database model_name accession numeric_id short_name description model_length metadata_status metadata_source CDD CHL00001 CHL00001 214330 rpoB RNA polymerase beta subunit 1070 matched cddid_all.tbl CDD CHL00002 CHL00002 214331 matK maturase K 504 matched cddid_all.tbl CDD CHL00003 CHL00003 176948 psbA photosystem II protein D1 338 matched cddid_all.tbl CDD CHL00004 CHL00004 176949 psbD photosystem II protein D2 353 matched cddid_all.tbl CDD CHL00005 CHL00005 176950 rps16 ribosomal protein S16 82 matched cddid_all.tbl CDD CHL00008 CHL00008 176951 petG cytochrome b6/f complex subunit V 37 matched cddid_all.tbl CDD CHL00009 CHL00009 176952 petN cytochrome b6/f complex subunit VIII 29 matched cddid_all.tbl CDD CHL00010 CHL00010 214332 infA translation initiation factor 1 78 matched cddid_all.tbl CDD CHL00011 CHL00011 176954 ndhD NADH dehydrogenase subunit 4 498 matched cddid_all.tbl CDD CHL00012 CHL00012 176955 ndhJ NADH dehydrogenase subunit J 158 matched cddid_all.tbl CDD CHL00013 CHL00013 214333 rpoA RNA polymerase alpha subunit 327 matched cddid_all.tbl CDD CHL00014 CHL00014 214334 ndhI NADH dehydrogenase subunit I 167 matched cddid_all.tbl CDD CHL00015 CHL00015 176958 ndhE NADH dehydrogenase subunit 4L 101 matched cddid_all.tbl CDD CHL00016 CHL00016 214335 ndhG NADH dehydrogenase subunit 6 182 matched cddid_all.tbl CDD CHL00017 CHL00017 176960 ndhH NADH dehydrogenase subunit 7 393 matched cddid_all.tbl CDD CHL00018 CHL00018 214336 rpoC1 RNA polymerase beta' subunit 663 matched cddid_all.tbl CDD CHL00019 CHL00019 176962 atpF ATP synthase CF0 B subunit 184 matched cddid_all.tbl CDD CHL00020 CHL00020 176963 psbN photosystem II protein N 43 matched cddid_all.tbl CDD CHL00022 CHL00022 176964 ndhC NADH dehydrogenase subunit 3 120 matched cddid_all.tbl CDD CHL00023 CHL00023 214337 ndhK NADH dehydrogenase subunit K 225 matched cddid_all.tbl CDD CHL00024 CHL00024 176966 psbI photosystem II protein I 36 matched cddid_all.tbl CDD CHL00025 CHL00025 214338 ndhF NADH dehydrogenase subunit 5 741 matched cddid_all.tbl CDD CHL00027 CHL00027 214339 rps15 ribosomal protein S15 90 matched cddid_all.tbl CDD CHL00028 CHL00028 214340 clpP ATP-dependent Clp protease proteolytic subunit 200 matched cddid_all.tbl CDD CHL00029 CHL00029 176970 rpl36 ribosomal protein L36 26 matched cddid_all.tbl CDD CHL00030 CHL00030 176971 rpl23 ribosomal protein L23 93 matched cddid_all.tbl CDD CHL00031 CHL00031 176972 psbT photosystem II protein T 33 matched cddid_all.tbl CDD CHL00032 CHL00032 214341 ndhA NADH dehydrogenase subunit 1 363 matched cddid_all.tbl CDD CHL00033 CHL00033 176974 ycf3 photosystem I assembly protein Ycf3 168 matched cddid_all.tbl CDD CHL00034 CHL00034 214342 rpl22 ribosomal protein L22 117 matched cddid_all.tbl CDD CHL00035 CHL00035 214343 psbC photosystem II 44 kDa protein 473 matched cddid_all.tbl CDD CHL00036 CHL00036 176977 ycf4 photosystem I assembly protein Ycf4 184 matched cddid_all.tbl CDD CHL00037 CHL00037 176978 petA cytochrome f 320 matched cddid_all.tbl CDD CHL00038 CHL00038 176979 psbL photosystem II protein L 38 matched cddid_all.tbl CDD CHL00039 CHL00039 176980 psbF photosystem II protein VI 39 matched cddid_all.tbl CDD CHL00040 CHL00040 176981 rbcL ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit 475 matched cddid_all.tbl CDD CHL00041 CHL00041 176982 rps11 ribosomal protein S11 116 matched cddid_all.tbl CDD CHL00042 CHL00042 214344 rps8 ribosomal protein S8 132 matched cddid_all.tbl CDD CHL00043 CHL00043 214345 cemA envelope membrane protein 261 matched cddid_all.tbl CDD CHL00044 CHL00044 176985 rpl16 ribosomal protein L16 135 matched cddid_all.tbl CDD CHL00045 CHL00045 214346 ccsA cytochrome c biogenesis protein 319 matched cddid_all.tbl CDD CHL00046 CHL00046 176987 atpI ATP synthase CF0 A subunit 228 matched cddid_all.tbl CDD CHL00047 CHL00047 214347 psbK photosystem II protein K 58 matched cddid_all.tbl CDD CHL00048 CHL00048 214348 rps3 ribosomal protein S3 214 matched cddid_all.tbl CDD CHL00049 CHL00049 176990 ndhB NADH dehydrogenase subunit 2 494 matched cddid_all.tbl CDD CHL00050 CHL00050 176991 rps19 ribosomal protein S19 92 matched cddid_all.tbl CDD CHL00051 CHL00051 176992 rps12 ribosomal protein S12 123 matched cddid_all.tbl CDD CHL00052 CHL00052 176993 rpl2 ribosomal protein L2 273 matched cddid_all.tbl CDD CHL00053 CHL00053 176994 rps7 ribosomal protein S7 155 matched cddid_all.tbl CDD CHL00054 CHL00054 176995 psaB photosystem I P700 chlorophyll a apoprotein A2 734 matched cddid_all.tbl CDD CHL00056 CHL00056 176996 psaA photosystem I P700 chlorophyll a apoprotein A1 750 matched cddid_all.tbl CDD CHL00057 CHL00057 176997 rpl14 ribosomal protein L14 122 matched cddid_all.tbl CDD CHL00058 CHL00058 176998 petD cytochrome b6/f complex subunit IV 160 matched cddid_all.tbl CDD CHL00059 CHL00059 176999 atpA ATP synthase CF1 alpha subunit 485 matched cddid_all.tbl CDD CHL00060 CHL00060 214349 atpB ATP synthase CF1 beta subunit 494 matched cddid_all.tbl CDD CHL00061 CHL00061 177001 atpH ATP synthase CF0 C subunit 81 matched cddid_all.tbl CDD CHL00062 CHL00062 214350 psbB photosystem II 47 kDa protein 504 matched cddid_all.tbl CDD CHL00063 CHL00063 214351 atpE ATP synthase CF1 epsilon subunit 134 matched cddid_all.tbl CDD CHL00064 CHL00064 177004 psbE photosystem II protein V 83 matched cddid_all.tbl CDD CHL00065 CHL00065 177005 psaC photosystem I subunit VII 81 matched cddid_all.tbl CDD CHL00066 CHL00066 177006 psbH photosystem II protein H 73 matched cddid_all.tbl CDD CHL00067 CHL00067 177007 rps2 ribosomal protein S2 230 matched cddid_all.tbl CDD CHL00068 CHL00068 214352 rpl20 ribosomal protein L20 115 matched cddid_all.tbl CDD CHL00070 CHL00070 177009 petB cytochrome b6 215 matched cddid_all.tbl CDD CHL00071 CHL00071 177010 tufA elongation factor Tu 409 matched cddid_all.tbl CDD CHL00072 CHL00072 177011 chlL photochlorophyllide reductase subunit L 290 matched cddid_all.tbl CDD CHL00073 CHL00073 214353 chlN photochlorophyllide reductase subunit N 457 matched cddid_all.tbl CDD CHL00074 CHL00074 214354 rps14 ribosomal protein S14 100 matched cddid_all.tbl CDD CHL00075 CHL00075 177014 rpl21 ribosomal protein L21 108 matched cddid_all.tbl CDD CHL00076 CHL00076 214355 chlB photochlorophyllide reductase subunit B 513 matched cddid_all.tbl CDD CHL00077 CHL00077 177016 rps18 ribosomal protein S18 86 matched cddid_all.tbl CDD CHL00078 CHL00078 214356 rpl5 ribosomal protein L5 181 matched cddid_all.tbl CDD CHL00079 CHL00079 214357 rps9 ribosomal protein S9 130 matched cddid_all.tbl CDD CHL00080 CHL00080 177019 psbM photosystem II protein M 34 matched cddid_all.tbl CDD CHL00081 CHL00081 177020 chlI Mg-protoporyphyrin IX chelatase 350 matched cddid_all.tbl CDD CHL00082 CHL00082 177021 psbZ photosystem II protein Z 62 matched cddid_all.tbl CDD CHL00083 CHL00083 214358 rpl12 ribosomal protein L12 131 matched cddid_all.tbl CDD CHL00084 CHL00084 177023 rpl19 ribosomal protein L19 117 matched cddid_all.tbl CDD CHL00085 CHL00085 214359 ycf24 putative ABC transporter 485 matched cddid_all.tbl CDD CHL00086 CHL00086 164492 apcA allophycocyanin alpha subunit 161 matched cddid_all.tbl CDD CHL00088 CHL00088 164493 apcB allophycocyanin beta subunit 161 matched cddid_all.tbl CDD CHL00089 CHL00089 100206 apcF allophycocyanin beta 18 subunit 169 matched cddid_all.tbl CDD CHL00090 CHL00090 164494 apcD allophycocyanin gamma subunit 161 matched cddid_all.tbl CDD CHL00091 CHL00091 164495 apcE phycobillisome linker protein 877 matched cddid_all.tbl CDD CHL00093 CHL00093 177025 groEL chaperonin GroEL 529 matched cddid_all.tbl CDD CHL00094 CHL00094 214360 dnaK heat shock protein 70 621 matched cddid_all.tbl CDD CHL00095 CHL00095 214361 clpC Clp protease ATP binding subunit 821 matched cddid_all.tbl CDD CHL00098 CHL00098 214362 tsf elongation factor Ts 200 matched cddid_all.tbl CDD CHL00099 CHL00099 214363 ilvB acetohydroxyacid synthase large subunit 585 matched cddid_all.tbl CDD CHL00100 CHL00100 214364 ilvH acetohydroxyacid synthase small subunit 174 matched cddid_all.tbl CDD CHL00101 CHL00101 214365 trpG anthranilate synthase component 2 190 matched cddid_all.tbl CDD CHL00102 CHL00102 214366 rps20 ribosomal protein S20 93 matched cddid_all.tbl CDD CHL00103 CHL00103 214367 rpl35 ribosomal protein L35 65 matched cddid_all.tbl CDD CHL00104 CHL00104 177033 rpl33 ribosomal protein L33 66 matched cddid_all.tbl CDD CHL00105 CHL00105 177034 psaJ photosystem I subunit IX 42 matched cddid_all.tbl CDD CHL00106 CHL00106 177035 petL cytochrome b6/f complex subunit VI 31 matched cddid_all.tbl CDD CHL00108 CHL00108 177036 psbJ photosystem II protein J 40 matched cddid_all.tbl CDD CHL00112 CHL00112 177037 rpl28 ribosomal protein L28; Provisional 63 matched cddid_all.tbl CDD CHL00113 CHL00113 177038 rps4 ribosomal protein S4; Reviewed 201 matched cddid_all.tbl CDD CHL00114 CHL00114 100224 psbX photosystem II protein X; Reviewed 39 matched cddid_all.tbl CDD CHL00115 CHL00115 177039 rpl34 ribosomal protein L34; Reviewed 46 matched cddid_all.tbl CDD CHL00117 CHL00117 214368 rpoC2 RNA polymerase beta'' subunit; Reviewed 1364 matched cddid_all.tbl CDD CHL00118 CHL00118 214369 atpG ATP synthase CF0 B' subunit; Validated 156 matched cddid_all.tbl CDD CHL00119 CHL00119 177042 atpD ATP synthase CF1 delta subunit; Validated 184 matched cddid_all.tbl CDD CHL00120 CHL00120 177043 psaL photosystem I subunit XI; Validated 143 matched cddid_all.tbl CDD CHL00121 CHL00121 214370 rpl27 ribosomal protein L27; Reviewed 86 matched cddid_all.tbl CDD CHL00122 CHL00122 214371 secA preprotein translocase subunit SecA; Validated 870 matched cddid_all.tbl CDD CHL00123 CHL00123 177046 rps6 ribosomal protein S6; Validated 97 matched cddid_all.tbl CDD CHL00124 CHL00124 177047 acpP acyl carrier protein; Validated 82 matched cddid_all.tbl CDD CHL00125 CHL00125 177048 psaE photosystem I subunit IV; Reviewed 64 matched cddid_all.tbl CDD CHL00127 CHL00127 177049 rpl11 ribosomal protein L11; Validated 140 matched cddid_all.tbl CDD CHL00128 CHL00128 177050 psbW photosystem II protein W; Reviewed 113 matched cddid_all.tbl CDD CHL00129 CHL00129 177051 rpl1 ribosomal protein L1; Reviewed 229 matched cddid_all.tbl CDD CHL00130 CHL00130 177052 rbcS ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit; Reviewed 138 matched cddid_all.tbl CDD CHL00131 CHL00131 214372 ycf16 sulfate ABC transporter protein; Validated 252 matched cddid_all.tbl CDD CHL00132 CHL00132 177054 psaF photosystem I subunit III; Validated 185 matched cddid_all.tbl CDD CHL00133 CHL00133 177055 psbV photosystem II cytochrome c550; Validated 163 matched cddid_all.tbl CDD CHL00134 CHL00134 177056 petF ferredoxin; Validated 99 matched cddid_all.tbl CDD CHL00135 CHL00135 177057 rps10 ribosomal protein S10; Validated 101 matched cddid_all.tbl CDD CHL00136 CHL00136 177058 rpl31 ribosomal protein L31; Validated 68 matched cddid_all.tbl CDD CHL00137 CHL00137 177059 rps13 ribosomal protein S13; Validated 122 matched cddid_all.tbl CDD CHL00138 CHL00138 177060 rps5 ribosomal protein S5; Validated 143 matched cddid_all.tbl CDD CHL00139 CHL00139 214373 rpl18 ribosomal protein L18; Validated 109 matched cddid_all.tbl CDD CHL00140 CHL00140 177062 rpl6 ribosomal protein L6; Validated 178 matched cddid_all.tbl CDD CHL00141 CHL00141 214374 rpl24 ribosomal protein L24; Validated 83 matched cddid_all.tbl CDD CHL00142 CHL00142 177064 rps17 ribosomal protein S17; Validated 84 matched cddid_all.tbl CDD CHL00143 CHL00143 177065 rpl3 ribosomal protein L3; Validated 207 matched cddid_all.tbl CDD CHL00144 CHL00144 177066 odpB pyruvate dehydrogenase E1 component beta subunit; Validated 327 matched cddid_all.tbl CDD CHL00145 CHL00145 177067 psaD photosystem I subunit II; Validated 139 matched cddid_all.tbl CDD CHL00147 CHL00147 214375 rpl4 ribosomal protein L4; Validated 215 matched cddid_all.tbl CDD CHL00148 CHL00148 214376 orf27 Ycf27; Reviewed 240 matched cddid_all.tbl CDD CHL00149 CHL00149 177069 odpA pyruvate dehydrogenase E1 component alpha subunit; Reviewed 341 matched cddid_all.tbl CDD CHL00151 CHL00151 164542 preA prenyl transferase; Reviewed 323 matched cddid_all.tbl CDD CHL00152 CHL00152 214377 rpl32 ribosomal protein L32; Validated 53 matched cddid_all.tbl CDD CHL00154 CHL00154 177071 rpl29 ribosomal protein L29; Validated 67 matched cddid_all.tbl CDD CHL00159 CHL00159 177072 rpl13 ribosomal protein L13; Validated 143 matched cddid_all.tbl CDD CHL00160 CHL00160 214378 rpl9 ribosomal protein L9; Provisional 153 matched cddid_all.tbl CDD CHL00161 CHL00161 214379 secY preprotein translocase subunit SecY; Validated 417 matched cddid_all.tbl CDD CHL00162 CHL00162 214380 thiG thiamin biosynthesis protein G; Validated 267 matched cddid_all.tbl CDD CHL00163 CHL00163 214381 ycf65 putative ribosomal protein 3; Validated 99 matched cddid_all.tbl CDD CHL00164 CHL00164 164550 psaK photosystem I subunit X; Validated 86 matched cddid_all.tbl CDD CHL00165 CHL00165 214382 ftrB ferredoxin thioreductase subunit beta; Validated 116 matched cddid_all.tbl CDD CHL00168 CHL00168 214383 pbsA heme oxygenase; Provisional 238 matched cddid_all.tbl CDD CHL00170 CHL00170 100270 cpcA phycocyanin alpha subunit; Reviewed 162 matched cddid_all.tbl CDD CHL00171 CHL00171 100271 cpcB phycocyanin beta subunit; Reviewed 172 matched cddid_all.tbl CDD CHL00172 CHL00172 133617 cpeB phycoerythrin beta subunit; Provisional 177 matched cddid_all.tbl CDD CHL00173 CHL00173 100273 cpeA phycoerythrin alpha subunit; Provisional 164 matched cddid_all.tbl CDD CHL00174 CHL00174 214384 accD acetyl-CoA carboxylase beta subunit; Reviewed 296 matched cddid_all.tbl CDD CHL00175 CHL00175 214385 minD septum-site determining protein; Validated 281 matched cddid_all.tbl CDD CHL00176 CHL00176 214386 ftsH cell division protein; Validated 638 matched cddid_all.tbl CDD CHL00177 CHL00177 214387 ccs1 c-type cytochrome biogenensis protein; Validated 426 matched cddid_all.tbl CDD CHL00180 CHL00180 177082 rbcR LysR transcriptional regulator; Provisional 305 matched cddid_all.tbl CDD CHL00181 CHL00181 177083 cbbX CbbX; Provisional 287 matched cddid_all.tbl CDD CHL00182 CHL00182 177084 tatC Sec-independent translocase component C; Provisional 249 matched cddid_all.tbl CDD CHL00183 CHL00183 177085 petJ cytochrome c553; Provisional 108 matched cddid_all.tbl CDD CHL00184 CHL00184 177086 ycf12 Ycf12; Provisional 33 matched cddid_all.tbl CDD CHL00185 CHL00185 177087 ycf59 magnesium-protoporphyrin IX monomethyl ester cyclase; Provisional 351 matched cddid_all.tbl CDD CHL00186 CHL00186 177088 psaI photosystem I subunit VIII; Validated 36 matched cddid_all.tbl CDD CHL00187 CHL00187 214388 cysT sulfate transport protein; Provisional 237 matched cddid_all.tbl CDD CHL00188 CHL00188 214389 hisH imidazole glycerol phosphate synthase subunit hisH; Provisional 210 matched cddid_all.tbl CDD CHL00189 CHL00189 177089 infB translation initiation factor 2; Provisional 742 matched cddid_all.tbl CDD CHL00190 CHL00190 177090 psaM photosystem I subunit XII; Provisional 30 matched cddid_all.tbl CDD CHL00191 CHL00191 214390 ycf61 DNA-directed RNA polymerase subunit omega; Provisional 76 matched cddid_all.tbl CDD CHL00192 CHL00192 214391 syfB phenylalanyl-tRNA synthetase beta chain; Provisional 704 matched cddid_all.tbl CDD CHL00193 CHL00193 177092 ycf35 Ycf35; Provisional 128 matched cddid_all.tbl CDD CHL00194 CHL00194 177093 ycf39 Ycf39; Provisional 317 matched cddid_all.tbl CDD CHL00195 CHL00195 177094 ycf46 Ycf46; Provisional 489 matched cddid_all.tbl CDD CHL00196 CHL00196 177095 psbY photosystem II protein Y; Provisional 36 matched cddid_all.tbl CDD CHL00197 CHL00197 214392 carA carbamoyl-phosphate synthase arginine-specific small subunit; Provisional 382 matched cddid_all.tbl CDD CHL00198 CHL00198 214393 accA acetyl-CoA carboxylase carboxyltransferase alpha subunit; Provisional 322 matched cddid_all.tbl CDD CHL00199 CHL00199 164575 infC translation initiation factor 3; Provisional 182 matched cddid_all.tbl CDD CHL00200 CHL00200 214394 trpA tryptophan synthase alpha subunit; Provisional 263 matched cddid_all.tbl CDD CHL00201 CHL00201 164576 syh histidine-tRNA synthetase; Provisional 430 matched cddid_all.tbl CDD CHL00202 CHL00202 133644 argB acetylglutamate kinase; Provisional 284 matched cddid_all.tbl CDD CHL00203 CHL00203 164577 fabH 3-oxoacyl-acyl-carrier-protein synthase 3; Provisional 326 matched cddid_all.tbl CDD CHL00204 CHL00204 214395 ycf1 Ycf1; Provisional 1832 matched cddid_all.tbl CDD CHL00206 CHL00206 214396 ycf2 Ycf2; Provisional 2281 matched cddid_all.tbl CDD CHL00207 CHL00207 214397 rpoB RNA polymerase beta subunit; Provisional 1077 matched cddid_all.tbl CDD COG0001 COG0001 439772 HemL Glutamate-1-semialdehyde aminotransferase [Coenzyme transport and metabolism]. Glutamate-1-semialdehyde aminotransferase is part of the Pathway/BioSystem: Heme biosynthesis 429 matched cddid_all.tbl CDD COG0002 COG0002 439773 ArgC N-acetyl-gamma-glutamylphosphate reductase [Amino acid transport and metabolism]. N-acetyl-gamma-glutamylphosphate reductase is part of the Pathway/BioSystem: Arginine biosynthesis 345 matched cddid_all.tbl CDD COG0003 COG0003 439774 ArsA Anion-transporting ATPase, ArsA/GET3 family [Inorganic ion transport and metabolism]. 299 matched cddid_all.tbl CDD COG0004 COG0004 439775 AmtB Ammonia channel protein AmtB [Inorganic ion transport and metabolism]. 413 matched cddid_all.tbl CDD COG0005 COG0005 439776 XapA Purine nucleoside phosphorylase [Nucleotide transport and metabolism]. Purine nucleoside phosphorylase is part of the Pathway/BioSystem: Purine salvage 241 matched cddid_all.tbl CDD COG0006 COG0006 439777 PepP Xaa-Pro aminopeptidase [Amino acid transport and metabolism]. 299 matched cddid_all.tbl CDD COG0007 COG0007 439778 CysG Uroporphyrinogen-III methylase (siroheme synthase) [Coenzyme transport and metabolism]. Uroporphyrinogen-III methylase (siroheme synthase) is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 245 matched cddid_all.tbl CDD COG0008 COG0008 439779 GlnS Glutamyl- or glutaminyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Glutamyl- or glutaminyl-tRNA synthetase is part of the Pathway/BioSystem: Heme biosynthesis 467 matched cddid_all.tbl CDD COG0009 COG0009 439780 TsaC tRNA A37 threonylcarbamoyladenosine synthetase subunit TsaC/SUA5/YrdC [Translation, ribosomal structure and biogenesis]. tRNA A37 threonylcarbamoyladenosine synthetase subunit TsaC/SUA5/YrdC is part of the Pathway/BioSystem: tRNA modification 204 matched cddid_all.tbl CDD COG0010 COG0010 439781 SpeB Arginase/agmatinase family enzyme [Amino acid transport and metabolism]. Arginase/agmatinase family enzyme is part of the Pathway/BioSystem: Urea cycle 283 matched cddid_all.tbl CDD COG0011 COG0011 439782 YqgV Thiamin-binding stress-response protein YqgV, UPF0045 family [Coenzyme transport and metabolism]. 98 matched cddid_all.tbl CDD COG0012 COG0012 439783 GTP1 Ribosome-binding ATPase YchF, GTP1/OBG family [Translation, ribosomal structure and biogenesis]. 362 matched cddid_all.tbl CDD COG0013 COG0013 439784 AlaS Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Alanyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 880 matched cddid_all.tbl CDD COG0014 COG0014 439785 ProA Gamma-glutamyl phosphate reductase [Amino acid transport and metabolism]. Gamma-glutamyl phosphate reductase is part of the Pathway/BioSystem: Proline biosynthesis 414 matched cddid_all.tbl CDD COG0015 COG0015 439786 PurB Adenylosuccinate lyase [Nucleotide transport and metabolism]. Adenylosuccinate lyase is part of the Pathway/BioSystem: Purine biosynthesis 436 matched cddid_all.tbl CDD COG0016 COG0016 439787 PheS Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]. Phenylalanyl-tRNA synthetase alpha subunit is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 339 matched cddid_all.tbl CDD COG0017 COG0017 439788 AsnS Aspartyl/asparaginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Aspartyl/asparaginyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 430 matched cddid_all.tbl CDD COG0018 COG0018 439789 ArgS Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Arginyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 574 matched cddid_all.tbl CDD COG0019 COG0019 439790 LysA Diaminopimelate decarboxylase [Amino acid transport and metabolism]. Diaminopimelate decarboxylase is part of the Pathway/BioSystem: Lysine biosynthesis 417 matched cddid_all.tbl CDD COG0020 COG0020 439791 UppS Undecaprenyl pyrophosphate synthase [Lipid transport and metabolism]. 248 matched cddid_all.tbl CDD COG0021 COG0021 439792 TktA Transketolase [Carbohydrate transport and metabolism]. Transketolase is part of the Pathway/BioSystem: Pentose phosphate pathway 661 matched cddid_all.tbl CDD COG0022 COG0022 439793 AcoB Pyruvate/2-oxoglutarate/acetoin dehydrogenase complex, dehydrogenase (E1) component, beta subunit [Energy production and conversion]. Pyruvate/2-oxoglutarate/acetoin dehydrogenase complex, dehydrogenase (E1) component, beta subunit is part of the Pathway/BioSystem: Pyruvate oxidation 325 matched cddid_all.tbl CDD COG0023 COG0023 439794 SUI1 Translation initiation factor 1 (eIF-1/SUI1) [Translation, ribosomal structure and biogenesis]. Translation initiation factor 1 (eIF-1/SUI1) is part of the Pathway/BioSystem: Translation factors 112 matched cddid_all.tbl CDD COG0024 COG0024 439795 Map Methionine aminopeptidase [Translation, ribosomal structure and biogenesis]. 250 matched cddid_all.tbl CDD COG0025 COG0025 439796 NhaP NhaP-type Na+/H+ or K+/H+ antiporter [Inorganic ion transport and metabolism]. 506 matched cddid_all.tbl CDD COG0026 COG0026 439797 PurK Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) [Nucleotide transport and metabolism]. Phosphoribosylaminoimidazole carboxylase (NCAIR synthetase) is part of the Pathway/BioSystem: Purine biosynthesis 353 matched cddid_all.tbl CDD COG0027 COG0027 439798 PurT Formate-dependent phosphoribosylglycinamide formyltransferase (GAR transformylase) [Nucleotide transport and metabolism]. Formate-dependent phosphoribosylglycinamide formyltransferase (GAR transformylase) is part of the Pathway/BioSystem: Purine biosynthesis 393 matched cddid_all.tbl CDD COG0028 COG0028 439799 IlvB Acetolactate synthase large subunit or other thiamine pyrophosphate-requiring enzyme [Amino acid transport and metabolism, Coenzyme transport and metabolism]. Acetolactate synthase large subunit or other thiamine pyrophosphate-requiring enzyme is part of the Pathway/BioSystem: Isoleucine, leucine, valine biosynthesis 548 matched cddid_all.tbl CDD COG0029 COG0029 439800 NadB Aspartate oxidase [Coenzyme transport and metabolism]. Aspartate oxidase is part of the Pathway/BioSystem: NAD biosynthesis 521 matched cddid_all.tbl CDD COG0030 COG0030 439801 RsmA 16S rRNA A1518 and A1519 N6-dimethyltransferase RsmA/KsgA/DIM1 (may also have DNA glycosylase/AP lyase activity) [Translation, ribosomal structure and biogenesis]. 16S rRNA A1518 and A1519 N6-dimethyltransferase RsmA/KsgA/DIM1 (may also have DNA glycosylase/AP lyase activity) is part of the Pathway/BioSystem: 16S rRNA modification 270 matched cddid_all.tbl CDD COG0031 COG0031 439802 CysK Cysteine synthase [Amino acid transport and metabolism]. Cysteine synthase is part of the Pathway/BioSystem: Cysteine biosynthesis 301 matched cddid_all.tbl CDD COG0033 COG0033 439803 Pgm Phosphoglucomutase/phosphomannomutase [Carbohydrate transport and metabolism]. 544 matched cddid_all.tbl CDD COG0034 COG0034 439804 PurF Glutamine phosphoribosylpyrophosphate amidotransferase [Nucleotide transport and metabolism]. Glutamine phosphoribosylpyrophosphate amidotransferase is part of the Pathway/BioSystem: Purine biosynthesis 464 matched cddid_all.tbl CDD COG0035 COG0035 439805 Upp Uracil phosphoribosyltransferase [Nucleotide transport and metabolism]. Uracil phosphoribosyltransferase is part of the Pathway/BioSystem: Pyrimidine salvage 209 matched cddid_all.tbl CDD COG0036 COG0036 439806 Rpe Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]. Pentose-5-phosphate-3-epimerase is part of the Pathway/BioSystem: Pentose phosphate pathway 218 matched cddid_all.tbl CDD COG0037 COG0037 439807 TilS tRNA(Ile)-lysidine synthase TilS/MesJ [Translation, ribosomal structure and biogenesis]. tRNA(Ile)-lysidine synthase TilS/MesJ is part of the Pathway/BioSystem: tRNA modification 235 matched cddid_all.tbl CDD COG0038 COG0038 439808 ClcA H+/Cl- antiporter ClcA [Inorganic ion transport and metabolism]. 415 matched cddid_all.tbl CDD COG0039 COG0039 439809 Mdh Malate/lactate dehydrogenase [Energy production and conversion]. Malate/lactate dehydrogenase is part of the Pathway/BioSystem: TCA cycle 302 matched cddid_all.tbl CDD COG0040 COG0040 439810 HisG ATP phosphoribosyltransferase [Amino acid transport and metabolism]. ATP phosphoribosyltransferase is part of the Pathway/BioSystem: Histidine biosynthesis 281 matched cddid_all.tbl CDD COG0041 COG0041 439811 PurE Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase [Nucleotide transport and metabolism]. Phosphoribosylcarboxyaminoimidazole (NCAIR) mutase is part of the Pathway/BioSystem: Purine biosynthesis 161 matched cddid_all.tbl CDD COG0042 COG0042 439812 DusA tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis]. tRNA-dihydrouridine synthase is part of the Pathway/BioSystem: tRNA modification 310 matched cddid_all.tbl CDD COG0043 COG0043 439813 UbiD 3-polyprenyl-4-hydroxybenzoate decarboxylase [Coenzyme transport and metabolism]. 3-polyprenyl-4-hydroxybenzoate decarboxylase is part of the Pathway/BioSystem: Ubiquinone biosynthesis 459 matched cddid_all.tbl CDD COG0044 COG0044 439814 AllB Dihydroorotase or related cyclic amidohydrolase [Nucleotide transport and metabolism]. Dihydroorotase or related cyclic amidohydrolase is part of the Pathway/BioSystem: Pyrimidine biosynthesis 439 matched cddid_all.tbl CDD COG0045 COG0045 439815 SucC Succinyl-CoA synthetase, beta subunit [Energy production and conversion]. Succinyl-CoA synthetase, beta subunit is part of the Pathway/BioSystem: TCA cycle 388 matched cddid_all.tbl CDD COG0046 COG0046 439816 PurL1 Phosphoribosylformylglycinamidine (FGAM) synthase, synthetase domain [Nucleotide transport and metabolism]. Phosphoribosylformylglycinamidine (FGAM) synthase, synthetase domain is part of the Pathway/BioSystem: Purine biosynthesis 747 matched cddid_all.tbl CDD COG0047 COG0047 439817 PurL2 Phosphoribosylformylglycinamidine (FGAM) synthase, glutamine amidotransferase domain [Nucleotide transport and metabolism]. Phosphoribosylformylglycinamidine (FGAM) synthase, glutamine amidotransferase domain is part of the Pathway/BioSystem: Purine biosynthesis 236 matched cddid_all.tbl CDD COG0048 COG0048 439818 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S12 is part of the Pathway/BioSystem: Ribosome 30S subunit 124 matched cddid_all.tbl CDD COG0049 COG0049 439819 RpsG Ribosomal protein S7 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S7 is part of the Pathway/BioSystem: Ribosome 30S subunit 156 matched cddid_all.tbl CDD COG0050 COG0050 439820 TufA Translation elongation factor EF-Tu, a GTPase [Translation, ribosomal structure and biogenesis]. Translation elongation factor EF-Tu, a GTPase is part of the Pathway/BioSystem: Translation factors 396 matched cddid_all.tbl CDD COG0051 COG0051 439821 RpsJ Ribosomal protein S10 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S10 is part of the Pathway/BioSystem: Ribosome 30S subunit 103 matched cddid_all.tbl CDD COG0052 COG0052 439822 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S2 is part of the Pathway/BioSystem: Ribosome 30S subunit 253 matched cddid_all.tbl CDD COG0053 COG0053 439823 FieF Divalent metal cation (Fe/Co/Zn/Cd) efflux pump [Inorganic ion transport and metabolism]. 284 matched cddid_all.tbl CDD COG0054 COG0054 439824 RibE 6,7-dimethyl-8-ribityllumazine synthase (Riboflavin synthase beta chain) [Coenzyme transport and metabolism]. 6,7-dimethyl-8-ribityllumazine synthase (Riboflavin synthase beta chain) is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis 152 matched cddid_all.tbl CDD COG0055 COG0055 439825 AtpD FoF1-type ATP synthase, beta subunit [Energy production and conversion]. FoF1-type ATP synthase, beta subunit is part of the Pathway/BioSystem: FoF1-type ATP synthase 468 matched cddid_all.tbl CDD COG0056 COG0056 439826 AtpA FoF1-type ATP synthase, alpha subunit [Energy production and conversion]. FoF1-type ATP synthase, alpha subunit is part of the Pathway/BioSystem: FoF1-type ATP synthase 504 matched cddid_all.tbl CDD COG0057 COG0057 439827 GapA Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]. Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase is part of the Pathway/BioSystem: Glycolysis 334 matched cddid_all.tbl CDD COG0058 COG0058 439828 GlgP Glucan phosphorylase [Carbohydrate transport and metabolism]. 795 matched cddid_all.tbl CDD COG0059 COG0059 439829 IlvC Ketol-acid reductoisomerase [Amino acid transport and metabolism, Coenzyme transport and metabolism]. Ketol-acid reductoisomerase is part of the Pathway/BioSystem: Isoleucine, leucine, valine biosynthesis 328 matched cddid_all.tbl CDD COG0060 COG0060 439830 IleS Isoleucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Isoleucyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 931 matched cddid_all.tbl CDD COG0061 COG0061 439831 NadK NAD kinase [Coenzyme transport and metabolism]. 279 matched cddid_all.tbl CDD COG0062 COG0062 439832 Nnr1 NAD(P)H-hydrate repair enzyme Nnr, NAD(P)H-hydrate epimerase domain [Nucleotide transport and metabolism]. 499 matched cddid_all.tbl CDD COG0063 COG0063 439833 Nnr2 NAD(P)H-hydrate repair enzyme Nnr, NAD(P)H-hydrate dehydratase domain [Nucleotide transport and metabolism]. 280 matched cddid_all.tbl CDD COG0064 COG0064 439834 GatB Asp-tRNAAsn/Glu-tRNAGln amidotransferase B subunit [Translation, ribosomal structure and biogenesis]. Asp-tRNAAsn/Glu-tRNAGln amidotransferase B subunit is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 477 matched cddid_all.tbl CDD COG0065 COG0065 439835 LeuC Homoaconitase/3-isopropylmalate dehydratase large subunit [Amino acid transport and metabolism]. Homoaconitase/3-isopropylmalate dehydratase large subunit is part of the Pathway/BioSystem: Isoleucine, leucine, valine biosynthesis 417 matched cddid_all.tbl CDD COG0066 COG0066 439836 LeuD 3-isopropylmalate dehydratase small subunit [Amino acid transport and metabolism]. 3-isopropylmalate dehydratase small subunit is part of the Pathway/BioSystem: Isoleucine, leucine, valine biosynthesis 195 matched cddid_all.tbl CDD COG0067 COG0067 439837 GltB1 Glutamate synthase domain 1 [Amino acid transport and metabolism]. Glutamate synthase domain 1 is part of the Pathway/BioSystem: Glutamine biosynthesis 1520 matched cddid_all.tbl CDD COG0068 COG0068 439838 HypF Hydrogenase maturation factor HypF (carbamoyltransferase) [Posttranslational modification, protein turnover, chaperones]. 757 matched cddid_all.tbl CDD COG0069 COG0069 439839 GltB2 Glutamate synthase domain 2 [Amino acid transport and metabolism]. Glutamate synthase domain 2 is part of the Pathway/BioSystem: Glutamine biosynthesis 728 matched cddid_all.tbl CDD COG0070 COG0070 439840 GltB3 Glutamate synthase domain 3 [Amino acid transport and metabolism]. Glutamate synthase domain 3 is part of the Pathway/BioSystem: Glutamine biosynthesis 1508 matched cddid_all.tbl CDD COG0071 COG0071 439841 IbpA Small heat shock protein IbpA, HSP20 family [Posttranslational modification, protein turnover, chaperones]. 105 matched cddid_all.tbl CDD COG0072 COG0072 439842 PheT Phenylalanyl-tRNA synthetase beta subunit [Translation, ribosomal structure and biogenesis]. Phenylalanyl-tRNA synthetase beta subunit is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 793 matched cddid_all.tbl CDD COG0073 COG0073 439843 EMAP tRNA-binding EMAP/Myf domain [Translation, ribosomal structure and biogenesis]. 773 matched cddid_all.tbl CDD COG0074 COG0074 439844 SucD Succinyl-CoA synthetase, alpha subunit [Energy production and conversion]. Succinyl-CoA synthetase, alpha subunit is part of the Pathway/BioSystem: TCA cycle 288 matched cddid_all.tbl CDD COG0075 COG0075 439845 PucG Archaeal aspartate aminotransferase or a related aminotransferase, includes purine catabolism protein PucG [Amino acid transport and metabolism, Nucleotide transport and metabolism]. Archaeal aspartate aminotransferase or a related aminotransferase, includes purine catabolism protein PucG is part of the Pathway/BioSystem: Serine biosynthesis 376 matched cddid_all.tbl CDD COG0076 COG0076 439846 GadA Glutamate or tyrosine decarboxylase or a related PLP-dependent protein [Amino acid transport and metabolism]. Glutamate or tyrosine decarboxylase or a related PLP-dependent protein is part of the Pathway/BioSystem: Pantothenate/CoA biosynthesis 460 matched cddid_all.tbl CDD COG0077 COG0077 439847 PheA2 Prephenate dehydratase [Amino acid transport and metabolism]. Prephenate dehydratase is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 274 matched cddid_all.tbl CDD COG0078 COG0078 439848 ArgF Ornithine carbamoyltransferase [Amino acid transport and metabolism]. Ornithine carbamoyltransferase is part of the Pathway/BioSystem: Arginine biosynthesis 310 matched cddid_all.tbl CDD COG0079 COG0079 439849 HisC Histidinol-phosphate/aromatic aminotransferase or cobyric acid decarboxylase [Amino acid transport and metabolism]. Histidinol-phosphate/aromatic aminotransferase or cobyric acid decarboxylase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 341 matched cddid_all.tbl CDD COG0080 COG0080 439850 RplK Ribosomal protein L11 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L11 is part of the Pathway/BioSystem: Ribosome 50S subunit 141 matched cddid_all.tbl CDD COG0081 COG0081 439851 RplA Ribosomal protein L1 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L1 is part of the Pathway/BioSystem: Ribosome 50S subunit 226 matched cddid_all.tbl CDD COG0082 COG0082 439852 AroC Chorismate synthase [Amino acid transport and metabolism]. Chorismate synthase is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 354 matched cddid_all.tbl CDD COG0083 COG0083 439853 ThrB Homoserine kinase [Amino acid transport and metabolism]. Homoserine kinase is part of the Pathway/BioSystem: Threonine biosynthesis 302 matched cddid_all.tbl CDD COG0084 COG0084 439854 TatD 3'->5' ssDNA/RNA exonuclease TatD [Cell motility]. 253 matched cddid_all.tbl CDD COG0085 COG0085 439855 RpoB DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]. DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase 1001 matched cddid_all.tbl CDD COG0086 COG0086 439856 RpoC DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]. DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase 1165 matched cddid_all.tbl CDD COG0087 COG0087 439857 RplC Ribosomal protein L3 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L3 is part of the Pathway/BioSystem: Ribosome 50S subunit 214 matched cddid_all.tbl CDD COG0088 COG0088 439858 RplD Ribosomal protein L4 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L4 is part of the Pathway/BioSystem: Ribosome 50S subunit 206 matched cddid_all.tbl CDD COG0089 COG0089 439859 RplW Ribosomal protein L23 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L23 is part of the Pathway/BioSystem: Ribosome 50S subunit 88 matched cddid_all.tbl CDD COG0090 COG0090 439860 RplB Ribosomal protein L2 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L2 is part of the Pathway/BioSystem: Ribosome 50S subunit 276 matched cddid_all.tbl CDD COG0091 COG0091 439861 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L22 is part of the Pathway/BioSystem: Ribosome 50S subunit 110 matched cddid_all.tbl CDD COG0092 COG0092 439862 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S3 is part of the Pathway/BioSystem: Ribosome 30S subunit 226 matched cddid_all.tbl CDD COG0093 COG0093 439863 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L14 is part of the Pathway/BioSystem: Ribosome 50S subunit 122 matched cddid_all.tbl CDD COG0094 COG0094 439864 RplE Ribosomal protein L5 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L5 is part of the Pathway/BioSystem: Ribosome 50S subunit 179 matched cddid_all.tbl CDD COG0095 COG0095 439865 LplA Lipoate-protein ligase A [Coenzyme transport and metabolism]. Lipoate-protein ligase A is part of the Pathway/BioSystem: Lipoate biosynthesis 246 matched cddid_all.tbl CDD COG0096 COG0096 439866 RpsH Ribosomal protein S8 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S8 is part of the Pathway/BioSystem: Ribosome 30S subunit 132 matched cddid_all.tbl CDD COG0097 COG0097 439867 RplF Ribosomal protein L6P/L9E [Translation, ribosomal structure and biogenesis]. Ribosomal protein L6P/L9E is part of the Pathway/BioSystem: Ribosome 50S subunit 177 matched cddid_all.tbl CDD COG0098 COG0098 439868 RpsE Ribosomal protein S5 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S5 is part of the Pathway/BioSystem: Ribosome 30S subunit 167 matched cddid_all.tbl CDD COG0099 COG0099 439869 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S13 is part of the Pathway/BioSystem: Ribosome 30S subunit 125 matched cddid_all.tbl CDD COG0100 COG0100 439870 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S11 is part of the Pathway/BioSystem: Ribosome 30S subunit 130 matched cddid_all.tbl CDD COG0101 COG0101 439871 TruA tRNA U38,U39,U40 pseudouridine synthase TruA [Translation, ribosomal structure and biogenesis]. tRNA U38,U39,U40 pseudouridine synthase TruA is part of the Pathway/BioSystem: tRNA modification 250 matched cddid_all.tbl CDD COG0102 COG0102 439872 RplM Ribosomal protein L13 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L13 is part of the Pathway/BioSystem: Ribosome 50S subunit 140 matched cddid_all.tbl CDD COG0103 COG0103 439873 RpsI Ribosomal protein S9 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S9 is part of the Pathway/BioSystem: Ribosome 30S subunit 130 matched cddid_all.tbl CDD COG0104 COG0104 439874 PurA Adenylosuccinate synthase [Nucleotide transport and metabolism]. Adenylosuccinate synthase is part of the Pathway/BioSystem: Purine biosynthesis 423 matched cddid_all.tbl CDD COG0105 COG0105 439875 Ndk Nucleoside diphosphate kinase [Nucleotide transport and metabolism]. Nucleoside diphosphate kinase is part of the Pathway/BioSystem: Pyrimidine biosynthesis 140 matched cddid_all.tbl CDD COG0106 COG0106 439876 HisA Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism]. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase is part of the Pathway/BioSystem: Histidine biosynthesis 236 matched cddid_all.tbl CDD COG0107 COG0107 439877 HisF Imidazole glycerol phosphate synthase subunit HisF [Amino acid transport and metabolism]. Imidazole glycerol phosphate synthase subunit HisF is part of the Pathway/BioSystem: Histidine biosynthesis 251 matched cddid_all.tbl CDD COG0108 COG0108 439878 RibB 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme transport and metabolism]. 3,4-dihydroxy-2-butanone 4-phosphate synthase is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis 201 matched cddid_all.tbl CDD COG0109 COG0109 439879 CyoE Polyprenyltransferase (heme O synthase) [Coenzyme transport and metabolism, Lipid transport and metabolism]. 299 matched cddid_all.tbl CDD COG0110 COG0110 439880 WbbJ Acetyltransferase, isoleucine patch superfamily [General function prediction only]. 140 matched cddid_all.tbl CDD COG0111 COG0111 439881 SerA Phosphoglycerate dehydrogenase or related dehydrogenase [Coenzyme transport and metabolism]. Phosphoglycerate dehydrogenase or related dehydrogenase is part of the Pathway/BioSystem: Serine biosynthesis 314 matched cddid_all.tbl CDD COG0112 COG0112 439882 GlyA Glycine/serine hydroxymethyltransferase [Amino acid transport and metabolism]. Glycine/serine hydroxymethyltransferase is part of the Pathway/BioSystem: Serine biosynthesis 414 matched cddid_all.tbl CDD COG0113 COG0113 439883 HemB Delta-aminolevulinic acid dehydratase, porphobilinogen synthase [Coenzyme transport and metabolism]. Delta-aminolevulinic acid dehydratase, porphobilinogen synthase is part of the Pathway/BioSystem: Heme biosynthesis 321 matched cddid_all.tbl CDD COG0114 COG0114 439884 FumC Fumarate hydratase class II [Energy production and conversion]. Fumarate hydratase class II is part of the Pathway/BioSystem: TCA cycle 461 matched cddid_all.tbl CDD COG0115 COG0115 439885 IlvE Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase [Amino acid transport and metabolism, Coenzyme transport and metabolism]. Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase is part of the Pathway/BioSystem: Isoleucine, leucine, valine biosynthesis 285 matched cddid_all.tbl CDD COG0116 COG0116 439886 RlmL 23S rRNA G2445 N2-methylase RlmL [Translation, ribosomal structure and biogenesis]. 23S rRNA G2445 N2-methylase RlmL is part of the Pathway/BioSystem: 23S rRNA modification 369 matched cddid_all.tbl CDD COG0117 COG0117 439887 RibD1 Riboflavin biosynthesis protein RibD, pyrimidine deaminase domain [Coenzyme transport and metabolism]. Riboflavin biosynthesis protein RibD, pyrimidine deaminase domain is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis 311 matched cddid_all.tbl CDD COG0118 COG0118 439888 HisH Imidazoleglycerol phosphate synthase glutamine amidotransferase subunit HisH [Amino acid transport and metabolism]. Imidazoleglycerol phosphate synthase glutamine amidotransferase subunit HisH is part of the Pathway/BioSystem: Histidine biosynthesis 196 matched cddid_all.tbl CDD COG0119 COG0119 439889 LeuA Isopropylmalate/homocitrate/citramalate synthases [Amino acid transport and metabolism]. Isopropylmalate/homocitrate/citramalate synthases is part of the Pathway/BioSystem: Isoleucine, leucine, valine biosynthesis 452 matched cddid_all.tbl CDD COG0120 COG0120 439890 RpiA Ribose 5-phosphate isomerase [Carbohydrate transport and metabolism]. Ribose 5-phosphate isomerase is part of the Pathway/BioSystem: Pentose phosphate pathway 225 matched cddid_all.tbl CDD COG0121 COG0121 439891 YafJ Predicted glutamine amidotransferase YafJ [General function prediction only]. 248 matched cddid_all.tbl CDD COG0122 COG0122 439892 AlkA 3-methyladenine DNA glycosylase/8-oxoguanine DNA glycosylase [Replication, recombination and repair]. 255 matched cddid_all.tbl CDD COG0123 COG0123 439893 AcuC Acetoin utilization deacetylase AcuC or a related deacetylase [Secondary metabolites biosynthesis, transport and catabolism]. 308 matched cddid_all.tbl CDD COG0124 COG0124 439894 HisS Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Histidyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 422 matched cddid_all.tbl CDD COG0125 COG0125 439895 Tmk Thymidylate kinase [Nucleotide transport and metabolism]. Thymidylate kinase is part of the Pathway/BioSystem: Thymidylate biosynthesis 206 matched cddid_all.tbl CDD COG0126 COG0126 439896 Pgk 3-phosphoglycerate kinase [Carbohydrate transport and metabolism]. 3-phosphoglycerate kinase is part of the Pathway/BioSystem: Glycolysis 389 matched cddid_all.tbl CDD COG0127 COG0127 439897 RdgB Inosine/xanthosine triphosphate pyrophosphatase, all-alpha NTP-PPase family [Nucleotide transport and metabolism]. 191 matched cddid_all.tbl CDD COG0128 COG0128 439898 AroA 5-enolpyruvylshikimate-3-phosphate synthase [Amino acid transport and metabolism]. 5-enolpyruvylshikimate-3-phosphate synthase is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 421 matched cddid_all.tbl CDD COG0129 COG0129 439899 IlvD Dihydroxyacid dehydratase/phosphogluconate dehydratase [Amino acid transport and metabolism, Carbohydrate transport and metabolism]. Dihydroxyacid dehydratase/phosphogluconate dehydratase is part of the Pathway/BioSystem: Isoleucine, leucine, valine biosynthesis 558 matched cddid_all.tbl CDD COG0130 COG0130 439900 TruB tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA [Translation, ribosomal structure and biogenesis]. tRNA U55 pseudouridine synthase TruB, may also work on U342 of tmRNA is part of the Pathway/BioSystem: tRNA modification 288 matched cddid_all.tbl CDD COG0131 COG0131 439901 HisB2 Imidazoleglycerol phosphate dehydratase HisB [Amino acid transport and metabolism]. Imidazoleglycerol phosphate dehydratase HisB is part of the Pathway/BioSystem: Histidine biosynthesis 183 matched cddid_all.tbl CDD COG0132 COG0132 439902 BioD Dethiobiotin synthetase [Coenzyme transport and metabolism]. Dethiobiotin synthetase is part of the Pathway/BioSystem: Biotin biosynthesis 222 matched cddid_all.tbl CDD COG0133 COG0133 439903 TrpB Tryptophan synthase beta chain [Amino acid transport and metabolism]. Tryptophan synthase beta chain is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 400 matched cddid_all.tbl CDD COG0134 COG0134 439904 TrpC Indole-3-glycerol phosphate synthase [Amino acid transport and metabolism]. Indole-3-glycerol phosphate synthase is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 257 matched cddid_all.tbl CDD COG0135 COG0135 439905 TrpF Phosphoribosylanthranilate isomerase [Amino acid transport and metabolism]. Phosphoribosylanthranilate isomerase is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 208 matched cddid_all.tbl CDD COG0136 COG0136 439906 Asd Aspartate-semialdehyde dehydrogenase [Amino acid transport and metabolism]. Aspartate-semialdehyde dehydrogenase is part of the Pathway/BioSystem: Lysine biosynthesis 333 matched cddid_all.tbl CDD COG0137 COG0137 439907 ArgG Argininosuccinate synthase [Amino acid transport and metabolism]. Argininosuccinate synthase is part of the Pathway/BioSystem: Arginine biosynthesis 397 matched cddid_all.tbl CDD COG0138 COG0138 439908 PurH AICAR transformylase/IMP cyclohydrolase PurH [Nucleotide transport and metabolism]. AICAR transformylase/IMP cyclohydrolase PurH is part of the Pathway/BioSystem: Purine biosynthesis 512 matched cddid_all.tbl CDD COG0139 COG0139 439909 HisI1 Phosphoribosyl-AMP cyclohydrolase [Amino acid transport and metabolism]. Phosphoribosyl-AMP cyclohydrolase is part of the Pathway/BioSystem: Histidine biosynthesis 106 matched cddid_all.tbl CDD COG0140 COG0140 439910 HisI2 Phosphoribosyl-ATP pyrophosphohydrolase [Amino acid transport and metabolism]. Phosphoribosyl-ATP pyrophosphohydrolase is part of the Pathway/BioSystem: Histidine biosynthesis 103 matched cddid_all.tbl CDD COG0141 COG0141 439911 HisD Histidinol dehydrogenase [Amino acid transport and metabolism]. Histidinol dehydrogenase is part of the Pathway/BioSystem: Histidine biosynthesis 429 matched cddid_all.tbl CDD COG0142 COG0142 439912 IspA Geranylgeranyl pyrophosphate synthase [Coenzyme transport and metabolism]. Geranylgeranyl pyrophosphate synthase is part of the Pathway/BioSystem: Isoprenoid biosynthesis 329 matched cddid_all.tbl CDD COG0143 COG0143 439913 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Methionyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 544 matched cddid_all.tbl CDD COG0144 COG0144 439914 RsmB 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]. 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family is part of the Pathway/BioSystem: 16S rRNA modification 441 matched cddid_all.tbl CDD COG0145 COG0145 439915 HyuA N-methylhydantoinase A/oxoprolinase/acetone carboxylase, beta subunit [Amino acid transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism]. 678 matched cddid_all.tbl CDD COG0146 COG0146 439916 HyuB N-methylhydantoinase B/oxoprolinase/acetone carboxylase, alpha subunit [Amino acid transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism]. 563 matched cddid_all.tbl CDD COG0147 COG0147 439917 TrpE Anthranilate/para-aminobenzoate synthases component I [Amino acid transport and metabolism, Coenzyme transport and metabolism]. Anthranilate/para-aminobenzoate synthases component I is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 416 matched cddid_all.tbl CDD COG0148 COG0148 439918 Eno Enolase [Carbohydrate transport and metabolism]. Enolase is part of the Pathway/BioSystem: Glycolysis 426 matched cddid_all.tbl CDD COG0149 COG0149 439919 TpiA Triosephosphate isomerase [Carbohydrate transport and metabolism]. Triosephosphate isomerase is part of the Pathway/BioSystem: Glycolysis 249 matched cddid_all.tbl CDD COG0150 COG0150 439920 PurM Phosphoribosylaminoimidazole (AIR) synthetase [Nucleotide transport and metabolism]. Phosphoribosylaminoimidazole (AIR) synthetase is part of the Pathway/BioSystem: Purine biosynthesis 343 matched cddid_all.tbl CDD COG0151 COG0151 439921 PurD Phosphoribosylamine-glycine ligase [Nucleotide transport and metabolism]. Phosphoribosylamine-glycine ligase is part of the Pathway/BioSystem: Purine biosynthesis 422 matched cddid_all.tbl CDD COG0152 COG0152 439922 PurC Phosphoribosylaminoimidazole-succinocarboxamide synthase [Nucleotide transport and metabolism]. Phosphoribosylaminoimidazole-succinocarboxamide synthase is part of the Pathway/BioSystem: Purine biosynthesis 245 matched cddid_all.tbl CDD COG0153 COG0153 439923 GalK Galactokinase [Carbohydrate transport and metabolism]. 380 matched cddid_all.tbl CDD COG0154 COG0154 439924 GatA Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit or related amidase [Translation, ribosomal structure and biogenesis]. Asp-tRNAAsn/Glu-tRNAGln amidotransferase A subunit or related amidase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 468 matched cddid_all.tbl CDD COG0155 COG0155 439925 CysI Sulfite reductase, beta subunit (hemoprotein) [Inorganic ion transport and metabolism]. Sulfite reductase, beta subunit (hemoprotein) is part of the Pathway/BioSystem: Cysteine biosynthesis 519 matched cddid_all.tbl CDD COG0156 COG0156 439926 BioF 7-keto-8-aminopelargonate synthetase or related enzyme [Coenzyme transport and metabolism]. 7-keto-8-aminopelargonate synthetase or related enzyme is part of the Pathway/BioSystem: Biotin biosynthesis 385 matched cddid_all.tbl CDD COG0157 COG0157 439927 NadC Nicotinate-nucleotide pyrophosphorylase [Coenzyme transport and metabolism]. Nicotinate-nucleotide pyrophosphorylase is part of the Pathway/BioSystem: NAD biosynthesis 272 matched cddid_all.tbl CDD COG0158 COG0158 439928 Fbp Fructose-1,6-bisphosphatase [Carbohydrate transport and metabolism]. Fructose-1,6-bisphosphatase is part of the Pathway/BioSystem: Gluconeogenesis 338 matched cddid_all.tbl CDD COG0159 COG0159 439929 TrpA Tryptophan synthase alpha chain [Amino acid transport and metabolism]. Tryptophan synthase alpha chain is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 262 matched cddid_all.tbl CDD COG0160 COG0160 439930 ArgD Acetylornithine aminotransferase/4-aminobutyrate aminotransferase [Amino acid transport and metabolism]. Acetylornithine aminotransferase/4-aminobutyrate aminotransferase is part of the Pathway/BioSystem: Arginine biosynthesis 429 matched cddid_all.tbl CDD COG0161 COG0161 439931 BioA Adenosylmethionine-8-amino-7-oxononanoate aminotransferase [Coenzyme transport and metabolism]. Adenosylmethionine-8-amino-7-oxononanoate aminotransferase is part of the Pathway/BioSystem: Biotin biosynthesis 446 matched cddid_all.tbl CDD COG0162 COG0162 439932 TyrS Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Tyrosyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 409 matched cddid_all.tbl CDD COG0163 COG0163 439933 UbiX Flavin prenyltransferase UbiX [Coenzyme transport and metabolism]. Flavin prenyltransferase UbiX is part of the Pathway/BioSystem: Ubiquinone biosynthesis 187 matched cddid_all.tbl CDD COG0164 COG0164 439934 RnhB Ribonuclease HII [Replication, recombination and repair]. 190 matched cddid_all.tbl CDD COG0165 COG0165 439935 ArgH Argininosuccinate lyase [Amino acid transport and metabolism]. Argininosuccinate lyase is part of the Pathway/BioSystem: Arginine biosynthesis 462 matched cddid_all.tbl CDD COG0166 COG0166 439936 Pgi Glucose-6-phosphate isomerase [Carbohydrate transport and metabolism]. Glucose-6-phosphate isomerase is part of the Pathway/BioSystem: Glycolysis 484 matched cddid_all.tbl CDD COG0167 COG0167 439937 PyrD Dihydroorotate dehydrogenase [Nucleotide transport and metabolism]. Dihydroorotate dehydrogenase is part of the Pathway/BioSystem: Pyrimidine biosynthesis 296 matched cddid_all.tbl CDD COG0168 COG0168 439938 TrkG Trk-type K+ transport system, membrane component [Inorganic ion transport and metabolism]. 414 matched cddid_all.tbl CDD COG0169 COG0169 439939 AroE Shikimate 5-dehydrogenase [Amino acid transport and metabolism]. Shikimate 5-dehydrogenase is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 270 matched cddid_all.tbl CDD COG0170 COG0170 439940 SEC59 Dolichol kinase [Posttranslational modification, protein turnover, chaperones, Cell wall/membrane/envelope biogenesis]. 190 matched cddid_all.tbl CDD COG0171 COG0171 439941 NadE NH3-dependent NAD+ synthetase [Coenzyme transport and metabolism]. NH3-dependent NAD+ synthetase is part of the Pathway/BioSystem: NAD biosynthesis 542 matched cddid_all.tbl CDD COG0172 COG0172 439942 SerS Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Seryl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 421 matched cddid_all.tbl CDD COG0173 COG0173 439943 AspS Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Aspartyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 589 matched cddid_all.tbl CDD COG0174 COG0174 439944 GlnA Glutamine synthetase [Amino acid transport and metabolism]. Glutamine synthetase is part of the Pathway/BioSystem: Glutamine biosynthesis 440 matched cddid_all.tbl CDD COG0175 COG0175 439945 CysD 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase or related enzyme [Amino acid transport and metabolism, Coenzyme transport and metabolism]. 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase or related enzyme is part of the Pathway/BioSystem: Cysteine biosynthesis 232 matched cddid_all.tbl CDD COG0176 COG0176 439946 TalA Transaldolase/fructose-6-phosphate aldolase [Carbohydrate transport and metabolism]. Transaldolase/fructose-6-phosphate aldolase is part of the Pathway/BioSystem: Pentose phosphate pathway 214 matched cddid_all.tbl CDD COG0177 COG0177 439947 Nth Endonuclease III [Replication, recombination and repair]. 198 matched cddid_all.tbl CDD COG0178 COG0178 439948 UvrA Excinuclease UvrABC ATPase subunit [Replication, recombination and repair]. 941 matched cddid_all.tbl CDD COG0179 COG0179 439949 YcgM 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (catechol pathway) [Secondary metabolites biosynthesis, transport and catabolism]. 206 matched cddid_all.tbl CDD COG0180 COG0180 439950 TrpS Tryptophanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Tryptophanyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 330 matched cddid_all.tbl CDD COG0181 COG0181 439951 HemC Porphobilinogen deaminase [Coenzyme transport and metabolism]. Porphobilinogen deaminase is part of the Pathway/BioSystem: Heme biosynthesis 306 matched cddid_all.tbl CDD COG0182 COG0182 439952 MtnA 5-methylthioribose/5-deoxyribulose 1-phosphate isomerase (methionine salvage pathway), a paralog of eIF-2B alpha subunit [Amino acid transport and metabolism]. 343 matched cddid_all.tbl CDD COG0183 COG0183 439953 PaaJ Acetyl-CoA acetyltransferase [Lipid transport and metabolism]. Acetyl-CoA acetyltransferase is part of the Pathway/BioSystem: Fatty acid biosynthesis 391 matched cddid_all.tbl CDD COG0184 COG0184 439954 RpsO Ribosomal protein S15P/S13E [Translation, ribosomal structure and biogenesis]. Ribosomal protein S15P/S13E is part of the Pathway/BioSystem: Ribosome 30S subunit 89 matched cddid_all.tbl CDD COG0185 COG0185 439955 RpsS Ribosomal protein S19 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S19 is part of the Pathway/BioSystem: Ribosome 30S subunit 95 matched cddid_all.tbl CDD COG0186 COG0186 439956 RpsQ Ribosomal protein S17 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S17 is part of the Pathway/BioSystem: Ribosome 30S subunit 87 matched cddid_all.tbl CDD COG0187 COG0187 439957 GyrB DNA gyrase/topoisomerase IV, subunit B [Replication, recombination and repair]. 635 matched cddid_all.tbl CDD COG0188 COG0188 439958 GyrA DNA gyrase/topoisomerase IV, subunit A [Replication, recombination and repair]. 804 matched cddid_all.tbl CDD COG0189 COG0189 439959 LysX Glutathione synthase, LysX or RimK-type ligase, ATP-grasp superfamily [Amino acid transport and metabolism, Coenzyme transport and metabolism, Translation, ribosomal structure and biogenesis, Secondary metabolites biosynthesis, transport and catabolism]. Glutathione synthase, LysX or RimK-type ligase, ATP-grasp superfamily is part of the Pathway/BioSystem: Lysine biosynthesis 289 matched cddid_all.tbl CDD COG0190 COG0190 439960 FolD 5,10-methylene-tetrahydrofolate dehydrogenase/Methenyl tetrahydrofolate cyclohydrolase [Coenzyme transport and metabolism]. 285 matched cddid_all.tbl CDD COG0191 COG0191 439961 Fba Fructose/tagatose bisphosphate aldolase [Carbohydrate transport and metabolism]. Fructose/tagatose bisphosphate aldolase is part of the Pathway/BioSystem: Glycolysis 283 matched cddid_all.tbl CDD COG0192 COG0192 439962 MetK S-adenosylmethionine synthetase [Coenzyme transport and metabolism]. S-adenosylmethionine synthetase is part of the Pathway/BioSystem: Methionine biosynthesis 384 matched cddid_all.tbl CDD COG0193 COG0193 439963 Pth Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]. Peptidyl-tRNA hydrolase is part of the Pathway/BioSystem: Translation factors 187 matched cddid_all.tbl CDD COG0194 COG0194 439964 Gmk Guanylate kinase [Nucleotide transport and metabolism]. 190 matched cddid_all.tbl CDD COG0195 COG0195 439965 NusA Transcription antitermination factor NusA, contains S1 and KH domains [Transcription]. 353 matched cddid_all.tbl CDD COG0196 COG0196 439966 RibF FAD synthase [Coenzyme transport and metabolism]. FAD synthase is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis 310 matched cddid_all.tbl CDD COG0197 COG0197 439967 RplP Ribosomal protein L16/L10AE [Translation, ribosomal structure and biogenesis]. Ribosomal protein L16/L10AE is part of the Pathway/BioSystem: Ribosome 50S subunit 136 matched cddid_all.tbl CDD COG0198 COG0198 439968 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L24 is part of the Pathway/BioSystem: Ribosome 50S subunit 104 matched cddid_all.tbl CDD COG0199 COG0199 439969 RpsN Ribosomal protein S14 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S14 is part of the Pathway/BioSystem: Ribosome 30S subunit 60 matched cddid_all.tbl CDD COG0200 COG0200 439970 RplO Ribosomal protein L15 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L15 is part of the Pathway/BioSystem: Ribosome 50S subunit 148 matched cddid_all.tbl CDD COG0201 COG0201 439971 SecY Preprotein translocase subunit SecY [Intracellular trafficking, secretion, and vesicular transport]. 427 matched cddid_all.tbl CDD COG0202 COG0202 439972 RpoA DNA-directed RNA polymerase, alpha subunit/40 kD subunit [Transcription]. DNA-directed RNA polymerase, alpha subunit/40 kD subunit is part of the Pathway/BioSystem: RNA polymerase 317 matched cddid_all.tbl CDD COG0203 COG0203 439973 RplQ Ribosomal protein L17 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L17 is part of the Pathway/BioSystem: Ribosome 50S subunit 121 matched cddid_all.tbl CDD COG0204 COG0204 439974 PlsC 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid transport and metabolism]. 1-acyl-sn-glycerol-3-phosphate acyltransferase is part of the Pathway/BioSystem: Phospholipid biosynthesis 215 matched cddid_all.tbl CDD COG0205 COG0205 439975 PfkA 6-phosphofructokinase [Carbohydrate transport and metabolism]. 6-phosphofructokinase is part of the Pathway/BioSystem: Glycolysis 344 matched cddid_all.tbl CDD COG0206 COG0206 439976 FtsZ Cell division GTPase FtsZ [Cell cycle control, cell division, chromosome partitioning]. 347 matched cddid_all.tbl CDD COG0207 COG0207 439977 ThyA Thymidylate synthase [Nucleotide transport and metabolism]. Thymidylate synthase is part of the Pathway/BioSystem: Thymidylate biosynthesis 264 matched cddid_all.tbl CDD COG0208 COG0208 439978 NrdB Ribonucleotide reductase beta subunit, ferritin-like domain [Nucleotide transport and metabolism]. Ribonucleotide reductase beta subunit, ferritin-like domain is part of the Pathway/BioSystem: Pyrimidine salvage 326 matched cddid_all.tbl CDD COG0209 COG0209 439979 NrdA Ribonucleotide reductase alpha subunit [Nucleotide transport and metabolism]. Ribonucleotide reductase alpha subunit is part of the Pathway/BioSystem: Pyrimidine salvage 665 matched cddid_all.tbl CDD COG0210 COG0210 439980 UvrD Superfamily I DNA or RNA helicase [Replication, recombination and repair]. 721 matched cddid_all.tbl CDD COG0211 COG0211 439981 RpmA Ribosomal protein L27 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L27 is part of the Pathway/BioSystem: Ribosome 50S subunit 82 matched cddid_all.tbl CDD COG0212 COG0212 439982 FAU1 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism]. 186 matched cddid_all.tbl CDD COG0213 COG0213 439983 DeoA Thymidine phosphorylase [Nucleotide transport and metabolism]. Thymidine phosphorylase is part of the Pathway/BioSystem: Pyrimidine salvage 431 matched cddid_all.tbl CDD COG0214 COG0214 439984 PdxS Pyridoxal 5'-phosphate synthase subunit PdxS [Coenzyme transport and metabolism]. Pyridoxal 5'-phosphate synthase subunit PdxS is part of the Pathway/BioSystem: Pyridoxal phosphate biosynthesis 293 matched cddid_all.tbl CDD COG0215 COG0215 439985 CysS Cysteinyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Cysteinyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 465 matched cddid_all.tbl CDD COG0216 COG0216 439986 PrfA Protein chain release factor RF1 [Translation, ribosomal structure and biogenesis]. Protein chain release factor RF1 is part of the Pathway/BioSystem: Translation factors 356 matched cddid_all.tbl CDD COG0217 COG0217 439987 TACO1 Transcriptional and/or translational regulatory protein YebC/TACO1 [Transcription, Translation, ribosomal structure and biogenesis]. 246 matched cddid_all.tbl CDD COG0218 COG0218 439988 EngB GTP-binding protein EngB required for normal cell division [Cell cycle control, cell division, chromosome partitioning]. 194 matched cddid_all.tbl CDD COG0219 COG0219 439989 TrmL tRNA(Leu) C34 or U34 (ribose-2'-O)-methylase TrmL, contains SPOUT domain [Translation, ribosomal structure and biogenesis]. tRNA(Leu) C34 or U34 (ribose-2'-O)-methylase TrmL, contains SPOUT domain is part of the Pathway/BioSystem: tRNA modification 153 matched cddid_all.tbl CDD COG0220 COG0220 439990 TrmB tRNA G46 N7-methylase TrmB [Translation, ribosomal structure and biogenesis]. tRNA G46 N7-methylase TrmB is part of the Pathway/BioSystem: tRNA modification 204 matched cddid_all.tbl CDD COG0221 COG0221 439991 Ppa Inorganic pyrophosphatase [Energy production and conversion]. 174 matched cddid_all.tbl CDD COG0222 COG0222 439992 RplL Ribosomal protein L7/L12 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L7/L12 is part of the Pathway/BioSystem: Ribosome 50S subunit 125 matched cddid_all.tbl CDD COG0223 COG0223 439993 Fmt Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis]. 308 matched cddid_all.tbl CDD COG0224 COG0224 439994 AtpG FoF1-type ATP synthase, gamma subunit [Energy production and conversion]. FoF1-type ATP synthase, gamma subunit is part of the Pathway/BioSystem: FoF1-type ATP synthase 288 matched cddid_all.tbl CDD COG0225 COG0225 439995 MsrA Peptide methionine sulfoxide reductase MsrA [Posttranslational modification, protein turnover, chaperones]. 177 matched cddid_all.tbl CDD COG0226 COG0226 439996 PstS ABC-type phosphate transport system, periplasmic component [Inorganic ion transport and metabolism]. 275 matched cddid_all.tbl CDD COG0227 COG0227 439997 RpmB Ribosomal protein L28 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L28 is part of the Pathway/BioSystem: Ribosome 50S subunit 68 matched cddid_all.tbl CDD COG0228 COG0228 439998 RpsP Ribosomal protein S16 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S16 is part of the Pathway/BioSystem: Ribosome 30S subunit 76 matched cddid_all.tbl CDD COG0229 COG0229 439999 MsrB Peptide methionine sulfoxide reductase MsrB [Posttranslational modification, protein turnover, chaperones]. 133 matched cddid_all.tbl CDD COG0230 COG0230 440000 RpmH Ribosomal protein L34 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L34 is part of the Pathway/BioSystem: Ribosome 50S subunit 44 matched cddid_all.tbl CDD COG0231 COG0231 440001 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]. Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) is part of the Pathway/BioSystem: Translation factors 186 matched cddid_all.tbl CDD COG0232 COG0232 440002 Dgt dGTP triphosphohydrolase [Nucleotide transport and metabolism]. 345 matched cddid_all.tbl CDD COG0233 COG0233 440003 Frr Ribosome recycling factor [Translation, ribosomal structure and biogenesis]. 185 matched cddid_all.tbl CDD COG0234 COG0234 440004 GroES Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones]. 95 matched cddid_all.tbl CDD COG0235 COG0235 440005 AraD 5-methylthioribulose/5-deoxyribulose/Fuculose 1-phosphate aldolase (methionine salvage, sugar degradation) [Amino acid transport and metabolism, Carbohydrate transport and metabolism]. 5-methylthioribulose/5-deoxyribulose/Fuculose 1-phosphate aldolase (methionine salvage, sugar degradation) is part of the Pathway/BioSystem: Urea cycle 208 matched cddid_all.tbl CDD COG0236 COG0236 440006 AcpP Acyl carrier protein [Lipid transport and metabolism]. Acyl carrier protein is part of the Pathway/BioSystem: Fatty acid biosynthesis 80 matched cddid_all.tbl CDD COG0237 COG0237 440007 CoaE Dephospho-CoA kinase [Coenzyme transport and metabolism]. Dephospho-CoA kinase is part of the Pathway/BioSystem: Pantothenate/CoA biosynthesis 193 matched cddid_all.tbl CDD COG0238 COG0238 440008 RpsR Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S18 is part of the Pathway/BioSystem: Ribosome 30S subunit 81 matched cddid_all.tbl CDD COG0239 COG0239 440009 CrcB Fluoride ion exporter CrcB/FEX, affects chromosome condensation [Cell cycle control, cell division, chromosome partitioning, Inorganic ion transport and metabolism]. 125 matched cddid_all.tbl CDD COG0240 COG0240 440010 GpsA Glycerol-3-phosphate dehydrogenase [Energy production and conversion]. Glycerol-3-phosphate dehydrogenase is part of the Pathway/BioSystem: Isoprenoid biosynthesis 327 matched cddid_all.tbl CDD COG0241 COG0241 440011 HisB1/GmhB Histidinol phosphatase/D-glycero-mannoheptose bisphosphatephosphatase, HAD superfamily [Amino acid transport and metabolism]. Histidinol phosphatase/D-glycero-mannoheptose bisphosphatephosphatase, HAD superfamily is part of the Pathway/BioSystem: Histidine biosynthesis 176 matched cddid_all.tbl CDD COG0242 COG0242 440012 Def Peptide deformylase [Translation, ribosomal structure and biogenesis]. 163 matched cddid_all.tbl CDD COG0243 COG0243 440013 BisC Anaerobic selenocysteine-containing dehydrogenase [Energy production and conversion]. 674 matched cddid_all.tbl CDD COG0244 COG0244 440014 RplJ Ribosomal protein L10 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L10 is part of the Pathway/BioSystem: Ribosome 50S subunit 172 matched cddid_all.tbl CDD COG0245 COG0245 440015 IspF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [Lipid transport and metabolism]. 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase is part of the Pathway/BioSystem: Isoprenoid biosynthesis 157 matched cddid_all.tbl CDD COG0246 COG0246 440016 MtlD Mannitol-1-phosphate/altronate dehydrogenases [Carbohydrate transport and metabolism]. 492 matched cddid_all.tbl CDD COG0247 COG0247 440017 GlpC Fe-S cluster-containing oxidoreductase, includes glycolate oxidase subunit GlcF [Energy production and conversion]. 420 matched cddid_all.tbl CDD COG0248 COG0248 440018 GppA Exopolyphosphatase/pppGpp-phosphohydrolase [Nucleotide transport and metabolism, Signal transduction mechanisms]. 314 matched cddid_all.tbl CDD COG0249 COG0249 440019 MutS DNA mismatch repair ATPase MutS [Replication, recombination and repair]. 861 matched cddid_all.tbl CDD COG0250 COG0250 440020 NusG Transcription termination/antitermination protein NusG [Transcription]. 171 matched cddid_all.tbl CDD COG0251 COG0251 440021 RidA Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 family [Defense mechanisms]. Enamine deaminase RidA, house cleaning of reactive enamine intermediates, YjgF/YER057c/UK114 family is part of the Pathway/BioSystem: Pyrimidine degradation 125 matched cddid_all.tbl CDD COG0252 COG0252 440022 AnsA L-asparaginase/archaeal Glu-tRNAGln amidotransferase subunit D [Translation, ribosomal structure and biogenesis, Amino acid transport and metabolism]. 325 matched cddid_all.tbl CDD COG0253 COG0253 440023 DapF Diaminopimelate epimerase [Amino acid transport and metabolism]. Diaminopimelate epimerase is part of the Pathway/BioSystem: Lysine biosynthesis 276 matched cddid_all.tbl CDD COG0254 COG0254 440024 RpmE Ribosomal protein L31 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L31 is part of the Pathway/BioSystem: Ribosome 50S subunit 72 matched cddid_all.tbl CDD COG0255 COG0255 440025 RpmC Ribosomal protein L29 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L29 is part of the Pathway/BioSystem: Ribosome 50S subunit 65 matched cddid_all.tbl CDD COG0256 COG0256 440026 RplR Ribosomal protein L18 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L18 is part of the Pathway/BioSystem: Ribosome 50S subunit 119 matched cddid_all.tbl CDD COG0257 COG0257 440027 RpmJ Ribosomal protein L36 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L36 is part of the Pathway/BioSystem: Ribosome 50S subunit 38 matched cddid_all.tbl CDD COG0258 COG0258 440028 ExoIX 5'-3' exonuclease Xni/ExoIX (flap endonuclease) [Replication, recombination and repair]. 286 matched cddid_all.tbl CDD COG0259 COG0259 440029 PdxH Pyridoxine/pyridoxamine 5'-phosphate oxidase [Coenzyme transport and metabolism]. Pyridoxine/pyridoxamine 5'-phosphate oxidase is part of the Pathway/BioSystem: Pyridoxal phosphate biosynthesis 212 matched cddid_all.tbl CDD COG0260 COG0260 440030 PepB Leucyl aminopeptidase [Amino acid transport and metabolism]. 492 matched cddid_all.tbl CDD COG0261 COG0261 440031 RplU Ribosomal protein L21 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L21 is part of the Pathway/BioSystem: Ribosome 50S subunit 103 matched cddid_all.tbl CDD COG0262 COG0262 440032 FolA Dihydrofolate reductase [Coenzyme transport and metabolism]. Dihydrofolate reductase is part of the Pathway/BioSystem: Folate biosynthesis 168 matched cddid_all.tbl CDD COG0263 COG0263 440033 ProB Glutamate 5-kinase [Amino acid transport and metabolism]. Glutamate 5-kinase is part of the Pathway/BioSystem: Proline biosynthesis 371 matched cddid_all.tbl CDD COG0264 COG0264 440034 Tsf Translation elongation factor EF-Ts [Translation, ribosomal structure and biogenesis]. Translation elongation factor EF-Ts is part of the Pathway/BioSystem: Translation factors 290 matched cddid_all.tbl CDD COG0265 COG0265 440035 DegQ Periplasmic serine protease, S1-C subfamily, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]. 274 matched cddid_all.tbl CDD COG0266 COG0266 440036 Nei Formamidopyrimidine-DNA glycosylase [Replication, recombination and repair]. 272 matched cddid_all.tbl CDD COG0267 COG0267 440037 RpmG Ribosomal protein L33 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L33 is part of the Pathway/BioSystem: Ribosome 50S subunit 52 matched cddid_all.tbl CDD COG0268 COG0268 440038 RpsT Ribosomal protein S20 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S20 is part of the Pathway/BioSystem: Ribosome 30S subunit 87 matched cddid_all.tbl CDD COG0269 COG0269 440039 UlaD 3-keto-L-gulonate-6-phosphate decarboxylase [Carbohydrate transport and metabolism]. 212 matched cddid_all.tbl CDD COG0270 COG0270 440040 Dcm DNA-cytosine methylase [Replication, recombination and repair]. 277 matched cddid_all.tbl CDD COG0271 COG0271 440041 BolA DNA-binding global transcriptional regulator BolA, affects cell shape, cell division and biofilm formation [Transcription, Signal transduction mechanisms]. 90 matched cddid_all.tbl CDD COG0272 COG0272 440042 Lig NAD-dependent DNA ligase [Replication, recombination and repair]. 668 matched cddid_all.tbl CDD COG0274 COG0274 440043 DeoC Deoxyribose-phosphate aldolase [Nucleotide transport and metabolism]. 219 matched cddid_all.tbl CDD COG0275 COG0275 440044 RmsH 16S rRNA C1402 N4-methylase RsmH [Translation, ribosomal structure and biogenesis]. 16S rRNA C1402 N4-methylase RsmH is part of the Pathway/BioSystem: 16S rRNA modification 312 matched cddid_all.tbl CDD COG0276 COG0276 440045 HemH Protoheme ferro-lyase (ferrochelatase) [Coenzyme transport and metabolism]. Protoheme ferro-lyase (ferrochelatase) is part of the Pathway/BioSystem: Heme biosynthesis 322 matched cddid_all.tbl CDD COG0277 COG0277 440046 GlcD FAD/FMN-containing lactate dehydrogenase/glycolate oxidase [Energy production and conversion]. 462 matched cddid_all.tbl CDD COG0278 COG0278 440047 GrxD Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]. 105 matched cddid_all.tbl CDD COG0279 COG0279 440048 GmhA Phosphoheptose isomerase [Carbohydrate transport and metabolism]. 189 matched cddid_all.tbl CDD COG0280 COG0280 440049 Pta Phosphotransacetylase (includes Pta, EutD and phosphobutyryltransferase) [Energy production and conversion]. 320 matched cddid_all.tbl CDD COG0281 COG0281 440050 SfcA Malic enzyme [Energy production and conversion]. Malic enzyme is part of the Pathway/BioSystem: Urea cycle 414 matched cddid_all.tbl CDD COG0282 COG0282 440051 AckA Acetate kinase [Energy production and conversion]. 395 matched cddid_all.tbl CDD COG0283 COG0283 440052 Cmk Cytidylate kinase [Nucleotide transport and metabolism]. 220 matched cddid_all.tbl CDD COG0284 COG0284 440053 PyrF Orotidine-5'-phosphate decarboxylase [Nucleotide transport and metabolism]. Orotidine-5'-phosphate decarboxylase is part of the Pathway/BioSystem: Pyrimidine biosynthesis 228 matched cddid_all.tbl CDD COG0285 COG0285 440054 FolC Folylpolyglutamate synthase/Dihydropteroate synthase [Coenzyme transport and metabolism]. Folylpolyglutamate synthase/Dihydropteroate synthase is part of the Pathway/BioSystem: Folate biosynthesis 423 matched cddid_all.tbl CDD COG0286 COG0286 440055 HsdM Type I restriction-modification system, DNA methylase subunit [Defense mechanisms]. 243 matched cddid_all.tbl CDD COG0287 COG0287 440056 TyrA Prephenate dehydrogenase [Amino acid transport and metabolism]. Prephenate dehydrogenase is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 278 matched cddid_all.tbl CDD COG0288 COG0288 440057 CynT Carbonic anhydrase [Inorganic ion transport and metabolism]. 204 matched cddid_all.tbl CDD COG0289 COG0289 440058 DapB 4-hydroxy-tetrahydrodipicolinate reductase [Amino acid transport and metabolism]. 4-hydroxy-tetrahydrodipicolinate reductase is part of the Pathway/BioSystem: Lysine biosynthesis 257 matched cddid_all.tbl CDD COG0290 COG0290 440059 InfC Translation initiation factor IF-3 [Translation, ribosomal structure and biogenesis]. Translation initiation factor IF-3 is part of the Pathway/BioSystem: Translation factors 175 matched cddid_all.tbl CDD COG0291 COG0291 440060 RpmI Ribosomal protein L35 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L35 is part of the Pathway/BioSystem: Ribosome 50S subunit 64 matched cddid_all.tbl CDD COG0292 COG0292 440061 RplT Ribosomal protein L20 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L20 is part of the Pathway/BioSystem: Ribosome 50S subunit 117 matched cddid_all.tbl CDD COG0293 COG0293 440062 RlmE 23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ [Translation, ribosomal structure and biogenesis]. 23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ is part of the Pathway/BioSystem: 23S rRNA modification 208 matched cddid_all.tbl CDD COG0294 COG0294 440063 FolP Dihydropteroate synthase [Coenzyme transport and metabolism]. Dihydropteroate synthase is part of the Pathway/BioSystem: Folate biosynthesis 274 matched cddid_all.tbl CDD COG0295 COG0295 440064 Cdd Cytidine deaminase [Nucleotide transport and metabolism]. Cytidine deaminase is part of the Pathway/BioSystem: Pyrimidine salvage 130 matched cddid_all.tbl CDD COG0296 COG0296 440065 GlgB 1,4-alpha-glucan branching enzyme [Carbohydrate transport and metabolism]. 625 matched cddid_all.tbl CDD COG0297 COG0297 440066 GlgA Glycogen synthase [Carbohydrate transport and metabolism]. 476 matched cddid_all.tbl CDD COG0298 COG0298 440067 HypC Hydrogenase maturation factor HybG, HypC/HupF family [Posttranslational modification, protein turnover, chaperones]. 78 matched cddid_all.tbl CDD COG0299 COG0299 440068 PurN Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]. Folate-dependent phosphoribosylglycinamide formyltransferase PurN is part of the Pathway/BioSystem: Purine biosynthesis 202 matched cddid_all.tbl CDD COG0300 COG0300 440069 YqjQ Short-chain dehydrogenase [General function prediction only]. 252 matched cddid_all.tbl CDD COG0301 COG0301 440070 ThiI Adenylyl- and sulfurtransferase ThiI (thiamine and tRNA 4-thiouridine biosynthesis) [Coenzyme transport and metabolism, Translation, ribosomal structure and biogenesis]. Adenylyl- and sulfurtransferase ThiI (thiamine and tRNA 4-thiouridine biosynthesis) is part of the Pathway/BioSystem: Thiamine biosynthesis 382 matched cddid_all.tbl CDD COG0302 COG0302 440071 FolE GTP cyclohydrolase I [Coenzyme transport and metabolism]. GTP cyclohydrolase I is part of the Pathway/BioSystem: Folate biosynthesis 186 matched cddid_all.tbl CDD COG0303 COG0303 440072 MoeA Molybdopterin Mo-transferase (molybdopterin biosynthesis) [Coenzyme transport and metabolism]. Molybdopterin Mo-transferase (molybdopterin biosynthesis) is part of the Pathway/BioSystem: Molybdopterin biosynthesis 401 matched cddid_all.tbl CDD COG0304 COG0304 440073 FabB 3-oxoacyl-(acyl-carrier-protein) synthase [Lipid transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism]. 3-oxoacyl-(acyl-carrier-protein) synthase is part of the Pathway/BioSystem: Fatty acid biosynthesis 409 matched cddid_all.tbl CDD COG0305 COG0305 440074 DnaB Replicative DNA helicase [Replication, recombination and repair]. 429 matched cddid_all.tbl CDD COG0306 COG0306 440075 PitA Phosphate/sulfate permease [Inorganic ion transport and metabolism]. 330 matched cddid_all.tbl CDD COG0307 COG0307 440076 RibC Riboflavin synthase alpha chain [Coenzyme transport and metabolism]. Riboflavin synthase alpha chain is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis 198 matched cddid_all.tbl CDD COG0308 COG0308 440077 PepN Aminopeptidase N, contains DUF3458 domain [Amino acid transport and metabolism]. 609 matched cddid_all.tbl CDD COG0309 COG0309 440078 HypE Carbamoyl dehydratase HypE (hydrogenase maturation factor) [Posttranslational modification, protein turnover, chaperones]. 328 matched cddid_all.tbl CDD COG0310 COG0310 440079 CbiM ABC-type Co2+ transport system, permease component [Inorganic ion transport and metabolism]. 198 matched cddid_all.tbl CDD COG0311 COG0311 440080 PdxT Pyridoxal 5'-phosphate synthase subunit PdxT (glutamine amidotransferase) [Coenzyme transport and metabolism]. Pyridoxal 5'-phosphate synthase subunit PdxT (glutamine amidotransferase) is part of the Pathway/BioSystem: Pyridoxal phosphate biosynthesis 191 matched cddid_all.tbl CDD COG0312 COG0312 440081 TldD Zn-dependent protease PmbA/TldA or its inactivated homolog [General function prediction only]. 443 matched cddid_all.tbl CDD COG0313 COG0313 440082 RsmI 16S rRNA C1402 (ribose-2'-O) methylase RsmI [Translation, ribosomal structure and biogenesis]. 16S rRNA C1402 (ribose-2'-O) methylase RsmI is part of the Pathway/BioSystem: 16S rRNA modification 219 matched cddid_all.tbl CDD COG0314 COG0314 440083 MoaE Molybdopterin synthase catalytic subunit MoaE [Coenzyme transport and metabolism]. Molybdopterin synthase catalytic subunit MoaE is part of the Pathway/BioSystem: Molybdopterin biosynthesis 143 matched cddid_all.tbl CDD COG0315 COG0315 440084 MoaC Molybdenum cofactor biosynthesis enzyme MoaC [Coenzyme transport and metabolism]. Molybdenum cofactor biosynthesis enzyme MoaC is part of the Pathway/BioSystem: Molybdopterin biosynthesis 153 matched cddid_all.tbl CDD COG0316 COG0316 440085 IscA Fe-S cluster assembly iron-binding protein IscA [Posttranslational modification, protein turnover, chaperones]. 107 matched cddid_all.tbl CDD COG0317 COG0317 440086 SpoT (p)ppGpp synthase/hydrolase, HD superfamily [Signal transduction mechanisms, Transcription]. 722 matched cddid_all.tbl CDD COG0318 COG0318 440087 MenE/FadK O-succinylbenzoic acid-CoA ligase MenE or related acyl-CoA synthetase (AMP-forming) [Lipid transport and metabolism]. O-succinylbenzoic acid-CoA ligase MenE or related acyl-CoA synthetase (AMP-forming) is part of the Pathway/BioSystem: Menaquinone biosynthesis 452 matched cddid_all.tbl CDD COG0319 COG0319 440088 YbeY ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme [Translation, ribosomal structure and biogenesis]. ssRNA-specific RNase YbeY, 16S rRNA maturation enzyme is part of the Pathway/BioSystem: 16S rRNA modification 144 matched cddid_all.tbl CDD COG0320 COG0320 440089 LipA Lipoate synthase [Coenzyme transport and metabolism]. Lipoate synthase is part of the Pathway/BioSystem: Lipoate biosynthesis 306 matched cddid_all.tbl CDD COG0321 COG0321 440090 LipB Lipoate-protein ligase B [Coenzyme transport and metabolism]. Lipoate-protein ligase B is part of the Pathway/BioSystem: Lipoate biosynthesis 211 matched cddid_all.tbl CDD COG0322 COG0322 440091 UvrC Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair]. 603 matched cddid_all.tbl CDD COG0323 COG0323 440092 MutL DNA mismatch repair ATPase MutL [Replication, recombination and repair]. 515 matched cddid_all.tbl CDD COG0324 COG0324 440093 MiaA tRNA A37 N6-isopentenylltransferase MiaA [Translation, ribosomal structure and biogenesis]. tRNA A37 N6-isopentenylltransferase MiaA is part of the Pathway/BioSystem: tRNA modification 306 matched cddid_all.tbl CDD COG0325 COG0325 440094 YggS Pyridoxal 5'-phosphate homeostasis protein YggS, UPF0001 family [Coenzyme transport and metabolism]. 227 matched cddid_all.tbl CDD COG0326 COG0326 440095 HtpG Molecular chaperone, HSP90 family [Posttranslational modification, protein turnover, chaperones]. 616 matched cddid_all.tbl CDD COG0327 COG0327 440096 NIF3 Putative GTP cyclohydrolase 1 type 2, NIF3 family [Coenzyme transport and metabolism]. Putative GTP cyclohydrolase 1 type 2, NIF3 family is part of the Pathway/BioSystem: Folate biosynthesis 254 matched cddid_all.tbl CDD COG0328 COG0328 440097 RnhA Ribonuclease HI [Replication, recombination and repair]. 136 matched cddid_all.tbl CDD COG0329 COG0329 440098 DapA 4-hydroxy-tetrahydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism, Cell wall/membrane/envelope biogenesis]. 4-hydroxy-tetrahydrodipicolinate synthase/N-acetylneuraminate lyase is part of the Pathway/BioSystem: Lysine biosynthesis 291 matched cddid_all.tbl CDD COG0330 COG0330 440099 HflC Regulator of protease activity HflC, stomatin/prohibitin superfamily [Posttranslational modification, protein turnover, chaperones]. 279 matched cddid_all.tbl CDD COG0331 COG0331 440100 FabD Malonyl CoA-acyl carrier protein transacylase [Lipid transport and metabolism]. Malonyl CoA-acyl carrier protein transacylase is part of the Pathway/BioSystem: Fatty acid biosynthesis 306 matched cddid_all.tbl CDD COG0332 COG0332 440101 FabH 3-oxoacyl-[acyl-carrier-protein] synthase III [Lipid transport and metabolism]. 3-oxoacyl-[acyl-carrier-protein] synthase III is part of the Pathway/BioSystem: Fatty acid biosynthesis 323 matched cddid_all.tbl CDD COG0333 COG0333 440102 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L32 is part of the Pathway/BioSystem: Ribosome 50S subunit 56 matched cddid_all.tbl CDD COG0334 COG0334 440103 GdhA Glutamate dehydrogenase/leucine dehydrogenase [Amino acid transport and metabolism]. Glutamate dehydrogenase/leucine dehydrogenase is part of the Pathway/BioSystem: Glutamine biosynthesis 411 matched cddid_all.tbl CDD COG0335 COG0335 440104 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L19 is part of the Pathway/BioSystem: Ribosome 50S subunit 116 matched cddid_all.tbl CDD COG0336 COG0336 440105 TrmD tRNA G37 N-methylase TrmD [Translation, ribosomal structure and biogenesis]. tRNA G37 N-methylase TrmD is part of the Pathway/BioSystem: tRNA modification 242 matched cddid_all.tbl CDD COG0337 COG0337 440106 AroB 3-dehydroquinate synthetase [Amino acid transport and metabolism]. 3-dehydroquinate synthetase is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 355 matched cddid_all.tbl CDD COG0338 COG0338 440107 Dam DNA-adenine methylase [Replication, recombination and repair]. 265 matched cddid_all.tbl CDD COG0339 COG0339 440108 Dcp Zn-dependent oligopeptidase, M3 family [Posttranslational modification, protein turnover, chaperones]. 682 matched cddid_all.tbl CDD COG0340 COG0340 440109 BirA2 Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme transport and metabolism]. Biotin-(acetyl-CoA carboxylase) ligase is part of the Pathway/BioSystem: Biotin biosynthesis 241 matched cddid_all.tbl CDD COG0341 COG0341 440110 SecF Preprotein translocase subunit SecF [Intracellular trafficking, secretion, and vesicular transport]. 291 matched cddid_all.tbl CDD COG0342 COG0342 440111 SecD Preprotein translocase subunit SecD [Intracellular trafficking, secretion, and vesicular transport]. 434 matched cddid_all.tbl CDD COG0343 COG0343 440112 Tgt Queuine/archaeosine tRNA-ribosyltransferase [Translation, ribosomal structure and biogenesis]. Queuine/archaeosine tRNA-ribosyltransferase is part of the Pathway/BioSystem: tRNA modification 370 matched cddid_all.tbl CDD COG0344 COG0344 440113 PlsY Phospholipid biosynthesis protein PlsY, probable glycerol-3-phosphate acyltransferase [Lipid transport and metabolism]. 194 matched cddid_all.tbl CDD COG0345 COG0345 440114 ProC Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism]. Pyrroline-5-carboxylate reductase is part of the Pathway/BioSystem: Proline biosynthesis 267 matched cddid_all.tbl CDD COG0346 COG0346 440115 GloA Catechol 2,3-dioxygenase or related enzyme, vicinal oxygen chelate (VOC) family [Secondary metabolites biosynthesis, transport and catabolism]. 125 matched cddid_all.tbl CDD COG0347 COG0347 440116 GlnK Nitrogen regulatory protein PII [Signal transduction mechanisms, Amino acid transport and metabolism]. 112 matched cddid_all.tbl CDD COG0348 COG0348 440117 NapH Polyferredoxin NapH [Energy production and conversion]. 263 matched cddid_all.tbl CDD COG0349 COG0349 440118 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]. 365 matched cddid_all.tbl CDD COG0350 COG0350 440119 AdaB DNA repair enzyme Ada (O6-methylguanine-DNA--protein-cysteine methyltransferase) [Replication, recombination and repair]. 163 matched cddid_all.tbl CDD COG0351 COG0351 440120 ThiD Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase [Coenzyme transport and metabolism]. Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase is part of the Pathway/BioSystem: Thiamine biosynthesis 254 matched cddid_all.tbl CDD COG0352 COG0352 440121 ThiE Thiamine monophosphate synthase [Coenzyme transport and metabolism]. Thiamine monophosphate synthase is part of the Pathway/BioSystem: Thiamine biosynthesis 206 matched cddid_all.tbl CDD COG0353 COG0353 440122 RecR Recombinational DNA repair protein RecR [Replication, recombination and repair]. 195 matched cddid_all.tbl CDD COG0354 COG0354 440123 YgfZ Folate-binding protein YgfZ, synthesis and repair of Fe-S clusters [Posttranslational modification, protein turnover, chaperones]. 317 matched cddid_all.tbl CDD COG0355 COG0355 440124 AtpC FoF1-type ATP synthase, epsilon subunit [Energy production and conversion]. FoF1-type ATP synthase, epsilon subunit is part of the Pathway/BioSystem: FoF1-type ATP synthase 131 matched cddid_all.tbl CDD COG0356 COG0356 440125 AtpB FoF1-type ATP synthase, membrane subunit a [Energy production and conversion]. FoF1-type ATP synthase, membrane subunit a is part of the Pathway/BioSystem: FoF1-type ATP synthase 212 matched cddid_all.tbl CDD COG0357 COG0357 440126 RsmG 16S rRNA G527 N7-methylase RsmG (former glucose-inhibited division protein B) [Translation, ribosomal structure and biogenesis]. 16S rRNA G527 N7-methylase RsmG (former glucose-inhibited division protein B) is part of the Pathway/BioSystem: 16S rRNA modification 211 matched cddid_all.tbl CDD COG0358 COG0358 440127 DnaG DNA primase (bacterial type) [Replication, recombination and repair]. 465 matched cddid_all.tbl CDD COG0359 COG0359 440128 RplI Ribosomal protein L9 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L9 is part of the Pathway/BioSystem: Ribosome 50S subunit 147 matched cddid_all.tbl CDD COG0360 COG0360 440129 RpsF Ribosomal protein S6 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S6 is part of the Pathway/BioSystem: Ribosome 30S subunit 107 matched cddid_all.tbl CDD COG0361 COG0361 440130 InfA Translation initiation factor IF-1 [Translation, ribosomal structure and biogenesis]. Translation initiation factor IF-1 is part of the Pathway/BioSystem: Translation factors 73 matched cddid_all.tbl CDD COG0362 COG0362 440131 Gnd 6-phosphogluconate dehydrogenase [Carbohydrate transport and metabolism]. 6-phosphogluconate dehydrogenase is part of the Pathway/BioSystem: Pentose phosphate pathway 467 matched cddid_all.tbl CDD COG0363 COG0363 440132 NagB 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase [Carbohydrate transport and metabolism]. 6-phosphogluconolactonase/Glucosamine-6-phosphate isomerase/deaminase is part of the Pathway/BioSystem: Pentose phosphate pathway 248 matched cddid_all.tbl CDD COG0364 COG0364 440133 Zwf Glucose-6-phosphate 1-dehydrogenase [Carbohydrate transport and metabolism]. Glucose-6-phosphate 1-dehydrogenase is part of the Pathway/BioSystem: Pentose phosphate pathway 495 matched cddid_all.tbl CDD COG0365 COG0365 440134 Acs Acyl-coenzyme A synthetase/AMP-(fatty) acid ligase [Lipid transport and metabolism]. 565 matched cddid_all.tbl CDD COG0366 COG0366 440135 AmyA Glycosidase/amylase (phosphorylase) [Carbohydrate transport and metabolism]. 413 matched cddid_all.tbl CDD COG0367 COG0367 440136 AsnB Asparagine synthetase B (glutamine-hydrolyzing) [Amino acid transport and metabolism]. Asparagine synthetase B (glutamine-hydrolyzing) is part of the Pathway/BioSystem: Asparagine biosynthesis 558 matched cddid_all.tbl CDD COG0368 COG0368 440137 CobS Cobalamin synthase CobS (adenosylcobinamide-GDP ribazoletransferase) [Coenzyme transport and metabolism]. Cobalamin synthase CobS (adenosylcobinamide-GDP ribazoletransferase) is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 246 matched cddid_all.tbl CDD COG0369 COG0369 440138 CysJ Flavoprotein (flavin reductase) subunit CysJ of sulfite and N-hydroxylaminopurine reductases [Nucleotide transport and metabolism, Inorganic ion transport and metabolism]. Flavoprotein (flavin reductase) subunit CysJ of sulfite and N-hydroxylaminopurine reductases is part of the Pathway/BioSystem: Cysteine biosynthesis 561 matched cddid_all.tbl CDD COG0370 COG0370 440139 FeoB Fe2+ transporter FeoB [Inorganic ion transport and metabolism]. 662 matched cddid_all.tbl CDD COG0371 COG0371 440140 GldA Glycerol dehydrogenase or related enzyme, iron-containing ADH family [Energy production and conversion]. Glycerol dehydrogenase or related enzyme, iron-containing ADH family is part of the Pathway/BioSystem: Isoprenoid biosynthesis 355 matched cddid_all.tbl CDD COG0372 COG0372 440141 GltA Citrate synthase [Energy production and conversion]. Citrate synthase is part of the Pathway/BioSystem: TCA cycle 387 matched cddid_all.tbl CDD COG0373 COG0373 440142 HemA Glutamyl-tRNA reductase [Coenzyme transport and metabolism]. Glutamyl-tRNA reductase is part of the Pathway/BioSystem: Heme biosynthesis 425 matched cddid_all.tbl CDD COG0374 COG0374 440143 HyaB Ni,Fe-hydrogenase I large subunit [Energy production and conversion]. 539 matched cddid_all.tbl CDD COG0375 COG0375 440144 HybF Hydrogenase maturation factor HypA/HybF, metallochaperone involved in Ni insertion [Posttranslational modification, protein turnover, chaperones]. 113 matched cddid_all.tbl CDD COG0376 COG0376 440145 KatG Catalase (peroxidase I) [Inorganic ion transport and metabolism]. 731 matched cddid_all.tbl CDD COG0377 COG0377 440146 NuoB NADH:ubiquinone oxidoreductase 20 kD subunit (chain B) or related Fe-S oxidoreductase [Energy production and conversion]. NADH:ubiquinone oxidoreductase 20 kD subunit (chain B) or related Fe-S oxidoreductase is part of the Pathway/BioSystem: NADH dehydrogenase 152 matched cddid_all.tbl CDD COG0378 COG0378 440147 HypB Hydrogenase/urease maturation factor HypB, Ni2+-binding GTPase [Posttranslational modification, protein turnover, chaperones]. 200 matched cddid_all.tbl CDD COG0379 COG0379 440148 NadA Quinolinate synthase [Coenzyme transport and metabolism]. Quinolinate synthase is part of the Pathway/BioSystem: NAD biosynthesis 299 matched cddid_all.tbl CDD COG0380 COG0380 440149 OtsA Trehalose-6-phosphate synthase, GT20 family [Carbohydrate transport and metabolism]. 474 matched cddid_all.tbl CDD COG0381 COG0381 440150 WecB UDP-N-acetylglucosamine 2-epimerase [Cell wall/membrane/envelope biogenesis]. 366 matched cddid_all.tbl CDD COG0382 COG0382 440151 UbiA 4-hydroxybenzoate polyprenyltransferase [Coenzyme transport and metabolism]. 4-hydroxybenzoate polyprenyltransferase is part of the Pathway/BioSystem: Ubiquinone biosynthesis 280 matched cddid_all.tbl CDD COG0383 COG0383 440152 MngB Alpha-mannosidase [Carbohydrate transport and metabolism]. 798 matched cddid_all.tbl CDD COG0384 COG0384 440153 YHI9 Predicted epimerase YddE/YHI9, PhzF superfamily [General function prediction only]. 281 matched cddid_all.tbl CDD COG0385 COG0385 440154 YfeH Predicted Na+-dependent transporter YfeH [General function prediction only]. 294 matched cddid_all.tbl CDD COG0386 COG0386 440155 BtuE Thioredoxin/glutathione peroxidase BtuE, reduces lipid peroxides [Defense mechanisms, Lipid transport and metabolism]. 161 matched cddid_all.tbl CDD COG0387 COG0387 440156 ChaA Cation (Ca2+/Na+/K+)/H+ antiporter ChaA [Inorganic ion transport and metabolism]. 362 matched cddid_all.tbl CDD COG0388 COG0388 440157 Nit2 Omega-amidase YafV/Nit2, hydrolyzes alpha-ketoglutaramate [Energy production and conversion]. 264 matched cddid_all.tbl CDD COG0389 COG0389 440158 DinP Nucleotidyltransferase/DNA polymerase DinP involved in DNA repair [Replication, recombination and repair]. 336 matched cddid_all.tbl CDD COG0390 COG0390 440159 FetB ABC-type iron transport system FetAB, permease component [Inorganic ion transport and metabolism]. 259 matched cddid_all.tbl CDD COG0391 COG0391 440160 CofD Archaeal 2-phospho-L-lactate transferase/Bacterial gluconeogenesis factor, CofD/UPF0052 family [Carbohydrate transport and metabolism, Coenzyme transport and metabolism]. 314 matched cddid_all.tbl CDD COG0392 COG0392 440161 AglD2 Predicted membrane flippase AglD2/YbhN, UPF0104 family [Cell wall/membrane/envelope biogenesis]. 289 matched cddid_all.tbl CDD COG0393 COG0393 440162 YbjQ Uncharacterized pentameric protein YbjQ, UPF0145 family [Function unknown]. 103 matched cddid_all.tbl CDD COG0394 COG0394 440163 Wzb Protein-tyrosine-phosphatase [Signal transduction mechanisms]. 137 matched cddid_all.tbl CDD COG0395 COG0395 440164 UgpE ABC-type glycerol-3-phosphate transport system, permease component [Carbohydrate transport and metabolism]. 282 matched cddid_all.tbl CDD COG0396 COG0396 440165 SufC Fe-S cluster assembly ATPase SufC [Posttranslational modification, protein turnover, chaperones]. 245 matched cddid_all.tbl CDD COG0397 COG0397 440166 SelO Protein adenylyltransferase (AMPylase) SelO/YdiU (selenoprotein O) [Posttranslational modification, protein turnover, chaperones]. 490 matched cddid_all.tbl CDD COG0398 COG0398 440167 TVP38 Uncharacterized membrane protein YdjX, related to fungal oxalate transporter, TVP38/TMEM64 family [Function unknown]. 209 matched cddid_all.tbl CDD COG0399 COG0399 440168 WecE dTDP-4-amino-4,6-dideoxygalactose transaminase [Cell wall/membrane/envelope biogenesis]. 364 matched cddid_all.tbl CDD COG0400 COG0400 440169 YpfH Predicted esterase [General function prediction only]. 200 matched cddid_all.tbl CDD COG0401 COG0401 440170 YqaE Membrane potential modulator PMP3/YqaE, plasma membrane proteolipid 3 (PMP3)/Esi3/RCI2/UPF0057 family [Energy production and conversion]. 53 matched cddid_all.tbl CDD COG0402 COG0402 440171 SsnA Cytosine/adenosine deaminase or related metal-dependent hydrolase [Nucleotide transport and metabolism, General function prediction only]. Cytosine/adenosine deaminase or related metal-dependent hydrolase is part of the Pathway/BioSystem: Pyrimidine salvage 416 matched cddid_all.tbl CDD COG0403 COG0403 440172 GcvP1 Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain [Amino acid transport and metabolism]. Glycine cleavage system protein P (pyridoxal-binding), N-terminal domain is part of the Pathway/BioSystem: Glycine cleavage 442 matched cddid_all.tbl CDD COG0404 COG0404 440173 GcvT Glycine cleavage system protein T (aminomethyltransferase) [Amino acid transport and metabolism]. Glycine cleavage system protein T (aminomethyltransferase) is part of the Pathway/BioSystem: Glycine cleavage 372 matched cddid_all.tbl CDD COG0405 COG0405 440174 Ggt Gamma-glutamyltranspeptidase [Amino acid transport and metabolism]. 507 matched cddid_all.tbl CDD COG0406 COG0406 440175 PhoE Broad specificity phosphatase PhoE [Carbohydrate transport and metabolism]. 195 matched cddid_all.tbl CDD COG0407 COG0407 440176 HemE Uroporphyrinogen-III decarboxylase HemE [Coenzyme transport and metabolism]. Uroporphyrinogen-III decarboxylase HemE is part of the Pathway/BioSystem: Heme biosynthesis 336 matched cddid_all.tbl CDD COG0408 COG0408 440177 HemF Coproporphyrinogen-III oxidase HemH, oxygen-dependent [Coenzyme transport and metabolism]. Coproporphyrinogen-III oxidase HemH, oxygen-dependent is part of the Pathway/BioSystem: Heme biosynthesis 298 matched cddid_all.tbl CDD COG0409 COG0409 440178 HypD Hydrogenase maturation factor HypD [Posttranslational modification, protein turnover, chaperones]. 367 matched cddid_all.tbl CDD COG0410 COG0410 440179 LivF ABC-type branched-chain amino acid transport system, ATPase component LivF [Amino acid transport and metabolism]. 236 matched cddid_all.tbl CDD COG0411 COG0411 440180 LivG ABC-type branched-chain amino acid transport system, ATPase component LivG [Amino acid transport and metabolism]. 257 matched cddid_all.tbl CDD COG0412 COG0412 440181 DLH Dienelactone hydrolase [Secondary metabolites biosynthesis, transport and catabolism]. 226 matched cddid_all.tbl CDD COG0413 COG0413 440182 PanB Ketopantoate hydroxymethyltransferase [Coenzyme transport and metabolism]. Ketopantoate hydroxymethyltransferase is part of the Pathway/BioSystem: Pantothenate/CoA biosynthesis 261 matched cddid_all.tbl CDD COG0414 COG0414 440183 PanC Panthothenate synthetase [Coenzyme transport and metabolism]. Panthothenate synthetase is part of the Pathway/BioSystem: Pantothenate/CoA biosynthesis 280 matched cddid_all.tbl CDD COG0415 COG0415 440184 PhrB Deoxyribodipyrimidine photolyase [Replication, recombination and repair]. 466 matched cddid_all.tbl CDD COG0416 COG0416 440185 PlsX Acyl-ACP:phosphate acyltransferase (fatty acid/phospholipid biosynthesis) [Lipid transport and metabolism]. 331 matched cddid_all.tbl CDD COG0417 COG0417 440186 PolB DNA polymerase B elongation subunit [Replication, recombination and repair]. 794 matched cddid_all.tbl CDD COG0418 COG0418 440187 PyrC Dihydroorotase [Nucleotide transport and metabolism]. Dihydroorotase is part of the Pathway/BioSystem: Pyrimidine biosynthesis 344 matched cddid_all.tbl CDD COG0419 COG0419 440188 SbcC DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]. 204 matched cddid_all.tbl CDD COG0420 COG0420 440189 SbcD DNA repair exonuclease SbcCD nuclease subunit [Replication, recombination and repair]. 250 matched cddid_all.tbl CDD COG0421 COG0421 440190 SpeE Spermidine synthase (polyamine aminopropyltransferase) [Amino acid transport and metabolism]. 195 matched cddid_all.tbl CDD COG0422 COG0422 440191 ThiC 4-amino-2-methyl-5-hydroxymethylpyrimidine (HMP) synthase ThiC [Coenzyme transport and metabolism]. 4-amino-2-methyl-5-hydroxymethylpyrimidine (HMP) synthase ThiC is part of the Pathway/BioSystem: Thiamine biosynthesis 430 matched cddid_all.tbl CDD COG0423 COG0423 440192 GRS1 Glycyl-tRNA synthetase, class II [Translation, ribosomal structure and biogenesis]. Glycyl-tRNA synthetase, class II is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 461 matched cddid_all.tbl CDD COG0424 COG0424 440193 Maf 7-methyl-GTP pyrophosphatase and related NTP pyrophosphatases, Maf/HAM1 superfamily [Secondary metabolites biosynthesis, transport and catabolism]. 189 matched cddid_all.tbl CDD COG0425 COG0425 440194 TusA Sulfur carrier protein TusA (tRNA thiolation, molybdenum cofactor biosynthesis) [Translation, ribosomal structure and biogenesis, Coenzyme transport and metabolism, Posttranslational modification, protein turnover, chaperones]. 70 matched cddid_all.tbl CDD COG0426 COG0426 440195 NorV Flavorubredoxin [Energy production and conversion]. 390 matched cddid_all.tbl CDD COG0427 COG0427 440196 ACH1 Propionyl CoA:succinate CoA transferase [Energy production and conversion]. 427 matched cddid_all.tbl CDD COG0428 COG0428 440197 ZupT Zinc transporter ZupT [Inorganic ion transport and metabolism]. 243 matched cddid_all.tbl CDD COG0429 COG0429 440198 YheT Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]. 323 matched cddid_all.tbl CDD COG0430 COG0430 440199 RCL1 RNA 3'-terminal phosphate cyclase [RNA processing and modification]. 340 matched cddid_all.tbl CDD COG0431 COG0431 440200 SsuE NAD(P)H-dependent FMN reductase [Energy production and conversion]. 162 matched cddid_all.tbl CDD COG0432 COG0432 440201 YjbQ Thiamin phosphate synthase YjbQ, UPF0047 family [Coenzyme transport and metabolism]. 133 matched cddid_all.tbl CDD COG0433 COG0433 440202 HerA Archaeal DNA helicase HerA or a related bacterial ATPase, contains HAS-barrel and ATPase domains [Replication, recombination and repair]. 388 matched cddid_all.tbl CDD COG0434 COG0434 440203 BtpA Membrane biogenesis protein, BtpA/SgcQ family [Cell wall/membrane/envelope biogenesis]. 268 matched cddid_all.tbl CDD COG0435 COG0435 440204 ECM4 Glutathionyl-hydroquinone reductase [Energy production and conversion]. 321 matched cddid_all.tbl CDD COG0436 COG0436 440205 AspB Aspartate/methionine/tyrosine aminotransferase [Amino acid transport and metabolism]. Aspartate/methionine/tyrosine aminotransferase is part of the Pathway/BioSystem: Isoleucine, leucine, valine biosynthesis 387 matched cddid_all.tbl CDD COG0437 COG0437 440206 HybA Fe-S-cluster-containing dehydrogenase component (DMSO reductase) [Energy production and conversion]. 184 matched cddid_all.tbl CDD COG0438 COG0438 440207 RfaB Glycosyltransferase involved in cell wall bisynthesis [Cell wall/membrane/envelope biogenesis]. 123 matched cddid_all.tbl CDD COG0439 COG0439 440208 AccC Biotin carboxylase [Lipid transport and metabolism]. Biotin carboxylase is part of the Pathway/BioSystem: Fatty acid biosynthesis 263 matched cddid_all.tbl CDD COG0440 COG0440 440209 IlvH Acetolactate synthase, small subunit [Amino acid transport and metabolism]. Acetolactate synthase, small subunit is part of the Pathway/BioSystem: Isoleucine, leucine, valine biosynthesis 160 matched cddid_all.tbl CDD COG0441 COG0441 440210 ThrS Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Threonyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 639 matched cddid_all.tbl CDD COG0442 COG0442 440211 ProS Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Prolyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 564 matched cddid_all.tbl CDD COG0443 COG0443 440212 DnaK Molecular chaperone DnaK (HSP70) [Posttranslational modification, protein turnover, chaperones]. 473 matched cddid_all.tbl CDD COG0444 COG0444 440213 DppD ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism, Inorganic ion transport and metabolism]. 320 matched cddid_all.tbl CDD COG0445 COG0445 440214 MnmG tRNA U34 5-carboxymethylaminomethyl modifying enzyme MnmG/GidA [Translation, ribosomal structure and biogenesis]. tRNA U34 5-carboxymethylaminomethyl modifying enzyme MnmG/GidA is part of the Pathway/BioSystem: tRNA modification 626 matched cddid_all.tbl CDD COG0446 COG0446 440215 FadH2 NADPH-dependent 2,4-dienoyl-CoA reductase, sulfur reductase, or a related oxidoreductase [Lipid transport and metabolism]. 322 matched cddid_all.tbl CDD COG0447 COG0447 440216 MenB 1,4-Dihydroxy-2-naphthoyl-CoA synthase [Coenzyme transport and metabolism]. 1,4-Dihydroxy-2-naphthoyl-CoA synthase is part of the Pathway/BioSystem: Menaquinone biosynthesis 281 matched cddid_all.tbl CDD COG0448 COG0448 440217 GlgC Glucose-1-phosphate adenylyltransferase (ADP-glucose pyrophosphorylase) [Carbohydrate transport and metabolism]. 377 matched cddid_all.tbl CDD COG0449 COG0449 440218 GlmS Glucosamine 6-phosphate synthetase, contains amidotransferase and phosphosugar isomerase domains [Cell wall/membrane/envelope biogenesis]. 610 matched cddid_all.tbl CDD COG0450 COG0450 440219 AhpC Alkyl hydroperoxide reductase subunit AhpC (peroxiredoxin) [Defense mechanisms]. 196 matched cddid_all.tbl CDD COG0451 COG0451 440220 WcaG Nucleoside-diphosphate-sugar epimerase [Cell wall/membrane/envelope biogenesis]. 295 matched cddid_all.tbl CDD COG0452 COG0452 440221 CoaBC Phosphopantothenoylcysteine synthetase/decarboxylase CoaBC [Coenzyme transport and metabolism]. Phosphopantothenoylcysteine synthetase/decarboxylase CoaBC is part of the Pathway/BioSystem: Pantothenate/CoA biosynthesis 399 matched cddid_all.tbl CDD COG0454 COG0454 440222 PhnO N-acetyltransferase, GNAT superfamily (includes histone acetyltransferase HPA2) [Transcription, General function prediction only]. 136 matched cddid_all.tbl CDD COG0455 COG0455 440223 FlhG MinD-like ATPase FlhG/YlxH, activator of the FlhF-type GTPase [Cell cycle control, cell division, chromosome partitioning, Cell motility]. 230 matched cddid_all.tbl CDD COG0456 COG0456 440224 RimI Ribosomal protein S18 acetylase RimI and related acetyltransferases [Translation, ribosomal structure and biogenesis]. 92 matched cddid_all.tbl CDD COG0457 COG0457 440225 TPR Tetratricopeptide (TPR) repeat [General function prediction only]. 245 matched cddid_all.tbl CDD COG0458 COG0458 440226 CarB Carbamoylphosphate synthase large subunit [Amino acid transport and metabolism, Nucleotide transport and metabolism]. Carbamoylphosphate synthase large subunit is part of the Pathway/BioSystem: Arginine biosynthesis 536 matched cddid_all.tbl CDD COG0459 COG0459 440227 GroEL Chaperonin GroEL (HSP60 family) [Posttranslational modification, protein turnover, chaperones]. 497 matched cddid_all.tbl CDD COG0460 COG0460 440228 ThrA Homoserine dehydrogenase [Amino acid transport and metabolism]. Homoserine dehydrogenase is part of the Pathway/BioSystem: Methionine biosynthesis 302 matched cddid_all.tbl CDD COG0461 COG0461 440229 PyrE Orotate phosphoribosyltransferase [Nucleotide transport and metabolism]. Orotate phosphoribosyltransferase is part of the Pathway/BioSystem: Pyrimidine biosynthesis 201 matched cddid_all.tbl CDD COG0462 COG0462 440230 PrsA Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism]. Phosphoribosylpyrophosphate synthetase is part of the Pathway/BioSystem: Histidine biosynthesis, Purine biosynthesis 311 matched cddid_all.tbl CDD COG0463 COG0463 440231 WcaA Glycosyltransferase involved in cell wall bisynthesis [Cell wall/membrane/envelope biogenesis]. 208 matched cddid_all.tbl CDD COG0464 COG0464 440232 SpoVK AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. 397 matched cddid_all.tbl CDD COG0465 COG0465 440233 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]. 583 matched cddid_all.tbl CDD COG0466 COG0466 440234 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]. 785 matched cddid_all.tbl CDD COG0467 COG0467 440235 RAD55 RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms]. 221 matched cddid_all.tbl CDD COG0468 COG0468 440236 RecA RecA/RadA recombinase [Replication, recombination and repair]. 351 matched cddid_all.tbl CDD COG0469 COG0469 440237 PykF Pyruvate kinase [Carbohydrate transport and metabolism]. Pyruvate kinase is part of the Pathway/BioSystem: Glycolysis 471 matched cddid_all.tbl CDD COG0470 COG0470 440238 HolB DNA polymerase III, delta prime subunit [Replication, recombination and repair]. 289 matched cddid_all.tbl CDD COG0471 COG0471 440239 CitT Di- and tricarboxylate antiporter [Carbohydrate transport and metabolism]. 369 matched cddid_all.tbl CDD COG0472 COG0472 440240 Rfe UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N-acetylglucosamine-1-phosphate transferase [Cell wall/membrane/envelope biogenesis]. UDP-N-acetylmuramyl pentapeptide phosphotransferase/UDP-N-acetylglucosamine-1-phosphate transferase is part of the Pathway/BioSystem: Mureine biosynthesis 288 matched cddid_all.tbl CDD COG0473 COG0473 440241 LeuB Isocitrate/isopropylmalate dehydrogenase [Energy production and conversion, Amino acid transport and metabolism]. Isocitrate/isopropylmalate dehydrogenase is part of the Pathway/BioSystem: TCA cycle 346 matched cddid_all.tbl CDD COG0474 COG0474 440242 MgtA Magnesium-transporting ATPase (P-type) [Inorganic ion transport and metabolism]. 874 matched cddid_all.tbl CDD COG0475 COG0475 440243 KefB Kef-type K+ transport system, membrane component KefB [Inorganic ion transport and metabolism]. 384 matched cddid_all.tbl CDD COG0476 COG0476 440244 ThiF Molybdopterin or thiamine biosynthesis adenylyltransferase [Coenzyme transport and metabolism]. Molybdopterin or thiamine biosynthesis adenylyltransferase is part of the Pathway/BioSystem: Molybdopterin biosynthesis 244 matched cddid_all.tbl CDD COG0477 COG0477 440245 ProP MFS family permease, includes anhydromuropeptide permease AmpG [Carbohydrate transport and metabolism, Amino acid transport and metabolism, Inorganic ion transport and metabolism, General function prediction only]. 295 matched cddid_all.tbl CDD COG0478 COG0478 440246 RIO2 RIO-like serine/threonine protein kinase fused to N-terminal HTH domain [Signal transduction mechanisms]. 183 matched cddid_all.tbl CDD COG0479 COG0479 440247 SdhB/FrdB Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit [Energy production and conversion]. Succinate dehydrogenase/fumarate reductase, Fe-S protein subunit is part of the Pathway/BioSystem: TCA cycle 230 matched cddid_all.tbl CDD COG0480 COG0480 440248 FusA Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]. Translation elongation factor EF-G, a GTPase is part of the Pathway/BioSystem: Translation factors 693 matched cddid_all.tbl CDD COG0481 COG0481 440249 LepA Translation elongation factor EF-4, membrane-bound GTPase [Translation, ribosomal structure and biogenesis]. 598 matched cddid_all.tbl CDD COG0482 COG0482 440250 MnmA tRNA U34 2-thiouridine synthase MnmA/TrmU, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]. tRNA U34 2-thiouridine synthase MnmA/TrmU, contains the PP-loop ATPase domain is part of the Pathway/BioSystem: tRNA modification 353 matched cddid_all.tbl CDD COG0483 COG0483 440251 SuhB Archaeal fructose-1,6-bisphosphatase or related enzyme, inositol monophosphatase family [Carbohydrate transport and metabolism]. Archaeal fructose-1,6-bisphosphatase or related enzyme, inositol monophosphatase family is part of the Pathway/BioSystem: Gluconeogenesis 255 matched cddid_all.tbl CDD COG0484 COG0484 440252 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]. 139 matched cddid_all.tbl CDD COG0486 COG0486 440253 MnmE tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE [Translation, ribosomal structure and biogenesis]. tRNA U34 5-carboxymethylaminomethyl modifying GTPase MnmE/TrmE is part of the Pathway/BioSystem: tRNA modification 448 matched cddid_all.tbl CDD COG0488 COG0488 440254 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]. 520 matched cddid_all.tbl CDD COG0489 COG0489 440255 Mrp Fe-S cluster carrier ATPase, Mrp/ApbC/NBP35 family [Cell cycle control, cell division, chromosome partitioning]. 289 matched cddid_all.tbl CDD COG0490 COG0490 440256 KhtT K+/H+ antiporter KhtSTU, c-di-AMP-binding regulatory subunit KhtT, contains RCK_C (TrkA_C) domain [Inorganic ion transport and metabolism, Signal transduction mechanisms]. 140 matched cddid_all.tbl CDD COG0491 COG0491 440257 GloB Glyoxylase or a related metal-dependent hydrolase, beta-lactamase superfamily II [General function prediction only]. 215 matched cddid_all.tbl CDD COG0492 COG0492 440258 TrxB Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones]. 305 matched cddid_all.tbl CDD COG0493 COG0493 440259 GltD NADPH-dependent glutamate synthase beta chain or related oxidoreductase [Amino acid transport and metabolism, General function prediction only]. NADPH-dependent glutamate synthase beta chain or related oxidoreductase is part of the Pathway/BioSystem: Glutamine biosynthesis 434 matched cddid_all.tbl CDD COG0494 COG0494 440260 MutT 8-oxo-dGTP pyrophosphatase MutT and related house-cleaning NTP pyrophosphohydrolases, NUDIX family [Defense mechanisms]. 143 matched cddid_all.tbl CDD COG0495 COG0495 440261 LeuS Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Leucyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 826 matched cddid_all.tbl CDD COG0496 COG0496 440262 SurE Broad specificity polyphosphatase and 5'/3'-nucleotidase SurE [Replication, recombination and repair]. 245 matched cddid_all.tbl CDD COG0497 COG0497 440263 RecN DNA repair ATPase RecN [Replication, recombination and repair]. 555 matched cddid_all.tbl CDD COG0498 COG0498 440264 ThrC Threonine synthase [Amino acid transport and metabolism]. Threonine synthase is part of the Pathway/BioSystem: Threonine biosynthesis 394 matched cddid_all.tbl CDD COG0499 COG0499 440265 SAM1 S-adenosylhomocysteine hydrolase [Coenzyme transport and metabolism]. 420 matched cddid_all.tbl CDD COG0500 COG0500 440266 SmtA SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, General function prediction only]. 199 matched cddid_all.tbl CDD COG0501 COG0501 440267 HtpX Zn-dependent protease with chaperone function [Posttranslational modification, protein turnover, chaperones]. 210 matched cddid_all.tbl CDD COG0502 COG0502 440268 BioB Biotin synthase or related enzyme [Coenzyme transport and metabolism]. Biotin synthase or related enzyme is part of the Pathway/BioSystem: Biotin biosynthesis 308 matched cddid_all.tbl CDD COG0503 COG0503 440269 Apt Adenine/guanine phosphoribosyltransferase or related PRPP-binding protein [Nucleotide transport and metabolism]. Adenine/guanine phosphoribosyltransferase or related PRPP-binding protein is part of the Pathway/BioSystem: Purine salvage 171 matched cddid_all.tbl CDD COG0504 COG0504 440270 PyrG CTP synthase (UTP-ammonia lyase) [Nucleotide transport and metabolism]. CTP synthase (UTP-ammonia lyase) is part of the Pathway/BioSystem: Pyrimidine biosynthesis 535 matched cddid_all.tbl CDD COG0505 COG0505 440271 CarA Carbamoylphosphate synthase small subunit [Amino acid transport and metabolism, Nucleotide transport and metabolism]. Carbamoylphosphate synthase small subunit is part of the Pathway/BioSystem: Arginine biosynthesis 361 matched cddid_all.tbl CDD COG0506 COG0506 440272 PutA Proline dehydrogenase [Amino acid transport and metabolism]. Proline dehydrogenase is part of the Pathway/BioSystem: Proline degradation 975 matched cddid_all.tbl CDD COG0507 COG0507 440273 RecD ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair]. 514 matched cddid_all.tbl CDD COG0508 COG0508 440274 AceF Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component [Energy production and conversion]. Pyruvate/2-oxoglutarate dehydrogenase complex, dihydrolipoamide acyltransferase (E2) component is part of the Pathway/BioSystem: Pyruvate oxidation 77 matched cddid_all.tbl CDD COG0509 COG0509 440275 GcvH Glycine cleavage system protein H (lipoate-binding) [Amino acid transport and metabolism]. Glycine cleavage system protein H (lipoate-binding) is part of the Pathway/BioSystem: Glycine cleavage 128 matched cddid_all.tbl CDD COG0510 COG0510 440276 CotS Thiamine kinase or a related kinase [Coenzyme transport and metabolism]. 156 matched cddid_all.tbl CDD COG0511 COG0511 440277 AccB Biotin carboxyl carrier protein [Lipid transport and metabolism]. Biotin carboxyl carrier protein is part of the Pathway/BioSystem: Fatty acid biosynthesis 136 matched cddid_all.tbl CDD COG0512 COG0512 440278 PabA Anthranilate/para-aminobenzoate synthase component II (glutamine amidotransferase) [Amino acid transport and metabolism, Coenzyme transport and metabolism]. Anthranilate/para-aminobenzoate synthase component II (glutamine amidotransferase) is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 189 matched cddid_all.tbl CDD COG0513 COG0513 440279 SrmB Superfamily II DNA and RNA helicase [Replication, recombination and repair]. 420 matched cddid_all.tbl CDD COG0514 COG0514 440280 RecQ Superfamily II DNA helicase RecQ [Replication, recombination and repair]. 489 matched cddid_all.tbl CDD COG0515 COG0515 440281 SPS1 Serine/threonine protein kinase [Signal transduction mechanisms]. 482 matched cddid_all.tbl CDD COG0516 COG0516 440282 GuaB IMP dehydrogenase/GMP reductase [Nucleotide transport and metabolism]. IMP dehydrogenase/GMP reductase is part of the Pathway/BioSystem: Purine biosynthesis 326 matched cddid_all.tbl CDD COG0517 COG0517 440283 CBS CBS domain [Signal transduction mechanisms]. 128 matched cddid_all.tbl CDD COG0518 COG0518 440284 GuaA1 GMP synthase, glutamine amidotransferase domain [Nucleotide transport and metabolism]. GMP synthase, glutamine amidotransferase domain is part of the Pathway/BioSystem: Purine biosynthesis 225 matched cddid_all.tbl CDD COG0519 COG0519 440285 GuaA2 GMP synthase, PP-ATPase domain/subunit [Nucleotide transport and metabolism]. GMP synthase, PP-ATPase domain/subunit is part of the Pathway/BioSystem: Purine biosynthesis 512 matched cddid_all.tbl CDD COG0520 COG0520 440286 CsdA Selenocysteine lyase/Cysteine desulfurase [Amino acid transport and metabolism]. 396 matched cddid_all.tbl CDD COG0521 COG0521 440287 MoaB Molybdopterin biosynthesis enzyme MoaB/MogA [Coenzyme transport and metabolism]. Molybdopterin biosynthesis enzyme MoaB/MogA is part of the Pathway/BioSystem: Molybdopterin biosynthesis 169 matched cddid_all.tbl CDD COG0522 COG0522 440288 RpsD Ribosomal protein S4 or related protein [Translation, ribosomal structure and biogenesis]. Ribosomal protein S4 or related protein is part of the Pathway/BioSystem: Ribosome 30S subunit 204 matched cddid_all.tbl CDD COG0523 COG0523 440289 YejR Zinc metallochaperone YeiR/ZagA and related GTPases, G3E family [General function prediction only]. 318 matched cddid_all.tbl CDD COG0524 COG0524 440290 RbsK Sugar or nucleoside kinase, ribokinase family [Carbohydrate transport and metabolism]. Sugar or nucleoside kinase, ribokinase family is part of the Pathway/BioSystem: Glycolysis 301 matched cddid_all.tbl CDD COG0525 COG0525 440291 ValS Valyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. Valyl-tRNA synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 877 matched cddid_all.tbl CDD COG0526 COG0526 440292 TrxA Thiol-disulfide isomerase or thioredoxin [Posttranslational modification, protein turnover, chaperones]. 139 matched cddid_all.tbl CDD COG0527 COG0527 440293 MetL1 Aspartate kinase [Amino acid transport and metabolism]. Aspartate kinase is part of the Pathway/BioSystem: Lysine biosynthesis 407 matched cddid_all.tbl CDD COG0528 COG0528 440294 PyrH Uridylate kinase [Nucleotide transport and metabolism]. Uridylate kinase is part of the Pathway/BioSystem: Pyrimidine biosynthesis 238 matched cddid_all.tbl CDD COG0529 COG0529 440295 CysC Adenylylsulfate kinase or related kinase [Inorganic ion transport and metabolism]. Adenylylsulfate kinase or related kinase is part of the Pathway/BioSystem: Cysteine biosynthesis 189 matched cddid_all.tbl CDD COG0530 COG0530 440296 ECM27 Ca2+/Na+ antiporter [Inorganic ion transport and metabolism]. 293 matched cddid_all.tbl CDD COG0531 COG0531 440297 PotE Serine transporter YbeC, amino acid:H+ symporter family [Amino acid transport and metabolism]. 438 matched cddid_all.tbl CDD COG0532 COG0532 440298 InfB Translation initiation factor IF-2, a GTPase [Translation, ribosomal structure and biogenesis]. Translation initiation factor IF-2, a GTPase is part of the Pathway/BioSystem: Translation factors 502 matched cddid_all.tbl CDD COG0533 COG0533 440299 TsaD tRNA A37 threonylcarbamoyltransferase TsaD [Translation, ribosomal structure and biogenesis]. tRNA A37 threonylcarbamoyltransferase TsaD is part of the Pathway/BioSystem: tRNA modification 333 matched cddid_all.tbl CDD COG0534 COG0534 440300 NorM Na+-driven multidrug efflux pump, DinF/NorM/MATE family [Defense mechanisms]. 427 matched cddid_all.tbl CDD COG0535 COG0535 440301 SkfB Radical SAM superfamily maturase, SkfB/NifB/PqqE family [Cell cycle control, cell division, chromosome partitioning, Coenzyme transport and metabolism]. 159 matched cddid_all.tbl CDD COG0536 COG0536 440302 Obg GTPase involved in cell partioning and DNA repair [Cell cycle control, cell division, chromosome partitioning, Replication, recombination, and repair]. 343 matched cddid_all.tbl CDD COG0537 COG0537 440303 HinT Purine nucleoside phosphoramidase/Ap4A hydrolase, histidine triade (HIT) family [Nucleotide transport and metabolism, General function prediction only]. 133 matched cddid_all.tbl CDD COG0538 COG0538 440304 Icd Isocitrate dehydrogenase [Energy production and conversion]. Isocitrate dehydrogenase is part of the Pathway/BioSystem: TCA cycle 409 matched cddid_all.tbl CDD COG0539 COG0539 440305 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S1 is part of the Pathway/BioSystem: Ribosome 30S subunit 348 matched cddid_all.tbl CDD COG0540 COG0540 440306 PyrB Aspartate carbamoyltransferase, catalytic subunit [Nucleotide transport and metabolism]. Aspartate carbamoyltransferase, catalytic subunit is part of the Pathway/BioSystem: Pyrimidine biosynthesis 306 matched cddid_all.tbl CDD COG0541 COG0541 440307 Ffh Signal recognition particle GTPase [Intracellular trafficking, secretion, and vesicular transport]. 423 matched cddid_all.tbl CDD COG0542 COG0542 440308 ClpA ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones]. 836 matched cddid_all.tbl CDD COG0543 COG0543 440309 Mcr1 NAD(P)H-flavin reductase [Coenzyme transport and metabolism, Energy production and conversion]. 247 matched cddid_all.tbl CDD COG0544 COG0544 440310 Tig FKBP-type peptidyl-prolyl cis-trans isomerase (trigger factor) [Posttranslational modification, protein turnover, chaperones]. 424 matched cddid_all.tbl CDD COG0545 COG0545 440311 FkpA FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]. 104 matched cddid_all.tbl CDD COG0546 COG0546 440312 Gph Phosphoglycolate phosphatase, HAD superfamily [Energy production and conversion]. 214 matched cddid_all.tbl CDD COG0547 COG0547 440313 TrpD Anthranilate phosphoribosyltransferase, glycosyltransferase domain [Amino acid transport and metabolism]. Anthranilate phosphoribosyltransferase, glycosyltransferase domain is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 327 matched cddid_all.tbl CDD COG0548 COG0548 440314 ArgB N-acetylglutamate kinase [Amino acid transport and metabolism]. N-acetylglutamate kinase is part of the Pathway/BioSystem: Arginine biosynthesis 283 matched cddid_all.tbl CDD COG0549 COG0549 440315 ArcC Carbamate kinase [Amino acid transport and metabolism]. 313 matched cddid_all.tbl CDD COG0550 COG0550 440316 TopA DNA topoisomerase IA [Replication, recombination and repair]. 541 matched cddid_all.tbl CDD COG0551 COG0551 440317 YrdD DNA topoisomerase I, ssDNA-binding Zn-finger and Zn-ribbon domains [Replication, recombination and repair]. 695 matched cddid_all.tbl CDD COG0552 COG0552 440318 FtsY Signal recognition particle GTPase FtsY [Intracellular trafficking, secretion, and vesicular transport]. 303 matched cddid_all.tbl CDD COG0553 COG0553 440319 HepA Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination, and repair]. 682 matched cddid_all.tbl CDD COG0554 COG0554 440320 GlpK Glycerol kinase [Energy production and conversion]. 496 matched cddid_all.tbl CDD COG0555 COG0555 440321 CysU ABC-type sulfate transport system, permease component [Inorganic ion transport and metabolism]. 268 matched cddid_all.tbl CDD COG0556 COG0556 440322 UvrB Excinuclease UvrABC helicase subunit UvrB [Replication, recombination and repair]. 657 matched cddid_all.tbl CDD COG0557 COG0557 440323 VacB Exoribonuclease R [Transcription]. 711 matched cddid_all.tbl CDD COG0558 COG0558 440324 PgsA Phosphatidylglycerophosphate synthase [Lipid transport and metabolism]. Phosphatidylglycerophosphate synthase is part of the Pathway/BioSystem: Phospholipid biosynthesis 177 matched cddid_all.tbl CDD COG0559 COG0559 440325 LivH Branched-chain amino acid ABC-type transport system, permease component [Amino acid transport and metabolism]. 290 matched cddid_all.tbl CDD COG0560 COG0560 440326 SerB Phosphoserine phosphatase [Amino acid transport and metabolism]. Phosphoserine phosphatase is part of the Pathway/BioSystem: Serine biosynthesis 221 matched cddid_all.tbl CDD COG0561 COG0561 440327 Cof Hydroxymethylpyrimidine pyrophosphatase and other HAD family phosphatases [Coenzyme transport and metabolism, General function prediction only]. 192 matched cddid_all.tbl CDD COG0562 COG0562 440328 Glf UDP-galactopyranose mutase [Cell wall/membrane/envelope biogenesis]. 365 matched cddid_all.tbl CDD COG0563 COG0563 440329 Adk Adenylate kinase or related kinase [Nucleotide transport and metabolism]. Adenylate kinase or related kinase is part of the Pathway/BioSystem: Pyrimidine biosynthesis 212 matched cddid_all.tbl CDD COG0564 COG0564 440330 RluA Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific [Translation, ribosomal structure and biogenesis]. Pseudouridine synthase RluA, 23S rRNA- or tRNA-specific is part of the Pathway/BioSystem: 23S rRNA modification 218 matched cddid_all.tbl CDD COG0565 COG0565 440331 TrmJ tRNA C32,U32 (ribose-2'-O)-methylase TrmJ or a related methyltransferase [Translation, ribosomal structure and biogenesis]. tRNA C32,U32 (ribose-2'-O)-methylase TrmJ or a related methyltransferase is part of the Pathway/BioSystem: tRNA modification 237 matched cddid_all.tbl CDD COG0566 COG0566 440332 SpoU tRNA G18 (ribose-2'-O)-methylase SpoU [Translation, ribosomal structure and biogenesis]. tRNA G18 (ribose-2'-O)-methylase SpoU is part of the Pathway/BioSystem: tRNA modification 265 matched cddid_all.tbl CDD COG0567 COG0567 440333 SucA 2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, and related enzymes [Energy production and conversion]. 2-oxoglutarate dehydrogenase complex, dehydrogenase (E1) component, and related enzymes is part of the Pathway/BioSystem: TCA cycle 935 matched cddid_all.tbl CDD COG0568 COG0568 440334 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]. DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase 268 matched cddid_all.tbl CDD COG0569 COG0569 440335 TrkA Trk/Ktr K+ transport system regulatory component TrkA/KtrA/KtrC, RCK domain [Inorganic ion transport and metabolism, Signal transduction mechanisms]. 296 matched cddid_all.tbl CDD COG0571 COG0571 440336 Rnc dsRNA-specific ribonuclease [Transcription]. 229 matched cddid_all.tbl CDD COG0572 COG0572 440337 Udk Uridine kinase [Nucleotide transport and metabolism]. Uridine kinase is part of the Pathway/BioSystem: Pyrimidine salvage 206 matched cddid_all.tbl CDD COG0573 COG0573 440338 PstC ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]. 303 matched cddid_all.tbl CDD COG0574 COG0574 440339 PpsA Phosphoenolpyruvate synthase/pyruvate phosphate dikinase [Carbohydrate transport and metabolism]. Phosphoenolpyruvate synthase/pyruvate phosphate dikinase is part of the Pathway/BioSystem: Gluconeogenesis 455 matched cddid_all.tbl CDD COG0575 COG0575 440340 CdsA CDP-diglyceride synthetase [Lipid transport and metabolism]. CDP-diglyceride synthetase is part of the Pathway/BioSystem: Phospholipid biosynthesis 211 matched cddid_all.tbl CDD COG0576 COG0576 440341 GrpE Molecular chaperone GrpE (heat shock protein HSP-70) [Posttranslational modification, protein turnover, chaperones]. 147 matched cddid_all.tbl CDD COG0577 COG0577 440342 SalY ABC-type antimicrobial peptide transport system, permease component [Defense mechanisms]. 339 matched cddid_all.tbl CDD COG0578 COG0578 440343 GlpA Glycerol-3-phosphate dehydrogenase [Energy production and conversion]. Glycerol-3-phosphate dehydrogenase is part of the Pathway/BioSystem: Isoprenoid biosynthesis 501 matched cddid_all.tbl CDD COG0579 COG0579 440344 LhgO L-2-hydroxyglutarate oxidase LhgO [Carbohydrate transport and metabolism]. 418 matched cddid_all.tbl CDD COG0580 COG0580 440345 GlpF Glycerol uptake facilitator or related aquaporin (Major Intrinsic protein Family) [Carbohydrate transport and metabolism]. 232 matched cddid_all.tbl CDD COG0581 COG0581 440346 PstA ABC-type phosphate transport system, permease component [Inorganic ion transport and metabolism]. 259 matched cddid_all.tbl CDD COG0582 COG0582 440347 FimB Integrase/recombinase, includes phage integrase [Replication, recombination and repair, Mobilome: prophages, transposons]. 391 matched cddid_all.tbl CDD COG0583 COG0583 440348 LysR DNA-binding transcriptional regulator, LysR family [Transcription]. 256 matched cddid_all.tbl CDD COG0584 COG0584 440349 UgpQ Glycerophosphoryl diester phosphodiesterase [Lipid transport and metabolism]. 238 matched cddid_all.tbl CDD COG0585 COG0585 440350 TruD tRNA(Glu) U13 pseudouridine synthase TruD [Translation, ribosomal structure and biogenesis]. tRNA(Glu) U13 pseudouridine synthase TruD is part of the Pathway/BioSystem: tRNA modification 349 matched cddid_all.tbl CDD COG0586 COG0586 440351 DedA Membrane integrity protein DedA, putative transporter, DedA/Tvp38 family [Cell wall/membrane/envelope biogenesis]. 201 matched cddid_all.tbl CDD COG0587 COG0587 440352 DnaE DNA polymerase III, alpha subunit [Replication, recombination and repair]. 1050 matched cddid_all.tbl CDD COG0588 COG0588 440353 GpmA Phosphoglycerate mutase (BPG-dependent) [Carbohydrate transport and metabolism]. Phosphoglycerate mutase (BPG-dependent) is part of the Pathway/BioSystem: Glycolysis 229 matched cddid_all.tbl CDD COG0589 COG0589 440354 UspA Nucleotide-binding universal stress protein, UspA family [Signal transduction mechanisms]. 136 matched cddid_all.tbl CDD COG0590 COG0590 440355 TadA tRNA(Arg) A34 adenosine deaminase TadA [Translation, ribosomal structure and biogenesis]. tRNA(Arg) A34 adenosine deaminase TadA is part of the Pathway/BioSystem: Pyrimidine salvagetRNA modification 148 matched cddid_all.tbl CDD COG0591 COG0591 440356 PutP Na+/proline symporter [Amino acid transport and metabolism]. 476 matched cddid_all.tbl CDD COG0592 COG0592 440357 DnaN DNA polymerase III sliding clamp (beta) subunit, PCNA homolog [Replication, recombination and repair]. 365 matched cddid_all.tbl CDD COG0593 COG0593 440358 DnaA Chromosomal replication initiation ATPase DnaA [Replication, recombination and repair]. 303 matched cddid_all.tbl CDD COG0594 COG0594 440359 RnpA RNase P protein component [Translation, ribosomal structure and biogenesis]. 99 matched cddid_all.tbl CDD COG0595 COG0595 440360 RnjA mRNA degradation ribonuclease J1/J2 [Translation, ribosomal structure and biogenesis]. 553 matched cddid_all.tbl CDD COG0596 COG0596 440361 MenH 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase MenH and related esterases, alpha/beta hydrolase fold [Coenzyme transport and metabolism, General function prediction only]. 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase MenH and related esterases, alpha/beta hydrolase fold is part of the Pathway/BioSystem: Menaquinone biosynthesis 221 matched cddid_all.tbl CDD COG0597 COG0597 440362 LspA Lipoprotein signal peptidase [Cell wall/membrane/envelope biogenesis, Intracellular trafficking, secretion, and vesicular transport]. 151 matched cddid_all.tbl CDD COG0598 COG0598 440363 CorA Mg2+ and Co2+ transporter CorA [Inorganic ion transport and metabolism]. 305 matched cddid_all.tbl CDD COG0599 COG0599 440364 YurZ Uncharacterized conserved protein YurZ, alkylhydroperoxidase/carboxymuconolactone decarboxylase family [General function prediction only]. 114 matched cddid_all.tbl CDD COG0600 COG0600 440365 TauC ABC-type nitrate/sulfonate/bicarbonate transport system, permease component [Inorganic ion transport and metabolism]. 254 matched cddid_all.tbl CDD COG0601 COG0601 440366 DppB ABC-type dipeptide/oligopeptide/nickel transport system, permease component [Amino acid transport and metabolism, Inorganic ion transport and metabolism]. 314 matched cddid_all.tbl CDD COG0602 COG0602 440367 QueE Organic radical activating enzyme NrdG/QueE [Coenzyme transport and metabolism]. Organic radical activating enzyme NrdG/QueE is part of the Pathway/BioSystem: tRNA modification 205 matched cddid_all.tbl CDD COG0603 COG0603 440368 QueC 7-cyano-7-deazaguanine synthase (queuosine biosynthesis) [Translation, ribosomal structure and biogenesis]. 7-cyano-7-deazaguanine synthase (queuosine biosynthesis) is part of the Pathway/BioSystem: tRNA modification 223 matched cddid_all.tbl CDD COG0604 COG0604 440369 Qor NADPH:quinone reductase or related Zn-dependent oxidoreductase [Energy production and conversion, General function prediction only]. 322 matched cddid_all.tbl CDD COG0605 COG0605 440370 SodA Superoxide dismutase [Inorganic ion transport and metabolism]. 192 matched cddid_all.tbl CDD COG0606 COG0606 440371 YifB Predicted Mg-chelatase, contains ChlI-like and ATPase domains, YifB family [Posttranslational modification, protein turnover, chaperones]. 502 matched cddid_all.tbl CDD COG0607 COG0607 440372 PspE Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism]. Rhodanese-related sulfurtransferase is part of the Pathway/BioSystem: Urea cycle 106 matched cddid_all.tbl CDD COG0608 COG0608 440373 RecJ ssDNA-specific exonuclease RecJ, DHH superfamily, may be involved in archaeal DNA replication intiation [Replication, recombination and repair]. 552 matched cddid_all.tbl CDD COG0609 COG0609 440374 FepD ABC-type Fe3+-siderophore transport system, permease component [Inorganic ion transport and metabolism]. 306 matched cddid_all.tbl CDD COG0610 COG0610 440375 COG0610 Type I site-specific restriction-modification system, R (restriction) subunit and related helicases ... [Defense mechanisms]. 936 matched cddid_all.tbl CDD COG0611 COG0611 440376 ThiL Thiamine monophosphate kinase [Coenzyme transport and metabolism]. Thiamine monophosphate kinase is part of the Pathway/BioSystem: Thiamine biosynthesis 321 matched cddid_all.tbl CDD COG0612 COG0612 440377 PqqL Predicted Zn-dependent peptidase, M16 family [General function prediction only]. 427 matched cddid_all.tbl CDD COG0613 COG0613 440378 YciV 5'-3' exoribonuclease TrpH/YciV (RNase AM), contains PHP domain [Nucleotide transport and metabolism]. 188 matched cddid_all.tbl CDD COG0614 COG0614 440379 FepB ABC-type Fe3+-hydroxamate transport system, periplasmic component [Inorganic ion transport and metabolism]. 264 matched cddid_all.tbl CDD COG0615 COG0615 440380 TagD Glycerol-3-phosphate cytidylyltransferase, cytidylyltransferase family [Cell wall/membrane/envelope biogenesis]. Glycerol-3-phosphate cytidylyltransferase, cytidylyltransferase family is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis 131 matched cddid_all.tbl CDD COG0616 COG0616 440381 SppA Periplasmic serine protease, ClpP class [Posttranslational modification, protein turnover, chaperones]. 215 matched cddid_all.tbl CDD COG0617 COG0617 440382 PcnB tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]. tRNA nucleotidyltransferase/poly(A) polymerase is part of the Pathway/BioSystem: tRNA modification 391 matched cddid_all.tbl CDD COG0618 COG0618 440383 NrnA nanoRNase/pAp phosphatase, hydrolyzes c-di-AMP and oligoRNAs [Nucleotide transport and metabolism, Signal transduction mechanisms]. 312 matched cddid_all.tbl CDD COG0619 COG0619 440384 EcfT ECF-type transporter transmembrane protein EcfT [Coenzyme transport and metabolism]. 249 matched cddid_all.tbl CDD COG0620 COG0620 440385 MetE Methionine synthase II (cobalamin-independent) [Amino acid transport and metabolism]. Methionine synthase II (cobalamin-independent) is part of the Pathway/BioSystem: Methionine biosynthesis 325 matched cddid_all.tbl CDD COG0621 COG0621 440386 MiaB tRNA A37 methylthiotransferase MiaB [Translation, ribosomal structure and biogenesis]. tRNA A37 methylthiotransferase MiaB is part of the Pathway/BioSystem: tRNA modification 435 matched cddid_all.tbl CDD COG0622 COG0622 440387 YfcE Predicted phosphodiesterase, calcineurin family [General function prediction only]. 183 matched cddid_all.tbl CDD COG0623 COG0623 440388 FabI Enoyl-[acyl-carrier-protein] reductase FabI [Lipid transport and metabolism]. Enoyl-[acyl-carrier-protein] reductase FabI is part of the Pathway/BioSystem: Fatty acid biosynthesis 254 matched cddid_all.tbl CDD COG0624 COG0624 440389 ArgE Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase or related deacylase [Amino acid transport and metabolism]. Acetylornithine deacetylase/Succinyl-diaminopimelate desuccinylase or related deacylase is part of the Pathway/BioSystem: Arginine biosynthesis 388 matched cddid_all.tbl CDD COG0625 COG0625 440390 GstA Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]. 205 matched cddid_all.tbl CDD COG0626 COG0626 440391 MetC Cystathionine beta-lyase/cystathionine gamma-synthase [Amino acid transport and metabolism]. Cystathionine beta-lyase/cystathionine gamma-synthase is part of the Pathway/BioSystem: Methionine biosynthesis 389 matched cddid_all.tbl CDD COG0627 COG0627 440392 FrmB S-formylglutathione hydrolase FrmB [Defense mechanisms]. 249 matched cddid_all.tbl CDD COG0628 COG0628 440393 PerM Predicted PurR-regulated permease PerM [General function prediction only]. 346 matched cddid_all.tbl CDD COG0629 COG0629 440394 Ssb Single-stranded DNA-binding protein [Replication, recombination and repair]. 116 matched cddid_all.tbl CDD COG0630 COG0630 440395 VirB11 Type IV secretory pathway ATPase VirB11/Archaellum biosynthesis ATPase ArlI/FlaI [Cell motility, Intracellular trafficking, secretion, and vesicular transport]. 462 matched cddid_all.tbl CDD COG0631 COG0631 440396 PTC1 Serine/threonine protein phosphatase PrpC [Signal transduction mechanisms]. 247 matched cddid_all.tbl CDD COG0632 COG0632 440397 RuvA Holliday junction resolvasome RuvABC DNA-binding subunit [Replication, recombination and repair]. 195 matched cddid_all.tbl CDD COG0633 COG0633 440398 Fdx Ferredoxin [Energy production and conversion]. 87 matched cddid_all.tbl CDD COG0634 COG0634 440399 HptA Hypoxanthine-guanine phosphoribosyltransferase [Nucleotide transport and metabolism]. Hypoxanthine-guanine phosphoribosyltransferase is part of the Pathway/BioSystem: Purine salvage 176 matched cddid_all.tbl CDD COG0635 COG0635 440400 HemN Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase [Coenzyme transport and metabolism]. Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase is part of the Pathway/BioSystem: Heme biosynthesis 400 matched cddid_all.tbl CDD COG0636 COG0636 440401 AtpE FoF1-type ATP synthase, membrane subunit c/Archaeal/vacuolar-type H+-ATPase, subunit K [Energy production and conversion]. FoF1-type ATP synthase, membrane subunit c/Archaeal/vacuolar-type H+-ATPase, subunit K is part of the Pathway/BioSystem: FoF1-type ATP synthase 75 matched cddid_all.tbl CDD COG0637 COG0637 440402 YcjU Beta-phosphoglucomutase, HAD superfamily [Carbohydrate transport and metabolism]. 208 matched cddid_all.tbl CDD COG0638 COG0638 440403 PRE1 20S proteasome, alpha and beta subunits [Posttranslational modification, protein turnover, chaperones]. 229 matched cddid_all.tbl CDD COG0639 COG0639 440404 ApaH Diadenosine tetraphosphatase ApaH/serine/threonine protein phosphatase, PP2A family [Signal transduction mechanisms]. 182 matched cddid_all.tbl CDD COG0640 COG0640 440405 ArsR DNA-binding transcriptional regulator, ArsR family [Transcription]. 92 matched cddid_all.tbl CDD COG0641 COG0641 440406 AslB Sulfatase maturation enzyme AslB, radical SAM superfamily [Posttranslational modification, protein turnover, chaperones]. 349 matched cddid_all.tbl CDD COG0642 COG0642 440407 BaeS Signal transduction histidine kinase [Signal transduction mechanisms]. 328 matched cddid_all.tbl CDD COG0643 COG0643 440408 CheA Chemotaxis protein histidine kinase CheA [Signal transduction mechanisms]. 563 matched cddid_all.tbl CDD COG0644 COG0644 440409 FixC Dehydrogenase (flavoprotein) [Energy production and conversion]. 281 matched cddid_all.tbl CDD COG0645 COG0645 440410 COG0645 Predicted kinase, contains AAA domain [General function prediction only]. 164 matched cddid_all.tbl CDD COG0646 COG0646 440411 MetH1 Methionine synthase I (cobalamin-dependent), methyltransferase domain [Amino acid transport and metabolism]. Methionine synthase I (cobalamin-dependent), methyltransferase domain is part of the Pathway/BioSystem: Methionine biosynthesis 809 matched cddid_all.tbl CDD COG0647 COG0647 440412 NagD Ribonucleotide monophosphatase NagD, HAD superfamily [Nucleotide transport and metabolism]. 259 matched cddid_all.tbl CDD COG0648 COG0648 440413 Nfo Endonuclease IV [Replication, recombination and repair]. 280 matched cddid_all.tbl CDD COG0649 COG0649 440414 NuoD NADH:ubiquinone oxidoreductase 49 kD subunit (chain D) [Energy production and conversion]. NADH:ubiquinone oxidoreductase 49 kD subunit (chain D) is part of the Pathway/BioSystem: NADH dehydrogenase 390 matched cddid_all.tbl CDD COG0650 COG0650 440415 HyfC Formate hydrogenlyase subunit HyfC [Energy production and conversion]. 303 matched cddid_all.tbl CDD COG0651 COG0651 440416 HyfB Formate hydrogenlyase subunit 3/Multisubunit Na+/H+ antiporter, MnhD subunit [Energy production and conversion, Inorganic ion transport and metabolism]. 430 matched cddid_all.tbl CDD COG0652 COG0652 440417 PpiB Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family [Posttranslational modification, protein turnover, chaperones]. 159 matched cddid_all.tbl CDD COG0653 COG0653 440418 SecA Preprotein translocase subunit SecA (ATPase, RNA helicase) [Intracellular trafficking, secretion, and vesicular transport]. 876 matched cddid_all.tbl CDD COG0654 COG0654 440419 UbiH 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme transport and metabolism, Energy production and conversion]. 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases is part of the Pathway/BioSystem: Ubiquinone biosynthesis 326 matched cddid_all.tbl CDD COG0655 COG0655 440420 WrbA Multimeric flavodoxin WrbA, includes NAD(P)H:quinone oxidoreductase [Energy production and conversion]. 181 matched cddid_all.tbl CDD COG0656 COG0656 440421 ARA1 Aldo/keto reductase, related to diketogulonate reductase [Secondary metabolites biosynthesis, transport and catabolism]. 259 matched cddid_all.tbl CDD COG0657 COG0657 440422 Aes Acetyl esterase/lipase [Lipid transport and metabolism]. 207 matched cddid_all.tbl CDD COG0658 COG0658 440423 ComEC DNA uptake channel protein ComEC, N-terminal domain [Intracellular trafficking, secretion, and vesicular transport]. 543 matched cddid_all.tbl CDD COG0659 COG0659 440424 SUL1 Sulfate permease or related transporter, MFS superfamily [Inorganic ion transport and metabolism]. 529 matched cddid_all.tbl CDD COG0661 COG0661 440425 AarF Predicted protein kinase regulating ubiquinone biosynthesis, AarF/ABC1/UbiB family [Coenzyme transport and metabolism, Signal transduction mechanisms]. Predicted protein kinase regulating ubiquinone biosynthesis, AarF/ABC1/UbiB family is part of the Pathway/BioSystem: Ubiquinone biosynthesis 487 matched cddid_all.tbl CDD COG0662 COG0662 440426 ManC Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism]. 114 matched cddid_all.tbl CDD COG0663 COG0663 440427 PaaY Carbonic anhydrase or acetyltransferase, isoleucine patch superfamily [General function prediction only]. 170 matched cddid_all.tbl CDD COG0664 COG0664 440428 Crp cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]. 207 matched cddid_all.tbl CDD COG0665 COG0665 440429 DadA Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]. 364 matched cddid_all.tbl CDD COG0666 COG0666 440430 ANKYR Ankyrin repeat [Signal transduction mechanisms]. 289 matched cddid_all.tbl CDD COG0667 COG0667 440431 PdxI Pyridoxal reductase PdxI or related oxidoreductase, aldo/keto reductase family [Coenzyme transport and metabolism, General function prediction only]. 316 matched cddid_all.tbl CDD COG0668 COG0668 440432 MscS Small-conductance mechanosensitive channel [Cell wall/membrane/envelope biogenesis]. 276 matched cddid_all.tbl CDD COG0669 COG0669 440433 CoaD Phosphopantetheine adenylyltransferase [Coenzyme transport and metabolism]. Phosphopantetheine adenylyltransferase is part of the Pathway/BioSystem: Pantothenate/CoA biosynthesis 159 matched cddid_all.tbl CDD COG0670 COG0670 440434 YbhL Integral membrane protein YbhL, putative Ca2+ regulator, Bax inhibitor (BI-1)/TMBIM family [Inorganic ion transport and metabolism]. 231 matched cddid_all.tbl CDD COG0671 COG0671 440435 PgpB Membrane-associated phospholipid phosphatase [Lipid transport and metabolism]. Membrane-associated phospholipid phosphatase is part of the Pathway/BioSystem: Phospholipid biosynthesis 189 matched cddid_all.tbl CDD COG0672 COG0672 440436 FTR1 High-affinity Fe2+/Pb2+ permease [Inorganic ion transport and metabolism]. 279 matched cddid_all.tbl CDD COG0673 COG0673 440437 MviM Predicted dehydrogenase [General function prediction only]. 295 matched cddid_all.tbl CDD COG0674 COG0674 440438 PorA Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, alpha subunit [Energy production and conversion]. Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, alpha subunit is part of the Pathway/BioSystem: Pyruvate oxidation 372 matched cddid_all.tbl CDD COG0675 COG0675 440439 InsQ Transposase [Mobilome: prophages, transposons]. 381 matched cddid_all.tbl CDD COG0676 COG0676 440440 YeaD D-hexose-6-phosphate mutarotase [Carbohydrate transport and metabolism]. 296 matched cddid_all.tbl CDD COG0677 COG0677 440441 WecC UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell wall/membrane/envelope biogenesis]. 413 matched cddid_all.tbl CDD COG0678 COG0678 440442 AHP1 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]. 160 matched cddid_all.tbl CDD COG0679 COG0679 440443 YfdV Predicted permease, AEC (auxin efflux carrier) family [General function prediction only]. 308 matched cddid_all.tbl CDD COG0680 COG0680 440444 HyaD Ni,Fe-hydrogenase maturation factor [Energy production and conversion]. 150 matched cddid_all.tbl CDD COG0681 COG0681 440445 LepB Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport]. 189 matched cddid_all.tbl CDD COG0682 COG0682 440446 Lgt Prolipoprotein diacylglyceryltransferase [Cell wall/membrane/envelope biogenesis]. 253 matched cddid_all.tbl CDD COG0683 COG0683 440447 LivK ABC-type branched-chain amino acid transport system, periplasmic component [Amino acid transport and metabolism]. 314 matched cddid_all.tbl CDD COG0684 COG0684 440448 RraA RNA degradosome component RraA (regulator of RNase E activity) [Translation, ribosomal structure and biogenesis]. 204 matched cddid_all.tbl CDD COG0685 COG0685 440449 MetF 5,10-methylenetetrahydrofolate reductase [Amino acid transport and metabolism]. 284 matched cddid_all.tbl CDD COG0686 COG0686 440450 Ald Alanine dehydrogenase (includes sporulation protein SpoVN) [Amino acid transport and metabolism]. Alanine dehydrogenase (includes sporulation protein SpoVN) is part of the Pathway/BioSystem: Urea cycle 372 matched cddid_all.tbl CDD COG0687 COG0687 440451 PotD Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]. 348 matched cddid_all.tbl CDD COG0688 COG0688 440452 Psd Phosphatidylserine decarboxylase [Lipid transport and metabolism]. Phosphatidylserine decarboxylase is part of the Pathway/BioSystem: Phospholipid biosynthesis 243 matched cddid_all.tbl CDD COG0689 COG0689 440453 Rph Ribonuclease PH [Translation, ribosomal structure and biogenesis]. 238 matched cddid_all.tbl CDD COG0690 COG0690 440454 SecE Preprotein translocase subunit SecE [Intracellular trafficking, secretion, and vesicular transport]. 68 matched cddid_all.tbl CDD COG0691 COG0691 440455 SmpB tmRNA-binding protein [Posttranslational modification, protein turnover, chaperones]. 153 matched cddid_all.tbl CDD COG0692 COG0692 440456 Ung Uracil-DNA glycosylase [Replication, recombination and repair]. 221 matched cddid_all.tbl CDD COG0693 COG0693 440457 YajL Protein/nucleotide deglycase, PfpI/YajL/DJ-1 family (repair of methylglyoxal-glycated proteins and nucleic acids) [Defense mechanisms]. 170 matched cddid_all.tbl CDD COG0694 COG0694 440458 NifU Fe-S cluster biogenesis protein NfuA, 4Fe-4S-binding domain [Posttranslational modification, protein turnover, chaperones]. 176 matched cddid_all.tbl CDD COG0695 COG0695 440459 GrxC Glutaredoxin [Posttranslational modification, protein turnover, chaperones]. 74 matched cddid_all.tbl CDD COG0696 COG0696 440460 GpmI Phosphoglycerate mutase (BPG-independent), AlkP superfamily [Carbohydrate transport and metabolism]. Phosphoglycerate mutase (BPG-independent), AlkP superfamily is part of the Pathway/BioSystem: Glycolysis 511 matched cddid_all.tbl CDD COG0697 COG0697 440461 RhaT Permease of the drug/metabolite transporter (DMT) superfamily [Carbohydrate transport and metabolism, Amino acid transport and metabolism, General function prediction only]. 290 matched cddid_all.tbl CDD COG0698 COG0698 440462 RpiB Ribose 5-phosphate isomerase RpiB [Carbohydrate transport and metabolism]. Ribose 5-phosphate isomerase RpiB is part of the Pathway/BioSystem: Pentose phosphate pathway 149 matched cddid_all.tbl CDD COG0699 COG0699 440463 CrfC Replication fork clamp-binding protein CrfC (dynamin-like GTPase family) [Replication, recombination and repair]. 582 matched cddid_all.tbl CDD COG0700 COG0700 440464 SpmB Spore maturation protein SpmB (function unknown) [Function unknown]. 172 matched cddid_all.tbl CDD COG0701 COG0701 440465 YraQ Uncharacterized membrane protein YraQ, UPF0718 family [Function unknown]. 296 matched cddid_all.tbl CDD COG0702 COG0702 440466 YbjT Uncharacterized conserved protein YbjT, contains NAD(P)-binding and DUF2867 domains [General function prediction only]. 215 matched cddid_all.tbl CDD COG0703 COG0703 440467 AroK Shikimate kinase [Amino acid transport and metabolism]. Shikimate kinase is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 165 matched cddid_all.tbl CDD COG0704 COG0704 440468 PhoU Phosphate uptake regulator PhoU [Inorganic ion transport and metabolism]. 213 matched cddid_all.tbl CDD COG0705 COG0705 440469 GlpG Membrane-associated serine protease, rhomboid family [Posttranslational modification, protein turnover, chaperones]. 189 matched cddid_all.tbl CDD COG0706 COG0706 440470 YidC Membrane protein insertase Oxa1/YidC/SpoIIIJ [Cell wall/membrane/envelope biogenesis]. 212 matched cddid_all.tbl CDD COG0707 COG0707 440471 MurG UDP-N-acetylglucosamine:LPS N-acetylglucosamine transferase [Cell wall/membrane/envelope biogenesis]. UDP-N-acetylglucosamine:LPS N-acetylglucosamine transferase is part of the Pathway/BioSystem: Mureine biosynthesis 363 matched cddid_all.tbl CDD COG0708 COG0708 440472 XthA Exonuclease III [Replication, recombination and repair]. 256 matched cddid_all.tbl CDD COG0709 COG0709 440473 SelD Selenophosphate synthase [Amino acid transport and metabolism]. 346 matched cddid_all.tbl CDD COG0710 COG0710 440474 AroD 3-dehydroquinate dehydratase [Amino acid transport and metabolism]. 3-dehydroquinate dehydratase is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 236 matched cddid_all.tbl CDD COG0711 COG0711 440475 AtpF FoF1-type ATP synthase, membrane subunit b or b' [Energy production and conversion]. FoF1-type ATP synthase, membrane subunit b or b' is part of the Pathway/BioSystem: FoF1-type ATP synthase 152 matched cddid_all.tbl CDD COG0712 COG0712 440476 AtpH FoF1-type ATP synthase, delta subunit [Energy production and conversion]. FoF1-type ATP synthase, delta subunit is part of the Pathway/BioSystem: FoF1-type ATP synthase 178 matched cddid_all.tbl CDD COG0713 COG0713 440477 NuoK NADH:ubiquinone oxidoreductase subunit 11 or 4L (chain K) [Energy production and conversion]. NADH:ubiquinone oxidoreductase subunit 11 or 4L (chain K) is part of the Pathway/BioSystem: NADH dehydrogenase 99 matched cddid_all.tbl CDD COG0714 COG0714 440478 MoxR MoxR-like ATPase [General function prediction only]. MoxR-like ATPase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 292 matched cddid_all.tbl CDD COG0715 COG0715 440479 TauA ABC-type nitrate/sulfonate/bicarbonate transport system, periplasmic component [Inorganic ion transport and metabolism]. 297 matched cddid_all.tbl CDD COG0716 COG0716 440480 FldA Flavodoxin [Energy production and conversion]. Flavodoxin is part of the Pathway/BioSystem: Heme biosynthesis 135 matched cddid_all.tbl CDD COG0717 COG0717 440481 Dcd dCTP deaminase [Nucleotide transport and metabolism]. dCTP deaminase is part of the Pathway/BioSystem: Thymidylate biosynthesis 180 matched cddid_all.tbl CDD COG0718 COG0718 440482 YbaB DNA-binding nucleoid-associated protein YbaB/EfbC [Transcription]. 100 matched cddid_all.tbl CDD COG0719 COG0719 440483 SufB Fe-S cluster assembly scaffold protein SufB [Posttranslational modification, protein turnover, chaperones]. 393 matched cddid_all.tbl CDD COG0720 COG0720 440484 QueD 6-pyruvoyl-tetrahydropterin synthase [Coenzyme transport and metabolism]. 6-pyruvoyl-tetrahydropterin synthase is part of the Pathway/BioSystem: tRNA modification 123 matched cddid_all.tbl CDD COG0721 COG0721 440485 GatC Asp-tRNAAsn/Glu-tRNAGln amidotransferase C subunit [Translation, ribosomal structure and biogenesis]. Asp-tRNAAsn/Glu-tRNAGln amidotransferase C subunit is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 95 matched cddid_all.tbl CDD COG0722 COG0722 440486 AroG1 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]. 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 351 matched cddid_all.tbl CDD COG0723 COG0723 440487 QcrA/PetC Rieske Fe-S protein [Energy production and conversion]. 118 matched cddid_all.tbl CDD COG0724 COG0724 440488 RRM RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]. 85 matched cddid_all.tbl CDD COG0725 COG0725 440489 ModA ABC-type molybdate transport system, periplasmic Mo-binding protein ModA [Inorganic ion transport and metabolism]. ABC-type molybdate transport system, periplasmic Mo-binding protein ModA is part of the Pathway/BioSystem: Molybdopterin biosynthesis 253 matched cddid_all.tbl CDD COG0726 COG0726 440490 CDA1 Peptidoglycan/xylan/chitin deacetylase, PgdA/NodB/CDA1 family [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis]. 195 matched cddid_all.tbl CDD COG0727 COG0727 440491 YkgJ Uncharacterized protein YkgJ, contains CxxCxxCC motif [General function prediction only]. 120 matched cddid_all.tbl CDD COG0728 COG0728 440492 MurJ Lipid II flippase MurJ/MviN (peptidoglycan biosynthesis) [Cell wall/membrane/envelope biogenesis]. 503 matched cddid_all.tbl CDD COG0729 COG0729 440493 TamA Outer membrane translocation and assembly module TamA [Cell wall/membrane/envelope biogenesis]. 574 matched cddid_all.tbl CDD COG0730 COG0730 440494 TauE Sulfite exporter TauE/SafE/YfcA and related permeases, UPF0721 family [Inorganic ion transport and metabolism]. 250 matched cddid_all.tbl CDD COG0731 COG0731 440495 Tyw1 Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily [Translation, ribosomal structure and biogenesis]. Wyosine [tRNA(Phe)-imidazoG37] synthetase, radical SAM superfamily is part of the Pathway/BioSystem: tRNA modification 248 matched cddid_all.tbl CDD COG0732 COG0732 440496 HsdS Restriction endonuclease S subunit [Defense mechanisms]. 88 matched cddid_all.tbl CDD COG0733 COG0733 440497 YocR Na+-dependent transporter, SNF family [General function prediction only]. 444 matched cddid_all.tbl CDD COG0735 COG0735 440498 Fur Fe2+ or Zn2+ uptake regulation protein Fur/Zur [Inorganic ion transport and metabolism]. 140 matched cddid_all.tbl CDD COG0736 COG0736 440499 AcpS Phosphopantetheinyl transferase (holo-ACP synthase) [Lipid transport and metabolism]. 122 matched cddid_all.tbl CDD COG0737 COG0737 440500 UshA 2',3'-cyclic-nucleotide 2'-phosphodiesterase/5'- or 3'-nucleotidase, 5'-nucleotidase family [Nucleotide transport and metabolism, Defense mechanisms]. 471 matched cddid_all.tbl CDD COG0738 COG0738 440501 FucP Fucose permease [Carbohydrate transport and metabolism]. 391 matched cddid_all.tbl CDD COG0739 COG0739 440502 NlpD Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell wall/membrane/envelope biogenesis]. 196 matched cddid_all.tbl CDD COG0740 COG0740 440503 ClpP ATP-dependent protease ClpP, protease subunit [Posttranslational modification, protein turnover, chaperones]. 194 matched cddid_all.tbl CDD COG0741 COG0741 440504 MltE Soluble lytic murein transglycosylase or regulatory protein s ( may contain LysM/invasin domain) [Cell wall/membrane/envelope biogenesis]. 244 matched cddid_all.tbl CDD COG0742 COG0742 440505 RsmD 16S rRNA G966 N2-methylase RsmD [Translation, ribosomal structure and biogenesis]. 16S rRNA G966 N2-methylase RsmD is part of the Pathway/BioSystem: 16S rRNA modification 183 matched cddid_all.tbl CDD COG0743 COG0743 440506 Dxr 1-deoxy-D-xylulose 5-phosphate reductoisomerase [Lipid transport and metabolism]. 1-deoxy-D-xylulose 5-phosphate reductoisomerase is part of the Pathway/BioSystem: Isoprenoid biosynthesis 385 matched cddid_all.tbl CDD COG0744 COG0744 440507 MrcB Penicillin-binding protein 1B/1F, peptidoglycan transglycosylase/transpeptidase [Cell wall/membrane/envelope biogenesis]. 630 matched cddid_all.tbl CDD COG0745 COG0745 440508 OmpR DNA-binding response regulator, OmpR family, contains REC and winged-helix (wHTH) domain [Signal transduction mechanisms, Transcription]. 204 matched cddid_all.tbl CDD COG0746 COG0746 440509 MobA Molybdopterin-guanine dinucleotide biosynthesis protein A [Coenzyme transport and metabolism]. Molybdopterin-guanine dinucleotide biosynthesis protein A is part of the Pathway/BioSystem: Molybdopterin biosynthesis 188 matched cddid_all.tbl CDD COG0747 COG0747 440510 DdpA ABC-type transport system, periplasmic component [Amino acid transport and metabolism]. 464 matched cddid_all.tbl CDD COG0748 COG0748 440511 HugZ Putative heme iron utilization protein, contains PNPOx domain [Inorganic ion transport and metabolism]. 221 matched cddid_all.tbl CDD COG0749 COG0749 440512 PolA DNA polymerase I, 3'-5' exonuclease and polymerase domains [Replication, recombination and repair]. 575 matched cddid_all.tbl CDD COG0750 COG0750 440513 RseP Membrane-associated protease RseP, regulator of RpoE activity [Posttranslational modification, protein turnover, chaperones, Transcription]. 349 matched cddid_all.tbl CDD COG0751 COG0751 440514 GlyS Glycyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]. Glycyl-tRNA synthetase, beta subunit is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 690 matched cddid_all.tbl CDD COG0752 COG0752 440515 GlyQ Glycyl-tRNA synthetase, alpha subunit [Translation, ribosomal structure and biogenesis]. Glycyl-tRNA synthetase, alpha subunit is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 283 matched cddid_all.tbl CDD COG0753 COG0753 440516 KatE Catalase [Inorganic ion transport and metabolism]. 489 matched cddid_all.tbl CDD COG0754 COG0754 440517 Gsp Glutathionylspermidine synthase, CHAP domain [Amino acid transport and metabolism]. 383 matched cddid_all.tbl CDD COG0755 COG0755 440518 CcmC ABC-type transport system involved in cytochrome c biogenesis, permease component [Posttranslational modification, protein turnover, chaperones]. 213 matched cddid_all.tbl CDD COG0756 COG0756 440519 Dut dUTP pyrophosphatase (dUTPase) [Nucleotide transport and metabolism, Defense mechanisms]. dUTP pyrophosphatase (dUTPase) is part of the Pathway/BioSystem: Thymidylate biosynthesis 143 matched cddid_all.tbl CDD COG0757 COG0757 440520 AroQ 3-dehydroquinate dehydratase [Amino acid transport and metabolism]. 3-dehydroquinate dehydratase is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 145 matched cddid_all.tbl CDD COG0758 COG0758 440521 Smf Predicted Rossmann fold nucleotide-binding protein DprA/Smf involved in DNA uptake [Replication, recombination and repair]. 360 matched cddid_all.tbl CDD COG0759 COG0759 440522 YidD Membrane-anchored protein YidD, putatitve component of membrane protein insertase Oxa1/YidC/SpoIIIJ [Cell wall/membrane/envelope biogenesis]. 71 matched cddid_all.tbl CDD COG0760 COG0760 440523 SurA Peptidyl-prolyl isomerase, parvulin family [Posttranslational modification, protein turnover, chaperones]. 143 matched cddid_all.tbl CDD COG0761 COG0761 440524 IspH 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid transport and metabolism]. 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH is part of the Pathway/BioSystem: Isoprenoid biosynthesis 289 matched cddid_all.tbl CDD COG0762 COG0762 440525 Ycf19 Cytochrome b6 maturation protein CCB3/Ycf19 and related maturases, YggT family [Posttranslational modification, protein turnover, chaperones]. 84 matched cddid_all.tbl CDD COG0763 COG0763 440526 LpxB Lipid A disaccharide synthetase [Cell wall/membrane/envelope biogenesis]. Lipid A disaccharide synthetase is part of the Pathway/BioSystem: Lipid A biosynthesis 378 matched cddid_all.tbl CDD COG0764 COG0764 440527 FabA 3-hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratase [Lipid transport and metabolism]. 3-hydroxymyristoyl/3-hydroxydecanoyl-(acyl carrier protein) dehydratase is part of the Pathway/BioSystem: Fatty acid biosynthesis 141 matched cddid_all.tbl CDD COG0765 COG0765 440528 HisM ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]. 218 matched cddid_all.tbl CDD COG0766 COG0766 440529 MurA UDP-N-acetylglucosamine enolpyruvyl transferase [Cell wall/membrane/envelope biogenesis]. UDP-N-acetylglucosamine enolpyruvyl transferase is part of the Pathway/BioSystem: Mureine biosynthesis 416 matched cddid_all.tbl CDD COG0767 COG0767 440530 MlaE Permease subunit MlaE of the ABC-type intermembrane phospholipid transporter Mla [Cell wall/membrane/envelope biogenesis]. 249 matched cddid_all.tbl CDD COG0768 COG0768 440531 FtsI Cell division protein FtsI, peptidoglycan transpeptidase (Penicillin-binding protein 2) [Cell cycle control, cell division, chromosome partitioning, Cell wall/membrane/envelope biogenesis]. 568 matched cddid_all.tbl CDD COG0769 COG0769 440532 MurE UDP-N-acetylmuramyl tripeptide synthase [Cell wall/membrane/envelope biogenesis]. UDP-N-acetylmuramyl tripeptide synthase is part of the Pathway/BioSystem: Mureine biosynthesis 459 matched cddid_all.tbl CDD COG0770 COG0770 440533 MurF UDP-N-acetylmuramyl pentapeptide synthase [Cell wall/membrane/envelope biogenesis]. UDP-N-acetylmuramyl pentapeptide synthase is part of the Pathway/BioSystem: Mureine biosynthesis 451 matched cddid_all.tbl CDD COG0771 COG0771 440534 MurD UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell wall/membrane/envelope biogenesis]. UDP-N-acetylmuramoylalanine-D-glutamate ligase is part of the Pathway/BioSystem: Mureine biosynthesis 445 matched cddid_all.tbl CDD COG0772 COG0772 440535 FtsW Peptodoglycan polymerase FtsW/RodA/SpoVE [Cell cycle control, cell division, chromosome partitioning]. 371 matched cddid_all.tbl CDD COG0773 COG0773 440536 MurC UDP-N-acetylmuramate-alanine ligase MurC and related ligases, MurC/Mpl family [Cell wall/membrane/envelope biogenesis]. UDP-N-acetylmuramate-alanine ligase MurC and related ligases, MurC/Mpl family is part of the Pathway/BioSystem: Mureine biosynthesis 451 matched cddid_all.tbl CDD COG0774 COG0774 440537 LpxC UDP-3-O-acyl-N-acetylglucosamine deacetylase [Cell wall/membrane/envelope biogenesis]. UDP-3-O-acyl-N-acetylglucosamine deacetylase is part of the Pathway/BioSystem: Lipid A biosynthesis 276 matched cddid_all.tbl CDD COG0775 COG0775 440538 MtnN Nucleoside phosphorylase/nucleosidase, includes 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase MtnN and futalosine hydrolase MqnB [Nucleotide transport and metabolism, Coenzyme transport and metabolism]. Nucleoside phosphorylase/nucleosidase, includes 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase MtnN and futalosine hydrolase MqnB is part of the Pathway/BioSystem: Menaquinone biosynthesis 231 matched cddid_all.tbl CDD COG0776 COG0776 440539 HimA Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair]. 92 matched cddid_all.tbl CDD COG0777 COG0777 440540 AccD Acetyl-CoA carboxylase beta subunit [Lipid transport and metabolism]. Acetyl-CoA carboxylase beta subunit is part of the Pathway/BioSystem: Fatty acid biosynthesis 280 matched cddid_all.tbl CDD COG0778 COG0778 440541 NfnB Nitroreductase [Energy production and conversion]. Nitroreductase is part of the Pathway/BioSystem: Pyrimidine degradation 163 matched cddid_all.tbl CDD COG0779 COG0779 440542 RimP Ribosome maturation factor RimP [Translation, ribosomal structure and biogenesis]. 151 matched cddid_all.tbl CDD COG0780 COG0780 440543 QueFC NADPH-dependent 7-cyano-7-deazaguanine reductase QueF, C-terminal domain, T-fold superfamily [Translation, ribosomal structure and biogenesis]. NADPH-dependent 7-cyano-7-deazaguanine reductase QueF, C-terminal domain, T-fold superfamily is part of the Pathway/BioSystem: tRNA modification 133 matched cddid_all.tbl CDD COG0781 COG0781 440544 NusB Transcription antitermination protein NusB [Transcription]. 128 matched cddid_all.tbl CDD COG0782 COG0782 440545 GreA Transcription elongation factor, GreA/GreB family [Transcription]. 156 matched cddid_all.tbl CDD COG0783 COG0783 440546 Dps DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism, Defense mechanisms]. 156 matched cddid_all.tbl CDD COG0784 COG0784 440547 CheY CheY-like REC (receiver) domain, includes chemotaxis protein CheY and sporulation regulator Spo0F [Signal transduction mechanisms]. 128 matched cddid_all.tbl CDD COG0785 COG0785 440548 CcdA Cytochrome c biogenesis protein CcdA [Energy production and conversion, Posttranslational modification, protein turnover, chaperones]. 193 matched cddid_all.tbl CDD COG0786 COG0786 440549 GltS Na+/glutamate symporter [Amino acid transport and metabolism]. 401 matched cddid_all.tbl CDD COG0787 COG0787 440550 Alr Alanine racemase [Cell wall/membrane/envelope biogenesis]. Alanine racemase is part of the Pathway/BioSystem: Mureine biosynthesis 368 matched cddid_all.tbl CDD COG0788 COG0788 440551 PurU Formyltetrahydrofolate hydrolase [Nucleotide transport and metabolism]. Formyltetrahydrofolate hydrolase is part of the Pathway/BioSystem: Purine biosynthesis 282 matched cddid_all.tbl CDD COG0789 COG0789 440552 SoxR DNA-binding transcriptional regulator, MerR family [Transcription]. 100 matched cddid_all.tbl CDD COG0790 COG0790 440553 TPR TPR repeat [General function prediction only]. 241 matched cddid_all.tbl CDD COG0791 COG0791 440554 NlpC Cell wall-associated hydrolase, NlpC_P60 family [Cell wall/membrane/envelope biogenesis]. 218 matched cddid_all.tbl CDD COG0792 COG0792 440555 YraN Predicted endonuclease distantly related to archaeal Holliday junction resolvase, YraN/UPF0102 family [Replication, recombination and repair]. 116 matched cddid_all.tbl CDD COG0793 COG0793 440556 CtpA C-terminal processing protease CtpA/Prc, contains a PDZ domain [Posttranslational modification, protein turnover, chaperones]. 341 matched cddid_all.tbl CDD COG0794 COG0794 440557 GutQ D-arabinose 5-phosphate isomerase GutQ [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis]. 317 matched cddid_all.tbl CDD COG0795 COG0795 440558 LptF Lipopolysaccharide export LptBFGC system, permease protein LptF [Cell wall/membrane/envelope biogenesis, Cell motility]. 357 matched cddid_all.tbl CDD COG0796 COG0796 440559 MurI Glutamate racemase [Cell wall/membrane/envelope biogenesis]. Glutamate racemase is part of the Pathway/BioSystem: Mureine biosynthesis 261 matched cddid_all.tbl CDD COG0797 COG0797 440560 RlpA Peptidoglycan lytic transglycosylase RlpA, contains C-terminal SPOR domain [Cell wall/membrane/envelope biogenesis]. 133 matched cddid_all.tbl CDD COG0798 COG0798 440561 ACR3 Arsenite efflux pump ArsB, ACR3 family [Inorganic ion transport and metabolism]. 335 matched cddid_all.tbl CDD COG0799 COG0799 440562 RsfS Ribosomal silencing factor RsfS, regulates association of 30S and 50S subunits [Translation, ribosomal structure and biogenesis]. 113 matched cddid_all.tbl CDD COG0800 COG0800 440563 Eda 2-keto-3-deoxy-6-phosphogluconate aldolase [Carbohydrate transport and metabolism]. 2-keto-3-deoxy-6-phosphogluconate aldolase is part of the Pathway/BioSystem: Entner-Doudoroff pathway 213 matched cddid_all.tbl CDD COG0801 COG0801 440564 FolK 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase (folate biosynthesis) [Coenzyme transport and metabolism]. 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase (folate biosynthesis) is part of the Pathway/BioSystem: Folate biosynthesis 155 matched cddid_all.tbl CDD COG0802 COG0802 440565 TsaE tRNA A37 threonylcarbamoyladenosine biosynthesis protein TsaE [Translation, ribosomal structure and biogenesis]. tRNA A37 threonylcarbamoyladenosine biosynthesis protein TsaE is part of the Pathway/BioSystem: tRNA modification 146 matched cddid_all.tbl CDD COG0803 COG0803 440566 ZnuA ABC-type Zn uptake system ZnuABC, Zn-binding component ZnuA [Inorganic ion transport and metabolism]. 286 matched cddid_all.tbl CDD COG0804 COG0804 440567 UreC Urease alpha subunit [Amino acid transport and metabolism]. 570 matched cddid_all.tbl CDD COG0805 COG0805 440568 TatC Twin-arginine protein secretion pathway component TatC [Intracellular trafficking, secretion, and vesicular transport]. 249 matched cddid_all.tbl CDD COG0806 COG0806 440569 RimM Ribosomal 30S subunit maturation factor RimM, required for 16S rRNA processing [Translation, ribosomal structure and biogenesis]. Ribosomal 30S subunit maturation factor RimM, required for 16S rRNA processing is part of the Pathway/BioSystem: 16S rRNA modification 173 matched cddid_all.tbl CDD COG0807 COG0807 440570 RibA GTP cyclohydrolase II [Coenzyme transport and metabolism]. GTP cyclohydrolase II is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis 398 matched cddid_all.tbl CDD COG0809 COG0809 440571 QueA S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase) [Translation, ribosomal structure and biogenesis]. S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase) is part of the Pathway/BioSystem: tRNA modification 340 matched cddid_all.tbl CDD COG0810 COG0810 440572 TonB Periplasmic protein TonB, links inner and outer membranes [Cell wall/membrane/envelope biogenesis]. 70 matched cddid_all.tbl CDD COG0811 COG0811 440573 TolQ Biopolymer transport protein ExbB/TolQ [Intracellular trafficking, secretion, and vesicular transport]. 199 matched cddid_all.tbl CDD COG0812 COG0812 440574 MurB UDP-N-acetylenolpyruvoylglucosamine reductase [Cell wall/membrane/envelope biogenesis]. UDP-N-acetylenolpyruvoylglucosamine reductase is part of the Pathway/BioSystem: Mureine biosynthesis 279 matched cddid_all.tbl CDD COG0813 COG0813 440575 DeoD Purine-nucleoside phosphorylase [Nucleotide transport and metabolism]. Purine-nucleoside phosphorylase is part of the Pathway/BioSystem: Purine salvage 236 matched cddid_all.tbl CDD COG0814 COG0814 440576 SdaC Amino acid permease [Amino acid transport and metabolism]. 401 matched cddid_all.tbl CDD COG0815 COG0815 440577 Lnt Apolipoprotein N-acyltransferase [Cell wall/membrane/envelope biogenesis]. 472 matched cddid_all.tbl CDD COG0816 COG0816 440578 YqgF YqgF/RuvX protein, pre-16S rRNA maturation RNase/Holliday junction resolvase/anti-termination factor [Translation, ribosomal structure and biogenesis, Replication, recombination and repair, Transcription]. 136 matched cddid_all.tbl CDD COG0817 COG0817 440579 RuvC Holliday junction resolvasome RuvABC endonuclease subunit RuvC [Replication, recombination and repair]. 152 matched cddid_all.tbl CDD COG0818 COG0818 440580 DgkA Diacylglycerol kinase [Lipid transport and metabolism]. 120 matched cddid_all.tbl CDD COG0819 COG0819 440581 TenA Aminopyrimidine aminohydrolase TenA (thiamine salvage pathway) [Coenzyme transport and metabolism]. 218 matched cddid_all.tbl CDD COG0820 COG0820 440582 RlmN Adenine C2-methylase RlmN of 23S rRNA A2503 and tRNA A37 [Translation, ribosomal structure and biogenesis]. Adenine C2-methylase RlmN of 23S rRNA A2503 and tRNA A37 is part of the Pathway/BioSystem: 23S rRNA modification 338 matched cddid_all.tbl CDD COG0821 COG0821 440583 IspG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase IspG/GcpE [Lipid transport and metabolism]. 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase IspG/GcpE is part of the Pathway/BioSystem: Isoprenoid biosynthesis 363 matched cddid_all.tbl CDD COG0822 COG0822 440584 IscU Fe-S cluster assembly scaffold protein IscU, NifU family [Posttranslational modification, protein turnover, chaperones]. 128 matched cddid_all.tbl CDD COG0823 COG0823 440585 TolB Periplasmic component TolB of the Tol biopolymer transport system [Intracellular trafficking, secretion, and vesicular transport]. 158 matched cddid_all.tbl CDD COG0824 COG0824 440586 FadM Acyl-CoA thioesterase FadM [Lipid transport and metabolism]. Acyl-CoA thioesterase FadM is part of the Pathway/BioSystem: Menaquinone biosynthesis 139 matched cddid_all.tbl CDD COG0825 COG0825 440587 AccA Acetyl-CoA carboxylase alpha subunit [Lipid transport and metabolism]. Acetyl-CoA carboxylase alpha subunit is part of the Pathway/BioSystem: Fatty acid biosynthesis 315 matched cddid_all.tbl CDD COG0826 COG0826 440588 RlhA 23S rRNA C2501 and tRNA U34 5'-hydroxylation protein RlhA/YrrN/YrrO, U32 peptidase family [Translation, ribosomal structure and biogenesis]. 23S rRNA C2501 and tRNA U34 5'-hydroxylation protein RlhA/YrrN/YrrO, U32 peptidase family is part of the Pathway/BioSystem: 23S rRNA modification 311 matched cddid_all.tbl CDD COG0827 COG0827 440589 YtxK Adenine-specific DNA N6-methylase [Replication, recombination and repair]. 327 matched cddid_all.tbl CDD COG0828 COG0828 440590 RpsU Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S21 is part of the Pathway/BioSystem: Ribosome 30S subunit 62 matched cddid_all.tbl CDD COG0829 COG0829 440591 UreH Urease accessory protein UreH [Posttranslational modification, protein turnover, chaperones]. 286 matched cddid_all.tbl CDD COG0830 COG0830 440592 UreF Urease accessory protein UreF [Posttranslational modification, protein turnover, chaperones]. 226 matched cddid_all.tbl CDD COG0831 COG0831 440593 UreA Urease gamma subunit [Amino acid transport and metabolism]. 102 matched cddid_all.tbl CDD COG0832 COG0832 440594 UreB Urease beta subunit [Amino acid transport and metabolism]. 101 matched cddid_all.tbl CDD COG0833 COG0833 440595 LysP Amino acid permease [Amino acid transport and metabolism]. 467 matched cddid_all.tbl CDD COG0834 COG0834 440596 HisJ ABC-type amino acid transport/signal transduction system, periplasmic component/domain [Amino acid transport and metabolism, Signal transduction mechanisms]. 223 matched cddid_all.tbl CDD COG0835 COG0835 440597 CheW Chemotaxis signal transduction protein CheW [Signal transduction mechanisms]. 151 matched cddid_all.tbl CDD COG0836 COG0836 440598 CpsB Mannose-1-phosphate guanylyltransferase [Cell wall/membrane/envelope biogenesis]. 347 matched cddid_all.tbl CDD COG0837 COG0837 440599 Glk Glucokinase [Carbohydrate transport and metabolism]. Glucokinase is part of the Pathway/BioSystem: Glycolysis 320 matched cddid_all.tbl CDD COG0838 COG0838 440600 NuoA NADH:ubiquinone oxidoreductase subunit 3 (chain A) [Energy production and conversion]. NADH:ubiquinone oxidoreductase subunit 3 (chain A) is part of the Pathway/BioSystem: NADH dehydrogenase 117 matched cddid_all.tbl CDD COG0839 COG0839 440601 NuoJ NADH:ubiquinone oxidoreductase subunit 6 (chain J) [Energy production and conversion]. NADH:ubiquinone oxidoreductase subunit 6 (chain J) is part of the Pathway/BioSystem: NADH dehydrogenase 162 matched cddid_all.tbl CDD COG0840 COG0840 440602 Tar Methyl-accepting chemotaxis protein (MCP) [Signal transduction mechanisms]. 533 matched cddid_all.tbl CDD COG0841 COG0841 440603 AcrB Multidrug efflux pump subunit AcrB [Defense mechanisms]. 1015 matched cddid_all.tbl CDD COG0842 COG0842 440604 YadH ABC-type multidrug transport system, permease component [Defense mechanisms]. 200 matched cddid_all.tbl CDD COG0843 COG0843 440605 CyoB Heme/copper-type cytochrome/quinol oxidase, subunit 1 [Energy production and conversion]. 535 matched cddid_all.tbl CDD COG0845 COG0845 440606 AcrA Multidrug efflux pump subunit AcrA (membrane-fusion protein) [Cell wall/membrane/envelope biogenesis, Defense mechanisms]. 324 matched cddid_all.tbl CDD COG0846 COG0846 440607 SIR2 NAD-dependent protein deacetylase, SIR2 family [Posttranslational modification, protein turnover, chaperones]. 243 matched cddid_all.tbl CDD COG0847 COG0847 440608 DnaQ DNA polymerase III, epsilon subunit or related 3'-5' exonuclease [Replication, recombination and repair]. 163 matched cddid_all.tbl CDD COG0848 COG0848 440609 ExbD Biopolymer transport protein ExbD [Intracellular trafficking, secretion, and vesicular transport]. 137 matched cddid_all.tbl CDD COG0849 COG0849 440610 FtsA Cell division ATPase FtsA [Cell cycle control, cell division, chromosome partitioning]. 402 matched cddid_all.tbl CDD COG0850 COG0850 440611 MinC Septum site-determining protein MinC [Cell cycle control, cell division, chromosome partitioning]. 223 matched cddid_all.tbl CDD COG0851 COG0851 440612 MinE Septum formation topological specificity factor MinE [Cell cycle control, cell division, chromosome partitioning]. 84 matched cddid_all.tbl CDD COG0852 COG0852 440613 NuoC NADH:ubiquinone oxidoreductase 27 kD subunit (chain C) [Energy production and conversion]. NADH:ubiquinone oxidoreductase 27 kD subunit (chain C) is part of the Pathway/BioSystem: NADH dehydrogenase 164 matched cddid_all.tbl CDD COG0853 COG0853 440614 PanD Aspartate 1-decarboxylase [Coenzyme transport and metabolism]. Aspartate 1-decarboxylase is part of the Pathway/BioSystem: Pantothenate/CoA biosynthesis 119 matched cddid_all.tbl CDD COG0854 COG0854 440615 PdxJ Pyridoxine 5'-phosphate synthase PdxJ [Coenzyme transport and metabolism]. Pyridoxine 5'-phosphate synthase PdxJ is part of the Pathway/BioSystem: Pyridoxal phosphate biosynthesis 235 matched cddid_all.tbl CDD COG0855 COG0855 440616 Ppk Polyphosphate kinase [Inorganic ion transport and metabolism]. 685 matched cddid_all.tbl CDD COG0856 COG0856 440617 PyrE2 Orotate phosphoribosyltransferase homolog [Nucleotide transport and metabolism]. 201 matched cddid_all.tbl CDD COG0857 COG0857 440618 PtaN BioD-like N-terminal domain of phosphotransacetylase [General function prediction only]. 697 matched cddid_all.tbl CDD COG0858 COG0858 440619 RbfA Ribosome-binding factor RbfA [Translation, ribosomal structure and biogenesis]. 118 matched cddid_all.tbl CDD COG0859 COG0859 440620 RfaF ADP-heptose:LPS heptosyltransferase [Cell wall/membrane/envelope biogenesis]. 336 matched cddid_all.tbl CDD COG0860 COG0860 440621 AmiC N-acetylmuramoyl-L-alanine amidase [Cell wall/membrane/envelope biogenesis]. 204 matched cddid_all.tbl CDD COG0861 COG0861 440622 TerC Tellurite resistance membrane protein TerC [Inorganic ion transport and metabolism]. 225 matched cddid_all.tbl CDD COG0863 COG0863 440623 YhdJ DNA modification methylase [Replication, recombination and repair]. 236 matched cddid_all.tbl CDD COG0864 COG0864 440624 NikR Metal-responsive transcriptional regulator, contains CopG/Arc/MetJ DNA-binding domain [Transcription]. 132 matched cddid_all.tbl CDD COG1001 COG1001 440625 AdeC Adenine deaminase [Nucleotide transport and metabolism]. 559 matched cddid_all.tbl CDD COG1002 COG1002 440626 YeeA Type II restriction/modification system, endonuclease and methylase domains [Defense mechanisms]. 838 matched cddid_all.tbl CDD COG1003 COG1003 440627 GcvP2 Glycine cleavage system protein P (pyridoxal-binding), C-terminal domain [Amino acid transport and metabolism]. Glycine cleavage system protein P (pyridoxal-binding), C-terminal domain is part of the Pathway/BioSystem: Glycine cleavage 468 matched cddid_all.tbl CDD COG1004 COG1004 440628 Ugd UDP-glucose 6-dehydrogenase [Cell wall/membrane/envelope biogenesis]. 436 matched cddid_all.tbl CDD COG1005 COG1005 440629 NuoH NADH:ubiquinone oxidoreductase subunit 1 (chain H) [Energy production and conversion]. NADH:ubiquinone oxidoreductase subunit 1 (chain H) is part of the Pathway/BioSystem: NADH dehydrogenase 329 matched cddid_all.tbl CDD COG1006 COG1006 440630 MnhC Multisubunit Na+/H+ antiporter, MnhC subunit [Inorganic ion transport and metabolism]. 113 matched cddid_all.tbl CDD COG1007 COG1007 440631 NuoN NADH:ubiquinone oxidoreductase subunit 2 (chain N) [Energy production and conversion]. NADH:ubiquinone oxidoreductase subunit 2 (chain N) is part of the Pathway/BioSystem: NADH dehydrogenase 473 matched cddid_all.tbl CDD COG1008 COG1008 440632 NuoM NADH:ubiquinone oxidoreductase subunit 4 (chain M) [Energy production and conversion]. NADH:ubiquinone oxidoreductase subunit 4 (chain M) is part of the Pathway/BioSystem: NADH dehydrogenase 488 matched cddid_all.tbl CDD COG1009 COG1009 440633 NuoL Membrane H+-translocase/NADH:ubiquinone oxidoreductase subunit 5 (chain L)/Multisubunit Na+/H+ antiporter, MnhA subunit [Energy production and conversion]. Membrane H+-translocase/NADH:ubiquinone oxidoreductase subunit 5 (chain L)/Multisubunit Na+/H+ antiporter, MnhA subunit is part of the Pathway/BioSystem: NADH dehydrogenase 608 matched cddid_all.tbl CDD COG1010 COG1010 440634 CobJ Precorrin-3B methylase [Coenzyme transport and metabolism]. Precorrin-3B methylase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 250 matched cddid_all.tbl CDD COG1011 COG1011 440635 YigB FMN and 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB, HAD superfamily (riboflavin biosynthesis) [Coenzyme transport and metabolism]. 220 matched cddid_all.tbl CDD COG1012 COG1012 440636 AdhE Acyl-CoA reductase or other NAD-dependent aldehyde dehydrogenase [Lipid transport and metabolism]. Acyl-CoA reductase or other NAD-dependent aldehyde dehydrogenase is part of the Pathway/BioSystem: Proline degradation 479 matched cddid_all.tbl CDD COG1013 COG1013 440637 PorB Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, beta subunit [Energy production and conversion]. Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, beta subunit is part of the Pathway/BioSystem: Pyruvate oxidation 262 matched cddid_all.tbl CDD COG1014 COG1014 440638 PorG Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, gamma subunit [Energy production and conversion]. Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, gamma subunit is part of the Pathway/BioSystem: Pyruvate oxidation 424 matched cddid_all.tbl CDD COG1015 COG1015 440639 DeoB Phosphopentomutase [Carbohydrate transport and metabolism]. 385 matched cddid_all.tbl CDD COG1017 COG1017 440640 Hmp Hemoglobin-like flavoprotein [Energy production and conversion]. 135 matched cddid_all.tbl CDD COG1018 COG1018 440641 Fpr Flavodoxin/ferredoxin--NADP reductase [Energy production and conversion]. 231 matched cddid_all.tbl CDD COG1019 COG1019 440642 CAB4 Phosphopantetheine adenylyltransferase [Coenzyme transport and metabolism]. Phosphopantetheine adenylyltransferase is part of the Pathway/BioSystem: Pantothenate/CoA biosynthesis 154 matched cddid_all.tbl CDD COG1020 COG1020 440643 EntF EntF, seryl-AMP synthase component of non-ribosomal peptide synthetase [Secondary metabolites biosynthesis, transport and catabolism]. 1329 matched cddid_all.tbl CDD COG1021 COG1021 440644 EntE EntE, 2,3-dihydroxybenzoate-AMP synthase component of non-ribosomal peptide synthetase [Secondary metabolites biosynthesis, transport and catabolism]. 533 matched cddid_all.tbl CDD COG1022 COG1022 440645 FAA1 Long-chain acyl-CoA synthetase (AMP-forming) [Lipid transport and metabolism]. 603 matched cddid_all.tbl CDD COG1023 COG1023 440646 YqeC 6-phosphogluconate dehydrogenase (decarboxylating) [Carbohydrate transport and metabolism]. 300 matched cddid_all.tbl CDD COG1024 COG1024 440647 CaiD Enoyl-CoA hydratase/carnithine racemase [Lipid transport and metabolism]. Enoyl-CoA hydratase/carnithine racemase is part of the Pathway/BioSystem: Fatty acid biosynthesis 249 matched cddid_all.tbl CDD COG1025 COG1025 440648 Ptr Secreted/periplasmic Zn-dependent peptidases, insulinase-like [Posttranslational modification, protein turnover, chaperones]. 956 matched cddid_all.tbl CDD COG1026 COG1026 440649 Cym1 Zn-dependent peptidase, M16 (insulinase) family [Posttranslational modification, protein turnover, chaperones]. 974 matched cddid_all.tbl CDD COG1027 COG1027 440650 AspA Aspartate ammonia-lyase [Amino acid transport and metabolism]. 460 matched cddid_all.tbl CDD COG1028 COG1028 440651 FabG NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family [Lipid transport and metabolism]. NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family is part of the Pathway/BioSystem: Fatty acid biosynthesis 249 matched cddid_all.tbl CDD COG1029 COG1029 440652 FwdB Formylmethanofuran dehydrogenase subunit B [Energy production and conversion]. 428 matched cddid_all.tbl CDD COG1030 COG1030 440653 NfeD Membrane-bound serine protease NfeD, ClpP class [Posttranslational modification, protein turnover, chaperones]. 413 matched cddid_all.tbl CDD COG1031 COG1031 440654 TM1601 Radical SAM superfamily enzyme with C-terminal helix-hairpin-helix motif [General function prediction only]. 555 matched cddid_all.tbl CDD COG1032 COG1032 440655 YgiQ Radical SAM superfamily enzyme YgiQ, UPF0313 family [General function prediction only]. 394 matched cddid_all.tbl CDD COG1033 COG1033 440656 MMPL Predicted exporter protein, RND superfamily [General function prediction only]. 767 matched cddid_all.tbl CDD COG1034 COG1034 440657 NuoG NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G) [Energy production and conversion]. NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G) is part of the Pathway/BioSystem: NADH dehydrogenase 453 matched cddid_all.tbl CDD COG1035 COG1035 440658 FrhB Coenzyme F420-reducing hydrogenase, beta subunit [Energy production and conversion]. 269 matched cddid_all.tbl CDD COG1036 COG1036 440659 AfpA Archaeal flavoprotein [Energy production and conversion]. 174 matched cddid_all.tbl CDD COG1038 COG1038 440660 PycA Pyruvate carboxylase [Energy production and conversion]. Pyruvate carboxylase is part of the Pathway/BioSystem: Urea cycle 1144 matched cddid_all.tbl CDD COG1039 COG1039 440661 RnhC Ribonuclease HIII [Replication, recombination and repair]. 302 matched cddid_all.tbl CDD COG1040 COG1040 440662 ComFC DNA utilization protein ComFC/GntX, contains phosphoribosyltransferase domain [General function prediction only]. 196 matched cddid_all.tbl CDD COG1041 COG1041 440663 Trm11 tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]. tRNA G10 N-methylase Trm11 is part of the Pathway/BioSystem: tRNA modification 172 matched cddid_all.tbl CDD COG1042 COG1042 440664 PatZN Acyl-CoA synthetase (NDP forming) [Energy production and conversion]. 708 matched cddid_all.tbl CDD COG1043 COG1043 440665 LpxA Acyl-[acyl carrier protein]--UDP-N-acetylglucosamine O-acyltransferase [Cell wall/membrane/envelope biogenesis]. Acyl-[acyl carrier protein]--UDP-N-acetylglucosamine O-acyltransferase is part of the Pathway/BioSystem: Lipid A biosynthesis 258 matched cddid_all.tbl CDD COG1044 COG1044 440666 LpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase [Cell wall/membrane/envelope biogenesis]. UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase is part of the Pathway/BioSystem: Lipid A biosynthesis 335 matched cddid_all.tbl CDD COG1045 COG1045 440667 CysE Serine acetyltransferase [Amino acid transport and metabolism]. Serine acetyltransferase is part of the Pathway/BioSystem: Cysteine biosynthesis 174 matched cddid_all.tbl CDD COG1047 COG1047 440668 SlpA Peptidyl-prolyl cis-trans isomerase, FKBP type [Posttranslational modification, protein turnover, chaperones]. 138 matched cddid_all.tbl CDD COG1048 COG1048 440669 AcnA Aconitase A [Energy production and conversion]. Aconitase A is part of the Pathway/BioSystem: Lysine biosynthesisTCA cycle 891 matched cddid_all.tbl CDD COG1049 COG1049 440670 AcnB Aconitase B [Energy production and conversion]. Aconitase B is part of the Pathway/BioSystem: TCA cycle 852 matched cddid_all.tbl CDD COG1051 COG1051 440671 YjhB ADP-ribose pyrophosphatase YjhB, NUDIX family [Nucleotide transport and metabolism]. 125 matched cddid_all.tbl CDD COG1052 COG1052 440672 LdhA Lactate dehydrogenase or related 2-hydroxyacid dehydrogenase [Energy production and conversion, Coenzyme transport and metabolism, General function prediction only]. Lactate dehydrogenase or related 2-hydroxyacid dehydrogenase is part of the Pathway/BioSystem: Pyridoxal phosphate biosynthesis 316 matched cddid_all.tbl CDD COG1053 COG1053 440673 SdhA Succinate dehydrogenase/fumarate reductase, flavoprotein subunit [Energy production and conversion]. Succinate dehydrogenase/fumarate reductase, flavoprotein subunit is part of the Pathway/BioSystem: TCA cycle 443 matched cddid_all.tbl CDD COG1054 COG1054 440674 TrhO tRNA U34 5'-hydroxylase TrhO, rhodanese family [Translation, ribosomal structure and biogenesis]. 304 matched cddid_all.tbl CDD COG1055 COG1055 440675 ArsB Na+/H+ antiporter NhaD or related arsenite permease [Inorganic ion transport and metabolism]. 415 matched cddid_all.tbl CDD COG1056 COG1056 440676 NadR Nicotinamide mononucleotide adenylyltransferase [Coenzyme transport and metabolism]. Nicotinamide mononucleotide adenylyltransferase is part of the Pathway/BioSystem: NAD biosynthesis 162 matched cddid_all.tbl CDD COG1057 COG1057 440677 NadD Nicotinate-nucleotide adenylyltransferase NadD [Coenzyme transport and metabolism]. Nicotinate-nucleotide adenylyltransferase NadD is part of the Pathway/BioSystem: NAD biosynthesis 197 matched cddid_all.tbl CDD COG1058 COG1058 440678 CinA ADP-ribose pyrophosphatase domain of DNA damage- and competence-inducible protein CinA [Replication, recombination and repair]. 249 matched cddid_all.tbl CDD COG1059 COG1059 440679 ENDO3c Thermostable 8-oxoguanine DNA glycosylase [Replication, recombination and repair, Defense mechanisms]. 206 matched cddid_all.tbl CDD COG1060 COG1060 440680 ThiH 2-iminoacetate synthase ThiH/Menaquinone biosynthesis enzymes MqnC and MqnE [Coenzyme transport and metabolism]. 2-iminoacetate synthase ThiH/Menaquinone biosynthesis enzymes MqnC and MqnE is part of the Pathway/BioSystem: Thiamine biosynthesis 351 matched cddid_all.tbl CDD COG1061 COG1061 440681 SSL2 Superfamily II DNA or RNA helicase [Transcription, Replication, recombination, and repair]. 566 matched cddid_all.tbl CDD COG1062 COG1062 440682 FrmA Zn-dependent alcohol/formaldehyde dehydrogenase [Energy production and conversion]. 355 matched cddid_all.tbl CDD COG1063 COG1063 440683 Tdh Threonine dehydrogenase or related Zn-dependent dehydrogenase [Amino acid transport and metabolism, General function prediction only]. Threonine dehydrogenase or related Zn-dependent dehydrogenase is part of the Pathway/BioSystem: Non-phosphorylated Entner-Doudoroff pathway 341 matched cddid_all.tbl CDD COG1064 COG1064 440684 AdhP D-arabinose 1-dehydrogenase, Zn-dependent alcohol dehydrogenase family [Carbohydrate transport and metabolism]. 332 matched cddid_all.tbl CDD COG1066 COG1066 440685 Sms DNA repair protein RadA/Sms, contains AAA+ ATPase domain [Replication, recombination and repair]. 453 matched cddid_all.tbl CDD COG1067 COG1067 440686 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]. 742 matched cddid_all.tbl CDD COG1069 COG1069 440687 AraB Ribulose kinase [Carbohydrate transport and metabolism]. 532 matched cddid_all.tbl CDD COG1070 COG1070 440688 XylB Sugar (pentulose or hexulose) kinase [Carbohydrate transport and metabolism]. Sugar (pentulose or hexulose) kinase is part of the Pathway/BioSystem: Non-phosphorylated Entner-Doudoroff pathway 494 matched cddid_all.tbl CDD COG1071 COG1071 440689 AcoA TPP-dependent pyruvate or acetoin dehydrogenase subunit alpha [Energy production and conversion]. TPP-dependent pyruvate or acetoin dehydrogenase subunit alpha is part of the Pathway/BioSystem: Pyruvate oxidation 348 matched cddid_all.tbl CDD COG1072 COG1072 440690 CoaA Panthothenate kinase [Coenzyme transport and metabolism]. Panthothenate kinase is part of the Pathway/BioSystem: Pantothenate/CoA biosynthesis 309 matched cddid_all.tbl CDD COG1073 COG1073 440691 FrsA Fermentation-respiration switch esterase FrsA, DUF1100 family [Signal transduction mechanisms]. 253 matched cddid_all.tbl CDD COG1074 COG1074 440692 RecB 3#-5# helicase subunit RecB of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair]. 866 matched cddid_all.tbl CDD COG1075 COG1075 440693 EstA Triacylglycerol esterase/lipase EstA, alpha/beta hydrolase fold [Lipid transport and metabolism]. 106 matched cddid_all.tbl CDD COG1076 COG1076 440694 DjlA DnaJ domain-containing protein [Posttranslational modification, protein turnover, chaperones]. 75 matched cddid_all.tbl CDD COG1077 COG1077 440695 MreB Cell shape-determining ATPase MreB, actin-like superfamily [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]. 339 matched cddid_all.tbl CDD COG1078 COG1078 440696 YdhJ HD superfamily phosphohydrolase [General function prediction only]. 340 matched cddid_all.tbl CDD COG1079 COG1079 440697 NupQ ABC-type guanosine uptake system NupNOPQ, permease subunit NupQ [Nucleotide transport and metabolism]. 309 matched cddid_all.tbl CDD COG1080 COG1080 440698 PtsA Phosphoenolpyruvate-protein kinase (PTS system EI component in bacteria) [Carbohydrate transport and metabolism]. 571 matched cddid_all.tbl CDD COG1082 COG1082 440699 YcjR Sugar phosphate isomerase/epimerase [Carbohydrate transport and metabolism]. 254 matched cddid_all.tbl CDD COG1083 COG1083 440700 NeuA CMP-N-acetylneuraminic acid synthetase, NeuA/PseF family [Cell wall/membrane/envelope biogenesis]. 228 matched cddid_all.tbl CDD COG1084 COG1084 440701 Nog1 GTP-binding protein, GTP1/Obg family [General function prediction only]. 330 matched cddid_all.tbl CDD COG1085 COG1085 440702 GalT Galactose-1-phosphate uridylyltransferase [Carbohydrate transport and metabolism]. 336 matched cddid_all.tbl CDD COG1086 COG1086 440703 FlaA1 NDP-sugar epimerase, includes UDP-GlcNAc-inverting 4,6-dehydratase FlaA1 and capsular polysaccharide biosynthesis protein EpsC [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones]. 121 matched cddid_all.tbl CDD COG1087 COG1087 440704 GalE UDP-glucose 4-epimerase [Cell wall/membrane/envelope biogenesis]. 328 matched cddid_all.tbl CDD COG1088 COG1088 440705 RfbB dTDP-D-glucose 4,6-dehydratase [Cell wall/membrane/envelope biogenesis]. 333 matched cddid_all.tbl CDD COG1089 COG1089 440706 Gmd GDP-D-mannose dehydratase [Cell wall/membrane/envelope biogenesis]. 321 matched cddid_all.tbl CDD COG1090 COG1090 440707 YfcH NAD dependent epimerase/dehydratase family enzyme [General function prediction only]. 298 matched cddid_all.tbl CDD COG1091 COG1091 440708 RfbD dTDP-4-dehydrorhamnose reductase [Cell wall/membrane/envelope biogenesis]. 279 matched cddid_all.tbl CDD COG1092 COG1092 440709 RlmK 23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI [Translation, ribosomal structure and biogenesis]. 23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI is part of the Pathway/BioSystem: 23S rRNA modification 392 matched cddid_all.tbl CDD COG1093 COG1093 440710 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]. Translation initiation factor 2, alpha subunit (eIF-2alpha) is part of the Pathway/BioSystem: Translation factors 259 matched cddid_all.tbl CDD COG1094 COG1094 440711 Krr1 rRNA processing protein Krr1/Pno1, contains KH domain [Translation, ribosomal structure and biogenesis]. 177 matched cddid_all.tbl CDD COG1095 COG1095 440712 RPB7 DNA-directed RNA polymerase, subunit E'/Rpb7 [Transcription]. DNA-directed RNA polymerase, subunit E'/Rpb7 is part of the Pathway/BioSystem: RNA polymerase 171 matched cddid_all.tbl CDD COG1096 COG1096 440713 Csl4 Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Intracellular trafficking, secretion, and vesicular transport]. 191 matched cddid_all.tbl CDD COG1097 COG1097 440714 Rrp4 Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Intracellular trafficking, secretion, and vesicular transport]. 234 matched cddid_all.tbl CDD COG1098 COG1098 440715 YabR Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain [General function prediction only]. 130 matched cddid_all.tbl CDD COG1099 COG1099 440716 COG1099 Predicted metal-dependent hydrolase, TIM-barrel fold [General function prediction only]. 260 matched cddid_all.tbl CDD COG1100 COG1100 440717 Gem1 GTPase SAR1 family domain [General function prediction only]. 177 matched cddid_all.tbl CDD COG1101 COG1101 440718 PhnK ABC-type uncharacterized transport system, ATPase component [General function prediction only]. 264 matched cddid_all.tbl CDD COG1102 COG1102 440719 CmkB Cytidylate kinase [Nucleotide transport and metabolism]. 188 matched cddid_all.tbl CDD COG1103 COG1103 440720 COG1103 Archaeal Cys-tRNA synthase (O-phospho-L-seryl-tRNA:Cys-tRNA synthase) [Translation, ribosomal structure and biogenesis]. 390 matched cddid_all.tbl CDD COG1104 COG1104 440721 NifS Cysteine desulfurase/Cysteine sulfinate desulfinase IscS or related enzyme, NifS family [Amino acid transport and metabolism]. 381 matched cddid_all.tbl CDD COG1105 COG1105 440722 FruK 1-phosphofructokinase or 6-phosphofructokinase II [Carbohydrate transport and metabolism]. 304 matched cddid_all.tbl CDD COG1106 COG1106 440723 COG1106 ATPase/GTPase, AAA15 family [General function prediction only]. 330 matched cddid_all.tbl CDD COG1107 COG1107 440724 COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [Replication, recombination and repair]. 626 matched cddid_all.tbl CDD COG1108 COG1108 440725 ZnuB ABC-type Mn2+/Zn2+ transport system, permease component [Inorganic ion transport and metabolism]. 260 matched cddid_all.tbl CDD COG1109 COG1109 440726 ManB Phosphomannomutase [Carbohydrate transport and metabolism]. 456 matched cddid_all.tbl CDD COG1110 COG1110 440727 TopG2 Reverse gyrase [Replication, recombination and repair]. 1219 matched cddid_all.tbl CDD COG1111 COG1111 440728 MPH1 ERCC4-related helicase [Replication, recombination and repair]. 718 matched cddid_all.tbl CDD COG1112 COG1112 440729 DNA2 Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]. 819 matched cddid_all.tbl CDD COG1113 COG1113 440730 AnsP L-asparagine transporter or related permease [Amino acid transport and metabolism]. 458 matched cddid_all.tbl CDD COG1114 COG1114 440731 BrnQ Branched-chain amino acid permease [Amino acid transport and metabolism]. 433 matched cddid_all.tbl CDD COG1115 COG1115 440732 AlsT Na+/alanine symporter [Amino acid transport and metabolism]. 450 matched cddid_all.tbl CDD COG1116 COG1116 440733 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]. 260 matched cddid_all.tbl CDD COG1117 COG1117 440734 PstB ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]. 258 matched cddid_all.tbl CDD COG1118 COG1118 440735 CysA ABC-type sulfate/molybdate transport systems, ATPase component [Inorganic ion transport and metabolism]. 348 matched cddid_all.tbl CDD COG1119 COG1119 440736 ModF ABC-type molybdenum transport system, ATPase component ModF/photorepair protein PhrA [Inorganic ion transport and metabolism]. 250 matched cddid_all.tbl CDD COG1120 COG1120 440737 FepC ABC-type cobalamin/Fe3+-siderophores transport system, ATPase component [Inorganic ion transport and metabolism, Coenzyme transport and metabolism]. 254 matched cddid_all.tbl CDD COG1121 COG1121 440738 ZnuC ABC-type Mn2+/Zn2+ transport system, ATPase component [Inorganic ion transport and metabolism]. 245 matched cddid_all.tbl CDD COG1122 COG1122 440739 EcfA2 Energy-coupling factor transporter ATP-binding protein EcfA2 [Inorganic ion transport and metabolism, General function prediction only]. 230 matched cddid_all.tbl CDD COG1123 COG1123 440740 GsiA ABC-type glutathione transport system ATPase component, contains duplicated ATPase domain [Posttranslational modification, protein turnover, chaperones]. 514 matched cddid_all.tbl CDD COG1124 COG1124 440741 DppF ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism, Inorganic ion transport and metabolism]. 248 matched cddid_all.tbl CDD COG1125 COG1125 440742 OpuBA ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]. 306 matched cddid_all.tbl CDD COG1126 COG1126 440743 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]. 239 matched cddid_all.tbl CDD COG1127 COG1127 440744 MlaF ATPase subunit MlaF of the ABC-type intermembrane phospholipid transporter Mla [Cell wall/membrane/envelope biogenesis]. 241 matched cddid_all.tbl CDD COG1129 COG1129 440745 MglA ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]. 497 matched cddid_all.tbl CDD COG1131 COG1131 440746 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]. 236 matched cddid_all.tbl CDD COG1132 COG1132 440747 MdlB ABC-type multidrug transport system, ATPase and permease component [Defense mechanisms]. 579 matched cddid_all.tbl CDD COG1133 COG1133 440748 SbmA Peptide antibiotic transporter SbmA/BacA, ABC-type permease family [Defense mechanisms]. 408 matched cddid_all.tbl CDD COG1134 COG1134 440749 TagH ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism]. 245 matched cddid_all.tbl CDD COG1135 COG1135 440750 AbcC ABC-type methionine transport system, ATPase component [Amino acid transport and metabolism]. 339 matched cddid_all.tbl CDD COG1136 COG1136 440751 LolD ABC-type lipoprotein export system, ATPase component [Cell wall/membrane/envelope biogenesis]. 227 matched cddid_all.tbl CDD COG1137 COG1137 440752 LptB ABC-type lipopolysaccharide export system, ATPase component [Cell wall/membrane/envelope biogenesis]. 240 matched cddid_all.tbl CDD COG1138 COG1138 440753 CcmF Cytochrome c biogenesis protein CcmF [Energy production and conversion, Posttranslational modification, protein turnover, chaperones]. 650 matched cddid_all.tbl CDD COG1139 COG1139 440754 LutB L-lactate utilization protein LutB, contains a ferredoxin-type domain [Energy production and conversion]. 465 matched cddid_all.tbl CDD COG1140 COG1140 440755 NarY Nitrate reductase beta subunit [Energy production and conversion, Inorganic ion transport and metabolism]. 485 matched cddid_all.tbl CDD COG1141 COG1141 440756 Fer Ferredoxin [Energy production and conversion]. 63 matched cddid_all.tbl CDD COG1142 COG1142 440757 HycB Fe-S-cluster-containing hydrogenase component 2 [Energy production and conversion]. 138 matched cddid_all.tbl CDD COG1143 COG1143 440758 NuoI Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) [Energy production and conversion]. Formate hydrogenlyase subunit 6/NADH:ubiquinone oxidoreductase 23 kD subunit (chain I) is part of the Pathway/BioSystem: NADH dehydrogenase 66 matched cddid_all.tbl CDD COG1144 COG1144 440759 PorD Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, delta subunit [Energy production and conversion]. Pyruvate:ferredoxin oxidoreductase or related 2-oxoacid:ferredoxin oxidoreductase, delta subunit is part of the Pathway/BioSystem: Pyruvate oxidation 84 matched cddid_all.tbl CDD COG1145 COG1145 440760 NapF Ferredoxin [Energy production and conversion]. 238 matched cddid_all.tbl CDD COG1146 COG1146 440761 PreA NAD-dependent dihydropyrimidine dehydrogenase, PreA subunit [Nucleotide transport and metabolism]. 67 matched cddid_all.tbl CDD COG1148 COG1148 440762 HdrA Heterodisulfide reductase, subunit A (polyferredoxin) [Energy production and conversion]. 563 matched cddid_all.tbl CDD COG1149 COG1149 440763 COG1149 MinD superfamily P-loop ATPase, contains an inserted ferredoxin domain [General function prediction only]. 68 matched cddid_all.tbl CDD COG1150 COG1150 440764 HdrC Heterodisulfide reductase, subunit C [Energy production and conversion]. 79 matched cddid_all.tbl CDD COG1151 COG1151 440765 Hcp Hydroxylamine reductase (hybrid-cluster protein) [Energy production and conversion]. 613 matched cddid_all.tbl CDD COG1152 COG1152 440766 CdhA CO dehydrogenase/acetyl-CoA synthase alpha subunit [Energy production and conversion]. 215 matched cddid_all.tbl CDD COG1153 COG1153 440767 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion]. 127 matched cddid_all.tbl CDD COG1154 COG1154 440768 Dxs Deoxyxylulose-5-phosphate synthase [Coenzyme transport and metabolism, Lipid transport and metabolism]. Deoxyxylulose-5-phosphate synthase is part of the Pathway/BioSystem: Pyridoxal phosphate biosynthesis 623 matched cddid_all.tbl CDD COG1155 COG1155 440769 NtpA Archaeal/vacuolar-type H+-ATPase catalytic subunit A/Vma1 [Energy production and conversion]. Archaeal/vacuolar-type H+-ATPase catalytic subunit A/Vma1 is part of the Pathway/BioSystem: A/V-type ATP synthase 583 matched cddid_all.tbl CDD COG1156 COG1156 440770 NtpB Archaeal/vacuolar-type H+-ATPase subunit B/Vma2 [Energy production and conversion]. Archaeal/vacuolar-type H+-ATPase subunit B/Vma2 is part of the Pathway/BioSystem: A/V-type ATP synthase 462 matched cddid_all.tbl CDD COG1157 COG1157 440771 FliI Flagellar biosynthesis/type III secretory pathway ATPase FliI [Cell motility, Intracellular trafficking, secretion, and vesicular transport]. 433 matched cddid_all.tbl CDD COG1158 COG1158 440772 Rho Transcription termination factor Rho [Transcription]. 373 matched cddid_all.tbl CDD COG1159 COG1159 440773 Era GTPase Era, involved in 16S rRNA processing [Translation, ribosomal structure and biogenesis]. 290 matched cddid_all.tbl CDD COG1160 COG1160 440774 Der Double Era-like domain GTPase Der [Translation, ribosomal structure and biogenesis]. 438 matched cddid_all.tbl CDD COG1161 COG1161 440775 RbgA Ribosome biogenesis GTPase RbgA [Translation, ribosomal structure and biogenesis]. 279 matched cddid_all.tbl CDD COG1162 COG1162 440776 RsgA Ribosome biogenesis GTPase RsgA [Translation, ribosomal structure and biogenesis]. 300 matched cddid_all.tbl CDD COG1163 COG1163 440777 Rbg1 Ribosome-interacting GTPase RBG1 [Translation, ribosomal structure and biogenesis]. 368 matched cddid_all.tbl CDD COG1164 COG1164 440778 PepF Oligoendopeptidase F [Amino acid transport and metabolism]. 600 matched cddid_all.tbl CDD COG1165 COG1165 440779 MenD 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase [Coenzyme transport and metabolism]. 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase is part of the Pathway/BioSystem: Menaquinone biosynthesis 567 matched cddid_all.tbl CDD COG1166 COG1166 440780 SpeA Arginine decarboxylase (spermidine biosynthesis) [Amino acid transport and metabolism]. 633 matched cddid_all.tbl CDD COG1167 COG1167 440781 ARO8 DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain [Transcription, Amino acid transport and metabolism]. DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain is part of the Pathway/BioSystem: Lysine biosynthesis 471 matched cddid_all.tbl CDD COG1168 COG1168 440782 MalY Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism, General function prediction only]. 387 matched cddid_all.tbl CDD COG1169 COG1169 440783 MenF Isochorismate synthase EntC [Coenzyme transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism]. Isochorismate synthase EntC is part of the Pathway/BioSystem: Menaquinone biosynthesis 353 matched cddid_all.tbl CDD COG1171 COG1171 440784 IlvA Threonine deaminase [Amino acid transport and metabolism]. Threonine deaminase is part of the Pathway/BioSystem: Isoleucine, leucine, valine biosynthesis 327 matched cddid_all.tbl CDD COG1172 COG1172 440785 AraH Ribose/xylose/arabinose/galactoside ABC-type transport system, permease component [Carbohydrate transport and metabolism]. 322 matched cddid_all.tbl CDD COG1173 COG1173 440786 DppC ABC-type dipeptide/oligopeptide/nickel transport system, permease component [Amino acid transport and metabolism, Inorganic ion transport and metabolism]. 275 matched cddid_all.tbl CDD COG1174 COG1174 440787 OpuBB ABC-type proline/glycine betaine transport system, permease component [Amino acid transport and metabolism]. 212 matched cddid_all.tbl CDD COG1175 COG1175 440788 UgpA ABC-type sugar transport system, permease component [Carbohydrate transport and metabolism]. 298 matched cddid_all.tbl CDD COG1176 COG1176 440789 PotB ABC-type spermidine/putrescine transport system, permease component I [Amino acid transport and metabolism]. 287 matched cddid_all.tbl CDD COG1177 COG1177 440790 PotC ABC-type spermidine/putrescine transport system, permease component II [Amino acid transport and metabolism]. 262 matched cddid_all.tbl CDD COG1178 COG1178 440791 FbpB ABC-type Fe3+ transport system, permease component [Inorganic ion transport and metabolism]. 538 matched cddid_all.tbl CDD COG1179 COG1179 440792 TcdA tRNA A37 threonylcarbamoyladenosine dehydratase [Translation, ribosomal structure and biogenesis]. tRNA A37 threonylcarbamoyladenosine dehydratase is part of the Pathway/BioSystem: tRNA modification 247 matched cddid_all.tbl CDD COG1180 COG1180 440793 PflA Pyruvate-formate lyase-activating enzyme [Posttranslational modification, protein turnover, chaperones]. 242 matched cddid_all.tbl CDD COG1181 COG1181 440794 DdlA D-alanine-D-alanine ligase or related ATP-grasp enzyme [Cell wall/membrane/envelope biogenesis, General function prediction only]. D-alanine-D-alanine ligase or related ATP-grasp enzyme is part of the Pathway/BioSystem: Mureine biosynthesis 303 matched cddid_all.tbl CDD COG1182 COG1182 440795 AzoR FMN-dependent NADH-azoreductase [Energy production and conversion]. 205 matched cddid_all.tbl CDD COG1183 COG1183 440796 PssA Phosphatidylserine synthase [Lipid transport and metabolism]. 237 matched cddid_all.tbl CDD COG1184 COG1184 440797 GCD2 Translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]. Translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family is part of the Pathway/BioSystem: Translation factors 304 matched cddid_all.tbl CDD COG1185 COG1185 440798 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]. 686 matched cddid_all.tbl CDD COG1186 COG1186 440799 PrfB Protein chain release factor PrfB [Translation, ribosomal structure and biogenesis]. Protein chain release factor PrfB is part of the Pathway/BioSystem: Translation factors 140 matched cddid_all.tbl CDD COG1187 COG1187 440800 RsuA Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 [Translation, ribosomal structure and biogenesis]. Pseudouridylate synthase RsuA, specific for 16S rRNA U516 and 23S rRNA U2605 is part of the Pathway/BioSystem: 16S rRNA modification 226 matched cddid_all.tbl CDD COG1188 COG1188 440801 HslR Ribosomal 50S subunit-recycling heat shock protein, contains S4 domain [Translation, ribosomal structure and biogenesis]. 120 matched cddid_all.tbl CDD COG1189 COG1189 440802 YqxC Predicted rRNA methylase YqxC, contains S4 and FtsJ domains [Translation, ribosomal structure and biogenesis]. 248 matched cddid_all.tbl CDD COG1190 COG1190 440803 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]. Lysyl-tRNA synthetase (class II) is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 495 matched cddid_all.tbl CDD COG1191 COG1191 440804 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]. DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase 236 matched cddid_all.tbl CDD COG1192 COG1192 440805 ParA ParA-like ATPase involved in chromosome/plasmid partitioning or cellulose biosynthesis protein BcsQ [Cell cycle control, cell division, chromosome partitioning, Cell motility]. 253 matched cddid_all.tbl CDD COG1193 COG1193 440806 MutS2 dsDNA-specific endonuclease/ATPase MutS2 [Replication, recombination and repair]. 784 matched cddid_all.tbl CDD COG1194 COG1194 440807 MutY Adenine-specific DNA glycosylase, acts on AG and A-oxoG pairs [Replication, recombination and repair]. 350 matched cddid_all.tbl CDD COG1195 COG1195 440808 RecF Recombinational DNA repair ATPase RecF [Replication, recombination and repair]. 352 matched cddid_all.tbl CDD COG1196 COG1196 440809 Smc Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]. 983 matched cddid_all.tbl CDD COG1197 COG1197 440810 Mfd Transcription-repair coupling factor (superfamily II helicase) [Replication, recombination and repair, Transcription]. 1130 matched cddid_all.tbl CDD COG1198 COG1198 440811 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [Replication, recombination and repair]. 728 matched cddid_all.tbl CDD COG1199 COG1199 440812 DinG Rad3-related DNA helicase DinG [Replication, recombination and repair]. 629 matched cddid_all.tbl CDD COG1200 COG1200 440813 RecG RecG-like helicase [Replication, recombination and repair]. 684 matched cddid_all.tbl CDD COG1201 COG1201 440814 Lhr Lhr-like helicase [Replication, recombination and repair]. 850 matched cddid_all.tbl CDD COG1202 COG1202 440815 COG1202 Superfamily II helicase, archaea-specific [Replication, recombination and repair]. 790 matched cddid_all.tbl CDD COG1203 COG1203 440816 Cas3 CRISPR-Cas type I system-associated endonuclease/helicase Cas3 [Defense mechanisms]. CRISPR-Cas type I system-associated endonuclease/helicase Cas3 is part of the Pathway/BioSystem: CRISPR-Cas system 535 matched cddid_all.tbl CDD COG1204 COG1204 440817 BRR2 Replicative superfamily II helicase [Replication, recombination and repair]. 529 matched cddid_all.tbl CDD COG1205 COG1205 440818 YprA ATP-dependent helicase YprA, contains C-terminal metal-binding DUF1998 domain [Replication, recombination and repair]. 758 matched cddid_all.tbl CDD COG1206 COG1206 440819 TrmFO Folate-dependent tRNA-U54 methylase TrmFO/GidA [Translation, ribosomal structure and biogenesis]. Folate-dependent tRNA-U54 methylase TrmFO/GidA is part of the Pathway/BioSystem: tRNA modification 436 matched cddid_all.tbl CDD COG1207 COG1207 440820 GlmU Bifunctional protein GlmU, N-acetylglucosamine-1-phosphate-uridyltransferase/glucosamine-1-phosphate-acetyltransferase [Cell wall/membrane/envelope biogenesis]. 457 matched cddid_all.tbl CDD COG1208 COG1208 440821 GCD1 NDP-sugar pyrophosphorylase, includes eIF-2Bgamma, eIF-2Bepsilon, and LPS biosynthesis protein s [Translation, ribosomal structure and biogenesis, Cell wall/membrane/envelope biogenesis]. 238 matched cddid_all.tbl CDD COG1209 COG1209 440822 RmlA1 dTDP-glucose pyrophosphorylase [Cell wall/membrane/envelope biogenesis]. 294 matched cddid_all.tbl CDD COG1210 COG1210 440823 GalU UTP-glucose-1-phosphate uridylyltransferase [Cell wall/membrane/envelope biogenesis]. 288 matched cddid_all.tbl CDD COG1211 COG1211 440824 IspD 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase [Lipid transport and metabolism]. 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase is part of the Pathway/BioSystem: Isoprenoid biosynthesis 224 matched cddid_all.tbl CDD COG1212 COG1212 440825 KdsB CMP-2-keto-3-deoxyoctulosonic acid synthetase [Cell wall/membrane/envelope biogenesis]. CMP-2-keto-3-deoxyoctulosonic acid synthetase is part of the Pathway/BioSystem: Lipid A biosynthesis 242 matched cddid_all.tbl CDD COG1213 COG1213 440826 COG1213 Choline kinase [Lipid transport and metabolism]. 236 matched cddid_all.tbl CDD COG1214 COG1214 440827 TsaB tRNA A37 threonylcarbamoyladenosine modification protein TsaB [Translation, ribosomal structure and biogenesis]. tRNA A37 threonylcarbamoyladenosine modification protein TsaB is part of the Pathway/BioSystem: tRNA modification 227 matched cddid_all.tbl CDD COG1215 COG1215 440828 BcsA Glycosyltransferase, catalytic subunit of cellulose synthase and poly-beta-1,6-N-acetylglucosamine synthase [Cell motility]. 303 matched cddid_all.tbl CDD COG1216 COG1216 440829 WcaE Glycosyltransferase, GT2 family [Carbohydrate transport and metabolism]. 202 matched cddid_all.tbl CDD COG1217 COG1217 440830 TypA Predicted membrane GTPase TypA/BipA involved in stress response [Signal transduction mechanisms]. 606 matched cddid_all.tbl CDD COG1218 COG1218 440831 CysQ 3'-Phosphoadenosine 5'-phosphosulfate (PAPS) 3'-phosphatase [Inorganic ion transport and metabolism]. 260 matched cddid_all.tbl CDD COG1219 COG1219 440832 ClpX ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein turnover, chaperones]. 409 matched cddid_all.tbl CDD COG1220 COG1220 440833 HslU ATP-dependent protease HslVU (ClpYQ), ATPase subunit HslU [Posttranslational modification, protein turnover, chaperones]. 454 matched cddid_all.tbl CDD COG1221 COG1221 440834 PspF Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain [Transcription, Signal transduction mechanisms]. 835 matched cddid_all.tbl CDD COG1222 COG1222 440835 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]. 326 matched cddid_all.tbl CDD COG1223 COG1223 440836 COG1223 Predicted ATPase, AAA+ superfamily [General function prediction only]. 246 matched cddid_all.tbl CDD COG1224 COG1224 440837 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]. 452 matched cddid_all.tbl CDD COG1225 COG1225 440838 Bcp Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]. 136 matched cddid_all.tbl CDD COG1226 COG1226 440839 Kch Voltage-gated potassium channel Kch [Inorganic ion transport and metabolism]. 279 matched cddid_all.tbl CDD COG1227 COG1227 440840 PPX1 Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion]. 307 matched cddid_all.tbl CDD COG1228 COG1228 440841 HutI Imidazolonepropionase or related amidohydrolase [Secondary metabolites biosynthesis, transport and catabolism]. 386 matched cddid_all.tbl CDD COG1229 COG1229 440842 FwdA Formylmethanofuran dehydrogenase subunit A [Energy production and conversion]. 554 matched cddid_all.tbl CDD COG1230 COG1230 440843 CzcD Co/Zn/Cd efflux system component [Inorganic ion transport and metabolism]. 294 matched cddid_all.tbl CDD COG1231 COG1231 440844 YobN Monoamine oxidase [Amino acid transport and metabolism]. 440 matched cddid_all.tbl CDD COG1232 COG1232 440845 HemY Protoporphyrinogen oxidase HemY/PPOX [Coenzyme transport and metabolism]. Protoporphyrinogen oxidase HemY/PPOX is part of the Pathway/BioSystem: Heme biosynthesis 443 matched cddid_all.tbl CDD COG1233 COG1233 440846 COG1233 Phytoene dehydrogenase-related protein [Secondary metabolites biosynthesis, transport and catabolism]. 491 matched cddid_all.tbl CDD COG1234 COG1234 440847 ElaC Ribonuclease BN, tRNA processing enzyme [Translation, ribosomal structure and biogenesis]. 250 matched cddid_all.tbl CDD COG1235 COG1235 440848 PhnP Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase [Inorganic ion transport and metabolism]. 259 matched cddid_all.tbl CDD COG1236 COG1236 440849 YSH1 RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis]. 404 matched cddid_all.tbl CDD COG1237 COG1237 440850 COG1237 Metal-dependent hydrolase, beta-lactamase superfamily II [General function prediction only]. 273 matched cddid_all.tbl CDD COG1238 COG1238 440851 YqaA Uncharacterized membrane protein YqaA, VTT domain [Function unknown]. 162 matched cddid_all.tbl CDD COG1239 COG1239 440852 ChlI Mg-chelatase subunit ChlI [Coenzyme transport and metabolism]. 344 matched cddid_all.tbl CDD COG1240 COG1240 440853 ChlD vWFA (von Willebrand factor type A) domain of Mg and Co chelatases [Coenzyme transport and metabolism]. 262 matched cddid_all.tbl CDD COG1241 COG1241 440854 Mcm2 DNA replicative helicase MCM subunit Mcm2, Cdc46/Mcm family [Replication, recombination and repair]. 682 matched cddid_all.tbl CDD COG1242 COG1242 440855 YhcC Radical SAM superfamily enzyme [General function prediction only]. 301 matched cddid_all.tbl CDD COG1243 COG1243 440856 ELP3 tRNA U34 5-carboxymethylaminomethylation enzyme Elp3 (RNA elongator complex protein 3), contains radical SAM and acetyltransferase domains [Translation, ribosomal structure and biogenesis]. 432 matched cddid_all.tbl CDD COG1244 COG1244 440857 RaSEA Archaeosine formation enzyme, radical SAM superfamily [Translation, ribosomal structure and biogenesis]. 346 matched cddid_all.tbl CDD COG1245 COG1245 440858 Rli1 Translation initiation factor RLI1, contains Fe-S and AAA+ ATPase domains [Translation, ribosomal structure and biogenesis]. 592 matched cddid_all.tbl CDD COG1246 COG1246 440859 ArgA N-acetylglutamate synthase or related acetyltransferase, GNAT family [Amino acid transport and metabolism]. N-acetylglutamate synthase or related acetyltransferase, GNAT family is part of the Pathway/BioSystem: Arginine biosynthesis 132 matched cddid_all.tbl CDD COG1247 COG1247 440860 MnaT L-amino acid N-acyltransferase MnaT [Amino acid transport and metabolism]. 163 matched cddid_all.tbl CDD COG1249 COG1249 440861 Lpd Dihydrolipoamide dehydrogenase (E3) component of pyruvate/2-oxoglutarate dehydrogenase complex or glutathione oxidoreductase [Energy production and conversion]. Dihydrolipoamide dehydrogenase (E3) component of pyruvate/2-oxoglutarate dehydrogenase complex or glutathione oxidoreductase is part of the Pathway/BioSystem: Glycine cleavagePyruvate oxidation 456 matched cddid_all.tbl CDD COG1250 COG1250 440862 FadB 3-hydroxyacyl-CoA dehydrogenase [Lipid transport and metabolism]. 3-hydroxyacyl-CoA dehydrogenase is part of the Pathway/BioSystem: Fatty acid biosynthesis 281 matched cddid_all.tbl CDD COG1251 COG1251 440863 NirB NAD(P)H-nitrite reductase, large subunit [Energy production and conversion]. 402 matched cddid_all.tbl CDD COG1252 COG1252 440864 Ndh NADH dehydrogenase, FAD-containing subunit [Energy production and conversion]. 386 matched cddid_all.tbl CDD COG1253 COG1253 440865 TlyC Hemolysin-related protein, contains CBS domains, UPF0053 family [General function prediction only]. 435 matched cddid_all.tbl CDD COG1254 COG1254 440866 AcyP Acylphosphatase [Energy production and conversion]. 89 matched cddid_all.tbl CDD COG1255 COG1255 440867 MTH1000 Predicted small methyltransferase MTH1000, UPF0146 family [General function prediction only]. 133 matched cddid_all.tbl CDD COG1256 COG1256 440868 FlgK Flagellar hook-associated protein FlgK [Cell motility]. 479 matched cddid_all.tbl CDD COG1257 COG1257 440869 HMG1 Hydroxymethylglutaryl-CoA reductase [Lipid transport and metabolism]. Hydroxymethylglutaryl-CoA reductase is part of the Pathway/BioSystem: Isoprenoid biosynthesis 409 matched cddid_all.tbl CDD COG1258 COG1258 440870 Pus10 tRNA U54 and U55 pseudouridine synthase Pus10 [Translation, ribosomal structure and biogenesis]. tRNA U54 and U55 pseudouridine synthase Pus10 is part of the Pathway/BioSystem: tRNA modification 411 matched cddid_all.tbl CDD COG1259 COG1259 440871 COG1259 Bifunctional DNase/RNase [General function prediction only]. 138 matched cddid_all.tbl CDD COG1260 COG1260 440872 INO1 Myo-inositol-1-phosphate synthase [Lipid transport and metabolism]. 356 matched cddid_all.tbl CDD COG1261 COG1261 440873 FlgA Flagellar basal body P-ring formation protein FlgA [Cell motility]. 158 matched cddid_all.tbl CDD COG1262 COG1262 440874 YfmG Formylglycine-generating enzyme, required for sulfatase activity, contains SUMF1/FGE domain [Posttranslational modification, protein turnover, chaperones]. 238 matched cddid_all.tbl CDD COG1263 COG1263 440875 PtsG1 Phosphotransferase system IIC components, glucose/maltose/N-acetylglucosamine-specific [Carbohydrate transport and metabolism]. 463 matched cddid_all.tbl CDD COG1264 COG1264 440876 PtsG2 Phosphotransferase system IIB components [Carbohydrate transport and metabolism]. 76 matched cddid_all.tbl CDD COG1266 COG1266 440877 YdiL Membrane protease YdiL, CAAX protease family [Posttranslational modification, protein turnover, chaperones]. 97 matched cddid_all.tbl CDD COG1267 COG1267 440878 PgpA Phosphatidylglycerophosphatase A [Lipid transport and metabolism]. Phosphatidylglycerophosphatase A is part of the Pathway/BioSystem: Phospholipid biosynthesis 148 matched cddid_all.tbl CDD COG1268 COG1268 440879 BioY Biotin transporter BioY [Coenzyme transport and metabolism]. 173 matched cddid_all.tbl CDD COG1269 COG1269 440880 NtpI Archaeal/vacuolar-type H+-ATPase subunit I/STV1 [Energy production and conversion]. Archaeal/vacuolar-type H+-ATPase subunit I/STV1 is part of the Pathway/BioSystem: A/V-type ATP synthase 645 matched cddid_all.tbl CDD COG1270 COG1270 440881 CbiB Cobalamin biosynthesis protein CobD/CbiB [Coenzyme transport and metabolism]. Cobalamin biosynthesis protein CobD/CbiB is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 318 matched cddid_all.tbl CDD COG1271 COG1271 440882 AppC Cytochrome bd-type quinol oxidase, subunit 1 [Energy production and conversion]. 442 matched cddid_all.tbl CDD COG1272 COG1272 440883 YqfA Predicted membrane channel-forming protein YqfA, hemolysin III family [Intracellular trafficking, secretion, and vesicular transport]. 213 matched cddid_all.tbl CDD COG1273 COG1273 440884 YkoV Non-homologous end joining protein Ku, dsDNA break repair [Replication, recombination and repair]. 279 matched cddid_all.tbl CDD COG1274 COG1274 440885 PepCK Phosphoenolpyruvate carboxykinase, GTP-dependent [Energy production and conversion]. Phosphoenolpyruvate carboxykinase, GTP-dependent is part of the Pathway/BioSystem: Gluconeogenesis 605 matched cddid_all.tbl CDD COG1275 COG1275 440886 TehA Tellurite resistance protein TehA and related permeases [Defense mechanisms]. 323 matched cddid_all.tbl CDD COG1276 COG1276 440887 PcoD Putative copper export protein [Inorganic ion transport and metabolism]. 282 matched cddid_all.tbl CDD COG1277 COG1277 440888 NosY ABC-type transport system involved in multi-copper enzyme maturation, permease component [Posttranslational modification, protein turnover, chaperones]. 201 matched cddid_all.tbl CDD COG1278 COG1278 440889 CspC Cold shock protein, CspA family [Transcription]. 67 matched cddid_all.tbl CDD COG1279 COG1279 440890 ArgO Arginine exporter protein ArgO [Amino acid transport and metabolism]. 204 matched cddid_all.tbl CDD COG1280 COG1280 440891 RhtB Threonine/homoserine/homoserine lactone efflux protein [Amino acid transport and metabolism]. 205 matched cddid_all.tbl CDD COG1281 COG1281 440892 HslO Redox-regulated molecular chaperone, HSP33 family [Posttranslational modification, protein turnover, chaperones]. 291 matched cddid_all.tbl CDD COG1282 COG1282 440893 PntB NAD/NADP transhydrogenase beta subunit [Energy production and conversion]. 458 matched cddid_all.tbl CDD COG1283 COG1283 440894 NptA Na+/phosphate symporter [Inorganic ion transport and metabolism]. 540 matched cddid_all.tbl CDD COG1284 COG1284 440895 YitT Uncharacterized membrane-anchored protein YitT, contains DUF161 and DUF2179 domains [Function unknown]. 285 matched cddid_all.tbl CDD COG1285 COG1285 440896 SapB Magnesium uptake protein YhiD/SapB, involved in acid resistance [Inorganic ion transport and metabolism]. 198 matched cddid_all.tbl CDD COG1286 COG1286 440897 CvpA Colicin V production accessory protein CvpA, regulator of purF expression and biofilm formation [Nucleotide transport and metabolism, Cell wall/membrane/envelope biogenesis]. 161 matched cddid_all.tbl CDD COG1287 COG1287 440898 Stt3 Asparagine N-glycosylation enzyme, membrane subunit Stt3 [Posttranslational modification, protein turnover, chaperones]. 774 matched cddid_all.tbl CDD COG1288 COG1288 440899 YfcC Predicted membrane transporter YfcC, affects glyoxylate shunt [General function prediction only]. 464 matched cddid_all.tbl CDD COG1289 COG1289 440900 YccC Uncharacterized membrane protein YccC [Function unknown]. 280 matched cddid_all.tbl CDD COG1290 COG1290 440901 QcrB/PetB Cytochrome b subunit of the bc complex [Energy production and conversion]. 393 matched cddid_all.tbl CDD COG1291 COG1291 440902 MotA Flagellar motor component MotA [Cell motility]. 258 matched cddid_all.tbl CDD COG1292 COG1292 440903 BetT Choline-glycine betaine transporter [Cell wall/membrane/envelope biogenesis]. 512 matched cddid_all.tbl CDD COG1293 COG1293 440904 RqcH Ribosome quality control (RQC) protein RqcH, Rqc2/NEMF/Tae2 family, contains fibronectin-(FbpA) and RNA- (NFACT) binding domains [Translation, ribosomal structure and biogenesis, Posttranslational modification, protein turnover, chaperones]. 578 matched cddid_all.tbl CDD COG1294 COG1294 440905 AppB Cytochrome bd-type quinol oxidase, subunit 2 [Energy production and conversion]. 333 matched cddid_all.tbl CDD COG1295 COG1295 440906 BrkB Uncharacterized membrane protein, BrkB/YihY/UPF0761 family (not an RNase) [Function unknown]. 289 matched cddid_all.tbl CDD COG1296 COG1296 440907 AzlC Predicted branched-chain amino acid permease (azaleucine resistance) [Amino acid transport and metabolism]. 225 matched cddid_all.tbl CDD COG1297 COG1297 440908 OPT Predicted oligopeptide transporter, OPT family [General function prediction only]. 633 matched cddid_all.tbl CDD COG1298 COG1298 440909 FlhA Flagellar biosynthesis protein FlhA [Cell motility]. 676 matched cddid_all.tbl CDD COG1299 COG1299 440910 FrwC Phosphotransferase system, fructose-specific IIC component [Carbohydrate transport and metabolism]. 469 matched cddid_all.tbl CDD COG1300 COG1300 440911 SpoIIM Stage II sporulation protein SpoIIM, component of the engulfment complex [Cell cycle control, cell division, chromosome partitioning]. 303 matched cddid_all.tbl CDD COG1301 COG1301 440912 GltP Na+/H+-dicarboxylate symporter [Energy production and conversion]. 406 matched cddid_all.tbl CDD COG1302 COG1302 440913 YloU Uncharacterized conserved protein YloU, alkaline shock protein (Asp23) family [Function unknown]. 118 matched cddid_all.tbl CDD COG1303 COG1303 440914 TRM56 tRNA C56-2-O'-methylase, SpoU family [Translation, ribosomal structure and biogenesis]. 174 matched cddid_all.tbl CDD COG1304 COG1304 440915 LldD FMN-dependent dehydrogenase, includes L-lactate dehydrogenase and type II isopentenyl diphosphate isomerase [Energy production and conversion, Lipid transport and metabolism, General function prediction only]. FMN-dependent dehydrogenase, includes L-lactate dehydrogenase and type II isopentenyl diphosphate isomerase is part of the Pathway/BioSystem: Isoprenoid biosynthesis 357 matched cddid_all.tbl CDD COG1305 COG1305 440916 YebA Transglutaminase-like enzyme, putative cysteine protease [Posttranslational modification, protein turnover, chaperones]. 174 matched cddid_all.tbl CDD COG1306 COG1306 440917 COG1306 Predicted glycosyl hydrolase, alpha amylase family [General function prediction only]. 407 matched cddid_all.tbl CDD COG1307 COG1307 440918 DegV Fatty acid-binding protein DegV (function unknown) [Lipid transport and metabolism]. 278 matched cddid_all.tbl CDD COG1308 COG1308 440919 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]. 116 matched cddid_all.tbl CDD COG1309 COG1309 440920 AcrR DNA-binding protein, AcrR family, includes nucleoid occlusion protein SlmA [Transcription]. 156 matched cddid_all.tbl CDD COG1310 COG1310 440921 Rri1 Proteasome lid subunit RPN8/RPN11, contains Jab1/MPN domain metalloenzyme (JAMM) motif [Posttranslational modification, protein turnover, chaperones]. 127 matched cddid_all.tbl CDD COG1311 COG1311 440922 HYS2 Archaeal DNA polymerase II, small subunit/DNA polymerase delta, subunit B [Replication, recombination and repair]. 411 matched cddid_all.tbl CDD COG1312 COG1312 440923 UxuA D-mannonate dehydratase [Carbohydrate transport and metabolism]. 388 matched cddid_all.tbl CDD COG1313 COG1313 440924 PflX Radical SAM superfamily enzyme PflX [General function prediction only]. 295 matched cddid_all.tbl CDD COG1314 COG1314 440925 SecG Protein translocase subunit SecG [Intracellular trafficking, secretion, and vesicular transport]. 91 matched cddid_all.tbl CDD COG1315 COG1315 440926 FapA Flagellar assembly protein FapA, interacts with EIIAGlc [Cell motility]. 401 matched cddid_all.tbl CDD COG1316 COG1316 440927 Cps2a Anionic cell wall polymer biosynthesis enzyme TagV/TagU, LytR-Cps2A-Psr (LCP) family (peptidoglycan teichoic acid transferase) [Cell wall/membrane/envelope biogenesis]. 264 matched cddid_all.tbl CDD COG1317 COG1317 440928 FliH Flagellar biosynthesis/type III secretory pathway protein FliH [Cell motility, Intracellular trafficking, secretion, and vesicular transport]. 172 matched cddid_all.tbl CDD COG1318 COG1318 440929 COG1318 Predicted transcriptional regulator [Transcription]. 143 matched cddid_all.tbl CDD COG1319 COG1319 440930 CutB Aldehyde, CO, or xanthine dehydrogenase, FAD-binding subunit [Energy production and conversion]. Aldehyde, CO, or xanthine dehydrogenase, FAD-binding subunit is part of the Pathway/BioSystem: Non-phosphorylated Entner-Doudoroff pathway 285 matched cddid_all.tbl CDD COG1320 COG1320 440931 MnhG Multisubunit Na+/H+ antiporter, MnhG subunit [Inorganic ion transport and metabolism]. 110 matched cddid_all.tbl CDD COG1321 COG1321 440932 MntR Mn-dependent transcriptional regulator MntR, DtxR family [Transcription]. 135 matched cddid_all.tbl CDD COG1322 COG1322 440933 RmuC DNA anti-recombination protein (rearrangement mutator) RmuC [Replication, recombination and repair]. 342 matched cddid_all.tbl CDD COG1323 COG1323 440934 TmcAL tRNA-Met C34-N4-acetylcytidine synthase TmcAL [Translation, ribosomal structure and biogenesis]. tRNA-Met C34-N4-acetylcytidine synthase TmcAL is part of the Pathway/BioSystem: tRNA modification 401 matched cddid_all.tbl CDD COG1324 COG1324 440935 CutA1 Divalent cation tolerance protein CutA [Inorganic ion transport and metabolism]. 104 matched cddid_all.tbl CDD COG1325 COG1325 440936 COG1325 Exosome subunit, RNA binding protein with dsRBD fold [Intracellular trafficking, secretion, and vesicular transport]. 142 matched cddid_all.tbl CDD COG1326 COG1326 440937 COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]. 207 matched cddid_all.tbl CDD COG1327 COG1327 440938 NrdR Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains [Transcription]. 153 matched cddid_all.tbl CDD COG1328 COG1328 440939 NrdD Anaerobic ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]. Anaerobic ribonucleoside-triphosphate reductase is part of the Pathway/BioSystem: Thymidylate biosynthesis 671 matched cddid_all.tbl CDD COG1329 COG1329 440940 CdnL RNA polymerase-interacting regulator, CarD/CdnL/TRCF family [Transcription]. 155 matched cddid_all.tbl CDD COG1330 COG1330 440941 RecC Scaffold subunit RecC of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair]. 1087 matched cddid_all.tbl CDD COG1331 COG1331 440942 YyaL Uncharacterized conserved protein YyaL, SSP411 family, contains thoiredoxin and six-hairpin glycosidase-like domains [General function prediction only]. 672 matched cddid_all.tbl CDD COG1332 COG1332 440943 Csm5 CRISPR-Cas system type III CSM-effector complex subunit Csm5, RAMP superfamily Cas7 group [Defense mechanisms]. CRISPR-Cas system type III CSM-effector complex subunit Csm5, RAMP superfamily Cas7 group is part of the Pathway/BioSystem: CRISPR-Cas system 371 matched cddid_all.tbl CDD COG1333 COG1333 440944 ResB Cytochrome c biogenesis protein ResB [Energy production and conversion, Posttranslational modification, protein turnover, chaperones]. 479 matched cddid_all.tbl CDD COG1334 COG1334 440945 FlaG Uncharacterized conserved protein, FlaG/YvyC family [General function prediction only]. 122 matched cddid_all.tbl CDD COG1335 COG1335 440946 PncA Nicotinamidase-related amidase [Coenzyme transport and metabolism, General function prediction only]. Nicotinamidase-related amidase is part of the Pathway/BioSystem: Pyrimidine degradation 169 matched cddid_all.tbl CDD COG1336 COG1336 440947 Cmr4 CRISPR-Cas system type III CMR-effector complex subunit Cmr4, RAMP superfamily Cas7 group [Defense mechanisms]. CRISPR-Cas system type III CMR-effector complex subunit Cmr4, RAMP superfamily Cas7 group is part of the Pathway/BioSystem: CRISPR-Cas system 279 matched cddid_all.tbl CDD COG1337 COG1337 440948 Csm3 CRISPR-Cas system type III CSM-effector complex subunit Csm3, RAMP superfamily Cas7 group [Defense mechanisms]. CRISPR-Cas system type III CSM-effector complex subunit Csm3, RAMP superfamily Cas7 group is part of the Pathway/BioSystem: CRISPR-Cas system 212 matched cddid_all.tbl CDD COG1338 COG1338 440949 FliP Flagellar biosynthesis protein FliP [Cell motility]. 249 matched cddid_all.tbl CDD COG1339 COG1339 440950 Rfk Archaeal CTP-dependent riboflavin kinase [Coenzyme transport and metabolism]. Archaeal CTP-dependent riboflavin kinase is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis 219 matched cddid_all.tbl CDD COG1340 COG1340 440951 COG1340 Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]. 297 matched cddid_all.tbl CDD COG1341 COG1341 440952 Grc3 Polynucleotide 5'-kinase, involved in rRNA processing [Translation, ribosomal structure and biogenesis]. 353 matched cddid_all.tbl CDD COG1342 COG1342 440953 COG1342 Predicted DNA-binding protein, UPF0251 family [General function prediction only]. 99 matched cddid_all.tbl CDD COG1343 COG1343 440954 Cas2 CRISPR/Cas system-associated endoribonuclease Cas2 [Defense mechanisms]. CRISPR/Cas system-associated endoribonuclease Cas2 is part of the Pathway/BioSystem: CRISPR-Cas system 89 matched cddid_all.tbl CDD COG1344 COG1344 440955 FlgL Flagellin and related hook-associated protein FlgL [Cell motility]. 245 matched cddid_all.tbl CDD COG1345 COG1345 440956 FliD Flagellar capping protein FliD [Cell motility]. 450 matched cddid_all.tbl CDD COG1346 COG1346 440957 LrgB Putative effector of murein hydrolase [Cell wall/membrane/envelope biogenesis]. 230 matched cddid_all.tbl CDD COG1347 COG1347 440958 NqrD Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrD [Energy production and conversion]. Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrD is part of the Pathway/BioSystem: Na+-translocating NADH dehydrogenase 208 matched cddid_all.tbl CDD COG1348 COG1348 440959 NifH/CfbC Nitrogenase ATPase subunit NifH/coenzyme F430 biosynthesis subunit CfbC [Coenzyme transport and metabolism, Inorganic ion transport and metabolism]. 276 matched cddid_all.tbl CDD COG1349 COG1349 440960 GlpR DNA-binding transcriptional regulator of sugar metabolism, DeoR/GlpR family [Transcription, Carbohydrate transport and metabolism]. 254 matched cddid_all.tbl CDD COG1350 COG1350 440961 COG1350 Predicted alternative tryptophan synthase beta-subunit (paralog of TrpB) [Amino acid transport and metabolism]. Predicted alternative tryptophan synthase beta-subunit (paralog of TrpB) is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 433 matched cddid_all.tbl CDD COG1351 COG1351 440962 ThyX Thymidylate synthase ThyX, FAD-dependent family [Nucleotide transport and metabolism]. Thymidylate synthase ThyX, FAD-dependent family is part of the Pathway/BioSystem: Thymidylate biosynthesis 197 matched cddid_all.tbl CDD COG1352 COG1352 440963 CheR Methylase of chemotaxis methyl-accepting proteins [Signal transduction mechanisms]. 272 matched cddid_all.tbl CDD COG1353 COG1353 440964 Cas10 CRISPR/Cas system-associated protein Cas10, large subunit of type III CRISPR-Cas systems, contains HD superfamily nuclease domain [Defense mechanisms]. CRISPR/Cas system-associated protein Cas10, large subunit of type III CRISPR-Cas systems, contains HD superfamily nuclease domain is part of the Pathway/BioSystem: CRISPR-Cas system 477 matched cddid_all.tbl CDD COG1354 COG1354 440965 ScpA Chromatin segregation and condensation protein Rec8/ScpA/Scc1, kleisin family [Replication, recombination and repair]. 237 matched cddid_all.tbl CDD COG1355 COG1355 440966 Mho1 Predicted class III extradiol dioxygenase, MEMO1 family [General function prediction only]. 274 matched cddid_all.tbl CDD COG1356 COG1356 440967 COG1356 Transcriptional regulator [Transcription]. 139 matched cddid_all.tbl CDD COG1357 COG1357 440968 YjbI Uncharacterized conserved protein YjbI, contains pentapeptide repeats [Function unknown]. 178 matched cddid_all.tbl CDD COG1358 COG1358 440969 Rpl7Ae Ribosomal protein L7Ae or related RNA K-turn-binding protein [Translation, ribosomal structure and biogenesis]. Ribosomal protein L7Ae or related RNA K-turn-binding protein is part of the Pathway/BioSystem: Ribosome 50S subunit 98 matched cddid_all.tbl CDD COG1359 COG1359 440970 YgiN Quinol monooxygenase YgiN [Energy production and conversion]. 91 matched cddid_all.tbl CDD COG1360 COG1360 440971 MotB Flagellar motor protein MotB [Cell motility]. 174 matched cddid_all.tbl CDD COG1361 COG1361 440972 MJ0795 S-layer protein MJ0795, predicted component of type IV pili-like system [General function prediction only]. 409 matched cddid_all.tbl CDD COG1362 COG1362 440973 LAP4 Aspartyl aminopeptidase [Amino acid transport and metabolism]. 430 matched cddid_all.tbl CDD COG1363 COG1363 440974 FrvX Putative aminopeptidase FrvX [Amino acid transport and metabolism, Carbohydrate transport and metabolism]. 353 matched cddid_all.tbl CDD COG1364 COG1364 440975 ArgJ Glutamate N-acetyltransferase (ornithine transacetylase) [Amino acid transport and metabolism]. Glutamate N-acetyltransferase (ornithine transacetylase) is part of the Pathway/BioSystem: Arginine biosynthesis 402 matched cddid_all.tbl CDD COG1365 COG1365 440976 COG1365 Predicted ATPase, PP-loop superfamily [General function prediction only]. 256 matched cddid_all.tbl CDD COG1366 COG1366 440977 SpoIIAA Anti-anti-sigma regulatory factor (antagonist of anti-sigma factor) [Signal transduction mechanisms]. 93 matched cddid_all.tbl CDD COG1367 COG1367 440978 Cmr1 CRISPR-Cas system type III CMR-effector complex subunit Cmr1, RAMP superfamily Cas7 group [Defense mechanisms]. CRISPR-Cas system type III CMR-effector complex subunit Cmr1, RAMP superfamily Cas7 group is part of the Pathway/BioSystem: CRISPR-Cas system 272 matched cddid_all.tbl CDD COG1368 COG1368 440979 MdoB Phosphoglycerol transferase MdoB/OpgB, AlkP superfamily [Cell wall/membrane/envelope biogenesis]. 576 matched cddid_all.tbl CDD COG1369 COG1369 440980 POP5 RNase P/RNase MRP subunit POP5 [Translation, ribosomal structure and biogenesis]. 110 matched cddid_all.tbl CDD COG1370 COG1370 440981 ArcTGT tRNA-guanine transglycosylase, archaeosine-15-forming, contains TGT and PUA domains [Translation, ribosomal structure and biogenesis]. 157 matched cddid_all.tbl CDD COG1371 COG1371 440982 ARCH Archease, activates RNA ligation by RtcB (tRNA splicing) [Translation, ribosomal structure and biogenesis]. 139 matched cddid_all.tbl CDD COG1372 COG1372 440983 Hop Intein/homing endonuclease [Replication, recombination and repair, Mobilome: prophages, transposons]. 866 matched cddid_all.tbl CDD COG1373 COG1373 440984 COG1373 Predicted ATPase, AAA+ superfamily [General function prediction only]. 405 matched cddid_all.tbl CDD COG1374 COG1374 440985 NIP7 Rbosome biogenesis protein Nip4, contains PUA domain [Translation, ribosomal structure and biogenesis]. 166 matched cddid_all.tbl CDD COG1376 COG1376 440986 ErfK Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis]. 121 matched cddid_all.tbl CDD COG1377 COG1377 440987 FlhB Flagellar biosynthesis protein FlhB [Cell motility]. 352 matched cddid_all.tbl CDD COG1378 COG1378 440988 YrhO Sugar-specific transcriptional regulator TrmB [Transcription]. 238 matched cddid_all.tbl CDD COG1379 COG1379 440989 YqxK PHP family phosphoesterase with a Zn ribbon [General function prediction only]. 402 matched cddid_all.tbl CDD COG1380 COG1380 440990 YohJ Putative effector of murein hydrolase LrgA, UPF0299 family [General function prediction only]. 120 matched cddid_all.tbl CDD COG1381 COG1381 440991 RecO Recombinational DNA repair protein RecO (RecF pathway) [Replication, recombination and repair]. 245 matched cddid_all.tbl CDD COG1382 COG1382 440992 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]. 121 matched cddid_all.tbl CDD COG1383 COG1383 440993 RPS17A Ribosomal protein S17E [Translation, ribosomal structure and biogenesis]. Ribosomal protein S17E is part of the Pathway/BioSystem: Archaeal ribosomal proteins 63 matched cddid_all.tbl CDD COG1384 COG1384 440994 LysS Lysyl-tRNA synthetase, class I [Translation, ribosomal structure and biogenesis]. Lysyl-tRNA synthetase, class I is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 525 matched cddid_all.tbl CDD COG1385 COG1385 440995 RsmE 16S rRNA U1498 N3-methylase RsmE [Translation, ribosomal structure and biogenesis]. 16S rRNA U1498 N3-methylase RsmE is part of the Pathway/BioSystem: 16S rRNA modification 245 matched cddid_all.tbl CDD COG1386 COG1386 440996 ScpB Chromosome segregation and condensation protein ScpB [Transcription]. 181 matched cddid_all.tbl CDD COG1387 COG1387 440997 HIS2 Histidinol phosphatase or related hydrolase of the PHP family [Amino acid transport and metabolism, General function prediction only]. Histidinol phosphatase or related hydrolase of the PHP family is part of the Pathway/BioSystem: Histidine biosynthesis 232 matched cddid_all.tbl CDD COG1388 COG1388 440998 LysM LysM repeat [Cell wall/membrane/envelope biogenesis]. 156 matched cddid_all.tbl CDD COG1389 COG1389 440999 COG1389 DNA topoisomerase VI, subunit B [Replication, recombination and repair]. 530 matched cddid_all.tbl CDD COG1390 COG1390 441000 NtpE Archaeal/vacuolar-type H+-ATPase subunit E/Vma4 [Energy production and conversion]. Archaeal/vacuolar-type H+-ATPase subunit E/Vma4 is part of the Pathway/BioSystem: A/V-type ATP synthase 196 matched cddid_all.tbl CDD COG1391 COG1391 441001 GlnE1 Glutamine synthetase adenylyltransferase [Posttranslational modification, protein turnover, chaperones]. 948 matched cddid_all.tbl CDD COG1392 COG1392 441002 YkaA Phosphate transport regulator YkaA, distantly related to PhoU, UPF0111/DUF47 family [Inorganic ion transport and metabolism]. 205 matched cddid_all.tbl CDD COG1393 COG1393 441003 ArsC Arsenate reductase or related protein, glutaredoxin family [Inorganic ion transport and metabolism]. 115 matched cddid_all.tbl CDD COG1394 COG1394 441004 NtpD Archaeal/vacuolar-type H+-ATPase subunit D/Vma8 [Energy production and conversion]. Archaeal/vacuolar-type H+-ATPase subunit D/Vma8 is part of the Pathway/BioSystem: A/V-type ATP synthase 202 matched cddid_all.tbl CDD COG1395 COG1395 441005 COG1395 Predicted transcriptional regulator [Transcription]. 313 matched cddid_all.tbl CDD COG1396 COG1396 441006 HipB Transcriptional regulator, contains XRE-family HTH domain [Transcription]. 83 matched cddid_all.tbl CDD COG1397 COG1397 441007 DraG ADP-ribosylglycohydrolase [Posttranslational modification, protein turnover, chaperones]. 256 matched cddid_all.tbl CDD COG1398 COG1398 441008 OLE1 Fatty-acid desaturase [Lipid transport and metabolism]. 286 matched cddid_all.tbl CDD COG1399 COG1399 441009 YceD 23S rRNA accumulation protein YceD (essential in plants, uncharacterized in bacteria) [Translation, ribosomal structure and biogenesis]. 169 matched cddid_all.tbl CDD COG1400 COG1400 441010 SEC65 Signal recognition particle subunit SEC65 [Intracellular trafficking, secretion, and vesicular transport]. 96 matched cddid_all.tbl CDD COG1401 COG1401 441011 McrB 5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB [Defense mechanisms]. 477 matched cddid_all.tbl CDD COG1402 COG1402 441012 ArfB Creatinine amidohydrolase/Fe(II)-dependent FAPy formamide hydrolase (riboflavin and F420 biosynthesis) [Coenzyme transport and metabolism]. Creatinine amidohydrolase/Fe(II)-dependent FAPy formamide hydrolase (riboflavin and F420 biosynthesis) is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis 236 matched cddid_all.tbl CDD COG1403 COG1403 441013 McrA 5-methylcytosine-specific restriction endonuclease McrA [Defense mechanisms]. 64 matched cddid_all.tbl CDD COG1404 COG1404 441014 AprE Serine protease, subtilisin family [Posttranslational modification, protein turnover, chaperones]. 456 matched cddid_all.tbl CDD COG1405 COG1405 441015 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]. 309 matched cddid_all.tbl CDD COG1406 COG1406 441016 CheX Chemotaxis protein CheX, a CheY~P-specific phosphatase [Cell motility]. 155 matched cddid_all.tbl CDD COG1407 COG1407 441017 COG1407 Metallophosphoesterase superfamily enzyme [General function prediction only]. 224 matched cddid_all.tbl CDD COG1408 COG1408 441018 YaeI Predicted phosphohydrolase, MPP superfamily [General function prediction only]. 268 matched cddid_all.tbl CDD COG1409 COG1409 441019 CpdA 3',5'-cyclic AMP phosphodiesterase CpdA [Signal transduction mechanisms]. 234 matched cddid_all.tbl CDD COG1410 COG1410 441020 MetH2 Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]. Methionine synthase I, cobalamin-binding domain is part of the Pathway/BioSystem: Methionine biosynthesis 1141 matched cddid_all.tbl CDD COG1411 COG1411 441021 COG1411 Uncharacterized conserved protein related to proFAR isomerase (HisA) [General function prediction only]. 229 matched cddid_all.tbl CDD COG1412 COG1412 441022 Fcf1 rRNA-processing protein FCF1 [Translation, ribosomal structure and biogenesis]. 123 matched cddid_all.tbl CDD COG1413 COG1413 441023 HEAT HEAT repeat [General function prediction only]. 137 matched cddid_all.tbl CDD COG1414 COG1414 441024 IclR DNA-binding transcriptional regulator, IclR family [Transcription]. 253 matched cddid_all.tbl CDD COG1415 COG1415 441025 COG1415 Uncharacterized conserved protein, DUF763 domain [Function unknown]. 375 matched cddid_all.tbl CDD COG1416 COG1416 441026 COG1416 Intracellular sulfur oxidation protein, DsrE/DsrF family [Inorganic ion transport and metabolism]. 139 matched cddid_all.tbl CDD COG1417 COG1417 441027 COG1417 Uncharacterized conserved protein, DUF22 domain [Function unknown]. 126 matched cddid_all.tbl CDD COG1418 COG1418 441028 RnaY HD superfamily phosphodieaserase, includes HD domain of RNase Y [Translation, ribosomal structure and biogenesis, General function prediction only]. 191 matched cddid_all.tbl CDD COG1419 COG1419 441029 FlhF Flagellar biosynthesis GTPase FlhF [Cell motility]. 361 matched cddid_all.tbl CDD COG1420 COG1420 441030 HrcA Transcriptional regulator of heat shock response [Transcription]. 339 matched cddid_all.tbl CDD COG1421 COG1421 441031 Csm2 CRISPR-Cas system type III CSM-effector complex small subunit Csm2 [Defense mechanisms]. CRISPR-Cas system type III CSM-effector complex small subunit Csm2 is part of the Pathway/BioSystem: CRISPR-Cas system 128 matched cddid_all.tbl CDD COG1422 COG1422 441032 YidC Archaeal YidC/Oxa1-related membrane protein, DUF106 family [Cell wall/membrane/envelope biogenesis]. 198 matched cddid_all.tbl CDD COG1423 COG1423 441033 COG1423 ATP-dependent RNA circularization protein, DNA/RNA ligase (PAB1020) family [Replication, recombination and repair]. 373 matched cddid_all.tbl CDD COG1424 COG1424 441034 BioW Pimeloyl-CoA synthetase [Coenzyme transport and metabolism]. Pimeloyl-CoA synthetase is part of the Pathway/BioSystem: Biotin biosynthesis 250 matched cddid_all.tbl CDD COG1426 COG1426 441035 RodZ Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell division, chromosome partitioning]. 71 matched cddid_all.tbl CDD COG1427 COG1427 441036 MqnA Chorismate dehydratase (menaquinone biosynthesis, futalosine pathway) [Coenzyme transport and metabolism]. Chorismate dehydratase (menaquinone biosynthesis, futalosine pathway) is part of the Pathway/BioSystem: Menaquinone biosynthesis 268 matched cddid_all.tbl CDD COG1428 COG1428 441037 Dck Deoxyadenosine/deoxycytidine kinase [Nucleotide transport and metabolism]. 205 matched cddid_all.tbl CDD COG1429 COG1429 441038 CobN Cobalamin biosynthesis protein CobN, Mg-chelatase [Coenzyme transport and metabolism]. Cobalamin biosynthesis protein CobN, Mg-chelatase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 1180 matched cddid_all.tbl CDD COG1430 COG1430 441039 COG1430 Uncharacterized conserved membrane protein, UPF0127 family [Function unknown]. 138 matched cddid_all.tbl CDD COG1431 COG1431 441040 PIWI PIWI domain, catalyzes dsRNA-guided hydrolysis of ssRNA, involved in RNA silencing, RNA metabolism and antiviral defense [Translation, ribosomal structure and biogenesis, Defense mechanisms]. 616 matched cddid_all.tbl CDD COG1432 COG1432 441041 LabA NYN domain, predicted PIN-related RNAse, tRNA/rRNA maturation [General function prediction only]. 164 matched cddid_all.tbl CDD COG1433 COG1433 441042 NifX Predicted Fe-Mo cluster-binding protein, NifX family [Posttranslational modification, protein turnover, chaperones]. 108 matched cddid_all.tbl CDD COG1434 COG1434 441043 ElyC Lipid carrier protein ElyC involved in cell wall biogenesis, DUF218 family [Cell wall/membrane/envelope biogenesis]. 212 matched cddid_all.tbl CDD COG1435 COG1435 441044 Tdk Thymidine kinase [Nucleotide transport and metabolism]. Thymidine kinase is part of the Pathway/BioSystem: Pyrimidine salvage 192 matched cddid_all.tbl CDD COG1436 COG1436 441045 NtpF Archaeal/vacuolar-type H+-ATPase subunit F/Vma7 [Energy production and conversion]. Archaeal/vacuolar-type H+-ATPase subunit F/Vma7 is part of the Pathway/BioSystem: A/V-type ATP synthase 101 matched cddid_all.tbl CDD COG1437 COG1437 441046 CyaB Adenylate cyclase class IV, CYTH domain (includes archaeal enzymes of unknown function) [Signal transduction mechanisms, General function prediction only]. 173 matched cddid_all.tbl CDD COG1438 COG1438 441047 ArgR Arginine repressor [Transcription]. 152 matched cddid_all.tbl CDD COG1439 COG1439 441048 Nob1 rRNA maturation endonuclease Nob1 [Translation, ribosomal structure and biogenesis]. 155 matched cddid_all.tbl CDD COG1440 COG1440 441049 CelA Phosphotransferase system cellobiose-specific component IIB [Carbohydrate transport and metabolism]. 100 matched cddid_all.tbl CDD COG1441 COG1441 441050 MenC O-succinylbenzoate synthase [Coenzyme transport and metabolism]. O-succinylbenzoate synthase is part of the Pathway/BioSystem: Menaquinone biosynthesis 325 matched cddid_all.tbl CDD COG1442 COG1442 441051 RfaJ Lipopolysaccharide biosynthesis protein, LPS:glycosyltransferase [Cell wall/membrane/envelope biogenesis]. 301 matched cddid_all.tbl CDD COG1443 COG1443 441052 Idi Isopentenyldiphosphate isomerase [Lipid transport and metabolism]. Isopentenyldiphosphate isomerase is part of the Pathway/BioSystem: Isoprenoid biosynthesis 162 matched cddid_all.tbl CDD COG1444 COG1444 441053 TmcA tRNA(Met) C34 N-acetyltransferase TmcA [Translation, ribosomal structure and biogenesis]. tRNA(Met) C34 N-acetyltransferase TmcA is part of the Pathway/BioSystem: tRNA modification 703 matched cddid_all.tbl CDD COG1445 COG1445 441054 FrwB Phosphotransferase system fructose-specific component IIB [Carbohydrate transport and metabolism]. 99 matched cddid_all.tbl CDD COG1446 COG1446 441055 IaaA Isoaspartyl peptidase or L-asparaginase, Ntn-hydrolase superfamily [Amino acid transport and metabolism]. 305 matched cddid_all.tbl CDD COG1447 COG1447 441056 CelC Phosphotransferase system cellobiose-specific component IIA [Carbohydrate transport and metabolism]. 100 matched cddid_all.tbl CDD COG1448 COG1448 441057 TyrB Aspartate/aromatic aminotransferase [Amino acid transport and metabolism]. Aspartate/aromatic aminotransferase is part of the Pathway/BioSystem: Isoleucine, leucine, valine biosynthesis 396 matched cddid_all.tbl CDD COG1449 COG1449 441058 COG1449 Alpha-amylase/alpha-mannosidase, GH57 family [Carbohydrate transport and metabolism]. 410 matched cddid_all.tbl CDD COG1450 COG1450 441059 PulD Type II secretory pathway component GspD/PulD (secretin) [Intracellular trafficking, secretion, and vesicular transport]. 333 matched cddid_all.tbl CDD COG1451 COG1451 441060 YgjP UTP pyrophosphatase, metal-dependent hydrolase family [General function prediction only]. 236 matched cddid_all.tbl CDD COG1452 COG1452 441061 LptD LPS assembly outer membrane protein LptD (organic solvent tolerance protein OstA) [Cell wall/membrane/envelope biogenesis]. 702 matched cddid_all.tbl CDD COG1453 COG1453 441062 COG1453 Predicted oxidoreductase of the aldo/keto reductase family [General function prediction only]. 365 matched cddid_all.tbl CDD COG1454 COG1454 441063 EutG Alcohol dehydrogenase, class IV [Energy production and conversion]. 381 matched cddid_all.tbl CDD COG1455 COG1455 441064 CelB Phosphotransferase system cellobiose-specific component IIC [Carbohydrate transport and metabolism]. 423 matched cddid_all.tbl CDD COG1456 COG1456 441065 CdhE CO dehydrogenase/acetyl-CoA synthase gamma subunit (corrinoid Fe-S protein) [Energy production and conversion]. 442 matched cddid_all.tbl CDD COG1457 COG1457 441066 CodB Purine-cytosine permease or related protein [Nucleotide transport and metabolism]. 448 matched cddid_all.tbl CDD COG1458 COG1458 441067 COG1458 Predicted RNase MK1237, contains PIN domain, UPF0278 family [General function prediction only]. 219 matched cddid_all.tbl CDD COG1459 COG1459 441068 PulF Type II secretory pathway, component PulF [Cell motility, Intracellular trafficking, secretion, and vesicular transport, Extracellular structures]. 399 matched cddid_all.tbl CDD COG1460 COG1460 441069 RpoF DNA-directed RNA polymerase, subunit F [Transcription]. DNA-directed RNA polymerase, subunit F is part of the Pathway/BioSystem: RNA polymerase 114 matched cddid_all.tbl CDD COG1461 COG1461 441070 YloV Predicted kinase related to dihydroxyacetone kinase [General function prediction only]. 541 matched cddid_all.tbl CDD COG1462 COG1462 441071 CsgG Curli biogenesis system outer membrane secretion channel CsgG [Cell wall/membrane/envelope biogenesis]. 263 matched cddid_all.tbl CDD COG1463 COG1463 441072 MlaD Periplasmic subunit MlaD of the ABC-type intermembrane phospholipid transporter Mla [Cell wall/membrane/envelope biogenesis]. 260 matched cddid_all.tbl CDD COG1464 COG1464 441073 NlpA ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]. 270 matched cddid_all.tbl CDD COG1465 COG1465 441074 AroB2 3-dehydroquinate synthase, class II [Amino acid transport and metabolism]. 351 matched cddid_all.tbl CDD COG1466 COG1466 441075 HolA DNA polymerase III, delta subunit [Replication, recombination and repair]. 305 matched cddid_all.tbl CDD COG1467 COG1467 441076 PRI1 Eukaryotic-type DNA primase, catalytic (small) subunit [Replication, recombination and repair]. 371 matched cddid_all.tbl CDD COG1468 COG1468 441077 Cas4 CRISPR/Cas system-associated exonuclease Cas4, RecB family [Defense mechanisms]. CRISPR/Cas system-associated exonuclease Cas4, RecB family is part of the Pathway/BioSystem: CRISPR-Cas system 184 matched cddid_all.tbl CDD COG1469 COG1469 441078 FolE2 GTP cyclohydrolase FolE2 [Coenzyme transport and metabolism]. GTP cyclohydrolase FolE2 is part of the Pathway/BioSystem: Folate biosynthesis 271 matched cddid_all.tbl CDD COG1470 COG1470 441079 COG1470 Uncharacterized membrane protein [Function unknown]. 475 matched cddid_all.tbl CDD COG1471 COG1471 441080 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]. Ribosomal protein S4E is part of the Pathway/BioSystem: Archaeal ribosomal proteins 239 matched cddid_all.tbl CDD COG1472 COG1472 441081 BglX Periplasmic beta-glucosidase and related glycosidases [Carbohydrate transport and metabolism]. 463 matched cddid_all.tbl CDD COG1473 COG1473 441082 AbgB Metal-dependent amidase/aminoacylase/carboxypeptidase [General function prediction only]. Metal-dependent amidase/aminoacylase/carboxypeptidase is part of the Pathway/BioSystem: Lysine biosynthesis 386 matched cddid_all.tbl CDD COG1474 COG1474 441083 CDC6 Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair]. 389 matched cddid_all.tbl CDD COG1475 COG1475 441084 Spo0J Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, cell division, chromosome partitioning]. 241 matched cddid_all.tbl CDD COG1476 COG1476 441085 XRE DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription]. 68 matched cddid_all.tbl CDD COG1477 COG1477 441086 ApbE FAD:protein FMN transferase ApbE [Coenzyme transport and metabolism, Posttranslational modification, protein turnover, chaperones]. 294 matched cddid_all.tbl CDD COG1478 COG1478 441087 CofE F420-0:Gamma-glutamyl ligase (F420 biosynthesis) [Coenzyme transport and metabolism]. 255 matched cddid_all.tbl CDD COG1479 COG1479 441088 GmrSD DNAse/DNA nickase specific for phosphorothioated or glycosylated phage DNA, GmrSD/DndB/SspE family, contains DUF262 and HNH nuclease domains [Defense mechanisms]. 544 matched cddid_all.tbl CDD COG1480 COG1480 441089 PgpH Cyclic di-AMP-specific phosphodiesterase PgpH, HD superfamily [Signal transduction mechanisms]. 692 matched cddid_all.tbl CDD COG1481 COG1481 441090 WhiA DNA-binding transcriptional regulator WhiA, involved in cell division [Transcription]. 309 matched cddid_all.tbl CDD COG1482 COG1482 441091 ManA Mannose-6-phosphate isomerase, class I [Carbohydrate transport and metabolism]. 324 matched cddid_all.tbl CDD COG1483 COG1483 441092 COG1483 Predicted ATPase, AAA+ superfamily [General function prediction only]. 992 matched cddid_all.tbl CDD COG1484 COG1484 441093 DnaC DNA replication protein DnaC [Replication, recombination and repair]. 242 matched cddid_all.tbl CDD COG1485 COG1485 441094 ZapE Cell division protein ZapE (Z ring-associated ATPase), AFG1 superfamily [Cell cycle control, cell division, chromosome partitioning]. 365 matched cddid_all.tbl CDD COG1486 COG1486 441095 CelF Alpha-galactosidase/6-phospho-beta-glucosidase, family 4 of glycosyl hydrolase [Carbohydrate transport and metabolism]. 423 matched cddid_all.tbl CDD COG1487 COG1487 441096 VapC Ribonuclease/mRNA interferase VapC, contains PIN domain [Defense mechanisms]. 128 matched cddid_all.tbl CDD COG1488 COG1488 441097 PncB Nicotinic acid phosphoribosyltransferase [Coenzyme transport and metabolism]. Nicotinic acid phosphoribosyltransferase is part of the Pathway/BioSystem: NAD biosynthesis 445 matched cddid_all.tbl CDD COG1489 COG1489 441098 SfsA DNA-binding protein, stimulates sugar fermentation [Carbohydrate transport and metabolism, Signal transduction mechanisms]. 231 matched cddid_all.tbl CDD COG1490 COG1490 441099 Dtd D-aminoacyl-tRNA deacylase [Translation, ribosomal structure and biogenesis]. 147 matched cddid_all.tbl CDD COG1491 COG1491 441100 COG1491 Predicted nucleic acid-binding OB-fold protein [General function prediction only]. 189 matched cddid_all.tbl CDD COG1492 COG1492 441101 CobQ Cobyric acid synthase [Coenzyme transport and metabolism]. Cobyric acid synthase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 493 matched cddid_all.tbl CDD COG1493 COG1493 441102 HprK Serine kinase of the HPr protein, regulates carbohydrate metabolism [Signal transduction mechanisms]. 142 matched cddid_all.tbl CDD COG1494 COG1494 441103 GlpX Fructose-1,6-bisphosphatase/sedoheptulose 1,7-bisphosphatase or related protein [Carbohydrate transport and metabolism]. 311 matched cddid_all.tbl CDD COG1495 COG1495 441104 DsbB Disulfide bond formation protein DsbB [Posttranslational modification, protein turnover, chaperones]. 153 matched cddid_all.tbl CDD COG1496 COG1496 441105 YfiH Copper oxidase (laccase) domain [Inorganic ion transport and metabolism]. 246 matched cddid_all.tbl CDD COG1497 COG1497 441106 MJ0558 Predicted transcriptional regulator MJ0558, contains a CRP-type HTH domain [Transcription]. 261 matched cddid_all.tbl CDD COG1498 COG1498 441107 SIK1 Box C/D ribonucleoprotein Nop56/Prp31/SIK1 subunit [Translation, ribosomal structure and biogenesis]. 352 matched cddid_all.tbl CDD COG1499 COG1499 441108 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]. 352 matched cddid_all.tbl CDD COG1500 COG1500 441109 Sdo1 Ribosome maturation protein Sdo1 [Translation, ribosomal structure and biogenesis]. 232 matched cddid_all.tbl CDD COG1501 COG1501 441110 YicI Alpha-glucosidase/xylosidase, GH31 family [Carbohydrate transport and metabolism]. 609 matched cddid_all.tbl CDD COG1502 COG1502 441111 Cls Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase [Lipid transport and metabolism]. Phosphatidylserine/phosphatidylglycerophosphate/cardiolipin synthase is part of the Pathway/BioSystem: Phospholipid biosynthesis 367 matched cddid_all.tbl CDD COG1503 COG1503 441112 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]. Peptide chain release factor 1 (eRF1) is part of the Pathway/BioSystem: Translation factors 384 matched cddid_all.tbl CDD COG1504 COG1504 441113 COG1504 Uncharacterized conserved protein, DUF498 domain [Function unknown]. 115 matched cddid_all.tbl CDD COG1505 COG1505 441114 PreP Prolyl endopeptidase PreP, S9A serine peptidase family [Amino acid transport and metabolism]. 673 matched cddid_all.tbl CDD COG1506 COG1506 441115 DAP2 Dipeptidyl aminopeptidase/acylaminoacyl peptidase [Amino acid transport and metabolism]. 234 matched cddid_all.tbl CDD COG1507 COG1507 441116 COG1507 Uncharacterized conserved protein, DUF501 family [Function unknown]. 175 matched cddid_all.tbl CDD COG1508 COG1508 441117 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]. DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog is part of the Pathway/BioSystem: RNA polymerase 413 matched cddid_all.tbl CDD COG1509 COG1509 441118 EpmB L-lysine 2,3-aminomutase (EF-P beta-lysylation pathway) [Amino acid transport and metabolism]. 345 matched cddid_all.tbl CDD COG1510 COG1510 441119 GbsR DNA-binding transcriptional regulator GbsR, MarR family [Transcription]. 164 matched cddid_all.tbl CDD COG1511 COG1511 441120 YhgE Uncharacterized membrane protein YhgE, phage infection protein (PIP) family [Function unknown]. 225 matched cddid_all.tbl CDD COG1512 COG1512 441121 YgcG Uncharacterized membrane protein YgcG, contains a TPM-fold domain [Function unknown]. 259 matched cddid_all.tbl CDD COG1513 COG1513 441122 CynS Cyanate lyase [Inorganic ion transport and metabolism]. 145 matched cddid_all.tbl CDD COG1514 COG1514 441123 ThpR RNA 2',3'-cyclic phosphodiesterase (2'-5' RNA ligase) [Translation, ribosomal structure and biogenesis]. 181 matched cddid_all.tbl CDD COG1515 COG1515 441124 Nfi Deoxyinosine 3'-endonuclease (endonuclease V) [Replication, recombination and repair]. 221 matched cddid_all.tbl CDD COG1516 COG1516 441125 FliS Flagellin-specific chaperone FliS [Cell motility, Intracellular trafficking, secretion, and vesicular transport]. 113 matched cddid_all.tbl CDD COG1517 COG1517 441126 Csx1 CRISPR/Cas system-associated protein Csx1, contains CARF domain [Defense mechanisms]. CRISPR/Cas system-associated protein Csx1, contains CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system 439 matched cddid_all.tbl CDD COG1518 COG1518 441127 Cas1 CRISPR-Cas system-associated integrase Cas1 [Defense mechanisms]. CRISPR-Cas system-associated integrase Cas1 is part of the Pathway/BioSystem: CRISPR-Cas system 329 matched cddid_all.tbl CDD COG1519 COG1519 441128 KdtA 3-deoxy-D-manno-octulosonic-acid transferase [Cell wall/membrane/envelope biogenesis]. 3-deoxy-D-manno-octulosonic-acid transferase is part of the Pathway/BioSystem: Lipid A biosynthesis 424 matched cddid_all.tbl CDD COG1520 COG1520 441129 PQQ Outer membrane protein assembly factor BamB, contains PQQ-like beta-propeller repeat [Cell wall/membrane/envelope biogenesis]. 370 matched cddid_all.tbl CDD COG1521 COG1521 441130 CoaX Pantothenate kinase type III [Coenzyme transport and metabolism]. 250 matched cddid_all.tbl CDD COG1522 COG1522 441131 Lrp DNA-binding transcriptional regulator, Lrp family [Transcription]. 138 matched cddid_all.tbl CDD COG1523 COG1523 441132 PulA Pullulanase/glycogen debranching enzyme [Carbohydrate transport and metabolism]. 690 matched cddid_all.tbl CDD COG1524 COG1524 441133 AtaC c-di-AMP phosphodiesterase AtaC or nucleotide pyrophosphatase, AlkP superfamily [Signal transduction mechanisms]. 370 matched cddid_all.tbl CDD COG1525 COG1525 441134 YncB Endonuclease YncB, thermonuclease family [Replication, recombination and repair]. 164 matched cddid_all.tbl CDD COG1526 COG1526 441135 FdhD Formate dehydrogenase assembly factor FdhD, a sulfurtransferase [Energy production and conversion]. 260 matched cddid_all.tbl CDD COG1527 COG1527 441136 NtpC Archaeal/vacuolar-type H+-ATPase subunit C/Vma6 [Energy production and conversion]. Archaeal/vacuolar-type H+-ATPase subunit C/Vma6 is part of the Pathway/BioSystem: A/V-type ATP synthase 348 matched cddid_all.tbl CDD COG1528 COG1528 441137 FtnA Ferritin [Inorganic ion transport and metabolism]. 158 matched cddid_all.tbl CDD COG1529 COG1529 441138 CoxL Aldehyde, CO or xanthine dehydrogenase, Mo-binding subunit [Energy production and conversion]. Aldehyde, CO or xanthine dehydrogenase, Mo-binding subunit is part of the Pathway/BioSystem: Non-phosphorylated Entner-Doudoroff pathway 741 matched cddid_all.tbl CDD COG1530 COG1530 441139 CafA Ribonuclease G or E [Translation, ribosomal structure and biogenesis]. 490 matched cddid_all.tbl CDD COG1531 COG1531 441140 COG1531 Uncharacterized conserved protein, UPF0248 family [Function unknown]. 78 matched cddid_all.tbl CDD COG1532 COG1532 441141 COG1532 Predicted RNA-binding protein [General function prediction only]. 60 matched cddid_all.tbl CDD COG1533 COG1533 441142 SplB DNA repair photolyase [Replication, recombination and repair]. 272 matched cddid_all.tbl CDD COG1534 COG1534 441143 YhbY RNA-binding protein YhbY [Translation, ribosomal structure and biogenesis]. 95 matched cddid_all.tbl CDD COG1535 COG1535 441144 EntB1 Isochorismate hydrolase [Secondary metabolites biosynthesis, transport and catabolism]. 204 matched cddid_all.tbl CDD COG1536 COG1536 441145 FliG Flagellar motor switch protein FliG [Cell motility]. 337 matched cddid_all.tbl CDD COG1537 COG1537 441146 PelA Stalled ribosome rescue protein Dom34, pelota family [Translation, ribosomal structure and biogenesis]. 351 matched cddid_all.tbl CDD COG1538 COG1538 441147 TolC Outer membrane protein TolC [Cell wall/membrane/envelope biogenesis]. 367 matched cddid_all.tbl CDD COG1539 COG1539 441148 FolB Dihydroneopterin aldolase [Coenzyme transport and metabolism]. Dihydroneopterin aldolase is part of the Pathway/BioSystem: Folate biosynthesis 118 matched cddid_all.tbl CDD COG1540 COG1540 441149 PxpA 5-oxoprolinase subunit A [Amino acid transport and metabolism]. 250 matched cddid_all.tbl CDD COG1541 COG1541 441150 PaaK Phenylacetate-coenzyme A ligase PaaK, adenylate-forming domain family [Coenzyme transport and metabolism]. 423 matched cddid_all.tbl CDD COG1542 COG1542 441151 COG1542 Uncharacterized conserved protein, DUF505 domain [Function unknown]. 594 matched cddid_all.tbl CDD COG1543 COG1543 441152 COG1543 Predicted glycosyl hydrolase, contains GH57 and DUF1957 domains [Carbohydrate transport and metabolism]. 528 matched cddid_all.tbl CDD COG1544 COG1544 441153 RaiA Ribosome-associated translation inhibitor RaiA [Translation, ribosomal structure and biogenesis]. 101 matched cddid_all.tbl CDD COG1545 COG1545 441154 COG1545 Uncharacterized OB-fold protein, contains Zn-ribbon domain [General function prediction only]. 116 matched cddid_all.tbl CDD COG1546 COG1546 441155 PncC Nicotinamide mononucleotide (NMN) deamidase PncC [Coenzyme transport and metabolism]. Nicotinamide mononucleotide (NMN) deamidase PncC is part of the Pathway/BioSystem: NAD biosynthesis 154 matched cddid_all.tbl CDD COG1547 COG1547 441156 YpuF Predicted metal-dependent hydrolase [Function unknown]. 92 matched cddid_all.tbl CDD COG1548 COG1548 441157 MfnF Methanofuran synthetase MfnF, hydantoinase/oxoprolinase family [Coenzyme transport and metabolism]. 339 matched cddid_all.tbl CDD COG1549 COG1549 441158 ArcS Archaeosine tRNA-ribosyltransferase, contains uracil-DNA-glycosylase and PUA domains [Translation, ribosomal structure and biogenesis]. 572 matched cddid_all.tbl CDD COG1550 COG1550 441159 YlxP Stress-induced protein YlxP, DUF503 family [Function unknown]. 93 matched cddid_all.tbl CDD COG1551 COG1551 441160 CsrA sRNA-binding carbon storage regulator CsrA [Signal transduction mechanisms]. 61 matched cddid_all.tbl CDD COG1552 COG1552 441161 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]. Ribosomal protein L40E is part of the Pathway/BioSystem: Archaeal ribosomal proteins 50 matched cddid_all.tbl CDD COG1553 COG1553 441162 DsrE Sulfur relay (sulfurtransferase) complex TusBCD TusD component, DsrE family [Inorganic ion transport and metabolism]. 118 matched cddid_all.tbl CDD COG1554 COG1554 441163 ATH1 Kojibiose phosphorylase YcjT [Carbohydrate transport and metabolism]. 761 matched cddid_all.tbl CDD COG1555 COG1555 441164 ComEA DNA uptake protein ComE or related DNA-binding protein [Replication, recombination and repair]. 72 matched cddid_all.tbl CDD COG1556 COG1556 441165 LutC L-lactate utilization protein LutC, contains LUD domain [Energy production and conversion]. 206 matched cddid_all.tbl CDD COG1558 COG1558 441166 FlgC Flagellar basal body rod protein FlgC [Cell motility]. 135 matched cddid_all.tbl CDD COG1559 COG1559 441167 MltG Endolytic transglycosylase MltG, terminates peptidoglycan polymerization [Cell wall/membrane/envelope biogenesis]. 333 matched cddid_all.tbl CDD COG1560 COG1560 441168 LpxP Palmitoleoyl-ACP: Kdo2-lipid-IV acyltransferase (lipid A biosynthesis) [Lipid transport and metabolism]. Palmitoleoyl-ACP: Kdo2-lipid-IV acyltransferase (lipid A biosynthesis) is part of the Pathway/BioSystem: Lipid A biosynthesis 271 matched cddid_all.tbl CDD COG1561 COG1561 441169 YicC Uncharacterized stationary-phase protein YicC, UPF0701 family [Function unknown]. 292 matched cddid_all.tbl CDD COG1562 COG1562 441170 ERG9 Phytoene/squalene synthetase [Lipid transport and metabolism]. 278 matched cddid_all.tbl CDD COG1563 COG1563 441171 COG1563 Uncharacterized MnhB-related membrane protein [General function prediction only]. 81 matched cddid_all.tbl CDD COG1564 COG1564 441172 ThiN Thiamine pyrophosphokinase [Coenzyme transport and metabolism]. Thiamine pyrophosphokinase is part of the Pathway/BioSystem: Thiamine biosynthesis 209 matched cddid_all.tbl CDD COG1565 COG1565 441173 MidA SAM-dependent methyltransferase, MidA family [General function prediction only]. 376 matched cddid_all.tbl CDD COG1566 COG1566 441174 EmrA Multidrug resistance efflux pump EmrA [Defense mechanisms]. 331 matched cddid_all.tbl CDD COG1567 COG1567 441175 Csm4 CRISPR-Cas system type III CSM-effector complex subunit Csm4, RAMP superfamily Cas5 group [Defense mechanisms]. CRISPR-Cas system type III CSM-effector complex subunit Csm4, RAMP superfamily Cas5 group is part of the Pathway/BioSystem: CRISPR-Cas system 313 matched cddid_all.tbl CDD COG1568 COG1568 441176 BpsA Aminopropyltransferase BpsA, N(4)-bis(aminopropyl)spermidine biosynthesis [Secondary metabolites biosynthesis, transport and catabolism]. 354 matched cddid_all.tbl CDD COG1569 COG1569 441177 COG1569 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]. 136 matched cddid_all.tbl CDD COG1570 COG1570 441178 XseA Exonuclease VII, large subunit [Replication, recombination and repair]. 400 matched cddid_all.tbl CDD COG1571 COG1571 441179 TiaS tRNA(Ile2) C34 agmatinyltransferase TiaS [Translation, ribosomal structure and biogenesis]. tRNA(Ile2) C34 agmatinyltransferase TiaS is part of the Pathway/BioSystem: tRNA modification 199 matched cddid_all.tbl CDD COG1572 COG1572 441180 COG1572 Serine protease, subtilase family [Posttranslational modification, protein turnover, chaperones]. 459 matched cddid_all.tbl CDD COG1573 COG1573 441181 Udg4 Uracil-DNA glycosylase [Replication, recombination and repair]. 189 matched cddid_all.tbl CDD COG1574 COG1574 441182 YtcJ Predicted amidohydrolase YtcJ [General function prediction only]. 535 matched cddid_all.tbl CDD COG1575 COG1575 441183 MenA 1,4-dihydroxy-2-naphthoate polyprenyltransferase [Coenzyme transport and metabolism]. 1,4-dihydroxy-2-naphthoate polyprenyltransferase is part of the Pathway/BioSystem: Menaquinone biosynthesis 290 matched cddid_all.tbl CDD COG1576 COG1576 441184 RlmH 23S rRNA pseudoU1915 N3-methylase RlmH [Translation, ribosomal structure and biogenesis]. 23S rRNA pseudoU1915 N3-methylase RlmH is part of the Pathway/BioSystem: 23S rRNA modification 156 matched cddid_all.tbl CDD COG1577 COG1577 441185 ERG12 Mevalonate kinase [Lipid transport and metabolism]. Mevalonate kinase is part of the Pathway/BioSystem: Isoprenoid biosynthesis 277 matched cddid_all.tbl CDD COG1578 COG1578 441186 DUF89 House-cleaning carbohydrate phosphatase, DUF89 family [Defense mechanisms]. 282 matched cddid_all.tbl CDD COG1579 COG1579 441187 DR0291 Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only]. 236 matched cddid_all.tbl CDD COG1580 COG1580 441188 FliL Flagellar basal body-associated protein FliL [Cell motility]. 153 matched cddid_all.tbl CDD COG1581 COG1581 441189 AlbA DNA/RNA-binding protein AlbA/Ssh10b [Transcription]. 87 matched cddid_all.tbl CDD COG1582 COG1582 441190 SwrD Swarming motility protein SwrD [Cell motility]. 61 matched cddid_all.tbl CDD COG1583 COG1583 441191 Cas6 CRISPR/Cas system endoribonuclease Cas6, RAMP superfamily [Defense mechanisms]. CRISPR/Cas system endoribonuclease Cas6, RAMP superfamily is part of the Pathway/BioSystem: CRISPR-Cas system 237 matched cddid_all.tbl CDD COG1584 COG1584 441192 SatP Succinate-acetate transporter SatP [Energy production and conversion]. 187 matched cddid_all.tbl CDD COG1585 COG1585 441193 YbbJ Membrane protein implicated in regulation of membrane protease activity [Posttranslational modification, protein turnover, chaperones]. 143 matched cddid_all.tbl CDD COG1586 COG1586 441194 SpeD S-adenosylmethionine decarboxylase [Amino acid transport and metabolism]. 118 matched cddid_all.tbl CDD COG1587 COG1587 441195 HemD Uroporphyrinogen-III synthase [Coenzyme transport and metabolism]. Uroporphyrinogen-III synthase is part of the Pathway/BioSystem: Heme biosynthesis 229 matched cddid_all.tbl CDD COG1588 COG1588 441196 POP4 RNase P/RNase MRP subunit p29 [Translation, ribosomal structure and biogenesis]. 94 matched cddid_all.tbl CDD COG1589 COG1589 441197 FtsQ Cell division septal protein FtsQ [Cell cycle control, cell division, chromosome partitioning]. 241 matched cddid_all.tbl CDD COG1590 COG1590 441198 Tyw3 tRNA(Phe) wybutosine-synthesizing methylase Tyw3 [Translation, ribosomal structure and biogenesis]. tRNA(Phe) wybutosine-synthesizing methylase Tyw3 is part of the Pathway/BioSystem: tRNA modification 194 matched cddid_all.tbl CDD COG1591 COG1591 441199 COG1591 Holliday junction resolvase Hjc, archaeal type [Replication, recombination and repair]. 140 matched cddid_all.tbl CDD COG1592 COG1592 441200 YotD Rubrerythrin [Energy production and conversion]. 180 matched cddid_all.tbl CDD COG1593 COG1593 441201 DctQ TRAP-type C4-dicarboxylate transport system, large permease component [Carbohydrate transport and metabolism]. 426 matched cddid_all.tbl CDD COG1594 COG1594 441202 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]. DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS is part of the Pathway/BioSystem: RNA polymerase 103 matched cddid_all.tbl CDD COG1595 COG1595 441203 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]. DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase 181 matched cddid_all.tbl CDD COG1596 COG1596 441204 Wza Periplasmic protein Wza involved in polysaccharide export, contains SLBB domain of the beta-grasp fold [Cell wall/membrane/envelope biogenesis]. 182 matched cddid_all.tbl CDD COG1597 COG1597 441205 LCB5 Phosphatidylglycerol kinase, diacylglycerol kinase family [Lipid transport and metabolism, General function prediction only]. 295 matched cddid_all.tbl CDD COG1598 COG1598 441206 HicB Antitoxin component HicB of the HicAB toxin-antitoxin system [Defense mechanisms]. 65 matched cddid_all.tbl CDD COG1599 COG1599 441207 RFA1 ssDNA-binding replication factor A, large subunit [Replication, recombination and repair]. 282 matched cddid_all.tbl CDD COG1600 COG1600 441208 QueG Epoxyqueuosine reductase QueG (queuosine biosynthesis) [Translation, ribosomal structure and biogenesis]. Epoxyqueuosine reductase QueG (queuosine biosynthesis) is part of the Pathway/BioSystem: tRNA modification 345 matched cddid_all.tbl CDD COG1601 COG1601 441209 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]. Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain is part of the Pathway/BioSystem: Translation factors 133 matched cddid_all.tbl CDD COG1602 COG1602 441210 NreA Archaeal DNA repair protein NreA [Replication, recombination and repair]. 414 matched cddid_all.tbl CDD COG1603 COG1603 441211 RPP1 RNase P/RNase MRP subunit p30 [Translation, ribosomal structure and biogenesis]. 231 matched cddid_all.tbl CDD COG1604 COG1604 441212 Cmr6 CRISPR/Cas system CMR subunit Cmr6, Cas7 group, RAMP superfamily [Defense mechanisms]. CRISPR/Cas system CMR subunit Cmr6, Cas7 group, RAMP superfamily is part of the Pathway/BioSystem: CRISPR-Cas system 239 matched cddid_all.tbl CDD COG1605 COG1605 441213 PheA Chorismate mutase [Amino acid transport and metabolism]. Chorismate mutase is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 166 matched cddid_all.tbl CDD COG1606 COG1606 441214 COG1606 ATP-utilizing enzyme, PP-loop superfamily [General function prediction only]. 265 matched cddid_all.tbl CDD COG1607 COG1607 441215 YciA Acyl-CoA hydrolase [Lipid transport and metabolism]. 146 matched cddid_all.tbl CDD COG1608 COG1608 441216 COG1608 Isopentenyl phosphate kinase [Lipid transport and metabolism]. 254 matched cddid_all.tbl CDD COG1609 COG1609 441217 PurR DNA-binding transcriptional regulator, LacI/PurR family [Transcription]. 335 matched cddid_all.tbl CDD COG1610 COG1610 441218 YqeY Uncharacterized conserved protein YqeY, may have tRNA amino acid amidase activity [General function prediction only]. 147 matched cddid_all.tbl CDD COG1611 COG1611 441219 PpnN Nucleotide monophosphate nucleosidase PpnN/YdgH, Lonely Guy (LOG) family [Nucleotide transport and metabolism]. 184 matched cddid_all.tbl CDD COG1612 COG1612 441220 CtaA Heme A synthase [Coenzyme transport and metabolism]. 318 matched cddid_all.tbl CDD COG1613 COG1613 441221 Sbp ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]. 340 matched cddid_all.tbl CDD COG1614 COG1614 441222 CdhC CO dehydrogenase/acetyl-CoA synthase beta subunit [Energy production and conversion]. 399 matched cddid_all.tbl CDD COG1615 COG1615 441223 COG1615 Uncharacterized membrane protein, UPF0182 family [Function unknown]. 926 matched cddid_all.tbl CDD COG1617 COG1617 441224 Cgi121 tRNA threonylcarbamoyladenosine modification (KEOPS) complex, Cgi121 subunit [Translation, ribosomal structure and biogenesis]. tRNA threonylcarbamoyladenosine modification (KEOPS) complex, Cgi121 subunit is part of the Pathway/BioSystem: tRNA modification 164 matched cddid_all.tbl CDD COG1618 COG1618 441225 THEP1 Nucleoside-triphosphatase THEP1 [Nucleotide transport and metabolism]. 175 matched cddid_all.tbl CDD COG1619 COG1619 441226 LdcA Muramoyltetrapeptide carboxypeptidase LdcA (peptidoglycan recycling) [Cell wall/membrane/envelope biogenesis]. 304 matched cddid_all.tbl CDD COG1620 COG1620 441227 LldP L-lactate permease [Energy production and conversion]. 520 matched cddid_all.tbl CDD COG1621 COG1621 441228 SacC Sucrose-6-phosphate hydrolase SacC, GH32 family [Carbohydrate transport and metabolism]. 459 matched cddid_all.tbl CDD COG1622 COG1622 441229 CyoA Heme/copper-type cytochrome/quinol oxidase, subunit 2 [Energy production and conversion]. 229 matched cddid_all.tbl CDD COG1623 COG1623 441230 DisA c-di-AMP synthetase DisA, contains DisA_N, linker and DNA-binding domains [Signal transduction mechanisms]. 353 matched cddid_all.tbl CDD COG1624 COG1624 441231 DisA c-di-AMP synthetase, contains DisA_N domain [Signal transduction mechanisms]. 245 matched cddid_all.tbl CDD COG1625 COG1625 441232 NifB Fe-S oxidoreductase, related to NifB/MoaA family [Energy production and conversion]. 441 matched cddid_all.tbl CDD COG1626 COG1626 441233 TreA Neutral trehalase [Carbohydrate transport and metabolism]. 438 matched cddid_all.tbl CDD COG1627 COG1627 441234 MJ0835 Uncharacterized conserved protein MJ0835, predicted component of type IV pili-like system, DUF1515 family [General function prediction only]. 421 matched cddid_all.tbl CDD COG1628 COG1628 441235 COG1628 Endonuclease V homolog, UPF0215 family [General function prediction only]. 189 matched cddid_all.tbl CDD COG1629 COG1629 441236 CirA Outer membrane receptor protein, Fe transport [Inorganic ion transport and metabolism]. 644 matched cddid_all.tbl CDD COG1630 COG1630 441237 NurA ssDNA and dsDNA 5'-3' nuclease NurA, repair of double-stranded DNA breaks [Replication, recombination and repair]. 370 matched cddid_all.tbl CDD COG1631 COG1631 441238 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]. Ribosomal protein L44E is part of the Pathway/BioSystem: Archaeal ribosomal proteins 91 matched cddid_all.tbl CDD COG1632 COG1632 441239 RPL15A Ribosomal protein L15E [Translation, ribosomal structure and biogenesis]. Ribosomal protein L15E is part of the Pathway/BioSystem: Archaeal ribosomal proteins 196 matched cddid_all.tbl CDD COG1633 COG1633 441240 YhjR Rubrerythrin, includes spore coat protein YhjR [Inorganic ion transport and metabolism]. 141 matched cddid_all.tbl CDD COG1634 COG1634 441241 FolK 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase MptE (tetrahydrofolate and tetrahydromethanopterin biosynthesis) [Coenzyme transport and metabolism]. 227 matched cddid_all.tbl CDD COG1635 COG1635 441242 THI4 Thiazole synthase/Archaeal ribulose 1,5-bisphosphate synthetase [Carbohydrate transport and metabolism, Coenzyme transport and metabolism]. 254 matched cddid_all.tbl CDD COG1636 COG1636 441243 QueH Epoxyqueuosine reductase QueH (tRNA modification) [Translation, ribosomal structure and biogenesis]. 192 matched cddid_all.tbl CDD COG1637 COG1637 441244 NucS Endonuclease NucS, RecB family [Replication, recombination and repair]. 209 matched cddid_all.tbl CDD COG1638 COG1638 441245 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]. 329 matched cddid_all.tbl CDD COG1639 COG1639 441246 HDOD HD-like signal output (HDOD) domain, no enzymatic activity [Signal transduction mechanisms]. 244 matched cddid_all.tbl CDD COG1640 COG1640 441247 MalQ 4-alpha-glucanotransferase [Carbohydrate transport and metabolism]. 505 matched cddid_all.tbl CDD COG1641 COG1641 441248 LarC CTP-dependent cyclometallase, nickel-pincer nucleotide (NPN) cofactor biosynthesis [Coenzyme transport and metabolism]. 392 matched cddid_all.tbl CDD COG1643 COG1643 441249 HrpA HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]. 836 matched cddid_all.tbl CDD COG1644 COG1644 441250 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]. 62 matched cddid_all.tbl CDD COG1645 COG1645 441251 COG1645 Uncharacterized Zn-finger containing protein, UPF0148 family [General function prediction only]. 116 matched cddid_all.tbl CDD COG1646 COG1646 441252 PcrB Glycerol-1-phosphate heptaprenyltransferase [Lipid transport and metabolism]. 241 matched cddid_all.tbl CDD COG1647 COG1647 441253 YvaK Esterase/lipase [Secondary metabolites biosynthesis, transport and catabolism]. 246 matched cddid_all.tbl CDD COG1648 COG1648 441254 CysG2 Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) [Coenzyme transport and metabolism]. Siroheme synthase (precorrin-2 oxidase/ferrochelatase domain) is part of the Pathway/BioSystem: Heme biosynthesis 211 matched cddid_all.tbl CDD COG1649 COG1649 441255 YddW Uncharacterized lipoprotein YddW, UPF0748 family [Function unknown]. 451 matched cddid_all.tbl CDD COG1650 COG1650 441256 COG1650 D-tyrosyl-tRNA(Tyr) deacylase [Translation, ribosomal structure and biogenesis]. 267 matched cddid_all.tbl CDD COG1651 COG1651 441257 DsbG Protein thiol-disulfide isomerase DsbC [Posttranslational modification, protein turnover, chaperones]. 152 matched cddid_all.tbl CDD COG1652 COG1652 441258 XkdP Cytoplasmic potassium-binding protein Kbp/XkdP/YgaU, contains LysM domain [Inorganic ion transport and metabolism]. 163 matched cddid_all.tbl CDD COG1653 COG1653 441259 UgpB ABC-type glycerol-3-phosphate transport system, periplasmic component [Carbohydrate transport and metabolism]. 363 matched cddid_all.tbl CDD COG1654 COG1654 441260 BirA Biotin operon repressor [Transcription]. 324 matched cddid_all.tbl CDD COG1655 COG1655 441261 COG1655 Uncharacterized conserved protein, DUF2225 family [Function unknown]. 228 matched cddid_all.tbl CDD COG1656 COG1656 441262 Mut7-C Uncharacterized conserved protein, contains PIN-related Mut7-C RNAse domain [General function prediction only]. 155 matched cddid_all.tbl CDD COG1657 COG1657 441263 SqhC Terpene cyclase SqhC [Lipid transport and metabolism]. 644 matched cddid_all.tbl CDD COG1658 COG1658 441264 RnmV 5S rRNA maturation ribonuclease M5, contains TOPRIM domain [Translation, ribosomal structure and biogenesis]. 184 matched cddid_all.tbl CDD COG1659 COG1659 441265 CFP29 Bacteriocin, linocin/CFP29 family [Defense mechanisms]. 265 matched cddid_all.tbl CDD COG1660 COG1660 441266 RapZ RNase adaptor protein RapZ for GlmZ sRNA degradation, contains a P-loop ATPase domain [Signal transduction mechanisms]. 286 matched cddid_all.tbl CDD COG1661 COG1661 441267 AF0104 Predicted DNA-binding protein with PD1-like DNA-binding motif, PPC/DUF296 domain [General function prediction only]. 139 matched cddid_all.tbl CDD COG1662 COG1662 441268 InsB Transposase and inactivated derivatives, IS1 family [Mobilome: prophages, transposons]. 193 matched cddid_all.tbl CDD COG1663 COG1663 441269 LpxK Tetraacyldisaccharide-1-P 4'-kinase (Lipid A 4'-kinase) [Cell wall/membrane/envelope biogenesis]. Tetraacyldisaccharide-1-P 4'-kinase (Lipid A 4'-kinase) is part of the Pathway/BioSystem: Lipid A biosynthesis 349 matched cddid_all.tbl CDD COG1664 COG1664 441270 CcmA Cytoskeletal protein CcmA, bactofilin family [Cytoskeleton]. 129 matched cddid_all.tbl CDD COG1665 COG1665 441271 AF1967 Predicted nucleotidyltransferase AF1967 [General function prediction only]. 316 matched cddid_all.tbl CDD COG1666 COG1666 441272 YajQ Cyclic di-GMP-binding protein YajQ, UPF0234 family [Signal transduction mechanisms]. 160 matched cddid_all.tbl CDD COG1667 COG1667 441273 AF1501 Uncharacterized conserved protein AF1501, DUF2226 family [Function unknown]. 214 matched cddid_all.tbl CDD COG1668 COG1668 441274 NatB ABC-type Na+ efflux pump, permease component NatB [Energy production and conversion, Inorganic ion transport and metabolism]. 402 matched cddid_all.tbl CDD COG1669 COG1669 441275 MJ0435 Predicted nucleotidyltransferase MJ0435 [General function prediction only]. 96 matched cddid_all.tbl CDD COG1670 COG1670 441276 RimL Protein N-acetyltransferase, RimJ/RimL family [Translation, ribosomal structure and biogenesis, Posttranslational modification, protein turnover, chaperones]. 173 matched cddid_all.tbl CDD COG1671 COG1671 441277 YaiI Uncharacterized conserved protein YaiI, UPF0178 family [Function unknown]. 149 matched cddid_all.tbl CDD COG1672 COG1672 441278 COG1672 Predicted ATPase, archaeal AAA+ ATPase superfamily [General function prediction only]. 324 matched cddid_all.tbl CDD COG1673 COG1673 441279 COG1673 Predicted RNA-binding protein, contains PUA-like EVE domain [General function prediction only]. 143 matched cddid_all.tbl CDD COG1674 COG1674 441280 FtsK DNA segregation ATPase FtsK/SpoIIIE or related protein [Cell cycle control, cell division, chromosome partitioning]. 611 matched cddid_all.tbl CDD COG1675 COG1675 441281 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]. 172 matched cddid_all.tbl CDD COG1676 COG1676 441282 SEN2 tRNA splicing endonuclease subunit SEN34 [Translation, ribosomal structure and biogenesis]. tRNA splicing endonuclease subunit SEN34 is part of the Pathway/BioSystem: tRNA modification 173 matched cddid_all.tbl CDD COG1677 COG1677 441283 FliE Flagellar hook-basal body complex protein FliE [Cell motility]. 105 matched cddid_all.tbl CDD COG1678 COG1678 441284 AlgH Putative transcriptional regulator, AlgH/UPF0301 family [Transcription]. 180 matched cddid_all.tbl CDD COG1679 COG1679 441285 AcnX1 Mevalonate 5-phosphate dehydratase subunit 1, aconitase superfamily (modified mevalonate pathway) [Lipid transport and metabolism]. 411 matched cddid_all.tbl CDD COG1680 COG1680 441286 AmpC CubicO group peptidase, beta-lactamase class C family [Defense mechanisms]. 355 matched cddid_all.tbl CDD COG1681 COG1681 441287 FlaB Archaellin (archaeal flagellin) [Cell motility]. 207 matched cddid_all.tbl CDD COG1682 COG1682 441288 TagG ABC-type polysaccharide/teichoic acid/polyol phosphate export permease [Carbohydrate transport and metabolism]. 258 matched cddid_all.tbl CDD COG1683 COG1683 441289 YbbK Uncharacterized conserved protein YbbK, DUF523 family [Function unknown]. 149 matched cddid_all.tbl CDD COG1684 COG1684 441290 FliR Flagellar biosynthesis protein FliR [Cell motility]. 253 matched cddid_all.tbl CDD COG1685 COG1685 441291 AroK2 Archaeal shikimate kinase [Amino acid transport and metabolism]. Archaeal shikimate kinase is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 282 matched cddid_all.tbl CDD COG1686 COG1686 441292 DacC D-alanyl-D-alanine carboxypeptidase [Cell wall/membrane/envelope biogenesis]. 324 matched cddid_all.tbl CDD COG1687 COG1687 441293 AzlD Branched-chain amino acid transport protein AzlD [Amino acid transport and metabolism]. 108 matched cddid_all.tbl CDD COG1688 COG1688 441294 Cas5 CRISPR/Cas system-associated protein Cas5, RAMP superfamily [Defense mechanisms]. CRISPR/Cas system-associated protein Cas5, RAMP superfamily is part of the Pathway/BioSystem: CRISPR-Cas system 210 matched cddid_all.tbl CDD COG1689 COG1689 441295 AF1543 Class II terpene cyclase family protein AF1543 [General function prediction only]. 272 matched cddid_all.tbl CDD COG1690 COG1690 441296 RtcB RNA-splicing ligase RtcB, repairs tRNA damage [Translation, ribosomal structure and biogenesis]. 454 matched cddid_all.tbl CDD COG1691 COG1691 441297 COG1691 NCAIR mutase (PurE)-related protein [Nucleotide transport and metabolism]. 248 matched cddid_all.tbl CDD COG1692 COG1692 441298 YmdB 2',3'- and 3',5'-cNMP phosphodiesterase YmdB, calcineurin family [Signal transduction mechanisms]. 264 matched cddid_all.tbl CDD COG1693 COG1693 441299 COG1693 Repressor of nif and glnA expression [Transcription]. 327 matched cddid_all.tbl CDD COG1694 COG1694 441300 MazG NTP pyrophosphatase, house-cleaning of non-canonical NTPs [Defense mechanisms]. 95 matched cddid_all.tbl CDD COG1695 COG1695 441301 PadR DNA-binding transcriptional regulator, PadR family [Transcription]. 102 matched cddid_all.tbl CDD COG1696 COG1696 441302 DltB D-alanyl-lipoteichoic acid acyltransferase DltB, MBOAT superfamily [Cell wall/membrane/envelope biogenesis]. 472 matched cddid_all.tbl CDD COG1697 COG1697 441303 Spo11 DNA topoisomerase VI, subunit A [Replication, recombination and repair]. 360 matched cddid_all.tbl CDD COG1698 COG1698 441304 COG1698 Uncharacterized conserved protein, UPF0147 family [Function unknown]. 88 matched cddid_all.tbl CDD COG1699 COG1699 441305 FliW Flagellar assembly factor FliW [Cell motility]. 139 matched cddid_all.tbl CDD COG1700 COG1700 441306 AQ645 Predicted anti-virus defense system component AQ645, contains DUF2357 and PD-(D/E)xK nuclease domains [Defense mechanisms]. 724 matched cddid_all.tbl CDD COG1701 COG1701 441307 aPPS Archaeal phosphopantothenate synthetase [Coenzyme transport and metabolism]. Archaeal phosphopantothenate synthetase is part of the Pathway/BioSystem: Pantothenate/CoA biosynthesis 251 matched cddid_all.tbl CDD COG1702 COG1702 441308 PhoH Phosphate starvation-inducible protein PhoH, predicted ATPase [Signal transduction mechanisms]. 325 matched cddid_all.tbl CDD COG1703 COG1703 441309 ArgK GTPase of the G3E family (not a periplasmic protein kinase) [Posttranslational modification, protein turnover, chaperones]. 317 matched cddid_all.tbl CDD COG1704 COG1704 441310 LemA Magnetosome formation protein MamQ, lipoprotein antigen LemA family [Cell wall/membrane/envelope biogenesis]. 187 matched cddid_all.tbl CDD COG1705 COG1705 441311 FlgJ Flagellum-specific peptidoglycan hydrolase FlgJ [Cell wall/membrane/envelope biogenesis, Cell motility]. 276 matched cddid_all.tbl CDD COG1706 COG1706 441312 FlgI Flagellar basal body P-ring protein FlgI [Cell motility]. 367 matched cddid_all.tbl CDD COG1707 COG1707 441313 AF1403 Uncharacterized protein, contains ACT and PBP-like DUF5612 domains, MJ1458 family [General function prediction only]. 216 matched cddid_all.tbl CDD COG1708 COG1708 441314 MJ0604 Predicted nucleotidyltransferase, MJ0604 family [General function prediction only]. 95 matched cddid_all.tbl CDD COG1709 COG1709 441315 COG1709 Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription]. 234 matched cddid_all.tbl CDD COG1710 COG1710 441316 MJ1475 Predicted DNA-binding protein MJ1475, contains C-terminal HTH domain [General function prediction only]. 135 matched cddid_all.tbl CDD COG1711 COG1711 441317 COG1711 DNA replication initiation complex subunit, GINS family [Replication, recombination and repair]. 222 matched cddid_all.tbl CDD COG1712 COG1712 441318 AspD L-aspartate dehydrogenase, NAD(P)-dependent [Amino acid transport and metabolism]. 263 matched cddid_all.tbl CDD COG1713 COG1713 441319 YqeK Diadenosine tetraphosphatase YqeK or a related HD superfamily phosphohydrolase [Signal transduction mechanisms, General function prediction only]. 184 matched cddid_all.tbl CDD COG1714 COG1714 441320 YckC Uncharacterized membrane protein YckC, RDD family [Function unknown]. 143 matched cddid_all.tbl CDD COG1715 COG1715 441321 Mrr Restriction endonuclease Mrr [Defense mechanisms]. 157 matched cddid_all.tbl CDD COG1716 COG1716 441322 FHA Forkhead associated (FHA) domain, binds pSer, pThr, pTyr [Signal transduction mechanisms]. 96 matched cddid_all.tbl CDD COG1717 COG1717 441323 Rpl32e Ribosomal protein L32E [Translation, ribosomal structure and biogenesis]. Ribosomal protein L32E is part of the Pathway/BioSystem: Archaeal ribosomal proteins 132 matched cddid_all.tbl CDD COG1718 COG1718 441324 RIO1 Serine/threonine-protein kinase RIO1 [Signal transduction mechanisms]. 252 matched cddid_all.tbl CDD COG1719 COG1719 441325 COG1719 Predicted hydrocarbon binding protein, contains 4VR domain [General function prediction only]. 137 matched cddid_all.tbl CDD COG1720 COG1720 441326 TrmO tRNA (Thr-GGU) A37 N6-methylase [Translation, ribosomal structure and biogenesis]. tRNA (Thr-GGU) A37 N6-methylase is part of the Pathway/BioSystem: tRNA modification 152 matched cddid_all.tbl CDD COG1721 COG1721 441327 YeaD2 Uncharacterized conserved protein, DUF58 family, contains vWF domain [Function unknown]. 287 matched cddid_all.tbl CDD COG1722 COG1722 441328 XseB Exonuclease VII small subunit [Replication, recombination and repair]. 74 matched cddid_all.tbl CDD COG1723 COG1723 441329 Rmd1 Mitochondrial translation protein, Rmd1/RMND1/DUF155 family [Translation, ribosomal structure and biogenesis]. 261 matched cddid_all.tbl CDD COG1724 COG1724 441330 YcfA Predicted RNA binding protein YcfA, dsRBD-like fold, HicA-like mRNA interferase family [General function prediction only]. 72 matched cddid_all.tbl CDD COG1725 COG1725 441331 YhcF DNA-binding transcriptional regulator YhcF, GntR family [Transcription]. 114 matched cddid_all.tbl CDD COG1726 COG1726 441332 NqrA Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrA [Energy production and conversion]. Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrA is part of the Pathway/BioSystem: Na+-translocating NADH dehydrogenase 445 matched cddid_all.tbl CDD COG1727 COG1727 441333 RPL18A Ribosomal protein L18E [Translation, ribosomal structure and biogenesis]. Ribosomal protein L18E is part of the Pathway/BioSystem: Archaeal ribosomal proteins 114 matched cddid_all.tbl CDD COG1728 COG1728 441334 YaaR Uncharacterized conserved protein YaaR, TM1646/DUF327 family [Function unknown]. 148 matched cddid_all.tbl CDD COG1729 COG1729 441335 CpoB Cell division protein CpoB, coordinates peptidoglycan biosynthesis and outer membrane constriction [Cell cycle control, cell division, chromosome partitioning]. 113 matched cddid_all.tbl CDD COG1730 COG1730 441336 GIM5 Prefoldin subunit 5 [Posttranslational modification, protein turnover, chaperones]. 145 matched cddid_all.tbl CDD COG1731 COG1731 441337 RibC2 Archaeal riboflavin synthase [Coenzyme transport and metabolism]. Archaeal riboflavin synthase is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis 155 matched cddid_all.tbl CDD COG1732 COG1732 441338 OsmF Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell wall/membrane/envelope biogenesis]. 294 matched cddid_all.tbl CDD COG1733 COG1733 441339 HxlR DNA-binding transcriptional regulator, HxlR family [Transcription]. 108 matched cddid_all.tbl CDD COG1734 COG1734 441340 DksA RNA polymerase-binding transcription factor DksA [Transcription]. 119 matched cddid_all.tbl CDD COG1735 COG1735 441341 Php Predicted metal-dependent hydrolase, phosphotriesterase family [General function prediction only]. 305 matched cddid_all.tbl CDD COG1736 COG1736 441342 DPH2 Diphthamide synthase subunit DPH2 [Translation, ribosomal structure and biogenesis]. 328 matched cddid_all.tbl CDD COG1737 COG1737 441343 RpiR DNA-binding transcriptional regulator, MurR/RpiR family, contains HTH and SIS domains [Transcription]. 286 matched cddid_all.tbl CDD COG1738 COG1738 441344 YhhQ Queuosine precursor transporter YhhQ, DUF165 family [Translation, ribosomal structure and biogenesis]. 220 matched cddid_all.tbl CDD COG1739 COG1739 441345 YIH1 Putative translation regulator, IMPACT (imprinted ancient) protein family [General function prediction only]. 198 matched cddid_all.tbl CDD COG1740 COG1740 441346 HyaA Ni,Fe-hydrogenase I small subunit [Energy production and conversion]. 364 matched cddid_all.tbl CDD COG1741 COG1741 441347 YhaK Redox-sensitive bicupin YhaK, pirin superfamily [General function prediction only]. 253 matched cddid_all.tbl CDD COG1742 COG1742 441348 YnfA Uncharacterized inner membrane protein YnfA, drug/metabolite transporter superfamily [General function prediction only]. 108 matched cddid_all.tbl CDD COG1743 COG1743 441349 COG1743 Adenine-specific DNA methylase, contains a Zn-ribbon domain [Replication, recombination and repair]. 871 matched cddid_all.tbl CDD COG1744 COG1744 441350 Med Lipoprotein Med, regulator of KinD/Spo0A, PBP1-ABC superfamily, includes NupN [Signal transduction mechanisms]. 300 matched cddid_all.tbl CDD COG1745 COG1745 441351 COG1745 Uncharacterized metal-binding protein MJ1132, UPF0058 family [Function unknown]. 90 matched cddid_all.tbl CDD COG1746 COG1746 441352 CCA1 tRNA nucleotidyltransferase (CCA-adding enzyme) [Translation, ribosomal structure and biogenesis]. tRNA nucleotidyltransferase (CCA-adding enzyme) is part of the Pathway/BioSystem: tRNA modification 448 matched cddid_all.tbl CDD COG1747 COG1747 441353 COG1747 Uncharacterized N-terminal domain of the transcription elongation factor GreA [Function unknown]. 890 matched cddid_all.tbl CDD COG1748 COG1748 441354 Lys9 Saccharopine dehydrogenase, NADP-dependent [Amino acid transport and metabolism]. Saccharopine dehydrogenase, NADP-dependent is part of the Pathway/BioSystem: Lysine biosynthesis 352 matched cddid_all.tbl CDD COG1749 COG1749 441355 FlgE Flagellar hook protein FlgE [Cell motility]. 414 matched cddid_all.tbl CDD COG1750 COG1750 441356 COG1750 Predicted archaeal serine protease, S18 family [General function prediction only]. 213 matched cddid_all.tbl CDD COG1751 COG1751 441357 PK Ligand-binding C-terminal domain of pyruvate kinase, DUF1867 [Carbohydrate transport and metabolism, Signal transduction mechanisms]. 189 matched cddid_all.tbl CDD COG1752 COG1752 441358 RssA Predicted acylesterase/phospholipase RssA, containd patatin domain [General function prediction only]. 261 matched cddid_all.tbl CDD COG1753 COG1753 441359 VapB3 Predicted antitoxin, CopG family [Defense mechanisms]. 76 matched cddid_all.tbl CDD COG1754 COG1754 441360 COG1754 Uncharacterized C-terminal domain of topoisomerase IA [Function unknown]. 892 matched cddid_all.tbl CDD COG1755 COG1755 441361 YpbQ Uncharacterized conserved protein YpbQ, isoprenylcysteine carboxyl methyltransferase (ICMT) family [Function unknown]. 171 matched cddid_all.tbl CDD COG1756 COG1756 441362 Emg1 rRNA pseudouridine-1189 N-methylase Emg1, Nep1/Mra1 family [Translation, ribosomal structure and biogenesis]. 224 matched cddid_all.tbl CDD COG1757 COG1757 441363 NhaC Na+/H+ antiporter NhaC/MleN [Energy production and conversion]. 418 matched cddid_all.tbl CDD COG1758 COG1758 441364 RpoZ DNA-directed RNA polymerase, subunit K/omega [Transcription]. DNA-directed RNA polymerase, subunit K/omega is part of the Pathway/BioSystem: RNA polymerase 64 matched cddid_all.tbl CDD COG1759 COG1759 441365 PurP 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase (purine biosynthesis) [Nucleotide transport and metabolism]. 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase (purine biosynthesis) is part of the Pathway/BioSystem: Purine biosynthesis 363 matched cddid_all.tbl CDD COG1760 COG1760 441366 SdaA L-serine deaminase [Amino acid transport and metabolism]. 275 matched cddid_all.tbl CDD COG1761 COG1761 441367 RPB11 DNA-directed RNA polymerase, subunit L/RPAC2 [Transcription]. DNA-directed RNA polymerase, subunit L/RPAC2 is part of the Pathway/BioSystem: RNA polymerase 88 matched cddid_all.tbl CDD COG1762 COG1762 441368 PtsN Phosphotransferase system mannitol/fructose-specific IIA domain (Ntr-type) [Carbohydrate transport and metabolism, Signal transduction mechanisms]. 150 matched cddid_all.tbl CDD COG1763 COG1763 441369 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme transport and metabolism]. Molybdopterin-guanine dinucleotide biosynthesis protein is part of the Pathway/BioSystem: Molybdopterin biosynthesis 162 matched cddid_all.tbl CDD COG1764 COG1764 441370 OsmC Organic hydroperoxide reductase OsmC/OhrA [Defense mechanisms]. 140 matched cddid_all.tbl CDD COG1765 COG1765 441371 YhfA Uncharacterized OsmC-related protein [General function prediction only]. 126 matched cddid_all.tbl CDD COG1766 COG1766 441372 FliF Flagellar biosynthesis/type III secretory pathway M-ring protein FliF/YscJ [Cell motility, Intracellular trafficking, secretion, and vesicular transport]. 541 matched cddid_all.tbl CDD COG1767 COG1767 441373 CitG Triphosphoribosyl-dephospho-CoA synthetase [Coenzyme transport and metabolism]. 295 matched cddid_all.tbl CDD COG1768 COG1768 441374 DR1119 Predicted phosphohydrolase, DR1119 family, metallophosphatase superfamily [General function prediction only]. 230 matched cddid_all.tbl CDD COG1769 COG1769 441375 Cmr3 CRISPR-Cas system type III CMR-effector complex subunit Cmr3, RAMP superfamily Cas5 group [Defense mechanisms]. CRISPR-Cas system type III CMR-effector complex subunit Cmr3, RAMP superfamily Cas5 group is part of the Pathway/BioSystem: CRISPR-Cas system 371 matched cddid_all.tbl CDD COG1770 COG1770 441376 PtrB Protease II [Amino acid transport and metabolism]. 686 matched cddid_all.tbl CDD COG1771 COG1771 441377 COG1771 Uncharacterized conserved protein, contains N-terminal Zn-finger domain [Function unknown]. 430 matched cddid_all.tbl CDD COG1772 COG1772 441378 COG1772 Uncharacterized conserved protein, DUF531 domain [Function unknown]. 173 matched cddid_all.tbl CDD COG1773 COG1773 441379 NorV Flavorubredoxin [Inorganic ion transport and metabolism]. 53 matched cddid_all.tbl CDD COG1774 COG1774 441380 YaaT Cell fate regulator YaaT, PSP1 superfamily (controls sporulation, competence, biofilm development) [Signal transduction mechanisms]. 269 matched cddid_all.tbl CDD COG1775 COG1775 441381 HgdB Benzoyl-CoA reductase/2-hydroxyglutaryl-CoA dehydratase subunit, BcrC/BadD/HgdB [Amino acid transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism]. 384 matched cddid_all.tbl CDD COG1776 COG1776 441382 CheC Phosphoaspartate phosphatase CheC, specific for CheY-P [Signal transduction mechanisms]. 199 matched cddid_all.tbl CDD COG1777 COG1777 441383 COG1777 Predicted transcriptional regulator, ArsR family [Transcription]. 113 matched cddid_all.tbl CDD COG1778 COG1778 441384 KdsC 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC and related HAD superfamily phosphatases [Cell wall/membrane/envelope biogenesis, General function prediction only]. 170 matched cddid_all.tbl CDD COG1779 COG1779 441385 Zpr1 C4-type Zn-finger protein [General function prediction only]. 191 matched cddid_all.tbl CDD COG1780 COG1780 441386 NrdI Flavodoxin NrdI, NrdF-interacting activator of class Ib ribonucleotide reductase [Nucleotide transport and metabolism]. 135 matched cddid_all.tbl CDD COG1781 COG1781 441387 PyrI Aspartate carbamoyltransferase, regulatory subunit [Nucleotide transport and metabolism]. 151 matched cddid_all.tbl CDD COG1782 COG1782 441388 COG1782 Predicted metal-dependent RNase, contains metallo-beta-lactamase and KH domains [General function prediction only]. 460 matched cddid_all.tbl CDD COG1783 COG1783 441389 XtmB Phage terminase large subunit [Mobilome: prophages, transposons]. 408 matched cddid_all.tbl CDD COG1784 COG1784 441390 COG1784 TctA family transporter [General function prediction only]. 411 matched cddid_all.tbl CDD COG1785 COG1785 441391 PhoA Alkaline phosphatase [Inorganic ion transport and metabolism, General function prediction only]. Alkaline phosphatase is part of the Pathway/BioSystem: Folate biosynthesis 401 matched cddid_all.tbl CDD COG1786 COG1786 441392 AcnX2 Mevalonate 5-phosphate dehydratase subunit 2, swiveling domain (modified mevalonate pathway) [Lipid transport and metabolism]. 131 matched cddid_all.tbl CDD COG1787 COG1787 441393 COG1787 Endonuclease, HJR/Mrr/RecB family [Defense mechanisms]. 119 matched cddid_all.tbl CDD COG1788 COG1788 441394 AtoD Acyl CoA:acetate/3-ketoacid CoA transferase, alpha subunit [Lipid transport and metabolism]. 226 matched cddid_all.tbl CDD COG1790 COG1790 441395 COG1790 Uncharacterized conserved protein, DUF483 domain [Function unknown]. 188 matched cddid_all.tbl CDD COG1791 COG1791 441396 Adi1 Acireductone dioxygenase (methionine salvage), cupin superfamily [Amino acid transport and metabolism]. 180 matched cddid_all.tbl CDD COG1792 COG1792 441397 MreC Cell shape-determining protein MreC [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]. 282 matched cddid_all.tbl CDD COG1793 COG1793 441398 CDC9 ATP-dependent DNA ligase [Replication, recombination and repair]. 435 matched cddid_all.tbl CDD COG1794 COG1794 441399 RacX Amino acid racemase YgeA [Cell wall/membrane/envelope biogenesis]. 228 matched cddid_all.tbl CDD COG1795 COG1795 441400 Fae Formaldehyde-activating enzyme (5,6,7,8-tetrahydromethanopterin hydrolyase) [Energy production and conversion]. 171 matched cddid_all.tbl CDD COG1796 COG1796 441401 PolX DNA polymerase/3'-5' exonuclease PolX [Replication, recombination and repair]. 567 matched cddid_all.tbl CDD COG1797 COG1797 441402 CobB Cobyrinic acid a,c-diamide synthase [Coenzyme transport and metabolism]. Cobyrinic acid a,c-diamide synthase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 459 matched cddid_all.tbl CDD COG1798 COG1798 441403 DPH5 Diphthamide biosynthesis methyltransferase [Translation, ribosomal structure and biogenesis]. 255 matched cddid_all.tbl CDD COG1799 COG1799 441404 SepF Cell division protein SepF/YlmF, interacts with FtsZ [Cell cycle control, cell division, chromosome partitioning]. 142 matched cddid_all.tbl CDD COG1800 COG1800 441405 COG1800 Predicted transglutaminase-like protease, UPF0252 family [General function prediction only]. 266 matched cddid_all.tbl CDD COG1801 COG1801 441406 YecE Sugar isomerase-related protein YecE, UPF0759/DUF72 family [General function prediction only]. 241 matched cddid_all.tbl CDD COG1802 COG1802 441407 GntR DNA-binding transcriptional regulator, GntR family [Transcription]. 222 matched cddid_all.tbl CDD COG1803 COG1803 441408 MgsA Methylglyoxal synthase [Carbohydrate transport and metabolism]. 122 matched cddid_all.tbl CDD COG1804 COG1804 441409 CaiB Crotonobetainyl-CoA:carnitine CoA-transferase CaiB and related acyl-CoA transferases [Lipid transport and metabolism]. 397 matched cddid_all.tbl CDD COG1805 COG1805 441410 NqrB Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrB [Energy production and conversion]. Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrB is part of the Pathway/BioSystem: Na+-translocating NADH dehydrogenase 402 matched cddid_all.tbl CDD COG1806 COG1806 441411 PpsR Regulator of PEP synthase PpsR, kinase-PPPase family (combines ADP:protein kinase and phosphorylase activities) [Signal transduction mechanisms]. 272 matched cddid_all.tbl CDD COG1807 COG1807 441412 ArnT PMT family glycosyltransferase ArnT/Agl22, involved in glycosylation of proteins and lipid IVA [Cell wall/membrane/envelope biogenesis]. 309 matched cddid_all.tbl CDD COG1808 COG1808 441413 AF0785 Uncharacterized membrane protein AF0785, contains DUF389 domain [Function unknown]. 211 matched cddid_all.tbl CDD COG1809 COG1809 441414 ComA Phosphosulfolactate synthase, CoM biosynthesis protein A [Coenzyme transport and metabolism]. 261 matched cddid_all.tbl CDD COG1810 COG1810 441415 COG1810 Uncharacterized conserved protein, DUF166 domain [Function unknown]. 230 matched cddid_all.tbl CDD COG1811 COG1811 441416 YqgA Uncharacterized membrane protein YqgA, affects biofilm formation [Function unknown]. 229 matched cddid_all.tbl CDD COG1812 COG1812 441417 MetK2 Archaeal S-adenosylmethionine synthetase [Coenzyme transport and metabolism]. Archaeal S-adenosylmethionine synthetase is part of the Pathway/BioSystem: Methionine biosynthesis 399 matched cddid_all.tbl CDD COG1813 COG1813 441418 aMBF1 Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and HTH domains [Translation, ribosomal structure and biogenesis]. 70 matched cddid_all.tbl CDD COG1814 COG1814 441419 Ccc1 Predicted Fe2+/Mn2+ transporter, VIT1/CCC1 family [Inorganic ion transport and metabolism]. 229 matched cddid_all.tbl CDD COG1815 COG1815 441420 FlgB Flagellar basal body rod protein FlgB [Cell motility]. 135 matched cddid_all.tbl CDD COG1816 COG1816 441421 Add Adenosine deaminase [Nucleotide transport and metabolism]. Adenosine deaminase is part of the Pathway/BioSystem: Menaquinone biosynthesis 326 matched cddid_all.tbl CDD COG1817 COG1817 441422 COG1817 Predicted glycosyltransferase [General function prediction only]. 342 matched cddid_all.tbl CDD COG1818 COG1818 441423 Tan1 tRNA(Ser,Leu) C12 N-acetylase TAN1, contains THUMP domain [Translation, ribosomal structure and biogenesis]. tRNA(Ser,Leu) C12 N-acetylase TAN1, contains THUMP domain is part of the Pathway/BioSystem: tRNA modification 162 matched cddid_all.tbl CDD COG1819 COG1819 441424 YjiC UDP:flavonoid glycosyltransferase YjiC, YdhE family [Carbohydrate transport and metabolism]. 268 matched cddid_all.tbl CDD COG1820 COG1820 441425 NagA N-acetylglucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism]. 373 matched cddid_all.tbl CDD COG1821 COG1821 441426 MfnD Tyramine-glutamate ligase MfnD (methanofuran biosynthesis), ATP-grasp superfamily [Coenzyme transport and metabolism]. 323 matched cddid_all.tbl CDD COG1822 COG1822 441427 MJ0419 Uncharacterized membrane protein MJ0419, predicted role in archaeal polysaccharide biosynthesis [Cell wall/membrane/envelope biogenesis]. 344 matched cddid_all.tbl CDD COG1823 COG1823 441428 TcyP L-cystine transporter TcyP, sodium:dicarboxylate symporter family [Amino acid transport and metabolism]. 463 matched cddid_all.tbl CDD COG1824 COG1824 441429 MgtE2 Permease, similar to cation transporters [Inorganic ion transport and metabolism]. 188 matched cddid_all.tbl CDD COG1825 COG1825 441430 RplY Ribosomal protein L25 (general stress protein Ctc) [Translation, ribosomal structure and biogenesis]. Ribosomal protein L25 (general stress protein Ctc) is part of the Pathway/BioSystem: Ribosome 50S subunit 182 matched cddid_all.tbl CDD COG1826 COG1826 441431 TatA Twin-arginine protein secretion pathway components TatA and TatB [Intracellular trafficking, secretion, and vesicular transport]. 72 matched cddid_all.tbl CDD COG1827 COG1827 441432 NiaR Transcriptional regulator of NAD metabolism, contains HTH and 3H domains [Transcription, Coenzyme transport and metabolism]. 171 matched cddid_all.tbl CDD COG1828 COG1828 441433 PurS Phosphoribosylformylglycinamidine (FGAM) synthase, PurS subunit [Nucleotide transport and metabolism]. Phosphoribosylformylglycinamidine (FGAM) synthase, PurS subunit is part of the Pathway/BioSystem: Purine biosynthesis 82 matched cddid_all.tbl CDD COG1829 COG1829 441434 COG1829 Archaeal pantoate kinase [Coenzyme transport and metabolism]. Archaeal pantoate kinase is part of the Pathway/BioSystem: Pantothenate/CoA biosynthesis 285 matched cddid_all.tbl CDD COG1830 COG1830 441435 FbaB Fructose-bisphosphate aldolase class Ia, DhnA family [Carbohydrate transport and metabolism]. Fructose-bisphosphate aldolase class Ia, DhnA family is part of the Pathway/BioSystem: Glycolysis 259 matched cddid_all.tbl CDD COG1831 COG1831 441436 COG1831 Predicted metal-dependent hydrolase, urease superfamily [General function prediction only]. 285 matched cddid_all.tbl CDD COG1832 COG1832 441437 YccU Predicted CoA-binding protein [General function prediction only]. 138 matched cddid_all.tbl CDD COG1833 COG1833 441438 COG1833 Uri superfamily endonuclease [General function prediction only]. 142 matched cddid_all.tbl CDD COG1834 COG1834 441439 DdaH N-Dimethylarginine dimethylaminohydrolase [Amino acid transport and metabolism]. 264 matched cddid_all.tbl CDD COG1835 COG1835 441440 OafA Peptidoglycan/LPS O-acetylase OafA/YrhL, contains acyltransferase and SGNH-hydrolase domains [Cell wall/membrane/envelope biogenesis]. 309 matched cddid_all.tbl CDD COG1836 COG1836 441441 COG1836 Cytidylyltransferase family enzyme [General function prediction only]. 243 matched cddid_all.tbl CDD COG1837 COG1837 441442 YlqC Predicted RNA-binding protein YlqC, contains KH domain, UPF0109 family [General function prediction only]. 76 matched cddid_all.tbl CDD COG1838 COG1838 441443 FumA Tartrate dehydratase beta subunit/Fumarate hydratase class I, C-terminal domain [Energy production and conversion]. Tartrate dehydratase beta subunit/Fumarate hydratase class I, C-terminal domain is part of the Pathway/BioSystem: TCA cycle 190 matched cddid_all.tbl CDD COG1839 COG1839 441444 COG1839 Adenosine/AMP kinase [Nucleotide transport and metabolism]. 160 matched cddid_all.tbl CDD COG1840 COG1840 441445 AfuA ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]. 286 matched cddid_all.tbl CDD COG1841 COG1841 441446 RpmD Ribosomal protein L30/L7E [Translation, ribosomal structure and biogenesis]. Ribosomal protein L30/L7E is part of the Pathway/BioSystem: Ribosome 50S subunit 58 matched cddid_all.tbl CDD COG1842 COG1842 441447 PspA Phage shock protein A [Transcription, Signal transduction mechanisms]. 217 matched cddid_all.tbl CDD COG1843 COG1843 441448 FlgD Flagellar hook-capping protein FlgD [Cell motility]. 223 matched cddid_all.tbl CDD COG1844 COG1844 441449 COG1844 Uncharacterized conserved protein, DUF356 domain [Function unknown]. 127 matched cddid_all.tbl CDD COG1845 COG1845 441450 CyoC Heme/copper-type cytochrome/quinol oxidase, subunit 3 [Energy production and conversion]. 192 matched cddid_all.tbl CDD COG1846 COG1846 441451 MarR DNA-binding transcriptional regulator, MarR family [Transcription]. 142 matched cddid_all.tbl CDD COG1847 COG1847 441452 Jag Predicted RNA-binding protein Jag (SpoIIIJ-associated), conains KH and R3H domains [General function prediction only]. 143 matched cddid_all.tbl CDD COG1848 COG1848 441453 VapC VapC family ribonuclease, toxin component of the VapBC toxin-antitoxin module, contains PIN domain [Defense mechanisms]. 134 matched cddid_all.tbl CDD COG1849 COG1849 441454 COG1849 Uncharacterized conserved protein [Function unknown]. 90 matched cddid_all.tbl CDD COG1850 COG1850 441455 RbcL Ribulose 1,5-bisphosphate carboxylase, large subunit, or a RuBisCO-like protein [Carbohydrate transport and metabolism]. 417 matched cddid_all.tbl CDD COG1851 COG1851 441456 COG1851 Uncharacterized conserved protein, UPF0128 family [Function unknown]. 221 matched cddid_all.tbl CDD COG1852 COG1852 441457 COG1852 Predicted redox protein with CxxCxxC motif, DUF116 family [General function prediction only]. 178 matched cddid_all.tbl CDD COG1853 COG1853 441458 RutF FMN reductase RutF, DIM6/NTAB family [Energy production and conversion]. FMN reductase RutF, DIM6/NTAB family is part of the Pathway/BioSystem: Pyrimidine degradation 160 matched cddid_all.tbl CDD COG1854 COG1854 441459 LuxS S-ribosylhomocysteine lyase LuxS, autoinducer biosynthesis [Signal transduction mechanisms]. 149 matched cddid_all.tbl CDD COG1855 COG1855 441460 PilT Predicted ATPase, PilT family, contains N-terminal PIN domain [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures]. 605 matched cddid_all.tbl CDD COG1856 COG1856 441461 COG1856 Uncharacterized conserved protein, radical SAM superfamily [General function prediction only]. 314 matched cddid_all.tbl CDD COG1857 COG1857 441462 Cas7 CRISPR-Cas system type I effector complex subunit Cas7, RAMP superfamily [Defense mechanisms]. CRISPR-Cas system type I effector complex subunit Cas7, RAMP superfamily is part of the Pathway/BioSystem: CRISPR-Cas system 313 matched cddid_all.tbl CDD COG1858 COG1858 441463 MauG Cytochrome c peroxidase [Posttranslational modification, protein turnover, chaperones]. 283 matched cddid_all.tbl CDD COG1859 COG1859 441464 KptA RNA:NAD 2'-phosphotransferase, TPT1/KptA family [Translation, ribosomal structure and biogenesis]. 181 matched cddid_all.tbl CDD COG1860 COG1860 441465 COG1860 Predicted metal-binding protein, contains two cysteine clusters, UPF0179 family [Nucleotide transport and metabolism, Replication, recombination, and repair]. 145 matched cddid_all.tbl CDD COG1861 COG1861 441466 SpsF Spore coat polysaccharide biosynthesis protein SpsF, cytidylyltransferase family [Cell wall/membrane/envelope biogenesis]. 245 matched cddid_all.tbl CDD COG1862 COG1862 441467 YajC Protein translocase subunit YajC [Intracellular trafficking, secretion, and vesicular transport]. 102 matched cddid_all.tbl CDD COG1863 COG1863 441468 MnhE Multisubunit Na+/H+ antiporter, MnhE subunit [Inorganic ion transport and metabolism]. 162 matched cddid_all.tbl CDD COG1864 COG1864 441469 NUC1 DNA/RNA endonuclease G, NUC1 [Nucleotide transport and metabolism]. 238 matched cddid_all.tbl CDD COG1865 COG1865 441470 CbiZ Adenosylcobinamide amidohydrolase [Coenzyme transport and metabolism]. 224 matched cddid_all.tbl CDD COG1866 COG1866 441471 PckA Phosphoenolpyruvate carboxykinase, ATP-dependent [Energy production and conversion]. Phosphoenolpyruvate carboxykinase, ATP-dependent is part of the Pathway/BioSystem: Gluconeogenesis 529 matched cddid_all.tbl CDD COG1867 COG1867 441472 TRM1 tRNA G26 N,N-dimethylase Trm1 [Translation, ribosomal structure and biogenesis]. tRNA G26 N,N-dimethylase Trm1 is part of the Pathway/BioSystem: tRNA modification 383 matched cddid_all.tbl CDD COG1868 COG1868 441473 FliM Flagellar motor switch protein FliM [Cell motility]. 326 matched cddid_all.tbl CDD COG1869 COG1869 441474 RbsD D-ribose pyranose/furanose isomerase RbsD [Carbohydrate transport and metabolism]. 129 matched cddid_all.tbl CDD COG1871 COG1871 441475 CheD Chemotaxis receptor (MCP) glutamine deamidase CheD [Signal transduction mechanisms]. 164 matched cddid_all.tbl CDD COG1872 COG1872 441476 YggU Uncharacterized conserved protein YggU, UPF0235/DUF167 family [Function unknown]. 81 matched cddid_all.tbl CDD COG1873 COG1873 441477 YlmC Sporulation protein YlmC, YlmC/YmxH family, contains PRC-barrel domain [General function prediction only]. 70 matched cddid_all.tbl CDD COG1874 COG1874 441478 GanA Beta-galactosidase GanA [Carbohydrate transport and metabolism]. 609 matched cddid_all.tbl CDD COG1875 COG1875 441479 YlaK Predicted ribonuclease YlaK, contains NYN-type RNase and PhoH-family ATPase domains [General function prediction only]. 441 matched cddid_all.tbl CDD COG1876 COG1876 441480 LdcB LD-carboxypeptidase LdcB, LAS superfamily [Cell wall/membrane/envelope biogenesis]. 168 matched cddid_all.tbl CDD COG1877 COG1877 441481 OtsB Trehalose-6-phosphate phosphatase [Carbohydrate transport and metabolism]. 242 matched cddid_all.tbl CDD COG1878 COG1878 441482 COG1878 Kynurenine formamidase [Amino acid transport and metabolism]. 216 matched cddid_all.tbl CDD COG1879 COG1879 441483 RbsB ABC-type sugar transport system, periplasmic component, contains N-terminal xre family HTH domain [Carbohydrate transport and metabolism]. 307 matched cddid_all.tbl CDD COG1880 COG1880 441484 CdhB CO dehydrogenase/acetyl-CoA synthase epsilon subunit [Energy production and conversion]. 168 matched cddid_all.tbl CDD COG1881 COG1881 441485 PEBP Uncharacterized conserved protein, phosphatidylethanolamine-binding protein (PEBP) family [General function prediction only]. 151 matched cddid_all.tbl CDD COG1882 COG1882 441486 PflD Pyruvate-formate lyase [Energy production and conversion]. Pyruvate-formate lyase is part of the Pathway/BioSystem: Pyruvate oxidation 789 matched cddid_all.tbl CDD COG1883 COG1883 441487 OadB Na+-transporting oxaloacetate/methylmalonyl-CoA decarboxylase, beta subunit [Energy production and conversion]. 373 matched cddid_all.tbl CDD COG1884 COG1884 441488 Sbm Methylmalonyl-CoA mutase, N-terminal domain/subunit [Lipid transport and metabolism]. 533 matched cddid_all.tbl CDD COG1885 COG1885 441489 COG1885 Uncharacterized conserved protein, UPF0212 family [Function unknown]. 112 matched cddid_all.tbl CDD COG1886 COG1886 441490 FliN Flagellar motor switch/type III secretory pathway protein FliN [Cell motility, Intracellular trafficking, secretion, and vesicular transport]. 172 matched cddid_all.tbl CDD COG1887 COG1887 441491 TagB CDP-glycerol glycerophosphotransferase, TagB/SpsB family [Cell wall/membrane/envelope biogenesis, Lipid transport and metabolism]. 369 matched cddid_all.tbl CDD COG1888 COG1888 441492 COG1888 Uncharacterized conserved protein, DUF211 domain [Function unknown]. 88 matched cddid_all.tbl CDD COG1889 COG1889 441493 NOP1 Fibrillarin-like rRNA 2'-O-methylase NOP1 [Translation, ribosomal structure and biogenesis]. 222 matched cddid_all.tbl CDD COG1890 COG1890 441494 RPS3A Ribosomal protein S3AE [Translation, ribosomal structure and biogenesis]. Ribosomal protein S3AE is part of the Pathway/BioSystem: Archaeal ribosomal proteins 208 matched cddid_all.tbl CDD COG1891 COG1891 441495 MfnB 4-(hydroxymethyl)-2-furancarboxaldehyde phosphate synthase MfnB [Coenzyme transport and metabolism]. 227 matched cddid_all.tbl CDD COG1892 COG1892 441496 PpcA Phosphoenolpyruvate carboxylase [Carbohydrate transport and metabolism]. 509 matched cddid_all.tbl CDD COG1893 COG1893 441497 PanE Ketopantoate reductase [Coenzyme transport and metabolism]. Ketopantoate reductase is part of the Pathway/BioSystem: Pantothenate/CoA biosynthesis 305 matched cddid_all.tbl CDD COG1894 COG1894 441498 NuoF NADH:ubiquinone oxidoreductase, NADH-binding 51 kD subunit (chain F) [Energy production and conversion]. NADH:ubiquinone oxidoreductase, NADH-binding 51 kD subunit (chain F) is part of the Pathway/BioSystem: NADH dehydrogenase 418 matched cddid_all.tbl CDD COG1895 COG1895 441499 HEPN HEPN domain protein, predicted toxin of MNT-HEPN system [Defense mechanisms]. 120 matched cddid_all.tbl CDD COG1896 COG1896 441500 YfbR 5'-deoxynucleotidase YfbR and related HD superfamily hydrolases [Nucleotide transport and metabolism, General function prediction only]. 162 matched cddid_all.tbl CDD COG1897 COG1897 441501 MetA Homoserine O-succinyltransferase [Amino acid transport and metabolism]. Homoserine O-succinyltransferase is part of the Pathway/BioSystem: Methionine biosynthesis 309 matched cddid_all.tbl CDD COG1898 COG1898 441502 RfbC dTDP-4-dehydrorhamnose 3,5-epimerase or related enzyme [Cell wall/membrane/envelope biogenesis]. 177 matched cddid_all.tbl CDD COG1899 COG1899 441503 DYS1 Deoxyhypusine synthase [Posttranslational modification, protein turnover, chaperones, Translation, ribosomal structure and biogenesis]. 323 matched cddid_all.tbl CDD COG1900 COG1900 441504 HcyBio Sulfur incorporation enzyme MA1821 (anaerobic homocysteine biosynthesis), HcyBio/DUF39 family [Amino acid transport and metabolism]. 386 matched cddid_all.tbl CDD COG1901 COG1901 441505 TrmY tRNA pseudouridine-54 N-methylase [Translation, ribosomal structure and biogenesis]. tRNA pseudouridine-54 N-methylase is part of the Pathway/BioSystem: tRNA modification 200 matched cddid_all.tbl CDD COG1902 COG1902 441506 FadH 2,4-dienoyl-CoA reductase or related NADH-dependent reductase, Old Yellow Enzyme (OYE) family [Energy production and conversion]. 365 matched cddid_all.tbl CDD COG1903 COG1903 441507 CbiD Cobalamin biosynthesis protein CbiD (cobalt-precorrin-5B C-methyltransferase) [Coenzyme transport and metabolism]. Cobalamin biosynthesis protein CbiD (cobalt-precorrin-5B C-methyltransferase) is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 368 matched cddid_all.tbl CDD COG1904 COG1904 441508 UxaC Glucuronate isomerase [Carbohydrate transport and metabolism]. 460 matched cddid_all.tbl CDD COG1905 COG1905 441509 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit (chain E) [Energy production and conversion]. NADH:ubiquinone oxidoreductase 24 kD subunit (chain E) is part of the Pathway/BioSystem: NADH dehydrogenase 159 matched cddid_all.tbl CDD COG1906 COG1906 441510 COG1906 Predicted GntP-related membrane permease AF0261, DUF401 family [General function prediction only]. 407 matched cddid_all.tbl CDD COG1907 COG1907 441511 bRFAP Beta-ribofuranosylaminobenzene 5'-phosphate synthase (methanopterin biosynthesis) [Coenzyme transport and metabolism]. 316 matched cddid_all.tbl CDD COG1908 COG1908 441512 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]. 137 matched cddid_all.tbl CDD COG1909 COG1909 441513 DPCK Archaeal dephospho-CoA kinase [Coenzyme transport and metabolism]. 169 matched cddid_all.tbl CDD COG1910 COG1910 441514 YvgK Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]. 328 matched cddid_all.tbl CDD COG1911 COG1911 441515 RPL30E Ribosomal protein L30E [Translation, ribosomal structure and biogenesis]. Ribosomal protein L30E is part of the Pathway/BioSystem: Archaeal ribosomal proteins 97 matched cddid_all.tbl CDD COG1912 COG1912 441516 COG1912 Stereoselective (R,S)-S-adenosylmethionine hydrolase (adenosine-forming) [Coenzyme transport and metabolism, Defense mechanisms]. 257 matched cddid_all.tbl CDD COG1913 COG1913 441517 COG1913 Predicted Zn-dependent protease [General function prediction only]. 175 matched cddid_all.tbl CDD COG1914 COG1914 441518 MntH Mn2+ or Fe2+ transporter, NRAMP family [Inorganic ion transport and metabolism]. 405 matched cddid_all.tbl CDD COG1915 COG1915 441519 COG1915 Uncharacterized conserved protein AF1278, contains saccharopine dehydrogenase N-terminal (SDHN) domain [Function unknown]. 409 matched cddid_all.tbl CDD COG1916 COG1916 441520 COG1916 Pheromone shutdown protein TraB, contains GTxH motif (function unknown) [Function unknown]. 392 matched cddid_all.tbl CDD COG1917 COG1917 441521 QdoI Cupin domain protein related to quercetin dioxygenase [General function prediction only]. 99 matched cddid_all.tbl CDD COG1918 COG1918 441522 FeoA Fe2+ transport protein FeoA [Inorganic ion transport and metabolism]. 73 matched cddid_all.tbl CDD COG1920 COG1920 441523 COG1920 2-phospho-L-lactate guanylyltransferase, coenzyme F420 biosynthesis enzyme, CobY/MobA/RfbA family [Coenzyme transport and metabolism]. 205 matched cddid_all.tbl CDD COG1921 COG1921 441524 SelA Seryl-tRNA(Sec) selenium transferase [Translation, ribosomal structure and biogenesis]. 399 matched cddid_all.tbl CDD COG1922 COG1922 441525 WecG UDP-N-acetyl-D-mannosaminuronic acid transferase, WecB/TagA/CpsF family [Cell wall/membrane/envelope biogenesis]. 244 matched cddid_all.tbl CDD COG1923 COG1923 441526 Hfq sRNA-binding regulator protein Hfq [Signal transduction mechanisms]. 67 matched cddid_all.tbl CDD COG1924 COG1924 441527 YjiL Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) [Lipid transport and metabolism]. 264 matched cddid_all.tbl CDD COG1925 COG1925 441528 PtsH HPr or related phosphotransfer protein [Signal transduction mechanisms, Carbohydrate transport and metabolism]. 88 matched cddid_all.tbl CDD COG1926 COG1926 441529 COG1926 Predicted phosphoribosyltransferase [General function prediction only]. 209 matched cddid_all.tbl CDD COG1927 COG1927 441530 Mtd F420-dependent methylenetetrahydromethanopterin dehydrogenase [Energy production and conversion]. 277 matched cddid_all.tbl CDD COG1928 COG1928 441531 PMT1 Dolichyl-phosphate-mannose--protein O-mannosyl transferase [Posttranslational modification, protein turnover, chaperones]. 495 matched cddid_all.tbl CDD COG1929 COG1929 441532 GlxK Glycerate kinase [Carbohydrate transport and metabolism]. Glycerate kinase is part of the Pathway/BioSystem: Non-phosphorylated Entner-Doudoroff pathway 373 matched cddid_all.tbl CDD COG1930 COG1930 441533 CbiN ABC-type cobalt transport system, periplasmic component [Inorganic ion transport and metabolism]. 99 matched cddid_all.tbl CDD COG1931 COG1931 441534 COG1931 Predicted RNA binding protein with dsRBD fold, UPF0201 family [General function prediction only]. 141 matched cddid_all.tbl CDD COG1932 COG1932 441535 SerC Phosphoserine aminotransferase [Coenzyme transport and metabolism, Amino acid transport and metabolism]. Phosphoserine aminotransferase is part of the Pathway/BioSystem: Serine biosynthesis 358 matched cddid_all.tbl CDD COG1933 COG1933 441536 PolC Archaeal DNA polymerase II, large subunit [Replication, recombination and repair]. 1075 matched cddid_all.tbl CDD COG1934 COG1934 441537 LptA Lipopolysaccharide export system protein LptA [Cell wall/membrane/envelope biogenesis]. 164 matched cddid_all.tbl CDD COG1935 COG1935 441538 COG1935 Uncharacterized conserved protein, DUF473 domain [Function unknown]. 129 matched cddid_all.tbl CDD COG1936 COG1936 441539 Fap7 Broad-specificity NMP kinase [Nucleotide transport and metabolism]. 173 matched cddid_all.tbl CDD COG1937 COG1937 441540 FrmR DNA-binding transcriptional regulator, FrmR family [Transcription]. 82 matched cddid_all.tbl CDD COG1938 COG1938 441541 COG1938 Predicted ATP-dependent carboligase, ATP-grasp superfamily [General function prediction only]. 236 matched cddid_all.tbl CDD COG1939 COG1939 441542 MrnC 23S rRNA maturation mini-RNase III [Translation, ribosomal structure and biogenesis]. 23S rRNA maturation mini-RNase III is part of the Pathway/BioSystem: 23S rRNA modification 130 matched cddid_all.tbl CDD COG1940 COG1940 441543 NagC Sugar kinase of the NBD/HSP70 family, may contain an N-terminal HTH domain [Carbohydrate transport and metabolism, Transcription]. 306 matched cddid_all.tbl CDD COG1941 COG1941 441544 FrhG Coenzyme F420-reducing hydrogenase, gamma subunit [Energy production and conversion]. 262 matched cddid_all.tbl CDD COG1942 COG1942 441545 PptA Phenylpyruvate tautomerase PptA, 4-oxalocrotonate tautomerase family [Secondary metabolites biosynthesis, transport and catabolism]. 58 matched cddid_all.tbl CDD COG1943 COG1943 441546 RAYT REP element-mobilizing transposase RayT [Mobilome: prophages, transposons]. 138 matched cddid_all.tbl CDD COG1944 COG1944 441547 YcaO Ribosomal protein S12 methylthiotransferase accessory factor YcaO [Translation, ribosomal structure and biogenesis]. 397 matched cddid_all.tbl CDD COG1945 COG1945 441548 PdaD Pyruvoyl-dependent arginine decarboxylase [Amino acid transport and metabolism]. 158 matched cddid_all.tbl CDD COG1946 COG1946 441549 TesB Acyl-CoA thioesterase [Lipid transport and metabolism]. 273 matched cddid_all.tbl CDD COG1947 COG1947 441550 IspE 4-diphosphocytidyl-2C-methyl-D-erythritol kinase [Lipid transport and metabolism]. 4-diphosphocytidyl-2C-methyl-D-erythritol kinase is part of the Pathway/BioSystem: Isoprenoid biosynthesis 281 matched cddid_all.tbl CDD COG1948 COG1948 441551 MUS81 ERCC4-type crossover junction endonuclease [Replication, recombination and repair]. 214 matched cddid_all.tbl CDD COG1949 COG1949 441552 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]. 177 matched cddid_all.tbl CDD COG1950 COG1950 441553 YvlD Uncharacterized membrane protein YvlD, DUF360 family [Function unknown]. 116 matched cddid_all.tbl CDD COG1951 COG1951 441554 TtdA Tartrate dehydratase alpha subunit/Fumarate hydratase class I, N-terminal domain [Energy production and conversion]. Tartrate dehydratase alpha subunit/Fumarate hydratase class I, N-terminal domain is part of the Pathway/BioSystem: TCA cycle 289 matched cddid_all.tbl CDD COG1952 COG1952 441555 SecB Preprotein translocase subunit SecB [Intracellular trafficking, secretion, and vesicular transport]. 158 matched cddid_all.tbl CDD COG1953 COG1953 441556 FUI1 Cytosine/uracil/thiamine/allantoin permease [Nucleotide transport and metabolism, Coenzyme transport and metabolism]. 483 matched cddid_all.tbl CDD COG1954 COG1954 441557 GlpP Glycerol-3-phosphate responsive antiterminator (mRNA-binding) [Transcription]. 178 matched cddid_all.tbl CDD COG1955 COG1955 441558 ArlJ Archaellum biogenesis protein ArlJ/FlaJ, TadC family [Cell motility]. 525 matched cddid_all.tbl CDD COG1956 COG1956 441559 MsrC GAF domain-containing protein, putative methionine-R-sulfoxide reductase [Defense mechanisms, Signal transduction mechanisms]. 156 matched cddid_all.tbl CDD COG1957 COG1957 441560 URH1 Inosine-uridine nucleoside N-ribohydrolase [Nucleotide transport and metabolism]. Inosine-uridine nucleoside N-ribohydrolase is part of the Pathway/BioSystem: Pyrimidine salvage 310 matched cddid_all.tbl CDD COG1958 COG1958 441561 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]. 71 matched cddid_all.tbl CDD COG1959 COG1959 441562 IscR DNA-binding transcriptional regulator, IscR family [Transcription]. 141 matched cddid_all.tbl CDD COG1960 COG1960 441563 CaiA Acyl-CoA dehydrogenase related to the alkylation response protein AidB [Lipid transport and metabolism]. Acyl-CoA dehydrogenase related to the alkylation response protein AidB is part of the Pathway/BioSystem: Fatty acid biosynthesis 381 matched cddid_all.tbl CDD COG1961 COG1961 441564 SpoIVCA Site-specific DNA recombinase SpoIVCA/DNA invertase PinE [Replication, recombination and repair]. 388 matched cddid_all.tbl CDD COG1962 COG1962 441565 MtrH Tetrahydromethanopterin S-methyltransferase, subunit H [Coenzyme transport and metabolism]. 308 matched cddid_all.tbl CDD COG1963 COG1963 441566 YuiD Acid phosphatase family membrane protein YuiD [General function prediction only]. 148 matched cddid_all.tbl CDD COG1964 COG1964 441567 MoaA2 C-terminal domain of the GTP 3',8'-cyclase MoaA, radical SAM superfamily (molybdenum cofactor biosynthesis) [Coenzyme transport and metabolism]. 473 matched cddid_all.tbl CDD COG1965 COG1965 441568 CyaY Fe-S cluster assembly protein CyaY, frataxin homolog [Inorganic ion transport and metabolism]. Fe-S cluster assembly protein CyaY, frataxin homolog is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 106 matched cddid_all.tbl CDD COG1966 COG1966 441569 CstA Carbon starvation protein CstA (peptide/pyruvate transporter) [Energy production and conversion, Amino acid transport and metabolism]. 534 matched cddid_all.tbl CDD COG1967 COG1967 441570 COG1967 Uncharacterized membrane protein [Function unknown]. 290 matched cddid_all.tbl CDD COG1968 COG1968 441571 UppP Undecaprenyl pyrophosphate phosphatase [Lipid transport and metabolism]. 265 matched cddid_all.tbl CDD COG1969 COG1969 441572 HyaC Ni,Fe-hydrogenase I cytochrome b subunit [Energy production and conversion]. 228 matched cddid_all.tbl CDD COG1970 COG1970 441573 MscL Large-conductance mechanosensitive channel [Cell wall/membrane/envelope biogenesis]. 132 matched cddid_all.tbl CDD COG1971 COG1971 441574 MntP Putative Mn2+ efflux pump MntP [Inorganic ion transport and metabolism]. 180 matched cddid_all.tbl CDD COG1972 COG1972 441575 NupC Nucleoside permease NupC [Nucleotide transport and metabolism]. 406 matched cddid_all.tbl CDD COG1973 COG1973 441576 HypE2 Hydrogenase maturation factor HypE [Posttranslational modification, protein turnover, chaperones]. 441 matched cddid_all.tbl CDD COG1974 COG1974 441577 LexA SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase) [Transcription, Signal transduction mechanisms]. 199 matched cddid_all.tbl CDD COG1975 COG1975 441578 XdhC Molybdoenzyme maturation factor PaoD (Mo cofactor insertion), XdhC/CoxF family [Posttranslational modification, protein turnover, chaperones]. 303 matched cddid_all.tbl CDD COG1976 COG1976 441579 TIF6 Translation initiation factor 6 (eIF-6) [Translation, ribosomal structure and biogenesis]. Translation initiation factor 6 (eIF-6) is part of the Pathway/BioSystem: Translation factors 221 matched cddid_all.tbl CDD COG1977 COG1977 441580 MoaD Molybdopterin synthase sulfur carrier subunit MoaD [Coenzyme transport and metabolism]. Molybdopterin synthase sulfur carrier subunit MoaD is part of the Pathway/BioSystem: Molybdopterin biosynthesis 82 matched cddid_all.tbl CDD COG1978 COG1978 441581 YkuK Predicted RNase H-related nuclease YkuK, DUF458 family [General function prediction only]. 157 matched cddid_all.tbl CDD COG1979 COG1979 441582 YqdH Alcohol dehydrogenase YqhD, Fe-dependent ADH family [Energy production and conversion]. 387 matched cddid_all.tbl CDD COG1980 COG1980 441583 FbpA Archaeal fructose 1,6-bisphosphatase [Carbohydrate transport and metabolism]. 363 matched cddid_all.tbl CDD COG1981 COG1981 441584 HemJ Protoporphyrinogen oxidase HemJ (unrelated to HemG or HemY) [Coenzyme transport and metabolism]. 140 matched cddid_all.tbl CDD COG1982 COG1982 441585 LdcC Arginine/lysine/ornithine decarboxylase [Amino acid transport and metabolism]. 486 matched cddid_all.tbl CDD COG1983 COG1983 441586 PspC Phage shock protein PspC (stress-responsive transcriptional regulator) [Transcription, Signal transduction mechanisms]. 65 matched cddid_all.tbl CDD COG1984 COG1984 441587 PxpC 5-oxoprolinase subunit C/Allophanate hydrolase subunit 2 [Amino acid transport and metabolism]. 285 matched cddid_all.tbl CDD COG1985 COG1985 441588 RibD Pyrimidine reductase, riboflavin biosynthesis [Coenzyme transport and metabolism]. Pyrimidine reductase, riboflavin biosynthesis is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis 217 matched cddid_all.tbl CDD COG1986 COG1986 441589 YjjX Non-canonical (house-cleaning) NTP pyrophosphatase, all-alpha NTP-PPase family [Nucleotide transport and metabolism, Defense mechanisms]. 171 matched cddid_all.tbl CDD COG1987 COG1987 441590 FliQ Flagellar biosynthesis protein FliQ [Cell motility]. 88 matched cddid_all.tbl CDD COG1988 COG1988 441591 YbcI Membrane-bound metal-dependent hydrolase YbcI, DUF457 family [General function prediction only]. 159 matched cddid_all.tbl CDD COG1989 COG1989 441592 PulO Prepilin signal peptidase PulO (type II secretory pathway) or related peptidase [Cell motility, Intracellular trafficking, secretion, and vesicular transport]. 256 matched cddid_all.tbl CDD COG1990 COG1990 441593 Pth2 Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]. 117 matched cddid_all.tbl CDD COG1991 COG1991 441594 MJ0832 Uncharacterized conserved protein MJ0832_1, predicted component of type IV pili-like system, UPF0333 family [General function prediction only]. 135 matched cddid_all.tbl CDD COG1992 COG1992 441595 COG1992 Predicted transcriptional regulator fused phosphomethylpyrimidine kinase (thiamin biosynthesis) [General function prediction only]. 432 matched cddid_all.tbl CDD COG1993 COG1993 441596 COG1993 PII-like signaling protein [Signal transduction mechanisms]. 101 matched cddid_all.tbl CDD COG1994 COG1994 441597 SpoIVFB Zn-dependent protease (includes sporulation protein SpoIVFB) [Posttranslational modification, protein turnover, chaperones]. 175 matched cddid_all.tbl CDD COG1995 COG1995 441598 PdxA 4-hydroxy-L-threonine phosphate dehydrogenase PdxA [Coenzyme transport and metabolism]. 4-hydroxy-L-threonine phosphate dehydrogenase PdxA is part of the Pathway/BioSystem: Pyridoxal phosphate biosynthesis 330 matched cddid_all.tbl CDD COG1996 COG1996 441599 RPC10 DNA-directed RNA polymerase, subunit RPC12/RpoP, contains C4-type Zn-finger [Transcription]. DNA-directed RNA polymerase, subunit RPC12/RpoP, contains C4-type Zn-finger is part of the Pathway/BioSystem: RNA polymerase 48 matched cddid_all.tbl CDD COG1997 COG1997 441600 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]. Ribosomal protein L37AE/L43A is part of the Pathway/BioSystem: Archaeal ribosomal proteins 87 matched cddid_all.tbl CDD COG1998 COG1998 441601 RPS27ae Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]. Ribosomal protein S27AE is part of the Pathway/BioSystem: Archaeal ribosomal proteins 56 matched cddid_all.tbl CDD COG1999 COG1999 441602 Sco1 Cytochrome oxidase Cu insertion factor, SCO1/SenC/PrrC family [Posttranslational modification, protein turnover, chaperones]. 156 matched cddid_all.tbl CDD COG2000 COG2000 441603 COG2000 Uncharacterized Fe-S cluster-containing protein [General function prediction only]. 212 matched cddid_all.tbl CDD COG2001 COG2001 441604 MraZ MraZ, DNA-binding transcriptional regulator and inhibitor of RsmH methyltransferase activity [Translation, ribosomal structure and biogenesis]. 144 matched cddid_all.tbl CDD COG2002 COG2002 441605 AbrB Bifunctional DNA-binding transcriptional regulator of stationary/sporulation/toxin gene expression and antitoxin component of the YhaV-PrlF toxin-antitoxin module [Transcription, Defense mechanisms]. 70 matched cddid_all.tbl CDD COG2003 COG2003 441606 RadC DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, recombination and repair]. 224 matched cddid_all.tbl CDD COG2004 COG2004 441607 RPS24A Ribosomal protein S24E [Translation, ribosomal structure and biogenesis]. Ribosomal protein S24E is part of the Pathway/BioSystem: Archaeal ribosomal proteins 97 matched cddid_all.tbl CDD COG2005 COG2005 441608 ModE DNA-binding transcriptional regulator ModE (molybdenum-dependent) [Transcription]. 118 matched cddid_all.tbl CDD COG2006 COG2006 441609 COG2006 Uncharacterized conserved protein, DUF362 family [Function unknown]. 282 matched cddid_all.tbl CDD COG2007 COG2007 441610 RPS8A Ribosomal protein S8E [Translation, ribosomal structure and biogenesis]. Ribosomal protein S8E is part of the Pathway/BioSystem: Archaeal ribosomal proteins 127 matched cddid_all.tbl CDD COG2008 COG2008 441611 GLY1 Threonine aldolase [Amino acid transport and metabolism]. 333 matched cddid_all.tbl CDD COG2009 COG2009 441612 SdhC Succinate dehydrogenase/fumarate reductase, cytochrome b subunit [Energy production and conversion]. 128 matched cddid_all.tbl CDD COG2010 COG2010 441613 CccA Cytochrome c, mono- and diheme variants [Energy production and conversion]. 169 matched cddid_all.tbl CDD COG2011 COG2011 441614 MetP ABC-type methionine transport system, permease component [Amino acid transport and metabolism]. 220 matched cddid_all.tbl CDD COG2012 COG2012 441615 RPB5 DNA-directed RNA polymerase, subunit H, RpoH/RPB5 [Transcription]. DNA-directed RNA polymerase, subunit H, RpoH/RPB5 is part of the Pathway/BioSystem: RNA polymerase 80 matched cddid_all.tbl CDD COG2013 COG2013 441616 AIM24 AIM24 protein, required for mitochondrial respiration [Energy production and conversion]. 210 matched cddid_all.tbl CDD COG2014 COG2014 441617 COG2014 Uncharacterized conserved protein, contains DUF4213 and DUF364 domains [Function unknown]. 249 matched cddid_all.tbl CDD COG2015 COG2015 441618 BDS1 Alkyl sulfatase BDS1 and related hydrolases, metallo-beta-lactamase superfamily [Secondary metabolites biosynthesis, transport and catabolism]. 629 matched cddid_all.tbl CDD COG2016 COG2016 441619 Tma20 Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ribosomal structure and biogenesis]. 154 matched cddid_all.tbl CDD COG2017 COG2017 441620 GalM Galactose mutarotase or related enzyme [Carbohydrate transport and metabolism]. 309 matched cddid_all.tbl CDD COG2018 COG2018 441621 COG2018 Predicted regulator of Ras-like GTPase activity, Roadblock/LC7/MglB family [Signal transduction mechanisms]. 123 matched cddid_all.tbl CDD COG2019 COG2019 441622 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]. 172 matched cddid_all.tbl CDD COG2020 COG2020 441623 STE14 Protein-S-isoprenylcysteine O-methyltransferase Ste14 [Posttranslational modification, protein turnover, chaperones]. 113 matched cddid_all.tbl CDD COG2021 COG2021 441624 MET2 Homoserine O-acetyltransferase [Amino acid transport and metabolism]. Homoserine O-acetyltransferase is part of the Pathway/BioSystem: Methionine biosynthesis 355 matched cddid_all.tbl CDD COG2022 COG2022 441625 ThiG Thiazole synthase ThiGH, ThiG subunit (thiamin biosynthesis) [Coenzyme transport and metabolism]. Thiazole synthase ThiGH, ThiG subunit (thiamin biosynthesis) is part of the Pathway/BioSystem: Thiamine biosynthesis 259 matched cddid_all.tbl CDD COG2023 COG2023 441626 RPR2 Ribonuclease P protein subunit RPR2 [Translation, ribosomal structure and biogenesis]. 90 matched cddid_all.tbl CDD COG2024 COG2024 441627 SepRS O-phosphoseryl-tRNA(Cys) synthetase [Translation, ribosomal structure and biogenesis]. O-phosphoseryl-tRNA(Cys) synthetase is part of the Pathway/BioSystem: Aminoacyl-tRNA synthetases 528 matched cddid_all.tbl CDD COG2025 COG2025 441628 FixB Electron transfer flavoprotein, alpha subunit FixB [Energy production and conversion]. 323 matched cddid_all.tbl CDD COG2026 COG2026 441629 RelE mRNA-degrading endonuclease RelE, toxin component of the RelBE toxin-antitoxin system [Defense mechanisms]. 85 matched cddid_all.tbl CDD COG2027 COG2027 441630 DacB D-alanyl-D-alanine carboxypeptidase [Cell wall/membrane/envelope biogenesis]. 464 matched cddid_all.tbl CDD COG2028 COG2028 441631 ASCH ASCH domain, putative RNA-binding protein, DUF365 family [General function prediction only]. 107 matched cddid_all.tbl CDD COG2029 COG2029 441632 COG2029 Uncharacterized conserved protein, DUF366 domain [Function unknown]. 186 matched cddid_all.tbl CDD COG2030 COG2030 441633 MaoC Acyl-CoA dehydratase PaaZ [Lipid transport and metabolism]. 140 matched cddid_all.tbl CDD COG2031 COG2031 441634 AtoE Short chain fatty acids transporter [Lipid transport and metabolism]. 442 matched cddid_all.tbl CDD COG2032 COG2032 441635 SodC Cu/Zn superoxide dismutase [Inorganic ion transport and metabolism]. 171 matched cddid_all.tbl CDD COG2033 COG2033 441636 SORL Desulfoferrodoxin, superoxide reductase-like (SORL) domain [Energy production and conversion]. 125 matched cddid_all.tbl CDD COG2034 COG2034 441637 COG2034 Uncharacterized membrane protein, DUF131 family [Function unknown]. 80 matched cddid_all.tbl CDD COG2035 COG2035 441638 COG2035 Uncharacterized membrane protein, DUF368 family [Function unknown]. 291 matched cddid_all.tbl CDD COG2036 COG2036 441639 HHT1 Archaeal histone H3/H4 [Chromatin structure and dynamics]. 67 matched cddid_all.tbl CDD COG2037 COG2037 441640 Ftr Formylmethanofuran:tetrahydromethanopterin formyltransferase [Energy production and conversion]. 296 matched cddid_all.tbl CDD COG2038 COG2038 441641 CobT NaMN:DMB phosphoribosyltransferase [Coenzyme transport and metabolism]. NaMN:DMB phosphoribosyltransferase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 351 matched cddid_all.tbl CDD COG2039 COG2039 441642 Pcp Pyrrolidone-carboxylate peptidase (N-terminal pyroglutamyl peptidase) [Posttranslational modification, protein turnover, chaperones]. 203 matched cddid_all.tbl CDD COG2040 COG2040 441643 MHT1 Homocysteine/selenocysteine methylase (S-methylmethionine-dependent) [Amino acid transport and metabolism]. 301 matched cddid_all.tbl CDD COG2041 COG2041 441644 MsrP Molybdopterin-dependent catalytic subunit of periplasmic DMSO/TMAO and protein-methionine-sulfoxide reductases [Energy production and conversion]. 183 matched cddid_all.tbl CDD COG2042 COG2042 441645 Tsr3 Ribosome biogenesis protein Tsr3 (rRNA maturation) [Translation, ribosomal structure and biogenesis]. 170 matched cddid_all.tbl CDD COG2043 COG2043 441646 COG2043 Uncharacterized conserved protein, DUF169 family [Function unknown]. 237 matched cddid_all.tbl CDD COG2044 COG2044 441647 COG2044 Predicted peroxiredoxin, DsrE/DsrF-like family [General function prediction only]. 121 matched cddid_all.tbl CDD COG2045 COG2045 441648 ComB Phosphosulfolactate phosphohydrolase or related enzyme [Coenzyme transport and metabolism]. 240 matched cddid_all.tbl CDD COG2046 COG2046 441649 MET3 ATP sulfurylase (sulfate adenylyltransferase) [Inorganic ion transport and metabolism]. ATP sulfurylase (sulfate adenylyltransferase) is part of the Pathway/BioSystem: Cysteine biosynthesis 388 matched cddid_all.tbl CDD COG2047 COG2047 441650 COG2047 Proteasome assembly chaperone (PAC2) family protein [General function prediction only]. 253 matched cddid_all.tbl CDD COG2048 COG2048 441651 HdrB Heterodisulfide reductase, subunit B [Energy production and conversion]. 285 matched cddid_all.tbl CDD COG2049 COG2049 441652 PxpB 5-oxoprolinase subunit B/Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]. 229 matched cddid_all.tbl CDD COG2050 COG2050 441653 PaaI Acyl-CoA thioesterase PaaI, contains HGG motif [Secondary metabolites biosynthesis, transport and catabolism]. 138 matched cddid_all.tbl CDD COG2051 COG2051 441654 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]. Ribosomal protein S27E is part of the Pathway/BioSystem: Archaeal ribosomal proteins 60 matched cddid_all.tbl CDD COG2052 COG2052 441655 RemA Regulator of extracellular matrix RemA, YlzA/DUF370 family [Cell wall/membrane/envelope biogenesis]. 78 matched cddid_all.tbl CDD COG2053 COG2053 441656 RPS28A Ribosomal protein S28E/S33 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S28E/S33 is part of the Pathway/BioSystem: Archaeal ribosomal proteins 73 matched cddid_all.tbl CDD COG2054 COG2054 441657 MfnE 5-(aminomethyl)-3-furanmethanol-phosphate kinase MfnE (methanofuran biosynthesis) [Coenzyme transport and metabolism]. 206 matched cddid_all.tbl CDD COG2055 COG2055 441658 AllD Malate/lactate/ureidoglycolate dehydrogenase, LDH2 family [Energy production and conversion]. Malate/lactate/ureidoglycolate dehydrogenase, LDH2 family is part of the Pathway/BioSystem: TCA cycle 337 matched cddid_all.tbl CDD COG2056 COG2056 441659 YuiF Predicted histidine transporter YuiF, NhaC family [Amino acid transport and metabolism]. 439 matched cddid_all.tbl CDD COG2057 COG2057 441660 AtoA Acyl-CoA:acetate/3-ketoacid CoA transferase, beta subunit [Lipid transport and metabolism]. 235 matched cddid_all.tbl CDD COG2058 COG2058 441661 RPP1A Ribosomal protein L12E/L44/L45/RPP1/RPP2 [Translation, ribosomal structure and biogenesis]. Ribosomal protein L12E/L44/L45/RPP1/RPP2 is part of the Pathway/BioSystem: Archaeal ribosomal proteins 103 matched cddid_all.tbl CDD COG2059 COG2059 441662 ChrA Chromate transport protein ChrA [Inorganic ion transport and metabolism]. 174 matched cddid_all.tbl CDD COG2060 COG2060 441663 KdpA K+-transporting ATPase, KdpA subunit [Inorganic ion transport and metabolism]. 565 matched cddid_all.tbl CDD COG2061 COG2061 441664 COG2061 Uncharacterized conserved protein, contains ACT domain [General function prediction only]. 401 matched cddid_all.tbl CDD COG2062 COG2062 441665 SixA Phosphohistidine phosphatase SixA [Signal transduction mechanisms]. 153 matched cddid_all.tbl CDD COG2063 COG2063 441666 FlgH Flagellar basal body L-ring protein FlgH [Cell motility]. 218 matched cddid_all.tbl CDD COG2064 COG2064 441667 TadC Flp pilus assembly protein TadC [Extracellular structures]. 191 matched cddid_all.tbl CDD COG2065 COG2065 441668 PyrR Pyrimidine operon attenuation protein PyrR/uracil phosphoribosyltransferase [Nucleotide transport and metabolism]. Pyrimidine operon attenuation protein PyrR/uracil phosphoribosyltransferase is part of the Pathway/BioSystem: Pyrimidine salvage 178 matched cddid_all.tbl CDD COG2066 COG2066 441669 GlsA Glutaminase [Amino acid transport and metabolism]. 300 matched cddid_all.tbl CDD COG2067 COG2067 441670 FadL Long-chain fatty acid transport protein [Lipid transport and metabolism]. 403 matched cddid_all.tbl CDD COG2068 COG2068 441671 MocA CTP:molybdopterin cytidylyltransferase MocA [Coenzyme transport and metabolism]. 195 matched cddid_all.tbl CDD COG2069 COG2069 441672 CdhD CO dehydrogenase/acetyl-CoA synthase delta subunit (corrinoid Fe-S protein) [Energy production and conversion]. 317 matched cddid_all.tbl CDD COG2070 COG2070 441673 YrpB NAD(P)H-dependent flavin oxidoreductase YrpB, nitropropane dioxygenase family [General function prediction only]. 302 matched cddid_all.tbl CDD COG2071 COG2071 441674 PuuD Gamma-glutamyl-gamma-aminobutyrate hydrolase PuuD (putrescine degradation), contains GATase1-like domain [Amino acid transport and metabolism]. 231 matched cddid_all.tbl CDD COG2072 COG2072 441675 CzcO Predicted flavoprotein CzcO associated with the cation diffusion facilitator CzcD [Inorganic ion transport and metabolism]. 414 matched cddid_all.tbl CDD COG2073 COG2073 441676 CbiG Cobalamin biosynthesis protein CbiG [Coenzyme transport and metabolism]. Cobalamin biosynthesis protein CbiG is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 334 matched cddid_all.tbl CDD COG2074 COG2074 441677 Pgk2 2-phosphoglycerate kinase/Mevalonate-3-phosphate 5-kinase [Carbohydrate transport and metabolism, Lipid transport and metabolism]. 207 matched cddid_all.tbl CDD COG2075 COG2075 441678 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]. Ribosomal protein L24E is part of the Pathway/BioSystem: Archaeal ribosomal proteins 63 matched cddid_all.tbl CDD COG2076 COG2076 441679 EmrE Multidrug transporter EmrE and related cation transporters [Defense mechanisms]. 105 matched cddid_all.tbl CDD COG2077 COG2077 441680 Tpx Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]. 168 matched cddid_all.tbl CDD COG2078 COG2078 441681 AMMECR1 Predicted RNA modification protein, AMMECR1 domain [General function prediction only]. 184 matched cddid_all.tbl CDD COG2079 COG2079 441682 PrpD 2-methylcitrate dehydratase PrpD [Carbohydrate transport and metabolism]. 446 matched cddid_all.tbl CDD COG2080 COG2080 441683 CutS Aldehyde, CO, or xanthine dehydrogenase, Fe-S subunit, CoxS/CutS family [Energy production and conversion]. Aldehyde, CO, or xanthine dehydrogenase, Fe-S subunit, CoxS/CutS family is part of the Pathway/BioSystem: Non-phosphorylated Entner-Doudoroff pathway 155 matched cddid_all.tbl CDD COG2081 COG2081 441684 YhiN Predicted flavoprotein YhiN [General function prediction only]. 402 matched cddid_all.tbl CDD COG2082 COG2082 441685 CobH Precorrin-8X methylmutase CbiC/CobH [Coenzyme transport and metabolism]. Precorrin-8X methylmutase CbiC/CobH is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 203 matched cddid_all.tbl CDD COG2083 COG2083 441686 COG2083 Uncharacterized conserved protein, UPF0216 family [Function unknown]. 137 matched cddid_all.tbl CDD COG2084 COG2084 441687 MmsB 3-hydroxyisobutyrate dehydrogenase or related beta-hydroxyacid dehydrogenase [Lipid transport and metabolism]. 285 matched cddid_all.tbl CDD COG2085 COG2085 441688 COG2085 Predicted dinucleotide-binding enzyme [General function prediction only]. 205 matched cddid_all.tbl CDD COG2086 COG2086 441689 FixA Electron transfer flavoprotein, alpha and beta subunits [Energy production and conversion]. 261 matched cddid_all.tbl CDD COG2087 COG2087 441690 CobU Adenosyl cobinamide kinase/adenosyl cobinamide phosphate guanylyltransferase [Coenzyme transport and metabolism]. Adenosyl cobinamide kinase/adenosyl cobinamide phosphate guanylyltransferase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 172 matched cddid_all.tbl CDD COG2088 COG2088 441691 SpoVG DNA-binding protein SpoVG, cell septation regulator [Cell cycle control, cell division, chromosome partitioning]. 84 matched cddid_all.tbl CDD COG2089 COG2089 441692 SpsE Sialic acid synthase SpsE, contains C-terminal SAF domain [Cell wall/membrane/envelope biogenesis]. 335 matched cddid_all.tbl CDD COG2090 COG2090 441693 COG2090 Uncharacterized conserved protein, DUF371 domain [Function unknown]. 140 matched cddid_all.tbl CDD COG2091 COG2091 441694 Sfp Phosphopantetheinyl transferase [Coenzyme transport and metabolism]. 177 matched cddid_all.tbl CDD COG2092 COG2092 441695 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]. Translation elongation factor EF-1beta is part of the Pathway/BioSystem: Translation factors 89 matched cddid_all.tbl CDD COG2093 COG2093 441696 Spt4 RNA polymerase subunit RPABC4/transcription elongation factor Spt4 [Transcription]. RNA polymerase subunit RPABC4/transcription elongation factor Spt4 is part of the Pathway/BioSystem: RNA polymerase 63 matched cddid_all.tbl CDD COG2094 COG2094 441697 Mpg 3-methyladenine DNA glycosylase Mpg [Replication, recombination and repair]. 193 matched cddid_all.tbl CDD COG2095 COG2095 441698 MarC Small neutral amino acid transporter SnatA, MarC family [Amino acid transport and metabolism]. 206 matched cddid_all.tbl CDD COG2096 COG2096 441699 PduO Cob(II)alamin adenosyltransferase [Coenzyme transport and metabolism]. Cob(II)alamin adenosyltransferase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 180 matched cddid_all.tbl CDD COG2097 COG2097 441700 RPL31A Ribosomal protein L31E [Translation, ribosomal structure and biogenesis]. Ribosomal protein L31E is part of the Pathway/BioSystem: Archaeal ribosomal proteins 89 matched cddid_all.tbl CDD COG2098 COG2098 441701 MptD 7,8-dihydroneopterin aldolase MptD (tetrahydrofolate and tetrahydromethanopterin biosynthesis) [Coenzyme transport and metabolism]. 117 matched cddid_all.tbl CDD COG2099 COG2099 441702 CobK Precorrin-6x reductase [Coenzyme transport and metabolism]. Precorrin-6x reductase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 251 matched cddid_all.tbl CDD COG2100 COG2100 441703 COG2100 Uncharacterized Fe-S cluster-containing enzyme, radical SAM superfamily [General function prediction only]. 344 matched cddid_all.tbl CDD COG2101 COG2101 441704 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]. 180 matched cddid_all.tbl CDD COG2102 COG2102 441705 Dph6 Diphthamide synthase (EF-2-diphthine--ammonia ligase) [Translation, ribosomal structure and biogenesis]. 213 matched cddid_all.tbl CDD COG2103 COG2103 441706 MurQ N-acetylmuramic acid 6-phosphate (MurNAc-6-P) etherase [Cell wall/membrane/envelope biogenesis]. 301 matched cddid_all.tbl CDD COG2104 COG2104 441707 ThiS Sulfur carrier protein ThiS (thiamine biosynthesis) [Coenzyme transport and metabolism]. Sulfur carrier protein ThiS (thiamine biosynthesis) is part of the Pathway/BioSystem: Thiamine biosynthesis 66 matched cddid_all.tbl CDD COG2105 COG2105 441708 YtfP Predicted gamma-glutamylamine cyclotransferase YtfP, GGCT/AIG2-like family [Amino acid transport and metabolism]. 114 matched cddid_all.tbl CDD COG2106 COG2106 441709 MTH1 Predicted RNA methylase MTH1, SPOUT superfamily [General function prediction only]. 266 matched cddid_all.tbl CDD COG2107 COG2107 441710 MqnD 1,4-dihydroxy-6-naphtoate synthase (menaquinone biosynthesis, futalosine pathway) [Coenzyme transport and metabolism]. 1,4-dihydroxy-6-naphtoate synthase (menaquinone biosynthesis, futalosine pathway) is part of the Pathway/BioSystem: Menaquinone biosynthesis 276 matched cddid_all.tbl CDD COG2108 COG2108 441711 COG2108 Uncharacterized radical SAM domain-containing protein [Function unknown]. 361 matched cddid_all.tbl CDD COG2109 COG2109 441712 BtuR ATP:corrinoid adenosyltransferase [Coenzyme transport and metabolism]. ATP:corrinoid adenosyltransferase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 182 matched cddid_all.tbl CDD COG2110 COG2110 441713 YmdB O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ribosomal structure and biogenesis]. 168 matched cddid_all.tbl CDD COG2111 COG2111 441714 MnhB Multisubunit Na+/H+ antiporter, MnhB subunit [Inorganic ion transport and metabolism]. 750 matched cddid_all.tbl CDD COG2112 COG2112 441715 COG2112 Predicted Ser/Thr protein kinase [Signal transduction mechanisms]. 225 matched cddid_all.tbl CDD COG2113 COG2113 441716 ProX ABC-type proline/glycine betaine transport system, periplasmic component [Amino acid transport and metabolism]. 297 matched cddid_all.tbl CDD COG2114 COG2114 441717 AcyC Adenylate cyclase, class 3 [Signal transduction mechanisms]. 407 matched cddid_all.tbl CDD COG2115 COG2115 441718 XylA Xylose isomerase [Carbohydrate transport and metabolism]. 439 matched cddid_all.tbl CDD COG2116 COG2116 441719 FocA Formate/nitrite transporter FocA, FNT family [Inorganic ion transport and metabolism]. 258 matched cddid_all.tbl CDD COG2117 COG2117 441720 COG2117 Predicted subunit of tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]. Predicted subunit of tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain is part of the Pathway/BioSystem: tRNA modification 196 matched cddid_all.tbl CDD COG2118 COG2118 441721 PDCD5 DNA-binding TFAR19-related protein, PDSD5 family [General function prediction only]. 114 matched cddid_all.tbl CDD COG2119 COG2119 441722 Gdt1 Putative Ca2+/H+ antiporter, TMEM165/GDT1 family [General function prediction only]. 192 matched cddid_all.tbl CDD COG2120 COG2120 441723 LmbE N-acetylglucosaminyl deacetylase, LmbE family [Carbohydrate transport and metabolism]. 201 matched cddid_all.tbl CDD COG2121 COG2121 441724 COG2121 Uncharacterized conserved protein, lysophospholipid acyltransferase (LPLAT) superfamily [Function unknown]. 225 matched cddid_all.tbl CDD COG2122 COG2122 441725 COG2122 Uncharacterized conserved protein, UPF0280 family, ApbE superfamily [Function unknown]. 240 matched cddid_all.tbl CDD COG2123 COG2123 441726 Rrp42 Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Intracellular trafficking, secretion, and vesicular transport]. 264 matched cddid_all.tbl CDD COG2124 COG2124 441727 CypX Cytochrome P450 [Secondary metabolites biosynthesis, transport and catabolism, Defense mechanisms]. Cytochrome P450 is part of the Pathway/BioSystem: Biotin biosynthesis 400 matched cddid_all.tbl CDD COG2125 COG2125 441728 RPS6A Ribosomal protein S6E (S10) [Translation, ribosomal structure and biogenesis]. Ribosomal protein S6E (S10) is part of the Pathway/BioSystem: Archaeal ribosomal proteins 133 matched cddid_all.tbl CDD COG2126 COG2126 441729 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]. Ribosomal protein L37E is part of the Pathway/BioSystem: Archaeal ribosomal proteins 52 matched cddid_all.tbl CDD COG2127 COG2127 441730 ClpS ATP-dependent Clp protease adapter protein ClpS [Posttranslational modification, protein turnover, chaperones]. 94 matched cddid_all.tbl CDD COG2128 COG2128 441731 YciW Alkylhydroperoxidase family enzyme, contains CxxC motif [Inorganic ion transport and metabolism]. 142 matched cddid_all.tbl CDD COG2129 COG2129 441732 COG2129 Predicted phosphoesterase, related to the Icc protein [General function prediction only]. 211 matched cddid_all.tbl CDD COG2130 COG2130 441733 CurA NADPH-dependent curcumin reductase CurA [Secondary metabolites biosynthesis, transport and catabolism, General function prediction only]. 333 matched cddid_all.tbl CDD COG2131 COG2131 441734 ComEB Deoxycytidylate deaminase [Nucleotide transport and metabolism]. 154 matched cddid_all.tbl CDD COG2132 COG2132 441735 SufI Multicopper oxidase with three cupredoxin domains (includes cell division protein FtsP and spore coat protein CotA) [Cell cycle control, cell division, chromosome partitioning, Inorganic ion transport and metabolism, Cell wall/membrane/envelope biogenesis]. 423 matched cddid_all.tbl CDD COG2133 COG2133 441736 YliI Glucose/arabinose dehydrogenase, beta-propeller fold [Carbohydrate transport and metabolism]. 365 matched cddid_all.tbl CDD COG2134 COG2134 441737 Cdh CDP-diacylglycerol pyrophosphatase [Lipid transport and metabolism]. 255 matched cddid_all.tbl CDD COG2135 COG2135 441738 SRAP ssDNA abasic site-binding protein YedK/HMCES, SRAP family [Replication, recombination and repair]. 222 matched cddid_all.tbl CDD COG2136 COG2136 441739 IMP4 rRNA maturation protein Rpf1, contains Brix/IMP4 (anticodon-binding) domain [Translation, ribosomal structure and biogenesis]. rRNA maturation protein Rpf1, contains Brix/IMP4 (anticodon-binding) domain is part of the Pathway/BioSystem: 16S rRNA modification 173 matched cddid_all.tbl CDD COG2137 COG2137 441740 RecX SOS response regulatory protein OraA/RecX, interacts with RecA [Posttranslational modification, protein turnover, chaperones]. 154 matched cddid_all.tbl CDD COG2138 COG2138 441741 SirB Sirohydrochlorin ferrochelatase [Coenzyme transport and metabolism]. Sirohydrochlorin ferrochelatase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 230 matched cddid_all.tbl CDD COG2139 COG2139 441742 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]. Ribosomal protein L21E is part of the Pathway/BioSystem: Archaeal ribosomal proteins 96 matched cddid_all.tbl CDD COG2140 COG2140 441743 OxdD Oxalate decarboxylase/archaeal phosphoglucose isomerase, cupin superfamily [Carbohydrate transport and metabolism]. Oxalate decarboxylase/archaeal phosphoglucose isomerase, cupin superfamily is part of the Pathway/BioSystem: Glycolysis 115 matched cddid_all.tbl CDD COG2141 COG2141 441744 SsuD Flavin-dependent oxidoreductase, luciferase family (includes alkanesulfonate monooxygenase SsuD and methylene tetrahydromethanopterin reductase) [Coenzyme transport and metabolism, General function prediction only]. Flavin-dependent oxidoreductase, luciferase family (includes alkanesulfonate monooxygenase SsuD and methylene tetrahydromethanopterin reductase) is part of the Pathway/BioSystem: Pyrimidine degradation 301 matched cddid_all.tbl CDD COG2142 COG2142 441745 SdhD Succinate dehydrogenase, hydrophobic anchor subunit [Energy production and conversion]. 124 matched cddid_all.tbl CDD COG2143 COG2143 441746 SoxW Thioredoxin-related protein SoxW [Posttranslational modification, protein turnover, chaperones]. 146 matched cddid_all.tbl CDD COG2144 COG2144 441747 COG2144 Selenophosphate synthetase-related protein [General function prediction only]. 323 matched cddid_all.tbl CDD COG2145 COG2145 441748 ThiM Hydroxyethylthiazole kinase, sugar kinase family [Coenzyme transport and metabolism]. Hydroxyethylthiazole kinase, sugar kinase family is part of the Pathway/BioSystem: Thiamine biosynthesis 264 matched cddid_all.tbl CDD COG2146 COG2146 441749 NirD Ferredoxin subunit of nitrite reductase or a ring-hydroxylating dioxygenase [Inorganic ion transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism]. 103 matched cddid_all.tbl CDD COG2147 COG2147 441750 RPL19A Ribosomal protein L19E [Translation, ribosomal structure and biogenesis]. Ribosomal protein L19E is part of the Pathway/BioSystem: Archaeal ribosomal proteins 148 matched cddid_all.tbl CDD COG2148 COG2148 441751 WcaJ Sugar transferase involved in LPS biosynthesis (colanic, teichoic acid) [Cell wall/membrane/envelope biogenesis]. 322 matched cddid_all.tbl CDD COG2149 COG2149 441752 YidH Uncharacterized membrane protein YidH, DUF202 family [Function unknown]. 126 matched cddid_all.tbl CDD COG2150 COG2150 441753 COG2150 Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only]. 167 matched cddid_all.tbl CDD COG2151 COG2151 441754 PaaD Metal-sulfur cluster biosynthetic enzyme [Posttranslational modification, protein turnover, chaperones]. 102 matched cddid_all.tbl CDD COG2152 COG2152 441755 COG2152 Predicted glycosyl hydrolase, GH43/DUF377 family [Carbohydrate transport and metabolism]. 304 matched cddid_all.tbl CDD COG2153 COG2153 441756 ElaA Predicted N-acyltransferase, GNAT family [General function prediction only]. 134 matched cddid_all.tbl CDD COG2154 COG2154 441757 PhhB Pterin-4a-carbinolamine dehydratase [Coenzyme transport and metabolism]. 99 matched cddid_all.tbl CDD COG2155 COG2155 441758 YuzA Uncharacterized membrane protein YuzA, DUF378 family [Function unknown]. 70 matched cddid_all.tbl CDD COG2156 COG2156 441759 KdpC K+-transporting ATPase, KdpC subunit [Inorganic ion transport and metabolism]. 188 matched cddid_all.tbl CDD COG2157 COG2157 441760 RPL20A Ribosomal protein L20A (L18A) [Translation, ribosomal structure and biogenesis]. Ribosomal protein L20A (L18A) is part of the Pathway/BioSystem: Archaeal ribosomal proteins 75 matched cddid_all.tbl CDD COG2158 COG2158 441761 COG2158 Uncharacterized conserved protein, contains a Zn-finger-like domain [General function prediction only]. 107 matched cddid_all.tbl CDD COG2159 COG2159 441762 LigW 5-carboxyvanillate decarboxylase LigW (lignin degradation), amidohydro domain [Carbohydrate transport and metabolism]. 253 matched cddid_all.tbl CDD COG2160 COG2160 441763 AraA L-arabinose isomerase [Carbohydrate transport and metabolism]. 495 matched cddid_all.tbl CDD COG2161 COG2161 441764 StbD Antitoxin component YafN of the YafNO toxin-antitoxin module, PHD/YefM family [Defense mechanisms]. 83 matched cddid_all.tbl CDD COG2162 COG2162 441765 NhoA Arylamine N-acetyltransferase [Secondary metabolites biosynthesis, transport and catabolism]. 256 matched cddid_all.tbl CDD COG2163 COG2163 441766 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]. Ribosomal protein L14E/L6E/L27E is part of the Pathway/BioSystem: Ribosome 50S subunit 88 matched cddid_all.tbl CDD COG2164 COG2164 441767 COG2164 Uncharacterized protein with cyclophilin fold, contains DUF369 domain [General function prediction only]. 122 matched cddid_all.tbl CDD COG2165 COG2165 441768 PulG Type II secretory pathway, pseudopilin PulG [Cell motility, Intracellular trafficking, secretion, and vesicular transport, Extracellular structures]. 99 matched cddid_all.tbl CDD COG2166 COG2166 441769 SufE Sulfur transfer protein SufE, Fe-S cluster assembly [Posttranslational modification, protein turnover, chaperones]. 140 matched cddid_all.tbl CDD COG2167 COG2167 441770 RPL39 Ribosomal protein L39E [Translation, ribosomal structure and biogenesis]. Ribosomal protein L39E is part of the Pathway/BioSystem: Archaeal ribosomal proteins 51 matched cddid_all.tbl CDD COG2168 COG2168 441771 TusB Sulfur transfer complex TusBCD TusB component, DsrH family [Translation, ribosomal structure and biogenesis]. 96 matched cddid_all.tbl CDD COG2169 COG2169 441772 AdaA Methylphosphotriester-DNA--protein-cysteine methyltransferase (N-terminal fragment of Ada), contains Zn-binding and two AraC-type DNA-binding domains [Replication, recombination and repair]. 358 matched cddid_all.tbl CDD COG2170 COG2170 441773 YbdK Gamma-glutamyl:cysteine ligase YbdK, ATP-grasp superfamily [Posttranslational modification, protein turnover, chaperones]. 373 matched cddid_all.tbl CDD COG2171 COG2171 441774 DapD Tetrahydrodipicolinate N-succinyltransferase [Amino acid transport and metabolism]. Tetrahydrodipicolinate N-succinyltransferase is part of the Pathway/BioSystem: Lysine biosynthesis 268 matched cddid_all.tbl CDD COG2172 COG2172 441775 RsbW Anti-sigma regulatory factor (Ser/Thr protein kinase) [Signal transduction mechanisms]. 127 matched cddid_all.tbl CDD COG2173 COG2173 441776 DdpX D-alanyl-D-alanine dipeptidase [Cell wall/membrane/envelope biogenesis]. 207 matched cddid_all.tbl CDD COG2174 COG2174 441777 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]. Ribosomal protein L34E is part of the Pathway/BioSystem: Archaeal ribosomal proteins 88 matched cddid_all.tbl CDD COG2175 COG2175 441778 TauD Taurine dioxygenase, alpha-ketoglutarate-dependent [Secondary metabolites biosynthesis, transport and catabolism]. 275 matched cddid_all.tbl CDD COG2176 COG2176 441779 PolC DNA polymerase III, alpha subunit (gram-positive type) [Replication, recombination and repair]. 181 matched cddid_all.tbl CDD COG2177 COG2177 441780 FtsX Cell division protein FtsX [Cell cycle control, cell division, chromosome partitioning]. 292 matched cddid_all.tbl CDD COG2178 COG2178 441781 COG2178 Predicted RNA- or ssDNA-binding protein, translin family [General function prediction only]. 205 matched cddid_all.tbl CDD COG2179 COG2179 441782 YqeG Predicted phosphohydrolase YqeG, HAD superfamily [General function prediction only]. 164 matched cddid_all.tbl CDD COG2180 COG2180 441783 NarJ Nitrate reductase assembly protein NarJ, required for insertion of molybdenum cofactor [Energy production and conversion, Inorganic ion transport and metabolism, Posttranslational modification, protein turnover, chaperones]. 181 matched cddid_all.tbl CDD COG2181 COG2181 441784 NarI Nitrate reductase gamma subunit [Energy production and conversion, Inorganic ion transport and metabolism]. 230 matched cddid_all.tbl CDD COG2182 COG2182 441785 MalE Maltose-binding periplasmic protein MalE [Carbohydrate transport and metabolism]. 410 matched cddid_all.tbl CDD COG2183 COG2183 441786 Tex Transcriptional accessory protein Tex/SPT6 [Transcription]. 719 matched cddid_all.tbl CDD COG2184 COG2184 441787 FIDO Fido, protein-threonine AMPylation domain [Signal transduction mechanisms]. 196 matched cddid_all.tbl CDD COG2185 COG2185 441788 Sbm Methylmalonyl-CoA mutase, C-terminal domain/subunit (cobalamin-binding) [Lipid transport and metabolism]. 134 matched cddid_all.tbl CDD COG2186 COG2186 441789 FadR DNA-binding transcriptional regulator, FadR family [Transcription]. 232 matched cddid_all.tbl CDD COG2187 COG2187 441790 COG2187 Aminoglycoside phosphotransferase family enzyme [General function prediction only]. 341 matched cddid_all.tbl CDD COG2188 COG2188 441791 MngR DNA-binding transcriptional regulator, GntR family [Transcription]. 238 matched cddid_all.tbl CDD COG2189 COG2189 441792 Mod Adenine specific DNA methylase Mod [Replication, recombination and repair]. 491 matched cddid_all.tbl CDD COG2190 COG2190 441793 NagE Phosphotransferase system IIA component [Carbohydrate transport and metabolism]. 154 matched cddid_all.tbl CDD COG2191 COG2191 441794 FwdE Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]. 192 matched cddid_all.tbl CDD COG2192 COG2192 441795 COG2192 Predicted carbamoyl transferase, NodU family [General function prediction only]. 568 matched cddid_all.tbl CDD COG2193 COG2193 441796 Bfr Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]. 152 matched cddid_all.tbl CDD COG2194 COG2194 441797 OpgE Phosphoethanolamine transferase for periplasmic glucans OpgE, AlkP superfamily [Cell wall/membrane/envelope biogenesis]. 537 matched cddid_all.tbl CDD COG2195 COG2195 441798 PepD2 Di- or tripeptidase [Amino acid transport and metabolism]. 364 matched cddid_all.tbl CDD COG2197 COG2197 441799 CitB DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription]. 131 matched cddid_all.tbl CDD COG2198 COG2198 441800 HPtr HPt (histidine-containing phosphotransfer) domain [Signal transduction mechanisms]. 871 matched cddid_all.tbl CDD COG2199 COG2199 441801 GGDEF GGDEF domain, diguanylate cyclase (c-di-GMP synthetase) or its enzymatically inactive variants [Signal transduction mechanisms]. 275 matched cddid_all.tbl CDD COG2200 COG2200 441802 EAL EAL domain, c-di-GMP-specific phosphodiesterase class I (or its enzymatically inactive variant) [Signal transduction mechanisms]. 576 matched cddid_all.tbl CDD COG2201 COG2201 441803 CheB Chemotaxis response regulator CheB, contains REC and protein-glutamate methylesterase domains [Signal transduction mechanisms]. 193 matched cddid_all.tbl CDD COG2202 COG2202 441804 PAS PAS domain [Signal transduction mechanisms]. 258 matched cddid_all.tbl CDD COG2203 COG2203 441805 GAF GAF domain [Signal transduction mechanisms]. 712 matched cddid_all.tbl CDD COG2204 COG2204 441806 AtoC DNA-binding transcriptional response regulator, NtrC family, contains REC, AAA-type ATPase, and a Fis-type DNA-binding domains [Signal transduction mechanisms]. 418 matched cddid_all.tbl CDD COG2205 COG2205 441807 KdpD K+-sensing histidine kinase KdpD [Signal transduction mechanisms]. 239 matched cddid_all.tbl CDD COG2206 COG2206 441808 HDGYP HD-GYP domain, c-di-GMP phosphodiesterase class II (or its inactivated variant) [Signal transduction mechanisms]. 316 matched cddid_all.tbl CDD COG2207 COG2207 441809 AraC AraC-type DNA-binding domain and AraC-containing proteins [Transcription]. 258 matched cddid_all.tbl CDD COG2208 COG2208 441810 RsbU Phosphoserine phosphatase RsbU, regulator of sigma subunit [Signal transduction mechanisms, Transcription]. 435 matched cddid_all.tbl CDD COG2209 COG2209 441811 NqrE Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrE [Energy production and conversion]. Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrE is part of the Pathway/BioSystem: Na+-translocating NADH dehydrogenase 202 matched cddid_all.tbl CDD COG2210 COG2210 441812 YrkE Peroxiredoxin family protein [Energy production and conversion]. 156 matched cddid_all.tbl CDD COG2211 COG2211 441813 MelB Na+/melibiose symporter or related transporter [Carbohydrate transport and metabolism]. 447 matched cddid_all.tbl CDD COG2212 COG2212 441814 MnhF Multisubunit Na+/H+ antiporter, MnhF subunit [Inorganic ion transport and metabolism]. 84 matched cddid_all.tbl CDD COG2213 COG2213 441815 MtlA Phosphotransferase system, mannitol-specific IIBC component [Carbohydrate transport and metabolism]. 479 matched cddid_all.tbl CDD COG2214 COG2214 441816 CbpA Curved DNA-binding protein CbpA, contains a DnaJ-like domain [Transcription]. 91 matched cddid_all.tbl CDD COG2215 COG2215 441817 RcnA ABC-type nickel/cobalt efflux system, permease component RcnA [Inorganic ion transport and metabolism]. 261 matched cddid_all.tbl CDD COG2216 COG2216 441818 KdpB K+ transport ATPase, ATPase subunit KdpB [Inorganic ion transport and metabolism]. 683 matched cddid_all.tbl CDD COG2217 COG2217 441819 ZntA Cation-transporting P-type ATPase [Inorganic ion transport and metabolism]. 717 matched cddid_all.tbl CDD COG2218 COG2218 441820 FwdC Formylmethanofuran dehydrogenase subunit C [Energy production and conversion]. 264 matched cddid_all.tbl CDD COG2219 COG2219 441821 PRI2 Eukaryotic-type DNA primase, large subunit [Replication, recombination and repair]. 346 matched cddid_all.tbl CDD COG2220 COG2220 441822 UlaG L-ascorbate lactonase UlaG, metallo-beta-lactamase superfamily [Carbohydrate transport and metabolism]. 224 matched cddid_all.tbl CDD COG2221 COG2221 441823 DsrA Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Inorganic ion transport and metabolism]. 69 matched cddid_all.tbl CDD COG2222 COG2222 441824 AgaS Fructoselysine-6-P-deglycase FrlB or related protein, duplicated sugar isomerase (SIS) domain [Cell wall/membrane/envelope biogenesis]. 336 matched cddid_all.tbl CDD COG2223 COG2223 441825 NarK Nitrate/nitrite transporter NarK [Inorganic ion transport and metabolism]. 392 matched cddid_all.tbl CDD COG2224 COG2224 441826 AceA Isocitrate lyase [Energy production and conversion]. Isocitrate lyase is part of the Pathway/BioSystem: TCA cycle, glyoxylate bypass 425 matched cddid_all.tbl CDD COG2225 COG2225 441827 AceB Malate synthase [Energy production and conversion]. Malate synthase is part of the Pathway/BioSystem: TCA cycle, glyoxylate bypass 530 matched cddid_all.tbl CDD COG2226 COG2226 441828 UbiE Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]. Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG is part of the Pathway/BioSystem: Biotin biosynthesis 143 matched cddid_all.tbl CDD COG2227 COG2227 441829 UbiG 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and metabolism]. 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase is part of the Pathway/BioSystem: Ubiquinone biosynthesis 126 matched cddid_all.tbl CDD COG2229 COG2229 441830 Srp102 Signal recognition particle receptor subunit beta, a GTPase [Intracellular trafficking, secretion, and vesicular transport]. 189 matched cddid_all.tbl CDD COG2230 COG2230 441831 Cfa Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport and metabolism]. 158 matched cddid_all.tbl CDD COG2231 COG2231 441832 HP0602 3-Methyladenine DNA glycosylase, HhH-GPD/Endo3 superfamily [Replication, recombination and repair]. 220 matched cddid_all.tbl CDD COG2232 COG2232 441833 PylC Pyrrolysine biosynthesis ligase PylC and related enzymes, ATP-grasp superfamily [Amino acid transport and metabolism]. 370 matched cddid_all.tbl CDD COG2233 COG2233 441834 UraA Xanthine/uracil permease [Nucleotide transport and metabolism]. Xanthine/uracil permease is part of the Pathway/BioSystem: Pyrimidine degradation 439 matched cddid_all.tbl CDD COG2234 COG2234 441835 Iap Zn-dependent amino- or carboxypeptidase, M28 family [Posttranslational modification, protein turnover, chaperones, Amino acid transport and metabolism]. 257 matched cddid_all.tbl CDD COG2235 COG2235 441836 ArcA Arginine deiminase [Amino acid transport and metabolism]. 406 matched cddid_all.tbl CDD COG2236 COG2236 441837 Hpt1 Hypoxanthine phosphoribosyltransferase [Coenzyme transport and metabolism]. Hypoxanthine phosphoribosyltransferase is part of the Pathway/BioSystem: Purine salvage 153 matched cddid_all.tbl CDD COG2237 COG2237 441838 COG2237 Uncharacterized membrane protein [Function unknown]. 365 matched cddid_all.tbl CDD COG2238 COG2238 441839 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]. Ribosomal protein S19E (S16A) is part of the Pathway/BioSystem: Archaeal ribosomal proteins 151 matched cddid_all.tbl CDD COG2239 COG2239 441840 MgtE Mg/Co/Ni transporter MgtE (contains CBS domain) [Inorganic ion transport and metabolism]. 443 matched cddid_all.tbl CDD COG2240 COG2240 441841 PdxK Pyridoxal/pyridoxine/pyridoxamine kinase [Coenzyme transport and metabolism]. Pyridoxal/pyridoxine/pyridoxamine kinase is part of the Pathway/BioSystem: Pyridoxal phosphate biosynthesis 272 matched cddid_all.tbl CDD COG2241 COG2241 441842 CobL Precorrin-6B methylase 1 [Coenzyme transport and metabolism]. Precorrin-6B methylase 1 is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 207 matched cddid_all.tbl CDD COG2242 COG2242 441843 CobL Precorrin-6B methylase 2 [Coenzyme transport and metabolism]. Precorrin-6B methylase 2 is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 403 matched cddid_all.tbl CDD COG2243 COG2243 441844 CobF Precorrin-2 methylase [Coenzyme transport and metabolism]. Precorrin-2 methylase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 229 matched cddid_all.tbl CDD COG2244 COG2244 441845 RfbX Membrane protein involved in the export of O-antigen and teichoic acid [Cell wall/membrane/envelope biogenesis]. 366 matched cddid_all.tbl CDD COG2245 COG2245 441846 COG2245 Uncharacterized membrane protein, contains DUF996 domain [Function unknown]. 181 matched cddid_all.tbl CDD COG2246 COG2246 441847 GtrA Putative flippase GtrA (transmembrane translocase of bactoprenol-linked glucose) [Lipid transport and metabolism]. 133 matched cddid_all.tbl CDD COG2247 COG2247 441848 LytB Putative cell wall-binding domain (amidase enhancer), LytB superfamily [Cell wall/membrane/envelope biogenesis]. 472 matched cddid_all.tbl CDD COG2248 COG2248 441849 COG2248 Predicted hydrolase, metallo-beta-lactamase superfamily [General function prediction only]. 300 matched cddid_all.tbl CDD COG2249 COG2249 441850 MdaB Putative NADPH-quinone reductase (modulator of drug activity B) [General function prediction only]. 190 matched cddid_all.tbl CDD COG2250 COG2250 441851 HEPN HEPN domain protein, predicted toxin of MNT-HEPN system [Defense mechanisms]. 121 matched cddid_all.tbl CDD COG2251 COG2251 441852 COG2251 Predicted nuclease, RecB family [General function prediction only]. 508 matched cddid_all.tbl CDD COG2252 COG2252 441853 NCS2 Xanthine/guanine/uracil/vitamin C permease GhxP/GhxQ, nucleobase:cation symporter 2 ( NCS2) family [Nucleotide transport and metabolism]. 435 matched cddid_all.tbl CDD COG2253 COG2253 441854 COG2253 Predicted nucleotidyltransferase component of viral defense system [Defense mechanisms]. 256 matched cddid_all.tbl CDD COG2254 COG2254 441855 Cas3 CRISPR/Cas system-associated endonuclease Cas3-HD [Defense mechanisms]. CRISPR/Cas system-associated endonuclease Cas3-HD is part of the Pathway/BioSystem: CRISPR-Cas system 224 matched cddid_all.tbl CDD COG2255 COG2255 441856 RuvB Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, recombination and repair]. 337 matched cddid_all.tbl CDD COG2256 COG2256 441857 RarA Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, recombination and repair]. 439 matched cddid_all.tbl CDD COG2257 COG2257 441858 YlqH Type III secretion system substrate exporter, FlhB-like [Intracellular trafficking, secretion, and vesicular transport]. 95 matched cddid_all.tbl CDD COG2258 COG2258 441859 YiiM N-hydroxylaminopurine reductase YiiM, contains MOSC domain [Nucleotide transport and metabolism, Defense mechanisms]. 162 matched cddid_all.tbl CDD COG2259 COG2259 441860 DoxX Uncharacterized membrane protein YphA, DoxX/SURF4 family [Function unknown]. 134 matched cddid_all.tbl CDD COG2260 COG2260 441861 Nop10 rRNA maturation protein Nop10, contains Zn-ribbon domain [Translation, ribosomal structure and biogenesis]. rRNA maturation protein Nop10, contains Zn-ribbon domain is part of the Pathway/BioSystem: 16S rRNA modification 51 matched cddid_all.tbl CDD COG2261 COG2261 441862 YeaQ Uncharacterized membrane protein YeaQ/YmgE, transglycosylase-associated protein family [General function prediction only]. 85 matched cddid_all.tbl CDD COG2262 COG2262 441863 HflX 50S ribosomal subunit-associated GTPase HflX [Translation, ribosomal structure and biogenesis]. 419 matched cddid_all.tbl CDD COG2263 COG2263 441864 COG2263 Predicted RNA methylase [General function prediction only]. 199 matched cddid_all.tbl CDD COG2264 COG2264 441865 PrmA Ribosomal protein L11 methylase PrmA [Translation, ribosomal structure and biogenesis]. 284 matched cddid_all.tbl CDD COG2265 COG2265 441866 TrmA tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]. tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family is part of the Pathway/BioSystem: tRNA modification 377 matched cddid_all.tbl CDD COG2266 COG2266 441867 COG2266 GTP:adenosylcobinamide-phosphate guanylyltransferase [Coenzyme transport and metabolism]. GTP:adenosylcobinamide-phosphate guanylyltransferase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 185 matched cddid_all.tbl CDD COG2267 COG2267 441868 PldB Lysophospholipase, alpha-beta hydrolase superfamily [Lipid transport and metabolism]. 221 matched cddid_all.tbl CDD COG2268 COG2268 441869 YqiK Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown]. 439 matched cddid_all.tbl CDD COG2269 COG2269 441870 EpmA Elongation factor P--beta-lysine ligase (EF-P beta-lysylation pathway) [Translation, ribosomal structure and biogenesis]. 309 matched cddid_all.tbl CDD COG2270 COG2270 441871 BtlA MFS-type transporter involved in bile tolerance, Atg22 family [General function prediction only]. 424 matched cddid_all.tbl CDD COG2271 COG2271 441872 UhpC Sugar phosphate permease [Carbohydrate transport and metabolism]. 363 matched cddid_all.tbl CDD COG2272 COG2272 441873 PnbA Carboxylesterase type B [Lipid transport and metabolism]. 500 matched cddid_all.tbl CDD COG2273 COG2273 441874 BglS Beta-glucanase, GH16 family [Carbohydrate transport and metabolism]. 259 matched cddid_all.tbl CDD COG2274 COG2274 441875 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]. 711 matched cddid_all.tbl CDD COG2301 COG2301 441876 CitE Citrate lyase beta subunit [Carbohydrate transport and metabolism]. 288 matched cddid_all.tbl CDD COG2302 COG2302 441877 YlmH RNA-binding protein YlmH, contains S4-like domain [General function prediction only]. 260 matched cddid_all.tbl CDD COG2303 COG2303 441878 BetA Choline dehydrogenase or related flavoprotein [Lipid transport and metabolism, General function prediction only]. Choline dehydrogenase or related flavoprotein is part of the Pathway/BioSystem: Non-phosphorylated Entner-Doudoroff pathway 531 matched cddid_all.tbl CDD COG2304 COG2304 441879 YfbK Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]. 289 matched cddid_all.tbl CDD COG2306 COG2306 441880 COG2306 Predicted RNA-binding protein, associated with RNAse of E/G family, DUF402 domain [General function prediction only]. 135 matched cddid_all.tbl CDD COG2307 COG2307 441881 Alpha-E Uncharacterized conserved protein, Alpha-E superfamily [Function unknown]. 314 matched cddid_all.tbl CDD COG2308 COG2308 441882 COG2308 Circularly permuted ATP-grasp protein [General function prediction only]. 782 matched cddid_all.tbl CDD COG2309 COG2309 441883 AmpS Leucyl aminopeptidase (aminopeptidase T) [Amino acid transport and metabolism]. 360 matched cddid_all.tbl CDD COG2310 COG2310 441884 TerZ Stress response protein SCP2 [Signal transduction mechanisms]. 187 matched cddid_all.tbl CDD COG2311 COG2311 441885 YeiB Uncharacterized membrane protein YeiB [Function unknown]. 389 matched cddid_all.tbl CDD COG2312 COG2312 441886 YbfO Erythromycin esterase homolog [Secondary metabolites biosynthesis, transport and catabolism]. 426 matched cddid_all.tbl CDD COG2313 COG2313 441887 PsuG Pseudouridine-5'-phosphate glycosidase (pseudoU degradation) [Nucleotide transport and metabolism]. 303 matched cddid_all.tbl CDD COG2314 COG2314 441888 TM2 Uncharacterized membrane protein YozV, TM2 domain, contains pTyr [General function prediction only]. 79 matched cddid_all.tbl CDD COG2315 COG2315 441889 MmcQ Predicted DNA-binding protein with #double-wing# structural motif, MmcQ/YjbR family [Transcription]. 115 matched cddid_all.tbl CDD COG2316 COG2316 441890 COG2316 Predicted hydrolase, HD superfamily [General function prediction only]. 185 matched cddid_all.tbl CDD COG2317 COG2317 441891 YpwA Zn-dependent carboxypeptidase, M32 family [Posttranslational modification, protein turnover, chaperones]. 496 matched cddid_all.tbl CDD COG2318 COG2318 441892 DinB Bacillithiol/mycothiol S-transferase BstA/DinB, DinB/YfiT family (unrelated to E. coli DinB) [Secondary metabolites biosynthesis, transport and catabolism]. 145 matched cddid_all.tbl CDD COG2319 COG2319 441893 WD40 WD40 repeat [General function prediction only]. 403 matched cddid_all.tbl CDD COG2320 COG2320 441894 GrpB GrpB domain, predicted nucleotidyltransferase, UPF0157 family [General function prediction only]. 166 matched cddid_all.tbl CDD COG2321 COG2321 441895 YpfJ Predicted metalloprotease [General function prediction only]. 285 matched cddid_all.tbl CDD COG2322 COG2322 441896 YozB Predicted membrane metallochaperone YozB (3H, Sco1 fusion), DUF420 family [General function prediction only]. 177 matched cddid_all.tbl CDD COG2323 COG2323 441897 YcaP Uncharacterized membrane protein YcaP, DUF421 family [Function unknown]. 181 matched cddid_all.tbl CDD COG2324 COG2324 441898 COG2324 Uncharacterized membrane protein [Function unknown]. 257 matched cddid_all.tbl CDD COG2326 COG2326 441899 PPK2 Polyphosphate kinase 2, PPK2 family [Energy production and conversion]. 240 matched cddid_all.tbl CDD COG2327 COG2327 441900 WcaK Polysaccharide pyruvyl transferase family protein WcaK (colanic acid biosynthesis) [Cell wall/membrane/envelope biogenesis]. 357 matched cddid_all.tbl CDD COG2329 COG2329 441901 HmoA Heme-degrading monooxygenase HmoA and related ABM domain proteins [Coenzyme transport and metabolism]. 98 matched cddid_all.tbl CDD COG2331 COG2331 441902 COG2331 Predicted nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]. 77 matched cddid_all.tbl CDD COG2332 COG2332 441903 CcmE Cytochrome c biogenesis protein CcmE [Energy production and conversion, Posttranslational modification, protein turnover, chaperones]. 148 matched cddid_all.tbl CDD COG2333 COG2333 441904 ComEC DNA uptake channel protein ComEC C-terminal domain, metallo-beta-lactamase superfamily [Intracellular trafficking, secretion, and vesicular transport]. 253 matched cddid_all.tbl CDD COG2334 COG2334 441905 SrkA Ser/Thr protein kinase RdoA involved in Cpx stress response, MazF antagonist [Signal transduction mechanisms]. Ser/Thr protein kinase RdoA involved in Cpx stress response, MazF antagonist is part of the Pathway/BioSystem: Threonine biosynthesis 297 matched cddid_all.tbl CDD COG2335 COG2335 441906 FAS1 Uncaracterized surface protein containing fasciclin (FAS1) repeats [General function prediction only]. 164 matched cddid_all.tbl CDD COG2336 COG2336 441907 MazE Antitoxin component MazE of the MazEF toxin-antitoxin module [Defense mechanisms]. 80 matched cddid_all.tbl CDD COG2337 COG2337 441908 MazF mRNA-degrading endonuclease MazF, toxin component of the MazEF toxin-antitoxin module [Defense mechanisms]. 111 matched cddid_all.tbl CDD COG2339 COG2339 441909 PrsW Membrane proteinase PrsW, cleaves anti-sigma factor RsiW, M82 family [Signal transduction mechanisms]. 251 matched cddid_all.tbl CDD COG2340 COG2340 441910 YkwD Spore germination protein YkwD and related proteins with CAP (CSP/antigen 5/PR1) domain [Cell cycle control, cell division, chromosome partitioning, General function prediction only]. 144 matched cddid_all.tbl CDD COG2342 COG2342 441911 COG2342 Endo alpha-1,4 polygalactosaminidase, GH114 family (was erroneously annotated as Cys-tRNA synthetase) [Carbohydrate transport and metabolism]. 276 matched cddid_all.tbl CDD COG2343 COG2343 441912 COG2343 Uncharacterized conserved protein, DUF427 family [Function unknown]. 123 matched cddid_all.tbl CDD COG2344 COG2344 441913 Rex NADH/NAD ratio-sensing transcriptional regulator Rex [Transcription]. 214 matched cddid_all.tbl CDD COG2345 COG2345 441914 COG2345 Predicted transcriptional regulator, ArsR family [Transcription]. 217 matched cddid_all.tbl CDD COG2346 COG2346 441915 YjbI Truncated hemoglobin YjbI [Inorganic ion transport and metabolism]. 120 matched cddid_all.tbl CDD COG2348 COG2348 441916 FmhB Lipid II:glycine glycyltransferase (Peptidoglycan interpeptide bridge formation enzyme) [Cell wall/membrane/envelope biogenesis]. 344 matched cddid_all.tbl CDD COG2350 COG2350 441917 YciI YciI superfamily enzyme, includes 5-CHQ dehydrochlorinase, contains active-site pHis [Secondary metabolites biosynthesis, transport and catabolism, General function prediction only]. 93 matched cddid_all.tbl CDD COG2351 COG2351 441918 HiuH 5-hydroxyisourate hydrolase (purine catabolism), transthyretin-related family [Nucleotide transport and metabolism]. 111 matched cddid_all.tbl CDD COG2352 COG2352 441919 Ppc Phosphoenolpyruvate carboxylase [Energy production and conversion]. Phosphoenolpyruvate carboxylase is part of the Pathway/BioSystem: Urea cycle 932 matched cddid_all.tbl CDD COG2353 COG2353 441920 YceI Polyisoprenoid-binding periplasmic protein YceI [General function prediction only]. 184 matched cddid_all.tbl CDD COG2354 COG2354 441921 MutK Membrane protein MutK/YedI, may be involved in DNA repair [Replication, recombination and repair]. 315 matched cddid_all.tbl CDD COG2355 COG2355 441922 COG2355 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Posttranslational modification, protein turnover, chaperones, Amino acid transport and metabolism]. 319 matched cddid_all.tbl CDD COG2356 COG2356 441923 EndA Endonuclease I [Replication, recombination and repair]. 165 matched cddid_all.tbl CDD COG2357 COG2357 441924 YjbM ppGpp synthetase catalytic domain (RelA/SpoT-type nucleotidyltranferase) [Nucleotide transport and metabolism, Signal transduction mechanisms]. 286 matched cddid_all.tbl CDD COG2358 COG2358 441925 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]. 303 matched cddid_all.tbl CDD COG2359 COG2359 441926 SpoVS Stage V sporulation protein SpoVS, predicted DNA-binding, AlbA superfamily [Function unknown]. 88 matched cddid_all.tbl CDD COG2360 COG2360 441927 Aat Leu/Phe-tRNA-protein transferase [Posttranslational modification, protein turnover, chaperones]. 215 matched cddid_all.tbl CDD COG2361 COG2361 441928 HEPN HEPN domain protein, predicted toxin of MNT-HEPN system [Defense mechanisms]. 115 matched cddid_all.tbl CDD COG2362 COG2362 441929 DppA D-aminopeptidase [Amino acid transport and metabolism]. 274 matched cddid_all.tbl CDD COG2363 COG2363 441930 YgdD Uncharacterized membrane protein YgdD, TMEM256/DUF423 family [Function unknown]. 126 matched cddid_all.tbl CDD COG2364 COG2364 441931 YczE Uncharacterized membrane protein YczE [Function unknown]. 207 matched cddid_all.tbl CDD COG2365 COG2365 441932 Oca4 Protein tyrosine/serine phosphatase Oca4 [Signal transduction mechanisms]. 248 matched cddid_all.tbl CDD COG2366 COG2366 441933 PvdQ Acyl-homoserine lactone (AHL) acylase PvdQ [Secondary metabolites biosynthesis, transport and catabolism]. 795 matched cddid_all.tbl CDD COG2367 COG2367 441934 PenP Beta-lactamase class A [Defense mechanisms]. 276 matched cddid_all.tbl CDD COG2368 COG2368 441935 YoaI Aromatic ring hydroxylase [Secondary metabolites biosynthesis, transport and catabolism]. 479 matched cddid_all.tbl CDD COG2369 COG2369 441936 COG2369 Uncharacterized protein, contains phage Mu head morphogenesis gpF-like domain [Mobilome: prophages, transposons]. 201 matched cddid_all.tbl CDD COG2370 COG2370 441937 HupE Hydrogenase/urease accessory protein HupE [Posttranslational modification, protein turnover, chaperones]. 196 matched cddid_all.tbl CDD COG2371 COG2371 441938 UreE Urease accessory protein UreE [Posttranslational modification, protein turnover, chaperones]. 126 matched cddid_all.tbl CDD COG2372 COG2372 441939 CopC Copper-binding protein CopC (methionine-rich) [Inorganic ion transport and metabolism]. 125 matched cddid_all.tbl CDD COG2373 COG2373 441940 YfaS Uncharacterized conserved protein YfaS, alpha-2-macroglobulin family [General function prediction only]. 1605 matched cddid_all.tbl CDD COG2374 COG2374 441941 COG2374 Predicted extracellular nuclease [General function prediction only]. 362 matched cddid_all.tbl CDD COG2375 COG2375 441942 ViuB NADPH-dependent ferric siderophore reductase, contains FAD-binding and SIP domains [Inorganic ion transport and metabolism]. 260 matched cddid_all.tbl CDD COG2376 COG2376 441943 DAK1 Dihydroxyacetone kinase [Carbohydrate transport and metabolism]. Dihydroxyacetone kinase is part of the Pathway/BioSystem: Isoprenoid biosynthesis 206 matched cddid_all.tbl CDD COG2377 COG2377 441944 AnmK 1,6-Anhydro-N-acetylmuramate kinase [Cell wall/membrane/envelope biogenesis]. 363 matched cddid_all.tbl CDD COG2378 COG2378 441945 YobV Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains [Transcription]. 314 matched cddid_all.tbl CDD COG2379 COG2379 441946 GckA Glycerate-2-kinase [Carbohydrate transport and metabolism]. Glycerate-2-kinase is part of the Pathway/BioSystem: Non-phosphorylated Entner-Doudoroff pathway 421 matched cddid_all.tbl CDD COG2380 COG2380 441947 NurA2 NurA-like predicted nuclease, RNAse H fold [General function prediction only]. 313 matched cddid_all.tbl CDD COG2382 COG2382 441948 Fes Enterochelin esterase or related enzyme [Inorganic ion transport and metabolism]. 314 matched cddid_all.tbl CDD COG2383 COG2383 441949 COG2383 Uncharacterized membrane protein, Fun14 family [Function unknown]. 107 matched cddid_all.tbl CDD COG2384 COG2384 441950 TrmK tRNA A22 N1-methylase [Translation, ribosomal structure and biogenesis]. tRNA A22 N1-methylase is part of the Pathway/BioSystem: tRNA modification 228 matched cddid_all.tbl CDD COG2385 COG2385 441951 SpoIID Peptidoglycan hydrolase (amidase) enhancer domain SpoIID [Cell wall/membrane/envelope biogenesis]. 357 matched cddid_all.tbl CDD COG2386 COG2386 441952 CcmB ABC-type transport system involved in cytochrome c biogenesis, permease component [Posttranslational modification, protein turnover, chaperones]. 219 matched cddid_all.tbl CDD COG2388 COG2388 441953 YidJ Predicted acetyltransferase, GNAT superfamily [General function prediction only]. 88 matched cddid_all.tbl CDD COG2389 COG2389 441954 COG2389 Uncharacterized metal-binding protein, DUF2227 family [Function unknown]. 178 matched cddid_all.tbl CDD COG2390 COG2390 441955 DeoR DNA-binding transcriptional regulator LsrR, DeoR family [Transcription]. 301 matched cddid_all.tbl CDD COG2391 COG2391 441956 YedE Uncharacterized membrane protein YedE/YeeE, contains two sulfur transport domains [General function prediction only]. 143 matched cddid_all.tbl CDD COG2401 COG2401 441957 MK0520 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]. 222 matched cddid_all.tbl CDD COG2402 COG2402 441958 COG2402 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]. 135 matched cddid_all.tbl CDD COG2403 COG2403 441959 YjiA Zn/Ni/Co-binding GTPase YjiA, predicted metallochaperone, CobW/Nha3/YciC family [Inorganic ion transport and metabolism]. 441 matched cddid_all.tbl CDD COG2404 COG2404 441960 DhhP Oligoribonuclease NrnA/c-di-AMP phosphodiesterase DhhP, DHH superfamily [Translation, ribosomal structure and biogenesis, Signal transduction mechanisms]. 307 matched cddid_all.tbl CDD COG2405 COG2405 441961 COG2405 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]. 164 matched cddid_all.tbl CDD COG2406 COG2406 441962 DPS Ferritin-like DNA-binding protein, DPS (DNA Protection under Starvation) family [Replication, recombination and repair]. 165 matched cddid_all.tbl CDD COG2407 COG2407 441963 FucI L-fucose isomerase or related protein [Carbohydrate transport and metabolism]. 462 matched cddid_all.tbl CDD COG2409 COG2409 441964 YdfJ Predicted lipid transporter YdfJ, MMPL/SSD domain, RND superfamily [General function prediction only]. 697 matched cddid_all.tbl CDD COG2410 COG2410 441965 COG2410 Predicted nuclease (RNAse H fold) [General function prediction only]. 186 matched cddid_all.tbl CDD COG2411 COG2411 441966 ASCH Predicted RNA-binding protein, contains PUA-like ASCH domain [General function prediction only]. 103 matched cddid_all.tbl CDD COG2412 COG2412 441967 COG2412 Uncharacterized conserved protein, DUF424 domain [Function unknown]. 98 matched cddid_all.tbl CDD COG2413 COG2413 441968 COG2413 Predicted nucleotidyltransferase [General function prediction only]. 240 matched cddid_all.tbl CDD COG2414 COG2414 441969 YdhV Aldehyde:ferredoxin oxidoreductase [Energy production and conversion]. 610 matched cddid_all.tbl CDD COG2419 COG2419 441970 TRM10 tRNA (A,G)9-N-methylase TRM10 [Translation, ribosomal structure and biogenesis]. tRNA (A,G)9-N-methylase TRM10 is part of the Pathway/BioSystem: tRNA modification 335 matched cddid_all.tbl CDD COG2421 COG2421 441971 FmdA Acetamidase/formamidase [Energy production and conversion]. 304 matched cddid_all.tbl CDD COG2423 COG2423 441972 OCDMu Ornithine cyclodeaminase/archaeal alanine dehydrogenase, mu-crystallin family [Amino acid transport and metabolism]. Ornithine cyclodeaminase/archaeal alanine dehydrogenase, mu-crystallin family is part of the Pathway/BioSystem: Proline biosynthesis 322 matched cddid_all.tbl CDD COG2425 COG2425 441973 ViaA Uncharacterized conserved protein, contains a von Willebrand factor type A (vWA) domain [Function unknown]. 263 matched cddid_all.tbl CDD COG2426 COG2426 441974 COG2426 Uncharacterized membrane protein [Function unknown]. 152 matched cddid_all.tbl CDD COG2427 COG2427 441975 YjgD Uncharacterized conserved protein YjgD, DUF1641 family [Function unknown]. 153 matched cddid_all.tbl CDD COG2428 COG2428 441976 Sfm1 Rps3 or RNA methylase involved in ribosome biogenesis, SPOUT family [Translation, ribosomal structure and biogenesis]. 203 matched cddid_all.tbl CDD COG2429 COG2429 441977 Gch31 Archaeal GTP cyclohydrolase III [Nucleotide transport and metabolism]. Archaeal GTP cyclohydrolase III is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis 246 matched cddid_all.tbl CDD COG2430 COG2430 441978 COG2430 Uncharacterized conserved protein, DUF432 domain [Function unknown]. 233 matched cddid_all.tbl CDD COG2431 COG2431 441979 LysO Lysine export protein LysO/YbjE, DUF340 family [Amino acid transport and metabolism]. 196 matched cddid_all.tbl CDD COG2433 COG2433 441980 COG2433 Possible nuclease of RNase H fold, RuvC/YqgF family [General function prediction only]. 644 matched cddid_all.tbl CDD COG2440 COG2440 441981 FixX Ferredoxin-like protein FixX [Energy production and conversion]. 87 matched cddid_all.tbl CDD COG2441 COG2441 441982 COG2441 Predicted butyrate kinase, DUF1464 family [General function prediction only]. 361 matched cddid_all.tbl CDD COG2442 COG2442 441983 COG2442 Predicted antitoxin component of a toxin-antitoxin system, DUF433 family [Defense mechanisms]. 68 matched cddid_all.tbl CDD COG2443 COG2443 441984 Sss1 Preprotein translocase subunit Sss1 [Intracellular trafficking, secretion, and vesicular transport]. 63 matched cddid_all.tbl CDD COG2445 COG2445 441985 YutE Uncharacterized HEPN domain protein YutE, UPF0331/DUF86 family [General function prediction only]. 132 matched cddid_all.tbl CDD COG2450 COG2450 441986 SepFarc Predicted archaeal cell division protein, SepF family [Cell cycle control, cell division, chromosome partitioning]. 122 matched cddid_all.tbl CDD COG2451 COG2451 441987 Rpl35A Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]. Ribosomal protein L35AE/L33A is part of the Pathway/BioSystem: Archaeal ribosomal proteins 85 matched cddid_all.tbl CDD COG2452 COG2452 441988 COG2452 Predicted site-specific integrase-resolvase [Mobilome: prophages, transposons]. 178 matched cddid_all.tbl CDD COG2453 COG2453 441989 CDC14 Protein-tyrosine phosphatase [Signal transduction mechanisms]. 140 matched cddid_all.tbl CDD COG2454 COG2454 441990 COG2454 Predicted nuclease, contains PIN domain [General function prediction only]. 220 matched cddid_all.tbl CDD COG2456 COG2456 441991 COG2456 Uncharacterized conserved protein, DUF2304 domain [Function unknown]. 118 matched cddid_all.tbl CDD COG2457 COG2457 441992 COG2457 Uncharacterized conserved protein, DUF447 domain [Function unknown]. 183 matched cddid_all.tbl CDD COG2461 COG2461 441993 COG2461 Uncharacterized conserved protein AF0170, contains SAB, hemerythrin HHE, and PAS domains [General function prediction only]. 400 matched cddid_all.tbl CDD COG2469 COG2469 441994 CheF Archaeal chemotaxis protein CheF [Signal transduction mechanisms]. 295 matched cddid_all.tbl CDD COG2501 COG2501 441995 YbcJ Ribosome-associated protein YbcJ, S4-like RNA-binding protein [Translation, ribosomal structure and biogenesis]. 61 matched cddid_all.tbl CDD COG2502 COG2502 441996 AsnA Asparagine synthetase A [Amino acid transport and metabolism]. Asparagine synthetase A is part of the Pathway/BioSystem: Asparagine biosynthesis 336 matched cddid_all.tbl CDD COG2503 COG2503 441997 COG2503 Predicted secreted acid phosphatase [General function prediction only]. 269 matched cddid_all.tbl CDD COG2508 COG2508 441998 PucR DNA-binding transcriptional regulator, PucR/PutR family [Transcription]. 257 matched cddid_all.tbl CDD COG2509 COG2509 441999 COG2509 FAD-dependent dehydrogenase [General function prediction only]. 466 matched cddid_all.tbl CDD COG2510 COG2510 442000 RibN Riboflavin transporter RibN, EamA domain [Coenzyme transport and metabolism]. 138 matched cddid_all.tbl CDD COG2511 COG2511 442001 GatE Archaeal Glu-tRNAGln amidotransferase subunit E, contains GAD domain [Translation, ribosomal structure and biogenesis]. 630 matched cddid_all.tbl CDD COG2512 COG2512 442002 COG2512 Predicted transcriptional regulator, contains CW (cell wall-binding) repeats and an HTH domain [General function prediction only]. 80 matched cddid_all.tbl CDD COG2513 COG2513 442003 PrpB 2-Methylisocitrate lyase and related enzymes, PEP mutase family [Carbohydrate transport and metabolism]. 288 matched cddid_all.tbl CDD COG2514 COG2514 442004 CatE Catechol-2,3-dioxygenase [Secondary metabolites biosynthesis, transport and catabolism]. 141 matched cddid_all.tbl CDD COG2515 COG2515 442005 Acd 1-aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase, PLP-dependent ACC family [Amino acid transport and metabolism]. 317 matched cddid_all.tbl CDD COG2516 COG2516 442006 COG2516 Biotin synthase-related protein, radical SAM superfamily [General function prediction only]. 322 matched cddid_all.tbl CDD COG2517 COG2517 442007 COG2517 Predicted RNA-binding protein, contains C-terminal EMAP domain [General function prediction only]. 232 matched cddid_all.tbl CDD COG2518 COG2518 442008 Pcm Protein-L-isoaspartate O-methyltransferase [Posttranslational modification, protein turnover, chaperones]. 197 matched cddid_all.tbl CDD COG2519 COG2519 442009 Gcd14 tRNA A58 N-methylase Trm61 [Translation, ribosomal structure and biogenesis]. tRNA A58 N-methylase Trm61 is part of the Pathway/BioSystem: tRNA modification 249 matched cddid_all.tbl CDD COG2520 COG2520 442010 Trm5 tRNA G37 N-methylase Trm5 [Translation, ribosomal structure and biogenesis]. tRNA G37 N-methylase Trm5 is part of the Pathway/BioSystem: tRNA modification 333 matched cddid_all.tbl CDD COG2521 COG2521 442011 COG2521 Predicted archaeal methyltransferase [General function prediction only]. 285 matched cddid_all.tbl CDD COG2522 COG2522 442012 AF0184 Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription]. 99 matched cddid_all.tbl CDD COG2524 COG2524 442013 COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]. 206 matched cddid_all.tbl CDD COG2602 COG2602 442014 YbxI Beta-lactamase class D [Defense mechanisms]. 267 matched cddid_all.tbl CDD COG2603 COG2603 442015 SelU tRNA 2-selenouridine synthase SelU, contains rhodanese domain [Translation, ribosomal structure and biogenesis]. tRNA 2-selenouridine synthase SelU, contains rhodanese domain is part of the Pathway/BioSystem: tRNA modification 341 matched cddid_all.tbl CDD COG2604 COG2604 442016 COG2604 Uncharacterized conserved protein [Function unknown]. 491 matched cddid_all.tbl CDD COG2605 COG2605 442017 COG2605 Predicted kinase related to galactokinase and mevalonate kinase [General function prediction only]. 328 matched cddid_all.tbl CDD COG2606 COG2606 442018 EbsC Cys-tRNA(Pro) deacylase, prolyl-tRNA editing enzyme YbaK/EbsC [Translation, ribosomal structure and biogenesis]. 152 matched cddid_all.tbl CDD COG2607 COG2607 442019 Atu1564 Predicted ATPase, AAA+ superfamily [General function prediction only]. 286 matched cddid_all.tbl CDD COG2608 COG2608 442020 CopZ Copper chaperone CopZ [Inorganic ion transport and metabolism]. 71 matched cddid_all.tbl CDD COG2609 COG2609 442021 AceE Pyruvate dehydrogenase complex, dehydrogenase (E1) component [Energy production and conversion]. Pyruvate dehydrogenase complex, dehydrogenase (E1) component is part of the Pathway/BioSystem: Pyruvate oxidation 891 matched cddid_all.tbl CDD COG2610 COG2610 442022 GntT H+/gluconate symporter GntT or related permease, GntP/DsdX family [Carbohydrate transport and metabolism]. 440 matched cddid_all.tbl CDD COG2703 COG2703 442023 COG2703 Hemerythrin [Signal transduction mechanisms]. 132 matched cddid_all.tbl CDD COG2704 COG2704 442024 DcuA Anaerobic C4-dicarboxylate transporter [Carbohydrate transport and metabolism]. 440 matched cddid_all.tbl CDD COG2706 COG2706 442025 Pgl 6-phosphogluconolactonase, cycloisomerase 2 family [Carbohydrate transport and metabolism]. 352 matched cddid_all.tbl CDD COG2707 COG2707 442026 YeaL Uncharacterized membrane protein, DUF441 family [Function unknown]. 149 matched cddid_all.tbl CDD COG2710 COG2710 442027 NifD/CfbD Nitrogenase Mo-Fe protein NifD/coenzyme F430 biosynthesis subunit CfbD [Coenzyme transport and metabolism, Inorganic ion transport and metabolism]. 416 matched cddid_all.tbl CDD COG2715 COG2715 442028 SpmA Spore maturation protein SpmA (function unknown) [General function prediction only]. 197 matched cddid_all.tbl CDD COG2716 COG2716 442029 GcvR Glycine cleavage system regulator GcvR [Amino acid transport and metabolism]. 174 matched cddid_all.tbl CDD COG2717 COG2717 442030 MsrQ Heme-binding membrane subunit of periplasmic DMSO/TMAO and protein-methionine-sulfoxide reductases [Energy production and conversion]. 200 matched cddid_all.tbl CDD COG2718 COG2718 442031 YeaH Uncharacterized conserved protein YeaH/YhbH, required for sporulation, DUF444 family [General function prediction only]. 385 matched cddid_all.tbl CDD COG2719 COG2719 442032 SpoVR Stage V sporulation protein SpoVR/YcgB, involved in spore cortex formation (function unknown) [Cell cycle control, cell division, chromosome partitioning]. 502 matched cddid_all.tbl CDD COG2720 COG2720 442033 YoaR Vancomycin resistance protein YoaR (function unknown), contains peptidoglycan-binding and VanW domains [Defense mechanisms]. 449 matched cddid_all.tbl CDD COG2721 COG2721 442034 UxaA Altronate dehydratase [Carbohydrate transport and metabolism]. 498 matched cddid_all.tbl CDD COG2723 COG2723 442035 BglB Beta-glucosidase/6-phospho-beta-glucosidase/beta-galactosidase [Carbohydrate transport and metabolism]. 445 matched cddid_all.tbl CDD COG2730 COG2730 442036 BglC Aryl-phospho-beta-D-glucosidase BglC, GH1 family [Carbohydrate transport and metabolism]. 295 matched cddid_all.tbl CDD COG2731 COG2731 442037 EbgC Beta-galactosidase, beta subunit [Carbohydrate transport and metabolism]. 138 matched cddid_all.tbl CDD COG2732 COG2732 442038 BarS Barstar, RNAse (barnase) inhibitor [Transcription]. 90 matched cddid_all.tbl CDD COG2733 COG2733 442039 YjiN Uncharacterized membrane-anchored protein YjiN, DUF445 family [Function unknown]. 421 matched cddid_all.tbl CDD COG2738 COG2738 442040 YugP Zn-dependent membrane protease YugP [Posttranslational modification, protein turnover, chaperones]. 226 matched cddid_all.tbl CDD COG2739 COG2739 442041 YlxM Predicted DNA-binding protein YlxM, UPF0122 family [Transcription]. 112 matched cddid_all.tbl CDD COG2740 COG2740 442042 YlxR Nucleoid-associated protein YlxR, Predicted RNA-binding, DUF448 family [General function prediction only]. 93 matched cddid_all.tbl CDD COG2746 COG2746 442043 YokD Aminoglycoside N3'-acetyltransferase [Defense mechanisms]. 256 matched cddid_all.tbl CDD COG2747 COG2747 442044 FlgM Negative regulator of flagellin synthesis (anti-sigma28 factor) [Transcription, Cell motility]. 101 matched cddid_all.tbl CDD COG2755 COG2755 442045 TesA Lysophospholipase L1 or related esterase. Includes spore coat protein LipC/YcsK [Cell cycle control, cell division, chromosome partitioning, Lipid transport and metabolism]. 191 matched cddid_all.tbl CDD COG2759 COG2759 442046 MIS1 Formyltetrahydrofolate synthetase [Nucleotide transport and metabolism]. 556 matched cddid_all.tbl CDD COG2761 COG2761 442047 FrnE Predicted dithiol-disulfide isomerase, DsbA/YjbH family (virulence, stress resistance) [Posttranslational modification, protein turnover, chaperones]. 205 matched cddid_all.tbl CDD COG2764 COG2764 442048 PhnB Zn-dependent glyoxalase, PhnB family [Energy production and conversion]. 118 matched cddid_all.tbl CDD COG2766 COG2766 442049 PrkA Predicted Ser/Thr protein kinase [Signal transduction mechanisms]. 675 matched cddid_all.tbl CDD COG2768 COG2768 442050 COG2768 Uncharacterized Fe-S cluster protein [Function unknown]. 74 matched cddid_all.tbl CDD COG2770 COG2770 442051 HAMP HAMP domain [Signal transduction mechanisms]. 631 matched cddid_all.tbl CDD COG2771 COG2771 442052 CsgD DNA-binding transcriptional regulator, CsgD family [Transcription]. 188 matched cddid_all.tbl CDD COG2801 COG2801 442053 Tra5 Transposase InsO and inactivated derivatives [Mobilome: prophages, transposons]. 309 matched cddid_all.tbl CDD COG2802 COG2802 442054 LON/PUA Uncharacterized conserved protein, LON_N-like domain, ASCH/PUA-like superfamily [Function unknown]. 194 matched cddid_all.tbl CDD COG2804 COG2804 442055 PulE Type II secretory pathway ATPase GspE/PulE or T4P pilus assembly pathway ATPase PilB [Cell motility, Intracellular trafficking, secretion, and vesicular transport, Extracellular structures]. 561 matched cddid_all.tbl CDD COG2805 COG2805 442056 PilT Type IV pilus assembly protein PilT, pilus retraction ATPase [Cell motility, Extracellular structures]. 342 matched cddid_all.tbl CDD COG2807 COG2807 442057 CynX Cyanate permease [Inorganic ion transport and metabolism]. 399 matched cddid_all.tbl CDD COG2808 COG2808 442058 PaiB Predicted FMN-binding regulatory protein PaiB [Signal transduction mechanisms]. 200 matched cddid_all.tbl CDD COG2810 COG2810 442059 COG2810 Predicted type IV restriction endonuclease [Defense mechanisms]. 340 matched cddid_all.tbl CDD COG2811 COG2811 442060 NtpH Archaeal/vacuolar-type H+-ATPase subunit H [Energy production and conversion]. Archaeal/vacuolar-type H+-ATPase subunit H is part of the Pathway/BioSystem: A/V-type ATP synthase 108 matched cddid_all.tbl CDD COG2812 COG2812 442061 DnaX DNA polymerase III, gamma/tau subunits [Replication, recombination and repair]. 340 matched cddid_all.tbl CDD COG2813 COG2813 442062 RsmC 16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]. 16S rRNA G1207 methylase RsmC is part of the Pathway/BioSystem: 16S rRNA modification 191 matched cddid_all.tbl CDD COG2814 COG2814 442063 AraJ Predicted arabinose efflux permease AraJ, MFS family [Carbohydrate transport and metabolism]. 348 matched cddid_all.tbl CDD COG2815 COG2815 442064 PASTA PASTA domain, binds beta-lactams [Cell wall/membrane/envelope biogenesis]. 220 matched cddid_all.tbl CDD COG2816 COG2816 442065 NPY1 NADH pyrophosphatase NudC, Nudix superfamily [Nucleotide transport and metabolism]. 288 matched cddid_all.tbl CDD COG2818 COG2818 442066 Tag 3-methyladenine DNA glycosylase Tag [Replication, recombination and repair]. 191 matched cddid_all.tbl CDD COG2819 COG2819 442067 YbbA Predicted hydrolase of the alpha/beta superfamily [General function prediction only]. 250 matched cddid_all.tbl CDD COG2820 COG2820 442068 Udp Uridine phosphorylase [Nucleotide transport and metabolism]. Uridine phosphorylase is part of the Pathway/BioSystem: Pyrimidine salvage 251 matched cddid_all.tbl CDD COG2821 COG2821 442069 MltA Membrane-bound lytic murein transglycosylase [Cell wall/membrane/envelope biogenesis]. 388 matched cddid_all.tbl CDD COG2822 COG2822 442070 EfeO Iron uptake system EfeUOB, periplasmic (or lipoprotein) component EfeO/EfeM [Inorganic ion transport and metabolism]. 305 matched cddid_all.tbl CDD COG2823 COG2823 442071 OsmY Osmotically-inducible protein OsmY, contains BON domain [Cell wall/membrane/envelope biogenesis]. 157 matched cddid_all.tbl CDD COG2824 COG2824 442072 PhnA Uncharacterized Zn-ribbon-containing protein [General function prediction only]. 114 matched cddid_all.tbl CDD COG2825 COG2825 442073 HlpA Periplasmic chaperone for outer membrane proteins, Skp family [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones]. 171 matched cddid_all.tbl CDD COG2826 COG2826 442074 Tra8 Transposase and inactivated derivatives, IS30 family [Mobilome: prophages, transposons]. 325 matched cddid_all.tbl CDD COG2827 COG2827 442075 YhbQ Predicted endonuclease, GIY-YIG superfamily [Replication, recombination and repair]. 82 matched cddid_all.tbl CDD COG2828 COG2828 442076 PrpF 2-Methylaconitate cis-trans-isomerase PrpF (2-methyl citrate pathway) [Energy production and conversion]. 373 matched cddid_all.tbl CDD COG2829 COG2829 442077 PldA Outer membrane phospholipase A [Cell wall/membrane/envelope biogenesis]. 253 matched cddid_all.tbl CDD COG2830 COG2830 442078 COG2830 Uncharacterized conserved protein, DUF452 domain [Function unknown]. 218 matched cddid_all.tbl CDD COG2831 COG2831 442079 FhaC Hemolysin activation/secretion protein [Intracellular trafficking, secretion, and vesicular transport]. 547 matched cddid_all.tbl CDD COG2832 COG2832 442080 YbaN Uncharacterized membrane protein YbaN, DUF454 family [Function unknown]. 125 matched cddid_all.tbl CDD COG2833 COG2833 442081 COG2833 Uncharacterized protein, contains ferritin-like DUF455 domain [Function unknown]. 265 matched cddid_all.tbl CDD COG2834 COG2834 442082 LolA Outer membrane lipoprotein-sorting protein [Cell wall/membrane/envelope biogenesis]. 211 matched cddid_all.tbl CDD COG2835 COG2835 442083 Trm112 RNA methyltransferase activator Trm112/YbaR [Translation, ribosomal structure and biogenesis]. 60 matched cddid_all.tbl CDD COG2836 COG2836 442084 DsbD Uncharacterized membrane protein, DsbD domain [Function unknown]. 226 matched cddid_all.tbl CDD COG2837 COG2837 442085 EfeB Periplasmic deferrochelatase/peroxidase EfeB [Inorganic ion transport and metabolism]. 334 matched cddid_all.tbl CDD COG2838 COG2838 442086 IcdM Monomeric isocitrate dehydrogenase [Energy production and conversion]. Monomeric isocitrate dehydrogenase is part of the Pathway/BioSystem: TCA cycle 739 matched cddid_all.tbl CDD COG2839 COG2839 442087 YqgC Uncharacterized conserved protein YqgC, DUF456 family [Function unknown]. 158 matched cddid_all.tbl CDD COG2840 COG2840 442088 SmrA DNA-nicking endonuclease, Smr domain [Replication, recombination and repair]. 177 matched cddid_all.tbl CDD COG2841 COG2841 442089 YdcH Uncharacterized conserved protein YdcH, DUF465 family [Function unknown]. 71 matched cddid_all.tbl CDD COG2842 COG2842 442090 COG2842 Bacteriophage DNA transposition protein, AAA+ family ATPase [Mobilome: prophages, transposons]. 254 matched cddid_all.tbl CDD COG2843 COG2843 442091 CapA Poly-gamma-glutamate biosynthesis protein CapA/YwtB (capsule formation), metallophosphatase superfamily [Cell wall/membrane/envelope biogenesis]. 310 matched cddid_all.tbl CDD COG2844 COG2844 442092 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms]. 864 matched cddid_all.tbl CDD COG2845 COG2845 442093 COG2845 Peptidoglycan O-acetyltransferase, SGNH hydrolase family [Cell wall/membrane/envelope biogenesis]. 229 matched cddid_all.tbl CDD COG2846 COG2846 442094 RIC Iron-sulfur cluster repair protein YtfE, RIC family, contains ScdAN and hemerythrin domains [Posttranslational modification, protein turnover, chaperones]. 237 matched cddid_all.tbl CDD COG2847 COG2847 442095 COG2847 Copper(I)-binding protein [Inorganic ion transport and metabolism]. 145 matched cddid_all.tbl CDD COG2848 COG2848 442096 COG2848 Uncharacterized conserved protein, UPF0210 family [Cell cycle control, cell division, chromosome partitioning]. 452 matched cddid_all.tbl CDD COG2849 COG2849 442097 YwqK Antitoxin component YwqK of the YwqJK toxin-antitoxin module [Defense mechanisms]. 163 matched cddid_all.tbl CDD COG2850 COG2850 442098 RoxA Ribosomal protein L16 Arg81 hydroxylase, contains JmjC domain [Translation, ribosomal structure and biogenesis]. 274 matched cddid_all.tbl CDD COG2851 COG2851 442099 CitM Mg2+/citrate symporter [Energy production and conversion]. 435 matched cddid_all.tbl CDD COG2852 COG2852 442100 YcjD Very-short-patch-repair endonuclease [Replication, recombination and repair]. 104 matched cddid_all.tbl CDD COG2853 COG2853 442101 MlaA Lipoprotein subunit MlaA of the ABC-type intermembrane phospholipid transporter Mla [Cell wall/membrane/envelope biogenesis]. 236 matched cddid_all.tbl CDD COG2854 COG2854 442102 MlaC Periplasmic subunit MlaC of the ABC-type intermembrane phospholipid transporter Mla [Cell wall/membrane/envelope biogenesis]. 181 matched cddid_all.tbl CDD COG2855 COG2855 442103 YeiH Uncharacterized membrane protein YadS, UPF0324 family [Function unknown]. 332 matched cddid_all.tbl CDD COG2856 COG2856 442104 ImmA Zn-dependent peptidase ImmA, M78 family [Posttranslational modification, protein turnover, chaperones]. 105 matched cddid_all.tbl CDD COG2857 COG2857 442105 CYT1 Cytochrome c1 [Energy production and conversion]. 213 matched cddid_all.tbl CDD COG2859 COG2859 442106 SIMPL Outer membrane channel-forming protein BP26/OMP28, SIMPL family [Cell wall/membrane/envelope biogenesis]. 241 matched cddid_all.tbl CDD COG2860 COG2860 442107 YadS Uncharacterized membrane protein YeiH [Function unknown]. 199 matched cddid_all.tbl CDD COG2861 COG2861 442108 YibQ Uncharacterized conserved protein YibQ, putative polysaccharide deacetylase 2 family [Carbohydrate transport and metabolism]. 334 matched cddid_all.tbl CDD COG2862 COG2862 442109 YqhA Uncharacterized membrane protein YqhA [Function unknown]. 170 matched cddid_all.tbl CDD COG2863 COG2863 442110 CytC553 Cytochrome c553 [Energy production and conversion]. 98 matched cddid_all.tbl CDD COG2864 COG2864 442111 FdnI Cytochrome b subunit of formate dehydrogenase [Energy production and conversion]. 217 matched cddid_all.tbl CDD COG2865 COG2865 442112 COG2865 Predicted transcriptional regulator, contains HTH domain [Transcription]. 123 matched cddid_all.tbl CDD COG2866 COG2866 442113 MpaA Murein tripeptide amidase MpaA [Cell wall/membrane/envelope biogenesis]. 337 matched cddid_all.tbl CDD COG2867 COG2867 442114 PasT Ribosome association toxin PasT (RatA) of the RatAB toxin-antitoxin module [Translation, ribosomal structure and biogenesis]. 137 matched cddid_all.tbl CDD COG2868 COG2868 442115 YsxB Uncharacterized conserved protein YsxB, DUF464 family [Function unknown]. 103 matched cddid_all.tbl CDD COG2869 COG2869 442116 NqrC Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrC [Energy production and conversion]. Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrC is part of the Pathway/BioSystem: Na+-translocating NADH dehydrogenase 257 matched cddid_all.tbl CDD COG2870 COG2870 442117 RfaE ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell wall/membrane/envelope biogenesis]. 321 matched cddid_all.tbl CDD COG2871 COG2871 442118 NqrF Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrF [Energy production and conversion]. Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrF is part of the Pathway/BioSystem: Na+-translocating NADH dehydrogenase 396 matched cddid_all.tbl CDD COG2872 COG2872 442119 AlaX Ser-tRNA(Ala) deacylase AlaX (editing enzyme) [Translation, ribosomal structure and biogenesis]. 238 matched cddid_all.tbl CDD COG2873 COG2873 442120 MET17 O-acetylhomoserine/O-acetylserine sulfhydrylase, pyridoxal phosphate-dependent [Amino acid transport and metabolism]. O-acetylhomoserine/O-acetylserine sulfhydrylase, pyridoxal phosphate-dependent is part of the Pathway/BioSystem: Methionine biosynthesis 428 matched cddid_all.tbl CDD COG2874 COG2874 442121 FlaH Archaellum biogenesis ATPase ArlH/FlaH [Cell motility]. 230 matched cddid_all.tbl CDD COG2875 COG2875 442122 CobM Precorrin-4 methylase [Coenzyme transport and metabolism]. Precorrin-4 methylase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 256 matched cddid_all.tbl CDD COG2876 COG2876 442123 AroGA 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]. 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 283 matched cddid_all.tbl CDD COG2877 COG2877 442124 KdsA 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell wall/membrane/envelope biogenesis]. 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase is part of the Pathway/BioSystem: Lipid A biosynthesis 265 matched cddid_all.tbl CDD COG2878 COG2878 442125 RnfB Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfB subunit [Energy production and conversion]. Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfB subunit is part of the Pathway/BioSystem: Na+-translocating Fd:NADH oxidoreductase 254 matched cddid_all.tbl CDD COG2879 COG2879 442126 YbdD Uncharacterized short protein YbdD, DUF466 family [Function unknown]. 64 matched cddid_all.tbl CDD COG2880 COG2880 442127 COG2880 Predicted DNA-binding protein, potential antitoxin AbrB/MazE fold [General function prediction only]. 63 matched cddid_all.tbl CDD COG2881 COG2881 442128 Yip1 GTPase-interacting Yip1 domain [General function prediction only]. 191 matched cddid_all.tbl CDD COG2882 COG2882 442129 FliJ Flagellar biosynthesis chaperone FliJ [Cell motility]. 142 matched cddid_all.tbl CDD COG2884 COG2884 442130 FtsE Cell division ATPase FtsE [Cell cycle control, cell division, chromosome partitioning]. 223 matched cddid_all.tbl CDD COG2885 COG2885 442131 OmpA Outer membrane protein OmpA and related peptidoglycan-associated (lipo)proteins [Cell wall/membrane/envelope biogenesis]. 294 matched cddid_all.tbl CDD COG2886 COG2886 442132 COG2886 Predicted antitoxin, contains HTH domain [General function prediction only]. 85 matched cddid_all.tbl CDD COG2887 COG2887 442133 Slr0479 RecB family exonuclease [Replication, recombination and repair]. 248 matched cddid_all.tbl CDD COG2888 COG2888 442134 COG2888 Predicted RNA-binding protein involved in translation, contains Zn-ribbon domain, DUF1610 family [General function prediction only]. 52 matched cddid_all.tbl CDD COG2890 COG2890 442135 HemK Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis]. 282 matched cddid_all.tbl CDD COG2891 COG2891 442136 MreD Cell shape-determining protein MreD [Cell wall/membrane/envelope biogenesis]. 165 matched cddid_all.tbl CDD COG2892 COG2892 442137 Pcc1 tRNA threonylcarbamoyladenosine modification (KEOPS) complex, Pcc1 subunit [Translation, ribosomal structure and biogenesis]. tRNA threonylcarbamoyladenosine modification (KEOPS) complex, Pcc1 subunit is part of the Pathway/BioSystem: tRNA modification 82 matched cddid_all.tbl CDD COG2893 COG2893 442138 ManX Phosphotransferase system, mannose/fructose-specific component IIA [Carbohydrate transport and metabolism]. 126 matched cddid_all.tbl CDD COG2894 COG2894 442139 MinD Septum site-determining ATPase MinD [Cell cycle control, cell division, chromosome partitioning]. 258 matched cddid_all.tbl CDD COG2895 COG2895 442140 CysN Sulfate adenylyltransferase subunit 1, EFTu-like GTPase family [Inorganic ion transport and metabolism]. Sulfate adenylyltransferase subunit 1, EFTu-like GTPase family is part of the Pathway/BioSystem: Cysteine biosynthesis 430 matched cddid_all.tbl CDD COG2896 COG2896 442141 MoaA GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) [Coenzyme transport and metabolism]. GTP 3',8-cyclase (molybdenum cofactor biosynthesis protein MoaA) is part of the Pathway/BioSystem: Molybdopterin biosynthesis 329 matched cddid_all.tbl CDD COG2897 COG2897 442142 SseA 3-mercaptopyruvate sulfurtransferase SseA, contains two rhodanese domains [Inorganic ion transport and metabolism]. 262 matched cddid_all.tbl CDD COG2898 COG2898 442143 MprF2 Lysylphosphatidylglycerol synthetase MprF, lysyl-tRNA-binding C-terminal domain [Lipid transport and metabolism]. 588 matched cddid_all.tbl CDD COG2899 COG2899 442144 TerC2 Uncharacterized TerC-related membrane protein, DUF475 domain [Inorganic ion transport and metabolism]. 340 matched cddid_all.tbl CDD COG2900 COG2900 442145 SlyX Uncharacterized coiled-coil protein SlyX (sensitive to lysis X) [Function unknown]. 67 matched cddid_all.tbl CDD COG2901 COG2901 442146 Fis DNA-binding protein Fis (factor for inversion stimulation) [Transcription]. 83 matched cddid_all.tbl CDD COG2902 COG2902 442147 Gdh2 NAD-specific glutamate dehydrogenase [Amino acid transport and metabolism]. 1607 matched cddid_all.tbl CDD COG2904 COG2904 442148 QueFN NADPH-dependent 7-cyano-7-deazaguanine reductase QueF, N-terminal domain [Translation, ribosomal structure and biogenesis]. 277 matched cddid_all.tbl CDD COG2905 COG2905 442149 COG2905 Signal-transduction protein containing cAMP-binding, CBS, and nucleotidyltransferase domains [Signal transduction mechanisms]. 124 matched cddid_all.tbl CDD COG2906 COG2906 442150 Bfd Bacterioferritin-associated ferredoxin [Inorganic ion transport and metabolism]. 54 matched cddid_all.tbl CDD COG2907 COG2907 442151 Ppro0129 Predicted flavin-containing amine oxidase [General function prediction only]. 423 matched cddid_all.tbl CDD COG2908 COG2908 442152 LpxH UDP-2,3-diacylglucosamine pyrophosphatase LpxH [Cell wall/membrane/envelope biogenesis]. 238 matched cddid_all.tbl CDD COG2909 COG2909 442153 MalT ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription]. 184 matched cddid_all.tbl CDD COG2910 COG2910 442154 YwnB Putative NADH-flavin reductase [General function prediction only]. 205 matched cddid_all.tbl CDD COG2911 COG2911 442155 TamB Autotransporter translocation and assembly protein TamB [Intracellular trafficking, secretion, and vesicular transport]. 766 matched cddid_all.tbl CDD COG2912 COG2912 442156 SirB1 Regulator of sirC expression, contains transglutaminase-like and TPR domains [Signal transduction mechanisms]. 264 matched cddid_all.tbl CDD COG2913 COG2913 442157 BamE Outer membrane protein assembly factor BamE, lipoprotein component of the BamABCDE complex [Cell wall/membrane/envelope biogenesis]. 128 matched cddid_all.tbl CDD COG2914 COG2914 442158 PasI Putative antitoxin component PasI (RatB) of the RatAB toxin-antitoxin module, ubiquitin-RnfH superfamily [Defense mechanisms]. 92 matched cddid_all.tbl CDD COG2915 COG2915 442159 HflD Regulator of phage lambda lysogenization HflD, binds to CII and stimulates its degradation [Mobilome: prophages, transposons, Signal transduction mechanisms]. 206 matched cddid_all.tbl CDD COG2916 COG2916 442160 Hns DNA-binding protein H-NS [Transcription]. 109 matched cddid_all.tbl CDD COG2917 COG2917 442161 YciB Intracellular septation protein A [Cell cycle control, cell division, chromosome partitioning]. 181 matched cddid_all.tbl CDD COG2918 COG2918 442162 GshA Gamma-glutamylcysteine synthetase [Coenzyme transport and metabolism]. 518 matched cddid_all.tbl CDD COG2919 COG2919 442163 FtsB Cell division protein FtsB [Cell cycle control, cell division, chromosome partitioning]. 96 matched cddid_all.tbl CDD COG2920 COG2920 442164 TusE Sulfur transfer complex TusBCD TusE component, DsrC family (tRNA 2-thiouridine synthesizing protein C) [Translation, ribosomal structure and biogenesis]. 108 matched cddid_all.tbl CDD COG2921 COG2921 442165 YbeD Putative lipoate-binding regulatory protein, UPF0250 family [Signal transduction mechanisms]. 88 matched cddid_all.tbl CDD COG2922 COG2922 442166 Smg Uncharacterized conserved protein Smg, DUF494 family [Function unknown]. 153 matched cddid_all.tbl CDD COG2923 COG2923 442167 DsrF Sulfur transfer complex TusBCD TusC component, DsrF family [Translation, ribosomal structure and biogenesis]. 118 matched cddid_all.tbl CDD COG2924 COG2924 442168 YggX Fe-S cluster biosynthesis and repair protein YggX [Inorganic ion transport and metabolism, Posttranslational modification, protein turnover, chaperones]. 90 matched cddid_all.tbl CDD COG2925 COG2925 442169 SbcB Exonuclease I (degrades ssDNA) [Replication, recombination and repair]. 474 matched cddid_all.tbl CDD COG2926 COG2926 442170 YeeX Uncharacterized conserved protein YeeX, DUF496 family [Function unknown]. 100 matched cddid_all.tbl CDD COG2927 COG2927 442171 HolC DNA polymerase III, chi subunit [Replication, recombination and repair]. 136 matched cddid_all.tbl CDD COG2928 COG2928 442172 COG2928 Uncharacterized membrane protein [Function unknown]. 208 matched cddid_all.tbl CDD COG2929 COG2929 442173 COG2929 Uncharacterized conserved protein, DUF497 family [Function unknown]. 92 matched cddid_all.tbl CDD COG2930 COG2930 442174 SYLF Lipid-binding SYLF domain, Ysc84/FYVE family [Lipid transport and metabolism]. 188 matched cddid_all.tbl CDD COG2931 COG2931 442175 COG2931 Ca2+-binding protein, RTX toxin-related [Secondary metabolites biosynthesis, transport and catabolism]. 252 matched cddid_all.tbl CDD COG2932 COG2932 442176 COG2932 Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: prophages, transposons]. 121 matched cddid_all.tbl CDD COG2933 COG2933 442177 RlmM 23S rRNA C2498 (ribose-2'-O)-methylase RlmM [Translation, ribosomal structure and biogenesis]. 23S rRNA C2498 (ribose-2'-O)-methylase RlmM is part of the Pathway/BioSystem: 23S rRNA modification 356 matched cddid_all.tbl CDD COG2935 COG2935 442178 Ate1 Arginyl-tRNA--protein-N-Asp/Glu arginylyltransferase [Posttranslational modification, protein turnover, chaperones]. 240 matched cddid_all.tbl CDD COG2936 COG2936 442179 COG2936 Predicted acyl esterase [General function prediction only]. 555 matched cddid_all.tbl CDD COG2937 COG2937 442180 PlsB Glycerol-3-phosphate O-acyltransferase [Lipid transport and metabolism]. Glycerol-3-phosphate O-acyltransferase is part of the Pathway/BioSystem: Phospholipid biosynthesis 707 matched cddid_all.tbl CDD COG2938 COG2938 442181 SdhE Succinate dehydrogenase flavin-adding protein, antitoxin component of the CptAB toxin-antitoxin module [Posttranslational modification, protein turnover, chaperones]. 84 matched cddid_all.tbl CDD COG2939 COG2939 442182 Kex1 Carboxypeptidase C (cathepsin A) [Amino acid transport and metabolism]. 506 matched cddid_all.tbl CDD COG2940 COG2940 442183 SET SET domain-containing protein (function unknown) [General function prediction only]. 134 matched cddid_all.tbl CDD COG2941 COG2941 442184 Coq7 Demethoxyubiquinone hydroxylase, CLK1/Coq7/Cat5 family (ubiquinone biosynthesis) [Coenzyme transport and metabolism]. Demethoxyubiquinone hydroxylase, CLK1/Coq7/Cat5 family (ubiquinone biosynthesis) is part of the Pathway/BioSystem: Ubiquinone biosynthesis 208 matched cddid_all.tbl CDD COG2942 COG2942 442185 YihS Mannose or cellobiose epimerase, N-acyl-D-glucosamine 2-epimerase family [Carbohydrate transport and metabolism]. 380 matched cddid_all.tbl CDD COG2943 COG2943 442186 MdoH Membrane glycosyltransferase [Cell wall/membrane/envelope biogenesis, Carbohydrate transport and metabolism]. 661 matched cddid_all.tbl CDD COG2944 COG2944 442187 YiaG DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription]. 64 matched cddid_all.tbl CDD COG2945 COG2945 442188 COG2945 Alpha/beta superfamily hydrolase [General function prediction only]. 201 matched cddid_all.tbl CDD COG2946 COG2946 442189 NicK DNA relaxase NicK [Replication, recombination and repair]. 302 matched cddid_all.tbl CDD COG2947 COG2947 442190 EVE Predicted RNA-binding protein, contains EVE domain [General function prediction only]. 135 matched cddid_all.tbl CDD COG2948 COG2948 442191 VirB10 Type IV secretory pathway, VirB10 component [Intracellular trafficking, secretion, and vesicular transport]. 309 matched cddid_all.tbl CDD COG2949 COG2949 442192 SanA Uncharacterized periplasmic protein SanA, affects membrane permeability for vancomycin [Cell wall/membrane/envelope biogenesis]. 214 matched cddid_all.tbl CDD COG2951 COG2951 442193 MltB Membrane-bound lytic murein transglycosylase B [Cell wall/membrane/envelope biogenesis]. 326 matched cddid_all.tbl CDD COG2952 COG2952 442194 COG2952 Uncharacterized conserved protein, DUF507 domain [Function unknown]. 183 matched cddid_all.tbl CDD COG2954 COG2954 442195 CYTH CYTH domain, found in class IV adenylate cyclase and various triphosphatases [General function prediction only]. 157 matched cddid_all.tbl CDD COG2956 COG2956 442196 LapB Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis]. 275 matched cddid_all.tbl CDD COG2957 COG2957 442197 AguA Agmatine/peptidylarginine deiminase [Amino acid transport and metabolism]. 328 matched cddid_all.tbl CDD COG2958 COG2958 442198 COG2958 Uncharacterized conserved protein [Function unknown]. 301 matched cddid_all.tbl CDD COG2959 COG2959 442199 HemX Proteobacterial HemX domain, involved in 2-ketogluconate production (unrelated to B. subtilis HemX, COG0755, no evidence of involvement in heme biosynthesis) [General function prediction only]. 361 matched cddid_all.tbl CDD COG2960 COG2960 442200 UbiK Ubiquinone biosynthesis accessory factor UbiK [Coenzyme transport and metabolism]. 83 matched cddid_all.tbl CDD COG2961 COG2961 442201 RlmJ 23S rRNA A2030 N6-methylase RlmJ [Translation, ribosomal structure and biogenesis]. 23S rRNA A2030 N6-methylase RlmJ is part of the Pathway/BioSystem: 23S rRNA modification 278 matched cddid_all.tbl CDD COG2962 COG2962 442202 RarD Membrane protein RarD, contains two EamA domains, drug/metabolite transporter family [General function prediction only]. 297 matched cddid_all.tbl CDD COG2963 COG2963 442203 InsE Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons]. 93 matched cddid_all.tbl CDD COG2964 COG2964 442204 YheO Predicted transcriptional regulator YheO, contains PAS and DNA-binding HTH domains [Transcription]. 214 matched cddid_all.tbl CDD COG2965 COG2965 442205 PriB Primosomal replication protein N [Replication, recombination and repair]. 98 matched cddid_all.tbl CDD COG2966 COG2966 442206 YjjP Uncharacterized membrane protein YjjP, DUF1212 family [Function unknown]. 409 matched cddid_all.tbl CDD COG2967 COG2967 442207 ApaG Uncharacterized conserved protein ApaG affecting Mg2+/Co2+ transport [Inorganic ion transport and metabolism]. 119 matched cddid_all.tbl CDD COG2968 COG2968 442208 YggE Uncharacterized conserved protein YggE, contains kinase-interacting SIMPL domain [Function unknown]. 234 matched cddid_all.tbl CDD COG2969 COG2969 442209 SspB Stringent starvation protein B, binds SsrA peptide [Posttranslational modification, protein turnover, chaperones]. 138 matched cddid_all.tbl CDD COG2971 COG2971 442210 BadF BadF-type ATPase, related to human N-acetylglucosamine kinase [Carbohydrate transport and metabolism]. 298 matched cddid_all.tbl CDD COG2972 COG2972 442211 YesM Sensor histidine kinase YesM [Signal transduction mechanisms]. 445 matched cddid_all.tbl CDD COG2973 COG2973 442212 TrpR Trp operon repressor [Transcription]. 99 matched cddid_all.tbl CDD COG2974 COG2974 442213 RdgC DNA recombination-dependent growth factor RdgC [Replication, recombination and repair]. 302 matched cddid_all.tbl CDD COG2975 COG2975 442214 IscX Fe-S-cluster formation regulator IscX/YfhJ [Posttranslational modification, protein turnover, chaperones]. 64 matched cddid_all.tbl CDD COG2976 COG2976 442215 YfgM Putative negative regulator of RcsB-dependent stress response, UPF0070 family [Signal transduction mechanisms]. 207 matched cddid_all.tbl CDD COG2977 COG2977 442216 EntD 4'-phosphopantetheinyl transferase EntD (siderophore biosynthesis) [Secondary metabolites biosynthesis, transport and catabolism]. 205 matched cddid_all.tbl CDD COG2978 COG2978 442217 AbgT p-Aminobenzoyl-glutamate transporter AbgT [Coenzyme transport and metabolism]. 508 matched cddid_all.tbl CDD COG2979 COG2979 442218 YebE Uncharacterized membrane protein YebE, DUF533 family [Function unknown]. 220 matched cddid_all.tbl CDD COG2980 COG2980 442219 LptE Outer membrane lipoprotein LptE/RlpB (LPS assembly) [Cell wall/membrane/envelope biogenesis]. 172 matched cddid_all.tbl CDD COG2981 COG2981 442220 CysZ Sulfate transporter CysZ [Amino acid transport and metabolism, Inorganic ion transport and metabolism]. 248 matched cddid_all.tbl CDD COG2982 COG2982 442221 AsmA Uncharacterized conserved protein AsmA involved in outer membrane biogenesis [Cell wall/membrane/envelope biogenesis]. 491 matched cddid_all.tbl CDD COG2983 COG2983 442222 YcgN Uncharacterized cysteine cluster protein YcgN, CxxCxxCC family [General function prediction only]. 148 matched cddid_all.tbl CDD COG2984 COG2984 442223 COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]. 284 matched cddid_all.tbl CDD COG2985 COG2985 442224 YbjL Uncharacterized membrane protein YbjL, putative transporter [General function prediction only]. 543 matched cddid_all.tbl CDD COG2986 COG2986 442225 HutH Histidine ammonia-lyase [Amino acid transport and metabolism]. 503 matched cddid_all.tbl CDD COG2987 COG2987 442226 HutU Urocanate hydratase [Amino acid transport and metabolism]. 567 matched cddid_all.tbl CDD COG2988 COG2988 442227 AstE Succinylglutamate desuccinylase [Amino acid transport and metabolism]. 305 matched cddid_all.tbl CDD COG2989 COG2989 442228 YcbB Murein L,D-transpeptidase YcbB/YkuD [Cell wall/membrane/envelope biogenesis]. 529 matched cddid_all.tbl CDD COG2990 COG2990 442229 VirK Outer membrane protein VirK/YbjX involved in antimicrobial peptide resistance, DUF535 family [Function unknown]. 307 matched cddid_all.tbl CDD COG2991 COG2991 442230 NqrM Na+-NQR maturation protein NqrM [Energy production and conversion, Posttranslational modification, protein turnover, chaperones]. Na+-NQR maturation protein NqrM is part of the Pathway/BioSystem: Na+-translocating NADH dehydrogenase 67 matched cddid_all.tbl CDD COG2992 COG2992 442231 Bax Uncharacterized FlgJ-related protein [General function prediction only]. 253 matched cddid_all.tbl CDD COG2993 COG2993 442232 CcoO Cbb3-type cytochrome oxidase, cytochrome c subunit FixO [Energy production and conversion]. 227 matched cddid_all.tbl CDD COG2994 COG2994 442233 HlyC ACP:hemolysin acyltransferase (hemolysin-activating protein) [Posttranslational modification, protein turnover, chaperones]. 143 matched cddid_all.tbl CDD COG2995 COG2995 442234 PqiA Intermembrane transporter PqiABC subunit PqiA [Cell wall/membrane/envelope biogenesis]. 211 matched cddid_all.tbl CDD COG2996 COG2996 442235 CvfB Predicted RNA-binding protein YitL, contains S1 domains, virulence factor B family [General function prediction only]. 264 matched cddid_all.tbl CDD COG2998 COG2998 442236 TupB ABC-type tungstate transport system, permease component TupA [Inorganic ion transport and metabolism]. 272 matched cddid_all.tbl CDD COG2999 COG2999 442237 GrxB Glutaredoxin 2 [Posttranslational modification, protein turnover, chaperones]. 215 matched cddid_all.tbl CDD COG3000 COG3000 442238 ERG3 Sterol desaturase/sphingolipid hydroxylase, fatty acid hydroxylase superfamily [Lipid transport and metabolism]. 158 matched cddid_all.tbl CDD COG3001 COG3001 442239 FN3K Fructosamine-3-kinase [Carbohydrate transport and metabolism]. 287 matched cddid_all.tbl CDD COG3002 COG3002 442240 MpsB Na+-translocating membrane potential-generating system subunit MpsB, UPF0753/DUF2309 family [Energy production and conversion]. 819 matched cddid_all.tbl CDD COG3004 COG3004 442241 NhaA Na+/H+ antiporter NhaA [Energy production and conversion, Inorganic ion transport and metabolism]. 387 matched cddid_all.tbl CDD COG3005 COG3005 442242 NapC Tetraheme cytochrome c subunit NapC of nitrate or TMAO reductase [Energy production and conversion]. 161 matched cddid_all.tbl CDD COG3006 COG3006 442243 MukF Chromosome condensin MukBEF, kleisin-like MukF subunit [Cell cycle control, cell division, chromosome partitioning]. 440 matched cddid_all.tbl CDD COG3007 COG3007 442244 COG3007 Trans-2-enoyl-CoA reductase [Lipid transport and metabolism]. 394 matched cddid_all.tbl CDD COG3008 COG3008 442245 PqiB Intermembrane transporter PqiABC subunit PqiB [Cell wall/membrane/envelope biogenesis]. 542 matched cddid_all.tbl CDD COG3009 COG3009 442246 PqiC Intermembrane transporter PqiABC lipoprotein subunit PqiC [Cell wall/membrane/envelope biogenesis]. 198 matched cddid_all.tbl CDD COG3010 COG3010 442247 NanE Putative N-acetylmannosamine-6-phosphate epimerase [Carbohydrate transport and metabolism]. 226 matched cddid_all.tbl CDD COG3011 COG3011 442248 YuxK Predicted thiol-disulfide oxidoreductase YuxK, DCC family [General function prediction only]. 133 matched cddid_all.tbl CDD COG3012 COG3012 442249 YchJ Uncharacterized conserved protein YchJ, contains N- and C-terminal SEC-C domains [Function unknown]. 144 matched cddid_all.tbl CDD COG3013 COG3013 442250 YfbU Uncharacterized conserved protein YfbU, UPF0304 family [Function unknown]. 168 matched cddid_all.tbl CDD COG3014 COG3014 442251 COG3014 Uncharacterized conserved protein [Function unknown]. 439 matched cddid_all.tbl CDD COG3015 COG3015 442252 CutF Uncharacterized lipoprotein NlpE involved in copper resistance [Cell wall/membrane/envelope biogenesis, Defense mechanisms]. 147 matched cddid_all.tbl CDD COG3016 COG3016 442253 PhuW Putative heme-binding protein PhuW [General function prediction only]. 287 matched cddid_all.tbl CDD COG3017 COG3017 442254 LolB Outer membrane lipoprotein LolB, involved in outer membrane biogenesis [Cell wall/membrane/envelope biogenesis]. 200 matched cddid_all.tbl CDD COG3018 COG3018 442255 FlgP Flagellar basal body lipoprotein FlgP, LPP20 family [Cell motility]. 140 matched cddid_all.tbl CDD COG3019 COG3019 442256 COG3019 Uncharacterized metal-binding protein, DUF411 family [Function unknown]. 152 matched cddid_all.tbl CDD COG3021 COG3021 442257 YafD Uncharacterized conserved protein YafD, endonuclease/exonuclease/phosphatase (EEP) superfamily [General function prediction only]. 310 matched cddid_all.tbl CDD COG3022 COG3022 442258 YaaA DNA-binding protein YaaA associated with the oxidative stress response [Replication, recombination and repair]. 250 matched cddid_all.tbl CDD COG3023 COG3023 442259 AmpD N-acetyl-anhydromuramyl-L-alanine amidase AmpD [Cell wall/membrane/envelope biogenesis]. 167 matched cddid_all.tbl CDD COG3024 COG3024 442260 YacG Endogenous inhibitor of DNA gyrase, YacG/DUF329 family [Replication, recombination and repair]. 58 matched cddid_all.tbl CDD COG3025 COG3025 442261 PPPi Inorganic triphosphatase YgiF, contains CYTH and CHAD domains [Inorganic ion transport and metabolism]. 261 matched cddid_all.tbl CDD COG3026 COG3026 442262 RseB RseB, negative regulator of sigma E activity [Signal transduction mechanisms]. 322 matched cddid_all.tbl CDD COG3027 COG3027 442263 ZapA Cell division protein ZapA, inhibits GTPase activity of FtsZ [Cell cycle control, cell division, chromosome partitioning]. 94 matched cddid_all.tbl CDD COG3028 COG3028 442264 YjgA Ribosomal 50S subunit-associated protein YjgA, DUF615 family [Translation, ribosomal structure and biogenesis]. 174 matched cddid_all.tbl CDD COG3029 COG3029 442265 FrdC Fumarate reductase subunit C [Energy production and conversion]. 128 matched cddid_all.tbl CDD COG3030 COG3030 442266 FxsA FxsA protein affecting phage T7 exclusion by the F plasmid, UPF0716 family [General function prediction only]. 144 matched cddid_all.tbl CDD COG3031 COG3031 442267 PulC Type II secretory pathway, component PulC [Intracellular trafficking, secretion, and vesicular transport]. 220 matched cddid_all.tbl CDD COG3033 COG3033 442268 TnaA Tryptophanase [Amino acid transport and metabolism]. 460 matched cddid_all.tbl CDD COG3034 COG3034 442269 YafK Murein L,D-transpeptidase YafK [Cell wall/membrane/envelope biogenesis]. 163 matched cddid_all.tbl CDD COG3036 COG3036 442270 ArfA Stalled ribosome alternative rescue factor ArfA [Translation, ribosomal structure and biogenesis]. 65 matched cddid_all.tbl CDD COG3037 COG3037 442271 UlaA Ascorbate-specific PTS system IIC component UlaA [Carbohydrate transport and metabolism]. 430 matched cddid_all.tbl CDD COG3038 COG3038 442272 CybB Cytochrome b561 [Energy production and conversion]. 183 matched cddid_all.tbl CDD COG3039 COG3039 442273 IS5 Transposase and inactivated derivatives, IS5 family [Mobilome: prophages, transposons]. 316 matched cddid_all.tbl CDD COG3040 COG3040 442274 Blc Bacterial lipocalin Blc [Cell wall/membrane/envelope biogenesis]. 178 matched cddid_all.tbl CDD COG3041 COG3041 442275 YafQ mRNA-degrading endonuclease YafQ (mRNA interferase), toxin component of the YafQ-DinJ toxin-antitoxin module [Translation, ribosomal structure and biogenesis, Defense mechanisms]. 88 matched cddid_all.tbl CDD COG3042 COG3042 442276 Hlx Putative hemolysin [General function prediction only]. 82 matched cddid_all.tbl CDD COG3043 COG3043 442277 NapB Nitrate reductase cytochrome c-type subunit NapB [Energy production and conversion, Inorganic ion transport and metabolism]. 150 matched cddid_all.tbl CDD COG3044 COG3044 442278 COG3044 Predicted ATPase of the ABC class [General function prediction only]. 569 matched cddid_all.tbl CDD COG3045 COG3045 442279 CreA Periplasmic catabolite regulation protein CreA (function unknown) [Signal transduction mechanisms]. 155 matched cddid_all.tbl CDD COG3046 COG3046 442280 COG3046 Uncharacterized conserved protein related to deoxyribodipyrimidine photolyase [General function prediction only]. 508 matched cddid_all.tbl CDD COG3047 COG3047 442281 OmpW Outer membrane protein OmpW [Cell wall/membrane/envelope biogenesis]. 216 matched cddid_all.tbl CDD COG3048 COG3048 442282 DsdA D-serine dehydratase [Amino acid transport and metabolism]. 446 matched cddid_all.tbl CDD COG3049 COG3049 442283 YxeI Penicillin V acylase or related amidase, Ntn superfamily [Cell wall/membrane/envelope biogenesis, General function prediction only]. 337 matched cddid_all.tbl CDD COG3050 COG3050 442284 HolD DNA polymerase III, psi subunit [Replication, recombination and repair]. 136 matched cddid_all.tbl CDD COG3051 COG3051 442285 CitF Citrate lyase, alpha subunit [Energy production and conversion]. 497 matched cddid_all.tbl CDD COG3052 COG3052 442286 CitD Acyl-carrier protein (citrate lyase gamma subunit) [Energy production and conversion]. 91 matched cddid_all.tbl CDD COG3053 COG3053 442287 CitC Citrate lyase synthetase CitC [Energy production and conversion]. 330 matched cddid_all.tbl CDD COG3054 COG3054 442288 YtfJ Predicted transcriptional regulator YtfJ [General function prediction only]. 185 matched cddid_all.tbl CDD COG3055 COG3055 442289 NanM N-acetylneuraminic acid mutarotase [Cell wall/membrane/envelope biogenesis]. 277 matched cddid_all.tbl CDD COG3056 COG3056 442290 YajG Uncharacterized lipoprotein YajG [Function unknown]. 192 matched cddid_all.tbl CDD COG3057 COG3057 442291 SeqA Negative regulator of replication initiation SeqA [Replication, recombination and repair]. 184 matched cddid_all.tbl CDD COG3058 COG3058 442292 FdhE Formate dehydrogenase maturation protein FdhE [Energy production and conversion, Posttranslational modification, protein turnover, chaperones]. 302 matched cddid_all.tbl CDD COG3059 COG3059 442293 YkgB Reactive chlorine resistance protein RclC/YkgB, DUF417 family [Defense mechanisms]. 162 matched cddid_all.tbl CDD COG3060 COG3060 442294 MetJ Transcriptional regulator MetJ (met regulon) [Transcription, Amino acid transport and metabolism]. 107 matched cddid_all.tbl CDD COG3061 COG3061 442295 OapA Cell division protein YtfB/OapA (opacity-associated protein A) [Cell cycle control, cell division, chromosome partitioning]. 425 matched cddid_all.tbl CDD COG3062 COG3062 442296 NapD Cytoplasmic chaperone NapD for the signal peptide of periplasmic nitrate reductase NapAB [Posttranslational modification, protein turnover, chaperones]. 86 matched cddid_all.tbl CDD COG3063 COG3063 442297 PilF Type IV pilus assembly protein PilF/PilW [Cell motility, Extracellular structures]. 94 matched cddid_all.tbl CDD COG3064 COG3064 442298 TolA Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]. 485 matched cddid_all.tbl CDD COG3065 COG3065 442299 Slp Starvation-inducible outer membrane lipoprotein Slp [Cell wall/membrane/envelope biogenesis]. 172 matched cddid_all.tbl CDD COG3066 COG3066 442300 MutH DNA mismatch repair protein MutH [Replication, recombination and repair]. 225 matched cddid_all.tbl CDD COG3067 COG3067 442301 NhaB Na+/H+ antiporter NhaB [Energy production and conversion, Inorganic ion transport and metabolism]. 498 matched cddid_all.tbl CDD COG3068 COG3068 442302 YjaG Uncharacterized conserved protein YjaG, DUF416 family [Function unknown]. 192 matched cddid_all.tbl CDD COG3069 COG3069 442303 DcuC C4-dicarboxylate transporter DcuC [Energy production and conversion]. 454 matched cddid_all.tbl CDD COG3070 COG3070 442304 TfoX Transcriptional regulator of competence genes, TfoX/Sxy family [Transcription]. 114 matched cddid_all.tbl CDD COG3071 COG3071 442305 HemYx Uncharacterized protein HemY, contains HemY_N domain and TPR repeats (unrelated to protoporphyrinogen oxidase HemY) [Function unknown]. 323 matched cddid_all.tbl CDD COG3072 COG3072 442306 CyaA Adenylate cyclase, class I [Signal transduction mechanisms]. 930 matched cddid_all.tbl CDD COG3073 COG3073 442307 RseA RseA, negative regulator of sigma E activity [Signal transduction mechanisms]. 166 matched cddid_all.tbl CDD COG3074 COG3074 442308 ZapB Cell division protein ZapB, interacts with FtsZ [Cell cycle control, cell division, chromosome partitioning]. 79 matched cddid_all.tbl CDD COG3075 COG3075 442309 GlpB Anaerobic glycerol-3-phosphate dehydrogenase [Amino acid transport and metabolism]. 415 matched cddid_all.tbl CDD COG3076 COG3076 442310 RraB Regulator of RNase E activity RraB [Translation, ribosomal structure and biogenesis]. 114 matched cddid_all.tbl CDD COG3077 COG3077 442311 RelB Antitoxin component of the RelBE or YafQ-DinJ toxin-antitoxin module [Defense mechanisms]. 82 matched cddid_all.tbl CDD COG3078 COG3078 442312 YihI Ribosome assembly protein YihI, activator of Der GTPase [Translation, ribosomal structure and biogenesis]. 181 matched cddid_all.tbl CDD COG3079 COG3079 442313 YgfB Uncharacterized conserved protein YgfB, UPF0149 family [Function unknown]. 187 matched cddid_all.tbl CDD COG3080 COG3080 442314 FrdD Fumarate reductase subunit D [Energy production and conversion]. 120 matched cddid_all.tbl CDD COG3081 COG3081 442315 NdpA dsDNA-binding nucleoid-associated protein YejK/NdpA [Replication, recombination and repair]. 339 matched cddid_all.tbl CDD COG3082 COG3082 442316 YejL Uncharacterized conserved protein YejL, UPF0352 family [Function unknown]. 70 matched cddid_all.tbl CDD COG3083 COG3083 442317 YejM Periplasmic protein PbgA/YejM, regulator of the LPS biosynthesis, AlkP superfamily [Cell wall/membrane/envelope biogenesis, Signal transduction mechanisms]. 603 matched cddid_all.tbl CDD COG3084 COG3084 442318 YihD Uncharacterized conserved protein YihD, DUF1040 family [Function unknown]. 89 matched cddid_all.tbl CDD COG3085 COG3085 442319 YifE Uncharacterized conserved protein YifE, UPF0438 family [Function unknown]. 116 matched cddid_all.tbl CDD COG3086 COG3086 442320 RseC RseC, positive regulator of sigma E activity [Signal transduction mechanisms]. 149 matched cddid_all.tbl CDD COG3087 COG3087 442321 FtsN Cell division protein FtsN [Cell cycle control, cell division, chromosome partitioning]. 198 matched cddid_all.tbl CDD COG3088 COG3088 442322 NrfF Cytochrome c-type biogenesis protein CcmH/NrfF [Energy production and conversion, Posttranslational modification, protein turnover, chaperones]. 149 matched cddid_all.tbl CDD COG3089 COG3089 442323 YheU Uncharacterized conserved protein YheU, UPF0270 family [Function unknown]. 76 matched cddid_all.tbl CDD COG3090 COG3090 442324 DctM TRAP-type C4-dicarboxylate transport system, small permease component YiaM [Carbohydrate transport and metabolism]. 168 matched cddid_all.tbl CDD COG3091 COG3091 442325 SprT Predicted Zn-dependent metalloprotease, SprT family [General function prediction only]. 159 matched cddid_all.tbl CDD COG3092 COG3092 442326 YfbV Uncharacterized membrane protein YfbV, UPF0208 family [Function unknown]. 145 matched cddid_all.tbl CDD COG3093 COG3093 442327 VapI Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense mechanisms]. 87 matched cddid_all.tbl CDD COG3094 COG3094 442328 SirB2 Uncharacterized membrane protein SirB2 [Function unknown]. 126 matched cddid_all.tbl CDD COG3095 COG3095 442329 MukE Chromosome condensin MukBEF, MukE localization factor [Cell cycle control, cell division, chromosome partitioning]. 242 matched cddid_all.tbl CDD COG3096 COG3096 442330 MukB Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell division, chromosome partitioning]. 1470 matched cddid_all.tbl CDD COG3097 COG3097 442331 YqfB Uncharacterized conserved protein YqfB, UPF0267 family [Function unknown]. 102 matched cddid_all.tbl CDD COG3098 COG3098 442332 YqcC Uncharacterized conserved protein YqcC, DUF446 family [Function unknown]. 109 matched cddid_all.tbl CDD COG3099 COG3099 442333 YciU Uncharacterized conserved protein YciU, UPF0263 family [Function unknown]. 107 matched cddid_all.tbl CDD COG3100 COG3100 442334 YcgL Uncharacterized conserved protein YcgL, UPF0745 family [Function unknown]. 85 matched cddid_all.tbl CDD COG3101 COG3101 442335 EpmC Elongation factor P hydroxylase EpmC (EF-P beta-lysylation pathway) [Translation, ribosomal structure and biogenesis]. 180 matched cddid_all.tbl CDD COG3102 COG3102 442336 YecM Uncharacterized conserved protein YecM, predicted metalloenzyme [General function prediction only]. 187 matched cddid_all.tbl CDD COG3103 COG3103 442337 YgiM Uncharacterized conserved protein YgiM, contains N-terminal SH3 domain, DUF1202 family [General function prediction only]. 119 matched cddid_all.tbl CDD COG3104 COG3104 442338 PTR2 Dipeptide/tripeptide permease [Amino acid transport and metabolism]. 479 matched cddid_all.tbl CDD COG3105 COG3105 442339 YhcB Uncharacterized membrane-anchored protein YhcB, DUF1043 family [Function unknown]. 139 matched cddid_all.tbl CDD COG3106 COG3106 442340 YcjX Ras-like GTP-binding stress-induced protein YcjX, DUF463 family [Signal transduction mechanisms]. 467 matched cddid_all.tbl CDD COG3107 COG3107 442341 LpoA Outer membrane lipoprotein LpoA, binds and activates PBP1a [Cell wall/membrane/envelope biogenesis]. 610 matched cddid_all.tbl CDD COG3108 COG3108 442342 YcbK Uncharacterized conserved protein YcbK, DUF882 family [Function unknown]. 138 matched cddid_all.tbl CDD COG3109 COG3109 442343 ProQ sRNA-binding protein ProQ [Signal transduction mechanisms]. 153 matched cddid_all.tbl CDD COG3110 COG3110 442344 YccT Uncharacterized conserved protein YccT, UPF0319 family [Function unknown]. 215 matched cddid_all.tbl CDD COG3111 COG3111 442345 YdeI Predicted periplasmic protein YdeI with OB-fold, BOF family [Function unknown]. 125 matched cddid_all.tbl CDD COG3112 COG3112 442346 YacL Uncharacterized conserved protein YacL, UPF0231 family [Function unknown]. 122 matched cddid_all.tbl CDD COG3113 COG3113 442347 MlaB Binding protein subunit MlaB of the ABC-type intermembrane phospholipid transporter Mla, contains STAS domain [Cell wall/membrane/envelope biogenesis]. 97 matched cddid_all.tbl CDD COG3114 COG3114 442348 CcmD Heme exporter protein D [Intracellular trafficking, secretion, and vesicular transport]. 65 matched cddid_all.tbl CDD COG3115 COG3115 442349 ZipA Cell division protein ZipA, interacts with FtsZ [Cell cycle control, cell division, chromosome partitioning]. 298 matched cddid_all.tbl CDD COG3116 COG3116 442350 FtsL Cell division protein FtsL, interacts with FtsB and FtsQ [Cell cycle control, cell division, chromosome partitioning]. 88 matched cddid_all.tbl CDD COG3117 COG3117 442351 YrbK Lipopolysaccharide export system protein LptC [Cell wall/membrane/envelope biogenesis]. 183 matched cddid_all.tbl CDD COG3118 COG3118 442352 CnoX Chaperedoxin CnoX, contains thioredoxin-like and TPR-like domains, YbbN/TrxSC family [Posttranslational modification, protein turnover, chaperones]. 105 matched cddid_all.tbl CDD COG3119 COG3119 442353 AslA Arylsulfatase A or related enzyme, AlkP superfamily [Inorganic ion transport and metabolism]. 393 matched cddid_all.tbl CDD COG3120 COG3120 442354 MatP Macrodomain Ter protein organizer, MatP/YcbG family [Replication, recombination and repair]. 149 matched cddid_all.tbl CDD COG3121 COG3121 442355 FimC P pilus assembly protein, chaperone PapD [Extracellular structures]. 237 matched cddid_all.tbl CDD COG3122 COG3122 442356 YaiL Uncharacterized conserved protein YaiL, DUF2058 family [Function unknown]. 180 matched cddid_all.tbl CDD COG3123 COG3123 442357 PpnP Pyrimidine/purine nucleoside phosphorylase YaiE/PpnP, UPF0345/DUF1255 family [Nucleotide transport and metabolism]. 99 matched cddid_all.tbl CDD COG3124 COG3124 442358 AcpH Acyl carrier protein phosphodiesterase [Lipid transport and metabolism]. 196 matched cddid_all.tbl CDD COG3125 COG3125 442359 CyoD Heme/copper-type cytochrome/quinol oxidase, subunit 4 [Energy production and conversion]. 109 matched cddid_all.tbl CDD COG3126 COG3126 442360 YbaY Uncharacterized lipoprotein YbaY [Function unknown]. 142 matched cddid_all.tbl CDD COG3127 COG3127 442361 YbbP Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport and catabolism]. 830 matched cddid_all.tbl CDD COG3128 COG3128 442362 PiuC Predicted 2-oxoglutarate- and Fe(II)-dependent dioxygenase YbiX [General function prediction only]. 225 matched cddid_all.tbl CDD COG3129 COG3129 442363 RlmF 23S rRNA A1618 N6-methylase RlmF [Translation, ribosomal structure and biogenesis]. 23S rRNA A1618 N6-methylase RlmF is part of the Pathway/BioSystem: 23S rRNA modification 292 matched cddid_all.tbl CDD COG3130 COG3130 442364 Rmf Ribosome modulation factor [Translation, ribosomal structure and biogenesis]. 57 matched cddid_all.tbl CDD COG3131 COG3131 442365 MdoG Periplasmic glucan biosynthesis protein OpgG [Cell wall/membrane/envelope biogenesis]. 519 matched cddid_all.tbl CDD COG3132 COG3132 442366 YceH Uncharacterized conserved protein YceH, UPF0502 family [Function unknown]. 213 matched cddid_all.tbl CDD COG3133 COG3133 442367 SlyB Outer membrane lipoprotein SlyB [Cell wall/membrane/envelope biogenesis]. 152 matched cddid_all.tbl CDD COG3134 COG3134 442368 YcfJ Uncharacterized conserved protein YcfJ, contains glycine zipper 2TM domain [Function unknown]. 176 matched cddid_all.tbl CDD COG3135 COG3135 442369 BenE Predicted benzoate:H+ symporter BenE [Secondary metabolites biosynthesis, transport and catabolism]. 391 matched cddid_all.tbl CDD COG3136 COG3136 442370 GlpM Dual-topology membrane protein YdgC, GlpM family [Function unknown]. 112 matched cddid_all.tbl CDD COG3137 COG3137 442371 YdiY Putative salt-induced outer membrane protein YdiY [Cell wall/membrane/envelope biogenesis]. 245 matched cddid_all.tbl CDD COG3138 COG3138 442372 AstA Arginine/ornithine N-succinyltransferase beta subunit [Amino acid transport and metabolism]. 338 matched cddid_all.tbl CDD COG3139 COG3139 442373 yeaC Uncharacterized conserved protein YeaC, DUF1315 family [Function unknown]. 92 matched cddid_all.tbl CDD COG3140 COG3140 442374 yoaH Uncharacterized conserved protein YoaH, UPF0181 family [Function unknown]. 58 matched cddid_all.tbl CDD COG3141 COG3141 442375 YebG dsDNA-binding SOS-regulon protein YebG, induction by DNA damage requires cAMP [Replication, recombination and repair]. 100 matched cddid_all.tbl CDD COG3142 COG3142 442376 CutC Copper homeostasis protein CutC [Inorganic ion transport and metabolism]. 240 matched cddid_all.tbl CDD COG3143 COG3143 442377 CheZ Phosphoaspartate phosphatase CheZ, dephosphorylates CheY~P [Cell motility, Signal transduction mechanisms]. 235 matched cddid_all.tbl CDD COG3144 COG3144 442378 FliK Flagellar hook-length control protein FliK [Cell motility]. 234 matched cddid_all.tbl CDD COG3145 COG3145 442379 AlkB Alkylated DNA repair dioxygenase AlkB [Replication, recombination and repair]. 200 matched cddid_all.tbl CDD COG3146 COG3146 442380 COG3146 Predicted N-acyltransferase [General function prediction only]. 378 matched cddid_all.tbl CDD COG3147 COG3147 442381 DedD Cell division protein DedD (periplasmic protein involved in septation) [Cell cycle control, cell division, chromosome partitioning]. 140 matched cddid_all.tbl CDD COG3148 COG3148 442382 TapT tRNA U47 aminocarboxypropyltransferaseTapT/TuaA/ YfiP, DTW domain [Translation, ribosomal structure and biogenesis]. 211 matched cddid_all.tbl CDD COG3149 COG3149 442383 PulM Type II secretory pathway, component PulM [Intracellular trafficking, secretion, and vesicular transport]. 165 matched cddid_all.tbl CDD COG3150 COG3150 442384 YcfP Predicted esterase YcpF, UPF0227 family [General function prediction only]. 190 matched cddid_all.tbl CDD COG3151 COG3151 442385 yqiB Uncharacterized conserved protein YqiB, DUF1249 family [Function unknown]. 145 matched cddid_all.tbl CDD COG3152 COG3152 442386 yhaH Uncharacterized membrane protein YhaH, DUF805 family [Function unknown]. 118 matched cddid_all.tbl CDD COG3153 COG3153 442387 yhbS Predicted N-acetyltransferase YhbS [General function prediction only]. 142 matched cddid_all.tbl CDD COG3154 COG3154 442388 UbiT Ubiquinone biosynthesis accessory factor UbiT, lipid carrier SCP2 domain [Coenzyme transport and metabolism]. 161 matched cddid_all.tbl CDD COG3155 COG3155 442389 ElbB Glyoxalase ElbB, DJ-1 superfamily [Defense mechanisms]. 215 matched cddid_all.tbl CDD COG3156 COG3156 442390 PulK Type II secretory pathway, component PulK [Intracellular trafficking, secretion, and vesicular transport]. 307 matched cddid_all.tbl CDD COG3157 COG3157 442391 Hcp Type VI protein secretion system component Hcp (secreted cytotoxin) [Intracellular trafficking, secretion, and vesicular transport]. 162 matched cddid_all.tbl CDD COG3158 COG3158 442392 Kup K+ uptake protein Kup [Inorganic ion transport and metabolism]. 630 matched cddid_all.tbl CDD COG3159 COG3159 442393 YigA Uncharacterized conserved protein YigA, DUF484 family [Function unknown]. 218 matched cddid_all.tbl CDD COG3160 COG3160 442394 Rsd Regulator of sigma D [Transcription]. 160 matched cddid_all.tbl CDD COG3161 COG3161 442395 UbiC 4-hydroxybenzoate synthetase (chorismate-pyruvate lyase) [Coenzyme transport and metabolism]. 4-hydroxybenzoate synthetase (chorismate-pyruvate lyase) is part of the Pathway/BioSystem: Ubiquinone biosynthesis 177 matched cddid_all.tbl CDD COG3162 COG3162 442396 YjcH Uncharacterized membrane protein, DUF485 family [Function unknown]. 104 matched cddid_all.tbl CDD COG3164 COG3164 442397 YhdR Uncharacterized conserved protein YhdP, contains DUF3971 and AsmA2 domains [Function unknown]. 1289 matched cddid_all.tbl CDD COG3165 COG3165 442398 UbiJ Ubiquinone biosynthesis protein UbiJ, contains SCP2 domain [Coenzyme transport and metabolism]. 204 matched cddid_all.tbl CDD COG3166 COG3166 442399 PilN Type IV pilus assembly protein PilN [Cell motility, Extracellular structures]. 185 matched cddid_all.tbl CDD COG3167 COG3167 442400 PilO Type IV pilus assembly protein PilO [Cell motility, Extracellular structures]. 202 matched cddid_all.tbl CDD COG3168 COG3168 442401 PilP Type IV pilus assembly protein PilP [Cell motility, Extracellular structures]. 171 matched cddid_all.tbl CDD COG3169 COG3169 442402 COG3169 Uncharacterized membrane protein, DMT/DUF486 family [Function unknown]. 112 matched cddid_all.tbl CDD COG3170 COG3170 442403 FimV Type IV pilus assembly protein FimV [Cell motility, Extracellular structures]. 508 matched cddid_all.tbl CDD COG3171 COG3171 442404 YggL Uncharacterized conserved protein YggL, DUF469 family [Function unknown]. 110 matched cddid_all.tbl CDD COG3172 COG3172 442405 NadR3 Nicotinamide riboside kinase [Coenzyme transport and metabolism]. Nicotinamide riboside kinase is part of the Pathway/BioSystem: NAD biosynthesis 178 matched cddid_all.tbl CDD COG3173 COG3173 442406 YcbJ Predicted kinase, aminoglycoside phosphotransferase (APT) family [General function prediction only]. 284 matched cddid_all.tbl CDD COG3174 COG3174 442407 MgtC Membrane component of predicted Mg2+ transport system, contains DUF4010 domain [Inorganic ion transport and metabolism]. 423 matched cddid_all.tbl CDD COG3175 COG3175 442408 COX11 Cytochrome c oxidase assembly protein Cox11 [Energy production and conversion, Posttranslational modification, protein turnover, chaperones]. 189 matched cddid_all.tbl CDD COG3176 COG3176 442409 COG3176 Putative hemolysin [General function prediction only]. 270 matched cddid_all.tbl CDD COG3177 COG3177 442410 COG3177 Fic family protein [Transcription]. 316 matched cddid_all.tbl CDD COG3178 COG3178 442411 COG3178 Predicted phosphotransferase, aminoglycoside/choline kinase (APH/ChoK) family [General function prediction only]. 327 matched cddid_all.tbl CDD COG3179 COG3179 442412 GH19 Chitinase, GH19 family [Carbohydrate transport and metabolism]. 193 matched cddid_all.tbl CDD COG3180 COG3180 442413 AbrB Uncharacterized membrane protein AbrB, regulator of aidB expression [General function prediction only]. 352 matched cddid_all.tbl CDD COG3181 COG3181 442414 TctC Tripartite-type tricarboxylate transporter, extracytoplasmic receptor component TctC [Energy production and conversion]. 324 matched cddid_all.tbl CDD COG3182 COG3182 442415 PiuB PepSY-associated TM region [Function unknown]. 379 matched cddid_all.tbl CDD COG3183 COG3183 442416 COG3183 Predicted restriction endonuclease, HNH family [Defense mechanisms]. 112 matched cddid_all.tbl CDD COG3184 COG3184 442417 COG3184 Uncharacterized conserved protein, contains DUF2059 domain [Function unknown]. 163 matched cddid_all.tbl CDD COG3185 COG3185 442418 HppD 4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism, General function prediction only]. 333 matched cddid_all.tbl CDD COG3186 COG3186 442419 PhhA Phenylalanine-4-hydroxylase [Amino acid transport and metabolism]. 279 matched cddid_all.tbl CDD COG3187 COG3187 442420 HslJ Heat shock protein HslJ [Posttranslational modification, protein turnover, chaperones]. 110 matched cddid_all.tbl CDD COG3188 COG3188 442421 FimD Outer membrane usher protein FimD/PapC [Cell motility, Extracellular structures]. 817 matched cddid_all.tbl CDD COG3189 COG3189 442422 YeaO Uncharacterized conserved protein YeaO, DUF488 family [Function unknown]. 119 matched cddid_all.tbl CDD COG3190 COG3190 442423 FliO Flagellar biogenesis protein FliO [Cell motility]. 122 matched cddid_all.tbl CDD COG3191 COG3191 442424 DmpA L-aminopeptidase/D-esterase [Amino acid transport and metabolism]. 309 matched cddid_all.tbl CDD COG3192 COG3192 442425 EutH Ethanolamine transporter EutH, required for ethanolamine utilization at low pH [Amino acid transport and metabolism]. 367 matched cddid_all.tbl CDD COG3193 COG3193 442426 GlcG Heme-binding protein HbpS, GlcG/HbpS family [Signal transduction mechanisms]. 135 matched cddid_all.tbl CDD COG3194 COG3194 442427 AllA Ureidoglycolate hydrolase (allantoin degradation) [Nucleotide transport and metabolism]. 164 matched cddid_all.tbl CDD COG3195 COG3195 442428 PucL 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) decarboxylase (uric acid degradation) [Nucleotide transport and metabolism]. 169 matched cddid_all.tbl CDD COG3196 COG3196 442429 CbrC Colicin E2 tolerance protein CbrC, UPF0167 family [General function prediction only]. 176 matched cddid_all.tbl CDD COG3197 COG3197 442430 FixS Cytochrome oxidase maturation protein, CcoS/FixS family [Posttranslational modification, protein turnover, chaperones]. 60 matched cddid_all.tbl CDD COG3198 COG3198 442431 COG3198 Uncharacterized conserved protein [Function unknown]. 168 matched cddid_all.tbl CDD COG3199 COG3199 442432 COG3199 NAD kinase [Nucleotide transport and metabolism]. 367 matched cddid_all.tbl CDD COG3200 COG3200 442433 AroG2 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase, class II [Amino acid transport and metabolism]. 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase, class II is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 447 matched cddid_all.tbl CDD COG3201 COG3201 442434 PnuC Nicotinamide riboside transporter PnuC [Coenzyme transport and metabolism]. 203 matched cddid_all.tbl CDD COG3202 COG3202 442435 TlcC ATP/ADP translocase [Energy production and conversion]. 430 matched cddid_all.tbl CDD COG3203 COG3203 442436 OmpC Outer membrane porin OmpC/OmpF/PhoE [Cell wall/membrane/envelope biogenesis]. 336 matched cddid_all.tbl CDD COG3204 COG3204 442437 YjiK Uncharacterized Ca-binding beta-propeller protein YjiK [General function prediction only]. 271 matched cddid_all.tbl CDD COG3205 COG3205 442438 COG3205 Uncharacterized membrane protein, DUF2061 family [Function unknown]. 64 matched cddid_all.tbl CDD COG3206 COG3206 442439 GumC Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis]. 687 matched cddid_all.tbl CDD COG3207 COG3207 442440 Dit1 Pyoverdine/dityrosine biosynthesis protein Dit1 [Secondary metabolites biosynthesis, transport and catabolism]. 313 matched cddid_all.tbl CDD COG3208 COG3208 442441 GrsT Surfactin synthase thioesterase subunit [Secondary metabolites biosynthesis, transport and catabolism]. 237 matched cddid_all.tbl CDD COG3209 COG3209 442442 RhsA Uncharacterized conserved protein RhaS, contains 28 RHS repeats [General function prediction only]. 1103 matched cddid_all.tbl CDD COG3210 COG3210 442443 FhaB Large exoprotein involved in heme utilization or adhesion [Intracellular trafficking, secretion, and vesicular transport]. 1698 matched cddid_all.tbl CDD COG3211 COG3211 442444 PhoX Secreted phosphatase, PhoX family [General function prediction only]. 568 matched cddid_all.tbl CDD COG3212 COG3212 442445 YkoI PepSY domain containing protein, regulator of zincin peptidase activity [Posttranslational modification, protein turnover, chaperones]. 66 matched cddid_all.tbl CDD COG3213 COG3213 442446 NnrS Nitric oxide response protein NnrS [Signal transduction mechanisms]. 393 matched cddid_all.tbl CDD COG3214 COG3214 442447 YcaQ DNA glycosylase YcaQ, repair of DNA interstrand crosslinks [Replication, recombination and repair]. 400 matched cddid_all.tbl CDD COG3215 COG3215 442448 PilZ Type IV pilus assembly protein PilZ [Cell motility, Extracellular structures]. 117 matched cddid_all.tbl CDD COG3216 COG3216 442449 COG3216 Uncharacterized conserved protein, DUF2062 family [Function unknown]. 169 matched cddid_all.tbl CDD COG3217 COG3217 442450 YcbX N-hydroxylaminopurine reductase subunit YcbX, contains MOSC domain [Nucleotide transport and metabolism, Defense mechanisms]. 240 matched cddid_all.tbl CDD COG3218 COG3218 442451 COG3218 ABC-type uncharacterized transport system, auxiliary component [General function prediction only]. 202 matched cddid_all.tbl CDD COG3219 COG3219 442452 COG3219 Uncharacterized conserved protein, DUF2063 family [Function unknown]. 249 matched cddid_all.tbl CDD COG3220 COG3220 442453 COG3220 Uncharacterized conserved protein, UPF0276 family [Function unknown]. 276 matched cddid_all.tbl CDD COG3221 COG3221 442454 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]. 250 matched cddid_all.tbl CDD COG3222 COG3222 442455 COG3222 Uncharacterized conserved protein, glycosyltransferase A (GT-A) superfamily, DUF2064 family [Function unknown]. 211 matched cddid_all.tbl CDD COG3223 COG3223 442456 PsiE Phosphate starvation-inducible membrane PsiE (function unknown) [General function prediction only]. 130 matched cddid_all.tbl CDD COG3224 COG3224 442457 COG3224 Antibiotic biosynthesis monooxygenase (ABM) superfamily enzyme [General function prediction only]. 183 matched cddid_all.tbl CDD COG3225 COG3225 442458 GldG ABC-type uncharacterized transport system involved in gliding motility, auxiliary component [Cell motility]. 494 matched cddid_all.tbl CDD COG3226 COG3226 442459 YbjK DNA-binding transcriptional regulator YbjK [Transcription]. 191 matched cddid_all.tbl CDD COG3227 COG3227 442460 LasB Zn-dependent metalloprotease (Neutral protease B) [Posttranslational modification, protein turnover, chaperones]. 608 matched cddid_all.tbl CDD COG3228 COG3228 442461 MtfA Mlc titration factor MtfA, regulates ptsG expression [Signal transduction mechanisms]. 253 matched cddid_all.tbl CDD COG3230 COG3230 442462 HemO Heme oxygenase [Inorganic ion transport and metabolism]. 192 matched cddid_all.tbl CDD COG3231 COG3231 442463 Aph Aminoglycoside phosphotransferase [Translation, ribosomal structure and biogenesis]. 258 matched cddid_all.tbl CDD COG3232 COG3232 442464 HpaF 5-carboxymethyl-2-hydroxymuconate isomerase [Amino acid transport and metabolism]. 121 matched cddid_all.tbl CDD COG3233 COG3233 442465 COG3233 Predicted deacetylase [General function prediction only]. 244 matched cddid_all.tbl CDD COG3234 COG3234 442466 yfaT Uncharacterized conserved protein YfaT, DUF1175 family [Function unknown]. 231 matched cddid_all.tbl CDD COG3235 COG3235 442467 COG3235 Uncharacterized membrane protein [Function unknown]. 221 matched cddid_all.tbl CDD COG3236 COG3236 442468 RibX N-glycosidase YbiA/RibX (riboflavin biosynthesis, damage control), NADAR superfamily [Coenzyme transport and metabolism, Defense mechanisms]. 148 matched cddid_all.tbl CDD COG3237 COG3237 442469 yjbJ Uncharacterized conserved protein YjbJ, UPF0337 family [Function unknown]. 65 matched cddid_all.tbl CDD COG3238 COG3238 442470 ydcZ Uncharacterized membrane protein YdcZ, DUF606 family [Function unknown]. 148 matched cddid_all.tbl CDD COG3239 COG3239 442471 DesA Fatty acid desaturase [Lipid transport and metabolism]. 319 matched cddid_all.tbl CDD COG3240 COG3240 442472 COG3240 Phospholipase/lecithinase/hemolysin [Lipid transport and metabolism, General function prediction only]. 305 matched cddid_all.tbl CDD COG3241 COG3241 442473 BlueCu Azurin [Energy production and conversion]. 158 matched cddid_all.tbl CDD COG3242 COG3242 442474 yjeT Uncharacterized conserved protein YjeT, DUF2065 family [Function unknown]. 62 matched cddid_all.tbl CDD COG3243 COG3243 442475 PhaC Poly-beta-hydroxybutyrate synthase [Lipid transport and metabolism]. 545 matched cddid_all.tbl CDD COG3245 COG3245 442476 CytC5 Cytochrome c5 [Energy production and conversion]. 108 matched cddid_all.tbl CDD COG3246 COG3246 442477 COG3246 Uncharacterized conserved protein, DUF849 family [Function unknown]. 276 matched cddid_all.tbl CDD COG3247 COG3247 442478 HdeD Acid resistance membrane protein HdeD, DUF308 family [General function prediction only]. 178 matched cddid_all.tbl CDD COG3248 COG3248 442479 Tsx Nucleoside-specific outer membrane channel protein Tsx [Cell wall/membrane/envelope biogenesis]. 267 matched cddid_all.tbl CDD COG3249 COG3249 442480 COG3249 Uncharacterized conserved protein, DUF2066 domain [Function unknown]. 347 matched cddid_all.tbl CDD COG3250 COG3250 442481 LacZ Beta-galactosidase/beta-glucuronidase [Carbohydrate transport and metabolism]. 638 matched cddid_all.tbl CDD COG3251 COG3251 442482 MbtH MbtH family protein, regulates adenylation domains of NRPSs [Secondary metabolites biosynthesis, transport and catabolism]. 71 matched cddid_all.tbl CDD COG3252 COG3252 442483 Mch Methenyltetrahydromethanopterin cyclohydrolase [Coenzyme transport and metabolism]. 315 matched cddid_all.tbl CDD COG3253 COG3253 442484 HemQ Coproheme decarboxylase/chlorite dismutase [Coenzyme transport and metabolism, Inorganic ion transport and metabolism]. 231 matched cddid_all.tbl CDD COG3254 COG3254 442485 RhaM L-rhamnose mutarotase [Cell wall/membrane/envelope biogenesis]. 104 matched cddid_all.tbl CDD COG3255 COG3255 442486 SCP2 Putative sterol carrier protein, contains SCP2 domain [Lipid transport and metabolism]. 104 matched cddid_all.tbl CDD COG3256 COG3256 442487 NorB Nitric oxide reductase large subunit [Inorganic ion transport and metabolism]. 738 matched cddid_all.tbl CDD COG3257 COG3257 442488 AllE Ureidoglycine aminohydrolase [Nucleotide transport and metabolism]. 262 matched cddid_all.tbl CDD COG3258 COG3258 442489 TsdA Thiosulfate dehydrogenase TsdA, contains C-terminal cytochrome c domain [Inorganic ion transport and metabolism]. 216 matched cddid_all.tbl CDD COG3259 COG3259 442490 FrhA Coenzyme F420-reducing hydrogenase, alpha subunit [Energy production and conversion]. 458 matched cddid_all.tbl CDD COG3260 COG3260 442491 HycG Ni,Fe-hydrogenase III small subunit [Energy production and conversion]. 137 matched cddid_all.tbl CDD COG3261 COG3261 442492 HycE2 Ni,Fe-hydrogenase III large subunit [Energy production and conversion]. 479 matched cddid_all.tbl CDD COG3262 COG3262 442493 HycE1 Ni,Fe-hydrogenase III component G [Energy production and conversion]. 523 matched cddid_all.tbl CDD COG3263 COG3263 442494 NhaP2 NhaP-type Na+/H+ and K+/H+ antiporter with C-terminal TrkAC and CorC domains [Energy production and conversion, Inorganic ion transport and metabolism]. 502 matched cddid_all.tbl CDD COG3264 COG3264 442495 MscK Small-conductance mechanosensitive channel MscK [Cell wall/membrane/envelope biogenesis]. 281 matched cddid_all.tbl CDD COG3265 COG3265 442496 GntK Gluconate kinase [Carbohydrate transport and metabolism]. Gluconate kinase is part of the Pathway/BioSystem: Non-phosphorylated Entner-Doudoroff pathway 164 matched cddid_all.tbl CDD COG3266 COG3266 442497 DamX Cell division protein DamX, binds to the septal ring, contains C-terminal SPOR domain [Cell cycle control, cell division, chromosome partitioning]. 455 matched cddid_all.tbl CDD COG3267 COG3267 442498 ExeA Type II secretory pathway ATPase component GspA/ExeA/MshM [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures]. 261 matched cddid_all.tbl CDD COG3268 COG3268 442499 COG3268 Uncharacterized conserved protein, related to short-chain dehydrogenases [Function unknown]. 368 matched cddid_all.tbl CDD COG3269 COG3269 442500 COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]. 129 matched cddid_all.tbl CDD COG3270 COG3270 442501 Ncl1 Ribosome biogenesis protein, NOL1/NOP2/FMU family [Translation, ribosomal structure and biogenesis]. 452 matched cddid_all.tbl CDD COG3271 COG3271 442502 C39G Predicted double-glycine leader peptidase, C39-like (CLD) domain [Intracellular trafficking, secretion, and vesicular transport]. 179 matched cddid_all.tbl CDD COG3272 COG3272 442503 YbgA Uncharacterized conserved protein YbgA, DUF1722 family [Function unknown]. 246 matched cddid_all.tbl CDD COG3273 COG3273 442504 COG3273 Uncharacterized protein, contains PhoU and TrkA_C domains [General function prediction only]. 387 matched cddid_all.tbl CDD COG3274 COG3274 442505 WecH Surface polysaccharide O-acyltransferase WecH [Cell wall/membrane/envelope biogenesis]. 345 matched cddid_all.tbl CDD COG3275 COG3275 442506 LytS Sensor histidine kinase, LytS/YehU family [Signal transduction mechanisms]. 352 matched cddid_all.tbl CDD COG3276 COG3276 442507 SelB Selenocysteine-specific translation elongation factor SelB [Translation, ribosomal structure and biogenesis]. Selenocysteine-specific translation elongation factor SelB is part of the Pathway/BioSystem: Translation factors 630 matched cddid_all.tbl CDD COG3277 COG3277 442508 GAR1 rRNA processing protein Gar1 [Translation, ribosomal structure and biogenesis]. rRNA processing protein Gar1 is part of the Pathway/BioSystem: 16S rRNA modification 76 matched cddid_all.tbl CDD COG3278 COG3278 442509 CcoN Cbb3-type cytochrome oxidase, subunit 1 [Energy production and conversion]. 474 matched cddid_all.tbl CDD COG3279 COG3279 442510 LytT DNA-binding response regulator, LytR/AlgR family [Transcription, Signal transduction mechanisms]. 235 matched cddid_all.tbl CDD COG3280 COG3280 442511 TreY Maltooligosyltrehalose synthase [Carbohydrate transport and metabolism]. 915 matched cddid_all.tbl CDD COG3281 COG3281 442512 Ble Predicted trehalose synthase [Carbohydrate transport and metabolism]. 1004 matched cddid_all.tbl CDD COG3283 COG3283 442513 TyrR Transcriptional regulator TyrR of aromatic amino acids metabolism [Transcription, Amino acid transport and metabolism]. 514 matched cddid_all.tbl CDD COG3284 COG3284 442514 AcoR Transcriptional regulator DhaR of acetoin/glycerol metabolism [Transcription]. 625 matched cddid_all.tbl CDD COG3285 COG3285 442515 LigD Eukaryotic-type DNA primase [Replication, recombination and repair]. 300 matched cddid_all.tbl CDD COG3286 COG3286 442516 COG3286 Uncharacterized conserved protein, DUF2067 domain [Function unknown]. 205 matched cddid_all.tbl CDD COG3287 COG3287 442517 FIST FIST domain protein MJ1623, contains FIST_N and FIST_C domains [Signal transduction mechanisms]. 382 matched cddid_all.tbl CDD COG3288 COG3288 442518 PntA NAD/NADP transhydrogenase alpha subunit [Energy production and conversion]. 359 matched cddid_all.tbl CDD COG3290 COG3290 442519 CitA Sensor histidine kinase DipB regulating citrate/malate metabolism [Signal transduction mechanisms]. 389 matched cddid_all.tbl CDD COG3291 COG3291 442520 COG3291 Uncharacterized conserved protein, PKD repeat domain [Function unknown]. 333 matched cddid_all.tbl CDD COG3292 COG3292 442521 COG3292 Periplasmic ligand-binding sensor domain [Signal transduction mechanisms]. 924 matched cddid_all.tbl CDD COG3293 COG3293 442522 COG3293 Transposase [Mobilome: prophages, transposons]. 98 matched cddid_all.tbl CDD COG3294 COG3294 442523 COG3294 Metal-dependent phosphatase/phosphodiesterase, HD supefamily [General function prediction only]. 259 matched cddid_all.tbl CDD COG3295 COG3295 442524 COG3295 Uncharacterized conserved protein [Function unknown]. 209 matched cddid_all.tbl CDD COG3296 COG3296 442525 Tic20a Uncharacterized Tic20-related protein, DUF4870 domain [General function prediction only]. 119 matched cddid_all.tbl CDD COG3297 COG3297 442526 PulL Type II secretory pathway, component PulL [Intracellular trafficking, secretion, and vesicular transport]. 404 matched cddid_all.tbl CDD COG3298 COG3298 442527 COG3298 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB [Replication, recombination and repair]. 211 matched cddid_all.tbl CDD COG3299 COG3299 442528 JayE Uncharacterized phage protein gp47/JayE [Mobilome: prophages, transposons]. 340 matched cddid_all.tbl CDD COG3300 COG3300 442529 MHYT MHYT domain, NO-binding membrane sensor [Signal transduction mechanisms]. 440 matched cddid_all.tbl CDD COG3301 COG3301 442530 NrfD Nitrite/polysulfide reductase, membrane component NrfD/PsrC [Inorganic ion transport and metabolism]. 297 matched cddid_all.tbl CDD COG3302 COG3302 442531 DmsC DMSO reductase anchor subunit DmsC [Energy production and conversion]. 282 matched cddid_all.tbl CDD COG3303 COG3303 442532 NrfA Formate-dependent nitrite reductase, periplasmic cytochrome c552 subunit [Inorganic ion transport and metabolism]. 464 matched cddid_all.tbl CDD COG3304 COG3304 442533 YccF Uncharacterized membrane protein YccF, DUF307 family [Function unknown]. 130 matched cddid_all.tbl CDD COG3305 COG3305 442534 COG3305 Uncharacterized membrane protein, DUF2068 family [Function unknown]. 148 matched cddid_all.tbl CDD COG3306 COG3306 442535 COG3306 Glycosyltransferase involved in LPS biosynthesis, GR25 family [Cell wall/membrane/envelope biogenesis]. 238 matched cddid_all.tbl CDD COG3307 COG3307 442536 RfaL O-antigen ligase [Cell wall/membrane/envelope biogenesis]. 239 matched cddid_all.tbl CDD COG3308 COG3308 442537 COG3308 Uncharacterized membrane protein [Function unknown]. 127 matched cddid_all.tbl CDD COG3309 COG3309 442538 VapD Virulence-associated protein VapD, endoribonuclease [Defense mechanisms]. 98 matched cddid_all.tbl CDD COG3310 COG3310 442539 COG3310 Uncharacterized conserved protein, DUF1415 family [Function unknown]. 184 matched cddid_all.tbl CDD COG3311 COG3311 442540 AlpA DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons]. 64 matched cddid_all.tbl CDD COG3312 COG3312 442541 AtpI FoF1-type ATP synthase accessory protein AtpI [Energy production and conversion]. FoF1-type ATP synthase accessory protein AtpI is part of the Pathway/BioSystem: FoF1-type ATP synthase 124 matched cddid_all.tbl CDD COG3313 COG3313 442542 YdhL Predicted Fe-S protein YdhL, DUF1289 family [General function prediction only]. 59 matched cddid_all.tbl CDD COG3314 COG3314 442543 SpoVV Spore dipicolinate transporter SpoVV/YjiH/YlbJ, contains nucleoside recognition GATE domain [Cell cycle control, cell division, chromosome partitioning, Amino acid transport and metabolism]. 434 matched cddid_all.tbl CDD COG3315 COG3315 442544 YktD O-Methyltransferase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport and catabolism]. 246 matched cddid_all.tbl CDD COG3316 COG3316 442545 Rve Transposase (or an inactivated derivative), DDE domain [Mobilome: prophages, transposons]. 235 matched cddid_all.tbl CDD COG3317 COG3317 442546 BamC Outer membrane beta-barrel protein assembly factor BamC [Cell wall/membrane/envelope biogenesis]. 354 matched cddid_all.tbl CDD COG3318 COG3318 442547 YecA Uncharacterized conserved protein YecA, UPF0149 family, contains C-terminal Zn-binding SEC-C motif [Function unknown]. 45 matched cddid_all.tbl CDD COG3319 COG3319 442548 EntF2 Thioesterase domain of type I polyketide synthase or non-ribosomal peptide synthetase [Secondary metabolites biosynthesis, transport and catabolism]. 855 matched cddid_all.tbl CDD COG3320 COG3320 442549 Lys2b Thioester reductase domain of alpha aminoadipate reductase Lys2 and NRPSs [Secondary metabolites biosynthesis, transport and catabolism]. Thioester reductase domain of alpha aminoadipate reductase Lys2 and NRPSs is part of the Pathway/BioSystem: Lysine biosynthesis 265 matched cddid_all.tbl CDD COG3321 COG3321 442550 PksD Acyl transferase domain in polyketide synthase (PKS) enzymes [Secondary metabolites biosynthesis, transport and catabolism]. 1386 matched cddid_all.tbl CDD COG3322 COG3322 442551 CHASE4 Extracellular (periplasmic) sensor domain CHASE (specificity unknown) [Signal transduction mechanisms]. 724 matched cddid_all.tbl CDD COG3323 COG3323 442552 YqfO PII-like insert in the uncharacterized protein YqfO, YbgI/NIF3 family [Function unknown]. 360 matched cddid_all.tbl CDD COG3324 COG3324 442553 VOC Lactoylglutathione lyase-related enzyme, vicinal oxygen chelate (VOC) family [General function prediction only]. 119 matched cddid_all.tbl CDD COG3325 COG3325 442554 ChiA Chitinase, GH18 family [Carbohydrate transport and metabolism]. 391 matched cddid_all.tbl CDD COG3326 COG3326 442555 YsdA Uncharacterized membrane protein YsdA, DUF1294 family [Function unknown]. 90 matched cddid_all.tbl CDD COG3327 COG3327 442556 PaaX DNA-binding transcriptional regulator PaaX (phenylacetic acid degradation) [Transcription]. 281 matched cddid_all.tbl CDD COG3328 COG3328 442557 IS285 Transposase (or an inactivated derivative) [Mobilome: prophages, transposons]. 400 matched cddid_all.tbl CDD COG3329 COG3329 442558 COG3329 Uncharacterized conserved protein Alr0986 [Function unknown]. 327 matched cddid_all.tbl CDD COG3330 COG3330 442559 COG3330 Uncharacterized conserved protein BH1414 [Function unknown]. 195 matched cddid_all.tbl CDD COG3331 COG3331 442560 YotM Penicillin-binding protein-related factor A, putative recombinase [General function prediction only]. 197 matched cddid_all.tbl CDD COG3332 COG3332 442561 Tango2 Uncharacterized stress-responsive protein, TANGO2 (Transport and Golgi organisation 2) family, contains NRDE motif [General function prediction only]. 257 matched cddid_all.tbl CDD COG3333 COG3333 442562 COG3333 TctA family transporter [General function prediction only]. 493 matched cddid_all.tbl CDD COG3334 COG3334 442563 MotE Flagellar motility protein MotE, a chaperone for MotC folding [Cell motility]. 129 matched cddid_all.tbl CDD COG3335 COG3335 442564 COG3335 Transposase [Mobilome: prophages, transposons]. 292 matched cddid_all.tbl CDD COG3336 COG3336 442565 CtaG Cytochrome c oxidase assembly protein CtaG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones]. 272 matched cddid_all.tbl CDD COG3337 COG3337 442566 Cmr5 CRISPR-Cas system type III CMR-effector complex small subunit Cmr5 [Defense mechanisms]. CRISPR-Cas system type III CMR-effector complex small subunit Cmr5 is part of the Pathway/BioSystem: CRISPR-Cas system 132 matched cddid_all.tbl CDD COG3338 COG3338 442567 Cah Carbonic anhydrase [Inorganic ion transport and metabolism]. 247 matched cddid_all.tbl CDD COG3339 COG3339 442568 YkvA Uncharacterized membrane protein YkvA, DUF1232 family [Function unknown]. 104 matched cddid_all.tbl CDD COG3340 COG3340 442569 PepE Peptidase E [Amino acid transport and metabolism]. 212 matched cddid_all.tbl CDD COG3341 COG3341 442570 Rnh1 Ribonuclease HI-related protein, contains viroplasmin and RNaseH domains [General function prediction only]. 203 matched cddid_all.tbl CDD COG3342 COG3342 442571 COG3342 Uncharacterized conserved protein, Ntn-hydrolase superfamily [General function prediction only]. 209 matched cddid_all.tbl CDD COG3343 COG3343 442572 RpoE DNA-directed RNA polymerase, delta subunit [Transcription]. DNA-directed RNA polymerase, delta subunit is part of the Pathway/BioSystem: RNA polymerase 90 matched cddid_all.tbl CDD COG3344 COG3344 442573 YkfC Retron-type reverse transcriptase [Mobilome: prophages, transposons]. 434 matched cddid_all.tbl CDD COG3345 COG3345 442574 GalA Alpha-galactosidase [Carbohydrate transport and metabolism]. 219 matched cddid_all.tbl CDD COG3346 COG3346 442575 Shy1 Cytochrome oxidase assembly protein ShyY1 [Posttranslational modification, protein turnover, chaperones]. 245 matched cddid_all.tbl CDD COG3347 COG3347 442576 RhaD Rhamnose utilisation protein RhaD, predicted bifunctional aldolase and dehydrogenase [Carbohydrate transport and metabolism]. 674 matched cddid_all.tbl CDD COG3349 COG3349 442577 COG3349 Uncharacterized protein, contains NAD-binding domain and a Fe-S cluster [General function prediction only]. 445 matched cddid_all.tbl CDD COG3350 COG3350 442578 YHS Heavy metal-bindng TRASH/YHS domain, predicted Cu/Ag metallochaperone [Inorganic ion transport and metabolism]. 56 matched cddid_all.tbl CDD COG3351 COG3351 442579 FlaD Archaellum component ArlD/FlaD/FlaE [Cell motility]. 118 matched cddid_all.tbl CDD COG3352 COG3352 442580 FlaC Archaellum component ArlC/FlaC [Cell motility]. 270 matched cddid_all.tbl CDD COG3353 COG3353 442581 FlaF Archaellum component FlaF, FlaF/FlaG flagellin family [Cell motility]. 144 matched cddid_all.tbl CDD COG3354 COG3354 442582 FlaG Archaellum component FlaG, FlaF/FlaG flagellin family [Cell motility]. 151 matched cddid_all.tbl CDD COG3355 COG3355 442583 COG3355 Predicted transcriptional regulator [Transcription]. 131 matched cddid_all.tbl CDD COG3356 COG3356 442584 COG3356 Predicted membrane-associated lipid hydrolase, neutral ceramidase superfamily [Lipid transport and metabolism]. 588 matched cddid_all.tbl CDD COG3357 COG3357 442585 COG3357 Predicted transcriptional regulator, contains HTH and Zn-ribbon domains [Transcription]. 92 matched cddid_all.tbl CDD COG3358 COG3358 442586 COG3358 Uncharacterized conserved protein, DUF1684 family [Function unknown]. 188 matched cddid_all.tbl CDD COG3359 COG3359 442587 YprB Uncharacterized conserved protein YprB, contains RNaseH-like and TPR domains [General function prediction only]. 198 matched cddid_all.tbl CDD COG3360 COG3360 442588 COG3360 Flavin-binding protein dodecin [General function prediction only]. 68 matched cddid_all.tbl CDD COG3361 COG3361 442589 YqjF Uncharacterized conserved protein YqjF, DUF2071 family [Function unknown]. 235 matched cddid_all.tbl CDD COG3363 COG3363 442590 PurO Archaeal IMP cyclohydrolase [Nucleotide transport and metabolism]. Archaeal IMP cyclohydrolase is part of the Pathway/BioSystem: Purine biosynthesis 203 matched cddid_all.tbl CDD COG3364 COG3364 442591 COG3364 Predicted nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]. 127 matched cddid_all.tbl CDD COG3365 COG3365 442592 COG3365 Uncharacterized conserved protein, DUF2073 family [Function unknown]. 121 matched cddid_all.tbl CDD COG3366 COG3366 442593 COG3366 Uncharacterized membrane protein [Function unknown]. 312 matched cddid_all.tbl CDD COG3367 COG3367 442594 COG3367 Uncharacterized conserved protein, NAD-dependent epimerase/dehydratase family [General function prediction only]. 347 matched cddid_all.tbl CDD COG3368 COG3368 442595 COG3368 Predicted permease [General function prediction only]. 489 matched cddid_all.tbl CDD COG3369 COG3369 442596 COG3369 Uncharacterized conserved protein, contains Zn-finger domain of CDGSH type [Function unknown]. 68 matched cddid_all.tbl CDD COG3370 COG3370 442597 COG3370 Uncharacterized conserved protein AF1964, DsrE/DsrF-like family [General function prediction only]. 112 matched cddid_all.tbl CDD COG3371 COG3371 442598 COG3371 Uncharacterized membrane protein [Function unknown]. 194 matched cddid_all.tbl CDD COG3372 COG3372 442599 COG3372 Predicted nuclease of restriction endonuclease-like (RecB) superfamily, implicated in nucleotide excision repair [General function prediction only]. 403 matched cddid_all.tbl CDD COG3373 COG3373 442600 COG3373 Predicted transcriptional regulator, contains HTH domain [Transcription]. 112 matched cddid_all.tbl CDD COG3374 COG3374 442601 COG3374 Uncharacterized membrane protein [Function unknown]. 197 matched cddid_all.tbl CDD COG3375 COG3375 442602 COG3375 Predicted acetyltransferase, GNAT superfamily [General function prediction only]. 271 matched cddid_all.tbl CDD COG3376 COG3376 442603 HoxN High-affinity nickel/cobalt permease [Inorganic ion transport and metabolism]. 342 matched cddid_all.tbl CDD COG3377 COG3377 442604 YunC Uncharacterized conserved protein YunC, DUF1805 family [Function unknown]. 95 matched cddid_all.tbl CDD COG3378 COG3378 442605 COG3378 DNA primase, phage- or plasmid-associated [Mobilome: prophages, transposons]. 403 matched cddid_all.tbl CDD COG3379 COG3379 442606 COG3379 Predicted phosphohydrolase or phosphomutase, AlkP superfamily [General function prediction only]. 472 matched cddid_all.tbl CDD COG3380 COG3380 442607 COG3380 Predicted NAD/FAD-dependent oxidoreductase [General function prediction only]. 331 matched cddid_all.tbl CDD COG3381 COG3381 442608 TorD Cytoplasmic chaperone TorD involved in molybdoenzyme TorA maturation [Posttranslational modification, protein turnover, chaperones]. 205 matched cddid_all.tbl CDD COG3382 COG3382 442609 B3/B4 B3/B4 domain (DNA/RNA-binding domain of Phe-tRNA-synthetase) [General function prediction only]. 233 matched cddid_all.tbl CDD COG3383 COG3383 442610 YjgC Predicted molibdopterin-dependent oxidoreductase YjgC [General function prediction only]. 684 matched cddid_all.tbl CDD COG3384 COG3384 442611 LigB Aromatic ring-opening dioxygenase, catalytic subunit, LigB family [Secondary metabolites biosynthesis, transport and catabolism]. 260 matched cddid_all.tbl CDD COG3385 COG3385 442612 InsG IS4 transposase InsG [Mobilome: prophages, transposons]. 385 matched cddid_all.tbl CDD COG3386 COG3386 442613 YvrE Sugar lactone lactonase YvrE [Carbohydrate transport and metabolism]. Sugar lactone lactonase YvrE is part of the Pathway/BioSystem: Non-phosphorylated Entner-Doudoroff pathway 266 matched cddid_all.tbl CDD COG3387 COG3387 442614 SGA1 Glucoamylase (glucan-1,4-alpha-glucosidase), GH15 family [Carbohydrate transport and metabolism]. 585 matched cddid_all.tbl CDD COG3388 COG3388 442615 COG3388 Predicted transcriptional regulator [Transcription]. 99 matched cddid_all.tbl CDD COG3389 COG3389 442616 COG3389 Presenilin-like membrane protease, A22 family [Posttranslational modification, protein turnover, chaperones]. 327 matched cddid_all.tbl CDD COG3390 COG3390 442617 COG3390 Replication protein A (RPA) family protein [Replication, recombination and repair]. 278 matched cddid_all.tbl CDD COG3391 COG3391 442618 YncE DNA-binding beta-propeller fold protein YncE [General function prediction only]. 237 matched cddid_all.tbl CDD COG3392 COG3392 442619 COG3392 Adenine-specific DNA methylase [Replication, recombination and repair]. 338 matched cddid_all.tbl CDD COG3393 COG3393 442620 COG3393 Predicted acetyltransferase, GNAT family [General function prediction only]. 86 matched cddid_all.tbl CDD COG3394 COG3394 442621 ChbG Chitooligosaccharide deacetylase ChbG, YdjC/CelG family [Carbohydrate transport and metabolism]. 271 matched cddid_all.tbl CDD COG3395 COG3395 442622 OtnK D-threonate/D-erythronate kinase OtnK and related C4-acid sugar kinases, YgbK/DUF1537 family [Carbohydrate transport and metabolism]. 415 matched cddid_all.tbl CDD COG3396 COG3396 442623 YdbO 1,2-phenylacetyl-CoA epoxidase, catalytic subunit [Secondary metabolites biosynthesis, transport and catabolism]. 264 matched cddid_all.tbl CDD COG3397 COG3397 442624 COG3397 Predicted carbohydrate-binding protein, contains CBM5 and CBM33 domains [General function prediction only]. 294 matched cddid_all.tbl CDD COG3398 COG3398 442625 COG3398 Predicted transcriptional regulator, contains two HTH domains [Transcription]. 159 matched cddid_all.tbl CDD COG3399 COG3399 442626 COG3399 Uncharacterized conserved protein [Function unknown]. 147 matched cddid_all.tbl CDD COG3400 COG3400 442627 COG3400 Uncharacterized protein AQ_414, contains TrkA and USP-like domains [General function prediction only]. 472 matched cddid_all.tbl CDD COG3401 COG3401 442628 FN3 Fibronectin type 3 domain [General function prediction only]. 603 matched cddid_all.tbl CDD COG3402 COG3402 442629 YdbS Uncharacterized membrane protein YdbS, contains bPH2 (bacterial pleckstrin homology) domain [Function unknown]. 143 matched cddid_all.tbl CDD COG3403 COG3403 442630 YcgG Uncharacterized conserved protein YcgG, contains conserved FPC and CPF motifs [Function unknown]. 240 matched cddid_all.tbl CDD COG3404 COG3404 442631 FtcD Formiminotetrahydrofolate cyclodeaminase [Amino acid transport and metabolism]. 209 matched cddid_all.tbl CDD COG3405 COG3405 442632 BcsZ Endo-1,4-beta-D-glucanase Y [Carbohydrate transport and metabolism]. 359 matched cddid_all.tbl CDD COG3407 COG3407 442633 MVD1 Mevalonate pyrophosphate decarboxylase [Lipid transport and metabolism]. Mevalonate pyrophosphate decarboxylase is part of the Pathway/BioSystem: Isoprenoid biosynthesis 322 matched cddid_all.tbl CDD COG3408 COG3408 442634 GDB1 Glycogen debranching enzyme (alpha-1,6-glucosidase) [Carbohydrate transport and metabolism]. 353 matched cddid_all.tbl CDD COG3409 COG3409 442635 PGRP Peptidoglycan-binding (PGRP) domain of peptidoglycan hydrolases [Cell wall/membrane/envelope biogenesis]. 69 matched cddid_all.tbl CDD COG3410 COG3410 442636 BH3996 Uncharacterized conserved protein, DUF2075 family [Function unknown]. 609 matched cddid_all.tbl CDD COG3411 COG3411 442637 COG3411 2Fe-2S ferredoxin [Energy production and conversion]. 2Fe-2S ferredoxin is part of the Pathway/BioSystem: 2Fe2S 96 matched cddid_all.tbl CDD COG3412 COG3412 442638 DhaM Phosphotransferase subunit DhaM of the dihydroxyacetone kinase DhaKLM complex, contains PTS-EIIA, HPr, and PEP-utilizing domains [Signal transduction mechanisms]. 126 matched cddid_all.tbl CDD COG3413 COG3413 442639 DmsR Predicted transcriptional regulator, contains HTH domain [General function prediction only]. 143 matched cddid_all.tbl CDD COG3414 COG3414 442640 SgaB Phosphotransferase system, galactitol-specific IIB component [Carbohydrate transport and metabolism]. 94 matched cddid_all.tbl CDD COG3415 COG3415 442641 Csa3 CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]. CRISPR-associated protein Csa3, CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system 325 matched cddid_all.tbl CDD COG3416 COG3416 442642 COG3416 Uncharacterized conserved protein, DUF2076 domain [Function unknown]. 237 matched cddid_all.tbl CDD COG3417 COG3417 442643 LpoB Outer membrane lipoprotein LpoB, binds and activates PBP1b [Cell wall/membrane/envelope biogenesis]. 190 matched cddid_all.tbl CDD COG3418 COG3418 442644 FlgN Flagellar biosynthesis/type III secretory pathway chaperone FlgN [Cell motility, Intracellular trafficking, secretion, and vesicular transport]. 153 matched cddid_all.tbl CDD COG3419 COG3419 442645 PilY1 Type IV pilus assembly protein, tip-associated adhesin PilY1 [Cell motility, Extracellular structures]. 877 matched cddid_all.tbl CDD COG3420 COG3420 442646 NosD Nitrous oxide reductase accessory protein NosD, contains tandem CASH domains [Inorganic ion transport and metabolism]. 343 matched cddid_all.tbl CDD COG3421 COG3421 442647 ResIII Type III restriction endonuclease [Defense mechanisms]. 883 matched cddid_all.tbl CDD COG3422 COG3422 442648 YegP Uncharacterized conserved protein YegP, UPF0339 family [Function unknown]. 58 matched cddid_all.tbl CDD COG3423 COG3423 442649 SfsB Predicted transcriptional regulator, lambda repressor-like DNA-binding domain [Transcription]. 69 matched cddid_all.tbl CDD COG3424 COG3424 442650 BH0617 Predicted naringenin-chalcone synthase [Secondary metabolites biosynthesis, transport and catabolism]. 351 matched cddid_all.tbl CDD COG3425 COG3425 442651 PksG 3-hydroxy-3-methylglutaryl CoA synthase [Lipid transport and metabolism]. 3-hydroxy-3-methylglutaryl CoA synthase is part of the Pathway/BioSystem: Isoprenoid biosynthesis 382 matched cddid_all.tbl CDD COG3426 COG3426 442652 Buk Butyrate kinase [Energy production and conversion]. 357 matched cddid_all.tbl CDD COG3427 COG3427 442653 CoxG Carbon monoxide dehydrogenase subunit CoxG [Energy production and conversion]. 145 matched cddid_all.tbl CDD COG3428 COG3428 442654 YdbT Uncharacterized membrane protein YdbT, contains bPH2 (bacterial pleckstrin homology) domain [Function unknown]. 410 matched cddid_all.tbl CDD COG3429 COG3429 442655 OpcA Glucose-6-phosphate dehydrogenase assembly protein OpcA, contains a peptidoglycan-binding domain [Carbohydrate transport and metabolism]. 312 matched cddid_all.tbl CDD COG3430 COG3430 442656 COG3430 Archaeal flagellin (archaellin), FlaG/FlaF family [Cell motility]. 91 matched cddid_all.tbl CDD COG3431 COG3431 442657 COG3431 Uncharacterized membrane protein, DUF373 family [Function unknown]. 150 matched cddid_all.tbl CDD COG3432 COG3432 442658 COG3432 Predicted transcriptional regulator [Transcription]. 83 matched cddid_all.tbl CDD COG3433 COG3433 442659 AcpA Acyl carrier protein/domain [Lipid transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism]. 295 matched cddid_all.tbl CDD COG3434 COG3434 442660 YuxH c-di-GMP phosphodiesterase YuxH/PdeH, contains EAL and HDOD domains [Signal transduction mechanisms]. 407 matched cddid_all.tbl CDD COG3435 COG3435 442661 COG3435 Gentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport and catabolism]. 316 matched cddid_all.tbl CDD COG3436 COG3436 442662 COG3436 Transposase [Mobilome: prophages, transposons]. 416 matched cddid_all.tbl CDD COG3437 COG3437 442663 RpfG Response regulator c-di-GMP phosphodiesterase, RpfG family, contains REC and HD-GYP domains [Signal transduction mechanisms]. 224 matched cddid_all.tbl CDD COG3439 COG3439 442664 COG3439 Uncharacterized conserved protein, DUF302 family [Function unknown]. 128 matched cddid_all.tbl CDD COG3440 COG3440 442665 COG3440 Predicted restriction endonuclease [Defense mechanisms]. 150 matched cddid_all.tbl CDD COG3442 COG3442 442666 COG3442 Glutamine amidotransferase related to the GATase domain of CobQ [General function prediction only]. 241 matched cddid_all.tbl CDD COG3443 COG3443 442667 ZinT Periplasmic Zn/Cd-binding protein ZinT [Inorganic ion transport and metabolism]. 191 matched cddid_all.tbl CDD COG3444 COG3444 442668 AgaB Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIB [Carbohydrate transport and metabolism]. 157 matched cddid_all.tbl CDD COG3445 COG3445 442669 GrcA Autonomous glycyl radical cofactor GrcA [Coenzyme transport and metabolism]. 125 matched cddid_all.tbl CDD COG3447 COG3447 442670 MASE1 Integral membrane sensor domain MASE1 [Signal transduction mechanisms]. 637 matched cddid_all.tbl CDD COG3448 COG3448 442671 COG3448 CBS-domain-containing membrane protein [Signal transduction mechanisms]. 136 matched cddid_all.tbl CDD COG3449 COG3449 442672 SbmC DNA gyrase inhibitor GyrI/SbmC [Replication, recombination and repair]. 286 matched cddid_all.tbl CDD COG3450 COG3450 442673 COG3450 Predicted enzyme of the cupin superfamily [General function prediction only]. 108 matched cddid_all.tbl CDD COG3451 COG3451 442674 VirB4 Type IV secretory pathway, VirB4 component [Intracellular trafficking, secretion, and vesicular transport]. 546 matched cddid_all.tbl CDD COG3452 COG3452 442675 CHASE Extracellular (periplasmic) sensor domain CHASE (specificity unknown) [Signal transduction mechanisms]. 785 matched cddid_all.tbl CDD COG3453 COG3453 442676 COG3453 Predicted phosphohydrolase, protein tyrosine phosphatase (PTP) superfamily, DUF442 family [General function prediction only]. 125 matched cddid_all.tbl CDD COG3454 COG3454 442677 PhnM Alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase PhnM [Inorganic ion transport and metabolism]. 383 matched cddid_all.tbl CDD COG3455 COG3455 442678 DotU Type VI protein secretion system component TssL/VasF/DotU [Intracellular trafficking, secretion, and vesicular transport]. 233 matched cddid_all.tbl CDD COG3456 COG3456 442679 COG3456 Predicted component of the type VI protein secretion system, contains a FHA domain [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport]. 402 matched cddid_all.tbl CDD COG3457 COG3457 442680 YhfX Predicted amino acid racemase [Amino acid transport and metabolism]. 356 matched cddid_all.tbl CDD COG3458 COG3458 442681 Axe1 Cephalosporin-C deacetylase or related acetyl esterase [Secondary metabolites biosynthesis, transport and catabolism]. 318 matched cddid_all.tbl CDD COG3459 COG3459 442682 COG3459 Cellobiose phosphorylase [Carbohydrate transport and metabolism]. 794 matched cddid_all.tbl CDD COG3460 COG3460 442683 PaaB 1,2-phenylacetyl-CoA epoxidase, PaaB subunit [Secondary metabolites biosynthesis, transport and catabolism]. 98 matched cddid_all.tbl CDD COG3461 COG3461 442684 COG3461 Uncharacterized conserved protein [Function unknown]. 117 matched cddid_all.tbl CDD COG3462 COG3462 442685 TM0315 Uncharacterized protein, contains short C-terminal (SHOCT) domain [Function unknown]. 80 matched cddid_all.tbl CDD COG3463 COG3463 442686 COG3463 Uncharacterized membrane protein [Function unknown]. 554 matched cddid_all.tbl CDD COG3464 COG3464 442687 COG3464 Transposase [Mobilome: prophages, transposons]. 287 matched cddid_all.tbl CDD COG3465 COG3465 442688 YwgA Uncharacterized conserved protein YwgA [Function unknown]. 168 matched cddid_all.tbl CDD COG3466 COG3466 442689 ISA1214 Putative transposon-encoded protein [Mobilome: prophages, transposons]. 54 matched cddid_all.tbl CDD COG3467 COG3467 442690 NimA Nitroimidazole reductase NimA or a related FMN-containing flavoprotein, pyridoxamine 5'-phosphate oxidase superfamily [Defense mechanisms]. 144 matched cddid_all.tbl CDD COG3468 COG3468 442691 AidA Autotransporter adhesin AidA [Cell wall/membrane/envelope biogenesis, Intracellular trafficking, secretion, and vesicular transport]. 846 matched cddid_all.tbl CDD COG3469 COG3469 442692 Chi1 Chitinase [Carbohydrate transport and metabolism]. 534 matched cddid_all.tbl CDD COG3470 COG3470 442693 Tpd Uncharacterized conserved protein probably involved in high-affinity Fe2+ transport [Cell wall/membrane/envelope biogenesis, Lipid transport and metabolism]. 172 matched cddid_all.tbl CDD COG3471 COG3471 442694 COG3471 Predicted secreted (periplasmic) protein [Function unknown]. 233 matched cddid_all.tbl CDD COG3472 COG3472 442695 COG3472 Uncharacterized conserved protein domain, often C-terminal to DUF262 [Function unknown]. 566 matched cddid_all.tbl CDD COG3473 COG3473 442696 COG3473 Maleate cis-trans isomerase [Secondary metabolites biosynthesis, transport and catabolism]. 242 matched cddid_all.tbl CDD COG3474 COG3474 442697 Cyc7 Cytochrome c2 [Energy production and conversion]. 101 matched cddid_all.tbl CDD COG3475 COG3475 442698 LicD Phosphorylcholine metabolism protein LicD [Lipid transport and metabolism]. 266 matched cddid_all.tbl CDD COG3476 COG3476 442699 TspO Tryptophan-rich sensory protein TspO/CrtK (mitochondrial benzodiazepine receptor homolog) [Signal transduction mechanisms]. 152 matched cddid_all.tbl CDD COG3477 COG3477 442700 YagU Uncharacterized membrane protein YagU, involved in acid resistance, DUF1440 family [Function unknown]. 176 matched cddid_all.tbl CDD COG3478 COG3478 442701 YpzJ Predicted nucleic-acid-binding protein, contains Zn-ribbon domain [General function prediction only]. 69 matched cddid_all.tbl CDD COG3479 COG3479 442702 PadC Phenolic acid decarboxylase [Secondary metabolites biosynthesis, transport and catabolism]. 168 matched cddid_all.tbl CDD COG3480 COG3480 442703 SdrC Predicted secreted protein YlbL, contains PDZ domain [Signal transduction mechanisms]. 344 matched cddid_all.tbl CDD COG3481 COG3481 442704 YhaM 3'-5' exoribonuclease YhaM, can participate in 23S rRNA maturation, HD superfamily [Translation, ribosomal structure and biogenesis]. 3'-5' exoribonuclease YhaM, can participate in 23S rRNA maturation, HD superfamily is part of the Pathway/BioSystem: 23S rRNA modification 316 matched cddid_all.tbl CDD COG3482 COG3482 442705 COG3482 Uncharacterized conserved protein [Function unknown]. 216 matched cddid_all.tbl CDD COG3483 COG3483 442706 TDO2 Tryptophan 2,3-dioxygenase (vermilion) [Amino acid transport and metabolism]. 276 matched cddid_all.tbl CDD COG3484 COG3484 442707 COG3484 Predicted proteasome-type protease [Posttranslational modification, protein turnover, chaperones]. 236 matched cddid_all.tbl CDD COG3485 COG3485 442708 PcaH Protocatechuate 3,4-dioxygenase beta subunit [Secondary metabolites biosynthesis, transport and catabolism]. 171 matched cddid_all.tbl CDD COG3486 COG3486 442709 IucD Lysine/ornithine N-monooxygenase [Secondary metabolites biosynthesis, transport and catabolism]. 440 matched cddid_all.tbl CDD COG3487 COG3487 442710 IrpA Imelysin-like iron-regulated protein IrpA, duplicated M75 peptidase-like domain [Function unknown]. 416 matched cddid_all.tbl CDD COG3488 COG3488 442711 COG3488 Uncharacterized conserved protein with two CxxC motifs, DUF1111 family [General function prediction only]. 461 matched cddid_all.tbl CDD COG3489 COG3489 442712 IrpA2 Imelysin-like iron-regulated protein IrpA, duplicated M75 peptidase-like domain [General function prediction only]. 365 matched cddid_all.tbl CDD COG3490 COG3490 442713 COG3490 Uncharacterized conserved protein, DUF1513 domain [Function unknown]. 365 matched cddid_all.tbl CDD COG3491 COG3491 442714 PcbC Isopenicillin N synthase and related dioxygenases [Secondary metabolites biosynthesis, transport and catabolism]. 320 matched cddid_all.tbl CDD COG3492 COG3492 442715 COG3492 Uncharacterized conserved protein, DUF1244 family [Function unknown]. 96 matched cddid_all.tbl CDD COG3493 COG3493 442716 CitS Na+/citrate or Na+/malate symporter [Energy production and conversion]. 432 matched cddid_all.tbl CDD COG3494 COG3494 442717 COG3494 Uncharacterized conserved protein, DUF1009 family [Function unknown]. 265 matched cddid_all.tbl CDD COG3495 COG3495 442718 COG3495 Uncharacterized conserved protein, DUF3299 family [Function unknown]. 166 matched cddid_all.tbl CDD COG3496 COG3496 442719 COG3496 Uncharacterized conserved protein, DUF1365 family [Function unknown]. 255 matched cddid_all.tbl CDD COG3497 COG3497 442720 COG3497 Phage tail sheath protein FI [Mobilome: prophages, transposons]. 273 matched cddid_all.tbl CDD COG3498 COG3498 442721 COG3498 Phage tail tube protein FII [Mobilome: prophages, transposons]. 167 matched cddid_all.tbl CDD COG3499 COG3499 442722 COG3499 Phage protein U [Mobilome: prophages, transposons]. 123 matched cddid_all.tbl CDD COG3500 COG3500 442723 gpD Phage protein D [Mobilome: prophages, transposons]. 336 matched cddid_all.tbl CDD COG3501 COG3501 442724 VgrG Uncharacterized conserved protein VgrG, implicated in type VI secretion and phage assembly [Intracellular trafficking, secretion, and vesicular transport, Mobilome: prophages, transposons, General function prediction only]. 743 matched cddid_all.tbl CDD COG3502 COG3502 442725 COG3502 Uncharacterized conserved protein, DUF952 family [Function unknown]. 113 matched cddid_all.tbl CDD COG3503 COG3503 442726 COG3503 Uncharacterized membrane protein, DUF1624 family [Function unknown]. 273 matched cddid_all.tbl CDD COG3504 COG3504 442727 VirB9 Type IV secretory pathway, VirB9 components [Intracellular trafficking, secretion, and vesicular transport]. 229 matched cddid_all.tbl CDD COG3505 COG3505 442728 VirD4 Type IV secretory pathway, VirD4 component, TraG/TraD family ATPase [Intracellular trafficking, secretion, and vesicular transport]. 402 matched cddid_all.tbl CDD COG3506 COG3506 442729 Ree1 Regulation of enolase protein 1 (function unknown), concanavalin A-like superfamily [Function unknown]. 195 matched cddid_all.tbl CDD COG3507 COG3507 442730 XynB2 Beta-xylosidase [Carbohydrate transport and metabolism]. 351 matched cddid_all.tbl CDD COG3508 COG3508 442731 HmgA Homogentisate 1,2-dioxygenase [Secondary metabolites biosynthesis, transport and catabolism]. 382 matched cddid_all.tbl CDD COG3509 COG3509 442732 LpqC Acetyl xylan esterase AxeA and related esterases, LpqC family [Carbohydrate transport and metabolism]. 284 matched cddid_all.tbl CDD COG3510 COG3510 442733 CmcI Cephalosporin hydroxylase [Defense mechanisms]. 239 matched cddid_all.tbl CDD COG3511 COG3511 442734 PlcC Phospholipase C [Cell wall/membrane/envelope biogenesis]. 392 matched cddid_all.tbl CDD COG3512 COG3512 226043 Cas2 CRISPR/Cas system-associated protein Cas2, endoribonuclease [Defense mechanisms]. 116 matched cddid_all.tbl CDD COG3513 COG3513 442735 Cas9 CRISPR-Cas system type-II protein Cas9 [Defense mechanisms]. CRISPR-Cas system type-II protein Cas9 is part of the Pathway/BioSystem: CRISPR-Cas system 812 matched cddid_all.tbl CDD COG3514 COG3514 442736 COG3514 Uncharacterized conserved protein, DUF4415 family [Function unknown]. 91 matched cddid_all.tbl CDD COG3515 COG3515 442737 TssA1 Type VI protein secretion system component TssA1/VasJ/EvfE, contains ImpA_N domain [Intracellular trafficking, secretion, and vesicular transport]. 342 matched cddid_all.tbl CDD COG3516 COG3516 442738 TssB Predicted component TssA of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]. 171 matched cddid_all.tbl CDD COG3517 COG3517 442739 COG3517 Predicted component TssB of the type VI protein secretion system, VipA/VipB/TssB family [Intracellular trafficking, secretion, and vesicular transport]. 474 matched cddid_all.tbl CDD COG3518 COG3518 442740 COG3518 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]. 162 matched cddid_all.tbl CDD COG3519 COG3519 442741 VasA Type VI protein secretion system component VasA [Intracellular trafficking, secretion, and vesicular transport]. 607 matched cddid_all.tbl CDD COG3520 COG3520 442742 COG3520 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]. 341 matched cddid_all.tbl CDD COG3521 COG3521 442743 COG3521 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]. 168 matched cddid_all.tbl CDD COG3522 COG3522 442744 COG3522 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]. 446 matched cddid_all.tbl CDD COG3523 COG3523 442745 IcmF Type VI protein secretion system component VasK [Intracellular trafficking, secretion, and vesicular transport]. 1192 matched cddid_all.tbl CDD COG3524 COG3524 442746 KpsE Capsule polysaccharide export protein KpsE/RkpR [Cell wall/membrane/envelope biogenesis]. 370 matched cddid_all.tbl CDD COG3525 COG3525 442747 Chb N-acetyl-beta-hexosaminidase [Carbohydrate transport and metabolism]. 578 matched cddid_all.tbl CDD COG3526 COG3526 442748 COG3526 Predicted selenoprotein, Rdx family [General function prediction only]. 93 matched cddid_all.tbl CDD COG3527 COG3527 442749 AlsD Alpha-acetolactate decarboxylase [Secondary metabolites biosynthesis, transport and catabolism]. 241 matched cddid_all.tbl CDD COG3528 COG3528 442750 COG3528 Uncharacterized conserved protein, DUF2219 family [Function unknown]. 326 matched cddid_all.tbl CDD COG3529 COG3529 442751 COG3529 Predicted nucleic-acid-binding protein, contains Zn-ribbon domain [General function prediction only]. 67 matched cddid_all.tbl CDD COG3530 COG3530 442752 COG3530 Uncharacterized conserved protein, DUF3820 family [Function unknown]. 73 matched cddid_all.tbl CDD COG3531 COG3531 442753 COG3531 Predicted protein-disulfide isomerase, contains CxxC motif [Posttranslational modification, protein turnover, chaperones]. 206 matched cddid_all.tbl CDD COG3533 COG3533 442754 HybA1 Beta-L-arabinofuranosidase, GH127 family [Carbohydrate transport and metabolism]. 597 matched cddid_all.tbl CDD COG3534 COG3534 442755 AbfA Alpha-L-arabinofuranosidase [Carbohydrate transport and metabolism]. 487 matched cddid_all.tbl CDD COG3535 COG3535 442756 COG3535 Uncharacterized conserved protein, DUF917 family [Function unknown]. 358 matched cddid_all.tbl CDD COG3536 COG3536 442757 COG3536 Uncharacterized conserved protein, DUF971 family [Function unknown]. 124 matched cddid_all.tbl CDD COG3537 COG3537 442758 COG3537 Putative alpha-1,2-mannosidase [Carbohydrate transport and metabolism]. 750 matched cddid_all.tbl CDD COG3538 COG3538 442759 COG3538 Meiotically up-regulated gene 157 (Mug157) protein (function unknown) [Function unknown]. 445 matched cddid_all.tbl CDD COG3539 COG3539 442760 FimA Pilin (type 1 fimbrial protein) [Cell motility]. 172 matched cddid_all.tbl CDD COG3540 COG3540 442761 PhoD Phosphodiesterase/alkaline phosphatase D [Inorganic ion transport and metabolism]. 482 matched cddid_all.tbl CDD COG3541 COG3541 442762 YcgL Predicted nucleotidyltransferase YcgL [General function prediction only]. 249 matched cddid_all.tbl CDD COG3542 COG3542 442763 CFF1 Predicted sugar epimerase, cupin superfamily [General function prediction only]. 149 matched cddid_all.tbl CDD COG3543 COG3543 442764 COG3543 Uncharacterized conserved protein, DUF1284 domain [Function unknown]. 130 matched cddid_all.tbl CDD COG3544 COG3544 442765 COG3544 Uncharacterized conserved protein, DUF305 family [Function unknown]. 75 matched cddid_all.tbl CDD COG3545 COG3545 442766 YdeN Predicted esterase of the alpha/beta hydrolase fold [General function prediction only]. 170 matched cddid_all.tbl CDD COG3546 COG3546 442767 CotJC Mn-containing catalase (includes spore coat protein CotJC) [Inorganic ion transport and metabolism]. 253 matched cddid_all.tbl CDD COG3547 COG3547 442768 COG3547 Transposase [Mobilome: prophages, transposons]. 349 matched cddid_all.tbl CDD COG3548 COG3548 442769 COG3548 Uncharacterized membrane protein [Function unknown]. 203 matched cddid_all.tbl CDD COG3549 COG3549 442770 HigB Plasmid maintenance system killer protein [Defense mechanisms]. 92 matched cddid_all.tbl CDD COG3550 COG3550 442771 HipA Serine/threonine protein kinase HipA, toxin component of the HipAB toxin-antitoxin module [Signal transduction mechanisms]. 398 matched cddid_all.tbl CDD COG3551 COG3551 442772 COG3551 Uncharacterized conserved protein [Function unknown]. 253 matched cddid_all.tbl CDD COG3552 COG3552 442773 CoxE Uncharacterized protein CoxE, contains von Willebrand factor type A (vWA) domain [Function unknown]. 371 matched cddid_all.tbl CDD COG3553 COG3553 442774 COG3553 Uncharacterized conserved protein, DUF2218 domain [Function unknown]. 94 matched cddid_all.tbl CDD COG3554 COG3554 442775 COG3554 Uncharacterized conserved protein [Function unknown]. 181 matched cddid_all.tbl CDD COG3555 COG3555 442776 LpxO2 Aspartyl/asparaginyl beta-hydroxylase, cupin superfamily [Posttranslational modification, protein turnover, chaperones]. 220 matched cddid_all.tbl CDD COG3556 COG3556 442777 COG3556 Uncharacterized membrane protein [Function unknown]. 149 matched cddid_all.tbl CDD COG3557 COG3557 442778 YgaC Uncharacterized conserved protein associated with RNAses G and E, UPF0374/DUF402 family [Function unknown]. 177 matched cddid_all.tbl CDD COG3558 COG3558 442779 COG3558 Uncharacterized conserved protein, nuclear transport factor 2 (NTF2) superfamily [Function unknown]. 154 matched cddid_all.tbl CDD COG3559 COG3559 442780 NodJ Putative exporter of oligosaccharides and polyketide antibiotics DrrB/NodJ, ABC-2 family [Intracellular trafficking, secretion, and vesicular transport]. 529 matched cddid_all.tbl CDD COG3560 COG3560 442781 FMR2 Fatty acid repression mutant protein (predicted oxidoreductase) [General function prediction only]. 196 matched cddid_all.tbl CDD COG3561 COG3561 442782 COG3561 Phage anti-repressor protein Ant [Mobilome: prophages, transposons]. 231 matched cddid_all.tbl CDD COG3562 COG3562 442783 KpsS Capsule polysaccharide modification protein KpsS [Cell wall/membrane/envelope biogenesis]. 421 matched cddid_all.tbl CDD COG3563 COG3563 442784 KpsC Capsule polysaccharide export protein KpsC/LpsZ [Cell wall/membrane/envelope biogenesis]. 675 matched cddid_all.tbl CDD COG3564 COG3564 442785 COG3564 Uncharacterized conserved protein, DUF779 family [Function unknown]. 123 matched cddid_all.tbl CDD COG3565 COG3565 442786 COG3565 Predicted dioxygenase of extradiol dioxygenase family [General function prediction only]. 139 matched cddid_all.tbl CDD COG3566 COG3566 442787 COG3566 Uncharacterized conserved protein, DUF2213 domain [Function unknown]. 370 matched cddid_all.tbl CDD COG3567 COG3567 442788 COG3567 Uncharacterized conserved protein, DUF1073 domain [Function unknown]. 453 matched cddid_all.tbl CDD COG3568 COG3568 442789 ElsH Metal-dependent hydrolase, endonuclease/exonuclease/phosphatase family [General function prediction only]. 167 matched cddid_all.tbl CDD COG3569 COG3569 442790 Top1 DNA topoisomerase IB [Replication, recombination and repair]. 345 matched cddid_all.tbl CDD COG3570 COG3570 442791 StrB Streptomycin 6-kinase [Defense mechanisms]. 301 matched cddid_all.tbl CDD COG3571 COG3571 442792 COG3571 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]. 202 matched cddid_all.tbl CDD COG3572 COG3572 442793 Gsh2 Gamma-glutamylcysteine synthetase [Coenzyme transport and metabolism]. 454 matched cddid_all.tbl CDD COG3573 COG3573 442794 COG3573 Predicted oxidoreductase [General function prediction only]. 551 matched cddid_all.tbl CDD COG3575 COG3575 442795 COG3575 Uncharacterized conserved protein [Function unknown]. 180 matched cddid_all.tbl CDD COG3576 COG3576 442796 COG3576 Predicted flavin-nucleotide-binding protein, pyridoxine 5'-phosphate oxidase superfamily [General function prediction only]. 189 matched cddid_all.tbl CDD COG3577 COG3577 442797 COG3577 Predicted aspartyl protease [General function prediction only]. 152 matched cddid_all.tbl CDD COG3579 COG3579 442798 PepC Aminopeptidase C [Amino acid transport and metabolism]. 440 matched cddid_all.tbl CDD COG3580 COG3580 442799 COG3580 Predicted nucleotide-binding protein, sugar kinase/HSP70/actin superfamily [General function prediction only]. 343 matched cddid_all.tbl CDD COG3581 COG3581 442800 COG3581 Predicted nucleotide-binding protein, sugar kinase/HSP70/actin superfamily [General function prediction only]. 407 matched cddid_all.tbl CDD COG3582 COG3582 442801 CUZ1 CDC48-associated ubiquitin-like protein CUZ1, contains AN1-type Zn-finger (protection from As/Sb toxicity) [Defense mechanisms]. 279 matched cddid_all.tbl CDD COG3583 COG3583 442802 YabE Uncharacterized conserved protein YabE, contains G5 and tandem DUF348 domains [Function unknown]. 335 matched cddid_all.tbl CDD COG3584 COG3584 442803 COG3584 3D (Asp-Asp-Asp) domain, usually in lytic transglycosylases [Function unknown]. 3D (Asp-Asp-Asp) domain, usually in lytic transglycosylases is part of the Pathway/BioSystem: 3D 92 matched cddid_all.tbl CDD COG3585 COG3585 442804 MopI Molybdopterin-binding protein MopI [Coenzyme transport and metabolism]. 141 matched cddid_all.tbl CDD COG3586 COG3586 442805 COG3586 Uncharacterized protein domain, C-terminal to COG1479 DNAse/DNA nickase [General function prediction only]. 313 matched cddid_all.tbl CDD COG3587 COG3587 442806 PM0699 Restriction endonuclease, type III RM system [Defense mechanisms]. 983 matched cddid_all.tbl CDD COG3588 COG3588 442807 Fba1 Fructose-bisphosphate aldolase class 1 [Carbohydrate transport and metabolism]. Fructose-bisphosphate aldolase class 1 is part of the Pathway/BioSystem: Glycolysis 302 matched cddid_all.tbl CDD COG3589 COG3589 442808 COG3589 Uncharacterized conserved protein, DUF871 domain [Function unknown]. 356 matched cddid_all.tbl CDD COG3590 COG3590 442809 PepO Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]. 674 matched cddid_all.tbl CDD COG3591 COG3591 442810 eMpr V8-like Glu-specific endopeptidase [Posttranslational modification, protein turnover, chaperones]. 194 matched cddid_all.tbl CDD COG3592 COG3592 442811 YjdI Uncharacterized Fe-S cluster protein YjdI [Function unknown]. 71 matched cddid_all.tbl CDD COG3593 COG3593 442812 YbjD Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM domains [Replication, recombination and repair]. 359 matched cddid_all.tbl CDD COG3594 COG3594 442813 NolL Fucose 4-O-acetylase or related acetyltransferase [Carbohydrate transport and metabolism]. 270 matched cddid_all.tbl CDD COG3595 COG3595 442814 YvlB Uncharacterized conserved protein YvlB, contains DUF4097 and DUF4098 domains [Function unknown]. 254 matched cddid_all.tbl CDD COG3596 COG3596 442815 YeeP Predicted GTPase [General function prediction only]. 318 matched cddid_all.tbl CDD COG3597 COG3597 442816 COG3597 Uncharacterized conserved protein, DUF697 family [Function unknown]. 367 matched cddid_all.tbl CDD COG3598 COG3598 442817 RepA RecA-family ATPase [Replication, recombination and repair]. 313 matched cddid_all.tbl CDD COG3599 COG3599 442818 DivIVA Cell division septum initiation protein DivIVA, interacts with FtsZ and MinD [Cell cycle control, cell division, chromosome partitioning]. 125 matched cddid_all.tbl CDD COG3600 COG3600 442819 GepA Uncharacterized phage-associated protein, contains DUF4065 domain [Mobilome: prophages, transposons]. 146 matched cddid_all.tbl CDD COG3601 COG3601 442820 FmnP Riboflavin transporter FmnP [Coenzyme transport and metabolism]. 180 matched cddid_all.tbl CDD COG3602 COG3602 442821 ACT-3 ACT domain, ACT-3 family [Signal transduction mechanisms]. 135 matched cddid_all.tbl CDD COG3603 COG3603 442822 ACT-7 ACT domain, ACT-7 family [Signal transduction mechanisms]. 120 matched cddid_all.tbl CDD COG3604 COG3604 442823 FhlA FhlA-type transcriptional regulator, contains GAF, AAA-type ATPase, and DNA-binding Fis domains [Transcription, Signal transduction mechanisms]. 338 matched cddid_all.tbl CDD COG3605 COG3605 442824 PtsP Signal transduction protein containing GAF and PtsI domains [Signal transduction mechanisms]. 188 matched cddid_all.tbl CDD COG3607 COG3607 442825 COG3607 Lactoylglutathione lyase-related enzyme, vicinal oxygen chelate (VOC) family [General function prediction only]. 126 matched cddid_all.tbl CDD COG3608 COG3608 442826 COG3608 Predicted deacylase [General function prediction only]. 296 matched cddid_all.tbl CDD COG3609 COG3609 442827 ParD Transcriptional regulator, contains Arc/MetJ-type RHH (ribbon-helix-helix) DNA-binding domain [Transcription]. 77 matched cddid_all.tbl CDD COG3610 COG3610 442828 YjjB Uncharacterized membrane protein YjjB, DUF3815 family [Function unknown]. 150 matched cddid_all.tbl CDD COG3611 COG3611 442829 DnaB2 Replication initiation and membrane attachment protein DnaB [Replication, recombination and repair]. 455 matched cddid_all.tbl CDD COG3612 COG3612 442830 COG3612 Predicted DNA-binding protein AF1194, contains HTH domain, DUF2240 family [Function unknown]. 153 matched cddid_all.tbl CDD COG3613 COG3613 442831 RCL Nucleoside 2-deoxyribosyltransferase [Nucleotide transport and metabolism]. 142 matched cddid_all.tbl CDD COG3614 COG3614 442832 CHASE1 Extracytoplasmic sensor domain CHASE1 (specificity unknown) [Signal transduction mechanisms]. 588 matched cddid_all.tbl CDD COG3615 COG3615 442833 TehB Tellurite resistance protein TehB, SAM-dependent methylase, cupin superfamily [Inorganic ion transport and metabolism]. 104 matched cddid_all.tbl CDD COG3616 COG3616 442834 Dsd1 D-serine deaminase, pyridoxal phosphate-dependent [Amino acid transport and metabolism]. 357 matched cddid_all.tbl CDD COG3617 COG3617 442835 COG3617 Prophage antirepressor [Mobilome: prophages, transposons]. 106 matched cddid_all.tbl CDD COG3618 COG3618 442836 COG3618 Predicted metal-dependent hydrolase, TIM-barrel fold [General function prediction only]. 272 matched cddid_all.tbl CDD COG3619 COG3619 442837 YoaK Uncharacterized membrane protein YoaK, UPF0700 family [Function unknown]. 228 matched cddid_all.tbl CDD COG3620 COG3620 442838 AF2118 Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain CBS pair) [Transcription]. 95 matched cddid_all.tbl CDD COG3621 COG3621 442839 PATA Patatin-like phospholipase/acyl hydrolase, includes sporulation protein CotR [General function prediction only]. 296 matched cddid_all.tbl CDD COG3622 COG3622 442840 Hyi Hydroxypyruvate/dehydroerythronate isomerase, Hyi/OtnI family [Carbohydrate transport and metabolism]. 260 matched cddid_all.tbl CDD COG3623 COG3623 442841 SgaU L-ribulose-5-phosphate 3-epimerase UlaE [Carbohydrate transport and metabolism]. 277 matched cddid_all.tbl CDD COG3624 COG3624 442842 PhnG Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnG [Inorganic ion transport and metabolism]. 150 matched cddid_all.tbl CDD COG3625 COG3625 442843 PhnH Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnH [Inorganic ion transport and metabolism]. 190 matched cddid_all.tbl CDD COG3626 COG3626 442844 PhnI Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnI [Inorganic ion transport and metabolism]. 369 matched cddid_all.tbl CDD COG3627 COG3627 442845 PhnJ Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase PhnJ [Inorganic ion transport and metabolism]. 290 matched cddid_all.tbl CDD COG3628 COG3628 442846 COG3628 Phage baseplate assembly protein W [Mobilome: prophages, transposons]. 119 matched cddid_all.tbl CDD COG3629 COG3629 442847 DnrI DNA-binding transcriptional regulator DnrI/AfsR/EmbR, SARP family, contains BTAD domain [Transcription]. 244 matched cddid_all.tbl CDD COG3630 COG3630 442848 OadG Na+-transporting oxaloacetate/methylmalonyl-CoA decarboxylase, gamma subunit [Energy production and conversion]. 80 matched cddid_all.tbl CDD COG3631 COG3631 442849 YesE Ketosteroid isomerase-related protein [General function prediction only]. 126 matched cddid_all.tbl CDD COG3633 COG3633 442850 SstT Na+/serine and Na+/threonine symporter SstT [Amino acid transport and metabolism]. 406 matched cddid_all.tbl CDD COG3634 COG3634 442851 AhpF Alkyl hydroperoxide reductase subunit AhpF [Defense mechanisms]. 200 matched cddid_all.tbl CDD COG3635 COG3635 442852 ApgM 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, archeal type [Carbohydrate transport and metabolism]. 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, archeal type is part of the Pathway/BioSystem: Glycolysis 398 matched cddid_all.tbl CDD COG3636 COG3636 442853 PA5055 Uncharacterized Zn-binding protein, DUF971 domain [Mobilome: prophages, transposons]. 92 matched cddid_all.tbl CDD COG3637 COG3637 442854 LomR Opacity protein LomR and related surface antigens [Cell wall/membrane/envelope biogenesis]. 154 matched cddid_all.tbl CDD COG3638 COG3638 442855 PhnC ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]. 249 matched cddid_all.tbl CDD COG3639 COG3639 442856 PhnE ABC-type phosphate/phosphonate transport system, permease component [Inorganic ion transport and metabolism]. 244 matched cddid_all.tbl CDD COG3640 COG3640 442857 CooC CO dehydrogenase nickel-insertion accessory protein CooC1 [Posttranslational modification, protein turnover, chaperones]. 249 matched cddid_all.tbl CDD COG3641 COG3641 442858 PfoR Membrane regulatory protein PfoR, PTS_EIIC_2 domain (does not regulate perfringolysin expression) [Signal transduction mechanisms]. 345 matched cddid_all.tbl CDD COG3642 COG3642 442859 Bud32 tRNA A-37 threonylcarbamoyl transferase component Bud32 [Translation, ribosomal structure and biogenesis]. tRNA A-37 threonylcarbamoyl transferase component Bud32 is part of the Pathway/BioSystem: tRNA modification 159 matched cddid_all.tbl CDD COG3643 COG3643 442860 GluFT Glutamate formiminotransferase [Amino acid transport and metabolism]. 303 matched cddid_all.tbl CDD COG3644 COG3644 442861 COG3644 Uncharacterized conserved protein, DUF2239 domain [Function unknown]. 199 matched cddid_all.tbl CDD COG3645 COG3645 442862 KilAC Phage antirepressor protein YoqD, KilAC domain [Mobilome: prophages, transposons]. 249 matched cddid_all.tbl CDD COG3646 COG3646 442863 pRha Phage regulatory protein Rha [Mobilome: prophages, transposons]. 211 matched cddid_all.tbl CDD COG3647 COG3647 442864 YjdF Uncharacterized membrane protein YjdF [Function unknown]. 201 matched cddid_all.tbl CDD COG3648 COG3648 442865 UriC Uricase (urate oxidase) [Secondary metabolites biosynthesis, transport and catabolism]. 287 matched cddid_all.tbl CDD COG3649 COG3649 442866 Cas7 CRISPR-Cas system type I effector complex subunit Cas7, RAMP superfamily [Defense mechanisms]. CRISPR-Cas system type I effector complex subunit Cas7, RAMP superfamily is part of the Pathway/BioSystem: CRISPR-Cas system 290 matched cddid_all.tbl CDD COG3650 COG3650 442867 COG3650 Uncharacterized membrane protein [Function unknown]. 186 matched cddid_all.tbl CDD COG3651 COG3651 442868 COG3651 Uncharacterized conserved protein, DUF2237 family [Function unknown]. 124 matched cddid_all.tbl CDD COG3652 COG3652 442869 COG3652 Predicted outer membrane protein, contains DUF4142 domain [Function unknown]. 176 matched cddid_all.tbl CDD COG3653 COG3653 442870 COG3653 N-acyl-D-aspartate/D-glutamate deacylase [Secondary metabolites biosynthesis, transport and catabolism]. 528 matched cddid_all.tbl CDD COG3654 COG3654 442871 Doc Prophage maintenance system killer protein [Mobilome: prophages, transposons]. 130 matched cddid_all.tbl CDD COG3655 COG3655 442872 YozG DNA-binding transcriptional regulator, XRE family [Transcription]. 69 matched cddid_all.tbl CDD COG3656 COG3656 442873 COG3656 Predicted periplasmic protein [Function unknown]. 161 matched cddid_all.tbl CDD COG3657 COG3657 442874 COG3657 Putative component of the toxin-antitoxin plasmid stabilization module [Defense mechanisms]. 103 matched cddid_all.tbl CDD COG3658 COG3658 442875 CytB Cytochrome b subunit of Ni2+-dependent hydrogenase [Energy production and conversion]. 195 matched cddid_all.tbl CDD COG3659 COG3659 442876 OprB Carbohydrate-selective porin OprB [Cell wall/membrane/envelope biogenesis]. 440 matched cddid_all.tbl CDD COG3660 COG3660 442877 ELM1 Mitochondrial fission protein ELM1 [Cell cycle control, cell division, chromosome partitioning]. 324 matched cddid_all.tbl CDD COG3661 COG3661 442878 AguA2 Alpha-glucuronidase [Carbohydrate transport and metabolism]. 688 matched cddid_all.tbl CDD COG3662 COG3662 442879 COG3662 Uncharacterized conserved protein, DUF2236 family [Function unknown]. 287 matched cddid_all.tbl CDD COG3663 COG3663 442880 Mug G:T/U-mismatch repair DNA glycosylase [Replication, recombination and repair]. 157 matched cddid_all.tbl CDD COG3664 COG3664 442881 XynB Beta-xylosidase [Carbohydrate transport and metabolism]. 490 matched cddid_all.tbl CDD COG3665 COG3665 442882 YcgI Uncharacterized conserved protein YcgI, DUF1989 family [Function unknown]. 221 matched cddid_all.tbl CDD COG3666 COG3666 442883 COG3666 Transposase, IS1182 family [Mobilome: prophages, transposons]. 169 matched cddid_all.tbl CDD COG3667 COG3667 442884 PcoB Uncharacterized conserved protein involved in copper resistance [Inorganic ion transport and metabolism]. 268 matched cddid_all.tbl CDD COG3668 COG3668 442885 ParE Plasmid stabilization system protein ParE [Mobilome: prophages, transposons]. 96 matched cddid_all.tbl CDD COG3669 COG3669 442886 AfuC Alpha-L-fucosidase [Carbohydrate transport and metabolism]. 401 matched cddid_all.tbl CDD COG3670 COG3670 442887 COG3670 Carotenoid cleavage dioxygenase or a related enzyme [Secondary metabolites biosynthesis, transport and catabolism]. 470 matched cddid_all.tbl CDD COG3671 COG3671 442888 COG3671 Uncharacterized membrane protein [Function unknown]. 117 matched cddid_all.tbl CDD COG3672 COG3672 442889 COG3672 Predicted transglutaminase-like protein [Posttranslational modification, protein turnover, chaperones]. 197 matched cddid_all.tbl CDD COG3673 COG3673 442890 COG3673 Uncharacterized conserved protein, PA2063/DUF2235 family [Function unknown]. 347 matched cddid_all.tbl CDD COG3675 COG3675 442891 Lip2 Predicted lipase [Lipid transport and metabolism]. 266 matched cddid_all.tbl CDD COG3676 COG3676 442892 COG3676 Transposase and inactivated derivatives [Mobilome: prophages, transposons]. 249 matched cddid_all.tbl CDD COG3677 COG3677 442893 InsA Transposase InsA [Mobilome: prophages, transposons]. 241 matched cddid_all.tbl CDD COG3678 COG3678 442894 CpxP Periplasmic chaperone Spy, Spy/CpxP family [Posttranslational modification, protein turnover, chaperones]. 141 matched cddid_all.tbl CDD COG3679 COG3679 442895 YlbF Cell fate regulator YlbF, YheA/YmcA/DUF963 family (controls sporulation, competence, biofilm development) [Signal transduction mechanisms]. 112 matched cddid_all.tbl CDD COG3680 COG3680 442896 COG3680 Uncharacterized protein, contains GIY-YIG domain [Function unknown]. 253 matched cddid_all.tbl CDD COG3681 COG3681 442897 CdsB L-cysteine desulfidase YhaM [Amino acid transport and metabolism]. 429 matched cddid_all.tbl CDD COG3682 COG3682 442898 CopY Transcriptional regulator, CopY/TcrY family [Transcription]. 125 matched cddid_all.tbl CDD COG3683 COG3683 442899 COG3683 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]. 221 matched cddid_all.tbl CDD COG3684 COG3684 442900 LacD Tagatose-1,6-bisphosphate/sulfofructosephosphate aldolase [Carbohydrate transport and metabolism, Inorganic ion transport and metabolism]. 330 matched cddid_all.tbl CDD COG3685 COG3685 442901 YciE Ferritin-like metal-binding protein YciE [Inorganic ion transport and metabolism]. 165 matched cddid_all.tbl CDD COG3686 COG3686 442902 COG3686 Uncharacterized conserved protein, MAPEG superfamily [Function unknown]. 130 matched cddid_all.tbl CDD COG3687 COG3687 442903 COG3687 Predicted metal-dependent hydrolase [General function prediction only]. 284 matched cddid_all.tbl CDD COG3688 COG3688 442904 Rae1 EndoRNase involved in mRNA decay, NYN (Nedd4-BP1/Rae1/YacP nuclease) family, contains PIN domain [Translation, ribosomal structure and biogenesis]. 168 matched cddid_all.tbl CDD COG3689 COG3689 442905 YcgQ Uncharacterized membrane protein YcgQ, UPF0703/DUF1980 family [Function unknown]. 111 matched cddid_all.tbl CDD COG3691 COG3691 442906 YfcZ Uncharacterized conserved protein YfcZ, UPF0381/DUF406 family [Function unknown]. 98 matched cddid_all.tbl CDD COG3692 COG3692 442907 YifN Uncharacterized conserved protein YifN, PemK superfamily [Function unknown]. 132 matched cddid_all.tbl CDD COG3693 COG3693 442908 XynA Endo-1,4-beta-xylanase, GH35 family [Carbohydrate transport and metabolism]. 328 matched cddid_all.tbl CDD COG3694 COG3694 442909 COG3694 ABC-type uncharacterized transport system, permease component [General function prediction only]. 262 matched cddid_all.tbl CDD COG3695 COG3695 442910 Atl1 Alkylated DNA nucleotide flippase Atl1, participates in nucleotide excision repair, Ada-like DNA-binding domain [Transcription]. 104 matched cddid_all.tbl CDD COG3696 COG3696 442911 CusA Cu/Ag efflux pump CusA [Inorganic ion transport and metabolism]. 1031 matched cddid_all.tbl CDD COG3697 COG3697 442912 CitX Phosphoribosyl-dephospho-CoA transferase (holo-ACP synthetase) [Coenzyme transport and metabolism, Lipid transport and metabolism]. 176 matched cddid_all.tbl CDD COG3698 COG3698 442913 YigE Uncharacterized conserved protein YigE, DUF2233 family [Function unknown]. 239 matched cddid_all.tbl CDD COG3700 COG3700 442914 AphA Acid phosphatase, class B [Inorganic ion transport and metabolism, General function prediction only]. 237 matched cddid_all.tbl CDD COG3701 COG3701 442915 TrbF Type IV secretory pathway, TrbF component [Intracellular trafficking, secretion, and vesicular transport]. 223 matched cddid_all.tbl CDD COG3702 COG3702 442916 VirB3 Type IV secretory pathway, VirB3 component [Intracellular trafficking, secretion, and vesicular transport]. 97 matched cddid_all.tbl CDD COG3703 COG3703 442917 ChaC2 Gamma-glutamylcyclotransferase ChaC2 (glutathione degradation) [Inorganic ion transport and metabolism]. 190 matched cddid_all.tbl CDD COG3704 COG3704 442918 VirB6 Type IV secretory pathway, VirB6 component [Intracellular trafficking, secretion, and vesicular transport]. 300 matched cddid_all.tbl CDD COG3705 COG3705 442919 HisZ ATP phosphoribosyltransferase regulatory subunit HisZ [Amino acid transport and metabolism]. 312 matched cddid_all.tbl CDD COG3706 COG3706 442920 PleD Two-component response regulator, PleD family, consists of two REC domains and a diguanylate cyclase (GGDEF) domain [Signal transduction mechanisms, Transcription]. 179 matched cddid_all.tbl CDD COG3707 COG3707 442921 AmiR Two-component response regulator, AmiR/NasT family, consists of REC and RNA-binding antiterminator (ANTAR) domains [Signal transduction mechanisms, Transcription]. 194 matched cddid_all.tbl CDD COG3708 COG3708 442922 YdeE Predicted transcriptional regulator YdeE, contains AraC-type DNA-binding domain [Transcription]. 157 matched cddid_all.tbl CDD COG3709 COG3709 442923 PhnN Ribose 1,5-bisphosphate kinase PhnN [Carbohydrate transport and metabolism]. 188 matched cddid_all.tbl CDD COG3710 COG3710 442924 CadC1 DNA-binding winged helix-turn-helix (wHTH) domain [Transcription]. 106 matched cddid_all.tbl CDD COG3711 COG3711 442925 BglG Transcriptional antiterminator [Transcription]. 618 matched cddid_all.tbl CDD COG3712 COG3712 442926 FecR Periplasmic ferric-dicitrate binding protein FecR, regulates iron transport [Inorganic ion transport and metabolism, Signal transduction mechanisms]. 269 matched cddid_all.tbl CDD COG3713 COG3713 442927 OmpV Outer membrane scaffolding protein for murein synthesis, MipA/OmpV family [Cell wall/membrane/envelope biogenesis]. 256 matched cddid_all.tbl CDD COG3714 COG3714 442928 YhhN Uncharacterized membrane protein YhhN [Function unknown]. 215 matched cddid_all.tbl CDD COG3715 COG3715 442929 ManY Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific IIC component [Carbohydrate transport and metabolism]. 259 matched cddid_all.tbl CDD COG3716 COG3716 442930 ManZ Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific IID component [Carbohydrate transport and metabolism]. 271 matched cddid_all.tbl CDD COG3717 COG3717 442931 KduI 5-keto 4-deoxyuronate isomerase [Carbohydrate transport and metabolism]. 275 matched cddid_all.tbl CDD COG3718 COG3718 442932 IolB 5-deoxy-D-glucuronate isomerase [Carbohydrate transport and metabolism]. 275 matched cddid_all.tbl CDD COG3719 COG3719 442933 RnaI Ribonuclease I [Translation, ribosomal structure and biogenesis]. 222 matched cddid_all.tbl CDD COG3720 COG3720 442934 HemS Putative heme degradation protein [Inorganic ion transport and metabolism]. 338 matched cddid_all.tbl CDD COG3721 COG3721 442935 HugX Putative heme iron utilization protein [Inorganic ion transport and metabolism]. 162 matched cddid_all.tbl CDD COG3722 COG3722 442936 MtlR DNA-binding transcriptional regulator, MltR family [Transcription]. 174 matched cddid_all.tbl CDD COG3723 COG3723 442937 RecT Recombinational DNA repair protein RecT [Replication, recombination and repair]. 264 matched cddid_all.tbl CDD COG3724 COG3724 442938 AstB Succinylarginine dihydrolase [Amino acid transport and metabolism]. 443 matched cddid_all.tbl CDD COG3725 COG3725 442939 AmpE Membrane protein AmpE required for beta-lactamase induction [Defense mechanisms]. 289 matched cddid_all.tbl CDD COG3726 COG3726 442940 AhpA Uncharacterized membrane protein Smp affecting hemolysin expression [Function unknown]. 208 matched cddid_all.tbl CDD COG3727 COG3727 442941 Vsr G:T-mismatch repair DNA endonuclease Vsr, very short patch repair protein [Replication, recombination and repair]. 141 matched cddid_all.tbl CDD COG3728 COG3728 442942 XtmA Phage terminase, small subunit [Mobilome: prophages, transposons]. 131 matched cddid_all.tbl CDD COG3729 COG3729 442943 GsiB General stress protein YciG, contains tandem KGG domains [General function prediction only]. 64 matched cddid_all.tbl CDD COG3730 COG3730 442944 SrlA Phosphotransferase system sorbitol-specific IIC component [Carbohydrate transport and metabolism]. 175 matched cddid_all.tbl CDD COG3731 COG3731 442945 SrlB Phosphotransferase system sorbitol-specific IIA component [Carbohydrate transport and metabolism]. 117 matched cddid_all.tbl CDD COG3732 COG3732 442946 SrlE Phosphotransferase system sorbitol-specific IIB component [Carbohydrate transport and metabolism]. 339 matched cddid_all.tbl CDD COG3733 COG3733 442947 TynA Cu2+-containing amine oxidase [Secondary metabolites biosynthesis, transport and catabolism]. 646 matched cddid_all.tbl CDD COG3734 COG3734 442948 DgoK 2-keto-3-deoxy-galactonokinase [Carbohydrate transport and metabolism]. 306 matched cddid_all.tbl CDD COG3735 COG3735 442949 TraB Uncharacterized conserved protein YbaP, TraB family [Function unknown]. 293 matched cddid_all.tbl CDD COG3736 COG3736 442950 VirB8 Type IV secretory pathway, component VirB8 [Intracellular trafficking, secretion, and vesicular transport]. 230 matched cddid_all.tbl CDD COG3737 COG3737 442951 COG3737 Uncharacterized protein, contains Mth938-like domain [Function unknown]. 121 matched cddid_all.tbl CDD COG3738 COG3738 442952 YiijF Uncharacterized conserved protein YijF, DUF1287 family [Function unknown]. 197 matched cddid_all.tbl CDD COG3739 COG3739 442953 YoaT Uncharacterized membrane protein YoaT, DUF817 family [Function unknown]. 279 matched cddid_all.tbl CDD COG3740 COG3740 442954 COG3740 Phage head maturation protease [Mobilome: prophages, transposons]. 183 matched cddid_all.tbl CDD COG3741 COG3741 442955 HutG N-formylglutamate amidohydrolase [Amino acid transport and metabolism]. 273 matched cddid_all.tbl CDD COG3742 COG3742 442956 VapC VapC family ribonuclease, contains PIN domain [Defense mechanisms]. 129 matched cddid_all.tbl CDD COG3743 COG3743 442957 H3TH Predicted 5' DNA nuclease, flap endonuclease-1-like, helix-3-turn-helix (H3TH) domain [Replication, recombination and repair]. 92 matched cddid_all.tbl CDD COG3744 COG3744 442958 COG3744 PIN domain nuclease, a component of toxin-antitoxin system (PIN domain) [Defense mechanisms]. 128 matched cddid_all.tbl CDD COG3745 COG3745 442959 CpaB Flp pilus assembly protein CpaB [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures]. 259 matched cddid_all.tbl CDD COG3746 COG3746 442960 OprP Phosphate-selective porin [Inorganic ion transport and metabolism]. 388 matched cddid_all.tbl CDD COG3747 COG3747 442961 COG3747 Phage terminase, small subunit [Mobilome: prophages, transposons]. 148 matched cddid_all.tbl CDD COG3748 COG3748 442962 COG3748 Uncharacterized membrane protein [Function unknown]. 400 matched cddid_all.tbl CDD COG3749 COG3749 442963 COG3749 Uncharacterized conserved protein, DUF934 family [Function unknown]. 161 matched cddid_all.tbl CDD COG3750 COG3750 442964 COG3750 Uncharacterized conserved protein, UPF0335 family [Function unknown]. 81 matched cddid_all.tbl CDD COG3751 COG3751 442965 EGL9 Proline 4-hydroxylase (includes Rps23 Pro-64 3,4-dihydroxylase Tpa1), contains SM-20 domain [Translation, ribosomal structure and biogenesis, Posttranslational modification, protein turnover, chaperones]. 195 matched cddid_all.tbl CDD COG3752 COG3752 442966 COG3752 Steroid 5-alpha reductase family enzyme [General function prediction only]. 264 matched cddid_all.tbl CDD COG3753 COG3753 442967 YidB Uncharacterized conserved protein YidB, DUF937 family [Function unknown]. 123 matched cddid_all.tbl CDD COG3754 COG3754 442968 RgpF Lipopolysaccharide biosynthesis protein [Cell wall/membrane/envelope biogenesis]. 152 matched cddid_all.tbl CDD COG3755 COG3755 442969 YecT Uncharacterized conserved protein YecT, DUF1311 family [Function unknown]. 121 matched cddid_all.tbl CDD COG3756 COG3756 442970 YdaU Uncharacterized conserved protein YdaU, DUF1376 family [Function unknown]. 124 matched cddid_all.tbl CDD COG3757 COG3757 442971 Acm Lyzozyme M1 (1,4-beta-N-acetylmuramidase), GH25 family [Cell wall/membrane/envelope biogenesis]. 208 matched cddid_all.tbl CDD COG3758 COG3758 442972 Ves Various environmental stresses-induced protein Ves (function unknown) [Function unknown]. 196 matched cddid_all.tbl CDD COG3759 COG3759 442973 COG3759 Uncharacterized membrane protein [Function unknown]. 120 matched cddid_all.tbl CDD COG3760 COG3760 442974 ProX Predicted aminoacyl-tRNA deacylase, YbaK-like aminoacyl-tRNA editing domain [General function prediction only]. 162 matched cddid_all.tbl CDD COG3761 COG3761 442975 NDUFA12 NADH:ubiquinone oxidoreductase NDUFA12 subunit (Leigh syndrome) [Energy production and conversion]. NADH:ubiquinone oxidoreductase NDUFA12 subunit (Leigh syndrome) is part of the Pathway/BioSystem: NADH dehydrogenase 132 matched cddid_all.tbl CDD COG3762 COG3762 442976 COG3762 Uncharacterized membrane protein [Function unknown]. 146 matched cddid_all.tbl CDD COG3763 COG3763 442977 YneF Uncharacterized conserved protein YneF, UPF0154 family [Function unknown]. 71 matched cddid_all.tbl CDD COG3764 COG3764 442978 SrtA Sortase (surface protein transpeptidase) [Cell wall/membrane/envelope biogenesis]. 144 matched cddid_all.tbl CDD COG3765 COG3765 442979 WzzB LPS O-antigen chain length determinant protein, WzzB/FepE family [Cell wall/membrane/envelope biogenesis]. 364 matched cddid_all.tbl CDD COG3766 COG3766 442980 YjfL Uncharacterized membrane protein YjfL, UPF0719 family [Function unknown]. 133 matched cddid_all.tbl CDD COG3767 COG3767 442981 COG3767 Uncharacterized low-complexity protein [Function unknown]. 102 matched cddid_all.tbl CDD COG3768 COG3768 442982 YcjF Uncharacterized membrane protein YcjF, UPF0283 family [Function unknown]. 339 matched cddid_all.tbl CDD COG3769 COG3769 442983 YedP Mannosyl-3-phosphoglycerate phosphatase YedP/MpgP, HAD superfamily [Carbohydrate transport and metabolism]. 268 matched cddid_all.tbl CDD COG3770 COG3770 442984 MepA Murein endopeptidase MepA (D-alanyl-D-alanine-endopeptidase) [Cell wall/membrane/envelope biogenesis]. 288 matched cddid_all.tbl CDD COG3771 COG3771 442985 YciS Lipopolysaccharide assembly protein YciS/LapA, DUF1049 family [Function unknown]. 96 matched cddid_all.tbl CDD COG3772 COG3772 442986 RrrD Phage-related lysozyme (muramidase), GH24 family [Cell wall/membrane/envelope biogenesis]. 146 matched cddid_all.tbl CDD COG3773 COG3773 442987 CwlJ Cell wall hydrolase CwlJ, involved in spore germination [Cell cycle control, cell division, chromosome partitioning, Cell wall/membrane/envelope biogenesis]. 124 matched cddid_all.tbl CDD COG3774 COG3774 442988 OCH1 Mannosyltransferase OCH1 or related enzyme [Cell wall/membrane/envelope biogenesis]. 136 matched cddid_all.tbl CDD COG3775 COG3775 442989 SgcC Phosphotransferase system, galactitol-specific IIC component [Carbohydrate transport and metabolism]. 451 matched cddid_all.tbl CDD COG3776 COG3776 442990 YhhL Uncharacterized conserved protein YhhL, DUF1145 family [Function unknown]. 91 matched cddid_all.tbl CDD COG3777 COG3777 442991 HTD2 Hydroxyacyl-ACP dehydratase HTD2, hotdog domain [Lipid transport and metabolism]. 281 matched cddid_all.tbl CDD COG3778 COG3778 442992 YmfQ Uncharacterized conserved protein YmfQ in lambdoid prophage, DUF2313 family [Mobilome: prophages, transposons]. 193 matched cddid_all.tbl CDD COG3779 COG3779 442993 YegJ Uncharacterized conserved protein YegJ, DUF2314 family [Function unknown]. 158 matched cddid_all.tbl CDD COG3780 COG3780 442994 COG3780 DNA endonuclease related to intein-encoded endonucleases [Replication, recombination and repair]. 273 matched cddid_all.tbl CDD COG3781 COG3781 442995 YneE Predicted membrane chloride channel, bestrophin family [Inorganic ion transport and metabolism]. 306 matched cddid_all.tbl CDD COG3782 COG3782 442996 COG3782 Uncharacterized conserved protein, DUF1853 domain [Function unknown]. 286 matched cddid_all.tbl CDD COG3783 COG3783 442997 CybC Soluble cytochrome b562 [Energy production and conversion]. 128 matched cddid_all.tbl CDD COG3784 COG3784 442998 YdbL Uncharacterized conserved protein YdbL, DUF1318 family [Function unknown]. 114 matched cddid_all.tbl CDD COG3785 COG3785 442999 HspQ Heat shock protein HspQ [Posttranslational modification, protein turnover, chaperones]. 107 matched cddid_all.tbl CDD COG3786 COG3786 443000 COG3786 L,D-peptidoglycan transpeptidase YkuD, ErfK/YbiS/YcfS/YnhG family [Cell wall/membrane/envelope biogenesis]. 189 matched cddid_all.tbl CDD COG3787 COG3787 443001 YhbP Uncharacterized conserved protein YhbP, UPF0306 family [Function unknown]. 146 matched cddid_all.tbl CDD COG3788 COG3788 443002 YecN Uncharacterized membrane protein YecN, MAPEG domain [Function unknown]. 131 matched cddid_all.tbl CDD COG3789 COG3789 443003 YjfI Uncharacterized conserved protein YjfI, DUF2170 family [Function unknown]. 142 matched cddid_all.tbl CDD COG3790 COG3790 443004 YbgE Predicted membrane protein, encoded in cydAB operon [Function unknown]. 98 matched cddid_all.tbl CDD COG3791 COG3791 443005 COG3791 Uncharacterized conserved protein [Function unknown]. 132 matched cddid_all.tbl CDD COG3792 COG3792 443006 COG3792 Uncharacterized conserved protein, DUF596 domain [Function unknown]. 108 matched cddid_all.tbl CDD COG3793 COG3793 443007 TerB Tellurite resistance protein TerB [Inorganic ion transport and metabolism]. 128 matched cddid_all.tbl CDD COG3794 COG3794 443008 PetE Plastocyanin [Energy production and conversion]. 76 matched cddid_all.tbl CDD COG3795 COG3795 443009 YCII 5-chloro-2-hydroxyhydroquinone dehydrochlorinase TtfG, YCII superfamily [Secondary metabolites biosynthesis, transport and catabolism]. 118 matched cddid_all.tbl CDD COG3797 COG3797 443010 COG3797 Uncharacterized conserved protein, DUF1697 family [Function unknown]. 180 matched cddid_all.tbl CDD COG3798 COG3798 443011 COG3798 Uncharacterized conserved protein, DUF2171 domain [Function unknown]. 77 matched cddid_all.tbl CDD COG3799 COG3799 443012 Mal Methylaspartate ammonia-lyase [Amino acid transport and metabolism]. 413 matched cddid_all.tbl CDD COG3800 COG3800 443013 COG3800 Predicted transcriptional regulator [General function prediction only]. 447 matched cddid_all.tbl CDD COG3801 COG3801 443014 COG3801 Uncharacterized conserved protein [Function unknown]. 114 matched cddid_all.tbl CDD COG3802 COG3802 443015 GguC Uncharacterized conserved protein GguC, FAA hydrolase family [Function unknown]. 331 matched cddid_all.tbl CDD COG3803 COG3803 443016 COG3803 Uncharacterized conserved protein, DUF924 family [Function unknown]. 181 matched cddid_all.tbl CDD COG3804 COG3804 443017 COG3804 Uncharacterized conserved protein [Function unknown]. 338 matched cddid_all.tbl CDD COG3805 COG3805 443018 DodA Aromatic ring-cleaving dioxygenase [Secondary metabolites biosynthesis, transport and catabolism]. 114 matched cddid_all.tbl CDD COG3806 COG3806 443019 ChrR Anti-sigma factor ChrR, cupin superfamily [Signal transduction mechanisms]. 157 matched cddid_all.tbl CDD COG3807 COG3807 443020 SH3 SH3-like domain [Function unknown]. 150 matched cddid_all.tbl CDD COG3808 COG3808 443021 OVP1 Na+ or H+-translocating membrane pyrophosphatase [Energy production and conversion]. 660 matched cddid_all.tbl CDD COG3809 COG3809 443022 COG3809 Predicted nucleic acid-binding protein, contains Zn-finger domain [General function prediction only]. 59 matched cddid_all.tbl CDD COG3811 COG3811 443023 YjhX Uncharacterized conserved protein YjhX, UPF0386/DUF2084 family [Function unknown]. 85 matched cddid_all.tbl CDD COG3812 COG3812 443024 COG3812 Uncharacterized conserved protein, DUF1993 domain [Function unknown]. 170 matched cddid_all.tbl CDD COG3813 COG3813 443025 COG3813 Uncharacterized conserved protein, DUF1272 domain [Function unknown]. 83 matched cddid_all.tbl CDD COG3814 COG3814 443026 SspB2 SspB-like protein, predicted to bind SsrA peptide [Posttranslational modification, protein turnover, chaperones]. 166 matched cddid_all.tbl CDD COG3815 COG3815 443027 COG3815 Uncharacterized membrane protein [Function unknown]. 115 matched cddid_all.tbl CDD COG3816 COG3816 443028 COG3816 Uncharacterized conserved protein, DUF1285 family [Function unknown]. 186 matched cddid_all.tbl CDD COG3817 COG3817 443029 COG3817 Uncharacterized membrane protein [Function unknown]. 316 matched cddid_all.tbl CDD COG3818 COG3818 443030 COG3818 Predicted N-acetyltransferase, GNAT superfamily [General function prediction only]. 168 matched cddid_all.tbl CDD COG3819 COG3819 443031 COG3819 Uncharacterized membrane protein [Function unknown]. 230 matched cddid_all.tbl CDD COG3820 COG3820 443032 COG3820 Uncharacterized conserved protein, DUF1013 family [Function unknown]. 228 matched cddid_all.tbl CDD COG3821 COG3821 443033 COG3821 Uncharacterized membrane protein [Function unknown]. 230 matched cddid_all.tbl CDD COG3822 COG3822 443034 YdaE D-lyxose ketol-isomerase [Carbohydrate transport and metabolism]. 224 matched cddid_all.tbl CDD COG3823 COG3823 443035 COG3823 Glutamine cyclotransferase [Posttranslational modification, protein turnover, chaperones]. 237 matched cddid_all.tbl CDD COG3824 COG3824 443036 COG3824 Predicted Zn-dependent protease, minimal metalloprotease (MMP)-like domain [Posttranslational modification, protein turnover, chaperones]. 122 matched cddid_all.tbl CDD COG3825 COG3825 443037 CoxE2 Uncharacterized CoxE-like protein, contains von Willebrand factor type A (vWA) domain [Function unknown]. 390 matched cddid_all.tbl CDD COG3826 COG3826 443038 COG3826 Uncharacterized conserved protein [Function unknown]. 237 matched cddid_all.tbl CDD COG3827 COG3827 443039 PopZ Cell pole-organizing protein PopZ [Cell cycle control, cell division, chromosome partitioning]. 81 matched cddid_all.tbl CDD COG3828 COG3828 443040 COG3828 Type 1 glutamine amidotransferase (GATase1)-like domain [General function prediction only]. 222 matched cddid_all.tbl CDD COG3829 COG3829 443041 RocR RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis domains [Transcription, Signal transduction mechanisms]. 448 matched cddid_all.tbl CDD COG3830 COG3830 443042 ACT ACT domain, binds amino acids and other small ligands [Signal transduction mechanisms]. 212 matched cddid_all.tbl CDD COG3831 COG3831 443043 WGR WGR domain, predicted DNA-binding domain in MolR [Transcription]. 83 matched cddid_all.tbl CDD COG3832 COG3832 443044 YndB Chalcone/flavanone-binding protein YndB, AHSA1/START/SRPBCC domain [Lipid transport and metabolism]. 142 matched cddid_all.tbl CDD COG3833 COG3833 443045 MalG ABC-type maltose transport system, permease component MalG [Carbohydrate transport and metabolism]. 282 matched cddid_all.tbl CDD COG3835 COG3835 443046 CdaR Sugar diacid utilization regulator CdaR [Transcription, Signal transduction mechanisms]. 301 matched cddid_all.tbl CDD COG3836 COG3836 443047 HpcH 2-keto-3-deoxy-L-rhamnonate aldolase RhmA [Carbohydrate transport and metabolism]. 237 matched cddid_all.tbl CDD COG3837 COG3837 443048 COG3837 Uncharacterized conserved protein, cupin superfamily [Function unknown]. 115 matched cddid_all.tbl CDD COG3838 COG3838 443049 VirB2 Type IV secretory pathway, VirB2 component (pilin) [Intracellular trafficking, secretion, and vesicular transport]. 109 matched cddid_all.tbl CDD COG3839 COG3839 443050 MalK ABC-type sugar transport system, ATPase component MalK [Carbohydrate transport and metabolism]. 352 matched cddid_all.tbl CDD COG3840 COG3840 443051 ThiQ ABC-type thiamine transport system, ATPase component ThiQ [Coenzyme transport and metabolism]. 232 matched cddid_all.tbl CDD COG3842 COG3842 443052 PotA ABC-type Fe3+/spermidine/putrescine transport systems, ATPase component [Amino acid transport and metabolism]. 353 matched cddid_all.tbl CDD COG3843 COG3843 443053 VirD2 Type IV secretory pathway, VirD2 component (relaxase) [Intracellular trafficking, secretion, and vesicular transport]. 652 matched cddid_all.tbl CDD COG3844 COG3844 443054 Bna5 Kynureninase [Amino acid transport and metabolism]. 420 matched cddid_all.tbl CDD COG3845 COG3845 443055 NupO ABC-type guanosine uptake system NupNOPQ, ATPase component NupO [Nucleotide transport and metabolism]. 504 matched cddid_all.tbl CDD COG3846 COG3846 443056 TrbL Type IV secretory pathway, TrbL components [Intracellular trafficking, secretion, and vesicular transport]. 443 matched cddid_all.tbl CDD COG3847 COG3847 443057 Flp Flp pilus assembly protein, pilin Flp [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures]. 58 matched cddid_all.tbl CDD COG3848 COG3848 443058 PykA2 Phosphohistidine swiveling domain of PEP-utilizing enzymes [Signal transduction mechanisms]. 321 matched cddid_all.tbl CDD COG3850 COG3850 443059 NarQ Signal transduction histidine kinase NarQ, nitrate/nitrite-specific [Signal transduction mechanisms]. 448 matched cddid_all.tbl CDD COG3851 COG3851 443060 UhpB Signal transduction histidine kinase UhpB, glucose-6-phosphate specific [Signal transduction mechanisms]. 493 matched cddid_all.tbl CDD COG3852 COG3852 443061 NtrB Signal transduction histidine kinase NtrB, nitrogen specific [Signal transduction mechanisms]. 361 matched cddid_all.tbl CDD COG3853 COG3853 443062 YaaN Uncharacterized conserved protein YaaN involved in tellurite resistance [Defense mechanisms]. 389 matched cddid_all.tbl CDD COG3854 COG3854 443063 SpoIIIAA Stage III sporulation protein SpoIIIAA [Cell cycle control, cell division, chromosome partitioning]. 309 matched cddid_all.tbl CDD COG3855 COG3855 443064 Fbp2 Fructose-1,6-bisphosphatase [Carbohydrate transport and metabolism]. Fructose-1,6-bisphosphatase is part of the Pathway/BioSystem: Gluconeogenesis 654 matched cddid_all.tbl CDD COG3856 COG3856 443065 Sbp Small basic protein Sbp (function unknown), DUF1290 domain [Function unknown]. 108 matched cddid_all.tbl CDD COG3857 COG3857 443066 AddB ATP-dependent helicase/DNAse subunit B [Replication, recombination and repair]. 1019 matched cddid_all.tbl CDD COG3858 COG3858 443067 SleL Spore cortex hydrolase SleL/YaaH, N-acetylglucosaminidase of GH18 family [Cell cycle control, cell division, chromosome partitioning]. 22 matched cddid_all.tbl CDD COG3859 COG3859 443068 ThiT Thiamine transporter ThiT [Coenzyme transport and metabolism]. 179 matched cddid_all.tbl CDD COG3860 COG3860 443069 COG3860 Uncharacterized conserved protein, DUF2087 family [Function unknown]. 170 matched cddid_all.tbl CDD COG3861 COG3861 443070 YsnF Stress response protein YsnF (function unknown) [Function unknown]. 133 matched cddid_all.tbl CDD COG3862 COG3862 443071 COG3862 Uncharacterized conserved protein with two CxxC motifs [Function unknown]. 117 matched cddid_all.tbl CDD COG3863 COG3863 443072 YycO Uncharacterized conserved protein YycO, NlpC/P60 family [Function unknown]. 166 matched cddid_all.tbl CDD COG3864 COG3864 443073 COG3864 Predicted metal-dependent peptidase [General function prediction only]. 384 matched cddid_all.tbl CDD COG3865 COG3865 443074 COG3865 Glyoxalase superfamily enzyme, possible 3-demethylubiquinone-9 3-methyltransferase [General function prediction only]. 156 matched cddid_all.tbl CDD COG3866 COG3866 443075 PelB Pectate lyase [Carbohydrate transport and metabolism]. 326 matched cddid_all.tbl CDD COG3867 COG3867 443076 GanB Arabinogalactan endo-1,4-beta-galactosidase [Carbohydrate transport and metabolism]. 382 matched cddid_all.tbl CDD COG3868 COG3868 443077 COG3868 Predicted glycosyl hydrolase, GH114 family [Carbohydrate transport and metabolism]. 272 matched cddid_all.tbl CDD COG3869 COG3869 443078 McsB Protein-arginine kinase McsB [Posttranslational modification, protein turnover, chaperones]. 353 matched cddid_all.tbl CDD COG3870 COG3870 443079 DarA Cyclic di-AMP receptor DarA/PstA [Signal transduction mechanisms]. 109 matched cddid_all.tbl CDD COG3871 COG3871 443080 YzzA General stress protein 26 (function unknown) [Function unknown]. 132 matched cddid_all.tbl CDD COG3872 COG3872 443081 YqhQ Uncharacterized conserved protein YqhQ, DUF1385 family [Function unknown]. 298 matched cddid_all.tbl CDD COG3874 COG3874 443082 YtfJ Uncharacterized spore protein YtfJ [Function unknown]. 133 matched cddid_all.tbl CDD COG3875 COG3875 443083 LarA Nickel-dependent lactate racemase [Cell wall/membrane/envelope biogenesis]. 418 matched cddid_all.tbl CDD COG3876 COG3876 443084 YbbC Uncharacterized conserved protein YbbC, DUF1343 family [Function unknown]. 382 matched cddid_all.tbl CDD COG3877 COG3877 443085 COG3877 Predicted DNA-binding transcriptional regulator with XRE-family HTH domain, DUF2089 family [Transcription]. 120 matched cddid_all.tbl CDD COG3878 COG3878 443086 YwqG Uncharacterized conserved protein YwqG, DUF1963 family [Function unknown]. 241 matched cddid_all.tbl CDD COG3879 COG3879 443087 YlxW Uncharacterized conserved protein YlxW, UPF0749 family [Function unknown]. 240 matched cddid_all.tbl CDD COG3880 COG3880 443088 McsA Protein-arginine kinase activator protein McsA [Posttranslational modification, protein turnover, chaperones]. 173 matched cddid_all.tbl CDD COG3881 COG3881 443089 YrrD Uncharacterized conserved protein YrrD, contains PRC-barrel domain [Function unknown]. 161 matched cddid_all.tbl CDD COG3882 COG3882 443090 FkbH Predicted enzyme involved in methoxymalonyl-ACP biosynthesis [Lipid transport and metabolism]. 375 matched cddid_all.tbl CDD COG3883 COG3883 443091 CwlO1 Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown]. 379 matched cddid_all.tbl CDD COG3884 COG3884 443092 FatA Acyl-ACP thioesterase [Lipid transport and metabolism]. 242 matched cddid_all.tbl CDD COG3885 COG3885 443093 COG3885 Aromatic ring-opening dioxygenase, LigB subunit [Secondary metabolites biosynthesis, transport and catabolism]. 273 matched cddid_all.tbl CDD COG3886 COG3886 443094 COG3886 HKD family nuclease [Replication, recombination and repair]. 941 matched cddid_all.tbl CDD COG3887 COG3887 443095 GdpP Cyclic di-AMP phosphodiesterase GdpP, contains GGDEF-like and DHH domains [Signal transduction mechanisms]. 662 matched cddid_all.tbl CDD COG3888 COG3888 443096 COG3888 Predicted transcriptional regulator [Transcription]. 328 matched cddid_all.tbl CDD COG3889 COG3889 443097 COG3889 Extracellular solute-binding protein, contains Ig-fold domain [General function prediction only]. 878 matched cddid_all.tbl CDD COG3890 COG3890 443098 ERG8 Phosphomevalonate kinase [Lipid transport and metabolism]. Phosphomevalonate kinase is part of the Pathway/BioSystem: Isoprenoid biosynthesis 319 matched cddid_all.tbl CDD COG3892 COG3892 443099 IolC Myo-inositol catabolism protein LolC [Carbohydrate transport and metabolism]. 640 matched cddid_all.tbl CDD COG3893 COG3893 443100 COG3893 Inactivated superfamily I helicase [Replication, recombination and repair]. 965 matched cddid_all.tbl CDD COG3894 COG3894 443101 COG3894 Uncharacterized 2Fe-2S and 4Fe-4S clusters-containing protein, contains DUF4445 domain [Function unknown]. 621 matched cddid_all.tbl CDD COG3895 COG3895 443102 MliC Membrane-bound inhibitor of C-type lysozyme [Cell wall/membrane/envelope biogenesis]. 108 matched cddid_all.tbl CDD COG3896 COG3896 443103 COG3896 Chloramphenicol 3-O-phosphotransferase [Defense mechanisms]. 182 matched cddid_all.tbl CDD COG3897 COG3897 443104 Nnt1 Protein N-terminal and lysine N-methylase, NNT1/EFM7 family [Posttranslational modification, protein turnover, chaperones]. 216 matched cddid_all.tbl CDD COG3898 COG3898 443105 HemYx Uncharacterized protein HemY, contains HemY_N domain and TPR repeats (unrelated to HemY-type protoporphyrinogen oxidase) [Function unknown]. 468 matched cddid_all.tbl CDD COG3899 COG3899 443106 COG3899 Predicted ATPase [General function prediction only]. 1244 matched cddid_all.tbl CDD COG3900 COG3900 443107 COG3900 Predicted periplasmic protein [Function unknown]. 260 matched cddid_all.tbl CDD COG3901 COG3901 443108 NosR Transcriptional regulator NosR of nitric oxide reductase [Transcription]. 713 matched cddid_all.tbl CDD COG3903 COG3903 443109 COG3903 Predicted ATPase [General function prediction only]. 933 matched cddid_all.tbl CDD COG3904 COG3904 443110 COG3904 Predicted periplasmic protein [Function unknown]. 197 matched cddid_all.tbl CDD COG3905 COG3905 443111 PutA1 Predicted transcriptional regulator, contains ribbon-helix-helix (RHH_1) domain [Transcription]. 69 matched cddid_all.tbl CDD COG3906 COG3906 443112 YrzB Uncharacterized conserved protein YrzB, UPF0473 family [Function unknown]. 94 matched cddid_all.tbl CDD COG3907 COG3907 443113 COG3907 Membrane-associated enzyme, PAP2 (acid phosphatase) superfamily [General function prediction only]. 236 matched cddid_all.tbl CDD COG3908 COG3908 443114 COG3908 Uncharacterized conserved protein, DUF2093 domain [Function unknown]. 73 matched cddid_all.tbl CDD COG3909 COG3909 443115 CytC556 Cytochrome c556 [Energy production and conversion]. 150 matched cddid_all.tbl CDD COG3910 COG3910 443116 COG3910 Predicted ATPase [General function prediction only]. 239 matched cddid_all.tbl CDD COG3911 COG3911 443117 COG3911 Predicted ATPase [General function prediction only]. 180 matched cddid_all.tbl CDD COG3913 COG3913 443118 SciT Regulator of T6SS expression TagF, TagF/ImpM/SciT family (unrelated to teichoic acid polymerase TagF of B.subtilis, COG1887) [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport]. 222 matched cddid_all.tbl CDD COG3914 COG3914 443119 Spy Predicted O-linked N-acetylglucosamine transferase, SPINDLY family [Posttranslational modification, protein turnover, chaperones]. 658 matched cddid_all.tbl CDD COG3915 COG3915 443120 COG3915 Uncharacterized conserved protein [Function unknown]. 167 matched cddid_all.tbl CDD COG3916 COG3916 443121 LasI N-acyl-homoserine lactone synthase LasI (autoinducer biosynthesis) [Signal transduction mechanisms]. 201 matched cddid_all.tbl CDD COG3917 COG3917 443122 NahD 2-hydroxychromene-2-carboxylate isomerase [Secondary metabolites biosynthesis, transport and catabolism]. 196 matched cddid_all.tbl CDD COG3918 COG3918 443123 COG3918 Uncharacterized membrane protein [Function unknown]. 155 matched cddid_all.tbl CDD COG3919 COG3919 443124 COG3919 Predicted ATP-dependent carboligase, ATP-grasp superfamily [General function prediction only]. 382 matched cddid_all.tbl CDD COG3920 COG3920 443125 COG3920 Two-component sensor histidine kinase, HisKA and HATPase domains [Signal transduction mechanisms]. 495 matched cddid_all.tbl CDD COG3921 COG3921 443126 COG3921 Uncharacterized conserved protein, contains Extensin-like_C domain [Function unknown]. 238 matched cddid_all.tbl CDD COG3923 COG3923 443127 PriC Primosomal replication protein N'' [Replication, recombination and repair]. 179 matched cddid_all.tbl CDD COG3924 COG3924 443128 YhdT Uncharacterized membrane protein YhdT [Function unknown]. 82 matched cddid_all.tbl CDD COG3925 COG3925 443129 FruA N-terminal domain of the PTS fructose-specific IIB component [Carbohydrate transport and metabolism, Signal transduction mechanisms]. 563 matched cddid_all.tbl CDD COG3926 COG3926 443130 ZliS Lysozyme family protein [General function prediction only]. 167 matched cddid_all.tbl CDD COG3930 COG3930 443131 COG3930 Uncharacterized conserved protein, DUF1704 domain [Function unknown]. 391 matched cddid_all.tbl CDD COG3931 COG3931 443132 HutG2 Predicted N-formylglutamate amidohydrolase [Amino acid transport and metabolism]. 252 matched cddid_all.tbl CDD COG3932 COG3932 443133 ExoD Exopolysaccharide synthesis protein ExoD [Cell wall/membrane/envelope biogenesis]. 206 matched cddid_all.tbl CDD COG3933 COG3933 443134 LevR Transcriptional regulatory protein LevR, contains PRD, AAA+ and EIIA domains [Transcription]. 916 matched cddid_all.tbl CDD COG3934 COG3934 443135 COG3934 Endo-1,4-beta-mannosidase [Carbohydrate transport and metabolism]. 331 matched cddid_all.tbl CDD COG3935 COG3935 443136 DnaD DNA replication protein DnaD [Replication, recombination and repair]. 103 matched cddid_all.tbl CDD COG3936 COG3936 443137 YfiQ Membrane-bound acyltransferase YfiQ, involved in biofilm formation [Carbohydrate transport and metabolism]. 334 matched cddid_all.tbl CDD COG3937 COG3937 443138 PhaF Polyhydroxyalkanoate synthesis regulator phasin [Secondary metabolites biosynthesis, transport and catabolism, Signal transduction mechanisms]. 103 matched cddid_all.tbl CDD COG3938 COG3938 443139 PrdF Proline racemase/hydroxyproline epimerase [Amino acid transport and metabolism]. 335 matched cddid_all.tbl CDD COG3940 COG3940 443140 COG3940 Beta-xylosidase, GH43 family [Carbohydrate transport and metabolism]. 309 matched cddid_all.tbl CDD COG3941 COG3941 443141 HI1514 Phage tail tape-measure protein, controls tail length [Mobilome: prophages, transposons]. 833 matched cddid_all.tbl CDD COG3942 COG3942 443142 COG3942 Surface antigen [Cell wall/membrane/envelope biogenesis]. 129 matched cddid_all.tbl CDD COG3943 COG3943 443143 RhuM Uncharacterized protein RhuM, Salmonella virulence factor [Function unknown]. 130 matched cddid_all.tbl CDD COG3944 COG3944 443144 YveK Capsular polysaccharide biosynthesis protein YveK [Cell wall/membrane/envelope biogenesis]. 309 matched cddid_all.tbl CDD COG3945 COG3945 443145 COG3945 Hemerythrin domain [General function prediction only]. 180 matched cddid_all.tbl CDD COG3946 COG3946 443146 VirJ Type IV secretory pathway, VirJ component [Intracellular trafficking, secretion, and vesicular transport]. 231 matched cddid_all.tbl CDD COG3947 COG3947 443147 SAPR Two-component response regulator, SAPR family, consists of REC, wHTH and BTAD domains [Signal transduction mechanisms, Transcription]. 16 matched cddid_all.tbl CDD COG3948 COG3948 443148 COG3948 Phage-related baseplate assembly protein [Mobilome: prophages, transposons]. 296 matched cddid_all.tbl CDD COG3949 COG3949 443149 YkvI Uncharacterized membrane protein YkvI [Function unknown]. 352 matched cddid_all.tbl CDD COG3950 COG3950 443150 COG3950 Predicted ATP-binding protein involved in virulence [General function prediction only]. 276 matched cddid_all.tbl CDD COG3951 COG3951 443151 FlgJ1 Rod binding protein domain [Cell motility]. 107 matched cddid_all.tbl CDD COG3952 COG3952 443152 LABN Uncharacterized N-terminal domain of lipid-A-disaccharide synthase [General function prediction only]. 105 matched cddid_all.tbl CDD COG3953 COG3953 443153 SLT SLT domain protein [Mobilome: prophages, transposons]. 325 matched cddid_all.tbl CDD COG3954 COG3954 443154 PrkB Phosphoribulokinase [Carbohydrate transport and metabolism]. 289 matched cddid_all.tbl CDD COG3955 COG3955 443155 COG3955 Uncharacterized conserved protein, DUF1919 family [Cell wall/membrane/envelope biogenesis]. 212 matched cddid_all.tbl CDD COG3956 COG3956 443156 YabN Uncharacterized conserved protein YabN, contains tetrapyrrole methylase and MazG-like pyrophosphatase domain [General function prediction only]. 268 matched cddid_all.tbl CDD COG3957 COG3957 443157 XFP Phosphoketolase [Carbohydrate transport and metabolism]. 785 matched cddid_all.tbl CDD COG3958 COG3958 443158 TktA2 Transketolase, C-terminal subunit [Carbohydrate transport and metabolism]. 308 matched cddid_all.tbl CDD COG3959 COG3959 443159 TktA1 Transketolase, N-terminal subunit [Carbohydrate transport and metabolism]. 277 matched cddid_all.tbl CDD COG3960 COG3960 443160 Gcl Glyoxylate carboligase [Secondary metabolites biosynthesis, transport and catabolism]. 588 matched cddid_all.tbl CDD COG3961 COG3961 443161 PDC1 TPP-dependent 2-oxoacid decarboxylase, includes indolepyruvate decarboxylase [Carbohydrate transport and metabolism, Coenzyme transport and metabolism, General function prediction only]. TPP-dependent 2-oxoacid decarboxylase, includes indolepyruvate decarboxylase is part of the Pathway/BioSystem: Pyruvate oxidation 545 matched cddid_all.tbl CDD COG3962 COG3962 443162 IolD TPP-dependent trihydroxycyclohexane-1,2-dione (THcHDO) dehydratase, myo-inositol metabolism [Carbohydrate transport and metabolism]. 622 matched cddid_all.tbl CDD COG3963 COG3963 443163 COG3963 Phosphatidylethanolamine N-methyltransferase [Lipid transport and metabolism]. 193 matched cddid_all.tbl CDD COG3964 COG3964 443164 COG3964 Predicted amidohydrolase [General function prediction only]. 376 matched cddid_all.tbl CDD COG3965 COG3965 443165 COG3965 Predicted Co/Zn/Cd cation transporter, cation efflux family [Inorganic ion transport and metabolism]. 300 matched cddid_all.tbl CDD COG3966 COG3966 443166 DltD Poly-D-alanine transfer protein DltD, involved in esterification of teichoic acids [Cell wall/membrane/envelope biogenesis]. 413 matched cddid_all.tbl CDD COG3967 COG3967 443167 DltE Short-chain dehydrogenase involved in D-alanine esterification of teichoic acids [Cell wall/membrane/envelope biogenesis, Lipid transport and metabolism]. 246 matched cddid_all.tbl CDD COG3968 COG3968 443168 GlnA3 Glutamine synthetase type III [Amino acid transport and metabolism]. 727 matched cddid_all.tbl CDD COG3969 COG3969 443169 YbdN Predicted phosphoadenosine phosphosulfate sulfurtransferase, contains C-terminal DUF3440 domain [General function prediction only]. 402 matched cddid_all.tbl CDD COG3970 COG3970 443170 COG3970 Fumarylacetoacetate (FAA) hydrolase family protein [General function prediction only]. 335 matched cddid_all.tbl CDD COG3971 COG3971 443171 MhpD 2-keto-4-pentenoate hydratase [Secondary metabolites biosynthesis, transport and catabolism]. 259 matched cddid_all.tbl CDD COG3972 COG3972 443172 COG3972 Superfamily I DNA and RNA helicases [Replication, recombination and repair]. 565 matched cddid_all.tbl CDD COG3973 COG3973 443173 HelD DNA helicase IV [Replication, recombination and repair]. 699 matched cddid_all.tbl CDD COG3975 COG3975 443174 COG3975 Predicted metalloprotease, contains C-terminal PDZ domain [General function prediction only]. 591 matched cddid_all.tbl CDD COG3976 COG3976 443175 COG3976 Uncharacterized conserved protein, contains FMN-binding domain [General function prediction only]. 116 matched cddid_all.tbl CDD COG3977 COG3977 443176 AvtA Alanine-alpha-ketoisovalerate (or valine-pyruvate) aminotransferase [Amino acid transport and metabolism]. 414 matched cddid_all.tbl CDD COG3978 COG3978 443177 IlvM Acetolactate synthase small subunit, contains ACT domain [Amino acid transport and metabolism]. 75 matched cddid_all.tbl CDD COG3979 COG3979 443178 COG3979 Chitodextrinase [Carbohydrate transport and metabolism]. 369 matched cddid_all.tbl CDD COG3980 COG3980 443179 SpsG Spore coat polysaccharide biosynthesis protein SpsG, predicted glycosyltransferase [Cell wall/membrane/envelope biogenesis]. 342 matched cddid_all.tbl CDD COG3981 COG3981 443180 COG3981 Predicted acetyltransferase [General function prediction only]. 170 matched cddid_all.tbl CDD COG4001 COG4001 443181 COG4001 Uncharacterized conserved protein [Function unknown]. 491 matched cddid_all.tbl CDD COG4002 COG4002 443182 COG4002 Predicted methyltransferase MtxX, methanogen marker protein 4 [General function prediction only]. 258 matched cddid_all.tbl CDD COG4003 COG4003 443183 COG4003 Uncharacterized conserved protein, DUF2095 family [Function unknown]. 105 matched cddid_all.tbl CDD COG4004 COG4004 443184 COG4004 Uncharacterized protein, contains DUF5611 domain [Function unknown]. 101 matched cddid_all.tbl CDD COG4006 COG4006 443185 Csm6 CRISPR-Cas system-associated protein Csm6, contains CARF domain [Defense mechanisms]. CRISPR-Cas system-associated protein Csm6, contains CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system 229 matched cddid_all.tbl CDD COG4007 COG4007 443186 COG4007 Predicted dehydrogenase related to H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase [General function prediction only]. 341 matched cddid_all.tbl CDD COG4008 COG4008 443187 COG4008 Predicted metal-binding transcription factor, methanogenesis marker domain 9 [Transcription]. 361 matched cddid_all.tbl CDD COG4009 COG4009 443188 COG4009 Uncharacterized conserved protein, DUF749 domain [Function unknown]. 90 matched cddid_all.tbl CDD COG4010 COG4010 443189 COG4010 Uncharacterized conserved protein, DUF2096 domain [Function unknown]. 175 matched cddid_all.tbl CDD COG4012 COG4012 443190 AF0413 Uncharacterized protein, DUF1786 family, actin-like ATPase superfamily [General function prediction only]. 345 matched cddid_all.tbl CDD COG4013 COG4013 443191 COG4013 Uncharacterized conserved protein, DUF2097 domain [Function unknown]. 91 matched cddid_all.tbl CDD COG4014 COG4014 443192 COG4014 Uncharacterized protein MTH814, DUF2098 family [Function unknown]. 98 matched cddid_all.tbl CDD COG4015 COG4015 443193 COG4015 Predicted dinucleotide-utilizing enzyme of the ThiF/HesA family [General function prediction only]. 211 matched cddid_all.tbl CDD COG4016 COG4016 443194 HcgF Iron-guanylylpyridinol (FeGP) cofactor biosynthesis protein HcgF, CinA family [Coenzyme transport and metabolism]. 172 matched cddid_all.tbl CDD COG4017 COG4017 443195 HcgC Iron-guanylylpyridinol (FeGP) cofactor biosynthesis protein, methyltransferase HcgC [Coenzyme transport and metabolism]. 253 matched cddid_all.tbl CDD COG4018 COG4018 443196 HcgG Iron-guanylylpyridinol (FeGP) cofactor biosynthesis protein, fibrillarin family [Coenzyme transport and metabolism]. 505 matched cddid_all.tbl CDD COG4019 COG4019 443197 HcgB Iron-guanylylpyridinol (FeGP) cofactor biosynthesis protein HcgB, guanylyltransferase [Coenzyme transport and metabolism]. 154 matched cddid_all.tbl CDD COG4020 COG4020 443198 MK0078 Predicted ATPase/kinase of ASKHA (acetate and sugar kinases, HSC70, actin) superfamily [General function prediction only]. 319 matched cddid_all.tbl CDD COG4021 COG4021 443199 Thg1 tRNA(His) 5'-end guanylyltransferase [Translation, ribosomal structure and biogenesis]. tRNA(His) 5'-end guanylyltransferase is part of the Pathway/BioSystem: tRNA modification 235 matched cddid_all.tbl CDD COG4022 COG4022 443200 COG4022 Uncharacterized conserved protein, DUF2099 domain [Function unknown]. 285 matched cddid_all.tbl CDD COG4023 COG4023 443201 SBH1 Preprotein translocase subunit SecG (Sec61beta) [Intracellular trafficking, secretion, and vesicular transport]. 55 matched cddid_all.tbl CDD COG4024 COG4024 443202 COG4024 Uncharacterized conserved protein, DUF2100 domain [Function unknown]. 209 matched cddid_all.tbl CDD COG4025 COG4025 443203 MTH423 Uncharacterized conserved protein MTH423, predicted component of type IV pili-like system, DUF2101 family [General function prediction only]. 236 matched cddid_all.tbl CDD COG4026 COG4026 443204 COG4026 Uncharacterized conserved protein, contains TOPRIM domain, potential nuclease [General function prediction only]. 287 matched cddid_all.tbl CDD COG4027 COG4027 443205 COG4027 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase [Nucleotide transport and metabolism]. 435 matched cddid_all.tbl CDD COG4028 COG4028 443206 COG4028 Predicted P-loop ATPase/GTPase [General function prediction only]. 288 matched cddid_all.tbl CDD COG4029 COG4029 443207 COG4029 Uncharacterized conserved protein MJ0498 [Function unknown]. 138 matched cddid_all.tbl CDD COG4030 COG4030 443208 COG4030 Predicted phosphohydrolase, HAD superfamily [General function prediction only]. 342 matched cddid_all.tbl CDD COG4031 COG4031 443209 COG4031 Uncharacterized metal-binding protein, DUF2103 family [Function unknown]. 123 matched cddid_all.tbl CDD COG4032 COG4032 443210 COG4032 Sulfopyruvate decarboxylase, TPP-binding subunit (coenzyme M biosynthesis) [Coenzyme transport and metabolism]. 168 matched cddid_all.tbl CDD COG4033 COG4033 443211 COG4033 Uncharacterized conserved protein MJ0453 [Function unknown]. 92 matched cddid_all.tbl CDD COG4034 COG4034 443212 COG4034 Uncharacterized conserved protein, DUF1152 domain [Function unknown]. 309 matched cddid_all.tbl CDD COG4035 COG4035 443213 EhaL Energy-converting hydrogenase Eha subunit L [Energy production and conversion]. 106 matched cddid_all.tbl CDD COG4036 COG4036 443214 EhaG Energy-converting hydrogenase Eha subunit G [Energy production and conversion]. 201 matched cddid_all.tbl CDD COG4037 COG4037 443215 EhaF Energy-converting hydrogenase Eha subunit F [Energy production and conversion]. 156 matched cddid_all.tbl CDD COG4038 COG4038 443216 EhaE Energy-converting hydrogenase Eha subunit E [Energy production and conversion]. 84 matched cddid_all.tbl CDD COG4039 COG4039 443217 EhaD Energy-converting hydrogenase Eha subunit D [Energy production and conversion]. 86 matched cddid_all.tbl CDD COG4040 COG4040 443218 EhaC Energy-converting hydrogenase Eha subunit C [Energy production and conversion]. 81 matched cddid_all.tbl CDD COG4041 COG4041 443219 EhaB Energy-converting hydrogenase Eha subunit B [Energy production and conversion]. 163 matched cddid_all.tbl CDD COG4042 COG4042 443220 EhaA Energy-converting hydrogenase Eha subunit A [Energy production and conversion]. 97 matched cddid_all.tbl CDD COG4043 COG4043 443221 ASCH ASC-1 homology (ASCH) domain, predicted RNA-binding domain [General function prediction only]. 113 matched cddid_all.tbl CDD COG4044 COG4044 443222 COG4044 Uncharacterized conserved protein, DUF2110 domain [Function unknown]. 222 matched cddid_all.tbl CDD COG4046 COG4046 443223 COG4046 Uncharacterized protein, contains DUF1512 domain [Function unknown]. 372 matched cddid_all.tbl CDD COG4047 COG4047 443224 COG4047 N-glycosylase/DNA lyase (8-oxoguanine DNA glycosylase) [Replication, recombination and repair]. 275 matched cddid_all.tbl CDD COG4048 COG4048 443225 COG4048 Uncharacterized conserved protein, DUF2111 domain [Function unknown]. 116 matched cddid_all.tbl CDD COG4049 COG4049 443226 COG4049 Uncharacterized conserved protein, contains archaeal-type C2H2 Zn-finger [General function prediction only]. 63 matched cddid_all.tbl CDD COG4050 COG4050 443227 COG4050 Uncharacterized conserved protein, DUF2112 domain [Function unknown]. 149 matched cddid_all.tbl CDD COG4051 COG4051 443228 COG4051 Uncharacterized conserved protein MJ0802, methanogenesis marker protein 17, contains DUF2113 domain [Function unknown]. 193 matched cddid_all.tbl CDD COG4052 COG4052 443229 COG4052 Uncharacterized conserved protein related to methyl-CoM reductase subunit C, methanogenesis marker protein 7 [General function prediction only]. 308 matched cddid_all.tbl CDD COG4053 COG4053 443230 COG4053 Uncharacterized conserved protein [Function unknown]. 239 matched cddid_all.tbl CDD COG4054 COG4054 443231 McorB Methyl coenzyme M reductase, beta subunit [Coenzyme transport and metabolism]. 443 matched cddid_all.tbl CDD COG4055 COG4055 443232 McorD Methyl coenzyme M reductase, subunit D [Coenzyme transport and metabolism]. 160 matched cddid_all.tbl CDD COG4056 COG4056 443233 McorC Methyl coenzyme M reductase, subunit C [Coenzyme transport and metabolism]. 204 matched cddid_all.tbl CDD COG4057 COG4057 443234 McorG Methyl coenzyme M reductase, gamma subunit [Coenzyme transport and metabolism]. 252 matched cddid_all.tbl CDD COG4058 COG4058 443235 McorA Methyl coenzyme M reductase, alpha subunit [Coenzyme transport and metabolism]. 554 matched cddid_all.tbl CDD COG4059 COG4059 443236 MtrE Tetrahydromethanopterin S-methyltransferase, subunit E [Coenzyme transport and metabolism]. 296 matched cddid_all.tbl CDD COG4060 COG4060 443237 MtrD Tetrahydromethanopterin S-methyltransferase, subunit D [Coenzyme transport and metabolism]. 237 matched cddid_all.tbl CDD COG4061 COG4061 443238 MtrC Tetrahydromethanopterin S-methyltransferase, subunit C [Coenzyme transport and metabolism]. 271 matched cddid_all.tbl CDD COG4062 COG4062 443239 MtrB Tetrahydromethanopterin S-methyltransferase, subunit B [Coenzyme transport and metabolism]. 96 matched cddid_all.tbl CDD COG4063 COG4063 443240 MtrA Tetrahydromethanopterin S-methyltransferase, subunit A [Coenzyme transport and metabolism]. 240 matched cddid_all.tbl CDD COG4064 COG4064 443241 MtrG Tetrahydromethanopterin S-methyltransferase, subunit G [Coenzyme transport and metabolism]. 79 matched cddid_all.tbl CDD COG4065 COG4065 443242 COG4065 Uncharacterized conserved protein MJ1451 [Function unknown]. 483 matched cddid_all.tbl CDD COG4066 COG4066 443243 COG4066 Uncharacterized conserved protein MTH_811, UPF0305 family [Function unknown]. 177 matched cddid_all.tbl CDD COG4067 COG4067 443244 COG4067 Uncharacterized conserved protein [Function unknown]. 150 matched cddid_all.tbl CDD COG4068 COG4068 443245 COG4068 Predicted nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]. 64 matched cddid_all.tbl CDD COG4069 COG4069 443246 COG4069 Uncharacterized conserved protein, DUF2117 domain [Function unknown]. 370 matched cddid_all.tbl CDD COG4070 COG4070 443247 MJ1412 Cyclophilin family protein MJ1412, methanogenesis marker protein 3 [General function prediction only]. 508 matched cddid_all.tbl CDD COG4071 COG4071 443248 COG4071 Gamma-glutamyl ligase family protein MJ1361 [General function prediction only]. 279 matched cddid_all.tbl CDD COG4072 COG4072 443249 COG4072 Uncharacterized conserved protein, DUF2118 domain [Function unknown]. 152 matched cddid_all.tbl CDD COG4073 COG4073 443250 COG4073 Uncharacterized conserved protein MJ0501 [Function unknown]. 198 matched cddid_all.tbl CDD COG4074 COG4074 443251 Mth 5,10-methenyltetrahydromethanopterin hydrogenase [Energy production and conversion]. 340 matched cddid_all.tbl CDD COG4075 COG4075 443252 COG4075 Uncharacterized conserved protein MJ1244, distantly related to nitrogen regulatory protein PII [Function unknown]. 108 matched cddid_all.tbl CDD COG4076 COG4076 443253 COG4076 Predicted RNA methylase [General function prediction only]. 230 matched cddid_all.tbl CDD COG4077 COG4077 443254 COG4077 Uncharacterized conserved protein MJ0491 [Function unknown]. 145 matched cddid_all.tbl CDD COG4078 COG4078 443255 EhaH Energy-converting hydrogenase Eha subunit H [Energy production and conversion]. 220 matched cddid_all.tbl CDD COG4079 COG4079 443256 COG4079 Uncharacterized conserved protein, DUF2121 domain [Function unknown]. 305 matched cddid_all.tbl CDD COG4080 COG4080 443257 COG4080 SpoU rRNA methylase family enzyme [Translation, ribosomal structure and biogenesis]. 151 matched cddid_all.tbl CDD COG4081 COG4081 443258 COG4081 Uncharacterized conserved protein MJ0452 [Function unknown]. 152 matched cddid_all.tbl CDD COG4083 COG4083 443259 COG4083 Exosortase/Archaeosortase [Intracellular trafficking, secretion, and vesicular transport]. 282 matched cddid_all.tbl CDD COG4084 COG4084 443260 EhaM Energy-converting hydrogenase A subunit M [Energy production and conversion]. 133 matched cddid_all.tbl CDD COG4085 COG4085 443261 YhcR DNA/RNA endonuclease YhcR, contains UshA esterase domain [RNA processing and modification]. 131 matched cddid_all.tbl CDD COG4086 COG4086 443262 YpuA Uncharacterized conserved protein YpuA, DUF1002 family [Function unknown]. 298 matched cddid_all.tbl CDD COG4087 COG4087 443263 COG4087 Soluble P-type ATPase [General function prediction only]. 156 matched cddid_all.tbl CDD COG4088 COG4088 443264 Kti12 tRNA uridine 5-carbamoylmethylation protein Kti12 (Killer toxin insensitivity protein) [Translation, ribosomal structure and biogenesis, Defense mechanisms]. 179 matched cddid_all.tbl CDD COG4089 COG4089 443265 COG4089 Uncharacterized membrane protein [Function unknown]. 229 matched cddid_all.tbl CDD COG4090 COG4090 443266 COG4090 Uncharacterized conserved protein MTH_862 [Function unknown]. 155 matched cddid_all.tbl CDD COG4091 COG4091 443267 COG4091 Predicted homoserine dehydrogenase, contains C-terminal SAF domain [Amino acid transport and metabolism]. 429 matched cddid_all.tbl CDD COG4092 COG4092 443268 COG4092 Predicted glycosyltransferase involved in capsule biosynthesis [Cell wall/membrane/envelope biogenesis]. 543 matched cddid_all.tbl CDD COG4093 COG4093 443269 COG4093 Uncharacterized conserved protein, DUF2125 domain [Function unknown]. 339 matched cddid_all.tbl CDD COG4094 COG4094 443270 COG4094 Uncharacterized membrane protein [Function unknown]. 219 matched cddid_all.tbl CDD COG4095 COG4095 443271 SWEET Sugar transporter, SemiSWEET family, contains PQ motif [Carbohydrate transport and metabolism]. 83 matched cddid_all.tbl CDD COG4096 COG4096 443272 HsdR Type I site-specific restriction endonuclease, part of a restriction-modification system [Defense mechanisms]. 806 matched cddid_all.tbl CDD COG4097 COG4097 443273 COG4097 Predicted ferric reductase [Inorganic ion transport and metabolism]. 442 matched cddid_all.tbl CDD COG4098 COG4098 443274 ComFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [Replication, recombination and repair]. 451 matched cddid_all.tbl CDD COG4099 COG4099 443275 COG4099 Predicted peptidase [General function prediction only]. 235 matched cddid_all.tbl CDD COG4100 COG4100 443276 YnbB Cystathionine beta-lyase family protein involved in aluminum resistance [Inorganic ion transport and metabolism, General function prediction only]. 409 matched cddid_all.tbl CDD COG4101 COG4101 443277 RmlC Uncharacterized conserved protein, RmlC-like cupin domain [General function prediction only]. 146 matched cddid_all.tbl CDD COG4102 COG4102 443278 COG4102 Uncharacterized conserved protein, DUF1501 family [Function unknown]. 395 matched cddid_all.tbl CDD COG4103 COG4103 443279 TerB2 Tellurite resistance protein TerB [Inorganic ion transport and metabolism]. 149 matched cddid_all.tbl CDD COG4104 COG4104 443280 PAAR Zn-binding Pro-Ala-Ala-Arg (PAAR) domain, involved in Type VI secretion [Intracellular trafficking, secretion, and vesicular transport]. 87 matched cddid_all.tbl CDD COG4105 COG4105 443281 BamD Outer membrane protein assembly factor BamD, BamD/ComL family [Cell wall/membrane/envelope biogenesis]. 254 matched cddid_all.tbl CDD COG4106 COG4106 443282 Tam Trans-aconitate methyltransferase [Energy production and conversion]. 100 matched cddid_all.tbl CDD COG4107 COG4107 443283 PhnK ABC-type phosphonate transport system, ATPase component PhnK [Inorganic ion transport and metabolism]. 262 matched cddid_all.tbl CDD COG4108 COG4108 443284 PrfC Peptide chain release factor RF-3 [Translation, ribosomal structure and biogenesis]. Peptide chain release factor RF-3 is part of the Pathway/BioSystem: Translation factors 528 matched cddid_all.tbl CDD COG4109 COG4109 443285 YtoI Predicted transcriptional regulator containing CBS domains [Transcription]. 135 matched cddid_all.tbl CDD COG4110 COG4110 443286 TerA Tellurium resistance protein TerA/TerD [Defense mechanisms]. 385 matched cddid_all.tbl CDD COG4111 COG4111 443287 COG4111 Uncharacterized conserved protein [Function unknown]. 170 matched cddid_all.tbl CDD COG4112 COG4112 443288 YmaB Predicted phosphoesterase YmaB, NUDIX family [General function prediction only]. 194 matched cddid_all.tbl CDD COG4113 COG4113 443289 VapC RNA interferase (RNase) VapC, contains PIN domain [Defense mechanisms]. 125 matched cddid_all.tbl CDD COG4114 COG4114 443290 FhuF Ferric iron reductase protein FhuF, involved in iron transport [Inorganic ion transport and metabolism]. 187 matched cddid_all.tbl CDD COG4115 COG4115 443291 COG4115 Toxin component of the Txe-Axe toxin-antitoxin module, Txe/YoeB family [Defense mechanisms]. 84 matched cddid_all.tbl CDD COG4116 COG4116 443292 YjbK Predicted triphosphatase or cyclase YjbK, contains CYTH domain [General function prediction only]. 191 matched cddid_all.tbl CDD COG4117 COG4117 443293 YdhU Thiosulfate reductase cytochrome b subunit [Inorganic ion transport and metabolism]. 204 matched cddid_all.tbl CDD COG4118 COG4118 443294 Phd Antitoxin component of toxin-antitoxin stability system, DNA-binding transcriptional repressor [Defense mechanisms]. 65 matched cddid_all.tbl CDD COG4119 COG4119 443295 COG4119 Predicted NTP pyrophosphohydrolase, NUDIX family [Nucleotide transport and metabolism, General function prediction only]. 153 matched cddid_all.tbl CDD COG4120 COG4120 443296 COG4120 ABC-type uncharacterized transport system, permease component [General function prediction only]. 296 matched cddid_all.tbl CDD COG4121 COG4121 443297 MnmC tRNA U34 5-methylaminomethyl-2-thiouridine-forming methyltransferase MnmC [Translation, ribosomal structure and biogenesis]. tRNA U34 5-methylaminomethyl-2-thiouridine-forming methyltransferase MnmC is part of the Pathway/BioSystem: tRNA modification 245 matched cddid_all.tbl CDD COG4122 COG4122 443298 TrmR tRNA 5-hydroxyU34 O-methylase TrmR/YrrM [Translation, ribosomal structure and biogenesis]. tRNA 5-hydroxyU34 O-methylase TrmR/YrrM is part of the Pathway/BioSystem: tRNA modification 173 matched cddid_all.tbl CDD COG4123 COG4123 443299 TrmN6 tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]. tRNA1(Val) A37 N6-methylase TrmN6 is part of the Pathway/BioSystem: tRNA modification 238 matched cddid_all.tbl CDD COG4124 COG4124 443300 ManB2 Beta-mannanase [Carbohydrate transport and metabolism]. 330 matched cddid_all.tbl CDD COG4125 COG4125 443301 COG4125 Uncharacterized membrane protein [Function unknown]. 144 matched cddid_all.tbl CDD COG4126 COG4126 443302 Dcg1 Asp/Glu/hydantoin racemase [Amino acid transport and metabolism]. 237 matched cddid_all.tbl CDD COG4127 COG4127 443303 COG4127 Predicted restriction endonuclease, Mrr-cat superfamily [General function prediction only]. 187 matched cddid_all.tbl CDD COG4128 COG4128 443304 Zot Zona occludens toxin, predicted ATPase [General function prediction only]. 276 matched cddid_all.tbl CDD COG4129 COG4129 443305 YgaE Uncharacterized membrane protein YgaE, UPF0421/DUF939 family [Function unknown]. 197 matched cddid_all.tbl CDD COG4130 COG4130 443306 COG4130 Predicted sugar epimerase, xylose isomerase-like family [Carbohydrate transport and metabolism]. 272 matched cddid_all.tbl CDD COG4132 COG4132 443307 COG4132 ABC-type uncharacterized transport system, permease component [General function prediction only]. 286 matched cddid_all.tbl CDD COG4133 COG4133 443308 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]. 206 matched cddid_all.tbl CDD COG4134 COG4134 443309 YnjB ABC-type uncharacterized transport system YnjBCD, periplasmic component [General function prediction only]. 401 matched cddid_all.tbl CDD COG4135 COG4135 443310 YnjC ABC-type uncharacterized transport system YnjBCD, permease component [General function prediction only]. 564 matched cddid_all.tbl CDD COG4136 COG4136 443311 YnjD ABC-type uncharacterized transport system YnjBCD, ATPase component [General function prediction only]. 211 matched cddid_all.tbl CDD COG4137 COG4137 443312 YpjD ABC-type uncharacterized transport system, permease component [General function prediction only]. 269 matched cddid_all.tbl CDD COG4138 COG4138 443313 BtuD ABC-type cobalamin transport system, ATPase component BtuD [Coenzyme transport and metabolism]. 248 matched cddid_all.tbl CDD COG4139 COG4139 443314 BtuC ABC-type cobalamin transport system, permease component BtuC [Coenzyme transport and metabolism]. 327 matched cddid_all.tbl CDD COG4143 COG4143 443315 TbpA ABC-type thiamine transport system, periplasmic component TbpA [Coenzyme transport and metabolism]. 343 matched cddid_all.tbl CDD COG4145 COG4145 443316 PanF Na+/panthothenate symporter [Coenzyme transport and metabolism]. 484 matched cddid_all.tbl CDD COG4146 COG4146 443317 YidK Uncharacterized membrane permease YidK, sodium:solute symporter family [General function prediction only]. 444 matched cddid_all.tbl CDD COG4147 COG4147 443318 ActP Na+(or H+)/acetate symporter ActP [Energy production and conversion]. 526 matched cddid_all.tbl CDD COG4148 COG4148 443319 ModC ABC-type molybdate transport system, ATPase component ModC [Inorganic ion transport and metabolism]. ABC-type molybdate transport system, ATPase component ModC is part of the Pathway/BioSystem: Molybdopterin biosynthesis 358 matched cddid_all.tbl CDD COG4149 COG4149 443320 ModB ABC-type molybdate transport system, permease component ModB [Inorganic ion transport and metabolism]. ABC-type molybdate transport system, permease component ModB is part of the Pathway/BioSystem: Molybdopterin biosynthesis 223 matched cddid_all.tbl CDD COG4150 COG4150 443321 CysP ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]. 334 matched cddid_all.tbl CDD COG4152 COG4152 443322 YhaQ ABC-type uncharacterized transport system, ATPase component [General function prediction only]. 298 matched cddid_all.tbl CDD COG4154 COG4154 443323 FucU L-fucose mutarotase/ribose pyranase, RbsD/FucU family [Carbohydrate transport and metabolism]. 143 matched cddid_all.tbl CDD COG4158 COG4158 443324 COG4158 Predicted ABC-type sugar transport system, permease component [General function prediction only]. 334 matched cddid_all.tbl CDD COG4160 COG4160 443325 ArtM ABC-type arginine/histidine transport system, permease component [Amino acid transport and metabolism]. 229 matched cddid_all.tbl CDD COG4161 COG4161 443326 ArtP ABC-type arginine transport system, ATPase component [Amino acid transport and metabolism]. 242 matched cddid_all.tbl CDD COG4166 COG4166 443327 OppA ABC-type oligopeptide transport system, periplasmic component [Amino acid transport and metabolism]. 543 matched cddid_all.tbl CDD COG4167 COG4167 443328 SapF ABC-type antimicrobial peptide export system, ATPase component SapF [Defense mechanisms]. 265 matched cddid_all.tbl CDD COG4168 COG4168 443329 SapB ABC-type antimicrobial peptide export system, permease component SapB [Defense mechanisms]. 321 matched cddid_all.tbl CDD COG4170 COG4170 443330 SapD ABC-type antimicrobial peptide export system, ATPase component SapD [Defense mechanisms]. 331 matched cddid_all.tbl CDD COG4171 COG4171 443331 SapC ABC-type antimicrobial peptide export system, permease component SapC [Defense mechanisms]. 296 matched cddid_all.tbl CDD COG4172 COG4172 443332 YejF ABC-type microcin C transport system, duplicated ATPase component YejF [Secondary metabolites biosynthesis, transport and catabolism]. 533 matched cddid_all.tbl CDD COG4174 COG4174 443333 YejB ABC-type microcin C transport system, permease component YejB [Secondary metabolites biosynthesis, transport and catabolism]. 363 matched cddid_all.tbl CDD COG4175 COG4175 443334 ProV ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]. 389 matched cddid_all.tbl CDD COG4176 COG4176 443335 ProW ABC-type proline/glycine betaine transport system, permease component [Amino acid transport and metabolism]. 275 matched cddid_all.tbl CDD COG4177 COG4177 443336 LivM ABC-type branched-chain amino acid transport system, permease component [Amino acid transport and metabolism]. 285 matched cddid_all.tbl CDD COG4178 COG4178 443337 YddA ABC-type uncharacterized transport system, permease and ATPase components [General function prediction only]. 571 matched cddid_all.tbl CDD COG4181 COG4181 443338 YbbA Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component [Secondary metabolites biosynthesis, transport and catabolism]. 233 matched cddid_all.tbl CDD COG4185 COG4185 443339 COG4185 Predicted ABC-type ATPase or kinase [General function prediction only]. 197 matched cddid_all.tbl CDD COG4186 COG4186 443340 COG4186 Uncharacterized conserved protein MJ1445, calcineurin-like phosphoesterase superfamily [General function prediction only]. 167 matched cddid_all.tbl CDD COG4187 COG4187 443341 RocB Arginine utilization protein RocB [Amino acid transport and metabolism]. 550 matched cddid_all.tbl CDD COG4188 COG4188 443342 COG4188 Predicted dienelactone hydrolase [General function prediction only]. 326 matched cddid_all.tbl CDD COG4189 COG4189 443343 COG4189 Predicted transcriptional regulator, ArsR family [Transcription]. 97 matched cddid_all.tbl CDD COG4190 COG4190 443344 COG4190 Predicted transcriptional regulator, contains HTH domain [Transcription]. 121 matched cddid_all.tbl CDD COG4191 COG4191 443345 COG4191 Signal transduction histidine kinase regulating C4-dicarboxylate transport system [Signal transduction mechanisms]. 361 matched cddid_all.tbl CDD COG4192 COG4192 443346 COG4192 Signal transduction histidine kinase regulating phosphoglycerate transport system [Signal transduction mechanisms]. 640 matched cddid_all.tbl CDD COG4193 COG4193 443347 LytD Beta- N-acetylglucosaminidase [Carbohydrate transport and metabolism]. 423 matched cddid_all.tbl CDD COG4194 COG4194 443348 COG4194 Uncharacterized membrane protein, DUF1648 family [Function unknown]. 366 matched cddid_all.tbl CDD COG4195 COG4195 443349 YjqB Phage-related replication protein YjqB, UPF0714/DUF867 family [Mobilome: prophages, transposons]. 214 matched cddid_all.tbl CDD COG4196 COG4196 443350 COG4196 Uncharacterized conserved protein, DUF2126 family [Function unknown]. 1101 matched cddid_all.tbl CDD COG4197 COG4197 443351 YdaS DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription]. 68 matched cddid_all.tbl CDD COG4198 COG4198 443352 COG4198 Uncharacterized conserved protein, DUF1015 family [Function unknown]. 412 matched cddid_all.tbl CDD COG4199 COG4199 443353 RecJ ssDNA-specific exonuclease RecJ [Replication, recombination and repair]. 774 matched cddid_all.tbl CDD COG4200 COG4200 443354 EfiE Predicted lantabiotic-exporting membrane pepmease, EfiE/EfiG/ABC2 family [Defense mechanisms]. 250 matched cddid_all.tbl CDD COG4206 COG4206 443355 BtuB Outer membrane cobalamin receptor protein BtuB [Coenzyme transport and metabolism]. 276 matched cddid_all.tbl CDD COG4208 COG4208 443356 CysW ABC-type sulfate transport system, permease component [Inorganic ion transport and metabolism]. 281 matched cddid_all.tbl CDD COG4209 COG4209 443357 LplB ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]. 316 matched cddid_all.tbl CDD COG4211 COG4211 443358 MglC ABC-type glucose/galactose transport system, permease component [Carbohydrate transport and metabolism]. 336 matched cddid_all.tbl CDD COG4213 COG4213 443359 XylF ABC-type xylose transport system, periplasmic component [Carbohydrate transport and metabolism]. 310 matched cddid_all.tbl CDD COG4214 COG4214 443360 XylH ABC-type xylose transport system, permease component [Carbohydrate transport and metabolism]. 393 matched cddid_all.tbl CDD COG4215 COG4215 443361 ArtQ ABC-type arginine transport system, permease component [Amino acid transport and metabolism]. 238 matched cddid_all.tbl CDD COG4218 COG4218 443362 MtrF Tetrahydromethanopterin S-methyltransferase, subunit F [Coenzyme transport and metabolism]. 68 matched cddid_all.tbl CDD COG4219 COG4219 443363 MecR1 Signal transducer regulating beta-lactamase production, contains metallopeptidase domain [Signal transduction mechanisms]. 337 matched cddid_all.tbl CDD COG4220 COG4220 443364 Nu1 Phage DNA packaging protein, Nu1 subunit of terminase [Mobilome: prophages, transposons]. 170 matched cddid_all.tbl CDD COG4221 COG4221 443365 YdfG NADP-dependent 3-hydroxy acid dehydrogenase YdfG [Energy production and conversion]. NADP-dependent 3-hydroxy acid dehydrogenase YdfG is part of the Pathway/BioSystem: Pyrimidine degradation 240 matched cddid_all.tbl CDD COG4222 COG4222 443366 COG4222 Uncharacterized conserved protein, contains a phytase-like domain [Function unknown]. 360 matched cddid_all.tbl CDD COG4223 COG4223 443367 COG4223 Uncharacterized conserved protein [Function unknown]. 259 matched cddid_all.tbl CDD COG4224 COG4224 443368 YnzC Uncharacterized conserved protein YnzC, UPF0291/DUF896 family [Function unknown]. 75 matched cddid_all.tbl CDD COG4225 COG4225 443369 YesR Rhamnogalacturonyl hydrolase YesR [Carbohydrate transport and metabolism]. 336 matched cddid_all.tbl CDD COG4226 COG4226 443370 HicB Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]. 110 matched cddid_all.tbl CDD COG4227 COG4227 443371 ArdC Antirestriction protein ArdC [Replication, recombination and repair]. 303 matched cddid_all.tbl CDD COG4228 COG4228 443372 COG4228 Mu-like prophage DNA circulation protein [Mobilome: prophages, transposons]. 406 matched cddid_all.tbl CDD COG4229 COG4229 443373 Utr4 Enolase-phosphatase E1 involved in merthionine salvage [Amino acid transport and metabolism]. 227 matched cddid_all.tbl CDD COG4230 COG4230 443374 PutA2 Delta 1-pyrroline-5-carboxylate dehydrogenase [Amino acid transport and metabolism]. 1156 matched cddid_all.tbl CDD COG4231 COG4231 443375 IorA TPP-dependent indolepyruvate ferredoxin oxidoreductase, alpha subunit [Energy production and conversion]. 76 matched cddid_all.tbl CDD COG4232 COG4232 443376 DsbD Thiol:disulfide interchange protein DsbD [Posttranslational modification, protein turnover, chaperones]. 416 matched cddid_all.tbl CDD COG4233 COG4233 443377 COG4233 Thiol-disulfide interchange protein, contains DsbC and DsbD domains [Posttranslational modification, protein turnover, chaperones, Energy production and conversion]. 681 matched cddid_all.tbl CDD COG4235 COG4235 443378 NrfG Cytochrome c-type biogenesis protein CcmH/NrfG [Energy production and conversion, Posttranslational modification, protein turnover, chaperones]. 131 matched cddid_all.tbl CDD COG4237 COG4237 443379 HyfE Hydrogenase-4 membrane subunit HyfE [Energy production and conversion]. 216 matched cddid_all.tbl CDD COG4238 COG4238 443380 Lpp Outer membrane murein-binding lipoprotein Lpp [Cell wall/membrane/envelope biogenesis]. 77 matched cddid_all.tbl CDD COG4239 COG4239 443381 YejE ABC-type microcin C transport system, permease component YejE [Secondary metabolites biosynthesis, transport and catabolism]. 342 matched cddid_all.tbl CDD COG4240 COG4240 443382 Tda10 Pantothenate kinase-related protein Tda10 (topoisomerase I damage affected protein) [General function prediction only]. 298 matched cddid_all.tbl CDD COG4241 COG4241 443383 YybS Uncharacterized conserved protein YybS, DUF2232 family [Function unknown]. 318 matched cddid_all.tbl CDD COG4242 COG4242 443384 CphB Cyanophycinase and related exopeptidases [Secondary metabolites biosynthesis, transport and catabolism, General function prediction only]. 276 matched cddid_all.tbl CDD COG4243 COG4243 443385 COG4243 Vitamin K epoxide reductase (VKOR) family protein, predicted involvement in disulfide bond formation [General function prediction only]. 161 matched cddid_all.tbl CDD COG4244 COG4244 443386 COG4244 Uncharacterized membrane protein [Function unknown]. 159 matched cddid_all.tbl CDD COG4245 COG4245 443387 TerY Uncharacterized conserved protein YegL, contains vWA domain of TerY type [Function unknown]. 196 matched cddid_all.tbl CDD COG4246 COG4246 443388 COG4246 Uncharacterized conserved protein, contains a phytase-like domain [Function unknown]. 340 matched cddid_all.tbl CDD COG4247 COG4247 443389 Phy 3-phytase (myo-inositol-hexaphosphate 3-phosphohydrolase) [Lipid transport and metabolism]. 348 matched cddid_all.tbl CDD COG4248 COG4248 443390 YegI Uncharacterized conserved protein YegI with protein kinase and helix-hairpin-helix DNA-binding domains [General function prediction only]. 476 matched cddid_all.tbl CDD COG4249 COG4249 443391 COG4249 Uncharacterized conserved protein, contains caspase domain [General function prediction only]. 238 matched cddid_all.tbl CDD COG4250 COG4250 443392 DICT DICT sensory domain found in diguanylate cyclases and two-component systems [Signal transduction mechanisms]. 178 matched cddid_all.tbl CDD COG4251 COG4251 443393 COG4251 Bacteriophytochrome (light-regulated signal transduction histidine kinase) [Signal transduction mechanisms]. 503 matched cddid_all.tbl CDD COG4252 COG4252 443394 CHASE2 Extracytoplasmic sensor domain CHASE2 (specificity unknown) [Signal transduction mechanisms]. 608 matched cddid_all.tbl CDD COG4253 COG4253 443395 COG4253 Uncharacterized conserved protein, DUF2345 family [Function unknown]. 900 matched cddid_all.tbl CDD COG4254 COG4254 443396 COG4254 Uncharacterized peptidoglycan binding protein, contains LysM and FecR domains [General function prediction only]. 207 matched cddid_all.tbl CDD COG4255 COG4255 443397 COG4255 Uncharacterized conserved protein [Function unknown]. 339 matched cddid_all.tbl CDD COG4256 COG4256 443398 HemP Hemin uptake protein HemP [Coenzyme transport and metabolism]. 60 matched cddid_all.tbl CDD COG4257 COG4257 443399 Vgb Streptogramin lyase [Defense mechanisms]. 270 matched cddid_all.tbl CDD COG4258 COG4258 443400 COG4258 Predicted exporter [General function prediction only]. 783 matched cddid_all.tbl CDD COG4259 COG4259 443401 COG4259 Uncharacterized conserved protein, DUF4810 domain [Function unknown]. 119 matched cddid_all.tbl CDD COG4260 COG4260 443402 YdjI Membrane protease subunit, stomatin/prohibitin family, contains C-terminal Zn-ribbon domain [Posttranslational modification, protein turnover, chaperones]. 337 matched cddid_all.tbl CDD COG4261 COG4261 443403 COG4261 Predicted acyltransferase, LPLAT superfamily [General function prediction only]. 300 matched cddid_all.tbl CDD COG4262 COG4262 443404 COG4262 Predicted spermidine synthase with an N-terminal membrane domain [General function prediction only]. 426 matched cddid_all.tbl CDD COG4263 COG4263 443405 NosZ Nitrous oxide reductase [Inorganic ion transport and metabolism]. 621 matched cddid_all.tbl CDD COG4264 COG4264 443406 IucA Siderophore synthetase component IucA/IucC/SbnC [Inorganic ion transport and metabolism]. 590 matched cddid_all.tbl CDD COG4266 COG4266 443407 Alc Allantoicase [Nucleotide transport and metabolism]. 331 matched cddid_all.tbl CDD COG4267 COG4267 443408 COG4267 Uncharacterized membrane protein [Function unknown]. 462 matched cddid_all.tbl CDD COG4268 COG4268 443409 McrC 5-methylcytosine-specific restriction endonuclease McrBC, regulatory subunit McrC [Defense mechanisms]. 388 matched cddid_all.tbl CDD COG4269 COG4269 443410 YjgN Uncharacterized membrane protein YjgN, DUF898 family [Function unknown]. 348 matched cddid_all.tbl CDD COG4270 COG4270 443411 COG4270 Uncharacterized membrane protein [Function unknown]. 124 matched cddid_all.tbl CDD COG4271 COG4271 443412 COG4271 Predicted nucleotide-binding protein containing TIR -like domain [General function prediction only]. 153 matched cddid_all.tbl CDD COG4272 COG4272 443413 COG4272 Uncharacterized membrane protein [Function unknown]. 123 matched cddid_all.tbl CDD COG4273 COG4273 443414 COG4273 Uncharacterized conserved protein, contains metal-binding DGC domain [Function unknown]. 122 matched cddid_all.tbl CDD COG4274 COG4274 443415 COG4274 Uncharacterized conserved protein, contains GYD domain [Function unknown]. 97 matched cddid_all.tbl CDD COG4275 COG4275 443416 ChrB1 Chromate resistance protein ChrB1 [Inorganic ion transport and metabolism]. 254 matched cddid_all.tbl CDD COG4276 COG4276 443417 SRPBCC Ligand-binding SRPBCC domain [General function prediction only]. 153 matched cddid_all.tbl CDD COG4277 COG4277 443418 COG4277 Predicted DNA modification or repair protein, contains radical SAM and helix-hairpin-helix domains [General function prediction only]. 414 matched cddid_all.tbl CDD COG4278 COG4278 443419 COG4278 Uncharacterized conserved protein [Function unknown]. 140 matched cddid_all.tbl CDD COG4279 COG4279 443420 COG4279 Uncharacterized protein, contains SWIM-type Zn finger domain [Function unknown]. 193 matched cddid_all.tbl CDD COG4280 COG4280 443421 COG4280 Uncharacterized membrane protein [Function unknown]. 241 matched cddid_all.tbl CDD COG4281 COG4281 443422 ACB Acyl-CoA-binding protein [Lipid transport and metabolism]. 87 matched cddid_all.tbl CDD COG4282 COG4282 443423 SMI1 Cell wall assembly regulator SMI1 (Killer toxin-resistance protein 4) [Cell wall/membrane/envelope biogenesis]. 188 matched cddid_all.tbl CDD COG4283 COG4283 443424 DfsB Uncharacterized conserved protein DfsB/IRC4, DUF1706 (PF08020) domain [General function prediction only]. 167 matched cddid_all.tbl CDD COG4284 COG4284 443425 QRI1 UDP-N-acetylglucosamine pyrophosphorylase [Carbohydrate transport and metabolism]. 402 matched cddid_all.tbl CDD COG4285 COG4285 443426 COG4285 Uncharacterized conserved protein, conains N-terminal glutamine amidotransferase (GATase1)-like domain [General function prediction only]. 221 matched cddid_all.tbl CDD COG4286 COG4286 443427 COG4286 Uncharacterized conserved protein, UPF0160 family [Function unknown]. 302 matched cddid_all.tbl CDD COG4287 COG4287 443428 PqaA PhoPQ-activated pathogenicity-related protein [General function prediction only]. 440 matched cddid_all.tbl CDD COG4288 COG4288 443429 COG4288 Uncharacterized conserved protein [Function unknown]. 123 matched cddid_all.tbl CDD COG4289 COG4289 443430 COG4289 Uncharacterized conserved protein, DUF2264 domain [Function unknown]. 386 matched cddid_all.tbl CDD COG4290 COG4290 443431 COG4290 Guanyl-specific ribonuclease Sa [Nucleotide transport and metabolism]. 124 matched cddid_all.tbl CDD COG4291 COG4291 443432 COG4291 Uncharacterized membrane protein [Function unknown]. 221 matched cddid_all.tbl CDD COG4292 COG4292 443433 LtrA Low temperature requirement protein LtrA (function unknown) [Function unknown]. 388 matched cddid_all.tbl CDD COG4293 COG4293 443434 COG4293 Uncharacterized conserved protein, DUF1802 family [Function unknown]. 183 matched cddid_all.tbl CDD COG4294 COG4294 443435 Uve UV DNA damage repair endonuclease [Replication, recombination and repair]. 313 matched cddid_all.tbl CDD COG4295 COG4295 443436 COG4295 Predicted RNA repair component, a phosphatase of H2Macro superfamily, DUF2263 family [General function prediction only]. 274 matched cddid_all.tbl CDD COG4296 COG4296 443437 COG4296 Uncharacterized conserved protein, DUF2262 domain [Function unknown]. 154 matched cddid_all.tbl CDD COG4297 COG4297 443438 YjlB Uncharacterized conserved protein YjlB, cupin superfamily [Function unknown]. 170 matched cddid_all.tbl CDD COG4298 COG4298 443439 YiaAB Uncharacterized conserved protein, YiaAB domain [Function unknown]. 88 matched cddid_all.tbl CDD COG4299 COG4299 443440 COG4299 Predicted acyltransferase, DUF1624 domain [General function prediction only]. 370 matched cddid_all.tbl CDD COG4300 COG4300 443441 CadD Cadmium resistance protein CadD, predicted permease [Inorganic ion transport and metabolism]. 211 matched cddid_all.tbl CDD COG4301 COG4301 443442 COG4301 Uncharacterized protein, contains predicted SAM-dependent methyltransferase domain [General function prediction only]. 316 matched cddid_all.tbl CDD COG4302 COG4302 443443 EutC Ethanolamine ammonia-lyase, small subunit [Amino acid transport and metabolism]. 265 matched cddid_all.tbl CDD COG4303 COG4303 443444 EutB Ethanolamine ammonia-lyase, large subunit [Amino acid transport and metabolism]. 460 matched cddid_all.tbl CDD COG4304 COG4304 443445 COG4304 Uncharacterized conserved protein, DUF2247 domain [Function unknown]. 164 matched cddid_all.tbl CDD COG4305 COG4305 443446 YoaJ Peptidoglycan-binding domain, expansin YoaJ [Cell wall/membrane/envelope biogenesis]. 226 matched cddid_all.tbl CDD COG4306 COG4306 443447 COG4306 Uncharacterized conserved protein, DUF2321 domain [Function unknown]. 88 matched cddid_all.tbl CDD COG4307 COG4307 443448 COG4307 Uncharacterized conserved protein, DUF2248 family [Function unknown]. 354 matched cddid_all.tbl CDD COG4308 COG4308 443449 LimA Limonene-1,2-epoxide hydrolase LimA/EphG [Secondary metabolites biosynthesis, transport and catabolism]. 119 matched cddid_all.tbl CDD COG4309 COG4309 443450 COG4309 SirA-like two-layered alpha/beta sandwich domain, DUF2249 family [General function prediction only]. 83 matched cddid_all.tbl CDD COG4310 COG4310 443451 COG4310 Uncharacterized conserved protein, cotains an aminopeptidase-like domain [General function prediction only]. 422 matched cddid_all.tbl CDD COG4311 COG4311 443452 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]. 94 matched cddid_all.tbl CDD COG4312 COG4312 443453 COG4312 Predicted dithiol-disulfide oxidoreductase, DUF899 family [General function prediction only]. 233 matched cddid_all.tbl CDD COG4313 COG4313 443454 SphA Sphingosine uptake channel SphA-related outer membrane channel [Cell wall/membrane/envelope biogenesis]. 303 matched cddid_all.tbl CDD COG4314 COG4314 443455 NosL Nitrous oxide reductase accessory protein NosL [Inorganic ion transport and metabolism]. 156 matched cddid_all.tbl CDD COG4315 COG4315 443456 COG4315 Predicted lipoprotein with conserved Yx(FWY)xxD motif (function unknown) [Function unknown]. 108 matched cddid_all.tbl CDD COG4316 COG4316 443457 COG4316 Uncharacterized conserved protein, DUF2251 domain [Function unknown]. 134 matched cddid_all.tbl CDD COG4317 COG4317 443458 XapX Xanthosine utilization system component, XapX domain [Nucleotide transport and metabolism]. 53 matched cddid_all.tbl CDD COG4318 COG4318 443459 COG4318 Uncharacterized conserved protein [Function unknown]. 215 matched cddid_all.tbl CDD COG4319 COG4319 443460 YybH Ketosteroid isomerase homolog YybH [General function prediction only]. 131 matched cddid_all.tbl CDD COG4320 COG4320 443461 COG4320 Uncharacterized conserved protein, DUF2252 family [Function unknown]. 428 matched cddid_all.tbl CDD COG4321 COG4321 443462 COG4321 Predicted DNA-binding protein, contains ribbon-helix-helix (RHH) domain [General function prediction only]. 93 matched cddid_all.tbl CDD COG4322 COG4322 443463 COG4322 Uncharacterized protein, contains DUF2272 domain [Function unknown]. 249 matched cddid_all.tbl CDD COG4323 COG4323 443464 COG4323 Uncharacterized conserved protein, DUF962 domain [Function unknown]. 107 matched cddid_all.tbl CDD COG4324 COG4324 443465 COG4324 Predicted aminopeptidase [General function prediction only]. 355 matched cddid_all.tbl CDD COG4325 COG4325 443466 COG4325 Uncharacterized membrane protein [Function unknown]. 437 matched cddid_all.tbl CDD COG4326 COG4326 443467 Spo0M Stage 0 sporulation-control protein Spo0M [Cell cycle control, cell division, chromosome partitioning]. 258 matched cddid_all.tbl CDD COG4327 COG4327 443468 COG4327 Uncharacterized membrane protein, DUF4212 domain [Function unknown]. 87 matched cddid_all.tbl CDD COG4328 COG4328 443469 COG4328 Predicted nuclease (RNAse H fold) [General function prediction only]. 258 matched cddid_all.tbl CDD COG4329 COG4329 443470 COG4329 Uncharacterized membrane protein, DUF2243 domain [Function unknown]. 165 matched cddid_all.tbl CDD COG4330 COG4330 443471 COG4330 Uncharacterized membrane protein, DUF1361 domain [Function unknown]. 214 matched cddid_all.tbl CDD COG4331 COG4331 443472 COG4331 Uncharacterized membrane protein, DUF2127 domain [Function unknown]. 171 matched cddid_all.tbl CDD COG4332 COG4332 443473 COG4332 Uncharacterized conserved protein, DUF1062 domain [Function unknown]. 196 matched cddid_all.tbl CDD COG4333 COG4333 443474 COG4333 Uncharacterized conserved protein, DUF1643 domain [Function unknown]. 167 matched cddid_all.tbl CDD COG4334 COG4334 443475 COG4334 Uncharacterized conserved protein, DUF2255 domain [Function unknown]. 124 matched cddid_all.tbl CDD COG4335 COG4335 443476 AlkC 3-methylpurine DNA glycosylase AlkC [Replication, recombination and repair]. 369 matched cddid_all.tbl CDD COG4336 COG4336 443477 YcsI Uncharacterized conserved protein YcsI, UPF0317/DUF1446 family [Function unknown]. 265 matched cddid_all.tbl CDD COG4337 COG4337 443478 COG4337 Uncharacterized conserved protein [Function unknown]. 182 matched cddid_all.tbl CDD COG4338 COG4338 443479 COG4338 Uncharacterized conserved protein, DUF2256 family [Function unknown]. 52 matched cddid_all.tbl CDD COG4339 COG4339 443480 COG4339 Predicted metal-dependent phosphohydrolase, HD superfamily [General function prediction only]. 202 matched cddid_all.tbl CDD COG4340 COG4340 443481 COG4340 Predicted dioxygenase, 2-oxoglutarate and Fe-dependent (2OG-Fe) dioxygenase superfamily [General function prediction only]. 231 matched cddid_all.tbl CDD COG4341 COG4341 443482 COG4341 Predicted HD phosphohydrolase [General function prediction only]. 182 matched cddid_all.tbl CDD COG4342 COG4342 443483 COG4342 Phage integrase/recombinase [Mobilome: prophages, transposons]. 278 matched cddid_all.tbl CDD COG4343 COG4343 443484 Cas4 CRISPR/Cas system-associated exonuclease Cas4, RecB family [Defense mechanisms]. CRISPR/Cas system-associated exonuclease Cas4, RecB family is part of the Pathway/BioSystem: CRISPR-Cas system 296 matched cddid_all.tbl CDD COG4344 COG4344 443485 COG4344 Predicted transciptional regulator, contains HTH domain [Transcription]. 96 matched cddid_all.tbl CDD COG4345 COG4345 443486 PF1044 Predicted DNA binding protein, Pae2254/DUF2258 family [General function prediction only]. 111 matched cddid_all.tbl CDD COG4346 COG4346 443487 COG4346 Predicted membrane-bound dolichyl-phosphate-mannose-protein mannosyltransferase [Posttranslational modification, protein turnover, chaperones]. 379 matched cddid_all.tbl CDD COG4347 COG4347 443488 YpjA Uncharacterized membrane protein YpjA [Function unknown]. 196 matched cddid_all.tbl CDD COG4352 COG4352 443489 RPL13 Ribosomal protein L13E [Translation, ribosomal structure and biogenesis]. Ribosomal protein L13E is part of the Pathway/BioSystem: Archaeal ribosomal proteins 78 matched cddid_all.tbl CDD COG4353 COG4353 443490 COG4353 Acetyltransferase superfamily protein, DUF1122 family [General function prediction only]. 183 matched cddid_all.tbl CDD COG4354 COG4354 443491 COG4354 Uncharacterized conserved protein, contains GBA2_N and DUF608 domains [Function unknown]. 744 matched cddid_all.tbl CDD COG4357 COG4357 443492 COG4357 Uncharacterized conserved protein, contains Zn-finger domain of CHY type [Function unknown]. 107 matched cddid_all.tbl CDD COG4359 COG4359 443493 MtnX 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase (methionine salvage) [Amino acid transport and metabolism]. 209 matched cddid_all.tbl CDD COG4360 COG4360 443494 APA2 ATP adenylyltransferase (5',5'''-P-1,P-4-tetraphosphate phosphorylase II) [Nucleotide transport and metabolism]. 293 matched cddid_all.tbl CDD COG4362 COG4362 443495 COG4362 Nitric oxide synthase, oxygenase domain [Inorganic ion transport and metabolism]. 360 matched cddid_all.tbl CDD COG4365 COG4365 443496 BshC Putative cysteine ligase BshC/YllA (bacillithiol biosynthesis) [Secondary metabolites biosynthesis, transport and catabolism]. 543 matched cddid_all.tbl CDD COG4367 COG4367 443497 COG4367 Uncharacterized conserved protein, DUF2316 domain [Function unknown]. 96 matched cddid_all.tbl CDD COG4370 COG4370 443498 COG4370 Uncharacterized conserved protein [Function unknown]. 396 matched cddid_all.tbl CDD COG4371 COG4371 443499 COG4371 Uncharacterized membrane protein [Function unknown]. 238 matched cddid_all.tbl CDD COG4372 COG4372 443500 COG4372 Uncharacterized protein, contains DUF3084 domain [Function unknown]. 370 matched cddid_all.tbl CDD COG4373 COG4373 443501 COG4373 Mu-like prophage FluMu protein gp28 [Mobilome: prophages, transposons]. 512 matched cddid_all.tbl CDD COG4374 COG4374 443502 COG4374 PIN domain nuclease, a component of toxin-antitoxin system (PIN domain) [Defense mechanisms]. 126 matched cddid_all.tbl CDD COG4377 COG4377 443503 YhfC Predicted metal-dependent membrane protease YhfC, DUF2324 family [General function prediction only]. 265 matched cddid_all.tbl CDD COG4378 COG4378 443504 COG4378 Uncharacterized conserved protein, DUF2325 domain [Function unknown]. 88 matched cddid_all.tbl CDD COG4379 COG4379 443505 COG4379 Mu-like prophage tail protein gpP [Mobilome: prophages, transposons]. 351 matched cddid_all.tbl CDD COG4380 COG4380 443506 COG4380 Uncharacterized conserved protein, DUF799 domain [Function unknown]. 219 matched cddid_all.tbl CDD COG4381 COG4381 443507 gp46 Mu-like prophage protein gp46 [Mobilome: prophages, transposons]. 145 matched cddid_all.tbl CDD COG4382 COG4382 443508 gp16 Mu-like prophage protein gp16 [Mobilome: prophages, transposons]. 150 matched cddid_all.tbl CDD COG4383 COG4383 443509 gp29 Mu-like prophage protein gp29 [Mobilome: prophages, transposons]. 526 matched cddid_all.tbl CDD COG4384 COG4384 443510 gp45 Mu-like prophage protein gp45 [Mobilome: prophages, transposons]. 185 matched cddid_all.tbl CDD COG4385 COG4385 443511 gpI Bacteriophage P2-related tail formation protein [Mobilome: prophages, transposons]. 155 matched cddid_all.tbl CDD COG4386 COG4386 443512 gpL Mu-like prophage tail sheath protein gpL [Mobilome: prophages, transposons]. 489 matched cddid_all.tbl CDD COG4387 COG4387 443513 gp36 Mu-like prophage protein gp36 [Mobilome: prophages, transposons]. 142 matched cddid_all.tbl CDD COG4388 COG4388 443514 COG4388 Mu-like prophage I protein [Mobilome: prophages, transposons]. 358 matched cddid_all.tbl CDD COG4389 COG4389 443515 COG4389 Site-specific recombinase [Replication, recombination and repair]. 667 matched cddid_all.tbl CDD COG4390 COG4390 443516 COG4390 Uncharacterized conserved protein, DUF2322 domain [Function unknown]. 104 matched cddid_all.tbl CDD COG4391 COG4391 443517 COG4391 Uncharacterized protein, contains Zn-finger domain [Function unknown]. 54 matched cddid_all.tbl CDD COG4392 COG4392 443518 AzlD2 Branched-chain amino acid transport protein [Amino acid transport and metabolism]. 107 matched cddid_all.tbl CDD COG4393 COG4393 443519 COG4393 Uncharacterized membrane protein [Function unknown]. 171 matched cddid_all.tbl CDD COG4394 COG4394 443520 EarP Elongation factor P Arg32-rhamnosyltransferase EarP [Translation, ribosomal structure and biogenesis]. 376 matched cddid_all.tbl CDD COG4395 COG4395 443521 Tim44 Predicted lipid-binding transport protein, Tim44 family [Lipid transport and metabolism]. 186 matched cddid_all.tbl CDD COG4396 COG4396 443522 Gam Mu-like prophage host-nuclease inhibitor protein Gam [Mobilome: prophages, transposons]. 169 matched cddid_all.tbl CDD COG4397 COG4397 443523 gpT Mu-like prophage major head subunit gpT [Mobilome: prophages, transposons]. 296 matched cddid_all.tbl CDD COG4398 COG4398 443524 FIST Small ligand-binding sensory domain FIST [Signal transduction mechanisms]. 386 matched cddid_all.tbl CDD COG4399 COG4399 443525 YheB Uncharacterized membrane protein YheB, UPF0754 family [Function unknown]. 210 matched cddid_all.tbl CDD COG4401 COG4401 443526 AroH Chorismate mutase AroH [Amino acid transport and metabolism]. Chorismate mutase AroH is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis 122 matched cddid_all.tbl CDD COG4402 COG4402 443527 COG4402 Uncharacterized conserved protein, DUF2330 domain [Function unknown]. 339 matched cddid_all.tbl CDD COG4403 COG4403 443528 LcnDR2 Lantibiotic modifying enzyme [Defense mechanisms]. 405 matched cddid_all.tbl CDD COG4405 COG4405 443529 YhfF Predicted RNA-binding protein YhfF, contains PUA-like ASCH domain [General function prediction only]. 156 matched cddid_all.tbl CDD COG4408 COG4408 443530 COG4408 Uncharacterized conserved protein [Function unknown]. 429 matched cddid_all.tbl CDD COG4409 COG4409 443531 NanH Neuraminidase (sialidase) NanH, contains C-terminal autotransporter domain [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis]. 376 matched cddid_all.tbl CDD COG4412 COG4412 443532 COG4412 Bacillopeptidase F, M6 metalloprotease family [Posttranslational modification, protein turnover, chaperones]. 524 matched cddid_all.tbl CDD COG4413 COG4413 443533 Utp Urea transporter [Amino acid transport and metabolism]. 302 matched cddid_all.tbl CDD COG4416 COG4416 443534 Com Mu-like prophage FluMu protein Com [Mobilome: prophages, transposons]. 59 matched cddid_all.tbl CDD COG4420 COG4420 443535 COG4420 Uncharacterized membrane protein [Function unknown]. 175 matched cddid_all.tbl CDD COG4421 COG4421 443536 COG4421 Capsular polysaccharide biosynthesis protein [Cell wall/membrane/envelope biogenesis]. 258 matched cddid_all.tbl CDD COG4422 COG4422 443537 COG4422 Bacteriophage protein gp37 [Mobilome: prophages, transposons]. 241 matched cddid_all.tbl CDD COG4423 COG4423 443538 COG4423 Uncharacterized conserved protein [Function unknown]. 83 matched cddid_all.tbl CDD COG4424 COG4424 443539 LpsS LPS sulfotransferase NodH [Cell wall/membrane/envelope biogenesis]. 238 matched cddid_all.tbl CDD COG4425 COG4425 443540 COG4425 Uncharacterized membrane protein [Function unknown]. 550 matched cddid_all.tbl CDD COG4427 COG4427 443541 COG4427 Uncharacterized conserved protein, DUF2332 domain [Function unknown]. 350 matched cddid_all.tbl CDD COG4430 COG4430 443542 YdeI Uncharacterized conserved protein YdeI, YjbR/CyaY-like superfamily, DUF1801 family [Function unknown]. 189 matched cddid_all.tbl CDD COG4443 COG4443 443543 COG4443 Uncharacterized conserved protein [Function unknown]. 70 matched cddid_all.tbl CDD COG4445 COG4445 443544 MiaE tRNA isopentenyl-2-thiomethyl-A-37 hydroxylase MiaE (synthesis of 2-methylthio-cis-ribozeatin) [Translation, ribosomal structure and biogenesis]. tRNA isopentenyl-2-thiomethyl-A-37 hydroxylase MiaE (synthesis of 2-methylthio-cis-ribozeatin) is part of the Pathway/BioSystem: tRNA modification 198 matched cddid_all.tbl CDD COG4446 COG4446 443545 COG4446 Uncharacterized conserved protein, DUF1499 family [Function unknown]. 135 matched cddid_all.tbl CDD COG4447 COG4447 443546 COG4447 Uncharacterized conserved protein related to plant photosystem II stability/assembly factor [General function prediction only]. 156 matched cddid_all.tbl CDD COG4448 COG4448 443547 AnsA2 L-asparaginase II [Amino acid transport and metabolism]. 336 matched cddid_all.tbl CDD COG4449 COG4449 443548 COG4449 Predicted protease, Abi (CAAX) family [General function prediction only]. 176 matched cddid_all.tbl CDD COG4451 COG4451 443549 RbcS Ribulose bisphosphate carboxylase small subunit [Carbohydrate transport and metabolism]. 102 matched cddid_all.tbl CDD COG4452 COG4452 443550 CreD Inner membrane protein CreD involved in colicin E2 resistance [Defense mechanisms]. 449 matched cddid_all.tbl CDD COG4453 COG4453 443551 COG4453 Uncharacterized conserved protein, DUF1778 family [Function unknown]. 89 matched cddid_all.tbl CDD COG4454 COG4454 443552 COG4454 Uncharacterized copper-binding protein, cupredoxin-like subfamily [General function prediction only]. 151 matched cddid_all.tbl CDD COG4455 COG4455 443553 ImpE Protein of avirulence locus involved in temperature-dependent protein secretion [General function prediction only]. 266 matched cddid_all.tbl CDD COG4456 COG4456 443554 VagC Virulence-associated protein VagC (function unknown) [Function unknown]. 74 matched cddid_all.tbl CDD COG4457 COG4457 443555 SrfB Virulence factor SrfB-related protein [Secondary metabolites biosynthesis, transport and catabolism]. 998 matched cddid_all.tbl CDD COG4458 COG4458 443556 SrfC Virulence factor SrfC-related protein [Secondary metabolites biosynthesis, transport and catabolism]. 894 matched cddid_all.tbl CDD COG4459 COG4459 443557 NapE Periplasmic nitrate reductase system, NapE component [Energy production and conversion]. 52 matched cddid_all.tbl CDD COG4460 COG4460 443558 COG4460 Uncharacterized conserved protein, DUF4440 domain [Function unknown]. 130 matched cddid_all.tbl CDD COG4461 COG4461 443559 LprI Lysozyme inhibitor LprI [Defense mechanisms]. 109 matched cddid_all.tbl CDD COG4463 COG4463 443560 CtsR Transcriptional regulator CtsR [Transcription]. 154 matched cddid_all.tbl CDD COG4464 COG4464 443561 YwqE Tyrosine-protein phosphatase YwqE [Signal transduction mechanisms]. 239 matched cddid_all.tbl CDD COG4465 COG4465 443562 CodY GTP-sensing pleiotropic transcriptional regulator CodY [Transcription]. 259 matched cddid_all.tbl CDD COG4466 COG4466 443563 COG4466 Uncharacterized conserved protein Veg, DUF1021 family [Function unknown]. 87 matched cddid_all.tbl CDD COG4467 COG4467 443564 YabA Regulator of replication initiation timing YabA [Replication, recombination and repair]. 107 matched cddid_all.tbl CDD COG4468 COG4468 443565 GalT2 Galactose-1-phosphate uridylyltransferase [Carbohydrate transport and metabolism]. 499 matched cddid_all.tbl CDD COG4469 COG4469 443566 CoiA Competence protein CoiA, contains predicted nuclease domain [General function prediction only]. 147 matched cddid_all.tbl CDD COG4470 COG4470 443567 YutD Uncharacterized conserved protein YutD, DUF1027 family [Function unknown]. 91 matched cddid_all.tbl CDD COG4471 COG4471 443568 YlbG Uncharacterized conserved protein YlbG, UPF0298 family [Function unknown]. 92 matched cddid_all.tbl CDD COG4472 COG4472 443569 COG4472 Uncharacterized conserved protein, UPF0297 family [Function unknown]. 81 matched cddid_all.tbl CDD COG4473 COG4473 443570 EcsB Predicted ABC-type exoprotein transport system, permease component [Intracellular trafficking, secretion, and vesicular transport]. 402 matched cddid_all.tbl CDD COG4474 COG4474 443571 YoqJ Uncharacterized SPBc2 prophage-derived protein YoqJ [Mobilome: prophages, transposons]. 184 matched cddid_all.tbl CDD COG4475 COG4475 443572 YwlG Uncharacterized conserved protein YwlG, UPF0340 family [Function unknown]. 181 matched cddid_all.tbl CDD COG4476 COG4476 443573 YktA Uncharacterized conserved protein YktA, UPF0223 family [Function unknown]. 86 matched cddid_all.tbl CDD COG4477 COG4477 443574 EzrA Septation ring formation regulator EzrA [Cell cycle control, cell division, chromosome partitioning]. 567 matched cddid_all.tbl CDD COG4478 COG4478 443575 COG4478 Uncharacterized membrane protein [Function unknown]. 206 matched cddid_all.tbl CDD COG4479 COG4479 443576 YozE Uncharacterized conserved protein YozE, UPF0346 family [Function unknown]. 70 matched cddid_all.tbl CDD COG4481 COG4481 443577 COG4481 Uncharacterized conserved protein, DUF951 family [Function unknown]. 58 matched cddid_all.tbl CDD COG4483 COG4483 443578 YqgQ Uncharacterized conserved protein YqgQ, DUF910 family [Function unknown]. 65 matched cddid_all.tbl CDD COG4485 COG4485 443579 YfhO Uncharacterized membrane protein YfhO [Function unknown]. 860 matched cddid_all.tbl CDD COG4487 COG4487 443580 COG4487 Uncharacterized conserved protein, contains DUF2130 domain [Function unknown]. 425 matched cddid_all.tbl CDD COG4492 COG4492 443581 PheB ACT domain-containing protein, UPF0735 family [General function prediction only]. 147 matched cddid_all.tbl CDD COG4493 COG4493 443582 YktB Uncharacterized conserved protein YktB, UPF0637 family [Function unknown]. 208 matched cddid_all.tbl CDD COG4495 COG4495 443583 COG4495 Uncharacterized conserved protein, DUF4176 domain [Function unknown]. 97 matched cddid_all.tbl CDD COG4496 COG4496 443584 YerC Predicted DNA-binding transcriptional regulator YerC, contains ArsR-like HTH domain [General function prediction only]. 92 matched cddid_all.tbl CDD COG4499 COG4499 443585 YukC ESX protein secretion system component YukC [Intracellular trafficking, secretion, and vesicular transport]. 435 matched cddid_all.tbl CDD COG4502 COG4502 443586 YorC 5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism]. 177 matched cddid_all.tbl CDD COG4506 COG4506 443587 YwiB Uncharacterized beta-barrel protein YwiB, DUF1934 family [Function unknown]. 136 matched cddid_all.tbl CDD COG4508 COG4508 443588 Dut2 Dimeric dUTPase, all-alpha-NTP-PPase (MazG) superfamily [Nucleotide transport and metabolism]. Dimeric dUTPase, all-alpha-NTP-PPase (MazG) superfamily is part of the Pathway/BioSystem: Thymidylate biosynthesis 163 matched cddid_all.tbl CDD COG4509 COG4509 443589 COG4509 Uncharacterized conserved protein [Function unknown]. 245 matched cddid_all.tbl CDD COG4512 COG4512 443590 AgrB Accessory gene regulator protein AgrB [Transcription, Signal transduction mechanisms]. 198 matched cddid_all.tbl CDD COG4517 COG4517 443591 COG4517 Uncharacterized conserved protein, DUF1820 domain [Function unknown]. 108 matched cddid_all.tbl CDD COG4518 COG4518 443592 gp41 Mu-like prophage FluMu protein gp41 [Mobilome: prophages, transposons]. 120 matched cddid_all.tbl CDD COG4519 COG4519 443593 COG4519 Uncharacterized conserved protein [Function unknown]. 96 matched cddid_all.tbl CDD COG4520 COG4520 443594 LipA17 Surface antigen [Cell wall/membrane/envelope biogenesis]. 155 matched cddid_all.tbl CDD COG4521 COG4521 443595 TauA ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]. 332 matched cddid_all.tbl CDD COG4525 COG4525 443596 TauB ABC-type taurine transport system, ATPase component [Inorganic ion transport and metabolism]. 262 matched cddid_all.tbl CDD COG4529 COG4529 443597 YdhS Uncharacterized NAD(P)/FAD-binding protein YdhS [General function prediction only]. 466 matched cddid_all.tbl CDD COG4530 COG4530 443598 COG4530 Uncharacterized conserved protein [Function unknown]. 36 matched cddid_all.tbl CDD COG4531 COG4531 443599 ZnuA ABC-type Zn2+ transport system, periplasmic component/surface adhesin ZnuA [Inorganic ion transport and metabolism]. 300 matched cddid_all.tbl CDD COG4533 COG4533 443600 SgrR DNA-binding transcriptional regulator SgrR of sgrS sRNA, contains a MarR-type HTH domain and a periplasmic-type solute-binding domain [Transcription]. 574 matched cddid_all.tbl CDD COG4535 COG4535 443601 CorC Mg2+ and Co2+ transporter CorC, contains CBS pair and CorC-HlyC domains [Inorganic ion transport and metabolism]. 288 matched cddid_all.tbl CDD COG4536 COG4536 443602 CorB Mg2+ and Co2+ transporter CorB, contains DUF21, CBS pair, and CorC-HlyC domains [Inorganic ion transport and metabolism]. 420 matched cddid_all.tbl CDD COG4537 COG4537 443603 ComGC Competence protein ComGC [Mobilome: prophages, transposons]. 108 matched cddid_all.tbl CDD COG4538 COG4538 443604 SnoaL Uncharacterized conserved protein, contains SnoaL-like domain [Function unknown]. 113 matched cddid_all.tbl CDD COG4539 COG4539 443605 MPO1 2-hydroxy fatty acid dioxygenase MPO1 (alpha-oxidation of fatty acids) [Lipid transport and metabolism]. 153 matched cddid_all.tbl CDD COG4540 COG4540 443606 gpV Phage P2 baseplate assembly protein gpV [Mobilome: prophages, transposons]. 167 matched cddid_all.tbl CDD COG4541 COG4541 443607 COG4541 Uncharacterized membrane protein [Function unknown]. 99 matched cddid_all.tbl CDD COG4542 COG4542 443608 PduX PduX protein involved in propanediol utilization and related proteins [Secondary metabolites biosynthesis, transport and catabolism]. 286 matched cddid_all.tbl CDD COG4544 COG4544 443609 COG4544 Uncharacterized conserved protein [Function unknown]. 230 matched cddid_all.tbl CDD COG4545 COG4545 443610 COG4545 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]. 87 matched cddid_all.tbl CDD COG4547 COG4547 443611 CobT2 Cobalamin biosynthesis cobaltochelatase CobT subunit [Coenzyme transport and metabolism]. Cobalamin biosynthesis cobaltochelatase CobT subunit is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 608 matched cddid_all.tbl CDD COG4548 COG4548 443612 NorD Nitric oxide reductase activation protein [Inorganic ion transport and metabolism]. 439 matched cddid_all.tbl CDD COG4549 COG4549 443613 YcnI Uncharacterized conserved protein YcnI, contains cohesin/reeler-like domain [Function unknown]. 179 matched cddid_all.tbl CDD COG4550 COG4550 443614 YmcA Cell fate regulator YmcA, YheA/YmcA/DUF963 family (controls sporulation, competence, biofilm development) [Signal transduction mechanisms]. 135 matched cddid_all.tbl CDD COG4551 COG4551 443615 COG4551 Predicted protein tyrosine phosphatase [General function prediction only]. 109 matched cddid_all.tbl CDD COG4552 COG4552 443616 Eis Predicted acetyltransferase [General function prediction only]. 393 matched cddid_all.tbl CDD COG4553 COG4553 443617 DepA Poly-beta-hydroxyalkanoate depolymerase [Lipid transport and metabolism]. 412 matched cddid_all.tbl CDD COG4555 COG4555 443618 NatA ABC-type Na+ transport system, ATPase component NatA [Energy production and conversion, Inorganic ion transport and metabolism]. 243 matched cddid_all.tbl CDD COG4558 COG4558 443619 ChuT ABC-type hemin transport system, periplasmic component [Inorganic ion transport and metabolism]. 285 matched cddid_all.tbl CDD COG4559 COG4559 443620 COG4559 ABC-type hemin transport system, ATPase component [Inorganic ion transport and metabolism]. 258 matched cddid_all.tbl CDD COG4564 COG4564 443621 COG4564 Signal transduction histidine kinase [Signal transduction mechanisms]. 510 matched cddid_all.tbl CDD COG4565 COG4565 443622 CitB DNA-binding response regulator DpiB of citrate/malate metabolism [Transcription, Signal transduction mechanisms]. 138 matched cddid_all.tbl CDD COG4566 COG4566 443623 FixJ DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription]. 196 matched cddid_all.tbl CDD COG4567 COG4567 443624 COG4567 DNA-binding response regulator, ActR/RegA family, consists of REC and Fis-type HTH domains [Signal transduction mechanisms, Transcription]. 177 matched cddid_all.tbl CDD COG4568 COG4568 443625 Rof Transcriptional antiterminator Rof (Rho-off) [Transcription]. 87 matched cddid_all.tbl CDD COG4569 COG4569 443626 MhpF Acetaldehyde dehydrogenase (acetylating) [Secondary metabolites biosynthesis, transport and catabolism]. 295 matched cddid_all.tbl CDD COG4570 COG4570 443627 RusA Holliday junction resolvase RusA (prophage-encoded endonuclease) [Replication, recombination and repair]. 120 matched cddid_all.tbl CDD COG4571 COG4571 443628 OmpT Outer membrane protease [Cell wall/membrane/envelope biogenesis]. 315 matched cddid_all.tbl CDD COG4572 COG4572 443629 ChaB Cation transport regulator ChaB [Inorganic ion transport and metabolism]. 75 matched cddid_all.tbl CDD COG4573 COG4573 443630 GatZ Tagatose-1,6-bisphosphate aldolase non-catalytic subunit AgaZ/GatZ [Carbohydrate transport and metabolism]. 423 matched cddid_all.tbl CDD COG4574 COG4574 443631 Eco Serine protease inhibitor ecotin [Posttranslational modification, protein turnover, chaperones]. 162 matched cddid_all.tbl CDD COG4575 COG4575 443632 ElaB Membrane-anchored ribosome-binding protein ElaB, inhibits growth in stationary phase, YqjD/DUF883 family [Translation, ribosomal structure and biogenesis]. 108 matched cddid_all.tbl CDD COG4576 COG4576 443633 CcmL Carboxysome shell and ethanolamine utilization microcompartment protein CcmK/EutM [Secondary metabolites biosynthesis, transport and catabolism, Energy production and conversion]. 90 matched cddid_all.tbl CDD COG4577 COG4577 443634 CcmK Carboxysome shell and ethanolamine utilization microcompartment protein CcmL/EutN [Secondary metabolites biosynthesis, transport and catabolism, Energy production and conversion]. 86 matched cddid_all.tbl CDD COG4578 COG4578 443635 GutM DNA-binding transcriptional regulator of glucitol operon [Transcription]. 127 matched cddid_all.tbl CDD COG4579 COG4579 443636 AceK Isocitrate dehydrogenase kinase/phosphatase [Signal transduction mechanisms]. 579 matched cddid_all.tbl CDD COG4580 COG4580 443637 LamB Maltoporin (phage lambda and maltose receptor) [Carbohydrate transport and metabolism]. 408 matched cddid_all.tbl CDD COG4581 COG4581 443638 Dob10 Superfamily II RNA helicase [Replication, recombination and repair]. 751 matched cddid_all.tbl CDD COG4582 COG4582 443639 ZapD Cell division protein ZapD, interacts with FtsZ [Cell cycle control, cell division, chromosome partitioning]. 253 matched cddid_all.tbl CDD COG4583 COG4583 443640 SoxG Sarcosine oxidase gamma subunit [Amino acid transport and metabolism]. 169 matched cddid_all.tbl CDD COG4584 COG4584 443641 COG4584 Transposase [Mobilome: prophages, transposons]. 484 matched cddid_all.tbl CDD COG4585 COG4585 443642 ComP Signal transduction histidine kinase ComP [Signal transduction mechanisms]. 252 matched cddid_all.tbl CDD COG4586 COG4586 443643 COG4586 ABC-type uncharacterized transport system, ATPase component [General function prediction only]. 323 matched cddid_all.tbl CDD COG4587 COG4587 443644 COG4587 ABC-type uncharacterized transport system, permease component [General function prediction only]. 266 matched cddid_all.tbl CDD COG4588 COG4588 443645 AcfC Accessory colonization factor AcfC, contains ABC-type periplasmic domain [Cell wall/membrane/envelope biogenesis]. 232 matched cddid_all.tbl CDD COG4589 COG4589 443646 YnbB Predicted CDP-diglyceride synthetase/phosphatidate cytidylyltransferase [General function prediction only]. 267 matched cddid_all.tbl CDD COG4590 COG4590 443647 COG4590 ABC-type uncharacterized transport system, permease component [General function prediction only]. 757 matched cddid_all.tbl CDD COG4591 COG4591 443648 LolE ABC-type transport system involved in lipoprotein release, permease component LolC [Cell wall/membrane/envelope biogenesis]. 283 matched cddid_all.tbl CDD COG4592 COG4592 443649 FepB ABC-type Fe2+-enterobactin transport system, periplasmic component [Inorganic ion transport and metabolism]. 330 matched cddid_all.tbl CDD COG4594 COG4594 443650 FecB ABC-type Fe3+-citrate transport system, periplasmic component [Inorganic ion transport and metabolism]. 316 matched cddid_all.tbl CDD COG4597 COG4597 443651 BatB ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]. 397 matched cddid_all.tbl CDD COG4598 COG4598 443652 HisP ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]. 259 matched cddid_all.tbl CDD COG4603 COG4603 443653 NupP ABC-type guanosine uptake system NupNOPQ, permease component NupP [Nucleotide transport and metabolism]. 356 matched cddid_all.tbl CDD COG4604 COG4604 443654 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]. 252 matched cddid_all.tbl CDD COG4605 COG4605 443655 CeuC ABC-type enterochelin transport system, permease component [Inorganic ion transport and metabolism]. 317 matched cddid_all.tbl CDD COG4606 COG4606 443656 CeuB ABC-type enterochelin transport system, permease component [Inorganic ion transport and metabolism]. 318 matched cddid_all.tbl CDD COG4607 COG4607 443657 CeuA ABC-type enterochelin transport system, periplasmic component [Inorganic ion transport and metabolism]. 310 matched cddid_all.tbl CDD COG4608 COG4608 443658 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]. 329 matched cddid_all.tbl CDD COG4615 COG4615 443659 PvdE ABC-type siderophore export system, fused ATPase and permease components [Inorganic ion transport and metabolism]. 547 matched cddid_all.tbl CDD COG4618 COG4618 443660 ArpD ABC-type protease/lipase transport system, ATPase and permease components [Intracellular trafficking, secretion, and vesicular transport]. 563 matched cddid_all.tbl CDD COG4619 COG4619 443661 FetA ABC-type iron transporter FetAB, ATPase component [Inorganic ion transport and metabolism]. 209 matched cddid_all.tbl CDD COG4623 COG4623 443662 MltF Membrane-bound lytic murein transglycosylase MltF [Cell wall/membrane/envelope biogenesis, Signal transduction mechanisms]. 421 matched cddid_all.tbl CDD COG4624 COG4624 443663 Nar1 Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion]. 450 matched cddid_all.tbl CDD COG4625 COG4625 443664 COG4625 Uncharacterized conserved protein, contains a C-terminal beta-barrel porin domain [Function unknown]. 900 matched cddid_all.tbl CDD COG4626 COG4626 443665 YmfN Phage terminase-like protein, large subunit, contains N-terminal HTH domain [Mobilome: prophages, transposons]. 559 matched cddid_all.tbl CDD COG4627 COG4627 443666 COG4627 Predicted SAM-depedendent methyltransferase [General function prediction only]. 161 matched cddid_all.tbl CDD COG4628 COG4628 443667 COG4628 Uncharacterized conserved protein, DUF2132 family [Function unknown]. 74 matched cddid_all.tbl CDD COG4630 COG4630 443668 XdhA Xanthine dehydrogenase, Fe-S cluster and FAD-binding subunit XdhA [Nucleotide transport and metabolism]. 476 matched cddid_all.tbl CDD COG4631 COG4631 443669 XdhB Xanthine dehydrogenase, molybdopterin-binding subunit XdhB [Nucleotide transport and metabolism]. 769 matched cddid_all.tbl CDD COG4632 COG4632 443670 NAGPA Sugar-P-sugar glycosidase (uncovering enzyme, UCE), NAGPA superfamily [Carbohydrate transport and metabolism]. 310 matched cddid_all.tbl CDD COG4633 COG4633 443671 COG4633 Plastocyanin domain containing protein [General function prediction only]. 121 matched cddid_all.tbl CDD COG4634 COG4634 443672 COG4634 Predicted nuclease, contains PIN domain, potential toxin-antitoxin system component [General function prediction only]. 113 matched cddid_all.tbl CDD COG4635 COG4635 443673 HemG Protoporphyrinogen IX oxidase, menaquinone-dependent (flavodoxin domain) [Coenzyme transport and metabolism]. 179 matched cddid_all.tbl CDD COG4636 COG4636 443674 Uma2 Endonuclease, Uma2 family (restriction endonuclease fold) [General function prediction only]. 187 matched cddid_all.tbl CDD COG4637 COG4637 443675 COG4637 Predicted ATPase [General function prediction only]. 371 matched cddid_all.tbl CDD COG4638 COG4638 443676 HcaE Phenylpropionate dioxygenase or related ring-hydroxylating dioxygenase, large terminal subunit [Inorganic ion transport and metabolism, General function prediction only]. 298 matched cddid_all.tbl CDD COG4639 COG4639 443677 COG4639 Predicted kinase [General function prediction only]. 145 matched cddid_all.tbl CDD COG4640 COG4640 443678 YvbJ Uncharacterized protein YvbJ, contains N-terminal Zn ribbon domain [Function unknown]. 445 matched cddid_all.tbl CDD COG4641 COG4641 443679 COG4641 Spore maturation protein CgeB [Cell cycle control, cell division, chromosome partitioning]. 303 matched cddid_all.tbl CDD COG4642 COG4642 443680 COG4642 Uncharacterized conserved protein [Function unknown]. 271 matched cddid_all.tbl CDD COG4643 COG4643 443681 COG4643 Uncharacterized domain associated with phage/plasmid primase [Mobilome: prophages, transposons]. 435 matched cddid_all.tbl CDD COG4644 COG4644 443682 COG4644 Transposase and inactivated derivatives, TnpA family [Mobilome: prophages, transposons]. 490 matched cddid_all.tbl CDD COG4645 COG4645 443683 OpgC Predicted acyltransferase [General function prediction only]. 372 matched cddid_all.tbl CDD COG4646 COG4646 443684 COG4646 Adenine-specific DNA methylase, N12 class [Replication, recombination and repair]. 1711 matched cddid_all.tbl CDD COG4647 COG4647 443685 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport and catabolism]. 117 matched cddid_all.tbl CDD COG4648 COG4648 443686 COG4648 Uncharacterized membrane protein [Function unknown]. 193 matched cddid_all.tbl CDD COG4649 COG4649 443687 TPR1 TPR-like repeat domain [Function unknown]. 222 matched cddid_all.tbl CDD COG4650 COG4650 443688 RtcR Sigma54-dependent transcription regulator containing an AAA-type ATPase domain and a DNA-binding domain [Transcription, Signal transduction mechanisms]. 534 matched cddid_all.tbl CDD COG4651 COG4651 443689 RosB Predicted Kef-type K+ transport protein, K+/H+ antiporter domain [Inorganic ion transport and metabolism]. 564 matched cddid_all.tbl CDD COG4652 COG4652 443690 COG4652 Uncharacterized conserved protein, DUF1430 domain [Function unknown]. 583 matched cddid_all.tbl CDD COG4653 COG4653 443691 gp36 Predicted phage phi-C31 gp36 major capsid-like protein [Mobilome: prophages, transposons]. 304 matched cddid_all.tbl CDD COG4654 COG4654 443692 CytC552 Cytochrome c551/c552 [Energy production and conversion]. 88 matched cddid_all.tbl CDD COG4655 COG4655 443693 TadX Uncharacterized conserved protein, contains TadX/Tad_C domain [General function prediction only]. 516 matched cddid_all.tbl CDD COG4656 COG4656 443694 RnfC Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfC subunit [Energy production and conversion]. Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfC subunit is part of the Pathway/BioSystem: Na+-translocating Fd:NADH oxidoreductase 451 matched cddid_all.tbl CDD COG4657 COG4657 443695 RnfA Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfA subunit [Energy production and conversion]. Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfA subunit is part of the Pathway/BioSystem: Na+-translocating Fd:NADH oxidoreductase 193 matched cddid_all.tbl CDD COG4658 COG4658 443696 RnfD Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfD subunit [Energy production and conversion]. Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfD subunit is part of the Pathway/BioSystem: Na+-translocating Fd:NADH oxidoreductase 332 matched cddid_all.tbl CDD COG4659 COG4659 443697 RnfG Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfG subunit [Energy production and conversion]. Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfG subunit is part of the Pathway/BioSystem: Na+-translocating Fd:NADH oxidoreductase 192 matched cddid_all.tbl CDD COG4660 COG4660 443698 RnfE Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfE subunit [Energy production and conversion]. Na+-translocating ferredoxin:NAD+ oxidoreductase RNF, RnfE subunit is part of the Pathway/BioSystem: Na+-translocating Fd:NADH oxidoreductase 209 matched cddid_all.tbl CDD COG4662 COG4662 443699 TupA ABC-type tungstate transport system, periplasmic component [Inorganic ion transport and metabolism]. 232 matched cddid_all.tbl CDD COG4663 COG4663 443700 FcbT1 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport and catabolism]. 356 matched cddid_all.tbl CDD COG4664 COG4664 443701 FcbT3 TRAP-type mannitol/chloroaromatic compound transport system, large permease component [Secondary metabolites biosynthesis, transport and catabolism]. 435 matched cddid_all.tbl CDD COG4665 COG4665 443702 FcbT2 TRAP-type mannitol/chloroaromatic compound transport system, small permease component [Secondary metabolites biosynthesis, transport and catabolism]. 170 matched cddid_all.tbl CDD COG4666 COG4666 443703 COG4666 TRAP-type uncharacterized transport system, fused permease components [General function prediction only]. 635 matched cddid_all.tbl CDD COG4667 COG4667 443704 YjjU Predicted phospholipase, patatin/cPLA2 family [Lipid transport and metabolism]. 281 matched cddid_all.tbl CDD COG4668 COG4668 443705 MtlA2 Mannitol/fructose-specific phosphotransferase system, IIA domain [Carbohydrate transport and metabolism]. 143 matched cddid_all.tbl CDD COG4669 COG4669 443706 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking, secretion, and vesicular transport]. 236 matched cddid_all.tbl CDD COG4670 COG4670 443707 YdiF Acyl CoA:acetate/3-ketoacid CoA transferase [Lipid transport and metabolism]. 511 matched cddid_all.tbl CDD COG4671 COG4671 443708 COG4671 Predicted glycosyl transferase [General function prediction only]. 391 matched cddid_all.tbl CDD COG4672 COG4672 443709 gp18 Phage tail protein [Mobilome: prophages, transposons]. 233 matched cddid_all.tbl CDD COG4674 COG4674 443710 COG4674 ABC-type uncharacterized transport system, ATPase component [General function prediction only]. 250 matched cddid_all.tbl CDD COG4675 COG4675 443711 MdpB Phage tail collar domain [Mobilome: prophages, transposons]. 173 matched cddid_all.tbl CDD COG4676 COG4676 443712 YfaP Uncharacterized conserved protein YfaP, DUF2135 family [Function unknown]. 125 matched cddid_all.tbl CDD COG4677 COG4677 443713 PemB Pectin methylesterase and related acyl-CoA thioesterases [Carbohydrate transport and metabolism, Lipid transport and metabolism]. 307 matched cddid_all.tbl CDD COG4678 COG4678 443714 COG4678 Muramidase (phage lambda lysozyme) [Cell wall/membrane/envelope biogenesis, Mobilome: prophages, transposons]. 166 matched cddid_all.tbl CDD COG4679 COG4679 443715 COG4679 Phage-related protein [Mobilome: prophages, transposons]. 113 matched cddid_all.tbl CDD COG4680 COG4680 443716 HigB mRNA-degrading endonuclease (mRNA interferase) HigB, toxic component of the HigAB toxin-antitoxin module [Translation, ribosomal structure and biogenesis, Defense mechanisms]. 89 matched cddid_all.tbl CDD COG4681 COG4681 443717 YaeQ Uncharacterized conserved protein YaeQ, suppresses RfaH defect [Function unknown]. 180 matched cddid_all.tbl CDD COG4682 COG4682 443718 YiaA Uncharacterized membrane protein YiaA [Function unknown]. 138 matched cddid_all.tbl CDD COG4683 COG4683 443719 COG4683 Uncharacterized conserved protein [Function unknown]. 119 matched cddid_all.tbl CDD COG4684 COG4684 443720 COG4684 Uncharacterized membrane protein [Function unknown]. 196 matched cddid_all.tbl CDD COG4685 COG4685 443721 YfaA Uncharacterized conserved protein YfaA, DUF2138 family [Function unknown]. 557 matched cddid_all.tbl CDD COG4687 COG4687 443722 COG4687 Uncharacterized conserved protein [Function unknown]. 125 matched cddid_all.tbl CDD COG4688 COG4688 443723 COG4688 Uncharacterized conserved protein [Function unknown]. 646 matched cddid_all.tbl CDD COG4689 COG4689 443724 Adc Acetoacetate decarboxylase [Secondary metabolites biosynthesis, transport and catabolism]. 246 matched cddid_all.tbl CDD COG4690 COG4690 443725 PepD Dipeptidase [Amino acid transport and metabolism]. 469 matched cddid_all.tbl CDD COG4691 COG4691 443726 StbC1 Plasmid stability protein StbC1, contains ribbon-helix-helix domain [Defense mechanisms]. 79 matched cddid_all.tbl CDD COG4692 COG4692 443727 COG4692 Predicted neuraminidase (sialidase) [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis]. 353 matched cddid_all.tbl CDD COG4693 COG4693 443728 PchG Oxidoreductase (NAD-binding), involved in siderophore biosynthesis [Inorganic ion transport and metabolism]. 362 matched cddid_all.tbl CDD COG4694 COG4694 443729 RloC Wobble nucleotide-excising tRNase [Translation, ribosomal structure and biogenesis]. 692 matched cddid_all.tbl CDD COG4695 COG4695 443730 BeeE Phage portal protein BeeE [Mobilome: prophages, transposons]. 393 matched cddid_all.tbl CDD COG4696 COG4696 443731 MazG2 NTP pyrophosphatase, MazG superfamily [Nucleotide transport and metabolism]. 130 matched cddid_all.tbl CDD COG4697 COG4697 443732 COG4697 Uncharacterized conserved protein, DUF2139 domain [Function unknown]. 488 matched cddid_all.tbl CDD COG4698 COG4698 443733 YpmS Uncharacterized conserved protein YpmS, DUF2140 family [Function unknown]. 196 matched cddid_all.tbl CDD COG4699 COG4699 443734 COG4699 Uncharacterized conserved protein, DUF1033 domain [Function unknown]. 104 matched cddid_all.tbl CDD COG4700 COG4700 443735 COG4700 Uncharacterized conserved protein ECs_4300, contains TPR-like domain [Function unknown]. 249 matched cddid_all.tbl CDD COG4701 COG4701 443736 COG4701 Uncharacterized conserved protein [Function unknown]. 145 matched cddid_all.tbl CDD COG4702 COG4702 443737 COG4702 Uncharacterized conserved protein, UPF0303 family [Function unknown]. 160 matched cddid_all.tbl CDD COG4703 COG4703 443738 YkuJ Uncharacterized conserved protein YkuJ, DUF1797 family [Function unknown]. 73 matched cddid_all.tbl CDD COG4704 COG4704 443739 COG4704 Uncharacterized conserved protein, DUF2141 family [Function unknown]. 140 matched cddid_all.tbl CDD COG4705 COG4705 443740 COG4705 Uncharacterized membrane-anchored protein [Function unknown]. 259 matched cddid_all.tbl CDD COG4706 COG4706 443741 COG4706 Predicted 3-hydroxylacyl-ACP dehydratase, HotDog domain [Lipid transport and metabolism]. 149 matched cddid_all.tbl CDD COG4707 COG4707 443742 COG4707 Prophage pi2 protein 07 [Mobilome: prophages, transposons]. 102 matched cddid_all.tbl CDD COG4708 COG4708 443743 QueT ECF-type transporter of queuosine precursor, membrane (S) component [Nucleotide transport and metabolism, Translation, ribosomal structure and biogenesis]. 158 matched cddid_all.tbl CDD COG4709 COG4709 443744 COG4709 Uncharacterized membrane protein [Function unknown]. 179 matched cddid_all.tbl CDD COG4710 COG4710 443745 COG4710 Predicted DNA-binding protein with an HTH domain [General function prediction only]. 76 matched cddid_all.tbl CDD COG4711 COG4711 443746 COG4711 Uncharacterized membrane protein [Function unknown]. 130 matched cddid_all.tbl CDD COG4712 COG4712 443747 DdrA Predicted ssDNA annealing protein, contains HHH motif, Rad42/Rad22/RecT/erf family [Replication, recombination and repair]. 213 matched cddid_all.tbl CDD COG4713 COG4713 443748 COG4713 Uncharacterized membrane protein [Function unknown]. 362 matched cddid_all.tbl CDD COG4714 COG4714 443749 COG4714 Uncharacterized membrane-anchored protein [Function unknown]. 292 matched cddid_all.tbl CDD COG4715 COG4715 443750 SWIM Uncharacterized protein, contains SWIM-type Zn finger domain [Function unknown]. 508 matched cddid_all.tbl CDD COG4716 COG4716 443751 COG4716 Myosin-crossreactive antigen (function unknown) [Function unknown]. 578 matched cddid_all.tbl CDD COG4717 COG4717 443752 YhaN Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]. 641 matched cddid_all.tbl CDD COG4718 COG4718 443753 COG4718 Phage tail protein [Mobilome: prophages, transposons]. 111 matched cddid_all.tbl CDD COG4719 COG4719 443754 COG4719 Uncharacterized conserved protein, UCP014979 family [Function unknown]. 167 matched cddid_all.tbl CDD COG4720 COG4720 443755 ECF-S ECF-type riboflavin transporter, membrane (S) component [Coenzyme transport and metabolism]. 170 matched cddid_all.tbl CDD COG4721 COG4721 443756 YkoE ABC-type thiamine/hydroxymethylpyrimidine transport system, permease component [Coenzyme transport and metabolism]. 197 matched cddid_all.tbl CDD COG4722 COG4722 443757 YomH Phage-related protein YomH [Mobilome: prophages, transposons]. 237 matched cddid_all.tbl CDD COG4723 COG4723 443758 COG4723 Phage-related protein, tail assembly protein I [Mobilome: prophages, transposons]. 197 matched cddid_all.tbl CDD COG4724 COG4724 443759 COG4724 Endo-beta-N-acetylglucosaminidase D [Carbohydrate transport and metabolism]. 662 matched cddid_all.tbl CDD COG4725 COG4725 443760 IME4 N6-adenosine-specific RNA methylase IME4 [Translation, ribosomal structure and biogenesis]. 193 matched cddid_all.tbl CDD COG4726 COG4726 443761 PilX Type IV pilus assembly protein PilX [Cell motility, Extracellular structures]. 175 matched cddid_all.tbl CDD COG4727 COG4727 443762 COG4727 Uncharacterized conserved protein, DUF2145 domain [Function unknown]. 273 matched cddid_all.tbl CDD COG4728 COG4728 443763 COG4728 Uncharacterized conserved protein, DUF1653 family [Function unknown]. 68 matched cddid_all.tbl CDD COG4729 COG4729 443764 COG4729 Uncharacterized conserved protein, DUF1850 family [Function unknown]. 152 matched cddid_all.tbl CDD COG4731 COG4731 443765 COG4731 Uncharacterized conserved protein, DUF2147 family [Function unknown]. 141 matched cddid_all.tbl CDD COG4732 COG4732 443766 ThiW ECF-type thiazole transporter, membrane (S) component ThiW [Coenzyme transport and metabolism]. 165 matched cddid_all.tbl CDD COG4733 COG4733 443767 COG4733 Phage-related protein, tail protein J [Mobilome: prophages, transposons]. 978 matched cddid_all.tbl CDD COG4734 COG4734 443768 ArdA Antirestriction protein ArdA [Defense mechanisms]. 173 matched cddid_all.tbl CDD COG4735 COG4735 443769 YaaW Uncharacterized conserved protein YaaW, UPF0174 family [Function unknown]. 172 matched cddid_all.tbl CDD COG4736 COG4736 443770 CcoQ Cbb3-type cytochrome oxidase, subunit 3 [Energy production and conversion]. 50 matched cddid_all.tbl CDD COG4737 COG4737 443771 COG4737 Uncharacterized conserved protein [Function unknown]. 123 matched cddid_all.tbl CDD COG4738 COG4738 443772 COG4738 Predicted transcriptional regulator [Transcription]. 123 matched cddid_all.tbl CDD COG4739 COG4739 443773 COG4739 Uncharacterized conserved protein, contains ferredoxin domain [Function unknown]. 182 matched cddid_all.tbl CDD COG4740 COG4740 443774 COG4740 Predicted metalloprotease [General function prediction only]. 176 matched cddid_all.tbl CDD COG4741 COG4741 443775 COG4741 Predicted secreted endonuclease distantly related to archaeal Holliday junction resolvase [Nucleotide transport and metabolism]. 159 matched cddid_all.tbl CDD COG4742 COG4742 443776 COG4742 Predicted transcriptional regulator, contains HTH domain [Transcription]. 267 matched cddid_all.tbl CDD COG4743 COG4743 443777 COG4743 Uncharacterized membrane protein, DUF1616 domain [Function unknown]. 333 matched cddid_all.tbl CDD COG4744 COG4744 443778 COG4744 Uncharacterized conserved protein, DUF2149 domain [Function unknown]. 111 matched cddid_all.tbl CDD COG4745 COG4745 443779 PMT Predicted membrane-bound mannosyltransferase, involved in protein glycosylation [General function prediction only]. 550 matched cddid_all.tbl CDD COG4746 COG4746 443780 COG4746 Uncharacterized conserved protein [Function unknown]. 78 matched cddid_all.tbl CDD COG4747 COG4747 443781 ACTx2 ACT domain-containing protein [General function prediction only]. 129 matched cddid_all.tbl CDD COG4748 COG4748 443782 COG4748 Uncharacterized conserved protein, contains restriction enzyme R protein N terminal (HSDR_N) domain [Function unknown]. 355 matched cddid_all.tbl CDD COG4749 COG4749 443783 COG4749 Uncharacterized conserved protein, DUF2150 domain [Function unknown]. 203 matched cddid_all.tbl CDD COG4750 COG4750 443784 LicC CTP:phosphocholine cytidylyltransferase LicC [Cell wall/membrane/envelope biogenesis, Lipid transport and metabolism]. 228 matched cddid_all.tbl CDD COG4752 COG4752 443785 COG4752 Uncharacterized conserved protein [Function unknown]. 185 matched cddid_all.tbl CDD COG4753 COG4753 443786 YesN Two-component response regulator, YesN/AraC family, consists of REC and AraC-type DNA-binding domains [Signal transduction mechanisms, Transcription]. 103 matched cddid_all.tbl CDD COG4754 COG4754 443787 COG4754 Extracellular substrate-binding protein [General function prediction only]. 435 matched cddid_all.tbl CDD COG4755 COG4755 443788 COG4755 Uncharacterized conserved protein, DUF2153 domain [Function unknown]. 143 matched cddid_all.tbl CDD COG4756 COG4756 443789 COG4756 Predicted cation transporter [General function prediction only]. 346 matched cddid_all.tbl CDD COG4757 COG4757 443790 COG4757 Predicted alpha/beta hydrolase [General function prediction only]. 289 matched cddid_all.tbl CDD COG4758 COG4758 443791 LiaF Membrane protein LiaF, inhibitor of the LiaRS two-component envelope stress sensory system [Signal transduction mechanisms]. 235 matched cddid_all.tbl CDD COG4759 COG4759 443792 COG4759 Uncharacterized conserved protein, contains thioredoxin-like domain [General function prediction only]. 314 matched cddid_all.tbl CDD COG4760 COG4760 443793 COG4760 Uncharacterized membrane protein, YccA/Bax inhibitor family [Function unknown]. 250 matched cddid_all.tbl CDD COG4762 COG4762 443794 COG4762 Uncharacterized conserved protein, UPF0548 family [Function unknown]. 175 matched cddid_all.tbl CDD COG4763 COG4763 443795 YcfT Uncharacterized membrane protein YcfT [Function unknown]. 342 matched cddid_all.tbl CDD COG4764 COG4764 443796 SLT Predicted transglycosylase, contains SLT domain [General function prediction only]. 199 matched cddid_all.tbl CDD COG4765 COG4765 443797 COG4765 Uncharacterized conserved protein, DUF2155 domain [Function unknown]. 125 matched cddid_all.tbl CDD COG4766 COG4766 443798 EutQ Ethanolamine utilization protein EutQ, cupin superfamily (function unknown) [Amino acid transport and metabolism]. 123 matched cddid_all.tbl CDD COG4767 COG4767 443799 VanZ Glycopeptide antibiotics resistance protein [Defense mechanisms]. 91 matched cddid_all.tbl CDD COG4768 COG4768 443800 COG4768 Uncharacterized conserved protein YoxC, contains an MCP-like domain [Function unknown]. 132 matched cddid_all.tbl CDD COG4769 COG4769 443801 COG4769 Uncharacterized membrane protein [Function unknown]. 161 matched cddid_all.tbl CDD COG4770 COG4770 443802 PccA Acetyl/propionyl-CoA carboxylase, alpha subunit [Lipid transport and metabolism]. 466 matched cddid_all.tbl CDD COG4771 COG4771 443803 FepA Outer membrane receptor for ferrienterochelin and colicins [Inorganic ion transport and metabolism]. 612 matched cddid_all.tbl CDD COG4772 COG4772 443804 FecA Outer membrane receptor for Fe3+-dicitrate [Inorganic ion transport and metabolism]. 681 matched cddid_all.tbl CDD COG4773 COG4773 443805 FhuE Outer membrane receptor for ferric coprogen and ferric-rhodotorulic acid [Inorganic ion transport and metabolism]. 692 matched cddid_all.tbl CDD COG4774 COG4774 443806 Fiu Outer membrane receptor for monomeric catechols [Inorganic ion transport and metabolism]. 639 matched cddid_all.tbl CDD COG4775 COG4775 443807 BamA Outer membrane protein assembly factor BamA [Cell wall/membrane/envelope biogenesis]. 711 matched cddid_all.tbl CDD COG4776 COG4776 443808 Rnb Exoribonuclease II [Transcription]. 644 matched cddid_all.tbl CDD COG4778 COG4778 443809 PhnL Alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit PhnL [Inorganic ion transport and metabolism]. 229 matched cddid_all.tbl CDD COG4779 COG4779 443810 FepG ABC-type enterobactin transport system, permease component [Inorganic ion transport and metabolism]. 344 matched cddid_all.tbl CDD COG4781 COG4781 443811 UgpQ1 Membrane-anchored glycerophosphoryl diester phosphodiesterase (GDPDase), membrane domain [Lipid transport and metabolism]. 575 matched cddid_all.tbl CDD COG4782 COG4782 443812 COG4782 Esterase/lipase superfamily enzyme [General function prediction only]. 357 matched cddid_all.tbl CDD COG4783 COG4783 443813 BepA Outer membrane protein chaperone/metalloprotease BepA/YfgC, contains M48 and TPR domains [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones]. 139 matched cddid_all.tbl CDD COG4784 COG4784 443814 COG4784 Putative Zn-dependent protease [General function prediction only]. 488 matched cddid_all.tbl CDD COG4785 COG4785 443815 NlpI Lipoprotein NlpI, contains TPR repeats [Cell wall/membrane/envelope biogenesis]. 223 matched cddid_all.tbl CDD COG4786 COG4786 443816 FlgG Flagellar basal body rod protein FlgG [Cell motility]. 260 matched cddid_all.tbl CDD COG4787 COG4787 443817 FlgF Flagellar basal body rod protein FlgF [Cell motility]. 246 matched cddid_all.tbl CDD COG4789 COG4789 443818 EscV Type III secretory pathway, component EscV [Intracellular trafficking, secretion, and vesicular transport]. 688 matched cddid_all.tbl CDD COG4790 COG4790 443819 EscR Type III secretory pathway, EscR/YscR component [Intracellular trafficking, secretion, and vesicular transport]. 216 matched cddid_all.tbl CDD COG4791 COG4791 443820 EscT Type III secretory pathway, EscT/YscT component [Intracellular trafficking, secretion, and vesicular transport]. 255 matched cddid_all.tbl CDD COG4792 COG4792 443821 EscU Type III secretory pathway, EscU/YscU component [Intracellular trafficking, secretion, and vesicular transport]. 344 matched cddid_all.tbl CDD COG4794 COG4794 443822 EscS Type III secretory pathway, EscS/YscS component [Intracellular trafficking, secretion, and vesicular transport]. 88 matched cddid_all.tbl CDD COG4795 COG4795 443823 PulJ Type II secretory pathway, PulJ/GspJ component [Intracellular trafficking, secretion, and vesicular transport]. 118 matched cddid_all.tbl CDD COG4796 COG4796 443824 HofQ Type II secretory pathway, component HofQ [Intracellular trafficking, secretion, and vesicular transport]. 570 matched cddid_all.tbl CDD COG4797 COG4797 443825 COG4797 Predicted regulatory domain of a methyltransferase [General function prediction only]. 460 matched cddid_all.tbl CDD COG4798 COG4798 443826 COG4798 Predicted methyltransferase [General function prediction only]. 274 matched cddid_all.tbl CDD COG4799 COG4799 443827 MmdA Acetyl-CoA carboxylase, carboxyltransferase component [Lipid transport and metabolism]. 508 matched cddid_all.tbl CDD COG4800 COG4800 443828 COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]. 173 matched cddid_all.tbl CDD COG4801 COG4801 443829 COG4801 Predicted acyltransferase, contains DUF342 domain [General function prediction only]. 283 matched cddid_all.tbl CDD COG4802 COG4802 443830 FtrB Ferredoxin-thioredoxin reductase, catalytic subunit [Energy production and conversion]. 118 matched cddid_all.tbl CDD COG4803 COG4803 443831 COG4803 Uncharacterized membrane protein [Function unknown]. 161 matched cddid_all.tbl CDD COG4804 COG4804 443832 YhcG Predicted nuclease of restriction endonuclease-like (RecB) superfamily, DUF1016 family [General function prediction only]. 341 matched cddid_all.tbl CDD COG4805 COG4805 443833 COG4805 Uncharacterized conserved protein, DUF885 family [Function unknown]. 587 matched cddid_all.tbl CDD COG4806 COG4806 443834 RhaA L-rhamnose isomerase [Carbohydrate transport and metabolism]. 420 matched cddid_all.tbl CDD COG4807 COG4807 443835 YehS Uncharacterized conserved protein YehS, DUF1456 family [Function unknown]. 153 matched cddid_all.tbl CDD COG4808 COG4808 443836 YehR Uncharacterized lipoprotein YehR, DUF1307 family [Function unknown]. 152 matched cddid_all.tbl CDD COG4809 COG4809 443837 Pfk2 Archaeal ADP-dependent glucokinase/phosphofructokinase [Carbohydrate transport and metabolism]. Archaeal ADP-dependent glucokinase/phosphofructokinase is part of the Pathway/BioSystem: Glycolysis 456 matched cddid_all.tbl CDD COG4810 COG4810 443838 EutS Ethanolamine utilization protein EutS, microcompartment shell protein [Amino acid transport and metabolism]. 117 matched cddid_all.tbl CDD COG4811 COG4811 443839 YobD Uncharacterized membrane protein YobD, UPF0266 family [Function unknown]. 150 matched cddid_all.tbl CDD COG4812 COG4812 443840 EutT Ethanolamine utilization protein EutT, cobalamin adenosyltransferase [Amino acid transport and metabolism]. 258 matched cddid_all.tbl CDD COG4813 COG4813 443841 ThuA Trehalose utilization protein [Carbohydrate transport and metabolism]. 244 matched cddid_all.tbl CDD COG4814 COG4814 443842 COG4814 Uncharacterized conserved protein with an alpha/beta hydrolase fold [Function unknown]. 286 matched cddid_all.tbl CDD COG4815 COG4815 443843 COG4815 Uncharacterized conserved protein [Function unknown]. 148 matched cddid_all.tbl CDD COG4816 COG4816 443844 EutL Ethanolamine utilization protein EutL, microcompartment shell protein [Amino acid transport and metabolism]. 216 matched cddid_all.tbl CDD COG4817 COG4817 443845 GINS DNA-binding ferritin-like protein (Dps family) [Replication, recombination and repair]. 117 matched cddid_all.tbl CDD COG4818 COG4818 443846 COG4818 Uncharacterized membrane protein MJ1443, UPF0132 family [Function unknown]. 105 matched cddid_all.tbl CDD COG4819 COG4819 443847 EutA Ethanolamine utilization protein EutA, possible chaperonin [Amino acid transport and metabolism]. 477 matched cddid_all.tbl CDD COG4820 COG4820 443848 EutJ Ethanolamine utilization protein EutJ, possible chaperonin [Amino acid transport and metabolism]. 270 matched cddid_all.tbl CDD COG4821 COG4821 443849 COG4821 Uncharacterized conserved protein, contains SIS (Sugar ISomerase) phosphosugar binding domain [General function prediction only]. 250 matched cddid_all.tbl CDD COG4822 COG4822 443850 CbiK Cobalamin biosynthesis protein CbiK, Co2+ chelatase [Coenzyme transport and metabolism]. Cobalamin biosynthesis protein CbiK, Co2+ chelatase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis 265 matched cddid_all.tbl CDD COG4823 COG4823 443851 AbiF Abortive infection bacteriophage resistance protein [Defense mechanisms]. 295 matched cddid_all.tbl CDD COG4824 COG4824 443852 COG4824 Phage-related holin (Lysis protein) [Mobilome: prophages, transposons]. 135 matched cddid_all.tbl CDD COG4825 COG4825 443853 MT1736 Uncharacterized conserved protein, contains thiamine pyrophosphokinase N- and C- domains [General function prediction only]. 386 matched cddid_all.tbl CDD COG4826 COG4826 443854 SERPIN Serine protease inhibitor [Posttranslational modification, protein turnover, chaperones]. 411 matched cddid_all.tbl CDD COG4827 COG4827 443855 COG4827 Predicted transporter [General function prediction only]. 231 matched cddid_all.tbl CDD COG4828 COG4828 443856 COG4828 Uncharacterized membrane protein [Function unknown]. 114 matched cddid_all.tbl CDD COG4829 COG4829 443857 CatC1 Muconolactone delta-isomerase [Secondary metabolites biosynthesis, transport and catabolism]. 96 matched cddid_all.tbl CDD COG4830 COG4830 443858 RPS26B Ribosomal protein S26e [Translation, ribosomal structure and biogenesis]. Ribosomal protein S26e is part of the Pathway/BioSystem: Archaeal ribosomal proteins 94 matched cddid_all.tbl CDD COG4831 COG4831 443859 COG4831 Roadblock/LC7 domain [Signal transduction mechanisms]. 108 matched cddid_all.tbl CDD COG4832 COG4832 443860 MA1133 Cyclopropanoid cyclopropyl hydrolase, GyrI-like domain [Defense mechanisms, Signal transduction mechanisms]. 202 matched cddid_all.tbl CDD COG4833 COG4833 443861 COG4833 Predicted alpha-1,6-mannanase, GH76 family [Carbohydrate transport and metabolism]. 348 matched cddid_all.tbl CDD COG4834 COG4834 443862 COG4834 Uncharacterized conserved protein, DUF2184 domain [Function unknown]. 314 matched cddid_all.tbl CDD COG4835 COG4835 443863 COG4835 Uncharacterized conserved protein [Function unknown]. 123 matched cddid_all.tbl CDD COG4836 COG4836 443864 YwzB Uncharacterized membrane protein YwzB [Function unknown]. 75 matched cddid_all.tbl CDD COG4837 COG4837 443865 YuzD Disulfide oxidoreductase YuzD [Posttranslational modification, protein turnover, chaperones]. 99 matched cddid_all.tbl CDD COG4838 COG4838 443866 YlaN Uncharacterized conserved protein YlaN, UPF0358 family [Function unknown]. 90 matched cddid_all.tbl CDD COG4839 COG4839 443867 FtsL2 Cell division protein FtsL [Cell cycle control, cell division, chromosome partitioning]. 123 matched cddid_all.tbl CDD COG4840 COG4840 443868 YfkK Uncharacterized conserved protein YfkK, UPF0435 family [Function unknown]. 74 matched cddid_all.tbl CDD COG4841 COG4841 443869 YneR Uncharacterized conserved protein YneR, related to HesB/YadR/YfhF family [Function unknown]. 95 matched cddid_all.tbl CDD COG4842 COG4842 443870 EsxA Secreted virulence factor YukE/EsxA, WXG100 family [Defense mechanisms]. 93 matched cddid_all.tbl CDD COG4843 COG4843 443871 YebE Uncharacterized conserved protein YebE, UPF0316/DUF2179 family [Function unknown]. 181 matched cddid_all.tbl CDD COG4844 COG4844 443872 YuzB Uncharacterized conserved protein YuzB, UPF0349 family [Function unknown]. 80 matched cddid_all.tbl CDD COG4845 COG4845 443873 CatA Chloramphenicol O-acetyltransferase [Defense mechanisms]. 210 matched cddid_all.tbl CDD COG4846 COG4846 443874 CcdC Cytochrome c biogenesis protein CcdC [Energy production and conversion, Posttranslational modification, protein turnover, chaperones]. 157 matched cddid_all.tbl CDD COG4847 COG4847 443875 COG4847 Uncharacterized conserved protein, DUF2175 family [Function unknown]. 106 matched cddid_all.tbl CDD COG4848 COG4848 443876 YtpQ YtpQ protein involved in methylglyoxal resistance, DUF1444/UPF0354 family [General function prediction only]. 186 matched cddid_all.tbl CDD COG4849 COG4849 443877 COG4849 Predicted nucleotidyltransferase [General function prediction only]. 283 matched cddid_all.tbl CDD COG4850 COG4850 443878 App1 Phosphatidate phosphatase APP1 [Lipid transport and metabolism]. 348 matched cddid_all.tbl CDD COG4851 COG4851 443879 CamS Uncharacterized conserved protein involved in sex pheromone biosynthesis [General function prediction only]. 384 matched cddid_all.tbl CDD COG4852 COG4852 443880 COG4852 Uncharacterized membrane protein [Function unknown]. 133 matched cddid_all.tbl CDD COG4853 COG4853 443881 YycI YycI protein, regulator of the WalKR two-component signal transduction system [Signal transduction mechanisms]. 259 matched cddid_all.tbl CDD COG4854 COG4854 443882 COG4854 Uncharacterized membrane protein AF1626, predicted component of bacteriocin or quorum sensing system, DUF2178 family [Function unknown]. 127 matched cddid_all.tbl CDD COG4855 COG4855 443883 COG4855 Uncharacterized conserved protein [Nucleotide transport and metabolism]. 70 matched cddid_all.tbl CDD COG4856 COG4856 443884 YbbR Cyclic di-AMP synthase regulator CdaR, YbbR domain [Signal transduction mechanisms]. 392 matched cddid_all.tbl CDD COG4857 COG4857 443885 MthN 5-Methylthioribose/5-deoxyribose kinase, methionine salvage pathway [Amino acid transport and metabolism]. 404 matched cddid_all.tbl CDD COG4858 COG4858 443886 COG4858 Uncharacterized membrane-anchored protein [Function unknown]. 230 matched cddid_all.tbl CDD COG4859 COG4859 443887 COG4859 Uncharacterized protein, contains DUF2185 domain [Function unknown]. 106 matched cddid_all.tbl CDD COG4860 COG4860 443888 COG4860 Predicted DNA-binding transcriptional regulator, ArsR family [Transcription]. 169 matched cddid_all.tbl CDD COG4861 COG4861 443889 COG4861 Uncharacterized conserved protein [Function unknown]. 333 matched cddid_all.tbl CDD COG4862 COG4862 443890 MecA Negative regulator MecA of genetic competence, sporulation and motility [Transcription, Signal transduction mechanisms, Cell motility]. 212 matched cddid_all.tbl CDD COG4863 COG4863 443891 YycH YycH protein, regulator of the WalKR two-component signal transduction system [Signal transduction mechanisms]. 442 matched cddid_all.tbl CDD COG4864 COG4864 443892 YqfA Uncharacterized conserved protein YqfA, UPF0365 family [Function unknown]. 330 matched cddid_all.tbl CDD COG4865 COG4865 443893 GlmE Glutamate mutase epsilon subunit [Amino acid transport and metabolism]. 483 matched cddid_all.tbl CDD COG4866 COG4866 443894 COG4866 Uncharacterized protein, contains DUF2156 domain [Function unknown]. 296 matched cddid_all.tbl CDD COG4867 COG4867 443895 COG4867 Uncharacterized conserved protein, contains von Willebrand factor type A (vWFA) domain [Function unknown]. 371 matched cddid_all.tbl CDD COG4868 COG4868 443896 COG4868 Uncharacterized conserved protein, UPF0371 family [Function unknown]. 493 matched cddid_all.tbl CDD COG4869 COG4869 443897 PduL Propanediol utilization protein [Secondary metabolites biosynthesis, transport and catabolism]. 210 matched cddid_all.tbl CDD COG4870 COG4870 443898 COG4870 Cysteine protease, C1A family [Posttranslational modification, protein turnover, chaperones]. 426 matched cddid_all.tbl CDD COG4871 COG4871 443899 COG4871 Metal-binding trascriptional regulator, contains Fe-S cluster and ArsR family DNA binding domain [Transcription]. 177 matched cddid_all.tbl CDD COG4872 COG4872 443900 COG4872 Uncharacterized membrane protein [Function unknown]. 361 matched cddid_all.tbl CDD COG4873 COG4873 443901 YkvS Uncharacterized conserved protein YkvS, DUF2187 family [Function unknown]. 68 matched cddid_all.tbl CDD COG4874 COG4874 443902 COG4874 Uncharacterized conserved protein [Function unknown]. 308 matched cddid_all.tbl CDD COG4875 COG4875 443903 CaMKIID Protein kinase association domain CaMKII_AD, NTF2-like superfamily [Posttranslational modification, protein turnover, chaperones]. 156 matched cddid_all.tbl CDD COG4876 COG4876 443904 YdaT Uncharacterized conserved protein YdaT [Function unknown]. 122 matched cddid_all.tbl CDD COG4877 COG4877 443905 COG4877 Uncharacterized conserved protein [Function unknown]. 62 matched cddid_all.tbl CDD COG4878 COG4878 443906 COG4878 Uncharacterized conserved protein, DUF2194 domain [Function unknown]. 600 matched cddid_all.tbl CDD COG4879 COG4879 443907 COG4879 Uncharacterized protein, contains DUF2192 domain [Function unknown]. 248 matched cddid_all.tbl CDD COG4880 COG4880 443908 COG4880 Secreted protein containing C-terminal beta-propeller domain distantly related to WD-40 repeats [General function prediction only]. 590 matched cddid_all.tbl CDD COG4881 COG4881 443909 COG4881 Predicted membrane anchor for polysulfide/nitrite-type reductase, PsrC/NrfD syperfamily [Inorganic ion transport and metabolism]. 386 matched cddid_all.tbl CDD COG4882 COG4882 443910 COG4882 Predicted aminopeptidase, Iap family [General function prediction only]. 480 matched cddid_all.tbl CDD COG4883 COG4883 443911 COG4883 Uncharacterized conserved protein, DUF2193 domain [Function unknown]. 499 matched cddid_all.tbl CDD COG4884 COG4884 443912 YfeS Uncharacterized conserved protein YfeS, contains WGR domain [Function unknown]. 172 matched cddid_all.tbl CDD COG4885 COG4885 443913 COG4885 Uncharacterized conserved protein [Function unknown]. 335 matched cddid_all.tbl CDD COG4886 COG4886 443914 LRR Leucine-rich repeat (LRR) protein [Transcription]. 414 matched cddid_all.tbl CDD COG4887 COG4887 443915 COG4887 Uncharacterized metal-binding protein MJ0455, DUF1847 family [Function unknown]. 211 matched cddid_all.tbl CDD COG4888 COG4888 443916 Elf1 Transcription elongation factor Elf1, contains Zn-ribbon domain [Transcription]. 109 matched cddid_all.tbl CDD COG4889 COG4889 443917 COG4889 Predicted helicase [General function prediction only]. 1571 matched cddid_all.tbl CDD COG4890 COG4890 443918 COG4890 Predicted outer membrane lipoprotein [Function unknown]. 38 matched cddid_all.tbl CDD COG4891 COG4891 443919 COG4891 Uncharacterized conserved protein [Function unknown]. 138 matched cddid_all.tbl CDD COG4892 COG4892 443920 COG4892 Predicted heme/steroid binding protein [General function prediction only]. 75 matched cddid_all.tbl CDD COG4893 COG4893 443921 COG4893 Uncharacterized conserved protein, DUF2195 domain [Function unknown]. 126 matched cddid_all.tbl CDD COG4894 COG4894 443922 YxjI Putative phospholipid scramblase YxjI, Tubby2 superfamily [Lipid transport and metabolism]. 163 matched cddid_all.tbl CDD COG4895 COG4895 443923 YwbE Uncharacterized conserved protein YwbE, DUF2196 family [Function unknown]. 64 matched cddid_all.tbl CDD COG4896 COG4896 443924 YlaI Uncharacterized conserved protein YlaI, DUF2197 family [Function unknown]. 66 matched cddid_all.tbl CDD COG4897 COG4897 443925 CsbA General stress protein CsbA (function unknown) [Function unknown]. 77 matched cddid_all.tbl CDD COG4898 COG4898 443926 COG4898 Uncharacterized conserved protein [Function unknown]. 115 matched cddid_all.tbl CDD COG4899 COG4899 443927 COG4899 Uncharacterized conserved protein, DUF2199 domain [Function unknown]. 169 matched cddid_all.tbl CDD COG4900 COG4900 443928 COG4900 Predicted metallopeptidase [General function prediction only]. 124 matched cddid_all.tbl CDD COG4901 COG4901 443929 RPS25 Ribosomal protein S25e [Translation, ribosomal structure and biogenesis]. Ribosomal protein S25e is part of the Pathway/BioSystem: Archaeal ribosomal proteins 108 matched cddid_all.tbl CDD COG4902 COG4902 443930 MJ0754 Ferritin-like protein MJ0754, DUF2202 family [General function prediction only]. 202 matched cddid_all.tbl CDD COG4903 COG4903 443931 ComK Competence transcription factor ComK [Transcription]. 171 matched cddid_all.tbl CDD COG4904 COG4904 443932 COG4904 Uncharacterized conserved protein [Function unknown]. 178 matched cddid_all.tbl CDD COG4905 COG4905 443933 COG4905 Uncharacterized membrane protein [Function unknown]. 179 matched cddid_all.tbl CDD COG4906 COG4906 443934 COG4906 Uncharacterized membrane protein [Function unknown]. 719 matched cddid_all.tbl CDD COG4907 COG4907 443935 COG4907 Uncharacterized membrane protein [Function unknown]. 601 matched cddid_all.tbl CDD COG4908 COG4908 443936 COG4908 Uncharacterized conserved protein, contains a NRPS condensation (elongation) domain [General function prediction only]. 243 matched cddid_all.tbl CDD COG4909 COG4909 443937 PduC Propanediol dehydratase, large subunit [Secondary metabolites biosynthesis, transport and catabolism]. 554 matched cddid_all.tbl CDD COG4910 COG4910 443938 PduE Propanediol dehydratase, small subunit [Secondary metabolites biosynthesis, transport and catabolism]. 167 matched cddid_all.tbl CDD COG4911 COG4911 443939 COG4911 Uncharacterized conserved protein, DUF2203 domain [Function unknown]. 129 matched cddid_all.tbl CDD COG4912 COG4912 443940 AlkD 3-methyladenine DNA glycosylase AlkD [Replication, recombination and repair]. 216 matched cddid_all.tbl CDD COG4913 COG4913 443941 COG4913 Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]. 1089 matched cddid_all.tbl CDD COG4914 COG4914 443942 COG4914 Predicted nucleotidyltransferase [General function prediction only]. 188 matched cddid_all.tbl CDD COG4915 COG4915 443943 XpaC 5-bromo-4-chloroindolyl phosphatase XpaC [Secondary metabolites biosynthesis, transport and catabolism, General function prediction only]. 208 matched cddid_all.tbl CDD COG4916 COG4916 443944 COG4916 Uncharacterized conserved protein [Function unknown]. 236 matched cddid_all.tbl CDD COG4917 COG4917 443945 EutP Ethanolamine utilization protein EutP, contains a P-loop NTPase domain [Amino acid transport and metabolism]. 145 matched cddid_all.tbl CDD COG4918 COG4918 443946 YqkB Predicted Fe-S cluster biosynthesis protein YqkB [General function prediction only]. 112 matched cddid_all.tbl CDD COG4919 COG4919 443947 RPS30 Ribosomal protein S30 [Translation, ribosomal structure and biogenesis]. Ribosomal protein S30 is part of the Pathway/BioSystem: Archaeal ribosomal proteins 52 matched cddid_all.tbl CDD COG4920 COG4920 443948 COG4920 Uncharacterized membrane protein [Function unknown]. 252 matched cddid_all.tbl CDD COG4921 COG4921 443949 COG4921 Uncharacterized conserved protein, DUF2209 domain [Function unknown]. 129 matched cddid_all.tbl CDD COG4922 COG4922 443950 COG4922 Predicted SnoaL-like aldol condensation-catalyzing enzyme [General function prediction only]. 129 matched cddid_all.tbl CDD COG4923 COG4923 443951 COG4923 Predicted nuclease (RNAse H fold) [General function prediction only]. 240 matched cddid_all.tbl CDD COG4924 COG4924 443952 COG4924 Uncharacterized conserved protein [Function unknown]. 384 matched cddid_all.tbl CDD COG4925 COG4925 443953 COG4925 Uncharacterized conserved protein [Function unknown]. 125 matched cddid_all.tbl CDD COG4926 COG4926 443954 PblB Phage-related protein [Mobilome: prophages, transposons]. 438 matched cddid_all.tbl CDD COG4927 COG4927 443955 COG4927 Predicted choloylglycine hydrolase [General function prediction only]. 242 matched cddid_all.tbl CDD COG4928 COG4928 443956 COG4928 Predicted P-loop ATPase, KAP-like [General function prediction only]. 386 matched cddid_all.tbl CDD COG4929 COG4929 443957 COG4929 Uncharacterized membrane-anchored protein [Function unknown]. 178 matched cddid_all.tbl CDD COG4930 COG4930 443958 COG4930 Predicted ATP-dependent Lon-type protease [Posttranslational modification, protein turnover, chaperones]. 672 matched cddid_all.tbl CDD COG4932 COG4932 443959 ClfA Clumping factor A-related surface protein, MSCRAMM (microbial surface components recognizing adhesive matrix molecules) family, DEv-IgG fold [Cell wall/membrane/envelope biogenesis]. 689 matched cddid_all.tbl CDD COG4933 COG4933 443960 COG4933 Predicted transcriptional regulator, contains an HTH and PUA-like domains [Transcription]. 137 matched cddid_all.tbl CDD COG4934 COG4934 443961 COG4934 Serine protease, subtilase family [Posttranslational modification, protein turnover, chaperones]. 519 matched cddid_all.tbl CDD COG4935 COG4935 443962 COG4935 Regulatory P domain of the subtilisin-like proprotein convertases and other proteases [Posttranslational modification, protein turnover, chaperones]. 641 matched cddid_all.tbl CDD COG4936 COG4936 443963 PocR Ligand-binding sensor domain [Signal transduction mechanisms]. 415 matched cddid_all.tbl CDD COG4937 COG4937 443964 FDXACB Ferredoxin-fold anticodon binding domain [Translation, ribosomal structure and biogenesis]. 443 matched cddid_all.tbl CDD COG4938 COG4938 443965 COG4938 Predicted ATPase [General function prediction only]. 277 matched cddid_all.tbl CDD COG4939 COG4939 443966 Tpp15 Membrane-anchored lipoprotein Tpp15, major membrane immunogen [Function unknown]. 115 matched cddid_all.tbl CDD COG4940 COG4940 443967 ComGF Competence protein ComGF [Mobilome: prophages, transposons]. 153 matched cddid_all.tbl CDD COG4941 COG4941 443968 COG4941 Predicted RNA polymerase sigma factor, contains C-terminal TPR domain [Transcription]. 412 matched cddid_all.tbl CDD COG4942 COG4942 443969 EnvC Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]. 377 matched cddid_all.tbl CDD COG4943 COG4943 443970 YjcC Redox-sensing c-di-GMP phosphodiesterase, contains CSS-motif and EAL domains [Signal transduction mechanisms]. 528 matched cddid_all.tbl CDD COG4944 COG4944 443971 COG4944 Uncharacterized conserved protein [Function unknown]. 213 matched cddid_all.tbl CDD COG4945 COG4945 443972 DOMON Carbohydrate-binding DOMON domain [Carbohydrate transport and metabolism, Signal transduction mechanisms]. 689 matched cddid_all.tbl CDD COG4946 COG4946 443973 COG4946 Uncharacterized N-terminal domain of tricorn protease, contains WD40 repeats [Function unknown]. 1072 matched cddid_all.tbl CDD COG4947 COG4947 443974 COG4947 Esterase/lipase superfamily enzyme [General function prediction only]. 244 matched cddid_all.tbl CDD COG4948 COG4948 443975 RspA L-alanine-DL-glutamate epimerase or related enzyme of enolase superfamily [Cell wall/membrane/envelope biogenesis, General function prediction only]. L-alanine-DL-glutamate epimerase or related enzyme of enolase superfamily is part of the Pathway/BioSystem: Non-phosphorylated Entner-Doudoroff pathway 359 matched cddid_all.tbl CDD COG4949 COG4949 443976 COG4949 Uncharacterized membrane-anchored protein [Function unknown]. 428 matched cddid_all.tbl CDD COG4950 COG4950 443977 YciW1 N-terminal domain of uncharacterized protein YciW (function unknown) [Function unknown]. 177 matched cddid_all.tbl CDD COG4951 COG4951 443978 COG4951 Uncharacterized conserved protein [Function unknown]. 793 matched cddid_all.tbl CDD COG4952 COG4952 443979 COG4952 L-rhamnose isomerase [Cell wall/membrane/envelope biogenesis]. 408 matched cddid_all.tbl CDD COG4953 COG4953 443980 PbpC Membrane carboxypeptidase/penicillin-binding protein PbpC [Cell wall/membrane/envelope biogenesis]. 773 matched cddid_all.tbl CDD COG4954 COG4954 443981 COG4954 Uncharacterized conserved protein, DUF2000 domain [Function unknown]. 134 matched cddid_all.tbl CDD COG4955 COG4955 443982 YpbB Uncharacterized conserved protein YpbB, contains C-terminal HTH domain [Function unknown]. 346 matched cddid_all.tbl CDD COG4956 COG4956 443983 COG4956 Uncharacterized conserved protein YacL, contains PIN and TRAM domains [General function prediction only]. 355 matched cddid_all.tbl CDD COG4957 COG4957 443984 COG4957 Predicted transcriptional regulator [Transcription]. 141 matched cddid_all.tbl CDD COG4959 COG4959 443985 TraF Type IV secretory pathway, protease TraF [Posttranslational modification, protein turnover, chaperones, Intracellular trafficking, secretion, and vesicular transport]. 114 matched cddid_all.tbl CDD COG4960 COG4960 443986 CpaA Flp pilus assembly protein, peptidase CpaA [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms]. 161 matched cddid_all.tbl CDD COG4961 COG4961 443987 TadG Flp pilus assembly protein TadG, includes N-terminal TadE domain [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures]. 152 matched cddid_all.tbl CDD COG4962 COG4962 443988 CpaF Pilus assembly protein, ATPase of CpaF family [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures]. 386 matched cddid_all.tbl CDD COG4963 COG4963 443989 CpaE Flp pilus assembly ATPase CpaE/TadZ, contains N-terminal REC/TadZ_N domain [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures]. 358 matched cddid_all.tbl CDD COG4964 COG4964 443990 CpaC Flp pilus assembly protein, secretin CpaC [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures]. 456 matched cddid_all.tbl CDD COG4965 COG4965 443991 TadB Flp pilus assembly protein TadB [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures]. 214 matched cddid_all.tbl CDD COG4966 COG4966 443992 PilW Type IV pilus assembly protein PilW [Cell motility, Extracellular structures]. 158 matched cddid_all.tbl CDD COG4967 COG4967 443993 PilV Type IV pilus assembly protein PilV [Cell motility, Extracellular structures]. 86 matched cddid_all.tbl CDD COG4968 COG4968 443994 PilE Type IV pilus assembly protein PilE [Cell motility, Extracellular structures]. 124 matched cddid_all.tbl CDD COG4969 COG4969 443995 PilA Type IV pilus assembly protein, major pilin PilA [Cell motility, Extracellular structures]. 134 matched cddid_all.tbl CDD COG4970 COG4970 443996 FimT Type IV pilus assembly protein FimT [Cell motility, Extracellular structures]. 73 matched cddid_all.tbl CDD COG4972 COG4972 443997 PilM Type IV pilus assembly protein, ATPase PilM [Cell motility, Extracellular structures]. 294 matched cddid_all.tbl CDD COG4973 COG4973 443998 XerC Site-specific recombinase XerC [Replication, recombination and repair]. 287 matched cddid_all.tbl CDD COG4974 COG4974 443999 XerD Site-specific recombinase XerD [Replication, recombination and repair]. 291 matched cddid_all.tbl CDD COG4975 COG4975 444000 GlcU Glucose uptake protein GlcU [Carbohydrate transport and metabolism]. 288 matched cddid_all.tbl CDD COG4976 COG4976 444001 COG4976 Predicted methyltransferase, contains TPR repeat [General function prediction only]. 181 matched cddid_all.tbl CDD COG4977 COG4977 444002 GlxA Transcriptional regulator GlxA, contains an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]. 318 matched cddid_all.tbl CDD COG4978 COG4978 444003 BltR2 GyrI-like small molecule binding domain [Signal transduction mechanisms]. 144 matched cddid_all.tbl CDD COG4980 COG4980 444004 GvpP Gas vesicle protein YhaH [General function prediction only]. 106 matched cddid_all.tbl CDD COG4981 COG4981 444005 COG4981 Enoyl reductase domain of yeast-type fatty acid synthase [Lipid transport and metabolism]. 3064 matched cddid_all.tbl CDD COG4982 COG4982 444006 FabG2 3-oxoacyl-ACP reductase domain of yeast-type fatty acid synthase FAS1 [Lipid transport and metabolism]. 3088 matched cddid_all.tbl CDD COG4983 COG4983 444007 COG4983 Primase-polymerase (Primpol) domain protein [Mobilome: prophages, transposons]. 511 matched cddid_all.tbl CDD COG4984 COG4984 444008 COG4984 Uncharacterized membrane protein [Function unknown]. 319 matched cddid_all.tbl CDD COG4985 COG4985 444009 PstA ABC-type phosphate transport system, auxiliary component PstA [Inorganic ion transport and metabolism]. 545 matched cddid_all.tbl CDD COG4986 COG4986 444010 COG4986 ABC-type anion transport system, duplicated permease component [Inorganic ion transport and metabolism]. 576 matched cddid_all.tbl CDD COG4987 COG4987 444011 CydC ABC-type transport system involved in cytochrome bd biosynthesis, fused ATPase and permease components [Energy production and conversion, Posttranslational modification, protein turnover, chaperones]. 569 matched cddid_all.tbl CDD COG4988 COG4988 444012 CydD ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion, Posttranslational modification, protein turnover, chaperones]. 563 matched cddid_all.tbl CDD COG4989 COG4989 444013 YdhF Predicted oxidoreductase YdhF [General function prediction only]. 299 matched cddid_all.tbl CDD COG4990 COG4990 444014 YvpB Predicted cysteine peptidase, C39 family [General function prediction only]. 303 matched cddid_all.tbl CDD COG4991 COG4991 444015 YraI Uncharacterized conserved protein YraI [Function unknown]. 92 matched cddid_all.tbl CDD COG4992 COG4992 444016 ArgD Acetylornithine/succinyldiaminopimelate/putrescine aminotransferase [Amino acid transport and metabolism]. Acetylornithine/succinyldiaminopimelate/putrescine aminotransferase is part of the Pathway/BioSystem: Arginine biosynthesis 396 matched cddid_all.tbl CDD COG4993 COG4993 444017 Gcd Glucose dehydrogenase, PQQ-dependent [Carbohydrate transport and metabolism]. 515 matched cddid_all.tbl CDD COG4994 COG4994 444018 COG4994 Uncharacterized protein CV0675, UCP033623 family [Function unknown]. 121 matched cddid_all.tbl CDD COG4995 COG4995 444019 COG4995 Uncharacterized conserved protein, contains CHAT domain [Function unknown]. 711 matched cddid_all.tbl CDD COG4996 COG4996 444020 COG4996 Predicted phosphatase [General function prediction only]. 165 matched cddid_all.tbl CDD COG4997 COG4997 444021 COG4997 Predicted house-cleaning noncanonical NTP pyrophosphatase, all-alpha NTP-PPase (MazG) superfamily [General function prediction only]. 108 matched cddid_all.tbl CDD COG4998 COG4998 444022 RecB2 Predicted endonuclease, RecB family [Replication, recombination and repair]. 223 matched cddid_all.tbl CDD COG4999 COG4999 444023 BarA5 Uncharacterized domain of signal transduction histidine kinase BarA [Signal transduction mechanisms]. 921 matched cddid_all.tbl CDD COG5000 COG5000 444024 NtrY Signal transduction histidine kinase NtrY involved in nitrogen fixation and metabolism regulation [Signal transduction mechanisms]. 422 matched cddid_all.tbl CDD COG5001 COG5001 444025 COG5001 Cyclic di-GMP metabolism protein, combines GGDEF and EAL domains with a 6TM membrane domain [Signal transduction mechanisms]. 678 matched cddid_all.tbl CDD COG5002 COG5002 444026 WalK Sensor histidine kinase WalK [Signal transduction mechanisms]. 390 matched cddid_all.tbl CDD COG5003 COG5003 444027 gp37 Mu-like prophage protein gp37 [Mobilome: prophages, transposons]. 143 matched cddid_all.tbl CDD COG5004 COG5004 444028 gpX P2-like prophage tail protein X [Mobilome: prophages, transposons]. 69 matched cddid_all.tbl CDD COG5005 COG5005 444029 gpG Mu-like prophage protein gpG [Mobilome: prophages, transposons]. 146 matched cddid_all.tbl CDD COG5006 COG5006 444030 RhtA Threonine/homoserine efflux transporter RhtA [Amino acid transport and metabolism]. 290 matched cddid_all.tbl CDD COG5007 COG5007 444031 IbaG Acid stress protein IbaG/YrbA, BolA-like family [Signal transduction mechanisms]. 81 matched cddid_all.tbl CDD COG5008 COG5008 444032 PilU Type IV pilus assembly protein, ATPase PilU [Cell motility, Extracellular structures]. 370 matched cddid_all.tbl CDD COG5009 COG5009 444033 MrcA Membrane carboxypeptidase/penicillin-binding protein [Cell wall/membrane/envelope biogenesis]. 785 matched cddid_all.tbl CDD COG5010 COG5010 444034 TadD Flp pilus assembly protein TadD, contains TPR repeats [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures]. 155 matched cddid_all.tbl CDD COG5011 COG5011 444035 COG5011 Uncharacterized conserved protein, DUF2344 family [Function unknown]. 213 matched cddid_all.tbl CDD COG5012 COG5012 444036 MtbC1 Methanogenic corrinoid protein MtbC1 [Energy production and conversion]. 219 matched cddid_all.tbl CDD COG5013 COG5013 444037 NarG Nitrate reductase alpha subunit [Energy production and conversion, Inorganic ion transport and metabolism]. 1231 matched cddid_all.tbl CDD COG5014 COG5014 444038 TM0948 Uncharacterized conserved protein TM0948, MoaA-related, radical SAM superfamily [General function prediction only]. 261 matched cddid_all.tbl CDD COG5015 COG5015 444039 COG5015 Pyridoxamine 5'-phosphate oxidase (PNPOx-like) family protein [General function prediction only]. 130 matched cddid_all.tbl CDD COG5016 COG5016 444040 OadA1 Pyruvate/oxaloacetate carboxyltransferase [Energy production and conversion]. Pyruvate/oxaloacetate carboxyltransferase is part of the Pathway/BioSystem: Urea cycle 540 matched cddid_all.tbl CDD COG5017 COG5017 444041 COG5017 UDP-N-acetylglucosamine transferase subunit ALG13 [Carbohydrate transport and metabolism]. 164 matched cddid_all.tbl CDD COG5018 COG5018 444042 KapD 3'-5' exonuclease KapD, inhibitor of KinA-controlled sporulation [Signal transduction mechanisms]. 181 matched cddid_all.tbl CDD COG5019 COG5019 227352 CDC3 Septin family protein [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]. 373 matched cddid_all.tbl CDD COG5020 COG5020 227353 KTR1 Mannosyltransferase [Carbohydrate transport and metabolism]. 399 matched cddid_all.tbl CDD COG5021 COG5021 227354 HUL4 Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]. 872 matched cddid_all.tbl CDD COG5022 COG5022 227355 COG5022 Myosin heavy chain [General function prediction only]. 1463 matched cddid_all.tbl CDD COG5023 COG5023 444043 COG5023 Tubulin [Cytoskeleton]. 491 matched cddid_all.tbl CDD COG5024 COG5024 227357 COG5024 Cyclin [Cell division and chromosome partitioning]. 440 matched cddid_all.tbl CDD COG5025 COG5025 227358 COG5025 Transcription factor of the Forkhead/HNF3 family [Transcription]. 610 matched cddid_all.tbl CDD COG5026 COG5026 444044 COG5026 Hexokinase [Carbohydrate transport and metabolism]. Hexokinase is part of the Pathway/BioSystem: Glycolysis 434 matched cddid_all.tbl CDD COG5027 COG5027 227360 SAS2 Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]. 395 matched cddid_all.tbl CDD COG5028 COG5028 227361 COG5028 Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]. 861 matched cddid_all.tbl CDD COG5029 COG5029 444045 CAL1 Prenyltransferase, beta subunit [Posttranslational modification, protein turnover, chaperones, Lipid transport and metabolism]. 259 matched cddid_all.tbl CDD COG5030 COG5030 227363 APS2 Clathrin adaptor complex, small subunit [Intracellular trafficking and secretion]. 152 matched cddid_all.tbl CDD COG5031 COG5031 444046 COQ4 Ubiquinone biosynthesis protein Coq4 [Coenzyme transport and metabolism]. Ubiquinone biosynthesis protein Coq4 is part of the Pathway/BioSystem: Ubiquinone biosynthesis 232 matched cddid_all.tbl CDD COG5032 COG5032 227365 TEL1 Phosphatidylinositol kinase or protein kinase, PI-3 family [Signal transduction mechanisms]. 2105 matched cddid_all.tbl CDD COG5033 COG5033 227366 TFG3 Transcription initiation factor IIF, auxiliary subunit [Transcription]. 225 matched cddid_all.tbl CDD COG5034 COG5034 227367 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]. 271 matched cddid_all.tbl CDD COG5035 COG5035 227368 CDC50 Cell cycle control protein [Cell division and chromosome partitioning / Transcription / Signal transduction mechanisms]. 372 matched cddid_all.tbl CDD COG5036 COG5036 444047 COG5036 SPX domain-containing protein involved in vacuolar polyphosphate accumulation [Inorganic ion transport and metabolism, Intracellular trafficking, secretion, and vesicular transport]. 241 matched cddid_all.tbl CDD COG5037 COG5037 227370 TOS9 Gluconate transport-inducing protein [Signal transduction mechanisms / Carbohydrate transport and metabolism]. 248 matched cddid_all.tbl CDD COG5038 COG5038 227371 COG5038 Ca2+-dependent lipid-binding protein, contains C2 domain [General function prediction only]. 1227 matched cddid_all.tbl CDD COG5039 COG5039 444048 EpsI Exopolysaccharide biosynthesis protein EpsI, predicted pyruvyl transferase [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis]. 330 matched cddid_all.tbl CDD COG5040 COG5040 227373 BMH1 14-3-3 family protein [Signal transduction mechanisms]. 268 matched cddid_all.tbl CDD COG5041 COG5041 227374 SKB2 Casein kinase II, beta subunit [Signal transduction mechanisms / Cell division and chromosome partitioning / Transcription]. 242 matched cddid_all.tbl CDD COG5042 COG5042 444049 NUP Purine nucleoside permease [Nucleotide transport and metabolism]. 356 matched cddid_all.tbl CDD COG5043 COG5043 227376 MRS6 Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]. 2552 matched cddid_all.tbl CDD COG5044 COG5044 227377 MRS6 RAB proteins geranylgeranyltransferase component A (RAB escort protein) [Posttranslational modification, protein turnover, chaperones]. 434 matched cddid_all.tbl CDD COG5045 COG5045 227378 COG5045 Ribosomal protein S10E [Translation, ribosomal structure and biogenesis]. 105 matched cddid_all.tbl CDD COG5046 COG5046 227379 MAF1 Protein involved in Mod5 protein sorting [Posttranslational modification, protein turnover, chaperones]. 282 matched cddid_all.tbl CDD COG5047 COG5047 227380 SEC23 Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking and secretion]. 755 matched cddid_all.tbl CDD COG5048 COG5048 227381 COG5048 FOG: Zn-finger [General function prediction only]. 467 matched cddid_all.tbl CDD COG5049 COG5049 227382 XRN1 5'-3' exonuclease [Replication, recombination and repair]. 953 matched cddid_all.tbl CDD COG5050 COG5050 444050 EPT1 sn-1,2-diacylglycerol ethanolamine- and cholinephosphotranferases [Lipid transport and metabolism]. 176 matched cddid_all.tbl CDD COG5051 COG5051 227384 RPL36A Ribosomal protein L36E [Translation, ribosomal structure and biogenesis]. 97 matched cddid_all.tbl CDD COG5052 COG5052 227385 YOP1 Protein involved in membrane traffic [Intracellular trafficking and secretion]. 186 matched cddid_all.tbl CDD COG5053 COG5053 227386 CDC33 Translation initiation factor 4E (eIF-4E) [Translation, ribosomal structure and biogenesis]. 217 matched cddid_all.tbl CDD COG5054 COG5054 227387 ERV1 Mitochondrial sulfhydryl oxidase involved in the biogenesis of cytosolic Fe/S proteins [Posttranslational modification, protein turnover, chaperones]. 181 matched cddid_all.tbl CDD COG5055 COG5055 444051 RAD52 Recombinational DNA repair protein (RAD52 pathway) [Replication, recombination and repair]. 300 matched cddid_all.tbl CDD COG5056 COG5056 227389 ARE1 Acyl-CoA cholesterol acyltransferase [Lipid metabolism]. 512 matched cddid_all.tbl CDD COG5057 COG5057 227390 LAG1 Phosphotyrosyl phosphatase activator [Cell division and chromosome partitioning / Signal transduction mechanisms]. 353 matched cddid_all.tbl CDD COG5058 COG5058 227391 LAG1 Protein transporter of the TRAM (translocating chain-associating membrane) superfamily, longevity assurance factor [Intracellular trafficking and secretion]. 395 matched cddid_all.tbl CDD COG5059 COG5059 227392 KIP1 Kinesin-like protein [Cytoskeleton]. 568 matched cddid_all.tbl CDD COG5061 COG5061 227393 ERO1 Oxidoreductin, endoplasmic reticulum membrane-associated protein involved in disulfide bond formation [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]. 425 matched cddid_all.tbl CDD COG5062 COG5062 227394 COG5062 Uncharacterized membrane protein [Function unknown]. 429 matched cddid_all.tbl CDD COG5063 COG5063 227395 CTH1 CCCH-type Zn-finger protein [General function prediction only]. 351 matched cddid_all.tbl CDD COG5064 COG5064 227396 SRP1 Karyopherin (importin) alpha [Intracellular trafficking and secretion]. 526 matched cddid_all.tbl CDD COG5065 COG5065 227397 PHO88 Protein involved in inorganic phosphate transport [Inorganic ion transport and metabolism]. 185 matched cddid_all.tbl CDD COG5066 COG5066 227398 SCS2 VAMP-associated protein involved in inositol metabolism [Intracellular trafficking and secretion]. 242 matched cddid_all.tbl CDD COG5067 COG5067 227399 DBF4 Protein kinase essential for the initiation of DNA replication [DNA replication, recombination, and repair / Cell division and chromosome partitioning]. 468 matched cddid_all.tbl CDD COG5068 COG5068 227400 ARG80 Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription]. 412 matched cddid_all.tbl CDD COG5069 COG5069 227401 SAC6 Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton]. 612 matched cddid_all.tbl CDD COG5070 COG5070 227402 VRG4 Nucleotide-sugar transporter [Carbohydrate transport and metabolism / Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]. 309 matched cddid_all.tbl CDD COG5071 COG5071 227403 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]. 439 matched cddid_all.tbl CDD COG5072 COG5072 227404 ALK1 Serine/threonine kinase of the haspin family [Cell division and chromosome partitioning]. 488 matched cddid_all.tbl CDD COG5073 COG5073 227405 VID24 Vacuolar import and degradation protein [Intracellular trafficking and secretion]. 272 matched cddid_all.tbl CDD COG5074 COG5074 227406 COG5074 t-SNARE complex subunit, syntaxin [Intracellular trafficking, secretion, and vesicular transport]. 280 matched cddid_all.tbl CDD COG5075 COG5075 227407 COG5075 Uncharacterized conserved protein [Function unknown]. 305 matched cddid_all.tbl CDD COG5076 COG5076 227408 COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]. 371 matched cddid_all.tbl CDD COG5077 COG5077 227409 COG5077 Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]. 1089 matched cddid_all.tbl CDD COG5078 COG5078 444052 COG5078 Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]. 146 matched cddid_all.tbl CDD COG5079 COG5079 227411 SAC3 Nuclear protein export factor [Intracellular trafficking and secretion / Cell division and chromosome partitioning]. 646 matched cddid_all.tbl CDD COG5080 COG5080 227412 YIP1 Rab GTPase interacting factor, Golgi membrane protein [Intracellular trafficking and secretion]. 227 matched cddid_all.tbl CDD COG5081 COG5081 227413 COG5081 Predicted membrane protein [Function unknown]. 180 matched cddid_all.tbl CDD COG5082 COG5082 227414 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]. 190 matched cddid_all.tbl CDD COG5083 COG5083 444053 SMP2 Phosphatidate phosphatase PAH1, contains Lipin and LNS2 domains. can be involved in plasmid maintenance [Lipid transport and metabolism]. 353 matched cddid_all.tbl CDD COG5084 COG5084 227416 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]. 285 matched cddid_all.tbl CDD COG5085 COG5085 227417 COG5085 Predicted membrane protein [Function unknown]. 230 matched cddid_all.tbl CDD COG5086 COG5086 227418 COG5086 Uncharacterized conserved protein [Function unknown]. 218 matched cddid_all.tbl CDD COG5087 COG5087 227419 RTT109 Uncharacterized conserved protein [Function unknown]. 349 matched cddid_all.tbl CDD COG5088 COG5088 227420 SOH1 Rad5p-binding protein [General function prediction only]. 114 matched cddid_all.tbl CDD COG5090 COG5090 227421 TFG2 Transcription initiation factor IIF, small subunit (RAP30) [Transcription]. 297 matched cddid_all.tbl CDD COG5091 COG5091 227422 SGT1 Suppressor of G2 allele of skp1 and related proteins [General function prediction only]. 368 matched cddid_all.tbl CDD COG5092 COG5092 227423 NMT1 N-myristoyl transferase [Lipid metabolism]. 451 matched cddid_all.tbl CDD COG5093 COG5093 227424 COG5093 Uncharacterized conserved protein [Function unknown]. 185 matched cddid_all.tbl CDD COG5094 COG5094 227425 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]. 145 matched cddid_all.tbl CDD COG5095 COG5095 227426 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]. 450 matched cddid_all.tbl CDD COG5096 COG5096 227427 COG5096 Vesicle coat complex, various subunits [Intracellular trafficking, secretion, and vesicular transport]. 757 matched cddid_all.tbl CDD COG5097 COG5097 227428 MED6 RNA polymerase II transcriptional regulation mediator [Transcription]. 210 matched cddid_all.tbl CDD COG5098 COG5098 227429 COG5098 Chromosome condensation complex Condensin, subunit D2 [Chromatin structure and dynamics / Cell division and chromosome partitioning]. 1128 matched cddid_all.tbl CDD COG5099 COG5099 227430 COG5099 RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis]. 777 matched cddid_all.tbl CDD COG5100 COG5100 227431 NPL4 Nuclear pore protein [Nuclear structure]. 571 matched cddid_all.tbl CDD COG5101 COG5101 227432 CRM1 Importin beta-related nuclear transport receptor [Nuclear structure / Intracellular trafficking and secretion]. 1053 matched cddid_all.tbl CDD COG5102 COG5102 227433 SFT2 Membrane protein involved in ER to Golgi transport [Intracellular trafficking and secretion]. 201 matched cddid_all.tbl CDD COG5103 COG5103 227434 CDC39 Cell division control protein, negative regulator of transcription [Cell division and chromosome partitioning / Transcription]. 2005 matched cddid_all.tbl CDD COG5104 COG5104 227435 PRP40 Splicing factor [RNA processing and modification]. 590 matched cddid_all.tbl CDD COG5105 COG5105 227436 MIH1 Mitotic inducer, protein phosphatase [Cell division and chromosome partitioning]. 427 matched cddid_all.tbl CDD COG5106 COG5106 227437 RPF2 Uncharacterized conserved protein [Function unknown]. 316 matched cddid_all.tbl CDD COG5107 COG5107 227438 RNA14 Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification]. 660 matched cddid_all.tbl CDD COG5108 COG5108 444054 RPO41 Mitochondrial DNA-directed RNA polymerase [Transcription]. 826 matched cddid_all.tbl CDD COG5109 COG5109 227440 COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]. 396 matched cddid_all.tbl CDD COG5110 COG5110 227441 RPN1 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]. 881 matched cddid_all.tbl CDD COG5111 COG5111 227442 RPC34 DNA-directed RNA polymerase III, subunit C34 [Transcription]. 301 matched cddid_all.tbl CDD COG5112 COG5112 227443 UFD2 U1-like Zn-finger-containing protein [General function prediction only]. 126 matched cddid_all.tbl CDD COG5113 COG5113 227444 UFD2 Ubiquitin fusion degradation protein 2 [Posttranslational modification, protein turnover, chaperones]. 929 matched cddid_all.tbl CDD COG5114 COG5114 227445 COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]. 432 matched cddid_all.tbl CDD COG5116 COG5116 227446 RPN2 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]. 926 matched cddid_all.tbl CDD COG5117 COG5117 227447 NOC3 Protein involved in the nuclear export of pre-ribosomes [Translation, ribosomal structure and biogenesis / Intracellular trafficking and secretion]. 657 matched cddid_all.tbl CDD COG5118 COG5118 227448 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]. 507 matched cddid_all.tbl CDD COG5119 COG5119 444055 COG5119 Uncharacterized conserved protein, contains ParB-like nuclease domain [General function prediction only]. 87 matched cddid_all.tbl CDD COG5120 COG5120 227450 GOT1 Membrane protein involved in Golgi transport [Intracellular trafficking and secretion]. 129 matched cddid_all.tbl CDD COG5122 COG5122 227451 TRS23 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]. 134 matched cddid_all.tbl CDD COG5123 COG5123 227452 TOA2 Transcription initiation factor IIA, gamma subunit [Transcription]. 113 matched cddid_all.tbl CDD COG5124 COG5124 227453 COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]. 209 matched cddid_all.tbl CDD COG5125 COG5125 227454 COG5125 Uncharacterized conserved protein [Function unknown]. 259 matched cddid_all.tbl CDD COG5126 COG5126 444056 FRQ1 Ca2+-binding protein, EF-hand superfamily [Signal transduction mechanisms]. 137 matched cddid_all.tbl CDD COG5127 COG5127 227456 COG5127 Vacuolar H+-ATPase V1 sector, subunit C [Energy production and conversion]. 383 matched cddid_all.tbl CDD COG5128 COG5128 227457 COG5128 Transport protein particle (TRAPP) complex subunit [Intracellular trafficking and secretion]. 208 matched cddid_all.tbl CDD COG5129 COG5129 227458 MAK16 Nuclear protein with HMG-like acidic region [General function prediction only]. 303 matched cddid_all.tbl CDD COG5130 COG5130 227459 YIP3 Prenylated rab acceptor 1 and related proteins [Intracellular trafficking and secretion / Signal transduction mechanisms]. 169 matched cddid_all.tbl CDD COG5131 COG5131 444057 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]. 81 matched cddid_all.tbl CDD COG5132 COG5132 227461 BUD31 Cell cycle control protein, G10 family [Transcription / Cell division and chromosome partitioning]. 146 matched cddid_all.tbl CDD COG5133 COG5133 227462 COG5133 Uncharacterized conserved protein [Function unknown]. 181 matched cddid_all.tbl CDD COG5134 COG5134 227463 COG5134 Uncharacterized conserved protein [Function unknown]. 272 matched cddid_all.tbl CDD COG5135 COG5135 444058 COG5135 Uncharacterized conserved protein [Function unknown]. 193 matched cddid_all.tbl CDD COG5136 COG5136 227465 COG5136 U1 snRNP-specific protein C [RNA processing and modification]. 188 matched cddid_all.tbl CDD COG5137 COG5137 227466 COG5137 Histone chaperone involved in gene silencing [Transcription / Chromatin structure and dynamics]. 279 matched cddid_all.tbl CDD COG5138 COG5138 227467 COG5138 Uncharacterized conserved protein [Function unknown]. 168 matched cddid_all.tbl CDD COG5139 COG5139 227468 COG5139 Uncharacterized conserved protein [Function unknown]. 397 matched cddid_all.tbl CDD COG5140 COG5140 227469 UFD1 Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones]. 331 matched cddid_all.tbl CDD COG5141 COG5141 227470 COG5141 PHD zinc finger-containing protein [General function prediction only]. 669 matched cddid_all.tbl CDD COG5142 COG5142 227471 OXR1 Oxidation resistance protein [DNA replication, recombination, and repair]. 212 matched cddid_all.tbl CDD COG5143 COG5143 227472 SNC1 Synaptobrevin/VAMP-like protein [Intracellular trafficking and secretion]. 190 matched cddid_all.tbl CDD COG5144 COG5144 227473 TFB2 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription / DNA replication, recombination, and repair]. 447 matched cddid_all.tbl CDD COG5145 COG5145 227474 RAD14 DNA excision repair protein [DNA replication, recombination, and repair]. 292 matched cddid_all.tbl CDD COG5146 COG5146 444059 PanK Pantothenate kinase [Coenzyme transport and metabolism]. Pantothenate kinase is part of the Pathway/BioSystem: Pantothenate/CoA biosynthesis 270 matched cddid_all.tbl CDD COG5147 COG5147 227476 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]. 512 matched cddid_all.tbl CDD COG5148 COG5148 444060 COG5148 vWFA (von Willebrand factor type A) domain-containing protein [Function unknown]. 304 matched cddid_all.tbl CDD COG5149 COG5149 227478 TOA1 Transcription initiation factor IIA, large chain [Transcription]. 293 matched cddid_all.tbl CDD COG5150 COG5150 227479 COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]. 148 matched cddid_all.tbl CDD COG5151 COG5151 227480 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]. 421 matched cddid_all.tbl CDD COG5152 COG5152 227481 COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]. 259 matched cddid_all.tbl CDD COG5153 COG5153 444061 CVT17 Putative lipase ATG15 (essential for vacuolar disintegration of autophagic bodies) [Intracellular trafficking, secretion, and vesicular transport]. 405 matched cddid_all.tbl CDD COG5154 COG5154 227483 BRX1 RNA-binding protein required for 60S ribosomal subunit biogenesis [Translation, ribosomal structure and biogenesis]. 283 matched cddid_all.tbl CDD COG5155 COG5155 227484 ESP1 Separase, a protease involved in sister chromatid separation [Cell division and chromosome partitioning / Posttranslational modification, protein turnover, chaperones]. 1622 matched cddid_all.tbl CDD COG5156 COG5156 227485 DOC1 Anaphase-promoting complex (APC), subunit 10 [Cell division and chromosome partitioning / Posttranslational modification, protein turnover, chaperones]. 189 matched cddid_all.tbl CDD COG5157 COG5157 227486 CDC73 RNA polymerase II assessory factor [Transcription]. 362 matched cddid_all.tbl CDD COG5158 COG5158 227487 SEC1 Proteins involved in synaptic transmission and general secretion, Sec1 family [Intracellular trafficking and secretion]. 582 matched cddid_all.tbl CDD COG5159 COG5159 227488 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]. 421 matched cddid_all.tbl CDD COG5160 COG5160 444062 ULP1 Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones]. 296 matched cddid_all.tbl CDD COG5161 COG5161 227490 SFT1 Pre-mRNA cleavage and polyadenylation specificity factor [RNA processing and modification]. 1319 matched cddid_all.tbl CDD COG5162 COG5162 227491 COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]. 197 matched cddid_all.tbl CDD COG5163 COG5163 227492 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]. 591 matched cddid_all.tbl CDD COG5164 COG5164 444063 SPT5 Transcription elongation factor SPT5 [Transcription]. 495 matched cddid_all.tbl CDD COG5165 COG5165 227494 POB3 Nucleosome-binding factor SPN, POB3 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]. 508 matched cddid_all.tbl CDD COG5166 COG5166 227495 COG5166 Uncharacterized conserved protein [Function unknown]. 657 matched cddid_all.tbl CDD COG5167 COG5167 227496 VID27 Protein involved in vacuole import and degradation [Intracellular trafficking and secretion]. 776 matched cddid_all.tbl CDD COG5169 COG5169 227497 HSF1 Heat shock transcription factor [Transcription]. 282 matched cddid_all.tbl CDD COG5170 COG5170 227498 CDC55 Serine/threonine protein phosphatase 2A, regulatory subunit [Signal transduction mechanisms]. 460 matched cddid_all.tbl CDD COG5171 COG5171 227499 YRB1 Ran GTPase-activating protein (Ran-binding protein) [Intracellular trafficking and secretion]. 211 matched cddid_all.tbl CDD COG5173 COG5173 227500 SEC6 Exocyst complex subunit SEC6 [Intracellular trafficking and secretion]. 742 matched cddid_all.tbl CDD COG5174 COG5174 227501 TFA2 Transcription initiation factor IIE, beta subunit [Transcription]. 285 matched cddid_all.tbl CDD COG5175 COG5175 227502 MOT2 Transcriptional repressor [Transcription]. 480 matched cddid_all.tbl CDD COG5176 COG5176 227503 MSL5 Splicing factor (branch point binding protein) [RNA processing and modification]. 269 matched cddid_all.tbl CDD COG5177 COG5177 227504 COG5177 Uncharacterized conserved protein [Function unknown]. 769 matched cddid_all.tbl CDD COG5178 COG5178 227505 PRP8 U5 snRNP spliceosome subunit [RNA processing and modification]. 2365 matched cddid_all.tbl CDD COG5179 COG5179 227506 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]. 968 matched cddid_all.tbl CDD COG5180 COG5180 444064 PBP1 PAB1-binding protein, interacts with poly(A)-binding protein [RNA processing and modification]. 548 matched cddid_all.tbl CDD COG5181 COG5181 227508 HSH155 U2 snRNP spliceosome subunit [RNA processing and modification]. 975 matched cddid_all.tbl CDD COG5182 COG5182 227509 CUS1 Splicing factor 3b, subunit 2 [RNA processing and modification]. 429 matched cddid_all.tbl CDD COG5183 COG5183 227510 SSM4 E3 ubiquitin-protein ligase DOA10 [Posttranslational modification, protein turnover, chaperones]. 1175 matched cddid_all.tbl CDD COG5184 COG5184 444065 ATS1 Alpha-tubulin suppressor ATS1 and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]. 343 matched cddid_all.tbl CDD COG5185 COG5185 444066 HEC1 Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell division, chromosome partitioning]. 594 matched cddid_all.tbl CDD COG5186 COG5186 444067 PAP1 Poly(A) polymerase Pap1 [RNA processing and modification]. 983 matched cddid_all.tbl CDD COG5187 COG5187 227514 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]. 412 matched cddid_all.tbl CDD COG5188 COG5188 227515 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]. 470 matched cddid_all.tbl CDD COG5189 COG5189 227516 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]. 423 matched cddid_all.tbl CDD COG5190 COG5190 444068 FCP1 TFIIF-interacting CTD phosphatase, includes NLI-interacting factor [Transcription]. 176 matched cddid_all.tbl CDD COG5191 COG5191 227518 COG5191 Uncharacterized conserved protein, contains HAT (Half-A-TPR) repeat [General function prediction only]. 435 matched cddid_all.tbl CDD COG5192 COG5192 227519 BMS1 GTP-binding protein required for 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis]. 1077 matched cddid_all.tbl CDD COG5193 COG5193 227520 LHP1 La protein, small RNA-binding pol III transcript stabilizing protein and related La-motif-containing proteins involved in translation [Posttranslational modification, protein turnover, chaperones / Translation, ribosomal structure and biogenesis]. 438 matched cddid_all.tbl CDD COG5194 COG5194 227521 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]. 88 matched cddid_all.tbl CDD COG5195 COG5195 227522 COG5195 Uncharacterized conserved protein [Function unknown]. 118 matched cddid_all.tbl CDD COG5196 COG5196 227523 ERD2 ER lumen protein retaining receptor [Intracellular trafficking and secretion]. 214 matched cddid_all.tbl CDD COG5197 COG5197 227524 COG5197 Predicted membrane protein [Function unknown]. 284 matched cddid_all.tbl CDD COG5198 COG5198 227525 Ptpl Protein tyrosine phosphatase-like protein (contains Pro instead of catalytic Arg) [General function prediction only]. 209 matched cddid_all.tbl CDD COG5199 COG5199 227526 SCP1 Calponin [Cytoskeleton]. 178 matched cddid_all.tbl CDD COG5200 COG5200 227527 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]. 258 matched cddid_all.tbl CDD COG5201 COG5201 227528 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]. 158 matched cddid_all.tbl CDD COG5202 COG5202 227529 COG5202 Predicted membrane protein [Function unknown]. 512 matched cddid_all.tbl CDD COG5204 COG5204 227530 SPT4 Transcription elongation factor SPT4 [Transcription]. 112 matched cddid_all.tbl CDD COG5206 COG5206 444069 GPI8 Glycosylphosphatidylinositol transamidase (GPIT), subunit GPI8 [Posttranslational modification, protein turnover, chaperones]. 716 matched cddid_all.tbl CDD COG5207 COG5207 444070 UBP14 Uncharacterized Zn-finger protein, UBP-type [General function prediction only]. 84 matched cddid_all.tbl CDD COG5208 COG5208 227533 HAP5 CCAAT-binding factor, subunit C [Transcription]. 286 matched cddid_all.tbl CDD COG5209 COG5209 227534 RCD1 Uncharacterized protein involved in cell differentiation/sexual development [General function prediction only]. 315 matched cddid_all.tbl CDD COG5210 COG5210 227535 COG5210 GTPase-activating protein [General function prediction only]. 496 matched cddid_all.tbl CDD COG5211 COG5211 227536 SSU72 RNA polymerase II-interacting protein involved in transcription start site selection [Transcription]. 197 matched cddid_all.tbl CDD COG5212 COG5212 444071 PDE1 cAMP phosphodiesterase [Signal transduction mechanisms]. 300 matched cddid_all.tbl CDD COG5213 COG5213 227538 FIP1 Polyadenylation factor I complex, subunit FIP1 [RNA processing and modification]. 266 matched cddid_all.tbl CDD COG5214 COG5214 227539 POL12 DNA polymerase alpha-primase complex, polymerase-associated subunit B [DNA replication, recombination, and repair]. 581 matched cddid_all.tbl CDD COG5215 COG5215 227540 KAP95 Karyopherin (importin) beta [Intracellular trafficking and secretion]. 858 matched cddid_all.tbl CDD COG5216 COG5216 227541 COG5216 Uncharacterized conserved protein [Function unknown]. 67 matched cddid_all.tbl CDD COG5217 COG5217 227542 BIM1 Microtubule-binding protein involved in cell cycle control [Cell division and chromosome partitioning / Cytoskeleton]. 342 matched cddid_all.tbl CDD COG5218 COG5218 227543 YCG1 Chromosome condensation complex Condensin, subunit G [Chromatin structure and dynamics / Cell division and chromosome partitioning]. 885 matched cddid_all.tbl CDD COG5219 COG5219 227544 COG5219 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]. 1525 matched cddid_all.tbl CDD COG5220 COG5220 227545 TFB3 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB3 [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]. 314 matched cddid_all.tbl CDD COG5221 COG5221 227546 DOP1 Dopey and related predicted leucine zipper transcription factors [Transcription]. 1618 matched cddid_all.tbl CDD COG5222 COG5222 227547 COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]. 427 matched cddid_all.tbl CDD COG5223 COG5223 227548 COG5223 Uncharacterized conserved protein [Function unknown]. 240 matched cddid_all.tbl CDD COG5224 COG5224 227549 HAP2 CCAAT-binding factor, subunit B [Transcription]. 248 matched cddid_all.tbl CDD COG5225 COG5225 227550 RRS1 Uncharacterized protein involved in ribosome biogenesis [Translation, ribosomal structure and biogenesis]. 172 matched cddid_all.tbl CDD COG5226 COG5226 227551 CEG1 mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]. 404 matched cddid_all.tbl CDD COG5227 COG5227 227552 SMT3 Ubiquitin-like protein (sentrin) [Posttranslational modification, protein turnover, chaperones]. 103 matched cddid_all.tbl CDD COG5228 COG5228 227553 POP2 mRNA deadenylase subunit [RNA processing and modification]. 299 matched cddid_all.tbl CDD COG5229 COG5229 227554 LOC7 Chromosome condensation complex Condensin, subunit H [Chromatin structure and dynamics / Cell division and chromosome partitioning]. 662 matched cddid_all.tbl CDD COG5230 COG5230 227555 COG5230 Uncharacterized conserved protein [Function unknown]. 194 matched cddid_all.tbl CDD COG5231 COG5231 227556 VMA13 Vacuolar H+-ATPase V1 sector, subunit H [Energy production and conversion]. 432 matched cddid_all.tbl CDD COG5232 COG5232 227557 SEC62 Preprotein translocase subunit Sec62 [Intracellular trafficking and secretion]. 259 matched cddid_all.tbl CDD COG5233 COG5233 227558 GRH1 Peripheral Golgi membrane protein [Intracellular trafficking and secretion]. 417 matched cddid_all.tbl CDD COG5234 COG5234 227559 CIN1 Beta-tubulin folding cofactor D [Posttranslational modification, protein turnover, chaperones / Cytoskeleton]. 993 matched cddid_all.tbl CDD COG5235 COG5235 227560 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]. 258 matched cddid_all.tbl CDD COG5236 COG5236 227561 COG5236 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]. 493 matched cddid_all.tbl CDD COG5237 COG5237 227562 PER1 Predicted membrane protein [Function unknown]. 319 matched cddid_all.tbl CDD COG5238 COG5238 444072 RNA1 Ran GTPase-activating protein (RanGAP) involved in mRNA processing and transport [Translation, ribosomal structure and biogenesis]. 434 matched cddid_all.tbl CDD COG5239 COG5239 227564 CCR4 mRNA deadenylase, 3'-5' endonuclease subunit Ccr4 [RNA processing and modification]. 378 matched cddid_all.tbl CDD COG5240 COG5240 227565 SEC21 Vesicle coat complex COPI, gamma subunit [Intracellular trafficking and secretion]. 898 matched cddid_all.tbl CDD COG5241 COG5241 227566 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]. 224 matched cddid_all.tbl CDD COG5242 COG5242 227567 TFB4 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair]. 296 matched cddid_all.tbl CDD COG5243 COG5243 227568 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]. 491 matched cddid_all.tbl CDD COG5244 COG5244 227569 NIP100 Dynactin complex subunit involved in mitotic spindle partitioning in anaphase B [Cell cycle control, cell division, chromosome partitioning]. 669 matched cddid_all.tbl CDD COG5245 COG5245 227570 DYN1 Dynein, heavy chain [Cytoskeleton]. 3164 matched cddid_all.tbl CDD COG5246 COG5246 227571 PRP11 Splicing factor 3a, subunit 2 [RNA processing and modification]. 222 matched cddid_all.tbl CDD COG5247 COG5247 227572 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]. 113 matched cddid_all.tbl CDD COG5248 COG5248 227573 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]. 126 matched cddid_all.tbl CDD COG5249 COG5249 227574 RER1 Golgi protein involved in Golgi-to-ER retrieval [Intracellular trafficking and secretion]. 180 matched cddid_all.tbl CDD COG5250 COG5250 227575 RPB4 RNA polymerase II, fourth largest subunit [Transcription]. 138 matched cddid_all.tbl CDD COG5251 COG5251 227576 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]. 199 matched cddid_all.tbl CDD COG5252 COG5252 227577 COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]. 299 matched cddid_all.tbl CDD COG5253 COG5253 227578 MSS4 Phosphatidylinositol-4-phosphate 5-kinase [Signal transduction mechanisms]. 612 matched cddid_all.tbl CDD COG5254 COG5254 227579 ARV1 Predicted membrane protein [Function unknown]. 239 matched cddid_all.tbl CDD COG5255 COG5255 444073 COG5255 Uncharacterized conserved protein [Function unknown]. 228 matched cddid_all.tbl CDD COG5256 COG5256 444074 TEF1 Translation elongation factor EF-1alpha (GTPase) [Translation, ribosomal structure and biogenesis]. Translation elongation factor EF-1alpha (GTPase) is part of the Pathway/BioSystem: Translation factors 423 matched cddid_all.tbl CDD COG5257 COG5257 444075 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]. Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) is part of the Pathway/BioSystem: Translation factors 408 matched cddid_all.tbl CDD COG5258 COG5258 444076 GTPBP1 GTPase [General function prediction only]. 531 matched cddid_all.tbl CDD COG5259 COG5259 227584 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]. 531 matched cddid_all.tbl CDD COG5260 COG5260 227585 TRF4 DNA polymerase sigma [Replication, recombination and repair]. 482 matched cddid_all.tbl CDD COG5261 COG5261 227586 IQG1 Protein involved in regulation of cellular morphogenesis/cytokinesis [Cell division and chromosome partitioning / Signal transduction mechanisms]. 1054 matched cddid_all.tbl CDD COG5262 COG5262 227587 HTA1 Histone H2A [Chromatin structure and dynamics]. 132 matched cddid_all.tbl CDD COG5263 COG5263 444077 COG5263 Glucan-binding domain (YG repeat) [Carbohydrate transport and metabolism]. 486 matched cddid_all.tbl CDD COG5264 COG5264 227589 VTC1 Vacuolar transporter chaperone [Posttranslational modification, protein turnover, chaperones]. 126 matched cddid_all.tbl CDD COG5265 COG5265 444078 ATM1 ABC-type transport system involved in Fe-S cluster assembly, permease and ATPase components [Posttranslational modification, protein turnover, chaperones]. 605 matched cddid_all.tbl CDD COG5266 COG5266 444079 COG5266 Uncharacterized protein, contains GH25 family domain [General function prediction only]. 261 matched cddid_all.tbl CDD COG5267 COG5267 444080 COG5267 Uncharacterized conserved protein, DUF1800 family [Function unknown]. 439 matched cddid_all.tbl CDD COG5268 COG5268 444081 TrbD Type IV secretory pathway, TrbD component [Intracellular trafficking, secretion, and vesicular transport]. 88 matched cddid_all.tbl CDD COG5269 COG5269 227594 ZUO1 Ribosome-associated chaperone zuotin [Translation, ribosomal structure and biogenesis / Posttranslational modification, protein turnover, chaperones]. 379 matched cddid_all.tbl CDD COG5270 COG5270 444082 PUA PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]. 488 matched cddid_all.tbl CDD COG5271 COG5271 444083 MDN1 Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]. 1028 matched cddid_all.tbl CDD COG5272 COG5272 444084 UBI4 Ubiquitin [Posttranslational modification, protein turnover, chaperones]. 213 matched cddid_all.tbl CDD COG5273 COG5273 227598 COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]. 309 matched cddid_all.tbl CDD COG5274 COG5274 444085 CYB5 Cytochrome b involved in lipid metabolism [Energy production and conversion, Lipid transport and metabolism]. 93 matched cddid_all.tbl CDD COG5275 COG5275 444086 COG5275 BRCT domain type II [General function prediction only]. 288 matched cddid_all.tbl CDD COG5276 COG5276 444087 COG5276 Uncharacterized secreted protein, contains LVIVD repeats, choice-of-anchor domain [Function unknown]. 320 matched cddid_all.tbl CDD COG5277 COG5277 444088 COG5277 Actin-related protein [Cytoskeleton]. 424 matched cddid_all.tbl CDD COG5278 COG5278 444089 CHASE3 Extracytoplasmic sensor domain CHASE3 (specificity unknown) [Signal transduction mechanisms]. 530 matched cddid_all.tbl CDD COG5279 COG5279 444090 CYK3 Cytokinesis protein 3, contains TGc (transglutaminase/protease-like) domain [Cell cycle control, cell division, chromosome partitioning]. 250 matched cddid_all.tbl CDD COG5280 COG5280 444091 YqbO Phage-related minor tail protein [Mobilome: prophages, transposons]. 962 matched cddid_all.tbl CDD COG5281 COG5281 444092 COG5281 Phage-related minor tail protein [Mobilome: prophages, transposons]. 603 matched cddid_all.tbl CDD COG5282 COG5282 444093 Zincin Zn-dependent metallopeptidase, zincin/DUF2342 superfamily [Posttranslational modification, protein turnover, chaperones]. 378 matched cddid_all.tbl CDD COG5283 COG5283 444094 COG5283 Phage-related tail protein [Mobilome: prophages, transposons]. 747 matched cddid_all.tbl CDD COG5285 COG5285 444095 PhyH Ectoine hydroxylase-related dioxygenase, phytanoyl-CoA dioxygenase (PhyH) family [Secondary metabolites biosynthesis, transport and catabolism]. 237 matched cddid_all.tbl CDD COG5290 COG5290 227610 COG5290 IkappaB kinase complex, IKAP component [Transcription]. 1243 matched cddid_all.tbl CDD COG5291 COG5291 227611 COG5291 Predicted membrane protein [Function unknown]. 313 matched cddid_all.tbl CDD COG5293 COG5293 444096 YydB Uncharacterized conserved protein YydD, contains DUF2326 domain [Function unknown]. 572 matched cddid_all.tbl CDD COG5294 COG5294 444097 YxeA Uncharacterized conserved protein YxeA, DUF1093 family [Function unknown]. 121 matched cddid_all.tbl CDD COG5295 COG5295 444098 Hia Autotransporter adhesin [Intracellular trafficking, secretion, and vesicular transport, Extracellular structures]. 785 matched cddid_all.tbl CDD COG5296 COG5296 227615 COG5296 Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]. 521 matched cddid_all.tbl CDD COG5297 COG5297 444099 CelA1 Cellulase/cellobiase CelA1 [Carbohydrate transport and metabolism]. 301 matched cddid_all.tbl CDD COG5298 COG5298 444100 YdaL Predicted metal-dependent carbohydrate esterase YdaL, contains NodB-like catalytic (CE4) domain [General function prediction only]. 479 matched cddid_all.tbl CDD COG5301 COG5301 444101 COG5301 Phage-related tail fiber protein [Mobilome: prophages, transposons]. 254 matched cddid_all.tbl CDD COG5302 COG5302 444102 COG5302 Post-segregation antitoxin (ccd killing mechanism protein) encoded by the F plasmid [Mobilome: prophages, transposons]. 80 matched cddid_all.tbl CDD COG5304 COG5304 444103 COG5304 Predicted DNA binding protein, CopG/RHH family [Transcription]. 90 matched cddid_all.tbl CDD COG5305 COG5305 444104 COG5305 Uncharacterized membrane protein PF0508, contains N-terminal glycosyltransferase domain of PMT family [General function prediction only]. 402 matched cddid_all.tbl CDD COG5306 COG5306 444105 MJ1470 Uncharacterized conserved protein MJ1470, contains DUF2341 domain, predicted component of type IV pili-like system [General function prediction only]. 529 matched cddid_all.tbl CDD COG5307 COG5307 444106 COG5307 Guanine-nucleotide exchange factor YEL1, contains Sec7 domain [General function prediction only]. 301 matched cddid_all.tbl CDD COG5308 COG5308 227624 NUP170 Nuclear pore complex subunit [Intracellular trafficking and secretion]. 1263 matched cddid_all.tbl CDD COG5309 COG5309 444107 Scw11 Exo-beta-1,3-glucanase, GH17 family [Carbohydrate transport and metabolism]. 512 matched cddid_all.tbl CDD COG5310 COG5310 444108 COG5310 Homospermidine synthase [Secondary metabolites biosynthesis, transport and catabolism]. 467 matched cddid_all.tbl CDD COG5314 COG5314 444109 COG5314 Conjugal transfer/entry exclusion protein [Mobilome: prophages, transposons]. 249 matched cddid_all.tbl CDD COG5316 COG5316 444110 COG5316 Uncharacterized protein, contains DUF4139 domain [Function unknown]. 451 matched cddid_all.tbl CDD COG5317 COG5317 444111 COG5317 Uncharacterized conserved protein, DUF1465 domain [Function unknown]. 170 matched cddid_all.tbl CDD COG5319 COG5319 444112 COG5319 Uncharacterized conserved protein, DUF1178 domain [Function unknown]. 150 matched cddid_all.tbl CDD COG5321 COG5321 444113 COG5321 Uncharacterized conserved protein [Function unknown]. 157 matched cddid_all.tbl CDD COG5322 COG5322 444114 COG5322 Predicted amino acid dehydrogenase [General function prediction only]. 362 matched cddid_all.tbl CDD COG5323 COG5323 444115 COG5323 Phage large terminase packaging protein [Mobilome: prophages, transposons]. 431 matched cddid_all.tbl CDD COG5324 COG5324 444116 Trl1 tRNA splicing ligase [Translation, ribosomal structure and biogenesis]. tRNA splicing ligase is part of the Pathway/BioSystem: tRNA modification 664 matched cddid_all.tbl CDD COG5325 COG5325 227635 COG5325 t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]. 283 matched cddid_all.tbl CDD COG5328 COG5328 444117 COG5328 Uncharacterized conserved protein, UPF0262 family [Function unknown]. 161 matched cddid_all.tbl CDD COG5329 COG5329 227637 COG5329 Phosphoinositide polyphosphatase (Sac family) [Signal transduction mechanisms]. 570 matched cddid_all.tbl CDD COG5330 COG5330 444118 COG5330 Uncharacterized conserved protein, DUF2336 family [Function unknown]. 351 matched cddid_all.tbl CDD COG5331 COG5331 444119 COG5331 Uncharacterized conserved protein [Function unknown]. 140 matched cddid_all.tbl CDD COG5333 COG5333 227640 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]. 297 matched cddid_all.tbl CDD COG5336 COG5336 444120 AtpZ FoF1-type ATP synthase AtpZ/Atp1/AtpQ subunit, putative Ca2+/Mg2+ transporter [Energy production and conversion]. FoF1-type ATP synthase AtpZ/Atp1/AtpQ subunit, putative Ca2+/Mg2+ transporter is part of the Pathway/BioSystem: FoF1-type ATP synthase 78 matched cddid_all.tbl CDD COG5337 COG5337 444121 CotH Spore coat protein CotH [Cell wall/membrane/envelope biogenesis]. 394 matched cddid_all.tbl CDD COG5338 COG5338 444122 COG5338 Uncharacterized conserved protein [Function unknown]. 386 matched cddid_all.tbl CDD COG5339 COG5339 444123 YdgA Uncharacterized conserved protein YdgA, DUF945 family [Function unknown]. 465 matched cddid_all.tbl CDD COG5340 COG5340 444124 AbiEi Abortive phage infection protein AbiEi, antitoxin conponent of an AbiEi-AbiEii TA system [Defense mechanisms]. 203 matched cddid_all.tbl CDD COG5341 COG5341 444125 COG5341 Uncharacterized conserved protein [Function unknown]. 126 matched cddid_all.tbl CDD COG5342 COG5342 444126 IalB Invasion protein IalB, involved in pathogenesis [General function prediction only]. 177 matched cddid_all.tbl CDD COG5343 COG5343 444127 RskA Anti-sigma-K factor RskA [Signal transduction mechanisms]. 239 matched cddid_all.tbl CDD COG5345 COG5345 444128 COG5345 Uncharacterized conserved protein, DUF2333 domain [Function unknown]. 354 matched cddid_all.tbl CDD COG5346 COG5346 444129 COG5346 Uncharacterized membrane protein [Function unknown]. 142 matched cddid_all.tbl CDD COG5347 COG5347 227651 COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]. 319 matched cddid_all.tbl CDD COG5349 COG5349 444130 COG5349 Uncharacterized conserved protein, DUF983 family [Function unknown]. 128 matched cddid_all.tbl CDD COG5350 COG5350 444131 COG5350 Predicted protein tyrosine phosphatase [General function prediction only]. 165 matched cddid_all.tbl CDD COG5351 COG5351 444132 COG5351 Uncharacterized conserved protein, DUF2169 domain [Function unknown]. 342 matched cddid_all.tbl CDD COG5352 COG5352 444133 COG5352 Uncharacterized conserved protein [Function unknown]. 171 matched cddid_all.tbl CDD COG5353 COG5353 444134 YpmB Uncharacterized conserved protein YpmB, contains C-terminal PepSY domain [Function unknown]. 158 matched cddid_all.tbl CDD COG5354 COG5354 227657 COG5354 Uncharacterized protein, contains Trp-Asp (WD) repeat [General function prediction only]. 561 matched cddid_all.tbl CDD COG5360 COG5360 444135 COG5360 Uncharacterized conserved protein, heparinase superfamily [General function prediction only]. 557 matched cddid_all.tbl CDD COG5361 COG5361 444136 COG5361 Uncharacterized conserved protein [Mobilome: prophages, transposons]. 463 matched cddid_all.tbl CDD COG5362 COG5362 444137 COG5362 Phage terminase large subunit [Mobilome: prophages, transposons]. 472 matched cddid_all.tbl CDD COG5366 COG5366 227661 COG5366 Protein involved in propagation of M2 dsRNA satellite of L-A virus [General function prediction only]. 531 matched cddid_all.tbl CDD COG5368 COG5368 444138 COG5368 Endo-beta-1,2-glucanase, glucoamylase superfamily [Carbohydrate transport and metabolism]. 422 matched cddid_all.tbl CDD COG5369 COG5369 227663 COG5369 Uncharacterized conserved protein [Function unknown]. 743 matched cddid_all.tbl CDD COG5371 COG5371 444139 GDA1 Nucleoside diphosphatase, GDA1/CD39 family [Nucleotide transport and metabolism]. 225 matched cddid_all.tbl CDD COG5373 COG5373 444140 COG5373 Uncharacterized membrane protein [Function unknown]. 854 matched cddid_all.tbl CDD COG5374 COG5374 227666 COG5374 Uncharacterized conserved protein [Function unknown]. 192 matched cddid_all.tbl CDD COG5375 COG5375 444141 COG5375 Uncharacterized conserved protein [Function unknown]. 224 matched cddid_all.tbl CDD COG5377 COG5377 444142 COG5377 Phage-related protein, predicted endonuclease [Mobilome: prophages, transposons]. 313 matched cddid_all.tbl CDD COG5378 COG5378 444143 COG5378 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]. 141 matched cddid_all.tbl CDD COG5379 COG5379 444144 BtaA S-adenosylmethionine:diacylglycerol 3-amino-3-carboxypropyl transferase [Lipid transport and metabolism]. 387 matched cddid_all.tbl CDD COG5380 COG5380 444145 LimK Lipase chaperone LimK [Posttranslational modification, protein turnover, chaperones]. 304 matched cddid_all.tbl CDD COG5381 COG5381 444146 COG5381 Uncharacterized conserved protein [Function unknown]. 193 matched cddid_all.tbl CDD COG5383 COG5383 444147 YdcJ Uncharacterized metalloenzyme YdcJ, glyoxalase superfamily [General function prediction only]. 196 matched cddid_all.tbl CDD COG5384 COG5384 227674 Mpp10 U3 small nucleolar ribonucleoprotein component [Translation, ribosomal structure and biogenesis]. 569 matched cddid_all.tbl CDD COG5385 COG5385 444148 HPt Histidine phosphotransfer protein ChpT, HPt domain [Signal transduction mechanisms]. 202 matched cddid_all.tbl CDD COG5386 COG5386 444149 NEAT Heme-binding NEAT domain [Inorganic ion transport and metabolism]. 302 matched cddid_all.tbl CDD COG5387 COG5387 444150 Atp12 Mitochondrial FoF1-type ATP synthase assembly chaperone ATP12 [Posttranslational modification, protein turnover, chaperones]. 235 matched cddid_all.tbl CDD COG5388 COG5388 444151 COG5388 Uncharacterized conserved protein [Function unknown]. 170 matched cddid_all.tbl CDD COG5389 COG5389 444152 COG5389 Uncharacterized conserved protein, DUF721 domain [Function unknown]. 163 matched cddid_all.tbl CDD COG5391 COG5391 227680 COG5391 Phox homology (PX) domain protein [Intracellular trafficking and secretion / General function prediction only]. 524 matched cddid_all.tbl CDD COG5393 COG5393 444153 YqjE Uncharacterized membrane protein YqjE [Function unknown]. 130 matched cddid_all.tbl CDD COG5394 COG5394 444154 COG5394 Polyhydroxyalkanoate (PHA) synthesis regulator protein, binds DNA and PHA [Secondary metabolites biosynthesis, transport and catabolism, Signal transduction mechanisms]. 181 matched cddid_all.tbl CDD COG5395 COG5395 444155 COG5395 Uncharacterized membrane protein [Function unknown]. 133 matched cddid_all.tbl CDD COG5397 COG5397 444156 COG5397 Uncharacterized conserved protein [Function unknown]. 334 matched cddid_all.tbl CDD COG5398 COG5398 444157 COG5398 Heme oxygenase [Coenzyme transport and metabolism]. 211 matched cddid_all.tbl CDD COG5399 COG5399 444158 COG5399 Uncharacterized conserved protein, DUF2286 domain [Function unknown]. 146 matched cddid_all.tbl CDD COG5400 COG5400 444159 COG5400 Uncharacterized conserved protein [Function unknown]. 202 matched cddid_all.tbl CDD COG5401 COG5401 444160 GerM Spore germination protein GerM [Cell cycle control, cell division, chromosome partitioning]. 163 matched cddid_all.tbl CDD COG5402 COG5402 444161 COG5402 Uncharacterized protein, contains DUF1214 domain [Function unknown]. 192 matched cddid_all.tbl CDD COG5403 COG5403 444162 COG5403 Uncharacterized conserved protein, DUF937 domain [Function unknown]. 184 matched cddid_all.tbl CDD COG5404 COG5404 444163 SulA Cell division inhibitor SulA, prevents FtsZ ring assembly [Cell cycle control, cell division, chromosome partitioning]. 152 matched cddid_all.tbl CDD COG5405 COG5405 444164 HslV ATP-dependent protease HslVU (ClpYQ), peptidase subunit [Posttranslational modification, protein turnover, chaperones]. 174 matched cddid_all.tbl CDD COG5406 COG5406 227693 COG5406 Nucleosome binding factor SPN, SPT16 subunit [Transcription, Replication, recombination and repair, Chromatin structure and dynamics]. 1001 matched cddid_all.tbl CDD COG5407 COG5407 444165 SEC63 Preprotein translocase subunit Sec63 [Intracellular trafficking, secretion, and vesicular transport]. 61 matched cddid_all.tbl CDD COG5408 COG5408 227695 COG5408 SPX domain-containing protein [Signal transduction mechanisms]. 296 matched cddid_all.tbl CDD COG5409 COG5409 227696 COG5409 EXS domain-containing protein [Signal transduction mechanisms]. 384 matched cddid_all.tbl CDD COG5410 COG5410 444166 COG5410 Uncharacterized conserved protein [Function unknown]. 479 matched cddid_all.tbl CDD COG5411 COG5411 227698 COG5411 Phosphatidylinositol 5-phosphate phosphatase [Signal transduction mechanisms]. 460 matched cddid_all.tbl CDD COG5412 COG5412 444167 COG5412 Phage-related protein [Mobilome: prophages, transposons]. 704 matched cddid_all.tbl CDD COG5413 COG5413 444168 COG5413 Uncharacterized integral membrane protein [Function unknown]. 210 matched cddid_all.tbl CDD COG5414 COG5414 227701 Taf7 TATA-binding protein-associated factor Taf7, part of the TFIID transcription initiation complex [Transcription]. 392 matched cddid_all.tbl CDD COG5415 COG5415 227702 COG5415 Predicted integral membrane metal-binding protein [General function prediction only]. 251 matched cddid_all.tbl CDD COG5416 COG5416 444169 YrvD Uncharacterized integral membrane protein YrvD [Function unknown]. 96 matched cddid_all.tbl CDD COG5417 COG5417 444170 YukD ESX protein secretion system component YukD [Intracellular trafficking, secretion, and vesicular transport]. 78 matched cddid_all.tbl CDD COG5418 COG5418 444171 COG5418 Predicted secreted protein [Function unknown]. 168 matched cddid_all.tbl CDD COG5419 COG5419 444172 COG5419 Uncharacterized conserved protein, DUF2285 domain [Function unknown]. 169 matched cddid_all.tbl CDD COG5420 COG5420 444173 COG5420 Uncharacterized protein, UPF0437 family [Function unknown]. 66 matched cddid_all.tbl CDD COG5421 COG5421 444174 COG5421 Transposase [Mobilome: prophages, transposons]. 490 matched cddid_all.tbl CDD COG5422 COG5422 227709 ROM1 RhoGEF, Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases [Signal transduction mechanisms]. 1175 matched cddid_all.tbl CDD COG5423 COG5423 444175 COG5423 Predicted metal-binding protein [Function unknown]. 183 matched cddid_all.tbl CDD COG5424 COG5424 444176 PqqC Pyrroloquinoline quinone (PQQ) biosynthesis protein C [Coenzyme transport and metabolism]. 228 matched cddid_all.tbl CDD COG5425 COG5425 444177 Usg Usg protein (tryptophan operon, function unknown) [Function unknown]. 89 matched cddid_all.tbl CDD COG5426 COG5426 444178 COG5426 Uncharacterized protein STM3548, contains class I glutamine amidotransferase domain [General function prediction only]. 738 matched cddid_all.tbl CDD COG5427 COG5427 444179 COG5427 Predicted membrane glycosyltransferase AF0583, Arch_YYY/DUF2298 family [Function unknown]. 735 matched cddid_all.tbl CDD COG5428 COG5428 444180 YuzE Predicted antitoxin component YuzE of a toxin-antitoxin system, DUF2283 family [Defense mechanisms]. 63 matched cddid_all.tbl CDD COG5429 COG5429 444181 COG5429 Uncharacterized conserved protein, DUF1223 domain [Function unknown]. 244 matched cddid_all.tbl CDD COG5430 COG5430 444182 SCPU Fimbrial subunit ScuA/B, ScuA/B/SCPU domain [Extracellular structures]. 162 matched cddid_all.tbl CDD COG5431 COG5431 444183 COG5431 Predicted nucleic acid-binding protein, contains SWIM-type Zn-finger domain [General function prediction only]. 119 matched cddid_all.tbl CDD COG5432 COG5432 227719 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]. 391 matched cddid_all.tbl CDD COG5433 COG5433 444184 YhhI Predicted transposase YbfD/YdcC associated with H repeats [Mobilome: prophages, transposons]. 331 matched cddid_all.tbl CDD COG5434 COG5434 444185 Pgu1 Polygalacturonase [Carbohydrate transport and metabolism]. 373 matched cddid_all.tbl CDD COG5435 COG5435 444186 COG5435 Uncharacterized conserved protein [Function unknown]. 137 matched cddid_all.tbl CDD COG5436 COG5436 444187 COG5436 Uncharacterized membrane protein [Function unknown]. 182 matched cddid_all.tbl CDD COG5437 COG5437 444188 LmaA Phage tail protein, TP901-1 family [Mobilome: prophages, transposons]. 138 matched cddid_all.tbl CDD COG5438 COG5438 444189 COG5438 Uncharacterized membrane protein [Function unknown]. 361 matched cddid_all.tbl CDD COG5439 COG5439 444190 STAS STAS domain [General function prediction only]. 114 matched cddid_all.tbl CDD COG5440 COG5440 444191 YbjN Global stress regulator YbjN, DUF2299 family [Signal transduction mechanisms]. 154 matched cddid_all.tbl CDD COG5441 COG5441 444192 Tm-1N ATP-binding helicase-inhibiting domain, Tm-1/UPF0261 family [Defense mechanisms]. 407 matched cddid_all.tbl CDD COG5442 COG5442 444193 FlaF Flagellar biosynthesis regulator FlaF [Cell motility]. 120 matched cddid_all.tbl CDD COG5443 COG5443 444194 FlbT Flagellar biosynthesis regulator FlbT [Cell motility]. 132 matched cddid_all.tbl CDD COG5444 COG5444 444195 YeeF Predicted ribonuclease, toxin component of the YeeF-YezG toxin-antitoxin module [Defense mechanisms]. 366 matched cddid_all.tbl CDD COG5445 COG5445 444196 YfaQ Uncharacterized conserved protein YfaQ, DUF2300 domain [Function unknown]. 548 matched cddid_all.tbl CDD COG5446 COG5446 444197 CbtA Putative cobalt transporter membrane subunit CbtA [Inorganic ion transport and metabolism]. 239 matched cddid_all.tbl CDD COG5447 COG5447 444198 COG5447 Uncharacterized conserved protein, DUF1491 domain [Function unknown]. 105 matched cddid_all.tbl CDD COG5448 COG5448 444199 COG5448 Uncharacterized conserved protein, DUF2460 domain [Function unknown]. 211 matched cddid_all.tbl CDD COG5449 COG5449 444200 COG5449 Uncharacterized conserved protein, DUF2163 domain [Function unknown]. 272 matched cddid_all.tbl CDD COG5450 COG5450 444201 VapB6 Transcription regulator of the Arc/MetJ class [Transcription]. 62 matched cddid_all.tbl CDD COG5451 COG5451 444202 COG5451 Predicted secreted protein [Function unknown]. 127 matched cddid_all.tbl CDD COG5452 COG5452 444203 COG5452 Uncharacterized conserved protein [Function unknown]. 178 matched cddid_all.tbl CDD COG5453 COG5453 444204 COG5453 Uncharacterized conserved protein [Function unknown]. 95 matched cddid_all.tbl CDD COG5454 COG5454 444205 COG5454 Predicted secreted protein [Function unknown]. 88 matched cddid_all.tbl CDD COG5455 COG5455 444206 RcnB Periplasmic regulator RcnB of Ni and Co efflux [Inorganic ion transport and metabolism]. 121 matched cddid_all.tbl CDD COG5456 COG5456 444207 FixH Nitrogen fixation protein FixH [Inorganic ion transport and metabolism]. 166 matched cddid_all.tbl CDD COG5457 COG5457 444208 YjiS Uncharacterized conserved protein YjiS, DUF1127 family [Function unknown]. 61 matched cddid_all.tbl CDD COG5458 COG5458 444209 COG5458 Uncharacterized conserved protein, DUF1489 domain [Function unknown]. 140 matched cddid_all.tbl CDD COG5459 COG5459 444210 Rsm22 Ribosomal protein RSM22 (predicted mitochondrial rRNA methylase) [Translation, ribosomal structure and biogenesis]. Ribosomal protein RSM22 (predicted mitochondrial rRNA methylase) is part of the Pathway/BioSystem: Archaeal ribosomal proteins 306 matched cddid_all.tbl CDD COG5460 COG5460 444211 COG5460 Uncharacterized conserved protein, DUF2164 family [Function unknown]. 79 matched cddid_all.tbl CDD COG5461 COG5461 444212 CpaD Type IV pilus biogenesis protein CpaD/CtpE [Extracellular structures]. 230 matched cddid_all.tbl CDD COG5462 COG5462 444213 COG5462 Predicted secreted (periplasmic) protein [Function unknown]. 116 matched cddid_all.tbl CDD COG5463 COG5463 444214 YgiB Uncharacterized conserved protein YgiB, UPF0441/DUF1190 family, involved in bioifilm formation [Function unknown]. 203 matched cddid_all.tbl CDD COG5464 COG5464 444215 RpnC Recombination-promoting DNA endonuclease RpnC/YadD [Replication, recombination and repair]. 301 matched cddid_all.tbl CDD COG5465 COG5465 444216 YbjN Uncharacterized conserved protein YbjN, helps stabilize unstable proteins [General function prediction only]. 166 matched cddid_all.tbl CDD COG5466 COG5466 444217 COG5466 Predicted small metal-binding protein [Function unknown]. 58 matched cddid_all.tbl CDD COG5467 COG5467 444218 COG5467 Uncharacterized conserved protein, DUF1476 domain [Function unknown]. 106 matched cddid_all.tbl CDD COG5468 COG5468 444219 COG5468 Predicted lipoprotein involved in lipopolysaccharide assembly [Function unknown]. 172 matched cddid_all.tbl CDD COG5469 COG5469 444220 COG5469 Predicted metal-binding protein [Function unknown]. 128 matched cddid_all.tbl CDD COG5470 COG5470 444221 COG5470 Uncharacterized conserved protein, DUF1330 family [Function unknown]. 95 matched cddid_all.tbl CDD COG5471 COG5471 444222 COG5471 Predicted phage recombinase, RecA/RadA family [Mobilome: prophages, transposons]. 107 matched cddid_all.tbl CDD COG5472 COG5472 444223 COG5472 Predicted small integral membrane protein [Function unknown]. 165 matched cddid_all.tbl CDD COG5473 COG5473 444224 COG5473 Uncharacterized membrane protein [Function unknown]. 263 matched cddid_all.tbl CDD COG5474 COG5474 444225 CRR6 NAD(P)H dehydrogenase cyanobacteria/chloroplast-specific assembly factor CRR6 [Energy production and conversion]. 157 matched cddid_all.tbl CDD COG5475 COG5475 444226 YodC Uncharacterized conserved protein YodC, DUF2158 family [Function unknown]. 53 matched cddid_all.tbl CDD COG5476 COG5476 444227 COG5476 Microcystin degradation protein MlrC, contains DUF1485 domain [General function prediction only]. 485 matched cddid_all.tbl CDD COG5477 COG5477 444228 COG5477 Predicted small integral membrane protein [Function unknown]. 90 matched cddid_all.tbl CDD COG5478 COG5478 444229 Fet4 Low affinity Fe/Cu permease [Inorganic ion transport and metabolism]. 140 matched cddid_all.tbl CDD COG5479 COG5479 444230 Psp3 LGFP repeat-containing protein, may be involved in cell wall binding [Cell wall/membrane/envelope biogenesis]. 246 matched cddid_all.tbl CDD COG5480 COG5480 444231 COG5480 Uncharacterized membrane protein [Function unknown]. 142 matched cddid_all.tbl CDD COG5481 COG5481 444232 COG5481 Uncharacterized conserved protein, DUF465 domain [Function unknown]. 68 matched cddid_all.tbl CDD COG5482 COG5482 444233 COG5482 Uncharacterized conserved protein, DUF2161 domain [Function unknown]. 227 matched cddid_all.tbl CDD COG5483 COG5483 444234 COG5483 Uncharacterized conserved protein, DUF488 family [Function unknown]. 147 matched cddid_all.tbl CDD COG5484 COG5484 444235 YjcR Uncharacterized conserved protein YjcR, contains N-terminal HTH domain [Function unknown]. 586 matched cddid_all.tbl CDD COG5485 COG5485 444236 COG5485 Predicted ester cyclase [General function prediction only]. 130 matched cddid_all.tbl CDD COG5486 COG5486 444237 COG5486 Predicted metal-binding membrane protein [Function unknown]. 234 matched cddid_all.tbl CDD COG5487 COG5487 444238 YtjA Uncharacterized membrane protein YtjA, UPF0391 family [Function unknown]. 54 matched cddid_all.tbl CDD COG5488 COG5488 444239 COG5488 Uncharacterized membrane protein [Function unknown]. 166 matched cddid_all.tbl CDD COG5489 COG5489 444240 COG5489 Uncharacterized conserved protein, DUF736 family [Function unknown]. 107 matched cddid_all.tbl CDD COG5490 COG5490 444241 Phasin Predicted polyhydroxyalkanoate (PHA)-binding protein, phasin family [Function unknown]. 143 matched cddid_all.tbl CDD COG5491 COG5491 444242 Did4 Archaeal cell division protein CdvB, Snf7/Vps24/ESCRT-III family [Cell cycle control, cell division, chromosome partitioning]. 201 matched cddid_all.tbl CDD COG5492 COG5492 444243 YjdB Uncharacterized conserved protein YjdB, contains Ig-like domain [General function prediction only]. 613 matched cddid_all.tbl CDD COG5493 COG5493 444244 COG5493 Uncharacterized protein, contains PD-(D/E)XK nuclease domain [General function prediction only]. 239 matched cddid_all.tbl CDD COG5494 COG5494 444245 COG5494 Predicted thioredoxin/glutaredoxin [Posttranslational modification, protein turnover, chaperones]. 259 matched cddid_all.tbl CDD COG5495 COG5495 444246 COG5495 Predicted oxidoreductase, contains short-chain dehydrogenase (SDR) and DUF2520 domains [General function prediction only]. 286 matched cddid_all.tbl CDD COG5496 COG5496 444247 COG5496 Predicted thioesterase [General function prediction only]. 129 matched cddid_all.tbl CDD COG5497 COG5497 444248 COG5497 Predicted secreted protein [Function unknown]. 243 matched cddid_all.tbl CDD COG5498 COG5498 444249 Acf2 Endoglucanase Acf2 [Carbohydrate transport and metabolism]. 871 matched cddid_all.tbl CDD COG5499 COG5499 444250 HigA Antitoxin component HigA of the HigAB toxin-antitoxin module, contains an N-terminal HTH domain [Defense mechanisms]. 127 matched cddid_all.tbl CDD COG5500 COG5500 444251 COG5500 Uncharacterized membrane protein [Function unknown]. 158 matched cddid_all.tbl CDD COG5501 COG5501 444252 SoxY Sulfur oxidation protein SoxY [Function unknown]. 148 matched cddid_all.tbl CDD COG5502 COG5502 444253 COG5502 Uncharacterized conserved protein, DUF2267 family [Function unknown]. 133 matched cddid_all.tbl CDD COG5503 COG5503 444254 RpoEps DNA-dependent RNA polymerase auxiliary subunit epsilon [Transcription, Defense mechanisms]. DNA-dependent RNA polymerase auxiliary subunit epsilon is part of the Pathway/BioSystem: RNA polymerase 69 matched cddid_all.tbl CDD COG5504 COG5504 444255 YjaZ Predicted Zn-dependent protease YjaZ, DUF2268 family [General function prediction only]. 269 matched cddid_all.tbl CDD COG5505 COG5505 444256 COG5505 Uncharacterized membrane protein YjcL [Function unknown]. 394 matched cddid_all.tbl CDD COG5506 COG5506 444257 YueI Uncharacterized conserved protein YueI, DUF2278 family [Function unknown]. 151 matched cddid_all.tbl CDD COG5507 COG5507 444258 YbaA Uncharacterized conserved protein YbaA, DUF1428 family [Function unknown]. 117 matched cddid_all.tbl CDD COG5508 COG5508 444259 COG5508 Uncharacterized conserved protein, DUF1674 domain [Function unknown]. 61 matched cddid_all.tbl CDD COG5509 COG5509 444260 COG5509 Uncharacterized small protein, DUF1192 family [Function unknown]. 62 matched cddid_all.tbl CDD COG5510 COG5510 444261 COG5510 Predicted small secreted protein [Function unknown]. 45 matched cddid_all.tbl CDD COG5511 COG5511 444262 COG5511 Phage portal protein [Mobilome: prophages, transposons]. May form a hole, or portal, that enables DNA passage during packaging and ejection, and also form the junction between the phage head (capsid) and the tail proteins. 512 matched cddid_all.tbl CDD COG5512 COG5512 444263 COG5512 Predicted nucleic acid-binding protein, contains Zn-ribbon domain (includes truncated derivatives) [General function prediction only]. 116 matched cddid_all.tbl CDD COG5513 COG5513 444264 ICP Chagasin-like inhibitor of cysteine peptidase, I42 family [Posttranslational modification, protein turnover, chaperones]. 115 matched cddid_all.tbl CDD COG5514 COG5514 444265 COG5514 Uncharacterized conserved protein, DUF1794 domain [Function unknown]. 200 matched cddid_all.tbl CDD COG5515 COG5515 444266 COG5515 Uncharacterized conserved protein, DUF1737 domain [Function unknown]. 68 matched cddid_all.tbl CDD COG5516 COG5516 444267 COG5516 Uncharacterized conserved protein containing a Zn-ribbon-like motif, possibly RNA-binding [General function prediction only]. 193 matched cddid_all.tbl CDD COG5517 COG5517 444268 HcaF 3-phenylpropionate/cinnamic acid dioxygenase, small subunit [Secondary metabolites biosynthesis, transport and catabolism]. 162 matched cddid_all.tbl CDD COG5518 COG5518 444269 COG5518 Phage capsid portal protein XkdE [Mobilome: prophages, transposons]. 333 matched cddid_all.tbl CDD COG5519 COG5519 444270 COG5519 Predicted ATPase domain of Cch-like helicases, DUF927 family [General function prediction only]. 592 matched cddid_all.tbl CDD COG5520 COG5520 444271 XynC O-Glycosyl hydrolase [Cell wall/membrane/envelope biogenesis]. 445 matched cddid_all.tbl CDD COG5521 COG5521 444272 YvdJ Maltodextrin utilization protein YvdJ (function unknown) [Carbohydrate transport and metabolism]. 276 matched cddid_all.tbl CDD COG5522 COG5522 444273 YwaF Uncharacterized membrane protein YwaF [Function unknown]. 244 matched cddid_all.tbl CDD COG5523 COG5523 444274 COG5523 Uncharacterized membrane protein [Function unknown]. 195 matched cddid_all.tbl CDD COG5524 COG5524 444275 COG5524 Bacteriorhodopsin [Energy production and conversion, Signal transduction mechanisms]. 234 matched cddid_all.tbl CDD COG5525 COG5525 444276 gpA1 Phage terminase, large subunit GpA [Mobilome: prophages, transposons]. 635 matched cddid_all.tbl CDD COG5526 COG5526 444277 COG5526 Lysozyme family protein [General function prediction only]. 189 matched cddid_all.tbl CDD COG5527 COG5527 444278 COG5527 Protein involved in initiation of plasmid replication [Mobilome: prophages, transposons]. 259 matched cddid_all.tbl CDD COG5528 COG5528 444279 COG5528 Uncharacterized membrane protein [Function unknown]. 155 matched cddid_all.tbl CDD COG5529 COG5529 444280 ECs1768 Phage-encoded DNA-binding protein ECs1768, contains HTH and DnaT DNA-binding domains [Mobilome: prophages, transposons]. 104 matched cddid_all.tbl CDD COG5530 COG5530 444281 COG5530 Uncharacterized membrane protein [Function unknown]. 226 matched cddid_all.tbl CDD COG5531 COG5531 444282 Rsc6 DNA-binding SWIB/MDM2 domain [Chromatin structure and dynamics]. 85 matched cddid_all.tbl CDD COG5532 COG5532 444283 yfdQ Uncharacterized conserved protein YfdQ, DUF2303 family [Function unknown]. 274 matched cddid_all.tbl CDD COG5533 COG5533 444284 COG5533 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]. 284 matched cddid_all.tbl CDD COG5534 COG5534 444285 RepA Plasmid replication initiator protein [Mobilome: prophages, transposons]. 289 matched cddid_all.tbl CDD COG5535 COG5535 227822 RAD4 DNA repair protein RAD4 [DNA replication, recombination, and repair]. 650 matched cddid_all.tbl CDD COG5536 COG5536 227823 BET4 Protein prenyltransferase, alpha subunit [Posttranslational modification, protein turnover, chaperones]. 328 matched cddid_all.tbl CDD COG5537 COG5537 227824 IRR1 Cohesin [Cell division and chromosome partitioning]. 740 matched cddid_all.tbl CDD COG5538 COG5538 227825 SEC66 Endoplasmic reticulum translocation complex, subunit SEC66 [Cell motility and secretion]. 180 matched cddid_all.tbl CDD COG5539 COG5539 227826 COG5539 Predicted cysteine protease (OTU family) [Posttranslational modification, protein turnover, chaperones]. 306 matched cddid_all.tbl CDD COG5540 COG5540 227827 COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]. 374 matched cddid_all.tbl CDD COG5541 COG5541 227828 RET3 Vesicle coat complex COPI, zeta subunit [Posttranslational modification, protein turnover, chaperones]. 187 matched cddid_all.tbl CDD COG5542 COG5542 444286 COG5542 Mannosyltransferase related to Gpi18 [Carbohydrate transport and metabolism]. 208 matched cddid_all.tbl CDD COG5543 COG5543 227830 COG5543 Uncharacterized conserved protein [Function unknown]. 1400 matched cddid_all.tbl CDD COG5544 COG5544 444287 yfiM Uncharacterized conserved protein YfiM, DUF2279 family [Function unknown]. 108 matched cddid_all.tbl CDD COG5545 COG5545 444288 COG5545 Predicted P-loop ATPase and inactivated derivatives [Mobilome: prophages, transposons]. 615 matched cddid_all.tbl CDD COG5546 COG5546 444289 COG5546 Uncharacterized membrane protein [Function unknown]. 87 matched cddid_all.tbl CDD COG5547 COG5547 444290 COG5547 Uncharacterized membrane protein [Function unknown]. 73 matched cddid_all.tbl CDD COG5548 COG5548 444291 COG5548 Uncharacterized membrane protein, UPF0136 family [Function unknown]. 106 matched cddid_all.tbl CDD COG5549 COG5549 444292 COG5549 Predicted Zn-dependent protease [Posttranslational modification, protein turnover, chaperones]. 234 matched cddid_all.tbl CDD COG5550 COG5550 444293 COG5550 Predicted aspartyl protease [Posttranslational modification, protein turnover, chaperones]. 117 matched cddid_all.tbl CDD COG5551 COG5551 444294 Cas6a CRISPR/Cas system endoribonuclease Cas6, RAMP superfamily [Defense mechanisms]. CRISPR/Cas system endoribonuclease Cas6, RAMP superfamily is part of the Pathway/BioSystem: CRISPR-Cas system 257 matched cddid_all.tbl CDD COG5552 COG5552 444295 COG5552 Uncharacterized conserved protein, DUF2277 domain [Function unknown]. 90 matched cddid_all.tbl CDD COG5553 COG5553 444296 COG5553 Predicted metal-dependent enzyme of the double-stranded beta helix superfamily [General function prediction only]. 179 matched cddid_all.tbl CDD COG5554 COG5554 444297 NifT Nitrogen fixation protein NifT [Secondary metabolites biosynthesis, transport and catabolism]. 67 matched cddid_all.tbl CDD COG5555 COG5555 444298 COG5555 Cytolysin, a secreted calcineurin-like phosphatase [Intracellular trafficking, secretion, and vesicular transport]. 325 matched cddid_all.tbl CDD COG5556 COG5556 444299 COG5556 Uncharacterized conserved protein [Function unknown]. 149 matched cddid_all.tbl CDD COG5557 COG5557 444300 HybB Ni/Fe-hydrogenase 2 integral membrane subunit HybB [Energy production and conversion]. 408 matched cddid_all.tbl CDD COG5558 COG5558 444301 COG5558 Transposase [Mobilome: prophages, transposons]. 319 matched cddid_all.tbl CDD COG5559 COG5559 444302 COG5559 Uncharacterized conserved protein, DUF2281 domain [Function unknown]. 56 matched cddid_all.tbl CDD COG5560 COG5560 227847 UBP12 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]. 823 matched cddid_all.tbl CDD COG5561 COG5561 444303 CGGC Predicted metal-binding protein, contains CGGC domain [Function unknown]. 110 matched cddid_all.tbl CDD COG5562 COG5562 444304 YbcV Prophage-encoded protein YbcV, DUF1398 family [Mobilome: prophages, transposons]. 132 matched cddid_all.tbl CDD COG5563 COG5563 444305 COG5563 Uncharacterized conserved protein CPn0794, contains PKD-like HAF repeats [Function unknown]. 265 matched cddid_all.tbl CDD COG5564 COG5564 444306 COG5564 Predicted TIM-barrel enzyme [Function unknown]. 275 matched cddid_all.tbl CDD COG5565 COG5565 444307 COG5565 Phage terminase large (ATPase) subunit and inactivated derivatives [Mobilome: prophages, transposons]. 481 matched cddid_all.tbl CDD COG5566 COG5566 444308 Mor Transcriptional regulator, middle operon regulator (Mor) family [Transcription, Mobilome: prophages, transposons]. 120 matched cddid_all.tbl CDD COG5567 COG5567 444309 YifL Small periplasmic lipoprotein YifL (function unknown) [Function unknown]. 43 matched cddid_all.tbl CDD COG5568 COG5568 444310 COG5568 Uncharacterized conserved protein, DUF1150 family [Function unknown]. 84 matched cddid_all.tbl CDD COG5569 COG5569 444311 CusF Periplasmic Cu and Ag efflux protein CusF [Inorganic ion transport and metabolism]. 101 matched cddid_all.tbl CDD COG5570 COG5570 444312 COG5570 Uncharacterized conserved protein, DUF465 domain [Function unknown]. 57 matched cddid_all.tbl CDD COG5571 COG5571 444313 YhjY Uncharacterized conserved protein YhjY, contains autotransporter beta-barrel domain [General function prediction only]. 648 matched cddid_all.tbl CDD COG5572 COG5572 444314 COG5572 Uncharacterized membrane protein [Function unknown]. 89 matched cddid_all.tbl CDD COG5573 COG5573 444315 COG5573 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]. 140 matched cddid_all.tbl CDD COG5574 COG5574 227861 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]. 271 matched cddid_all.tbl CDD COG5575 COG5575 227862 ORC2 Origin recognition complex, subunit 2 [DNA replication, recombination, and repair]. 535 matched cddid_all.tbl CDD COG5576 COG5576 227863 COG5576 Homeodomain-containing transcription factor [Transcription]. 156 matched cddid_all.tbl CDD COG5577 COG5577 444316 CotF Spore coat protein CotF [Cell wall/membrane/envelope biogenesis]. 84 matched cddid_all.tbl CDD COG5578 COG5578 444317 YesL Uncharacterized membrane protein YesL [Function unknown]. 210 matched cddid_all.tbl CDD COG5579 COG5579 444318 Mll0975 Uncharacterized conserved protein, DUF1810 family [Function unknown]. 140 matched cddid_all.tbl CDD COG5580 COG5580 444319 COG5580 Activator of HSP90 ATPase [Posttranslational modification, protein turnover, chaperones]. 129 matched cddid_all.tbl CDD COG5581 COG5581 444320 YcgR Cyclic di-GMP-binding flagellar brake protein FlgZ/YcgR, contains PilZNR(YcgR) and PilZ domains [Cell motility]. 205 matched cddid_all.tbl CDD COG5582 COG5582 444321 YpiB Uncharacterized conserved protein YpiB, UPF0302 family [Function unknown]. 180 matched cddid_all.tbl CDD COG5583 COG5583 444322 COG5583 Uncharacterized conserved protein YezD [Function unknown]. 57 matched cddid_all.tbl CDD COG5584 COG5584 444323 COG5584 Uncharacterized conserved protein YtzB [Function unknown]. 103 matched cddid_all.tbl CDD COG5585 COG5585 444324 COG5585 Putative phage head morphogenesis protein, F of phage Mu or gp7 of SPP1 [Mobilome: prophages, transposons]. 223 matched cddid_all.tbl CDD COG5586 COG5586 444325 COG5586 Uncharacterized protein, contains DUF2293 domain [Function unknown]. 97 matched cddid_all.tbl CDD COG5587 COG5587 444326 COG5587 Uncharacterized protein, contains DUF2461 domain [Function unknown]. 223 matched cddid_all.tbl CDD COG5588 COG5588 444327 COG5588 Uncharacterized conserved protein, DUF1326 domain [Function unknown]. 205 matched cddid_all.tbl CDD COG5589 COG5589 444328 COG5589 Uncharacterized conserved protein, DUF2390 domain [Function unknown]. 165 matched cddid_all.tbl CDD COG5590 COG5590 444329 COG5590 Ubiquinone biosynthesis protein COQ9 [Coenzyme transport and metabolism]. 214 matched cddid_all.tbl CDD COG5591 COG5591 444330 COG5591 Uncharacterized conserved protein [Function unknown]. 88 matched cddid_all.tbl CDD COG5592 COG5592 444331 COG5592 Hemerythrin domain-containing protein [General function prediction only]. 151 matched cddid_all.tbl CDD COG5593 COG5593 227880 COG5593 Nucleic-acid-binding protein possibly involved in ribosomal biogenesis [Translation, ribosomal structure and biogenesis]. 821 matched cddid_all.tbl CDD COG5594 COG5594 227881 COG5594 Uncharacterized integral membrane protein [Function unknown]. 827 matched cddid_all.tbl CDD COG5595 COG5595 444332 COG5595 Predicted nucleic acid-binding protein, contains Zn-ribbon domain [General function prediction only]. 256 matched cddid_all.tbl CDD COG5596 COG5596 227883 TIM22 Mitochondrial import inner membrane translocase, subunit TIM22 [Posttranslational modification, protein turnover, chaperones]. 191 matched cddid_all.tbl CDD COG5597 COG5597 444333 Gnt1 N-acetylglucosaminyl transferase [Cell wall/membrane/envelope biogenesis]. 279 matched cddid_all.tbl CDD COG5598 COG5598 444334 MttB2 Trimethylamine:corrinoid methyltransferase [Coenzyme transport and metabolism]. 469 matched cddid_all.tbl CDD COG5599 COG5599 444335 COG5599 Protein tyrosine phosphatase [Signal transduction mechanisms]. 282 matched cddid_all.tbl CDD COG5600 COG5600 227887 COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]. 413 matched cddid_all.tbl CDD COG5601 COG5601 227888 CDC36 General negative regulator of transcription subunit [Transcription]. 172 matched cddid_all.tbl CDD COG5602 COG5602 227889 Sin3 Histone deacetylase complex, regulatory component SIN3 [Chromatin structure and dynamics]. 1163 matched cddid_all.tbl CDD COG5603 COG5603 227890 TRS20 Subunit of TRAPP, an ER-Golgi tethering complex [Cell motility and secretion]. 136 matched cddid_all.tbl CDD COG5604 COG5604 227891 COG5604 Uncharacterized conserved protein [Function unknown]. 523 matched cddid_all.tbl CDD COG5605 COG5605 444336 COX4 Cytochrome c oxidase subunit IV [Energy production and conversion]. 112 matched cddid_all.tbl CDD COG5606 COG5606 444337 COG5606 Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only]. 105 matched cddid_all.tbl CDD COG5607 COG5607 444338 CHAD CHAD domain, binds inorganic polyphosphates [Function unknown]. 284 matched cddid_all.tbl CDD COG5608 COG5608 444339 LEA Dessication stress tolerance protein, LEA/WHy domain [Defense mechanisms]. 138 matched cddid_all.tbl CDD COG5609 COG5609 444340 MpsC Na+-translocating membrane potential-generating system subunit MpsC, DUF2294 family [Energy production and conversion]. 122 matched cddid_all.tbl CDD COG5610 COG5610 444341 COG5610 Predicted sugar hydrolase, contains GT1 and HAD domains [General function prediction only]. 501 matched cddid_all.tbl CDD COG5611 COG5611 444342 COG5611 Predicted nucleic-acid-binding protein, contains PIN domain [General function prediction only]. 128 matched cddid_all.tbl CDD COG5612 COG5612 444343 CnrX Ni/Co/Cd-binding protein CnrX (heavy-metal resistance) [Inorganic ion transport and metabolism]. 155 matched cddid_all.tbl CDD COG5613 COG5613 444344 SseC Type III secretion system effector SseC (host membrane pore formation) [Intracellular trafficking, secretion, and vesicular transport]. 395 matched cddid_all.tbl CDD COG5614 COG5614 444345 COG5614 Phage head-tail adaptor [Mobilome: prophages, transposons]. 107 matched cddid_all.tbl CDD COG5615 COG5615 444346 COG5615 Uncharacterized membrane protein [Function unknown]. 155 matched cddid_all.tbl CDD COG5616 COG5616 444347 TolBN TolB amino-terminal domain (function unknown) [Signal transduction mechanisms]. 135 matched cddid_all.tbl CDD COG5617 COG5617 444348 PTPS Predicted membrane glycosyltransferase TK1552, contains 6-pyruvoyl-tetrahydropterin synthase (PTPS)-related domain [General function prediction only]. 560 matched cddid_all.tbl CDD COG5618 COG5618 444349 COG5618 Predicted periplasmic lipoprotein [Function unknown]. 215 matched cddid_all.tbl CDD COG5619 COG5619 444350 COG5619 Uncharacterized conserved protein, DUF2290 domain [Function unknown]. 221 matched cddid_all.tbl CDD COG5620 COG5620 444351 COG5620 Uncharacterized conserved protein, DUF1851 domain [Function unknown]. 196 matched cddid_all.tbl CDD COG5621 COG5621 444352 CrtC Predicted lipocalin, contains AttH/CrtC domain [General function prediction only]. 359 matched cddid_all.tbl CDD COG5622 COG5622 444353 COG5622 Protein required for attachment to host cells [Cell wall/membrane/envelope biogenesis]. 148 matched cddid_all.tbl CDD COG5623 COG5623 227910 CLP1 Predicted GTPase subunit of the pre-mRNA cleavage complex [Translation, ribosomal structure and biogenesis]. 424 matched cddid_all.tbl CDD COG5624 COG5624 227911 COG5624 Transcription initiation factor TFIID, subunit TAF12 [Transcription]. 505 matched cddid_all.tbl CDD COG5625 COG5625 444354 COG5625 Predicted DNA-binding transcriptional regulator, contains HTH domain [Transcription]. 90 matched cddid_all.tbl CDD COG5626 COG5626 444355 Ssr3000 Uncharacterized protein Ssr3000, DUF2288 family [Function unknown]. 84 matched cddid_all.tbl CDD COG5627 COG5627 227914 COG5627 SUMO ligase MMS21, Smc5/6 complex, required for cell growth and DNA repair [Replication, recombination and repair]. 275 matched cddid_all.tbl CDD COG5628 COG5628 444356 COG5628 Predicted acetyltransferase [General function prediction only]. 163 matched cddid_all.tbl CDD COG5629 COG5629 227916 COG5629 Predicted metal-binding protein [Function unknown]. 321 matched cddid_all.tbl CDD COG5630 COG5630 444357 ARG2 N-acetylglutamate synthase (arginine biosynthesis) [Amino acid transport and metabolism]. 437 matched cddid_all.tbl CDD COG5631 COG5631 444358 COG5631 Predicted transcription regulator, contains HTH domain, MarR family [Transcription]. 177 matched cddid_all.tbl CDD COG5632 COG5632 444359 CwlA N-acetylmuramoyl-L-alanine amidase CwlA [Cell wall/membrane/envelope biogenesis]. 177 matched cddid_all.tbl CDD COG5633 COG5633 444360 YcfL Uncharacterized conserved protein YcfL [Function unknown]. 128 matched cddid_all.tbl CDD COG5634 COG5634 444361 YukJ Uncharacterized conserved protein YukJ, DUF2278 family [Function unknown]. 332 matched cddid_all.tbl CDD COG5635 COG5635 444362 NACHT Predicted NTPase, NACHT family domain [Signal transduction mechanisms]. 935 matched cddid_all.tbl CDD COG5636 COG5636 227923 COG5636 Uncharacterized conserved protein, contains Zn-ribbon-like motif [Function unknown]. 284 matched cddid_all.tbl CDD COG5637 COG5637 444363 COG5637 Uncharacterized protein, contains SRPBCC domain [Function unknown]. 154 matched cddid_all.tbl CDD COG5638 COG5638 227925 COG5638 Uncharacterized conserved protein [Function unknown]. 622 matched cddid_all.tbl CDD COG5639 COG5639 444364 COG5639 Uncharacterized conserved protein, DUF2274 domain [Function unknown]. 78 matched cddid_all.tbl CDD COG5640 COG5640 444365 COG5640 Secreted trypsin-like serine protease [Posttranslational modification, protein turnover, chaperones]. 262 matched cddid_all.tbl CDD COG5641 COG5641 227928 GAT1 GATA Zn-finger-containing transcription factor [Transcription]. 498 matched cddid_all.tbl CDD COG5642 COG5642 444366 COG5642 Uncharacterized conserved protein, DUF2384 family [Function unknown]. 139 matched cddid_all.tbl CDD COG5643 COG5643 444367 COG5643 Uncharacterized conserved protein containing a metal-binding domain [General function prediction only]. 375 matched cddid_all.tbl CDD COG5644 COG5644 227931 COG5644 U3 small nucleolar RNA-associated protein 14 [Function unknown]. 869 matched cddid_all.tbl CDD COG5645 COG5645 444368 YceK Uncharacterized conserved protein YceK [Function unknown]. 100 matched cddid_all.tbl CDD COG5646 COG5646 444369 Fra Iron-binding protein Fra/YdhG, frataxin family (Fe-S cluster biosynthesis) [Posttranslational modification, protein turnover, chaperones, Inorganic ion transport and metabolism]. 112 matched cddid_all.tbl CDD COG5647 COG5647 227934 COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]. 773 matched cddid_all.tbl CDD COG5648 COG5648 227935 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]. 211 matched cddid_all.tbl CDD COG5649 COG5649 444370 COG5649 Uncharacterized conserved protein, DUF1801 domain [Function unknown]. 120 matched cddid_all.tbl CDD COG5650 COG5650 444371 COG5650 Uncharacterized membrane protein [Function unknown]. 411 matched cddid_all.tbl CDD COG5651 COG5651 444372 PPE PPE-repeat protein [Function unknown]. 385 matched cddid_all.tbl CDD COG5652 COG5652 444373 VanZ VanZ-like family protein (function unknown) [Function unknown]. 128 matched cddid_all.tbl CDD COG5653 COG5653 444374 BcsL Acetyltransferase involved in cellulose biosynthesis, CelD/BcsL family [Cell motility]. 374 matched cddid_all.tbl CDD COG5654 COG5654 444375 RES Uncharacterized protein, contains RES domain [Function unknown]. 152 matched cddid_all.tbl CDD COG5655 COG5655 444376 REP Replication initiaton protein REP (rolling circle plasmid replication) [Mobilome: prophages, transposons]. 255 matched cddid_all.tbl CDD COG5656 COG5656 227943 SXM1 Importin, protein involved in nuclear import [Posttranslational modification, protein turnover, chaperones]. 970 matched cddid_all.tbl CDD COG5657 COG5657 227944 CSE1 CAS/CSE protein involved in chromosome segregation [Cell division and chromosome partitioning]. 947 matched cddid_all.tbl CDD COG5658 COG5658 444377 SdpI Bacterial immunity/signal transduction membrane protein SdpI, SdpI/YbgB/DUF1648 family [Defense mechanisms]. 216 matched cddid_all.tbl CDD COG5659 COG5659 444378 Srso17 SRSO17 transposase [Mobilome: prophages, transposons]. 417 matched cddid_all.tbl CDD COG5660 COG5660 444379 YlaD Anti-sigma-YlaC factor YlaD, contains Zn-finger domain [Signal transduction mechanisms]. 219 matched cddid_all.tbl CDD COG5661 COG5661 444380 COG5661 Predicted secreted Zn-dependent protease [Posttranslational modification, protein turnover, chaperones]. 179 matched cddid_all.tbl CDD COG5662 COG5662 444381 RsiW Transmembrane transcriptional regulator RsiW (anti-sigma-W factor) [Transcription]. 155 matched cddid_all.tbl CDD COG5663 COG5663 444382 YqfW Uncharacterized conserved protein YqfW, HAD superfamily [General function prediction only]. 187 matched cddid_all.tbl CDD COG5664 COG5664 444383 COG5664 Predicted secreted Zn-dependent protease [Posttranslational modification, protein turnover, chaperones]. 198 matched cddid_all.tbl CDD COG5665 COG5665 444384 Not5 CCR4-NOT transcriptional regulation complex, NOT5 subunit [Transcription]. 874 matched cddid_all.tbl CDD COG5671 COG5671 444385 NdhL NAD(P)H dehydrogenase cyanobacteria/chloroplast subunit L [Energy production and conversion]. 70 matched cddid_all.tbl CDD COG5672 COG5672 444386 NdhM NAD(P)H dehydrogenase cyanobacteria/chloroplast subunit M [Energy production and conversion]. 114 matched cddid_all.tbl CDD COG5673 COG5673 444387 NdhN NAD(P)H dehydrogenase cyanobacteria/chloroplast subunit N [Energy production and conversion]. 156 matched cddid_all.tbl CDD COG5674 COG5674 444388 NdhO NAD(P)H dehydrogenase cyanobacteria/chloroplast subunit O [Energy production and conversion]. 69 matched cddid_all.tbl CDD COG5675 COG5675 444389 PetH Ferredoxin-NADP+ oxidoreductase PetH, often fused with N-terminal CpcD domain [Energy production and conversion]. 405 matched cddid_all.tbl CDD COG5676 COG5676 444390 CytM Cytochrome cM [Energy production and conversion]. 124 matched cddid_all.tbl CDD COG5677 COG5677 444391 PetJ Cytochrome c6 [Energy production and conversion]. 112 matched cddid_all.tbl CDD COG5678 COG5678 444392 PetA Cytochrome b6f complex cytochrome f subunit, PetA [Energy production and conversion]. 329 matched cddid_all.tbl CDD COG5679 COG5679 444393 PetD Cytochrome b6f complex subunit IV, PetD, 17 kd cytochrome b [Energy production and conversion]. 161 matched cddid_all.tbl CDD COG5680 COG5680 444394 PetG Cytochrome b6f complex subunit V, PetG [Energy production and conversion]. 38 matched cddid_all.tbl CDD COG5681 COG5681 444395 PetL Cytochrome b6f complex subunit VI, PetL/Ycf7 [Energy production and conversion]. 31 matched cddid_all.tbl CDD COG5682 COG5682 444396 PetM Cytochrome b6f complex subunit VII, PetM/Ycf31 [Energy production and conversion]. 34 matched cddid_all.tbl CDD COG5683 COG5683 444397 PetN Cytochrome b6f complex subunit VIII, PetN/Ycf6 [Energy production and conversion]. 29 matched cddid_all.tbl CDD COG5684 COG5684 444398 ApcA Allophycocyanin alpha chain [Energy production and conversion]. 161 matched cddid_all.tbl CDD COG5685 COG5685 444399 ApcB Allophycocyanin beta chain [Energy production and conversion]. 162 matched cddid_all.tbl CDD COG5686 COG5686 444400 ApcC Phycobilisome linker polypeptide [Energy production and conversion]. 66 matched cddid_all.tbl CDD COG5687 COG5687 444401 CpcA Phycocyanin alpha chain, CpcA/CpeB [Energy production and conversion]. 162 matched cddid_all.tbl CDD COG5688 COG5688 444402 CpcB Phycocyanin/phycoerythrin beta chain, CpcB/CpeB [Energy production and conversion]. 172 matched cddid_all.tbl CDD COG5689 COG5689 444403 CpcD Phycobilisome linker protein CpcD [Energy production and conversion]. 82 matched cddid_all.tbl CDD COG5690 COG5690 444404 Ycf58 Phycocyanobilin lyase CpeS/CpcS (= Ycf58) [Energy production and conversion]. 170 matched cddid_all.tbl CDD COG5691 COG5691 444405 CpeT Phycocyanobilin lyase CpeT/CpcT [Energy production and conversion]. 195 matched cddid_all.tbl CDD COG5692 COG5692 444406 PcyA Phycocyanobilin:ferredoxin oxidoreductase [Energy production and conversion]. 242 matched cddid_all.tbl CDD COG5693 COG5693 444407 ApcE Phycobilisome linker protein ApcE [Energy production and conversion]. 904 matched cddid_all.tbl CDD COG5694 COG5694 444408 ApcE-CpcD Phycobilisome linker ApcECpcD fusion protein [Energy production and conversion]. 286 matched cddid_all.tbl CDD COG5695 COG5695 444409 NdhP NAD(P)H dehydrogenase cyanobacteria/chloroplast subunit P [Energy production and conversion]. 40 matched cddid_all.tbl CDD COG5696 COG5696 444410 NdhQ NAD(P)H dehydrogenase cyanobacteria/chloroplast subunitQ [Energy production and conversion]. 45 matched cddid_all.tbl CDD COG5701 COG5701 444411 PsaA Photosystem I reaction center subunit A1, PsaA [Energy production and conversion]. Photosystem I reaction center subunit A1, PsaA is part of the Pathway/BioSystem: Photosystem I 755 matched cddid_all.tbl CDD COG5702 COG5702 444412 PsaB Photosystem I reaction center subunit A2, PsaB [Energy production and conversion]. Photosystem I reaction center subunit A2, PsaB is part of the Pathway/BioSystem: Photosystem I 741 matched cddid_all.tbl CDD COG5703 COG5703 444413 PsaC Photosystem I reaction center iron-sulfur center subunit VII, PsaC [Energy production and conversion]. Photosystem I reaction center iron-sulfur center subunit VII, PsaC is part of the Pathway/BioSystem: Photosystem I 82 matched cddid_all.tbl CDD COG5704 COG5704 444414 PsaD Photosystem I reaction center subunit II, PsaD [Energy production and conversion]. Photosystem I reaction center subunit II, PsaD is part of the Pathway/BioSystem: Photosystem I 142 matched cddid_all.tbl CDD COG5705 COG5705 444415 PsaE Photosystem I reaction center subunit IV, PsaE [Energy production and conversion]. Photosystem I reaction center subunit IV, PsaE is part of the Pathway/BioSystem: Photosystem I 68 matched cddid_all.tbl CDD COG5706 COG5706 444416 PsaF Photosystem I reaction center subunit III, PsaF [Energy production and conversion]. Photosystem I reaction center subunit III, PsaF is part of the Pathway/BioSystem: Photosystem I 164 matched cddid_all.tbl CDD COG5707 COG5707 444417 PsaI Photosystem I reaction center subunit VIII, PsaI [Energy production and conversion]. Photosystem I reaction center subunit VIII, PsaI is part of the Pathway/BioSystem: Photosystem I 38 matched cddid_all.tbl CDD COG5708 COG5708 444418 PsaJ Photosystem I reaction center subunit IX, PsaJ [Energy production and conversion]. Photosystem I reaction center subunit IX, PsaJ is part of the Pathway/BioSystem: Photosystem I 42 matched cddid_all.tbl CDD COG5709 COG5709 444419 PsaK Photosystem I reaction center subunit X, PsaK [Energy production and conversion]. Photosystem I reaction center subunit X, PsaK is part of the Pathway/BioSystem: Photosystem I 90 matched cddid_all.tbl CDD COG5710 COG5710 444420 PsaL Photosystem I reaction center subunit XI, PsaL [Energy production and conversion]. Photosystem I reaction center subunit XI, PsaL is part of the Pathway/BioSystem: Photosystem I 165 matched cddid_all.tbl CDD COG5711 COG5711 444421 PsaM Photosystem I reaction center subunit XII, PsaM [Energy production and conversion]. Photosystem I reaction center subunit XII, PsaM is part of the Pathway/BioSystem: Photosystem I 29 matched cddid_all.tbl CDD COG5712 COG5712 444422 Ycf4 Photosystem I assembly protein Ycf4 [Energy production and conversion]. Photosystem I assembly protein Ycf4 is part of the Pathway/BioSystem: Photosystem I 188 matched cddid_all.tbl CDD COG5713 COG5713 444423 Ycf3 Photosystem I assembly protein Ycf3, contains TPR repeats [Energy production and conversion]. Photosystem I assembly protein Ycf3, contains TPR repeats is part of the Pathway/BioSystem: Photosystem I 173 matched cddid_all.tbl CDD COG5714 COG5714 444424 Ycf37 Photosystem I assembly protein Ycf37, contains TPR repeats [Energy production and conversion]. Photosystem I assembly protein Ycf37, contains TPR repeats is part of the Pathway/BioSystem: Photosystem I 176 matched cddid_all.tbl CDD COG5715 COG5715 444425 Ycf33 Photosystem I auxiliary component Ycf33, involved in cyclic electron transport [Energy production and conversion]. Photosystem I auxiliary component Ycf33, involved in cyclic electron transport is part of the Pathway/BioSystem: Photosystem I 67 matched cddid_all.tbl CDD COG5716 COG5716 444426 PsbA Photosystem II reaction center D1, PsbA [Energy production and conversion]. Photosystem II reaction center D1, PsbA is part of the Pathway/BioSystem: Photosystem II 356 matched cddid_all.tbl CDD COG5717 COG5717 444427 PsbB Photosystem II reaction center chlorophyll a-binding protein CP47, PsbB [Energy production and conversion]. Photosystem II reaction center chlorophyll a-binding protein CP47, PsbB is part of the Pathway/BioSystem: Photosystem II 510 matched cddid_all.tbl CDD COG5718 COG5718 444428 PsbC Photosystem II reaction center chlorophyll a-binding protein CP43, PsbC [Energy production and conversion]. Photosystem II reaction center chlorophyll a-binding protein CP43, PsbC is part of the Pathway/BioSystem: Photosystem II 462 matched cddid_all.tbl CDD COG5719 COG5719 444429 PsbD Photosystem II reaction center D2, PsbD [Energy production and conversion]. Photosystem II reaction center D2, PsbD is part of the Pathway/BioSystem: Photosystem II 316 matched cddid_all.tbl CDD COG5720 COG5720 444430 PsbE Photosystem II cytochrome b559 alpha subunit, PsbE [Energy production and conversion]. Photosystem II cytochrome b559 alpha subunit, PsbE is part of the Pathway/BioSystem: Photosystem II 83 matched cddid_all.tbl CDD COG5721 COG5721 444431 PsbF Photosystem II cytochrome b559 beta chain, PsbF [Energy production and conversion]. Photosystem II cytochrome b559 beta chain, PsbF is part of the Pathway/BioSystem: Photosystem II 45 matched cddid_all.tbl CDD COG5722 COG5722 444432 PsbH Photosystem II reaction center 10 kDa phosphoprotein, PsbH [Energy production and conversion]. Photosystem II reaction center 10 kDa phosphoprotein, PsbH is part of the Pathway/BioSystem: Photosystem II 67 matched cddid_all.tbl CDD COG5723 COG5723 444433 PsbI Photosystem II reaction center protein I, PsbI, oxygen-evolving center [Energy production and conversion]. Photosystem II reaction center protein I, PsbI, oxygen-evolving center is part of the Pathway/BioSystem: Photosystem II 38 matched cddid_all.tbl CDD COG5724 COG5724 444434 PsbJ Photosystem II reaction center protein J, PsbJ [Energy production and conversion]. Photosystem II reaction center protein J, PsbJ is part of the Pathway/BioSystem: Photosystem II 38 matched cddid_all.tbl CDD COG5725 COG5725 444435 PsbK Photosystem II reaction center protein K, PsbK [Energy production and conversion]. Photosystem II reaction center protein K, PsbK is part of the Pathway/BioSystem: Photosystem II 45 matched cddid_all.tbl CDD COG5726 COG5726 444436 PsbL Photosystem II reaction center protein L, PsbL [Energy production and conversion]. Photosystem II reaction center protein L, PsbL is part of the Pathway/BioSystem: Photosystem II 38 matched cddid_all.tbl CDD COG5727 COG5727 444437 PsbM Photosystem II reaction center protein M, PsbM [Energy production and conversion]. Photosystem II reaction center protein M, PsbM is part of the Pathway/BioSystem: Photosystem II 36 matched cddid_all.tbl CDD COG5728 COG5728 444438 PsbN Photosystem II reaction center protein N, PsbN [Energy production and conversion]. Photosystem II reaction center protein N, PsbN is part of the Pathway/BioSystem: Photosystem II 43 matched cddid_all.tbl CDD COG5729 COG5729 444439 PsbO Photosystem II reaction center Mn-stabilizing protein, PsbO [Energy production and conversion]. Photosystem II reaction center Mn-stabilizing protein, PsbO is part of the Pathway/BioSystem: Photosystem II 275 matched cddid_all.tbl CDD COG5730 COG5730 444440 PsbP Photosystem II reaction center protein P, PsbP [Energy production and conversion]. Photosystem II reaction center protein P, PsbP is part of the Pathway/BioSystem: Photosystem II 180 matched cddid_all.tbl CDD COG5731 COG5731 444441 PsbT Photosystem II reaction center protein T, PsbT/Ycf8 [Energy production and conversion]. Photosystem II reaction center protein T, PsbT/Ycf8 is part of the Pathway/BioSystem: Photosystem II 33 matched cddid_all.tbl CDD COG5732 COG5732 444442 PsbW Photosystem II reaction center protein W, PsbW/Psb28/Ycf79 [Energy production and conversion]. Photosystem II reaction center protein W, PsbW/Psb28/Ycf79 is part of the Pathway/BioSystem: Photosystem II 111 matched cddid_all.tbl CDD COG5733 COG5733 444443 PsbX Photosystem II reaction center protein X, PsbX [Energy production and conversion]. Photosystem II reaction center protein X, PsbX is part of the Pathway/BioSystem: Photosystem II 39 matched cddid_all.tbl CDD COG5734 COG5734 444444 PsbY Photosystem II reaction center protein Y, PsbY [Energy production and conversion]. Photosystem II reaction center protein Y, PsbY is part of the Pathway/BioSystem: Photosystem II 39 matched cddid_all.tbl CDD COG5735 COG5735 444445 PsbZ Photosystem II reaction center protein Z, PsbZ/Ycf9 [Energy production and conversion]. Photosystem II reaction center protein Z, PsbZ/Ycf9 is part of the Pathway/BioSystem: Photosystem II 61 matched cddid_all.tbl CDD COG5736 COG5736 444446 Psb27 Photosystem II reaction center 11 kD protein, Psb27 [Energy production and conversion]. Photosystem II reaction center 11 kD protein, Psb27 is part of the Pathway/BioSystem: Photosystem II 132 matched cddid_all.tbl CDD COG5737 COG5737 444447 PsbU Photosystem II 12 kDa extrinsic protein PsbU [Energy production and conversion]. Photosystem II 12 kDa extrinsic protein PsbU is part of the Pathway/BioSystem: Photosystem II 143 matched cddid_all.tbl CDD COG5738 COG5738 444448 PsbV Photosystem II cytochrome c550, PsbV [Energy production and conversion]. Photosystem II cytochrome c550, PsbV is part of the Pathway/BioSystem: Photosystem II 163 matched cddid_all.tbl CDD COG5739 COG5739 444449 PsbQ Photosystem II oxygen-evolving enhancer PsbQ/CyanoQ [Energy production and conversion]. Photosystem II oxygen-evolving enhancer PsbQ/CyanoQ is part of the Pathway/BioSystem: Photosystem II 148 matched cddid_all.tbl CDD COG5740 COG5740 444450 THF1 Photosystem II biogenesis protein Psb29 (thylakoid formation protein THF1) [Energy production and conversion]. Photosystem II biogenesis protein Psb29 (thylakoid formation protein THF1) is part of the Pathway/BioSystem: Photosystem II 226 matched cddid_all.tbl CDD COG5741 COG5741 444451 Ycf12 Photosystem II subunit Psb30 (=Ycf12) [Energy production and conversion]. Photosystem II subunit Psb30 (=Ycf12) is part of the Pathway/BioSystem: Photosystem II 41 matched cddid_all.tbl CDD COG5742 COG5742 444452 IsiA Chlorophyll-binding protein PcbABC/IsiA [Energy production and conversion]. 346 matched cddid_all.tbl CDD COG5743 COG5743 444453 LHCA5 Photosystem I light harvesting complex protein, LHCA5/LHCA6/HLI5/Ycf17 family [Energy production and conversion]. Photosystem I light harvesting complex protein, LHCA5/LHCA6/HLI5/Ycf17 family is part of the Pathway/BioSystem: Photosystem I 62 matched cddid_all.tbl CDD COG5744 COG5744 444454 PsbC2 PsbC-PsaL fusion protein [Energy production and conversion]. 498 matched cddid_all.tbl CDD COG5745 COG5745 444455 PsaX Photosystem I protein PsaX [Energy production and conversion]. Photosystem I protein PsaX is part of the Pathway/BioSystem: Photosystem I 38 matched cddid_all.tbl CDD COG5746 COG5746 444456 BchB Light-independent protochlorophyllide reductase subunit B, BchB (= ChlB) [Coenzyme transport and metabolism]. 536 matched cddid_all.tbl CDD COG5747 COG5747 444457 BchN Light-independent protochlorophyllide reductase subunit N, BchN (=ChlN) [Coenzyme transport and metabolism]. 423 matched cddid_all.tbl CDD COG5748 COG5748 444458 LPOR Light-dependent NADPH-protochlorophyllide oxidoreductase [Coenzyme transport and metabolism]. 324 matched cddid_all.tbl CDD COG5749 COG5749 444459 PobA Chlorophyllide a oxygenase/letal leaf spot protein [Coenzyme transport and metabolism]. 349 matched cddid_all.tbl CDD COG5750 COG5750 444460 Ycf53 Chlorophyll biosynthesis regulator GUN4/Ycf53 domain [Signal transduction mechanisms]. 233 matched cddid_all.tbl CDD COG5751 COG5751 444461 A-ycf53 Photosynthetic regulator, contains GUN4/Ycf53 domain and N-terminal all-alpha domain [Signal transduction mechanisms]. 240 matched cddid_all.tbl CDD COG5752 COG5752 444462 K-ycf53 Signaling protein combining a Ser/Thr protein kinase domain and the GUN4/Ycf53 porphyrin-binding domain [Signal transduction mechanisms]. 466 matched cddid_all.tbl CDD COG5753 COG5753 444463 BchX Bacteriochlorophyllide reductase subunit BchX [Coenzyme transport and metabolism]. 304 matched cddid_all.tbl CDD COG5754 COG5754 444464 BchY Bacteriochlorophyllide reductase subunit BchY [Coenzyme transport and metabolism]. 509 matched cddid_all.tbl CDD COG5755 COG5755 444465 BchZ Bacteriochlorophyllide reductase subunit BchZ [Coenzyme transport and metabolism]. 479 matched cddid_all.tbl CDD COG5756 COG5756 444466 Atp1 FoF1-type ATP synthase subunit Atp1, cyanobacterial family [Energy production and conversion]. FoF1-type ATP synthase subunit Atp1, cyanobacterial family is part of the Pathway/BioSystem: FoF1-type ATP synthase 139 matched cddid_all.tbl CDD COG5757 COG5757 444467 AtpR Na+-translocating membrane ATPase (N-ATPase) assembly subunit AtpR [Energy production and conversion]. Na+-translocating membrane ATPase (N-ATPase) assembly subunit AtpR is part of the Pathway/BioSystem: FoF1-type ATP synthase 100 matched cddid_all.tbl CDD COG5758 COG5758 444468 Tab2 RNA-binding protein Tab2, reqiured for psaB translation [Energy production and conversion, Translation, ribosomal structure and biogenesis]. 282 matched cddid_all.tbl CDD COG5759 COG5759 444469 Ycf59 Mg-protoporphyrin IX monomethyl ester cyclase BchE, aerobic (=Ycf59) [Coenzyme transport and metabolism]. 352 matched cddid_all.tbl CDD COG5760 COG5760 444470 PetP Cyanobacterial/red algae cytochrome b6f complex subunit PetP (= Ycf86), DUF2862 (PF11061) family [Energy production and conversion]. 63 matched cddid_all.tbl CDD COG5761 COG5761 444471 Cp12 Cyanobacterial/chloroplast protein CP12, regulates Calvin cycle by forming a complex with GAPDH and phosphoribulokinase [Energy production and conversion]. 74 matched cddid_all.tbl CDD COG5762 COG5762 444472 PM23 Uncharacterized cyanobacterial/plant protein PM23 (seed maturation protein), contains DUF760 (PF05542) domain [Energy production and conversion]. 113 matched cddid_all.tbl CDD COG5763 COG5763 444473 Ycf20 Cyanobacterial/chloroplast protein Ycf20, involved in dissipation of absorbed light energy, DUF565 (PF04483) domain [Energy production and conversion]. 110 matched cddid_all.tbl CDD COG5764 COG5764 444474 Ycf34 Cyanobacterial/chloroplast FeS cluster protein Ycf34, regulator of photosynthetic electron transport, PF10718 domain [Energy production and conversion, Signal transduction mechanisms]. 82 matched cddid_all.tbl CDD COG5765 COG5765 444475 Ycf35 Uncharacterized cyanobacterial/chloroplast stress-induced protein Ycf35, DUF1257 domain [Energy production and conversion]. 123 matched cddid_all.tbl CDD COG5766 COG5766 444476 Ycf36 Uncharacterized cyanobacterial/chloroplast membrane protein Ycf36, DUF1230 (PF06799) domain [Energy production and conversion]. 165 matched cddid_all.tbl CDD COG5767 COG5767 444477 Ycf51 Uncharacterized cyanobacterial/chloroplast membrane protein Ycf51, DUF2518 (PF10726) domain [Energy production and conversion]. 172 matched cddid_all.tbl CDD COG5768 COG5768 444478 Ycf55 Cyanobacterial response regulator with REC-Ycf55 domain architecture [Energy production and conversion, Signal transduction mechanisms]. 579 matched cddid_all.tbl CDD COG5769 COG5769 444479 Tic20 Cyanobacterial/chloroplast membrane protein Tic20/Ycf60, involved in chloroplast protein import [Energy production and conversion]. 159 matched cddid_all.tbl CDD COG5770 COG5770 444480 Ycf66 Uncharacterized cyanobacterial protein with Ycf66_N domain [Energy production and conversion]. 92 matched cddid_all.tbl CDD COG5771 COG5771 444481 Pro0776 Uncharacterized cyanobacterial/chloroplast protein Pro0776, algal eyespot protein with methylated Arg, DUF1350 (PF07082) domain [Energy production and conversion]. 252 matched cddid_all.tbl CDD COG5772 COG5772 444482 Tic21 Cyanobacterial/chloroplast membrane protein Tic21, involved in chloroplast protein import, DUF3611 (PF12263) domain [Energy production and conversion]. 189 matched cddid_all.tbl CDD COG5773 COG5773 444483 Pro0765 Uncharacterized cyanobacterial/plant membrane protein Pro0765, DUF3082 (PF11282) domain [Energy production and conversion]. 107 matched cddid_all.tbl CDD COG5774 COG5774 444484 Ccb1 Cytochrome b6 maturation protein CCB1 [Energy production and conversion, Posttranslational modification, protein turnover, chaperones]. 176 matched cddid_all.tbl CDD COG5775 COG5775 444485 Ccr2 Thylakoid membrane protein DAC/CCR2, involved in assembly of b6/f complex and response to cold stress, DUF3007 (PF11460) family [Energy production and conversion]. 103 matched cddid_all.tbl CDD COG5776 COG5776 444486 PH Bacterial PH (pleckstrin homology) domain [Energy production and conversion]. 128 matched cddid_all.tbl CDD COG5777 COG5777 444487 Pro0498 Uncharacterized cyanobacterial/plant membrane protein Pro0498, contains N-terminal TPR repeats [Energy production and conversion]. 172 matched cddid_all.tbl CDD COG5778 COG5778 444488 Pam68 Photosystem II assembly factor PAM68, DUF3464 (PF11947) domain [Energy production and conversion]. 158 matched cddid_all.tbl CDD COG5779 COG5779 444489 TAP/TPM Thylakoid acid phosphatase, contains TAP/TPM domain [Energy production and conversion]. 268 matched cddid_all.tbl CDD COG5780 COG5780 444490 Ape1 Acclimation of photosynthesis to environment protein APE1, affects chlorophyll fluorescence, DUF2854 (PF11016) domain [Energy production and conversion, Signal transduction mechanisms]. 181 matched cddid_all.tbl CDD COG5781 COG5781 444491 Ccb2 Cytochrome b6 maturation protein CCB2 [Energy production and conversion, Posttranslational modification, protein turnover, chaperones]. 220 matched cddid_all.tbl CDD COG5782 COG5782 444492 NdhV NAD(P)H dehydrogenase cyanobacteria/chloroplast-specific subunit NdhV, DUF2996 (PF11210) domain [Energy production and conversion]. 151 matched cddid_all.tbl CDD COG5783 COG5783 444493 CSAP Chloroplast senescence-associated protein CSAP, DUF1997 (PF09366) domain [Energy production and conversion]. 181 matched cddid_all.tbl CDD COG5784 COG5784 444494 Pro1025 Uncharacterized cyanobacterial/plant protein Pro1025, DUF3531 (PF12049) domain [Energy production and conversion]. 148 matched cddid_all.tbl CDD COG5785 COG5785 444495 Cr066 Uncharacterized cyanobacterial/chloroplast protein CR066, DUF3172 (PF11371) domain [Energy production and conversion]. 181 matched cddid_all.tbl CDD COG5786 COG5786 444496 LPA3 Cyanobacterial/plant protein LPA3, possible role in PSII assembly, DUF1995 (PF09353) domain [Energy production and conversion]. 248 matched cddid_all.tbl CDD COG5787 COG5787 444497 Alr2454 Uncharacterized cyanobacterial/plant protein Alr2454, DUF3067 (PF11267) family [Energy production and conversion]. 102 matched cddid_all.tbl CDD COG5788 COG5788 444498 SipA Cyanobacterial/chloroplast protein SipA, regulator of sensor kinase NblS (Hik33), DUF3148 (PF11347) family [Energy production and conversion, Signal transduction mechanisms]. 73 matched cddid_all.tbl CDD COG5789 COG5789 444499 Pro1627 Uncharacterized cyanobacterial/plant protein Pro1627, DUF3143 (PF11341) family [Energy production and conversion]. 90 matched cddid_all.tbl CDD COG5790 COG5790 444500 NdhS NAD(P)H dehydrogenase cyanobacteria/chloroplast-specific subunit S (CRR31) [Energy production and conversion]. 59 matched cddid_all.tbl CDD COG5791 COG5791 444501 CRR7 NAD(P)H dehydrogenase cyanobacteria/chloroplast-specific auxiliary subunit CRR7 [Energy production and conversion]. 85 matched cddid_all.tbl CDD COG5792 COG5792 444502 CBS-CP12 Fusion of CP12 with N-terminal CBS domain pair [Energy production and conversion, Signal transduction mechanisms]. 203 matched cddid_all.tbl CDD COG5801 COG5801 444503 Spo0A Stage 0 sporulation initiation regulator Spo0A (response regulator, REC-HTH domains) [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. 264 matched cddid_all.tbl CDD COG5802 COG5802 444504 Spo0B Stage 0 sporulation initiation phosphotransferase Spo0B [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. 170 matched cddid_all.tbl CDD COG5803 COG5803 444505 Spo0F Stage 0 sporulation initiation response regulator Spo0F [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. 119 matched cddid_all.tbl CDD COG5804 COG5804 444506 Spo0E Stage 0 sporulation regulatory phosphatase Spo0E [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. 55 matched cddid_all.tbl CDD COG5805 COG5805 444507 KinA Sporulation sensor histidine kinase A (Stage II sporulation protein SpoIIF/SpoIIJ) [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. 496 matched cddid_all.tbl CDD COG5806 COG5806 444508 KinB Sporulation sensor histidine kinase B [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. 412 matched cddid_all.tbl CDD COG5807 COG5807 444509 KinC Sporulation sensor histidine kinase C [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. 358 matched cddid_all.tbl CDD COG5808 COG5808 444510 KinD Sporulation sensor histidine kinase D [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. 454 matched cddid_all.tbl CDD COG5809 COG5809 444511 KinE Sporulation sensor histidine kinase E [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. 489 matched cddid_all.tbl CDD COG5810 COG5810 444512 KbaA Sporulation protein KbaA, activator of histidine kinase KinB [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. 211 matched cddid_all.tbl CDD COG5811 COG5811 444513 SigE Sporulation sigma factor SigE (mother cell-specific, SpoIIGB) [Cell cycle control, cell division, chromosome partitioning, Transcription]. 232 matched cddid_all.tbl CDD COG5812 COG5812 444514 SigF Sporulation sigma factor SigF (forespore-specific, SpoIIAC) [Cell cycle control, cell division, chromosome partitioning, Transcription]. 245 matched cddid_all.tbl CDD COG5813 COG5813 444515 SigG Sporulation sigma factor SigG (forespore-specific, SpoIIIG) [Cell cycle control, cell division, chromosome partitioning, Transcription]. 257 matched cddid_all.tbl CDD COG5814 COG5814 444516 SigK Sporulation sigma factor SigK (mother cell-specific, SpoIIIC/SpoIVCB) [Cell cycle control, cell division, chromosome partitioning, Transcription]. 234 matched cddid_all.tbl CDD COG5815 COG5815 444517 SpoIIAA Stage II sporulation protein SpoIIAA (antagonist of anti-sigma F factor) [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. 110 matched cddid_all.tbl CDD COG5816 COG5816 444518 SpoIIB Stage II sporulation protein SpoIIB (spatial and temporal regulation of the dissolution of septal peptidoglycan during engulfment) [Cell cycle control, cell division, chromosome partitioning]. 322 matched cddid_all.tbl CDD COG5817 COG5817 444519 SpoIIE Stage II sporulation protein SpoIIE/SpoIIH (serine phosphatase - sigma-F activation) [Cell cycle control, cell division, chromosome partitioning]. 803 matched cddid_all.tbl CDD COG5818 COG5818 444520 SpoIIGA Stage II sporulation protein SpoIIGA (protease, processing of pro-sigma-E to active sigma-E) [Cell cycle control, cell division, chromosome partitioning, Transcription, Posttranslational modification, protein turnover, chaperones]. 301 matched cddid_all.tbl CDD COG5819 COG5819 444521 SpoIIP Stage II sporulation protein SpoIIP, required for dissolution of the septal cell wall [Cell cycle control, cell division, chromosome partitioning]. 256 matched cddid_all.tbl CDD COG5820 COG5820 444522 SpoIIQ Stage II sporulation protein SpoIIQ, required for engulfement [Cell cycle control, cell division, chromosome partitioning]. 224 matched cddid_all.tbl CDD COG5821 COG5821 444523 SpoIIQ2 Stage II sporulation protein SpoIIQ, clostridial version, metallopeptidase M23 family [Cell cycle control, cell division, chromosome partitioning]. 200 matched cddid_all.tbl CDD COG5822 COG5822 444524 SpoIIR Stage II sporulation protein SpoIIR, required for processing of pro-sigma-E [Cell cycle control, cell division, chromosome partitioning]. 211 matched cddid_all.tbl CDD COG5823 COG5823 444525 SpoIIIAB Stage III sporulation protein SpoIIIAB, component of the engulfment complex [Cell cycle control, cell division, chromosome partitioning]. 172 matched cddid_all.tbl CDD COG5824 COG5824 444526 SpoIIIAC Stage III sporulation protein SpoIIIAC, component of the engulfment complex [Cell cycle control, cell division, chromosome partitioning]. 65 matched cddid_all.tbl CDD COG5825 COG5825 444527 SpoIIIAD Stage III sporulation protein SpoIIIAD, component of the engulfment complex [Cell cycle control, cell division, chromosome partitioning]. 127 matched cddid_all.tbl CDD COG5826 COG5826 444528 SpoIIIAE Stage III sporulation protein SpoIIIAE, component of the engulfment complex [Cell cycle control, cell division, chromosome partitioning]. 394 matched cddid_all.tbl CDD COG5827 COG5827 444529 SpoIIIAF Stage III sporulation protein SpoIIIAF, component of the engulfment complex [Cell cycle control, cell division, chromosome partitioning]. 204 matched cddid_all.tbl CDD COG5828 COG5828 444530 SpoIIIAG Stage III sporulation protein SpoIIIAG, component of the engulfment complex [Cell cycle control, cell division, chromosome partitioning]. 202 matched cddid_all.tbl CDD COG5829 COG5829 444531 SpoIIIAH Stage III sporulation protein SpoIIIAH, component of the engulfment complex [Cell cycle control, cell division, chromosome partitioning]. 187 matched cddid_all.tbl CDD COG5830 COG5830 444532 SpoIIID Stage III sporulation protein SpoIIID, transcriptional regulator of sigma-E- and sigma-K-dependent genes [Cell cycle control, cell division, chromosome partitioning, Transcription]. 84 matched cddid_all.tbl CDD COG5831 COG5831 444533 SpoIVA Stage IV sporulation protein SpoIVA, required for spore cortex formation and coat assembly [Cell cycle control, cell division, chromosome partitioning]. 492 matched cddid_all.tbl CDD COG5832 COG5832 444534 SpoIVB Stage IV sporulation protein SpoIVB, serine protease, degrades SpoIIQ, SpoIVFA [Cell cycle control, cell division, chromosome partitioning, Posttranslational modification, protein turnover, chaperones]. 438 matched cddid_all.tbl CDD COG5833 COG5833 444535 SpoIVFA Stage IV sporulation protein SpoIVFA, regulates SpoIVFB [Cell cycle control, cell division, chromosome partitioning]. 219 matched cddid_all.tbl CDD COG5834 COG5834 444536 SpoVAA Stage V sporulation protein SpoVAA, subunit of dipicolinate uptake complex [Cell cycle control, cell division, chromosome partitioning, Amino acid transport and metabolism]. 206 matched cddid_all.tbl CDD COG5835 COG5835 444537 SpoVAB Stage V sporulation protein SpoVAB, subunit of dipicolinate uptake complex [Cell cycle control, cell division, chromosome partitioning, Amino acid transport and metabolism]. 136 matched cddid_all.tbl CDD COG5836 COG5836 444538 SpoVAC Stage V sporulation protein SpoVAC, subunit of dipicolinate uptake complex [Cell cycle control, cell division, chromosome partitioning, Amino acid transport and metabolism]. 149 matched cddid_all.tbl CDD COG5837 COG5837 444539 SpoVAD Stage V sporulation protein SpoVAD, subunit of dipicolinate uptake complex [Cell cycle control, cell division, chromosome partitioning, Amino acid transport and metabolism]. 336 matched cddid_all.tbl CDD COG5838 COG5838 444540 SpoVAEA Stage V sporulation protein SpoVAEA, mutants lead to the production of immature spores [Cell cycle control, cell division, chromosome partitioning]. 193 matched cddid_all.tbl CDD COG5839 COG5839 444541 SpoVAEB Stage V sporulation protein SpoVAEB, subunit of dipicolinate uptake complex [Cell cycle control, cell division, chromosome partitioning, Amino acid transport and metabolism]. 116 matched cddid_all.tbl CDD COG5840 COG5840 444542 SpoVAF Stage V sporulation protein SpoVAF, subunit of dipicolinate uptake complex, GerA superfamily [Cell cycle control, cell division, chromosome partitioning, Amino acid transport and metabolism]. 488 matched cddid_all.tbl CDD COG5841 COG5841 444543 SpoVB Stage V sporulation protein SpoVB/SpoIIIF, required for spore cortex synthesis [Cell cycle control, cell division, chromosome partitioning]. 532 matched cddid_all.tbl CDD COG5842 COG5842 444544 DpaA Dipicolinate synthase subunit A (sporulation protein SpoVFA) [Cell cycle control, cell division, chromosome partitioning, Amino acid transport and metabolism]. 288 matched cddid_all.tbl CDD COG5843 COG5843 444545 DpaB Dipicolinate synthase subunit B (sporulation protein SpoVFB) [Cell cycle control, cell division, chromosome partitioning, Amino acid transport and metabolism]. 195 matched cddid_all.tbl CDD COG5844 COG5844 444546 SpoVM Stage V sporulation protein SpoVM, required for spore cortex and coat synthesis [Cell cycle control, cell division, chromosome partitioning]. 26 matched cddid_all.tbl CDD COG5845 COG5845 444547 SpoVT Stage V sporulation protein SpoVT, regulator of stationary/sporulation gene expression [Cell cycle control, cell division, chromosome partitioning, Transcription]. 180 matched cddid_all.tbl CDD COG5846 COG5846 444548 SpoVID Stage VI sporulation protein SpoVID (LysM domain), required for assembly of the spore coat [Cell cycle control, cell division, chromosome partitioning]. 398 matched cddid_all.tbl CDD COG5847 COG5847 444549 SpoVIF Stage VI sporulation protein SpoVIF, required for heat resistance [Cell cycle control, cell division, chromosome partitioning]. 85 matched cddid_all.tbl CDD COG5848 COG5848 444550 BofA SigmaK-processing regulatory protein BofA (Bypass-of-forespore protein A) [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. 88 matched cddid_all.tbl CDD COG5849 COG5849 444551 BofC SigmaK checkpoint regulator BofC (Bypass-of-forespore protein C) [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. 183 matched cddid_all.tbl CDD COG5850 COG5850 444552 RsfA Prespore-specific transcriptional regulator RsfA [Cell cycle control, cell division, chromosome partitioning, Transcription]. 204 matched cddid_all.tbl CDD COG5851 COG5851 444553 Sda Stage 0 sporulation inhibitor Sda, checkpoint for initiation of sporulation and replication [Cell cycle control, cell division, chromosome partitioning, Replication, recombination, and repair]. 46 matched cddid_all.tbl CDD COG5852 COG5852 444554 SspA/SspB/SspC/SspD Small acid-soluble spore protein SspA/SspB/SspC/SspD (alpha/beta-type) [Cell cycle control, cell division, chromosome partitioning]. 70 matched cddid_all.tbl CDD COG5853 COG5853 444555 SspE Small acid-soluble spore protein SspE (gamma-type) [Cell cycle control, cell division, chromosome partitioning]. 69 matched cddid_all.tbl CDD COG5854 COG5854 444556 SspF Small acid-soluble spore protein SspF (alpha/beta-type) [Cell cycle control, cell division, chromosome partitioning]. 60 matched cddid_all.tbl CDD COG5855 COG5855 444557 SspH Small acid-soluble spore protein SspH/YfjU [Cell cycle control, cell division, chromosome partitioning]. 59 matched cddid_all.tbl CDD COG5856 COG5856 444558 SspI Small acid-soluble spore protein SspI [Cell cycle control, cell division, chromosome partitioning]. 66 matched cddid_all.tbl CDD COG5857 COG5857 444559 SspK Small acid-soluble spore protein SspK [Cell cycle control, cell division, chromosome partitioning]. 47 matched cddid_all.tbl CDD COG5858 COG5858 444560 SspL Small acid-soluble spore protein SspL [Cell cycle control, cell division, chromosome partitioning]. 44 matched cddid_all.tbl CDD COG5859 COG5859 444561 SspN Small acid-soluble spore protein SspN [Cell cycle control, cell division, chromosome partitioning]. 47 matched cddid_all.tbl CDD COG5860 COG5860 444562 SspO Small acid-soluble spore protein SspO/CotK [Cell cycle control, cell division, chromosome partitioning]. 49 matched cddid_all.tbl CDD COG5861 COG5861 444563 SspP Small acid-soluble spore protein SspP/CotL [Cell cycle control, cell division, chromosome partitioning]. 48 matched cddid_all.tbl CDD COG5862 COG5862 444564 CsgA Small acid-soluble spore protein CsgA [Cell cycle control, cell division, chromosome partitioning]. 82 matched cddid_all.tbl CDD COG5863 COG5863 444565 Tlp Small acid-soluble spore protein Tlp (thioredoxin-like protein) [Cell cycle control, cell division, chromosome partitioning]. 69 matched cddid_all.tbl CDD COG5864 COG5864 444566 SASP Small acid-soluble spore protein SAS2, clostridial type [Cell cycle control, cell division, chromosome partitioning]. 67 matched cddid_all.tbl CDD COG5865 COG5865 444567 CsfB Forespore-specific anti-sigma-G factor CsfB/Gin [Cell cycle control, cell division, chromosome partitioning, Transcription]. 63 matched cddid_all.tbl CDD COG5866 COG5866 444568 YabG Sporulation-specific protease YabG [Cell cycle control, cell division, chromosome partitioning, Posttranslational modification, protein turnover, chaperones]. 289 matched cddid_all.tbl CDD COG5867 COG5867 444569 YabK Anti-sigma-F factor Fin [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]. 76 matched cddid_all.tbl CDD COG5868 COG5868 444570 YabP Sporulation protein YabP [Cell cycle control, cell division, chromosome partitioning]. 94 matched cddid_all.tbl CDD COG5869 COG5869 444571 YabQ Spore cortex formation membrane protein YabQ [Cell cycle control, cell division, chromosome partitioning]. 187 matched cddid_all.tbl CDD COG5870 COG5870 444572 YbaK Uncharacterized sporulation protein YbaK, contains DUF2521 domain (not related to E. coli deacylase YbaK, COG2606) [Cell cycle control, cell division, chromosome partitioning, Transcription]. 146 matched cddid_all.tbl CDD COG5871 COG5871 444573 YqfC Spore cortex protein YqfC, YabP family [Cell cycle control, cell division, chromosome partitioning]. 93 matched cddid_all.tbl CDD COG5872 COG5872 444574 YqfD Stage IV sporulation protein YqfD [Cell cycle control, cell division, chromosome partitioning]. 399 matched cddid_all.tbl CDD COG5873 COG5873 444575 YqzE Uncharacterized sporulation protein YqzE [Cell cycle control, cell division, chromosome partitioning]. 58 matched cddid_all.tbl CDD COG5874 COG5874 444576 YtxC Uncharacterized sporulation protein YtxC [Cell cycle control, cell division, chromosome partitioning]. 298 matched cddid_all.tbl CDD COG5875 COG5875 444577 YunB Uncharacterized sporulation protein YunB [Cell cycle control, cell division, chromosome partitioning]. 227 matched cddid_all.tbl CDD COG5876 COG5876 444578 COG5876 Uncharacterized sporulation protein YozQ [Function unknown]. 53 matched cddid_all.tbl CDD COG5877 COG5877 444579 YjcM1 Stand-alone amidase domain [Cell cycle control, cell division, chromosome partitioning]. 172 matched cddid_all.tbl CDD COG5878 COG5878 444580 YyaC Uncharacterized sporulation protein YyaC,contains DUF1256 domain [Cell cycle control, cell division, chromosome partitioning]. 195 matched cddid_all.tbl CDD COG5879 COG5879 444581 CotD Spore coat protein CotD [Cell cycle control, cell division, chromosome partitioning]. 87 matched cddid_all.tbl CDD COG5880 COG5880 444582 CotE Spore coat protein CotE [Cell cycle control, cell division, chromosome partitioning]. 177 matched cddid_all.tbl CDD COG5881 COG5881 444583 CotI Spore coat protein CotI/CotS, protein kinase superfamily [Cell cycle control, cell division, chromosome partitioning]. 331 matched cddid_all.tbl CDD COG5882 COG5882 444584 CotJA Spore coat protein CotJA, required for the assembly of CotJC [Cell cycle control, cell division, chromosome partitioning]. 73 matched cddid_all.tbl CDD COG5883 COG5883 444585 CotJB Spore coat protein CotJB [Cell cycle control, cell division, chromosome partitioning]. 85 matched cddid_all.tbl CDD COG5884 COG5884 444586 CotN Spore coat protein CotN/TasA [Cell cycle control, cell division, chromosome partitioning]. 196 matched cddid_all.tbl CDD COG5885 COG5885 444587 CotO Spore coat protein CotO/YjbX [Cell cycle control, cell division, chromosome partitioning]. 174 matched cddid_all.tbl CDD COG5886 COG5886 444588 CotV Spore coat protein CotV/CotX (outer spore coat) [Cell cycle control, cell division, chromosome partitioning]. 148 matched cddid_all.tbl CDD COG5887 COG5887 444589 CotW Spore coat protein CotW (outer spore coat) [Cell cycle control, cell division, chromosome partitioning]. 81 matched cddid_all.tbl CDD COG5888 COG5888 444590 CotY Spore coat protein CotY/CotZ (outer spore coat) [Cell cycle control, cell division, chromosome partitioning]. 153 matched cddid_all.tbl CDD COG5889 COG5889 444591 GerQ Spore coat protein GerQ/YwdL (inner spore coat) [Cell cycle control, cell division, chromosome partitioning]. 161 matched cddid_all.tbl CDD COG5890 COG5890 444592 YhbB Uncharacterized sporulation proteins YjcM and YhbB, contain C-terminal amidase domain [Cell cycle control, cell division, chromosome partitioning]. 269 matched cddid_all.tbl CDD COG5891 COG5891 444593 YheC Spore coat protein YheC/YheD, ATP-grasp superfamily [Cell cycle control, cell division, chromosome partitioning]. 400 matched cddid_all.tbl CDD COG5892 COG5892 444594 YlbD Spore coat protein YlbD, FlgN family [Cell cycle control, cell division, chromosome partitioning]. 132 matched cddid_all.tbl CDD COG5893 COG5893 444595 YmaG Spore coat protein YmaG [Cell cycle control, cell division, chromosome partitioning]. 71 matched cddid_all.tbl CDD COG5894 COG5894 444596 YppG Spore coat protein YppG [Cell cycle control, cell division, chromosome partitioning]. 112 matched cddid_all.tbl CDD COG5895 COG5895 444597 YpzA Uncharacterized sporulation protein YpzA, contains DUF2564 domain [Cell cycle control, cell division, chromosome partitioning]. 82 matched cddid_all.tbl CDD COG5896 COG5896 444598 YraG Spore coat protein YraE/YraG [Cell cycle control, cell division, chromosome partitioning]. 65 matched cddid_all.tbl CDD COG5897 COG5897 444599 YsxE Spore coat protein YsxE, aminoglycoside phosphotransferase family [Cell cycle control, cell division, chromosome partitioning]. 335 matched cddid_all.tbl CDD COG5898 COG5898 444600 YuzC Spore coat protein YuzC (inner spore coat) [Cell cycle control, cell division, chromosome partitioning]. 117 matched cddid_all.tbl CDD COG5899 COG5899 444601 YwqH Spore coat protein YwqH [Cell cycle control, cell division, chromosome partitioning]. 134 matched cddid_all.tbl CDD COG5900 COG5900 444602 YybI Spore coat protein YybI (inner spore coat) [Cell cycle control, cell division, chromosome partitioning]. 242 matched cddid_all.tbl CDD COG5901 COG5901 444603 GerAA Spore germination receptor GerABC, GerA subunit (L-alanine receptor) [Cell cycle control, cell division, chromosome partitioning]. 483 matched cddid_all.tbl CDD COG5902 COG5902 444604 GerAB Spore germination receptor GerABC, GerB subunit (amino acid transporter) [Cell cycle control, cell division, chromosome partitioning]. 365 matched cddid_all.tbl CDD COG5903 COG5903 444605 GerAC Spore germination receptor GerABC, GerC subunit [Cell cycle control, cell division, chromosome partitioning]. 369 matched cddid_all.tbl CDD COG5904 COG5904 444606 GerD Spore germination receptor GerD [Cell cycle control, cell division, chromosome partitioning]. 210 matched cddid_all.tbl CDD COG5905 COG5905 444607 GerE Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription]. 76 matched cddid_all.tbl CDD COG5906 COG5906 444608 GerPA Spore germination protein GerPA/GerPF (inner spore coat) [Cell cycle control, cell division, chromosome partitioning]. 73 matched cddid_all.tbl CDD COG5907 COG5907 444609 GerPB Spore germination protein GerPB, DUF2539 family (inner spore coat) [Cell cycle control, cell division, chromosome partitioning]. 70 matched cddid_all.tbl CDD COG5908 COG5908 444610 GerPC Spore germination protein GerPC (inner spore coat) [Cell cycle control, cell division, chromosome partitioning]. 201 matched cddid_all.tbl CDD COG5909 COG5909 444611 GerPD Spore germination protein GerPD (inner spore coat) [Cell cycle control, cell division, chromosome partitioning]. 55 matched cddid_all.tbl CDD COG5910 COG5910 444612 GerPE Spore germination protein GerPE (inner spore coat) [Cell cycle control, cell division, chromosome partitioning]. 126 matched cddid_all.tbl CDD COG5911 COG5911 444613 Gpr Spore germination protease Gpr [Cell cycle control, cell division, chromosome partitioning]. 330 matched cddid_all.tbl CDD COG5912 COG5912 444614 CoxA Spore cortex protein CoxA (YrbB), YhcN/YlaJ family [Cell cycle control, cell division, chromosome partitioning]. 181 matched cddid_all.tbl CDD COG5914 COG5914 444615 YpeB Spore germination protein YpeB, HAD superfamily, activates cortex-lytic enzyme SleB [Cell cycle control, cell division, chromosome partitioning]. 449 matched cddid_all.tbl CDD COG5915 COG5915 444616 Tgl Transglutaminase [Cell cycle control, cell division, chromosome partitioning]. 268 matched cddid_all.tbl CDD COG5916 COG5916 444617 YfkD Uncharacterized sporulation protein YfkD [Cell cycle control, cell division, chromosome partitioning]. 266 matched cddid_all.tbl CDD COG5917 COG5917 444618 YjbA Uncharacterized sporulation protein YjbA, contains UPF0736/DUF3603 domain [Cell cycle control, cell division, chromosome partitioning]. 248 matched cddid_all.tbl CDD COG5918 COG5918 444619 YmfJ Uncharacterized sporulation protein YmfJ, contains DUF3243 domain [Cell cycle control, cell division, chromosome partitioning]. 85 matched cddid_all.tbl CDD COG5919 COG5919 444620 YodI Uncharacterized sporulation protein YodI [Cell cycle control, cell division, chromosome partitioning]. 86 matched cddid_all.tbl CDD COG5920 COG5920 444621 YqfT Uncharacterized sporulation protein YqfT, contains DUF2624 domain [Cell cycle control, cell division, chromosome partitioning]. 84 matched cddid_all.tbl CDD COG5921 COG5921 444622 YqfX Uncharacterized sporulation protein YqfX, contains DUF308 domain [Cell cycle control, cell division, chromosome partitioning]. 83 matched cddid_all.tbl CDD COG5922 COG5922 444623 YqhG Uncharacterized sporulation protein YqhG [Cell cycle control, cell division, chromosome partitioning]. 261 matched cddid_all.tbl CDD COG5923 COG5923 444624 YrzE Uncharacterized sporulation membrane protein YrzE, contains DUF3792 domain [Cell cycle control, cell division, chromosome partitioning]. 125 matched cddid_all.tbl CDD COG5924 COG5924 444625 YtfI Uncharacterized sporulation protein YtfI, contains DUF2953 domain [Cell cycle control, cell division, chromosome partitioning]. 220 matched cddid_all.tbl CDD COG5925 COG5925 444626 YtrH Uncharacterized sporulation membrane protein YtrH/SpoVIGA [Cell cycle control, cell division, chromosome partitioning]. 110 matched cddid_all.tbl CDD COG5926 COG5926 444627 YtrI Uncharacterized sporulation protein YtrI [Cell cycle control, cell division, chromosome partitioning]. 167 matched cddid_all.tbl CDD COG5930 COG5930 444628 Cas10d CRISPR-Cas system type I-D effector complex large subunit Cas10d/Csc3, contains HD superfamily nuclease domain [Defense mechanisms]. CRISPR-Cas system type I-D effector complex large subunit Cas10d/Csc3, contains HD superfamily nuclease domain is part of the Pathway/BioSystem: CRISPR-Cas system 1032 matched cddid_all.tbl CDD COG5931 COG5931 444629 Cas12a CRISPR-Cas system type-V protein Cas12a [Defense mechanisms]. CRISPR-Cas system type-V protein Cas12a is part of the Pathway/BioSystem: CRISPR-Cas system 1243 matched cddid_all.tbl CDD COG5932 COG5932 444630 Cas3f CRISPR-Cas type I-F system-associated endonuclease/helicase Cas3f, fused to Cas2 domain [Defense mechanisms]. CRISPR-Cas type I-F system-associated endonuclease/helicase Cas3f, fused to Cas2 domain is part of the Pathway/BioSystem: CRISPR-Cas system 1094 matched cddid_all.tbl CDD COG5933 COG5933 444631 Cas5f CRISPR-Cas system type I-F effector complex subunit Cas5f/Csy2, RAMP superfamily [Defense mechanisms]. CRISPR-Cas system type I-F effector complex subunit Cas5f/Csy2, RAMP superfamily is part of the Pathway/BioSystem: CRISPR-Cas system 319 matched cddid_all.tbl CDD COG5934 COG5934 444632 Cas6e CRISPR-Cas system endoribonuclease Cas6e, RAMP superfamily [Defense mechanisms]. CRISPR-Cas system endoribonuclease Cas6e, RAMP superfamily is part of the Pathway/BioSystem: CRISPR-Cas system 363 matched cddid_all.tbl CDD COG5935 COG5935 444633 Cas6f CRISPR-Cas system endoribonuclease Cas6f/Csy4, RAMP superfamily [Defense mechanisms]. CRISPR-Cas system endoribonuclease Cas6f/Csy4, RAMP superfamily is part of the Pathway/BioSystem: CRISPR-Cas system 187 matched cddid_all.tbl CDD COG5936 COG5936 444634 Cas7f CRISPR-Cas system type I-F effector complex subunit Cas7f/Csy3, RAMP superfamily [Defense mechanisms]. CRISPR-Cas system type I-F effector complex subunit Cas7f/Csy3, RAMP superfamily is part of the Pathway/BioSystem: CRISPR-Cas system 337 matched cddid_all.tbl CDD COG5937 COG5937 444635 Cas8a4 CRISPR-Cas system type I-A effector complex large subunit Cas8a4 [Defense mechanisms]. CRISPR-Cas system type I-A effector complex large subunit Cas8a4 is part of the Pathway/BioSystem: CRISPR-Cas system 583 matched cddid_all.tbl CDD COG5938 COG5938 444636 Cas8b1 CRISPR-Cas system type I-B effector complex large subunit Cas8b1 [Defense mechanisms]. CRISPR-Cas system type I-B effector complex large subunit Cas8b1 is part of the Pathway/BioSystem: CRISPR-Cas system 600 matched cddid_all.tbl CDD COG5939 COG5939 444637 Cas8b2 CRISPR-Cas system type I-B effector complex large subunit Cas8b2 [Defense mechanisms]. CRISPR-Cas system type I-B effector complex large subunit Cas8b2 is part of the Pathway/BioSystem: CRISPR-Cas system 336 matched cddid_all.tbl CDD COG5940 COG5940 444638 Cas8b3 CRISPR-Cas system type I-B effector complex large subunit Cas8b3 [Defense mechanisms]. CRISPR-Cas system type I-B effector complex large subunit Cas8b3 is part of the Pathway/BioSystem: CRISPR-Cas system 503 matched cddid_all.tbl CDD COG5941 COG5941 444639 Cas8c CRISPR-Cas system type I-C effector complex large subunit Cas8c [Defense mechanisms]. CRISPR-Cas system type I-C effector complex large subunit Cas8c is part of the Pathway/BioSystem: CRISPR-Cas system 576 matched cddid_all.tbl CDD COG5942 COG5942 444640 Cas8e CRISPR-Cas system type I-E effector complex large subunit Cas8e [Defense mechanisms]. CRISPR-Cas system type I-E effector complex large subunit Cas8e is part of the Pathway/BioSystem: CRISPR-Cas system 484 matched cddid_all.tbl CDD COG5943 COG5943 444641 Cas8f CRISPR-Cas system type I-F effector complex large subunit Cas8f [Defense mechanisms]. CRISPR-Cas system type I-F effector complex large subunit Cas8f is part of the Pathway/BioSystem: CRISPR-Cas system 432 matched cddid_all.tbl CDD COG5944 COG5944 444642 Cas8g1 CRISPR-Cas system type I-G effector complex large subunit Cas8g1 [Defense mechanisms]. CRISPR-Cas system type I-G effector complex large subunit Cas8g1 is part of the Pathway/BioSystem: CRISPR-Cas system 360 matched cddid_all.tbl CDD COG5945 COG5945 444643 Csb1gr7 CRISPR-Cas system type I-G effector complex subunit Csb1, RAMP superfamily Cas7 group [Defense mechanisms]. CRISPR-Cas system type I-G effector complex subunit Csb1, RAMP superfamily Cas7 group is part of the Pathway/BioSystem: CRISPR-Cas system 384 matched cddid_all.tbl CDD COG5946 COG5946 444644 Csb5gr5 CRISPR-Cas system type I-G effector complex subunit Csb5, RAMP superfamily Cas5 group [Defense mechanisms]. CRISPR-Cas system type I-G effector complex subunit Csb5, RAMP superfamily Cas5 group is part of the Pathway/BioSystem: CRISPR-Cas system 478 matched cddid_all.tbl CDD COG5947 COG5947 444645 Csc1gr5 CRISPR-Cas system type I-D effector complex subunit Csc1, RAMP superfamily Cas5 group [Defense mechanisms]. CRISPR-Cas system type I-D effector complex subunit Csc1, RAMP superfamily Cas5 group is part of the Pathway/BioSystem: CRISPR-Cas system 231 matched cddid_all.tbl CDD COG5948 COG5948 444646 Csc2gr7 CRISPR-Cas system type I-D effector complex subunit Csc2, RAMP superfamily Cas7 group [Defense mechanisms]. CRISPR-Cas system type I-D effector complex subunit Csc2, RAMP superfamily Cas7 group is part of the Pathway/BioSystem: CRISPR-Cas system 323 matched cddid_all.tbl CDD COG5949 COG5949 444647 Cse2gr11 CRISPR-Cas system type I-E effector complex small subunit Cse2 [Defense mechanisms]. CRISPR-Cas system type I-E effector complex small subunit Cse2 is part of the Pathway/BioSystem: CRISPR-Cas system 179 matched cddid_all.tbl CDD COG5950 COG5950 444648 Csx10gr5 CRISPR-Cas system type II-D effector complex subunit Csx10, RAMP superfamily Cas5 group [Defense mechanisms]. CRISPR-Cas system type II-D effector complex subunit Csx10, RAMP superfamily Cas5 group is part of the Pathway/BioSystem: CRISPR-Cas system 367 matched cddid_all.tbl CDD KOG0001 KOG0001 227953 KOG0001 KOG0001, Ubiquitin and ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones, General function prediction only] 75 matched cddid_all.tbl CDD KOG0002 KOG0002 227954 KOG0002 KOG0002, 60s ribosomal protein L39 [Translation, ribosomal structure and biogenesis] 48 matched cddid_all.tbl CDD KOG0003 KOG0003 227955 KOG0003 KOG0003, Ubiquitin/60s ribosomal protein L40 fusion [Translation, ribosomal structure and biogenesis] 128 matched cddid_all.tbl CDD KOG0004 KOG0004 227956 KOG0004 KOG0004, Ubiquitin/40S ribosomal protein S27a fusion [Translation, ribosomal structure and biogenesis] 156 matched cddid_all.tbl CDD KOG0005 KOG0005 227957 KOG0005 KOG0005, Ubiquitin-like protein [Cell cycle control, cell division, chromosome partitioning, Posttranslational modification, protein turnover, chaperones] 70 matched cddid_all.tbl CDD KOG0006 KOG0006 227958 KOG0006 KOG0006, E3 ubiquitin-protein ligase (Parkin protein) [Posttranslational modification, protein turnover, chaperones] 446 matched cddid_all.tbl CDD KOG0007 KOG0007 227959 KOG0007 KOG0007, Splicing factor 3a, subunit 1 [RNA processing and modification] 341 matched cddid_all.tbl CDD KOG0008 KOG0008 227960 KOG0008 KOG0008, Transcription initiation factor TFIID, subunit TAF1 [Transcription] 1563 matched cddid_all.tbl CDD KOG0009 KOG0009 227961 KOG0009 KOG0009, Ubiquitin-like/40S ribosomal S30 protein fusion [Translation, ribosomal structure and biogenesis, Posttranslational modification, protein turnover, chaperones] 62 matched cddid_all.tbl CDD KOG0010 KOG0010 227962 KOG0010 KOG0010, Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones, General function prediction only] 493 matched cddid_all.tbl CDD KOG0011 KOG0011 227963 KOG0011 KOG0011, Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair] 340 matched cddid_all.tbl CDD KOG0012 KOG0012 227964 KOG0012 KOG0012, DNA damage inducible protein [Replication, recombination and repair] 380 matched cddid_all.tbl CDD KOG0013 KOG0013 227965 KOG0013 KOG0013, Uncharacterized conserved protein [Function unknown] 231 matched cddid_all.tbl CDD KOG0014 KOG0014 227966 KOG0014 KOG0014, MADS box transcription factor [Transcription] 195 matched cddid_all.tbl CDD KOG0015 KOG0015 227967 KOG0015 KOG0015, Regulator of arginine metabolism and related MADS box-containing transcription factors [Transcription] 338 matched cddid_all.tbl CDD KOG0016 KOG0016 227968 KOG0016 KOG0016, Enoyl-CoA hydratase/isomerase [Lipid transport and metabolism] 266 matched cddid_all.tbl CDD KOG0018 KOG0018 227969 KOG0018 KOG0018, Structural maintenance of chromosome protein 1 (sister chromatid cohesion complex Cohesin, subunit SMC1) [Cell cycle control, cell division, chromosome partitioning] 1141 matched cddid_all.tbl CDD KOG0019 KOG0019 227970 KOG0019 KOG0019, Molecular chaperone (HSP90 family) [Posttranslational modification, protein turnover, chaperones] 656 matched cddid_all.tbl CDD KOG0020 KOG0020 227971 KOG0020 KOG0020, Endoplasmic reticulum glucose-regulated protein (GRP94/endoplasmin), HSP90 family [Posttranslational modification, protein turnover, chaperones] 785 matched cddid_all.tbl CDD KOG0021 KOG0021 227972 KOG0021 KOG0021, Glutathione synthetase [Secondary metabolites biosynthesis, transport and catabolism] 468 matched cddid_all.tbl CDD KOG0022 KOG0022 227973 KOG0022 KOG0022, Alcohol dehydrogenase, class III [Secondary metabolites biosynthesis, transport and catabolism] 375 matched cddid_all.tbl CDD KOG0023 KOG0023 227974 KOG0023 KOG0023, Alcohol dehydrogenase, class V [Secondary metabolites biosynthesis, transport and catabolism] 360 matched cddid_all.tbl CDD KOG0024 KOG0024 227975 KOG0024 KOG0024, Sorbitol dehydrogenase [Secondary metabolites biosynthesis, transport and catabolism] 354 matched cddid_all.tbl CDD KOG0025 KOG0025 227976 KOG0025 KOG0025, Zn2+-binding dehydrogenase (nuclear receptor binding factor-1) [Transcription, Energy production and conversion] 354 matched cddid_all.tbl CDD KOG0026 KOG0026 227977 KOG0026 KOG0026, Anthranilate synthase, beta chain [Amino acid transport and metabolism] 223 matched cddid_all.tbl CDD KOG0027 KOG0027 227978 KOG0027 KOG0027, Calmodulin and related proteins (EF-Hand superfamily) [Signal transduction mechanisms] 151 matched cddid_all.tbl CDD KOG0028 KOG0028 227979 KOG0028 KOG0028, Ca2+-binding protein (centrin/caltractin), EF-Hand superfamily protein [Cytoskeleton, Cell cycle control, cell division, chromosome partitioning] 172 matched cddid_all.tbl CDD KOG0029 KOG0029 227980 KOG0029 KOG0029, Amine oxidase [Secondary metabolites biosynthesis, transport and catabolism] 501 matched cddid_all.tbl CDD KOG0030 KOG0030 227981 KOG0030 KOG0030, Myosin essential light chain, EF-Hand protein superfamily [Cytoskeleton] 152 matched cddid_all.tbl CDD KOG0031 KOG0031 227982 KOG0031 KOG0031, Myosin regulatory light chain, EF-Hand protein superfamily [Cytoskeleton] 171 matched cddid_all.tbl CDD KOG0032 KOG0032 227983 KOG0032 KOG0032, Ca2+/calmodulin-dependent protein kinase, EF-Hand protein superfamily [Signal transduction mechanisms] 382 matched cddid_all.tbl CDD KOG0033 KOG0033 227984 KOG0033 KOG0033, Ca2+/calmodulin-dependent protein kinase, EF-Hand protein superfamily [Signal transduction mechanisms] 355 matched cddid_all.tbl CDD KOG0034 KOG0034 227985 KOG0034 KOG0034, Ca2+/calmodulin-dependent protein phosphatase (calcineurin subunit B), EF-Hand superfamily protein [Signal transduction mechanisms] 187 matched cddid_all.tbl CDD KOG0035 KOG0035 227986 KOG0035 KOG0035, Ca2+-binding actin-bundling protein (actinin), alpha chain (EF-Hand protein superfamily) [Cytoskeleton] 890 matched cddid_all.tbl CDD KOG0036 KOG0036 227987 KOG0036 KOG0036, Predicted mitochondrial carrier protein [Nucleotide transport and metabolism] 463 matched cddid_all.tbl CDD KOG0037 KOG0037 227988 KOG0037 KOG0037, Ca2+-binding protein, EF-Hand protein superfamily [Signal transduction mechanisms] 221 matched cddid_all.tbl CDD KOG0038 KOG0038 227989 KOG0038 KOG0038, Ca2+-binding kinase interacting protein (KIP) (EF-Hand protein superfamily) [General function prediction only] 189 matched cddid_all.tbl CDD KOG0039 KOG0039 227990 KOG0039 KOG0039, Ferric reductase, NADH/NADPH oxidase and related proteins [Inorganic ion transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism] 601 matched cddid_all.tbl CDD KOG0040 KOG0040 227991 KOG0040 KOG0040, Ca2+-binding actin-bundling protein (spectrin), alpha chain (EF-Hand protein superfamily) [Cytoskeleton] 2399 matched cddid_all.tbl CDD KOG0041 KOG0041 227992 KOG0041 KOG0041, Predicted Ca2+-binding protein, EF-Hand protein superfamily [General function prediction only] 244 matched cddid_all.tbl CDD KOG0042 KOG0042 227993 KOG0042 KOG0042, Glycerol-3-phosphate dehydrogenase [Energy production and conversion] 680 matched cddid_all.tbl CDD KOG0043 KOG0043 227994 KOG0043 KOG0043, Uncharacterized conserved protein, contains DM10 domain [Function unknown] 452 matched cddid_all.tbl CDD KOG0044 KOG0044 227995 KOG0044 KOG0044, Ca2+ sensor (EF-Hand superfamily) [Signal transduction mechanisms] 193 matched cddid_all.tbl CDD KOG0045 KOG0045 227996 KOG0045 KOG0045, Cytosolic Ca2+-dependent cysteine protease (calpain), large subunit (EF-Hand protein superfamily) [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms] 612 matched cddid_all.tbl CDD KOG0046 KOG0046 227997 KOG0046 KOG0046, Ca2+-binding actin-bundling protein (fimbrin/plastin), EF-Hand protein superfamily [Cytoskeleton] 627 matched cddid_all.tbl CDD KOG0047 KOG0047 227998 KOG0047 KOG0047, Catalase [Inorganic ion transport and metabolism] 505 matched cddid_all.tbl CDD KOG0048 KOG0048 227999 KOG0048 KOG0048, Transcription factor, Myb superfamily [Transcription] 238 matched cddid_all.tbl CDD KOG0049 KOG0049 228000 KOG0049 KOG0049, Transcription factor, Myb superfamily [Transcription] 939 matched cddid_all.tbl CDD KOG0050 KOG0050 228001 KOG0050 KOG0050, mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification, Cell cycle control, cell division, chromosome partitioning] 617 matched cddid_all.tbl CDD KOG0051 KOG0051 228002 KOG0051 KOG0051, RNA polymerase I termination factor, Myb superfamily [Transcription] 607 matched cddid_all.tbl CDD KOG0052 KOG0052 228003 KOG0052 KOG0052, Translation elongation factor EF-1 alpha/Tu [Translation, ribosomal structure and biogenesis] 391 matched cddid_all.tbl CDD KOG0053 KOG0053 228004 KOG0053 KOG0053, Cystathionine beta-lyases/cystathionine gamma-synthases [Amino acid transport and metabolism] 409 matched cddid_all.tbl CDD KOG0054 KOG0054 228005 KOG0054 KOG0054, Multidrug resistance-associated protein/mitoxantrone resistance protein, ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism] 1381 matched cddid_all.tbl CDD KOG0055 KOG0055 228006 KOG0055 KOG0055, Multidrug/pheromone exporter, ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism] 1181 matched cddid_all.tbl CDD KOG0056 KOG0056 228007 KOG0056 KOG0056, Heavy metal exporter HMT1, ABC superfamily [Inorganic ion transport and metabolism] 790 matched cddid_all.tbl CDD KOG0057 KOG0057 228008 KOG0057 KOG0057, Mitochondrial Fe/S cluster exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport] 591 matched cddid_all.tbl CDD KOG0058 KOG0058 228009 KOG0058 KOG0058, Peptide exporter, ABC superfamily [Intracellular trafficking, secretion, and vesicular transport] 716 matched cddid_all.tbl CDD KOG0059 KOG0059 228010 KOG0059 KOG0059, Lipid exporter ABCA1 and related proteins, ABC superfamily [Lipid transport and metabolism, General function prediction only] 885 matched cddid_all.tbl CDD KOG0060 KOG0060 228011 KOG0060 KOG0060, Long-chain acyl-CoA transporter, ABC superfamily (involved in peroxisome organization and biogenesis) [Lipid transport and metabolism, General function prediction only] 659 matched cddid_all.tbl CDD KOG0061 KOG0061 228012 KOG0061 KOG0061, Transporter, ABC superfamily (Breast cancer resistance protein) [Secondary metabolites biosynthesis, transport and catabolism] 578 matched cddid_all.tbl CDD KOG0062 KOG0062 228013 KOG0062 KOG0062, ATPase component of ABC transporters with duplicated ATPase domains/Translation elongation factor EF-3b [Amino acid transport and metabolism, Translation, ribosomal structure and biogenesis] 582 matched cddid_all.tbl CDD KOG0063 KOG0063 228014 KOG0063 KOG0063, RNAse L inhibitor, ABC superfamily [RNA processing and modification] 592 matched cddid_all.tbl CDD KOG0064 KOG0064 228015 KOG0064 KOG0064, Peroxisomal long-chain acyl-CoA transporter, ABC superfamily [Lipid transport and metabolism] 728 matched cddid_all.tbl CDD KOG0065 KOG0065 228016 KOG0065 KOG0065, Pleiotropic drug resistance proteins (PDR1-15), ABC superfamily [Secondary metabolites biosynthesis, transport and catabolism] 1391 matched cddid_all.tbl CDD KOG0066 KOG0066 228017 KOG0066 KOG0066, eIF2-interacting protein ABC50 (ABC superfamily) [Translation, ribosomal structure and biogenesis] 807 matched cddid_all.tbl CDD KOG0067 KOG0067 228018 KOG0067 KOG0067, Transcription factor CtBP [Transcription] 435 matched cddid_all.tbl CDD KOG0068 KOG0068 228019 KOG0068 KOG0068, D-3-phosphoglycerate dehydrogenase, D-isomer-specific 2-hydroxy acid dehydrogenase superfamily [Amino acid transport and metabolism] 406 matched cddid_all.tbl CDD KOG0069 KOG0069 228020 KOG0069 KOG0069, Glyoxylate/hydroxypyruvate reductase (D-isomer-specific 2-hydroxy acid dehydrogenase superfamily) [Energy production and conversion] 336 matched cddid_all.tbl CDD KOG0070 KOG0070 228021 KOG0070 KOG0070, GTP-binding ADP-ribosylation factor Arf1 [Intracellular trafficking, secretion, and vesicular transport] 181 matched cddid_all.tbl CDD KOG0071 KOG0071 228022 KOG0071 KOG0071, GTP-binding ADP-ribosylation factor Arf6 (dArf3) [Intracellular trafficking, secretion, and vesicular transport] 180 matched cddid_all.tbl CDD KOG0072 KOG0072 228023 KOG0072 KOG0072, GTP-binding ADP-ribosylation factor-like protein ARL1 [Intracellular trafficking, secretion, and vesicular transport] 182 matched cddid_all.tbl CDD KOG0073 KOG0073 228024 KOG0073 KOG0073, GTP-binding ADP-ribosylation factor-like protein ARL2 [Intracellular trafficking, secretion, and vesicular transport, Cytoskeleton] 185 matched cddid_all.tbl CDD KOG0074 KOG0074 228025 KOG0074 KOG0074, GTP-binding ADP-ribosylation factor-like protein ARL3 [General function prediction only] 185 matched cddid_all.tbl CDD KOG0075 KOG0075 228026 KOG0075 KOG0075, GTP-binding ADP-ribosylation factor-like protein [General function prediction only] 186 matched cddid_all.tbl CDD KOG0076 KOG0076 228027 KOG0076 KOG0076, GTP-binding ADP-ribosylation factor-like protein yARL3 [Intracellular trafficking, secretion, and vesicular transport] 197 matched cddid_all.tbl CDD KOG0077 KOG0077 228028 KOG0077 KOG0077, Vesicle coat complex COPII, GTPase subunit SAR1 [Intracellular trafficking, secretion, and vesicular transport] 193 matched cddid_all.tbl CDD KOG0078 KOG0078 228029 KOG0078 KOG0078, GTP-binding protein SEC4, small G protein superfamily, and related Ras family GTP-binding proteins [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 207 matched cddid_all.tbl CDD KOG0079 KOG0079 228030 KOG0079 KOG0079, GTP-binding protein H-ray, small G protein superfamily [General function prediction only] 198 matched cddid_all.tbl CDD KOG0080 KOG0080 228031 KOG0080 KOG0080, GTPase Rab18, small G protein superfamily [General function prediction only] 209 matched cddid_all.tbl CDD KOG0081 KOG0081 228032 KOG0081 KOG0081, GTPase Rab27, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport] 219 matched cddid_all.tbl CDD KOG0082 KOG0082 228033 KOG0082 KOG0082, G-protein alpha subunit (small G protein superfamily) [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms] 354 matched cddid_all.tbl CDD KOG0083 KOG0083 228034 KOG0083 KOG0083, GTPase Rab26/Rab37, small G protein superfamily [General function prediction only] 192 matched cddid_all.tbl CDD KOG0084 KOG0084 228035 KOG0084 KOG0084, GTPase Rab1/YPT1, small G protein superfamily, and related GTP-binding proteins [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 205 matched cddid_all.tbl CDD KOG0085 KOG0085 228036 KOG0085 KOG0085, G protein subunit Galphaq/Galphay, small G protein superfamily [Signal transduction mechanisms] 359 matched cddid_all.tbl CDD KOG0086 KOG0086 228037 KOG0086 KOG0086, GTPase Rab4, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport] 214 matched cddid_all.tbl CDD KOG0087 KOG0087 228038 KOG0087 KOG0087, GTPase Rab11/YPT3, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport] 222 matched cddid_all.tbl CDD KOG0088 KOG0088 228039 KOG0088 KOG0088, GTPase Rab21, small G protein superfamily [General function prediction only] 218 matched cddid_all.tbl CDD KOG0089 KOG0089 228040 KOG0089 KOG0089, Methylenetetrahydrofolate dehydrogenase/methylenetetrahydrofolate cyclohydrolase [Coenzyme transport and metabolism] 309 matched cddid_all.tbl CDD KOG0090 KOG0090 228041 KOG0090 KOG0090, Signal recognition particle receptor, beta subunit (small G protein superfamily) [Intracellular trafficking, secretion, and vesicular transport] 238 matched cddid_all.tbl CDD KOG0091 KOG0091 228042 KOG0091 KOG0091, GTPase Rab39, small G protein superfamily [General function prediction only] 213 matched cddid_all.tbl CDD KOG0092 KOG0092 228043 KOG0092 KOG0092, GTPase Rab5/YPT51 and related small G protein superfamily GTPases [Intracellular trafficking, secretion, and vesicular transport] 200 matched cddid_all.tbl CDD KOG0093 KOG0093 228044 KOG0093 KOG0093, GTPase Rab3, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport] 193 matched cddid_all.tbl CDD KOG0094 KOG0094 228045 KOG0094 KOG0094, GTPase Rab6/YPT6/Ryh1, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport] 221 matched cddid_all.tbl CDD KOG0095 KOG0095 228046 KOG0095 KOG0095, GTPase Rab30, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport] 213 matched cddid_all.tbl CDD KOG0096 KOG0096 228047 KOG0096 KOG0096, GTPase Ran/TC4/GSP1 (nuclear protein transport pathway), small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport] 216 matched cddid_all.tbl CDD KOG0097 KOG0097 228048 KOG0097 KOG0097, GTPase Rab14, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport] 215 matched cddid_all.tbl CDD KOG0098 KOG0098 228049 KOG0098 KOG0098, GTPase Rab2, small G protein superfamily [Intracellular trafficking, secretion, and vesicular transport] 216 matched cddid_all.tbl CDD KOG0099 KOG0099 228050 KOG0099 KOG0099, G protein subunit Galphas, small G protein superfamily [Signal transduction mechanisms] 379 matched cddid_all.tbl CDD KOG0100 KOG0100 228051 KOG0100 KOG0100, Molecular chaperones GRP78/BiP/KAR2, HSP70 superfamily [Posttranslational modification, protein turnover, chaperones] 663 matched cddid_all.tbl CDD KOG0101 KOG0101 228052 KOG0101 KOG0101, Molecular chaperones HSP70/HSC70, HSP70 superfamily [Posttranslational modification, protein turnover, chaperones] 620 matched cddid_all.tbl CDD KOG0102 KOG0102 228053 KOG0102 KOG0102, Molecular chaperones mortalin/PBP74/GRP75, HSP70 superfamily [Posttranslational modification, protein turnover, chaperones] 640 matched cddid_all.tbl CDD KOG0103 KOG0103 228054 KOG0103 KOG0103, Molecular chaperones HSP105/HSP110/SSE1, HSP70 superfamily [Posttranslational modification, protein turnover, chaperones] 727 matched cddid_all.tbl CDD KOG0104 KOG0104 228055 KOG0104 KOG0104, Molecular chaperones GRP170/SIL1, HSP70 superfamily [Posttranslational modification, protein turnover, chaperones] 902 matched cddid_all.tbl CDD KOG0105 KOG0105 228056 KOG0105 KOG0105, Alternative splicing factor ASF/SF2 (RRM superfamily) [RNA processing and modification] 241 matched cddid_all.tbl CDD KOG0106 KOG0106 228057 KOG0106 KOG0106, Alternative splicing factor SRp55/B52/SRp75 (RRM superfamily) [RNA processing and modification] 216 matched cddid_all.tbl CDD KOG0107 KOG0107 228058 KOG0107 KOG0107, Alternative splicing factor SRp20/9G8 (RRM superfamily) [RNA processing and modification] 195 matched cddid_all.tbl CDD KOG0108 KOG0108 228059 KOG0108 KOG0108, mRNA cleavage and polyadenylation factor I complex, subunit RNA15 [RNA processing and modification] 435 matched cddid_all.tbl CDD KOG0109 KOG0109 228060 KOG0109 KOG0109, RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains [RNA processing and modification, General function prediction only] 346 matched cddid_all.tbl CDD KOG0110 KOG0110 228061 KOG0110 KOG0110, RNA-binding protein (RRM superfamily) [General function prediction only] 725 matched cddid_all.tbl CDD KOG0111 KOG0111 228062 KOG0111 KOG0111, Cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones] 298 matched cddid_all.tbl CDD KOG0112 KOG0112 228063 KOG0112 KOG0112, Large RNA-binding protein (RRM superfamily) [General function prediction only] 975 matched cddid_all.tbl CDD KOG0113 KOG0113 228064 KOG0113 KOG0113, U1 small nuclear ribonucleoprotein (RRM superfamily) [RNA processing and modification] 335 matched cddid_all.tbl CDD KOG0114 KOG0114 228065 KOG0114 KOG0114, Predicted RNA-binding protein (RRM superfamily) [General function prediction only] 124 matched cddid_all.tbl CDD KOG0115 KOG0115 228066 KOG0115 KOG0115, RNA-binding protein p54nrb (RRM superfamily) [RNA processing and modification] 275 matched cddid_all.tbl CDD KOG0116 KOG0116 228067 KOG0116 KOG0116, RasGAP SH3 binding protein rasputin, contains NTF2 and RRM domains [Signal transduction mechanisms] 419 matched cddid_all.tbl CDD KOG0117 KOG0117 228068 KOG0117 KOG0117, Heterogeneous nuclear ribonucleoprotein R (RRM superfamily) [RNA processing and modification] 506 matched cddid_all.tbl CDD KOG0119 KOG0119 228069 KOG0119 KOG0119, Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification] 554 matched cddid_all.tbl CDD KOG0120 KOG0120 228070 KOG0120 KOG0120, Splicing factor U2AF, large subunit (RRM superfamily) [RNA processing and modification] 500 matched cddid_all.tbl CDD KOG0121 KOG0121 228071 KOG0121 KOG0121, Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification] 153 matched cddid_all.tbl CDD KOG0122 KOG0122 228072 KOG0122 KOG0122, Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis] 270 matched cddid_all.tbl CDD KOG0123 KOG0123 228073 KOG0123 KOG0123, Polyadenylate-binding protein (RRM superfamily) [RNA processing and modification, Translation, ribosomal structure and biogenesis] 369 matched cddid_all.tbl CDD KOG0124 KOG0124 228074 KOG0124 KOG0124, Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification] 544 matched cddid_all.tbl CDD KOG0125 KOG0125 228075 KOG0125 KOG0125, Ataxin 2-binding protein (RRM superfamily) [General function prediction only] 376 matched cddid_all.tbl CDD KOG0126 KOG0126 228076 KOG0126 KOG0126, Predicted RNA-binding protein (RRM superfamily) [General function prediction only] 219 matched cddid_all.tbl CDD KOG0127 KOG0127 228077 KOG0127 KOG0127, Nucleolar protein fibrillarin NOP77 (RRM superfamily) [RNA processing and modification] 678 matched cddid_all.tbl CDD KOG0128 KOG0128 228078 KOG0128 KOG0128, RNA-binding protein SART3 (RRM superfamily) [RNA processing and modification] 844 matched cddid_all.tbl CDD KOG0129 KOG0129 228079 KOG0129 KOG0129, Predicted RNA-binding protein (RRM superfamily) [Translation, ribosomal structure and biogenesis] 520 matched cddid_all.tbl CDD KOG0130 KOG0130 228080 KOG0130 KOG0130, RNA-binding protein RBM8/Tsunagi (RRM superfamily) [General function prediction only] 170 matched cddid_all.tbl CDD KOG0131 KOG0131 228081 KOG0131 KOG0131, Splicing factor 3b, subunit 4 [RNA processing and modification] 203 matched cddid_all.tbl CDD KOG0132 KOG0132 228082 KOG0132 KOG0132, RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification, Transcription] 894 matched cddid_all.tbl CDD KOG0133 KOG0133 228083 KOG0133 KOG0133, Deoxyribodipyrimidine photolyase/cryptochrome [Replication, recombination and repair, Signal transduction mechanisms] 531 matched cddid_all.tbl CDD KOG0134 KOG0134 228084 KOG0134 KOG0134, NADH:flavin oxidoreductase/12-oxophytodienoate reductase [Energy production and conversion, General function prediction only] 400 matched cddid_all.tbl CDD KOG0135 KOG0135 228085 KOG0135 KOG0135, Pristanoyl-CoA/acyl-CoA oxidase [Lipid transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism] 661 matched cddid_all.tbl CDD KOG0136 KOG0136 228086 KOG0136 KOG0136, Acyl-CoA oxidase [Lipid transport and metabolism] 670 matched cddid_all.tbl CDD KOG0137 KOG0137 228087 KOG0137 KOG0137, Very-long-chain acyl-CoA dehydrogenase [Lipid transport and metabolism] 634 matched cddid_all.tbl CDD KOG0138 KOG0138 228088 KOG0138 KOG0138, Glutaryl-CoA dehydrogenase [Amino acid transport and metabolism] 432 matched cddid_all.tbl CDD KOG0139 KOG0139 228089 KOG0139 KOG0139, Short-chain acyl-CoA dehydrogenase [Lipid transport and metabolism] 398 matched cddid_all.tbl CDD KOG0140 KOG0140 228090 KOG0140 KOG0140, Medium-chain acyl-CoA dehydrogenase [Lipid transport and metabolism] 408 matched cddid_all.tbl CDD KOG0141 KOG0141 228091 KOG0141 KOG0141, Isovaleryl-CoA dehydrogenase [Amino acid transport and metabolism, Lipid transport and metabolism] 421 matched cddid_all.tbl CDD KOG0142 KOG0142 228092 KOG0142 KOG0142, Isopentenyl pyrophosphate:dimethylallyl pyrophosphate isomerase [Secondary metabolites biosynthesis, transport and catabolism] 225 matched cddid_all.tbl CDD KOG0143 KOG0143 228093 KOG0143 KOG0143, Iron/ascorbate family oxidoreductases [Secondary metabolites biosynthesis, transport and catabolism, General function prediction only] 322 matched cddid_all.tbl CDD KOG0144 KOG0144 228094 KOG0144 KOG0144, RNA-binding protein CUGBP1/BRUNO (RRM superfamily) [RNA processing and modification] 510 matched cddid_all.tbl CDD KOG0145 KOG0145 228095 KOG0145 KOG0145, RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification] 360 matched cddid_all.tbl CDD KOG0146 KOG0146 228096 KOG0146 KOG0146, RNA-binding protein ETR-3 (RRM superfamily) [RNA processing and modification] 371 matched cddid_all.tbl CDD KOG0147 KOG0147 228097 KOG0147 KOG0147, Transcriptional coactivator CAPER (RRM superfamily) [Transcription] 549 matched cddid_all.tbl CDD KOG0148 KOG0148 228098 KOG0148 KOG0148, Apoptosis-promoting RNA-binding protein TIA-1/TIAR (RRM superfamily) [RNA processing and modification, Translation, ribosomal structure and biogenesis] 321 matched cddid_all.tbl CDD KOG0149 KOG0149 228099 KOG0149 KOG0149, Predicted RNA-binding protein SEB4 (RRM superfamily) [General function prediction only] 247 matched cddid_all.tbl CDD KOG0150 KOG0150 228100 KOG0150 KOG0150, Spliceosomal protein FBP21 [RNA processing and modification] 336 matched cddid_all.tbl CDD KOG0151 KOG0151 228101 KOG0151 KOG0151, Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only] 877 matched cddid_all.tbl CDD KOG0152 KOG0152 228102 KOG0152 KOG0152, Spliceosomal protein FBP11/Splicing factor PRP40 [RNA processing and modification] 463 matched cddid_all.tbl CDD KOG0153 KOG0153 228103 KOG0153 KOG0153, Predicted RNA-binding protein (RRM superfamily) [General function prediction only] 377 matched cddid_all.tbl CDD KOG0154 KOG0154 228104 KOG0154 KOG0154, RNA-binding protein RBM5 and related proteins, contain G-patch and RRM domains [General function prediction only] 573 matched cddid_all.tbl CDD KOG0155 KOG0155 228105 KOG0155 KOG0155, Transcription factor CA150 [Transcription] 617 matched cddid_all.tbl CDD KOG0156 KOG0156 228106 KOG0156 KOG0156, Cytochrome P450 CYP2 subfamily [Secondary metabolites biosynthesis, transport and catabolism] 489 matched cddid_all.tbl CDD KOG0157 KOG0157 228107 KOG0157 KOG0157, Cytochrome P450 CYP4/CYP19/CYP26 subfamilies [Secondary metabolites biosynthesis, transport and catabolism, Lipid transport and metabolism] 497 matched cddid_all.tbl CDD KOG0158 KOG0158 228108 KOG0158 KOG0158, Cytochrome P450 CYP3/CYP5/CYP6/CYP9 subfamilies [Secondary metabolites biosynthesis, transport and catabolism] 499 matched cddid_all.tbl CDD KOG0159 KOG0159 228109 KOG0159 KOG0159, Cytochrome P450 CYP11/CYP12/CYP24/CYP27 subfamilies [Secondary metabolites biosynthesis, transport and catabolism] 519 matched cddid_all.tbl CDD KOG0160 KOG0160 228110 KOG0160 KOG0160, Myosin class V heavy chain [Cytoskeleton] 862 matched cddid_all.tbl CDD KOG0161 KOG0161 228111 KOG0161 KOG0161, Myosin class II heavy chain [Cytoskeleton] 1930 matched cddid_all.tbl CDD KOG0162 KOG0162 228112 KOG0162 KOG0162, Myosin class I heavy chain [Cytoskeleton] 1106 matched cddid_all.tbl CDD KOG0163 KOG0163 228113 KOG0163 KOG0163, Myosin class VI heavy chain [Cytoskeleton] 1259 matched cddid_all.tbl CDD KOG0164 KOG0164 228114 KOG0164 KOG0164, Myosin class I heavy chain [Cytoskeleton] 1001 matched cddid_all.tbl CDD KOG0165 KOG0165 228115 KOG0165 KOG0165, Microtubule-associated protein Asp [Cytoskeleton] 1023 matched cddid_all.tbl CDD KOG0166 KOG0166 228116 KOG0166 KOG0166, Karyopherin (importin) alpha [Intracellular trafficking, secretion, and vesicular transport] 514 matched cddid_all.tbl CDD KOG0168 KOG0168 228117 KOG0168 KOG0168, Putative ubiquitin fusion degradation protein [Posttranslational modification, protein turnover, chaperones] 1051 matched cddid_all.tbl CDD KOG0169 KOG0169 228118 KOG0169 KOG0169, Phosphoinositide-specific phospholipase C [Signal transduction mechanisms] 746 matched cddid_all.tbl CDD KOG0170 KOG0170 228119 KOG0170 KOG0170, E3 ubiquitin protein ligase [Posttranslational modification, protein turnover, chaperones] 621 matched cddid_all.tbl CDD KOG0171 KOG0171 228120 KOG0171 KOG0171, Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones] 176 matched cddid_all.tbl CDD KOG0172 KOG0172 228121 KOG0172 KOG0172, Lysine-ketoglutarate reductase/saccharopine dehydrogenase [Amino acid transport and metabolism] 445 matched cddid_all.tbl CDD KOG0173 KOG0173 228122 KOG0173 KOG0173, 20S proteasome, regulatory subunit beta type PSMB7/PSMB10/PUP1 [Posttranslational modification, protein turnover, chaperones] 271 matched cddid_all.tbl CDD KOG0174 KOG0174 228123 KOG0174 KOG0174, 20S proteasome, regulatory subunit beta type PSMB6/PSMB9/PRE3 [Posttranslational modification, protein turnover, chaperones] 224 matched cddid_all.tbl CDD KOG0175 KOG0175 228124 KOG0175 KOG0175, 20S proteasome, regulatory subunit beta type PSMB5/PSMB8/PRE2 [Posttranslational modification, protein turnover, chaperones] 285 matched cddid_all.tbl CDD KOG0176 KOG0176 228125 KOG0176 KOG0176, 20S proteasome, regulatory subunit alpha type PSMA5/PUP2 [Posttranslational modification, protein turnover, chaperones] 241 matched cddid_all.tbl CDD KOG0177 KOG0177 228126 KOG0177 KOG0177, 20S proteasome, regulatory subunit beta type PSMB2/PRE1 [Posttranslational modification, protein turnover, chaperones] 200 matched cddid_all.tbl CDD KOG0178 KOG0178 228127 KOG0178 KOG0178, 20S proteasome, regulatory subunit alpha type PSMA4/PRE9 [Posttranslational modification, protein turnover, chaperones] 249 matched cddid_all.tbl CDD KOG0179 KOG0179 228128 KOG0179 KOG0179, 20S proteasome, regulatory subunit beta type PSMB1/PRE7 [Posttranslational modification, protein turnover, chaperones] 235 matched cddid_all.tbl CDD KOG0180 KOG0180 228129 KOG0180 KOG0180, 20S proteasome, regulatory subunit beta type PSMB3/PUP3 [Posttranslational modification, protein turnover, chaperones] 204 matched cddid_all.tbl CDD KOG0181 KOG0181 228130 KOG0181 KOG0181, 20S proteasome, regulatory subunit alpha type PSMA2/PRE8 [Posttranslational modification, protein turnover, chaperones] 233 matched cddid_all.tbl CDD KOG0182 KOG0182 228131 KOG0182 KOG0182, 20S proteasome, regulatory subunit alpha type PSMA6/SCL1 [Posttranslational modification, protein turnover, chaperones] 246 matched cddid_all.tbl CDD KOG0183 KOG0183 228132 KOG0183 KOG0183, 20S proteasome, regulatory subunit alpha type PSMA7/PRE6 [Posttranslational modification, protein turnover, chaperones] 249 matched cddid_all.tbl CDD KOG0184 KOG0184 228133 KOG0184 KOG0184, 20S proteasome, regulatory subunit alpha type PSMA3/PRE10 [Posttranslational modification, protein turnover, chaperones] 254 matched cddid_all.tbl CDD KOG0185 KOG0185 228134 KOG0185 KOG0185, 20S proteasome, regulatory subunit beta type PSMB4/PRE4 [Posttranslational modification, protein turnover, chaperones] 256 matched cddid_all.tbl CDD KOG0186 KOG0186 228135 KOG0186 KOG0186, Proline oxidase [Amino acid transport and metabolism] 506 matched cddid_all.tbl CDD KOG0187 KOG0187 228136 KOG0187 KOG0187, 40S ribosomal protein S17 [Translation, ribosomal structure and biogenesis] 134 matched cddid_all.tbl CDD KOG0188 KOG0188 228137 KOG0188 KOG0188, Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 895 matched cddid_all.tbl CDD KOG0189 KOG0189 228138 KOG0189 KOG0189, Phosphoadenosine phosphosulfate reductase [Amino acid transport and metabolism] 261 matched cddid_all.tbl CDD KOG0190 KOG0190 228139 KOG0190 KOG0190, Protein disulfide isomerase (prolyl 4-hydroxylase beta subunit) [Posttranslational modification, protein turnover, chaperones] 493 matched cddid_all.tbl CDD KOG0191 KOG0191 228140 KOG0191 KOG0191, Thioredoxin/protein disulfide isomerase [Posttranslational modification, protein turnover, chaperones] 383 matched cddid_all.tbl CDD KOG0192 KOG0192 228141 KOG0192 KOG0192, Tyrosine kinase specific for activated (GTP-bound) p21cdc42Hs [Signal transduction mechanisms] 362 matched cddid_all.tbl CDD KOG0193 KOG0193 228142 KOG0193 KOG0193, Serine/threonine protein kinase RAF [Signal transduction mechanisms] 678 matched cddid_all.tbl CDD KOG0194 KOG0194 228143 KOG0194 KOG0194, Protein tyrosine kinase [Signal transduction mechanisms] 474 matched cddid_all.tbl CDD KOG0195 KOG0195 228144 KOG0195 KOG0195, Integrin-linked kinase [Signal transduction mechanisms] 448 matched cddid_all.tbl CDD KOG0196 KOG0196 228145 KOG0196 KOG0196, Tyrosine kinase, EPH (ephrin) receptor family [Signal transduction mechanisms] 996 matched cddid_all.tbl CDD KOG0197 KOG0197 228146 KOG0197 KOG0197, Tyrosine kinases [Signal transduction mechanisms] 468 matched cddid_all.tbl CDD KOG0198 KOG0198 228147 KOG0198 KOG0198, MEKK and related serine/threonine protein kinases [Signal transduction mechanisms] 313 matched cddid_all.tbl CDD KOG0199 KOG0199 228148 KOG0199 KOG0199, ACK and related non-receptor tyrosine kinases [Signal transduction mechanisms] 1039 matched cddid_all.tbl CDD KOG0200 KOG0200 228149 KOG0200 KOG0200, Fibroblast/platelet-derived growth factor receptor and related receptor tyrosine kinases [Signal transduction mechanisms] 609 matched cddid_all.tbl CDD KOG0201 KOG0201 228150 KOG0201 KOG0201, Serine/threonine protein kinase [Signal transduction mechanisms] 467 matched cddid_all.tbl CDD KOG0202 KOG0202 228151 KOG0202 KOG0202, Ca2+ transporting ATPase [Inorganic ion transport and metabolism] 972 matched cddid_all.tbl CDD KOG0203 KOG0203 228152 KOG0203 KOG0203, Na+/K+ ATPase, alpha subunit [Inorganic ion transport and metabolism] 1019 matched cddid_all.tbl CDD KOG0204 KOG0204 228153 KOG0204 KOG0204, Calcium transporting ATPase [Inorganic ion transport and metabolism] 1034 matched cddid_all.tbl CDD KOG0205 KOG0205 228154 KOG0205 KOG0205, Plasma membrane H+-transporting ATPase [Inorganic ion transport and metabolism] 942 matched cddid_all.tbl CDD KOG0206 KOG0206 228155 KOG0206 KOG0206, P-type ATPase [General function prediction only] 1151 matched cddid_all.tbl CDD KOG0207 KOG0207 228156 KOG0207 KOG0207, Cation transport ATPase [Inorganic ion transport and metabolism] 951 matched cddid_all.tbl CDD KOG0208 KOG0208 228157 KOG0208 KOG0208, Cation transport ATPase [Inorganic ion transport and metabolism] 1140 matched cddid_all.tbl CDD KOG0209 KOG0209 228158 KOG0209 KOG0209, P-type ATPase [Inorganic ion transport and metabolism] 1160 matched cddid_all.tbl CDD KOG0210 KOG0210 228159 KOG0210 KOG0210, P-type ATPase [Inorganic ion transport and metabolism] 1051 matched cddid_all.tbl CDD KOG0211 KOG0211 228160 KOG0211 KOG0211, Protein phosphatase 2A regulatory subunit A and related proteins [Signal transduction mechanisms] 759 matched cddid_all.tbl CDD KOG0212 KOG0212 228161 KOG0212 KOG0212, Uncharacterized conserved protein [Function unknown] 675 matched cddid_all.tbl CDD KOG0213 KOG0213 228162 KOG0213 KOG0213, Splicing factor 3b, subunit 1 [RNA processing and modification] 1172 matched cddid_all.tbl CDD KOG0214 KOG0214 228163 KOG0214 KOG0214, RNA polymerase II, second largest subunit [Transcription] 1141 matched cddid_all.tbl CDD KOG0215 KOG0215 228164 KOG0215 KOG0215, RNA polymerase III, second largest subunit [Transcription] 1153 matched cddid_all.tbl CDD KOG0216 KOG0216 228165 KOG0216 KOG0216, RNA polymerase I, second largest subunit [Transcription] 1111 matched cddid_all.tbl CDD KOG0217 KOG0217 228166 KOG0217 KOG0217, Mismatch repair ATPase MSH6 (MutS family) [Replication, recombination and repair] 1125 matched cddid_all.tbl CDD KOG0218 KOG0218 228167 KOG0218 KOG0218, Mismatch repair MSH3 [Replication, recombination and repair] 1070 matched cddid_all.tbl CDD KOG0219 KOG0219 228168 KOG0219 KOG0219, Mismatch repair ATPase MSH2 (MutS family) [Replication, recombination and repair] 845 matched cddid_all.tbl CDD KOG0220 KOG0220 228169 KOG0220 KOG0220, Mismatch repair ATPase MSH4 (MutS family) [Replication, recombination and repair] 867 matched cddid_all.tbl CDD KOG0221 KOG0221 228170 KOG0221 KOG0221, Mismatch repair ATPase MSH5 (MutS family) [Replication, recombination and repair] 849 matched cddid_all.tbl CDD KOG0222 KOG0222 228171 KOG0222 KOG0222, Phenylalanine and histidine ammonia-lyase [Secondary metabolites biosynthesis, transport and catabolism] 715 matched cddid_all.tbl CDD KOG0223 KOG0223 228172 KOG0223 KOG0223, Aquaporin (major intrinsic protein family) [Carbohydrate transport and metabolism] 238 matched cddid_all.tbl CDD KOG0224 KOG0224 228173 KOG0224 KOG0224, Aquaporin (major intrinsic protein family) [Carbohydrate transport and metabolism] 316 matched cddid_all.tbl CDD KOG0225 KOG0225 228174 KOG0225 KOG0225, Pyruvate dehydrogenase E1, alpha subunit [Energy production and conversion] 394 matched cddid_all.tbl CDD KOG0226 KOG0226 228175 KOG0226 KOG0226, RNA-binding proteins [General function prediction only] 290 matched cddid_all.tbl CDD KOG0227 KOG0227 228176 KOG0227 KOG0227, Splicing factor 3a, subunit 2 [RNA processing and modification] 222 matched cddid_all.tbl CDD KOG0228 KOG0228 228177 KOG0228 KOG0228, Beta-fructofuranosidase (invertase) [Carbohydrate transport and metabolism] 571 matched cddid_all.tbl CDD KOG0229 KOG0229 228178 KOG0229 KOG0229, Phosphatidylinositol-4-phosphate 5-kinase [Signal transduction mechanisms] 420 matched cddid_all.tbl CDD KOG0230 KOG0230 228179 KOG0230 KOG0230, Phosphatidylinositol-4-phosphate 5-kinase and related FYVE finger-containing proteins [Signal transduction mechanisms] 1598 matched cddid_all.tbl CDD KOG0231 KOG0231 228180 KOG0231 KOG0231, Junctional membrane complex protein Junctophilin and related MORN repeat proteins [General function prediction only] 455 matched cddid_all.tbl CDD KOG0232 KOG0232 228181 KOG0232 KOG0232, Vacuolar H+-ATPase V0 sector, subunits c/c' [Energy production and conversion] 156 matched cddid_all.tbl CDD KOG0233 KOG0233 228182 KOG0233 KOG0233, Vacuolar H+-ATPase V0 sector, subunit c'' [Energy production and conversion] 196 matched cddid_all.tbl CDD KOG0234 KOG0234 228183 KOG0234 KOG0234, Fructose-6-phosphate 2-kinase/fructose-2,6-biphosphatase [Carbohydrate transport and metabolism] 438 matched cddid_all.tbl CDD KOG0235 KOG0235 228184 KOG0235 KOG0235, Phosphoglycerate mutase [Carbohydrate transport and metabolism] 214 matched cddid_all.tbl CDD KOG0236 KOG0236 228185 KOG0236 KOG0236, Sulfate/bicarbonate/oxalate exchanger SAT-1 and related transporters (SLC26 family) [Inorganic ion transport and metabolism] 665 matched cddid_all.tbl CDD KOG0237 KOG0237 228186 KOG0237 KOG0237, Glycinamide ribonucleotide synthetase (GARS)/Aminoimidazole ribonucleotide synthetase (AIRS) [Nucleotide transport and metabolism] 788 matched cddid_all.tbl CDD KOG0238 KOG0238 228187 KOG0238 KOG0238, 3-Methylcrotonyl-CoA carboxylase, biotin-containing subunit/Propionyl-CoA carboxylase, alpha chain/Acetyl-CoA carboxylase, biotin carboxylase subunit [Lipid transport and metabolism, Amino acid transport and metabolism] 670 matched cddid_all.tbl CDD KOG0239 KOG0239 228188 KOG0239 KOG0239, Kinesin (KAR3 subfamily) [Cytoskeleton] 670 matched cddid_all.tbl CDD KOG0240 KOG0240 228189 KOG0240 KOG0240, Kinesin (SMY1 subfamily) [Cytoskeleton] 607 matched cddid_all.tbl CDD KOG0241 KOG0241 228190 KOG0241 KOG0241, Kinesin-like protein [Cytoskeleton] 1714 matched cddid_all.tbl CDD KOG0242 KOG0242 228191 KOG0242 KOG0242, Kinesin-like protein [Cytoskeleton] 675 matched cddid_all.tbl CDD KOG0243 KOG0243 228192 KOG0243 KOG0243, Kinesin-like protein [Cytoskeleton] 1041 matched cddid_all.tbl CDD KOG0244 KOG0244 228193 KOG0244 KOG0244, Kinesin-like protein [Cytoskeleton] 913 matched cddid_all.tbl CDD KOG0245 KOG0245 228194 KOG0245 KOG0245, Kinesin-like protein [Cytoskeleton] 1221 matched cddid_all.tbl CDD KOG0246 KOG0246 228195 KOG0246 KOG0246, Kinesin-like protein [Cytoskeleton] 676 matched cddid_all.tbl CDD KOG0247 KOG0247 228196 KOG0247 KOG0247, Kinesin-like protein [Cytoskeleton] 809 matched cddid_all.tbl CDD KOG0248 KOG0248 228197 KOG0248 KOG0248, Cytoplasmic protein Max-1, contains PH, MyTH4 and FERM domains [Cytoskeleton] 936 matched cddid_all.tbl CDD KOG0249 KOG0249 228198 KOG0249 KOG0249, LAR-interacting protein and related proteins [General function prediction only] 916 matched cddid_all.tbl CDD KOG0250 KOG0250 228199 KOG0250 KOG0250, DNA repair protein RAD18 (SMC family protein) [Replication, recombination and repair] 1074 matched cddid_all.tbl CDD KOG0251 KOG0251 228200 KOG0251 KOG0251, Clathrin assembly protein AP180 and related proteins, contain ENTH domain [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 491 matched cddid_all.tbl CDD KOG0252 KOG0252 228201 KOG0252 KOG0252, Inorganic phosphate transporter [Inorganic ion transport and metabolism] 538 matched cddid_all.tbl CDD KOG0253 KOG0253 228202 KOG0253 KOG0253, Synaptic vesicle transporter SV2 (major facilitator superfamily) [General function prediction only] 528 matched cddid_all.tbl CDD KOG0254 KOG0254 228203 KOG0254 KOG0254, Predicted transporter (major facilitator superfamily) [General function prediction only] 513 matched cddid_all.tbl CDD KOG0255 KOG0255 228204 KOG0255 KOG0255, Synaptic vesicle transporter SVOP and related transporters (major facilitator superfamily) [General function prediction only] 521 matched cddid_all.tbl CDD KOG0256 KOG0256 228205 KOG0256 KOG0256, 1-aminocyclopropane-1-carboxylate synthase, and related proteins [Signal transduction mechanisms] 471 matched cddid_all.tbl CDD KOG0257 KOG0257 228206 KOG0257 KOG0257, Kynurenine aminotransferase, glutamine transaminase K [Amino acid transport and metabolism] 420 matched cddid_all.tbl CDD KOG0258 KOG0258 228207 KOG0258 KOG0258, Alanine aminotransferase [Amino acid transport and metabolism] 475 matched cddid_all.tbl CDD KOG0259 KOG0259 228208 KOG0259 KOG0259, Tyrosine aminotransferase [Amino acid transport and metabolism] 447 matched cddid_all.tbl CDD KOG0260 KOG0260 228209 KOG0260 KOG0260, RNA polymerase II, large subunit [Transcription] 1605 matched cddid_all.tbl CDD KOG0261 KOG0261 228210 KOG0261 KOG0261, RNA polymerase III, large subunit [Transcription] 1386 matched cddid_all.tbl CDD KOG0262 KOG0262 228211 KOG0262 KOG0262, RNA polymerase I, large subunit [Transcription] 1640 matched cddid_all.tbl CDD KOG0263 KOG0263 228212 KOG0263 KOG0263, Transcription initiation factor TFIID, subunit TAF5 (also component of histone acetyltransferase SAGA) [Transcription] 707 matched cddid_all.tbl CDD KOG0264 KOG0264 228213 KOG0264 KOG0264, Nucleosome remodeling factor, subunit CAF1/NURF55/MSI1 [Chromatin structure and dynamics] 422 matched cddid_all.tbl CDD KOG0265 KOG0265 228214 KOG0265 KOG0265, U5 snRNP-specific protein-like factor and related proteins [RNA processing and modification] 338 matched cddid_all.tbl CDD KOG0266 KOG0266 228215 KOG0266 KOG0266, WD40 repeat-containing protein [General function prediction only] 456 matched cddid_all.tbl CDD KOG0267 KOG0267 228216 KOG0267 KOG0267, Microtubule severing protein katanin p80 subunit B (contains WD40 repeats) [Cell cycle control, cell division, chromosome partitioning] 825 matched cddid_all.tbl CDD KOG0268 KOG0268 228217 KOG0268 KOG0268, Sof1-like rRNA processing protein (contains WD40 repeats) [RNA processing and modification] 433 matched cddid_all.tbl CDD KOG0269 KOG0269 228218 KOG0269 KOG0269, WD40 repeat-containing protein [Function unknown] 839 matched cddid_all.tbl CDD KOG0270 KOG0270 228219 KOG0270 KOG0270, WD40 repeat-containing protein [Function unknown] 463 matched cddid_all.tbl CDD KOG0271 KOG0271 228220 KOG0271 KOG0271, Notchless-like WD40 repeat-containing protein [Function unknown] 480 matched cddid_all.tbl CDD KOG0272 KOG0272 228221 KOG0272 KOG0272, U4/U6 small nuclear ribonucleoprotein Prp4 (contains WD40 repeats) [RNA processing and modification] 459 matched cddid_all.tbl CDD KOG0273 KOG0273 228222 KOG0273 KOG0273, Beta-transducin family (WD-40 repeat) protein [Chromatin structure and dynamics] 524 matched cddid_all.tbl CDD KOG0274 KOG0274 228223 KOG0274 KOG0274, Cdc4 and related F-box and WD-40 proteins [General function prediction only] 537 matched cddid_all.tbl CDD KOG0275 KOG0275 228224 KOG0275 KOG0275, Conserved WD40 repeat-containing protein [General function prediction only] 508 matched cddid_all.tbl CDD KOG0276 KOG0276 228225 KOG0276 KOG0276, Vesicle coat complex COPI, beta' subunit [Intracellular trafficking, secretion, and vesicular transport] 794 matched cddid_all.tbl CDD KOG0277 KOG0277 228226 KOG0277 KOG0277, Peroxisomal targeting signal type 2 receptor [Intracellular trafficking, secretion, and vesicular transport] 311 matched cddid_all.tbl CDD KOG0278 KOG0278 228227 KOG0278 KOG0278, Serine/threonine kinase receptor-associated protein [Lipid transport and metabolism] 334 matched cddid_all.tbl CDD KOG0279 KOG0279 228228 KOG0279 KOG0279, G protein beta subunit-like protein [Signal transduction mechanisms] 315 matched cddid_all.tbl CDD KOG0280 KOG0280 228229 KOG0280 KOG0280, Uncharacterized conserved protein [Amino acid transport and metabolism] 339 matched cddid_all.tbl CDD KOG0281 KOG0281 228230 KOG0281 KOG0281, Beta-TrCP (transducin repeats containing)/Slimb proteins [Function unknown] 499 matched cddid_all.tbl CDD KOG0282 KOG0282 228231 KOG0282 KOG0282, mRNA splicing factor [Function unknown] 503 matched cddid_all.tbl CDD KOG0283 KOG0283 228232 KOG0283 KOG0283, WD40 repeat-containing protein [Function unknown] 712 matched cddid_all.tbl CDD KOG0284 KOG0284 228233 KOG0284 KOG0284, Polyadenylation factor I complex, subunit PFS2 [RNA processing and modification] 464 matched cddid_all.tbl CDD KOG0285 KOG0285 228234 KOG0285 KOG0285, Pleiotropic regulator 1 [RNA processing and modification] 460 matched cddid_all.tbl CDD KOG0286 KOG0286 228235 KOG0286 KOG0286, G-protein beta subunit [General function prediction only] 343 matched cddid_all.tbl CDD KOG0287 KOG0287 228236 KOG0287 KOG0287, Postreplication repair protein RAD18 [Replication, recombination and repair] 442 matched cddid_all.tbl CDD KOG0288 KOG0288 228237 KOG0288 KOG0288, WD40 repeat protein TipD [General function prediction only] 459 matched cddid_all.tbl CDD KOG0289 KOG0289 228238 KOG0289 KOG0289, mRNA splicing factor [General function prediction only] 506 matched cddid_all.tbl CDD KOG0290 KOG0290 228239 KOG0290 KOG0290, Conserved WD40 repeat-containing protein AN11 [Function unknown] 364 matched cddid_all.tbl CDD KOG0291 KOG0291 228240 KOG0291 KOG0291, WD40-repeat-containing subunit of the 18S rRNA processing complex [RNA processing and modification] 893 matched cddid_all.tbl CDD KOG0292 KOG0292 228241 KOG0292 KOG0292, Vesicle coat complex COPI, alpha subunit [Intracellular trafficking, secretion, and vesicular transport] 1202 matched cddid_all.tbl CDD KOG0293 KOG0293 228242 KOG0293 KOG0293, WD40 repeat-containing protein [Function unknown] 519 matched cddid_all.tbl CDD KOG0294 KOG0294 228243 KOG0294 KOG0294, WD40 repeat-containing protein [Function unknown] 362 matched cddid_all.tbl CDD KOG0295 KOG0295 228244 KOG0295 KOG0295, WD40 repeat-containing protein [Function unknown] 406 matched cddid_all.tbl CDD KOG0296 KOG0296 228245 KOG0296 KOG0296, Angio-associated migratory cell protein (contains WD40 repeats) [Function unknown] 399 matched cddid_all.tbl CDD KOG0297 KOG0297 228246 KOG0297 KOG0297, TNF receptor-associated factor [Signal transduction mechanisms] 391 matched cddid_all.tbl CDD KOG0298 KOG0298 228247 KOG0298 KOG0298, DEAD box-containing helicase-like transcription factor/DNA repair protein [Replication, recombination and repair] 1394 matched cddid_all.tbl CDD KOG0299 KOG0299 228248 KOG0299 KOG0299, U3 snoRNP-associated protein (contains WD40 repeats) [RNA processing and modification] 479 matched cddid_all.tbl CDD KOG0300 KOG0300 228249 KOG0300 KOG0300, WD40 repeat-containing protein [Function unknown] 481 matched cddid_all.tbl CDD KOG0301 KOG0301 228250 KOG0301 KOG0301, Phospholipase A2-activating protein (contains WD40 repeats) [Lipid transport and metabolism] 745 matched cddid_all.tbl CDD KOG0302 KOG0302 228251 KOG0302 KOG0302, Ribosome Assembly protein [General function prediction only] 440 matched cddid_all.tbl CDD KOG0303 KOG0303 228252 KOG0303 KOG0303, Actin-binding protein Coronin, contains WD40 repeats [Cytoskeleton] 472 matched cddid_all.tbl CDD KOG0304 KOG0304 228253 KOG0304 KOG0304, mRNA deadenylase subunit [RNA processing and modification] 239 matched cddid_all.tbl CDD KOG0305 KOG0305 228254 KOG0305 KOG0305, Anaphase promoting complex, Cdc20, Cdh1, and Ama1 subunits [Cell cycle control, cell division, chromosome partitioning, Posttranslational modification, protein turnover, chaperones] 484 matched cddid_all.tbl CDD KOG0306 KOG0306 228255 KOG0306 KOG0306, WD40-repeat-containing subunit of the 18S rRNA processing complex [RNA processing and modification] 888 matched cddid_all.tbl CDD KOG0307 KOG0307 228256 KOG0307 KOG0307, Vesicle coat complex COPII, subunit SEC31 [Intracellular trafficking, secretion, and vesicular transport] 1049 matched cddid_all.tbl CDD KOG0308 KOG0308 228257 KOG0308 KOG0308, Conserved WD40 repeat-containing protein [Function unknown] 735 matched cddid_all.tbl CDD KOG0309 KOG0309 228258 KOG0309 KOG0309, Conserved WD40 repeat-containing protein [Function unknown] 1081 matched cddid_all.tbl CDD KOG0310 KOG0310 228259 KOG0310 KOG0310, Conserved WD40 repeat-containing protein [Function unknown] 487 matched cddid_all.tbl CDD KOG0311 KOG0311 228260 KOG0311 KOG0311, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 381 matched cddid_all.tbl CDD KOG0312 KOG0312 228261 KOG0312 KOG0312, Uncharacterized conserved protein [Function unknown] 563 matched cddid_all.tbl CDD KOG0313 KOG0313 228262 KOG0313 KOG0313, Microtubule binding protein YTM1 (contains WD40 repeats) [Cytoskeleton] 423 matched cddid_all.tbl CDD KOG0314 KOG0314 228263 KOG0314 KOG0314, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 448 matched cddid_all.tbl CDD KOG0315 KOG0315 228264 KOG0315 KOG0315, G-protein beta subunit-like protein (contains WD40 repeats) [General function prediction only] 311 matched cddid_all.tbl CDD KOG0316 KOG0316 228265 KOG0316 KOG0316, Conserved WD40 repeat-containing protein [Function unknown] 307 matched cddid_all.tbl CDD KOG0317 KOG0317 228266 KOG0317 KOG0317, Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones] 293 matched cddid_all.tbl CDD KOG0318 KOG0318 228267 KOG0318 KOG0318, WD40 repeat stress protein/actin interacting protein [Cytoskeleton] 603 matched cddid_all.tbl CDD KOG0319 KOG0319 228268 KOG0319 KOG0319, WD40-repeat-containing subunit of the 18S rRNA processing complex [RNA processing and modification] 775 matched cddid_all.tbl CDD KOG0320 KOG0320 228269 KOG0320 KOG0320, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 187 matched cddid_all.tbl CDD KOG0321 KOG0321 228270 KOG0321 KOG0321, WD40 repeat-containing protein L2DTL [Function unknown] 720 matched cddid_all.tbl CDD KOG0322 KOG0322 228271 KOG0322 KOG0322, G-protein beta subunit-like protein GNB1L, contains WD repeats [General function prediction only] 323 matched cddid_all.tbl CDD KOG0323 KOG0323 228272 KOG0323 KOG0323, TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription] 635 matched cddid_all.tbl CDD KOG0324 KOG0324 228273 KOG0324 KOG0324, Uncharacterized conserved protein [Function unknown] 214 matched cddid_all.tbl CDD KOG0325 KOG0325 228274 KOG0325 KOG0325, Lipoyltransferase [Energy production and conversion, Coenzyme transport and metabolism] 226 matched cddid_all.tbl CDD KOG0326 KOG0326 228275 KOG0326 KOG0326, ATP-dependent RNA helicase [RNA processing and modification] 459 matched cddid_all.tbl CDD KOG0327 KOG0327 228276 KOG0327 KOG0327, Translation initiation factor 4F, helicase subunit (eIF-4A) and related helicases [Translation, ribosomal structure and biogenesis] 397 matched cddid_all.tbl CDD KOG0328 KOG0328 228277 KOG0328 KOG0328, Predicted ATP-dependent RNA helicase FAL1, involved in rRNA maturation, DEAD-box superfamily [Translation, ribosomal structure and biogenesis] 400 matched cddid_all.tbl CDD KOG0329 KOG0329 228278 KOG0329 KOG0329, ATP-dependent RNA helicase [RNA processing and modification] 387 matched cddid_all.tbl CDD KOG0330 KOG0330 228279 KOG0330 KOG0330, ATP-dependent RNA helicase [RNA processing and modification] 476 matched cddid_all.tbl CDD KOG0331 KOG0331 228280 KOG0331 KOG0331, ATP-dependent RNA helicase [RNA processing and modification] 519 matched cddid_all.tbl CDD KOG0332 KOG0332 228281 KOG0332 KOG0332, ATP-dependent RNA helicase [RNA processing and modification] 477 matched cddid_all.tbl CDD KOG0333 KOG0333 228282 KOG0333 KOG0333, U5 snRNP-like RNA helicase subunit [RNA processing and modification] 673 matched cddid_all.tbl CDD KOG0334 KOG0334 228283 KOG0334 KOG0334, RNA helicase [RNA processing and modification] 997 matched cddid_all.tbl CDD KOG0335 KOG0335 228284 KOG0335 KOG0335, ATP-dependent RNA helicase [RNA processing and modification] 482 matched cddid_all.tbl CDD KOG0336 KOG0336 228285 KOG0336 KOG0336, ATP-dependent RNA helicase [RNA processing and modification] 552 matched cddid_all.tbl CDD KOG0337 KOG0337 228286 KOG0337 KOG0337, ATP-dependent RNA helicase [RNA processing and modification] 529 matched cddid_all.tbl CDD KOG0338 KOG0338 228287 KOG0338 KOG0338, ATP-dependent RNA helicase [RNA processing and modification] 691 matched cddid_all.tbl CDD KOG0339 KOG0339 228288 KOG0339 KOG0339, ATP-dependent RNA helicase [RNA processing and modification] 731 matched cddid_all.tbl CDD KOG0340 KOG0340 228289 KOG0340 KOG0340, ATP-dependent RNA helicase [RNA processing and modification] 442 matched cddid_all.tbl CDD KOG0341 KOG0341 228290 KOG0341 KOG0341, DEAD-box protein abstrakt [RNA processing and modification] 610 matched cddid_all.tbl CDD KOG0342 KOG0342 228291 KOG0342 KOG0342, ATP-dependent RNA helicase pitchoune [RNA processing and modification] 543 matched cddid_all.tbl CDD KOG0343 KOG0343 228292 KOG0343 KOG0343, RNA Helicase [RNA processing and modification] 758 matched cddid_all.tbl CDD KOG0344 KOG0344 228293 KOG0344 KOG0344, ATP-dependent RNA helicase [RNA processing and modification] 593 matched cddid_all.tbl CDD KOG0345 KOG0345 228294 KOG0345 KOG0345, ATP-dependent RNA helicase [RNA processing and modification] 567 matched cddid_all.tbl CDD KOG0346 KOG0346 228295 KOG0346 KOG0346, RNA helicase [RNA processing and modification] 569 matched cddid_all.tbl CDD KOG0347 KOG0347 228296 KOG0347 KOG0347, RNA helicase [RNA processing and modification] 731 matched cddid_all.tbl CDD KOG0348 KOG0348 228297 KOG0348 KOG0348, ATP-dependent RNA helicase [RNA processing and modification] 708 matched cddid_all.tbl CDD KOG0349 KOG0349 228298 KOG0349 KOG0349, Putative DEAD-box RNA helicase DDX1 [RNA processing and modification] 725 matched cddid_all.tbl CDD KOG0350 KOG0350 228299 KOG0350 KOG0350, DEAD-box ATP-dependent RNA helicase [RNA processing and modification] 620 matched cddid_all.tbl CDD KOG0351 KOG0351 228300 KOG0351 KOG0351, ATP-dependent DNA helicase [Replication, recombination and repair] 941 matched cddid_all.tbl CDD KOG0352 KOG0352 228301 KOG0352 KOG0352, ATP-dependent DNA helicase [Replication, recombination and repair] 641 matched cddid_all.tbl CDD KOG0353 KOG0353 228302 KOG0353 KOG0353, ATP-dependent DNA helicase [General function prediction only] 695 matched cddid_all.tbl CDD KOG0354 KOG0354 228303 KOG0354 KOG0354, DEAD-box like helicase [General function prediction only] 746 matched cddid_all.tbl CDD KOG0355 KOG0355 228304 KOG0355 KOG0355, DNA topoisomerase type II [Chromatin structure and dynamics] 842 matched cddid_all.tbl CDD KOG0356 KOG0356 228305 KOG0356 KOG0356, Mitochondrial chaperonin, Cpn60/Hsp60p [Posttranslational modification, protein turnover, chaperones] 550 matched cddid_all.tbl CDD KOG0357 KOG0357 228306 KOG0357 KOG0357, Chaperonin complex component, TCP-1 epsilon subunit (CCT5) [Posttranslational modification, protein turnover, chaperones] 400 matched cddid_all.tbl CDD KOG0358 KOG0358 228307 KOG0358 KOG0358, Chaperonin complex component, TCP-1 delta subunit (CCT4) [Posttranslational modification, protein turnover, chaperones] 534 matched cddid_all.tbl CDD KOG0359 KOG0359 228308 KOG0359 KOG0359, Chaperonin complex component, TCP-1 zeta subunit (CCT6) [Posttranslational modification, protein turnover, chaperones] 520 matched cddid_all.tbl CDD KOG0360 KOG0360 228309 KOG0360 KOG0360, Chaperonin complex component, TCP-1 alpha subunit (CCT1) [Posttranslational modification, protein turnover, chaperones] 545 matched cddid_all.tbl CDD KOG0361 KOG0361 228310 KOG0361 KOG0361, Chaperonin complex component, TCP-1 eta subunit (CCT7) [Posttranslational modification, protein turnover, chaperones] 543 matched cddid_all.tbl CDD KOG0362 KOG0362 228311 KOG0362 KOG0362, Chaperonin complex component, TCP-1 theta subunit (CCT8) [Posttranslational modification, protein turnover, chaperones] 537 matched cddid_all.tbl CDD KOG0363 KOG0363 228312 KOG0363 KOG0363, Chaperonin complex component, TCP-1 beta subunit (CCT2) [Posttranslational modification, protein turnover, chaperones] 527 matched cddid_all.tbl CDD KOG0364 KOG0364 228313 KOG0364 KOG0364, Chaperonin complex component, TCP-1 gamma subunit (CCT3) [Posttranslational modification, protein turnover, chaperones] 527 matched cddid_all.tbl CDD KOG0365 KOG0365 228314 KOG0365 KOG0365, Beta subunit of farnesyltransferase [Posttranslational modification, protein turnover, chaperones] 423 matched cddid_all.tbl CDD KOG0366 KOG0366 228315 KOG0366 KOG0366, Protein geranylgeranyltransferase type II, beta subunit [Posttranslational modification, protein turnover, chaperones] 329 matched cddid_all.tbl CDD KOG0367 KOG0367 228316 KOG0367 KOG0367, Protein geranylgeranyltransferase Type I, beta subunit [Posttranslational modification, protein turnover, chaperones] 347 matched cddid_all.tbl CDD KOG0368 KOG0368 228317 KOG0368 KOG0368, Acetyl-CoA carboxylase [Lipid transport and metabolism] 2196 matched cddid_all.tbl CDD KOG0369 KOG0369 228318 KOG0369 KOG0369, Pyruvate carboxylase [Energy production and conversion] 1176 matched cddid_all.tbl CDD KOG0370 KOG0370 228319 KOG0370 KOG0370, Multifunctional pyrimidine synthesis protein CAD (includes carbamoyl-phophate synthetase, aspartate transcarbamylase, and glutamine amidotransferase) [General function prediction only] 1435 matched cddid_all.tbl CDD KOG0371 KOG0371 228320 KOG0371 KOG0371, Serine/threonine protein phosphatase 2A, catalytic subunit [Signal transduction mechanisms] 319 matched cddid_all.tbl CDD KOG0372 KOG0372 228321 KOG0372 KOG0372, Serine/threonine specific protein phosphatase involved in glycogen accumulation, PP2A-related [Carbohydrate transport and metabolism, Signal transduction mechanisms] 303 matched cddid_all.tbl CDD KOG0373 KOG0373 228322 KOG0373 KOG0373, Serine/threonine specific protein phosphatase involved in cell cycle control, PP2A-related [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms] 306 matched cddid_all.tbl CDD KOG0374 KOG0374 228323 KOG0374 KOG0374, Serine/threonine specific protein phosphatase PP1, catalytic subunit [Signal transduction mechanisms, General function prediction only] 331 matched cddid_all.tbl CDD KOG0375 KOG0375 228324 KOG0375 KOG0375, Serine-threonine phosphatase 2B, catalytic subunit [General function prediction only] 517 matched cddid_all.tbl CDD KOG0376 KOG0376 228325 KOG0376 KOG0376, Serine-threonine phosphatase 2A, catalytic subunit [General function prediction only] 476 matched cddid_all.tbl CDD KOG0377 KOG0377 228326 KOG0377 KOG0377, Protein serine/threonine phosphatase RDGC/PPEF, contains STphosphatase and EF-hand domains [Signal transduction mechanisms] 631 matched cddid_all.tbl CDD KOG0378 KOG0378 228327 KOG0378 KOG0378, 40S ribosomal protein S4 [Translation, ribosomal structure and biogenesis] 263 matched cddid_all.tbl CDD KOG0379 KOG0379 228328 KOG0379 KOG0379, Kelch repeat-containing proteins [General function prediction only] 482 matched cddid_all.tbl CDD KOG0380 KOG0380 228329 KOG0380 KOG0380, Sterol O-acyltransferase/Diacylglycerol O-acyltransferase [Lipid transport and metabolism] 523 matched cddid_all.tbl CDD KOG0381 KOG0381 228330 KOG0381 KOG0381, HMG box-containing protein [General function prediction only] 96 matched cddid_all.tbl CDD KOG0382 KOG0382 228331 KOG0382 KOG0382, Carbonic anhydrase [General function prediction only] 262 matched cddid_all.tbl CDD KOG0383 KOG0383 228332 KOG0383 KOG0383, Predicted helicase [General function prediction only] 696 matched cddid_all.tbl CDD KOG0384 KOG0384 228333 KOG0384 KOG0384, Chromodomain-helicase DNA-binding protein [Transcription] 1373 matched cddid_all.tbl CDD KOG0385 KOG0385 228334 KOG0385 KOG0385, Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription] 971 matched cddid_all.tbl CDD KOG0386 KOG0386 228335 KOG0386 KOG0386, Chromatin remodeling complex SWI/SNF, component SWI2 and related ATPases (DNA/RNA helicase superfamily) [Chromatin structure and dynamics, Transcription] 1157 matched cddid_all.tbl CDD KOG0387 KOG0387 228336 KOG0387 KOG0387, Transcription-coupled repair protein CSB/RAD26 (contains SNF2 family DNA-dependent ATPase domain) [Transcription, Replication, recombination and repair] 923 matched cddid_all.tbl CDD KOG0388 KOG0388 228337 KOG0388 KOG0388, SNF2 family DNA-dependent ATPase [Replication, recombination and repair] 1185 matched cddid_all.tbl CDD KOG0389 KOG0389 228338 KOG0389 KOG0389, SNF2 family DNA-dependent ATPase [Chromatin structure and dynamics] 941 matched cddid_all.tbl CDD KOG0390 KOG0390 228339 KOG0390 KOG0390, DNA repair protein, SNF2 family [Replication, recombination and repair] 776 matched cddid_all.tbl CDD KOG0391 KOG0391 228340 KOG0391 KOG0391, SNF2 family DNA-dependent ATPase [General function prediction only] 1958 matched cddid_all.tbl CDD KOG0392 KOG0392 228341 KOG0392 KOG0392, SNF2 family DNA-dependent ATPase domain-containing protein [Transcription] 1549 matched cddid_all.tbl CDD KOG0393 KOG0393 228342 KOG0393 KOG0393, Ras-related small GTPase, Rho type [General function prediction only] 198 matched cddid_all.tbl CDD KOG0394 KOG0394 228343 KOG0394 KOG0394, Ras-related GTPase [General function prediction only] 210 matched cddid_all.tbl CDD KOG0395 KOG0395 228344 KOG0395 KOG0395, Ras-related GTPase [General function prediction only] 196 matched cddid_all.tbl CDD KOG0396 KOG0396 228345 KOG0396 KOG0396, Uncharacterized conserved protein [Function unknown] 389 matched cddid_all.tbl CDD KOG0397 KOG0397 228346 KOG0397 KOG0397, 60S ribosomal protein L11 [Translation, ribosomal structure and biogenesis] 176 matched cddid_all.tbl CDD KOG0398 KOG0398 228347 KOG0398 KOG0398, Mitochondrial/chloroplast ribosomal protein L5/L7 [Translation, ribosomal structure and biogenesis] 278 matched cddid_all.tbl CDD KOG0399 KOG0399 228348 KOG0399 KOG0399, Glutamate synthase [Amino acid transport and metabolism] 2142 matched cddid_all.tbl CDD KOG0400 KOG0400 228349 KOG0400 KOG0400, 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis] 151 matched cddid_all.tbl CDD KOG0401 KOG0401 228350 KOG0401 KOG0401, Translation initiation factor 4F, ribosome/mRNA-bridging subunit (eIF-4G) [Translation, ribosomal structure and biogenesis] 970 matched cddid_all.tbl CDD KOG0402 KOG0402 228351 KOG0402 KOG0402, 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis] 92 matched cddid_all.tbl CDD KOG0403 KOG0403 228352 KOG0403 KOG0403, Neoplastic transformation suppressor Pdcd4/MA-3, contains MA3 domain [Signal transduction mechanisms] 645 matched cddid_all.tbl CDD KOG0404 KOG0404 228353 KOG0404 KOG0404, Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones] 322 matched cddid_all.tbl CDD KOG0405 KOG0405 228354 KOG0405 KOG0405, Pyridine nucleotide-disulphide oxidoreductase [Secondary metabolites biosynthesis, transport and catabolism] 478 matched cddid_all.tbl CDD KOG0406 KOG0406 228355 KOG0406 KOG0406, Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones] 231 matched cddid_all.tbl CDD KOG0407 KOG0407 228356 KOG0407 KOG0407, 40S ribosomal protein S14 [Translation, ribosomal structure and biogenesis] 139 matched cddid_all.tbl CDD KOG0408 KOG0408 228357 KOG0408 KOG0408, Mitochondrial/chloroplast ribosomal protein S11 [Translation, ribosomal structure and biogenesis] 190 matched cddid_all.tbl CDD KOG0409 KOG0409 228358 KOG0409 KOG0409, Predicted dehydrogenase [General function prediction only] 327 matched cddid_all.tbl CDD KOG0410 KOG0410 228359 KOG0410 KOG0410, Predicted GTP binding protein [General function prediction only] 410 matched cddid_all.tbl CDD KOG0411 KOG0411 228360 KOG0411 KOG0411, Uncharacterized membrane protein [Function unknown] 405 matched cddid_all.tbl CDD KOG0412 KOG0412 228361 KOG0412 KOG0412, Golgi transport complex COD1 protein [Intracellular trafficking, secretion, and vesicular transport] 773 matched cddid_all.tbl CDD KOG0413 KOG0413 228362 KOG0413 KOG0413, Uncharacterized conserved protein related to condensin complex subunit 1 [Function unknown] 1529 matched cddid_all.tbl CDD KOG0414 KOG0414 228363 KOG0414 KOG0414, Chromosome condensation complex Condensin, subunit D2 [Chromatin structure and dynamics, Cell cycle control, cell division, chromosome partitioning] 1251 matched cddid_all.tbl CDD KOG0415 KOG0415 228364 KOG0415 KOG0415, Predicted peptidyl prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones] 479 matched cddid_all.tbl CDD KOG0416 KOG0416 228365 KOG0416 KOG0416, Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones] 189 matched cddid_all.tbl CDD KOG0417 KOG0417 228366 KOG0417 KOG0417, Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones] 148 matched cddid_all.tbl CDD KOG0418 KOG0418 228367 KOG0418 KOG0418, Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones] 200 matched cddid_all.tbl CDD KOG0419 KOG0419 228368 KOG0419 KOG0419, Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones] 152 matched cddid_all.tbl CDD KOG0420 KOG0420 228369 KOG0420 KOG0420, Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones] 184 matched cddid_all.tbl CDD KOG0421 KOG0421 228370 KOG0421 KOG0421, Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones] 175 matched cddid_all.tbl CDD KOG0422 KOG0422 228371 KOG0422 KOG0422, Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones] 153 matched cddid_all.tbl CDD KOG0423 KOG0423 228372 KOG0423 KOG0423, Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones] 223 matched cddid_all.tbl CDD KOG0424 KOG0424 228373 KOG0424 KOG0424, Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones] 158 matched cddid_all.tbl CDD KOG0425 KOG0425 228374 KOG0425 KOG0425, Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones] 171 matched cddid_all.tbl CDD KOG0426 KOG0426 228375 KOG0426 KOG0426, Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones] 165 matched cddid_all.tbl CDD KOG0427 KOG0427 228376 KOG0427 KOG0427, Ubiquitin conjugating enzyme [Posttranslational modification, protein turnover, chaperones] 161 matched cddid_all.tbl CDD KOG0428 KOG0428 228377 KOG0428 KOG0428, Non-canonical ubiquitin conjugating enzyme 1 [Posttranslational modification, protein turnover, chaperones] 314 matched cddid_all.tbl CDD KOG0429 KOG0429 228378 KOG0429 KOG0429, Ubiquitin-conjugating enzyme-related protein Ft1, involved in programmed cell death [Posttranslational modification, protein turnover, chaperones] 258 matched cddid_all.tbl CDD KOG0430 KOG0430 228379 KOG0430 KOG0430, Xanthine dehydrogenase [Nucleotide transport and metabolism] 1257 matched cddid_all.tbl CDD KOG0431 KOG0431 228380 KOG0431 KOG0431, Auxilin-like protein and related proteins containing DnaJ domain [General function prediction only] 453 matched cddid_all.tbl CDD KOG0432 KOG0432 228381 KOG0432 KOG0432, Valyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 995 matched cddid_all.tbl CDD KOG0433 KOG0433 228382 KOG0433 KOG0433, Isoleucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 937 matched cddid_all.tbl CDD KOG0434 KOG0434 228383 KOG0434 KOG0434, Isoleucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 1070 matched cddid_all.tbl CDD KOG0435 KOG0435 228384 KOG0435 KOG0435, Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 876 matched cddid_all.tbl CDD KOG0436 KOG0436 228385 KOG0436 KOG0436, Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 578 matched cddid_all.tbl CDD KOG0437 KOG0437 228386 KOG0437 KOG0437, Leucyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 1080 matched cddid_all.tbl CDD KOG0438 KOG0438 228387 KOG0438 KOG0438, Mitochondrial/chloroplast ribosomal protein L2 [Translation, ribosomal structure and biogenesis] 312 matched cddid_all.tbl CDD KOG0439 KOG0439 228388 KOG0439 KOG0439, VAMP-associated protein involved in inositol metabolism [Intracellular trafficking, secretion, and vesicular transport] 218 matched cddid_all.tbl CDD KOG0440 KOG0440 228389 KOG0440 KOG0440, Cell cycle-associated protein Mob1-1 [Cell cycle control, cell division, chromosome partitioning] 243 matched cddid_all.tbl CDD KOG0441 KOG0441 228390 KOG0441 KOG0441, Cu2+/Zn2+ superoxide dismutase SOD1 [Inorganic ion transport and metabolism] 154 matched cddid_all.tbl CDD KOG0442 KOG0442 228391 KOG0442 KOG0442, Structure-specific endonuclease ERCC1-XPF, catalytic component XPF/ERCC4 [Replication, recombination and repair] 892 matched cddid_all.tbl CDD KOG0443 KOG0443 228392 KOG0443 KOG0443, Actin regulatory proteins (gelsolin/villin family) [Cytoskeleton] 827 matched cddid_all.tbl CDD KOG0444 KOG0444 228393 KOG0444 KOG0444, Cytoskeletal regulator Flightless-I (contains leucine-rich and gelsolin repeats) [Cytoskeleton] 1255 matched cddid_all.tbl CDD KOG0445 KOG0445 228394 KOG0445 KOG0445, Actin regulatory protein supervillin (gelsolin/villin family) [Cytoskeleton] 919 matched cddid_all.tbl CDD KOG0446 KOG0446 228395 KOG0446 KOG0446, Vacuolar sorting protein VPS1, dynamin, and related proteins [Intracellular trafficking, secretion, and vesicular transport, General function prediction only] 657 matched cddid_all.tbl CDD KOG0447 KOG0447 228396 KOG0447 KOG0447, Dynamin-like GTP binding protein [General function prediction only] 980 matched cddid_all.tbl CDD KOG0448 KOG0448 228397 KOG0448 KOG0448, Mitofusin 1 GTPase, involved in mitochondrila biogenesis [Posttranslational modification, protein turnover, chaperones] 749 matched cddid_all.tbl CDD KOG0449 KOG0449 228398 KOG0449 KOG0449, Succinate dehydrogenase, cytochrome b subunit [Carbohydrate transport and metabolism] 168 matched cddid_all.tbl CDD KOG0450 KOG0450 228399 KOG0450 KOG0450, 2-oxoglutarate dehydrogenase, E1 subunit [Carbohydrate transport and metabolism] 1017 matched cddid_all.tbl CDD KOG0451 KOG0451 228400 KOG0451 KOG0451, Predicted 2-oxoglutarate dehydrogenase, E1 subunit [Carbohydrate transport and metabolism] 913 matched cddid_all.tbl CDD KOG0452 KOG0452 228401 KOG0452 KOG0452, RNA-binding translational regulator IRP (aconitase superfamily) [RNA processing and modification, Translation, ribosomal structure and biogenesis] 892 matched cddid_all.tbl CDD KOG0453 KOG0453 228402 KOG0453 KOG0453, Aconitase/homoaconitase (aconitase superfamily) [Energy production and conversion, Amino acid transport and metabolism] 778 matched cddid_all.tbl CDD KOG0454 KOG0454 228403 KOG0454 KOG0454, 3-isopropylmalate dehydratase (aconitase superfamily) [Amino acid transport and metabolism] 502 matched cddid_all.tbl CDD KOG0455 KOG0455 228404 KOG0455 KOG0455, Homoserine dehydrogenase [Amino acid transport and metabolism] 364 matched cddid_all.tbl CDD KOG0456 KOG0456 228405 KOG0456 KOG0456, Aspartate kinase [Amino acid transport and metabolism] 559 matched cddid_all.tbl CDD KOG0457 KOG0457 228406 KOG0457 KOG0457, Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics] 438 matched cddid_all.tbl CDD KOG0458 KOG0458 228407 KOG0458 KOG0458, Elongation factor 1 alpha [Translation, ribosomal structure and biogenesis] 603 matched cddid_all.tbl CDD KOG0459 KOG0459 228408 KOG0459 KOG0459, Polypeptide release factor 3 [Translation, ribosomal structure and biogenesis] 501 matched cddid_all.tbl CDD KOG0460 KOG0460 228409 KOG0460 KOG0460, Mitochondrial translation elongation factor Tu [Translation, ribosomal structure and biogenesis] 449 matched cddid_all.tbl CDD KOG0461 KOG0461 228410 KOG0461 KOG0461, Selenocysteine-specific elongation factor [Translation, ribosomal structure and biogenesis] 522 matched cddid_all.tbl CDD KOG0462 KOG0462 228411 KOG0462 KOG0462, Elongation factor-type GTP-binding protein [Translation, ribosomal structure and biogenesis] 650 matched cddid_all.tbl CDD KOG0463 KOG0463 228412 KOG0463 KOG0463, GTP-binding protein GP-1 [General function prediction only] 641 matched cddid_all.tbl CDD KOG0464 KOG0464 228413 KOG0464 KOG0464, Elongation factor G [Translation, ribosomal structure and biogenesis] 753 matched cddid_all.tbl CDD KOG0465 KOG0465 228414 KOG0465 KOG0465, Mitochondrial elongation factor [Translation, ribosomal structure and biogenesis] 721 matched cddid_all.tbl CDD KOG0466 KOG0466 228415 KOG0466 KOG0466, Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis] 466 matched cddid_all.tbl CDD KOG0467 KOG0467 228416 KOG0467 KOG0467, Translation elongation factor 2/ribosome biogenesis protein RIA1 and related proteins [Translation, ribosomal structure and biogenesis] 887 matched cddid_all.tbl CDD KOG0468 KOG0468 228417 KOG0468 KOG0468, U5 snRNP-specific protein [Translation, ribosomal structure and biogenesis] 971 matched cddid_all.tbl CDD KOG0469 KOG0469 228418 KOG0469 KOG0469, Elongation factor 2 [Translation, ribosomal structure and biogenesis] 842 matched cddid_all.tbl CDD KOG0470 KOG0470 228419 KOG0470 KOG0470, 1,4-alpha-glucan branching enzyme/starch branching enzyme II [Carbohydrate transport and metabolism] 757 matched cddid_all.tbl CDD KOG0471 KOG0471 228420 KOG0471 KOG0471, Alpha-amylase [Carbohydrate transport and metabolism] 545 matched cddid_all.tbl CDD KOG0472 KOG0472 228421 KOG0472 KOG0472, Leucine-rich repeat protein [Function unknown] 565 matched cddid_all.tbl CDD KOG0473 KOG0473 228422 KOG0473 KOG0473, Leucine-rich repeat protein [Function unknown] 326 matched cddid_all.tbl CDD KOG0474 KOG0474 228423 KOG0474 KOG0474, Cl- channel CLC-7 and related proteins (CLC superfamily) [Inorganic ion transport and metabolism] 762 matched cddid_all.tbl CDD KOG0475 KOG0475 228424 KOG0475 KOG0475, Cl- channel CLC-3 and related proteins (CLC superfamily) [Inorganic ion transport and metabolism] 696 matched cddid_all.tbl CDD KOG0476 KOG0476 228425 KOG0476 KOG0476, Cl- channel CLC-2 and related proteins (CLC superfamily) [Inorganic ion transport and metabolism] 931 matched cddid_all.tbl CDD KOG0477 KOG0477 228426 KOG0477 KOG0477, DNA replication licensing factor, MCM2 component [Replication, recombination and repair] 854 matched cddid_all.tbl CDD KOG0478 KOG0478 228427 KOG0478 KOG0478, DNA replication licensing factor, MCM4 component [Replication, recombination and repair] 804 matched cddid_all.tbl CDD KOG0479 KOG0479 228428 KOG0479 KOG0479, DNA replication licensing factor, MCM3 component [Replication, recombination and repair] 818 matched cddid_all.tbl CDD KOG0480 KOG0480 228429 KOG0480 KOG0480, DNA replication licensing factor, MCM6 component [Replication, recombination and repair] 764 matched cddid_all.tbl CDD KOG0481 KOG0481 228430 KOG0481 KOG0481, DNA replication licensing factor, MCM5 component [Replication, recombination and repair] 729 matched cddid_all.tbl CDD KOG0482 KOG0482 228431 KOG0482 KOG0482, DNA replication licensing factor, MCM7 component [Replication, recombination and repair] 721 matched cddid_all.tbl CDD KOG0483 KOG0483 228432 KOG0483 KOG0483, Transcription factor HEX, contains HOX and HALZ domains [Transcription] 198 matched cddid_all.tbl CDD KOG0484 KOG0484 228433 KOG0484 KOG0484, Transcription factor PHOX2/ARIX, contains HOX domain [Transcription] 125 matched cddid_all.tbl CDD KOG0485 KOG0485 228434 KOG0485 KOG0485, Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription] 268 matched cddid_all.tbl CDD KOG0486 KOG0486 228435 KOG0486 KOG0486, Transcription factor PTX1, contains HOX domain [Transcription] 351 matched cddid_all.tbl CDD KOG0487 KOG0487 228436 KOG0487 KOG0487, Transcription factor Abd-B, contains HOX domain [Transcription] 308 matched cddid_all.tbl CDD KOG0488 KOG0488 228437 KOG0488 KOG0488, Transcription factor BarH and related HOX domain proteins [General function prediction only] 309 matched cddid_all.tbl CDD KOG0489 KOG0489 228438 KOG0489 KOG0489, Transcription factor zerknullt and related HOX domain proteins [General function prediction only] 261 matched cddid_all.tbl CDD KOG0490 KOG0490 228439 KOG0490 KOG0490, Transcription factor, contains HOX domain [General function prediction only] 235 matched cddid_all.tbl CDD KOG0491 KOG0491 228440 KOG0491 KOG0491, Transcription factor BSH, contains HOX domain [General function prediction only] 194 matched cddid_all.tbl CDD KOG0492 KOG0492 228441 KOG0492 KOG0492, Transcription factor MSH, contains HOX domain [General function prediction only] 246 matched cddid_all.tbl CDD KOG0493 KOG0493 228442 KOG0493 KOG0493, Transcription factor Engrailed, contains HOX domain [General function prediction only] 342 matched cddid_all.tbl CDD KOG0494 KOG0494 228443 KOG0494 KOG0494, Transcription factor CHX10 and related HOX domain proteins [General function prediction only] 332 matched cddid_all.tbl CDD KOG0495 KOG0495 228444 KOG0495 KOG0495, HAT repeat protein [RNA processing and modification] 913 matched cddid_all.tbl CDD KOG0496 KOG0496 228445 KOG0496 KOG0496, Beta-galactosidase [Carbohydrate transport and metabolism] 649 matched cddid_all.tbl CDD KOG0497 KOG0497 228446 KOG0497 KOG0497, Oxidosqualene-lanosterol cyclase and related proteins [Lipid transport and metabolism] 760 matched cddid_all.tbl CDD KOG0498 KOG0498 228447 KOG0498 KOG0498, K+-channel ERG and related proteins, contain PAS/PAC sensor domain [Inorganic ion transport and metabolism, Signal transduction mechanisms] 727 matched cddid_all.tbl CDD KOG0499 KOG0499 228448 KOG0499 KOG0499, Cyclic nucleotide-gated cation channel CNCG4 [Inorganic ion transport and metabolism, Signal transduction mechanisms] 815 matched cddid_all.tbl CDD KOG0500 KOG0500 228449 KOG0500 KOG0500, Cyclic nucleotide-gated cation channel CNGA1-3 and related proteins [Inorganic ion transport and metabolism, Signal transduction mechanisms] 536 matched cddid_all.tbl CDD KOG0501 KOG0501 228450 KOG0501 KOG0501, K+-channel KCNQ [Inorganic ion transport and metabolism] 971 matched cddid_all.tbl CDD KOG0502 KOG0502 228451 KOG0502 KOG0502, Integral membrane ankyrin-repeat protein Kidins220 (protein kinase D substrate) [General function prediction only] 296 matched cddid_all.tbl CDD KOG0503 KOG0503 228452 KOG0503 KOG0503, Asparaginase [Amino acid transport and metabolism] 368 matched cddid_all.tbl CDD KOG0505 KOG0505 228453 KOG0505 KOG0505, Myosin phosphatase, regulatory subunit [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms] 527 matched cddid_all.tbl CDD KOG0506 KOG0506 228454 KOG0506 KOG0506, Glutaminase (contains ankyrin repeat) [Amino acid transport and metabolism] 622 matched cddid_all.tbl CDD KOG0507 KOG0507 228455 KOG0507 KOG0507, CASK-interacting adaptor protein (caskin) and related proteins with ankyrin repeats and SAM domain [Signal transduction mechanisms] 854 matched cddid_all.tbl CDD KOG0508 KOG0508 228456 KOG0508 KOG0508, Ankyrin repeat protein [General function prediction only] 615 matched cddid_all.tbl CDD KOG0509 KOG0509 228457 KOG0509 KOG0509, Ankyrin repeat and DHHC-type Zn-finger domain containing proteins [General function prediction only] 600 matched cddid_all.tbl CDD KOG0510 KOG0510 228458 KOG0510 KOG0510, Ankyrin repeat protein [General function prediction only] 929 matched cddid_all.tbl CDD KOG0511 KOG0511 228459 KOG0511 KOG0511, Ankyrin repeat protein [General function prediction only] 516 matched cddid_all.tbl CDD KOG0512 KOG0512 228460 KOG0512 KOG0512, Fetal globin-inducing factor (contains ankyrin repeats) [Transcription] 228 matched cddid_all.tbl CDD KOG0513 KOG0513 228461 KOG0513 KOG0513, Ca2+-independent phospholipase A2 [Lipid transport and metabolism] 503 matched cddid_all.tbl CDD KOG0514 KOG0514 228462 KOG0514 KOG0514, Ankyrin repeat protein [General function prediction only] 452 matched cddid_all.tbl CDD KOG0515 KOG0515 228463 KOG0515 KOG0515, p53-interacting protein 53BP/ASPP, contains ankyrin and SH3 domains [Cell cycle control, cell division, chromosome partitioning] 752 matched cddid_all.tbl CDD KOG0516 KOG0516 228464 KOG0516 KOG0516, Dystonin, GAS (Growth-arrest-specific protein), and related proteins [Cytoskeleton] 1047 matched cddid_all.tbl CDD KOG0517 KOG0517 228465 KOG0517 KOG0517, Beta-spectrin [Cytoskeleton] 2473 matched cddid_all.tbl CDD KOG0518 KOG0518 228466 KOG0518 KOG0518, Actin-binding cytoskeleton protein, filamin [Cytoskeleton] 1113 matched cddid_all.tbl CDD KOG0519 KOG0519 228467 KOG0519 KOG0519, Sensory transduction histidine kinase [Signal transduction mechanisms] 786 matched cddid_all.tbl CDD KOG0520 KOG0520 228468 KOG0520 KOG0520, Uncharacterized conserved protein, contains IPT/TIG domain [Function unknown] 975 matched cddid_all.tbl CDD KOG0521 KOG0521 228469 KOG0521 KOG0521, Putative GTPase activating proteins (GAPs) [Signal transduction mechanisms] 785 matched cddid_all.tbl CDD KOG0522 KOG0522 228470 KOG0522 KOG0522, Ankyrin repeat protein [General function prediction only] 560 matched cddid_all.tbl CDD KOG0523 KOG0523 228471 KOG0523 KOG0523, Transketolase [Carbohydrate transport and metabolism] 632 matched cddid_all.tbl CDD KOG0524 KOG0524 228472 KOG0524 KOG0524, Pyruvate dehydrogenase E1, beta subunit [Energy production and conversion] 359 matched cddid_all.tbl CDD KOG0525 KOG0525 228473 KOG0525 KOG0525, Branched chain alpha-keto acid dehydrogenase E1, beta subunit [Energy production and conversion] 362 matched cddid_all.tbl CDD KOG0526 KOG0526 228474 KOG0526 KOG0526, Nucleosome-binding factor SPN, POB3 subunit [Transcription, Replication, recombination and repair, Chromatin structure and dynamics] 615 matched cddid_all.tbl CDD KOG0527 KOG0527 228475 KOG0527 KOG0527, HMG-box transcription factor [Transcription] 331 matched cddid_all.tbl CDD KOG0528 KOG0528 228476 KOG0528 KOG0528, HMG-box transcription factor SOX5 [Transcription] 511 matched cddid_all.tbl CDD KOG0529 KOG0529 228477 KOG0529 KOG0529, Protein geranylgeranyltransferase type II, alpha subunit [Posttranslational modification, protein turnover, chaperones] 421 matched cddid_all.tbl CDD KOG0530 KOG0530 228478 KOG0530 KOG0530, Protein farnesyltransferase, alpha subunit/protein geranylgeranyltransferase type I, alpha subunit [Posttranslational modification, protein turnover, chaperones] 318 matched cddid_all.tbl CDD KOG0531 KOG0531 228479 KOG0531 KOG0531, Protein phosphatase 1, regulatory subunit, and related proteins [Signal transduction mechanisms] 414 matched cddid_all.tbl CDD KOG0532 KOG0532 228480 KOG0532 KOG0532, Leucine-rich repeat (LRR) protein, contains calponin homology domain [Cytoskeleton] 722 matched cddid_all.tbl CDD KOG0533 KOG0533 228481 KOG0533 KOG0533, RRM motif-containing protein [RNA processing and modification] 243 matched cddid_all.tbl CDD KOG0534 KOG0534 228482 KOG0534 KOG0534, NADH-cytochrome b-5 reductase [Coenzyme transport and metabolism, Energy production and conversion] 286 matched cddid_all.tbl CDD KOG0535 KOG0535 228483 KOG0535 KOG0535, Sulfite oxidase, molybdopterin-binding component [Energy production and conversion] 381 matched cddid_all.tbl CDD KOG0536 KOG0536 228484 KOG0536 KOG0536, Flavohemoprotein b5+b5R [Energy production and conversion] 145 matched cddid_all.tbl CDD KOG0537 KOG0537 228485 KOG0537 KOG0537, Cytochrome b5 [Energy production and conversion] 124 matched cddid_all.tbl CDD KOG0538 KOG0538 228486 KOG0538 KOG0538, Glycolate oxidase [Energy production and conversion] 363 matched cddid_all.tbl CDD KOG0539 KOG0539 228487 KOG0539 KOG0539, Sphingolipid fatty acid hydroxylase [Lipid transport and metabolism] 240 matched cddid_all.tbl CDD KOG0540 KOG0540 228488 KOG0540 KOG0540, 3-Methylcrotonyl-CoA carboxylase, non-biotin containing subunit/Acetyl-CoA carboxylase carboxyl transferase, subunit beta [Amino acid transport and metabolism, Lipid transport and metabolism] 536 matched cddid_all.tbl CDD KOG0541 KOG0541 228489 KOG0541 KOG0541, Alkyl hydroperoxide reductase/peroxiredoxin [Posttranslational modification, protein turnover, chaperones] 171 matched cddid_all.tbl CDD KOG0542 KOG0542 228490 KOG0542 KOG0542, Predicted exonuclease [Replication, recombination and repair] 280 matched cddid_all.tbl CDD KOG0543 KOG0543 228491 KOG0543 KOG0543, FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones] 397 matched cddid_all.tbl CDD KOG0544 KOG0544 228492 KOG0544 KOG0544, FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones] 108 matched cddid_all.tbl CDD KOG0545 KOG0545 228493 KOG0545 KOG0545, Aryl-hydrocarbon receptor-interacting protein [Posttranslational modification, protein turnover, chaperones] 329 matched cddid_all.tbl CDD KOG0546 KOG0546 228494 KOG0546 KOG0546, HSP90 co-chaperone CPR7/Cyclophilin [Posttranslational modification, protein turnover, chaperones] 372 matched cddid_all.tbl CDD KOG0547 KOG0547 228495 KOG0547 KOG0547, Translocase of outer mitochondrial membrane complex, subunit TOM70/TOM72 [Intracellular trafficking, secretion, and vesicular transport] 606 matched cddid_all.tbl CDD KOG0548 KOG0548 228496 KOG0548 KOG0548, Molecular co-chaperone STI1 [Posttranslational modification, protein turnover, chaperones] 539 matched cddid_all.tbl CDD KOG0549 KOG0549 228497 KOG0549 KOG0549, FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones] 188 matched cddid_all.tbl CDD KOG0550 KOG0550 228498 KOG0550 KOG0550, Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones] 486 matched cddid_all.tbl CDD KOG0551 KOG0551 228499 KOG0551 KOG0551, Hsp90 co-chaperone CNS1 (contains TPR repeats) [Posttranslational modification, protein turnover, chaperones] 390 matched cddid_all.tbl CDD KOG0552 KOG0552 228500 KOG0552 KOG0552, FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones] 226 matched cddid_all.tbl CDD KOG0553 KOG0553 228501 KOG0553 KOG0553, TPR repeat-containing protein [General function prediction only] 304 matched cddid_all.tbl CDD KOG0554 KOG0554 228502 KOG0554 KOG0554, Asparaginyl-tRNA synthetase (mitochondrial) [Translation, ribosomal structure and biogenesis] 446 matched cddid_all.tbl CDD KOG0555 KOG0555 228503 KOG0555 KOG0555, Asparaginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 545 matched cddid_all.tbl CDD KOG0556 KOG0556 228504 KOG0556 KOG0556, Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 533 matched cddid_all.tbl CDD KOG0557 KOG0557 228505 KOG0557 KOG0557, Dihydrolipoamide acetyltransferase [Energy production and conversion] 470 matched cddid_all.tbl CDD KOG0558 KOG0558 228506 KOG0558 KOG0558, Dihydrolipoamide transacylase (alpha-keto acid dehydrogenase E2 subunit) [Energy production and conversion] 474 matched cddid_all.tbl CDD KOG0559 KOG0559 228507 KOG0559 KOG0559, Dihydrolipoamide succinyltransferase (2-oxoglutarate dehydrogenase, E2 subunit) [Energy production and conversion] 457 matched cddid_all.tbl CDD KOG0560 KOG0560 228508 KOG0560 KOG0560, Sulfite reductase (ferredoxin) [Inorganic ion transport and metabolism] 638 matched cddid_all.tbl CDD KOG0561 KOG0561 228509 KOG0561 KOG0561, bHLH transcription factor [Transcription] 373 matched cddid_all.tbl CDD KOG0562 KOG0562 228510 KOG0562 KOG0562, Predicted hydrolase (HIT family) [General function prediction only] 184 matched cddid_all.tbl CDD KOG0563 KOG0563 228511 KOG0563 KOG0563, Glucose-6-phosphate 1-dehydrogenase [Carbohydrate transport and metabolism] 499 matched cddid_all.tbl CDD KOG0564 KOG0564 228512 KOG0564 KOG0564, 5,10-methylenetetrahydrofolate reductase [Amino acid transport and metabolism] 590 matched cddid_all.tbl CDD KOG0565 KOG0565 228513 KOG0565 KOG0565, Inositol polyphosphate 5-phosphatase and related proteins [Intracellular trafficking, secretion, and vesicular transport] 145 matched cddid_all.tbl CDD KOG0566 KOG0566 228514 KOG0566 KOG0566, Inositol-1,4,5-triphosphate 5-phosphatase (synaptojanin), INP51/INP52/INP53 family [Intracellular trafficking, secretion, and vesicular transport] 1080 matched cddid_all.tbl CDD KOG0567 KOG0567 228515 KOG0567 KOG0567, HEAT repeat-containing protein [General function prediction only] 289 matched cddid_all.tbl CDD KOG0568 KOG0568 228516 KOG0568 KOG0568, Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones] 342 matched cddid_all.tbl CDD KOG0569 KOG0569 228517 KOG0569 KOG0569, Permease of the major facilitator superfamily [Carbohydrate transport and metabolism] 485 matched cddid_all.tbl CDD KOG0570 KOG0570 228518 KOG0570 KOG0570, Transcriptional coactivator [Transcription] 223 matched cddid_all.tbl CDD KOG0571 KOG0571 228519 KOG0571 KOG0571, Asparagine synthase (glutamine-hydrolyzing) [Amino acid transport and metabolism] 543 matched cddid_all.tbl CDD KOG0572 KOG0572 228520 KOG0572 KOG0572, Glutamine phosphoribosylpyrophosphate amidotransferase [Nucleotide transport and metabolism] 474 matched cddid_all.tbl CDD KOG0573 KOG0573 228521 KOG0573 KOG0573, Asparagine synthase [Amino acid transport and metabolism] 520 matched cddid_all.tbl CDD KOG0574 KOG0574 228522 KOG0574 KOG0574, STE20-like serine/threonine kinase MST [Signal transduction mechanisms] 502 matched cddid_all.tbl CDD KOG0575 KOG0575 228523 KOG0575 KOG0575, Polo-like serine/threonine protein kinase [Cell cycle control, cell division, chromosome partitioning] 592 matched cddid_all.tbl CDD KOG0576 KOG0576 228524 KOG0576 KOG0576, Mitogen-activated protein kinase kinase kinase kinase (MAP4K), germinal center kinase family [Signal transduction mechanisms] 829 matched cddid_all.tbl CDD KOG0577 KOG0577 228525 KOG0577 KOG0577, Serine/threonine protein kinase [Signal transduction mechanisms] 948 matched cddid_all.tbl CDD KOG0578 KOG0578 228526 KOG0578 KOG0578, p21-activated serine/threonine protein kinase [Signal transduction mechanisms] 550 matched cddid_all.tbl CDD KOG0579 KOG0579 228527 KOG0579 KOG0579, Ste20-like serine/threonine protein kinase [Signal transduction mechanisms] 1187 matched cddid_all.tbl CDD KOG0580 KOG0580 228528 KOG0580 KOG0580, Serine/threonine protein kinase [Cell cycle control, cell division, chromosome partitioning] 281 matched cddid_all.tbl CDD KOG0581 KOG0581 228529 KOG0581 KOG0581, Mitogen-activated protein kinase kinase (MAP2K) [Signal transduction mechanisms] 364 matched cddid_all.tbl CDD KOG0582 KOG0582 228530 KOG0582 KOG0582, Ste20-like serine/threonine protein kinase [Signal transduction mechanisms] 516 matched cddid_all.tbl CDD KOG0583 KOG0583 228531 KOG0583 KOG0583, Serine/threonine protein kinase [Signal transduction mechanisms] 370 matched cddid_all.tbl CDD KOG0584 KOG0584 228532 KOG0584 KOG0584, Serine/threonine protein kinase [General function prediction only] 632 matched cddid_all.tbl CDD KOG0585 KOG0585 228533 KOG0585 KOG0585, Ca2+/calmodulin-dependent protein kinase kinase beta and related serine/threonine protein kinases [Signal transduction mechanisms] 576 matched cddid_all.tbl CDD KOG0586 KOG0586 228534 KOG0586 KOG0586, Serine/threonine protein kinase [General function prediction only] 596 matched cddid_all.tbl CDD KOG0587 KOG0587 228535 KOG0587 KOG0587, Traf2- and Nck-interacting kinase and related germinal center kinase (GCK) family protein kinases [Signal transduction mechanisms] 953 matched cddid_all.tbl CDD KOG0588 KOG0588 228536 KOG0588 KOG0588, Serine/threonine protein kinase [Cell cycle control, cell division, chromosome partitioning] 786 matched cddid_all.tbl CDD KOG0589 KOG0589 228537 KOG0589 KOG0589, Serine/threonine protein kinase [General function prediction only] 426 matched cddid_all.tbl CDD KOG0590 KOG0590 228538 KOG0590 KOG0590, Checkpoint kinase and related serine/threonine protein kinases [Cell cycle control, cell division, chromosome partitioning] 601 matched cddid_all.tbl CDD KOG0591 KOG0591 228539 KOG0591 KOG0591, NIMA (never in mitosis)-related G2-specific serine/threonine protein kinase [Cell cycle control, cell division, chromosome partitioning] 375 matched cddid_all.tbl CDD KOG0592 KOG0592 228540 KOG0592 KOG0592, 3-phosphoinositide-dependent protein kinase (PDK1) [Signal transduction mechanisms] 604 matched cddid_all.tbl CDD KOG0593 KOG0593 228541 KOG0593 KOG0593, Predicted protein kinase KKIAMRE [General function prediction only] 396 matched cddid_all.tbl CDD KOG0594 KOG0594 228542 KOG0594 KOG0594, Protein kinase PCTAIRE and related kinases [General function prediction only] 323 matched cddid_all.tbl CDD KOG0595 KOG0595 228543 KOG0595 KOG0595, Serine/threonine-protein kinase involved in autophagy [Posttranslational modification, protein turnover, chaperones, Intracellular trafficking, secretion, and vesicular transport, Signal transduction mechanisms] 429 matched cddid_all.tbl CDD KOG0596 KOG0596 228544 KOG0596 KOG0596, Dual specificity; serine/threonine and tyrosine kinase [Cell cycle control, cell division, chromosome partitioning] 677 matched cddid_all.tbl CDD KOG0597 KOG0597 228545 KOG0597 KOG0597, Serine-threonine protein kinase FUSED [General function prediction only] 808 matched cddid_all.tbl CDD KOG0598 KOG0598 228546 KOG0598 KOG0598, Ribosomal protein S6 kinase and related proteins [General function prediction only, Signal transduction mechanisms] 357 matched cddid_all.tbl CDD KOG0599 KOG0599 228547 KOG0599 KOG0599, Phosphorylase kinase gamma subunit [Carbohydrate transport and metabolism] 411 matched cddid_all.tbl CDD KOG0600 KOG0600 228548 KOG0600 KOG0600, Cdc2-related protein kinase [Cell cycle control, cell division, chromosome partitioning] 560 matched cddid_all.tbl CDD KOG0601 KOG0601 228549 KOG0601 KOG0601, Cyclin-dependent kinase WEE1 [Cell cycle control, cell division, chromosome partitioning] 524 matched cddid_all.tbl CDD KOG0602 KOG0602 228550 KOG0602 KOG0602, Neutral trehalase [Carbohydrate transport and metabolism] 600 matched cddid_all.tbl CDD KOG0603 KOG0603 228551 KOG0603 KOG0603, Ribosomal protein S6 kinase [Signal transduction mechanisms] 612 matched cddid_all.tbl CDD KOG0604 KOG0604 228552 KOG0604 KOG0604, MAP kinase-activated protein kinase 2 [Signal transduction mechanisms] 400 matched cddid_all.tbl CDD KOG0605 KOG0605 228553 KOG0605 KOG0605, NDR and related serine/threonine kinases [General function prediction only] 550 matched cddid_all.tbl CDD KOG0606 KOG0606 228554 KOG0606 KOG0606, Microtubule-associated serine/threonine kinase and related proteins [Signal transduction mechanisms, General function prediction only] 1205 matched cddid_all.tbl CDD KOG0607 KOG0607 228555 KOG0607 KOG0607, MAP kinase-interacting kinase and related serine/threonine protein kinases [Signal transduction mechanisms] 463 matched cddid_all.tbl CDD KOG0608 KOG0608 228556 KOG0608 KOG0608, Warts/lats-like serine threonine kinases [Cell cycle control, cell division, chromosome partitioning] 1034 matched cddid_all.tbl CDD KOG0609 KOG0609 228557 KOG0609 KOG0609, Calcium/calmodulin-dependent serine protein kinase/membrane-associated guanylate kinase [Signal transduction mechanisms] 542 matched cddid_all.tbl CDD KOG0610 KOG0610 228558 KOG0610 KOG0610, Putative serine/threonine protein kinase [General function prediction only] 459 matched cddid_all.tbl CDD KOG0611 KOG0611 228559 KOG0611 KOG0611, Predicted serine/threonine protein kinase [General function prediction only] 668 matched cddid_all.tbl CDD KOG0612 KOG0612 228560 KOG0612 KOG0612, Rho-associated, coiled-coil containing protein kinase [Signal transduction mechanisms] 1317 matched cddid_all.tbl CDD KOG0613 KOG0613 228561 KOG0613 KOG0613, Projectin/twitchin and related proteins [Cytoskeleton] 1205 matched cddid_all.tbl CDD KOG0614 KOG0614 228562 KOG0614 KOG0614, cGMP-dependent protein kinase [Signal transduction mechanisms] 732 matched cddid_all.tbl CDD KOG0615 KOG0615 228563 KOG0615 KOG0615, Serine/threonine protein kinase Chk2 and related proteins [Cell cycle control, cell division, chromosome partitioning] 475 matched cddid_all.tbl CDD KOG0616 KOG0616 228564 KOG0616 KOG0616, cAMP-dependent protein kinase catalytic subunit (PKA) [Signal transduction mechanisms] 355 matched cddid_all.tbl CDD KOG0617 KOG0617 228565 KOG0617 KOG0617, Ras suppressor protein (contains leucine-rich repeats) [Signal transduction mechanisms] 264 matched cddid_all.tbl CDD KOG0618 KOG0618 228566 KOG0618 KOG0618, Serine/threonine phosphatase 2C containing leucine-rich repeats, similar to SCN circadian oscillatory protein (SCOP) [Signal transduction mechanisms] 1081 matched cddid_all.tbl CDD KOG0620 KOG0620 228567 KOG0620 KOG0620, Glucose-repressible alcohol dehydrogenase transcriptional effector CCR4 and related proteins [Transcription] 361 matched cddid_all.tbl CDD KOG0621 KOG0621 228568 KOG0621 KOG0621, Phospholipid scramblase [Cell wall/membrane/envelope biogenesis] 292 matched cddid_all.tbl CDD KOG0622 KOG0622 228569 KOG0622 KOG0622, Ornithine decarboxylase [Amino acid transport and metabolism] 448 matched cddid_all.tbl CDD KOG0623 KOG0623 228570 KOG0623 KOG0623, Glutamine amidotransferase/cyclase [Amino acid transport and metabolism] 541 matched cddid_all.tbl CDD KOG0624 KOG0624 228571 KOG0624 KOG0624, dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms] 504 matched cddid_all.tbl CDD KOG0625 KOG0625 228572 KOG0625 KOG0625, Phosphoglucomutase [Carbohydrate transport and metabolism] 558 matched cddid_all.tbl CDD KOG0626 KOG0626 228573 KOG0626 KOG0626, Beta-glucosidase, lactase phlorizinhydrolase, and related proteins [Carbohydrate transport and metabolism] 471 matched cddid_all.tbl CDD KOG0627 KOG0627 228574 KOG0627 KOG0627, Heat shock transcription factor [Transcription] 304 matched cddid_all.tbl CDD KOG0628 KOG0628 228575 KOG0628 KOG0628, Aromatic-L-amino-acid/L-histidine decarboxylase [Amino acid transport and metabolism] 511 matched cddid_all.tbl CDD KOG0629 KOG0629 228576 KOG0629 KOG0629, Glutamate decarboxylase and related proteins [Amino acid transport and metabolism] 510 matched cddid_all.tbl CDD KOG0630 KOG0630 228577 KOG0630 KOG0630, Predicted pyridoxal-dependent decarboxylase [Amino acid transport and metabolism] 838 matched cddid_all.tbl CDD KOG0631 KOG0631 228578 KOG0631 KOG0631, Galactokinase [Carbohydrate transport and metabolism] 489 matched cddid_all.tbl CDD KOG0632 KOG0632 228579 KOG0632 KOG0632, Phytochelatin synthase [Inorganic ion transport and metabolism] 388 matched cddid_all.tbl CDD KOG0633 KOG0633 228580 KOG0633 KOG0633, Histidinol phosphate aminotransferase [Amino acid transport and metabolism] 375 matched cddid_all.tbl CDD KOG0634 KOG0634 228581 KOG0634 KOG0634, Aromatic amino acid aminotransferase and related proteins [Amino acid transport and metabolism] 472 matched cddid_all.tbl CDD KOG0635 KOG0635 228582 KOG0635 KOG0635, Adenosine 5'-phosphosulfate kinase [Inorganic ion transport and metabolism] 207 matched cddid_all.tbl CDD KOG0636 KOG0636 228583 KOG0636 KOG0636, ATP sulfurylase (sulfate adenylyltransferase) [Inorganic ion transport and metabolism] 466 matched cddid_all.tbl CDD KOG0637 KOG0637 228584 KOG0637 KOG0637, Sucrose transporter and related proteins [Carbohydrate transport and metabolism] 498 matched cddid_all.tbl CDD KOG0638 KOG0638 228585 KOG0638 KOG0638, 4-hydroxyphenylpyruvate dioxygenase [Amino acid transport and metabolism] 381 matched cddid_all.tbl CDD KOG0639 KOG0639 228586 KOG0639 KOG0639, Transducin-like enhancer of split protein (contains WD40 repeats) [Chromatin structure and dynamics] 705 matched cddid_all.tbl CDD KOG0640 KOG0640 228587 KOG0640 KOG0640, mRNA cleavage stimulating factor complex; subunit 1 [RNA processing and modification] 430 matched cddid_all.tbl CDD KOG0641 KOG0641 228588 KOG0641 KOG0641, WD40 repeat protein [General function prediction only] 350 matched cddid_all.tbl CDD KOG0642 KOG0642 228589 KOG0642 KOG0642, Cell-cycle nuclear protein, contains WD-40 repeats [Cell cycle control, cell division, chromosome partitioning] 577 matched cddid_all.tbl CDD KOG0643 KOG0643 228590 KOG0643 KOG0643, Translation initiation factor 3, subunit i (eIF-3i)/TGF-beta receptor-interacting protein (TRIP-1) [Translation, ribosomal structure and biogenesis, Signal transduction mechanisms] 327 matched cddid_all.tbl CDD KOG0644 KOG0644 228591 KOG0644 KOG0644, Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only] 1113 matched cddid_all.tbl CDD KOG0645 KOG0645 228592 KOG0645 KOG0645, WD40 repeat protein [General function prediction only] 312 matched cddid_all.tbl CDD KOG0646 KOG0646 228593 KOG0646 KOG0646, WD40 repeat protein [General function prediction only] 476 matched cddid_all.tbl CDD KOG0647 KOG0647 228594 KOG0647 KOG0647, mRNA export protein (contains WD40 repeats) [RNA processing and modification] 347 matched cddid_all.tbl CDD KOG0648 KOG0648 228595 KOG0648 KOG0648, Predicted NUDIX hydrolase FGF-2 and related proteins [Signal transduction mechanisms] 295 matched cddid_all.tbl CDD KOG0649 KOG0649 228596 KOG0649 KOG0649, WD40 repeat protein [General function prediction only] 325 matched cddid_all.tbl CDD KOG0650 KOG0650 228597 KOG0650 KOG0650, WD40 repeat nucleolar protein Bop1, involved in ribosome biogenesis [Translation, ribosomal structure and biogenesis] 733 matched cddid_all.tbl CDD KOG0651 KOG0651 228598 KOG0651 KOG0651, 26S proteasome regulatory complex, ATPase RPT4 [Posttranslational modification, protein turnover, chaperones] 388 matched cddid_all.tbl CDD KOG0652 KOG0652 228599 KOG0652 KOG0652, 26S proteasome regulatory complex, ATPase RPT5 [Posttranslational modification, protein turnover, chaperones] 424 matched cddid_all.tbl CDD KOG0653 KOG0653 228600 KOG0653 KOG0653, Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning] 391 matched cddid_all.tbl CDD KOG0654 KOG0654 228601 KOG0654 KOG0654, G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning] 359 matched cddid_all.tbl CDD KOG0655 KOG0655 228602 KOG0655 KOG0655, G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning] 408 matched cddid_all.tbl CDD KOG0656 KOG0656 228603 KOG0656 KOG0656, G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning] 335 matched cddid_all.tbl CDD KOG0657 KOG0657 228604 KOG0657 KOG0657, Glyceraldehyde 3-phosphate dehydrogenase [Carbohydrate transport and metabolism] 285 matched cddid_all.tbl CDD KOG0658 KOG0658 228605 KOG0658 KOG0658, Glycogen synthase kinase-3 [Carbohydrate transport and metabolism] 364 matched cddid_all.tbl CDD KOG0659 KOG0659 228606 KOG0659 KOG0659, Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, kinase subunit CDK7 [Cell cycle control, cell division, chromosome partitioning, Transcription, Replication, recombination and repair] 318 matched cddid_all.tbl CDD KOG0660 KOG0660 228607 KOG0660 KOG0660, Mitogen-activated protein kinase [Signal transduction mechanisms] 359 matched cddid_all.tbl CDD KOG0661 KOG0661 228608 KOG0661 KOG0661, MAPK related serine/threonine protein kinase [Signal transduction mechanisms] 538 matched cddid_all.tbl CDD KOG0662 KOG0662 228609 KOG0662 KOG0662, Cyclin-dependent kinase CDK5 [Intracellular trafficking, secretion, and vesicular transport, Signal transduction mechanisms] 292 matched cddid_all.tbl CDD KOG0663 KOG0663 228610 KOG0663 KOG0663, Protein kinase PITSLRE and related kinases [General function prediction only] 419 matched cddid_all.tbl CDD KOG0664 KOG0664 228611 KOG0664 KOG0664, Nemo-like MAPK-related serine/threonine protein kinase [Signal transduction mechanisms] 449 matched cddid_all.tbl CDD KOG0665 KOG0665 228612 KOG0665 KOG0665, Jun-N-terminal kinase (JNK) [Signal transduction mechanisms] 369 matched cddid_all.tbl CDD KOG0666 KOG0666 228613 KOG0666 KOG0666, Cyclin C-dependent kinase CDK8 [Transcription] 438 matched cddid_all.tbl CDD KOG0667 KOG0667 228614 KOG0667 KOG0667, Dual-specificity tyrosine-phosphorylation regulated kinase [General function prediction only] 586 matched cddid_all.tbl CDD KOG0668 KOG0668 228615 KOG0668 KOG0668, Casein kinase II, alpha subunit [Signal transduction mechanisms, Cell cycle control, cell division, chromosome partitioning, Transcription] 338 matched cddid_all.tbl CDD KOG0669 KOG0669 228616 KOG0669 KOG0669, Cyclin T-dependent kinase CDK9 [Cell cycle control, cell division, chromosome partitioning] 376 matched cddid_all.tbl CDD KOG0670 KOG0670 228617 KOG0670 KOG0670, U4/U6-associated splicing factor PRP4 [RNA processing and modification] 752 matched cddid_all.tbl CDD KOG0671 KOG0671 228618 KOG0671 KOG0671, LAMMER dual specificity kinases [Signal transduction mechanisms] 415 matched cddid_all.tbl CDD KOG0672 KOG0672 228619 KOG0672 KOG0672, Halotolerance protein HAL3 (contains flavoprotein domain) [Inorganic ion transport and metabolism, Cell cycle control, cell division, chromosome partitioning] 218 matched cddid_all.tbl CDD KOG0673 KOG0673 228620 KOG0673 KOG0673, Thymidylate synthase [Nucleotide transport and metabolism] 293 matched cddid_all.tbl CDD KOG0674 KOG0674 228621 KOG0674 KOG0674, Calreticulin [Posttranslational modification, protein turnover, chaperones] 406 matched cddid_all.tbl CDD KOG0675 KOG0675 228622 KOG0675 KOG0675, Calnexin [Posttranslational modification, protein turnover, chaperones] 558 matched cddid_all.tbl CDD KOG0676 KOG0676 228623 KOG0676 KOG0676, Actin and related proteins [Cytoskeleton] 372 matched cddid_all.tbl CDD KOG0677 KOG0677 228624 KOG0677 KOG0677, Actin-related protein Arp2/3 complex, subunit Arp2 [Cytoskeleton] 389 matched cddid_all.tbl CDD KOG0678 KOG0678 228625 KOG0678 KOG0678, Actin-related protein Arp2/3 complex, subunit Arp3 [Cytoskeleton] 415 matched cddid_all.tbl CDD KOG0679 KOG0679 228626 KOG0679 KOG0679, Actin-related protein - Arp4p/Act3p [Cytoskeleton] 426 matched cddid_all.tbl CDD KOG0680 KOG0680 228627 KOG0680 KOG0680, Actin-related protein - Arp6p [Cytoskeleton] 400 matched cddid_all.tbl CDD KOG0681 KOG0681 228628 KOG0681 KOG0681, Actin-related protein - Arp5p [Cytoskeleton] 645 matched cddid_all.tbl CDD KOG0682 KOG0682 228629 KOG0682 KOG0682, Ammonia permease [Inorganic ion transport and metabolism] 500 matched cddid_all.tbl CDD KOG0683 KOG0683 228630 KOG0683 KOG0683, Glutamine synthetase [Amino acid transport and metabolism] 380 matched cddid_all.tbl CDD KOG0684 KOG0684 228631 KOG0684 KOG0684, Cytochrome P450 [Secondary metabolites biosynthesis, transport and catabolism] 486 matched cddid_all.tbl CDD KOG0685 KOG0685 228632 KOG0685 KOG0685, Flavin-containing amine oxidase [Coenzyme transport and metabolism] 498 matched cddid_all.tbl CDD KOG0686 KOG0686 228633 KOG0686 KOG0686, COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms] 466 matched cddid_all.tbl CDD KOG0687 KOG0687 228634 KOG0687 KOG0687, 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones] 393 matched cddid_all.tbl CDD KOG0688 KOG0688 228635 KOG0688 KOG0688, Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis] 431 matched cddid_all.tbl CDD KOG0689 KOG0689 228636 KOG0689 KOG0689, Guanine nucleotide exchange factor for Rho and Rac GTPases [Signal transduction mechanisms] 448 matched cddid_all.tbl CDD KOG0690 KOG0690 228637 KOG0690 KOG0690, Serine/threonine protein kinase [Signal transduction mechanisms] 516 matched cddid_all.tbl CDD KOG0691 KOG0691 228638 KOG0691 KOG0691, Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones] 296 matched cddid_all.tbl CDD KOG0692 KOG0692 228639 KOG0692 KOG0692, Pentafunctional AROM protein [Amino acid transport and metabolism] 595 matched cddid_all.tbl CDD KOG0693 KOG0693 228640 KOG0693 KOG0693, Myo-inositol-1-phosphate synthase [Lipid transport and metabolism] 512 matched cddid_all.tbl CDD KOG0694 KOG0694 228641 KOG0694 KOG0694, Serine/threonine protein kinase [Signal transduction mechanisms] 694 matched cddid_all.tbl CDD KOG0695 KOG0695 228642 KOG0695 KOG0695, Serine/threonine protein kinase [Signal transduction mechanisms] 593 matched cddid_all.tbl CDD KOG0696 KOG0696 228643 KOG0696 KOG0696, Serine/threonine protein kinase [Signal transduction mechanisms] 683 matched cddid_all.tbl CDD KOG0697 KOG0697 228644 KOG0697 KOG0697, Protein phosphatase 1B (formerly 2C) [Signal transduction mechanisms] 379 matched cddid_all.tbl CDD KOG0698 KOG0698 228645 KOG0698 KOG0698, Serine/threonine protein phosphatase [Signal transduction mechanisms] 330 matched cddid_all.tbl CDD KOG0699 KOG0699 228646 KOG0699 KOG0699, Serine/threonine protein phosphatase [Signal transduction mechanisms] 542 matched cddid_all.tbl CDD KOG0700 KOG0700 228647 KOG0700 KOG0700, Protein phosphatase 2C/pyruvate dehydrogenase (lipoamide) phosphatase [Signal transduction mechanisms] 390 matched cddid_all.tbl CDD KOG0701 KOG0701 228648 KOG0701 KOG0701, dsRNA-specific nuclease Dicer and related ribonucleases [RNA processing and modification] 1606 matched cddid_all.tbl CDD KOG0702 KOG0702 228649 KOG0702 KOG0702, Predicted GTPase-activating protein [Signal transduction mechanisms] 524 matched cddid_all.tbl CDD KOG0703 KOG0703 228650 KOG0703 KOG0703, Predicted GTPase-activating protein [Signal transduction mechanisms] 287 matched cddid_all.tbl CDD KOG0704 KOG0704 228651 KOG0704 KOG0704, ADP-ribosylation factor GTPase activator [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport, Cytoskeleton] 386 matched cddid_all.tbl CDD KOG0705 KOG0705 228652 KOG0705 KOG0705, GTPase-activating protein Centaurin gamma (contains Ras-like GTPase, PH and ankyrin repeat domains) [Signal transduction mechanisms] 749 matched cddid_all.tbl CDD KOG0706 KOG0706 228653 KOG0706 KOG0706, Predicted GTPase-activating protein [Signal transduction mechanisms] 454 matched cddid_all.tbl CDD KOG0707 KOG0707 228654 KOG0707 KOG0707, Guanylate kinase [Nucleotide transport and metabolism] 231 matched cddid_all.tbl CDD KOG0708 KOG0708 228655 KOG0708 KOG0708, Membrane-associated guanylate kinase MAGUK (contains PDZ, SH3, HOOK and GUK domains) [Nucleotide transport and metabolism] 359 matched cddid_all.tbl CDD KOG0709 KOG0709 228656 KOG0709 KOG0709, CREB/ATF family transcription factor [Transcription] 472 matched cddid_all.tbl CDD KOG0710 KOG0710 228657 KOG0710 KOG0710, Molecular chaperone (small heat-shock protein Hsp26/Hsp42) [Posttranslational modification, protein turnover, chaperones] 196 matched cddid_all.tbl CDD KOG0711 KOG0711 228658 KOG0711 KOG0711, Polyprenyl synthetase [Coenzyme transport and metabolism] 347 matched cddid_all.tbl CDD KOG0712 KOG0712 228659 KOG0712 KOG0712, Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones] 337 matched cddid_all.tbl CDD KOG0713 KOG0713 228660 KOG0713 KOG0713, Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones] 336 matched cddid_all.tbl CDD KOG0714 KOG0714 228661 KOG0714 KOG0714, Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones] 306 matched cddid_all.tbl CDD KOG0715 KOG0715 228662 KOG0715 KOG0715, Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones] 288 matched cddid_all.tbl CDD KOG0716 KOG0716 228663 KOG0716 KOG0716, Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones] 279 matched cddid_all.tbl CDD KOG0717 KOG0717 228664 KOG0717 KOG0717, Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones] 508 matched cddid_all.tbl CDD KOG0718 KOG0718 228665 KOG0718 KOG0718, Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones] 546 matched cddid_all.tbl CDD KOG0719 KOG0719 228666 KOG0719 KOG0719, Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones] 264 matched cddid_all.tbl CDD KOG0720 KOG0720 228667 KOG0720 KOG0720, Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones] 490 matched cddid_all.tbl CDD KOG0721 KOG0721 228668 KOG0721 KOG0721, Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones] 230 matched cddid_all.tbl CDD KOG0722 KOG0722 228669 KOG0722 KOG0722, Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones] 329 matched cddid_all.tbl CDD KOG0723 KOG0723 228670 KOG0723 KOG0723, Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones] 112 matched cddid_all.tbl CDD KOG0724 KOG0724 228671 KOG0724 KOG0724, Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones] 335 matched cddid_all.tbl CDD KOG0725 KOG0725 228672 KOG0725 KOG0725, Reductases with broad range of substrate specificities [General function prediction only] 270 matched cddid_all.tbl CDD KOG0726 KOG0726 228673 KOG0726 KOG0726, 26S proteasome regulatory complex, ATPase RPT2 [Posttranslational modification, protein turnover, chaperones] 440 matched cddid_all.tbl CDD KOG0727 KOG0727 228674 KOG0727 KOG0727, 26S proteasome regulatory complex, ATPase RPT3 [Posttranslational modification, protein turnover, chaperones] 408 matched cddid_all.tbl CDD KOG0728 KOG0728 228675 KOG0728 KOG0728, 26S proteasome regulatory complex, ATPase RPT6 [Posttranslational modification, protein turnover, chaperones] 404 matched cddid_all.tbl CDD KOG0729 KOG0729 228676 KOG0729 KOG0729, 26S proteasome regulatory complex, ATPase RPT1 [Posttranslational modification, protein turnover, chaperones] 435 matched cddid_all.tbl CDD KOG0730 KOG0730 228677 KOG0730 KOG0730, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones] 693 matched cddid_all.tbl CDD KOG0731 KOG0731 228678 KOG0731 KOG0731, AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones] 774 matched cddid_all.tbl CDD KOG0732 KOG0732 228679 KOG0732 KOG0732, AAA+-type ATPase containing the bromodomain [Posttranslational modification, protein turnover, chaperones] 1080 matched cddid_all.tbl CDD KOG0733 KOG0733 228680 KOG0733 KOG0733, Nuclear AAA ATPase (VCP subfamily) [Posttranslational modification, protein turnover, chaperones] 802 matched cddid_all.tbl CDD KOG0734 KOG0734 228681 KOG0734 KOG0734, AAA+-type ATPase containing the peptidase M41 domain [Posttranslational modification, protein turnover, chaperones] 752 matched cddid_all.tbl CDD KOG0735 KOG0735 228682 KOG0735 KOG0735, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones] 952 matched cddid_all.tbl CDD KOG0736 KOG0736 228683 KOG0736 KOG0736, Peroxisome assembly factor 2 containing the AAA+-type ATPase domain [Posttranslational modification, protein turnover, chaperones] 953 matched cddid_all.tbl CDD KOG0737 KOG0737 228684 KOG0737 KOG0737, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones] 386 matched cddid_all.tbl CDD KOG0738 KOG0738 228685 KOG0738 KOG0738, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones] 491 matched cddid_all.tbl CDD KOG0739 KOG0739 228686 KOG0739 KOG0739, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones] 439 matched cddid_all.tbl CDD KOG0740 KOG0740 228687 KOG0740 KOG0740, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones] 428 matched cddid_all.tbl CDD KOG0741 KOG0741 228688 KOG0741 KOG0741, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones] 744 matched cddid_all.tbl CDD KOG0742 KOG0742 228689 KOG0742 KOG0742, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones] 592 matched cddid_all.tbl CDD KOG0743 KOG0743 228690 KOG0743 KOG0743, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones] 457 matched cddid_all.tbl CDD KOG0744 KOG0744 228691 KOG0744 KOG0744, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones] 423 matched cddid_all.tbl CDD KOG0745 KOG0745 228692 KOG0745 KOG0745, Putative ATP-dependent Clp-type protease (AAA+ ATPase superfamily) [Posttranslational modification, protein turnover, chaperones] 564 matched cddid_all.tbl CDD KOG0746 KOG0746 228693 KOG0746 KOG0746, 60S ribosomal protein L3 and related proteins [Translation, ribosomal structure and biogenesis] 384 matched cddid_all.tbl CDD KOG0747 KOG0747 228694 KOG0747 KOG0747, Putative NAD+-dependent epimerases [Carbohydrate transport and metabolism] 331 matched cddid_all.tbl CDD KOG0748 KOG0748 228695 KOG0748 KOG0748, Predicted membrane proteins, contain hemolysin III domain [General function prediction only, Signal transduction mechanisms] 286 matched cddid_all.tbl CDD KOG0749 KOG0749 228696 KOG0749 KOG0749, Mitochondrial ADP/ATP carrier proteins [Energy production and conversion] 298 matched cddid_all.tbl CDD KOG0750 KOG0750 228697 KOG0750 KOG0750, Mitochondrial solute carrier protein [Energy production and conversion] 304 matched cddid_all.tbl CDD KOG0751 KOG0751 228698 KOG0751 KOG0751, Mitochondrial aspartate/glutamate carrier protein Aralar/Citrin (contains EF-hand Ca2+-binding domains) [Energy production and conversion] 694 matched cddid_all.tbl CDD KOG0752 KOG0752 228699 KOG0752 KOG0752, Mitochondrial solute carrier protein [Energy production and conversion] 320 matched cddid_all.tbl CDD KOG0753 KOG0753 228700 KOG0753 KOG0753, Mitochondrial fatty acid anion carrier protein/Uncoupling protein [Energy production and conversion] 317 matched cddid_all.tbl CDD KOG0754 KOG0754 228701 KOG0754 KOG0754, Mitochondrial oxodicarboxylate carrier protein [Energy production and conversion] 294 matched cddid_all.tbl CDD KOG0755 KOG0755 228702 KOG0755 KOG0755, Mitochondrial oxaloacetate carrier protein [Energy production and conversion] 320 matched cddid_all.tbl CDD KOG0756 KOG0756 228703 KOG0756 KOG0756, Mitochondrial tricarboxylate/dicarboxylate carrier proteins [Energy production and conversion] 299 matched cddid_all.tbl CDD KOG0757 KOG0757 228704 KOG0757 KOG0757, Mitochondrial carrier protein - Rim2p/Mrs12p [Energy production and conversion] 319 matched cddid_all.tbl CDD KOG0758 KOG0758 228705 KOG0758 KOG0758, Mitochondrial carnitine-acylcarnitine carrier protein [Energy production and conversion] 297 matched cddid_all.tbl CDD KOG0759 KOG0759 228706 KOG0759 KOG0759, Mitochondrial oxoglutarate/malate carrier proteins [Energy production and conversion] 286 matched cddid_all.tbl CDD KOG0760 KOG0760 228707 KOG0760 KOG0760, Mitochondrial carrier protein MRS3/4 [Energy production and conversion] 302 matched cddid_all.tbl CDD KOG0761 KOG0761 228708 KOG0761 KOG0761, Mitochondrial carrier protein CGI-69 [Energy production and conversion] 361 matched cddid_all.tbl CDD KOG0762 KOG0762 228709 KOG0762 KOG0762, Mitochondrial carrier protein [Energy production and conversion] 311 matched cddid_all.tbl CDD KOG0763 KOG0763 228710 KOG0763 KOG0763, Mitochondrial ornithine transporter [Energy production and conversion] 301 matched cddid_all.tbl CDD KOG0764 KOG0764 228711 KOG0764 KOG0764, Mitochondrial FAD carrier protein [Energy production and conversion] 299 matched cddid_all.tbl CDD KOG0765 KOG0765 228712 KOG0765 KOG0765, Predicted mitochondrial carrier protein [Energy production and conversion] 333 matched cddid_all.tbl CDD KOG0766 KOG0766 228713 KOG0766 KOG0766, Predicted mitochondrial carrier protein [Energy production and conversion] 297 matched cddid_all.tbl CDD KOG0767 KOG0767 228714 KOG0767 KOG0767, Mitochondrial phosphate carrier protein [Energy production and conversion] 333 matched cddid_all.tbl CDD KOG0768 KOG0768 228715 KOG0768 KOG0768, Mitochondrial carrier protein PET8 [Energy production and conversion] 323 matched cddid_all.tbl CDD KOG0769 KOG0769 228716 KOG0769 KOG0769, Predicted mitochondrial carrier protein [Energy production and conversion] 308 matched cddid_all.tbl CDD KOG0770 KOG0770 228717 KOG0770 KOG0770, Predicted mitochondrial carrier protein [Energy production and conversion] 353 matched cddid_all.tbl CDD KOG0771 KOG0771 228718 KOG0771 KOG0771, Prolactin regulatory element-binding protein/Protein transport protein SEC12p [Intracellular trafficking, secretion, and vesicular transport] 398 matched cddid_all.tbl CDD KOG0772 KOG0772 228719 KOG0772 KOG0772, Uncharacterized conserved protein, contains WD40 repeat [Function unknown] 641 matched cddid_all.tbl CDD KOG0773 KOG0773 228720 KOG0773 KOG0773, Transcription factor MEIS1 and related HOX domain proteins [Transcription] 342 matched cddid_all.tbl CDD KOG0774 KOG0774 228721 KOG0774 KOG0774, Transcription factor PBX and related HOX domain proteins [Transcription] 334 matched cddid_all.tbl CDD KOG0775 KOG0775 228722 KOG0775 KOG0775, Transcription factor SIX and related HOX domain proteins [Transcription] 304 matched cddid_all.tbl CDD KOG0776 KOG0776 228723 KOG0776 KOG0776, Geranylgeranyl pyrophosphate synthase/Polyprenyl synthetase [Coenzyme transport and metabolism] 384 matched cddid_all.tbl CDD KOG0777 KOG0777 228724 KOG0777 KOG0777, Geranylgeranyl pyrophosphate synthase/Polyprenyl synthetase [Coenzyme transport and metabolism] 322 matched cddid_all.tbl CDD KOG0778 KOG0778 228725 KOG0778 KOG0778, Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones] 511 matched cddid_all.tbl CDD KOG0779 KOG0779 228726 KOG0779 KOG0779, Protease, Ulp1 family [Posttranslational modification, protein turnover, chaperones] 595 matched cddid_all.tbl CDD KOG0780 KOG0780 228727 KOG0780 KOG0780, Signal recognition particle, subunit Srp54 [Intracellular trafficking, secretion, and vesicular transport] 483 matched cddid_all.tbl CDD KOG0781 KOG0781 228728 KOG0781 KOG0781, Signal recognition particle receptor, alpha subunit [Intracellular trafficking, secretion, and vesicular transport] 587 matched cddid_all.tbl CDD KOG0782 KOG0782 228729 KOG0782 KOG0782, Predicted diacylglycerol kinase [Signal transduction mechanisms] 1004 matched cddid_all.tbl CDD KOG0783 KOG0783 228730 KOG0783 KOG0783, Uncharacterized conserved protein, contains ankyrin and BTB/POZ domains [Function unknown] 1267 matched cddid_all.tbl CDD KOG0784 KOG0784 228731 KOG0784 KOG0784, Isocitrate dehydrogenase, gamma subunit [Amino acid transport and metabolism] 375 matched cddid_all.tbl CDD KOG0785 KOG0785 228732 KOG0785 KOG0785, Isocitrate dehydrogenase, alpha subunit [Amino acid transport and metabolism] 365 matched cddid_all.tbl CDD KOG0786 KOG0786 228733 KOG0786 KOG0786, 3-isopropylmalate dehydrogenase [Amino acid transport and metabolism] 363 matched cddid_all.tbl CDD KOG0787 KOG0787 228734 KOG0787 KOG0787, Dehydrogenase kinase [Signal transduction mechanisms] 414 matched cddid_all.tbl CDD KOG0788 KOG0788 228735 KOG0788 KOG0788, S-adenosylmethionine decarboxylase [Signal transduction mechanisms] 334 matched cddid_all.tbl CDD KOG0789 KOG0789 228736 KOG0789 KOG0789, Protein tyrosine phosphatase [Signal transduction mechanisms] 415 matched cddid_all.tbl CDD KOG0790 KOG0790 228737 KOG0790 KOG0790, Protein tyrosine phosphatase Corkscrew and related SH2 domain enzymes [Signal transduction mechanisms] 600 matched cddid_all.tbl CDD KOG0791 KOG0791 228738 KOG0791 KOG0791, Protein tyrosine phosphatase, contains fn3 domain [Signal transduction mechanisms] 374 matched cddid_all.tbl CDD KOG0792 KOG0792 228739 KOG0792 KOG0792, Protein tyrosine phosphatase PTPMEG, contains FERM domain [Signal transduction mechanisms] 1144 matched cddid_all.tbl CDD KOG0793 KOG0793 228740 KOG0793 KOG0793, Protein tyrosine phosphatase [Signal transduction mechanisms] 1004 matched cddid_all.tbl CDD KOG0794 KOG0794 228741 KOG0794 KOG0794, CDK8 kinase-activating protein cyclin C [Transcription] 264 matched cddid_all.tbl CDD KOG0795 KOG0795 228742 KOG0795 KOG0795, Chorismate mutase [Amino acid transport and metabolism] 262 matched cddid_all.tbl CDD KOG0796 KOG0796 228743 KOG0796 KOG0796, Spliceosome subunit [RNA processing and modification] 319 matched cddid_all.tbl CDD KOG0797 KOG0797 228744 KOG0797 KOG0797, Actin-related protein [Cytoskeleton] 618 matched cddid_all.tbl CDD KOG0798 KOG0798 228745 KOG0798 KOG0798, Uncharacterized conserved protein [Cell cycle control, cell division, chromosome partitioning] 380 matched cddid_all.tbl CDD KOG0799 KOG0799 228746 KOG0799 KOG0799, Branching enzyme [Carbohydrate transport and metabolism] 439 matched cddid_all.tbl CDD KOG0801 KOG0801 228747 KOG0801 KOG0801, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 205 matched cddid_all.tbl CDD KOG0802 KOG0802 228748 KOG0802 KOG0802, E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 543 matched cddid_all.tbl CDD KOG0803 KOG0803 228749 KOG0803 KOG0803, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 1312 matched cddid_all.tbl CDD KOG0804 KOG0804 228750 KOG0804 KOG0804, Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only] 493 matched cddid_all.tbl CDD KOG0805 KOG0805 228751 KOG0805 KOG0805, Carbon-nitrogen hydrolase [Amino acid transport and metabolism] 337 matched cddid_all.tbl CDD KOG0806 KOG0806 228752 KOG0806 KOG0806, Carbon-nitrogen hydrolase [Amino acid transport and metabolism] 298 matched cddid_all.tbl CDD KOG0807 KOG0807 228753 KOG0807 KOG0807, Carbon-nitrogen hydrolase [Amino acid transport and metabolism] 295 matched cddid_all.tbl CDD KOG0808 KOG0808 228754 KOG0808 KOG0808, Carbon-nitrogen hydrolase [Amino acid transport and metabolism] 387 matched cddid_all.tbl CDD KOG0809 KOG0809 228755 KOG0809 KOG0809, SNARE protein TLG2/Syntaxin 16 [Intracellular trafficking, secretion, and vesicular transport] 305 matched cddid_all.tbl CDD KOG0810 KOG0810 228756 KOG0810 KOG0810, SNARE protein Syntaxin 1 and related proteins [Intracellular trafficking, secretion, and vesicular transport] 297 matched cddid_all.tbl CDD KOG0811 KOG0811 228757 KOG0811 KOG0811, SNARE protein PEP12/VAM3/Syntaxin 7/Syntaxin 17 [Intracellular trafficking, secretion, and vesicular transport] 269 matched cddid_all.tbl CDD KOG0812 KOG0812 228758 KOG0812 KOG0812, SNARE protein SED5/Syntaxin 5 [Intracellular trafficking, secretion, and vesicular transport] 311 matched cddid_all.tbl CDD KOG0813 KOG0813 228759 KOG0813 KOG0813, Glyoxylase [General function prediction only] 265 matched cddid_all.tbl CDD KOG0814 KOG0814 228760 KOG0814 KOG0814, Glyoxylase [General function prediction only] 237 matched cddid_all.tbl CDD KOG0815 KOG0815 228761 KOG0815 KOG0815, 60S acidic ribosomal protein P0 [Translation, ribosomal structure and biogenesis] 245 matched cddid_all.tbl CDD KOG0816 KOG0816 228762 KOG0816 KOG0816, Protein involved in mRNA turnover [RNA processing and modification] 223 matched cddid_all.tbl CDD KOG0817 KOG0817 228763 KOG0817 KOG0817, Acyl-CoA-binding protein [Lipid transport and metabolism] 142 matched cddid_all.tbl CDD KOG0818 KOG0818 228764 KOG0818 KOG0818, GTPase-activating proteins of the GIT family [Signal transduction mechanisms] 669 matched cddid_all.tbl CDD KOG0819 KOG0819 228765 KOG0819 KOG0819, Annexin [Intracellular trafficking, secretion, and vesicular transport] 321 matched cddid_all.tbl CDD KOG0820 KOG0820 228766 KOG0820 KOG0820, Ribosomal RNA adenine dimethylase [RNA processing and modification] 315 matched cddid_all.tbl CDD KOG0821 KOG0821 228767 KOG0821 KOG0821, Predicted ribosomal RNA adenine dimethylase [RNA processing and modification] 326 matched cddid_all.tbl CDD KOG0822 KOG0822 228768 KOG0822 KOG0822, Protein kinase inhibitor [Cell cycle control, cell division, chromosome partitioning] 649 matched cddid_all.tbl CDD KOG0823 KOG0823 228769 KOG0823 KOG0823, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 230 matched cddid_all.tbl CDD KOG0824 KOG0824 228770 KOG0824 KOG0824, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 324 matched cddid_all.tbl CDD KOG0825 KOG0825 228771 KOG0825 KOG0825, PHD Zn-finger protein [General function prediction only] 1134 matched cddid_all.tbl CDD KOG0826 KOG0826 228772 KOG0826 KOG0826, Predicted E3 ubiquitin ligase involved in peroxisome organization [Posttranslational modification, protein turnover, chaperones] 357 matched cddid_all.tbl CDD KOG0827 KOG0827 228773 KOG0827 KOG0827, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 465 matched cddid_all.tbl CDD KOG0828 KOG0828 228774 KOG0828 KOG0828, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 636 matched cddid_all.tbl CDD KOG0829 KOG0829 228775 KOG0829 KOG0829, 60S ribosomal protein L18A [Translation, ribosomal structure and biogenesis] 169 matched cddid_all.tbl CDD KOG0830 KOG0830 228776 KOG0830 KOG0830, 40S ribosomal protein SA (P40)/Laminin receptor 1 [Translation, ribosomal structure and biogenesis] 254 matched cddid_all.tbl CDD KOG0831 KOG0831 228777 KOG0831 KOG0831, Acyl-CoA:diacylglycerol acyltransferase (DGAT) [Lipid transport and metabolism] 334 matched cddid_all.tbl CDD KOG0832 KOG0832 228778 KOG0832 KOG0832, Mitochondrial/chloroplast ribosomal protein S2 [Translation, ribosomal structure and biogenesis] 251 matched cddid_all.tbl CDD KOG0833 KOG0833 228779 KOG0833 KOG0833, Cytidine deaminase [Nucleotide transport and metabolism] 173 matched cddid_all.tbl CDD KOG0834 KOG0834 228780 KOG0834 KOG0834, CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning] 323 matched cddid_all.tbl CDD KOG0835 KOG0835 228781 KOG0835 KOG0835, Cyclin L [General function prediction only] 367 matched cddid_all.tbl CDD KOG0836 KOG0836 228782 KOG0836 KOG0836, F-actin capping protein, alpha subunit [Cytoskeleton] 282 matched cddid_all.tbl CDD KOG0837 KOG0837 228783 KOG0837 KOG0837, Transcriptional activator of the JUN family [Transcription] 279 matched cddid_all.tbl CDD KOG0838 KOG0838 228784 KOG0838 KOG0838, RNA Methylase, SpoU family [RNA processing and modification] 271 matched cddid_all.tbl CDD KOG0839 KOG0839 228785 KOG0839 KOG0839, RNA Methylase, SpoU family [RNA processing and modification] 1477 matched cddid_all.tbl CDD KOG0840 KOG0840 228786 KOG0840 KOG0840, ATP-dependent Clp protease, proteolytic subunit [Posttranslational modification, protein turnover, chaperones] 275 matched cddid_all.tbl CDD KOG0841 KOG0841 228787 KOG0841 KOG0841, Multifunctional chaperone (14-3-3 family) [Posttranslational modification, protein turnover, chaperones] 247 matched cddid_all.tbl CDD KOG0842 KOG0842 228788 KOG0842 KOG0842, Transcription factor tinman/NKX2-3, contains HOX domain [Transcription] 307 matched cddid_all.tbl CDD KOG0843 KOG0843 228789 KOG0843 KOG0843, Transcription factor EMX1 and related HOX domain proteins [Transcription] 197 matched cddid_all.tbl CDD KOG0844 KOG0844 228790 KOG0844 KOG0844, Transcription factor EVX1, contains HOX domain [Transcription] 408 matched cddid_all.tbl CDD KOG0845 KOG0845 228791 KOG0845 KOG0845, Nuclear pore complex, Nup98 component (sc Nup145/Nup100/Nup116) [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 903 matched cddid_all.tbl CDD KOG0846 KOG0846 228792 KOG0846 KOG0846, Mitochondrial/chloroplast ribosomal protein L15/L10 [Translation, ribosomal structure and biogenesis] 274 matched cddid_all.tbl CDD KOG0847 KOG0847 228793 KOG0847 KOG0847, Transcription factor, contains HOX domain [Transcription] 288 matched cddid_all.tbl CDD KOG0848 KOG0848 228794 KOG0848 KOG0848, Transcription factor Caudal, contains HOX domain [Transcription] 317 matched cddid_all.tbl CDD KOG0849 KOG0849 228795 KOG0849 KOG0849, Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription] 354 matched cddid_all.tbl CDD KOG0850 KOG0850 228796 KOG0850 KOG0850, Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription] 245 matched cddid_all.tbl CDD KOG0851 KOG0851 228797 KOG0851 KOG0851, Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [Replication, recombination and repair] 139 matched cddid_all.tbl CDD KOG0852 KOG0852 228798 KOG0852 KOG0852, Alkyl hydroperoxide reductase, thiol specific antioxidant and related enzymes [Posttranslational modification, protein turnover, chaperones] 196 matched cddid_all.tbl CDD KOG0853 KOG0853 228799 KOG0853 KOG0853, Glycosyltransferase [Cell wall/membrane/envelope biogenesis] 495 matched cddid_all.tbl CDD KOG0854 KOG0854 228800 KOG0854 KOG0854, Alkyl hydroperoxide reductase, thiol specific antioxidant and related enzymes [Posttranslational modification, protein turnover, chaperones] 224 matched cddid_all.tbl CDD KOG0855 KOG0855 228801 KOG0855 KOG0855, Alkyl hydroperoxide reductase, thiol specific antioxidant and related enzymes [Posttranslational modification, protein turnover, chaperones] 211 matched cddid_all.tbl CDD KOG0856 KOG0856 228802 KOG0856 KOG0856, Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones] 146 matched cddid_all.tbl CDD KOG0857 KOG0857 228803 KOG0857 KOG0857, 60s ribosomal protein L10 [Translation, ribosomal structure and biogenesis] 212 matched cddid_all.tbl CDD KOG0858 KOG0858 228804 KOG0858 KOG0858, Predicted membrane protein [Function unknown] 239 matched cddid_all.tbl CDD KOG0859 KOG0859 228805 KOG0859 KOG0859, Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport] 217 matched cddid_all.tbl CDD KOG0860 KOG0860 228806 KOG0860 KOG0860, Synaptobrevin/VAMP-like protein [Intracellular trafficking, secretion, and vesicular transport] 116 matched cddid_all.tbl CDD KOG0861 KOG0861 228807 KOG0861 KOG0861, SNARE protein YKT6, synaptobrevin/VAMP syperfamily [Intracellular trafficking, secretion, and vesicular transport] 198 matched cddid_all.tbl CDD KOG0862 KOG0862 228808 KOG0862 KOG0862, Synaptobrevin/VAMP-like protein SEC22 [Intracellular trafficking, secretion, and vesicular transport] 216 matched cddid_all.tbl CDD KOG0863 KOG0863 228809 KOG0863 KOG0863, 20S proteasome, regulatory subunit alpha type PSMA1/PRE5 [Posttranslational modification, protein turnover, chaperones] 264 matched cddid_all.tbl CDD KOG0864 KOG0864 228810 KOG0864 KOG0864, Ran-binding protein RANBP1 and related RanBD domain proteins [Intracellular trafficking, secretion, and vesicular transport] 215 matched cddid_all.tbl CDD KOG0865 KOG0865 228811 KOG0865 KOG0865, Cyclophilin type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones] 167 matched cddid_all.tbl CDD KOG0866 KOG0866 228812 KOG0866 KOG0866, Ran-binding protein RANBP3 [Intracellular trafficking, secretion, and vesicular transport] 327 matched cddid_all.tbl CDD KOG0867 KOG0867 228813 KOG0867 KOG0867, Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones] 226 matched cddid_all.tbl CDD KOG0868 KOG0868 228814 KOG0868 KOG0868, Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones] 217 matched cddid_all.tbl CDD KOG0869 KOG0869 228815 KOG0869 KOG0869, CCAAT-binding factor, subunit A (HAP3) [Transcription] 168 matched cddid_all.tbl CDD KOG0870 KOG0870 228816 KOG0870 KOG0870, DNA polymerase epsilon, subunit D [Transcription] 172 matched cddid_all.tbl CDD KOG0871 KOG0871 228817 KOG0871 KOG0871, Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription] 156 matched cddid_all.tbl CDD KOG0872 KOG0872 228818 KOG0872 KOG0872, Sterol C5 desaturase [Lipid transport and metabolism] 312 matched cddid_all.tbl CDD KOG0873 KOG0873 228819 KOG0873 KOG0873, C-4 sterol methyl oxidase [Lipid transport and metabolism] 283 matched cddid_all.tbl CDD KOG0874 KOG0874 228820 KOG0874 KOG0874, Sphingolipid hydroxylase [Lipid transport and metabolism] 287 matched cddid_all.tbl CDD KOG0875 KOG0875 228821 KOG0875 KOG0875, 60S ribosomal protein L5 [Translation, ribosomal structure and biogenesis] 264 matched cddid_all.tbl CDD KOG0876 KOG0876 228822 KOG0876 KOG0876, Manganese superoxide dismutase [Inorganic ion transport and metabolism] 234 matched cddid_all.tbl CDD KOG0877 KOG0877 228823 KOG0877 KOG0877, 40S ribosomal protein S2/30S ribosomal protein S5 [Translation, ribosomal structure and biogenesis] 213 matched cddid_all.tbl CDD KOG0878 KOG0878 228824 KOG0878 KOG0878, 60S ribosomal protein L32 [Translation, ribosomal structure and biogenesis] 124 matched cddid_all.tbl CDD KOG0879 KOG0879 228825 KOG0879 KOG0879, U-snRNP-associated cyclophilin type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones] 177 matched cddid_all.tbl CDD KOG0880 KOG0880 228826 KOG0880 KOG0880, Peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones] 217 matched cddid_all.tbl CDD KOG0881 KOG0881 228827 KOG0881 KOG0881, Cyclophilin type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones] 164 matched cddid_all.tbl CDD KOG0882 KOG0882 228828 KOG0882 KOG0882, Cyclophilin-related peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones] 558 matched cddid_all.tbl CDD KOG0883 KOG0883 228829 KOG0883 KOG0883, Cyclophilin type, U box-containing peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones] 518 matched cddid_all.tbl CDD KOG0884 KOG0884 228830 KOG0884 KOG0884, Similar to cyclophilin-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones] 161 matched cddid_all.tbl CDD KOG0885 KOG0885 228831 KOG0885 KOG0885, Peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones] 439 matched cddid_all.tbl CDD KOG0886 KOG0886 228832 KOG0886 KOG0886, 40S ribosomal protein S2 [Translation, ribosomal structure and biogenesis] 167 matched cddid_all.tbl CDD KOG0887 KOG0887 228833 KOG0887 KOG0887, 60S ribosomal protein L35A/L37 [Translation, ribosomal structure and biogenesis] 111 matched cddid_all.tbl CDD KOG0888 KOG0888 228834 KOG0888 KOG0888, Nucleoside diphosphate kinase [Nucleotide transport and metabolism] 156 matched cddid_all.tbl CDD KOG0889 KOG0889 228835 KOG0889 KOG0889, Histone acetyltransferase SAGA, TRRAP/TRA1 component, PI-3 kinase superfamily [Signal transduction mechanisms, Chromatin structure and dynamics, Replication, recombination and repair, Cell cycle control, cell division, chromosome partitioning] 3550 matched cddid_all.tbl CDD KOG0890 KOG0890 228836 KOG0890 KOG0890, Protein kinase of the PI-3 kinase family involved in mitotic growth, DNA repair and meiotic recombination [Signal transduction mechanisms, Chromatin structure and dynamics, Replication, recombination and repair, Cell cycle control, cell division, chromosome partitioning] 2382 matched cddid_all.tbl CDD KOG0891 KOG0891 228837 KOG0891 KOG0891, DNA-dependent protein kinase [Replication, recombination and repair] 2341 matched cddid_all.tbl CDD KOG0892 KOG0892 228838 KOG0892 KOG0892, Protein kinase ATM/Tel1, involved in telomere length regulation and DNA repair [Signal transduction mechanisms, Chromatin structure and dynamics, Replication, recombination and repair, Cell cycle control, cell division, chromosome partitioning] 2806 matched cddid_all.tbl CDD KOG0893 KOG0893 228839 KOG0893 KOG0893, 60S ribosomal protein L31 [Translation, ribosomal structure and biogenesis] 125 matched cddid_all.tbl CDD KOG0894 KOG0894 228840 KOG0894 KOG0894, Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones] 244 matched cddid_all.tbl CDD KOG0895 KOG0895 228841 KOG0895 KOG0895, Ubiquitin-conjugating enzyme [Posttranslational modification, protein turnover, chaperones] 1101 matched cddid_all.tbl CDD KOG0896 KOG0896 228842 KOG0896 KOG0896, Ubiquitin-conjugating enzyme E2 [Posttranslational modification, protein turnover, chaperones] 138 matched cddid_all.tbl CDD KOG0897 KOG0897 228843 KOG0897 KOG0897, Predicted ubiquitin-conjugating enzyme [Posttranslational modification, protein turnover, chaperones] 122 matched cddid_all.tbl CDD KOG0898 KOG0898 228844 KOG0898 KOG0898, 40S ribosomal protein S15 [Translation, ribosomal structure and biogenesis] 152 matched cddid_all.tbl CDD KOG0899 KOG0899 228845 KOG0899 KOG0899, Mitochondrial/chloroplast ribosomal protein S19 [Translation, ribosomal structure and biogenesis] 93 matched cddid_all.tbl CDD KOG0900 KOG0900 228846 KOG0900 KOG0900, 40S ribosomal protein S20 [Translation, ribosomal structure and biogenesis] 121 matched cddid_all.tbl CDD KOG0901 KOG0901 228847 KOG0901 KOG0901, 60S ribosomal protein L14/L17/L23 [Translation, ribosomal structure and biogenesis] 145 matched cddid_all.tbl CDD KOG0902 KOG0902 228848 KOG0902 KOG0902, Phosphatidylinositol 4-kinase [Signal transduction mechanisms] 1803 matched cddid_all.tbl CDD KOG0903 KOG0903 228849 KOG0903 KOG0903, Phosphatidylinositol 4-kinase, involved in intracellular trafficking and secretion [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 847 matched cddid_all.tbl CDD KOG0904 KOG0904 228850 KOG0904 KOG0904, Phosphatidylinositol 3-kinase catalytic subunit (p110) [Signal transduction mechanisms] 1076 matched cddid_all.tbl CDD KOG0905 KOG0905 228851 KOG0905 KOG0905, Phosphoinositide 3-kinase [Signal transduction mechanisms] 1639 matched cddid_all.tbl CDD KOG0906 KOG0906 228852 KOG0906 KOG0906, Phosphatidylinositol 3-kinase VPS34, involved in signal transduction [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 843 matched cddid_all.tbl CDD KOG0907 KOG0907 228853 KOG0907 KOG0907, Thioredoxin [Posttranslational modification, protein turnover, chaperones] 106 matched cddid_all.tbl CDD KOG0908 KOG0908 228854 KOG0908 KOG0908, Thioredoxin-like protein [Posttranslational modification, protein turnover, chaperones] 288 matched cddid_all.tbl CDD KOG0909 KOG0909 228855 KOG0909 KOG0909, Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones] 500 matched cddid_all.tbl CDD KOG0910 KOG0910 228856 KOG0910 KOG0910, Thioredoxin-like protein [Posttranslational modification, protein turnover, chaperones] 150 matched cddid_all.tbl CDD KOG0911 KOG0911 228857 KOG0911 KOG0911, Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones] 227 matched cddid_all.tbl CDD KOG0912 KOG0912 228858 KOG0912 KOG0912, Thiol-disulfide isomerase and thioredoxin [Posttranslational modification, protein turnover, chaperones, Energy production and conversion] 375 matched cddid_all.tbl CDD KOG0913 KOG0913 228859 KOG0913 KOG0913, Thiol-disulfide isomerase and thioredoxin [Posttranslational modification, protein turnover, chaperones, Energy production and conversion] 248 matched cddid_all.tbl CDD KOG0914 KOG0914 228860 KOG0914 KOG0914, Thioredoxin-like protein [Posttranslational modification, protein turnover, chaperones] 265 matched cddid_all.tbl CDD KOG0915 KOG0915 228861 KOG0915 KOG0915, Uncharacterized conserved protein [Function unknown] 1702 matched cddid_all.tbl CDD KOG0916 KOG0916 228862 KOG0916 KOG0916, 1,3-beta-glucan synthase/callose synthase catalytic subunit [Cell wall/membrane/envelope biogenesis] 1679 matched cddid_all.tbl CDD KOG0917 KOG0917 228863 KOG0917 KOG0917, Uncharacterized conserved protein [Function unknown] 338 matched cddid_all.tbl CDD KOG0918 KOG0918 228864 KOG0918 KOG0918, Selenium-binding protein [Inorganic ion transport and metabolism] 476 matched cddid_all.tbl CDD KOG0919 KOG0919 228865 KOG0919 KOG0919, C-5 cytosine-specific DNA methylase [Transcription] 338 matched cddid_all.tbl CDD KOG0920 KOG0920 228866 KOG0920 KOG0920, ATP-dependent RNA helicase A [RNA processing and modification] 924 matched cddid_all.tbl CDD KOG0921 KOG0921 228867 KOG0921 KOG0921, Dosage compensation complex, subunit MLE [Transcription] 1282 matched cddid_all.tbl CDD KOG0922 KOG0922 228868 KOG0922 KOG0922, DEAH-box RNA helicase [RNA processing and modification] 674 matched cddid_all.tbl CDD KOG0923 KOG0923 228869 KOG0923 KOG0923, mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification] 902 matched cddid_all.tbl CDD KOG0924 KOG0924 228870 KOG0924 KOG0924, mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification] 1042 matched cddid_all.tbl CDD KOG0925 KOG0925 228871 KOG0925 KOG0925, mRNA splicing factor ATP-dependent RNA helicase [RNA processing and modification] 699 matched cddid_all.tbl CDD KOG0926 KOG0926 228872 KOG0926 KOG0926, DEAH-box RNA helicase [RNA processing and modification, Translation, ribosomal structure and biogenesis] 1172 matched cddid_all.tbl CDD KOG0927 KOG0927 228873 KOG0927 KOG0927, Predicted transporter (ABC superfamily) [General function prediction only] 614 matched cddid_all.tbl CDD KOG0928 KOG0928 228874 KOG0928 KOG0928, Pattern-formation protein/guanine nucleotide exchange factor [Intracellular trafficking, secretion, and vesicular transport] 1386 matched cddid_all.tbl CDD KOG0929 KOG0929 228875 KOG0929 KOG0929, Guanine nucleotide exchange factor [Intracellular trafficking, secretion, and vesicular transport] 1514 matched cddid_all.tbl CDD KOG0930 KOG0930 228876 KOG0930 KOG0930, Guanine nucleotide exchange factor Cytohesin, contains PH and Sec7 domains [Intracellular trafficking, secretion, and vesicular transport] 395 matched cddid_all.tbl CDD KOG0931 KOG0931 228877 KOG0931 KOG0931, Predicted guanine nucleotide exchange factor, contains Sec7 domain [Intracellular trafficking, secretion, and vesicular transport] 627 matched cddid_all.tbl CDD KOG0932 KOG0932 228878 KOG0932 KOG0932, Guanine nucleotide exchange factor EFA6 [Intracellular trafficking, secretion, and vesicular transport] 774 matched cddid_all.tbl CDD KOG0933 KOG0933 228879 KOG0933 KOG0933, Structural maintenance of chromosome protein 2 (chromosome condensation complex Condensin, subunit E) [Chromatin structure and dynamics, Cell cycle control, cell division, chromosome partitioning] 1174 matched cddid_all.tbl CDD KOG0934 KOG0934 228880 KOG0934 KOG0934, Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport] 145 matched cddid_all.tbl CDD KOG0935 KOG0935 228881 KOG0935 KOG0935, Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport] 143 matched cddid_all.tbl CDD KOG0936 KOG0936 228882 KOG0936 KOG0936, Clathrin adaptor complex, small subunit [Intracellular trafficking, secretion, and vesicular transport] 182 matched cddid_all.tbl CDD KOG0937 KOG0937 228883 KOG0937 KOG0937, Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport] 424 matched cddid_all.tbl CDD KOG0938 KOG0938 228884 KOG0938 KOG0938, Adaptor complexes medium subunit family [Intracellular trafficking, secretion, and vesicular transport] 446 matched cddid_all.tbl CDD KOG0939 KOG0939 228885 KOG0939 KOG0939, E3 ubiquitin-protein ligase/Putative upstream regulatory element binding protein [Posttranslational modification, protein turnover, chaperones, Transcription] 720 matched cddid_all.tbl CDD KOG0940 KOG0940 228886 KOG0940 KOG0940, Ubiquitin protein ligase RSP5/NEDD4 [Posttranslational modification, protein turnover, chaperones] 358 matched cddid_all.tbl CDD KOG0941 KOG0941 228887 KOG0941 KOG0941, E3 ubiquitin protein ligase [Posttranslational modification, protein turnover, chaperones] 850 matched cddid_all.tbl CDD KOG0942 KOG0942 228888 KOG0942 KOG0942, E3 ubiquitin protein ligase [Posttranslational modification, protein turnover, chaperones] 1001 matched cddid_all.tbl CDD KOG0943 KOG0943 228889 KOG0943 KOG0943, Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones] 3015 matched cddid_all.tbl CDD KOG0944 KOG0944 228890 KOG0944 KOG0944, Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones] 763 matched cddid_all.tbl CDD KOG0945 KOG0945 228891 KOG0945 KOG0945, Alpha-aminoadipic semialdehyde dehydrogenase-phosphopantetheinyl transferase [Amino acid transport and metabolism, Coenzyme transport and metabolism] 289 matched cddid_all.tbl CDD KOG0946 KOG0946 228892 KOG0946 KOG0946, ER-Golgi vesicle-tethering protein p115 [Intracellular trafficking, secretion, and vesicular transport] 970 matched cddid_all.tbl CDD KOG0947 KOG0947 228893 KOG0947 KOG0947, Cytoplasmic exosomal RNA helicase SKI2, DEAD-box superfamily [RNA processing and modification] 1248 matched cddid_all.tbl CDD KOG0948 KOG0948 228894 KOG0948 KOG0948, Nuclear exosomal RNA helicase MTR4, DEAD-box superfamily [RNA processing and modification] 1041 matched cddid_all.tbl CDD KOG0949 KOG0949 228895 KOG0949 KOG0949, Predicted helicase, DEAD-box superfamily [General function prediction only] 1330 matched cddid_all.tbl CDD KOG0950 KOG0950 228896 KOG0950 KOG0950, DNA polymerase theta/eta, DEAD-box superfamily [General function prediction only] 1008 matched cddid_all.tbl CDD KOG0951 KOG0951 228897 KOG0951 KOG0951, RNA helicase BRR2, DEAD-box superfamily [RNA processing and modification] 1674 matched cddid_all.tbl CDD KOG0952 KOG0952 228898 KOG0952 KOG0952, DNA/RNA helicase MER3/SLH1, DEAD-box superfamily [RNA processing and modification] 1230 matched cddid_all.tbl CDD KOG0953 KOG0953 228899 KOG0953 KOG0953, Mitochondrial RNA helicase SUV3, DEAD-box superfamily [RNA processing and modification] 700 matched cddid_all.tbl CDD KOG0954 KOG0954 228900 KOG0954 KOG0954, PHD finger protein [General function prediction only] 893 matched cddid_all.tbl CDD KOG0955 KOG0955 228901 KOG0955 KOG0955, PHD finger protein BR140/LIN-49 [General function prediction only] 1051 matched cddid_all.tbl CDD KOG0956 KOG0956 228902 KOG0956 KOG0956, PHD finger protein AF10 [General function prediction only] 900 matched cddid_all.tbl CDD KOG0957 KOG0957 228903 KOG0957 KOG0957, PHD finger protein [General function prediction only] 707 matched cddid_all.tbl CDD KOG0958 KOG0958 228904 KOG0958 KOG0958, DNA damage-responsive repressor GIS1/RPH1, jumonji superfamily [Replication, recombination and repair] 690 matched cddid_all.tbl CDD KOG0959 KOG0959 228905 KOG0959 KOG0959, N-arginine dibasic convertase NRD1 and related Zn2+-dependent endopeptidases, insulinase superfamily [Posttranslational modification, protein turnover, chaperones] 974 matched cddid_all.tbl CDD KOG0960 KOG0960 228906 KOG0960 KOG0960, Mitochondrial processing peptidase, beta subunit, and related enzymes (insulinase superfamily) [Posttranslational modification, protein turnover, chaperones] 467 matched cddid_all.tbl CDD KOG0961 KOG0961 228907 KOG0961 KOG0961, Predicted Zn2+-dependent endopeptidase, insulinase superfamily [Posttranslational modification, protein turnover, chaperones] 1022 matched cddid_all.tbl CDD KOG0962 KOG0962 228908 KOG0962 KOG0962, DNA repair protein RAD50, ABC-type ATPase/SMC superfamily [Replication, recombination and repair] 1294 matched cddid_all.tbl CDD KOG0963 KOG0963 228909 KOG0963 KOG0963, Transcription factor/CCAAT displacement protein CDP1 [Transcription] 629 matched cddid_all.tbl CDD KOG0964 KOG0964 228910 KOG0964 KOG0964, Structural maintenance of chromosome protein 3 (sister chromatid cohesion complex Cohesin, subunit SMC3) [Cell cycle control, cell division, chromosome partitioning] 1200 matched cddid_all.tbl CDD KOG0965 KOG0965 228911 KOG0965 KOG0965, Predicted RNA-binding protein, contains SWAP and G-patch domains [General function prediction only] 988 matched cddid_all.tbl CDD KOG0966 KOG0966 228912 KOG0966 KOG0966, ATP-dependent DNA ligase IV [Replication, recombination and repair] 881 matched cddid_all.tbl CDD KOG0967 KOG0967 228913 KOG0967 KOG0967, ATP-dependent DNA ligase I [Replication, recombination and repair] 714 matched cddid_all.tbl CDD KOG0968 KOG0968 228914 KOG0968 KOG0968, DNA polymerase zeta, catalytic subunit [Replication, recombination and repair] 1488 matched cddid_all.tbl CDD KOG0969 KOG0969 228915 KOG0969 KOG0969, DNA polymerase delta, catalytic subunit [Replication, recombination and repair] 1066 matched cddid_all.tbl CDD KOG0970 KOG0970 228916 KOG0970 KOG0970, DNA polymerase alpha, catalytic subunit [Replication, recombination and repair] 1429 matched cddid_all.tbl CDD KOG0971 KOG0971 228917 KOG0971 KOG0971, Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton] 1243 matched cddid_all.tbl CDD KOG0972 KOG0972 228918 KOG0972 KOG0972, Huntingtin interacting protein 1 (Hip1) interactor Hippi [Signal transduction mechanisms] 384 matched cddid_all.tbl CDD KOG0973 KOG0973 228919 KOG0973 KOG0973, Histone transcription regulator HIRA, WD repeat superfamily [Cell cycle control, cell division, chromosome partitioning, Transcription] 942 matched cddid_all.tbl CDD KOG0974 KOG0974 228920 KOG0974 KOG0974, WD-repeat protein WDR6, WD repeat superfamily [General function prediction only] 967 matched cddid_all.tbl CDD KOG0975 KOG0975 228921 KOG0975 KOG0975, Branched chain aminotransferase BCAT1, pyridoxal phosphate enzymes type IV superfamily [Amino acid transport and metabolism] 379 matched cddid_all.tbl CDD KOG0976 KOG0976 228922 KOG0976 KOG0976, Rho/Rac1-interacting serine/threonine kinase Citron [Signal transduction mechanisms] 1265 matched cddid_all.tbl CDD KOG0977 KOG0977 228923 KOG0977 KOG0977, Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning, Nuclear structure] 546 matched cddid_all.tbl CDD KOG0978 KOG0978 228924 KOG0978 KOG0978, E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones] 698 matched cddid_all.tbl CDD KOG0979 KOG0979 228925 KOG0979 KOG0979, Structural maintenance of chromosome protein SMC5/Spr18, SMC superfamily [Chromatin structure and dynamics, Cell cycle control, cell division, chromosome partitioning, Replication, recombination and repair] 985 matched cddid_all.tbl CDD KOG0980 KOG0980 228926 KOG0980 KOG0980, Actin-binding protein SLA2/Huntingtin-interacting protein Hip1 [Cytoskeleton] 980 matched cddid_all.tbl CDD KOG0981 KOG0981 228927 KOG0981 KOG0981, DNA topoisomerase I [Replication, recombination and repair] 759 matched cddid_all.tbl CDD KOG0982 KOG0982 228928 KOG0982 KOG0982, Centrosomal protein Nuf [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton] 502 matched cddid_all.tbl CDD KOG0983 KOG0983 228929 KOG0983 KOG0983, Mitogen-activated protein kinase (MAPK) kinase MKK7/JNKK2 [Signal transduction mechanisms] 391 matched cddid_all.tbl CDD KOG0984 KOG0984 228930 KOG0984 KOG0984, Mitogen-activated protein kinase (MAPK) kinase MKK3/MKK6 [Signal transduction mechanisms] 282 matched cddid_all.tbl CDD KOG0985 KOG0985 228931 KOG0985 KOG0985, Vesicle coat protein clathrin, heavy chain [Intracellular trafficking, secretion, and vesicular transport] 1666 matched cddid_all.tbl CDD KOG0986 KOG0986 228932 KOG0986 KOG0986, G protein-coupled receptor kinase [Signal transduction mechanisms] 591 matched cddid_all.tbl CDD KOG0987 KOG0987 228933 KOG0987 KOG0987, DNA helicase PIF1/RRM3 [Cell cycle control, cell division, chromosome partitioning] 540 matched cddid_all.tbl CDD KOG0988 KOG0988 228934 KOG0988 KOG0988, RNA-directed RNA polymerase QDE-1 required for posttranscriptional gene silencing and RNA interference [RNA processing and modification] 1145 matched cddid_all.tbl CDD KOG0989 KOG0989 228935 KOG0989 KOG0989, Replication factor C, subunit RFC4 [Replication, recombination and repair] 346 matched cddid_all.tbl CDD KOG0990 KOG0990 228936 KOG0990 KOG0990, Replication factor C, subunit RFC5 [Replication, recombination and repair] 360 matched cddid_all.tbl CDD KOG0991 KOG0991 228937 KOG0991 KOG0991, Replication factor C, subunit RFC2 [Replication, recombination and repair] 333 matched cddid_all.tbl CDD KOG0992 KOG0992 228938 KOG0992 KOG0992, Uncharacterized conserved protein [Function unknown] 613 matched cddid_all.tbl CDD KOG0993 KOG0993 228939 KOG0993 KOG0993, Rab5 GTPase effector Rabaptin-5 [Intracellular trafficking, secretion, and vesicular transport] 542 matched cddid_all.tbl CDD KOG0994 KOG0994 228940 KOG0994 KOG0994, Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures] 1758 matched cddid_all.tbl CDD KOG0995 KOG0995 228941 KOG0995 KOG0995, Centromere-associated protein HEC1 [Cell cycle control, cell division, chromosome partitioning] 581 matched cddid_all.tbl CDD KOG0996 KOG0996 228942 KOG0996 KOG0996, Structural maintenance of chromosome protein 4 (chromosome condensation complex Condensin, subunit C) [Chromatin structure and dynamics, Cell cycle control, cell division, chromosome partitioning] 1293 matched cddid_all.tbl CDD KOG0997 KOG0997 228943 KOG0997 KOG0997, Uncharacterized conserved protein Sand [Function unknown] 523 matched cddid_all.tbl CDD KOG0998 KOG0998 228944 KOG0998 KOG0998, Synaptic vesicle protein EHS-1 and related EH domain proteins [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 847 matched cddid_all.tbl CDD KOG0999 KOG0999 228945 KOG0999 KOG0999, Microtubule-associated protein Bicaudal-D [Intracellular trafficking, secretion, and vesicular transport] 772 matched cddid_all.tbl CDD KOG1000 KOG1000 228946 KOG1000 KOG1000, Chromatin remodeling protein HARP/SMARCAL1, DEAD-box superfamily [Chromatin structure and dynamics] 689 matched cddid_all.tbl CDD KOG1001 KOG1001 228947 KOG1001 KOG1001, Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription, Replication, recombination and repair] 674 matched cddid_all.tbl CDD KOG1002 KOG1002 228948 KOG1002 KOG1002, Nucleotide excision repair protein RAD16 [Replication, recombination and repair] 791 matched cddid_all.tbl CDD KOG1003 KOG1003 228949 KOG1003 KOG1003, Actin filament-coating protein tropomyosin [Cytoskeleton] 205 matched cddid_all.tbl CDD KOG1004 KOG1004 228950 KOG1004 KOG1004, Exosomal 3'-5' exoribonuclease complex subunit Rrp40 [Translation, ribosomal structure and biogenesis] 230 matched cddid_all.tbl CDD KOG1005 KOG1005 228951 KOG1005 KOG1005, Telomerase catalytic subunit/reverse transcriptase TERT [Replication, recombination and repair, Chromatin structure and dynamics] 888 matched cddid_all.tbl CDD KOG1006 KOG1006 228952 KOG1006 KOG1006, Mitogen-activated protein kinase (MAPK) kinase MKK4 [Signal transduction mechanisms] 361 matched cddid_all.tbl CDD KOG1007 KOG1007 228953 KOG1007 KOG1007, WD repeat protein TSSC1, WD repeat superfamily [Function unknown] 370 matched cddid_all.tbl CDD KOG1008 KOG1008 228954 KOG1008 KOG1008, Uncharacterized conserved protein, contains WD40 repeats [Function unknown] 783 matched cddid_all.tbl CDD KOG1009 KOG1009 228955 KOG1009 KOG1009, Chromatin assembly complex 1 subunit B/CAC2 (contains WD40 repeats) [Chromatin structure and dynamics, Replication, recombination and repair] 434 matched cddid_all.tbl CDD KOG1010 KOG1010 228956 KOG1010 KOG1010, Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning] 920 matched cddid_all.tbl CDD KOG1011 KOG1011 228957 KOG1011 KOG1011, Neurotransmitter release regulator, UNC-13 [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 1283 matched cddid_all.tbl CDD KOG1012 KOG1012 228958 KOG1012 KOG1012, Ca2+-dependent lipid-binding protein CLB1/vesicle protein vp115/Granuphilin A, contains C2 domain [General function prediction only] 136 matched cddid_all.tbl CDD KOG1013 KOG1013 228959 KOG1013 KOG1013, Synaptic vesicle protein rabphilin-3A [Intracellular trafficking, secretion, and vesicular transport] 362 matched cddid_all.tbl CDD KOG1014 KOG1014 228960 KOG1014 KOG1014, 17 beta-hydroxysteroid dehydrogenase type 3, HSD17B3 [Lipid transport and metabolism] 312 matched cddid_all.tbl CDD KOG1015 KOG1015 228961 KOG1015 KOG1015, Transcription regulator XNP/ATRX, DEAD-box superfamily [Transcription] 1567 matched cddid_all.tbl CDD KOG1016 KOG1016 228962 KOG1016 KOG1016, Predicted DNA helicase, DEAD-box superfamily [General function prediction only] 1387 matched cddid_all.tbl CDD KOG1017 KOG1017 228963 KOG1017 KOG1017, Predicted uracil phosphoribosyltransferase [General function prediction only] 267 matched cddid_all.tbl CDD KOG1018 KOG1018 228964 KOG1018 KOG1018, Cytosine deaminase FCY1 and related enzymes [Nucleotide transport and metabolism] 169 matched cddid_all.tbl CDD KOG1019 KOG1019 228965 KOG1019 KOG1019, Retinoblastoma pathway protein LIN-9/chromatin-associated protein Aly [Chromatin structure and dynamics, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms] 837 matched cddid_all.tbl CDD KOG1020 KOG1020 228966 KOG1020 KOG1020, Sister chromatid cohesion protein SCC2/Nipped-B [Chromatin structure and dynamics, Cell cycle control, cell division, chromosome partitioning, Replication, recombination and repair] 1692 matched cddid_all.tbl CDD KOG1021 KOG1021 228967 KOG1021 KOG1021, Acetylglucosaminyltransferase EXT1/exostosin 1 [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis, Extracellular structures] 464 matched cddid_all.tbl CDD KOG1022 KOG1022 228968 KOG1022 KOG1022, Acetylglucosaminyltransferase EXT2/exostosin 2 [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis, Extracellular structures] 691 matched cddid_all.tbl CDD KOG1023 KOG1023 228969 KOG1023 KOG1023, Natriuretic peptide receptor, guanylate cyclase [Signal transduction mechanisms] 484 matched cddid_all.tbl CDD KOG1024 KOG1024 228970 KOG1024 KOG1024, Receptor-like protein tyrosine kinase RYK/derailed [Signal transduction mechanisms] 523 matched cddid_all.tbl CDD KOG1025 KOG1025 228971 KOG1025 KOG1025, Epidermal growth factor receptor EGFR and related tyrosine kinases [Signal transduction mechanisms] 1177 matched cddid_all.tbl CDD KOG1026 KOG1026 228972 KOG1026 KOG1026, Nerve growth factor receptor TRKA and related tyrosine kinases [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 774 matched cddid_all.tbl CDD KOG1027 KOG1027 228973 KOG1027 KOG1027, Serine/threonine protein kinase and endoribonuclease ERN1/IRE1, sensor of the unfolded protein response pathway [Signal transduction mechanisms] 903 matched cddid_all.tbl CDD KOG1028 KOG1028 228974 KOG1028 KOG1028, Ca2+-dependent phospholipid-binding protein Synaptotagmin, required for synaptic vesicle and secretory granule exocytosis [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 421 matched cddid_all.tbl CDD KOG1029 KOG1029 228975 KOG1029 KOG1029, Endocytic adaptor protein intersectin [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 1118 matched cddid_all.tbl CDD KOG1030 KOG1030 228976 KOG1030 KOG1030, Predicted Ca2+-dependent phospholipid-binding protein [General function prediction only] 168 matched cddid_all.tbl CDD KOG1031 KOG1031 228977 KOG1031 KOG1031, Predicted Ca2+-dependent phospholipid-binding protein [General function prediction only] 1169 matched cddid_all.tbl CDD KOG1032 KOG1032 228978 KOG1032 KOG1032, Uncharacterized conserved protein, contains GRAM domain [Function unknown] 590 matched cddid_all.tbl CDD KOG1033 KOG1033 228979 KOG1033 KOG1033, eIF-2alpha kinase PEK/EIF2AK3 [Translation, ribosomal structure and biogenesis] 516 matched cddid_all.tbl CDD KOG1034 KOG1034 228980 KOG1034 KOG1034, Transcriptional repressor EED/ESC/FIE, required for transcriptional silencing, WD repeat superfamily [Transcription] 385 matched cddid_all.tbl CDD KOG1035 KOG1035 228981 KOG1035 KOG1035, eIF-2alpha kinase GCN2 [Translation, ribosomal structure and biogenesis] 1351 matched cddid_all.tbl CDD KOG1036 KOG1036 228982 KOG1036 KOG1036, Mitotic spindle checkpoint protein BUB3, WD repeat superfamily [Cell cycle control, cell division, chromosome partitioning] 323 matched cddid_all.tbl CDD KOG1037 KOG1037 228983 KOG1037 KOG1037, NAD+ ADP-ribosyltransferase Parp, required for poly-ADP ribosylation of nuclear proteins [Transcription, Replication, recombination and repair, Posttranslational modification, protein turnover, chaperones] 531 matched cddid_all.tbl CDD KOG1038 KOG1038 228984 KOG1038 KOG1038, Mitochondrial/chloroplast DNA-directed RNA polymerase RPO41, provides primers for DNA replication-initiation [Transcription, Replication, recombination and repair] 1088 matched cddid_all.tbl CDD KOG1039 KOG1039 228985 KOG1039 KOG1039, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 344 matched cddid_all.tbl CDD KOG1040 KOG1040 228986 KOG1040 KOG1040, Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification] 325 matched cddid_all.tbl CDD KOG1041 KOG1041 228987 KOG1041 KOG1041, Translation initiation factor 2C (eIF-2C) and related proteins [Translation, ribosomal structure and biogenesis] 876 matched cddid_all.tbl CDD KOG1042 KOG1042 228988 KOG1042 KOG1042, Germ-line stem cell division protein Hiwi/Piwi; negative developmental regulator [Cell cycle control, cell division, chromosome partitioning] 845 matched cddid_all.tbl CDD KOG1043 KOG1043 228989 KOG1043 KOG1043, Ca2+-binding transmembrane protein LETM1/MRS7 [Function unknown] 499 matched cddid_all.tbl CDD KOG1044 KOG1044 228990 KOG1044 KOG1044, Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms, Cytoskeleton] 670 matched cddid_all.tbl CDD KOG1045 KOG1045 228991 KOG1045 KOG1045, Uncharacterized conserved protein HEN1/CORYMBOSA2 [Function unknown] 404 matched cddid_all.tbl CDD KOG1046 KOG1046 228992 KOG1046 KOG1046, Puromycin-sensitive aminopeptidase and related aminopeptidases [Amino acid transport and metabolism, Posttranslational modification, protein turnover, chaperones] 843 matched cddid_all.tbl CDD KOG1047 KOG1047 228993 KOG1047 KOG1047, Bifunctional leukotriene A4 hydrolase/aminopeptidase LTA4H [Lipid transport and metabolism, Posttranslational modification, protein turnover, chaperones, Defense mechanisms, Amino acid transport and metabolism] 613 matched cddid_all.tbl CDD KOG1048 KOG1048 228994 KOG1048 KOG1048, Neural adherens junction protein Plakophilin and related Armadillo repeat proteins [Signal transduction mechanisms, Extracellular structures] 717 matched cddid_all.tbl CDD KOG1049 KOG1049 228995 KOG1049 KOG1049, Polyadenylation factor I complex, subunit FIP1 [RNA processing and modification] 538 matched cddid_all.tbl CDD KOG1050 KOG1050 228996 KOG1050 KOG1050, Trehalose-6-phosphate synthase component TPS1 and related subunits [Carbohydrate transport and metabolism] 732 matched cddid_all.tbl CDD KOG1051 KOG1051 228997 KOG1051 KOG1051, Chaperone HSP104 and related ATP-dependent Clp proteases [Posttranslational modification, protein turnover, chaperones] 898 matched cddid_all.tbl CDD KOG1052 KOG1052 228998 KOG1052 KOG1052, Glutamate-gated kainate-type ion channel receptor subunit GluR5 and related subunits [Inorganic ion transport and metabolism, Amino acid transport and metabolism, Signal transduction mechanisms] 656 matched cddid_all.tbl CDD KOG1053 KOG1053 228999 KOG1053 KOG1053, Glutamate-gated NMDA-type ion channel receptor subunit GRIN2A and related subunits [Inorganic ion transport and metabolism, Amino acid transport and metabolism, Signal transduction mechanisms] 1258 matched cddid_all.tbl CDD KOG1054 KOG1054 229000 KOG1054 KOG1054, Glutamate-gated AMPA-type ion channel receptor subunit GluR2 and related subunits [Inorganic ion transport and metabolism, Amino acid transport and metabolism, Signal transduction mechanisms] 897 matched cddid_all.tbl CDD KOG1055 KOG1055 229001 KOG1055 KOG1055, GABA-B ion channel receptor subunit GABABR1 and related subunits, G-protein coupled receptor superfamily [Inorganic ion transport and metabolism, Amino acid transport and metabolism, Signal transduction mechanisms] 865 matched cddid_all.tbl CDD KOG1056 KOG1056 229002 KOG1056 KOG1056, Glutamate-gated metabotropic ion channel receptor subunit GRM2 and related subunits, G-protein coupled receptor superfamily [Inorganic ion transport and metabolism, Signal transduction mechanisms] 878 matched cddid_all.tbl CDD KOG1057 KOG1057 229003 KOG1057 KOG1057, Arp2/3 complex-interacting protein VIP1/Asp1, involved in regulation of actin cytoskeleton [Cytoskeleton] 1018 matched cddid_all.tbl CDD KOG1058 KOG1058 229004 KOG1058 KOG1058, Vesicle coat complex COPI, beta subunit [Intracellular trafficking, secretion, and vesicular transport] 948 matched cddid_all.tbl CDD KOG1059 KOG1059 229005 KOG1059 KOG1059, Vesicle coat complex AP-3, delta subunit [Intracellular trafficking, secretion, and vesicular transport] 877 matched cddid_all.tbl CDD KOG1060 KOG1060 229006 KOG1060 KOG1060, Vesicle coat complex AP-3, beta subunit [Intracellular trafficking, secretion, and vesicular transport] 968 matched cddid_all.tbl CDD KOG1061 KOG1061 229007 KOG1061 KOG1061, Vesicle coat complex AP-1/AP-2/AP-4, beta subunit [Intracellular trafficking, secretion, and vesicular transport] 734 matched cddid_all.tbl CDD KOG1062 KOG1062 229008 KOG1062 KOG1062, Vesicle coat complex AP-1, gamma subunit [Intracellular trafficking, secretion, and vesicular transport] 866 matched cddid_all.tbl CDD KOG1063 KOG1063 229009 KOG1063 KOG1063, RNA polymerase II elongator complex, subunit ELP2, WD repeat superfamily [Chromatin structure and dynamics, Transcription] 764 matched cddid_all.tbl CDD KOG1064 KOG1064 229010 KOG1064 KOG1064, RAVE (regulator of V-ATPase assembly) complex subunit RAV1/DMX protein, WD repeat superfamily [General function prediction only] 2439 matched cddid_all.tbl CDD KOG1065 KOG1065 229011 KOG1065 KOG1065, Maltase glucoamylase and related hydrolases, glycosyl hydrolase family 31 [Carbohydrate transport and metabolism] 805 matched cddid_all.tbl CDD KOG1066 KOG1066 229012 KOG1066 KOG1066, Glucosidase II catalytic (alpha) subunit and related enzymes, glycosyl hydrolase family 31 [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones] 915 matched cddid_all.tbl CDD KOG1067 KOG1067 229013 KOG1067 KOG1067, Predicted RNA-binding polyribonucleotide nucleotidyltransferase [General function prediction only] 760 matched cddid_all.tbl CDD KOG1068 KOG1068 229014 KOG1068 KOG1068, Exosomal 3'-5' exoribonuclease complex, subunit Rrp41 and related exoribonucleases [Translation, ribosomal structure and biogenesis] 245 matched cddid_all.tbl CDD KOG1069 KOG1069 229015 KOG1069 KOG1069, Exosomal 3'-5' exoribonuclease complex, subunit Rrp46 [Translation, ribosomal structure and biogenesis] 217 matched cddid_all.tbl CDD KOG1070 KOG1070 229016 KOG1070 KOG1070, rRNA processing protein Rrp5 [RNA processing and modification] 1710 matched cddid_all.tbl CDD KOG1071 KOG1071 229017 KOG1071 KOG1071, Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis] 340 matched cddid_all.tbl CDD KOG1073 KOG1073 229018 KOG1073 KOG1073, Uncharacterized mRNA-associated protein RAP55 [Intracellular trafficking, secretion, and vesicular transport] 361 matched cddid_all.tbl CDD KOG1074 KOG1074 229019 KOG1074 KOG1074, Transcriptional repressor SALM [Transcription] 958 matched cddid_all.tbl CDD KOG1076 KOG1076 229020 KOG1076 KOG1076, Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis] 843 matched cddid_all.tbl CDD KOG1077 KOG1077 229021 KOG1077 KOG1077, Vesicle coat complex AP-2, alpha subunit [Intracellular trafficking, secretion, and vesicular transport] 938 matched cddid_all.tbl CDD KOG1078 KOG1078 229022 KOG1078 KOG1078, Vesicle coat complex COPI, gamma subunit [Intracellular trafficking, secretion, and vesicular transport] 865 matched cddid_all.tbl CDD KOG1079 KOG1079 229023 KOG1079 KOG1079, Transcriptional repressor EZH1 [Transcription] 739 matched cddid_all.tbl CDD KOG1080 KOG1080 229024 KOG1080 KOG1080, Histone H3 (Lys4) methyltransferase complex, subunit SET1 and related methyltransferases [Chromatin structure and dynamics, Transcription] 1005 matched cddid_all.tbl CDD KOG1081 KOG1081 229025 KOG1081 KOG1081, Transcription factor NSD1 and related SET domain proteins [Transcription] 463 matched cddid_all.tbl CDD KOG1082 KOG1082 229026 KOG1082 KOG1082, Histone H3 (Lys9) methyltransferase SUV39H1/Clr4, required for transcriptional silencing [Chromatin structure and dynamics, Transcription] 364 matched cddid_all.tbl CDD KOG1083 KOG1083 229027 KOG1083 KOG1083, Putative transcription factor ASH1/LIN-59 [Transcription] 1306 matched cddid_all.tbl CDD KOG1084 KOG1084 229028 KOG1084 KOG1084, Transcription factor TCF20 [Transcription] 375 matched cddid_all.tbl CDD KOG1085 KOG1085 229029 KOG1085 KOG1085, Predicted methyltransferase (contains a SET domain) [General function prediction only] 392 matched cddid_all.tbl CDD KOG1086 KOG1086 229030 KOG1086 KOG1086, Cytosolic sorting protein/ADP-ribosylation factor effector GGA [Intracellular trafficking, secretion, and vesicular transport] 594 matched cddid_all.tbl CDD KOG1087 KOG1087 229031 KOG1087 KOG1087, Cytosolic sorting protein GGA2/TOM1 [Intracellular trafficking, secretion, and vesicular transport] 470 matched cddid_all.tbl CDD KOG1088 KOG1088 229032 KOG1088 KOG1088, Uncharacterized conserved protein [Function unknown] 124 matched cddid_all.tbl CDD KOG1089 KOG1089 229033 KOG1089 KOG1089, Myotubularin-related phosphatidylinositol 3-phosphate 3-phosphatase MTM6 [General function prediction only] 573 matched cddid_all.tbl CDD KOG1090 KOG1090 229034 KOG1090 KOG1090, Predicted dual-specificity phosphatase [General function prediction only] 1732 matched cddid_all.tbl CDD KOG1091 KOG1091 229035 KOG1091 KOG1091, Ypt/Rab-specific GTPase-activating protein GYP6 [Intracellular trafficking, secretion, and vesicular transport] 625 matched cddid_all.tbl CDD KOG1092 KOG1092 229036 KOG1092 KOG1092, Ypt/Rab-specific GTPase-activating protein GYP1 [Intracellular trafficking, secretion, and vesicular transport] 484 matched cddid_all.tbl CDD KOG1093 KOG1093 229037 KOG1093 KOG1093, Predicted protein kinase (contains TBC and RHOD domains) [General function prediction only] 725 matched cddid_all.tbl CDD KOG1094 KOG1094 229038 KOG1094 KOG1094, Discoidin domain receptor DDR1 [Signal transduction mechanisms] 807 matched cddid_all.tbl CDD KOG1095 KOG1095 229039 KOG1095 KOG1095, Protein tyrosine kinase [Signal transduction mechanisms] 1025 matched cddid_all.tbl CDD KOG1096 KOG1096 229040 KOG1096 KOG1096, Adenosine monophosphate deaminase [Nucleotide transport and metabolism] 768 matched cddid_all.tbl CDD KOG1097 KOG1097 229041 KOG1097 KOG1097, Adenine deaminase/adenosine deaminase [Nucleotide transport and metabolism] 399 matched cddid_all.tbl CDD KOG1098 KOG1098 229042 KOG1098 KOG1098, Putative SAM-dependent rRNA methyltransferase SPB1 [RNA processing and modification, General function prediction only] 780 matched cddid_all.tbl CDD KOG1099 KOG1099 229043 KOG1099 KOG1099, SAM-dependent methyltransferase/cell division protein FtsJ [Cell cycle control, cell division, chromosome partitioning, General function prediction only] 294 matched cddid_all.tbl CDD KOG1100 KOG1100 229044 KOG1100 KOG1100, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 207 matched cddid_all.tbl CDD KOG1101 KOG1101 229045 KOG1101 KOG1101, Apoptosis inhibitor IAP1 and related BIR domain proteins [Cell cycle control, cell division, chromosome partitioning, General function prediction only] 147 matched cddid_all.tbl CDD KOG1102 KOG1102 229046 KOG1102 KOG1102, Rab6 GTPase activator GAPCenA and related TBC domain proteins [General function prediction only] 397 matched cddid_all.tbl CDD KOG1103 KOG1103 229047 KOG1103 KOG1103, Predicted coiled-coil protein [Function unknown] 561 matched cddid_all.tbl CDD KOG1104 KOG1104 229048 KOG1104 KOG1104, Nuclear cap-binding complex, subunit NCBP1/CBP80 [RNA processing and modification] 759 matched cddid_all.tbl CDD KOG1105 KOG1105 229049 KOG1105 KOG1105, Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription] 296 matched cddid_all.tbl CDD KOG1106 KOG1106 229050 KOG1106 KOG1106, Uncharacterized conserved protein [Function unknown] 177 matched cddid_all.tbl CDD KOG1107 KOG1107 229051 KOG1107 KOG1107, Membrane coat complex Retromer, subunit VPS35 [Intracellular trafficking, secretion, and vesicular transport] 760 matched cddid_all.tbl CDD KOG1108 KOG1108 229052 KOG1108 KOG1108, Predicted heme/steroid binding protein [General function prediction only] 281 matched cddid_all.tbl CDD KOG1109 KOG1109 229053 KOG1109 KOG1109, Vacuole membrane protein VMP1 [General function prediction only] 440 matched cddid_all.tbl CDD KOG1110 KOG1110 229054 KOG1110 KOG1110, Putative steroid membrane receptor Hpr6.6/25-Dx [General function prediction only] 183 matched cddid_all.tbl CDD KOG1111 KOG1111 229055 KOG1111 KOG1111, N-acetylglucosaminyltransferase complex, subunit PIG-A/SPT14, required for phosphatidylinositol biosynthesis/Sulfolipid synthase [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones, Lipid transport and metabolism] 426 matched cddid_all.tbl CDD KOG1112 KOG1112 229056 KOG1112 KOG1112, Ribonucleotide reductase, alpha subunit [Nucleotide transport and metabolism] 796 matched cddid_all.tbl CDD KOG1113 KOG1113 229057 KOG1113 KOG1113, cAMP-dependent protein kinase types I and II, regulatory subunit [Signal transduction mechanisms] 368 matched cddid_all.tbl CDD KOG1114 KOG1114 229058 KOG1114 KOG1114, Tripeptidyl peptidase II [Posttranslational modification, protein turnover, chaperones] 1304 matched cddid_all.tbl CDD KOG1115 KOG1115 229059 KOG1115 KOG1115, Ceramide kinase [Lipid transport and metabolism, Signal transduction mechanisms] 516 matched cddid_all.tbl CDD KOG1116 KOG1116 229060 KOG1116 KOG1116, Sphingosine kinase, involved in sphingolipid metabolism [Lipid transport and metabolism, Signal transduction mechanisms] 579 matched cddid_all.tbl CDD KOG1117 KOG1117 229061 KOG1117 KOG1117, Rho- and Arf-GTPase activating protein ARAP3 [Signal transduction mechanisms, Cytoskeleton] 1186 matched cddid_all.tbl CDD KOG1118 KOG1118 229062 KOG1118 KOG1118, Lysophosphatidic acid acyltransferase endophilin/SH3GL, involved in synaptic vesicle formation [Lipid transport and metabolism, Signal transduction mechanisms] 366 matched cddid_all.tbl CDD KOG1119 KOG1119 229063 KOG1119 KOG1119, Mitochondrial Fe-S cluster biosynthesis protein ISA2 (contains a HesB-like domain) [Energy production and conversion, Intracellular trafficking, secretion, and vesicular transport] 199 matched cddid_all.tbl CDD KOG1120 KOG1120 229064 KOG1120 KOG1120, Fe-S cluster biosynthesis protein ISA1 (contains a HesB-like domain) [Inorganic ion transport and metabolism] 134 matched cddid_all.tbl CDD KOG1121 KOG1121 229065 KOG1121 KOG1121, Tam3-transposase (Ac family) [Replication, recombination and repair] 641 matched cddid_all.tbl CDD KOG1122 KOG1122 229066 KOG1122 KOG1122, tRNA and rRNA cytosine-C5-methylase (nucleolar protein NOL1/NOP2) [RNA processing and modification] 460 matched cddid_all.tbl CDD KOG1123 KOG1123 229067 KOG1123 KOG1123, RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription, Replication, recombination and repair] 776 matched cddid_all.tbl CDD KOG1125 KOG1125 229068 KOG1125 KOG1125, TPR repeat-containing protein [General function prediction only] 579 matched cddid_all.tbl CDD KOG1126 KOG1126 229069 KOG1126 KOG1126, DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning] 638 matched cddid_all.tbl CDD KOG1127 KOG1127 229070 KOG1127 KOG1127, TPR repeat-containing protein [RNA processing and modification] 1238 matched cddid_all.tbl CDD KOG1128 KOG1128 229071 KOG1128 KOG1128, Uncharacterized conserved protein, contains TPR repeats [General function prediction only] 777 matched cddid_all.tbl CDD KOG1129 KOG1129 229072 KOG1129 KOG1129, TPR repeat-containing protein [General function prediction only] 478 matched cddid_all.tbl CDD KOG1130 KOG1130 229073 KOG1130 KOG1130, Predicted G-alpha GTPase interaction protein, contains GoLoco domain [Signal transduction mechanisms] 639 matched cddid_all.tbl CDD KOG1131 KOG1131 229074 KOG1131 KOG1131, RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 5'-3' helicase subunit RAD3 [Transcription, Replication, recombination and repair] 755 matched cddid_all.tbl CDD KOG1132 KOG1132 229075 KOG1132 KOG1132, Helicase of the DEAD superfamily [Replication, recombination and repair] 945 matched cddid_all.tbl CDD KOG1133 KOG1133 229076 KOG1133 KOG1133, Helicase of the DEAD superfamily [Replication, recombination and repair] 821 matched cddid_all.tbl CDD KOG1134 KOG1134 229077 KOG1134 KOG1134, Uncharacterized conserved protein [General function prediction only] 728 matched cddid_all.tbl CDD KOG1135 KOG1135 229078 KOG1135 KOG1135, mRNA cleavage and polyadenylation factor II complex, subunit CFT2 (CPSF subunit) [RNA processing and modification] 764 matched cddid_all.tbl CDD KOG1136 KOG1136 229079 KOG1136 KOG1136, Predicted cleavage and polyadenylation specificity factor (CPSF subunit) [RNA processing and modification] 501 matched cddid_all.tbl CDD KOG1137 KOG1137 229080 KOG1137 KOG1137, mRNA cleavage and polyadenylation factor II complex, BRR5 (CPSF subunit) [RNA processing and modification] 668 matched cddid_all.tbl CDD KOG1138 KOG1138 229081 KOG1138 KOG1138, Predicted cleavage and polyadenylation specificity factor (CPSF subunit) [RNA processing and modification] 653 matched cddid_all.tbl CDD KOG1139 KOG1139 229082 KOG1139 KOG1139, Predicted ubiquitin-protein ligase of the N-recognin family [Posttranslational modification, protein turnover, chaperones] 784 matched cddid_all.tbl CDD KOG1140 KOG1140 229083 KOG1140 KOG1140, N-end rule pathway, recognition component UBR1 [Posttranslational modification, protein turnover, chaperones] 1738 matched cddid_all.tbl CDD KOG1141 KOG1141 229084 KOG1141 KOG1141, Predicted histone methyl transferase [Chromatin structure and dynamics] 1262 matched cddid_all.tbl CDD KOG1142 KOG1142 229085 KOG1142 KOG1142, Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription] 258 matched cddid_all.tbl CDD KOG1143 KOG1143 229086 KOG1143 KOG1143, Predicted translation elongation factor [Translation, ribosomal structure and biogenesis] 591 matched cddid_all.tbl CDD KOG1144 KOG1144 229087 KOG1144 KOG1144, Translation initiation factor 5B (eIF-5B) [Translation, ribosomal structure and biogenesis] 1064 matched cddid_all.tbl CDD KOG1145 KOG1145 229088 KOG1145 KOG1145, Mitochondrial translation initiation factor 2 (IF-2; GTPase) [Translation, ribosomal structure and biogenesis] 683 matched cddid_all.tbl CDD KOG1146 KOG1146 229089 KOG1146 KOG1146, Homeobox protein [General function prediction only] 1406 matched cddid_all.tbl CDD KOG1147 KOG1147 229090 KOG1147 KOG1147, Glutamyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 712 matched cddid_all.tbl CDD KOG1148 KOG1148 229091 KOG1148 KOG1148, Glutaminyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 764 matched cddid_all.tbl CDD KOG1149 KOG1149 229092 KOG1149 KOG1149, Glutamyl-tRNA synthetase (mitochondrial) [Translation, ribosomal structure and biogenesis] 524 matched cddid_all.tbl CDD KOG1150 KOG1150 229093 KOG1150 KOG1150, Predicted molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones] 250 matched cddid_all.tbl CDD KOG1151 KOG1151 229094 KOG1151 KOG1151, Tousled-like protein kinase [Signal transduction mechanisms] 775 matched cddid_all.tbl CDD KOG1152 KOG1152 229095 KOG1152 KOG1152, Signal transduction serine/threonine kinase with PAS/PAC sensor domain [Signal transduction mechanisms] 772 matched cddid_all.tbl CDD KOG1153 KOG1153 229096 KOG1153 KOG1153, Subtilisin-related protease/Vacuolar protease B [Posttranslational modification, protein turnover, chaperones] 501 matched cddid_all.tbl CDD KOG1154 KOG1154 229097 KOG1154 KOG1154, Gamma-glutamyl kinase [Amino acid transport and metabolism] 285 matched cddid_all.tbl CDD KOG1155 KOG1155 229098 KOG1155 KOG1155, Anaphase-promoting complex (APC), Cdc23 subunit [Cell cycle control, cell division, chromosome partitioning, Posttranslational modification, protein turnover, chaperones] 559 matched cddid_all.tbl CDD KOG1156 KOG1156 229099 KOG1156 KOG1156, N-terminal acetyltransferase [Chromatin structure and dynamics] 700 matched cddid_all.tbl CDD KOG1157 KOG1157 229100 KOG1157 KOG1157, Predicted guanosine polyphosphate pyrophosphohydrolase/synthase [Signal transduction mechanisms] 543 matched cddid_all.tbl CDD KOG1158 KOG1158 229101 KOG1158 KOG1158, NADP/FAD dependent oxidoreductase [Energy production and conversion] 645 matched cddid_all.tbl CDD KOG1159 KOG1159 229102 KOG1159 KOG1159, NADP-dependent flavoprotein reductase [Energy production and conversion] 574 matched cddid_all.tbl CDD KOG1160 KOG1160 229103 KOG1160 KOG1160, Fe-S oxidoreductase [Energy production and conversion] 601 matched cddid_all.tbl CDD KOG1161 KOG1161 229104 KOG1161 KOG1161, Protein involved in vacuolar polyphosphate accumulation, contains SPX domain [Inorganic ion transport and metabolism] 310 matched cddid_all.tbl CDD KOG1162 KOG1162 229105 KOG1162 KOG1162, Predicted small molecule transporter [Intracellular trafficking, secretion, and vesicular transport] 617 matched cddid_all.tbl CDD KOG1163 KOG1163 229106 KOG1163 KOG1163, Casein kinase (serine/threonine/tyrosine protein kinase) [Signal transduction mechanisms] 341 matched cddid_all.tbl CDD KOG1164 KOG1164 229107 KOG1164 KOG1164, Casein kinase (serine/threonine/tyrosine protein kinase) [Signal transduction mechanisms] 322 matched cddid_all.tbl CDD KOG1165 KOG1165 229108 KOG1165 KOG1165, Casein kinase (serine/threonine/tyrosine protein kinase) [Signal transduction mechanisms] 449 matched cddid_all.tbl CDD KOG1166 KOG1166 229109 KOG1166 KOG1166, Mitotic checkpoint serine/threonine protein kinase [Cell cycle control, cell division, chromosome partitioning] 974 matched cddid_all.tbl CDD KOG1167 KOG1167 229110 KOG1167 KOG1167, Serine/threonine protein kinase of the CDC7 subfamily involved in DNA synthesis, repair and recombination [Replication, recombination and repair] 418 matched cddid_all.tbl CDD KOG1168 KOG1168 229111 KOG1168 KOG1168, Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription] 385 matched cddid_all.tbl CDD KOG1169 KOG1169 229112 KOG1169 KOG1169, Diacylglycerol kinase [Lipid transport and metabolism, Signal transduction mechanisms] 634 matched cddid_all.tbl CDD KOG1170 KOG1170 229113 KOG1170 KOG1170, Diacylglycerol kinase [Lipid transport and metabolism] 1099 matched cddid_all.tbl CDD KOG1171 KOG1171 229114 KOG1171 KOG1171, Metallothionein-like protein [Inorganic ion transport and metabolism] 406 matched cddid_all.tbl CDD KOG1172 KOG1172 229115 KOG1172 KOG1172, Na+-independent Cl/HCO3 exchanger AE1 and related transporters (SLC4 family) [Inorganic ion transport and metabolism] 876 matched cddid_all.tbl CDD KOG1173 KOG1173 229116 KOG1173 KOG1173, Anaphase-promoting complex (APC), Cdc16 subunit [Cell cycle control, cell division, chromosome partitioning, Posttranslational modification, protein turnover, chaperones] 611 matched cddid_all.tbl CDD KOG1174 KOG1174 229117 KOG1174 KOG1174, Anaphase-promoting complex (APC), subunit 7 [Cell cycle control, cell division, chromosome partitioning, Posttranslational modification, protein turnover, chaperones] 564 matched cddid_all.tbl CDD KOG1175 KOG1175 229118 KOG1175 KOG1175, Acyl-CoA synthetase [Lipid transport and metabolism] 626 matched cddid_all.tbl CDD KOG1176 KOG1176 229119 KOG1176 KOG1176, Acyl-CoA synthetase [Lipid transport and metabolism] 537 matched cddid_all.tbl CDD KOG1177 KOG1177 229120 KOG1177 KOG1177, Long chain fatty acid acyl-CoA ligase [Lipid transport and metabolism] 596 matched cddid_all.tbl CDD KOG1178 KOG1178 229121 KOG1178 KOG1178, Non-ribosomal peptide synthetase/alpha-aminoadipate reductase and related enzymes [Secondary metabolites biosynthesis, transport and catabolism] 1032 matched cddid_all.tbl CDD KOG1179 KOG1179 229122 KOG1179 KOG1179, Very long-chain acyl-CoA synthetase/fatty acid transporter [Lipid transport and metabolism] 649 matched cddid_all.tbl CDD KOG1180 KOG1180 229123 KOG1180 KOG1180, Acyl-CoA synthetase [Lipid transport and metabolism] 678 matched cddid_all.tbl CDD KOG1182 KOG1182 229124 KOG1182 KOG1182, Branched chain alpha-keto acid dehydrogenase complex, alpha subunit [Energy production and conversion] 432 matched cddid_all.tbl CDD KOG1183 KOG1183 229125 KOG1183 KOG1183, N-acetylglucosaminyltransferase complex, subunit PIG-Q/GPI1, required for phosphatidylinositol biosynthesis [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones] 623 matched cddid_all.tbl CDD KOG1184 KOG1184 229126 KOG1184 KOG1184, Thiamine pyrophosphate-requiring enzyme [Amino acid transport and metabolism, Coenzyme transport and metabolism] 561 matched cddid_all.tbl CDD KOG1185 KOG1185 229127 KOG1185 KOG1185, Thiamine pyrophosphate-requiring enzyme [Amino acid transport and metabolism, Coenzyme transport and metabolism] 571 matched cddid_all.tbl CDD KOG1186 KOG1186 229128 KOG1186 KOG1186, Copper amine oxidase [Secondary metabolites biosynthesis, transport and catabolism] 670 matched cddid_all.tbl CDD KOG1187 KOG1187 229129 KOG1187 KOG1187, Serine/threonine protein kinase [Signal transduction mechanisms] 361 matched cddid_all.tbl CDD KOG1188 KOG1188 229130 KOG1188 KOG1188, WD40 repeat protein [General function prediction only] 376 matched cddid_all.tbl CDD KOG1189 KOG1189 229131 KOG1189 KOG1189, Global transcriptional regulator, cell division control protein [Amino acid transport and metabolism] 960 matched cddid_all.tbl CDD KOG1190 KOG1190 229132 KOG1190 KOG1190, Polypyrimidine tract-binding protein [RNA processing and modification] 492 matched cddid_all.tbl CDD KOG1191 KOG1191 229133 KOG1191 KOG1191, Mitochondrial GTPase [Translation, ribosomal structure and biogenesis] 531 matched cddid_all.tbl CDD KOG1192 KOG1192 229134 KOG1192 KOG1192, UDP-glucuronosyl and UDP-glucosyl transferase [Carbohydrate transport and metabolism, Energy production and conversion] 304 matched cddid_all.tbl CDD KOG1193 KOG1193 229135 KOG1193 KOG1193, Arginyl-tRNA-protein transferase [Posttranslational modification, protein turnover, chaperones] 511 matched cddid_all.tbl CDD KOG1194 KOG1194 229136 KOG1194 KOG1194, Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription] 534 matched cddid_all.tbl CDD KOG1195 KOG1195 229137 KOG1195 KOG1195, Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 567 matched cddid_all.tbl CDD KOG1196 KOG1196 229138 KOG1196 KOG1196, Predicted NAD-dependent oxidoreductase [General function prediction only] 343 matched cddid_all.tbl CDD KOG1197 KOG1197 229139 KOG1197 KOG1197, Predicted quinone oxidoreductase [Energy production and conversion, General function prediction only] 336 matched cddid_all.tbl CDD KOG1198 KOG1198 229140 KOG1198 KOG1198, Zinc-binding oxidoreductase [Energy production and conversion, General function prediction only] 347 matched cddid_all.tbl CDD KOG1199 KOG1199 229141 KOG1199 KOG1199, Short-chain alcohol dehydrogenase/3-hydroxyacyl-CoA dehydrogenase [Secondary metabolites biosynthesis, transport and catabolism] 260 matched cddid_all.tbl CDD KOG1200 KOG1200 229142 KOG1200 KOG1200, Mitochondrial/plastidial beta-ketoacyl-ACP reductase [Lipid transport and metabolism] 256 matched cddid_all.tbl CDD KOG1201 KOG1201 229143 KOG1201 KOG1201, Hydroxysteroid 17-beta dehydrogenase 11 [Secondary metabolites biosynthesis, transport and catabolism] 300 matched cddid_all.tbl CDD KOG1202 KOG1202 229144 KOG1202 KOG1202, Animal-type fatty acid synthase and related proteins [Lipid transport and metabolism] 2376 matched cddid_all.tbl CDD KOG1203 KOG1203 229145 KOG1203 KOG1203, Predicted dehydrogenase [Carbohydrate transport and metabolism] 411 matched cddid_all.tbl CDD KOG1204 KOG1204 229146 KOG1204 KOG1204, Predicted dehydrogenase [Secondary metabolites biosynthesis, transport and catabolism] 253 matched cddid_all.tbl CDD KOG1205 KOG1205 229147 KOG1205 KOG1205, Predicted dehydrogenase [Secondary metabolites biosynthesis, transport and catabolism] 282 matched cddid_all.tbl CDD KOG1206 KOG1206 229148 KOG1206 KOG1206, Peroxisomal multifunctional beta-oxidation protein and related enzymes [Lipid transport and metabolism] 272 matched cddid_all.tbl CDD KOG1207 KOG1207 229149 KOG1207 KOG1207, Diacetyl reductase/L-xylulose reductase [Secondary metabolites biosynthesis, transport and catabolism] 245 matched cddid_all.tbl CDD KOG1208 KOG1208 229150 KOG1208 KOG1208, Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases) [Secondary metabolites biosynthesis, transport and catabolism] 314 matched cddid_all.tbl CDD KOG1209 KOG1209 229151 KOG1209 KOG1209, 1-Acyl dihydroxyacetone phosphate reductase and related dehydrogenases [Secondary metabolites biosynthesis, transport and catabolism] 289 matched cddid_all.tbl CDD KOG1210 KOG1210 229152 KOG1210 KOG1210, Predicted 3-ketosphinganine reductase [Secondary metabolites biosynthesis, transport and catabolism] 331 matched cddid_all.tbl CDD KOG1211 KOG1211 229153 KOG1211 KOG1211, Amidases [Translation, ribosomal structure and biogenesis] 506 matched cddid_all.tbl CDD KOG1212 KOG1212 229154 KOG1212 KOG1212, Amidases [Translation, ribosomal structure and biogenesis, Lipid transport and metabolism, Signal transduction mechanisms] 560 matched cddid_all.tbl CDD KOG1213 KOG1213 229155 KOG1213 KOG1213, Sister chromatid cohesion complex Cohesin, subunit RAD21/SCC1 [Cell cycle control, cell division, chromosome partitioning] 614 matched cddid_all.tbl CDD KOG1214 KOG1214 229156 KOG1214 KOG1214, Nidogen and related basement membrane protein proteins [Cell wall/membrane/envelope biogenesis, Extracellular structures] 1289 matched cddid_all.tbl CDD KOG1215 KOG1215 229157 KOG1215 KOG1215, Low-density lipoprotein receptors containing Ca2+-binding EGF-like domains [Signal transduction mechanisms] 877 matched cddid_all.tbl CDD KOG1216 KOG1216 229158 KOG1216 KOG1216, von Willebrand factor and related coagulation proteins [Extracellular structures, Defense mechanisms] 553 matched cddid_all.tbl CDD KOG1217 KOG1217 229159 KOG1217 KOG1217, Fibrillins and related proteins containing Ca2+-binding EGF-like domains [Signal transduction mechanisms] 487 matched cddid_all.tbl CDD KOG1218 KOG1218 229160 KOG1218 KOG1218, Proteins containing Ca2+-binding EGF-like domains [Signal transduction mechanisms] 316 matched cddid_all.tbl CDD KOG1219 KOG1219 229161 KOG1219 KOG1219, Uncharacterized conserved protein, contains laminin, cadherin and EGF domains [Signal transduction mechanisms] 4289 matched cddid_all.tbl CDD KOG1220 KOG1220 229162 KOG1220 KOG1220, Phosphoglucomutase/phosphomannomutase [Carbohydrate transport and metabolism] 607 matched cddid_all.tbl CDD KOG1221 KOG1221 229163 KOG1221 KOG1221, Acyl-CoA reductase [Lipid transport and metabolism] 411 matched cddid_all.tbl CDD KOG1222 KOG1222 229164 KOG1222 KOG1222, Kinesin associated protein KAP [Intracellular trafficking, secretion, and vesicular transport] 791 matched cddid_all.tbl CDD KOG1223 KOG1223 229165 KOG1223 KOG1223, Isochorismate synthase [Amino acid transport and metabolism] 508 matched cddid_all.tbl CDD KOG1224 KOG1224 229166 KOG1224 KOG1224, Para-aminobenzoate (PABA) synthase ABZ1 [Translation, ribosomal structure and biogenesis] 767 matched cddid_all.tbl CDD KOG1225 KOG1225 229167 KOG1225 KOG1225, Teneurin-1 and related extracellular matrix proteins, contain EGF-like repeats [Signal transduction mechanisms, Extracellular structures] 525 matched cddid_all.tbl CDD KOG1226 KOG1226 229168 KOG1226 KOG1226, Integrin beta subunit (N-terminal portion of extracellular region) [Signal transduction mechanisms, Extracellular structures] 783 matched cddid_all.tbl CDD KOG1227 KOG1227 229169 KOG1227 KOG1227, Putative methyltransferase [General function prediction only] 351 matched cddid_all.tbl CDD KOG1228 KOG1228 229170 KOG1228 KOG1228, Uncharacterized conserved protein [Function unknown] 256 matched cddid_all.tbl CDD KOG1229 KOG1229 229171 KOG1229 KOG1229, 3'5'-cyclic nucleotide phosphodiesterases [Signal transduction mechanisms] 775 matched cddid_all.tbl CDD KOG1230 KOG1230 229172 KOG1230 KOG1230, Protein containing repeated kelch motifs [General function prediction only] 521 matched cddid_all.tbl CDD KOG1231 KOG1231 229173 KOG1231 KOG1231, Proteins containing the FAD binding domain [Energy production and conversion] 505 matched cddid_all.tbl CDD KOG1232 KOG1232 229174 KOG1232 KOG1232, Proteins containing the FAD binding domain [Energy production and conversion] 511 matched cddid_all.tbl CDD KOG1233 KOG1233 229175 KOG1233 KOG1233, Alkyl-dihydroxyacetonephosphate synthase [General function prediction only] 613 matched cddid_all.tbl CDD KOG1234 KOG1234 229176 KOG1234 KOG1234, ABC (ATP binding cassette) 1 protein [General function prediction only] 363 matched cddid_all.tbl CDD KOG1235 KOG1235 229177 KOG1235 KOG1235, Predicted unusual protein kinase [General function prediction only] 538 matched cddid_all.tbl CDD KOG1236 KOG1236 229178 KOG1236 KOG1236, Predicted unusual protein kinase [General function prediction only] 565 matched cddid_all.tbl CDD KOG1237 KOG1237 229179 KOG1237 KOG1237, H+/oligopeptide symporter [Amino acid transport and metabolism] 571 matched cddid_all.tbl CDD KOG1238 KOG1238 229180 KOG1238 KOG1238, Glucose dehydrogenase/choline dehydrogenase/mandelonitrile lyase (GMC oxidoreductase family) [General function prediction only] 623 matched cddid_all.tbl CDD KOG1239 KOG1239 229181 KOG1239 KOG1239, Inner membrane protein translocase involved in respiratory chain assembly [Posttranslational modification, protein turnover, chaperones, Intracellular trafficking, secretion, and vesicular transport] 372 matched cddid_all.tbl CDD KOG1240 KOG1240 229182 KOG1240 KOG1240, Protein kinase containing WD40 repeats [Signal transduction mechanisms] 1431 matched cddid_all.tbl CDD KOG1241 KOG1241 229183 KOG1241 KOG1241, Karyopherin (importin) beta 1 [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 859 matched cddid_all.tbl CDD KOG1242 KOG1242 229184 KOG1242 KOG1242, Protein containing adaptin N-terminal region [Translation, ribosomal structure and biogenesis] 569 matched cddid_all.tbl CDD KOG1243 KOG1243 229185 KOG1243 KOG1243, Protein kinase [General function prediction only] 690 matched cddid_all.tbl CDD KOG1244 KOG1244 229186 KOG1244 KOG1244, Predicted transcription factor Requiem/NEURO-D4 [Transcription] 336 matched cddid_all.tbl CDD KOG1245 KOG1245 229187 KOG1245 KOG1245, Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics] 1404 matched cddid_all.tbl CDD KOG1246 KOG1246 229188 KOG1246 KOG1246, DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only] 904 matched cddid_all.tbl CDD KOG1247 KOG1247 229189 KOG1247 KOG1247, Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 567 matched cddid_all.tbl CDD KOG1248 KOG1248 229190 KOG1248 KOG1248, Uncharacterized conserved protein [Function unknown] 1176 matched cddid_all.tbl CDD KOG1249 KOG1249 229191 KOG1249 KOG1249, Predicted GTPases [General function prediction only] 572 matched cddid_all.tbl CDD KOG1250 KOG1250 229192 KOG1250 KOG1250, Threonine/serine dehydratases [Amino acid transport and metabolism] 457 matched cddid_all.tbl CDD KOG1251 KOG1251 229193 KOG1251 KOG1251, Serine racemase [Signal transduction mechanisms, Amino acid transport and metabolism] 323 matched cddid_all.tbl CDD KOG1252 KOG1252 229194 KOG1252 KOG1252, Cystathionine beta-synthase and related enzymes [Amino acid transport and metabolism] 362 matched cddid_all.tbl CDD KOG1253 KOG1253 229195 KOG1253 KOG1253, tRNA methyltransferase [Translation, ribosomal structure and biogenesis] 525 matched cddid_all.tbl CDD KOG1254 KOG1254 229196 KOG1254 KOG1254, ATP-citrate lyase [Energy production and conversion] 600 matched cddid_all.tbl CDD KOG1255 KOG1255 229197 KOG1255 KOG1255, Succinyl-CoA synthetase, alpha subunit [Energy production and conversion] 329 matched cddid_all.tbl CDD KOG1256 KOG1256 229198 KOG1256 KOG1256, Long-chain acyl-CoA synthetases (AMP-forming) [Lipid transport and metabolism] 691 matched cddid_all.tbl CDD KOG1257 KOG1257 229199 KOG1257 KOG1257, NADP+-dependent malic enzyme [Energy production and conversion] 582 matched cddid_all.tbl CDD KOG1258 KOG1258 229200 KOG1258 KOG1258, mRNA processing protein [RNA processing and modification] 577 matched cddid_all.tbl CDD KOG1259 KOG1259 229201 KOG1259 KOG1259, Nischarin, modulator of integrin alpha5 subunit action [Signal transduction mechanisms, Cytoskeleton] 490 matched cddid_all.tbl CDD KOG1260 KOG1260 229202 KOG1260 KOG1260, Isocitrate lyase [Energy production and conversion] 492 matched cddid_all.tbl CDD KOG1261 KOG1261 229203 KOG1261 KOG1261, Malate synthase [Energy production and conversion] 552 matched cddid_all.tbl CDD KOG1262 KOG1262 229204 KOG1262 KOG1262, FAD-binding protein DIMINUTO [General function prediction only] 543 matched cddid_all.tbl CDD KOG1263 KOG1263 229205 KOG1263 KOG1263, Multicopper oxidases [Secondary metabolites biosynthesis, transport and catabolism] 563 matched cddid_all.tbl CDD KOG1264 KOG1264 229206 KOG1264 KOG1264, Phospholipase C [Lipid transport and metabolism] 1267 matched cddid_all.tbl CDD KOG1265 KOG1265 229207 KOG1265 KOG1265, Phospholipase C [Lipid transport and metabolism] 1189 matched cddid_all.tbl CDD KOG1266 KOG1266 229208 KOG1266 KOG1266, Protein kinase [Signal transduction mechanisms] 458 matched cddid_all.tbl CDD KOG1267 KOG1267 229209 KOG1267 KOG1267, Mitochondrial transcription termination factor, mTERF [Transcription, General function prediction only] 413 matched cddid_all.tbl CDD KOG1268 KOG1268 229210 KOG1268 KOG1268, Glucosamine 6-phosphate synthetases, contain amidotransferase and phosphosugar isomerase domains [Cell wall/membrane/envelope biogenesis] 670 matched cddid_all.tbl CDD KOG1269 KOG1269 229211 KOG1269 KOG1269, SAM-dependent methyltransferases [Lipid transport and metabolism, General function prediction only] 364 matched cddid_all.tbl CDD KOG1270 KOG1270 229212 KOG1270 KOG1270, Methyltransferases [Coenzyme transport and metabolism] 282 matched cddid_all.tbl CDD KOG1271 KOG1271 229213 KOG1271 KOG1271, Methyltransferases [General function prediction only] 227 matched cddid_all.tbl CDD KOG1272 KOG1272 229214 KOG1272 KOG1272, WD40-repeat-containing subunit of the 18S rRNA processing complex [RNA processing and modification] 545 matched cddid_all.tbl CDD KOG1273 KOG1273 229215 KOG1273 KOG1273, WD40 repeat protein [General function prediction only] 405 matched cddid_all.tbl CDD KOG1274 KOG1274 229216 KOG1274 KOG1274, WD40 repeat protein [General function prediction only] 933 matched cddid_all.tbl CDD KOG1275 KOG1275 229217 KOG1275 KOG1275, PAB-dependent poly(A) ribonuclease, subunit PAN2 [Replication, recombination and repair] 1118 matched cddid_all.tbl CDD KOG1276 KOG1276 229218 KOG1276 KOG1276, Protoporphyrinogen oxidase [Coenzyme transport and metabolism] 491 matched cddid_all.tbl CDD KOG1277 KOG1277 229219 KOG1277 KOG1277, Endosomal membrane proteins, EMP70 [Intracellular trafficking, secretion, and vesicular transport] 593 matched cddid_all.tbl CDD KOG1278 KOG1278 229220 KOG1278 KOG1278, Endosomal membrane proteins, EMP70 [Intracellular trafficking, secretion, and vesicular transport] 628 matched cddid_all.tbl CDD KOG1279 KOG1279 229221 KOG1279 KOG1279, Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics] 506 matched cddid_all.tbl CDD KOG1280 KOG1280 229222 KOG1280 KOG1280, Uncharacterized conserved protein containing ZZ-type Zn-finger [General function prediction only] 381 matched cddid_all.tbl CDD KOG1281 KOG1281 229223 KOG1281 KOG1281, Na+/dicarboxylate, Na+/tricarboxylate and phosphate transporters [Inorganic ion transport and metabolism] 586 matched cddid_all.tbl CDD KOG1282 KOG1282 229224 KOG1282 KOG1282, Serine carboxypeptidases (lysosomal cathepsin A) [Amino acid transport and metabolism, Posttranslational modification, protein turnover, chaperones] 454 matched cddid_all.tbl CDD KOG1283 KOG1283 229225 KOG1283 KOG1283, Serine carboxypeptidases [Posttranslational modification, protein turnover, chaperones] 414 matched cddid_all.tbl CDD KOG1284 KOG1284 229226 KOG1284 KOG1284, Bifunctional GTP cyclohydrolase II/3,4-dihydroxy-2butanone-4-phosphate synthase [Coenzyme transport and metabolism] 357 matched cddid_all.tbl CDD KOG1285 KOG1285 229227 KOG1285 KOG1285, Beta, beta-carotene 15,15'-dioxygenase and related enzymes [Secondary metabolites biosynthesis, transport and catabolism] 582 matched cddid_all.tbl CDD KOG1286 KOG1286 229228 KOG1286 KOG1286, Amino acid transporters [Amino acid transport and metabolism] 554 matched cddid_all.tbl CDD KOG1287 KOG1287 229229 KOG1287 KOG1287, Amino acid transporters [Amino acid transport and metabolism] 479 matched cddid_all.tbl CDD KOG1288 KOG1288 229230 KOG1288 KOG1288, Amino acid transporters [Amino acid transport and metabolism] 945 matched cddid_all.tbl CDD KOG1289 KOG1289 229231 KOG1289 KOG1289, Amino acid transporters [Amino acid transport and metabolism] 550 matched cddid_all.tbl CDD KOG1290 KOG1290 229232 KOG1290 KOG1290, Serine/threonine protein kinase [Signal transduction mechanisms] 590 matched cddid_all.tbl CDD KOG1291 KOG1291 229233 KOG1291 KOG1291, Mn2+ and Fe2+ transporters of the NRAMP family [Inorganic ion transport and metabolism] 503 matched cddid_all.tbl CDD KOG1292 KOG1292 229234 KOG1292 KOG1292, Xanthine/uracil transporters [Nucleotide transport and metabolism] 510 matched cddid_all.tbl CDD KOG1293 KOG1293 229235 KOG1293 KOG1293, Proteins containing armadillo/beta-catenin-like repeat [General function prediction only] 678 matched cddid_all.tbl CDD KOG1294 KOG1294 229236 KOG1294 KOG1294, Apurinic/apyrimidinic endonuclease and related enzymes [Replication, recombination and repair] 335 matched cddid_all.tbl CDD KOG1295 KOG1295 229237 KOG1295 KOG1295, Nonsense-mediated decay protein Upf3 [RNA processing and modification] 376 matched cddid_all.tbl CDD KOG1296 KOG1296 229238 KOG1296 KOG1296, Uncharacterized conserved protein [Function unknown] 161 matched cddid_all.tbl CDD KOG1297 KOG1297 229239 KOG1297 KOG1297, Uncharacterized conserved protein [Function unknown] 249 matched cddid_all.tbl CDD KOG1298 KOG1298 229240 KOG1298 KOG1298, Squalene monooxygenase [Lipid transport and metabolism] 509 matched cddid_all.tbl CDD KOG1299 KOG1299 229241 KOG1299 KOG1299, Vacuolar sorting protein VPS45/Stt10 (Sec1 family) [Intracellular trafficking, secretion, and vesicular transport] 549 matched cddid_all.tbl CDD KOG1300 KOG1300 229242 KOG1300 KOG1300, Vesicle trafficking protein Sec1 [Intracellular trafficking, secretion, and vesicular transport] 593 matched cddid_all.tbl CDD KOG1301 KOG1301 229243 KOG1301 KOG1301, Vesicle trafficking protein Sly1 (Sec1 family) [Intracellular trafficking, secretion, and vesicular transport] 621 matched cddid_all.tbl CDD KOG1302 KOG1302 229244 KOG1302 KOG1302, Vacuolar sorting protein VPS33/slp1 (Sec1 family) [Intracellular trafficking, secretion, and vesicular transport] 600 matched cddid_all.tbl CDD KOG1303 KOG1303 229245 KOG1303 KOG1303, Amino acid transporters [Amino acid transport and metabolism] 437 matched cddid_all.tbl CDD KOG1304 KOG1304 229246 KOG1304 KOG1304, Amino acid transporters [Amino acid transport and metabolism] 449 matched cddid_all.tbl CDD KOG1305 KOG1305 229247 KOG1305 KOG1305, Amino acid transporter protein [Amino acid transport and metabolism] 411 matched cddid_all.tbl CDD KOG1306 KOG1306 229248 KOG1306 KOG1306, Ca2+/Na+ exchanger NCX1 and related proteins [Inorganic ion transport and metabolism, Signal transduction mechanisms] 596 matched cddid_all.tbl CDD KOG1307 KOG1307 229249 KOG1307 KOG1307, K+-dependent Ca2+/Na+ exchanger NCKX1 and related proteins [Inorganic ion transport and metabolism, Signal transduction mechanisms] 588 matched cddid_all.tbl CDD KOG1308 KOG1308 229250 KOG1308 KOG1308, Hsp70-interacting protein Hip/Transient component of progesterone receptor complexes and an Hsp70-binding protein [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms] 377 matched cddid_all.tbl CDD KOG1309 KOG1309 229251 KOG1309 KOG1309, Suppressor of G2 allele of skp1 [Signal transduction mechanisms] 196 matched cddid_all.tbl CDD KOG1310 KOG1310 229252 KOG1310 KOG1310, WD40 repeat protein [General function prediction only] 758 matched cddid_all.tbl CDD KOG1311 KOG1311 229253 KOG1311 KOG1311, DHHC-type Zn-finger proteins [General function prediction only] 251 matched cddid_all.tbl CDD KOG1312 KOG1312 229254 KOG1312 KOG1312, DHHC-type Zn-finger proteins [General function prediction only] 341 matched cddid_all.tbl CDD KOG1313 KOG1313 229255 KOG1313 KOG1313, DHHC-type Zn-finger proteins [General function prediction only] 309 matched cddid_all.tbl CDD KOG1314 KOG1314 229256 KOG1314 KOG1314, DHHC-type Zn-finger protein [General function prediction only] 414 matched cddid_all.tbl CDD KOG1315 KOG1315 229257 KOG1315 KOG1315, Predicted DHHC-type Zn-finger protein [General function prediction only] 307 matched cddid_all.tbl CDD KOG1316 KOG1316 229258 KOG1316 KOG1316, Argininosuccinate lyase [Amino acid transport and metabolism] 464 matched cddid_all.tbl CDD KOG1317 KOG1317 229259 KOG1317 KOG1317, Fumarase [Energy production and conversion] 487 matched cddid_all.tbl CDD KOG1318 KOG1318 229260 KOG1318 KOG1318, Helix loop helix transcription factor EB [Transcription] 411 matched cddid_all.tbl CDD KOG1319 KOG1319 229261 KOG1319 KOG1319, bHLHZip transcription factor BIGMAX [Transcription] 229 matched cddid_all.tbl CDD KOG1320 KOG1320 229262 KOG1320 KOG1320, Serine protease [Posttranslational modification, protein turnover, chaperones] 473 matched cddid_all.tbl CDD KOG1321 KOG1321 229263 KOG1321 KOG1321, Protoheme ferro-lyase (ferrochelatase) [Coenzyme transport and metabolism] 395 matched cddid_all.tbl CDD KOG1322 KOG1322 229264 KOG1322 KOG1322, GDP-mannose pyrophosphorylase/mannose-1-phosphate guanylyltransferase [Cell wall/membrane/envelope biogenesis] 371 matched cddid_all.tbl CDD KOG1323 KOG1323 229265 KOG1323 KOG1323, Serine/threonine phosphatase [Signal transduction mechanisms] 493 matched cddid_all.tbl CDD KOG1324 KOG1324 229266 KOG1324 KOG1324, Dihydrofolate reductase [Coenzyme transport and metabolism] 190 matched cddid_all.tbl CDD KOG1325 KOG1325 229267 KOG1325 KOG1325, Lysophospholipase [Lipid transport and metabolism] 571 matched cddid_all.tbl CDD KOG1326 KOG1326 229268 KOG1326 KOG1326, Membrane-associated protein FER-1 and related ferlins, contain multiple C2 domains [Cell wall/membrane/envelope biogenesis] 1105 matched cddid_all.tbl CDD KOG1327 KOG1327 229269 KOG1327 KOG1327, Copine [Signal transduction mechanisms] 529 matched cddid_all.tbl CDD KOG1328 KOG1328 229270 KOG1328 KOG1328, Synaptic vesicle protein BAIAP3, involved in vesicle priming/regulation [Intracellular trafficking, secretion, and vesicular transport, Signal transduction mechanisms] 1103 matched cddid_all.tbl CDD KOG1329 KOG1329 229271 KOG1329 KOG1329, Phospholipase D1 [Lipid transport and metabolism] 887 matched cddid_all.tbl CDD KOG1330 KOG1330 229272 KOG1330 KOG1330, Sugar transporter/spinster transmembrane protein [Carbohydrate transport and metabolism] 493 matched cddid_all.tbl CDD KOG1331 KOG1331 229273 KOG1331 KOG1331, Predicted methyltransferase [General function prediction only] 293 matched cddid_all.tbl CDD KOG1332 KOG1332 229274 KOG1332 KOG1332, Vesicle coat complex COPII, subunit SEC13 [Intracellular trafficking, secretion, and vesicular transport] 299 matched cddid_all.tbl CDD KOG1333 KOG1333 229275 KOG1333 KOG1333, Uncharacterized conserved protein [Function unknown] 241 matched cddid_all.tbl CDD KOG1334 KOG1334 229276 KOG1334 KOG1334, WD40 repeat protein [General function prediction only] 559 matched cddid_all.tbl CDD KOG1335 KOG1335 229277 KOG1335 KOG1335, Dihydrolipoamide dehydrogenase [Energy production and conversion] 506 matched cddid_all.tbl CDD KOG1336 KOG1336 229278 KOG1336 KOG1336, Monodehydroascorbate/ferredoxin reductase [General function prediction only] 478 matched cddid_all.tbl CDD KOG1337 KOG1337 229279 KOG1337 KOG1337, N-methyltransferase [General function prediction only] 472 matched cddid_all.tbl CDD KOG1338 KOG1338 229280 KOG1338 KOG1338, Uncharacterized conserved protein [Function unknown] 466 matched cddid_all.tbl CDD KOG1339 KOG1339 229281 KOG1339 KOG1339, Aspartyl protease [Posttranslational modification, protein turnover, chaperones] 398 matched cddid_all.tbl CDD KOG1340 KOG1340 229282 KOG1340 KOG1340, Prosaposin [Lipid transport and metabolism, Carbohydrate transport and metabolism] 218 matched cddid_all.tbl CDD KOG1341 KOG1341 229283 KOG1341 KOG1341, Na+/K+ transporter [Inorganic ion transport and metabolism] 854 matched cddid_all.tbl CDD KOG1342 KOG1342 229284 KOG1342 KOG1342, Histone deacetylase complex, catalytic component RPD3 [Chromatin structure and dynamics] 425 matched cddid_all.tbl CDD KOG1343 KOG1343 229285 KOG1343 KOG1343, Histone deacetylase complex, catalytic component HDA1 [Chromatin structure and dynamics] 797 matched cddid_all.tbl CDD KOG1344 KOG1344 229286 KOG1344 KOG1344, Predicted histone deacetylase [Chromatin structure and dynamics] 324 matched cddid_all.tbl CDD KOG1345 KOG1345 229287 KOG1345 KOG1345, Serine/threonine kinase [Signal transduction mechanisms] 378 matched cddid_all.tbl CDD KOG1346 KOG1346 229288 KOG1346 KOG1346, Programmed cell death 8 (apoptosis-inducing factor) [Signal transduction mechanisms] 659 matched cddid_all.tbl CDD KOG1347 KOG1347 229289 KOG1347 KOG1347, Uncharacterized membrane protein, predicted efflux pump [General function prediction only] 473 matched cddid_all.tbl CDD KOG1348 KOG1348 229290 KOG1348 KOG1348, Asparaginyl peptidases [Posttranslational modification, protein turnover, chaperones] 477 matched cddid_all.tbl CDD KOG1349 KOG1349 229291 KOG1349 KOG1349, Gpi-anchor transamidase [Posttranslational modification, protein turnover, chaperones] 309 matched cddid_all.tbl CDD KOG1350 KOG1350 229292 KOG1350 KOG1350, F0F1-type ATP synthase, beta subunit [Energy production and conversion] 521 matched cddid_all.tbl CDD KOG1351 KOG1351 229293 KOG1351 KOG1351, Vacuolar H+-ATPase V1 sector, subunit B [Energy production and conversion] 489 matched cddid_all.tbl CDD KOG1352 KOG1352 229294 KOG1352 KOG1352, Vacuolar H+-ATPase V1 sector, subunit A [Energy production and conversion] 618 matched cddid_all.tbl CDD KOG1353 KOG1353 229295 KOG1353 KOG1353, F0F1-type ATP synthase, alpha subunit [Energy production and conversion] 340 matched cddid_all.tbl CDD KOG1354 KOG1354 229296 KOG1354 KOG1354, Serine/threonine protein phosphatase 2A, regulatory subunit [Signal transduction mechanisms] 433 matched cddid_all.tbl CDD KOG1355 KOG1355 229297 KOG1355 KOG1355, Adenylosuccinate synthase [Nucleotide transport and metabolism] 455 matched cddid_all.tbl CDD KOG1356 KOG1356 229298 KOG1356 KOG1356, Putative transcription factor 5qNCA, contains JmjC domain [Transcription] 889 matched cddid_all.tbl CDD KOG1357 KOG1357 229299 KOG1357 KOG1357, Serine palmitoyltransferase [Posttranslational modification, protein turnover, chaperones] 519 matched cddid_all.tbl CDD KOG1358 KOG1358 229300 KOG1358 KOG1358, Serine palmitoyltransferase [Posttranslational modification, protein turnover, chaperones] 467 matched cddid_all.tbl CDD KOG1359 KOG1359 229301 KOG1359 KOG1359, Glycine C-acetyltransferase/2-amino-3-ketobutyrate-CoA ligase [Amino acid transport and metabolism] 417 matched cddid_all.tbl CDD KOG1360 KOG1360 229302 KOG1360 KOG1360, 5-aminolevulinate synthase [Coenzyme transport and metabolism] 570 matched cddid_all.tbl CDD KOG1361 KOG1361 229303 KOG1361 KOG1361, Predicted hydrolase involved in interstrand cross-link repair [Replication, recombination and repair] 481 matched cddid_all.tbl CDD KOG1362 KOG1362 229304 KOG1362 KOG1362, Choline transporter-like protein [Lipid transport and metabolism] 577 matched cddid_all.tbl CDD KOG1363 KOG1363 229305 KOG1363 KOG1363, Predicted regulator of the ubiquitin pathway (contains UAS and UBX domains) [Signal transduction mechanisms] 460 matched cddid_all.tbl CDD KOG1364 KOG1364 229306 KOG1364 KOG1364, Predicted ubiquitin regulatory protein, contains UAS and UBX domains [Posttranslational modification, protein turnover, chaperones] 356 matched cddid_all.tbl CDD KOG1365 KOG1365 229307 KOG1365 KOG1365, RNA-binding protein Fusilli, contains RRM domain [RNA processing and modification, General function prediction only] 508 matched cddid_all.tbl CDD KOG1366 KOG1366 229308 KOG1366 KOG1366, Alpha-macroglobulin [Posttranslational modification, protein turnover, chaperones] 1436 matched cddid_all.tbl CDD KOG1367 KOG1367 229309 KOG1367 KOG1367, 3-phosphoglycerate kinase [Carbohydrate transport and metabolism] 416 matched cddid_all.tbl CDD KOG1368 KOG1368 229310 KOG1368 KOG1368, Threonine aldolase [Amino acid transport and metabolism] 384 matched cddid_all.tbl CDD KOG1369 KOG1369 229311 KOG1369 KOG1369, Hexokinase [Carbohydrate transport and metabolism] 474 matched cddid_all.tbl CDD KOG1370 KOG1370 229312 KOG1370 KOG1370, S-adenosylhomocysteine hydrolase [Coenzyme transport and metabolism] 434 matched cddid_all.tbl CDD KOG1371 KOG1371 229313 KOG1371 KOG1371, UDP-glucose 4-epimerase/UDP-sulfoquinovose synthase [Cell wall/membrane/envelope biogenesis] 343 matched cddid_all.tbl CDD KOG1372 KOG1372 229314 KOG1372 KOG1372, GDP-mannose 4,6 dehydratase [Carbohydrate transport and metabolism] 376 matched cddid_all.tbl CDD KOG1373 KOG1373 229315 KOG1373 KOG1373, Transport protein Sec61, alpha subunit [Intracellular trafficking, secretion, and vesicular transport, Posttranslational modification, protein turnover, chaperones] 476 matched cddid_all.tbl CDD KOG1374 KOG1374 229316 KOG1374 KOG1374, Gamma tubulin [Cytoskeleton] 448 matched cddid_all.tbl CDD KOG1375 KOG1375 229317 KOG1375 KOG1375, Beta tubulin [Cytoskeleton] 369 matched cddid_all.tbl CDD KOG1376 KOG1376 229318 KOG1376 KOG1376, Alpha tubulin [Cytoskeleton] 407 matched cddid_all.tbl CDD KOG1377 KOG1377 229319 KOG1377 KOG1377, Uridine 5'- monophosphate synthase/orotate phosphoribosyltransferase [Nucleotide transport and metabolism] 261 matched cddid_all.tbl CDD KOG1378 KOG1378 229320 KOG1378 KOG1378, Purple acid phosphatase [Carbohydrate transport and metabolism] 452 matched cddid_all.tbl CDD KOG1379 KOG1379 229321 KOG1379 KOG1379, Serine/threonine protein phosphatase [Signal transduction mechanisms] 330 matched cddid_all.tbl CDD KOG1380 KOG1380 229322 KOG1380 KOG1380, Heme A farnesyltransferase [Coenzyme transport and metabolism] 409 matched cddid_all.tbl CDD KOG1381 KOG1381 229323 KOG1381 KOG1381, Para-hydroxybenzoate-polyprenyl transferase [Coenzyme transport and metabolism] 353 matched cddid_all.tbl CDD KOG1382 KOG1382 229324 KOG1382 KOG1382, Multiple inositol polyphosphate phosphatase [General function prediction only] 467 matched cddid_all.tbl CDD KOG1383 KOG1383 229325 KOG1383 KOG1383, Glutamate decarboxylase/sphingosine phosphate lyase [Amino acid transport and metabolism] 491 matched cddid_all.tbl CDD KOG1384 KOG1384 229326 KOG1384 KOG1384, tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis] 348 matched cddid_all.tbl CDD KOG1385 KOG1385 229327 KOG1385 KOG1385, Nucleoside phosphatase [Nucleotide transport and metabolism] 453 matched cddid_all.tbl CDD KOG1386 KOG1386 229328 KOG1386 KOG1386, Nucleoside phosphatase [Nucleotide transport and metabolism] 501 matched cddid_all.tbl CDD KOG1387 KOG1387 229329 KOG1387 KOG1387, Glycosyltransferase [Cell wall/membrane/envelope biogenesis] 465 matched cddid_all.tbl CDD KOG1388 KOG1388 229330 KOG1388 KOG1388, Attractin and platelet-activating factor acetylhydrolase [Signal transduction mechanisms, Defense mechanisms] 217 matched cddid_all.tbl CDD KOG1389 KOG1389 229331 KOG1389 KOG1389, 3-oxoacyl CoA thiolase [Lipid transport and metabolism] 435 matched cddid_all.tbl CDD KOG1390 KOG1390 229332 KOG1390 KOG1390, Acetyl-CoA acetyltransferase [Lipid transport and metabolism] 396 matched cddid_all.tbl CDD KOG1391 KOG1391 229333 KOG1391 KOG1391, Acetyl-CoA acetyltransferase [Lipid transport and metabolism] 396 matched cddid_all.tbl CDD KOG1392 KOG1392 229334 KOG1392 KOG1392, Acetyl-CoA acetyltransferase [Lipid transport and metabolism] 465 matched cddid_all.tbl CDD KOG1393 KOG1393 229335 KOG1393 KOG1393, Hydroxymethylglutaryl-CoA synthase [Lipid transport and metabolism] 462 matched cddid_all.tbl CDD KOG1394 KOG1394 229336 KOG1394 KOG1394, 3-oxoacyl-(acyl-carrier-protein) synthase (I and II) [Lipid transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism] 440 matched cddid_all.tbl CDD KOG1395 KOG1395 229337 KOG1395 KOG1395, Tryptophan synthase beta chain [Amino acid transport and metabolism] 477 matched cddid_all.tbl CDD KOG1396 KOG1396 229338 KOG1396 KOG1396, Uncharacterized conserved protein [Function unknown] 530 matched cddid_all.tbl CDD KOG1397 KOG1397 229339 KOG1397 KOG1397, Ca2+/H+ antiporter VCX1 and related proteins [Inorganic ion transport and metabolism] 441 matched cddid_all.tbl CDD KOG1398 KOG1398 229340 KOG1398 KOG1398, Uncharacterized conserved protein [Function unknown] 460 matched cddid_all.tbl CDD KOG1399 KOG1399 229341 KOG1399 KOG1399, Flavin-containing monooxygenase [Secondary metabolites biosynthesis, transport and catabolism] 448 matched cddid_all.tbl CDD KOG1400 KOG1400 229342 KOG1400 KOG1400, Predicted ATP-dependent protease PIL, contains LON domain [General function prediction only] 371 matched cddid_all.tbl CDD KOG1401 KOG1401 229343 KOG1401 KOG1401, Acetylornithine aminotransferase [Amino acid transport and metabolism] 433 matched cddid_all.tbl CDD KOG1402 KOG1402 229344 KOG1402 KOG1402, Ornithine aminotransferase [Amino acid transport and metabolism] 427 matched cddid_all.tbl CDD KOG1403 KOG1403 229345 KOG1403 KOG1403, Predicted alanine-glyoxylate aminotransferase [General function prediction only] 452 matched cddid_all.tbl CDD KOG1404 KOG1404 229346 KOG1404 KOG1404, Alanine-glyoxylate aminotransferase AGT2 [Amino acid transport and metabolism] 442 matched cddid_all.tbl CDD KOG1405 KOG1405 229347 KOG1405 KOG1405, 4-aminobutyrate aminotransferase [Amino acid transport and metabolism] 484 matched cddid_all.tbl CDD KOG1406 KOG1406 229348 KOG1406 KOG1406, Peroxisomal 3-ketoacyl-CoA-thiolase P-44/SCP2 [Lipid transport and metabolism] 408 matched cddid_all.tbl CDD KOG1407 KOG1407 229349 KOG1407 KOG1407, WD40 repeat protein [Function unknown] 313 matched cddid_all.tbl CDD KOG1408 KOG1408 229350 KOG1408 KOG1408, WD40 repeat protein [Function unknown] 1080 matched cddid_all.tbl CDD KOG1409 KOG1409 229351 KOG1409 KOG1409, Uncharacterized conserved protein, contains WD40 repeats and FYVE domains [Function unknown] 404 matched cddid_all.tbl CDD KOG1410 KOG1410 229352 KOG1410 KOG1410, Nuclear transport receptor RanBP16 (importin beta superfamily) [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 1082 matched cddid_all.tbl CDD KOG1411 KOG1411 229353 KOG1411 KOG1411, Aspartate aminotransferase/Glutamic oxaloacetic transaminase AAT1/GOT2 [Amino acid transport and metabolism] 427 matched cddid_all.tbl CDD KOG1412 KOG1412 229354 KOG1412 KOG1412, Aspartate aminotransferase/Glutamic oxaloacetic transaminase AAT2/GOT1 [Amino acid transport and metabolism] 410 matched cddid_all.tbl CDD KOG1413 KOG1413 229355 KOG1413 KOG1413, N-acetylglucosaminyltransferase I [Carbohydrate transport and metabolism] 411 matched cddid_all.tbl CDD KOG1414 KOG1414 229356 KOG1414 KOG1414, Transcriptional activator FOSB/c-Fos and related bZIP transcription factors [Transcription] 395 matched cddid_all.tbl CDD KOG1415 KOG1415 229357 KOG1415 KOG1415, Ubiquitin C-terminal hydrolase UCHL1 [Posttranslational modification, protein turnover, chaperones] 222 matched cddid_all.tbl CDD KOG1416 KOG1416 229358 KOG1416 KOG1416, tRNA(1-methyladenosine) methyltransferase, subunit GCD10 [Translation, ribosomal structure and biogenesis] 475 matched cddid_all.tbl CDD KOG1417 KOG1417 229359 KOG1417 KOG1417, Homogentisate 1,2-dioxygenase [Amino acid transport and metabolism] 446 matched cddid_all.tbl CDD KOG1418 KOG1418 229360 KOG1418 KOG1418, Tandem pore domain K+ channel [Inorganic ion transport and metabolism] 433 matched cddid_all.tbl CDD KOG1419 KOG1419 229361 KOG1419 KOG1419, Voltage-gated K+ channel KCNQ [Inorganic ion transport and metabolism] 654 matched cddid_all.tbl CDD KOG1420 KOG1420 229362 KOG1420 KOG1420, Ca2+-activated K+ channel Slowpoke, alpha subunit [Inorganic ion transport and metabolism, Signal transduction mechanisms] 1103 matched cddid_all.tbl CDD KOG1421 KOG1421 229363 KOG1421 KOG1421, Predicted signaling-associated protein (contains a PDZ domain) [General function prediction only] 955 matched cddid_all.tbl CDD KOG1422 KOG1422 229364 KOG1422 KOG1422, Intracellular Cl- channel CLIC, contains GST domain [Inorganic ion transport and metabolism] 221 matched cddid_all.tbl CDD KOG1423 KOG1423 229365 KOG1423 KOG1423, Ras-like GTPase ERA [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms] 379 matched cddid_all.tbl CDD KOG1424 KOG1424 229366 KOG1424 KOG1424, Predicted GTP-binding protein MMR1 [General function prediction only] 562 matched cddid_all.tbl CDD KOG1425 KOG1425 229367 KOG1425 KOG1425, Microfibrillar-associated protein MFAP1 [Cytoskeleton] 430 matched cddid_all.tbl CDD KOG1427 KOG1427 229368 KOG1427 KOG1427, Uncharacterized conserved protein, contains RCC1 domain [Function unknown] 443 matched cddid_all.tbl CDD KOG1428 KOG1428 229369 KOG1428 KOG1428, Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms] 3738 matched cddid_all.tbl CDD KOG1429 KOG1429 229370 KOG1429 KOG1429, dTDP-glucose 4-6-dehydratase/UDP-glucuronic acid decarboxylase [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis] 350 matched cddid_all.tbl CDD KOG1430 KOG1430 229371 KOG1430 KOG1430, C-3 sterol dehydrogenase/3-beta-hydroxysteroid dehydrogenase and related dehydrogenases [Lipid transport and metabolism, Amino acid transport and metabolism] 361 matched cddid_all.tbl CDD KOG1431 KOG1431 229372 KOG1431 KOG1431, GDP-L-fucose synthetase [Carbohydrate transport and metabolism, Posttranslational modification, protein turnover, chaperones] 315 matched cddid_all.tbl CDD KOG1432 KOG1432 229373 KOG1432 KOG1432, Predicted DNA repair exonuclease SIA1 [General function prediction only] 379 matched cddid_all.tbl CDD KOG1433 KOG1433 229374 KOG1433 KOG1433, DNA repair protein RAD51/RHP55 [Replication, recombination and repair] 283 matched cddid_all.tbl CDD KOG1434 KOG1434 229375 KOG1434 KOG1434, Meiotic recombination protein Dmc1 [Energy production and conversion, Replication, recombination and repair] 335 matched cddid_all.tbl CDD KOG1435 KOG1435 229376 KOG1435 KOG1435, Sterol reductase/lamin B receptor [Lipid transport and metabolism, Signal transduction mechanisms] 428 matched cddid_all.tbl CDD KOG1436 KOG1436 229377 KOG1436 KOG1436, Dihydroorotate dehydrogenase [Nucleotide transport and metabolism] 398 matched cddid_all.tbl CDD KOG1437 KOG1437 229378 KOG1437 KOG1437, Fasciclin and related adhesion glycoproteins [Cell wall/membrane/envelope biogenesis, Extracellular structures] 682 matched cddid_all.tbl CDD KOG1438 KOG1438 229379 KOG1438 KOG1438, Anthranilate phosphoribosyltransferase [Amino acid transport and metabolism] 373 matched cddid_all.tbl CDD KOG1439 KOG1439 229380 KOG1439 KOG1439, RAB proteins geranylgeranyltransferase component A (RAB escort protein) [Posttranslational modification, protein turnover, chaperones] 440 matched cddid_all.tbl CDD KOG1440 KOG1440 229381 KOG1440 KOG1440, CDP-diacylglycerol synthase [Lipid transport and metabolism] 432 matched cddid_all.tbl CDD KOG1441 KOG1441 229382 KOG1441 KOG1441, Glucose-6-phosphate/phosphate and phosphoenolpyruvate/phosphate antiporter [Carbohydrate transport and metabolism, Amino acid transport and metabolism] 316 matched cddid_all.tbl CDD KOG1442 KOG1442 229383 KOG1442 KOG1442, GDP-fucose transporter [Carbohydrate transport and metabolism, Posttranslational modification, protein turnover, chaperones, Intracellular trafficking, secretion, and vesicular transport] 347 matched cddid_all.tbl CDD KOG1443 KOG1443 229384 KOG1443 KOG1443, Predicted integral membrane protein [Function unknown] 349 matched cddid_all.tbl CDD KOG1444 KOG1444 229385 KOG1444 KOG1444, Nucleotide-sugar transporter VRG4/SQV-7 [Carbohydrate transport and metabolism, Posttranslational modification, protein turnover, chaperones, Intracellular trafficking, secretion, and vesicular transport] 314 matched cddid_all.tbl CDD KOG1445 KOG1445 229386 KOG1445 KOG1445, Tumor-specific antigen (contains WD repeats) [Cytoskeleton] 1012 matched cddid_all.tbl CDD KOG1446 KOG1446 229387 KOG1446 KOG1446, Histone H3 (Lys4) methyltransferase complex and RNA cleavage factor II complex, subunit SWD2 [RNA processing and modification, Chromatin structure and dynamics, Posttranslational modification, protein turnover, chaperones] 311 matched cddid_all.tbl CDD KOG1447 KOG1447 229388 KOG1447 KOG1447, GTP-specific succinyl-CoA synthetase, beta subunit [Energy production and conversion] 412 matched cddid_all.tbl CDD KOG1448 KOG1448 229389 KOG1448 KOG1448, Ribose-phosphate pyrophosphokinase [Nucleotide transport and metabolism, Amino acid transport and metabolism] 316 matched cddid_all.tbl CDD KOG1449 KOG1449 229390 KOG1449 KOG1449, Predicted Rho GTPase-activating protein CdGAPr [Signal transduction mechanisms] 670 matched cddid_all.tbl CDD KOG1450 KOG1450 229391 KOG1450 KOG1450, Predicted Rho GTPase-activating protein [Signal transduction mechanisms] 650 matched cddid_all.tbl CDD KOG1451 KOG1451 229392 KOG1451 KOG1451, Oligophrenin-1 and related Rho GTPase-activating proteins [Signal transduction mechanisms] 812 matched cddid_all.tbl CDD KOG1452 KOG1452 229393 KOG1452 KOG1452, Predicted Rho GTPase-activating protein [Signal transduction mechanisms] 442 matched cddid_all.tbl CDD KOG1453 KOG1453 229394 KOG1453 KOG1453, Chimaerin and related Rho GTPase activating proteins [Signal transduction mechanisms] 918 matched cddid_all.tbl CDD KOG1454 KOG1454 229395 KOG1454 KOG1454, Predicted hydrolase/acyltransferase (alpha/beta hydrolase superfamily) [General function prediction only] 326 matched cddid_all.tbl CDD KOG1455 KOG1455 229396 KOG1455 KOG1455, Lysophospholipase [Lipid transport and metabolism] 313 matched cddid_all.tbl CDD KOG1456 KOG1456 229397 KOG1456 KOG1456, Heterogeneous nuclear ribonucleoprotein L (contains RRM repeats) [RNA processing and modification] 494 matched cddid_all.tbl CDD KOG1457 KOG1457 229398 KOG1457 KOG1457, RNA binding protein (contains RRM repeats) [General function prediction only] 284 matched cddid_all.tbl CDD KOG1458 KOG1458 229399 KOG1458 KOG1458, Fructose-1,6-bisphosphatase [Carbohydrate transport and metabolism] 343 matched cddid_all.tbl CDD KOG1459 KOG1459 229400 KOG1459 KOG1459, Squalene synthetase [Lipid transport and metabolism] 413 matched cddid_all.tbl CDD KOG1460 KOG1460 229401 KOG1460 KOG1460, GDP-mannose pyrophosphorylase [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones] 407 matched cddid_all.tbl CDD KOG1461 KOG1461 229402 KOG1461 KOG1461, Translation initiation factor 2B, epsilon subunit (eIF-2Bepsilon/GCD6) [Translation, ribosomal structure and biogenesis] 673 matched cddid_all.tbl CDD KOG1462 KOG1462 229403 KOG1462 KOG1462, Translation initiation factor 2B, gamma subunit (eIF-2Bgamma/GCD1) [Translation, ribosomal structure and biogenesis] 433 matched cddid_all.tbl CDD KOG1463 KOG1463 229404 KOG1463 KOG1463, 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones] 411 matched cddid_all.tbl CDD KOG1464 KOG1464 229405 KOG1464 KOG1464, COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms] 440 matched cddid_all.tbl CDD KOG1465 KOG1465 229406 KOG1465 KOG1465, Translation initiation factor 2B, beta subunit (eIF-2Bbeta/GCD7) [Translation, ribosomal structure and biogenesis] 353 matched cddid_all.tbl CDD KOG1466 KOG1466 229407 KOG1466 KOG1466, Translation initiation factor 2B, alpha subunit (eIF-2Balpha/GCN3) [Translation, ribosomal structure and biogenesis] 313 matched cddid_all.tbl CDD KOG1467 KOG1467 229408 KOG1467 KOG1467, Translation initiation factor 2B, delta subunit (eIF-2Bdelta/GCD2) [Translation, ribosomal structure and biogenesis] 556 matched cddid_all.tbl CDD KOG1468 KOG1468 229409 KOG1468 KOG1468, Predicted translation initiation factor related to eIF-2B alpha/beta/delta subunits (CIG2/IDI2) [Translation, ribosomal structure and biogenesis] 354 matched cddid_all.tbl CDD KOG1469 KOG1469 229410 KOG1469 KOG1469, Predicted acyl-CoA dehydrogenase [General function prediction only] 392 matched cddid_all.tbl CDD KOG1470 KOG1470 229411 KOG1470 KOG1470, Phosphatidylinositol transfer protein PDR16 and related proteins [Lipid transport and metabolism] 324 matched cddid_all.tbl CDD KOG1471 KOG1471 229412 KOG1471 KOG1471, Phosphatidylinositol transfer protein SEC14 and related proteins [Lipid transport and metabolism] 317 matched cddid_all.tbl CDD KOG1472 KOG1472 229413 KOG1472 KOG1472, Histone acetyltransferase SAGA/ADA, catalytic subunit PCAF/GCN5 and related proteins [Chromatin structure and dynamics, Transcription] 720 matched cddid_all.tbl CDD KOG1473 KOG1473 229414 KOG1473 KOG1473, Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics, Transcription] 1414 matched cddid_all.tbl CDD KOG1474 KOG1474 229415 KOG1474 KOG1474, Transcription initiation factor TFIID, subunit BDF1 and related bromodomain proteins [Transcription] 640 matched cddid_all.tbl CDD KOG1475 KOG1475 229416 KOG1475 KOG1475, Ribosomal protein RPL1/RPL2/RL4L4 [RNA processing and modification] 290 matched cddid_all.tbl CDD KOG1476 KOG1476 229417 KOG1476 KOG1476, Beta-1,3-glucuronyltransferase B3GAT1/SQV-8 [Posttranslational modification, protein turnover, chaperones] 330 matched cddid_all.tbl CDD KOG1477 KOG1477 229418 KOG1477 KOG1477, SPRY domain-containing proteins [General function prediction only] 469 matched cddid_all.tbl CDD KOG1478 KOG1478 229419 KOG1478 KOG1478, 3-keto sterol reductase [Lipid transport and metabolism] 341 matched cddid_all.tbl CDD KOG1479 KOG1479 229420 KOG1479 KOG1479, Nucleoside transporter [Nucleotide transport and metabolism] 406 matched cddid_all.tbl CDD KOG1480 KOG1480 229421 KOG1480 KOG1480, Netrin transmembrane receptor unc-5 [Signal transduction mechanisms] 909 matched cddid_all.tbl CDD KOG1481 KOG1481 229422 KOG1481 KOG1481, Cysteine synthase [Amino acid transport and metabolism] 391 matched cddid_all.tbl CDD KOG1482 KOG1482 229423 KOG1482 KOG1482, Zn2+ transporter [Inorganic ion transport and metabolism] 379 matched cddid_all.tbl CDD KOG1483 KOG1483 229424 KOG1483 KOG1483, Zn2+ transporter ZNT1 and related Cd2+/Zn2+ transporters (cation diffusion facilitator superfamily) [Inorganic ion transport and metabolism] 404 matched cddid_all.tbl CDD KOG1484 KOG1484 229425 KOG1484 KOG1484, Putative Zn2+ transporter MSC2 (cation diffusion facilitator superfamily) [Inorganic ion transport and metabolism] 354 matched cddid_all.tbl CDD KOG1485 KOG1485 229426 KOG1485 KOG1485, Mitochondrial Fe2+ transporter MMT1 and related transporters (cation diffusion facilitator superfamily) [Inorganic ion transport and metabolism] 412 matched cddid_all.tbl CDD KOG1486 KOG1486 229427 KOG1486 KOG1486, GTP-binding protein DRG2 (ODN superfamily) [Signal transduction mechanisms] 364 matched cddid_all.tbl CDD KOG1487 KOG1487 229428 KOG1487 KOG1487, GTP-binding protein DRG1 (ODN superfamily) [Signal transduction mechanisms] 358 matched cddid_all.tbl CDD KOG1488 KOG1488 229429 KOG1488 KOG1488, Translational repressor Pumilio/PUF3 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis] 503 matched cddid_all.tbl CDD KOG1489 KOG1489 229430 KOG1489 KOG1489, Predicted GTP-binding protein (ODN superfamily) [General function prediction only] 366 matched cddid_all.tbl CDD KOG1490 KOG1490 229431 KOG1490 KOG1490, GTP-binding protein CRFG/NOG1 (ODN superfamily) [General function prediction only] 504 matched cddid_all.tbl CDD KOG1491 KOG1491 229432 KOG1491 KOG1491, Predicted GTP-binding protein (ODN superfamily) [General function prediction only] 391 matched cddid_all.tbl CDD KOG1492 KOG1492 229433 KOG1492 KOG1492, C3H1-type Zn-finger protein [General function prediction only] 377 matched cddid_all.tbl CDD KOG1493 KOG1493 229434 KOG1493 KOG1493, Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning, Posttranslational modification, protein turnover, chaperones] 84 matched cddid_all.tbl CDD KOG1494 KOG1494 229435 KOG1494 KOG1494, NAD-dependent malate dehydrogenase [Energy production and conversion] 345 matched cddid_all.tbl CDD KOG1495 KOG1495 229436 KOG1495 KOG1495, Lactate dehydrogenase [Energy production and conversion] 332 matched cddid_all.tbl CDD KOG1496 KOG1496 229437 KOG1496 KOG1496, Malate dehydrogenase [Energy production and conversion] 332 matched cddid_all.tbl CDD KOG1497 KOG1497 229438 KOG1497 KOG1497, COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms] 399 matched cddid_all.tbl CDD KOG1498 KOG1498 229439 KOG1498 KOG1498, 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones] 439 matched cddid_all.tbl CDD KOG1499 KOG1499 229440 KOG1499 KOG1499, Protein arginine N-methyltransferase PRMT1 and related enzymes [Posttranslational modification, protein turnover, chaperones, Transcription, Signal transduction mechanisms] 346 matched cddid_all.tbl CDD KOG1500 KOG1500 229441 KOG1500 KOG1500, Protein arginine N-methyltransferase CARM1 [Posttranslational modification, protein turnover, chaperones, Transcription] 517 matched cddid_all.tbl CDD KOG1501 KOG1501 229442 KOG1501 KOG1501, Arginine N-methyltransferase [General function prediction only] 636 matched cddid_all.tbl CDD KOG1502 KOG1502 229443 KOG1502 KOG1502, Flavonol reductase/cinnamoyl-CoA reductase [Defense mechanisms] 327 matched cddid_all.tbl CDD KOG1503 KOG1503 229444 KOG1503 KOG1503, Phosphoribosylpyrophosphate synthetase-associated protein [Amino acid transport and metabolism, Nucleotide transport and metabolism] 354 matched cddid_all.tbl CDD KOG1504 KOG1504 229445 KOG1504 KOG1504, Ornithine carbamoyltransferase OTC/ARG3 [Amino acid transport and metabolism] 346 matched cddid_all.tbl CDD KOG1505 KOG1505 229446 KOG1505 KOG1505, Lysophosphatidic acid acyltransferase LPAAT and related acyltransferases [Lipid transport and metabolism] 346 matched cddid_all.tbl CDD KOG1506 KOG1506 229447 KOG1506 KOG1506, S-adenosylmethionine synthetase [Coenzyme transport and metabolism] 383 matched cddid_all.tbl CDD KOG1507 KOG1507 229448 KOG1507 KOG1507, Nucleosome assembly protein NAP-1 [Chromatin structure and dynamics, Cell cycle control, cell division, chromosome partitioning] 358 matched cddid_all.tbl CDD KOG1508 KOG1508 229449 KOG1508 KOG1508, DNA replication factor/protein phosphatase inhibitor SET/SPR-2 [Replication, recombination and repair] 260 matched cddid_all.tbl CDD KOG1509 KOG1509 229450 KOG1509 KOG1509, Predicted nucleic acid-binding protein ASMTL [Cell cycle control, cell division, chromosome partitioning] 209 matched cddid_all.tbl CDD KOG1510 KOG1510 229451 KOG1510 KOG1510, RNA polymerase II holoenzyme and mediator subcomplex, subunit SURB7/SRB7 [Transcription] 139 matched cddid_all.tbl CDD KOG1511 KOG1511 229452 KOG1511 KOG1511, Mevalonate kinase MVK/ERG12 [Lipid transport and metabolism] 397 matched cddid_all.tbl CDD KOG1512 KOG1512 229453 KOG1512 KOG1512, PHD Zn-finger protein [General function prediction only] 381 matched cddid_all.tbl CDD KOG1513 KOG1513 229454 KOG1513 KOG1513, Nuclear helicase MOP-3/SNO (DEAD-box superfamily) [Transcription, Signal transduction mechanisms] 1300 matched cddid_all.tbl CDD KOG1514 KOG1514 229455 KOG1514 KOG1514, Origin recognition complex, subunit 1, and related proteins [Replication, recombination and repair] 767 matched cddid_all.tbl CDD KOG1515 KOG1515 229456 KOG1515 KOG1515, Arylacetamide deacetylase [Defense mechanisms] 336 matched cddid_all.tbl CDD KOG1516 KOG1516 229457 KOG1516 KOG1516, Carboxylesterase and related proteins [General function prediction only] 545 matched cddid_all.tbl CDD KOG1517 KOG1517 229458 KOG1517 KOG1517, Guanine nucleotide binding protein MIP1 [Cell cycle control, cell division, chromosome partitioning] 1387 matched cddid_all.tbl CDD KOG1518 KOG1518 229459 KOG1518 KOG1518, Coproporphyrinogen III oxidase CPO/HEM13 [Coenzyme transport and metabolism] 382 matched cddid_all.tbl CDD KOG1519 KOG1519 229460 KOG1519 KOG1519, Predicted mitochondrial carrier protein [General function prediction only] 297 matched cddid_all.tbl CDD KOG1520 KOG1520 229461 KOG1520 KOG1520, Predicted alkaloid synthase/Surface mucin Hemomucin [General function prediction only] 376 matched cddid_all.tbl CDD KOG1521 KOG1521 229462 KOG1521 KOG1521, RNA polymerase I and III, subunit RPA40/RPC40 [Transcription] 338 matched cddid_all.tbl CDD KOG1522 KOG1522 229463 KOG1522 KOG1522, RNA polymerase II, subunit POLR2C/RPB3 [Transcription] 285 matched cddid_all.tbl CDD KOG1523 KOG1523 229464 KOG1523 KOG1523, Actin-related protein Arp2/3 complex, subunit ARPC1/p41-ARC [Cytoskeleton] 361 matched cddid_all.tbl CDD KOG1524 KOG1524 229465 KOG1524 KOG1524, WD40 repeat-containing protein CHE-2 [General function prediction only] 737 matched cddid_all.tbl CDD KOG1525 KOG1525 229466 KOG1525 KOG1525, Sister chromatid cohesion complex Cohesin, subunit PDS5 [Cell cycle control, cell division, chromosome partitioning] 1266 matched cddid_all.tbl CDD KOG1526 KOG1526 229467 KOG1526 KOG1526, NADP-dependent isocitrate dehydrogenase [Energy production and conversion] 383 matched cddid_all.tbl CDD KOG1527 KOG1527 229468 KOG1527 KOG1527, Uroporphyrin III methyltransferase [Coenzyme transport and metabolism] 506 matched cddid_all.tbl CDD KOG1528 KOG1528 229469 KOG1528 KOG1528, Salt-sensitive 3'-phosphoadenosine-5'-phosphatase HAL2/SAL1 [Nucleotide transport and metabolism, Inorganic ion transport and metabolism] 351 matched cddid_all.tbl CDD KOG1529 KOG1529 229470 KOG1529 KOG1529, Mercaptopyruvate sulfurtransferase/thiosulfate sulfurtransferase [Defense mechanisms] 286 matched cddid_all.tbl CDD KOG1530 KOG1530 229471 KOG1530 KOG1530, Rhodanese-related sulfurtransferase [Inorganic ion transport and metabolism] 136 matched cddid_all.tbl CDD KOG1531 KOG1531 229472 KOG1531 KOG1531, F0F1-type ATP synthase, gamma subunit [Energy production and conversion] 304 matched cddid_all.tbl CDD KOG1532 KOG1532 229473 KOG1532 KOG1532, GTPase XAB1, interacts with DNA repair protein XPA [Replication, recombination and repair] 366 matched cddid_all.tbl CDD KOG1533 KOG1533 229474 KOG1533 KOG1533, Predicted GTPase [General function prediction only] 290 matched cddid_all.tbl CDD KOG1534 KOG1534 229475 KOG1534 KOG1534, Putative transcription factor FET5 [Transcription] 273 matched cddid_all.tbl CDD KOG1535 KOG1535 229476 KOG1535 KOG1535, Predicted fumarylacetoacetate hydralase [General function prediction only] 217 matched cddid_all.tbl CDD KOG1536 KOG1536 229477 KOG1536 KOG1536, Biotin holocarboxylase synthetase/biotin-protein ligase [Coenzyme transport and metabolism] 649 matched cddid_all.tbl CDD KOG1537 KOG1537 229478 KOG1537 KOG1537, Homoserine kinase [Amino acid transport and metabolism] 355 matched cddid_all.tbl CDD KOG1538 KOG1538 229479 KOG1538 KOG1538, Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only] 1038 matched cddid_all.tbl CDD KOG1539 KOG1539 229480 KOG1539 KOG1539, WD repeat protein [General function prediction only] 910 matched cddid_all.tbl CDD KOG1540 KOG1540 229481 KOG1540 KOG1540, Ubiquinone biosynthesis methyltransferase COQ5 [Coenzyme transport and metabolism] 296 matched cddid_all.tbl CDD KOG1541 KOG1541 229482 KOG1541 KOG1541, Predicted protein carboxyl methylase [General function prediction only] 270 matched cddid_all.tbl CDD KOG1542 KOG1542 229483 KOG1542 KOG1542, Cysteine proteinase Cathepsin F [Posttranslational modification, protein turnover, chaperones] 372 matched cddid_all.tbl CDD KOG1543 KOG1543 229484 KOG1543 KOG1543, Cysteine proteinase Cathepsin L [Posttranslational modification, protein turnover, chaperones] 325 matched cddid_all.tbl CDD KOG1544 KOG1544 229485 KOG1544 KOG1544, Predicted cysteine proteinase TIN-ag [General function prediction only] 470 matched cddid_all.tbl CDD KOG1545 KOG1545 229486 KOG1545 KOG1545, Voltage-gated shaker-like K+ channel KCNA [Inorganic ion transport and metabolism] 507 matched cddid_all.tbl CDD KOG1546 KOG1546 229487 KOG1546 KOG1546, Metacaspase involved in regulation of apoptosis [Cell cycle control, cell division, chromosome partitioning, Posttranslational modification, protein turnover, chaperones] 362 matched cddid_all.tbl CDD KOG1547 KOG1547 229488 KOG1547 KOG1547, Septin CDC10 and related P-loop GTPases [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms, Cytoskeleton] 336 matched cddid_all.tbl CDD KOG1548 KOG1548 229489 KOG1548 KOG1548, Transcription elongation factor TAT-SF1 [Transcription] 382 matched cddid_all.tbl CDD KOG1549 KOG1549 229490 KOG1549 KOG1549, Cysteine desulfurase NFS1 [Amino acid transport and metabolism] 428 matched cddid_all.tbl CDD KOG1550 KOG1550 229491 KOG1550 KOG1550, Extracellular protein SEL-1 and related proteins [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms] 552 matched cddid_all.tbl CDD KOG1551 KOG1551 229492 KOG1551 KOG1551, Uncharacterized conserved protein [Function unknown] 371 matched cddid_all.tbl CDD KOG1552 KOG1552 229493 KOG1552 KOG1552, Predicted alpha/beta hydrolase [General function prediction only] 258 matched cddid_all.tbl CDD KOG1553 KOG1553 229494 KOG1553 KOG1553, Predicted alpha/beta hydrolase BAT5 [General function prediction only] 517 matched cddid_all.tbl CDD KOG1554 KOG1554 229495 KOG1554 KOG1554, COP9 signalosome, subunit CSN5 [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms] 347 matched cddid_all.tbl CDD KOG1555 KOG1555 229496 KOG1555 KOG1555, 26S proteasome regulatory complex, subunit RPN11 [Posttranslational modification, protein turnover, chaperones] 316 matched cddid_all.tbl CDD KOG1556 KOG1556 229497 KOG1556 KOG1556, 26S proteasome regulatory complex, subunit RPN8/PSMD7 [Posttranslational modification, protein turnover, chaperones] 309 matched cddid_all.tbl CDD KOG1557 KOG1557 229498 KOG1557 KOG1557, Fructose-biphosphate aldolase [Carbohydrate transport and metabolism] 363 matched cddid_all.tbl CDD KOG1558 KOG1558 229499 KOG1558 KOG1558, Fe2+/Zn2+ regulated transporter [Inorganic ion transport and metabolism] 327 matched cddid_all.tbl CDD KOG1559 KOG1559 229500 KOG1559 KOG1559, Gamma-glutamyl hydrolase [Coenzyme transport and metabolism] 340 matched cddid_all.tbl CDD KOG1560 KOG1560 229501 KOG1560 KOG1560, Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis] 339 matched cddid_all.tbl CDD KOG1561 KOG1561 229502 KOG1561 KOG1561, CCAAT-binding factor, subunit B (HAP2) [Transcription] 307 matched cddid_all.tbl CDD KOG1562 KOG1562 229503 KOG1562 KOG1562, Spermidine synthase [Amino acid transport and metabolism] 337 matched cddid_all.tbl CDD KOG1563 KOG1563 229504 KOG1563 KOG1563, Mitochondrial protein Surfeit 1/SURF1/SHY1, required for expression of cytochrome oxidase [Energy production and conversion] 288 matched cddid_all.tbl CDD KOG1564 KOG1564 229505 KOG1564 KOG1564, DNA repair protein RHP57 [Replication, recombination and repair] 351 matched cddid_all.tbl CDD KOG1565 KOG1565 229506 KOG1565 KOG1565, Gelatinase A and related matrix metalloproteases [Posttranslational modification, protein turnover, chaperones, Extracellular structures] 469 matched cddid_all.tbl CDD KOG1566 KOG1566 229507 KOG1566 KOG1566, Conserved protein Mo25 [Function unknown] 342 matched cddid_all.tbl CDD KOG1567 KOG1567 229508 KOG1567 KOG1567, Ribonucleotide reductase, beta subunit [Nucleotide transport and metabolism] 344 matched cddid_all.tbl CDD KOG1568 KOG1568 229509 KOG1568 KOG1568, Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones, Intracellular trafficking, secretion, and vesicular transport] 174 matched cddid_all.tbl CDD KOG1569 KOG1569 229510 KOG1569 KOG1569, 50S ribosomal protein L1 [Translation, ribosomal structure and biogenesis] 323 matched cddid_all.tbl CDD KOG1570 KOG1570 229511 KOG1570 KOG1570, 60S ribosomal protein L10A [Translation, ribosomal structure and biogenesis] 218 matched cddid_all.tbl CDD KOG1571 KOG1571 229512 KOG1571 KOG1571, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 355 matched cddid_all.tbl CDD KOG1572 KOG1572 229513 KOG1572 KOG1572, Predicted protein tyrosine phosphatase [Defense mechanisms] 249 matched cddid_all.tbl CDD KOG1573 KOG1573 229514 KOG1573 KOG1573, Aldehyde reductase [General function prediction only] 204 matched cddid_all.tbl CDD KOG1574 KOG1574 229515 KOG1574 KOG1574, Predicted cell growth/differentiation regulator, contains RA domain [Extracellular structures] 375 matched cddid_all.tbl CDD KOG1575 KOG1575 229516 KOG1575 KOG1575, Voltage-gated shaker-like K+ channel, subunit beta/KCNAB [Energy production and conversion] 336 matched cddid_all.tbl CDD KOG1576 KOG1576 229517 KOG1576 KOG1576, Predicted oxidoreductase [Energy production and conversion] 342 matched cddid_all.tbl CDD KOG1577 KOG1577 229518 KOG1577 KOG1577, Aldo/keto reductase family proteins [General function prediction only] 300 matched cddid_all.tbl CDD KOG1578 KOG1578 229519 KOG1578 KOG1578, Predicted carbonic anhydrase involved in protection against oxidative damage [Inorganic ion transport and metabolism] 276 matched cddid_all.tbl CDD KOG1579 KOG1579 229520 KOG1579 KOG1579, Homocysteine S-methyltransferase [Amino acid transport and metabolism] 317 matched cddid_all.tbl CDD KOG1580 KOG1580 229521 KOG1580 KOG1580, UDP-galactose transporter related protein [Carbohydrate transport and metabolism] 337 matched cddid_all.tbl CDD KOG1581 KOG1581 229522 KOG1581 KOG1581, UDP-galactose transporter related protein [Carbohydrate transport and metabolism] 327 matched cddid_all.tbl CDD KOG1582 KOG1582 229523 KOG1582 KOG1582, UDP-galactose transporter related protein [Carbohydrate transport and metabolism] 367 matched cddid_all.tbl CDD KOG1583 KOG1583 229524 KOG1583 KOG1583, UDP-N-acetylglucosamine transporter [Carbohydrate transport and metabolism] 330 matched cddid_all.tbl CDD KOG1584 KOG1584 229525 KOG1584 KOG1584, Sulfotransferase [General function prediction only] 297 matched cddid_all.tbl CDD KOG1585 KOG1585 229526 KOG1585 KOG1585, Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport] 308 matched cddid_all.tbl CDD KOG1586 KOG1586 229527 KOG1586 KOG1586, Protein required for fusion of vesicles in vesicular transport, alpha-SNAP [Intracellular trafficking, secretion, and vesicular transport] 288 matched cddid_all.tbl CDD KOG1587 KOG1587 229528 KOG1587 KOG1587, Cytoplasmic dynein intermediate chain [Cytoskeleton] 555 matched cddid_all.tbl CDD KOG1588 KOG1588 229529 KOG1588 KOG1588, RNA-binding protein Sam68 and related KH domain proteins [RNA processing and modification] 259 matched cddid_all.tbl CDD KOG1589 KOG1589 229530 KOG1589 KOG1589, Uncharacterized conserved protein [Function unknown] 118 matched cddid_all.tbl CDD KOG1590 KOG1590 229531 KOG1590 KOG1590, Uncharacterized conserved protein [Function unknown] 132 matched cddid_all.tbl CDD KOG1591 KOG1591 229532 KOG1591 KOG1591, Prolyl 4-hydroxylase alpha subunit [Amino acid transport and metabolism] 289 matched cddid_all.tbl CDD KOG1592 KOG1592 229533 KOG1592 KOG1592, Asparaginase [Amino acid transport and metabolism] 326 matched cddid_all.tbl CDD KOG1593 KOG1593 229534 KOG1593 KOG1593, Asparaginase [Amino acid transport and metabolism] 349 matched cddid_all.tbl CDD KOG1594 KOG1594 229535 KOG1594 KOG1594, Uncharacterized enzymes related to aldose 1-epimerase [Carbohydrate transport and metabolism] 305 matched cddid_all.tbl CDD KOG1595 KOG1595 229536 KOG1595 KOG1595, CCCH-type Zn-finger protein [General function prediction only] 528 matched cddid_all.tbl CDD KOG1596 KOG1596 229537 KOG1596 KOG1596, Fibrillarin and related nucleolar RNA-binding proteins [RNA processing and modification] 317 matched cddid_all.tbl CDD KOG1597 KOG1597 229538 KOG1597 KOG1597, Transcription initiation factor TFIIB [Transcription] 308 matched cddid_all.tbl CDD KOG1598 KOG1598 229539 KOG1598 KOG1598, Transcription initiation factor TFIIIB, Brf1 subunit [Transcription] 521 matched cddid_all.tbl CDD KOG1599 KOG1599 229540 KOG1599 KOG1599, Uricase (urate oxidase) [Secondary metabolites biosynthesis, transport and catabolism] 297 matched cddid_all.tbl CDD KOG1600 KOG1600 229541 KOG1600 KOG1600, Fatty acid desaturase [Lipid transport and metabolism] 321 matched cddid_all.tbl CDD KOG1601 KOG1601 229542 KOG1601 KOG1601, GATA-4/5/6 transcription factors [Transcription] 340 matched cddid_all.tbl CDD KOG1602 KOG1602 229543 KOG1602 KOG1602, Cis-prenyltransferase [Lipid transport and metabolism] 271 matched cddid_all.tbl CDD KOG1603 KOG1603 229544 KOG1603 KOG1603, Copper chaperone [Inorganic ion transport and metabolism] 73 matched cddid_all.tbl CDD KOG1604 KOG1604 229545 KOG1604 KOG1604, Predicted mutarotase [Carbohydrate transport and metabolism] 353 matched cddid_all.tbl CDD KOG1605 KOG1605 229546 KOG1605 KOG1605, TFIIF-interacting CTD phosphatase, including NLI-interacting factor (involved in RNA polymerase II regulation) [Transcription] 262 matched cddid_all.tbl CDD KOG1606 KOG1606 229547 KOG1606 KOG1606, Stationary phase-induced protein, SOR/SNZ family [Coenzyme transport and metabolism] 296 matched cddid_all.tbl CDD KOG1607 KOG1607 229548 KOG1607 KOG1607, Protein transporter of the TRAM (translocating chain-associating membrane) superfamily [Intracellular trafficking, secretion, and vesicular transport] 318 matched cddid_all.tbl CDD KOG1608 KOG1608 229549 KOG1608 KOG1608, Protein transporter of the TRAM (translocating chain-associating membrane) superfamily [Intracellular trafficking, secretion, and vesicular transport] 374 matched cddid_all.tbl CDD KOG1609 KOG1609 229550 KOG1609 KOG1609, Protein involved in mRNA turnover and stability [RNA processing and modification] 323 matched cddid_all.tbl CDD KOG1610 KOG1610 229551 KOG1610 KOG1610, Corticosteroid 11-beta-dehydrogenase and related short chain-type dehydrogenases [Secondary metabolites biosynthesis, transport and catabolism, General function prediction only] 322 matched cddid_all.tbl CDD KOG1611 KOG1611 229552 KOG1611 KOG1611, Predicted short chain-type dehydrogenase [General function prediction only] 249 matched cddid_all.tbl CDD KOG1612 KOG1612 229553 KOG1612 KOG1612, Exosomal 3'-5' exoribonuclease complex, subunit Rrp42 [Translation, ribosomal structure and biogenesis] 288 matched cddid_all.tbl CDD KOG1613 KOG1613 229554 KOG1613 KOG1613, Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis] 298 matched cddid_all.tbl CDD KOG1614 KOG1614 229555 KOG1614 KOG1614, Exosomal 3'-5' exoribonuclease complex, subunit Rrp45 [Translation, ribosomal structure and biogenesis] 291 matched cddid_all.tbl CDD KOG1615 KOG1615 229556 KOG1615 KOG1615, Phosphoserine phosphatase [Amino acid transport and metabolism] 227 matched cddid_all.tbl CDD KOG1616 KOG1616 229557 KOG1616 KOG1616, Protein involved in Snf1 protein kinase complex assembly [Carbohydrate transport and metabolism] 289 matched cddid_all.tbl CDD KOG1617 KOG1617 229558 KOG1617 KOG1617, CDP-alcohol phosphatidyltransferase/Phosphatidylglycerol-phosphate synthase [Lipid transport and metabolism] 243 matched cddid_all.tbl CDD KOG1618 KOG1618 229559 KOG1618 KOG1618, Predicted phosphatase [General function prediction only] 389 matched cddid_all.tbl CDD KOG1619 KOG1619 229560 KOG1619 KOG1619, Cytochrome b [Energy production and conversion] 245 matched cddid_all.tbl CDD KOG1620 KOG1620 229561 KOG1620 KOG1620, Inositol polyphosphate multikinase, component of the ARGR transcription regulatory complex [Transcription, Lipid transport and metabolism, Signal transduction mechanisms] 284 matched cddid_all.tbl CDD KOG1621 KOG1621 229562 KOG1621 KOG1621, 1D-myo-inositol-triphosphate 3-kinase A [Lipid transport and metabolism] 458 matched cddid_all.tbl CDD KOG1622 KOG1622 229563 KOG1622 KOG1622, GMP synthase [Nucleotide transport and metabolism] 552 matched cddid_all.tbl CDD KOG1623 KOG1623 229564 KOG1623 KOG1623, Multitransmembrane protein [General function prediction only] 243 matched cddid_all.tbl CDD KOG1624 KOG1624 229565 KOG1624 KOG1624, Mitochondrial/chloroplast ribosomal protein L4 [Translation, ribosomal structure and biogenesis] 290 matched cddid_all.tbl CDD KOG1625 KOG1625 229566 KOG1625 KOG1625, DNA polymerase alpha-primase complex, polymerase-associated subunit B [Replication, recombination and repair] 600 matched cddid_all.tbl CDD KOG1626 KOG1626 229567 KOG1626 KOG1626, Inorganic pyrophosphatase/Nucleosome remodeling factor, subunit NURF38 [Energy production and conversion] 279 matched cddid_all.tbl CDD KOG1627 KOG1627 229568 KOG1627 KOG1627, Translation elongation factor EF-1 gamma [Translation, ribosomal structure and biogenesis] 160 matched cddid_all.tbl CDD KOG1628 KOG1628 229569 KOG1628 KOG1628, 40S ribosomal protein S3A [Translation, ribosomal structure and biogenesis] 249 matched cddid_all.tbl CDD KOG1629 KOG1629 229570 KOG1629 KOG1629, Bax-mediated apoptosis inhibitor TEGT/BI-1 [Defense mechanisms] 235 matched cddid_all.tbl CDD KOG1630 KOG1630 229571 KOG1630 KOG1630, Growth hormone-induced protein and related proteins [Signal transduction mechanisms] 336 matched cddid_all.tbl CDD KOG1631 KOG1631 229572 KOG1631 KOG1631, Translocon-associated complex TRAP, alpha subunit [Intracellular trafficking, secretion, and vesicular transport] 261 matched cddid_all.tbl CDD KOG1632 KOG1632 229573 KOG1632 KOG1632, Uncharacterized PHD Zn-finger protein [General function prediction only] 345 matched cddid_all.tbl CDD KOG1633 KOG1633 229574 KOG1633 KOG1633, F-box protein JEMMA and related proteins with JmjC, PHD, F-box and LRR domains [Chromatin structure and dynamics] 776 matched cddid_all.tbl CDD KOG1634 KOG1634 229575 KOG1634 KOG1634, Predicted transcription factor DATF1, contains PHD and TFS2M domains [Transcription] 778 matched cddid_all.tbl CDD KOG1635 KOG1635 229576 KOG1635 KOG1635, Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones] 191 matched cddid_all.tbl CDD KOG1636 KOG1636 229577 KOG1636 KOG1636, DNA polymerase delta processivity factor (proliferating cell nuclear antigen) [Replication, recombination and repair] 260 matched cddid_all.tbl CDD KOG1637 KOG1637 229578 KOG1637 KOG1637, Threonyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 560 matched cddid_all.tbl CDD KOG1638 KOG1638 229579 KOG1638 KOG1638, Steroid reductase [Lipid transport and metabolism] 257 matched cddid_all.tbl CDD KOG1639 KOG1639 229580 KOG1639 KOG1639, Steroid reductase required for elongation of the very long chain fatty acids [Lipid transport and metabolism] 297 matched cddid_all.tbl CDD KOG1640 KOG1640 229581 KOG1640 KOG1640, Predicted steroid reductase [Lipid transport and metabolism] 304 matched cddid_all.tbl CDD KOG1641 KOG1641 229582 KOG1641 KOG1641, Mitochondrial chaperonin [Posttranslational modification, protein turnover, chaperones] 104 matched cddid_all.tbl CDD KOG1642 KOG1642 229583 KOG1642 KOG1642, Ribonuclease, T2 family [RNA processing and modification] 263 matched cddid_all.tbl CDD KOG1643 KOG1643 229584 KOG1643 KOG1643, Triosephosphate isomerase [Carbohydrate transport and metabolism] 247 matched cddid_all.tbl CDD KOG1644 KOG1644 229585 KOG1644 KOG1644, U2-associated snRNP A' protein [RNA processing and modification] 233 matched cddid_all.tbl CDD KOG1645 KOG1645 229586 KOG1645 KOG1645, RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 463 matched cddid_all.tbl CDD KOG1646 KOG1646 229587 KOG1646 KOG1646, 40S ribosomal protein S6 [Translation, ribosomal structure and biogenesis] 237 matched cddid_all.tbl CDD KOG1647 KOG1647 229588 KOG1647 KOG1647, Vacuolar H+-ATPase V1 sector, subunit D [Energy production and conversion] 255 matched cddid_all.tbl CDD KOG1648 KOG1648 229589 KOG1648 KOG1648, Uncharacterized conserved protein, contains RUN, BRK and TBC domains [General function prediction only] 813 matched cddid_all.tbl CDD KOG1649 KOG1649 229590 KOG1649 KOG1649, SWI-SNF chromatin remodeling complex, Snf5 subunit [Chromatin structure and dynamics, Transcription] 397 matched cddid_all.tbl CDD KOG1650 KOG1650 229591 KOG1650 KOG1650, Predicted K+/H+-antiporter [Inorganic ion transport and metabolism] 769 matched cddid_all.tbl CDD KOG1651 KOG1651 229592 KOG1651 KOG1651, Glutathione peroxidase [Posttranslational modification, protein turnover, chaperones] 171 matched cddid_all.tbl CDD KOG1652 KOG1652 229593 KOG1652 KOG1652, Mitochondrial import inner membrane translocase, subunit TIM17 [Intracellular trafficking, secretion, and vesicular transport] 183 matched cddid_all.tbl CDD KOG1653 KOG1653 229594 KOG1653 KOG1653, Single-stranded DNA-binding protein [Replication, recombination and repair] 175 matched cddid_all.tbl CDD KOG1654 KOG1654 229595 KOG1654 KOG1654, Microtubule-associated anchor protein involved in autophagy and membrane trafficking [Cytoskeleton] 116 matched cddid_all.tbl CDD KOG1655 KOG1655 229596 KOG1655 KOG1655, Protein involved in vacuolar protein sorting [Intracellular trafficking, secretion, and vesicular transport] 218 matched cddid_all.tbl CDD KOG1656 KOG1656 229597 KOG1656 KOG1656, Protein involved in glucose derepression and pre-vacuolar endosome protein sorting [Intracellular trafficking, secretion, and vesicular transport] 221 matched cddid_all.tbl CDD KOG1657 KOG1657 229598 KOG1657 KOG1657, CCAAT-binding factor, subunit C (HAP5) [Transcription] 236 matched cddid_all.tbl CDD KOG1658 KOG1658 229599 KOG1658 KOG1658, DNA polymerase epsilon, subunit C [Replication, recombination and repair] 162 matched cddid_all.tbl CDD KOG1659 KOG1659 229600 KOG1659 KOG1659, Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription] 224 matched cddid_all.tbl CDD KOG1660 KOG1660 229601 KOG1660 KOG1660, Sorting nexin SNX6/TFAF2, contains PX domain [Defense mechanisms] 399 matched cddid_all.tbl CDD KOG1661 KOG1661 229602 KOG1661 KOG1661, Protein-L-isoaspartate(D-aspartate) O-methyltransferase [Posttranslational modification, protein turnover, chaperones] 237 matched cddid_all.tbl CDD KOG1662 KOG1662 229603 KOG1662 KOG1662, Mitochondrial F1F0-ATP synthase, subunit OSCP/ATP5 [Energy production and conversion] 210 matched cddid_all.tbl CDD KOG1663 KOG1663 229604 KOG1663 KOG1663, O-methyltransferase [Secondary metabolites biosynthesis, transport and catabolism] 237 matched cddid_all.tbl CDD KOG1664 KOG1664 229605 KOG1664 KOG1664, Vacuolar H+-ATPase V1 sector, subunit E [Energy production and conversion] 220 matched cddid_all.tbl CDD KOG1665 KOG1665 229606 KOG1665 KOG1665, AFH1-interacting protein FIP2, contains BTB/POZ domain and pentapeptide repeats [General function prediction only] 302 matched cddid_all.tbl CDD KOG1666 KOG1666 229607 KOG1666 KOG1666, V-SNARE [Intracellular trafficking, secretion, and vesicular transport] 220 matched cddid_all.tbl CDD KOG1667 KOG1667 229608 KOG1667 KOG1667, Zn2+-binding protein Melusin/RAR1, contains CHORD domain [General function prediction only] 320 matched cddid_all.tbl CDD KOG1668 KOG1668 229609 KOG1668 KOG1668, Elongation factor 1 beta/delta chain [Transcription] 231 matched cddid_all.tbl CDD KOG1669 KOG1669 229610 KOG1669 KOG1669, Predicted mRNA cap-binding protein related to eIF-4E [Translation, ribosomal structure and biogenesis] 208 matched cddid_all.tbl CDD KOG1670 KOG1670 229611 KOG1670 KOG1670, Translation initiation factor 4F, cap-binding subunit (eIF-4E) and related cap-binding proteins [Translation, ribosomal structure and biogenesis] 212 matched cddid_all.tbl CDD KOG1671 KOG1671 229612 KOG1671 KOG1671, Ubiquinol cytochrome c reductase, subunit RIP1 [Energy production and conversion] 210 matched cddid_all.tbl CDD KOG1672 KOG1672 229613 KOG1672 KOG1672, ATP binding protein [Posttranslational modification, protein turnover, chaperones, Energy production and conversion] 211 matched cddid_all.tbl CDD KOG1673 KOG1673 229614 KOG1673 KOG1673, Ras GTPases [General function prediction only] 205 matched cddid_all.tbl CDD KOG1674 KOG1674 229615 KOG1674 KOG1674, Cyclin [General function prediction only] 218 matched cddid_all.tbl CDD KOG1675 KOG1675 229616 KOG1675 KOG1675, Predicted cyclin [General function prediction only] 343 matched cddid_all.tbl CDD KOG1676 KOG1676 229617 KOG1676 KOG1676, K-homology type RNA binding proteins [RNA processing and modification] 600 matched cddid_all.tbl CDD KOG1677 KOG1677 229618 KOG1677 KOG1677, CCCH-type Zn-finger protein [General function prediction only] 332 matched cddid_all.tbl CDD KOG1678 KOG1678 229619 KOG1678 KOG1678, 60s ribosomal protein L15 [Translation, ribosomal structure and biogenesis] 204 matched cddid_all.tbl CDD KOG1679 KOG1679 229620 KOG1679 KOG1679, Enoyl-CoA hydratase [Lipid transport and metabolism] 291 matched cddid_all.tbl CDD KOG1680 KOG1680 229621 KOG1680 KOG1680, Enoyl-CoA hydratase [Lipid transport and metabolism] 290 matched cddid_all.tbl CDD KOG1681 KOG1681 229622 KOG1681 KOG1681, Enoyl-CoA isomerase [Lipid transport and metabolism] 292 matched cddid_all.tbl CDD KOG1682 KOG1682 229623 KOG1682 KOG1682, Enoyl-CoA isomerase [Lipid transport and metabolism] 287 matched cddid_all.tbl CDD KOG1683 KOG1683 229624 KOG1683 KOG1683, Hydroxyacyl-CoA dehydrogenase/enoyl-CoA hydratase [Lipid transport and metabolism] 380 matched cddid_all.tbl CDD KOG1684 KOG1684 229625 KOG1684 KOG1684, Enoyl-CoA hydratase [Lipid transport and metabolism] 401 matched cddid_all.tbl CDD KOG1685 KOG1685 229626 KOG1685 KOG1685, Uncharacterized conserved protein [Function unknown] 343 matched cddid_all.tbl CDD KOG1686 KOG1686 229627 KOG1686 KOG1686, Mitochondrial/chloroplast ribosomal L21 protein [Translation, ribosomal structure and biogenesis] 151 matched cddid_all.tbl CDD KOG1687 KOG1687 229628 KOG1687 KOG1687, NADH-ubiquinone oxidoreductase, NUFS7/PSST/20 kDa subunit [Energy production and conversion] 168 matched cddid_all.tbl CDD KOG1688 KOG1688 229629 KOG1688 KOG1688, Golgi proteins involved in ER retention (RER) [Intracellular trafficking, secretion, and vesicular transport] 188 matched cddid_all.tbl CDD KOG1689 KOG1689 229630 KOG1689 KOG1689, mRNA cleavage factor I subunit [RNA processing and modification] 221 matched cddid_all.tbl CDD KOG1690 KOG1690 229631 KOG1690 KOG1690, emp24/gp25L/p24 family of membrane trafficking proteins [Intracellular trafficking, secretion, and vesicular transport] 215 matched cddid_all.tbl CDD KOG1691 KOG1691 229632 KOG1691 KOG1691, emp24/gp25L/p24 family of membrane trafficking proteins [Intracellular trafficking, secretion, and vesicular transport] 210 matched cddid_all.tbl CDD KOG1692 KOG1692 229633 KOG1692 KOG1692, Putative cargo transport protein EMP24 (p24 protein family) [Intracellular trafficking, secretion, and vesicular transport] 201 matched cddid_all.tbl CDD KOG1693 KOG1693 229634 KOG1693 KOG1693, emp24/gp25L/p24 family of membrane trafficking proteins [Intracellular trafficking, secretion, and vesicular transport] 209 matched cddid_all.tbl CDD KOG1694 KOG1694 229635 KOG1694 KOG1694, 60s ribosomal protein L6 [Translation, ribosomal structure and biogenesis] 152 matched cddid_all.tbl CDD KOG1695 KOG1695 229636 KOG1695 KOG1695, Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones] 206 matched cddid_all.tbl CDD KOG1696 KOG1696 229637 KOG1696 KOG1696, 60s ribosomal protein L19 [Translation, ribosomal structure and biogenesis] 193 matched cddid_all.tbl CDD KOG1697 KOG1697 229638 KOG1697 KOG1697, Mitochondrial/chloroplast ribosomal protein S9 [Translation, ribosomal structure and biogenesis] 275 matched cddid_all.tbl CDD KOG1698 KOG1698 229639 KOG1698 KOG1698, Mitochondrial/chloroplast ribosomal protein L19 [Translation, ribosomal structure and biogenesis] 201 matched cddid_all.tbl CDD KOG1699 KOG1699 229640 KOG1699 KOG1699, O-acetyltransferase [General function prediction only] 442 matched cddid_all.tbl CDD KOG1700 KOG1700 229641 KOG1700 KOG1700, Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms, Cytoskeleton] 200 matched cddid_all.tbl CDD KOG1701 KOG1701 229642 KOG1701 KOG1701, Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms] 468 matched cddid_all.tbl CDD KOG1702 KOG1702 229643 KOG1702 KOG1702, Nebulin repeat protein [Cytoskeleton] 264 matched cddid_all.tbl CDD KOG1703 KOG1703 229644 KOG1703 KOG1703, Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms, Cytoskeleton] 479 matched cddid_all.tbl CDD KOG1705 KOG1705 229645 KOG1705 KOG1705, Uncharacterized conserved protein, contains CXXC motifs [Function unknown] 110 matched cddid_all.tbl CDD KOG1706 KOG1706 229646 KOG1706 KOG1706, Argininosuccinate synthase [Amino acid transport and metabolism] 412 matched cddid_all.tbl CDD KOG1707 KOG1707 229647 KOG1707 KOG1707, Predicted Ras related/Rac-GTP binding protein [Defense mechanisms] 625 matched cddid_all.tbl CDD KOG1708 KOG1708 229648 KOG1708 KOG1708, Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis] 236 matched cddid_all.tbl CDD KOG1709 KOG1709 229649 KOG1709 KOG1709, Guanidinoacetate methyltransferase and related proteins [Amino acid transport and metabolism] 271 matched cddid_all.tbl CDD KOG1710 KOG1710 229650 KOG1710 KOG1710, MYND Zn-finger and ankyrin repeat protein [General function prediction only] 396 matched cddid_all.tbl CDD KOG1711 KOG1711 229651 KOG1711 KOG1711, Mitochondrial/chloroplast ribosomal protein L22 [Translation, ribosomal structure and biogenesis] 218 matched cddid_all.tbl CDD KOG1712 KOG1712 229652 KOG1712 KOG1712, Adenine phosphoribosyl transferases [Nucleotide transport and metabolism] 183 matched cddid_all.tbl CDD KOG1713 KOG1713 229653 KOG1713 KOG1713, NADH-ubiquinone oxidoreductase, NDUFS3/30 kDa subunit [Energy production and conversion] 191 matched cddid_all.tbl CDD KOG1714 KOG1714 229654 KOG1714 KOG1714, 60s ribosomal protein L18 [Translation, ribosomal structure and biogenesis] 188 matched cddid_all.tbl CDD KOG1715 KOG1715 229655 KOG1715 KOG1715, Mitochondrial/chloroplast ribosomal protein L12 [Translation, ribosomal structure and biogenesis] 187 matched cddid_all.tbl CDD KOG1716 KOG1716 229656 KOG1716 KOG1716, Dual specificity phosphatase [Defense mechanisms] 285 matched cddid_all.tbl CDD KOG1717 KOG1717 229657 KOG1717 KOG1717, Dual specificity phosphatase [Defense mechanisms] 343 matched cddid_all.tbl CDD KOG1718 KOG1718 229658 KOG1718 KOG1718, Dual specificity phosphatase [Defense mechanisms] 198 matched cddid_all.tbl CDD KOG1719 KOG1719 229659 KOG1719 KOG1719, Dual specificity phosphatase [Defense mechanisms] 183 matched cddid_all.tbl CDD KOG1720 KOG1720 229660 KOG1720 KOG1720, Protein tyrosine phosphatase CDC14 [Defense mechanisms] 225 matched cddid_all.tbl CDD KOG1722 KOG1722 229661 KOG1722 KOG1722, 60s ribosomal protein L24 [Translation, ribosomal structure and biogenesis] 155 matched cddid_all.tbl CDD KOG1723 KOG1723 229662 KOG1723 KOG1723, 60s ribosomal protein L30 isolog [Translation, ribosomal structure and biogenesis] 162 matched cddid_all.tbl CDD KOG1724 KOG1724 229663 KOG1724 KOG1724, SCF ubiquitin ligase, Skp1 component [Posttranslational modification, protein turnover, chaperones] 162 matched cddid_all.tbl CDD KOG1725 KOG1725 229664 KOG1725 KOG1725, Protein involved in membrane traffic (YOP1/TB2/DP1/HVA22 family) [Intracellular trafficking, secretion, and vesicular transport] 186 matched cddid_all.tbl CDD KOG1726 KOG1726 229665 KOG1726 KOG1726, HVA22/DP1 gene product-related proteins [Defense mechanisms] 225 matched cddid_all.tbl CDD KOG1727 KOG1727 229666 KOG1727 KOG1727, Microtubule-binding protein (translationally controlled tumor protein) [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton] 169 matched cddid_all.tbl CDD KOG1728 KOG1728 229667 KOG1728 KOG1728, 40S ribosomal protein S11 [Translation, ribosomal structure and biogenesis] 156 matched cddid_all.tbl CDD KOG1729 KOG1729 229668 KOG1729 KOG1729, FYVE finger containing protein [General function prediction only] 288 matched cddid_all.tbl CDD KOG1730 KOG1730 229669 KOG1730 KOG1730, Thioredoxin-like protein [Posttranslational modification, protein turnover, chaperones] 206 matched cddid_all.tbl CDD KOG1731 KOG1731 229670 KOG1731 KOG1731, FAD-dependent sulfhydryl oxidase/quiescin and related proteins [Cell cycle control, cell division, chromosome partitioning] 606 matched cddid_all.tbl CDD KOG1732 KOG1732 229671 KOG1732 KOG1732, 60S ribosomal protein L21 [Translation, ribosomal structure and biogenesis] 160 matched cddid_all.tbl CDD KOG1733 KOG1733 229672 KOG1733 KOG1733, Mitochondrial import inner membrane translocase, subunit TIM13 [Intracellular trafficking, secretion, and vesicular transport] 97 matched cddid_all.tbl CDD KOG1734 KOG1734 229673 KOG1734 KOG1734, Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 328 matched cddid_all.tbl CDD KOG1735 KOG1735 229674 KOG1735 KOG1735, Actin depolymerizing factor [Cytoskeleton] 146 matched cddid_all.tbl CDD KOG1736 KOG1736 229675 KOG1736 KOG1736, Glia maturation factor beta [Extracellular structures] 143 matched cddid_all.tbl CDD KOG1737 KOG1737 229676 KOG1737 KOG1737, Oxysterol-binding protein [Lipid transport and metabolism] 764 matched cddid_all.tbl CDD KOG1738 KOG1738 229677 KOG1738 KOG1738, Membrane-associated guanylate kinase-interacting protein/connector enhancer of KSR-like [Nucleotide transport and metabolism] 638 matched cddid_all.tbl CDD KOG1739 KOG1739 229678 KOG1739 KOG1739, Serine/threonine protein kinase GPBP [Signal transduction mechanisms, Defense mechanisms] 611 matched cddid_all.tbl CDD KOG1740 KOG1740 229679 KOG1740 KOG1740, Predicted mitochondrial/chloroplast ribosomal protein S17 [Translation, ribosomal structure and biogenesis] 107 matched cddid_all.tbl CDD KOG1741 KOG1741 229680 KOG1741 KOG1741, Mitochondrial/chloroplast ribosomal protein S14/S29 [Translation, ribosomal structure and biogenesis] 103 matched cddid_all.tbl CDD KOG1742 KOG1742 229681 KOG1742 KOG1742, 60s ribosomal protein L15/L27 [Translation, ribosomal structure and biogenesis] 147 matched cddid_all.tbl CDD KOG1743 KOG1743 229682 KOG1743 KOG1743, Ferric reductase-like proteins [Inorganic ion transport and metabolism] 137 matched cddid_all.tbl CDD KOG1744 KOG1744 229683 KOG1744 KOG1744, Histone H2B [Chromatin structure and dynamics] 127 matched cddid_all.tbl CDD KOG1745 KOG1745 229684 KOG1745 KOG1745, Histones H3 and H4 [Chromatin structure and dynamics] 137 matched cddid_all.tbl CDD KOG1746 KOG1746 229685 KOG1746 KOG1746, Defender against cell death protein/oligosaccharyltransferase, epsilon subunit [Cell cycle control, cell division, chromosome partitioning, Posttranslational modification, protein turnover, chaperones] 115 matched cddid_all.tbl CDD KOG1747 KOG1747 229686 KOG1747 KOG1747, Protein tyrosine kinase 9/actin monomer-binding protein [Extracellular structures] 342 matched cddid_all.tbl CDD KOG1748 KOG1748 229687 KOG1748 KOG1748, Acyl carrier protein/NADH-ubiquinone oxidoreductase, NDUFAB1/SDAP subunit [Energy production and conversion, Lipid transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism] 131 matched cddid_all.tbl CDD KOG1749 KOG1749 229688 KOG1749 KOG1749, 40S ribosomal protein S23 [Translation, ribosomal structure and biogenesis] 143 matched cddid_all.tbl CDD KOG1750 KOG1750 229689 KOG1750 KOG1750, Mitochondrial/chloroplast ribosomal protein S12 [Translation, ribosomal structure and biogenesis] 139 matched cddid_all.tbl CDD KOG1751 KOG1751 229690 KOG1751 KOG1751, 60s ribosomal protein L23 [Translation, ribosomal structure and biogenesis] 157 matched cddid_all.tbl CDD KOG1752 KOG1752 229691 KOG1752 KOG1752, Glutaredoxin and related proteins [Posttranslational modification, protein turnover, chaperones] 104 matched cddid_all.tbl CDD KOG1753 KOG1753 229692 KOG1753 KOG1753, 40S ribosomal protein S16 [Translation, ribosomal structure and biogenesis] 145 matched cddid_all.tbl CDD KOG1754 KOG1754 229693 KOG1754 KOG1754, 40S ribosomal protein S15/S22 [Translation, ribosomal structure and biogenesis] 130 matched cddid_all.tbl CDD KOG1755 KOG1755 229694 KOG1755 KOG1755, Profilin [Cytoskeleton] 128 matched cddid_all.tbl CDD KOG1756 KOG1756 229695 KOG1756 KOG1756, Histone 2A [Chromatin structure and dynamics] 131 matched cddid_all.tbl CDD KOG1757 KOG1757 229696 KOG1757 KOG1757, Histone 2A [Chromatin structure and dynamics] 131 matched cddid_all.tbl CDD KOG1758 KOG1758 229697 KOG1758 KOG1758, Mitochondrial F1F0-ATP synthase, subunit delta/ATP16 [Energy production and conversion] 159 matched cddid_all.tbl CDD KOG1759 KOG1759 229698 KOG1759 KOG1759, Macrophage migration inhibitory factor [Defense mechanisms] 115 matched cddid_all.tbl CDD KOG1760 KOG1760 229699 KOG1760 KOG1760, Molecular chaperone Prefoldin, subunit 4 [Posttranslational modification, protein turnover, chaperones] 131 matched cddid_all.tbl CDD KOG1761 KOG1761 229700 KOG1761 KOG1761, Signal recognition particle, subunit Srp14 [Intracellular trafficking, secretion, and vesicular transport] 116 matched cddid_all.tbl CDD KOG1762 KOG1762 229701 KOG1762 KOG1762, 60s acidic ribosomal protein P1 [Translation, ribosomal structure and biogenesis] 114 matched cddid_all.tbl CDD KOG1763 KOG1763 229702 KOG1763 KOG1763, Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only] 343 matched cddid_all.tbl CDD KOG1764 KOG1764 229703 KOG1764 KOG1764, 5'-AMP-activated protein kinase, gamma subunit [Energy production and conversion] 381 matched cddid_all.tbl CDD KOG1765 KOG1765 229704 KOG1765 KOG1765, Regulator of ribosome synthesis [Translation, ribosomal structure and biogenesis] 181 matched cddid_all.tbl CDD KOG1766 KOG1766 229705 KOG1766 KOG1766, Enhancer of rudimentary [General function prediction only] 104 matched cddid_all.tbl CDD KOG1767 KOG1767 229706 KOG1767 KOG1767, 40S ribosomal protein S25 [Translation, ribosomal structure and biogenesis] 110 matched cddid_all.tbl CDD KOG1768 KOG1768 229707 KOG1768 KOG1768, 40s ribosomal protein S26 [Translation, ribosomal structure and biogenesis] 115 matched cddid_all.tbl CDD KOG1769 KOG1769 229708 KOG1769 KOG1769, Ubiquitin-like proteins [Posttranslational modification, protein turnover, chaperones] 99 matched cddid_all.tbl CDD KOG1770 KOG1770 229709 KOG1770 KOG1770, Translation initiation factor 1 (eIF-1/SUI1) [Translation, ribosomal structure and biogenesis] 112 matched cddid_all.tbl CDD KOG1771 KOG1771 229710 KOG1771 KOG1771, GPI-alpha-mannosyltransferase III (GPI10/PIG-B) involved in glycosylphosphatidylinositol anchor biosynthesis [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones] 464 matched cddid_all.tbl CDD KOG1772 KOG1772 229711 KOG1772 KOG1772, Vacuolar H+-ATPase V1 sector, subunit G [Energy production and conversion] 108 matched cddid_all.tbl CDD KOG1773 KOG1773 229712 KOG1773 KOG1773, Stress responsive protein [General function prediction only] 63 matched cddid_all.tbl CDD KOG1774 KOG1774 229713 KOG1774 KOG1774, Small nuclear ribonucleoprotein E [RNA processing and modification] 88 matched cddid_all.tbl CDD KOG1775 KOG1775 229714 KOG1775 KOG1775, U6 snRNA-associated Sm-like protein [RNA processing and modification] 84 matched cddid_all.tbl CDD KOG1776 KOG1776 229715 KOG1776 KOG1776, Zn-binding protein Push [Signal transduction mechanisms] 1110 matched cddid_all.tbl CDD KOG1777 KOG1777 229716 KOG1777 KOG1777, Putative Zn-finger protein [General function prediction only] 625 matched cddid_all.tbl CDD KOG1778 KOG1778 229717 KOG1778 KOG1778, CREB binding protein/P300 and related TAZ Zn-finger proteins [Transcription] 319 matched cddid_all.tbl CDD KOG1779 KOG1779 229718 KOG1779 KOG1779, 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis] 84 matched cddid_all.tbl CDD KOG1780 KOG1780 229719 KOG1780 KOG1780, Small Nuclear ribonucleoprotein G [RNA processing and modification] 77 matched cddid_all.tbl CDD KOG1781 KOG1781 229720 KOG1781 KOG1781, Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] 108 matched cddid_all.tbl CDD KOG1782 KOG1782 229721 KOG1782 KOG1782, Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] 129 matched cddid_all.tbl CDD KOG1783 KOG1783 229722 KOG1783 KOG1783, Small nuclear ribonucleoprotein F [RNA processing and modification] 77 matched cddid_all.tbl CDD KOG1784 KOG1784 229723 KOG1784 KOG1784, Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification] 96 matched cddid_all.tbl CDD KOG1785 KOG1785 229724 KOG1785 KOG1785, Tyrosine kinase negative regulator CBL [Defense mechanisms] 563 matched cddid_all.tbl CDD KOG1786 KOG1786 229725 KOG1786 KOG1786, Lysosomal trafficking regulator LYST and related BEACH and WD40 repeat proteins [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 1081 matched cddid_all.tbl CDD KOG1787 KOG1787 229726 KOG1787 KOG1787, Kinase A-anchor protein Neurobeachin and related BEACH and WD40 repeat proteins [Intracellular trafficking, secretion, and vesicular transport] 1126 matched cddid_all.tbl CDD KOG1788 KOG1788 229727 KOG1788 KOG1788, Uncharacterized conserved protein [Function unknown] 2799 matched cddid_all.tbl CDD KOG1789 KOG1789 229728 KOG1789 KOG1789, Endocytosis protein RME-8, contains DnaJ domain [Intracellular trafficking, secretion, and vesicular transport, Posttranslational modification, protein turnover, chaperones] 2235 matched cddid_all.tbl CDD KOG1790 KOG1790 229729 KOG1790 KOG1790, 60s ribosomal protein L34 [Translation, ribosomal structure and biogenesis] 121 matched cddid_all.tbl CDD KOG1791 KOG1791 229730 KOG1791 KOG1791, Uncharacterized conserved protein [Function unknown] 1758 matched cddid_all.tbl CDD KOG1792 KOG1792 229731 KOG1792 KOG1792, Reticulon [Intracellular trafficking, secretion, and vesicular transport] 230 matched cddid_all.tbl CDD KOG1793 KOG1793 229732 KOG1793 KOG1793, Uncharacterized conserved protein [Function unknown] 417 matched cddid_all.tbl CDD KOG1794 KOG1794 229733 KOG1794 KOG1794, N-Acetylglucosamine kinase [Carbohydrate transport and metabolism] 336 matched cddid_all.tbl CDD KOG1795 KOG1795 229734 KOG1795 KOG1795, U5 snRNP spliceosome subunit [RNA processing and modification] 2321 matched cddid_all.tbl CDD KOG1796 KOG1796 229735 KOG1796 KOG1796, Vacuolar protein sorting-associated protein [Intracellular trafficking, secretion, and vesicular transport] 609 matched cddid_all.tbl CDD KOG1797 KOG1797 229736 KOG1797 KOG1797, Uncharacterized conserved protein (Neuroblastoma-amplified protein) [Function unknown] 1660 matched cddid_all.tbl CDD KOG1798 KOG1798 229737 KOG1798 KOG1798, DNA polymerase epsilon, catalytic subunit A [Replication, recombination and repair] 2173 matched cddid_all.tbl CDD KOG1799 KOG1799 229738 KOG1799 KOG1799, Dihydropyrimidine dehydrogenase [Nucleotide transport and metabolism] 471 matched cddid_all.tbl CDD KOG1800 KOG1800 229739 KOG1800 KOG1800, Ferredoxin/adrenodoxin reductase [Nucleotide transport and metabolism] 468 matched cddid_all.tbl CDD KOG1801 KOG1801 229740 KOG1801 KOG1801, tRNA-splicing endonuclease positive effector (SEN1) [RNA processing and modification] 827 matched cddid_all.tbl CDD KOG1802 KOG1802 229741 KOG1802 KOG1802, RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification] 935 matched cddid_all.tbl CDD KOG1803 KOG1803 229742 KOG1803 KOG1803, DNA helicase [Replication, recombination and repair] 649 matched cddid_all.tbl CDD KOG1804 KOG1804 229743 KOG1804 KOG1804, RNA helicase [RNA processing and modification] 733 matched cddid_all.tbl CDD KOG1805 KOG1805 229744 KOG1805 KOG1805, DNA replication helicase [Replication, recombination and repair] 1100 matched cddid_all.tbl CDD KOG1806 KOG1806 229745 KOG1806 KOG1806, DEAD box containing helicases [Replication, recombination and repair] 1320 matched cddid_all.tbl CDD KOG1807 KOG1807 229746 KOG1807 KOG1807, Helicases [Replication, recombination and repair] 1025 matched cddid_all.tbl CDD KOG1808 KOG1808 229747 KOG1808 KOG1808, AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only] 1856 matched cddid_all.tbl CDD KOG1809 KOG1809 229748 KOG1809 KOG1809, Vacuolar protein sorting-associated protein [Intracellular trafficking, secretion, and vesicular transport] 1827 matched cddid_all.tbl CDD KOG1810 KOG1810 229749 KOG1810 KOG1810, Cell cycle-associated protein [Cell cycle control, cell division, chromosome partitioning] 1417 matched cddid_all.tbl CDD KOG1811 KOG1811 229750 KOG1811 KOG1811, Predicted Zn2+-binding protein, contains FYVE domain [General function prediction only] 1141 matched cddid_all.tbl CDD KOG1812 KOG1812 229751 KOG1812 KOG1812, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 384 matched cddid_all.tbl CDD KOG1813 KOG1813 229752 KOG1813 KOG1813, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 313 matched cddid_all.tbl CDD KOG1814 KOG1814 229753 KOG1814 KOG1814, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 445 matched cddid_all.tbl CDD KOG1815 KOG1815 229754 KOG1815 KOG1815, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 444 matched cddid_all.tbl CDD KOG1816 KOG1816 229755 KOG1816 KOG1816, Ubiquitin fusion-degradation protein [Posttranslational modification, protein turnover, chaperones] 308 matched cddid_all.tbl CDD KOG1817 KOG1817 229756 KOG1817 KOG1817, Ribonuclease [RNA processing and modification] 533 matched cddid_all.tbl CDD KOG1818 KOG1818 229757 KOG1818 KOG1818, Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 634 matched cddid_all.tbl CDD KOG1819 KOG1819 229758 KOG1819 KOG1819, FYVE finger-containing proteins [General function prediction only] 953 matched cddid_all.tbl CDD KOG1820 KOG1820 229759 KOG1820 KOG1820, Microtubule-associated protein [Cytoskeleton] 815 matched cddid_all.tbl CDD KOG1821 KOG1821 229760 KOG1821 KOG1821, Uncharacterized conserved protein [Function unknown] 662 matched cddid_all.tbl CDD KOG1822 KOG1822 229761 KOG1822 KOG1822, Uncharacterized conserved protein [Function unknown] 2067 matched cddid_all.tbl CDD KOG1823 KOG1823 229762 KOG1823 KOG1823, DRIM (Down-regulated in metastasis)-like proteins [Defense mechanisms] 1364 matched cddid_all.tbl CDD KOG1824 KOG1824 229763 KOG1824 KOG1824, TATA-binding protein-interacting protein [General function prediction only] 1233 matched cddid_all.tbl CDD KOG1825 KOG1825 229764 KOG1825 KOG1825, Fry-like conserved proteins [General function prediction only] 2206 matched cddid_all.tbl CDD KOG1826 KOG1826 229765 KOG1826 KOG1826, Ras GTPase activating protein RasGAP/neurofibromin [Defense mechanisms] 2724 matched cddid_all.tbl CDD KOG1827 KOG1827 229766 KOG1827 KOG1827, Chromatin remodeling complex RSC, subunit RSC1/Polybromo and related proteins [Chromatin structure and dynamics, Transcription] 629 matched cddid_all.tbl CDD KOG1828 KOG1828 229767 KOG1828 KOG1828, IRF-2-binding protein CELTIX-1, contains BROMO domain [Transcription] 418 matched cddid_all.tbl CDD KOG1829 KOG1829 229768 KOG1829 KOG1829, Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms] 580 matched cddid_all.tbl CDD KOG1830 KOG1830 229769 KOG1830 KOG1830, Wiskott Aldrich syndrome proteins [Cytoskeleton] 518 matched cddid_all.tbl CDD KOG1831 KOG1831 229770 KOG1831 KOG1831, Negative regulator of transcription [Transcription] 1591 matched cddid_all.tbl CDD KOG1832 KOG1832 229771 KOG1832 KOG1832, HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning] 1516 matched cddid_all.tbl CDD KOG1833 KOG1833 229772 KOG1833 KOG1833, Nuclear pore complex, gp210 component [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 679 matched cddid_all.tbl CDD KOG1834 KOG1834 229773 KOG1834 KOG1834, Calsyntenin [Extracellular structures] 952 matched cddid_all.tbl CDD KOG1835 KOG1835 229774 KOG1835 KOG1835, Uncharacterized conserved protein [Function unknown] 1704 matched cddid_all.tbl CDD KOG1836 KOG1836 229775 KOG1836 KOG1836, Extracellular matrix glycoprotein Laminin subunits alpha and gamma [Extracellular structures] 1705 matched cddid_all.tbl CDD KOG1837 KOG1837 229776 KOG1837 KOG1837, Uncharacterized conserved protein [Function unknown] 1621 matched cddid_all.tbl CDD KOG1838 KOG1838 229777 KOG1838 KOG1838, Alpha/beta hydrolase [General function prediction only] 409 matched cddid_all.tbl CDD KOG1839 KOG1839 229778 KOG1839 KOG1839, Uncharacterized protein CLU1/cluA/TIF31 involved in mitochondrial morphology/distribution, also found associated with eIF-3 [General function prediction only] 1236 matched cddid_all.tbl CDD KOG1840 KOG1840 229779 KOG1840 KOG1840, Kinesin light chain [Cytoskeleton] 508 matched cddid_all.tbl CDD KOG1841 KOG1841 229780 KOG1841 KOG1841, Smad anchor for receptor activation [Defense mechanisms] 1287 matched cddid_all.tbl CDD KOG1842 KOG1842 229781 KOG1842 KOG1842, FYVE finger-containing protein [General function prediction only] 505 matched cddid_all.tbl CDD KOG1843 KOG1843 229782 KOG1843 KOG1843, Uncharacterized conserved protein [Function unknown] 473 matched cddid_all.tbl CDD KOG1844 KOG1844 229783 KOG1844 KOG1844, PHD Zn-finger proteins [General function prediction only] 508 matched cddid_all.tbl CDD KOG1845 KOG1845 229784 KOG1845 KOG1845, MORC family ATPases [Cell cycle control, cell division, chromosome partitioning] 775 matched cddid_all.tbl CDD KOG1846 KOG1846 229785 KOG1846 KOG1846, Uncharacterized conserved protein, contains Sec7 domain [Intracellular trafficking, secretion, and vesicular transport] 1777 matched cddid_all.tbl CDD KOG1847 KOG1847 229786 KOG1847 KOG1847, mRNA splicing factor [RNA processing and modification] 878 matched cddid_all.tbl CDD KOG1848 KOG1848 229787 KOG1848 KOG1848, Uncharacterized conserved protein [Function unknown] 1610 matched cddid_all.tbl CDD KOG1849 KOG1849 229788 KOG1849 KOG1849, Regulator of spindle pole body duplication [Cell cycle control, cell division, chromosome partitioning] 1319 matched cddid_all.tbl CDD KOG1850 KOG1850 229789 KOG1850 KOG1850, Myosin-like coiled-coil protein [Cytoskeleton] 391 matched cddid_all.tbl CDD KOG1851 KOG1851 229790 KOG1851 KOG1851, Uncharacterized conserved protein [Function unknown] 1710 matched cddid_all.tbl CDD KOG1852 KOG1852 229791 KOG1852 KOG1852, Cell cycle-associated protein [Cell cycle control, cell division, chromosome partitioning] 223 matched cddid_all.tbl CDD KOG1853 KOG1853 229792 KOG1853 KOG1853, LIS1-interacting protein NUDE [Cytoskeleton] 333 matched cddid_all.tbl CDD KOG1854 KOG1854 229793 KOG1854 KOG1854, Mitochondrial inner membrane protein (mitofilin) [Cell wall/membrane/envelope biogenesis] 657 matched cddid_all.tbl CDD KOG1855 KOG1855 229794 KOG1855 KOG1855, Predicted RNA-binding protein [General function prediction only] 484 matched cddid_all.tbl CDD KOG1856 KOG1856 229795 KOG1856 KOG1856, Transcription elongation factor SPT6 [RNA processing and modification] 1299 matched cddid_all.tbl CDD KOG1857 KOG1857 229796 KOG1857 KOG1857, Transcription accessory protein TEX, contains S1 domain [Transcription] 623 matched cddid_all.tbl CDD KOG1858 KOG1858 229797 KOG1858 KOG1858, Anaphase-promoting complex (APC), subunit 1 (meiotic check point regulator/Tsg24) [Cell cycle control, cell division, chromosome partitioning, Posttranslational modification, protein turnover, chaperones] 1496 matched cddid_all.tbl CDD KOG1859 KOG1859 229798 KOG1859 KOG1859, Leucine-rich repeat proteins [General function prediction only] 1096 matched cddid_all.tbl CDD KOG1860 KOG1860 229799 KOG1860 KOG1860, Nuclear protein export factor [Intracellular trafficking, secretion, and vesicular transport, Cell cycle control, cell division, chromosome partitioning] 927 matched cddid_all.tbl CDD KOG1861 KOG1861 229800 KOG1861 KOG1861, Leucine permease transcriptional regulator [Transcription] 540 matched cddid_all.tbl CDD KOG1862 KOG1862 229801 KOG1862 KOG1862, GYF domain containing proteins [General function prediction only] 673 matched cddid_all.tbl CDD KOG1863 KOG1863 229802 KOG1863 KOG1863, Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones] 1093 matched cddid_all.tbl CDD KOG1864 KOG1864 229803 KOG1864 KOG1864, Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones] 587 matched cddid_all.tbl CDD KOG1865 KOG1865 229804 KOG1865 KOG1865, Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones] 545 matched cddid_all.tbl CDD KOG1866 KOG1866 229805 KOG1866 KOG1866, Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones] 944 matched cddid_all.tbl CDD KOG1867 KOG1867 229806 KOG1867 KOG1867, Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones] 492 matched cddid_all.tbl CDD KOG1868 KOG1868 229807 KOG1868 KOG1868, Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones] 653 matched cddid_all.tbl CDD KOG1869 KOG1869 229808 KOG1869 KOG1869, Splicing coactivator SRm160/300, subunit SRm300 [RNA processing and modification] 425 matched cddid_all.tbl CDD KOG1870 KOG1870 229809 KOG1870 KOG1870, Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones] 842 matched cddid_all.tbl CDD KOG1871 KOG1871 229810 KOG1871 KOG1871, Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones] 420 matched cddid_all.tbl CDD KOG1872 KOG1872 229811 KOG1872 KOG1872, Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones] 473 matched cddid_all.tbl CDD KOG1873 KOG1873 229812 KOG1873 KOG1873, Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones] 877 matched cddid_all.tbl CDD KOG1874 KOG1874 229813 KOG1874 KOG1874, KEKE-like motif-containing transcription regulator (Rlr1)/suppressor of sin4 [Transcription] 1477 matched cddid_all.tbl CDD KOG1875 KOG1875 229814 KOG1875 KOG1875, Thyroid hormone receptor-associated coactivator complex component (TRAP170) [Transcription] 1322 matched cddid_all.tbl CDD KOG1876 KOG1876 229815 KOG1876 KOG1876, Actin-related protein Arp2/3 complex, subunit ARPC4 [Cytoskeleton] 168 matched cddid_all.tbl CDD KOG1877 KOG1877 229816 KOG1877 KOG1877, Putative transmembrane protein cmp44E [General function prediction only] 819 matched cddid_all.tbl CDD KOG1878 KOG1878 229817 KOG1878 KOG1878, Nuclear receptor coregulator SMRT/SMRTER, contains Myb-like domains [Transcription] 1672 matched cddid_all.tbl CDD KOG1879 KOG1879 229818 KOG1879 KOG1879, UDP-glucose:glycoprotein glucosyltransferase [Carbohydrate transport and metabolism] 1470 matched cddid_all.tbl CDD KOG1880 KOG1880 229819 KOG1880 KOG1880, Nuclear inhibitor of phosphatase-1 [General function prediction only] 337 matched cddid_all.tbl CDD KOG1881 KOG1881 229820 KOG1881 KOG1881, Anion exchanger adaptor protein Kanadaptin, contains FHA domain [General function prediction only] 793 matched cddid_all.tbl CDD KOG1882 KOG1882 229821 KOG1882 KOG1882, Transcriptional regulator SNIP1, contains FHA domain [Signal transduction mechanisms] 293 matched cddid_all.tbl CDD KOG1883 KOG1883 229822 KOG1883 KOG1883, Cofactor required for Sp1 transcriptional activation, subunit 3 [Transcription] 1517 matched cddid_all.tbl CDD KOG1884 KOG1884 229823 KOG1884 KOG1884, Uncharacterized conserved protein [Function unknown] 1498 matched cddid_all.tbl CDD KOG1885 KOG1885 229824 KOG1885 KOG1885, Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis] 560 matched cddid_all.tbl CDD KOG1886 KOG1886 229825 KOG1886 KOG1886, BAH domain proteins [Transcription] 464 matched cddid_all.tbl CDD KOG1887 KOG1887 229826 KOG1887 KOG1887, Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones] 806 matched cddid_all.tbl CDD KOG1888 KOG1888 229827 KOG1888 KOG1888, Putative phosphoinositide phosphatase [Lipid transport and metabolism] 868 matched cddid_all.tbl CDD KOG1889 KOG1889 229828 KOG1889 KOG1889, Putative phosphoinositide phosphatase [Lipid transport and metabolism] 579 matched cddid_all.tbl CDD KOG1890 KOG1890 229829 KOG1890 KOG1890, Phosphoinositide phosphatase SAC1 [Lipid transport and metabolism] 949 matched cddid_all.tbl CDD KOG1891 KOG1891 229830 KOG1891 KOG1891, Proline binding protein WW45 [General function prediction only] 271 matched cddid_all.tbl CDD KOG1892 KOG1892 229831 KOG1892 KOG1892, Actin filament-binding protein Afadin [Cytoskeleton] 1629 matched cddid_all.tbl CDD KOG1893 KOG1893 229832 KOG1893 KOG1893, Uncharacterized conserved protein [Function unknown] 861 matched cddid_all.tbl CDD KOG1894 KOG1894 229833 KOG1894 KOG1894, Uncharacterized conserved protein [Function unknown] 412 matched cddid_all.tbl CDD KOG1895 KOG1895 229834 KOG1895 KOG1895, mRNA cleavage and polyadenylation factor II complex, subunit PTA1 [RNA processing and modification] 957 matched cddid_all.tbl CDD KOG1896 KOG1896 229835 KOG1896 KOG1896, mRNA cleavage and polyadenylation factor II complex, subunit CFT1 (CPSF subunit) [RNA processing and modification] 1366 matched cddid_all.tbl CDD KOG1897 KOG1897 229836 KOG1897 KOG1897, Damage-specific DNA binding complex, subunit DDB1 [Replication, recombination and repair] 1096 matched cddid_all.tbl CDD KOG1898 KOG1898 229837 KOG1898 KOG1898, Splicing factor 3b, subunit 3 [RNA processing and modification] 1205 matched cddid_all.tbl CDD KOG1899 KOG1899 229838 KOG1899 KOG1899, LAR transmembrane tyrosine phosphatase-interacting protein liprin [General function prediction only] 861 matched cddid_all.tbl CDD KOG1900 KOG1900 229839 KOG1900 KOG1900, Nuclear pore complex, Nup155 component (D Nup154, sc Nup157/Nup170) [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 1311 matched cddid_all.tbl CDD KOG1901 KOG1901 229840 KOG1901 KOG1901, Uncharacterized high-glucose-regulated protein [General function prediction only] 487 matched cddid_all.tbl CDD KOG1902 KOG1902 229841 KOG1902 KOG1902, Putative signal transduction protein involved in RNA splicing [Signal transduction mechanisms, RNA processing and modification] 441 matched cddid_all.tbl CDD KOG1903 KOG1903 229842 KOG1903 KOG1903, Cell cycle-associated protein [Cell cycle control, cell division, chromosome partitioning] 217 matched cddid_all.tbl CDD KOG1904 KOG1904 229843 KOG1904 KOG1904, Transcription coactivator [Transcription] 496 matched cddid_all.tbl CDD KOG1905 KOG1905 229844 KOG1905 KOG1905, Class IV sirtuins (SIR2 family) [Chromatin structure and dynamics, Transcription] 353 matched cddid_all.tbl CDD KOG1906 KOG1906 229845 KOG1906 KOG1906, DNA polymerase sigma [Replication, recombination and repair] 514 matched cddid_all.tbl CDD KOG1907 KOG1907 229846 KOG1907 KOG1907, Phosphoribosylformylglycinamidine synthase [Nucleotide transport and metabolism] 1320 matched cddid_all.tbl CDD KOG1908 KOG1908 229847 KOG1908 KOG1908, Ribonuclease inhibitor type leucine-rich repeat proteins [RNA processing and modification] 165 matched cddid_all.tbl CDD KOG1909 KOG1909 229848 KOG1909 KOG1909, Ran GTPase-activating protein [RNA processing and modification, Nuclear structure, Signal transduction mechanisms] 382 matched cddid_all.tbl CDD KOG1910 KOG1910 229849 KOG1910 KOG1910, Uncharacterized conserved protein [Function unknown] 2306 matched cddid_all.tbl CDD KOG1911 KOG1911 229850 KOG1911 KOG1911, Heterochromatin-associated protein HP1 and related CHROMO domain proteins [Chromatin structure and dynamics] 270 matched cddid_all.tbl CDD KOG1912 KOG1912 229851 KOG1912 KOG1912, WD40 repeat protein [General function prediction only] 1062 matched cddid_all.tbl CDD KOG1913 KOG1913 229852 KOG1913 KOG1913, Regucalcin gene promoter region-related protein (RGPR) [Transcription] 1423 matched cddid_all.tbl CDD KOG1914 KOG1914 229853 KOG1914 KOG1914, mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification] 656 matched cddid_all.tbl CDD KOG1915 KOG1915 229854 KOG1915 KOG1915, Cell cycle control protein (crooked neck) [Cell cycle control, cell division, chromosome partitioning] 677 matched cddid_all.tbl CDD KOG1916 KOG1916 229855 KOG1916 KOG1916, Nuclear protein, contains WD40 repeats [General function prediction only] 1283 matched cddid_all.tbl CDD KOG1917 KOG1917 229856 KOG1917 KOG1917, Membrane-associated hematopoietic protein [General function prediction only] 1125 matched cddid_all.tbl CDD KOG1918 KOG1918 229857 KOG1918 KOG1918, 3-methyladenine DNA glycosidase [Replication, recombination and repair] 254 matched cddid_all.tbl CDD KOG1919 KOG1919 229858 KOG1919 KOG1919, RNA pseudouridylate synthases [RNA processing and modification] 371 matched cddid_all.tbl CDD KOG1920 KOG1920 229859 KOG1920 KOG1920, IkappaB kinase complex, IKAP component [Transcription] 1265 matched cddid_all.tbl CDD KOG1921 KOG1921 229860 KOG1921 KOG1921, Endonuclease III [Replication, recombination and repair] 286 matched cddid_all.tbl CDD KOG1922 KOG1922 229861 KOG1922 KOG1922, Rho GTPase effector BNI1 and related formins [Signal transduction mechanisms, Cytoskeleton] 833 matched cddid_all.tbl CDD KOG1923 KOG1923 229862 KOG1923 KOG1923, Rac1 GTPase effector FRL [Signal transduction mechanisms, Cytoskeleton] 830 matched cddid_all.tbl CDD KOG1924 KOG1924 229863 KOG1924 KOG1924, RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms, Cytoskeleton] 1102 matched cddid_all.tbl CDD KOG1925 KOG1925 229864 KOG1925 KOG1925, Rac1 GTPase effector FHOS [Signal transduction mechanisms, Cytoskeleton] 817 matched cddid_all.tbl CDD KOG1926 KOG1926 229865 KOG1926 KOG1926, Predicted regulator of rRNA gene transcription (MYB-binding protein) [Transcription] 1129 matched cddid_all.tbl CDD KOG1927 KOG1927 229866 KOG1927 KOG1927, R-kappa-B and related transcription factors [Transcription] 1274 matched cddid_all.tbl CDD KOG1928 KOG1928 229867 KOG1928 KOG1928, Alpha-1,4-N-acetylglucosaminyltransferase [Carbohydrate transport and metabolism] 409 matched cddid_all.tbl CDD KOG1929 KOG1929 229868 KOG1929 KOG1929, Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair] 811 matched cddid_all.tbl CDD KOG1930 KOG1930 229869 KOG1930 KOG1930, Focal adhesion protein Tensin, contains PTB domain [Signal transduction mechanisms, Cytoskeleton] 483 matched cddid_all.tbl CDD KOG1931 KOG1931 229870 KOG1931 KOG1931, Putative transmembrane protein [General function prediction only] 1156 matched cddid_all.tbl CDD KOG1932 KOG1932 229871 KOG1932 KOG1932, TATA binding protein associated factor [Transcription] 1180 matched cddid_all.tbl CDD KOG1933 KOG1933 229872 KOG1933 KOG1933, Cholesterol transport protein (Niemann-Pick C disease protein) [Lipid transport and metabolism] 1201 matched cddid_all.tbl CDD KOG1934 KOG1934 229873 KOG1934 KOG1934, Predicted membrane protein (patched superfamily) [General function prediction only] 868 matched cddid_all.tbl CDD KOG1935 KOG1935 229874 KOG1935 KOG1935, Membrane protein Patched/PTCH [Signal transduction mechanisms] 1143 matched cddid_all.tbl CDD KOG1936 KOG1936 229875 KOG1936 KOG1936, Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 518 matched cddid_all.tbl CDD KOG1937 KOG1937 229876 KOG1937 KOG1937, Uncharacterized conserved protein [Function unknown] 521 matched cddid_all.tbl CDD KOG1938 KOG1938 229877 KOG1938 KOG1938, Protein with predicted involvement in meiosis (GSG1) [Cell cycle control, cell division, chromosome partitioning] 960 matched cddid_all.tbl CDD KOG1939 KOG1939 229878 KOG1939 KOG1939, Oxoprolinase [Amino acid transport and metabolism] 1247 matched cddid_all.tbl CDD KOG1940 KOG1940 229879 KOG1940 KOG1940, Zn-finger protein [General function prediction only] 276 matched cddid_all.tbl CDD KOG1941 KOG1941 229880 KOG1941 KOG1941, Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures] 518 matched cddid_all.tbl CDD KOG1942 KOG1942 229881 KOG1942 KOG1942, DNA helicase, TBP-interacting protein [Replication, recombination and repair] 456 matched cddid_all.tbl CDD KOG1943 KOG1943 229882 KOG1943 KOG1943, Beta-tubulin folding cofactor D [Posttranslational modification, protein turnover, chaperones] 1133 matched cddid_all.tbl CDD KOG1944 KOG1944 229883 KOG1944 KOG1944, Peroxisomal membrane protein MPV17 and related proteins [General function prediction only] 222 matched cddid_all.tbl CDD KOG1945 KOG1945 229884 KOG1945 KOG1945, Protein phosphatase 1 binding protein spinophilin/neurabin II [Signal transduction mechanisms] 377 matched cddid_all.tbl CDD KOG1946 KOG1946 229885 KOG1946 KOG1946, RNA polymerase I transcription factor UAF [Transcription] 240 matched cddid_all.tbl CDD KOG1947 KOG1947 229886 KOG1947 KOG1947, Leucine rich repeat proteins, some proteins contain F-box [General function prediction only] 482 matched cddid_all.tbl CDD KOG1948 KOG1948 229887 KOG1948 KOG1948, Metalloproteinase-related collagenase pM5 [Posttranslational modification, protein turnover, chaperones] 1165 matched cddid_all.tbl CDD KOG1949 KOG1949 229888 KOG1949 KOG1949, Uncharacterized conserved protein [Function unknown] 1005 matched cddid_all.tbl CDD KOG1950 KOG1950 229889 KOG1950 KOG1950, Glycosyl transferase, family 8 - glycogenin [Carbohydrate transport and metabolism] 369 matched cddid_all.tbl CDD KOG1951 KOG1951 229890 KOG1951 KOG1951, GTP-binding protein AARP2 involved in 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis] 115 matched cddid_all.tbl CDD KOG1952 KOG1952 229891 KOG1952 KOG1952, Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription] 950 matched cddid_all.tbl CDD KOG1953 KOG1953 229892 KOG1953 KOG1953, Targeting complex (TRAPP) subunit [Intracellular trafficking, secretion, and vesicular transport] 1235 matched cddid_all.tbl CDD KOG1954 KOG1954 229893 KOG1954 KOG1954, Endocytosis/signaling protein EHD1 [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 532 matched cddid_all.tbl CDD KOG1955 KOG1955 229894 KOG1955 KOG1955, Ral-GTPase effector RALBP1 [Intracellular trafficking, secretion, and vesicular transport] 737 matched cddid_all.tbl CDD KOG1956 KOG1956 229895 KOG1956 KOG1956, DNA topoisomerase III alpha [Replication, recombination and repair] 758 matched cddid_all.tbl CDD KOG1957 KOG1957 229896 KOG1957 KOG1957, DNA topoisomerase III beta [Replication, recombination and repair] 555 matched cddid_all.tbl CDD KOG1958 KOG1958 229897 KOG1958 KOG1958, Glycosyl hydrolase, family 38 - alpha-mannosidase [Carbohydrate transport and metabolism] 1129 matched cddid_all.tbl CDD KOG1959 KOG1959 229898 KOG1959 KOG1959, Glycosyl hydrolase, family 38 - alpha-mannosidase [Carbohydrate transport and metabolism] 996 matched cddid_all.tbl CDD KOG1960 KOG1960 229899 KOG1960 KOG1960, Predicted RNA-binding protein, contains KH domains [RNA processing and modification] 531 matched cddid_all.tbl CDD KOG1961 KOG1961 229900 KOG1961 KOG1961, Vacuolar sorting protein VPS52/suppressor of actin Sac2 [Intracellular trafficking, secretion, and vesicular transport, Cytoskeleton] 683 matched cddid_all.tbl CDD KOG1962 KOG1962 229901 KOG1962 KOG1962, B-cell receptor-associated protein and related proteins [Defense mechanisms] 216 matched cddid_all.tbl CDD KOG1963 KOG1963 229902 KOG1963 KOG1963, WD40 repeat protein [General function prediction only] 792 matched cddid_all.tbl CDD KOG1964 KOG1964 229903 KOG1964 KOG1964, Nuclear pore complex, rNup107 component (sc Nup84) [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 800 matched cddid_all.tbl CDD KOG1965 KOG1965 229904 KOG1965 KOG1965, Sodium/hydrogen exchanger protein [Inorganic ion transport and metabolism] 575 matched cddid_all.tbl CDD KOG1966 KOG1966 229905 KOG1966 KOG1966, Sodium/hydrogen exchanger protein [Inorganic ion transport and metabolism] 670 matched cddid_all.tbl CDD KOG1967 KOG1967 229906 KOG1967 KOG1967, DNA repair/transcription protein Mms19 [Replication, recombination and repair, Transcription] 1030 matched cddid_all.tbl CDD KOG1968 KOG1968 229907 KOG1968 KOG1968, Replication factor C, subunit RFC1 (large subunit) [Replication, recombination and repair] 871 matched cddid_all.tbl CDD KOG1969 KOG1969 229908 KOG1969 KOG1969, DNA replication checkpoint protein CHL12/CTF18 [Energy production and conversion, Replication, recombination and repair] 877 matched cddid_all.tbl CDD KOG1970 KOG1970 229909 KOG1970 KOG1970, Checkpoint RAD17-RFC complex, RAD17/RAD24 component [Energy production and conversion, Replication, recombination and repair] 634 matched cddid_all.tbl CDD KOG1971 KOG1971 229910 KOG1971 KOG1971, Lysyl hydroxylase [Posttranslational modification, protein turnover, chaperones] 415 matched cddid_all.tbl CDD KOG1972 KOG1972 229911 KOG1972 KOG1972, Uncharacterized conserved protein [Function unknown] 913 matched cddid_all.tbl CDD KOG1973 KOG1973 229912 KOG1973 KOG1973, Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics] 274 matched cddid_all.tbl CDD KOG1974 KOG1974 229913 KOG1974 KOG1974, DNA topoisomerase I-interacting protein [Replication, recombination and repair] 1229 matched cddid_all.tbl CDD KOG1975 KOG1975 229914 KOG1975 KOG1975, mRNA cap methyltransferase [RNA processing and modification] 389 matched cddid_all.tbl CDD KOG1976 KOG1976 229915 KOG1976 KOG1976, Inositol polyphosphate 5-phosphatase, type I [Lipid transport and metabolism] 391 matched cddid_all.tbl CDD KOG1977 KOG1977 229916 KOG1977 KOG1977, DNA mismatch repair protein - MLH3 family [Replication, recombination and repair] 1142 matched cddid_all.tbl CDD KOG1978 KOG1978 229917 KOG1978 KOG1978, DNA mismatch repair protein - MLH2/PMS1/Pms2 family [Replication, recombination and repair] 672 matched cddid_all.tbl CDD KOG1979 KOG1979 229918 KOG1979 KOG1979, DNA mismatch repair protein - MLH1 family [Replication, recombination and repair] 694 matched cddid_all.tbl CDD KOG1980 KOG1980 229919 KOG1980 KOG1980, Uncharacterized conserved protein [Function unknown] 754 matched cddid_all.tbl CDD KOG1981 KOG1981 229920 KOG1981 KOG1981, SOK1 kinase belonging to the STE20/SPS1/GC kinase family [Signal transduction mechanisms] 513 matched cddid_all.tbl CDD KOG1982 KOG1982 229921 KOG1982 KOG1982, Nuclear 5'-3' exoribonuclease-interacting protein, Rai1p [Replication, recombination and repair] 359 matched cddid_all.tbl CDD KOG1983 KOG1983 229922 KOG1983 KOG1983, Tomosyn and related SNARE-interacting proteins [Intracellular trafficking, secretion, and vesicular transport] 993 matched cddid_all.tbl CDD KOG1984 KOG1984 229923 KOG1984 KOG1984, Vesicle coat complex COPII, subunit SFB3 [Intracellular trafficking, secretion, and vesicular transport] 1007 matched cddid_all.tbl CDD KOG1985 KOG1985 229924 KOG1985 KOG1985, Vesicle coat complex COPII, subunit SEC24/subunit SFB2 [Intracellular trafficking, secretion, and vesicular transport] 887 matched cddid_all.tbl CDD KOG1986 KOG1986 229925 KOG1986 KOG1986, Vesicle coat complex COPII, subunit SEC23 [Intracellular trafficking, secretion, and vesicular transport] 745 matched cddid_all.tbl CDD KOG1987 KOG1987 229926 KOG1987 KOG1987, Speckle-type POZ protein SPOP and related proteins with TRAF, MATH and BTB/POZ domains [Cell cycle control, cell division, chromosome partitioning, General function prediction only] 297 matched cddid_all.tbl CDD KOG1988 KOG1988 229927 KOG1988 KOG1988, Uncharacterized conserved protein [Function unknown] 970 matched cddid_all.tbl CDD KOG1989 KOG1989 229928 KOG1989 KOG1989, ARK protein kinase family [Signal transduction mechanisms] 738 matched cddid_all.tbl CDD KOG1990 KOG1990 229929 KOG1990 KOG1990, Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair] 564 matched cddid_all.tbl CDD KOG1991 KOG1991 229930 KOG1991 KOG1991, Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 1010 matched cddid_all.tbl CDD KOG1992 KOG1992 229931 KOG1992 KOG1992, Nuclear export receptor CSE1/CAS (importin beta superfamily) [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 960 matched cddid_all.tbl CDD KOG1993 KOG1993 229932 KOG1993 KOG1993, Nuclear transport receptor KAP120 (importin beta superfamily) [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 978 matched cddid_all.tbl CDD KOG1994 KOG1994 229933 KOG1994 KOG1994, Predicted RNA binding protein, contains G-patch and Zn-finger domains [RNA processing and modification] 268 matched cddid_all.tbl CDD KOG1995 KOG1995 229934 KOG1995 KOG1995, Conserved Zn-finger protein [General function prediction only] 351 matched cddid_all.tbl CDD KOG1996 KOG1996 229935 KOG1996 KOG1996, mRNA splicing factor [RNA processing and modification] 378 matched cddid_all.tbl CDD KOG1997 KOG1997 229936 KOG1997 KOG1997, PH domain-containing protein [Signal transduction mechanisms] 1518 matched cddid_all.tbl CDD KOG1998 KOG1998 229937 KOG1998 KOG1998, Signaling protein DOCK180 [Signal transduction mechanisms] 1548 matched cddid_all.tbl CDD KOG1999 KOG1999 229938 KOG1999 KOG1999, RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription] 1024 matched cddid_all.tbl CDD KOG2000 KOG2000 229939 KOG2000 KOG2000, Gamma-tubulin complex, DGRIP91/SPC98 component [Cytoskeleton] 879 matched cddid_all.tbl CDD KOG2001 KOG2001 229940 KOG2001 KOG2001, Gamma-tubulin complex, DGRIP84/SPC97 component [Cytoskeleton] 734 matched cddid_all.tbl CDD KOG2002 KOG2002 229941 KOG2002 KOG2002, TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism] 1018 matched cddid_all.tbl CDD KOG2003 KOG2003 229942 KOG2003 KOG2003, TPR repeat-containing protein [General function prediction only] 840 matched cddid_all.tbl CDD KOG2004 KOG2004 229943 KOG2004 KOG2004, Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones] 906 matched cddid_all.tbl CDD KOG2005 KOG2005 229944 KOG2005 KOG2005, 26S proteasome regulatory complex, subunit RPN1/PSMD2 [Posttranslational modification, protein turnover, chaperones] 878 matched cddid_all.tbl CDD KOG2006 KOG2006 229945 KOG2006 KOG2006, WD40 repeat protein [General function prediction only] 1023 matched cddid_all.tbl CDD KOG2007 KOG2007 229946 KOG2007 KOG2007, Cysteinyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 586 matched cddid_all.tbl CDD KOG2008 KOG2008 229947 KOG2008 KOG2008, BTK-associated SH3-domain binding protein SAB [Signal transduction mechanisms] 426 matched cddid_all.tbl CDD KOG2009 KOG2009 229948 KOG2009 KOG2009, Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription] 584 matched cddid_all.tbl CDD KOG2010 KOG2010 229949 KOG2010 KOG2010, Double stranded RNA binding protein [General function prediction only] 405 matched cddid_all.tbl CDD KOG2011 KOG2011 229950 KOG2011 KOG2011, Sister chromatid cohesion complex Cohesin, subunit STAG/IRR1/SCC3 [Cell cycle control, cell division, chromosome partitioning] 1048 matched cddid_all.tbl CDD KOG2012 KOG2012 229951 KOG2012 KOG2012, Ubiquitin activating enzyme UBA1 [Posttranslational modification, protein turnover, chaperones] 1013 matched cddid_all.tbl CDD KOG2013 KOG2013 229952 KOG2013 KOG2013, SMT3/SUMO-activating complex, catalytic component UBA2 [Posttranslational modification, protein turnover, chaperones] 603 matched cddid_all.tbl CDD KOG2014 KOG2014 229953 KOG2014 KOG2014, SMT3/SUMO-activating complex, AOS1/RAD31 component [Posttranslational modification, protein turnover, chaperones] 331 matched cddid_all.tbl CDD KOG2015 KOG2015 229954 KOG2015 KOG2015, NEDD8-activating complex, catalytic component UBA3 [Posttranslational modification, protein turnover, chaperones] 422 matched cddid_all.tbl CDD KOG2016 KOG2016 229955 KOG2016 KOG2016, NEDD8-activating complex, APP-BP1/UBA5 component [Posttranslational modification, protein turnover, chaperones] 523 matched cddid_all.tbl CDD KOG2017 KOG2017 229956 KOG2017 KOG2017, Molybdopterin synthase sulfurylase [Coenzyme transport and metabolism] 427 matched cddid_all.tbl CDD KOG2018 KOG2018 229957 KOG2018 KOG2018, Predicted dinucleotide-utilizing enzyme involved in molybdopterin and thiamine biosynthesis [Posttranslational modification, protein turnover, chaperones] 430 matched cddid_all.tbl CDD KOG2019 KOG2019 229958 KOG2019 KOG2019, Metalloendoprotease HMP1 (insulinase superfamily) [General function prediction only, Posttranslational modification, protein turnover, chaperones] 998 matched cddid_all.tbl CDD KOG2020 KOG2020 229959 KOG2020 KOG2020, Nuclear transport receptor CRM1/MSN5 (importin beta superfamily) [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 1041 matched cddid_all.tbl CDD KOG2021 KOG2021 229960 KOG2021 KOG2021, Nuclear mRNA export factor receptor LOS1/Exportin-t (importin beta superfamily) [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport, Translation, ribosomal structure and biogenesis] 980 matched cddid_all.tbl CDD KOG2022 KOG2022 229961 KOG2022 KOG2022, Nuclear transport receptor LGL2 (importin beta superfamily) [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 982 matched cddid_all.tbl CDD KOG2023 KOG2023 229962 KOG2023 KOG2023, Nuclear transport receptor Karyopherin-beta2/Transportin (importin beta superfamily) [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 885 matched cddid_all.tbl CDD KOG2024 KOG2024 229963 KOG2024 KOG2024, Beta-Glucuronidase GUSB (glycosylhydrolase superfamily 2) [Carbohydrate transport and metabolism] 297 matched cddid_all.tbl CDD KOG2025 KOG2025 229964 KOG2025 KOG2025, Chromosome condensation complex Condensin, subunit G [Chromatin structure and dynamics, Cell cycle control, cell division, chromosome partitioning] 892 matched cddid_all.tbl CDD KOG2026 KOG2026 229965 KOG2026 KOG2026, Spindle pole body protein - Sad1p [Cytoskeleton] 442 matched cddid_all.tbl CDD KOG2027 KOG2027 229966 KOG2027 KOG2027, Spindle pole body protein [Cytoskeleton] 388 matched cddid_all.tbl CDD KOG2028 KOG2028 229967 KOG2028 KOG2028, ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair] 554 matched cddid_all.tbl CDD KOG2029 KOG2029 229968 KOG2029 KOG2029, Uncharacterized conserved protein [Function unknown] 697 matched cddid_all.tbl CDD KOG2030 KOG2030 229969 KOG2030 KOG2030, Predicted RNA-binding protein [General function prediction only] 911 matched cddid_all.tbl CDD KOG2031 KOG2031 229970 KOG2031 KOG2031, Tyrosyl-DNA phosphodiesterase [Replication, recombination and repair] 519 matched cddid_all.tbl CDD KOG2032 KOG2032 229971 KOG2032 KOG2032, Uncharacterized conserved protein [Function unknown] 533 matched cddid_all.tbl CDD KOG2033 KOG2033 229972 KOG2033 KOG2033, Low density lipoprotein B-like protein [Lipid transport and metabolism] 863 matched cddid_all.tbl CDD KOG2034 KOG2034 229973 KOG2034 KOG2034, Vacuolar sorting protein PEP3/VPS18 [Intracellular trafficking, secretion, and vesicular transport] 911 matched cddid_all.tbl CDD KOG2035 KOG2035 229974 KOG2035 KOG2035, Replication factor C, subunit RFC3 [Energy production and conversion, Replication, recombination and repair] 351 matched cddid_all.tbl CDD KOG2036 KOG2036 229975 KOG2036 KOG2036, Predicted P-loop ATPase fused to an acetyltransferase [General function prediction only] 1011 matched cddid_all.tbl CDD KOG2037 KOG2037 229976 KOG2037 KOG2037, Guanylate-binding protein [General function prediction only] 552 matched cddid_all.tbl CDD KOG2038 KOG2038 229977 KOG2038 KOG2038, CAATT-binding transcription factor/60S ribosomal subunit biogenesis protein [Translation, ribosomal structure and biogenesis, Transcription] 988 matched cddid_all.tbl CDD KOG2039 KOG2039 229978 KOG2039 KOG2039, Transcriptional coactivator p100 [Transcription] 875 matched cddid_all.tbl CDD KOG2040 KOG2040 229979 KOG2040 KOG2040, Glycine dehydrogenase (decarboxylating) [Amino acid transport and metabolism] 1001 matched cddid_all.tbl CDD KOG2041 KOG2041 229980 KOG2041 KOG2041, WD40 repeat protein [General function prediction only] 1189 matched cddid_all.tbl CDD KOG2042 KOG2042 229981 KOG2042 KOG2042, Ubiquitin fusion degradation protein-2 [Posttranslational modification, protein turnover, chaperones] 943 matched cddid_all.tbl CDD KOG2043 KOG2043 229982 KOG2043 KOG2043, Signaling protein SWIFT and related BRCT domain proteins [Transcription, Signal transduction mechanisms, Cell cycle control, cell division, chromosome partitioning, Replication, recombination and repair] 896 matched cddid_all.tbl CDD KOG2044 KOG2044 229983 KOG2044 KOG2044, 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair, RNA processing and modification] 931 matched cddid_all.tbl CDD KOG2045 KOG2045 229984 KOG2045 KOG2045, 5'-3' exonuclease XRN1/KEM1/SEP1 involved in DNA strand exchange and mRNA turnover [Replication, recombination and repair, Cell cycle control, cell division, chromosome partitioning] 1493 matched cddid_all.tbl CDD KOG2046 KOG2046 229985 KOG2046 KOG2046, Calponin [Cytoskeleton] 193 matched cddid_all.tbl CDD KOG2047 KOG2047 229986 KOG2047 KOG2047, mRNA splicing factor [RNA processing and modification] 835 matched cddid_all.tbl CDD KOG2048 KOG2048 229987 KOG2048 KOG2048, WD40 repeat protein [General function prediction only] 691 matched cddid_all.tbl CDD KOG2049 KOG2049 229988 KOG2049 KOG2049, Translational repressor MPT5/PUF4 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis] 536 matched cddid_all.tbl CDD KOG2050 KOG2050 229989 KOG2050 KOG2050, Puf family RNA-binding protein [Translation, ribosomal structure and biogenesis] 652 matched cddid_all.tbl CDD KOG2051 KOG2051 229990 KOG2051 KOG2051, Nonsense-mediated mRNA decay 2 protein [RNA processing and modification] 1128 matched cddid_all.tbl CDD KOG2052 KOG2052 229991 KOG2052 KOG2052, Activin A type IB receptor, serine/threonine protein kinase [Signal transduction mechanisms] 513 matched cddid_all.tbl CDD KOG2053 KOG2053 229992 KOG2053 KOG2053, Mitochondrial inheritance and actin cytoskeleton organization protein [Cytoskeleton] 932 matched cddid_all.tbl CDD KOG2054 KOG2054 229993 KOG2054 KOG2054, Nucleolar RNA-associated protein (NRAP) [Function unknown] 1121 matched cddid_all.tbl CDD KOG2055 KOG2055 229994 KOG2055 KOG2055, WD40 repeat protein [General function prediction only] 514 matched cddid_all.tbl CDD KOG2056 KOG2056 229995 KOG2056 KOG2056, Equilibrative nucleoside transporter protein [Nucleotide transport and metabolism] 336 matched cddid_all.tbl CDD KOG2057 KOG2057 229996 KOG2057 KOG2057, Predicted equilibrative nucleoside transporter protein [Nucleotide transport and metabolism] 499 matched cddid_all.tbl CDD KOG2058 KOG2058 229997 KOG2058 KOG2058, Ypt/Rab GTPase activating protein [Intracellular trafficking, secretion, and vesicular transport] 436 matched cddid_all.tbl CDD KOG2059 KOG2059 229998 KOG2059 KOG2059, Ras GTPase-activating protein [Signal transduction mechanisms] 800 matched cddid_all.tbl CDD KOG2060 KOG2060 229999 KOG2060 KOG2060, Rab3 effector RIM1 and related proteins, contain PDZ and C2 domains [Intracellular trafficking, secretion, and vesicular transport] 405 matched cddid_all.tbl CDD KOG2061 KOG2061 230000 KOG2061 KOG2061, Uncharacterized MYND Zn-finger protein [General function prediction only] 362 matched cddid_all.tbl CDD KOG2062 KOG2062 230001 KOG2062 KOG2062, 26S proteasome regulatory complex, subunit RPN2/PSMD1 [Posttranslational modification, protein turnover, chaperones] 929 matched cddid_all.tbl CDD KOG2063 KOG2063 230002 KOG2063 KOG2063, Vacuolar assembly/sorting proteins VPS39/VAM6/VPS3 [Intracellular trafficking, secretion, and vesicular transport] 877 matched cddid_all.tbl CDD KOG2064 KOG2064 230003 KOG2064 KOG2064, Poly(ADP-ribose) glycohydrolase [Signal transduction mechanisms] 517 matched cddid_all.tbl CDD KOG2065 KOG2065 230004 KOG2065 KOG2065, Gamma-tubulin ring complex protein [Cytoskeleton] 679 matched cddid_all.tbl CDD KOG2066 KOG2066 230005 KOG2066 KOG2066, Vacuolar assembly/sorting protein VPS41 [Intracellular trafficking, secretion, and vesicular transport] 846 matched cddid_all.tbl CDD KOG2067 KOG2067 230006 KOG2067 KOG2067, Mitochondrial processing peptidase, alpha subunit [Posttranslational modification, protein turnover, chaperones] 472 matched cddid_all.tbl CDD KOG2068 KOG2068 230007 KOG2068 KOG2068, MOT2 transcription factor [Transcription] 327 matched cddid_all.tbl CDD KOG2069 KOG2069 230008 KOG2069 KOG2069, Golgi transport complex subunit [Intracellular trafficking, secretion, and vesicular transport] 581 matched cddid_all.tbl CDD KOG2070 KOG2070 230009 KOG2070 KOG2070, Guanine nucleotide exchange factor [Nucleotide transport and metabolism] 661 matched cddid_all.tbl CDD KOG2071 KOG2071 230010 KOG2071 KOG2071, mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification] 579 matched cddid_all.tbl CDD KOG2072 KOG2072 230011 KOG2072 KOG2072, Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis] 988 matched cddid_all.tbl CDD KOG2073 KOG2073 230012 KOG2073 KOG2073, SAP family cell cycle dependent phosphatase-associated protein [Cell cycle control, cell division, chromosome partitioning] 838 matched cddid_all.tbl CDD KOG2074 KOG2074 230013 KOG2074 KOG2074, RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB1 [Transcription, Replication, recombination and repair] 548 matched cddid_all.tbl CDD KOG2075 KOG2075 230014 KOG2075 KOG2075, Topoisomerase TOP1-interacting protein BTBD1 [Function unknown] 521 matched cddid_all.tbl CDD KOG2076 KOG2076 230015 KOG2076 KOG2076, RNA polymerase III transcription factor TFIIIC [Transcription] 895 matched cddid_all.tbl CDD KOG2077 KOG2077 230016 KOG2077 KOG2077, JNK/SAPK-associated protein-1 [Signal transduction mechanisms] 832 matched cddid_all.tbl CDD KOG2078 KOG2078 230017 KOG2078 KOG2078, tRNA modification enzyme [RNA processing and modification] 495 matched cddid_all.tbl CDD KOG2079 KOG2079 230018 KOG2079 KOG2079, Vacuolar assembly/sorting protein VPS8 [Intracellular trafficking, secretion, and vesicular transport] 1206 matched cddid_all.tbl CDD KOG2080 KOG2080 230019 KOG2080 KOG2080, Uncharacterized conserved protein, contains DENN and RUN domains [Signal transduction mechanisms] 1295 matched cddid_all.tbl CDD KOG2081 KOG2081 230020 KOG2081 KOG2081, Nuclear transport regulator [Intracellular trafficking, secretion, and vesicular transport] 559 matched cddid_all.tbl CDD KOG2082 KOG2082 230021 KOG2082 KOG2082, K+/Cl- cotransporter KCC1 and related transporters [Inorganic ion transport and metabolism] 1075 matched cddid_all.tbl CDD KOG2083 KOG2083 230022 KOG2083 KOG2083, Na+/K+ symporter [Inorganic ion transport and metabolism] 643 matched cddid_all.tbl CDD KOG2084 KOG2084 230023 KOG2084 KOG2084, Predicted histone tail methylase containing SET domain [Chromatin structure and dynamics] 482 matched cddid_all.tbl CDD KOG2085 KOG2085 230024 KOG2085 KOG2085, Serine/threonine protein phosphatase 2A, regulatory subunit [Signal transduction mechanisms] 457 matched cddid_all.tbl CDD KOG2086 KOG2086 230025 KOG2086 KOG2086, Protein tyrosine phosphatase SHP1/Cofactor for p97 ATPase-mediated vesicle membrane fusion [Nuclear structure] 380 matched cddid_all.tbl CDD KOG2087 KOG2087 230026 KOG2087 KOG2087, Glycoprotein hormone receptor [Signal transduction mechanisms] 363 matched cddid_all.tbl CDD KOG2088 KOG2088 230027 KOG2088 KOG2088, Predicted lipase/calmodulin-binding heat-shock protein [Lipid transport and metabolism, Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms] 596 matched cddid_all.tbl CDD KOG2089 KOG2089 230028 KOG2089 KOG2089, Metalloendopeptidase family - saccharolysin & thimet oligopeptidase [Posttranslational modification, protein turnover, chaperones] 718 matched cddid_all.tbl CDD KOG2090 KOG2090 230029 KOG2090 KOG2090, Metalloendopeptidase family - mitochondrial intermediate peptidase [Posttranslational modification, protein turnover, chaperones] 704 matched cddid_all.tbl CDD KOG2091 KOG2091 230030 KOG2091 KOG2091, Predicted member of glycosyl hydrolase family 18 [Carbohydrate transport and metabolism] 392 matched cddid_all.tbl CDD KOG2092 KOG2092 230031 KOG2092 KOG2092, Uncharacterized conserved protein [Function unknown] 381 matched cddid_all.tbl CDD KOG2093 KOG2093 230032 KOG2093 KOG2093, Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair] 1016 matched cddid_all.tbl CDD KOG2094 KOG2094 230033 KOG2094 KOG2094, Predicted DNA damage inducible protein [Replication, recombination and repair] 490 matched cddid_all.tbl CDD KOG2095 KOG2095 230034 KOG2095 KOG2095, DNA polymerase iota/DNA damage inducible protein [Replication, recombination and repair] 656 matched cddid_all.tbl CDD KOG2096 KOG2096 230035 KOG2096 KOG2096, WD40 repeat protein [General function prediction only] 420 matched cddid_all.tbl CDD KOG2097 KOG2097 230036 KOG2097 KOG2097, Predicted N6-adenine methylase involved in transcription regulation [Transcription] 397 matched cddid_all.tbl CDD KOG2098 KOG2098 230037 KOG2098 KOG2098, Predicted N6-adenine RNA methylase [RNA processing and modification] 591 matched cddid_all.tbl CDD KOG2099 KOG2099 230038 KOG2099 KOG2099, Glycogen phosphorylase [Carbohydrate transport and metabolism] 843 matched cddid_all.tbl CDD KOG2100 KOG2100 230039 KOG2100 KOG2100, Dipeptidyl aminopeptidase [Posttranslational modification, protein turnover, chaperones] 755 matched cddid_all.tbl CDD KOG2101 KOG2101 230040 KOG2101 KOG2101, Intermediate filament-like protein, sorting nexins, and related proteins containing PX (PhoX) domain(s) [Cytoskeleton, Intracellular trafficking, secretion, and vesicular transport, Cell cycle control, cell division, chromosome partitioning] 362 matched cddid_all.tbl CDD KOG2102 KOG2102 230041 KOG2102 KOG2102, Exosomal 3'-5' exoribonuclease complex, subunit Rrp44/Dis3 [Translation, ribosomal structure and biogenesis] 941 matched cddid_all.tbl CDD KOG2103 KOG2103 230042 KOG2103 KOG2103, Uncharacterized conserved protein [Function unknown] 910 matched cddid_all.tbl CDD KOG2104 KOG2104 230043 KOG2104 KOG2104, Nuclear transport factor 2 [Intracellular trafficking, secretion, and vesicular transport] 126 matched cddid_all.tbl CDD KOG2105 KOG2105 230044 KOG2105 KOG2105, Predicted metal-dependent hydrolase, contains AlaS domain [General function prediction only] 415 matched cddid_all.tbl CDD KOG2106 KOG2106 230045 KOG2106 KOG2106, Uncharacterized conserved protein, contains HELP and WD40 domains [Function unknown] 626 matched cddid_all.tbl CDD KOG2107 KOG2107 230046 KOG2107 KOG2107, Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown] 179 matched cddid_all.tbl CDD KOG2108 KOG2108 230047 KOG2108 KOG2108, 3'-5' DNA helicase [Replication, recombination and repair] 853 matched cddid_all.tbl CDD KOG2109 KOG2109 230048 KOG2109 KOG2109, WD40 repeat protein [General function prediction only] 788 matched cddid_all.tbl CDD KOG2110 KOG2110 230049 KOG2110 KOG2110, Uncharacterized conserved protein, contains WD40 repeats [Function unknown] 391 matched cddid_all.tbl CDD KOG2111 KOG2111 230050 KOG2111 KOG2111, Uncharacterized conserved protein, contains WD40 repeats [Function unknown] 346 matched cddid_all.tbl CDD KOG2112 KOG2112 230051 KOG2112 KOG2112, Lysophospholipase [Lipid transport and metabolism] 206 matched cddid_all.tbl CDD KOG2113 KOG2113 230052 KOG2113 KOG2113, Predicted RNA binding protein, contains KH domain [General function prediction only] 394 matched cddid_all.tbl CDD KOG2114 KOG2114 230053 KOG2114 KOG2114, Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport] 933 matched cddid_all.tbl CDD KOG2115 KOG2115 230054 KOG2115 KOG2115, Vacuolar sorting protein VPS45 [Intracellular trafficking, secretion, and vesicular transport] 951 matched cddid_all.tbl CDD KOG2116 KOG2116 230055 KOG2116 KOG2116, Protein involved in plasmid maintenance/nuclear protein involved in lipid metabolism [Cell motility, Lipid transport and metabolism] 738 matched cddid_all.tbl CDD KOG2117 KOG2117 230056 KOG2117 KOG2117, Uncharacterized conserved protein [Function unknown] 379 matched cddid_all.tbl CDD KOG2118 KOG2118 230057 KOG2118 KOG2118, Predicted membrane protein, contains two CBS domains [Function unknown] 498 matched cddid_all.tbl CDD KOG2119 KOG2119 230058 KOG2119 KOG2119, Predicted bile acid beta-glucosidase [Carbohydrate transport and metabolism] 879 matched cddid_all.tbl CDD KOG2120 KOG2120 230059 KOG2120 KOG2120, SCF ubiquitin ligase, Skp2 component [Posttranslational modification, protein turnover, chaperones] 419 matched cddid_all.tbl CDD KOG2121 KOG2121 230060 KOG2121 KOG2121, Predicted metal-dependent hydrolase (beta-lactamase superfamily) [General function prediction only] 746 matched cddid_all.tbl CDD KOG2122 KOG2122 230061 KOG2122 KOG2122, Beta-catenin-binding protein APC, contains ARM repeats [Signal transduction mechanisms, Cytoskeleton] 2195 matched cddid_all.tbl CDD KOG2123 KOG2123 230062 KOG2123 KOG2123, Uncharacterized conserved protein [Function unknown] 388 matched cddid_all.tbl CDD KOG2124 KOG2124 230063 KOG2124 KOG2124, Glycosylphosphatidylinositol anchor synthesis protein [Signal transduction mechanisms] 883 matched cddid_all.tbl CDD KOG2125 KOG2125 230064 KOG2125 KOG2125, Glycosylphosphatidylinositol anchor synthesis protein [Signal transduction mechanisms] 760 matched cddid_all.tbl CDD KOG2126 KOG2126 230065 KOG2126 KOG2126, Glycosylphosphatidylinositol anchor synthesis protein [Signal transduction mechanisms] 895 matched cddid_all.tbl CDD KOG2127 KOG2127 230066 KOG2127 KOG2127, Calmodulin-binding protein CRAG, contains DENN domain [Signal transduction mechanisms] 1020 matched cddid_all.tbl CDD KOG2128 KOG2128 230067 KOG2128 KOG2128, Ras GTPase-activating protein family - IQGAP [Signal transduction mechanisms] 1401 matched cddid_all.tbl CDD KOG2129 KOG2129 230068 KOG2129 KOG2129, Uncharacterized conserved protein H4 [Function unknown] 552 matched cddid_all.tbl CDD KOG2130 KOG2130 230069 KOG2130 KOG2130, Phosphatidylserine-specific receptor PtdSerR, contains JmjC domain [Chromatin structure and dynamics, Signal transduction mechanisms] 407 matched cddid_all.tbl CDD KOG2131 KOG2131 230070 KOG2131 KOG2131, Uncharacterized conserved protein, contains JmjC domain [Chromatin structure and dynamics, Signal transduction mechanisms] 427 matched cddid_all.tbl CDD KOG2132 KOG2132 230071 KOG2132 KOG2132, Uncharacterized conserved protein, contains JmjC domain [Chromatin structure and dynamics, Signal transduction mechanisms] 355 matched cddid_all.tbl CDD KOG2133 KOG2133 230072 KOG2133 KOG2133, Transcriptional corepressor Atrophin-1/DRPLA [General function prediction only] 1229 matched cddid_all.tbl CDD KOG2134 KOG2134 230073 KOG2134 KOG2134, Polynucleotide kinase 3' phosphatase [Replication, recombination and repair] 422 matched cddid_all.tbl CDD KOG2135 KOG2135 230074 KOG2135 KOG2135, Proteins containing the RNA recognition motif [General function prediction only] 526 matched cddid_all.tbl CDD KOG2136 KOG2136 230075 KOG2136 KOG2136, Transcriptional regulators binding to the GC-rich sequences [Transcription] 434 matched cddid_all.tbl CDD KOG2137 KOG2137 230076 KOG2137 KOG2137, Protein kinase [Signal transduction mechanisms] 700 matched cddid_all.tbl CDD KOG2138 KOG2138 230077 KOG2138 KOG2138, Predicted RNA binding protein, contains G-patch domain [RNA processing and modification] 883 matched cddid_all.tbl CDD KOG2139 KOG2139 230078 KOG2139 KOG2139, WD40 repeat protein [General function prediction only] 445 matched cddid_all.tbl CDD KOG2140 KOG2140 230079 KOG2140 KOG2140, Uncharacterized conserved protein [General function prediction only] 739 matched cddid_all.tbl CDD KOG2141 KOG2141 230080 KOG2141 KOG2141, Protein involved in high osmolarity signaling pathway [Signal transduction mechanisms] 822 matched cddid_all.tbl CDD KOG2142 KOG2142 230081 KOG2142 KOG2142, Molybdenum cofactor sulfurase [Coenzyme transport and metabolism] 728 matched cddid_all.tbl CDD KOG2143 KOG2143 230082 KOG2143 KOG2143, Uncharacterized conserved protein [Function unknown] 854 matched cddid_all.tbl CDD KOG2144 KOG2144 230083 KOG2144 KOG2144, Tyrosyl-tRNA synthetase, cytoplasmic [Translation, ribosomal structure and biogenesis] 360 matched cddid_all.tbl CDD KOG2145 KOG2145 230084 KOG2145 KOG2145, Cytoplasmic tryptophanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 397 matched cddid_all.tbl CDD KOG2146 KOG2146 230085 KOG2146 KOG2146, Splicing coactivator SRm160/300, subunit SRm160 (contains PWI domain) [RNA processing and modification, General function prediction only] 354 matched cddid_all.tbl CDD KOG2147 KOG2147 230086 KOG2147 KOG2147, Nucleolar protein involved in 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis] 823 matched cddid_all.tbl CDD KOG2148 KOG2148 230087 KOG2148 KOG2148, Exocyst protein Sec3 [Intracellular trafficking, secretion, and vesicular transport] 867 matched cddid_all.tbl CDD KOG2149 KOG2149 230088 KOG2149 KOG2149, Uncharacterized conserved protein [Function unknown] 393 matched cddid_all.tbl CDD KOG2150 KOG2150 230089 KOG2150 KOG2150, CCR4-NOT transcriptional regulation complex, NOT5 subunit [Transcription] 575 matched cddid_all.tbl CDD KOG2151 KOG2151 230090 KOG2151 KOG2151, Predicted transcriptional regulator [Transcription, Cell cycle control, cell division, chromosome partitioning, General function prediction only] 312 matched cddid_all.tbl CDD KOG2152 KOG2152 230091 KOG2152 KOG2152, Sister chromatid cohesion protein [Cell cycle control, cell division, chromosome partitioning] 865 matched cddid_all.tbl CDD KOG2153 KOG2153 230092 KOG2153 KOG2153, Protein involved in the nuclear export of pre-ribosomes [Translation, ribosomal structure and biogenesis, Intracellular trafficking, secretion, and vesicular transport] 704 matched cddid_all.tbl CDD KOG2154 KOG2154 230093 KOG2154 KOG2154, Predicted nucleolar protein involved in ribosome biogenesis [Translation, ribosomal structure and biogenesis] 505 matched cddid_all.tbl CDD KOG2155 KOG2155 230094 KOG2155 KOG2155, Tubulin-tyrosine ligase-related protein [Posttranslational modification, protein turnover, chaperones] 631 matched cddid_all.tbl CDD KOG2156 KOG2156 230095 KOG2156 KOG2156, Tubulin-tyrosine ligase-related protein [Posttranslational modification, protein turnover, chaperones] 662 matched cddid_all.tbl CDD KOG2157 KOG2157 230096 KOG2157 KOG2157, Predicted tubulin-tyrosine ligase [Posttranslational modification, protein turnover, chaperones] 497 matched cddid_all.tbl CDD KOG2158 KOG2158 230097 KOG2158 KOG2158, Tubulin-tyrosine ligase-related protein [Posttranslational modification, protein turnover, chaperones] 565 matched cddid_all.tbl CDD KOG2159 KOG2159 230098 KOG2159 KOG2159, tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis] 416 matched cddid_all.tbl CDD KOG2160 KOG2160 230099 KOG2160 KOG2160, Armadillo/beta-catenin-like repeat-containing protein [Posttranslational modification, protein turnover, chaperones] 342 matched cddid_all.tbl CDD KOG2161 KOG2161 230100 KOG2161 KOG2161, Glucosidase I [Carbohydrate transport and metabolism] 849 matched cddid_all.tbl CDD KOG2162 KOG2162 230101 KOG2162 KOG2162, Nonsense-mediated mRNA decay protein [RNA processing and modification] 862 matched cddid_all.tbl CDD KOG2163 KOG2163 230102 KOG2163 KOG2163, Centromere/kinetochore protein zw10 involved in mitotic chromosome segregation [Cell cycle control, cell division, chromosome partitioning] 719 matched cddid_all.tbl CDD KOG2164 KOG2164 230103 KOG2164 KOG2164, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 513 matched cddid_all.tbl CDD KOG2165 KOG2165 230104 KOG2165 KOG2165, Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning, Posttranslational modification, protein turnover, chaperones] 765 matched cddid_all.tbl CDD KOG2166 KOG2166 230105 KOG2166 KOG2166, Cullins [Cell cycle control, cell division, chromosome partitioning] 475 matched cddid_all.tbl CDD KOG2167 KOG2167 230106 KOG2167 KOG2167, Cullins [Cell cycle control, cell division, chromosome partitioning] 661 matched cddid_all.tbl CDD KOG2168 KOG2168 230107 KOG2168 KOG2168, Cullins [Cell cycle control, cell division, chromosome partitioning] 835 matched cddid_all.tbl CDD KOG2169 KOG2169 230108 KOG2169 KOG2169, Zn-finger transcription factor [Transcription] 636 matched cddid_all.tbl CDD KOG2170 KOG2170 230109 KOG2170 KOG2170, ATPase of the AAA+ superfamily [General function prediction only] 344 matched cddid_all.tbl CDD KOG2171 KOG2171 230110 KOG2171 KOG2171, Karyopherin (importin) beta 3 [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 1075 matched cddid_all.tbl CDD KOG2172 KOG2172 230111 KOG2172 KOG2172, Uncharacterized conserved protein [Function unknown] 654 matched cddid_all.tbl CDD KOG2173 KOG2173 230112 KOG2173 KOG2173, Integral membrane protein [General function prediction only] 849 matched cddid_all.tbl CDD KOG2174 KOG2174 230113 KOG2174 KOG2174, Leptin receptor gene-related protein [Signal transduction mechanisms] 131 matched cddid_all.tbl CDD KOG2175 KOG2175 230114 KOG2175 KOG2175, Protein predicted to be involved in carbohydrate metabolism [Carbohydrate transport and metabolism] 458 matched cddid_all.tbl CDD KOG2176 KOG2176 230115 KOG2176 KOG2176, Exocyst complex, subunit SEC15 [Intracellular trafficking, secretion, and vesicular transport] 296 matched cddid_all.tbl CDD KOG2177 KOG2177 230116 KOG2177 KOG2177, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 326 matched cddid_all.tbl CDD KOG2178 KOG2178 230117 KOG2178 KOG2178, Predicted sugar kinase [Carbohydrate transport and metabolism] 409 matched cddid_all.tbl CDD KOG2179 KOG2179 230118 KOG2179 KOG2179, Nucleotide excision repair complex XPC-HR23B, subunit XPC/DPB11 [Replication, recombination and repair] 669 matched cddid_all.tbl CDD KOG2180 KOG2180 230119 KOG2180 KOG2180, Late Golgi protein sorting complex, subunit Vps53 [Intracellular trafficking, secretion, and vesicular transport] 793 matched cddid_all.tbl CDD KOG2181 KOG2181 230120 KOG2181 KOG2181, LIM domain binding protein LDB1/NLI/CLIM [Transcription] 415 matched cddid_all.tbl CDD KOG2182 KOG2182 230121 KOG2182 KOG2182, Hydrolytic enzymes of the alpha/beta hydrolase fold [Posttranslational modification, protein turnover, chaperones, General function prediction only] 514 matched cddid_all.tbl CDD KOG2183 KOG2183 230122 KOG2183 KOG2183, Prolylcarboxypeptidase (angiotensinase C) [Posttranslational modification, protein turnover, chaperones, General function prediction only] 492 matched cddid_all.tbl CDD KOG2184 KOG2184 230123 KOG2184 KOG2184, Tuftelin-interacting protein TIP39, contains G-patch domain [RNA processing and modification] 767 matched cddid_all.tbl CDD KOG2185 KOG2185 230124 KOG2185 KOG2185, Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification] 486 matched cddid_all.tbl CDD KOG2186 KOG2186 230125 KOG2186 KOG2186, Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning] 276 matched cddid_all.tbl CDD KOG2187 KOG2187 230126 KOG2187 KOG2187, tRNA uracil-5-methyltransferase and related tRNA-modifying enzymes [Translation, ribosomal structure and biogenesis] 534 matched cddid_all.tbl CDD KOG2188 KOG2188 230127 KOG2188 KOG2188, Predicted RNA-binding protein, contains Pumilio domains [Translation, ribosomal structure and biogenesis] 650 matched cddid_all.tbl CDD KOG2189 KOG2189 230128 KOG2189 KOG2189, Vacuolar H+-ATPase V0 sector, subunit a [Energy production and conversion] 829 matched cddid_all.tbl CDD KOG2190 KOG2190 230129 KOG2190 KOG2190, PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification, General function prediction only] 485 matched cddid_all.tbl CDD KOG2191 KOG2191 230130 KOG2191 KOG2191, RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification, General function prediction only] 402 matched cddid_all.tbl CDD KOG2192 KOG2192 230131 KOG2192 KOG2192, PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification, General function prediction only] 390 matched cddid_all.tbl CDD KOG2193 KOG2193 230132 KOG2193 KOG2193, IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification, General function prediction only] 584 matched cddid_all.tbl CDD KOG2194 KOG2194 230133 KOG2194 KOG2194, Aminopeptidases of the M20 family [Posttranslational modification, protein turnover, chaperones, General function prediction only] 834 matched cddid_all.tbl CDD KOG2195 KOG2195 230134 KOG2195 KOG2195, Transferrin receptor and related proteins containing the protease-associated (PA) domain [Posttranslational modification, protein turnover, chaperones, Inorganic ion transport and metabolism, General function prediction only] 702 matched cddid_all.tbl CDD KOG2196 KOG2196 230135 KOG2196 KOG2196, Nuclear porin [Nuclear structure] 254 matched cddid_all.tbl CDD KOG2197 KOG2197 230136 KOG2197 KOG2197, Ypt/Rab-specific GTPase-activating protein GYP7 and related proteins [Signal transduction mechanisms] 488 matched cddid_all.tbl CDD KOG2198 KOG2198 230137 KOG2198 KOG2198, tRNA cytosine-5-methylases and related enzymes of the NOL1/NOP2/sun superfamily [Translation, ribosomal structure and biogenesis] 375 matched cddid_all.tbl CDD KOG2199 KOG2199 230138 KOG2199 KOG2199, Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms] 462 matched cddid_all.tbl CDD KOG2200 KOG2200 230139 KOG2200 KOG2200, Tumour suppressor protein p122-RhoGAP/DLC1 [Signal transduction mechanisms] 674 matched cddid_all.tbl CDD KOG2201 KOG2201 230140 KOG2201 KOG2201, Pantothenate kinase PanK and related proteins [Coenzyme transport and metabolism] 371 matched cddid_all.tbl CDD KOG2202 KOG2202 230141 KOG2202 KOG2202, U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification] 260 matched cddid_all.tbl CDD KOG2203 KOG2203 230142 KOG2203 KOG2203, GTP-binding protein [General function prediction only] 772 matched cddid_all.tbl CDD KOG2204 KOG2204 230143 KOG2204 KOG2204, Mannosyl-oligosaccharide alpha-1,2-mannosidase and related glycosyl hydrolases [Carbohydrate transport and metabolism] 625 matched cddid_all.tbl CDD KOG2205 KOG2205 230144 KOG2205 KOG2205, Uncharacterized conserved protein [Function unknown] 424 matched cddid_all.tbl CDD KOG2206 KOG2206 230145 KOG2206 KOG2206, Exosome 3'-5' exoribonuclease complex, subunit PM/SCL-100 (Rrp6) [Translation, ribosomal structure and biogenesis] 687 matched cddid_all.tbl CDD KOG2207 KOG2207 230146 KOG2207 KOG2207, Predicted 3'-5' exonuclease [Replication, recombination and repair] 617 matched cddid_all.tbl CDD KOG2208 KOG2208 230147 KOG2208 KOG2208, Vigilin [Lipid transport and metabolism] 753 matched cddid_all.tbl CDD KOG2209 KOG2209 230148 KOG2209 KOG2209, Oxysterol-binding protein [Signal transduction mechanisms] 445 matched cddid_all.tbl CDD KOG2210 KOG2210 230149 KOG2210 KOG2210, Oxysterol-binding protein [Signal transduction mechanisms] 392 matched cddid_all.tbl CDD KOG2211 KOG2211 230150 KOG2211 KOG2211, Predicted Golgi transport complex 1 protein [Intracellular trafficking, secretion, and vesicular transport] 797 matched cddid_all.tbl CDD KOG2212 KOG2212 230151 KOG2212 KOG2212, Alpha-amylase [Carbohydrate transport and metabolism] 504 matched cddid_all.tbl CDD KOG2213 KOG2213 230152 KOG2213 KOG2213, Apoptosis inhibitor 5/fibroblast growth factor 2-interacting factor 2, and related proteins [Signal transduction mechanisms] 460 matched cddid_all.tbl CDD KOG2214 KOG2214 230153 KOG2214 KOG2214, Predicted esterase of the alpha-beta hydrolase superfamily [General function prediction only] 543 matched cddid_all.tbl CDD KOG2215 KOG2215 230154 KOG2215 KOG2215, Exocyst complex subunit [Intracellular trafficking, secretion, and vesicular transport] 673 matched cddid_all.tbl CDD KOG2216 KOG2216 230155 KOG2216 KOG2216, Conserved coiled/coiled coil protein [Function unknown] 303 matched cddid_all.tbl CDD KOG2217 KOG2217 230156 KOG2217 KOG2217, U4/U6.U5 snRNP associated protein [RNA processing and modification] 705 matched cddid_all.tbl CDD KOG2218 KOG2218 230157 KOG2218 KOG2218, ER to golgi transport protein/RAD50-interacting protein 1 [Intracellular trafficking, secretion, and vesicular transport, Cell cycle control, cell division, chromosome partitioning] 737 matched cddid_all.tbl CDD KOG2219 KOG2219 230158 KOG2219 KOG2219, Uncharacterized conserved protein [Function unknown] 864 matched cddid_all.tbl CDD KOG2220 KOG2220 230159 KOG2220 KOG2220, Predicted signal transduction protein [General function prediction only] 714 matched cddid_all.tbl CDD KOG2221 KOG2221 230160 KOG2221 KOG2221, PDZ-domain interacting protein EPI64, contains TBC domain [Intracellular trafficking, secretion, and vesicular transport] 267 matched cddid_all.tbl CDD KOG2222 KOG2222 230161 KOG2222 KOG2222, Uncharacterized conserved protein, contains TBC, SH3 and RUN domains [Signal transduction mechanisms, General function prediction only] 848 matched cddid_all.tbl CDD KOG2223 KOG2223 230162 KOG2223 KOG2223, Uncharacterized conserved protein, contains TBC domain [Signal transduction mechanisms, General function prediction only] 586 matched cddid_all.tbl CDD KOG2224 KOG2224 230163 KOG2224 KOG2224, Uncharacterized conserved protein, contains TBC domain [Signal transduction mechanisms, General function prediction only] 781 matched cddid_all.tbl CDD KOG2225 KOG2225 230164 KOG2225 KOG2225, Proteins containing regions of low-complexity [General function prediction only] 695 matched cddid_all.tbl CDD KOG2226 KOG2226 230165 KOG2226 KOG2226, Proteins containing regions of low-complexity [General function prediction only] 786 matched cddid_all.tbl CDD KOG2227 KOG2227 230166 KOG2227 KOG2227, Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase [Replication, recombination and repair, Cell cycle control, cell division, chromosome partitioning] 529 matched cddid_all.tbl CDD KOG2228 KOG2228 230167 KOG2228 KOG2228, Origin recognition complex, subunit 4 [Replication, recombination and repair] 408 matched cddid_all.tbl CDD KOG2229 KOG2229 230168 KOG2229 KOG2229, Protein required for actin cytoskeleton organization and cell cycle progression [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton] 616 matched cddid_all.tbl CDD KOG2230 KOG2230 230169 KOG2230 KOG2230, Predicted beta-mannosidase [Carbohydrate transport and metabolism] 867 matched cddid_all.tbl CDD KOG2231 KOG2231 230170 KOG2231 KOG2231, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 669 matched cddid_all.tbl CDD KOG2232 KOG2232 230171 KOG2232 KOG2232, Ceramidases [Signal transduction mechanisms] 734 matched cddid_all.tbl CDD KOG2233 KOG2233 230172 KOG2233 KOG2233, Alpha-N-acetylglucosaminidase [Intracellular trafficking, secretion, and vesicular transport] 666 matched cddid_all.tbl CDD KOG2234 KOG2234 230173 KOG2234 KOG2234, Predicted UDP-galactose transporter [Carbohydrate transport and metabolism] 345 matched cddid_all.tbl CDD KOG2235 KOG2235 230174 KOG2235 KOG2235, Uncharacterized conserved protein [Function unknown] 776 matched cddid_all.tbl CDD KOG2236 KOG2236 230175 KOG2236 KOG2236, Uncharacterized conserved protein [Function unknown] 483 matched cddid_all.tbl CDD KOG2237 KOG2237 230176 KOG2237 KOG2237, Predicted serine protease [Posttranslational modification, protein turnover, chaperones] 712 matched cddid_all.tbl CDD KOG2238 KOG2238 230177 KOG2238 KOG2238, Uncharacterized conserved protein TEX2, contains PH domain [General function prediction only] 795 matched cddid_all.tbl CDD KOG2239 KOG2239 230178 KOG2239 KOG2239, Transcription factor containing NAC and TS-N domains [Transcription] 209 matched cddid_all.tbl CDD KOG2240 KOG2240 230179 KOG2240 KOG2240, RNA polymerase II general transcription factor BTF3 and related proteins [Transcription] 162 matched cddid_all.tbl CDD KOG2241 KOG2241 230180 KOG2241 KOG2241, tRNA-binding protein [Translation, ribosomal structure and biogenesis] 255 matched cddid_all.tbl CDD KOG2242 KOG2242 230181 KOG2242 KOG2242, Scaffold/matrix specific factor hnRNP-U/SAF-A, contains SPRY domain [RNA processing and modification] 558 matched cddid_all.tbl CDD KOG2243 KOG2243 230182 KOG2243 KOG2243, Ca2+ release channel (ryanodine receptor) [Signal transduction mechanisms] 5019 matched cddid_all.tbl CDD KOG2244 KOG2244 230183 KOG2244 KOG2244, Highly conserved protein containing a thioredoxin domain [General function prediction only] 786 matched cddid_all.tbl CDD KOG2245 KOG2245 230184 KOG2245 KOG2245, Poly(A) polymerase and related nucleotidyltransferases [RNA processing and modification] 562 matched cddid_all.tbl CDD KOG2246 KOG2246 230185 KOG2246 KOG2246, Galactosyltransferases [Carbohydrate transport and metabolism] 364 matched cddid_all.tbl CDD KOG2247 KOG2247 230186 KOG2247 KOG2247, WD40 repeat-containing protein [General function prediction only] 615 matched cddid_all.tbl CDD KOG2248 KOG2248 230187 KOG2248 KOG2248, 3'-5' exonuclease [Replication, recombination and repair] 380 matched cddid_all.tbl CDD KOG2249 KOG2249 230188 KOG2249 KOG2249, 3'-5' exonuclease [Replication, recombination and repair] 280 matched cddid_all.tbl CDD KOG2250 KOG2250 230189 KOG2250 KOG2250, Glutamate/leucine/phenylalanine/valine dehydrogenases [Amino acid transport and metabolism] 514 matched cddid_all.tbl CDD KOG2251 KOG2251 230190 KOG2251 KOG2251, Homeobox transcription factor [Transcription] 228 matched cddid_all.tbl CDD KOG2252 KOG2252 230191 KOG2252 KOG2252, CCAAT displacement protein and related homeoproteins [Transcription] 558 matched cddid_all.tbl CDD KOG2253 KOG2253 230192 KOG2253 KOG2253, U1 snRNP complex, subunit SNU71 and related PWI-motif proteins [RNA processing and modification] 668 matched cddid_all.tbl CDD KOG2254 KOG2254 230193 KOG2254 KOG2254, Predicted endo-1,3-beta-glucanase [Carbohydrate transport and metabolism] 747 matched cddid_all.tbl CDD KOG2255 KOG2255 230194 KOG2255 KOG2255, Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis] 224 matched cddid_all.tbl CDD KOG2256 KOG2256 230195 KOG2256 KOG2256, Predicted protein involved in nuclear export of pre-ribosomes [Translation, ribosomal structure and biogenesis] 661 matched cddid_all.tbl CDD KOG2257 KOG2257 230196 KOG2257 KOG2257, N-acetylglucosaminyltransferase complex, subunit PIG-P, required for phosphatidylinositol biosynthesis [Function unknown] 135 matched cddid_all.tbl CDD KOG2258 KOG2258 230197 KOG2258 KOG2258, Glycerophosphoryl diester phosphodiesterase [Energy production and conversion] 341 matched cddid_all.tbl CDD KOG2259 KOG2259 230198 KOG2259 KOG2259, Uncharacterized conserved protein [Function unknown] 823 matched cddid_all.tbl CDD KOG2260 KOG2260 230199 KOG2260 KOG2260, Cell division cycle 37 protein, CDC37 [Cell cycle control, cell division, chromosome partitioning] 372 matched cddid_all.tbl CDD KOG2261 KOG2261 230200 KOG2261 KOG2261, Polycomb enhancer protein, EPC [Transcription] 716 matched cddid_all.tbl CDD KOG2262 KOG2262 230201 KOG2262 KOG2262, Sexual differentiation process protein ISP4 [Signal transduction mechanisms] 761 matched cddid_all.tbl CDD KOG2263 KOG2263 230202 KOG2263 KOG2263, Methionine synthase II (cobalamin-independent) [Amino acid transport and metabolism] 765 matched cddid_all.tbl CDD KOG2264 KOG2264 230203 KOG2264 KOG2264, Exostosin EXT1L [Signal transduction mechanisms] 907 matched cddid_all.tbl CDD KOG2265 KOG2265 230204 KOG2265 KOG2265, Nuclear distribution protein NUDC [Signal transduction mechanisms] 179 matched cddid_all.tbl CDD KOG2266 KOG2266 230205 KOG2266 KOG2266, Chromatin-associated protein Dek and related proteins, contains SAP DNA binding domain [Chromatin structure and dynamics] 594 matched cddid_all.tbl CDD KOG2267 KOG2267 230206 KOG2267 KOG2267, Eukaryotic-type DNA primase, large subunit [Replication, recombination and repair] 475 matched cddid_all.tbl CDD KOG2268 KOG2268 230207 KOG2268 KOG2268, Serine/threonine protein kinase [Signal transduction mechanisms, General function prediction only] 465 matched cddid_all.tbl CDD KOG2269 KOG2269 230208 KOG2269 KOG2269, Serine/threonine protein kinase [Signal transduction mechanisms] 531 matched cddid_all.tbl CDD KOG2270 KOG2270 230209 KOG2270 KOG2270, Serine/threonine protein kinase involved in cell cycle control [Signal transduction mechanisms, Cell cycle control, cell division, chromosome partitioning] 520 matched cddid_all.tbl CDD KOG2271 KOG2271 230210 KOG2271 KOG2271, Nuclear pore complex component (sc Nup85) [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 678 matched cddid_all.tbl CDD KOG2272 KOG2272 230211 KOG2272 KOG2272, Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms, Cytoskeleton] 332 matched cddid_all.tbl CDD KOG2273 KOG2273 230212 KOG2273 KOG2273, Membrane coat complex Retromer, subunit VPS5/SNX1, Sorting nexins, and related PX domain-containing proteins [Intracellular trafficking, secretion, and vesicular transport] 503 matched cddid_all.tbl CDD KOG2274 KOG2274 230213 KOG2274 KOG2274, Predicted importin 9 [Intracellular trafficking, secretion, and vesicular transport, Nuclear structure] 1005 matched cddid_all.tbl CDD KOG2275 KOG2275 230214 KOG2275 KOG2275, Aminoacylase ACY1 and related metalloexopeptidases [Amino acid transport and metabolism] 420 matched cddid_all.tbl CDD KOG2276 KOG2276 230215 KOG2276 KOG2276, Metalloexopeptidases [Amino acid transport and metabolism] 473 matched cddid_all.tbl CDD KOG2277 KOG2277 230216 KOG2277 KOG2277, S-M checkpoint control protein CID1 and related nucleotidyltransferases [Cell cycle control, cell division, chromosome partitioning] 596 matched cddid_all.tbl CDD KOG2278 KOG2278 230217 KOG2278 KOG2278, RNA:NAD 2'-phosphotransferase TPT1 [Translation, ribosomal structure and biogenesis] 207 matched cddid_all.tbl CDD KOG2279 KOG2279 230218 KOG2279 KOG2279, Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms] 608 matched cddid_all.tbl CDD KOG2280 KOG2280 230219 KOG2280 KOG2280, Vacuolar assembly/sorting protein VPS16 [Intracellular trafficking, secretion, and vesicular transport] 829 matched cddid_all.tbl CDD KOG2281 KOG2281 230220 KOG2281 KOG2281, Dipeptidyl aminopeptidases/acylaminoacyl-peptidases [Posttranslational modification, protein turnover, chaperones] 867 matched cddid_all.tbl CDD KOG2282 KOG2282 230221 KOG2282 KOG2282, NADH-ubiquinone oxidoreductase, NDUFS1/75 kDa subunit [Energy production and conversion] 708 matched cddid_all.tbl CDD KOG2283 KOG2283 230222 KOG2283 KOG2283, Clathrin coat dissociation kinase GAK/PTEN/Auxilin and related tyrosine phosphatases [Signal transduction mechanisms, General function prediction only] 434 matched cddid_all.tbl CDD KOG2284 KOG2284 230223 KOG2284 KOG2284, E3 ubiquitin ligase, Cullin 2 component [Posttranslational modification, protein turnover, chaperones] 728 matched cddid_all.tbl CDD KOG2285 KOG2285 230224 KOG2285 KOG2285, E3 ubiquitin ligase, Cullin 1 component [Posttranslational modification, protein turnover, chaperones] 777 matched cddid_all.tbl CDD KOG2286 KOG2286 230225 KOG2286 KOG2286, Exocyst complex subunit SEC6 [Intracellular trafficking, secretion, and vesicular transport] 667 matched cddid_all.tbl CDD KOG2287 KOG2287 230226 KOG2287 KOG2287, Galactosyltransferases [Carbohydrate transport and metabolism] 349 matched cddid_all.tbl CDD KOG2288 KOG2288 230227 KOG2288 KOG2288, Galactosyltransferases [Carbohydrate transport and metabolism] 274 matched cddid_all.tbl CDD KOG2289 KOG2289 230228 KOG2289 KOG2289, Rhomboid family proteins [Signal transduction mechanisms] 316 matched cddid_all.tbl CDD KOG2290 KOG2290 230229 KOG2290 KOG2290, Rhomboid family proteins [Signal transduction mechanisms] 652 matched cddid_all.tbl CDD KOG2291 KOG2291 230230 KOG2291 KOG2291, Oligosaccharyltransferase, alpha subunit (ribophorin I) [Posttranslational modification, protein turnover, chaperones] 602 matched cddid_all.tbl CDD KOG2292 KOG2292 230231 KOG2292 KOG2292, Oligosaccharyltransferase, STT3 subunit [Posttranslational modification, protein turnover, chaperones] 751 matched cddid_all.tbl CDD KOG2293 KOG2293 230232 KOG2293 KOG2293, Daxx-interacting protein MSP58/p78, contains FHA domain [Transcription, Signal transduction mechanisms] 547 matched cddid_all.tbl CDD KOG2294 KOG2294 230233 KOG2294 KOG2294, Transcription factor of the Forkhead/HNF3 family [Transcription] 454 matched cddid_all.tbl CDD KOG2295 KOG2295 230234 KOG2295 KOG2295, C2H2 Zn-finger protein [General function prediction only] 648 matched cddid_all.tbl CDD KOG2296 KOG2296 230235 KOG2296 KOG2296, Integral membrane protein [General function prediction only] 673 matched cddid_all.tbl CDD KOG2297 KOG2297 230236 KOG2297 KOG2297, Predicted translation factor, contains W2 domain [Translation, ribosomal structure and biogenesis] 412 matched cddid_all.tbl CDD KOG2298 KOG2298 230237 KOG2298 KOG2298, Glycyl-tRNA synthetase and related class II tRNA synthetase [Translation, ribosomal structure and biogenesis] 599 matched cddid_all.tbl CDD KOG2299 KOG2299 230238 KOG2299 KOG2299, Ribonuclease HI [Replication, recombination and repair] 301 matched cddid_all.tbl CDD KOG2300 KOG2300 230239 KOG2300 KOG2300, Uncharacterized conserved protein [Function unknown] 629 matched cddid_all.tbl CDD KOG2301 KOG2301 230240 KOG2301 KOG2301, Voltage-gated Ca2+ channels, alpha1 subunits [Inorganic ion transport and metabolism, Signal transduction mechanisms] 1592 matched cddid_all.tbl CDD KOG2302 KOG2302 230241 KOG2302 KOG2302, T-type voltage-gated Ca2+ channel, pore-forming alpha1I subunit [Inorganic ion transport and metabolism, Signal transduction mechanisms] 1956 matched cddid_all.tbl CDD KOG2303 KOG2303 230242 KOG2303 KOG2303, Predicted NAD synthase, contains CN hydrolase domain [Coenzyme transport and metabolism, General function prediction only] 706 matched cddid_all.tbl CDD KOG2304 KOG2304 230243 KOG2304 KOG2304, 3-hydroxyacyl-CoA dehydrogenase [Lipid transport and metabolism] 298 matched cddid_all.tbl CDD KOG2305 KOG2305 230244 KOG2305 KOG2305, 3-hydroxyacyl-CoA dehydrogenase [Lipid transport and metabolism] 313 matched cddid_all.tbl CDD KOG2306 KOG2306 230245 KOG2306 KOG2306, Uncharacterized conserved protein [Function unknown] 609 matched cddid_all.tbl CDD KOG2307 KOG2307 230246 KOG2307 KOG2307, Low density lipoprotein receptor [Intracellular trafficking, secretion, and vesicular transport] 705 matched cddid_all.tbl CDD KOG2308 KOG2308 230247 KOG2308 KOG2308, Phosphatidic acid-preferring phospholipase A1, contains DDHD domain [Lipid transport and metabolism, Intracellular trafficking, secretion, and vesicular transport] 741 matched cddid_all.tbl CDD KOG2309 KOG2309 230248 KOG2309 KOG2309, 60s ribosomal protein L2/L8 [Translation, ribosomal structure and biogenesis] 248 matched cddid_all.tbl CDD KOG2310 KOG2310 230249 KOG2310 KOG2310, DNA repair exonuclease MRE11 [Replication, recombination and repair] 646 matched cddid_all.tbl CDD KOG2311 KOG2311 230250 KOG2311 KOG2311, NAD/FAD-utilizing protein possibly involved in translation [Translation, ribosomal structure and biogenesis] 679 matched cddid_all.tbl CDD KOG2312 KOG2312 230251 KOG2312 KOG2312, Predicted transcriptional regulator, contains ARID domain [Transcription] 847 matched cddid_all.tbl CDD KOG2313 KOG2313 230252 KOG2313 KOG2313, Stress-induced protein UVI31+ [Signal transduction mechanisms] 100 matched cddid_all.tbl CDD KOG2314 KOG2314 230253 KOG2314 KOG2314, Translation initiation factor 3, subunit b (eIF-3b) [Translation, ribosomal structure and biogenesis] 698 matched cddid_all.tbl CDD KOG2315 KOG2315 230254 KOG2315 KOG2315, Predicted translation initiation factor related to eIF-3a [Translation, ribosomal structure and biogenesis] 566 matched cddid_all.tbl CDD KOG2316 KOG2316 230255 KOG2316 KOG2316, Predicted ATPase (PP-loop superfamily) [General function prediction only] 277 matched cddid_all.tbl CDD KOG2317 KOG2317 230256 KOG2317 KOG2317, Putative translation initiation inhibitor UK114/IBM1 [Translation, ribosomal structure and biogenesis] 138 matched cddid_all.tbl CDD KOG2318 KOG2318 230257 KOG2318 KOG2318, Uncharacterized conserved protein [Function unknown] 650 matched cddid_all.tbl CDD KOG2319 KOG2319 230258 KOG2319 KOG2319, Vacuolar assembly/sorting protein VPS9 [Intracellular trafficking, secretion, and vesicular transport] 477 matched cddid_all.tbl CDD KOG2320 KOG2320 230259 KOG2320 KOG2320, RAS effector RIN1 (contains VPS domain) [Intracellular trafficking, secretion, and vesicular transport] 651 matched cddid_all.tbl CDD KOG2321 KOG2321 230260 KOG2321 KOG2321, WD40 repeat protein [General function prediction only] 703 matched cddid_all.tbl CDD KOG2322 KOG2322 230261 KOG2322 KOG2322, N-methyl-D-aspartate receptor glutamate-binding subunit [Signal transduction mechanisms] 237 matched cddid_all.tbl CDD KOG2323 KOG2323 230262 KOG2323 KOG2323, Pyruvate kinase [Carbohydrate transport and metabolism] 501 matched cddid_all.tbl CDD KOG2324 KOG2324 230263 KOG2324 KOG2324, Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 457 matched cddid_all.tbl CDD KOG2325 KOG2325 230264 KOG2325 KOG2325, Predicted transporter/transmembrane protein [General function prediction only] 488 matched cddid_all.tbl CDD KOG2326 KOG2326 230265 KOG2326 KOG2326, DNA-binding subunit of a DNA-dependent protein kinase (Ku80 autoantigen) [Replication, recombination and repair] 669 matched cddid_all.tbl CDD KOG2327 KOG2327 230266 KOG2327 KOG2327, DNA-binding subunit of a DNA-dependent protein kinase (Ku70 autoantigen) [Replication, recombination and repair] 602 matched cddid_all.tbl CDD KOG2328 KOG2328 230267 KOG2328 KOG2328, Chromosome condensation complex Condensin, subunit H [Chromatin structure and dynamics, Cell cycle control, cell division, chromosome partitioning] 702 matched cddid_all.tbl CDD KOG2329 KOG2329 230268 KOG2329 KOG2329, Alkaline ceramidase [Lipid transport and metabolism] 276 matched cddid_all.tbl CDD KOG2330 KOG2330 230269 KOG2330 KOG2330, Splicing factor 3b, subunit 2 [RNA processing and modification] 500 matched cddid_all.tbl CDD KOG2331 KOG2331 230270 KOG2331 KOG2331, Predicted glycosylhydrolase [General function prediction only] 526 matched cddid_all.tbl CDD KOG2332 KOG2332 230271 KOG2332 KOG2332, Ferritin [Inorganic ion transport and metabolism] 178 matched cddid_all.tbl CDD KOG2333 KOG2333 230272 KOG2333 KOG2333, Uncharacterized conserved protein [General function prediction only] 614 matched cddid_all.tbl CDD KOG2334 KOG2334 230273 KOG2334 KOG2334, tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis] 477 matched cddid_all.tbl CDD KOG2335 KOG2335 230274 KOG2335 KOG2335, tRNA-dihydrouridine synthase [Translation, ribosomal structure and biogenesis] 358 matched cddid_all.tbl CDD KOG2336 KOG2336 230275 KOG2336 KOG2336, Molybdopterin biosynthesis-related protein [Coenzyme transport and metabolism] 422 matched cddid_all.tbl CDD KOG2337 KOG2337 230276 KOG2337 KOG2337, Ubiquitin activating E1 enzyme-like protein [Coenzyme transport and metabolism] 669 matched cddid_all.tbl CDD KOG2338 KOG2338 230277 KOG2338 KOG2338, Transcriptional effector CCR4-related protein [Transcription] 495 matched cddid_all.tbl CDD KOG2339 KOG2339 230278 KOG2339 KOG2339, Uncharacterized conserved protein [Function unknown] 624 matched cddid_all.tbl CDD KOG2340 KOG2340 230279 KOG2340 KOG2340, Uncharacterized conserved protein [Function unknown] 698 matched cddid_all.tbl CDD KOG2341 KOG2341 230280 KOG2341 KOG2341, TATA box binding protein (TBP)-associated factor, RNA polymerase II [Transcription] 563 matched cddid_all.tbl CDD KOG2342 KOG2342 230281 KOG2342 KOG2342, Uncharacterized conserved protein [Function unknown] 280 matched cddid_all.tbl CDD KOG2343 KOG2343 230282 KOG2343 KOG2343, Glucose-repressible protein and related proteins [General function prediction only] 689 matched cddid_all.tbl CDD KOG2344 KOG2344 230283 KOG2344 KOG2344, Exocyst component protein and related proteins [Intracellular trafficking, secretion, and vesicular transport] 623 matched cddid_all.tbl CDD KOG2345 KOG2345 230284 KOG2345 KOG2345, Serine/threonine protein kinase/TGF-beta stimulated factor [Transcription, Lipid transport and metabolism, Signal transduction mechanisms] 302 matched cddid_all.tbl CDD KOG2346 KOG2346 230285 KOG2346 KOG2346, Uncharacterized conserved protein [Function unknown] 636 matched cddid_all.tbl CDD KOG2347 KOG2347 230286 KOG2347 KOG2347, Sec5 subunit of exocyst complex [Intracellular trafficking, secretion, and vesicular transport] 934 matched cddid_all.tbl CDD KOG2348 KOG2348 230287 KOG2348 KOG2348, Urea transporter [Amino acid transport and metabolism] 667 matched cddid_all.tbl CDD KOG2349 KOG2349 230288 KOG2349 KOG2349, Na+:iodide/myo-inositol/multivitamin symporters [Inorganic ion transport and metabolism] 585 matched cddid_all.tbl CDD KOG2350 KOG2350 230289 KOG2350 KOG2350, Zn-finger protein joined to JAZF1 (predicted suppressor) [General function prediction only] 221 matched cddid_all.tbl CDD KOG2351 KOG2351 230290 KOG2351 KOG2351, RNA polymerase II, fourth largest subunit [Transcription] 134 matched cddid_all.tbl CDD KOG2352 KOG2352 230291 KOG2352 KOG2352, Predicted spermine/spermidine synthase [Amino acid transport and metabolism] 482 matched cddid_all.tbl CDD KOG2353 KOG2353 230292 KOG2353 KOG2353, L-type voltage-dependent Ca2+ channel, alpha2/delta subunit [Inorganic ion transport and metabolism, Signal transduction mechanisms] 1104 matched cddid_all.tbl CDD KOG2354 KOG2354 230293 KOG2354 KOG2354, RNA Polymerase C (III) 37 kDa subunit [Transcription] 446 matched cddid_all.tbl CDD KOG2355 KOG2355 230294 KOG2355 KOG2355, Predicted ABC-type transport, ATPase component/CCR4 associated factor [General function prediction only, Transcription] 291 matched cddid_all.tbl CDD KOG2356 KOG2356 230295 KOG2356 KOG2356, Transcriptional activator, adenine-specific DNA methyltransferase [Transcription, Signal transduction mechanisms] 366 matched cddid_all.tbl CDD KOG2357 KOG2357 230296 KOG2357 KOG2357, Uncharacterized conserved protein [Function unknown] 440 matched cddid_all.tbl CDD KOG2358 KOG2358 230297 KOG2358 KOG2358, NifU-like domain-containing proteins [Posttranslational modification, protein turnover, chaperones] 213 matched cddid_all.tbl CDD KOG2359 KOG2359 230298 KOG2359 KOG2359, Uncharacterized conserved protein [Function unknown] 688 matched cddid_all.tbl CDD KOG2360 KOG2360 230299 KOG2360 KOG2360, Proliferation-associated nucleolar protein (NOL1) [Cell cycle control, cell division, chromosome partitioning] 413 matched cddid_all.tbl CDD KOG2361 KOG2361 230300 KOG2361 KOG2361, Predicted methyltransferase [General function prediction only] 264 matched cddid_all.tbl CDD KOG2362 KOG2362 230301 KOG2362 KOG2362, Uncharacterized Fe-S protein [General function prediction only] 336 matched cddid_all.tbl CDD KOG2363 KOG2363 230302 KOG2363 KOG2363, Protein subunit of nuclear ribonuclease P (RNase P) [Translation, ribosomal structure and biogenesis] 247 matched cddid_all.tbl CDD KOG2364 KOG2364 230303 KOG2364 KOG2364, Predicted pseudouridylate synthase [Translation, ribosomal structure and biogenesis] 433 matched cddid_all.tbl CDD KOG2365 KOG2365 230304 KOG2365 KOG2365, Uncharacterized membrane protein [Function unknown] 808 matched cddid_all.tbl CDD KOG2366 KOG2366 230305 KOG2366 KOG2366, Alpha-D-galactosidase (melibiase) [Carbohydrate transport and metabolism] 414 matched cddid_all.tbl CDD KOG2367 KOG2367 230306 KOG2367 KOG2367, Alpha-isopropylmalate synthase/homocitrate synthase [Amino acid transport and metabolism] 560 matched cddid_all.tbl CDD KOG2368 KOG2368 230307 KOG2368 KOG2368, Hydroxymethylglutaryl-CoA lyase [Energy production and conversion, Amino acid transport and metabolism] 316 matched cddid_all.tbl CDD KOG2369 KOG2369 230308 KOG2369 KOG2369, Lecithin:cholesterol acyltransferase (LCAT)/Acyl-ceramide synthase [Lipid transport and metabolism] 473 matched cddid_all.tbl CDD KOG2370 KOG2370 230309 KOG2370 KOG2370, Cactin [Signal transduction mechanisms] 623 matched cddid_all.tbl CDD KOG2371 KOG2371 230310 KOG2371 KOG2371, Molybdopterin biosynthesis protein [Coenzyme transport and metabolism] 411 matched cddid_all.tbl CDD KOG2372 KOG2372 230311 KOG2372 KOG2372, Oxidation resistance protein [Replication, recombination and repair] 241 matched cddid_all.tbl CDD KOG2373 KOG2373 230312 KOG2373 KOG2373, Predicted mitochondrial DNA helicase twinkle [Replication, recombination and repair] 514 matched cddid_all.tbl CDD KOG2374 KOG2374 230313 KOG2374 KOG2374, Uncharacterized conserved protein [Function unknown] 661 matched cddid_all.tbl CDD KOG2375 KOG2375 230314 KOG2375 KOG2375, Protein interacting with poly(A)-binding protein [RNA processing and modification] 756 matched cddid_all.tbl CDD KOG2376 KOG2376 230315 KOG2376 KOG2376, Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport] 652 matched cddid_all.tbl CDD KOG2377 KOG2377 230316 KOG2377 KOG2377, Uncharacterized conserved protein [Function unknown] 657 matched cddid_all.tbl CDD KOG2378 KOG2378 230317 KOG2378 KOG2378, cAMP-regulated guanine nucleotide exchange factor [Signal transduction mechanisms] 573 matched cddid_all.tbl CDD KOG2379 KOG2379 230318 KOG2379 KOG2379, Endonuclease MUS81 [Replication, recombination and repair] 501 matched cddid_all.tbl CDD KOG2380 KOG2380 230319 KOG2380 KOG2380, Prephenate dehydrogenase (NADP+) [Amino acid transport and metabolism] 480 matched cddid_all.tbl CDD KOG2381 KOG2381 230320 KOG2381 KOG2381, Phosphatidylinositol 4-kinase [Signal transduction mechanisms] 286 matched cddid_all.tbl CDD KOG2382 KOG2382 230321 KOG2382 KOG2382, Predicted alpha/beta hydrolase [General function prediction only] 315 matched cddid_all.tbl CDD KOG2383 KOG2383 230322 KOG2383 KOG2383, Predicted ATPase [General function prediction only] 467 matched cddid_all.tbl CDD KOG2384 KOG2384 230323 KOG2384 KOG2384, Major histocompatibility complex protein BAT4, contains G-patch and ankyrin domains [General function prediction only] 223 matched cddid_all.tbl CDD KOG2385 KOG2385 230324 KOG2385 KOG2385, Uncharacterized conserved protein [Function unknown] 633 matched cddid_all.tbl CDD KOG2386 KOG2386 230325 KOG2386 KOG2386, mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification] 393 matched cddid_all.tbl CDD KOG2387 KOG2387 230326 KOG2387 KOG2387, CTP synthase (UTP-ammonia lyase) [Nucleotide transport and metabolism] 585 matched cddid_all.tbl CDD KOG2388 KOG2388 230327 KOG2388 KOG2388, UDP-N-acetylglucosamine pyrophosphorylase [Cell wall/membrane/envelope biogenesis] 477 matched cddid_all.tbl CDD KOG2389 KOG2389 230328 KOG2389 KOG2389, Predicted bromodomain transcription factor [Transcription] 353 matched cddid_all.tbl CDD KOG2390 KOG2390 230329 KOG2390 KOG2390, Uncharacterized conserved protein [Function unknown] 669 matched cddid_all.tbl CDD KOG2391 KOG2391 230330 KOG2391 KOG2391, Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones, Intracellular trafficking, secretion, and vesicular transport] 365 matched cddid_all.tbl CDD KOG2392 KOG2392 230331 KOG2392 KOG2392, Serpin [Defense mechanisms] 380 matched cddid_all.tbl CDD KOG2393 KOG2393 230332 KOG2393 KOG2393, Transcription initiation factor IIF, large subunit (RAP74) [Transcription] 555 matched cddid_all.tbl CDD KOG2394 KOG2394 230333 KOG2394 KOG2394, WD40 protein DMR-N9 [General function prediction only] 636 matched cddid_all.tbl CDD KOG2395 KOG2395 230334 KOG2395 KOG2395, Protein involved in vacuole import and degradation [Intracellular trafficking, secretion, and vesicular transport] 644 matched cddid_all.tbl CDD KOG2396 KOG2396 230335 KOG2396 KOG2396, HAT (Half-A-TPR) repeat-containing protein [General function prediction only] 568 matched cddid_all.tbl CDD KOG2397 KOG2397 230336 KOG2397 KOG2397, Protein kinase C substrate, 80 KD protein, heavy chain [Signal transduction mechanisms] 480 matched cddid_all.tbl CDD KOG2398 KOG2398 230337 KOG2398 KOG2398, Predicted proline-serine-threonine phosphatase-interacting protein (PSTPIP) [Cell cycle control, cell division, chromosome partitioning] 611 matched cddid_all.tbl CDD KOG2399 KOG2399 230338 KOG2399 KOG2399, K+-dependent Na+:Ca2+ antiporter [Inorganic ion transport and metabolism] 506 matched cddid_all.tbl CDD KOG2400 KOG2400 230339 KOG2400 KOG2400, Nuclear protein ZAP [Defense mechanisms] 82 matched cddid_all.tbl CDD KOG2401 KOG2401 230340 KOG2401 KOG2401, Predicted MutS-related protein involved in mismatch repair [Replication, recombination and repair] 448 matched cddid_all.tbl CDD KOG2402 KOG2402 230341 KOG2402 KOG2402, Paf1/RNA polymerase II complex, RTF1 component (involved in regulation of TATA box-binding protein) [Transcription] 525 matched cddid_all.tbl CDD KOG2403 KOG2403 230342 KOG2403 KOG2403, Succinate dehydrogenase, flavoprotein subunit [Energy production and conversion] 642 matched cddid_all.tbl CDD KOG2404 KOG2404 230343 KOG2404 KOG2404, Fumarate reductase, flavoprotein subunit [Energy production and conversion] 477 matched cddid_all.tbl CDD KOG2405 KOG2405 230344 KOG2405 KOG2405, Predicted 3'-5' exonuclease [Replication, recombination and repair] 458 matched cddid_all.tbl CDD KOG2406 KOG2406 230345 KOG2406 KOG2406, MADS box transcription factor [Transcription] 635 matched cddid_all.tbl CDD KOG2407 KOG2407 230346 KOG2407 KOG2407, GPI transamidase complex, GPI16/PIG-T component, involved in glycosylphosphatidylinositol anchor biosynthesis [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones] 575 matched cddid_all.tbl CDD KOG2408 KOG2408 230347 KOG2408 KOG2408, Peroxidase/oxygenase [General function prediction only] 719 matched cddid_all.tbl CDD KOG2409 KOG2409 230348 KOG2409 KOG2409, KRR1-interacting protein involved in 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis] 647 matched cddid_all.tbl CDD KOG2410 KOG2410 230349 KOG2410 KOG2410, Gamma-glutamyltransferase [Amino acid transport and metabolism] 579 matched cddid_all.tbl CDD KOG2411 KOG2411 230350 KOG2411 KOG2411, Aspartyl-tRNA synthetase, mitochondrial [Translation, ribosomal structure and biogenesis] 628 matched cddid_all.tbl CDD KOG2412 KOG2412 230351 KOG2412 KOG2412, Nuclear-export-signal (NES)-containing protein/polyadenylated-RNA export factor [RNA processing and modification] 591 matched cddid_all.tbl CDD KOG2413 KOG2413 230352 KOG2413 KOG2413, Xaa-Pro aminopeptidase [Amino acid transport and metabolism] 550 matched cddid_all.tbl CDD KOG2414 KOG2414 230353 KOG2414 KOG2414, Putative Xaa-Pro aminopeptidase [Amino acid transport and metabolism] 488 matched cddid_all.tbl CDD KOG2415 KOG2415 230354 KOG2415 KOG2415, Electron transfer flavoprotein ubiquinone oxidoreductase [Energy production and conversion] 621 matched cddid_all.tbl CDD KOG2416 KOG2416 230355 KOG2416 KOG2416, Acinus (induces apoptotic chromatin condensation) [Chromatin structure and dynamics] 718 matched cddid_all.tbl CDD KOG2417 KOG2417 230356 KOG2417 KOG2417, Predicted G-protein coupled receptor [Signal transduction mechanisms] 462 matched cddid_all.tbl CDD KOG2418 KOG2418 230357 KOG2418 KOG2418, Microtubule-associated protein TAU [Cytoskeleton] 448 matched cddid_all.tbl CDD KOG2419 KOG2419 230358 KOG2419 KOG2419, Phosphatidylserine decarboxylase [Lipid transport and metabolism] 975 matched cddid_all.tbl CDD KOG2420 KOG2420 230359 KOG2420 KOG2420, Phosphatidylserine decarboxylase [Lipid transport and metabolism] 382 matched cddid_all.tbl CDD KOG2421 KOG2421 230360 KOG2421 KOG2421, Predicted starch-binding protein [General function prediction only] 417 matched cddid_all.tbl CDD KOG2422 KOG2422 230361 KOG2422 KOG2422, Uncharacterized conserved protein [Function unknown] 665 matched cddid_all.tbl CDD KOG2423 KOG2423 230362 KOG2423 KOG2423, Nucleolar GTPase [General function prediction only] 572 matched cddid_all.tbl CDD KOG2424 KOG2424 230363 KOG2424 KOG2424, Protein involved in transcription start site selection [Transcription] 195 matched cddid_all.tbl CDD KOG2425 KOG2425 230364 KOG2425 KOG2425, Nuclear protein involved in cell morphogenesis and cell surface growth [General function prediction only] 599 matched cddid_all.tbl CDD KOG2426 KOG2426 230365 KOG2426 KOG2426, Dihydroxyacetone kinase/glycerone kinase [Carbohydrate transport and metabolism] 582 matched cddid_all.tbl CDD KOG2427 KOG2427 230366 KOG2427 KOG2427, Uncharacterized conserved protein [Function unknown] 391 matched cddid_all.tbl CDD KOG2428 KOG2428 230367 KOG2428 KOG2428, Uncharacterized conserved protein [Function unknown] 443 matched cddid_all.tbl CDD KOG2429 KOG2429 230368 KOG2429 KOG2429, Glycosyl hydrolase, family 47 [Carbohydrate transport and metabolism] 622 matched cddid_all.tbl CDD KOG2430 KOG2430 230369 KOG2430 KOG2430, Glycosyl hydrolase, family 47 [Carbohydrate transport and metabolism] 587 matched cddid_all.tbl CDD KOG2431 KOG2431 230370 KOG2431 KOG2431, 1, 2-alpha-mannosidase [Carbohydrate transport and metabolism] 546 matched cddid_all.tbl CDD KOG2432 KOG2432 230371 KOG2432 KOG2432, Uncharacterized conserved protein [Function unknown] 565 matched cddid_all.tbl CDD KOG2433 KOG2433 230372 KOG2433 KOG2433, Uncharacterized conserved protein [Function unknown] 577 matched cddid_all.tbl CDD KOG2434 KOG2434 230373 KOG2434 KOG2434, RNA polymerase I transcription factor [Transcription] 500 matched cddid_all.tbl CDD KOG2435 KOG2435 230374 KOG2435 KOG2435, Uncharacterized conserved protein [Function unknown] 323 matched cddid_all.tbl CDD KOG2436 KOG2436 230375 KOG2436 KOG2436, Acetylglutamate kinase/acetylglutamate synthase [Amino acid transport and metabolism] 520 matched cddid_all.tbl CDD KOG2437 KOG2437 230376 KOG2437 KOG2437, Muskelin [Signal transduction mechanisms] 723 matched cddid_all.tbl CDD KOG2438 KOG2438 230377 KOG2438 KOG2438, Glutamyl-tRNA amidotransferase subunit B [Translation, ribosomal structure and biogenesis] 505 matched cddid_all.tbl CDD KOG2439 KOG2439 230378 KOG2439 KOG2439, Nuclear architecture related protein [Nuclear structure] 459 matched cddid_all.tbl CDD KOG2440 KOG2440 230379 KOG2440 KOG2440, Pyrophosphate-dependent phosphofructo-1-kinase [Carbohydrate transport and metabolism] 666 matched cddid_all.tbl CDD KOG2441 KOG2441 230380 KOG2441 KOG2441, mRNA splicing factor/probable chromatin binding snw family nuclear protein [RNA processing and modification, Chromatin structure and dynamics] 506 matched cddid_all.tbl CDD KOG2442 KOG2442 230381 KOG2442 KOG2442, Uncharacterized conserved protein, contains PA domain [General function prediction only] 541 matched cddid_all.tbl CDD KOG2443 KOG2443 230382 KOG2443 KOG2443, Uncharacterized conserved protein [Function unknown] 362 matched cddid_all.tbl CDD KOG2444 KOG2444 230383 KOG2444 KOG2444, WD40 repeat protein [General function prediction only] 238 matched cddid_all.tbl CDD KOG2445 KOG2445 230384 KOG2445 KOG2445, Nuclear pore complex component (sc Seh1) [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 361 matched cddid_all.tbl CDD KOG2446 KOG2446 230385 KOG2446 KOG2446, Glucose-6-phosphate isomerase [Carbohydrate transport and metabolism] 546 matched cddid_all.tbl CDD KOG2447 KOG2447 230386 KOG2447 KOG2447, Oligosaccharyltransferase, delta subunit (ribophorin II) [Posttranslational modification, protein turnover, chaperones] 287 matched cddid_all.tbl CDD KOG2448 KOG2448 230387 KOG2448 KOG2448, Dihydroxy-acid dehydratase [Amino acid transport and metabolism] 596 matched cddid_all.tbl CDD KOG2449 KOG2449 230388 KOG2449 KOG2449, Methylmalonate semialdehyde dehydrogenase [Amino acid transport and metabolism, Carbohydrate transport and metabolism] 157 matched cddid_all.tbl CDD KOG2450 KOG2450 230389 KOG2450 KOG2450, Aldehyde dehydrogenase [Energy production and conversion] 501 matched cddid_all.tbl CDD KOG2451 KOG2451 230390 KOG2451 KOG2451, Aldehyde dehydrogenase [Energy production and conversion] 503 matched cddid_all.tbl CDD KOG2452 KOG2452 230391 KOG2452 KOG2452, Formyltetrahydrofolate dehydrogenase [Nucleotide transport and metabolism] 881 matched cddid_all.tbl CDD KOG2453 KOG2453 230392 KOG2453 KOG2453, Aldehyde dehydrogenase [Energy production and conversion] 507 matched cddid_all.tbl CDD KOG2454 KOG2454 230393 KOG2454 KOG2454, Betaine aldehyde dehydrogenase [Energy production and conversion] 583 matched cddid_all.tbl CDD KOG2455 KOG2455 230394 KOG2455 KOG2455, Delta-1-pyrroline-5-carboxylate dehydrogenase [Amino acid transport and metabolism] 561 matched cddid_all.tbl CDD KOG2456 KOG2456 230395 KOG2456 KOG2456, Aldehyde dehydrogenase [Energy production and conversion] 477 matched cddid_all.tbl CDD KOG2457 KOG2457 230396 KOG2457 KOG2457, A/G-specific adenine DNA glycosylase [Replication, recombination and repair] 555 matched cddid_all.tbl CDD KOG2458 KOG2458 230397 KOG2458 KOG2458, Endoplasmic reticulum protein EP58, contains filamin rod domain and KDEL motif [General function prediction only] 528 matched cddid_all.tbl CDD KOG2459 KOG2459 230398 KOG2459 KOG2459, GPI transamidase complex, GPI17/PIG-S component, involved in glycosylphosphatidylinositol anchor biosynthesis [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones] 536 matched cddid_all.tbl CDD KOG2460 KOG2460 230399 KOG2460 KOG2460, Signal recognition particle, subunit Srp68 [Intracellular trafficking, secretion, and vesicular transport] 593 matched cddid_all.tbl CDD KOG2461 KOG2461 230400 KOG2461 KOG2461, Transcription factor BLIMP-1/PRDI-BF1, contains C2H2-type Zn-finger and SET domains [Transcription] 396 matched cddid_all.tbl CDD KOG2462 KOG2462 230401 KOG2462 KOG2462, C2H2-type Zn-finger protein [Transcription] 279 matched cddid_all.tbl CDD KOG2463 KOG2463 230402 KOG2463 KOG2463, Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones] 376 matched cddid_all.tbl CDD KOG2464 KOG2464 230403 KOG2464 KOG2464, Serine/threonine kinase (haspin family) [Cell cycle control, cell division, chromosome partitioning] 246 matched cddid_all.tbl CDD KOG2465 KOG2465 230404 KOG2465 KOG2465, Uncharacterized conserved protein [Function unknown] 390 matched cddid_all.tbl CDD KOG2466 KOG2466 230405 KOG2466 KOG2466, Uridine permease/thiamine transporter/allantoin transport [Nucleotide transport and metabolism, Coenzyme transport and metabolism] 572 matched cddid_all.tbl CDD KOG2467 KOG2467 230406 KOG2467 KOG2467, Glycine/serine hydroxymethyltransferase [Amino acid transport and metabolism] 477 matched cddid_all.tbl CDD KOG2468 KOG2468 230407 KOG2468 KOG2468, Dolichol kinase [Lipid transport and metabolism] 510 matched cddid_all.tbl CDD KOG2469 KOG2469 230408 KOG2469 KOG2469, IMP-GMP specific 5'-nucleotidase [Nucleotide transport and metabolism] 424 matched cddid_all.tbl CDD KOG2470 KOG2470 230409 KOG2470 KOG2470, Similar to IMP-GMP specific 5'-nucleotidase [Nucleotide transport and metabolism] 510 matched cddid_all.tbl CDD KOG2471 KOG2471 230410 KOG2471 KOG2471, TPR repeat-containing protein [General function prediction only] 696 matched cddid_all.tbl CDD KOG2472 KOG2472 230411 KOG2472 KOG2472, Phenylalanyl-tRNA synthetase beta subunit [Translation, ribosomal structure and biogenesis] 578 matched cddid_all.tbl CDD KOG2473 KOG2473 230412 KOG2473 KOG2473, RNA polymerase III transcription factor (TF)IIIC subunit [Transcription] 484 matched cddid_all.tbl CDD KOG2474 KOG2474 230413 KOG2474 KOG2474, Zinc transporter and related ZIP domain-containing proteins [Inorganic ion transport and metabolism] 406 matched cddid_all.tbl CDD KOG2475 KOG2475 230414 KOG2475 KOG2475, CDC45 (cell division cycle 45)-like protein [Replication, recombination and repair] 587 matched cddid_all.tbl CDD KOG2476 KOG2476 230415 KOG2476 KOG2476, Uncharacterized conserved protein [Function unknown] 528 matched cddid_all.tbl CDD KOG2477 KOG2477 230416 KOG2477 KOG2477, Uncharacterized conserved protein [Function unknown] 628 matched cddid_all.tbl CDD KOG2478 KOG2478 230417 KOG2478 KOG2478, Putative RNA polymerase II regulator [Transcription] 452 matched cddid_all.tbl CDD KOG2479 KOG2479 230418 KOG2479 KOG2479, Translation initiation factor 3, subunit d (eIF-3d) [Translation, ribosomal structure and biogenesis] 549 matched cddid_all.tbl CDD KOG2480 KOG2480 230419 KOG2480 KOG2480, 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase [Lipid transport and metabolism] 602 matched cddid_all.tbl CDD KOG2481 KOG2481 230420 KOG2481 KOG2481, Protein required for normal rRNA processing [RNA processing and modification] 570 matched cddid_all.tbl CDD KOG2482 KOG2482 230421 KOG2482 KOG2482, Predicted C2H2-type Zn-finger protein [Transcription] 423 matched cddid_all.tbl CDD KOG2483 KOG2483 230422 KOG2483 KOG2483, Upstream transcription factor 2/L-myc-2 protein [Transcription] 232 matched cddid_all.tbl CDD KOG2484 KOG2484 230423 KOG2484 KOG2484, GTPase [General function prediction only] 435 matched cddid_all.tbl CDD KOG2485 KOG2485 230424 KOG2485 KOG2485, Conserved ATP/GTP binding protein [General function prediction only] 335 matched cddid_all.tbl CDD KOG2486 KOG2486 230425 KOG2486 KOG2486, Predicted GTPase [General function prediction only] 320 matched cddid_all.tbl CDD KOG2487 KOG2487 230426 KOG2487 KOG2487, RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription, Replication, recombination and repair] 314 matched cddid_all.tbl CDD KOG2488 KOG2488 230427 KOG2488 KOG2488, Acetyltransferase (GNAT) domain-containing protein [General function prediction only] 202 matched cddid_all.tbl CDD KOG2489 KOG2489 230428 KOG2489 KOG2489, Transmembrane protein [General function prediction only] 592 matched cddid_all.tbl CDD KOG2490 KOG2490 230429 KOG2490 KOG2490, Predicted membrane protein [Function unknown] 601 matched cddid_all.tbl CDD KOG2491 KOG2491 230430 KOG2491 KOG2491, Nuclear matrix protein [Nuclear structure] 674 matched cddid_all.tbl CDD KOG2492 KOG2492 230431 KOG2492 KOG2492, CDK5 activator-binding protein [Signal transduction mechanisms] 552 matched cddid_all.tbl CDD KOG2493 KOG2493 230432 KOG2493 KOG2493, Na+/Pi symporter [Inorganic ion transport and metabolism] 512 matched cddid_all.tbl CDD KOG2494 KOG2494 230433 KOG2494 KOG2494, C3H1-type Zn-finger protein [Transcription] 331 matched cddid_all.tbl CDD KOG2495 KOG2495 230434 KOG2495 KOG2495, NADH-dehydrogenase (ubiquinone) [Energy production and conversion] 491 matched cddid_all.tbl CDD KOG2496 KOG2496 230435 KOG2496 KOG2496, Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell cycle control, cell division, chromosome partitioning, Transcription, Replication, recombination and repair] 325 matched cddid_all.tbl CDD KOG2497 KOG2497 230436 KOG2497 KOG2497, Predicted methyltransferase [General function prediction only] 262 matched cddid_all.tbl CDD KOG2498 KOG2498 230437 KOG2498 KOG2498, IK cytokine down-regulator of HLA class II [Signal transduction mechanisms] 544 matched cddid_all.tbl CDD KOG2499 KOG2499 230438 KOG2499 KOG2499, Beta-N-acetylhexosaminidase [Carbohydrate transport and metabolism] 542 matched cddid_all.tbl CDD KOG2500 KOG2500 230439 KOG2500 KOG2500, Uncharacterized conserved protein [Function unknown] 253 matched cddid_all.tbl CDD KOG2501 KOG2501 230440 KOG2501 KOG2501, Thioredoxin, nucleoredoxin and related proteins [General function prediction only] 157 matched cddid_all.tbl CDD KOG2502 KOG2502 230441 KOG2502 KOG2502, Tub family proteins [General function prediction only] 355 matched cddid_all.tbl CDD KOG2503 KOG2503 230442 KOG2503 KOG2503, Tubby superfamily protein TULP4 [General function prediction only] 565 matched cddid_all.tbl CDD KOG2504 KOG2504 230443 KOG2504 KOG2504, Monocarboxylate transporter [Carbohydrate transport and metabolism] 509 matched cddid_all.tbl CDD KOG2505 KOG2505 230444 KOG2505 KOG2505, Ankyrin repeat protein [General function prediction only] 591 matched cddid_all.tbl CDD KOG2506 KOG2506 230445 KOG2506 KOG2506, SpoU rRNA Methylase family protein [Translation, ribosomal structure and biogenesis] 371 matched cddid_all.tbl CDD KOG2507 KOG2507 230446 KOG2507 KOG2507, Ubiquitin regulatory protein UBXD2, contains UAS and UBX domains [General function prediction only] 506 matched cddid_all.tbl CDD KOG2508 KOG2508 230447 KOG2508 KOG2508, Predicted phospholipase [Lipid transport and metabolism] 437 matched cddid_all.tbl CDD KOG2509 KOG2509 230448 KOG2509 KOG2509, Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 455 matched cddid_all.tbl CDD KOG2510 KOG2510 230449 KOG2510 KOG2510, SWI-SNF chromatin-remodeling complex protein [Chromatin structure and dynamics] 532 matched cddid_all.tbl CDD KOG2511 KOG2511 230450 KOG2511 KOG2511, Nicotinic acid phosphoribosyltransferase [Coenzyme transport and metabolism] 420 matched cddid_all.tbl CDD KOG2512 KOG2512 230451 KOG2512 KOG2512, Beta-tubulin folding cofactor C [Posttranslational modification, protein turnover, chaperones] 337 matched cddid_all.tbl CDD KOG2513 KOG2513 230452 KOG2513 KOG2513, Protein required for meiotic chromosome segregation [Cell cycle control, cell division, chromosome partitioning] 647 matched cddid_all.tbl CDD KOG2514 KOG2514 230453 KOG2514 KOG2514, Uncharacterized conserved protein [Function unknown] 861 matched cddid_all.tbl CDD KOG2515 KOG2515 230454 KOG2515 KOG2515, Mannosyltransferase [Cell wall/membrane/envelope biogenesis, Intracellular trafficking, secretion, and vesicular transport] 568 matched cddid_all.tbl CDD KOG2516 KOG2516 230455 KOG2516 KOG2516, Protein involved in dolichol pathway for N-glycosylation (mannosyltransferase family) [Cell wall/membrane/envelope biogenesis, Intracellular trafficking, secretion, and vesicular transport] 517 matched cddid_all.tbl CDD KOG2517 KOG2517 230456 KOG2517 KOG2517, Ribulose kinase and related carbohydrate kinases [Carbohydrate transport and metabolism] 516 matched cddid_all.tbl CDD KOG2518 KOG2518 230457 KOG2518 KOG2518, 5'-3' exonuclease [Replication, recombination and repair] 556 matched cddid_all.tbl CDD KOG2519 KOG2519 230458 KOG2519 KOG2519, 5'-3' exonuclease [Replication, recombination and repair] 449 matched cddid_all.tbl CDD KOG2520 KOG2520 230459 KOG2520 KOG2520, 5'-3' exonuclease [Replication, recombination and repair] 815 matched cddid_all.tbl CDD KOG2521 KOG2521 230460 KOG2521 KOG2521, Uncharacterized conserved protein [Function unknown] 350 matched cddid_all.tbl CDD KOG2522 KOG2522 230461 KOG2522 KOG2522, Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis] 560 matched cddid_all.tbl CDD KOG2523 KOG2523 230462 KOG2523 KOG2523, Predicted RNA-binding protein with PUA domain [Translation, ribosomal structure and biogenesis] 181 matched cddid_all.tbl CDD KOG2524 KOG2524 230463 KOG2524 KOG2524, Cobyrinic acid a,c-diamide synthase [Coenzyme transport and metabolism] 338 matched cddid_all.tbl CDD KOG2525 KOG2525 230464 KOG2525 KOG2525, Folylpolyglutamate synthase [Coenzyme transport and metabolism] 496 matched cddid_all.tbl CDD KOG2526 KOG2526 230465 KOG2526 KOG2526, Predicted aminopeptidases - M20/M25/M40 family [Amino acid transport and metabolism] 555 matched cddid_all.tbl CDD KOG2527 KOG2527 230466 KOG2527 KOG2527, Sorting nexin SNX11 [Intracellular trafficking, secretion, and vesicular transport] 144 matched cddid_all.tbl CDD KOG2528 KOG2528 230467 KOG2528 KOG2528, Sorting nexin SNX9/SH3PX1 and related proteins [Intracellular trafficking, secretion, and vesicular transport] 490 matched cddid_all.tbl CDD KOG2529 KOG2529 230468 KOG2529 KOG2529, Pseudouridine synthase [Translation, ribosomal structure and biogenesis] 395 matched cddid_all.tbl CDD KOG2530 KOG2530 230469 KOG2530 KOG2530, Members of tubulin/FtsZ family [Cytoskeleton] 483 matched cddid_all.tbl CDD KOG2531 KOG2531 230470 KOG2531 KOG2531, Sugar (pentulose and hexulose) kinases [Carbohydrate transport and metabolism] 545 matched cddid_all.tbl CDD KOG2532 KOG2532 230471 KOG2532 KOG2532, Permease of the major facilitator superfamily [Carbohydrate transport and metabolism] 466 matched cddid_all.tbl CDD KOG2533 KOG2533 230472 KOG2533 KOG2533, Permease of the major facilitator superfamily [Carbohydrate transport and metabolism] 495 matched cddid_all.tbl CDD KOG2534 KOG2534 230473 KOG2534 KOG2534, DNA polymerase IV (family X) [Replication, recombination and repair] 353 matched cddid_all.tbl CDD KOG2535 KOG2535 230474 KOG2535 KOG2535, RNA polymerase II elongator complex, subunit ELP3/histone acetyltransferase [Chromatin structure and dynamics, Transcription] 554 matched cddid_all.tbl CDD KOG2536 KOG2536 230475 KOG2536 KOG2536, MAM33, mitochondrial matrix glycoprotein [Energy production and conversion] 263 matched cddid_all.tbl CDD KOG2537 KOG2537 230476 KOG2537 KOG2537, Phosphoglucomutase/phosphomannomutase [Carbohydrate transport and metabolism] 539 matched cddid_all.tbl CDD KOG2538 KOG2538 230477 KOG2538 KOG2538, Origin recognition complex, subunit 3 [Replication, recombination and repair] 578 matched cddid_all.tbl CDD KOG2539 KOG2539 230478 KOG2539 KOG2539, Mitochondrial/chloroplast ribosome small subunit component [Translation, ribosomal structure and biogenesis] 491 matched cddid_all.tbl CDD KOG2540 KOG2540 230479 KOG2540 KOG2540, Cytochrome oxidase assembly factor COX11 [Posttranslational modification, protein turnover, chaperones] 269 matched cddid_all.tbl CDD KOG2541 KOG2541 230480 KOG2541 KOG2541, Palmitoyl protein thioesterase [Lipid transport and metabolism, Posttranslational modification, protein turnover, chaperones] 296 matched cddid_all.tbl CDD KOG2542 KOG2542 230481 KOG2542 KOG2542, Uncharacterized conserved protein (YdiU family) [Function unknown] 500 matched cddid_all.tbl CDD KOG2543 KOG2543 230482 KOG2543 KOG2543, Origin recognition complex, subunit 5 [Replication, recombination and repair] 438 matched cddid_all.tbl CDD KOG2544 KOG2544 230483 KOG2544 KOG2544, Dihydropteroate synthase/7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase/Dihydroneopterin aldolase [Coenzyme transport and metabolism] 711 matched cddid_all.tbl CDD KOG2545 KOG2545 230484 KOG2545 KOG2545, Conserved membrane protein [Function unknown] 543 matched cddid_all.tbl CDD KOG2546 KOG2546 230485 KOG2546 KOG2546, Abl interactor ABI-1, contains SH3 domain [Signal transduction mechanisms, Cytoskeleton] 483 matched cddid_all.tbl CDD KOG2547 KOG2547 230486 KOG2547 KOG2547, Ceramide glucosyltransferase [Lipid transport and metabolism, Cell wall/membrane/envelope biogenesis] 431 matched cddid_all.tbl CDD KOG2548 KOG2548 230487 KOG2548 KOG2548, SWAP mRNA splicing regulator [RNA processing and modification] 653 matched cddid_all.tbl CDD KOG2549 KOG2549 230488 KOG2549 KOG2549, Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription] 576 matched cddid_all.tbl CDD KOG2550 KOG2550 230489 KOG2550 KOG2550, IMP dehydrogenase/GMP reductase [Nucleotide transport and metabolism] 503 matched cddid_all.tbl CDD KOG2551 KOG2551 230490 KOG2551 KOG2551, Phospholipase/carboxyhydrolase [Amino acid transport and metabolism] 230 matched cddid_all.tbl CDD KOG2552 KOG2552 230491 KOG2552 KOG2552, Major facilitator superfamily permease - Cdc91p [General function prediction only] 388 matched cddid_all.tbl CDD KOG2553 KOG2553 230492 KOG2553 KOG2553, Pseudouridylate synthase [Translation, ribosomal structure and biogenesis] 416 matched cddid_all.tbl CDD KOG2554 KOG2554 230493 KOG2554 KOG2554, Pseudouridylate synthase [Translation, ribosomal structure and biogenesis] 425 matched cddid_all.tbl CDD KOG2555 KOG2555 230494 KOG2555 KOG2555, AICAR transformylase/IMP cyclohydrolase/methylglyoxal synthase [Nucleotide transport and metabolism] 588 matched cddid_all.tbl CDD KOG2556 KOG2556 230495 KOG2556 KOG2556, Leishmanolysin-like peptidase (Peptidase M8 family) [Cell wall/membrane/envelope biogenesis, Defense mechanisms] 666 matched cddid_all.tbl CDD KOG2557 KOG2557 230496 KOG2557 KOG2557, Uncharacterized conserved protein, contains TLDc domain [Function unknown] 427 matched cddid_all.tbl CDD KOG2558 KOG2558 230497 KOG2558 KOG2558, Negative regulator of histones [Transcription] 532 matched cddid_all.tbl CDD KOG2559 KOG2559 230498 KOG2559 KOG2559, Predicted pseudouridine synthase [Translation, ribosomal structure and biogenesis] 318 matched cddid_all.tbl CDD KOG2560 KOG2560 230499 KOG2560 KOG2560, RNA splicing factor - Slu7p [RNA processing and modification] 529 matched cddid_all.tbl CDD KOG2561 KOG2561 230500 KOG2561 KOG2561, Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms] 568 matched cddid_all.tbl CDD KOG2562 KOG2562 230501 KOG2562 KOG2562, Protein phosphatase 2 regulatory subunit [RNA processing and modification] 493 matched cddid_all.tbl CDD KOG2563 KOG2563 230502 KOG2563 KOG2563, Permease of the major facilitator superfamily [General function prediction only] 480 matched cddid_all.tbl CDD KOG2564 KOG2564 230503 KOG2564 KOG2564, Predicted acetyltransferases and hydrolases with the alpha/beta hydrolase fold [General function prediction only] 343 matched cddid_all.tbl CDD KOG2565 KOG2565 230504 KOG2565 KOG2565, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only] 469 matched cddid_all.tbl CDD KOG2566 KOG2566 230505 KOG2566 KOG2566, Beta-glucocerebrosidase [Carbohydrate transport and metabolism] 518 matched cddid_all.tbl CDD KOG2567 KOG2567 230506 KOG2567 KOG2567, Uncharacterized conserved protein [Function unknown] 179 matched cddid_all.tbl CDD KOG2568 KOG2568 230507 KOG2568 KOG2568, Predicted membrane protein [Function unknown] 518 matched cddid_all.tbl CDD KOG2569 KOG2569 230508 KOG2569 KOG2569, G protein-coupled seven transmembrane receptor [Signal transduction mechanisms] 440 matched cddid_all.tbl CDD KOG2570 KOG2570 230509 KOG2570 KOG2570, SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics, Transcription] 420 matched cddid_all.tbl CDD KOG2571 KOG2571 230510 KOG2571 KOG2571, Chitin synthase/hyaluronan synthase (glycosyltransferases) [Cell wall/membrane/envelope biogenesis] 862 matched cddid_all.tbl CDD KOG2572 KOG2572 230511 KOG2572 KOG2572, Ribosome biogenesis protein - Nop58p/Nop5p [RNA processing and modification, Translation, ribosomal structure and biogenesis] 498 matched cddid_all.tbl CDD KOG2573 KOG2573 230512 KOG2573 KOG2573, Ribosome biogenesis protein - Nop56p/Sik1p [RNA processing and modification, Translation, ribosomal structure and biogenesis] 498 matched cddid_all.tbl CDD KOG2574 KOG2574 230513 KOG2574 KOG2574, mRNA splicing factor PRP31 [RNA processing and modification] 492 matched cddid_all.tbl CDD KOG2575 KOG2575 230514 KOG2575 KOG2575, Glucosyltransferase - Alg6p [Carbohydrate transport and metabolism, Amino acid transport and metabolism] 510 matched cddid_all.tbl CDD KOG2576 KOG2576 230515 KOG2576 KOG2576, Glucosyltransferase - Alg8p [Transcription] 500 matched cddid_all.tbl CDD KOG2577 KOG2577 230516 KOG2577 KOG2577, Transcription factor E2F/dimerization partner (TDP) [Transcription] 354 matched cddid_all.tbl CDD KOG2578 KOG2578 230517 KOG2578 KOG2578, Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription] 388 matched cddid_all.tbl CDD KOG2579 KOG2579 230518 KOG2579 KOG2579, Ficolin and related extracellular proteins [General function prediction only] 338 matched cddid_all.tbl CDD KOG2580 KOG2580 230519 KOG2580 KOG2580, Mitochondrial import inner membrane translocase, subunit TIM44 [Intracellular trafficking, secretion, and vesicular transport] 459 matched cddid_all.tbl CDD KOG2581 KOG2581 230520 KOG2581 KOG2581, 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones] 493 matched cddid_all.tbl CDD KOG2582 KOG2582 230521 KOG2582 KOG2582, COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms] 422 matched cddid_all.tbl CDD KOG2583 KOG2583 230522 KOG2583 KOG2583, Ubiquinol cytochrome c reductase, subunit QCR2 [Energy production and conversion] 429 matched cddid_all.tbl CDD KOG2584 KOG2584 230523 KOG2584 KOG2584, Dihydroorotase and related enzymes [Nucleotide transport and metabolism] 522 matched cddid_all.tbl CDD KOG2585 KOG2585 230524 KOG2585 KOG2585, Uncharacterized conserved protein [Function unknown] 453 matched cddid_all.tbl CDD KOG2586 KOG2586 230525 KOG2586 KOG2586, Pyridoxamine-phosphate oxidase [Coenzyme transport and metabolism] 228 matched cddid_all.tbl CDD KOG2587 KOG2587 230526 KOG2587 KOG2587, RNA polymerase III (C) subunit [Transcription] 551 matched cddid_all.tbl CDD KOG2588 KOG2588 230527 KOG2588 KOG2588, Predicted DNA-binding protein [Transcription] 953 matched cddid_all.tbl CDD KOG2589 KOG2589 230528 KOG2589 KOG2589, Histone tail methylase [Chromatin structure and dynamics] 453 matched cddid_all.tbl CDD KOG2590 KOG2590 230529 KOG2590 KOG2590, RNA-binding protein LARP/SRO9 and related La domain proteins [Posttranslational modification, protein turnover, chaperones, Translation, ribosomal structure and biogenesis] 448 matched cddid_all.tbl CDD KOG2591 KOG2591 230530 KOG2591 KOG2591, c-Mpl binding protein, contains La domain [Signal transduction mechanisms] 684 matched cddid_all.tbl CDD KOG2592 KOG2592 230531 KOG2592 KOG2592, Tumor differentially expressed (TDE) protein [Function unknown] 426 matched cddid_all.tbl CDD KOG2593 KOG2593 230532 KOG2593 KOG2593, Transcription initiation factor IIE, alpha subunit [Transcription] 436 matched cddid_all.tbl CDD KOG2594 KOG2594 230533 KOG2594 KOG2594, Uncharacterized conserved protein [Function unknown] 396 matched cddid_all.tbl CDD KOG2595 KOG2595 230534 KOG2595 KOG2595, Predicted GTPase activator protein [Signal transduction mechanisms] 395 matched cddid_all.tbl CDD KOG2596 KOG2596 230535 KOG2596 KOG2596, Aminopeptidase I zinc metalloprotease (M18) [Amino acid transport and metabolism] 479 matched cddid_all.tbl CDD KOG2597 KOG2597 230536 KOG2597 KOG2597, Predicted aminopeptidase of the M17 family [General function prediction only] 513 matched cddid_all.tbl CDD KOG2598 KOG2598 230537 KOG2598 KOG2598, Phosphomethylpyrimidine kinase [Coenzyme transport and metabolism, Transcription] 523 matched cddid_all.tbl CDD KOG2599 KOG2599 230538 KOG2599 KOG2599, Pyridoxal/pyridoxine/pyridoxamine kinase [Coenzyme transport and metabolism] 308 matched cddid_all.tbl CDD KOG2600 KOG2600 230539 KOG2600 KOG2600, U3 small nucleolar ribonucleoprotein (snoRNP) subunit - Mpp10p [RNA processing and modification] 596 matched cddid_all.tbl CDD KOG2601 KOG2601 230540 KOG2601 KOG2601, Iron transporter [Inorganic ion transport and metabolism] 503 matched cddid_all.tbl CDD KOG2602 KOG2602 230541 KOG2602 KOG2602, Predicted cell surface protein homologous to bacterial outer membrane proteins [General function prediction only] 457 matched cddid_all.tbl CDD KOG2603 KOG2603 230542 KOG2603 KOG2603, Oligosaccharyltransferase, gamma subunit [Posttranslational modification, protein turnover, chaperones] 331 matched cddid_all.tbl CDD KOG2604 KOG2604 230543 KOG2604 KOG2604, Subunit of cis-Golgi transport vesicle tethering complex - Sec34p [Intracellular trafficking, secretion, and vesicular transport] 733 matched cddid_all.tbl CDD KOG2605 KOG2605 230544 KOG2605 KOG2605, OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms, Posttranslational modification, protein turnover, chaperones] 371 matched cddid_all.tbl CDD KOG2606 KOG2606 230545 KOG2606 KOG2606, OTU (ovarian tumor)-like cysteine protease [Signal transduction mechanisms, Posttranslational modification, protein turnover, chaperones] 302 matched cddid_all.tbl CDD KOG2607 KOG2607 230546 KOG2607 KOG2607, CDK5 activator-binding protein [Signal transduction mechanisms] 505 matched cddid_all.tbl CDD KOG2608 KOG2608 230547 KOG2608 KOG2608, Endoplasmic reticulum membrane-associated oxidoreductin involved in disulfide bond formation [Posttranslational modification, protein turnover, chaperones, Intracellular trafficking, secretion, and vesicular transport] 469 matched cddid_all.tbl CDD KOG2609 KOG2609 230548 KOG2609 KOG2609, Cyclin D-interacting protein GCIP [Cell cycle control, cell division, chromosome partitioning, RNA processing and modification] 228 matched cddid_all.tbl CDD KOG2610 KOG2610 230549 KOG2610 KOG2610, Uncharacterized conserved protein [Function unknown] 491 matched cddid_all.tbl CDD KOG2611 KOG2611 230550 KOG2611 KOG2611, Neurochondrin/leucine-rich protein (Neurochondrin) [Function unknown] 698 matched cddid_all.tbl CDD KOG2612 KOG2612 230551 KOG2612 KOG2612, Predicted integral membrane protein [Function unknown] 103 matched cddid_all.tbl CDD KOG2613 KOG2613 230552 KOG2613 KOG2613, NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis] 502 matched cddid_all.tbl CDD KOG2614 KOG2614 230553 KOG2614 KOG2614, Kynurenine 3-monooxygenase and related flavoprotein monooxygenases [Energy production and conversion, General function prediction only] 420 matched cddid_all.tbl CDD KOG2615 KOG2615 230554 KOG2615 KOG2615, Permease of the major facilitator superfamily [General function prediction only] 451 matched cddid_all.tbl CDD KOG2616 KOG2616 230555 KOG2616 KOG2616, Pyridoxalphosphate-dependent enzyme/predicted threonine synthase [Amino acid transport and metabolism] 266 matched cddid_all.tbl CDD KOG2617 KOG2617 230556 KOG2617 KOG2617, Citrate synthase [Energy production and conversion] 458 matched cddid_all.tbl CDD KOG2618 KOG2618 230557 KOG2618 KOG2618, Uncharacterized conserved protein [Function unknown] 366 matched cddid_all.tbl CDD KOG2619 KOG2619 230558 KOG2619 KOG2619, Fucosyltransferase [Carbohydrate transport and metabolism, Amino acid transport and metabolism] 372 matched cddid_all.tbl CDD KOG2620 KOG2620 230559 KOG2620 KOG2620, Prohibitins and stomatins of the PID superfamily [Energy production and conversion] 301 matched cddid_all.tbl CDD KOG2621 KOG2621 230560 KOG2621 KOG2621, Prohibitins and stomatins of the PID superfamily [Energy production and conversion] 288 matched cddid_all.tbl CDD KOG2622 KOG2622 230561 KOG2622 KOG2622, Putative myrosinase precursor [Defense mechanisms] 510 matched cddid_all.tbl CDD KOG2623 KOG2623 230562 KOG2623 KOG2623, Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 467 matched cddid_all.tbl CDD KOG2624 KOG2624 230563 KOG2624 KOG2624, Triglyceride lipase-cholesterol esterase [Lipid transport and metabolism] 403 matched cddid_all.tbl CDD KOG2625 KOG2625 230564 KOG2625 KOG2625, Uncharacterized conserved protein [Function unknown] 348 matched cddid_all.tbl CDD KOG2626 KOG2626 230565 KOG2626 KOG2626, Histone H3 (Lys4) methyltransferase complex, subunit CPS60/ASH2/BRE2 [Chromatin structure and dynamics, Transcription] 544 matched cddid_all.tbl CDD KOG2627 KOG2627 230566 KOG2627 KOG2627, Nuclear protein ES2 [General function prediction only] 488 matched cddid_all.tbl CDD KOG2628 KOG2628 230567 KOG2628 KOG2628, Farnesyl cysteine-carboxyl methyltransferase [Posttranslational modification, protein turnover, chaperones] 201 matched cddid_all.tbl CDD KOG2629 KOG2629 230568 KOG2629 KOG2629, Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis,Posttranslational modification, protein turnover, chaperones , Intracellular trafficking, secretion, and vesicular transport] 300 matched cddid_all.tbl CDD KOG2630 KOG2630 230569 KOG2630 KOG2630, Enolase-phosphatase E-1 [Amino acid transport and metabolism] 254 matched cddid_all.tbl CDD KOG2631 KOG2631 230570 KOG2631 KOG2631, Class II aldolase/adducin N-terminal domain protein [Carbohydrate transport and metabolism] 238 matched cddid_all.tbl CDD KOG2632 KOG2632 230571 KOG2632 KOG2632, Rhomboid family proteins [Function unknown] 258 matched cddid_all.tbl CDD KOG2633 KOG2633 230572 KOG2633 KOG2633, Hismacro and SEC14 domain-containing proteins [Chromatin structure and dynamics, Transcription] 200 matched cddid_all.tbl CDD KOG2634 KOG2634 230573 KOG2634 KOG2634, Initiator tRNA phosphoribosyl-transferase [RNA processing and modification] 476 matched cddid_all.tbl CDD KOG2635 KOG2635 230574 KOG2635 KOG2635, Medium subunit of clathrin adaptor complex [Intracellular trafficking, secretion, and vesicular transport] 512 matched cddid_all.tbl CDD KOG2636 KOG2636 230575 KOG2636 KOG2636, Splicing factor 3a, subunit 3 [RNA processing and modification] 497 matched cddid_all.tbl CDD KOG2637 KOG2637 230576 KOG2637 KOG2637, Uncharacterized conserved protein [Function unknown] 446 matched cddid_all.tbl CDD KOG2638 KOG2638 230577 KOG2638 KOG2638, UDP-glucose pyrophosphorylase [Carbohydrate transport and metabolism] 498 matched cddid_all.tbl CDD KOG2639 KOG2639 230578 KOG2639 KOG2639, Sodium sulfate symporter and related arsenite permeases [Inorganic ion transport and metabolism] 685 matched cddid_all.tbl CDD KOG2640 KOG2640 230579 KOG2640 KOG2640, Thioredoxin [Function unknown] 319 matched cddid_all.tbl CDD KOG2641 KOG2641 230580 KOG2641 KOG2641, Predicted seven transmembrane receptor - rhodopsin family [Signal transduction mechanisms] 386 matched cddid_all.tbl CDD KOG2642 KOG2642 230581 KOG2642 KOG2642, Alpha-1,2 glucosyltransferase/transcriptional activator [Posttranslational modification, protein turnover, chaperones, Transcription, Lipid transport and metabolism, Signal transduction mechanisms] 446 matched cddid_all.tbl CDD KOG2643 KOG2643 230582 KOG2643 KOG2643, Ca2+ binding protein, contains EF-hand motifs [Inorganic ion transport and metabolism] 489 matched cddid_all.tbl CDD KOG2644 KOG2644 230583 KOG2644 KOG2644, 3'-phosphoadenosine 5'-phosphosulfate sulfotransferase (PAPS reductase)/FAD synthetase and related enzymes [Amino acid transport and metabolism, Coenzyme transport and metabolism] 282 matched cddid_all.tbl CDD KOG2645 KOG2645 230584 KOG2645 KOG2645, Type I phosphodiesterase/nucleotide pyrophosphatase [General function prediction only] 418 matched cddid_all.tbl CDD KOG2646 KOG2646 230585 KOG2646 KOG2646, Ribosomal protein S5 [Translation, ribosomal structure and biogenesis] 396 matched cddid_all.tbl CDD KOG2647 KOG2647 230586 KOG2647 KOG2647, Predicted Dolichyl-phosphate-mannose-protein mannosyltransferase [General function prediction only] 444 matched cddid_all.tbl CDD KOG2648 KOG2648 230587 KOG2648 KOG2648, Diphthamide biosynthesis protein [Translation, ribosomal structure and biogenesis] 453 matched cddid_all.tbl CDD KOG2649 KOG2649 230588 KOG2649 KOG2649, Zinc carboxypeptidase [General function prediction only] 500 matched cddid_all.tbl CDD KOG2650 KOG2650 230589 KOG2650 KOG2650, Zinc carboxypeptidase [Function unknown] 418 matched cddid_all.tbl CDD KOG2651 KOG2651 230590 KOG2651 KOG2651, rRNA adenine N-6-methyltransferase [RNA processing and modification] 476 matched cddid_all.tbl CDD KOG2652 KOG2652 230591 KOG2652 KOG2652, RNA polymerase II transcription initiation factor TFIIA, large chain [Transcription] 348 matched cddid_all.tbl CDD KOG2653 KOG2653 230592 KOG2653 KOG2653, 6-phosphogluconate dehydrogenase [Carbohydrate transport and metabolism] 487 matched cddid_all.tbl CDD KOG2654 KOG2654 230593 KOG2654 KOG2654, Uncharacterized conserved protein [Function unknown] 461 matched cddid_all.tbl CDD KOG2655 KOG2655 230594 KOG2655 KOG2655, Septin family protein (P-loop GTPase) [Cell cycle control, cell division, chromosome partitioning, Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 366 matched cddid_all.tbl CDD KOG2656 KOG2656 230595 KOG2656 KOG2656, DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics, Transcription] 445 matched cddid_all.tbl CDD KOG2657 KOG2657 230596 KOG2657 KOG2657, Transmembrane glycoprotein nicastrin [Signal transduction mechanisms, Posttranslational modification, protein turnover, chaperones] 596 matched cddid_all.tbl CDD KOG2658 KOG2658 230597 KOG2658 KOG2658, NADH:ubiquinone oxidoreductase, NDUFV1/51kDa subunit [Energy production and conversion] 478 matched cddid_all.tbl CDD KOG2659 KOG2659 230598 KOG2659 KOG2659, LisH motif-containing protein [Cytoskeleton] 228 matched cddid_all.tbl CDD KOG2660 KOG2660 230599 KOG2660 KOG2660, Locus-specific chromosome binding proteins [Function unknown] 331 matched cddid_all.tbl CDD KOG2661 KOG2661 230600 KOG2661 KOG2661, Peptidase family M48 [Posttranslational modification, protein turnover, chaperones] 424 matched cddid_all.tbl CDD KOG2662 KOG2662 230601 KOG2662 KOG2662, Magnesium transporters: CorA family [Inorganic ion transport and metabolism] 414 matched cddid_all.tbl CDD KOG2663 KOG2663 230602 KOG2663 KOG2663, Acetolactate synthase, small subunit [Amino acid transport and metabolism] 309 matched cddid_all.tbl CDD KOG2664 KOG2664 230603 KOG2664 KOG2664, Small nuclear RNA activating protein complex - 50kD subunit (SNAP50) [Transcription] 396 matched cddid_all.tbl CDD KOG2665 KOG2665 230604 KOG2665 KOG2665, Predicted FAD-dependent oxidoreductase [Function unknown] 453 matched cddid_all.tbl CDD KOG2666 KOG2666 230605 KOG2666 KOG2666, UDP-glucose/GDP-mannose dehydrogenase [Carbohydrate transport and metabolism, Signal transduction mechanisms] 481 matched cddid_all.tbl CDD KOG2667 KOG2667 230606 KOG2667 KOG2667, COPII vesicle protein [Intracellular trafficking, secretion, and vesicular transport] 379 matched cddid_all.tbl CDD KOG2668 KOG2668 230607 KOG2668 KOG2668, Flotillins [Intracellular trafficking, secretion, and vesicular transport, Cytoskeleton] 428 matched cddid_all.tbl CDD KOG2669 KOG2669 230608 KOG2669 KOG2669, Regulator of nuclear mRNA [RNA processing and modification] 325 matched cddid_all.tbl CDD KOG2670 KOG2670 230609 KOG2670 KOG2670, Enolase [Carbohydrate transport and metabolism] 433 matched cddid_all.tbl CDD KOG2671 KOG2671 230610 KOG2671 KOG2671, Putative RNA methylase [Replication, recombination and repair] 421 matched cddid_all.tbl CDD KOG2672 KOG2672 230611 KOG2672 KOG2672, Lipoate synthase [Coenzyme transport and metabolism] 360 matched cddid_all.tbl CDD KOG2673 KOG2673 230612 KOG2673 KOG2673, Uncharacterized conserved protein, contains PSP domain [Function unknown] 485 matched cddid_all.tbl CDD KOG2674 KOG2674 230613 KOG2674 KOG2674, Cysteine protease required for autophagy - Apg4p/Aut2p [Cytoskeleton, Intracellular trafficking, secretion, and vesicular transport] 409 matched cddid_all.tbl CDD KOG2675 KOG2675 230614 KOG2675 KOG2675, Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton, Signal transduction mechanisms] 480 matched cddid_all.tbl CDD KOG2676 KOG2676 230615 KOG2676 KOG2676, Uncharacterized conserved protein [Function unknown] 478 matched cddid_all.tbl CDD KOG2677 KOG2677 230616 KOG2677 KOG2677, Stoned B synaptic vesicle biogenesis protein [Intracellular trafficking, secretion, and vesicular transport] 922 matched cddid_all.tbl CDD KOG2678 KOG2678 230617 KOG2678 KOG2678, Predicted membrane protein [Function unknown] 244 matched cddid_all.tbl CDD KOG2679 KOG2679 230618 KOG2679 KOG2679, Purple (tartrate-resistant) acid phosphatase [Posttranslational modification, protein turnover, chaperones] 336 matched cddid_all.tbl CDD KOG2680 KOG2680 230619 KOG2680 KOG2680, DNA helicase TIP49, TBP-interacting protein [Transcription] 454 matched cddid_all.tbl CDD KOG2681 KOG2681 230620 KOG2681 KOG2681, Metal-dependent phosphohydrolase [Function unknown] 498 matched cddid_all.tbl CDD KOG2682 KOG2682 230621 KOG2682 KOG2682, NAD-dependent histone deacetylases and class I sirtuins (SIR2 family) [Chromatin structure and dynamics, Transcription] 314 matched cddid_all.tbl CDD KOG2683 KOG2683 230622 KOG2683 KOG2683, Sirtuin 4 and related class II sirtuins (SIR2 family) [Chromatin structure and dynamics, Transcription] 305 matched cddid_all.tbl CDD KOG2684 KOG2684 230623 KOG2684 KOG2684, Sirtuin 5 and related class III sirtuins (SIR2 family) [Chromatin structure and dynamics, Transcription] 412 matched cddid_all.tbl CDD KOG2685 KOG2685 230624 KOG2685 KOG2685, Cystoskeletal protein Tektin [Cytoskeleton] 421 matched cddid_all.tbl CDD KOG2686 KOG2686 230625 KOG2686 KOG2686, Choline kinase [Cell wall/membrane/envelope biogenesis] 366 matched cddid_all.tbl CDD KOG2687 KOG2687 230626 KOG2687 KOG2687, Spindle pole body protein, contains UNC-84 domain [Cell cycle control, cell division, chromosome partitioning] 414 matched cddid_all.tbl CDD KOG2688 KOG2688 230627 KOG2688 KOG2688, Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning] 394 matched cddid_all.tbl CDD KOG2689 KOG2689 230628 KOG2689 KOG2689, Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones] 290 matched cddid_all.tbl CDD KOG2690 KOG2690 230629 KOG2690 KOG2690, Uncharacterized conserved protein, contains BSD domain [Function unknown] 331 matched cddid_all.tbl CDD KOG2691 KOG2691 230630 KOG2691 KOG2691, RNA polymerase II subunit 9 [Transcription] 113 matched cddid_all.tbl CDD KOG2692 KOG2692 230631 KOG2692 KOG2692, Sialyltransferase [Carbohydrate transport and metabolism] 376 matched cddid_all.tbl CDD KOG2693 KOG2693 230632 KOG2693 KOG2693, Putative zinc transporter [Inorganic ion transport and metabolism] 453 matched cddid_all.tbl CDD KOG2694 KOG2694 230633 KOG2694 KOG2694, Putative zinc transporter [Inorganic ion transport and metabolism] 361 matched cddid_all.tbl CDD KOG2695 KOG2695 230634 KOG2695 KOG2695, WD40 repeat protein [General function prediction only] 425 matched cddid_all.tbl CDD KOG2696 KOG2696 230635 KOG2696 KOG2696, Histone acetyltransferase type b catalytic subunit [Chromatin structure and dynamics] 403 matched cddid_all.tbl CDD KOG2697 KOG2697 230636 KOG2697 KOG2697, Histidinol dehydrogenase [Amino acid transport and metabolism] 446 matched cddid_all.tbl CDD KOG2698 KOG2698 230637 KOG2698 KOG2698, GTP cyclohydrolase I [Coenzyme transport and metabolism] 247 matched cddid_all.tbl CDD KOG2699 KOG2699 230638 KOG2699 KOG2699, Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones] 407 matched cddid_all.tbl CDD KOG2700 KOG2700 230639 KOG2700 KOG2700, Adenylosuccinate lyase [Nucleotide transport and metabolism] 481 matched cddid_all.tbl CDD KOG2701 KOG2701 230640 KOG2701 KOG2701, Uncharacterized conserved protein [Function unknown] 608 matched cddid_all.tbl CDD KOG2702 KOG2702 230641 KOG2702 KOG2702, Predicted panthothenate kinase/uridine kinase-related protein [Nucleotide transport and metabolism, Coenzyme transport and metabolism] 323 matched cddid_all.tbl CDD KOG2703 KOG2703 230642 KOG2703 KOG2703, C4-type Zn-finger protein [General function prediction only] 460 matched cddid_all.tbl CDD KOG2704 KOG2704 230643 KOG2704 KOG2704, Predicted membrane protein [Function unknown] 480 matched cddid_all.tbl CDD KOG2705 KOG2705 230644 KOG2705 KOG2705, Predicted membrane protein [Function unknown] 471 matched cddid_all.tbl CDD KOG2706 KOG2706 230645 KOG2706 KOG2706, Predicted membrane protein [Function unknown] 476 matched cddid_all.tbl CDD KOG2707 KOG2707 230646 KOG2707 KOG2707, Predicted metalloprotease with chaperone activity (RNAse H/HSP70 fold) [Posttranslational modification, protein turnover, chaperones] 405 matched cddid_all.tbl CDD KOG2708 KOG2708 230647 KOG2708 KOG2708, Predicted metalloprotease with chaperone activity (RNAse H/HSP70 fold) [Posttranslational modification, protein turnover, chaperones] 336 matched cddid_all.tbl CDD KOG2709 KOG2709 230648 KOG2709 KOG2709, Uncharacterized conserved protein [Function unknown] 560 matched cddid_all.tbl CDD KOG2710 KOG2710 230649 KOG2710 KOG2710, Rho GTPase-activating protein [Signal transduction mechanisms, Cytoskeleton] 412 matched cddid_all.tbl CDD KOG2711 KOG2711 230650 KOG2711 KOG2711, Glycerol-3-phosphate dehydrogenase/dihydroxyacetone 3-phosphate reductase [Energy production and conversion] 372 matched cddid_all.tbl CDD KOG2712 KOG2712 230651 KOG2712 KOG2712, Transcriptional coactivator [Transcription] 108 matched cddid_all.tbl CDD KOG2713 KOG2713 230652 KOG2713 KOG2713, Mitochondrial tryptophanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 347 matched cddid_all.tbl CDD KOG2714 KOG2714 230653 KOG2714 KOG2714, SETA binding protein SB1 and related proteins, contain BTB/POZ domain [General function prediction only] 465 matched cddid_all.tbl CDD KOG2715 KOG2715 230654 KOG2715 KOG2715, Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only] 210 matched cddid_all.tbl CDD KOG2716 KOG2716 230655 KOG2716 KOG2716, Polymerase delta-interacting protein PDIP1 and related proteins, contain BTB/POZ domain [Inorganic ion transport and metabolism] 230 matched cddid_all.tbl CDD KOG2717 KOG2717 230656 KOG2717 KOG2717, Uncharacterized conserved protein with similarity to embryogenesis protein H beta 58 and VPS26 [General function prediction only] 313 matched cddid_all.tbl CDD KOG2718 KOG2718 230657 KOG2718 KOG2718, Na+-bile acid cotransporter [Inorganic ion transport and metabolism] 371 matched cddid_all.tbl CDD KOG2719 KOG2719 230658 KOG2719 KOG2719, Metalloprotease [General function prediction only] 428 matched cddid_all.tbl CDD KOG2720 KOG2720 230659 KOG2720 KOG2720, Predicted hydrolase (HIT family) [General function prediction only] 431 matched cddid_all.tbl CDD KOG2721 KOG2721 230660 KOG2721 KOG2721, Uncharacterized conserved protein [Function unknown] 260 matched cddid_all.tbl CDD KOG2722 KOG2722 230661 KOG2722 KOG2722, Predicted membrane protein [Function unknown] 408 matched cddid_all.tbl CDD KOG2723 KOG2723 230662 KOG2723 KOG2723, Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only] 221 matched cddid_all.tbl CDD KOG2724 KOG2724 230663 KOG2724 KOG2724, Nuclear pore complex component NPAP60L/NUP50 [Intracellular trafficking, secretion, and vesicular transport] 487 matched cddid_all.tbl CDD KOG2725 KOG2725 230664 KOG2725 KOG2725, Cytochrome oxidase assembly factor COX15 [Posttranslational modification, protein turnover, chaperones] 411 matched cddid_all.tbl CDD KOG2726 KOG2726 230665 KOG2726 KOG2726, Mitochondrial polypeptide chain release factor [Translation, ribosomal structure and biogenesis] 386 matched cddid_all.tbl CDD KOG2727 KOG2727 230666 KOG2727 KOG2727, Rab3 GTPase-activating protein, non-catalytic subunit [Intracellular trafficking, secretion, and vesicular transport] 1244 matched cddid_all.tbl CDD KOG2728 KOG2728 230667 KOG2728 KOG2728, Uncharacterized conserved protein with similarity to phosphopantothenoylcysteine synthetase/decarboxylase [General function prediction only] 302 matched cddid_all.tbl CDD KOG2729 KOG2729 230668 KOG2729 KOG2729, ER vesicle integral membrane protein involved in establishing cell polarity, signaling and protein degradation [Posttranslational modification, protein turnover, chaperones, Intracellular trafficking, secretion, and vesicular transport, Signal transduction mechanisms] 137 matched cddid_all.tbl CDD KOG2730 KOG2730 230669 KOG2730 KOG2730, Methylase [General function prediction only] 263 matched cddid_all.tbl CDD KOG2731 KOG2731 230670 KOG2731 KOG2731, DNA alkylation damage repair protein [RNA processing and modification] 378 matched cddid_all.tbl CDD KOG2732 KOG2732 230671 KOG2732 KOG2732, DNA polymerase delta, regulatory subunit 55 [Replication, recombination and repair] 435 matched cddid_all.tbl CDD KOG2733 KOG2733 230672 KOG2733 KOG2733, Uncharacterized membrane protein [Function unknown] 423 matched cddid_all.tbl CDD KOG2734 KOG2734 230673 KOG2734 KOG2734, Uncharacterized conserved protein [Function unknown] 536 matched cddid_all.tbl CDD KOG2735 KOG2735 230674 KOG2735 KOG2735, Phosphatidylserine synthase [Lipid transport and metabolism] 466 matched cddid_all.tbl CDD KOG2736 KOG2736 230675 KOG2736 KOG2736, Presenilin [Signal transduction mechanisms] 406 matched cddid_all.tbl CDD KOG2737 KOG2737 230676 KOG2737 KOG2737, Putative metallopeptidase [General function prediction only] 492 matched cddid_all.tbl CDD KOG2738 KOG2738 230677 KOG2738 KOG2738, Putative methionine aminopeptidase [Posttranslational modification, protein turnover, chaperones] 369 matched cddid_all.tbl CDD KOG2739 KOG2739 230678 KOG2739 KOG2739, Leucine-rich acidic nuclear protein [Cell cycle control, cell division, chromosome partitioning, General function prediction only] 260 matched cddid_all.tbl CDD KOG2740 KOG2740 230679 KOG2740 KOG2740, Clathrin-associated protein medium chain [Intracellular trafficking, secretion, and vesicular transport] 418 matched cddid_all.tbl CDD KOG2741 KOG2741 230680 KOG2741 KOG2741, Dimeric dihydrodiol dehydrogenase [Carbohydrate transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism] 351 matched cddid_all.tbl CDD KOG2742 KOG2742 230681 KOG2742 KOG2742, Predicted oxidoreductase [General function prediction only] 367 matched cddid_all.tbl CDD KOG2743 KOG2743 230682 KOG2743 KOG2743, Cobalamin synthesis protein [Coenzyme transport and metabolism] 391 matched cddid_all.tbl CDD KOG2744 KOG2744 230683 KOG2744 KOG2744, DNA-binding proteins Bright/BRCAA1/RBP1 and related proteins containing BRIGHT domain [Transcription] 512 matched cddid_all.tbl CDD KOG2745 KOG2745 230684 KOG2745 KOG2745, Mitochondrial carrier protein [General function prediction only] 321 matched cddid_all.tbl CDD KOG2746 KOG2746 230685 KOG2746 KOG2746, HMG-box transcription factor Capicua and related proteins [Transcription] 683 matched cddid_all.tbl CDD KOG2747 KOG2747 230686 KOG2747 KOG2747, Histone acetyltransferase (MYST family) [Chromatin structure and dynamics] 396 matched cddid_all.tbl CDD KOG2748 KOG2748 230687 KOG2748 KOG2748, Uncharacterized conserved protein, contains chromo domain [Chromatin structure and dynamics] 369 matched cddid_all.tbl CDD KOG2749 KOG2749 230688 KOG2749 KOG2749, mRNA cleavage and polyadenylation factor IA/II complex, subunit CLP1 [RNA processing and modification] 415 matched cddid_all.tbl CDD KOG2750 KOG2750 230689 KOG2750 KOG2750, Uncharacterized conserved protein similar to ATP/GTP-binding protein [General function prediction only] 587 matched cddid_all.tbl CDD KOG2751 KOG2751 230690 KOG2751 KOG2751, Beclin-like protein [Signal transduction mechanisms] 447 matched cddid_all.tbl CDD KOG2752 KOG2752 230691 KOG2752 KOG2752, Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only] 345 matched cddid_all.tbl CDD KOG2753 KOG2753 230692 KOG2753 KOG2753, Uncharacterized conserved protein, contains PCI domain [General function prediction only] 378 matched cddid_all.tbl CDD KOG2754 KOG2754 230693 KOG2754 KOG2754, Oligosaccharyltransferase, beta subunit [Posttranslational modification, protein turnover, chaperones] 443 matched cddid_all.tbl CDD KOG2755 KOG2755 230694 KOG2755 KOG2755, Oxidoreductase [General function prediction only] 334 matched cddid_all.tbl CDD KOG2756 KOG2756 230695 KOG2756 KOG2756, Predicted Mg2+-dependent phosphodiesterase TTRAP [Signal transduction mechanisms] 349 matched cddid_all.tbl CDD KOG2757 KOG2757 230696 KOG2757 KOG2757, Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism] 411 matched cddid_all.tbl CDD KOG2758 KOG2758 230697 KOG2758 KOG2758, Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis] 432 matched cddid_all.tbl CDD KOG2759 KOG2759 230698 KOG2759 KOG2759, Vacuolar H+-ATPase V1 sector, subunit H [Energy production and conversion] 406 matched cddid_all.tbl CDD KOG2760 KOG2760 230699 KOG2760 KOG2760, Vacuolar sorting protein VPS36 [Intracellular trafficking, secretion, and vesicular transport] 432 matched cddid_all.tbl CDD KOG2761 KOG2761 230700 KOG2761 KOG2761, START domain-containing proteins involved in steroidogenesis/phosphatidylcholine transfer [Lipid transport and metabolism] 219 matched cddid_all.tbl CDD KOG2762 KOG2762 230701 KOG2762 KOG2762, Mannosyltransferase [Carbohydrate transport and metabolism] 429 matched cddid_all.tbl CDD KOG2763 KOG2763 230702 KOG2763 KOG2763, Acyl-CoA thioesterase [Lipid transport and metabolism] 357 matched cddid_all.tbl CDD KOG2764 KOG2764 230703 KOG2764 KOG2764, Putative transcriptional regulator DJ-1 [General function prediction only, Defense mechanisms] 247 matched cddid_all.tbl CDD KOG2765 KOG2765 230704 KOG2765 KOG2765, Predicted membrane protein [Function unknown] 416 matched cddid_all.tbl CDD KOG2766 KOG2766 230705 KOG2766 KOG2766, Predicted membrane protein [Function unknown] 336 matched cddid_all.tbl CDD KOG2767 KOG2767 230706 KOG2767 KOG2767, Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis] 400 matched cddid_all.tbl CDD KOG2768 KOG2768 230707 KOG2768 KOG2768, Translation initiation factor 2, beta subunit (eIF-2beta) [Translation, ribosomal structure and biogenesis] 231 matched cddid_all.tbl CDD KOG2769 KOG2769 230708 KOG2769 KOG2769, Putative u4/u6 small nuclear ribonucleoprotein [RNA processing and modification] 522 matched cddid_all.tbl CDD KOG2770 KOG2770 230709 KOG2770 KOG2770, Aminomethyl transferase [Amino acid transport and metabolism] 401 matched cddid_all.tbl CDD KOG2771 KOG2771 230710 KOG2771 KOG2771, Subunit of tRNA-specific adenosine-34 deaminase [RNA processing and modification] 344 matched cddid_all.tbl CDD KOG2772 KOG2772 230711 KOG2772 KOG2772, Transaldolase [Carbohydrate transport and metabolism] 337 matched cddid_all.tbl CDD KOG2773 KOG2773 230712 KOG2773 KOG2773, Apoptosis antagonizing transcription factor/protein transport protein [Transcription, Intracellular trafficking, secretion, and vesicular transport] 483 matched cddid_all.tbl CDD KOG2774 KOG2774 230713 KOG2774 KOG2774, NAD dependent epimerase [General function prediction only] 366 matched cddid_all.tbl CDD KOG2775 KOG2775 230714 KOG2775 KOG2775, Metallopeptidase [General function prediction only] 397 matched cddid_all.tbl CDD KOG2776 KOG2776 230715 KOG2776 KOG2776, Metallopeptidase [General function prediction only] 398 matched cddid_all.tbl CDD KOG2777 KOG2777 230716 KOG2777 KOG2777, tRNA-specific adenosine deaminase 1 [RNA processing and modification] 542 matched cddid_all.tbl CDD KOG2778 KOG2778 230717 KOG2778 KOG2778, Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones] 328 matched cddid_all.tbl CDD KOG2779 KOG2779 230718 KOG2779 KOG2779, N-myristoyl transferase [Lipid transport and metabolism] 421 matched cddid_all.tbl CDD KOG2780 KOG2780 230719 KOG2780 KOG2780, Ribosome biogenesis protein RPF1, contains IMP4 domain [RNA processing and modification] 302 matched cddid_all.tbl CDD KOG2781 KOG2781 230720 KOG2781 KOG2781, U3 small nucleolar ribonucleoprotein (snoRNP) component [RNA processing and modification] 290 matched cddid_all.tbl CDD KOG2782 KOG2782 230721 KOG2782 KOG2782, Putative SAM dependent methyltransferases [General function prediction only] 303 matched cddid_all.tbl CDD KOG2783 KOG2783 230722 KOG2783 KOG2783, Phenylalanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 436 matched cddid_all.tbl CDD KOG2784 KOG2784 230723 KOG2784 KOG2784, Phenylalanyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis] 483 matched cddid_all.tbl CDD KOG2785 KOG2785 230724 KOG2785 KOG2785, C2H2-type Zn-finger protein [General function prediction only] 390 matched cddid_all.tbl CDD KOG2786 KOG2786 230725 KOG2786 KOG2786, Putative glutamate/ornithine acetyltransferase [Amino acid transport and metabolism] 431 matched cddid_all.tbl CDD KOG2787 KOG2787 230726 KOG2787 KOG2787, Lanthionine synthetase C-like protein 1 [Defense mechanisms] 403 matched cddid_all.tbl CDD KOG2788 KOG2788 230727 KOG2788 KOG2788, Glycosyltransferase [Carbohydrate transport and metabolism] 418 matched cddid_all.tbl CDD KOG2789 KOG2789 230728 KOG2789 KOG2789, Putative Zn-finger protein [General function prediction only] 482 matched cddid_all.tbl CDD KOG2790 KOG2790 230729 KOG2790 KOG2790, Phosphoserine aminotransferase [Coenzyme transport and metabolism, Amino acid transport and metabolism] 370 matched cddid_all.tbl CDD KOG2791 KOG2791 230730 KOG2791 KOG2791, N-acetylglucosaminyltransferase [Carbohydrate transport and metabolism] 455 matched cddid_all.tbl CDD KOG2792 KOG2792 230731 KOG2792 KOG2792, Putative cytochrome C oxidase assembly protein [Energy production and conversion] 280 matched cddid_all.tbl CDD KOG2793 KOG2793 230732 KOG2793 KOG2793, Putative N2,N2-dimethylguanosine tRNA methyltransferase [RNA processing and modification] 248 matched cddid_all.tbl CDD KOG2794 KOG2794 230733 KOG2794 KOG2794, Delta-aminolevulinic acid dehydratase [Coenzyme transport and metabolism] 340 matched cddid_all.tbl CDD KOG2795 KOG2795 230734 KOG2795 KOG2795, Catalytic subunit of the meiotic double strand break transesterase [Replication, recombination and repair] 372 matched cddid_all.tbl CDD KOG2796 KOG2796 230735 KOG2796 KOG2796, Uncharacterized conserved protein [Function unknown] 366 matched cddid_all.tbl CDD KOG2797 KOG2797 230736 KOG2797 KOG2797, Prephenate dehydratase [Amino acid transport and metabolism] 377 matched cddid_all.tbl CDD KOG2798 KOG2798 230737 KOG2798 KOG2798, Putative trehalase [Carbohydrate transport and metabolism] 369 matched cddid_all.tbl CDD KOG2799 KOG2799 230738 KOG2799 KOG2799, Succinyl-CoA synthetase, beta subunit [Energy production and conversion] 434 matched cddid_all.tbl CDD KOG2800 KOG2800 230739 KOG2800 KOG2800, Conserved developmentally regulated protein [General function prediction only] 389 matched cddid_all.tbl CDD KOG2801 KOG2801 230740 KOG2801 KOG2801, Probable Rab-GAPs [Intracellular trafficking, secretion, and vesicular transport] 559 matched cddid_all.tbl CDD KOG2802 KOG2802 230741 KOG2802 KOG2802, Membrane protein HUEL (cation efflux superfamily) [General function prediction only] 503 matched cddid_all.tbl CDD KOG2803 KOG2803 230742 KOG2803 KOG2803, Choline phosphate cytidylyltransferase/Predicted CDP-ethanolamine synthase [Lipid transport and metabolism] 358 matched cddid_all.tbl CDD KOG2804 KOG2804 230743 KOG2804 KOG2804, Phosphorylcholine transferase/cholinephosphate cytidylyltransferase [Lipid transport and metabolism] 348 matched cddid_all.tbl CDD KOG2805 KOG2805 230744 KOG2805 KOG2805, tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Translation, ribosomal structure and biogenesis] 377 matched cddid_all.tbl CDD KOG2806 KOG2806 230745 KOG2806 KOG2806, Chitinase [Carbohydrate transport and metabolism] 432 matched cddid_all.tbl CDD KOG2807 KOG2807 230746 KOG2807 KOG2807, RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription, Replication, recombination and repair] 378 matched cddid_all.tbl CDD KOG2808 KOG2808 230747 KOG2808 KOG2808, U5 snRNP-associated RNA splicing factor [RNA processing and modification] 341 matched cddid_all.tbl CDD KOG2809 KOG2809 230748 KOG2809 KOG2809, Telomerase elongation inhibitor/RNA maturation protein PINX1 [RNA processing and modification, Cell cycle control, cell division, chromosome partitioning] 326 matched cddid_all.tbl CDD KOG2810 KOG2810 230749 KOG2810 KOG2810, Checkpoint 9-1-1 complex, RAD9 component [Energy production and conversion, Replication, recombination and repair] 394 matched cddid_all.tbl CDD KOG2811 KOG2811 230750 KOG2811 KOG2811, Uncharacterized conserved protein [Function unknown] 420 matched cddid_all.tbl CDD KOG2812 KOG2812 230751 KOG2812 KOG2812, Uncharacterized conserved protein [Function unknown] 426 matched cddid_all.tbl CDD KOG2813 KOG2813 230752 KOG2813 KOG2813, Predicted molecular chaperone, contains DnaJ domain [Posttranslational modification, protein turnover, chaperones] 406 matched cddid_all.tbl CDD KOG2814 KOG2814 230753 KOG2814 KOG2814, Transcription coactivator complex, P50 component (LigT RNA ligase/phosphodiesterase family) [Transcription] 345 matched cddid_all.tbl CDD KOG2815 KOG2815 230754 KOG2815 KOG2815, Mitochondrial/choloroplast ribosomal protein S15 [Translation, ribosomal structure and biogenesis] 256 matched cddid_all.tbl CDD KOG2816 KOG2816 230755 KOG2816 KOG2816, Predicted transporter ADD1 (major facilitator superfamily) [General function prediction only] 463 matched cddid_all.tbl CDD KOG2817 KOG2817 230756 KOG2817 KOG2817, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 394 matched cddid_all.tbl CDD KOG2818 KOG2818 230757 KOG2818 KOG2818, Predicted undecaprenyl diphosphate synthase [Lipid transport and metabolism] 263 matched cddid_all.tbl CDD KOG2819 KOG2819 230758 KOG2819 KOG2819, Uncharacterized conserved protein [Function unknown] 413 matched cddid_all.tbl CDD KOG2820 KOG2820 230759 KOG2820 KOG2820, FAD-dependent oxidoreductase [General function prediction only] 399 matched cddid_all.tbl CDD KOG2821 KOG2821 230760 KOG2821 KOG2821, RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin A [Transcription] 433 matched cddid_all.tbl CDD KOG2822 KOG2822 230761 KOG2822 KOG2822, Sphingoid base-phosphate phosphatase [Lipid transport and metabolism] 407 matched cddid_all.tbl CDD KOG2823 KOG2823 230762 KOG2823 KOG2823, Cellular protein (glioma tumor suppressor candidate region gene 2) [General function prediction only] 438 matched cddid_all.tbl CDD KOG2824 KOG2824 230763 KOG2824 KOG2824, Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones] 281 matched cddid_all.tbl CDD KOG2825 KOG2825 230764 KOG2825 KOG2825, Putative arsenite-translocating ATPase [Inorganic ion transport and metabolism] 323 matched cddid_all.tbl CDD KOG2826 KOG2826 230765 KOG2826 KOG2826, Actin-related protein Arp2/3 complex, subunit ARPC2 [Cytoskeleton] 301 matched cddid_all.tbl CDD KOG2827 KOG2827 230766 KOG2827 KOG2827, Uncharacterized conserved protein [Function unknown] 322 matched cddid_all.tbl CDD KOG2828 KOG2828 230767 KOG2828 KOG2828, Acetyl-CoA hydrolase [Energy production and conversion] 454 matched cddid_all.tbl CDD KOG2829 KOG2829 230768 KOG2829 KOG2829, E2F-like protein [Transcription] 326 matched cddid_all.tbl CDD KOG2830 KOG2830 230769 KOG2830 KOG2830, Protein phosphatase 2A-associated protein [Signal transduction mechanisms] 324 matched cddid_all.tbl CDD KOG2831 KOG2831 230770 KOG2831 KOG2831, ATP phosphoribosyltransferase [Amino acid transport and metabolism] 308 matched cddid_all.tbl CDD KOG2832 KOG2832 230771 KOG2832 KOG2832, TFIIF-interacting CTD phosphatase, including NLI-interacting factor (involved in RNA polymerase II regulation) [Transcription] 393 matched cddid_all.tbl CDD KOG2833 KOG2833 230772 KOG2833 KOG2833, Mevalonate pyrophosphate decarboxylase [Lipid transport and metabolism] 395 matched cddid_all.tbl CDD KOG2834 KOG2834 230773 KOG2834 KOG2834, Nuclear pore complex, rNpl4 component (sc Npl4) [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 510 matched cddid_all.tbl CDD KOG2835 KOG2835 230774 KOG2835 KOG2835, Phosphoribosylamidoimidazole-succinocarboxamide synthase [Nucleotide transport and metabolism] 373 matched cddid_all.tbl CDD KOG2836 KOG2836 230775 KOG2836 KOG2836, Protein tyrosine phosphatase IVA1 [Signal transduction mechanisms] 173 matched cddid_all.tbl CDD KOG2837 KOG2837 230776 KOG2837 KOG2837, Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification] 309 matched cddid_all.tbl CDD KOG2838 KOG2838 230777 KOG2838 KOG2838, Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only] 401 matched cddid_all.tbl CDD KOG2839 KOG2839 230778 KOG2839 KOG2839, Diadenosine and diphosphoinositol polyphosphate phosphohydrolase [Signal transduction mechanisms] 145 matched cddid_all.tbl CDD KOG2840 KOG2840 230779 KOG2840 KOG2840, Uncharacterized conserved protein with similarity to predicted ATPase of the PP-loop superfamily [General function prediction only] 347 matched cddid_all.tbl CDD KOG2841 KOG2841 230780 KOG2841 KOG2841, Structure-specific endonuclease ERCC1-XPF, ERCC1 component [Replication, recombination and repair] 254 matched cddid_all.tbl CDD KOG2842 KOG2842 230781 KOG2842 KOG2842, Interferon-related protein PC4 like [Cytoskeleton] 427 matched cddid_all.tbl CDD KOG2843 KOG2843 230782 KOG2843 KOG2843, Fumarylacetoacetase [Carbohydrate transport and metabolism] 420 matched cddid_all.tbl CDD KOG2844 KOG2844 230783 KOG2844 KOG2844, Dimethylglycine dehydrogenase precursor [Amino acid transport and metabolism] 856 matched cddid_all.tbl CDD KOG2845 KOG2845 230784 KOG2845 KOG2845, Activating signal cointegrator 1 [Transcription] 331 matched cddid_all.tbl CDD KOG2846 KOG2846 230785 KOG2846 KOG2846, Predicted membrane protein [Function unknown] 328 matched cddid_all.tbl CDD KOG2847 KOG2847 230786 KOG2847 KOG2847, Phosphate acyltransferase [Lipid transport and metabolism] 286 matched cddid_all.tbl CDD KOG2848 KOG2848 230787 KOG2848 KOG2848, 1-acyl-sn-glycerol-3-phosphate acyltransferase [Lipid transport and metabolism] 276 matched cddid_all.tbl CDD KOG2849 KOG2849 230788 KOG2849 KOG2849, Placental protein 11 [General function prediction only] 388 matched cddid_all.tbl CDD KOG2850 KOG2850 230789 KOG2850 KOG2850, Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only] 186 matched cddid_all.tbl CDD KOG2851 KOG2851 230790 KOG2851 KOG2851, Eukaryotic-type DNA primase, catalytic (small) subunit [Replication, recombination and repair] 412 matched cddid_all.tbl CDD KOG2852 KOG2852 230791 KOG2852 KOG2852, Possible oxidoreductase [General function prediction only] 380 matched cddid_all.tbl CDD KOG2853 KOG2853 230792 KOG2853 KOG2853, Possible oxidoreductase [General function prediction only] 509 matched cddid_all.tbl CDD KOG2854 KOG2854 230793 KOG2854 KOG2854, Possible pfkB family carbohydrate kinase [Carbohydrate transport and metabolism] 343 matched cddid_all.tbl CDD KOG2855 KOG2855 230794 KOG2855 KOG2855, Ribokinase [Carbohydrate transport and metabolism] 330 matched cddid_all.tbl CDD KOG2856 KOG2856 230795 KOG2856 KOG2856, Adaptor protein PACSIN [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport, Cytoskeleton] 472 matched cddid_all.tbl CDD KOG2857 KOG2857 230796 KOG2857 KOG2857, Predicted MYND Zn-finger protein/hormone receptor interactor [Transcription] 157 matched cddid_all.tbl CDD KOG2858 KOG2858 230797 KOG2858 KOG2858, Uncharacterized conserved protein [General function prediction only] 390 matched cddid_all.tbl CDD KOG2859 KOG2859 230798 KOG2859 KOG2859, DNA repair protein, member of the recA/RAD51 family [Replication, recombination and repair] 293 matched cddid_all.tbl CDD KOG2860 KOG2860 230799 KOG2860 KOG2860, Uncharacterized conserved protein, contains TraB domain [Signal transduction mechanisms] 359 matched cddid_all.tbl CDD KOG2861 KOG2861 230800 KOG2861 KOG2861, Uncharacterized conserved protein [Function unknown] 399 matched cddid_all.tbl CDD KOG2862 KOG2862 230801 KOG2862 KOG2862, Alanine-glyoxylate aminotransferase AGT1 [General function prediction only] 385 matched cddid_all.tbl CDD KOG2863 KOG2863 230802 KOG2863 KOG2863, RNA lariat debranching enzyme [RNA processing and modification] 456 matched cddid_all.tbl CDD KOG2864 KOG2864 230803 KOG2864 KOG2864, Nuclear division RFT1 protein [Cell cycle control, cell division, chromosome partitioning] 530 matched cddid_all.tbl CDD KOG2865 KOG2865 230804 KOG2865 KOG2865, NADH:ubiquinone oxidoreductase, NDUFA9/39kDa subunit [Energy production and conversion] 391 matched cddid_all.tbl CDD KOG2866 KOG2866 230805 KOG2866 KOG2866, Uncharacterized conserved protein [Function unknown] 349 matched cddid_all.tbl CDD KOG2867 KOG2867 230806 KOG2867 KOG2867, Phosphotyrosyl phosphatase activator [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms] 367 matched cddid_all.tbl CDD KOG2868 KOG2868 230807 KOG2868 KOG2868, Decapping enzyme complex component DCP1 [Transcription, RNA processing and modification] 335 matched cddid_all.tbl CDD KOG2869 KOG2869 230808 KOG2869 KOG2869, Meiotic cell division protein Pelota/DOM34 [Translation, ribosomal structure and biogenesis] 379 matched cddid_all.tbl CDD KOG2870 KOG2870 230809 KOG2870 KOG2870, NADH:ubiquinone oxidoreductase, NDUFS2/49 kDa subunit [Energy production and conversion] 452 matched cddid_all.tbl CDD KOG2871 KOG2871 230810 KOG2871 KOG2871, Uncharacterized conserved protein [Function unknown] 449 matched cddid_all.tbl CDD KOG2872 KOG2872 230811 KOG2872 KOG2872, Uroporphyrinogen decarboxylase [Coenzyme transport and metabolism] 359 matched cddid_all.tbl CDD KOG2873 KOG2873 230812 KOG2873 KOG2873, Ubiquinol cytochrome c reductase assembly protein CBP3 [Energy production and conversion] 284 matched cddid_all.tbl CDD KOG2874 KOG2874 230813 KOG2874 KOG2874, rRNA processing protein [Translation, ribosomal structure and biogenesis, Cell cycle control, cell division, chromosome partitioning] 356 matched cddid_all.tbl CDD KOG2875 KOG2875 230814 KOG2875 KOG2875, 8-oxoguanine DNA glycosylase [Replication, recombination and repair] 323 matched cddid_all.tbl CDD KOG2876 KOG2876 230815 KOG2876 KOG2876, Molybdenum cofactor biosynthesis pathway protein [Coenzyme transport and metabolism] 323 matched cddid_all.tbl CDD KOG2877 KOG2877 230816 KOG2877 KOG2877, sn-1,2-diacylglycerol ethanolamine- and cholinephosphotranferases [Lipid transport and metabolism] 389 matched cddid_all.tbl CDD KOG2878 KOG2878 230817 KOG2878 KOG2878, Predicted kinase [General function prediction only] 282 matched cddid_all.tbl CDD KOG2879 KOG2879 230818 KOG2879 KOG2879, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 298 matched cddid_all.tbl CDD KOG2880 KOG2880 230819 KOG2880 KOG2880, SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms] 424 matched cddid_all.tbl CDD KOG2881 KOG2881 230820 KOG2881 KOG2881, Predicted membrane protein [Function unknown] 294 matched cddid_all.tbl CDD KOG2882 KOG2882 230821 KOG2882 KOG2882, p-Nitrophenyl phosphatase [Inorganic ion transport and metabolism] 306 matched cddid_all.tbl CDD KOG2883 KOG2883 230822 KOG2883 KOG2883, NIPSNAP1 protein [Function unknown] 253 matched cddid_all.tbl CDD KOG2884 KOG2884 230823 KOG2884 KOG2884, 26S proteasome regulatory complex, subunit RPN10/PSMD4 [Posttranslational modification, protein turnover, chaperones] 259 matched cddid_all.tbl CDD KOG2885 KOG2885 230824 KOG2885 KOG2885, Uncharacterized conserved protein [Function unknown] 325 matched cddid_all.tbl CDD KOG2886 KOG2886 230825 KOG2886 KOG2886, Uncharacterized conserved protein [Function unknown] 209 matched cddid_all.tbl CDD KOG2887 KOG2887 230826 KOG2887 KOG2887, Membrane protein involved in ER to Golgi transport [Intracellular trafficking, secretion, and vesicular transport] 175 matched cddid_all.tbl CDD KOG2888 KOG2888 230827 KOG2888 KOG2888, Putative RNA binding protein [General function prediction only] 453 matched cddid_all.tbl CDD KOG2889 KOG2889 230828 KOG2889 KOG2889, Predicted PRP38-like splicing factor [Function unknown] 204 matched cddid_all.tbl CDD KOG2890 KOG2890 230829 KOG2890 KOG2890, Predicted membrane protein [Function unknown] 326 matched cddid_all.tbl CDD KOG2891 KOG2891 230830 KOG2891 KOG2891, Surface glycoprotein [General function prediction only] 445 matched cddid_all.tbl CDD KOG2892 KOG2892 230831 KOG2892 KOG2892, Porphobilinogen deaminase [Coenzyme transport and metabolism] 320 matched cddid_all.tbl CDD KOG2893 KOG2893 230832 KOG2893 KOG2893, Zn finger protein [General function prediction only] 341 matched cddid_all.tbl CDD KOG2894 KOG2894 230833 KOG2894 KOG2894, Uncharacterized conserved protein XAP-5 [Function unknown] 331 matched cddid_all.tbl CDD KOG2895 KOG2895 230834 KOG2895 KOG2895, Uncharacterized conserved protein [Function unknown] 408 matched cddid_all.tbl CDD KOG2896 KOG2896 230835 KOG2896 KOG2896, UV radiation resistance associated protein [General function prediction only] 377 matched cddid_all.tbl CDD KOG2897 KOG2897 230836 KOG2897 KOG2897, DNA-binding protein YL1 and related proteins [General function prediction only] 390 matched cddid_all.tbl CDD KOG2898 KOG2898 230837 KOG2898 KOG2898, Predicted phosphate acyltransferase, contains PlsC domain [Lipid transport and metabolism] 354 matched cddid_all.tbl CDD KOG2899 KOG2899 230838 KOG2899 KOG2899, Predicted methyltransferase [General function prediction only] 288 matched cddid_all.tbl CDD KOG2900 KOG2900 230839 KOG2900 KOG2900, Biotin synthase [Coenzyme transport and metabolism] 380 matched cddid_all.tbl CDD KOG2901 KOG2901 230840 KOG2901 KOG2901, Uncharacterized conserved protein [Function unknown] 415 matched cddid_all.tbl CDD KOG2902 KOG2902 230841 KOG2902 KOG2902, Dihydroorotase [Nucleotide transport and metabolism] 344 matched cddid_all.tbl CDD KOG2903 KOG2903 230842 KOG2903 KOG2903, Predicted glutathione S-transferase [Posttranslational modification, protein turnover, chaperones] 319 matched cddid_all.tbl CDD KOG2904 KOG2904 230843 KOG2904 KOG2904, Predicted methyltransferase [General function prediction only] 328 matched cddid_all.tbl CDD KOG2905 KOG2905 230844 KOG2905 KOG2905, Transcription initiation factor IIF, small subunit (RAP30) [Transcription] 254 matched cddid_all.tbl CDD KOG2906 KOG2906 230845 KOG2906 KOG2906, RNA polymerase III subunit C11 [Transcription] 105 matched cddid_all.tbl CDD KOG2907 KOG2907 230846 KOG2907 KOG2907, RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription] 116 matched cddid_all.tbl CDD KOG2908 KOG2908 230847 KOG2908 KOG2908, 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones] 380 matched cddid_all.tbl CDD KOG2909 KOG2909 230848 KOG2909 KOG2909, Vacuolar H+-ATPase V1 sector, subunit C [Energy production and conversion] 381 matched cddid_all.tbl CDD KOG2910 KOG2910 230849 KOG2910 KOG2910, Uncharacterized conserved protein predicted to be involved in protein sorting [General function prediction only] 209 matched cddid_all.tbl CDD KOG2911 KOG2911 230850 KOG2911 KOG2911, Uncharacterized conserved protein [Function unknown] 439 matched cddid_all.tbl CDD KOG2912 KOG2912 230851 KOG2912 KOG2912, Predicted DNA methylase [Function unknown] 419 matched cddid_all.tbl CDD KOG2913 KOG2913 230852 KOG2913 KOG2913, Predicted membrane protein [Function unknown] 260 matched cddid_all.tbl CDD KOG2914 KOG2914 230853 KOG2914 KOG2914, Predicted haloacid-halidohydrolase and related hydrolases [General function prediction only] 222 matched cddid_all.tbl CDD KOG2915 KOG2915 230854 KOG2915 KOG2915, tRNA(1-methyladenosine) methyltransferase, subunit GCD14 [Translation, ribosomal structure and biogenesis] 314 matched cddid_all.tbl CDD KOG2916 KOG2916 230855 KOG2916 KOG2916, Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis] 304 matched cddid_all.tbl CDD KOG2917 KOG2917 230856 KOG2917 KOG2917, Predicted exosome subunit [Translation, ribosomal structure and biogenesis] 250 matched cddid_all.tbl CDD KOG2918 KOG2918 230857 KOG2918 KOG2918, Carboxymethyl transferase [Posttranslational modification, protein turnover, chaperones] 335 matched cddid_all.tbl CDD KOG2919 KOG2919 230858 KOG2919 KOG2919, Guanine nucleotide-binding protein [General function prediction only] 406 matched cddid_all.tbl CDD KOG2920 KOG2920 230859 KOG2920 KOG2920, Predicted methyltransferase [General function prediction only] 282 matched cddid_all.tbl CDD KOG2921 KOG2921 230860 KOG2921 KOG2921, Intramembrane metalloprotease (sterol-regulatory element-binding protein (SREBP) protease) [Posttranslational modification, protein turnover, chaperones] 484 matched cddid_all.tbl CDD KOG2922 KOG2922 230861 KOG2922 KOG2922, Uncharacterized conserved protein [Function unknown] 335 matched cddid_all.tbl CDD KOG2923 KOG2923 230862 KOG2923 KOG2923, Uncharacterized conserved protein [Function unknown] 67 matched cddid_all.tbl CDD KOG2924 KOG2924 230863 KOG2924 KOG2924, Deoxyhypusine synthase [Posttranslational modification, protein turnover, chaperones] 366 matched cddid_all.tbl CDD KOG2925 KOG2925 230864 KOG2925 KOG2925, Predicted translation initiation factor related to eIF-1A [Translation, ribosomal structure and biogenesis] 167 matched cddid_all.tbl CDD KOG2926 KOG2926 230865 KOG2926 KOG2926, Malonyl-CoA:ACP transacylase [Lipid transport and metabolism] 386 matched cddid_all.tbl CDD KOG2927 KOG2927 230866 KOG2927 KOG2927, Membrane component of ER protein translocation complex [Intracellular trafficking, secretion, and vesicular transport] 372 matched cddid_all.tbl CDD KOG2928 KOG2928 230867 KOG2928 KOG2928, Origin recognition complex, subunit 2 [Replication, recombination and repair] 518 matched cddid_all.tbl CDD KOG2929 KOG2929 230868 KOG2929 KOG2929, Transcription factor, component of CCR4 transcriptional complex [Transcription] 348 matched cddid_all.tbl CDD KOG2930 KOG2930 230869 KOG2930 KOG2930, SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones] 114 matched cddid_all.tbl CDD KOG2931 KOG2931 230870 KOG2931 KOG2931, Differentiation-related gene 1 protein (NDR1 protein), related proteins [Function unknown] 222 matched cddid_all.tbl CDD KOG2932 KOG2932 230871 KOG2932 KOG2932, E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones] 389 matched cddid_all.tbl CDD KOG2933 KOG2933 230872 KOG2933 KOG2933, Uncharacterized conserved protein [Function unknown] 334 matched cddid_all.tbl CDD KOG2934 KOG2934 230873 KOG2934 KOG2934, Uncharacterized conserved protein, contains Josephin domain [General function prediction only] 204 matched cddid_all.tbl CDD KOG2935 KOG2935 230874 KOG2935 KOG2935, Ataxin 3/Josephin [General function prediction only] 315 matched cddid_all.tbl CDD KOG2936 KOG2936 230875 KOG2936 KOG2936, Uncharacterized conserved protein [Function unknown] 301 matched cddid_all.tbl CDD KOG2937 KOG2937 230876 KOG2937 KOG2937, Decapping enzyme complex, predicted pyrophosphatase DCP2 [RNA processing and modification] 348 matched cddid_all.tbl CDD KOG2938 KOG2938 230877 KOG2938 KOG2938, Predicted inosine-uridine preferring nucleoside hydrolase [Nucleotide transport and metabolism] 350 matched cddid_all.tbl CDD KOG2939 KOG2939 230878 KOG2939 KOG2939, Uncharacterized conserved protein [Function unknown] 502 matched cddid_all.tbl CDD KOG2940 KOG2940 230879 KOG2940 KOG2940, Predicted methyltransferase [General function prediction only] 325 matched cddid_all.tbl CDD KOG2941 KOG2941 230880 KOG2941 KOG2941, Beta-1,4-mannosyltransferase [Posttranslational modification, protein turnover, chaperones] 444 matched cddid_all.tbl CDD KOG2942 KOG2942 230881 KOG2942 KOG2942, Uncharacterized conserved protein [Function unknown] 361 matched cddid_all.tbl CDD KOG2943 KOG2943 230882 KOG2943 KOG2943, Predicted glyoxalase [Carbohydrate transport and metabolism] 299 matched cddid_all.tbl CDD KOG2944 KOG2944 230883 KOG2944 KOG2944, Glyoxalase [Carbohydrate transport and metabolism] 170 matched cddid_all.tbl CDD KOG2945 KOG2945 230884 KOG2945 KOG2945, Predicted RNA-binding protein [General function prediction only] 365 matched cddid_all.tbl CDD KOG2946 KOG2946 230885 KOG2946 KOG2946, Uncharacterized conserved protein [Function unknown] 234 matched cddid_all.tbl CDD KOG2947 KOG2947 230886 KOG2947 KOG2947, Carbohydrate kinase [Carbohydrate transport and metabolism] 308 matched cddid_all.tbl CDD KOG2948 KOG2948 230887 KOG2948 KOG2948, Predicted metal-binding protein [General function prediction only] 327 matched cddid_all.tbl CDD KOG2949 KOG2949 230888 KOG2949 KOG2949, Ketopantoate hydroxymethyltransferase [Coenzyme transport and metabolism] 306 matched cddid_all.tbl CDD KOG2950 KOG2950 230889 KOG2950 KOG2950, Uncharacterized protein involved in protein-protein interaction, contains polyproline-binding GYF domain [General function prediction only] 348 matched cddid_all.tbl CDD KOG2951 KOG2951 230890 KOG2951 KOG2951, Inositol monophosphatase [Carbohydrate transport and metabolism] 279 matched cddid_all.tbl CDD KOG2952 KOG2952 230891 KOG2952 KOG2952, Cell cycle control protein [Cell cycle control, cell division, chromosome partitioning, Transcription, Signal transduction mechanisms] 351 matched cddid_all.tbl CDD KOG2953 KOG2953 230892 KOG2953 KOG2953, mRNA-binding protein Encore [RNA processing and modification] 432 matched cddid_all.tbl CDD KOG2954 KOG2954 230893 KOG2954 KOG2954, Mitochondrial carrier protein [General function prediction only] 427 matched cddid_all.tbl CDD KOG2955 KOG2955 230894 KOG2955 KOG2955, Uncharacterized conserved protein [Function unknown] 1069 matched cddid_all.tbl CDD KOG2956 KOG2956 230895 KOG2956 KOG2956, CLIP-associating protein [General function prediction only] 516 matched cddid_all.tbl CDD KOG2957 KOG2957 230896 KOG2957 KOG2957, Vacuolar H+-ATPase V0 sector, subunit d [Energy production and conversion] 350 matched cddid_all.tbl CDD KOG2958 KOG2958 230897 KOG2958 KOG2958, Galactose-1-phosphate uridylyltransferase [Energy production and conversion] 354 matched cddid_all.tbl CDD KOG2959 KOG2959 230898 KOG2959 KOG2959, Transcriptional regulator [Transcription] 238 matched cddid_all.tbl CDD KOG2960 KOG2960 230899 KOG2960 KOG2960, Protein involved in thiamine biosynthesis and DNA damage tolerance [General function prediction only] 328 matched cddid_all.tbl CDD KOG2961 KOG2961 230900 KOG2961 KOG2961, Predicted hydrolase (HAD superfamily) [General function prediction only] 190 matched cddid_all.tbl CDD KOG2962 KOG2962 230901 KOG2962 KOG2962, Prohibitin-related membrane protease subunits [General function prediction only] 322 matched cddid_all.tbl CDD KOG2963 KOG2963 230902 KOG2963 KOG2963, RNA-binding protein required for 60S ribosomal subunit biogenesis [Translation, ribosomal structure and biogenesis] 405 matched cddid_all.tbl CDD KOG2964 KOG2964 230903 KOG2964 KOG2964, Arginase family protein [Amino acid transport and metabolism] 361 matched cddid_all.tbl CDD KOG2965 KOG2965 230904 KOG2965 KOG2965, Arginase [Amino acid transport and metabolism] 318 matched cddid_all.tbl CDD KOG2966 KOG2966 230905 KOG2966 KOG2966, Uncharacterized conserved protein [General function prediction only] 325 matched cddid_all.tbl CDD KOG2967 KOG2967 230906 KOG2967 KOG2967, Uncharacterized conserved protein [Function unknown] 314 matched cddid_all.tbl CDD KOG2968 KOG2968 230907 KOG2968 KOG2968, Predicted esterase of the alpha-beta hydrolase superfamily (Neuropathy target esterase), contains cAMP-binding domains [General function prediction only] 1158 matched cddid_all.tbl CDD KOG2969 KOG2969 230908 KOG2969 KOG2969, Uncharacterized conserved protein [Function unknown] 264 matched cddid_all.tbl CDD KOG2970 KOG2970 230909 KOG2970 KOG2970, Predicted membrane protein [Function unknown] 319 matched cddid_all.tbl CDD KOG2971 KOG2971 230910 KOG2971 KOG2971, RNA-binding protein required for biogenesis of the ribosomal 60S subunit [Translation, ribosomal structure and biogenesis] 299 matched cddid_all.tbl CDD KOG2972 KOG2972 230911 KOG2972 KOG2972, Uncharacterized conserved protein [Function unknown] 276 matched cddid_all.tbl CDD KOG2973 KOG2973 230912 KOG2973 KOG2973, Uncharacterized conserved protein [Function unknown] 353 matched cddid_all.tbl CDD KOG2974 KOG2974 230913 KOG2974 KOG2974, Uncharacterized conserved protein [Function unknown] 241 matched cddid_all.tbl CDD KOG2975 KOG2975 230914 KOG2975 KOG2975, Translation initiation factor 3, subunit f (eIF-3f) [Translation, ribosomal structure and biogenesis] 288 matched cddid_all.tbl CDD KOG2976 KOG2976 230915 KOG2976 KOG2976, Protein involved in autophagy and nutrient starvation [Posttranslational modification, protein turnover, chaperones] 278 matched cddid_all.tbl CDD KOG2977 KOG2977 230916 KOG2977 KOG2977, Glycosyltransferase [General function prediction only] 323 matched cddid_all.tbl CDD KOG2978 KOG2978 230917 KOG2978 KOG2978, Dolichol-phosphate mannosyltransferase [General function prediction only] 238 matched cddid_all.tbl CDD KOG2979 KOG2979 230918 KOG2979 KOG2979, Protein involved in DNA repair [General function prediction only] 262 matched cddid_all.tbl CDD KOG2980 KOG2980 230919 KOG2980 KOG2980, Integral membrane protease of the rhomboid family involved in different forms of regulated intramembrane proteolysis [Signal transduction mechanisms] 310 matched cddid_all.tbl CDD KOG2981 KOG2981 230920 KOG2981 KOG2981, Protein involved in autophagocytosis during starvation [General function prediction only] 295 matched cddid_all.tbl CDD KOG2982 KOG2982 230921 KOG2982 KOG2982, Uncharacterized conserved protein [Function unknown] 418 matched cddid_all.tbl CDD KOG2983 KOG2983 230922 KOG2983 KOG2983, Uncharacterized conserved protein [Function unknown] 334 matched cddid_all.tbl CDD KOG2984 KOG2984 230923 KOG2984 KOG2984, Predicted hydrolase [General function prediction only] 277 matched cddid_all.tbl CDD KOG2985 KOG2985 230924 KOG2985 KOG2985, Uncharacterized conserved protein [Function unknown] 306 matched cddid_all.tbl CDD KOG2986 KOG2986 230925 KOG2986 KOG2986, Uncharacterized conserved protein [Function unknown] 313 matched cddid_all.tbl CDD KOG2987 KOG2987 230926 KOG2987 KOG2987, Fatty acid desaturase [Lipid transport and metabolism] 324 matched cddid_all.tbl CDD KOG2988 KOG2988 230927 KOG2988 KOG2988, 60S ribosomal protein L30 [Translation, ribosomal structure and biogenesis] 112 matched cddid_all.tbl CDD KOG2989 KOG2989 230928 KOG2989 KOG2989, Uncharacterized conserved protein [Function unknown] 253 matched cddid_all.tbl CDD KOG2990 KOG2990 230929 KOG2990 KOG2990, C2C2-type Zn-finger protein [Function unknown] 317 matched cddid_all.tbl CDD KOG2991 KOG2991 230930 KOG2991 KOG2991, Splicing regulator [RNA processing and modification] 330 matched cddid_all.tbl CDD KOG2992 KOG2992 230931 KOG2992 KOG2992, Nucleolar GTPase/ATPase p130 [Nuclear structure] 446 matched cddid_all.tbl CDD KOG2993 KOG2993 230932 KOG2993 KOG2993, Cytoplasm to vacuole targeting protein [Intracellular trafficking, secretion, and vesicular transport] 1738 matched cddid_all.tbl CDD KOG2994 KOG2994 230933 KOG2994 KOG2994, Uracil DNA glycosylase [Replication, recombination and repair] 297 matched cddid_all.tbl CDD KOG2996 KOG2996 230934 KOG2996 KOG2996, Rho guanine nucleotide exchange factor VAV3 [Signal transduction mechanisms] 865 matched cddid_all.tbl CDD KOG2997 KOG2997 230935 KOG2997 KOG2997, F-box protein FBX9 [General function prediction only] 366 matched cddid_all.tbl CDD KOG2998 KOG2998 230936 KOG2998 KOG2998, Uncharacterized conserved protein [Function unknown] 302 matched cddid_all.tbl CDD KOG2999 KOG2999 230937 KOG2999 KOG2999, Regulator of Rac1, required for phagocytosis and cell migration [Signal transduction mechanisms] 713 matched cddid_all.tbl CDD KOG3000 KOG3000 230938 KOG3000 KOG3000, Microtubule-binding protein involved in cell cycle control [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton] 295 matched cddid_all.tbl CDD KOG3001 KOG3001 230939 KOG3001 KOG3001, Dosage compensation regulatory complex/histone acetyltransferase complex, subunit MSL-3/MRG15/EAF3, and related CHROMO domain-containing proteins [Chromatin structure and dynamics, Transcription] 391 matched cddid_all.tbl CDD KOG3002 KOG3002 230940 KOG3002 KOG3002, Zn finger protein [General function prediction only] 299 matched cddid_all.tbl CDD KOG3003 KOG3003 230941 KOG3003 KOG3003, Molecular chaperone of the GrpE family [Posttranslational modification, protein turnover, chaperones] 236 matched cddid_all.tbl CDD KOG3004 KOG3004 230942 KOG3004 KOG3004, Meiotic chromosome segregation protein [Cell cycle control, cell division, chromosome partitioning] 305 matched cddid_all.tbl CDD KOG3005 KOG3005 230943 KOG3005 KOG3005, GIY-YIG type nuclease [General function prediction only] 276 matched cddid_all.tbl CDD KOG3006 KOG3006 230944 KOG3006 KOG3006, Transthyretin and related proteins [Lipid transport and metabolism] 132 matched cddid_all.tbl CDD KOG3007 KOG3007 230945 KOG3007 KOG3007, Mu-crystallin [Amino acid transport and metabolism] 333 matched cddid_all.tbl CDD KOG3008 KOG3008 230946 KOG3008 KOG3008, Quinolinate phosphoribosyl transferase [Nucleotide transport and metabolism] 300 matched cddid_all.tbl CDD KOG3009 KOG3009 230947 KOG3009 KOG3009, Predicted carbohydrate kinase, contains PfkB domain [General function prediction only] 614 matched cddid_all.tbl CDD KOG3010 KOG3010 230948 KOG3010 KOG3010, Methyltransferase [General function prediction only] 261 matched cddid_all.tbl CDD KOG3011 KOG3011 230949 KOG3011 KOG3011, Ubiquitin-conjugating enzyme [Posttranslational modification, protein turnover, chaperones] 293 matched cddid_all.tbl CDD KOG3012 KOG3012 230950 KOG3012 KOG3012, Uncharacterized conserved protein [Function unknown] 259 matched cddid_all.tbl CDD KOG3013 KOG3013 230951 KOG3013 KOG3013, Exosomal 3'-5' exoribonuclease complex, subunit Rrp4 [RNA processing and modification] 301 matched cddid_all.tbl CDD KOG3014 KOG3014 230952 KOG3014 KOG3014, Protein involved in establishing cohesion between sister chromatids during DNA replication [Replication, recombination and repair] 257 matched cddid_all.tbl CDD KOG3015 KOG3015 230953 KOG3015 KOG3015, F1-ATP synthase assembly protein [Energy production and conversion] 283 matched cddid_all.tbl CDD KOG3016 KOG3016 230954 KOG3016 KOG3016, Acyl-CoA thioesterase [Lipid transport and metabolism] 294 matched cddid_all.tbl CDD KOG3017 KOG3017 230955 KOG3017 KOG3017, Defense-related protein containing SCP domain [Function unknown] 225 matched cddid_all.tbl CDD KOG3018 KOG3018 230956 KOG3018 KOG3018, Malonyl-CoA decarboxylase [Carbohydrate transport and metabolism] 362 matched cddid_all.tbl CDD KOG3019 KOG3019 230957 KOG3019 KOG3019, Predicted nucleoside-diphosphate sugar epimerase [Nucleotide transport and metabolism] 315 matched cddid_all.tbl CDD KOG3020 KOG3020 230958 KOG3020 KOG3020, TatD-related DNase [Replication, recombination and repair] 296 matched cddid_all.tbl CDD KOG3021 KOG3021 230959 KOG3021 KOG3021, Predicted kinase [General function prediction only] 313 matched cddid_all.tbl CDD KOG3022 KOG3022 230960 KOG3022 KOG3022, Predicted ATPase, nucleotide-binding [Cell cycle control, cell division, chromosome partitioning] 300 matched cddid_all.tbl CDD KOG3023 KOG3023 230961 KOG3023 KOG3023, Glutamate-cysteine ligase regulatory subunit [Amino acid transport and metabolism] 285 matched cddid_all.tbl CDD KOG3024 KOG3024 230962 KOG3024 KOG3024, Uncharacterized conserved protein [Function unknown] 312 matched cddid_all.tbl CDD KOG3025 KOG3025 230963 KOG3025 KOG3025, Mitochondrial F1F0-ATP synthase, subunit c/ATP9/proteolipid [Energy production and conversion] 137 matched cddid_all.tbl CDD KOG3026 KOG3026 230964 KOG3026 KOG3026, Splicing factor SPF30 [RNA processing and modification] 262 matched cddid_all.tbl CDD KOG3027 KOG3027 230965 KOG3027 KOG3027, Mitochondrial outer membrane protein Metaxin 2, Metaxin 1-binding protein [Cell wall/membrane/envelope biogenesis, Intracellular trafficking, secretion, and vesicular transport] 257 matched cddid_all.tbl CDD KOG3028 KOG3028 230966 KOG3028 KOG3028, Translocase of outer mitochondrial membrane complex, subunit TOM37/Metaxin 1 [Intracellular trafficking, secretion, and vesicular transport] 313 matched cddid_all.tbl CDD KOG3029 KOG3029 230967 KOG3029 KOG3029, Glutathione S-transferase-related protein [General function prediction only] 370 matched cddid_all.tbl CDD KOG3030 KOG3030 230968 KOG3030 KOG3030, Lipid phosphate phosphatase and related enzymes of the PAP2 family [Lipid transport and metabolism] 317 matched cddid_all.tbl CDD KOG3031 KOG3031 230969 KOG3031 KOG3031, Protein required for biogenesis of the ribosomal 60S subunit [Translation, ribosomal structure and biogenesis] 307 matched cddid_all.tbl CDD KOG3032 KOG3032 230970 KOG3032 KOG3032, Uncharacterized conserved protein [Function unknown] 264 matched cddid_all.tbl CDD KOG3033 KOG3033 230971 KOG3033 KOG3033, Predicted PhzC/PhzF-type epimerase [General function prediction only] 286 matched cddid_all.tbl CDD KOG3034 KOG3034 230972 KOG3034 KOG3034, Isoamyl acetate-hydrolyzing esterase and related enzymes [General function prediction only] 308 matched cddid_all.tbl CDD KOG3035 KOG3035 230973 KOG3035 KOG3035, Isoamyl acetate-hydrolyzing esterase [Lipid transport and metabolism] 245 matched cddid_all.tbl CDD KOG3036 KOG3036 230974 KOG3036 KOG3036, Protein involved in cell differentiation/sexual development [General function prediction only] 293 matched cddid_all.tbl CDD KOG3037 KOG3037 230975 KOG3037 KOG3037, Cell membrane glycoprotein [General function prediction only] 330 matched cddid_all.tbl CDD KOG3038 KOG3038 230976 KOG3038 KOG3038, Histone acetyltransferase SAGA associated factor SGF29 [General function prediction only] 264 matched cddid_all.tbl CDD KOG3039 KOG3039 230977 KOG3039 KOG3039, Uncharacterized conserved protein [Function unknown] 303 matched cddid_all.tbl CDD KOG3040 KOG3040 230978 KOG3040 KOG3040, Predicted sugar phosphatase (HAD superfamily) [General function prediction only] 262 matched cddid_all.tbl CDD KOG3041 KOG3041 230979 KOG3041 KOG3041, Nucleoside diphosphate-sugar hydrolase of the MutT (NUDIX) family [Replication, recombination and repair] 225 matched cddid_all.tbl CDD KOG3042 KOG3042 230980 KOG3042 KOG3042, Panthothenate synthetase [Coenzyme transport and metabolism] 283 matched cddid_all.tbl CDD KOG3043 KOG3043 230981 KOG3043 KOG3043, Predicted hydrolase related to dienelactone hydrolase [General function prediction only] 242 matched cddid_all.tbl CDD KOG3044 KOG3044 230982 KOG3044 KOG3044, Uncharacterized conserved protein [Function unknown] 307 matched cddid_all.tbl CDD KOG3045 KOG3045 230983 KOG3045 KOG3045, Predicted RNA methylase involved in rRNA processing [RNA processing and modification] 325 matched cddid_all.tbl CDD KOG3046 KOG3046 230984 KOG3046 KOG3046, Transcription factor, subunit of SRB subcomplex of RNA polymerase II [Transcription] 147 matched cddid_all.tbl CDD KOG3047 KOG3047 230985 KOG3047 KOG3047, Predicted transcriptional regulator UXT [Transcription] 157 matched cddid_all.tbl CDD KOG3048 KOG3048 230986 KOG3048 KOG3048, Molecular chaperone Prefoldin, subunit 5 [Posttranslational modification, protein turnover, chaperones] 153 matched cddid_all.tbl CDD KOG3049 KOG3049 230987 KOG3049 KOG3049, Succinate dehydrogenase, Fe-S protein subunit [Energy production and conversion] 288 matched cddid_all.tbl CDD KOG3050 KOG3050 230988 KOG3050 KOG3050, COP9 signalosome, subunit CSN6 [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms] 299 matched cddid_all.tbl CDD KOG3051 KOG3051 230989 KOG3051 KOG3051, RNA binding/translational regulation protein of the SUA5 family [Translation, ribosomal structure and biogenesis] 261 matched cddid_all.tbl CDD KOG3052 KOG3052 230990 KOG3052 KOG3052, Cytochrome c1 [Energy production and conversion] 311 matched cddid_all.tbl CDD KOG3053 KOG3053 230991 KOG3053 KOG3053, Uncharacterized conserved protein [Function unknown] 293 matched cddid_all.tbl CDD KOG3054 KOG3054 230992 KOG3054 KOG3054, Uncharacterized conserved protein [Function unknown] 299 matched cddid_all.tbl CDD KOG3055 KOG3055 230993 KOG3055 KOG3055, Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase [Amino acid transport and metabolism] 263 matched cddid_all.tbl CDD KOG3056 KOG3056 230994 KOG3056 KOG3056, Protein required for S-phase initiation or completion [Cell cycle control, cell division, chromosome partitioning] 578 matched cddid_all.tbl CDD KOG3057 KOG3057 230995 KOG3057 KOG3057, Cytochrome c oxidase, subunit VIb/COX12 [Energy production and conversion] 112 matched cddid_all.tbl CDD KOG3058 KOG3058 230996 KOG3058 KOG3058, Uncharacterized conserved protein [Function unknown] 351 matched cddid_all.tbl CDD KOG3059 KOG3059 230997 KOG3059 KOG3059, N-acetylglucosaminyltransferase complex, subunit PIG-C/GPI2, required for phosphatidylinositol biosynthesis [Lipid transport and metabolism] 292 matched cddid_all.tbl CDD KOG3060 KOG3060 230998 KOG3060 KOG3060, Uncharacterized conserved protein [Function unknown] 289 matched cddid_all.tbl CDD KOG3061 KOG3061 230999 KOG3061 KOG3061, Proteasome maturation factor [Posttranslational modification, protein turnover, chaperones] 137 matched cddid_all.tbl CDD KOG3062 KOG3062 231000 KOG3062 KOG3062, RNA polymerase II elongator associated protein [General function prediction only] 281 matched cddid_all.tbl CDD KOG3063 KOG3063 231001 KOG3063 KOG3063, Membrane coat complex Retromer, subunit VPS26 [Intracellular trafficking, secretion, and vesicular transport] 301 matched cddid_all.tbl CDD KOG3064 KOG3064 231002 KOG3064 KOG3064, RNA-binding nuclear protein (MAK16) containing a distinct C4 Zn-finger [RNA processing and modification] 303 matched cddid_all.tbl CDD KOG3065 KOG3065 231003 KOG3065 KOG3065, SNAP-25 (synaptosome-associated protein) component of SNARE complex [Intracellular trafficking, secretion, and vesicular transport] 273 matched cddid_all.tbl CDD KOG3066 KOG3066 231004 KOG3066 KOG3066, Translin-associated protein X [General function prediction only] 271 matched cddid_all.tbl CDD KOG3067 KOG3067 231005 KOG3067 KOG3067, Translin family protein [General function prediction only] 226 matched cddid_all.tbl CDD KOG3068 KOG3068 231006 KOG3068 KOG3068, mRNA splicing factor [RNA processing and modification] 268 matched cddid_all.tbl CDD KOG3069 KOG3069 231007 KOG3069 KOG3069, Peroxisomal NUDIX hydrolase [Replication, recombination and repair] 246 matched cddid_all.tbl CDD KOG3070 KOG3070 231008 KOG3070 KOG3070, Predicted RNA-binding protein containing PIN domain and invovled in translation or RNA processing [Translation, ribosomal structure and biogenesis] 235 matched cddid_all.tbl CDD KOG3071 KOG3071 231009 KOG3071 KOG3071, Fatty acyl-CoA elongase/Polyunsaturated fatty acid specific elongation enzyme [Lipid transport and metabolism] 274 matched cddid_all.tbl CDD KOG3072 KOG3072 231010 KOG3072 KOG3072, Long chain fatty acid elongase [Lipid transport and metabolism] 282 matched cddid_all.tbl CDD KOG3073 KOG3073 231011 KOG3073 KOG3073, Protein required for 18S rRNA maturation and 40S ribosome biogenesis [Translation, ribosomal structure and biogenesis] 236 matched cddid_all.tbl CDD KOG3074 KOG3074 231012 KOG3074 KOG3074, Transcriptional regulator of the PUR family, single-stranded-DNA-binding [Transcription] 263 matched cddid_all.tbl CDD KOG3075 KOG3075 231013 KOG3075 KOG3075, Ribose 5-phosphate isomerase [Carbohydrate transport and metabolism] 261 matched cddid_all.tbl CDD KOG3076 KOG3076 231014 KOG3076 KOG3076, 5'-phosphoribosylglycinamide formyltransferase [Carbohydrate transport and metabolism] 206 matched cddid_all.tbl CDD KOG3077 KOG3077 231015 KOG3077 KOG3077, Uncharacterized conserved protein [Function unknown] 260 matched cddid_all.tbl CDD KOG3078 KOG3078 231016 KOG3078 KOG3078, Adenylate kinase [Nucleotide transport and metabolism] 235 matched cddid_all.tbl CDD KOG3079 KOG3079 231017 KOG3079 KOG3079, Uridylate kinase/adenylate kinase [Nucleotide transport and metabolism] 195 matched cddid_all.tbl CDD KOG3080 KOG3080 231018 KOG3080 KOG3080, Nucleolar protein-like/EBNA1-binding protein [RNA processing and modification] 328 matched cddid_all.tbl CDD KOG3081 KOG3081 231019 KOG3081 KOG3081, Vesicle coat complex COPI, epsilon subunit [Intracellular trafficking, secretion, and vesicular transport] 299 matched cddid_all.tbl CDD KOG3082 KOG3082 231020 KOG3082 KOG3082, Methionyl-tRNA formyltransferase [Translation, ribosomal structure and biogenesis] 338 matched cddid_all.tbl CDD KOG3083 KOG3083 231021 KOG3083 KOG3083, Prohibitin [Posttranslational modification, protein turnover, chaperones] 271 matched cddid_all.tbl CDD KOG3084 KOG3084 231022 KOG3084 KOG3084, NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair] 345 matched cddid_all.tbl CDD KOG3085 KOG3085 231023 KOG3085 KOG3085, Predicted hydrolase (HAD superfamily) [General function prediction only] 237 matched cddid_all.tbl CDD KOG3086 KOG3086 231024 KOG3086 KOG3086, Predicted dioxygenase [General function prediction only] 296 matched cddid_all.tbl CDD KOG3087 KOG3087 231025 KOG3087 KOG3087, Serine/threonine protein kinase [General function prediction only] 229 matched cddid_all.tbl CDD KOG3088 KOG3088 231026 KOG3088 KOG3088, Secretory carrier membrane protein [Intracellular trafficking, secretion, and vesicular transport] 313 matched cddid_all.tbl CDD KOG3089 KOG3089 231027 KOG3089 KOG3089, Predicted DEAD-box-containing helicase [General function prediction only] 271 matched cddid_all.tbl CDD KOG3090 KOG3090 231028 KOG3090 KOG3090, Prohibitin-like protein [Posttranslational modification, protein turnover, chaperones] 290 matched cddid_all.tbl CDD KOG3091 KOG3091 231029 KOG3091 KOG3091, Nuclear pore complex, p54 component (sc Nup57) [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 508 matched cddid_all.tbl CDD KOG3092 KOG3092 231030 KOG3092 KOG3092, Casein kinase II, beta subunit [Signal transduction mechanisms, Cell cycle control, cell division, chromosome partitioning, Transcription] 216 matched cddid_all.tbl CDD KOG3093 KOG3093 231031 KOG3093 KOG3093, 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism] 200 matched cddid_all.tbl CDD KOG3094 KOG3094 231032 KOG3094 KOG3094, Predicted membrane protein [Function unknown] 284 matched cddid_all.tbl CDD KOG3095 KOG3095 231033 KOG3095 KOG3095, Transcription initiation factor IIE, beta subunit [Transcription] 284 matched cddid_all.tbl CDD KOG3096 KOG3096 231034 KOG3096 KOG3096, Spliceosome-associated coiled-coil protein [Function unknown] 225 matched cddid_all.tbl CDD KOG3097 KOG3097 231035 KOG3097 KOG3097, Predicted membrane protein [Function unknown] 390 matched cddid_all.tbl CDD KOG3098 KOG3098 231036 KOG3098 KOG3098, Uncharacterized conserved protein [Function unknown] 461 matched cddid_all.tbl CDD KOG3099 KOG3099 231037 KOG3099 KOG3099, Bisphosphate 3'-nucleotidase BPNT1/Inositol polyphosphate 1-phosphatase [Nucleotide transport and metabolism] 340 matched cddid_all.tbl CDD KOG3100 KOG3100 231038 KOG3100 KOG3100, Uncharacterized conserved protein [Function unknown] 206 matched cddid_all.tbl CDD KOG3101 KOG3101 231039 KOG3101 KOG3101, Esterase D [General function prediction only] 283 matched cddid_all.tbl CDD KOG3102 KOG3102 231040 KOG3102 KOG3102, Uncharacterized conserved protein [Function unknown] 269 matched cddid_all.tbl CDD KOG3103 KOG3103 231041 KOG3103 KOG3103, Rab GTPase interacting factor, Golgi membrane protein [Intracellular trafficking, secretion, and vesicular transport] 249 matched cddid_all.tbl CDD KOG3104 KOG3104 231042 KOG3104 KOG3104, Mod5 protein sorting/negative effector of RNA Pol III synthesis [Transcription] 264 matched cddid_all.tbl CDD KOG3105 KOG3105 231043 KOG3105 KOG3105, DNA-binding centromere protein B (CENP-B) [Chromatin structure and dynamics, Cell cycle control, cell division, chromosome partitioning] 488 matched cddid_all.tbl CDD KOG3106 KOG3106 231044 KOG3106 KOG3106, ER lumen protein retaining receptor [Intracellular trafficking, secretion, and vesicular transport] 212 matched cddid_all.tbl CDD KOG3107 KOG3107 231045 KOG3107 KOG3107, Predicted haloacid dehalogenase-like hydrolase (eyes absent) [General function prediction only] 468 matched cddid_all.tbl CDD KOG3108 KOG3108 231046 KOG3108 KOG3108, Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [Replication, recombination and repair] 265 matched cddid_all.tbl CDD KOG3109 KOG3109 231047 KOG3109 KOG3109, Haloacid dehalogenase-like hydrolase [General function prediction only] 244 matched cddid_all.tbl CDD KOG3110 KOG3110 231048 KOG3110 KOG3110, Riboflavin kinase [Coenzyme transport and metabolism] 153 matched cddid_all.tbl CDD KOG3111 KOG3111 231049 KOG3111 KOG3111, D-ribulose-5-phosphate 3-epimerase [Carbohydrate transport and metabolism] 224 matched cddid_all.tbl CDD KOG3112 KOG3112 231050 KOG3112 KOG3112, Uncharacterized conserved protein [Function unknown] 262 matched cddid_all.tbl CDD KOG3113 KOG3113 231051 KOG3113 KOG3113, Uncharacterized conserved protein [Function unknown] 293 matched cddid_all.tbl CDD KOG3114 KOG3114 231052 KOG3114 KOG3114, Uncharacterized conserved protein [Function unknown] 290 matched cddid_all.tbl CDD KOG3115 KOG3115 231053 KOG3115 KOG3115, Methyltransferase-like protein [General function prediction only] 249 matched cddid_all.tbl CDD KOG3116 KOG3116 231054 KOG3116 KOG3116, Predicted C3H1-type Zn-finger protein [General function prediction only] 177 matched cddid_all.tbl CDD KOG3117 KOG3117 231055 KOG3117 KOG3117, Protein involved in rRNA processing [RNA processing and modification] 340 matched cddid_all.tbl CDD KOG3118 KOG3118 231056 KOG3118 KOG3118, Disrupter of silencing SAS10 [Chromatin structure and dynamics] 517 matched cddid_all.tbl CDD KOG3119 KOG3119 231057 KOG3119 KOG3119, Basic region leucine zipper transcription factor [Transcription] 269 matched cddid_all.tbl CDD KOG3120 KOG3120 231058 KOG3120 KOG3120, Predicted haloacid dehalogenase-like hydrolase [General function prediction only] 256 matched cddid_all.tbl CDD KOG3121 KOG3121 231059 KOG3121 KOG3121, Dynactin, subunit p25 [Cytoskeleton] 184 matched cddid_all.tbl CDD KOG3122 KOG3122 231060 KOG3122 KOG3122, DNA-directed RNA polymerase III subunit [Transcription] 310 matched cddid_all.tbl CDD KOG3123 KOG3123 231061 KOG3123 KOG3123, Diphthine synthase [Translation, ribosomal structure and biogenesis] 272 matched cddid_all.tbl CDD KOG3124 KOG3124 231062 KOG3124 KOG3124, Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism] 267 matched cddid_all.tbl CDD KOG3125 KOG3125 231063 KOG3125 KOG3125, Thymidine kinase [Nucleotide transport and metabolism] 234 matched cddid_all.tbl CDD KOG3126 KOG3126 231064 KOG3126 KOG3126, Porin/voltage-dependent anion-selective channel protein [Inorganic ion transport and metabolism] 281 matched cddid_all.tbl CDD KOG3127 KOG3127 231065 KOG3127 KOG3127, Deoxycytidylate deaminase [Nucleotide transport and metabolism] 230 matched cddid_all.tbl CDD KOG3128 KOG3128 231066 KOG3128 KOG3128, Uncharacterized conserved protein [Function unknown] 298 matched cddid_all.tbl CDD KOG3129 KOG3129 231067 KOG3129 KOG3129, 26S proteasome regulatory complex, subunit PSMD9 [Posttranslational modification, protein turnover, chaperones] 231 matched cddid_all.tbl CDD KOG3130 KOG3130 231068 KOG3130 KOG3130, Uncharacterized conserved protein [Function unknown] 514 matched cddid_all.tbl CDD KOG3131 KOG3131 231069 KOG3131 KOG3131, Uncharacterized conserved protein [Function unknown] 281 matched cddid_all.tbl CDD KOG3132 KOG3132 231070 KOG3132 KOG3132, m3G-cap-specific nuclear import receptor (Snurportin1) [RNA processing and modification] 325 matched cddid_all.tbl CDD KOG3133 KOG3133 231071 KOG3133 KOG3133, 40 kDa farnesylated protein associated with peroxisomes [Intracellular trafficking, secretion, and vesicular transport] 267 matched cddid_all.tbl CDD KOG3134 KOG3134 231072 KOG3134 KOG3134, Predicted membrane protein [Function unknown] 225 matched cddid_all.tbl CDD KOG3135 KOG3135 231073 KOG3135 KOG3135, 1,4-benzoquinone reductase-like; Trp repressor binding protein-like/protoplast-secreted protein [General function prediction only] 203 matched cddid_all.tbl CDD KOG3136 KOG3136 231074 KOG3136 KOG3136, Uncharacterized conserved protein [Function unknown] 196 matched cddid_all.tbl CDD KOG3137 KOG3137 231075 KOG3137 KOG3137, Peptide deformylase [Translation, ribosomal structure and biogenesis] 267 matched cddid_all.tbl CDD KOG3138 KOG3138 231076 KOG3138 KOG3138, Predicted N-acetyltransferase [General function prediction only] 187 matched cddid_all.tbl CDD KOG3139 KOG3139 231077 KOG3139 KOG3139, N-acetyltransferase [General function prediction only] 165 matched cddid_all.tbl CDD KOG3140 KOG3140 231078 KOG3140 KOG3140, Predicted membrane protein [Function unknown] 275 matched cddid_all.tbl CDD KOG3141 KOG3141 231079 KOG3141 KOG3141, Mitochondrial/chloroplast ribosomal protein L3 [Translation, ribosomal structure and biogenesis] 310 matched cddid_all.tbl CDD KOG3142 KOG3142 231080 KOG3142 KOG3142, Prenylated rab acceptor 1 [Intracellular trafficking, secretion, and vesicular transport] 187 matched cddid_all.tbl CDD KOG3143 KOG3143 231081 KOG3143 KOG3143, Imidazoleglycerol-phosphate dehydratase [Amino acid transport and metabolism] 219 matched cddid_all.tbl CDD KOG3144 KOG3144 231082 KOG3144 KOG3144, Ethanolamine-P-transferase GPI11/PIG-F, involved in glycosylphosphatidylinositol anchor biosynthesis [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones] 196 matched cddid_all.tbl CDD KOG3145 KOG3145 231083 KOG3145 KOG3145, Cystine transporter Cystinosin [Amino acid transport and metabolism] 372 matched cddid_all.tbl CDD KOG3146 KOG3146 231084 KOG3146 KOG3146, Dolichyl pyrophosphate phosphatase and related acid phosphatases [Lipid transport and metabolism] 228 matched cddid_all.tbl CDD KOG3147 KOG3147 231085 KOG3147 KOG3147, 6-phosphogluconolactonase - like protein [Carbohydrate transport and metabolism] 252 matched cddid_all.tbl CDD KOG3148 KOG3148 231086 KOG3148 KOG3148, Glucosamine-6-phosphate isomerase [Carbohydrate transport and metabolism] 273 matched cddid_all.tbl CDD KOG3149 KOG3149 231087 KOG3149 KOG3149, Transcription initiation factor IIF, auxiliary subunit [Transcription] 249 matched cddid_all.tbl CDD KOG3150 KOG3150 231088 KOG3150 KOG3150, Uncharacterized conserved protein [Function unknown] 182 matched cddid_all.tbl CDD KOG3151 KOG3151 231089 KOG3151 KOG3151, 26S proteasome regulatory complex, subunit RPN12/PSMD8 [Posttranslational modification, protein turnover, chaperones] 260 matched cddid_all.tbl CDD KOG3152 KOG3152 231090 KOG3152 KOG3152, TBP-binding protein, activator of basal transcription (contains rrm motif) [Transcription] 278 matched cddid_all.tbl CDD KOG3153 KOG3153 231091 KOG3153 KOG3153, Thiamine pyrophosphokinase [Coenzyme transport and metabolism] 250 matched cddid_all.tbl CDD KOG3154 KOG3154 231092 KOG3154 KOG3154, Uncharacterized conserved protein [Function unknown] 263 matched cddid_all.tbl CDD KOG3155 KOG3155 231093 KOG3155 KOG3155, Actin-related protein Arp2/3 complex, subunit ARPC3 [Cytoskeleton] 173 matched cddid_all.tbl CDD KOG3156 KOG3156 231094 KOG3156 KOG3156, Uncharacterized membrane protein [Function unknown] 220 matched cddid_all.tbl CDD KOG3157 KOG3157 231095 KOG3157 KOG3157, Proline synthetase co-transcribed protein [General function prediction only] 244 matched cddid_all.tbl CDD KOG3158 KOG3158 231096 KOG3158 KOG3158, HSP90 co-chaperone p23 [Posttranslational modification, protein turnover, chaperones] 180 matched cddid_all.tbl CDD KOG3159 KOG3159 231097 KOG3159 KOG3159, Lipoate-protein ligase A [Coenzyme transport and metabolism] 336 matched cddid_all.tbl CDD KOG3160 KOG3160 231098 KOG3160 KOG3160, Gamma-interferon inducible lysosomal thiol reductase [Posttranslational modification, protein turnover, chaperones] 220 matched cddid_all.tbl CDD KOG3161 KOG3161 231099 KOG3161 KOG3161, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 861 matched cddid_all.tbl CDD KOG3162 KOG3162 231100 KOG3162 KOG3162, Mitochondrial/chloroplast ribosomal protein S18 [Translation, ribosomal structure and biogenesis] 159 matched cddid_all.tbl CDD KOG3163 KOG3163 231101 KOG3163 KOG3163, Uncharacterized conserved protein related to ribosomal protein S8E [General function prediction only] 260 matched cddid_all.tbl CDD KOG3164 KOG3164 231102 KOG3164 KOG3164, Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only] 236 matched cddid_all.tbl CDD KOG3165 KOG3165 231103 KOG3165 KOG3165, Predicted nucleic-acid-binding protein, contains PIN domain [General function prediction only] 195 matched cddid_all.tbl CDD KOG3166 KOG3166 231104 KOG3166 KOG3166, 60S ribosomal protein L7A [Translation, ribosomal structure and biogenesis] 209 matched cddid_all.tbl CDD KOG3167 KOG3167 231105 KOG3167 KOG3167, Box H/ACA snoRNP component, involved in ribosomal RNA pseudouridinylation [RNA processing and modification] 153 matched cddid_all.tbl CDD KOG3168 KOG3168 231106 KOG3168 KOG3168, U1 snRNP component [Transcription] 177 matched cddid_all.tbl CDD KOG3169 KOG3169 231107 KOG3169 KOG3169, RNA polymerase II transcriptional regulation mediator [Transcription] 208 matched cddid_all.tbl CDD KOG3170 KOG3170 231108 KOG3170 KOG3170, Conserved phosducin-like protein [Signal transduction mechanisms] 240 matched cddid_all.tbl CDD KOG3171 KOG3171 231109 KOG3171 KOG3171, Conserved phosducin-like protein [Signal transduction mechanisms] 273 matched cddid_all.tbl CDD KOG3172 KOG3172 231110 KOG3172 KOG3172, Small nuclear ribonucleoprotein Sm D3 [RNA processing and modification] 119 matched cddid_all.tbl CDD KOG3173 KOG3173 231111 KOG3173 KOG3173, Predicted Zn-finger protein [General function prediction only] 167 matched cddid_all.tbl CDD KOG3174 KOG3174 231112 KOG3174 KOG3174, F-actin capping protein, beta subunit [Cytoskeleton] 275 matched cddid_all.tbl CDD KOG3175 KOG3175 231113 KOG3175 KOG3175, Protein phosphatase 4 regulatory subunit 2 related protein [General function prediction only] 366 matched cddid_all.tbl CDD KOG3176 KOG3176 231114 KOG3176 KOG3176, Predicted alpha-helical protein, potentially involved in replication/repair [Replication, recombination and repair] 223 matched cddid_all.tbl CDD KOG3177 KOG3177 231115 KOG3177 KOG3177, Oligoketide cyclase/lipid transport protein [Lipid transport and metabolism] 227 matched cddid_all.tbl CDD KOG3178 KOG3178 231116 KOG3178 KOG3178, Hydroxyindole-O-methyltransferase and related SAM-dependent methyltransferases [General function prediction only] 342 matched cddid_all.tbl CDD KOG3179 KOG3179 231117 KOG3179 KOG3179, Predicted glutamine synthetase [Nucleotide transport and metabolism] 245 matched cddid_all.tbl CDD KOG3180 KOG3180 231118 KOG3180 KOG3180, Electron transfer flavoprotein, beta subunit [Energy production and conversion] 254 matched cddid_all.tbl CDD KOG3181 KOG3181 231119 KOG3181 KOG3181, 40S ribosomal protein S3 [Translation, ribosomal structure and biogenesis] 244 matched cddid_all.tbl CDD KOG3182 KOG3182 231120 KOG3182 KOG3182, Predicted cation transporter [Inorganic ion transport and metabolism] 212 matched cddid_all.tbl CDD KOG3183 KOG3183 231121 KOG3183 KOG3183, Predicted Zn-finger protein [General function prediction only] 250 matched cddid_all.tbl CDD KOG3184 KOG3184 231122 KOG3184 KOG3184, 60S ribosomal protein L7 [Translation, ribosomal structure and biogenesis] 235 matched cddid_all.tbl CDD KOG3185 KOG3185 231123 KOG3185 KOG3185, Translation initiation factor 6 (eIF-6) [Translation, ribosomal structure and biogenesis] 245 matched cddid_all.tbl CDD KOG3186 KOG3186 231124 KOG3186 KOG3186, Mitotic spindle checkpoint protein [Cell cycle control, cell division, chromosome partitioning] 202 matched cddid_all.tbl CDD KOG3187 KOG3187 231125 KOG3187 KOG3187, Protein tyrosine phosphatase-like protein PTPLA (contains Pro instead of catalytic Arg) [General function prediction only] 223 matched cddid_all.tbl CDD KOG3188 KOG3188 231126 KOG3188 KOG3188, Uncharacterized conserved protein [Function unknown] 246 matched cddid_all.tbl CDD KOG3189 KOG3189 231127 KOG3189 KOG3189, Phosphomannomutase [Lipid transport and metabolism] 252 matched cddid_all.tbl CDD KOG3190 KOG3190 231128 KOG3190 KOG3190, Uncharacterized conserved protein [Function unknown] 256 matched cddid_all.tbl CDD KOG3191 KOG3191 231129 KOG3191 KOG3191, Predicted N6-DNA-methyltransferase [Translation, ribosomal structure and biogenesis] 209 matched cddid_all.tbl CDD KOG3192 KOG3192 231130 KOG3192 KOG3192, Mitochondrial J-type chaperone [Posttranslational modification, protein turnover, chaperones] 168 matched cddid_all.tbl CDD KOG3193 KOG3193 231131 KOG3193 KOG3193, K+ channel subunit [Inorganic ion transport and metabolism] 1087 matched cddid_all.tbl CDD KOG3194 KOG3194 231132 KOG3194 KOG3194, Checkpoint 9-1-1 complex, RAD1 component [Energy production and conversion, Replication, recombination and repair] 279 matched cddid_all.tbl CDD KOG3195 KOG3195 231133 KOG3195 KOG3195, Uncharacterized membrane protein NPD008/CGI-148 [General function prediction only] 213 matched cddid_all.tbl CDD KOG3196 KOG3196 231134 KOG3196 KOG3196, NADH:ubiquinone oxidoreductase, NDUFV2/24 kD subunit [Energy production and conversion] 233 matched cddid_all.tbl CDD KOG3197 KOG3197 231135 KOG3197 KOG3197, Predicted hydrolases of HD superfamily [General function prediction only] 210 matched cddid_all.tbl CDD KOG3198 KOG3198 231136 KOG3198 KOG3198, Signal recognition particle, subunit Srp19 [Intracellular trafficking, secretion, and vesicular transport] 152 matched cddid_all.tbl CDD KOG3199 KOG3199 231137 KOG3199 KOG3199, Nicotinamide mononucleotide adenylyl transferase [Coenzyme transport and metabolism] 234 matched cddid_all.tbl CDD KOG3200 KOG3200 231138 KOG3200 KOG3200, Uncharacterized conserved protein [Function unknown] 224 matched cddid_all.tbl CDD KOG3201 KOG3201 231139 KOG3201 KOG3201, Uncharacterized conserved protein [Function unknown] 201 matched cddid_all.tbl CDD KOG3202 KOG3202 231140 KOG3202 KOG3202, SNARE protein TLG1/Syntaxin 6 [Intracellular trafficking, secretion, and vesicular transport] 235 matched cddid_all.tbl CDD KOG3203 KOG3203 231141 KOG3203 KOG3203, Mitochondrial/chloroplast ribosomal protein L13 [Translation, ribosomal structure and biogenesis] 165 matched cddid_all.tbl CDD KOG3204 KOG3204 231142 KOG3204 KOG3204, 60S ribosomal protein L13a [Translation, ribosomal structure and biogenesis] 197 matched cddid_all.tbl CDD KOG3205 KOG3205 231143 KOG3205 KOG3205, Rho GDP-dissociation inhibitor [Signal transduction mechanisms] 200 matched cddid_all.tbl CDD KOG3206 KOG3206 231144 KOG3206 KOG3206, Alpha-tubulin folding cofactor B [Posttranslational modification, protein turnover, chaperones] 234 matched cddid_all.tbl CDD KOG3207 KOG3207 231145 KOG3207 KOG3207, Beta-tubulin folding cofactor E [Posttranslational modification, protein turnover, chaperones] 505 matched cddid_all.tbl CDD KOG3208 KOG3208 231146 KOG3208 KOG3208, SNARE protein GS28 [Intracellular trafficking, secretion, and vesicular transport] 231 matched cddid_all.tbl CDD KOG3209 KOG3209 231147 KOG3209 KOG3209, WW domain-containing protein [General function prediction only] 984 matched cddid_all.tbl CDD KOG3210 KOG3210 231148 KOG3210 KOG3210, Imidazoleglycerol-phosphate synthase subunit H-like [Coenzyme transport and metabolism] 226 matched cddid_all.tbl CDD KOG3211 KOG3211 231149 KOG3211 KOG3211, Predicted endoplasmic reticulum membrane protein Lec35/MPDU1 involved in monosaccharide-P-dolichol utilization [General function prediction only] 230 matched cddid_all.tbl CDD KOG3212 KOG3212 231150 KOG3212 KOG3212, Uncharacterized conserved protein related to IojAP [Function unknown] 208 matched cddid_all.tbl CDD KOG3213 KOG3213 231151 KOG3213 KOG3213, Transcription factor IIB [Transcription] 238 matched cddid_all.tbl CDD KOG3214 KOG3214 231152 KOG3214 KOG3214, Uncharacterized Zn ribbon-containing protein [Function unknown] 109 matched cddid_all.tbl CDD KOG3215 KOG3215 231153 KOG3215 KOG3215, Uncharacterized conserved protein [Function unknown] 222 matched cddid_all.tbl CDD KOG3216 KOG3216 231154 KOG3216 KOG3216, Diamine acetyltransferase [Amino acid transport and metabolism] 163 matched cddid_all.tbl CDD KOG3217 KOG3217 231155 KOG3217 KOG3217, Protein tyrosine phosphatase [Signal transduction mechanisms] 159 matched cddid_all.tbl CDD KOG3218 KOG3218 231156 KOG3218 KOG3218, RNA polymerase, 25-kDa subunit (common to polymerases I, II and III) [Transcription] 208 matched cddid_all.tbl CDD KOG3219 KOG3219 231157 KOG3219 KOG3219, Transcription initiation factor TFIID, subunit TAF11 [Transcription] 195 matched cddid_all.tbl CDD KOG3220 KOG3220 231158 KOG3220 KOG3220, Similar to bacterial dephospho-CoA kinase [Coenzyme transport and metabolism] 225 matched cddid_all.tbl CDD KOG3221 KOG3221 231159 KOG3221 KOG3221, Glycolipid transfer protein [Carbohydrate transport and metabolism] 199 matched cddid_all.tbl CDD KOG3222 KOG3222 231160 KOG3222 KOG3222, Inosine triphosphate pyrophosphatase [Nucleotide transport and metabolism] 195 matched cddid_all.tbl CDD KOG3223 KOG3223 231161 KOG3223 KOG3223, Uncharacterized conserved protein [Function unknown] 221 matched cddid_all.tbl CDD KOG3224 KOG3224 231162 KOG3224 KOG3224, Uncharacterized conserved protein [Function unknown] 278 matched cddid_all.tbl CDD KOG3225 KOG3225 231163 KOG3225 KOG3225, Mitochondrial import inner membrane translocase, subunit TIM22 [Intracellular trafficking, secretion, and vesicular transport] 168 matched cddid_all.tbl CDD KOG3226 KOG3226 231164 KOG3226 KOG3226, DNA repair protein [Replication, recombination and repair] 508 matched cddid_all.tbl CDD KOG3227 KOG3227 231165 KOG3227 KOG3227, Calcium-responsive transcription coactivator [Transcription] 231 matched cddid_all.tbl CDD KOG3228 KOG3228 231166 KOG3228 KOG3228, Uncharacterized conserved protein [Function unknown] 226 matched cddid_all.tbl CDD KOG3229 KOG3229 231167 KOG3229 KOG3229, Vacuolar sorting protein VPS24 [Intracellular trafficking, secretion, and vesicular transport] 227 matched cddid_all.tbl CDD KOG3230 KOG3230 231168 KOG3230 KOG3230, Vacuolar assembly/sorting protein DID4 [Intracellular trafficking, secretion, and vesicular transport] 224 matched cddid_all.tbl CDD KOG3231 KOG3231 231169 KOG3231 KOG3231, Predicted assembly/vacuolar sorting protein [Intracellular trafficking, secretion, and vesicular transport] 208 matched cddid_all.tbl CDD KOG3232 KOG3232 231170 KOG3232 KOG3232, Vacuolar assembly/sorting protein DID2 [Intracellular trafficking, secretion, and vesicular transport] 203 matched cddid_all.tbl CDD KOG3233 KOG3233 231171 KOG3233 KOG3233, RNA polymerase III, subunit C34 [Transcription] 297 matched cddid_all.tbl CDD KOG3234 KOG3234 231172 KOG3234 KOG3234, Acetyltransferase, (GNAT) family [General function prediction only] 173 matched cddid_all.tbl CDD KOG3235 KOG3235 231173 KOG3235 KOG3235, Subunit of the major N alpha-acetyltransferase [General function prediction only] 193 matched cddid_all.tbl CDD KOG3236 KOG3236 231174 KOG3236 KOG3236, Predicted membrane protein [Function unknown] 225 matched cddid_all.tbl CDD KOG3237 KOG3237 231175 KOG3237 KOG3237, Uncharacterized conserved protein [Function unknown] 250 matched cddid_all.tbl CDD KOG3238 KOG3238 231176 KOG3238 KOG3238, Chloride ion current inducer protein [Inorganic ion transport and metabolism] 216 matched cddid_all.tbl CDD KOG3239 KOG3239 231177 KOG3239 KOG3239, Density-regulated protein related to translation initiation factor 1 (eIF-1/SUI1) [General function prediction only] 193 matched cddid_all.tbl CDD KOG3240 KOG3240 231178 KOG3240 KOG3240, Phosphatidylinositol synthase [Lipid transport and metabolism] 218 matched cddid_all.tbl CDD KOG3241 KOG3241 231179 KOG3241 KOG3241, Uncharacterized conserved protein [Function unknown] 227 matched cddid_all.tbl CDD KOG3242 KOG3242 231180 KOG3242 KOG3242, Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification] 208 matched cddid_all.tbl CDD KOG3243 KOG3243 231181 KOG3243 KOG3243, 6,7-dimethyl-8-ribityllumazine synthase [Coenzyme transport and metabolism] 158 matched cddid_all.tbl CDD KOG3244 KOG3244 231182 KOG3244 KOG3244, Protein involved in ubiquinone biosynthesis [Coenzyme transport and metabolism] 267 matched cddid_all.tbl CDD KOG3245 KOG3245 231183 KOG3245 KOG3245, Uncharacterized conserved protein [Function unknown] 106 matched cddid_all.tbl CDD KOG3246 KOG3246 231184 KOG3246 KOG3246, Sentrin-specific cysteine protease (Ulp1 family) [General function prediction only] 223 matched cddid_all.tbl CDD KOG3247 KOG3247 231185 KOG3247 KOG3247, Uncharacterized conserved protein [Function unknown] 466 matched cddid_all.tbl CDD KOG3248 KOG3248 231186 KOG3248 KOG3248, Transcription factor TCF-4 [Transcription] 421 matched cddid_all.tbl CDD KOG3249 KOG3249 231187 KOG3249 KOG3249, Uncharacterized conserved protein [Function unknown] 181 matched cddid_all.tbl CDD KOG3250 KOG3250 231188 KOG3250 KOG3250, COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms] 258 matched cddid_all.tbl CDD KOG3251 KOG3251 231189 KOG3251 KOG3251, Golgi SNAP receptor complex member [Intracellular trafficking, secretion, and vesicular transport] 213 matched cddid_all.tbl CDD KOG3252 KOG3252 231190 KOG3252 KOG3252, Uncharacterized conserved protein [Function unknown] 217 matched cddid_all.tbl CDD KOG3253 KOG3253 231191 KOG3253 KOG3253, Predicted alpha/beta hydrolase [General function prediction only] 784 matched cddid_all.tbl CDD KOG3254 KOG3254 231192 KOG3254 KOG3254, Mitochondrial/chloroplast ribosomal protein L6 [Translation, ribosomal structure and biogenesis] 211 matched cddid_all.tbl CDD KOG3255 KOG3255 231193 KOG3255 KOG3255, 60S ribosomal protein L9 [Translation, ribosomal structure and biogenesis] 179 matched cddid_all.tbl CDD KOG3256 KOG3256 231194 KOG3256 KOG3256, NADH:ubiquinone oxidoreductase, NDUFS8/23 kDa subunit [Energy production and conversion] 212 matched cddid_all.tbl CDD KOG3257 KOG3257 231195 KOG3257 KOG3257, Mitochondrial/chloroplast ribosomal protein L11 [Translation, ribosomal structure and biogenesis] 168 matched cddid_all.tbl CDD KOG3258 KOG3258 231196 KOG3258 KOG3258, Parvulin-like peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones] 133 matched cddid_all.tbl CDD KOG3259 KOG3259 231197 KOG3259 KOG3259, Peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones] 163 matched cddid_all.tbl CDD KOG3260 KOG3260 231198 KOG3260 KOG3260, Calcyclin-binding protein CacyBP [Signal transduction mechanisms] 224 matched cddid_all.tbl CDD KOG3261 KOG3261 231199 KOG3261 KOG3261, Uncharacterized conserved protein [Function unknown] 202 matched cddid_all.tbl CDD KOG3262 KOG3262 231200 KOG3262 KOG3262, H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis] 215 matched cddid_all.tbl CDD KOG3263 KOG3263 231201 KOG3263 KOG3263, Nucleic acid binding protein [General function prediction only] 196 matched cddid_all.tbl CDD KOG3264 KOG3264 231202 KOG3264 KOG3264, Uncharacterized conserved protein [Function unknown] 221 matched cddid_all.tbl CDD KOG3265 KOG3265 231203 KOG3265 KOG3265, Histone chaperone involved in gene silencing [Transcription, Chromatin structure and dynamics] 250 matched cddid_all.tbl CDD KOG3266 KOG3266 231204 KOG3266 KOG3266, Predicted glycine cleavage system H protein [Amino acid transport and metabolism] 172 matched cddid_all.tbl CDD KOG3267 KOG3267 231205 KOG3267 KOG3267, Uncharacterized conserved protein [Function unknown] 138 matched cddid_all.tbl CDD KOG3268 KOG3268 231206 KOG3268 KOG3268, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 234 matched cddid_all.tbl CDD KOG3269 KOG3269 231207 KOG3269 KOG3269, Predicted membrane protein [Function unknown] 180 matched cddid_all.tbl CDD KOG3270 KOG3270 231208 KOG3270 KOG3270, Uncharacterized conserved protein [Function unknown] 244 matched cddid_all.tbl CDD KOG3271 KOG3271 231209 KOG3271 KOG3271, Translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis] 156 matched cddid_all.tbl CDD KOG3272 KOG3272 231210 KOG3272 KOG3272, Predicted coiled-coil protein [General function prediction only] 207 matched cddid_all.tbl CDD KOG3273 KOG3273 231211 KOG3273 KOG3273, Predicted RNA-binding protein Pno1p interacting with Nob1p and involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones] 252 matched cddid_all.tbl CDD KOG3274 KOG3274 231212 KOG3274 KOG3274, Uncharacterized conserved protein, AMMECR1 [Function unknown] 210 matched cddid_all.tbl CDD KOG3275 KOG3275 231213 KOG3275 KOG3275, Zinc-binding protein of the histidine triad (HIT) family [Signal transduction mechanisms] 127 matched cddid_all.tbl CDD KOG3276 KOG3276 231214 KOG3276 KOG3276, Uncharacterized conserved protein, contains YggU domain [Function unknown] 125 matched cddid_all.tbl CDD KOG3277 KOG3277 231215 KOG3277 KOG3277, Uncharacterized conserved protein [Function unknown] 165 matched cddid_all.tbl CDD KOG3278 KOG3278 231216 KOG3278 KOG3278, Mitochondrial/chloroplast ribosomal protein L28 [Translation, ribosomal structure and biogenesis] 215 matched cddid_all.tbl CDD KOG3279 KOG3279 231217 KOG3279 KOG3279, Uncharacterized conserved protein (melanoma antigen P15) [Function unknown] 283 matched cddid_all.tbl CDD KOG3280 KOG3280 231218 KOG3280 KOG3280, Mitochondrial/chloroplast ribosomal protein L17 [Translation, ribosomal structure and biogenesis] 171 matched cddid_all.tbl CDD KOG3281 KOG3281 231219 KOG3281 KOG3281, Mitochondrial F1-ATPase assembly protein [Posttranslational modification, protein turnover, chaperones] 273 matched cddid_all.tbl CDD KOG3282 KOG3282 231220 KOG3282 KOG3282, Uncharacterized conserved protein [Function unknown] 190 matched cddid_all.tbl CDD KOG3283 KOG3283 231221 KOG3283 KOG3283, 40S ribosomal protein S8 [Translation, ribosomal structure and biogenesis] 200 matched cddid_all.tbl CDD KOG3284 KOG3284 231222 KOG3284 KOG3284, Vacuolar sorting protein VPS28 [Intracellular trafficking, secretion, and vesicular transport] 213 matched cddid_all.tbl CDD KOG3285 KOG3285 231223 KOG3285 KOG3285, Spindle assembly checkpoint protein [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton] 203 matched cddid_all.tbl CDD KOG3286 KOG3286 231224 KOG3286 KOG3286, Selenoprotein T [General function prediction only] 226 matched cddid_all.tbl CDD KOG3287 KOG3287 231225 KOG3287 KOG3287, Membrane trafficking protein, emp24/gp25L/p24 family [Intracellular trafficking, secretion, and vesicular transport] 236 matched cddid_all.tbl CDD KOG3288 KOG3288 231226 KOG3288 KOG3288, OTU-like cysteine protease [Signal transduction mechanisms, Posttranslational modification, protein turnover, chaperones] 307 matched cddid_all.tbl CDD KOG3289 KOG3289 231227 KOG3289 KOG3289, Uncharacterized conserved protein encoded by sequence overlapping the COX4 gene [General function prediction only] 199 matched cddid_all.tbl CDD KOG3290 KOG3290 231228 KOG3290 KOG3290, Peroxisomal phytanoyl-CoA hydroxylase [Lipid transport and metabolism] 286 matched cddid_all.tbl CDD KOG3291 KOG3291 231229 KOG3291 KOG3291, Ribosomal protein S7 [Translation, ribosomal structure and biogenesis] 208 matched cddid_all.tbl CDD KOG3292 KOG3292 231230 KOG3292 KOG3292, Predicted membrane protein [Function unknown] 196 matched cddid_all.tbl CDD KOG3293 KOG3293 231231 KOG3293 KOG3293, Small nuclear ribonucleoprotein (snRNP) [RNA processing and modification] 134 matched cddid_all.tbl CDD KOG3294 KOG3294 231232 KOG3294 KOG3294, WW domain binding protein WBP-2, contains GRAM domain [Signal transduction mechanisms] 261 matched cddid_all.tbl CDD KOG3295 KOG3295 231233 KOG3295 KOG3295, 60S Ribosomal protein L13 [Translation, ribosomal structure and biogenesis] 205 matched cddid_all.tbl CDD KOG3296 KOG3296 231234 KOG3296 KOG3296, Translocase of outer mitochondrial membrane complex, subunit TOM40 [Intracellular trafficking, secretion, and vesicular transport] 308 matched cddid_all.tbl CDD KOG3297 KOG3297 231235 KOG3297 KOG3297, DNA-directed RNA polymerase subunit E' [Transcription] 202 matched cddid_all.tbl CDD KOG3298 KOG3298 231236 KOG3298 KOG3298, DNA-directed RNA polymerase subunit E' [Transcription] 170 matched cddid_all.tbl CDD KOG3299 KOG3299 231237 KOG3299 KOG3299, Uncharacterized conserved protein [Function unknown] 206 matched cddid_all.tbl CDD KOG3300 KOG3300 231238 KOG3300 KOG3300, NADH:ubiquinone oxidoreductase, B16.6 subunit/cell death-regulatory protein [Energy production and conversion, Cell cycle control, cell division, chromosome partitioning] 146 matched cddid_all.tbl CDD KOG3301 KOG3301 231239 KOG3301 KOG3301, Ribosomal protein S4 [Translation, ribosomal structure and biogenesis] 183 matched cddid_all.tbl CDD KOG3302 KOG3302 231240 KOG3302 KOG3302, TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription] 200 matched cddid_all.tbl CDD KOG3303 KOG3303 231241 KOG3303 KOG3303, Predicted alpha-helical protein, potentially involved in replication/repair [Replication, recombination and repair] 192 matched cddid_all.tbl CDD KOG3304 KOG3304 231242 KOG3304 KOG3304, Surfeit family protein 5 [General function prediction only] 148 matched cddid_all.tbl CDD KOG3305 KOG3305 231243 KOG3305 KOG3305, Uncharacterized conserved protein [Function unknown] 121 matched cddid_all.tbl CDD KOG3306 KOG3306 231244 KOG3306 KOG3306, Predicted membrane protein [Function unknown] 185 matched cddid_all.tbl CDD KOG3307 KOG3307 231245 KOG3307 KOG3307, Molybdopterin converting factor subunit 2 [Coenzyme transport and metabolism] 150 matched cddid_all.tbl CDD KOG3308 KOG3308 231246 KOG3308 KOG3308, Uncharacterized protein of the uridine kinase family [Nucleotide transport and metabolism] 225 matched cddid_all.tbl CDD KOG3309 KOG3309 231247 KOG3309 KOG3309, Ferredoxin [Energy production and conversion] 159 matched cddid_all.tbl CDD KOG3310 KOG3310 231248 KOG3310 KOG3310, Riboflavin synthase alpha chain [Coenzyme transport and metabolism] 210 matched cddid_all.tbl CDD KOG3311 KOG3311 231249 KOG3311 KOG3311, Ribosomal protein S18 [Translation, ribosomal structure and biogenesis] 152 matched cddid_all.tbl CDD KOG3312 KOG3312 231250 KOG3312 KOG3312, Predicted membrane protein [Function unknown] 186 matched cddid_all.tbl CDD KOG3313 KOG3313 231251 KOG3313 KOG3313, Molecular chaperone Prefoldin, subunit 3 [Posttranslational modification, protein turnover, chaperones] 187 matched cddid_all.tbl CDD KOG3314 KOG3314 231252 KOG3314 KOG3314, Ku70-binding protein [Replication, recombination and repair] 194 matched cddid_all.tbl CDD KOG3315 KOG3315 231253 KOG3315 KOG3315, Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport] 191 matched cddid_all.tbl CDD KOG3316 KOG3316 231254 KOG3316 KOG3316, Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport] 163 matched cddid_all.tbl CDD KOG3317 KOG3317 231255 KOG3317 KOG3317, Translocon-associated complex TRAP, beta subunit [Intracellular trafficking, secretion, and vesicular transport] 188 matched cddid_all.tbl CDD KOG3318 KOG3318 231256 KOG3318 KOG3318, Predicted membrane protein [Function unknown] 178 matched cddid_all.tbl CDD KOG3319 KOG3319 231257 KOG3319 KOG3319, Predicted membrane protein [Function unknown] 153 matched cddid_all.tbl CDD KOG3320 KOG3320 231258 KOG3320 KOG3320, 40S ribosomal protein S7 [Translation, ribosomal structure and biogenesis] 192 matched cddid_all.tbl CDD KOG3321 KOG3321 231259 KOG3321 KOG3321, Mitochondrial ribosomal protein S10 [Translation, ribosomal structure and biogenesis] 175 matched cddid_all.tbl CDD KOG3322 KOG3322 231260 KOG3322 KOG3322, Ribonucleases P/MRP protein subunit [RNA processing and modification] 688 matched cddid_all.tbl CDD KOG3323 KOG3323 231261 KOG3323 KOG3323, D-Tyr-tRNA (Tyr) deacylase [Translation, ribosomal structure and biogenesis] 149 matched cddid_all.tbl CDD KOG3324 KOG3324 231262 KOG3324 KOG3324, Mitochondrial import inner membrane translocase, subunit TIM23 [Intracellular trafficking, secretion, and vesicular transport] 206 matched cddid_all.tbl CDD KOG3325 KOG3325 231263 KOG3325 KOG3325, Membrane coat complex Retromer, subunit VPS29/PEP11 [Intracellular trafficking, secretion, and vesicular transport] 183 matched cddid_all.tbl CDD KOG3326 KOG3326 231264 KOG3326 KOG3326, Uncharacterized conserved protein [Function unknown] 154 matched cddid_all.tbl CDD KOG3327 KOG3327 231265 KOG3327 KOG3327, Thymidylate kinase/adenylate kinase [Nucleotide transport and metabolism] 208 matched cddid_all.tbl CDD KOG3328 KOG3328 231266 KOG3328 KOG3328, HGG motif-containing thioesterase [General function prediction only] 148 matched cddid_all.tbl CDD KOG3329 KOG3329 231267 KOG3329 KOG3329, RAN guanine nucleotide release factor [Signal transduction mechanisms] 185 matched cddid_all.tbl CDD KOG3330 KOG3330 231268 KOG3330 KOG3330, Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport] 183 matched cddid_all.tbl CDD KOG3331 KOG3331 231269 KOG3331 KOG3331, Mitochondrial/chloroplast ribosomal protein L4/L29 [Translation, ribosomal structure and biogenesis] 213 matched cddid_all.tbl CDD KOG3332 KOG3332 231270 KOG3332 KOG3332, N-acetylglucosaminyl phosphatidylinositol de-N-acetylase [Cell wall/membrane/envelope biogenesis] 247 matched cddid_all.tbl CDD KOG3333 KOG3333 231271 KOG3333 KOG3333, Mitochondrial/chloroplast ribosomal protein L18 [Translation, ribosomal structure and biogenesis] 188 matched cddid_all.tbl CDD KOG3334 KOG3334 231272 KOG3334 KOG3334, Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription] 148 matched cddid_all.tbl CDD KOG3335 KOG3335 231273 KOG3335 KOG3335, Predicted coiled-coil protein [General function prediction only] 181 matched cddid_all.tbl CDD KOG3336 KOG3336 231274 KOG3336 KOG3336, Predicted member of the intramitochondrial sorting protein family [Intracellular trafficking, secretion, and vesicular transport] 185 matched cddid_all.tbl CDD KOG3337 KOG3337 231275 KOG3337 KOG3337, Protein similar to predicted member of the intramitochondrial sorting protein family [Intracellular trafficking, secretion, and vesicular transport] 201 matched cddid_all.tbl CDD KOG3338 KOG3338 231276 KOG3338 KOG3338, Divalent cation tolerance-related protein [Inorganic ion transport and metabolism] 153 matched cddid_all.tbl CDD KOG3339 KOG3339 231277 KOG3339 KOG3339, Predicted glycosyltransferase [General function prediction only] 211 matched cddid_all.tbl CDD KOG3340 KOG3340 231278 KOG3340 KOG3340, Alpha-L-fucosidase [Carbohydrate transport and metabolism] 454 matched cddid_all.tbl CDD KOG3341 KOG3341 231279 KOG3341 KOG3341, RNA polymerase II transcription factor complex subunit [Transcription] 249 matched cddid_all.tbl CDD KOG3342 KOG3342 231280 KOG3342 KOG3342, Signal peptidase I [Intracellular trafficking, secretion, and vesicular transport] 180 matched cddid_all.tbl CDD KOG3343 KOG3343 231281 KOG3343 KOG3343, Vesicle coat complex COPI, zeta subunit [Intracellular trafficking, secretion, and vesicular transport] 175 matched cddid_all.tbl CDD KOG3344 KOG3344 231282 KOG3344 KOG3344, 40s ribosomal protein s10 [Translation, ribosomal structure and biogenesis] 150 matched cddid_all.tbl CDD KOG3345 KOG3345 231283 KOG3345 KOG3345, Uncharacterized conserved protein [Function unknown] 275 matched cddid_all.tbl CDD KOG3346 KOG3346 231284 KOG3346 KOG3346, Phosphatidylethanolamine binding protein [General function prediction only] 185 matched cddid_all.tbl CDD KOG3347 KOG3347 231285 KOG3347 KOG3347, Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism] 176 matched cddid_all.tbl CDD KOG3348 KOG3348 231286 KOG3348 KOG3348, BolA (bacterial stress-induced morphogen)-related protein [Signal transduction mechanisms] 85 matched cddid_all.tbl CDD KOG3349 KOG3349 231287 KOG3349 KOG3349, Predicted glycosyltransferase [General function prediction only] 170 matched cddid_all.tbl CDD KOG3350 KOG3350 231288 KOG3350 KOG3350, Uncharacterized conserved protein [Function unknown] 217 matched cddid_all.tbl CDD KOG3351 KOG3351 231289 KOG3351 KOG3351, Predicted nucleotidyltransferase [General function prediction only] 293 matched cddid_all.tbl CDD KOG3352 KOG3352 231290 KOG3352 KOG3352, Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion] 153 matched cddid_all.tbl CDD KOG3353 KOG3353 231291 KOG3353 KOG3353, 60S ribosomal protein L22 [Translation, ribosomal structure and biogenesis] 175 matched cddid_all.tbl CDD KOG3354 KOG3354 231292 KOG3354 KOG3354, Gluconate kinase [Carbohydrate transport and metabolism] 191 matched cddid_all.tbl CDD KOG3355 KOG3355 231293 KOG3355 KOG3355, Mitochondrial sulfhydryl oxidase involved in the biogenesis of cytosolic Fe/S proteins [Posttranslational modification, protein turnover, chaperones] 177 matched cddid_all.tbl CDD KOG3356 KOG3356 231294 KOG3356 KOG3356, Predicted membrane protein [Function unknown] 147 matched cddid_all.tbl CDD KOG3357 KOG3357 231295 KOG3357 KOG3357, Uncharacterized conserved protein [Function unknown] 167 matched cddid_all.tbl CDD KOG3358 KOG3358 231296 KOG3358 KOG3358, Uncharacterized secreted protein SDF2 (Stromal cell-derived factor 2), contains MIR domains [General function prediction only] 211 matched cddid_all.tbl CDD KOG3359 KOG3359 231297 KOG3359 KOG3359, Dolichyl-phosphate-mannose:protein O-mannosyl transferase [Posttranslational modification, protein turnover, chaperones] 723 matched cddid_all.tbl CDD KOG3360 KOG3360 231298 KOG3360 KOG3360, Acylphosphatase [Energy production and conversion] 98 matched cddid_all.tbl CDD KOG3361 KOG3361 231299 KOG3361 KOG3361, Iron binding protein involved in Fe-S cluster formation [Energy production and conversion] 157 matched cddid_all.tbl CDD KOG3362 KOG3362 231300 KOG3362 KOG3362, Predicted BBOX Zn-finger protein [General function prediction only] 156 matched cddid_all.tbl CDD KOG3363 KOG3363 231301 KOG3363 KOG3363, Uncharacterized conserved nuclear protein [Function unknown] 196 matched cddid_all.tbl CDD KOG3364 KOG3364 231302 KOG3364 KOG3364, Membrane protein involved in organellar division [Cell wall/membrane/envelope biogenesis] 149 matched cddid_all.tbl CDD KOG3365 KOG3365 231303 KOG3365 KOG3365, NADH:ubiquinone oxidoreductase, NDUFA5/B13 subunit [Energy production and conversion] 145 matched cddid_all.tbl CDD KOG3366 KOG3366 231304 KOG3366 KOG3366, Mitochondrial F1F0-ATP synthase, subunit d/ATP7 [Energy production and conversion] 172 matched cddid_all.tbl CDD KOG3367 KOG3367 231305 KOG3367 KOG3367, Hypoxanthine-guanine phosphoribosyltransferase [Nucleotide transport and metabolism] 216 matched cddid_all.tbl CDD KOG3368 KOG3368 231306 KOG3368 KOG3368, Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport] 140 matched cddid_all.tbl CDD KOG3369 KOG3369 231307 KOG3369 KOG3369, Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport] 199 matched cddid_all.tbl CDD KOG3370 KOG3370 231308 KOG3370 KOG3370, dUTPase [Nucleotide transport and metabolism] 140 matched cddid_all.tbl CDD KOG3371 KOG3371 231309 KOG3371 KOG3371, Uncharacterized conserved protein [Function unknown] 243 matched cddid_all.tbl CDD KOG3372 KOG3372 231310 KOG3372 KOG3372, Signal peptidase complex subunit [Intracellular trafficking, secretion, and vesicular transport] 176 matched cddid_all.tbl CDD KOG3373 KOG3373 231311 KOG3373 KOG3373, Glycine cleavage system H protein (lipoate-binding) [Amino acid transport and metabolism] 172 matched cddid_all.tbl CDD KOG3374 KOG3374 231312 KOG3374 KOG3374, Cellular repressor of transcription [Transcription] 210 matched cddid_all.tbl CDD KOG3375 KOG3375 231313 KOG3375 KOG3375, Phosphoprotein/predicted coiled-coil protein [General function prediction only] 174 matched cddid_all.tbl CDD KOG3376 KOG3376 231314 KOG3376 KOG3376, Uncharacterized conserved protein [Function unknown] 249 matched cddid_all.tbl CDD KOG3377 KOG3377 231315 KOG3377 KOG3377, Uncharacterized conserved protein [Function unknown] 143 matched cddid_all.tbl CDD KOG3378 KOG3378 231316 KOG3378 KOG3378, Hemoglobin-like flavoprotein [Energy production and conversion] 385 matched cddid_all.tbl CDD KOG3379 KOG3379 231317 KOG3379 KOG3379, Diadenosine polyphosphate hydrolase and related proteins of the histidine triad (HIT) family [Nucleotide transport and metabolism, General function prediction only] 150 matched cddid_all.tbl CDD KOG3380 KOG3380 231318 KOG3380 KOG3380, Actin-related protein Arp2/3 complex, subunit ARPC5 [Cytoskeleton] 152 matched cddid_all.tbl CDD KOG3381 KOG3381 231319 KOG3381 KOG3381, Uncharacterized conserved protein [Function unknown] 161 matched cddid_all.tbl CDD KOG3382 KOG3382 231320 KOG3382 KOG3382, NADH:ubiquinone oxidoreductase, B17.2 subunit [Energy production and conversion] 151 matched cddid_all.tbl CDD KOG3383 KOG3383 231321 KOG3383 KOG3383, Uncharacterized conserved protein [Function unknown] 187 matched cddid_all.tbl CDD KOG3384 KOG3384 231322 KOG3384 KOG3384, Selenoprotein [General function prediction only] 154 matched cddid_all.tbl CDD KOG3385 KOG3385 231323 KOG3385 KOG3385, V-SNARE [Intracellular trafficking, secretion, and vesicular transport] 118 matched cddid_all.tbl CDD KOG3386 KOG3386 231324 KOG3386 KOG3386, Copper transporter [Inorganic ion transport and metabolism] 155 matched cddid_all.tbl CDD KOG3387 KOG3387 231325 KOG3387 KOG3387, 60S ribosomal protein 15.5kD/SNU13, NHP2/L7A family (includes ribonuclease P subunit p38), involved in splicing [RNA processing and modification, Translation, ribosomal structure and biogenesis] 131 matched cddid_all.tbl CDD KOG3388 KOG3388 231326 KOG3388 KOG3388, Predicted transcription regulator/nuclease, contains ParB domain [Replication, recombination and repair] 136 matched cddid_all.tbl CDD KOG3389 KOG3389 231327 KOG3389 KOG3389, NADH:ubiquinone oxidoreductase, NDUFS4/18 kDa subunit [Energy production and conversion] 178 matched cddid_all.tbl CDD KOG3390 KOG3390 231328 KOG3390 KOG3390, General control of amino-acid synthesis 5-like 1 [Transcription] 120 matched cddid_all.tbl CDD KOG3391 KOG3391 231329 KOG3391 KOG3391, Transcriptional co-repressor component [Transcription] 151 matched cddid_all.tbl CDD KOG3392 KOG3392 231330 KOG3392 KOG3392, Exon-exon junction complex, Magoh component [RNA processing and modification] 147 matched cddid_all.tbl CDD KOG3393 KOG3393 231331 KOG3393 KOG3393, Predicted membrane protein [Function unknown] 157 matched cddid_all.tbl CDD KOG3394 KOG3394 231332 KOG3394 KOG3394, Protein OS-9 [General function prediction only] 502 matched cddid_all.tbl CDD KOG3395 KOG3395 231333 KOG3395 KOG3395, Uncharacterized conserved protein [Function unknown] 246 matched cddid_all.tbl CDD KOG3396 KOG3396 231334 KOG3396 KOG3396, Glucosamine-phosphate N-acetyltransferase [Cell wall/membrane/envelope biogenesis] 150 matched cddid_all.tbl CDD KOG3397 KOG3397 231335 KOG3397 KOG3397, Acetyltransferases [General function prediction only] 225 matched cddid_all.tbl CDD KOG3398 KOG3398 231336 KOG3398 KOG3398, Transcription factor MBF1 [Transcription] 135 matched cddid_all.tbl CDD KOG3399 KOG3399 231337 KOG3399 KOG3399, Predicted Yippee-type zinc-binding protein [General function prediction only] 122 matched cddid_all.tbl CDD KOG3400 KOG3400 231338 KOG3400 KOG3400, RNA polymerase subunit 8 [Transcription] 143 matched cddid_all.tbl CDD KOG3401 KOG3401 231339 KOG3401 KOG3401, 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis] 145 matched cddid_all.tbl CDD KOG3402 KOG3402 231340 KOG3402 KOG3402, Predicted membrane protein [Function unknown] 101 matched cddid_all.tbl CDD KOG3403 KOG3403 231341 KOG3403 KOG3403, Translation initiation factor 1A (eIF-1A) [Translation, ribosomal structure and biogenesis] 145 matched cddid_all.tbl CDD KOG3404 KOG3404 231342 KOG3404 KOG3404, G10 protein/predicted nuclear transcription regulator [Transcription] 145 matched cddid_all.tbl CDD KOG3405 KOG3405 231343 KOG3405 KOG3405, RNA polymerase subunit K [Transcription] 136 matched cddid_all.tbl CDD KOG3406 KOG3406 231344 KOG3406 KOG3406, 40S ribosomal protein S12 [Translation, ribosomal structure and biogenesis] 134 matched cddid_all.tbl CDD KOG3407 KOG3407 231345 KOG3407 KOG3407, Uncharacterized conserved protein [Function unknown] 151 matched cddid_all.tbl CDD KOG3408 KOG3408 231346 KOG3408 KOG3408, U1-like Zn-finger-containing protein, probabl erole in RNA processing/splicing [RNA processing and modification] 129 matched cddid_all.tbl CDD KOG3409 KOG3409 231347 KOG3409 KOG3409, Exosomal 3'-5' exoribonuclease complex, subunit ski4 (Csl4) [Translation, ribosomal structure and biogenesis] 193 matched cddid_all.tbl CDD KOG3410 KOG3410 231348 KOG3410 KOG3410, Conserved alpha-helical protein [Function unknown] 120 matched cddid_all.tbl CDD KOG3411 KOG3411 231349 KOG3411 KOG3411, 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis] 143 matched cddid_all.tbl CDD KOG3412 KOG3412 231350 KOG3412 KOG3412, 60S ribosomal protein L28 [Translation, ribosomal structure and biogenesis] 133 matched cddid_all.tbl CDD KOG3413 KOG3413 231351 KOG3413 KOG3413, Mitochondrial matrix protein frataxin, involved in Fe/S protein biosynthesis [Inorganic ion transport and metabolism] 156 matched cddid_all.tbl CDD KOG3414 KOG3414 231352 KOG3414 KOG3414, Component of the U4/U6.U5 snRNP/mitosis protein DIM1 [RNA processing and modification, Cell cycle control, cell division, chromosome partitioning] 142 matched cddid_all.tbl CDD KOG3415 KOG3415 231353 KOG3415 KOG3415, Putative Rab5-interacting protein [Intracellular trafficking, secretion, and vesicular transport] 129 matched cddid_all.tbl CDD KOG3416 KOG3416 231354 KOG3416 KOG3416, Predicted nucleic acid binding protein [General function prediction only] 134 matched cddid_all.tbl CDD KOG3417 KOG3417 231355 KOG3417 KOG3417, Ras1 guanine nucleotide exchange factor [Signal transduction mechanisms] 840 matched cddid_all.tbl CDD KOG3418 KOG3418 231356 KOG3418 KOG3418, 60S ribosomal protein L27 [Translation, ribosomal structure and biogenesis] 136 matched cddid_all.tbl CDD KOG3419 KOG3419 231357 KOG3419 KOG3419, Mitochondrial/chloroplast ribosomal protein S16 [Translation, ribosomal structure and biogenesis] 112 matched cddid_all.tbl CDD KOG3420 KOG3420 231358 KOG3420 KOG3420, Predicted RNA methylase [Translation, ribosomal structure and biogenesis] 185 matched cddid_all.tbl CDD KOG3421 KOG3421 231359 KOG3421 KOG3421, 60S ribosomal protein L14 [Translation, ribosomal structure and biogenesis] 136 matched cddid_all.tbl CDD KOG3422 KOG3422 231360 KOG3422 KOG3422, Mitochondrial ribosomal protein L16 [Translation, ribosomal structure and biogenesis] 221 matched cddid_all.tbl CDD KOG3423 KOG3423 231361 KOG3423 KOG3423, Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription] 176 matched cddid_all.tbl CDD KOG3424 KOG3424 231362 KOG3424 KOG3424, 40S ribosomal protein S24 [Translation, ribosomal structure and biogenesis] 132 matched cddid_all.tbl CDD KOG3425 KOG3425 231363 KOG3425 KOG3425, Uncharacterized conserved protein [Function unknown] 128 matched cddid_all.tbl CDD KOG3426 KOG3426 231364 KOG3426 KOG3426, NADH:ubiquinone oxidoreductase, NDUFA6/B14 subunit [Energy production and conversion] 124 matched cddid_all.tbl CDD KOG3427 KOG3427 231365 KOG3427 KOG3427, Polyglutamine tract-binding protein PQBP-1 [Transcription] 222 matched cddid_all.tbl CDD KOG3428 KOG3428 231366 KOG3428 KOG3428, Small nuclear ribonucleoprotein SMD1 and related snRNPs [RNA processing and modification] 109 matched cddid_all.tbl CDD KOG3429 KOG3429 231367 KOG3429 KOG3429, Predicted peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis] 172 matched cddid_all.tbl CDD KOG3430 KOG3430 231368 KOG3430 KOG3430, Dynein light chain type 1 [Cytoskeleton] 90 matched cddid_all.tbl CDD KOG3431 KOG3431 231369 KOG3431 KOG3431, Apoptosis-related protein/predicted DNA-binding protein [Cell cycle control, cell division, chromosome partitioning] 129 matched cddid_all.tbl CDD KOG3432 KOG3432 231370 KOG3432 KOG3432, Vacuolar H+-ATPase V1 sector, subunit F [Energy production and conversion] 121 matched cddid_all.tbl CDD KOG3433 KOG3433 231371 KOG3433 KOG3433, Protein involved in meiotic recombination/predicted coiled-coil protein [Cell cycle control, cell division, chromosome partitioning, General function prediction only] 203 matched cddid_all.tbl CDD KOG3434 KOG3434 231372 KOG3434 KOG3434, 60S ribosomal protein L22 [Translation, ribosomal structure and biogenesis] 125 matched cddid_all.tbl CDD KOG3435 KOG3435 231373 KOG3435 KOG3435, Mitochondrial/chloroplast ribosomal protein L54/L37 [Translation, ribosomal structure and biogenesis] 127 matched cddid_all.tbl CDD KOG3436 KOG3436 231374 KOG3436 KOG3436, 60S ribosomal protein L35 [Translation, ribosomal structure and biogenesis] 123 matched cddid_all.tbl CDD KOG3437 KOG3437 231375 KOG3437 KOG3437, Anaphase-promoting complex (APC), subunit 10 [Cell cycle control, cell division, chromosome partitioning, Posttranslational modification, protein turnover, chaperones] 184 matched cddid_all.tbl CDD KOG3438 KOG3438 231376 KOG3438 KOG3438, DNA-directed RNA polymerase, subunit L [Transcription] 105 matched cddid_all.tbl CDD KOG3439 KOG3439 231377 KOG3439 KOG3439, Protein conjugation factor involved in autophagy [Posttranslational modification, protein turnover, chaperones] 116 matched cddid_all.tbl CDD KOG3440 KOG3440 231378 KOG3440 KOG3440, Ubiquinol cytochrome c reductase, subunit QCR7 [Energy production and conversion] 122 matched cddid_all.tbl CDD KOG3441 KOG3441 231379 KOG3441 KOG3441, Mitochondrial ribosomal protein L14 [Translation, ribosomal structure and biogenesis] 149 matched cddid_all.tbl CDD KOG3442 KOG3442 231380 KOG3442 KOG3442, Uncharacterized conserved protein [Function unknown] 132 matched cddid_all.tbl CDD KOG3443 KOG3443 231381 KOG3443 KOG3443, Uncharacterized conserved protein [Function unknown] 184 matched cddid_all.tbl CDD KOG3444 KOG3444 231382 KOG3444 KOG3444, Uncharacterized conserved protein [Function unknown] 121 matched cddid_all.tbl CDD KOG3445 KOG3445 231383 KOG3445 KOG3445, Mitochondrial/chloroplast ribosomal protein 36a [Translation, ribosomal structure and biogenesis] 145 matched cddid_all.tbl CDD KOG3446 KOG3446 231384 KOG3446 KOG3446, NADH:ubiquinone oxidoreductase NDUFA2/B8 subunit [Energy production and conversion] 97 matched cddid_all.tbl CDD KOG3447 KOG3447 231385 KOG3447 KOG3447, Mitochondrial/chloroplast ribosomal S17-like protein [Translation, ribosomal structure and biogenesis] 150 matched cddid_all.tbl CDD KOG3448 KOG3448 231386 KOG3448 KOG3448, Predicted snRNP core protein [RNA processing and modification] 96 matched cddid_all.tbl CDD KOG3449 KOG3449 231387 KOG3449 KOG3449, 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis] 112 matched cddid_all.tbl CDD KOG3450 KOG3450 231388 KOG3450 KOG3450, Huntingtin interacting protein HYPK [General function prediction only] 119 matched cddid_all.tbl CDD KOG3451 KOG3451 231389 KOG3451 KOG3451, Uncharacterized conserved protein [Function unknown] 71 matched cddid_all.tbl CDD KOG3452 KOG3452 231390 KOG3452 KOG3452, 60S ribosomal protein L36 [Translation, ribosomal structure and biogenesis] 102 matched cddid_all.tbl CDD KOG3453 KOG3453 231391 KOG3453 KOG3453, Cytochrome c [Energy production and conversion] 110 matched cddid_all.tbl CDD KOG3454 KOG3454 231392 KOG3454 KOG3454, U1 snRNP-specific protein C [RNA processing and modification] 165 matched cddid_all.tbl CDD KOG3455 KOG3455 231393 KOG3455 KOG3455, Predicted membrane protein [Function unknown] 139 matched cddid_all.tbl CDD KOG3456 KOG3456 231394 KOG3456 KOG3456, NADH:ubiquinone oxidoreductase, NDUFS6/13 kDa subunit [Energy production and conversion] 120 matched cddid_all.tbl CDD KOG3457 KOG3457 231395 KOG3457 KOG3457, Sec61 protein translocation complex, beta subunit [Posttranslational modification, protein turnover, chaperones] 88 matched cddid_all.tbl CDD KOG3458 KOG3458 231396 KOG3458 KOG3458, NADH:ubiquinone oxidoreductase, NDUFA8/PGIV/19 kDa subunit [Energy production and conversion] 170 matched cddid_all.tbl CDD KOG3459 KOG3459 231397 KOG3459 KOG3459, Small nuclear ribonucleoprotein (snRNP) Sm core protein [RNA processing and modification] 114 matched cddid_all.tbl CDD KOG3460 KOG3460 231398 KOG3460 KOG3460, Small nuclear ribonucleoprotein (snRNP) LSM3 [RNA processing and modification] 91 matched cddid_all.tbl CDD KOG3461 KOG3461 231399 KOG3461 KOG3461, CDGSH-type Zn-finger containing protein [General function prediction only] 132 matched cddid_all.tbl CDD KOG3462 KOG3462 231400 KOG3462 KOG3462, Predicted membrane protein [Function unknown] 105 matched cddid_all.tbl CDD KOG3463 KOG3463 231401 KOG3463 KOG3463, Transcription initiation factor IIA, gamma subunit [Transcription] 109 matched cddid_all.tbl CDD KOG3464 KOG3464 231402 KOG3464 KOG3464, 60S ribosomal protein L44 [Translation, ribosomal structure and biogenesis] 106 matched cddid_all.tbl CDD KOG3465 KOG3465 231403 KOG3465 KOG3465, Signal recognition particle, subunit Srp9 [Intracellular trafficking, secretion, and vesicular transport] 86 matched cddid_all.tbl CDD KOG3466 KOG3466 231404 KOG3466 KOG3466, NADH:ubiquinone oxidoreductase, NDUFB9/B22 subunit [Energy production and conversion] 157 matched cddid_all.tbl CDD KOG3467 KOG3467 231405 KOG3467 KOG3467, Histone H4 [Chromatin structure and dynamics] 103 matched cddid_all.tbl CDD KOG3468 KOG3468 231406 KOG3468 KOG3468, NADH:ubiquinone oxidoreductase, NDUFB7/B18 subunit [Energy production and conversion] 128 matched cddid_all.tbl CDD KOG3469 KOG3469 231407 KOG3469 KOG3469, Cytochrome c oxidase, subunit VIa/COX13 [Energy production and conversion] 112 matched cddid_all.tbl CDD KOG3470 KOG3470 231408 KOG3470 KOG3470, Beta-tubulin folding cofactor A [Posttranslational modification, protein turnover, chaperones] 107 matched cddid_all.tbl CDD KOG3471 KOG3471 231409 KOG3471 KOG3471, RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription, Replication, recombination and repair] 465 matched cddid_all.tbl CDD KOG3472 KOG3472 231410 KOG3472 KOG3472, Predicted small membrane protein [Function unknown] 112 matched cddid_all.tbl CDD KOG3473 KOG3473 231411 KOG3473 KOG3473, RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin C [Transcription] 112 matched cddid_all.tbl CDD KOG3474 KOG3474 231412 KOG3474 KOG3474, Molybdopterin converting factor, small subunit [Energy production and conversion] 84 matched cddid_all.tbl CDD KOG3475 KOG3475 231413 KOG3475 KOG3475, 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis] 92 matched cddid_all.tbl CDD KOG3476 KOG3476 231414 KOG3476 KOG3476, Microtubule-associated protein CRIPT [Cytoskeleton] 100 matched cddid_all.tbl CDD KOG3477 KOG3477 231415 KOG3477 KOG3477, Putative cytochrome c oxidase, subunit COX19 [Energy production and conversion] 97 matched cddid_all.tbl CDD KOG3478 KOG3478 231416 KOG3478 KOG3478, Prefoldin subunit 6, KE2 family [Posttranslational modification, protein turnover, chaperones] 120 matched cddid_all.tbl CDD KOG3479 KOG3479 231417 KOG3479 KOG3479, Mitochondrial import inner membrane translocase, subunit TIM9 [Intracellular trafficking, secretion, and vesicular transport] 83 matched cddid_all.tbl CDD KOG3480 KOG3480 231418 KOG3480 KOG3480, Mitochondrial import inner membrane translocase, subunits TIM10/TIM12 [Intracellular trafficking, secretion, and vesicular transport] 90 matched cddid_all.tbl CDD KOG3481 KOG3481 231419 KOG3481 KOG3481, Uncharacterized conserved protein [Function unknown] 87 matched cddid_all.tbl CDD KOG3482 KOG3482 231420 KOG3482 KOG3482, Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification] 79 matched cddid_all.tbl CDD KOG3483 KOG3483 231421 KOG3483 KOG3483, Uncharacterized conserved protein [Function unknown] 94 matched cddid_all.tbl CDD KOG3484 KOG3484 231422 KOG3484 KOG3484, Cyclin-dependent protein kinase CDC28, regulatory subunit CKS1, and related proteins [Cell cycle control, cell division, chromosome partitioning] 91 matched cddid_all.tbl CDD KOG3485 KOG3485 231423 KOG3485 KOG3485, Uncharacterized conserved protein [Function unknown] 86 matched cddid_all.tbl CDD KOG3486 KOG3486 231424 KOG3486 KOG3486, 40S ribosomal protein S21 [Translation, ribosomal structure and biogenesis] 83 matched cddid_all.tbl CDD KOG3487 KOG3487 231425 KOG3487 KOG3487, TRAPP 20 K subunit [Intracellular trafficking, secretion, and vesicular transport] 139 matched cddid_all.tbl CDD KOG3488 KOG3488 231426 KOG3488 KOG3488, Dolichol phosphate-mannose regulatory protein (DPM2) [Posttranslational modification, protein turnover, chaperones] 81 matched cddid_all.tbl CDD KOG3489 KOG3489 231427 KOG3489 KOG3489, Mitochondrial import inner membrane translocase, subunit TIM8 [Intracellular trafficking, secretion, and vesicular transport] 86 matched cddid_all.tbl CDD KOG3490 KOG3490 231428 KOG3490 KOG3490, Transcription elongation factor SPT4 [Transcription] 111 matched cddid_all.tbl CDD KOG3491 KOG3491 231429 KOG3491 KOG3491, Predicted membrane protein [Function unknown] 65 matched cddid_all.tbl CDD KOG3492 KOG3492 231430 KOG3492 KOG3492, Ribosome biogenesis protein NIP7 [Translation, ribosomal structure and biogenesis] 180 matched cddid_all.tbl CDD KOG3493 KOG3493 231431 KOG3493 KOG3493, Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones] 73 matched cddid_all.tbl CDD KOG3494 KOG3494 231432 KOG3494 KOG3494, Ubiquinol cytochrome c oxidoreductase, subunit QCR9 [Energy production and conversion] 72 matched cddid_all.tbl CDD KOG3495 KOG3495 231433 KOG3495 KOG3495, Mitochondrial F1F0-ATP synthase, subunit epsilon/ATP15 [Energy production and conversion] 50 matched cddid_all.tbl CDD KOG3496 KOG3496 231434 KOG3496 KOG3496, Cytochrome c oxidase assembly protein/Cu2+ chaperone COX17 [Posttranslational modification, protein turnover, chaperones] 72 matched cddid_all.tbl CDD KOG3497 KOG3497 231435 KOG3497 KOG3497, DNA-directed RNA polymerase, subunit RPB10 [Transcription] 69 matched cddid_all.tbl CDD KOG3498 KOG3498 231436 KOG3498 KOG3498, Preprotein translocase, gamma subunit [Intracellular trafficking, secretion, and vesicular transport] 67 matched cddid_all.tbl CDD KOG3499 KOG3499 231437 KOG3499 KOG3499, 60S ribosomal protein L38 [Translation, ribosomal structure and biogenesis] 69 matched cddid_all.tbl CDD KOG3500 KOG3500 231438 KOG3500 KOG3500, Vacuolar H+-ATPase V0 sector, subunit M9.7 (M9.2) [Energy production and conversion] 84 matched cddid_all.tbl CDD KOG3501 KOG3501 231439 KOG3501 KOG3501, Molecular chaperone Prefoldin, subunit 1 [Posttranslational modification, protein turnover, chaperones] 114 matched cddid_all.tbl CDD KOG3502 KOG3502 231440 KOG3502 KOG3502, 40S ribosomal protein S28 [Translation, ribosomal structure and biogenesis] 66 matched cddid_all.tbl CDD KOG3503 KOG3503 231441 KOG3503 KOG3503, H/ACA snoRNP complex, subunit NOP10 [RNA processing and modification] 64 matched cddid_all.tbl CDD KOG3504 KOG3504 231442 KOG3504 KOG3504, 60S ribosomal protein L29 [Translation, ribosomal structure and biogenesis] 84 matched cddid_all.tbl CDD KOG3505 KOG3505 231443 KOG3505 KOG3505, Mitochondrial/chloroplast ribosomal protein L33-like [Translation, ribosomal structure and biogenesis] 55 matched cddid_all.tbl CDD KOG3506 KOG3506 231444 KOG3506 KOG3506, 40S ribosomal protein S29 [Translation, ribosomal structure and biogenesis] 56 matched cddid_all.tbl CDD KOG3507 KOG3507 231445 KOG3507 KOG3507, DNA-directed RNA polymerase, subunit RPB7.0 [Transcription] 62 matched cddid_all.tbl CDD KOG3508 KOG3508 231446 KOG3508 KOG3508, GTPase-activating protein [General function prediction only] 932 matched cddid_all.tbl CDD KOG3509 KOG3509 231447 KOG3509 KOG3509, Basement membrane-specific heparan sulfate proteoglycan (HSPG) core protein [Posttranslational modification, protein turnover, chaperones] 964 matched cddid_all.tbl CDD KOG3511 KOG3511 231448 KOG3511 KOG3511, Sortilin and related receptors [General function prediction only] 720 matched cddid_all.tbl CDD KOG3512 KOG3512 231449 KOG3512 KOG3512, Netrin, axonal chemotropic factor [Signal transduction mechanisms] 592 matched cddid_all.tbl CDD KOG3513 KOG3513 231450 KOG3513 KOG3513, Neural cell adhesion molecule L1 [Signal transduction mechanisms] 1051 matched cddid_all.tbl CDD KOG3514 KOG3514 231451 KOG3514 KOG3514, Neurexin III-alpha [Signal transduction mechanisms] 1591 matched cddid_all.tbl CDD KOG3515 KOG3515 231452 KOG3515 KOG3515, Predicted transmembrane protein of the immunoglobulin family of cell adhesion molecules [General function prediction only] 741 matched cddid_all.tbl CDD KOG3516 KOG3516 231453 KOG3516 KOG3516, Neurexin IV [Signal transduction mechanisms] 1306 matched cddid_all.tbl CDD KOG3517 KOG3517 231454 KOG3517 KOG3517, Transcription factor PAX1/9 [Transcription] 334 matched cddid_all.tbl CDD KOG3518 KOG3518 231455 KOG3518 KOG3518, Putative guanine nucleotide exchange factor [General function prediction only] 521 matched cddid_all.tbl CDD KOG3519 KOG3519 231456 KOG3519 KOG3519, Invasion-inducing protein TIAM1/CDC24 and related RhoGEF GTPases [Signal transduction mechanisms] 756 matched cddid_all.tbl CDD KOG3520 KOG3520 231457 KOG3520 KOG3520, Predicted guanine nucleotide exchange factor [Signal transduction mechanisms] 1167 matched cddid_all.tbl CDD KOG3521 KOG3521 231458 KOG3521 KOG3521, Predicted guanine nucleotide exchange factor [Signal transduction mechanisms] 846 matched cddid_all.tbl CDD KOG3522 KOG3522 231459 KOG3522 KOG3522, Predicted guanine nucleotide exchange factor [Signal transduction mechanisms] 925 matched cddid_all.tbl CDD KOG3523 KOG3523 231460 KOG3523 KOG3523, Putative guanine nucleotide exchange factor TIM [Signal transduction mechanisms] 695 matched cddid_all.tbl CDD KOG3524 KOG3524 231461 KOG3524 KOG3524, Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms] 850 matched cddid_all.tbl CDD KOG3525 KOG3525 231462 KOG3525 KOG3525, Subtilisin-like proprotein convertase [Posttranslational modification, protein turnover, chaperones] 431 matched cddid_all.tbl CDD KOG3526 KOG3526 231463 KOG3526 KOG3526, Subtilisin-like proprotein convertase [Posttranslational modification, protein turnover, chaperones] 629 matched cddid_all.tbl CDD KOG3527 KOG3527 231464 KOG3527 KOG3527, Erythrocyte membrane protein 4.1 and related proteins of the ERM family [General function prediction only] 805 matched cddid_all.tbl CDD KOG3529 KOG3529 231465 KOG3529 KOG3529, Radixin, moesin and related proteins of the ERM family [General function prediction only] 596 matched cddid_all.tbl CDD KOG3530 KOG3530 231466 KOG3530 KOG3530, FERM domain protein EHM2 [General function prediction only] 616 matched cddid_all.tbl CDD KOG3531 KOG3531 231467 KOG3531 KOG3531, Rho guanine nucleotide exchange factor CDEP [Signal transduction mechanisms] 1036 matched cddid_all.tbl CDD KOG3532 KOG3532 231468 KOG3532 KOG3532, Predicted protein kinase [General function prediction only] 1051 matched cddid_all.tbl CDD KOG3533 KOG3533 231469 KOG3533 KOG3533, Inositol 1,4,5-trisphosphate receptor [Signal transduction mechanisms] 2706 matched cddid_all.tbl CDD KOG3534 KOG3534 231470 KOG3534 KOG3534, p53 inducible protein PIR121 [General function prediction only] 1253 matched cddid_all.tbl CDD KOG3535 KOG3535 231471 KOG3535 KOG3535, Adaptor protein Disabled [Signal transduction mechanisms] 557 matched cddid_all.tbl CDD KOG3536 KOG3536 231472 KOG3536 KOG3536, Adaptor protein CED-6, contains PTB domain [General function prediction only] 321 matched cddid_all.tbl CDD KOG3537 KOG3537 231473 KOG3537 KOG3537, Adaptor protein NUMB [Signal transduction mechanisms] 543 matched cddid_all.tbl CDD KOG3538 KOG3538 231474 KOG3538 KOG3538, Disintegrin metalloproteinases with thrombospondin repeats [Posttranslational modification, protein turnover, chaperones] 845 matched cddid_all.tbl CDD KOG3539 KOG3539 231475 KOG3539 KOG3539, Spondins, extracellular matrix proteins [Extracellular structures] 508 matched cddid_all.tbl CDD KOG3540 KOG3540 231476 KOG3540 KOG3540, Beta amyloid precursor protein [General function prediction only] 615 matched cddid_all.tbl CDD KOG3541 KOG3541 231477 KOG3541 KOG3541, Predicted guanine nucleotide exchange factor [Signal transduction mechanisms] 477 matched cddid_all.tbl CDD KOG3542 KOG3542 231478 KOG3542 KOG3542, cAMP-regulated guanine nucleotide exchange factor [Signal transduction mechanisms] 1283 matched cddid_all.tbl CDD KOG3543 KOG3543 231479 KOG3543 KOG3543, Ca2+-dependent activator protein [Signal transduction mechanisms] 1218 matched cddid_all.tbl CDD KOG3544 KOG3544 231480 KOG3544 KOG3544, Collagens (type IV and type XIII), and related proteins [Extracellular structures] 327 matched cddid_all.tbl CDD KOG3545 KOG3545 231481 KOG3545 KOG3545, Olfactomedin and related extracellular matrix glycoproteins [Extracellular structures] 249 matched cddid_all.tbl CDD KOG3546 KOG3546 231482 KOG3546 KOG3546, Collagens (type XV) [Extracellular structures] 1167 matched cddid_all.tbl CDD KOG3547 KOG3547 231483 KOG3547 KOG3547, Bestrophin (Best vitelliform macular dystrophy-associated protein) [General function prediction only] 450 matched cddid_all.tbl CDD KOG3548 KOG3548 231484 KOG3548 KOG3548, DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair] 1176 matched cddid_all.tbl CDD KOG3549 KOG3549 231485 KOG3549 KOG3549, Syntrophins (type gamma) [Extracellular structures] 505 matched cddid_all.tbl CDD KOG3550 KOG3550 231486 KOG3550 KOG3550, Receptor targeting protein Lin-7 [Extracellular structures] 207 matched cddid_all.tbl CDD KOG3551 KOG3551 231487 KOG3551 KOG3551, Syntrophins (type beta) [Extracellular structures] 506 matched cddid_all.tbl CDD KOG3552 KOG3552 231488 KOG3552 KOG3552, FERM domain protein FRM-8 [General function prediction only] 1298 matched cddid_all.tbl CDD KOG3553 KOG3553 231489 KOG3553 KOG3553, Tax interaction protein TIP1 [Cell wall/membrane/envelope biogenesis] 124 matched cddid_all.tbl CDD KOG3554 KOG3554 231490 KOG3554 KOG3554, Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics] 693 matched cddid_all.tbl CDD KOG3555 KOG3555 231491 KOG3555 KOG3555, Ca2+-binding proteoglycan Testican [General function prediction only] 434 matched cddid_all.tbl CDD KOG3556 KOG3556 231492 KOG3556 KOG3556, Familial cylindromatosis protein [General function prediction only] 724 matched cddid_all.tbl CDD KOG3557 KOG3557 231493 KOG3557 KOG3557, Epidermal growth factor receptor kinase substrate [Signal transduction mechanisms] 721 matched cddid_all.tbl CDD KOG3558 KOG3558 231494 KOG3558 KOG3558, Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms, Transcription] 768 matched cddid_all.tbl CDD KOG3559 KOG3559 231495 KOG3559 KOG3559, Transcriptional regulator SIM1 [Transcription] 598 matched cddid_all.tbl CDD KOG3560 KOG3560 231496 KOG3560 KOG3560, Aryl-hydrocarbon receptor [Transcription] 712 matched cddid_all.tbl CDD KOG3561 KOG3561 231497 KOG3561 KOG3561, Aryl-hydrocarbon receptor nuclear translocator [Transcription] 803 matched cddid_all.tbl CDD KOG3562 KOG3562 231498 KOG3562 KOG3562, Forkhead/HNF-3-related transcription factor [Transcription] 277 matched cddid_all.tbl CDD KOG3563 KOG3563 231499 KOG3563 KOG3563, Forkhead/HNF-3-related transcription factor [Transcription] 454 matched cddid_all.tbl CDD KOG3564 KOG3564 231500 KOG3564 KOG3564, GTPase-activating protein [General function prediction only] 604 matched cddid_all.tbl CDD KOG3565 KOG3565 231501 KOG3565 KOG3565, Cdc42-interacting protein CIP4 [Cytoskeleton] 640 matched cddid_all.tbl CDD KOG3566 KOG3566 231502 KOG3566 KOG3566, Glycosylphosphatidylinositol anchor attachment protein GAA1 [Posttranslational modification, protein turnover, chaperones] 617 matched cddid_all.tbl CDD KOG3567 KOG3567 231503 KOG3567 KOG3567, Peptidylglycine alpha-amidating monooxygenase [Posttranslational modification, protein turnover, chaperones] 501 matched cddid_all.tbl CDD KOG3568 KOG3568 231504 KOG3568 KOG3568, Dopamine beta-monooxygenase [Amino acid transport and metabolism] 603 matched cddid_all.tbl CDD KOG3569 KOG3569 231505 KOG3569 KOG3569, RAS signaling inhibitor ST5 [Signal transduction mechanisms] 425 matched cddid_all.tbl CDD KOG3570 KOG3570 231506 KOG3570 KOG3570, MAPK-activating protein DENN [Signal transduction mechanisms] 1588 matched cddid_all.tbl CDD KOG3571 KOG3571 231507 KOG3571 KOG3571, Dishevelled 3 and related proteins [General function prediction only] 626 matched cddid_all.tbl CDD KOG3572 KOG3572 231508 KOG3572 KOG3572, Uncharacterized conserved protein, contains DEP domain [Signal transduction mechanisms] 1701 matched cddid_all.tbl CDD KOG3573 KOG3573 231509 KOG3573 KOG3573, Caspase, apoptotic cysteine protease [Cell cycle control, cell division, chromosome partitioning] 195 matched cddid_all.tbl CDD KOG3574 KOG3574 231510 KOG3574 KOG3574, Acetyl-CoA transporter [Inorganic ion transport and metabolism] 510 matched cddid_all.tbl CDD KOG3576 KOG3576 231511 KOG3576 KOG3576, Ovo and related transcription factors [Transcription] 267 matched cddid_all.tbl CDD KOG3577 KOG3577 231512 KOG3577 KOG3577, Smoothened and related G-protein-coupled receptors [Signal transduction mechanisms] 482 matched cddid_all.tbl CDD KOG3578 KOG3578 231513 KOG3578 KOG3578, Uncharacterized conserved protein [Function unknown] 1058 matched cddid_all.tbl CDD KOG3579 KOG3579 231514 KOG3579 KOG3579, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 352 matched cddid_all.tbl CDD KOG3580 KOG3580 231515 KOG3580 KOG3580, Tight junction proteins [Signal transduction mechanisms] 1027 matched cddid_all.tbl CDD KOG3581 KOG3581 231516 KOG3581 KOG3581, Creatine kinases [Energy production and conversion] 363 matched cddid_all.tbl CDD KOG3582 KOG3582 231517 KOG3582 KOG3582, Mlx interactors and related transcription factors [Transcription] 856 matched cddid_all.tbl CDD KOG3583 KOG3583 231518 KOG3583 KOG3583, Uncharacterized conserved protein [Function unknown] 279 matched cddid_all.tbl CDD KOG3584 KOG3584 231519 KOG3584 KOG3584, cAMP response element binding protein and related transcription factors [Transcription] 348 matched cddid_all.tbl CDD KOG3585 KOG3585 231520 KOG3585 KOG3585, TBX2 and related T-box transcription factors [Transcription] 328 matched cddid_all.tbl CDD KOG3586 KOG3586 231521 KOG3586 KOG3586, TBX1 and related T-box transcription factors [Transcription] 437 matched cddid_all.tbl CDD KOG3587 KOG3587 231522 KOG3587 KOG3587, Galectin, galactose-binding lectin [Extracellular structures] 143 matched cddid_all.tbl CDD KOG3588 KOG3588 231523 KOG3588 KOG3588, Chondroitin synthase 1 [Carbohydrate transport and metabolism] 494 matched cddid_all.tbl CDD KOG3589 KOG3589 231524 KOG3589 KOG3589, G protein signaling regulators [Signal transduction mechanisms] 221 matched cddid_all.tbl CDD KOG3590 KOG3590 231525 KOG3590 KOG3590, Protein kinase A anchoring protein [Signal transduction mechanisms] 602 matched cddid_all.tbl CDD KOG3591 KOG3591 231526 KOG3591 KOG3591, Alpha crystallins [Posttranslational modification, protein turnover, chaperones] 173 matched cddid_all.tbl CDD KOG3592 KOG3592 231527 KOG3592 KOG3592, Microtubule-associated proteins [Cytoskeleton] 934 matched cddid_all.tbl CDD KOG3593 KOG3593 231528 KOG3593 KOG3593, Predicted receptor-like serine/threonine kinase [Signal transduction mechanisms] 355 matched cddid_all.tbl CDD KOG3595 KOG3595 231529 KOG3595 KOG3595, Dyneins, heavy chain [Cytoskeleton] 1227 matched cddid_all.tbl CDD KOG3596 KOG3596 231530 KOG3596 KOG3596, Uncharacterized conserved protein [Function unknown] 1984 matched cddid_all.tbl CDD KOG3597 KOG3597 231531 KOG3597 KOG3597, Proteoglycan [General function prediction only] 442 matched cddid_all.tbl CDD KOG3598 KOG3598 231532 KOG3598 KOG3598, Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription] 2220 matched cddid_all.tbl CDD KOG3599 KOG3599 231533 KOG3599 KOG3599, Ca2+-modulated nonselective cation channel polycystin [Inorganic ion transport and metabolism, Signal transduction mechanisms] 798 matched cddid_all.tbl CDD KOG3600 KOG3600 231534 KOG3600 KOG3600, Thyroid hormone receptor-associated protein complex, subunit TRAP240 [Transcription] 2238 matched cddid_all.tbl CDD KOG3601 KOG3601 231535 KOG3601 KOG3601, Adaptor protein GRB2, contains SH2 and SH3 domains [Signal transduction mechanisms] 222 matched cddid_all.tbl CDD KOG3602 KOG3602 231536 KOG3602 KOG3602, WD40 repeat-containing protein [General function prediction only] 1459 matched cddid_all.tbl CDD KOG3603 KOG3603 231537 KOG3603 KOG3603, Predicted phospholipase D [General function prediction only] 456 matched cddid_all.tbl CDD KOG3604 KOG3604 231538 KOG3604 KOG3604, Pecanex [Function unknown] 560 matched cddid_all.tbl CDD KOG3605 KOG3605 231539 KOG3605 KOG3605, Beta amyloid precursor-binding protein [General function prediction only] 678 matched cddid_all.tbl CDD KOG3606 KOG3606 231540 KOG3606 KOG3606, Cell polarity protein PAR6 [Signal transduction mechanisms] 358 matched cddid_all.tbl CDD KOG3607 KOG3607 231541 KOG3607 KOG3607, Meltrins, fertilins and related Zn-dependent metalloproteinases of the ADAMs family [Posttranslational modification, protein turnover, chaperones] 716 matched cddid_all.tbl CDD KOG3608 KOG3608 231542 KOG3608 KOG3608, Zn finger proteins [General function prediction only] 467 matched cddid_all.tbl CDD KOG3609 KOG3609 231543 KOG3609 KOG3609, Receptor-activated Ca2+-permeable cation channels (STRPC family) [Inorganic ion transport and metabolism, Signal transduction mechanisms] 822 matched cddid_all.tbl CDD KOG3610 KOG3610 231544 KOG3610 KOG3610, Plexins (functional semaphorin receptors) [Signal transduction mechanisms] 1025 matched cddid_all.tbl CDD KOG3611 KOG3611 231545 KOG3611 KOG3611, Semaphorins [Signal transduction mechanisms] 737 matched cddid_all.tbl CDD KOG3612 KOG3612 231546 KOG3612 KOG3612, PHD Zn-finger protein [General function prediction only] 588 matched cddid_all.tbl CDD KOG3613 KOG3613 231547 KOG3613 KOG3613, Dopey and related predicted leucine zipper transcription factors [Transcription] 1749 matched cddid_all.tbl CDD KOG3614 KOG3614 231548 KOG3614 KOG3614, Ca2+/Mg2+-permeable cation channels (LTRPC family) [Inorganic ion transport and metabolism, Signal transduction mechanisms] 1381 matched cddid_all.tbl CDD KOG3615 KOG3615 231549 KOG3615 KOG3615, Uncharacterized conserved protein [Function unknown] 1014 matched cddid_all.tbl CDD KOG3616 KOG3616 231550 KOG3616 KOG3616, Selective LIM binding factor [Transcription] 1636 matched cddid_all.tbl CDD KOG3617 KOG3617 231551 KOG3617 KOG3617, WD40 and TPR repeat-containing protein [General function prediction only] 1416 matched cddid_all.tbl CDD KOG3618 KOG3618 231552 KOG3618 KOG3618, Adenylyl cyclase [General function prediction only] 1318 matched cddid_all.tbl CDD KOG3619 KOG3619 231553 KOG3619 KOG3619, Adenylate/guanylate cyclase [Energy production and conversion] 774 matched cddid_all.tbl CDD KOG3620 KOG3620 231554 KOG3620 KOG3620, Uncharacterized conserved protein [Function unknown] 1626 matched cddid_all.tbl CDD KOG3621 KOG3621 231555 KOG3621 KOG3621, WD40 repeat-containing protein [General function prediction only] 726 matched cddid_all.tbl CDD KOG3622 KOG3622 231556 KOG3622 KOG3622, Uncharacterized conserved protein [Function unknown] 1572 matched cddid_all.tbl CDD KOG3623 KOG3623 231557 KOG3623 KOG3623, Homeobox transcription factor SIP1 [Transcription] 1007 matched cddid_all.tbl CDD KOG3624 KOG3624 231558 KOG3624 KOG3624, M13 family peptidase [Amino acid transport and metabolism] 687 matched cddid_all.tbl CDD KOG3625 KOG3625 231559 KOG3625 KOG3625, Alpha amylase [Carbohydrate transport and metabolism] 1521 matched cddid_all.tbl CDD KOG3626 KOG3626 231560 KOG3626 KOG3626, Organic anion transporter [Secondary metabolites biosynthesis, transport and catabolism] 735 matched cddid_all.tbl CDD KOG3627 KOG3627 231561 KOG3627 KOG3627, Trypsin [Amino acid transport and metabolism] 256 matched cddid_all.tbl CDD KOG3628 KOG3628 231562 KOG3628 KOG3628, Predicted AMP-binding protein [General function prediction only] 1363 matched cddid_all.tbl CDD KOG3629 KOG3629 231563 KOG3629 KOG3629, Guanine-nucleotide releasing factor [Signal transduction mechanisms] 728 matched cddid_all.tbl CDD KOG3630 KOG3630 231564 KOG3630 KOG3630, Nuclear pore complex, Nup214/CAN component [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 1405 matched cddid_all.tbl CDD KOG3631 KOG3631 231565 KOG3631 KOG3631, Alpha-parvin and related focal adhesion proteins [Cytoskeleton] 365 matched cddid_all.tbl CDD KOG3632 KOG3632 231566 KOG3632 KOG3632, Peripheral benzodiazepine receptor PRAX-1 [Signal transduction mechanisms, Cytoskeleton] 1335 matched cddid_all.tbl CDD KOG3633 KOG3633 231567 KOG3633 KOG3633, BAG family molecular chaperone regulator 2 [Posttranslational modification, protein turnover, chaperones] 219 matched cddid_all.tbl CDD KOG3634 KOG3634 231568 KOG3634 KOG3634, Troponin [Cytoskeleton] 361 matched cddid_all.tbl CDD KOG3635 KOG3635 231569 KOG3635 KOG3635, Phosphorylase kinase [Carbohydrate transport and metabolism] 1150 matched cddid_all.tbl CDD KOG3636 KOG3636 231570 KOG3636 KOG3636, Uncharacterized conserved protein, contains TBC and Rhodanese domains [General function prediction only] 669 matched cddid_all.tbl CDD KOG3637 KOG3637 231571 KOG3637 KOG3637, Vitronectin receptor, alpha subunit [Extracellular structures] 1030 matched cddid_all.tbl CDD KOG3638 KOG3638 231572 KOG3638 KOG3638, Sonic hedgehog and related proteins [Signal transduction mechanisms] 414 matched cddid_all.tbl CDD KOG3639 KOG3639 231573 KOG3639 KOG3639, C2 Ca2+-binding motif-containing protein [General function prediction only] 1239 matched cddid_all.tbl CDD KOG3640 KOG3640 231574 KOG3640 KOG3640, Actin binding protein Anillin [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton] 1116 matched cddid_all.tbl CDD KOG3641 KOG3641 231575 KOG3641 KOG3641, Zinc carboxypeptidase [Amino acid transport and metabolism] 650 matched cddid_all.tbl CDD KOG3642 KOG3642 231576 KOG3642 KOG3642, GABA receptor [Signal transduction mechanisms] 466 matched cddid_all.tbl CDD KOG3643 KOG3643 231577 KOG3643 KOG3643, GABA receptor [Signal transduction mechanisms] 459 matched cddid_all.tbl CDD KOG3644 KOG3644 231578 KOG3644 KOG3644, Ligand-gated ion channel [Signal transduction mechanisms] 457 matched cddid_all.tbl CDD KOG3645 KOG3645 231579 KOG3645 KOG3645, Acetylcholine receptor [Signal transduction mechanisms] 449 matched cddid_all.tbl CDD KOG3646 KOG3646 231580 KOG3646 KOG3646, Acetylcholine receptor [Intracellular trafficking, secretion, and vesicular transport] 486 matched cddid_all.tbl CDD KOG3647 KOG3647 231581 KOG3647 KOG3647, Predicted coiled-coil protein [General function prediction only] 338 matched cddid_all.tbl CDD KOG3648 KOG3648 231582 KOG3648 KOG3648, Golgi apparatus protein (cysteine-rich fibroblast growth factor receptor) [Intracellular trafficking, secretion, and vesicular transport] 1179 matched cddid_all.tbl CDD KOG3650 KOG3650 231583 KOG3650 KOG3650, Predicted coiled-coil protein [General function prediction only] 120 matched cddid_all.tbl CDD KOG3651 KOG3651 231584 KOG3651 KOG3651, Protein kinase C, alpha binding protein [Signal transduction mechanisms] 429 matched cddid_all.tbl CDD KOG3652 KOG3652 231585 KOG3652 KOG3652, Uncharacterized conserved protein [Function unknown] 1215 matched cddid_all.tbl CDD KOG3653 KOG3653 231586 KOG3653 KOG3653, Transforming growth factor beta/activin receptor subfamily of serine/threonine kinases [Signal transduction mechanisms] 534 matched cddid_all.tbl CDD KOG3654 KOG3654 231587 KOG3654 KOG3654, Uncharacterized CH domain protein [Cytoskeleton] 708 matched cddid_all.tbl CDD KOG3655 KOG3655 231588 KOG3655 KOG3655, Drebrins and related actin binding proteins [Cytoskeleton] 484 matched cddid_all.tbl CDD KOG3657 KOG3657 231589 KOG3657 KOG3657, Mitochondrial DNA polymerase gamma, catalytic subunit [Replication, recombination and repair] 1075 matched cddid_all.tbl CDD KOG3658 KOG3658 231590 KOG3658 KOG3658, Tumor necrosis factor-alpha-converting enzyme (TACE/ADAM17) and related metalloproteases [Extracellular structures] 764 matched cddid_all.tbl CDD KOG3659 KOG3659 231591 KOG3659 KOG3659, Sodium-neurotransmitter symporter [Signal transduction mechanisms] 629 matched cddid_all.tbl CDD KOG3660 KOG3660 231592 KOG3660 KOG3660, Sodium-neurotransmitter symporter [Signal transduction mechanisms] 629 matched cddid_all.tbl CDD KOG3661 KOG3661 231593 KOG3661 KOG3661, Uncharacterized conserved protein [Function unknown] 1019 matched cddid_all.tbl CDD KOG3662 KOG3662 231594 KOG3662 KOG3662, Cell division control protein/predicted DNA repair exonuclease [Replication, recombination and repair] 410 matched cddid_all.tbl CDD KOG3663 KOG3663 231595 KOG3663 KOG3663, Nuclear factor I [Transcription] 518 matched cddid_all.tbl CDD KOG3664 KOG3664 231596 KOG3664 KOG3664, Predicted patched transmembrane receptor [Signal transduction mechanisms] 999 matched cddid_all.tbl CDD KOG3665 KOG3665 231597 KOG3665 KOG3665, ZYG-1-like serine/threonine protein kinases [General function prediction only] 699 matched cddid_all.tbl CDD KOG3666 KOG3666 231598 KOG3666 KOG3666, Uncharacterized conserved protein [Function unknown] 1141 matched cddid_all.tbl CDD KOG3667 KOG3667 231599 KOG3667 KOG3667, STAT protein [Transcription, Signal transduction mechanisms] 682 matched cddid_all.tbl CDD KOG3668 KOG3668 231600 KOG3668 KOG3668, Phosphatidylinositol transfer protein [Lipid transport and metabolism, Signal transduction mechanisms] 269 matched cddid_all.tbl CDD KOG3669 KOG3669 231601 KOG3669 KOG3669, Uncharacterized conserved protein, contains dysferlin, TECPR and PH domains [General function prediction only] 705 matched cddid_all.tbl CDD KOG3670 KOG3670 231602 KOG3670 KOG3670, Phospholipase [Lipid transport and metabolism] 397 matched cddid_all.tbl CDD KOG3671 KOG3671 231603 KOG3671 KOG3671, Actin regulatory protein (Wiskott-Aldrich syndrome protein) [Signal transduction mechanisms, Cytoskeleton] 569 matched cddid_all.tbl CDD KOG3672 KOG3672 231604 KOG3672 KOG3672, Histidine acid phosphatase [General function prediction only] 487 matched cddid_all.tbl CDD KOG3673 KOG3673 231605 KOG3673 KOG3673, FtsJ-like RNA methyltransferase [RNA processing and modification] 845 matched cddid_all.tbl CDD KOG3674 KOG3674 231606 KOG3674 KOG3674, FtsJ-like RNA methyltransferase [RNA processing and modification] 696 matched cddid_all.tbl CDD KOG3675 KOG3675 231607 KOG3675 KOG3675, Dipeptidyl peptidase III [General function prediction only] 381 matched cddid_all.tbl CDD KOG3676 KOG3676 231608 KOG3676 KOG3676, Ca2+-permeable cation channel OSM-9 and related channels (OTRPC family) [Inorganic ion transport and metabolism, Signal transduction mechanisms] 782 matched cddid_all.tbl CDD KOG3677 KOG3677 231609 KOG3677 KOG3677, RNA polymerase I-associated factor - PAF67 [Translation, ribosomal structure and biogenesis, Transcription] 525 matched cddid_all.tbl CDD KOG3678 KOG3678 231610 KOG3678 KOG3678, SARM protein (with sterile alpha and armadillo motifs) [Extracellular structures] 832 matched cddid_all.tbl CDD KOG3679 KOG3679 231611 KOG3679 KOG3679, Predicted coiled-coil protein [General function prediction only] 802 matched cddid_all.tbl CDD KOG3680 KOG3680 231612 KOG3680 KOG3680, Uncharacterized conserved protein [Function unknown] 830 matched cddid_all.tbl CDD KOG3681 KOG3681 231613 KOG3681 KOG3681, Alpha-catenin [Extracellular structures] 835 matched cddid_all.tbl CDD KOG3682 KOG3682 231614 KOG3682 KOG3682, Predicted membrane protein (associated with esophageal cancer in humans) [Function unknown] 930 matched cddid_all.tbl CDD KOG3683 KOG3683 231615 KOG3683 KOG3683, Uncharacterized conserved protein [Function unknown] 460 matched cddid_all.tbl CDD KOG3684 KOG3684 231616 KOG3684 KOG3684, Ca2+-activated K+ channel proteins (intermediate/small conductance classes) [Inorganic ion transport and metabolism] 489 matched cddid_all.tbl CDD KOG3685 KOG3685 231617 KOG3685 KOG3685, Uncharacterized conserved protein [Function unknown] 1338 matched cddid_all.tbl CDD KOG3686 KOG3686 231618 KOG3686 KOG3686, Rap1-GTPase-activating protein (Rap1GAP) [Signal transduction mechanisms] 740 matched cddid_all.tbl CDD KOG3687 KOG3687 231619 KOG3687 KOG3687, Tuberin - Rap/ran-GTPase-activating protein [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms] 1697 matched cddid_all.tbl CDD KOG3688 KOG3688 231620 KOG3688 KOG3688, Cyclic GMP phosphodiesterase [Signal transduction mechanisms] 554 matched cddid_all.tbl CDD KOG3689 KOG3689 231621 KOG3689 KOG3689, Cyclic nucleotide phosphodiesterase [Signal transduction mechanisms] 707 matched cddid_all.tbl CDD KOG3690 KOG3690 231622 KOG3690 KOG3690, Angiotensin I-converting enzymes - M2 family peptidases [Amino acid transport and metabolism] 646 matched cddid_all.tbl CDD KOG3691 KOG3691 231623 KOG3691 KOG3691, Exocyst complex subunit Sec8 [Intracellular trafficking, secretion, and vesicular transport] 982 matched cddid_all.tbl CDD KOG3692 KOG3692 231624 KOG3692 KOG3692, Uncharacterized conserved protein [Function unknown] 881 matched cddid_all.tbl CDD KOG3693 KOG3693 231625 KOG3693 KOG3693, Uncharacterized conserved protein [Function unknown] 1117 matched cddid_all.tbl CDD KOG3694 KOG3694 231626 KOG3694 KOG3694, Protein required for meiosis [Cell cycle control, cell division, chromosome partitioning] 313 matched cddid_all.tbl CDD KOG3695 KOG3695 231627 KOG3695 KOG3695, Uncharacterized conserved protein [Function unknown] 825 matched cddid_all.tbl CDD KOG3696 KOG3696 231628 KOG3696 KOG3696, Aspartyl beta-hydroxylase [Posttranslational modification, protein turnover, chaperones] 334 matched cddid_all.tbl CDD KOG3697 KOG3697 231629 KOG3697 KOG3697, Adaptor protein SHC and related proteins [Signal transduction mechanisms] 345 matched cddid_all.tbl CDD KOG3698 KOG3698 231630 KOG3698 KOG3698, Hyaluronoglucosaminidase [Posttranslational modification, protein turnover, chaperones] 891 matched cddid_all.tbl CDD KOG3699 KOG3699 231631 KOG3699 KOG3699, Cytoskeletal protein Adducin [Signal transduction mechanisms, Cytoskeleton] 440 matched cddid_all.tbl CDD KOG3700 KOG3700 231632 KOG3700 KOG3700, Predicted acyltransferase [General function prediction only] 660 matched cddid_all.tbl CDD KOG3701 KOG3701 231633 KOG3701 KOG3701, TGFbeta receptor signaling protein SMAD and related proteins [Signal transduction mechanisms, Transcription] 411 matched cddid_all.tbl CDD KOG3702 KOG3702 231634 KOG3702 KOG3702, Nuclear polyadenylated RNA binding protein [RNA processing and modification] 681 matched cddid_all.tbl CDD KOG3703 KOG3703 231635 KOG3703 KOG3703, Heparan sulfate N-deacetylase/N-sulfotransferase [Posttranslational modification, protein turnover, chaperones] 873 matched cddid_all.tbl CDD KOG3704 KOG3704 231636 KOG3704 KOG3704, Heparan sulfate D-glucosaminyl 3-O-sulfotransferase [Posttranslational modification, protein turnover, chaperones] 360 matched cddid_all.tbl CDD KOG3705 KOG3705 231637 KOG3705 KOG3705, Glycoprotein 6-alpha-L-fucosyltransferase [Posttranslational modification, protein turnover, chaperones] 580 matched cddid_all.tbl CDD KOG3706 KOG3706 231638 KOG3706 KOG3706, Uncharacterized conserved protein [Function unknown] 629 matched cddid_all.tbl CDD KOG3707 KOG3707 231639 KOG3707 KOG3707, Uncharacterized conserved protein [Function unknown] 844 matched cddid_all.tbl CDD KOG3708 KOG3708 231640 KOG3708 KOG3708, Uncharacterized conserved protein [Function unknown] 681 matched cddid_all.tbl CDD KOG3709 KOG3709 231641 KOG3709 KOG3709, PACS-1 cytosolic sorting protein [Intracellular trafficking, secretion, and vesicular transport] 778 matched cddid_all.tbl CDD KOG3710 KOG3710 231642 KOG3710 KOG3710, EGL-Nine (EGLN) protein [Signal transduction mechanisms] 280 matched cddid_all.tbl CDD KOG3711 KOG3711 231643 KOG3711 KOG3711, Uncharacterized conserved protein [Function unknown] 719 matched cddid_all.tbl CDD KOG3712 KOG3712 231644 KOG3712 KOG3712, RFX family transcription factor [Transcription] 736 matched cddid_all.tbl CDD KOG3713 KOG3713 231645 KOG3713 KOG3713, Voltage-gated K+ channel KCNB/KCNC [Inorganic ion transport and metabolism] 477 matched cddid_all.tbl CDD KOG3714 KOG3714 231646 KOG3714 KOG3714, Meprin A metalloprotease [Posttranslational modification, protein turnover, chaperones] 411 matched cddid_all.tbl CDD KOG3715 KOG3715 231647 KOG3715 KOG3715, LST7 amino acid permease Golgi transport protein [Intracellular trafficking, secretion, and vesicular transport, Amino acid transport and metabolism] 344 matched cddid_all.tbl CDD KOG3716 KOG3716 231648 KOG3716 KOG3716, Carnitine O-acyltransferase CPTI [Lipid transport and metabolism] 764 matched cddid_all.tbl CDD KOG3717 KOG3717 231649 KOG3717 KOG3717, Carnitine O-acyltransferase CRAT [Lipid transport and metabolism] 612 matched cddid_all.tbl CDD KOG3718 KOG3718 231650 KOG3718 KOG3718, Carnitine O-acyltransferase CROT [Lipid transport and metabolism] 609 matched cddid_all.tbl CDD KOG3719 KOG3719 231651 KOG3719 KOG3719, Carnitine O-acyltransferase CPT2/YAT1 [Lipid transport and metabolism] 638 matched cddid_all.tbl CDD KOG3720 KOG3720 231652 KOG3720 KOG3720, Lysosomal & prostatic acid phosphatases [Lipid transport and metabolism] 411 matched cddid_all.tbl CDD KOG3721 KOG3721 231653 KOG3721 KOG3721, Mitochondrial endonuclease [Nucleotide transport and metabolism] 302 matched cddid_all.tbl CDD KOG3722 KOG3722 231654 KOG3722 KOG3722, Lipocalin-interacting membrane receptor (LIMR) [Defense mechanisms] 538 matched cddid_all.tbl CDD KOG3723 KOG3723 231655 KOG3723 KOG3723, PH domain protein Melted [Signal transduction mechanisms] 851 matched cddid_all.tbl CDD KOG3724 KOG3724 231656 KOG3724 KOG3724, Negative regulator of COPII vesicle formation [Intracellular trafficking, secretion, and vesicular transport] 973 matched cddid_all.tbl CDD KOG3725 KOG3725 231657 KOG3725 KOG3725, SH3 domain protein SH3GLB [Signal transduction mechanisms] 375 matched cddid_all.tbl CDD KOG3726 KOG3726 231658 KOG3726 KOG3726, Uncharacterized conserved protein [Function unknown] 717 matched cddid_all.tbl CDD KOG3727 KOG3727 231659 KOG3727 KOG3727, Mitogen inducible gene product (contains ERM and PH domains) [Cell cycle control, cell division, chromosome partitioning] 664 matched cddid_all.tbl CDD KOG3728 KOG3728 231660 KOG3728 KOG3728, Uridine phosphorylase [Nucleotide transport and metabolism] 308 matched cddid_all.tbl CDD KOG3729 KOG3729 231661 KOG3729 KOG3729, Mitochondrial glycerol-3-phosphate acyltransferase GPAT [Lipid transport and metabolism] 715 matched cddid_all.tbl CDD KOG3730 KOG3730 231662 KOG3730 KOG3730, Acyl-CoA:dihydroxyactetone-phosphate acyltransferase DHAPAT [Lipid transport and metabolism] 521 matched cddid_all.tbl CDD KOG3731 KOG3731 231663 KOG3731 KOG3731, Sulfatases [Carbohydrate transport and metabolism] 541 matched cddid_all.tbl CDD KOG3732 KOG3732 231664 KOG3732 KOG3732, Staufen and related double-stranded-RNA-binding proteins [Intracellular trafficking, secretion, and vesicular transport, Transcription] 339 matched cddid_all.tbl CDD KOG3733 KOG3733 231665 KOG3733 KOG3733, Mucolipidin and related proteins (TRML subfamily of transient receptor potential proteins) [Inorganic ion transport and metabolism] 566 matched cddid_all.tbl CDD KOG3734 KOG3734 231666 KOG3734 KOG3734, Predicted phosphoglycerate mutase [Carbohydrate transport and metabolism] 272 matched cddid_all.tbl CDD KOG3735 KOG3735 231667 KOG3735 KOG3735, Tropomodulin and leiomodulin [Cytoskeleton] 353 matched cddid_all.tbl CDD KOG3736 KOG3736 231668 KOG3736 KOG3736, Polypeptide N-acetylgalactosaminyltransferase [Posttranslational modification, protein turnover, chaperones] 578 matched cddid_all.tbl CDD KOG3737 KOG3737 231669 KOG3737 KOG3737, Predicted polypeptide N-acetylgalactosaminyltransferase [Posttranslational modification, protein turnover, chaperones] 603 matched cddid_all.tbl CDD KOG3738 KOG3738 231670 KOG3738 KOG3738, Predicted polypeptide N-acetylgalactosaminyltransferase [Posttranslational modification, protein turnover, chaperones] 559 matched cddid_all.tbl CDD KOG3739 KOG3739 231671 KOG3739 KOG3739, Stress-activated MAP kinase-interacting protein, Sin1p [Signal transduction mechanisms] 634 matched cddid_all.tbl CDD KOG3740 KOG3740 231672 KOG3740 KOG3740, Uncharacterized conserved protein [Function unknown] 706 matched cddid_all.tbl CDD KOG3741 KOG3741 231673 KOG3741 KOG3741, Poly(A) ribonuclease subunit [RNA processing and modification] 655 matched cddid_all.tbl CDD KOG3742 KOG3742 231674 KOG3742 KOG3742, Glycogen synthase [Carbohydrate transport and metabolism] 692 matched cddid_all.tbl CDD KOG3743 KOG3743 231675 KOG3743 KOG3743, Recombination signal binding protein-J kappa(CBF1, Su(H), HS2NF5) [Transcription] 622 matched cddid_all.tbl CDD KOG3744 KOG3744 231676 KOG3744 KOG3744, Uncharacterized conserved protein [Function unknown] 311 matched cddid_all.tbl CDD KOG3745 KOG3745 231677 KOG3745 KOG3745, Exocyst subunit - Sec10p [Intracellular trafficking, secretion, and vesicular transport] 763 matched cddid_all.tbl CDD KOG3746 KOG3746 231678 KOG3746 KOG3746, Uncharacterized conserved protein [Function unknown] 553 matched cddid_all.tbl CDD KOG3747 KOG3747 231679 KOG3747 KOG3747, Concentrative Na+-nucleoside cotransporter CNT1/CNT2 [Nucleotide transport and metabolism, Inorganic ion transport and metabolism] 602 matched cddid_all.tbl CDD KOG3748 KOG3748 231680 KOG3748 KOG3748, Uncharacterized conserved protein [Function unknown] 477 matched cddid_all.tbl CDD KOG3749 KOG3749 231681 KOG3749 KOG3749, Phosphoenolpyruvate carboxykinase [Energy production and conversion] 640 matched cddid_all.tbl CDD KOG3750 KOG3750 231682 KOG3750 KOG3750, Inositol phospholipid synthesis protein, Scs3p [Lipid transport and metabolism] 270 matched cddid_all.tbl CDD KOG3751 KOG3751 231683 KOG3751 KOG3751, Growth factor receptor-bound proteins (GRB7, GRB10, GRB14) [Signal transduction mechanisms] 622 matched cddid_all.tbl CDD KOG3752 KOG3752 231684 KOG3752 KOG3752, Ribonuclease H [Replication, recombination and repair] 371 matched cddid_all.tbl CDD KOG3753 KOG3753 231685 KOG3753 KOG3753, Circadian clock protein period [Signal transduction mechanisms] 1114 matched cddid_all.tbl CDD KOG3754 KOG3754 231686 KOG3754 KOG3754, Gamma-glutamylcysteine synthetase [Coenzyme transport and metabolism] 640 matched cddid_all.tbl CDD KOG3755 KOG3755 231687 KOG3755 KOG3755, SATB1 matrix attachment region binding protein [Transcription] 769 matched cddid_all.tbl CDD KOG3756 KOG3756 231688 KOG3756 KOG3756, Pinin (desmosome-associated protein) [Cytoskeleton] 340 matched cddid_all.tbl CDD KOG3757 KOG3757 231689 KOG3757 KOG3757, Microtubule assembly protein Doublecortin and related proteins, contain DCX domain [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton] 301 matched cddid_all.tbl CDD KOG3758 KOG3758 231690 KOG3758 KOG3758, Uncharacterized conserved protein [Function unknown] 655 matched cddid_all.tbl CDD KOG3759 KOG3759 231691 KOG3759 KOG3759, Uncharacterized RUN domain protein [Signal transduction mechanisms] 621 matched cddid_all.tbl CDD KOG3760 KOG3760 231692 KOG3760 KOG3760, Heparan sulfate-glucuronic acid C5-epimerase [Carbohydrate transport and metabolism] 594 matched cddid_all.tbl CDD KOG3761 KOG3761 231693 KOG3761 KOG3761, Choline transporter [Lipid transport and metabolism] 591 matched cddid_all.tbl CDD KOG3762 KOG3762 231694 KOG3762 KOG3762, Predicted transporter [General function prediction only] 618 matched cddid_all.tbl CDD KOG3763 KOG3763 231695 KOG3763 KOG3763, mRNA export factor TAP/MEX67 [RNA processing and modification] 585 matched cddid_all.tbl CDD KOG3764 KOG3764 231696 KOG3764 KOG3764, Vesicular amine transporter [Intracellular trafficking, secretion, and vesicular transport] 464 matched cddid_all.tbl CDD KOG3765 KOG3765 231697 KOG3765 KOG3765, Predicted glycosyltransferase [Carbohydrate transport and metabolism] 386 matched cddid_all.tbl CDD KOG3766 KOG3766 231698 KOG3766 KOG3766, Polycomb group protein SCM/L(3)MBT (tumor-supressor in Drosophila and humans) [Transcription] 478 matched cddid_all.tbl CDD KOG3767 KOG3767 231699 KOG3767 KOG3767, Sideroflexin [General function prediction only] 328 matched cddid_all.tbl CDD KOG3768 KOG3768 231700 KOG3768 KOG3768, DEAD box RNA helicase [General function prediction only] 888 matched cddid_all.tbl CDD KOG3769 KOG3769 231701 KOG3769 KOG3769, Ribonuclease III domain proteins [Translation, ribosomal structure and biogenesis] 333 matched cddid_all.tbl CDD KOG3770 KOG3770 231702 KOG3770 KOG3770, Acid sphingomyelinase and PHM5 phosphate metabolism protein [Lipid transport and metabolism] 577 matched cddid_all.tbl CDD KOG3771 KOG3771 231703 KOG3771 KOG3771, Amphiphysin [Intracellular trafficking, secretion, and vesicular transport] 460 matched cddid_all.tbl CDD KOG3772 KOG3772 231704 KOG3772 KOG3772, M-phase inducer phosphatase [Cell cycle control, cell division, chromosome partitioning] 325 matched cddid_all.tbl CDD KOG3773 KOG3773 231705 KOG3773 KOG3773, Adiponutrin and related vesicular transport proteins; predicted alpha/beta hydrolase [Intracellular trafficking, secretion, and vesicular transport] 354 matched cddid_all.tbl CDD KOG3774 KOG3774 231706 KOG3774 KOG3774, Uncharacterized conserved protein Lama [Signal transduction mechanisms] 563 matched cddid_all.tbl CDD KOG3775 KOG3775 231707 KOG3775 KOG3775, Mitogen-activated protein kinase scaffold protein JIP [Signal transduction mechanisms] 482 matched cddid_all.tbl CDD KOG3776 KOG3776 231708 KOG3776 KOG3776, Plasma membrane glycoprotein CD36 and related membrane receptors [Signal transduction mechanisms] 507 matched cddid_all.tbl CDD KOG3777 KOG3777 231709 KOG3777 KOG3777, Uncharacterized conserved protein [Function unknown] 443 matched cddid_all.tbl CDD KOG3778 KOG3778 231710 KOG3778 KOG3778, Uncharacterized conserved protein [Function unknown] 603 matched cddid_all.tbl CDD KOG3779 KOG3779 231711 KOG3779 KOG3779, Homeobox transcription factor prospero [Transcription] 737 matched cddid_all.tbl CDD KOG3780 KOG3780 231712 KOG3780 KOG3780, Thioredoxin binding protein TBP-2/VDUP1 [General function prediction only] 427 matched cddid_all.tbl CDD KOG3781 KOG3781 231713 KOG3781 KOG3781, Dystroglycan [Extracellular structures] 559 matched cddid_all.tbl CDD KOG3782 KOG3782 231714 KOG3782 KOG3782, Predicted membrane protein, contains type II SA sequence [General function prediction only] 189 matched cddid_all.tbl CDD KOG3783 KOG3783 231715 KOG3783 KOG3783, Uncharacterized conserved protein [Function unknown] 546 matched cddid_all.tbl CDD KOG3784 KOG3784 231716 KOG3784 KOG3784, Sorting nexin protein SNX27 [General function prediction only, Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 407 matched cddid_all.tbl CDD KOG3785 KOG3785 231717 KOG3785 KOG3785, Uncharacterized conserved protein [Function unknown] 557 matched cddid_all.tbl CDD KOG3786 KOG3786 231718 KOG3786 KOG3786, RNA polymerase II assessory factor Cdc73p [Transcription] 395 matched cddid_all.tbl CDD KOG3787 KOG3787 231719 KOG3787 KOG3787, Glutamate/aspartate and neutral amino acid transporters [Amino acid transport and metabolism] 507 matched cddid_all.tbl CDD KOG3788 KOG3788 231720 KOG3788 KOG3788, Predicted divalent cation transporter [Inorganic ion transport and metabolism] 348 matched cddid_all.tbl CDD KOG3789 KOG3789 231721 KOG3789 KOG3789, Nitrogen permease regulator NLRG/NPR2 [Inorganic ion transport and metabolism] 396 matched cddid_all.tbl CDD KOG3790 KOG3790 231722 KOG3790 KOG3790, Uncharacterized conserved protein [Function unknown] 529 matched cddid_all.tbl CDD KOG3791 KOG3791 231723 KOG3791 KOG3791, Predicted RNA-binding protein involved in translational regulation [Translation, ribosomal structure and biogenesis, Signal transduction mechanisms] 569 matched cddid_all.tbl CDD KOG3792 KOG3792 231724 KOG3792 KOG3792, Transcription factor NFAT, subunit NF90 [General function prediction only] 816 matched cddid_all.tbl CDD KOG3793 KOG3793 231725 KOG3793 KOG3793, Transcription factor NFAT, subunit NF45 [Transcription] 362 matched cddid_all.tbl CDD KOG3794 KOG3794 231726 KOG3794 KOG3794, CBF1-interacting corepressor CIR and related proteins [Transcription] 453 matched cddid_all.tbl CDD KOG3795 KOG3795 231727 KOG3795 KOG3795, Uncharacterized conserved protein [Function unknown] 230 matched cddid_all.tbl CDD KOG3796 KOG3796 231728 KOG3796 KOG3796, Ammonium transporter RHBG [Intracellular trafficking, secretion, and vesicular transport, General function prediction only] 442 matched cddid_all.tbl CDD KOG3797 KOG3797 231729 KOG3797 KOG3797, Peripheral-type benzodiazepine receptor and related proteins [Signal transduction mechanisms] 168 matched cddid_all.tbl CDD KOG3798 KOG3798 231730 KOG3798 KOG3798, Predicted Zn-dependent hydrolase (beta-lactamase superfamily) [General function prediction only] 343 matched cddid_all.tbl CDD KOG3799 KOG3799 231731 KOG3799 KOG3799, Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport] 169 matched cddid_all.tbl CDD KOG3800 KOG3800 231732 KOG3800 KOG3800, Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones] 300 matched cddid_all.tbl CDD KOG3801 KOG3801 231733 KOG3801 KOG3801, Uncharacterized conserved protein BCN92 [RNA processing and modification] 94 matched cddid_all.tbl CDD KOG3802 KOG3802 231734 KOG3802 KOG3802, Transcription factor OCT-1, contains POU and HOX domains [Transcription] 398 matched cddid_all.tbl CDD KOG3803 KOG3803 231735 KOG3803 KOG3803, Transcription factor containing C2HC type Zn finger [Transcription] 968 matched cddid_all.tbl CDD KOG3804 KOG3804 231736 KOG3804 KOG3804, Transcription factor NERF and related proteins, contain ETS domain [Transcription] 390 matched cddid_all.tbl CDD KOG3805 KOG3805 231737 KOG3805 KOG3805, ERG and related ETS transcription factors [Transcription] 361 matched cddid_all.tbl CDD KOG3806 KOG3806 231738 KOG3806 KOG3806, Predicted transcription factor [Transcription] 177 matched cddid_all.tbl CDD KOG3807 KOG3807 231739 KOG3807 KOG3807, Predicted membrane protein ST7 (tumor suppressor in humans) [General function prediction only] 556 matched cddid_all.tbl CDD KOG3808 KOG3808 231740 KOG3808 KOG3808, Uncharacterized conserved protein [Function unknown] 74 matched cddid_all.tbl CDD KOG3809 KOG3809 231741 KOG3809 KOG3809, Microtubule-binding protein MIP-T3 [Cytoskeleton] 583 matched cddid_all.tbl CDD KOG3810 KOG3810 231742 KOG3810 KOG3810, Micronutrient transporters (folate transporter family) [Coenzyme transport and metabolism] 433 matched cddid_all.tbl CDD KOG3811 KOG3811 231743 KOG3811 KOG3811, Transcription factor AP-2 [Transcription] 434 matched cddid_all.tbl CDD KOG3812 KOG3812 231744 KOG3812 KOG3812, L-type voltage-dependent Ca2+ channel, beta subunit [Inorganic ion transport and metabolism, Signal transduction mechanisms] 393 matched cddid_all.tbl CDD KOG3813 KOG3813 231745 KOG3813 KOG3813, Uncharacterized conserved protein (tumor-suppressor AXUD1 in humans) [General function prediction only] 640 matched cddid_all.tbl CDD KOG3814 KOG3814 231746 KOG3814 KOG3814, Signaling protein van gogh/strabismus [Signal transduction mechanisms] 531 matched cddid_all.tbl CDD KOG3815 KOG3815 231747 KOG3815 KOG3815, Transcription factor Doublesex [Transcription] 322 matched cddid_all.tbl CDD KOG3816 KOG3816 231748 KOG3816 KOG3816, Cell differentiation regulator of the Headcase family [Signal transduction mechanisms] 526 matched cddid_all.tbl CDD KOG3817 KOG3817 231749 KOG3817 KOG3817, Uncharacterized conserved protein [Function unknown] 452 matched cddid_all.tbl CDD KOG3818 KOG3818 231750 KOG3818 KOG3818, DNA polymerase epsilon, subunit B [Replication, recombination and repair] 525 matched cddid_all.tbl CDD KOG3819 KOG3819 231751 KOG3819 KOG3819, Uncharacterized conserved proteins (Hepatitis delta antigen-interacting protein A) [Function unknown] 513 matched cddid_all.tbl CDD KOG3820 KOG3820 231752 KOG3820 KOG3820, Aromatic amino acid hydroxylase [Amino acid transport and metabolism] 461 matched cddid_all.tbl CDD KOG3821 KOG3821 231753 KOG3821 KOG3821, Heparin sulfate cell surface proteoglycan [Signal transduction mechanisms] 563 matched cddid_all.tbl CDD KOG3822 KOG3822 231754 KOG3822 KOG3822, Succinyl-CoA:alpha-ketoacid-CoA transferase [Energy production and conversion] 516 matched cddid_all.tbl CDD KOG3823 KOG3823 231755 KOG3823 KOG3823, Uncharacterized conserved protein [Function unknown] 630 matched cddid_all.tbl CDD KOG3824 KOG3824 231756 KOG3824 KOG3824, Huntingtin interacting protein HYPE [General function prediction only] 472 matched cddid_all.tbl CDD KOG3825 KOG3825 231757 KOG3825 KOG3825, Deoxyribonuclease II [Replication, recombination and repair] 316 matched cddid_all.tbl CDD KOG3826 KOG3826 231758 KOG3826 KOG3826, Na+/H+ antiporter [Inorganic ion transport and metabolism] 252 matched cddid_all.tbl CDD KOG3827 KOG3827 231759 KOG3827 KOG3827, Inward rectifier K+ channel [Inorganic ion transport and metabolism] 400 matched cddid_all.tbl CDD KOG3828 KOG3828 231760 KOG3828 KOG3828, Uncharacterized conserved protein [Function unknown] 457 matched cddid_all.tbl CDD KOG3829 KOG3829 231761 KOG3829 KOG3829, Uncharacterized conserved protein [Function unknown] 486 matched cddid_all.tbl CDD KOG3830 KOG3830 231762 KOG3830 KOG3830, Uncharacterized conserved protein [Function unknown] 542 matched cddid_all.tbl CDD KOG3831 KOG3831 231763 KOG3831 KOG3831, Uncharacterized conserved protein [Function unknown] 196 matched cddid_all.tbl CDD KOG3832 KOG3832 231764 KOG3832 KOG3832, Predicted amino acid transporter [General function prediction only] 319 matched cddid_all.tbl CDD KOG3833 KOG3833 231765 KOG3833 KOG3833, Uncharacterized conserved protein, contains RtcB domain [Function unknown] 505 matched cddid_all.tbl CDD KOG3834 KOG3834 231766 KOG3834 KOG3834, Golgi reassembly stacking protein GRASP65, contains PDZ domain [Intracellular trafficking, secretion, and vesicular transport] 462 matched cddid_all.tbl CDD KOG3835 KOG3835 231767 KOG3835 KOG3835, Transcriptional corepressor NAB1 [Transcription] 495 matched cddid_all.tbl CDD KOG3836 KOG3836 231768 KOG3836 KOG3836, HLH transcription factor EBF/Olf-1 and related DNA binding proteins [Transcription] 605 matched cddid_all.tbl CDD KOG3837 KOG3837 231769 KOG3837 KOG3837, Uncharacterized conserved protein, contains DM14 and C2 domains [General function prediction only] 523 matched cddid_all.tbl CDD KOG3838 KOG3838 231770 KOG3838 KOG3838, Mannose lectin ERGIC-53, involved in glycoprotein traffic [Intracellular trafficking, secretion, and vesicular transport] 497 matched cddid_all.tbl CDD KOG3839 KOG3839 231771 KOG3839 KOG3839, Lectin VIP36, involved in the transport of glycoproteins carrying high mannose-type glycans [Intracellular trafficking, secretion, and vesicular transport] 351 matched cddid_all.tbl CDD KOG3840 KOG3840 231772 KOG3840 KOG3840, Uncharaterized conserved protein, contains BTB/POZ domain [General function prediction only] 438 matched cddid_all.tbl CDD KOG3841 KOG3841 231773 KOG3841 KOG3841, TEF-1 and related transcription factor, TEAD family [Transcription] 455 matched cddid_all.tbl CDD KOG3842 KOG3842 231774 KOG3842 KOG3842, Adaptor protein Pellino [Signal transduction mechanisms] 429 matched cddid_all.tbl CDD KOG3843 KOG3843 231775 KOG3843 KOG3843, Predicted serine hydroxymethyltransferase SLA/LP (autoimmune hepatitis marker in humans) [Translation, ribosomal structure and biogenesis] 432 matched cddid_all.tbl CDD KOG3844 KOG3844 231776 KOG3844 KOG3844, Predicted component of NuA3 histone acetyltransferase complex [Chromatin structure and dynamics] 476 matched cddid_all.tbl CDD KOG3845 KOG3845 231777 KOG3845 KOG3845, MLN, STAR and related lipid-binding proteins [Lipid transport and metabolism] 241 matched cddid_all.tbl CDD KOG3846 KOG3846 231778 KOG3846 KOG3846, L-kynurenine hydrolase [Amino acid transport and metabolism] 465 matched cddid_all.tbl CDD KOG3847 KOG3847 231779 KOG3847 KOG3847, Phospholipase A2 (platelet-activating factor acetylhydrolase in humans) [Lipid transport and metabolism] 399 matched cddid_all.tbl CDD KOG3848 KOG3848 231780 KOG3848 KOG3848, Extracellular protein TEM7, contains PSI domain (tumor endothelial marker in humans) [Extracellular structures] 516 matched cddid_all.tbl CDD KOG3849 KOG3849 231781 KOG3849 KOG3849, GDP-fucose protein O-fucosyltransferase [Posttranslational modification, protein turnover, chaperones] 386 matched cddid_all.tbl CDD KOG3850 KOG3850 231782 KOG3850 KOG3850, Predicted membrane protein [Function unknown] 455 matched cddid_all.tbl CDD KOG3851 KOG3851 231783 KOG3851 KOG3851, Sulfide:quinone oxidoreductase/flavo-binding protein [Energy production and conversion] 446 matched cddid_all.tbl CDD KOG3852 KOG3852 231784 KOG3852 KOG3852, Uncharacterized conserved protein [Function unknown] 426 matched cddid_all.tbl CDD KOG3853 KOG3853 231785 KOG3853 KOG3853, Inositol monophosphatase [Signal transduction mechanisms] 350 matched cddid_all.tbl CDD KOG3854 KOG3854 231786 KOG3854 KOG3854, SPRT-like metalloprotease [Function unknown] 505 matched cddid_all.tbl CDD KOG3855 KOG3855 231787 KOG3855 KOG3855, Monooxygenase involved in coenzyme Q (ubiquinone) biosynthesis [Coenzyme transport and metabolism, Energy production and conversion] 481 matched cddid_all.tbl CDD KOG3856 KOG3856 231788 KOG3856 KOG3856, Uncharacterized conserved protein [Function unknown] 135 matched cddid_all.tbl CDD KOG3857 KOG3857 231789 KOG3857 KOG3857, Alcohol dehydrogenase, class IV [Energy production and conversion] 465 matched cddid_all.tbl CDD KOG3858 KOG3858 231790 KOG3858 KOG3858, Ephrin, ligand for Eph receptor tyrosine kinase [Signal transduction mechanisms] 233 matched cddid_all.tbl CDD KOG3859 KOG3859 231791 KOG3859 KOG3859, Septins (P-loop GTPases) [Cell cycle control, cell division, chromosome partitioning] 406 matched cddid_all.tbl CDD KOG3860 KOG3860 231792 KOG3860 KOG3860, Acyltransferase required for palmitoylation of Hedgehog (Hh) family of secreted signaling proteins [Signal transduction mechanisms] 494 matched cddid_all.tbl CDD KOG3861 KOG3861 231793 KOG3861 KOG3861, Sensory cilia assembly protein [Extracellular structures] 438 matched cddid_all.tbl CDD KOG3862 KOG3862 231794 KOG3862 KOG3862, Transcription factor PAX2/5/8, contains PAX domain [Transcription] 327 matched cddid_all.tbl CDD KOG3863 KOG3863 231795 KOG3863 KOG3863, bZIP transcription factor NRF1 [Transcription] 604 matched cddid_all.tbl CDD KOG3864 KOG3864 231796 KOG3864 KOG3864, Uncharacterized conserved protein [Function unknown] 221 matched cddid_all.tbl CDD KOG3865 KOG3865 231797 KOG3865 KOG3865, Arrestin [Signal transduction mechanisms] 402 matched cddid_all.tbl CDD KOG3866 KOG3866 231798 KOG3866 KOG3866, DNA-binding protein of the nucleobindin family [General function prediction only] 442 matched cddid_all.tbl CDD KOG3867 KOG3867 231799 KOG3867 KOG3867, Sulfatase [General function prediction only] 528 matched cddid_all.tbl CDD KOG3868 KOG3868 231800 KOG3868 KOG3868, Vacuolar H+-ATPase V0 sector, accessory subunit S1 (Ac45) [Energy production and conversion] 411 matched cddid_all.tbl CDD KOG3869 KOG3869 231801 KOG3869 KOG3869, Uncharacterized conserved protein [Function unknown] 450 matched cddid_all.tbl CDD KOG3870 KOG3870 231802 KOG3870 KOG3870, Uncharacterized conserved protein [Function unknown] 434 matched cddid_all.tbl CDD KOG3871 KOG3871 231803 KOG3871 KOG3871, Cell adhesion complex protein bystin [Extracellular structures] 449 matched cddid_all.tbl CDD KOG3873 KOG3873 231804 KOG3873 KOG3873, Sphingomyelinase family protein [Signal transduction mechanisms] 422 matched cddid_all.tbl CDD KOG3874 KOG3874 231805 KOG3874 KOG3874, Uncharacterized conserved protein [Function unknown] 504 matched cddid_all.tbl CDD KOG3875 KOG3875 231806 KOG3875 KOG3875, Peroxisomal biogenesis protein peroxin [Intracellular trafficking, secretion, and vesicular transport] 362 matched cddid_all.tbl CDD KOG3876 KOG3876 231807 KOG3876 KOG3876, Arfaptin and related proteins [Signal transduction mechanisms] 341 matched cddid_all.tbl CDD KOG3877 KOG3877 231808 KOG3877 KOG3877, NADH:ubiquinone oxidoreductase, NDUFA10/42kDa subunit [Energy production and conversion] 393 matched cddid_all.tbl CDD KOG3878 KOG3878 231809 KOG3878 KOG3878, Protein involved in maintenance of Golgi structure and ER-Golgi transport [Intracellular trafficking, secretion, and vesicular transport] 469 matched cddid_all.tbl CDD KOG3879 KOG3879 231810 KOG3879 KOG3879, Predicted membrane protein [Function unknown] 267 matched cddid_all.tbl CDD KOG3880 KOG3880 231811 KOG3880 KOG3880, Predicted small molecule transporter involved in cellular pH homeostasis (Batten disease protein in human) [General function prediction only] 409 matched cddid_all.tbl CDD KOG3881 KOG3881 231812 KOG3881 KOG3881, Uncharacterized conserved protein [Function unknown] 412 matched cddid_all.tbl CDD KOG3882 KOG3882 231813 KOG3882 KOG3882, Tetraspanin family integral membrane protein [General function prediction only] 237 matched cddid_all.tbl CDD KOG3883 KOG3883 231814 KOG3883 KOG3883, Ras family small GTPase [Signal transduction mechanisms] 198 matched cddid_all.tbl CDD KOG3884 KOG3884 231815 KOG3884 KOG3884, Neural proliferation, differentiation and control protein [Signal transduction mechanisms] 437 matched cddid_all.tbl CDD KOG3885 KOG3885 231816 KOG3885 KOG3885, Fibroblast growth factor [Signal transduction mechanisms] 155 matched cddid_all.tbl CDD KOG3886 KOG3886 231817 KOG3886 KOG3886, GTP-binding protein [Signal transduction mechanisms] 295 matched cddid_all.tbl CDD KOG3887 KOG3887 231818 KOG3887 KOG3887, Predicted small GTPase involved in nuclear protein import [Intracellular trafficking, secretion, and vesicular transport] 347 matched cddid_all.tbl CDD KOG3888 KOG3888 231819 KOG3888 KOG3888, Gamma-butyrobetaine,2-oxoglutarate dioxygenase [Lipid transport and metabolism] 407 matched cddid_all.tbl CDD KOG3889 KOG3889 231820 KOG3889 KOG3889, Predicted gamma-butyrobetaine,2-oxoglutarate dioxygenase [Lipid transport and metabolism] 371 matched cddid_all.tbl CDD KOG3890 KOG3890 231821 KOG3890 KOG3890, Mitochondrial 28S ribosomal protein S22 [Translation, ribosomal structure and biogenesis] 391 matched cddid_all.tbl CDD KOG3891 KOG3891 231822 KOG3891 KOG3891, Secretory vesicle-associated protein ICA69, contains Arfaptin domain [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 436 matched cddid_all.tbl CDD KOG3892 KOG3892 231823 KOG3892 KOG3892, N-acetyl-glucosamine-6-phosphate deacetylase [Carbohydrate transport and metabolism] 407 matched cddid_all.tbl CDD KOG3893 KOG3893 231824 KOG3893 KOG3893, Mannosyltransferase [Carbohydrate transport and metabolism] 405 matched cddid_all.tbl CDD KOG3894 KOG3894 231825 KOG3894 KOG3894, SNARE protein Syntaxin 18/UFE1 [Intracellular trafficking, secretion, and vesicular transport] 316 matched cddid_all.tbl CDD KOG3895 KOG3895 231826 KOG3895 KOG3895, Synaptic vesicle protein Synapsin [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 488 matched cddid_all.tbl CDD KOG3896 KOG3896 231827 KOG3896 KOG3896, Dynactin, subunit p62 [Cell motility] 449 matched cddid_all.tbl CDD KOG3897 KOG3897 231828 KOG3897 KOG3897, Conserved protein Knockout [Function unknown] 411 matched cddid_all.tbl CDD KOG3898 KOG3898 231829 KOG3898 KOG3898, Transcription factor NeuroD and related HTH proteins [Transcription] 254 matched cddid_all.tbl CDD KOG3899 KOG3899 231830 KOG3899 KOG3899, Uncharacterized conserved protein [Function unknown] 381 matched cddid_all.tbl CDD KOG3900 KOG3900 231831 KOG3900 KOG3900, Transforming growth factor beta, bone morphogenetic protein and related proteins [Signal transduction mechanisms] 413 matched cddid_all.tbl CDD KOG3901 KOG3901 231832 KOG3901 KOG3901, Transcription initiation factor IID subunit [Transcription] 109 matched cddid_all.tbl CDD KOG3902 KOG3902 231833 KOG3902 KOG3902, Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription] 352 matched cddid_all.tbl CDD KOG3903 KOG3903 231834 KOG3903 KOG3903, Mitotic checkpoint protein PRCC [Cell cycle control, cell division, chromosome partitioning] 410 matched cddid_all.tbl CDD KOG3904 KOG3904 231835 KOG3904 KOG3904, Predicted hydrolase RP2 (NUDIX/MutT superfamily) [Function unknown] 209 matched cddid_all.tbl CDD KOG3905 KOG3905 231836 KOG3905 KOG3905, Dynein light intermediate chain [Cell motility] 473 matched cddid_all.tbl CDD KOG3906 KOG3906 231837 KOG3906 KOG3906, Tryptophan 2,3-dioxygenase [Amino acid transport and metabolism] 399 matched cddid_all.tbl CDD KOG3907 KOG3907 231838 KOG3907 KOG3907, ZIP-like zinc transporter proteins [Intracellular trafficking, secretion, and vesicular transport] 303 matched cddid_all.tbl CDD KOG3908 KOG3908 231839 KOG3908 KOG3908, Queuine-tRNA ribosyltransferase [RNA processing and modification] 396 matched cddid_all.tbl CDD KOG3909 KOG3909 231840 KOG3909 KOG3909, Queuine-tRNA ribosyltransferase [RNA processing and modification] 414 matched cddid_all.tbl CDD KOG3910 KOG3910 231841 KOG3910 KOG3910, Helix loop helix transcription factor [Transcription] 632 matched cddid_all.tbl CDD KOG3911 KOG3911 231842 KOG3911 KOG3911, Nucleolar protein NOP52/RRP1 [RNA processing and modification] 378 matched cddid_all.tbl CDD KOG3912 KOG3912 231843 KOG3912 KOG3912, Predicted integral membrane protein [General function prediction only] 372 matched cddid_all.tbl CDD KOG3913 KOG3913 231844 KOG3913 KOG3913, Wnt family of developmental regulators [Signal transduction mechanisms] 356 matched cddid_all.tbl CDD KOG3914 KOG3914 231845 KOG3914 KOG3914, WD repeat protein WDR4 [Function unknown] 390 matched cddid_all.tbl CDD KOG3915 KOG3915 231846 KOG3915 KOG3915, Transcription regulator dachshund, contains SKI/SNO domain [Transcription] 641 matched cddid_all.tbl CDD KOG3916 KOG3916 231847 KOG3916 KOG3916, UDP-Gal:glucosylceramide beta-1,4-galactosyltransferase [Carbohydrate transport and metabolism] 372 matched cddid_all.tbl CDD KOG3917 KOG3917 231848 KOG3917 KOG3917, Beta-1,4-galactosyltransferase B4GALT7/SQV-3 [Carbohydrate transport and metabolism] 310 matched cddid_all.tbl CDD KOG3918 KOG3918 231849 KOG3918 KOG3918, Predicted membrane protein [Function unknown] 129 matched cddid_all.tbl CDD KOG3919 KOG3919 231850 KOG3919 KOG3919, Kinesin-associated fasciculation and elongation protein involved in axonal transport [Intracellular trafficking, secretion, and vesicular transport] 374 matched cddid_all.tbl CDD KOG3920 KOG3920 231851 KOG3920 KOG3920, Uncharacterized conserved protein, contains PA domain [General function prediction only] 193 matched cddid_all.tbl CDD KOG3921 KOG3921 231852 KOG3921 KOG3921, Uncharacterized conserved protein [Function unknown] 360 matched cddid_all.tbl CDD KOG3922 KOG3922 231853 KOG3922 KOG3922, Sulfotransferases [Posttranslational modification, protein turnover, chaperones] 361 matched cddid_all.tbl CDD KOG3923 KOG3923 231854 KOG3923 KOG3923, D-aspartate oxidase [Amino acid transport and metabolism] 342 matched cddid_all.tbl CDD KOG3924 KOG3924 231855 KOG3924 KOG3924, Putative protein methyltransferase involved in meiosis and transcriptional silencing (Dot1) [Cell cycle control, cell division, chromosome partitioning, Transcription] 419 matched cddid_all.tbl CDD KOG3925 KOG3925 231856 KOG3925 KOG3925, Uncharacterized conserved protein [Function unknown] 371 matched cddid_all.tbl CDD KOG3926 KOG3926 231857 KOG3926 KOG3926, F-box proteins [Amino acid transport and metabolism] 332 matched cddid_all.tbl CDD KOG3927 KOG3927 231858 KOG3927 KOG3927, Na+/K+ ATPase, beta subunit [Inorganic ion transport and metabolism] 300 matched cddid_all.tbl CDD KOG3928 KOG3928 231859 KOG3928 KOG3928, Mitochondrial ribosome small subunit component, mediator of apoptosis DAP3 [Translation, ribosomal structure and biogenesis] 461 matched cddid_all.tbl CDD KOG3929 KOG3929 231860 KOG3929 KOG3929, Uncharacterized conserved protein [Function unknown] 363 matched cddid_all.tbl CDD KOG3930 KOG3930 231861 KOG3930 KOG3930, Uncharacterized conserved protein [Function unknown] 389 matched cddid_all.tbl CDD KOG3931 KOG3931 231862 KOG3931 KOG3931, Uncharacterized conserved protein [Function unknown] 484 matched cddid_all.tbl CDD KOG3932 KOG3932 231863 KOG3932 KOG3932, CDK5 kinase activator p35/Nck5a [Cell cycle control, cell division, chromosome partitioning] 357 matched cddid_all.tbl CDD KOG3933 KOG3933 231864 KOG3933 KOG3933, Mitochondrial ribosomal protein S28 [Translation, ribosomal structure and biogenesis] 296 matched cddid_all.tbl CDD KOG3934 KOG3934 231865 KOG3934 KOG3934, Histone mRNA stem-loop binding protein [RNA processing and modification] 333 matched cddid_all.tbl CDD KOG3935 KOG3935 231866 KOG3935 KOG3935, Predicted glycerate kinase [Carbohydrate transport and metabolism] 446 matched cddid_all.tbl CDD KOG3936 KOG3936 231867 KOG3936 KOG3936, Nitroreductases [Energy production and conversion] 100 matched cddid_all.tbl CDD KOG3937 KOG3937 231868 KOG3937 KOG3937, mRNA splicing factor [RNA processing and modification] 371 matched cddid_all.tbl CDD KOG3938 KOG3938 231869 KOG3938 KOG3938, RGS-GAIP interacting protein GIPC, contains PDZ domain [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 334 matched cddid_all.tbl CDD KOG3939 KOG3939 231870 KOG3939 KOG3939, Selenophosphate synthetase [Signal transduction mechanisms] 312 matched cddid_all.tbl CDD KOG3940 KOG3940 231871 KOG3940 KOG3940, Uncharacterized conserved protein [Function unknown] 351 matched cddid_all.tbl CDD KOG3941 KOG3941 231872 KOG3941 KOG3941, Intermediate in Toll signal transduction pathway (ECSIT) [Signal transduction mechanisms] 406 matched cddid_all.tbl CDD KOG3942 KOG3942 231873 KOG3942 KOG3942, MIF4G domain-containing protein [Translation, ribosomal structure and biogenesis] 348 matched cddid_all.tbl CDD KOG3943 KOG3943 231874 KOG3943 KOG3943, THUMP domain-containing proteins [General function prediction only] 291 matched cddid_all.tbl CDD KOG3944 KOG3944 231875 KOG3944 KOG3944, Uncharacterized conserved protein [Function unknown] 291 matched cddid_all.tbl CDD KOG3945 KOG3945 231876 KOG3945 KOG3945, Uncharacterized conserved protein [Function unknown] 149 matched cddid_all.tbl CDD KOG3946 KOG3946 231877 KOG3946 KOG3946, Glutaminyl cyclase [Posttranslational modification, protein turnover, chaperones] 338 matched cddid_all.tbl CDD KOG3947 KOG3947 231878 KOG3947 KOG3947, Phosphoesterases [General function prediction only] 305 matched cddid_all.tbl CDD KOG3948 KOG3948 231879 KOG3948 KOG3948, Mediator of U snRNA nuclear export PHAX [RNA processing and modification] 369 matched cddid_all.tbl CDD KOG3949 KOG3949 231880 KOG3949 KOG3949, RNA polymerase II elongator complex, subunit ELP4 [Chromatin structure and dynamics, Transcription] 360 matched cddid_all.tbl CDD KOG3950 KOG3950 231881 KOG3950 KOG3950, Gamma/delta sarcoglycan [Cytoskeleton] 292 matched cddid_all.tbl CDD KOG3951 KOG3951 231882 KOG3951 KOG3951, Uncharacterized conserved protein [Function unknown] 321 matched cddid_all.tbl CDD KOG3952 KOG3952 231883 KOG3952 KOG3952, Uncharacterized conserved protein [Function unknown] 304 matched cddid_all.tbl CDD KOG3953 KOG3953 231884 KOG3953 KOG3953, SOCS box protein SSB-1, contains SPRY domain [General function prediction only] 242 matched cddid_all.tbl CDD KOG3954 KOG3954 231885 KOG3954 KOG3954, Electron transfer flavoprotein, alpha subunit [Energy production and conversion] 336 matched cddid_all.tbl CDD KOG3955 KOG3955 231886 KOG3955 KOG3955, Heparan sulfate 6-O-sulfotransferase [Cell wall/membrane/envelope biogenesis, Carbohydrate transport and metabolism] 361 matched cddid_all.tbl CDD KOG3956 KOG3956 231887 KOG3956 KOG3956, Alpha 2-macroglobulin receptor-associated protein [Posttranslational modification, protein turnover, chaperones, Intracellular trafficking, secretion, and vesicular transport, Signal transduction mechanisms, Lipid transport and metabolism, Defense mechanisms] 359 matched cddid_all.tbl CDD KOG3957 KOG3957 231888 KOG3957 KOG3957, Predicted L-carnitine dehydratase/alpha-methylacyl-CoA racemase [Lipid transport and metabolism] 387 matched cddid_all.tbl CDD KOG3958 KOG3958 231889 KOG3958 KOG3958, Putative dynamitin [Cytoskeleton] 371 matched cddid_all.tbl CDD KOG3959 KOG3959 231890 KOG3959 KOG3959, 2-Oxoglutarate- and iron-dependent dioxygenase-related proteins [General function prediction only] 306 matched cddid_all.tbl CDD KOG3960 KOG3960 231891 KOG3960 KOG3960, Myogenic helix-loop-helix transcription factor [Transcription] 284 matched cddid_all.tbl CDD KOG3961 KOG3961 231892 KOG3961 KOG3961, Uncharacterized conserved protein [Function unknown] 262 matched cddid_all.tbl CDD KOG3962 KOG3962 231893 KOG3962 KOG3962, Predicted actin-bundling protein [Cytoskeleton] 246 matched cddid_all.tbl CDD KOG3963 KOG3963 231894 KOG3963 KOG3963, Mab-21-like cell fate specification proteins [Signal transduction mechanisms] 382 matched cddid_all.tbl CDD KOG3964 KOG3964 231895 KOG3964 KOG3964, Phosphatidylglycerolphosphate synthase [Lipid transport and metabolism] 469 matched cddid_all.tbl CDD KOG3965 KOG3965 231896 KOG3965 KOG3965, Uncharacterized conserved protein [Function unknown] 160 matched cddid_all.tbl CDD KOG3966 KOG3966 231897 KOG3966 KOG3966, p53-mediated apoptosis protein EI24/PIG8 [Signal transduction mechanisms, Defense mechanisms] 360 matched cddid_all.tbl CDD KOG3967 KOG3967 231898 KOG3967 KOG3967, Uncharacterized conserved protein [Function unknown] 297 matched cddid_all.tbl CDD KOG3968 KOG3968 231899 KOG3968 KOG3968, Atrazine chlorohydrolase/guanine deaminase [Nucleotide transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism] 439 matched cddid_all.tbl CDD KOG3969 KOG3969 231900 KOG3969 KOG3969, Uncharacterized conserved protein [Function unknown] 310 matched cddid_all.tbl CDD KOG3970 KOG3970 231901 KOG3970 KOG3970, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 299 matched cddid_all.tbl CDD KOG3971 KOG3971 231902 KOG3971 KOG3971, SAP-90/PSD-95 associated protein-related protein (Vulcan) [Signal transduction mechanisms] 640 matched cddid_all.tbl CDD KOG3972 KOG3972 231903 KOG3972 KOG3972, Predicted membrane protein [Function unknown] 252 matched cddid_all.tbl CDD KOG3973 KOG3973 231904 KOG3973 KOG3973, Uncharacterized conserved glycine-rich protein [Function unknown] 465 matched cddid_all.tbl CDD KOG3974 KOG3974 231905 KOG3974 KOG3974, Predicted sugar kinase [Carbohydrate transport and metabolism] 306 matched cddid_all.tbl CDD KOG3975 KOG3975 231906 KOG3975 KOG3975, Uncharacterized conserved protein [Function unknown] 301 matched cddid_all.tbl CDD KOG3976 KOG3976 231907 KOG3976 KOG3976, Mitochondrial F1F0-ATP synthase, subunit b/ATP4 [Energy production and conversion] 247 matched cddid_all.tbl CDD KOG3977 KOG3977 231908 KOG3977 KOG3977, Troponin I [Cytoskeleton] 221 matched cddid_all.tbl CDD KOG3978 KOG3978 231909 KOG3978 KOG3978, Predicted membrane protein [Function unknown] 469 matched cddid_all.tbl CDD KOG3979 KOG3979 231910 KOG3979 KOG3979, FGF receptor activating protein 1 [Signal transduction mechanisms] 296 matched cddid_all.tbl CDD KOG3980 KOG3980 231911 KOG3980 KOG3980, RNA 3'-terminal phosphate cyclase [RNA processing and modification] 361 matched cddid_all.tbl CDD KOG3981 KOG3981 231912 KOG3981 KOG3981, Deoxyribose-phosphate aldolase [Nucleotide transport and metabolism] 326 matched cddid_all.tbl CDD KOG3982 KOG3982 231913 KOG3982 KOG3982, Runt and related transcription factors [Transcription] 475 matched cddid_all.tbl CDD KOG3983 KOG3983 231914 KOG3983 KOG3983, Golgi protein [Intracellular trafficking, secretion, and vesicular transport] 275 matched cddid_all.tbl CDD KOG3984 KOG3984 231915 KOG3984 KOG3984, Purine nucleoside phosphorylase [Nucleotide transport and metabolism] 286 matched cddid_all.tbl CDD KOG3985 KOG3985 231916 KOG3985 KOG3985, Methylthioadenosine phosphorylase MTAP [Nucleotide transport and metabolism] 283 matched cddid_all.tbl CDD KOG3986 KOG3986 231917 KOG3986 KOG3986, Protein phosphatase, regulatory subunit PPP1R3C/D [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms] 526 matched cddid_all.tbl CDD KOG3987 KOG3987 231918 KOG3987 KOG3987, Uncharacterized conserved protein DREV/CGI-81 [Function unknown] 288 matched cddid_all.tbl CDD KOG3988 KOG3988 231919 KOG3988 KOG3988, Protein-tyrosine sulfotransferase TPST1/TPST2 [Posttranslational modification, protein turnover, chaperones] 378 matched cddid_all.tbl CDD KOG3989 KOG3989 231920 KOG3989 KOG3989, Beta-2-glycoprotein I [Extracellular structures] 224 matched cddid_all.tbl CDD KOG3990 KOG3990 231921 KOG3990 KOG3990, Uncharacterized conserved protein [Function unknown] 305 matched cddid_all.tbl CDD KOG3991 KOG3991 231922 KOG3991 KOG3991, Uncharacterized conserved protein [Function unknown] 256 matched cddid_all.tbl CDD KOG3992 KOG3992 231923 KOG3992 KOG3992, Uncharacterized conserved protein [Function unknown] 314 matched cddid_all.tbl CDD KOG3993 KOG3993 231924 KOG3993 KOG3993, Transcription factor (contains Zn finger) [Transcription] 500 matched cddid_all.tbl CDD KOG3994 KOG3994 231925 KOG3994 KOG3994, Uncharacterized conserved protein [Function unknown] 291 matched cddid_all.tbl CDD KOG3995 KOG3995 231926 KOG3995 KOG3995, 3-hydroxyanthranilate oxygenase HAAO [Amino acid transport and metabolism] 279 matched cddid_all.tbl CDD KOG3996 KOG3996 231927 KOG3996 KOG3996, Holocytochrome c synthase/heme-lyase [Energy production and conversion, Posttranslational modification, protein turnover, chaperones] 256 matched cddid_all.tbl CDD KOG3997 KOG3997 231928 KOG3997 KOG3997, Major apurinic/apyrimidinic endonuclease/3'-repair diesterase APN1 [Replication, recombination and repair] 281 matched cddid_all.tbl CDD KOG3998 KOG3998 231929 KOG3998 KOG3998, Putative cargo transport protein ERV29 [Intracellular trafficking, secretion, and vesicular transport] 270 matched cddid_all.tbl CDD KOG3999 KOG3999 231930 KOG3999 KOG3999, Checkpoint 9-1-1 complex, HUS1 component [Energy production and conversion, Replication, recombination and repair] 284 matched cddid_all.tbl CDD KOG4000 KOG4000 231931 KOG4000 KOG4000, Uncharacterized conserved protein [Function unknown] 291 matched cddid_all.tbl CDD KOG4001 KOG4001 231932 KOG4001 KOG4001, Axonemal dynein light chain [Cytoskeleton] 259 matched cddid_all.tbl CDD KOG4002 KOG4002 231933 KOG4002 KOG4002, Uncharacterized integral membrane protein [Function unknown] 264 matched cddid_all.tbl CDD KOG4003 KOG4003 231934 KOG4003 KOG4003, Pyrazinamidase/nicotinamidase PNC1 [Defense mechanisms] 223 matched cddid_all.tbl CDD KOG4004 KOG4004 231935 KOG4004 KOG4004, Matricellular protein Osteonectin/SPARC/BM-40 [Extracellular structures] 259 matched cddid_all.tbl CDD KOG4005 KOG4005 231936 KOG4005 KOG4005, Transcription factor XBP-1 [Transcription] 292 matched cddid_all.tbl CDD KOG4006 KOG4006 231937 KOG4006 KOG4006, Anti-proliferation factor BTG1/TOB [Signal transduction mechanisms, General function prediction only] 311 matched cddid_all.tbl CDD KOG4007 KOG4007 231938 KOG4007 KOG4007, Uncharacterized conserved protein [Function unknown] 229 matched cddid_all.tbl CDD KOG4008 KOG4008 231939 KOG4008 KOG4008, rRNA processing protein RRP7 [RNA processing and modification] 261 matched cddid_all.tbl CDD KOG4009 KOG4009 231940 KOG4009 KOG4009, NADH-ubiquinone oxidoreductase, subunit NDUFB10/PDSW [Energy production and conversion] 156 matched cddid_all.tbl CDD KOG4010 KOG4010 231941 KOG4010 KOG4010, Coiled-coil protein TPD52 [General function prediction only] 208 matched cddid_all.tbl CDD KOG4011 KOG4011 231942 KOG4011 KOG4011, Transcription initiation factor TFIID, subunit TAF7 [Transcription] 330 matched cddid_all.tbl CDD KOG4012 KOG4012 231943 KOG4012 KOG4012, Histone H1 [Chromatin structure and dynamics] 243 matched cddid_all.tbl CDD KOG4013 KOG4013 231944 KOG4013 KOG4013, Predicted Cu2+ homeostasis protein CutC [Inorganic ion transport and metabolism] 255 matched cddid_all.tbl CDD KOG4014 KOG4014 231945 KOG4014 KOG4014, Uncharacterized conserved protein (contains TPR repeat) [Function unknown] 248 matched cddid_all.tbl CDD KOG4015 KOG4015 231946 KOG4015 KOG4015, Fatty acid-binding protein FABP [Lipid transport and metabolism] 133 matched cddid_all.tbl CDD KOG4016 KOG4016 231947 KOG4016 KOG4016, Synaptic vesicle protein Synaptogyrin involved in regulation of Ca2+-dependent exocytosis [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 233 matched cddid_all.tbl CDD KOG4017 KOG4017 231948 KOG4017 KOG4017, DNA excision repair protein XPA/XPAC/RAD14 [Replication, recombination and repair] 274 matched cddid_all.tbl CDD KOG4018 KOG4018 231949 KOG4018 KOG4018, Uncharacterized conserved protein, contains RWD domain [Function unknown] 215 matched cddid_all.tbl CDD KOG4019 KOG4019 231950 KOG4019 KOG4019, Calcineurin-mediated signaling pathway inhibitor DSCR1 [Signal transduction mechanisms, General function prediction only] 193 matched cddid_all.tbl CDD KOG4020 KOG4020 231951 KOG4020 KOG4020, Protein DRE2, required for cell viability [Function unknown] 257 matched cddid_all.tbl CDD KOG4021 KOG4021 231952 KOG4021 KOG4021, Mitochondrial ribosomal protein S18b [Translation, ribosomal structure and biogenesis] 239 matched cddid_all.tbl CDD KOG4022 KOG4022 231953 KOG4022 KOG4022, Dihydropteridine reductase DHPR/QDPR [Amino acid transport and metabolism] 236 matched cddid_all.tbl CDD KOG4023 KOG4023 231954 KOG4023 KOG4023, Uncharacterized conserved protein [Function unknown] 108 matched cddid_all.tbl CDD KOG4024 KOG4024 231955 KOG4024 KOG4024, Complement component 1, Q subcomponent binding protein/mRNA splicing factor SF2, subunit P32 [Defense mechanisms] 266 matched cddid_all.tbl CDD KOG4025 KOG4025 231956 KOG4025 KOG4025, Putative apoptosis related protein [Function unknown] 207 matched cddid_all.tbl CDD KOG4026 KOG4026 231957 KOG4026 KOG4026, Uncharacterized conserved protein [Function unknown] 207 matched cddid_all.tbl CDD KOG4027 KOG4027 231958 KOG4027 KOG4027, Uncharacterized conserved protein [Function unknown] 187 matched cddid_all.tbl CDD KOG4028 KOG4028 231959 KOG4028 KOG4028, Uncharacterized conserved protein [Function unknown] 175 matched cddid_all.tbl CDD KOG4029 KOG4029 231960 KOG4029 KOG4029, Transcription factor HAND2/Transcription factor TAL1/TAL2/LYL1 [Transcription] 228 matched cddid_all.tbl CDD KOG4030 KOG4030 231961 KOG4030 KOG4030, Uncharacterized conserved protein, contains SPRY domain [Function unknown] 197 matched cddid_all.tbl CDD KOG4031 KOG4031 231962 KOG4031 KOG4031, Vesicle coat protein clathrin, light chain [Intracellular trafficking, secretion, and vesicular transport] 216 matched cddid_all.tbl CDD KOG4032 KOG4032 231963 KOG4032 KOG4032, Uncharacterized conserved protein [Function unknown] 184 matched cddid_all.tbl CDD KOG4033 KOG4033 231964 KOG4033 KOG4033, Uncharacterized conserved protein [Function unknown] 314 matched cddid_all.tbl CDD KOG4034 KOG4034 231965 KOG4034 KOG4034, Uncharacterized conserved protein NOF (Neighbor of FAU) [Function unknown] 169 matched cddid_all.tbl CDD KOG4035 KOG4035 231966 KOG4035 KOG4035, Coeffector of mDia Rho GTPase, regulates actin polymerization and cell adhesion turnover [Signal transduction mechanisms, Cytoskeleton] 411 matched cddid_all.tbl CDD KOG4036 KOG4036 231967 KOG4036 KOG4036, Uncharacterized conserved protein [Function unknown] 236 matched cddid_all.tbl CDD KOG4037 KOG4037 231968 KOG4037 KOG4037, Photoreceptor synaptic vesicle protein HRG4/UNC-119 [Intracellular trafficking, secretion, and vesicular transport, Signal transduction mechanisms] 240 matched cddid_all.tbl CDD KOG4038 KOG4038 231969 KOG4038 KOG4038, cGMP-phosphodiesterase, delta subunit [Signal transduction mechanisms] 150 matched cddid_all.tbl CDD KOG4039 KOG4039 231970 KOG4039 KOG4039, Serine/threonine kinase TIP30/CC3 [Signal transduction mechanisms] 238 matched cddid_all.tbl CDD KOG4040 KOG4040 231971 KOG4040 KOG4040, NADH:ubiquinone oxidoreductase, NDUFB8/ASHI subunit [Energy production and conversion] 186 matched cddid_all.tbl CDD KOG4041 KOG4041 231972 KOG4041 KOG4041, Protein phosphatase 1, regulatory (inhibitor) subunit PPP1R2 [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms] 182 matched cddid_all.tbl CDD KOG4042 KOG4042 231973 KOG4042 KOG4042, Dynactin subunit p27/WS-3, involved in transport of organelles along microtubules [Intracellular trafficking, secretion, and vesicular transport, Cytoskeleton] 190 matched cddid_all.tbl CDD KOG4043 KOG4043 231974 KOG4043 KOG4043, Uncharacterized conserved protein [Function unknown] 214 matched cddid_all.tbl CDD KOG4044 KOG4044 231975 KOG4044 KOG4044, Mitochondrial associated endoribonuclease MAR1 (isochorismatase superfamily) [General function prediction only] 201 matched cddid_all.tbl CDD KOG4045 KOG4045 231976 KOG4045 KOG4045, Uncharacterized conserved protein [Function unknown] 168 matched cddid_all.tbl CDD KOG4046 KOG4046 231977 KOG4046 KOG4046, RNase MRP and P, subunit POP4/p29 [RNA processing and modification] 224 matched cddid_all.tbl CDD KOG4047 KOG4047 231978 KOG4047 KOG4047, Docking protein 1 (p62dok) [Signal transduction mechanisms] 429 matched cddid_all.tbl CDD KOG4048 KOG4048 231979 KOG4048 KOG4048, Uncharacterized conserved protein [Function unknown] 201 matched cddid_all.tbl CDD KOG4049 KOG4049 231980 KOG4049 KOG4049, Proliferation-related protein MLF [Function unknown] 248 matched cddid_all.tbl CDD KOG4050 KOG4050 231981 KOG4050 KOG4050, Glutamate transporter EAAC1-interacting protein GTRAP3-18 [Amino acid transport and metabolism, Signal transduction mechanisms] 188 matched cddid_all.tbl CDD KOG4051 KOG4051 231982 KOG4051 KOG4051, Uncharacterized conserved protein [Function unknown] 214 matched cddid_all.tbl CDD KOG4052 KOG4052 231983 KOG4052 KOG4052, Uncharacterized conserved protein [Function unknown] 190 matched cddid_all.tbl CDD KOG4053 KOG4053 231984 KOG4053 KOG4053, Ataxin-1, involved in Ca2+ homeostasis [Function unknown] 224 matched cddid_all.tbl CDD KOG4054 KOG4054 231985 KOG4054 KOG4054, Uncharacterized conserved protein [Function unknown] 183 matched cddid_all.tbl CDD KOG4055 KOG4055 231986 KOG4055 KOG4055, Uncharacterized conserved protein [Function unknown] 213 matched cddid_all.tbl CDD KOG4056 KOG4056 231987 KOG4056 KOG4056, Translocase of outer mitochondrial membrane complex, subunit TOM20 [Intracellular trafficking, secretion, and vesicular transport] 143 matched cddid_all.tbl CDD KOG4057 KOG4057 231988 KOG4057 KOG4057, Uncharacterized conserved protein [Function unknown] 180 matched cddid_all.tbl CDD KOG4058 KOG4058 231989 KOG4058 KOG4058, Uncharacterized conserved protein [Function unknown] 199 matched cddid_all.tbl CDD KOG4059 KOG4059 231990 KOG4059 KOG4059, Uncharacterized conserved protein [Function unknown] 193 matched cddid_all.tbl CDD KOG4060 KOG4060 231991 KOG4060 KOG4060, Uncharacterized conserved protein [Function unknown] 176 matched cddid_all.tbl CDD KOG4061 KOG4061 231992 KOG4061 KOG4061, DMQ mono-oxygenase/Ubiquinone biosynthesis protein COQ7/CLK-1/CAT5 [General function prediction only] 217 matched cddid_all.tbl CDD KOG4062 KOG4062 231993 KOG4062 KOG4062, 6-O-methylguanine-DNA methyltransferase MGMT/MGT1, involved in DNA repair [Replication, recombination and repair] 178 matched cddid_all.tbl CDD KOG4063 KOG4063 231994 KOG4063 KOG4063, Major epididymal secretory protein HE1 [Function unknown] 158 matched cddid_all.tbl CDD KOG4064 KOG4064 231995 KOG4064 KOG4064, Cysteine dioxygenase CDO1 [Amino acid transport and metabolism] 196 matched cddid_all.tbl CDD KOG4065 KOG4065 231996 KOG4065 KOG4065, Uncharacterized conserved protein [Function unknown] 144 matched cddid_all.tbl CDD KOG4066 KOG4066 231997 KOG4066 KOG4066, Cell growth regulatory protein CGR11 [Function unknown] 177 matched cddid_all.tbl CDD KOG4067 KOG4067 231998 KOG4067 KOG4067, Uncharacterized conserved protein [Function unknown] 195 matched cddid_all.tbl CDD KOG4068 KOG4068 231999 KOG4068 KOG4068, Uncharacterized conserved protein [Function unknown] 174 matched cddid_all.tbl CDD KOG4069 KOG4069 232000 KOG4069 KOG4069, Uncharacterized conserved protein [Function unknown] 154 matched cddid_all.tbl CDD KOG4070 KOG4070 232001 KOG4070 KOG4070, Putative signal transduction protein p25 [General function prediction only, Signal transduction mechanisms] 180 matched cddid_all.tbl CDD KOG4071 KOG4071 232002 KOG4071 KOG4071, Uncharacterized conserved protein [Function unknown] 187 matched cddid_all.tbl CDD KOG4072 KOG4072 232003 KOG4072 KOG4072, Signal peptidase complex, subunit SPC25 [Intracellular trafficking, secretion, and vesicular transport] 127 matched cddid_all.tbl CDD KOG4073 KOG4073 232004 KOG4073 KOG4073, Pterin carbinolamine dehydratase PCBD/dimerization cofactor of HNF1 [Transcription] 104 matched cddid_all.tbl CDD KOG4074 KOG4074 232005 KOG4074 KOG4074, Leucine zipper nuclear factor [Function unknown] 383 matched cddid_all.tbl CDD KOG4075 KOG4075 232006 KOG4075 KOG4075, Cytochrome c oxidase, subunit IV/COX5b [Energy production and conversion] 167 matched cddid_all.tbl CDD KOG4076 KOG4076 232007 KOG4076 KOG4076, Regulator of ATP-sensitive K+ channels Alpha-endosulfine/ARPP-19 and related cAMP-regulated phosphoproteins [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 121 matched cddid_all.tbl CDD KOG4077 KOG4077 232008 KOG4077 KOG4077, Cytochrome c oxidase, subunit Va/COX6 [Energy production and conversion] 149 matched cddid_all.tbl CDD KOG4078 KOG4078 232009 KOG4078 KOG4078, Putative mitochondrial ribosomal protein mRpS35 [Translation, ribosomal structure and biogenesis] 173 matched cddid_all.tbl CDD KOG4079 KOG4079 232010 KOG4079 KOG4079, Putative mitochondrial ribosomal protein mRpS25 [Translation, ribosomal structure and biogenesis] 169 matched cddid_all.tbl CDD KOG4080 KOG4080 232011 KOG4080 KOG4080, Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis] 176 matched cddid_all.tbl CDD KOG4081 KOG4081 232012 KOG4081 KOG4081, Dynein light chain [Cell motility] 115 matched cddid_all.tbl CDD KOG4082 KOG4082 232013 KOG4082 KOG4082, Uncharacterized conserved protein [Function unknown] 268 matched cddid_all.tbl CDD KOG4083 KOG4083 232014 KOG4083 KOG4083, Head-elevated expression protein [Transcription] 192 matched cddid_all.tbl CDD KOG4084 KOG4084 232015 KOG4084 KOG4084, Transmembrane protein [General function prediction only] 149 matched cddid_all.tbl CDD KOG4085 KOG4085 232016 KOG4085 KOG4085, Uncharacterized conserved protein [Function unknown] 175 matched cddid_all.tbl CDD KOG4086 KOG4086 232017 KOG4086 KOG4086, Transcriptional regulator SOH1 [Transcription, Replication, recombination and repair] 130 matched cddid_all.tbl CDD KOG4087 KOG4087 232018 KOG4087 KOG4087, Phospholipase A2 [Lipid transport and metabolism] 144 matched cddid_all.tbl CDD KOG4088 KOG4088 232019 KOG4088 KOG4088, Translocon-associated complex TRAP, delta subunit [Intracellular trafficking, secretion, and vesicular transport] 167 matched cddid_all.tbl CDD KOG4089 KOG4089 232020 KOG4089 KOG4089, Predicted mitochondrial ribosomal protein L23 [Translation, ribosomal structure and biogenesis] 165 matched cddid_all.tbl CDD KOG4090 KOG4090 232021 KOG4090 KOG4090, Uncharacterized conserved protein [Function unknown] 157 matched cddid_all.tbl CDD KOG4091 KOG4091 232022 KOG4091 KOG4091, Transcription factor [Transcription] 463 matched cddid_all.tbl CDD KOG4092 KOG4092 232023 KOG4092 KOG4092, Mitochondrial F1F0-ATP synthase, subunit f [Energy production and conversion] 108 matched cddid_all.tbl CDD KOG4093 KOG4093 232024 KOG4093 KOG4093, Uncharacterized conserved protein [Function unknown] 144 matched cddid_all.tbl CDD KOG4094 KOG4094 232025 KOG4094 KOG4094, Uncharacterized conserved protein [Function unknown] 178 matched cddid_all.tbl CDD KOG4095 KOG4095 232026 KOG4095 KOG4095, Uncharacterized conserved protein (tumor-specific protein BCL7 in humans) [General function prediction only] 165 matched cddid_all.tbl CDD KOG4096 KOG4096 232027 KOG4096 KOG4096, Uncharacterized conserved protein [Function unknown] 75 matched cddid_all.tbl CDD KOG4097 KOG4097 232028 KOG4097 KOG4097, Succinate dehydrogenase membrane anchor subunit and related proteins [Energy production and conversion, Intracellular trafficking, secretion, and vesicular transport] 178 matched cddid_all.tbl CDD KOG4098 KOG4098 232029 KOG4098 KOG4098, Molecular chaperone Prefoldin, subunit 2 [Posttranslational modification, protein turnover, chaperones] 140 matched cddid_all.tbl CDD KOG4099 KOG4099 232030 KOG4099 KOG4099, Predicted membrane protein [Function unknown] 138 matched cddid_all.tbl CDD KOG4100 KOG4100 232031 KOG4100 KOG4100, Uncharacterized conserved protein [Function unknown] 125 matched cddid_all.tbl CDD KOG4101 KOG4101 232032 KOG4101 KOG4101, Cysteine-rich hydrophobic proteins [General function prediction only] 175 matched cddid_all.tbl CDD KOG4102 KOG4102 232033 KOG4102 KOG4102, Uncharacterized conserved protein [Function unknown] 121 matched cddid_all.tbl CDD KOG4103 KOG4103 232034 KOG4103 KOG4103, Mitochondrial F1F0-ATP synthase, subunit g/ATP20 [Energy production and conversion] 103 matched cddid_all.tbl CDD KOG4104 KOG4104 232035 KOG4104 KOG4104, Ganglioside-induced differentiation associated protein 3 [Signal transduction mechanisms] 113 matched cddid_all.tbl CDD KOG4105 KOG4105 232036 KOG4105 KOG4105, 6-pyruvoyl tetrahydrobiopterin synthase [Coenzyme transport and metabolism] 141 matched cddid_all.tbl CDD KOG4106 KOG4106 232037 KOG4106 KOG4106, Uncharacterized conserved protein [Function unknown] 125 matched cddid_all.tbl CDD KOG4107 KOG4107 232038 KOG4107 KOG4107, MP1 adaptor interacting protein P14 [Signal transduction mechanisms] 125 matched cddid_all.tbl CDD KOG4108 KOG4108 232039 KOG4108 KOG4108, Dynein light chain [Cell motility] 174 matched cddid_all.tbl CDD KOG4109 KOG4109 232040 KOG4109 KOG4109, Histone H3 (Lys4) methyltransferase complex, subunit CPS25/DPY-30 [Transcription] 116 matched cddid_all.tbl CDD KOG4110 KOG4110 232041 KOG4110 KOG4110, NADH:ubiquinone oxidoreductase, NDUFS5/15kDa [Energy production and conversion] 120 matched cddid_all.tbl CDD KOG4111 KOG4111 232042 KOG4111 KOG4111, Translocase of outer mitochondrial membrane complex, subunit TOM22 [Intracellular trafficking, secretion, and vesicular transport] 136 matched cddid_all.tbl CDD KOG4112 KOG4112 232043 KOG4112 KOG4112, Signal peptidase subunit [Intracellular trafficking, secretion, and vesicular transport] 101 matched cddid_all.tbl CDD KOG4113 KOG4113 232044 KOG4113 KOG4113, Guanine nucleotide exchange factor [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 99 matched cddid_all.tbl CDD KOG4114 KOG4114 232045 KOG4114 KOG4114, Cytochrome c oxidase assembly protein PET191 [Posttranslational modification, protein turnover, chaperones] 73 matched cddid_all.tbl CDD KOG4115 KOG4115 232046 KOG4115 KOG4115, Dynein-associated protein Roadblock [Cell cycle control, cell division, chromosome partitioning, Cell motility] 97 matched cddid_all.tbl CDD KOG4116 KOG4116 232047 KOG4116 KOG4116, Ubiquinol cytochrome c reductase, subunit QCR8 [Energy production and conversion] 90 matched cddid_all.tbl CDD KOG4117 KOG4117 232048 KOG4117 KOG4117, Heat shock factor binding protein [Transcription, Posttranslational modification, protein turnover, chaperones] 73 matched cddid_all.tbl CDD KOG4118 KOG4118 232049 KOG4118 KOG4118, Uncharacterized conserved protein [Function unknown] 74 matched cddid_all.tbl CDD KOG4119 KOG4119 232050 KOG4119 KOG4119, G protein gamma subunit [Signal transduction mechanisms] 71 matched cddid_all.tbl CDD KOG4120 KOG4120 232051 KOG4120 KOG4120, G/T mismatch-specific thymine DNA glycosylase [Replication, recombination and repair] 426 matched cddid_all.tbl CDD KOG4121 KOG4121 232052 KOG4121 KOG4121, Nuclear pore complex, Nup133 component (sc Nup133) [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 1128 matched cddid_all.tbl CDD KOG4122 KOG4122 232053 KOG4122 KOG4122, Mitochondrial/chloroplast ribosomal protein L36 [Translation, ribosomal structure and biogenesis] 38 matched cddid_all.tbl CDD KOG4123 KOG4123 232054 KOG4123 KOG4123, Putative alpha 1,2 mannosyltransferase [Carbohydrate transport and metabolism] 550 matched cddid_all.tbl CDD KOG4124 KOG4124 232055 KOG4124 KOG4124, Putative transcriptional repressor regulating G2/M transition [Transcription, Cell cycle control, cell division, chromosome partitioning] 442 matched cddid_all.tbl CDD KOG4125 KOG4125 232056 KOG4125 KOG4125, Acid trehalase [Carbohydrate transport and metabolism] 682 matched cddid_all.tbl CDD KOG4126 KOG4126 232057 KOG4126 KOG4126, Alkaline phosphatase [Inorganic ion transport and metabolism] 529 matched cddid_all.tbl CDD KOG4127 KOG4127 232058 KOG4127 KOG4127, Renal dipeptidase [Posttranslational modification, protein turnover, chaperones] 419 matched cddid_all.tbl CDD KOG4128 KOG4128 232059 KOG4128 KOG4128, Bleomycin hydrolases and aminopeptidases of cysteine protease family [Amino acid transport and metabolism] 457 matched cddid_all.tbl CDD KOG4129 KOG4129 232060 KOG4129 KOG4129, Exopolyphosphatases and related proteins [Energy production and conversion] 377 matched cddid_all.tbl CDD KOG4130 KOG4130 232061 KOG4130 KOG4130, Prenyl protein protease [Posttranslational modification, protein turnover, chaperones] 291 matched cddid_all.tbl CDD KOG4131 KOG4131 232062 KOG4131 KOG4131, Ngg1-interacting factor 3 protein NIF3L1 [General function prediction only] 272 matched cddid_all.tbl CDD KOG4132 KOG4132 232063 KOG4132 KOG4132, Uroporphyrinogen III synthase UROS/HEM4 [Coenzyme transport and metabolism] 260 matched cddid_all.tbl CDD KOG4133 KOG4133 232064 KOG4133 KOG4133, tRNA splicing endonuclease [Translation, ribosomal structure and biogenesis] 290 matched cddid_all.tbl CDD KOG4134 KOG4134 232065 KOG4134 KOG4134, DNA-dependent RNA polymerase I [Transcription] 253 matched cddid_all.tbl CDD KOG4135 KOG4135 232066 KOG4135 KOG4135, Predicted phosphoglucosamine acetyltransferase [Carbohydrate transport and metabolism] 185 matched cddid_all.tbl CDD KOG4136 KOG4136 232067 KOG4136 KOG4136, Predicted mitochondrial cholesterol transporter [Signal transduction mechanisms, Lipid transport and metabolism] 198 matched cddid_all.tbl CDD KOG4137 KOG4137 232068 KOG4137 KOG4137, Uncharacterized conserved protein [Function unknown] 102 matched cddid_all.tbl CDD KOG4138 KOG4138 232069 KOG4138 KOG4138, Unchracterized conserved protein (estrogen up-regulated protein E2IG2 in human) [General function prediction only] 96 matched cddid_all.tbl CDD KOG4139 KOG4139 232070 KOG4139 KOG4139, Protein kinase essential for the initiation of DNA replication [Replication, recombination and repair, Cell cycle control, cell division, chromosome partitioning] 520 matched cddid_all.tbl CDD KOG4140 KOG4140 232071 KOG4140 KOG4140, Nuclear protein Ataxin-7 [Chromatin structure and dynamics] 659 matched cddid_all.tbl CDD KOG4141 KOG4141 232072 KOG4141 KOG4141, DNA repair and recombination protein RAD52/RAD22 [Replication, recombination and repair] 222 matched cddid_all.tbl CDD KOG4142 KOG4142 232073 KOG4142 KOG4142, Phospholipid methyltransferase [Lipid transport and metabolism] 208 matched cddid_all.tbl CDD KOG4143 KOG4143 232074 KOG4143 KOG4143, Sigma receptor and C-8 sterol isomerase [Signal transduction mechanisms] 218 matched cddid_all.tbl CDD KOG4144 KOG4144 232075 KOG4144 KOG4144, Arylalkylamine N-acetyltransferase [General function prediction only] 190 matched cddid_all.tbl CDD KOG4145 KOG4145 232076 KOG4145 KOG4145, Allantoicase [Nucleotide transport and metabolism] 340 matched cddid_all.tbl CDD KOG4146 KOG4146 232077 KOG4146 KOG4146, Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones] 101 matched cddid_all.tbl CDD KOG4147 KOG4147 232078 KOG4147 KOG4147, Uncharacterized conserved protein [Function unknown] 127 matched cddid_all.tbl CDD KOG4148 KOG4148 232079 KOG4148 KOG4148, Uncharacterized conserved protein [Function unknown] 106 matched cddid_all.tbl CDD KOG4149 KOG4149 232080 KOG4149 KOG4149, Uncharacterized conserved protein [Function unknown] 129 matched cddid_all.tbl CDD KOG4150 KOG4150 232081 KOG4150 KOG4150, Predicted ATP-dependent RNA helicase [RNA processing and modification] 1034 matched cddid_all.tbl CDD KOG4151 KOG4151 232082 KOG4151 KOG4151, Myosin assembly protein/sexual cycle protein and related proteins [Posttranslational modification, protein turnover, chaperones, Cell cycle control, cell division, chromosome partitioning, General function prediction only] 748 matched cddid_all.tbl CDD KOG4152 KOG4152 232083 KOG4152 KOG4152, Host cell transcription factor HCFC1 [Cell cycle control, cell division, chromosome partitioning, Transcription] 830 matched cddid_all.tbl CDD KOG4153 KOG4153 232084 KOG4153 KOG4153, Fructose 1,6-bisphosphate aldolase [Carbohydrate transport and metabolism] 358 matched cddid_all.tbl CDD KOG4154 KOG4154 232085 KOG4154 KOG4154, Arginine-rich protein [General function prediction only] 178 matched cddid_all.tbl CDD KOG4156 KOG4156 232086 KOG4156 KOG4156, Claspin, protein mediating phosphorylation and activation of Chk1 protein kinase in the DNA replication checkpoint response [Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms] 1329 matched cddid_all.tbl CDD KOG4157 KOG4157 232087 KOG4157 KOG4157, beta-1,6-N-acetylglucosaminyltransferase, contains WSC domain [Carbohydrate transport and metabolism, Posttranslational modification, protein turnover, chaperones] 418 matched cddid_all.tbl CDD KOG4158 KOG4158 232088 KOG4158 KOG4158, BRPK/PTEN-induced protein kinase [Signal transduction mechanisms] 598 matched cddid_all.tbl CDD KOG4159 KOG4159 232089 KOG4159 KOG4159, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 398 matched cddid_all.tbl CDD KOG4160 KOG4160 232090 KOG4160 KOG4160, BPI/LBP/CETP family protein [Defense mechanisms] 492 matched cddid_all.tbl CDD KOG4161 KOG4161 232091 KOG4161 KOG4161, Methyl-CpG binding transcription regulators [Transcription, Chromatin structure and dynamics] 272 matched cddid_all.tbl CDD KOG4162 KOG4162 232092 KOG4162 KOG4162, Predicted calmodulin-binding protein [Signal transduction mechanisms] 799 matched cddid_all.tbl CDD KOG4163 KOG4163 232093 KOG4163 KOG4163, Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 551 matched cddid_all.tbl CDD KOG4164 KOG4164 232094 KOG4164 KOG4164, Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning] 497 matched cddid_all.tbl CDD KOG4165 KOG4165 232095 KOG4165 KOG4165, Gamma-glutamyl phosphate reductase [Amino acid transport and metabolism] 433 matched cddid_all.tbl CDD KOG4166 KOG4166 232096 KOG4166 KOG4166, Thiamine pyrophosphate-requiring enzyme [Amino acid transport and metabolism, Coenzyme transport and metabolism] 675 matched cddid_all.tbl CDD KOG4167 KOG4167 232097 KOG4167 KOG4167, Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription] 907 matched cddid_all.tbl CDD KOG4168 KOG4168 232098 KOG4168 KOG4168, Predicted RNA polymerase III subunit C17 [Transcription] 149 matched cddid_all.tbl CDD KOG4169 KOG4169 232099 KOG4169 KOG4169, 15-hydroxyprostaglandin dehydrogenase and related dehydrogenases [Lipid transport and metabolism, General function prediction only] 261 matched cddid_all.tbl CDD KOG4170 KOG4170 232100 KOG4170 KOG4170, 2-enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase/Peroxisomal 3-ketoacyl-CoA-thiolase, sterol-binding domain and related enzymes [Lipid transport and metabolism] 113 matched cddid_all.tbl CDD KOG4171 KOG4171 232101 KOG4171 KOG4171, Adenylate/guanylate kinase [Nucleotide transport and metabolism] 671 matched cddid_all.tbl CDD KOG4172 KOG4172 232102 KOG4172 KOG4172, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 62 matched cddid_all.tbl CDD KOG4173 KOG4173 232103 KOG4173 KOG4173, Alpha-SNAP protein [Intracellular trafficking, secretion, and vesicular transport] 253 matched cddid_all.tbl CDD KOG4174 KOG4174 232104 KOG4174 KOG4174, Uncharacterized conserved protein [Function unknown] 282 matched cddid_all.tbl CDD KOG4175 KOG4175 232105 KOG4175 KOG4175, Tryptophan synthase alpha chain [Amino acid transport and metabolism] 268 matched cddid_all.tbl CDD KOG4176 KOG4176 232106 KOG4176 KOG4176, Uncharacterized conserved protein [Function unknown] 323 matched cddid_all.tbl CDD KOG4177 KOG4177 232107 KOG4177 KOG4177, Ankyrin [Cell wall/membrane/envelope biogenesis] 1143 matched cddid_all.tbl CDD KOG4178 KOG4178 232108 KOG4178 KOG4178, Soluble epoxide hydrolase [Lipid transport and metabolism] 322 matched cddid_all.tbl CDD KOG4179 KOG4179 232109 KOG4179 KOG4179, Lysyl hydrolase/glycosyltransferase family 25 [Posttranslational modification, protein turnover, chaperones] 568 matched cddid_all.tbl CDD KOG4180 KOG4180 232110 KOG4180 KOG4180, Predicted kinase [General function prediction only] 395 matched cddid_all.tbl CDD KOG4181 KOG4181 232111 KOG4181 KOG4181, Uncharacterized conserved protein [Function unknown] 491 matched cddid_all.tbl CDD KOG4182 KOG4182 232112 KOG4182 KOG4182, Uncharacterized conserved protein [Function unknown] 828 matched cddid_all.tbl CDD KOG4183 KOG4183 232113 KOG4183 KOG4183, RNA polymerase I 49 kDa subunit [Transcription] 413 matched cddid_all.tbl CDD KOG4184 KOG4184 232114 KOG4184 KOG4184, Predicted sugar kinase [Carbohydrate transport and metabolism, General function prediction only] 478 matched cddid_all.tbl CDD KOG4185 KOG4185 232115 KOG4185 KOG4185, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 296 matched cddid_all.tbl CDD KOG4186 KOG4186 232116 KOG4186 KOG4186, Peroxisomal biogenesis protein (peroxin) [Intracellular trafficking, secretion, and vesicular transport] 233 matched cddid_all.tbl CDD KOG4187 KOG4187 232117 KOG4187 KOG4187, Proprotein convertase (PC) 2 chaperone involved in secretion (neuroendocrine protein 7B2) [Posttranslational modification, protein turnover, chaperones, Intracellular trafficking, secretion, and vesicular transport] 228 matched cddid_all.tbl CDD KOG4188 KOG4188 232118 KOG4188 KOG4188, Uncharacterized conserved protein [Function unknown] 159 matched cddid_all.tbl CDD KOG4189 KOG4189 232119 KOG4189 KOG4189, Uncharacterized conserved protein [Function unknown] 209 matched cddid_all.tbl CDD KOG4190 KOG4190 232120 KOG4190 KOG4190, Uncharacterized conserved protein [Function unknown] 1034 matched cddid_all.tbl CDD KOG4191 KOG4191 232121 KOG4191 KOG4191, Histone acetyltransferases PCAF/SAGA/ADA, subunit TADA3L/NGG1 [Chromatin structure and dynamics] 516 matched cddid_all.tbl CDD KOG4192 KOG4192 232122 KOG4192 KOG4192, Uncharacterized conserved protein [Function unknown] 134 matched cddid_all.tbl CDD KOG4193 KOG4193 232123 KOG4193 KOG4193, G protein-coupled receptors [Signal transduction mechanisms] 610 matched cddid_all.tbl CDD KOG4194 KOG4194 232124 KOG4194 KOG4194, Membrane glycoprotein LIG-1 [Signal transduction mechanisms] 873 matched cddid_all.tbl CDD KOG4195 KOG4195 232125 KOG4195 KOG4195, Transient receptor potential-related channel 7 [Inorganic ion transport and metabolism] 275 matched cddid_all.tbl CDD KOG4196 KOG4196 232126 KOG4196 KOG4196, bZIP transcription factor MafK [Transcription] 135 matched cddid_all.tbl CDD KOG4198 KOG4198 232127 KOG4198 KOG4198, RNA-binding Ran Zn-finger protein and related proteins [General function prediction only] 280 matched cddid_all.tbl CDD KOG4199 KOG4199 232128 KOG4199 KOG4199, Uncharacterized conserved protein [Function unknown] 461 matched cddid_all.tbl CDD KOG4200 KOG4200 232129 KOG4200 KOG4200, Uncharacterized conserved protein [Function unknown] 398 matched cddid_all.tbl CDD KOG4201 KOG4201 232130 KOG4201 KOG4201, Anthranilate synthase component II [Amino acid transport and metabolism] 289 matched cddid_all.tbl CDD KOG4202 KOG4202 232131 KOG4202 KOG4202, Phosphoribosylanthranilate isomerase [Amino acid transport and metabolism] 227 matched cddid_all.tbl CDD KOG4203 KOG4203 232132 KOG4203 KOG4203, Armadillo/beta-Catenin/plakoglobin [Signal transduction mechanisms, Cytoskeleton] 473 matched cddid_all.tbl CDD KOG4204 KOG4204 232133 KOG4204 KOG4204, Histone deacetylase complex, SIN3 component [Chromatin structure and dynamics] 231 matched cddid_all.tbl CDD KOG4205 KOG4205 232134 KOG4205 KOG4205, RNA-binding protein musashi/mRNA cleavage and polyadenylation factor I complex, subunit HRP1 [RNA processing and modification] 311 matched cddid_all.tbl CDD KOG4206 KOG4206 232135 KOG4206 KOG4206, Spliceosomal protein snRNP-U1A/U2B [RNA processing and modification] 221 matched cddid_all.tbl CDD KOG4207 KOG4207 232136 KOG4207 KOG4207, Predicted splicing factor, SR protein superfamily [RNA processing and modification] 256 matched cddid_all.tbl CDD KOG4208 KOG4208 232137 KOG4208 KOG4208, Nucleolar RNA-binding protein NIFK [General function prediction only] 214 matched cddid_all.tbl CDD KOG4209 KOG4209 232138 KOG4209 KOG4209, Splicing factor RNPS1, SR protein superfamily [RNA processing and modification] 231 matched cddid_all.tbl CDD KOG4210 KOG4210 232139 KOG4210 KOG4210, Nuclear localization sequence binding protein [Transcription] 285 matched cddid_all.tbl CDD KOG4211 KOG4211 232140 KOG4211 KOG4211, Splicing factor hnRNP-F and related RNA-binding proteins [RNA processing and modification] 510 matched cddid_all.tbl CDD KOG4212 KOG4212 232141 KOG4212 KOG4212, RNA-binding protein hnRNP-M [RNA processing and modification] 608 matched cddid_all.tbl CDD KOG4213 KOG4213 232142 KOG4213 KOG4213, RNA-binding protein La [RNA processing and modification] 205 matched cddid_all.tbl CDD KOG4214 KOG4214 232143 KOG4214 KOG4214, Myotrophin and similar proteins [Transcription] 117 matched cddid_all.tbl CDD KOG4215 KOG4215 232144 KOG4215 KOG4215, Hepatocyte nuclear factor 4 and similar steroid hormone receptors [Transcription] 432 matched cddid_all.tbl CDD KOG4216 KOG4216 232145 KOG4216 KOG4216, Steroid hormone nuclear receptor [Transcription] 479 matched cddid_all.tbl CDD KOG4217 KOG4217 232146 KOG4217 KOG4217, Nuclear receptors of the nerve growth factor-induced protein B type [Transcription] 605 matched cddid_all.tbl CDD KOG4218 KOG4218 232147 KOG4218 KOG4218, Nuclear hormone receptor betaFTZ-F1 [Transcription] 475 matched cddid_all.tbl CDD KOG4219 KOG4219 232148 KOG4219 KOG4219, G protein-coupled receptor [Signal transduction mechanisms] 423 matched cddid_all.tbl CDD KOG4220 KOG4220 232149 KOG4220 KOG4220, Muscarinic acetylcholine receptor [Signal transduction mechanisms] 503 matched cddid_all.tbl CDD KOG4221 KOG4221 232150 KOG4221 KOG4221, Receptor mediating netrin-dependent axon guidance [Signal transduction mechanisms] 1381 matched cddid_all.tbl CDD KOG4222 KOG4222 232151 KOG4222 KOG4222, Axon guidance receptor Dscam [Signal transduction mechanisms] 1281 matched cddid_all.tbl CDD KOG4223 KOG4223 232152 KOG4223 KOG4223, Reticulocalbin, calumenin, DNA supercoiling factor, and related Ca2+-binding proteins of the CREC family (EF-Hand protein superfamily) [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 325 matched cddid_all.tbl CDD KOG4224 KOG4224 232153 KOG4224 KOG4224, Armadillo repeat protein VAC8 required for vacuole fusion, inheritance and cytosol-to-vacuole protein targeting [Intracellular trafficking, secretion, and vesicular transport] 550 matched cddid_all.tbl CDD KOG4225 KOG4225 232154 KOG4225 KOG4225, Sorbin and SH3 domain-containing protein [Signal transduction mechanisms] 489 matched cddid_all.tbl CDD KOG4226 KOG4226 232155 KOG4226 KOG4226, Adaptor protein NCK/Dock, contains SH2 and SH3 domains [Signal transduction mechanisms] 379 matched cddid_all.tbl CDD KOG4227 KOG4227 232156 KOG4227 KOG4227, WD40 repeat protein [General function prediction only] 609 matched cddid_all.tbl CDD KOG4228 KOG4228 232157 KOG4228 KOG4228, Protein tyrosine phosphatase [Signal transduction mechanisms] 1087 matched cddid_all.tbl CDD KOG4229 KOG4229 232158 KOG4229 KOG4229, Myosin VII, myosin IXB and related myosins [Cell motility] 1062 matched cddid_all.tbl CDD KOG4230 KOG4230 232159 KOG4230 KOG4230, C1-tetrahydrofolate synthase [Coenzyme transport and metabolism] 935 matched cddid_all.tbl CDD KOG4231 KOG4231 232160 KOG4231 KOG4231, Intracellular membrane-bound Ca2+-independent phospholipase A2 [Lipid transport and metabolism] 763 matched cddid_all.tbl CDD KOG4232 KOG4232 232161 KOG4232 KOG4232, Delta 6-fatty acid desaturase/delta-8 sphingolipid desaturase [Lipid transport and metabolism] 430 matched cddid_all.tbl CDD KOG4233 KOG4233 232162 KOG4233 KOG4233, DNA-bridging protein BAF [Chromatin structure and dynamics, Replication, recombination and repair] 90 matched cddid_all.tbl CDD KOG4234 KOG4234 232163 KOG4234 KOG4234, TPR repeat-containing protein [General function prediction only] 271 matched cddid_all.tbl CDD KOG4235 KOG4235 232164 KOG4235 KOG4235, Mitochondrial thymidine kinase 2/deoxyguanosine kinase [Nucleotide transport and metabolism] 244 matched cddid_all.tbl CDD KOG4236 KOG4236 232165 KOG4236 KOG4236, Serine/threonine protein kinase PKC mu/PKD and related proteins [Signal transduction mechanisms] 888 matched cddid_all.tbl CDD KOG4237 KOG4237 232166 KOG4237 KOG4237, Extracellular matrix protein slit, contains leucine-rich and EGF-like repeats [Extracellular structures, Signal transduction mechanisms] 498 matched cddid_all.tbl CDD KOG4238 KOG4238 232167 KOG4238 KOG4238, Bifunctional ATP sulfurylase/adenosine 5'-phosphosulfate kinase [Nucleotide transport and metabolism] 627 matched cddid_all.tbl CDD KOG4239 KOG4239 232168 KOG4239 KOG4239, Ras GTPase effector RASSF2 [Signal transduction mechanisms] 348 matched cddid_all.tbl CDD KOG4240 KOG4240 232169 KOG4240 KOG4240, Multidomain protein, contains SPEC repeats, PH, SH3, and separate rac-specific and rho-specific guanine nucleotide exchange factor domains [Signal transduction mechanisms] 1025 matched cddid_all.tbl CDD KOG4241 KOG4241 232170 KOG4241 KOG4241, Mitochondrial ribosomal protein L10 [Translation, ribosomal structure and biogenesis] 245 matched cddid_all.tbl CDD KOG4242 KOG4242 232171 KOG4242 KOG4242, Predicted myosin-I-binding protein [Cell motility] 553 matched cddid_all.tbl CDD KOG4243 KOG4243 232172 KOG4243 KOG4243, Macrophage maturation-associated protein [Defense mechanisms] 298 matched cddid_all.tbl CDD KOG4244 KOG4244 232173 KOG4244 KOG4244, Failed axon connections (fax) protein/glutathione S-transferase-like protein [Signal transduction mechanisms] 281 matched cddid_all.tbl CDD KOG4245 KOG4245 232174 KOG4245 KOG4245, Predicted metal-dependent hydrolase of the TIM-barrel fold [General function prediction only] 297 matched cddid_all.tbl CDD KOG4246 KOG4246 232175 KOG4246 KOG4246, Predicted DNA-binding protein, contains SAP domain [General function prediction only] 1194 matched cddid_all.tbl CDD KOG4247 KOG4247 232176 KOG4247 KOG4247, Mitochondrial DNA polymerase accessory subunit [Replication, recombination and repair] 175 matched cddid_all.tbl CDD KOG4248 KOG4248 232177 KOG4248 KOG4248, Ubiquitin-like protein, regulator of apoptosis [Posttranslational modification, protein turnover, chaperones] 1143 matched cddid_all.tbl CDD KOG4249 KOG4249 232178 KOG4249 KOG4249, Uncharacterized conserved protein [Function unknown] 408 matched cddid_all.tbl CDD KOG4250 KOG4250 232179 KOG4250 KOG4250, TANK binding protein kinase TBK1 [Signal transduction mechanisms] 732 matched cddid_all.tbl CDD KOG4251 KOG4251 232180 KOG4251 KOG4251, Calcium binding protein [General function prediction only] 362 matched cddid_all.tbl CDD KOG4252 KOG4252 232181 KOG4252 KOG4252, GTP-binding protein [Signal transduction mechanisms] 246 matched cddid_all.tbl CDD KOG4253 KOG4253 232182 KOG4253 KOG4253, Tryptophan-rich basic nuclear protein [General function prediction only] 175 matched cddid_all.tbl CDD KOG4254 KOG4254 232183 KOG4254 KOG4254, Phytoene desaturase [Coenzyme transport and metabolism] 561 matched cddid_all.tbl CDD KOG4255 KOG4255 232184 KOG4255 KOG4255, Uncharacterized conserved protein [Function unknown] 439 matched cddid_all.tbl CDD KOG4256 KOG4256 232185 KOG4256 KOG4256, Kinetochore component [Cell cycle control, cell division, chromosome partitioning] 2209 matched cddid_all.tbl CDD KOG4257 KOG4257 232186 KOG4257 KOG4257, Focal adhesion tyrosine kinase FAK, contains FERM domain [Signal transduction mechanisms] 974 matched cddid_all.tbl CDD KOG4258 KOG4258 232187 KOG4258 KOG4258, Insulin/growth factor receptor (contains protein kinase domain) [Signal transduction mechanisms] 1025 matched cddid_all.tbl CDD KOG4259 KOG4259 232188 KOG4259 KOG4259, Putative nucleic acid-binding protein Hcc-1/proliferation associated cytokine-inducible protein, contains SAP domain [Cell cycle control, cell division, chromosome partitioning] 260 matched cddid_all.tbl CDD KOG4260 KOG4260 232189 KOG4260 KOG4260, Uncharacterized conserved protein [Function unknown] 350 matched cddid_all.tbl CDD KOG4261 KOG4261 232190 KOG4261 KOG4261, Talin [Cytoskeleton] 1003 matched cddid_all.tbl CDD KOG4262 KOG4262 232191 KOG4262 KOG4262, Uncharacterized conserved protein [Function unknown] 496 matched cddid_all.tbl CDD KOG4263 KOG4263 232192 KOG4263 KOG4263, Putative receptor CCR1 [Signal transduction mechanisms] 299 matched cddid_all.tbl CDD KOG4264 KOG4264 232193 KOG4264 KOG4264, Nucleo-cytoplasmic protein MLN51 [General function prediction only] 694 matched cddid_all.tbl CDD KOG4265 KOG4265 232194 KOG4265 KOG4265, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 349 matched cddid_all.tbl CDD KOG4266 KOG4266 232195 KOG4266 KOG4266, Subtilisin kexin isozyme-1/site 1 protease, subtilase superfamily [Posttranslational modification, protein turnover, chaperones] 1033 matched cddid_all.tbl CDD KOG4267 KOG4267 232196 KOG4267 KOG4267, Predicted membrane protein [Function unknown] 110 matched cddid_all.tbl CDD KOG4268 KOG4268 232197 KOG4268 KOG4268, Uncharacterized conserved protein containing PAP2 domain [Function unknown] 189 matched cddid_all.tbl CDD KOG4269 KOG4269 232198 KOG4269 KOG4269, Rac GTPase-activating protein BCR/ABR [Signal transduction mechanisms] 1112 matched cddid_all.tbl CDD KOG4270 KOG4270 232199 KOG4270 KOG4270, GTPase-activator protein [Signal transduction mechanisms] 577 matched cddid_all.tbl CDD KOG4271 KOG4271 232200 KOG4271 KOG4271, Rho-GTPase activating protein [Signal transduction mechanisms] 1100 matched cddid_all.tbl CDD KOG4272 KOG4272 232201 KOG4272 KOG4272, Predicted GTP-binding protein [General function prediction only] 164 matched cddid_all.tbl CDD KOG4273 KOG4273 232202 KOG4273 KOG4273, Uncharacterized conserved protein [Function unknown] 418 matched cddid_all.tbl CDD KOG4274 KOG4274 232203 KOG4274 KOG4274, Positive cofactor 2 (PC2), subunit of a multiprotein coactivator of RNA polymerase II [Transcription] 742 matched cddid_all.tbl CDD KOG4275 KOG4275 232204 KOG4275 KOG4275, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 350 matched cddid_all.tbl CDD KOG4276 KOG4276 232205 KOG4276 KOG4276, Predicted hormone receptor interactor [General function prediction only] 113 matched cddid_all.tbl CDD KOG4277 KOG4277 232206 KOG4277 KOG4277, Uncharacterized conserved protein, contains thioredoxin domain [General function prediction only] 468 matched cddid_all.tbl CDD KOG4278 KOG4278 232207 KOG4278 KOG4278, Protein tyrosine kinase [Signal transduction mechanisms] 1157 matched cddid_all.tbl CDD KOG4279 KOG4279 232208 KOG4279 KOG4279, Serine/threonine protein kinase [Signal transduction mechanisms] 1226 matched cddid_all.tbl CDD KOG4280 KOG4280 232209 KOG4280 KOG4280, Kinesin-like protein [Cytoskeleton] 574 matched cddid_all.tbl CDD KOG4281 KOG4281 232210 KOG4281 KOG4281, Uncharacterized conserved protein [Function unknown] 236 matched cddid_all.tbl CDD KOG4282 KOG4282 232211 KOG4282 KOG4282, Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription] 345 matched cddid_all.tbl CDD KOG4283 KOG4283 232212 KOG4283 KOG4283, Transcription-coupled repair protein CSA, contains WD40 domain [Transcription, Replication, recombination and repair] 397 matched cddid_all.tbl CDD KOG4284 KOG4284 232213 KOG4284 KOG4284, DEAD box protein [Transcription] 980 matched cddid_all.tbl CDD KOG4285 KOG4285 232214 KOG4285 KOG4285, Mitotic phosphoprotein [Cell cycle control, cell division, chromosome partitioning] 350 matched cddid_all.tbl CDD KOG4286 KOG4286 232215 KOG4286 KOG4286, Dystrophin-like protein [Cell motility, Signal transduction mechanisms, Cytoskeleton] 966 matched cddid_all.tbl CDD KOG4287 KOG4287 232216 KOG4287 KOG4287, Pectin acetylesterase and similar proteins [Cell wall/membrane/envelope biogenesis] 402 matched cddid_all.tbl CDD KOG4288 KOG4288 232217 KOG4288 KOG4288, Predicted oxidoreductase [General function prediction only] 283 matched cddid_all.tbl CDD KOG4289 KOG4289 232218 KOG4289 KOG4289, Cadherin EGF LAG seven-pass G-type receptor [Signal transduction mechanisms] 2531 matched cddid_all.tbl CDD KOG4290 KOG4290 232219 KOG4290 KOG4290, Predicted membrane protein [Function unknown] 429 matched cddid_all.tbl CDD KOG4291 KOG4291 232220 KOG4291 KOG4291, Mucin/alpha-tectorin [Extracellular structures] 1043 matched cddid_all.tbl CDD KOG4292 KOG4292 232221 KOG4292 KOG4292, Cubilin, multiligand receptor mediating cobalamin absorption [Coenzyme transport and metabolism] 454 matched cddid_all.tbl CDD KOG4293 KOG4293 232222 KOG4293 KOG4293, Predicted membrane protein, contains DoH and Cytochrome b-561/ferric reductase transmembrane domains [Signal transduction mechanisms] 403 matched cddid_all.tbl CDD KOG4294 KOG4294 232223 KOG4294 KOG4294, Non voltage-gated ion channels (DEG/ENaC family) [Inorganic ion transport and metabolism, Signal transduction mechanisms] 520 matched cddid_all.tbl CDD KOG4295 KOG4295 232224 KOG4295 KOG4295, Serine proteinase inhibitor (KU family) [Posttranslational modification, protein turnover, chaperones] 295 matched cddid_all.tbl CDD KOG4296 KOG4296 232225 KOG4296 KOG4296, Epithelin/granulin [Signal transduction mechanisms] 90 matched cddid_all.tbl CDD KOG4297 KOG4297 232226 KOG4297 KOG4297, C-type lectin [Signal transduction mechanisms, Defense mechanisms] 170 matched cddid_all.tbl CDD KOG4298 KOG4298 232227 KOG4298 KOG4298, CAP-binding protein complex interacting protein 2 [RNA processing and modification] 245 matched cddid_all.tbl CDD KOG4299 KOG4299 232228 KOG4299 KOG4299, PHD Zn-finger protein [General function prediction only] 613 matched cddid_all.tbl CDD KOG4300 KOG4300 232229 KOG4300 KOG4300, Predicted methyltransferase [General function prediction only] 252 matched cddid_all.tbl CDD KOG4301 KOG4301 232230 KOG4301 KOG4301, Beta-dystrobrevin [Cytoskeleton] 434 matched cddid_all.tbl CDD KOG4302 KOG4302 232231 KOG4302 KOG4302, Microtubule-associated protein essential for anaphase spindle elongation [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton] 660 matched cddid_all.tbl CDD KOG4303 KOG4303 232232 KOG4303 KOG4303, Vesicular inhibitory amino acid transporter [Amino acid transport and metabolism, Signal transduction mechanisms] 524 matched cddid_all.tbl CDD KOG4304 KOG4304 232233 KOG4304 KOG4304, Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription] 250 matched cddid_all.tbl CDD KOG4305 KOG4305 232234 KOG4305 KOG4305, RhoGEF GTPase [Signal transduction mechanisms] 1029 matched cddid_all.tbl CDD KOG4306 KOG4306 232235 KOG4306 KOG4306, Glycosylphosphatidylinositol-specific phospholipase C [Signal transduction mechanisms] 306 matched cddid_all.tbl CDD KOG4307 KOG4307 232236 KOG4307 KOG4307, RNA binding protein RBM12/SWAN [General function prediction only] 944 matched cddid_all.tbl CDD KOG4308 KOG4308 232237 KOG4308 KOG4308, LRR-containing protein [Function unknown] 478 matched cddid_all.tbl CDD KOG4309 KOG4309 232238 KOG4309 KOG4309, Transcription mediator-related factor [Transcription] 217 matched cddid_all.tbl CDD KOG4310 KOG4310 232239 KOG4310 KOG4310, Synapse-associated protein [Intracellular trafficking, secretion, and vesicular transport] 373 matched cddid_all.tbl CDD KOG4311 KOG4311 232240 KOG4311 KOG4311, Histidinol dehydrogenase [Amino acid transport and metabolism] 359 matched cddid_all.tbl CDD KOG4312 KOG4312 232241 KOG4312 KOG4312, Predicted acyltransferase [General function prediction only] 449 matched cddid_all.tbl CDD KOG4313 KOG4313 232242 KOG4313 KOG4313, Thiamine pyrophosphokinase [Nucleotide transport and metabolism] 306 matched cddid_all.tbl CDD KOG4314 KOG4314 232243 KOG4314 KOG4314, Predicted carbohydrate/phosphate translocator [General function prediction only] 290 matched cddid_all.tbl CDD KOG4315 KOG4315 232244 KOG4315 KOG4315, G-patch nucleic acid binding protein [General function prediction only] 455 matched cddid_all.tbl CDD KOG4316 KOG4316 232245 KOG4316 KOG4316, Uncharacterized conserved protein [Function unknown] 172 matched cddid_all.tbl CDD KOG4317 KOG4317 232246 KOG4317 KOG4317, Predicted Zn-finger protein [Function unknown] 383 matched cddid_all.tbl CDD KOG4318 KOG4318 232247 KOG4318 KOG4318, Bicoid mRNA stability factor [RNA processing and modification] 1088 matched cddid_all.tbl CDD KOG4319 KOG4319 232248 KOG4319 KOG4319, DNA-binding nuclear protein p8 [Transcription] 70 matched cddid_all.tbl CDD KOG4320 KOG4320 232249 KOG4320 KOG4320, Uncharacterized conserved protein [Function unknown] 253 matched cddid_all.tbl CDD KOG4321 KOG4321 232250 KOG4321 KOG4321, Predicted phosphate acyltransferases [Lipid transport and metabolism] 279 matched cddid_all.tbl CDD KOG4322 KOG4322 232251 KOG4322 KOG4322, Anaphase-promoting complex (APC), subunit 5 [Cell cycle control, cell division, chromosome partitioning, Posttranslational modification, protein turnover, chaperones] 482 matched cddid_all.tbl CDD KOG4323 KOG4323 232252 KOG4323 KOG4323, Polycomb-like PHD Zn-finger protein [General function prediction only] 464 matched cddid_all.tbl CDD KOG4324 KOG4324 232253 KOG4324 KOG4324, Guanine nucleotide exchange factor [Intracellular trafficking, secretion, and vesicular transport] 476 matched cddid_all.tbl CDD KOG4325 KOG4325 232254 KOG4325 KOG4325, Uncharacterized conserved protein [Function unknown] 212 matched cddid_all.tbl CDD KOG4326 KOG4326 232255 KOG4326 KOG4326, Mitochondrial F1F0-ATP synthase, subunit e [Energy production and conversion] 81 matched cddid_all.tbl CDD KOG4327 KOG4327 232256 KOG4327 KOG4327, mRNA splicing protein SMN (survival motor neuron) [RNA processing and modification] 218 matched cddid_all.tbl CDD KOG4328 KOG4328 232257 KOG4328 KOG4328, WD40 protein [Function unknown] 498 matched cddid_all.tbl CDD KOG4329 KOG4329 232258 KOG4329 KOG4329, DNA-binding protein [General function prediction only] 445 matched cddid_all.tbl CDD KOG4330 KOG4330 232259 KOG4330 KOG4330, Uncharacterized conserved protein [Function unknown] 206 matched cddid_all.tbl CDD KOG4331 KOG4331 232260 KOG4331 KOG4331, Polytopic membrane protein Prominin [General function prediction only] 865 matched cddid_all.tbl CDD KOG4332 KOG4332 232261 KOG4332 KOG4332, Predicted sugar transporter [Carbohydrate transport and metabolism] 454 matched cddid_all.tbl CDD KOG4333 KOG4333 232262 KOG4333 KOG4333, Nuclear DEAF-1 related transcriptional regulator (suppressin) and related SAND domain proteins [Cell cycle control, cell division, chromosome partitioning, Transcription] 425 matched cddid_all.tbl CDD KOG4334 KOG4334 232263 KOG4334 KOG4334, Uncharacterized conserved protein, contains double-stranded RNA-binding motif and WW domain [General function prediction only] 650 matched cddid_all.tbl CDD KOG4335 KOG4335 232264 KOG4335 KOG4335, FERM domain-containing protein KRIT1 [Signal transduction mechanisms] 558 matched cddid_all.tbl CDD KOG4336 KOG4336 232265 KOG4336 KOG4336, TBP-associated transcription factor Prodos [Transcription] 323 matched cddid_all.tbl CDD KOG4337 KOG4337 232266 KOG4337 KOG4337, Microsomal triglyceride transfer protein [Lipid transport and metabolism, Intracellular trafficking, secretion, and vesicular transport] 896 matched cddid_all.tbl CDD KOG4338 KOG4338 232267 KOG4338 KOG4338, Predicted lipoprotein [Lipid transport and metabolism] 1680 matched cddid_all.tbl CDD KOG4339 KOG4339 232268 KOG4339 KOG4339, RPEL repeat-containing protein [General function prediction only] 533 matched cddid_all.tbl CDD KOG4340 KOG4340 232269 KOG4340 KOG4340, Uncharacterized conserved protein [Function unknown] 422 matched cddid_all.tbl CDD KOG4341 KOG4341 232270 KOG4341 KOG4341, F-box protein containing LRR [General function prediction only] 483 matched cddid_all.tbl CDD KOG4342 KOG4342 232271 KOG4342 KOG4342, Alpha-mannosidase [Carbohydrate transport and metabolism] 1078 matched cddid_all.tbl CDD KOG4343 KOG4343 232272 KOG4343 KOG4343, bZIP transcription factor ATF6 [Transcription] 655 matched cddid_all.tbl CDD KOG4344 KOG4344 232273 KOG4344 KOG4344, Uncharacterized conserved protein [Function unknown] 1121 matched cddid_all.tbl CDD KOG4345 KOG4345 232274 KOG4345 KOG4345, NF-kappa B regulator AP20/Cezanne [Signal transduction mechanisms] 774 matched cddid_all.tbl CDD KOG4346 KOG4346 232275 KOG4346 KOG4346, Uncharacterized conserved protein [Function unknown] 849 matched cddid_all.tbl CDD KOG4347 KOG4347 232276 KOG4347 KOG4347, GTPase-activating protein VRP [General function prediction only] 671 matched cddid_all.tbl CDD KOG4348 KOG4348 232277 KOG4348 KOG4348, Adaptor protein CMS/SETA [Signal transduction mechanisms] 627 matched cddid_all.tbl CDD KOG4349 KOG4349 232278 KOG4349 KOG4349, Uncharacterized conserved protein [Function unknown] 143 matched cddid_all.tbl CDD KOG4350 KOG4350 232279 KOG4350 KOG4350, Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only] 620 matched cddid_all.tbl CDD KOG4351 KOG4351 232280 KOG4351 KOG4351, Uncharacterized conserved protein [Function unknown] 244 matched cddid_all.tbl CDD KOG4352 KOG4352 232281 KOG4352 KOG4352, Fas-mediated apoptosis inhibitor FAIM [Signal transduction mechanisms] 187 matched cddid_all.tbl CDD KOG4353 KOG4353 232282 KOG4353 KOG4353, RNA export factor NXT1 [RNA processing and modification] 139 matched cddid_all.tbl CDD KOG4354 KOG4354 232283 KOG4354 KOG4354, N-acetyl-gamma-glutamyl-phosphate reductase [Amino acid transport and metabolism] 340 matched cddid_all.tbl CDD KOG4355 KOG4355 232284 KOG4355 KOG4355, Predicted Fe-S oxidoreductase [General function prediction only] 547 matched cddid_all.tbl CDD KOG4356 KOG4356 232285 KOG4356 KOG4356, Uncharacterized conserved protein [Function unknown] 310 matched cddid_all.tbl CDD KOG4357 KOG4357 232286 KOG4357 KOG4357, Uncharacterized conserved protein (involved in mesoderm differentiation in humans) [General function prediction only] 164 matched cddid_all.tbl CDD KOG4358 KOG4358 232287 KOG4358 KOG4358, Uncharacterized conserved protein [Function unknown] 584 matched cddid_all.tbl CDD KOG4359 KOG4359 232288 KOG4359 KOG4359, Protein kinase C inhibitor-like protein [General function prediction only] 166 matched cddid_all.tbl CDD KOG4360 KOG4360 232289 KOG4360 KOG4360, Uncharacterized coiled coil protein [Function unknown] 596 matched cddid_all.tbl CDD KOG4361 KOG4361 232290 KOG4361 KOG4361, BCL2-associated athanogene-like proteins and related BAG family chaperone regulators [Signal transduction mechanisms] 344 matched cddid_all.tbl CDD KOG4362 KOG4362 232291 KOG4362 KOG4362, Transcriptional regulator BRCA1 [Replication, recombination and repair, Transcription] 684 matched cddid_all.tbl CDD KOG4363 KOG4363 232292 KOG4363 KOG4363, Putative growth response protein [Signal transduction mechanisms] 270 matched cddid_all.tbl CDD KOG4364 KOG4364 232293 KOG4364 KOG4364, Chromatin assembly factor-I [Chromatin structure and dynamics] 811 matched cddid_all.tbl CDD KOG4365 KOG4365 232294 KOG4365 KOG4365, Uncharacterized conserved protein [Function unknown] 572 matched cddid_all.tbl CDD KOG4366 KOG4366 232295 KOG4366 KOG4366, Predicted thioesterase [General function prediction only] 213 matched cddid_all.tbl CDD KOG4367 KOG4367 232296 KOG4367 KOG4367, Predicted Zn-finger protein [Function unknown] 699 matched cddid_all.tbl CDD KOG4368 KOG4368 232297 KOG4368 KOG4368, Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only] 757 matched cddid_all.tbl CDD KOG4369 KOG4369 232298 KOG4369 KOG4369, RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms] 2131 matched cddid_all.tbl CDD KOG4370 KOG4370 232299 KOG4370 KOG4370, Ral-GTPase effector RLIP76 [Signal transduction mechanisms] 514 matched cddid_all.tbl CDD KOG4371 KOG4371 232300 KOG4371 KOG4371, Membrane-associated protein tyrosine phosphatase PTP-BAS and related proteins, contain FERM domain [Signal transduction mechanisms] 1332 matched cddid_all.tbl CDD KOG4372 KOG4372 232301 KOG4372 KOG4372, Predicted alpha/beta hydrolase [General function prediction only] 405 matched cddid_all.tbl CDD KOG4373 KOG4373 232302 KOG4373 KOG4373, Predicted 3'-5' exonuclease [General function prediction only] 319 matched cddid_all.tbl CDD KOG4374 KOG4374 232303 KOG4374 KOG4374, RNA-binding protein Bicaudal-C [RNA processing and modification] 216 matched cddid_all.tbl CDD KOG4375 KOG4375 232304 KOG4375 KOG4375, Scaffold protein Shank and related SAM domain proteins [Signal transduction mechanisms] 272 matched cddid_all.tbl CDD KOG4376 KOG4376 232305 KOG4376 KOG4376, Uncharacterized conserved protein [Function unknown] 161 matched cddid_all.tbl CDD KOG4377 KOG4377 232306 KOG4377 KOG4377, Zn-finger protein [General function prediction only] 480 matched cddid_all.tbl CDD KOG4378 KOG4378 232307 KOG4378 KOG4378, Nuclear protein COP1 [Signal transduction mechanisms] 673 matched cddid_all.tbl CDD KOG4379 KOG4379 232308 KOG4379 KOG4379, Uncharacterized conserved protein (tumor antigen CML66 in humans) [Function unknown] 596 matched cddid_all.tbl CDD KOG4380 KOG4380 232309 KOG4380 KOG4380, Carnitine deficiency associated protein [General function prediction only] 244 matched cddid_all.tbl CDD KOG4381 KOG4381 232310 KOG4381 KOG4381, RUN domain-containing protein [Signal transduction mechanisms] 368 matched cddid_all.tbl CDD KOG4382 KOG4382 232311 KOG4382 KOG4382, Uncharacterized conserved protein, contains DTW domain [Function unknown] 276 matched cddid_all.tbl CDD KOG4383 KOG4383 232312 KOG4383 KOG4383, Uncharacterized conserved protein [Function unknown] 1354 matched cddid_all.tbl CDD KOG4384 KOG4384 232313 KOG4384 KOG4384, Uncharacterized SAM domain protein [General function prediction only] 361 matched cddid_all.tbl CDD KOG4385 KOG4385 232314 KOG4385 KOG4385, Predicted forkhead transcription factor [Transcription] 581 matched cddid_all.tbl CDD KOG4386 KOG4386 232315 KOG4386 KOG4386, Uncharacterized conserved protein [Function unknown] 809 matched cddid_all.tbl CDD KOG4387 KOG4387 232316 KOG4387 KOG4387, Ornithine decarboxylase antizyme [Amino acid transport and metabolism] 191 matched cddid_all.tbl CDD KOG4388 KOG4388 232317 KOG4388 KOG4388, Hormone-sensitive lipase HSL [Lipid transport and metabolism] 880 matched cddid_all.tbl CDD KOG4389 KOG4389 232318 KOG4389 KOG4389, Acetylcholinesterase/Butyrylcholinesterase [Signal transduction mechanisms] 601 matched cddid_all.tbl CDD KOG4390 KOG4390 232319 KOG4390 KOG4390, Voltage-gated A-type K+ channel KCND [Inorganic ion transport and metabolism] 632 matched cddid_all.tbl CDD KOG4391 KOG4391 232320 KOG4391 KOG4391, Predicted alpha/beta hydrolase BEM46 [General function prediction only] 300 matched cddid_all.tbl CDD KOG4392 KOG4392 232321 KOG4392 KOG4392, RNA polymerase, subunit L [Transcription] 117 matched cddid_all.tbl CDD KOG4393 KOG4393 232322 KOG4393 KOG4393, Predicted pseudouridylate synthase [RNA processing and modification, Translation, ribosomal structure and biogenesis] 295 matched cddid_all.tbl CDD KOG4394 KOG4394 232323 KOG4394 KOG4394, RNase P subunit that is not also a subunit of RNase MRP, involved in pre-tRNA processing [RNA processing and modification] 116 matched cddid_all.tbl CDD KOG4395 KOG4395 232324 KOG4395 KOG4395, Transcription factor Atonal, contains HTH domain [Transcription] 285 matched cddid_all.tbl CDD KOG4396 KOG4396 232325 KOG4396 KOG4396, Predicted membrane-anchored protein [Function unknown] 691 matched cddid_all.tbl CDD KOG4397 KOG4397 232326 KOG4397 KOG4397, Uncharacterized conserved protein [Function unknown] 213 matched cddid_all.tbl CDD KOG4398 KOG4398 232327 KOG4398 KOG4398, Predicted coiled-coil protein [General function prediction only] 359 matched cddid_all.tbl CDD KOG4399 KOG4399 232328 KOG4399 KOG4399, C2HC-type Zn-finger protein [General function prediction only] 325 matched cddid_all.tbl CDD KOG4400 KOG4400 232329 KOG4400 KOG4400, E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones] 261 matched cddid_all.tbl CDD KOG4401 KOG4401 232330 KOG4401 KOG4401, Uncharacterized conserved protein [Function unknown] 184 matched cddid_all.tbl CDD KOG4402 KOG4402 232331 KOG4402 KOG4402, Uncharacterized conserved protein [Function unknown] 144 matched cddid_all.tbl CDD KOG4403 KOG4403 232332 KOG4403 KOG4403, Cell surface glycoprotein STIM, contains SAM domain [General function prediction only] 575 matched cddid_all.tbl CDD KOG4404 KOG4404 232333 KOG4404 KOG4404, Tandem pore domain K+ channel TASK3/THIK-1 [Inorganic ion transport and metabolism] 350 matched cddid_all.tbl CDD KOG4405 KOG4405 232334 KOG4405 KOG4405, GDP dissociation inhibitor [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 547 matched cddid_all.tbl CDD KOG4406 KOG4406 232335 KOG4406 KOG4406, CDC42 Rho GTPase-activating protein [Signal transduction mechanisms, Cytoskeleton] 467 matched cddid_all.tbl CDD KOG4407 KOG4407 232336 KOG4407 KOG4407, Predicted Rho GTPase-activating protein [General function prediction only] 1973 matched cddid_all.tbl CDD KOG4408 KOG4408 232337 KOG4408 KOG4408, Putative Mg2+ and Co2+ transporter CorD [Inorganic ion transport and metabolism] 386 matched cddid_all.tbl CDD KOG4409 KOG4409 232338 KOG4409 KOG4409, Predicted hydrolase/acyltransferase (alpha/beta hydrolase superfamily) [General function prediction only] 365 matched cddid_all.tbl CDD KOG4410 KOG4410 232339 KOG4410 KOG4410, 5-formyltetrahydrofolate cyclo-ligase [Coenzyme transport and metabolism] 396 matched cddid_all.tbl CDD KOG4411 KOG4411 232340 KOG4411 KOG4411, Phytoene/squalene synthetase [Lipid transport and metabolism] 292 matched cddid_all.tbl CDD KOG4412 KOG4412 232341 KOG4412 KOG4412, 26S proteasome regulatory complex, subunit PSMD10 [Posttranslational modification, protein turnover, chaperones] 226 matched cddid_all.tbl CDD KOG4413 KOG4413 232342 KOG4413 KOG4413, 26S proteasome regulatory complex, subunit PSMD5 [Posttranslational modification, protein turnover, chaperones] 524 matched cddid_all.tbl CDD KOG4414 KOG4414 232343 KOG4414 KOG4414, COP9 signalosome, subunit CSN8 [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms] 197 matched cddid_all.tbl CDD KOG4415 KOG4415 232344 KOG4415 KOG4415, Uncharacterized conserved protein [Function unknown] 247 matched cddid_all.tbl CDD KOG4416 KOG4416 232345 KOG4416 KOG4416, Uncharacterized conserved protein [Function unknown] 605 matched cddid_all.tbl CDD KOG4417 KOG4417 232346 KOG4417 KOG4417, Predicted endonuclease [General function prediction only] 261 matched cddid_all.tbl CDD KOG4418 KOG4418 232347 KOG4418 KOG4418, Predicted membrane protein [Function unknown] 438 matched cddid_all.tbl CDD KOG4419 KOG4419 232348 KOG4419 KOG4419, 5' nucleotidase [Nucleotide transport and metabolism] 602 matched cddid_all.tbl CDD KOG4420 KOG4420 232349 KOG4420 KOG4420, Uncharacterized conserved protein (Ganglioside-induced differentiation associated protein 1, GDAP1) [Function unknown] 325 matched cddid_all.tbl CDD KOG4421 KOG4421 232350 KOG4421 KOG4421, Uncharacterized conserved protein [Function unknown] 637 matched cddid_all.tbl CDD KOG4422 KOG4422 232351 KOG4422 KOG4422, Uncharacterized conserved protein [Function unknown] 625 matched cddid_all.tbl CDD KOG4423 KOG4423 232352 KOG4423 KOG4423, GTP-binding protein-like, RAS superfamily [Signal transduction mechanisms] 229 matched cddid_all.tbl CDD KOG4424 KOG4424 232353 KOG4424 KOG4424, Predicted Rho/Rac guanine nucleotide exchange factor/faciogenital dysplasia protein 3 [Signal transduction mechanisms] 623 matched cddid_all.tbl CDD KOG4425 KOG4425 232354 KOG4425 KOG4425, Uncharacterized conserved protein [Function unknown] 900 matched cddid_all.tbl CDD KOG4426 KOG4426 232355 KOG4426 KOG4426, Arginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis] 656 matched cddid_all.tbl CDD KOG4427 KOG4427 232356 KOG4427 KOG4427, E3 ubiquitin protein ligase [Posttranslational modification, protein turnover, chaperones] 1096 matched cddid_all.tbl CDD KOG4428 KOG4428 232357 KOG4428 KOG4428, Inositol-polyphosphate 4-phosphatase [Signal transduction mechanisms] 813 matched cddid_all.tbl CDD KOG4429 KOG4429 232358 KOG4429 KOG4429, Uncharacterized conserved protein, contains SH3 and FCH domains [General function prediction only] 421 matched cddid_all.tbl CDD KOG4430 KOG4430 232359 KOG4430 KOG4430, Topoisomerase I-binding arginine-serine-rich protein [Transcription] 553 matched cddid_all.tbl CDD KOG4431 KOG4431 232360 KOG4431 KOG4431, Uncharacterized protein, induced by hypoxia [General function prediction only] 100 matched cddid_all.tbl CDD KOG4432 KOG4432 232361 KOG4432 KOG4432, Uncharacterized NUDIX family hydrolase [General function prediction only] 405 matched cddid_all.tbl CDD KOG4433 KOG4433 232362 KOG4433 KOG4433, Tweety transmembrane/cell surface protein [General function prediction only] 526 matched cddid_all.tbl CDD KOG4434 KOG4434 232363 KOG4434 KOG4434, Molecular chaperone SEC63, endoplasmic reticulum translocon component [Intracellular trafficking, secretion, and vesicular transport, Posttranslational modification, protein turnover, chaperones] 520 matched cddid_all.tbl CDD KOG4435 KOG4435 232364 KOG4435 KOG4435, Predicted lipid kinase [Lipid transport and metabolism, Signal transduction mechanisms] 535 matched cddid_all.tbl CDD KOG4436 KOG4436 232365 KOG4436 KOG4436, Predicted GTPase activator NB4S/EVI5 (contains TBC domain)/Calmodulin-binding protein Pollux (contains PTB and TBC domains) [General function prediction only] 948 matched cddid_all.tbl CDD KOG4437 KOG4437 232366 KOG4437 KOG4437, ATP-dependent DNA ligase III [Replication, recombination and repair] 482 matched cddid_all.tbl CDD KOG4438 KOG4438 232367 KOG4438 KOG4438, Centromere-associated protein NUF2 [Cell cycle control, cell division, chromosome partitioning] 446 matched cddid_all.tbl CDD KOG4439 KOG4439 232368 KOG4439 KOG4439, RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription, Replication, recombination and repair] 901 matched cddid_all.tbl CDD KOG4440 KOG4440 232369 KOG4440 KOG4440, NMDA selective glutamate-gated ion channel receptor subunit GRIN1 [Inorganic ion transport and metabolism, Amino acid transport and metabolism, Signal transduction mechanisms] 993 matched cddid_all.tbl CDD KOG4441 KOG4441 232370 KOG4441 KOG4441, Proteins containing BTB/POZ and Kelch domains, involved in regulatory/signal transduction processes [Signal transduction mechanisms, General function prediction only] 571 matched cddid_all.tbl CDD KOG4442 KOG4442 232371 KOG4442 KOG4442, Clathrin coat binding protein/Huntingtin interacting protein HIP1, involved in regulation of endocytosis [Intracellular trafficking, secretion, and vesicular transport] 729 matched cddid_all.tbl CDD KOG4443 KOG4443 232372 KOG4443 KOG4443, Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only] 694 matched cddid_all.tbl CDD KOG4444 KOG4444 232373 KOG4444 KOG4444, Peroxisomal assembly protein PEX3 [Cell wall/membrane/envelope biogenesis, Intracellular trafficking, secretion, and vesicular transport] 359 matched cddid_all.tbl CDD KOG4445 KOG4445 232374 KOG4445 KOG4445, Uncharacterized conserved protein, contains RWD domain [Function unknown] 368 matched cddid_all.tbl CDD KOG4446 KOG4446 232375 KOG4446 KOG4446, Uncharacterized conserved protein [Function unknown] 471 matched cddid_all.tbl CDD KOG4447 KOG4447 232376 KOG4447 KOG4447, Transcription factor TWIST [Transcription] 173 matched cddid_all.tbl CDD KOG4448 KOG4448 232377 KOG4448 KOG4448, Uncharacterized conserved protein, contains phosphotyrosine interaction (PI) domain [Function unknown] 374 matched cddid_all.tbl CDD KOG4449 KOG4449 232378 KOG4449 KOG4449, Translocase of outer mitochondrial membrane complex, subunit TOM7 [Intracellular trafficking, secretion, and vesicular transport] 53 matched cddid_all.tbl CDD KOG4450 KOG4450 232379 KOG4450 KOG4450, Uncharacterized conserved protein [Function unknown] 168 matched cddid_all.tbl CDD KOG4451 KOG4451 232380 KOG4451 KOG4451, Uncharacterized conserved protein (tumor-associated antigen HCA127 in humans) [Function unknown] 286 matched cddid_all.tbl CDD KOG4452 KOG4452 232381 KOG4452 KOG4452, Predicted membrane protein [Function unknown] 79 matched cddid_all.tbl CDD KOG4453 KOG4453 232382 KOG4453 KOG4453, Predicted ER membrane protein [Function unknown] 269 matched cddid_all.tbl CDD KOG4454 KOG4454 232383 KOG4454 KOG4454, RNA binding protein (RRM superfamily) [General function prediction only] 267 matched cddid_all.tbl CDD KOG4455 KOG4455 232384 KOG4455 KOG4455, Uncharacterized conserved protein [Function unknown] 110 matched cddid_all.tbl CDD KOG4456 KOG4456 232385 KOG4456 KOG4456, Inner centromere protein (INCENP), C-terminal domain [Cell cycle control, cell division, chromosome partitioning] 134 matched cddid_all.tbl CDD KOG4457 KOG4457 232386 KOG4457 KOG4457, Uncharacterized conserved protein [Function unknown] 202 matched cddid_all.tbl CDD KOG4458 KOG4458 232387 KOG4458 KOG4458, Nitric oxide synthase-binding protein, contains PTB domain [Signal transduction mechanisms] 78 matched cddid_all.tbl CDD KOG4459 KOG4459 232388 KOG4459 KOG4459, Membrane-associated proteoglycan Leprecan [Function unknown] 471 matched cddid_all.tbl CDD KOG4460 KOG4460 232389 KOG4460 KOG4460, Nuclear pore complex, Nup88/rNup84 component [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 741 matched cddid_all.tbl CDD KOG4461 KOG4461 232390 KOG4461 KOG4461, Mitochondrial 28S ribosomal protein S30 [Translation, ribosomal structure and biogenesis] 473 matched cddid_all.tbl CDD KOG4462 KOG4462 232391 KOG4462 KOG4462, WASP-interacting protein VRP1/WIP, contains WH2 domain [Cytoskeleton] 437 matched cddid_all.tbl CDD KOG4463 KOG4463 232392 KOG4463 KOG4463, Uncharacterized conserved protein [Function unknown] 323 matched cddid_all.tbl CDD KOG4464 KOG4464 232393 KOG4464 KOG4464, Signaling protein RIC-8/synembryn (regulates neurotransmitter secretion) [Signal transduction mechanisms] 532 matched cddid_all.tbl CDD KOG4465 KOG4465 232394 KOG4465 KOG4465, Uncharacterized conserved protein [Function unknown] 598 matched cddid_all.tbl CDD KOG4466 KOG4466 232395 KOG4466 KOG4466, Component of histone deacetylase complex (breast carcinoma metastasis suppressor 1 protein in human) [Cell cycle control, cell division, chromosome partitioning, Transcription] 291 matched cddid_all.tbl CDD KOG4467 KOG4467 232396 KOG4467 KOG4467, Uncharacterized conserved protein [Function unknown] 557 matched cddid_all.tbl CDD KOG4468 KOG4468 232397 KOG4468 KOG4468, Polycomb-group transcriptional regulator [Transcription] 782 matched cddid_all.tbl CDD KOG4469 KOG4469 232398 KOG4469 KOG4469, Uncharacterized conserved protein [Function unknown] 391 matched cddid_all.tbl CDD KOG4470 KOG4470 232399 KOG4470 KOG4470, Proteasome activator subunit [Posttranslational modification, protein turnover, chaperones] 246 matched cddid_all.tbl CDD KOG4471 KOG4471 232400 KOG4471 KOG4471, Phosphatidylinositol 3-phosphate 3-phosphatase myotubularin MTM1 [Lipid transport and metabolism, Intracellular trafficking, secretion, and vesicular transport] 717 matched cddid_all.tbl CDD KOG4472 KOG4472 232401 KOG4472 KOG4472, Glycolipid 2-alpha-mannosyltransferase (alpha-1,2-mannosyltransferase) [Carbohydrate transport and metabolism] 399 matched cddid_all.tbl CDD KOG4473 KOG4473 232402 KOG4473 KOG4473, Uncharacterized membrane protein [Function unknown] 247 matched cddid_all.tbl CDD KOG4474 KOG4474 232403 KOG4474 KOG4474, Uncharacterized conserved protein [Function unknown] 253 matched cddid_all.tbl CDD KOG4476 KOG4476 232404 KOG4476 KOG4476, Gluconate transport-inducing protein [Signal transduction mechanisms, Carbohydrate transport and metabolism] 248 matched cddid_all.tbl CDD KOG4477 KOG4477 232405 KOG4477 KOG4477, RING1 interactor RYBP and related Zn-finger-containing proteins [Transcription] 228 matched cddid_all.tbl CDD KOG4478 KOG4478 232406 KOG4478 KOG4478, Uncharacterized membrane protein [Function unknown] 217 matched cddid_all.tbl CDD KOG4479 KOG4479 232407 KOG4479 KOG4479, Transcription factor e(y)2 [Transcription] 92 matched cddid_all.tbl CDD KOG4480 KOG4480 232408 KOG4480 KOG4480, Heme oxygenase [Inorganic ion transport and metabolism] 283 matched cddid_all.tbl CDD KOG4481 KOG4481 232409 KOG4481 KOG4481, Uncharacterized conserved protein [Function unknown] 194 matched cddid_all.tbl CDD KOG4482 KOG4482 232410 KOG4482 KOG4482, Sarcoglycan complex, alpha/epsilon subunits [Function unknown] 449 matched cddid_all.tbl CDD KOG4483 KOG4483 232411 KOG4483 KOG4483, Uncharacterized conserved protein [Function unknown] 528 matched cddid_all.tbl CDD KOG4484 KOG4484 232412 KOG4484 KOG4484, Uncharacterized conserved protein [Function unknown] 199 matched cddid_all.tbl CDD KOG4485 KOG4485 232413 KOG4485 KOG4485, Uncharacterized conserved protein, contains ankyrin and FN3 repeats [General function prediction only] 724 matched cddid_all.tbl CDD KOG4486 KOG4486 232414 KOG4486 KOG4486, 3-methyladenine DNA glycosylase [Replication, recombination and repair] 261 matched cddid_all.tbl CDD KOG4487 KOG4487 232415 KOG4487 KOG4487, Uncharacterized conserved protein [Function unknown] 110 matched cddid_all.tbl CDD KOG4488 KOG4488 232416 KOG4488 KOG4488, Small EDRK-rich protein H4F5 [General function prediction only] 70 matched cddid_all.tbl CDD KOG4489 KOG4489 232417 KOG4489 KOG4489, Uncharacterized conserved protein BC10 (implicated in bladder cancer in humans) [Function unknown] 87 matched cddid_all.tbl CDD KOG4490 KOG4490 232418 KOG4490 KOG4490, Translocon-associated complex TRAP, gamma subunit [Intracellular trafficking, secretion, and vesicular transport] 183 matched cddid_all.tbl CDD KOG4491 KOG4491 232419 KOG4491 KOG4491, Predicted membrane protein [Function unknown] 323 matched cddid_all.tbl CDD KOG4492 KOG4492 232420 KOG4492 KOG4492, Chorismate synthase [Amino acid transport and metabolism] 368 matched cddid_all.tbl CDD KOG4493 KOG4493 232421 KOG4493 KOG4493, Uncharacterized conserved protein [Function unknown] 219 matched cddid_all.tbl CDD KOG4494 KOG4494 232422 KOG4494 KOG4494, Cell surface ATP diphosphohydrolase Apyrase [Nucleotide transport and metabolism] 352 matched cddid_all.tbl CDD KOG4495 KOG4495 232423 KOG4495 KOG4495, RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin B [Transcription] 110 matched cddid_all.tbl CDD KOG4496 KOG4496 232424 KOG4496 KOG4496, Predicted coiled-coil protein [Function unknown] 194 matched cddid_all.tbl CDD KOG4497 KOG4497 232425 KOG4497 KOG4497, Uncharacterized conserved protein WDR8, contains WD repeats [General function prediction only] 447 matched cddid_all.tbl CDD KOG4498 KOG4498 232426 KOG4498 KOG4498, Uncharacterized conserved protein [Function unknown] 197 matched cddid_all.tbl CDD KOG4499 KOG4499 232427 KOG4499 KOG4499, Ca2+-binding protein Regucalcin/SMP30 [Inorganic ion transport and metabolism, Signal transduction mechanisms] 310 matched cddid_all.tbl CDD KOG4500 KOG4500 232428 KOG4500 KOG4500, Rho/Rac GTPase guanine nucleotide exchange factor smgGDS/Vimar [Signal transduction mechanisms] 604 matched cddid_all.tbl CDD KOG4501 KOG4501 232429 KOG4501 KOG4501, Transcription coactivator complex, P100 component [Transcription] 707 matched cddid_all.tbl CDD KOG4502 KOG4502 232430 KOG4502 KOG4502, Predicted membrane protein [Function unknown] 133 matched cddid_all.tbl CDD KOG4503 KOG4503 232431 KOG4503 KOG4503, Uncharacterized conserved membrane protein [Function unknown] 230 matched cddid_all.tbl CDD KOG4504 KOG4504 232432 KOG4504 KOG4504, Cation-independent mannose-6-phosphate receptor CI-MPR [Signal transduction mechanisms, Intracellular trafficking, secretion, and vesicular transport] 370 matched cddid_all.tbl CDD KOG4505 KOG4505 232433 KOG4505 KOG4505, Na+/H+ antiporter [Inorganic ion transport and metabolism] 467 matched cddid_all.tbl CDD KOG4506 KOG4506 232434 KOG4506 KOG4506, Uncharacterized conserved protein [Function unknown] 598 matched cddid_all.tbl CDD KOG4507 KOG4507 232435 KOG4507 KOG4507, Uncharacterized conserved protein, contains TPR repeats [Function unknown] 886 matched cddid_all.tbl CDD KOG4508 KOG4508 232436 KOG4508 KOG4508, Uncharacterized conserved protein [Function unknown] 522 matched cddid_all.tbl CDD KOG4509 KOG4509 232437 KOG4509 KOG4509, Uncharacterized conserved protein [Function unknown] 247 matched cddid_all.tbl CDD KOG4510 KOG4510 232438 KOG4510 KOG4510, Permease of the drug/metabolite transporter (DMT) superfamily [General function prediction only] 346 matched cddid_all.tbl CDD KOG4511 KOG4511 232439 KOG4511 KOG4511, Uncharacterized conserved protein [Function unknown] 335 matched cddid_all.tbl CDD KOG4512 KOG4512 232440 KOG4512 KOG4512, Vitamin D3 receptor interacting protein [Transcription, Signal transduction mechanisms] 625 matched cddid_all.tbl CDD KOG4513 KOG4513 232441 KOG4513 KOG4513, Phosphoglycerate mutase [Carbohydrate transport and metabolism] 531 matched cddid_all.tbl CDD KOG4514 KOG4514 232442 KOG4514 KOG4514, Uncharacterized conserved protein [Function unknown] 222 matched cddid_all.tbl CDD KOG4515 KOG4515 232443 KOG4515 KOG4515, Uncharacterized conserved protein [Function unknown] 217 matched cddid_all.tbl CDD KOG4516 KOG4516 232444 KOG4516 KOG4516, NADH:ubiquinone oxidoreductase, NDUFC2/B14.5B subunit [Energy production and conversion] 118 matched cddid_all.tbl CDD KOG4517 KOG4517 232445 KOG4517 KOG4517, Uncharacterized conserved protein [Function unknown] 117 matched cddid_all.tbl CDD KOG4518 KOG4518 232446 KOG4518 KOG4518, Hydroxypyruvate isomerase [Carbohydrate transport and metabolism] 264 matched cddid_all.tbl CDD KOG4519 KOG4519 232447 KOG4519 KOG4519, Phosphomevalonate kinase [Lipid transport and metabolism] 459 matched cddid_all.tbl CDD KOG4520 KOG4520 232448 KOG4520 KOG4520, Predicted coiled-coil protein [General function prediction only] 238 matched cddid_all.tbl CDD KOG4521 KOG4521 232449 KOG4521 KOG4521, Nuclear pore complex, Nup160 component [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 1480 matched cddid_all.tbl CDD KOG4522 KOG4522 232450 KOG4522 KOG4522, RNA polymerase II transcription mediator [Transcription] 1427 matched cddid_all.tbl CDD KOG4523 KOG4523 232451 KOG4523 KOG4523, Uncharacterized conserved protein [Function unknown] 157 matched cddid_all.tbl CDD KOG4524 KOG4524 232452 KOG4524 KOG4524, Uncharacterized conserved protein [Function unknown] 1014 matched cddid_all.tbl CDD KOG4525 KOG4525 232453 KOG4525 KOG4525, Jacalin-like lectin domain-containing protein [General function prediction only] 614 matched cddid_all.tbl CDD KOG4526 KOG4526 232454 KOG4526 KOG4526, Predicted membrane protein [Function unknown] 170 matched cddid_all.tbl CDD KOG4527 KOG4527 232455 KOG4527 KOG4527, Cytochrome c oxidase, subunit VIIc/COX8 [Energy production and conversion] 76 matched cddid_all.tbl CDD KOG4528 KOG4528 232456 KOG4528 KOG4528, Uncharacterized conserved protein [Function unknown] 168 matched cddid_all.tbl CDD KOG4529 KOG4529 232457 KOG4529 KOG4529, Uncharacterized conserved protein [Function unknown] 404 matched cddid_all.tbl CDD KOG4530 KOG4530 232458 KOG4530 KOG4530, Predicted flavoprotein [General function prediction only] 199 matched cddid_all.tbl CDD KOG4531 KOG4531 232459 KOG4531 KOG4531, M phase phosphoprotein 6 [Cell cycle control, cell division, chromosome partitioning] 165 matched cddid_all.tbl CDD KOG4532 KOG4532 232460 KOG4532 KOG4532, WD40-like repeat containing protein [General function prediction only] 344 matched cddid_all.tbl CDD KOG4533 KOG4533 232461 KOG4533 KOG4533, Uncharacterized conserved protein [Function unknown] 317 matched cddid_all.tbl CDD KOG4534 KOG4534 232462 KOG4534 KOG4534, Uncharacterized conserved protein [Function unknown] 349 matched cddid_all.tbl CDD KOG4535 KOG4535 232463 KOG4535 KOG4535, HEAT and armadillo repeat-containing protein [General function prediction only] 728 matched cddid_all.tbl CDD KOG4536 KOG4536 232464 KOG4536 KOG4536, Predicted membrane protein [Function unknown] 347 matched cddid_all.tbl CDD KOG4537 KOG4537 232465 KOG4537 KOG4537, Zn-ribbon-containing protein implicated in mitosis [Cell cycle control, cell division, chromosome partitioning, Defense mechanisms] 178 matched cddid_all.tbl CDD KOG4538 KOG4538 232466 KOG4538 KOG4538, Predicted coiled-coil protein [General function prediction only] 130 matched cddid_all.tbl CDD KOG4539 KOG4539 232467 KOG4539 KOG4539, Uncharacterized conserved protein [Function unknown] 274 matched cddid_all.tbl CDD KOG4540 KOG4540 232468 KOG4540 KOG4540, Putative lipase essential for disintegration of autophagic bodies inside the vacuole [Intracellular trafficking, secretion, and vesicular transport, Lipid transport and metabolism] 425 matched cddid_all.tbl CDD KOG4541 KOG4541 232469 KOG4541 KOG4541, Nuclear transport receptor exportin 4 (importin beta superfamily) [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 748 matched cddid_all.tbl CDD KOG4542 KOG4542 232470 KOG4542 KOG4542, Predicted membrane protein [Function unknown] 96 matched cddid_all.tbl CDD KOG4543 KOG4543 232471 KOG4543 KOG4543, Uncharacterized conserved protein [Function unknown] 208 matched cddid_all.tbl CDD KOG4544 KOG4544 232472 KOG4544 KOG4544, Uncharacterized conserved protein [Function unknown] 144 matched cddid_all.tbl CDD KOG4545 KOG4545 232473 KOG4545 KOG4545, Uncharacterized conserved protein [Function unknown] 197 matched cddid_all.tbl CDD KOG4546 KOG4546 232474 KOG4546 KOG4546, Peroxisomal biogenesis protein (peroxin 16) [Intracellular trafficking, secretion, and vesicular transport] 320 matched cddid_all.tbl CDD KOG4547 KOG4547 232475 KOG4547 KOG4547, WD40 repeat-containing protein [General function prediction only] 541 matched cddid_all.tbl CDD KOG4548 KOG4548 232476 KOG4548 KOG4548, Mitochondrial ribosomal protein L17 [Translation, ribosomal structure and biogenesis] 263 matched cddid_all.tbl CDD KOG4549 KOG4549 232477 KOG4549 KOG4549, Magnesium-dependent phosphatase [General function prediction only] 144 matched cddid_all.tbl CDD KOG4550 KOG4550 232478 KOG4550 KOG4550, Predicted membrane protein [Function unknown] 606 matched cddid_all.tbl CDD KOG4551 KOG4551 232479 KOG4551 KOG4551, GPI-GlcNAc transferase complex, PIG-H component, involved in glycosylphosphatidylinositol anchor biosynthesis [Cell wall/membrane/envelope biogenesis, Posttranslational modification, protein turnover, chaperones] 184 matched cddid_all.tbl CDD KOG4552 KOG4552 232480 KOG4552 KOG4552, Vitamin-D-receptor interacting protein complex component [Transcription] 272 matched cddid_all.tbl CDD KOG4553 KOG4553 232481 KOG4553 KOG4553, Uncharacterized conserved protein [Function unknown] 1398 matched cddid_all.tbl CDD KOG4554 KOG4554 232482 KOG4554 KOG4554, Protein involved in inorganic phosphate transport [Inorganic ion transport and metabolism] 185 matched cddid_all.tbl CDD KOG4555 KOG4555 232483 KOG4555 KOG4555, TPR repeat-containing protein [Function unknown] 175 matched cddid_all.tbl CDD KOG4556 KOG4556 232484 KOG4556 KOG4556, Predicted membrane protein [Function unknown] 205 matched cddid_all.tbl CDD KOG4557 KOG4557 232485 KOG4557 KOG4557, Origin recognition complex, subunit 6 [Replication, recombination and repair] 262 matched cddid_all.tbl CDD KOG4558 KOG4558 232486 KOG4558 KOG4558, Uncharacterized conserved protein [Function unknown] 251 matched cddid_all.tbl CDD KOG4559 KOG4559 232487 KOG4559 KOG4559, Uncharacterized conserved protein [Function unknown] 120 matched cddid_all.tbl CDD KOG4560 KOG4560 232488 KOG4560 KOG4560, Transcription factor IIIC box B binding (alpha) subunit [Transcription] 1897 matched cddid_all.tbl CDD KOG4561 KOG4561 232489 KOG4561 KOG4561, Uncharacterized conserved protein, contains TBC domain [Signal transduction mechanisms, General function prediction only] 281 matched cddid_all.tbl CDD KOG4562 KOG4562 232490 KOG4562 KOG4562, Uncharacterized conserved protein (tumor-rejection antigen MAGE in humans) [Function unknown] 329 matched cddid_all.tbl CDD KOG4563 KOG4563 232491 KOG4563 KOG4563, Cell cycle-regulated histone H1-binding protein [Chromatin structure and dynamics, Cell cycle control, cell division, chromosome partitioning] 400 matched cddid_all.tbl CDD KOG4564 KOG4564 232492 KOG4564 KOG4564, Adenylate cyclase-coupled calcitonin receptor [Signal transduction mechanisms] 473 matched cddid_all.tbl CDD KOG4565 KOG4565 232493 KOG4565 KOG4565, E93 protein involved in programmed cell death, putative transcription regulator [Transcription] 206 matched cddid_all.tbl CDD KOG4566 KOG4566 232494 KOG4566 KOG4566, Cytokine-inducible SH2 protein [Signal transduction mechanisms] 258 matched cddid_all.tbl CDD KOG4567 KOG4567 232495 KOG4567 KOG4567, GTPase-activating protein [General function prediction only] 370 matched cddid_all.tbl CDD KOG4568 KOG4568 232496 KOG4568 KOG4568, Cytoskeleton-associated protein and related proteins [Cytoskeleton, General function prediction only] 664 matched cddid_all.tbl CDD KOG4569 KOG4569 232497 KOG4569 KOG4569, Predicted lipase [Lipid transport and metabolism] 336 matched cddid_all.tbl CDD KOG4570 KOG4570 232498 KOG4570 KOG4570, Uncharacterized conserved protein [Function unknown] 418 matched cddid_all.tbl CDD KOG4571 KOG4571 232499 KOG4571 KOG4571, Activating transcription factor 4 [Transcription] 294 matched cddid_all.tbl CDD KOG4572 KOG4572 232500 KOG4572 KOG4572, Predicted DNA-binding transcription factor, interacts with stathmin [Transcription, General function prediction only, Signal transduction mechanisms] 1424 matched cddid_all.tbl CDD KOG4573 KOG4573 232501 KOG4573 KOG4573, Phosphoprotein involved in cytoplasm to vacuole targeting and autophagy [Intracellular trafficking, secretion, and vesicular transport] 705 matched cddid_all.tbl CDD KOG4574 KOG4574 232502 KOG4574 KOG4574, RNA-binding protein (contains RRM and Pumilio-like repeats) [General function prediction only] 1007 matched cddid_all.tbl CDD KOG4575 KOG4575 232503 KOG4575 KOG4575, TGc (transglutaminase/protease-like) domain-containing protein involved in cytokinesis [Cell cycle control, cell division, chromosome partitioning] 874 matched cddid_all.tbl CDD KOG4576 KOG4576 232504 KOG4576 KOG4576, Sulfite oxidase, heme-binding component [Energy production and conversion] 167 matched cddid_all.tbl CDD KOG4577 KOG4577 232505 KOG4577 KOG4577, Transcription factor LIM3, contains LIM and HOX domains [Transcription] 383 matched cddid_all.tbl CDD KOG4578 KOG4578 232506 KOG4578 KOG4578, Uncharacterized conserved protein, contains KAZAL and TY domains [General function prediction only] 421 matched cddid_all.tbl CDD KOG4579 KOG4579 232507 KOG4579 KOG4579, Leucine-rich repeat (LRR) protein associated with apoptosis in muscle tissue [General function prediction only] 177 matched cddid_all.tbl CDD KOG4580 KOG4580 232508 KOG4580 KOG4580, Component of vacuolar transporter chaperone (Vtc) involved in vacuole fusion [Intracellular trafficking, secretion, and vesicular transport, Posttranslational modification, protein turnover, chaperones] 112 matched cddid_all.tbl CDD KOG4581 KOG4581 232509 KOG4581 KOG4581, Predicted membrane protein [Function unknown] 359 matched cddid_all.tbl CDD KOG4582 KOG4582 232510 KOG4582 KOG4582, Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only] 278 matched cddid_all.tbl CDD KOG4583 KOG4583 232511 KOG4583 KOG4583, Membrane-associated ER protein involved in stress response (contains ubiquitin-like domain) [Posttranslational modification, protein turnover, chaperones] 391 matched cddid_all.tbl CDD KOG4584 KOG4584 232512 KOG4584 KOG4584, Uncharacterized conserved protein [General function prediction only] 348 matched cddid_all.tbl CDD KOG4585 KOG4585 232513 KOG4585 KOG4585, Predicted transposase [Replication, recombination and repair] 326 matched cddid_all.tbl CDD KOG4586 KOG4586 232514 KOG4586 KOG4586, CUB domain-containing protein [General function prediction only] 156 matched cddid_all.tbl CDD KOG4587 KOG4587 232515 KOG4587 KOG4587, Predicted membrane protein [Function unknown] 605 matched cddid_all.tbl CDD KOG4588 KOG4588 232516 KOG4588 KOG4588, Predicted ubiquitin-conjugating enzyme [Posttranslational modification, protein turnover, chaperones] 267 matched cddid_all.tbl CDD KOG4589 KOG4589 232517 KOG4589 KOG4589, Cell division protein FtsJ [Cell cycle control, cell division, chromosome partitioning] 232 matched cddid_all.tbl CDD KOG4590 KOG4590 232518 KOG4590 KOG4590, Signal transduction protein Enabled, contains WH1 domain [Signal transduction mechanisms] 285 matched cddid_all.tbl CDD KOG4591 KOG4591 232519 KOG4591 KOG4591, Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only] 280 matched cddid_all.tbl CDD KOG4592 KOG4592 232520 KOG4592 KOG4592, Uncharacterized conserved protein [Function unknown] 728 matched cddid_all.tbl CDD KOG4593 KOG4593 232521 KOG4593 KOG4593, Mitotic checkpoint protein MAD1 [Cell cycle control, cell division, chromosome partitioning] 716 matched cddid_all.tbl CDD KOG4594 KOG4594 232522 KOG4594 KOG4594, Sequence-specific single-stranded-DNA-binding protein [Replication, recombination and repair, Transcription, General function prediction only] 354 matched cddid_all.tbl CDD KOG4595 KOG4595 232523 KOG4595 KOG4595, Uncharacterized conserved protein [Function unknown] 139 matched cddid_all.tbl CDD KOG4596 KOG4596 232524 KOG4596 KOG4596, Uncharacterized conserved protein [Function unknown] 1936 matched cddid_all.tbl CDD KOG4597 KOG4597 232525 KOG4597 KOG4597, Serine proteinase inhibitor (KU family) with thrombospondin repeats [Posttranslational modification, protein turnover, chaperones] 560 matched cddid_all.tbl CDD KOG4598 KOG4598 232526 KOG4598 KOG4598, Putative ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones] 1203 matched cddid_all.tbl CDD KOG4599 KOG4599 232527 KOG4599 KOG4599, Putative mitochondrial/chloroplast ribosomal protein L45 [Translation, ribosomal structure and biogenesis] 379 matched cddid_all.tbl CDD KOG4600 KOG4600 232528 KOG4600 KOG4600, Mitochondrial ribosomal protein MRP7 (L2) [Translation, ribosomal structure and biogenesis] 144 matched cddid_all.tbl CDD KOG4601 KOG4601 232529 KOG4601 KOG4601, Uncharacterized conserved protein [Function unknown] 264 matched cddid_all.tbl CDD KOG4602 KOG4602 232530 KOG4602 KOG4602, Nanos and related proteins [General function prediction only] 318 matched cddid_all.tbl CDD KOG4603 KOG4603 232531 KOG4603 KOG4603, TBP-1 interacting protein [Signal transduction mechanisms] 201 matched cddid_all.tbl CDD KOG4604 KOG4604 232532 KOG4604 KOG4604, Uncharacterized conserved protein [Function unknown] 91 matched cddid_all.tbl CDD KOG4605 KOG4605 232533 KOG4605 KOG4605, Uncharacterized conserved protein containing CDGSH-type Zn-finger [Function unknown] 129 matched cddid_all.tbl CDD KOG4606 KOG4606 232534 KOG4606 KOG4606, Uncharacterized conserved protein [Function unknown] 126 matched cddid_all.tbl CDD KOG4607 KOG4607 232535 KOG4607 KOG4607, Mitochondrial ribosomal protein L9 [Translation, ribosomal structure and biogenesis] 222 matched cddid_all.tbl CDD KOG4608 KOG4608 232536 KOG4608 KOG4608, Uncharacterized conserved protein [Function unknown] 270 matched cddid_all.tbl CDD KOG4609 KOG4609 232537 KOG4609 KOG4609, Predicted phosphoglycerate mutase [General function prediction only] 284 matched cddid_all.tbl CDD KOG4610 KOG4610 232538 KOG4610 KOG4610, Uncharacterized conserved protein [Function unknown] 328 matched cddid_all.tbl CDD KOG4611 KOG4611 232539 KOG4611 KOG4611, Uncharacterized conserved protein [Function unknown] 747 matched cddid_all.tbl CDD KOG4612 KOG4612 232540 KOG4612 KOG4612, Mitochondrial ribosomal protein L34 [Translation, ribosomal structure and biogenesis] 105 matched cddid_all.tbl CDD KOG4613 KOG4613 232541 KOG4613 KOG4613, Predicted component of DNA replication checkpoint response mechanism (S-M checkpoint) [General function prediction only, Cell cycle control, cell division, chromosome partitioning] 133 matched cddid_all.tbl CDD KOG4614 KOG4614 232542 KOG4614 KOG4614, Inner membrane protein required for assembly of the F0 sector of ATP synthase [Posttranslational modification, protein turnover, chaperones] 287 matched cddid_all.tbl CDD KOG4615 KOG4615 232543 KOG4615 KOG4615, Uncharacterized conserved protein [Function unknown] 122 matched cddid_all.tbl CDD KOG4616 KOG4616 232544 KOG4616 KOG4616, Mitochondrial ribosomal protein L55 [Translation, ribosomal structure and biogenesis] 137 matched cddid_all.tbl CDD KOG4617 KOG4617 232545 KOG4617 KOG4617, Uncharacterized conserved protein [Function unknown] 249 matched cddid_all.tbl CDD KOG4618 KOG4618 232546 KOG4618 KOG4618, Uncharacterized conserved protein [Function unknown] 74 matched cddid_all.tbl CDD KOG4619 KOG4619 232547 KOG4619 KOG4619, Uncharacterized conserved protein [Function unknown] 105 matched cddid_all.tbl CDD KOG4620 KOG4620 232548 KOG4620 KOG4620, Uncharacterized conserved protein [Function unknown] 80 matched cddid_all.tbl CDD KOG4621 KOG4621 232549 KOG4621 KOG4621, Uncharacterized conserved protein [Function unknown] 167 matched cddid_all.tbl CDD KOG4622 KOG4622 232550 KOG4622 KOG4622, Predicted nucleotide kinase [General function prediction only] 291 matched cddid_all.tbl CDD KOG4623 KOG4623 232551 KOG4623 KOG4623, Uncharacterized conserved protein [Function unknown] 611 matched cddid_all.tbl CDD KOG4624 KOG4624 232552 KOG4624 KOG4624, Uncharacterized conserved protein [Function unknown] 104 matched cddid_all.tbl CDD KOG4625 KOG4625 232553 KOG4625 KOG4625, Notch signaling protein Neuralized, Nuez domain [Signal transduction mechanisms] 595 matched cddid_all.tbl CDD KOG4626 KOG4626 232554 KOG4626 KOG4626, O-linked N-acetylglucosamine transferase OGT [Carbohydrate transport and metabolism, Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms] 966 matched cddid_all.tbl CDD KOG4627 KOG4627 232555 KOG4627 KOG4627, Kynurenine formamidase [Amino acid transport and metabolism] 270 matched cddid_all.tbl CDD KOG4628 KOG4628 232556 KOG4628 KOG4628, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 348 matched cddid_all.tbl CDD KOG4629 KOG4629 232557 KOG4629 KOG4629, Predicted mechanosensitive ion channel [Cell wall/membrane/envelope biogenesis] 714 matched cddid_all.tbl CDD KOG4630 KOG4630 232558 KOG4630 KOG4630, NADH:ubiquinone oxidoreductase, NDUFA7/B14.5A subunit [Energy production and conversion] 142 matched cddid_all.tbl CDD KOG4631 KOG4631 232559 KOG4631 KOG4631, NADH:ubiquinone oxidoreductase, NDUFB3/B12 subunit [Energy production and conversion] 100 matched cddid_all.tbl CDD KOG4632 KOG4632 232560 KOG4632 KOG4632, NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit [Energy production and conversion] 187 matched cddid_all.tbl CDD KOG4633 KOG4633 232561 KOG4633 KOG4633, NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit [Energy production and conversion] 169 matched cddid_all.tbl CDD KOG4634 KOG4634 232562 KOG4634 KOG4634, Mitochondrial F1F0-ATP synthase, subunit Cf6 (coupling factor 6) [Energy production and conversion] 105 matched cddid_all.tbl CDD KOG4635 KOG4635 232563 KOG4635 KOG4635, Vacuolar import and degradation protein [Intracellular trafficking, secretion, and vesicular transport] 274 matched cddid_all.tbl CDD KOG4636 KOG4636 232564 KOG4636 KOG4636, Uncharacterized conserved protein with TLDc domain [Function unknown] 483 matched cddid_all.tbl CDD KOG4637 KOG4637 232565 KOG4637 KOG4637, Adaptor for phosphoinositide 3-kinase [Signal transduction mechanisms] 464 matched cddid_all.tbl CDD KOG4638 KOG4638 232566 KOG4638 KOG4638, Uncharacterized conserved protein [Function unknown] 371 matched cddid_all.tbl CDD KOG4639 KOG4639 232567 KOG4639 KOG4639, RNase P/RNase MRP subunit POP5 [Translation, ribosomal structure and biogenesis] 154 matched cddid_all.tbl CDD KOG4640 KOG4640 232568 KOG4640 KOG4640, Anaphase-promoting complex (APC), subunit 4 [Cell cycle control, cell division, chromosome partitioning, Posttranslational modification, protein turnover, chaperones] 665 matched cddid_all.tbl CDD KOG4642 KOG4642 232569 KOG4642 KOG4642, Chaperone-dependent E3 ubiquitin protein ligase (contains TPR repeats) [Posttranslational modification, protein turnover, chaperones] 284 matched cddid_all.tbl CDD KOG4643 KOG4643 232570 KOG4643 KOG4643, Uncharacterized coiled-coil protein [Function unknown] 1195 matched cddid_all.tbl CDD KOG4644 KOG4644 232571 KOG4644 KOG4644, L-fucose kinase [Carbohydrate transport and metabolism] 948 matched cddid_all.tbl CDD KOG4645 KOG4645 232572 KOG4645 KOG4645, MAPKKK (MAP kinase kinase kinase) SSK2 and related serine/threonine protein kinases [Signal transduction mechanisms] 1509 matched cddid_all.tbl CDD KOG4646 KOG4646 232573 KOG4646 KOG4646, Uncharacterized conserved protein, contains ARM repeats [Function unknown] 173 matched cddid_all.tbl CDD KOG4647 KOG4647 232574 KOG4647 KOG4647, Uncharacterized membrane protein [Function unknown] 263 matched cddid_all.tbl CDD KOG4648 KOG4648 232575 KOG4648 KOG4648, Uncharacterized conserved protein, contains LRR repeats [Function unknown] 536 matched cddid_all.tbl CDD KOG4649 KOG4649 232576 KOG4649 KOG4649, PQQ (pyrrolo-quinoline quinone) repeat protein [Secondary metabolites biosynthesis, transport and catabolism] 354 matched cddid_all.tbl CDD KOG4650 KOG4650 232577 KOG4650 KOG4650, Predicted steroid reductase [General function prediction only] 311 matched cddid_all.tbl CDD KOG4651 KOG4651 232578 KOG4651 KOG4651, Chondroitin 6-sulfotransferase and related sulfotransferases [Cell wall/membrane/envelope biogenesis, Extracellular structures] 324 matched cddid_all.tbl CDD KOG4652 KOG4652 232579 KOG4652 KOG4652, HORMA domain [Chromatin structure and dynamics] 324 matched cddid_all.tbl CDD KOG4653 KOG4653 232580 KOG4653 KOG4653, Uncharacterized conserved protein [Function unknown] 982 matched cddid_all.tbl CDD KOG4654 KOG4654 232581 KOG4654 KOG4654, Uncharacterized conserved protein [Function unknown] 252 matched cddid_all.tbl CDD KOG4655 KOG4655 232582 KOG4655 KOG4655, U3 small nucleolar ribonucleoprotein (snoRNP) component [RNA processing and modification] 181 matched cddid_all.tbl CDD KOG4656 KOG4656 232583 KOG4656 KOG4656, Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism] 247 matched cddid_all.tbl CDD KOG4657 KOG4657 232584 KOG4657 KOG4657, Uncharacterized conserved protein [Function unknown] 246 matched cddid_all.tbl CDD KOG4658 KOG4658 232585 KOG4658 KOG4658, Apoptotic ATPase [Signal transduction mechanisms] 889 matched cddid_all.tbl CDD KOG4659 KOG4659 232586 KOG4659 KOG4659, Uncharacterized conserved protein (Rhs family) [Function unknown] 1899 matched cddid_all.tbl CDD KOG4660 KOG4660 232587 KOG4660 KOG4660, Protein Mei2, essential for commitment to meiosis, and related proteins [Cell cycle control, cell division, chromosome partitioning] 549 matched cddid_all.tbl CDD KOG4661 KOG4661 232588 KOG4661 KOG4661, Hsp27-ERE-TATA-binding protein/Scaffold attachment factor (SAF-B) [Transcription] 940 matched cddid_all.tbl CDD KOG4662 KOG4662 232589 KOG4662 KOG4662, NADH dehydrogenase subunit 3 and related proteins [Energy production and conversion] 122 matched cddid_all.tbl CDD KOG4663 KOG4663 232590 KOG4663 KOG4663, Cytochrome b [Energy production and conversion] 210 matched cddid_all.tbl CDD KOG4664 KOG4664 232591 KOG4664 KOG4664, Cytochrome oxidase subunit III and related proteins [Energy production and conversion] 261 matched cddid_all.tbl CDD KOG4665 KOG4665 232592 KOG4665 KOG4665, ATP synthase F0 subunit 6 and related proteins [Energy production and conversion] 252 matched cddid_all.tbl CDD KOG4666 KOG4666 232593 KOG4666 KOG4666, Predicted phosphate acyltransferase, contains PlsC domain [Lipid transport and metabolism] 412 matched cddid_all.tbl CDD KOG4667 KOG4667 232594 KOG4667 KOG4667, Predicted esterase [Lipid transport and metabolism] 269 matched cddid_all.tbl CDD KOG4668 KOG4668 232595 KOG4668 KOG4668, NADH dehydrogenase subunits 2, 5, and related proteins [Energy production and conversion] 355 matched cddid_all.tbl CDD KOG4669 KOG4669 232596 KOG4669 KOG4669, NADH dehydrogenase subunit 4L and related proteins [Energy production and conversion] 100 matched cddid_all.tbl CDD KOG4670 KOG4670 232597 KOG4670 KOG4670, Uncharacterized conserved membrane protein [Function unknown] 602 matched cddid_all.tbl CDD KOG4671 KOG4671 232598 KOG4671 KOG4671, Brain cell membrane protein 1 (BCMP1) [General function prediction only] 201 matched cddid_all.tbl CDD KOG4672 KOG4672 232599 KOG4672 KOG4672, Uncharacterized conserved low complexity protein [Function unknown] 487 matched cddid_all.tbl CDD KOG4673 KOG4673 232600 KOG4673 KOG4673, Transcription factor TMF, TATA element modulatory factor [Transcription] 961 matched cddid_all.tbl CDD KOG4674 KOG4674 232601 KOG4674 KOG4674, Uncharacterized conserved coiled-coil protein [Function unknown] 1822 matched cddid_all.tbl CDD KOG4675 KOG4675 232602 KOG4675 KOG4675, Uncharacterized conserved protein, contains ENT domain [General function prediction only] 273 matched cddid_all.tbl CDD KOG4676 KOG4676 232603 KOG4676 KOG4676, Splicing factor, arginine/serine-rich [RNA processing and modification] 479 matched cddid_all.tbl CDD KOG4677 KOG4677 232604 KOG4677 KOG4677, Golgi integral membrane protein [Intracellular trafficking, secretion, and vesicular transport, General function prediction only] 554 matched cddid_all.tbl CDD KOG4679 KOG4679 232605 KOG4679 KOG4679, Uncharacterized protein PSP1 (suppressor of DNA polymerase alpha mutations in yeast) [General function prediction only] 572 matched cddid_all.tbl CDD KOG4680 KOG4680 232606 KOG4680 KOG4680, Uncharacterized conserved protein, contains ML domain [General function prediction only] 153 matched cddid_all.tbl CDD KOG4681 KOG4681 232607 KOG4681 KOG4681, Uncharacterized conserved protein [Function unknown] 280 matched cddid_all.tbl CDD KOG4682 KOG4682 232608 KOG4682 KOG4682, Uncharacterized conserved protein, contains BTB/POZ domain [General function prediction only] 488 matched cddid_all.tbl CDD KOG4683 KOG4683 232609 KOG4683 KOG4683, Uncharacterized conserved protein [Function unknown] 549 matched cddid_all.tbl CDD KOG4684 KOG4684 232610 KOG4684 KOG4684, Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only] 275 matched cddid_all.tbl CDD KOG4685 KOG4685 232611 KOG4685 KOG4685, tRNA splicing endonuclease SEN2 [Translation, ribosomal structure and biogenesis] 271 matched cddid_all.tbl CDD KOG4686 KOG4686 232612 KOG4686 KOG4686, Predicted sugar transporter [Carbohydrate transport and metabolism] 459 matched cddid_all.tbl CDD KOG4687 KOG4687 232613 KOG4687 KOG4687, Uncharacterized coiled-coil protein [Function unknown] 389 matched cddid_all.tbl CDD KOG4688 KOG4688 232614 KOG4688 KOG4688, Putative beta-catenin-Tcf/Lef signaling pathway component DRCTNNB1A [Signal transduction mechanisms] 503 matched cddid_all.tbl CDD KOG4689 KOG4689 232615 KOG4689 KOG4689, Predicted RNase [RNA processing and modification] 479 matched cddid_all.tbl CDD KOG4690 KOG4690 232616 KOG4690 KOG4690, Uncharacterized conserved protein [Function unknown] 165 matched cddid_all.tbl CDD KOG4691 KOG4691 232617 KOG4691 KOG4691, Uncharacterized conserved protein [Function unknown] 227 matched cddid_all.tbl CDD KOG4692 KOG4692 232618 KOG4692 KOG4692, Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones] 489 matched cddid_all.tbl CDD KOG4693 KOG4693 232619 KOG4693 KOG4693, Uncharacterized conserved protein, contains kelch repeat [General function prediction only] 392 matched cddid_all.tbl CDD KOG4694 KOG4694 232620 KOG4694 KOG4694, Predicted membrane protein [Function unknown] 174 matched cddid_all.tbl CDD KOG4695 KOG4695 232621 KOG4695 KOG4695, Uncharacterized conserved protein [Function unknown] 122 matched cddid_all.tbl CDD KOG4696 KOG4696 232622 KOG4696 KOG4696, Uncharacterized conserved protein [Function unknown] 393 matched cddid_all.tbl CDD KOG4697 KOG4697 232623 KOG4697 KOG4697, Integral membrane protein involved in transport between the late Golgi and endosome [Intracellular trafficking, secretion, and vesicular transport] 160 matched cddid_all.tbl CDD KOG4698 KOG4698 232624 KOG4698 KOG4698, Uncharacterized conserved protein [Function unknown] 475 matched cddid_all.tbl CDD KOG4699 KOG4699 232625 KOG4699 KOG4699, Preprotein translocase subunit Sec66 [Intracellular trafficking, secretion, and vesicular transport] 180 matched cddid_all.tbl CDD KOG4700 KOG4700 232626 KOG4700 KOG4700, Uncharacterized homolog of ribosome-binding factor A [General function prediction only] 207 matched cddid_all.tbl CDD KOG4701 KOG4701 232627 KOG4701 KOG4701, Chitinase [Cell wall/membrane/envelope biogenesis] 568 matched cddid_all.tbl CDD KOG4702 KOG4702 232628 KOG4702 KOG4702, Uncharacterized conserved protein [Function unknown] 77 matched cddid_all.tbl CDD KOG4703 KOG4703 232629 KOG4703 KOG4703, Uncharacterized conserved protein [Function unknown] 431 matched cddid_all.tbl CDD KOG4704 KOG4704 232630 KOG4704 KOG4704, Uncharacterized conserved protein [Function unknown] 431 matched cddid_all.tbl CDD KOG4705 KOG4705 232631 KOG4705 KOG4705, Uncharacterized conserved protein [Function unknown] 303 matched cddid_all.tbl CDD KOG4706 KOG4706 232632 KOG4706 KOG4706, Uncharacterized conserved protein [Function unknown] 196 matched cddid_all.tbl CDD KOG4707 KOG4707 232633 KOG4707 KOG4707, Mitochondrial/chloroplast ribosomal protein L20 [Translation, ribosomal structure and biogenesis] 147 matched cddid_all.tbl CDD KOG4708 KOG4708 232634 KOG4708 KOG4708, Mitochondrial ribosomal protein MRP17 [Translation, ribosomal structure and biogenesis] 141 matched cddid_all.tbl CDD KOG4709 KOG4709 232635 KOG4709 KOG4709, Uncharacterized conserved protein [Function unknown] 217 matched cddid_all.tbl CDD KOG4710 KOG4710 232636 KOG4710 KOG4710, E3 ubiquitin ligase, VHL component (von Hippel-Lindau tumor suppressor in humans) [Posttranslational modification, protein turnover, chaperones] 170 matched cddid_all.tbl CDD KOG4711 KOG4711 232637 KOG4711 KOG4711, Predicted membrane protein [General function prediction only] 625 matched cddid_all.tbl CDD KOG4712 KOG4712 232638 KOG4712 KOG4712, Uncharacterized conserved protein [Function unknown] 1335 matched cddid_all.tbl CDD KOG4713 KOG4713 232639 KOG4713 KOG4713, Cyclin-dependent kinase 2-associated protein [Signal transduction mechanisms, Cell cycle control, cell division, chromosome partitioning] 189 matched cddid_all.tbl CDD KOG4714 KOG4714 232640 KOG4714 KOG4714, Nucleoporin [Nuclear structure] 319 matched cddid_all.tbl CDD KOG4715 KOG4715 232641 KOG4715 KOG4715, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin [Chromatin structure and dynamics] 410 matched cddid_all.tbl CDD KOG4716 KOG4716 232642 KOG4716 KOG4716, Thioredoxin reductase [Posttranslational modification, protein turnover, chaperones] 503 matched cddid_all.tbl CDD KOG4717 KOG4717 232643 KOG4717 KOG4717, Serine/threonine protein kinase [Signal transduction mechanisms] 864 matched cddid_all.tbl CDD KOG4718 KOG4718 232644 KOG4718 KOG4718, Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics] 235 matched cddid_all.tbl CDD KOG4719 KOG4719 232645 KOG4719 KOG4719, Nuclear pore complex protein [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport] 1053 matched cddid_all.tbl CDD KOG4720 KOG4720 232646 KOG4720 KOG4720, Ethanolamine kinase [Lipid transport and metabolism] 391 matched cddid_all.tbl CDD KOG4721 KOG4721 232647 KOG4721 KOG4721, Serine/threonine protein kinase, contains leucine zipper domain [Signal transduction mechanisms] 904 matched cddid_all.tbl CDD KOG4722 KOG4722 232648 KOG4722 KOG4722, Zn-finger protein [General function prediction only] 672 matched cddid_all.tbl CDD KOG4723 KOG4723 232649 KOG4723 KOG4723, Uncharacterized conserved protein [Function unknown] 248 matched cddid_all.tbl CDD KOG4724 KOG4724 232650 KOG4724 KOG4724, Predicted Rho GTPase-activating protein [Signal transduction mechanisms] 741 matched cddid_all.tbl CDD KOG4725 KOG4725 232651 KOG4725 KOG4725, Uncharacterized conserved protein [Function unknown] 378 matched cddid_all.tbl CDD KOG4726 KOG4726 232652 KOG4726 KOG4726, Ultrahigh sulfur keratin-associated protein [Extracellular structures] 146 matched cddid_all.tbl CDD KOG4727 KOG4727 232653 KOG4727 KOG4727, U1-like Zn-finger protein [General function prediction only] 193 matched cddid_all.tbl CDD KOG4728 KOG4728 232654 KOG4728 KOG4728, Anti-apoptotic Bcl-2 family proteins, prevent opening of mitochondrial porin channel [Signal transduction mechanisms] 126 matched cddid_all.tbl CDD KOG4729 KOG4729 232655 KOG4729 KOG4729, Galactoside-binding lectin [General function prediction only] 265 matched cddid_all.tbl CDD KOG4730 KOG4730 232656 KOG4730 KOG4730, D-arabinono-1, 4-lactone oxidase [Defense mechanisms] 518 matched cddid_all.tbl CDD KOG4731 KOG4731 232657 KOG4731 KOG4731, Protein predicted to be involved in spindle matrix formation, contains DM13, DoH, and DOMON domains [Cell cycle control, cell division, chromosome partitioning] 512 matched cddid_all.tbl CDD KOG4732 KOG4732 232658 KOG4732 KOG4732, Uncharacterized conserved protein [Function unknown] 869 matched cddid_all.tbl CDD KOG4734 KOG4734 232659 KOG4734 KOG4734, Uncharacterized conserved protein [Function unknown] 537 matched cddid_all.tbl CDD KOG4735 KOG4735 232660 KOG4735 KOG4735, Extracellular protein with conserved cysteines [Function unknown] 472 matched cddid_all.tbl CDD KOG4736 KOG4736 232661 KOG4736 KOG4736, Uncharacterized conserved protein [Function unknown] 302 matched cddid_all.tbl CDD KOG4737 KOG4737 232662 KOG4737 KOG4737, ATPase membrane sector associated protein [Energy production and conversion] 326 matched cddid_all.tbl CDD KOG4738 KOG4738 232663 KOG4738 KOG4738, Predicted metallothionein [Inorganic ion transport and metabolism] 51 matched cddid_all.tbl CDD KOG4739 KOG4739 232664 KOG4739 KOG4739, Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning, General function prediction only] 233 matched cddid_all.tbl CDD KOG4740 KOG4740 232665 KOG4740 KOG4740, Uncharacterized conserved protein [Function unknown] 564 matched cddid_all.tbl CDD KOG4741 KOG4741 232666 KOG4741 KOG4741, Uncharacterized conserved protein [Function unknown] 173 matched cddid_all.tbl CDD KOG4742 KOG4742 232667 KOG4742 KOG4742, Predicted chitinase [General function prediction only] 286 matched cddid_all.tbl CDD KOG4743 KOG4743 232668 KOG4743 KOG4743, Cyclin-dependent kinase inhibitor [Signal transduction mechanisms] 195 matched cddid_all.tbl CDD KOG4744 KOG4744 232669 KOG4744 KOG4744, Uncharacterized conserved protein [Function unknown] 308 matched cddid_all.tbl CDD KOG4745 KOG4745 232670 KOG4745 KOG4745, Metalloproteinase inhibitor TIMP and related proteins [General function prediction only] 141 matched cddid_all.tbl CDD KOG4746 KOG4746 232671 KOG4746 KOG4746, Small nuclear RNA activating complex (SNAPc), subunit SNAP43 [RNA processing and modification] 423 matched cddid_all.tbl CDD KOG4747 KOG4747 232672 KOG4747 KOG4747, Two-component phosphorelay intermediate involved in MAP kinase cascade regulation [Signal transduction mechanisms] 150 matched cddid_all.tbl CDD KOG4748 KOG4748 232673 KOG4748 KOG4748, Subunit of Golgi mannosyltransferase complex [Carbohydrate transport and metabolism, Cell wall/membrane/envelope biogenesis] 364 matched cddid_all.tbl CDD KOG4749 KOG4749 232674 KOG4749 KOG4749, Inositol polyphosphate kinase [Signal transduction mechanisms] 375 matched cddid_all.tbl CDD KOG4750 KOG4750 232675 KOG4750 KOG4750, Serine O-acetyltransferase [Amino acid transport and metabolism] 269 matched cddid_all.tbl CDD KOG4751 KOG4751 232676 KOG4751 KOG4751, DNA recombinational repair protein BRCA2 [Replication, recombination and repair] 756 matched cddid_all.tbl CDD KOG4752 KOG4752 232677 KOG4752 KOG4752, Ribosomal protein L41 [Translation, ribosomal structure and biogenesis] 25 matched cddid_all.tbl CDD KOG4753 KOG4753 232678 KOG4753 KOG4753, Predicted membrane protein [Function unknown] 124 matched cddid_all.tbl CDD KOG4754 KOG4754 232679 KOG4754 KOG4754, Predicted phosphoglycerate mutase [Carbohydrate transport and metabolism] 248 matched cddid_all.tbl CDD KOG4755 KOG4755 232680 KOG4755 KOG4755, Predicted pyroglutamyl peptidase [Posttranslational modification, protein turnover, chaperones] 213 matched cddid_all.tbl CDD KOG4756 KOG4756 232681 KOG4756 KOG4756, Mitochondrial ribosomal protein L27 [Translation, ribosomal structure and biogenesis] 146 matched cddid_all.tbl CDD KOG4757 KOG4757 232682 KOG4757 KOG4757, Predicted telomere binding protein [General function prediction only] 522 matched cddid_all.tbl CDD KOG4758 KOG4758 232683 KOG4758 KOG4758, Predicted membrane protein [General function prediction only] 220 matched cddid_all.tbl CDD KOG4759 KOG4759 232684 KOG4759 KOG4759, Ribosome recycling factor [Translation, ribosomal structure and biogenesis] 263 matched cddid_all.tbl CDD KOG4760 KOG4760 232685 KOG4760 KOG4760, Uncharacterized conserved protein [Function unknown] 365 matched cddid_all.tbl CDD KOG4761 KOG4761 232686 KOG4761 KOG4761, Proteasome formation inhibitor PI31 [Posttranslational modification, protein turnover, chaperones] 266 matched cddid_all.tbl CDD KOG4762 KOG4762 232687 KOG4762 KOG4762, DNA replication factor [Replication, recombination and repair] 498 matched cddid_all.tbl CDD KOG4763 KOG4763 232688 KOG4763 KOG4763, Ubiquinol-cytochrome c reductase hinge protein [Energy production and conversion] 77 matched cddid_all.tbl CDD KOG4764 KOG4764 232689 KOG4764 KOG4764, Uncharacterized conserved protein [Function unknown] 70 matched cddid_all.tbl CDD KOG4765 KOG4765 232690 KOG4765 KOG4765, Uncharacterized conserved protein [Function unknown] 419 matched cddid_all.tbl CDD KOG4766 KOG4766 232691 KOG4766 KOG4766, Uncharacterized conserved protein [Function unknown] 64 matched cddid_all.tbl CDD KOG4767 KOG4767 232692 KOG4767 KOG4767, Cytochrome c oxidase, subunit II, and related proteins [Energy production and conversion] 231 matched cddid_all.tbl CDD KOG4768 KOG4768 232693 KOG4768 KOG4768, Mitochondrial mRNA maturase [RNA processing and modification] 796 matched cddid_all.tbl CDD KOG4769 KOG4769 232694 KOG4769 KOG4769, Cytochrome c oxidase, subunit I [Energy production and conversion] 182 matched cddid_all.tbl CDD KOG4770 KOG4770 232695 KOG4770 KOG4770, NADH dehydrogenase subunit 1 [Energy production and conversion] 315 matched cddid_all.tbl CDD KOG4771 KOG4771 232696 KOG4771 KOG4771, Nucleolar protein (NOP16) involved in 60S ribosomal subunit biogenesis [Translation, ribosomal structure and biogenesis] 210 matched cddid_all.tbl CDD KOG4772 KOG4772 232697 KOG4772 KOG4772, Predicted tRNA-splicing endonuclease subunit [Translation, ribosomal structure and biogenesis] 364 matched cddid_all.tbl CDD KOG4773 KOG4773 232698 KOG4773 KOG4773, NADPH oxidase [Energy production and conversion] 386 matched cddid_all.tbl CDD KOG4774 KOG4774 232699 KOG4774 KOG4774, Uncharacterized conserved protein [Function unknown] 190 matched cddid_all.tbl CDD KOG4775 KOG4775 232700 KOG4775 KOG4775, Uncharacterized protein SFI1 involved in G(2)-M transition [Cell cycle control, cell division, chromosome partitioning] 840 matched cddid_all.tbl CDD KOG4776 KOG4776 232701 KOG4776 KOG4776, Uncharacterized conserved protein BCNT [Function unknown] 235 matched cddid_all.tbl CDD KOG4777 KOG4777 232702 KOG4777 KOG4777, Aspartate-semialdehyde dehydrogenase [Amino acid transport and metabolism] 361 matched cddid_all.tbl CDD KOG4778 KOG4778 232703 KOG4778 KOG4778, Mitochondrial ribosomal protein L28 [Translation, ribosomal structure and biogenesis] 186 matched cddid_all.tbl CDD KOG4779 KOG4779 232704 KOG4779 KOG4779, Predicted membrane protein [Function unknown] 82 matched cddid_all.tbl CDD KOG4780 KOG4780 232705 KOG4780 KOG4780, Uncharacterized conserved protein [Function unknown] 467 matched cddid_all.tbl CDD KOG4781 KOG4781 232706 KOG4781 KOG4781, Uncharacterized conserved protein [Function unknown] 237 matched cddid_all.tbl CDD KOG4782 KOG4782 232707 KOG4782 KOG4782, Predicted membrane protein [Function unknown] 108 matched cddid_all.tbl CDD KOG4783 KOG4783 232708 KOG4783 KOG4783, Uncharacterized conserved protein [Function unknown] 102 matched cddid_all.tbl CDD KOG4784 KOG4784 232709 KOG4784 KOG4784, Uncharacterized conserved protein [Function unknown] 348 matched cddid_all.tbl CDD KOG4785 KOG4785 232710 KOG4785 KOG4785, Transcription factor CBF, beta subunit [Transcription] 177 matched cddid_all.tbl CDD KOG4786 KOG4786 232711 KOG4786 KOG4786, Ubinuclein, nuclear protein interacting with cellular and viral transcription factors [Transcription, Signal transduction mechanisms] 1136 matched cddid_all.tbl CDD KOG4787 KOG4787 232712 KOG4787 KOG4787, Uncharacterized conserved protein [Function unknown] 852 matched cddid_all.tbl CDD KOG4788 KOG4788 232713 KOG4788 KOG4788, Members of chemokine-like factor super family and related proteins [Defense mechanisms] 172 matched cddid_all.tbl CDD KOG4789 KOG4789 232714 KOG4789 KOG4789, Uncharacterized conserved protein [Function unknown] 668 matched cddid_all.tbl CDD KOG4790 KOG4790 232715 KOG4790 KOG4790, Uncharacterized conserved protein [Function unknown] 362 matched cddid_all.tbl CDD KOG4791 KOG4791 232716 KOG4791 KOG4791, Uncharacterized conserved protein [Function unknown] 667 matched cddid_all.tbl CDD KOG4792 KOG4792 232717 KOG4792 KOG4792, Crk family adapters [Signal transduction mechanisms] 293 matched cddid_all.tbl CDD KOG4793 KOG4793 232718 KOG4793 KOG4793, Three prime repair exonuclease [Replication, recombination and repair] 318 matched cddid_all.tbl CDD KOG4794 KOG4794 232719 KOG4794 KOG4794, Thymosin beta [Cell motility] 114 matched cddid_all.tbl CDD KOG4795 KOG4795 232720 KOG4795 KOG4795, Protein associated with transcriptional elongation factor ELL [Transcription] 264 matched cddid_all.tbl CDD KOG4796 KOG4796 232721 KOG4796 KOG4796, RNA polymerase II elongation factor [Transcription] 604 matched cddid_all.tbl CDD KOG4797 KOG4797 232722 KOG4797 KOG4797, Transcriptional regulator [Transcription] 123 matched cddid_all.tbl CDD KOG4798 KOG4798 232723 KOG4798 KOG4798, Uncharacterized conserved protein [Function unknown] 229 matched cddid_all.tbl CDD KOG4799 KOG4799 232724 KOG4799 KOG4799, Mitochondrial ribosomal protein L30 [Translation, ribosomal structure and biogenesis] 182 matched cddid_all.tbl CDD KOG4800 KOG4800 232725 KOG4800 KOG4800, Neuronal membrane glycoprotein/Myelin proteolipid protein [Function unknown] 248 matched cddid_all.tbl CDD KOG4801 KOG4801 232726 KOG4801 KOG4801, Member of the steroid/thyroid receptor superfamily [Signal transduction mechanisms] 321 matched cddid_all.tbl CDD KOG4802 KOG4802 232727 KOG4802 KOG4802, Adhesion-type protein [Extracellular structures] 516 matched cddid_all.tbl CDD KOG4803 KOG4803 232728 KOG4803 KOG4803, Uncharacterized conserved protein [Function unknown] 610 matched cddid_all.tbl CDD KOG4804 KOG4804 232729 KOG4804 KOG4804, Predicted membrane protein [General function prediction only] 243 matched cddid_all.tbl CDD KOG4805 KOG4805 232730 KOG4805 KOG4805, Uncharacterized conserved protein [Function unknown] 719 matched cddid_all.tbl CDD KOG4806 KOG4806 232731 KOG4806 KOG4806, Uncharacterized conserved protein [Function unknown] 454 matched cddid_all.tbl CDD KOG4807 KOG4807 232732 KOG4807 KOG4807, F-actin binding protein, regulates actin cytoskeletal organization [Cytoskeleton] 593 matched cddid_all.tbl CDD KOG4808 KOG4808 232733 KOG4808 KOG4808, Uncharacterized conserved protein [Function unknown] 151 matched cddid_all.tbl CDD KOG4809 KOG4809 232734 KOG4809 KOG4809, Rab6 GTPase-interacting protein involved in endosome-to-TGN transport [Intracellular trafficking, secretion, and vesicular transport] 654 matched cddid_all.tbl CDD KOG4810 KOG4810 232735 KOG4810 KOG4810, Uncharacterized conserved protein [Function unknown] 227 matched cddid_all.tbl CDD KOG4811 KOG4811 232736 KOG4811 KOG4811, Uncharacterized conserved protein [Function unknown] 127 matched cddid_all.tbl CDD KOG4812 KOG4812 232737 KOG4812 KOG4812, Golgi-associated protein/Nedd4 WW domain-binding protein [General function prediction only] 262 matched cddid_all.tbl CDD KOG4813 KOG4813 232738 KOG4813 KOG4813, Translation initiation factor eIF3, p35 subunit [Translation, ribosomal structure and biogenesis] 248 matched cddid_all.tbl CDD KOG4814 KOG4814 232739 KOG4814 KOG4814, Uncharacterized conserved protein [Function unknown] 872 matched cddid_all.tbl CDD KOG4815 KOG4815 232740 KOG4815 KOG4815, Muscular protein implicated in muscular dystrophy phenotype [General function prediction only] 511 matched cddid_all.tbl CDD KOG4816 KOG4816 232741 KOG4816 KOG4816, Uncharacterized conserved protein [Function unknown] 98 matched cddid_all.tbl CDD KOG4817 KOG4817 232742 KOG4817 KOG4817, Unnamed protein [Function unknown] 468 matched cddid_all.tbl CDD KOG4818 KOG4818 232743 KOG4818 KOG4818, Lysosomal-associated membrane protein [General function prediction only] 362 matched cddid_all.tbl CDD KOG4819 KOG4819 232744 KOG4819 KOG4819, Uncharacterized conserved protein [Function unknown] 106 matched cddid_all.tbl CDD KOG4820 KOG4820 232745 KOG4820 KOG4820, Involved in anesthetic response in C.elegans [General function prediction only] 933 matched cddid_all.tbl CDD KOG4821 KOG4821 232746 KOG4821 KOG4821, Predicted Na+-dependent cotransporter [General function prediction only] 287 matched cddid_all.tbl CDD KOG4822 KOG4822 232747 KOG4822 KOG4822, Predicted nuclear membrane protein involved in mRNA transport and sex determination via splicing modulation [RNA processing and modification, Signal transduction mechanisms] 1906 matched cddid_all.tbl CDD KOG4823 KOG4823 232748 KOG4823 KOG4823, Uncharacterized conserved protein [Function unknown] 328 matched cddid_all.tbl CDD KOG4824 KOG4824 232749 KOG4824 KOG4824, Apolipoprotein D/Lipocalin [Cell wall/membrane/envelope biogenesis] 224 matched cddid_all.tbl CDD KOG4825 KOG4825 232750 KOG4825 KOG4825, Component of synaptic membrane glycine-, glutamate- and thienylcyclohexylpiperidine-binding glycoprotein (43kDa) [Signal transduction mechanisms] 666 matched cddid_all.tbl CDD KOG4826 KOG4826 232751 KOG4826 KOG4826, C-8,7 sterol isomerase [Lipid transport and metabolism] 229 matched cddid_all.tbl CDD KOG4827 KOG4827 232752 KOG4827 KOG4827, Uncharacterized conserved protein [Function unknown] 279 matched cddid_all.tbl CDD KOG4828 KOG4828 232753 KOG4828 KOG4828, Uncharacterized conserved protein [Function unknown] 125 matched cddid_all.tbl CDD KOG4829 KOG4829 232754 KOG4829 KOG4829, Uncharacterized conserved protein [Function unknown] 236 matched cddid_all.tbl CDD KOG4830 KOG4830 232755 KOG4830 KOG4830, Predicted sugar transporter [Carbohydrate transport and metabolism] 412 matched cddid_all.tbl CDD KOG4831 KOG4831 232756 KOG4831 KOG4831, Unnamed protein [Function unknown] 125 matched cddid_all.tbl CDD KOG4832 KOG4832 232757 KOG4832 KOG4832, Uncharacterized conserved protein [Function unknown] 253 matched cddid_all.tbl CDD KOG4833 KOG4833 232758 KOG4833 KOG4833, Uncharacterized conserved protein [Function unknown] 573 matched cddid_all.tbl CDD KOG4834 KOG4834 232759 KOG4834 KOG4834, Predicted DNA-binding protein, contains SANT domain [General function prediction only] 280 matched cddid_all.tbl CDD KOG4835 KOG4835 232760 KOG4835 KOG4835, DNA-binding protein C1D involved in regulation of double-strand break repair [Replication, recombination and repair] 144 matched cddid_all.tbl CDD KOG4836 KOG4836 232761 KOG4836 KOG4836, Uncharacterized conserved protein [Function unknown] 215 matched cddid_all.tbl CDD KOG4837 KOG4837 232762 KOG4837 KOG4837, Uncharacterized conserved protein [Function unknown] 248 matched cddid_all.tbl CDD KOG4838 KOG4838 232763 KOG4838 KOG4838, Uncharacterized conserved protein [Function unknown] 312 matched cddid_all.tbl CDD KOG4839 KOG4839 232764 KOG4839 KOG4839, Uncharacterized conserved protein [Function unknown] 753 matched cddid_all.tbl CDD KOG4840 KOG4840 232765 KOG4840 KOG4840, Predicted hydrolases or acyltransferases (alpha/beta hydrolase superfamily) [General function prediction only] 299 matched cddid_all.tbl CDD KOG4841 KOG4841 232766 KOG4841 KOG4841, Dolichol-phosphate mannosyltransferase, subunit 3 [Posttranslational modification, protein turnover, chaperones, Signal transduction mechanisms] 95 matched cddid_all.tbl CDD KOG4842 KOG4842 232767 KOG4842 KOG4842, Protein involved in sister chromatid separation and/or segregation [Cell cycle control, cell division, chromosome partitioning] 278 matched cddid_all.tbl CDD KOG4843 KOG4843 232768 KOG4843 KOG4843, Uncharacterized conserved protein [Function unknown] 355 matched cddid_all.tbl CDD KOG4844 KOG4844 232769 KOG4844 KOG4844, Mitochondrial ribosomal protein S27 [Translation, ribosomal structure and biogenesis] 102 matched cddid_all.tbl CDD KOG4845 KOG4845 232770 KOG4845 KOG4845, NADH dehydrogenase, subunit 4 [Energy production and conversion] 452 matched cddid_all.tbl CDD KOG4846 KOG4846 232771 KOG4846 KOG4846, Nuclear receptor [Signal transduction mechanisms] 538 matched cddid_all.tbl CDD KOG4847 KOG4847 232772 KOG4847 KOG4847, Coiled coil protein involved in linking membrane proteins to cytoskeleton [General function prediction only] 483 matched cddid_all.tbl CDD KOG4848 KOG4848 232773 KOG4848 KOG4848, Extracellular matrix-associated peroxidase [Extracellular structures, Defense mechanisms] 225 matched cddid_all.tbl CDD KOG4849 KOG4849 232774 KOG4849 KOG4849, mRNA cleavage factor I subunit/CPSF subunit [RNA processing and modification] 498 matched cddid_all.tbl CDD KOG4850 KOG4850 232775 KOG4850 KOG4850, Uncharacterized conserved protein [Function unknown] 190 matched cddid_all.tbl CDD KOG4851 KOG4851 232776 KOG4851 KOG4851, Uncharacterized conserved protein [Function unknown] 156 matched cddid_all.tbl CDD KOG4852 KOG4852 232777 KOG4852 KOG4852, Uncharacterized conserved protein [Function unknown] 265 matched cddid_all.tbl CDD LOAD_ACT LOAD_ACT 40050 ACT small ligand binding domain. 76 matched cddid_all.tbl CDD LOAD_ATP_cone LOAD_ATP_cone 40051 ATP_cone ATP-cone domain, ATP binding allosteric domain seen in nucleotidereductases and other proteins. 89 matched cddid_all.tbl CDD LOAD_Ccd1 LOAD_Ccd1 88627 Ccd1 Conserved cysteine containing domain 1 (a predicted disulfide bond redox regulator). 71 matched cddid_all.tbl CDD LOAD_Ccd2 LOAD_Ccd2 40053 Ccd2 Conserved cysteine containing domain 2 (a predicted disulfide bond redox regulator). 114 matched cddid_all.tbl CDD LOAD_DAK2 LOAD_DAK2 40054 DAK2 predicted phosphatase domain of the Diacylglycerol kinase family. 202 matched cddid_all.tbl CDD LOAD_DSBH LOAD_DSBH 40055 DSBH Double stranded beta helix domain involved in carbohydrate binding and protein-protein interactions in different contexts. 66 matched cddid_all.tbl CDD LOAD_Dak1 LOAD_Dak1 40056 Dak1 Kinase domain of the Diacylglycerol kinase family. 329 matched cddid_all.tbl CDD LOAD_EF1B LOAD_EF1B 40057 EF1B Elongation factor 1B conserved domain. 89 matched cddid_all.tbl CDD LOAD_ERCC4 LOAD_ERCC4 40058 ERCC4 ERCC4 domain, Predicted nuclease domain. 84 matched cddid_all.tbl CDD LOAD_FCS LOAD_FCS 40059 FCS Zinc coordinating domain chromatinic proteins. 40 matched cddid_all.tbl CDD LOAD_HD LOAD_HD 40060 HD HD Metal dependent (phospho) Hydrolase domain. 114 matched cddid_all.tbl CDD LOAD_HisDeac1 LOAD_HisDeac1 40061 HisDeac1 RPD3 like Histone decetylase domain. 295 matched cddid_all.tbl CDD LOAD_Hrd LOAD_Hrd 40062 Hrd Conserved helical domain seen associated with recQ family helicases and RNASeD like nucleases. 77 matched cddid_all.tbl CDD LOAD_LSAT LOAD_LSAT 40063 LSAT Late Stage Acyl transferases. 278 matched cddid_all.tbl CDD LOAD_NTF2 LOAD_NTF2 40064 NTF2 Domain found in RNA transport proteins. 123 matched cddid_all.tbl CDD LOAD_S2Pmetalloprt LOAD_S2Pmetalloprt 40065 S2Pmetalloprt S2P metal dependent membrane associated protease domain. 148 matched cddid_all.tbl CDD LOAD_SKIP LOAD_SKIP 40066 SKIP Conserved domain found in chromatinic proteins. 168 matched cddid_all.tbl CDD LOAD_Toprim LOAD_Toprim 40067 Toprim The Topoisomerase- primase domain- a nucleotidyl transferase/hydrolase domain. 98 matched cddid_all.tbl CDD LOAD_USPA LOAD_USPA 40068 USPA An ATP binding domain seen as a stand alone in USPA. 135 matched cddid_all.tbl CDD LOAD_W2 LOAD_W2 40069 W2 conserved protein-protein interaction domain in translation factors like eIF2B. 116 matched cddid_all.tbl CDD LOAD_arc_metj LOAD_arc_metj 40070 arc_metj A small exclusively prokaryotic DNA binding domain with beta sheet DNA contact. 43 matched cddid_all.tbl CDD LOAD_bir LOAD_bir 88628 BIR Zn binding domain involved in protein protein interactions in caspase inhibition and spindle assembly. 65 matched cddid_all.tbl CDD LOAD_cdc45 LOAD_cdc45 40072 cdc45 Possible enzyme involved in DNA replication. 578 matched cddid_all.tbl CDD LOAD_cold LOAD_cold 40073 cold Cold Shock RNA binding domain of the OB fold. 67 matched cddid_all.tbl CDD LOAD_efts_N LOAD_efts_N 40074 efts_N Conserved 3 helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins. 41 matched cddid_all.tbl CDD LOAD_gas2groo LOAD_gas2groo 40075 gas2groo Conserved domain seen in Groovin and Gas2 proteins. 128 matched cddid_all.tbl CDD LOAD_gyf LOAD_gyf 40076 gyf Protein protein interaction domain involved in binding proline rich sequences. 69 matched cddid_all.tbl CDD LOAD_hismacro LOAD_hismacro 40077 hismacro Domain found in Macro histone 2 (predicted phosphoesterase). 170 matched cddid_all.tbl CDD LOAD_kelch LOAD_kelch 40078 kelch A beta propeller domain involved in protein-protein interactions and some enzymatic actvities like gycolate oxidase. 48 matched cddid_all.tbl CDD LOAD_ku LOAD_ku 40079 ku A family of DNA binding domains including those in Ku70/80. 521 matched cddid_all.tbl CDD LOAD_ligase LOAD_ligase 40080 ligase ATP and NAD dependent DNA ligases and capping enzymes. 184 matched cddid_all.tbl CDD LOAD_little_fing LOAD_little_fing 40081 little_fing Zinc coordinating RNA binding domain. 31 matched cddid_all.tbl CDD LOAD_mi LOAD_mi 40082 mi conserved alpha helical domain involved in protein-protein interactions in eukaryotic translation regulators. 122 matched cddid_all.tbl CDD LOAD_minC LOAD_minC 40083 minC Bacterial proteins involved in chromosomal partioning. 105 matched cddid_all.tbl CDD LOAD_nac LOAD_nac 40084 NAC Domain found in the archaeal and eukaryotic BTF proteins involved in translation and transcription. 61 matched cddid_all.tbl CDD LOAD_nic LOAD_nic 40085 nic Large alpha helical domain involved in protein-protein interactions in eIF4G, NMD2 and CBP80. 214 matched cddid_all.tbl CDD LOAD_nirV LOAD_nirV 40086 nirV Conserved bacterial and eukaryotic enzyme of unknown activity. 238 matched cddid_all.tbl CDD LOAD_osmc LOAD_osmc 40087 osmc domain with Conserved cysteine found in OsmC like proteins (predicted oxidative damage protective proteins). 134 matched cddid_all.tbl CDD LOAD_p29_RnaseP LOAD_p29_RnaseP 40088 p29_RnaseP subunit of RNA processing enzyme RNAse P. 92 matched cddid_all.tbl CDD LOAD_pex11 LOAD_pex11 40089 pex11 peroxisomal development protein. 223 matched cddid_all.tbl CDD LOAD_php LOAD_php 40090 php family of phosphoesterases. 206 matched cddid_all.tbl CDD LOAD_pua LOAD_pua 40091 pua Novel RNA binding domain. 76 matched cddid_all.tbl CDD LOAD_rna_Cyc LOAD_rna_Cyc 40092 rna_Cyc RNA 3' phosphate cyclase domain. 329 matched cddid_all.tbl CDD LOAD_sir2 LOAD_sir2 40093 sir2 Catalytic domain of the SIR2 like Histonde deacetylases and ADP ribosyl transferase. 217 matched cddid_all.tbl CDD LOAD_sis LOAD_sis 40094 sis phosphoSugar isomerase domain similar to glucose phosphate isomerase. 90 matched cddid_all.tbl CDD LOAD_surE LOAD_surE 40095 surE Conserved bacterial and eukaryotic enzyme of unknown activity. 192 matched cddid_all.tbl CDD LOAD_swib LOAD_swib 40096 swib Conserved domain involved in chromatin structure regulation. 85 matched cddid_all.tbl CDD LOAD_tam LOAD_tam 40097 tam DNA binding domain found in several chromosomal proteins including the Methyl CpG binding proteins. 75 matched cddid_all.tbl CDD LOAD_taz LOAD_taz 40098 taz Zinc binding domain involved in protein-protein interactions. 101 matched cddid_all.tbl CDD LOAD_tf2f LOAD_tf2f 40099 tf2f Conserved domain in TF2F, predicted chromatin modifying protein. 105 matched cddid_all.tbl CDD LOAD_uvrC_endov LOAD_uvrC_endov 40100 uvrC_endov DNASE domain found in UvrC and EndoV proteins. 123 matched cddid_all.tbl CDD LOAD_yugu LOAD_yugu 40101 yugu Conserved bacterial and eukaryotic enzyme of unknown activity. 135 matched cddid_all.tbl CDD LOAD_zz LOAD_zz 40102 zz Zinc binding domain seen in both chromatinic and cytoskeletal proteins. 48 matched cddid_all.tbl CDD MTH00001 MTH00001 177099 ND4L NADH dehydrogenase subunit 4L; Provisional 99 matched cddid_all.tbl CDD MTH00004 MTH00004 214398 ND5 NADH dehydrogenase subunit 5; Validated 602 matched cddid_all.tbl CDD MTH00005 MTH00005 164583 ATP6 ATP synthase F0 subunit 6; Provisional 231 matched cddid_all.tbl CDD MTH00007 MTH00007 133649 COX1 cytochrome c oxidase subunit I; Validated 511 matched cddid_all.tbl CDD MTH00008 MTH00008 164584 COX2 cytochrome c oxidase subunit II; Validated 228 matched cddid_all.tbl CDD MTH00009 MTH00009 177101 COX3 cytochrome c oxidase subunit III; Validated 259 matched cddid_all.tbl CDD MTH00010 MTH00010 164586 ND1 NADH dehydrogenase subunit 1; Validated 311 matched cddid_all.tbl CDD MTH00011 MTH00011 164587 ND2 NADH dehydrogenase subunit 2; Validated 330 matched cddid_all.tbl CDD MTH00012 MTH00012 164588 ND3 NADH dehydrogenase subunit 3; Validated 117 matched cddid_all.tbl CDD MTH00013 MTH00013 133655 ND4L NADH dehydrogenase subunit 4L; Validated 97 matched cddid_all.tbl CDD MTH00014 MTH00014 214399 ND4 NADH dehydrogenase subunit 4; Validated 452 matched cddid_all.tbl CDD MTH00015 MTH00015 164590 ND6 NADH dehydrogenase subunit 6; Validated 155 matched cddid_all.tbl CDD MTH00016 MTH00016 177102 CYTB cytochrome b; Validated 378 matched cddid_all.tbl CDD MTH00018 MTH00018 164592 ND3 NADH dehydrogenase subunit 3; Validated 113 matched cddid_all.tbl CDD MTH00020 MTH00020 214400 ND5 NADH dehydrogenase subunit 5; Reviewed 610 matched cddid_all.tbl CDD MTH00021 MTH00021 214401 ND6 NADH dehydrogenase subunit 6; Validated 188 matched cddid_all.tbl CDD MTH00022 MTH00022 164595 CYTB cytochrome b; Validated 379 matched cddid_all.tbl CDD MTH00023 MTH00023 214402 COX2 cytochrome c oxidase subunit II; Validated 240 matched cddid_all.tbl CDD MTH00024 MTH00024 214403 COX3 cytochrome c oxidase subunit III; Validated 261 matched cddid_all.tbl CDD MTH00025 MTH00025 214404 ATP8 ATP synthase F0 subunit 8; Validated 70 matched cddid_all.tbl CDD MTH00026 MTH00026 164599 COX1 cytochrome c oxidase subunit I; Provisional 534 matched cddid_all.tbl CDD MTH00027 MTH00027 214405 COX2 cytochrome c oxidase subunit II; Provisional 262 matched cddid_all.tbl CDD MTH00028 MTH00028 214406 COX3 cytochrome c oxidase subunit III; Provisional 297 matched cddid_all.tbl CDD MTH00029 MTH00029 177108 ND1 NADH dehydrogenase subunit 1; Provisional 343 matched cddid_all.tbl CDD MTH00030 MTH00030 164603 ND3 NADH dehydrogenase subunit 3; Provisional 123 matched cddid_all.tbl CDD MTH00032 MTH00032 214407 ND5 NADH dehydrogenase subunit 5; Provisional 669 matched cddid_all.tbl CDD MTH00033 MTH00033 133672 CYTB cytochrome b; Provisional 383 matched cddid_all.tbl CDD MTH00034 MTH00034 177109 CYTB cytochrome b; Validated 379 matched cddid_all.tbl CDD MTH00035 MTH00035 177110 ATP6 ATP synthase F0 subunit 6; Validated 229 matched cddid_all.tbl CDD MTH00036 MTH00036 214408 ATP8 ATP synthase F0 subunit 8; Validated 54 matched cddid_all.tbl CDD MTH00037 MTH00037 177112 COX1 cytochrome c oxidase subunit I; Provisional 517 matched cddid_all.tbl CDD MTH00038 MTH00038 177113 COX2 cytochrome c oxidase subunit II; Provisional 229 matched cddid_all.tbl CDD MTH00039 MTH00039 177114 COX3 cytochrome c oxidase subunit III; Validated 260 matched cddid_all.tbl CDD MTH00040 MTH00040 214409 ND1 NADH dehydrogenase subunit 1; Validated 323 matched cddid_all.tbl CDD MTH00041 MTH00041 177116 ND2 NADH dehydrogenase subunit 2; Validated 349 matched cddid_all.tbl CDD MTH00042 MTH00042 177117 ND3 NADH dehydrogenase subunit 3; Validated 116 matched cddid_all.tbl CDD MTH00043 MTH00043 214410 ND4L NADH dehydrogenase subunit 4L; Validated 98 matched cddid_all.tbl CDD MTH00044 MTH00044 214411 ND4 NADH dehydrogenase subunit 4; Validated 458 matched cddid_all.tbl CDD MTH00045 MTH00045 177120 ND6 NADH dehydrogenase subunit 6; Validated 162 matched cddid_all.tbl CDD MTH00046 MTH00046 177121 CYTB cytochrome b; Validated 355 matched cddid_all.tbl CDD MTH00047 MTH00047 214412 COX2 cytochrome c oxidase subunit II; Provisional 194 matched cddid_all.tbl CDD MTH00048 MTH00048 177123 COX1 cytochrome c oxidase subunit I; Provisional 511 matched cddid_all.tbl CDD MTH00049 MTH00049 177124 COX3 cytochrome c oxidase subunit III; Validated 215 matched cddid_all.tbl CDD MTH00050 MTH00050 177125 ATP6 ATP synthase F0 subunit 6; Validated 170 matched cddid_all.tbl CDD MTH00051 MTH00051 177126 COX2 cytochrome c oxidase subunit II; Provisional 234 matched cddid_all.tbl CDD MTH00052 MTH00052 164623 COX3 cytochrome c oxidase subunit III; Provisional 262 matched cddid_all.tbl CDD MTH00053 MTH00053 164624 CYTB cytochrome b; Provisional 381 matched cddid_all.tbl CDD MTH00054 MTH00054 177127 ND1 NADH dehydrogenase subunit 1; Provisional 324 matched cddid_all.tbl CDD MTH00055 MTH00055 177128 ND3 NADH dehydrogenase subunit 3; Provisional 118 matched cddid_all.tbl CDD MTH00057 MTH00057 177129 ND6 NADH dehydrogenase subunit 6; Provisional 186 matched cddid_all.tbl CDD MTH00058 MTH00058 177130 ND1 NADH dehydrogenase subunit 1; Provisional 293 matched cddid_all.tbl CDD MTH00059 MTH00059 177131 ND2 NADH dehydrogenase subunit 2; Provisional 289 matched cddid_all.tbl CDD MTH00060 MTH00060 177132 ND3 NADH dehydrogenase subunit 3; Provisional 116 matched cddid_all.tbl CDD MTH00061 MTH00061 177133 ND4L NADH dehydrogenase subunit 4L; Provisional 86 matched cddid_all.tbl CDD MTH00062 MTH00062 214413 ND4 NADH dehydrogenase subunit 4; Provisional 417 matched cddid_all.tbl CDD MTH00063 MTH00063 214414 ND5 NADH dehydrogenase subunit 5; Provisional 522 matched cddid_all.tbl CDD MTH00064 MTH00064 177136 ND6 NADH dehydrogenase subunit 6; Provisional 151 matched cddid_all.tbl CDD MTH00065 MTH00065 214415 ND6 NADH dehydrogenase subunit 6; Provisional 172 matched cddid_all.tbl CDD MTH00066 MTH00066 214416 ND5 NADH dehydrogenase subunit 5; Provisional 598 matched cddid_all.tbl CDD MTH00067 MTH00067 177139 ND4L NADH dehydrogenase subunit 4L; Provisional 98 matched cddid_all.tbl CDD MTH00068 MTH00068 214417 ND4 NADH dehydrogenase subunit 4; Provisional 458 matched cddid_all.tbl CDD MTH00069 MTH00069 177141 ND3 NADH dehydrogenase subunit 3; Provisional 114 matched cddid_all.tbl CDD MTH00070 MTH00070 177142 ND2 NADH dehydrogenase subunit 2; Provisional 346 matched cddid_all.tbl CDD MTH00071 MTH00071 214418 ND1 NADH dehydrogenase subunit 1; Provisional 322 matched cddid_all.tbl CDD MTH00072 MTH00072 164642 ATP8 ATP synthase F0 subunit 8; Provisional 54 matched cddid_all.tbl CDD MTH00073 MTH00073 177144 ATP6 ATP synthase F0 subunit 6; Provisional 227 matched cddid_all.tbl CDD MTH00074 MTH00074 177145 CYTB cytochrome b; Provisional 380 matched cddid_all.tbl CDD MTH00075 MTH00075 177146 COX3 cytochrome c oxidase subunit III; Provisional 261 matched cddid_all.tbl CDD MTH00076 MTH00076 164646 COX2 cytochrome c oxidase subunit II; Provisional 228 matched cddid_all.tbl CDD MTH00077 MTH00077 214419 COX1 cytochrome c oxidase subunit I; Provisional 514 matched cddid_all.tbl CDD MTH00079 MTH00079 177148 COX1 cytochrome c oxidase subunit I; Provisional 508 matched cddid_all.tbl CDD MTH00080 MTH00080 177149 COX2 cytochrome c oxidase subunit II; Provisional 231 matched cddid_all.tbl CDD MTH00083 MTH00083 177150 COX3 cytochrome c oxidase subunit III; Provisional 256 matched cddid_all.tbl CDD MTH00086 MTH00086 177151 CYTB cytochrome b; Provisional 355 matched cddid_all.tbl CDD MTH00087 MTH00087 177152 ATP6 ATP synthase F0 subunit 6; Provisional 195 matched cddid_all.tbl CDD MTH00090 MTH00090 177153 ND1 NADH dehydrogenase subunit 1; Provisional 284 matched cddid_all.tbl CDD MTH00091 MTH00091 177154 ND2 NADH dehydrogenase subunit 2; Provisional 273 matched cddid_all.tbl CDD MTH00092 MTH00092 177155 ND3 NADH dehydrogenase subunit 3; Provisional 111 matched cddid_all.tbl CDD MTH00093 MTH00093 177156 ND4L NADH dehydrogenase subunit 4L; Provisional 77 matched cddid_all.tbl CDD MTH00094 MTH00094 177157 ND4 NADH dehydrogenase subunit 4; Provisional 403 matched cddid_all.tbl CDD MTH00095 MTH00095 177158 ND5 NADH dehydrogenase subunit 5; Provisional 527 matched cddid_all.tbl CDD MTH00097 MTH00097 177159 ND6 NADH dehydrogenase subunit 6; Provisional 121 matched cddid_all.tbl CDD MTH00098 MTH00098 177160 COX2 cytochrome c oxidase subunit II; Validated 227 matched cddid_all.tbl CDD MTH00099 MTH00099 177161 COX3 cytochrome c oxidase subunit III; Validated 261 matched cddid_all.tbl CDD MTH00100 MTH00100 177162 CYTB cytochrome b; Provisional 379 matched cddid_all.tbl CDD MTH00101 MTH00101 177163 ATP6 ATP synthase F0 subunit 6; Validated 226 matched cddid_all.tbl CDD MTH00102 MTH00102 214420 ATP8 ATP synthase F0 subunit 8; Validated 67 matched cddid_all.tbl CDD MTH00103 MTH00103 177165 COX1 cytochrome c oxidase subunit I; Validated 513 matched cddid_all.tbl CDD MTH00104 MTH00104 177166 ND1 NADH dehydrogenase subunit 1; Provisional 318 matched cddid_all.tbl CDD MTH00105 MTH00105 177167 ND2 NADH dehydrogenase subunit 2; Provisional 347 matched cddid_all.tbl CDD MTH00106 MTH00106 177168 ND3 NADH dehydrogenase subunit 3; Provisional 115 matched cddid_all.tbl CDD MTH00107 MTH00107 177169 ND4L NADH dehydrogenase subunit 4L; Provisional 98 matched cddid_all.tbl CDD MTH00108 MTH00108 177170 ND5 NADH dehydrogenase subunit 5; Provisional 602 matched cddid_all.tbl CDD MTH00109 MTH00109 214421 ND6 NADH dehydrogenase subunit 6; Provisional 175 matched cddid_all.tbl CDD MTH00110 MTH00110 177172 ND4 NADH dehydrogenase subunit 4; Provisional 459 matched cddid_all.tbl CDD MTH00111 MTH00111 214422 ND1 NADH dehydrogenase subunit 1; Provisional 323 matched cddid_all.tbl CDD MTH00112 MTH00112 214423 ND2 NADH dehydrogenase subunit 2; Provisional 346 matched cddid_all.tbl CDD MTH00113 MTH00113 177175 ND3 NADH dehydrogenase subunit 3; Provisional 114 matched cddid_all.tbl CDD MTH00115 MTH00115 214424 ND6 NADH dehydrogenase subunit 6; Provisional 174 matched cddid_all.tbl CDD MTH00116 MTH00116 177177 COX1 cytochrome c oxidase subunit I; Provisional 515 matched cddid_all.tbl CDD MTH00117 MTH00117 177178 COX2 cytochrome c oxidase subunit II; Provisional 227 matched cddid_all.tbl CDD MTH00118 MTH00118 177179 COX3 cytochrome c oxidase subunit III; Provisional 261 matched cddid_all.tbl CDD MTH00119 MTH00119 214425 CYTB cytochrome b; Provisional 380 matched cddid_all.tbl CDD MTH00120 MTH00120 177181 ATP6 ATP synthase F0 subunit 6; Provisional 227 matched cddid_all.tbl CDD MTH00123 MTH00123 214426 ATP8 ATP synthase F0 subunit 8; Provisional 54 matched cddid_all.tbl CDD MTH00124 MTH00124 214427 ND4 NADH dehydrogenase subunit 4; Provisional 457 matched cddid_all.tbl CDD MTH00125 MTH00125 177184 ND4L NADH dehydrogenase subunit 4L; Provisional 98 matched cddid_all.tbl CDD MTH00126 MTH00126 177185 ND4L NADH dehydrogenase subunit 4L; Provisional 98 matched cddid_all.tbl CDD MTH00127 MTH00127 177186 ND4 NADH dehydrogenase subunit 4; Provisional 459 matched cddid_all.tbl CDD MTH00129 MTH00129 177187 COX2 cytochrome c oxidase subunit II; Provisional 230 matched cddid_all.tbl CDD MTH00130 MTH00130 177188 COX3 cytochrome c oxidase subunit III; Provisional 261 matched cddid_all.tbl CDD MTH00131 MTH00131 177189 CYTB cytochrome b; Provisional 380 matched cddid_all.tbl CDD MTH00132 MTH00132 177190 ATP6 ATP synthase F0 subunit 6; Provisional 227 matched cddid_all.tbl CDD MTH00133 MTH00133 177191 ATP8 ATP synthase F0 subunit 8; Provisional 55 matched cddid_all.tbl CDD MTH00134 MTH00134 177192 ND1 NADH dehydrogenase subunit 1; Provisional 324 matched cddid_all.tbl CDD MTH00135 MTH00135 177193 ND2 NADH dehydrogenase subunit 2; Provisional 347 matched cddid_all.tbl CDD MTH00136 MTH00136 177194 ND3 NADH dehydrogenase subunit 3; Provisional 116 matched cddid_all.tbl CDD MTH00137 MTH00137 214428 ND5 NADH dehydrogenase subunit 5; Provisional 611 matched cddid_all.tbl CDD MTH00138 MTH00138 177196 ND6 NADH dehydrogenase subunit 6; Provisional 173 matched cddid_all.tbl CDD MTH00139 MTH00139 214429 COX2 cytochrome c oxidase subunit II; Provisional 226 matched cddid_all.tbl CDD MTH00140 MTH00140 214430 COX2 cytochrome c oxidase subunit II; Provisional 228 matched cddid_all.tbl CDD MTH00141 MTH00141 177199 COX3 cytochrome c oxidase subunit III; Provisional 259 matched cddid_all.tbl CDD MTH00142 MTH00142 214431 COX1 cytochrome c oxidase subunit I; Provisional 511 matched cddid_all.tbl CDD MTH00143 MTH00143 177201 ND1 NADH dehydrogenase subunit 1; Provisional 307 matched cddid_all.tbl CDD MTH00144 MTH00144 214432 ND2 NADH dehydrogenase subunit 2; Provisional 328 matched cddid_all.tbl CDD MTH00145 MTH00145 177203 CYTB cytochrome b; Provisional 379 matched cddid_all.tbl CDD MTH00147 MTH00147 177204 ATP8 ATP synthase F0 subunit 8; Provisional 51 matched cddid_all.tbl CDD MTH00148 MTH00148 214433 ND3 NADH dehydrogenase subunit 3; Provisional 117 matched cddid_all.tbl CDD MTH00149 MTH00149 214434 ND4L NADH dehydrogenase subunit 4L; Provisional 97 matched cddid_all.tbl CDD MTH00150 MTH00150 214435 ND4 NADH dehydrogenase subunit 4; Provisional 417 matched cddid_all.tbl CDD MTH00151 MTH00151 214436 ND5 NADH dehydrogenase subunit 5; Provisional 565 matched cddid_all.tbl CDD MTH00152 MTH00152 214437 ND6 NADH dehydrogenase subunit 6; Provisional 163 matched cddid_all.tbl CDD MTH00153 MTH00153 177210 COX1 cytochrome c oxidase subunit I; Provisional 511 matched cddid_all.tbl CDD MTH00154 MTH00154 214438 COX2 cytochrome c oxidase subunit II; Provisional 227 matched cddid_all.tbl CDD MTH00155 MTH00155 214439 COX3 cytochrome c oxidase subunit III; Provisional 255 matched cddid_all.tbl CDD MTH00156 MTH00156 214440 CYTB cytochrome b; Provisional 356 matched cddid_all.tbl CDD MTH00157 MTH00157 214441 ATP6 ATP synthase F0 subunit 6; Provisional 223 matched cddid_all.tbl CDD MTH00158 MTH00158 177215 ATP8 ATP synthase F0 subunit 8; Provisional 32 matched cddid_all.tbl CDD MTH00160 MTH00160 214442 ND2 NADH dehydrogenase subunit 2; Provisional 335 matched cddid_all.tbl CDD MTH00161 MTH00161 177217 ND3 NADH dehydrogenase subunit 3; Provisional 113 matched cddid_all.tbl CDD MTH00162 MTH00162 177218 ND4L NADH dehydrogenase subunit 4L; Provisional 89 matched cddid_all.tbl CDD MTH00163 MTH00163 214443 ND4 NADH dehydrogenase subunit 4; Provisional 445 matched cddid_all.tbl CDD MTH00165 MTH00165 214444 ND5 NADH dehydrogenase subunit 5; Provisional 573 matched cddid_all.tbl CDD MTH00166 MTH00166 214445 ND6 NADH dehydrogenase subunit 6; Provisional 160 matched cddid_all.tbl CDD MTH00167 MTH00167 177222 COX1 cytochrome c oxidase subunit I; Provisional 512 matched cddid_all.tbl CDD MTH00168 MTH00168 177223 COX2 cytochrome c oxidase subunit II; Provisional 225 matched cddid_all.tbl CDD MTH00169 MTH00169 214446 ATP8 ATP synthase F0 subunit 8; Provisional 67 matched cddid_all.tbl CDD MTH00171 MTH00171 177225 ATP8 ATP synthase F0 subunit 8; Provisional 54 matched cddid_all.tbl CDD MTH00172 MTH00172 214447 ATP6 ATP synthase F0 subunit 6; Provisional 232 matched cddid_all.tbl CDD MTH00173 MTH00173 214448 ATP6 ATP synthase F0 subunit 6; Provisional 231 matched cddid_all.tbl CDD MTH00174 MTH00174 133799 ATP6 ATP synthase F0 subunit 6; Provisional 252 matched cddid_all.tbl CDD MTH00175 MTH00175 177228 ATP6 ATP synthase F0 subunit 6; Provisional 244 matched cddid_all.tbl CDD MTH00176 MTH00176 214449 ATP6 ATP synthase F0 subunit 6; Provisional 229 matched cddid_all.tbl CDD MTH00179 MTH00179 177230 ATP6 ATP synthase F0 subunit 6; Provisional 227 matched cddid_all.tbl CDD MTH00180 MTH00180 177231 ND4L NADH dehydrogenase subunit 4L; Provisional 99 matched cddid_all.tbl CDD MTH00181 MTH00181 214450 ND4L NADH dehydrogenase subunit 4L; Provisional 93 matched cddid_all.tbl CDD MTH00182 MTH00182 214451 COX1 cytochrome c oxidase subunit I; Provisional 525 matched cddid_all.tbl CDD MTH00183 MTH00183 177234 COX1 cytochrome c oxidase subunit I; Provisional 516 matched cddid_all.tbl CDD MTH00184 MTH00184 177235 COX1 cytochrome c oxidase subunit I; Provisional 519 matched cddid_all.tbl CDD MTH00185 MTH00185 164736 COX2 cytochrome c oxidase subunit II; Provisional 230 matched cddid_all.tbl CDD MTH00186 MTH00186 177236 ATP8 ATP synthase F0 subunit 8; Provisional 52 matched cddid_all.tbl CDD MTH00188 MTH00188 177237 ND4L NADH dehydrogenase subunit 4L; Provisional 97 matched cddid_all.tbl CDD MTH00189 MTH00189 177238 COX3 cytochrome c oxidase subunit III; Provisional 260 matched cddid_all.tbl CDD MTH00191 MTH00191 177239 CYTB cytochrome b; Provisional 365 matched cddid_all.tbl CDD MTH00192 MTH00192 177240 ND4L NADH dehydrogenase subunit 4L; Provisional 99 matched cddid_all.tbl CDD MTH00193 MTH00193 177241 ND1 NADH dehydrogenase subunit 1; Provisional 306 matched cddid_all.tbl CDD MTH00195 MTH00195 214452 ND1 NADH dehydrogenase subunit 1; Provisional 307 matched cddid_all.tbl CDD MTH00196 MTH00196 214453 ND2 NADH dehydrogenase subunit 2; Provisional 365 matched cddid_all.tbl CDD MTH00197 MTH00197 177244 ND2 NADH dehydrogenase subunit 2; Provisional 323 matched cddid_all.tbl CDD MTH00198 MTH00198 214454 ND2 NADH dehydrogenase subunit 2; Provisional 607 matched cddid_all.tbl CDD MTH00199 MTH00199 177245 ND2 NADH dehydrogenase subunit 2; Provisional 460 matched cddid_all.tbl CDD MTH00200 MTH00200 177246 ND2 NADH dehydrogenase subunit 2; Provisional 347 matched cddid_all.tbl CDD MTH00202 MTH00202 214455 ND3 NADH dehydrogenase subunit 3; Provisional 117 matched cddid_all.tbl CDD MTH00203 MTH00203 214456 ND3 NADH dehydrogenase subunit 3; Provisional 112 matched cddid_all.tbl CDD MTH00204 MTH00204 164750 ND4 NADH dehydrogenase subunit 4; Provisional 485 matched cddid_all.tbl CDD MTH00205 MTH00205 214457 ND4 NADH dehydrogenase subunit 4; Provisional 448 matched cddid_all.tbl CDD MTH00206 MTH00206 214458 ND4 NADH dehydrogenase subunit 4; Provisional 450 matched cddid_all.tbl CDD MTH00207 MTH00207 164753 ND5 NADH dehydrogenase subunit 5; Provisional 572 matched cddid_all.tbl CDD MTH00208 MTH00208 177251 ND5 NADH dehydrogenase subunit 5; Provisional 628 matched cddid_all.tbl CDD MTH00209 MTH00209 177252 ND5 NADH dehydrogenase subunit 5; Provisional 564 matched cddid_all.tbl CDD MTH00210 MTH00210 177253 ND5 NADH dehydrogenase subunit 5; Provisional 616 matched cddid_all.tbl CDD MTH00211 MTH00211 214459 ND5 NADH dehydrogenase subunit 5; Provisional 597 matched cddid_all.tbl CDD MTH00212 MTH00212 214460 ND6 NADH dehydrogenase subunit 6; Provisional 160 matched cddid_all.tbl CDD MTH00213 MTH00213 177256 ND6 NADH dehydrogenase subunit 6; Provisional 239 matched cddid_all.tbl CDD MTH00214 MTH00214 214461 ND6 NADH dehydrogenase subunit 6; Provisional 168 matched cddid_all.tbl CDD MTH00216 MTH00216 164761 ND1 NADH dehydrogenase subunit 1; Provisional 327 matched cddid_all.tbl CDD MTH00217 MTH00217 214462 ND4 NADH dehydrogenase subunit 4; Provisional 482 matched cddid_all.tbl CDD MTH00218 MTH00218 214463 ND1 NADH dehydrogenase subunit 1; Provisional 311 matched cddid_all.tbl CDD MTH00219 MTH00219 214464 COX3 cytochrome c oxidase subunit III; Provisional 262 matched cddid_all.tbl CDD MTH00222 MTH00222 164765 ATP9 ATP synthase F0 subunit 9; Provisional 77 matched cddid_all.tbl CDD MTH00223 MTH00223 177260 COX1 cytochrome c oxidase subunit I; Provisional 512 matched cddid_all.tbl CDD MTH00224 MTH00224 164767 CYTB cytochrome b; Provisional 379 matched cddid_all.tbl CDD MTH00225 MTH00225 214465 ND1 NADH dehydrogenase subunit 1; Provisional 305 matched cddid_all.tbl CDD MTH00226 MTH00226 214466 ND4 NADH dehydrogenase subunit 4; Provisional 505 matched cddid_all.tbl CDD MTH00260 MTH00260 164770 ATP8 ATP synthase F0 subunit 8; Provisional 53 matched cddid_all.tbl CDD MTH00261 MTH00261 177263 ATP8 ATP synthase F0 subunit 8; Provisional 68 matched cddid_all.tbl CDD NF000031 NF000031 411074 MFS_efflux_LmrA lincomycin efflux MFS transporter Lmr(A). 484 matched cddid_all.tbl CDD NF000040 NF000040 439388 Tn10_TetC tetracyline resistance-associated transcriptional repressor TetC. TetC, as found in composite transposon Tn10, is a transcriptional repressor of itself and of TetD, which is a transcriptional activator for some stress response proteins in the SoxS/MarA/Rob regulon in E. coli and which therefore contributes to antibiotic resistance. 197 matched cddid_all.tbl CDD NF000058 NF000058 411076 Erm41 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(41). 173 matched cddid_all.tbl CDD NF000060 NF000060 411077 MFS_efflux_LmrB lincomycin efflux MFS transporter Lmr(B). The lin-2 mutant, described in PMID:12499232, alters Lmr(B) expression in Bacillus subtilis and allows Lmr(B) to confer resistance to lincomycin. 479 matched cddid_all.tbl CDD NF000106 NF000106 411078 40850658_otr oxytetracycline efflux ABC transporter Otr(C) ATP-binding subunit. 351 matched cddid_all.tbl CDD NF000124 NF000124 439389 fos-Vibrio FosG/FosC2-related fosfomycin resistance glutathione transferase. 132 matched cddid_all.tbl CDD NF000140 NF000140 411079 AAC_6p_Salmo AAC(6')-Iy/Iaa family aminoglycoside 6'-N-acetyltransferase. Members of this family are chromosomal acetyltransferases from the genus Salmonella. Analysis has demonstrated a case in which a member designated AAC(6')-Iy, identical in two different strains isolated from a single patient, conferred resistance to tobramycin only in the isolate where a deletion event upstream of the gene resulted in high expression. Members of this family are therefore considered cryptic aminoglycoside N-acetyltransferases. which may or may not confer resistance, depending on expression levels. 145 matched cddid_all.tbl CDD NF000217 NF000217 411080 MATE_multi_FepA multidrug efflux MATE transporter FepA. 443 matched cddid_all.tbl CDD NF000342 NF000342 439391 glpA_Cterm aminoglycoside O-phosphotransferase APH(4)-Ib. The C-terminal half of CAA52372.1 shows homology to hygromycin-modifying enzyme APH(4)-Ia. The N-terminal region shows no homology to any other protein. The gene glpA was identified as one of two in a 3.0-kb DNA segment capable of conferring on E. coli the ability to degrade and use the phosphonate herbicide glyphosate as a sole carbon source. The expressed protein conferred minor (3-fold) increase in tolerance to hygromycin, but this protein probably should not be considered an aminoglycoside modifying enzyme associated with the spread of resistance in bacteria toward clinically important antimicrobials. 228 matched cddid_all.tbl CDD NF000349 NF000349 411082 mfpA_AE000516.2 pentapeptide repeat protein MfpA. 183 matched cddid_all.tbl CDD NF000391 NF000391 411083 EmrB multidrug efflux MFS transporter permease subunit EmrB. 501 matched cddid_all.tbl CDD NF000535 NF000535 467948 MSCRAMM_SdrC MSCRAMM family adhesin SdrC. Features of this protein family include a YSIRK-type signal peptide at the N-terminus and a variable-length C-terminal region of Ser-Asp (SD) repeats followed by an LPXTG motif for surface immobilization by sortase. 963 matched cddid_all.tbl CDD NF000536 NF000536 333720 YmiA YmiA family putative membrane protein. 42 matched cddid_all.tbl CDD NF000537 NF000537 333721 YncL stress response membrane protein YncL. 30 matched cddid_all.tbl CDD NF000539 NF000539 333722 plantaricin plantaricin C family lantibiotic. This family describes plantaricin C-like lantibiotic precursors. The seed alignment straddles the cleavage motif (typically GG), and includes both an extended leader peptide region and a Cys-rich core peptide region. Because of the mosaic structure of lantibiotic precursors, this family can be expected to overlap other lantibiotic precursor families in the same clan. 65 matched cddid_all.tbl CDD NF000540 NF000540 467949 alt_ValS valine--tRNA ligase. 827 matched cddid_all.tbl CDD NF012135 NF012135 411084 ANT_3pp_9_crypt aminoglycoside nucleotidyltransferase ANT(3'')/ANT(9). Known members of this family are restricted to Salmonella enterica. Activities as both a streptomycin 3''-O-adenylyltransferase and a spectinomycin 9-O-adenylyltransferase are cryptic because of a lack of expression, but detected if cells are grown on miminal rather than rich media (see PMID:21507083). 262 matched cddid_all.tbl CDD NF012136 NF012136 333724 SecA2_Lm accessory Sec system translocase SecA2. Members of this family are SecA2, part of a Sec-like preprotein translocase called accessory Sec. This SecA2 family is characteristic of Listeria species. 776 matched cddid_all.tbl CDD NF012138 NF012138 333725 exosort_XrtR exosortase R. 160 matched cddid_all.tbl CDD NF012139 NF012139 333726 exosort_XrtP exosortase P. 159 matched cddid_all.tbl CDD NF012144 NF012144 411085 ramA_TF RamA family antibiotic efflux transcriptional regulator. 108 matched cddid_all.tbl CDD NF012162 NF012162 467950 surf_Nterm_1 surface-anchored protein thioester-forming domain. This model describes a conserved region, fairly rich in insertions and deletions, located just past the signal peptide region in long, variable, and typically highly repetitive and sortase-dependent surface proteins. Members are found in a broad range of taxa, including many strains of Streptococcus pneumoniae. A conserved Cys forms a thioester bond, often to a host protein for covalent attachment. 234 matched cddid_all.tbl CDD NF012163 NF012163 411086 BaeS_SmeS sensor histidine kinase efflux regulator BaeS. 457 matched cddid_all.tbl CDD NF012164 NF012164 333728 AlbA subtilosin maturase AlbA. AlbA is a radical SAM/SPASM domain-containing protein responsible for introducing thioether crosslinks during that maturation of bacteriocins such subtilosin A. 442 matched cddid_all.tbl CDD NF012168 NF012168 411087 BlaI_of_BCL penicillinase repressor BlaI. 121 matched cddid_all.tbl CDD NF012179 NF012179 333729 CptA phosphoethanolamine transferase CptA. 556 matched cddid_all.tbl CDD NF012181 NF012181 467951 MSCRAMM_SdrD MSCRAMM family adhesin SdrD. Features of this protein family include a YSIRK-type signal peptide at the N-terminus and a variable-length C-terminal region of Ser-Asp (SD) repeats followed by an LPXTG motif for surface immobilization by sortase. 1379 matched cddid_all.tbl CDD NF012182 NF012182 333731 exosortase_XrtQ exosortase Q. 256 matched cddid_all.tbl CDD NF012196 NF012196 467952 Ig_like_ice Ig-like domain. This variant form of the Ig-like domain occurs as a repeat in a number of large adhesins, including a 1.5-MDa ice-binding adhesin, the Marinomonas primoryensis antifreeze protein. 108 matched cddid_all.tbl CDD NF012197 NF012197 467953 lonely_Cys lonely Cys domain. This model describes an unusual domain, over 700 amino acids long, that is largely restricted to the Streptomyces (prodigious producers of natural products) and that may occur ten or more times in giant proteins. The most striking feature is an extremely low cysteine composition, one residue per domain, and that in an essentially invariant position. 706 matched cddid_all.tbl CDD NF012198 NF012198 411088 MarA_TF MDR efflux pump AcrAB transcriptional activator MarA. 124 matched cddid_all.tbl CDD NF012200 NF012200 467954 choice_anch_D choice-of-anchor D domain. This HMM describes a repeat domain just over 100 amino acids long and usually found in tandem copies. Members appear to be extracellular proteins that have some C-terminal anchoring domain, such as type IX secrection (T9SS) or PEP-CTERM. 107 matched cddid_all.tbl CDD NF012201 NF012201 333735 WIAG-tail WIAG-tail domain. This 80-amino acid domain occurs in proteins in a single copy at the C-terminus. In most proteins, the domain immediately follows a long, variable run of tandem 10-amino acid repeats. The domain is named for its C-terminal motif, WIAxGx, hence the name WIAG-tail. 80 matched cddid_all.tbl CDD NF012204 NF012204 467955 adhes_FxxPxG leukotoxin LktA family filamentous adhesin N-terminal domain. This model, related to TIGR01901, describes a conserved single-copy N-terminal domain found in repeat-rich, extremely long proteins such as the leukotoxin LktA of Fusobacterium necrophorum. 152 matched cddid_all.tbl CDD NF012206 NF012206 333737 LktA_tand_53 leukotoxin LktA-type filamentous protein tandem repeat. This repeat, about 53 amino acids in length, may comprise most of the length of proteins over 3000 amino acids long. The best characterized protein with this repeat is the leukotoxin LktA of Fusobacterium necrophorum, where it is the major virulence factor. 53 matched cddid_all.tbl CDD NF012208 NF012208 411089 SDR_dihy_bifunc bifunctional dihydropteridine reductase/dihydrofolate reductase TmpR. Members of this family are SDR family oxidoreductases, unrelated to previously known families of dihydrofolate reductase (DHFR), one of which was demonstrated to be a bifunctional dihydropteridine reductase/dihydrofolate reductase. The DHFR activity can give a heterologously expressed protein the ability to confer resistance to trimethoprim, an inhibitor of most forms of DHFR. 233 matched cddid_all.tbl CDD NF012209 NF012209 333738 LEPR-8K LEPR-XLL family repeat protein signature domain. This model, just 24 amino acids long, describes an N-terminal single-copy region that contains the most highly conserved motif in a collection of repeat-filled giant proteins. Member proteins average over 8000 amino acids and include at least one longer than 35,000 in length. The signature motif is LEPRxLL 24 matched cddid_all.tbl CDD NF012210 NF012210 467956 PDxFFG PDxFFG domain. This model represents the conserved N-terminal domain of family of large proteins with signal peptides, found in Mycoplasma and Ureaplasma. A short conserved N-terminal domain and a large conserved C-terminal domain are separated by poorly conserved regions of variable length. This domain is named for its best conserved motif, PDxFFG. 269 matched cddid_all.tbl CDD NF012211 NF012211 333740 tand_rpt_95 tandem-95 repeat. This 95-amino acid repeat occurs in tandem in proteins that may be several thousand amino acids long. 98 matched cddid_all.tbl CDD NF012221 NF012221 467957 MARTX_Nterm MARTX multifunctional-autoprocessing repeats-in-toxin holotoxin N-terminal region. This model describes the N-terminal 1900 amino acids of MARTX family multifunctional-autoprocessing repeats-in-toxin holotoxins, which contain both repeat regions that facilitate their entry into eukaryotic target cells, and multiple effector domains. 1848 matched cddid_all.tbl CDD NF012226 NF012226 411090 AdeS_HK two-component sensor histidine kinase AdeS. Mutations in this component of the two-component regulatory system for the AdeABC efflux pump can confer adaptive resistance to certain antibiotics, including tigecycline. 353 matched cddid_all.tbl CDD NF012227 NF012227 411091 AdeR_RR efflux system response regulator transcription factor AdeR. This protein, the DNA-binding regulator AdeR, works with its two-component system partner AdeS, to modulate expression of the AdeABC efflux pump. 239 matched cddid_all.tbl CDD NF012228 NF012228 467958 RobA_TF MDR efflux pump AcrAB transcriptional activator RobA. The original characterization of RobA as a Right side Origin of replication Binding protein A (robA) may be misleading. Characterizations in large numbers of papers since then treat RobA as a transcriptional activator of the AcrAB antibiotic efflux pump. 286 matched cddid_all.tbl CDD NF012230 NF012230 333742 LWXIA_domain LWXIA domain. This domain occurs exclusively at the C-terminus of a set of long proteins (average length 4000 residues), and is separated form the rest of the protein sequence by a Pro and Ser-rich spacer region of poorly conserved, low-complexity sequence. This domain is named for its most conserved motif, LWxIA. Some but not all sequences in the seed alignment score well locally to the LysM domain model of PF01476, which may have a general peptidoglycan binding function. 74 matched cddid_all.tbl CDD NF028536 NF028536 333743 PAP2_near_MCR1 PAP2 family protein. Members of this family belong to the PAP2 superfamily (see PF01569). The founding members of this family are notable for being encoded next to mcr-1, a phosphoethanolamine--lipid A transferase that confers resistance to colistin. 237 matched cddid_all.tbl CDD NF028538 NF028538 467959 PAP2_lipid_A PAP2 family lipid A phosphatase. All members of the seed alignment for this family belong to the PAP2 superfamily and therefore share homology with the lipid A 1-phosphatase LpxE of Helicobacter pylori. LpxE removes one of two KDO sugar phosphates from lipid A, making it possible for a phosphoethanolamine--lipid A transferase to add the modifying group that increases resistance to colistin. All members of the seed alignment for this model are encoded close to the gene for a phosphoethanolamine--lipid A transferase, such as MCR-1. 224 matched cddid_all.tbl CDD NF032891 NF032891 467960 tail_200_repeat tandem large repeat. This HMM describes a domain of nearly 200 amino acids, found in up to 14 tandem repeats in the C-terminal region of very large protein, in Vibrio parahaemolyticus and related species. 192 matched cddid_all.tbl CDD NF032893 NF032893 467961 tail-700 PLxRFG domain. This domain, nearly 700 residues long, begins with a nearly invariant motif YxPLxRFGx[YF]. It occurs as the extreme C-terminal domain of large size, some over 5000 amino acids long with an average of nearly 3000. The function is unknown. 681 matched cddid_all.tbl CDD NF033069 NF033069 333747 acnA_upstr_60 acnA regulatory region 60-length spurious protein. This HMM describes an apparently spurious protein translation from the region upstream of the aconitase A gene acnA in Escherichia coli str. K-12 substr. MG1655, positions 1335595-1335774, and in related strains. Evidence against its expression as a real protein include a putative TTG start codon, the lack of good RBS, non-conservative substitutions where found, the absence of credible homologs in any species besides E. coli, and a DNA region in Salmonella enterica LT2 in which one third of the translation is present, but the other two thirds are missing. 60 matched cddid_all.tbl CDD NF033070 NF033070 333748 rSAM_AprD4 AprD4 family radical SAM diol-dehydratase. AprD4, as described originally in Streptoalloteichus hindustanus, is a radical SAM enzyme involved in C3-deoxygenation of the intermediate paromamine during biosynthesis of the aminoglycoside apramycin. It acts as a diol-dehydratase, and works with the partner protein, AprD3, a reductase. 456 matched cddid_all.tbl CDD NF033071 NF033071 467962 SusD starch-binding outer membrane lipoprotein SusD. SusD (Starch Uptake System D) is an outer membrane lipoprotein that binds starch and participates in a TonB-dependent nutrient uptake complex. Related proteins from similar TonB-dependent complexes that import other, usually multimeric nutrient substrates include RagB and NanU. 558 matched cddid_all.tbl CDD NF033072 NF033072 333750 NanU SusD family outer membrane lipoprotein NanU. NanU, related to SusD and RagB, is an outer membrane lipoprotein from a TonB-dependent nutrient uptake complex. 521 matched cddid_all.tbl CDD NF033073 NF033073 467963 LPXTG_double doubled motif LPXTG anchor domain. This unusual LPXTG-type C-terminal protein sorting domain occurs largely in the genus Clostridium and typically is separated from the main body of the protein by a glycine-rich linker sequence. In this domain, the classical sortase cleavage motif, LPXTG, has the consensus sequence VPLAxLPKTG. Much of this motif, the sequence VPLAxLP, is repeated an average 20 amino acids upstream within this domain. This unusual structure of a sortase recognition site-containing domain suggest a specialized form of interaction with its cognate sortase. 66 matched cddid_all.tbl CDD NF033092 NF033092 467964 HK_WalK cell wall metabolism sensor histidine kinase WalK. This model describes WalK as found in Staphylococcus aureus (sp|Q2G2U4.1|WALK_STAA8). A shorter version, as found in Streptococcus pneumoniae, called WalK(Spn) or VicK, is not included. WalK is part of a two-component system and works with partner protein WalR. 594 matched cddid_all.tbl CDD NF033093 NF033093 467965 HK_VicK cell wall metabolism sensor histidine kinase VicK. This model describes the protein VicK (or WalK) as found in Streptococcus pneumoniae, This protein is shorter than the WalK of Staphylococcus aureus, although apparently is functionally similar. Compare to model NF033092 (HK_WalK). VicK is a sensor histidine kinase involved in regulating cell wall metabolism. Its two component system partner is the response regulatory VicR. 448 matched cddid_all.tbl CDD NF033113 NF033113 380163 halo_ClmS chloramphenicol-biosynthetic FADH2-dependent halogenase CmlS. 570 matched cddid_all.tbl CDD NF033138 NF033138 411094 RND-peri-MexC MexC family multidrug efflux RND transporter periplasmic adaptor subunit. 375 matched cddid_all.tbl CDD NF033143 NF033143 467966 efflux_OM_AdeK multidrug efflux RND transporter AdeIJK outer membrane channel subunit AdeK. 480 matched cddid_all.tbl CDD NF033147 NF033147 411096 GXX_rpt_CTERM Gly-Xaa-Xaa repeat protein C-terminal domain. This model often occurs at the C-terminus, and companion model N_to_GlyXaaXaa (NF033172) at the N-terminus, of proteins that in between consist largely of variable numbers of Gly-Xaa-Xaa repeats, reminiscent of collagen repeats. Member proteins observed have been found so far only in Gram-positive bacteria. This domain contains a motif IPxTG near its C-terminus, suggesting it is processed by some form of sortase. 132 matched cddid_all.tbl CDD NF033153 NF033153 467967 phage_ICD_like "host cell division inhibitor Icd domain. Icd from temperate phage P1 inhibits cell division in its host. Homologous sequence is found in many other proteins, often as the C-terminal region of what appears to be a much larger protein. Putative phage proteins that contain this domain may be designated ""host cell division inhibitor Icd-like protein"". See PMID: 8491703 for a description of Icd. Many proteins with this domain also have the Ash domain described by PF10554, which also occurs in phage." 48 matched cddid_all.tbl CDD NF033154 NF033154 467968 endonuc_SmrA DNA endonuclease SmrA. YdaL is a small endonuclease with homology to the C-terminal domain found in the endonuclease MutS2, but not found in the related mismatch repair protein MutS. The biological role of this endonuclease is not yet known. As one of two Small MutS2-Related proteins in E. coli, This protein was designated SmrA by Gui, et al. (PMID:21276852). The term SMR is much better known for describing a large family of Small Multidrug Resistance (SMR) efflux transporters, but in that context is used with three capital letters. 189 matched cddid_all.tbl CDD NF033155 NF033155 380165 CatA_like_1 CatA-like O-acetyltransferase, family 1. Members of this family are homologs to members of the CatA family of chloramphenicol acetyltransferases, although less than 30% identical. There is no evidence that members of this family act on or confer resistance to chloramphenicol. 209 matched cddid_all.tbl CDD NF033157 NF033157 380166 SWFGD_domain SWFGD domain. This small domain (29 amino acids long) is named for its most conspicuous (although not invariant) motif, SWFGD. The motif occurs primarily, although not exclusively, in protein sequences with a BON domain (PF04972), suspected of involvement in attachment to phospholipid membranes, or with a DUF2171 domain (PF09939). Two copies of the motif may be found in a single protein. 29 matched cddid_all.tbl CDD NF033158 NF033158 380167 Myrrcad "MyrrCad domain. This domain appears at or near the C-terminus in expanded paralogous families of proteins in Mycoplasma and Candidatus Mycoplasma genomes. Proteins with this domain typically show an N-terminal sequence regions followed by a repeat region, highly variable in length and similar to the leucine-rich repeat. The center region of this domain resembles alpha-helical hydrophobic transmembrane segments. The domain ends with a cluster of basic residues, suggesting an orientation in which the C-terminal residues of the domain face the cytosol. The coinage ""MyrrCad"", rendered without full capitalization because it is an acronym rather than an amino acid sequence motif, signifies ""MYcoplasma Repeat-Rich protein C-terminal Anchor Domain""" 36 matched cddid_all.tbl CDD NF033160 NF033160 467969 lipo_LipL36 lipoprotein LipL36. Members of this family are lipoprotein LipL36, as described in Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 but found broadly in the genus Leptospira. Close homologs that are not lipoproteins by sequence are likely defective in their reported coding region. 383 matched cddid_all.tbl CDD NF033161 NF033161 467970 lipo_LipL41 lipoprotein LipL41. Members of this family are lipoprotein LipL41, as described in Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 but found broadly in the genus Leptospira. Close homologs that are not lipoproteins by sequence are likely defective in their reported coding region. 358 matched cddid_all.tbl CDD NF033162 NF033162 380170 lipo_LipL21 lipoprotein LipL21. Members of this family are lipoprotein LipL21, as described in Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 but found broadly in the genus Leptospira. Close homologs that are not lipoproteins by sequence are likely defective in their reported coding region. 191 matched cddid_all.tbl CDD NF033163 NF033163 467971 lipo_LipL71 lipoprotein LipL71. Members of this family are lipoprotein LipL71, also known as LruA, as described in Leptospira interrogans but found broadly in the genus Leptospira. Close homologs that are not lipoproteins by sequence are likely defective in their reported coding region. 472 matched cddid_all.tbl CDD NF033164 NF033164 380172 lipo_LipL46 lipoprotein LipL46. Members of this family are lipoprotein LipL46, as described in Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 but found broadly in the genus Leptospira. Close homologs that are not lipoproteins by sequence are likely defective in their reported coding region. 413 matched cddid_all.tbl CDD NF033165 NF033165 467972 lipo_LipL45 lipoprotein LipL45. Members of this family are lipoprotein LipL45, as described in Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 but found broadly in the genus Leptospira. Close homologs that are not lipoproteins by sequence are likely defective in their reported coding region. 391 matched cddid_all.tbl CDD NF033166 NF033166 380174 lipo_LipL31 lipoprotein LipL31. Members of this family are lipoprotein LipL31, as described in Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 but found broadly in the genus Leptospira. Close homologs that are not lipoproteins by sequence are likely defective in their reported coding region. 210 matched cddid_all.tbl CDD NF033167 NF033167 467973 lipo_LIC11695 LIC_11695/LIC_11696 family lipoprotein. Members of this family are lipoproteins found broadly in the genus Leptospira. Two paralogs, LIC_11695 and LIC_11696 are found in Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130 (a well-studied reference strain), where they are encoded by tandem genes, and are among the 25 proteins whose expression is up-regulated the most by the increase in osmolarity that signals entry into a host species. 186 matched cddid_all.tbl CDD NF033168 NF033168 467974 lipo_LIC10766 LIC_10766 family lipoprotein. Members of this family are lipoproteins found broadly in the genus Leptospira. 142 matched cddid_all.tbl CDD NF033169 NF033169 467975 lipo_LIC10494 LIC_10494 family lipoprotein. Members of this family are lipoproteins found broadly in the genus Leptospira. 213 matched cddid_all.tbl CDD NF033170 NF033170 467976 lipo_LIC13355 LIC_13355 family lipoprotein. Members of this family are lipoproteins found broadly in the genus Leptospira. 273 matched cddid_all.tbl CDD NF033171 NF033171 467977 lipo_LIC11139 LIC_11139 family putative lipoprotein. Members of this family are restricted to the genus Leptospira. They are putative lipoproteins with only a single Cys residue, invariant at the proposed lipoprotein signal cleavage site. Residues in the -1 position are unusual for lipoproteins in general, but consistent with observations in Leptospira, as described in PMID:26890609. 157 matched cddid_all.tbl CDD NF033172 NF033172 467978 N_to_GlyXaaXaa collagen-like repeat preface domain. All protein sequence used in the seed alignment for this model comes from the N-terminal region of proteins with extended collagen-like Gly-rich repeat regions, and occur in Firmicutes. 122 matched cddid_all.tbl CDD NF033173 NF033173 380181 anticapsin_BacC dihydroanticapsin 7-dehydrogenase. Members of this family are dihydroanticapsin 7-dehydrogenase (EC 1.1.1.385), one of seven key molecular markers for biosynthesis of the non-cognate amino acid anticapsin, a building block for the dipeptide antibiotic natural product bacilysin. 252 matched cddid_all.tbl CDD NF033175 NF033175 467979 fuso_auto_Nterm autotransporter-associated N-terminal domain. This domain typically is found in the genus Fusobacterium, in N-terminal regions of large proteins that are recognized as autotransporter proteins by C-terminal regions matching Pfam model PF03797. In paralogous families of such proteins, the N-terminal and C-terminal regions are fairly well-conserved, but the repetitive central region is poorly conserved in both length and sequence. 121 matched cddid_all.tbl CDD NF033176 NF033176 380183 auto_AIDA-I autotransporter adhesin AIDA-I. 1287 matched cddid_all.tbl CDD NF033177 NF033177 467980 auto_Ag43 Ag43/Cah family autotransporter adhesin. Members of this family, restricted to Escherichia coli (including E. coli K-12) are the autotransporter adhesin Ag43 (antigen 43), also known as flu, or its calcium-binding homolog Cah, differing mostly in the central region. The C-terminal region forms an outer membrane beta-barrel autotransporter domain, which enables type V secretion (autotransport). 948 matched cddid_all.tbl CDD NF033178 NF033178 467981 auto_BigA autotransporter adhesin BigA. Members of this family are the adhesin BigA, found in Salmonella. BigA is an autotranporter, meaning is has a C-terminal outer membrane beta-barrel, through which passenger regions of the proteins are transported. 1875 matched cddid_all.tbl CDD NF033179 NF033179 380186 TnsA_like_Actin TnsA-like heteromeric transposase endonuclease subunit. The transposase of transposon Tn7 contains multiple subunit. Members of this family are largely restricted to the Actinobacteria, resemble the endonuclease subunit TsnA of the multimeric transposase of Tn7 and its relatives, and occur in genomic neighborhoods that suggest a similar role in transposition. 212 matched cddid_all.tbl CDD NF033181 NF033181 467982 NiFeSe_hydrog nickel-dependent hydrogenase large subunit. Members of this family are the large subunit of the periplasmic nickel-dependent hydrogenase. Some members contain a selenocysteine residue. 509 matched cddid_all.tbl CDD NF033183 NF033183 467983 colliding_TM low-complexity tail membrane protein. Members of this family appear typically as an unusual gene pair with members of PF11998 (DUF3493). Strangely, members tend to have tail-to-tail overlapping regions, where the tail region from this protein is long, low-complexity, and typically rich in Asp, Glu, Asn, Gln, Ser, and Thr. These gene pairs occur broadly in Cyanobacteria. The function of this pair of convergently-transcribed overlapping proteins is unknown. The low-complexity region was trimmed from the seed alignment to build this HMM. 188 matched cddid_all.tbl CDD NF033184 NF033184 439394 B3_Acin_new1 putative subclass B3 metallo-beta-lactamase. This is one of two families of putative metallo-beta-lactamases of subclass B3 that are restricted to the genus Acinetobacter, and undescribed as of January 2017. 283 matched cddid_all.tbl CDD NF033185 NF033185 380189 B3_Acin_new2 putative subclass B3 metallo-beta-lactamase. This is one of two families of putative metallo-beta-lactamases of subclass B3 that are restricted to the genus Acinetobacter, and undescribed as of January 2017. 285 matched cddid_all.tbl CDD NF033186 NF033186 467984 internalin_K class 1 internalin InlK. Internalins, as found in the intracellular human pathogen Listeria monocytogenes, are paralogous surface-anchored proteins with an N-terminal signal peptide, leucine-rich repeats, and a C-terminal LPXTG processing and cell surface anchoring site. Members of this family are internalin K (InlK), a virulence factor. See articles PMID:17764999. for a general discussion of internalins, and PMID:21829365, PMID:22082958, and PMID:23958637 for more information about internalin K. 604 matched cddid_all.tbl CDD NF033187 NF033187 380191 internalin_J class 1 internalin InlJ. Internalins, as found in the intracellular human pathogen Listeria monocytogenes, are paralogous surface-anchored proteins with an N-terminal signal peptide, leucine-rich repeats, and a C-terminal LPXTG processing and cell surface anchoring site. See PMID:17764999 for a general discussion of internalins. Members of this family are internalin J (InlJ). 846 matched cddid_all.tbl CDD NF033188 NF033188 467985 internalin_H InlH/InlC2 family class 1 internalin. Internalins, as found in the intracellular human pathogen Listeria monocytogenes, are paralogous surface or secreted proteins with an N-terminal signal peptide, leucine-rich repeats, and usually a C-terminal LPXTG processing and cell surface anchoring site. See PMID:17764999 for a general discussion of internalins. Members of this family are internalin H (InlH), or internalin C2, two class 1 (LPXTG-type) internalins that are closely related, one apparently derived from the other through a recombination event. 548 matched cddid_all.tbl CDD NF033189 NF033189 380193 internalin_A class 1 internalin InlA. Internalins, as found in the intracellular human pathogen Listeria monocytogenes, are paralogous surface or secreted proteins with an N-terminal signal peptide, leucine-rich repeats, and usually a C-terminal LPXTG processing and cell surface anchoring site. See PMID:17764999 for a general discussion of internalins. Members of this family are internalin A (InlA), a class 1 (LPXTG-type) internalin. 799 matched cddid_all.tbl CDD NF033190 NF033190 467986 inl_like_NEAT_1 "NEAT domain-containing leucine-rich repeat protein. Members of this family have an N-terminal NEAT (near transporter) domain often associated with iron transport, followed by a leucine-rich repeat region with significant sequence similarity to the internalins of Listeria monocytogenes. However, since Bacillus cereus (from which this protein was described, in PMID:16978259) is not considered an intracellular pathogen, and the function may be iron transport rather than internalization, applying the name ""internalin"" to this family probably would be misleading." 754 matched cddid_all.tbl CDD NF033191 NF033191 467987 JDVT-CTERM JDVT-CTERM protein-sorting domain. This bacterial C-terminal protein-sorting domain, superficially similar to MYXO-CTERM (TIGR03901), occurs in a variety of Proteobacteria, including Janthinobacterium, Duganella, Vibrio breoganii, and Thioalkalivibrio, hence the name JDVT. Its local genomic context in species examined so far includes a homolog of eukaryotic type II CAAX prenylation site proteases (see PF02517). The architecture of the domain consists of a run of Gly residues and an invariant Cys residue (a probably modification site), followed by a hydrophobic predicted transmembrane alpha helix and then a cluster of basic residues, mostly Arg. 35 matched cddid_all.tbl CDD NF033192 NF033192 467988 JDVT-CAAX JDVT-CTERM system glutamic-type intramembrane protease. See NF033191. 98 matched cddid_all.tbl CDD NF033193 NF033193 467989 lipo_NDxxF NDxxF motif lipoprotein. Members of this family are lipoproteins, about 200 amino acids long in precursor form, found in Staphylococcus aureus, Bacillus cereus, and various other Firmicutes. The protein family is named for one of its several highly conserved motifs. 199 matched cddid_all.tbl CDD NF033194 NF033194 380197 lipo_EMYY EMYY motif lipoprotein. Members of this family are lipoproteins, about 300 amino acids long in precursor form, found broadly in the genus Staphylococcus and in some related species. 292 matched cddid_all.tbl CDD NF033195 NF033195 467990 F430_CfbB Ni-sirohydrochlorin a,c-diamide synthase. Members of this family are Ni-sirohydrochlorin a,c-diamide synthase, involving in synthesizing coenzyme F430, used in methanogens by coenzyme M reductase. Members of this family are restricted to archaeal methanogens, and resemble (and may be misannotated as) the enzyme cobyrinic acid a,c-diamide synthase, involved in cobalamin biosynthesis. 451 matched cddid_all.tbl CDD NF033196 NF033196 467991 c_type_nonphoto c-type cytochrome. Members of this family are apparent c-type cytochromes that resemble the photosynthetic reaction center c-type cytochrome (PF02276) but are smaller and found in non-photosynthetic organisms. 97 matched cddid_all.tbl CDD NF033197 NF033197 467992 F430_CfbE coenzyme F430 synthase. Members of this family are coenzyme F430 synthase, involving in synthesizing coenzyme F430, which is used in methanogens by coenzyme M reductase. Members of this family are restricted to archaeal methanogens, and resemble (and may be misannotated as) MurD, an enzyme of bacterial cell wall biosynthesis. 419 matched cddid_all.tbl CDD NF033198 NF033198 467993 F430_CfbA sirohydrochlorin nickelochelatase. Members of this family are sirohydrochlorin nickelochelatase, involving in synthesizing coenzyme F430, used in methanogens by coenzyme M reductase. Members of this family are restricted to archaeal methanogens, and resemble (and may be misannotated as) sirohydrochlorin cobaltochelatase , involved in cobalamin biosynthesis. Some members of this family are double in length because of a duplication. 124 matched cddid_all.tbl CDD NF033200 NF033200 380202 F430_CfbC Ni-sirohydrochlorin a,c-diamide reductive cyclase ATP-dependent reductase subunit. This family, very closely related to the nitrogenase iron protein, was identified as a subunit involved in biosynthesis of coenzyme F430 in archaeal methanogens and archaeal anaerobic methanotrophs. 260 matched cddid_all.tbl CDD NF033201 NF033201 467994 Vip_LPXTG_Lm cell invasion LPXTG protein Vip. Vip (Virulence protein), like the LPXTG-type internalins, is an LPXTG-anchored surface protein of the mammalian cell-invading pathogen Listeria monocytogenes, but absent from the related species Listeria innocua. For certain cell types, Vip is required for Listeria's ability to invade. It appears to bind the endoplasmic reticulum (ER) resident chaperone Gp96 as its receptor. 414 matched cddid_all.tbl CDD NF033202 NF033202 380204 GW_glycos_SH3 GW domain. The GW domain of Listeria belongs to the clan of SH3-like domains. A similar but broader model (PF13457) occurs in Pfam. The GW domain occurs as repeats on surface proteins of the cell-invading pathogenic bacterium Listeria monocytogenes, and is involved in binding to glycosaminoglycans. Members of this family include the GW-type internalin InlB and several paralogs. 81 matched cddid_all.tbl CDD NF033203 NF033203 380205 entero_EhxA enterohemolysin EhxA. Members of this family are the RTX toxin called enterohemolysin or EhxA, because it is found in enterohemorrhagic Escherichia coli (EHEC) strains such as O157:H7. 997 matched cddid_all.tbl CDD NF033205 NF033205 467995 IPExxxVDY IPExxxVDY family protein. This protein family is uncharacterized. Member proteins average about 160 amino acids in size, and feature two widely separated invariant Asn residues, as well as the larger (though less invariant) motif for which it is named. Members are found primarily in the Flavobacteriia branch of the Bacteroidetes. 152 matched cddid_all.tbl CDD NF033206 NF033206 467996 ScyE_fam ScyD/ScyE family protein. This family includes ScyE, a protein involved in scytomenin biosynthesis and export, and its paralog ScyD. Some members of the family contain a C-terminal PEP-CTERM domain that predictions anchoring to the outer membrane. 330 matched cddid_all.tbl CDD NF033207 NF033207 467997 midcut_by_XrtH midcut-by-XrtH protein. Members of this protein family occur in bacterial genomes that encode the exosortase/archaeosortase family member XrtH (exosortase H). While many targets of XrtH are C-terminal protein-processing signals described by TIGR04174, the IPTL-CTERM domain, members of this family have a version of that signal in the N-terminal half of the protein. This architecture suggests that XrtH may performs a cleavage that releases the C-terminal domain of midcut-by-XrtH proteins from the membrane, perhaps as part of some regulatory pathway. 171 matched cddid_all.tbl CDD NF033208 NF033208 467998 choice_anch_E choice-of-anchor E domain-containing protein. This HMM describes a domain just over 100 amino acids long and usually found in tandem copies. Members appear to be extracellular proteins that have some C-terminal anchoring domain, usually PEP-CTERM but occasionally a type IX secrection (T9SS) recognition domain. 171 matched cddid_all.tbl CDD NF033210 NF033210 467999 RBP7 reticulate body protein Rbp-7. Members of this family are the 7-kDa reticulate body protein found in several species of Chlamydia. The protein is often overlooked during genome structural annotation; members observed so far are 65 to 67 amino acids long. The protein has been demonstrated by mass spectroscopy, and shown to be present only in reticulate or intermediate bodies. 74 matched cddid_all.tbl CDD NF033212 NF033212 439396 SapB_AmfS_lanti SapB/AmfS family lanthipeptide. Members of this family are class III lanthipeptide precursors. These typically are short peptides, encoded next to the gene for the lanthipeptide synthetase that creates the characteristic lanthionine (or beta-methyl lanthionine) bridges for which these natural products are named. Members of this family include SapB and AmfS, which are considered morphogens rather than antibiotics. Members also include labionin-containing peptides such labyrinthopeptins A1 and A2. 40 matched cddid_all.tbl CDD NF033213 NF033213 411104 matur_PanM aspartate 1-decarboxylase autocleavage activator PanM. Members of this family, called PanM (or PanZ), although related to the GNAT family N-acetyltransferases, have a different function. Then enzyme PanD, aspartate 1-decarboxylase, has an active site modified Ser residue, created by cleavage of a precursor form. PanM promotes the maturation of the CoA biosynthesis enzyme PanD, but also inhibits its activity in the presence of CoA. Figure 6 in PMID:26276430 identifies residues considered critical to interaction with PanD; seed alignment sequences and cutoff scores were chosen to separate proposed PanM from functionally distinct relatives. 130 matched cddid_all.tbl CDD NF033214 NF033214 468000 ComC_Streptocco competence-stimulating peptide ComC. Members of this family are ComC, a secreted peptide that stimulates competence for natural transformation in Streptococcus. ComC peptides fall within the broader family of PF03047, a homology family of pheromone/bacteriocin precursors that is also restricted to Streptococcus. The PF03047 HMM runs only a few residues past the GlyGly precursor peptide cleavage site, and thus does not distinguish ComC from other pheromone precursors, such as BlpC. 41 matched cddid_all.tbl CDD NF033215 NF033215 380214 BlpC_Streptocco quorum-sensing system pheromone BlpC. Members of this family are BlpC, a peptide pheromone that stimulates production of BLP (bacteriocin-like peptides) family class II bacteriocins. BlpC peptides fall within the broader family of PF03047, a homology family of pheromone/bacteriocin precursors that is also restricted to Streptococcus. The PF03047 HMM runs only a few residues past the GlyGly precursor peptide cleavage site, and thus does not distinguish BlpC from other pheromone precursors, such as ComC. 51 matched cddid_all.tbl CDD NF033216 NF033216 468001 lipo_YgdI_YgdR YgdI/YgdR family lipoprotein. Members of this family are exclusively lipoproteins of small size, including YgdI and YgdR from E. coli K-12. 71 matched cddid_all.tbl CDD NF033217 NF033217 380216 Fur_reg_FbpC Fur-regulated basic protein FbpC. Members of this family are FbpC, Fur-regulated basic protein C. This protein has also been described as MrgC (metal-regulated gene C). Members of this family are found so far only in the genus Bacillus, although the small size may have interferred in gene-finding. 29 matched cddid_all.tbl CDD NF033218 NF033218 468002 anchor_AmaP alkaline shock response membrane anchor protein AmaP. The founding member of this family, AmaP (Asp23 membrane anchoring protein), is related to Asp23 through part of its length, but includes a highly hydrophobic N-terminal region that should make it an integral membrane protein. Asp23 (alkaline shock protein of 23 kDa), described in PMID:7864904, is a cytosolic protein in Staphylococcus aureus, strongly induced by a pH shift from 7 to 10, and also recruited to the membrane. AmaP appears to be the partner protein with an integral membrane segment and the ability to anchor Asp23 to the membrane. This model was built to identify full-length homologs of AmaP, while excluding Asp23. Some but not all members of this family score above the cutoffs of Pfam model version PF03780.11, but full-length homologs of Asp23 score considerably higher. Asp23 family members previously were known as DUF322. 166 matched cddid_all.tbl CDD NF033221 NF033221 468003 ANT_6_Ig "aminoglycoside nucleotidyltransferase ANT(6)-Ig. Article PMID:27154456 describes a streptomycin resistance protein, ""Campylobacter ANT-like protein A"", highly similar to WP_002785795.1, and reports internal primers that match exactly to genes encoding WP_002785795.1. Campylobacter ANT-like protein A was shown to confer resistance to streptomycin. This model identifies proteins from this family, including WP_002785795.1. The most closely related sequence found by database search was the family of ""Campylobacter ANT-like protein B"", such as WP_038855261.1, which also is found in Campylobacter coli but which could not be shown to confer resistance to streptomycin." 299 matched cddid_all.tbl CDD NF033222 NF033222 380218 listolys_S listeriolysin S family TOMM bacteriocin. Members of this family include listeriolysin S from some strains of Listeria monocytogenes, and staphylolysin S. Members are encoded in biosynthetic clusters similar to those for streptolysin S (found by model TIGR03602), a precursor similar in length, architecture, and composition, but different enough to require a different HMM. 32 matched cddid_all.tbl CDD NF033223 NF033223 380219 YHYH_alt YHYH domain. Proteins with this form of YHYH motif-containing domain have it located near the N-terminus of a protein just after a signal peptide region. The domain has two characteristic motifs, GxC and YH[YC]H, separated by a short spacer region of variable length. A different family of YHYH domain-domaining proteins, in which the YHYH domain is more C-terminal and is repeated, is described by Pfam model PF14240. 25 matched cddid_all.tbl CDD NF033224 NF033224 380220 PmrR LpxT activity modulator PmrR. Members of this family are PrmR, and extremely small protein at 29 amino acids in length. 29 matched cddid_all.tbl CDD NF033225 NF033225 380221 spore_CmpA cortex morphogenetic protein CmpA. Members of this family are CmpA (cortex morphogenetic protein A), a small protein (37 amino acids) involved in endospore formation and frequently missed during genome annotation. 36 matched cddid_all.tbl CDD NF033226 NF033226 468004 small_MntS manganase accumulation protein MntS. Members of this family are MntS, a small protein of about 42 amino acids that seems to play assist bacteria in accumulating manganese when iron is limiting. It may function as a manganese chaperone, or may inhibit manganese efflux transporters. 41 matched cddid_all.tbl CDD NF033227 NF033227 380223 Fur_reg_FbpB Fur-regulated basic protein FbpB. This model describes FbpB (Fur-regulated basic protein B), one of three paralogous small proteins recognized by Pfam model PF13040 in Bacillus subtilis. 43 matched cddid_all.tbl CDD NF033228 NF033228 380224 div_inhib_SidA cell division inhibitor SidA. This protein, SidA (SOS-induced inhibitor of cell division A), is found so far in Caulobacter and Phenylobacterium. It interacts with FtsW. 29 matched cddid_all.tbl CDD NF033229 NF033229 380225 small_MgtR protein MgtR. 30 matched cddid_all.tbl CDD NF033230 NF033230 411106 phage_region_01 phage region protein. Members of this family are found broadly in the Gammaproteobacteria and may be a marker of temperate phage or prophage. A member (YP_008766900.1) occurs in Shigella phage SfIV. 142 matched cddid_all.tbl CDD NF033231 NF033231 380226 small_Blr division septum protein Blr. Members of this family are Blr, named beta-lactam resistance protein because mutants have heightened sensitivity to beta-lactam antibiotics, but actually involved in cell division. The protein is very small. 40 matched cddid_all.tbl CDD NF033232 NF033232 380227 small_YtzI YtzI protein. Members of this family include YtzI from Bacillus subtilis, and homologs widely distributed in the Firmicutes. The pattern of sequence conservation suggests the protein begins with a hydrophobic stretch without any basic residue near the initiator Met residue. Members of this family average about 53 residues in length. At the time this model was constructed, members were included in Pfam model PF12606.6 (Tumour necrosis factor receptor superfamily member 19), seemingly in error. This model was constructed to separate the two families. 41 matched cddid_all.tbl CDD NF033233 NF033233 380228 twin_helix twin transmembrane helix small protein. Members of the seed alignment for this family are small (average length 68 residues), strictly bacterial, and extremely hydrophobic. Pfam model PF04588 (HIG_1_N) includes both eukaryotic proteins, including a protein from the fish Gillichthys mirabilis, and the members of this family. Similarity between those eukaryotic proteins and the members o this model may represent convergent evolution related to the similar composition of their transmembrane alpha-helical regions, rather than a common origin or common function. 58 matched cddid_all.tbl CDD NF033376 NF033376 380229 lat_flg_LafA_1 lateral flagellin LafA. This HMM describes rare second type of flagellin from E. coli and some closely related species, called LafA, where the familiar and common flagellin, FliC, is nearly universal and carries the H-antigen used for serotyping strains. In contrast to FliC, whose center region is highly variable, LafA shows little variability in sequence. In many E. coli strains, the Flag-2 locus either is absent or is cryptic, appearing degraded and non-functional. 304 matched cddid_all.tbl CDD NF033377 NF033377 468005 OMA_tautomer 4-oxalomesaconate tautomerase. 347 matched cddid_all.tbl CDD NF033379 NF033379 380231 FrucBisAld_I fructose-bisphosphate aldolase class I. This family consists of fructose-bisphosphate aldolase class I. All members of the seed alignment are from prokaryotes, although class I is the common form in plants and animals. The common form in prokaryotes is class II. 324 matched cddid_all.tbl CDD NF033380 NF033380 380232 Rlm_2499C5 23S rRNA (cytosine(2499)-C(5))-methyltransferase. This model describes a 23S rRNA modification related to RlmI of E. coli, but that modifies site C2499 rather than C1962. 391 matched cddid_all.tbl CDD NF033381 NF033381 468006 MonaBetaBRL_TX monalysin family beta-barrel pore-forming toxin. Members of this family are secreted in a water-soluble pro-toxin form, but undergo cleavage and oligomerization to form beta-barrel pore. The founding member of the family is monalysin from Pseudomonas entomophila. This family is built narrowly, and therefore excludes a set of pore-forming proteins (not necessarily toxins) from a eukaryote, Dictyostelium. Analogous (but perhaps not homologous) beta-type pore-forming toxins include aerolysin and leukocidin. 230 matched cddid_all.tbl CDD NF033382 NF033382 468007 OMP_33_36 porin Omp33-36. Members of this family are outer membrane beta-barrel proteins that facilitate passive transport from the extracellular milieu into the periplasm. Known members are limited to the genus Acinetobacter, and the name, Omp33-36, reflects variability of this protein across the lineage. Note that this HMM previously was named CarO in error. Both this protein and CarO affect carbapenem transport across the outer member and thus carbapenem susceptibility or resistance. 293 matched cddid_all.tbl CDD NF033383 NF033383 439397 induct_EntF EntF family bacteriocin induction factor. Members of this family have leader sequences like bacteriocins (see TIGR01847), but characterized examples function as signaling peptides that induce production of a nearby encoded bacteriocin, rather than as bacteriocins themselves. The founding member of this family is enterocin induction factor EntF. 39 matched cddid_all.tbl CDD NF033384 NF033384 380236 enterocin_MR10 enterocin L50 family leaderless bacteriocin. Members of this family are leaderless peptide components of bacteriocins in which the two subunits share about 74% identity with each other and are each about 43 amino acids long. Members include enterocin subunits L50A and L50B, MR10A and MR10B, etc. 43 matched cddid_all.tbl CDD NF033385 NF033385 380237 enterocin_LsbB LsbB family leaderless bacteriocin. Members of this family are leaderless peptide components of bacteriocins with a conserved motif KXXXGXXPWE. 35 matched cddid_all.tbl CDD NF033388 NF033388 468008 ubiq_like_UBact ubiquitin-like protein UBact. This HMM describes a protein family that includes most, but not all, of the proteins designated UBact (a ubiquitin-like protein) in the article first describing a biosystem related to bacterial pupylation. Protein modification by ubiquitin in eukaryotes, pupylation in many bacteria, and this system is a few other bacteria, is considered a signal that can trigger altered protein handling such as rapid degradation. Proteins that the authors consider members of the same family, but that show very little sequence similarity other than protein size and the final two residues, include WP_008669967.1 in the genus Rhodopirellula and OHA48658.1 in Candidatus Terrybacteria. 54 matched cddid_all.tbl CDD NF033389 NF033389 439398 scrub_typh_TSA22 major outer membrane protein TSA22. Members of this family are TSA22, one of three major outer membrane proteins, the so-called type-specific antigens, in two species of Orientia, including O. tsutsugamushi, causative agent of scrub typhus. The other type-specific antigens are TSA47 (a serine proteins in the DegP/HtrA family) and the much better known TSA56, which is quite variable in size and may be used for strain typing. 202 matched cddid_all.tbl CDD NF033390 NF033390 468009 Orientia_TSA56 "type-specific antigen TSA56. This protein is the immunodominant major cell surface protein of Orienta tsutsugamushi, known as ""56-kDa type-specific antigen"" or TSA56. It should not be confused with unrelated proteins TSA47 (a serine protease) or TSA22. An ortholog is found in Orientia chuto, and included in the seed alignment." 525 matched cddid_all.tbl CDD NF033391 NF033391 468010 lipid_A_LpxO lipid A hydroxylase LpxO. Members of this family are LpxO, an enzyme that modifies one of the lipid chains in lipid A by hydroxylation, with resulting changes in resistance to the host immune response and to the antibiotic colistin. This family, as built, includes LpxO1 from Pseudomonas aeruginosa, but not its paralog LpxO2. 297 matched cddid_all.tbl CDD NF033392 NF033392 380242 PSM_delta PSM-delta family phenol-soluble modulin. Members of this family are phenol-soluble modulins (short peptides, usually cytolysins) with an intact N-formyl-methionine at the N-terminus. 23 matched cddid_all.tbl CDD NF033393 NF033393 380243 TRP47_fam_Nterm TRP47 family tandem repeat effector N-terminal domain. This HMM describes a conserved N-terminal domain of a family of proteins found, so far, only in the genus Ehrlichia. The repeat region is followed by a long repeat region with a large content of acidic and serine residues, but other than in composition, the repeats themselves may be unrelated from one lineage to another. Characterized examples, such as TRP47 from Ehrlichia chaffeensis, are glycoproteins and are immunodominant antigens. 105 matched cddid_all.tbl CDD NF033394 NF033394 468011 capsid_maj_Podo phage major capsid protein. A founding member of this family, AKO59007.1, was identified as the major head protein in Brucella phage 02_19 during a comparison of Brucella phage genomes. The N-terminal half appears to the better conserved region with fewer insertions and deletions. 312 matched cddid_all.tbl CDD NF033395 NF033395 468012 fibronec_SfbI fibronectin-binding protein PrtF1/SfbI. PrtF1/SfbI is a fibronectin-binding protein a C-terminal region LPXTG region that mediates processing by sortase and covalent attachment to the cell wall. Near the N-terminus is a TED domain, which includes a Cys residue that forms a covalent thioester bond. 555 matched cddid_all.tbl CDD NF033396 NF033396 380246 pilus_ancill_1 pilus ancillary protein 1. 737 matched cddid_all.tbl CDD NF033399 NF033399 380247 thiazolyl_GetA GE37468 family thiazolyl peptide. 47 matched cddid_all.tbl CDD NF033400 NF033400 468013 thiazolyl_B thiazolylpeptide-type bacteriocin. 45 matched cddid_all.tbl CDD NF033401 NF033401 468014 thiazolyl_BerA thiocillin/thiostrepton family thiazolyl peptide. Members of this family include the precursor peptides for the antibiotics thiostrepton, nosiheptide, thiocillin, and berninamycin. 42 matched cddid_all.tbl CDD NF033402 NF033402 380250 linaridin_RiPP linaridin family RiPP. Linaridins are ribosomally translated, post-translationally modified peptide natural products, or RiPPs. Examples include cypemycin, SGR-1832, and legonaridin. 63 matched cddid_all.tbl CDD NF033403 NF033403 380251 linaridin_rel linaridin-like RiPP. Members of this family share N-terminal (leader peptide) sequence with the linaridin family of ribosomally translated, post-translationally modified natural product precursors. 64 matched cddid_all.tbl CDD NF033404 NF033404 468015 YneK putative protein YneK. Members of this family, YneK, are found so far only in Escherichia coli and Escherichia albertii, with 68% sequence identity but in identical gene neighborhoods. In E. coli O157:H7 strain Sakai, yneK has a nonsense mutation and is therefore truncated. The function is unknown. 371 matched cddid_all.tbl CDD NF033405 NF033405 439401 FosLL fosfomycin resistance glutathione transferase. This putative fosfomycin resistance glutathione transferase was detected in a mobile island in Acinetobacter baumannii D1279779 and is found in many other isolates as well. 135 matched cddid_all.tbl CDD NF033407 NF033407 468016 SnoaL_meth_ester SnoaL/DnrD family polyketide biosynthesis methyl ester cyclase. This HMM represents mutually closely related methyl ester cyclases from a number of polyketide biosynthesis pathways. Examples include proteins designated SnoaL (nogalamycin biosynthesis), DnrD (doxorubicin biosynthesis), RdmA (rhodomycin biosynthesis), etc. 144 matched cddid_all.tbl CDD NF033411 NF033411 380254 small_mem_YnhF YnhF family membrane protein. Members of this protein family, are small membrane proteins, about 29 amino acids in length. YnhF from E. coli was shown to have an intact fMet residue at the N-terminus and to be chloroform-soluble. The previously generated narrow cluster PRK14756 includes some members of this family. 29 matched cddid_all.tbl CDD NF033412 NF033412 380255 primase_PriX eukaryotic-type DNA primase noncatalytic subunit PriX. In most archaea, the eukaryotic-type DNA primase has catalytic subunit PriS and a regulatory subunit PriL. The proteins in this family are PriX, an essential second noncatalytic subunit found in a subset of the archaea. 98 matched cddid_all.tbl CDD NF033413 NF033413 380256 RiPP_TM1316 Cys-rich RiPP peptide. Member of this family include the small, Cys-rich peptide TM1316 of Thermotoga maritima, encoded near the peptide-modifying radical SAM/SPASM protein TM1317 (AE000512.1). TM1316 is expressed at very high levels in stationary phase. 31 matched cddid_all.tbl CDD NF033414 NF033414 380257 bottro_RiPP bottromycin family RiPP peptide. Bottromycins are one of the rarer known classes of ribosomally translated, post-translationally modified peptide (RiPP) antibiotics. 44 matched cddid_all.tbl CDD NF033415 NF033415 468017 thiovirid_RiPP thioviridamide family RiPP peptide. Thioviridamide represents one of the rarer known classes of ribosomally translated, post-translationally modified peptide (RiPP) antibiotics. 72 matched cddid_all.tbl CDD NF033416 NF033416 380259 YM-216391_RiPP YM-216391 family RiPP peptide. YM-216391 represents one of the rarer known classes of ribosomally translated, post-translationally modified peptide (RiPP) antibiotics. 35 matched cddid_all.tbl CDD NF033417 NF033417 468018 glycocin_F_RiPP glycocin F family RiPP peptide. Glycocin F, from Lactobacillus plantarum strain KW30, represents one of the rarer known classes of ribosomally translated, post-translationally modified peptide (RiPP) antibiotics. Members of the family are glycosylated, which is uncommon among RiPP natural products. 68 matched cddid_all.tbl CDD NF033418 NF033418 380261 T6SS_TagK type VI secretion system-associated protein TagK. Members of this family have full-length homology to SciF, a type VI secretion system (T6SS) protein from Salmonella typhimurium island SPI-6. Homologs occur in some but not all T6SS loci, and the broader family is now called TagK. 304 matched cddid_all.tbl CDD NF033419 NF033419 468019 T6SS_TagK_dom TagK family protein C-terminal domain. 127 matched cddid_all.tbl CDD NF033420 NF033420 411112 T6SS_PAAR_dom type VI secretion system PAAR domain. The PAAR domain is widespread, but this model represents a narrow clade that may occur in type VI secretion systems (T6SS), either free-standing or fused to a long extension. Effector domains of T6SS may be separate proteins, or may be fused to on of the tube or spike proteins: VgrG (spike), Hcp (tube), or this PAAR family (spike tip). Members of this family that have long extensions are likely to be T6SS effectors. 94 matched cddid_all.tbl CDD NF033422 NF033422 468020 onco_T4SS_CagA type IV secretion system oncogenic effector CagA. CagA, an effector injected into host cells by the type IV secretion system (T4SS) apparatus of Helicobacter pylori, is an oncogenic toxin. Tyrosine phosphorylation at multiple Glu-Pro-Ile-Tyr-Ala (EPIYA) motifs creates a scaffold that interacts with multiple host signaling systems and sometimes allows neoplasias to begin in gastric epithelial cells. 1056 matched cddid_all.tbl CDD NF033424 NF033424 468021 chlamy_CPAF protease-like activity factor CPAF. CPAF (chlamydial protease/proteasome-like activity factor) is a serine protease secreted various species of the intracellular pathogen Chlamydia. Early attribution of contributions of CPAF to virulence by cleavage of specific host cell substrates contains a number of errors, and the true role of CPAF, and its contributions to virulence, remain under study. 565 matched cddid_all.tbl CDD NF033425 NF033425 380267 PSM_alpha_1_2 alpha-1/alpha-2 family phenol-soluble modulin. Members of this family are extremely short proteins, about 21 amino acids long, that are known to retain an N-formyl-methionine (fMet) at the N-terminus. These proteins, phenol-soluble modulins of the alpha class, including alpha-1 and alpha-2 from Staphylococcus aureus, are exported by an ABC transporter, and affect the state of the host immune system in a number of ways. 21 matched cddid_all.tbl CDD NF033426 NF033426 380268 PSM_alpha_3 alpha-3 family phenol-soluble modulin. 22 matched cddid_all.tbl CDD NF033427 NF033427 380269 PSM_alpha_Shaem alpha family phenol-soluble modulin. This family is based on an alpha family Staphylococcus haemolyticus phenol-soluble modulin, somewhat similar to delta-lysin. 20 matched cddid_all.tbl CDD NF033428 NF033428 380270 PSM_epsilo epsilon family phenol-soluble modulin. Members of this family epsilon-family phenol-soluble modulins. Species with members include Staphylococcus epidermidis, Staphylococcus capitis, Staphylococcus lugdunensis, Staphylococcus pseudintermedius, and Staphylococcus schleiferi. 21 matched cddid_all.tbl CDD NF033429 NF033429 468022 ImuA_translesion "translesion DNA synthesis-associated protein ImuA. A three-gene cassette encoding ImuA, ImuB, and ImuC (""inducible mutagenesis"") is induced by DNA damage, is capable of DNA synthesis across DNA damage lesions, and consequently is associated with mutagenesis. This family, ImuA (previously misnamed SulA in Pseudomonas putida) shows some homology to SulA itself and to RecA. ImuB resembles Y-family polymerases but may be catalytically inactive. ImuC is a C-family polymerase, and catalytically active." 181 matched cddid_all.tbl CDD NF033430 NF033430 380272 TfxA_RiPP trifolitoxin family RiPP peptide. Trifolitoxin is ribosomally synthesized and post-translationally modified peptide natural product (RiPP) antibiotic produced by some strains of Rhizobium and active against others. At the time of building this model, only two variants sequences from this family are detected, both 42 amino acid-long TfxA peptides that differ at only two positions. 42 matched cddid_all.tbl CDD NF033431 NF033431 380273 cinnamycin_RiPP cinnamycin family lantibiotic. Members of this family are RiPP precursor peptides from which the lantibiotic cinnamycin is the most heavily studied. Mature cinnamycin is 19 amino acids long with nine post-translational modifications, including lanthionine, methyllanthionine, and lysinoalanine bridge modifications. 77 matched cddid_all.tbl CDD NF033432 NF033432 468023 ThioGly_TfuA_rel TfuA-related McrA-glycine thioamidation protein. 211 matched cddid_all.tbl CDD NF033433 NF033433 468024 NisI_immun_dup NisI/SpaI lantibiotic immunity lipoprotein domain. This HMM describes a domain that occurs twice in the nisin lantibiotic self-immunity lipoprotein NisI, and once in the subtilin lantibiotic self-immunity lipoprotein SpaI, and once or twice in numerous other known or putative lantibiotic resistance lipoproteins. 104 matched cddid_all.tbl CDD NF033434 NF033434 380276 AzmA_fam_RiPP azolemycin family RiPP peptide. The azolemycin precursor peptide, AzmA, contains a mature (core) peptide region derived from the sequence VVSTCTI. Examining genomic context from that RiPP precursor peptides related to AzmA are much more similar in the leader peptide region than in the core region, and that the proper length for the percursor peptide is probably about 36 amino acids. 36 matched cddid_all.tbl CDD NF033435 NF033435 468025 S-layer_Clost S-layer protein SlpA. In Clostridiodes difficile, the S-layer protein precursor, SlpA, is one member of a large paralogous family of protein that share several cell wall-binding repeats. SlpA is cleaved into a larger and smaller protein. The S-layer protein itself is important to adhesion, and portions of it are highly variable, and then N-terminal and C-terminal are well-conserved. 728 matched cddid_all.tbl CDD NF033436 NF033436 380278 SpoVM_broad stage V sporulation protein SpoVM. Members of this family are SpoVM (stage V sporulation protein M). 26 matched cddid_all.tbl CDD NF033437 NF033437 380279 YpdK membrane protein YpdK. 23 matched cddid_all.tbl CDD NF033438 NF033438 468026 BREX_BrxD BREX system ATP-binding protein BrxD. BrxD is an ATP-binding protein found in types 2 and 6 of BREX (bacteriophage exclusion) phage resistance systems. 423 matched cddid_all.tbl CDD NF033439 NF033439 380281 small_mem_YoeI membrane protein YoeI. YoeI, a hydrophobic protein of only 20 amino acids, is found in at least these genera: Escherichia, Salmonella, Citrobacter, Enterobacter, and Klebsiella. It is known to be expressed in E. coli. 20 matched cddid_all.tbl CDD NF033440 NF033440 380282 small_YrbN protein YrbN. YrbN, a small protein of only 26 amino acids, is found in at least these genera: Escherichia, Salmonella, Enterobacter, Klebsiella, and Yersinia. It is known to be expressed in E. coli. 26 matched cddid_all.tbl CDD NF033441 NF033441 468027 BREX_BrxC BREX system P-loop protein BrxC. BrxC is a P-loop-containing protein, and probable ATPase, from BREX (bacteriophage exclusion) systems of type 1. 1173 matched cddid_all.tbl CDD NF033442 NF033442 468028 BREX_PglW BREX system serine/threonine kinase PglW. Members of this family are PglW, a predicted serine/threonine kinase of the Pgl (phage growth limitation) system (now called BREX type 2) and the BREX type 3 system. 1387 matched cddid_all.tbl CDD NF033443 NF033443 468029 BREX_PglZ_6 BREX-6 system phosphatase PglZ. 958 matched cddid_all.tbl CDD NF033444 NF033444 380286 BREX_PglZ_5 BREX-5 system phosphatase PglZ. 704 matched cddid_all.tbl CDD NF033445 NF033445 468030 BREX_PglZ_4 BREX-4 system phosphatase PglZ. 734 matched cddid_all.tbl CDD NF033446 NF033446 468031 BREX_PglZ_2 BREX-2 system phosphatase PglZ. 890 matched cddid_all.tbl CDD NF033447 NF033447 468032 BrxE_fam BrxE family protein. This family is uncharacterized, but a subgroup within this family is BrxE, a protein of unknown function found in type 6 BREX phage resistance systems. 166 matched cddid_all.tbl CDD NF033448 NF033448 468033 BREX_6_BrxE BREX-6 system BrxE protein. Members of this family are BrxE, a protein of unknown function that is found in type 6 BREX systems of phage defense. 182 matched cddid_all.tbl CDD NF033449 NF033449 468034 BREX_PglZ_3 BREX-3 system phosphatase PglZ. BREX is a phage defense system (BacteRiophage EXclusion), with a number of described subtypes. The first described, PGL (phage growth limitation), is not called BREX-2. This model describes one of the two core proteins universal across the first six defined BREX subtypes, the phosphatase-like PglZ domain protein, as found in BREX-3 systems. 642 matched cddid_all.tbl CDD NF033450 NF033450 468035 BREX_PglZ_1_B BREX-1 system phosphatase PglZ type B. BREX (bacteriophage exclusion) is a phage resistance resistance, in which two protein families are core but other proteins are variable. BREX subtypes are based on PglZ domain protein, a putative phosphatase. This family is one of two major subtypes of PglZ as seen in type 1 BREX systems. Most members of this family contain an additional C-terminal domain that is not included in the seed alignment. Family TIGR02687 describes the alternative type A for PglZ of BREX-1. 672 matched cddid_all.tbl CDD NF033451 NF033451 468036 BREX_2_MTaseX BREX-2 system adenine-specific DNA-methyltransferase PglX. This protein, PglX, is a site-specific DNA methyltransferase associated with PGL (phage growth limitation), a type 2 BREX (bacteriophage exclusion) system. The phage resistance appears not be restriction, but does manage to inhibit phage replication. 1188 matched cddid_all.tbl CDD NF033452 NF033452 468037 BREX_1_MTaseX BREX-1 system adenine-specific DNA-methyltransferase PglX. This protein, PglX, is a site-specific DNA methyltransferase associated BREX (bacteriophage exclusion) type 1 systems. The phage resistance appears not to be through restriction-modification, as phage DNA appears not to get degraded, but it does manage to inhibit phage replication. 1187 matched cddid_all.tbl CDD NF033453 NF033453 468038 BREX_3_BrxF BREX-3 system P-loop-containing protein BrxF. This family of proteins that are about 150 amino acids in length includes BrxF from type 3 BREX (bacteriophage exclusion) systems. Most members have the P-loop motif GxxGxGKT, but the region is surprisingly poorly conserved in a sizable fraction of otherwise strongly similar proteins. 149 matched cddid_all.tbl CDD NF033454 NF033454 468039 BREX_5_MTaseX BREX-5 system adenine-specific DNA-methyltransferase PglX. 1401 matched cddid_all.tbl CDD NF033455 NF033455 468040 BREX_6_MTaseX BREX-6 system adenine-specific DNA-methyltransferase PglX. 1319 matched cddid_all.tbl CDD NF033456 NF033456 380298 RiPP_CCRG-2 CCRG-2 family RiPP leader. This model consists of the conserved leader peptide domain of CCRG-2 family ribosomal peptide natural products (RiPPs), up to the Gly-Gly presumptive cleavage site, plus one additional residue (hydrophobic, or another Gly). Members are found almost exclusively in the genus Prochlorococcus, in multiple instances per genome. 18 matched cddid_all.tbl CDD NF033457 NF033457 380299 elgicin_lanti elgicin/penisin family lantibiotic. The HMM describes the elgicin family of lanthipeptides active as bacteriocins. The leader domain occurs in additional proteins that lack homology in the core region, although sharing richness in Cys residues there. 64 matched cddid_all.tbl CDD NF033458 NF033458 380300 lipid_A_LpxG UDP-2,3-diacylglucosamine diphosphatase LpxG. Members of this family are LpxG, the lipid A biosynthesis enzyme UDP-2,3-diacylglucosamine diphosphatase ()EC 3.6.1.54). This family is unrelated to the more common LpxH, or to LpxI, which share the same activity. 321 matched cddid_all.tbl CDD NF033459 NF033459 380301 DksA_like RNA polymerase-binding protein DksA. 113 matched cddid_all.tbl CDD NF033460 NF033460 380302 glycerol3P_ox_II type 2 glycerol-3-phosphate oxidase. This FAD-dependent enzyme (EC 1.1.3.21), glycerol-3-phosphate oxidase, also called L-alpha-glycerophosphate oxidase, converts sn-glycerol 3-phosphate plus oxygen to glycerone phosphate plus hydrogen peroxide, which contributes to virulence. This form, called type 2, is shorter than type 1 and is found exclusively in Mycoplasmas and other members of the Mollicutes. 361 matched cddid_all.tbl CDD NF033461 NF033461 411122 glycerol3P_ox_1 type 1 glycerol-3-phosphate oxidase. Glycerol-3-phosphate oxidase, also called alpha-glycerophosphate oxidase (GlpO), is an FAD-dependent enzyme related to the glycerol-3-phosphate dehydrogenase GlpD. Notably, GlpO releases hydrogen peroxide, which can contribute to virulence. 607 matched cddid_all.tbl CDD NF033464 NF033464 380304 cyanoexo_CrtC cyanoexosortase C. Cyanosortase C (CrtC) belongs to the exosortase/archaeosortase family of multiple membrane proteins that act as cysteine proteases, and probably as transpeptidases, analogous to (but unrelated to) the sortases. CrtC is known so far only in Cyanobacteria, and appears so far primarily in the lesser-studied genera: Leptolyngbya, Oscillatoriales, Scytonema, Alkalinema, Phormidesmis, etc. 278 matched cddid_all.tbl CDD NF033465 NF033465 380305 PTPA-CTERM PTPA-CTERM protein sorting domain. This C-terminal sorting and processing signal, called PTPA-CTERM, is a variant of the widespread PEP-CTERM domain. It is restricted a subset of Cyanobacteria that encode the sorting enzyme named cyanoexosortase C. 23 matched cddid_all.tbl CDD NF033471 NF033471 380306 J25_fam_lasso acinetodin/klebsidin/J25 family lasso peptide. Members of this family include precursors of at least three lasso peptides, namely microcin J25, acinetodin and klebsidin. All members of the family are encoded as neighboring genes to homologs of the processing protein genes mcjB, mcjC, and mcjD. 39 matched cddid_all.tbl CDD NF033473 NF033473 439404 trim_sens_DfrEf trimethoprim-sensitive dihydrofolate reductase. This dihydrofolate reductase was originally described as the intrinsic dihydrofolate reductase of Enterococcus faecalis, sensitive to trimethoprim and incapable of conferring resistance to that antibiotic. Although the protein was referred to as DfrE by Coque, et al. (1999, PMID:9869579), to contrast it with the much rarer, resistance-conferring enzyme DfrF, we do not use the term DfrE, as a name in that series suggests a TMP-resistant form. Instead, we reserve the name DfrE for the trimethoprim-resistant enzyme WP_012655890.1 and close homologs, as described in PMID:34374564. 164 matched cddid_all.tbl CDD NF033474 NF033474 468041 DivGenRetAVD diversity-generating retroelement protein Avd. Avd (accessory variability determinant) is part of diversity-generating retroelement (GDR) system through which a portion of a protein-coding gene can be rewritten, creating diversity that can affect host range. The founding member of this family, bAvd, from a Bordetella bacteriophage, belongs to a retrohoming element called BPP-1. Members of this family are four-helix bundle proteins, related to those of family TIGR02436, some of whose members are found in long intervening sequence (IVS) regions in 23S rRNA. 104 matched cddid_all.tbl CDD NF033477 NF033477 380308 EmaA_autotrans collagen-binding adhesin autotransporter EmaA. EmaA (extracellular matrix protein adhesin ) is an outer membrane protein first described in Aggregatibacter (Actinobacillus) actinomycetemcomitans, a member of the Gammaproteobacteria. It is a glycoprotein, and has a C-terminal beta-barrel domain that marks it as an autotransporter. It serves as an adhesin that binds collagen, the most abundant material in the host extracellular matrix. It shares homology with the collagen-binding protein YadA of Yersinia enterocolitica. 1694 matched cddid_all.tbl CDD NF033479 NF033479 468042 Efa1_rel_toxin LifA/Efa1-related large cytotoxin. Members of this family are large and almost certainly multifunctional proteins found in various pathogens from genus Chlamydia, about 3000 amino acids in size and related to lymphostatin (Efa1/LifA) from enteropathogenic Escherichia coli. Roles have been suggested for Efa1 (EHEC factor for adherence) in adhesion, so some members have been annotated as adherence proteins rather than cytotoxins. 3223 matched cddid_all.tbl CDD NF033480 NF033480 468043 bifunc_MprF bifunctional lysylphosphatidylglycerol flippase/synthetase MprF. The C-terminal region of MprF tranfers lysine from a charged tRNA onto phosphatidylglycerol to make lysylphosphatidylglycerol (EC 2.3.2.3). The N-terminal region of MprF acts as a flippase. MprF helps confer resistance to antimicrobial cationic peptides. 839 matched cddid_all.tbl CDD NF033481 NF033481 411124 auto_Ata trimeric autotransporter adhesin Ata. Ata (Acinetobacter trimeric autotransporter) has an architecture that consists of a long signal peptide, a repetitive passenger domain that varies in length from strain to strain, and a C-terminal domain of four transmembrane beta stands that forms one third of the pore for autotransporter activity and anchoring in the outer membrane. 1862 matched cddid_all.tbl CDD NF033482 NF033482 468044 RiPP_thiocil thiocillin family RiPP. Members of this family are ribosomally synthesized and post-translationally modified peptide natural product (RiPP) precursors. Nearly all contain at least one Cys residues expected to be involved in thiazolyl peptide modifications, and are expected to behave at least in part as antibiotics. Genomes of some species (Bacillus atrophaeus, Streptomyces coelicoflavus, etc.) may contain multiple paralogs. 48 matched cddid_all.tbl CDD NF033483 NF033483 468045 PknB_PASTA_kin Stk1 family PASTA domain-containing Ser/Thr kinase. 563 matched cddid_all.tbl CDD NF033484 NF033484 468046 Stp1_PP2C_phos Stp1/IreP family PP2C-type Ser/Thr phosphatase. Many Gram-positive bacteria have a protein kinase/protein phosphatase gene pair that responds to peptidoglycan metabolites and can be instrumental in resistance to beta-lactam antibiotics. Characterized examples of the phosphatase component are Stp1 of Staphylococcus aureus and IreP of Enterococcus faecalis. 232 matched cddid_all.tbl CDD NF033485 NF033485 468047 small_SCO1431 SCO1431 family membrane protein. Members of this family, including SCO1431 from Streptomyces coelicolor A3(2), are small and extremely hydrophobic proteins that lack an N-terminal signal peptide. Known members are restricted to the genus Streptomyces, where the protein family is widespread. 47 matched cddid_all.tbl CDD NF033486 NF033486 411129 harvest_ssl1498 ssl1498 family light-harvesting-like protein. Members of this family appear restricted to the Cyanobacteria, and include ssl1498 from Synechocystis sp. PCC 6803. These proteins are small, usually about 56 amino acids, with an N-terminal half related to a number of light-harvesting proteins, and a highly hydrophobic C-terminal half likely to be embedded in membrane. 53 matched cddid_all.tbl CDD NF033487 NF033487 411130 Lacal_2735_fam Lacal_2735 family protein. This small protein is widespread but uncharacterized. Most members are shorter than 60 amino acids in length. 54 matched cddid_all.tbl CDD NF033488 NF033488 411131 lmo0937_fam_TM lmo0937 family membrane protein. Members of this family are very small (about 45 amino acids) and highly hydrophobic, suggesting a presence in the membrane, and have a broad phylogenetic distribution. The member protein lmo0937, from the pathogen Listeria monocytogenes, is described as up-regulated when the bacterium is in the mouse spleen, suggesting a role in stress response. 43 matched cddid_all.tbl CDD NF033490 NF033490 411132 small_SPW0924 SPW_0924 family protein. Members of this family average less than 44 amino acids in length, and are found exclusively in the Actinobacteria (mostly Streptomyces). The N-terminal half is organized like a signal peptide, beginning Met-Arg and then continuing with a hydrophobic stretch that is unusually rich in alanine. The C-terminal region has a nearly invariant motif TSPxPLLTTVP. The function is unknown. 44 matched cddid_all.tbl CDD NF033491 NF033491 411133 BA3454_fam BA3454 family stress response protein. BA3454, a protein less than 45 amino acids long, is up-regulated strongly by SpxA2 during stress conditions. Related proteins are found widely in the genus Bacillus, although not in Bacillus subtilis. 43 matched cddid_all.tbl CDD NF033492 NF033492 411134 podovir_small putative phage replication protein. Members of this family of very small, highly hydrophobic proteins are restricted to the genus Acinetobacter, and appear to be entirely of phage origin. One member is encoded in the Podoviral Bacteriophage YMC/09/02/B1251 ABA BP (although the coding region is not predicted in GenBank record JX403940.1). Evidence suggesting the reading frame really does encode protein includes the overlap of a TGA stop codon with an ATG start codon at both ends of this protein, suggesting translational coupling with the much larger adjacent genes immediately upstream and downstream. 36 matched cddid_all.tbl CDD NF033493 NF033493 411135 MetS_like_NSS MetS family NSS transporter small subunit. MetS, as described in the Gram-positive bacterium Corynebacterium glutamicum, is the small subunit of MetPS, an NSS (Neurotransmitter:Sodium Symporter) transporter involved in methionine and alanine import. While MetS itself is small, only 60 amino acids, homologs in gamma proteobacteria such as Vibrio sp., similarly found next to an NSS transporter large subunit, may be barely half that length and consist almost entirely of a predicted hydrophobic region that would localize to within the plasma membrane. 30 matched cddid_all.tbl CDD NF033494 NF033494 411136 NSS_import_MetS methionine/alanine import NSS transporter subunit MetS. 53 matched cddid_all.tbl CDD NF033495 NF033495 411137 phage_BC1881 BC1881 family protein. Members of this family of very small proteins (average length is about 50 residues) include BC1881 from the phBC6A51 prophage region of the Bacillus cereus ATCC 14579 genome. 45 matched cddid_all.tbl CDD NF033496 NF033496 411138 DUF2080_fam_acc DUF2080 family transposase-associated protein. Members of this family appear restricted to the archaea. They tend to be encoded upstream of predicted transposase genes within insertion sequences such as ISNagr11, ISHca1, ISH36, etc. The widespread distribution suggests this protein may be more than a mere passenger gene and may participate in some transposase-associated function. See PF09853, COG3466, and arCOG03884 for alternative (currently narrow) treatments of this family. 34 matched cddid_all.tbl CDD NF033497 NF033497 411139 rubre_like_arch rubrerythrin-like domain. This rubrerythrin-like domain is found primarily in the archaea, occasionally as part of a larger redox-active protein. It features two CxxC motifs with a spacer of 12 to 13 amino acids. 34 matched cddid_all.tbl CDD NF033498 NF033498 411140 YlcG_phage_expr YlcG family protein. Members of this family include YlcG from the DLP12 prophage region of Eschichia coli K-12, and homologs from the Gifsy-1 and Gifsy-2 prophage regions of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2. Members of this protein family are small, about 46 amino acids long. YlcG is known to be expressed. It is encoded immediately downstream of the Holliday junction resolvase RusA. 41 matched cddid_all.tbl CDD NF033499 NF033499 411141 Xis_Gifsy_1 excisionase Xis. Members of this family are excisionases such as Xis from the Gifsy-1 prophage of Salmonella enterica subsp. enterica serovar Typhimurium str. LT2. 92 matched cddid_all.tbl CDD NF033500 NF033500 411142 phi80_GamL host nuclease inhibitor GamL. Members of this family, including GamL from phage phi80, are phage inhibitors of host nucleases such as RecBCD and SbcCD. This family has a distant relationship to Gam (see PF06064), which inhibits RecBCD. 89 matched cddid_all.tbl CDD NF033501 NF033501 411143 ArfB_arch_rifla 2-amino-5-formylamino-6-ribosylaminopyrimidin-4(3H)-one 5'-monophosphate deformylase. MJ0116 from Methanocaldococcus jannaschii, the founding member of this family, was shown be 2-amino-5-formylamino-6-ribosylaminopyrimidin-4(3H)-one 5'-monophosphate deformylase, catalyzing the second step in archaeal riboflavin and Fo biosynthesis. 219 matched cddid_all.tbl CDD NF033503 NF033503 468048 LarB nickel pincer cofactor biosynthesis protein LarB. This protein, related to AIR carboxylase, is part of a three protein system involved in producing a specialized nicotinic acid-derived, nickel-containing cofactor, as used in the nickel-dependent lactate racemase of lactic acid bacteria. 209 matched cddid_all.tbl CDD NF033504 NF033504 468049 Ni_dep_LarA nickel-dependent lactate racemase. LarA from Lactobacillus plantarum is a nickel-dependent lactate racemase and the founding member of a family of isomerases that depend on a nicotinic acid-derived nickel pincer cofactor. While it is not yet clear which homologs of LarA act preferentially on lactate, this model identifies one clade of architecurally similar proteins from among a broader set of LarA homologs. Note that the crystal structure 4NAR, on deposit at PDB but not associated with any publication, represents a protein from Thermotoga maritima that falls outside the scope of this family and that is annotated in PDB as a putative uronate isomerase. 417 matched cddid_all.tbl CDD NF033505 NF033505 411146 paceosortase pacearchaeosortase. Members of this family, pacearchaeosortase, are archaeosortases from the uncultured (so far) Candidatus Pacearchaeota archaeon lineage and its close relatives. In most assemblies where pacearchaeosortase is found, only one protein can be found likely to make it the target for sorting and cleavage, and it is encoded by the adjacent gene. This dedicated arrangement suggests the adjacent gene encodes a critical surface protein, most likely one that helps form an S-layer. 167 matched cddid_all.tbl CDD NF033506 NF033506 468050 PACE-CTERM-PROT putative S-layer protein. Assembled genomes from the Candidatus Pacearchaeota archaeon group and its close relatives, so far all uncultured, have a single archaeosortase, called pacearchaseosortase. A search protein archaeosortase targets, with a C-terminal domain resembling other archaeosortase and exosortase sorting signal regions, found this family as the best candidate. It is nearly always encoded by a gene found adjacent to the pacearchaseosortase gene. This dedicated arrangement, a sorting enzyme encoded next to its only predicted sorting substrate, suggests that members of this family, called PACE-CTERM, may be an important and abundant surface protein, most likely the major S-layer protein. 558 matched cddid_all.tbl CDD NF033507 NF033507 411148 Loki-CTERM Loki-CTERM protein-sorting domain. 26 matched cddid_all.tbl CDD NF033510 NF033510 411149 Ca_tandemer Ca2+-stabilized adhesin repeat. This repeat is found in proteins such as the biofilm-associated protein Bap of Acinetobacter baumannii (which can exceed 8000 amino acids in length), the calcium-stabilized ice-binding adhesin of the Antarctic bacterium Marinomonas primoryensis, and the giant calcium-binding adhesin SiiE of Salmonella enterica. 97 matched cddid_all.tbl CDD NF033511 NF033511 411150 metallo_CpaA metalloendopeptidase CpaA. 575 matched cddid_all.tbl CDD NF033512 NF033512 468051 T2SS_chap_CpaB metalloprotease secretion chaperone CpaB. The cpaA and cpaB gene pair, as described in the genus Acinetobacter, consists of a metalloendopeptidase virulence factor, CpaA, and a tightly binding membrane-bound chaperone, CpaB, important for its secretion by a type II secretion system (T2SS). CpaA, in at least some Acinetobacter, is the most heavily secreted T2SS effector, and behaves as a virulence factor that cleaves factor V in blood and alters coagulation. 205 matched cddid_all.tbl CDD NF033515 NF033515 411152 lipo_6_6_Borrel Lp6.6 family lipoprotein. In Borrelia burgdorferi, the tiny lipoprotein Lp6.6 is plasmid-borne and was originally described as a major low-molecular-weight lipoprotein that could constitute 2% of the dry weight of defatted cells. Lp6.6 was later found to facilitate transmission from ticks to mice, and to be down-regulated after infection. 60 matched cddid_all.tbl CDD NF033516 NF033516 468052 transpos_IS3 IS3 family transposase. 369 matched cddid_all.tbl CDD NF033517 NF033517 468053 transpos_IS66 IS66 family transposase. Members of this protein family are DDE transposases from the IS66 family insertion sequences, which typically consist of two accessary genes (TnpA and TnpB) and the third gene encoding the transposase. 388 matched cddid_all.tbl CDD NF033518 NF033518 468054 transpos_IS607 IS607 family transposase. 187 matched cddid_all.tbl CDD NF033519 NF033519 468055 transpos_ISAzo13 ISAzo13 family transposase. 387 matched cddid_all.tbl CDD NF033520 NF033520 468056 transpos_IS982 IS982 family transposase. Currently, there are 46 seed sequences in this family. 243 matched cddid_all.tbl CDD NF033521 NF033521 468057 lasso_leader_L3 lasso RiPP family leader peptide. 20 matched cddid_all.tbl CDD NF033522 NF033522 468058 lasso_benenodin benenodin family lasso peptide. This family consists of both the leader (removed) and core (mature) portions of precursor peptides from the benenodin family of lasso peptides. 43 matched cddid_all.tbl CDD NF033523 NF033523 468059 lasso_peptidase Atxe2 family lasso peptide isopeptidase. 637 matched cddid_all.tbl CDD NF033524 NF033524 411161 lasso_PadeA_fam paeninodin family lasso peptide. Members of this family are lasso peptides in the paeninodin family, mostly from the genera Bacillus, Paenibacillus, and Thermobacillus. The HMM covers the leader peptide region but only about half of the core peptide region, since it is quite diverse. 30 matched cddid_all.tbl CDD NF033525 NF033525 468060 lasso_albusnod albusnodin family lasso peptide. Members of this family are lasso peptides in the family of albusnodin, and appear limited so far to the Actinobacteria. Members are more strongly conserved in the core peptide region than in the leader peptide region, which is unusual for ribosomally produced, post-translationally modified natural products. The founding member of this family is not only circularized by the formation of an isopeptide bond, but also acetylated. 40 matched cddid_all.tbl CDD NF033527 NF033527 468061 transpos_Tn3 Tn3 family transposase. 954 matched cddid_all.tbl CDD NF033528 NF033528 411164 lasso_cyano lasso peptide. Members of this family are lasso peptide precursors of a type common in the Cyanobacteria and so far restricted to them. Some members have a pair of Cys residues in the core peptide region, C-terminal the region modeled in the HMM, and therefore would form bicyclic compounds. 35 matched cddid_all.tbl CDD NF033529 NF033529 468062 transpos_ISLre2 ISLre2 family transposase. 378 matched cddid_all.tbl CDD NF033530 NF033530 468063 lasso_PqqD_Strm lasso peptide biosynthesis PqqD family chaperone. Members of this family are homologs of PqqD, a chaperone that binds RiPP peptide precursors for their modification into bioactive natural products. By context, this set is involved in the biosynthesis of threaded-lasso peptides. This model focuses on lasso peptide systems from Actinobacteria. Similar systems, with different subfamilies of PqqD-related peptides, occur in lasso peptide systems in other lineages. A characterized example is LarB1 from the lariatin system of Rhodococcus jostii. 78 matched cddid_all.tbl CDD NF033532 NF033532 468064 lone7para_assoc type VII secretion system-associated protein. Members of this family occur almost exclusively in the genus Streptomyces, in the context of type VII secretion systems (T7SS). Several paralogs may accompany a single T7SS. A few members of this family are large proteins with additional domains that add or remove, ADP-ribosylations, suggesting that all family members may have effector activity as well, and that the longer members of the family are multifunctional effector proteins. 162 matched cddid_all.tbl CDD NF033533 NF033533 468065 lone7_assoc_B type VII secretion system-associated protein. Members of this family are found almost entirely in the genus Streptomyces, and are associated with a type VII secretion system (T7SS). 135 matched cddid_all.tbl CDD NF033534 NF033534 411169 rhodolasso lasso peptide. Members of this family are lasso peptides as found in the genus Rhodothermus. The leader peptide region shows sequence relatedness to several other groups of lasso peptide precursors. Known members of this family have a pair of Cys residues in the core peptide region, suggesting a bicyclic product, with one cross-link from the signature lasso peptide isopeptide bond and the other from the cysteine disulfide bond. This subfamily of lasso peptide appears not to have been discussed in the literature yet. 49 matched cddid_all.tbl CDD NF033535 NF033535 468066 lass_lactam_cya lasso peptide isopeptide bond-forming cyclase. Members of this family are the isopeptide bond-forming cyclase of lasso peptide biosynthesis systems, from a subgroup that contains primarily cyanobacterial examples. These proteins resemble the glutamine-hydrolyzing asparagine synthase AsnB (EC 6.3.5.4). 668 matched cddid_all.tbl CDD NF033536 NF033536 468067 lasso_PqqD_Bac lasso peptide biosynthesis PqqD family chaperone. Members of this family are homologs of PqqD, a chaperone that binds RiPP peptide precursors for their modification into bioactive natural products. By context, this set is involved in the biosynthesis of threaded-lasso peptides. This model focuses on lasso peptide systems from Firmicutes. Similar systems, with different subfamilies of PqqD-related peptides, occur in lasso peptide systems in other lineages. 88 matched cddid_all.tbl CDD NF033537 NF033537 468068 lasso_biosyn_B2 lasso peptide biosynthesis B2 protein. 130 matched cddid_all.tbl CDD NF033538 NF033538 468069 transpos_IS91 IS91 family transposase. 376 matched cddid_all.tbl CDD NF033539 NF033539 468070 transpos_IS1380 IS1380 family transposase. Proteins of this family are DDE type transposases, which are encoded by IS1380 family elements. It was first identified and characterized in an Acetobacter pasteurianus mutant with ethanol oxidation deficiency caused by disruption of the cytochrome c gene by the IS1380 element. 417 matched cddid_all.tbl CDD NF033540 NF033540 468071 transpos_IS701 IS701 family transposase. Members of this family are transposases in the family of that of insertion element IS701, narrowly defined. Note that a molecular phylogenetic tree of the broader sets of transposases from IS elements classified as IS701 family or IS4 family by ISFINDER shows the two groups interleaved. This model represents an unambiguous clade that includes IS701 itself and the majority of proteins called IS701 family. The poorly conserved C-terminal region of members of this family is not included in the seed alignment. 345 matched cddid_all.tbl CDD NF033541 NF033541 468072 transpos_ISH3 ISH3 family transposase. This family contains transposases from the insertion element ISH3, and related transposases from other mobile elements with similar transposases. This model reproduces the classification from ISFinder except for ISC1439B-like transposases, since those are extremely different. 298 matched cddid_all.tbl CDD NF033542 NF033542 468073 transpos_IS110 IS110 family transposase. Proteins of this family are DEDD (Asp, Glu, Asp, Asp) type transposases, which are encoded by the IS110 family elements. 345 matched cddid_all.tbl CDD NF033543 NF033543 468074 transpos_IS256 IS256 family transposase. Members of this family belong to the branch of the IS256-like family of transposases that includes the founding member. It excludes the IS1249 group. 406 matched cddid_all.tbl CDD NF033544 NF033544 468075 transpos_IS1249 IS1249 family transposase. Members of this family belong to the IS1249 group branch of the broader IS256 family of transposases. This group differs sharply from the main branch, which includes founding member IS256 itself, by having an N-terminal region with two pairs of closely spaced Cys residues. 381 matched cddid_all.tbl CDD NF033545 NF033545 468076 transpos_IS630 IS630 family transposase. 298 matched cddid_all.tbl CDD NF033546 NF033546 468077 transpos_IS21 IS21 family transposase. 296 matched cddid_all.tbl CDD NF033547 NF033547 468078 transpos_IS1595 IS1595 family transposase. Most transposases of this family of transposases, IS1595, have an additional short N-terminal domain with a pair of CxxC motifs. 211 matched cddid_all.tbl CDD NF033550 NF033550 468079 transpos_ISL3 ISL3 family transposase. 369 matched cddid_all.tbl CDD NF033551 NF033551 468080 transpos_IS1182 IS1182 family transposase. Members of this family are transposases of the IS1182 family. About two-thirds of the members of this family have an extra domain between the middle and the C-terminal domain, about 50 amino acids in size and containing four invariant Cys residues. 437 matched cddid_all.tbl CDD NF033553 NF033553 468081 MerP_Gpos mercury resistance system substrate-binding protein MerP. Members of this family are MerP, a substrate-binding protein for a system in which toxic Hg(II) is transported into the cytosol, where it can be reduced to the much less toxic form Hg(0). Members of this family are found, so far, in Gram-positive bacteria. A related MerP family, as found in plasmid-borne systems in Gram-negative bacteria, is described by TIGR02052. 112 matched cddid_all.tbl CDD NF033554 NF033554 468082 floc_PepA flocculation-associated PEP-CTERM protein PepA. PepA was described in Zoogloea resiniphila as a PEP-CTERM protein regulated by the PrsK/PrsR two-component system. Knocking out that system blocks flocculation, after which expression of recombinant PepA can restore flocculation. 258 matched cddid_all.tbl CDD NF033556 NF033556 468083 MerTP_fusion mercuric transport protein MerTP. MerTP is a transport protein for the mercuric ion, Hg(II). Once imported to the cytosol, the highly toxic ion can be converted by MerA, mercury(II) reductase, to the less toxic Hg atom. 186 matched cddid_all.tbl CDD NF033557 NF033557 468084 LLB_putidacin putidacin L1 family lectin-like bacteriocin. Putidacin L1 is a well-described member of a family of lectin-like bacteriocins found almost exclusively in Pseudomonas. This subfamily is narrowly defined, and does not include the homolog pyocin L1. 274 matched cddid_all.tbl CDD NF033558 NF033558 468085 transpos_IS1 IS1 family transposase. Proteins of this family are DDE transposases encoded by the IS1 family elements usually through a translational frameshift mechanism. 199 matched cddid_all.tbl CDD NF033559 NF033559 468086 transpos_IS1634 IS1634 family transposase. Members of this protein family are DDE type transposases encoded by the IS1634 family elements, which were firstly identified and characterized in Mycoplasma mycoides. 463 matched cddid_all.tbl CDD NF033561 NF033561 468087 macrolact_Ik_Al albusnodin/ikarugamycin family macrolactam cyclase. Members of this family show homology enzymes known to form the lactam bond of the isopeptide linkage of lasso peptides. This family includes the peptide cyclase involved in biosynthesis of the lasso peptide albusnodin. However, another member of this family belongs to the biosynthesis cassette for ikarugamycin, a macrolactam whose biosynthesis relies on a hybrid PKS/NRPS system, not a ribosomally produced peptide. 561 matched cddid_all.tbl CDD NF033562 NF033562 411192 BH0509_fam BH0509 family protein. This family of unknown function appears restricted to the Firmicutes. Proteomics evidence for expression was provided for the member from Bacillus cereus by Dr. Samuel Payne, Pacific Northwest National Labs. The family is named, for now, after BH0509 from Bacillus halodurans. 43 matched cddid_all.tbl CDD NF033563 NF033563 468088 transpos_IS30 IS30 family transposase. 267 matched cddid_all.tbl CDD NF033564 NF033564 411194 transpos_ISAs1 ISAs1 family transposase. 314 matched cddid_all.tbl CDD NF033566 NF033566 411195 adhes_LIC20035 LIC20035 family adhesin. LIC20035 of Leptospira interrogans was characterized as a surface exposed adhesin that binds host extracellular matrix components. Orthologs appear restricted to the genus Leptospira. Member proteins average about 430 residues in length, much of which consists of repeats. All members are predicted lipoproteins. 428 matched cddid_all.tbl CDD NF033567 NF033567 468089 act_recrut_TARP type III secretion system actin-recruiting effector Tarp. The founding member of the Tarp (translocated actin-recruiting phosphoprotein) is CT456 from Chlamydia trachomatis. Tarp is a type III secretion system effector. Orthologs are found other Chlamydia, but are highly variable in length because many lack much of the repeat region. 761 matched cddid_all.tbl CDD NF033570 NF033570 411197 FIB_Spiroplas cytoskeletal motor fibril protein Fib. Fib, a 59K protein also called fibrillin, is the repeating subunit of the linear fibril that runs through the shortest path along the length of Spiroplasma cells, members of the Mollicutes that lack cells walls but have a spiral shape. The fibril is a linear contractile ribbon, and Fib is its only component. 511 matched cddid_all.tbl CDD NF033571 NF033571 468090 motil_scm1_spiro motility-associated protein Scm1. Scm1 (Spiroplasma citri motility gene 1) was shown by loss-of-function mutation to be involved in motility. The Scm1 family is widespread in the genus Spiroplasma, members of the Mollicutes (bacteria with no cell wall) that have a spiral shape organized around a contractile ribbon fibril made of repeating subunits of the Fib (fibril) protein. 401 matched cddid_all.tbl CDD NF033572 NF033572 468091 transpos_ISKra4 ISKra4 family transposase. 414 matched cddid_all.tbl CDD NF033573 NF033573 468092 transpos_IS200 IS200/IS605 family transposase. Most IS200/IS605 family insertion sequences encode both this transposase, TnpA, about 130 amino acids long, and larger accessory protein, TnpB, that may act as a methyltransferase. 126 matched cddid_all.tbl CDD NF033576 NF033576 468093 mCpol mCpol domain. The mCpol domain (minimal CRISPR polymerase) is named for its homology relationship to catalytic domain of the CRISPR polymerases (often called Cmr2 or Cas10). It is predicted to generate cyclic nucleotides, potentially sensed by CARF domains which in turn activate various effector domain including HEPN RNases, CARF sensor and effectors are found in conserved genome contexts. It is part of a broader class of conflict systems reliant on the production of second messenger nucleotide or nucleotide derivatives. The putative function of the mCpol domain implies that CRISPR polymerases of the type III CRISPR/Cas systems have a nucleotide synthetase functional role. 118 matched cddid_all.tbl CDD NF033577 NF033577 468094 transpos_IS481 IS481 family transposase. null 283 matched cddid_all.tbl CDD NF033578 NF033578 468095 transpos_IS5_1 IS5 family transposase. 415 matched cddid_all.tbl CDD NF033579 NF033579 468096 transpos_IS5_2 IS5 family transposase. 287 matched cddid_all.tbl CDD NF033580 NF033580 468097 transpos_IS5_3 IS5 family transposase. 257 matched cddid_all.tbl CDD NF033581 NF033581 468098 transpos_IS5_4 IS5 family transposase. 284 matched cddid_all.tbl CDD NF033583 NF033583 411207 staphy_B_SbnC staphyloferrin B biosynthesis protein SbnC. SbnC, related to siderophore biosynthesis protein IucA and IucC, is encoded in Staphylococcus aureus in the sbnABCDEFGHI locus responsible for the biosynthesis of staphyloferrin B, a carboxylate-type siderophore. SbnC is found in many species of Staphylococcus. 584 matched cddid_all.tbl CDD NF033586 NF033586 411208 staphy_B_SbnF staphyloferrin B biosynthesis protein SbnF. 577 matched cddid_all.tbl CDD NF033587 NF033587 411209 transpos_IS6 IS6 family transposase. 203 matched cddid_all.tbl CDD NF033588 NF033588 411210 transpos_ISC774 IS6 family transposase. ISC774 is an example of an outlier clade of IS6 family insertion sequences. Members so are appear restricted to the archaeal genus Sulfolobus. 195 matched cddid_all.tbl CDD NF033589 NF033589 411211 staphy_B_SbnI bifunctional transcriptional regulator/O-phospho-L-serine synthase SbnI. SbnI is a bifunctional protein involved in staphyloferrin B (staphylobactin) biosynthesis in Staphylococcus aureus and other members of the genus. It is a bifunctional protein. The N-terminal region is heme-binding, and loses the ability to bind DNA when heme is bound. Under low iron conditions, the biosynthesis operon for staphyloferrin B, a carboxylate-type siderophore, is derepressed. The C-terminal domain is a kinase that acts on free serine, producing O-phospho-L-serine, which is used as one of the precursors of staphyloferrin B. 254 matched cddid_all.tbl CDD NF033590 NF033590 468099 transpos_IS4_3 IS4 family transposase. 403 matched cddid_all.tbl CDD NF033591 NF033591 468100 transpos_IS4_2 IS4 family transposase. 340 matched cddid_all.tbl CDD NF033592 NF033592 468101 transpos_IS4_1 IS4 family transposase. 332 matched cddid_all.tbl CDD NF033593 NF033593 468102 transpos_ISNCY_1 ISNCY family transposase. The ISNCY insertion sequence family, as defined by ISFinder, encodes several apparently unrelated families of transposases. Members of this family resemble the transposases of ISNCY family elements such as ISRm17 from Sinorhizobium meliloti, ISMav9 from Mycobacterium avium, and ISNfl1 from Nostoc commune. 444 matched cddid_all.tbl CDD NF033594 NF033594 468103 transpos_ISNCY_2 ISNCY family transposase. The ISNCY insertion sequence family, as defined by ISFinder, encodes several apparently unrelated families of transposases. Members of this family resemble the transposases of ISNCY family elements such as IS1202, ISTde1, ISKpn21, and ISCARN1. 367 matched cddid_all.tbl CDD NF033595 NF033595 468104 denti_PrtP dentilisin complex serine proteinase subunit PrtP. PrtP, a chymotrypsin-like protease known as dentilisin, forms a complex with PrcB and PrcA. It is found in Treponema denticola and in numerous other Treponema species. Dentilisin from T. denticola plays a significant role in pathogen-host interactions in periodontal disease. 608 matched cddid_all.tbl CDD NF033596 NF033596 468105 denti_PrcB dentilisin complex subunit PrcB. 174 matched cddid_all.tbl CDD NF033597 NF033597 468106 denti_PrcA dentilisin complex subunit PrcA. PrcA is a lipoprotein that, together with PrcB and the serine proteinase subunit PrtP, form a chymotrypsin-like surface complex that is also known as dentilisin, after its discovery and characterization in Treponema denticola. Dentilisin is an important virulence factor in periodontal disease. 611 matched cddid_all.tbl CDD NF033598 NF033598 468107 elast_bind_EbpS elastin-binding protein EbpS. The elastin-binding protein EbpS is an adhesin described in Staphylococcus aureus, with orthologs found in many additional staphylococcal species. EbpS is a membrane protein that lacks an N-terminal signal peptide region, has extensive regions low-complexity sequence rich in Asn and Gln, and has a C-terminal LysM domain. 466 matched cddid_all.tbl CDD NF033599 NF033599 411221 His_racem_CntK histidine racemase CntK. CntK (cobalt and nickel transport system protein K) is a histidine racemase that performs the first step in the biosynthesis of staphylopine, a metallophore involved in the import of multiple divalent cations. It was first characterized in Staphylococcus aureus. 271 matched cddid_all.tbl CDD NF033600 NF033600 411222 staphylopine_DH staphylopine biosynthesis dehydrogenase. 424 matched cddid_all.tbl CDD NF033601 NF033601 411223 Sta_opine_CntL staphylopine biosynthesis enzyme CntL. CntL (cobalt and nickel transporter L) is an enzyme involved in biosynthesis of staphylopine, a metallophore involved in the import of zinc, cobalt, nickel, and other divalent cations. CntL transfers aminobutyrate from S-adenoyslmethionine, and is sometimes misannotated as a SAM-dependent methyltransferase. The staphylopine biosynthesis pathway was first characterized in Staphylococcus aureus. 255 matched cddid_all.tbl CDD NF033602 NF033602 411224 campy_sm_acidic highly acidic protein. This highly acidic protein, usually between 50 and 55 amino acids long, is found so far in Campylobacter jejuni and Campylobacter coli. A reanalysis of proteomics data, performed by Dr. Samuel Payne of Pacific Northwest National Labs, shows strong evidence for expression of AIW09513.1, founding member of the family. 50 matched cddid_all.tbl CDD NF033603 NF033603 468108 mini-MOMP_1 mini-MOMP protein. Mini-MOMP proteins, found in several species of Campylobacter, are small proteins (about 63 amino acids long before removal of the signal peptide) with strong homology to the N-terminal region of MOMP, the major outer membrane protein that is Campylobacter's major porin. 63 matched cddid_all.tbl CDD NF033604 NF033604 411226 epsi_CJH_07325 CJH_07325 family protein. Members of the CJH_07325 family are small proteins, shorter than 70 amino acids, expressed in members of the genera Campylobacter and Helicobacter. The function is unknown. 56 matched cddid_all.tbl CDD NF033605 NF033605 468109 Zn_bnd_ABC_AdcA zinc ABC transporter substrate-binding lipoprotein AdcA. 516 matched cddid_all.tbl CDD NF033607 NF033607 411229 disagg_AAA_ClpG AAA family protein disaggregase ClpG. ClpG, as characterized in Pseudomonas aeruginosa, is a Clp family member of the AAA+ family of ATPases. ClpG has stand-alone ability to disaggregate proteins from aggregates that result from heat stess. Both ClpG and its mobilized homolog ClpK provide increased survival of exposure to heat. 932 matched cddid_all.tbl CDD NF033608 NF033608 411230 type_I_tox_Fst type I toxin-antitoxin system Fst family toxin. 28 matched cddid_all.tbl CDD NF033609 NF033609 468110 MSCRAMM_ClfA MSCRAMM family adhesin clumping factor ClfA. Clumping factor A is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). It is heavily studied in Staphylococcus aureus both for its biological role in adhesion and for its potential for vaccination. Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif. 934 matched cddid_all.tbl CDD NF033610 NF033610 468111 SLATT_3 SLATT domain. The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family is always N-terminally fused to the SLATT_1 family, and is typically operonically linked to either inactive TIR domains or SLOG domains which could act as regulators of the SLATT channels. The SLATT domain defined here (170 residues long) is similar to the DUF4231 domain (105 residues long) described in Pfam model PF14015. 164 matched cddid_all.tbl CDD NF033611 NF033611 468112 SAVED SAVED domain. The SAVED (SMODS-Associated and fused to Various Effector Domains) domain is predicted to function as a sensor domain, sensing nucleotides or nucleotide derivatives generated by SMODS and other nucleotide synthetase domains. The sensing of ligands by SAVED is predicted to activate effectors deployed by a class of conflict systems which are reliant on the on the production and sensing of the nucleotide second messengers. 261 matched cddid_all.tbl CDD NF033615 NF033615 411234 CDF_MamM magnetosome biogenesis CDF transporter MamM. 290 matched cddid_all.tbl CDD NF033616 NF033616 411235 CDF_MamB magnetosome biogenesis CDF transporter MamB. 284 matched cddid_all.tbl CDD NF033617 NF033617 411236 RND_permease_2 multidrug efflux RND transporter permease subunit. 1009 matched cddid_all.tbl CDD NF033618 NF033618 411237 mlaB_1 lipid asymmetry maintenance protein MlaB. MlaB belongs to a system that maintains asymmetry in the outer membrane of Gram-negative bacteria, with LPS in the outer leaflet and phospholipids in the inner leaflet. Several components of the system share homology with typical ABC transporters. 94 matched cddid_all.tbl CDD NF033619 NF033619 411238 perm_MlaE_1 lipid asymmetry maintenance ABC transporter permease subunit MlaE. 253 matched cddid_all.tbl CDD NF033620 NF033620 468113 pqiC membrane integrity-associated transporter subunit PqiC. PqiC (YmbA), a lipoprotein, has been identified as part of the PqiABC system, a transporter that bridges the inner and outer membranes in species such as Escherichia coli and is important to membrane integrity. 185 matched cddid_all.tbl CDD NF033621 NF033621 468114 de_GSH_amidase deaminated glutathione amidase. 260 matched cddid_all.tbl CDD NF033622 NF033622 411241 repair_DdrC DNA damage response protein DdrC. DdrC is a DNA-binding protein that seems restricted to the genus Deinococcus, and that plays a role in the ability of members of that genus to recover from fragmentation of their DNA. Note that the region where DdrC is found in Deinococcus radiodurans R1 originally had incorrect structural annotation, with a feature designated DR_0003 shown on the opposite strand. 223 matched cddid_all.tbl CDD NF033623 NF033623 468115 urate_HpxO FAD-dependent urate hydroxylase HpxO. HpxO is an FAD-dependent urate hydroxylase (EC 1.14.13.113). Like the factor independent urate hydroxylase (EC 1.7.3.3), it consumes O2 and converts urate to 5-hydroxyisourate, which decomposes spontaneously to allantoin and CO2. However, HpxO oxidizes NADH to NAD(+), and produces H20, while EC 1.7.3.3 produces H202 as a byproduct. 382 matched cddid_all.tbl CDD NF033624 NF033624 411243 HpxX oxalurate catabolism protein HpxX. HpxX is a small protein of unknown function, about 60 residues in length, encoded in the set of four genes, hpxWXYZ, that belong to the oxalurate metabolism portion of a complete pathway for hypoxanthine (hpx) utilization, as in Klebsiella pneumoniae. 55 matched cddid_all.tbl CDD NF033625 NF033625 411244 HpxZ oxalurate catabolism protein HpxZ. HpxZ is not characterized, but it is encoded in the cluster hpxWXYZ, associated with oxalurate catabolism, within the larger hpx (hypoxanthine utilization) locus of species such as Klebsiella pneumoniae, where KPN_01771 is HpxZ. 122 matched cddid_all.tbl CDD NF033628 NF033628 411245 snapalysin snapalysin. Snapalysin (SnpA, or Small Neutral Protease A) belongs to the metzincin family of zinc-dependent metalloendopeptidases. 207 matched cddid_all.tbl CDD NF033629 NF033629 411246 RiPP_CPAC RiPP peptide. null 52 matched cddid_all.tbl CDD NF033630 NF033630 468116 SLATT_6 SLATT domain. The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family associates with a SMODS nucleotide synthetase domain fused to the predicted AGS-C sensor domain. It is sometimes further coupled to R-M systems. 179 matched cddid_all.tbl CDD NF033631 NF033631 468117 SLATT_5 SLATT domain. The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family contains an additional C-terminal alpha-helix, and strictly associates with a reverse transcriptase domain, part of a predicted retroelement with diversity-generating potential. 182 matched cddid_all.tbl CDD NF033632 NF033632 468118 SLATT_4 SLATT domain. The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family is often coupled to the SMODS nucleotide synthetase and is sometimes further embedded in other conflict systems like CRISPR/Cas or R-M systems. 154 matched cddid_all.tbl CDD NF033633 NF033633 468119 SLATT_2 SLATT domain. The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family is the only prokaryotic SLATT family to exist as a standalone domain, with no as-yet discernable genome associations. 181 matched cddid_all.tbl CDD NF033634 NF033634 468120 SLATT_1 SLATT domain. The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family is often C-terminally fused to the SLATT_3 family, and is typically operonically linked to either inactive TIR domains or SLOG domains which could act as regulators of the SLATT channels. In relatively rare instances, it is genomically linked as a standalone domain to the RelA/SpoT nucleotide synthetase and the predicted NA37/YejK sensor domain. 135 matched cddid_all.tbl CDD NF033635 NF033635 468121 SLATT_fungal SLATT domain. The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function in bacteria as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. The role of this fungal family is not yet understood, although the expansion of the family in many fungal lineages points to a potential role in conflict. 125 matched cddid_all.tbl CDD NF033638 NF033638 468122 RNase_AS polyadenylate-specific 3'-exoribonuclease AS. RNase AS is a 3'-exoribonuclease, found in Mycobacterium tuberculosis and other Actinobacteria, that acts specifically to degrade polyadenylate sequences from the 3'-end of RNA. 155 matched cddid_all.tbl CDD NF033640 NF033640 468123 N_Twi_rSAM twitch domain-containing radical SAM protein. Members of this family are unusual among radical SAM proteins in several ways. First, the N-terminal region consists of an iron-sulfur cluster-binding twitch domain (half of a SPASM domain), something usually found C-terminal to the radical SAM domain. Second, the radical SAM domains in many of the members of this family score poorly vs. the Pfam HMM, PF04055 (version 19), used to identify radical SAM. Lastly, the majority of members sequenced to date come from uncultured bacteria from marine or aquifer sources rather than from conventionally cultured bacterial isolates. The function is unknown. 396 matched cddid_all.tbl CDD NF033641 NF033641 468124 antiterm_LoaP antiterminator LoaP. LoaP is a paralog of NusG with an extensive presence in Firmicutes. The founding member, from Bacillus amyloliquefaciens, was shown to serve as an antiterminator for the transcription of genes involved in antibiotic biosynthesis. 166 matched cddid_all.tbl CDD NF033642 NF033642 411256 stress_AzuC stress response protein AzuC. AzuC is a basic, extremely small protein (28 amino acids in Escherichia coli K-12) whose expression is repressed by cyclic AMP response protein (CRP) and stimulated by acidic pH. 26 matched cddid_all.tbl CDD NF033643 NF033643 439409 EspJ_gen EspJ family T3SS effector ADP-ribosyltransferase. 216 matched cddid_all.tbl CDD NF033644 NF033644 468125 antiterm_UpxY UpxY family transcription antiterminator. The UpxY family of NusG-related transcription antiterminators was described originally from a paralogous family of eight members from Bacteriodes fragilis, UpaY to UphY, each of which was associated with a distinct capsular polysaccharide biosynthesis locus. There is no UpxY protein per se. 162 matched cddid_all.tbl CDD NF033645 NF033645 468126 pilus_FilE putative pilus assembly protein FilE. FilE is found almost exclusively in the genus Acinetobacter, and is assigned as a putative pilus system protein from local genomic contexts that include several additional putative pilus system proteins. Note that some members of this protein family have proline-rich repeat regions for which spurious translation in another reading frame can give a false-positive match to Pfam's collagen repeat region HMM, PF01391. 411 matched cddid_all.tbl CDD NF033647 NF033647 468127 adhesin_LEA LEA family epithelial adhesin N-terminal domain. LEA (Lactobacillus epithelium adhesin), as characterized in an adhesive commensal strain of Lactobacillus crispatus (ST1), is a large, repetitive protein with an N-terminal YSIRK-type signal peptide and a C-terminal LPXTG site for processing by sortase and attachment to the cell surface. Family members contain variable numbers of an 82 amino acid long repeats similar to Lactobacillus Rib/alpha-like repeats. This HMM describes the N-terminal region upstream of the repeat region, just over 600 amino acids long. 655 matched cddid_all.tbl CDD NF033649 NF033649 468128 LipDrop_Rv1109c lipid droplet-associated protein. RHA1_ro05869 from Rhodococcus jostii RHA1, an ortholog of Rv1109c from Mycobacterium tuberculosis, has been shown specifically with lipid droplets that consist of a neutral lipid core enveloped by a phospholipid monolayer and surface proteins. Lipid droplets of triacylglycerol can be especially prominent in members of the genus Rhodococcus, but occur also in Mycobacterium tuberculosis and can support dormancy of that pathogen. 199 matched cddid_all.tbl CDD NF033650 NF033650 411261 ANR_neg_reg ANR family transcriptional regulator. ANR family transcriptional regulators include the AggR-activated regulator Aar. The name ANR (AraC Negative Regulators) refers to an effect on, rather than homology to, certain AraC family transcriptional regulators. 54 matched cddid_all.tbl CDD NF033651 NF033651 468129 cyto_nec_fctrs CNF1 family cytotoxic necrotizing factor. CNF1 family of cytotoxic necrotizing factors, glutamine amidases that find their way to their eukaryotic host cells' cytosol and permanently activate certain GTPases, includes full-length homologs of CNF1, CNF2, CNF3, and CNFY, but it excludes smaller proteins such as the type 3 secretion system effector VopC. 1013 matched cddid_all.tbl CDD NF033652 NF033652 468130 LbtU_sider_porin LbtU family siderophore porin. LbtU, from Legionella pneumophila, a novel TonB-independent siderophore uptake outer membrane protein from a species that lacks TonB, is the founding member of a class of porins that may be involved generally in siderophore-mediated iron acquisition. 322 matched cddid_all.tbl CDD NF033656 NF033656 468131 DMQ_monoox_COQ7 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinone monooxygenase. 205 matched cddid_all.tbl CDD NF033657 NF033657 468132 choice_anch_F choice-of-anchor F family protein. Choice-of-anchor F is a domain found in prokaryotic proteins with a variety of C-terminal sorting and transit domains. These include the autotransporter outer membrane beta-barrel domain, the JDVT-CTERM domain, and variant forms of PEP-CTERM domains. 296 matched cddid_all.tbl CDD NF033662 NF033662 411265 acid_disulf_rpt acidic double-disulfide repeat. The acidic double-disulfide repeat is an Asp-rich repeat with four nearly invariant Cys residues in a repeat length of about 35 amino acids. 32 matched cddid_all.tbl CDD NF033663 NF033663 411266 AceI_fam_PACE AceI family chlorhexidine efflux PACE transporter. The AceI family of proton-coupled multidrug/biocide efflux transporters includes several shown to respond to the presence of the biocide chlorhexidine and improve resistance to it, among other biocides and antibiotics. Members of the family seen so far, including founding member AceI, have been chromosomal and restricted to the genus Acinetobacter. 136 matched cddid_all.tbl CDD NF033664 NF033664 411267 PACE_transport PACE efflux transporter. PACE transporters, including the chlorhexidine efflux transporter AceI, average about 140 amino acids in length and consist of two tandem homologous domains described by Pfam model PF05232. PACE transporters are single component efflux transporters that sit in the plasma membrane and couple proton import to substrate export. 130 matched cddid_all.tbl CDD NF033665 NF033665 411268 PACE_efflu_PCE multidrug/biocide efflux PACE transporter. PACE (proteobacterial antimicrobial compound efflux) transporters are single component proton-coupled efflux pumps that help confer resistance to a number of biocides and antibiotics. The family has also been named PCE (proteobacterial chlorhexidine efflux). Members of this subfamily of the PACE transporters, distinct from the AceI-like branch, include several whose expression is increased by exposure to chlorhexidine and/or help confer increased resistance to it. 130 matched cddid_all.tbl CDD NF033668 NF033668 468133 rSAM_PA0069 PA0069 family radical SAM protein. PA0069 from Pseudomonas aeruginosa is the founding member a family of radical SAM enzymes of unknown function. Note that inclusion of some members of this family in COG1533, along with some spore photoproduct lyase (SPL) proteins, has led to some family members being annotated as SPL. 348 matched cddid_all.tbl CDD NF033672 NF033672 411270 mbn_chaper_assoc copper uptake system-associated domain. Proteins from this family that may contain just an N-terminal signal peptide followed by this domain, or have a copper chaperone domain in addition, just past the signal peptide. A majority of bacteria that encode a peptide-derived methanobactin precursor encode a member of this family as well, strongly suggesting a role for this domain in copper acquisition. 104 matched cddid_all.tbl CDD NF033674 NF033674 468134 stress_OB_fold NirD/YgiW/YdeI family stress tolerance protein. Members of this family possess an N-terminal signal peptide, and are associated with tolerance to various toxic stresses. These include antimicrobial peptides (YdeI), hydrogen peroxide (YgiW and YdeI), and nickel (NcrY and NirD). 110 matched cddid_all.tbl CDD NF033675 NF033675 468135 NTTRR-F1 NTTRR-F1 domain. NTTRR-F1 (N-terminal To Repetitive Region - Firmicutes 1) is a homology domain found strictly as the N-terminal non-repetitive region of otherwise highly repetitive proteins of various Firmicutes. The repetitive region that follows typically is collagen-like, with every third residue a glycine. 155 matched cddid_all.tbl CDD NF033676 NF033676 411273 Lacb_SerRich_Nt serine-rich glycoprotein adhesin prefix domain. Lacb_SerRich_Nt describes a Lactobacillus-restricted N-terminal non-repetitive sequence region shared by proteins with extensive serine-rich repeat regions, all likely to function as adhesins. This region contains a variant form of the KxYKxGKxW motif (see TIGR03715) followed by a region related to serine-rich glycoprotein adhesins of the Streptococci. 80 matched cddid_all.tbl CDD NF033677 NF033677 411274 biofilm_BapA_N BapA prefix-like domain. Two largely unrelated repetitive proteins, both named biofilm-associated protein BapA (from Salmonella enterica and from Paracoccus denitrificans) share homology domains at the two ends. Both lack a typical signal peptide for translocation by Sec, and instead depend on type I secretion for export and for contribution to biofilm formation. The conserved prefix (i.e. N-terminal) domain is shared by a number of other large, repetitive proteins of Proteobacteria thought to be associated with adhesion or biofilm formation. 64 matched cddid_all.tbl CDD NF033678 NF033678 468136 C69_fam_dipept C69 family dipeptidase. Members of the MEROPS C69 family (subfamily 001) are dipeptidases (EC 3.4.13.-). 463 matched cddid_all.tbl CDD NF033679 NF033679 468137 DNRLRE_dom DNRLRE domain. The DNRLRE domain, with a length of about 160 amino acids, appears typically in large, repetitive surface proteins of bacteria and archaea, sometimes repeated several times. It occurs, notably, three times in the C-terminal region of the enzyme disaggregatase from the archaeal species Methanosarcina mazei, each time with the motif DNRLRE, for which the domain is named. Archaeal proteins within this family are described particularly well by the currently more narrowly defined Pfam model, PF06848. Note that the catalytic region of disaggregatase, in the N-terminal portion of the protein, is modeled by a different HMM, PF08480. 164 matched cddid_all.tbl CDD NF033680 NF033680 468138 exonuc_ExeM-GG extracellular exonuclease ExeM. ExeM, as described in Shewanella oneidensis, is a biofilm formation-associated exonuclease that cleaves extracellular DNA (eDNA), a biofilm component. Members of the ExeM family contain two or three pairs of Cys residues, presumed to form disulfide bonds, and a C-terminal GlyGly-CTERM membrane-anchoring segment. Strangely, engineered removal of the GlyGly-CTERM region did not result in net export from the cell and appearance of the enzyme in culture supernatants. 883 matched cddid_all.tbl CDD NF033681 NF033681 468139 ExeM_NucH_DNase ExeM/NucH family extracellular endonuclease. 545 matched cddid_all.tbl CDD NF033682 NF033682 468140 retention_LapA retention module-containing protein. The retention module, as described for the giant adhesin LapA of Pseudomonas fluorescens and for an ice-binding giant adhesin of an Antarctic bacterium, appears at the N-terminus of a number of very large repetitive proteins, many of which have C-terminal regions that make them substrates for type I secretion systems. 145 matched cddid_all.tbl CDD NF033683 NF033683 468141 di_4Fe-4S_YfhL YfhL family 4Fe-4S dicluster ferredoxin. 79 matched cddid_all.tbl CDD NF033684 NF033684 411281 suffix_2_RND transporter suffix domain. Members of this protein family contain a highly hydrophobic region about 70 amino acids long that usually occurs as essentially the full length of a small membrane protein, but in some cases occurs as a C-terminal suffix domain for RND efflux transporter permease subunit proteins. 69 matched cddid_all.tbl CDD NF033685 NF033685 411282 Tet_leader_L tetracycline resistance efflux system leader peptide. Stalling of the ribosomal translation of a tetracycline resistance system mRNA from inability to properly translate a short leader peptide can affect mRNA secondary structure, preventing early transcriptional termination and therefore inducing expression of the resistance protein. This leader peptide is found upstream of efflux transporters such as tet(L) and tet(45) (which occur in Gram-positive organisms), but on occasion may occur as a fused additional N-terminal domain of such efflux proteins. 20 matched cddid_all.tbl CDD NF033686 NF033686 411283 leader_PheM_1 pheST operon leader peptide PheM. 14 matched cddid_all.tbl CDD NF033688 NF033688 411284 MG406_fam MG406 family protein. Homologs to MG406 from Mycoplasma genitalium and MPN605 from Mycoplasma pneumoniae are about 150 amino acids long on average, highly hydrophobic, widespread in but restricted to the Mollicutes, and highly divergent there. MG406 itself appears to be an essential gene. 117 matched cddid_all.tbl CDD NF033689 NF033689 411285 N2Fix_CO_CowN N(2)-fixation sustaining protein CowN. Carbon monoxide inhibits the ability of Mo-nitrogenase to fix nitrogen, but expression of CowN is protective, and allows nitrogen fixation to continue. 89 matched cddid_all.tbl CDD NF033690 NF033690 411286 ErmCL_fam_lead ErmCL family antibiotic resistance leader peptide. 19 matched cddid_all.tbl CDD NF033691 NF033691 411287 immunity_MafI MafI family immunity protein. MafI proteins, as described in Neisseria species, are small proteins encoded in modules with MafB (multiple adhesin family B) secreted toxins. Homologs are found broadly, primarily in Proteobacterial genera such as Neisseria, Cronobacter, Enterobacter, Pseudomonas, etc. 67 matched cddid_all.tbl CDD NF033694 NF033694 468142 perox_inhi_SPIN SPIN family peroxidase inhibitor. SPIN (staphylococcal peroxidase inhibitor) binds to and inhibits human myeloperoxidase to resist killing after phagocytosis by neutrophils. 99 matched cddid_all.tbl CDD NF033695 NF033695 439412 trnsprt_adja_30 KPN_01571 family protein. Members of this family are very small, highly hydrophobic proteins regularly encoded adjacent to transporters and likely to be previously overlooked small subunits of transporters. 30 matched cddid_all.tbl CDD NF033696 NF033696 411289 CrpP_fam CrpP family protein. CrpP, described originally as a protein encoded by Pseudomonas aeruginosa plasmid pUM505, confers elevated resistance to ciprofloxacin, but not to four other fluoroquinoline-type antibiotics tested. The apparent mechanism is phosphorylation. However, CrpP appears more closely related to the ribosome modulation factor Rmf than to any known aminoglycoside phosphotransferase. 58 matched cddid_all.tbl CDD NF033697 NF033697 439413 leader_RseD rpoE leader peptide RseD. RseD, as described originally in Escherichia coli, is a leader peptide translationally coupled to the extracytoplasmic stress response sigma factor RpoE. It participates in the CrsA-mediated fine-tuning of the stress response. It is found also in Salmonella enterica, Cedecea neteri, etc. The corresponding locus in Klebsiella pneumoniae appears to be split into an upstream and a downstream peptide. 31 matched cddid_all.tbl CDD NF033701 NF033701 411291 yciY_fam YciY family protein. Members of the YciY family are named after the gene symbol given in E. coli K-12, but members of the family are found also in Salmonella, Klebsiella, Yersinia, Erwinia, etc. 56 matched cddid_all.tbl CDD NF033703 NF033703 468143 transcr_KstR cholesterol catabolism transcriptional regulator KstR. KstR, a protein characterized in Mycobacterium tuberculosis (MTB) and M. smegmatis is a TetR family transcriptional regulator that is essential for pathogenesis in MTB. In controls the expression of about 80 proteins involved in the earlier stages of cholesterol catabolism. KstR binds not to cholesterol itself, but to catabolites found early in the degradation pathway. 185 matched cddid_all.tbl CDD NF033704 NF033704 468144 helico_Hpn_like nickel-binding protein HpnL. The Hpn-like protein HpnL, or Hpn-2, including founding member HP1432, is a histidine and glutamine-rich metal-binding polypeptide that binds nickel, among other metals, any may help deliver sequestered nickel for the biosynthesis of urease, which is critical to the survival of Helicobacter pylori during exposures to strongly acidic conditions. This protein is a paralog to the histidine-rich nickel storage protein Hpn (e.g. HP1427). Both nickel-binding proteins are expressed in response to nickel, under control of the regulator NikR. 71 matched cddid_all.tbl CDD NF033705 NF033705 411294 helico_Hpn nickel storage protein Hpn. Hpn (Helicobacter pylori nickel) is a histidine-rich polypeptide, 60 amino acids in length, capable of binding nickel and several other metals. It can store a reserve of nickel for biosynthesis of active urease, critical to the ability of the bacterium to survive acid exposure during colonization, and hydrogenase. Hpn is closely related in its N-terminal region to a somewhat longer His and Gln-rich protein, called the Hpn-like protein. Both are expressed, under control of NikR, in response to nickel. 60 matched cddid_all.tbl CDD NF033706 NF033706 411295 Ni_bind_SCO4226 SCO4226 family nickel-binding protein. Members of the SCO4226 family belong to the larger family of DUF4242 domain-containing proteins, described by Pfam model PF14026. SCO4226 itself was shown to dimerize and bind four nickel atoms per homodimer. 82 matched cddid_all.tbl CDD NF033707 NF033707 468145 T9SS_sortase type IX secretion system sortase PorU. PorU, part of type IX secretion systems (T9SS), is the protease responsible for both removing the C-terminal sorting signal found in substrates and for its replacement by anionic LPS, through which most T9SS substrates become attached to the cell surface after secretion. 1056 matched cddid_all.tbl CDD NF033708 NF033708 468146 T9SS_Cterm_ChiA T9SS sorting signal type C. The sorting signals of type IX secretion systems (T9SS) in the CFB bacteria are long, compared to other prokaryotic C-terminal sorting motif-containing signals, including LPXTG, PEP-CTERM, and GlyGly-TERM, and they seem to contain multiple motifs. A few T9SS substrates, including ChiA, have a variant form of T9SS sorting signal that may score poorly to both TIGR04183 (type A) and TIGR04131 (type B), depend on T9SS for secretion, but are released from the cell rather than left anchored to the cell surface. 55 matched cddid_all.tbl CDD NF033709 NF033709 468147 PorV_fam PorV/PorQ family protein. Proteins closely related to PorV, and its paralog PorQ, are found regularly in species with type IX secretion systems (T9SS), the system associated with a type of gliding motility in many of the Bacteroidetes. 327 matched cddid_all.tbl CDD NF033710 NF033710 468148 T9SS_OM_PorV type IX secretion system outer membrane channel protein PorV. PorV, as characterized in oral pathogen Porphyromonas gingivalis, is a component of the type IX secretion system (T9SS) needed to process a subset of T9SS substrates. PorV is a paralog of PorQ. 368 matched cddid_all.tbl CDD NF033711 NF033711 468149 T9SS_PorQ type IX secretion system protein PorQ. 330 matched cddid_all.tbl CDD NF033712 NF033712 468150 B12_rSAM_KedN5 KedN5 family methylcobalamin-dependent radical SAM C-methyltransferase. KedN5, the founding member of a family of radical SAM enzymes with an N-terminal B12-binding domain, is a C-methyltransferase that relies on a methylcobalamin cofactor during natural product biosynthesis. 624 matched cddid_all.tbl CDD NF033713 NF033713 411302 DbpA DbpA. 166 matched cddid_all.tbl CDD NF033715 NF033715 468151 glycyl_HPDL_Lrg 4-hydroxyphenylacetate decarboxylase large subunit. 4-hydroxyphenylacetate decarboxylase, an enzyme with a glycyl radical active site, depends on a radical SAM enzyme for activation, and is found in strict anaerobes such as Clostridium difficile. It has a large and a small subunit. 901 matched cddid_all.tbl CDD NF033716 NF033716 411304 glycyl_HPDL_Sma 4-hydroxyphenylacetate decarboxylase small subunit. 4-hydroxyphenylacetate decarboxylase, an enzyme with a glycyl radical active site, depends on a radical SAM enzyme for activation, and is found in strict anaerobes such as Clostridium difficile. It has a large and a small subunit. 79 matched cddid_all.tbl CDD NF033717 NF033717 468152 HPDL_rSAM_activ 4-hydroxyphenylacetate decarboxylase activase. 4-hydroxyphenylacetate decarboxylase activase is a radical SAM enzyme, found in anaerobic bacteria where 4-hydroxyphenylacetate decarboxylase occurs and required to prepare the glycyl radical active site of the enzyme. 311 matched cddid_all.tbl CDD NF033718 NF033718 468153 indole_decarb indoleacetate decarboxylase. Indoleacetate decarboxylase is a single subunit glycyl radical enzyme that depends on a cognate radical SAM enzyme for its activation. It performs the final step in the anaerobic fermentation of tryptophan to skatole, a malodorous volatile compound. 868 matched cddid_all.tbl CDD NF033719 NF033719 411307 ind_deCO2_activ indoleacetate decarboxylase activase. 302 matched cddid_all.tbl CDD NF033720 NF033720 411308 DbpB decorin-binding protein DbpB. 182 matched cddid_all.tbl CDD NF033721 NF033721 468154 P12_lipo P12 family lipoprotein. 287 matched cddid_all.tbl CDD NF033723 NF033723 411310 S2_P23 S2/P23 family protein. 179 matched cddid_all.tbl CDD NF033724 NF033724 411311 P13_porin P13 family porin. 178 matched cddid_all.tbl CDD NF033725 NF033725 411312 borfam_49 chromosome replication/partitioning protein. 150 matched cddid_all.tbl CDD NF033726 NF033726 411313 borfam52 P52 family lipoprotein. 171 matched cddid_all.tbl CDD NF033728 NF033728 468155 borfam54_1 complement regulator-acquiring protein. 319 matched cddid_all.tbl CDD NF033729 NF033729 411315 borfam54_2 complement regulator-acquiring protein. 219 matched cddid_all.tbl CDD NF033730 NF033730 411316 borfam54_3 complement regulator-acquiring protein. 292 matched cddid_all.tbl CDD NF033731 NF033731 411317 borfam63 fibronectin-binding protein RevA. 160 matched cddid_all.tbl CDD NF033732 NF033732 411318 borfam95 exported protein A EppA. 176 matched cddid_all.tbl CDD NF033733 NF033733 468156 MFS_ArsK arsenite efflux MFS transporter ArsK. ArsK, a major facilitator superfamily (MFS) transporter, was shown in Agrobacterium tumefaciens to be induced by arsenite and antimonite, to reduce their accumulation, and to confer resistance when expressed heterologously. 388 matched cddid_all.tbl CDD NF033734 NF033734 468157 MFS_ArsJ organoarsenical effux MFS transporter ArsJ. ArkJ regularly is encoded next to a glyceraldehyde-3-phosphate dehydrogenase that can synthesize 1-arseno-3-phosphoglycerate in the presence of arsenate, and appears to provide arsenate resistance by exporting that organoarsenical compound before it spontaneously dissociates into arsenate and 3-phosphoglycerate. 392 matched cddid_all.tbl CDD NF033735 NF033735 468158 G3PDH_Arsen ArsJ-associated glyceraldehyde-3-phosphate dehydrogenase. 324 matched cddid_all.tbl CDD NF033737 NF033737 411322 Amm_Lyn_leader ammosamide/lymphostin biosynthesis leader domain. Precursors of the ammosamide (Amm6) and lymphostin family of natural products share both a strongly conserved leader peptide region that interacts with natural product biosynthesis enzymes, and a critical Trp residue at or near the C-terminus that is incorporated into the small molecule natural product eventually produced - a pyrroloquinoline alkaloid whose core is derived from tryptophan. An additional, shorter homolog, Xan, encoded in a less well understood natural production biosynthesis locus, lacks the critical Trp. It is thought to be a trans-acting leader peptide that does not need to be linked covalently to a core peptide, if that is the substrate of the natural product biosynthesis enzymes, in order to enable them to perform their modifications. 27 matched cddid_all.tbl CDD NF033738 NF033738 468159 microvirid_RiPP microviridin/marinostatin family tricyclic proteinase inhibitor. Members of the microviridin/marinostatin are ribosomally translated peptides whose post-translational processing converts them into tricyclic depsipeptides that serve as serine proteinase inhibitors. A single precursor usually has one core peptide region near the C-terminus, with a nearly invariant TxKYPSD motif, but may instead have two or three repeats of the core region. 47 matched cddid_all.tbl CDD NF033739 NF033739 468160 intramemb_PrsW glutamic-type intramembrane protease PrsW. PrsW, an intramembrane protease, cleaves the anti-sigma factor RsiW, which regulates the activity of the ECF-type sigma factor SigW. 209 matched cddid_all.tbl CDD NF033740 NF033740 468161 MarP_fam_protase MarP family serine protease. The founding member of this family of membrane-spanning serine proteases, which is restricted to Actinobacteria, is the acid resistance periplasmic serine protease MarP of Mycobacterium tuberculosis. Recent work shows that MarP is required to cleave and activate the peptidoglycan hydrolase RipA, and loss of RipA activity creates a defect in progeny separation during cell division. Therefore, the requirement for MarP in order to survive acidic conditions may be a consequence of peptidoglycan hydrolysis requirements, explaining why MarP family members are distributed more broadly in the Actinobacteria than the subset of species capable of surviving intracellularly as pathogens. 390 matched cddid_all.tbl CDD NF033741 NF033741 468162 NlpC_p60_RipA NlpC/P60 family peptidoglycan endopeptidase RipA. 457 matched cddid_all.tbl CDD NF033742 NF033742 468163 NlpC_p60_RipB NlpC/P60 family peptidoglycan endopeptidase RipB. 206 matched cddid_all.tbl CDD NF033743 NF033743 468164 NlpC_inact_RipD NlpC/P60 family peptidoglycan-binding protein RipD. RipD proteins, such as founding member Rv1566c from Mycobacterium tuberculosis, is a catalytically inactive paralog of the peptidoglycan endopeptidases RipA and RipB. A catalytically important Cys and His pair is replaced by Ala-83 and Ser-132. 177 matched cddid_all.tbl CDD NF033745 NF033745 468165 class_C_sortase class C sortase. 218 matched cddid_all.tbl CDD NF033746 NF033746 411330 class_D_sortase class D sortase. 135 matched cddid_all.tbl CDD NF033747 NF033747 468166 class_E_sortase class E sortase. 211 matched cddid_all.tbl CDD NF033748 NF033748 411332 class_F_sortase class F sortase. 155 matched cddid_all.tbl CDD NF033749 NF033749 468167 bact_hemeryth bacteriohemerythrin. Bacteriohemerythrin, an O2-carrying protein that lacks a heme moiety, is named based on its homology to eukaryotic proteins such as myohemerythrin. 129 matched cddid_all.tbl CDD NF033750 NF033750 468168 vWF_bind_Staph von Willebrand factor binding protein Vwb. The von Willebrand factor binding protein Vwb, like its paralog staphylocoagulase, is a coagulase and a virulence factor. It induces clotting, not by being an enzyme, but by activating prothrombin to generate fibrin. 510 matched cddid_all.tbl CDD NF033751 NF033751 468169 pallilysin_like pallilysin-related adhesin. In contrast to pallilysin itself (a bifunctional adhesin and protease), members of the pallilysin-related adhesin family average twice the length, lack the HEXXH motif essential to pallilysin's metalloprotease activity, and are likely to function in virulence only as an adhesin. Typical members of this family include TDE0840 from Treponema denticola and BB0038 from Borrelia burgdorferi, which share less than 20% pairwise amino acid sequence identity. 383 matched cddid_all.tbl CDD NF033752 NF033752 411336 linaridin_CypA "cypemycin family RiPP. The cypemycin precursor CypA belongs to the linaridin class (linear ""arid"" peptide, following dehydration modifications) of RiPP natural product precursors. The signature terminal motif CL[VI]C is modified by decarboxylation of the C-terminal Cys residue, followed by cyclization." 52 matched cddid_all.tbl CDD NF033753 NF033753 411337 RiPP_decarbCypD CypD family RiPP peptide-cysteine decarboxylase. CypD, a Cys decarboxylase flavoprotein, oxidatively removes the carboxyl moiety from the C-terminal Cys residue of CypA, the precursor of the RiPP natural product cypemycin. 182 matched cddid_all.tbl CDD NF033754 NF033754 468170 gliding_CglC adventurous gliding motility lipoprotein CglC. CglC (cell contact-dependent gliding (or conditional gliding) motility protein C, also called adventurous gliding motility protein AgmO, is found in delta-proteobacterial species that exhibit a taxonomically restricted form of gliding motility. 156 matched cddid_all.tbl CDD NF033755 NF033755 468171 gliding_CglE adventurous gliding motility protein CglE. 172 matched cddid_all.tbl CDD NF033756 NF033756 468172 gliding_GltC adventurous gliding motility protein GltC. GltC is a soluble periplasmic protein required for a type of gliding motility found in certain social delta-proteobacteria, including the model species Myxococcus xanthus. 621 matched cddid_all.tbl CDD NF033757 NF033757 468173 gliding_CglB adventurous gliding motility lipoprotein CglB. CglB is an outer membrane lipoprotein required for A-motility in Myxococcus xanthus and other delta-proteobacteria. It is transferable between cells that have a compatible TraAB system, and was therefore named conditional (or cell contact-dependent) gliding motility protein B, or CglB. 403 matched cddid_all.tbl CDD NF033758 NF033758 468174 gliding_GltE adventurous gliding motility TPR repeat lipoprotein GltE. GltE (also called AglT) is a tetratricopeptide repeat protein with a lipoprotein signal peptide and a role in A-motility (adventurous gliding motility) in Myxococcus xanthus and other delta-proteobacteria. 411 matched cddid_all.tbl CDD NF033759 NF033759 411343 exchanger_TraA outer membrane exchange protein TraA. TraA, together with its partner TraB, mediates a large scale exchange of outer membrane lipoproteins, and lipids, between closely related strains or clonally identical cells, certain delta-proteobacterial species such as Myxococcus xanthus. The exchange mechanism is likely to involve fusion of outer membrane, probably done to coordinate the social behaviors these bacteria display. 662 matched cddid_all.tbl CDD NF033760 NF033760 468175 gliding_GltG adventurous gliding motility protein GltG. GltG proteins, including the founding member MXAN_4867 from Myxococcus xanthus, occur in certain delta-proteobacteria and are involved in adventurous gliding (A-)motility. GltG has an N-terminal forkhead-associated (FHA) domain domain, often associated with signal transduction. 647 matched cddid_all.tbl CDD NF033761 NF033761 468176 gliding_GltJ adventurous gliding motility protein GltJ. Adventurous gliding motility protein GltJ, also known as AgmX, occurs in delta-proteobacteria such as Myxococcus xanthus. 671 matched cddid_all.tbl CDD NF033762 NF033762 411346 social_mot_Tgl social motility TPR repeat lipoprotein Tgl. Social motility in delta-proteobacterial species such as Myxococcus xanthus depends on a type VI pilus, which in turn depends on assembly of the PilQ secretin complex. Tgl, a tetratricopeptide repeat (TPR) outer membrane lipoprotein, is required for PilQ assembly. 252 matched cddid_all.tbl CDD NF033763 NF033763 411347 exchanger_TraB outer membrane exchange protein TraB. TraB, as described originally in the delta-proteobacterium, is a protein with a C-terminal OmpA-like domain, and is encoded in an operon with TraA. Together TraAB make it possible for bacterial cells with close enough kinship to exchange outer membrane lipoproteins, such that certain motility defects in mutant cells can be corrected through the exchange. This exchange most likely involves membrane fusion events, as large amounts of lipid are also exchanged, and it is restricted by a bi-directional kin recognition requirement. Among wild-type cells, these exchanges likely help coordinate various social behaviors. 522 matched cddid_all.tbl CDD NF033764 NF033764 468177 gliding_CglF adventurous gliding motility protein CglF. CglF, as originally described in Myxococcus xanthus, is a gliding motility protein. It has the property that motility in a cglF loss mutant can be restored by close contact with compatible kin strains where cglF is wild type. The restoration of motility depends on bidirectional kinship recognition, which is mediated by TraAB and leads to exchange of outer membrane proteins and lipids. This cell contact requirement leads to the gene symbol, cglF, meaning conditional (or, cell contact-dependent) gliding F. This protein has also been called GltF. 87 matched cddid_all.tbl CDD NF033765 NF033765 468178 gliding_CglD adventurous gliding motility lipoprotein CglD. 1124 matched cddid_all.tbl CDD NF033766 NF033766 468179 choice_anch_G choice-of-anchor G family protein. Choice-of-anchor proteins belong to homology families in which various branches carry C-terminal sorting signals known, or suspected, to be processed by transpeptidases as sortase, exosortase, archaeosortase, rhombosortase, or the type 9 secretion system sorting enzyme. Members of this family, called choice-of-anchor G, included sortase and exosortase targets, and are likely to be found on the cell surface. 282 matched cddid_all.tbl CDD NF033767 NF033767 411351 exosort_XrtS exosortase S. Members of the exosortase S family occur in the high GC Gram-positive order Micrococcales (a branch of the Actinobacteria), in genera such as Arthrobacter, Microbacterium, Curtobacterium, and Paenarthrobacter. 155 matched cddid_all.tbl CDD NF033768 NF033768 468180 myxo_SS_tail AgmX/PglI C-terminal domain. The AgmX/PglI C-terminal domain described by this HMM (myxo_SS_tail) occurs as the C-terminal domain in multiple proteins per genome for a number of species capable of surface gliding motility, e.g. 12 in Myxococcus xanthus. Member proteins include the adventurous gliding motility proteins AgmX (GltJ) and PglI in M. xanthus. The domain is about 92 amino acids long, and features a pair of Cys residues about 45 amino acids apart in almost all cases. 92 matched cddid_all.tbl CDD NF033769 NF033769 411353 after_VWA_1 after-VIT domain. The after-VIT domain is a bacterial surface protein C-terminal domain found on some proteins that have both the Vault protein Inter-alpha-Trypsin (VIT) domain and a von Willebrand factor type A domain. Note that some of after-VIT domain-containing proteins, such as members of TIGR03788, may have a known C-terminal sorting signal, such as LPXTG or PEP-CTERM, instead of the after-VIT domain. The after-VIT domain appears to be homologous to the myxo_SS_tail domain, some of whose member proteins are involved in adventurous gliding motility in Myxococcus xanthus, and it is similarly located. 90 matched cddid_all.tbl CDD NF033770 NF033770 411354 exosort_XrtT exosortase T. Exosortase T is a variant form of exosortase, typically found in Alphaproteobacteria in genera such as Pseudovibrio, Labrenzia, and Ruegeria. Members of this family may be dedicated enzymes, processing a single substrate encoded by a nearby gene, rather than processing multiple proteins like exosortases A and B. 472 matched cddid_all.tbl CDD NF033771 NF033771 439417 colonize_BriC biofilm-regulating peptide BriC. BriC (Biofilm-Regulating peptide Induced by Competence), as characterized in Streptococcus pneumoniae, is a cell-cell communication peptide, or peptide pheromone, that is induced by expression of ComE (a master regulator of competence). BriC contributes to biofilm formation, and to colonization in a mouse mole. 60 matched cddid_all.tbl CDD NF033772 NF033772 468181 pheromone_VP1 peptide pheromone VP1. VP1 (virulence peptide 1), as characterized in Streptococcus pneumoniae (a.k.a. pneumococcus), is part of a large panel of secreted regulatory peptides with paralogous leader domains, typically ending with the cleavage site GlyGly, but with highly variable core regions. VP1, along with other pneumococcal peptide pheromones such as BriC, participate to cell-cell communication to regulate pathogenic processes such as biofilm formation. 65 matched cddid_all.tbl CDD NF033773 NF033773 411357 tellur_TrgA TrgA family protein. TrgA, a protein associated with tellurium resistance (but less critical to the phenotype than TrgB, encoded by the adjacent gene), is the founding member of a family of hydrophobic proteins, about 150 amino acids in length, probably embedded in the membrane, and possibly involved in transport. 145 matched cddid_all.tbl CDD NF033774 NF033774 468182 phos_trans_PitA inorganic phosphate transporter PitA. PitA is a low-affinity transporter for inorganic phosphate. It imports phosphate complexed to divalent cations such as Mg(2+) or Ca(2+). Loss of PitA function can confer reduced sensitivity to high levels of Zn(2+). The PitA of Escherichia coli has a closely related paralog, PitB, that is functional but only minimally expressed. Note that the term PitA is used broadly. This exception-level HMM identifies a rather narrow clade of PitA transporters which, however, includes both PitA and PitB of E. coli K-12. 499 matched cddid_all.tbl CDD NF033775 NF033775 468183 P_type_ZntA Zn(II)/Cd(II)/Pb(II) translocating P-type ATPase ZntA. 732 matched cddid_all.tbl CDD NF033776 NF033776 411360 stress_YhcN peroxide/acid stress response protein YhcN. 87 matched cddid_all.tbl CDD NF033777 NF033777 411361 M_group_A_cterm M protein C-terminal domain. M protein (emm) is an important virulence protein and serology-defining surface antigen of Streptococcus pyogenes (group A Streptococcus). M protein has an amino-terminal YSIRK-type signal sequence (associated with cross-wall targeting in dividing cells), and a C-terminal LPXTG domain for processing by sortase and covalent attachment to the Gram-positive cell wall. Past the signal peptide, M protein has a hypervariable region, but this HMM describes only the well-conserved region C-terminal to the hypervariable region. It discriminates M protein from two related proteins, Enn and Mrp. 218 matched cddid_all.tbl CDD NF033778 NF033778 411362 trans_TimA TIM44-related membrane protein TimA. TimA was first described in Caulobacter crescentus, a member of the alpha-proteobacterial lineage that gave rise to the mitochondrion. It is notable because of homology to Tim44, a protein involved in protein translocation in both human and yeast mitochondria, although TimA itself is not considered involved in protein translocation. TimA is found localized to the plasma membrane, on the cytosolic face. The mitochondrial homolog, Tim44, is found as a peripheral protein of the inner face of the mitochondrial inner membrane, and serves as an adaptor to recruit other subunits into the translocation complex, rather than in transport channel itself. 198 matched cddid_all.tbl CDD NF033779 NF033779 468184 Tim44_TimA_adap Tim44/TimA family putative adaptor protein. Members of this family resemble both the eukaryotic protein Tim44, important to the assembly of a protein translocase in mitochondria, and the TimA protein of alpha-proteobacteria such as Caulobacter crescentus. TimA may assist in protein recruitment to the membrane, as Tim44, but appears not to be part of any complex associated with protein translocation. 215 matched cddid_all.tbl CDD NF033780 NF033780 468185 exosort_XrtU_C exosortase U C-terminal region. The XrtU family of exosortases is marked by a distinctive C-terminal region, modeled by the exosort_XrtU_C hidden Markov model. Because members of the archaeosortase and exosortase family perform cleavage of target proteins, in pathways thought to lead to new covalent attachment at the C-terminus and surface anchoring, the XrtU C-terminal domain may indicate the presence of a novel anchoring chemistry. 173 matched cddid_all.tbl CDD NF033782 NF033782 411365 lipoprot_Omp28 Omp28 family outer membrane lipoprotein. The Omp28 family of lipoproteins is named for a founding member described in Porphyromonas gingivalis, where it has been shown across many strains to be an expressed surface antigen. All members of the family are predicted lipoproteins. 263 matched cddid_all.tbl CDD NF033785 NF033785 411366 sulfur_OscA sulfur starvation response protein OscA. OscA (organosulfur compound A) is a small protein, about 60 amino acids in length, in the DUF2292 family. As characterized in Pseudomonas corrugata, OscA is required during sulfur starvation for obtaining it from organosulfur compounds. The pathway is required to remediate oxidative stress from chromate, so oscA was discovered by the loss of high resistance to chromate in Pseudomonas corrugata 28 when the gene is insertionally inactivated. The oscA gene tends to be found near sulfate transporter genes. 60 matched cddid_all.tbl CDD NF033787 NF033787 411367 HTH_BldC BldC family transcriptional regulator. BldC, a helix-turn-helix transcription factor with homology to the mercury resistance transcriptional regulator MerR, is a DNA-binding protein. It is considered the founding member of a subfamily of regulators with an asymmetric head-to-tail oligomerization for cooperative DNA binding, rather than classic dimerization. 49 matched cddid_all.tbl CDD NF033788 NF033788 411368 HTH_metalloreg metalloregulator ArsR/SmtB family transcription factor. Transcriptional repressors that sense toxic heavy metals such as arsenic or cadmium, and are released from DNA so that resistance factors will be expressed, include ArsR, SmtB, ZiaR, CadC, CadX, KmtR, etc. However, some members of this family, including the sporulation delaying system autorepressor SdpR and its family (see NF033789), may lack metal-binding cites and instead regulate other cellular processes. 76 matched cddid_all.tbl CDD NF033789 NF033789 411369 repress_SdpR autorepressor SdpR family transcription factor. Transcription factors in the family of the sporulation delaying system autorepressor SdpR (of Bacillus subtilis) resemble metalloregulatory transcriptional repressors such as ArsR, SmtB, CadX, ZiaR, etc., but may lack the key metal-binding residues. 79 matched cddid_all.tbl CDD NF033790 NF033790 411370 CnrY_NccY_antiS CnrY/NccY family anti-sigma factor. 95 matched cddid_all.tbl CDD NF033791 NF033791 411371 ActR_PrrA_rreg ActR/PrrA/RegA family redox response regulator transcription factor. ActR, PrrA, and RegA are examples of lineage-specific names given to a response regulator transcription factor that acts as a global regulator and belongs to a sensor-regulator pair that is highly conserved in the alpha-proteobacteria. Examples of this regulator include ActR (acid tolerance regulator) in Sinorhizobium meliloti, stationary phase response regulator SpdR in Caulobacter crescentus, 173 matched cddid_all.tbl CDD NF033792 NF033792 468186 ActS_PrrB_HisK ActS/PrrB/RegB family redox-sensitive histidine kinase. This redox-responsive histidine kinase, found in alpha-proteobacteria, shows strong sequence conservation, including the notable motif [VA]AAAAHELGTPxTI. It always acts as a partner to an ActR/PrrA/RegA family global response regulator transcription factor in a two-component sensory transduction system. Lineage-specific names and gene symbols given to this histidine kinase reflect downstream regulator changes such as entry into stationary phase, anaerobic expression of photosynthesis genes, and survival of exposure to low pH. 423 matched cddid_all.tbl CDD NF033793 NF033793 411373 peri_CopK periplasmic Cu(I)/Cu(II)-binding protein CopK. 88 matched cddid_all.tbl CDD NF033794 NF033794 411374 chaper_CopZ_Eh copper chaperone CopZ. Copper chaperone CopZ, as the name is used in Enterococcus hirae and related species, is a small copper-binding protein with close homology to domains found, sometimes in multiple copies, in various copper-translocating copper-translocating P-type ATPases, and to distinct families of other small copper chaperones that also named CopZ. 68 matched cddid_all.tbl CDD NF033795 NF033795 411375 chaper_CopZ_Bs copper chaperone CopZ. This model describes CopZ, a small copper chaperone, as found in Bacillus subtilis and related species. A number of longer protein, such as copper-translocating P-type ATPases, contain multiple CopZ-like domains, with its signature invariant CxxC motif. CopZ from other species may be more different in sequence from this family than some of those domains of longer proteins. 66 matched cddid_all.tbl CDD NF033796 NF033796 468187 selen_YedE_FdhT selenium metabolism membrane protein YedE/FdhT. Members of this family are predicted multiple membrane-spanning proteins, and therefore thought likely to be transporters. It appears that all species whose genomes encode a member of this family produce selenocysteine-containing enzymes, typically formate dehydrogenase. The family member from Campylobacter jejuni was show to be essential for formate dehydrogenase (a selenocysteine-containing enzyme) expression and activity, and so it was named a formate dehydrogenase accessory protein, FdhT. Note that this family is related to (but distinct from) that of TIGR04112, which is similarly restricted to species with pathways for selenium incorporation. 387 matched cddid_all.tbl CDD NF033797 NF033797 411377 phero_SHP2_SHP3 SHP2/SHP3 family peptide pheromone. 23 matched cddid_all.tbl CDD NF033798 NF033798 411378 biofilm_StcA StcA family protein. StcA (streptococcal charged A protein), as described in Streptococcus pyogenes, is a small, positively charged, secreted protein that participates in a quorum-sensing system, and promotes biofilm formation. Related proteins are found in several other Streptococcus spp. 89 matched cddid_all.tbl CDD NF033799 NF033799 411379 inhib_PhrA PhrA family phosphatase inhibitor. 44 matched cddid_all.tbl CDD NF033800 NF033800 411380 quorum_NprX quorum-signaling peptide NprX. NprX, also called NprRB, belongs to the NprR-NprX quorum-sensing system in Bacillus. The mature form of the peptide pheromone is the SKPDIVG heptapeptide. 43 matched cddid_all.tbl CDD NF033801 NF033801 411381 NprX_fam NprX family peptide pheromone. 42 matched cddid_all.tbl CDD NF033802 NF033802 411382 AimP_fam lysogeny pheromone AimP family peptide. AimP is the quorum signaling-like peptide pheromone of a phage system, called the arbitrium system, that detects environmental evidence of predecessor phage activity, in order to direct a lysis/lysogeny decision. 43 matched cddid_all.tbl CDD NF033803 NF033803 411383 TOMM_BorA TOMM family putative cytolysin BorA. The BorA family of thiazole/oxazole-modified microcin (TOMM) peptides that are putative cytolysins and virulence factors have been found, so far, encoded by plasmids in members of the genus Borreliella. 37 matched cddid_all.tbl CDD NF033804 NF033804 468188 Streccoc_I_II antigen I/II family LPXTG-anchored adhesin. Members of the antigen I/II family are adhesins with a glucan-binding domain, two types of repetitive regions, an isopeptide bond-forming domain associated with shear resistance, and a C-terminal LPXTG motif for anchoring to the cell wall. They occur in oral Streptococci, and tend to be major cell surface adhesins. Members of this family include SspA and SspB from Streptococcus gordonii, antigen I/II from S. mutans, etc. 1552 matched cddid_all.tbl CDD NF033805 NF033805 468189 invasion_CiaB invasion protein CiaB. CiaB (Campylobacter invasion antigen B) is important for host cell invasion by Campylobacter. It is found as well in a number of other species capable of invasion, including Campylobacter coli, Campylobacter rectus, and Helicobacter pullorum. 600 matched cddid_all.tbl CDD NF033806 NF033806 411386 laterosporulin laterosporulin family class IId bacteriocin. 52 matched cddid_all.tbl CDD NF033807 NF033807 468190 CopL_fam CopL family metal-binding regulatory protein. The founding member of this family was shown to be involved in the copper-responsive expression of a multicopper oxidase copA encoded downstream. The regulatory function likely involves copper-binding, but activity as a DNA-binding transcriptional regulator was not demonstrated directly. 129 matched cddid_all.tbl CDD NF033808 NF033808 468191 copper_CopD copper homeostasis membrane protein CopD. CopD is an inner membrane protein encoded in Gram-negative bacterial systems that provide resistance to excess copper. It is typically chromosomal, although the PcoD protein of the plasmid-borne pco copper resistance system is a exceptional member of the CopD family. 295 matched cddid_all.tbl CDD NF033814 NF033814 468192 copper_CopC copper homeostasis periplasmic binding protein CopC. 109 matched cddid_all.tbl CDD NF033816 NF033816 468193 Cj0069_fam Cj0069 family protein. Cj0069 from Campylobacter jejuni, described as a serological marker that can show a patient was previously infected with that organism, is the founding member of an uncommon broadly distributed family of proteins. Members of that family are found also in various Helicobacter spp., Bradyrhizobium spp., and Corynebacterium spp. 333 matched cddid_all.tbl CDD NF033817 NF033817 468194 Mplas_variab_LP variable surface lipoprotein signal domain. This HMM describes a homology domain of lipoprotein signal peptides restricted to the genus Mycoplasma, and found in paralogous families that typically are associated with antigenic phase variation, as expression of some members of the family is turned on, others turned off, by the means promoter region modifications by site-specific DNA invertases. The avg family of Mycoplasma agalactiae represents one such family of lipoproteins. 29 matched cddid_all.tbl CDD NF033819 NF033819 411392 IS66_TnpB IS66 family insertion sequence element accessory protein TnpB. The IS66 family insertion sequence element encodes a DDE transposase TnpC, and two accessory proteins, TnpA and TnpB. It has been assumed that the TnpA, TnpB, and TnpC proteins are produced independently in appropriate amounts and form a complex, which acts as a transposase to promote the transposition of an IS66 family element. 90 matched cddid_all.tbl CDD NF033820 NF033820 411393 STM0539_fam STM0539 family protein. STM0539, from Salmonella enterica strain LT2, is the founding member of family of proteins of unknown function, about 145 amino acids in length. 141 matched cddid_all.tbl CDD NF033821 NF033821 411394 YoaK YoaK family small membrane protein. YoaK is a small protein (about 32 amino acids) found in E. coli (from which it is named), Salmonella, Klebsiella, Pantoea, and related taxa. It associates with the inner membrane. 32 matched cddid_all.tbl CDD NF033823 NF033823 468195 archmetzin archaemetzincin family Zn-dependent metalloprotease. 170 matched cddid_all.tbl CDD NF033824 NF033824 411396 Myxo_non_zincin non-proteolytic archaemetzincin-like protein. Members of this family resemble the archaemetzincins, a mostly archaeal family of Zn-dependent metalloproteases, but it lacks the critical catalytic glutamate (E) in the signature motif HEXXH, within the longer pattern HEXXHXXGX3CX4CXMX17CXXC that defines the archaemetzincins. Members of this family are found in Myxococcus xanthus and related members of the Delta-proteobacteria. 174 matched cddid_all.tbl CDD NF033826 NF033826 411397 immun_CdiI ribonuclease toxin immunity protein CdiI. CdiI proteins, including the founding member from Escherichia coli strain STEC_O31, serve as immunity proteins for the toxic tRNA-cleaving ribonuclease toxin CdiA. The system confers contact-dependent inhibition (cdi) between different strains of bacteria. 118 matched cddid_all.tbl CDD NF033827 NF033827 468196 CDF_efflux_DmeF CDF family Co(II)/Ni(II) efflux transporter DmeF. DmeF, a metal efflux transporter belongs to the cation diffusion facilitator (CDF) family. Examples from different species have been described as primarily being induced by, or performing efflux of, different panels of metals, including Co(II) and Ni(II) for Rhizobium leguminosarum and Agrobacterium tumefaciens, and a broader spectrum Wautersia metallidurans CH34. 308 matched cddid_all.tbl CDD NF033828 NF033828 411399 entry_exc2_fam Exc2 family lipoprotein. Exc2, a plasmid-encoded predicted lipoprotein of small size, was once described as a plasmid entry exclusion protein (1985). However, a more recent article (1995), says entry exclusion activity should instead be ascribed to MbeD. 131 matched cddid_all.tbl CDD NF033829 NF033829 411400 plas_excl_MbeD MbeD family mobilization/exclusion protein. MbeD, as found in the ColE1 plasmid, was originally described as a plasmid mobilization protein. Later, it was shown that MbeD additionally was responsible for a plasmid entry exclusion phenotype that had previously been ascribed to products of the exc1 and exc2 genes. 69 matched cddid_all.tbl CDD NF033830 NF033830 468197 NleE_fam_methyl NleE/OspZ family T3SS effector cysteine methyltransferase. NleE from Escherichia coli O157:H7 strain Sakai, and its homolog OspZ from Shigella, are the founding members of a family of SAM-dependent protein--cysteine methyltransferases. Both are type III secretion system (T3SS) effectors involved in virulence, and have the host protein NF-kappa-B as substrates. 212 matched cddid_all.tbl CDD NF033831 NF033831 468198 sce7725_fam sce7725 family protein. This family of uncharacterized proteins is named for founding member sce7725 from Sorangium cellulosum, from the Deltaproteobacteria. It belongs a gene pair found sporadically in genera as diverse as Enterococcus, Lactobacillus, Staphylococcus, Streptococcus, Acinetobacter, and Klebsiella. The partner in each gene pair is a member of the sce7726 famly. 311 matched cddid_all.tbl CDD NF033832 NF033832 468199 sce7726_fam sce7726 family protein. This family of uncharacterized proteins is named for founding member sce7726 from Sorangium cellulosum, from the Deltaproteobacteria. It belongs a gene pair found sporadically in genera as diverse as Enterococcus, Lactobacillus, Staphylococcus, Streptococcus, Acinetobacter, and Klebsiella, or in phage from those lineages. The partner in each gene pair is a member of the sce7725 family. 182 matched cddid_all.tbl CDD NF033833 NF033833 411404 rhodan_ChrE rhodanese family chromate resistance protein ChrE. 108 matched cddid_all.tbl CDD NF033835 NF033835 468200 VraH_fam VraH family protein. 54 matched cddid_all.tbl CDD NF033837 NF033837 411406 GarQ_core garvicin Q family class II bacteriocin core domain. This HMM describes the core (mature) peptide region of GarQ, the class II bacteriocin garvicin (garvieacin) Q, and homologous peptide with similar core regions. Some members, such as GarQ itself, have a classical GlyGly-containing ComC/BlpC-like leader peptide, but others have N-terminal regions (probable leader peptides) of a different type. 42 matched cddid_all.tbl CDD NF033838 NF033838 468201 PspC_subgroup_1 pneumococcal surface protein PspC, choline-binding form. The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A. The other form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. 684 matched cddid_all.tbl CDD NF033839 NF033839 468202 PspC_subgroup_2 pneumococcal surface protein PspC, LPXTG-anchored form. The pneumococcal surface protein PspC, as described in Streptococcus pneumoniae, is a repetitive and highly variable protein, recognized by a conserved N-terminal domain and also by genomic location. This form, subgroup 2, is anchored covalently after cleavage by sortase at a C-terminal LPXTG site. The other form, subgroup 1, has variable numbers of a choline-binding repeat in the C-terminal region, and is also known as choline-binding protein A. 557 matched cddid_all.tbl CDD NF033840 NF033840 411409 PspC_relate_1 PspC-related protein choline-binding protein 1. Members of this family share C-terminal homology to the choline-binding form of the pneumococcal surface antigen PspC, but not to its allelic LPXTG-anchored forms because they lack the choline-binding repeat region. Members of this family should not be confused with PspC itself, whose identity and function reflect regions N-terminal to the choline-binding region. See Iannelli, et al. (PMID: 11891047) for information about the different allelic forms of PspC. 648 matched cddid_all.tbl CDD NF033841 NF033841 411410 small_YshB YshB family small membrane protein. YshB, a membrane-associated protein typically 36 to 40 amino acids in length, is found conserved in genera of the gamma-proteobacteria including Cronobacter, Enterobacter, Escherichia, Klebiella, Salmonella, and Serratia. The gene symbol derives from E. coli K-12. 40 matched cddid_all.tbl CDD NF033842 NF033842 411411 small_MgtS protein MgtS. MgtS, previously called YneM, is a small inner membrane protein that modulates Mg(2+) concentrations through its effects on the P-type transporter MgtA. 30 matched cddid_all.tbl CDD NF033843 NF033843 411412 small_YpfM protein YpfM. 19 matched cddid_all.tbl CDD NF033844 NF033844 411413 small_YqgB acid stress response protein YqgB. 40 matched cddid_all.tbl CDD NF033845 NF033845 468203 MSCRAMM_ClfB MSCRAMM family adhesin clumping factor ClfB. Clumping factor B is an MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules). Features of the sequence, but also of other MSCRAMM adhesins, include a long run of Ser-Asp dipeptide repeats and a C-terminal cell wall anchoring LPXTG motif. 871 matched cddid_all.tbl CDD NF033846 NF033846 411415 Rumino_NPXTG NPXTG family C-terminal sorting domain. Rumino_NPXTG represents a flavor of C-terminal protein sorting signal in species related to Ruminococcus albus. In that lineage, multiple sortases per genome may be found, including multiple B-type sortases. Proteins found by this HMM (more than 12 encoded in a representative complete genome) may represent substrates of a panel of related sortases, while additional proteins found in Ruminococcus genomes with below-cutoff hits to this model may be processed by other sortases. 29 matched cddid_all.tbl CDD NF033847 NF033847 468204 MCP_Sipho major capsid protein, Siphoviridae type. This protein is a phage major capsid protein, as reported in primary sequence submissions of a large number of Siphoviridae, many of which have hosts in the Mycobacterium and Gordonia genera of bacteria. 549 matched cddid_all.tbl CDD NF033848 NF033848 468205 VgrG_rel VgrG-related protein. Members of this family resemble Vgr proteins of type VI secretion systems (T6SS) as found in various proteobacteria. However, members of this family occur instead in genera such as Streptomyces and Roseiflexus. The biological roles and molecular functions of proteins in this family appear not to have been characterized. 547 matched cddid_all.tbl CDD NF033849 NF033849 468206 ser_rich_anae_1 serine-rich protein. This serine-rich protein belongs to a family with large size (over 1000 amino acids), which a highly serine-rich central region that averages over 300 aa in length. Species encoding members of this family of proteins tend to be anaerobic bacteria, including Gram-positive bacteria of the human gut microbiome and Chloroflexi from marine sediments. 1122 matched cddid_all.tbl CDD NF033850 NF033850 411419 LCxxNW mobility-associated LCxxNW protein. This protein belongs to a family of small proteins, about 65 amino acids long, with three invariant Cys residues, including one in the motif LCxxNW, for which the family is named. Member proteins are found in contexts that suggests they are accessory proteins of mobile elements. The context includes members of families PF01695, PF01610, and PF00665, all associated with transposition and/or integration. 61 matched cddid_all.tbl CDD NF033852 NF033852 468207 fulvocin_rel bacteriocin fulvocin C-related protein. Fulvocin C was described in 1981 as a bacteriocin from Myxococcus fulvus, 45 amino acids long with 8 cysteines. The precursor form was not described. However, the most closely related precursor-like proteins represent the founding members of a family of proteins that average over 225 amino acids in length, the majority of which have a C-terminal tail region in which the 8 Cys residues are essentially invariant. The long N-terminal region, and the sharp change in amino acid composition at the start of what appears to be the bacteriocin core peptide region, suggests that the N-terminal region may contribute directly in peptide maturation or transport, rather than merely providing for recognition by maturation proteins. 149 matched cddid_all.tbl CDD NF033853 NF033853 411421 KPN_two_small small membrane protein. Members of this family, including paralogs KPN_01023 and KPN_01923 from Klebsiella pneumoniae subsp. pneumoniae MGH 78578, are small proteins, typically 40 amino acids in length. A highly hydrophobic region, about 25 amino acids in length with a composition typical of transmembrane segments, is followed by a highly basic region of about 15 amino acids. Analogous proteins of similar size, with apparently similar hydrophobic regions, have been described as membrane-associated proteins expressed in response to various types of cell envelope stress. 37 matched cddid_all.tbl CDD NF033854 NF033854 468208 esterase_BioV pimelyl-ACP methyl ester esterase BioV. BioV, found in Helicobacter pylori and a number of related Epsilonproteobacteria replaces BioH as a pimelyl-ACP methyl ester esterase required for biotin biosynthesis. 167 matched cddid_all.tbl CDD NF033855 NF033855 468209 tRNA_MNMC2 tRNA (5-methylaminomethyl-2-thiouridine)(34)-methyltransferase MnmD. This HMM describes either the N-terminal region, called MNMC2, of the tRNA modification bifunctional enzyme MnmC, or a free-standing protein that performs the same methyltransferase function, in partnership with an FAD-dependent protein, or C-terminal region, called MNMC1 (see TIGR03197). 205 matched cddid_all.tbl CDD NF033856 NF033856 411424 T4SS_effec_BID T4SS effector BID domain. The BID domain (Bartonella intracellular delivery domain) is recognized by the type IV secretion system (T4SS) virB (not trw) of Bartonella and related taxa (e.g. Ochrobactrum), and is found in T4SS effector proteins such as BepA, BepB, BepC, etc. Multiple copies of the domain may be found in a single protein. 109 matched cddid_all.tbl CDD NF033857 NF033857 411425 BPSL0067_fam BPSL0067 family protein. null 115 matched cddid_all.tbl CDD NF033858 NF033858 468210 ABC2_perm_RbbA ribosome-associated ATPase/putative transporter RbbA. 907 matched cddid_all.tbl CDD NF033859 NF033859 411427 SMEK_N SMEK domain. The SMEK domain is named for four genera in which multiple, diverse members of this uncommon family of bacterial proteins are found: Staphylococcus, Mycoplasma, Escherichia, and Klebsiella. Members of the family are highly variable in length. This domain occurs as the N-terminal region. The four scattered invariant residues in the seed alignment, which may provide a clue to function, are Glu, Asp, Gln, and Lys. 97 matched cddid_all.tbl CDD NF033860 NF033860 468211 Wzy_O6_O28 oligosaccharide repeat unit polymerase. Members of this family are oligosaccharide repeat unit polymerases in a subfamily that includes the Wzy proteins for polymerization of the O-antigens O6, O28, O39, O59, and several others. 384 matched cddid_all.tbl CDD NF033861 NF033861 411429 sm_mem_Ecr Ecr family regulatory small membrane protein. Ecr, as described in the genus Enterobacter, is a small membrane protein predicted to span the inner membrane. It was found to modulate expression of PhoP, part of the PhoP-PhoQ two component system, which in turn induces the arnBCADTEF operon, leading to modification of LPS and conferring elevated resistance to colistin. The form described in PMID:31169899 (WP_048029797.1), at 72 amino acids in length, is aberrant compared with the typical length for the majority of family members, about 46 residues. 46 matched cddid_all.tbl CDD NF033863 NF033863 468212 immun_TipC_fam TipC family immunity protein. This family is named for founding member TipC1 (previously TipC), an immunity protein for the toxin TelC, which is a type VII secretion system (T7SS) effector lipid II phosphatase. 192 matched cddid_all.tbl CDD NF033864 NF033864 411431 cytochrome579 cytochrome 579. Cytochrome 579, as described originally in Leptospirillum from acid mine drainage, is an abundant red cytochrome that acts as an electron transfer protein involved in Fe(II) oxidation. 178 matched cddid_all.tbl CDD NF033865 NF033865 468213 fusolisin autotransporter serine protease fusolisin. 1003 matched cddid_all.tbl CDD NF033869 NF033869 411433 viru_reg_Rsp AraC family transcriptional regulator Rsp. Rsp (repressor of surface proteins), as described in Staphylococcus aureus, is a large protein with an AraC-like helix-turn-helix DNA-binding domain. Regulatory targets include the accessory gene regulator (agr) operon, which in turn regulates a large number of virulence factors. 701 matched cddid_all.tbl CDD NF033870 NF033870 411434 VOMP_auto_Cterm Vomp family autotransporter C-terminal domain. The Vomp (variably expressed outer-membrane proteins) family, as described in Bartonella, consists of autotransporter surface proteins including collagen-binding autotransporter adhesins VompA and VompC. 356 matched cddid_all.tbl CDD NF033871 NF033871 468214 deAMP_SidD deAMPylase SidD family protein. The founding member of this protein family, SidD from Legionella pneumophila, is a type IV secretion system effector that acts as a deAMPylase of the host protein. Homologs are found in several other Gammaproteobacteria, including several different Legionella and Coxiella species. 180 matched cddid_all.tbl CDD NF033872 NF033872 468215 SidA_fam T4SS effector SidA family protein. The founding member of this protein family, SidD from Legionella pneumophila, is a minimally characterized type IV secretion system substrate. Homologs are found in a wide range of Legionella species. 379 matched cddid_all.tbl CDD NF033873 NF033873 411437 SidJ_poly_Glu SidJ family T4SS effector polyglutamylation protein. SidJ, called a pseudokinase because its polyglutamylation activity differs from what might be expected from its kinase-like fold, is the founding member of a family of such pseudokinases. SidJ itself, as described in Legionella pneumophila, is exported by a type IV secretion system (T4SS), and modifies and modulates the activity of T4SS effector SidE. 758 matched cddid_all.tbl CDD NF033874 NF033874 468216 SidJ_rel_pseudo SidJ-related pseudokinase. Members of this family are uncharacterized but exhibit strong local sequence similarity to SidJ, a protein that exhibits a protein kinase fold, but that surprisingly exhibit a different activity. In the case of SidJ itself, the activity is polyglutamation activity. For this family, the activity is unknown. 508 matched cddid_all.tbl CDD NF033875 NF033875 411439 Agg_substance LPXTG-anchored aggregation substance. Aggregation substances, as described in Enterococcus, are LPXTG-anchored large surface proteins that contribute to virulence. Several closely related paralogs may be found in a single strain. 1306 matched cddid_all.tbl CDD NF033876 NF033876 468217 flagella_HExxH flagellinolysin. Flagellinolysin is a variant form of bacterial flagellin in with the normally hypervariable central region contains an M9 (MEROPS classification) family metalloprotease domain, with its signature HExxH motif. The founding member of the family, from the pathogen Clostridium haemolyticum, shows EDTA-sensitive metalloprotease activity. The large count of flagellin subunits in a complete flagellum means the capacity of flagellinolysin to perform as a protease may have implications for host-pathogen relationships. 380 matched cddid_all.tbl CDD NF033878 NF033878 468218 thiovarsolin thiovarsolin family RiPP. The thiovarsolins, named for a founding member from Streptomyces varsoviensis, are RiPPs (ribosomally synthesized and post-translationally modified peptide). As with the thioviridamides, thiovarsolin precursors are encoded in loci that encode YcaO and TfuA family proteins, suggesting post-translational modification by thioamidation. 89 matched cddid_all.tbl CDD NF033879 NF033879 411442 smalltalk smalltalk protein. Smalltalk is a membrane-associated protein of very small size (less than 35 amino acids), found broadly in Bacteroides and Prevotella, both of which are prevalent in human gut microbiomes. Genomic context suggests a role in crosstalk in the gut microbiome, whether that involve toxins and immunity, signaling, or some other form of interaction. The family was identified and discussed by Sberro, et al., in a screen for overlooked small proteins encoded within human microbiomes, and named smalltalk here for its small size and cross-talk role. 29 matched cddid_all.tbl CDD NF033880 NF033880 411443 Prli42 stressosome-associated protein Prli42. Prli42, as characterized in Listeria monocytogenes and found broadly in the Firmicutes, is a membrane protein of very small size, essential to the function of the stressosome. It appears to be related to DUF4044 (PF13253). 31 matched cddid_all.tbl CDD NF033881 NF033881 411444 aureocin_A53 aureocin A53 family class IId bacteriocin. Members of this family include leaderless, unmodified class IId bacteriocins such as lacticin Q, BacSp222, and the founding member aureocin A53. 48 matched cddid_all.tbl CDD NF033882 NF033882 468219 T4SS_lipo_DotD type IVB secretion system lipoprotein DotD. Members of this family are the lipoprotein DotD from type IVB secretion systems, which are also called Dot/Icm secretion systems. DotD is is related to conjugal transfer protein TraH as that term is used in IncI1 plasmid transfer regions. 143 matched cddid_all.tbl CDD NF033883 NF033883 468220 conj_TraQ_IncI1 conjugal transfer protein TraQ. 175 matched cddid_all.tbl CDD NF033884 NF033884 468221 conj_TraO_IncI1 conjugal transfer protein TraO. TraO, involved in the conjugal transfer of plasmids such as IncI1 plasmids, shares homology with IcmE of type IVB secretion systems. 381 matched cddid_all.tbl CDD NF033885 NF033885 468222 conj_TraP_IncI1 conjugal transfer protein TraP. Members of this family are the conjugal transfer protein TraP, as the term is used for the member protein from IncI1 plasmids and for their homologs. Note that the same terminology may be applied to unrelated proteins from other forms of conjugal transfer system. 217 matched cddid_all.tbl CDD NF033886 NF033886 468223 T4SS_DotA type IVB secretion system protein DotA. This HMM distinguishes DotA of type IVB secretion systems from TraY as the term is used in the conjugal transfer systems of IncI1 family plasmids. 777 matched cddid_all.tbl CDD NF033887 NF033887 468224 conj_TraX conjugal transfer protein TraX. 163 matched cddid_all.tbl CDD NF033888 NF033888 468225 conj_TraW conjugal transfer protein TraW. Members of this family are the TraW protein of conjugal plasmid transfer systems, as the term is used for certain transfer systems, including that of IncI1 family plasmids. Note that an unrelated protein, also designated TraW, participates in the assembly of F-pilin subunits, involved in transfer of F-plasmids. 380 matched cddid_all.tbl CDD NF033889 NF033889 468226 termin_lrg_T7 phage terminase large subunit. The phage terminase large subunit (TerL) is also called DNA maturase B. It oligomerizes into an ATPase that forces DNA into a pre-existing phage prohead to package the DNA. This TerL family includes members from phage T7 and phage T3, among others. 499 matched cddid_all.tbl CDD NF033890 NF033890 411453 DotM_IcmP_IVB type IVB secretion system coupling complex protein DotM/IcmP. 354 matched cddid_all.tbl CDD NF033891 NF033891 468227 surf_exc_IncI1 plasmid IncI1-type surface exclusion protein ExcA. The surface exclusion protein ExcA, as found in R64 and other IncI1 family plasmids, is not required for plasmid transfer. Instead, it is required for blocking transfer of closely related plasmids into the host cell. 210 matched cddid_all.tbl CDD NF033892 NF033892 468228 XcbB_CpsF_sero XcbB/CpsF family capsular polysaccharide biosynthesis protein. Two partially characterized members of this family are XcbB, as described in Neisseria meningitidis serotype X, and CpsF as described in Enterococcus faecalis serotype C. In the latter case, loss of CpsF converts capsular polysaccharide to serotype D. 291 matched cddid_all.tbl CDD NF033893 NF033893 411456 pheromone_ipd peptide pheromone inhibitor Ipd. The pheromone inhibitor iPD1, in mature form, is the last 8 amino acids of the product of the ipd gene. It was described in conjugative plasmids of Enterococcus faecalis. 21 matched cddid_all.tbl CDD NF033894 NF033894 468229 Eex_IncN EexN family lipoprotein. Members of this family are lipoproteins, typically associated with mobile elements such as phage, and related to the entry exclusion protein Eex of IncN-type plasmids. Members of this family tend to be small (shorter than 90 amino acids) with three invariant Cys residues, one of which belongs to the lipoprotein signal peptide. This family shares some similarities with TIGR04359, which includes the entry exclusion lipoprotein TrbK of IncPalpha-type plasmids. 65 matched cddid_all.tbl CDD NF033896 NF033896 411458 MFS_LfrA efflux MFS transporter LfrA. This efflux transporter, as characterized in Mycolicibacterium (Mycobacterium) smegmatis, provides low-level fluoroquinolone resistance (lfr) when overexpressed. 504 matched cddid_all.tbl CDD NF033897 NF033897 468230 GUMAP_C GUMAP protein C-terminal domain. GUMAP (Giant Ureaplasma Membrane-Anchored Protein) is a very large protein found in several species of the genus Ureaplasma, a lineage that resembles Gram-positive bacteria by ancestry but that lacks a peptidoglycan cell wall. GUMAP proteins average about 5000 amino acids in length. Near the C-terminus, these proteins have a strongly hydrophobic segment followed immediately by a cluster of basic residues, as is characteristic of proteins with a C-terminal membrane anchor. Because of the potentially large computation cost of performing database searches with a protein profile HMM that is thousands of residues long, this HMM models only about 750 amino acids of the C-terminal region of GUMAP proteins. 729 matched cddid_all.tbl CDD NF033898 NF033898 468231 QWxxN_dom QWxxN domain-containing protein. The QWxxN domain is about 125 amino acids long, and appears typically as the conserved core region in up to 9 tandem repeats, each about 200 amino acids long. Proteins with this domain are known so far only in the genus Enterococcus, and may reach over 3000 amino acids in length. 127 matched cddid_all.tbl CDD NF033899 NF033899 468232 T4SS_pilin_TrwL VirB2 family type IV secretion system major pilin TrwL. TrwL is the major pilin of Trw type IV secretion system (T4SS) of Bartonella species. It is related to VirB2 of related T4SS and to the conjugal transfer protein TrbC. The Trw system is unusual for having duplications of certain subunits, and TrwL has divergent, tandem-duplicated copies, named in series TrwL1, TrwL2, etc. 103 matched cddid_all.tbl CDD NF033900 NF033900 468233 T4SS_IcmE_DotG type IVB secretion system protein DotG/IcmE. 1012 matched cddid_all.tbl CDD NF033901 NF033901 411463 L_lactate_LldD FMN-dependent L-lactate dehydrogenase LldD. LldD is an FMN-dependent L-lactate dehydrogenase. It occurs in E. coli, Salmonella, and as one of two L-lactate dehydrogenases in Pseudomonas aeruginosa. It is unrelated to the NAD-dependent enzyme. 377 matched cddid_all.tbl CDD NF033902 NF033902 468234 iso_D2_wall_anc SpaH/EbpB family LPXTG-anchored major pilin. Members of this family are pilin major subunits whose structure includes an LPXTG motif-containing signal (see TIGR01167) near the C-terminus, for processing by sortases. Most contain a recognizable D2-type fimbrial isopeptide formation domain (see TIGR04226), in which Lys-to-Asn isopeptide bond formation provides additional structural integrity to support adhesion despite shear. For proper members of this subfamily, lengths fall typically in the range of 460 to 640 amino acids in length. Many members of this family contribute to the virulence of certain Gram-positive pathogens, including SpaA, SpaD, and SpaH from Corynebacterium diphtheriae, and EbpB and EbpC from Enterococcus faecalis. 533 matched cddid_all.tbl CDD NF033903 NF033903 468235 VaFE_rpt VaFE repeat. The VaFE domain, about 121 amino acids long, typically occurs as a tandem repeat in sortase-anchored surface proteins of Gram-positive bacteria. A single protein may from one to over fifteen VaFE domains. The domain is named for a particularly strong motif with a nearly invariant Phe-Glu residue pair. The function is for the VaFE domain is unknown. 121 matched cddid_all.tbl CDD NF033904 NF033904 468236 LlsX_fam LlsX family protein. LlsX, as found in Listeria monocytogenes, is a small protein of unknown function, encoded in the island responsible for listeriolysin S biosynthesis and processing. Related proteins are found in additional Gram-positive lineages, such as Streptococcus sobrinus and Lactobacillus sp. 90 matched cddid_all.tbl CDD NF033906 NF033906 411467 ExsE_fam T3SS regulon translocated regulator ExsE family protein. ExsE, through protein-protein interaction, serves in a regulatory cascade that modulates the role of ExsA, a transcriptional activator of Pseudomonas aeruginosa's type III secretion system (T3SS) regulon. ExsE itself is a substrate for translocation (i.e. removal) by the T3SS system, providing feedback that modulates expression of secretion system genes. Homologs found in multiple species of Aeromonas and Photorhabdus may be functionally equivalent. Note that VP1702 from Vibrio parahaemolyticus, given the same gene symbol and ascribed an equivalent function, appears unrelated in sequence. 77 matched cddid_all.tbl CDD NF033907 NF033907 468237 ExsE2_fam T3SS regulon translocated regulator ExsE2. ExsE2, as described in two Vibrio species, is called functionally equivalent to ExsE from Pseudomonas aeruginosa, but appears to lack detectable sequence homology. In each model organism, a type III secretion system (T3SS) contains a DNA-binding transcriptional activator ExsA, an anti-activator ExsD that binds ExsA and inhibits its activity, and a secretion chaperone ExsC that can bind to and counteract ExsD. ExsE2 (in V. alginolyticus) or ExsE (in P. aeruginosa) can bind its chaperone ExsC until it exits the cell by successful T3SS translocation, providing fine tuning of T3SS gene expression through these interactions. We renamed the Vibrio family from ExsE to ExsE2 to help minimize confusion between these two very dissimilar families. 93 matched cddid_all.tbl CDD NF033908 NF033908 468238 AcfA_fam_omp AcfA family outer membrane beta-barrel protein. AcfA (accessory colonization factor A), as discussed in Vibrio cholerae, is a porin-like outer membrane beta-barrel protein. It encoded in a locus with other proteins also termed accessory colonization factor, near the toxin-coregulated pilus genes, and its presence aids in intestinal colonization, but its molecular function is unknown. Members of the broader family, described by this HMM, are found in many species of Vibrio, Photobacterium, Aliivibrio, and related genera. The name AcfA is used also for a member of this family from Vibrio alginolyticus, that is no more than 40 percent identical in amino acid sequence, but it is unclear that all members of this family should be considered AcfA. 214 matched cddid_all.tbl CDD NF033909 NF033909 468239 opacity_OapA opacity-associated protein OapA. This family consists of full-length homologs to OapA, opacity-associated protein A as described in Haemophilus influenzae. OapA shares a C-terminal homology domain, called the OapA domain, with the Escherichia coli protein YtfB, which is now known to bind peptidoglycan through its OapA domain and to act as a cell division protein. 421 matched cddid_all.tbl CDD NF033910 NF033910 468240 LWR_salt "LWR-salt protein. This family of uncharacterized proteins was assigned the name LWR-salt (pronounced ""lower-salt"") to mark a well-conserved motif LWR (part of the longer motif WxFFRDxLWRG) and its restriction to the Halobacteria, a branch of the Archaea." 118 matched cddid_all.tbl CDD NF033911 NF033911 468241 botu_NTNH non-toxic nonhemagglutinin NTNH. The botulinum neurotoxin (BoNT) is always encoded together with associated non-toxic proteins (ANTPs) that are co-produced with it and form a complex that protects the toxin. Often, NtnH (non-toxic nonhemagglutinin) is one of these ANTPs, with the ntnh gene lying immediately upstream of the bont gene. 1164 matched cddid_all.tbl CDD NF033912 NF033912 468242 msc mechanosensitive ion channel. Proteins of this subfamily are mechanosensitive channels, involved in numerous biological functions. Representative proteins of this subfamily are WP_092311603 and WP_068170239 (TCDB accession: 1.A.23.8.3 and 1.A.23.8.5, respectively). 365 matched cddid_all.tbl CDD NF033913 NF033913 468243 fibronec_FbpA LPXTG-anchored fibronectin-binding protein FbpA. FbpA, a fibronectin-binding protein described in Streptococcus pyogenes, has a YSIRK-type (crosswall-targeting) signal peptide and a C-terminal LPXTG motif for covalent attachment to the cell wall. It is unrelated to the PavA-like protein from Streptococcus gordonii (see BlastRule NBR009716) that was given the identical name, so the phase LPXTG-anchored is added to the protein name for clarity. 386 matched cddid_all.tbl CDD NF033914 NF033914 411475 antiphage_ZorA_1 anti-phage ZorAB system protein ZorA. Proteins of this subfamily are putative H+ channel proteins, but it has been reported that they are also involved in anti-phage defense. 619 matched cddid_all.tbl CDD NF033915 NF033915 411476 antiphage_ZorA_2 anti-phage ZorAB system protein ZorA. Proteins of this subfamily are putative H+ channel proteins, but it has been reported that they are also involved in anti-phage defense. 383 matched cddid_all.tbl CDD NF033916 NF033916 411477 antiphage_ZorA_3 anti-phage ZorAB system protein ZorA. Proteins of this subfamily are putative H+ channel proteins, but it has been reported that they are also involved in anti-phage defense. 509 matched cddid_all.tbl CDD NF033917 NF033917 411478 antiphage_ZorA_4 anti-phage ZorAB system protein ZorA. Proteins of this subfamily are putative H+ channel proteins, but it has been reported that they are also involved in anti-phage defense. 417 matched cddid_all.tbl CDD NF033918 NF033918 411479 LGIC_1 ligand-gated ion channel. Prokaryotic ligand-gated ion channels (LGICs) are a large group of transmembrane transporters, which might contribute to adaptation to pH change. 305 matched cddid_all.tbl CDD NF033919 NF033919 468244 PA2779_fam PA2779 family protein. Homologs of PA2779, an uncharacterized protein, average about 130 amino acids in length. The most distinctive feature is an extremely hydrophobic region at or near the C-terminus, consisting almost entirely of the bulkier hydrophobic residues Val, Ile, Leu, and Phe. The function is unknown. 123 matched cddid_all.tbl CDD NF033920 NF033920 468245 C39_PA2778_fam PA2778 family cysteine peptidase. Members of this family are MEROPS classification C39 family cysteine peptidases, a group that includes many processing enzyme for peptide natural products such as lantibiotics and other bacteriocins. This family, more specifically, includes PA2778 as found in Pseudomonas aeruginosa. All members of the defining seed alignment are encoded in the vicinity of a homolog of PA2779 (see HMM NF033919). Note that the C-terminal region consists largely of tetratricopeptide repeats (TPR), so classification using this HMM must be based on comparing the top domain score to the second gathering threshold (GA2). 255 matched cddid_all.tbl CDD NF033921 NF033921 468246 por_somb iron uptake porin. Proteins of this family have typical porin structures. It has been reported that Synechococcus outer membrane (Som) porins (SomA and SomB) are involved in iron uptake in cyanobacterium Synechococcus. 481 matched cddid_all.tbl CDD NF033922 NF033922 468247 opr_porin_1 Opr family porin. Proteins hit by this HMM model are members of the Opr family porins, which are mainly found in Pseudomonas and other Gram-negative bacteria with different substrates. 328 matched cddid_all.tbl CDD NF033923 NF033923 411484 opr_proin_2 Opr family porin. Proteins hit by this HMM model are members of the Opr family porins, which are mainly found in Pseudomonas and other Gram-negative bacteria with different substrates. 386 matched cddid_all.tbl CDD NF033924 NF033924 411485 T3SS_LcrQ_reg type III secretion system exported negative regulator LcrQ/YscM1. The type III secretion system (T3SS) protein called LcrQ in Yersinia pseudotuberculosis and YscM1 in Yersinia enterocolitica is a post-transcriptional regulator of T3SS effector gene expression. Successful chaperone-dependent export by the T3SS allows the translation of T3SS effector proteins to proceed. 110 matched cddid_all.tbl CDD NF033925 NF033925 468248 pora_1 PorA family porin. This HMM hits Corynebacterial Porin A (PorA) family porins, which are short membrane proteins. 42 matched cddid_all.tbl CDD NF033926 NF033926 468249 msp_porin MSP porin. Members of this HMM are MSP porins (major outer sheath proteins) in Treponema. They may play a role in immune evasion and persistence. 512 matched cddid_all.tbl CDD NF033927 NF033927 411488 alph_xenorhab_B alpha-xenorhabdolysin family binary toxin subunit B. 223 matched cddid_all.tbl CDD NF033928 NF033928 468250 alph_xenorhab_A alpha-xenorhabdolysin family binary toxin subunit A. Alpha-xenorhabdolysin was the founding member of a family of alpha-helical pore-forming binary toxins. YaxAB from Yersinia enterocolitica has been studied structurally. This HMM represents subunit A proteins such as XaxA and YaxA, capable of binding to the membrane even in the absence of the B subunit. This family is related to the Bacillus haemolytic enterotoxin family (see PF05791.9), although thresholds for this HMM are set to exclude that family. 340 matched cddid_all.tbl CDD NF033930 NF033930 468251 pneumo_PspA pneumococcal surface protein A. The pneumococcal surface protein proteins, found in Streptococcus pneumoniae, are repetitive, with patterns of localized high sequence identity across pairs of proteins given different specific names that recombination may be presumed. This protein, PspA, has an N-terminal region that lacks a cross-wall-targeting YSIRK type extended signal peptide, in contrast to the closely related choline-binding protein CbpA which has a similar C-terminus but a YSIRK-containing region at the N-terminus. 660 matched cddid_all.tbl CDD NF033932 NF033932 468252 LapB_rpt_80 LapB C-terminal region repeat. This model describes a tandem repeat about 80 amino acids in length per repeat, found in at least 12 different surface-exposed proteins of the pathogen Listeria monocytogenes, and in particular found 10 times in tandem in the surface protein LapB, for which the repeat is named. 83 matched cddid_all.tbl CDD NF033934 NF033934 411492 KCU-star KCU-star family selenoprotein. This family is named KCU-star because nearly all member proteins end with tripeptide lysine-cysteine-selenocysteine, followed immediately by a stop codon (represented by an asterisk, or star). Members occur in primarily in species of Helicobacter (although not Helicobacter pylori, in which selenocysteine incorporation capability has been lost) and Campylobacter. This small family belongs to the larger YbdD/YjiX (DUF466) family described by Pfam model PF04328, which regularly occur in the company of CstA family pyruvate transport proteins, and may be part of the transporter. 57 matched cddid_all.tbl CDD NF033935 NF033935 411493 inclusion_IncB inclusion membrane protein IncB. When Chlamydia invades a cell, the host-derived membrane of the vacuole in which it resides becomes known as the inclusion membrane. The chlamydial type III secretion system (T3SS) delivers a number of effector proteins into the inclusion membrane, including this protein, IncB (inclusion membrane protein B). IncB proteins from different chlamydial species share a conserved hydrophobic C-terminal region, represented by this HMM, but their N-terminal regions vary considerably in length and sequence. 78 matched cddid_all.tbl CDD NF033936 NF033936 468253 CuZnOut_SO0444 SO_0444 family Cu/Zn efflux transporter. Members of this family are apparent metal cation efflux transporters. Architectural features include an average length of about 400 residues, with well conserved and highly hydrophobic N-terminal and C-terminal domains. The central region is highly variable in length and sequence, and rich in both Cys and His residues, as often seen in proteins produced in response to toxic concentrations of certain metals. The founding member, SO_0444, was shown to confer resistance to high levels of Cu and Zn ions. The best conserved region of the protein is a CSCG motif in the N-terminal region, found at least twice as in a selenocysteine-containing form, USCG. 336 matched cddid_all.tbl CDD NF033937 NF033937 411495 porH_1 PorH family porin. Proteins of this HMM family form major outer membrane hetero-oligomeric pores on the cell wall of Corynebacterium with PorA family porins. 97 matched cddid_all.tbl CDD NF033938 NF033938 468254 porH_2 PorH family porin. Proteins of this HMM family form major outer membrane hetero-oligomeric pores on the cell wall of Corynebacterium with PorA family porins. 63 matched cddid_all.tbl CDD NF033939 NF033939 468255 DESULF_POR1 outer membrane homotrimeric porin. Proteins of this HMM family are primarily identified in sulfate-reducing Desulfovibrio, but this HMM may also hit proteins from other Gram-negative bacteria. Porins of this family form transmembrane pores for the passive transport of small molecules across the outer membranes of Gram-negative bacteria. 455 matched cddid_all.tbl CDD NF033940 NF033940 411498 ErpA_rel ErpA-related iron-sulfur cluster insertion protein. null 95 matched cddid_all.tbl CDD NF033942 NF033942 468256 GjpA outer membrane porin GjpA. GjpA was first identified in Gordonia jacobaea strain MV-1 as an outer membrane channel-forming protein. It has been reported that GjpA could be of relevance in the import and export of negatively charged molecules across the cell wall. 331 matched cddid_all.tbl CDD NF033943 NF033943 468257 RTX_toxin RTX family hemolysin. RTX family toxin are secreted from the bacteria and inserted into the membranes of infected cells, causing host cell rupture. 875 matched cddid_all.tbl CDD NF033945 NF033945 411501 AcrIIA2_fam AcrIIA2 family anti-CRISPR protein. Anti-CRISPR proteins are phage proteins that defeat CRISPR-Cas systems for immunity based on phage-derived spacers found in arrays between CRISPR repeats. The founding member of this family, AcrIIA2, works against a CRISPR-Cas class II system. 118 matched cddid_all.tbl CDD NF033946 NF033946 468258 AcrIIA4_fam AcrIIA4 family anti-CRISPR protein. AcrIIA4 is an anti-CRISPR protein that affects Cas9, a class II CRISPR system protein used in biotechnology applications for targeted genome editing. 86 matched cddid_all.tbl CDD NF033947 NF033947 468259 PEP-cistern "cistern family PEP-CTERM protein. Members of this family are PEP-CTERM proteins, that is, surface proteins of Gram-negative organisms that carry a short C-terminal region used to help target proteins to their proper cellular location, hold them in position for post-translational modifications that might need to occur (such as glycosylation), and which is eventually removed by exosortase as the protein is ligated to something else. In this family the most conspicuous feature other than the PEP-CTERM sorting signal (with variants that include PEP, PAP, PTP, and SEP) is a pair of Cys residues about 6 amino acids apart from each other. The second Cys occurs in the middle of run of amino acids that are all either small (Gly, Ser, Ala) or else Asn. The local context suggests the Cys occurs at a turn at the end of a structural feature such as alpha-helix or beta-strand, rather than in the middle of one. The word ""cistern"" was assigned to suggest the proposed Cys-turn feature." 198 matched cddid_all.tbl CDD NF033948 NF033948 468260 AcrIIA3_fam anti-CRISPR protein AcrIIA3. AcrIIA3, as found in siphophages infecting Listeria and Streptococcus, is an anti-CRISPR protein that prevents Cas9-containing CRISPR systems from protecting against phage infection. 119 matched cddid_all.tbl CDD NF033949 NF033949 468261 Cas12b type V CRISPR-associated protein Cas12b. 1187 matched cddid_all.tbl CDD NF033950 NF033950 439422 Cas12c type V CRISPR-associated protein Cas12c. 1246 matched cddid_all.tbl CDD NF033951 NF033951 468262 Cas12d type V CRISPR-associated protein Cas12d. 1118 matched cddid_all.tbl CDD NF033952 NF033952 411508 AcrID1_fam AcrID1 family anti-CRISPR protein. The AcrID1 family of anti-CRISPR proteins occurs in virus infecting the Archaea, primarily Sulfolobus. It targets and inactivates type I-D CRISPR-Cas systems. 93 matched cddid_all.tbl CDD NF033953 NF033953 411509 AcrF10_fam AcrF10 family anti-CRISPR protein. Members of the AcrF10 family of anti-CRISPR proteins have been found in phage from various Vibrio, Shewanella, and their relatives. AcrF10 is considered a DNA mimic protein. 94 matched cddid_all.tbl CDD NF035921 NF035921 468263 staph_coagu staphylocoagulase. Past residue 485, the protein consists of a variable number of 27-amino acid tandem repeats (see PF04022). This HMM omits coverage of a portion of the repetitive C-terminal region. 520 matched cddid_all.tbl CDD NF035922 NF035922 411511 Trp_DH_ScyB tryptophan dehydrogenase ScyB. The tryptophan dehydrogenase (EC 1.4.1.19) ScyB performs a reversible NAD(+)-dependent deamination of L-Trp to 3-indolepyruvate. ScyB occurs in Cyanobacteria that biosynthesize scytonemin, a natural sunscreen, from tryptophan. 346 matched cddid_all.tbl CDD NF035923 NF035923 468264 TPP_ScyA scytonemin biosynthesis protein ScyA. This HMM distinguishes ScyA itself, found within the ScyABCDEF operon, from closely related paralogous TPP-binding ScyA-related proteins encoded outside the operon. 623 matched cddid_all.tbl CDD NF035924 NF035924 411513 scytonem_ScyC scytonemin biosynthesis cyclase/decarboxylase ScyC. Of the various markers of scytonemin biosynthesis, ScyC appears to be the clearest, as there are few or no close homologs from outside of the set of confidently predicted scytonemin producer bacteria. 312 matched cddid_all.tbl CDD NF035925 NF035925 468265 Geo26A_fam geobacillin-26 family protein. 197 matched cddid_all.tbl CDD NF035926 NF035926 411515 scyF_NHL_VPEP scytonemin biosynthesis PEP-CTERM protein ScyF. ScyF has multiple tandem copies of the NHL repeat, making it a beta-propellar protein. It has an N-terminal signal peptide, and a C-terminal PEP-CTERM domain for recognition and cleavage by exosortase, suggesting that ScyF is sorted to an extracellular location, perhaps the outer leaflet of the outer membrane, and attached there covalently. 376 matched cddid_all.tbl CDD NF035927 NF035927 411516 TPP_ScyA_rel ScyA-related TPP-binding enzyme. Members of this family are not ScyA itself, which is described in TPP_ScyA (NF035923), but instead are closely related paralogs that are likewise restricted to the Cyanobacteria. Nostoc punctiforme, for example, has ScyA itself, but also has three members of this family, all more closely related to each other than to ScyA. By homology, members of this family are expected to be thiamine pyrophosphate-binding enzymes. 551 matched cddid_all.tbl CDD NF035928 NF035928 411517 holin_1 bacteriophage holin. Holins form transmembrane pores for releasing endolysins that hydrolyze the cell wall and induce cell death. 117 matched cddid_all.tbl CDD NF035929 NF035929 468266 lectin_1 lectin. Lectins are important adhesin proteins, which bind carbohydrate structures on host cell surface. The carbohydrate specificity of diverse lectins to a large extent dictates bacteria tissue tropism by mediating specific attachment to unique host sites expressing the corresponding carbohydrate receptor. 837 matched cddid_all.tbl CDD NF035930 NF035930 468267 lectin_2 lectin. Lectins are important adhesin proteins, which bind carbohydrate structures on host cell surface. The carbohydrate specificity of diverse lectins to a large extent dictates bacteria tissue tropism by mediating specific attachment to unique host sites expressing the corresponding carbohydrate receptor. 238 matched cddid_all.tbl CDD NF035931 NF035931 411520 lectin_3 lectin. Lectins are important adhesin proteins, which bind carbohydrate structures on host cell surface. The carbohydrate specificity of diverse lectins to a large extent dictates bacteria tissue tropism by mediating specific attachment to unique host sites expressing the corresponding carbohydrate receptor. 226 matched cddid_all.tbl CDD NF035932 NF035932 468268 lectin_4 lectin. Lectins are important adhesin proteins, which bind carbohydrate structures on host cell surface. The carbohydrate specificity of diverse lectins to a large extent dictates bacteria tissue tropism by mediating specific attachment to unique host sites expressing the corresponding carbohydrate receptor. 318 matched cddid_all.tbl CDD NF035933 NF035933 468269 ESAT6_1 pore-forming ESAT-6 family protein. 107 matched cddid_all.tbl CDD NF035934 NF035934 411523 ESAT6_2 pore-forming ESAT-6 family protein. 96 matched cddid_all.tbl CDD NF035935 NF035935 411524 ESAT6_3 pore-forming ESAT-6 family protein. 98 matched cddid_all.tbl CDD NF035936 NF035936 468270 agg_sub_LPXTH serine-rich aggregation substance UasX. Members of this protein family are repetitive, serine-rich surface proteins of the Firmicutes, found primarily in the genus Leuconostoc. The variant form of sortase signal, LPXTH, is replaced by LPXTG in members from some lineages, such as Weissella oryzae, and therefore recognizable. Some members of this family have the KxYKxGKxW type signal peptide as seen in the glycoprotein adhesin GspB, a substrate of the accessory Sec system for secretion. WOSG25_050600 from Weissella oryzae SG25 is identified in a publication as an unnamed aggregation substance, a conclusion supported by the sorting signals and composition reported here. We assign the gene symbol uasX (unnamed aggregation substance X) based on our evaluation of the family. 281 matched cddid_all.tbl CDD NF035937 NF035937 411526 EboA_family EboA family metabolite traffic protein. This HMM describes a narrow, cyanobacterial-only clade of members of the EboA (eustigmatophyte/bacterial operon A) family. Members of this family appear required for transport of certain secondary metabolite precursors to the periplasm, including (but not limited) to precursors of scytonemin. More than half the members of this clade belong to scytonemin producers. 219 matched cddid_all.tbl CDD NF035938 NF035938 468271 EboA_domain EboA domain-containing protein. EboA (eustigmatophyte/bacterial operon A) belongs to a broadly distributed system of six proteins. The ebo system in general appears to involved in trafficking certain of certain natural product precursors whose biosynthesis requires export at least as far as the periplasm. Scytonemin is an example of one natural product whose biosynthesis requires an Ebo system. 141 matched cddid_all.tbl CDD NF035939 NF035939 468272 TIM_EboE metabolite traffic protein EboE. EboE (eustigmatophyte/bacterial operon E) belongs to the TIM barrel fold superfamily by homology, as shown by Pfam model PF01261. Although its exact function is unknown, EboE is encoded as part of a widely distributed system that appears to allow export of precursor metabolites of various secondary metabolites so that biosynthesis can be completed outside of the cytosol. 375 matched cddid_all.tbl CDD NF035940 NF035940 468273 prenyl_rel_EboC UbiA-like protein EboC. 292 matched cddid_all.tbl CDD NF035941 NF035941 411530 GBS_alph_likeN alpha-like surface protein N-terminal domain. Most Group B Streptococcus (GBS) have a member of a mosaic family of repetitive surface protein. The founding member is the alpha C protein (bca), but other named members with complete sequences include Alp2, Alp3, and Rib. This HMM describes the shared, non-repetitive N-terminal region, including a YSIRK-like signal peptide region. 225 matched cddid_all.tbl CDD NF035942 NF035942 411531 T3SS_eff_HopBF1 T3SS effector protein kinase HopBF1. HopBF1, found in plant pathogens such as Pseudomonas syringae and in the human pathogen Ewingella americana, it a type III secretion system effector that acts as a protein kinase. It phosphorylates the eukaryotic chaperone HSP90 on a serine residue, inhibiting its ATPase activity. The inhibition interferes with the proper folding of client proteins of HSP90 that are important to resistance to bacterial infection. 200 matched cddid_all.tbl CDD NF035943 NF035943 411532 exosort_XrtV exosortase V. 262 matched cddid_all.tbl CDD NF035944 NF035944 411533 PEPxxWA-CTERM PEPxxWA-CTERM sorting domain. This variant form of PEP-CTERM sorting signal shows unusually strong conservation across much of the hydrophobic transmembrane segment, including an unusual Trp (W) residue at position 6 of the seed alignment. The Trp is replaced by Tyr (Y) in a number of proteins hit by the HMM. The top-scoring members of this family tend to occur in Sphingomonas and related genera, encoded by genomes that also encode the sorting enzyme XrtV (exosortase V). 24 matched cddid_all.tbl CDD NF035945 NF035945 468274 Zn_serralysin serralysin family metalloprotease. 457 matched cddid_all.tbl CDD NF035950 NF035950 468275 RumC_sactiRiPP RumC family sactipeptide. The founding member of this family of radical SAM/SPASM-modified sactipeptide bacteriocins is ruminococcin C1, AEC03333.1 from Ruminococcus gnavus. This bacteriocin, from a human gut bacterium, is interesting because of its anti-clostridial activity. Known homologs to RumC1 average about 65 amino acids in length and have four invariant Cys residues. 63 matched cddid_all.tbl CDD NF035951 NF035951 411536 rSAM_RumMC RumMC family radical SAM sactipeptide maturase. The RumMC family of radical SAM/SPASM domain peptide modification enzymes creates sulfur-to-alpha-carbon (sactipeptide) linages in RiPP peptide natural products in the family of ruminococcin C. 510 matched cddid_all.tbl CDD NF035952 NF035952 468276 WxPxxD_TM WxPxxD family membrane protein. This uncommon, extremely hydrophobic protein of about 240 amino acids occurs sporadically in members of the Firmicutes, including the Listeria, Bacillus, Anoxybacillus, and Terribacillus genera. The protein is named for its most distinctive motif. The function is unknown, but the size and hydrophobicity suggests a transport-related function. 234 matched cddid_all.tbl CDD NF035953 NF035953 468277 integrity_Cei envelope integrity protein Cei. Cei (cell envelope integrity), as described for the founding member Rv2700 from Mycobacterium tuberculosis, is a transmembrane protein with an extracellular LytR_C domain. It lacks any DNA-binding domain and is not a transcriptional regulator. It shares homology to C-terminal regions present in some members of the LytR-CpsA-Psr family, a family in which some characterized members transfer teichoic acids to from carriers to mature peptidoglycan. 211 matched cddid_all.tbl CDD NF035954 NF035954 411539 ocin_CA_C0660 CA_C0660 family putative sactipeptide bacteriocin. Members of this family are Cys-rich peptides about 65 amino acids in length, regularly found in the vicinity of the radical SAM/SPASM domain enzymes. The most closely related such radical SAM enzyme is the RiPP modification enzyme that introduces sulfur-to-alpha-carbon peptide (sactipeptide) modification in ruminococcin C, whose precursor is very similar in length and in Cys content and arrangement. 64 matched cddid_all.tbl CDD NF037932 NF037932 411540 ocin_sys_WGxF bacteriocin-like WGxF protein. Members of this protein family of hydrophobic proteins about 60 amino acids long are found various members of the Firmicutes in three-gene contexts that suggest a role as a bacteriocin or an immunity protein. The protein is named for its most striking sequence feature, a nearly invariant WGxF motif. The two conserved neighboring families are TIGR01654-like (e.g. WP_149116529.1) and TIGR03608-like (e.g. WP_149116530.1). 59 matched cddid_all.tbl CDD NF037933 NF037933 468278 EpaQ_fam EpaQ family protein. EpaQ, as described in the Gram-positive bacterium Enterococcus faecalis, is encoded with the enterococcal polysaccharide antigen (epa) operon. It is distantly related to some O-antigen ligases of Gram-negative bacteria, and may have a similar molecular function. EpaQ contributes to biofilm formation and resistance to certain antibiotics. 377 matched cddid_all.tbl CDD NF037934 NF037934 468279 holdfast_HfaA holdfast anchoring protein HfaA. 115 matched cddid_all.tbl CDD NF037935 NF037935 411543 holdfast_HfaB holdfast anchoring protein HfaB. HfaB, part of the holdfast anchoring complex of Caulobacter and related bacteria, is a homolog of the outer membrane protein CsgG of curli biogenesis. 264 matched cddid_all.tbl CDD NF037936 NF037936 468280 holdfast_HfaD holdfast anchor protein HfaD. 373 matched cddid_all.tbl CDD NF037937 NF037937 468281 septum_RefZ forespore capture DNA-binding protein RefZ. RefZ (regulator of FtsZ), a DNA-binding protein in the family of TetR/AcrR family transcriptional regulators, participates in septum placement and in chromosome capture during the asymmetrical cell division in endospore formation. The five nearly palindromic DNA motifs (RBMs) to which RefZ binds affect chromosomal localization, not transcription, so RefZ is not considered a transcription factor. 195 matched cddid_all.tbl CDD NF037938 NF037938 411546 Myr_Ysa_major MyfA/PsaA family fimbrial adhesin. The related adhesins MyfA and PsaA are fimbrial major subunits of Myf fimbriae from Yersinia enterocolitica, and Psa (also known as pH6 antigen) fimbriae from Y. pestis. 158 matched cddid_all.tbl CDD NF037940 NF037940 468282 PKS_MbtD mycobactin polyketide synthase MbtD. 973 matched cddid_all.tbl CDD NF037941 NF037941 468283 PKS_NbtC nocobactin polyketide synthase NbtC. 1026 matched cddid_all.tbl CDD NF037942 NF037942 411549 ac_ACP_DH_MbtN mycobactin biosynthesis acyl-ACP dehydrogenase MbtN. MbtN belongs to a family of dehydrogenases that in most cases act on acyl groups carried on CoA. However, MbtN appears to act on an acyl group carried instead on the mycobactin biosynthesis acyl carrier protein MbtL. 376 matched cddid_all.tbl CDD NF037944 NF037944 411550 holin_2 bacteriophage holin. Proteins of this family are homologs of the mycobacterial phage holin Gp29. They can cause host cell lysis to release progeny phage particles. 64 matched cddid_all.tbl CDD NF037945 NF037945 411551 holin_3 bacteriophage holin. Bacteriophage holin can cause host cell lysis to release progeny phage particles. Proteins of this family have about 60 amino acids, and a transmembrane domain is usually found on the C-terminal. 37 matched cddid_all.tbl CDD NF037946 NF037946 468284 terminal_TopJ terminal organelle assembly protein TopJ. 440 matched cddid_all.tbl CDD NF037947 NF037947 411553 holin_4 bacteriophage holin. Bacteriophage holin can cause host cell lysis to release progeny phage particles. Proteins of this family usually have two transmembrane domains. 75 matched cddid_all.tbl CDD NF037948 NF037948 468285 signal_int_SinM signal integration modulator SinM. SinM (signal integration modulator) is a regulatory partner of the hybrid histidine kinase/response regulator SinK (signal integrating kinase). 387 matched cddid_all.tbl CDD NF037949 NF037949 411555 holin_5 bacteriophage holin. Proteins of this family can cause host cell lysis to release progeny phage particles. 64 matched cddid_all.tbl CDD NF037950 NF037950 411556 spanin2_1 bacteriophage spanin2 family protein. A number of bacteriophage proteins cause lysis of host cells. Holins and endolysins induce the disruption of inner membrane by degrading peptidoglycans. Then, spanin2 family proteins are involved in the final step in host cell lysis by disrupting the outer membrane. 130 matched cddid_all.tbl CDD NF037951 NF037951 411557 spanin2_2 bacteriophage spanin2 family protein. A number of bacteriophage proteins cause lysis of host cells. Holins and endolysins induce the disruption of inner membrane by degrading peptidoglycans. Then, spanin2 family proteins are involved in the final step in host cell lysis by disrupting the outer membrane. 107 matched cddid_all.tbl CDD NF037952 NF037952 468286 spanin2_3 bacteriophage spanin2 family protein. A number of bacteriophage proteins cause lysis of host cells. Holins and endolysins induce the disruption of inner membrane by degrading peptidoglycans. Then, spanin2 family proteins are involved in the final step in host cell lysis by disrupting the outer membrane. 98 matched cddid_all.tbl CDD NF037953 NF037953 468287 frad septal junction protein FraD. Proteins of this family are components of cyanobacterial septal junctions (microplasmodesmata) in heterocyst-forming cyanobacteria. 305 matched cddid_all.tbl CDD NF037954 NF037954 468288 het_cyst_PatD heterocyst frequency control protein PatD. 116 matched cddid_all.tbl CDD NF037955 NF037955 411561 mfs MFS transporter. 366 matched cddid_all.tbl CDD NF037957 NF037957 411562 freyrasin_like freyrasin family ranthipeptide. A ranthipeptide is a ribosomally synthesized and post-translationally modified peptide (RiPP) whose linkages from cysteine sulfur atoms are to something besides the alpha carbons of other amino acids. Thus, ranthipeptides differ from sactipeptides (sulfur-to-alpha carbon RiPP peptides). The founding member of this family is freyrasin itself, the PapA protein from Paenibacillus polymyxa (see SUA72395.1). All members so far are encoded next to radical SAM peptide maturases. 49 matched cddid_all.tbl CDD NF037958 NF037958 468289 QH_gamma quinohemoprotein amine dehydrogenase subunit gamma. 100 matched cddid_all.tbl CDD NF037959 NF037959 468290 MFS_SpdSyn fused MFS/spermidine synthase. Proteins of this family are fusion of a N-terminal MFS (Major Facilitator Superfamily) transporter domain and a C-terminal spermidine synthase (SpdSyn)-like domain. The encoding genes usually near the genes encoding S-adenosylmethionine decarboxylase (AdoMetDC) on many bacterial genomes. It has been shown in Shewanella oneidensis that the fused protein aminopropylates a substrate other than putrescine, and has a role outside of polyamine biosynthesis. 480 matched cddid_all.tbl CDD NF037960 NF037960 468291 MFS_trans MFS transporter. 382 matched cddid_all.tbl CDD NF037961 NF037961 411566 RodA_shape rod shape-determining protein RodA. Proteins of this family are members of the FtsW/RodA/SpoVE superfamily. It has been reported that RodA proteins play important roles in maintaining cell shape and antibiotic resistance in bacteria. 415 matched cddid_all.tbl CDD NF037962 NF037962 468292 arsenic_eff arsenic efflux protein. Most proteins of this family have 8 transmembrane domains with two 4 transmembrane halves separated by a hydrophilic loop of variable sizes. It has been reported that some proteins of this family are involved in arsenate/arsenite resistance. 286 matched cddid_all.tbl CDD NF037963 NF037963 468293 heterocyst_HetZ heterocyst differentiation protein HetZ. The HMM distinguishes HetZ itself, a heterocyst differentiation protein, from a closely related paralog. 366 matched cddid_all.tbl CDD NF037964 NF037964 411569 HetZ_related HetZ-related protein. Members of this cyanobacterial protein family are paralogs of the heterocyst differentiation protein HetZ and occur in largely the same set of genomes. 370 matched cddid_all.tbl CDD NF037965 NF037965 411570 HetZ_rel_2 HetZ-related protein 2. Members of this family are cyanobacterial proteins distantly related to heterocyst differentiation protein HetZ, which also has a much more closely related set of paralogs in heterocyst-forming species. 367 matched cddid_all.tbl CDD NF037966 NF037966 468294 HetP_family HetP family heterocyst commitment protein. HetP and its paralogs occur in heterocyst-forming members of the Cyanobacteria, and play a role in commitment to development into heterocysts, which specialize in nitrogen fixation rather than photosynthesis. 63 matched cddid_all.tbl CDD NF037967 NF037967 411572 SemiSWEET_1 SemiSWEET transporter. The SWEET (Sugars Will Eventually be Exported Transporter) is a superfamily of sugar transporters found in both eukaryotes and prokaryotes. Eukaryotic SWEETs usually have seven transmembrane helices (TMHs), but most prokaryotic SWEETs (SemiSWEETs) have only three TMHs. Proteins of this family have 7 TMHs. 196 matched cddid_all.tbl CDD NF037968 NF037968 411573 SemiSWEET_2 SemiSWEET transporter. The SWEET (Sugars Will Eventually be Exported Transporter) is a superfamily of sugar transporters found in both eukaryotes and prokaryotes. Eukaryotic SWEETs usually have seven transmembrane helices (TMHs), but most prokaryotic SWEETs (SemiSWEETs) have only three TMHs. Proteins of this family have 3 TMHs. 76 matched cddid_all.tbl CDD NF037969 NF037969 411574 SemiSWEET_3 SemiSWEET transporter. The SWEET (Sugars Will Eventually be Exported Transporter) is a superfamily of sugar transporters found in both eukaryotes and prokaryotes. Eukaryotic SWEETs usually have seven transmembrane helices (TMHs), but most prokaryotic SWEETs (SemiSWEETs) have only three TMHs. Proteins of this family have 3 TMHs. 97 matched cddid_all.tbl CDD NF037970 NF037970 468295 vanZ_1 VanZ family protein. VanZ was originally identified in Enterococcus faecium. VanZ increases teicoplanin resistance in Enterococcus faecium, but has no impact on vancomycin resistance. Proteins of this family are homologs of the VanZ protein. They may be involved in teicoplanin resistance. 107 matched cddid_all.tbl CDD NF037971 NF037971 411576 lipo_BcpO CDI system lipoprotein BcpO. BcpO is a small lipoprotein, about 74 amino acids long on average, encoded in Burkholderia bcpAIOB locus systems for two-partner secretion and contact dependent growth inhibition. 66 matched cddid_all.tbl CDD NF037972 NF037972 411577 HuaA_fam_RiPP huazacin family RiPP peptide. 40 matched cddid_all.tbl CDD NF037974 NF037974 468296 SslE_AcfD_Zn_LP SslE/AcfD family lipoprotein zinc metalloprotease. Members of this family are surface lipoprotein zinc metalloproteases, from the family that includes accessory colonization factor AcfD from Vibrio cholerae, SslE (YghJ ) from E. coli (Secreted and Surface-associated Lipoprotein from E. coli), and VPA1376 from Vibrio parahaemolyticus. Each is about 1500 amino acids long, and SslE is a known substrate of a type II secretion system (T2SS). SslE is known to have mucinase activity. 1389 matched cddid_all.tbl CDD NF037975 NF037975 411579 pilot_rel_YacC YacC family pilotin-like protein. Members of this, including YacC from Escherichia coli K-12, resemble the lipoprotein GspS of type II secretion systems (T2SS), but in general are not lipoproteins. In E. coli K-12, where the T2SS is cryptic (not expressed, but able to function after manipulation to force its express), YacC is encoded far from the locus where the main set of T2SS genes are found, and it is not clear that YacC is a true GspS. 115 matched cddid_all.tbl CDD NF037976 NF037976 411580 gtrA_1 GtrA family protein. The GtrA family proteins have 3-4 transmembrane domains. They are involved in translocation of lipid-linked glucose across the cytoplasmic membrane. 126 matched cddid_all.tbl CDD NF037977 NF037977 411581 Lpg0189_fam Lpg0189 family type II secretion system effector. 279 matched cddid_all.tbl CDD NF037978 NF037978 468297 T2SS_GspB type II secretion system assembly factor GspB. GspB (general secretory pathway B) occurs in type II secretion systems (T2SS) and is viewed as an accessory protein, a factor involved in the assembly process rather than integral to the completed T2SS apparatus. 158 matched cddid_all.tbl CDD NF037979 NF037979 468298 Na_transp sodium-dependent transporter. 417 matched cddid_all.tbl CDD NF037980 NF037980 468299 T2SS_GspK type II secretion system minor pseudopilin GspK. 311 matched cddid_all.tbl CDD NF037981 NF037981 468300 NCS2_1 purine/pyrimidine permease. Proteins of this family usually have 14 transmembrane domains. They belong to the NSC2 superfamily transporters. They are specific purine and/or pyrimidine permeases. 419 matched cddid_all.tbl CDD NF037982 NF037982 468301 Nramp_1 Nramp family divalent metal transporter. Nramp (natural resistance-associated macrophage protein) family divalent metal transporters are widely conserved divalent metal transporters, which enables manganese import in bacteria and dietary iron uptake in mammals. 404 matched cddid_all.tbl CDD NF037993 NF037993 468302 cyano_chori_ly cyanobacterial-type chorismate lyase. This variant form of chorismate lyase is widespread in the cyanobacteria, including founding example sll1797 from Synechocystis sp. PCC6803. Previously, members of this family were named DUF98 domain-containing protein, as found by Pfam model PF01947. The product, 4-hydroxybenzoate, is next prenylated by slr0926, during plastoquinone biosynthesis. 176 matched cddid_all.tbl CDD NF037994 NF037994 468303 DcuC_1 C4-dicarboxylate transporter DcuC. Proteins of this family usually have 11-12 transmembrane regions. They transport C4-dicarboxylates under anaerobic conditions, which plays an important role in anaerobic energy metabolism. 414 matched cddid_all.tbl CDD NF037995 NF037995 468304 TRAP_S1 TRAP transporter substrate-binding protein DctP. Proteins of this family are members of the superfamily of Tripartite ATP-independent Periplasmic Transporter (TRAP-T). They transport hydrophobic substrates, usually lipoprotein. 271 matched cddid_all.tbl CDD NF037996 NF037996 468305 B-4DMT B-4DMT family transporter. 139 matched cddid_all.tbl CDD NF037997 NF037997 411591 Na_Pi_symport Na/Pi symporter. Proteins of this family belong to the Phosphate:Na+ Symporter (PNaS) superfamily. 294 matched cddid_all.tbl CDD NF037998 NF037998 468306 RND_1 protein translocase SecDF, variant type. Members of this family are identified by TCDB as belonging to 2.A.6.4.4, a variant 12-TM type SecDF, as found in Spiroplasma, Mesoplasma, and Acholeplasma. 1237 matched cddid_all.tbl CDD NF037999 NF037999 411593 mutacin lantibiotic mutacin. Mutacins are lantibiotics in the epidermin/gallidermin/nisin family, found in the biofilm-forming dental caries pathogen Streptococcus mutans. Named members of the family include mutacin I and mutacin 1140. This HMM separates the mutacins (MutA) from paralog MutA' encoded nearby, which lacks mutacin activity. 63 matched cddid_all.tbl CDD NF038000 NF038000 411594 mutacin_prime mutacin-like lanthipeptide. MutA', a paralog of the nisin-like lantibiotic mutacin precursor MutA, is a lanthipeptide of unknown function, encoded in Streptococcus mutans within the same region. It is not required for mutacin function. 64 matched cddid_all.tbl CDD NF038001 NF038001 468307 HYExAFE HYExAFE family protein. This uncharacterized protein is named for its best conserved region, the motif HY[ED]xAFE, found near the N-terminus. It appears to limited in taxonomic range to members of the Planctomycetes. 164 matched cddid_all.tbl CDD NF038002 NF038002 468308 bifunc_CbiS bifunctional adenosylcobinamide hydrolase/alpha-ribazole phosphatase CbiS. 333 matched cddid_all.tbl CDD NF038004 NF038004 411597 darobactin_RiPP darobactin family peptide antibiotic. Darobactin, discovered in the genus Photorhabdus, is a peptide antibiotic, made from a ribosomally translated precursor, and modified by the radical SAM/SPASM peptide maturase DarE. Darobactin A is the founding member of a new class of antibiotic that appears to target BamA, a component of the outer membrane beta-barrel assembly machine. It is seven amino acids long, Trp1-Asn2-Trp3-Ser4-Lys5-Ser6-Phe7, with two crosslinks, one from Trp1 to Trp3, the other from Trp3 to Lys5. Homologs of the darobactin A precursor are encoded in various strains of Photorhabdus, Yersinia, and Vibrio. 45 matched cddid_all.tbl CDD NF038005 NF038005 411598 rSAM_mat_DarE darobactin maturation radical SAM/SPASM protein DarE. The radical SAM/SPASM protein DarE is a maturase for the ribosomally translated, post-translationally modified peptide natural product (RiPP) darobactin, including forms A, B, C, D, and E. The mature form is just seven amino acids long, with two cross-links, a Trp1-Trp3 linkage and a Trp3-Lys5 (or Arg5) linkage. 432 matched cddid_all.tbl CDD NF038006 NF038006 439423 NhaD_1 sodium:proton antiporter NhaD. Proteins of this family usually have 10-13 transmembrane regions. They extrudes Na+ or Li+ in exchange for H+. They have been identified and characterized in a number of bacterial species. 405 matched cddid_all.tbl CDD NF038007 NF038007 411600 ABC_ATP_DarD darobactin export ABC transporter ATP-binding protein. 218 matched cddid_all.tbl CDD NF038008 NF038008 468309 ABC_perm_DarB darobactin export ABC transporter permease subunit. 777 matched cddid_all.tbl CDD NF038009 NF038009 468310 TatB_1 twin-arginine translocation system-associated protein. This family is suggested by TCDB to be part of the twin-arginine translocation (TAT) system, but lacks detectable sequence similarity to subunits such as TatB. 70 matched cddid_all.tbl CDD NF038010 NF038010 411603 ABC_adapt_DarC darobactin export ABC transporter periplasmic adaptor subunit. 417 matched cddid_all.tbl CDD NF038011 NF038011 411604 PelF GT4 family glycosyltransferase PelF. Proteins of this family are components of the exopolysaccharide Pel transporter. It has been reported that PelF is a soluble glycosyltransferase that uses UDP-glucose as the substrate for the synthesis of exopolysaccharide Pel, whereas PelG is a Wzx-like and PST family exopolysaccharide transporter. 489 matched cddid_all.tbl CDD NF038012 NF038012 411605 DMT_1 DMT family transporter. Proteins of this family belong to the drug/metabolite transporter (DMT) superfamily. 276 matched cddid_all.tbl CDD NF038013 NF038013 411606 AceTr_1 acetate uptake transporter. Proteins of this family are acetate transporters, which usually have 6 transmembrane regions. The homologue in E. coli is YaaH. 176 matched cddid_all.tbl CDD NF038014 NF038014 468311 Chlamy_inclu_1 inclusion-associated protein. Proteins of this family are inclusion-associated proteins in Chlamydia. It has been shown that protein CPj0783, which is identical to the HMM seed protein WP_010892266, was localized on Chlamydial inclusion. CPj0783 interacted with host Huntingtin-protein14, which may play an important role in disturbing the vesicle transport system to escape host lysosomal or autophagosomal degradation. 236 matched cddid_all.tbl CDD NF038015 NF038015 468312 AztD zinc metallochaperone AztD. Proteins of this family are components of the AztABCD zinc-uptake system. AztC, AztB, and AztA are the extracellular solute-binding protein (SBP), permease, and ATP-binding protein, respectively. AztD is a zinc chaperone to AztC, and it may store zinc in the periplasm for transfer through the AztABCD transporter system. 352 matched cddid_all.tbl CDD NF038016 NF038016 411609 sporang_Gsm sporangiospore maturation cell wall hydrolase GsmA. The peptidoglycan-hydrolyzing enzyme GsmA occurs in some sporangia-forming members of the Actinobacteria, such as Actinoplanes missouriensis, and is required for proper separation of spores. GsmA proteins have one or two SH3 domains N-terminal to the hydrolase domain. 312 matched cddid_all.tbl CDD NF038017 NF038017 411610 ABC_perm1 ABC transporter permease. Proteins of this family are the permease subunit of an ABC transporter complex, which may be involved in tungstate uptake. 184 matched cddid_all.tbl CDD NF038018 NF038018 411611 qmoC quinone-interacting membrane-bound oxidoreductase complex subunit QmoC. Proteins of this family are the transmembrane subunit of the quinone-interacting membrane-bound oxidoreductase complex, which consists of the QmoA, QmoB, and QmoC proteins. It has been reported that the QmoABC complex is essential for efficiently delivering electron to adenosine 5'-phosphosulfate reductase AprAB, which is important in sulfate reduction in sulfate reducing prokaryotes (SRPs). 363 matched cddid_all.tbl CDD NF038019 NF038019 468313 PE_process_PecA PecA family PE domain-processing aspartic protease. PecA from Mycobacterium marinum, and by homology, three related paralogs from Mycobacterium tuberculosis (PE26, PE_PGRS35, and PE_PGRS16) are all PE domain-containing proteins secreted by a type VII secretion system (T7SS, also called ESX in Mycobacterium), and all share a C-terminal aspartic protease-like domain. PecA itself is now known to be a functional aspartic protease that cleaves within the PE domain of T7SS secretion substrates that have the domain, including itself. Members of this family typically contain a long, variable, low-complexity region. This HMM represents the aspartic protease region C-terminal to the low-complexity region. 278 matched cddid_all.tbl CDD NF038020 NF038020 411613 HeR heliorhodopsin HeR. This HMM represents heliorhodopsins, a group of phylogenetically distinct microbial rhodopsins, which play an important role in absorbing and transferring light energy for numerous biological processes in bacteria. Heliorhodopsin was initially identified and characterized in a Gram-positive actinobacterium based on functional metagenomics and photochemical approaches. Heliorhodopsin have seven transmembrane domains, and exhibit similar biological function as microbial rhodopsins. However, heliorhodopsin form a distinct cluster based on phylogenetic analyses. Most microbial rhodopsins are hit by the Pfam HMM PF01036, which does not hit heliorhodopsins. 244 matched cddid_all.tbl CDD NF038021 NF038021 411614 mannan_LmeA mannan chain length control protein LmeA. 264 matched cddid_all.tbl CDD NF038022 NF038022 468314 PorACj_fam PorACj family cell wall channel-forming small protein. Members of this unusual protein family are small (often 40 amino acids or shorter), variable, and detected so far only in the genus Corynebacterium. Despite its small size, the founding member reported to form into homooligomeric channels in the cell wall (not the plasma membrane). This family, as built, may also include PorA subunits of PorA/PorH heterooligomeric cell wall channels. 32 matched cddid_all.tbl CDD NF038023 NF038023 468315 S_layer_PS2 S-layer protein PS2. 499 matched cddid_all.tbl CDD NF038024 NF038024 468316 CRR6_slr1097 CRR6 family NdhI maturation factor. The protein Slr1097 and its functionally equivalent cyanobacterial homologs are required for proper maturation of NdhI, a subunit of NADPH dehydrogenase complexes, so that NDH-1 complexes can assemble properly. The related protein in the model plant species Arabidopsis thaliana is known as CRR6 (chlororespiratory reduction 6). 151 matched cddid_all.tbl CDD NF038025 NF038025 468317 dapto_LiaX daptomycin-sensing surface protein LiaX. LiaX (lipid-II-interacting antibiotics X), as described in Enterococcus faecalis, is expressed under control of the the LiaR response regulator, and is involved in the process of resistance to daptomycin and to antimicrobial peptides of the innate immune response. 513 matched cddid_all.tbl CDD NF038026 NF038026 411619 RsaX20_sORF putative metal homeostasis protein. Members of this family average just 38 amino acids in length, but are widely conserved among species of the Gram-positive genera that include Staphylococcus, Enterococcus, Leuconostoc, and Lactobacillus. Expression of an RNA designated RsaX20, which encodes a member of this family, was studied in a Staphylococcus aureus of possible structural RNAs, and shown to be controlled by Fur-like transcription factor Zur. The broad conservation of the coding region across multiple species and protein-like pattern of amino acid substitutions in multiple sequence alignments strongly suggests that that members of this family are indeed translated into functional proteins. 32 matched cddid_all.tbl CDD NF038027 NF038027 468318 TssQ_fam TssQ family T6SS-associated lipoprotein. The founding member of this protein family, TssQ (BB0812) from Bordetella bronchiseptica, is a lipoprotein, and possibly all other family members are as well. TssQ is encoded within a T6SS locus but its function remains unknown. 100 matched cddid_all.tbl CDD NF038028 NF038028 468319 spiralin_repeat spiralin repeat. The spiralin repeat is a domain that appears once in spiralin (the major lipoprotein of Spiroplasma species) and up to six times in related proteins. 88 matched cddid_all.tbl CDD NF038029 NF038029 411622 LP_plasma lipoprotein signal peptide. This HMM describes one of several homology families that can be found of mutually closely related lipoprotein signal peptides in the Mycoplasmas and closely related genera (Mesoplasma, Spiroplasma), but absent outside that taxonomic group. Member proteins include spiralin, the most abundant lipoprotein in Spiroplasma. 24 matched cddid_all.tbl CDD NF038030 NF038030 468320 spiralin_LP spiralin lipoprotein. Spiralin is the major lipoprotein in multiple species of Spiroplasma, a relative of the Mycoplasmas. 239 matched cddid_all.tbl CDD NF038031 NF038031 411624 PavB_Nterm PavB family adhesin N-terminal domain. This HMM describes the portion of PavB from Streptococcus pneumoniae, and closely related proteins from Streptococcus mitis and Streptococcus pseudopneumoniae, N-terminal to the repetitive region with variable numbers of SSURE (Streptococcal Surface REpeats) regions (see PF11966), which bind fibronectin. The PavB region is notable, in part, for its rare variant, WSIRR, of the YSIRK motif signal peptide. Full-length versions of proteins from this family have a C-terminal LPXTG-containing region for sortase-mediated anchoring to the cell wall. 128 matched cddid_all.tbl CDD NF038032 NF038032 468321 CehA_McbA_metalo CehA/McbA family metallohydrolase domain. This domain, a branch of the PHP superfamily, is found in several partially characterized metallohydrolases, including McbA and CehA. Both were studied as hydrolases of carbaryl, a xenobiotic compound that does not contain a phosphate group, suggesting that presuming members of this family to be phosphoesterases (like many PHP domain-containing proteins) may be incorrect. 315 matched cddid_all.tbl CDD NF038033 NF038033 411626 FEA1_rel_lipo FEA1-related lipoprotein. 406 matched cddid_all.tbl CDD NF038034 NF038034 411627 lactGbeta_entB lactococcin G-beta/enterocin 1071B family bacteriocin. This HMM was built to improve on Pfam model PF11632, which in version PF11632.8 had a two-member seed. It includes 12 residues of leader peptide and GlyGly cleavage motif (see TIGR01847), and has a shorter but more broadly conserved core peptide region. Characterized member proteins include lactococcin G and enterocin 1071B. 38 matched cddid_all.tbl CDD NF038035 NF038035 411628 lactGalph_entA lactococcin G-alpha/enterocin 1071A family bacteriocin. 34 matched cddid_all.tbl CDD NF038036 NF038036 411629 TCP11_Legionella TCP11-related protein. 927 matched cddid_all.tbl CDD NF038037 NF038037 411630 cytob_DsrM sulfate reduction electron transfer complex DsrMKJOP subunit DsrM. Proteins of this family are the DsrM subunit of the DsrMKJOP complex, which is a membrane-bound redox complex involved in sulfate reduction in Sulfate-reducing organisms (SROs). The dsrM gene encodes a cytochrome b reductase, which usually has six transmembrane helices and five conserved histidines. 320 matched cddid_all.tbl CDD NF038038 NF038038 468322 cytoc_DsrJ sulfate reduction electron transfer complex DsrMKJOP subunit DsrJ. Proteins of this family are the DsrJ subunit of the DsrMKJOP complex, which is a membrane-bound redox complex involved in sulfate reduction in Sulfate-reducing organisms (SROs). The dsrJ gene encodes a triheme periplasmic cytochrome c subunit, which contains three conserved heme c-binding sites (CXXCH) at the C terminal. 119 matched cddid_all.tbl CDD NF038039 NF038039 411632 WGxxGxxG-CTERM WGxxGxxG-CTERM domain. This domain, a possible protein-sorting signal, begins with the motif that usually takes the form DWGW, followed by a hydrophobic (and probably membrane-spanning) stretch xGxxGxxGxxG (where x is hydrophobic), and then a short patch of mostly basic residues at the C-terminus. This domain has a broad taxonomic range that includes Firmicutes, Cyanobacteria, and Deinococcus. Members from the Firmicutes tend to occur together with a DUF3231 (PF11553) family protein. 19 matched cddid_all.tbl CDD NF038040 NF038040 411633 phero_PhrK_fam PhrK family phosphatase-inhibitory pheromone. 40 matched cddid_all.tbl CDD NF038041 NF038041 468323 fim_Mfa1_fam Mfa1 family fimbria major subunit. 483 matched cddid_all.tbl CDD NF038042 NF038042 468324 actinodefensin actinodefensin. The actinodefensin family is named (here) as an Actinomyces-specific branch of the (otherwise eukaryotic) arthropod defensin family described by Pfam model PF01097. 70 matched cddid_all.tbl CDD NF038043 NF038043 411636 act_def_assoc_A actinodefensin-associated protein A. Actinodefensin (see family NF038042) is a bacterial branch of the arthropod defensin family. Members of that family occur in the Actinomyes lineage, have a distinctive N-terminal region that may reflect how processing and transport occur, and are found in a conserved gene neighborhood. Actinodefensin-associated protein A is found exclusively in these conserved gene neighborhoods. 379 matched cddid_all.tbl CDD NF038044 NF038044 411637 act_def_assoc_B actinodefensin-associated protein B. Members of this family are small proteins, averaging about 70 amino acids in length, restricted to the Actinomycetes. Member proteins typically occur in the vicinity of actinodefensin, which represents and Actinomycetes-restricted branch of the arthropod defensin family. The function of this protein is unknown. 63 matched cddid_all.tbl CDD NF038045 NF038045 468325 GEF_RalF T4SS guanine nucleotide exchange effector RalF. 341 matched cddid_all.tbl CDD NF038047 NF038047 468326 not_Tcp10 AAWKG family protein. Members of this family are found primarily in Streptomyces. The family is notable in part because a region outside of the N-terminal region modeled here contains 9-residue repeats that resemble the 18-residue repeats found by PF07202 in the C-terminal region of eukaryotic T-complex protein 10. The family is uncharacterized. This model was constructed, and named for family's most prominent motif, AAWKG, to head off any possible confusion with Tcp10. 398 matched cddid_all.tbl CDD NF038048 NF038048 411640 DIP1984_fam DIP1984 family protein. Members of this family, including the Corynebacterium diphtheriae protein DIP1984, which has a solved crystal structure, are uncharacterized with respect to function. Some members of this family previously have been annotated, incorrectly, as septolysin. This model was constructed to overrule and correct such errors. Note that septolysin O, and other members of the family of cholesterol-dependent cytolysins such as listeriolysin O (WP_003722731.1), are unrelated. 149 matched cddid_all.tbl CDD NF038049 NF038049 411641 SelD_rel_HyperS SelD-related putative sulfur metabolism protein. 465 matched cddid_all.tbl CDD NF038050 NF038050 411642 NrtS nitrate/nitrite transporter NrtS. NrtS family proteins were first identified and characterized in Synechococcus sp. PCC 7002. The homologous proteins NrtS1 and NrtS2 are encoded by two neighboring genes on Synechococcus sp. PCC 7002 genome. The heteromeric transporter was shown to transport nitrite as well as nitrate. This HMM hits both NrtS1 and NrtS2 proteins, which have extremely high sequence identity and conserved motifs. 56 matched cddid_all.tbl CDD NF038051 NF038051 411643 MamC magnetosome protein MamC. Magnetosomes are membrane-enclosed organelles containing crystals of magnetite (Fe3O4) that cause magnetotactic bacteria to orient in magnetic fields. MamC interacts with the magnetite surface and affect the size and shape of the growing crystal. 97 matched cddid_all.tbl CDD NF038052 NF038052 468327 histone_lik_HC2 histone H1-like DNA-binding protein Hc2. This model describes highly repetitive, Lys and Arg-rich histone H1-like protein Hc2, as found in the genus Chlamydia. 201 matched cddid_all.tbl CDD NF038053 NF038053 468328 hist_H1_lk_Burk histone H1-like DNA-binding protein. This model describes histone H1-like repetitive basic proteins as found in Burkholderia and related species. It excludes the Hc2 family found in Chlamydia and involved in DNA condensation for the formation of elementary bodies. 192 matched cddid_all.tbl CDD NF038054 NF038054 411646 T3SS_SctI type III secretion system inner rod subunit SctI. This model describes protein SctI (Secretion and Cellular Translocation I), an inner rod protein in the basal body of the type III secretion system (T3SS) as found in many pathogenic bacteria. SctI has some sequence similarity to the needle filament protein SctF. Lineage-specific names for SctI in various bacteria include BsaK, PrgJ, and MxiI. 76 matched cddid_all.tbl CDD NF038055 NF038055 411647 T3SS_SctB_pilot type III secretion system translocon subunit SctB. One SctB and four SctE subunits, located at the tip of the type III secretion system (T3SS) injectosome, combine to form the translocon (translocator pore) in the membrane of targeted cells. Species-specific names for this highly variable component of T3SS include YopD, EspB, IpaC, SipC, etc. 311 matched cddid_all.tbl CDD NF038058 NF038058 468329 adhes_P110_Nter P110/LppT family adhesin N-terminal domain. Members of this family include the multifunctional adhesin P110 (as the name is used in Mycoplasma hyopneumoniae, not Mycoplasma genitalium) and homologs presumed also to be adhesins. Homologs include LppT (lipoprotein T), which despite its name seems to lack the signal peptide region Cys residue required for conversion into a lipoprotein, and paralogs MHP683 and MHP684 from Mycoplasma hyopneumoniae. 202 matched cddid_all.tbl CDD NF038065 NF038065 411649 Pr6Pr Pr6Pr family membrane protein. This family is defined by TCDB as prokaryotic 6 TMS (Pr6Pr) family membrane protein(http://www.tcdb.org/search/result.php?tc=9.b.302). The function of this family proteins is not understood. 162 matched cddid_all.tbl CDD NF038066 NF038066 468330 MptB polyprenol phosphomannose-dependent alpha 1,6 mannosyltransferase MptB. Proteins of this family are Involved in the initiation of core alpha-(1,6) mannan biosynthesis of lipomannan (LM-A) and multi-mannosylated polymer (LM-B), extending triacylatedphosphatidyl-myo-inositol dimannoside (Ac1PIM2) and mannosylated glycolipid, 1,2-di-O-C16/C18:1-(alpha-D-mannopyranosyl)-(1->4)-(alpha-D-glucopyranosyluronic acid)-(1->3)-glycerol (Man1GlcAGroAc2), respectively. 554 matched cddid_all.tbl CDD NF038067 NF038067 411651 OMP_CarO ornithine uptake porin CarO. The outer membrane porin CarO (carbapenem resistance-associated outer membrane protein), found in Acinetobacter, is of clinical interest because of its role in allowing entry of carbapenem antibiotics and its variability from strain to strain. CarO should not be confused with Omp33-36, an essentially unrelated outer membrane protein that is similar in size and that also affects carbapenem susceptibility. 249 matched cddid_all.tbl CDD NF038068 NF038068 411652 LaoB_over_CadC L-arginine responsive protein LaoB. LaoB (L-arginine responsive overlapping gene) is a small, rare protein, encoded in an antisense frame to the gene for CadC in some strains of Escherichia coli. CadC, in response to acid stress and the presence of sufficient lysine, activates expression of a lysine decarboxlation and lysine/cadaverine antiport system, which provides resistance to the acidity. 41 matched cddid_all.tbl CDD NF038070 NF038070 411653 LmbU_fam_TF LmbU family transcriptional regulator. LmbU is a well-described member of a family of DNA-binding transcriptional activators for natural product biosynthesis in Streptomyces and related species. Besides LmbU (lincomycin), some other members include CouE (coumermycin A1), CloE (clorobiocin), and HrmB (hormaomycin). 171 matched cddid_all.tbl CDD NF038071 NF038071 468331 lat_flg_LafA_2 lateral flagellin LafA. 283 matched cddid_all.tbl CDD NF038072 NF038072 411655 IcmL_DotI_only type IVB secretion system apparatus protein IcmL/DotI. 200 matched cddid_all.tbl CDD NF038073 NF038073 468332 rSAM_STM4011 STM4011 family radical SAM protein. Members of this family are putative radical SAM proteins that (at the time of HMM construction) fall outside the scope of Pfam model PF04055 available at the time (version 21), as many radical SAM proteins do. The function is unknown. Members are somewhat variable in architecture, and found mostly in Streptomyces and related species. However, the family is named for a member in Salmonella enterica, in the model strain LT2, protein STM4011, whose function is unknown. 278 matched cddid_all.tbl CDD NF038074 NF038074 468333 fam_STM4014 STM4014 family protein. Members of this family are proteins of unknown function, regularly found in a conserved gene neighborhood that also includes two uncharacterized radical SAM proteins. The protein family is named for a founding member from the Salmonella enterica model strain LT2, although the system is rare in the Proteobacteria and relativly common in Streptomyces and related taxa. 350 matched cddid_all.tbl CDD NF038075 NF038075 468334 fam_STM4013 STM4013/SEN3800 family hydrolase. Members of this family are sulfatase-like metal-dependent hydrolases, of unknown function, regularly found in a conserved gene neighborhood that also includes two uncharacterized radical SAM proteins. See PF00884 for information on related proteins. 261 matched cddid_all.tbl CDD NF038076 NF038076 468335 fam_STM4015 STM4015 family protein. Members of this family are proteins of unknown function, regularly found in a conserved gene neighborhood that also includes two uncharacterized radical SAM proteins. The protein family is named for a founding member from the Salmonella enterica model strain LT2, although the system is rare in the Proteobacteria and relativly common in Streptomyces and related taxa. 286 matched cddid_all.tbl CDD NF038077 NF038077 411660 MFS_export_MxcK myxochelin export MFS transporter MxcK. 405 matched cddid_all.tbl CDD NF038078 NF038078 468336 NRPS_MxcG myxochelin non-ribosomal peptide synthetase MxcG. 1444 matched cddid_all.tbl CDD NF038079 NF038079 468337 TonB_sider_MxcH TonB-dependent siderophore myxochelin receptor MxcH. 796 matched cddid_all.tbl CDD NF038080 NF038080 411663 PG_bind_siph peptidoglycan-binding domain. This domain occurs shows apparent homology to known or putative peptidoglycan-binding domains in families such as PF01471. The domain occurs once, or twice, at the C-terminus of proteins such as cell wall amidases. In particular, member proteins can be found among putative lysins of phage of Streptomyces from the Siphoviridae family, such as phiBT1. 76 matched cddid_all.tbl CDD NF038081 NF038081 468338 BN159_2729_fam BN159_2729 family protein. This uncharacterized protein family occurs in Streptomyces and related species. Some members have insertions of long stretches of low-complexity sequences. 237 matched cddid_all.tbl CDD NF038082 NF038082 468339 phiSA1p31 phiSA1p31 domain. This domain occurs in Streptomyces and related lineages, in proteins with highly variable architectures, typically at or near the C-terminus. Member proteins include at least two from known temperate phage of Streptomyces, including phiSA1p31, for which it is named, from Streptomyces phage phiSASD1. 60 matched cddid_all.tbl CDD NF038083 NF038083 468340 CU044_5270_fam CU044_5270 family protein. Members of this family occur largely in Streptomyces and related species, often with several members per genome. Lengths average about 340 amino acids. The function is unknown. 284 matched cddid_all.tbl CDD NF038084 NF038084 411667 DHCW_cupin DHCW motif cupin fold protein. Members of this uncharacterized protein family resemble other cupin superfamily small barrel proteins. This family has a signature motif, DHCW, for which the family is named. 106 matched cddid_all.tbl CDD NF038085 NF038085 468341 MSMEG_6728_fam MSMEG_6728 family protein. 149 matched cddid_all.tbl CDD NF038086 NF038086 468342 anchor_synt_A protein sorting system archaetidylserine synthase. Members of this family are homologs of CDP-diacylglycerol--serine O-phosphatidyltransferase PssA of subclass II, as found in Gram-positive bacteria, but occur in a branch of the archaea. In Haloferax volcanii, the member of this family HVO_1143, together with the PssD-related decarboxylase HVO_0146, were both shown to be required for the archaeosortase ArtA to cause removal of the PGF-CTERM sorting signal and replacement with a prenyl-derived C-terminal lipid anchor. Based on these observations, members of this family are suggested to be CDP-2,3-di-O-geranylgeranyl-sn-glycerol:l-serine O-archaetidyltransferase, generating archaetidylserine en route to archaetidylethanolamine biosynthesis. 222 matched cddid_all.tbl CDD NF038087 NF038087 468343 arch_ser_synth archaetidylserine synthase. Members of this family, including founding member MTH_1027 from Methanothermobacter thermautotrophicus, resemble subclass II bacterial CDP-diacylglycerol--serine O-phosphatidyltransferase, but act as instead as CDP-2,3-Di-O-geranylgeranyl-sn-glycerol:L-serine O-archaetidyltransferase (archaetidylserine synthase). 216 matched cddid_all.tbl CDD NF038088 NF038088 468344 anchor_synt_D protein sorting system archaetidylserine decarboxylase. Members of this family, including founding member HVO_0146 from Haloferax volcanii, are archaeal homologs of bacterial phosphatidylserine decarboxylases (PssD). HVO_0146, and the PssA homolog HVO_1143, were shown be required for archaeosortase A (ArtA)-mediated removal of the PGF-CTERM protein-sorting signal and replacement with a large, prenyl-derived, C-terminal anchoring lipid moiety that is proposed to be archaetidylethanolamine. 196 matched cddid_all.tbl CDD NF038090 NF038090 411672 IscA_HesB_Se IscA/HesB family protein. Members of this family, a large fraction of which are selenoproteins, are homologous to proteins of iron-sulfur cluster biosynthesis such as IscA, and belong to the broader set of HesB-related proteins. 99 matched cddid_all.tbl CDD NF038091 NF038091 468345 T4SS_VirB10 type IV secretion system protein VirB10. Members of this family are VirB10, an outer membrane-associated protein from the apparatus of protein type IV secretion systems (T4SS). The model attempts to exclude related TraI proteins of conjugal transfer systems as well as the ComB10 protein of a DNA-translocating competence protein of Helicobacter pylori. Because the N-terminal regions of VirB10 proteins are highly variable, the model 197 matched cddid_all.tbl CDD NF038092 NF038092 468346 T4SS_ComB10 DNA type IV secretion system protein ComB10. ComB10, a VirB10 homolog, is an outer membrane-associated component of a DNA-translocating type IV secretion system (T4SS) involved in competence. Most T4SS translocate proteins, but both ComB10 as found in Helicobacter, and the T4SS of Agrobacterium, translocate DNA. 225 matched cddid_all.tbl CDD NF038093 NF038093 468347 GrdX GrdX family protein. GrdX is a small protein, of unknown function, encoded in grd operons for selenocysteine-dependent glycine reductase systems. A small number of GrdX proteins appear to be encoded with a UGA-encoded selenocysteine residue appearing close to the N-terminus, at sites that do not align with Cys residues in other members of the family. This arrangement suggests that the ability to complete translation of GrdX selenoproteins may have regulatory value, in addition to whatever may be the molecular function of GrdX itself. 118 matched cddid_all.tbl CDD NF038094 NF038094 468348 CueP_fam CueP family metal-binding protein. Members of this family including CueP itself, a copper-binding periplasmic metallochaperone, as found in Salmonella enterica serovar Typhimurium. Many family members, although not CueP itself, are lipoproteins. Several other members of the family are selenoproteins, including members from Bacillus selenitireducens, Bacillus beveridgei, and others. 146 matched cddid_all.tbl CDD NF038095 NF038095 468349 met_chaper_CueP copper-binding periplasmic metallochaperone CueP. This narrowly built model for CueP includes periplasmic proteins from Salmonella enterica, in which it contributes to an increased tolerance to copper, and from various other Gram-negative bacteria. It does not include CueP lipoproteins from species such as Corynebacterium diphtheriae. 177 matched cddid_all.tbl CDD NF038096 NF038096 411678 thylak_slr1796 thylakoid membrane photosystem I accumulation factor. Members of this family, restricted to the Cyanobacteria and chloroplasts, show homology to thioredoxins. However, the core region of family protein alignment shows either one Cys residue or zero, suggesting family members may share the thioredoxin-like fold but lack redox capability. The founding member of the family, slr1796, was shown by proteomics to localize to the thylakoid membrane, consistent with taxonomic restriction to the Cyanobacteria. Targeted mutation of slr1796 shows a role in successful translation and insertion of photosystem I proteins into the thylakoid membrane. 157 matched cddid_all.tbl CDD NF038097 NF038097 411679 KCGN_DNA_rpt KCGN motif-containing spurious repeat. This AntiFam-type HMM recognizes spurious protein translations, often with the motif KCGN, of a DNA repeat widespread in the genus Leptospira. 21 matched cddid_all.tbl CDD NF038098 NF038098 411680 GyrA_w_intein intein-containing DNA gyrase subunit A. 1232 matched cddid_all.tbl CDD NF038099 NF038099 468350 AsSugarArsM arsenosugar biosynthesis arsenite methyltransferase ArsM. This form of arsenite methyltransferase works together with the radical SAM enzyme ArsS in a pathway of arsenosugar biosynthesis. Examples of ArsM such as slr0303 from Synechocystis sp. PCC 6803 and alr3095 from Nostoc sp. PCC 7120 are encoded next to ArsS. 321 matched cddid_all.tbl CDD NF038101 NF038101 411682 Trm112_arch methytransferase partner Trm112. This HMM describes an archaeal branch of a small protein, Trm112, that is conserved in the three domains of life and that serves as general activator of methyltransferases for RNA or protein. 59 matched cddid_all.tbl CDD NF038104 NF038104 468351 lipo_NF038104 NF038104 family lipoprotein. This family of small lipoproteins of unknown function, about 68 amino acids long, occurs in genera that include Acinetobacter, Moraxella, Neisseria, and Psychrobacter. The N-terminal half, including the lipoprotein signal peptide, shows significant sequence similarity to the divisome-associated lipoprotein YraP, a three-fold longer protein, as found in Eschericia coli. 62 matched cddid_all.tbl CDD NF038105 NF038105 411684 acin_NF038105 NF038105 family protein. This family of small proteins, about 66 amino acids long, appears universal in the first 20 species of Acinetobacter examined, but absent outside the genus. 62 matched cddid_all.tbl CDD NF038106 NF038106 411685 gamma_NF038106 PA4642 family protein. Member of this family are small (about 95 amino acids), uncharacterized, and apparently restricted to the Gammaproteobacteria. Members include PA4642 from Pseudomonas aeruginosa PAO1. 93 matched cddid_all.tbl CDD NF038107 NF038107 468352 rSAM_NF038107 Cys-every-fifth radical SAM/SPASM peptide maturase CefB. Members of this family are radical SAM/SPASM domain proteins, most of which perform post-translational modification on RiPP peptide precursors or enzyme subunits. Target residues for modification often are Cys residues. Members of family NF038108, with a Cys Every Fifth position (CefA) over most of the short length of that family, are the putative target RiPP proteins. 444 matched cddid_all.tbl CDD NF038108 NF038108 411687 RiPP_NF038108 Cys-every-fifth RiPP peptide CefA. Members typically are shorter than 100 residues, with from nine to eleven Cys residues spaced strictly as every fifth residue and usually with at least one adjacent Gly. Most family members occur in the vicinity of a peptide-modifying radical SAM/SPASM domain protein, marking those family members as putative RiPP (ribosomally translated, post-translationally modified peptide) precursors. Because of the small size, richness in Cys and Gly residues, and strictly repetitive nature, it may be expected that some predicted proteins, scoring above the thresholds for the model, are related by convergent evolution rather than by homology, and are not themselves RiPP precursors. 65 matched cddid_all.tbl CDD NF038109 NF038109 439425 tapY2_fam TapY2 family type IVa secretion system protein. Members of this family average about 100 amino acids in length and include two invariant Cys residues. The family is named for TapY2 (Type IV Aeromonas Pilus Y2), which in PMID:18212071 is called the counterpart to PilY2 from the type IVa pilus system Pil in Pseudomonas aeruginosa. However, sequence similarity between TapY2 and PilY2 is very low, and is not certain to represent true homology. 91 matched cddid_all.tbl CDD NF038110 NF038110 468353 Lys_methyl_FliB flagellin lysine-N-methylase. 375 matched cddid_all.tbl CDD NF038111 NF038111 468354 rhom_dep_M36 rhombosortase-dependent M36 family metallopeptidase. Members of this bacterial protein family have an M36 family metallopeptidase domain, like fungalysin (see PF02128), and a C-terminal GlyGly-CTERM domain, recognized and cleaved by rhombosortase. 1312 matched cddid_all.tbl CDD NF038112 NF038112 468355 myxo_dep_M36 myxosortase-dependent M36 family metallopeptidase. Members of this bacterial protein family have an M36 family metallopeptidase domain, like fungalysin (see PF02128), and a C-terminal MYXO-CTERM domain (see TIGR03901), suggesting processing and surface-anchoring by the still-unknown putative transpeptidase, myxosortase. Members of this family include MXAN_3564 (mepA), part of the effector cargo of outer membrane vesicles that the species produces in large numbers during predation on other microbes. 1597 matched cddid_all.tbl CDD NF038113 NF038113 468356 T9SSA_dep_M36 T9SS-dependent M36 family metallopeptidase. Members of this family have an M36 family metallopeptidase domain, like fungalysin (see PF02128), and a C-terminal T9SS type A sorting domain (see TIGR04131). 868 matched cddid_all.tbl CDD NF038114 NF038114 468357 rightmost PxKF domain. The PxKF domain is found in a number of extracellular proteins, always as the most C-terminal domain (710 of 710 at the time of HMM construction). Upstream regions of proteins with the PxKF domain often mark them as members of largely surface-associated proteins, processed and anchored by the type IX secretion system, exosortases, rhombosortases, etc. The species distribution of PxKF domain-containing proteins is broad - mostly Actinobacteria, but also some Firmicutes, Deinococcus, etc. That broad taxonomic distribution, plus its large size (over 100 amino acids long) compared to most known N-terminal or C-terminal sorting signals that are recognized but then removed, suggests that the domain is retained in the mature protein, and has some function involved in surface-binding. 112 matched cddid_all.tbl CDD NF038115 NF038115 468358 SVAGG SVAGG family GlyGly-CTERM protein. The SVAGG (Shewanella/Vibrio/Aeromonas GlyGly-CTERM protein) family (defined and named here) averages about 420 amino acids in length. Member proteins have a C-terminal GlyGly-CTERM sorting signal, which implies cleavage by rhombosortase, export by a type II secretion system (T2SS), and covalent attachment to the outer membrane. 407 matched cddid_all.tbl CDD NF038116 NF038116 468359 Sden1266_dom choice-of-anchor H domain. The choice-of-anchor H domain is observed, in from one to four copies, in over 500 proteobacterial proteins with a C-terminal protein sorting signal, GlyGly-CTERM, that directs processing by rhombosortase, transport by a type II secretion system (T2SS), and (most likely) covalent attachment to the outer membrane. The domain is also observed occasionally, in up to 13 tandem copies, in proteins sorted and processed instead by a type IX secretion system (T9SS), which also implies transpeptidation and covalent attachment on the cell surface. One member of this family, Sden_1266, is toxic if expressed as a transgene in Escherichia coli, as might be expected given the lack of the required processing machinery in that species. 124 matched cddid_all.tbl CDD NF038117 NF038117 468360 choice_anch_I "choice-of-anchor I domain. This domain is found in the N-terminal third of the alkaline phosphatase PhoA of Synechocystis sp. PCC 6803 (see AGF50645.1), upstream of the region presumed to have phosphatase activity. It is found in a number of other cyanobacterial proteins called PhoA, although those annotations may be incorrect. Proteins with this domain include a number with the PEP-CTERM protein-sorting domain, but also a number with the LPXTG protein-sorting domain, making this a choice-of-anchor domain, that is, a new homology domain of what was previously ""dark matter"" (that is, lacking any HMM), whose members include proteins targeted for covalent attachment at the cell surface by at least two different protein-sorting systems." 461 matched cddid_all.tbl CDD NF038118 NF038118 468361 PEP_CTERM_CCXG CCXG family PEP-CTERM protein. This exosortase-dependent PEP-CTERM protein has an unusual CCXG motif, with two adjacent Cys residues. 199 matched cddid_all.tbl CDD NF038119 NF038119 468362 PEP_CTERM_MHFG MHFG family PEP-CTERM protein. This PEP-CTERM protein, dependent on exosortase for processing and export, is named for a distinctive MHFG motif. 260 matched cddid_all.tbl CDD NF038120 NF038120 468363 PEP_CTERM_QFxxD NF038120 family PEP-CTERM protein. This family of PEP-CTERM proteins has a notable motif, QFxxD, near the PEP-CTERM region, for which it is named. 217 matched cddid_all.tbl CDD NF038121 NF038121 468364 PEP_CTERM_LEVG LEVG family PEP-CTERM protein. This well-conserved family of PEP-CTERM proteins occurs in Cyanobacteria. 252 matched cddid_all.tbl CDD NF038122 NF038122 468365 metallo_LGF NF038122 family metalloprotease. Members of this family are marked as probable metalloproteases by striking local similarity of its HExxH motif-containing region that of PF00413. This family is notable in part for the large fraction, nearly half, with a PEP-CTERM domain or similar C-terminal signal for protein sorting and covalent attachment at the cell surface. 258 matched cddid_all.tbl CDD NF038123 NF038123 468366 NF038123_dom spondin domain. 208 matched cddid_all.tbl CDD NF038124 NF038124 468367 PEP_CTERM_TLD_A PEP_CTERM-anchored TLD domain-containing protein. Members of this family represent one branch of the TLD domain family, predicted to be a family of enzymes (see PF07534). All members furthermore have a C-terminal region, PEP-CTERM (TIGR02595 or one of its variants) for recognition and processing by an exosortase, and presumably attachment on the cell surface. 235 matched cddid_all.tbl CDD NF038125 NF038125 468368 PEP_CTERM_THxN THxN family PEP-CTERM protein. This family of PEP-CTERM proteins is named for one of several well-conserved motifs. The function is unknown, but DVUA0032 is mentioned as a member protein whose expression depends on a 54-dependent promoter. PEP-CTERMs are expected to be expressed covalently attached to outer membrane. 246 matched cddid_all.tbl CDD NF038126 NF038126 468369 PEP_CTERM_FxDxF FxDxF family PEP-CTERM protein. This family of PEP-CTERM protein is named for a well-conserved motif near its N-terminus, FxDxFxF. A few members of this family have two full copies, suggesting two sites, rather than just one at the C-terminus, for cleavage by exosortase and covalent attachment to the outer membrane. 165 matched cddid_all.tbl CDD NF038127 NF038127 468370 FDP_fam DVUA0089 family protein. This family is named after oldest member mentioned in a publication, the plasmid-encoded PEP-CTERM protein DVUA0089 from Desulfovibrio vulgaris Hildenborough. Nearly every member has the PEP-CTERM sequence at its C-terminus (or a related variant), a single for recognition and processing by exosortases, and probably for covalent attachment to components of the outer membrane after cleavage and transpeptidation. This HMM appears to be related to PF04151.15, which describes a domain often found in the C-terminal regions of peptidases. 147 matched cddid_all.tbl CDD NF038128 NF038128 468371 choice_anch_J choice-of-anchor J domain. The choice-of-anchor J domain, about 160 amino acids long, occurs as many as times in a protein, although most often only once. Proteins with the domain include proteins with serine hydrolase, metallohydrolase, or adhesin-associated domains. Notably, many members are also found with either the PEP-CTERM term domain, or the type IX secretion system type A domain, both associated with protein-sorting system expected to leave target proteins covalently attached to the bacterial outer membrane. 161 matched cddid_all.tbl CDD NF038129 NF038129 468372 PEP_NF038129 NF038129 family PEP-CTERM protein. 192 matched cddid_all.tbl CDD NF038130 NF038130 468373 PEP_NF038130 NF038130 family PEP-CTERM protein. This family of PEP-CTERM proteins occurs in Cyanobacteria such as Nostoc, but also in floc-forming bacteria such as Zoogloea ramigera and Candidatus Accumulibacter phosphatis. 283 matched cddid_all.tbl CDD NF038131 NF038131 468374 choice_anch_K choice-of-anchor K domain. The choice-of-anchor K is a rather uncommon extracellular domain about 170 amino acids long. A substantial fraction of member proteins have C-terminal regions that target them for sorting to the cell surface, including PEP-CTERM, its variant VPLPA-CTERM, and LPXTG. The domain is found occasionally in RTX toxin-like proteins. 169 matched cddid_all.tbl CDD NF038132 NF038132 468375 PEP_NF038132 NF038132 family protein. Most members of this family, but not all, are exosortase-dependent proteins with a PEP-CTERM protein-sorting signal at the C-terminus. This HMM excludes a set of related proteins with an additional insert region that features a near-invariant LFTART motif. 198 matched cddid_all.tbl CDD NF038133 NF038133 468376 choice_anch_L choice-of-anchor L domain. The choice-of-anchor L domain, about 220 amino acids long, is an extracellular domain found often with a C-terminal cell surface, such as PEP-CTERM or the type IX secretion system (T9SS) type B sorting signal. It tends to be found only once per protein, but the family contains some members proteins over 4000 residues long. 223 matched cddid_all.tbl CDD NF038134 NF038134 468377 choice_anch_M choice-of-anchor M domain. This model represents a domain about 180 amino acids long, often repeated and sometimes cyclically permuted, containing a signature region described by TIGR03769 (which is just 41 residues long). Many members of this family have either LPXTG or PEP-CTERM domains at the C-terminus, for covalent anchoring at the cell surface by sortases or exosortases, respectively. Other member proteins that lack such C-terminal regions may instead have lipoprotein signal peptides at the N-terminus. The domain is duplicated in members of TIGR03773, such as CmrA2. The related protein TroA (see TIGR03772), with regions homologous to most of the length of this model, appears to have a function related to zinc uptake. 184 matched cddid_all.tbl CDD NF038135 NF038135 468378 rSAM_Rv2578c Rv2578c family radical SAM protein. This radical SAM family, which includes Rv2578c from Mycobacterium tuberculosis, is uncharacterized, but is notable in part because inteins are found in many members of this family. Although inteins are viewed mostly as selfish genetic elements, they occur often in important housekeeping proteins, such as RecA, in a way that suggests domestication of the element into a regulatory system in which triggering intein excision results in an irreverisible change to the host protein. Intein-containing members of this family are found by HMM NF038136. Rv2578c itself appears to be part of the SOS regulon. 315 matched cddid_all.tbl CDD NF038136 NF038136 468379 rSAM_Rv_intein intein-containing Rv2578c family radical SAM protein. This radical SAM family consists of intein-containing radical SAM proteins related to (but not including) Rv2578c from Mycobacterium tuberculosisis. Rv2578c and its homologs are uncharacterized, but presence of inteins in multiple members of the family is notable. Although inteins are viewed mostly as selfish genetic elements, they occur often in important housekeeping proteins, such as RecA, in a way that suggests domestication of the element into a regulatory system in which triggering intein excision results in an irreverisible and situationally beneficial change to the host protein. 572 matched cddid_all.tbl CDD NF038137 NF038137 439452 leader_TrpLE_al trpE operon leader peptide TrpLE. This HMM describes a variant of the trp operon leader peptide, as found in Sinohizobium meliloti and other alphaproteobacteria. In Sinohizobium meliloti, tryptophan biosynthesis genes are divided into three different operons, and only the trpE-encoding operon is proceeded by a leader peptide, designated TrpLE. This family differs substantially from that of Pfam model PF08255. Melior, et al. (2020) describe an usual activity in trans, something not previously known for leader peptides, affecting expression of antibiotic efflux proteins. 14 matched cddid_all.tbl CDD NF038138 NF038138 468380 phena_PhzG phenazine biosynthesis FMN-dependent oxidase PhzG. 205 matched cddid_all.tbl CDD NF038139 NF038139 468381 Reg_Aceta_RamB acetate metabolism transcriptional regulator RamB. RamB (Regulator of Acetate Metabolism B), as described in Mycobacterium tuberculosis and Corynebacterium glutamicum, is a transcription factor with multiple targets connected to acetate metabolism. It features an N-terminal XRE (Xenobiotic Response Element) family DNA-binding domain and a DUF2083 (PF09856) domain-containing C-terminal region. 464 matched cddid_all.tbl CDD NF038140 NF038140 439455 amidase_Rv3717 Rv3717 family N-acetylmuramoyl-L-alanine amidase. This zinc-dependent amidase functions as a peptidoglycan hydrolase, and affects septum formation, cell division, and cell morphology. Model proteins for this family include Rv3717 from Mycobacterium tuberculosis (MTB) and MSMEG_6281 from Mycolicibacterium smegmatis, a fast-growing laboratory surrogate for MTB. 233 matched cddid_all.tbl CDD NF038141 NF038141 468382 choice_anch_N choice-of-anchor N domain. The choice-of-anchor N family occurs in both bacteria, with a PEP-CTERM sorting signal at the C-terminus, and in archaea with a PEF-CTERM sorting signal. Well-conserved motifs in the multiple sequence alignment include AxPxLQ near the N-terminus, and HFD and PxSHD near the C-terminus, the latter just upstream of the sorting signal region. 182 matched cddid_all.tbl CDD NF038142 NF038142 468383 exosort_XrtW exosortase W. Exosortase W is an EpsI domain-containing subtype of exosortase, a bacterial protein-sorting enzyme that is probably a transpeptidase rather than a simple hydrolase. It is most closely related to exosortase D, which is VPLPA-CTERM-specific. However, it is the sole exosortase in Candidatus Manganitrophus noduliformans, the nodule-forming Nitrospiraceae bacterium identified as the first manganese-oxidizing chemolithoautotroph. In that species, target proteins have the more classical PEP-CTERM sorting signal at the C-terminus. 494 matched cddid_all.tbl CDD NF038143 NF038143 468384 HYxxLL NF038143 family protein. This family is uncharacterized. 197 matched cddid_all.tbl CDD NF038144 NF038144 439459 PxxKW PxxKW family cysteine-rich protein. Members of this uncharacterized protein family are shorter than 100 residues, with four invariant Cys residues, including a CxGC motif. One branch of the family has three additional conserved Cys. Other notable motifs include PxxKW (for which the family is currently named), CNxATH, and NP[LI]KASKR near the C-terminus. 81 matched cddid_all.tbl CDD NF038145 NF038145 468385 Hvo_1808_fam Hvo_1808 family surface protein. Members of this family are secreted proteins from halophilic archaea. Essentially every member has lipoprotein signal peptide at the N-terminus, or else a PGF-CTERM sorting signal at the C-terminus, but not both. Both types of sorting signals are processed in such a way that, following removal, a lipid moiety left at the new terminus of the amino acid chain anchors the protein in the plasma membrane. 436 matched cddid_all.tbl CDD NF038146 NF038146 439461 LxmA_leader LxmA family RiPP leader domain. LxmA is the founding member of a family of ribosomally translated and post-translationally modified lanthipeptides whose lanthionine moiety is created by a novel class of enzyme. This HMM represents the leader domain, and the first four residues of the core peptide, of LxmA, its full-length homologs, and a number of other RiPPs that much lower sequence similarity outside the leader peptide region. 30 matched cddid_all.tbl CDD NF038147 NF038147 439462 lanti_IV_venA VenA family class IV lanthipeptide. Members of this family include VenA, precursor of the class IV lanthipeptide venezuelin, and all detectable homologs. 49 matched cddid_all.tbl CDD NF038148 NF038148 439463 lanti_IV_SflA "SflA family class IV lanthipeptide. SflA is the precursor peptide of a RiPP biosynthetic gene cluster (BGC) designated ""sfl"", for the Second-most abundant class Four (IV) Lanthipeptide." 52 matched cddid_all.tbl CDD NF038149 NF038149 439464 leader_PheL pheA operon leader peptide PheL. 15 matched cddid_all.tbl CDD NF038150 NF038150 468386 lanthi_synth_IV class IV lanthionine synthetase LanL. Several classes of lanthionine bridge-producing peptide-modifying enzymes (lanthionine synthases) have been defined. LanC enzymes are class I, LanM are class II, LanKC are class III, and LanL are class IV. Members of this family are the class IV enzyme, active in the maturation of class IV lanthipeptides, a large fraction of which act as lantibiotics. 853 matched cddid_all.tbl CDD NF038151 NF038151 468387 lanthi_synth_III class III lanthionine synthetase LanKC. 831 matched cddid_all.tbl CDD NF038152 NF038152 439467 TrpL_Coryne trp operon leader peptide. Member of this family are tryptophan biosynthesis operon leader peptide TrpL, as found in the genus Corynebacterium. It differs substantially from Trp-rich leader peptides documented in other lineages, such as in the gammaproteobacteria. 17 matched cddid_all.tbl CDD NF038153 NF038153 468388 lant_leader_L1a class I lanthipeptide leader domain. This HMM describes a homology domain found regularly as a leader peptide, ending with a GlyGly dipeptide (a leader peptide cleavage site), of putative lanthipeptides (probably lantibiotics in most cases) encoded in the vicinity of a class I lanthionine synthase, or LanC. The designation L1a reflects model construction for class I lantibiotics (L1), first in a possible series (L1a), from the lanthipeptide RiPP collection found in PMID:32493223. Because the leader peptide may reflect constraints on cleavage and export, it may be expected that some members of the family undergo modifications other than lanthionine bridge formation, or no special modifications at all. 32 matched cddid_all.tbl CDD NF038154 NF038154 468389 lanthi_III_a class III lanthipeptide. This family of putative class III lanthipeptides, here designated family lanthi_III_a, averages about 44 amino acids in length, has a strongly conserved N-terminal ten amino acids including an invariant motif LxLQ, and usually has Cys as its final residue. The designation III_a indicates that it is the first family defined here from the collection of putative class III lanthipeptides reported by Walker, et al. (PMID:32493223). 36 matched cddid_all.tbl CDD NF038155 NF038155 439470 lanthi_I_FDLD FDLD family class I lanthipeptide. This HMM finds a broad collection of putative class I lanthipeptides with a well-conserved motif FDLD near the N-terminus, and poorly conserved but typically Cys-rich core peptide regions. Some members belong to the more narrowly defined family of gallidermin/nisin-like lanthipeptides. 33 matched cddid_all.tbl CDD NF038156 NF038156 468390 lant_syn_V_LxmK class V lanthionine synthetase subunit LxmK. 347 matched cddid_all.tbl CDD NF038157 NF038157 439472 lanti_ALQxL ALQxL family lanthipeptide leader peptide. This 17-residue leader peptide region HMM identifies a family of lanthipeptides that average 40 residues in length, with typically 3 or 4 Cys residues C-terminal to this region. Most members of the family are classified as class IV lanthipeptides by proximity to class IV lanthionine synthases. 17 matched cddid_all.tbl CDD NF038158 NF038158 439473 lant_leader_L1b class I lanthipeptide leader domain. This HMM describes a homology domain found regularly as a leader peptide, ending with a GlyGly dipeptide (a leader peptide cleavage site), of putative lanthipeptides (probably lantibiotics in most cases) encoded in the vicinity of a class I lanthionine synthase, or LanC. The designation L1b reflects model construction for class I lantibiotics (L1), second in a possible series (L1b), from the lanthipeptide RiPP collection found in PMID:32493223. Because the leader peptide may reflect constraints on cleavage and export, it may be expected that some members of the family undergo modifications other than lanthionine bridge formation, or no special modifications at all, but amino acid composition of member proteins C-terminal to the leader domain suggests that all are lanthipeptides, and probably act as lantibiotics. 28 matched cddid_all.tbl CDD NF038159 NF038159 439474 lanthi_III_b class III lanthipeptide. Members of this family are class III lanthipeptides, most likely active as lantibiotics. They average about 43 amino acids in length, with two conserved Cys residues, the second of them often appearing as the final residue. The family lacks the GlyGly motif that many other RiPP precursors have as the cleavage site between leader peptide and core region. The designation III_b indicates that it is the second family defined here with no characterized member but with members in the collection of putative class III lanthipeptides reported by Walker, et al. (PMID:32493223). The family has some overlap with the SapB/AmfS family of class III lanthipeptides (NF033212 ) and with the lanthi_III_a family (NF038154). 38 matched cddid_all.tbl CDD NF038160 NF038160 439475 lanthi_III_c class III lanthipeptide. Members of this family are class III lanthipeptide precursors of unusually small size, 36 amino acids long on average. Most have a Cys-Cys dipeptide pair not far from the C-terminus. Members lack the Gly-Gly cleavage site that many RiPP precursor polypeptides have between leader and core peptide regions. The designation III_c indicates that it is the third family defined here with no characterized member but with members in the collection of putative class III lanthipeptides reported by Walker, et al. (PMID:32493223). 33 matched cddid_all.tbl CDD NF038161 NF038161 468391 lant_II_LchA2 class II lanthipeptide, LchA2/BrtA2 family. Members of this family are class II lanthipeptide precursors. Most members have three Cys residues in conserved positions among their last 15 amino acids. Named members include lichenicidin A2 (LchA2) and the birimositide beta chain, BrtA2. 50 matched cddid_all.tbl CDD NF038162 NF038162 468392 RctB_rel_intein intein-containing RctB family protein. 961 matched cddid_all.tbl CDD NF038163 NF038163 439478 bactofencin_A bactofencin A family cationic bacteriocin. Bactofencin A (BnfA), a class IId bacteriocin from Lactobacillus salivarius, is a disulfide bond-containing 22-amino-acid defensin-like peptide with a broad spectrum of activity. Precursor forms for BnfA and other members of the family average about 49 amino acids in length, with the core peptide starting immediately after the GlyGly motif of the leader peptide. 45 matched cddid_all.tbl CDD NF038164 NF038164 439479 garvicinKS_A GatA family leaderless bacteriocin. GatA is one component of the multipeptide leaderless bacteriocin designated garvicin KS, as found in Lactococcus garvieae KS1546. 22 matched cddid_all.tbl CDD NF038165 NF038165 439480 garvicinKS_B GatB family leaderless bacteriocin. GatB is one component of the multipeptide leaderless bacteriocin designated garvicin KS, as found in Lactococcus garvieae KS1546. 30 matched cddid_all.tbl CDD NF038167 NF038167 468393 cyan_ocin_like CTB family bacteriocin. Members of this family, which average about 85 amino acids in length, resemble class II bacteriocins. They show N-terminal sequence similarity to bacteriocin leader peptide domain TIGR01847 and lack Cys residues (enriched in lanthipeptides as well as disulfide-forming bacteriocins) almost entirely. They are undoubtedly cleaved at a GlyGly motif while being exported in the manner of bacteriocins, as they are regularly encoded next to homologs of families TIGR01193 and TIGR01000, involved in bacteriocin cleavage and export. Because multiple family members can be encoded in tandem in a single genome, such as the set of six in Cylindrospermum stagnale PCC 7417, we name the family CTB (Cyanobacterial Tandem Bacteriocin). 72 matched cddid_all.tbl CDD NF038168 NF038168 439482 phazolicin_TOMM phazolicin family TOMM bacteriocin. Phazolicin is a ribosome-targeting thiazole/oxazole-modified microcin (TOMM), also called a linear azol(in)e-containing peptides (LAP). 54 matched cddid_all.tbl CDD NF038169 NF038169 439483 lachnocin lachnocin family radical SAM-modified peptide. 42 matched cddid_all.tbl CDD NF038170 NF038170 439484 lachnocin_rSAM lachnocin radical SAM maturase. 440 matched cddid_all.tbl CDD NF038171 NF038171 439485 maturase_LodB lysine-epsilon-oxidase maturase LodB. L-lysine-epsilon-oxidase (LodA), which acts on free lysine and produces hydrogen peroxide, contains a cysteine tryptophylquinone cofactor. LodB, usually encoded next to LodA, is the maturase required for formation of the quinone moiety. Note that a related system consists of cysteine tryptophylquinone-dependent glycine oxidase, GoxA, and its maturase, GoxB. 362 matched cddid_all.tbl CDD NF038172 NF038172 468394 Lys_ox_CTQ_LodA CTQ-dependent lysine 6-oxidase LodA. LodA converts free L-lysine into 6-semialdehyde 2-aminoadipic acid, ammonia and hydrogen peroxide. It has antibacterial activity because of the hydrogen peroxide produced, and was originally named marinocine. The enzyme depends on a cysteine tryptophylquinone (CTQ) cofactor, formed by post-translational modification by an accessory protein, the maturase LodB. 684 matched cddid_all.tbl CDD NF038173 NF038173 468395 Gly_ox_CTQ_GoxA CTQ-dependent glycine oxidase GoxA. 668 matched cddid_all.tbl CDD NF038174 NF038174 468396 maturase_GoxB glycine oxidase maturase GoxB. GoxB, a flavoprotein, is responsible for the post-translational modification that forms the cysteine tryptophylquinone (CTQ) cofactor of the quinone glycine oxidase GoxA. 358 matched cddid_all.tbl CDD NF038175 NF038175 439489 IniB_NTERM IniB N-terminal domain. This domain is found as the N-terminal fifty amino acids of a number low-complexity proteins that often bear little or no similarity to each other elsewhere in the protein. The domain occurs twice in Mycobacterium tuberculosis strain H37Rv, in two adjacent proteins, Rv0340 and the isoniazid inducible protein IniB (Rv0341). 49 matched cddid_all.tbl CDD NF038176 NF038176 468397 Rv0340_fam Rv0340 family protein. Homologs of Rv0340 from Mycobacterium tuberculosis H37Rv are regularly found encoded upstream of the genes for IniB, IniA, and IniC. As with those families, mutation in this family can contribute to resistance to isoniazid, a front-line treatment for Mycobacterium tuberculosis that works by inhibiting cell wall biosynthesis. Rv0340 and glycine-rich repetive protein IniB are homologous across the N-terminal 50 amino acids of each, but otherwise dissimilar. 179 matched cddid_all.tbl CDD NF038177 NF038177 468398 epimerase_AlgG mannuronan 5-epimerase AlgG. 519 matched cddid_all.tbl CDD NF038178 NF038178 439492 AlgP_Nterm AlgP family protein N-terminal domain. This HMM describes the conserved N-terminal domain of a protein that has extensive lysine-rich repeats in the C-terminal half, typically PAAK, and is called histone-like for that reason. Some reports have called AlgP (also called AlgR3) a regulator of alginate biosynthesis, responsible for a mucoid phenotype in Pseudomonas aeruginosa, but recent work casts doubt on the specificity of the connection to alginate. 132 matched cddid_all.tbl CDD NF038179 NF038179 439493 stress_YobI stress response small protein YobI. YobI, as found in strains of Escherichia coli and Shigella sonnei, is a hydrophobic protein of very small size, 21 amino acids, whose expression increases after heat shock. 21 matched cddid_all.tbl CDD NF038180 NF038180 439494 leader_pinensin pinensin family lanthipeptide leader domain. This family of class I lanthipeptide leader peptide occurs in Gram-negative lineages such as Chitinophaga pinensis (for which pinensins, antifungal lantibiotics, are named), Fulvivirga, Longimicrobium, and Pedobacter. Most member sequences contain the motif SFVT, and the leader peptide ends with a typical GlyGly motif. 28 matched cddid_all.tbl CDD NF038181 NF038181 468399 reg_ATPase_IniR isoniazid response ATPase/transcriptional regulator IniR. Two unrelated first-line drugs for the treatment of tuberculosis, isoniazid and ethambutol, block different steps in the biosynthesis of the Mycobacterial cell envelope, and induce expression of the iniBAC operon, mutations in which often lead to adaptive resistance to those drugs. IniR (iniBAC Regulator), an ATPase but also a transcriptional regulator, with an N-terminal P-loop motif GGxGxGK[ST] and a C-terminal LuxR-like helix-turn-helix DNA-binding domain, responds to the envelope stress signal and induces IniB, IniA, and IniC. 827 matched cddid_all.tbl CDD NF038182 NF038182 439496 penta_rpt_SmQnr SmQnr family pentapeptide repeat protein. The pentapeptide repeat protein SmQnr is a chromosomal homolog of quinolone resistance proteins QnrA and QnrB, found in Stenotrophomonas maltophilia and related species. Most alleles appear to contribute little or no resistance to quinolones, but some exceptional alleles to reduce susceptibility. 215 matched cddid_all.tbl CDD NF038185 NF038185 468400 KdpD_non_kinase KdpD-like non-kinase potassium sensor. Members of this family contain the N-terminal sensor region, but lack the C-terminal histidine kinase region, of the sensor histidine kinase KdpD found broadly in species such as Escherichia coli, Mycobacterium tuberculosis, Clostridium acetobutylicum, and Staphylococcus aureus. Members are found in Bacillus anthracis and related species. 373 matched cddid_all.tbl CDD NF038186 NF038186 439498 YPDG_rpt YPDG domain. The YPDG domain may occur once in a protein, or up to 22 times in tandem repeats. It is common in proteins of Gram-positive bacteria with C-terminal LPXTG sites for anchoring on the cell surface. 98 matched cddid_all.tbl CDD NF038187 NF038187 439499 FadE_coli acyl-CoA dehydrogenase FadE. This HMM describes a narrow clade of medium-chain and long-chain acyl-CoA dehydrogenases that includes YafH from Escherichia coli K-12 and Salmonella enterica LT2 (also called FadF), now called FadE. 816 matched cddid_all.tbl CDD NF038188 NF038188 468401 cas13A_C2c2 type VI-A CRISPR-associated RNA-guided ribonuclease Cas13a. 1175 matched cddid_all.tbl CDD NF038189 NF038189 468402 VI_Cas13d type VI-D CRISPR-associated RNA-guided ribonuclease Cas13d. 879 matched cddid_all.tbl CDD NF038190 NF038190 468403 VI_Cas13b type VI-B CRISPR-associated RNA-guided ribonuclease Cas13b. 1067 matched cddid_all.tbl CDD NF038191 NF038191 468404 V_Cas12k type V CRISPR-associated protein Cas12k. Cas12k is the large effector protein of type V-K CRISPR systems, which belong to the class 2 systems. Cas12k has also been known as C2c5, and type V-K as type V-U5. 628 matched cddid_all.tbl CDD NF038192 NF038192 468405 V_cas_c2c8 type V CRISPR-associated protein C2c8. 449 matched cddid_all.tbl CDD NF038193 NF038193 468406 VI_Cas13c type VI-C CRISPR-associated RNA-guided ribonuclease Cas13c. 854 matched cddid_all.tbl CDD NF038194 NF038194 439506 AlgK_TPR_lipo alginate biosynthesis TPR repeat lipoprotein AlgK. 448 matched cddid_all.tbl CDD NF038196 NF038196 468407 ferrodoxin_EFR1 EFR1 family ferrodoxin. Members of the family have a C-terminal ferrodoxin domain, with eight conserved Cys residues in two CxxCxxCxxxCP motifs, each of which binds a 4Fe-4S cluster. The N-terminal region resembles flavodoxin domains, with some members of the family recognized by Pfam models PF12724 (Flavodoxin_5) or PF00258 (Flavodoxin_1). 243 matched cddid_all.tbl CDD NF038197 NF038197 468408 prim_adj_arch primase-associated protein. Members of this family are found exclusively in Archaea, always adjacent to a DNA primase-like protein. 495 matched cddid_all.tbl CDD NF038205 NF038205 468409 Campy_LoFi_RPT LOFI repeat. This weakly conserved (low-fidelity, or LOFI) repeat appears primarily in Campylobacteria, but not exclusively, in proteins such as Cj0967, Cj0736, and Cj0735. The HMM models a core region about 23 residues in length of repeats whose lengths vary typically between 35 and 50 residues in length. 23 matched cddid_all.tbl CDD NF038206 NF038206 468410 RGCVC_fam RGCVC family protein. This family of small proteins, averaging just over 60 amino acids in length, has conspicuous motifs CxxCxH, HD, and RGCVC. The last motif, for which the family is named, is distinctive. The family appears in GC-rich bacteria. The function is unknown. 54 matched cddid_all.tbl CDD NF038207 NF038207 439510 glyco_res_GraF glycopeptide resistance-associated protein GraF. GraF was discovered as a small stress protein expressed at higher levels in glycopeptide (vancomycin, teicoplanin)-intermediate strains of Staphylococcus aureus. Overexperssion leads to a thicker cell wall, and reduced sensitivities to glycopeptides and oxacillin. 44 matched cddid_all.tbl CDD NF038209 NF038209 468411 mft_etfA mycofactocin-associated electron transfer flavoprotein alpha subunit. Members of this small protein family are putative electron transfer flavoproteins, related to FixA from E. coli and EtfB from Methylophilus methylotrophus but clearly forming a distinctive clade. All members occur in species with a mycofactocin system. Mycofactocin is a small molecule redox carrier, synthesized from a pair of amino acids in the ribosomally translated peptide MftA, with aid from the radical SAM enzyme MftC, in a pathway analogous to the biosynthesis of PQQ. 304 matched cddid_all.tbl CDD NF038210 NF038210 439512 GMC_mycofac_3 mycofactocin system GMC family oxidoreductase MftG. This model describes a set of dehydrogenases belonging to the glucose-methanol-choline oxidoreductase (GMC oxidoreductase) family. Members of the present family appear to be restricted to the genus Dietzia, and occur in the context of mycofactocin biosynthesis genes and mycofactocin dependent oxidoreductase genes. 418 matched cddid_all.tbl CDD NF038211 NF038211 439513 MFT_alt_reg mycofactocin system transcriptional regulator MftR2. Member of this family bear almost no resemblance to the mycofactocin transcriptional regulator MftR (TIGR03968), but occur in the equivalent position, next to the start of the mycofactocin biosynthetic gene cluster and transcribed divergently from it. It is found primarily in the genus Nocardia, but also in a few species of Rhodococcus. 193 matched cddid_all.tbl CDD NF038212 NF038212 439514 argG_rel argininosuccinate synthase-related protein. Members of this family are related to, yet distinct from, the argininosuccinate synthase ArgG. 381 matched cddid_all.tbl CDD NF038213 NF038213 439515 SDR_TniO_fam SDR family oxidoreductase. 249 matched cddid_all.tbl CDD NF038214 NF038214 439516 IS21_help_AAA IS21-like element helper ATPase IstB. This protein family model resembles PF01695, but was built to hit full-length AAA+ ATPases of IS21 family IS (insertion sequence) elements. 232 matched cddid_all.tbl CDD NF038215 NF038215 439517 acineto_lipo_PV NF038215 family lipoprotein. This small lipoprotein, about 60 amino acids long on average in precursor form, is widespread in the genus Acinetobacter. The motif PVxxxDY is conserved in most members. The function is unknown. 55 matched cddid_all.tbl CDD NF038216 NF038216 468412 ABZJ_00895_fam ABZJ_00895 family protein. This family of proteins resembles transporters in their extensive hydrophobicity. The actual function is unknown, but family member ABZJ_00895 was one of a number of proteins whose expression was reduced signficantly in a lab-generated, colistin-resistant lpxC disruption mutant of Acinetobacter baumannii (see PMID:28275586). 134 matched cddid_all.tbl CDD NF038218 NF038218 468413 IcmG_DotF_IVB type IVB secretion system protein IcmG/DotF. 265 matched cddid_all.tbl CDD NF038219 NF038219 439520 IcmV_IVB type IVB secretion system protein IcmV. 149 matched cddid_all.tbl CDD NF038220 NF038220 468414 IcmT_TraK IcmT/TraK family protein. 80 matched cddid_all.tbl CDD NF038221 NF038221 468415 IcmJ_DotN_IVB type IVB secretion system protein IcmJDotN. 203 matched cddid_all.tbl CDD NF038222 NF038222 439523 IcmW_IVB type IVB secretion system protein IcmW. 139 matched cddid_all.tbl CDD NF038223 NF038223 468416 IcmN_DotK_IVB type IVB secretion system protein IcmN/DotK. 164 matched cddid_all.tbl CDD NF038224 NF038224 468417 OmpA_like_CmpA C-OmpA-like family protein CmpA. Proteins of this family are one of the six L. pneumophila proteins containing an OmpA-like domain. It has been reported that CmpA was important for efficient intracellular replication of Legionella pneumophila. 233 matched cddid_all.tbl CDD NF038225 NF038225 468418 IcmX_IVB type IVB secretion system protein IcmX. 436 matched cddid_all.tbl CDD NF038226 NF038226 439527 IcmF_IVB type IVB secretion system protein IcmF. 973 matched cddid_all.tbl CDD NF038227 NF038227 439528 IcmM_DotJ_IVB type IVB secretion system protein IcmM/DotJ. 94 matched cddid_all.tbl CDD NF038228 NF038228 439529 IcmH_DotU_IVB type IVB secretion system protein IcmH/DotU. 258 matched cddid_all.tbl CDD NF038229 NF038229 439530 Glyco4_Geo_Pelo GPMC system family 4 glycosyltransferase. Members of this family are family 4 glycosyltransferases of the GPMC (Geobacter/Pelobacter Mystery Cassette) system, in which the most distinctive signature is the TIGR04442 protein family. 338 matched cddid_all.tbl CDD NF038230 NF038230 468419 Regu_Geo_Pelo GPMC system transcriptional regulator. Members of this family are family are sigma 54-interacting transcriptional regulators of the GPMC (Geobacter/Pelobacter Mystery Cassette) system, in which the most distinctive signature is the TIGR04442 protein family. 935 matched cddid_all.tbl CDD NF038231 NF038231 439532 MBL_Geo_Pelo GPMC system MBL fold metallohydrolase. Members of this family, distantly related to metallo-beta-lactamases, are MBL fold hydrolases of the GPMC (Geobacter/Pelobacter Mystery Cassette) system, in which the most distinctive signature is the TIGR04442 protein family. 250 matched cddid_all.tbl CDD NF038232 NF038232 468420 STM3845_fam retron St85 family effector protein. Members of this family, such as STM3845 from a retron in Salmonella enterica called St-85, are found in the vicinity of reverse transcriptases (RNA-directed DNA polymerase) and retron structural RNA genes. The protein is not required for msDNA (Multicopy Single-Stranded DNA) biosynthesis, but instead is assigned an effector function. 277 matched cddid_all.tbl CDD NF038233 NF038233 468421 retron_St85_RT retron St85 family RNA-directed DNA polymerase. All members of the seed alignment are reverse transcriptases St85-like systems. However, members of this family may include reverse transcriptases from other types of retron system. 290 matched cddid_all.tbl CDD NF038234 NF038234 468422 retron_eff_Eco8 retron Eco8 family effector endonuclease. This ATPase, found as the effector protein partner next to a reverse transcriptase in Eco8 type retron systems, is a predicted OLD family endonuclease. 679 matched cddid_all.tbl CDD NF038235 NF038235 468423 retron_Ec48_2TM retron Ec48 family effector membrane protein. 219 matched cddid_all.tbl CDD NF038236 NF038236 439537 retron_eff_Se72 retron Se72 family effector protein. Members of this family are cold shock domain-containing proteins encoded adjacent to reverse transcriptases found in Se72-type retron systems, and considered effector proteins contributing to phage resistance. 62 matched cddid_all.tbl CDD NF038237 NF038237 468424 retron_Ec67_fus retron Ec67 family RNA-directed DNA polymerase/endonuclease. 575 matched cddid_all.tbl CDD NF038239 NF038239 468425 T6SS_TssL_short type VI secretion system protein TssL, short form. TssL is a type VI secretion system (T6SS) protein, related to IcmH/DotU of type IVb secretion systems (T4bSS). Some forms have a OmpA-related C-terminal extension domain, likely to mediated interaction with peptidoglycan, but this form, also called SciP, lacks that extension. 207 matched cddid_all.tbl CDD NF038240 NF038240 468426 fibro_bind_EfbA fibronectin-binding protein EfbA. The virulence factor EfbA (enterococcal fibronectin-binding protein A), like its close homolog PavA from Streptococcus pneumoniae, is an anchorless adhesin, meaning it has no site for processing by sortase and covalent attachment to the cell surface, but still contributes to adhesion that contributes to pathogenesis. 567 matched cddid_all.tbl CDD NF038241 NF038241 439541 RipB_Ich (R)-specific enoyl-CoA hydratase RipB/Ich. 175 matched cddid_all.tbl CDD NF038242 NF038242 439542 RipC_Ccl itaconate degradation C-C-lyase RipC. 268 matched cddid_all.tbl CDD NF038243 NF038243 468427 TRP75_fam_Nterm TRP75-like N-terminal domain. This N-terminal domain is found in TRP75 (tandem repeat protein, 75 kDa) of Ehrlichia chaffeensis and TRP95 of Ehrlichia canis, preceding the region of 24 amino acid long direct repeats. It appears also in non-repetitive proteins from Anaplasma and Wolbachia, which likewise are members of the alphaproteobacteria. 126 matched cddid_all.tbl CDD NF038244 NF038244 439544 pheromon_TrpTrp quorum-sensing system DWW-type pheromone. Members of this family are pheromone precursor peptides about 31 amino acids in length, including a signal peptide. The active pheromone is derived from the C-terminal few residues, containing a nearly invariant DWW motif. Member proteins are found encoded near Rgg-type quorum-sensing transcriptional regulators. 32 matched cddid_all.tbl CDD NF038245 NF038245 468428 bile_salt_hydro choloylglycine hydrolase. Bile salt hydrolase, also known as choloylglycine hydrolase, enables commensal or pathogenic bacteria in the digestive tract to escape the antimicrobial activity of bile acids, which are cholesterol derivatives conjugated to glycine or taurine. 314 matched cddid_all.tbl CDD NF038246 NF038246 468429 bile_salt_MFS conjugated bile salt MFS transporter. Members of this family are MFS transporters found regularly in the vicinity of bile acid hydrolases in Gram-positive bacteria such as Lactobacillus acidophilus and Enterococcus cecorum, and presumed to be bile salt MFS transporters, or transporter subunits. 409 matched cddid_all.tbl CDD NF038247 NF038247 439547 memb_stab_MspA membrane stabilizing protein MspA. 102 matched cddid_all.tbl CDD NF038248 NF038248 468430 FakA_VfrB fatty acid kinase catalytic subunit FakA. Fatty acid kinase A (FakA, also called VfrB), works with a fatty acid binding-protein partner (either FakB1 or FakB2 in Staphylococcus aureus, depending on the substrate) to assimilate host fatty acids for membrane biosynthesis. 549 matched cddid_all.tbl CDD NF038249 NF038249 468431 fatty_FakB1 fatty acid kinase binding subunit FakB1. FakB1 binds saturated fatty acids. Its paralog, FakB2 preferentially binds unsaturated fatty acids. 286 matched cddid_all.tbl CDD NF038250 NF038250 439550 nitrate_NreA nitrate respiration regulation accessory nitrate sensor NreA. NreA is a nitrate-binding, GAF domain-containing accessory protein to the two-component system NreBC. It is involved in the regulation of the the nitrate reductase operon narGHJI. 142 matched cddid_all.tbl CDD NF038251 NF038251 439551 AdcR_fam_Zn_TF zinc-dependent MarR family transcriptional regulator. This HMM represents one of several unusual clades within the MarR family transcription factors that bind Zn(2+) and regulate the response to zinc abundance or scarcity. Members include AdcR (adhesin competence regulator), which regulates expression of the high affinity zinc uptake transporter AdcABC and various other proteins. 143 matched cddid_all.tbl CDD NF038252 NF038252 439552 cable_major cable pilus major pilin CblA. 166 matched cddid_all.tbl CDD NF038253 NF038253 439553 GBS_IgA_bnd_BAC IgA Fc-binding protein BAC. The IgA Fc-region binding protein of Streptococcus agalactiae (group B streptococcus) is a surface-anchored virulence factor with a YSIRK-type signal sequence at the N-terminus and an LPXTG sorting signal near the C-terminus. It is also called beta-antigen. 1127 matched cddid_all.tbl CDD NF038254 NF038254 468432 T4SS_assoc_EirA T4SS-associated protein EirA. EirA (essential for intracellular replication A) was charactized in Coxiella burnetii as critical for replication in host vacuoles. Its absence appears to block secretion by the Dot/Icm type IV secretion system (T4SS), and family members occur strictly in species with T4SS. 152 matched cddid_all.tbl CDD NF038255 NF038255 468433 exopoly_VpsD VpsD family glycosyltransferase. Member of this family include VpsD (VC0920), involved in the biosynthesis of Vibrio polysaccharide, an exopolysaccharide component of biofilm matrix. 381 matched cddid_all.tbl CDD NF038256 NF038256 468434 exopoly_VpsF VpsF family polysaccharide biosynthesis protein. Vps genes contribute to biofilm formation by directing biosynthesis of the exopolysaccharide VPS (Vibrio polysaccharide), a major component of the biofilm matrix. Members of this family show some distant similarity to O-antigen ligases. 394 matched cddid_all.tbl CDD NF038257 NF038257 468435 exopoly_VpsP VpsP family polysaccharide biosynthesis protein. Vps genes contribute to biofilm formation by directing biosynthesis of the exopolysaccharide VPS (Vibrio polysaccharide), a major component of the biofilm matrix. The specific function of VpsP is not known. 213 matched cddid_all.tbl CDD NF038258 NF038258 468436 PBP4_Staph penicillin-binding protein PBP4. Members of this family penicillin-binding protein 4 (PBP4), as the name is used in Staphylococcus aureus and related species from the same genus. PBP4 is not essential. It has transpeptidase activity, provides low level beta-lactam resistance, and in mutant strains can contribute to high level beta-lactam resistance. 365 matched cddid_all.tbl CDD NF038259 NF038259 439559 ectoine_DoeA_2 ectoine hydrolase. This HMM describes a second family of ectoine hydrolase, related to TIGR02993. Members of both families carry the gene symbol DoeA. Ectoine is a compatible solute commonly used in halotolerant bacteria. This family was reported in halotolerant methylotrophs. 386 matched cddid_all.tbl CDD NF038260 NF038260 439560 ectoine_DoeB_2 N(2)-acetyl-L-2,4-diaminobutanoate deacetylase DoeB2. This HMM describes a second family of N-alpha-acetyl-L-2,4-diaminobutyrate deacetylase, unrelated to the previously recognized DoeB described in TIGR02994. Because of the lack of homology, we reassign the gene symbol for this family from doeB to doeB2 in the interest of clarity. Ectoine is a compatible solute commonly used in halotolerant bacteria. This family was reported in halotolerant methylotrophs. 378 matched cddid_all.tbl CDD NF038261 NF038261 468437 rhodoquin_RquA rhodoquinone biosynthesis methyltransferase RquA. 217 matched cddid_all.tbl CDD NF038262 NF038262 468438 SiaB_fam_kinase SiaB family protein kinase. 177 matched cddid_all.tbl CDD NF038263 NF038263 439563 prot_phos_SiaA biofilm regulation protein phosphatase SiaA. 658 matched cddid_all.tbl CDD NF038264 NF038264 439564 kinase_SiaB biofilm regulation protein kinase SiaB. 176 matched cddid_all.tbl CDD NF038265 NF038265 439565 phos_prot_SiaC biofilm regulation phosphoprotein SiaC. The founding member of the SiaC family, PA0170 from Pseudomonas aeruginosa (NP_248860.1), is phosphorylated on Thr-68, as part of a regulatory system that affects aggregate and biofilm formation. The broader family, originally named DUF1987, if described by Pfam model PF09345. 122 matched cddid_all.tbl CDD NF038266 NF038266 468439 diguan_SiaD biofilm regulation diguanylate cyclase SiaD. 252 matched cddid_all.tbl CDD NF038267 NF038267 468440 amidase_AmiC N-acetylmuramoyl-L-alanine amidase AmiC. 407 matched cddid_all.tbl CDD NF038268 NF038268 439568 TF_SarA global transcriptional regulator SarA. SarA (staphylococcal accessory regulator) is a transcription factor affecting multiple virulence-associated processes, such as biofilm formation and protease secretion. 121 matched cddid_all.tbl CDD NF038269 NF038269 439569 lipase_LipE lipase LipE. 407 matched cddid_all.tbl CDD NF038270 NF038270 468441 membran_MsaC Msa family membrane protein. Msa (SA1233) was first described in Staphylococcus aureus as Modulator of SarA, but later reports suggested the locus was actually a non-coding gene, msaC, in the 3'-untranslated region of cold shock protein CspA (msaB). To construct the seed alignment for this HMM, we found full-length homologs across a broad taxonomic range within the Firmicutes, with the appearance of well-organized transmembrane alpha-helices. We further note amino acid substitution patterns suggesting translation into functional protein, and generally (in our opinion) the look of real protein rather than spurious translation, such as richness in Lys and Arg residues at the C-terminus just after the last transmembrane segment. 130 matched cddid_all.tbl CDD NF038271 NF038271 468442 strep_PBP2X penicillin-binding protein PBP2X. 748 matched cddid_all.tbl CDD NF038272 NF038272 439572 strep_PBP1A streptococcal penicillin-binding protein PBP1A. PBP1a is a bifunctional enzyme of cell wall biosynthesis, performing both polymerization of GlcNAc-MurNAc chains (glycosyltransfer, GT) and peptide cross-linking (transpeptidation, TP). 657 matched cddid_all.tbl CDD NF038273 NF038273 468443 strep_PBP3 streptococcal D-alanyl-D-alanine carboxypeptidase PBP3. PBP3 (penicillin-binding protein 3) is the lone D-alanyl-D-alanine carboxypeptidase in Streptococcus pneumoniae. The gene is known as pbp3 or dacA. 407 matched cddid_all.tbl CDD NF038274 NF038274 468444 strep_PBP1B streptococcal penicillin-binding protein PBP1B. 745 matched cddid_all.tbl CDD NF038275 NF038275 439575 Myrrnad "MyrrNad domain. This HMM, the N-terminal domain counterpart to MyrrCad (NF033158), represents the N-terminal regions of a family of LRR-like repeat proteins. The coinage ""MyrrCad"", rendered without full capitalization because it is an acronym rather than an amino acid sequence motif, signifies ""MYcoplasma Repeat-Rich protein C-terminal Anchor Domain.""" 81 matched cddid_all.tbl CDD NF038276 NF038276 439576 strep_PBP2A streptococcal penicillin-binding protein PBP2A. 716 matched cddid_all.tbl CDD NF038277 NF038277 468445 accessory_MacP cell wall synthase accessory phosphoprotein MacP. MacP was characterized in Streptococcus pneumoniae as a partner protein to the cell wall synthase PBP2a, required for its activity. 98 matched cddid_all.tbl CDD NF038278 NF038278 468446 strep_PBP2B streptococcal penicillin-binding protein PBP2B. 678 matched cddid_all.tbl CDD NF038279 NF038279 439579 TF_CBS_SpxR CBS-HotDog domain-containing transcription factor SpxR. SpxR from Streptococcus pneumoniae, like its full-length homolog YtoI from Listeria monocytogenes, is a transcriptional regulator with an N-terminal DNA-binding domain, and with CBS and HotDog domains. SpxR regulates the pyruvate oxidase SpxB. 427 matched cddid_all.tbl CDD NF038280 NF038280 468447 IS607_TnpB IS607 family element RNA-guided endonuclease TnpB. 431 matched cddid_all.tbl CDD NF038281 NF038281 468448 IS200_TnpB IS200/IS605 family element RNA-guided endonuclease TnpB. 359 matched cddid_all.tbl CDD NF038282 NF038282 468449 LapC_YejM_PbgA LPS biosynthesis-modulating metalloenzyme YejM. YejM (LapC, PbgA) belongs to a regulatory system that controls the activity of LpxC, the enzyme that catalyzes the first committed step in the LPS synthesis. The earlier report (2015) by Dalebroux, et al (PMID: 25856753), which assigned a role in cardiolipin transport and introduced the name PbgA (phoPQ-barrier gene A), is no longer considered accurate. 584 matched cddid_all.tbl CDD NF038283 NF038283 468450 viperin_w_prok viperin family antiviral radical SAM protein. Homologs of a viral defense radical SAM enzyme found in Homo sapiens, viperin (RSAD2), occur in prokaryotes with a strong bias toward placement in phage defense islands, encoded next to CRISPR system and restriction enzyme genes. Further investigation shows members indeed perform the anti-viral function of synthesizing modified ribonucleotides such as ddhCTP, ddh-guanosine triphosphate (ddhGTP) and ddh-uridine triphosphate (ddhUTP). Those non-standard ribonucleotides can interfere with viral replication machinery. 280 matched cddid_all.tbl CDD NF038284 NF038284 439584 bifunc_DapF bifunctional diaminopimelate epimerase/glutamate racemase. 254 matched cddid_all.tbl CDD NF038285 NF038285 468451 deiodinase_rel deiodinase family protein. Members of this protein family are related to iodothyronine deiodinase, a human selenoprotein. Some members of this family (although not of the seed alignment) likewise are selenoproteins, with the selenium-containing motif GSYTUPPF. 347 matched cddid_all.tbl CDD NF038286 NF038286 439586 peptide_16_IlvX peptide IlvX. The very short peptide IlvX, 16 amino acids long, is found in Escherchia coli and related species as the apparent first encoded peptide from the ilvXGEDA operon, for which ilvL, further upstream, is the classical attentuator system leader peptide controlling expression. IlvX is preceded by a ribosome binding site, terminates just two nucleotides from ilvG, and has evidence of increased protein expression during isoleucine expression. Its biological role is unknown, and skepticism that IlvX has any molecular function after its biosynthesis may be appropriate. 16 matched cddid_all.tbl CDD NF038287 NF038287 468452 Amuc_1100_fam Amuc_1100 family pilus-like protein. 257 matched cddid_all.tbl CDD NF038288 NF038288 468453 chaper_GTP_ZigA zinc metallochaperone GTPase ZigA. The GTPase ZigA (Zur-induced GTPase A) is a zinc metallochaperone thought to be important for histidine utilization (HUT), supplying Zn to the histidine ammonia-lyase HutH when required under low-Zn conditions. 390 matched cddid_all.tbl CDD NF038289 NF038289 468454 Zn_piracy_ZnuD zinc piracy TonB-dependent receptor ZnuD. ZnuD, as described in Acinetobacter baumannii, works with the zinc uptake transporter ZnuABC to overcome sequestration of zinc by the host. ZnuD, TonB-dependent receptor, pirates zinc from the host protein calprotectin. A similar ZnuD family protein, outside the current scope of this model, has been characterized in Neisseria. 684 matched cddid_all.tbl CDD NF038290 NF038290 468455 repM_Acin replication initiation protein RepM. 304 matched cddid_all.tbl CDD NF038291 NF038291 468456 rep_pAB02_ORF2 plasmid replication DNA-binding protein. This uncharacterized protein, with an N-terminal DNA-binding helix-turn-helix domain, occurs in replication regions of a large number of Acinetobacter plasmids. The founding members of this family, AAR00518.1 and WP_000839337.1 from plasmids pAB02 and pMAC, are referred to as ORF2 there, sitting adjacent to RepM, which in turn is adjacent to the DNA repeat region at each plasmid's origin of replication. 172 matched cddid_all.tbl CDD NF038292 NF038292 439592 SagF_ScfC SagF family protein. This protein of unknown function SagF is encoded by the extended locus that includes the key proteins of streptolysin S biosynthesis. Because it is encoded just upstream of genes for ABC transporter permease and ATPase components of an ABC transporter, one group calls the protein a probable ABC transporter substrate-binding protein, designated ScfC (subcutaneous fitness C). However, the protein lacks any readily detected homology to any other ABC transporter substrate-binding protein. Additional members of the family are found in other loci producing RiPP class peptide natural products related to streptolysin S, such clostridiolysin S. 225 matched cddid_all.tbl CDD NF038293 NF038293 439593 permease_SagG SagG family ABC transporter permease subunit. Members of this family are ABC transporter permease subunits, typically found in extended loci for the production of bacterial cytotoxins such as streptolysin S and clostridiolysin S. 370 matched cddid_all.tbl CDD NF038294 NF038294 439594 lipo_LIC11966 ErpY-like lipoprotein. Members of this family are surface-exposed lipoproteins from the genus Leptospira. Members include the founding member LIC11966, reported to be a fibrinogen-binding protein. 158 matched cddid_all.tbl CDD NF038295 NF038295 468457 EPS_HpsP hormogonium polysaccharide biosynthesis glycosyltransferase HpsP. 388 matched cddid_all.tbl CDD NF038296 NF038296 468458 HisXaaSer_A2 His-Xaa-Ser repeat protein HxsA2. This model represents a short form of the His-Xaa-Ser repeat protein HxsA, while TIGR03979 represents a long form. In the short form, sequences average about 97 amino acids in length and end with the HXS repeat region. 96 matched cddid_all.tbl CDD NF038297 NF038297 468459 hybrid_HK_HrmK hybrid histidine kinase/response regulator HrmK. HrmK (hormogonium hybrid histidine kinase) is a regulator found in heterocyst-forming Cyanobacteria. It affects the formation of hormogonia, motility-conferring filaments produced only by heterocyst-forming cyanobacteria. 606 matched cddid_all.tbl CDD NF038298 NF038298 439598 EPS_HpsO hormogonium polysaccharide biosynthesis glycosyltransferase HpsO. 388 matched cddid_all.tbl CDD NF038299 NF038299 468460 EPS_HpsN hormogonium polysaccharide biosynthesis glycosyltransferase HpsN. 317 matched cddid_all.tbl CDD NF038300 NF038300 468461 EPS_HpsL hormogonium polysaccharide biosynthesis protein HpsL. 533 matched cddid_all.tbl CDD NF038301 NF038301 468462 EPS_HpsA hormogonium polysaccharide biosynthesis protein HpsA. 1486 matched cddid_all.tbl CDD NF038302 NF038302 439602 EPS_HpsE hormogonium polysaccharide biosynthesis glycosyltransferase HpsE. 307 matched cddid_all.tbl CDD NF038303 NF038303 468463 EPS_HpsB hormogonium polysaccharide secretion pseudopilin HpsB. 210 matched cddid_all.tbl CDD NF038304 NF038304 468464 EPS_HpsC hormogonium polysaccharide secretion pseudopilin HpsC. 315 matched cddid_all.tbl CDD NF038305 NF038305 468465 HpsJ_fam HpsJ family protein. HpsJ (hormogornium polysaccharide J) is thought to be involved in the biosynthesis or secretion of an extracellular polysaccharide shared by many Cyanobacteria. 230 matched cddid_all.tbl CDD NF038307 NF038307 439606 EPS_acetyl_HpsU hormogonium polysaccharide biosynthesis acetyltransferase HpsU. HpsU is related to the colanic acid biosynthesis acetyltransferase WcaF, which acts on a fucose residue in a disaccharide attached to a lipid carrier. 178 matched cddid_all.tbl CDD NF038308 NF038308 468466 RNA_repair_RtcR RNA repair transcriptional activator RtcR. 527 matched cddid_all.tbl CDD NF038309 NF038309 439608 HisXaaSer_A3 His-Xaa-Ser repeat protein HxsA3. This model represents an alternate form of the His-Xaa-Ser repeat protein HxsA, while TIGR03979 represents a more common form. The model covers a conserved N-terminal region, followed by the His-Xaa-Ser repeat region, but does not cover the C-terminal region, which is highly variable in this branch of His-Xaa-Ser repeat family protein. 81 matched cddid_all.tbl CDD NF038310 NF038310 468467 lysogeny_AimR AimR family lysis-lysogeny pheromone receptor. The founding member of this family, AimR (arbitrium receptor), is a DNA-binding phage regulatory protein that acts as a receptor for a 6-amino acid signaling peptide cleaved from the C-terminus of AimP. AimR controls expression of AimX, the third member of the quorum sensing-like arbitrium system and an inhibitor of phage lysogeny. 363 matched cddid_all.tbl CDD NF038312 NF038312 468468 SCO5918_fam SCO5918 family protein. 98 matched cddid_all.tbl CDD NF038313 NF038313 439611 HisXaaSer_A4 His-Xaa-Ser repeat protein HxsA4. 90 matched cddid_all.tbl CDD NF038314 NF038314 439612 epimerase_MslH lasso peptide C-terminal Trp epimerase. 439 matched cddid_all.tbl CDD NF038315 NF038315 468469 HxsD_rel HxsD-like protein. Members of this family resemble HxsD, although usually shorter. HxsD is a possible chaperone of a radical SAM-catalyzed peptide modification system. Members of this family often are found in the context of other Hxs system proteins, suggesting it may be one of a pair of chaperones in those systems. 62 matched cddid_all.tbl CDD NF038316 NF038316 468470 DrmE_fam DrmE family protein. Members of this extremely diverse family include DrmE, a protein of unknown function sometimes found as part of a DISARM antiphage defense systems. 832 matched cddid_all.tbl CDD NF038317 NF038317 468471 DISARM_DrmD DISARM system SNF2-like helicase DrmD, long form. DrmD, a SNF2-like helicase, is a component of class 1 DISARM (Defence Island System Associated with Restriction Modification), which contains a DNA adenine N6 methyltransferase. 1023 matched cddid_all.tbl CDD NF038318 NF038318 468472 DISARM_DrmD_b DISARM system SNF2-like helicase DrmD, short form. DrmD, a SNF2-like helicase, is a component of class 1 DISARM (Defence Island System Associated with Restriction Modification), which contains a DNA adenine N6 methyltransferase. This HMM describes a distinct form that is somewhat shorter than the majority of DrmD proteins. 868 matched cddid_all.tbl CDD NF038319 NF038319 468473 DISARM_DrmC_I DISARM system phospholipase D-like protein DrmC. DrmC, a phospholipase D (PLD) domain-containing protein, is a component of DISARM (Defence Island System Associated with Restriction Modification). This HMM represents most but not all DrmC of class I DISARM systems, which contain a DNA adenine N6 methyltransferase. DrmC appears to be an auxiliary rather than core component of DISARM, required for resistance to some phage but not others. 234 matched cddid_all.tbl CDD NF038322 NF038322 468474 ImpA_fam_HExGH ImpA family metalloprotease. Members of this family are metalloproteases related to the ImpA from Pseudomonas aeruginosa (PA0572 in strain PAO1), a virulence factor that cleaves CD44 on the surface of human macrophages, inhibiting phagocytosis. Members of this family are distinguished by a strong motif, CGxGCSGNPxD, just a few residues upstream of the familiar metalloprotease motif HExxH (typically HELGH here) and completely lacking in more distant homologs of ImpA. 879 matched cddid_all.tbl CDD NF038323 NF038323 439619 DISARM_DrmE DISARM system-associated protein DrmE. DrmE appears as an fifth component in a subset of class II DISARM phage defense systems. Its role in DISARM is unknown. 785 matched cddid_all.tbl CDD NF038324 NF038324 468475 DrmB_fam DrmB family protein. Members of the seed alignment for this HMM are the DISARM anti-phage system protein DrmB from both class I and class II. 594 matched cddid_all.tbl CDD NF038325 NF038325 468476 DISARM_DrmAS DISARM system helicase DrmA, short form. Members of the seed alignment for this family are DrmA helicases from representative DISARM anti-phage gene clusters, mostly from class I systems, but a few from class II systems. This HMM excludes those members of class II systems that both are divergent in sequence from this set and have a characteristic long insert. 1155 matched cddid_all.tbl CDD NF038326 NF038326 468477 DISARM_DrmAL DISARM system helicase DrmA, long form. This HMM identifies some DrmA helicases from class II DISARM anti-phage systems, and none from class I systems. Members distinguished from the shorter, more common form (see NF038325) both by sequence divergence in regions that align and by an insert that makes members of this set longer. 1321 matched cddid_all.tbl CDD NF038327 NF038327 439622 c-di-AMP_CdaM diadenylate cyclase CdaM. CdaM is one of several classes of diadenylate cyclase (the cyclic di-AMP synthesizing enzyme), characterized originally in Mycoplasma pneumoniae. 196 matched cddid_all.tbl CDD NF038328 NF038328 439623 c-di-AMP_CdaS sporulation-specific diadenylate cyclase CdaS. 191 matched cddid_all.tbl CDD NF038329 NF038329 468478 gly_rich_SclB LPXTG-anchored collagen-like adhesin Scl2/SclB. SclB (or Scl2 - streptococcal collagen-like protein 2) is an LPXTG-anchored surface-anchored adhesin with a variable-length region of triple helix-forming collagen-like Gly-Xaa-Xaa repeats. 440 matched cddid_all.tbl CDD NF038330 NF038330 468479 adhesin_SclA LPXTG-anchored collagen-like adhesin Scl1/SclA. Scl1 (streptococcal collagen-like protein 1), also called SclA, is an LPXTG-anchored surface-anchored adhesin with a variable-length region of triple helix-forming collagen-like Gly-Xaa-Xaa repeats. 388 matched cddid_all.tbl CDD NF038331 NF038331 439626 Tsi3_fam Tsi3 family protein. Members of this family are related Tsi3, the immunity protein for the type VI secretion system effector muramidase Tse3. 116 matched cddid_all.tbl CDD NF038332 NF038332 468480 rSAM_rare_HxsC4 radical SAM protein HxsC4. This rare radical SAM protein, closer to HxsC among previously defined families, shows up regularly in the context of putative RiPP target HxsA4 and additional members of the His-Xaa-Ser repeats system. 335 matched cddid_all.tbl CDD NF038334 NF038334 439628 malate_HK_MalK malate sensor histidine kinase MalK. 533 matched cddid_all.tbl CDD NF038335 NF038335 468481 YPO0640_fam YrhA family protein. Members of this family include YrhA from Escherichia coli, which is found as a pseudogene in the K-12 model strain, and YPO0640 from Yersinia pestis. Only full-length forms are used in the seed alignment for this HMM. The function of this protein family is unknown. 149 matched cddid_all.tbl CDD NF038336 NF038336 468482 YjiT_fam STY4851/ECs_5259 family protein. Full length members of this family, about 1100 amino acids long, include STY4851 from Salmonella enterica subsp. enterica serovar Typhi str. Ty2 and ECs_5259. The family also includes the half-length pseudogene translation YjiT from Escherichia coli str. K-12 substr. MG1655, for which the corresponding complete protein is WP_048814575. The function is unknown. 1086 matched cddid_all.tbl CDD NF038337 NF038337 439631 FAAL_FadD21 fatty-acid--AMP ligase FAAL21/FadD21. 579 matched cddid_all.tbl CDD NF038338 NF038338 439632 FAAL_FadD28 fatty-acid--AMP ligase FAAL28/FadD28. 580 matched cddid_all.tbl CDD NF038339 NF038339 468483 FAAL_FadD32 "long-chain-fatty-acid--AMP ligase FAAL32/FadD32. FadD32, also called FAAL32, is a marker enzyme for the biosynthesis of the type of mycolic acids, the very large ""eumycolic acids"", found in Mycobacterium." 625 matched cddid_all.tbl CDD NF038340 NF038340 468484 SAR2788_fam SAR2788 family putative toxin. 177 matched cddid_all.tbl CDD NF038341 NF038341 468485 ligase_FadD4 fatty-acid--CoA ligase FadD4. 504 matched cddid_all.tbl CDD NF038342 NF038342 439636 FACL_FadD6 long-chain-acyl-CoA synthetase FadD6. 584 matched cddid_all.tbl CDD NF038343 NF038343 439637 ligase_FadD11 fatty acid--CoA ligase FadD11. The fatty-acid-coA ligase FadD11 is disrupted in multiple strains of Mycobacterium tuberculosis, including the type strain H37Rv. This HMM represents full-length versions. 585 matched cddid_all.tbl CDD NF038344 NF038344 439638 bile_CoA_BaiB bile acid--CoA ligase BaiB. 504 matched cddid_all.tbl CDD NF038345 NF038345 468486 wall_hydro_RipC peptidoglycan hydrolase RipC. RipC is a peptidoglycan hydrolase, found in species such as Mycobacterium tuberculosis, that is activated by conformation change sent as a signal by the cell division-regulating transporter-like complex FtsEX. Members of this family are distinguished from more distant homologs by a Pro/Gly-rich region. 361 matched cddid_all.tbl CDD NF038346 NF038346 468487 FtsX_actino permease-like cell division protein FtsX. 307 matched cddid_all.tbl CDD NF038347 NF038347 468488 FtsX_Gpos permease-like cell division protein FtsX. The FtsEX complex resembles an ABC transporter, where FtsE is the ATPase and the membrane subunit FtsX resembles a permease subunit. But rather than transporting any substrate, the complex acts in cell division by undergoing conformational changes that alter the activity of cell wall hydrolases located outside the plasma membrane. The complex is widely conserved in bacteria, but also extremely divergent in sequence between different lineages. 296 matched cddid_all.tbl CDD NF038348 NF038348 439642 T2SS_HK histidine kinase. 574 matched cddid_all.tbl CDD NF038349 NF038349 439643 dPGM_arch 2,3-diphosphoglycerate-dependent phosphoglycerate mutase. 193 matched cddid_all.tbl CDD NF038350 NF038350 439644 taxis_HmpF pilus motility taxis protein HmpF. 553 matched cddid_all.tbl CDD NF038351 NF038351 439645 cyt_ox_assem_30 cytochrome oxidase small assembly protein. Members of this family are small proteins, averaging about 40 amino acids in length as predicted, with a conserved core region just 30 amino acids long. The conserved region contains a highly hydrophobic probable transmembrane alpha helix. Members regularly are found encoded in the context of much larger cytochrome oxidase complex subunits, in members of the Burkholderiales such as Bordetella pertussis and Burkholderia sp. 30 matched cddid_all.tbl CDD NF038353 NF038353 468489 FxLYD_dom FxLYD domain. The uncharacterized FxLYD domain, named for the strongest (but not invariant) motif, spans about 75 amino acids usually in the C-terminal region of a protein. 71 matched cddid_all.tbl CDD NF038354 NF038354 439647 trnsprt_adja_43 putative transporter small subunit. Members of this family are very small, highly hydrophobic proteins regularly encoded adjacent to transporters and likely to be previously overlooked small subunits of transporters. 39 matched cddid_all.tbl CDD NF038355 NF038355 439648 FDH3_beta formate dehydrogenase FDH3 subunit beta. Members of this family are the beta subunit of the FDH3 type of formate dehydrogenase as found in Methylorubrum (Methylobacterium) extorquens. 180 matched cddid_all.tbl CDD NF038356 NF038356 439649 actino_DLW39 DLW-39 family protein. DLW-39 is a small protein, restricted to the Actinobacteria. Its sequence features a highly hydrophobic stretch of about 15 amino acids, flanked by pairs of basic residues, and C-terminal region in which most members share the motif DLW. Members typically are about 39 amino acids in length when a start site supported by sequence conservation is chosen. The family is uncharacterized. 38 matched cddid_all.tbl CDD NF038357 NF038357 468490 BN6_48550_fam BN6_48550 family protein. This uncharacterized domain, named for its occurrence in the arbitrarily chosen protein BN6_48550, seems restricted to the Actinobacteria. This domain tends to be N-terminal in longer proteins that contain additional domains, such TIR-like (PF10137) or glycosyltransferase domains. The function is unknown. 338 matched cddid_all.tbl CDD NF038358 NF038358 468491 phophono_PhpG CMP-5'-phosphonoformate--3-phosphoglycerate phosphonoformyl transferase. Members of this family, including founding member PhpG, are inferred to be the enzyme CMP-5'-phosphonoformate--3-phosphoglycerate phosphonoformyl transferase, conserved in a number of phosphonate natural product biosynthesis pathways. 417 matched cddid_all.tbl CDD NF038360 NF038360 439653 rad_fix_GrcA3 autonomous glycyl radical cofactor GrcA3. This small protein, like GrcA and GrcA2, is a lineage-specific small protein related to the glycyl radical active site-containing C-terminal region of pyruvate formate-lyase (PFL, also called formate C-acetyltransferase) from similar species. Because PFL is prone to damage and inactivation, this protein is made as a spare part that fills in for the portion of the protein that was damaged and lost. The distinct families we now call GrcA, GrcA2, and GrcA3 all have the surprising property of being much more closely related to some full length PFL than to members of the other GrcA-series families. 78 matched cddid_all.tbl CDD NF038361 NF038361 439654 rSAM_Sden_1168 Sden_1168 family B12-binding radical SAM P-methyltransferase. 560 matched cddid_all.tbl CDD NF038362 NF038362 468492 Sden_1164_fam Sden_1164 family protein. Sden_1164, homologous to nucleotidyltransferases, is the founding member of a family that co-occurs with the Sden_1168 family of B12-binding radical SAM P-methyltransferases. The system to which these two protein families belong is uncharacterized. 266 matched cddid_all.tbl CDD NF038363 NF038363 439656 SecM_small secA translation cis-regulator SecM, small type. Members of this family are a short form of SecM, found in members of the Pasteurellale, only three-fifths as long as the SecM of Escherichia coli. It is likewise encoded immediately upstream of the gene for SecA. The speed of translation of SecM and processing of its signal peptide provides a control mechanism that fine-tunes the translation of SecA. 103 matched cddid_all.tbl CDD NF038364 NF038364 439657 AglZ_HisF2_fam AglZ/HisF2 family acetamidino modification protein. 248 matched cddid_all.tbl CDD NF038365 NF038365 468493 Sca4_fam Sca4 family spreading effector. Sca4 (surface cell antigen 4) is a surface protein of Rickettsia (intracellular pathogens) that mediates protrusion from an infected cell and engulfment by the adjacent cell, in order to mediate spreading. 1017 matched cddid_all.tbl CDD NF038367 NF038367 439660 OM_lipo_TUL4 TUL4 family lipoprotein. TUL4 family lipoproteins, including paralogs designated LpnA and LpnB, are highly expressed on the outer membrane in the genus Francisella. 149 matched cddid_all.tbl CDD NF038368 NF038368 439661 P2_Rz1 Rz1-like lysis system protein LysC. LysC is an Rz1-like component of a phage lytic system, substantially overlapping although not fully embedded in the gene for the Rz-like LysB component. The phage lysis defect in the absence of a functional LysB/LysC system is appears in the presence of high concentrations of divalent cations. 85 matched cddid_all.tbl CDD NF038369 NF038369 468494 GroEL3_Chlamy variant chaperonin GroEL3. GroEL3, as found in Chlamydia trachomatis, is an atypical paralog of the normal GroEL, divergent in function and not encoded next to a GroES. 506 matched cddid_all.tbl CDD NF038370 NF038370 439663 GroEL2_Chlamy variant chaperonin GroEL2. GroEL2, as found in Chlamydia trachomatis, is an atypical paralog of the normal GroEL, divergent in function and not encoded next to a GroES. 533 matched cddid_all.tbl CDD NF038371 NF038371 439664 phegan_RiPP_fam pheganomycin family RiPP precursor. 37 matched cddid_all.tbl CDD NF038372 NF038372 439665 tryptorubin_fam tryptorubin family RiPP precursor. Tryptorubin A is the founding member of the atropitides, a class of polycyclic RiPP natural product featuring crosslinks through aromatic amino acids. 26 matched cddid_all.tbl CDD NF038373 NF038373 468495 cittilin_RiPP cittilin family RiPP precursor. Cittilins, such as cittilin A from Myxococcus xanthus, are RiPP natural products. Known examples of the peptide precursor end with sequence YXYY. The precursor may be only 27 amino acids long. The mature form contains bicyclic tetrapeptide scaffold with biaryl and aryl-oxygen-aryl ether bonds. The biosynthetic gene cluster includes a cytochrome P450 enzyme and a methyltransferase. 27 matched cddid_all.tbl CDD NF038374 NF038374 439667 omphalotin_tail omphalotin family RiPP precursor domain. This HMM describes a RiPP cyclopeptide precursor peptide region that appears as the tail region of certain self-sacrificing fungal methyltransferases . The founding member of the family is omphalotin A precursor region. 40 matched cddid_all.tbl CDD NF038375 NF038375 439668 crocagin_RiPP crocagin A family RiPP precursor. 21 matched cddid_all.tbl CDD NF038376 NF038376 439669 microvionin microvionin family RiPP. The antibacterial RiPP peptide microvionin, from Microbacterium arborescens, is the founding member of lipolanthine-type natural products. 27 matched cddid_all.tbl CDD NF038377 NF038377 439670 TglA_fam_RiPP TglA family RiPP precursor. 49 matched cddid_all.tbl CDD NF038378 NF038378 439671 DNZ54_00345_fm DNZ54_00345 family phage region protein. Members of this uncharacterized protein family appear to be membrane proteins, and are found in bacteria encoded within prophage regions. 124 matched cddid_all.tbl CDD NF038379 NF038379 468496 amino_Aden_PurZ succino-amino-deoxyadenylate synthase PurZ. 292 matched cddid_all.tbl CDD NF038380 NF038380 468497 phage_DpoZ_1 aminoadenine-incorporating DNA polymerase DpoZ. 604 matched cddid_all.tbl CDD NF038381 NF038381 468498 phage_DpoZ_2 aminoadenine-incorporating DNA polymerase DpoZ. 753 matched cddid_all.tbl CDD NF038382 NF038382 439675 RaxX_RiPP RaxX family RiPP. RaxX (Required for Activation of XA21-mediated immunity X), produced by many strains of Xanthomonas, is a RiPP microbial peptide family. Characterized members have a sulfated tyrosine and interact with the rice immune receptor XA21. 58 matched cddid_all.tbl CDD NF038383 NF038383 468499 lipo_LIC12048 LIC12048 family lipoprotein. 1441 matched cddid_all.tbl CDD NF038384 NF038384 439677 zinc_YnfU_fam YnfU family zinc-binding protein. The founding member of this family of putative zinc-binding proteins is YnfU, from the Qin prophage region of E. coli K-12. 52 matched cddid_all.tbl CDD NF038385 NF038385 439678 IS66_access_TnpA IS66-like element accessory protein TnpA. 190 matched cddid_all.tbl CDD NF038387 NF038387 439679 CBS_CbpA cyclic di-AMP binding protein CbpA. The founding member of this family, Lmo0553 from Listeria monocytogenes, now called CbpA, binds cyclic di-AMP, a signaling molecule, through its CBS (cystathionine-beta-synthase ) domain. 209 matched cddid_all.tbl CDD NF038388 NF038388 439680 sigmaX_act_ComW sigma(X)-activator ComW. The pneumococcal DNA-binding protein ComW, critical for natural transformation, interacts with the sigma factor that is a master regulator for competence, sigma(X). 73 matched cddid_all.tbl CDD NF038389 NF038389 468500 ArsS_fam_HK ArsS family sensor histidine kinase. ArsS in Helicobacter pylori is a sensor histidine kinase participating in a two-component system that controls the response to acid conditiions encountered during the process of gastric colonization. This HMM identified ArsS itself but also a broader collection of apparent orthologs from closely related non-gastric colonizers such as Helicobacter hepaticus, Campylobacter jejuni and Wolinella succinogenes. See BlastRule NBR014349 for specific identification of ArsS itself, distinguished by a signature His residue that becomes protonated at low pH. 402 matched cddid_all.tbl CDD NF038390 NF038390 468501 Nsidase_PpnN nucleotide 5'-monophosphate nucleosidase PpnN. PpnN (pyrimidine/purine nucleotide 5'-monophosphate nucleosidase), widely conserved in gamma proteobacteria, plays a role in purine homeostasis. It can bind the the stringent response alarmones ppGpp and pppGpp and then, because of allosteric changes, have a much higher rate of cleavage of preferred substrate GMP. PpnN was previously known in E. coli as YgdH. 450 matched cddid_all.tbl CDD NF038391 NF038391 468502 streptophobe streptophobe family protein. Members of this family of uncharacterized probably membrane proteins are restricted almost entirely to the genus Streptomyces, and are highly hydrophobic through the aligned region, hence our coinage of the name streptophobe. Member SCO7274 from Streptomyces coelicolor A3(2) was shown to be expressed as protein. 403 matched cddid_all.tbl CDD NF038392 NF038392 439684 div_DrpB_YedR cell division protein DrpB. DrpB (division ring protein B) is a non-essential cell division protein with a limited taxonomic range, found in enteric bacteria such as Escherichia coli. 86 matched cddid_all.tbl CDD NF038393 NF038393 439685 lipo_LIC_10705 LIC_10705 family lipoprotein. The LIC_10705 family of lipoproteins, found in the genus Leptospira, includes tandem-encoded paralogs such as LIC_10705 and LIC_10706 in L. interrogans serovar Copenhageni str. Fiocruz L1-130. 178 matched cddid_all.tbl CDD NF038394 NF038394 439686 lipo_LipL32 major surface lipoprotein LipL32. LipL32, a surface lipoprotein, is found in the genus Leptospira only in pathogenic species, where it is the most abundant surface protein. LipL32 belongs to a broader family of surface lipoproteins (see PF12103) found also in other host-colonizing bacteria such as Pseudoalteromonas tunicata. 269 matched cddid_all.tbl CDD NF038395 NF038395 439687 nocathioamide nocathioamide family RiPP precursor. 49 matched cddid_all.tbl CDD NF038396 NF038396 439688 NF038396 NF038396 family protein. This small, highly hydrophobic, uncharacterized, strictly actinobacterial protein shows hints of sequence similarity to the envelope stress response protein PspG found in some proteobacteria. It sometimes occurs as a tail domain attached to dihydrofolate reductases. 59 matched cddid_all.tbl CDD NF038397 NF038397 439689 AB5_pltB_like subtilase family AB5 toxin binding subunit. Members of this family are the B subunit of AB5 toxins such as the ADP-ribosylating cytotoxin subtilase, which is related to pertussis toxin. These B subunits, in general, form homopentamers. This family does not include any related pertussis toxin subunits (such as PtxB, PtxC, or PtxE), although some members of this family may have carried legacy annotations saying they are pertussis toxin proteins. 132 matched cddid_all.tbl CDD NF038399 NF038399 439690 NH_RiPP_Os17 Os1348 family NHLP clan protein. This HMM describes a region about 63 amino acids in length, including RiPP precursors Os1348 and Franean1_4349, showing some sequence similarity to both NHLP family RiPP precursors and to the nitrile hydratase alpha subunit itself. Some members of the family are long proteins, with this domain at or near the N-terminus. 63 matched cddid_all.tbl CDD NF038402 NF038402 439691 TroA_like helical backbone metal receptor. 219 matched cddid_all.tbl CDD NF038403 NF038403 468503 perm_prefix_1 permease prefix domain 1. The permease prefix domain 1 is found as the N-terminal domain of putative permeases resembling ABC transporter permeases, and also of hypothetical proteins of unknown function. In at least some permease families, this prefix domain is only variably present, and may be replaced by a different, seemingly unrelated prefix domain. 59 matched cddid_all.tbl CDD NF038404 NF038404 439693 perm_prefix_2 permease prefix domain 2. The permease prefix domain 2 is found as the N-terminal domain of putative permeases resembling ABC transporter permeases. In at least some permease families, this prefix domain is only variably present, and may be replaced by a different, seemingly unrelated prefix domain. This domain is considerably less common than permease prefix domain 1 (NF038404). 62 matched cddid_all.tbl CDD NF039170 NF039170 468504 SdrH_fam_CTERM SdrH family protein C-terminal domain. The founding member of this family of staphylococcal proteins, SdrH from Staphylococcus epidermidis, is one of three MSCRAMM family proteins, but is atypical in lacking a recognizable LPXTG-like C-terminal recognition sequence for cell wall anchoring. This HMM represents the entire region C-terminal to the repetitive, low-complexity region that is a feature of all members of this family. That repetitive region consists mostly of Ser-Asp dipeptides in S. epidermidis but has radically different compositions in other species. 163 matched cddid_all.tbl CDD NF040463 NF040463 439695 all3515_fam all3515 family Zur-repressed PEP-CTERM protein. Full-length members of this family have an N-terminal signal peptide and a C-terminal PEP-CTERM (or related) recognition site for sorting and cleavage by exosortase, a probable transpeptidase for attachment to the outer membrane. The founding member of this family, all3515 from Anabaena sp. strain PCC 7120, showed the greatest upregulation of any protein to challenge by zinc deficiency, over 250 fold. 227 matched cddid_all.tbl CDD NF040464 NF040464 468505 SCO3374_fam "SCO3374 family protein. This HMM describes a family restricted to the genus Streptomyces. The HMM produces scores that are significant, although below the cutoffs set for this model, to about 10 percent of the proteins in the seed alignment of Pfam model PF09250.11, designated ""bifunctional DNA primase/polymerase, N-terminal""" 163 matched cddid_all.tbl CDD NF040465 NF040465 439697 T7_gp19.5 gp19.5 family protein. Members of this family are phage proteins in the family of gp19.5 of phage T7. 47 matched cddid_all.tbl CDD NF040466 NF040466 468506 ydjY_domain YdjY domain. The founding member of this family is the poorly characterized protein YdjY, an apparent lipoprotein, of Escherichia coli K-12. Many members are lipoproteins. YdjY and other members of its branch of the broader family have an invariant GCxxCxxxC motif. 181 matched cddid_all.tbl CDD NF040471 NF040471 439699 ydgH_STM1478 DUF1471 family protein YdgH. YdgH is the rare paralog in the DUF1471 family (PF07338) with three tandem copies of the DUF1471 domain instead of just one. Note that STM1478 from the Salmonella enterica model strain LT2 is also called SssB. 317 matched cddid_all.tbl CDD NF040473 NF040473 439700 peri_YbiM_McbA DUF1471 family periplasmic protein McbA. McbA (YbiM) is a member of the DUF1471 family found in Escherichia coli K-12, where it is one of many paralogs, but not found in Salmonella enterica LT2. Many members of the DUF1471 family of small enterobacterial periplasmic proteins participate in response to various forms of stress, such as low pH. 86 matched cddid_all.tbl CDD NF040474 NF040474 439701 peri_RclB reactive chlorine resistance periplasmic protein RclB. 78 matched cddid_all.tbl CDD NF040475 NF040475 439702 chlor_reg_RclR reactive chlorine-specific transcriptional regulator RclR. 284 matched cddid_all.tbl CDD NF040476 NF040476 439703 chlor_memb_RclC reactive chlorine resistance membrane protein RclC. 184 matched cddid_all.tbl CDD NF040477 NF040477 439704 chlor_oxi_RclA reactive chlorine resistance oxidoreductase RclA. 441 matched cddid_all.tbl CDD NF040479 NF040479 468507 porin_porB_Neis trimeric porin PorB. This HMM describes PorB, a trimeric porin found broadly within the genus Neisseria, including in N. gonorrhoeae and N. meningitidis. 343 matched cddid_all.tbl CDD NF040480 NF040480 439706 CGLAU_01105_fam CGLAU_01105 family protein. Members of this family are found, so far, almost entirely in the genus Corynebacterium. The function is unknown. The model was built, in part, to prevent misannotations that might result from a now-corrected improper inclusion of a family member in the seed alignment of Pfam model PF05407, which represents an endopeptidase of Rubella virus, MEROPS family C27. 168 matched cddid_all.tbl CDD NF040481 NF040481 439707 YdcK_fam YdcK family protein. 326 matched cddid_all.tbl CDD NF040482 NF040482 468508 auto_BafA_Cterm BafA family autotransporter C-terminal domain. BafA from both Bartonella henselae and Bartonella quintana, and possibly all Bartonella BafA, are mitogenic autotransporter virulence factors that help induce vasoproliferative lesions during infection. This HMM represents the more conserved C-terminal portion only, as the passenger region is more highly variable in length and sequence. 617 matched cddid_all.tbl CDD NF040483 NF040483 468509 serum_opaci_fac serum opacification domain. Serum opacity factors are virulence proteins from Streptococcus pyogenes and related bacterial pathogens. The opacification domain binds to apoA-I and apoA-II of HDL, and apparently in non-enzymatic fashion causes HDL to release the lipid it was carrying. That lipid then coalesces in serum, forming droplets that opacify mammalian serum. This HMM represents a region within the described opacification domain from which poorly conserved regions and sequences recognized as von Willebrand factor type A domain have been removed. 342 matched cddid_all.tbl CDD NF040485 NF040485 468510 ZirU_fam ZirU family protein. ZirU, as found in Salmonella, shares with ZirS the property of requiring ZirT for its type Vb-like secretion. This HMM describes a broader family of ZirU homologs. The N-terminal half of this HMM shows detectable homology (although scoring below the cutoffs set for the model) to ZirT (zinc regulated transporter), but no similarity to ZirS (zinc regulated secreted protein) 208 matched cddid_all.tbl CDD NF040486 NF040486 468511 SrfA_fam SrfA family protein. The virulence factor SrfA (SsrAB regulated factor A) from Salmonella enterica is a secreted effector. The mechanism of secretion is not known. SrfA belongs to a set of three SsrAB regulated factors, along with SrfB and SrfC. Operons related to srfABC are widely distributed in proteobacteria, suggesting coordinated action, and the three proteins appear able to form a complex. 437 matched cddid_all.tbl CDD NF040487 NF040487 468512 T3SS_CigR_fam anti-virulence regulator CigR family protein. Members of this family are full-length homologs of CigR, an inner membrane protein that appears to act as an anti-virulence factor. It was previously thought to be exported as a type III secretion system (T3SS) effector. A low-complexity, variable length repetitive region, rich in Gly, Pro, His, Lys, and Asn, separates a short, hydrophobic N-terminal domain from a longer, well-conserved C-terminal domain. A short stretch of that C-terminal domain, about 25 amino acids long, shows similarity to the C-terminal half of the domain described by Pfam model PF11776.10 (RcnB), but similarity between CigR and RcnB is not extensive. 147 matched cddid_all.tbl CDD NF040488 NF040488 439713 SCO5389_fam SCO5389 family protein. The function of this protein is unknown. A member of this family was shown to have two-fold increased protein expression in a strain of Streptomyces tsukubaensis under redox stress from knockout of the hydrogen peroxide-scavenging enzyme AhpC. A one-time classification of this protein family as a recurring spurious translation of shadow ORFs overlapping a different and real gene family appears to have been in error. 130 matched cddid_all.tbl CDD NF040489 NF040489 439714 variant_MftA variant-type mycofactocin precursor. Mycofactocin is a enzyme cofactor derived from the C-terminal amino acid pair, usually Val-Tyr, of the RiPP precursor peptide MftA. A rare variant form of MftA, with differences from the consensus for several key amino acids in the last ten, occurs in Deltaproteobacteria. The most notable amino acid replacement, true for all members of the seed alignment, although not necessarily for all members of this branch of the MftA family, is Ile replacing Val in the terminal dipeptide destined to become part of the mature cofactor. The variant form tends to co-occur with a variant, somewhat shorter form of the radical SAM maturase enzyme MftC. 23 matched cddid_all.tbl CDD NF040490 NF040490 439715 SDR_subfam_3 mycofactocin-coupled SDR family oxidoreductase. 268 matched cddid_all.tbl CDD NF040491 NF040491 468513 SDR_subfam_4 mycofactocin-coupled SDR family oxidoreductase. Members of this family are uncharacterized SDR family oxidoreductase regularly found encoded next to genes for mycofactocin biosynthesis proteins, and never found in genomes lacking mycofactocin. Members of this family are likely to represent a family of proteins that share a specific function. 256 matched cddid_all.tbl CDD NF040492 NF040492 439717 not_ScfB ScfB-related radical SAM/SPASM orphan maturase. Members of this rare protein family are SPASM domain-containing radical SAM enzymes that closely resembly ScfB, the thioether bridge-forming peptide modification enzyme of the SCIFF (Six Cysteines in Forty-Five residues) RiPP precursor. However, they form their own, distinctive clade within is ScfB-like family, are noticeably different toward the N-terminus, and are found in genomic contexts in which no ScfA-like encoded protein can be found. The protein is designated an orphan maturase because no substrate has been identified. 450 matched cddid_all.tbl CDD NF040493 NF040493 439718 TA_anti_VapB type II toxin-antitoxin system VapB family antitoxin. The term VapB has been used for the antitoxin component of various type II toxin-antitoxin systems called VapBC but showing little or no sequence identity. The family described here includes member proteins such as STM3034 from Salmonella enterica LT2 and VapB2 from Haemophilus influenzae, and is seeming unrelated to proteins called VapB in Mycobacterium tuberculosis. 73 matched cddid_all.tbl CDD NF040494 NF040494 468514 nitrored_ArsF nitrophenyl compound nitroreductase subunit ArsF family protein. The founding member of this family, ArsF, acts together with ArsE as a nitroreductase for trivalent forms (having As(III) instead of As(V)) of two synthetic aromatic organoarsenical biocides, nitarsone and roxarsone, reducing the nitro group to an amine, after which efflux confers resistance to the arsenical. Because the nitro group is rather far from the As(III) moiety of the known substrates, it is likely that conversed properties of members of this family include nitroreductase activity but not arsenical resistance activity. 106 matched cddid_all.tbl CDD NF040495 NF040495 439720 tranport_ArsG aromatic aminobenezylarsenical efflux permease ArsG family transporter. ArsG belongs to a broadly conserved ArsEFG cassette that was found in Shewanella putrefaciens as part of an organoarsenical resistance locus. ArsG performs efflux after the nitroreductase pair, ArsEF, converts a nitro group into an amine on the aromatic ring that elsewhere carries the arsenical group. TCDB names the system the Aminobenzyl Carbon-arsenic Defining Exporter (ABCDE) Family, 2.A.131. 225 matched cddid_all.tbl CDD NF040499 NF040499 439721 Bdr_N_group1 Bdr protein N-terminal domain. Bdr (Borrelia direct repeat) proteins have an N-terminal domain, a variable length region of repeats, typically 11 amino acids long with a KID repeat, and a non-repetitive C-terminal domain. This HMM describes the conserved N-terminal domain of families designated BdrA, BdrB, and BdrC. A related but non-overlapping model, NF040500, describes the N-terminal domain of additional Bdr families. 52 matched cddid_all.tbl CDD NF040500 NF040500 439722 Bdr_N_group2 Bdr protein N-terminal domain. Bdr (Borrelia direct repeat) proteins have an N-terminal domain, a variable length region of repeats, typically 11 amino acids long with a KID repeat, and a non-repetitive C-terminal domain. This HMM describes the conserved N-terminal domain of families other than BdrA, BdrB, and BdrC, which are described by sister model NF040499. 47 matched cddid_all.tbl CDD NF040502 NF040502 439723 PPT_acetyltrans phosphinothricin N-acetyltransferase. Phosphinothricin N-acetyltransferase (PAT) provides resistance to producers of the natural product phosphinothricin, non-proteinogenic amino acid antibiotic. 183 matched cddid_all.tbl CDD NF040505 NF040505 439724 ArsO_flavin_mono ArsO family NAD(P)H-dependent flavin-containing monooxygenase. All members of the seed alignment for this HMM, including founding member ArsO (ABB70173.1), are encoded in arsenic resistance islands. However, protein functions in this family maybe both variable and promiscuous. ArsO is related to the flavoprotein CzcO (see PMID:12100555), which was found to modestly enhance the activity of cation diffusion facilitator CzcD. 346 matched cddid_all.tbl CDD NF040506 NF040506 468515 PG0870_Nterm PG0870 family Cys-rich N-terminal domain. This protein N-terminal domain, about 60 amino acids long, has four nearly invariant Cys residues, two in the unusual motif VGRCxxxxxCGYH. The family is named for a member protein, PG0870. 56 matched cddid_all.tbl CDD NF040507 NF040507 439726 LBP_cg2779_fam LBP_cg2779 family protein. 58 matched cddid_all.tbl CDD NF040508 NF040508 439727 LVIS_2131_fam LVIS_2131 family protein. This uncharacterized protein, found in members of the Lactobacillales, is named after LVIS_2131 from Levilactobacillus (Lactobacillus) brevis. 202 matched cddid_all.tbl CDD NF040509 NF040509 468516 Lacto_palin_RPT translation of Lactobacillus palindromic repeat. This model was built for AntiFam to prevent false prediction of DNA repeat translations as proteins related to WP_020751851.1 40 matched cddid_all.tbl CDD NF040510 NF040510 468517 avirulen_svx Svx/AvrXca family virulence/avirulence protein. This family is named for Xanthomonas proteins such as AvrXca, called avirulence proteins, and the virulence factor Svx from Erwinia carotovora. Svx is described as secreted, regulated by a quorum-sensing system, and post-translationally modified. These proteins belong to the DUF6055 (PF19527) domain family. 601 matched cddid_all.tbl CDD NF040511 NF040511 439729 membrane_GPGG GPGG-motif small membrane protein. Members of this family are small membrane proteins, nearly all between 47 and 49 residues in length and very well conserved. 47 matched cddid_all.tbl CDD NF040512 NF040512 468518 histam_anti_2 histidine-histamine antiporter. Members of this histidine-histamine antiporter found in Firmicutes such as Lentilactobacillus parabuchneri and Clostridium thermobutyricum are more closely related to antiporters of different substrates than they are to TIGR04298 family histidine-histamine antiporters such as found in Haemophilus influenzae. Members of the seed alignment were selected with help from proximity to the hdcB gene. 477 matched cddid_all.tbl CDD NF040513 NF040513 468519 antiport_TyrP tyrosine-tyramine antiporter. 465 matched cddid_all.tbl CDD NF040514 NF040514 439732 CAL67264_fam CAL67264 family membrane protein. Members of this family are small, well-conserved, hydrophobic, lineage-restricted bacterial proteins, about 60 amino acids in length, with an essentially invariant C-terminal motif LKGRV. 57 matched cddid_all.tbl CDD NF040516 NF040516 439733 CapE_47_fam CapE family protein. Known members of this family are full-length homologs of CapE, a 47-amino acid linked to polyglutamate synthesis in Bacillus, or longer proteins sharing N-terminal homology with CapE. 39 matched cddid_all.tbl CDD NF040517 NF040517 468520 Lacto_Palin_RP2 translation of Lactobacillus palindromic repeat. This model was built for AntiFam to prevent false prediction of DNA repeat translations as proteins related to WP_015765070.1. Additional models represent translations from other reading frames from the same class of repeat. 24 matched cddid_all.tbl CDD NF040518 NF040518 468521 Lacto_Palin_RP3 translation of Lactobacillus palindromic repeat. This model was built for AntiFam to prevent false prediction of DNA repeat translations as proteins related to XXXX. Additional models represent translations from other reading frames from the same class of repeat. 23 matched cddid_all.tbl CDD NF040519 NF040519 439734 Sbal_3080_fam Sbal_3080 family lipoprotein. 136 matched cddid_all.tbl CDD NF040520 NF040520 468522 Ig_like_BLP2 Ig-like repeat protein Blp2. Blp2 (BAP-like protein 2), found broadly in the genus Acinetobacter, resembles the much larger biofilm-associated proteins Bap and Blp1 in N-terminal sequence and the presence of tandem Ig-like repeats. 729 matched cddid_all.tbl CDD NF040521 NF040521 468523 C45_proenzyme C45 family autoproteolytic acyltransferase/hydolase. Members of this family include hydrolases and N-acyltransferases, and belong to the Ntn (N-terminal nucleophile) hydrolase family. Members have an invariant Cys residue (Cys-103 in XP_002569112.1) required both for autoproteolytic processing into alpha and beta chains and for activity. The family is described by MEROPs as a cysteine protease, family C45, because of its autoproteolytic activity. Characterized members include TAN from Drosophila, which removes beta-alanine from both carcinine and N-beta-alanyl dopamine, and isopenicillin-N N-acyltransferase from various fungi. The latter has been heavily studied because of its role in penicillin biosynthesis. 312 matched cddid_all.tbl CDD NF040522 NF040522 439737 VC1465_fam VC1465 family Xer recombination activation factor. 111 matched cddid_all.tbl CDD NF040523 NF040523 468524 adhesin_AbpA amylase-binding adhesin AbpA. AbpA, an adhesin of oral streptococci, binds the host salivary protein alpha-amylase, contributing to colonization. Its C-terminal motif for cell wall attachment, LPKTxAVK-COOH, is recognized and processed by a dedicated B-type sortase. 203 matched cddid_all.tbl CDD NF040524 NF040524 439739 LPKTxAVK LPKTxAVK class sortase B sorting signal. 15 matched cddid_all.tbl CDD NF040525 NF040525 439740 SrtB_LPKTxSAVK class B sortase, LPKTxAVK-specific. This branch of the class B sortase family is found in multiple species of Streptococcus and Gemella. It processes target proteins that end with the motif LPKTxAVK-COOH, which differ from most sortase recognition sites in lacking an additional C-terminal transmembrane helix. Substrates of this sortase include the amylase-binding adhesin AbpA, as well of other proteins with similar N-terminal and C-terminal domains but unrelated central regions. 261 matched cddid_all.tbl CDD NF040526 NF040526 468525 SCO0930_lipo SCO0930 family lipoprotein. Members of this family are full-length homologs to the lipoprotein SCO0930, Streptomyces coelicolor A3(2). SCO0930 contains four copies of the repeat described by Pfam model PF03640. By comparison, PA5359 from Pseudomonas aeruginosa PAO1 has only two copies of the repeat, differs substantially in several regions, and is excluded from this family. 310 matched cddid_all.tbl CDD NF040528 NF040528 468526 SP_0198_lipo SP_0198 family lipoprotein. Members of this family, found only in Streptococcus, are lipoproteins with a lipoprotein signal peptide, a Ser-rich low-complexity region, and a C-terminal DUF3642 (PF12182) domain. 144 matched cddid_all.tbl CDD NF040533 NF040533 439743 endo_SpGH101 SpGH101 family endo-alpha-N-acetylgalactosaminidase. Members of this family are streptococcal surface proteins with a complex (and somewhat variable) architecture that includes a crosswall-targeting N-terminal YSIRK domain, a C-terminal cell wall-anchoring LPXTG domain, and a central endo-alpha-N-acetylgalactosaminidase that removes an O-linked disaccharide from host glycoproteins. 1694 matched cddid_all.tbl CDD NF040534 NF040534 439744 resp_reg_YycF response regulator YycF. 231 matched cddid_all.tbl CDD NF040535 NF040535 468527 LiaF_C_term cell wall-active antibiotics response protein LiaF, C-terminal domain. This HMM represents the conserved C-terminal domain of LiaF (called VraT in Staphylococcus), an additional key component of the histidine kinase LiaS and response regulator LiaR system. The system responds to cell envelop stress in the Firmicutes, and plays a role in resistance to cell wall-targeting antibiotics. 104 matched cddid_all.tbl CDD NF040536 NF040536 439746 export_ArsQ arsinothricin export permease ArsQ. 400 matched cddid_all.tbl CDD NF040537 NF040537 439747 radical_ArsL arsinothricin biosynthesis radical SAM protein ArsL. 424 matched cddid_all.tbl CDD NF040538 NF040538 439748 methyl_ArsM arsinothricin biosynthesis methyltransferase ArsM. The ArsM found in the arsinothricin (AST) biosynthesis can act as a typical arsenite methyltransferase, acting on inorganic arsenite, methylarsenicals, and aromatic arsenicals. In arsinothricin biosynthesis, the radical SAM enzyme ArsL acts first, synthesizing hydroxyarsinothricin (AST-OH) by adding 3-amino-3-carboxypropyl derived from S-adenosylmethionine (SAM) to As(III). This ArsM then methylates AST-OH, producing the naturally occurring arsenical antibiotic arsinothricin. Other forms of ArsM would not be expected to have this specific activity. 352 matched cddid_all.tbl CDD NF040539 NF040539 439749 AST_met_ArsM_2 putative arsinothricin biosynthesis methyltransferase ArsM. Galvan, et al. (PMID:34378964) identified a 3-gene cluster for biosynthesis and export of arsinothricin, an arsenic-containing antibiotic., with key enzyme ArsL, a radical SAM enzyme, catalyzing the first step. The cassette contains a methyltransferase, designated ArsM, capable both of completing arsinothricin biosynthesis and of methylating inorganic arsenite (see NF040538). Examination of additional genomic neighborhoods of ArsL showed that in species such as Paenibacillus sambharensis and Vogesella fluminis, this arsenite methyltransferase appears to replace NF040538. 262 matched cddid_all.tbl CDD NF040542 NF040542 439750 rSAM_RCCLKC RCCLKC-tail radical SAM protein. Members of this family radical SAM enzymes of unknown function with an intriguing, nearly invariant C-terminal motif RCCLKC-COOH. 423 matched cddid_all.tbl CDD NF040546 NF040546 468528 rSAM_CUAEP CUAEP/CCAEP-tail radical SAM protein. Members of this family are radical SAM enzymes with an N-terminal apparent B12-binding domain. Some members of the family have Cys-Cys motif about 10 amino acids before the C-terminus, but the majority of the family are selenoproteins with the second Cys replaced by selenocysteine, in a strongly conserved motif W[YF]C[CU]AEP. The proximity of the selenocysteine-encoding TGA codon to the C-terminus may have impeded recognition of this novel family of selenoproteins. 468 matched cddid_all.tbl CDD NF040549 NF040549 468529 Nt5e_LPXTG cell surface ecto-5'-nucleotidase Nt5e. Members of this family, found in Streptococcus sanguinis and related species, are LPXTG-anchored cell surface proteins. By hydrolyzing pro-inflammatory extracellular ATP in the host, it may blunt immune responses and contribute to virulence. Nt5e has also been called adenosine synthase AdsA. 730 matched cddid_all.tbl CDD NF040552 NF040552 439753 mini_lipo_xxCxC CGxCxC motif mini-lipoprotein. Members of this family, found so far only in the genus Akkermansia, are apparent lipoproteins of very small size, typically 45 amino acids. The mature form of the predicted lipoprotein begins CGxCxC and is only 26 amino acids long. 26 matched cddid_all.tbl CDD NF040553 NF040553 468530 SGO_0316_fam SGO_0316/SGO_0317 family LPXTG-anchored serine peptidase. Members of this family are cell wall-anchored streptococcal serine peptidases from MEROPS family S8, which contains subtilisin and its homologs. In several species, such as Streptococcus gordonii, two members of this family are encoded by a tandem gene pair. 1474 matched cddid_all.tbl CDD NF040554 NF040554 468531 mini_HHHH HHHH-motif protein. Proteins in this family are small in size, averaging just 46 amino acids in length, half of which belongs to an apparent signal peptide. The C-terminal region contains two invariant Cys residues, and between them, an HHHH motif, unusual in such a small protein. The function is unknown. 45 matched cddid_all.tbl CDD NF040555 NF040555 468532 Pro-rich_NTERM AAA family ATPase Pro-rich N-terminal domain. This HMM describes an extremely rich N-terminal domain that is well-conserved for a family of AAA family ATPases seen in Streptomyces. The HMM was built to support correct structural annotation of this unusual, low-complexity domain. 93 matched cddid_all.tbl CDD NF040556 NF040556 468533 CAS_Csx28 CRISPR-associated protein Csx28. 172 matched cddid_all.tbl CDD NF040557 NF040557 468534 CAS_Csx27 CRISPR-associated protein Csx27. 223 matched cddid_all.tbl CDD NF040558 NF040558 439759 CAS_Csx18 CRISPR-associated protein Csx18. 64 matched cddid_all.tbl CDD NF040559 NF040559 468535 CAS_Csx20 CRISPR-associated protein Csx20. 124 matched cddid_all.tbl CDD NF040560 NF040560 468536 CAS_Csx15 CRISPR-associated protein Csx15. 125 matched cddid_all.tbl CDD NF040561 NF040561 468537 PrimPol_Msp CRISPR-associated primase-polymerase type A1. 515 matched cddid_all.tbl CDD NF040562 NF040562 439763 PrimPol_Db CRISPR-associated primase-polymerase type B. 335 matched cddid_all.tbl CDD NF040563 NF040563 468538 guided_IscB RNA-guided endonuclease IscB. 315 matched cddid_all.tbl CDD NF040564 NF040564 439765 SCO2523_fam SCO2523 family variant P-loop protein. The family of proteins related to SCO2523 of Streptomyces coelicolor is limited to the Acintobacteria, and part of a conserved gene neighborhood encoding proteins SCO2521-SCO2524. The N-terminal half shows homology to P-loop-containing regions of multiple protein families, but the key motif differs substantially from the P-loop consensus, DKGGTGRS when GxxGxGK[ST] is typical. 305 matched cddid_all.tbl CDD NF040565 NF040565 468539 SCO2521_fam SCO2521 family protein. The family of proteins related to SCO2521 of Streptomyces coelicolor is limited to the Acintobacteria, and part of a conserved gene neighborhood encoding proteins SCO2521-SCO2524. 301 matched cddid_all.tbl CDD NF040566 NF040566 468540 SCO2522_fam SCO2522 family protein. The family of proteins related to SCO2522 of Streptomyces coelicolor is limited to the Acintobacteria, and part of a conserved gene neighborhood encoding proteins SCO2521-SCO2524. 313 matched cddid_all.tbl CDD NF040567 NF040567 468541 SCO2524_fam SCO2524 family protein. The family of proteins related to SCO2524 of Streptomyces coelicolor is limited to the Acintobacteria, and part of a conserved gene neighborhood encoding proteins SCO2521-SCO2524. 611 matched cddid_all.tbl CDD NF040568 NF040568 468542 SCO2525_fam SCO2525 family SAM-dependent methyltransferase. The founding member of this strictly actinobacterial family of class I SAM-dependent methyltransferases, SCO2525, appears to affect development, as inferred by mutant phenotype in Streptomyces coelicolor. SCO2525 belongs to a conserved gene neighborhood that also includes SCO2521-SCO2524. 241 matched cddid_all.tbl CDD NF040569 NF040569 468543 DUF2007_rel DUF2007-related protein. This family of small proteins, 74 amino acids in length on average, includes some proteins included in the seed alignment for Pfam model PF09413 (DUF2007), but most members of this HMM, apparently a distinctive branch within the family of DUF2007-related proteins, fall below the detection limits of PF09413. 74 matched cddid_all.tbl CDD NF040570 NF040570 468544 guided_TnpB RNA-guided endonuclease TnpB family protein. This family includes RNA-guided endonuclease TnpB from IS200/IS605 family elements (NF038281) and IS607 family elements (NF038280), but also many additional proteins. It exhibits homolog to or actually includes some CRISPR-associated (Cas) proteins such as the type V CRISPR-associated protein C2c8. For a long time, TnpB proteins were described as accessory proteins in IS (insertion sequence) elements, present as one of just one or two proteins encoded in the element but not necessary for transposition. The programmable RNA-guided endonuclease TnpB proteins may provide a CRISPR-like, widespread form of phage defense by RNA-guided DNA degradation. 384 matched cddid_all.tbl CDD NF040571 NF040571 468545 peroxidase_FMP peroxidase, FMP-type. This novel form of the heme-binding enzyme peroxidase was originally described as occurring in Flavobacterium meningosepticum (now called Elizabethkingia meningoseptica), hence FMP (F. meningosepticum peroxidase), although the species attribution may have been incorrect. 359 matched cddid_all.tbl CDD NF040572 NF040572 468546 heme_bind_FMP heme-binding protein, FMP family. 263 matched cddid_all.tbl CDD NF040573 NF040573 468547 holin_dep_muram holin-associated N-acetylmuramidase. Members of this family are N-acetylmuramidases (lysozymes) associated with the family of large, 3-transmembrane segment-type holins that is described by Pfam model PF11351. All members of the seed alignment for this HMM are encoded adjacent to a holin from that family, and may depend on the action of the holin to access the peptidoglycan layer. Systems including the holin/N-acetylmuramidase may include both gene transfer agents (which package DNA into particles that escape without lysing the host cell) and typical phage. 200 matched cddid_all.tbl CDD NF040574 NF040574 468548 T3SS_ATP_VscN2 type III secretion system ATPase VscN2. 420 matched cddid_all.tbl CDD NF040575 NF040575 468549 syringactin syringactin. Syringactin are close homologs of the normally eukaryotic protein actin, found in the plant pathogen Pseudomonas syringae and related species. This model was created, in part, to clarify that the family is real and distinct, rather than an artifact of eukaryotic contamination of bacterial genomic sequence data. As of the creation of this HMM, the family is uncharacterized. 132 matched cddid_all.tbl CDD NF040576 NF040576 468550 T2SS_GspM_XpsM type II secretion system protein GspM, XpsM type. This form of the type II secretion system (T2SS) protein GspM (general secretion pathway M - the old name for T2SS) is more closely related to the type IV pilus protein PilO than to other GspM. Note that PF04612 refers to this type of GspM as type b. 180 matched cddid_all.tbl CDD NF040577 NF040577 468551 cas_Cas7fv type I-Fv CRISPR-associated protein Cas7fv. Cas7fv is one of the CRISPR associated (Cas) proteins of type I-F variant (I-Fv) CRISPR-Cas system. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas modules are adaptive immune systems found in archaea and bacteria against foreign nucleic acids such as phages and plasmids via RNA-guided endonucleases. CRISPR-Cas systems are classified based on Cas protein content and arrangement in CRISPR-Cas loci into two main classes (1 and 2) and at least six types (I, II, III, IV, V, VI). Class 1 systems utilize multiple Cas proteins and CRISPR RNA (crRNA) to form an effector complex while class 2 systems employ a large, single effector with crRNA to mediate interference. Type I CRISPR-Cas systems are most widespread in nature and the Cas protein composition of the employed Cascade interference complexes differ between seven subtypes (A-F, U). Type I-F variant (I-Fv) is a subtype that rely on a minimal set of five Cas proteins and has structural differences with I-F and I-E Cascades. Double strand DNA recruitment and recognition in the type I-Fv Cascade is facilitated from the major groove side by Cas5fv instead of the large subunit Cas8 and the finger domain of Cas7fv. 323 matched cddid_all.tbl CDD NF040578 NF040578 468552 S1_dom_Ygs S1 domain-containing post-transcriptional regulator Ygs. Ygs, as first described in Staphylococcus epidermidis, is a full-length homolog of GSP13 (YugI) from Bacillus subtilis. Each has a single copy of the S1 domain, an RNA-binding domain repeated several times in ribosomal small subunit protein S1, and each has been shown to be induced by stress and improve survival. Ygs was shown in Staphylococcus epidermidis to affect polysaccharide intercellular adhesin biosynthesis, and through it, biofilm formation. More recently, the full-length homolog CvfD was shown to be a post-transcriptional regulator, suggesting all members of this family are. 122 matched cddid_all.tbl CDD NF040579 NF040579 468553 S1_dom_CvfD CvfD/Ygs/GSP13 family RNA-binding post-transcriptional regulator. CvfD, Ygs, and GSP13 form a family of full-length homologs of RNA-binding proteins from the Firmicutes with a single copy of the S1 domain. Several members of the family have been characterized as general stress proteins, and the most recently characterized, CvfD, was shown to act as a post-transcriptional regulator. 113 matched cddid_all.tbl CDD NF040580 NF040580 468554 MBL_fold_Vmh Vmh family MBL fold metallo-hydrolase. Members of this family are zinc-binding enzymes with a metallo-beta-lactamase fold. The founding member, Vmh from Vibrio vulnificus (AAO08273.1), was described as having actual beta-lactamase activity. Because the search for beta-lactamases in known and potential pathogens has been so intense for so long, the potential zinc-binding motifs differ so greatly from those of the well-characterized metallo-beta-lactamases, and reports of beta-lactamase activity have not been widespread throughout this family, the question of whether the beta-lactamase activity seen for Vmh is essential or incidental is not yet answered. 284 matched cddid_all.tbl CDD NF040581 NF040581 468555 cas_Crn1 CRISPR-associated ring nuclease Crn1. Ring nucleases cleave second messengers such as cyclic oligoadenylate produced by type III CRISPR system effectors, in order to provide an off-switch for the regulation of CRISPR activity. This family of ring nuclease, which includes Sso2081 from Sulfolobus solfataricus, is designated Crn1. 179 matched cddid_all.tbl CDD NF040582 NF040582 468556 STY4528_fam STY4528 family pathogenicity island replication protein. The founding member of this family, STY4528 from Salmonella pathogenicity island 7 (SPI-7) of Salmonella typhi, belongs to the core set of proteins of SPI-7-related conjugative elements, and is assigned to the replication region. Members include a protein designated Api5 from the Yersinia pseudotuberculosis adhesion pathogenicity island (YAPI). 323 matched cddid_all.tbl CDD NF040583 NF040583 468557 dnaB_SPI-7_type SPI-7-type island replicative DNA helicase. Members of this family are DnaB-PI, a pathogenicity island (PI) variant of the replicative DNA helicase DnaB. Members are found with other conjugative element replication proteins such as ParA, ParB in genetic islands whose core proteins (but not cargo proteins) are shared with the Salmonella typhi SPI-7 island. 434 matched cddid_all.tbl CDD NF040584 NF040584 468558 STY4534_fam STY4534 family ICE replication protein. Members of this family regularly are found near a TopB family topoisomerase, in mobile elements such as certain pathogenicity islands, in regions of those islands thought to be involved in replication. The founding member of the family is STY4534 in Salmonella pathogenicity island 7 (SPI-7), a core protein shared by members of SPI-7's subclass of integrative and conjugative element (ICE). 125 matched cddid_all.tbl CDD NF040585 NF040585 468559 SjiA_fam_FXSXX FXSXX-COOH family cyclophane-modified RiPP peptide SjiA. 59 matched cddid_all.tbl CDD NF040586 NF040586 468560 FxSxx_TPR FxSxx-COOH system tetratricopeptide repeat protein. Members of this family are typically about 850 amino acids long, or 1300 long because of an additional N-terminal domain. Proteins have a P-loop motif, GxGGxGKT, near the N-terminus of the region covered by this HMM, and a region over 400 residues long of tetratricopeptide repeat sequence. The family is found regularly next to other components of FxSxx-COOH systems, which feature an FxsB family radical SAM protein and a protein modified by it, FxsA. Members of this FxsA family typically have an FxSxx motif as the final five amino acids. 836 matched cddid_all.tbl CDD NF040587 NF040587 468561 rSAM_lost_HExxH FxsB C-terminal extension domain without HExxH motif. This HMM describes a branch of the TIGR04267 domain family in which the presumptive metal-binding motif, shared by many metallo-proteases, has been been lost. The domain appears as a C-terminal extension for some of the radical SAM enzyme family FxsB proteins, involved in post-translational modification of the 60-amino acid long RiPP precursor proteins, collectively named FxsA. 364 matched cddid_all.tbl CDD NF040588 NF040588 468562 FxsC_Nterm FxsC protein N-terminal TIR-like domain. Members of this protein family, FxsC, occur in the context of FxSxx-COOH class RiPP precursors (FxsA) and their radical SAM/SPASM domain maturases (FxsB). Most but not all members have an additional C-termimal domain (see TIGR04276). 181 matched cddid_all.tbl CDD NF040589 NF040589 468563 Synergist-CPBP SYNERG-CTERM system CAAX-type protease. 170 matched cddid_all.tbl CDD NF040590 NF040590 468564 Pyro_CPBP_1 CPBP family archaeomyxosortase MrtA. Members of this family are CPBP family (CAAX-like) intramembane metalloproteases that are found only in the branch of the Archaea that includes the genera Pyrococcus, Thermococcus, and Palaeococcus, and appear both universal and highly conserved in sequence within that lineage. Comparative genomics suggests this enzyme, distantly related to Rce1, processes the C-terminal sorting signal CGP-CTERM. Because CGP-CTERM resembles MYXO-CTERM, processed by bacterial myxosortases, we designate this protein archaeomyxosortase. 194 matched cddid_all.tbl CDD NF040591 NF040591 468565 choice_anch_O choice-of-anchor O protein. Members of this rare protein family have been observed with the JDVT-CTERM sorting signal at the C-terminus, or with a low-scoring variant of the GlyGly-CTERM domain (see WP_188923155.1), or with alternative sequence regions not currently recognizable as sorting signals or homology domains. The function is unknown. 629 matched cddid_all.tbl CDD NF040592 NF040592 468566 tRNA_mod_ArcS archaeosine synthase subunit alpha. 575 matched cddid_all.tbl CDD NF040593 NF040593 468567 CAAX_MXAN_2755 MXAN_2755 family glutamic-type intramembrane protease. Members of the family are restricted to the taxonomic order Myxococcales, within the Deltaproteobacteria. The N-terminal region is a domain unique to this family. The C-terminal domain is an CPBP family (Rce1-like) intramembrane protease domain (see PF02517), related to eukaryotic CAAX endopeptidases, which cleave at the site of a prenylated Cys residue in a C-terminal motif involved in protein sorting. 238 matched cddid_all.tbl CDD NF040594 NF040594 468568 CPBP_fam_mrtC MrtC family glutamic-type intramembrane protease. Members of the family are restricted to the taxonomic order Myxococcales, within the Deltaproteobacteria. The N-terminal region is a domain unique to this family. The C-terminal domain is a CPBP family intramembrane metalloprotease domain (see PF02517), related to eukaryotic CAAX endopeptidases, which cleave at the site of a prenylated Cys residue in a C-terminal motif involved in protein sorting. The founding member of this family is from Chondromyces crocatus. 221 matched cddid_all.tbl CDD NF040595 NF040595 468569 HTH_Cbp1 CRISPR DNA repeat-binding protein Cbp1. 135 matched cddid_all.tbl CDD NF040596 NF040596 468570 MXAN_2562_fam MXAN_2562 family outer membrane beta-barrel protein. This homology domain, found in Deltaproteobacteria such as Myxococcus xanthus, comprises the near full-length of proteins about 240 amino acids in size, or the C-terminal domain of longer proteins. A distant relationship to PF13505 suggests these proteins may form outer membrane beta-barrels. 208 matched cddid_all.tbl CDD NF040597 NF040597 468571 carb_anhyd carbonic anhydrase. 248 matched cddid_all.tbl CDD NF040598 NF040598 468572 Ala_zip_lipo Lpp/OprI family alanine-zipper lipoprotein. This model derives from PF11839 but is more narrowly focused. All member sequences of the seed alignment are bacterial lipoproteins between 78 and 103 amino acids in length. Members include OprI (major outer membrane lipoprotein I) from Pseudomonas aeruginosa, and Lpp (Braun's lipoprotein), called the most abundant protein in Escherichia coli. Lpp becomes covalently linked to the cell wall, while anchored in the inner leaflet of the outer membrane, providing structural stability to the cell envelope. 90 matched cddid_all.tbl CDD NF040599 NF040599 468573 LdtF_DpaA_YafK peptidoglycan meso-diaminopimelic acid protein amidase. DpaA (previously YafK and LdtF) murein L,D-transpeptidases, but actually functions as an amidase. In E. coli, the most abundant protein is the lipoprotein Lpp, anchored to the inner face of the outer membrane, but cross-linked to the peptidoglycan cell wall by the transpeptidases LdtA, LdtB, and LdtC. DpaA (peptidoglycan meso-diaminopimelic acid protein amidase A) is an amidase that hydrolyzes those linkages. 242 matched cddid_all.tbl CDD NF040601 NF040601 468574 TerS_not_xtmA phage terminase small subunit. Members of this family are phage terminase small subunit proteins, based on adjacency to terminase large subunit proteins, and on a small N-terminal homology domain, described by PF10668, about 67 amino acids in length, shared with TerS from PBSX (XtmA) and from phage related to PBSX. Terminase small subunits related to XtmA of defective prophage PBSX have a C-terminal PF03592 domain, accounting for most of the length of those proteins. Members of this family differ from XtmA-like TerS over most of the their lengths, C-terminal to the PF10668 domain, and show no trace of homology to PF03592. 229 matched cddid_all.tbl CDD NF040602 NF040602 468575 F420_dehyd_FpoD F420H2 dehydrogenase subunit FpoD. 372 matched cddid_all.tbl CDD NF040603 NF040603 468576 choice_anch_P choice-of-anchor P family protein. 186 matched cddid_all.tbl CDD NF040604 NF040604 468577 HacB_Meth homoaconitase small subunit. Part of the 2-oxosuberate biosynthesis pathway in methangoens 159 matched cddid_all.tbl CDD NF040605 NF040605 468578 mycolic_FabG1 3-oxoacyl-ACP reductase FabG1. 233 matched cddid_all.tbl CDD NF040606 NF040606 468579 CytoC_perox di-heme-cytochrome C peroxidase. 520 matched cddid_all.tbl CDD NF040607 NF040607 468580 mycolic_Pks13 polyketide synthase Pks13. 1671 matched cddid_all.tbl CDD NF040608 NF040608 468581 division_SteA putative cytokinetic ring protein SteA. Members of this family on membrane proteins from Actinobacteria were reported (in 2019) to be SteA (Sensitive To Ethambutol A), a cytokinetic ring protein that partners with SteB and contributes to proper cell division. A short region of sequence similarity to some proteins characterized as thiamine pyrophosphokinases may cause confusion in functional annotation. 369 matched cddid_all.tbl CDD NF040610 NF040610 468582 F420_dehyd_FpoH F420H2 dehydrogenase subunit FpoH. 339 matched cddid_all.tbl CDD NF040611 NF040611 468583 F420_dehyd_FpoC F420H2 dehydrogenase subunit FpoC. 158 matched cddid_all.tbl CDD NF040612 NF040612 468584 F420_dehyd_FpoI F420H2 dehydrogenase subunit FpoI. 135 matched cddid_all.tbl CDD NF040613 NF040613 468585 F420_dehyd_FpoJ F420H2 dehydrogenase subunit FpoJ. 81 matched cddid_all.tbl CDD NF040614 NF040614 468586 F420_dehyd_FpoK F420H2 dehydrogenase subunit FpoK. 98 matched cddid_all.tbl CDD NF040615 NF040615 468587 HacA_Meth homoaconitase large subunit. Part of the 2-oxosuberate biosynthesis pathway in methangoens 419 matched cddid_all.tbl CDD NF040616 NF040616 468588 F420_dehyd_FpoF F420H2 dehydrogenase subunit FpoF. 337 matched cddid_all.tbl CDD NF040617 NF040617 468589 F420_dehyd_FpoL F420H2 dehydrogenase subunit FpoL. 669 matched cddid_all.tbl CDD NF040618 NF040618 468590 PPA1309_fam PPA1309 family protein. This family of uncharacterized proteins, restricted to the Actinobacteria but absent from the genus Mycobacterium, is named for founding member PPA1309 from Cutibacterium (Propionibacterium) acnes. 164 matched cddid_all.tbl CDD NF040619 NF040619 468591 AksF_Meth homoisocitrate dehydrogenase. 332 matched cddid_all.tbl CDD NF040620 NF040620 468592 fused_HadA_HadB fused (3R)-hydroxyacyl-ACP dehydratase subunits HadA/HadB. 329 matched cddid_all.tbl CDD NF040621 NF040621 468593 Dietz_HadA (3R)-hydroxyacyl-ACP dehydratase subunit HadA. 132 matched cddid_all.tbl CDD NF040622 NF040622 468594 MfnE [5-(aminomethyl)furan-3-yl]methyl phosphate kinase. 211 matched cddid_all.tbl CDD NF040623 NF040623 468595 MfnF (4-{4-[2-(gamma-L-glutamylamino)ethyl]phenoxymethyl}furan-2-yl)methanamine synthase. 323 matched cddid_all.tbl CDD NF040624 NF040624 468596 HadA (3R)-hydroxyacyl-ACP dehydratase subunit HadA. 144 matched cddid_all.tbl CDD NF040625 NF040625 468597 HacB2_Meth homoaconitase small subunit. 161 matched cddid_all.tbl CDD NF040626 NF040626 468598 AksF2_Meth homoisocitrate dehydrogenase. 332 matched cddid_all.tbl CDD NF040627 NF040627 468599 GFPS_Meth geranylfarnesyl diphosphate synthase. 285 matched cddid_all.tbl CDD NF040628 NF040628 468600 GT-D_rel GT-D fold domain. This HMM describes a domain related to the GT-D fold glycotransferase domain described in Pfam model PF08759. The two families share the strong motif R[VIL]GDGE, and full-length homology, but only about 16 percent identity overall. As characterized sequences included in PF08759 include glycosyltransferase proteins or domains, members of this family are proposed also to be glycosyltransferases and to share the GT-D fold of PF08759. 223 matched cddid_all.tbl CDD NF040629 NF040629 468601 PGI_Meth glucose-6-phosphate isomerase. 396 matched cddid_all.tbl CDD NF040631 NF040631 468602 InhA NADH-dependent enoyl-ACP reductase InhA. 256 matched cddid_all.tbl CDD NF040633 NF040633 468603 FadD32_Coryne FadD32-like long-chain-fatty-acid--AMP ligase. Members of this family are found in the genus Corynebacterium, are most similar to the key mycolic acid biosynthesis protein FadD32 of any fatty acid--AMP ligase in Mycobacterium tuberculosis, and are likewise encoded next to Pks13. However, as the mycolic acids produced in Corynebacterium and in Mycobacterium differ substantially, it is not clear that assigning the same name in Corynebacterium is appropriate. 613 matched cddid_all.tbl CDD NF040636 NF040636 468604 AcpM meromycolate extension acyl carrier protein AcpM. 93 matched cddid_all.tbl CDD NF040637 NF040637 468605 CatA_like_2 CatA-like O-acetyltransferase, family 2. Members of this family are homologs to members of the CatA family of chloramphenicol acetyltransferases, although less than 30% identical. There is no evidence that members of this family act on or confer resistance to chloramphenicol. 203 matched cddid_all.tbl CDD NF040638 NF040638 468606 CatA_like_3 CatA-like O-acetyltransferase, family 3. Members of this family are homologs to members of the CatA family of chloramphenicol acetyltransferases, although less than 35% identical. There is no evidence that members of this family act on or confer resistance to chloramphenicol. 212 matched cddid_all.tbl CDD NF040639 NF040639 468607 LETM1_rel_film LETM1-related biofilm-associated protein. This bacterial protein family is related to the mitochondrial protein LETM1. The founding member, WP_060382447 from the fish pathogen Flavobacterium columnare, called a calcium-binding EF hand protein, was found highly up-regulated in expression during biofilm formation. 396 matched cddid_all.tbl CDD NF040640 NF040640 468608 YcgZ_fam regulatory protein YcgZ. YcgZ, as found in Escherichia coli, is a small protein of unknown function that appears to participate in regulatory cascades involved in processes such as biofilm formation and response to blue light. YcgZ is homologous to YmgB/AriR, a paralog also found in E. coli and described as having a role in regulatory cascades. 77 matched cddid_all.tbl CDD NF040641 NF040641 468609 bifunc_ST_SDO bifunctional sulfur transferase/dioxygenase Blh. 423 matched cddid_all.tbl CDD NF040642 NF040642 468610 sulf_sens_BigR sulfite-sensing transcriptional repressor BigR. BigR (biofilm growth-associated repressor) is a winged-helix DNA-binding protein active as a transcriptional regulator for Blh, a bifunctional sulfur transferase/dioxygenase found in a number of plant-associated bacteria. Oxidative conditions that allow disulfide bond formation between the invariant residues Cys42 and Cys108 cause BigR to lose DNA-binding transcriptional repressor activity. 95 matched cddid_all.tbl CDD NF040643 NF040643 468611 S6_alt_immun pyocin S6 family toxin immunity protein. All members of the seed alignment for this family are found in the genus Pseudomonas, always adjacent or close to proteins with the killing domain (see PF09000) of 16S rRNA-cleaving colicin E3 and pyocin S6 family toxins. This family is unrelated to that of PF03513, a well-characterized family of immunity protein for ribosome inactivating toxins in the family of colicin E3, pyocin S6, but is called an immunity protein for the same family of toxins by Dingemans, et al., (2016) in pyocin S6-encoding strain P. aeruginosa CF_PA39. In most strains with a toxin from family PF09000, an immunity protein is found either from this family, or from PF03513, but only occasionally from both. 78 matched cddid_all.tbl CDD NF040645 NF040645 468612 K_channel_Meth hyperpolarization-activated voltage-gated potassium channel. 203 matched cddid_all.tbl CDD NF040646 NF040646 468613 HPT_Archaea hypoxanthine/guanine phosphoribosyltransferase. 184 matched cddid_all.tbl CDD NF040647 NF040647 468614 IPPK_Arch isopentenyl phosphate kinase. 258 matched cddid_all.tbl CDD NF040648 NF040648 468615 lactal_redase_Meth lactaldehyde dehydrogenase. 463 matched cddid_all.tbl CDD NF040649 NF040649 468616 FucA_Meth L-fuculose phosphate aldolase. 179 matched cddid_all.tbl CDD NF040650 NF040650 468617 sulfolac_dhydr L-sulfolactate dehydrogenase. 339 matched cddid_all.tbl CDD NF040651 NF040651 468618 MtaB_Meth methanol--corrinoid protein co-methyltransferase MtaB. MtaABC catalyze the formation of methyl-coenzyme M from methanol and coenzyme M. MtaB methylates the corrinoid protein MtaC. 460 matched cddid_all.tbl CDD NF040652 NF040652 468619 Mbox_reg_Rv1535 Rv1535 family protein. Members of this family include Rv1535 from Mycobacterium tuberculosis, regulated in response to changes in Mg(2+) leves and encoded immediately downstream from an Mbox Mg(2+)-sensing riboswitch. 77 matched cddid_all.tbl CDD NF040653 NF040653 468620 Rv1535_dom Rv1535 domain. This HMM describes a domain found in the C-terminal region of Rv1535 from Mycobacterium tuberculosis, a protein whose expression is regulated by a Mg(2+)-sensing riboswitch, and as nearly the entire length of proteins of about half the size (about 40 amino acids in length) from other Actinobacterial lineages such as Nocardia. 31 matched cddid_all.tbl CDD NF040654 NF040654 468621 MtaA_Meth methylcobamide:CoM methyltransferase MtaA. MtaABC catalyze the formation of methyl-coenzyme M from methanol and coenzyme M. MtaA transfers the methyl group from methylated MtaC. 334 matched cddid_all.tbl CDD NF040655 NF040655 468622 MtaC_Meth methanol--corrinoid protein MtaC. MtaABC catalyze the formation of methyl-coenzyme M from methanol and coenzyme M. MtaC is methylated by MtaB and provides the methyl group that is transfered to coenzyme M by MtaA 253 matched cddid_all.tbl CDD NF040656 NF040656 468623 GHMP_GYDIA GYDIA family GHMP kinase. The GHMP kinase family is named for galactokinase (G), homoserine kinase (H), mevalonate kinase (M), and phosphomevalonate kinase (P). This uncharacterized protein family, most closely related to mevalonate kinase (see TIGR00549), has several distinctive nearly invariant motifs, including WGLG[ST]SSTL, GGSGYDIA (for which the family is named), and SLGAWGGF. 298 matched cddid_all.tbl CDD NF040657 NF040657 468624 immun_SitI3 SitI3 family protein. The founding member of this protein family, SitI3 from Myxococcus xanthus (WP_020478554.1), is an immunity protein encoded immediately downstream of a lipoprotein toxin, SitA3, that can move between cells by means of a transfer system for exchange of outer membrane lipoproteins involved in kin recognition. It is not yet clear what fraction of the members of this family are immunity proteins from other toxin/immunity-type conflict systems. 140 matched cddid_all.tbl CDD NF040658 NF040658 468625 Myxo_OME_TraC outer membrane exchange accessory lipoprotein TraC. This lipoprotein family, found Myxococcus xanthus and other members of the Myxococcocales branch of the Deltaproteobacteria, is involved in a kinship recognition-dependent system for exchange of outer membrane lipoproteins. TraC is described as an accessory protein to the TraAB pair that was shown to be critical to outer membrane exchange. 602 matched cddid_all.tbl CDD NF040660 NF040660 468626 mycolic_MTase cyclopropane mycolic acid synthase family methyltransferase. Members of this family include tailoring enzymes that make site-specific modifications to mycolic acid precursor molecules. These include Mycobacterium tuberculosis enzymes MmaA1-MmaA4, CmaA1-CmaA2, and PcaA. The family also includes UmaA, reported to be the lone member of this family not involved in mycolic acid biosynthesis. No members of this family are found in species that lack mycolic acids. This model excludes two more distantly related paralogs, Rv0447c (UfaA1 ) and Rv3720, that are also encoded in the Mycobacterium tuberculosis H37Rv genome. 283 matched cddid_all.tbl CDD NF040661 NF040661 468627 Osc7112_2153fam Osc7112_2153 family protein. This rare, small cyanobacterial protein, about 80 amino acids in length, has a signal peptide and a pair of invariant Cys residues that suggest disulfide bond formation. The protein regularly is found encoded just a few genes away from exosortase O (XrtO), but the significance of that finding is unclear. 75 matched cddid_all.tbl CDD NF040662 NF040662 468628 attach_TipJ_rel host specificity factor TipJ family phage tail protein. Members of this family form a family related to that of host specificity protein J of phage lambda, a tail tip protein that mediates attachment to LamB on the surface of E. coli. Binding of the phage tail to the LamB receptor triggers the injection of phage DNA into host cells. Proteins with this domain are likely also to be phage tail proteins. 473 matched cddid_all.tbl CDD NF040663 NF040663 468629 salivaricin_M salivaricin M family lantibiotic. Members of this family are type A2 lantibiotic precursors in the family of founding members EGX30806.1, called salivaricin M, from Streptococcus salivarius strain M18 (previously strain Mia), a commensal strain of the oral microbiome, and ALO23661.1, called salivaricin E. Salivaricin M affects the caries-causing oral pathogen Streptococcus mutans. 57 matched cddid_all.tbl CDD NF040664 NF040664 468630 HEC_x9_TCC_lant lacticin 481 family lantibiotic. The lacticin 481 group exert their antimicrobial action by disrupting the cytoplasmic membrane. This model contains a lipid II-binding motif. The docking of the lantibiotic with lipid II is part of the mechanism by which family members form a membrane-disrupting structure. The lacticin 481 group includes lacticin 481, mutacin H-29B, variacin, nukacin ISK-1, butyrivibriocin OR79A, streptococcin A-FF2, ruminococcin A, mutacin II, and salivaricin A. 39 matched cddid_all.tbl CDD NF040665 NF040665 468631 relax_SAG1250 SAG1250 family conjugative relaxase. 606 matched cddid_all.tbl CDD NF040666 NF040666 468632 Tn5252_Orf10 SAG1252 family conjugative relaxosome accessory protein. SAG1252, a member of the Tn5252 ORF10 family, occurs in mobile elements from a class associated with the movement of bacteriocins and antibiotic resistance proteins in Streptococcus. This HMM excludes related MobC proteins, such as the adjacent SAG1251, a homolog over the short length of these small proteins except for a small central region recognized by Pfam model PF05713 (MobC). 114 matched cddid_all.tbl CDD NF040667 NF040667 468633 hom_kin_desulfo homoserine kinase, Desulfovibrio type. 163 matched cddid_all.tbl CDD NF040668 NF040668 468634 regulator_TseB cell wall elongation/penicillin-binding protein regulator TseB. 161 matched cddid_all.tbl CDD NF040669 NF040669 468635 MtaC2_Meth methanol--corrinoid protein MtaC. 267 matched cddid_all.tbl CDD NF040670 NF040670 468636 wall_bind_EntA cell wall-binding protein EntA. This HMM describes the cell wall-binding protein EntA, as found in Bacillus cereus. EntA is related to EntB, EntC, and EndD, but it lacks the central region of KAXEXX repeats that EntB and EndC have. EntD also lacks those repeats. Ent proteins have a signal peptide, an N-terminal SH3 domain and a C-terminal 3D (Asp-Asp-Asp) domain. 291 matched cddid_all.tbl CDD NF040671 NF040671 468637 PLuB_AAA PLuB system helicase-like protein. The PLuB system is found in the genera Persicimonas, Lujinxingia, and Bradymonas, all members of the Deltaproteobacteria. This protein, with an AAA+ domain, shows strong local homology to various helicases. The system also includes a CPBP family intramembrane metalloprotease and a PQQ-binding-like beta-propeller repeat protein. 1256 matched cddid_all.tbl CDD NF040672 NF040672 468638 SCO2322_fam SCO2322 family protein. 144 matched cddid_all.tbl CDD NF040673 NF040673 468639 PLuB_PQQ_rpt PLuB system PQQ-binding repeat protein. Members of this family contain a region similar to the PQQ-binding repeats domain (see PF13360), and occur in a conserved gene neighborhood together with a helicase-like protein and a CPBP family intramembrane protease. This system, designated PLuB, is found in the genera Persicimonas, Lujinxingia, and Bradymonas, all members of the Deltaproteobacteria. 393 matched cddid_all.tbl CDD NF040674 NF040674 468640 PLuB_CAAX MrtP family glutamic-type intramembrane protease. 350 matched cddid_all.tbl CDD NF040675 NF040675 468641 wall_bind_EntD cell wall-binding protein EntD. This HMM describes the cell wall-binding protein EntD, as found in Bacillus cereus. EntD, like its close homolog EntA, is related to EntB and EntC, but lacks the central region of KAXEXX repeats that EntB and EndC share. Ent proteins have a signal peptide, an N-terminal SH3 domain and a C-terminal 3D (Asp-Asp-Asp) domain. They may play a role in maintenance of cell wall structure and stress responses that support virulence, and probably lack any direct role as enterotoxins. 310 matched cddid_all.tbl CDD NF040676 NF040676 468642 wall_bind_EntB cell wall-binding protein EntB. This HMM describes the cell wall-binding protein EntB, as found in Bacillus cereus. EntB is related to EntA, EntC, and EndD. All Ent family proteins have a signal peptide, an N-terminal SH3 domain and a C-terminal 3D (Asp-Asp-Asp) domain. EntB and EndC have a central region with a highly variable number of repeats resembling KAXEXX. The gene symbol derives from the notion that at least some members of the family function as enterotoxins, but more recent descriptions focus on roles in stress response and cell wall integrity. 476 matched cddid_all.tbl CDD NF040677 NF040677 468643 wall_bind_EntC cell wall-binding protein EntC. This HMM describes the cell wall-binding protein EntC, as found in Bacillus cereus. EntC is related to EntA, EntB, and EndD. All Ent family proteins have a signal peptide, an N-terminal SH3 domain and a C-terminal 3D (Asp-Asp-Asp) domain. EntB and EndC have a central region with a highly variable number of repeats resembling KAXEXX. The gene symbol derives from the notion that at least some members of the family function as enterotoxins, but more recent descriptions focus on roles in stress response and cell wall integrity. 422 matched cddid_all.tbl CDD NF040679 NF040679 468644 halocin_of_epi halocin C8 precursor-like protein. Members of this family are bacterial (mostly staphylococcal) homologs of the archaeal bacteriocin halocin C8 precursor. Members average about 245 amino acids in length, with the 76 amino acid Cys-rich mature peptide region at the C-terminus. Cutoff scores are set fairly high because this HMM is designed to identify full-length members of the family such as WP_002493350.1 from Staphylococcus epidermidis. 243 matched cddid_all.tbl CDD NF040680 NF040680 468645 chromo_anti enediyne antibiotic chromoprotein. Members of this family are the apoprotein polypeptides of chromophore-containing antibiotics such as neocarzinostatin and actinoxanthin, interesting in part for the roles as anticancer therapeutics. 133 matched cddid_all.tbl CDD NF040681 NF040681 468646 GPS-CTERM GPS-CTERM domain. The GPS-CTERM domain, defined by this HMM, is found in Actinobacteria such as Nocardia and Streptomyces, at the C-terminus of at least to otherwise unrelated protein families. It is an apparent novel protein-sorting domain. 30 matched cddid_all.tbl CDD NF040682 NF040682 468647 PorA_Arch pyruvate synthase subunit PorA. 388 matched cddid_all.tbl CDD NF040683 NF040683 468648 PorC_Meth_Thtga pyruvate synthase subunit PorC. 177 matched cddid_all.tbl CDD NF040684 NF040684 468649 PorD_Arch pyruvate synthase subunit PorD. 85 matched cddid_all.tbl CDD NF040685 NF040685 468650 conju_mem_TcpD conjugal transfer membrane protein TcpD. 114 matched cddid_all.tbl CDD NF040686 NF040686 468651 TcpD_dom TcpD family membrane protein. 63 matched cddid_all.tbl CDD NF040688 NF040688 468652 ADPRT_certhrax ADP-ribosyltransferase certhrax. The two members of the seed alignment include the originally described ADP-ribosyltransferase called certhrax, extended somewhat upstream of the originally predicted start codon, and a full length homolog from Bacillus toyonensis with 72 percent identity, likely to function in the same way and merit the same name. 531 matched cddid_all.tbl CDD NF040689 NF040689 468653 MtrAB_MtrA MtrAB system response regulator MtrA. 219 matched cddid_all.tbl CDD NF040690 NF040690 468654 mycolate_SDR mycolate reductase. Catalyzes the final step in mycolic acid biosynthesis 265 matched cddid_all.tbl CDD NF040691 NF040691 468655 MtrAB_MtrB MtrAB system histidine kinase MtrB. 507 matched cddid_all.tbl CDD NF040692 NF040692 468656 recomb_assoc gamma-mobile-trio protein GmtX. Members of this family are found regularly in the context of a XerC/XerD-related recombinase and with a member of family PF13009, called a putative integrase by Pfam. The family is named GmtX, for Gammaproteobacterial Mobile Trio system protein of unknown (X) function. Members of this family include VPA1268 found in a pathogenicity island of Vibrio parahaemolyticus. 206 matched cddid_all.tbl CDD NF040693 NF040693 468657 recomb_GmtY gamma-mobile-trio recombinase GmtY. GmtY (gamma-mobile-trio system tyrosine recombinase) is a putative integrase regularly found associated with two other proteins of unknown function, in a cassette found sporadically in various Gamma-proteobacteria. Members of this family include VPA1270, found in pathogenicity island 6 of Vibrio parahaemolyticus RIMD2210633. 441 matched cddid_all.tbl CDD NF040694 NF040694 468658 ribK_Meth CTP-dependent riboflavin kinase. 127 matched cddid_all.tbl CDD NF040695 NF040695 468659 FlaK_Arch preflagellin peptidase FlaK. 230 matched cddid_all.tbl CDD NF040696 NF040696 468660 isopcys_mtase protein-S-isoprenylcysteine O-methyltransferase. 190 matched cddid_all.tbl CDD NF040697 NF040697 468661 VPA1267_fam VPA1267 family protein. Members of this family occur in mobile elements, as for VPA1267 found in pathogenicity island 6 of Vibrio parahaemolyticus RIMD2210633. 143 matched cddid_all.tbl CDD NF040698 NF040698 468662 IdsA_Meth short chain isoprenyl diphosphate synthase IdsA. 328 matched cddid_all.tbl CDD NF040699 NF040699 468663 VPA1262_fam VPA1262 family protein. Members of this family occur in mobile elements, as for example VPA1262 found in pathogenicity island 6 of Vibrio parahaemolyticus RIMD2210633. 1024 matched cddid_all.tbl CDD NF040700 NF040700 468664 VPA1262_N_dom VPA1262 family N-terminal domain. The founding member VPA1262, of this domain family is a large protein of 1104 amino acids, found in a pathogenicity island of Vibrio parahaemolyticus RIMD 2210633. Many homologs of half that length share homology only to the N-terminal half. Members of the family share well-conserved DP[FY] and HDR motifs. The related model NF040699 describes full-length homologs of VPA1262. The function is unknown. 475 matched cddid_all.tbl CDD NF040701 NF040701 468665 RecJ_Meth single-stranded-DNA-specific exonuclease RecJ. 449 matched cddid_all.tbl CDD NF040702 NF040702 468666 ileS_w_GNAT isoleucine--tRNA ligase, N-acetyltransferase domain-containing. This unusual form of isoleucine--tRNA ligase, found in at least six different species of Moraxella, has a GNAT-type N-acetyltransferase domain, about 170 amino acids long, inserted after position 270 of forms lacking the insert, such as that of Escherichia coli. 1100 matched cddid_all.tbl CDD NF040703 NF040703 468667 cyclopro_CfaB C17 cyclopropane fatty acid synthase CfaB. 393 matched cddid_all.tbl CDD NF040704 NF040704 468668 IPP_alt_MvaD archaeal-type phosphomevalonate decarboxylase. The archaeal alternate mevalonate pathway generates isopentenyl diphosphate by decarboxylation of mevalonate monophosphate followed by phosphorylation of isopentyl phosphate. This model represents the enzyme responsible for the decarboxylation of mevalonate monophosphate that is found in halophilic archaea. 323 matched cddid_all.tbl CDD NF040705 NF040705 468669 sigma_mbnA methanobactin precursor domain-containing sigma factor. This variant form of sigma factor is found exclusively with a C-terminal methanobactin precursor domain. 272 matched cddid_all.tbl CDD NF040706 NF040706 468670 photo_cyt_PufC photosynthetic reaction center cytochrome PufC. 311 matched cddid_all.tbl CDD NF040707 NF040707 468671 Siroheme_Dcarb_AhbB siroheme decarboxylase subunit beta. 153 matched cddid_all.tbl CDD NF040708 NF040708 468672 Siroheme_Dcarb_AhbA siroheme decarboxylase subunit alpha. 149 matched cddid_all.tbl CDD NF040709 NF040709 468673 benzoate_BenM benzoate utilization transcription regulator BenM. The LysR family transcriptional regulator BenM is both a paralog and a neighbor of CatM. Both transcription factors sense the catabolite cis,cis-muconate in order to play a role in benzoate catabolism. This model describes BenM. 299 matched cddid_all.tbl CDD NF040710 NF040710 468674 benzoate_CatM cis,cis-muconate-binding transcription regulator CatM. 293 matched cddid_all.tbl CDD NF040711 NF040711 468675 partner_SinI SinI family autotransporter-associated protein. Members of this family, including SinI from Salmonella enterica LT2, are putative passenger proteins of a variant-type type V secretion system (T5SS), in which SinH or a homolog is an inverse autotransporter that transporters a member of this family as well as its own passenger domain. 288 matched cddid_all.tbl CDD NF040712 NF040712 468676 SepH septation protein SepH. Septation protein H (SepH) was firstly characterized in Streptomyces venezuelae, and homologs were identified in Mycobacterium smegmatis. SepH contains a N-terminal DUF3071 domain and a conserved C-terminal region. It binds directly to cell division protein FtsZ to stimulate the assembly of FtsZ protofilaments. 346 matched cddid_all.tbl CDD NF040713 NF040713 468677 ZapE cell division protein ZapE. 344 matched cddid_all.tbl CDD NF040714 NF040714 468678 streptamidine streptamidine family RiPP. Streptamidine is a ribosomally translated, post-translationally modified peptide (RiPP) whose modification depends on a YcaO family maturase. The mature product derives from the central hexapeptide HLSATH, or a similar peptide. See related model NF040715 for a similar family in which a related RiPP precursor domain occurs typically in two or more tandem repeats. 28 matched cddid_all.tbl CDD NF040715 NF040715 468679 AmiA_rel_RiPP2x streptamidine-related RiPP repeat. This HMM represents a family of streptamidine-related RiPP precursor proteins, most of which have two or more repeats of the 35 amino-acid long domain that contains the modification site. Modification is performed by a YcaO family peptide maturase. The related model NF040714 describes the family of RiPP precursor proteins that includes streptamidine (AmiA) itself and close homologs. While in the streptamidine precursor AmiA itself and its homologs, the core peptide is HLSATH or something similar, the six residues from this family that align are typically APQGPG, suggesting a very different mature product. 35 matched cddid_all.tbl CDD NF040716 NF040716 468680 YcaO_for_S12 30S ribosomal protein S12 methylthiotransferase accessory factor YcaO. YcaO acts as a partner for RimO to achieve the modification of ribosomal protein S12. Homologs of YcaO are involved a wide variety of RiPP (ribosomally translated, post-translationally modified peptide) natural product biosynthesis pathways. Some members of this family have an additional N-terminal OsmC-like domain. 571 matched cddid_all.tbl CDD NF040717 NF040717 468681 BcsR_only cellulose biosynthesis protein BcsR. BcsR (bacterial cellulose synthesis R, previously YhjR in Escherichia coli) is a small cytosolic protein essential for cellulose. It appears to form part of the Bcs macrocomplex that also includes membrane, periplasmic, and outer membrane components. BcsR shares homology with the N-terminal domain of BcsP, a longer protein with variable and repetitive C-terminal regions, found in beta-proteobacteria. See PF10945 for an HMM that describes the shared region. 42 matched cddid_all.tbl CDD NF040718 NF040718 468682 BcsP_of_Ic cellulose biosynthesis protein BcsP N-terminal domain. BcsP is a protein of bacterial cellulose biosynthesis, encode in the beta-proteobacteria in type Ic cellulose biosynthesis operons. Only the N-terminal region, homologous to the much smaller protein BcsR, is well-conserved. Pfam model PF10945 describes the region shared by BcsP, BcsR, and some other cellulose biosynthesis proteins. 55 matched cddid_all.tbl CDD NF040719 NF040719 468683 Lar0958_adhesin Lar_0958 family LPXTG-anchored mucus adhesin. 1030 matched cddid_all.tbl CDD NF040720 NF040720 468684 MptN_Meth tetrahydromethanopterin:alpha-L-glutamate ligase. 290 matched cddid_all.tbl CDD NF040721 NF040721 468685 Trm14_Arch tRNA (guanine(6)-N2)-methyltransferase. 370 matched cddid_all.tbl CDD NF040722 NF040722 468686 MfnD_Meth tyramine--L-glutamate ligase. 290 matched cddid_all.tbl CDD NF040723 NF040723 468687 UDP-GlcNAcDh_Arch UDP-N-acetylglucosamine 3-dehydrogenase. 302 matched cddid_all.tbl CDD NF040724 NF040724 468688 GpgS_Meth glucosyl-3-phosphoglycerate synthase. 402 matched cddid_all.tbl CDD NF040725 NF040725 468689 panto_kin_Meth pantoate kinase. 286 matched cddid_all.tbl CDD NF040726 NF040726 468690 BetaRFA-P_synth beta-ribofuranosylaminobenzene 5'-phosphate synthase. 327 matched cddid_all.tbl CDD NF040727 NF040727 468691 SBP_SaoB_CU ABC transporter substrate-binding (seleno)protein SaoB. Members of this family are apparent substrate-binding proteins of an ABC transporter, found in Clostridium difficile and a number of other anaerobic heterotrophs, as part of the SAO (selenocysteine organometallic-assisted) locus. Six of the nine core proteins of the SAO locus can be selenoproteins, including this protein and the permease subunit, SaoP, encoded next to it. 261 matched cddid_all.tbl CDD NF040728 NF040728 468692 MerB_rel_SaoL MerB-like organometallic lyase SaoL. Nearly all members of this family, SaoL, are selenoproteins with a CU motif that suggests interaction with a heavy metal such as mercury. While SaoL is homologous to the organomercurial lyase MerB, its context is different. SaoL occurs as part of the SAO (selenocysteine-assisted organomercurial) locus, with nine conserved proteins. Six SAO proteins can be selenoproteins, including multiple subunits of an unusual ABC transporter with one permease subunit but two associated substrate-binding proteins. 159 matched cddid_all.tbl CDD NF040729 NF040729 468693 ABC_ATP_SaoA ABC transporter ATP-binding protein SaoA. SaoA is the ATP-binding subunit of an ABC transporter in which both the permease subunit SaoP, and the substrate-binding protein SaoB, are nearly always selenoproteins that were unrecognized as such until recently (2022). The SAO system is found in Clostridium difficile and various other anaerobic heterotrophs. 248 matched cddid_all.tbl CDD NF040730 NF040730 468694 CxCC_doxin thioredoxin-like (seleno)protein SaoT. SaoT is a predicted cytosolic protein, usually a selenoprotein, from the SAO (selenocysteine-assisted organometallic) locus. Other proteins in the system include a putative metal efflux protein, a surface protein, an ABC transporter with multiple selenoprotein subunits, and the selenoprotein SaoL, a homolog of the organomercurial lyase MerB of some mercury resistance systems. The SAO system may use mercury or another heavy metal atom as a cofactor, incorporating it into an organometallic intermediate, associated with import of that metabolite, and then exporting the metal after its release for use in a subsequent cycle. 83 matched cddid_all.tbl CDD NF040731 NF040731 468695 flavo_sub_EftB electron transfer flavoprotein subunit beta. Members of this family electron transfer flavoprotein subunit beta (EftB) as found in pathways for leucine reduction to isocaproate as seen in the strict anaerobe Clostridium difficile. 260 matched cddid_all.tbl CDD NF040732 NF040732 468696 DsrE_rel_SaoD DsrE-related protein SaoD. 110 matched cddid_all.tbl CDD NF040733 NF040733 468697 ABC_perm_U ABC transporter permease subunit SaoP. SaoP, one of the nine proteins of the SAO (selenocysteine-associated organometallic) locus, is nearly always a selenoprotein, and is one of six novel selenoprotein families from that locus. The Sec (U) residue occurs at a position described in other ABC transporter permease homodimers as the channel-gating position. A role in importing (and perhaps even forming) organometallic compounds, in a cycle in which the metal atom is reexported and reused, as a cofactor that aids in utilization of some otherwise refractory substrate, has been suggested. The SAO system occurs in Clostridium difficile (a human gut pathogen), Brachyspira pilosicoli (an intestinal spirochete in chicken), Desulfopila aestuarii (a deltaproteobacterial sulfate reducer from estuary sediment), etc. 251 matched cddid_all.tbl CDD NF040734 NF040734 468698 CC-COOH_SaoC Cys-Cys-COOH (seleno)protein SaoC. Members of this family, now called SaoC, include CD2366 from Clostridium difficile. The most striking conserved motif in this family is a pair of cysteine residues at the C-terminus, which takes the form Cys-Sec (CU) in the occasional members of this family that are selenoproteins. Selenoprotein examples include WP_252346676.1 (Finegoldia magna), WP_252346670.1 (Merdimonas faecis), and WP_252346671.1 (Lachnospiraceae bacterium). The SAO (selenocysteine-assisted organometallic) system contains six selenoproteins overall, including three ABC transporter subunits and a homolog (SaoL) of organomercurial lyases. SaoC is proposed to play a role in chaperoning heavy metal atoms effluxed by SaoE to an ABC transporter with selenoprotein permease and substrate-binding proteins, for reuptake after covalent incorporation into an organometallic intermediate of some unknown class of fermentable nutrient. 147 matched cddid_all.tbl CDD NF040735 NF040735 468699 SBP_SaoX ABC transporter substrate-binding subunit SaoX. Members of this family include CD2365 from Clostridium difficile, and are identified as SaoX of the selenocysteine-assisted organometallic (SAO) system. SaoX, an ABC transporter substrate-binding subunit, is an occasional selenoprotein. Partner proteins SaoB (another substrate-binding protein) and SaoP (an ABC transporter permease subunit) are selenoproteins most of the time. The transporter complex likely imports some (currently unknown) organometallic compound, and might actually couple its formation to its transport, employing a heavy metal atom as an inorganic cofactor that lowers activation energies for anaerobic fermentation of refractory substrates. 330 matched cddid_all.tbl CDD NF040736 NF040736 468700 efflux_SaoE efflux transporter SaoE. Members of this family, including CD2367 from Clostridium difficile, are related to efflux proteins associated with resistance to arsenic or organoarsenicals, copper, and zinc. 352 matched cddid_all.tbl CDD NF040737 NF040737 468701 peroxi_PrxU thioredoxin-dependent peroxiredoxin. 233 matched cddid_all.tbl CDD NF040738 NF040738 468702 nickel_Mua nickel-binding protein Mua. Mua (modulator of urease activity), as found in the genus Helicobacter, is described as a nickel-binding protein 185 matched cddid_all.tbl CDD NF040739 NF040739 468703 ornith_OrtA 2-amino-4-oxopentanoate thiolase subunit OrtA. 93 matched cddid_all.tbl CDD NF040740 NF040740 468704 ornith_Ord 2,4-diaminopentanoate dehydrogenase. This model does not distinguish between 1.4.1.26 (NAD-only) and 1.4.1.12 (NAD or NADP). 335 matched cddid_all.tbl CDD NF040741 NF040741 468705 ornith_OrtB 2-amino-4-oxopentanoate thiolase subunit OrtB. 464 matched cddid_all.tbl CDD NF040742 NF040742 468706 racem_Orr ornithine racemase Orr. This type of ornithine racemase occurs in an operon for anaerobic oxidative degradation of L-ornithine as occurs in strict anaerobes such as Clostridium sticklandii. The enzyme from C. sticklandii was shown to act on the basic amino acids ornithine, lysine, and arginine. Additional close homologs, outside the family defined by this HMM, likely have similar activity profiles, but occur in different genomic contexts and would not receive the gene symbol orr. 351 matched cddid_all.tbl CDD NF040743 NF040743 468707 ornith_mutase_E D-ornithine 4,5-aminomutase subunit OraE. 730 matched cddid_all.tbl CDD NF040744 NF040744 468708 ornith_Or-4 GlmL-related ornithine degradation protein. Members of this uncharacterized protein family, given the temporary name Or-4, occur as a part of a conserved gene cluster for anaerobic oxidative degradation of L-ornithine. That cluster includes a B-12-dependent enzyme, D-ornithine 4,5-aminomutase. Or-4 is related to but distinct from GlmL, a protein of unknown function encoded next to subunits of a coenzyme B12-dependent glutamate mutase. 448 matched cddid_all.tbl CDD NF040745 NF040745 468709 accessory_GlmL methylaspartate mutase accessory protein GlmL. GlmL (glutamate mutase operon protein L), a protein with unknown activity, occurs invariably as part of a locus that also includes the E (epsilon) and S (sigma) subunits of methylaspartate mutase (also called glutamate mutase. A related protein occurs exclusively in a locus the anaerobic degradation of ornithine, where a different cobalamin-dependent enzyme occurs. It seems likely that GlmL is an accessory protein for the methylaspartate mutase. 460 matched cddid_all.tbl CDD NF040746 NF040746 468710 reduct_C_beta glycine/sarcosine/betaine reductase complex component C subunit beta. Protein C is the shared acetyl-phosphate-forming component of three types of selenoprotein-containing complexes, acting on glycine, sarcosine, or betaine. Protein C itself has a large subunit and a small subunit (sometimes fused), and does not contain selenocysteine. This HMM describes the large subunit, called beta. 477 matched cddid_all.tbl CDD NF040747 NF040747 468711 reduct_C_alpha glycine/sarcosine/betaine reductase complex component C subunit alpha. Protein C is the shared acetyl-phosphate-forming component of three types of selenoprotein-containing complexes, acting on glycine, sarcosine, or betaine. A different subunit, B, determines the substrate. Protein C itself has a large subunit and a small subunit (sometimes fused), and does not contain selenocysteine. This HMM describes the small subunit, called alpha. 380 matched cddid_all.tbl CDD NF040748 NF040748 468712 reduct_selen_A glycine/sarcosine/betaine reductase complex selenoprotein A. Selenoprotein A (GrdA) is the A subunit of a complex whose specificity is determined by a different subunit, B, in a glycine or sarcosine or betaine reductase complex. In some species, only one type of B subunit (also a selenoprotein) occurs. Protein C is usually a heterodimer of two subunits called beta (GrdC) and alpha (GrdD), and is not a selenoprotein. 151 matched cddid_all.tbl CDD NF040749 NF040749 468713 tetrathio_RR tetrathionate respiration response regulator TtrR. 191 matched cddid_all.tbl CDD NF040750 NF040750 468714 tetrathio_HK tetrathionate respiration histidine kinase TtrS. 554 matched cddid_all.tbl CDD NF040755 NF040755 468715 AgaR transcriptional repressor AgaR. 256 matched cddid_all.tbl CDD NF040756 NF040756 468716 corr_regen_AcsV corrinoid activation/regeneration protein AcsV. 632 matched cddid_all.tbl CDD NF040757 NF040757 468717 AgaW PTS N-acetylgalactosamine transporter subunit IIC. 248 matched cddid_all.tbl CDD NF040758 NF040758 468718 CODH_ACS_meth carbon monoxide dehydrogenase/acetyl-CoA synthase methytransferase subunit. 261 matched cddid_all.tbl CDD NF040759 NF040759 468719 WLP_AcsD acetyl-CoA decarbonylase/synthase complex subunit delta. This component of the acetyl-CoA decarbonylase/synthase complex, as found in acetogens with the Wood-Ljungdahl pathway, is the corrinoid iron-sulfur protein small subunit, AcsD. 312 matched cddid_all.tbl CDD NF040760 NF040760 468720 AgaE PTS N-acetylgalactosamine transporter subunit IID. 292 matched cddid_all.tbl CDD NF040761 NF040761 468721 AgaF PTS galactosamine/N-acetylgalactosamine transporter subunit IIA. 144 matched cddid_all.tbl CDD NF040762 NF040762 468722 Hydr_FeFe_Clost ferredoxin hydrogenase, clostridial type. Members of this family of hydrogenases share full-length homology with many other iron-only hydrogenases, but differ in transferrring electrons only to ferredoxins (EC 1.12.7.2) and not to NAD(P)+. 572 matched cddid_all.tbl CDD NF040763 NF040763 468723 FeFe_hydrog_A6 NADH-dependent [FeFe] hydrogenase, group A6. 571 matched cddid_all.tbl CDD NF040764 NF040764 468724 CODH_ACS_al_bet acetyl-CoA decarbonylase/synthase complex subunit alpha/beta. Members of this family have both alpha and beta regions. Proteins scoring between 400 and 800 have only the C-terminal (beta) region. 707 matched cddid_all.tbl CDD NF040765 NF040765 468725 adhesion_FAF adhesion factor FAF. FAF (Finegoldia adhesion factor) has firstly been identified and characterized in the opportunistic pathogen Finegoldia magna. FAF mediate bacterial adhesion to hosts through interactions with the basement membrane protein BM-40. 632 matched cddid_all.tbl CDD NF040766 NF040766 468726 CODH_aero_grp5 aerobic carbon-monoxide dehydrogenase large subunit, group V. 785 matched cddid_all.tbl CDD NF040768 NF040768 468727 Epx enterococcus pore-forming toxin Epx. 297 matched cddid_all.tbl CDD NF040769 NF040769 468728 SelL_rel_redox SelL-related redox protein. Members of this family are related to the C-terminal region of selenoprotein L (SelL), found in many non-mammalian animals. But while SelL itself has a pair of selenocysteine (U) residues (e.g. XP_029705782.1), typically in the motif ULPU, this family is defined more broadly. Most members of the seed alignment for this HMM are bacterial proteins that have one or zero selenocysteine residues, and are shorter than SelU, although SelU members are also included. 172 matched cddid_all.tbl CDD NF040770 NF040770 468729 hetero_SS_HdrA2 CoB-CoM heterodisulfide reductase HdrA2. HdrA2 represents a distinct subclass of the HdrA family, which is the A subunit of the CoB-CoM heterodisulfide reductase. HdrA2 from Methanosarcina acetivorans. A distinctive feature is a MvhD-like C-terminal domain, where MvhD is the signature delta subunit of the F420-non-reducing type of hydrogenase, Mvh. 777 matched cddid_all.tbl CDD NF040771 NF040771 468730 AAH_UGLYAH2 bifunctional allantoicase/(S)-ureidoglycine aminohydrolase, UGLYAH2 family. The UGLYAH2 family acts primarily as allantoicase (allantoate amidinohydrolase, EC 3.5.3.4), while unrelated to the AllC family of allantoicase enzymes. It belongs to a broader family of enzymes with (S)-ureidoglycine aminohydrolase activity (EC 3.5.3.26) carried out at the same active site. However, Puggioni, et al. consider that activity secondary, as (S)-ureidoglycine is an unstable compound expected only as a product of allantoate amidohydrolase (AAH) activity, and AAH is nearly always absent when UGLYAH2 is present. UGLYAH2 is an acronym for (S)-ureidoglycine aminohydrolase type 2. 267 matched cddid_all.tbl CDD NF040772 NF040772 468731 double_cubane double-cubane-cluster-containing anaerobic reductase. This subfamily of double-cubane proteins occurs strictly in anaerobes (facultative or obligate), such as Escherichia coli and Clostridium difficile. The enzyme always co-occurs with an accessory protein, an ATP-dependent activase. The cofactor contains a pair of 4Fe-4S cubane clusters, bridged by a sulfur atom, for an overall 8Fe-9S cofactor structure. However, we observe that that this family essentially always co-occurs in bacteria with SelD, the selenium donor protein required for biosynthesis of selenoproteins, selenouridine-modified tRNAs, selenium-dependent molybdenum hydroxylases, and selenoneine. 372 matched cddid_all.tbl CDD NF040775 NF040775 468732 endonuc_Nei2 endonuclease VIII Nei2. 251 matched cddid_all.tbl CDD NF040776 NF040776 468733 AlsR transcriptional repressor AlsR. 279 matched cddid_all.tbl CDD NF040779 NF040779 468734 Sec_lyase_SclA selenocysteine lyase SclA. In bacteria, selenocysteine lyase activity (EC 4.4.1.16) usually is seen as a secondary activity of a cysteine desulfurase (EC 2.8.1.7). However, SclA, as studied in Enterococcus faecalis, acts primary on selenocysteine, binding cysteine just as well but acting on cysteine with much lower catalytic efficiency. 378 matched cddid_all.tbl CDD NF040782 NF040782 468735 PG_glutam_Chrys protein-glutamine glutaminase. This HMM describes full-length protein-glutamine glutaminases that share end-to-end homology with the founding member from Chryseobacterium proteolyticum, can hydrolyze amino groups from the glutamine side-chains of proteins. Pfam model PF18626 identifies a central region, about one-third the length of this model, that includes the catalytic triad Cys-His-Asp. 321 matched cddid_all.tbl CDD NF040785 NF040785 468736 CD3324_fam CD3324 family protein. Members of this family include CD3324 and CD1583A from Clostridium difficile and YraL from Bacillus subtilis. Members show stretches of sequence homology to Mor, which is a transcriptional activator from phage Mu, and to other members of Pfam model PF08765. 82 matched cddid_all.tbl CDD NF040786 NF040786 468737 LysR_Sec_metab selenium metabolism-associated LysR family transcriptional regulator. LysR family transcriptional regulators regularly appear encoded adjacent to selenecysteine incorporation proteins such as SelB. This model represents one especially well-conserved subgroup of such transcription factors from species such as Merdimonas faecis, Sellimonas intestinalis, Syntrophotalea acetylenica, and Hydrogenivirga caldilitoris. Seed alignment members were selected by proximity to selB, but not all family members are expected to have similar genomic locations. 298 matched cddid_all.tbl CDD NF040787 NF040787 468738 S-lay_SlaA_Mtsph S-layer protein SlaA. 1356 matched cddid_all.tbl CDD NF040788 NF040788 468739 S-lay_SlaB_Mtsph S-layer protein SlaB. 416 matched cddid_all.tbl CDD NF040789 NF040789 468740 gerfarn_diphsyn geranylfarnesyl diphosphate synthase. 328 matched cddid_all.tbl CDD NF040790 NF040790 468741 glucon_galact_dh bifunctional D-gluconate/D-galactonate dehydratase. 390 matched cddid_all.tbl CDD NF040791 NF040791 468742 gly_kin_Thpl glycerate 2-kinase. 410 matched cddid_all.tbl CDD NF040792 NF040792 468743 glyc_ald_dh D-glyceraldehyde dehydrogenase. 488 matched cddid_all.tbl CDD NF040793 NF040793 468744 sarcosine_GrdG sarcosine reductase complex component B subunit alpha. 428 matched cddid_all.tbl CDD NF040794 NF040794 468745 sarcosine_GrdF sarcosine reductase complex component B subunit beta. 435 matched cddid_all.tbl CDD NF040795 NF040795 468746 betaine_GrdH betaine reductase selenoprotein B. 435 matched cddid_all.tbl CDD NF040796 NF040796 468747 toxic_TimP small toxic inner membrane protein TimP. The gene timP (toxic inner membrane protein) occurs within the small structural RNA ryfA. Proteins of the TimP family can be found encoded in Escherichia coli, Salmonella enterica, Citrobacter, and Klebsiella sp. 40 matched cddid_all.tbl CDD NF040801 NF040801 468748 spore_GerD spore germination lipoprotein GerD. This HMM describes the spore germination GerD, as found in Bacillus subtilis and other endospore-forming bacteria. It appears that every member of this family has a lipoprotein-type signal sequence. 174 matched cddid_all.tbl CDD NF040808 NF040808 468749 CspC_non_triad bile acid germinant receptor pseudoprotease CspC. Members of this family share homology with MEROPS S8 family serine proteases, but with substitutions that replace key catalytic residues, as seen in CD2246 from Clostridium difficile. The related germination-specific protease CspC of Clostridium perfringens, outside the scope of this model, retains its serine protease catalytic triad residues. Adjacent to CD2246 is the fusion protein CD2247, CspBA, in which the CspB region retains its subtilisin-like catalytic triad while the CspA, like CspC, has lost it. 556 matched cddid_all.tbl CDD NF040809 NF040809 468750 germ_prot_CspBA bifunctional germination protease/germinant receptor pseudoprotease CspBA. CspBA, as found in Clostridium difficile, is translated as a fusion protein, but cleaved into separate homologous CspB and CspA proteins during spore formation. CspB is a protease, required to active SleC by cleaving it in order to trigger germination. CspA, like the bile salt germinant receptor CspC (encoded by the adjacent gene), has lost the catalytic residues necessary for subtilisin-like serine protease activity. 1099 matched cddid_all.tbl CDD NF040810 NF040810 468751 BenC benzoate 1,2-dioxygenase electron transfer component BenC. 333 matched cddid_all.tbl CDD NF040811 NF040811 468752 BenD benzoate diol dehydrogenase BenD. 256 matched cddid_all.tbl CDD NF040813 NF040813 468753 pro_dh_Thprot D-proline dehydrogenase. 362 matched cddid_all.tbl CDD NF040814 NF040814 468754 tRNA_cyt_mtase tRNA (cytosine(49)-C(5))-methyltransferase. 305 matched cddid_all.tbl CDD NF040815 NF040815 468755 recomb_XerA_Arch tyrosine recombinase XerA. 282 matched cddid_all.tbl CDD NF040816 NF040816 468756 Fbpase1_Arch class I fructose-bisphosphate aldolase. 271 matched cddid_all.tbl CDD NF040817 NF040817 468757 GdhA_Arch glutamate dehydrogenase. 419 matched cddid_all.tbl CDD NF040818 NF040818 468758 GAPOR_Arch glyceraldehyde-3-phosphate:ferredoxin oxidoreductase. 654 matched cddid_all.tbl CDD NF040819 NF040819 468759 helicase_HerA DNA double-strand break repair helicase HerA. 561 matched cddid_all.tbl CDD NF040820 NF040820 468760 trans_reg_LrpA HTH-type transcriptional regulator LrpA. 141 matched cddid_all.tbl CDD NF040821 NF040821 468761 dipep_PepQ_Arch Xaa-Pro dipeptidase PepQ. 346 matched cddid_all.tbl CDD NF040822 NF040822 468762 lys_aminopep_Arch lysyl aminopeptidase. 345 matched cddid_all.tbl CDD NF040823 NF040823 468763 deglyc_PfpI deglycase PfpI. 166 matched cddid_all.tbl CDD NF040824 NF040824 468764 damage_ctl_Phtase damage-control phosphatase. 282 matched cddid_all.tbl CDD NF040825 NF040825 468765 UDPMaNacDH_Arch UDP-N-acetyl-D-mannosamine dehydrogenase. 418 matched cddid_all.tbl CDD NF040826 NF040826 468766 lxa_BCAM0308 BCAM0308 family protein. Members of this family average about 170 amino acids in length, and have a conserved pair of CxxC motifs, suggesting metal-binding. Many of this proteins register as part-length, borderline-scoring hits to Pfam model PF04981, which hits the N-terminal domain of Nmd3 (nonsense-mediated decay 3) in yeast, involving in export of the 60S ribosomal subunit from the nucleus, as well as archaeal homologs of Nmd3. This HMM was built to provide a clear separation of member proteins from that family. The family is named for BCAM0308 from Burkholderia cenocepacia, one of many proteins in the lxa (low oxygen-activated) locus, whose proteins are induced when oxygen concentrations are low. 153 matched cddid_all.tbl CDD NF040827 NF040827 468767 CotZ_rel CotZ-related putative spore coat protein. Members of this appear only in endospore-forming bacteria, and are distantly related to spore coat protein CotZ. 212 matched cddid_all.tbl CDD NF040828 NF040828 468768 sulfhyd_ShyA NAD(P)-dependent hydrogenase/sulfhydrogenase 2 subunit alpha. 415 matched cddid_all.tbl CDD NF040829 NF040829 468769 sulfhyd_ShyB NAD(P)-dependent hydrogenase/sulfhydrogenase 2 subunit beta. 334 matched cddid_all.tbl CDD NF040830 NF040830 468770 sulfhyd_ShyC NAD(P)-dependent hydrogenase/sulfhydrogenase 2 subunit gamma. 288 matched cddid_all.tbl CDD NF040831 NF040831 468771 sulfhyd_ShyD NAD(P)-dependent hydrogenase/sulfhydrogenase 2 subunit delta. 240 matched cddid_all.tbl CDD NF040832 NF040832 468772 sulfhyd_HydA NADPH-dependent hydrogenase/sulfhydrogenase 1 subunit alpha. 426 matched cddid_all.tbl CDD NF040833 NF040833 468773 sulfhyd_HydB NADPH-dependent hydrogenase/sulfhydrogenase 1 subunit beta. 367 matched cddid_all.tbl CDD NF040835 NF040835 468774 sulfhyd_HydG NADPH-dependent hydrogenase/sulfhydrogenase 1 subunit gamma. 292 matched cddid_all.tbl CDD NF040836 NF040836 468775 sulfhyd_HydD NADPH-dependent hydrogenase/sulfhydrogenase 1 subunit delta. 261 matched cddid_all.tbl CDD NF040837 NF040837 468776 BMC_EutD_Gpos ethanolamine utilization phosphate acetyltransferase EutD, CD1920-type. Members of this family of bacterial microcompartment (BMC) enzymes for ethanolamine utilization are thought to have the same phosphate acetyltransferase activity (EC 2.3.1.8) as EutD of Salmonella and E. coli, but lacking sequence similarity and instead being related to PduL, phosphate propanoyltransferase (EC 2.3.1.222) of propanediol utilization BMC enzymes. Examples discussed in the literature, such as Lmo1182 from Listeria monocytogenes and CD1920 from Clostridium difficile, are called EutD despite the lack of homology. 205 matched cddid_all.tbl CDD NF040838 NF040838 468777 T4_PilC_Neiss neisserial PilC family type IV pilus tip adhesin. PilC, as found in Neisseria meningitidis and Neisseria gonorrhoeae, is the tip adhesin of the type IV pilus. It also occurs in the bacterial outer membrane, and contributes to pilus biogenesis and to competence for transformation. Typically two paralogs are found, PilC1 and PilC2, and this HMM does not distinguish between them. PilC genes are phase-variable because of expression is controlled by frameshift mutations in a run of G residues in DNA encoding the signal peptide region. 1035 matched cddid_all.tbl CDD NF040839 NF040839 468778 tungstate_WtpB tungstate ABC transporter permease WtpB. 250 matched cddid_all.tbl CDD NF040840 NF040840 468779 tungstate_WtpC tungstate ABC transporter ATP-binding protein WtpC. 347 matched cddid_all.tbl CDD NF040841 NF040841 468780 AMEP412_fam AMEP412 family response elicitor. AMEP412 (WP_017418614.1) from Bacillus subtilis strain BU412, a 76-amino acid protein that is the founding member of this family, has been shown both to elicit a hypersensitive response in tobacco and have antimicrobial activity against Streptomyces scabiei. Members of this family are found regularly in the context of an apparent ABC transporter ATP-binding protein and a large (about 520 amino acid) protein whose hydrophobic nature suggest transporter permease function. 74 matched cddid_all.tbl CDD NF040842 NF040842 468781 elici_assc_perm AMEP412-like elicitor-associated permease-like protein. Members of this family are found as part of a conserved bacterial gene neighborhood, along with AMEP412 family proteins and an apparent ABC transporter ATP-binding protein. The hydrophobic nature of this protein suggests the protein is a transporter subunit associated with AMEP412 family protein export. Members of the AMEP412 family (see NF040841) are about 76 amino acids in length, and affect both plant cells (hypersensitive response in tobacco) and other bacterial cells (antimicrobial activity vs. the plant pathogen Streptomyces scabiei). 512 matched cddid_all.tbl CDD NF040843 NF040843 468782 SE2200_fam SE2200 family small protein. Members of this staphylococcal protein family are small, typically 33 amino acids long, with the first 18 amino acids resembling a signal-anchor domain for membrane insertion. A proteomics study demonstrates significant protein expression in Staphylococcus aureus, and conservation in the genus suggests purifying selection as would be expected for a real protein. This family, broadly distributed in the genus Staphylococcus, was once described as DUF2648 by Pfam model PF10855, but at the time this model was built (April 2022), that Pfam model had been retired under suspicion of not identifying real proteins. 33 matched cddid_all.tbl CDD NF040844 NF040844 468783 Lac_Quin_Ox_NO L-lactate dehydrogenase (quinone), SACOL2623 family. Members of this family, found primarily in the genus Streptococcus, were shown to be L-lactate dehydrogenase (quinone) (Lqo) although they have generally been misannotated as malate dehydrogenase (quinone). Staphylococcus can survive nitrous oxide exposure from host defense through a response in which L-lactate is excreted in large amounts. Lqo acts in L-lactate consumption after its reuptake. 489 matched cddid_all.tbl CDD NF040845 NF040845 468784 lmo0850_fam Lmo0850 family protein. This family of small proteins, averaging about 45 amino acids in length, occurs widely in Gram-positive genera such as Staphylococcus, Listeria, and Bacillus. The function is unknown, but the sRNA LhrA sRNA regulates expression of Lmo0850 in Listeria monocytogenes by negatively regulating the stability of its mRNA. The regulation depends on Hfq and involves an antisense interaction. 34 matched cddid_all.tbl CDD NF040846 NF040846 468785 SAS049_fam SAS049 family protein. This family of small proteins, about 59 amino acids in length, includes SAS049 from Staphylococcus aureus, SE1307 from Staphylococcus epidermidis, and closely related proteins from other staphylococcal species. The N-terminal region appears highly similar to Rv0909 from Mycobacterium tuberculosis, which appears to be the antitoxin member of a novel class of type 2 toxin-antitoxin system (see PF14013). 47 matched cddid_all.tbl CDD NF040847 NF040847 468786 mev_decarb mevalonate 3,5-bisphosphate decarboxylase. 350 matched cddid_all.tbl CDD NF040848 NF040848 468787 mev_kinase mevalonate-3-kinase. 323 matched cddid_all.tbl CDD NF040849 NF040849 468788 tRNAmod_TiaS tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS. 422 matched cddid_all.tbl CDD NF040850 NF040850 468789 Trm14_Thcoccales tRNA (guanine(6)-N2)-methyltransferase. 365 matched cddid_all.tbl CDD NF040851 NF040851 468790 tran_reg_TrmB HTH-type sugar-sensing transcriptional regulator TrmB. 338 matched cddid_all.tbl CDD NF040852 NF040852 468791 nitrile_Arch nitrilase. 262 matched cddid_all.tbl CDD NF040853 NF040853 468792 KEOPS_Pcc1 KEOPS complex subunit Pcc1. 78 matched cddid_all.tbl CDD NF040854 NF040854 468793 Hol_resolv_Hjc Holliday junction resolvase Hjc. 134 matched cddid_all.tbl CDD NF040855 NF040855 468794 iso_homocit_dh isocitrate--homoisocitrate dehydrogenase. 345 matched cddid_all.tbl CDD NF040857 NF040857 468795 condensinMksB Mks condensin complex protein MksB. 412 matched cddid_all.tbl CDD NF040858 NF040858 468796 condensinMksE Mks condensin complex protein MksE. 230 matched cddid_all.tbl CDD NF040859 NF040859 468797 condensinMksF Mks condensin complex protein MksF. 926 matched cddid_all.tbl CDD NF040861 NF040861 468798 pufA_517_ASD light-harvesting antenna LH1, alpha subunit. 41 matched cddid_all.tbl CDD NF040862 NF040862 468799 pufB_517_ASD light-harvesting antenna LH1, beta subunit. 42 matched cddid_all.tbl CDD NF040863 NF040863 468800 HgcA_corrinoid mercury methylation corrinoid protein HgcA. 327 matched cddid_all.tbl CDD NF040864 NF040864 468801 HgcB_ferredoxin mercury methylation ferredoxin HgcB. 94 matched cddid_all.tbl CDD NF040865 NF040865 468802 a_tRNA_ed_AlaXM alanyl-tRNA editing protein AlaXM. 234 matched cddid_all.tbl CDD NF040866 NF040866 468803 AraD_Arch arabinonate dehydratase. 372 matched cddid_all.tbl CDD NF040867 NF040867 468804 prot_deacyl_CobB NAD-dependent protein deacetylase. 242 matched cddid_all.tbl CDD NF040868 NF040868 468805 carboxypep_CpsA carboxypeptidase CpsA. 391 matched cddid_all.tbl CDD NF040869 NF040869 468806 G3PDH_Arch NADP-dependent glyceraldehyde-3-phosphate dehydrogenase. 502 matched cddid_all.tbl CDD NF040870 NF040870 468807 AztC zinc ABC transporter substrate-binding protein AztC. 277 matched cddid_all.tbl CDD NF040871 NF040871 468808 AztB zinc ABC transporter permease AztB. 254 matched cddid_all.tbl CDD NF040872 NF040872 468809 MFS_HP1165 HP1165 family MFS efflux transporter. HP1165, the founding member of this family of MFS efflux transporters, was shown to provide mild resistance to tetracycline after long exposure, but does not appear to be dedicated to resistance to specific antibiotics. It seems instead that expression may be raised by various factors including the effects of host response to infection. 385 matched cddid_all.tbl CDD NF040873 NF040873 468810 AztA zinc ABC transporter ATP-binding protein AztA. 191 matched cddid_all.tbl CDD NF040875 NF040875 468811 SAS053_fam SAS053 family protein. This small protein of Staphylococcus, Macrococcus, and Mammaliicoccus occurs in a conserved gene neighborhood, downstream of a larger uncharacterized protein distantly related to glucosamine-6-phosphate deaminases. The function is unknown, but its gene is known to be translated into protein. The family is named for founding protein SAS053 from Staphylococcus aureus subsp. aureus N315. 42 matched cddid_all.tbl CDD NF040876 NF040876 468812 RHE_PE00001_fam RHE_PE00001 family protein. RHE_PE00001, the founding member of this family, was shown to be essential for growth on rich medium, despite being encoded on a plasmid. Members of this family contain an apparent helix-turn-helix domain described by Pfam model PF11972, suggesting DNA-binding activity. 372 matched cddid_all.tbl CDD NF040877 NF040877 468813 SE1832_fam SE1832 family small protein. This small protein is known to be expressed, but its function is unknown. 51 matched cddid_all.tbl CDD NF040878 NF040878 468814 SE1561_fam SE1561 family small protein. 46 matched cddid_all.tbl CDD NF040879 NF040879 468815 SAR1012_fam SAR1012 family small protein. This small protein of unknown function is encoded in multiple species of Staphylococcus. It has been demonstrated by mass spectroscopy to be expressed with an unmodified N-terminal fMet residue. 30 matched cddid_all.tbl CDD NF040880 NF040880 468816 adnlytase_SelO protein adenylyltransferase SelO. 480 matched cddid_all.tbl CDD NF040881 NF040881 468817 PTS_reg_TmaR PTS system regulator TmaR. 103 matched cddid_all.tbl CDD NF040882 NF040882 468818 cfpA_ASD cytoplasmic filament protein CfpA. 605 matched cddid_all.tbl CDD NF040883 NF040883 468819 amid_act_ActS amidase activator ActS. 242 matched cddid_all.tbl CDD NF040884 NF040884 468820 acetylneur_anom N-acetylneuraminate anomerase. 155 matched cddid_all.tbl CDD NF040885 NF040885 468821 diguan_DgcJ diguanylate cyclase DgcJ. 490 matched cddid_all.tbl CDD NF040886 NF040886 468822 cyt_C_like_Sec multiheme c-type cytochrome (seleno)protein ExtKL. Most members of this family are selenoproteins. The gene symbol ExtKL predates recognition that a UGA codon separate ExtK from ExtL actually encodes a selenocysteine residue. 423 matched cddid_all.tbl CDD NF040887 NF040887 468823 trans_reg_YciT DNA-binding transcriptional regulator YciT. Involved in osmolarity control regulation 246 matched cddid_all.tbl CDD NF040888 NF040888 468824 trans_reg_YafC DNA-binding transcriptional regulator YafC. 293 matched cddid_all.tbl CDD NF040889 NF040889 468825 trans_reg_YeiE DNA-binding transcriptional regulator YeiE. 288 matched cddid_all.tbl CDD NF040890 NF040890 468826 trans_reg_YgbI DNA-binding transcriptional repressor YgbI. 253 matched cddid_all.tbl CDD NF040891 NF040891 468827 colicin_tol_CbrC PF03691 family colicin E2 tolerance protein CbrC. 195 matched cddid_all.tbl CDD NF040893 NF040893 468828 SAVMC3_10250 SAVMC3_10250 family protein. 236 matched cddid_all.tbl CDD NF040894 NF040894 468829 puhB_PGC photosynthetic complex putative assembly protein PuhB. 176 matched cddid_all.tbl CDD NF040895 NF040895 468830 MFS_effux_SdrM multidrug efflux MFS transporter SdrM. 441 matched cddid_all.tbl CDD NF040896 NF040896 468831 SP_0009_fam SP_0009 family protein. 32 matched cddid_all.tbl CDD NF040897 NF040897 468832 SPJ_0845_Nterm SPJ_0845 N-terminal domain. 25 matched cddid_all.tbl CDD NF040898 NF040898 468833 CC_mini_metal LDCC motif small metal-binding domain. This small and previously undescribed domain, just over 30 amino acids in length, occurs primarily in small proteins of unknown function. It is identified as a probable heavy metal-binding domain by its CysCys pair (seen often in mercury resistance proteins), by the presence of metal-binding or transport domains such PF00403, N-terminal or C-terminal to this domain, in longer members of the family, in some cases by local genomic context. 31 matched cddid_all.tbl CDD NF040899 NF040899 468834 ryptide_rSAM radical SAM/SPASM ryptide class RiPP maturase. 464 matched cddid_all.tbl CDD NF040900 NF040900 468835 porin_ExtI selenite/tellurite reduction operon porin ExtI. 399 matched cddid_all.tbl CDD NF040901 NF040901 468836 SeO3_TeO2_ExtH selenite/tellurite reduction operon rhodanese-like protein ExtH. 426 matched cddid_all.tbl CDD NF040902 NF040902 468837 NuoF_pre_CCxxC CCxxC motif-containing NuoF prefix domain. This domain of about 50 residues, containing seven invariant Cys residues, is a rare N-terminal extension to the NADH-quinone oxidoreductase subunit NuoF. 53 matched cddid_all.tbl CDD NF040903 NF040903 468838 GguC GguC family protein. 329 matched cddid_all.tbl CDD NF040904 NF040904 468839 PhrA_Strep PhrA family quorum-sensing system peptide. 56 matched cddid_all.tbl CDD NF040905 NF040905 468840 GguA sugar ABC transporter ATP-binding protein. 500 matched cddid_all.tbl CDD NF040906 NF040906 468841 GguB sugar ABC transporter permease. 375 matched cddid_all.tbl CDD NF040907 NF040907 468842 ChvE sugar ABC transporter substrate-binding protein. 319 matched cddid_all.tbl CDD NF040908 NF040908 468843 CPC_1213_fam CPC_1213 family protein. 42 matched cddid_all.tbl CDD NF040909 NF040909 468844 OadG_rel_small OadG-related small transporter subunit. Members of this family are transporter subunits of small size, related to the N-terminal region of OadG the oxaloacetate decarboxylase gamma subunit. OadG itself is described the longer model PF04277. 36 matched cddid_all.tbl CDD NF040910 NF040910 468845 CD1375_fam CD1375 family phage-related protein. Members of this family of usually small proteins are found typically in prophage regions of Gram-positive bacteria. 34 matched cddid_all.tbl CDD NF040911 NF040911 468846 KGW_Acineto KGW motif small protein. Members of this family of small proteins are found in the genus Acinetobacter. The family is named for KGW motif that is its best-conserved motif, at the midpoint of the 40 amino acid length sequence. C-terminal to that motif, the sequence is extremely hydrophobic. Members are found encoded next to a YqfO/Nif3 family protein. The function is unknown. 38 matched cddid_all.tbl CDD NF040912 NF040912 468847 SGM_5486_fam SGM_5486 family transporter-associated protein. Members of this family, found in the genus Streptomyces, regularly are found encoded next to an MFS transporter gene. Proteins average about 40 amino acids in length, with the last 25 extremely hydrophobic. 37 matched cddid_all.tbl CDD NF040913 NF040913 468848 DsrE_rel_ELSE SaoD/DsrE family protein. Members of this family are closely related to SaoD (see NF040732), and both families are distantly related to DsrE. 124 matched cddid_all.tbl CDD NF040914 NF040914 468849 Mrt_core myxosortase core domain. 108 matched cddid_all.tbl CDD NF040915 NF040915 468850 CPBP_fam_mrtZ MrtZ family glutamic-type intramembrane protease. 275 matched cddid_all.tbl CDD NF040916 NF040916 468851 MamD magnetosome protein MamD. 316 matched cddid_all.tbl CDD NF040917 NF040917 468852 Mms6 magnetic particle specific iron-binding protein Mms6. 155 matched cddid_all.tbl CDD NF040918 NF040918 468853 LPFR_fam LPFR motif small protein. This HMM describes an uncharacterized small, hydrophobic protein that is widespread in the genus Streptomyces. Multiple sequence alignment shows a well-conserved start site, patterns of conservative substitution of amino acids, and a best-conserved motif VTLPFRxxARLF. Coding regions for this protein have been systematically underreported previously because of small size, often less than 45 amino acids, and the lack of supporting evidence such as this HMM. 35 matched cddid_all.tbl CDD NF040919 NF040919 468854 Clostri_philic clostri-philic family protein. Members of this unusual, uncharacterized protein family are small in size (about 45 amino acids), rich in charged residues and therefore highly hydrophilic, and largely restricted to the genus Clostridium. We propose the name clostri-philic. The function is unknown. 38 matched cddid_all.tbl CDD NF040920 NF040920 468855 CD1871A_fam CD1871A family CXXC motif-containing protein. Members of this family typically are small proteins (often less than 50 amino acids in length) with a highly conserved C-terminal motif CLECxGIG that features an apparent redox-active disulfide bond. The N-terminal portion is hydrophobic and resembles a transmembrane alpha-helix. 38 matched cddid_all.tbl CDD NF040922 NF040922 468856 flgE_Caulobact flagellar hook protein FlgE. 497 matched cddid_all.tbl CDD NF040924 NF040924 468857 small_MgtU magnesium transporter protection protein MgtU. 28 matched cddid_all.tbl CDD NF040925 NF040925 468858 LD_carbox_ElsL cell wall-recycling L,D-carboxypeptidase ElsL. 164 matched cddid_all.tbl CDD NF040926 NF040926 468859 small_YadW small protein YadW. Next to a transporter, as common for small proteins. Supported by cross species conservation, proteomics, and ribosome profiling. Has some overlap with next gene, but hydrophobic then amphipathic, next to a transporter, looks good. 21 matched cddid_all.tbl CDD NF040927 NF040927 468860 ABC_perm_SloB metal ABC transporter permease subunit. Members of this family are metal ABC transporter permease subunits, including SloB from Streptococcus mutans and a number of others, closely related but characterized as acting on different panels of metals, and named in a variety of ways. The SloABC transporter, for example, is characterized as acting on manganese and iron, but its regulator SloR responds only to manganese. 271 matched cddid_all.tbl CDD NF040928 NF040928 468861 ABC_lipo_SloC metal ABC transporter substrate-binding lipoprotein. Members of this family, such as SloC from Streptococcus mutans, are lipoproteins found in metal ABC transporter cassettes. The panel of metals bound and transported can vary from member to member but typically includes manganese, and names provided in publications differ as well. It appears that some members of this so-called LraI family of lipoproteins moonlight as adhesins. 304 matched cddid_all.tbl CDD NF040929 NF040929 468862 quorum_TF_HapR LuxR/HapR/OpaR family quorum-sensing transcriptional regulator. Members of this family are closely related quorum-sensing master transcriptional regulators in the genus Vibrio, and belong to the broader TetR family, in the genus Vibrio. Members include the virulence gene master regulator HapR in V. cholerae, LuxR in Vibrio harveyi, OpaR in Vibrio parahaemolyticus, and SmcR in Vibrio vulnificus. 200 matched cddid_all.tbl CDD NF040930 NF040930 468863 ABC_arch_GlcS glucose ABC transporter substrate-binding protein GlcS. 443 matched cddid_all.tbl CDD NF040931 NF040931 468864 ABC_arch_GlcT glucose ABC transporter permease GlcT. 278 matched cddid_all.tbl CDD NF040932 NF040932 468865 ABC_arch_GlcU glucose ABC transporter permease GlcU. 272 matched cddid_all.tbl CDD NF040933 NF040933 468866 ABC_arch_GlcV glucose ABC transporter ATP-binding protein GlcV. 357 matched cddid_all.tbl CDD NF040935 NF040935 468867 helicase_Hel308 ATP-dependent DNA helicase Hel308. 704 matched cddid_all.tbl CDD NF040936 NF040936 468868 hexpp_archaea hexaprenyl pyrophosphate synthase. 275 matched cddid_all.tbl CDD NF040937 NF040937 468869 HerA_Thermprot DNA double-strand break repair helicase HerA. 487 matched cddid_all.tbl CDD NF040938 NF040938 468870 KDG_KDGal_kin bifunctional 2-dehydro-3-deoxygluconokinase/2-dehydro-3-deoxygalactonokinase. 305 matched cddid_all.tbl CDD NF040939 NF040939 468871 trans_reg_lrs14 HTH-type transcriptional regulator Lrs14. 118 matched cddid_all.tbl CDD NF040941 NF040941 468872 GGGWT_bact fibrinogen-like bacterial YCDxxxxGGGW domain. Pfam model PF00147, about 220 amino acids long, describes a conserved domain found in eukaryotic proteins such as fibrinogen beta and gamma chains, fincolin, and angiopoietin. This model describes a small homology domain, about 46 amino acids long, found in the PF00147 homology region of those proteins but also as a much shorter homology domain in bacterial proteins that may lack homology to those proteins, or to each other, outside this region. The signature motif, at the C-terminus of this domain, is YCDxTTDGGGWxLV. 46 matched cddid_all.tbl CDD NF040942 NF040942 468873 hypo_ExtJ selenite/tellurite reduction operon protein ExtJ. 105 matched cddid_all.tbl CDD NF040943 NF040943 468874 cytoc3_ExtM selenite/tellurite reduction operon c-type cytochrome ExtM. 599 matched cddid_all.tbl CDD NF040944 NF040944 468875 MYPE2350_fam MYPE2350 family membrane protein. Members of this family are membrane proteins as found in a paralogous family in Mycoplasma penetrans. Note that Pfam model PF07666 described this family first (incorrectly calling it family 26 instead of family 6), but that model also pulls in a large number of apparently unrelated hydrophobic bacterial proteins as well. This model is designated equivalog in order to give it higher precedence as an annotation rule than other rules that are less specific. 128 matched cddid_all.tbl CDD NF040945 NF040945 468876 CCC_membrane CCC motif membrane protein. Members of this family average about 150 amino acids in length and are hydrophobic, with several probable transmembrane alpha helices. A notable feature is a Cys-rich cluster, often CCC, starting at about position 22. Members of both this family and NF040944 previously were both included in Pfam model PF07666. But while both families are hydrophobic, they appear not to be truly homologous. NF040944 identifies members of a paralogous family in Mycoplasma penetrans that includes protein MYPE2350, and consequently some members of this family have carried names suggesting (improperly, we think) a relationship to that family. 99 matched cddid_all.tbl CDD NF040946 NF040946 468877 PSII_PsbP photosystem II reaction center PsbP. 180 matched cddid_all.tbl CDD NF040947 NF040947 468878 trans_reg_LysM HTH-type transcriptional regulator LysM. 136 matched cddid_all.tbl CDD NF040948 NF040948 468879 alpha_gluc_MalA alpha-glucosidase MalA. 626 matched cddid_all.tbl CDD NF040949 NF040949 468880 minchrom_main_MCM minichromosome maintenance protein MCM. 681 matched cddid_all.tbl CDD NF040950 NF040950 468881 archin_ph_syn archaetidylinositol phosphate synthase. 191 matched cddid_all.tbl CDD NF040951 NF040951 468882 CRSPR_nucase CRISPR system ring nuclease. 322 matched cddid_all.tbl CDD NF040952 NF040952 468883 Arch_mtprotase_TldD zinc metalloprotease TldD. 443 matched cddid_all.tbl CDD NF040953 NF040953 468884 Arch_udg type-4 uracil-DNA glycosylase. 183 matched cddid_all.tbl CDD NF040954 NF040954 468885 Arch_KDGaldase bifunctional 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase. 288 matched cddid_all.tbl CDD NF040955 NF040955 468886 Arch_DPS DNA protection during starvation protein. 177 matched cddid_all.tbl CDD NF040956 NF040956 468887 Arch_Xpf_endonucase 3'-flap repair endonuclease Xpf. 222 matched cddid_all.tbl CDD NF040957 NF040957 468888 Arch_PMK phosphomevalonate kinase. 316 matched cddid_all.tbl CDD NF040959 NF040959 468889 MamA magnetosome protein MamA. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. Proteins of this family typically contain five tetra-trico-peptide repeat (TPR) motifs. Based on structural analyses, MamA forms a large homooligomer through self-recognition to regulate protein-protein interaction in magnetosomes. 204 matched cddid_all.tbl CDD NF040960 NF040960 468890 MamE magnetosome formation protease MamE. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. Proteins of this family are serine proteases involved in the maturation (membrane growth) of magnetosomes through cleaving magnetosome proteins. 661 matched cddid_all.tbl CDD NF040961 NF040961 468891 MamO magnetosome protein MamO. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. Proteins of this family are essential in the formation of bacterial magnetosomes. MamO promotes crystal nucleation and activates the MamE protease. 648 matched cddid_all.tbl CDD NF040962 NF040962 468892 near_HgcAB HgcAB-associated protein. Nearly have the members of this mostly archaeal protein family occur in species with methylmercury formation proteins HgcA and HgcB, encoded next to HgcA. 70 matched cddid_all.tbl CDD NF040963 NF040963 468893 MamI magnetosome protein MamI. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. It has been reported that proteins of this family were involved in magnetosome nucleation in MTB and were essential for magnetosome formation. 69 matched cddid_all.tbl CDD NF040964 NF040964 468894 MamK MamK family actin-like protein. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. Proteins of this family include the magnetosome protein MamK, which is encoded by the mamK gene on the magnetosome island (MAI), and MamK paralogs/homologs. It has been reported that MamK and MamK paralogs are important for magnetosome chain formation in MTB. MamK family proteins can also be found in bacteria without magnetosomes. 333 matched cddid_all.tbl CDD NF040965 NF040965 468895 MamP magnetosome magnetite formation protein MamP. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. The MamP protein is involved in biomineralization through redox-control of magnetite formation in MTB. 286 matched cddid_all.tbl CDD NF040966 NF040966 468896 MamQ magnetosome protein MamQ. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. Proteins of this family are essential for magnetosome formation. 221 matched cddid_all.tbl CDD NF040967 NF040967 468897 cytc_ExtN selenite/tellurite reduction operon c-type cytochrome ExtN. 416 matched cddid_all.tbl CDD NF040968 NF040968 468898 FeS_ExtO selenite/tellurite reduction operon b-type cytochrome iron-sulfur cluster-binding subunit ExtO. 417 matched cddid_all.tbl CDD NF040969 NF040969 468899 cytb_ExtP selenite/tellurite reduction operon b-type cytochrome ExtP. 205 matched cddid_all.tbl CDD NF040970 NF040970 468900 memb_ExtQ selenite/tellurite reduction operon b-type cytochrome membrane protein ExtQ. 132 matched cddid_all.tbl CDD NF040971 NF040971 468901 cytc_ExtS selenite/tellurite reduction operon c-type cytochrome lipoprotein ExtS. 262 matched cddid_all.tbl CDD NF040972 NF040972 468902 T6SS_VF_TecA type 6 secretion system effector deamidase TecA. TecA (T6SS effector protein affecting cytoskeletal architecture), a type 6 secretion system effector confirmed as a virulence factor of Burkholderia cepacia in a mouse model, is a deamidase that inactivates RhoA and other Rho GTPases in host cells. 159 matched cddid_all.tbl CDD NF040973 NF040973 468903 restrict_Sau3AI Sau3AI family type II restriction endonuclease. Members of this family include type II restriction enzymes such as Sau3AI, while excluding proteins more closely related to the DNA repair protein MutH. Both Sau3AI and MutH endonucleases act on GATC sequences. 464 matched cddid_all.tbl CDD NF040974 NF040974 468904 RepABC_RepC plasmid replication protein RepC. 393 matched cddid_all.tbl CDD NF040975 NF040975 468905 leader_RepB_LM IncL/M-type plasmid replication leader peptide RepB. 16 matched cddid_all.tbl CDD NF040976 NF040976 468906 RepC_IncLM IncL/M type plasmid replication protein RepC. 75 matched cddid_all.tbl CDD NF040977 NF040977 468907 RepA_IncFII_LM plasmid replication initiator RepA. Members of this family are the plasmid replication initiator protein RepA, as the term is used in IncFII (see TIGR03474) and IncL/M plasmids. Other RepA proteins may have no readily detectable homology. 265 matched cddid_all.tbl CDD NF040978 NF040978 468908 Ve_IatC_Nterm inverse autotransporter adhesin IatC N-terminal domain. The inverse autotransporter (type Ve secretion protein) IatC contains a central region that is variable in the number of repeats seen, and averages about 3000 amino acids in length. This HMM describes a mostly non-repetitive region N-teminal to the architectural differences from different repeat counts are seen. IatC can contribute to biofilm formation. 1065 matched cddid_all.tbl CDD NF040979 NF040979 468909 Ve_Ilp_Nterm inverse autotransporter adhesin Ilp N-terminal domain. Ilp (Intimin/invasin-Like Protein), as found in Yersinia, is an inverse autotransporter (type Ve secretion protein) that can have over 40 repeats of the Bacterial Ig-like (BIG) domain (PF02369) and has an average length over 4000 amino acids. This HMM describes the non-repetitive N-terminal domain. 550 matched cddid_all.tbl CDD NF040980 NF040980 468910 Ve_Inv_Crono_N inverse autotransporter invasin Inv N-terminal domain. Inv, as the term is used in Cronobacter sakazakii, is an inverse autotransporter virulence factor that mediates invasion of host cells. Member proteins can have variable numbers of the Bacterial Ig-like (BIG) domain (PF02369). This HMM describes the non-repetitive N-terminal domain only. 350 matched cddid_all.tbl CDD NF040981 NF040981 468911 Ve_YrIlm_NTERM YrIlm family inverse autotransporter adhesin N-terminal domain. 477 matched cddid_all.tbl CDD NF040982 NF040982 468912 ComGD competence type IV pilus minor pilin ComGD. 140 matched cddid_all.tbl CDD NF040983 NF040983 468913 BimA_second trimeric autotransporter actin-nucleating factor BimA. This HMM describes BimA (Burkholderia intracellular motility A), WP_004266405.1-like proteins in Burkholderia mallei or B. pseudomallei. The term BimA has also been used for WP_011205626.1-like homologs that have a very different N-terminal half. 382 matched cddid_all.tbl CDD NF040984 NF040984 468914 BimA_first trimeric autotransporter actin-nucleating factor BimA. BimA (B. pseudomallei intracellular motility protein A) is a trimeric autotransporter, homologous in its C-terminal half to a number of trimeric autotransporter adhesins. It is a virulence factor that nucleates actin, so that actin polymerization can drive escape by B. pseudomallei out of one cell and into a neighboring cell. HMM NF040983 describes a homolog with similar activity but substantial difference in sequence architecture in the N-terminal region. 517 matched cddid_all.tbl CDD NF040985 NF040985 468915 MamG magnetosome protein MamG. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. Proteins of this family regulate magnetite crystal size during biomineralization. 102 matched cddid_all.tbl CDD NF040986 NF040986 468916 MamH magnetosome biogenesis transporter MamH. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. It has been reported that proteins of this family were iron transporters involved in biomineralization of magnetosomes. 419 matched cddid_all.tbl CDD NF040987 NF040987 468917 MamJ magnetosome protein MamJ. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. It has been reported that proteins of this family were involved in the assembly of magnetosome chains. 412 matched cddid_all.tbl CDD NF040988 NF040988 468918 MamL magnetosome protein MamL. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. Proteins of this family are involved in magnetite crystal maturation. 78 matched cddid_all.tbl CDD NF040989 NF040989 468919 MamN magnetosome biogenesis transporter MamN. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. Proteins of this family are probably ion transporters involved in biomineralization. 437 matched cddid_all.tbl CDD NF040990 NF040990 468920 MamR magnetosome protein MamR. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. Proteins of this family have a predicted DNA-binding domain and play an important role in crystal number and size control. 91 matched cddid_all.tbl CDD NF040991 NF040991 468921 MamS magnetosome protein MamS. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. Proteins of this family are involved in magnetite crystal growth. 186 matched cddid_all.tbl CDD NF040992 NF040992 468922 MamT magnetosome protein MamT. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. Proteins of this family have magnetochrome domains and may play a role in magnetite crystal maturation. 151 matched cddid_all.tbl CDD NF040993 NF040993 468923 MamU lipid kinase MamU. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. Proteins of this family are encoded by the mamU gene on the mamAB operon and predicted to be lipid kinases, but their roles in magnetosome formation have not been determined yet. 296 matched cddid_all.tbl CDD NF040994 NF040994 468924 MamV CDF transporter MamV. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. Proteins of this family are encoded by the mamV gene on the mamAB operon and predicted to be transporters, but their roles in magnetosome formation have not been determined yet. 319 matched cddid_all.tbl CDD NF040995 NF040995 468925 MamW magnetosome protein MamW. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. Proteins of this family are involved in magnetosome alignment. 117 matched cddid_all.tbl CDD NF040996 NF040996 468926 MamX magnetosome protein MamX. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. Proteins of this family are involved in biomineralization through redox control. 264 matched cddid_all.tbl CDD NF040997 NF040997 468927 MamY liposome tubulation protein MamY. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. Proteins of this family are involved in liposome tubulation during the formation of magnetosomes. 325 matched cddid_all.tbl CDD NF040998 NF040998 468928 MamZ magnetosome biogenesis transporter MamZ. Magnetosomes are special lipid-bound organelles that comprise magnetic mineral crystals in magnetotactic bacteria (MTB). Magnetosomes are important for MTB to search for preferred microaerophilic environment. Proteins of this family are predicted to be MFS transporter and involved in redox control of biomineralization. 632 matched cddid_all.tbl CDD NF040999 NF040999 468929 pilin_ComGC competence type IV pilus major pilin ComGC. ComGC, encoded in the comG operon, is the major pilin of a type IV pilus involved in natural transformation of monoderm bacteria (those lacking an outer membrane) such as Bacillus subtilis and Streptococcus pneumoniae. In the seed alignment, Bacillus proteins have a pair of Cys residues likely to form a disulfide bond while Streptococcus proteins lack Cys residues. 84 matched cddid_all.tbl CDD NF041000 NF041000 468930 ATPase_ComGA competence type IV pilus ATPase ComGA. 265 matched cddid_all.tbl CDD NF041002 NF041002 468931 pilin_ComGF competence type IV pilus minor pilin ComGF. ComGF is one of several minor pilins in the type IV pilus involved in the competence system of natural transformation by various Gram-positive bacteria. Oddly, while nearly all members have an N-terminal region with a consensus site for cleavage and methylation, ComGF from Bacillus subtilis appears N-terminally truncated, and may be functional despite the truncation. 138 matched cddid_all.tbl CDD NF041003 NF041003 468932 GGPP_syn geranylgeranyl diphosphate synthase. 326 matched cddid_all.tbl CDD NF041004 NF041004 468933 Beta_gal_BgaS beta-galactosidase BgaS. 479 matched cddid_all.tbl CDD NF041005 NF041005 468934 cell_div_CdvB1_B2 cell division protein CdvB1/B2. 212 matched cddid_all.tbl CDD NF041006 NF041006 468935 cell_div_CdvC cell division protein CdvC. 371 matched cddid_all.tbl CDD NF041007 NF041007 468936 cell_div_CdvA cell division protein CdvA. 235 matched cddid_all.tbl CDD NF041008 NF041008 468937 cell_div_CdvB cell division protein CdvB. 260 matched cddid_all.tbl CDD NF041009 NF041009 468938 cell_div_CdvB3 cell division protein CdvB3. 164 matched cddid_all.tbl CDD NF041010 NF041010 468939 glycosy_Agl16 glycosylation protein Agl16. 351 matched cddid_all.tbl CDD NF041011 NF041011 468940 dihydoor_dh_Arch dihydroorotate dehydrogenase PyrD. 289 matched cddid_all.tbl CDD NF041012 NF041012 468941 T4P_ComGB competence type IV pilus assembly protein ComGB. Members of this family occur in Gram-positive bacteria as part of a type IV pilus system used for DNA binding and uptake when species such as Streptococcus pneumoniae or Bacilus subtilis are in a competent state for natural transformation. Members of this family, typically called ComGB (second protein of the ComG operon), belong more broadly to the family of GspF, part of type 2 secretion systems (T2SS) in Gram-negative bacteria. 333 matched cddid_all.tbl CDD NF041013 NF041013 468942 T4P_ComGE competence type IV pilus minor pilin ComGE. 83 matched cddid_all.tbl CDD NF041014 NF041014 468943 pilin_ComGG_2 competence type IV pilus minor pilin ComGG. ComGG is an especially variable protein of ComG-like DNA binding/uptake type IV pilus formation systems. This HMM identifies ComGG proteins as found in Streptococcus pneumoniae, not Bacillus subtilis. 101 matched cddid_all.tbl CDD NF041015 NF041015 468944 UDPsulfquin_syn UDP-sulfoquinovose synthase. 384 matched cddid_all.tbl CDD NF041016 NF041016 468945 trans_reg_ArnR HTH-type transcriptional activator ArnR. 269 matched cddid_all.tbl CDD NF041017 NF041017 468946 DNA_import_CedB DNA import protein CedB. 590 matched cddid_all.tbl CDD NF041018 NF041018 468947 glyceraldDH_alpha glyceraldehyde dehydrogenase subunit alpha. 741 matched cddid_all.tbl CDD NF041019 NF041019 468948 glyceraldDH_beta glyceraldehyde dehydrogenase subunit beta. 280 matched cddid_all.tbl CDD NF041020 NF041020 468949 glyceraldDH_gamma glyceraldehyde dehydrogenase subunit gamma. 162 matched cddid_all.tbl CDD NF041021 NF041021 468950 SCO5717_Nterm SCO5717 family growth-regulating ATPase N-terminal domain. Members of this unusual protein family have a short domain described by this HMM at the N-terminus, then (typically) a long, low-complexity, typically Pro-rich region, then a AAA+ family ATPase domain, and then another region of low-complexity sequence. 48 matched cddid_all.tbl CDD NF041022 NF041022 468951 rodlin_AB rodlin. 134 matched cddid_all.tbl CDD NF041023 NF041023 468952 PP0621_fam PP0621 family protein. Members of this family of small proteins have an N-terminal signal peptide and three invariant Cys resisdues, two in a CXXC motif. 70 matched cddid_all.tbl CDD NF041024 NF041024 468953 acVLRF1_NCBI acVLRF1 family peptidyl-tRNA hydrolase. Members of this family, found in many Actinobacteria, share a consistent architecture and belong to the larger set of Vms1/Ankzf1 family peptidyl-tRNA hydrolase, which release nascent polypeptide chains from stalled ribosomes. The broader family is quite variable in domain architecture. 208 matched cddid_all.tbl CDD NF041025 NF041025 468954 antiphage_deaminase anti-phage dCTP deaminase. It has been shown that proteins of this family prevented bacteria from phage infections by depleting deoxycytidine triphosphate (dCTP), which are important for the replication of viruses. The anti-phage dCTP deaminases have an N-terminal kinase and a C-terminal dCTP deaminase domains, however, the housekeeping dCTP deaminases usually do not have the N-terminal kinase. 435 matched cddid_all.tbl CDD NF041026 NF041026 468955 antiphage_dGTPase anti-phage deoxyguanosine triphosphatase. Proteins of this family are distant homologues of human antiviral protein SAMHD1. It has been shown that proteins of this family protected bacteria from phage infection by degrading dGTP into phosphate-free deoxyguanosine. The anti-phage dGTPase may also be involved in other biological processes. 426 matched cddid_all.tbl CDD NF041027 NF041027 468956 GSU2204_Se_pt_1 GSU2204 family CXXCH-containing (seleno)protein, part 1. Most members of this family, including founding member GSU2204, are selenoproteins that average about 730 amino acids in length, with a cytochrome c-like CxxCH motif and also a selenocysteine site, typically GUA, about 145 amino acids from the proper C-terminus. This family was listed in Zhang, et al., in Biomolecules (2022). This HMM describes the family up to the residue immediately N-terminal to what is normally a selenocysteine residue. Cutoffs are set so as to exclude most homologs from related clades in which both the CXXCH and the U/C sites are missing, suggesting a similar architecture but different function. 578 matched cddid_all.tbl CDD NF041028 NF041028 468957 decahem_GSU2203 GSU2203 family decaheme c-type cytochrome. Members of this family are DmsE family decaheme c-type cytochromes (see TIGR03508), but belong to a narrow clade that includes GSU2203, and that co-occurs with a GSU2204 family protein, most of which are selenoproteins (see NF041027). 316 matched cddid_all.tbl CDD NF041029 NF041029 468958 Mre11_Pyroc DNA double-strand break repair protein Mre11. 438 matched cddid_all.tbl CDD NF041030 NF041030 468959 Mre11_Halo DNA double-strand break repair protein Mre11. 360 matched cddid_all.tbl CDD NF041031 NF041031 468960 Mre11_Sulfo DNA double-strand break repair protein Mre11. 373 matched cddid_all.tbl CDD NF041032 NF041032 468961 NurA_Pyro DNA double-strand break repair nuclease NurA. 448 matched cddid_all.tbl CDD NF041033 NF041033 468962 NurA_Sulf DNA double-strand break repair nuclease NurA. 331 matched cddid_all.tbl CDD NF041034 NF041034 468963 Rad50_Sulf DNA double-strand break repair ATPase Rad50. 872 matched cddid_all.tbl CDD NF041035 NF041035 468964 Rad50_Halo DNA double-strand break repair ATPase Rad50. 883 matched cddid_all.tbl CDD NF041036 NF041036 468965 decaheme_TF multiheme cytochrome-associated LysR family transcriptional regulator. Members of this family, including founding member GSU2202 from Geobacter sulfurreducens PCA, are LysR family transcriptional regulators found regularly in the vicinity of multiheme cytochromes such as GSU2203, a decaheme c-type cytochrome. 301 matched cddid_all.tbl CDD NF041037 NF041037 468966 microcin_B17 microcin B17 family TOMM. Microcin B17 is a thiazole/oxazole modified microcin (TOMM), a type of ribosomally translated and post-translationally modified natural product (RiPP). It is a toxin that corrupts gyrase activity and causes gyrase to to cleave chromosomal DNA, killing the cell. 69 matched cddid_all.tbl CDD NF041038 NF041038 468967 FslA rhizoferrin biosynthesis protein FslA. FslA and FslC are the two major enzymes involved in rhizoferrin synthesis in Francisella, which has a reduced genome and cannot directly use putrescine to synthesize siderophores. Rhizoferrin biosynthesis in Fransicella starts with ornithine as the substrate. First, FslA mediates the condensation of ornithine with citrates to produce N-citrylornithine, which is then decarboxylated by FslC to generate N-citrylputrescine. Finally, FslA mediates another round of condensation of N-citrylputrescine with citrates to generate rhizoferrin. 639 matched cddid_all.tbl CDD NF041039 NF041039 468968 FslC rhizoferrin biosystnesis N-citrylornithine decarboxylase FslC. FslA and FslC are the two major enzymes involved in rhizoferrin synthesis in Francisella, which has a reduced genome and cannot directly use putrescine to synthesize siderophores. Rhizoferrin biosynthesis in Fransicella starts with ornithine as the substrate. First, FslA mediates the condensation of ornithine with citrates to produce N-citrylornithine, which is then decarboxylated by FslC to generate N-citrylputrescine. Finally, FslA mediates another round of condensation of N-citrylputrescine with citrates to generate rhizoferrin. 418 matched cddid_all.tbl CDD NF041040 NF041040 468969 FslB rhizoferrin export MFS transporter FslB. 417 matched cddid_all.tbl CDD NF041041 NF041041 468970 FslD rhizoferrin import MFS transporter FslD. 396 matched cddid_all.tbl CDD NF041042 NF041042 468971 FslE rhizoferrin import outer membrane protein FslE. 505 matched cddid_all.tbl CDD NF041043 NF041043 468972 BPSS1780_fam BPSS1780 family membrane protein. 246 matched cddid_all.tbl CDD NF041044 NF041044 468973 GIVxVP GIVxVP protein. GIVxVP is a rare, small, uncharacterized protein found in Cyanobacteria such as Synechococcus lacustris, Cyanobium gracile, and Microcystis elabens, in a conserved gene neighborhood of unknown function. Member sequences are about 70 amino acids in length with two apparent transmembrane segments. 57 matched cddid_all.tbl CDD NF041045 NF041045 468974 RsbA_anti_sig anti-sigma factor RsbA family regulatory protein. Members of this family have MEDS sensory domain in the N-terminal region and a histidine kinase-like ATPase domain in the C-terminal region. RsbA of Streptomyces coelicolor, the founding member of this family, was suggested as an anti-sigma factor by genomic location preceding sigB, by homology to RsbW of Bacillus subtilis, and by binding to SigmaB and effects on its activity. Members of this family include full-length homologs, but it appears members they may perform different regulatory functions in different lineages. Therefore, the symbol RsbA will be inappropriate for some family members, such as PrsR from Streptomyces avermitilis. 304 matched cddid_all.tbl CDD NF041046 NF041046 468975 UGSC_fam "UGSC family (seleno)protein. This family includes selenoprotein members with a UGSC motif, and non-selenoprotein members with a CGSC motif. Selenoprotein members were discussed in Zhang, et al., ""Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective"" (2022)." 147 matched cddid_all.tbl CDD NF041047 NF041047 468976 GSU3128_fam GSU3128 family (seleno)protein. This selenoprotein family is described as distantly related to the peroxidase/peroxynitrite reductase system component AhpD. 84 matched cddid_all.tbl CDD NF041048 NF041048 468977 TusA_like_YeeD thiosulfate utilization sulfurtransferase TsuB/YeeD. YeeD (TsuB) is a TusA family putative sulfurtransferase associated with thiosulfate utilization. 72 matched cddid_all.tbl CDD NF041049 NF041049 468978 thio_trans_TsuA thiosulfate utilization transporter TsuA/YeeE. TsuA (YeeE) is one of two paralogous transporters in Escherichia coli described by Pfam model PF04143. TsuA, and adjacent putative sulfurtransferase TsuB, are involved in thiosulfate utilization. 348 matched cddid_all.tbl CDD NF041051 NF041051 468979 SelTWH_Campy SelT/SelW/SelH family (seleno)protein, Campylobacterial type. Members of this family are primarily (perhaps exclusively) selenoproteins, found in Campylobacter species such as C. lari, but also in members of several other lineages. The protein family is related to SelT, SelW, and SelH, and features a CXXU motif. 70 matched cddid_all.tbl CDD NF041052 NF041052 468980 OsmC_like_Se OsmC-related (seleno)protein. Members of this family are distantly related to the hydroperoxide resistance protein OsmC (osmotically inducible protein) of Escherichia. Proteins found by the HMM include large numbers of selenoproteins, most of which currently are known only from Metagenome-Assembled Genomes (MAGs) of uncultured organisms, a large fraction of which are assigned to the Chloroflexi. 144 matched cddid_all.tbl CDD NF041053 NF041053 468981 CobW_rel_Se CobW-related selenoprotein. 195 matched cddid_all.tbl CDD NF041054 NF041054 468982 WAxxUGC_long ResA-like WAxxUGC motif-containing protein, long form. Members of this family average about 350 amino acids in length. Many are selenoproteins, with a motif WAxxUGC, located in region homologous to smaller proteins such as the thiol-disulfide oxidoreductase ResA of Bacillus. 351 matched cddid_all.tbl CDD NF041055 NF041055 468983 ryptide_RrrA ryptide family R-Y-crosslinked RiPP peptide. 41 matched cddid_all.tbl CDD NF041056 NF041056 468984 ryptide_ex_MFS ryptide export MFS transporter. Members of this family are MFS transporters that belong to a system in which ryptide precursor RiPP peptides are produced, modified by a radical SAM/SPASM enzyme that introduces an arginine-tryptophan crosslink, and exported. 392 matched cddid_all.tbl CDD NF041057 NF041057 468985 Rcas_1661_fam_Se Rcas_1661 family thioredoxin-like (seleno)lipoprotein. Most known members of this lipoprotein family are selenoproteins, but the family is named for Rcas_1661 (WP_157042591.1), with a CXXC rather than UXXC motif. Members are found primarily among the Chloroflexi. 247 matched cddid_all.tbl CDD NF041059 NF041059 468986 DpdA tRNA-guanine transglycosylase DpdA. 405 matched cddid_all.tbl CDD NF041060 NF041060 468987 DpdB DGQHR domain-containing protein DpdB. 352 matched cddid_all.tbl CDD NF041061 NF041061 468988 DpdD protein DpdD. 703 matched cddid_all.tbl CDD NF041062 NF041062 468989 DpdE protein DpdE. 1048 matched cddid_all.tbl CDD NF041063 NF041063 468990 DpdF protein DpdF. 813 matched cddid_all.tbl CDD NF041064 NF041064 468991 DpdG protein DpdG. 291 matched cddid_all.tbl CDD NF041065 NF041065 468992 DpdH protein DpdH. 1005 matched cddid_all.tbl CDD NF041066 NF041066 468993 DpdI protein DpdI. 239 matched cddid_all.tbl CDD NF041067 NF041067 468994 DpdJ protein DpdJ. 1480 matched cddid_all.tbl CDD NF041068 NF041068 468995 DpdK phospholipase D-like domain-containing protein DpdK. 167 matched cddid_all.tbl CDD NF041069 NF041069 468996 IPMS_Sufob isopropylmalate synthase. 371 matched cddid_all.tbl CDD NF041070 NF041070 468997 carrier_LysW_Arch alpha-aminoadipate/glutamate carrier protein LysW/ArgW. involved in lysine biosynthesis via the alpha-aminoadipate pathway and also in arginine biosynthesis 56 matched cddid_all.tbl CDD NF041071 NF041071 468998 Trm10_mtase_Thprot tRNA (adenine(9)-N1)-methyltransferase Trm10. 293 matched cddid_all.tbl CDD NF041072 NF041072 468999 FtrB_double_U FtrB family double-selenoprotein. 121 matched cddid_all.tbl CDD NF041073 NF041073 469000 S-lay_SlaA_Sulfolob S-layer protein SlaA. 1462 matched cddid_all.tbl CDD NF041074 NF041074 469001 quin_ox_SoxA proton pump complex quinol oxidase subunit SoxA. 154 matched cddid_all.tbl CDD NF041075 NF041075 469002 quin_ox_SoxB proton pump complex quinol oxidase subunit SoxB. 468 matched cddid_all.tbl CDD NF041076 NF041076 469003 cyt_b_SoxC proton pump complex cytochrome B SoxC. 542 matched cddid_all.tbl CDD NF041077 NF041077 469004 tRNAmeth_TrmJ_Sulfolob tRNA (cytidine-2'-O-)-methyltransferase TrmJ. 229 matched cddid_all.tbl CDD NF041078 NF041078 469005 cGAS CBASS cGAMP synthase. 339 matched cddid_all.tbl CDD NF041079 NF041079 469006 CBASS_lipase CBASS cGAMP-activated phospholipase. 317 matched cddid_all.tbl CDD NF041080 NF041080 469007 DGGGPL_reductase digeranylgeranylglycerophospholipid reductase. 447 matched cddid_all.tbl CDD NF041081 NF041081 469008 prot_lys_mtase_Arch protein-lysine N-methyltransferase. 142 matched cddid_all.tbl CDD NF041082 NF041082 469009 thermosome_alpha thermosome subunit alpha. 518 matched cddid_all.tbl CDD NF041083 NF041083 469010 thermosome_beta thermosome subunit beta. 519 matched cddid_all.tbl CDD NF041084 NF041084 469011 trehalase_H1_Arch alpha,alpha-trehalase TreH1. 569 matched cddid_all.tbl CDD NF041085 NF041085 469012 trehalase_H2_Arch alpha,alpha-trehalase TreH2. 578 matched cddid_all.tbl CDD NF041086 NF041086 469013 STAUR_1299_fam STAUR_1299 family protein. Members of this family, including STAUR_1299 from Stigmatella aurantiaca, are found so far in genomes of cultured bacteria only if the bacterium belongs to the Deltaproteobacteria. The restriction to the Deltaproteobacteria is less absolute in MAGs (metagenome-assembled genomes). 112 matched cddid_all.tbl CDD NF041088 NF041088 469014 ala_glut_racmase_Arch bifunctional L-alanine/L-glutamate racemase. 381 matched cddid_all.tbl CDD NF041089 NF041089 469015 alpha_gluc_AglA alpha-glucosidase AglA. 464 matched cddid_all.tbl CDD NF041090 NF041090 469016 Cyc-maltodext_AglB cyclomaltodextrinase. 470 matched cddid_all.tbl CDD NF041091 NF041091 469017 asp_aminotase_Arch aspartate aminotransferase. 376 matched cddid_all.tbl CDD NF041092 NF041092 469018 beta-fruc_BfrA beta-fructosidase. 433 matched cddid_all.tbl CDD NF041093 NF041093 469019 CheC_Thtogales CheY-P phosphatase CheC. 201 matched cddid_all.tbl CDD NF041094 NF041094 469020 CheX_Thtogales CheY-P phosphatase CheX. 152 matched cddid_all.tbl CDD NF041095 NF041095 469021 dival_cat_tol_CutA divalent-cation tolerance protein CutA. 100 matched cddid_all.tbl CDD NF041096 NF041096 469022 esterase_EstD esterase EstD. 421 matched cddid_all.tbl CDD NF041097 NF041097 469023 keto_inos_dh_IolM scyllo-inosose 3-dehydrogenase. 385 matched cddid_all.tbl CDD NF041098 NF041098 469024 diketo_inos_hlase_IolN 3-dehydro-scyllo-inosose hydrolase. 307 matched cddid_all.tbl CDD NF041099 NF041099 469025 keto_glucon_epim_IolO 5-keto-L-gluconate epimerase. 269 matched cddid_all.tbl CDD NF041100 NF041100 469026 betagal_LacZ_Ttogales beta-galactosidase LacZ. 1090 matched cddid_all.tbl CDD NF041101 NF041101 469027 manno_glu_gly_synth mannosylglucosylglycerate synthase. 431 matched cddid_all.tbl CDD NF041102 NF041102 469028 endonuc_V_Ttgales endonuclease V. 215 matched cddid_all.tbl CDD NF041103 NF041103 469029 PFKA_PPi_Ttgales diphosphate--fructose-6-phosphate 1-phosphotransferase. 406 matched cddid_all.tbl CDD NF041106 NF041106 469030 ArsC_rel_Se_1 ArsC family (seleno)protein. Weak hits to Pfam model PF03960 and to COG1393 suggest a relationship to glutaredoxin-like arsenate reductase protein ArsC. This family contains significant numbers of selenoproteins. 107 matched cddid_all.tbl CDD NF041107 NF041107 469031 RQC_minor_1 "RQC-minor-1 family DNA-binding protein. The DNA-binding RQC domain (PF09382) appears primarily in RecQ, a DNA helicase involved in recombination, replication, and repair. However, it appears also in this uncharacterized protein family, to which we give the name ""RQC-minor-1 family DNA-binding protein."" A majority of members contain an additional C-terminal predicted zinc-ribbon domain. Members appear not to show any conserved gene neighborhood." 173 matched cddid_all.tbl CDD NF041108 NF041108 469032 RQC_minor_2 "RQC-minor-2 family DNA-binding protein. The DNA-binding RQC domain (PF09382) appears primarily in RecQ, a DNA helicase involved in recombination, replication, and repair. However, it appears also in this long, uncharacterized protein family, to which we give the name ""RQC-minor-2 family DNA-binding protein.""" 465 matched cddid_all.tbl CDD NF041109 NF041109 469033 VF_TspB_C_term virulence factor TspB C-terminus-like domain. Members of this family share a C-terminal domain, perhaps a surface-anchoring domain, with T and B Cell Stimulating Protein B (TspB) of Neisseria meningitidis, an IgG-binding protein that helps confer serum resistance. This short domain (51 residues long) contains two invariant Cys residues and an apparent C-terminal transmembrane segment, suggesting a role in anchoring to the surface of the outer membrane. Member proteins often are found in prophage regions. 51 matched cddid_all.tbl CDD NF041110 NF041110 469034 HPE1_fam_CxxC "plant virulence effector HPE1-like domain. This HMM describes the N-terminal 90 to 100 amino acids of a family bacterial proteins from plant-associated species. Most members of this family have some form of additional C-terminal domain of similar length. However, the best-studied members of this family are shorter proteins, virulence effectors from two plant pathogens, HPE1 (""hypothetical protein effector 1"") from Candidatus Liberibacter solanacearum, and CLIBASIA_00460 from Candidatus Liberibacter asiaticus. Members of this family begin with an N-terminal signal peptide, for apparent Sec-mediated secretion, and nearly all share a CxxC motif." 94 matched cddid_all.tbl CDD NF041111 NF041111 469035 effector_HPE1 "HPE1 family effector. The founding members of this family of virulence factors from bacterial pathogens of plants are HPE1 (""hypothetical protein effector 1"") from Candidatus Liberibacter solanacearum, and CLIBASIA_00460 from Candidatus Liberibacter asiaticus." 99 matched cddid_all.tbl CDD NF041112 NF041112 469036 chap_CsgH_alph curli-like amyloid fiber formation chaperone CsgH. The designation CsgH was given to the broad set of homologs, found outside the Enterobacteriales, of the curli amyloid fiber formation periplasmic chaperone CsgC from species such as Escherichia coli and Salmonella. Members of the seed alignment belong to the Alphaproteobacteria. Because CsgC and CsgH proteins are related, and CsgH is defined broadly, this model does not exclude CsgC proteins, although they are covered also by a more specific HMM NF007507 (PRK10102.1). 90 matched cddid_all.tbl CDD NF041114 NF041114 469037 UPxT_UxV_star UXX-star (seleno)protein family 1. 62 matched cddid_all.tbl CDD NF041115 NF041115 469038 UxxU_metal_bind metal-binding (seleno)protein. Known members of this family are selenoproteins with an exceptional UXXU motif, with two selenocysteines. Known members so far derive primarily from MAGs, and have an N-terminal signal peptide N-terminal to the region represented in the seed alignment. Note that this model represents a specific clade of a more widely distributed domain that frequently appears 3 or 4 times in a single protein, so the domain-specific cutoff is critical to identification. Homologous domains, outside the scope of this model, are found in CopZ family copper chaperones and heavy metal-translocating P-type ATPases. 74 matched cddid_all.tbl CDD NF041116 NF041116 469039 CBASS_cyclase_a CBASS oligonucleotide cyclase. 317 matched cddid_all.tbl CDD NF041117 NF041117 469040 CBASS_cyclase_b CBASS oligonucleotide cyclase. 273 matched cddid_all.tbl CDD NF041118 NF041118 469041 A_G_epim_Thtga L-Ala-D/L-Glu epimerase. 341 matched cddid_all.tbl CDD NF041119 NF041119 469042 CheD_Thtga chemoreceptor glutamine deamidase/glutamate methylesterase CheD. 158 matched cddid_all.tbl CDD NF041120 NF041120 469043 RqcH_arch ribosome rescue protein RqcH, archaeal type. This HMM (built with support from arCOG01695) describes archaeal homologs of the RqcH (Ribosome-associated Quality Control H), involved in release of defective mRNAs that lack a stop codons and so are stuck on ribosomes. Conservation of a role in ribosome rescue for this archaeal family is supported by presence in a conserved gene neighborhood with homologs of Pelota/Dom34 and ABCE1/Rli1 homologs, proteins involved in splitting the ribosome into large and small subunits. 642 matched cddid_all.tbl CDD NF041121 NF041121 469044 SAV_2336_NTERM SAV_2336 family N-terminal domain. This HMM describes an N-terminal domain shared by SAV_2336 (BAC70047.1) whose C-terminal region suggests restriction enzyme activity (PMID: 18456708), and with other proteins with unrelated C-terminal regions. A member protein was also identified in a kanamycin biosynthetic gene cluster (PMID:16766657), while N-terminal regions of two other member proteins were named Trypco1 in a bioinformatic study (PMID:32101166) of predicted bacterial conflict systems. 473 matched cddid_all.tbl CDD NF041122 NF041122 469045 panto_kin_Thplsm pantoate kinase. 298 matched cddid_all.tbl CDD NF041123 NF041123 469046 phpantohe_syn_Arch 4-phosphopantoate--beta-alanine ligase. 213 matched cddid_all.tbl CDD NF041124 NF041124 469047 CoaD_Thcocales phosphopantetheine adenylyltransferase. 156 matched cddid_all.tbl CDD NF041125 NF041125 469048 deph_CoA_kin_Thcocales GTP-dependent dephospho-CoA kinase. 175 matched cddid_all.tbl CDD NF041126 NF041126 469049 FBP_aldo_phos fructose-1,6-bisphosphate aldolase/phosphatase. 356 matched cddid_all.tbl CDD NF041127 NF041127 469050 exo_beta_glucsam exo-beta-D-glucosaminidase. 782 matched cddid_all.tbl CDD NF041128 NF041128 469051 glucosaP_deam_GlmD glucosamine-6-phosphate deaminase. 323 matched cddid_all.tbl CDD NF041129 NF041129 469052 maldex_phorlase_Thcocales maltodextrin phosphorylase. 816 matched cddid_all.tbl CDD NF041130 NF041130 469053 PenR_Burk_TF beta-lactamase transcriptional regulator PenR. PenR, as the term is used in Burkholderia, is a LysR-family transcriptional regulator of adjacent chromosomal class A beta-lactamase genes of the blaPEN family, which include blaPEN-A in B. multivorans, blaPEN-B in B. cenocepacia, etc. 292 matched cddid_all.tbl CDD NF041131 NF041131 469054 RicT_YaaT_fam regulatory iron-sulfur-containing complex subunit RicT. RicT in Bacillus subtilis (originally YaaT) was described as stage 0 sporulation protein affecting phosphorelay signals. However, RicT belongs to a iron-sulfur containing regulatory complex that is conserved also in many non-sporulating species, together with homologs of YmcA (RicA) and YlbF (RicF). 213 matched cddid_all.tbl CDD NF041132 NF041132 469055 DNA_protcyst_Mta_Thcoc methylated-DNA--protein-cysteine methyltransferase. 169 matched cddid_all.tbl CDD NF041133 NF041133 469056 branch_enz_Thcocales 1,4-alpha-glucan branching protein. 553 matched cddid_all.tbl CDD NF041134 NF041134 469057 R1P_kin_Thcocales ADP-dependent ribose-1-phosphate kinase. 291 matched cddid_all.tbl CDD NF041135 NF041135 469058 IPPtranDIPPsyn_Thcocales bifunctional L-myo-inositol-1-phosphate cytidylyltransferase/CDP-L-myo-inositol myo-inositolphosphotransferase. 419 matched cddid_all.tbl CDD NF041136 NF041136 469059 MrpORP iron-sulfur cluster carrier protein MrpORP. 365 matched cddid_all.tbl CDD NF041137 NF041137 469060 B3_blaSPR SPR family subclass B3 metallo-beta-lactamase. Members of this exceptional subfamily within the subclass B3 metallo-beta-lactamases, SPR (described originally in Serratia proteamaculans) have an altered zinc ion binding site that binds a single Zn(2+) only in the absence of substrate, but may recruit a second Zn(2+) after substrate binds. Purified enzyme is effective against benzylpenicillin. The assignment as subclass B3 enzyme is based on homology, not Zn-binding residues. Note that additional examples of functional B3 enzymes with altered Zn-binding sites have been described. 299 matched cddid_all.tbl CDD NF041139 NF041139 469061 TreT_Thcocales trehalose synthase. 412 matched cddid_all.tbl CDD NF041140 NF041140 469062 Trm10AGmtase_Thcocales tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase. 372 matched cddid_all.tbl CDD NF041141 NF041141 469063 tran_reg_TrmBL2 HTH-type transcriptional regulator TrmBL2. 264 matched cddid_all.tbl CDD NF041142 NF041142 469064 PCNA_Inhib PCNA-inhibitor. 65 matched cddid_all.tbl CDD NF041144 NF041144 469065 expansin_EXLX1 expansin EXLX1-like domain. This HMM represents nearly the full length of EXLX1 (YoaJ) of Bacillus subtilis, a cellulose-binding bacterial expansin, and similar domains in related bacteirial proteins. Expansins, which are small and non-catalytic, have the ability to loosen plant cell wall material and improve enzyme access, but an expansin domain can occur as an auxiliary domain in cellulases such as CelA of Clavibacter michiganensis, a bacterial pathogen of tomato plants. Pfam model PF01357 (expansin C-terminal domain), somewhat less than half the size, is related but is oriented toward plant expansin and hits relatively few members of this family above cutoffs (as of version PF01357.23). 192 matched cddid_all.tbl CDD NF041153 NF041153 469066 organophos_OPH organophosphate hydrolase OPH. The organophosphate hydrolase OPH, also called aryldialkylphosphatase (EC 3.1.8.1), Phosphotriesterase, and paraoxon hydrolase, is the product of opd (organophosphate degrading) gene clusters found in mobile elements. It is a zinc ion-binding lipoprotein. 365 matched cddid_all.tbl CDD NF041155 NF041155 469067 encap_f1 family 1 encapsulin nanocompartment shell protein. Capsid-like encapsulin nanocompartments are commonly found in bacteria and archaea. Encapsulin nanocompartments, which are assembled from shell proteins, encapsulate various cargo proteins, typically peroxidases or ferritin-like proteins, to protect cells from oxidative stress caused by peroxide. 260 matched cddid_all.tbl CDD NF041156 NF041156 469068 FolD_Thplmales bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD. 277 matched cddid_all.tbl CDD NF041157 NF041157 469069 Cit_synThplmales citrate synthase. 376 matched cddid_all.tbl CDD NF041158 NF041158 469070 Spm_actase_Thplmales spermidine N(1)-acetyltransferase. 115 matched cddid_all.tbl CDD NF041159 NF041159 469071 Rham_dhyd_Thplmales L-rhamnose 1-dehydrogenase. 253 matched cddid_all.tbl CDD NF041160 NF041160 469072 DGGPL_Thplmales digeranylgeranylglycerophospholipid reductase. 396 matched cddid_all.tbl CDD NF041162 NF041162 469073 encap_f2a family 2A encapsulin nanocompartment shell protein. Capsid-like encapsulin nanocompartments are commonly found in bacteria and archaea. Encapsulin nanocompartments, which are assembled from shell proteins, encapsulate various cargo proteins, typically peroxidases or ferritin-like proteins, to protect cells from oxidative stress caused by peroxide. 294 matched cddid_all.tbl CDD NF041163 NF041163 469074 encap_f2b family 2B encapsulin nanocompartment shell protein. Capsid-like encapsulin nanocompartments are commonly found in bacteria and archaea. Encapsulin nanocompartments, which are assembled from shell proteins, encapsulate various cargo proteins, typically peroxidases or ferritin-like proteins, to protect cells from oxidative stress caused by peroxide. 450 matched cddid_all.tbl CDD NF041164 NF041164 469075 NucKinThplmales nucleoside kinase. 295 matched cddid_all.tbl CDD NF041165 NF041165 469076 ZFX_Thplmales zinc-containing ferredoxin. 144 matched cddid_all.tbl CDD NF041166 NF041166 469077 f2_encap_cargo1 family 2A encapsulin nanocompartment cargo protein cysteine desulfurase. Capsid-like encapsulin nanocompartments are commonly found in bacteria and archaea. Encapsulin nanocompartments, which are assembled from shell proteins, encapsulate various cargo proteins, typically peroxidases or ferritin-like proteins, to protect cells from oxidative stress caused by peroxide. Proteins of this family are cysteine desulfurases with an additional N-terminal encapsulation targeting sequence (~200 aa) that is necessary and sufficient for compartmentalization. 623 matched cddid_all.tbl CDD NF041167 NF041167 469078 f2_encap_cargo2 family 2 encapsulin nanocompartment cargo protein terpene cyclase. 358 matched cddid_all.tbl CDD NF041168 NF041168 469079 f2_encap_cargo3 family 2 encapsulin nanocompartment cargo protein terpene cyclase. 733 matched cddid_all.tbl CDD NF041169 NF041169 469080 f2_encap_cargo4 family 2 encapsulin nanocompartment cargo protein polyprenyl transferase. 334 matched cddid_all.tbl CDD NF041170 NF041170 469081 Oxoac_fdxalpha_Archa 2-oxoacid:ferredoxin oxidoreductase subunit alpha. 635 matched cddid_all.tbl CDD NF041171 NF041171 469082 Oxoac_fdxbeta_Archa 2-oxoacid:ferredoxin oxidoreductase subunit beta. 296 matched cddid_all.tbl CDD NF041172 NF041172 469083 AcrlCoa_red_Thmprot acryloyl-coenzyme A reductase. 334 matched cddid_all.tbl CDD NF041173 NF041173 469084 Sug_nt_acttase_Thmprot bifunctional sugar-1-phosphate nucleotidylyltransferase/acetyltransferase. 404 matched cddid_all.tbl CDD NF041174 NF041174 469085 SDX_Thmprot sulredoxin. 109 matched cddid_all.tbl CDD NF041175 NF041175 469086 RNAseHI_Thmprot ribonuclease HI. 144 matched cddid_all.tbl CDD NF041176 NF041176 469087 GlyK_Thmprot glycerate 2-kinase. 395 matched cddid_all.tbl CDD NF041177 NF041177 469088 Cyp119_Thmprot cytochrome P450 Cyp119. 368 matched cddid_all.tbl CDD NF041178 NF041178 469089 TQO_small_DoxA thiosulfate:quinone oxidoreductase small subunit. 165 matched cddid_all.tbl CDD NF041179 NF041179 469090 TQO_large_DoxD thiosulfate:quinone oxidoreductase large subunit. 181 matched cddid_all.tbl CDD NF041183 NF041183 469091 Pks2_ls1_myc sulfolipid-1 biosynthesis phthioceranic/hydroxyphthioceranic acid synthase. 2085 matched cddid_all.tbl CDD NF041186 NF041186 469092 SenA selenoneine synthase SenA. Selenoneine is the selenium analog of ergothioneine, a sulfur-containing derivative of a hercynine, which derives from histidine by trimethylation of its amino group. SenA, a homolog of ergothioneine biosynthesis protein EgtB, completes selenoneine biosynthesis in a pathway that also requires a SelD protein to prepare selenophosphate, EgtD to prepare hercynine, and the selenosugar-producing glycosyltransferase SenB (TIGR04348). SenA catalyzes selenium-carbon bond formation between hercynine and selenosugar to produce selenoneine. Other enzymes that create carbon-selenium bonds include SelA, involved in selenocysteine biosynthesis, SelU, involved in selenouridine biosynthesis, and SbtM, a radical SAM enzyme involved in post-translational modification of the RiPP precursor SbtA (see PMID:34730336). 384 matched cddid_all.tbl CDD NF041188 NF041188 469093 encap_f3 family 3 encapsulin nanocompartment shell protein. Capsid-like encapsulin nanocompartments are commonly found in bacteria and archaea. Encapsulin nanocompartments, which are assembled from shell proteins, encapsulate various cargo proteins, typically peroxidases or ferritin-like proteins, to protect cells from oxidative stress caused by peroxide. 266 matched cddid_all.tbl CDD NF041190 NF041190 469094 encap_f4a family 4A encapsulin nanocompartment shell protein. Capsid-like encapsulin nanocompartments are commonly found in bacteria and archaea. Encapsulin nanocompartments, which are assembled from shell proteins, encapsulate various cargo proteins, typically peroxidases or ferritin-like proteins, to protect cells from oxidative stress caused by peroxide. 92 matched cddid_all.tbl CDD NF041191 NF041191 469095 encap_f4b family 4B encapsulin nanocompartment shell protein. Capsid-like encapsulin nanocompartments are commonly found in bacteria and archaea. Encapsulin nanocompartments, which are assembled from shell proteins, encapsulate various cargo proteins, typically peroxidases or ferritin-like proteins, to protect cells from oxidative stress caused by peroxide. 90 matched cddid_all.tbl CDD NF041192 NF041192 469096 encap_f4c family 4C encapsulin nanocompartment shell protein. Capsid-like encapsulin nanocompartments are commonly found in bacteria and archaea. Encapsulin nanocompartments, which are assembled from shell proteins, encapsulate various cargo proteins, typically peroxidases or ferritin-like proteins, to protect cells from oxidative stress caused by peroxide. 95 matched cddid_all.tbl CDD NF041193 NF041193 469097 lipo_SP0191 SP0191 family lipoprotein. 190 matched cddid_all.tbl CDD NF041194 NF041194 469098 LD_carboxy_LdcB LD-carboxypeptidase LdcB/DacB. 180 matched cddid_all.tbl CDD NF041195 NF041195 469099 ScbA_BarX_GamBu ScbA/BarX family gamma-butyrolactone biosynthesis protein. Members of this family initiate the biosynthesis of gamma-butyrolactone autoregulators, a class of compound that include A-factor in (2-isocapryloyl-3R-hydroxymethyl-y-butyrolactone) in Streptomyces griseus. Through its receptor, a member of the TetR/AcrR family of transcriptional regulators, gamma-butyrolactones can control various processes such as antibiotic biosynthesis. 288 matched cddid_all.tbl CDD NF041196 NF041196 469100 ScbR_bind_reg ScbR family autoregulator-binding transcription factor. 191 matched cddid_all.tbl CDD NF041197 NF041197 469101 CxxC_Se_CxxC dual CXXC motif small (seleno)protein. Members of this family have a pair of CxxC motifs. An additional Cys in the 16 amino region separating the two motifs occasionally is replaced by selenocysteine. This family was reported as OS_HP3 by Zhang et al. in PMID:17626042. 62 matched cddid_all.tbl CDD NF041198 NF041198 469102 UshA_like_PCGU UshA-like (seleno)protein. Members of this family are distantly related to hydrolases such as UshA and CpdB of Escherichia coli. Most members are selenoproteins with a PCGU motif. 519 matched cddid_all.tbl CDD NF041199 NF041199 469103 trx7_PDZ_seleno Trx7/PDZ domain-containing (seleno)protein. Members of this family, most of which are selenoproteins, have an average length of about 420 amino acids, with an N-terminal signal peptide and then a PF13899-type thioredoxin-like domain (Trx7), followed by a more C-terminal PDZ domain. The selenocysteine residue occurs in a CxxU or UxxU motif. 389 matched cddid_all.tbl CDD NF041200 NF041200 469104 mob_BfmA_Nterm BfmA/BtgA family mobilization N-terminal domain. BfmA was identified as a mobilization protein for a pathogenicity island that includes fragilysin (Bacteroides fragilis toxin, or BFT) and the fragilysin family metalloproteinase MP-II. BfmA has partner proteins BfmB (a member of the PF18976) and BfmC. The distantly related protein BtgA, also found in Bacteroides fragilis, is a mobilization factor for antibiotic resistance factors. 81 matched cddid_all.tbl CDD NF041201 NF041201 469105 recomb_XisF fdxN element excision recombinase XisF. 463 matched cddid_all.tbl CDD NF041202 NF041202 469106 StoA_CxxC endospore biogenesis thiol-disulfide oxidoreductase StoA. StoA (originally YkvV in Bacillus subtilis) is a paralog of ResA. It is involved in proper formation of the peptidoglycan cortex of the endospore, while ResA is involved in cytochrome c maturation. Both are membrane-bound and outside of the cytoplasm. This HMM separates StoA from the much larger set of ResA proteins. 163 matched cddid_all.tbl CDD NF041203 NF041203 469107 rhodanese_LYCAU rhodanese-related (seleno)protein. Most members of this family of rhodanese-related putative sulfurtransferases are selenoproteins with one or two selenocysteines in a CxU or UxU motif. 126 matched cddid_all.tbl CDD NF041204 NF041204 469108 VdcC non-oxidative hydroxyarylic acid decarboxylases subunit C. 467 matched cddid_all.tbl CDD NF041205 NF041205 469109 VdcD non-oxidative hydroxyarylic acid decarboxylases subunit D. 70 matched cddid_all.tbl CDD NF041206 NF041206 469110 VdcB non-oxidative hydroxyarylic acid decarboxylases subunit B. 184 matched cddid_all.tbl CDD NF041207 NF041207 469111 tRNA_bind_PBP11 tRNA-binding protein Pbp11. 104 matched cddid_all.tbl CDD NF041208 NF041208 469112 celldiv_DipM cell division endopeptidase DipM. 419 matched cddid_all.tbl CDD NF041209 NF041209 469113 resp_regPieR two component system response regulator PieR. 231 matched cddid_all.tbl CDD NF041210 NF041210 469114 his_kin_PieS two component system sensor histidine kinase PieS. 474 matched cddid_all.tbl CDD NF041211 NF041211 469115 CxxS_UxF_star SbtA. Members of this family have a HPDCxxS motif, instead of xxxCxxC or xxxUxxT as found in some homologs. Members tend to be selenoproteins, with a novel C-terminal UxF-COOH motif. 71 matched cddid_all.tbl CDD NF041212 NF041212 469116 Uxx_star Uxx-star family glutaredoxin-like (seleno)protein. A number of proteins with glutaredoxin-like folds, a length of about 75 amino acids, and a CxxC, C/UxxT, or CxxS motif near the N-terminus end with a UXX-COOH motif. That final motif typically is missed during coding region feature prediction by genome annotation pipelines. This HMM covers proteins from several distinctive families with this feature. The seed alignment illustrates the final selenocysteine or aligned Cys or Ser residues, but the HMM also hits proteins that lack an equivalent motif at the C-terminus. This C-terminal selenocysteine-containing motif has not yet been described in the literature. 70 matched cddid_all.tbl CDD NF041213 NF041213 469117 plasmid_TraA plasmid transfer protein TraA. 164 matched cddid_all.tbl CDD NF041214 NF041214 469118 plasmid_TraB plasmid transfer protein TraB. 639 matched cddid_all.tbl CDD NF041216 NF041216 469119 CU044_2847_fam CU044_2847 family protein. 89 matched cddid_all.tbl CDD NF041217 NF041217 469120 BagE_FevW bagremycin/ferroverdin synthetase BagE/FevW. 424 matched cddid_all.tbl CDD NF041218 NF041218 469121 BagM_FevK bagremycin/ferroverdin biosynthesis UbiX family decarboxylase BagM/FevK. 215 matched cddid_all.tbl CDD NF041219 NF041219 469122 BagN_FevL bagremycin/ferroverdin biosynthesis UbiD family decarboxylase BagN/FevL. 489 matched cddid_all.tbl CDD NF041220 NF041220 469123 BagH_FevF bagremycin/ferroverdin biosynthesis o-aminophenol oxidase BagH/FevF. 305 matched cddid_all.tbl CDD NF041221 NF041221 469124 BagZ_FevE bagremycin/ferroverdin biosynthesis copper chaperon BagZ/FevE. 122 matched cddid_all.tbl CDD NF041222 NF041222 469125 BagA_FevW bagremycin/ferroverdin biosynthesis tyrosine ammonia-lyase BagA/FevW. 517 matched cddid_all.tbl CDD NF041223 NF041223 469126 BagB_FevI bagremycin/ferroverdin biosynthesis DhnA-type aldolase BagB/FevI. 257 matched cddid_all.tbl CDD NF041224 NF041224 469127 BagC_FevH bagremycin/ferroverdin biosynthesis 3,4-AHBA synthase BagC/FevH. 368 matched cddid_all.tbl CDD NF041225 NF041225 469128 Cas_III-E_gRAMP type III-E CRISPR-associated gRAMP effector Cas7-11. The giant RAMP (gRAMP) effector of type III-E CRISPR/Cas systems, named Cas7-11 because of its multiple domains, works together with the caspase-like TPR-CHAT protease (Csx29) in a subset of type III-E systems. The complex of the Cas7-11 and the TPR-CHAT subunits is called craspase (CRISPR-guided caspase). 1629 matched cddid_all.tbl CDD NF041226 NF041226 469129 BagK_FevA1 bagremycin/ferroverdin biosynthesis FAD-dependent oxygenase BagK/FevA1. 453 matched cddid_all.tbl CDD NF041227 NF041227 469130 BagG_FevA2 bagremycin/ferroverdin biosynthesis FAD-dependent oxygenase BagG/FevA2. 455 matched cddid_all.tbl CDD NF041228 NF041228 469131 BagJ_FevB bagremycin/ferroverdin transporter BagJ/FevB. 452 matched cddid_all.tbl CDD NF041229 NF041229 469132 BagF_FevY phospho-2-dehydro-3-deoxyheptonate aldolase BagF/FevY. 340 matched cddid_all.tbl CDD NF041230 NF041230 469133 BagL_FevM MarR family transcriptional regulator BagL/FevM. 145 matched cddid_all.tbl CDD NF041231 NF041231 469134 BagI_FevR AfsR/SARP family transcriptional regulator BagI/FevR. 315 matched cddid_all.tbl CDD NF041232 NF041232 469135 BagY_FevT LuxR family transcriptional regulator BagY/FevT. 366 matched cddid_all.tbl CDD NF041234 NF041234 469136 CAS_csx30 type III-E CRISPR-associated protein Csx30. Csx30, encoded in type III-E CRISPR systems, was identified as the proteolytic target of craspase (CRISPR-guided caspase), which is a complex of the gRAMP (giant RAMP) protein Cas7-11 and the TPR-CHAT protein Csx29. 560 matched cddid_all.tbl CDD NF041235 NF041235 469137 CAS_csx31 type III-E CRISPR-associated protein Csx31. 373 matched cddid_all.tbl CDD NF041236 NF041236 469138 CAS_III-E_sigma type III-E CRISPR-associated RpoE-like sigma factor. 192 matched cddid_all.tbl CDD NF041237 NF041237 469139 CAS_csx29_CRASP type III-E CRISPR-associated TPR-CHAT protein Csx29. Csx29, the protease subunit of the craspase complex, is a TPR-CHAP family protein of type III-E CRISPR/Cas systems. Craspase is guided by crRNA, but cleaves protein, not nucleotide, and therefore is highly interesting for potential technological applications. 669 matched cddid_all.tbl CDD NF041238 NF041238 469140 AhpD_rel_CFYUT alkylhydroperoxidase-related (seleno)protein. Members of this family are almost entirely selenoproteins, with an average length of 370 amino acids and typically with the motif CFYUT. Cutoffs are set so that most incomplete proteins that run from the N-terminus to the selenocysteine-encoding TGA codon, ending CFY, still score above cutoffs. So far, the vast majority of family members are reported from uncultured organisms assembled out of metagenomic sequence. 354 matched cddid_all.tbl CDD NF041239 NF041239 469141 Moor_selen_rel CC/Se motif family (seleno)protein. Many members of this family have a double-Cys motif. Others, including several from the genus Moorella such as WP_263870381.1 and WP_263870380.1, have a selenocysteine at a similar location once structural annotation is corrected. 91 matched cddid_all.tbl CDD NF041240 NF041240 469142 YebF_not_Cmi protein YebF. This HMM identifies the exported protein YebF from E. coli, Salmonella, Providencia, Xenorhabdus, and other closely related lineages. It excludes the colicin M immunity protein Cmi, a YebF homolog. The related model from Pfam, PF13995, covers both families. 114 matched cddid_all.tbl CDD NF041241 NF041241 469143 YhfZ_full GntR family transcriptional regulator YhfZ. Full-length homologs of the transcriptional regulator YhfZ from Escherichia coli, with an N-terminal GntR-like domain, are quite divergent. See PF14503 (YhfZ_C) for the broader family. This HMM identifies a subset in which the motif MPLPYxxxYEGLA and the C-terminal PxY motifs are both well conserved, suggesting orthology with conserved function. 304 matched cddid_all.tbl CDD NF041242 NF041242 469144 T6SS_PdpE_Fran type VI secretion system protein PdpE. PdpE is encoded within the type VI secretion system (T6SS) locus in Francisella tularensis and several other members of the genus, is secreted by that system, but has not been shown to be essential to virulence and is therefore not currently named as a T6SS effector protein. So far, no homolog is detected outside of the genus Francisella. 192 matched cddid_all.tbl CDD NF041243 NF041243 469145 T6SS_IglJ type VI secretion system baseplate protein IglJ. IglJ (intracellular growth locus J), a encoded in the type VI secretion system (T6SS) of Francisella tularensis, is characterized component of the baseplate in a lineage-specific form of the T6SS apparatus. 223 matched cddid_all.tbl CDD NF041244 NF041244 469146 IglI_fam type VI secretion system protein IglI family protein. IglI (intracellular growth locus I), from Francisella tularensis, occurs within the type VI secretion system (T6SS) locus, and is important to virulence. This model describes a broad family of related proteins, the majority of which likewise encoded in the vicinity of other T6SS proteins such as baseplate subunit TssK. 292 matched cddid_all.tbl CDD NF041245 NF041245 469147 T6SS_IglE type VI secretion system lipoprotein IglE. IglE (intracellular growth locus E), as found in Francisella tularensis, is an outer membrane lipoprotein important to the role of the type VI secretion system locus that encodes it in pathgenesis. IglE is a distant homolog of TssJ, as revealed after multiple rounds of PSI-BLAST and seen in its similar crystal structure. 131 matched cddid_all.tbl CDD NF041246 NF041246 469148 T6SS_IglH_TssF type VI secretion system baseplate subunit TssF/IglH. 464 matched cddid_all.tbl CDD NF041247 NF041247 469149 UsfY protein UsfY. Proteins of this family are encoded by the usfY gene on Mycobacterium genomes. The usfY gene is tightly linked with the anti-sigma B factor rsbW (usfX). However, the function of UsfY is unknown. 95 matched cddid_all.tbl CDD NF041248 NF041248 469150 T6SS_IglG type VI secretion system PAAR-like protein IglG. 173 matched cddid_all.tbl CDD NF041249 NF041249 469151 T6SS_TssI_Fran type VI secretion system tip protein TssI/VgrG, short form. Members of this family are TssI/VgrG proteins of type VI secretion systems of a variant short form found in Francisella tularensis and related species. 163 matched cddid_all.tbl CDD NF041250 NF041250 469152 VI_TagQ type VI secretion system-associated lipoprotein TagQ. 301 matched cddid_all.tbl CDD NF041251 NF041251 469153 omp10_alpha_prot outer membrane lipoprotein Omp10. 122 matched cddid_all.tbl CDD NF041252 NF041252 469154 outer_memb_MapA outer membrane lipoprotein MapA. 213 matched cddid_all.tbl CDD NF041255 NF041255 469155 mycofact_MftM mycofactocin oligosaccharide methyltransferase MftM. Mature mycofactocin has an attached oligosaccharide chain of glucose residues with beta-1,4 linkages. In Mycolicibacterium smegmatis but not in Mycobacterium tuberculosis, the second glucose residue is 2-O-methylated by the SAM-dependent methyltransferase MftM. 289 matched cddid_all.tbl CDD NF041256 NF041256 469156 GntI_guanitoxin guanitoxin biosynthesis pre-guanitoxin N-oxide kinase GntI. 279 matched cddid_all.tbl CDD NF041257 NF041257 469157 GntH_guanitoxin guanitoxin biosynthesis MBL fold metallo-hydrolase GntH. 372 matched cddid_all.tbl CDD NF041258 NF041258 469158 motor_HelR_2 "RNA polymerase recycling motor ATPase HelR group 2. This HMM describes the second of at least two ""HelR"" subclasses of the RNA polymerase recycling motor protein HelD for which at least a few members have genes preceded by a Rifamycin Associated Element (RAE) and are known or predicted to be induced by rifampicin, a rifamycin-type antibiotic. HelD proteins, including HelR, are helicase-like motor proteins that play a role in transcription, removing and recycling stalled transcription complexes that could interfere with normal transcription or with DNA replication." 713 matched cddid_all.tbl CDD NF041259 NF041259 469159 mono_DmmA_fam dimethylamine monooxygenase subunit DmmA-like domain. 99 matched cddid_all.tbl CDD NF041260 NF041260 469160 actino_IHF integration host factor, actinobacterial type. Members of this family are nucleoid-associated dsDNA-binding proteins called integration host factor (mIHF in mycobacteria and sIHF in streptomycetes) because of similarities in cellular role, not in sequence, to the integration host factor proteins of Escherichia coli. Actinobacterial-type IHF actually shows more sequence similarity to 30S ribosomal subunit protein S13. Some members are fused to an additional guanylate kinase domain. This HMM assigns the gene symbol mihF broadly across the actinobacteria. 102 matched cddid_all.tbl CDD NF041261 NF041261 469161 RHS_core RHS element core protein. 1261 matched cddid_all.tbl CDD NF041262 NF041262 469162 colicin_Z_Cterm colicin Z C-terminal-like domain. 87 matched cddid_all.tbl CDD NF041263 NF041263 469163 colicin_Z_full colicin Z family toxin. This HMM represents full-length homologs of the colicin Z activity protein. The C-terminal is found more broadly, and is described by model NF041262. 229 matched cddid_all.tbl CDD NF041264 NF041264 469164 MobA plasmid mobilization protein MobA. 91 matched cddid_all.tbl CDD NF041265 NF041265 469165 NadS NadS family protein. 94 matched cddid_all.tbl CDD NF041266 NF041266 469166 YsgD_CorL YsgD/CorL family protein. 18 matched cddid_all.tbl CDD NF041267 NF041267 469167 relax_RlxS relaxase/mobilization nuclease RlxS. 654 matched cddid_all.tbl CDD NF041271 NF041271 469168 Phos_CheZ protein phosphatase CheZ. 242 matched cddid_all.tbl CDD NF041272 NF041272 469169 Chtaxis_ChePep chemotaxis regulatory protein ChePep. 530 matched cddid_all.tbl CDD NF041273 NF041273 469170 GlcN_kinase glucosamine kinase. 391 matched cddid_all.tbl CDD NF041274 NF041274 469171 isoleu_diox_hilA L-isoleucine 3(1)-dioxygenase. 285 matched cddid_all.tbl CDD NF041275 NF041275 469172 MurL_Xanthmoales UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-L-glutamate epimerase. 447 matched cddid_all.tbl CDD NF041276 NF041276 469173 treh_trans_TtfA trehalose monomycolate transport factor TtfA. 282 matched cddid_all.tbl CDD NF041277 NF041277 469174 coba_remo_CbiR cobamide remodeling phosphodiesterase CbiR. Rare cobamides, analogs of B12 with critical differences in the lower ligand, can become available for a salvage-like pathway to B12 biosynthesis through the action of enzymes that cleave the lower ligand. Members of this family are CbiR, a phosphodiesterase, which joins CbiZ, a previously discovered amidohydrolase, in the guild of cobamide remodeling enzymes. 249 matched cddid_all.tbl CDD NF041278 NF041278 469175 CmcJ_NvfI_EfuI CmcJ/NvfI family oxidoreductase. Members of this family are typically biosynthetic cluster enzymes, including the Fe(II)/2-oxoglutarate-dependent dioxygenase NvfI, the hydroxylase/desaturase EfuI, and the hydroxylase-like subunit CmcJ of the CmcI/CmcJ methoxylation complex involved in cephamycin biosynthesis. 263 matched cddid_all.tbl CDD NF041279 NF041279 469176 repress_GgpR glucosylglycerol biosynthesis transcriptional repressor GgpR. Members of this family, called GgpR, found so far exclusively in the genus Synechocystis, are encoded upstream of the glucosylglycerol-phosphate synthase GgpS and are characterized as essential to transcriptional repression of glucosylglycerol biosynthesis. 90 matched cddid_all.tbl CDD NF041280 NF041280 469177 mem_Micro_34 small membrane protein MtfM. Members of this family are typically 34 amino acids in length, consisting largely of one highly hydrophobic predicted transmembrane segment. Many are from the genera Micromonospora and Actinoplanes. Note that many annotation pipelines are unable to predict a bacterial protein this small without supporting homology evidence as from this HMM. We suggest the symbol MtfM (Membrane protein of length Thirty-Four from Micromonospora). 34 matched cddid_all.tbl CDD NF041281 NF041281 469178 TraA_gammapb TraA family conjugative transfer protein. 75 matched cddid_all.tbl CDD NF041282 NF041282 469179 TnpC_regulator Tn3 family transposase post-transcriptional regulator TnpC. 105 matched cddid_all.tbl CDD NF041283 NF041283 469180 PrgP ParA superfamily DNA segregation protein PrgP. 297 matched cddid_all.tbl CDD NF041284 NF041284 469181 PrgO DNA segregation protein PrgO. 90 matched cddid_all.tbl CDD NF041285 NF041285 469182 ABC_SBP_TrpX tryptophan ABC transporter substrate-binding protein. 322 matched cddid_all.tbl CDD NF041286 NF041286 469183 lipo_GerS germination lipoprotein GerS. 196 matched cddid_all.tbl CDD NF041287 NF041287 469184 lipo_GerS_rel germination lipoprotein GerS-related protein. Members of this family are related to the lipoprotein GerS that is found in the spore cortex of bacterial such as Clostridium difficile, and that regulates the activity of other spore cortex proteins. Similar between members of this family and GerS family lipoproteins 201 matched cddid_all.tbl CDD NF041288 NF041288 469185 YdaE_coli YdaE family protein. Members of this family include YdaE from the Rac prophage region of Escherichia coli K-12, a homolog from the Gifsy-1 prophage region of Salmonella enterica LT2, and related proteins from other closely related species. The presence of four conserved Cys residues has led to annotations as a zinc-binding protein or metallothionein, but the actual function seems unclear. 50 matched cddid_all.tbl CDD NF041289 NF041289 469186 KorA KorA family transcriptional regulator. 91 matched cddid_all.tbl CDD NF041290 NF041290 469187 StbA_2 plasmid stabilization protein StbA. 123 matched cddid_all.tbl CDD NF041291 NF041291 469188 StbC plasmid stabilization protein StbC. 122 matched cddid_all.tbl CDD NF041292 NF041292 469189 StbB StbB family protein. 233 matched cddid_all.tbl CDD NF041293 NF041293 469190 G6PDh_Azf NAD-dependent glucose-6-phosphate dehydrogenase Azf. 252 matched cddid_all.tbl CDD NF041294 NF041294 469191 Scnl_mescCoAtase succinyl-CoA:mesaconate CoA-transferase. 381 matched cddid_all.tbl CDD NF041295 NF041295 469192 dynobact_RiPP dynobactin A family peptide antibiotic. Members of this family are RiPP precursor peptides modified by radical SAM/SPASM enzyme maturases. The founding member of this family, from Photorhabdus australis, has the ten amino amino acids WNSNVHSYRF in the mature product called dynobactin A. This antibiotic targets BamA, involved in the insertion of beta-barrel proteins correctly into the outer membrane. 48 matched cddid_all.tbl CDD NF041296 NF041296 469193 RNAactase_tcmA_Halo tRNA(Met) cytidine acetyltransferase TmcA. 744 matched cddid_all.tbl CDD NF041297 NF041297 469194 UDPGDh_AglM UDP-glucose 6-dehydrogenase AglM. 429 matched cddid_all.tbl CDD NF041298 NF041298 469195 rSAM_mat_DynA dynobactin maturation radical SAM/SPASM protein DynA. Members of this family are the radical SAM/SPASM protein DynA responsible for the maturation of dynobactins. Dynobactin A is a BamA-targeting peptide antibiotic, with amino acid sequence WNSNVHSYRF, made from a RiPP precursor peptide through post-translational modification. 356 matched cddid_all.tbl CDD NF041299 NF041299 469196 RiPP_near_DynW DynW-associated RiPP peptide. This rare and poorly characterized RiPP family contains proteins encoded next to the DynW family of radical SAM/SPASM peptide maturases. This family was described by bioinformatic analysis of related families DynA (radical SAM/SPASM) and DynB (RiPP propeptide). 68 matched cddid_all.tbl CDD NF041300 NF041300 469197 rSAM_mat_DarW radical SAM/SPASM peptide maturase DarW. DarW is a radical SAM/SPASM domain-containing peptide maturase most closely related to the darobactin maturase DarE. 415 matched cddid_all.tbl CDD NF041301 NF041301 469198 Cit_synth_Halo_CitZ citrate synthase. 379 matched cddid_all.tbl CDD NF041302 NF041302 469199 HMG_CoAsyn_Halo hydroxymethylglutaryl-CoA synthase. 443 matched cddid_all.tbl CDD NF041303 NF041303 469200 Indglycph_syn_Halo_TrpC indole-3-glycerol phosphate synthase. 250 matched cddid_all.tbl CDD NF041304 NF041304 469201 AvrBs2 type III secretion system effector avirulence protein AvrBs2. 716 matched cddid_all.tbl CDD NF041305 NF041305 469202 SecF_Halo protein translocase subunit SecF. 287 matched cddid_all.tbl CDD NF041306 NF041306 469203 RnaseHI_Halo ribonuclease HI. 197 matched cddid_all.tbl CDD NF041307 NF041307 469204 AvrBs1 AvrBs1/Avra family type III secretion system effector. 435 matched cddid_all.tbl CDD NF041308 NF041308 469205 AvrBs3 type III secretion system effector avirulence protein AvrBs3. 1179 matched cddid_all.tbl CDD NF041309 NF041309 469206 XopB XopB/HopD1 family type III secretion system effector. 510 matched cddid_all.tbl CDD NF041310 NF041310 469207 Prot_Kin_Rio1_Halo serine/threonine-protein kinase Rio1. 273 matched cddid_all.tbl CDD NF041311 NF041311 469208 Sig_rec_Srp19_Halo signal recognition particle subunit SRP19. 93 matched cddid_all.tbl CDD NF041312 NF041312 469209 Superox_dis_Halo superoxide dismutase. 196 matched cddid_all.tbl CDD NF041313 NF041313 469210 UDPGP_AglF_Halo UTP--glucose-1-phosphate uridylyltransferase AglF. 234 matched cddid_all.tbl CDD NF041314 NF041314 469211 Malate_DH_Halo malate dehydrogenase. 304 matched cddid_all.tbl CDD NF041315 NF041315 469212 malate_syn_AceB_Halo malate synthase AceB. 429 matched cddid_all.tbl CDD NF041316 NF041316 469213 NleH type III secretion system effector kinase NleH. 304 matched cddid_all.tbl CDD NF041317 NF041317 469214 HtdO plasmid transfer protein HtdO. 153 matched cddid_all.tbl CDD NF041318 NF041318 469215 phage_rep_C1 phage repressor protein C1. 283 matched cddid_all.tbl CDD NF041319 NF041319 469216 PTS-HPr_Halo phosphocarrier protein HPr. 87 matched cddid_all.tbl CDD NF041320 NF041320 469217 pfkB_Halo 1-phosphofructokinase. 302 matched cddid_all.tbl CDD NF041321 NF041321 469218 Alpha-amyl_MalA_Halo alpha-amylase MalA. 667 matched cddid_all.tbl CDD NF041322 NF041322 469219 Anth_synII_Halo anthranilate synthase component II. 190 matched cddid_all.tbl CDD NF041323 NF041323 469220 Nitr_red_NasA_Halo assimilatory nitrate reductase NasA. 674 matched cddid_all.tbl CDD NF041324 NF041324 469221 Bacteroid_MobA conjugal transfer protein MobA. 131 matched cddid_all.tbl CDD NF041325 NF041325 469222 Bacteroid_MobB conjugal transfer protein MobB. 419 matched cddid_all.tbl CDD NF041326 NF041326 469223 Bacteroid_MobC conjugal transfer protein MobC. 652 matched cddid_all.tbl CDD NF041327 NF041327 469224 Bgr08870_fam Bgr_08870 family protein, N-terminal domain. This HMM describes the N-terminal region of Bgr_08870 from Bartonella grahamii. Homologs appear restricted to other species of the same genus. The C-terminal region includes extensive low-complexity sequence, but also regions of homology with other at least one other family of Bartonella proteins. 209 matched cddid_all.tbl CDD NF041328 NF041328 469225 C_rich_MXAN6577 MXAN_6577-like cysteine-rich domain. 145 matched cddid_all.tbl CDD NF041329 NF041329 469226 CmeU CmeU family protein. 75 matched cddid_all.tbl CDD NF041330 NF041330 469227 BimD protein BimD. 121 matched cddid_all.tbl CDD NF041331 NF041331 469228 LigA_Halo ATP-dependent DNA ligase LigA. 549 matched cddid_all.tbl CDD NF041332 NF041332 469229 KDG_KDGal_kin_Halo bifunctional 2-dehydro-3-deoxygluconokinase/2-dehydro-3-deoxygalactonokinase. 318 matched cddid_all.tbl CDD NF041333 NF041333 469230 CruF_Halo bisanhydrobacterioruberin hydratase. 267 matched cddid_all.tbl CDD NF041334 NF041334 469231 XopJ YopJ family type III secretion system effector XopJ. 348 matched cddid_all.tbl CDD NF041335 NF041335 469232 surf_glcprot_Halo cell surface glycoprotein. 862 matched cddid_all.tbl CDD NF041336 NF041336 469233 CheA_Halo chemotaxis protein CheA. 666 matched cddid_all.tbl CDD NF041337 NF041337 469234 XopD Ulp1 family type III secretion system effector isopeptidase XopD. 731 matched cddid_all.tbl CDD NF041338 NF041338 469235 XopE XopE/AvrPphe family type III secretion system effector. 358 matched cddid_all.tbl CDD NF041344 NF041344 469236 XopF XopF/Hpa4 family type III secretion system effector. 548 matched cddid_all.tbl CDD NF041345 NF041345 469237 XopF1 type III secretion system effector XopF1. 668 matched cddid_all.tbl CDD NF041346 NF041346 469238 XopF2 type III secretion system effector XopF2. 541 matched cddid_all.tbl CDD NF041347 NF041347 469239 XopG XopG/HopH/AvrPtoH family type III secretion system effector. 200 matched cddid_all.tbl CDD NF041348 NF041348 469240 XopH type III secretion system effector XopH. 368 matched cddid_all.tbl CDD NF041349 NF041349 469241 XopI type III secretion system effector F-box protein XopI. 453 matched cddid_all.tbl CDD NF041350 NF041350 469242 XopK type III secretion system effector XopK. 876 matched cddid_all.tbl CDD NF041351 NF041351 469243 XopL type III secretion system leucine-rich repeat domain-containing effector XopL. 481 matched cddid_all.tbl CDD NF041352 NF041352 469244 XopN type III secretion system effector XopN. 719 matched cddid_all.tbl CDD NF041353 NF041353 469245 XopO XopO/AvrRps4 family type III secretion system effector. 218 matched cddid_all.tbl CDD NF041354 NF041354 469246 XopP type III secretion system effector XopP. 627 matched cddid_all.tbl CDD NF041355 NF041355 469247 XopQ type III secretion system effector XopQ. 402 matched cddid_all.tbl CDD NF041356 NF041356 469248 XopR type III secretion system effector protein XopR. 406 matched cddid_all.tbl CDD NF041357 NF041357 469249 XopU type III secretion system effector protein XopU. 984 matched cddid_all.tbl CDD NF041358 NF041358 469250 GntT_guanitoxin guanitoxin biosynthesis MATE family efflux transporter GntT. 438 matched cddid_all.tbl CDD NF041359 NF041359 469251 GntG_guanitoxin GntG family PLP-dependent aldolase. 342 matched cddid_all.tbl CDD NF041360 NF041360 469252 GntF_guanitoxin guanitoxin biosynthesis pre-guanitoxin forming N-methyltransferase GntF. 273 matched cddid_all.tbl CDD NF041362 NF041362 469253 GntE_guanitoxin guanitoxin biosynthesis PLP-dependent transaminase GntE. 426 matched cddid_all.tbl CDD NF041363 NF041363 469254 GntD_guanitoxin guanitoxin biosynthesis L-enduracididine beta-hydroxylase GntD. 340 matched cddid_all.tbl CDD NF041364 NF041364 469255 GntC_guanitoxin guanitoxin biosynthesis PLP-dependent (S)-gamma-hydroxy-L-arginine cyclodehydratase GntC. 354 matched cddid_all.tbl CDD NF041365 NF041365 469256 GntB_guanitoxin guanitoxin biosynthesis L-arginine gamma (S) hydroxylase. 308 matched cddid_all.tbl CDD NF041366 NF041366 469257 GntA_guanitoxin guanitoxin biosynthesis heme-dependent pre-guanitoxin N-hydroxylase GntA. 232 matched cddid_all.tbl CDD NF041367 NF041367 469258 CheY_Halo chemotaxis protein CheY. 114 matched cddid_all.tbl CDD NF041368 NF041368 469259 Fbpase2_Halo class II fructose-bisphosphate aldolase. 333 matched cddid_all.tbl CDD NF041369 NF041369 469260 Dhydh_Halo D-2-hydroxyacid dehydrogenase. 305 matched cddid_all.tbl CDD NF041370 NF041370 469261 desamp_Halo desampylase. 133 matched cddid_all.tbl CDD NF041371 NF041371 469262 Diadnylcyc_Halo diadenylate cyclase DacZ. 270 matched cddid_all.tbl CDD NF041372 NF041372 469263 DUF166_seleno DUF166 family (seleno)protein DfsP. DfsP (DUF166 Family Seleno-Protein) is a well-separated clade within the DUF166 family (see PF02593). The motif UC, in selenoprotein members, aligns to a CC motif in non-selenoprotein members. Members of this family appear restricted to the Desulfobacterales. 203 matched cddid_all.tbl CDD NF041373 NF041373 469264 HGG_STG HGGxSTG domain. 38 matched cddid_all.tbl CDD NF041374 NF041374 469265 GDCCVxC GDCCVxC domain. 58 matched cddid_all.tbl CDD NF041375 NF041375 469266 XopV XopV/AopV family type III secretion system effector. 266 matched cddid_all.tbl CDD NF041376 NF041376 469267 XopW type III secretion system effector XopW. 206 matched cddid_all.tbl CDD NF041377 NF041377 469268 XopX XopX family type III secretion system effector. 571 matched cddid_all.tbl CDD NF041378 NF041378 469269 XopZ XopZ family type III secretion system effector. 1293 matched cddid_all.tbl CDD NF041379 NF041379 469270 OS_HP4_CYCXC CYCXC family (seleno)protein. Most members of this family, called OS_HP4 in a review by Zhang, et al., are selenoproteins. 90 matched cddid_all.tbl CDD NF041380 NF041380 469271 XopAA type III secretion system effector XopAA. 690 matched cddid_all.tbl CDD NF041381 NF041381 469272 XopAC XopAC/AvrAC family type III secretion system effector. 453 matched cddid_all.tbl CDD NF041382 NF041382 469273 Trx_VPGUxxT_one VPGUxxT family thioredoxin-like (seleno)protein, type 1. Type 1 members of the VPGUxxT family thioredoxin-like (seleno)protein have a single site where selenocysteine residues appear. 349 matched cddid_all.tbl CDD NF041383 NF041383 469274 Trx_VPGUxxT_two VPGUxxT family thioredoxin-like (seleno)protein, type 2. Type 2 members of the VPGUxxT family thioredoxin-like (seleno)protein have two sites where selenocysteine residues appear, with motifs EVPGUxxC and UFWxGE. 287 matched cddid_all.tbl CDD NF041384 NF041384 469275 YHS_seleno_dom YHS domain-containing (seleno)protein. 113 matched cddid_all.tbl CDD NF041385 NF041385 469276 Dggglyphlred_Halo digeranylgeranylglycerophospholipid reductase. 405 matched cddid_all.tbl CDD NF041386 NF041386 469277 dihyfolred_HdrA_Halo dihydrofolate reductase HdrA. 158 matched cddid_all.tbl CDD NF041387 NF041387 469278 DNArepr_NreA_Halo DNA repair protein NreA. 419 matched cddid_all.tbl CDD NF041388 NF041388 469279 DNAstvprot_Halo DNA starvation/stationary phase protection protein DpsA. 171 matched cddid_all.tbl CDD NF041389 NF041389 469280 dodecin_Halo dodecin. 65 matched cddid_all.tbl CDD NF041390 NF041390 469281 TadE_Rv3655c TadE family type IV pilus minor pilin. This HMM somewhat overlaps with Pfam model PF07811 but extends coverage to include Rv3655c from Mycobacterium tuberculosis and related species. Rv3655c belongs to a cassette that produces an Flp-like type IV pilus structure, and has been ascribed an ability to suppress macrophage apoptosis. 100 matched cddid_all.tbl CDD NF041391 NF041391 469282 DPhHxTase_Halo dolichyl-phosphate hexose transferase. 213 matched cddid_all.tbl CDD NF041392 NF041392 469283 XylDh_Gfo6_Halo D-xylose 1-dehydrogenase Gfo6. 350 matched cddid_all.tbl CDD NF041393 NF041393 469284 Frdxn_Halo ferredoxin Fer. 128 matched cddid_all.tbl CDD NF041394 NF041394 469285 GtaseAglG_Halo glucosyl-dolichyl phosphate glucuronosyltransferase. 304 matched cddid_all.tbl CDD NF041395 NF041395 469286 TranRegLrpA1_Halo HTH-type transcriptional regulator LrpA1. 142 matched cddid_all.tbl CDD NF041396 NF041396 469287 TranRegLrp_Halo HTH-type transcriptional regulator Lrp. 149 matched cddid_all.tbl CDD NF041397 NF041397 469288 TranRegGlpR_Halo HTH-type transcriptional regulator GlpR. 253 matched cddid_all.tbl CDD NF041398 NF041398 469289 GluDhGdhB_Halo glutamate dehydrogenase GdhB. 412 matched cddid_all.tbl CDD NF041399 NF041399 469290 XopAD XopAD/skwp family type III secretion system effector. 1961 matched cddid_all.tbl CDD NF041400 NF041400 469291 XopAE type III secretion system effector XopAE. 478 matched cddid_all.tbl CDD NF041401 NF041401 469292 XopAF XopAF/AvrXv3 family type III secretion system effector. 205 matched cddid_all.tbl CDD NF041402 NF041402 469293 XopAG XopAG/AvrGf1 family type III secretion system effector. 432 matched cddid_all.tbl CDD NF041403 NF041403 469294 XopAH XopAH/AvrB family type III secretion system effector. 286 matched cddid_all.tbl CDD NF041404 NF041404 469295 XopAI type III secretion system effector XopAI. 232 matched cddid_all.tbl CDD NF041405 NF041405 469296 XopAJ XopAJ/AvrRxo1 family type III secretion system effector zeta toxin. 324 matched cddid_all.tbl CDD NF041406 NF041406 469297 XopAK XopAK family type III secretion system effector. 173 matched cddid_all.tbl CDD NF041407 NF041407 469298 XopAP XopAP family type III secretion system effector. 317 matched cddid_all.tbl CDD NF041408 NF041408 469299 XopAU XopAU family type III secretion system effector serine/threonine kinase. 498 matched cddid_all.tbl CDD NF041409 NF041409 469300 XopAV type III secretion system effector XopAV. 238 matched cddid_all.tbl CDD NF041410 NF041410 469301 XopAW XopAW family type III secretion system calcium-binding effector. 227 matched cddid_all.tbl CDD NF041411 NF041411 469302 XopAX XopAX family type III secretion system effector. 305 matched cddid_all.tbl CDD NF041412 NF041412 469303 XopC XopC/Rsp1239 family type III secretion system effector. 828 matched cddid_all.tbl CDD NF041413 NF041413 469304 ArsR_Rv2640c_fam Rv2640c family ArsR-like transcriptional regulator. Mycobacterium tuberculosis has several ArsR-related transcriptional regulators, including Rv2640c, a member of this family, and Rv2642, encoded nearby. Members of the Rv2640c family have two invariant CC motifs, one at (or a single amino acid away from) the C-terminus. 118 matched cddid_all.tbl CDD NF041414 NF041414 469305 ArsI_CadI_VOC ArsI/CadI family heavy metal resistance metalloenzyme. This family belong to the broader VOC (Vicinal Oxygen Chelate) domain family (see PF00903), which includes glyoxalase I, fosfomycin resistance proteins FosA and FosB, and dioxygenases such as 4-hydroxyphenylpyruvate dioxygenase. Members of this specific family include none of those, but instead include CadI from Mycobacterium tuberculosis and ArsI from Bacillus sp. MD1. They have an invariant CC motif at about position 95, and have poorly conserved C-terminal extension regions that nearly always contain at least one addition CC motif, often several. ArsI has been characterized as an organoarsenical lyase. 144 matched cddid_all.tbl CDD NF041415 NF041415 469306 halo_CC_star halo-CC-star protein HcsS. Members of this family average about 65 amino acids in length, and nearly every members ends with a double-cysteine (CC) motif at the extreme C-terminus of the protein, suggesting binding to a heavy metal atom. Members are found primarily in the Halobacteria, a branch of the Archaea. The gene symbol HcsS (Halo-CC-Star-Short) shows the similarity the adjacent HcsL (Halo-CC-Star-Long) protein. The greater context contains homologs of arsenic resistance proteins ArsD (a chaperone), ArsA (a transporter), and sometimes ArsM (arsenite methyltransferase), suggesting the HcsS and HcsL act in arsenical metabolism. 55 matched cddid_all.tbl CDD NF041416 NF041416 469307 halo_CC_star_2 halo-CC-star protein HcsL. Members of this family belong to the broader YlbF family described by Pfam model PF06133. Members occur in halophilic archaea, and are the larger (HcsL) of two related small proteins that have the CC-star terminal motif (Cys-Cys-COOH). The rare CC-star motif seems most common in proteins such as HgcB that interact with heavy metals. The gene symbol is represents the descriptive name Halo-CC-Star motif Large protein, while its partner is HcsS (Halo-CC-Star motif Small protein). 113 matched cddid_all.tbl CDD NF041417 NF041417 469308 ArsA_halo arsenical pump-driving ATPase, halobacterial type. Members of this family of arsenical pump-driving ATPase (ArsA) occur typically in Halobacteria (a branch of the archaea), accompanied by homologs of ArsD and by HcsL and HcsS (halo-CC-Star proteins, long and short), two proteins that both end with Cys-Cys-COOH motifs indicative of interaction with heavy metal atoms. 617 matched cddid_all.tbl CDD NF041418 NF041418 469309 MbpA mobilization protein MbpA. 93 matched cddid_all.tbl CDD NF041419 NF041419 469310 CC_star_Cory cory-CC-star protein. Members of this family have the CC-star motif (Cys-Cys-COOH), that is, a pair of Cys residues as the final two residues. A founding member is WP_085549354.1 from Corynebacterium pollutisoli. Members of this family typical are encoded next to an ArsA family ATPase (e.g. WP_085549353.1), suggesting a role in heavy metal metabolism, and predicted carbon starvation protein A (e.g. WP_085549355.1). 80 matched cddid_all.tbl CDD NF041420 NF041420 469311 MbpB mobilization protein MbpB. 260 matched cddid_all.tbl CDD NF041421 NF041421 469312 MbpC mobilization protein MbpC. 148 matched cddid_all.tbl CDD NF041422 NF041422 469313 VirB10_subf VirB10/TraB/TrbI family type IV secretion system protein. 404 matched cddid_all.tbl CDD NF041423 NF041423 469314 MobC_subf MobC family replication-relaxation protein. 239 matched cddid_all.tbl CDD NF041424 NF041424 469315 Brachy_memb_1 WESB_1763 family membrane protein. Members of this family are highly hydrophobic proteins that appear so far to be restricted to the genus Brachyspira, a spirochete lineage. The function is unknown. 306 matched cddid_all.tbl CDD NF041425 NF041425 469316 OS_HP2_seleno OS_HP2 family (seleno)domain. Members of this family contain a branch of the DUF1573 (PF07610) domain. A majority are selenoproteins, with a UGC motif. 98 matched cddid_all.tbl CDD NF041426 NF041426 469317 TrsA conjugative transfer protein TrsA. 324 matched cddid_all.tbl CDD NF041427 NF041427 469318 TrsD TrsD/TraD family conjugative transfer protein. 201 matched cddid_all.tbl CDD NF041428 NF041428 469319 TrsH TrsH/TraH family protein. 147 matched cddid_all.tbl CDD NF041429 NF041429 469320 EexR EexR/EexS family entry exclusion protein. 142 matched cddid_all.tbl CDD NF041430 NF041430 469321 UrfF plasmid repression protein F. 68 matched cddid_all.tbl CDD NF041431 NF041431 469322 S_layer_MEMAR MEMAR_RS02690 family S-layer glycoprotein. Members of this family are archaeal S-layer glycoproteins in the family of MEMAR_RS02690. Most members of this family have the PGF-CTERM domain, recognized and processed by the archaeosortase A (ArtA). Surprisingly, while MEMAR_RS02690 itself, from Methanoculleus marisnigri, a methanogen from the Order Methanomicrobiales, has the PGF-CTERM domain, and ArtA is encoded in the species, cleavage and lipidation was not successfully shown. All seed alignment members contain the PGF-CTERM sorting signal at the C-terminus, but additional members of the family differ at the C-terminus, and appear not to be ArtA-dependent surface proteins. 811 matched cddid_all.tbl CDD NF041432 NF041432 469323 MchS3 MchS3 family protein. 105 matched cddid_all.tbl CDD NF041433 NF041433 469324 UmoA UmoA family protein. 178 matched cddid_all.tbl CDD NF041434 NF041434 469325 UmoC UmoC family protein. 105 matched cddid_all.tbl CDD NF041435 NF041435 469326 UmoD UmoD family protein. 150 matched cddid_all.tbl CDD NF041436 NF041436 469327 Wzy_Strepto oligosaccharide repeat unit polymerase Wzy. 395 matched cddid_all.tbl CDD NF041437 NF041437 469328 TfpZ TfpX/TfpZ family type IV pilin accessory protein. 240 matched cddid_all.tbl CDD NF041438 NF041438 469329 SepM_fam_S16 SepM family pheromone-processing serine protease. This HMM describes a peptide pheromone-processing S16-type serine protease found broadly in Gram-positive bacteria, and named for the founding member from Streptococcus mutans (see BlastRule NBR014542). The Lon-like catalytic domain is located toward the C-terminus, and has a Ser-Lys active site dyad rather than the more common Ser-His-Asp triad found in large numbers of serine proteases. Members of this family also have a PDZ domain. 340 matched cddid_all.tbl CDD NF041439 NF041439 469330 TraE_Enteroc type IV conjugative transfer system protein TraE. 99 matched cddid_all.tbl CDD NF041440 NF041440 469331 hydrolase_YghX YghX family hydrolase. YghX is a predicted hydrolase, homologous to dienelactone hydrolases, but its function is unknown. YghX is encoded intact in Escherichia coli O157:H7 str. Sakai, but is a frameshifted pseudogene in Escherichia coli K-12 MG1655, and consequently is used occasionally as a site for minimally disruptive genetic engineering. 292 matched cddid_all.tbl CDD NF041442 NF041442 469332 YgjJ protein YgjJ. YgjJ proteins are widespread in the Gammaproteobacteria, and named for the founding member from Escherichia coli K-12. 341 matched cddid_all.tbl CDD NF041443 NF041443 469333 DDRRRQL_YjdP DDRRRQL repeat protein YjdP. Members of this family average 108 amino acids in length, with a signal peptide and with a highly charged C-terminal region of typically five tandem 7-mer repeats approximated by DDRRRQL. The family is named for founding member YjdP from Escherichia coli K-12. 102 matched cddid_all.tbl CDD NF041444 NF041444 469334 SASP_CD1290 CD1290 family small acid-soluble spore protein. CD1290 (CD630_12900) from Clostridioides difficile 630 is the founding member group of small acid-soluble spore proteins (SASP). Members are related to the alpha/beta family described by Pfam model PF00269, but are shorter on average and typically score below thresholds for that model. Sequences that resemble germination protease GPR cleavage motifs are EIAx[D/E] and [E/D]IIEN. 61 matched cddid_all.tbl CDD NF041447 NF041447 469335 TrbC_conju F-type conjugative transfer protein TrbC. 685 matched cddid_all.tbl CDD NF041448 NF041448 469336 stress_YjaA YjaA family stress response protein. 125 matched cddid_all.tbl CDD NF041449 NF041449 469337 K_carrageenase kappa-carrageenase. 283 matched cddid_all.tbl CDD NF041450 NF041450 469338 MobP1 MobP1 family relaxase. 321 matched cddid_all.tbl CDD NF041451 NF041451 469339 DDP1 DNA distortion polypeptide 1. 169 matched cddid_all.tbl CDD NF041452 NF041452 469340 DDP3 DNA distortion polypeptide 3. 116 matched cddid_all.tbl CDD NF041453 NF041453 469341 Bac51 bacteriocin 51 precursor BacA. 107 matched cddid_all.tbl CDD NF041454 NF041454 469342 FspA flagellum-secreted nonflagellar protein FspA. 138 matched cddid_all.tbl CDD NF041455 NF041455 469343 DSF_Ax21 diffusible signal factor-reguated Ax21 faimly protein. 184 matched cddid_all.tbl CDD NF041456 NF041456 469344 surv_prot_CiaI intracellular survival protein CiaI. 186 matched cddid_all.tbl CDD NF041457 NF041457 469345 reg_protDegQ_Bacil degradation enzyme regulation protein DegQ. gene synonym sacQ 46 matched cddid_all.tbl CDD NF041458 NF041458 469346 antiadapt_SpxO anti-adapter protein SpxO. 54 matched cddid_all.tbl CDD NF041459 NF041459 469347 antitoxMazE_Staph type II toxin-antitoxin system antitoxin MazE. 54 matched cddid_all.tbl CDD NF041460 NF041460 469348 kinGactiv_GlnX protein kinase G-activating protein GlnX. 439 matched cddid_all.tbl CDD NF041461 NF041461 469349 C_hydro_YcaC isochorismate family cysteine hydrolase YcaC. YcaC is a well-conserved cysteine hydrolase of unknown function, found in both Pseudomonas aeruginosa and Escherichia coli K-12, with an isochorismate family crystal structure. 201 matched cddid_all.tbl CDD NF041462 NF041462 469350 GalA beta-galactosidase GalA. 757 matched cddid_all.tbl CDD NF041463 NF041463 469351 GalB beta-galactosidase GalB. 799 matched cddid_all.tbl CDD NF041464 NF041464 469352 HelD_BACSU RNA polymerase recycling motor HelD (Bacillota-type). 772 matched cddid_all.tbl CDD NF041465 NF041465 469353 HelD_MYCSM RNA polymerase recycling motor HelD (Actinomycetota-type). 719 matched cddid_all.tbl CDD NF041466 NF041466 469354 factorH_bind factor H-binding protein. 279 matched cddid_all.tbl CDD NF041467 NF041467 469355 caps_synth_Cap8I type 8 capsular polysaccharide synthesis protein Cap8I. 463 matched cddid_all.tbl CDD NF041468 NF041468 469356 anti_sig_RseA anti-sigma E factor RseA. 134 matched cddid_all.tbl CDD NF041469 NF041469 469357 spor_prot_SB stage II sporulation protein SB. 58 matched cddid_all.tbl CDD NF041470 NF041470 469358 sec_prot_XpsN general secretion pathway protein XpsN. 260 matched cddid_all.tbl CDD NF041471 NF041471 469359 phage_reg_YmfL YmfL family putative phage regulatory protein. Members of this family are homologs of the e14 prophage region protein YmfL from Escherichia coli K-12. Distant homology to phage regulatory protein CII, as described by Pfam model PF06892, suggests a similar function. 143 matched cddid_all.tbl CDD NF041472 NF041472 469360 toxin_DinQ damage-inducible type I toxin DinQ. Members of this family include DinQ as seen in Escherichia coli K-12 and a family of closely related DinQ-like type I toxins termed DqlA. See model NF041473 for the more distantly related DqlB type I toxins. 22 matched cddid_all.tbl CDD NF041473 NF041473 469361 DinQ_rel DinQ-like type I toxin DqlB. 31 matched cddid_all.tbl CDD NF041474 NF041474 469362 membrane_YkgR small membrane protein YkgR. This family of stress response membrane proteins is named for the founding protein YkgR from Escherichia coli K-12. YkgR expression is induced by the cyclic AMP response protein (CRP), and the expressed protein is inserted into the inner membrane. 33 matched cddid_all.tbl CDD NF041475 NF041475 469363 membrane_YoaI small membrane protein YoaI. YoaI, a small membrane protein found in Escherchia coli, Salmonella enterica, Citrobacter rodentium, and other members of the Enterobacterales, averages about 34 amino acids in length. The founding member of this family, from Escherichia coli K-12, was shown to be regulated as part of the phosphate regulon. 34 matched cddid_all.tbl CDD NF041476 NF041476 469364 membrane_YldA small membrane protein YldA. This family of small membrane proteins, averaging about 29 amino acids in length, is named for YldA of Escherichia coli K-12 but is found in multiple members of the Enterobacterales. The family appears homologous to YoaI, also found in Escherichia coli K-12. 29 matched cddid_all.tbl CDD NF041477 NF041477 469365 YnaM_YnfT_fam YnaM/YnfT family protein. This uncharacterized protein family is named for two identical proteins found in prophage regions of Escherichia coli K-12, YnaM (Rac prophage) and YnfT (Qin prophage). 34 matched cddid_all.tbl CDD NF041478 NF041478 469366 spor_prot_SspM acid-soluble spore protein SspM. 34 matched cddid_all.tbl CDD NF041479 NF041479 469367 spor_membprot_YtrI sporulation membrane protein YtrI. 167 matched cddid_all.tbl CDD NF041480 NF041480 469368 flag_mot_ctl_ZomB flagellar motor control protein ZomB. 630 matched cddid_all.tbl CDD NF041481 NF041481 469369 beta_arabfuran_tase terminal beta-(1->2)-arabinofuranosyltransferase. 628 matched cddid_all.tbl CDD NF041482 NF041482 469370 ADPrt_Strmyces ADP-ribosyltransferase. 207 matched cddid_all.tbl CDD NF041483 NF041483 469371 growth_prot_Scy polarized growth protein Scy. 1293 matched cddid_all.tbl CDD NF041484 NF041484 469372 membrane_YmiC small membrane protein YmiC. YmiC is an uncharacterized predicted protein about 32 amino acids long, hypothesized to be real and a membrane protein based on conservation across multiple gammaproteobacteria with constant length and constant hydrophobic character suggesting insertion into membrane. Expression was verified for a construct with an added C-terminal epitope. Homologs tend to show a pattern of conservative amino acid substitutions. Thus, comparative genomics also suggests YmiC is a real protein. An usual feature is three perfectly invariant Trp residues, and a highly conserved fourth, in a stretch of 19 residues. 30 matched cddid_all.tbl CDD NF041485 NF041485 469373 spor_mat_CgeC spore maturation protein CgeC. 101 matched cddid_all.tbl CDD NF041486 NF041486 469374 rep_init_RepSA replication initiator protein RepSA. 443 matched cddid_all.tbl CDD NF041487 NF041487 469375 copper_ox_MnxG manganese-oxidizing multicopper oxidase MnxG. 1895 matched cddid_all.tbl CDD NF041488 NF041488 469376 caps_synth_Cps4B capsular polysaccharide biosynthesis protein Cps4B. 243 matched cddid_all.tbl CDD NF041489 NF041489 469377 sigO_reg_RsoA sigma-O factor regulator RsoA. 77 matched cddid_all.tbl CDD NF041490 NF041490 469378 trans_reg_SutA transcriptional regulator SutA. 109 matched cddid_all.tbl CDD NF041491 NF041491 469379 membrane_YniD small membrane protein YniD. YniD, an uncharacterized protein, is named for the founding member of the protein family in Escherichia coli K-12. Length and hydrophobic character are well-conserved and most amino acid substitutions appear conservative, suggesting YniD is expressed and functional in some way. 34 matched cddid_all.tbl CDD NF041492 NF041492 469380 MobF MobF family relaxase. 288 matched cddid_all.tbl CDD NF041493 NF041493 469381 MobT MobT family relaxase. 383 matched cddid_all.tbl CDD NF041494 NF041494 469382 MobH MobH family relaxase. 340 matched cddid_all.tbl CDD NF041495 NF041495 469383 MobB_relaxase MobB family relaxase. 267 matched cddid_all.tbl CDD NF041496 NF041496 469384 MobQ MobQ family relaxase. 197 matched cddid_all.tbl CDD NF041497 NF041497 469385 MobV MobV family relaxase. 187 matched cddid_all.tbl CDD NF041498 NF041498 469386 MobP2 MobP2 family relaxase. 333 matched cddid_all.tbl CDD NF041499 NF041499 469387 MobP3 MobP3 family relaxase. 311 matched cddid_all.tbl CDD NF041501 NF041501 469388 cola_mem FGLLP motif-containing membrane domain. Members of this family average about 700 amino acids in length, with variable N-terminal regions but a shared hydrophobic C-domain, modeled by this HMM, about 300 amino acids in length. 311 matched cddid_all.tbl CDD NF041502 NF041502 469389 integrase_1 site-specific integrase. 484 matched cddid_all.tbl CDD NF041503 NF041503 469390 WZX_like O-unit flippase-like protein. 429 matched cddid_all.tbl CDD NF041504 NF041504 469391 AccA_sub carboxyltransferase subunit alpha. 257 matched cddid_all.tbl CDD NF041505 NF041505 469392 HrpD6 HrpD6 family protein. 80 matched cddid_all.tbl CDD NF041506 NF041506 469393 VapD VapD family protein. 91 matched cddid_all.tbl CDD NF041507 NF041507 469394 HrpE_Xanth HrpE family protein. 85 matched cddid_all.tbl CDD NF041508 NF041508 469395 BacL2 BacL2 family protein. 200 matched cddid_all.tbl CDD NF041510 NF041510 469396 AMED_5909_fam AMED_5909 family protein. Most members of this family of uncharacterized proteins are about 80 amino acids in length, and are found in members of the Actinomycetota, such as the genera Amycolatopsis, Lentzea, Pseudonocardiales, Saccharomonospora, and Saccharothrix. The family is named for one of its members, AMED_5909 from Amycolatopsis mediterranei (ADJ47652). 69 matched cddid_all.tbl CDD NF041511 NF041511 469397 PA2816_fam PA2816 family glutamine-rich protein. Members of this family, including PA2816 from Pseudomonas aeruginosa, average about 140 amino acids in length, with an N-terminal signal peptide. The last 100 amino acids are extremely glutamine-rich. The family appears restricted to the genus Pseudomonas. The function is unknown. 138 matched cddid_all.tbl CDD NF041512 NF041512 469398 PA2817_fam PA2817 family protein. This family is named for uncharacterized protein PA2817 from Pseudomonas aeruginosa. Many members of the family have been annotated previously with the name dehydrogenase, but no source for that annotation, nor homology to any characterized enzyme or solved crystal structure, could be found as this HMM was built. 136 matched cddid_all.tbl CDD NF041513 NF041513 469399 formate_DH_Act formate dehydrogenase. Members of this family are the enzyme formate dehydrogenase, of a type found in the Actinomycetota, as in the genera Streptomyces, Nocardiopsis, Gordonia, and Saccharomonospora. Many are selenoproteins. 1066 matched cddid_all.tbl CDD NF041514 NF041514 469400 Legion_RtxA_N enhanced entry virulence factor RtxA, N-terminal domain. This HMM describes the N-terminal, non-repetitive portion of the Legionella virulence factor RxtA, named for the presence of tandem repeats-in-toxin (RTX) domains. RtxA can be four to six thousand amino acids long. In some isolates, the toxin is divided into two tandem ORFs but presumably re-form by recombination. RtxA is involved in adherence and cell entry. 335 matched cddid_all.tbl CDD NF041515 NF041515 469401 GspC_delta type II secretion system protein GspC, deltaproteobacterial-type. Members of this family are GspC (general secretion protein C), a component of type II secretion systems (T2SS), of a form found prmarily in deltaproteobacteria. This HMM is designed to be complementary to other HMMs that identify GspC rather that to separate a distinct subtype. 310 matched cddid_all.tbl CDD NF041516 NF041516 469402 PA2928_fam PA2928 family protein. This family is named for the locus PA2928 of Pseudomonas aeroginosa PAO1, as the family member most frequently cited in the literature, although PA2928 itself is significantly shorter at the N-terminus than most other members of this family, and is probably non-functional. WP_017001489.1 represents an intact equivalent to the PA2928 pseudogene. 345 matched cddid_all.tbl CDD NF041518 NF041518 469403 choice_anch_Q choice-of-anchor Q domain. 58 matched cddid_all.tbl CDD NF041519 NF041519 469404 bluetail bluetail putative surface-anchoring domain. Bluetail is a short protein domain, about 55 amino acids long, found primarily in Cyanobacteria (blue), at the extreme C-terminus of proteins (tail), that otherwise may differ in length and domain content. This pattern of occurrence suggests a role in anchoring proteins on the cell surface, although bluetail does not have the tripartide structure of signature motif, then transmembrane alpha helix, then cluster of Arg residues like the sorting domains PEP-CTERM, Gly-Gly-CTERM, MYXO-CTERM, etc. 55 matched cddid_all.tbl CDD NF041520 NF041520 469405 flexitail flexitail putative surface-anchoring domain. The flexitail domain is found several hundred proteins from metagenome-assembled genomes (MAGs) of Chloroflexi bacteria. As a rule, the flexitail domain, which averages about 110 amino acids in length, is located at the protein C-terminus, and is separated from other recognizable domains by stretches of low complexity sequences. This resembles the pattens seen for short, tripartite, C-terminal protein-sorting signals for surface-anchored proteins, such as PEP-CTERM, GlyGly-CTERM, or MYXO-CTERM, or the LPXTG signal in tripartite form as described by TIGR01167, or longer C-terminal sorting signals such as type IX secretion system (T9SS) signals. At the time of model creation, no example had yet appeared among the more than 200 million collected proteins from genomes of cultured prokaryotes in the RefSeq collection. This suggests that the flexitail domain may represent an adaptation to a lifestyle that has not been conducive to isolation in culture conditions known so far. 106 matched cddid_all.tbl CDD NF041521 NF041521 469406 HhoA_HhoB_HtrA HhoA/HhoB/HtrA family serine endopeptidase. Members of this family include the paralogous serine proteases HhoA, HhoB, and HtrA of the model cyanobacterial isolate Synechocystis sp. PCC 6803. They resemble the paralogous trio of serine proteases DegQ, DegP, and DegS of Escherichia coli. 334 matched cddid_all.tbl CDD NF041522 NF041522 469407 TPR_sll0314 Sll0314/Alr1548 family TPR repeat-containing protein. Members of this cyanobacterial family have signal peptides and are called periplasmic. The body of the protein contains regions of homology to tetratricopeptide repeats (TPR). Member protein Sll0314 was found to be upregulated as part of the iron deprivation stress regulon. 275 matched cddid_all.tbl CDD NF041523 NF041523 469408 post_COAP_1 post-COAP-1 domain. Post-COAP-1 was identified as a C-terminal domain, about 115 amino acids in length, found in a subset of proteins with the choice-of-anchor P (COAP) domain (see NF040603). This domain is seen primarily in non-cultured prokaryotes with a broad taxonomic bacteria and archaea. 115 matched cddid_all.tbl CDD NF041524 NF041524 469409 Gltr_6 family 6 glucosyltransferase. 226 matched cddid_all.tbl CDD NF041525 NF041525 469410 HrpD5 HrpD5 family protein. 314 matched cddid_all.tbl CDD NF041526 NF041526 469411 Hpa3 Hpa3 family type III secretion system protein. 123 matched cddid_all.tbl CDD NF041527 NF041527 469412 SCO1860_LAETG SCO1860 family LAETG-anchored protein. Members of this poorly characterized family, including SCO1860 from Streptomyces coelicolor, are surface proteins whose C-terminus contains a variant type sortase recognition and cleavage sorting signal. The sorting signal motif, LAETG, is compatible with processing by a SrtE family sortase enzyme. 305 matched cddid_all.tbl CDD NF041528 NF041528 469413 strep_LAETG LAETG motif sortase-processing domain. This HMM describes a Streptomyces-specific variant of the widespread LPXTG motif-containing sortase recognition and processing domain. 35 matched cddid_all.tbl CDD NF041529 NF041529 469414 LvhB7 T4SS-associated protein LvhB7. 45 matched cddid_all.tbl CDD NF041530 NF041530 469415 LvrD T4SS-associated protein LvrD. 126 matched cddid_all.tbl CDD NF041531 NF041531 469416 HrpV HrpV family type III secretion system protein. 117 matched cddid_all.tbl CDD NF041532 NF041532 469417 HprT HrpT family type III secretion system protein. 51 matched cddid_all.tbl CDD NF041533 NF041533 469418 trans_reg_TagK transcriptional regulator TagK. 178 matched cddid_all.tbl CDD NF041534 NF041534 469419 rodZ_Strepcoccus cytoskeleton protein RodZ. 275 matched cddid_all.tbl CDD NF041535 NF041535 469420 TonB_rec_PqqU TonB-dependent receptor PqqU. 673 matched cddid_all.tbl CDD NF041536 NF041536 469421 ArsM_DUF2284_UU arsenite methyltransferase/DUF2284 domain selenoprotein. Members of the seed alignment for this protein are selenoproteins with two selenocysteine-containing motifs. The first is in the N-terminal arsenite methyltransferase region, typically QUEGG, and the second is in a C-terminal DUF2284 domain, typically TUPSG. 459 matched cddid_all.tbl CDD NF041537 NF041537 469422 ArsM_AhpD_UU arsenite methyltransferase/AhpD domain selenoprotein. Members of the seed alignment for this protein are selenoproteins, most with two selenocysteine-containing motifs. The first is in the N-terminal arsenite methyltransferase region, typically UXGGA, and the second is in the C-terminal AhpD-like region, typically GCEPU. 345 matched cddid_all.tbl CDD NF041538 NF041538 469423 PEP_EDSA_1 EDSAP-1 family PEP-CTERM protein. Members of this family, designated EDSA-1 (exosortase-dependent surface-anchored protein 1), have an N-terminal signal peptide and a C-terminal PEP-CTERM region for recognition and processing by an exosortase. 306 matched cddid_all.tbl CDD NF041539 NF041539 469424 choice_anch_R choice-of-anchor R domain. The most frequent C-terminal anchoring domain for members of this family is PEP-CTERM (see TIGR02595) or a PEP-CTERM-related variant sorting signal domain processed by one of the specialty exosortases. Some member proteins are found instead with dockerin-like C-terminal repeats and a GC motif at the extreme C-terminus. The GC-type dockerin domain occurs, so far, primarily in metagenome-assembled genomes from the taxonomic class Phycisphaerae, within the Planctomycetota, where it seems to anchor a number of otherwise unrelated proteins. 156 matched cddid_all.tbl CDD NF041540 NF041540 469425 dockerin_GC GC-type dockerin-like domain. This domain begins and ends with a near invariant C, and GC, respectively. It occurs strictly at the C-terminus of proteins, and those protein are found almost exclusively in metagenome-assembled genomes of the taxonomic class Phycisphaerae, within the Planctomycetota. It shows apparent sequence homology to the type I dockerin domain (see PF00404), which likewise contains an internal repeat and which appears in strictly C-terminal positions of otherwise unrelated proteins. Type I dockerin domains occur in proteins that are organized by interaction with the cohesin domain (PF00963) in order to form the cellulosome. However, the GC-type dockerin domain described here is uncharacterized, and cohesin domains identifiable by PF00963 are not found in the same proteomes. 67 matched cddid_all.tbl CDD NF041541 NF041541 469426 fosBx1_fam FosBx1 family fosfomycin resistance bacillithiol transferase. Members of this family, found in Bacillus cereus and related species that synthesis bacillithiol rather than glutathione, are VOC family thiol transferases. They provide resistance to the antibiotic fosfomycin by transferring either bacillithiol or cysteine (but not glutathione) to fosfomycin, leaving it inactive. Note that this family is drawn rather narrowly, and several such families, all non-overlapping, appear in B. cereus and its close relatives. This family includes proteins that have been named FosBx1 (although the original source of that name is hard to trace), and the protein studied crystallographically by Thompson, et al. (see PMID:24004181). 138 matched cddid_all.tbl CDD NF041542 NF041542 469427 fosX-Cc fosfomycin resistance hydrolase FosXCC. FosXCC (FosX from Campylobacter coli) is rare, mobile antimicrobial resistance protein. Most members of the family are seen not only outside of the genus Campylobacter, but in Gram-positive species such as C. difficile. 130 matched cddid_all.tbl CDD NF041543 NF041543 469428 XopA_Hpa1 XopA/Hpa1 family type III secretion system protein. 131 matched cddid_all.tbl CDD NF041544 NF041544 469429 ParC ParC family partition-associated protein. 80 matched cddid_all.tbl CDD NF041545 NF041545 469430 GrdB_like_no_Se GrdB-related putative oxidoreductase. Members of this family are not selenoproteins, but are homologs to the N-terminal domain of GrdB, a selenoprotein subunit in the glycine reductase complex. Members of this family are found in a different context, not near other glycine reductase subunits. 171 matched cddid_all.tbl CDD NF041546 NF041546 469431 ParA_partition ParA family partition ATPase. 202 matched cddid_all.tbl CDD NF041547 NF041547 469432 GntR_LSA1692 GntR family transcriptional regulator, LSA1692 subfamily. 233 matched cddid_all.tbl CDD NF041548 NF041548 469433 PssE PssE/Cps14G family polysaccharide biosynthesis glycosyltransferase. 146 matched cddid_all.tbl CDD NF041549 NF041549 469434 PssD PssD/Cps14F family polysaccharide biosynthesis glycosyltransferase. 151 matched cddid_all.tbl CDD NF041550 NF041550 469435 CesT_sub type III secretion system chaperone. 143 matched cddid_all.tbl CDD NF041551 NF041551 469436 YlcI_YnfO_N YlcI/YnfO family protein. The seed alignment of this HMM (86 proteins after non-redundification to a maximum 80 percent amino acid identity) represents are a large expansion relative to PF13132.9 (3 proteins), named DUF3950. Members are small bacterial proteins, often from prophage regions. This model is short (42 amino acids), which high sequence diversity among seed members, and has relatively high cutoffs for its length. Some family members and additional apparent homologs scoring below the current cutoffs of the model include putative DNA-binding proteins such as HicB family antitoxin components of type II toxin-antitoxin systems. 42 matched cddid_all.tbl CDD NF041552 NF041552 469437 TF_PrdR sigma-54 dependent transcriptional regulator PrdR. 577 matched cddid_all.tbl CDD NF041553 NF041553 469438 CBO2463_dom CBO2463/CBO2479 domain. This domain occurs in proteins encoded typically between known subunits of the selenocysteine-containing D-proline reductase complex, a key contributor to Stickland metabolism. In Stickland metabolism, amino acids proline or glycine, or certain other compounds such as betaine or sarcosine, can be reduced, enabling energy-generating oxidation of various substrates such as other amino acids. Some members of this protein family have two copies of this domain. 60 matched cddid_all.tbl CDD NF041554 NF041554 469439 SA1362_fam SA1362 family protein. Members of this family include SA1362 from Staphylococcus aureus. The N-terminal 50 amino acids are highly hydrophobic and suggest two transmembrane alpha-helical regions. The C-terminal region rich in basic residues, variable in length, and often somewhat repetitive. The family is widespread in Gram-positive species. 70 matched cddid_all.tbl CDD NF041555 NF041555 469440 tannase_A subtype A tannase. 617 matched cddid_all.tbl CDD NF041556 NF041556 469441 tannase_B subtype B tannase. 461 matched cddid_all.tbl CDD NF041557 NF041557 469442 AmoA_BACT bacterial ammonia monooxygenase, subunit AmoA. 234 matched cddid_all.tbl CDD NF041558 NF041558 469443 NosP nitric oxide-sensing protein NosP. 368 matched cddid_all.tbl CDD NF041559 NF041559 469444 BTH_I2691_fam T6SS effector BTH_I2691 family protein. 848 matched cddid_all.tbl CDD NF041560 NF041560 469445 T6SS_Burk_ExIF putative type VI secretion system effector, ExIF family. Members of this family are found typically in type VI secretion system (T6SS) regions of Burkholderia, Paraburkholderia, Acinetobacter, and related lineages, and may be effector proteins. The family is provisionally named ExIF after a motif well conserved across most family members. 233 matched cddid_all.tbl CDD NF041561 NF041561 469446 PraA alkane oxidation protein activator PraA. 166 matched cddid_all.tbl CDD NF041562 NF041562 469447 PraB alkane oxidation protein activator PraB. 163 matched cddid_all.tbl CDD NF041563 NF041563 469448 amorph_syn (-)-alpha-amorphene synthase. 304 matched cddid_all.tbl CDD NF041564 NF041564 469449 eudesmol_syn 7-epi-alpha-eudesmol synthase. 341 matched cddid_all.tbl CDD NF041565 NF041565 469450 selin_dien_syn selina-4(15),7(11)-diene synthase. 345 matched cddid_all.tbl CDD NF041566 NF041566 469451 branchenz_Thermus 1,4-alpha-glucan branching protein. 527 matched cddid_all.tbl CDD NF041567 NF041567 469452 mtaseRsmF_Thermus 16S rRNA (cytosine(1407)-C(5))-methyltransferase RsmF. 443 matched cddid_all.tbl CDD NF041568 NF041568 469453 Jag_EloR RNA-binding cell elongation regulator Jag/EloR. Members of this family are nucleic acid-binding proteins (RNA or single-stranded DNA) with a KH domain at the N-terminus, an R3H domain at the C-terminus, and additional regions of homology. The founding member of this family was JAG (spoIIIJ Associated Gene) from Bacillus subtilis, but later work in other lineages, such as Streptococcus pneumoniae, as established a role in controlling cell elongation and the operation of the elongasome. The S. pneumoniae protein, a protein that undergoes regulatory phosphorylation and dephosphorylation, is also called RNA-binding cell elongation regulator EloR, and also KhpB. 203 matched cddid_all.tbl CDD NF041569 NF041569 469454 A-tRNAntase A-adding tRNA nucleotidyltransferase. 880 matched cddid_all.tbl CDD NF041570 NF041570 469455 acyltasePE acyltransferase PE. 354 matched cddid_all.tbl CDD NF041571 NF041571 469456 alkn_up_AupA alkane uptake protein AupA. 444 matched cddid_all.tbl CDD NF041572 NF041572 469457 rhamnosid_Flavobac alpha-L-rhamnosidase. 946 matched cddid_all.tbl CDD NF041573 NF041573 469458 rhamnosid_Stmyc alpha-L-rhamnosidase. 1028 matched cddid_all.tbl CDD NF041574 NF041574 469459 antitoxPezT_Strep type II toxin-antitoxin system toxin PezT. 251 matched cddid_all.tbl CDD NF041575 NF041575 469460 antitoxPezA_Strep type II toxin-antitoxin system antitoxin PezA. 158 matched cddid_all.tbl CDD NF041576 NF041576 469461 bacphytchrmBphP bacteriophytochrome BphP. 622 matched cddid_all.tbl CDD NF041577 NF041577 469462 nside_bi_sphtase 3',5'-nucleoside bisphosphate phosphatase. 276 matched cddid_all.tbl CDD NF041578 NF041578 469463 betaarabinsidaseHypBA2 beta-L-arabinobiosidase HypBA2. 1708 matched cddid_all.tbl CDD NF041579 NF041579 469464 betaxyl_Flavo beta-xylosidase. 716 matched cddid_all.tbl CDD NF041580 NF041580 469465 DidA DNA damage-induced SOS-independent cell division inhibitor A. 73 matched cddid_all.tbl CDD NF041581 NF041581 469466 SosA DNA damage-induced cell division inhibitor SosA. 77 matched cddid_all.tbl CDD NF041582 NF041582 469467 malolactic malolactic enzyme. Malolactic enzyme converts L-malate anaerobically to L-lactate and carbon dioxide. 536 matched cddid_all.tbl CDD NF041583 NF041583 469468 SOS_SulA_aeru SOS-induced cell division inhibitor SulA, Pseudomonas type. SulA, as found in Pseudomonas aeruginosa, is a cell division inhibitor induced by the SOS response. It interacts with FtsZ to halt cell division. SulA proteins, like FtsZ, differ greatly by lineage; SulA of Escherichia coli is architecturally somewhat different and is described by a different model, TIGR00623. 157 matched cddid_all.tbl CDD NF041584 NF041584 469469 MqnP_SCO4491 menaquinone biosynthesis prenyltransferase MqnP, SCO4491 family. This model is one of three built to describe UbiA-like prenyltransferases thought to be menaquinone biosynthesis prenyltransferase MqnP. This family contains the founding protein SCO4491. 285 matched cddid_all.tbl CDD NF041585 NF041585 469470 MqnP_Cj_Hp menaquinone biosynthesis prenyltransferase MqnP, HP1360 family. 281 matched cddid_all.tbl CDD NF041586 NF041586 469471 MqnP_DT menaquinone biosynthesis prenyltransferase MqnP, Deinococcus/Thermus-type. 277 matched cddid_all.tbl CDD NF041587 NF041587 469472 YmgF cell division-associated protein YmgF. 72 matched cddid_all.tbl CDD NF041588 NF041588 469473 AQJ64_40280_fam AQJ64_40280 family protein. Members of this family occur almost exclusively in the genus Streptomyces. The function is unknown. Some members, such as AQJ64_40280 (KUN75916.1) for which we name the family, previously were annotated as amine oxidase, but the source of that annotation could not be traced during model construction. 116 matched cddid_all.tbl CDD NF041589 NF041589 469474 PepG1 type I toxin-antitoxin system toxin PepG1. 46 matched cddid_all.tbl CDD NF041591 NF041591 469475 CxxC_VVA0879 VVA0879 family protein. Members of this rare but broadly distributed family average about 120 amino acids in length, including an apparent redox-active disulfide motif CxxC and two other invariant Cys residues. The family is named for VVA0879 from Vibrio vulnificus but occurs also in Gram-positive species such as Clostridium botulinum. 100 matched cddid_all.tbl CDD NF041592 NF041592 469476 carboxyl_red carboxylic acid reductase. 1161 matched cddid_all.tbl CDD NF041593 NF041593 469477 histid_kinase_PdhS cell-division control histidine kinase PdhS. 1038 matched cddid_all.tbl CDD NF041594 NF041594 469478 dam_ctlPhtase_Archglob damage-control phosphatase. 287 matched cddid_all.tbl CDD NF041595 NF041595 469479 dap_A_syn_DdaF dapdiamide A synthase. 424 matched cddid_all.tbl CDD NF041596 NF041596 469480 fum_diaprop_lig_DdaG fumarate--(S)-2,3-diaminopropanoate ligase. 390 matched cddid_all.tbl CDD NF041597 NF041597 469481 T3SS_coreg_PtrC type III secretion system co-regulatory protein PtrC. PtrC (Pseudomonas type III repressor gene C), represented by locus PA2486 in Pseudomonas aeruginosa PAO1, is a small protein, typically around 64 amino acids, rich in charged residues. Overexpression represses T3SS expression, although the mechanism is not described and may depend on protein-protein interaction rather than direct interaction with DNA. 52 matched cddid_all.tbl CDD NF041598 NF041598 469482 small_PA2485 PA2485 family small membrane protein. Members of this family are small, uncharacterized, N-terminally hydrophobic proteins, 37 to 39 amino acids in length, regularly found encoded next the small regulatory protein PtrC (NF041597 ) in species of Pseudomonas. The family is named for Pseudomonas aeruginosa PAO1 protein PA2485, which originally was predicted to be longer. 37 matched cddid_all.tbl CDD NF041599 NF041599 469483 reg_PtrA_PA2808 co-regulatory protein PtrA N-terminal domain. This HMM describes a shared N-terminal region of several families of proteins, some of which contain a C-terminal DUF2790 (PF10976) domain. The founding member of this family, PA2808 of Pseudomonas aeruginosa PAO1, was found to suppress expression of the type III secretion system (T3SS) via a protein-protein interaction with the T3SS transcriptional activator ExsA. It was named PtrA (Pseudomonas type III repressor A). Homologs are found broadly throughout the Pseudomonas genus. 46 matched cddid_all.tbl CDD NF041600 NF041600 469484 cyt_ox_CcoM cytochrome c oxidase subunit CcoM. 34 matched cddid_all.tbl CDD NF041601 NF041601 469485 PA5502_lipo PA5502 family lipoprotein. 237 matched cddid_all.tbl CDD NF041602 NF041602 469486 VF_A0006_fam VF_A0006 family four-cysteine protein. Members of this family, including VF_A0006 of Vibrio fischeri, PSPA7_2531 of Pseudomonas aeruginosa, and BPSL3341 from Burkholderia pseudomallei, have an N-terminal signal peptide and four invariant Cys residues suggesting the formation of two disulfide bonds. The function is unknown. 89 matched cddid_all.tbl CDD NF041603 NF041603 469487 Cys_rich_47 PSPA7_2676 family Cys-rich small protein. Members of this family are small proteins, averaging 47 amino acids in length with four invariant Cys residues (two in a CxxC motif) and typically six overall. The richness in Cys residues, as in the motif CxCCxxC motif found in many members, suggests metal-binding activity. 39 matched cddid_all.tbl CDD NF041604 NF041604 469488 CSP_NTE_dom cold shock protein N-terminal extension domain. Members of this family have a C-terminal cold shock domain, but also a longer, hydrophobic N-terminal domain. Members are found primarily in the genus Pseudomonas, including in P. aeruginosa. 112 matched cddid_all.tbl CDD NF041605 NF041605 469489 gln_syn_GlnII glutamine synthetase GlnII. 333 matched cddid_all.tbl CDD NF041606 NF041606 469490 dguan_cyc_DgcA diguanylate cyclase DgcA. 340 matched cddid_all.tbl CDD NF041607 NF041607 469491 dimeth_corrin_MtbC dimethylamine corrinoid protein MtbC. 203 matched cddid_all.tbl CDD NF041608 NF041608 469492 methylcob_mtaseMtbA methylcobamide:CoM methyltransferase MtbA. 339 matched cddid_all.tbl CDD NF041609 NF041609 469493 esterase_EstP esterase EstP. 640 matched cddid_all.tbl CDD NF041610 NF041610 469494 alph_arabinopyran exo-alpha-(1->6)-L-arabinopyranosidase. 738 matched cddid_all.tbl CDD NF041611 NF041611 469495 exoglucan_CbhB exoglucanase CbhB. 994 matched cddid_all.tbl CDD NF041612 NF041612 469496 fdxn_Clost 2Fe-2S ferredoxin. 102 matched cddid_all.tbl CDD NF041613 NF041613 469497 fdxn_Azotob 2Fe-2S ferredoxin. 107 matched cddid_all.tbl CDD NF041614 NF041614 469498 FeSrepair_DnrN iron-sulfur cluster repair protein DnrN. 157 matched cddid_all.tbl CDD NF041615 NF041615 469499 Feoxidase_Iro iron oxidase. 90 matched cddid_all.tbl CDD NF041616 NF041616 469500 T2SS_C_SYNERG type II secretion system protein GspC, SYNERG-CTERM-associated variant. This HMM describes the GspC subunit of a rare variant form of type II secretion system (T2SS) found exclusively in the Synergistota, with the SYNERG-CTERM protein-sorting system. SYNERG-CTERM is a C-terminal sorting signal with an invariant Cys residue in its signature domain. The sorting enzyme for SYNERG-CTERM proteins, MrtS (myxosortase S), is a homolog of the MYXO-CTERM-processing enzyme MrtX and of the eukaryotic CAAX prenyl protease Rce1. SYNERG-CTERM proteins are predicted to become surface-anchored by a lipid group attached to a C-terminal Cys sidechain. 296 matched cddid_all.tbl CDD NF041617 NF041617 469501 T2SS_L_SYNERG type II secretion system protein GspL, SYNERG-CTERM-associated variant. This HMM describes the GspL subunit of a rare variant form of type II secretion system (T2SS) found exclusively in the Synergistota, with the SYNERG-CTERM protein-sorting system. SYNERG-CTERM is a C-terminal sorting signal with an invariant Cys residue in its signature domain. The sorting enzyme for SYNERG-CTERM proteins, MrtS (myxosortase S), is a homolog of the MYXO-CTERM-processing enzyme MrtX and of the eukaryotic CAAX prenyl protease Rce1. SYNERG-CTERM proteins are predicted to become surface-anchored by a lipid group attached to a C-terminal Cys sidechain. 387 matched cddid_all.tbl CDD NF041618 NF041618 469502 T2SS_M_SYNERG type II secretion system protein GspM, SYNERG-CTERM-associated variant. This HMM describes the GspM subunit of a rare variant form of type II secretion system (T2SS) found exclusively in the Synergistota, with the SYNERG-CTERM protein-sorting system. SYNERG-CTERM is a C-terminal sorting signal with an invariant Cys residue in its signature domain. The sorting enzyme for SYNERG-CTERM proteins, MrtS (myxosortase S), is a homolog of the MYXO-CTERM-processing enzyme MrtX and of the eukaryotic CAAX prenyl protease Rce1. SYNERG-CTERM proteins are predicted to become surface-anchored by a lipid group attached to a C-terminal Cys sidechain. 157 matched cddid_all.tbl CDD NF041619 NF041619 469503 T2SS_N_SYNERG type II secretion system protein GspN, SYNERG-CTERM-associated variant. This HMM describes the GspN subunit of a rare variant form of type II secretion system (T2SS) found exclusively in the Synergistota, with the SYNERG-CTERM protein-sorting system. SYNERG-CTERM is a C-terminal sorting signal with an invariant Cys residue in its signature domain. The sorting enzyme for SYNERG-CTERM proteins, MrtS (myxosortase S), is a homolog of the MYXO-CTERM-processing enzyme MrtX and of the eukaryotic CAAX prenyl protease Rce1. SYNERG-CTERM proteins are predicted to become surface-anchored by a lipid group attached to a C-terminal Cys sidechain. 194 matched cddid_all.tbl CDD NF041620 NF041620 469504 MXAN_5187_fam MXAN_5187 family protein. 597 matched cddid_all.tbl CDD NF041621 NF041621 469505 MXAN_5187_C_dom MXAN_5187 C-terminal domain. This domain occurs at the C-terminus of MXAN_5187 from Myxococcus xanthus. Member proteins, most of which belong to Myxococcales branch of the Deltaproteobacteria, can have very different architectures outside of this domain. 70 matched cddid_all.tbl CDD NF041622 NF041622 469506 KwaA anti-phage protein KwaA. 182 matched cddid_all.tbl CDD NF041623 NF041623 469507 KwaB anti-phage protein KwaB. 306 matched cddid_all.tbl CDD NF041624 NF041624 469508 isoafr_syn isoafricanol synthase. 351 matched cddid_all.tbl CDD NF041625 NF041625 469509 methfumCoahyd_Halo 2-methylfumaryl-CoA hydratase. 358 matched cddid_all.tbl CDD NF041626 NF041626 469510 malyCoAlyase_Halo L-malyl-CoA/beta-methylmalyl-CoA lyase. 339 matched cddid_all.tbl CDD NF041627 NF041627 469511 NaLiK_antip_UmpA Na,Li,K/H(+) antiporter subunit UmpA. 243 matched cddid_all.tbl CDD NF041628 NF041628 469512 NaLiK_antip_UmpB Na,Li,K/H(+) antiporter subunit UmpB. 252 matched cddid_all.tbl CDD NF041629 NF041629 469513 anti_IS1548_end IS1548 end spurious translation. 27 matched cddid_all.tbl CDD NF041630 NF041630 469514 CBS_CbpB cyclic-di-AMP-binding protein CbpB. CbpB (c-di-AMP-binding protein B) has two CBS (cystathionine beta synthase) domains (see PF00571). When levels of c-di-AMP are low, CbpB activates RelA, a bifunctional (p)ppGpp synthetase/hydrolase. 143 matched cddid_all.tbl CDD NF041631 NF041631 469515 KRQAASG_repeat KRQAASG repeat spurious translation. This AntiFam-like HMM describes spurious translations from an intergenic repeat common in Burkholderia. 21 matched cddid_all.tbl CDD NF041633 NF041633 469516 trifunc_aldol KHG/KDPG aldolase/sugar kinase fusion protein. The N-terminal region of this protein resembles the bifunctional KHG/KDPG aldolase (4.1.2.14 and 4.1.3.16), while the C-terminal region resembles 2-dehydro-3-deoxygluconokinase and 2-dehydro-3-deoxygalactonokinase. 577 matched cddid_all.tbl CDD NF041634 NF041634 469517 HAEPLYID HAEPLYID family protein. This family is named for start of a long and nearly invariant motif near the protein N-terminus. Many members of this family previously carried an untraceable and probably incorrect annotation as phosphoribosylformylglycinamidine synthase. 268 matched cddid_all.tbl CDD NF041635 NF041635 469518 STM3941_fam STM3941 family protein. 157 matched cddid_all.tbl CDD NF041636 NF041636 469519 slam_lipo Slam-dependent surface lipoprotein. 155 matched cddid_all.tbl CDD NF041637 NF041637 469520 FGAM_small_mem phosphoribosylformylglycinamidine synthase-associated small membrane protein. This small protein averages less than 40 amino acids, nearly all of which, for the last 30, are hydrophobic and suggest integration into membrane. Members are regularly found encoded between or next to PurS and PurQ subunits of phosphoribosylformylglycinamidine synthase. The family appears to occur only in the Hyphomicrobiales, a branch of the Alphaproteobacteria. 33 matched cddid_all.tbl CDD NF041638 NF041638 469521 QRL_CxxC_CxxC RRQRL motif-containing zinc-binding protein. Members of this family, found in multiple species of Streptomyces, are judged by be zinc-binding by the pair of CxxC motifs in the C-terminal region. The family is named for a near-invariant QRL motif (usually RRQRL) closer to the N-terminus. 98 matched cddid_all.tbl CDD NF041639 NF041639 469522 YicS_fam YicS family protein. Members of the YicS protein family, found in Escherichia coli and related species, average 100 amino acids in size, with a signal peptide and two widely spaced invariant Cys residues. 96 matched cddid_all.tbl CDD NF041640 NF041640 469523 AmoB_BACT bacterial ammonia monooxygenase, subunit AmoB. 409 matched cddid_all.tbl CDD NF041641 NF041641 469524 AmoC_BACT bacterial ammonia monooxygenase, subunit AmoC. 250 matched cddid_all.tbl CDD NF041642 NF041642 469525 RAxF_45 RAxF-45 family protein. Members of this family of small proteins are found broadly within the order Bacillales. The family is named for its best conserved motif, a nearly invariant RAxF motif, and its small size, about 45 amino acids in length. 39 matched cddid_all.tbl CDD NF041644 NF041644 469526 CBO0543_fam CBO0543 family protein. This family is named for an uncharacterized founding protein from Clostridium botulinum. The family is rather hydrophobic, about 165 amino acids in length, and found in genera such as Bacillus, Paenibacillus, Desulfosporosinus, and Weizmannia. The function is unknown. 116 matched cddid_all.tbl CDD NF041645 NF041645 469527 prot_kin_PA4780 PA4780 family RIO1-like protein kinase. Members of this family are putative serine/threonine-protein kinases, closely related to founding member PA4780 from Pseudomonas aeruginosa PAO1, which was shown to be upregulated by and important for the biodegradation of phenanthrene and naphthalene. Members belong more generally to the RIO1 atypical kinase family (see PF01163). 274 matched cddid_all.tbl CDD NF041646 NF041646 469528 VC0807_fam VC0807 family protein. Members of this broadly distributed bacterial protein family are hydrophobic in nature, and apparently homologous to members of the DUF3159 (PF11361) family. 189 matched cddid_all.tbl CDD NF041647 NF041647 469529 ABC_perm_CPBP ABC transporter permease subunit/CPBP intramembrane protease. The C-terminal region of this ABC transporter permease contains a CPBP family glutamic-type intramembrane protease domain, related to the eukaryotic type 2 CAAX prenyl protease Rce1. 641 matched cddid_all.tbl CDD NF041648 NF041648 469530 spore_exo_CotA CotA family spore coat protein. CotA, as the term is used in Clostridium difficile, is a spore coat protein also reportedly detected also in exosporium. Homologs are found in a number of related endospore-forming bacteria. 214 matched cddid_all.tbl CDD NF041649 NF041649 469531 ceramidase_neut neutral ceramidase. 636 matched cddid_all.tbl CDD NF041650 NF041650 469532 nod_mtase_NodS nodulation methyltransferase NodS. 190 matched cddid_all.tbl CDD NF041651 NF041651 469533 nodul_NodU nodulation protein NodU. 556 matched cddid_all.tbl CDD NF041652 NF041652 469534 Nud_hyd_Dein Nudix hydrolase. 152 matched cddid_all.tbl CDD NF041653 NF041653 469535 Nud_hyd_Meth Nudix hydrolase. 170 matched cddid_all.tbl CDD NF041654 NF041654 469536 GlcNAcase beta-N-acetylglucosaminidase. 733 matched cddid_all.tbl CDD NF041655 NF041655 469537 MM0924_fam MM0924 family protein. Members of this family occur in both archaea and bacteria, and share some sequence homology with the domain DUF2642 (PF10842). 57 matched cddid_all.tbl CDD NF041656 NF041656 469538 CPBP_MmRce1 MmRce1 family CPBP family CAAX prenyl protease. MmRce1, an archaeal member of the same family CPBP integral membrane glutamic-type protease as the eukaryotic type II CAAX prenyl endopeptidase Rce1 (Ras and a-factor converting enzyme 1), was crystalized and studied to gain insights into Rce1 function. It was shown to act as an endopeptidase on the eukaryotic protein-derived synthetic substrate ARSGAKASGCLVS, only if Cys residue is farnesylated. This model substrate ends with a CAAX motif (Cys-Aliphatic-Aliphatic-Anything). 271 matched cddid_all.tbl CDD NF041657 NF041657 469539 ompB_ricketsia outer membrane protein OmpB. 1655 matched cddid_all.tbl CDD NF041658 NF041658 469540 ornithlipidmtase_OlsG ornithine lipid N-methyltransferase. 191 matched cddid_all.tbl CDD NF041659 NF041659 469541 Papain_Inhib cysteine/serine endopeptidase inhibitor. 130 matched cddid_all.tbl CDD NF041660 NF041660 469542 oxygluDhInhib_OdhI oxoglutarate dehydrogenase inhibitor Odhl. 141 matched cddid_all.tbl CDD NF041661 NF041661 469543 Cycl_ph_dihydrol phosphoribosyl 1,2-cyclic phosphate 1,2-diphosphodiesterase. 259 matched cddid_all.tbl CDD NF041662 NF041662 469544 ampC_Kaer CMY2-MIR-ACT-EC family cephalosporin-hydrolyzing class C beta-lactamase. This narrowly defined subfamily of AmpC class C beta-lactamases covers chromosomal ly encoded proteins apparently restricted to and universal in Klebsiella (previously Enterobacter) aerogenes. Strains encoding this enzyme tend to be resistant to penicillins and first and second generation cephalosporins. 381 matched cddid_all.tbl CDD NF041663 NF041663 469545 ampC_Sliq cephalosporin-hydrolyzing class C beta-lactamase. 378 matched cddid_all.tbl CDD NF041664 NF041664 469546 RNAP_arch_Epp archaeal transcription elongation factor subunit Spt4. Spt4, an archaeal zinc-binding protein, averaging about 64 amino acids in length, forms a heterodimer with Spt5. The Spt4/5 heterodimer is now considered a transcription elongation factor, responsible for making the archaeal DNA-directed RNA polymerase (RNAP) processive. Previously, Spt4 was treated as a part of the RNAP itself and was designated subnit E''. 57 matched cddid_all.tbl CDD NF041665 NF041665 469547 blaPSZ PSZ family class C beta-lactamase. 379 matched cddid_all.tbl CDD NF041666 NF041666 469548 ampC_Ecan CMY2-MIR-ACT-EC family cephalosporin-hydrolyzing class C beta-lactamase. This HMM identifies a small subset of chromosomal class C beta-lactamases (AmpC) typical of Enterobacter cancerogenus. 381 matched cddid_all.tbl CDD NF041667 NF041667 469549 GvpU gas vesicle accessory protein GvpU. 117 matched cddid_all.tbl CDD NF041668 NF041668 469550 trim_DfrL trimethoprim-resistant dihydrofolate reductase DfrL. 176 matched cddid_all.tbl CDD NF041669 NF041669 469551 GvpT GvpT/GvpP family gas vesicle accessory protein. 122 matched cddid_all.tbl CDD NF041670 NF041670 469552 GvpQ gas vesicle protein GvpQ. 137 matched cddid_all.tbl CDD NF041671 NF041671 469553 peri_hyde_PaoC aldehyde oxidoreductase molybdenum-binding subunit PaoC. PaoC is the molybdopterin-cytosine-dinucleotide cofactor-binding subunit of the periplasmic aldehyde oxidoreductase PaoABC. The enzyme is known formally as carboxylate reductase (EC 1.2.99.6). 735 matched cddid_all.tbl CDD NF041672 NF041672 469554 ADPriboarghdlase ADP-ribosylarginine hydrolase Tri1. 360 matched cddid_all.tbl CDD NF041673 NF041673 469555 transregRamA acetate metabolism transcriptional regulator RamA. 280 matched cddid_all.tbl CDD NF041674 NF041674 469556 RNA-bind_Rsr RNA-binding protein Rsr. 531 matched cddid_all.tbl CDD NF041675 NF041675 469557 sarc_dimgly_mtase sarcosine/dimethylglycine N-methyltransferase. 278 matched cddid_all.tbl CDD PHA00002 PHA00002 222768 A DNA replication initiation protein gpA 515 matched cddid_all.tbl CDD PHA00003 PHA00003 222769 B internal scaffolding protein 120 matched cddid_all.tbl CDD PHA00006 PHA00006 164773 D external scaffolding protein 151 matched cddid_all.tbl CDD PHA00007 PHA00007 164774 E cell lysis protein 91 matched cddid_all.tbl CDD PHA00008 PHA00008 222770 J DNA packaging protein 25 matched cddid_all.tbl CDD PHA00009 PHA00009 164775 F capsid protein 427 matched cddid_all.tbl CDD PHA00010 PHA00010 164776 G major spike protein 179 matched cddid_all.tbl CDD PHA00012 PHA00012 222771 I assembly protein 361 matched cddid_all.tbl CDD PHA00019 PHA00019 222772 IV phage assembly protein 428 matched cddid_all.tbl CDD PHA00022 PHA00022 164777 VII minor coat protein 28 matched cddid_all.tbl CDD PHA00024 PHA00024 106880 IX minor coat protein 33 matched cddid_all.tbl CDD PHA00025 PHA00025 222773 VIII major coat protein 76 matched cddid_all.tbl CDD PHA00026 PHA00026 133846 cp coat protein 129 matched cddid_all.tbl CDD PHA00027 PHA00027 133847 lys lysis protein 58 matched cddid_all.tbl CDD PHA00028 PHA00028 222774 rep RNA replicase, beta subunit 561 matched cddid_all.tbl CDD PHA00080 PHA00080 222775 PHA00080 DksA-like zinc finger domain containing protein 72 matched cddid_all.tbl CDD PHA00094 PHA00094 106886 VI minor coat protein 112 matched cddid_all.tbl CDD PHA00097 PHA00097 164779 K protein K 56 matched cddid_all.tbl CDD PHA00098 PHA00098 222776 PHA00098 hypothetical protein 112 matched cddid_all.tbl CDD PHA00099 PHA00099 164781 PHA00099 minor capsid protein 147 matched cddid_all.tbl CDD PHA00101 PHA00101 177266 PHA00101 internal virion protein B 194 matched cddid_all.tbl CDD PHA00144 PHA00144 222777 PHA00144 major head protein 438 matched cddid_all.tbl CDD PHA00147 PHA00147 133855 PHA00147 upper collar protein 308 matched cddid_all.tbl CDD PHA00148 PHA00148 222778 PHA00148 lower collar protein 242 matched cddid_all.tbl CDD PHA00149 PHA00149 222779 PHA00149 DNA encapsidation protein 331 matched cddid_all.tbl CDD PHA00159 PHA00159 177267 PHA00159 endonuclease I 148 matched cddid_all.tbl CDD PHA00198 PHA00198 222780 PHA00198 nonstructural protein 86 matched cddid_all.tbl CDD PHA00201 PHA00201 177268 PHA00201 major capsid protein 343 matched cddid_all.tbl CDD PHA00202 PHA00202 164786 PHA00202 DNA replication initiation protein 388 matched cddid_all.tbl CDD PHA00212 PHA00212 164787 PHA00212 putative transcription regulator 63 matched cddid_all.tbl CDD PHA00276 PHA00276 222781 PHA00276 phage lambda Rz-like lysis protein 144 matched cddid_all.tbl CDD PHA00280 PHA00280 106901 PHA00280 putative NHN endonuclease 121 matched cddid_all.tbl CDD PHA00327 PHA00327 164789 PHA00327 minor capsid protein 187 matched cddid_all.tbl CDD PHA00330 PHA00330 222782 PHA00330 putative replication initiation protein 316 matched cddid_all.tbl CDD PHA00350 PHA00350 222783 PHA00350 putative assembly protein 399 matched cddid_all.tbl CDD PHA00360 PHA00360 177271 II replication initiation protein 421 matched cddid_all.tbl CDD PHA00363 PHA00363 222784 PHA00363 major capsid protein 557 matched cddid_all.tbl CDD PHA00368 PHA00368 222785 PHA00368 internal virion protein D 1315 matched cddid_all.tbl CDD PHA00369 PHA00369 164794 H minor spike protein 325 matched cddid_all.tbl CDD PHA00370 PHA00370 164795 III attachment protein 297 matched cddid_all.tbl CDD PHA00371 PHA00371 222786 mat maturation protein 418 matched cddid_all.tbl CDD PHA00380 PHA00380 133872 PHA00380 tail protein 599 matched cddid_all.tbl CDD PHA00404 PHA00404 164796 PHA00404 hypothetical protein 42 matched cddid_all.tbl CDD PHA00405 PHA00405 222787 PHA00405 hypothetical protein 85 matched cddid_all.tbl CDD PHA00406 PHA00406 164797 PHA00406 hypothetical protein 48 matched cddid_all.tbl CDD PHA00407 PHA00407 164798 PHA00407 phage lambda Rz1-like protein 84 matched cddid_all.tbl CDD PHA00415 PHA00415 222788 25 baseplate wedge subunit 131 matched cddid_all.tbl CDD PHA00422 PHA00422 133878 PHA00422 hypothetical protein 69 matched cddid_all.tbl CDD PHA00425 PHA00425 164800 PHA00425 DNA packaging protein, small subunit 88 matched cddid_all.tbl CDD PHA00426 PHA00426 164801 PHA00426 type II holin 67 matched cddid_all.tbl CDD PHA00428 PHA00428 222789 PHA00428 tail tubular protein A 193 matched cddid_all.tbl CDD PHA00430 PHA00430 222790 PHA00430 tail fiber protein 568 matched cddid_all.tbl CDD PHA00431 PHA00431 222791 PHA00431 internal virion protein C 746 matched cddid_all.tbl CDD PHA00432 PHA00432 177277 PHA00432 internal virion protein A 137 matched cddid_all.tbl CDD PHA00435 PHA00435 222792 PHA00435 capsid assembly protein 306 matched cddid_all.tbl CDD PHA00437 PHA00437 222793 PHA00437 tail assembly protein 94 matched cddid_all.tbl CDD PHA00438 PHA00438 133887 PHA00438 hypothetical protein 81 matched cddid_all.tbl CDD PHA00439 PHA00439 222794 PHA00439 exonuclease 286 matched cddid_all.tbl CDD PHA00440 PHA00440 133889 PHA00440 host protein H-NS-interacting protein 98 matched cddid_all.tbl CDD PHA00441 PHA00441 222795 PHA00441 hypothetical protein 89 matched cddid_all.tbl CDD PHA00442 PHA00442 222796 PHA00442 host recBCD nuclease inhibitor 59 matched cddid_all.tbl CDD PHA00446 PHA00446 177281 PHA00446 hypothetical protein 89 matched cddid_all.tbl CDD PHA00447 PHA00447 177282 PHA00447 lysozyme 142 matched cddid_all.tbl CDD PHA00448 PHA00448 133894 PHA00448 hypothetical protein 70 matched cddid_all.tbl CDD PHA00450 PHA00450 164812 PHA00450 host dGTPase inhibitor 85 matched cddid_all.tbl CDD PHA00451 PHA00451 177283 PHA00451 protein kinase 362 matched cddid_all.tbl CDD PHA00452 PHA00452 222797 PHA00452 T3/T7-like RNA polymerase 807 matched cddid_all.tbl CDD PHA00453 PHA00453 164815 PHA00453 hypothetical protein 41 matched cddid_all.tbl CDD PHA00454 PHA00454 222798 PHA00454 ATP-dependent DNA ligase 315 matched cddid_all.tbl CDD PHA00455 PHA00455 133900 PHA00455 hypothetical protein 85 matched cddid_all.tbl CDD PHA00456 PHA00456 164817 PHA00456 hypothetical protein 34 matched cddid_all.tbl CDD PHA00457 PHA00457 222799 PHA00457 inhibitor of host bacterial RNA polymerase 63 matched cddid_all.tbl CDD PHA00458 PHA00458 222800 PHA00458 single-stranded DNA-binding protein 233 matched cddid_all.tbl CDD PHA00476 PHA00476 222801 PHA00476 hypothetical protein 110 matched cddid_all.tbl CDD PHA00489 PHA00489 133905 PHA00489 scaffolding protein 101 matched cddid_all.tbl CDD PHA00490 PHA00490 133906 PHA00490 terminal protein 266 matched cddid_all.tbl CDD PHA00497 PHA00497 222802 pol RNA-dependent RNA polymerase 673 matched cddid_all.tbl CDD PHA00510 PHA00510 133907 PHA00510 transcriptional regulator 125 matched cddid_all.tbl CDD PHA00514 PHA00514 222803 PHA00514 dsDNA binding protein 98 matched cddid_all.tbl CDD PHA00515 PHA00515 133909 PHA00515 hypothetical protein 53 matched cddid_all.tbl CDD PHA00520 PHA00520 222804 PHA00520 packaging NTPase P4 330 matched cddid_all.tbl CDD PHA00527 PHA00527 222805 PHA00527 hypothetical protein 129 matched cddid_all.tbl CDD PHA00540 PHA00540 133910 PHA00540 hypothetical protein 715 matched cddid_all.tbl CDD PHA00542 PHA00542 106954 PHA00542 putative Cro-like protein 82 matched cddid_all.tbl CDD PHA00547 PHA00547 164822 PHA00547 hypothetical protein 337 matched cddid_all.tbl CDD PHA00616 PHA00616 177288 PHA00616 hypothetical protein 44 matched cddid_all.tbl CDD PHA00617 PHA00617 177289 PHA00617 ribbon-helix-helix domain containing protein 80 matched cddid_all.tbl CDD PHA00619 PHA00619 177290 PHA00619 CRISPR-associated Cas4-like protein 201 matched cddid_all.tbl CDD PHA00626 PHA00626 106959 PHA00626 hypothetical protein 59 matched cddid_all.tbl CDD PHA00645 PHA00645 222806 PHA00645 hypothetical protein 125 matched cddid_all.tbl CDD PHA00646 PHA00646 133916 PHA00646 hypothetical protein 65 matched cddid_all.tbl CDD PHA00649 PHA00649 106962 PHA00649 hypothetical protein 83 matched cddid_all.tbl CDD PHA00650 PHA00650 106963 PHA00650 hypothetical protein 82 matched cddid_all.tbl CDD PHA00652 PHA00652 106964 PHA00652 hypothetical protein 128 matched cddid_all.tbl CDD PHA00653 PHA00653 164824 mtd major tropism determinant 381 matched cddid_all.tbl CDD PHA00657 PHA00657 106966 PHA00657 crystallin beta/gamma motif-containing protein 2052 matched cddid_all.tbl CDD PHA00658 PHA00658 106967 PHA00658 putative lysin 720 matched cddid_all.tbl CDD PHA00660 PHA00660 133918 PHA00660 hypothetical protein 215 matched cddid_all.tbl CDD PHA00661 PHA00661 106970 PHA00661 hypothetical protein 734 matched cddid_all.tbl CDD PHA00662 PHA00662 222807 PHA00662 hypothetical protein 215 matched cddid_all.tbl CDD PHA00663 PHA00663 106972 PHA00663 hypothetical protein 68 matched cddid_all.tbl CDD PHA00664 PHA00664 106973 PHA00664 hypothetical protein 140 matched cddid_all.tbl CDD PHA00665 PHA00665 106974 PHA00665 major capsid protein 329 matched cddid_all.tbl CDD PHA00666 PHA00666 222808 PHA00666 putative protease 233 matched cddid_all.tbl CDD PHA00667 PHA00667 106976 PHA00667 hypothetical protein 158 matched cddid_all.tbl CDD PHA00669 PHA00669 222809 PHA00669 hypothetical protein 114 matched cddid_all.tbl CDD PHA00670 PHA00670 106978 PHA00670 hypothetical protein 540 matched cddid_all.tbl CDD PHA00671 PHA00671 106979 PHA00671 hypothetical protein 135 matched cddid_all.tbl CDD PHA00672 PHA00672 133920 PHA00672 hypothetical protein 152 matched cddid_all.tbl CDD PHA00673 PHA00673 106981 PHA00673 acetyltransferase domain containing protein 154 matched cddid_all.tbl CDD PHA00675 PHA00675 106982 PHA00675 hypothetical protein 78 matched cddid_all.tbl CDD PHA00676 PHA00676 106983 PHA00676 hypothetical protein 96 matched cddid_all.tbl CDD PHA00679 PHA00679 106984 PHA00679 hypothetical protein 71 matched cddid_all.tbl CDD PHA00680 PHA00680 106985 PHA00680 hypothetical protein 143 matched cddid_all.tbl CDD PHA00684 PHA00684 222810 PHA00684 hypothetical protein 128 matched cddid_all.tbl CDD PHA00687 PHA00687 106987 PHA00687 hypothetical protein 56 matched cddid_all.tbl CDD PHA00689 PHA00689 106988 PHA00689 hypothetical protein 62 matched cddid_all.tbl CDD PHA00691 PHA00691 106989 PHA00691 hypothetical protein 68 matched cddid_all.tbl CDD PHA00692 PHA00692 106990 PHA00692 hypothetical protein 74 matched cddid_all.tbl CDD PHA00724 PHA00724 222811 PHA00724 hypothetical protein 83 matched cddid_all.tbl CDD PHA00725 PHA00725 177293 PHA00725 hypothetical protein 81 matched cddid_all.tbl CDD PHA00726 PHA00726 177294 PHA00726 hypothetical protein 89 matched cddid_all.tbl CDD PHA00727 PHA00727 222812 PHA00727 hypothetical protein 278 matched cddid_all.tbl CDD PHA00728 PHA00728 177296 PHA00728 hypothetical protein 151 matched cddid_all.tbl CDD PHA00729 PHA00729 177297 PHA00729 NTP-binding motif containing protein 226 matched cddid_all.tbl CDD PHA00730 PHA00730 222813 int integrase 337 matched cddid_all.tbl CDD PHA00731 PHA00731 222814 PHA00731 hypothetical protein 96 matched cddid_all.tbl CDD PHA00732 PHA00732 177300 PHA00732 hypothetical protein 79 matched cddid_all.tbl CDD PHA00733 PHA00733 177301 PHA00733 hypothetical protein 128 matched cddid_all.tbl CDD PHA00734 PHA00734 177302 PHA00734 hypothetical protein 95 matched cddid_all.tbl CDD PHA00735 PHA00735 177303 PHA00735 hypothetical protein 808 matched cddid_all.tbl CDD PHA00736 PHA00736 177304 PHA00736 hypothetical protein 79 matched cddid_all.tbl CDD PHA00738 PHA00738 177305 PHA00738 putative HTH transcription regulator 108 matched cddid_all.tbl CDD PHA00739 PHA00739 177306 V3 structural protein VP3 92 matched cddid_all.tbl CDD PHA00742 PHA00742 222815 PHA00742 hypothetical protein 211 matched cddid_all.tbl CDD PHA00743 PHA00743 177308 PHA00743 helix-turn-helix protein 51 matched cddid_all.tbl CDD PHA00771 PHA00771 164842 PHA00771 head assembly protein 151 matched cddid_all.tbl CDD PHA00780 PHA00780 107010 PHA00780 hypothetical protein 80 matched cddid_all.tbl CDD PHA00781 PHA00781 133939 PHA00781 hypothetical protein 59 matched cddid_all.tbl CDD PHA00821 PHA00821 164843 PHA00821 hypothetical protein 295 matched cddid_all.tbl CDD PHA00911 PHA00911 222816 21 prohead core scaffolding protein and protease 212 matched cddid_all.tbl CDD PHA00965 PHA00965 222817 PHA00965 tail protein 588 matched cddid_all.tbl CDD PHA00979 PHA00979 177310 PHA00979 putative major coat protein 77 matched cddid_all.tbl CDD PHA01075 PHA01075 222818 PHA01075 major capsid protein 408 matched cddid_all.tbl CDD PHA01076 PHA01076 107017 PHA01076 putative encapsidation protein 378 matched cddid_all.tbl CDD PHA01077 PHA01077 222819 PHA01077 putative lower collar protein 251 matched cddid_all.tbl CDD PHA01078 PHA01078 164848 PHA01078 putative upper collar protein 249 matched cddid_all.tbl CDD PHA01079 PHA01079 164849 PHA01079 hypothetical protein 48 matched cddid_all.tbl CDD PHA01080 PHA01080 164850 PHA01080 hypothetical protein 80 matched cddid_all.tbl CDD PHA01081 PHA01081 133945 PHA01081 putative minor coat protein 104 matched cddid_all.tbl CDD PHA01082 PHA01082 222820 PHA01082 putative transcription regulator 133 matched cddid_all.tbl CDD PHA01083 PHA01083 164851 PHA01083 hypothetical protein 149 matched cddid_all.tbl CDD PHA01159 PHA01159 107025 PHA01159 hypothetical protein 114 matched cddid_all.tbl CDD PHA01160 PHA01160 107026 PHA01160 nonstructural protein 40 matched cddid_all.tbl CDD PHA01327 PHA01327 222821 PHA01327 hypothetical protein 49 matched cddid_all.tbl CDD PHA01346 PHA01346 164853 PHA01346 hypothetical protein 53 matched cddid_all.tbl CDD PHA01351 PHA01351 107029 PHA01351 putative minor structural protein 1070 matched cddid_all.tbl CDD PHA01365 PHA01365 107030 PHA01365 hypothetical protein 91 matched cddid_all.tbl CDD PHA01366 PHA01366 222822 PHA01366 hypothetical protein 337 matched cddid_all.tbl CDD PHA01399 PHA01399 133949 PHA01399 membrane protein P6 242 matched cddid_all.tbl CDD PHA01474 PHA01474 164854 PHA01474 nonstructural protein 52 matched cddid_all.tbl CDD PHA01486 PHA01486 107034 PHA01486 nonstructural protein 32 matched cddid_all.tbl CDD PHA01511 PHA01511 107035 PHA01511 coat protein 430 matched cddid_all.tbl CDD PHA01513 PHA01513 164855 mnt Mnt 82 matched cddid_all.tbl CDD PHA01514 PHA01514 107037 PHA01514 O-antigen conversion protein C 485 matched cddid_all.tbl CDD PHA01516 PHA01516 107038 PHA01516 hypothetical protein 98 matched cddid_all.tbl CDD PHA01519 PHA01519 107039 PHA01519 hypothetical protein 115 matched cddid_all.tbl CDD PHA01547 PHA01547 177311 PHA01547 putative internal virion protein A 206 matched cddid_all.tbl CDD PHA01548 PHA01548 222823 PHA01548 hypothetical protein 167 matched cddid_all.tbl CDD PHA01622 PHA01622 164858 PHA01622 CRISPR-associated Cas4-like protein 204 matched cddid_all.tbl CDD PHA01623 PHA01623 222824 PHA01623 hypothetical protein 56 matched cddid_all.tbl CDD PHA01624 PHA01624 222825 PHA01624 hypothetical protein 102 matched cddid_all.tbl CDD PHA01625 PHA01625 164860 PHA01625 hypothetical protein 249 matched cddid_all.tbl CDD PHA01627 PHA01627 222826 PHA01627 DNA binding protein 107 matched cddid_all.tbl CDD PHA01630 PHA01630 164861 PHA01630 putative group 1 glycosyl transferase 331 matched cddid_all.tbl CDD PHA01631 PHA01631 164862 PHA01631 hypothetical protein 176 matched cddid_all.tbl CDD PHA01632 PHA01632 133953 PHA01632 hypothetical protein 64 matched cddid_all.tbl CDD PHA01633 PHA01633 107050 PHA01633 putative glycosyl transferase group 1 335 matched cddid_all.tbl CDD PHA01634 PHA01634 133954 PHA01634 hypothetical protein 156 matched cddid_all.tbl CDD PHA01635 PHA01635 222827 PHA01635 hypothetical protein 231 matched cddid_all.tbl CDD PHA01707 PHA01707 107053 dut 2'-deoxyuridine 5'-triphosphatase 158 matched cddid_all.tbl CDD PHA01732 PHA01732 222828 PHA01732 proline-rich protein 94 matched cddid_all.tbl CDD PHA01733 PHA01733 107055 PHA01733 hypothetical protein 153 matched cddid_all.tbl CDD PHA01735 PHA01735 222829 PHA01735 hypothetical protein 76 matched cddid_all.tbl CDD PHA01740 PHA01740 133956 PHA01740 putative single-stranded DNA-binding protein 158 matched cddid_all.tbl CDD PHA01745 PHA01745 222830 PHA01745 hypothetical protein 306 matched cddid_all.tbl CDD PHA01746 PHA01746 107059 PHA01746 hypothetical protein 131 matched cddid_all.tbl CDD PHA01747 PHA01747 222831 PHA01747 putative ATP-dependent protease 425 matched cddid_all.tbl CDD PHA01748 PHA01748 222832 PHA01748 hypothetical protein 60 matched cddid_all.tbl CDD PHA01749 PHA01749 177316 PHA01749 coat protein 134 matched cddid_all.tbl CDD PHA01750 PHA01750 107063 PHA01750 hypothetical protein 75 matched cddid_all.tbl CDD PHA01751 PHA01751 222833 PHA01751 hypothetical protein 110 matched cddid_all.tbl CDD PHA01752 PHA01752 177317 PHA01752 hypothetical protein 488 matched cddid_all.tbl CDD PHA01753 PHA01753 133958 PHA01753 Holliday junction resolvase 121 matched cddid_all.tbl CDD PHA01754 PHA01754 133959 PHA01754 hypothetical protein 69 matched cddid_all.tbl CDD PHA01755 PHA01755 222834 PHA01755 hypothetical protein 562 matched cddid_all.tbl CDD PHA01756 PHA01756 107069 PHA01756 hypothetical protein 268 matched cddid_all.tbl CDD PHA01757 PHA01757 222835 PHA01757 hypothetical protein 98 matched cddid_all.tbl CDD PHA01769 PHA01769 222836 PHA01769 hypothetical protein 98 matched cddid_all.tbl CDD PHA01782 PHA01782 177318 PHA01782 hypothetical protein 177 matched cddid_all.tbl CDD PHA01790 PHA01790 164869 PHA01790 streptodornase 326 matched cddid_all.tbl CDD PHA01794 PHA01794 222837 PHA01794 hypothetical protein 134 matched cddid_all.tbl CDD PHA01795 PHA01795 177320 PHA01795 hypothetical protein 280 matched cddid_all.tbl CDD PHA01806 PHA01806 222838 PHA01806 hypothetical protein 200 matched cddid_all.tbl CDD PHA01807 PHA01807 222839 PHA01807 hypothetical protein 153 matched cddid_all.tbl CDD PHA01808 PHA01808 164872 PHA01808 putative structural protein 98 matched cddid_all.tbl CDD PHA01809 PHA01809 107079 PHA01809 hypothetical protein 65 matched cddid_all.tbl CDD PHA01810 PHA01810 177323 PHA01810 hypothetical protein 100 matched cddid_all.tbl CDD PHA01811 PHA01811 177324 PHA01811 hypothetical protein 78 matched cddid_all.tbl CDD PHA01812 PHA01812 177325 PHA01812 hypothetical protein 122 matched cddid_all.tbl CDD PHA01813 PHA01813 107083 PHA01813 hypothetical protein 58 matched cddid_all.tbl CDD PHA01814 PHA01814 107084 PHA01814 hypothetical protein 137 matched cddid_all.tbl CDD PHA01815 PHA01815 107085 PHA01815 hypothetical protein 55 matched cddid_all.tbl CDD PHA01816 PHA01816 107086 PHA01816 hypothetical protein 160 matched cddid_all.tbl CDD PHA01817 PHA01817 177326 PHA01817 hypothetical protein 479 matched cddid_all.tbl CDD PHA01818 PHA01818 107088 PHA01818 hypothetical protein 458 matched cddid_all.tbl CDD PHA01819 PHA01819 107089 PHA01819 hypothetical protein 129 matched cddid_all.tbl CDD PHA01886 PHA01886 222840 PHA01886 TM2 domain-containing protein 78 matched cddid_all.tbl CDD PHA01929 PHA01929 177328 PHA01929 putative scaffolding protein 306 matched cddid_all.tbl CDD PHA01971 PHA01971 222841 PHA01971 hypothetical protein 123 matched cddid_all.tbl CDD PHA01972 PHA01972 222842 PHA01972 structural protein 828 matched cddid_all.tbl CDD PHA01976 PHA01976 177330 PHA01976 helix-turn-helix protein 67 matched cddid_all.tbl CDD PHA02004 PHA02004 177331 PHA02004 capsid protein 332 matched cddid_all.tbl CDD PHA02030 PHA02030 222843 PHA02030 hypothetical protein 336 matched cddid_all.tbl CDD PHA02031 PHA02031 222844 PHA02031 putative DnaG-like primase 266 matched cddid_all.tbl CDD PHA02046 PHA02046 222845 PHA02046 hypothetical protein 99 matched cddid_all.tbl CDD PHA02047 PHA02047 222846 PHA02047 phage lambda Rz1-like protein 101 matched cddid_all.tbl CDD PHA02053 PHA02053 177336 PHA02053 hypothetical protein 115 matched cddid_all.tbl CDD PHA02054 PHA02054 177337 PHA02054 hypothetical protein 94 matched cddid_all.tbl CDD PHA02057 PHA02057 177338 PHA02057 ADP-ribosylation superfamily-like protein 319 matched cddid_all.tbl CDD PHA02067 PHA02067 164889 PHA02067 hypothetical protein 221 matched cddid_all.tbl CDD PHA02078 PHA02078 177339 PHA02078 hypothetical protein 54 matched cddid_all.tbl CDD PHA02085 PHA02085 164890 PHA02085 hypothetical protein 87 matched cddid_all.tbl CDD PHA02086 PHA02086 107108 PHA02086 hypothetical protein 88 matched cddid_all.tbl CDD PHA02087 PHA02087 107109 PHA02087 hypothetical protein 83 matched cddid_all.tbl CDD PHA02088 PHA02088 107110 PHA02088 hypothetical protein 125 matched cddid_all.tbl CDD PHA02090 PHA02090 177340 PHA02090 hypothetical protein 79 matched cddid_all.tbl CDD PHA02091 PHA02091 177341 PHA02091 hypothetical protein 72 matched cddid_all.tbl CDD PHA02092 PHA02092 177342 PHA02092 hypothetical protein 108 matched cddid_all.tbl CDD PHA02094 PHA02094 177343 PHA02094 hypothetical protein 81 matched cddid_all.tbl CDD PHA02095 PHA02095 107115 PHA02095 hypothetical protein 84 matched cddid_all.tbl CDD PHA02096 PHA02096 107116 PHA02096 hypothetical protein 103 matched cddid_all.tbl CDD PHA02097 PHA02097 177344 PHA02097 hypothetical protein 59 matched cddid_all.tbl CDD PHA02098 PHA02098 107118 PHA02098 hypothetical protein 56 matched cddid_all.tbl CDD PHA02099 PHA02099 107119 PHA02099 hypothetical protein 84 matched cddid_all.tbl CDD PHA02100 PHA02100 107120 PHA02100 hypothetical protein 112 matched cddid_all.tbl CDD PHA02101 PHA02101 177345 PHA02101 hypothetical protein 101 matched cddid_all.tbl CDD PHA02102 PHA02102 222847 PHA02102 hypothetical protein 72 matched cddid_all.tbl CDD PHA02103 PHA02103 222848 PHA02103 hypothetical protein 135 matched cddid_all.tbl CDD PHA02104 PHA02104 177347 PHA02104 hypothetical protein 89 matched cddid_all.tbl CDD PHA02105 PHA02105 133990 PHA02105 hypothetical protein 68 matched cddid_all.tbl CDD PHA02106 PHA02106 177348 PHA02106 hypothetical protein 91 matched cddid_all.tbl CDD PHA02107 PHA02107 164900 PHA02107 hypothetical protein 216 matched cddid_all.tbl CDD PHA02108 PHA02108 177349 PHA02108 hypothetical protein 48 matched cddid_all.tbl CDD PHA02109 PHA02109 222849 PHA02109 hypothetical protein 233 matched cddid_all.tbl CDD PHA02110 PHA02110 107130 PHA02110 hypothetical protein 98 matched cddid_all.tbl CDD PHA02114 PHA02114 107131 PHA02114 hypothetical protein 127 matched cddid_all.tbl CDD PHA02115 PHA02115 164902 PHA02115 hypothetical protein 105 matched cddid_all.tbl CDD PHA02117 PHA02117 177351 PHA02117 glutathionylspermidine synthase domain-containing protein 397 matched cddid_all.tbl CDD PHA02118 PHA02118 107134 PHA02118 hypothetical protein 202 matched cddid_all.tbl CDD PHA02119 PHA02119 107135 PHA02119 hypothetical protein 87 matched cddid_all.tbl CDD PHA02122 PHA02122 177352 PHA02122 hypothetical protein 65 matched cddid_all.tbl CDD PHA02123 PHA02123 107137 PHA02123 hypothetical protein 146 matched cddid_all.tbl CDD PHA02125 PHA02125 133998 PHA02125 thioredoxin-like protein 75 matched cddid_all.tbl CDD PHA02126 PHA02126 222850 PHA02126 hypothetical protein 153 matched cddid_all.tbl CDD PHA02127 PHA02127 107140 PHA02127 hypothetical protein 57 matched cddid_all.tbl CDD PHA02128 PHA02128 107141 PHA02128 hypothetical protein 151 matched cddid_all.tbl CDD PHA02130 PHA02130 107142 PHA02130 hypothetical protein 81 matched cddid_all.tbl CDD PHA02131 PHA02131 107143 PHA02131 hypothetical protein 70 matched cddid_all.tbl CDD PHA02132 PHA02132 107144 PHA02132 hypothetical protein 86 matched cddid_all.tbl CDD PHA02135 PHA02135 107145 PHA02135 hypothetical protein 122 matched cddid_all.tbl CDD PHA02141 PHA02141 177353 PHA02141 hypothetical protein 105 matched cddid_all.tbl CDD PHA02142 PHA02142 134000 PHA02142 putative RNA ligase 366 matched cddid_all.tbl CDD PHA02145 PHA02145 107148 PHA02145 hypothetical protein 230 matched cddid_all.tbl CDD PHA02146 PHA02146 107149 PHA02146 hypothetical protein 86 matched cddid_all.tbl CDD PHA02148 PHA02148 107150 PHA02148 hypothetical protein 110 matched cddid_all.tbl CDD PHA02150 PHA02150 134001 PHA02150 hypothetical protein 77 matched cddid_all.tbl CDD PHA02151 PHA02151 177354 PHA02151 hypothetical protein 217 matched cddid_all.tbl CDD PHA02152 PHA02152 107153 PHA02152 hypothetical protein 96 matched cddid_all.tbl CDD PHA02239 PHA02239 107154 PHA02239 putative protein phosphatase 235 matched cddid_all.tbl CDD PHA02241 PHA02241 107155 PHA02241 hypothetical protein 182 matched cddid_all.tbl CDD PHA02243 PHA02243 107156 PHA02243 hypothetical protein 160 matched cddid_all.tbl CDD PHA02244 PHA02244 107157 PHA02244 ATPase-like protein 383 matched cddid_all.tbl CDD PHA02246 PHA02246 177355 PHA02246 hypothetical protein 192 matched cddid_all.tbl CDD PHA02248 PHA02248 134004 PHA02248 hypothetical protein 204 matched cddid_all.tbl CDD PHA02256 PHA02256 177356 PHA02256 hypothetical protein 113 matched cddid_all.tbl CDD PHA02264 PHA02264 107161 PHA02264 hypothetical protein 152 matched cddid_all.tbl CDD PHA02265 PHA02265 164905 PHA02265 hypothetical protein 103 matched cddid_all.tbl CDD PHA02275 PHA02275 107163 PHA02275 hypothetical protein 125 matched cddid_all.tbl CDD PHA02277 PHA02277 107164 PHA02277 hypothetical protein 150 matched cddid_all.tbl CDD PHA02278 PHA02278 177357 PHA02278 thioredoxin-like protein 103 matched cddid_all.tbl CDD PHA02283 PHA02283 107166 PHA02283 hypothetical protein 210 matched cddid_all.tbl CDD PHA02284 PHA02284 107167 PHA02284 hypothetical protein 251 matched cddid_all.tbl CDD PHA02290 PHA02290 107168 PHA02290 hypothetical protein 234 matched cddid_all.tbl CDD PHA02291 PHA02291 177358 PHA02291 hypothetical protein 132 matched cddid_all.tbl CDD PHA02310 PHA02310 177359 PHA02310 hypothetical protein 130 matched cddid_all.tbl CDD PHA02324 PHA02324 164907 PHA02324 hypothetical protein 47 matched cddid_all.tbl CDD PHA02325 PHA02325 177360 PHA02325 hypothetical protein 72 matched cddid_all.tbl CDD PHA02334 PHA02334 164909 PHA02334 hypothetical protein 64 matched cddid_all.tbl CDD PHA02335 PHA02335 164910 PHA02335 hypothetical protein 118 matched cddid_all.tbl CDD PHA02337 PHA02337 177361 PHA02337 putative high light inducible protein 35 matched cddid_all.tbl CDD PHA02357 PHA02357 164912 PHA02357 hypothetical protein 81 matched cddid_all.tbl CDD PHA02358 PHA02358 222851 PHA02358 hypothetical protein 194 matched cddid_all.tbl CDD PHA02360 PHA02360 107178 PHA02360 hypothetical protein 70 matched cddid_all.tbl CDD PHA02414 PHA02414 107179 PHA02414 hypothetical protein 111 matched cddid_all.tbl CDD PHA02415 PHA02415 177362 PHA02415 DNA primase domain-containing protein 930 matched cddid_all.tbl CDD PHA02416 PHA02416 107181 PHA02416 hypothetical protein 167 matched cddid_all.tbl CDD PHA02417 PHA02417 164914 PHA02417 hypothetical protein 83 matched cddid_all.tbl CDD PHA02436 PHA02436 107183 PHA02436 hypothetical protein 52 matched cddid_all.tbl CDD PHA02446 PHA02446 177363 PHA02446 hypothetical protein 166 matched cddid_all.tbl CDD PHA02447 PHA02447 164916 PHA02447 hypothetical protein 86 matched cddid_all.tbl CDD PHA02448 PHA02448 107186 PHA02448 hypothetical protein 192 matched cddid_all.tbl CDD PHA02450 PHA02450 134010 PHA02450 hypothetical protein 53 matched cddid_all.tbl CDD PHA02451 PHA02451 177364 PHA02451 hypothetical protein 54 matched cddid_all.tbl CDD PHA02456 PHA02456 164918 PHA02456 zinc metallopeptidase motif-containing protein 141 matched cddid_all.tbl CDD PHA02458 PHA02458 164919 A protein A*; Reviewed 341 matched cddid_all.tbl CDD PHA02503 PHA02503 177365 PHA02503 putative transcription regulator; Provisional 57 matched cddid_all.tbl CDD PHA02508 PHA02508 107192 PHA02508 putative minor coat protein; Provisional 93 matched cddid_all.tbl CDD PHA02510 PHA02510 222852 X gene X product; Reviewed 116 matched cddid_all.tbl CDD PHA02513 PHA02513 177367 V1 structural protein V1; Reviewed 135 matched cddid_all.tbl CDD PHA02515 PHA02515 107197 PHA02515 hypothetical protein; Provisional 508 matched cddid_all.tbl CDD PHA02516 PHA02516 134016 W baseplate wedge subunit; Provisional 103 matched cddid_all.tbl CDD PHA02517 PHA02517 222853 PHA02517 putative transposase OrfB; Reviewed 277 matched cddid_all.tbl CDD PHA02518 PHA02518 222854 PHA02518 ParA-like protein; Provisional 211 matched cddid_all.tbl CDD PHA02519 PHA02519 107201 PHA02519 plasmid partition protein SopA; Reviewed 387 matched cddid_all.tbl CDD PHA02523 PHA02523 164924 43B DNA polymerase subunit B; Provisional 391 matched cddid_all.tbl CDD PHA02524 PHA02524 164925 43A DNA polymerase subunit A; Provisional 498 matched cddid_all.tbl CDD PHA02528 PHA02528 177369 43 DNA polymerase; Provisional 881 matched cddid_all.tbl CDD PHA02529 PHA02529 222855 O capsid-scaffolding protein; Provisional 278 matched cddid_all.tbl CDD PHA02530 PHA02530 222856 pseT polynucleotide kinase; Provisional 300 matched cddid_all.tbl CDD PHA02531 PHA02531 222857 20 portal vertex protein; Provisional 514 matched cddid_all.tbl CDD PHA02533 PHA02533 222858 17 large terminase protein; Provisional 534 matched cddid_all.tbl CDD PHA02535 PHA02535 222859 P terminase ATPase subunit; Provisional 581 matched cddid_all.tbl CDD PHA02536 PHA02536 222860 Q portal vertex protein; Provisional 346 matched cddid_all.tbl CDD PHA02537 PHA02537 222861 M terminase endonuclease subunit; Provisional 230 matched cddid_all.tbl CDD PHA02538 PHA02538 164934 N capsid protein; Provisional 348 matched cddid_all.tbl CDD PHA02539 PHA02539 222862 18 tail sheath protein; Provisional 648 matched cddid_all.tbl CDD PHA02540 PHA02540 222863 61 DNA primase; Provisional 337 matched cddid_all.tbl CDD PHA02541 PHA02541 177376 23 major capsid protein; Provisional 518 matched cddid_all.tbl CDD PHA02542 PHA02542 222864 41 41 helicase; Provisional 473 matched cddid_all.tbl CDD PHA02543 PHA02543 222865 regA translation repressor protein; Provisional 125 matched cddid_all.tbl CDD PHA02544 PHA02544 222866 44 clamp loader, small subunit; Provisional 316 matched cddid_all.tbl CDD PHA02545 PHA02545 177380 45 sliding clamp; Provisional 223 matched cddid_all.tbl CDD PHA02546 PHA02546 222867 47 endonuclease subunit; Provisional 340 matched cddid_all.tbl CDD PHA02547 PHA02547 222868 55 RNA polymerase sigma factor; Provisional 179 matched cddid_all.tbl CDD PHA02548 PHA02548 177383 24 capsid vertex protein; Provisional 412 matched cddid_all.tbl CDD PHA02550 PHA02550 222869 32 single-stranded DNA binding protein; Provisional 304 matched cddid_all.tbl CDD PHA02551 PHA02551 177385 19 tail tube protein; Provisional 163 matched cddid_all.tbl CDD PHA02552 PHA02552 222870 4 head completion protein; Provisional 151 matched cddid_all.tbl CDD PHA02553 PHA02553 222871 6 baseplate wedge subunit; Provisional 611 matched cddid_all.tbl CDD PHA02554 PHA02554 177388 13 neck protein; Provisional 311 matched cddid_all.tbl CDD PHA02555 PHA02555 222872 14 neck protein; Provisional 216 matched cddid_all.tbl CDD PHA02556 PHA02556 222873 15 tail sheath stabilizer and completion protein; Provisional 273 matched cddid_all.tbl CDD PHA02557 PHA02557 222874 22 prohead core protein; Provisional 271 matched cddid_all.tbl CDD PHA02558 PHA02558 222875 uvsW UvsW helicase; Provisional 501 matched cddid_all.tbl CDD PHA02559 PHA02559 222876 59 59 protein; Provisional 216 matched cddid_all.tbl CDD PHA02560 PHA02560 164955 FI major tail sheath protein; Provisional 388 matched cddid_all.tbl CDD PHA02561 PHA02561 222877 D tail protein; Provisional 351 matched cddid_all.tbl CDD PHA02562 PHA02562 222878 46 endonuclease subunit; Provisional 562 matched cddid_all.tbl CDD PHA02563 PHA02563 222879 PHA02563 DNA polymerase; Provisional 630 matched cddid_all.tbl CDD PHA02564 PHA02564 222880 V virion protein; Provisional 141 matched cddid_all.tbl CDD PHA02565 PHA02565 177395 49 recombination endonuclease VII; Provisional 157 matched cddid_all.tbl CDD PHA02566 PHA02566 222881 alt ADP-ribosyltransferase; Provisional 684 matched cddid_all.tbl CDD PHA02567 PHA02567 222882 rnh RnaseH; Provisional 304 matched cddid_all.tbl CDD PHA02568 PHA02568 164963 J baseplate assembly protein; Provisional 300 matched cddid_all.tbl CDD PHA02569 PHA02569 177398 39 DNA topoisomerase II large subunit; Provisional 602 matched cddid_all.tbl CDD PHA02570 PHA02570 177399 dexA exonuclease; Provisional 220 matched cddid_all.tbl CDD PHA02571 PHA02571 177400 a-gt.4 hypothetical protein; Provisional 109 matched cddid_all.tbl CDD PHA02572 PHA02572 222883 nrdA ribonucleoside-diphosphate reductase subunit alpha; Provisional 753 matched cddid_all.tbl CDD PHA02573 PHA02573 222884 30.3 hypothetical protein; Provisional 148 matched cddid_all.tbl CDD PHA02574 PHA02574 177403 57B hypothetical protein; Provisional 149 matched cddid_all.tbl CDD PHA02575 PHA02575 222885 1 deoxynucleoside monophosphate kinase; Provisional 227 matched cddid_all.tbl CDD PHA02576 PHA02576 177405 3 tail completion and sheath stabilizer protein; Provisional 177 matched cddid_all.tbl CDD PHA02577 PHA02577 222886 2 DNA end protector protein; Provisional 181 matched cddid_all.tbl CDD PHA02578 PHA02578 177407 53 baseplate wedge subunit; Provisional 181 matched cddid_all.tbl CDD PHA02579 PHA02579 177408 7 baseplate wedge subunit; Provisional 1030 matched cddid_all.tbl CDD PHA02580 PHA02580 177409 8 baseplate wedge subunit; Provisional 331 matched cddid_all.tbl CDD PHA02581 PHA02581 222887 9 baseplate wedge tail fiber connector; Provisional 284 matched cddid_all.tbl CDD PHA02582 PHA02582 222888 10 baseplate wedge subunit and tail pin; Provisional 604 matched cddid_all.tbl CDD PHA02583 PHA02583 222889 11 baseplate wedge subunit and tail pin; Provisional 218 matched cddid_all.tbl CDD PHA02584 PHA02584 222890 34 long tail fiber, proximal subunit; Provisional 1229 matched cddid_all.tbl CDD PHA02585 PHA02585 222891 16 small terminase protein; Provisional 161 matched cddid_all.tbl CDD PHA02586 PHA02586 222892 68 prohead core protein; Provisional 140 matched cddid_all.tbl CDD PHA02587 PHA02587 222893 30 DNA ligase; Provisional 488 matched cddid_all.tbl CDD PHA02588 PHA02588 222894 cd deoxycytidylate deaminase; Provisional 168 matched cddid_all.tbl CDD PHA02589 PHA02589 222895 rnlA RNA ligase A; Provisional 378 matched cddid_all.tbl CDD PHA02590 PHA02590 164985 PHA02590 hypothetical protein; Provisional 105 matched cddid_all.tbl CDD PHA02591 PHA02591 164986 PHA02591 hypothetical protein; Provisional 83 matched cddid_all.tbl CDD PHA02592 PHA02592 222896 52 DNA topisomerase II medium subunit; Provisional 439 matched cddid_all.tbl CDD PHA02593 PHA02593 222897 62 clamp loader small subunit; Provisional 191 matched cddid_all.tbl CDD PHA02594 PHA02594 222898 nadV nicotinamide phosphoribosyl transferase; Provisional 470 matched cddid_all.tbl CDD PHA02595 PHA02595 222899 tk.4 hypothetical protein; Provisional 154 matched cddid_all.tbl CDD PHA02596 PHA02596 222900 5 baseplate hub subunit and tail lysozyme; Provisional 576 matched cddid_all.tbl CDD PHA02597 PHA02597 222901 30.2 hypothetical protein; Provisional 197 matched cddid_all.tbl CDD PHA02598 PHA02598 222902 denA endonuclease II; Provisional 138 matched cddid_all.tbl CDD PHA02599 PHA02599 222903 dsbA double-stranded DNA binding protein; Provisional 91 matched cddid_all.tbl CDD PHA02600 PHA02600 164995 FII major tail tube protein; Provisional 169 matched cddid_all.tbl CDD PHA02601 PHA02601 222904 int integrase; Provisional 333 matched cddid_all.tbl CDD PHA02602 PHA02602 177427 56 dCTP pyrophosphatase; Provisional 172 matched cddid_all.tbl CDD PHA02603 PHA02603 222905 nrdC.11 hypothetical protein; Provisional 330 matched cddid_all.tbl CDD PHA02604 PHA02604 177429 rI.-1 hypothetical protein; Provisional 126 matched cddid_all.tbl CDD PHA02605 PHA02605 177430 54 baseplate subunit; Provisional 305 matched cddid_all.tbl CDD PHA02606 PHA02606 222906 5.1 hypothetical protein; Provisional 179 matched cddid_all.tbl CDD PHA02607 PHA02607 177432 wac fibritin; Provisional 454 matched cddid_all.tbl CDD PHA02608 PHA02608 177433 67 prohead core protein; Provisional 80 matched cddid_all.tbl CDD PHA02609 PHA02609 165004 uvsW.1 hypothetical protein; Provisional 76 matched cddid_all.tbl CDD PHA02610 PHA02610 165005 uvsY.-2 hypothetical protein; Provisional 53 matched cddid_all.tbl CDD PHA02611 PHA02611 222907 51 baseplate hub assembly protein; Provisional 249 matched cddid_all.tbl CDD PHA02612 PHA02612 222908 27 baseplate hub subunit; Provisional 372 matched cddid_all.tbl CDD PHA02613 PHA02613 222909 48 baseplate subunit; Provisional 361 matched cddid_all.tbl CDD PHA02614 PHA02614 222910 PHA02614 Major capsid protein VP1; Provisional 363 matched cddid_all.tbl CDD PHA02616 PHA02616 222911 PHA02616 VP2/VP3; Provisional 259 matched cddid_all.tbl CDD PHA02620 PHA02620 177439 PHA02620 VP3; Provisional 353 matched cddid_all.tbl CDD PHA02621 PHA02621 177440 PHA02621 agnoprotein; Provisional 68 matched cddid_all.tbl CDD PHA02624 PHA02624 222912 PHA02624 large T antigen; Provisional 647 matched cddid_all.tbl CDD PHA02627 PHA02627 177442 PHA02627 hypothetical protein; Provisional 73 matched cddid_all.tbl CDD PHA02629 PHA02629 165015 PHA02629 A-type inclusion body protein; Provisional 61 matched cddid_all.tbl CDD PHA02633 PHA02633 165016 PHA02633 hypothetical protein; Provisional 63 matched cddid_all.tbl CDD PHA02634 PHA02634 165017 PHA02634 hypothetical protein; Provisional 49 matched cddid_all.tbl CDD PHA02635 PHA02635 165018 PHA02635 ankyrin-like protein; Provisional 61 matched cddid_all.tbl CDD PHA02636 PHA02636 165019 PHA02636 hypothetical protein; Provisional 47 matched cddid_all.tbl CDD PHA02637 PHA02637 222913 PHA02637 TNF-alpha-receptor-like protein; Provisional 127 matched cddid_all.tbl CDD PHA02638 PHA02638 165021 PHA02638 CC chemokine receptor-like protein; Provisional 417 matched cddid_all.tbl CDD PHA02639 PHA02639 165022 PHA02639 EEV host range protein; Provisional 295 matched cddid_all.tbl CDD PHA02641 PHA02641 165023 PHA02641 hypothetical protein; Provisional 188 matched cddid_all.tbl CDD PHA02642 PHA02642 165024 PHA02642 C-type lectin-like protein; Provisional 216 matched cddid_all.tbl CDD PHA02643 PHA02643 165025 PHA02643 hypothetical protein; Provisional 82 matched cddid_all.tbl CDD PHA02644 PHA02644 165026 PHA02644 hypothetical protein; Provisional 112 matched cddid_all.tbl CDD PHA02646 PHA02646 165027 PHA02646 virion protein; Provisional 156 matched cddid_all.tbl CDD PHA02649 PHA02649 165029 PHA02649 hypothetical protein; Provisional 95 matched cddid_all.tbl CDD PHA02650 PHA02650 165030 PHA02650 hypothetical protein; Provisional 81 matched cddid_all.tbl CDD PHA02651 PHA02651 165031 PHA02651 IL-1 receptor antagonist; Provisional 165 matched cddid_all.tbl CDD PHA02652 PHA02652 165032 PHA02652 hypothetical protein; Provisional 70 matched cddid_all.tbl CDD PHA02653 PHA02653 177443 PHA02653 RNA helicase NPH-II; Provisional 675 matched cddid_all.tbl CDD PHA02655 PHA02655 165034 PHA02655 hypothetical protein; Provisional 94 matched cddid_all.tbl CDD PHA02656 PHA02656 165035 PHA02656 viral TNFR II-like protein; Provisional 199 matched cddid_all.tbl CDD PHA02657 PHA02657 165036 PHA02657 hypothetical protein; Provisional 95 matched cddid_all.tbl CDD PHA02658 PHA02658 165037 PHA02658 hypothetical protein; Provisional 92 matched cddid_all.tbl CDD PHA02659 PHA02659 165038 PHA02659 endothelin precursor; Provisional 70 matched cddid_all.tbl CDD PHA02660 PHA02660 165039 PHA02660 serpin-like protein; Provisional 364 matched cddid_all.tbl CDD PHA02661 PHA02661 177444 PHA02661 vascular endothelial growth factor like protein; Provisional 146 matched cddid_all.tbl CDD PHA02662 PHA02662 177445 PHA02662 ORF131 putative membrane protein; Provisional 226 matched cddid_all.tbl CDD PHA02663 PHA02663 177446 PHA02663 hypothetical protein; Provisional 172 matched cddid_all.tbl CDD PHA02664 PHA02664 177447 PHA02664 hypothetical protein; Provisional 534 matched cddid_all.tbl CDD PHA02665 PHA02665 177448 PHA02665 hypothetical protein; Provisional 322 matched cddid_all.tbl CDD PHA02666 PHA02666 222914 PHA02666 hypothetical protein; Provisional 287 matched cddid_all.tbl CDD PHA02668 PHA02668 177450 PHA02668 GM-CSF/IL-2 inhibition factor; Provisional 265 matched cddid_all.tbl CDD PHA02669 PHA02669 177451 PHA02669 hypothetical protein; Provisional 210 matched cddid_all.tbl CDD PHA02670 PHA02670 222915 PHA02670 ORF112 putative chemokine-binding protein; Provisional 287 matched cddid_all.tbl CDD PHA02671 PHA02671 177453 PHA02671 hypothetical protein; Provisional 179 matched cddid_all.tbl CDD PHA02672 PHA02672 177454 PHA02672 ORF110 EEV glycoprotein; Provisional 166 matched cddid_all.tbl CDD PHA02673 PHA02673 177455 PHA02673 ORF109 EEV glycoprotein; Provisional 161 matched cddid_all.tbl CDD PHA02674 PHA02674 177456 PHA02674 ORF107 virion morphogenesis; Provisional 60 matched cddid_all.tbl CDD PHA02675 PHA02675 177457 PHA02675 ORF104 fusion protein; Provisional 90 matched cddid_all.tbl CDD PHA02676 PHA02676 177458 PHA02676 A-type inclusion protein; Provisional 520 matched cddid_all.tbl CDD PHA02677 PHA02677 222916 PHA02677 hypothetical protein; Provisional 108 matched cddid_all.tbl CDD PHA02678 PHA02678 177460 PHA02678 hypothetical protein; Provisional 89 matched cddid_all.tbl CDD PHA02679 PHA02679 177461 PHA02679 ORF091 IMV membrane protein; Provisional 53 matched cddid_all.tbl CDD PHA02680 PHA02680 177462 PHA02680 ORF090 IMV phosphorylated membrane protein; Provisional 91 matched cddid_all.tbl CDD PHA02681 PHA02681 222917 PHA02681 ORF089 virion membrane protein; Provisional 92 matched cddid_all.tbl CDD PHA02682 PHA02682 177464 PHA02682 ORF080 virion core protein; Provisional 280 matched cddid_all.tbl CDD PHA02683 PHA02683 177465 PHA02683 ORF078 thioredoxin-like protein; Provisional 75 matched cddid_all.tbl CDD PHA02684 PHA02684 177466 PHA02684 ORF066 virion protein; Provisional 221 matched cddid_all.tbl CDD PHA02685 PHA02685 177467 PHA02685 ORF065 virion protein; Provisional 155 matched cddid_all.tbl CDD PHA02686 PHA02686 177468 PHA02686 hypothetical protein; Provisional 138 matched cddid_all.tbl CDD PHA02687 PHA02687 222918 PHA02687 ORF061 late transcription factor VLTF-4; Provisional 231 matched cddid_all.tbl CDD PHA02688 PHA02688 222919 PHA02688 ORF059 IMV protein VP55; Provisional 323 matched cddid_all.tbl CDD PHA02689 PHA02689 177471 PHA02689 ORF051 putative membrane protein; Provisional 128 matched cddid_all.tbl CDD PHA02690 PHA02690 222920 PHA02690 hypothetical protein; Provisional 90 matched cddid_all.tbl CDD PHA02691 PHA02691 177473 PHA02691 hypothetical protein; Provisional 110 matched cddid_all.tbl CDD PHA02692 PHA02692 177474 PHA02692 hypothetical protein; Provisional 70 matched cddid_all.tbl CDD PHA02693 PHA02693 177475 PHA02693 hypothetical protein; Provisional 710 matched cddid_all.tbl CDD PHA02694 PHA02694 177476 PHA02694 hypothetical protein; Provisional 292 matched cddid_all.tbl CDD PHA02695 PHA02695 177477 PHA02695 hypothetical protein; Provisional 725 matched cddid_all.tbl CDD PHA02696 PHA02696 222921 PHA02696 hypothetical protein; Provisional 79 matched cddid_all.tbl CDD PHA02697 PHA02697 222922 PHA02697 hypothetical protein; Provisional 255 matched cddid_all.tbl CDD PHA02698 PHA02698 177480 PHA02698 hypothetical protein; Provisional 89 matched cddid_all.tbl CDD PHA02699 PHA02699 165075 PHA02699 hypothetical protein; Provisional 466 matched cddid_all.tbl CDD PHA02700 PHA02700 177481 PHA02700 ORF017 DNA-binding phosphoprotein; Provisional 106 matched cddid_all.tbl CDD PHA02701 PHA02701 177482 PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional 183 matched cddid_all.tbl CDD PHA02702 PHA02702 177483 PHA02702 ORF033 IMV membrane protein; Provisional 78 matched cddid_all.tbl CDD PHA02703 PHA02703 165079 PHA02703 ORF007 dUTPase; Provisional 165 matched cddid_all.tbl CDD PHA02705 PHA02705 165080 PHA02705 hypothetical protein; Provisional 72 matched cddid_all.tbl CDD PHA02706 PHA02706 165081 PHA02706 hypothetical protein; Provisional 58 matched cddid_all.tbl CDD PHA02707 PHA02707 165082 PHA02707 hypothetical protein; Provisional 37 matched cddid_all.tbl CDD PHA02708 PHA02708 177484 PHA02708 hypothetical protein; Provisional 148 matched cddid_all.tbl CDD PHA02709 PHA02709 165084 PHA02709 hypothetical protein; Provisional 44 matched cddid_all.tbl CDD PHA02711 PHA02711 165085 PHA02711 Toll/IL-receptor-like protein; Provisional 190 matched cddid_all.tbl CDD PHA02713 PHA02713 165086 PHA02713 hypothetical protein; Provisional 557 matched cddid_all.tbl CDD PHA02714 PHA02714 165087 PHA02714 CD-30-like protein; Provisional 110 matched cddid_all.tbl CDD PHA02715 PHA02715 165088 PHA02715 hypothetical protein; Provisional 202 matched cddid_all.tbl CDD PHA02716 PHA02716 165089 PHA02716 CPXV016; CPX019; EVM010; Provisional 764 matched cddid_all.tbl CDD PHA02718 PHA02718 165090 PHA02718 hypothetical protein; Provisional 69 matched cddid_all.tbl CDD PHA02723 PHA02723 165092 PHA02723 hypothetical protein; Provisional 77 matched cddid_all.tbl CDD PHA02724 PHA02724 165093 PHA02724 hydrophobic IMV membrane protein; Provisional 53 matched cddid_all.tbl CDD PHA02725 PHA02725 165094 PHA02725 hypothetical protein; Provisional 170 matched cddid_all.tbl CDD PHA02726 PHA02726 165095 PHA02726 hypothetical protein; Provisional 94 matched cddid_all.tbl CDD PHA02728 PHA02728 165096 PHA02728 uncharacterized protein; Provisional 184 matched cddid_all.tbl CDD PHA02729 PHA02729 165097 PHA02729 hypothetical protein; Provisional 94 matched cddid_all.tbl CDD PHA02730 PHA02730 165098 PHA02730 ankyrin-like protein; Provisional 672 matched cddid_all.tbl CDD PHA02731 PHA02731 177485 PHA02731 putative integrase; Provisional 231 matched cddid_all.tbl CDD PHA02732 PHA02732 165099 PHA02732 hypothetical protein; Provisional 1467 matched cddid_all.tbl CDD PHA02734 PHA02734 165101 PHA02734 coat protein; Provisional 149 matched cddid_all.tbl CDD PHA02735 PHA02735 165102 PHA02735 putative DNA polymerase type B; Provisional 716 matched cddid_all.tbl CDD PHA02736 PHA02736 165103 PHA02736 Viral ankyrin protein; Provisional 154 matched cddid_all.tbl CDD PHA02737 PHA02737 165104 PHA02737 hypothetical protein; Provisional 72 matched cddid_all.tbl CDD PHA02738 PHA02738 222923 PHA02738 hypothetical protein; Provisional 320 matched cddid_all.tbl CDD PHA02739 PHA02739 222924 PHA02739 hypothetical protein; Provisional 116 matched cddid_all.tbl CDD PHA02740 PHA02740 165107 PHA02740 protein tyrosine phosphatase; Provisional 298 matched cddid_all.tbl CDD PHA02741 PHA02741 165108 PHA02741 hypothetical protein; Provisional 169 matched cddid_all.tbl CDD PHA02742 PHA02742 165109 PHA02742 protein tyrosine phosphatase; Provisional 303 matched cddid_all.tbl CDD PHA02743 PHA02743 222925 PHA02743 Viral ankyrin protein; Provisional 166 matched cddid_all.tbl CDD PHA02744 PHA02744 165111 PHA02744 hypothetical protein; Provisional 88 matched cddid_all.tbl CDD PHA02745 PHA02745 222926 PHA02745 hypothetical protein; Provisional 265 matched cddid_all.tbl CDD PHA02746 PHA02746 165113 PHA02746 protein tyrosine phosphatase; Provisional 323 matched cddid_all.tbl CDD PHA02747 PHA02747 165114 PHA02747 protein tyrosine phosphatase; Provisional 312 matched cddid_all.tbl CDD PHA02748 PHA02748 165115 PHA02748 viral inexin-like protein; Provisional 360 matched cddid_all.tbl CDD PHA02749 PHA02749 165116 PHA02749 hypothetical protein; Provisional 322 matched cddid_all.tbl CDD PHA02750 PHA02750 165117 PHA02750 hypothetical protein; Provisional 240 matched cddid_all.tbl CDD PHA02751 PHA02751 165118 PHA02751 hypothetical protein; Provisional 233 matched cddid_all.tbl CDD PHA02752 PHA02752 177486 PHA02752 hypothetical protein; Provisional 242 matched cddid_all.tbl CDD PHA02753 PHA02753 165120 PHA02753 hypothetical protein; Provisional 298 matched cddid_all.tbl CDD PHA02754 PHA02754 165121 PHA02754 hypothetical protein; Provisional 67 matched cddid_all.tbl CDD PHA02755 PHA02755 165122 PHA02755 hypothetical protein; Provisional 96 matched cddid_all.tbl CDD PHA02756 PHA02756 165123 PHA02756 hypothetical protein; Provisional 164 matched cddid_all.tbl CDD PHA02757 PHA02757 165124 PHA02757 hypothetical protein; Provisional 75 matched cddid_all.tbl CDD PHA02758 PHA02758 165125 PHA02758 hypothetical protein; Provisional 321 matched cddid_all.tbl CDD PHA02759 PHA02759 165126 PHA02759 virus coat protein VP2; Provisional 245 matched cddid_all.tbl CDD PHA02762 PHA02762 165127 PHA02762 hypothetical protein; Provisional 62 matched cddid_all.tbl CDD PHA02763 PHA02763 177487 PHA02763 hypothetical protein; Provisional 102 matched cddid_all.tbl CDD PHA02764 PHA02764 165129 PHA02764 hypothetical protein; Provisional 399 matched cddid_all.tbl CDD PHA02765 PHA02765 165130 PHA02765 hypothetical protein; Provisional 117 matched cddid_all.tbl CDD PHA02766 PHA02766 165131 PHA02766 hypothetical protein; Provisional 73 matched cddid_all.tbl CDD PHA02767 PHA02767 165132 PHA02767 hypothetical protein; Provisional 101 matched cddid_all.tbl CDD PHA02768 PHA02768 165133 PHA02768 hypothetical protein; Provisional 55 matched cddid_all.tbl CDD PHA02769 PHA02769 165134 PHA02769 hypothetical protein; Provisional 154 matched cddid_all.tbl CDD PHA02770 PHA02770 165135 PHA02770 hypothetical protein; Provisional 81 matched cddid_all.tbl CDD PHA02771 PHA02771 165136 PHA02771 hypothetical protein; Provisional 90 matched cddid_all.tbl CDD PHA02772 PHA02772 165137 PHA02772 hypothetical protein; Provisional 95 matched cddid_all.tbl CDD PHA02773 PHA02773 165138 PHA02773 hypothetical protein; Provisional 112 matched cddid_all.tbl CDD PHA02774 PHA02774 222927 PHA02774 E1; Provisional 613 matched cddid_all.tbl CDD PHA02775 PHA02775 165140 PHA02775 E6; Provisional 160 matched cddid_all.tbl CDD PHA02776 PHA02776 165141 PHA02776 E7 protein; Provisional 101 matched cddid_all.tbl CDD PHA02777 PHA02777 165142 PHA02777 major capsid L1 protein; Provisional 555 matched cddid_all.tbl CDD PHA02778 PHA02778 222928 PHA02778 major capsid L1 protein; Provisional 503 matched cddid_all.tbl CDD PHA02779 PHA02779 222929 PHA02779 E6 protein; Provisional 150 matched cddid_all.tbl CDD PHA02780 PHA02780 177490 PHA02780 hypothetical protein; Provisional 73 matched cddid_all.tbl CDD PHA02781 PHA02781 165146 PHA02781 hypothetical protein; Provisional 78 matched cddid_all.tbl CDD PHA02782 PHA02782 165147 PHA02782 hypothetical protein; Provisional 503 matched cddid_all.tbl CDD PHA02783 PHA02783 165148 PHA02783 uncharacterized protein; Provisional 181 matched cddid_all.tbl CDD PHA02785 PHA02785 165149 PHA02785 IL-beta-binding protein; Provisional 326 matched cddid_all.tbl CDD PHA02786 PHA02786 222930 PHA02786 uncharacterized protein; Provisional 192 matched cddid_all.tbl CDD PHA02789 PHA02789 165152 PHA02789 uncharacterized protein; Provisional 173 matched cddid_all.tbl CDD PHA02790 PHA02790 165153 PHA02790 Kelch-like protein; Provisional 480 matched cddid_all.tbl CDD PHA02791 PHA02791 165154 PHA02791 ankyrin-like protein; Provisional 284 matched cddid_all.tbl CDD PHA02792 PHA02792 165155 PHA02792 ankyrin-like protein; Provisional 631 matched cddid_all.tbl CDD PHA02793 PHA02793 165156 PHA02793 hypothetical protein; Provisional 66 matched cddid_all.tbl CDD PHA02795 PHA02795 165157 PHA02795 ankyrin-like protein; Provisional 437 matched cddid_all.tbl CDD PHA02798 PHA02798 222931 PHA02798 ankyrin-like protein; Provisional 489 matched cddid_all.tbl CDD PHA02800 PHA02800 165159 PHA02800 hypothetical protein; Provisional 161 matched cddid_all.tbl CDD PHA02807 PHA02807 165161 PHA02807 hypothetical protein; Provisional 155 matched cddid_all.tbl CDD PHA02809 PHA02809 222932 PHA02809 hypothetical protein; Provisional 111 matched cddid_all.tbl CDD PHA02811 PHA02811 165163 PHA02811 putative host range protein; Provisional 197 matched cddid_all.tbl CDD PHA02813 PHA02813 165164 PHA02813 hypothetical protein; Provisional 354 matched cddid_all.tbl CDD PHA02815 PHA02815 165165 PHA02815 hypothetical protein; Provisional 64 matched cddid_all.tbl CDD PHA02816 PHA02816 222933 PHA02816 hypothetical protein; Provisional 106 matched cddid_all.tbl CDD PHA02817 PHA02817 165167 PHA02817 EEV Host range protein; Provisional 225 matched cddid_all.tbl CDD PHA02818 PHA02818 165168 PHA02818 hypothetical protein; Provisional 92 matched cddid_all.tbl CDD PHA02819 PHA02819 165169 PHA02819 hypothetical protein; Provisional 71 matched cddid_all.tbl CDD PHA02820 PHA02820 222934 PHA02820 phospholipase-D-like protein; Provisional 424 matched cddid_all.tbl CDD PHA02823 PHA02823 222935 PHA02823 chemokine binding protein; Provisional 255 matched cddid_all.tbl CDD PHA02825 PHA02825 177491 PHA02825 LAP/PHD finger-like protein; Provisional 162 matched cddid_all.tbl CDD PHA02826 PHA02826 165173 PHA02826 IL-1 receptor-like protein; Provisional 227 matched cddid_all.tbl CDD PHA02827 PHA02827 177492 PHA02827 hypothetical protein; Provisional 150 matched cddid_all.tbl CDD PHA02828 PHA02828 165175 PHA02828 putative transmembrane protein; Provisional 100 matched cddid_all.tbl CDD PHA02831 PHA02831 165176 PHA02831 EEV host range protein; Provisional 268 matched cddid_all.tbl CDD PHA02834 PHA02834 165177 PHA02834 chemokine receptor-like protein; Provisional 323 matched cddid_all.tbl CDD PHA02835 PHA02835 165178 PHA02835 putative secreted protein; Provisional 186 matched cddid_all.tbl CDD PHA02836 PHA02836 165179 PHA02836 putative transmembrane protein; Provisional 153 matched cddid_all.tbl CDD PHA02837 PHA02837 165180 PHA02837 uncharacterized protein; Provisional 190 matched cddid_all.tbl CDD PHA02838 PHA02838 165181 PHA02838 hypothetical protein; Provisional 68 matched cddid_all.tbl CDD PHA02839 PHA02839 165182 PHA02839 Il-24-like protein; Provisional 156 matched cddid_all.tbl CDD PHA02840 PHA02840 165183 PHA02840 hypothetical protein; Provisional 82 matched cddid_all.tbl CDD PHA02841 PHA02841 165184 PHA02841 hypothetical protein; Provisional 103 matched cddid_all.tbl CDD PHA02843 PHA02843 165185 PHA02843 hypothetical protein; Provisional 73 matched cddid_all.tbl CDD PHA02844 PHA02844 165186 PHA02844 putative transmembrane protein; Provisional 75 matched cddid_all.tbl CDD PHA02845 PHA02845 165187 PHA02845 hypothetical protein; Provisional 91 matched cddid_all.tbl CDD PHA02849 PHA02849 165188 PHA02849 putative transmembrane protein; Provisional 82 matched cddid_all.tbl CDD PHA02851 PHA02851 165189 PHA02851 EEV glycoprotein; Provisional 223 matched cddid_all.tbl CDD PHA02852 PHA02852 165190 PHA02852 putative virion structural protein; Provisional 153 matched cddid_all.tbl CDD PHA02854 PHA02854 165191 PHA02854 putative host range protein; Provisional 178 matched cddid_all.tbl CDD PHA02855 PHA02855 222936 PHA02855 anti-apoptotic membrane protein; Provisional 180 matched cddid_all.tbl CDD PHA02857 PHA02857 165193 PHA02857 monoglyceride lipase; Provisional 276 matched cddid_all.tbl CDD PHA02858 PHA02858 165194 PHA02858 EIF2a-like PKR inhibitor; Provisional 86 matched cddid_all.tbl CDD PHA02859 PHA02859 165195 PHA02859 ankyrin repeat protein; Provisional 209 matched cddid_all.tbl CDD PHA02861 PHA02861 165196 PHA02861 uncharacterized protein; Provisional 149 matched cddid_all.tbl CDD PHA02862 PHA02862 165197 PHA02862 5L protein; Provisional 156 matched cddid_all.tbl CDD PHA02864 PHA02864 222937 PHA02864 hypothetical protein; Provisional 240 matched cddid_all.tbl CDD PHA02865 PHA02865 165199 PHA02865 MHC-like TNF binding protein; Provisional 338 matched cddid_all.tbl CDD PHA02866 PHA02866 165200 PHA02866 Hypothetical protein; Provisional 333 matched cddid_all.tbl CDD PHA02867 PHA02867 165201 PHA02867 C-type lectin protein; Provisional 167 matched cddid_all.tbl CDD PHA02869 PHA02869 165202 PHA02869 C4L/C10L-like gene family protein; Provisional 418 matched cddid_all.tbl CDD PHA02871 PHA02871 165203 PHA02871 hypothetical protein; Provisional 222 matched cddid_all.tbl CDD PHA02872 PHA02872 222938 PHA02872 EFc gene family protein; Provisional 124 matched cddid_all.tbl CDD PHA02874 PHA02874 165205 PHA02874 ankyrin repeat protein; Provisional 434 matched cddid_all.tbl CDD PHA02875 PHA02875 165206 PHA02875 ankyrin repeat protein; Provisional 413 matched cddid_all.tbl CDD PHA02876 PHA02876 165207 PHA02876 ankyrin repeat protein; Provisional 682 matched cddid_all.tbl CDD PHA02878 PHA02878 222939 PHA02878 ankyrin repeat protein; Provisional 477 matched cddid_all.tbl CDD PHA02880 PHA02880 222940 PHA02880 hypothetical protein; Provisional 189 matched cddid_all.tbl CDD PHA02881 PHA02881 165210 PHA02881 hypothetical protein; Provisional 161 matched cddid_all.tbl CDD PHA02882 PHA02882 165211 PHA02882 putative serine/threonine kinase; Provisional 294 matched cddid_all.tbl CDD PHA02884 PHA02884 165212 PHA02884 ankyrin repeat protein; Provisional 300 matched cddid_all.tbl CDD PHA02885 PHA02885 165213 PHA02885 putative interleukin binding protein; Provisional 135 matched cddid_all.tbl CDD PHA02887 PHA02887 165214 PHA02887 EGF-like protein; Provisional 126 matched cddid_all.tbl CDD PHA02888 PHA02888 165215 PHA02888 hypothetical protein; Provisional 96 matched cddid_all.tbl CDD PHA02889 PHA02889 165216 PHA02889 hypothetical protein; Provisional 241 matched cddid_all.tbl CDD PHA02890 PHA02890 165217 PHA02890 hypothetical protein; Provisional 278 matched cddid_all.tbl CDD PHA02891 PHA02891 165218 PHA02891 hypothetical protein; Provisional 120 matched cddid_all.tbl CDD PHA02892 PHA02892 165219 PHA02892 hypothetical protein; Provisional 75 matched cddid_all.tbl CDD PHA02893 PHA02893 165220 PHA02893 hypothetical protein; Provisional 88 matched cddid_all.tbl CDD PHA02894 PHA02894 165221 PHA02894 hypothetical protein; Provisional 97 matched cddid_all.tbl CDD PHA02896 PHA02896 165222 PHA02896 A-type inclusion like protein; Provisional 616 matched cddid_all.tbl CDD PHA02898 PHA02898 165223 PHA02898 virion envelope protein; Provisional 92 matched cddid_all.tbl CDD PHA02901 PHA02901 222941 PHA02901 virus redox protein; Provisional 75 matched cddid_all.tbl CDD PHA02902 PHA02902 165225 PHA02902 putative IMV membrane protein; Provisional 70 matched cddid_all.tbl CDD PHA02907 PHA02907 165226 PHA02907 hypothetical protein; Provisional 182 matched cddid_all.tbl CDD PHA02909 PHA02909 165227 PHA02909 hypothetical protein; Provisional 72 matched cddid_all.tbl CDD PHA02910 PHA02910 165228 PHA02910 hypothetical protein; Provisional 171 matched cddid_all.tbl CDD PHA02911 PHA02911 177496 PHA02911 C-type lectin-like protein; Provisional 213 matched cddid_all.tbl CDD PHA02913 PHA02913 177497 PHA02913 TGF-beta-like protein; Provisional 172 matched cddid_all.tbl CDD PHA02914 PHA02914 165230 PHA02914 Immunoglobulin-like domain protein; Provisional 500 matched cddid_all.tbl CDD PHA02917 PHA02917 165231 PHA02917 ankyrin-like protein; Provisional 661 matched cddid_all.tbl CDD PHA02919 PHA02919 165232 PHA02919 host-range protein; Provisional 150 matched cddid_all.tbl CDD PHA02920 PHA02920 165233 PHA02920 putative virulence factor; Provisional 117 matched cddid_all.tbl CDD PHA02922 PHA02922 165234 PHA02922 hypothetical protein; Provisional 153 matched cddid_all.tbl CDD PHA02923 PHA02923 165235 PHA02923 hypothetical protein; Provisional 315 matched cddid_all.tbl CDD PHA02924 PHA02924 222942 PHA02924 hypothetical protein; Provisional 156 matched cddid_all.tbl CDD PHA02926 PHA02926 165237 PHA02926 zinc finger-like protein; Provisional 242 matched cddid_all.tbl CDD PHA02927 PHA02927 222943 PHA02927 secreted complement-binding protein; Provisional 263 matched cddid_all.tbl CDD PHA02928 PHA02928 165239 PHA02928 Hypothetical protein; Provisional 214 matched cddid_all.tbl CDD PHA02929 PHA02929 222944 PHA02929 N1R/p28-like protein; Provisional 238 matched cddid_all.tbl CDD PHA02930 PHA02930 165241 PHA02930 hypothetical protein; Provisional 81 matched cddid_all.tbl CDD PHA02931 PHA02931 165242 PHA02931 hypothetical protein; Provisional 72 matched cddid_all.tbl CDD PHA02932 PHA02932 222945 PHA02932 hypothetical protein; Provisional 221 matched cddid_all.tbl CDD PHA02933 PHA02933 165244 PHA02933 unchracterized protein; Provisional 149 matched cddid_all.tbl CDD PHA02934 PHA02934 165245 PHA02934 Hypothetical protein; Provisional 253 matched cddid_all.tbl CDD PHA02935 PHA02935 222946 PHA02935 Hypothetical protein; Provisional 349 matched cddid_all.tbl CDD PHA02937 PHA02937 165247 PHA02937 hypothetical protein; Provisional 310 matched cddid_all.tbl CDD PHA02938 PHA02938 165248 PHA02938 hypothetical protein; Provisional 361 matched cddid_all.tbl CDD PHA02939 PHA02939 222947 PHA02939 hypothetical protein; Provisional 144 matched cddid_all.tbl CDD PHA02940 PHA02940 165250 PHA02940 hypothetical protein; Provisional 315 matched cddid_all.tbl CDD PHA02941 PHA02941 222948 PHA02941 hypothetical protein; Provisional 356 matched cddid_all.tbl CDD PHA02942 PHA02942 165252 PHA02942 putative transposase; Provisional 383 matched cddid_all.tbl CDD PHA02943 PHA02943 165253 PHA02943 hypothetical protein; Provisional 165 matched cddid_all.tbl CDD PHA02944 PHA02944 165254 PHA02944 hypothetical protein; Provisional 180 matched cddid_all.tbl CDD PHA02945 PHA02945 165255 PHA02945 interferon resistance protein; Provisional 88 matched cddid_all.tbl CDD PHA02946 PHA02946 165256 PHA02946 ankyin-like protein; Provisional 446 matched cddid_all.tbl CDD PHA02947 PHA02947 222949 PHA02947 S-S bond formation pathway protein; Provisional 215 matched cddid_all.tbl CDD PHA02948 PHA02948 165258 PHA02948 serine protease inhibitor-like protein; Provisional 373 matched cddid_all.tbl CDD PHA02949 PHA02949 165259 PHA02949 Hypothetical protein; Provisional 65 matched cddid_all.tbl CDD PHA02951 PHA02951 177499 PHA02951 Hypothetical protein; Provisional 337 matched cddid_all.tbl CDD PHA02952 PHA02952 222950 PHA02952 EEV maturation protein; Provisional 648 matched cddid_all.tbl CDD PHA02953 PHA02953 165262 PHA02953 IEV and EEV membrane glycoprotein; Provisional 170 matched cddid_all.tbl CDD PHA02954 PHA02954 165263 PHA02954 EEV membrane glycoprotein; Provisional 317 matched cddid_all.tbl CDD PHA02955 PHA02955 165264 PHA02955 hypothetical protein; Provisional 213 matched cddid_all.tbl CDD PHA02956 PHA02956 165265 PHA02956 hypothetical protein; Provisional 189 matched cddid_all.tbl CDD PHA02957 PHA02957 165266 PHA02957 hypothetical protein; Provisional 206 matched cddid_all.tbl CDD PHA02961 PHA02961 165267 PHA02961 hypothetical protein; Provisional 658 matched cddid_all.tbl CDD PHA02962 PHA02962 165268 PHA02962 hypothetical protein; Provisional 722 matched cddid_all.tbl CDD PHA02963 PHA02963 165269 PHA02963 hypothetical protein; Provisional 210 matched cddid_all.tbl CDD PHA02965 PHA02965 165270 PHA02965 hypothetical protein; Provisional 466 matched cddid_all.tbl CDD PHA02966 PHA02966 165271 PHA02966 hypothetical protein; Provisional 67 matched cddid_all.tbl CDD PHA02967 PHA02967 165272 PHA02967 hypothetical protein; Provisional 128 matched cddid_all.tbl CDD PHA02968 PHA02968 165273 PHA02968 hypothetical protein; Provisional 414 matched cddid_all.tbl CDD PHA02969 PHA02969 165274 PHA02969 hypothetical protein; Provisional 111 matched cddid_all.tbl CDD PHA02970 PHA02970 222951 PHA02970 hypothetical protein; Provisional 115 matched cddid_all.tbl CDD PHA02972 PHA02972 165276 PHA02972 hypothetical protein; Provisional 109 matched cddid_all.tbl CDD PHA02973 PHA02973 165277 PHA02973 hypothetical protein; Provisional 102 matched cddid_all.tbl CDD PHA02974 PHA02974 165278 PHA02974 putative IMV membrane protein; Provisional 81 matched cddid_all.tbl CDD PHA02975 PHA02975 165279 PHA02975 hypothetical protein; Provisional 69 matched cddid_all.tbl CDD PHA02976 PHA02976 165280 PHA02976 hypothetical protein; Provisional 181 matched cddid_all.tbl CDD PHA02977 PHA02977 165281 PHA02977 hypothetical protein; Provisional 201 matched cddid_all.tbl CDD PHA02978 PHA02978 165282 PHA02978 hypothetical protein; Provisional 135 matched cddid_all.tbl CDD PHA02979 PHA02979 165283 PHA02979 hypothetical protein; Provisional 140 matched cddid_all.tbl CDD PHA02980 PHA02980 165284 PHA02980 hypothetical protein; Provisional 160 matched cddid_all.tbl CDD PHA02982 PHA02982 165285 PHA02982 hypothetical protein; Provisional 251 matched cddid_all.tbl CDD PHA02983 PHA02983 222952 PHA02983 hypothetical protein; Provisional 180 matched cddid_all.tbl CDD PHA02984 PHA02984 165287 PHA02984 hypothetical protein; Provisional 286 matched cddid_all.tbl CDD PHA02985 PHA02985 165288 PHA02985 hypothetical protein; Provisional 271 matched cddid_all.tbl CDD PHA02986 PHA02986 222953 PHA02986 hypothetical protein; Provisional 141 matched cddid_all.tbl CDD PHA02987 PHA02987 165290 PHA02987 Ig domain OX-2-like protein; Provisional 189 matched cddid_all.tbl CDD PHA02988 PHA02988 165291 PHA02988 hypothetical protein; Provisional 283 matched cddid_all.tbl CDD PHA02989 PHA02989 222954 PHA02989 ankyrin repeat protein; Provisional 494 matched cddid_all.tbl CDD PHA02991 PHA02991 222955 PHA02991 HT motif gene family protein; Provisional 120 matched cddid_all.tbl CDD PHA02992 PHA02992 222956 PHA02992 hypothetical protein; Provisional 728 matched cddid_all.tbl CDD PHA02993 PHA02993 165295 PHA02993 hypothetical protein; Provisional 147 matched cddid_all.tbl CDD PHA02994 PHA02994 222957 PHA02994 hypothetical protein; Provisional 218 matched cddid_all.tbl CDD PHA02995 PHA02995 165297 PHA02995 DNA-binding virion core protein; Provisional 101 matched cddid_all.tbl CDD PHA02996 PHA02996 177503 PHA02996 poly(A) polymerase large subunit; Provisional 467 matched cddid_all.tbl CDD PHA02998 PHA02998 222958 PHA02998 RNA polymerase subunit; Provisional 195 matched cddid_all.tbl CDD PHA02999 PHA02999 222959 PHA02999 Hypothetical protein; Provisional 382 matched cddid_all.tbl CDD PHA03000 PHA03000 177505 PHA03000 Hypothetical protein; Provisional 566 matched cddid_all.tbl CDD PHA03001 PHA03001 222960 PHA03001 putative virion core protein; Provisional 132 matched cddid_all.tbl CDD PHA03002 PHA03002 165303 PHA03002 Hypothetical protein; Provisional 679 matched cddid_all.tbl CDD PHA03003 PHA03003 177506 PHA03003 palmytilated EEV membrane glycoprotein; Provisional 369 matched cddid_all.tbl CDD PHA03004 PHA03004 177507 PHA03004 putative membrane protein; Provisional 270 matched cddid_all.tbl CDD PHA03005 PHA03005 222961 PHA03005 sulfhydryl oxidase; Provisional 96 matched cddid_all.tbl CDD PHA03006 PHA03006 165307 PHA03006 hypothetical protein; Provisional 323 matched cddid_all.tbl CDD PHA03007 PHA03007 165308 PHA03007 hypothetical protein; Provisional 540 matched cddid_all.tbl CDD PHA03008 PHA03008 165309 PHA03008 hypothetical protein; Provisional 234 matched cddid_all.tbl CDD PHA03010 PHA03010 165310 PHA03010 hypothetical protein; Provisional 546 matched cddid_all.tbl CDD PHA03011 PHA03011 165311 PHA03011 hypothetical protein; Provisional 120 matched cddid_all.tbl CDD PHA03012 PHA03012 165312 PHA03012 hypothetical protein; Provisional 279 matched cddid_all.tbl CDD PHA03013 PHA03013 165313 PHA03013 hypothetical protein; Provisional 109 matched cddid_all.tbl CDD PHA03014 PHA03014 165314 PHA03014 hypothetical protein; Provisional 163 matched cddid_all.tbl CDD PHA03016 PHA03016 165315 PHA03016 hypothetical protein; Provisional 441 matched cddid_all.tbl CDD PHA03017 PHA03017 165316 PHA03017 hypothetical protein; Provisional 228 matched cddid_all.tbl CDD PHA03018 PHA03018 165317 PHA03018 hypothetical protein; Provisional 174 matched cddid_all.tbl CDD PHA03019 PHA03019 165318 PHA03019 hypothetical protein; Provisional 77 matched cddid_all.tbl CDD PHA03020 PHA03020 165319 PHA03020 hypothetical protein; Provisional 352 matched cddid_all.tbl CDD PHA03022 PHA03022 165320 PHA03022 hypothetical protein; Provisional 335 matched cddid_all.tbl CDD PHA03023 PHA03023 165321 PHA03023 hypothetical protein; Provisional 112 matched cddid_all.tbl CDD PHA03024 PHA03024 165322 PHA03024 hypothetical protein; Provisional 229 matched cddid_all.tbl CDD PHA03025 PHA03025 165323 PHA03025 hypothetical protein; Provisional 68 matched cddid_all.tbl CDD PHA03026 PHA03026 165324 PHA03026 hypothetical protein; Provisional 421 matched cddid_all.tbl CDD PHA03027 PHA03027 165325 PHA03027 hypothetical protein; Provisional 325 matched cddid_all.tbl CDD PHA03028 PHA03028 165326 PHA03028 hypothetical protein; Provisional 185 matched cddid_all.tbl CDD PHA03029 PHA03029 165327 PHA03029 hypothetical protein; Provisional 92 matched cddid_all.tbl CDD PHA03030 PHA03030 165328 PHA03030 hypothetical protein; Provisional 122 matched cddid_all.tbl CDD PHA03031 PHA03031 165329 PHA03031 hypothetical protein; Provisional 449 matched cddid_all.tbl CDD PHA03033 PHA03033 165330 PHA03033 hypothetical protein; Provisional 142 matched cddid_all.tbl CDD PHA03034 PHA03034 165331 PHA03034 hypothetical protein; Provisional 145 matched cddid_all.tbl CDD PHA03035 PHA03035 165332 PHA03035 hypothetical protein; Provisional 158 matched cddid_all.tbl CDD PHA03036 PHA03036 222962 PHA03036 DNA polymerase; Provisional 1004 matched cddid_all.tbl CDD PHA03041 PHA03041 222963 PHA03041 virion core protein; Provisional 153 matched cddid_all.tbl CDD PHA03042 PHA03042 222964 PHA03042 CD47-like protein; Provisional 286 matched cddid_all.tbl CDD PHA03043 PHA03043 165336 PHA03043 hypothetical protein; Provisional 130 matched cddid_all.tbl CDD PHA03044 PHA03044 165337 PHA03044 IMV membrane protein; Provisional 74 matched cddid_all.tbl CDD PHA03045 PHA03045 177510 PHA03045 IMV membrane protein; Provisional 113 matched cddid_all.tbl CDD PHA03046 PHA03046 165339 PHA03046 Hypothetical protein; Provisional 142 matched cddid_all.tbl CDD PHA03047 PHA03047 165340 PHA03047 IMV membrane receptor-like protein; Provisional 53 matched cddid_all.tbl CDD PHA03048 PHA03048 165341 PHA03048 IMV membrane protein; Provisional 93 matched cddid_all.tbl CDD PHA03049 PHA03049 165342 PHA03049 IMV membrane protein; Provisional 68 matched cddid_all.tbl CDD PHA03050 PHA03050 165343 PHA03050 glutaredoxin; Provisional 108 matched cddid_all.tbl CDD PHA03051 PHA03051 165344 PHA03051 Hypothetical protein; Provisional 88 matched cddid_all.tbl CDD PHA03052 PHA03052 165345 PHA03052 Hypothetical protein; Provisional 69 matched cddid_all.tbl CDD PHA03054 PHA03054 165346 PHA03054 IMV membrane protein; Provisional 72 matched cddid_all.tbl CDD PHA03055 PHA03055 165347 PHA03055 Hypothetical protein; Provisional 79 matched cddid_all.tbl CDD PHA03056 PHA03056 165348 PHA03056 putative myristoylated protein; Provisional 165 matched cddid_all.tbl CDD PHA03057 PHA03057 222965 PHA03057 Hypothetical protein; Provisional 146 matched cddid_all.tbl CDD PHA03058 PHA03058 222966 PHA03058 Hypothetical protein; Provisional 124 matched cddid_all.tbl CDD PHA03060 PHA03060 222967 PHA03060 Hypothetical protein; Provisional 71 matched cddid_all.tbl CDD PHA03061 PHA03061 177511 PHA03061 putative DNA-binding virion core protein; Provisional 311 matched cddid_all.tbl CDD PHA03062 PHA03062 177512 PHA03062 putative IMV membrane protein; Provisional 78 matched cddid_all.tbl CDD PHA03065 PHA03065 222968 PHA03065 Hypothetical protein; Provisional 438 matched cddid_all.tbl CDD PHA03066 PHA03066 165355 PHA03066 Hypothetical protein; Provisional 110 matched cddid_all.tbl CDD PHA03067 PHA03067 222969 PHA03067 hypothetical protein; Provisional 383 matched cddid_all.tbl CDD PHA03068 PHA03068 177515 PHA03068 DNA-binding phosphoprotein; Provisional 270 matched cddid_all.tbl CDD PHA03069 PHA03069 165358 PHA03069 DNA-binding protein; Provisional 119 matched cddid_all.tbl CDD PHA03070 PHA03070 177516 PHA03070 DNA-binding virion core protein; Provisional 249 matched cddid_all.tbl CDD PHA03071 PHA03071 165360 PHA03071 late transcription factor VLTF-1; Provisional 260 matched cddid_all.tbl CDD PHA03072 PHA03072 222970 PHA03072 putative viral membrane protein; Provisional 190 matched cddid_all.tbl CDD PHA03073 PHA03073 177518 PHA03073 late transcription factor VLTF-2; Provisional 150 matched cddid_all.tbl CDD PHA03074 PHA03074 165363 PHA03074 late transcription factor VLTF-3; Provisional 225 matched cddid_all.tbl CDD PHA03075 PHA03075 177519 PHA03075 glutaredoxin-like protein; Provisional 123 matched cddid_all.tbl CDD PHA03078 PHA03078 222971 PHA03078 transcriptional elongation factor; Provisional 219 matched cddid_all.tbl CDD PHA03079 PHA03079 165366 PHA03079 hypothetical protein; Provisional 87 matched cddid_all.tbl CDD PHA03080 PHA03080 222972 PHA03080 putative virion core protein; Provisional 366 matched cddid_all.tbl CDD PHA03081 PHA03081 222973 PHA03081 putative metalloprotease; Provisional 595 matched cddid_all.tbl CDD PHA03082 PHA03082 222974 PHA03082 DNA-dependent RNA polymerase subunit; Provisional 63 matched cddid_all.tbl CDD PHA03083 PHA03083 222975 PHA03083 poxvirus myristoylprotein; Provisional 334 matched cddid_all.tbl CDD PHA03087 PHA03087 222976 PHA03087 G protein-coupled chemokine receptor-like protein; Provisional 335 matched cddid_all.tbl CDD PHA03089 PHA03089 222977 PHA03089 late transcription factor VLTF-4; Provisional 191 matched cddid_all.tbl CDD PHA03091 PHA03091 222978 PHA03091 putative alpha aminitin-sensitive protein; Provisional 232 matched cddid_all.tbl CDD PHA03092 PHA03092 165374 PHA03092 semaphorin-like protein; Provisional 134 matched cddid_all.tbl CDD PHA03093 PHA03093 222979 PHA03093 EEV glycoprotein; Provisional 185 matched cddid_all.tbl CDD PHA03094 PHA03094 165376 PHA03094 dUTPase; Provisional 144 matched cddid_all.tbl CDD PHA03095 PHA03095 222980 PHA03095 ankyrin-like protein; Provisional 471 matched cddid_all.tbl CDD PHA03096 PHA03096 222981 PHA03096 p28-like protein; Provisional 284 matched cddid_all.tbl CDD PHA03097 PHA03097 222982 PHA03097 C-type lectin-like protein; Provisional 157 matched cddid_all.tbl CDD PHA03098 PHA03098 222983 PHA03098 kelch-like protein; Provisional 534 matched cddid_all.tbl CDD PHA03099 PHA03099 165381 PHA03099 epidermal growth factor-like protein (EGF-like protein); Provisional 139 matched cddid_all.tbl CDD PHA03100 PHA03100 222984 PHA03100 ankyrin repeat protein; Provisional 422 matched cddid_all.tbl CDD PHA03101 PHA03101 222985 PHA03101 DNA topoisomerase type I; Provisional 314 matched cddid_all.tbl CDD PHA03102 PHA03102 222986 PHA03102 Small T antigen; Reviewed 153 matched cddid_all.tbl CDD PHA03103 PHA03103 222987 PHA03103 double-strand RNA-binding protein; Provisional 183 matched cddid_all.tbl CDD PHA03105 PHA03105 222988 PHA03105 EEV glycoprotein; Provisional 188 matched cddid_all.tbl CDD PHA03108 PHA03108 165387 PHA03108 poly(A) polymerase small subunit; Provisional 300 matched cddid_all.tbl CDD PHA03111 PHA03111 222989 PHA03111 Ser/Thr kinase; Provisional 444 matched cddid_all.tbl CDD PHA03112 PHA03112 222990 PHA03112 IL-18 binding protein; Provisional 141 matched cddid_all.tbl CDD PHA03115 PHA03115 177532 PHA03115 hypothetical protein; Provisional 340 matched cddid_all.tbl CDD PHA03118 PHA03118 165391 PHA03118 multifunctional expression regulator; Provisional 474 matched cddid_all.tbl CDD PHA03119 PHA03119 222991 PHA03119 helicase-primase primase subunit; Provisional 1085 matched cddid_all.tbl CDD PHA03120 PHA03120 165393 PHA03120 tegument protein VP22; Provisional 310 matched cddid_all.tbl CDD PHA03123 PHA03123 165395 PHA03123 dUTPase; Provisional 402 matched cddid_all.tbl CDD PHA03124 PHA03124 165396 PHA03124 dUTPase; Provisional 418 matched cddid_all.tbl CDD PHA03125 PHA03125 222992 PHA03125 dUTPase; Provisional 376 matched cddid_all.tbl CDD PHA03126 PHA03126 165398 PHA03126 dUTPase; Provisional 326 matched cddid_all.tbl CDD PHA03127 PHA03127 222993 PHA03127 dUTPase; Provisional 322 matched cddid_all.tbl CDD PHA03128 PHA03128 165400 PHA03128 dUTPase; Provisional 376 matched cddid_all.tbl CDD PHA03129 PHA03129 222994 PHA03129 dUTPase; Provisional 436 matched cddid_all.tbl CDD PHA03130 PHA03130 222995 PHA03130 dUTPase; Provisional 368 matched cddid_all.tbl CDD PHA03131 PHA03131 222996 PHA03131 dUTPase; Provisional 286 matched cddid_all.tbl CDD PHA03132 PHA03132 222997 PHA03132 thymidine kinase; Provisional 580 matched cddid_all.tbl CDD PHA03133 PHA03133 165405 PHA03133 thymidine kinase; Provisional 368 matched cddid_all.tbl CDD PHA03134 PHA03134 177537 PHA03134 thymidine kinase; Provisional 340 matched cddid_all.tbl CDD PHA03135 PHA03135 165407 PHA03135 thymidine kinase; Provisional 343 matched cddid_all.tbl CDD PHA03136 PHA03136 177538 PHA03136 thymidine kinase; Provisional 378 matched cddid_all.tbl CDD PHA03138 PHA03138 165410 PHA03138 thymidine kinase; Provisional 340 matched cddid_all.tbl CDD PHA03139 PHA03139 165411 PHA03139 helicase-primase primase subunit; Provisional 860 matched cddid_all.tbl CDD PHA03140 PHA03140 222998 PHA03140 helicase-primase primase subunit; Provisional 772 matched cddid_all.tbl CDD PHA03141 PHA03141 177540 PHA03141 helicase-primase primase subunit; Provisional 101 matched cddid_all.tbl CDD PHA03142 PHA03142 222999 PHA03142 helicase-primase primase subunit BSLF1; Provisional 835 matched cddid_all.tbl CDD PHA03144 PHA03144 223000 PHA03144 helicase-primase primase subunit; Provisional 746 matched cddid_all.tbl CDD PHA03145 PHA03145 165416 PHA03145 helicase-primase primase subunit; Provisional 1058 matched cddid_all.tbl CDD PHA03146 PHA03146 177543 PHA03146 helicase-primase primase subunit; Provisional 1075 matched cddid_all.tbl CDD PHA03147 PHA03147 165418 PHA03147 hypothetical protein; Provisional 280 matched cddid_all.tbl CDD PHA03148 PHA03148 223001 PHA03148 hypothetical protein; Provisional 289 matched cddid_all.tbl CDD PHA03149 PHA03149 165420 PHA03149 hypothetical protein; Provisional 66 matched cddid_all.tbl CDD PHA03150 PHA03150 223002 PHA03150 hypothetical protein; Provisional 456 matched cddid_all.tbl CDD PHA03151 PHA03151 177546 PHA03151 hypothetical protein; Provisional 259 matched cddid_all.tbl CDD PHA03152 PHA03152 165423 PHA03152 hypothetical protein; Provisional 138 matched cddid_all.tbl CDD PHA03154 PHA03154 165425 PHA03154 hypothetical protein; Provisional 304 matched cddid_all.tbl CDD PHA03155 PHA03155 165426 PHA03155 hypothetical protein; Provisional 115 matched cddid_all.tbl CDD PHA03156 PHA03156 165427 PHA03156 hypothetical protein; Provisional 90 matched cddid_all.tbl CDD PHA03158 PHA03158 165429 PHA03158 hypothetical protein; Provisional 273 matched cddid_all.tbl CDD PHA03159 PHA03159 165430 PHA03159 hypothetical protein; Provisional 160 matched cddid_all.tbl CDD PHA03160 PHA03160 165431 PHA03160 hypothetical protein; Provisional 499 matched cddid_all.tbl CDD PHA03161 PHA03161 165432 PHA03161 hypothetical protein; Provisional 150 matched cddid_all.tbl CDD PHA03162 PHA03162 165433 PHA03162 hypothetical protein; Provisional 135 matched cddid_all.tbl CDD PHA03163 PHA03163 165434 PHA03163 hypothetical protein; Provisional 92 matched cddid_all.tbl CDD PHA03164 PHA03164 177547 PHA03164 hypothetical protein; Provisional 88 matched cddid_all.tbl CDD PHA03165 PHA03165 165436 PHA03165 hypothetical protein; Provisional 57 matched cddid_all.tbl CDD PHA03166 PHA03166 177548 PHA03166 hypothetical protein; Provisional 580 matched cddid_all.tbl CDD PHA03169 PHA03169 223003 PHA03169 hypothetical protein; Provisional 413 matched cddid_all.tbl CDD PHA03170 PHA03170 165441 PHA03170 UL37 tegument protein; Provisional 293 matched cddid_all.tbl CDD PHA03171 PHA03171 165442 PHA03171 UL37 tegument protein; Provisional 499 matched cddid_all.tbl CDD PHA03172 PHA03172 165443 PHA03172 UL37 tegument protein; Provisional 951 matched cddid_all.tbl CDD PHA03173 PHA03173 223004 PHA03173 UL37 tegument protein; Provisional 1028 matched cddid_all.tbl CDD PHA03175 PHA03175 177551 PHA03175 UL43 envelope protein; Provisional 413 matched cddid_all.tbl CDD PHA03176 PHA03176 223005 PHA03176 UL43 envelope protein; Provisional 420 matched cddid_all.tbl CDD PHA03178 PHA03178 177552 PHA03178 UL43 envelope protein; Provisional 403 matched cddid_all.tbl CDD PHA03179 PHA03179 223006 PHA03179 UL43 envelope protein; Provisional 387 matched cddid_all.tbl CDD PHA03180 PHA03180 165451 PHA03180 helicase-primase primase subunit; Provisional 1071 matched cddid_all.tbl CDD PHA03181 PHA03181 165452 PHA03181 helicase-primase primase subunit; Provisional 764 matched cddid_all.tbl CDD PHA03185 PHA03185 177553 PHA03185 UL14 tegument protein; Provisional 214 matched cddid_all.tbl CDD PHA03187 PHA03187 223007 PHA03187 UL14 tegument protein; Provisional 322 matched cddid_all.tbl CDD PHA03188 PHA03188 165458 PHA03188 UL14 tegument protein; Provisional 199 matched cddid_all.tbl CDD PHA03189 PHA03189 223008 PHA03189 UL14 tegument protein; Provisional 348 matched cddid_all.tbl CDD PHA03190 PHA03190 165460 PHA03190 UL14 tegument protein; Provisional 196 matched cddid_all.tbl CDD PHA03191 PHA03191 165461 PHA03191 UL14 tegument protein; Provisional 238 matched cddid_all.tbl CDD PHA03193 PHA03193 177555 PHA03193 tegument protein VP11/12; Provisional 594 matched cddid_all.tbl CDD PHA03195 PHA03195 177556 PHA03195 tegument protein VP11/12; Provisional 746 matched cddid_all.tbl CDD PHA03199 PHA03199 165466 PHA03199 uracil DNA glycosylase; Provisional 304 matched cddid_all.tbl CDD PHA03200 PHA03200 165467 PHA03200 uracil DNA glycosylase; Provisional 255 matched cddid_all.tbl CDD PHA03201 PHA03201 165468 PHA03201 uracil DNA glycosylase; Provisional 318 matched cddid_all.tbl CDD PHA03202 PHA03202 165469 PHA03202 uracil DNA glycosylase; Provisional 313 matched cddid_all.tbl CDD PHA03204 PHA03204 165471 PHA03204 uracil DNA glycosylase; Provisional 322 matched cddid_all.tbl CDD PHA03207 PHA03207 165473 PHA03207 serine/threonine kinase US3; Provisional 392 matched cddid_all.tbl CDD PHA03209 PHA03209 177557 PHA03209 serine/threonine kinase US3; Provisional 357 matched cddid_all.tbl CDD PHA03210 PHA03210 165476 PHA03210 serine/threonine kinase US3; Provisional 501 matched cddid_all.tbl CDD PHA03211 PHA03211 223009 PHA03211 serine/threonine kinase US3; Provisional 461 matched cddid_all.tbl CDD PHA03212 PHA03212 165478 PHA03212 serine/threonine kinase US3; Provisional 391 matched cddid_all.tbl CDD PHA03214 PHA03214 165479 PHA03214 nuclear protein UL24; Provisional 252 matched cddid_all.tbl CDD PHA03215 PHA03215 223010 PHA03215 nuclear protein UL24; Provisional 262 matched cddid_all.tbl CDD PHA03216 PHA03216 177558 PHA03216 nuclear protein UL24; Provisional 272 matched cddid_all.tbl CDD PHA03218 PHA03218 223011 PHA03218 nuclear protein UL24; Provisional 306 matched cddid_all.tbl CDD PHA03219 PHA03219 165484 PHA03219 nuclear protein UL24; Provisional 300 matched cddid_all.tbl CDD PHA03222 PHA03222 165485 PHA03222 single-stranded binding protein UL29; Provisional 337 matched cddid_all.tbl CDD PHA03225 PHA03225 165486 PHA03225 DNA packaging protein UL33; Provisional 125 matched cddid_all.tbl CDD PHA03229 PHA03229 223012 PHA03229 DNA packaging protein UL33; Provisional 132 matched cddid_all.tbl CDD PHA03230 PHA03230 223013 PHA03230 nuclear protein UL55; Provisional 180 matched cddid_all.tbl CDD PHA03231 PHA03231 223014 PHA03231 glycoprotein BALF4; Provisional 829 matched cddid_all.tbl CDD PHA03232 PHA03232 223015 PHA03232 DNA packaging protein UL32; Provisional 586 matched cddid_all.tbl CDD PHA03233 PHA03233 223016 PHA03233 DNA packaging protein UL32; Provisional 518 matched cddid_all.tbl CDD PHA03234 PHA03234 177562 PHA03234 DNA packaging protein UL33; Provisional 338 matched cddid_all.tbl CDD PHA03235 PHA03235 223017 PHA03235 DNA packaging protein UL33; Provisional 409 matched cddid_all.tbl CDD PHA03236 PHA03236 223018 PHA03236 DNA packaging protein UL33; Provisional 127 matched cddid_all.tbl CDD PHA03237 PHA03237 223019 PHA03237 envelope glycoprotein M; Provisional 424 matched cddid_all.tbl CDD PHA03239 PHA03239 177565 PHA03239 envelope glycoprotein M; Provisional 429 matched cddid_all.tbl CDD PHA03240 PHA03240 165499 PHA03240 envelope glycoprotein M; Provisional 258 matched cddid_all.tbl CDD PHA03242 PHA03242 177566 PHA03242 envelope glycoprotein M; Provisional 428 matched cddid_all.tbl CDD PHA03244 PHA03244 177567 PHA03244 large tegument protein UL36; Provisional 478 matched cddid_all.tbl CDD PHA03246 PHA03246 223020 PHA03246 large tegument protein UL36; Provisional 3095 matched cddid_all.tbl CDD PHA03247 PHA03247 223021 PHA03247 large tegument protein UL36; Provisional 3151 matched cddid_all.tbl CDD PHA03248 PHA03248 223022 PHA03248 DNA packaging tegument protein UL25; Provisional 583 matched cddid_all.tbl CDD PHA03249 PHA03249 223023 PHA03249 DNA packaging tegument protein UL25; Provisional 653 matched cddid_all.tbl CDD PHA03250 PHA03250 165509 PHA03250 UL35; Provisional 564 matched cddid_all.tbl CDD PHA03252 PHA03252 223024 PHA03252 DNA packaging tegument protein UL25; Provisional 589 matched cddid_all.tbl CDD PHA03253 PHA03253 223025 PHA03253 UL35; Provisional 609 matched cddid_all.tbl CDD PHA03255 PHA03255 165513 PHA03255 BDLF3; Provisional 234 matched cddid_all.tbl CDD PHA03256 PHA03256 165514 PHA03256 BDLF3; Provisional 77 matched cddid_all.tbl CDD PHA03257 PHA03257 177569 PHA03257 Capsid triplex subunit 2; Provisional 316 matched cddid_all.tbl CDD PHA03258 PHA03258 165516 PHA03258 Capsid triplex subunit 2; Provisional 304 matched cddid_all.tbl CDD PHA03259 PHA03259 165517 PHA03259 Capsid triplex subunit 2; Provisional 302 matched cddid_all.tbl CDD PHA03260 PHA03260 165518 PHA03260 Capsid triplex subunit 2; Provisional 339 matched cddid_all.tbl CDD PHA03261 PHA03261 223026 PHA03261 Capsid triplex subunit 1; Provisional 469 matched cddid_all.tbl CDD PHA03262 PHA03262 223027 PHA03262 Capsid triplex subunit 1; Provisional 264 matched cddid_all.tbl CDD PHA03263 PHA03263 223028 PHA03263 Capsid triplex subunit 1; Provisional 332 matched cddid_all.tbl CDD PHA03264 PHA03264 223029 PHA03264 envelope glycoprotein D; Provisional 416 matched cddid_all.tbl CDD PHA03265 PHA03265 165523 PHA03265 envelope glycoprotein D; Provisional 402 matched cddid_all.tbl CDD PHA03269 PHA03269 165527 PHA03269 envelope glycoprotein C; Provisional 566 matched cddid_all.tbl CDD PHA03270 PHA03270 165528 PHA03270 envelope glycoprotein C; Provisional 466 matched cddid_all.tbl CDD PHA03271 PHA03271 223030 PHA03271 envelope glycoprotein C; Provisional 490 matched cddid_all.tbl CDD PHA03273 PHA03273 223031 PHA03273 envelope glycoprotein C; Provisional 486 matched cddid_all.tbl CDD PHA03275 PHA03275 177573 PHA03275 envelope glycoprotein K; Provisional 340 matched cddid_all.tbl CDD PHA03276 PHA03276 165533 PHA03276 envelope glycoprotein K; Provisional 337 matched cddid_all.tbl CDD PHA03278 PHA03278 177574 PHA03278 envelope glycoprotein K; Provisional 347 matched cddid_all.tbl CDD PHA03279 PHA03279 165536 PHA03279 envelope glycoprotein K; Provisional 361 matched cddid_all.tbl CDD PHA03281 PHA03281 165538 PHA03281 envelope glycoprotein E; Provisional 642 matched cddid_all.tbl CDD PHA03282 PHA03282 165539 PHA03282 envelope glycoprotein E; Provisional 540 matched cddid_all.tbl CDD PHA03283 PHA03283 223032 PHA03283 envelope glycoprotein E; Provisional 542 matched cddid_all.tbl CDD PHA03286 PHA03286 177576 PHA03286 envelope glycoprotein E; Provisional 492 matched cddid_all.tbl CDD PHA03289 PHA03289 165546 PHA03289 envelope glycoprotein I; Provisional 352 matched cddid_all.tbl CDD PHA03290 PHA03290 165547 PHA03290 envelope glycoprotein I; Provisional 357 matched cddid_all.tbl CDD PHA03291 PHA03291 223033 PHA03291 envelope glycoprotein I; Provisional 401 matched cddid_all.tbl CDD PHA03292 PHA03292 177577 PHA03292 envelope glycoprotein I; Provisional 413 matched cddid_all.tbl CDD PHA03293 PHA03293 223034 PHA03293 deoxyribonuclease; Provisional 523 matched cddid_all.tbl CDD PHA03294 PHA03294 223035 PHA03294 envelope glycoprotein H; Provisional 835 matched cddid_all.tbl CDD PHA03295 PHA03295 223036 PHA03295 envelope glycoprotein H; Provisional 714 matched cddid_all.tbl CDD PHA03296 PHA03296 165553 PHA03296 envelope glycoprotein H; Provisional 814 matched cddid_all.tbl CDD PHA03297 PHA03297 165554 PHA03297 envelope glycoprotein L; Provisional 185 matched cddid_all.tbl CDD PHA03298 PHA03298 165555 PHA03298 envelope glycoprotein L; Provisional 167 matched cddid_all.tbl CDD PHA03299 PHA03299 165556 PHA03299 envelope glycoprotein L; Provisional 195 matched cddid_all.tbl CDD PHA03301 PHA03301 223037 PHA03301 envelope glycoprotein L; Provisional 226 matched cddid_all.tbl CDD PHA03302 PHA03302 223038 PHA03302 envelope glycoprotein L; Provisional 253 matched cddid_all.tbl CDD PHA03303 PHA03303 165560 PHA03303 envelope glycoprotein L; Provisional 159 matched cddid_all.tbl CDD PHA03307 PHA03307 223039 PHA03307 transcriptional regulator ICP4; Provisional 1352 matched cddid_all.tbl CDD PHA03308 PHA03308 165563 PHA03308 transcriptional regulator ICP4; Provisional 1463 matched cddid_all.tbl CDD PHA03309 PHA03309 165564 PHA03309 transcriptional regulator ICP4; Provisional 2033 matched cddid_all.tbl CDD PHA03311 PHA03311 223040 PHA03311 helicase-primase subunit BBLF4; Provisional 782 matched cddid_all.tbl CDD PHA03312 PHA03312 177582 PHA03312 helicase-primase subunit BBLF2/3; Provisional 709 matched cddid_all.tbl CDD PHA03321 PHA03321 223041 PHA03321 tegument protein VP11/12; Provisional 694 matched cddid_all.tbl CDD PHA03322 PHA03322 223042 PHA03322 tegument protein VP11/12; Provisional 674 matched cddid_all.tbl CDD PHA03323 PHA03323 223043 PHA03323 nuclear egress membrane protein UL34; Provisional 272 matched cddid_all.tbl CDD PHA03324 PHA03324 165570 PHA03324 nuclear egress membrane protein UL34; Provisional 274 matched cddid_all.tbl CDD PHA03325 PHA03325 223044 PHA03325 nuclear-egress-membrane-like protein; Provisional 418 matched cddid_all.tbl CDD PHA03326 PHA03326 223045 PHA03326 nuclear egress membrane protein; Provisional 275 matched cddid_all.tbl CDD PHA03328 PHA03328 223046 PHA03328 nuclear egress lamina protein UL31; Provisional 316 matched cddid_all.tbl CDD PHA03330 PHA03330 165574 PHA03330 putative primase; Provisional 771 matched cddid_all.tbl CDD PHA03332 PHA03332 223047 PHA03332 membrane glycoprotein; Provisional 1328 matched cddid_all.tbl CDD PHA03333 PHA03333 223048 PHA03333 putative ATPase subunit of terminase; Provisional 752 matched cddid_all.tbl CDD PHA03334 PHA03334 223049 PHA03334 putative DNA polymerase catalytic subunit; Provisional 1545 matched cddid_all.tbl CDD PHA03335 PHA03335 223050 PHA03335 hypothetical protein; Provisional 385 matched cddid_all.tbl CDD PHA03336 PHA03336 223051 PHA03336 uncharacterized protein; Provisional 462 matched cddid_all.tbl CDD PHA03338 PHA03338 165582 PHA03338 US22 family homolog; Provisional 344 matched cddid_all.tbl CDD PHA03342 PHA03342 165586 PHA03342 US22 family homolog; Provisional 511 matched cddid_all.tbl CDD PHA03343 PHA03343 165587 PHA03343 US22 family homolog; Provisional 578 matched cddid_all.tbl CDD PHA03344 PHA03344 165588 PHA03344 US22 family homolog; Provisional 672 matched cddid_all.tbl CDD PHA03346 PHA03346 223052 PHA03346 US22 family homolog; Provisional 520 matched cddid_all.tbl CDD PHA03347 PHA03347 177588 PHA03347 uracil DNA glycosylase; Provisional 252 matched cddid_all.tbl CDD PHA03348 PHA03348 177589 PHA03348 tegument protein UL21; Provisional 526 matched cddid_all.tbl CDD PHA03349 PHA03349 177590 PHA03349 tegument protein UL16; Provisional 343 matched cddid_all.tbl CDD PHA03351 PHA03351 177591 PHA03351 tegument protein UL16; Provisional 235 matched cddid_all.tbl CDD PHA03352 PHA03352 223053 PHA03352 tegument protein UL16; Provisional 340 matched cddid_all.tbl CDD PHA03354 PHA03354 177593 PHA03354 Alkaline exonuclease; Provisional 81 matched cddid_all.tbl CDD PHA03356 PHA03356 177594 PHA03356 tegument protein UL11; Provisional 93 matched cddid_all.tbl CDD PHA03357 PHA03357 177595 PHA03357 Alkaline exonuclease; Provisional 81 matched cddid_all.tbl CDD PHA03358 PHA03358 177596 PHA03358 Alkaline exonuclease; Provisional 75 matched cddid_all.tbl CDD PHA03359 PHA03359 223054 PHA03359 UL17 tegument protein; Provisional 686 matched cddid_all.tbl CDD PHA03360 PHA03360 177598 PHA03360 tegument protein; Provisional 442 matched cddid_all.tbl CDD PHA03361 PHA03361 223055 PHA03361 UL7 tegument protein; Provisional 302 matched cddid_all.tbl CDD PHA03362 PHA03362 223056 PHA03362 single-stranded binding protein UL29; Provisional 1189 matched cddid_all.tbl CDD PHA03364 PHA03364 223057 PHA03364 hypothetical protein; Provisional 264 matched cddid_all.tbl CDD PHA03365 PHA03365 177602 PHA03365 hypothetical protein; Provisional 419 matched cddid_all.tbl CDD PHA03366 PHA03366 223058 PHA03366 FGAM-synthase; Provisional 1304 matched cddid_all.tbl CDD PHA03367 PHA03367 223059 PHA03367 single-stranded DNA binding protein; Provisional 1115 matched cddid_all.tbl CDD PHA03368 PHA03368 223060 PHA03368 DNA packaging terminase subunit 1; Provisional 738 matched cddid_all.tbl CDD PHA03369 PHA03369 223061 PHA03369 capsid maturational protease; Provisional 663 matched cddid_all.tbl CDD PHA03370 PHA03370 177607 PHA03370 virion protein US2; Provisional 269 matched cddid_all.tbl CDD PHA03371 PHA03371 177608 PHA03371 circ protein; Provisional 240 matched cddid_all.tbl CDD PHA03372 PHA03372 177609 PHA03372 DNA packaging terminase subunit 1; Provisional 668 matched cddid_all.tbl CDD PHA03373 PHA03373 223062 PHA03373 tegument protein; Provisional 247 matched cddid_all.tbl CDD PHA03374 PHA03374 223063 PHA03374 hypothetical protein; Provisional 730 matched cddid_all.tbl CDD PHA03375 PHA03375 223064 PHA03375 hypothetical protein; Provisional 844 matched cddid_all.tbl CDD PHA03376 PHA03376 177613 PHA03376 BARF1; Provisional 221 matched cddid_all.tbl CDD PHA03377 PHA03377 177614 PHA03377 EBNA-3C; Provisional 1000 matched cddid_all.tbl CDD PHA03378 PHA03378 223065 PHA03378 EBNA-3B; Provisional 991 matched cddid_all.tbl CDD PHA03379 PHA03379 223066 PHA03379 EBNA-3A; Provisional 935 matched cddid_all.tbl CDD PHA03380 PHA03380 223067 PHA03380 transactivating tegument protein VP16; Provisional 432 matched cddid_all.tbl CDD PHA03381 PHA03381 177618 PHA03381 tegument protein VP22; Provisional 290 matched cddid_all.tbl CDD PHA03383 PHA03383 177619 PHA03383 PCNA-like protein; Provisional 262 matched cddid_all.tbl CDD PHA03384 PHA03384 223068 PHA03384 early DNA-binding protein E2A; Provisional 445 matched cddid_all.tbl CDD PHA03385 PHA03385 177621 IX capsid protein IX,hexon associated protein IX; Provisional 135 matched cddid_all.tbl CDD PHA03386 PHA03386 177622 P10 fibrous body protein; Provisional 94 matched cddid_all.tbl CDD PHA03387 PHA03387 177623 gp37 spherodin-like protein; Provisional 267 matched cddid_all.tbl CDD PHA03388 PHA03388 177624 ORF1_granulin Granulin; Provisional 248 matched cddid_all.tbl CDD PHA03389 PHA03389 177625 polh polyhedrin; Provisional 246 matched cddid_all.tbl CDD PHA03390 PHA03390 223069 pk1 serine/threonine-protein kinase 1; Provisional 267 matched cddid_all.tbl CDD PHA03391 PHA03391 223070 p47 viral transcription regulator p47; Provisional 395 matched cddid_all.tbl CDD PHA03392 PHA03392 223071 egt ecdysteroid UDP-glucosyltransferase; Provisional 507 matched cddid_all.tbl CDD PHA03393 PHA03393 223072 odv-e66 occlusion-derived virus envelope protein E66; Provisional 682 matched cddid_all.tbl CDD PHA03394 PHA03394 223073 lef-8 DNA-directed RNA polymerase subunit beta-like protein; Provisional 865 matched cddid_all.tbl CDD PHA03395 PHA03395 177631 p10 fibrous body protein; Provisional 87 matched cddid_all.tbl CDD PHA03396 PHA03396 223074 lef-9 late expression factor 9; Provisional 493 matched cddid_all.tbl CDD PHA03397 PHA03397 177633 vlf-1 very late expression factor 1; Provisional 363 matched cddid_all.tbl CDD PHA03398 PHA03398 223075 PHA03398 viral phosphatase superfamily protein; Provisional 303 matched cddid_all.tbl CDD PHA03399 PHA03399 223076 pif3 per os infectivity factor 3; Provisional 200 matched cddid_all.tbl CDD PHA03402 PHA03402 223077 PHA03402 hypothetical protein; Provisional 81 matched cddid_all.tbl CDD PHA03405 PHA03405 177637 PHA03405 hypothetical protein; Provisional 130 matched cddid_all.tbl CDD PHA03410 PHA03410 223078 PHA03410 hypothetical protein; Provisional 170 matched cddid_all.tbl CDD PHA03411 PHA03411 177639 PHA03411 putative methyltransferase; Provisional 279 matched cddid_all.tbl CDD PHA03412 PHA03412 177640 PHA03412 putative methyltransferase; Provisional 241 matched cddid_all.tbl CDD PHA03413 PHA03413 177641 PHA03413 putative internal core protein; Provisional 1304 matched cddid_all.tbl CDD PHA03414 PHA03414 177642 PHA03414 virion protein; Provisional 1337 matched cddid_all.tbl CDD PHA03415 PHA03415 177643 PHA03415 putative internal virion protein; Provisional 1019 matched cddid_all.tbl CDD PHA03416 PHA03416 177644 PHA03416 hypothetical E4 protein; Provisional 92 matched cddid_all.tbl CDD PHA03417 PHA03417 177645 PHA03417 E4 protein; Provisional 118 matched cddid_all.tbl CDD PHA03418 PHA03418 177646 PHA03418 hypothetical E4 protein; Provisional 230 matched cddid_all.tbl CDD PHA03419 PHA03419 223079 PHA03419 E4 protein; Provisional 200 matched cddid_all.tbl CDD PHA03420 PHA03420 177648 PHA03420 E4 protein; Provisional 137 matched cddid_all.tbl CDD PLN00009 PLN00009 177649 PLN00009 cyclin-dependent kinase A; Provisional 294 matched cddid_all.tbl CDD PLN00010 PLN00010 215027 PLN00010 cyclin-dependent kinases regulatory subunit; Provisional 86 matched cddid_all.tbl CDD PLN00011 PLN00011 177651 PLN00011 cysteine synthase 323 matched cddid_all.tbl CDD PLN00012 PLN00012 215028 PLN00012 chlorophyll synthetase; Provisional 375 matched cddid_all.tbl CDD PLN00014 PLN00014 177653 PLN00014 light-harvesting-like protein 3; Provisional 250 matched cddid_all.tbl CDD PLN00015 PLN00015 177654 PLN00015 protochlorophyllide reductase 308 matched cddid_all.tbl CDD PLN00016 PLN00016 215029 PLN00016 RNA-binding protein; Provisional 378 matched cddid_all.tbl CDD PLN00017 PLN00017 177656 PLN00017 photosystem I reaction centre subunit VI; Provisional 90 matched cddid_all.tbl CDD PLN00019 PLN00019 215030 PLN00019 photosystem I reaction center subunit III; Provisional 223 matched cddid_all.tbl CDD PLN00020 PLN00020 215031 PLN00020 ribulose bisphosphate carboxylase/oxygenase activase -RuBisCO activase (RCA); Provisional 413 matched cddid_all.tbl CDD PLN00021 PLN00021 177659 PLN00021 chlorophyllase 313 matched cddid_all.tbl CDD PLN00022 PLN00022 215032 PLN00022 electron transfer flavoprotein subunit alpha; Provisional 356 matched cddid_all.tbl CDD PLN00023 PLN00023 177661 PLN00023 GTP-binding protein; Provisional 334 matched cddid_all.tbl CDD PLN00025 PLN00025 215033 PLN00025 photosystem II light harvesting chlorophyll a/b binding protein; Provisional 262 matched cddid_all.tbl CDD PLN00026 PLN00026 177663 PLN00026 aquaporin NIP; Provisional 298 matched cddid_all.tbl CDD PLN00027 PLN00027 177664 PLN00027 aquaporin TIP; Provisional 252 matched cddid_all.tbl CDD PLN00028 PLN00028 177665 PLN00028 nitrate transmembrane transporter; Provisional 476 matched cddid_all.tbl CDD PLN00032 PLN00032 215034 PLN00032 DNA-directed RNA polymerase; Provisional 71 matched cddid_all.tbl CDD PLN00033 PLN00033 215035 PLN00033 photosystem II stability/assembly factor; Provisional 398 matched cddid_all.tbl CDD PLN00034 PLN00034 215036 PLN00034 mitogen-activated protein kinase kinase; Provisional 353 matched cddid_all.tbl CDD PLN00035 PLN00035 177669 PLN00035 histone H4; Provisional 103 matched cddid_all.tbl CDD PLN00036 PLN00036 177670 PLN00036 40S ribosomal protein S4; Provisional 261 matched cddid_all.tbl CDD PLN00037 PLN00037 177671 PLN00037 photosystem II oxygen-evolving enhancer protein 1; Provisional 313 matched cddid_all.tbl CDD PLN00038 PLN00038 215037 PLN00038 photosystem I reaction center subunit XI (PsaL); Provisional 165 matched cddid_all.tbl CDD PLN00039 PLN00039 177673 PLN00039 photosystem II reaction center Psb28 protein; Provisional 111 matched cddid_all.tbl CDD PLN00040 PLN00040 215038 PLN00040 Protein MAK16 homolog; Provisional 233 matched cddid_all.tbl CDD PLN00041 PLN00041 215039 PLN00041 photosystem I reaction center subunit II; Provisional 196 matched cddid_all.tbl CDD PLN00042 PLN00042 177676 PLN00042 photosystem II oxygen-evolving enhancer protein 2; Provisional 260 matched cddid_all.tbl CDD PLN00043 PLN00043 165621 PLN00043 elongation factor 1-alpha; Provisional 447 matched cddid_all.tbl CDD PLN00044 PLN00044 165622 PLN00044 multi-copper oxidase-related protein; Provisional 596 matched cddid_all.tbl CDD PLN00045 PLN00045 177677 PLN00045 photosystem I reaction center subunit IV; Provisional 101 matched cddid_all.tbl CDD PLN00046 PLN00046 215040 PLN00046 photosystem I reaction center subunit O; Provisional 141 matched cddid_all.tbl CDD PLN00047 PLN00047 177679 PLN00047 photosystem II biogenesis protein Psb29; Provisional 283 matched cddid_all.tbl CDD PLN00048 PLN00048 177680 PLN00048 photosystem I light harvesting chlorophyll a/b binding protein 3; Provisional 262 matched cddid_all.tbl CDD PLN00049 PLN00049 177681 PLN00049 carboxyl-terminal processing protease; Provisional 389 matched cddid_all.tbl CDD PLN00050 PLN00050 165628 PLN00050 expansin A; Provisional 247 matched cddid_all.tbl CDD PLN00051 PLN00051 177682 PLN00051 RNA-binding S4 domain-containing protein; Provisional 267 matched cddid_all.tbl CDD PLN00052 PLN00052 177683 PLN00052 prolyl 4-hydroxylase; Provisional 310 matched cddid_all.tbl CDD PLN00053 PLN00053 215041 PLN00053 photosystem II subunit R; Provisional 117 matched cddid_all.tbl CDD PLN00054 PLN00054 215042 PLN00054 photosystem I reaction center subunit N; Provisional 139 matched cddid_all.tbl CDD PLN00055 PLN00055 177686 PLN00055 photosystem II reaction center protein H; Provisional 73 matched cddid_all.tbl CDD PLN00056 PLN00056 177687 PLN00056 photosystem Q(B) protein; Provisional 353 matched cddid_all.tbl CDD PLN00057 PLN00057 177688 PLN00057 proliferating cell nuclear antigen; Provisional 263 matched cddid_all.tbl CDD PLN00058 PLN00058 177689 PLN00058 photosystem II reaction center subunit T; Provisional 103 matched cddid_all.tbl CDD PLN00059 PLN00059 177690 PLN00059 PsbP domain-containing protein 1; Provisional 286 matched cddid_all.tbl CDD PLN00060 PLN00060 177691 PLN00060 meiotic recombination protein SPO11-2; Provisional 384 matched cddid_all.tbl CDD PLN00061 PLN00061 215043 PLN00061 photosystem II protein Psb27; Provisional 150 matched cddid_all.tbl CDD PLN00062 PLN00062 177693 PLN00062 TATA-box-binding protein; Provisional 179 matched cddid_all.tbl CDD PLN00063 PLN00063 215044 PLN00063 photosystem II core complex proteins psbY; Provisional 194 matched cddid_all.tbl CDD PLN00064 PLN00064 215045 PLN00064 photosystem II protein Psb27; Provisional 166 matched cddid_all.tbl CDD PLN00066 PLN00066 215046 PLN00066 PsbP domain-containing protein 4; Provisional 262 matched cddid_all.tbl CDD PLN00067 PLN00067 177697 PLN00067 PsbP domain-containing protein 6; Provisional 263 matched cddid_all.tbl CDD PLN00068 PLN00068 177698 PLN00068 photosystem II CP47 chlorophyll A apoprotein; Provisional 508 matched cddid_all.tbl CDD PLN00070 PLN00070 215047 PLN00070 aconitate hydratase 936 matched cddid_all.tbl CDD PLN00071 PLN00071 177700 PLN00071 photosystem I subunit VII; Provisional 81 matched cddid_all.tbl CDD PLN00072 PLN00072 177701 PLN00072 3-isopropylmalate isomerase/dehydratase small subunit; Provisional 246 matched cddid_all.tbl CDD PLN00074 PLN00074 215048 PLN00074 photosystem II D2 protein (PsbD); Provisional 353 matched cddid_all.tbl CDD PLN00075 PLN00075 215049 PLN00075 Photosystem II reaction center protein K; Provisional 52 matched cddid_all.tbl CDD PLN00077 PLN00077 215050 PLN00077 photosystem II reaction centre W protein; Provisional 128 matched cddid_all.tbl CDD PLN00078 PLN00078 165653 PLN00078 photosystem I reaction center subunit N (PsaN); Provisional 122 matched cddid_all.tbl CDD PLN00081 PLN00081 165655 PLN00081 photosystem I reaction center subunit V (PsaG); Provisional 141 matched cddid_all.tbl CDD PLN00082 PLN00082 215051 PLN00082 photosystem II reaction centre W protein (PsbW); Provisional 67 matched cddid_all.tbl CDD PLN00083 PLN00083 177706 PLN00083 photosystem II subunit R; Provisional 101 matched cddid_all.tbl CDD PLN00084 PLN00084 177707 PLN00084 photosystem II subunit S (PsbS); Provisional 214 matched cddid_all.tbl CDD PLN00085 PLN00085 177708 PLN00085 photosystem II reaction center protein M (PsbM); Provisional 149 matched cddid_all.tbl CDD PLN00088 PLN00088 177709 PLN00088 predicted protein; Provisional 127 matched cddid_all.tbl CDD PLN00089 PLN00089 177710 PLN00089 fucoxanthin-chlorophyll a/c binding protein; Provisional 209 matched cddid_all.tbl CDD PLN00090 PLN00090 165663 PLN00090 photosystem II reaction center M protein; Provisional 113 matched cddid_all.tbl CDD PLN00091 PLN00091 215052 PLN00091 photosystem I reaction center subunit V (PsaG); Provisional 160 matched cddid_all.tbl CDD PLN00092 PLN00092 177712 PLN00092 photosystem I reaction center subunit V (PsaG); Provisional 137 matched cddid_all.tbl CDD PLN00093 PLN00093 177713 PLN00093 geranylgeranyl diphosphate reductase; Provisional 450 matched cddid_all.tbl CDD PLN00094 PLN00094 215053 PLN00094 aconitate hydratase 2; Provisional 938 matched cddid_all.tbl CDD PLN00095 PLN00095 165668 PLN00095 chlorophyllide a oxygenase; Provisional 394 matched cddid_all.tbl CDD PLN00096 PLN00096 177715 PLN00096 isocitrate dehydrogenase (NADP+); Provisional 393 matched cddid_all.tbl CDD PLN00097 PLN00097 165670 PLN00097 photosystem I light harvesting complex Lhca2/4, chlorophyll a/b binding; Provisional 244 matched cddid_all.tbl CDD PLN00098 PLN00098 177716 PLN00098 light-harvesting complex I chlorophyll a/b-binding protein (Lhac); Provisional 267 matched cddid_all.tbl CDD PLN00099 PLN00099 177717 PLN00099 light-harvesting complex IChlorophyll A-B binding protein Lhca1; Provisional 243 matched cddid_all.tbl CDD PLN00100 PLN00100 215054 PLN00100 light-harvesting complex chlorophyll-a/b protein of photosystem I (Lhca); Provisional 246 matched cddid_all.tbl CDD PLN00101 PLN00101 215055 PLN00101 Photosystem I light-harvesting complex type 4 protein; Provisional 250 matched cddid_all.tbl CDD PLN00103 PLN00103 177720 PLN00103 isocitrate dehydrogenase (NADP+); Provisional 410 matched cddid_all.tbl CDD PLN00104 PLN00104 215056 PLN00104 MYST -like histone acetyltransferase; Provisional 450 matched cddid_all.tbl CDD PLN00105 PLN00105 215057 PLN00105 malate/L-lactate dehydrogenase; Provisional 330 matched cddid_all.tbl CDD PLN00106 PLN00106 215058 PLN00106 malate dehydrogenase 323 matched cddid_all.tbl CDD PLN00107 PLN00107 165679 PLN00107 FAD-dependent oxidoreductase; Provisional 257 matched cddid_all.tbl CDD PLN00108 PLN00108 177724 PLN00108 unknown protein; Provisional 257 matched cddid_all.tbl CDD PLN00110 PLN00110 177725 PLN00110 flavonoid 3',5'-hydroxylase (F3'5'H); Provisional 504 matched cddid_all.tbl CDD PLN00111 PLN00111 215059 PLN00111 accumulation of photosystem one; Provisional 399 matched cddid_all.tbl CDD PLN00112 PLN00112 215060 PLN00112 malate dehydrogenase (NADP); Provisional 444 matched cddid_all.tbl CDD PLN00113 PLN00113 215061 PLN00113 leucine-rich repeat receptor-like protein kinase; Provisional 968 matched cddid_all.tbl CDD PLN00115 PLN00115 177729 PLN00115 pollen allergen group 3; Provisional 118 matched cddid_all.tbl CDD PLN00116 PLN00116 177730 PLN00116 translation elongation factor EF-2 subunit; Provisional 843 matched cddid_all.tbl CDD PLN00118 PLN00118 215062 PLN00118 isocitrate dehydrogenase (NAD+) 372 matched cddid_all.tbl CDD PLN00119 PLN00119 177732 PLN00119 endoglucanase 489 matched cddid_all.tbl CDD PLN00120 PLN00120 215063 PLN00120 fucoxanthin-chlorophyll a-c binding protein; Provisional 202 matched cddid_all.tbl CDD PLN00121 PLN00121 177733 PLN00121 histone H3; Provisional 136 matched cddid_all.tbl CDD PLN00122 PLN00122 215064 PLN00122 serine/threonine protein phosphatase 2A; Provisional 170 matched cddid_all.tbl CDD PLN00123 PLN00123 215065 PLN00123 isocitrate dehydrogenase (NAD+) 360 matched cddid_all.tbl CDD PLN00124 PLN00124 177736 PLN00124 succinyl-CoA ligase [GDP-forming] subunit beta; Provisional 422 matched cddid_all.tbl CDD PLN00125 PLN00125 215066 PLN00125 Succinyl-CoA ligase [GDP-forming] subunit alpha 300 matched cddid_all.tbl CDD PLN00126 PLN00126 165695 PLN00126 succinate dehydrogenase, cytochrome b subunit family; Provisional 129 matched cddid_all.tbl CDD PLN00127 PLN00127 177738 PLN00127 succinate dehydrogenase (ubiquinone) cytochrome b subunit; Provisional 178 matched cddid_all.tbl CDD PLN00128 PLN00128 177739 PLN00128 Succinate dehydrogenase [ubiquinone] flavoprotein subunit 635 matched cddid_all.tbl CDD PLN00129 PLN00129 215067 PLN00129 succinate dehydrogenase [ubiquinone] iron-sulfur subunit 276 matched cddid_all.tbl CDD PLN00130 PLN00130 177741 PLN00130 succinate dehydrogenase (SDH3); Provisional 213 matched cddid_all.tbl CDD PLN00131 PLN00131 165700 PLN00131 hypothetical protein; Provisional 218 matched cddid_all.tbl CDD PLN00133 PLN00133 215068 PLN00133 class I-fumerate hydratase; Provisional 576 matched cddid_all.tbl CDD PLN00134 PLN00134 215069 PLN00134 fumarate hydratase; Provisional 458 matched cddid_all.tbl CDD PLN00135 PLN00135 177744 PLN00135 malate dehydrogenase 309 matched cddid_all.tbl CDD PLN00136 PLN00136 215070 PLN00136 silicon transporter; Provisional 482 matched cddid_all.tbl CDD PLN00137 PLN00137 215071 PLN00137 NHAD transporter family protein; Provisional 424 matched cddid_all.tbl CDD PLN00138 PLN00138 165706 PLN00138 large subunit ribosomal protein LP2; Provisional 113 matched cddid_all.tbl CDD PLN00139 PLN00139 165707 PLN00139 hypothetical protein; Provisional 320 matched cddid_all.tbl CDD PLN00140 PLN00140 165708 PLN00140 alcohol acetyltransferase family protein; Provisional 444 matched cddid_all.tbl CDD PLN00141 PLN00141 215072 PLN00141 Tic62-NAD(P)-related group II protein; Provisional 251 matched cddid_all.tbl CDD PLN00142 PLN00142 215073 PLN00142 sucrose synthase 815 matched cddid_all.tbl CDD PLN00143 PLN00143 165711 PLN00143 tyrosine/nicotianamine aminotransferase; Provisional 409 matched cddid_all.tbl CDD PLN00144 PLN00144 177748 PLN00144 acetylornithine transaminase 382 matched cddid_all.tbl CDD PLN00145 PLN00145 215074 PLN00145 tyrosine/nicotianamine aminotransferase; Provisional 430 matched cddid_all.tbl CDD PLN00146 PLN00146 215075 PLN00146 40S ribosomal protein S15a; Provisional 130 matched cddid_all.tbl CDD PLN00147 PLN00147 215076 PLN00147 light-harvesting complex I chlorophyll-a/b binding protein Lhca5; Provisional 252 matched cddid_all.tbl CDD PLN00148 PLN00148 215077 PLN00148 potassium transporter; Provisional 785 matched cddid_all.tbl CDD PLN00149 PLN00149 177753 PLN00149 potassium transporter; Provisional 779 matched cddid_all.tbl CDD PLN00150 PLN00150 215078 PLN00150 potassium ion transporter family protein; Provisional 779 matched cddid_all.tbl CDD PLN00151 PLN00151 215079 PLN00151 potassium transporter; Provisional 852 matched cddid_all.tbl CDD PLN00152 PLN00152 177755 PLN00152 DNA-directed RNA polymerase; Provisional 130 matched cddid_all.tbl CDD PLN00153 PLN00153 165721 PLN00153 histone H2A; Provisional 129 matched cddid_all.tbl CDD PLN00154 PLN00154 177756 PLN00154 histone H2A; Provisional 136 matched cddid_all.tbl CDD PLN00155 PLN00155 165723 PLN00155 histone H2A; Provisional 58 matched cddid_all.tbl CDD PLN00156 PLN00156 215080 PLN00156 histone H2AX; Provisional 139 matched cddid_all.tbl CDD PLN00157 PLN00157 177758 PLN00157 histone H2A; Provisional 132 matched cddid_all.tbl CDD PLN00158 PLN00158 215081 PLN00158 histone H2B; Provisional 116 matched cddid_all.tbl CDD PLN00160 PLN00160 165727 PLN00160 histone H3; Provisional 97 matched cddid_all.tbl CDD PLN00161 PLN00161 215082 PLN00161 histone H3; Provisional 135 matched cddid_all.tbl CDD PLN00162 PLN00162 215083 PLN00162 transport protein sec23; Provisional 761 matched cddid_all.tbl CDD PLN00163 PLN00163 165730 PLN00163 histone H4; Provisional 59 matched cddid_all.tbl CDD PLN00164 PLN00164 215084 PLN00164 glucosyltransferase; Provisional 480 matched cddid_all.tbl CDD PLN00165 PLN00165 165732 PLN00165 hypothetical protein; Provisional 88 matched cddid_all.tbl CDD PLN00166 PLN00166 165733 PLN00166 aquaporin TIP2; Provisional 250 matched cddid_all.tbl CDD PLN00167 PLN00167 215085 PLN00167 aquaporin TIP5; Provisional 256 matched cddid_all.tbl CDD PLN00168 PLN00168 215086 PLN00168 Cytochrome P450; Provisional 519 matched cddid_all.tbl CDD PLN00169 PLN00169 177765 PLN00169 CETS family protein; Provisional 175 matched cddid_all.tbl CDD PLN00170 PLN00170 215087 PLN00170 photosystem II light-harvesting-Chl-binding protein Lhcb6 (CP24); Provisional 255 matched cddid_all.tbl CDD PLN00171 PLN00171 215088 PLN00171 photosystem light-harvesting complex -chlorophyll a/b binding protein Lhcb7; Provisional 324 matched cddid_all.tbl CDD PLN00172 PLN00172 177768 PLN00172 ubiquitin conjugating enzyme; Provisional 147 matched cddid_all.tbl CDD PLN00174 PLN00174 177769 PLN00174 predicted protein; Provisional 160 matched cddid_all.tbl CDD PLN00175 PLN00175 215089 PLN00175 aminotransferase family protein; Provisional 413 matched cddid_all.tbl CDD PLN00176 PLN00176 215090 PLN00176 galactinol synthase 333 matched cddid_all.tbl CDD PLN00177 PLN00177 177772 PLN00177 sulfite oxidase; Provisional 393 matched cddid_all.tbl CDD PLN00178 PLN00178 177773 PLN00178 sulfite reductase 623 matched cddid_all.tbl CDD PLN00179 PLN00179 215091 PLN00179 acyl- [acyl-carrier protein] desaturase 390 matched cddid_all.tbl CDD PLN00180 PLN00180 177775 PLN00180 NDF6 (NDH-dependent flow 6); Provisional 180 matched cddid_all.tbl CDD PLN00181 PLN00181 177776 PLN00181 protein SPA1-RELATED; Provisional 793 matched cddid_all.tbl CDD PLN00182 PLN00182 165748 PLN00182 putative aquaporin NIP4; Provisional 283 matched cddid_all.tbl CDD PLN00183 PLN00183 215092 PLN00183 putative aquaporin NIP7; Provisional 274 matched cddid_all.tbl CDD PLN00184 PLN00184 177778 PLN00184 aquaporin NIP1; Provisional 296 matched cddid_all.tbl CDD PLN00185 PLN00185 177779 PLN00185 60S ribosomal protein L4-1; Provisional 405 matched cddid_all.tbl CDD PLN00186 PLN00186 215093 PLN00186 ribosomal protein S26; Provisional 109 matched cddid_all.tbl CDD PLN00187 PLN00187 177781 PLN00187 photosystem II light-harvesting complex II protein Lhcb4; Provisional 286 matched cddid_all.tbl CDD PLN00188 PLN00188 215094 PLN00188 enhanced disease resistance protein (EDR2); Provisional 719 matched cddid_all.tbl CDD PLN00189 PLN00189 177783 PLN00189 40S ribosomal protein S9; Provisional 194 matched cddid_all.tbl CDD PLN00190 PLN00190 177784 PLN00190 60S ribosomal protein L21; Provisional 158 matched cddid_all.tbl CDD PLN00191 PLN00191 215095 PLN00191 enolase 457 matched cddid_all.tbl CDD PLN00192 PLN00192 215096 PLN00192 aldehyde oxidase 1344 matched cddid_all.tbl CDD PLN00193 PLN00193 215097 PLN00193 expansin-A; Provisional 256 matched cddid_all.tbl CDD PLN00194 PLN00194 215098 PLN00194 aldose 1-epimerase; Provisional 337 matched cddid_all.tbl CDD PLN00196 PLN00196 165762 PLN00196 alpha-amylase; Provisional 428 matched cddid_all.tbl CDD PLN00197 PLN00197 215099 PLN00197 beta-amylase; Provisional 573 matched cddid_all.tbl CDD PLN00198 PLN00198 215100 PLN00198 anthocyanidin reductase; Provisional 338 matched cddid_all.tbl CDD PLN00200 PLN00200 177791 PLN00200 argininosuccinate synthase; Provisional 404 matched cddid_all.tbl CDD PLN00202 PLN00202 177792 PLN00202 beta-ureidopropionase 405 matched cddid_all.tbl CDD PLN00203 PLN00203 215101 PLN00203 glutamyl-tRNA reductase 519 matched cddid_all.tbl CDD PLN00204 PLN00204 215102 PLN00204 CP12 gene family protein; Provisional 126 matched cddid_all.tbl CDD PLN00205 PLN00205 177795 PLN00205 ribisomal protein L13 family protein; Provisional 191 matched cddid_all.tbl CDD PLN00206 PLN00206 215103 PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional 518 matched cddid_all.tbl CDD PLN00207 PLN00207 215104 PLN00207 polyribonucleotide nucleotidyltransferase; Provisional 891 matched cddid_all.tbl CDD PLN00208 PLN00208 177798 PLN00208 translation initiation factor (eIF); Provisional 145 matched cddid_all.tbl CDD PLN00209 PLN00209 165774 PLN00209 ribosomal protein S27; Provisional 86 matched cddid_all.tbl CDD PLN00210 PLN00210 177799 PLN00210 40S ribosomal protein S16; Provisional 141 matched cddid_all.tbl CDD PLN00212 PLN00212 215106 PLN00212 glutelin; Provisional 493 matched cddid_all.tbl CDD PLN00213 PLN00213 165778 PLN00213 predicted protein; Provisional 118 matched cddid_all.tbl CDD PLN00214 PLN00214 177800 PLN00214 putative protein; Provisional 115 matched cddid_all.tbl CDD PLN00215 PLN00215 165780 PLN00215 predicted protein; Provisional 110 matched cddid_all.tbl CDD PLN00216 PLN00216 165781 PLN00216 predicted protein; Provisional 69 matched cddid_all.tbl CDD PLN00217 PLN00217 165782 PLN00217 predicted protein; Provisional 210 matched cddid_all.tbl CDD PLN00218 PLN00218 165783 PLN00218 predicted protein; Provisional 151 matched cddid_all.tbl CDD PLN00219 PLN00219 165784 PLN00219 predicted protein; Provisional 65 matched cddid_all.tbl CDD PLN00220 PLN00220 215107 PLN00220 tubulin beta chain; Provisional 447 matched cddid_all.tbl CDD PLN00221 PLN00221 177802 PLN00221 tubulin alpha chain; Provisional 450 matched cddid_all.tbl CDD PLN00222 PLN00222 215108 PLN00222 tubulin gamma chain; Provisional 454 matched cddid_all.tbl CDD PLN00223 PLN00223 165788 PLN00223 ADP-ribosylation factor; Provisional 181 matched cddid_all.tbl CDD PLN00410 PLN00410 215109 PLN00410 U5 snRNP protein, DIM1 family; Provisional 142 matched cddid_all.tbl CDD PLN00411 PLN00411 177805 PLN00411 nodulin MtN21 family protein; Provisional 358 matched cddid_all.tbl CDD PLN00412 PLN00412 215110 PLN00412 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase; Provisional 496 matched cddid_all.tbl CDD PLN00413 PLN00413 165792 PLN00413 triacylglycerol lipase 479 matched cddid_all.tbl CDD PLN00414 PLN00414 177807 PLN00414 glycosyltransferase family protein 446 matched cddid_all.tbl CDD PLN00415 PLN00415 177808 PLN00415 3-ketoacyl-CoA synthase 466 matched cddid_all.tbl CDD PLN00416 PLN00416 177809 PLN00416 carbonate dehydratase 258 matched cddid_all.tbl CDD PLN00417 PLN00417 177810 PLN00417 oxidoreductase, 2OG-Fe(II) oxygenase family protein 348 matched cddid_all.tbl CDD PLN02150 PLN02150 177811 PLN02150 terpene synthase/cyclase family protein 96 matched cddid_all.tbl CDD PLN02151 PLN02151 177812 PLN02151 trehalose-phosphatase 354 matched cddid_all.tbl CDD PLN02152 PLN02152 177813 PLN02152 indole-3-acetate beta-glucosyltransferase 455 matched cddid_all.tbl CDD PLN02153 PLN02153 177814 PLN02153 epithiospecifier protein 341 matched cddid_all.tbl CDD PLN02154 PLN02154 215111 PLN02154 carbonic anhydrase 290 matched cddid_all.tbl CDD PLN02155 PLN02155 165802 PLN02155 polygalacturonase 394 matched cddid_all.tbl CDD PLN02156 PLN02156 177816 PLN02156 gibberellin 2-beta-dioxygenase 335 matched cddid_all.tbl CDD PLN02157 PLN02157 177817 PLN02157 3-hydroxyisobutyryl-CoA hydrolase-like protein 401 matched cddid_all.tbl CDD PLN02159 PLN02159 177818 PLN02159 Fe(2+) transport protein 337 matched cddid_all.tbl CDD PLN02160 PLN02160 177819 PLN02160 thiosulfate sulfurtransferase 136 matched cddid_all.tbl CDD PLN02161 PLN02161 177820 PLN02161 beta-amylase 531 matched cddid_all.tbl CDD PLN02162 PLN02162 177821 PLN02162 triacylglycerol lipase 475 matched cddid_all.tbl CDD PLN02164 PLN02164 177822 PLN02164 sulfotransferase 346 matched cddid_all.tbl CDD PLN02165 PLN02165 177823 PLN02165 adenylate isopentenyltransferase 334 matched cddid_all.tbl CDD PLN02166 PLN02166 165812 PLN02166 dTDP-glucose 4,6-dehydratase 436 matched cddid_all.tbl CDD PLN02167 PLN02167 215112 PLN02167 UDP-glycosyltransferase family protein 475 matched cddid_all.tbl CDD PLN02168 PLN02168 215113 PLN02168 copper ion binding / pectinesterase 545 matched cddid_all.tbl CDD PLN02169 PLN02169 177826 PLN02169 fatty acid (omega-1)-hydroxylase/midchain alkane hydroxylase 500 matched cddid_all.tbl CDD PLN02170 PLN02170 215114 PLN02170 probable pectinesterase/pectinesterase inhibitor 529 matched cddid_all.tbl CDD PLN02171 PLN02171 215115 PLN02171 endoglucanase 629 matched cddid_all.tbl CDD PLN02172 PLN02172 215116 PLN02172 flavin-containing monooxygenase FMO GS-OX 461 matched cddid_all.tbl CDD PLN02173 PLN02173 177830 PLN02173 UDP-glucosyl transferase family protein 449 matched cddid_all.tbl CDD PLN02174 PLN02174 177831 PLN02174 aldehyde dehydrogenase family 3 member H1 484 matched cddid_all.tbl CDD PLN02175 PLN02175 177832 PLN02175 endoglucanase 484 matched cddid_all.tbl CDD PLN02176 PLN02176 215117 PLN02176 putative pectinesterase 340 matched cddid_all.tbl CDD PLN02177 PLN02177 215118 PLN02177 glycerol-3-phosphate acyltransferase 497 matched cddid_all.tbl CDD PLN02178 PLN02178 177834 PLN02178 cinnamyl-alcohol dehydrogenase 375 matched cddid_all.tbl CDD PLN02179 PLN02179 177835 PLN02179 carbonic anhydrase 235 matched cddid_all.tbl CDD PLN02180 PLN02180 177836 PLN02180 gamma-glutamyl transpeptidase 4 639 matched cddid_all.tbl CDD PLN02182 PLN02182 177837 PLN02182 cytidine deaminase 339 matched cddid_all.tbl CDD PLN02183 PLN02183 165828 PLN02183 ferulate 5-hydroxylase 516 matched cddid_all.tbl CDD PLN02184 PLN02184 177838 PLN02184 superoxide dismutase [Fe] 212 matched cddid_all.tbl CDD PLN02187 PLN02187 215119 PLN02187 rooty/superroot1 462 matched cddid_all.tbl CDD PLN02188 PLN02188 215120 PLN02188 polygalacturonase/glycoside hydrolase family protein 404 matched cddid_all.tbl CDD PLN02189 PLN02189 215121 PLN02189 cellulose synthase 1040 matched cddid_all.tbl CDD PLN02190 PLN02190 215122 PLN02190 cellulose synthase-like protein 756 matched cddid_all.tbl CDD PLN02191 PLN02191 177843 PLN02191 L-ascorbate oxidase 574 matched cddid_all.tbl CDD PLN02192 PLN02192 215123 PLN02192 3-ketoacyl-CoA synthase 511 matched cddid_all.tbl CDD PLN02193 PLN02193 177844 PLN02193 nitrile-specifier protein 470 matched cddid_all.tbl CDD PLN02194 PLN02194 177845 PLN02194 cytochrome-c oxidase 265 matched cddid_all.tbl CDD PLN02195 PLN02195 215124 PLN02195 cellulose synthase A 977 matched cddid_all.tbl CDD PLN02196 PLN02196 177847 PLN02196 abscisic acid 8'-hydroxylase 463 matched cddid_all.tbl CDD PLN02197 PLN02197 177848 PLN02197 pectinesterase 588 matched cddid_all.tbl CDD PLN02198 PLN02198 177849 PLN02198 glutathione gamma-glutamylcysteinyltransferase 573 matched cddid_all.tbl CDD PLN02199 PLN02199 177850 PLN02199 shikimate kinase 303 matched cddid_all.tbl CDD PLN02200 PLN02200 215125 PLN02200 adenylate kinase family protein 234 matched cddid_all.tbl CDD PLN02201 PLN02201 177852 PLN02201 probable pectinesterase/pectinesterase inhibitor 520 matched cddid_all.tbl CDD PLN02202 PLN02202 177853 PLN02202 carbonate dehydratase 284 matched cddid_all.tbl CDD PLN02203 PLN02203 165847 PLN02203 aldehyde dehydrogenase 484 matched cddid_all.tbl CDD PLN02204 PLN02204 215126 PLN02204 diacylglycerol kinase 601 matched cddid_all.tbl CDD PLN02205 PLN02205 177855 PLN02205 alpha,alpha-trehalose-phosphate synthase [UDP-forming] 854 matched cddid_all.tbl CDD PLN02206 PLN02206 177856 PLN02206 UDP-glucuronate decarboxylase 442 matched cddid_all.tbl CDD PLN02207 PLN02207 177857 PLN02207 UDP-glycosyltransferase 468 matched cddid_all.tbl CDD PLN02208 PLN02208 177858 PLN02208 glycosyltransferase family protein 442 matched cddid_all.tbl CDD PLN02209 PLN02209 177859 PLN02209 serine carboxypeptidase 437 matched cddid_all.tbl CDD PLN02210 PLN02210 215127 PLN02210 UDP-glucosyl transferase 456 matched cddid_all.tbl CDD PLN02211 PLN02211 215128 PLN02211 methyl indole-3-acetate methyltransferase 273 matched cddid_all.tbl CDD PLN02213 PLN02213 165857 PLN02213 sinapoylglucose-malate O-sinapoyltransferase/ carboxypeptidase 319 matched cddid_all.tbl CDD PLN02214 PLN02214 177862 PLN02214 cinnamoyl-CoA reductase 342 matched cddid_all.tbl CDD PLN02216 PLN02216 215129 PLN02216 protein SRG1 357 matched cddid_all.tbl CDD PLN02217 PLN02217 215130 PLN02217 probable pectinesterase/pectinesterase inhibitor 670 matched cddid_all.tbl CDD PLN02218 PLN02218 177865 PLN02218 polygalacturonase ADPG 431 matched cddid_all.tbl CDD PLN02219 PLN02219 165863 PLN02219 probable galactinol--sucrose galactosyltransferase 2 775 matched cddid_all.tbl CDD PLN02220 PLN02220 177866 PLN02220 delta-9 acyl-lipid desaturase 299 matched cddid_all.tbl CDD PLN02221 PLN02221 177867 PLN02221 asparaginyl-tRNA synthetase 572 matched cddid_all.tbl CDD PLN02222 PLN02222 177868 PLN02222 phosphoinositide phospholipase C 2 581 matched cddid_all.tbl CDD PLN02223 PLN02223 165867 PLN02223 phosphoinositide phospholipase C 537 matched cddid_all.tbl CDD PLN02224 PLN02224 177869 PLN02224 methionine-tRNA ligase 616 matched cddid_all.tbl CDD PLN02225 PLN02225 177870 PLN02225 1-deoxy-D-xylulose-5-phosphate synthase 701 matched cddid_all.tbl CDD PLN02226 PLN02226 177871 PLN02226 2-oxoglutarate dehydrogenase E2 component 463 matched cddid_all.tbl CDD PLN02227 PLN02227 177872 PLN02227 fructose-bisphosphate aldolase I 399 matched cddid_all.tbl CDD PLN02228 PLN02228 177873 PLN02228 Phosphoinositide phospholipase C 567 matched cddid_all.tbl CDD PLN02229 PLN02229 177874 PLN02229 alpha-galactosidase 427 matched cddid_all.tbl CDD PLN02230 PLN02230 177875 PLN02230 phosphoinositide phospholipase C 4 598 matched cddid_all.tbl CDD PLN02231 PLN02231 177876 PLN02231 alanine transaminase 534 matched cddid_all.tbl CDD PLN02232 PLN02232 165876 PLN02232 ubiquinone biosynthesis methyltransferase 160 matched cddid_all.tbl CDD PLN02233 PLN02233 177877 PLN02233 ubiquinone biosynthesis methyltransferase 261 matched cddid_all.tbl CDD PLN02234 PLN02234 177878 PLN02234 1-deoxy-D-xylulose-5-phosphate synthase 641 matched cddid_all.tbl CDD PLN02235 PLN02235 177879 PLN02235 ATP citrate (pro-S)-lyase 423 matched cddid_all.tbl CDD PLN02236 PLN02236 177880 PLN02236 choline kinase 344 matched cddid_all.tbl CDD PLN02237 PLN02237 215131 PLN02237 glyceraldehyde-3-phosphate dehydrogenase B 442 matched cddid_all.tbl CDD PLN02238 PLN02238 215132 PLN02238 hypoxanthine phosphoribosyltransferase 189 matched cddid_all.tbl CDD PLN02240 PLN02240 177883 PLN02240 UDP-glucose 4-epimerase 352 matched cddid_all.tbl CDD PLN02241 PLN02241 215133 PLN02241 glucose-1-phosphate adenylyltransferase 436 matched cddid_all.tbl CDD PLN02242 PLN02242 215134 PLN02242 methionine gamma-lyase 418 matched cddid_all.tbl CDD PLN02243 PLN02243 177886 PLN02243 S-adenosylmethionine synthase 386 matched cddid_all.tbl CDD PLN02244 PLN02244 215135 PLN02244 tocopherol O-methyltransferase 340 matched cddid_all.tbl CDD PLN02245 PLN02245 215136 PLN02245 ATP phosphoribosyl transferase 403 matched cddid_all.tbl CDD PLN02246 PLN02246 215137 PLN02246 4-coumarate--CoA ligase 537 matched cddid_all.tbl CDD PLN02247 PLN02247 165890 PLN02247 indole-3-acetic acid-amido synthetase 606 matched cddid_all.tbl CDD PLN02248 PLN02248 215138 PLN02248 cellulose synthase-like protein 1135 matched cddid_all.tbl CDD PLN02249 PLN02249 177891 PLN02249 indole-3-acetic acid-amido synthetase 597 matched cddid_all.tbl CDD PLN02250 PLN02250 215139 PLN02250 lipid phosphate phosphatase 314 matched cddid_all.tbl CDD PLN02251 PLN02251 215140 PLN02251 pyrophosphate-dependent phosphofructokinase 568 matched cddid_all.tbl CDD PLN02252 PLN02252 215141 PLN02252 nitrate reductase [NADPH] 888 matched cddid_all.tbl CDD PLN02253 PLN02253 177895 PLN02253 xanthoxin dehydrogenase 280 matched cddid_all.tbl CDD PLN02254 PLN02254 215142 PLN02254 gibberellin 3-beta-dioxygenase 358 matched cddid_all.tbl CDD PLN02255 PLN02255 215143 PLN02255 H(+) -translocating inorganic pyrophosphatase 765 matched cddid_all.tbl CDD PLN02256 PLN02256 215144 PLN02256 arogenate dehydrogenase 304 matched cddid_all.tbl CDD PLN02257 PLN02257 177899 PLN02257 phosphoribosylamine--glycine ligase 434 matched cddid_all.tbl CDD PLN02258 PLN02258 215145 PLN02258 9-cis-epoxycarotenoid dioxygenase NCED 590 matched cddid_all.tbl CDD PLN02259 PLN02259 177901 PLN02259 branched-chain-amino-acid aminotransferase 2 388 matched cddid_all.tbl CDD PLN02260 PLN02260 215146 PLN02260 probable rhamnose biosynthetic enzyme 668 matched cddid_all.tbl CDD PLN02262 PLN02262 215147 PLN02262 fructose-1,6-bisphosphatase 340 matched cddid_all.tbl CDD PLN02263 PLN02263 177904 PLN02263 serine decarboxylase 470 matched cddid_all.tbl CDD PLN02264 PLN02264 215148 PLN02264 lipoxygenase 919 matched cddid_all.tbl CDD PLN02265 PLN02265 215149 PLN02265 probable phenylalanyl-tRNA synthetase beta chain 597 matched cddid_all.tbl CDD PLN02266 PLN02266 215150 PLN02266 endoglucanase 510 matched cddid_all.tbl CDD PLN02267 PLN02267 215151 PLN02267 enoyl-CoA hydratase/isomerase family protein 239 matched cddid_all.tbl CDD PLN02268 PLN02268 177909 PLN02268 probable polyamine oxidase 435 matched cddid_all.tbl CDD PLN02269 PLN02269 215152 PLN02269 Pyruvate dehydrogenase E1 component subunit alpha 362 matched cddid_all.tbl CDD PLN02270 PLN02270 165912 PLN02270 phospholipase D alpha 808 matched cddid_all.tbl CDD PLN02271 PLN02271 215153 PLN02271 serine hydroxymethyltransferase 586 matched cddid_all.tbl CDD PLN02272 PLN02272 177912 PLN02272 glyceraldehyde-3-phosphate dehydrogenase 421 matched cddid_all.tbl CDD PLN02274 PLN02274 215154 PLN02274 inosine-5'-monophosphate dehydrogenase 505 matched cddid_all.tbl CDD PLN02275 PLN02275 215155 PLN02275 transferase, transferring glycosyl groups 371 matched cddid_all.tbl CDD PLN02276 PLN02276 215156 PLN02276 gibberellin 20-oxidase 361 matched cddid_all.tbl CDD PLN02277 PLN02277 177916 PLN02277 H(+) -translocating inorganic pyrophosphatase 730 matched cddid_all.tbl CDD PLN02278 PLN02278 215157 PLN02278 succinic semialdehyde dehydrogenase 498 matched cddid_all.tbl CDD PLN02279 PLN02279 177918 PLN02279 ent-kaur-16-ene synthase 784 matched cddid_all.tbl CDD PLN02280 PLN02280 215158 PLN02280 IAA-amino acid hydrolase 478 matched cddid_all.tbl CDD PLN02281 PLN02281 177920 PLN02281 chlorophyllide a oxygenase 536 matched cddid_all.tbl CDD PLN02282 PLN02282 165923 PLN02282 phosphoglycerate kinase 401 matched cddid_all.tbl CDD PLN02283 PLN02283 177921 PLN02283 alpha-dioxygenase 633 matched cddid_all.tbl CDD PLN02284 PLN02284 177922 PLN02284 glutamine synthetase 354 matched cddid_all.tbl CDD PLN02285 PLN02285 215159 PLN02285 methionyl-tRNA formyltransferase 334 matched cddid_all.tbl CDD PLN02286 PLN02286 215160 PLN02286 arginine-tRNA ligase 576 matched cddid_all.tbl CDD PLN02287 PLN02287 215161 PLN02287 3-ketoacyl-CoA thiolase 452 matched cddid_all.tbl CDD PLN02288 PLN02288 215162 PLN02288 mannose-6-phosphate isomerase 394 matched cddid_all.tbl CDD PLN02289 PLN02289 215163 PLN02289 ribulose-bisphosphate carboxylase small chain 176 matched cddid_all.tbl CDD PLN02290 PLN02290 215164 PLN02290 cytokinin trans-hydroxylase 516 matched cddid_all.tbl CDD PLN02291 PLN02291 177928 PLN02291 phospho-2-dehydro-3-deoxyheptonate aldolase 474 matched cddid_all.tbl CDD PLN02292 PLN02292 215165 PLN02292 ferric-chelate reductase 702 matched cddid_all.tbl CDD PLN02293 PLN02293 177930 PLN02293 adenine phosphoribosyltransferase 187 matched cddid_all.tbl CDD PLN02294 PLN02294 177931 PLN02294 cytochrome c oxidase subunit Vb 174 matched cddid_all.tbl CDD PLN02295 PLN02295 215166 PLN02295 glycerol kinase 512 matched cddid_all.tbl CDD PLN02296 PLN02296 215167 PLN02296 carbonate dehydratase 269 matched cddid_all.tbl CDD PLN02297 PLN02297 177934 PLN02297 ribose-phosphate pyrophosphokinase 326 matched cddid_all.tbl CDD PLN02298 PLN02298 165939 PLN02298 hydrolase, alpha/beta fold family protein 330 matched cddid_all.tbl CDD PLN02299 PLN02299 215168 PLN02299 1-aminocyclopropane-1-carboxylate oxidase 321 matched cddid_all.tbl CDD PLN02300 PLN02300 215169 PLN02300 lactoylglutathione lyase 286 matched cddid_all.tbl CDD PLN02301 PLN02301 215170 PLN02301 pectinesterase/pectinesterase inhibitor 548 matched cddid_all.tbl CDD PLN02302 PLN02302 215171 PLN02302 ent-kaurenoic acid oxidase 490 matched cddid_all.tbl CDD PLN02303 PLN02303 215172 PLN02303 urease 837 matched cddid_all.tbl CDD PLN02304 PLN02304 215173 PLN02304 probable pectinesterase 379 matched cddid_all.tbl CDD PLN02305 PLN02305 215174 PLN02305 lipoxygenase 918 matched cddid_all.tbl CDD PLN02306 PLN02306 177941 PLN02306 hydroxypyruvate reductase 386 matched cddid_all.tbl CDD PLN02307 PLN02307 177942 PLN02307 phosphoglucomutase 579 matched cddid_all.tbl CDD PLN02308 PLN02308 177943 PLN02308 endoglucanase 492 matched cddid_all.tbl CDD PLN02309 PLN02309 215175 PLN02309 5'-adenylylsulfate reductase 457 matched cddid_all.tbl CDD PLN02310 PLN02310 215176 PLN02310 triacylglycerol lipase 405 matched cddid_all.tbl CDD PLN02311 PLN02311 215177 PLN02311 chalcone isomerase 271 matched cddid_all.tbl CDD PLN02312 PLN02312 215178 PLN02312 acyl-CoA oxidase 680 matched cddid_all.tbl CDD PLN02313 PLN02313 177947 PLN02313 Pectinesterase/pectinesterase inhibitor 587 matched cddid_all.tbl CDD PLN02314 PLN02314 215179 PLN02314 pectinesterase 586 matched cddid_all.tbl CDD PLN02315 PLN02315 177949 PLN02315 aldehyde dehydrogenase family 7 member 508 matched cddid_all.tbl CDD PLN02316 PLN02316 215180 PLN02316 synthase/transferase 1036 matched cddid_all.tbl CDD PLN02317 PLN02317 215181 PLN02317 arogenate dehydratase 382 matched cddid_all.tbl CDD PLN02318 PLN02318 177952 PLN02318 phosphoribulokinase/uridine kinase 656 matched cddid_all.tbl CDD PLN02319 PLN02319 177953 PLN02319 aminomethyltransferase 404 matched cddid_all.tbl CDD PLN02320 PLN02320 177954 PLN02320 seryl-tRNA synthetase 502 matched cddid_all.tbl CDD PLN02321 PLN02321 215182 PLN02321 2-isopropylmalate synthase 632 matched cddid_all.tbl CDD PLN02322 PLN02322 177956 PLN02322 acyl-CoA thioesterase 154 matched cddid_all.tbl CDD PLN02323 PLN02323 215183 PLN02323 probable fructokinase 330 matched cddid_all.tbl CDD PLN02324 PLN02324 177958 PLN02324 triacylglycerol lipase 415 matched cddid_all.tbl CDD PLN02325 PLN02325 215184 PLN02325 nudix hydrolase 144 matched cddid_all.tbl CDD PLN02326 PLN02326 215185 PLN02326 3-oxoacyl-[acyl-carrier-protein] synthase III 379 matched cddid_all.tbl CDD PLN02327 PLN02327 215186 PLN02327 CTP synthase 557 matched cddid_all.tbl CDD PLN02328 PLN02328 215187 PLN02328 lysine-specific histone demethylase 1 homolog 808 matched cddid_all.tbl CDD PLN02329 PLN02329 215188 PLN02329 3-isopropylmalate dehydrogenase 409 matched cddid_all.tbl CDD PLN02330 PLN02330 215189 PLN02330 4-coumarate--CoA ligase-like 1 546 matched cddid_all.tbl CDD PLN02331 PLN02331 177965 PLN02331 phosphoribosylglycinamide formyltransferase 207 matched cddid_all.tbl CDD PLN02332 PLN02332 215190 PLN02332 membrane bound O-acyl transferase (MBOAT) family protein 465 matched cddid_all.tbl CDD PLN02333 PLN02333 215191 PLN02333 glucose-6-phosphate 1-dehydrogenase 604 matched cddid_all.tbl CDD PLN02334 PLN02334 215192 PLN02334 ribulose-phosphate 3-epimerase 229 matched cddid_all.tbl CDD PLN02335 PLN02335 177969 PLN02335 anthranilate synthase 222 matched cddid_all.tbl CDD PLN02336 PLN02336 177970 PLN02336 phosphoethanolamine N-methyltransferase 475 matched cddid_all.tbl CDD PLN02337 PLN02337 215193 PLN02337 lipoxygenase 866 matched cddid_all.tbl CDD PLN02338 PLN02338 177972 PLN02338 3-phosphoshikimate 1-carboxyvinyltransferase 443 matched cddid_all.tbl CDD PLN02339 PLN02339 177973 PLN02339 NAD+ synthase (glutamine-hydrolysing) 700 matched cddid_all.tbl CDD PLN02340 PLN02340 215194 PLN02340 endoglucanase 614 matched cddid_all.tbl CDD PLN02341 PLN02341 215195 PLN02341 pfkB-type carbohydrate kinase family protein 470 matched cddid_all.tbl CDD PLN02342 PLN02342 177976 PLN02342 ornithine carbamoyltransferase 348 matched cddid_all.tbl CDD PLN02343 PLN02343 177977 PLN02343 allene oxide cyclase 229 matched cddid_all.tbl CDD PLN02344 PLN02344 177978 PLN02344 chorismate mutase 284 matched cddid_all.tbl CDD PLN02345 PLN02345 177979 PLN02345 endoglucanase 469 matched cddid_all.tbl CDD PLN02346 PLN02346 215196 PLN02346 histidine biosynthesis bifunctional protein hisIE 271 matched cddid_all.tbl CDD PLN02347 PLN02347 215197 PLN02347 GMP synthetase 536 matched cddid_all.tbl CDD PLN02348 PLN02348 215198 PLN02348 phosphoribulokinase 395 matched cddid_all.tbl CDD PLN02349 PLN02349 215199 PLN02349 glycerol-3-phosphate acyltransferase 426 matched cddid_all.tbl CDD PLN02350 PLN02350 215200 PLN02350 phosphogluconate dehydrogenase (decarboxylating) 493 matched cddid_all.tbl CDD PLN02351 PLN02351 215201 PLN02351 cytochromes b561 family protein 242 matched cddid_all.tbl CDD PLN02352 PLN02352 215202 PLN02352 phospholipase D epsilon 758 matched cddid_all.tbl CDD PLN02353 PLN02353 177986 PLN02353 probable UDP-glucose 6-dehydrogenase 473 matched cddid_all.tbl CDD PLN02354 PLN02354 177987 PLN02354 copper ion binding / oxidoreductase 552 matched cddid_all.tbl CDD PLN02355 PLN02355 215203 PLN02355 probable galactinol--sucrose galactosyltransferase 1 758 matched cddid_all.tbl CDD PLN02356 PLN02356 215204 PLN02356 phosphateglycerate kinase 423 matched cddid_all.tbl CDD PLN02357 PLN02357 215205 PLN02357 serine acetyltransferase 360 matched cddid_all.tbl CDD PLN02358 PLN02358 165999 PLN02358 glyceraldehyde-3-phosphate dehydrogenase 338 matched cddid_all.tbl CDD PLN02359 PLN02359 166000 PLN02359 ethanolaminephosphotransferase 389 matched cddid_all.tbl CDD PLN02360 PLN02360 166001 PLN02360 probable 6-phosphogluconolactonase 268 matched cddid_all.tbl CDD PLN02361 PLN02361 177990 PLN02361 alpha-amylase 401 matched cddid_all.tbl CDD PLN02362 PLN02362 215206 PLN02362 hexokinase 509 matched cddid_all.tbl CDD PLN02363 PLN02363 215207 PLN02363 phosphoribosylanthranilate isomerase 256 matched cddid_all.tbl CDD PLN02364 PLN02364 166005 PLN02364 L-ascorbate peroxidase 1 250 matched cddid_all.tbl CDD PLN02365 PLN02365 177993 PLN02365 2-oxoglutarate-dependent dioxygenase 300 matched cddid_all.tbl CDD PLN02366 PLN02366 215208 PLN02366 spermidine synthase 308 matched cddid_all.tbl CDD PLN02367 PLN02367 177995 PLN02367 lactoylglutathione lyase 233 matched cddid_all.tbl CDD PLN02368 PLN02368 177996 PLN02368 alanine transaminase 407 matched cddid_all.tbl CDD PLN02369 PLN02369 215209 PLN02369 ribose-phosphate pyrophosphokinase 302 matched cddid_all.tbl CDD PLN02370 PLN02370 215210 PLN02370 acyl-ACP thioesterase 419 matched cddid_all.tbl CDD PLN02371 PLN02371 215211 PLN02371 phosphoglucosamine mutase family protein 583 matched cddid_all.tbl CDD PLN02372 PLN02372 215212 PLN02372 violaxanthin de-epoxidase 455 matched cddid_all.tbl CDD PLN02373 PLN02373 178001 PLN02373 soluble inorganic pyrophosphatase 188 matched cddid_all.tbl CDD PLN02374 PLN02374 215213 PLN02374 pyruvate dehydrogenase (acetyl-transferring) 433 matched cddid_all.tbl CDD PLN02375 PLN02375 178003 PLN02375 molybderin biosynthesis protein CNX3 270 matched cddid_all.tbl CDD PLN02376 PLN02376 178004 PLN02376 1-aminocyclopropane-1-carboxylate synthase 496 matched cddid_all.tbl CDD PLN02377 PLN02377 166018 PLN02377 3-ketoacyl-CoA synthase 502 matched cddid_all.tbl CDD PLN02378 PLN02378 166019 PLN02378 glutathione S-transferase DHAR1 213 matched cddid_all.tbl CDD PLN02379 PLN02379 178005 PLN02379 pfkB-type carbohydrate kinase family protein 367 matched cddid_all.tbl CDD PLN02380 PLN02380 178006 PLN02380 1-acyl-sn-glycerol-3-phosphate acyltransferase 376 matched cddid_all.tbl CDD PLN02381 PLN02381 215214 PLN02381 valyl-tRNA synthetase 1066 matched cddid_all.tbl CDD PLN02382 PLN02382 178008 PLN02382 probable sucrose-phosphatase 413 matched cddid_all.tbl CDD PLN02383 PLN02383 178009 PLN02383 aspartate semialdehyde dehydrogenase 344 matched cddid_all.tbl CDD PLN02384 PLN02384 215215 PLN02384 ribose-5-phosphate isomerase 264 matched cddid_all.tbl CDD PLN02385 PLN02385 215216 PLN02385 hydrolase; alpha/beta fold family protein 349 matched cddid_all.tbl CDD PLN02386 PLN02386 166027 PLN02386 superoxide dismutase [Cu-Zn] 152 matched cddid_all.tbl CDD PLN02387 PLN02387 215217 PLN02387 long-chain-fatty-acid-CoA ligase family protein 696 matched cddid_all.tbl CDD PLN02388 PLN02388 215218 PLN02388 phosphopantetheine adenylyltransferase 177 matched cddid_all.tbl CDD PLN02389 PLN02389 215219 PLN02389 biotin synthase 379 matched cddid_all.tbl CDD PLN02390 PLN02390 178014 PLN02390 molybdopterin synthase catalytic subunit 111 matched cddid_all.tbl CDD PLN02392 PLN02392 178015 PLN02392 probable steroid reductase DET2 260 matched cddid_all.tbl CDD PLN02393 PLN02393 215220 PLN02393 leucoanthocyanidin dioxygenase like protein 362 matched cddid_all.tbl CDD PLN02394 PLN02394 215221 PLN02394 trans-cinnamate 4-monooxygenase 503 matched cddid_all.tbl CDD PLN02395 PLN02395 166036 PLN02395 glutathione S-transferase 215 matched cddid_all.tbl CDD PLN02396 PLN02396 178018 PLN02396 hexaprenyldihydroxybenzoate methyltransferase 322 matched cddid_all.tbl CDD PLN02397 PLN02397 215222 PLN02397 aspartate transaminase 423 matched cddid_all.tbl CDD PLN02398 PLN02398 215223 PLN02398 hydroxyacylglutathione hydrolase 329 matched cddid_all.tbl CDD PLN02399 PLN02399 178021 PLN02399 phospholipid hydroperoxide glutathione peroxidase 236 matched cddid_all.tbl CDD PLN02400 PLN02400 215224 PLN02400 cellulose synthase 1085 matched cddid_all.tbl CDD PLN02401 PLN02401 215225 PLN02401 diacylglycerol o-acyltransferase 446 matched cddid_all.tbl CDD PLN02402 PLN02402 178024 PLN02402 cytidine deaminase 303 matched cddid_all.tbl CDD PLN02403 PLN02403 178025 PLN02403 aminocyclopropanecarboxylate oxidase 303 matched cddid_all.tbl CDD PLN02404 PLN02404 178026 PLN02404 6,7-dimethyl-8-ribityllumazine synthase 141 matched cddid_all.tbl CDD PLN02405 PLN02405 215226 PLN02405 hexokinase 497 matched cddid_all.tbl CDD PLN02406 PLN02406 215227 PLN02406 ethanolamine-phosphate cytidylyltransferase 418 matched cddid_all.tbl CDD PLN02407 PLN02407 178029 PLN02407 diphosphomevalonate decarboxylase 343 matched cddid_all.tbl CDD PLN02408 PLN02408 215228 PLN02408 phospholipase A1 365 matched cddid_all.tbl CDD PLN02409 PLN02409 178031 PLN02409 serine--glyoxylate aminotransaminase 401 matched cddid_all.tbl CDD PLN02410 PLN02410 178032 PLN02410 UDP-glucoronosyl/UDP-glucosyl transferase family protein 451 matched cddid_all.tbl CDD PLN02411 PLN02411 178033 PLN02411 12-oxophytodienoate reductase 391 matched cddid_all.tbl CDD PLN02412 PLN02412 166053 PLN02412 probable glutathione peroxidase 167 matched cddid_all.tbl CDD PLN02413 PLN02413 215229 PLN02413 choline-phosphate cytidylyltransferase 294 matched cddid_all.tbl CDD PLN02414 PLN02414 178035 PLN02414 glycine dehydrogenase (decarboxylating) 993 matched cddid_all.tbl CDD PLN02415 PLN02415 178036 PLN02415 uricase 304 matched cddid_all.tbl CDD PLN02416 PLN02416 178037 PLN02416 probable pectinesterase/pectinesterase inhibitor 541 matched cddid_all.tbl CDD PLN02417 PLN02417 178038 PLN02417 dihydrodipicolinate synthase 280 matched cddid_all.tbl CDD PLN02418 PLN02418 215230 PLN02418 delta-1-pyrroline-5-carboxylate synthase 718 matched cddid_all.tbl CDD PLN02419 PLN02419 166060 PLN02419 methylmalonate-semialdehyde dehydrogenase [acylating] 604 matched cddid_all.tbl CDD PLN02420 PLN02420 178040 PLN02420 endoglucanase 525 matched cddid_all.tbl CDD PLN02421 PLN02421 215231 PLN02421 phosphotransferase, alcohol group as acceptor/kinase 330 matched cddid_all.tbl CDD PLN02422 PLN02422 215232 PLN02422 dephospho-CoA kinase 232 matched cddid_all.tbl CDD PLN02423 PLN02423 178043 PLN02423 phosphomannomutase 245 matched cddid_all.tbl CDD PLN02424 PLN02424 215233 PLN02424 ketopantoate hydroxymethyltransferase 332 matched cddid_all.tbl CDD PLN02425 PLN02425 215234 PLN02425 probable fructose-bisphosphate aldolase 390 matched cddid_all.tbl CDD PLN02426 PLN02426 215235 PLN02426 cytochrome P450, family 94, subfamily C protein 502 matched cddid_all.tbl CDD PLN02427 PLN02427 178047 PLN02427 UDP-apiose/xylose synthase 386 matched cddid_all.tbl CDD PLN02428 PLN02428 215236 PLN02428 lipoic acid synthase 349 matched cddid_all.tbl CDD PLN02429 PLN02429 166070 PLN02429 triosephosphate isomerase 315 matched cddid_all.tbl CDD PLN02430 PLN02430 178049 PLN02430 long-chain-fatty-acid-CoA ligase 660 matched cddid_all.tbl CDD PLN02431 PLN02431 178050 PLN02431 ferredoxin--nitrite reductase 587 matched cddid_all.tbl CDD PLN02432 PLN02432 178051 PLN02432 putative pectinesterase 293 matched cddid_all.tbl CDD PLN02433 PLN02433 215237 PLN02433 uroporphyrinogen decarboxylase 345 matched cddid_all.tbl CDD PLN02434 PLN02434 178053 PLN02434 fatty acid hydroxylase 237 matched cddid_all.tbl CDD PLN02435 PLN02435 215238 PLN02435 probable UDP-N-acetylglucosamine pyrophosphorylase 493 matched cddid_all.tbl CDD PLN02436 PLN02436 215239 PLN02436 cellulose synthase A 1094 matched cddid_all.tbl CDD PLN02437 PLN02437 178056 PLN02437 ribonucleoside--diphosphate reductase large subunit 813 matched cddid_all.tbl CDD PLN02438 PLN02438 178057 PLN02438 inositol-3-phosphate synthase 510 matched cddid_all.tbl CDD PLN02439 PLN02439 215240 PLN02439 arginine decarboxylase 559 matched cddid_all.tbl CDD PLN02440 PLN02440 215241 PLN02440 amidophosphoribosyltransferase 479 matched cddid_all.tbl CDD PLN02441 PLN02441 215242 PLN02441 cytokinin dehydrogenase 525 matched cddid_all.tbl CDD PLN02442 PLN02442 178061 PLN02442 S-formylglutathione hydrolase 283 matched cddid_all.tbl CDD PLN02443 PLN02443 178062 PLN02443 acyl-coenzyme A oxidase 664 matched cddid_all.tbl CDD PLN02444 PLN02444 215243 PLN02444 HMP-P synthase 642 matched cddid_all.tbl CDD PLN02445 PLN02445 215244 PLN02445 anthranilate synthase component I 523 matched cddid_all.tbl CDD PLN02446 PLN02446 215245 PLN02446 (5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase 262 matched cddid_all.tbl CDD PLN02447 PLN02447 215246 PLN02447 1,4-alpha-glucan-branching enzyme 758 matched cddid_all.tbl CDD PLN02448 PLN02448 215247 PLN02448 UDP-glycosyltransferase family protein 459 matched cddid_all.tbl CDD PLN02449 PLN02449 178068 PLN02449 ferrochelatase 485 matched cddid_all.tbl CDD PLN02450 PLN02450 178069 PLN02450 1-aminocyclopropane-1-carboxylate synthase 468 matched cddid_all.tbl CDD PLN02451 PLN02451 215248 PLN02451 homoserine kinase 370 matched cddid_all.tbl CDD PLN02452 PLN02452 178071 PLN02452 phosphoserine transaminase 365 matched cddid_all.tbl CDD PLN02453 PLN02453 178072 PLN02453 complex I subunit 105 matched cddid_all.tbl CDD PLN02454 PLN02454 215249 PLN02454 triacylglycerol lipase 414 matched cddid_all.tbl CDD PLN02455 PLN02455 178074 PLN02455 fructose-bisphosphate aldolase 358 matched cddid_all.tbl CDD PLN02456 PLN02456 215250 PLN02456 citrate synthase 455 matched cddid_all.tbl CDD PLN02457 PLN02457 215251 PLN02457 phenylalanine ammonia-lyase 706 matched cddid_all.tbl CDD PLN02458 PLN02458 215252 PLN02458 transferase, transferring glycosyl groups 346 matched cddid_all.tbl CDD PLN02459 PLN02459 215253 PLN02459 probable adenylate kinase 261 matched cddid_all.tbl CDD PLN02460 PLN02460 215254 PLN02460 indole-3-glycerol-phosphate synthase 338 matched cddid_all.tbl CDD PLN02461 PLN02461 215255 PLN02461 Probable pyruvate kinase 511 matched cddid_all.tbl CDD PLN02462 PLN02462 215256 PLN02462 sedoheptulose-1,7-bisphosphatase 304 matched cddid_all.tbl CDD PLN02463 PLN02463 178082 PLN02463 lycopene beta cyclase 447 matched cddid_all.tbl CDD PLN02464 PLN02464 215257 PLN02464 glycerol-3-phosphate dehydrogenase 627 matched cddid_all.tbl CDD PLN02465 PLN02465 215258 PLN02465 L-galactono-1,4-lactone dehydrogenase 573 matched cddid_all.tbl CDD PLN02466 PLN02466 215259 PLN02466 aldehyde dehydrogenase family 2 member 538 matched cddid_all.tbl CDD PLN02467 PLN02467 215260 PLN02467 betaine aldehyde dehydrogenase 503 matched cddid_all.tbl CDD PLN02468 PLN02468 178087 PLN02468 putative pectinesterase/pectinesterase inhibitor 565 matched cddid_all.tbl CDD PLN02469 PLN02469 178088 PLN02469 hydroxyacylglutathione hydrolase 258 matched cddid_all.tbl CDD PLN02470 PLN02470 215261 PLN02470 acetolactate synthase 585 matched cddid_all.tbl CDD PLN02471 PLN02471 215262 PLN02471 superoxide dismutase [Mn] 231 matched cddid_all.tbl CDD PLN02472 PLN02472 215263 PLN02472 uncharacterized protein 246 matched cddid_all.tbl CDD PLN02473 PLN02473 166114 PLN02473 glutathione S-transferase 214 matched cddid_all.tbl CDD PLN02474 PLN02474 178092 PLN02474 UTP--glucose-1-phosphate uridylyltransferase 469 matched cddid_all.tbl CDD PLN02475 PLN02475 215264 PLN02475 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase 766 matched cddid_all.tbl CDD PLN02476 PLN02476 178094 PLN02476 O-methyltransferase 278 matched cddid_all.tbl CDD PLN02477 PLN02477 178095 PLN02477 glutamate dehydrogenase 410 matched cddid_all.tbl CDD PLN02478 PLN02478 215265 PLN02478 alternative oxidase 328 matched cddid_all.tbl CDD PLN02479 PLN02479 178097 PLN02479 acetate-CoA ligase 567 matched cddid_all.tbl CDD PLN02480 PLN02480 178098 PLN02480 Probable pectinesterase 343 matched cddid_all.tbl CDD PLN02481 PLN02481 215266 PLN02481 Omega-hydroxypalmitate O-feruloyl transferase 436 matched cddid_all.tbl CDD PLN02482 PLN02482 178100 PLN02482 glutamate-1-semialdehyde 2,1-aminomutase 474 matched cddid_all.tbl CDD PLN02483 PLN02483 178101 PLN02483 serine palmitoyltransferase 489 matched cddid_all.tbl CDD PLN02484 PLN02484 178102 PLN02484 probable pectinesterase/pectinesterase inhibitor 587 matched cddid_all.tbl CDD PLN02485 PLN02485 215267 PLN02485 oxidoreductase 329 matched cddid_all.tbl CDD PLN02486 PLN02486 178104 PLN02486 aminoacyl-tRNA ligase 383 matched cddid_all.tbl CDD PLN02487 PLN02487 215268 PLN02487 zeta-carotene desaturase 569 matched cddid_all.tbl CDD PLN02488 PLN02488 178106 PLN02488 probable pectinesterase/pectinesterase inhibitor 509 matched cddid_all.tbl CDD PLN02489 PLN02489 215269 PLN02489 homocysteine S-methyltransferase 335 matched cddid_all.tbl CDD PLN02490 PLN02490 215270 PLN02490 MPBQ/MSBQ methyltransferase 340 matched cddid_all.tbl CDD PLN02491 PLN02491 215271 PLN02491 carotenoid 9,10(9',10')-cleavage dioxygenase 545 matched cddid_all.tbl CDD PLN02492 PLN02492 215272 PLN02492 ribonucleoside-diphosphate reductase 324 matched cddid_all.tbl CDD PLN02493 PLN02493 166134 PLN02493 probable peroxisomal (S)-2-hydroxy-acid oxidase 367 matched cddid_all.tbl CDD PLN02494 PLN02494 178111 PLN02494 adenosylhomocysteinase 477 matched cddid_all.tbl CDD PLN02495 PLN02495 215273 PLN02495 oxidoreductase, acting on the CH-CH group of donors 385 matched cddid_all.tbl CDD PLN02496 PLN02496 215274 PLN02496 probable phosphopantothenoylcysteine decarboxylase 209 matched cddid_all.tbl CDD PLN02497 PLN02497 178113 PLN02497 probable pectinesterase 331 matched cddid_all.tbl CDD PLN02498 PLN02498 215275 PLN02498 omega-3 fatty acid desaturase 450 matched cddid_all.tbl CDD PLN02499 PLN02499 178115 PLN02499 glycerol-3-phosphate acyltransferase 498 matched cddid_all.tbl CDD PLN02500 PLN02500 215276 PLN02500 cytochrome P450 90B1 490 matched cddid_all.tbl CDD PLN02501 PLN02501 215277 PLN02501 digalactosyldiacylglycerol synthase 794 matched cddid_all.tbl CDD PLN02502 PLN02502 215278 PLN02502 lysyl-tRNA synthetase 553 matched cddid_all.tbl CDD PLN02503 PLN02503 215279 PLN02503 fatty acyl-CoA reductase 2 605 matched cddid_all.tbl CDD PLN02504 PLN02504 178120 PLN02504 nitrilase 346 matched cddid_all.tbl CDD PLN02505 PLN02505 178121 PLN02505 omega-6 fatty acid desaturase 381 matched cddid_all.tbl CDD PLN02506 PLN02506 215280 PLN02506 putative pectinesterase/pectinesterase inhibitor 537 matched cddid_all.tbl CDD PLN02507 PLN02507 215281 PLN02507 glutathione reductase 499 matched cddid_all.tbl CDD PLN02508 PLN02508 178124 PLN02508 magnesium-protoporphyrin IX monomethyl ester [oxidative] cyclase 357 matched cddid_all.tbl CDD PLN02509 PLN02509 178125 PLN02509 cystathionine beta-lyase 464 matched cddid_all.tbl CDD PLN02510 PLN02510 178126 PLN02510 probable 1-acyl-sn-glycerol-3-phosphate acyltransferase 374 matched cddid_all.tbl CDD PLN02511 PLN02511 215282 PLN02511 hydrolase 388 matched cddid_all.tbl CDD PLN02512 PLN02512 178128 PLN02512 acetylglutamate kinase 309 matched cddid_all.tbl CDD PLN02513 PLN02513 178129 PLN02513 adenylosuccinate synthase 427 matched cddid_all.tbl CDD PLN02514 PLN02514 166155 PLN02514 cinnamyl-alcohol dehydrogenase 357 matched cddid_all.tbl CDD PLN02515 PLN02515 178130 PLN02515 naringenin,2-oxoglutarate 3-dioxygenase 358 matched cddid_all.tbl CDD PLN02516 PLN02516 178131 PLN02516 methylenetetrahydrofolate dehydrogenase (NADP+) 299 matched cddid_all.tbl CDD PLN02517 PLN02517 178132 PLN02517 phosphatidylcholine-sterol O-acyltransferase 642 matched cddid_all.tbl CDD PLN02518 PLN02518 215283 PLN02518 pheophorbide a oxygenase 539 matched cddid_all.tbl CDD PLN02519 PLN02519 215284 PLN02519 isovaleryl-CoA dehydrogenase 404 matched cddid_all.tbl CDD PLN02520 PLN02520 178135 PLN02520 bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase 529 matched cddid_all.tbl CDD PLN02521 PLN02521 215285 PLN02521 galactokinase 497 matched cddid_all.tbl CDD PLN02522 PLN02522 178137 PLN02522 ATP citrate (pro-S)-lyase 608 matched cddid_all.tbl CDD PLN02523 PLN02523 215286 PLN02523 galacturonosyltransferase 559 matched cddid_all.tbl CDD PLN02524 PLN02524 215287 PLN02524 S-adenosylmethionine decarboxylase 355 matched cddid_all.tbl CDD PLN02525 PLN02525 215288 PLN02525 phosphatidic acid phosphatase family protein 352 matched cddid_all.tbl CDD PLN02526 PLN02526 178141 PLN02526 acyl-coenzyme A oxidase 412 matched cddid_all.tbl CDD PLN02527 PLN02527 178142 PLN02527 aspartate carbamoyltransferase 306 matched cddid_all.tbl CDD PLN02528 PLN02528 215289 PLN02528 2-oxoisovalerate dehydrogenase E2 component 416 matched cddid_all.tbl CDD PLN02529 PLN02529 178144 PLN02529 lysine-specific histone demethylase 1 738 matched cddid_all.tbl CDD PLN02530 PLN02530 178145 PLN02530 histidine-tRNA ligase 487 matched cddid_all.tbl CDD PLN02531 PLN02531 215290 PLN02531 GTP cyclohydrolase I 469 matched cddid_all.tbl CDD PLN02532 PLN02532 215291 PLN02532 asparagine-tRNA synthetase 633 matched cddid_all.tbl CDD PLN02533 PLN02533 215292 PLN02533 probable purple acid phosphatase 427 matched cddid_all.tbl CDD PLN02534 PLN02534 215293 PLN02534 UDP-glycosyltransferase 491 matched cddid_all.tbl CDD PLN02535 PLN02535 215294 PLN02535 glycolate oxidase 364 matched cddid_all.tbl CDD PLN02536 PLN02536 178151 PLN02536 diaminopimelate epimerase 267 matched cddid_all.tbl CDD PLN02537 PLN02537 178152 PLN02537 diaminopimelate decarboxylase 410 matched cddid_all.tbl CDD PLN02538 PLN02538 215295 PLN02538 2,3-bisphosphoglycerate-independent phosphoglycerate mutase 558 matched cddid_all.tbl CDD PLN02539 PLN02539 178154 PLN02539 glucose-6-phosphate 1-dehydrogenase 491 matched cddid_all.tbl CDD PLN02540 PLN02540 215296 PLN02540 methylenetetrahydrofolate reductase 565 matched cddid_all.tbl CDD PLN02541 PLN02541 215297 PLN02541 uracil phosphoribosyltransferase 244 matched cddid_all.tbl CDD PLN02542 PLN02542 215298 PLN02542 fructose-1,6-bisphosphatase 412 matched cddid_all.tbl CDD PLN02543 PLN02543 215299 PLN02543 pfkB-type carbohydrate kinase family protein 496 matched cddid_all.tbl CDD PLN02544 PLN02544 178159 PLN02544 phosphoribosylaminoimidazole-succinocarboxamide synthase 370 matched cddid_all.tbl CDD PLN02545 PLN02545 215300 PLN02545 3-hydroxybutyryl-CoA dehydrogenase 295 matched cddid_all.tbl CDD PLN02546 PLN02546 215301 PLN02546 glutathione reductase 558 matched cddid_all.tbl CDD PLN02547 PLN02547 215302 PLN02547 dUTP pyrophosphatase 157 matched cddid_all.tbl CDD PLN02548 PLN02548 178163 PLN02548 adenosine kinase 332 matched cddid_all.tbl CDD PLN02549 PLN02549 178164 PLN02549 asparagine synthase (glutamine-hydrolyzing) 578 matched cddid_all.tbl CDD PLN02550 PLN02550 178165 PLN02550 threonine dehydratase 591 matched cddid_all.tbl CDD PLN02551 PLN02551 178166 PLN02551 aspartokinase 521 matched cddid_all.tbl CDD PLN02552 PLN02552 215303 PLN02552 isopentenyl-diphosphate delta-isomerase 247 matched cddid_all.tbl CDD PLN02553 PLN02553 178168 PLN02553 inositol-phosphate phosphatase 270 matched cddid_all.tbl CDD PLN02554 PLN02554 215304 PLN02554 UDP-glycosyltransferase family protein 481 matched cddid_all.tbl CDD PLN02555 PLN02555 178170 PLN02555 limonoid glucosyltransferase 480 matched cddid_all.tbl CDD PLN02556 PLN02556 178171 PLN02556 cysteine synthase/L-3-cyanoalanine synthase 368 matched cddid_all.tbl CDD PLN02557 PLN02557 178172 PLN02557 phosphoribosylformylglycinamidine cyclo-ligase 379 matched cddid_all.tbl CDD PLN02558 PLN02558 166199 PLN02558 CDP-diacylglycerol-glycerol-3-phosphate/ 3-phosphatidyltransferase 203 matched cddid_all.tbl CDD PLN02559 PLN02559 178173 PLN02559 chalcone--flavonone isomerase 230 matched cddid_all.tbl CDD PLN02560 PLN02560 178174 PLN02560 enoyl-CoA reductase 308 matched cddid_all.tbl CDD PLN02561 PLN02561 178175 PLN02561 triosephosphate isomerase 253 matched cddid_all.tbl CDD PLN02562 PLN02562 215305 PLN02562 UDP-glycosyltransferase 448 matched cddid_all.tbl CDD PLN02563 PLN02563 178177 PLN02563 aminoacyl-tRNA ligase 963 matched cddid_all.tbl CDD PLN02564 PLN02564 178178 PLN02564 6-phosphofructokinase 484 matched cddid_all.tbl CDD PLN02565 PLN02565 166206 PLN02565 cysteine synthase 322 matched cddid_all.tbl CDD PLN02566 PLN02566 215306 PLN02566 amine oxidase (copper-containing) 646 matched cddid_all.tbl CDD PLN02567 PLN02567 215307 PLN02567 alpha,alpha-trehalase 554 matched cddid_all.tbl CDD PLN02568 PLN02568 215308 PLN02568 polyamine oxidase 539 matched cddid_all.tbl CDD PLN02569 PLN02569 178182 PLN02569 threonine synthase 484 matched cddid_all.tbl CDD PLN02571 PLN02571 215309 PLN02571 triacylglycerol lipase 413 matched cddid_all.tbl CDD PLN02572 PLN02572 215310 PLN02572 UDP-sulfoquinovose synthase 442 matched cddid_all.tbl CDD PLN02573 PLN02573 215311 PLN02573 pyruvate decarboxylase 578 matched cddid_all.tbl CDD PLN02574 PLN02574 215312 PLN02574 4-coumarate--CoA ligase-like 560 matched cddid_all.tbl CDD PLN02575 PLN02575 215313 PLN02575 haloacid dehalogenase-like hydrolase 381 matched cddid_all.tbl CDD PLN02576 PLN02576 215314 PLN02576 protoporphyrinogen oxidase 496 matched cddid_all.tbl CDD PLN02577 PLN02577 178189 PLN02577 hydroxymethylglutaryl-CoA synthase 459 matched cddid_all.tbl CDD PLN02578 PLN02578 215315 PLN02578 hydrolase 354 matched cddid_all.tbl CDD PLN02579 PLN02579 215316 PLN02579 sphingolipid delta-4 desaturase 323 matched cddid_all.tbl CDD PLN02580 PLN02580 215317 PLN02580 trehalose-phosphatase 384 matched cddid_all.tbl CDD PLN02581 PLN02581 215318 PLN02581 red chlorophyll catabolite reductase 267 matched cddid_all.tbl CDD PLN02582 PLN02582 178194 PLN02582 1-deoxy-D-xylulose-5-phosphate synthase 677 matched cddid_all.tbl CDD PLN02583 PLN02583 178195 PLN02583 cinnamoyl-CoA reductase 297 matched cddid_all.tbl CDD PLN02584 PLN02584 178196 PLN02584 5'-methylthioadenosine nucleosidase 249 matched cddid_all.tbl CDD PLN02585 PLN02585 215319 PLN02585 magnesium protoporphyrin IX methyltransferase 315 matched cddid_all.tbl CDD PLN02586 PLN02586 166227 PLN02586 probable cinnamyl alcohol dehydrogenase 360 matched cddid_all.tbl CDD PLN02587 PLN02587 178198 PLN02587 L-galactose dehydrogenase 314 matched cddid_all.tbl CDD PLN02588 PLN02588 215320 PLN02588 glycerol-3-phosphate acyltransferase 525 matched cddid_all.tbl CDD PLN02589 PLN02589 166230 PLN02589 caffeoyl-CoA O-methyltransferase 247 matched cddid_all.tbl CDD PLN02590 PLN02590 178200 PLN02590 probable tyrosine decarboxylase 539 matched cddid_all.tbl CDD PLN02591 PLN02591 178201 PLN02591 tryptophan synthase 250 matched cddid_all.tbl CDD PLN02592 PLN02592 215321 PLN02592 ent-copalyl diphosphate synthase 800 matched cddid_all.tbl CDD PLN02593 PLN02593 178203 PLN02593 adrenodoxin-like ferredoxin protein 117 matched cddid_all.tbl CDD PLN02594 PLN02594 215322 PLN02594 phosphatidate cytidylyltransferase 342 matched cddid_all.tbl CDD PLN02595 PLN02595 178205 PLN02595 cytochrome c oxidase subunit VI protein 102 matched cddid_all.tbl CDD PLN02596 PLN02596 178206 PLN02596 hexokinase-like 490 matched cddid_all.tbl CDD PLN02597 PLN02597 178207 PLN02597 phosphoenolpyruvate carboxykinase [ATP] 555 matched cddid_all.tbl CDD PLN02598 PLN02598 215323 PLN02598 omega-6 fatty acid desaturase 421 matched cddid_all.tbl CDD PLN02599 PLN02599 178209 PLN02599 dihydroorotase 364 matched cddid_all.tbl CDD PLN02600 PLN02600 178210 PLN02600 enoyl-CoA hydratase 251 matched cddid_all.tbl CDD PLN02601 PLN02601 178211 PLN02601 beta-carotene hydroxylase 303 matched cddid_all.tbl CDD PLN02602 PLN02602 178212 PLN02602 lactate dehydrogenase 350 matched cddid_all.tbl CDD PLN02603 PLN02603 178213 PLN02603 asparaginyl-tRNA synthetase 565 matched cddid_all.tbl CDD PLN02604 PLN02604 215324 PLN02604 oxidoreductase 566 matched cddid_all.tbl CDD PLN02605 PLN02605 215325 PLN02605 monogalactosyldiacylglycerol synthase 382 matched cddid_all.tbl CDD PLN02606 PLN02606 215326 PLN02606 palmitoyl-protein thioesterase 306 matched cddid_all.tbl CDD PLN02607 PLN02607 215327 PLN02607 1-aminocyclopropane-1-carboxylate synthase 447 matched cddid_all.tbl CDD PLN02608 PLN02608 178218 PLN02608 L-ascorbate peroxidase 289 matched cddid_all.tbl CDD PLN02609 PLN02609 215328 PLN02609 catalase 492 matched cddid_all.tbl CDD PLN02610 PLN02610 215329 PLN02610 probable methionyl-tRNA synthetase 801 matched cddid_all.tbl CDD PLN02611 PLN02611 178221 PLN02611 glutamate--cysteine ligase 482 matched cddid_all.tbl CDD PLN02612 PLN02612 215330 PLN02612 phytoene desaturase 567 matched cddid_all.tbl CDD PLN02613 PLN02613 215331 PLN02613 endoglucanase 498 matched cddid_all.tbl CDD PLN02614 PLN02614 166255 PLN02614 long-chain acyl-CoA synthetase 666 matched cddid_all.tbl CDD PLN02615 PLN02615 178224 PLN02615 arginase 338 matched cddid_all.tbl CDD PLN02616 PLN02616 215332 PLN02616 tetrahydrofolate dehydrogenase/cyclohydrolase, putative 364 matched cddid_all.tbl CDD PLN02617 PLN02617 178226 PLN02617 imidazole glycerol phosphate synthase hisHF 538 matched cddid_all.tbl CDD PLN02618 PLN02618 215333 PLN02618 tryptophan synthase, beta chain 410 matched cddid_all.tbl CDD PLN02619 PLN02619 178228 PLN02619 nucleoside-diphosphate kinase 238 matched cddid_all.tbl CDD PLN02620 PLN02620 166261 PLN02620 indole-3-acetic acid-amido synthetase 612 matched cddid_all.tbl CDD PLN02621 PLN02621 178229 PLN02621 nicotinamidase 197 matched cddid_all.tbl CDD PLN02622 PLN02622 166263 PLN02622 iron superoxide dismutase 261 matched cddid_all.tbl CDD PLN02623 PLN02623 215334 PLN02623 pyruvate kinase 581 matched cddid_all.tbl CDD PLN02624 PLN02624 215335 PLN02624 ornithine-delta-aminotransferase 474 matched cddid_all.tbl CDD PLN02625 PLN02625 178232 PLN02625 uroporphyrin-III C-methyltransferase 263 matched cddid_all.tbl CDD PLN02626 PLN02626 215336 PLN02626 malate synthase 551 matched cddid_all.tbl CDD PLN02627 PLN02627 178234 PLN02627 glutamyl-tRNA synthetase 535 matched cddid_all.tbl CDD PLN02628 PLN02628 215337 PLN02628 fructose-1,6-bisphosphatase family protein 351 matched cddid_all.tbl CDD PLN02629 PLN02629 215338 PLN02629 powdery mildew resistance 5 387 matched cddid_all.tbl CDD PLN02630 PLN02630 178237 PLN02630 pfkB-type carbohydrate kinase family protein 335 matched cddid_all.tbl CDD PLN02631 PLN02631 178238 PLN02631 ferric-chelate reductase 699 matched cddid_all.tbl CDD PLN02632 PLN02632 215339 PLN02632 phytoene synthase 334 matched cddid_all.tbl CDD PLN02633 PLN02633 178240 PLN02633 palmitoyl protein thioesterase family protein 314 matched cddid_all.tbl CDD PLN02634 PLN02634 215340 PLN02634 probable pectinesterase 359 matched cddid_all.tbl CDD PLN02635 PLN02635 215341 PLN02635 disproportionating enzyme 538 matched cddid_all.tbl CDD PLN02636 PLN02636 215342 PLN02636 acyl-coenzyme A oxidase 686 matched cddid_all.tbl CDD PLN02638 PLN02638 215343 PLN02638 cellulose synthase A (UDP-forming), catalytic subunit 1079 matched cddid_all.tbl CDD PLN02639 PLN02639 178245 PLN02639 oxidoreductase, 2OG-Fe(II) oxygenase family protein 337 matched cddid_all.tbl CDD PLN02640 PLN02640 215344 PLN02640 glucose-6-phosphate 1-dehydrogenase 573 matched cddid_all.tbl CDD PLN02641 PLN02641 215345 PLN02641 anthranilate phosphoribosyltransferase 343 matched cddid_all.tbl CDD PLN02642 PLN02642 178248 PLN02642 copper, zinc superoxide dismutase 164 matched cddid_all.tbl CDD PLN02643 PLN02643 215346 PLN02643 ADP-glucose phosphorylase 336 matched cddid_all.tbl CDD PLN02644 PLN02644 215347 PLN02644 acetyl-CoA C-acetyltransferase 394 matched cddid_all.tbl CDD PLN02645 PLN02645 178251 PLN02645 phosphoglycolate phosphatase 311 matched cddid_all.tbl CDD PLN02646 PLN02646 215348 PLN02646 argininosuccinate lyase 474 matched cddid_all.tbl CDD PLN02647 PLN02647 215349 PLN02647 acyl-CoA thioesterase 437 matched cddid_all.tbl CDD PLN02648 PLN02648 215350 PLN02648 allene oxide synthase 480 matched cddid_all.tbl CDD PLN02649 PLN02649 215351 PLN02649 glucose-6-phosphate isomerase 560 matched cddid_all.tbl CDD PLN02650 PLN02650 178256 PLN02650 dihydroflavonol-4-reductase 351 matched cddid_all.tbl CDD PLN02651 PLN02651 178257 PLN02651 cysteine desulfurase 364 matched cddid_all.tbl CDD PLN02652 PLN02652 215352 PLN02652 hydrolase; alpha/beta fold family protein 395 matched cddid_all.tbl CDD PLN02653 PLN02653 178259 PLN02653 GDP-mannose 4,6-dehydratase 340 matched cddid_all.tbl CDD PLN02654 PLN02654 215353 PLN02654 acetate-CoA ligase 666 matched cddid_all.tbl CDD PLN02655 PLN02655 215354 PLN02655 ent-kaurene oxidase 466 matched cddid_all.tbl CDD PLN02656 PLN02656 178262 PLN02656 tyrosine transaminase 409 matched cddid_all.tbl CDD PLN02657 PLN02657 178263 PLN02657 3,8-divinyl protochlorophyllide a 8-vinyl reductase 390 matched cddid_all.tbl CDD PLN02658 PLN02658 215355 PLN02658 homogentisate 1,2-dioxygenase 435 matched cddid_all.tbl CDD PLN02659 PLN02659 215356 PLN02659 Probable galacturonosyltransferase 534 matched cddid_all.tbl CDD PLN02660 PLN02660 178266 PLN02660 pantoate--beta-alanine ligase 284 matched cddid_all.tbl CDD PLN02661 PLN02661 178267 PLN02661 Putative thiazole synthesis 357 matched cddid_all.tbl CDD PLN02662 PLN02662 178268 PLN02662 cinnamyl-alcohol dehydrogenase family protein 322 matched cddid_all.tbl CDD PLN02663 PLN02663 166304 PLN02663 hydroxycinnamoyl-CoA:shikimate/quinate hydroxycinnamoyltransferase 431 matched cddid_all.tbl CDD PLN02664 PLN02664 178269 PLN02664 enoyl-CoA hydratase/delta3,5-delta2,4-dienoyl-CoA isomerase 275 matched cddid_all.tbl CDD PLN02665 PLN02665 215357 PLN02665 pectinesterase family protein 366 matched cddid_all.tbl CDD PLN02666 PLN02666 215358 PLN02666 5-oxoprolinase 1275 matched cddid_all.tbl CDD PLN02667 PLN02667 215359 PLN02667 inositol polyphosphate multikinase 286 matched cddid_all.tbl CDD PLN02668 PLN02668 178273 PLN02668 indole-3-acetate carboxyl methyltransferase 386 matched cddid_all.tbl CDD PLN02669 PLN02669 178274 PLN02669 xylulokinase 556 matched cddid_all.tbl CDD PLN02670 PLN02670 178275 PLN02670 transferase, transferring glycosyl groups 472 matched cddid_all.tbl CDD PLN02671 PLN02671 178276 PLN02671 pectinesterase 359 matched cddid_all.tbl CDD PLN02672 PLN02672 215360 PLN02672 methionine S-methyltransferase 1082 matched cddid_all.tbl CDD PLN02673 PLN02673 215361 PLN02673 quinolinate synthetase A 724 matched cddid_all.tbl CDD PLN02674 PLN02674 178279 PLN02674 adenylate kinase 244 matched cddid_all.tbl CDD PLN02676 PLN02676 215362 PLN02676 polyamine oxidase 487 matched cddid_all.tbl CDD PLN02677 PLN02677 215363 PLN02677 mevalonate kinase 387 matched cddid_all.tbl CDD PLN02678 PLN02678 215364 PLN02678 seryl-tRNA synthetase 448 matched cddid_all.tbl CDD PLN02679 PLN02679 178283 PLN02679 hydrolase, alpha/beta fold family protein 360 matched cddid_all.tbl CDD PLN02680 PLN02680 215365 PLN02680 carbon-monoxide oxygenase 232 matched cddid_all.tbl CDD PLN02681 PLN02681 215366 PLN02681 proline dehydrogenase 455 matched cddid_all.tbl CDD PLN02682 PLN02682 215367 PLN02682 pectinesterase family protein 369 matched cddid_all.tbl CDD PLN02683 PLN02683 215368 PLN02683 pyruvate dehydrogenase E1 component subunit beta 356 matched cddid_all.tbl CDD PLN02684 PLN02684 166325 PLN02684 Probable galactinol--sucrose galactosyltransferase 750 matched cddid_all.tbl CDD PLN02685 PLN02685 215369 PLN02685 iron superoxide dismutase 299 matched cddid_all.tbl CDD PLN02686 PLN02686 215370 PLN02686 cinnamoyl-CoA reductase 367 matched cddid_all.tbl CDD PLN02687 PLN02687 215371 PLN02687 flavonoid 3'-monooxygenase 517 matched cddid_all.tbl CDD PLN02688 PLN02688 178291 PLN02688 pyrroline-5-carboxylate reductase 266 matched cddid_all.tbl CDD PLN02689 PLN02689 215372 PLN02689 Bifunctional isoaspartyl peptidase/L-asparaginase 318 matched cddid_all.tbl CDD PLN02690 PLN02690 178293 PLN02690 Agmatine deiminase 374 matched cddid_all.tbl CDD PLN02691 PLN02691 215373 PLN02691 porphobilinogen deaminase 351 matched cddid_all.tbl CDD PLN02692 PLN02692 178295 PLN02692 alpha-galactosidase 412 matched cddid_all.tbl CDD PLN02693 PLN02693 178296 PLN02693 IAA-amino acid hydrolase 437 matched cddid_all.tbl CDD PLN02694 PLN02694 178297 PLN02694 serine O-acetyltransferase 294 matched cddid_all.tbl CDD PLN02695 PLN02695 178298 PLN02695 GDP-D-mannose-3',5'-epimerase 370 matched cddid_all.tbl CDD PLN02696 PLN02696 215374 PLN02696 1-deoxy-D-xylulose-5-phosphate reductoisomerase 454 matched cddid_all.tbl CDD PLN02697 PLN02697 215375 PLN02697 lycopene epsilon cyclase 529 matched cddid_all.tbl CDD PLN02698 PLN02698 178301 PLN02698 Probable pectinesterase/pectinesterase inhibitor 497 matched cddid_all.tbl CDD PLN02699 PLN02699 215376 PLN02699 Bifunctional molybdopterin adenylyltransferase/molybdopterin molybdenumtransferase 659 matched cddid_all.tbl CDD PLN02700 PLN02700 215377 PLN02700 homoserine dehydrogenase family protein 377 matched cddid_all.tbl CDD PLN02701 PLN02701 178304 PLN02701 alpha-mannosidase 1050 matched cddid_all.tbl CDD PLN02702 PLN02702 215378 PLN02702 L-idonate 5-dehydrogenase 364 matched cddid_all.tbl CDD PLN02703 PLN02703 178306 PLN02703 beta-fructofuranosidase 618 matched cddid_all.tbl CDD PLN02704 PLN02704 166345 PLN02704 flavonol synthase 335 matched cddid_all.tbl CDD PLN02705 PLN02705 178307 PLN02705 beta-amylase 681 matched cddid_all.tbl CDD PLN02706 PLN02706 178308 PLN02706 glucosamine 6-phosphate N-acetyltransferase 150 matched cddid_all.tbl CDD PLN02707 PLN02707 178309 PLN02707 Soluble inorganic pyrophosphatase 267 matched cddid_all.tbl CDD PLN02708 PLN02708 215379 PLN02708 Probable pectinesterase/pectinesterase inhibitor 553 matched cddid_all.tbl CDD PLN02709 PLN02709 178311 PLN02709 nudix hydrolase 222 matched cddid_all.tbl CDD PLN02710 PLN02710 215380 PLN02710 farnesyltranstransferase subunit beta 439 matched cddid_all.tbl CDD PLN02711 PLN02711 215381 PLN02711 Probable galactinol--sucrose galactosyltransferase 777 matched cddid_all.tbl CDD PLN02712 PLN02712 215382 PLN02712 arogenate dehydrogenase 667 matched cddid_all.tbl CDD PLN02713 PLN02713 215383 PLN02713 Probable pectinesterase/pectinesterase inhibitor 566 matched cddid_all.tbl CDD PLN02714 PLN02714 178316 PLN02714 thiamin pyrophosphokinase 229 matched cddid_all.tbl CDD PLN02715 PLN02715 178317 PLN02715 lipid phosphate phosphatase 327 matched cddid_all.tbl CDD PLN02716 PLN02716 178318 PLN02716 nicotinate-nucleotide diphosphorylase (carboxylating) 308 matched cddid_all.tbl CDD PLN02717 PLN02717 178319 PLN02717 uridine nucleosidase 316 matched cddid_all.tbl CDD PLN02718 PLN02718 178320 PLN02718 Probable galacturonosyltransferase 603 matched cddid_all.tbl CDD PLN02719 PLN02719 178321 PLN02719 triacylglycerol lipase 518 matched cddid_all.tbl CDD PLN02720 PLN02720 178322 PLN02720 complex II 140 matched cddid_all.tbl CDD PLN02721 PLN02721 178323 PLN02721 threonine aldolase 353 matched cddid_all.tbl CDD PLN02722 PLN02722 166363 PLN02722 indole-3-acetamide amidohydrolase 422 matched cddid_all.tbl CDD PLN02723 PLN02723 178324 PLN02723 3-mercaptopyruvate sulfurtransferase 320 matched cddid_all.tbl CDD PLN02724 PLN02724 215384 PLN02724 Molybdenum cofactor sulfurase 805 matched cddid_all.tbl CDD PLN02725 PLN02725 178326 PLN02725 GDP-4-keto-6-deoxymannose-3,5-epimerase-4-reductase 306 matched cddid_all.tbl CDD PLN02726 PLN02726 215385 PLN02726 dolichyl-phosphate beta-D-mannosyltransferase 243 matched cddid_all.tbl CDD PLN02727 PLN02727 215386 PLN02727 NAD kinase 986 matched cddid_all.tbl CDD PLN02728 PLN02728 215387 PLN02728 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 252 matched cddid_all.tbl CDD PLN02729 PLN02729 215388 PLN02729 PSII-Q subunit 220 matched cddid_all.tbl CDD PLN02730 PLN02730 178331 PLN02730 enoyl-[acyl-carrier-protein] reductase 303 matched cddid_all.tbl CDD PLN02731 PLN02731 178332 PLN02731 Putative lipid phosphate phosphatase 333 matched cddid_all.tbl CDD PLN02732 PLN02732 215389 PLN02732 Probable NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 159 matched cddid_all.tbl CDD PLN02733 PLN02733 215390 PLN02733 phosphatidylcholine-sterol O-acyltransferase 440 matched cddid_all.tbl CDD PLN02734 PLN02734 178335 PLN02734 glycyl-tRNA synthetase 684 matched cddid_all.tbl CDD PLN02735 PLN02735 215391 PLN02735 carbamoyl-phosphate synthase 1102 matched cddid_all.tbl CDD PLN02736 PLN02736 178337 PLN02736 long-chain acyl-CoA synthetase 651 matched cddid_all.tbl CDD PLN02737 PLN02737 215392 PLN02737 inositol monophosphatase family protein 363 matched cddid_all.tbl CDD PLN02738 PLN02738 215393 PLN02738 carotene beta-ring hydroxylase 633 matched cddid_all.tbl CDD PLN02739 PLN02739 215394 PLN02739 serine acetyltransferase 355 matched cddid_all.tbl CDD PLN02740 PLN02740 178341 PLN02740 Alcohol dehydrogenase-like 381 matched cddid_all.tbl CDD PLN02741 PLN02741 178342 PLN02741 riboflavin synthase 194 matched cddid_all.tbl CDD PLN02742 PLN02742 215395 PLN02742 Probable galacturonosyltransferase 534 matched cddid_all.tbl CDD PLN02743 PLN02743 215396 PLN02743 nicotinamidase 239 matched cddid_all.tbl CDD PLN02744 PLN02744 215397 PLN02744 dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex 539 matched cddid_all.tbl CDD PLN02745 PLN02745 178346 PLN02745 Putative pectinesterase/pectinesterase inhibitor 596 matched cddid_all.tbl CDD PLN02746 PLN02746 178347 PLN02746 hydroxymethylglutaryl-CoA lyase 347 matched cddid_all.tbl CDD PLN02747 PLN02747 215398 PLN02747 N-carbamolyputrescine amidase 296 matched cddid_all.tbl CDD PLN02748 PLN02748 215399 PLN02748 tRNA dimethylallyltransferase 468 matched cddid_all.tbl CDD PLN02749 PLN02749 178350 PLN02749 Uncharacterized protein At1g47420 173 matched cddid_all.tbl CDD PLN02750 PLN02750 178351 PLN02750 oxidoreductase, 2OG-Fe(II) oxygenase family protein 345 matched cddid_all.tbl CDD PLN02751 PLN02751 215400 PLN02751 glutamyl-tRNA(Gln) amidotransferase 544 matched cddid_all.tbl CDD PLN02752 PLN02752 215401 PLN02752 [acyl-carrier protein] S-malonyltransferase 343 matched cddid_all.tbl CDD PLN02753 PLN02753 178354 PLN02753 triacylglycerol lipase 531 matched cddid_all.tbl CDD PLN02754 PLN02754 215402 PLN02754 chorismate synthase 413 matched cddid_all.tbl CDD PLN02755 PLN02755 178356 PLN02755 complex I subunit 71 matched cddid_all.tbl CDD PLN02756 PLN02756 166397 PLN02756 S-methyl-5-thioribose kinase 418 matched cddid_all.tbl CDD PLN02757 PLN02757 215403 PLN02757 sirohydrochlorine ferrochelatase 154 matched cddid_all.tbl CDD PLN02758 PLN02758 215404 PLN02758 oxidoreductase, 2OG-Fe(II) oxygenase family protein 361 matched cddid_all.tbl CDD PLN02759 PLN02759 178359 PLN02759 Formate--tetrahydrofolate ligase 637 matched cddid_all.tbl CDD PLN02760 PLN02760 215405 PLN02760 4-aminobutyrate:pyruvate transaminase 504 matched cddid_all.tbl CDD PLN02761 PLN02761 215406 PLN02761 lipase class 3 family protein 527 matched cddid_all.tbl CDD PLN02762 PLN02762 215407 PLN02762 pyruvate kinase complex alpha subunit 509 matched cddid_all.tbl CDD PLN02763 PLN02763 215408 PLN02763 hydrolase, hydrolyzing O-glycosyl compounds 978 matched cddid_all.tbl CDD PLN02764 PLN02764 178364 PLN02764 glycosyltransferase family protein 453 matched cddid_all.tbl CDD PLN02765 PLN02765 215409 PLN02765 pyruvate kinase 526 matched cddid_all.tbl CDD PLN02766 PLN02766 215410 PLN02766 coniferyl-aldehyde dehydrogenase 501 matched cddid_all.tbl CDD PLN02768 PLN02768 215411 PLN02768 AMP deaminase 835 matched cddid_all.tbl CDD PLN02769 PLN02769 215412 PLN02769 Probable galacturonosyltransferase 629 matched cddid_all.tbl CDD PLN02770 PLN02770 215413 PLN02770 haloacid dehalogenase-like hydrolase family protein 248 matched cddid_all.tbl CDD PLN02771 PLN02771 178370 PLN02771 carbamoyl-phosphate synthase (glutamine-hydrolyzing) 415 matched cddid_all.tbl CDD PLN02772 PLN02772 215414 PLN02772 guanylate kinase 398 matched cddid_all.tbl CDD PLN02773 PLN02773 178372 PLN02773 pectinesterase 317 matched cddid_all.tbl CDD PLN02774 PLN02774 178373 PLN02774 brassinosteroid-6-oxidase 463 matched cddid_all.tbl CDD PLN02775 PLN02775 178374 PLN02775 Probable dihydrodipicolinate reductase 286 matched cddid_all.tbl CDD PLN02776 PLN02776 215415 PLN02776 prenyltransferase 341 matched cddid_all.tbl CDD PLN02777 PLN02777 178376 PLN02777 photosystem I P subunit (PSI-P) 167 matched cddid_all.tbl CDD PLN02778 PLN02778 178377 PLN02778 3,5-epimerase/4-reductase 298 matched cddid_all.tbl CDD PLN02779 PLN02779 215416 PLN02779 haloacid dehalogenase-like hydrolase family protein 286 matched cddid_all.tbl CDD PLN02780 PLN02780 166421 PLN02780 ketoreductase/ oxidoreductase 320 matched cddid_all.tbl CDD PLN02781 PLN02781 215417 PLN02781 Probable caffeoyl-CoA O-methyltransferase 234 matched cddid_all.tbl CDD PLN02782 PLN02782 215418 PLN02782 Branched-chain amino acid aminotransferase 403 matched cddid_all.tbl CDD PLN02783 PLN02783 178380 PLN02783 diacylglycerol O-acyltransferase 315 matched cddid_all.tbl CDD PLN02784 PLN02784 215419 PLN02784 alpha-amylase 894 matched cddid_all.tbl CDD PLN02785 PLN02785 215420 PLN02785 Protein HOTHEAD 587 matched cddid_all.tbl CDD PLN02786 PLN02786 178383 PLN02786 isochorismate synthase 533 matched cddid_all.tbl CDD PLN02787 PLN02787 215421 PLN02787 3-oxoacyl-[acyl-carrier-protein] synthase II 540 matched cddid_all.tbl CDD PLN02788 PLN02788 215422 PLN02788 phenylalanine-tRNA synthetase 402 matched cddid_all.tbl CDD PLN02789 PLN02789 215423 PLN02789 farnesyltranstransferase 320 matched cddid_all.tbl CDD PLN02790 PLN02790 215424 PLN02790 transketolase 654 matched cddid_all.tbl CDD PLN02791 PLN02791 215425 PLN02791 Nudix hydrolase homolog 770 matched cddid_all.tbl CDD PLN02792 PLN02792 178389 PLN02792 oxidoreductase 536 matched cddid_all.tbl CDD PLN02793 PLN02793 215426 PLN02793 Probable polygalacturonase 443 matched cddid_all.tbl CDD PLN02794 PLN02794 178391 PLN02794 cardiolipin synthase 341 matched cddid_all.tbl CDD PLN02795 PLN02795 178392 PLN02795 allantoinase 505 matched cddid_all.tbl CDD PLN02796 PLN02796 215427 PLN02796 D-glycerate 3-kinase 347 matched cddid_all.tbl CDD PLN02797 PLN02797 178394 PLN02797 phosphatidyl-N-dimethylethanolamine N-methyltransferase 164 matched cddid_all.tbl CDD PLN02798 PLN02798 215428 PLN02798 nitrilase 286 matched cddid_all.tbl CDD PLN02799 PLN02799 215429 PLN02799 Molybdopterin synthase sulfur carrier subunit 82 matched cddid_all.tbl CDD PLN02800 PLN02800 215430 PLN02800 imidazoleglycerol-phosphate dehydratase 261 matched cddid_all.tbl CDD PLN02801 PLN02801 215431 PLN02801 beta-amylase 517 matched cddid_all.tbl CDD PLN02802 PLN02802 215432 PLN02802 triacylglycerol lipase 509 matched cddid_all.tbl CDD PLN02803 PLN02803 178400 PLN02803 beta-amylase 548 matched cddid_all.tbl CDD PLN02804 PLN02804 178401 PLN02804 chalcone isomerase 206 matched cddid_all.tbl CDD PLN02805 PLN02805 178402 PLN02805 D-lactate dehydrogenase [cytochrome] 555 matched cddid_all.tbl CDD PLN02806 PLN02806 178403 PLN02806 complex I subunit 81 matched cddid_all.tbl CDD PLN02807 PLN02807 215433 PLN02807 diaminohydroxyphosphoribosylaminopyrimidine deaminase 380 matched cddid_all.tbl CDD PLN02808 PLN02808 166449 PLN02808 alpha-galactosidase 386 matched cddid_all.tbl CDD PLN02809 PLN02809 178405 PLN02809 4-hydroxybenzoate nonaprenyltransferase 289 matched cddid_all.tbl CDD PLN02810 PLN02810 178406 PLN02810 carbon-monoxide oxygenase 231 matched cddid_all.tbl CDD PLN02811 PLN02811 178407 PLN02811 hydrolase 220 matched cddid_all.tbl CDD PLN02812 PLN02812 178408 PLN02812 5-formyltetrahydrofolate cyclo-ligase 211 matched cddid_all.tbl CDD PLN02813 PLN02813 215434 PLN02813 pfkB-type carbohydrate kinase family protein 426 matched cddid_all.tbl CDD PLN02814 PLN02814 215435 PLN02814 beta-glucosidase 504 matched cddid_all.tbl CDD PLN02815 PLN02815 215436 PLN02815 L-aspartate oxidase 594 matched cddid_all.tbl CDD PLN02816 PLN02816 215437 PLN02816 mannosyltransferase 546 matched cddid_all.tbl CDD PLN02817 PLN02817 166458 PLN02817 glutathione dehydrogenase (ascorbate) 265 matched cddid_all.tbl CDD PLN02818 PLN02818 215438 PLN02818 tocopherol cyclase 403 matched cddid_all.tbl CDD PLN02819 PLN02819 215439 PLN02819 lysine-ketoglutarate reductase/saccharopine dehydrogenase 1042 matched cddid_all.tbl CDD PLN02820 PLN02820 178415 PLN02820 3-methylcrotonyl-CoA carboxylase, beta chain 569 matched cddid_all.tbl CDD PLN02821 PLN02821 215440 PLN02821 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase 460 matched cddid_all.tbl CDD PLN02822 PLN02822 178417 PLN02822 serine palmitoyltransferase 481 matched cddid_all.tbl CDD PLN02823 PLN02823 178418 PLN02823 spermine synthase 336 matched cddid_all.tbl CDD PLN02824 PLN02824 178419 PLN02824 hydrolase, alpha/beta fold family protein 294 matched cddid_all.tbl CDD PLN02825 PLN02825 215441 PLN02825 amino-acid N-acetyltransferase 515 matched cddid_all.tbl CDD PLN02826 PLN02826 178421 PLN02826 dihydroorotate dehydrogenase 409 matched cddid_all.tbl CDD PLN02827 PLN02827 215442 PLN02827 Alcohol dehydrogenase-like 378 matched cddid_all.tbl CDD PLN02828 PLN02828 178422 PLN02828 formyltetrahydrofolate deformylase 268 matched cddid_all.tbl CDD PLN02829 PLN02829 215443 PLN02829 Probable galacturonosyltransferase 639 matched cddid_all.tbl CDD PLN02830 PLN02830 215444 PLN02830 UDP-sugar pyrophosphorylase 615 matched cddid_all.tbl CDD PLN02831 PLN02831 215445 PLN02831 Bifunctional GTP cyclohydrolase II/ 3,4-dihydroxy-2-butanone-4-phosphate synthase 450 matched cddid_all.tbl CDD PLN02832 PLN02832 215446 PLN02832 glutamine amidotransferase subunit of pyridoxal 5'-phosphate synthase complex 248 matched cddid_all.tbl CDD PLN02833 PLN02833 215447 PLN02833 glycerol acyltransferase family protein 376 matched cddid_all.tbl CDD PLN02834 PLN02834 215448 PLN02834 3-dehydroquinate synthase 433 matched cddid_all.tbl CDD PLN02835 PLN02835 178429 PLN02835 oxidoreductase 539 matched cddid_all.tbl CDD PLN02836 PLN02836 215449 PLN02836 3-oxoacyl-[acyl-carrier-protein] synthase 437 matched cddid_all.tbl CDD PLN02837 PLN02837 215450 PLN02837 threonine-tRNA ligase 614 matched cddid_all.tbl CDD PLN02838 PLN02838 166479 PLN02838 3-hydroxyacyl-CoA dehydratase subunit of elongase 221 matched cddid_all.tbl CDD PLN02839 PLN02839 178432 PLN02839 nudix hydrolase 372 matched cddid_all.tbl CDD PLN02840 PLN02840 215451 PLN02840 tRNA dimethylallyltransferase 421 matched cddid_all.tbl CDD PLN02841 PLN02841 178434 PLN02841 GPI mannosyltransferase 440 matched cddid_all.tbl CDD PLN02842 PLN02842 178435 PLN02842 nucleotide kinase 505 matched cddid_all.tbl CDD PLN02843 PLN02843 215452 PLN02843 isoleucyl-tRNA synthetase 974 matched cddid_all.tbl CDD PLN02844 PLN02844 215453 PLN02844 oxidoreductase/ferric-chelate reductase 722 matched cddid_all.tbl CDD PLN02845 PLN02845 215454 PLN02845 Branched-chain-amino-acid aminotransferase-like protein 336 matched cddid_all.tbl CDD PLN02846 PLN02846 166487 PLN02846 digalactosyldiacylglycerol synthase 462 matched cddid_all.tbl CDD PLN02847 PLN02847 178439 PLN02847 triacylglycerol lipase 633 matched cddid_all.tbl CDD PLN02848 PLN02848 178440 PLN02848 adenylosuccinate lyase 458 matched cddid_all.tbl CDD PLN02849 PLN02849 215455 PLN02849 beta-glucosidase 503 matched cddid_all.tbl CDD PLN02850 PLN02850 215456 PLN02850 aspartate-tRNA ligase 530 matched cddid_all.tbl CDD PLN02851 PLN02851 178443 PLN02851 3-hydroxyisobutyryl-CoA hydrolase-like protein 407 matched cddid_all.tbl CDD PLN02852 PLN02852 215457 PLN02852 ferredoxin-NADP+ reductase 491 matched cddid_all.tbl CDD PLN02853 PLN02853 215458 PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain 492 matched cddid_all.tbl CDD PLN02854 PLN02854 215459 PLN02854 3-ketoacyl-CoA synthase 521 matched cddid_all.tbl CDD PLN02855 PLN02855 215460 PLN02855 Bifunctional selenocysteine lyase/cysteine desulfurase 424 matched cddid_all.tbl CDD PLN02856 PLN02856 215461 PLN02856 fumarylacetoacetase 424 matched cddid_all.tbl CDD PLN02857 PLN02857 215462 PLN02857 octaprenyl-diphosphate synthase 416 matched cddid_all.tbl CDD PLN02858 PLN02858 215463 PLN02858 fructose-bisphosphate aldolase 1378 matched cddid_all.tbl CDD PLN02859 PLN02859 178450 PLN02859 glutamine-tRNA ligase 788 matched cddid_all.tbl CDD PLN02860 PLN02860 215464 PLN02860 o-succinylbenzoate-CoA ligase 563 matched cddid_all.tbl CDD PLN02861 PLN02861 178452 PLN02861 long-chain-fatty-acid-CoA ligase 660 matched cddid_all.tbl CDD PLN02862 PLN02862 178453 PLN02862 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase 216 matched cddid_all.tbl CDD PLN02863 PLN02863 215465 PLN02863 UDP-glucoronosyl/UDP-glucosyl transferase family protein 477 matched cddid_all.tbl CDD PLN02864 PLN02864 178455 PLN02864 enoyl-CoA hydratase 310 matched cddid_all.tbl CDD PLN02865 PLN02865 215466 PLN02865 galactokinase 423 matched cddid_all.tbl CDD PLN02866 PLN02866 215467 PLN02866 phospholipase D 1068 matched cddid_all.tbl CDD PLN02867 PLN02867 178458 PLN02867 Probable galacturonosyltransferase 535 matched cddid_all.tbl CDD PLN02868 PLN02868 178459 PLN02868 acyl-CoA thioesterase family protein 413 matched cddid_all.tbl CDD PLN02869 PLN02869 166510 PLN02869 fatty aldehyde decarbonylase 620 matched cddid_all.tbl CDD PLN02870 PLN02870 215468 PLN02870 Probable galacturonosyltransferase 533 matched cddid_all.tbl CDD PLN02871 PLN02871 215469 PLN02871 UDP-sulfoquinovose:DAG sulfoquinovosyltransferase 465 matched cddid_all.tbl CDD PLN02872 PLN02872 215470 PLN02872 triacylglycerol lipase 395 matched cddid_all.tbl CDD PLN02873 PLN02873 215471 PLN02873 coproporphyrinogen-III oxidase 274 matched cddid_all.tbl CDD PLN02874 PLN02874 178462 PLN02874 3-hydroxyisobutyryl-CoA hydrolase-like protein 379 matched cddid_all.tbl CDD PLN02875 PLN02875 215472 PLN02875 4-hydroxyphenylpyruvate dioxygenase 398 matched cddid_all.tbl CDD PLN02876 PLN02876 215473 PLN02876 acyl-CoA dehydrogenase 822 matched cddid_all.tbl CDD PLN02877 PLN02877 215474 PLN02877 alpha-amylase/limit dextrinase 970 matched cddid_all.tbl CDD PLN02878 PLN02878 178466 PLN02878 homogentisate phytyltransferase 280 matched cddid_all.tbl CDD PLN02879 PLN02879 178467 PLN02879 L-ascorbate peroxidase 251 matched cddid_all.tbl CDD PLN02880 PLN02880 215475 PLN02880 tyrosine decarboxylase 490 matched cddid_all.tbl CDD PLN02881 PLN02881 215476 PLN02881 tetrahydrofolylpolyglutamate synthase 530 matched cddid_all.tbl CDD PLN02882 PLN02882 215477 PLN02882 aminoacyl-tRNA ligase 1159 matched cddid_all.tbl CDD PLN02883 PLN02883 178471 PLN02883 Branched-chain amino acid aminotransferase 384 matched cddid_all.tbl CDD PLN02884 PLN02884 178472 PLN02884 6-phosphofructokinase 411 matched cddid_all.tbl CDD PLN02885 PLN02885 178473 PLN02885 nicotinate phosphoribosyltransferase 545 matched cddid_all.tbl CDD PLN02886 PLN02886 215478 PLN02886 aminoacyl-tRNA ligase 389 matched cddid_all.tbl CDD PLN02887 PLN02887 215479 PLN02887 hydrolase family protein 580 matched cddid_all.tbl CDD PLN02888 PLN02888 215480 PLN02888 enoyl-CoA hydratase 265 matched cddid_all.tbl CDD PLN02889 PLN02889 215481 PLN02889 oxo-acid-lyase/anthranilate synthase 918 matched cddid_all.tbl CDD PLN02890 PLN02890 178478 PLN02890 geranyl diphosphate synthase 422 matched cddid_all.tbl CDD PLN02891 PLN02891 178479 PLN02891 IMP cyclohydrolase 547 matched cddid_all.tbl CDD PLN02892 PLN02892 215482 PLN02892 isocitrate lyase 570 matched cddid_all.tbl CDD PLN02893 PLN02893 215483 PLN02893 Cellulose synthase-like protein 734 matched cddid_all.tbl CDD PLN02894 PLN02894 215484 PLN02894 hydrolase, alpha/beta fold family protein 402 matched cddid_all.tbl CDD PLN02895 PLN02895 215485 PLN02895 phosphoacetylglucosamine mutase 562 matched cddid_all.tbl CDD PLN02896 PLN02896 178484 PLN02896 cinnamyl-alcohol dehydrogenase 353 matched cddid_all.tbl CDD PLN02897 PLN02897 178485 PLN02897 tetrahydrofolate dehydrogenase/cyclohydrolase, putative 345 matched cddid_all.tbl CDD PLN02898 PLN02898 215486 PLN02898 HMP-P kinase/thiamin-monophosphate pyrophosphorylase 502 matched cddid_all.tbl CDD PLN02899 PLN02899 178487 PLN02899 alpha-galactosidase 633 matched cddid_all.tbl CDD PLN02900 PLN02900 215487 PLN02900 alanyl-tRNA synthetase 936 matched cddid_all.tbl CDD PLN02901 PLN02901 215488 PLN02901 1-acyl-sn-glycerol-3-phosphate acyltransferase 214 matched cddid_all.tbl CDD PLN02902 PLN02902 215489 PLN02902 pantothenate kinase 876 matched cddid_all.tbl CDD PLN02903 PLN02903 215490 PLN02903 aminoacyl-tRNA ligase 652 matched cddid_all.tbl CDD PLN02904 PLN02904 178492 PLN02904 oxidoreductase 357 matched cddid_all.tbl CDD PLN02905 PLN02905 178493 PLN02905 beta-amylase 702 matched cddid_all.tbl CDD PLN02906 PLN02906 215491 PLN02906 xanthine dehydrogenase 1319 matched cddid_all.tbl CDD PLN02907 PLN02907 215492 PLN02907 glutamate-tRNA ligase 722 matched cddid_all.tbl CDD PLN02908 PLN02908 178496 PLN02908 threonyl-tRNA synthetase 686 matched cddid_all.tbl CDD PLN02909 PLN02909 178497 PLN02909 Endoglucanase 486 matched cddid_all.tbl CDD PLN02910 PLN02910 215493 PLN02910 polygalacturonate 4-alpha-galacturonosyltransferase 657 matched cddid_all.tbl CDD PLN02911 PLN02911 178499 PLN02911 inositol-phosphate phosphatase 296 matched cddid_all.tbl CDD PLN02912 PLN02912 178500 PLN02912 oxidoreductase, 2OG-Fe(II) oxygenase family protein 348 matched cddid_all.tbl CDD PLN02913 PLN02913 178501 PLN02913 dihydrofolate synthetase 510 matched cddid_all.tbl CDD PLN02914 PLN02914 178502 PLN02914 hexokinase 490 matched cddid_all.tbl CDD PLN02915 PLN02915 215494 PLN02915 cellulose synthase A [UDP-forming], catalytic subunit 1044 matched cddid_all.tbl CDD PLN02916 PLN02916 178504 PLN02916 pectinesterase family protein 502 matched cddid_all.tbl CDD PLN02917 PLN02917 215495 PLN02917 CMP-KDO synthetase 293 matched cddid_all.tbl CDD PLN02918 PLN02918 215496 PLN02918 pyridoxine (pyridoxamine) 5'-phosphate oxidase 544 matched cddid_all.tbl CDD PLN02919 PLN02919 215497 PLN02919 haloacid dehalogenase-like hydrolase family protein 1057 matched cddid_all.tbl CDD PLN02920 PLN02920 215498 PLN02920 pantothenate kinase 1 398 matched cddid_all.tbl CDD PLN02921 PLN02921 178509 PLN02921 naphthoate synthase 327 matched cddid_all.tbl CDD PLN02922 PLN02922 215499 PLN02922 prenyltransferase 315 matched cddid_all.tbl CDD PLN02923 PLN02923 178511 PLN02923 xylose isomerase 478 matched cddid_all.tbl CDD PLN02924 PLN02924 178512 PLN02924 thymidylate kinase 220 matched cddid_all.tbl CDD PLN02925 PLN02925 178513 PLN02925 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase 733 matched cddid_all.tbl CDD PLN02926 PLN02926 215500 PLN02926 histidinol dehydrogenase 431 matched cddid_all.tbl CDD PLN02927 PLN02927 178515 PLN02927 antheraxanthin epoxidase/zeaxanthin epoxidase 668 matched cddid_all.tbl CDD PLN02928 PLN02928 215501 PLN02928 oxidoreductase family protein 347 matched cddid_all.tbl CDD PLN02929 PLN02929 215502 PLN02929 NADH kinase 301 matched cddid_all.tbl CDD PLN02930 PLN02930 178518 PLN02930 CDP-diacylglycerol-serine O-phosphatidyltransferase 353 matched cddid_all.tbl CDD PLN02931 PLN02931 215503 PLN02931 nucleoside diphosphate kinase family protein 177 matched cddid_all.tbl CDD PLN02932 PLN02932 178520 PLN02932 3-ketoacyl-CoA synthase 478 matched cddid_all.tbl CDD PLN02933 PLN02933 178521 PLN02933 Probable pectinesterase/pectinesterase inhibitor 530 matched cddid_all.tbl CDD PLN02934 PLN02934 215504 PLN02934 triacylglycerol lipase 515 matched cddid_all.tbl CDD PLN02935 PLN02935 215505 PLN02935 Bifunctional NADH kinase/NAD(+) kinase 508 matched cddid_all.tbl CDD PLN02936 PLN02936 178524 PLN02936 epsilon-ring hydroxylase 489 matched cddid_all.tbl CDD PLN02937 PLN02937 215506 PLN02937 Putative isoaspartyl peptidase/L-asparaginase 414 matched cddid_all.tbl CDD PLN02938 PLN02938 178526 PLN02938 phosphatidylserine decarboxylase 428 matched cddid_all.tbl CDD PLN02939 PLN02939 215507 PLN02939 transferase, transferring glycosyl groups 977 matched cddid_all.tbl CDD PLN02940 PLN02940 178528 PLN02940 riboflavin kinase 382 matched cddid_all.tbl CDD PLN02941 PLN02941 215508 PLN02941 inositol-tetrakisphosphate 1-kinase 328 matched cddid_all.tbl CDD PLN02942 PLN02942 178530 PLN02942 dihydropyrimidinase 486 matched cddid_all.tbl CDD PLN02943 PLN02943 215509 PLN02943 aminoacyl-tRNA ligase 958 matched cddid_all.tbl CDD PLN02945 PLN02945 178531 PLN02945 nicotinamide-nucleotide adenylyltransferase/nicotinate-nucleotide adenylyltransferase 236 matched cddid_all.tbl CDD PLN02946 PLN02946 178532 PLN02946 cysteine-tRNA ligase 557 matched cddid_all.tbl CDD PLN02947 PLN02947 215510 PLN02947 oxidoreductase 374 matched cddid_all.tbl CDD PLN02948 PLN02948 178534 PLN02948 phosphoribosylaminoimidazole carboxylase 577 matched cddid_all.tbl CDD PLN02949 PLN02949 215511 PLN02949 transferase, transferring glycosyl groups 463 matched cddid_all.tbl CDD PLN02950 PLN02950 215512 PLN02950 4-alpha-glucanotransferase 909 matched cddid_all.tbl CDD PLN02951 PLN02951 215513 PLN02951 Molybderin biosynthesis protein CNX2 373 matched cddid_all.tbl CDD PLN02952 PLN02952 178538 PLN02952 phosphoinositide phospholipase C 599 matched cddid_all.tbl CDD PLN02953 PLN02953 178539 PLN02953 phosphatidate cytidylyltransferase 403 matched cddid_all.tbl CDD PLN02954 PLN02954 215514 PLN02954 phosphoserine phosphatase 224 matched cddid_all.tbl CDD PLN02955 PLN02955 178541 PLN02955 8-amino-7-oxononanoate synthase 476 matched cddid_all.tbl CDD PLN02956 PLN02956 215515 PLN02956 PSII-Q subunit 185 matched cddid_all.tbl CDD PLN02957 PLN02957 215516 PLN02957 copper, zinc superoxide dismutase 238 matched cddid_all.tbl CDD PLN02958 PLN02958 215517 PLN02958 diacylglycerol kinase/D-erythro-sphingosine kinase 481 matched cddid_all.tbl CDD PLN02959 PLN02959 215518 PLN02959 aminoacyl-tRNA ligase 1084 matched cddid_all.tbl CDD PLN02960 PLN02960 215519 PLN02960 alpha-amylase 897 matched cddid_all.tbl CDD PLN02961 PLN02961 178546 PLN02961 alanine-tRNA ligase 223 matched cddid_all.tbl CDD PLN02962 PLN02962 178547 PLN02962 hydroxyacylglutathione hydrolase 251 matched cddid_all.tbl CDD PLN02964 PLN02964 215520 PLN02964 phosphatidylserine decarboxylase 644 matched cddid_all.tbl CDD PLN02965 PLN02965 178549 PLN02965 Probable pheophorbidase 255 matched cddid_all.tbl CDD PLN02966 PLN02966 178550 PLN02966 cytochrome P450 83A1 502 matched cddid_all.tbl CDD PLN02967 PLN02967 215521 PLN02967 kinase 581 matched cddid_all.tbl CDD PLN02968 PLN02968 215522 PLN02968 Probable N-acetyl-gamma-glutamyl-phosphate reductase 381 matched cddid_all.tbl CDD PLN02969 PLN02969 215523 PLN02969 9-cis-epoxycarotenoid dioxygenase 610 matched cddid_all.tbl CDD PLN02970 PLN02970 215524 PLN02970 serine racemase 328 matched cddid_all.tbl CDD PLN02971 PLN02971 166612 PLN02971 tryptophan N-hydroxylase 543 matched cddid_all.tbl CDD PLN02972 PLN02972 215525 PLN02972 Histidyl-tRNA synthetase 763 matched cddid_all.tbl CDD PLN02973 PLN02973 178556 PLN02973 beta-fructofuranosidase 571 matched cddid_all.tbl CDD PLN02974 PLN02974 215526 PLN02974 adenosylmethionine-8-amino-7-oxononanoate transaminase 817 matched cddid_all.tbl CDD PLN02975 PLN02975 166616 PLN02975 complex I subunit 97 matched cddid_all.tbl CDD PLN02976 PLN02976 215527 PLN02976 amine oxidase 1713 matched cddid_all.tbl CDD PLN02977 PLN02977 215528 PLN02977 glutathione synthetase 478 matched cddid_all.tbl CDD PLN02978 PLN02978 215529 PLN02978 pyridoxal kinase 308 matched cddid_all.tbl CDD PLN02979 PLN02979 166620 PLN02979 glycolate oxidase 366 matched cddid_all.tbl CDD PLN02980 PLN02980 215530 PLN02980 2-oxoglutarate decarboxylase/ hydro-lyase/ magnesium ion binding / thiamin pyrophosphate binding 1655 matched cddid_all.tbl CDD PLN02981 PLN02981 215531 PLN02981 glucosamine:fructose-6-phosphate aminotransferase 680 matched cddid_all.tbl CDD PLN02982 PLN02982 215532 PLN02982 galactinol-raffinose galactosyltransferase/ghydrolase, hydrolyzing O-glycosyl compounds 865 matched cddid_all.tbl CDD PLN02983 PLN02983 215533 PLN02983 biotin carboxyl carrier protein of acetyl-CoA carboxylase 274 matched cddid_all.tbl CDD PLN02984 PLN02984 215534 PLN02984 oxidoreductase, 2OG-Fe(II) oxygenase family protein 341 matched cddid_all.tbl CDD PLN02985 PLN02985 178566 PLN02985 squalene monooxygenase 514 matched cddid_all.tbl CDD PLN02986 PLN02986 178567 PLN02986 cinnamyl-alcohol dehydrogenase family protein 322 matched cddid_all.tbl CDD PLN02987 PLN02987 166628 PLN02987 Cytochrome P450, family 90, subfamily A 472 matched cddid_all.tbl CDD PLN02988 PLN02988 178568 PLN02988 3-hydroxyisobutyryl-CoA hydrolase 381 matched cddid_all.tbl CDD PLN02989 PLN02989 178569 PLN02989 cinnamyl-alcohol dehydrogenase family protein 325 matched cddid_all.tbl CDD PLN02990 PLN02990 215535 PLN02990 Probable pectinesterase/pectinesterase inhibitor 572 matched cddid_all.tbl CDD PLN02991 PLN02991 215536 PLN02991 oxidoreductase 543 matched cddid_all.tbl CDD PLN02992 PLN02992 178572 PLN02992 coniferyl-alcohol glucosyltransferase 481 matched cddid_all.tbl CDD PLN02993 PLN02993 215537 PLN02993 lupeol synthase 763 matched cddid_all.tbl CDD PLN02994 PLN02994 166635 PLN02994 1-aminocyclopropane-1-carboxylate synthase 153 matched cddid_all.tbl CDD PLN02995 PLN02995 178574 PLN02995 Probable pectinesterase/pectinesterase inhibitor 539 matched cddid_all.tbl CDD PLN02996 PLN02996 215538 PLN02996 fatty acyl-CoA reductase 491 matched cddid_all.tbl CDD PLN02997 PLN02997 178576 PLN02997 flavonol synthase 325 matched cddid_all.tbl CDD PLN02998 PLN02998 215539 PLN02998 beta-glucosidase 497 matched cddid_all.tbl CDD PLN02999 PLN02999 178577 PLN02999 photosystem II oxygen-evolving enhancer 3 protein (PsbQ) 190 matched cddid_all.tbl CDD PLN03000 PLN03000 178578 PLN03000 amine oxidase 881 matched cddid_all.tbl CDD PLN03001 PLN03001 166642 PLN03001 oxidoreductase, 2OG-Fe(II) oxygenase family protein 262 matched cddid_all.tbl CDD PLN03002 PLN03002 178579 PLN03002 oxidoreductase, 2OG-Fe(II) oxygenase family protein 332 matched cddid_all.tbl CDD PLN03003 PLN03003 178580 PLN03003 Probable polygalacturonase At3g15720 456 matched cddid_all.tbl CDD PLN03004 PLN03004 178581 PLN03004 UDP-glycosyltransferase 451 matched cddid_all.tbl CDD PLN03005 PLN03005 178582 PLN03005 beta-fructofuranosidase 550 matched cddid_all.tbl CDD PLN03006 PLN03006 178583 PLN03006 carbonate dehydratase 301 matched cddid_all.tbl CDD PLN03007 PLN03007 178584 PLN03007 UDP-glucosyltransferase family protein 482 matched cddid_all.tbl CDD PLN03008 PLN03008 178585 PLN03008 Phospholipase D delta 868 matched cddid_all.tbl CDD PLN03009 PLN03009 166650 PLN03009 cellulase 495 matched cddid_all.tbl CDD PLN03010 PLN03010 215540 PLN03010 polygalacturonase 409 matched cddid_all.tbl CDD PLN03012 PLN03012 166653 PLN03012 Camelliol C synthase 759 matched cddid_all.tbl CDD PLN03013 PLN03013 178587 PLN03013 cysteine synthase 429 matched cddid_all.tbl CDD PLN03014 PLN03014 178588 PLN03014 carbonic anhydrase 347 matched cddid_all.tbl CDD PLN03015 PLN03015 178589 PLN03015 UDP-glucosyl transferase 470 matched cddid_all.tbl CDD PLN03016 PLN03016 178590 PLN03016 sinapoylglucose-malate O-sinapoyltransferase 433 matched cddid_all.tbl CDD PLN03017 PLN03017 178591 PLN03017 trehalose-phosphatase 366 matched cddid_all.tbl CDD PLN03018 PLN03018 178592 PLN03018 homomethionine N-hydroxylase 534 matched cddid_all.tbl CDD PLN03019 PLN03019 166660 PLN03019 carbonic anhydrase 330 matched cddid_all.tbl CDD PLN03020 PLN03020 215541 PLN03020 low-temperature-induced protein; Provisional 556 matched cddid_all.tbl CDD PLN03021 PLN03021 178593 PLN03021 Low-temperature-induced protein; Provisional 619 matched cddid_all.tbl CDD PLN03023 PLN03023 215542 PLN03023 Expansin-like B1; Provisional 247 matched cddid_all.tbl CDD PLN03024 PLN03024 178595 PLN03024 Putative EG45-like domain containing protein 1; Provisional 125 matched cddid_all.tbl CDD PLN03025 PLN03025 178596 PLN03025 replication factor C subunit; Provisional 319 matched cddid_all.tbl CDD PLN03026 PLN03026 178597 PLN03026 histidinol-phosphate aminotransferase; Provisional 380 matched cddid_all.tbl CDD PLN03028 PLN03028 215543 PLN03028 pyrophosphate--fructose-6-phosphate 1-phosphotransferase; Provisional 610 matched cddid_all.tbl CDD PLN03029 PLN03029 215544 PLN03029 type-a response regulator protein; Provisional 222 matched cddid_all.tbl CDD PLN03030 PLN03030 215545 PLN03030 cationic peroxidase; Provisional 324 matched cddid_all.tbl CDD PLN03031 PLN03031 215546 PLN03031 hypothetical protein; Provisional 102 matched cddid_all.tbl CDD PLN03032 PLN03032 166673 PLN03032 serine decarboxylase; Provisional 374 matched cddid_all.tbl CDD PLN03033 PLN03033 178601 PLN03033 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional 290 matched cddid_all.tbl CDD PLN03034 PLN03034 178602 PLN03034 phosphoglycerate kinase; Provisional 481 matched cddid_all.tbl CDD PLN03036 PLN03036 178603 PLN03036 glutamine synthetase; Provisional 432 matched cddid_all.tbl CDD PLN03037 PLN03037 215547 PLN03037 lipase class 3 family protein; Provisional 525 matched cddid_all.tbl CDD PLN03039 PLN03039 166679 PLN03039 ethanolaminephosphotransferase; Provisional 337 matched cddid_all.tbl CDD PLN03042 PLN03042 215548 PLN03042 Lactoylglutathione lyase; Provisional 185 matched cddid_all.tbl CDD PLN03043 PLN03043 178606 PLN03043 Probable pectinesterase/pectinesterase inhibitor; Provisional 538 matched cddid_all.tbl CDD PLN03044 PLN03044 215549 PLN03044 GTP cyclohydrolase I; Provisional 188 matched cddid_all.tbl CDD PLN03046 PLN03046 178608 PLN03046 D-glycerate 3-kinase; Provisional 460 matched cddid_all.tbl CDD PLN03049 PLN03049 215550 PLN03049 pyridoxine (pyridoxamine) 5'-phosphate oxidase; Provisional 462 matched cddid_all.tbl CDD PLN03050 PLN03050 215551 PLN03050 pyridoxine (pyridoxamine) 5'-phosphate oxidase; Provisional 246 matched cddid_all.tbl CDD PLN03051 PLN03051 215552 PLN03051 acyl-activating enzyme; Provisional 499 matched cddid_all.tbl CDD PLN03052 PLN03052 215553 PLN03052 acetate--CoA ligase; Provisional 728 matched cddid_all.tbl CDD PLN03055 PLN03055 178613 PLN03055 AMP deaminase; Provisional 602 matched cddid_all.tbl CDD PLN03058 PLN03058 166697 PLN03058 dynein light chain type 1 family protein; Provisional 128 matched cddid_all.tbl CDD PLN03059 PLN03059 166698 PLN03059 beta-galactosidase; Provisional 840 matched cddid_all.tbl CDD PLN03060 PLN03060 215554 PLN03060 inositol phosphatase-like protein; Provisional 206 matched cddid_all.tbl CDD PLN03063 PLN03063 215555 PLN03063 alpha,alpha-trehalose-phosphate synthase (UDP-forming); Provisional 797 matched cddid_all.tbl CDD PLN03064 PLN03064 215556 PLN03064 alpha,alpha-trehalose-phosphate synthase (UDP-forming); Provisional 934 matched cddid_all.tbl CDD PLN03065 PLN03065 178617 PLN03065 isocitrate dehydrogenase (NADP+); Provisional 483 matched cddid_all.tbl CDD PLN03069 PLN03069 215557 PLN03069 magnesiumprotoporphyrin-IX chelatase subunit H; Provisional 1220 matched cddid_all.tbl CDD PLN03070 PLN03070 178619 PLN03070 photosystem I reaction center subunit psaK 247; Provisional 128 matched cddid_all.tbl CDD PLN03071 PLN03071 178620 PLN03071 GTP-binding nuclear protein Ran; Provisional 219 matched cddid_all.tbl CDD PLN03072 PLN03072 178621 PLN03072 60S ribosomal protein L12; Provisional 166 matched cddid_all.tbl CDD PLN03073 PLN03073 215558 PLN03073 ABC transporter F family; Provisional 718 matched cddid_all.tbl CDD PLN03074 PLN03074 215559 PLN03074 auxin influx permease; Provisional 473 matched cddid_all.tbl CDD PLN03075 PLN03075 178624 PLN03075 nicotianamine synthase; Provisional 296 matched cddid_all.tbl CDD PLN03076 PLN03076 215560 PLN03076 ARF guanine nucleotide exchange factor (ARF-GEF); Provisional 1780 matched cddid_all.tbl CDD PLN03077 PLN03077 215561 PLN03077 Protein ECB2; Provisional 857 matched cddid_all.tbl CDD PLN03078 PLN03078 215562 PLN03078 Putative tRNA pseudouridine synthase; Provisional 513 matched cddid_all.tbl CDD PLN03079 PLN03079 178628 PLN03079 Uncharacterized protein At4g33100; Provisional 91 matched cddid_all.tbl CDD PLN03080 PLN03080 178629 PLN03080 Probable beta-xylosidase; Provisional 779 matched cddid_all.tbl CDD PLN03081 PLN03081 215563 PLN03081 pentatricopeptide (PPR) repeat-containing protein; Provisional 697 matched cddid_all.tbl CDD PLN03082 PLN03082 215564 PLN03082 Iron-sulfur cluster assembly; Provisional 163 matched cddid_all.tbl CDD PLN03083 PLN03083 215565 PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional 803 matched cddid_all.tbl CDD PLN03084 PLN03084 178633 PLN03084 alpha/beta hydrolase fold protein; Provisional 383 matched cddid_all.tbl CDD PLN03085 PLN03085 215566 PLN03085 nucleobase:cation symporter-1; Provisional 221 matched cddid_all.tbl CDD PLN03086 PLN03086 178635 PLN03086 PRLI-interacting factor K; Provisional 567 matched cddid_all.tbl CDD PLN03087 PLN03087 215567 PLN03087 BODYGUARD 1 domain containing hydrolase; Provisional 481 matched cddid_all.tbl CDD PLN03088 PLN03088 215568 PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional 356 matched cddid_all.tbl CDD PLN03089 PLN03089 215569 PLN03089 hypothetical protein; Provisional 373 matched cddid_all.tbl CDD PLN03090 PLN03090 178639 PLN03090 auxin-responsive family protein; Provisional 104 matched cddid_all.tbl CDD PLN03091 PLN03091 215570 PLN03091 hypothetical protein; Provisional 459 matched cddid_all.tbl CDD PLN03093 PLN03093 178641 PLN03093 Protein SENSITIVITY TO RED LIGHT REDUCED 1; Provisional 273 matched cddid_all.tbl CDD PLN03094 PLN03094 178642 PLN03094 Substrate binding subunit of ER-derived-lipid transporter; Provisional 370 matched cddid_all.tbl CDD PLN03095 PLN03095 215571 PLN03095 NADH:ubiquinone oxidoreductase 18 kDa subunit; Provisional 115 matched cddid_all.tbl CDD PLN03096 PLN03096 215572 PLN03096 glyceraldehyde-3-phosphate dehydrogenase A; Provisional 395 matched cddid_all.tbl CDD PLN03097 PLN03097 178645 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional 846 matched cddid_all.tbl CDD PLN03098 PLN03098 215573 LPA1 LOW PSII ACCUMULATION1; Provisional 453 matched cddid_all.tbl CDD PLN03099 PLN03099 215574 PIR Protein PIR; Provisional 1232 matched cddid_all.tbl CDD PLN03100 PLN03100 215575 PLN03100 Permease subunit of ER-derived-lipid transporter; Provisional 292 matched cddid_all.tbl CDD PLN03102 PLN03102 215576 PLN03102 acyl-activating enzyme; Provisional 579 matched cddid_all.tbl CDD PLN03103 PLN03103 215577 PLN03103 GDP-L-galactose-hexose-1-phosphate guanyltransferase; Provisional 403 matched cddid_all.tbl CDD PLN03104 PLN03104 215578 FHL FAR-RED-ELONGATED HYPOCOTYL1-LIKE; Provisional 201 matched cddid_all.tbl CDD PLN03105 PLN03105 178652 TCP24 transcription factor TCP24 (TEOSINTE BRANCHED1, CYCLOIDEA, AND PCF FAMILY 24); Provisional 324 matched cddid_all.tbl CDD PLN03106 PLN03106 215579 TCP2 Protein TCP2; Provisional 447 matched cddid_all.tbl CDD PLN03107 PLN03107 215580 PLN03107 eukaryotic translation initiation factor 5A; Provisional 159 matched cddid_all.tbl CDD PLN03108 PLN03108 178655 PLN03108 Rab family protein; Provisional 210 matched cddid_all.tbl CDD PLN03109 PLN03109 215581 PLN03109 ETHYLENE-INSENSITIVE3-like3 protein; Provisional 599 matched cddid_all.tbl CDD PLN03110 PLN03110 178657 PLN03110 Rab GTPase; Provisional 216 matched cddid_all.tbl CDD PLN03111 PLN03111 215582 PLN03111 DNA-directed RNA polymerase II subunit family protein; Provisional 206 matched cddid_all.tbl CDD PLN03112 PLN03112 215583 PLN03112 cytochrome P450 family protein; Provisional 514 matched cddid_all.tbl CDD PLN03113 PLN03113 215584 PLN03113 DNA ligase 1; Provisional 744 matched cddid_all.tbl CDD PLN03114 PLN03114 178661 PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional 395 matched cddid_all.tbl CDD PLN03115 PLN03115 215585 PLN03115 ferredoxin--NADP(+) reductase; Provisional 367 matched cddid_all.tbl CDD PLN03116 PLN03116 215586 PLN03116 ferredoxin--NADP+ reductase; Provisional 307 matched cddid_all.tbl CDD PLN03117 PLN03117 178664 PLN03117 Branched-chain-amino-acid aminotransferase; Provisional 355 matched cddid_all.tbl CDD PLN03118 PLN03118 215587 PLN03118 Rab family protein; Provisional 211 matched cddid_all.tbl CDD PLN03119 PLN03119 178666 PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional 648 matched cddid_all.tbl CDD PLN03120 PLN03120 215588 PLN03120 nucleic acid binding protein; Provisional 260 matched cddid_all.tbl CDD PLN03121 PLN03121 215589 PLN03121 nucleic acid binding protein; Provisional 243 matched cddid_all.tbl CDD PLN03122 PLN03122 178669 PLN03122 Poly [ADP-ribose] polymerase; Provisional 815 matched cddid_all.tbl CDD PLN03123 PLN03123 215590 PLN03123 poly [ADP-ribose] polymerase; Provisional 981 matched cddid_all.tbl CDD PLN03124 PLN03124 215591 PLN03124 poly [ADP-ribose] polymerase; Provisional 643 matched cddid_all.tbl CDD PLN03126 PLN03126 215592 PLN03126 Elongation factor Tu; Provisional 478 matched cddid_all.tbl CDD PLN03127 PLN03127 178673 PLN03127 Elongation factor Tu; Provisional 447 matched cddid_all.tbl CDD PLN03128 PLN03128 215593 PLN03128 DNA topoisomerase 2; Provisional 1135 matched cddid_all.tbl CDD PLN03129 PLN03129 215594 PLN03129 NADP-dependent malic enzyme; Provisional 581 matched cddid_all.tbl CDD PLN03130 PLN03130 215595 PLN03130 ABC transporter C family member; Provisional 1622 matched cddid_all.tbl CDD PLN03131 PLN03131 178677 PLN03131 hypothetical protein; Provisional 705 matched cddid_all.tbl CDD PLN03132 PLN03132 178678 PLN03132 NADH dehydrogenase (ubiquinone) flavoprotein 1; Provisional 461 matched cddid_all.tbl CDD PLN03133 PLN03133 215596 PLN03133 beta-1,3-galactosyltransferase; Provisional 636 matched cddid_all.tbl CDD PLN03134 PLN03134 178680 PLN03134 glycine-rich RNA-binding protein 4; Provisional 144 matched cddid_all.tbl CDD PLN03136 PLN03136 178681 PLN03136 Ferredoxin; Provisional 148 matched cddid_all.tbl CDD PLN03137 PLN03137 215597 PLN03137 ATP-dependent DNA helicase; Q4-like; Provisional 1195 matched cddid_all.tbl CDD PLN03138 PLN03138 215598 PLN03138 Protein TOC75; Provisional 796 matched cddid_all.tbl CDD PLN03139 PLN03139 178684 PLN03139 formate dehydrogenase; Provisional 386 matched cddid_all.tbl CDD PLN03140 PLN03140 215599 PLN03140 ABC transporter G family member; Provisional 1470 matched cddid_all.tbl CDD PLN03141 PLN03141 215600 PLN03141 3-epi-6-deoxocathasterone 23-monooxygenase; Provisional 452 matched cddid_all.tbl CDD PLN03142 PLN03142 215601 PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional 1033 matched cddid_all.tbl CDD PLN03143 PLN03143 215602 PLN03143 nudix hydrolase; Provisional 291 matched cddid_all.tbl CDD PLN03144 PLN03144 178689 PLN03144 Carbon catabolite repressor protein 4 homolog; Provisional 606 matched cddid_all.tbl CDD PLN03145 PLN03145 215603 PLN03145 Protein phosphatase 2c; Provisional 365 matched cddid_all.tbl CDD PLN03146 PLN03146 178691 PLN03146 aspartyl protease family protein; Provisional 431 matched cddid_all.tbl CDD PLN03147 PLN03147 178692 PLN03147 ribosomal protein S19; Provisional 92 matched cddid_all.tbl CDD PLN03148 PLN03148 178693 PLN03148 Blue copper-like protein; Provisional 167 matched cddid_all.tbl CDD PLN03149 PLN03149 178694 PLN03149 peptidyl-prolyl isomerase H (cyclophilin H); Provisional 186 matched cddid_all.tbl CDD PLN03150 PLN03150 178695 PLN03150 hypothetical protein; Provisional 623 matched cddid_all.tbl CDD PLN03151 PLN03151 215604 PLN03151 cation/calcium exchanger; Provisional 650 matched cddid_all.tbl CDD PLN03152 PLN03152 178697 PLN03152 hypothetical protein; Provisional 241 matched cddid_all.tbl CDD PLN03153 PLN03153 215605 PLN03153 hypothetical protein; Provisional 537 matched cddid_all.tbl CDD PLN03154 PLN03154 215606 PLN03154 putative allyl alcohol dehydrogenase; Provisional 348 matched cddid_all.tbl CDD PLN03155 PLN03155 178700 PLN03155 cytochrome c oxidase subunit 5C; Provisional 63 matched cddid_all.tbl CDD PLN03156 PLN03156 178701 PLN03156 GDSL esterase/lipase; Provisional 351 matched cddid_all.tbl CDD PLN03157 PLN03157 178702 PLN03157 spermidine hydroxycinnamoyl transferase; Provisional 447 matched cddid_all.tbl CDD PLN03158 PLN03158 215607 PLN03158 methionine aminopeptidase; Provisional 396 matched cddid_all.tbl CDD PLN03159 PLN03159 215608 PLN03159 cation/H(+) antiporter 15; Provisional 832 matched cddid_all.tbl CDD PLN03160 PLN03160 215609 PLN03160 uncharacterized protein; Provisional 219 matched cddid_all.tbl CDD PLN03161 PLN03161 178706 PLN03161 Probable xyloglucan endotransglucosylase/hydrolase protein; Provisional 291 matched cddid_all.tbl CDD PLN03162 PLN03162 178707 PLN03162 golden-2 like transcription factor; Provisional 526 matched cddid_all.tbl CDD PLN03164 PLN03164 215610 PLN03164 3-oxo-5-alpha-steroid 4-dehydrogenase, C-terminal domain containing protein; Provisional 323 matched cddid_all.tbl CDD PLN03165 PLN03165 178709 PLN03165 chaperone protein dnaJ-related; Provisional 111 matched cddid_all.tbl CDD PLN03166 PLN03166 178710 PLN03166 60S ribosomal protein L34; Provisional 96 matched cddid_all.tbl CDD PLN03167 PLN03167 215611 PLN03167 Chaperonin-60 beta subunit; Provisional 600 matched cddid_all.tbl CDD PLN03168 PLN03168 178712 PLN03168 chalcone synthase; Provisional 389 matched cddid_all.tbl CDD PLN03169 PLN03169 215612 PLN03169 chalcone synthase family protein; Provisional 391 matched cddid_all.tbl CDD PLN03170 PLN03170 178714 PLN03170 chalcone synthase; Provisional 401 matched cddid_all.tbl CDD PLN03171 PLN03171 178715 PLN03171 chalcone synthase-like protein; Provisional 399 matched cddid_all.tbl CDD PLN03172 PLN03172 178716 PLN03172 chalcone synthase family protein; Provisional 393 matched cddid_all.tbl CDD PLN03173 PLN03173 178717 PLN03173 chalcone synthase; Provisional 391 matched cddid_all.tbl CDD PLN03174 PLN03174 215613 PLN03174 Chalcone-flavanone isomerase-related; Provisional 278 matched cddid_all.tbl CDD PLN03175 PLN03175 178719 PLN03175 hypothetical protein; Provisional 415 matched cddid_all.tbl CDD PLN03176 PLN03176 178720 PLN03176 flavanone-3-hydroxylase; Provisional 120 matched cddid_all.tbl CDD PLN03178 PLN03178 215614 PLN03178 leucoanthocyanidin dioxygenase; Provisional 360 matched cddid_all.tbl CDD PLN03180 PLN03180 215615 PLN03180 reversibly glycosylated polypeptide; Provisional 346 matched cddid_all.tbl CDD PLN03181 PLN03181 215616 PLN03181 glycosyltransferase; Provisional 453 matched cddid_all.tbl CDD PLN03182 PLN03182 215617 PLN03182 xyloglucan 6-xylosyltransferase; Provisional 429 matched cddid_all.tbl CDD PLN03183 PLN03183 178725 PLN03183 acetylglucosaminyltransferase family protein; Provisional 421 matched cddid_all.tbl CDD PLN03184 PLN03184 215618 PLN03184 chloroplast Hsp70; Provisional 673 matched cddid_all.tbl CDD PLN03185 PLN03185 215619 PLN03185 phosphatidylinositol phosphate kinase; Provisional 765 matched cddid_all.tbl CDD PLN03186 PLN03186 178728 PLN03186 DNA repair protein RAD51 homolog; Provisional 342 matched cddid_all.tbl CDD PLN03187 PLN03187 215620 PLN03187 meiotic recombination protein DMC1 homolog; Provisional 344 matched cddid_all.tbl CDD PLN03188 PLN03188 215621 PLN03188 kinesin-12 family protein; Provisional 1320 matched cddid_all.tbl CDD PLN03189 PLN03189 215622 PLN03189 Protease specific for SMALL UBIQUITIN-RELATED MODIFIER (SUMO); Provisional 490 matched cddid_all.tbl CDD PLN03190 PLN03190 215623 PLN03190 aminophospholipid translocase; Provisional 1178 matched cddid_all.tbl CDD PLN03191 PLN03191 215624 PLN03191 Type I inositol-1,4,5-trisphosphate 5-phosphatase 2; Provisional 621 matched cddid_all.tbl CDD PLN03192 PLN03192 215625 PLN03192 Voltage-dependent potassium channel; Provisional 823 matched cddid_all.tbl CDD PLN03193 PLN03193 178735 PLN03193 beta-1,3-galactosyltransferase; Provisional 408 matched cddid_all.tbl CDD PLN03194 PLN03194 215626 PLN03194 putative disease resistance protein; Provisional 187 matched cddid_all.tbl CDD PLN03195 PLN03195 215627 PLN03195 fatty acid omega-hydroxylase; Provisional 516 matched cddid_all.tbl CDD PLN03196 PLN03196 215628 PLN03196 MOC1-like protein; Provisional 487 matched cddid_all.tbl CDD PLN03198 PLN03198 178739 PLN03198 delta6-acyl-lipid desaturase; Provisional 526 matched cddid_all.tbl CDD PLN03199 PLN03199 178740 PLN03199 delta6-acyl-lipid desaturase-like protein; Provisional 485 matched cddid_all.tbl CDD PLN03200 PLN03200 215629 PLN03200 cellulose synthase-interactive protein; Provisional 2102 matched cddid_all.tbl CDD PLN03201 PLN03201 215630 PLN03201 RAB geranylgeranyl transferase beta-subunit; Provisional 316 matched cddid_all.tbl CDD PLN03202 PLN03202 215631 PLN03202 protein argonaute; Provisional 900 matched cddid_all.tbl CDD PLN03205 PLN03205 178744 PLN03205 ATR interacting protein; Provisional 652 matched cddid_all.tbl CDD PLN03206 PLN03206 178745 PLN03206 phosphoribosylformylglycinamidine synthase; Provisional 1307 matched cddid_all.tbl CDD PLN03207 PLN03207 215632 PLN03207 stomagen; Provisional 113 matched cddid_all.tbl CDD PLN03208 PLN03208 178747 PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional 193 matched cddid_all.tbl CDD PLN03209 PLN03209 178748 PLN03209 translocon at the inner envelope of chloroplast subunit 62; Provisional 576 matched cddid_all.tbl CDD PLN03210 PLN03210 215633 PLN03210 Resistant to P. syringae 6; Provisional 1153 matched cddid_all.tbl CDD PLN03211 PLN03211 215634 PLN03211 ABC transporter G-25; Provisional 659 matched cddid_all.tbl CDD PLN03212 PLN03212 178751 PLN03212 Transcription repressor MYB5; Provisional 249 matched cddid_all.tbl CDD PLN03213 PLN03213 178752 PLN03213 repressor of silencing 3; Provisional 759 matched cddid_all.tbl CDD PLN03214 PLN03214 215635 PLN03214 probable enoyl-CoA hydratase/isomerase; Provisional 278 matched cddid_all.tbl CDD PLN03215 PLN03215 178754 PLN03215 ascorbic acid mannose pathway regulator 1; Provisional 373 matched cddid_all.tbl CDD PLN03216 PLN03216 178755 PLN03216 actin depolymerizing factor; Provisional 141 matched cddid_all.tbl CDD PLN03217 PLN03217 178756 PLN03217 transcription factor ATBS1; Provisional 93 matched cddid_all.tbl CDD PLN03218 PLN03218 215636 PLN03218 maturation of RBCL 1; Provisional 1060 matched cddid_all.tbl CDD PLN03219 PLN03219 178758 PLN03219 uncharacterized protein; Provisional 108 matched cddid_all.tbl CDD PLN03220 PLN03220 178759 PLN03220 uncharacterized protein; Provisional 105 matched cddid_all.tbl CDD PLN03221 PLN03221 178760 PLN03221 rapid alkalinization factor 23; Provisional 137 matched cddid_all.tbl CDD PLN03222 PLN03222 178761 PLN03222 rapid alkalinization factor 23-like protein; Provisional 119 matched cddid_all.tbl CDD PLN03223 PLN03223 215637 PLN03223 Polycystin cation channel protein; Provisional 1634 matched cddid_all.tbl CDD PLN03224 PLN03224 178763 PLN03224 probable serine/threonine protein kinase; Provisional 507 matched cddid_all.tbl CDD PLN03225 PLN03225 215638 PLN03225 Serine/threonine-protein kinase SNT7; Provisional 566 matched cddid_all.tbl CDD PLN03226 PLN03226 215639 PLN03226 serine hydroxymethyltransferase; Provisional 475 matched cddid_all.tbl CDD PLN03227 PLN03227 178766 PLN03227 serine palmitoyltransferase-like protein; Provisional 392 matched cddid_all.tbl CDD PLN03228 PLN03228 178767 PLN03228 methylthioalkylmalate synthase; Provisional 503 matched cddid_all.tbl CDD PLN03229 PLN03229 178768 PLN03229 acetyl-coenzyme A carboxylase carboxyl transferase subunit alpha; Provisional 762 matched cddid_all.tbl CDD PLN03230 PLN03230 178769 PLN03230 acetyl-coenzyme A carboxylase carboxyl transferase; Provisional 431 matched cddid_all.tbl CDD PLN03231 PLN03231 178770 PLN03231 putative alpha-galactosidase; Provisional 357 matched cddid_all.tbl CDD PLN03232 PLN03232 215640 PLN03232 ABC transporter C family member; Provisional 1495 matched cddid_all.tbl CDD PLN03233 PLN03233 178772 PLN03233 putative glutamate-tRNA ligase; Provisional 523 matched cddid_all.tbl CDD PLN03234 PLN03234 178773 PLN03234 cytochrome P450 83B1; Provisional 499 matched cddid_all.tbl CDD PLN03236 PLN03236 178774 PLN03236 4-alpha-glucanotransferase; Provisional 745 matched cddid_all.tbl CDD PLN03237 PLN03237 215641 PLN03237 DNA topoisomerase 2; Provisional 1465 matched cddid_all.tbl CDD PLN03238 PLN03238 215642 PLN03238 probable histone acetyltransferase MYST; Provisional 290 matched cddid_all.tbl CDD PLN03239 PLN03239 178777 PLN03239 histone acetyltransferase; Provisional 351 matched cddid_all.tbl CDD PLN03240 PLN03240 178778 PLN03240 putative Low-temperature-induced protein; Provisional 626 matched cddid_all.tbl CDD PLN03241 PLN03241 215643 PLN03241 magnesium chelatase subunit H; Provisional 1315 matched cddid_all.tbl CDD PLN03242 PLN03242 178780 PLN03242 diacylglycerol o-acyltransferase; Provisional 410 matched cddid_all.tbl CDD PLN03243 PLN03243 215644 PLN03243 haloacid dehalogenase-like hydrolase; Provisional 260 matched cddid_all.tbl CDD PLN03244 PLN03244 178782 PLN03244 alpha-amylase; Provisional 872 matched cddid_all.tbl CDD PLN03246 PLN03246 215645 PLN03246 26S proteasome regulatory subunit; Provisional 303 matched cddid_all.tbl CDD PRK00006 PRK00006 234568 fabZ 3-hydroxyacyl-ACP dehydratase FabZ. 147 matched cddid_all.tbl CDD PRK00009 PRK00009 234570 PRK00009 phosphoenolpyruvate carboxylase; Reviewed 911 matched cddid_all.tbl CDD PRK00010 PRK00010 178791 rplE 50S ribosomal protein L5; Validated 179 matched cddid_all.tbl CDD PRK00011 PRK00011 234571 glyA serine hydroxymethyltransferase; Reviewed 416 matched cddid_all.tbl CDD PRK00013 PRK00013 234573 groEL chaperonin GroEL; Reviewed 542 matched cddid_all.tbl CDD PRK00015 PRK00015 234574 rnhB ribonuclease HII; Validated 197 matched cddid_all.tbl CDD PRK00019 PRK00019 234576 rpmE 50S ribosomal protein L31; Reviewed 72 matched cddid_all.tbl CDD PRK00021 PRK00021 234577 truA tRNA pseudouridine(38-40) synthase TruA. 244 matched cddid_all.tbl CDD PRK00024 PRK00024 178801 PRK00024 DNA repair protein RadC. 224 matched cddid_all.tbl CDD PRK00026 PRK00026 234581 trmD tRNA (guanine-N(1)-)-methyltransferase; Reviewed 244 matched cddid_all.tbl CDD PRK00029 PRK00029 234583 PRK00029 YdiU family protein. 487 matched cddid_all.tbl CDD PRK00031 PRK00031 178807 lolA outer membrane lipoprotein chaperone LolA. 195 matched cddid_all.tbl CDD PRK00033 PRK00033 178809 clpS ATP-dependent Clp protease adaptor protein ClpS; Reviewed 100 matched cddid_all.tbl CDD PRK00034 PRK00034 178810 gatC Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC. 95 matched cddid_all.tbl CDD PRK00035 PRK00035 234585 hemH ferrochelatase; Reviewed 333 matched cddid_all.tbl CDD PRK00038 PRK00038 134052 rnpA ribonuclease P protein component. 123 matched cddid_all.tbl CDD PRK00039 PRK00039 234587 ruvC Holliday junction resolvase; Reviewed 164 matched cddid_all.tbl CDD PRK00042 PRK00042 234589 tpiA triosephosphate isomerase; Provisional 250 matched cddid_all.tbl CDD PRK00043 PRK00043 234590 thiE thiamine phosphate synthase. 212 matched cddid_all.tbl CDD PRK00044 PRK00044 234591 psd phosphatidylserine decarboxylase; Reviewed 288 matched cddid_all.tbl CDD PRK00045 PRK00045 234592 hemA glutamyl-tRNA reductase; Reviewed 423 matched cddid_all.tbl CDD PRK00046 PRK00046 234593 murB UDP-N-acetylmuramate dehydrogenase. 334 matched cddid_all.tbl CDD PRK00047 PRK00047 234594 glpK glycerol kinase GlpK. 498 matched cddid_all.tbl CDD PRK00049 PRK00049 234596 PRK00049 elongation factor Tu; Reviewed 396 matched cddid_all.tbl CDD PRK00051 PRK00051 234598 hisI phosphoribosyl-AMP cyclohydrolase; Reviewed 125 matched cddid_all.tbl CDD PRK00052 PRK00052 234599 PRK00052 prolipoprotein diacylglyceryl transferase; Reviewed 269 matched cddid_all.tbl CDD PRK00053 PRK00053 234600 alr alanine racemase; Reviewed 363 matched cddid_all.tbl CDD PRK00054 PRK00054 234601 PRK00054 dihydroorotate dehydrogenase electron transfer subunit; Reviewed 250 matched cddid_all.tbl CDD PRK00055 PRK00055 234602 PRK00055 ribonuclease Z; Reviewed 270 matched cddid_all.tbl CDD PRK00059 PRK00059 234605 prsA peptidylprolyl isomerase; Provisional 336 matched cddid_all.tbl CDD PRK00061 PRK00061 234606 ribH 6,7-dimethyl-8-ribityllumazine synthase; Provisional 154 matched cddid_all.tbl CDD PRK00062 PRK00062 234607 PRK00062 glutamate-1-semialdehyde 2,1-aminomutase. 426 matched cddid_all.tbl CDD PRK00064 PRK00064 234608 recF recombination protein F; Reviewed 361 matched cddid_all.tbl CDD PRK00066 PRK00066 178836 ldh L-lactate dehydrogenase; Reviewed 315 matched cddid_all.tbl CDD PRK00068 PRK00068 234609 PRK00068 hypothetical protein; Validated 970 matched cddid_all.tbl CDD PRK00070 PRK00070 234610 acpS 4'-phosphopantetheinyl transferase; Provisional 126 matched cddid_all.tbl CDD PRK00071 PRK00071 234611 nadD nicotinate-nucleotide adenylyltransferase. 203 matched cddid_all.tbl CDD PRK00073 PRK00073 234613 pgk phosphoglycerate kinase; Provisional 389 matched cddid_all.tbl CDD PRK00074 PRK00074 234614 guaA GMP synthase; Reviewed 511 matched cddid_all.tbl CDD PRK00075 PRK00075 234615 cbiD cobalt-precorrin-6A synthase; Reviewed 361 matched cddid_all.tbl CDD PRK00077 PRK00077 234617 eno enolase; Provisional 425 matched cddid_all.tbl CDD PRK00078 PRK00078 234618 PRK00078 Maf-like protein; Reviewed 192 matched cddid_all.tbl CDD PRK00080 PRK00080 234619 ruvB Holliday junction branch migration DNA helicase RuvB. 328 matched cddid_all.tbl CDD PRK00087 PRK00087 234623 PRK00087 bifunctional 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/30S ribosomal protein S1. 647 matched cddid_all.tbl CDD PRK00089 PRK00089 234624 era GTPase Era; Reviewed 292 matched cddid_all.tbl CDD PRK00092 PRK00092 234627 PRK00092 ribosome maturation protein RimP; Reviewed 154 matched cddid_all.tbl CDD PRK00093 PRK00093 234628 PRK00093 GTP-binding protein Der; Reviewed 435 matched cddid_all.tbl CDD PRK00094 PRK00094 234629 gpsA NAD(P)H-dependent glycerol-3-phosphate dehydrogenase. 325 matched cddid_all.tbl CDD PRK00095 PRK00095 234630 mutL DNA mismatch repair endonuclease MutL. 617 matched cddid_all.tbl CDD PRK00098 PRK00098 234631 PRK00098 GTPase RsgA; Reviewed 298 matched cddid_all.tbl CDD PRK00099 PRK00099 234632 rplJ 50S ribosomal protein L10; Reviewed 172 matched cddid_all.tbl CDD PRK00103 PRK00103 234634 PRK00103 rRNA large subunit methyltransferase; Provisional 157 matched cddid_all.tbl CDD PRK00104 PRK00104 234635 scpA segregation and condensation protein A; Reviewed 242 matched cddid_all.tbl CDD PRK00105 PRK00105 234636 cobT nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase; Reviewed 335 matched cddid_all.tbl CDD PRK00106 PRK00106 178867 PRK00106 ribonuclease Y. 535 matched cddid_all.tbl CDD PRK00109 PRK00109 234639 PRK00109 Holliday junction resolvase RuvX. 138 matched cddid_all.tbl CDD PRK00110 PRK00110 234640 PRK00110 YebC/PmpR family DNA-binding transcriptional regulator. 245 matched cddid_all.tbl CDD PRK00111 PRK00111 234641 PRK00111 hypothetical protein; Provisional 180 matched cddid_all.tbl CDD PRK00114 PRK00114 234643 hslO Hsp33 family molecular chaperone HslO. 293 matched cddid_all.tbl CDD PRK00116 PRK00116 234645 ruvA Holliday junction branch migration protein RuvA. 192 matched cddid_all.tbl CDD PRK00117 PRK00117 234646 recX recombination regulator RecX; Reviewed 157 matched cddid_all.tbl CDD PRK00118 PRK00118 234647 PRK00118 putative DNA-binding protein; Validated 104 matched cddid_all.tbl CDD PRK00120 PRK00120 234648 PRK00120 dITP/XTP pyrophosphatase; Reviewed 196 matched cddid_all.tbl CDD PRK00121 PRK00121 234649 trmB tRNA (guanine-N(7)-)-methyltransferase; Reviewed 202 matched cddid_all.tbl CDD PRK00122 PRK00122 234650 rimM 16S rRNA-processing protein RimM; Provisional 172 matched cddid_all.tbl CDD PRK00124 PRK00124 178882 PRK00124 YaiI/YqxD family protein. 151 matched cddid_all.tbl CDD PRK00125 PRK00125 234651 pyrF orotidine 5'-phosphate decarboxylase; Reviewed 278 matched cddid_all.tbl CDD PRK00129 PRK00129 234653 upp uracil phosphoribosyltransferase; Reviewed 209 matched cddid_all.tbl CDD PRK00131 PRK00131 234654 aroK shikimate kinase; Reviewed 175 matched cddid_all.tbl CDD PRK00132 PRK00132 178888 rpsI 30S ribosomal protein S9; Reviewed 130 matched cddid_all.tbl CDD PRK00133 PRK00133 234655 metG methionyl-tRNA synthetase; Reviewed 673 matched cddid_all.tbl CDD PRK00134 PRK00134 234656 ccrB fluoride efflux transporter family protein. 104 matched cddid_all.tbl CDD PRK00135 PRK00135 234657 scpB segregation and condensation protein B; Reviewed 188 matched cddid_all.tbl CDD PRK00136 PRK00136 234658 rpsH 30S ribosomal protein S8; Validated 130 matched cddid_all.tbl CDD PRK00139 PRK00139 234660 murE UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase; Provisional 460 matched cddid_all.tbl CDD PRK00140 PRK00140 234661 rplK 50S ribosomal protein L11; Validated 141 matched cddid_all.tbl CDD PRK00142 PRK00142 234663 PRK00142 rhodanese-related sulfurtransferase. 314 matched cddid_all.tbl CDD PRK00143 PRK00143 234664 mnmA tRNA-specific 2-thiouridylase MnmA; Reviewed 346 matched cddid_all.tbl CDD PRK00145 PRK00145 234665 PRK00145 putative inner membrane protein translocase component YidC; Provisional 223 matched cddid_all.tbl CDD PRK00147 PRK00147 234666 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional 342 matched cddid_all.tbl CDD PRK00149 PRK00149 234667 dnaA chromosomal replication initiator protein DnaA. 401 matched cddid_all.tbl CDD PRK00150 PRK00150 234668 def peptide deformylase; Reviewed 165 matched cddid_all.tbl CDD PRK00155 PRK00155 234670 ispD D-ribitol-5-phosphate cytidylyltransferase. 227 matched cddid_all.tbl CDD PRK00159 PRK00159 178907 PRK00159 putative septation inhibitor protein; Reviewed 87 matched cddid_all.tbl CDD PRK00162 PRK00162 178908 glpE thiosulfate sulfurtransferase GlpE. 108 matched cddid_all.tbl CDD PRK00164 PRK00164 234672 moaA GTP 3',8-cyclase MoaA. 331 matched cddid_all.tbl CDD PRK00166 PRK00166 234673 apaH symmetrical bis(5'-nucleosyl)-tetraphosphatase. 275 matched cddid_all.tbl CDD PRK00170 PRK00170 234675 PRK00170 azoreductase; Reviewed 201 matched cddid_all.tbl CDD PRK00173 PRK00173 178914 rph ribonuclease PH; Reviewed 238 matched cddid_all.tbl CDD PRK00174 PRK00174 234677 PRK00174 acetyl-CoA synthetase; Provisional 637 matched cddid_all.tbl CDD PRK00175 PRK00175 234678 metX homoserine O-acetyltransferase; Provisional 379 matched cddid_all.tbl CDD PRK00179 PRK00179 234679 pgi glucose-6-phosphate isomerase; Reviewed 548 matched cddid_all.tbl CDD PRK00180 PRK00180 234680 PRK00180 acetate kinase A/propionate kinase 2; Reviewed 402 matched cddid_all.tbl CDD PRK00182 PRK00182 234681 tatB Sec-independent protein translocase subunit TatB. 160 matched cddid_all.tbl CDD PRK00183 PRK00183 166842 PRK00183 hypothetical protein; Provisional 157 matched cddid_all.tbl CDD PRK00187 PRK00187 166843 PRK00187 NorM family multidrug efflux MATE transporter. 464 matched cddid_all.tbl CDD PRK00188 PRK00188 234682 trpD anthranilate phosphoribosyltransferase; Provisional 339 matched cddid_all.tbl CDD PRK00191 PRK00191 234683 tatA twin arginine translocase protein A; Provisional 84 matched cddid_all.tbl CDD PRK00192 PRK00192 234684 PRK00192 mannosyl-3-phosphoglycerate phosphatase; Reviewed 273 matched cddid_all.tbl CDD PRK00194 PRK00194 178923 PRK00194 ACT domain-containing protein. 90 matched cddid_all.tbl CDD PRK00197 PRK00197 234685 proA gamma-glutamyl phosphate reductase; Provisional 417 matched cddid_all.tbl CDD PRK00199 PRK00199 178925 ihfB integration host factor subunit beta; Reviewed 94 matched cddid_all.tbl CDD PRK00202 PRK00202 234686 nusB transcription antitermination factor NusB. 137 matched cddid_all.tbl CDD PRK00203 PRK00203 178927 rnhA ribonuclease H; Reviewed 150 matched cddid_all.tbl CDD PRK00207 PRK00207 178928 PRK00207 sulfurtransferase complex subunit TusD. 128 matched cddid_all.tbl CDD PRK00208 PRK00208 234687 thiG thiazole synthase; Reviewed 250 matched cddid_all.tbl CDD PRK00211 PRK00211 178930 PRK00211 sulfurtransferase complex subunit TusC. 119 matched cddid_all.tbl CDD PRK00216 PRK00216 234689 ubiE bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol methylase UbiE. 239 matched cddid_all.tbl CDD PRK00218 PRK00218 234690 PRK00218 lysogenization regulator HflD. 207 matched cddid_all.tbl CDD PRK00220 PRK00220 234691 PRK00220 glycerol-3-phosphate 1-O-acyltransferase PlsY. 198 matched cddid_all.tbl CDD PRK00226 PRK00226 234693 greA transcription elongation factor GreA; Reviewed 157 matched cddid_all.tbl CDD PRK00227 PRK00227 178937 glnD [protein-PII] uridylyltransferase. 693 matched cddid_all.tbl CDD PRK00228 PRK00228 234694 PRK00228 YqgE/AlgH family protein. 191 matched cddid_all.tbl CDD PRK00230 PRK00230 234695 PRK00230 orotidine-5'-phosphate decarboxylase. 230 matched cddid_all.tbl CDD PRK00232 PRK00232 234696 pdxA 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed 332 matched cddid_all.tbl CDD PRK00235 PRK00235 234697 cobS cobalamin synthase; Reviewed 249 matched cddid_all.tbl CDD PRK00236 PRK00236 234698 xerC site-specific tyrosine recombinase XerC; Reviewed 297 matched cddid_all.tbl CDD PRK00241 PRK00241 234699 nudC NAD(+) diphosphatase. 256 matched cddid_all.tbl CDD PRK00247 PRK00247 178945 PRK00247 putative inner membrane protein translocase component YidC; Validated 429 matched cddid_all.tbl CDD PRK00249 PRK00249 234700 flgH flagellar basal body L-ring protein FlgH. 222 matched cddid_all.tbl CDD PRK00253 PRK00253 178948 fliE flagellar hook-basal body protein FliE; Reviewed 108 matched cddid_all.tbl CDD PRK00254 PRK00254 234702 PRK00254 ski2-like helicase; Provisional 720 matched cddid_all.tbl CDD PRK00257 PRK00257 166874 PRK00257 4-phosphoerythronate dehydrogenase PdxB. 381 matched cddid_all.tbl CDD PRK00258 PRK00258 234703 aroE shikimate 5-dehydrogenase; Reviewed 278 matched cddid_all.tbl CDD PRK00259 PRK00259 234704 PRK00259 intracellular septation protein A; Reviewed 179 matched cddid_all.tbl CDD PRK00275 PRK00275 234709 glnD PII uridylyl-transferase; Provisional 895 matched cddid_all.tbl CDD PRK00276 PRK00276 178954 infA translation initiation factor IF-1; Validated 72 matched cddid_all.tbl CDD PRK00277 PRK00277 178955 clpP ATP-dependent Clp protease proteolytic subunit; Reviewed 200 matched cddid_all.tbl CDD PRK00278 PRK00278 234710 trpC indole-3-glycerol phosphate synthase TrpC. 260 matched cddid_all.tbl CDD PRK00279 PRK00279 234711 adk adenylate kinase; Reviewed 215 matched cddid_all.tbl CDD PRK00281 PRK00281 234712 PRK00281 undecaprenyl-diphosphate phosphatase. 268 matched cddid_all.tbl CDD PRK00283 PRK00283 234713 xerD tyrosine recombinase. 299 matched cddid_all.tbl CDD PRK00284 PRK00284 178960 pqqA pyrroloquinoline quinone precursor peptide PqqA. 23 matched cddid_all.tbl CDD PRK00285 PRK00285 178961 ihfA integration host factor subunit alpha; Reviewed 99 matched cddid_all.tbl CDD PRK00290 PRK00290 234715 dnaK molecular chaperone DnaK; Provisional 627 matched cddid_all.tbl CDD PRK00292 PRK00292 234716 glk glucokinase; Provisional 316 matched cddid_all.tbl CDD PRK00293 PRK00293 234717 dipZ thiol:disulfide interchange protein precursor; Provisional 571 matched cddid_all.tbl CDD PRK00294 PRK00294 166894 hscB co-chaperone HscB; Provisional 173 matched cddid_all.tbl CDD PRK00295 PRK00295 166895 PRK00295 hypothetical protein; Provisional 68 matched cddid_all.tbl CDD PRK00296 PRK00296 234718 minE cell division topological specificity factor MinE; Reviewed 86 matched cddid_all.tbl CDD PRK00299 PRK00299 178967 PRK00299 sulfurtransferase TusA. 81 matched cddid_all.tbl CDD PRK00300 PRK00300 234719 gmk guanylate kinase; Provisional 205 matched cddid_all.tbl CDD PRK00302 PRK00302 234721 lnt apolipoprotein N-acyltransferase; Reviewed 505 matched cddid_all.tbl CDD PRK00304 PRK00304 166901 PRK00304 hypothetical protein; Provisional 75 matched cddid_all.tbl CDD PRK00311 PRK00311 234723 panB 3-methyl-2-oxobutanoate hydroxymethyltransferase; Reviewed 264 matched cddid_all.tbl CDD PRK00312 PRK00312 178974 pcm protein-L-isoaspartate(D-aspartate) O-methyltransferase. 212 matched cddid_all.tbl CDD PRK00315 PRK00315 234724 PRK00315 potassium-transporting ATPase subunit KdpC. 193 matched cddid_all.tbl CDD PRK00317 PRK00317 234725 mobA molybdopterin-guanine dinucleotide biosynthesis protein MobA; Reviewed 193 matched cddid_all.tbl CDD PRK00321 PRK00321 234726 rdgC recombination associated protein; Reviewed 303 matched cddid_all.tbl CDD PRK00325 PRK00325 234727 algL polysaccharide lyase. 359 matched cddid_all.tbl CDD PRK00326 PRK00326 234728 PRK00326 transcriptional regulator MraZ. 139 matched cddid_all.tbl CDD PRK00329 PRK00329 178979 PRK00329 GIY-YIG nuclease superfamily protein; Validated 86 matched cddid_all.tbl CDD PRK00331 PRK00331 234729 PRK00331 isomerizing glutamine--fructose-6-phosphate transaminase. 604 matched cddid_all.tbl CDD PRK00341 PRK00341 166914 PRK00341 DUF493 domain-containing protein. 91 matched cddid_all.tbl CDD PRK00346 PRK00346 234732 surE 5'(3')-nucleotidase/polyphosphatase; Provisional 250 matched cddid_all.tbl CDD PRK00349 PRK00349 234734 uvrA excinuclease ABC subunit UvrA. 943 matched cddid_all.tbl CDD PRK00357 PRK00357 178985 rpsS 30S ribosomal protein S19; Reviewed 92 matched cddid_all.tbl CDD PRK00364 PRK00364 178988 groES co-chaperonin GroES; Reviewed 95 matched cddid_all.tbl CDD PRK00366 PRK00366 234737 ispG flavodoxin-dependent (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase. 360 matched cddid_all.tbl CDD PRK00369 PRK00369 234738 pyrC dihydroorotase; Provisional 392 matched cddid_all.tbl CDD PRK00373 PRK00373 178991 PRK00373 V-type ATP synthase subunit D; Reviewed 204 matched cddid_all.tbl CDD PRK00377 PRK00377 234740 cbiT cobalt-precorrin-6Y C(15)-methyltransferase; Provisional 198 matched cddid_all.tbl CDD PRK00378 PRK00378 178993 PRK00378 nucleoid-associated protein NdpA; Validated 334 matched cddid_all.tbl CDD PRK00389 PRK00389 234742 gcvT glycine cleavage system aminomethyltransferase GcvT. 359 matched cddid_all.tbl CDD PRK00392 PRK00392 234744 rpoZ DNA-directed RNA polymerase subunit omega; Reviewed 69 matched cddid_all.tbl CDD PRK00393 PRK00393 234745 ribA GTP cyclohydrolase II RibA. 197 matched cddid_all.tbl CDD PRK00394 PRK00394 234746 PRK00394 transcription factor; Reviewed 179 matched cddid_all.tbl CDD PRK00395 PRK00395 179001 hfq RNA-binding protein Hfq; Provisional 79 matched cddid_all.tbl CDD PRK00398 PRK00398 234747 rpoP DNA-directed RNA polymerase subunit P; Provisional 46 matched cddid_all.tbl CDD PRK00400 PRK00400 179005 hisE phosphoribosyl-ATP diphosphatase. 105 matched cddid_all.tbl CDD PRK00402 PRK00402 234748 PRK00402 3-isopropylmalate dehydratase large subunit; Reviewed 418 matched cddid_all.tbl CDD PRK00405 PRK00405 234749 rpoB DNA-directed RNA polymerase subunit beta; Reviewed 1112 matched cddid_all.tbl CDD PRK00407 PRK00407 179008 Archease Archease protein family (MTH1598/TM1083). This archease family of proteins, has two SHS2 domains, with one inserted into another. It is predicted to be an enzyme. It is predicted to act as a chaperone in DNA/RNA metabolism. 139 matched cddid_all.tbl CDD PRK00409 PRK00409 234750 PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed 782 matched cddid_all.tbl CDD PRK00411 PRK00411 234751 cdc6 ORC1-type DNA replication protein. 394 matched cddid_all.tbl CDD PRK00414 PRK00414 179012 gmhA D-sedoheptulose 7-phosphate isomerase. 192 matched cddid_all.tbl CDD PRK00415 PRK00415 179013 rps27e 30S ribosomal protein S27e; Reviewed 59 matched cddid_all.tbl CDD PRK00418 PRK00418 234754 PRK00418 DNA gyrase inhibitor YacG. 62 matched cddid_all.tbl CDD PRK00419 PRK00419 234755 PRK00419 DNA primase small subunit PriS. 376 matched cddid_all.tbl CDD PRK00420 PRK00420 234756 PRK00420 hypothetical protein; Validated 112 matched cddid_all.tbl CDD PRK00423 PRK00423 234758 tfb transcription initiation factor IIB; Reviewed 310 matched cddid_all.tbl CDD PRK00430 PRK00430 179020 fis DNA-binding transcriptional regulator Fis. 95 matched cddid_all.tbl CDD PRK00431 PRK00431 234759 PRK00431 ADP-ribose-binding protein. 177 matched cddid_all.tbl CDD PRK00432 PRK00432 234760 PRK00432 30S ribosomal protein S27ae; Validated 50 matched cddid_all.tbl CDD PRK00435 PRK00435 179023 ef1B elongation factor 1-beta; Validated 88 matched cddid_all.tbl CDD PRK00439 PRK00439 234762 leuD 3-isopropylmalate dehydratase small subunit; Reviewed 163 matched cddid_all.tbl CDD PRK00440 PRK00440 234763 rfc replication factor C small subunit; Reviewed 319 matched cddid_all.tbl CDD PRK00441 PRK00441 179027 argR arginine repressor; Provisional 149 matched cddid_all.tbl CDD PRK00442 PRK00442 234764 tatA twin-arginine translocase TatA/TatE family subunit. 92 matched cddid_all.tbl CDD PRK00443 PRK00443 179028 nagB glucosamine-6-phosphate deaminase; Provisional 261 matched cddid_all.tbl CDD PRK00446 PRK00446 234765 cyaY frataxin-like protein; Provisional 105 matched cddid_all.tbl CDD PRK00447 PRK00447 234766 PRK00447 hypothetical protein; Provisional 144 matched cddid_all.tbl CDD PRK00448 PRK00448 234767 polC DNA polymerase III PolC; Validated 1437 matched cddid_all.tbl CDD PRK00451 PRK00451 234769 PRK00451 aminomethyl-transferring glycine dehydrogenase subunit GcvPA. 447 matched cddid_all.tbl CDD PRK00455 PRK00455 234771 pyrE orotate phosphoribosyltransferase; Validated 202 matched cddid_all.tbl CDD PRK00465 PRK00465 179039 rpmJ 50S ribosomal protein L36; Reviewed 37 matched cddid_all.tbl CDD PRK00466 PRK00466 166979 PRK00466 acetyl-lysine deacetylase; Validated 346 matched cddid_all.tbl CDD PRK00468 PRK00468 179040 PRK00468 KH domain-containing protein. 75 matched cddid_all.tbl CDD PRK00474 PRK00474 179041 rps9p 30S ribosomal protein S9P; Reviewed 134 matched cddid_all.tbl CDD PRK00476 PRK00476 234775 aspS aspartyl-tRNA synthetase; Validated 588 matched cddid_all.tbl CDD PRK00478 PRK00478 234776 scpA segregation and condensation protein ScpA. 505 matched cddid_all.tbl CDD PRK00481 PRK00481 234777 PRK00481 NAD-dependent deacetylase; Provisional 242 matched cddid_all.tbl CDD PRK00484 PRK00484 234778 lysS lysyl-tRNA synthetase; Reviewed 491 matched cddid_all.tbl CDD PRK00485 PRK00485 234779 fumC fumarate hydratase; Reviewed 464 matched cddid_all.tbl CDD PRK00504 PRK00504 234783 rpmG 50S ribosomal protein L33; Validated 50 matched cddid_all.tbl CDD PRK00509 PRK00509 234785 PRK00509 argininosuccinate synthase; Provisional 399 matched cddid_all.tbl CDD PRK00513 PRK00513 179052 minC septum formation inhibitor; Reviewed 214 matched cddid_all.tbl CDD PRK00517 PRK00517 234786 prmA 50S ribosomal protein L11 methyltransferase. 250 matched cddid_all.tbl CDD PRK00521 PRK00521 234787 rbfA 30S ribosome-binding factor RbfA. 120 matched cddid_all.tbl CDD PRK00522 PRK00522 179055 tpx thiol peroxidase. 167 matched cddid_all.tbl CDD PRK00523 PRK00523 179056 PRK00523 hypothetical protein; Provisional 72 matched cddid_all.tbl CDD PRK00528 PRK00528 179057 rpmE 50S ribosomal protein L31; Reviewed 71 matched cddid_all.tbl CDD PRK00529 PRK00529 234788 PRK00529 elongation factor P; Validated 186 matched cddid_all.tbl CDD PRK00536 PRK00536 134311 speE spermidine synthase; Provisional 262 matched cddid_all.tbl CDD PRK00539 PRK00539 179059 atpC F0F1 ATP synthase subunit epsilon; Validated 133 matched cddid_all.tbl CDD PRK00549 PRK00549 234789 PRK00549 competence damage-inducible protein A; Provisional 414 matched cddid_all.tbl CDD PRK00550 PRK00550 234790 rpsE 30S ribosomal protein S5; Validated 168 matched cddid_all.tbl CDD PRK00553 PRK00553 179062 PRK00553 ribose-phosphate pyrophosphokinase; Provisional 332 matched cddid_all.tbl CDD PRK00555 PRK00555 179063 PRK00555 galactokinase; Provisional 363 matched cddid_all.tbl CDD PRK00556 PRK00556 234791 minC septum formation inhibitor; Reviewed 194 matched cddid_all.tbl CDD PRK00558 PRK00558 234792 uvrC excinuclease ABC subunit UvrC. 598 matched cddid_all.tbl CDD PRK00560 PRK00560 167003 PRK00560 molybdenum cofactor guanylyltransferase MobA. 196 matched cddid_all.tbl CDD PRK00561 PRK00561 100598 ppnK NAD(+) kinase. 259 matched cddid_all.tbl CDD PRK00564 PRK00564 179066 hypA hydrogenase nickel incorporation protein; Provisional 117 matched cddid_all.tbl CDD PRK00566 PRK00566 234794 PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional 1156 matched cddid_all.tbl CDD PRK00567 PRK00567 234795 mscL large-conductance mechanosensitive channel protein MscL. 134 matched cddid_all.tbl CDD PRK00568 PRK00568 134322 PRK00568 carbon storage regulator; Provisional 76 matched cddid_all.tbl CDD PRK00571 PRK00571 234796 atpC F0F1 ATP synthase subunit epsilon; Validated 135 matched cddid_all.tbl CDD PRK00575 PRK00575 234797 tatA Sec-independent protein translocase subunit TatA. 92 matched cddid_all.tbl CDD PRK00576 PRK00576 234798 PRK00576 molybdopterin-guanine dinucleotide biosynthesis protein A; Provisional 178 matched cddid_all.tbl CDD PRK00591 PRK00591 234801 prfA peptide chain release factor 1; Validated 359 matched cddid_all.tbl CDD PRK00595 PRK00595 179075 rpmG 50S ribosomal protein L33; Validated 53 matched cddid_all.tbl CDD PRK00596 PRK00596 179076 rpsJ 30S ribosomal protein S10; Reviewed 102 matched cddid_all.tbl CDD PRK00601 PRK00601 234802 dut dUTP diphosphatase. 150 matched cddid_all.tbl CDD PRK00611 PRK00611 100616 PRK00611 putative disulfide oxidoreductase; Provisional 135 matched cddid_all.tbl CDD PRK00615 PRK00615 234803 PRK00615 glutamate-1-semialdehyde aminotransferase; Provisional 433 matched cddid_all.tbl CDD PRK00624 PRK00624 167014 PRK00624 glycine cleavage system protein H; Provisional 114 matched cddid_all.tbl CDD PRK00625 PRK00625 134335 PRK00625 shikimate kinase; Provisional 173 matched cddid_all.tbl CDD PRK00629 PRK00629 234804 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed 791 matched cddid_all.tbl CDD PRK00630 PRK00630 234805 PRK00630 nickel responsive regulator; Provisional 148 matched cddid_all.tbl CDD PRK00635 PRK00635 234806 PRK00635 excinuclease ABC subunit A; Provisional 1809 matched cddid_all.tbl CDD PRK00642 PRK00642 179080 PRK00642 inorganic pyrophosphatase; Provisional 205 matched cddid_all.tbl CDD PRK00647 PRK00647 100624 PRK00647 hypothetical protein; Validated 96 matched cddid_all.tbl CDD PRK00648 PRK00648 234807 PRK00648 Maf-like protein; Reviewed 191 matched cddid_all.tbl CDD PRK00652 PRK00652 234808 lpxK tetraacyldisaccharide 4'-kinase; Reviewed 325 matched cddid_all.tbl CDD PRK00654 PRK00654 234809 glgA glycogen synthase GlgA. 466 matched cddid_all.tbl CDD PRK00665 PRK00665 179084 petG cytochrome b6-f complex subunit PetG; Reviewed 37 matched cddid_all.tbl CDD PRK00668 PRK00668 179085 ndk mulitfunctional nucleoside diphosphate kinase/apyrimidinic endonuclease/3'-; Validated 134 matched cddid_all.tbl CDD PRK00676 PRK00676 234810 hemA glutamyl-tRNA reductase; Validated 338 matched cddid_all.tbl CDD PRK00685 PRK00685 234811 PRK00685 metal-dependent hydrolase; Provisional 228 matched cddid_all.tbl CDD PRK00694 PRK00694 234812 PRK00694 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Validated 606 matched cddid_all.tbl CDD PRK00696 PRK00696 234813 sucC ADP-forming succinate--CoA ligase subunit beta. 388 matched cddid_all.tbl CDD PRK00701 PRK00701 234815 PRK00701 divalent metal cation transporter MntH. 439 matched cddid_all.tbl CDD PRK00702 PRK00702 234816 PRK00702 ribose-5-phosphate isomerase RpiA. 220 matched cddid_all.tbl CDD PRK00704 PRK00704 234817 PRK00704 photosystem I reaction center protein subunit XI; Provisional 160 matched cddid_all.tbl CDD PRK00711 PRK00711 234819 PRK00711 D-amino acid dehydrogenase. 416 matched cddid_all.tbl CDD PRK00714 PRK00714 234820 PRK00714 RNA pyrophosphohydrolase; Reviewed 156 matched cddid_all.tbl CDD PRK00719 PRK00719 234821 PRK00719 alkanesulfonate monooxygenase; Provisional 378 matched cddid_all.tbl CDD PRK00720 PRK00720 234822 tatA twin-arginine translocase TatA/TatE family subunit. 78 matched cddid_all.tbl CDD PRK00723 PRK00723 179097 PRK00723 phosphatidylserine decarboxylase; Provisional 297 matched cddid_all.tbl CDD PRK00724 PRK00724 234823 PRK00724 formate dehydrogenase accessory sulfurtransferase FdhD. 263 matched cddid_all.tbl CDD PRK00725 PRK00725 234824 glgC glucose-1-phosphate adenylyltransferase; Provisional 425 matched cddid_all.tbl CDD PRK00726 PRK00726 234825 murG undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional 357 matched cddid_all.tbl CDD PRK00732 PRK00732 179101 fliE flagellar hook-basal body complex protein FliE. 102 matched cddid_all.tbl CDD PRK00733 PRK00733 234827 hppA membrane-bound proton-translocating pyrophosphatase; Validated 666 matched cddid_all.tbl CDD PRK00736 PRK00736 179103 PRK00736 hypothetical protein; Provisional 68 matched cddid_all.tbl CDD PRK00737 PRK00737 179104 PRK00737 small nuclear ribonucleoprotein; Provisional 72 matched cddid_all.tbl CDD PRK00741 PRK00741 179105 prfC peptide chain release factor 3; Provisional 526 matched cddid_all.tbl CDD PRK00742 PRK00742 234828 PRK00742 chemotaxis-specific protein-glutamate methyltransferase CheB. 354 matched cddid_all.tbl CDD PRK00745 PRK00745 179107 PRK00745 4-oxalocrotonate tautomerase; Provisional 62 matched cddid_all.tbl CDD PRK00748 PRK00748 179108 PRK00748 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Validated 233 matched cddid_all.tbl CDD PRK00750 PRK00750 234829 lysK lysyl-tRNA synthetase; Reviewed 510 matched cddid_all.tbl CDD PRK00753 PRK00753 134373 psbL photosystem II reaction center L; Provisional 39 matched cddid_all.tbl CDD PRK00754 PRK00754 179110 PRK00754 signal recognition particle protein Srp19; Provisional 95 matched cddid_all.tbl CDD PRK00756 PRK00756 179111 PRK00756 acyltransferase NodA; Provisional 196 matched cddid_all.tbl CDD PRK00758 PRK00758 179112 PRK00758 GMP synthase subunit A; Validated 184 matched cddid_all.tbl CDD PRK00762 PRK00762 179113 hypA hydrogenase maturation nickel metallochaperone HypA. 124 matched cddid_all.tbl CDD PRK00766 PRK00766 234830 PRK00766 hypothetical protein; Provisional 194 matched cddid_all.tbl CDD PRK00767 PRK00767 179115 PRK00767 transcriptional regulator BetI; Validated 197 matched cddid_all.tbl CDD PRK00768 PRK00768 234831 nadE ammonia-dependent NAD(+) synthetase. 268 matched cddid_all.tbl CDD PRK00770 PRK00770 179117 PRK00770 deoxyhypusine synthase. 384 matched cddid_all.tbl CDD PRK00771 PRK00771 179118 PRK00771 signal recognition particle protein Srp54; Provisional 437 matched cddid_all.tbl CDD PRK00772 PRK00772 234832 PRK00772 3-isopropylmalate dehydrogenase; Provisional 358 matched cddid_all.tbl CDD PRK00773 PRK00773 234833 rplX 50S ribosomal protein LX; Validated 76 matched cddid_all.tbl CDD PRK00777 PRK00777 234834 PRK00777 pantetheine-phosphate adenylyltransferase. 153 matched cddid_all.tbl CDD PRK00779 PRK00779 234835 PRK00779 ornithine carbamoyltransferase; Provisional 304 matched cddid_all.tbl CDD PRK00782 PRK00782 234836 PRK00782 MEMO1 family protein. 267 matched cddid_all.tbl CDD PRK00783 PRK00783 234837 PRK00783 DNA-directed RNA polymerase subunit D; Provisional 263 matched cddid_all.tbl CDD PRK00784 PRK00784 234838 PRK00784 cobyric acid synthase. 488 matched cddid_all.tbl CDD PRK00790 PRK00790 179126 fliE flagellar hook-basal body complex protein FliE. 109 matched cddid_all.tbl CDD PRK00794 PRK00794 179127 flbT flagellar biosynthesis repressor FlbT; Reviewed 132 matched cddid_all.tbl CDD PRK00801 PRK00801 234839 PRK00801 hypothetical protein; Provisional 201 matched cddid_all.tbl CDD PRK00802 PRK00802 234840 PRK00802 DNA-3-methyladenine glycosylase. 188 matched cddid_all.tbl CDD PRK00805 PRK00805 234841 PRK00805 putative deoxyhypusine synthase; Provisional 329 matched cddid_all.tbl CDD PRK00807 PRK00807 179131 PRK00807 50S ribosomal protein L24e; Validated 52 matched cddid_all.tbl CDD PRK00808 PRK00808 179132 PRK00808 bacteriohemerythrin. 150 matched cddid_all.tbl CDD PRK00809 PRK00809 179133 PRK00809 hypothetical protein; Provisional 144 matched cddid_all.tbl CDD PRK00810 PRK00810 234842 nifW nitrogenase stabilizing/protective protein NifW. 113 matched cddid_all.tbl CDD PRK00811 PRK00811 234843 PRK00811 polyamine aminopropyltransferase. 283 matched cddid_all.tbl CDD PRK00816 PRK00816 234844 rnfD electron transport complex protein RnfD; Reviewed 350 matched cddid_all.tbl CDD PRK00819 PRK00819 179136 PRK00819 RNA 2'-phosphotransferase; Reviewed 179 matched cddid_all.tbl CDD PRK00823 PRK00823 234845 phhB pterin-4-alpha-carbinolamine dehydratase; Validated 97 matched cddid_all.tbl CDD PRK00831 PRK00831 179138 rpmJ 50S ribosomal protein L36; Validated 41 matched cddid_all.tbl CDD PRK00843 PRK00843 179139 egsA NAD(P)-dependent glycerol-1-phosphate dehydrogenase; Reviewed 350 matched cddid_all.tbl CDD PRK00844 PRK00844 234846 glgC glucose-1-phosphate adenylyltransferase; Provisional 407 matched cddid_all.tbl CDD PRK00846 PRK00846 179141 PRK00846 hypothetical protein; Provisional 77 matched cddid_all.tbl CDD PRK00854 PRK00854 234848 rocD ornithine--oxo-acid transaminase; Reviewed 401 matched cddid_all.tbl CDD PRK00855 PRK00855 179143 PRK00855 argininosuccinate lyase; Provisional 459 matched cddid_all.tbl CDD PRK00856 PRK00856 234849 pyrB aspartate carbamoyltransferase catalytic subunit. 305 matched cddid_all.tbl CDD PRK00861 PRK00861 234850 PRK00861 putative lipid kinase; Reviewed 300 matched cddid_all.tbl CDD PRK00865 PRK00865 234851 PRK00865 glutamate racemase; Provisional 261 matched cddid_all.tbl CDD PRK00870 PRK00870 179147 PRK00870 haloalkane dehalogenase; Provisional 302 matched cddid_all.tbl CDD PRK00871 PRK00871 234852 PRK00871 glutathione-regulated potassium-efflux system oxidoreductase KefF. 176 matched cddid_all.tbl CDD PRK00872 PRK00872 179149 PRK00872 hypothetical protein; Provisional 157 matched cddid_all.tbl CDD PRK00876 PRK00876 179150 nadE NAD(+) synthase. 326 matched cddid_all.tbl CDD PRK00877 PRK00877 234853 hisD bifunctional histidinal dehydrogenase/ histidinol dehydrogenase; Reviewed 425 matched cddid_all.tbl CDD PRK00881 PRK00881 234854 purH bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase; Provisional 513 matched cddid_all.tbl CDD PRK00886 PRK00886 234857 PRK00886 2-phosphosulfolactate phosphatase family protein. 240 matched cddid_all.tbl CDD PRK00888 PRK00888 179156 ftsB cell division protein FtsB; Reviewed 105 matched cddid_all.tbl CDD PRK00889 PRK00889 179157 PRK00889 adenylylsulfate kinase; Provisional 175 matched cddid_all.tbl CDD PRK00892 PRK00892 234858 lpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional 343 matched cddid_all.tbl CDD PRK00893 PRK00893 234859 PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed 152 matched cddid_all.tbl CDD PRK00901 PRK00901 234860 PRK00901 methylated-DNA--protein-cysteine methyltransferase; Provisional 155 matched cddid_all.tbl CDD PRK00907 PRK00907 179161 PRK00907 hypothetical protein; Provisional 92 matched cddid_all.tbl CDD PRK00911 PRK00911 234861 PRK00911 dihydroxy-acid dehydratase; Provisional 552 matched cddid_all.tbl CDD PRK00912 PRK00912 234862 PRK00912 ribonuclease P protein component 3; Provisional 237 matched cddid_all.tbl CDD PRK00913 PRK00913 234863 PRK00913 multifunctional aminopeptidase A; Provisional 483 matched cddid_all.tbl CDD PRK00915 PRK00915 234864 PRK00915 2-isopropylmalate synthase; Validated 513 matched cddid_all.tbl CDD PRK00923 PRK00923 234865 PRK00923 sirohydrochlorin nickelochelatase. 126 matched cddid_all.tbl CDD PRK00924 PRK00924 179169 PRK00924 5-keto-4-deoxyuronate isomerase; Provisional 276 matched cddid_all.tbl CDD PRK00927 PRK00927 234866 PRK00927 tryptophanyl-tRNA synthetase; Reviewed 333 matched cddid_all.tbl CDD PRK00933 PRK00933 234867 PRK00933 ribosomal biogenesis protein; Validated 165 matched cddid_all.tbl CDD PRK00934 PRK00934 234868 PRK00934 ribose-phosphate pyrophosphokinase; Provisional 285 matched cddid_all.tbl CDD PRK00939 PRK00939 179173 PRK00939 stress response translation initiation inhibitor YciH. 99 matched cddid_all.tbl CDD PRK00942 PRK00942 234869 PRK00942 acetylglutamate kinase; Provisional 283 matched cddid_all.tbl CDD PRK00943 PRK00943 234870 PRK00943 selenide, water dikinase SelD. 347 matched cddid_all.tbl CDD PRK00944 PRK00944 234871 PRK00944 hypothetical protein; Provisional 195 matched cddid_all.tbl CDD PRK00951 PRK00951 234873 hisB imidazoleglycerol-phosphate dehydratase HisB. 195 matched cddid_all.tbl CDD PRK00956 PRK00956 179181 thyA thymidylate synthase; Provisional 208 matched cddid_all.tbl CDD PRK00957 PRK00957 234875 PRK00957 methionine synthase; Provisional 305 matched cddid_all.tbl CDD PRK00960 PRK00960 234876 PRK00960 seryl-tRNA synthetase; Provisional 517 matched cddid_all.tbl CDD PRK00961 PRK00961 179184 PRK00961 H(2)-dependent methylenetetrahydromethanopterin dehydrogenase; Provisional 342 matched cddid_all.tbl CDD PRK00962 PRK00962 179185 PRK00962 hypothetical protein; Provisional 165 matched cddid_all.tbl CDD PRK00964 PRK00964 234877 PRK00964 tetrahydromethanopterin S-methyltransferase subunit A; Provisional 225 matched cddid_all.tbl CDD PRK00965 PRK00965 179187 PRK00965 tetrahydromethanopterin S-methyltransferase subunit B; Provisional 96 matched cddid_all.tbl CDD PRK00967 PRK00967 179188 PRK00967 hypothetical protein; Provisional 105 matched cddid_all.tbl CDD PRK00971 PRK00971 234880 PRK00971 glutaminase; Provisional 307 matched cddid_all.tbl CDD PRK00973 PRK00973 179193 PRK00973 glucose-6-phosphate isomerase; Provisional 446 matched cddid_all.tbl CDD PRK00977 PRK00977 179195 PRK00977 exodeoxyribonuclease VII small subunit; Provisional 80 matched cddid_all.tbl CDD PRK00979 PRK00979 234883 PRK00979 tetrahydromethanopterin S-methyltransferase subunit H; Provisional 308 matched cddid_all.tbl CDD PRK00982 PRK00982 179197 acpP acyl carrier protein; Provisional 78 matched cddid_all.tbl CDD PRK00984 PRK00984 234884 truD tRNA pseudouridine synthase D; Reviewed 341 matched cddid_all.tbl CDD PRK00994 PRK00994 234885 PRK00994 F420-dependent methylenetetrahydromethanopterin dehydrogenase. 277 matched cddid_all.tbl CDD PRK01001 PRK01001 234887 PRK01001 putative inner membrane protein translocase component YidC; Provisional 795 matched cddid_all.tbl CDD PRK01002 PRK01002 179203 PRK01002 nickel responsive regulator; Provisional 141 matched cddid_all.tbl CDD PRK01005 PRK01005 179204 PRK01005 V-type ATP synthase subunit E; Provisional 207 matched cddid_all.tbl CDD PRK01008 PRK01008 134464 PRK01008 queuine tRNA-ribosyltransferase; Provisional 372 matched cddid_all.tbl CDD PRK01018 PRK01018 179205 PRK01018 50S ribosomal protein L30e; Reviewed 99 matched cddid_all.tbl CDD PRK01021 PRK01021 167141 lpxB lipid-A-disaccharide synthase; Reviewed 608 matched cddid_all.tbl CDD PRK01022 PRK01022 234888 PRK01022 hypothetical protein; Provisional 167 matched cddid_all.tbl CDD PRK01024 PRK01024 179207 PRK01024 Na(+)-translocating NADH-quinone reductase subunit B; Provisional 503 matched cddid_all.tbl CDD PRK01026 PRK01026 179208 PRK01026 tetrahydromethanopterin S-methyltransferase subunit G; Provisional 77 matched cddid_all.tbl CDD PRK01029 PRK01029 234889 tolB Tol-Pal system protein TolB. 428 matched cddid_all.tbl CDD PRK01037 PRK01037 234892 trmD tRNA (guanine-N(1)-)-methyltransferase/unknown domain fusion protein; Reviewed 357 matched cddid_all.tbl CDD PRK01045 PRK01045 234893 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed 298 matched cddid_all.tbl CDD PRK01059 PRK01059 234894 PRK01059 ATP:guanido phosphotransferase; Provisional 346 matched cddid_all.tbl CDD PRK01060 PRK01060 179214 PRK01060 endonuclease IV; Provisional 281 matched cddid_all.tbl CDD PRK01061 PRK01061 234895 PRK01061 Na(+)-translocating NADH-quinone reductase subunit E; Provisional 244 matched cddid_all.tbl CDD PRK01064 PRK01064 179216 PRK01064 hypothetical protein; Provisional 78 matched cddid_all.tbl CDD PRK01066 PRK01066 167150 PRK01066 porphobilinogen deaminase; Provisional 231 matched cddid_all.tbl CDD PRK01076 PRK01076 179217 PRK01076 L-rhamnose isomerase; Provisional 419 matched cddid_all.tbl CDD PRK01077 PRK01077 234896 PRK01077 cobyrinate a,c-diamide synthase. 451 matched cddid_all.tbl CDD PRK01096 PRK01096 234897 PRK01096 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional 440 matched cddid_all.tbl CDD PRK01099 PRK01099 179220 rpoK DNA-directed RNA polymerase subunit K; Provisional 62 matched cddid_all.tbl CDD PRK01100 PRK01100 234898 PRK01100 accessory gene regulator ArgB-like protein. 210 matched cddid_all.tbl CDD PRK01103 PRK01103 234899 PRK01103 bifunctional DNA-formamidopyrimidine glycosylase/DNA-(apurinic or apyrimidinic site) lyase. 274 matched cddid_all.tbl CDD PRK01109 PRK01109 234900 PRK01109 ATP-dependent DNA ligase; Provisional 590 matched cddid_all.tbl CDD PRK01112 PRK01112 234902 PRK01112 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase. 228 matched cddid_all.tbl CDD PRK01115 PRK01115 234903 PRK01115 DNA polymerase sliding clamp; Validated 247 matched cddid_all.tbl CDD PRK01117 PRK01117 234904 PRK01117 adenylosuccinate synthetase; Provisional 430 matched cddid_all.tbl CDD PRK01119 PRK01119 179228 PRK01119 putative heavy metal-binding protein. 106 matched cddid_all.tbl CDD PRK01130 PRK01130 234907 PRK01130 putative N-acetylmannosamine-6-phosphate 2-epimerase. 221 matched cddid_all.tbl CDD PRK01143 PRK01143 234908 rpl11p 50S ribosomal protein L11P; Validated 163 matched cddid_all.tbl CDD PRK01146 PRK01146 234909 PRK01146 DNA-directed RNA polymerase subunit L; Provisional 85 matched cddid_all.tbl CDD PRK01151 PRK01151 179234 rps17E 30S ribosomal protein S17e; Validated 58 matched cddid_all.tbl CDD PRK01153 PRK01153 179235 PRK01153 nicotinamide-nucleotide adenylyltransferase; Provisional 174 matched cddid_all.tbl CDD PRK01156 PRK01156 100796 PRK01156 chromosome segregation protein; Provisional 895 matched cddid_all.tbl CDD PRK01158 PRK01158 234910 PRK01158 phosphoglycolate phosphatase; Provisional 230 matched cddid_all.tbl CDD PRK01160 PRK01160 234911 PRK01160 hypothetical protein; Provisional 178 matched cddid_all.tbl CDD PRK01170 PRK01170 234912 PRK01170 bifunctional pantetheine-phosphate adenylyltransferase/NTP phosphatase. 322 matched cddid_all.tbl CDD PRK01172 PRK01172 100801 PRK01172 ATP-dependent DNA helicase. 674 matched cddid_all.tbl CDD PRK01175 PRK01175 234913 PRK01175 phosphoribosylformylglycinamidine synthase I; Provisional 261 matched cddid_all.tbl CDD PRK01177 PRK01177 167170 PRK01177 hypothetical protein; Provisional 140 matched cddid_all.tbl CDD PRK01178 PRK01178 179239 rps24e 30S ribosomal protein S24e; Reviewed 99 matched cddid_all.tbl CDD PRK01184 PRK01184 234914 PRK01184 flagellar hook-basal body complex protein FliE. 184 matched cddid_all.tbl CDD PRK01185 PRK01185 179241 ppnK NAD(+) kinase. 271 matched cddid_all.tbl CDD PRK01189 PRK01189 100807 PRK01189 V-type ATP synthase subunit F; Provisional 104 matched cddid_all.tbl CDD PRK01192 PRK01192 234916 PRK01192 50S ribosomal protein L31e; Reviewed 89 matched cddid_all.tbl CDD PRK01194 PRK01194 100810 PRK01194 V-type ATP synthase subunit E; Provisional 185 matched cddid_all.tbl CDD PRK01198 PRK01198 234917 PRK01198 V-type ATP synthase subunit C; Provisional 352 matched cddid_all.tbl CDD PRK01202 PRK01202 234918 PRK01202 glycine cleavage system protein GcvH. 127 matched cddid_all.tbl CDD PRK01207 PRK01207 100814 PRK01207 methionine synthase; Provisional 343 matched cddid_all.tbl CDD PRK01209 PRK01209 234919 cobD cobalamin biosynthesis protein. 312 matched cddid_all.tbl CDD PRK01211 PRK01211 179247 PRK01211 dihydroorotase; Provisional 409 matched cddid_all.tbl CDD PRK01212 PRK01212 234920 PRK01212 homoserine kinase; Provisional 301 matched cddid_all.tbl CDD PRK01213 PRK01213 234921 PRK01213 phosphoribosylformylglycinamidine synthase subunit PurL. 724 matched cddid_all.tbl CDD PRK01215 PRK01215 179250 PRK01215 nicotinamide mononucleotide deamidase-related protein. 264 matched cddid_all.tbl CDD PRK01216 PRK01216 179251 PRK01216 DNA polymerase IV; Validated 351 matched cddid_all.tbl CDD PRK01217 PRK01217 179252 PRK01217 hypothetical protein; Provisional 114 matched cddid_all.tbl CDD PRK01220 PRK01220 179253 PRK01220 malonate decarboxylase subunit delta; Provisional 99 matched cddid_all.tbl CDD PRK01221 PRK01221 234922 PRK01221 deoxyhypusine synthase. 312 matched cddid_all.tbl CDD PRK01222 PRK01222 234923 PRK01222 phosphoribosylanthranilate isomerase. 210 matched cddid_all.tbl CDD PRK01229 PRK01229 234924 PRK01229 N-glycosylase/DNA lyase; Provisional 208 matched cddid_all.tbl CDD PRK01231 PRK01231 179257 ppnK NAD(+) kinase. 295 matched cddid_all.tbl CDD PRK01237 PRK01237 234927 PRK01237 triphosphoribosyl-dephospho-CoA synthase; Validated 289 matched cddid_all.tbl CDD PRK01242 PRK01242 179261 rpl39e 50S ribosomal protein L39e; Validated 50 matched cddid_all.tbl CDD PRK01250 PRK01250 179262 PRK01250 inorganic diphosphatase. 176 matched cddid_all.tbl CDD PRK01253 PRK01253 179263 PRK01253 preprotein translocase subunit Sec61beta. 54 matched cddid_all.tbl CDD PRK01259 PRK01259 234929 PRK01259 ribose-phosphate diphosphokinase. 309 matched cddid_all.tbl CDD PRK01261 PRK01261 234930 aroD 3-dehydroquinate dehydratase; Provisional 229 matched cddid_all.tbl CDD PRK01265 PRK01265 234931 PRK01265 heat shock protein HtpX; Provisional 324 matched cddid_all.tbl CDD PRK01271 PRK01271 179269 PRK01271 tautomerase PptA. 76 matched cddid_all.tbl CDD PRK01278 PRK01278 179270 argD acetylornithine transaminase protein; Provisional 389 matched cddid_all.tbl CDD PRK01285 PRK01285 234933 PRK01285 pyruvoyl-dependent arginine decarboxylase; Reviewed 155 matched cddid_all.tbl CDD PRK01286 PRK01286 234934 PRK01286 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional 336 matched cddid_all.tbl CDD PRK01287 PRK01287 234935 xerC site-specific tyrosine recombinase XerC; Reviewed 358 matched cddid_all.tbl CDD PRK01293 PRK01293 234936 PRK01293 phosphoribosyl-dephospho-CoA transferase; Provisional 207 matched cddid_all.tbl CDD PRK01294 PRK01294 234937 PRK01294 lipase secretion chaperone. 336 matched cddid_all.tbl CDD PRK01295 PRK01295 167205 PRK01295 phosphoglyceromutase; Provisional 206 matched cddid_all.tbl CDD PRK01297 PRK01297 234938 PRK01297 ATP-dependent RNA helicase RhlB; Provisional 475 matched cddid_all.tbl CDD PRK01305 PRK01305 234939 PRK01305 arginyl-tRNA-protein transferase; Provisional 240 matched cddid_all.tbl CDD PRK01310 PRK01310 167208 PRK01310 hypothetical protein; Validated 104 matched cddid_all.tbl CDD PRK01315 PRK01315 234941 PRK01315 putative inner membrane protein translocase component YidC; Provisional 329 matched cddid_all.tbl CDD PRK01318 PRK01318 234942 PRK01318 membrane protein insertase; Provisional 521 matched cddid_all.tbl CDD PRK01322 PRK01322 179280 PRK01322 6-carboxyhexanoate--CoA ligase; Provisional 242 matched cddid_all.tbl CDD PRK01326 PRK01326 179281 prsA foldase protein PrsA; Reviewed 310 matched cddid_all.tbl CDD PRK01343 PRK01343 234943 PRK01343 zinc-binding protein; Provisional 57 matched cddid_all.tbl CDD PRK01345 PRK01345 234944 PRK01345 heat shock protein HtpX; Provisional 317 matched cddid_all.tbl CDD PRK01346 PRK01346 234945 PRK01346 enhanced intracellular survival protein Eis. 411 matched cddid_all.tbl CDD PRK01355 PRK01355 234946 PRK01355 azoreductase; Reviewed 199 matched cddid_all.tbl CDD PRK01356 PRK01356 167217 hscB co-chaperone HscB; Provisional 166 matched cddid_all.tbl CDD PRK01371 PRK01371 179287 PRK01371 Sec-independent protein translocase protein TatB. 137 matched cddid_all.tbl CDD PRK01372 PRK01372 234948 ddl D-alanine--D-alanine ligase; Reviewed 304 matched cddid_all.tbl CDD PRK01379 PRK01379 134546 cyaY iron donor protein CyaY. 103 matched cddid_all.tbl CDD PRK01388 PRK01388 234949 PRK01388 arginine deiminase; Provisional 406 matched cddid_all.tbl CDD PRK01392 PRK01392 234951 citX 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA:apo-citrate lyase; Reviewed 180 matched cddid_all.tbl CDD PRK01395 PRK01395 179293 PRK01395 V-type ATP synthase subunit F; Provisional 104 matched cddid_all.tbl CDD PRK01397 PRK01397 179294 PRK01397 50S ribosomal protein L31; Provisional 78 matched cddid_all.tbl CDD PRK01402 PRK01402 234952 hslO Hsp33-like chaperonin; Reviewed 328 matched cddid_all.tbl CDD PRK01415 PRK01415 167229 PRK01415 hypothetical protein; Validated 247 matched cddid_all.tbl CDD PRK01424 PRK01424 234954 PRK01424 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional 366 matched cddid_all.tbl CDD PRK01433 PRK01433 234955 hscA chaperone protein HscA; Provisional 595 matched cddid_all.tbl CDD PRK01441 PRK01441 167232 PRK01441 Maf-like protein; Reviewed 207 matched cddid_all.tbl CDD PRK01470 PRK01470 179298 tatA twin arginine translocase protein A; Provisional 51 matched cddid_all.tbl CDD PRK01474 PRK01474 100879 atpC F0F1 ATP synthase subunit epsilon; Validated 112 matched cddid_all.tbl CDD PRK01482 PRK01482 134562 fliE flagellar hook-basal body complex protein FliE. 108 matched cddid_all.tbl CDD PRK01530 PRK01530 134567 PRK01530 hypothetical protein; Reviewed 105 matched cddid_all.tbl CDD PRK01544 PRK01544 234958 PRK01544 bifunctional N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase/tRNA (m7G46) methyltransferase; Reviewed 506 matched cddid_all.tbl CDD PRK01546 PRK01546 100891 PRK01546 hypothetical protein; Provisional 79 matched cddid_all.tbl CDD PRK01558 PRK01558 179302 PRK01558 V-type ATP synthase subunit E; Provisional 198 matched cddid_all.tbl CDD PRK01581 PRK01581 234961 speE polyamine aminopropyltransferase. 374 matched cddid_all.tbl CDD PRK01584 PRK01584 234962 PRK01584 alanyl-tRNA synthetase; Provisional 594 matched cddid_all.tbl CDD PRK01610 PRK01610 234963 PRK01610 putative voltage-gated ClC-type chloride channel ClcB; Provisional 418 matched cddid_all.tbl CDD PRK01611 PRK01611 234964 argS arginyl-tRNA synthetase; Reviewed 507 matched cddid_all.tbl CDD PRK01614 PRK01614 234965 tatE Sec-independent protein translocase subunit TatA. 85 matched cddid_all.tbl CDD PRK01617 PRK01617 234966 PRK01617 hypothetical protein; Provisional 154 matched cddid_all.tbl CDD PRK01622 PRK01622 179310 PRK01622 membrane protein insertase YidC. 256 matched cddid_all.tbl CDD PRK01625 PRK01625 179311 sspH acid-soluble spore protein H; Provisional 59 matched cddid_all.tbl CDD PRK01631 PRK01631 167247 PRK01631 hypothetical protein; Provisional 76 matched cddid_all.tbl CDD PRK01636 PRK01636 179312 ccrB fluoride efflux transporter CrcB. 118 matched cddid_all.tbl CDD PRK01637 PRK01637 179313 PRK01637 virulence factor BrkB family protein. 286 matched cddid_all.tbl CDD PRK01641 PRK01641 179314 leuD 3-isopropylmalate dehydratase small subunit. 200 matched cddid_all.tbl CDD PRK01642 PRK01642 234967 cls cardiolipin synthetase; Reviewed 483 matched cddid_all.tbl CDD PRK01655 PRK01655 179316 spxA transcriptional regulator Spx; Reviewed 131 matched cddid_all.tbl CDD PRK01658 PRK01658 167253 PRK01658 CidA/LrgA family holin-like protein. 122 matched cddid_all.tbl CDD PRK01663 PRK01663 234968 PRK01663 C4-dicarboxylate transporter DctA; Reviewed 428 matched cddid_all.tbl CDD PRK01678 PRK01678 234969 rpmE2 type B 50S ribosomal protein L31. 87 matched cddid_all.tbl CDD PRK01683 PRK01683 234970 PRK01683 trans-aconitate 2-methyltransferase; Provisional 258 matched cddid_all.tbl CDD PRK01699 PRK01699 179322 fliE flagellar hook-basal body complex protein FliE. 99 matched cddid_all.tbl CDD PRK01712 PRK01712 234973 PRK01712 carbon storage regulator CsrA. 64 matched cddid_all.tbl CDD PRK01713 PRK01713 167263 PRK01713 ornithine carbamoyltransferase; Provisional 334 matched cddid_all.tbl CDD PRK01723 PRK01723 234975 PRK01723 3-deoxy-D-manno-octulosonic-acid kinase; Reviewed 239 matched cddid_all.tbl CDD PRK01736 PRK01736 234976 PRK01736 hypothetical protein; Reviewed 190 matched cddid_all.tbl CDD PRK01747 PRK01747 234978 mnmC bifunctional tRNA (5-methylaminomethyl-2-thiouridine)(34)-methyltransferase MnmD/FAD-dependent 5-carboxymethylaminomethyl-2-thiouridine(34) oxidoreductase MnmC. 662 matched cddid_all.tbl CDD PRK01749 PRK01749 234979 PRK01749 disulfide bond formation protein DsbB. 176 matched cddid_all.tbl CDD PRK01752 PRK01752 179332 PRK01752 YchJ family protein. 156 matched cddid_all.tbl CDD PRK01759 PRK01759 234980 glnD bifunctional uridylyltransferase/uridylyl-removing protein GlnD. 854 matched cddid_all.tbl CDD PRK01766 PRK01766 234981 PRK01766 multidrug efflux protein; Reviewed 456 matched cddid_all.tbl CDD PRK01773 PRK01773 179335 hscB Fe-S protein assembly co-chaperone HscB. 173 matched cddid_all.tbl CDD PRK01777 PRK01777 234982 PRK01777 RnfH family protein. 95 matched cddid_all.tbl CDD PRK01810 PRK01810 179337 PRK01810 DNA polymerase IV; Validated 407 matched cddid_all.tbl CDD PRK01816 PRK01816 179338 PRK01816 hypothetical protein; Provisional 143 matched cddid_all.tbl CDD PRK01821 PRK01821 234983 PRK01821 hypothetical protein; Provisional 133 matched cddid_all.tbl CDD PRK01827 PRK01827 234984 thyA thymidylate synthase; Reviewed 264 matched cddid_all.tbl CDD PRK01833 PRK01833 167284 tatA Sec-independent protein translocase subunit TatA. 74 matched cddid_all.tbl CDD PRK01842 PRK01842 234985 PRK01842 hypothetical protein; Provisional 149 matched cddid_all.tbl CDD PRK01844 PRK01844 100947 PRK01844 YneF family protein. 72 matched cddid_all.tbl CDD PRK01862 PRK01862 234987 PRK01862 voltage-gated chloride channel ClcB. 574 matched cddid_all.tbl CDD PRK01885 PRK01885 179345 greB transcription elongation factor GreB; Reviewed 157 matched cddid_all.tbl CDD PRK01889 PRK01889 234988 PRK01889 GTPase RsgA; Reviewed 356 matched cddid_all.tbl CDD PRK01903 PRK01903 234989 rnpA ribonuclease P protein component. 133 matched cddid_all.tbl CDD PRK01904 PRK01904 234990 PRK01904 DUF2057 domain-containing protein. 219 matched cddid_all.tbl CDD PRK01905 PRK01905 179348 PRK01905 Fis family transcriptional regulator. 77 matched cddid_all.tbl CDD PRK01908 PRK01908 179350 PRK01908 electron transport complex protein RnfG; Validated 205 matched cddid_all.tbl CDD PRK01909 PRK01909 234991 pdxA 4-hydroxythreonine-4-phosphate dehydrogenase PdxA. 329 matched cddid_all.tbl CDD PRK01911 PRK01911 179352 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional 292 matched cddid_all.tbl CDD PRK01917 PRK01917 179353 PRK01917 cation-binding hemerythrin HHE family protein; Provisional 139 matched cddid_all.tbl CDD PRK01964 PRK01964 179355 PRK01964 4-oxalocrotonate tautomerase; Provisional 64 matched cddid_all.tbl CDD PRK01966 PRK01966 234993 ddl D-alanine--D-alanine ligase. 333 matched cddid_all.tbl CDD PRK02001 PRK02001 179358 PRK02001 ribosome assembly cofactor RimP. 152 matched cddid_all.tbl CDD PRK02047 PRK02047 179360 PRK02047 hypothetical protein; Provisional 91 matched cddid_all.tbl CDD PRK02048 PRK02048 179361 PRK02048 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase; Provisional 611 matched cddid_all.tbl CDD PRK02079 PRK02079 179362 PRK02079 pyrroloquinoline quinone biosynthesis peptide chaperone PqqD. 88 matched cddid_all.tbl CDD PRK02090 PRK02090 234997 PRK02090 phosphoadenylyl-sulfate reductase. 241 matched cddid_all.tbl CDD PRK02101 PRK02101 234999 PRK02101 peroxide stress protein YaaA. 255 matched cddid_all.tbl CDD PRK02102 PRK02102 179366 PRK02102 ornithine carbamoyltransferase; Validated 331 matched cddid_all.tbl CDD PRK02103 PRK02103 179367 PRK02103 malonate decarboxylase acyl carrier protein. 105 matched cddid_all.tbl CDD PRK02106 PRK02106 235000 PRK02106 choline dehydrogenase; Validated 560 matched cddid_all.tbl CDD PRK02110 PRK02110 235002 PRK02110 disulfide bond formation protein B; Provisional 169 matched cddid_all.tbl CDD PRK02113 PRK02113 179371 PRK02113 MBL fold metallo-hydrolase. 252 matched cddid_all.tbl CDD PRK02114 PRK02114 235003 PRK02114 formylmethanofuran--tetrahydromethanopterin formyltransferase; Provisional 297 matched cddid_all.tbl CDD PRK02118 PRK02118 179373 PRK02118 V-type ATP synthase subunit B; Provisional 436 matched cddid_all.tbl CDD PRK02119 PRK02119 235004 PRK02119 hypothetical protein; Provisional 73 matched cddid_all.tbl CDD PRK02122 PRK02122 235005 PRK02122 glucosamine-6-phosphate deaminase-like protein; Validated 652 matched cddid_all.tbl CDD PRK02126 PRK02126 235006 PRK02126 ribonuclease Z; Provisional 334 matched cddid_all.tbl CDD PRK02134 PRK02134 235007 PRK02134 chitin disaccharide deacetylase. 249 matched cddid_all.tbl CDD PRK02135 PRK02135 235008 PRK02135 hypothetical protein; Provisional 201 matched cddid_all.tbl CDD PRK02141 PRK02141 235009 PRK02141 Maf-like protein; Reviewed 207 matched cddid_all.tbl CDD PRK02155 PRK02155 179379 ppnK NAD kinase. 291 matched cddid_all.tbl CDD PRK02166 PRK02166 167325 PRK02166 hypothetical protein; Reviewed 184 matched cddid_all.tbl CDD PRK02186 PRK02186 235010 PRK02186 argininosuccinate lyase; Provisional 887 matched cddid_all.tbl CDD PRK02190 PRK02190 235011 PRK02190 agmatinase; Provisional 301 matched cddid_all.tbl CDD PRK02193 PRK02193 179381 truB tRNA pseudouridine synthase B; Provisional 279 matched cddid_all.tbl CDD PRK02195 PRK02195 179382 PRK02195 V-type ATP synthase subunit D; Provisional 201 matched cddid_all.tbl CDD PRK02201 PRK02201 235012 PRK02201 putative inner membrane protein translocase component YidC; Provisional 357 matched cddid_all.tbl CDD PRK02220 PRK02220 235013 PRK02220 4-oxalocrotonate tautomerase; Provisional 61 matched cddid_all.tbl CDD PRK02224 PRK02224 179385 PRK02224 DNA double-strand break repair Rad50 ATPase. 880 matched cddid_all.tbl CDD PRK02227 PRK02227 235014 PRK02227 (5-formylfuran-3-yl)methyl phosphate synthase. 238 matched cddid_all.tbl CDD PRK02228 PRK02228 179387 PRK02228 V-type ATP synthase subunit F; Provisional 100 matched cddid_all.tbl CDD PRK02230 PRK02230 179388 PRK02230 inorganic pyrophosphatase; Provisional 184 matched cddid_all.tbl CDD PRK02231 PRK02231 167337 ppnK NAD(+) kinase. 272 matched cddid_all.tbl CDD PRK02234 PRK02234 235015 recU Holliday junction-specific endonuclease; Reviewed 195 matched cddid_all.tbl CDD PRK02237 PRK02237 235016 PRK02237 YnfA family protein. 109 matched cddid_all.tbl CDD PRK02240 PRK02240 179391 PRK02240 GTP cyclohydrolase IIa. 254 matched cddid_all.tbl CDD PRK02249 PRK02249 179392 PRK02249 DNA primase regulatory subunit PriL. 343 matched cddid_all.tbl CDD PRK02250 PRK02250 179393 PRK02250 hypothetical protein; Provisional 166 matched cddid_all.tbl CDD PRK02251 PRK02251 179394 PRK02251 cell division protein CrgA. 87 matched cddid_all.tbl CDD PRK02253 PRK02253 179395 PRK02253 deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional 167 matched cddid_all.tbl CDD PRK02256 PRK02256 235018 PRK02256 putative aminopeptidase 1; Provisional 462 matched cddid_all.tbl CDD PRK02259 PRK02259 235019 PRK02259 aspartoacylase; Provisional 288 matched cddid_all.tbl CDD PRK02260 PRK02260 179399 PRK02260 S-ribosylhomocysteine lyase. 158 matched cddid_all.tbl CDD PRK02261 PRK02261 179400 PRK02261 methylaspartate mutase subunit S; Provisional 137 matched cddid_all.tbl CDD PRK02265 PRK02265 179402 PRK02265 acetoacetate decarboxylase; Provisional 246 matched cddid_all.tbl CDD PRK02268 PRK02268 235021 PRK02268 hypothetical protein; Provisional 141 matched cddid_all.tbl CDD PRK02269 PRK02269 167353 PRK02269 ribose-phosphate diphosphokinase. 320 matched cddid_all.tbl CDD PRK02271 PRK02271 235022 PRK02271 methylenetetrahydromethanopterin reductase; Provisional 325 matched cddid_all.tbl CDD PRK02277 PRK02277 235023 PRK02277 orotate phosphoribosyltransferase-like protein; Provisional 200 matched cddid_all.tbl CDD PRK02287 PRK02287 235024 PRK02287 DUF367 family protein. 171 matched cddid_all.tbl CDD PRK02289 PRK02289 179406 PRK02289 4-oxalocrotonate tautomerase; Provisional 60 matched cddid_all.tbl CDD PRK02290 PRK02290 235025 PRK02290 3-dehydroquinate synthase II family protein. 344 matched cddid_all.tbl CDD PRK02292 PRK02292 235026 PRK02292 V-type ATP synthase subunit E; Provisional 188 matched cddid_all.tbl CDD PRK02301 PRK02301 235027 PRK02301 deoxyhypusine synthase. 316 matched cddid_all.tbl CDD PRK02302 PRK02302 179410 PRK02302 hypothetical protein; Provisional 89 matched cddid_all.tbl CDD PRK02304 PRK02304 235028 PRK02304 adenine phosphoribosyltransferase; Provisional 175 matched cddid_all.tbl CDD PRK02308 PRK02308 235029 uvsE putative UV damage endonuclease; Provisional 303 matched cddid_all.tbl CDD PRK02315 PRK02315 235030 PRK02315 adaptor protein MecA. 233 matched cddid_all.tbl CDD PRK02318 PRK02318 235031 PRK02318 mannitol-1-phosphate 5-dehydrogenase; Provisional 381 matched cddid_all.tbl CDD PRK02362 PRK02362 235032 PRK02362 ATP-dependent DNA helicase. 737 matched cddid_all.tbl CDD PRK02382 PRK02382 179417 PRK02382 dihydroorotase; Provisional 443 matched cddid_all.tbl CDD PRK02391 PRK02391 179418 PRK02391 heat shock protein HtpX; Provisional 296 matched cddid_all.tbl CDD PRK02395 PRK02395 235034 PRK02395 hypothetical protein; Provisional 279 matched cddid_all.tbl CDD PRK02399 PRK02399 179420 PRK02399 hypothetical protein; Provisional 406 matched cddid_all.tbl CDD PRK02406 PRK02406 235035 PRK02406 DNA polymerase IV; Validated 343 matched cddid_all.tbl CDD PRK02412 PRK02412 235036 aroD type I 3-dehydroquinate dehydratase. 253 matched cddid_all.tbl CDD PRK02427 PRK02427 235037 PRK02427 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional 435 matched cddid_all.tbl CDD PRK02436 PRK02436 235038 xerD site-specific tyrosine recombinase XerD. 245 matched cddid_all.tbl CDD PRK02458 PRK02458 235039 PRK02458 ribose-phosphate pyrophosphokinase; Provisional 323 matched cddid_all.tbl CDD PRK02463 PRK02463 235040 PRK02463 OxaA-like protein precursor; Provisional 307 matched cddid_all.tbl CDD PRK02471 PRK02471 179427 PRK02471 bifunctional glutamate--cysteine ligase GshA/glutathione synthetase GshB. 752 matched cddid_all.tbl CDD PRK02478 PRK02478 167380 PRK02478 Maf-like protein; Reviewed 199 matched cddid_all.tbl CDD PRK02487 PRK02487 179430 PRK02487 heme-degrading domain-containing protein. 163 matched cddid_all.tbl CDD PRK02491 PRK02491 179431 PRK02491 putative deoxyribonucleotide triphosphate pyrophosphatase/unknown domain fusion protein; Reviewed 328 matched cddid_all.tbl CDD PRK02492 PRK02492 235043 PRK02492 deoxyhypusine synthase. 347 matched cddid_all.tbl CDD PRK02496 PRK02496 179433 adk adenylate kinase; Provisional 184 matched cddid_all.tbl CDD PRK02504 PRK02504 235044 PRK02504 NAD(P)H-quinone oxidoreductase subunit N. 513 matched cddid_all.tbl CDD PRK02506 PRK02506 235045 PRK02506 dihydroorotate dehydrogenase 1A; Reviewed 310 matched cddid_all.tbl CDD PRK02507 PRK02507 235046 PRK02507 proton extrusion protein PcxA; Provisional 422 matched cddid_all.tbl CDD PRK02509 PRK02509 235047 PRK02509 hypothetical protein; Provisional 973 matched cddid_all.tbl CDD PRK02515 PRK02515 235048 psbU photosystem II complex extrinsic protein PsbU. 132 matched cddid_all.tbl CDD PRK02529 PRK02529 134722 petN cytochrome b6-f complex subunit PetN; Provisional 33 matched cddid_all.tbl CDD PRK02539 PRK02539 179440 PRK02539 DUF896 family protein. 85 matched cddid_all.tbl CDD PRK02542 PRK02542 179441 PRK02542 photosystem I assembly protein Ycf4; Provisional 188 matched cddid_all.tbl CDD PRK02546 PRK02546 235050 PRK02546 NAD(P)H-quinone oxidoreductase subunit 4; Provisional 525 matched cddid_all.tbl CDD PRK02551 PRK02551 179443 PRK02551 flavoprotein NrdI; Provisional 154 matched cddid_all.tbl CDD PRK02553 PRK02553 167396 psbK photosystem II reaction center protein K; Provisional 45 matched cddid_all.tbl CDD PRK02557 PRK02557 179444 psbE cytochrome b559 subunit alpha; Provisional 81 matched cddid_all.tbl CDD PRK02561 PRK02561 235051 psbF cytochrome b559 subunit beta; Provisional 44 matched cddid_all.tbl CDD PRK02565 PRK02565 179446 PRK02565 photosystem II reaction center protein J; Provisional 39 matched cddid_all.tbl CDD PRK02597 PRK02597 235052 rpoC2 DNA-directed RNA polymerase subunit beta'; Provisional 1331 matched cddid_all.tbl CDD PRK02603 PRK02603 179448 PRK02603 photosystem I assembly protein Ycf3; Provisional 172 matched cddid_all.tbl CDD PRK02610 PRK02610 235053 PRK02610 histidinol-phosphate transaminase. 374 matched cddid_all.tbl CDD PRK02615 PRK02615 235054 PRK02615 thiamine phosphate synthase. 347 matched cddid_all.tbl CDD PRK02624 PRK02624 179451 psbH photosystem II reaction center protein PsbH. 64 matched cddid_all.tbl CDD PRK02625 PRK02625 235055 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional 627 matched cddid_all.tbl CDD PRK02627 PRK02627 235056 PRK02627 acetylornithine aminotransferase; Provisional 396 matched cddid_all.tbl CDD PRK02628 PRK02628 235057 nadE NAD synthetase; Reviewed 679 matched cddid_all.tbl CDD PRK02645 PRK02645 179455 ppnK NAD(+) kinase. 305 matched cddid_all.tbl CDD PRK02649 PRK02649 179456 ppnK NAD(+) kinase. 305 matched cddid_all.tbl CDD PRK02654 PRK02654 235058 PRK02654 putative inner membrane protein translocase component YidC; Provisional 375 matched cddid_all.tbl CDD PRK02655 PRK02655 179459 psbI photosystem II reaction center protein I. 38 matched cddid_all.tbl CDD PRK02693 PRK02693 179460 PRK02693 apocytochrome f; Reviewed 312 matched cddid_all.tbl CDD PRK02714 PRK02714 235061 PRK02714 o-succinylbenzoate synthase. 320 matched cddid_all.tbl CDD PRK02724 PRK02724 235062 PRK02724 30S ribosomal protein PSRP-3. 104 matched cddid_all.tbl CDD PRK02726 PRK02726 235063 PRK02726 molybdenum cofactor guanylyltransferase. 200 matched cddid_all.tbl CDD PRK02733 PRK02733 235065 PRK02733 photosystem I reaction center subunit IX; Provisional 42 matched cddid_all.tbl CDD PRK02746 PRK02746 235066 pdxA 4-hydroxythreonine-4-phosphate dehydrogenase PdxA. 345 matched cddid_all.tbl CDD PRK02749 PRK02749 179468 PRK02749 photosystem I reaction center subunit IV; Provisional 71 matched cddid_all.tbl CDD PRK02759 PRK02759 235067 PRK02759 bifunctional phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP diphosphatase HisIE. 203 matched cddid_all.tbl CDD PRK02769 PRK02769 235068 PRK02769 histidine decarboxylase; Provisional 380 matched cddid_all.tbl CDD PRK02793 PRK02793 179472 PRK02793 phi X174 lysis protein; Provisional 72 matched cddid_all.tbl CDD PRK02794 PRK02794 179473 PRK02794 DNA polymerase IV; Provisional 419 matched cddid_all.tbl CDD PRK02797 PRK02797 235070 PRK02797 TDP-N-acetylfucosamine:lipid II N-acetylfucosaminyltransferase. 322 matched cddid_all.tbl CDD PRK02812 PRK02812 235072 PRK02812 ribose-phosphate pyrophosphokinase; Provisional 330 matched cddid_all.tbl CDD PRK02813 PRK02813 235073 PRK02813 putative aminopeptidase 2; Provisional 428 matched cddid_all.tbl CDD PRK02816 PRK02816 179478 PRK02816 phycocyanobilin:ferredoxin oxidoreductase; Validated 243 matched cddid_all.tbl CDD PRK02821 PRK02821 179479 PRK02821 RNA-binding protein. 77 matched cddid_all.tbl CDD PRK02833 PRK02833 235075 PRK02833 phosphate-starvation-inducible protein PsiE; Provisional 133 matched cddid_all.tbl CDD PRK02842 PRK02842 235076 PRK02842 ferredoxin:protochlorophyllide reductase (ATP-dependent) subunit N. 427 matched cddid_all.tbl CDD PRK02853 PRK02853 235077 PRK02853 hypothetical protein; Provisional 161 matched cddid_all.tbl CDD PRK02854 PRK02854 179484 PRK02854 primosomal protein DnaT. 179 matched cddid_all.tbl CDD PRK02862 PRK02862 179486 glgC glucose-1-phosphate adenylyltransferase; Provisional 429 matched cddid_all.tbl CDD PRK02866 PRK02866 235079 PRK02866 cyanate hydratase; Validated 147 matched cddid_all.tbl CDD PRK02868 PRK02868 235080 PRK02868 hypothetical protein; Provisional 245 matched cddid_all.tbl CDD PRK02870 PRK02870 235081 PRK02870 heat shock protein HtpX; Provisional 336 matched cddid_all.tbl CDD PRK02877 PRK02877 179490 PRK02877 hypothetical protein; Provisional 106 matched cddid_all.tbl CDD PRK02886 PRK02886 179491 PRK02886 hypothetical protein; Provisional 87 matched cddid_all.tbl CDD PRK02888 PRK02888 235082 PRK02888 nitrous-oxide reductase; Validated 635 matched cddid_all.tbl CDD PRK02898 PRK02898 179494 PRK02898 energy-coupling factor ABC transporter substrate-binding protein. 100 matched cddid_all.tbl CDD PRK02899 PRK02899 179495 PRK02899 genetic competence negative regulator. 197 matched cddid_all.tbl CDD PRK02901 PRK02901 235084 PRK02901 O-succinylbenzoate synthase; Provisional 327 matched cddid_all.tbl CDD PRK02909 PRK02909 179497 PRK02909 flagellar transcriptional regulator FlhD. 105 matched cddid_all.tbl CDD PRK02910 PRK02910 235085 PRK02910 ferredoxin:protochlorophyllide reductase (ATP-dependent) subunit B. 519 matched cddid_all.tbl CDD PRK02913 PRK02913 179499 PRK02913 hypothetical protein; Provisional 150 matched cddid_all.tbl CDD PRK02919 PRK02919 235086 PRK02919 oxaloacetate decarboxylase subunit gamma; Provisional 82 matched cddid_all.tbl CDD PRK02922 PRK02922 179501 PRK02922 cell surface composition regulator GlgS. 67 matched cddid_all.tbl CDD PRK02925 PRK02925 235087 PRK02925 glucuronate isomerase; Reviewed 466 matched cddid_all.tbl CDD PRK02929 PRK02929 179503 PRK02929 L-arabinose isomerase; Provisional 499 matched cddid_all.tbl CDD PRK02935 PRK02935 179504 PRK02935 hypothetical protein; Provisional 110 matched cddid_all.tbl CDD PRK02936 PRK02936 179505 argD acetylornithine transaminase. 377 matched cddid_all.tbl CDD PRK02939 PRK02939 179506 PRK02939 YnfC family lipoprotein. 236 matched cddid_all.tbl CDD PRK02943 PRK02943 235088 PRK02943 secA regulator SecM. 167 matched cddid_all.tbl CDD PRK02944 PRK02944 179508 PRK02944 YidC family membrane integrase SpoIIIJ. 255 matched cddid_all.tbl CDD PRK02946 PRK02946 235089 aceK bifunctional isocitrate dehydrogenase kinase/phosphatase protein; Validated 575 matched cddid_all.tbl CDD PRK02947 PRK02947 179510 PRK02947 sugar isomerase domain-containing protein. 246 matched cddid_all.tbl CDD PRK02948 PRK02948 179511 PRK02948 IscS subfamily cysteine desulfurase. 381 matched cddid_all.tbl CDD PRK02951 PRK02951 235090 PRK02951 DNA replication terminus site-binding protein; Provisional 309 matched cddid_all.tbl CDD PRK02955 PRK02955 179513 PRK02955 small acid-soluble spore protein SspI; Provisional 68 matched cddid_all.tbl CDD PRK02958 PRK02958 235091 tatA Sec-independent protein translocase subunit TatA. 73 matched cddid_all.tbl CDD PRK02963 PRK02963 235092 PRK02963 carbon starvation induced protein CsiD. 316 matched cddid_all.tbl CDD PRK02967 PRK02967 235093 PRK02967 nickel-responsive transcriptional regulator NikR. 139 matched cddid_all.tbl CDD PRK02971 PRK02971 235094 PRK02971 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnF; Provisional 129 matched cddid_all.tbl CDD PRK02975 PRK02975 179518 PRK02975 O-antigen assembly polymerase. 450 matched cddid_all.tbl CDD PRK02983 PRK02983 235095 lysS bifunctional lysylphosphatidylglycerol synthetase/lysine--tRNA ligase LysX. 1094 matched cddid_all.tbl CDD PRK02984 PRK02984 179520 sspO acid-soluble spore protein O; Provisional 49 matched cddid_all.tbl CDD PRK02991 PRK02991 235096 PRK02991 D-serine dehydratase; Provisional 441 matched cddid_all.tbl CDD PRK02998 PRK02998 179522 prsA peptidylprolyl isomerase; Reviewed 283 matched cddid_all.tbl CDD PRK02999 PRK02999 235097 PRK02999 malate synthase G; Provisional 726 matched cddid_all.tbl CDD PRK03001 PRK03001 179524 PRK03001 zinc metalloprotease HtpX. 283 matched cddid_all.tbl CDD PRK03002 PRK03002 101162 prsA peptidylprolyl isomerase PrsA. 285 matched cddid_all.tbl CDD PRK03003 PRK03003 179525 PRK03003 GTP-binding protein Der; Reviewed 472 matched cddid_all.tbl CDD PRK03007 PRK03007 235098 PRK03007 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional 428 matched cddid_all.tbl CDD PRK03011 PRK03011 235099 PRK03011 butyrate kinase; Provisional 358 matched cddid_all.tbl CDD PRK03057 PRK03057 179529 PRK03057 hypothetical protein; Provisional 180 matched cddid_all.tbl CDD PRK03059 PRK03059 235101 PRK03059 PII uridylyl-transferase; Provisional 856 matched cddid_all.tbl CDD PRK03065 PRK03065 179531 hutP anti-terminator HutP; Provisional 148 matched cddid_all.tbl CDD PRK03072 PRK03072 235102 PRK03072 heat shock protein HtpX; Provisional 288 matched cddid_all.tbl CDD PRK03080 PRK03080 235103 PRK03080 phosphoserine transaminase. 378 matched cddid_all.tbl CDD PRK03081 PRK03081 179534 sspK small, acid-soluble spore protein K. 50 matched cddid_all.tbl CDD PRK03092 PRK03092 179535 PRK03092 ribose-phosphate diphosphokinase. 304 matched cddid_all.tbl CDD PRK03094 PRK03094 179536 PRK03094 hypothetical protein; Provisional 80 matched cddid_all.tbl CDD PRK03095 PRK03095 179537 prsA peptidylprolyl isomerase PrsA. 287 matched cddid_all.tbl CDD PRK03103 PRK03103 235104 PRK03103 DNA polymerase IV; Reviewed 409 matched cddid_all.tbl CDD PRK03113 PRK03113 179540 PRK03113 putative disulfide oxidoreductase; Provisional 139 matched cddid_all.tbl CDD PRK03114 PRK03114 179541 PRK03114 DUF84 family protein. 169 matched cddid_all.tbl CDD PRK03137 PRK03137 179543 PRK03137 1-pyrroline-5-carboxylate dehydrogenase; Provisional 514 matched cddid_all.tbl CDD PRK03140 PRK03140 179544 PRK03140 phosphatidylserine decarboxylase; Provisional 259 matched cddid_all.tbl CDD PRK03147 PRK03147 179545 PRK03147 thiol-disulfide oxidoreductase ResA. 173 matched cddid_all.tbl CDD PRK03174 PRK03174 179548 sspH small acid-soluble spore protein H. 59 matched cddid_all.tbl CDD PRK03180 PRK03180 235108 ligB ATP-dependent DNA ligase; Reviewed 508 matched cddid_all.tbl CDD PRK03187 PRK03187 235109 tgl transglutaminase; Provisional 272 matched cddid_all.tbl CDD PRK03188 PRK03188 235110 PRK03188 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional 300 matched cddid_all.tbl CDD PRK03195 PRK03195 179552 PRK03195 DUF721 family protein. 186 matched cddid_all.tbl CDD PRK03202 PRK03202 235111 PRK03202 ATP-dependent 6-phosphofructokinase. 320 matched cddid_all.tbl CDD PRK03204 PRK03204 179554 PRK03204 haloalkane dehalogenase; Provisional 286 matched cddid_all.tbl CDD PRK03244 PRK03244 235112 argD acetylornithine transaminase. 398 matched cddid_all.tbl CDD PRK03298 PRK03298 235114 PRK03298 endonuclease NucS. 224 matched cddid_all.tbl CDD PRK03317 PRK03317 235115 PRK03317 histidinol-phosphate aminotransferase; Provisional 368 matched cddid_all.tbl CDD PRK03321 PRK03321 179559 PRK03321 putative aminotransferase; Provisional 352 matched cddid_all.tbl CDD PRK03333 PRK03333 179560 coaE dephospho-CoA kinase/protein folding accessory domain-containing protein; Provisional 395 matched cddid_all.tbl CDD PRK03341 PRK03341 235116 PRK03341 arginine repressor; Provisional 168 matched cddid_all.tbl CDD PRK03343 PRK03343 235117 PRK03343 transaldolase; Validated 368 matched cddid_all.tbl CDD PRK03348 PRK03348 235118 PRK03348 DNA polymerase IV; Provisional 454 matched cddid_all.tbl CDD PRK03352 PRK03352 179564 PRK03352 DNA polymerase IV; Validated 346 matched cddid_all.tbl CDD PRK03354 PRK03354 179566 PRK03354 crotonobetainyl-CoA dehydrogenase; Validated 380 matched cddid_all.tbl CDD PRK03355 PRK03355 179567 PRK03355 glycerol-3-phosphate 1-O-acyltransferase. 783 matched cddid_all.tbl CDD PRK03356 PRK03356 179568 PRK03356 L-carnitine/gamma-butyrobetaine antiport BCCT transporter. 504 matched cddid_all.tbl CDD PRK03359 PRK03359 179569 PRK03359 putative electron transfer flavoprotein FixA; Reviewed 256 matched cddid_all.tbl CDD PRK03363 PRK03363 235120 fixB electron transfer flavoprotein subunit alpha/FixB family protein. 313 matched cddid_all.tbl CDD PRK03371 PRK03371 179572 pdxA D-threonate 4-phosphate dehydrogenase. 326 matched cddid_all.tbl CDD PRK03372 PRK03372 235121 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional 306 matched cddid_all.tbl CDD PRK03378 PRK03378 235122 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional 292 matched cddid_all.tbl CDD PRK03379 PRK03379 179575 PRK03379 vitamin B12-transporter protein BtuF; Provisional 260 matched cddid_all.tbl CDD PRK03381 PRK03381 235123 PRK03381 PII uridylyl-transferase; Provisional 774 matched cddid_all.tbl CDD PRK03430 PRK03430 235125 PRK03430 hypothetical protein; Validated 157 matched cddid_all.tbl CDD PRK03437 PRK03437 179579 PRK03437 3-isopropylmalate dehydrogenase; Provisional 344 matched cddid_all.tbl CDD PRK03449 PRK03449 179580 PRK03449 putative inner membrane protein translocase component YidC; Provisional 304 matched cddid_all.tbl CDD PRK03459 PRK03459 235126 rnpA ribonuclease P; Reviewed 122 matched cddid_all.tbl CDD PRK03467 PRK03467 235127 PRK03467 hypothetical protein; Provisional 144 matched cddid_all.tbl CDD PRK03482 PRK03482 179583 PRK03482 phosphoglycerate mutase GpmB. 215 matched cddid_all.tbl CDD PRK03501 PRK03501 179584 ppnK NAD kinase. 264 matched cddid_all.tbl CDD PRK03512 PRK03512 179586 PRK03512 thiamine phosphate synthase. 211 matched cddid_all.tbl CDD PRK03515 PRK03515 179587 PRK03515 ornithine carbamoyltransferase subunit I; Provisional 336 matched cddid_all.tbl CDD PRK03522 PRK03522 235128 rumB 23S rRNA (uracil(747)-C(5))-methyltransferase RlmC. 315 matched cddid_all.tbl CDD PRK03525 PRK03525 179589 PRK03525 L-carnitine CoA-transferase. 405 matched cddid_all.tbl CDD PRK03537 PRK03537 235129 PRK03537 molybdate ABC transporter substrate-binding protein. 188 matched cddid_all.tbl CDD PRK03545 PRK03545 179591 PRK03545 putative arabinose transporter; Provisional 390 matched cddid_all.tbl CDD PRK03554 PRK03554 179592 tatA Sec-independent protein translocase subunit TatA. 89 matched cddid_all.tbl CDD PRK03557 PRK03557 235130 PRK03557 CDF family zinc transporter ZitB. 312 matched cddid_all.tbl CDD PRK03562 PRK03562 235131 PRK03562 glutathione-regulated potassium-efflux system protein KefC; Provisional 621 matched cddid_all.tbl CDD PRK03564 PRK03564 179595 PRK03564 formate dehydrogenase accessory protein FdhE; Provisional 309 matched cddid_all.tbl CDD PRK03573 PRK03573 179596 PRK03573 transcriptional regulator SlyA; Provisional 144 matched cddid_all.tbl CDD PRK03577 PRK03577 235132 PRK03577 acid shock protein. 102 matched cddid_all.tbl CDD PRK03578 PRK03578 235133 hscB Fe-S protein assembly co-chaperone HscB. 176 matched cddid_all.tbl CDD PRK03580 PRK03580 179599 PRK03580 crotonobetainyl-CoA hydratase. 261 matched cddid_all.tbl CDD PRK03584 PRK03584 235134 PRK03584 acetoacetate--CoA ligase. 655 matched cddid_all.tbl CDD PRK03592 PRK03592 235135 PRK03592 haloalkane dehalogenase; Provisional 295 matched cddid_all.tbl CDD PRK03598 PRK03598 235136 PRK03598 putative efflux pump membrane fusion protein; Provisional 331 matched cddid_all.tbl CDD PRK03601 PRK03601 235137 PRK03601 HTH-type transcriptional regulator HdfR. 275 matched cddid_all.tbl CDD PRK03604 PRK03604 235138 moaC bifunctional molybdenum cofactor biosynthesis protein MoaC/MogA; Provisional 312 matched cddid_all.tbl CDD PRK03606 PRK03606 179606 PRK03606 ureidoglycolate lyase. 162 matched cddid_all.tbl CDD PRK03609 PRK03609 179607 umuC translesion error-prone DNA polymerase V subunit UmuC. 422 matched cddid_all.tbl CDD PRK03612 PRK03612 235139 PRK03612 polyamine aminopropyltransferase. 521 matched cddid_all.tbl CDD PRK03619 PRK03619 235140 PRK03619 phosphoribosylformylglycinamidine synthase subunit PurQ. 219 matched cddid_all.tbl CDD PRK03620 PRK03620 235141 PRK03620 5-dehydro-4-deoxyglucarate dehydratase; Provisional 303 matched cddid_all.tbl CDD PRK03624 PRK03624 235142 PRK03624 putative acetyltransferase; Provisional 140 matched cddid_all.tbl CDD PRK03625 PRK03625 179612 tatE twin-arginine translocase subunit TatE. 67 matched cddid_all.tbl CDD PRK03633 PRK03633 179614 PRK03633 putative MFS family transporter protein; Provisional 381 matched cddid_all.tbl CDD PRK03634 PRK03634 179615 PRK03634 rhamnulose-1-phosphate aldolase; Provisional 274 matched cddid_all.tbl CDD PRK03635 PRK03635 235144 PRK03635 ArgP/LysG family DNA-binding transcriptional regulator. 294 matched cddid_all.tbl CDD PRK03636 PRK03636 235145 PRK03636 hypothetical protein; Provisional 179 matched cddid_all.tbl CDD PRK03640 PRK03640 235146 PRK03640 o-succinylbenzoate--CoA ligase. 483 matched cddid_all.tbl CDD PRK03641 PRK03641 179619 PRK03641 DUF2057 family protein. 220 matched cddid_all.tbl CDD PRK03642 PRK03642 179620 PRK03642 putative periplasmic esterase; Provisional 432 matched cddid_all.tbl CDD PRK03643 PRK03643 235147 PRK03643 tagaturonate reductase. 471 matched cddid_all.tbl CDD PRK03646 PRK03646 179622 dadX catabolic alanine racemase. 355 matched cddid_all.tbl CDD PRK03655 PRK03655 235148 PRK03655 putative ion channel protein; Provisional 414 matched cddid_all.tbl CDD PRK03657 PRK03657 235149 PRK03657 2-oxo-tetronate isomerase. 170 matched cddid_all.tbl CDD PRK03659 PRK03659 179625 PRK03659 glutathione-regulated potassium-efflux system protein KefB; Provisional 601 matched cddid_all.tbl CDD PRK03661 PRK03661 179627 PRK03661 nicotinamide-nucleotide amidase. 164 matched cddid_all.tbl CDD PRK03669 PRK03669 179628 PRK03669 mannosyl-3-phosphoglycerate phosphatase-related protein. 271 matched cddid_all.tbl CDD PRK03670 PRK03670 167581 PRK03670 competence damage-inducible protein A; Provisional 252 matched cddid_all.tbl CDD PRK03673 PRK03673 179629 PRK03673 nicotinamide mononucleotide deamidase-related protein YfaY. 396 matched cddid_all.tbl CDD PRK03681 PRK03681 179630 hypA hydrogenase/urease nickel incorporation protein HypA. 114 matched cddid_all.tbl CDD PRK03692 PRK03692 179631 PRK03692 putative UDP-N-acetyl-D-mannosaminuronic acid transferase; Provisional 243 matched cddid_all.tbl CDD PRK03695 PRK03695 235150 PRK03695 vitamin B12-transporter ATPase; Provisional 248 matched cddid_all.tbl CDD PRK03699 PRK03699 235151 PRK03699 putative transporter; Provisional 394 matched cddid_all.tbl CDD PRK03705 PRK03705 235152 PRK03705 glycogen debranching protein GlgX. 658 matched cddid_all.tbl CDD PRK03708 PRK03708 179635 ppnK NAD(+) kinase. 277 matched cddid_all.tbl CDD PRK03715 PRK03715 179636 argD acetylornithine transaminase protein; Provisional 395 matched cddid_all.tbl CDD PRK03717 PRK03717 167589 PRK03717 ribonuclease P protein component 2; Provisional 120 matched cddid_all.tbl CDD PRK03719 PRK03719 179637 PRK03719 ecotin; Provisional 166 matched cddid_all.tbl CDD PRK03731 PRK03731 235153 aroL shikimate kinase AroL. 171 matched cddid_all.tbl CDD PRK03732 PRK03732 167593 PRK03732 hypothetical protein; Provisional 114 matched cddid_all.tbl CDD PRK03735 PRK03735 179639 PRK03735 cytochrome b6; Provisional 223 matched cddid_all.tbl CDD PRK03739 PRK03739 235154 PRK03739 2-isopropylmalate synthase; Validated 552 matched cddid_all.tbl CDD PRK03743 PRK03743 179641 pdxA 4-hydroxythreonine-4-phosphate dehydrogenase PdxA. 332 matched cddid_all.tbl CDD PRK03745 PRK03745 235155 PRK03745 signal recognition particle protein Srp19; Provisional 100 matched cddid_all.tbl CDD PRK03757 PRK03757 179642 PRK03757 YceI family protein. 191 matched cddid_all.tbl CDD PRK03759 PRK03759 235156 PRK03759 isopentenyl-diphosphate Delta-isomerase. 184 matched cddid_all.tbl CDD PRK03760 PRK03760 235157 PRK03760 hypothetical protein; Provisional 117 matched cddid_all.tbl CDD PRK03761 PRK03761 235158 PRK03761 LPS assembly outer membrane complex protein LptD; Provisional 778 matched cddid_all.tbl CDD PRK03767 PRK03767 179647 PRK03767 NAD(P)H:quinone oxidoreductase; Provisional 200 matched cddid_all.tbl CDD PRK03776 PRK03776 179648 PRK03776 phosphatidylglycerol--membrane-oligosaccharide glycerophosphotransferase. 762 matched cddid_all.tbl CDD PRK03784 PRK03784 235159 PRK03784 vtamin B12-transporter permease; Provisional 331 matched cddid_all.tbl CDD PRK03814 PRK03814 235161 PRK03814 oxaloacetate decarboxylase subunit gamma; Provisional 85 matched cddid_all.tbl CDD PRK03817 PRK03817 235163 PRK03817 galactokinase; Provisional 351 matched cddid_all.tbl CDD PRK03818 PRK03818 179654 PRK03818 putative transporter; Validated 552 matched cddid_all.tbl CDD PRK03822 PRK03822 179655 lplA lipoate-protein ligase A; Provisional 338 matched cddid_all.tbl CDD PRK03824 PRK03824 235164 hypA hydrogenase nickel incorporation protein HypA. 135 matched cddid_all.tbl CDD PRK03826 PRK03826 235165 PRK03826 5'-nucleotidase; Provisional 195 matched cddid_all.tbl CDD PRK03837 PRK03837 235166 PRK03837 transcriptional regulator NanR; Provisional 241 matched cddid_all.tbl CDD PRK03839 PRK03839 179660 PRK03839 putative kinase; Provisional 180 matched cddid_all.tbl CDD PRK03846 PRK03846 179661 PRK03846 adenylylsulfate kinase; Provisional 198 matched cddid_all.tbl CDD PRK03854 PRK03854 235167 opgC glucans biosynthesis protein MdoC. 375 matched cddid_all.tbl CDD PRK03858 PRK03858 179663 PRK03858 DNA polymerase IV; Validated 396 matched cddid_all.tbl CDD PRK03868 PRK03868 235168 PRK03868 glucose-6-phosphate isomerase; Provisional 410 matched cddid_all.tbl CDD PRK03879 PRK03879 235169 PRK03879 ribonuclease P protein component 1; Validated 96 matched cddid_all.tbl CDD PRK03887 PRK03887 167628 PRK03887 methylated-DNA--protein-cysteine methyltransferase; Provisional 175 matched cddid_all.tbl CDD PRK03892 PRK03892 179667 PRK03892 Ribonuclease P protein component 3. 216 matched cddid_all.tbl CDD PRK03893 PRK03893 179668 PRK03893 putative sialic acid transporter; Provisional 496 matched cddid_all.tbl CDD PRK03902 PRK03902 179669 PRK03902 transcriptional regulator MntR. 142 matched cddid_all.tbl CDD PRK03903 PRK03903 235171 PRK03903 transaldolase; Provisional 274 matched cddid_all.tbl CDD PRK03906 PRK03906 235172 PRK03906 mannonate dehydratase; Provisional 385 matched cddid_all.tbl CDD PRK03907 PRK03907 235173 fliE flagellar hook-basal body complex protein FliE. 97 matched cddid_all.tbl CDD PRK03910 PRK03910 179673 PRK03910 D-cysteine desulfhydrase; Validated 331 matched cddid_all.tbl CDD PRK03911 PRK03911 235174 PRK03911 HrcA family transcriptional regulator. 260 matched cddid_all.tbl CDD PRK03918 PRK03918 235175 PRK03918 DNA double-strand break repair ATPase Rad50. 880 matched cddid_all.tbl CDD PRK03922 PRK03922 179676 PRK03922 hypothetical protein; Provisional 113 matched cddid_all.tbl CDD PRK03926 PRK03926 179677 PRK03926 mevalonate kinase; Provisional 302 matched cddid_all.tbl CDD PRK03932 PRK03932 235176 asnC asparaginyl-tRNA synthetase; Validated 450 matched cddid_all.tbl CDD PRK03934 PRK03934 235177 PRK03934 phosphatidylserine decarboxylase; Provisional 265 matched cddid_all.tbl CDD PRK03941 PRK03941 235178 PRK03941 NTPase; Reviewed 174 matched cddid_all.tbl CDD PRK03946 PRK03946 179681 pdxA 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional 307 matched cddid_all.tbl CDD PRK03954 PRK03954 235180 PRK03954 ribonuclease P protein component 4; Validated 121 matched cddid_all.tbl CDD PRK03955 PRK03955 179684 PRK03955 DUF126 domain-containing protein. 131 matched cddid_all.tbl CDD PRK03957 PRK03957 179685 PRK03957 V-type ATP synthase subunit F; Provisional 100 matched cddid_all.tbl CDD PRK03958 PRK03958 235181 PRK03958 tRNA 2'-O-methylase; Reviewed 176 matched cddid_all.tbl CDD PRK03963 PRK03963 167649 PRK03963 V-type ATP synthase subunit E; Provisional 198 matched cddid_all.tbl CDD PRK03968 PRK03968 235182 PRK03968 DNA primase large subunit PriL. 399 matched cddid_all.tbl CDD PRK03971 PRK03971 179688 PRK03971 deoxyhypusine synthase. 334 matched cddid_all.tbl CDD PRK03972 PRK03972 179689 PRK03972 ribosomal biogenesis protein; Validated 208 matched cddid_all.tbl CDD PRK03975 PRK03975 179690 tfx putative transcriptional regulator; Provisional 141 matched cddid_all.tbl CDD PRK03976 PRK03976 235183 rpl37ae 50S ribosomal protein L37Ae; Reviewed 90 matched cddid_all.tbl CDD PRK03979 PRK03979 235184 PRK03979 ADP-specific phosphofructokinase; Provisional 463 matched cddid_all.tbl CDD PRK03980 PRK03980 235185 PRK03980 flap endonuclease-1; Provisional 292 matched cddid_all.tbl CDD PRK03982 PRK03982 235186 PRK03982 heat shock protein HtpX; Provisional 288 matched cddid_all.tbl CDD PRK03983 PRK03983 235187 PRK03983 exosome complex exonuclease Rrp41; Provisional 244 matched cddid_all.tbl CDD PRK03987 PRK03987 235188 PRK03987 translation initiation factor IF-2 subunit alpha; Validated 262 matched cddid_all.tbl CDD PRK03988 PRK03988 235189 PRK03988 translation initiation factor IF-2 subunit beta; Validated 138 matched cddid_all.tbl CDD PRK03991 PRK03991 235190 PRK03991 threonyl-tRNA synthetase; Validated 613 matched cddid_all.tbl CDD PRK03992 PRK03992 179699 PRK03992 proteasome-activating nucleotidase; Provisional 389 matched cddid_all.tbl CDD PRK03995 PRK03995 235191 PRK03995 D-aminoacyl-tRNA deacylase. 267 matched cddid_all.tbl CDD PRK03996 PRK03996 235192 PRK03996 archaeal proteasome endopeptidase complex subunit alpha. 241 matched cddid_all.tbl CDD PRK03999 PRK03999 235193 PRK03999 translation initiation factor IF-5A; Provisional 129 matched cddid_all.tbl CDD PRK04000 PRK04000 235194 PRK04000 translation initiation factor IF-2 subunit gamma; Validated 411 matched cddid_all.tbl CDD PRK04004 PRK04004 235195 PRK04004 translation initiation factor IF-2; Validated 586 matched cddid_all.tbl CDD PRK04005 PRK04005 235196 PRK04005 50S ribosomal protein L18e; Provisional 111 matched cddid_all.tbl CDD PRK04007 PRK04007 235197 rps28e 30S ribosomal protein S28e; Validated 70 matched cddid_all.tbl CDD PRK04012 PRK04012 179708 PRK04012 translation initiation factor IF-1A; Provisional 100 matched cddid_all.tbl CDD PRK04013 PRK04013 101376 argD acetylornithine/acetyl-lysine aminotransferase; Provisional 364 matched cddid_all.tbl CDD PRK04015 PRK04015 235199 PRK04015 DNA/RNA-binding protein AlbA. 91 matched cddid_all.tbl CDD PRK04016 PRK04016 235200 PRK04016 DNA-directed RNA polymerase subunit N; Provisional 62 matched cddid_all.tbl CDD PRK04017 PRK04017 179711 PRK04017 hypothetical protein; Provisional 132 matched cddid_all.tbl CDD PRK04019 PRK04019 179712 rplP0 acidic ribosomal protein P0; Validated 330 matched cddid_all.tbl CDD PRK04021 PRK04021 167678 PRK04021 hypothetical protein; Reviewed 92 matched cddid_all.tbl CDD PRK04023 PRK04023 235202 PRK04023 DNA polymerase II large subunit; Validated 1121 matched cddid_all.tbl CDD PRK04024 PRK04024 235203 PRK04024 2,3-bisphosphoglycerate-independent phosphoglycerate mutase. 412 matched cddid_all.tbl CDD PRK04027 PRK04027 235204 PRK04027 30S ribosomal protein S7P; Reviewed 195 matched cddid_all.tbl CDD PRK04028 PRK04028 235205 PRK04028 Glu-tRNA(Gln) amidotransferase subunit GatE. 630 matched cddid_all.tbl CDD PRK04031 PRK04031 235206 PRK04031 DNA primase; Provisional 408 matched cddid_all.tbl CDD PRK04032 PRK04032 235207 PRK04032 CDP-2,3-bis-(O-geranylgeranyl)-sn-glycerol synthase. 159 matched cddid_all.tbl CDD PRK04034 PRK04034 179721 rps8p 30S ribosomal protein S8P; Reviewed 130 matched cddid_all.tbl CDD PRK04036 PRK04036 235208 PRK04036 DNA-directed DNA polymerase II small subunit. 504 matched cddid_all.tbl CDD PRK04038 PRK04038 235209 rps19p 30S ribosomal protein S19P; Provisional 134 matched cddid_all.tbl CDD PRK04040 PRK04040 235210 PRK04040 adenylate kinase; Provisional 188 matched cddid_all.tbl CDD PRK04043 PRK04043 235212 tolB Tol-Pal system protein TolB. 419 matched cddid_all.tbl CDD PRK04044 PRK04044 235213 rps5p 30S ribosomal protein S5P; Reviewed 211 matched cddid_all.tbl CDD PRK04046 PRK04046 179728 PRK04046 translation initiation factor IF-6; Provisional 222 matched cddid_all.tbl CDD PRK04049 PRK04049 235214 PRK04049 30S ribosomal protein S8e; Validated 127 matched cddid_all.tbl CDD PRK04051 PRK04051 179730 rps4p 30S ribosomal protein S4P; Validated 177 matched cddid_all.tbl CDD PRK04053 PRK04053 235215 rps13p 30S ribosomal protein S13P; Reviewed 149 matched cddid_all.tbl CDD PRK04056 PRK04056 179732 PRK04056 septum formation inhibitor Maf. 180 matched cddid_all.tbl CDD PRK04057 PRK04057 235216 PRK04057 30S ribosomal protein S3Ae; Validated 203 matched cddid_all.tbl CDD PRK04059 PRK04059 179734 rpl34e 50S ribosomal protein L34e; Validated 88 matched cddid_all.tbl CDD PRK04069 PRK04069 235217 PRK04069 serine-protein kinase RsbW; Provisional 161 matched cddid_all.tbl CDD PRK04073 PRK04073 179736 rocD ornithine--oxo-acid transaminase; Provisional 396 matched cddid_all.tbl CDD PRK04081 PRK04081 235218 PRK04081 hypothetical protein; Provisional 207 matched cddid_all.tbl CDD PRK04101 PRK04101 179740 PRK04101 metallothiol transferase FosB. 139 matched cddid_all.tbl CDD PRK04115 PRK04115 235220 PRK04115 hypothetical protein; Provisional 137 matched cddid_all.tbl CDD PRK04123 PRK04123 235221 PRK04123 ribulokinase; Provisional 548 matched cddid_all.tbl CDD PRK04125 PRK04125 235222 PRK04125 antiholin-like protein LrgA. 141 matched cddid_all.tbl CDD PRK04128 PRK04128 167709 PRK04128 1-(5-phosphoribosyl)-5- ((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase. 228 matched cddid_all.tbl CDD PRK04132 PRK04132 235223 PRK04132 replication factor C small subunit; Provisional 846 matched cddid_all.tbl CDD PRK04135 PRK04135 179745 PRK04135 2,3-bisphosphoglycerate-independent phosphoglycerate mutase. 395 matched cddid_all.tbl CDD PRK04136 PRK04136 179746 rpl40e 50S ribosomal protein L40e; Provisional 48 matched cddid_all.tbl CDD PRK04140 PRK04140 235224 PRK04140 transcriptional regulator. 317 matched cddid_all.tbl CDD PRK04143 PRK04143 235225 PRK04143 protein-ADP-ribose hydrolase. 264 matched cddid_all.tbl CDD PRK04147 PRK04147 179749 PRK04147 N-acetylneuraminate lyase; Provisional 293 matched cddid_all.tbl CDD PRK04148 PRK04148 235226 PRK04148 hypothetical protein; Provisional 134 matched cddid_all.tbl CDD PRK04149 PRK04149 235227 sat sulfate adenylyltransferase; Reviewed 391 matched cddid_all.tbl CDD PRK04151 PRK04151 179752 PRK04151 IMP cyclohydrolase; Provisional 197 matched cddid_all.tbl CDD PRK04155 PRK04155 235228 PRK04155 protein deglycase HchA. 287 matched cddid_all.tbl CDD PRK04156 PRK04156 235229 gltX glutamyl-tRNA synthetase; Provisional 567 matched cddid_all.tbl CDD PRK04158 PRK04158 235230 PRK04158 GTP-sensing pleiotropic transcriptional regulator CodY. 256 matched cddid_all.tbl CDD PRK04161 PRK04161 235232 PRK04161 tagatose 1,6-diphosphate aldolase; Reviewed 329 matched cddid_all.tbl CDD PRK04163 PRK04163 235233 PRK04163 exosome complex protein Rrp4. 235 matched cddid_all.tbl CDD PRK04164 PRK04164 235234 PRK04164 hypothetical protein; Provisional 181 matched cddid_all.tbl CDD PRK04165 PRK04165 235235 PRK04165 acetyl-CoA decarbonylase/synthase complex subunit gamma; Provisional 450 matched cddid_all.tbl CDD PRK04168 PRK04168 235236 PRK04168 tungstate ABC transporter substrate-binding protein WtpA. 334 matched cddid_all.tbl CDD PRK04169 PRK04169 235237 PRK04169 heptaprenylglyceryl phosphate synthase. 232 matched cddid_all.tbl CDD PRK04171 PRK04171 235238 PRK04171 16S rRNA (pseudouridine)(914)-N(1))-methyltransferase Nep1. 222 matched cddid_all.tbl CDD PRK04172 PRK04172 235239 pheS phenylalanine--tRNA ligase subunit alpha. 489 matched cddid_all.tbl CDD PRK04173 PRK04173 235240 PRK04173 glycyl-tRNA synthetase; Provisional 456 matched cddid_all.tbl CDD PRK04179 PRK04179 235242 rpl37e 50S ribosomal protein L37e; Reviewed 62 matched cddid_all.tbl CDD PRK04180 PRK04180 179769 PRK04180 pyridoxal 5'-phosphate synthase lyase subunit PdxS. 293 matched cddid_all.tbl CDD PRK04181 PRK04181 235243 PRK04181 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional 257 matched cddid_all.tbl CDD PRK04182 PRK04182 235244 PRK04182 cytidylate kinase; Provisional 180 matched cddid_all.tbl CDD PRK04183 PRK04183 235245 PRK04183 Glu-tRNA(Gln) amidotransferase subunit GatD. 419 matched cddid_all.tbl CDD PRK04184 PRK04184 235246 PRK04184 DNA topoisomerase VI subunit B; Validated 535 matched cddid_all.tbl CDD PRK04190 PRK04190 179774 PRK04190 glucose-6-phosphate isomerase; Provisional 191 matched cddid_all.tbl CDD PRK04191 PRK04191 235247 rps3p 30S ribosomal protein S3P; Reviewed 207 matched cddid_all.tbl CDD PRK04192 PRK04192 235248 PRK04192 V-type ATP synthase subunit A; Provisional 586 matched cddid_all.tbl CDD PRK04195 PRK04195 235250 PRK04195 replication factor C large subunit; Provisional 482 matched cddid_all.tbl CDD PRK04196 PRK04196 235251 PRK04196 V-type ATP synthase subunit B; Provisional 460 matched cddid_all.tbl CDD PRK04199 PRK04199 235252 rpl10e 50S ribosomal protein L16. 172 matched cddid_all.tbl CDD PRK04200 PRK04200 179781 PRK04200 cofactor-independent phosphoglycerate mutase; Provisional 395 matched cddid_all.tbl CDD PRK04201 PRK04201 235253 PRK04201 zinc transporter ZupT; Provisional 265 matched cddid_all.tbl CDD PRK04203 PRK04203 235254 rpl1P 50S ribosomal protein L1P; Reviewed 215 matched cddid_all.tbl CDD PRK04204 PRK04204 235255 PRK04204 RNA 3'-terminal phosphate cyclase. 343 matched cddid_all.tbl CDD PRK04207 PRK04207 179786 PRK04207 type II glyceraldehyde-3-phosphate dehydrogenase. 341 matched cddid_all.tbl CDD PRK04208 PRK04208 179787 rbcL ribulose bisophosphate carboxylase; Reviewed 468 matched cddid_all.tbl CDD PRK04210 PRK04210 235256 PRK04210 phosphoenolpyruvate carboxykinase (GTP). 601 matched cddid_all.tbl CDD PRK04211 PRK04211 235257 rps12P 30S ribosomal protein S12P; Reviewed 145 matched cddid_all.tbl CDD PRK04213 PRK04213 179790 PRK04213 GTP-binding protein EngB. 201 matched cddid_all.tbl CDD PRK04214 PRK04214 179791 rbn ribonuclease BN/unknown domain fusion protein; Reviewed 412 matched cddid_all.tbl CDD PRK04217 PRK04217 235258 PRK04217 hypothetical protein; Provisional 110 matched cddid_all.tbl CDD PRK04219 PRK04219 235259 rpl5p 50S ribosomal protein L5P; Reviewed 177 matched cddid_all.tbl CDD PRK04220 PRK04220 179793 PRK04220 2-phosphoglycerate kinase; Provisional 301 matched cddid_all.tbl CDD PRK04223 PRK04223 179794 rpl22p 50S ribosomal protein L22P; Reviewed 153 matched cddid_all.tbl CDD PRK04231 PRK04231 235260 rpl3p 50S ribosomal protein L3P; Reviewed 337 matched cddid_all.tbl CDD PRK04233 PRK04233 235261 PRK04233 hypothetical protein; Provisional 129 matched cddid_all.tbl CDD PRK04235 PRK04235 235262 PRK04235 hypothetical protein; Provisional 196 matched cddid_all.tbl CDD PRK04239 PRK04239 179798 PRK04239 DNA-binding protein. 110 matched cddid_all.tbl CDD PRK04243 PRK04243 235263 PRK04243 50S ribosomal protein L15e; Validated 196 matched cddid_all.tbl CDD PRK04247 PRK04247 235264 PRK04247 endonuclease NucS. 238 matched cddid_all.tbl CDD PRK04250 PRK04250 235265 PRK04250 dihydroorotase; Provisional 398 matched cddid_all.tbl CDD PRK04257 PRK04257 179802 PRK04257 hypothetical protein; Provisional 78 matched cddid_all.tbl CDD PRK04260 PRK04260 179803 PRK04260 acetylornithine transaminase. 375 matched cddid_all.tbl CDD PRK04262 PRK04262 235266 PRK04262 hypothetical protein; Provisional 347 matched cddid_all.tbl CDD PRK04266 PRK04266 235267 PRK04266 fibrillarin-like rRNA/tRNA 2'-O-methyltransferase. 226 matched cddid_all.tbl CDD PRK04270 PRK04270 179806 PRK04270 RNA-guided pseudouridylation complex pseudouridine synthase subunit Cbf5. 300 matched cddid_all.tbl CDD PRK04280 PRK04280 179807 PRK04280 transcriptional regulator ArgR. 148 matched cddid_all.tbl CDD PRK04282 PRK04282 235268 PRK04282 exosome complex protein Rrp42. 271 matched cddid_all.tbl CDD PRK04284 PRK04284 235269 PRK04284 ornithine carbamoyltransferase; Provisional 332 matched cddid_all.tbl CDD PRK04286 PRK04286 235270 PRK04286 hypothetical protein; Provisional 298 matched cddid_all.tbl CDD PRK04288 PRK04288 179810 PRK04288 antiholin-like protein LrgB; Provisional 232 matched cddid_all.tbl CDD PRK04290 PRK04290 235271 PRK04290 30S ribosomal protein S6e; Validated 115 matched cddid_all.tbl CDD PRK04293 PRK04293 179812 PRK04293 adenylosuccinate synthetase; Provisional 333 matched cddid_all.tbl CDD PRK04296 PRK04296 235272 PRK04296 thymidine kinase; Provisional 190 matched cddid_all.tbl CDD PRK04301 PRK04301 235273 radA DNA repair and recombination protein RadA; Validated 317 matched cddid_all.tbl CDD PRK04302 PRK04302 235274 PRK04302 triosephosphate isomerase; Provisional 223 matched cddid_all.tbl CDD PRK04306 PRK04306 235275 PRK04306 50S ribosomal protein L21e; Reviewed 98 matched cddid_all.tbl CDD PRK04307 PRK04307 235276 PRK04307 protein-disulfide oxidoreductase DsbI. 218 matched cddid_all.tbl CDD PRK04309 PRK04309 235277 PRK04309 DNA-directed RNA polymerase subunit A''; Validated 383 matched cddid_all.tbl CDD PRK04313 PRK04313 179820 PRK04313 30S ribosomal protein S4e; Validated 237 matched cddid_all.tbl CDD PRK04319 PRK04319 235279 PRK04319 acetyl-CoA synthetase; Provisional 570 matched cddid_all.tbl CDD PRK04322 PRK04322 235280 PRK04322 peptidyl-tRNA hydrolase; Provisional 113 matched cddid_all.tbl CDD PRK04323 PRK04323 179823 PRK04323 hypothetical protein; Provisional 91 matched cddid_all.tbl CDD PRK04325 PRK04325 179824 PRK04325 hypothetical protein; Provisional 74 matched cddid_all.tbl CDD PRK04326 PRK04326 179825 PRK04326 methionine synthase; Provisional 330 matched cddid_all.tbl CDD PRK04328 PRK04328 235281 PRK04328 hypothetical protein; Provisional 249 matched cddid_all.tbl CDD PRK04330 PRK04330 235282 PRK04330 hypothetical protein; Provisional 88 matched cddid_all.tbl CDD PRK04333 PRK04333 235283 PRK04333 50S ribosomal protein L14e; Validated 84 matched cddid_all.tbl CDD PRK04334 PRK04334 235284 PRK04334 hypothetical protein; Provisional 251 matched cddid_all.tbl CDD PRK04337 PRK04337 179831 PRK04337 50S ribosomal protein L35Ae; Validated 87 matched cddid_all.tbl CDD PRK04338 PRK04338 235286 PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional 382 matched cddid_all.tbl CDD PRK04342 PRK04342 235287 PRK04342 DNA topoisomerase IV subunit A. 367 matched cddid_all.tbl CDD PRK04346 PRK04346 235288 PRK04346 tryptophan synthase subunit beta; Validated 397 matched cddid_all.tbl CDD PRK04350 PRK04350 235289 PRK04350 thymidine phosphorylase; Provisional 490 matched cddid_all.tbl CDD PRK04351 PRK04351 235290 PRK04351 SprT family protein. 149 matched cddid_all.tbl CDD PRK04358 PRK04358 235291 PRK04358 hypothetical protein; Provisional 217 matched cddid_all.tbl CDD PRK04366 PRK04366 235292 PRK04366 aminomethyl-transferring glycine dehydrogenase subunit GcvPB. 481 matched cddid_all.tbl CDD PRK04374 PRK04374 179839 PRK04374 [protein-PII] uridylyltransferase. 869 matched cddid_all.tbl CDD PRK04375 PRK04375 235293 PRK04375 protoheme IX farnesyltransferase; Provisional 296 matched cddid_all.tbl CDD PRK04387 PRK04387 179841 PRK04387 hypothetical protein; Provisional 90 matched cddid_all.tbl CDD PRK04388 PRK04388 235294 PRK04388 disulfide bond formation protein B; Provisional 172 matched cddid_all.tbl CDD PRK04405 PRK04405 235295 prsA peptidylprolyl isomerase; Provisional 298 matched cddid_all.tbl CDD PRK04406 PRK04406 235296 PRK04406 hypothetical protein; Provisional 75 matched cddid_all.tbl CDD PRK04423 PRK04423 235297 PRK04423 LPS-assembly protein LptD. 798 matched cddid_all.tbl CDD PRK04424 PRK04424 179847 PRK04424 transcription factor FapR. 185 matched cddid_all.tbl CDD PRK04435 PRK04435 179848 PRK04435 ACT domain-containing protein. 147 matched cddid_all.tbl CDD PRK04439 PRK04439 235298 PRK04439 methionine adenosyltransferase. 399 matched cddid_all.tbl CDD PRK04443 PRK04443 235299 PRK04443 [LysW]-lysine hydrolase. 348 matched cddid_all.tbl CDD PRK04447 PRK04447 235300 PRK04447 hypothetical protein; Provisional 351 matched cddid_all.tbl CDD PRK04452 PRK04452 235301 PRK04452 acetyl-CoA decarbonylase/synthase complex subunit delta; Provisional 319 matched cddid_all.tbl CDD PRK04456 PRK04456 235302 PRK04456 acetyl-CoA decarbonylase/synthase complex subunit beta; Reviewed 463 matched cddid_all.tbl CDD PRK04457 PRK04457 179854 PRK04457 polyamine aminopropyltransferase. 262 matched cddid_all.tbl CDD PRK04460 PRK04460 179855 PRK04460 nickel-responsive transcriptional regulator NikR. 137 matched cddid_all.tbl CDD PRK04517 PRK04517 235303 PRK04517 hypothetical protein; Provisional 216 matched cddid_all.tbl CDD PRK04523 PRK04523 235304 PRK04523 N-acetylornithine carbamoyltransferase; Reviewed 335 matched cddid_all.tbl CDD PRK04527 PRK04527 235305 PRK04527 argininosuccinate synthase; Provisional 400 matched cddid_all.tbl CDD PRK04531 PRK04531 235306 PRK04531 acetylglutamate kinase; Provisional 398 matched cddid_all.tbl CDD PRK04537 PRK04537 235307 PRK04537 ATP-dependent RNA helicase RhlB; Provisional 572 matched cddid_all.tbl CDD PRK04539 PRK04539 179862 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional 296 matched cddid_all.tbl CDD PRK04542 PRK04542 179863 PRK04542 elongation factor P; Provisional 189 matched cddid_all.tbl CDD PRK04561 PRK04561 179864 tatA twin arginine translocase protein A; Provisional 75 matched cddid_all.tbl CDD PRK04598 PRK04598 179867 tatA twin-arginine translocase subunit TatA. 81 matched cddid_all.tbl CDD PRK04612 PRK04612 179868 argD acetylornithine transaminase. 408 matched cddid_all.tbl CDD PRK04654 PRK04654 135173 PRK04654 sec-independent translocase; Provisional 214 matched cddid_all.tbl CDD PRK04694 PRK04694 179873 PRK04694 Maf-like protein; Reviewed 190 matched cddid_all.tbl CDD PRK04750 PRK04750 235310 ubiB putative ubiquinone biosynthesis protein UbiB; Reviewed 537 matched cddid_all.tbl CDD PRK04758 PRK04758 179875 PRK04758 hypothetical protein; Validated 181 matched cddid_all.tbl CDD PRK04761 PRK04761 179876 ppnK inorganic polyphosphate/ATP-NAD kinase; Reviewed 246 matched cddid_all.tbl CDD PRK04778 PRK04778 179877 PRK04778 septation ring formation regulator EzrA; Provisional 569 matched cddid_all.tbl CDD PRK04813 PRK04813 235313 PRK04813 D-alanine--poly(phosphoribitol) ligase subunit DltA. 503 matched cddid_all.tbl CDD PRK04833 PRK04833 179883 PRK04833 argininosuccinate lyase; Provisional 455 matched cddid_all.tbl CDD PRK04837 PRK04837 235314 PRK04837 ATP-dependent RNA helicase RhlB; Provisional 423 matched cddid_all.tbl CDD PRK04841 PRK04841 235315 PRK04841 HTH-type transcriptional regulator MalT. 903 matched cddid_all.tbl CDD PRK04860 PRK04860 179886 PRK04860 SprT family zinc-dependent metalloprotease. 160 matched cddid_all.tbl CDD PRK04863 PRK04863 235316 mukB chromosome partition protein MukB. 1486 matched cddid_all.tbl CDD PRK04885 PRK04885 235317 ppnK inorganic polyphosphate/ATP-NAD kinase; Provisional 265 matched cddid_all.tbl CDD PRK04897 PRK04897 235318 PRK04897 heat shock protein HtpX; Provisional 298 matched cddid_all.tbl CDD PRK04914 PRK04914 235319 PRK04914 RNA polymerase-associated protein RapA. 956 matched cddid_all.tbl CDD PRK04923 PRK04923 179893 PRK04923 ribose-phosphate diphosphokinase. 319 matched cddid_all.tbl CDD PRK04926 PRK04926 235320 dgt deoxyguanosinetriphosphate triphosphohydrolase; Provisional 503 matched cddid_all.tbl CDD PRK04930 PRK04930 179895 PRK04930 glutathione-regulated potassium-efflux system ancillary protein KefG; Provisional 184 matched cddid_all.tbl CDD PRK04940 PRK04940 179896 PRK04940 hypothetical protein; Provisional 180 matched cddid_all.tbl CDD PRK04946 PRK04946 235321 PRK04946 endonuclease SmrB. 181 matched cddid_all.tbl CDD PRK04949 PRK04949 179898 PRK04949 putative sulfate transport protein CysZ; Validated 251 matched cddid_all.tbl CDD PRK04950 PRK04950 235322 PRK04950 ProP expression regulator; Provisional 213 matched cddid_all.tbl CDD PRK04960 PRK04960 235323 PRK04960 universal stress protein UspB; Provisional 111 matched cddid_all.tbl CDD PRK04964 PRK04964 179901 PRK04964 hypothetical protein; Provisional 66 matched cddid_all.tbl CDD PRK04965 PRK04965 179902 PRK04965 NADH:flavorubredoxin reductase NorW. 377 matched cddid_all.tbl CDD PRK04966 PRK04966 179903 PRK04966 hypothetical protein; Provisional 72 matched cddid_all.tbl CDD PRK04968 PRK04968 235324 PRK04968 SecY interacting protein Syd; Provisional 181 matched cddid_all.tbl CDD PRK04972 PRK04972 179905 PRK04972 putative transporter; Provisional 558 matched cddid_all.tbl CDD PRK04974 PRK04974 235325 PRK04974 glycerol-3-phosphate 1-O-acyltransferase PlsB. 818 matched cddid_all.tbl CDD PRK04976 PRK04976 235326 torD chaperone protein TorD; Validated 202 matched cddid_all.tbl CDD PRK04980 PRK04980 179908 PRK04980 hypothetical protein; Provisional 102 matched cddid_all.tbl CDD PRK04984 PRK04984 179909 PRK04984 fatty acid metabolism transcriptional regulator FadR. 239 matched cddid_all.tbl CDD PRK04987 PRK04987 235327 PRK04987 fumarate reductase subunit FrdC. 130 matched cddid_all.tbl CDD PRK04989 PRK04989 235328 psbM photosystem II reaction center protein M; Provisional 35 matched cddid_all.tbl CDD PRK04998 PRK04998 179912 PRK04998 hypothetical protein; Provisional 88 matched cddid_all.tbl CDD PRK05007 PRK05007 235329 PRK05007 bifunctional uridylyltransferase/uridylyl-removing protein GlnD. 884 matched cddid_all.tbl CDD PRK05014 PRK05014 179914 hscB co-chaperone HscB; Provisional 171 matched cddid_all.tbl CDD PRK05015 PRK05015 235330 PRK05015 aminopeptidase B; Provisional 424 matched cddid_all.tbl CDD PRK05022 PRK05022 235331 PRK05022 nitric oxide reductase transcriptional regulator NorR. 509 matched cddid_all.tbl CDD PRK05031 PRK05031 235332 PRK05031 tRNA (uracil-5-)-methyltransferase; Validated 362 matched cddid_all.tbl CDD PRK05035 PRK05035 235334 PRK05035 electron transport complex protein RnfC; Provisional 695 matched cddid_all.tbl CDD PRK05054 PRK05054 179920 PRK05054 exoribonuclease II; Provisional 644 matched cddid_all.tbl CDD PRK05057 PRK05057 235335 aroK shikimate kinase AroK. 172 matched cddid_all.tbl CDD PRK05066 PRK05066 179922 PRK05066 transcriptional regulator ArgR. 156 matched cddid_all.tbl CDD PRK05070 PRK05070 179923 PRK05070 DNA mismatch repair protein; Provisional 218 matched cddid_all.tbl CDD PRK05074 PRK05074 235336 PRK05074 non-canonical purine NTP phosphatase. 173 matched cddid_all.tbl CDD PRK05077 PRK05077 235337 frsA esterase FrsA. 414 matched cddid_all.tbl CDD PRK05082 PRK05082 235338 PRK05082 N-acetylmannosamine kinase; Provisional 291 matched cddid_all.tbl CDD PRK05084 PRK05084 235339 xerS site-specific tyrosine recombinase XerS; Reviewed 357 matched cddid_all.tbl CDD PRK05087 PRK05087 179929 PRK05087 D-alanine--poly(phosphoribitol) ligase subunit DltC. 78 matched cddid_all.tbl CDD PRK05089 PRK05089 235341 PRK05089 cytochrome C oxidase assembly protein; Provisional 188 matched cddid_all.tbl CDD PRK05090 PRK05090 179931 PRK05090 hypothetical protein; Validated 95 matched cddid_all.tbl CDD PRK05092 PRK05092 235342 PRK05092 PII uridylyl-transferase; Provisional 931 matched cddid_all.tbl CDD PRK05093 PRK05093 179933 argD acetylornithine/succinyldiaminopimelate transaminase. 403 matched cddid_all.tbl CDD PRK05094 PRK05094 179934 PRK05094 dsDNA-mimic protein; Reviewed 107 matched cddid_all.tbl CDD PRK05096 PRK05096 235343 PRK05096 guanosine 5'-monophosphate oxidoreductase; Provisional 346 matched cddid_all.tbl CDD PRK05097 PRK05097 235344 PRK05097 macrodomain Ter protein MatP. 150 matched cddid_all.tbl CDD PRK05101 PRK05101 179937 PRK05101 galactokinase; Provisional 382 matched cddid_all.tbl CDD PRK05105 PRK05105 235345 PRK05105 O-succinylbenzoate synthase; Provisional 322 matched cddid_all.tbl CDD PRK05111 PRK05111 235346 PRK05111 acetylornithine deacetylase; Provisional 383 matched cddid_all.tbl CDD PRK05113 PRK05113 235347 PRK05113 electron transport complex protein RnfB; Provisional 191 matched cddid_all.tbl CDD PRK05114 PRK05114 179941 PRK05114 YoaH family protein. 59 matched cddid_all.tbl CDD PRK05122 PRK05122 235348 PRK05122 major facilitator superfamily transporter; Provisional 399 matched cddid_all.tbl CDD PRK05124 PRK05124 235349 cysN sulfate adenylyltransferase subunit 1; Provisional 474 matched cddid_all.tbl CDD PRK05151 PRK05151 235352 PRK05151 electron transport complex protein RsxA; Provisional 193 matched cddid_all.tbl CDD PRK05159 PRK05159 235354 aspC aspartyl-tRNA synthetase; Provisional 437 matched cddid_all.tbl CDD PRK05166 PRK05166 179950 PRK05166 histidinol-phosphate transaminase. 371 matched cddid_all.tbl CDD PRK05170 PRK05170 235356 PRK05170 YcgN family cysteine cluster protein. 147 matched cddid_all.tbl CDD PRK05174 PRK05174 179953 PRK05174 bifunctional 3-hydroxydecanoyl-ACP dehydratase/trans-2-decenoyl-ACP isomerase. 172 matched cddid_all.tbl CDD PRK05179 PRK05179 235358 rpsM 30S ribosomal protein S13; Validated 122 matched cddid_all.tbl CDD PRK05182 PRK05182 235359 PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional 310 matched cddid_all.tbl CDD PRK05183 PRK05183 235360 hscA chaperone protein HscA; Provisional 616 matched cddid_all.tbl CDD PRK05184 PRK05184 235361 PRK05184 pyrroloquinoline quinone biosynthesis protein PqqB; Provisional 302 matched cddid_all.tbl CDD PRK05185 PRK05185 179959 rplT 50S ribosomal protein L20; Provisional 114 matched cddid_all.tbl CDD PRK05198 PRK05198 235363 PRK05198 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional 264 matched cddid_all.tbl CDD PRK05201 PRK05201 235364 hslU ATP-dependent protease ATPase subunit HslU. 443 matched cddid_all.tbl CDD PRK05205 PRK05205 235365 PRK05205 bifunctional pyr operon transcriptional regulator/uracil phosphoribosyltransferase PyrR. 176 matched cddid_all.tbl CDD PRK05218 PRK05218 235366 PRK05218 heat shock protein 90; Provisional 613 matched cddid_all.tbl CDD PRK05222 PRK05222 235367 PRK05222 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; Provisional 758 matched cddid_all.tbl CDD PRK05225 PRK05225 235368 PRK05225 ketol-acid reductoisomerase; Validated 487 matched cddid_all.tbl CDD PRK05231 PRK05231 235369 PRK05231 homoserine kinase; Provisional 319 matched cddid_all.tbl CDD PRK05234 PRK05234 179969 mgsA methylglyoxal synthase; Validated 142 matched cddid_all.tbl CDD PRK05244 PRK05244 235370 PRK05244 Der GTPase-activating protein YihI. 177 matched cddid_all.tbl CDD PRK05246 PRK05246 235371 PRK05246 glutathione synthetase; Provisional 316 matched cddid_all.tbl CDD PRK05248 PRK05248 235372 PRK05248 hypothetical protein; Provisional 121 matched cddid_all.tbl CDD PRK05249 PRK05249 235373 PRK05249 Si-specific NAD(P)(+) transhydrogenase. 461 matched cddid_all.tbl CDD PRK05253 PRK05253 235375 PRK05253 sulfate adenylyltransferase subunit CysD. 301 matched cddid_all.tbl CDD PRK05254 PRK05254 235376 PRK05254 uracil-DNA glycosylase; Provisional 224 matched cddid_all.tbl CDD PRK05255 PRK05255 235377 PRK05255 ribosome-associated protein. 171 matched cddid_all.tbl CDD PRK05256 PRK05256 235378 PRK05256 chromosome partition protein MukE. 238 matched cddid_all.tbl CDD PRK05257 PRK05257 179979 PRK05257 malate:quinone oxidoreductase; Validated 494 matched cddid_all.tbl CDD PRK05260 PRK05260 179980 PRK05260 chromosome partition protein MukF. 440 matched cddid_all.tbl CDD PRK05261 PRK05261 235379 PRK05261 phosphoketolase. 785 matched cddid_all.tbl CDD PRK05264 PRK05264 179982 PRK05264 met regulon transcriptional regulator MetJ. 105 matched cddid_all.tbl CDD PRK05265 PRK05265 235380 PRK05265 pyridoxine 5'-phosphate synthase; Provisional 239 matched cddid_all.tbl CDD PRK05269 PRK05269 235381 PRK05269 transaldolase B; Provisional 318 matched cddid_all.tbl CDD PRK05270 PRK05270 235382 PRK05270 UDP-glucose--hexose-1-phosphate uridylyltransferase. 493 matched cddid_all.tbl CDD PRK05274 PRK05274 235384 PRK05274 2-keto-3-deoxygluconate permease; Provisional 326 matched cddid_all.tbl CDD PRK05277 PRK05277 235385 PRK05277 H(+)/Cl(-) exchange transporter ClcA. 438 matched cddid_all.tbl CDD PRK05279 PRK05279 235386 PRK05279 N-acetylglutamate synthase; Validated 441 matched cddid_all.tbl CDD PRK05282 PRK05282 179990 PRK05282 dipeptidase PepE. 233 matched cddid_all.tbl CDD PRK05286 PRK05286 235388 PRK05286 quinone-dependent dihydroorotate dehydrogenase. 344 matched cddid_all.tbl CDD PRK05287 PRK05287 235389 PRK05287 cell division protein ZapD. 250 matched cddid_all.tbl CDD PRK05289 PRK05289 235390 PRK05289 acyl-ACP--UDP-N-acetylglucosamine O-acyltransferase. 262 matched cddid_all.tbl CDD PRK05290 PRK05290 235391 PRK05290 hybrid cluster protein; Provisional 546 matched cddid_all.tbl CDD PRK05291 PRK05291 235392 trmE tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE. 449 matched cddid_all.tbl CDD PRK05293 PRK05293 179997 glgC glucose-1-phosphate adenylyltransferase; Provisional 380 matched cddid_all.tbl CDD PRK05294 PRK05294 235393 carB carbamoyl-phosphate synthase large subunit. 1066 matched cddid_all.tbl CDD PRK05297 PRK05297 235394 PRK05297 phosphoribosylformylglycinamidine synthase; Provisional 1290 matched cddid_all.tbl CDD PRK05298 PRK05298 235395 PRK05298 excinuclease ABC subunit UvrB. 652 matched cddid_all.tbl CDD PRK05299 PRK05299 235396 rpsB 30S ribosomal protein S2; Provisional 258 matched cddid_all.tbl CDD PRK05302 PRK05302 235398 PRK05302 30S ribosomal protein S7; Validated 156 matched cddid_all.tbl CDD PRK05303 PRK05303 235399 flgI flagellar basal body P-ring protein FlgI. 367 matched cddid_all.tbl CDD PRK05305 PRK05305 235400 PRK05305 phosphatidylserine decarboxylase family protein. 206 matched cddid_all.tbl CDD PRK05309 PRK05309 180007 PRK05309 30S ribosomal protein S11; Validated 128 matched cddid_all.tbl CDD PRK05312 PRK05312 235402 pdxA 4-hydroxythreonine-4-phosphate dehydrogenase PdxA. 336 matched cddid_all.tbl CDD PRK05313 PRK05313 180009 PRK05313 hypothetical protein; Provisional 452 matched cddid_all.tbl CDD PRK05318 PRK05318 235403 PRK05318 deoxyguanosinetriphosphate triphosphohydrolase-like protein; Provisional 432 matched cddid_all.tbl CDD PRK05320 PRK05320 235405 PRK05320 rhodanese superfamily protein; Provisional 257 matched cddid_all.tbl CDD PRK05321 PRK05321 235406 PRK05321 nicotinate phosphoribosyltransferase; Provisional 400 matched cddid_all.tbl CDD PRK05322 PRK05322 235407 PRK05322 galactokinase; Provisional 387 matched cddid_all.tbl CDD PRK05324 PRK05324 235408 PRK05324 succinylglutamate desuccinylase; Provisional 329 matched cddid_all.tbl CDD PRK05325 PRK05325 235409 PRK05325 hypothetical protein; Provisional 401 matched cddid_all.tbl CDD PRK05326 PRK05326 235410 PRK05326 potassium/proton antiporter. 562 matched cddid_all.tbl CDD PRK05327 PRK05327 235411 rpsD 30S ribosomal protein S4; Validated 203 matched cddid_all.tbl CDD PRK05329 PRK05329 235412 PRK05329 glycerol-3-phosphate dehydrogenase subunit GlpB. 422 matched cddid_all.tbl CDD PRK05330 PRK05330 235413 PRK05330 oxygen-dependent coproporphyrinogen oxidase. 300 matched cddid_all.tbl CDD PRK05333 PRK05333 235415 PRK05333 NAD-dependent protein deacetylase. 285 matched cddid_all.tbl CDD PRK05335 PRK05335 235416 PRK05335 tRNA (uracil-5-)-methyltransferase Gid; Reviewed 436 matched cddid_all.tbl CDD PRK05337 PRK05337 235417 PRK05337 beta-hexosaminidase; Provisional 337 matched cddid_all.tbl CDD PRK05338 PRK05338 235418 rplS 50S ribosomal protein L19; Provisional 116 matched cddid_all.tbl CDD PRK05339 PRK05339 235419 PRK05339 pyruvate, phosphate dikinase/phosphoenolpyruvate synthase regulator. 269 matched cddid_all.tbl CDD PRK05340 PRK05340 235420 PRK05340 UDP-2,3-diacylglucosamine hydrolase; Provisional 241 matched cddid_all.tbl CDD PRK05342 PRK05342 235422 clpX ATP-dependent Clp protease ATP-binding subunit ClpX. 412 matched cddid_all.tbl CDD PRK05346 PRK05346 235423 PRK05346 Na(+)-translocating NADH-quinone reductase subunit C; Provisional 256 matched cddid_all.tbl CDD PRK05347 PRK05347 235424 PRK05347 glutaminyl-tRNA synthetase; Provisional 554 matched cddid_all.tbl CDD PRK05349 PRK05349 235425 PRK05349 Na(+)-translocating NADH-quinone reductase subunit B; Provisional 405 matched cddid_all.tbl CDD PRK05350 PRK05350 180033 PRK05350 acyl carrier protein; Provisional 82 matched cddid_all.tbl CDD PRK05352 PRK05352 235426 PRK05352 Na(+)-translocating NADH-quinone reductase subunit A; Provisional 448 matched cddid_all.tbl CDD PRK05354 PRK05354 235427 PRK05354 biosynthetic arginine decarboxylase. 634 matched cddid_all.tbl CDD PRK05355 PRK05355 235428 PRK05355 3-phosphoserine/phosphohydroxythreonine transaminase. 360 matched cddid_all.tbl CDD PRK05359 PRK05359 235429 PRK05359 oligoribonuclease; Provisional 181 matched cddid_all.tbl CDD PRK05362 PRK05362 235430 PRK05362 phosphopentomutase; Provisional 394 matched cddid_all.tbl CDD PRK05363 PRK05363 235431 PRK05363 protein-methionine-sulfoxide reductase catalytic subunit MsrP. 280 matched cddid_all.tbl CDD PRK05365 PRK05365 180040 PRK05365 malonic semialdehyde reductase; Provisional 195 matched cddid_all.tbl CDD PRK05368 PRK05368 235433 PRK05368 homoserine O-succinyltransferase; Provisional 302 matched cddid_all.tbl CDD PRK05370 PRK05370 235434 PRK05370 argininosuccinate synthase; Validated 447 matched cddid_all.tbl CDD PRK05371 PRK05371 235435 PRK05371 x-prolyl-dipeptidyl aminopeptidase; Provisional 767 matched cddid_all.tbl CDD PRK05377 PRK05377 180045 PRK05377 fructose-1,6-bisphosphate aldolase; Reviewed 296 matched cddid_all.tbl CDD PRK05379 PRK05379 235436 PRK05379 bifunctional nicotinamide-nucleotide adenylyltransferase/Nudix hydroxylase. 340 matched cddid_all.tbl CDD PRK05380 PRK05380 235437 pyrG CTP synthetase; Validated 533 matched cddid_all.tbl CDD PRK05382 PRK05382 235438 PRK05382 chorismate synthase; Validated 359 matched cddid_all.tbl CDD PRK05388 PRK05388 235441 argJ bifunctional glutamate N-acetyltransferase/amino-acid acetyltransferase ArgJ. 395 matched cddid_all.tbl CDD PRK05395 PRK05395 235443 PRK05395 type II 3-dehydroquinate dehydratase. 146 matched cddid_all.tbl CDD PRK05396 PRK05396 180054 tdh L-threonine 3-dehydrogenase; Validated 341 matched cddid_all.tbl CDD PRK05398 PRK05398 180055 PRK05398 formyl-coenzyme A transferase; Provisional 416 matched cddid_all.tbl CDD PRK05399 PRK05399 235444 PRK05399 DNA mismatch repair protein MutS; Provisional 854 matched cddid_all.tbl CDD PRK05402 PRK05402 235445 PRK05402 1,4-alpha-glucan branching protein GlgB. 726 matched cddid_all.tbl CDD PRK05406 PRK05406 235446 PRK05406 5-oxoprolinase subunit PxpA. 246 matched cddid_all.tbl CDD PRK05408 PRK05408 180059 PRK05408 oxidative damage protection protein; Provisional 90 matched cddid_all.tbl CDD PRK05409 PRK05409 235447 PRK05409 hypothetical protein; Provisional 281 matched cddid_all.tbl CDD PRK05412 PRK05412 180061 PRK05412 putative nucleotide-binding protein; Reviewed 161 matched cddid_all.tbl CDD PRK05414 PRK05414 235448 PRK05414 urocanate hydratase; Provisional 556 matched cddid_all.tbl CDD PRK05416 PRK05416 235450 PRK05416 RNase adapter RapZ. 288 matched cddid_all.tbl CDD PRK05417 PRK05417 235451 PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional 191 matched cddid_all.tbl CDD PRK05419 PRK05419 235452 PRK05419 protein-methionine-sulfoxide reductase heme-binding subunit MsrQ. 205 matched cddid_all.tbl CDD PRK05420 PRK05420 235453 PRK05420 aquaporin Z; Provisional 231 matched cddid_all.tbl CDD PRK05421 PRK05421 235454 PRK05421 endonuclease/exonuclease/phosphatase family protein. 263 matched cddid_all.tbl CDD PRK05422 PRK05422 235455 smpB SsrA-binding protein SmpB. 148 matched cddid_all.tbl CDD PRK05423 PRK05423 180070 PRK05423 DUF496 family protein. 104 matched cddid_all.tbl CDD PRK05427 PRK05427 235458 PRK05427 putative manganese-dependent inorganic pyrophosphatase; Provisional 308 matched cddid_all.tbl CDD PRK05428 PRK05428 235459 PRK05428 HPr kinase/phosphorylase; Provisional 308 matched cddid_all.tbl CDD PRK05431 PRK05431 235461 PRK05431 seryl-tRNA synthetase; Provisional 425 matched cddid_all.tbl CDD PRK05434 PRK05434 235463 PRK05434 2,3-bisphosphoglycerate-independent phosphoglycerate mutase. 507 matched cddid_all.tbl CDD PRK05435 PRK05435 235464 rpmA 50S ribosomal protein L27; Validated 82 matched cddid_all.tbl CDD PRK05441 PRK05441 235467 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed 299 matched cddid_all.tbl CDD PRK05442 PRK05442 235468 PRK05442 malate dehydrogenase; Provisional 326 matched cddid_all.tbl CDD PRK05443 PRK05443 235469 PRK05443 polyphosphate kinase; Provisional 691 matched cddid_all.tbl CDD PRK05444 PRK05444 235470 PRK05444 1-deoxy-D-xylulose-5-phosphate synthase; Provisional 580 matched cddid_all.tbl CDD PRK05445 PRK05445 180087 PRK05445 YfbU family protein. 164 matched cddid_all.tbl CDD PRK05446 PRK05446 235471 PRK05446 bifunctional histidinol-phosphatase/imidazoleglycerol-phosphate dehydratase HisB. 354 matched cddid_all.tbl CDD PRK05447 PRK05447 235472 PRK05447 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional 385 matched cddid_all.tbl CDD PRK05449 PRK05449 180090 PRK05449 aspartate alpha-decarboxylase; Provisional 126 matched cddid_all.tbl CDD PRK05450 PRK05450 235473 PRK05450 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional 245 matched cddid_all.tbl CDD PRK05452 PRK05452 235475 PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional 479 matched cddid_all.tbl CDD PRK05454 PRK05454 235476 PRK05454 glucans biosynthesis glucosyltransferase MdoH. 605 matched cddid_all.tbl CDD PRK05456 PRK05456 235477 PRK05456 ATP-dependent protease subunit HslV. 172 matched cddid_all.tbl CDD PRK05457 PRK05457 235478 PRK05457 protease HtpX. 284 matched cddid_all.tbl CDD PRK05458 PRK05458 235479 PRK05458 guanosine 5'-monophosphate oxidoreductase; Provisional 326 matched cddid_all.tbl CDD PRK05461 PRK05461 180098 apaG CO2+/MG2+ efflux protein ApaG; Reviewed 127 matched cddid_all.tbl CDD PRK05462 PRK05462 235480 PRK05462 adenosylmethionine decarboxylase. 266 matched cddid_all.tbl CDD PRK05463 PRK05463 180100 PRK05463 putative hydro-lyase. 262 matched cddid_all.tbl CDD PRK05465 PRK05465 235482 PRK05465 ethanolamine ammonia-lyase subunit EutC. 260 matched cddid_all.tbl CDD PRK05467 PRK05467 235483 PRK05467 Fe(II)-dependent oxygenase superfamily protein; Provisional 226 matched cddid_all.tbl CDD PRK05469 PRK05469 235484 PRK05469 tripeptide aminopeptidase PepT. 408 matched cddid_all.tbl CDD PRK05470 PRK05470 180105 PRK05470 fumarate reductase subunit FrdD. 118 matched cddid_all.tbl CDD PRK05471 PRK05471 235485 PRK05471 CDP-diacylglycerol pyrophosphatase; Provisional 252 matched cddid_all.tbl CDD PRK05472 PRK05472 235486 PRK05472 redox-sensing transcriptional repressor Rex; Provisional 213 matched cddid_all.tbl CDD PRK05473 PRK05473 180108 IreB-like IreB family regulatory phosphoprotein. IreB (EF1202) was characterized in Enterococcus faecalis as a small protein, well-conserved in the Firmicutes. It belongs to a system that includes the Ser/Thr protein kinase IreK, and phosphatase IreP, undergoes phosphorylation on threonine residues, and is involved in regulating cephalosporin resistance. This family was previously named DUF965 by Pfam model pfam06135 86 matched cddid_all.tbl CDD PRK05474 PRK05474 235487 PRK05474 xylose isomerase; Provisional 437 matched cddid_all.tbl CDD PRK05476 PRK05476 235488 PRK05476 S-adenosyl-L-homocysteine hydrolase; Provisional 425 matched cddid_all.tbl CDD PRK05477 PRK05477 235489 gatB Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB. 474 matched cddid_all.tbl CDD PRK05478 PRK05478 235490 PRK05478 3-isopropylmalate dehydratase large subunit. 466 matched cddid_all.tbl CDD PRK05479 PRK05479 235491 PRK05479 ketol-acid reductoisomerase; Provisional 330 matched cddid_all.tbl CDD PRK05480 PRK05480 235492 PRK05480 uridine/cytidine kinase; Provisional 209 matched cddid_all.tbl CDD PRK05481 PRK05481 235493 PRK05481 lipoyl synthase; Provisional 289 matched cddid_all.tbl CDD PRK05500 PRK05500 180119 PRK05500 bifunctional orotidine-5'-phosphate decarboxylase/orotate phosphoribosyltransferase. 477 matched cddid_all.tbl CDD PRK05506 PRK05506 180120 PRK05506 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional 632 matched cddid_all.tbl CDD PRK05508 PRK05508 180121 PRK05508 methionine-R-sulfoxide reductase. 119 matched cddid_all.tbl CDD PRK05518 PRK05518 235496 rpl6p 50S ribosomal protein L6P; Reviewed 180 matched cddid_all.tbl CDD PRK05528 PRK05528 235497 PRK05528 peptide-methionine (S)-S-oxide reductase. 156 matched cddid_all.tbl CDD PRK05529 PRK05529 135428 PRK05529 cell division protein FtsQ; Provisional 255 matched cddid_all.tbl CDD PRK05537 PRK05537 180124 PRK05537 bifunctional sulfate adenylyltransferase/adenylylsulfate kinase. 568 matched cddid_all.tbl CDD PRK05541 PRK05541 235498 PRK05541 adenylylsulfate kinase; Provisional 176 matched cddid_all.tbl CDD PRK05550 PRK05550 235499 PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional 283 matched cddid_all.tbl CDD PRK05557 PRK05557 235500 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Validated 248 matched cddid_all.tbl CDD PRK05559 PRK05559 235501 PRK05559 DNA topoisomerase IV subunit B; Reviewed 631 matched cddid_all.tbl CDD PRK05560 PRK05560 235502 PRK05560 DNA gyrase subunit A; Validated 805 matched cddid_all.tbl CDD PRK05561 PRK05561 235503 PRK05561 DNA topoisomerase 4 subunit A. 742 matched cddid_all.tbl CDD PRK05562 PRK05562 235504 PRK05562 NAD(P)-dependent oxidoreductase. 223 matched cddid_all.tbl CDD PRK05563 PRK05563 235505 PRK05563 DNA polymerase III subunits gamma and tau; Validated 559 matched cddid_all.tbl CDD PRK05564 PRK05564 180132 PRK05564 DNA polymerase III subunit delta'; Validated 313 matched cddid_all.tbl CDD PRK05565 PRK05565 235506 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional 247 matched cddid_all.tbl CDD PRK05568 PRK05568 235508 PRK05568 flavodoxin; Provisional 142 matched cddid_all.tbl CDD PRK05569 PRK05569 135442 PRK05569 flavodoxin; Provisional 141 matched cddid_all.tbl CDD PRK05571 PRK05571 235509 PRK05571 ribose-5-phosphate isomerase B; Provisional 148 matched cddid_all.tbl CDD PRK05572 PRK05572 180137 PRK05572 RNA polymerase sporulation sigma factor, SigF/SigG family. 252 matched cddid_all.tbl CDD PRK05573 PRK05573 235510 rplU 50S ribosomal protein L21; Validated 103 matched cddid_all.tbl CDD PRK05575 PRK05575 180140 cbiC precorrin-8X methylmutase; Validated 204 matched cddid_all.tbl CDD PRK05576 PRK05576 235512 PRK05576 cobalt-factor II C(20)-methyltransferase. 229 matched cddid_all.tbl CDD PRK05578 PRK05578 180142 PRK05578 cytidine deaminase; Validated 131 matched cddid_all.tbl CDD PRK05579 PRK05579 235513 PRK05579 bifunctional phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Validated 399 matched cddid_all.tbl CDD PRK05580 PRK05580 235514 PRK05580 primosome assembly protein PriA; Validated 679 matched cddid_all.tbl CDD PRK05581 PRK05581 235515 PRK05581 ribulose-phosphate 3-epimerase; Validated 220 matched cddid_all.tbl CDD PRK05583 PRK05583 235517 PRK05583 ribosomal protein L7Ae family protein; Provisional 104 matched cddid_all.tbl CDD PRK05584 PRK05584 180148 PRK05584 5'-methylthioadenosine/adenosylhomocysteine nucleosidase. 230 matched cddid_all.tbl CDD PRK05585 PRK05585 235518 yajC preprotein translocase subunit YajC; Validated 106 matched cddid_all.tbl CDD PRK05586 PRK05586 180150 PRK05586 acetyl-CoA carboxylase biotin carboxylase subunit. 447 matched cddid_all.tbl CDD PRK05588 PRK05588 235519 PRK05588 histidinol phosphate phosphatase. 255 matched cddid_all.tbl CDD PRK05589 PRK05589 235520 PRK05589 peptide chain release factor 2; Provisional 325 matched cddid_all.tbl CDD PRK05590 PRK05590 235521 PRK05590 hypothetical protein; Provisional 166 matched cddid_all.tbl CDD PRK05595 PRK05595 235525 PRK05595 replicative DNA helicase; Provisional 444 matched cddid_all.tbl CDD PRK05597 PRK05597 235526 PRK05597 molybdopterin biosynthesis protein MoeB; Validated 355 matched cddid_all.tbl CDD PRK05599 PRK05599 235527 PRK05599 SDR family oxidoreductase. 246 matched cddid_all.tbl CDD PRK05600 PRK05600 235528 PRK05600 thiamine biosynthesis protein ThiF; Validated 370 matched cddid_all.tbl CDD PRK05601 PRK05601 235529 PRK05601 DNA polymerase III subunit epsilon; Validated 377 matched cddid_all.tbl CDD PRK05602 PRK05602 235530 PRK05602 RNA polymerase sigma factor; Reviewed 186 matched cddid_all.tbl CDD PRK05605 PRK05605 235531 PRK05605 long-chain-fatty-acid--CoA ligase; Validated 573 matched cddid_all.tbl CDD PRK05610 PRK05610 235532 rpsQ 30S ribosomal protein S17; Reviewed 84 matched cddid_all.tbl CDD PRK05611 PRK05611 180163 rpmD 50S ribosomal protein L30; Reviewed 59 matched cddid_all.tbl CDD PRK05613 PRK05613 168128 PRK05613 O-acetylhomoserine/O-acetylserine sulfhydrylase. 437 matched cddid_all.tbl CDD PRK05614 PRK05614 180164 gltA citrate synthase. 419 matched cddid_all.tbl CDD PRK05617 PRK05617 235533 PRK05617 3-hydroxyisobutyryl-CoA hydrolase; Provisional 342 matched cddid_all.tbl CDD PRK05618 PRK05618 235534 PRK05618 50S ribosomal protein L25/general stress protein Ctc; Reviewed 197 matched cddid_all.tbl CDD PRK05620 PRK05620 180167 PRK05620 long-chain fatty-acid--CoA ligase. 576 matched cddid_all.tbl CDD PRK05621 PRK05621 235535 PRK05621 F0F1 ATP synthase subunit gamma; Validated 284 matched cddid_all.tbl CDD PRK05625 PRK05625 180169 PRK05625 5-amino-6-(5-phosphoribosylamino)uracil reductase; Validated 217 matched cddid_all.tbl CDD PRK05626 PRK05626 180170 rpsO 30S ribosomal protein S15; Reviewed 89 matched cddid_all.tbl CDD PRK05627 PRK05627 235536 PRK05627 bifunctional riboflavin kinase/FAD synthetase. 305 matched cddid_all.tbl CDD PRK05629 PRK05629 180173 PRK05629 hypothetical protein; Validated 318 matched cddid_all.tbl CDD PRK05632 PRK05632 235537 PRK05632 phosphate acetyltransferase; Reviewed 684 matched cddid_all.tbl CDD PRK05634 PRK05634 235538 PRK05634 nucleosidase; Provisional 185 matched cddid_all.tbl CDD PRK05636 PRK05636 180177 PRK05636 replicative DNA helicase; Provisional 505 matched cddid_all.tbl CDD PRK05637 PRK05637 180178 PRK05637 anthranilate synthase component II; Provisional 208 matched cddid_all.tbl CDD PRK05638 PRK05638 235539 PRK05638 threonine synthase; Validated 442 matched cddid_all.tbl CDD PRK05639 PRK05639 168145 PRK05639 acetyl ornithine aminotransferase family protein. 457 matched cddid_all.tbl CDD PRK05640 PRK05640 101884 PRK05640 putative monovalent cation/H+ antiporter subunit B; Reviewed 151 matched cddid_all.tbl CDD PRK05641 PRK05641 235540 PRK05641 putative acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated 153 matched cddid_all.tbl CDD PRK05643 PRK05643 235541 PRK05643 DNA polymerase III subunit beta; Validated 367 matched cddid_all.tbl CDD PRK05644 PRK05644 235542 gyrB DNA gyrase subunit B; Validated 638 matched cddid_all.tbl CDD PRK05645 PRK05645 135493 PRK05645 lysophospholipid acyltransferase. 295 matched cddid_all.tbl CDD PRK05646 PRK05646 235543 PRK05646 lipid A biosynthesis lauroyl acyltransferase; Provisional 310 matched cddid_all.tbl CDD PRK05650 PRK05650 235545 PRK05650 SDR family oxidoreductase. 270 matched cddid_all.tbl CDD PRK05653 PRK05653 235546 fabG 3-oxoacyl-ACP reductase FabG. 246 matched cddid_all.tbl CDD PRK05656 PRK05656 168156 PRK05656 acetyl-CoA C-acetyltransferase. 393 matched cddid_all.tbl CDD PRK05657 PRK05657 235548 PRK05657 RNA polymerase sigma factor RpoS; Validated 325 matched cddid_all.tbl CDD PRK05658 PRK05658 235549 PRK05658 RNA polymerase sigma factor RpoD; Validated 619 matched cddid_all.tbl CDD PRK05665 PRK05665 168162 PRK05665 amidotransferase; Provisional 240 matched cddid_all.tbl CDD PRK05670 PRK05670 235552 PRK05670 anthranilate synthase component II; Provisional 189 matched cddid_all.tbl CDD PRK05671 PRK05671 168165 PRK05671 aspartate-semialdehyde dehydrogenase; Reviewed 336 matched cddid_all.tbl CDD PRK05672 PRK05672 235553 dnaE2 error-prone DNA polymerase; Validated 1046 matched cddid_all.tbl CDD PRK05673 PRK05673 235554 dnaE DNA polymerase III subunit alpha; Validated 1135 matched cddid_all.tbl CDD PRK05674 PRK05674 168168 PRK05674 gamma-carboxygeranoyl-CoA hydratase; Validated 265 matched cddid_all.tbl CDD PRK05677 PRK05677 168170 PRK05677 long-chain-fatty-acid--CoA ligase; Validated 562 matched cddid_all.tbl CDD PRK05678 PRK05678 180194 PRK05678 succinyl-CoA synthetase subunit alpha; Validated 291 matched cddid_all.tbl CDD PRK05679 PRK05679 235555 PRK05679 pyridoxal 5'-phosphate synthase. 195 matched cddid_all.tbl CDD PRK05681 PRK05681 235556 flgC flagellar basal body rod protein FlgC; Reviewed 135 matched cddid_all.tbl CDD PRK05682 PRK05682 235557 flgE flagellar hook protein FlgE; Validated 407 matched cddid_all.tbl CDD PRK05683 PRK05683 235558 flgK flagellar hook-associated protein FlgK; Validated 676 matched cddid_all.tbl CDD PRK05684 PRK05684 235559 flgJ flagellar assembly peptidoglycan hydrolase FlgJ. 312 matched cddid_all.tbl CDD PRK05686 PRK05686 235561 fliG flagellar motor switch protein G; Validated 339 matched cddid_all.tbl CDD PRK05687 PRK05687 235562 fliH flagellar assembly protein FliH. 246 matched cddid_all.tbl CDD PRK05688 PRK05688 168181 fliI flagellar protein export ATPase FliI. 451 matched cddid_all.tbl CDD PRK05689 PRK05689 235563 fliJ flagella biosynthesis chaperone FliJ. 147 matched cddid_all.tbl CDD PRK05690 PRK05690 180204 PRK05690 molybdopterin biosynthesis protein MoeB; Provisional 245 matched cddid_all.tbl CDD PRK05691 PRK05691 235564 PRK05691 peptide synthase; Validated 4334 matched cddid_all.tbl CDD PRK05692 PRK05692 180206 PRK05692 hydroxymethylglutaryl-CoA lyase; Provisional 287 matched cddid_all.tbl CDD PRK05693 PRK05693 168186 PRK05693 SDR family oxidoreductase. 274 matched cddid_all.tbl CDD PRK05696 PRK05696 180207 fliL flagellar basal body-associated protein FliL; Reviewed 170 matched cddid_all.tbl CDD PRK05697 PRK05697 235565 PRK05697 flagellar basal body-associated protein FliL-like protein; Validated 137 matched cddid_all.tbl CDD PRK05698 PRK05698 168189 fliN flagellar motor switch protein FliN. 155 matched cddid_all.tbl CDD PRK05699 PRK05699 235566 fliP flagellar biosynthesis protein FliP; Reviewed 245 matched cddid_all.tbl CDD PRK05700 PRK05700 235567 fliQ flagellar type III secretion system protein FliQ. 89 matched cddid_all.tbl CDD PRK05701 PRK05701 235568 fliR flagellar type III secretion system protein FliR. 242 matched cddid_all.tbl CDD PRK05702 PRK05702 235569 flhB flagellar type III secretion system protein FlhB. 359 matched cddid_all.tbl CDD PRK05703 PRK05703 235570 flhF flagellar biosynthesis protein FlhF. 424 matched cddid_all.tbl CDD PRK05704 PRK05704 235571 PRK05704 2-oxoglutarate dehydrogenase complex dihydrolipoyllysine-residue succinyltransferase. 407 matched cddid_all.tbl CDD PRK05707 PRK05707 180215 PRK05707 DNA polymerase III subunit delta'; Validated 328 matched cddid_all.tbl CDD PRK05708 PRK05708 235572 PRK05708 putative 2-dehydropantoate 2-reductase. 305 matched cddid_all.tbl CDD PRK05710 PRK05710 235573 PRK05710 tRNA glutamyl-Q(34) synthetase GluQRS. 299 matched cddid_all.tbl CDD PRK05711 PRK05711 235574 PRK05711 DNA polymerase III subunit epsilon; Provisional 240 matched cddid_all.tbl CDD PRK05713 PRK05713 235575 PRK05713 iron-sulfur-binding ferredoxin reductase. 312 matched cddid_all.tbl CDD PRK05714 PRK05714 168201 PRK05714 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Provisional 405 matched cddid_all.tbl CDD PRK05715 PRK05715 180218 PRK05715 NADH-quinone oxidoreductase subunit NuoK. 100 matched cddid_all.tbl CDD PRK05716 PRK05716 235576 PRK05716 methionine aminopeptidase; Validated 252 matched cddid_all.tbl CDD PRK05717 PRK05717 168204 PRK05717 SDR family oxidoreductase. 255 matched cddid_all.tbl CDD PRK05718 PRK05718 235577 PRK05718 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional 212 matched cddid_all.tbl CDD PRK05720 PRK05720 235578 mtnA methylthioribose-1-phosphate isomerase; Reviewed 344 matched cddid_all.tbl CDD PRK05722 PRK05722 235579 PRK05722 glucose-6-phosphate 1-dehydrogenase; Validated 495 matched cddid_all.tbl CDD PRK05723 PRK05723 168208 PRK05723 flavodoxin; Provisional 151 matched cddid_all.tbl CDD PRK05724 PRK05724 235580 PRK05724 acetyl-CoA carboxylase carboxyltransferase subunit alpha; Validated 319 matched cddid_all.tbl CDD PRK05728 PRK05728 235581 PRK05728 DNA polymerase III subunit chi; Validated 142 matched cddid_all.tbl CDD PRK05729 PRK05729 235582 valS valyl-tRNA synthetase; Reviewed 874 matched cddid_all.tbl CDD PRK05731 PRK05731 235583 PRK05731 thiamine monophosphate kinase; Provisional 318 matched cddid_all.tbl CDD PRK05732 PRK05732 235584 PRK05732 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated 395 matched cddid_all.tbl CDD PRK05733 PRK05733 235585 PRK05733 single-stranded DNA-binding protein; Provisional 172 matched cddid_all.tbl CDD PRK05738 PRK05738 235586 rplW 50S ribosomal protein L23; Reviewed 92 matched cddid_all.tbl CDD PRK05740 PRK05740 235587 secE preprotein translocase subunit SecE; Reviewed 92 matched cddid_all.tbl CDD PRK05748 PRK05748 180232 PRK05748 replicative DNA helicase; Provisional 448 matched cddid_all.tbl CDD PRK05749 PRK05749 235589 PRK05749 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed 425 matched cddid_all.tbl CDD PRK05751 PRK05751 180234 PRK05751 preprotein translocase subunit SecB; Validated 156 matched cddid_all.tbl CDD PRK05752 PRK05752 235590 PRK05752 uroporphyrinogen-III synthase; Validated 255 matched cddid_all.tbl CDD PRK05753 PRK05753 180236 PRK05753 nucleoside diphosphate kinase regulator; Provisional 137 matched cddid_all.tbl CDD PRK05755 PRK05755 235591 PRK05755 DNA polymerase I; Provisional 880 matched cddid_all.tbl CDD PRK05756 PRK05756 235592 PRK05756 pyridoxal kinase PdxY. 286 matched cddid_all.tbl CDD PRK05758 PRK05758 235593 PRK05758 F0F1 ATP synthase subunit delta; Validated 177 matched cddid_all.tbl CDD PRK05759 PRK05759 180240 PRK05759 F0F1 ATP synthase subunit B; Validated 156 matched cddid_all.tbl CDD PRK05760 PRK05760 180241 PRK05760 F0F1 ATP synthase subunit I; Validated 124 matched cddid_all.tbl CDD PRK05761 PRK05761 235594 PRK05761 DNA-directed DNA polymerase I. 787 matched cddid_all.tbl CDD PRK05762 PRK05762 235595 PRK05762 DNA polymerase II; Reviewed 786 matched cddid_all.tbl CDD PRK05764 PRK05764 235596 PRK05764 aspartate aminotransferase; Provisional 393 matched cddid_all.tbl CDD PRK05765 PRK05765 235597 PRK05765 precorrin-3B C17-methyltransferase; Provisional 246 matched cddid_all.tbl CDD PRK05766 PRK05766 235598 rps14P 30S ribosomal protein S14P; Reviewed 52 matched cddid_all.tbl CDD PRK05767 PRK05767 180247 rpl44e 50S ribosomal protein L44e; Validated 92 matched cddid_all.tbl CDD PRK05769 PRK05769 235599 PRK05769 acetyl ornithine aminotransferase family protein. 441 matched cddid_all.tbl CDD PRK05771 PRK05771 235600 PRK05771 V-type ATP synthase subunit I; Validated 646 matched cddid_all.tbl CDD PRK05772 PRK05772 168237 PRK05772 S-methyl-5-thioribose-1-phosphate isomerase. 363 matched cddid_all.tbl CDD PRK05773 PRK05773 235601 PRK05773 3,4-dihydroxy-2-butanone 4-phosphate synthase; Validated 219 matched cddid_all.tbl CDD PRK05776 PRK05776 235602 PRK05776 DNA topoisomerase I; Provisional 670 matched cddid_all.tbl CDD PRK05777 PRK05777 235603 PRK05777 NADH-quinone oxidoreductase subunit NuoN. 476 matched cddid_all.tbl CDD PRK05778 PRK05778 235604 PRK05778 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Validated 301 matched cddid_all.tbl CDD PRK05782 PRK05782 235605 PRK05782 bifunctional sirohydrochlorin cobalt chelatase/precorrin-8X methylmutase; Validated 335 matched cddid_all.tbl CDD PRK05783 PRK05783 235606 PRK05783 hypothetical protein; Provisional 84 matched cddid_all.tbl CDD PRK05785 PRK05785 235607 PRK05785 hypothetical protein; Provisional 226 matched cddid_all.tbl CDD PRK05786 PRK05786 235608 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional 238 matched cddid_all.tbl CDD PRK05787 PRK05787 235609 PRK05787 cobalt-precorrin-7 (C(5))-methyltransferase. 210 matched cddid_all.tbl CDD PRK05788 PRK05788 235610 PRK05788 cobalt-precorrin 5A hydrolase. 315 matched cddid_all.tbl CDD PRK05790 PRK05790 180261 PRK05790 putative acyltransferase; Provisional 393 matched cddid_all.tbl CDD PRK05793 PRK05793 235611 PRK05793 amidophosphoribosyltransferase; Provisional 469 matched cddid_all.tbl CDD PRK05800 PRK05800 235612 cobU adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase; Validated 170 matched cddid_all.tbl CDD PRK05802 PRK05802 235613 PRK05802 sulfide/dihydroorotate dehydrogenase-like FAD/NAD-binding protein. 320 matched cddid_all.tbl CDD PRK05803 PRK05803 180266 PRK05803 RNA polymerase sporulation sigma factor SigK. 233 matched cddid_all.tbl CDD PRK05805 PRK05805 180267 PRK05805 phosphate butyryltransferase; Validated 301 matched cddid_all.tbl CDD PRK05807 PRK05807 235614 PRK05807 RNA-binding protein S1. 136 matched cddid_all.tbl CDD PRK05808 PRK05808 180269 PRK05808 3-hydroxybutyryl-CoA dehydrogenase; Validated 282 matched cddid_all.tbl CDD PRK05809 PRK05809 180270 PRK05809 short-chain-enoyl-CoA hydratase. 260 matched cddid_all.tbl CDD PRK05812 PRK05812 235615 secD preprotein translocase subunit SecD; Reviewed 462 matched cddid_all.tbl CDD PRK05813 PRK05813 235616 PRK05813 single-stranded DNA-binding protein; Provisional 219 matched cddid_all.tbl CDD PRK05815 PRK05815 235617 PRK05815 F0F1 ATP synthase subunit A; Validated 227 matched cddid_all.tbl CDD PRK05818 PRK05818 235618 PRK05818 DNA polymerase III subunit delta'; Validated 261 matched cddid_all.tbl CDD PRK05819 PRK05819 180275 deoD DeoD-type purine-nucleoside phosphorylase. 235 matched cddid_all.tbl CDD PRK05820 PRK05820 180276 deoA thymidine phosphorylase; Reviewed 440 matched cddid_all.tbl CDD PRK05826 PRK05826 235619 PRK05826 pyruvate kinase; Provisional 465 matched cddid_all.tbl CDD PRK05828 PRK05828 180278 PRK05828 acyl carrier protein; Validated 84 matched cddid_all.tbl CDD PRK05834 PRK05834 180279 PRK05834 hypothetical protein; Provisional 194 matched cddid_all.tbl CDD PRK05835 PRK05835 180280 PRK05835 class II fructose-1,6-bisphosphate aldolase. 307 matched cddid_all.tbl CDD PRK05839 PRK05839 180281 PRK05839 succinyldiaminopimelate transaminase. 374 matched cddid_all.tbl CDD PRK05841 PRK05841 235620 flgE flagellar hook protein FlgE; Validated 603 matched cddid_all.tbl CDD PRK05842 PRK05842 235621 flgD flagellar hook assembly protein FlgD. 295 matched cddid_all.tbl CDD PRK05844 PRK05844 180284 PRK05844 pyruvate flavodoxin oxidoreductase subunit gamma; Validated 186 matched cddid_all.tbl CDD PRK05846 PRK05846 235622 PRK05846 NADH:ubiquinone oxidoreductase subunit M; Reviewed 497 matched cddid_all.tbl CDD PRK05849 PRK05849 235623 PRK05849 hypothetical protein; Provisional 783 matched cddid_all.tbl CDD PRK05850 PRK05850 235624 PRK05850 acyl-CoA synthetase; Validated 578 matched cddid_all.tbl CDD PRK05851 PRK05851 180289 PRK05851 long-chain-fatty acid--ACP ligase MbtM. 525 matched cddid_all.tbl CDD PRK05852 PRK05852 235625 PRK05852 fatty acid--CoA ligase family protein. 534 matched cddid_all.tbl CDD PRK05853 PRK05853 235626 PRK05853 hypothetical protein; Validated 161 matched cddid_all.tbl CDD PRK05854 PRK05854 235627 PRK05854 SDR family oxidoreductase. 313 matched cddid_all.tbl CDD PRK05855 PRK05855 235628 PRK05855 SDR family oxidoreductase. 582 matched cddid_all.tbl CDD PRK05857 PRK05857 180293 PRK05857 fatty acid--CoA ligase. 540 matched cddid_all.tbl CDD PRK05858 PRK05858 235629 PRK05858 acetolactate synthase. 542 matched cddid_all.tbl CDD PRK05862 PRK05862 180295 PRK05862 enoyl-CoA hydratase; Provisional 257 matched cddid_all.tbl CDD PRK05864 PRK05864 168278 PRK05864 enoyl-CoA hydratase; Provisional 276 matched cddid_all.tbl CDD PRK05865 PRK05865 235630 PRK05865 sugar epimerase family protein. 854 matched cddid_all.tbl CDD PRK05866 PRK05866 235631 PRK05866 SDR family oxidoreductase. 293 matched cddid_all.tbl CDD PRK05867 PRK05867 135631 PRK05867 SDR family oxidoreductase. 253 matched cddid_all.tbl CDD PRK05868 PRK05868 180297 PRK05868 FAD-binding protein. 372 matched cddid_all.tbl CDD PRK05869 PRK05869 235632 PRK05869 enoyl-CoA hydratase; Validated 222 matched cddid_all.tbl CDD PRK05870 PRK05870 180298 PRK05870 enoyl-CoA hydratase; Provisional 249 matched cddid_all.tbl CDD PRK05872 PRK05872 235633 PRK05872 short chain dehydrogenase; Provisional 296 matched cddid_all.tbl CDD PRK05874 PRK05874 102036 PRK05874 L-fuculose-phosphate aldolase; Validated 217 matched cddid_all.tbl CDD PRK05875 PRK05875 180300 PRK05875 short chain dehydrogenase; Provisional 276 matched cddid_all.tbl CDD PRK05876 PRK05876 135637 PRK05876 short chain dehydrogenase; Provisional 275 matched cddid_all.tbl CDD PRK05877 PRK05877 235634 PRK05877 aminodeoxychorismate synthase component I; Provisional 405 matched cddid_all.tbl CDD PRK05878 PRK05878 235635 PRK05878 pyruvate phosphate dikinase; Provisional 530 matched cddid_all.tbl CDD PRK05880 PRK05880 180303 PRK05880 F0F1 ATP synthase subunit C; Validated 81 matched cddid_all.tbl CDD PRK05883 PRK05883 180304 PRK05883 acyl carrier protein; Validated 91 matched cddid_all.tbl CDD PRK05884 PRK05884 135642 PRK05884 SDR family oxidoreductase. 223 matched cddid_all.tbl CDD PRK05886 PRK05886 235636 yajC preprotein translocase subunit YajC; Validated 109 matched cddid_all.tbl CDD PRK05888 PRK05888 235637 PRK05888 NADH-quinone oxidoreductase subunit NuoI. 164 matched cddid_all.tbl CDD PRK05889 PRK05889 180306 PRK05889 biotin/lipoyl-binding carrier protein. 71 matched cddid_all.tbl CDD PRK05892 PRK05892 180307 PRK05892 nucleoside diphosphate kinase regulator; Provisional 158 matched cddid_all.tbl CDD PRK05896 PRK05896 235638 PRK05896 DNA polymerase III subunits gamma and tau; Validated 605 matched cddid_all.tbl CDD PRK05898 PRK05898 135648 dnaE DNA polymerase III subunit alpha. 971 matched cddid_all.tbl CDD PRK05899 PRK05899 235639 PRK05899 transketolase; Reviewed 586 matched cddid_all.tbl CDD PRK05901 PRK05901 235640 PRK05901 RNA polymerase sigma factor; Provisional 509 matched cddid_all.tbl CDD PRK05904 PRK05904 235641 PRK05904 coproporphyrinogen III oxidase; Provisional 353 matched cddid_all.tbl CDD PRK05905 PRK05905 235642 PRK05905 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase. 258 matched cddid_all.tbl CDD PRK05906 PRK05906 168292 PRK05906 lipid A biosynthesis lauroyl acyltransferase; Provisional 454 matched cddid_all.tbl CDD PRK05907 PRK05907 235643 PRK05907 hypothetical protein; Provisional 311 matched cddid_all.tbl CDD PRK05910 PRK05910 168293 PRK05910 type III secretion system protein; Validated 584 matched cddid_all.tbl CDD PRK05911 PRK05911 235644 PRK05911 RNA polymerase sigma factor sigma-28; Reviewed 257 matched cddid_all.tbl CDD PRK05917 PRK05917 102059 PRK05917 DNA polymerase III subunit delta'; Validated 290 matched cddid_all.tbl CDD PRK05920 PRK05920 180312 PRK05920 aromatic acid decarboxylase; Validated 204 matched cddid_all.tbl CDD PRK05922 PRK05922 102061 PRK05922 type III secretion system ATPase; Validated 434 matched cddid_all.tbl CDD PRK05925 PRK05925 235646 PRK05925 aspartate kinase; Provisional 440 matched cddid_all.tbl CDD PRK05926 PRK05926 168296 PRK05926 hypothetical protein; Provisional 370 matched cddid_all.tbl CDD PRK05927 PRK05927 135660 PRK05927 dehypoxanthine futalosine cyclase. 350 matched cddid_all.tbl CDD PRK05928 PRK05928 235647 hemD uroporphyrinogen-III synthase; Reviewed 249 matched cddid_all.tbl CDD PRK05932 PRK05932 235648 PRK05932 RNA polymerase factor sigma-54; Reviewed 455 matched cddid_all.tbl CDD PRK05933 PRK05933 180315 PRK05933 type III secretion system protein; Validated 372 matched cddid_all.tbl CDD PRK05934 PRK05934 168300 PRK05934 type III secretion system protein; Validated 341 matched cddid_all.tbl CDD PRK05935 PRK05935 235649 PRK05935 biotin--protein ligase; Provisional 190 matched cddid_all.tbl CDD PRK05937 PRK05937 102071 PRK05937 8-amino-7-oxononanoate synthase; Provisional 370 matched cddid_all.tbl CDD PRK05939 PRK05939 235650 PRK05939 cystathionine gamma-synthase family protein. 397 matched cddid_all.tbl CDD PRK05940 PRK05940 235651 PRK05940 anthranilate synthase component I. 463 matched cddid_all.tbl CDD PRK05942 PRK05942 180317 PRK05942 aspartate aminotransferase; Provisional 394 matched cddid_all.tbl CDD PRK05943 PRK05943 180318 PRK05943 50S ribosomal protein L25; Reviewed 94 matched cddid_all.tbl CDD PRK05945 PRK05945 180319 sdhA succinate dehydrogenase/fumarate reductase flavoprotein subunit. 575 matched cddid_all.tbl CDD PRK05948 PRK05948 180320 PRK05948 precorrin-2 C(20)-methyltransferase. 238 matched cddid_all.tbl CDD PRK05949 PRK05949 180321 PRK05949 RNA polymerase sigma factor; Validated 327 matched cddid_all.tbl CDD PRK05950 PRK05950 235652 sdhB succinate dehydrogenase iron-sulfur subunit; Reviewed 232 matched cddid_all.tbl CDD PRK05951 PRK05951 180323 ubiA prenyltransferase; Reviewed 296 matched cddid_all.tbl CDD PRK05952 PRK05952 235653 PRK05952 beta-ketoacyl-ACP synthase. 381 matched cddid_all.tbl CDD PRK05953 PRK05953 180325 PRK05953 Precorrin-8X methylmutase. 208 matched cddid_all.tbl CDD PRK05954 PRK05954 180326 PRK05954 precorrin-8X methylmutase; Provisional 203 matched cddid_all.tbl CDD PRK05957 PRK05957 235654 PRK05957 pyridoxal phosphate-dependent aminotransferase. 389 matched cddid_all.tbl CDD PRK05958 PRK05958 235655 PRK05958 8-amino-7-oxononanoate synthase; Reviewed 385 matched cddid_all.tbl CDD PRK05962 PRK05962 168315 PRK05962 amidase; Validated 424 matched cddid_all.tbl CDD PRK05963 PRK05963 180328 PRK05963 beta-ketoacyl-ACP synthase III. 326 matched cddid_all.tbl CDD PRK05964 PRK05964 235656 PRK05964 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional 423 matched cddid_all.tbl CDD PRK05965 PRK05965 180330 PRK05965 hypothetical protein; Provisional 459 matched cddid_all.tbl CDD PRK05967 PRK05967 235657 PRK05967 cystathionine beta-lyase; Provisional 395 matched cddid_all.tbl CDD PRK05968 PRK05968 168320 PRK05968 hypothetical protein; Provisional 389 matched cddid_all.tbl CDD PRK05972 PRK05972 235658 ligD ATP-dependent DNA ligase; Reviewed 860 matched cddid_all.tbl CDD PRK05973 PRK05973 168322 PRK05973 replicative DNA helicase; Provisional 237 matched cddid_all.tbl CDD PRK05974 PRK05974 235659 PRK05974 phosphoribosylformylglycinamidine synthase subunit PurS; Reviewed 80 matched cddid_all.tbl CDD PRK05975 PRK05975 168324 PRK05975 3-carboxy-cis,cis-muconate cycloisomerase; Provisional 351 matched cddid_all.tbl CDD PRK05978 PRK05978 180334 PRK05978 hypothetical protein; Provisional 148 matched cddid_all.tbl CDD PRK05980 PRK05980 180335 PRK05980 crotonase/enoyl-CoA hydratase family protein. 260 matched cddid_all.tbl CDD PRK05981 PRK05981 235661 PRK05981 enoyl-CoA hydratase/isomerase. 266 matched cddid_all.tbl CDD PRK05985 PRK05985 180337 PRK05985 cytosine deaminase; Provisional 391 matched cddid_all.tbl CDD PRK05986 PRK05986 235662 PRK05986 cob(I)yrinic acid a,c-diamide adenosyltransferase. 191 matched cddid_all.tbl CDD PRK05988 PRK05988 180339 PRK05988 formate dehydrogenase subunit gamma; Validated 156 matched cddid_all.tbl CDD PRK05989 PRK05989 235663 cobN cobaltochelatase subunit CobN; Reviewed 1244 matched cddid_all.tbl CDD PRK05990 PRK05990 180341 PRK05990 precorrin-2 C(20)-methyltransferase; Reviewed 241 matched cddid_all.tbl CDD PRK05991 PRK05991 180342 PRK05991 precorrin-3B C17-methyltransferase; Provisional 250 matched cddid_all.tbl CDD PRK05993 PRK05993 180343 PRK05993 SDR family oxidoreductase. 277 matched cddid_all.tbl CDD PRK05994 PRK05994 180344 PRK05994 O-acetylhomoserine aminocarboxypropyltransferase; Validated 427 matched cddid_all.tbl CDD PRK05995 PRK05995 235664 PRK05995 enoyl-CoA hydratase; Provisional 262 matched cddid_all.tbl CDD PRK05996 PRK05996 235665 motB MotB family protein. 423 matched cddid_all.tbl CDD PRK06002 PRK06002 235666 fliI flagellar protein export ATPase FliI. 450 matched cddid_all.tbl CDD PRK06003 PRK06003 168340 flgB flagellar basal body rod protein FlgB; Reviewed 126 matched cddid_all.tbl CDD PRK06004 PRK06004 235667 flgB flagellar basal body rod protein FlgB; Reviewed 127 matched cddid_all.tbl CDD PRK06005 PRK06005 180347 flgA flagellar basal body P-ring formation protein FlgA. 160 matched cddid_all.tbl CDD PRK06008 PRK06008 235669 flgL flagellar hook-associated family protein. 348 matched cddid_all.tbl CDD PRK06009 PRK06009 235670 flgD flagellar hook assembly protein FlgD. 140 matched cddid_all.tbl CDD PRK06010 PRK06010 235671 fliQ flagellar biosynthesis protein FliQ; Reviewed 88 matched cddid_all.tbl CDD PRK06012 PRK06012 235672 flhA flagellar type III secretion system protein FlhA. 697 matched cddid_all.tbl CDD PRK06015 PRK06015 168348 PRK06015 2-dehydro-3-deoxy-phosphogluconate aldolase. 201 matched cddid_all.tbl CDD PRK06018 PRK06018 235673 PRK06018 putative acyl-CoA synthetase; Provisional 542 matched cddid_all.tbl CDD PRK06019 PRK06019 235674 PRK06019 phosphoribosylaminoimidazole carboxylase ATPase subunit; Reviewed 372 matched cddid_all.tbl CDD PRK06023 PRK06023 168351 PRK06023 crotonase/enoyl-CoA hydratase family protein. 251 matched cddid_all.tbl CDD PRK06025 PRK06025 235675 PRK06025 acetyl-CoA C-acetyltransferase. 417 matched cddid_all.tbl CDD PRK06026 PRK06026 180353 PRK06026 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Validated 212 matched cddid_all.tbl CDD PRK06027 PRK06027 235676 purU formyltetrahydrofolate deformylase; Reviewed 286 matched cddid_all.tbl CDD PRK06029 PRK06029 235677 PRK06029 UbiX family flavin prenyltransferase. 185 matched cddid_all.tbl CDD PRK06030 PRK06030 180356 PRK06030 hypothetical protein; Provisional 124 matched cddid_all.tbl CDD PRK06031 PRK06031 235678 PRK06031 phosphoribosyltransferase; Provisional 233 matched cddid_all.tbl CDD PRK06032 PRK06032 235679 fliH flagellar assembly protein H; Validated 199 matched cddid_all.tbl CDD PRK06033 PRK06033 180359 PRK06033 flagellar motor switch protein FliN. 83 matched cddid_all.tbl CDD PRK06034 PRK06034 235680 PRK06034 hypothetical protein; Provisional 279 matched cddid_all.tbl CDD PRK06035 PRK06035 180361 PRK06035 3-hydroxyacyl-CoA dehydrogenase; Validated 291 matched cddid_all.tbl CDD PRK06036 PRK06036 180362 PRK06036 S-methyl-5-thioribose-1-phosphate isomerase. 339 matched cddid_all.tbl CDD PRK06038 PRK06038 180363 PRK06038 N-ethylammeline chlorohydrolase; Provisional 430 matched cddid_all.tbl CDD PRK06041 PRK06041 235682 PRK06041 archaellar assembly protein FlaJ. 553 matched cddid_all.tbl CDD PRK06043 PRK06043 180366 PRK06043 fumarate hydratase; Provisional 192 matched cddid_all.tbl CDD PRK06048 PRK06048 180368 PRK06048 acetolactate synthase large subunit. 561 matched cddid_all.tbl CDD PRK06049 PRK06049 235683 rpl30p 50S ribosomal protein L30P; Reviewed 154 matched cddid_all.tbl CDD PRK06052 PRK06052 235684 PRK06052 methionine synthase. 344 matched cddid_all.tbl CDD PRK06057 PRK06057 180371 PRK06057 short chain dehydrogenase; Provisional 255 matched cddid_all.tbl CDD PRK06058 PRK06058 235685 PRK06058 4-aminobutyrate--2-oxoglutarate transaminase. 443 matched cddid_all.tbl CDD PRK06059 PRK06059 180373 PRK06059 lipid-transfer protein; Provisional 399 matched cddid_all.tbl CDD PRK06060 PRK06060 180374 PRK06060 p-hydroxybenzoic acid--AMP ligase FadD22. 705 matched cddid_all.tbl CDD PRK06061 PRK06061 235686 PRK06061 amidase; Provisional 483 matched cddid_all.tbl CDD PRK06062 PRK06062 235687 PRK06062 hypothetical protein; Provisional 451 matched cddid_all.tbl CDD PRK06063 PRK06063 180377 PRK06063 DEDDh family exonuclease. 313 matched cddid_all.tbl CDD PRK06064 PRK06064 235688 PRK06064 thiolase domain-containing protein. 389 matched cddid_all.tbl CDD PRK06065 PRK06065 180379 PRK06065 thiolase domain-containing protein. 392 matched cddid_all.tbl CDD PRK06066 PRK06066 180380 PRK06066 thiolase domain-containing protein. 385 matched cddid_all.tbl CDD PRK06067 PRK06067 180381 PRK06067 flagellar accessory protein FlaH; Validated 234 matched cddid_all.tbl CDD PRK06069 PRK06069 235689 sdhA succinate dehydrogenase/fumarate reductase flavoprotein subunit. 577 matched cddid_all.tbl CDD PRK06072 PRK06072 168377 PRK06072 enoyl-CoA hydratase; Provisional 248 matched cddid_all.tbl CDD PRK06073 PRK06073 235690 PRK06073 NADH dehydrogenase subunit A; Validated 124 matched cddid_all.tbl CDD PRK06074 PRK06074 235691 PRK06074 NADH dehydrogenase subunit C; Provisional 189 matched cddid_all.tbl CDD PRK06075 PRK06075 180385 PRK06075 NADH-quinone oxidoreductase subunit D. 392 matched cddid_all.tbl CDD PRK06076 PRK06076 235692 PRK06076 NADH-quinone oxidoreductase subunit NuoH. 322 matched cddid_all.tbl CDD PRK06077 PRK06077 235693 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional 252 matched cddid_all.tbl CDD PRK06078 PRK06078 180387 PRK06078 pyrimidine-nucleoside phosphorylase; Reviewed 434 matched cddid_all.tbl CDD PRK06079 PRK06079 235694 PRK06079 enoyl-[acyl-carrier-protein] reductase FabI. 252 matched cddid_all.tbl CDD PRK06080 PRK06080 235695 PRK06080 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Validated 293 matched cddid_all.tbl CDD PRK06082 PRK06082 180390 PRK06082 aspartate aminotransferase family protein. 459 matched cddid_all.tbl CDD PRK06084 PRK06084 180392 PRK06084 bifunctional O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase. 425 matched cddid_all.tbl CDD PRK06087 PRK06087 180393 PRK06087 medium-chain fatty-acid--CoA ligase. 547 matched cddid_all.tbl CDD PRK06090 PRK06090 180394 PRK06090 DNA polymerase III subunit delta'; Validated 319 matched cddid_all.tbl CDD PRK06091 PRK06091 180395 PRK06091 membrane protein FdrA; Validated 555 matched cddid_all.tbl CDD PRK06092 PRK06092 235696 PRK06092 4-amino-4-deoxychorismate lyase; Reviewed 268 matched cddid_all.tbl CDD PRK06096 PRK06096 180397 PRK06096 molybdenum transport protein ModD; Provisional 284 matched cddid_all.tbl CDD PRK06099 PRK06099 235697 PRK06099 F0F1 ATP synthase subunit I; Validated 126 matched cddid_all.tbl CDD PRK06100 PRK06100 180398 PRK06100 DNA polymerase III subunit psi; Provisional 132 matched cddid_all.tbl CDD PRK06101 PRK06101 180399 PRK06101 SDR family oxidoreductase. 240 matched cddid_all.tbl CDD PRK06102 PRK06102 235698 PRK06102 amidase. 452 matched cddid_all.tbl CDD PRK06105 PRK06105 180401 PRK06105 aminotransferase; Provisional 460 matched cddid_all.tbl CDD PRK06107 PRK06107 180403 PRK06107 aspartate transaminase. 402 matched cddid_all.tbl CDD PRK06108 PRK06108 180404 PRK06108 pyridoxal phosphate-dependent aminotransferase. 382 matched cddid_all.tbl CDD PRK06110 PRK06110 235699 PRK06110 threonine dehydratase. 322 matched cddid_all.tbl CDD PRK06111 PRK06111 180406 PRK06111 acetyl-CoA carboxylase biotin carboxylase subunit; Validated 450 matched cddid_all.tbl CDD PRK06112 PRK06112 235700 PRK06112 acetolactate synthase catalytic subunit; Validated 578 matched cddid_all.tbl CDD PRK06113 PRK06113 135765 PRK06113 7-alpha-hydroxysteroid dehydrogenase; Validated 255 matched cddid_all.tbl CDD PRK06114 PRK06114 180408 PRK06114 SDR family oxidoreductase. 254 matched cddid_all.tbl CDD PRK06116 PRK06116 235701 PRK06116 glutathione reductase; Validated 450 matched cddid_all.tbl CDD PRK06123 PRK06123 180411 PRK06123 SDR family oxidoreductase. 248 matched cddid_all.tbl CDD PRK06124 PRK06124 235702 PRK06124 SDR family oxidoreductase. 256 matched cddid_all.tbl CDD PRK06125 PRK06125 235703 PRK06125 short chain dehydrogenase; Provisional 259 matched cddid_all.tbl CDD PRK06126 PRK06126 235704 PRK06126 hypothetical protein; Provisional 545 matched cddid_all.tbl CDD PRK06127 PRK06127 235705 PRK06127 enoyl-CoA hydratase; Provisional 269 matched cddid_all.tbl CDD PRK06128 PRK06128 180413 PRK06128 SDR family oxidoreductase. 300 matched cddid_all.tbl CDD PRK06129 PRK06129 235706 PRK06129 3-hydroxyacyl-CoA dehydrogenase; Validated 308 matched cddid_all.tbl CDD PRK06130 PRK06130 235707 PRK06130 3-hydroxybutyryl-CoA dehydrogenase; Validated 311 matched cddid_all.tbl CDD PRK06131 PRK06131 235708 PRK06131 dihydroxy-acid dehydratase; Validated 571 matched cddid_all.tbl CDD PRK06132 PRK06132 235709 PRK06132 hypothetical protein; Provisional 359 matched cddid_all.tbl CDD PRK06133 PRK06133 235710 PRK06133 glutamate carboxypeptidase; Reviewed 410 matched cddid_all.tbl CDD PRK06134 PRK06134 180419 PRK06134 putative FAD-binding dehydrogenase; Reviewed 581 matched cddid_all.tbl CDD PRK06136 PRK06136 235711 PRK06136 uroporphyrinogen-III C-methyltransferase. 249 matched cddid_all.tbl CDD PRK06138 PRK06138 235712 PRK06138 SDR family oxidoreductase. 252 matched cddid_all.tbl CDD PRK06139 PRK06139 235713 PRK06139 SDR family oxidoreductase. 330 matched cddid_all.tbl CDD PRK06141 PRK06141 180421 PRK06141 ornithine cyclodeaminase family protein. 314 matched cddid_all.tbl CDD PRK06142 PRK06142 235714 PRK06142 crotonase/enoyl-CoA hydratase family protein. 272 matched cddid_all.tbl CDD PRK06143 PRK06143 180423 PRK06143 enoyl-CoA hydratase; Provisional 256 matched cddid_all.tbl CDD PRK06144 PRK06144 180424 PRK06144 enoyl-CoA hydratase; Provisional 262 matched cddid_all.tbl CDD PRK06145 PRK06145 102207 PRK06145 acyl-CoA synthetase; Validated 497 matched cddid_all.tbl CDD PRK06147 PRK06147 235715 PRK06147 3-oxoacyl-(acyl carrier protein) synthase; Validated 348 matched cddid_all.tbl CDD PRK06148 PRK06148 180426 PRK06148 hypothetical protein; Provisional 1013 matched cddid_all.tbl CDD PRK06149 PRK06149 235716 PRK06149 aminotransferase. 972 matched cddid_all.tbl CDD PRK06151 PRK06151 180428 PRK06151 N-ethylammeline chlorohydrolase; Provisional 488 matched cddid_all.tbl CDD PRK06153 PRK06153 235717 PRK06153 hypothetical protein; Provisional 393 matched cddid_all.tbl CDD PRK06154 PRK06154 235718 PRK06154 thiamine pyrophosphate-requiring protein. 565 matched cddid_all.tbl CDD PRK06155 PRK06155 235719 PRK06155 crotonobetaine/carnitine-CoA ligase; Provisional 542 matched cddid_all.tbl CDD PRK06156 PRK06156 235720 PRK06156 dipeptidase. 520 matched cddid_all.tbl CDD PRK06157 PRK06157 180433 PRK06157 acetyl-CoA acetyltransferase; Validated 398 matched cddid_all.tbl CDD PRK06158 PRK06158 180434 PRK06158 thiolase; Provisional 384 matched cddid_all.tbl CDD PRK06161 PRK06161 180435 PRK06161 putative monovalent cation/H+ antiporter subunit F; Reviewed 89 matched cddid_all.tbl CDD PRK06163 PRK06163 235721 PRK06163 hypothetical protein; Provisional 202 matched cddid_all.tbl CDD PRK06164 PRK06164 235722 PRK06164 acyl-CoA synthetase; Validated 540 matched cddid_all.tbl CDD PRK06169 PRK06169 180437 PRK06169 putative amidase; Provisional 466 matched cddid_all.tbl CDD PRK06170 PRK06170 235723 PRK06170 amidase; Provisional 490 matched cddid_all.tbl CDD PRK06171 PRK06171 180439 PRK06171 sorbitol-6-phosphate 2-dehydrogenase; Provisional 266 matched cddid_all.tbl CDD PRK06172 PRK06172 180440 PRK06172 SDR family oxidoreductase. 253 matched cddid_all.tbl CDD PRK06175 PRK06175 180442 PRK06175 L-aspartate oxidase; Provisional 433 matched cddid_all.tbl CDD PRK06176 PRK06176 180443 PRK06176 cystathionine gamma-synthase. 380 matched cddid_all.tbl CDD PRK06178 PRK06178 235724 PRK06178 acyl-CoA synthetase; Validated 567 matched cddid_all.tbl CDD PRK06179 PRK06179 235725 PRK06179 short chain dehydrogenase; Provisional 270 matched cddid_all.tbl CDD PRK06180 PRK06180 180446 PRK06180 short chain dehydrogenase; Provisional 277 matched cddid_all.tbl CDD PRK06181 PRK06181 235726 PRK06181 SDR family oxidoreductase. 263 matched cddid_all.tbl CDD PRK06182 PRK06182 180448 PRK06182 short chain dehydrogenase; Validated 273 matched cddid_all.tbl CDD PRK06183 PRK06183 235727 mhpA bifunctional 3-(3-hydroxy-phenyl)propionate/3-hydroxycinnamic acid hydroxylase. 500 matched cddid_all.tbl CDD PRK06184 PRK06184 235728 PRK06184 hypothetical protein; Provisional 502 matched cddid_all.tbl CDD PRK06185 PRK06185 235729 PRK06185 FAD-dependent oxidoreductase. 407 matched cddid_all.tbl CDD PRK06186 PRK06186 180452 PRK06186 hypothetical protein; Validated 229 matched cddid_all.tbl CDD PRK06187 PRK06187 235730 PRK06187 long-chain-fatty-acid--CoA ligase; Validated 521 matched cddid_all.tbl CDD PRK06188 PRK06188 235731 PRK06188 acyl-CoA synthetase; Validated 524 matched cddid_all.tbl CDD PRK06189 PRK06189 235732 PRK06189 allantoinase; Provisional 451 matched cddid_all.tbl CDD PRK06190 PRK06190 235733 PRK06190 enoyl-CoA hydratase; Provisional 258 matched cddid_all.tbl CDD PRK06193 PRK06193 235734 PRK06193 hypothetical protein; Provisional 206 matched cddid_all.tbl CDD PRK06194 PRK06194 180458 PRK06194 hypothetical protein; Provisional 287 matched cddid_all.tbl CDD PRK06195 PRK06195 235735 PRK06195 DNA polymerase III subunit epsilon; Validated 309 matched cddid_all.tbl CDD PRK06196 PRK06196 235736 PRK06196 oxidoreductase; Provisional 315 matched cddid_all.tbl CDD PRK06197 PRK06197 235737 PRK06197 short chain dehydrogenase; Provisional 306 matched cddid_all.tbl CDD PRK06198 PRK06198 180462 PRK06198 short chain dehydrogenase; Provisional 260 matched cddid_all.tbl CDD PRK06199 PRK06199 235738 PRK06199 ornithine cyclodeaminase; Validated 379 matched cddid_all.tbl CDD PRK06200 PRK06200 235739 PRK06200 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase; Provisional 263 matched cddid_all.tbl CDD PRK06201 PRK06201 180465 PRK06201 hypothetical protein; Validated 221 matched cddid_all.tbl CDD PRK06202 PRK06202 180466 PRK06202 hypothetical protein; Provisional 232 matched cddid_all.tbl CDD PRK06203 PRK06203 235740 aroB 3-dehydroquinate synthase; Reviewed 389 matched cddid_all.tbl CDD PRK06205 PRK06205 235741 PRK06205 acetyl-CoA C-acetyltransferase. 404 matched cddid_all.tbl CDD PRK06207 PRK06207 235742 PRK06207 pyridoxal phosphate-dependent aminotransferase. 405 matched cddid_all.tbl CDD PRK06208 PRK06208 235743 PRK06208 class II aldolase/adducin family protein. 274 matched cddid_all.tbl CDD PRK06209 PRK06209 180471 PRK06209 glutamate-1-semialdehyde 2,1-aminomutase; Provisional 431 matched cddid_all.tbl CDD PRK06210 PRK06210 180472 PRK06210 enoyl-CoA hydratase; Provisional 272 matched cddid_all.tbl CDD PRK06213 PRK06213 235744 PRK06213 crotonase/enoyl-CoA hydratase family protein. 229 matched cddid_all.tbl CDD PRK06214 PRK06214 235745 PRK06214 sulfite reductase subunit alpha. 530 matched cddid_all.tbl CDD PRK06215 PRK06215 235746 PRK06215 hypothetical protein; Provisional 238 matched cddid_all.tbl CDD PRK06217 PRK06217 168472 PRK06217 hypothetical protein; Validated 183 matched cddid_all.tbl CDD PRK06222 PRK06222 235747 PRK06222 sulfide/dihydroorotate dehydrogenase-like FAD/NAD-binding protein. 281 matched cddid_all.tbl CDD PRK06223 PRK06223 180477 PRK06223 malate dehydrogenase; Reviewed 307 matched cddid_all.tbl CDD PRK06224 PRK06224 235748 PRK06224 citryl-CoA lyase. 263 matched cddid_all.tbl CDD PRK06225 PRK06225 235749 PRK06225 pyridoxal phosphate-dependent aminotransferase. 380 matched cddid_all.tbl CDD PRK06228 PRK06228 235750 PRK06228 F0F1 ATP synthase subunit epsilon; Validated 131 matched cddid_all.tbl CDD PRK06231 PRK06231 180481 PRK06231 F0F1 ATP synthase subunit B; Validated 205 matched cddid_all.tbl CDD PRK06233 PRK06233 180482 PRK06233 vitamin B12 independent methionine synthase. 372 matched cddid_all.tbl CDD PRK06234 PRK06234 168478 PRK06234 methionine gamma-lyase; Provisional 400 matched cddid_all.tbl CDD PRK06241 PRK06241 235751 PRK06241 phosphoenolpyruvate synthase; Validated 871 matched cddid_all.tbl CDD PRK06242 PRK06242 180484 PRK06242 flavodoxin; Provisional 150 matched cddid_all.tbl CDD PRK06245 PRK06245 180485 cofG FO synthase subunit 1; Reviewed 336 matched cddid_all.tbl CDD PRK06246 PRK06246 180486 PRK06246 fumarate hydratase; Provisional 280 matched cddid_all.tbl CDD PRK06247 PRK06247 180487 PRK06247 pyruvate kinase; Provisional 476 matched cddid_all.tbl CDD PRK06249 PRK06249 180488 PRK06249 putative 2-dehydropantoate 2-reductase. 313 matched cddid_all.tbl CDD PRK06251 PRK06251 235752 PRK06251 V-type ATP synthase subunit K; Validated 102 matched cddid_all.tbl CDD PRK06252 PRK06252 235753 PRK06252 methylcobalamin:coenzyme M methyltransferase; Validated 339 matched cddid_all.tbl CDD PRK06259 PRK06259 235756 PRK06259 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Provisional 486 matched cddid_all.tbl CDD PRK06263 PRK06263 235758 sdhA succinate dehydrogenase flavoprotein subunit; Reviewed 543 matched cddid_all.tbl CDD PRK06264 PRK06264 235759 cbiC cobalt-precorrin-8 methylmutase. 210 matched cddid_all.tbl CDD PRK06265 PRK06265 235760 PRK06265 cobalt transporter CbiM. 199 matched cddid_all.tbl CDD PRK06266 PRK06266 235761 PRK06266 transcription initiation factor E subunit alpha; Validated 178 matched cddid_all.tbl CDD PRK06267 PRK06267 235762 PRK06267 hypothetical protein; Provisional 350 matched cddid_all.tbl CDD PRK06270 PRK06270 235763 PRK06270 homoserine dehydrogenase; Provisional 341 matched cddid_all.tbl CDD PRK06271 PRK06271 180501 PRK06271 V-type ATP synthase subunit K; Validated 213 matched cddid_all.tbl CDD PRK06273 PRK06273 235764 PRK06273 ferredoxin; Provisional 165 matched cddid_all.tbl CDD PRK06274 PRK06274 235765 PRK06274 indolepyruvate oxidoreductase subunit beta. 197 matched cddid_all.tbl CDD PRK06276 PRK06276 235766 PRK06276 acetolactate synthase large subunit. 586 matched cddid_all.tbl CDD PRK06277 PRK06277 235767 PRK06277 energy conserving hydrogenase EhbF. 478 matched cddid_all.tbl CDD PRK06278 PRK06278 180505 PRK06278 cobyrinic acid a,c-diamide synthase; Validated 476 matched cddid_all.tbl CDD PRK06279 PRK06279 180506 PRK06279 putative monovalent cation/H+ antiporter subunit E; Reviewed 100 matched cddid_all.tbl CDD PRK06280 PRK06280 235768 PRK06280 hypothetical protein; Provisional 77 matched cddid_all.tbl CDD PRK06281 PRK06281 180508 PRK06281 putative monovalent cation/H+ antiporter subunit B; Reviewed 154 matched cddid_all.tbl CDD PRK06285 PRK06285 180509 PRK06285 chorismate mutase; Provisional 96 matched cddid_all.tbl CDD PRK06286 PRK06286 235769 PRK06286 putative monovalent cation/H+ antiporter subunit G; Reviewed 91 matched cddid_all.tbl CDD PRK06287 PRK06287 180511 PRK06287 cobalt transport protein CbiN; Validated 107 matched cddid_all.tbl CDD PRK06288 PRK06288 235770 PRK06288 RNA polymerase sigma factor WhiG; Reviewed 268 matched cddid_all.tbl CDD PRK06289 PRK06289 235771 PRK06289 acetyl-CoA acetyltransferase; Provisional 403 matched cddid_all.tbl CDD PRK06290 PRK06290 235772 PRK06290 LL-diaminopimelate aminotransferase. 410 matched cddid_all.tbl CDD PRK06291 PRK06291 235773 PRK06291 aspartate kinase; Provisional 465 matched cddid_all.tbl CDD PRK06292 PRK06292 235774 PRK06292 dihydrolipoamide dehydrogenase; Validated 460 matched cddid_all.tbl CDD PRK06293 PRK06293 180517 PRK06293 single-stranded DNA-binding protein; Provisional 161 matched cddid_all.tbl CDD PRK06298 PRK06298 180519 PRK06298 type III secretion system protein; Validated 356 matched cddid_all.tbl CDD PRK06299 PRK06299 235775 rpsA 30S ribosomal protein S1; Reviewed 565 matched cddid_all.tbl CDD PRK06300 PRK06300 235776 PRK06300 enoyl-(acyl carrier protein) reductase; Provisional 299 matched cddid_all.tbl CDD PRK06305 PRK06305 180523 PRK06305 DNA polymerase III subunits gamma and tau; Validated 451 matched cddid_all.tbl CDD PRK06309 PRK06309 180524 PRK06309 DNA polymerase III subunit epsilon; Validated 232 matched cddid_all.tbl CDD PRK06310 PRK06310 180525 PRK06310 DNA polymerase III subunit epsilon; Validated 250 matched cddid_all.tbl CDD PRK06319 PRK06319 235778 PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated 860 matched cddid_all.tbl CDD PRK06321 PRK06321 180528 PRK06321 replicative DNA helicase; Provisional 472 matched cddid_all.tbl CDD PRK06327 PRK06327 235779 PRK06327 dihydrolipoamide dehydrogenase; Validated 475 matched cddid_all.tbl CDD PRK06328 PRK06328 180530 PRK06328 HrpE/YscL family type III secretion apparatus protein. 223 matched cddid_all.tbl CDD PRK06330 PRK06330 235780 PRK06330 transcript cleavage factor/unknown domain fusion protein; Validated 718 matched cddid_all.tbl CDD PRK06333 PRK06333 235781 PRK06333 beta-ketoacyl-ACP synthase. 424 matched cddid_all.tbl CDD PRK06334 PRK06334 180533 PRK06334 long chain fatty acid--[acyl-carrier-protein] ligase; Validated 539 matched cddid_all.tbl CDD PRK06341 PRK06341 235782 PRK06341 single-stranded DNA-binding protein; Provisional 166 matched cddid_all.tbl CDD PRK06342 PRK06342 180535 PRK06342 transcription elongation factor GreA. 160 matched cddid_all.tbl CDD PRK06347 PRK06347 180536 PRK06347 1,4-beta-N-acetylmuramoylhydrolase. 592 matched cddid_all.tbl CDD PRK06348 PRK06348 180537 PRK06348 pyridoxal phosphate-dependent aminotransferase. 384 matched cddid_all.tbl CDD PRK06349 PRK06349 235783 PRK06349 homoserine dehydrogenase; Provisional 426 matched cddid_all.tbl CDD PRK06354 PRK06354 235784 PRK06354 pyruvate kinase; Provisional 590 matched cddid_all.tbl CDD PRK06357 PRK06357 180541 PRK06357 hypothetical protein; Provisional 216 matched cddid_all.tbl CDD PRK06361 PRK06361 180543 PRK06361 histidinol phosphate phosphatase domain-containing protein. 212 matched cddid_all.tbl CDD PRK06365 PRK06365 235785 PRK06365 thiolase domain-containing protein. 430 matched cddid_all.tbl CDD PRK06366 PRK06366 102340 PRK06366 acetyl-CoA C-acetyltransferase. 388 matched cddid_all.tbl CDD PRK06369 PRK06369 235786 nac nascent polypeptide-associated complex protein; Reviewed 115 matched cddid_all.tbl CDD PRK06370 PRK06370 235787 PRK06370 FAD-containing oxidoreductase. 463 matched cddid_all.tbl CDD PRK06371 PRK06371 180547 PRK06371 S-methyl-5-thioribose-1-phosphate isomerase. 329 matched cddid_all.tbl CDD PRK06372 PRK06372 235788 PRK06372 translation initiation factor IF-2B subunit delta; Provisional 253 matched cddid_all.tbl CDD PRK06380 PRK06380 180548 PRK06380 metal-dependent hydrolase; Provisional 418 matched cddid_all.tbl CDD PRK06381 PRK06381 235789 PRK06381 threonine synthase; Validated 319 matched cddid_all.tbl CDD PRK06386 PRK06386 235790 PRK06386 replication factor A; Reviewed 358 matched cddid_all.tbl CDD PRK06389 PRK06389 235791 PRK06389 argininosuccinate lyase; Provisional 434 matched cddid_all.tbl CDD PRK06392 PRK06392 102354 PRK06392 homoserine dehydrogenase; Provisional 326 matched cddid_all.tbl CDD PRK06393 PRK06393 102355 rpoE DNA-directed RNA polymerase subunit E''; Validated 64 matched cddid_all.tbl CDD PRK06394 PRK06394 235793 rpl13p 50S ribosomal protein L13P; Reviewed 146 matched cddid_all.tbl CDD PRK06397 PRK06397 135898 PRK06397 V-type ATP synthase subunit H; Validated 111 matched cddid_all.tbl CDD PRK06398 PRK06398 235794 PRK06398 aldose dehydrogenase; Validated 258 matched cddid_all.tbl CDD PRK06402 PRK06402 235795 rpl12p 50S ribosomal protein L12P; Reviewed 106 matched cddid_all.tbl CDD PRK06404 PRK06404 102361 PRK06404 anthranilate synthase component I; Reviewed 351 matched cddid_all.tbl CDD PRK06406 PRK06406 235796 PRK06406 vitamin B12-dependent ribonucleotide reductase. 771 matched cddid_all.tbl CDD PRK06407 PRK06407 180556 PRK06407 ornithine cyclodeaminase; Provisional 301 matched cddid_all.tbl CDD PRK06411 PRK06411 235797 PRK06411 NADH-quinone oxidoreductase subunit NuoB. 183 matched cddid_all.tbl CDD PRK06416 PRK06416 235798 PRK06416 dihydrolipoamide dehydrogenase; Reviewed 462 matched cddid_all.tbl CDD PRK06418 PRK06418 180559 PRK06418 transcription elongation factor NusA-like protein; Validated 166 matched cddid_all.tbl CDD PRK06423 PRK06423 102368 PRK06423 phosphoribosylformylglycinamidine synthase; Provisional 73 matched cddid_all.tbl CDD PRK06425 PRK06425 102370 PRK06425 histidinol-phosphate aminotransferase; Validated 332 matched cddid_all.tbl CDD PRK06427 PRK06427 180561 PRK06427 bifunctional hydroxy-methylpyrimidine kinase/ hydroxy-phosphomethylpyrimidine kinase; Reviewed 266 matched cddid_all.tbl CDD PRK06432 PRK06432 102372 PRK06432 NADH dehydrogenase subunit A; Validated 144 matched cddid_all.tbl CDD PRK06433 PRK06433 180562 PRK06433 NADH dehydrogenase subunit J; Provisional 88 matched cddid_all.tbl CDD PRK06434 PRK06434 102374 PRK06434 cystathionine gamma-lyase; Validated 384 matched cddid_all.tbl CDD PRK06436 PRK06436 235800 PRK06436 2-hydroxyacid dehydrogenase. 303 matched cddid_all.tbl CDD PRK06437 PRK06437 135906 PRK06437 hypothetical protein; Provisional 67 matched cddid_all.tbl CDD PRK06438 PRK06438 102377 PRK06438 hypothetical protein; Provisional 292 matched cddid_all.tbl CDD PRK06439 PRK06439 102378 PRK06439 NADH dehydrogenase subunit J; Provisional 72 matched cddid_all.tbl CDD PRK06443 PRK06443 235801 PRK06443 chorismate mutase; Validated 177 matched cddid_all.tbl CDD PRK06444 PRK06444 102381 PRK06444 prephenate dehydrogenase; Provisional 197 matched cddid_all.tbl CDD PRK06445 PRK06445 180563 PRK06445 acetyl-CoA C-acetyltransferase. 394 matched cddid_all.tbl CDD PRK06446 PRK06446 235802 PRK06446 hypothetical protein; Provisional 436 matched cddid_all.tbl CDD PRK06450 PRK06450 180565 PRK06450 threonine synthase; Validated 338 matched cddid_all.tbl CDD PRK06451 PRK06451 235803 PRK06451 NADP-dependent isocitrate dehydrogenase. 412 matched cddid_all.tbl CDD PRK06452 PRK06452 180567 sdhA succinate dehydrogenase flavoprotein subunit; Reviewed 566 matched cddid_all.tbl CDD PRK06455 PRK06455 235804 PRK06455 riboflavin synthase; Provisional 155 matched cddid_all.tbl CDD PRK06456 PRK06456 180569 PRK06456 acetolactate synthase large subunit. 572 matched cddid_all.tbl CDD PRK06457 PRK06457 180570 PRK06457 pyruvate dehydrogenase; Provisional 549 matched cddid_all.tbl CDD PRK06458 PRK06458 235805 PRK06458 hydrogenase 4 subunit F; Validated 490 matched cddid_all.tbl CDD PRK06459 PRK06459 235806 PRK06459 hydrogenase 4 subunit B; Validated 585 matched cddid_all.tbl CDD PRK06460 PRK06460 235807 PRK06460 hypothetical protein; Provisional 376 matched cddid_all.tbl CDD PRK06461 PRK06461 180574 PRK06461 single-stranded DNA-binding protein; Reviewed 129 matched cddid_all.tbl CDD PRK06462 PRK06462 235808 PRK06462 asparagine synthetase A; Reviewed 335 matched cddid_all.tbl CDD PRK06463 PRK06463 180576 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional 255 matched cddid_all.tbl CDD PRK06464 PRK06464 235809 PRK06464 phosphoenolpyruvate synthase; Validated 795 matched cddid_all.tbl CDD PRK06466 PRK06466 180578 PRK06466 acetolactate synthase 3 large subunit. 574 matched cddid_all.tbl CDD PRK06473 PRK06473 235810 PRK06473 NADH-quinone oxidoreductase subunit M. 500 matched cddid_all.tbl CDD PRK06474 PRK06474 235811 PRK06474 hypothetical protein; Provisional 178 matched cddid_all.tbl CDD PRK06475 PRK06475 180582 PRK06475 FAD-binding protein. 400 matched cddid_all.tbl CDD PRK06476 PRK06476 235812 PRK06476 pyrroline-5-carboxylate reductase; Reviewed 258 matched cddid_all.tbl CDD PRK06481 PRK06481 180584 PRK06481 flavocytochrome c. 506 matched cddid_all.tbl CDD PRK06482 PRK06482 235813 PRK06482 SDR family oxidoreductase. 276 matched cddid_all.tbl CDD PRK06483 PRK06483 180586 PRK06483 dihydromonapterin reductase; Provisional 236 matched cddid_all.tbl CDD PRK06484 PRK06484 168574 PRK06484 short chain dehydrogenase; Validated 520 matched cddid_all.tbl CDD PRK06486 PRK06486 235814 PRK06486 aldolase. 262 matched cddid_all.tbl CDD PRK06487 PRK06487 180588 PRK06487 2-hydroxyacid dehydrogenase. 317 matched cddid_all.tbl CDD PRK06489 PRK06489 235815 PRK06489 hypothetical protein; Provisional 360 matched cddid_all.tbl CDD PRK06490 PRK06490 180590 PRK06490 glutamine amidotransferase; Provisional 239 matched cddid_all.tbl CDD PRK06494 PRK06494 180591 PRK06494 enoyl-CoA hydratase; Provisional 259 matched cddid_all.tbl CDD PRK06495 PRK06495 168580 PRK06495 enoyl-CoA hydratase/isomerase family protein. 257 matched cddid_all.tbl CDD PRK06498 PRK06498 180592 PRK06498 isocitrate lyase; Provisional 531 matched cddid_all.tbl CDD PRK06500 PRK06500 235816 PRK06500 SDR family oxidoreductase. 249 matched cddid_all.tbl CDD PRK06501 PRK06501 235817 PRK06501 beta-ketoacyl-ACP synthase. 425 matched cddid_all.tbl CDD PRK06504 PRK06504 180595 PRK06504 acetyl-CoA C-acetyltransferase. 390 matched cddid_all.tbl CDD PRK06505 PRK06505 180596 PRK06505 enoyl-[acyl-carrier-protein] reductase FabI. 271 matched cddid_all.tbl CDD PRK06508 PRK06508 180597 PRK06508 acyl carrier protein; Provisional 93 matched cddid_all.tbl CDD PRK06512 PRK06512 180598 PRK06512 thiamine phosphate synthase. 221 matched cddid_all.tbl CDD PRK06518 PRK06518 235818 PRK06518 hypothetical protein; Provisional 177 matched cddid_all.tbl CDD PRK06519 PRK06519 235819 PRK06519 beta-ketoacyl-ACP synthase. 398 matched cddid_all.tbl CDD PRK06520 PRK06520 180601 PRK06520 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase. 368 matched cddid_all.tbl CDD PRK06521 PRK06521 235820 PRK06521 hydrogenase 4 subunit B; Validated 667 matched cddid_all.tbl CDD PRK06522 PRK06522 235821 PRK06522 2-dehydropantoate 2-reductase; Reviewed 304 matched cddid_all.tbl CDD PRK06523 PRK06523 180604 PRK06523 short chain dehydrogenase; Provisional 260 matched cddid_all.tbl CDD PRK06524 PRK06524 180605 PRK06524 biotin carboxylase-like protein; Validated 493 matched cddid_all.tbl CDD PRK06525 PRK06525 180606 PRK06525 hydrogenase 4 subunit D; Validated 479 matched cddid_all.tbl CDD PRK06526 PRK06526 180607 PRK06526 transposase; Provisional 254 matched cddid_all.tbl CDD PRK06529 PRK06529 180608 PRK06529 amidase; Provisional 482 matched cddid_all.tbl CDD PRK06531 PRK06531 235822 yajC preprotein translocase subunit YajC; Validated 113 matched cddid_all.tbl CDD PRK06539 PRK06539 180610 PRK06539 ribonucleoside-diphosphate reductase subunit alpha. 822 matched cddid_all.tbl CDD PRK06541 PRK06541 235823 PRK06541 aspartate aminotransferase family protein. 460 matched cddid_all.tbl CDD PRK06545 PRK06545 235824 PRK06545 prephenate dehydrogenase; Validated 359 matched cddid_all.tbl CDD PRK06546 PRK06546 180614 PRK06546 pyruvate dehydrogenase; Provisional 578 matched cddid_all.tbl CDD PRK06547 PRK06547 235825 PRK06547 hypothetical protein; Provisional 172 matched cddid_all.tbl CDD PRK06548 PRK06548 75628 PRK06548 ribonuclease H; Provisional 161 matched cddid_all.tbl CDD PRK06549 PRK06549 235826 PRK06549 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated 130 matched cddid_all.tbl CDD PRK06550 PRK06550 180617 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional 235 matched cddid_all.tbl CDD PRK06552 PRK06552 180618 PRK06552 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional 213 matched cddid_all.tbl CDD PRK06553 PRK06553 235827 PRK06553 lipid A biosynthesis lauroyl acyltransferase; Provisional 308 matched cddid_all.tbl CDD PRK06555 PRK06555 180620 PRK06555 pyrophosphate--fructose-6-phosphate 1-phosphotransferase; Validated 403 matched cddid_all.tbl CDD PRK06556 PRK06556 235828 PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated 953 matched cddid_all.tbl CDD PRK06557 PRK06557 235829 PRK06557 L-ribulose-5-phosphate 4-epimerase; Validated 221 matched cddid_all.tbl CDD PRK06558 PRK06558 235830 PRK06558 V-type ATP synthase subunit K; Validated 159 matched cddid_all.tbl CDD PRK06563 PRK06563 180625 PRK06563 crotonase/enoyl-CoA hydratase family protein. 255 matched cddid_all.tbl CDD PRK06565 PRK06565 180626 PRK06565 amidase; Validated 566 matched cddid_all.tbl CDD PRK06567 PRK06567 235832 PRK06567 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Validated 1028 matched cddid_all.tbl CDD PRK06568 PRK06568 168615 PRK06568 F0F1 ATP synthase subunit B; Validated 154 matched cddid_all.tbl CDD PRK06569 PRK06569 180627 PRK06569 F0F1 ATP synthase subunit B'; Validated 155 matched cddid_all.tbl CDD PRK06580 PRK06580 180628 PRK06580 putative monovalent cation/H+ antiporter subunit E; Reviewed 103 matched cddid_all.tbl CDD PRK06581 PRK06581 235833 PRK06581 DNA polymerase III subunit delta'; Validated 263 matched cddid_all.tbl CDD PRK06582 PRK06582 180630 PRK06582 coproporphyrinogen III oxidase; Provisional 390 matched cddid_all.tbl CDD PRK06585 PRK06585 235834 holA DNA polymerase III subunit delta; Reviewed 343 matched cddid_all.tbl CDD PRK06588 PRK06588 168619 PRK06588 putative monovalent cation/H+ antiporter subunit D; Reviewed 506 matched cddid_all.tbl CDD PRK06589 PRK06589 235835 PRK06589 putative monovalent cation/H+ antiporter subunit D; Reviewed 489 matched cddid_all.tbl CDD PRK06590 PRK06590 235836 PRK06590 NADH:ubiquinone oxidoreductase subunit L; Reviewed 624 matched cddid_all.tbl CDD PRK06591 PRK06591 235837 PRK06591 putative monovalent cation/H+ antiporter subunit D; Reviewed 432 matched cddid_all.tbl CDD PRK06596 PRK06596 235838 PRK06596 RNA polymerase factor sigma-32; Reviewed 284 matched cddid_all.tbl CDD PRK06598 PRK06598 235839 PRK06598 aspartate-semialdehyde dehydrogenase; Reviewed 369 matched cddid_all.tbl CDD PRK06599 PRK06599 235840 PRK06599 DNA topoisomerase I; Validated 675 matched cddid_all.tbl CDD PRK06602 PRK06602 180638 PRK06602 NADH:ubiquinone oxidoreductase subunit A; Validated 121 matched cddid_all.tbl CDD PRK06603 PRK06603 168626 PRK06603 enoyl-[acyl-carrier-protein] reductase FabI. 260 matched cddid_all.tbl CDD PRK06606 PRK06606 235841 PRK06606 branched-chain amino acid transaminase. 306 matched cddid_all.tbl CDD PRK06608 PRK06608 235842 PRK06608 serine/threonine dehydratase. 338 matched cddid_all.tbl CDD PRK06617 PRK06617 168629 PRK06617 2-octaprenyl-6-methoxyphenyl hydroxylase; Validated 374 matched cddid_all.tbl CDD PRK06620 PRK06620 168630 PRK06620 hypothetical protein; Validated 214 matched cddid_all.tbl CDD PRK06628 PRK06628 102471 PRK06628 lipid A biosynthesis lauroyl acyltransferase; Provisional 290 matched cddid_all.tbl CDD PRK06630 PRK06630 168631 PRK06630 hypothetical protein; Provisional 99 matched cddid_all.tbl CDD PRK06633 PRK06633 168632 PRK06633 acetyl-CoA C-acetyltransferase. 392 matched cddid_all.tbl CDD PRK06635 PRK06635 235843 PRK06635 aspartate kinase; Reviewed 404 matched cddid_all.tbl CDD PRK06638 PRK06638 235844 PRK06638 NADH-quinone oxidoreductase subunit J. 198 matched cddid_all.tbl CDD PRK06642 PRK06642 135984 PRK06642 single-stranded DNA-binding protein; Provisional 152 matched cddid_all.tbl CDD PRK06645 PRK06645 180643 PRK06645 DNA polymerase III subunits gamma and tau; Validated 507 matched cddid_all.tbl CDD PRK06646 PRK06646 102480 PRK06646 DNA polymerase III subunit chi; Provisional 154 matched cddid_all.tbl CDD PRK06647 PRK06647 235845 PRK06647 DNA polymerase III subunits gamma and tau; Validated 563 matched cddid_all.tbl CDD PRK06649 PRK06649 180645 PRK06649 V-type ATP synthase subunit K; Validated 143 matched cddid_all.tbl CDD PRK06654 PRK06654 235846 fliL flagellar basal body-associated protein FliL; Reviewed 181 matched cddid_all.tbl CDD PRK06655 PRK06655 235847 flgD flagellar hook assembly protein FlgD. 225 matched cddid_all.tbl CDD PRK06661 PRK06661 168637 PRK06661 hypothetical protein; Provisional 231 matched cddid_all.tbl CDD PRK06663 PRK06663 180648 PRK06663 flagellar hook-associated protein 3. 419 matched cddid_all.tbl CDD PRK06664 PRK06664 235848 fliD flagellar hook-associated protein FliD; Validated 661 matched cddid_all.tbl CDD PRK06665 PRK06665 180650 flgK flagellar hook-associated protein FlgK; Validated 627 matched cddid_all.tbl CDD PRK06666 PRK06666 235849 fliM flagellar motor switch protein FliM; Validated 337 matched cddid_all.tbl CDD PRK06667 PRK06667 180652 motB flagellar motor protein MotB; Validated 252 matched cddid_all.tbl CDD PRK06669 PRK06669 235850 fliH flagellar assembly protein H; Validated 281 matched cddid_all.tbl CDD PRK06672 PRK06672 180654 PRK06672 hypothetical protein; Validated 341 matched cddid_all.tbl CDD PRK06676 PRK06676 235851 rpsA 30S ribosomal protein S1; Reviewed 390 matched cddid_all.tbl CDD PRK06680 PRK06680 180656 PRK06680 D-amino acid aminotransferase; Reviewed 286 matched cddid_all.tbl CDD PRK06683 PRK06683 136002 PRK06683 hypothetical protein; Provisional 82 matched cddid_all.tbl CDD PRK06687 PRK06687 180657 PRK06687 TRZ/ATZ family protein. 419 matched cddid_all.tbl CDD PRK06688 PRK06688 235852 PRK06688 enoyl-CoA hydratase; Provisional 259 matched cddid_all.tbl CDD PRK06690 PRK06690 180659 PRK06690 acetyl-CoA C-acyltransferase. 361 matched cddid_all.tbl CDD PRK06696 PRK06696 180660 PRK06696 uridine kinase; Validated 223 matched cddid_all.tbl CDD PRK06698 PRK06698 136007 PRK06698 bifunctional 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase/phosphatase; Validated 459 matched cddid_all.tbl CDD PRK06701 PRK06701 235853 PRK06701 short chain dehydrogenase; Provisional 290 matched cddid_all.tbl CDD PRK06702 PRK06702 102505 PRK06702 bifunctional O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase. 432 matched cddid_all.tbl CDD PRK06703 PRK06703 235854 PRK06703 flavodoxin; Provisional 151 matched cddid_all.tbl CDD PRK06704 PRK06704 180663 PRK06704 RNA polymerase subunit sigma-70. 228 matched cddid_all.tbl CDD PRK06705 PRK06705 180664 PRK06705 argininosuccinate lyase; Provisional 502 matched cddid_all.tbl CDD PRK06707 PRK06707 235855 PRK06707 amidase; Provisional 536 matched cddid_all.tbl CDD PRK06710 PRK06710 180666 PRK06710 long-chain-fatty-acid--CoA ligase; Validated 563 matched cddid_all.tbl CDD PRK06714 PRK06714 168652 PRK06714 S-adenosylhomocysteine nucleosidase; Validated 236 matched cddid_all.tbl CDD PRK06718 PRK06718 180667 PRK06718 NAD(P)-binding protein. 202 matched cddid_all.tbl CDD PRK06719 PRK06719 180668 PRK06719 precorrin-2 dehydrogenase; Validated 157 matched cddid_all.tbl CDD PRK06720 PRK06720 180669 PRK06720 hypothetical protein; Provisional 169 matched cddid_all.tbl CDD PRK06722 PRK06722 180670 PRK06722 exonuclease; Provisional 281 matched cddid_all.tbl CDD PRK06724 PRK06724 180671 PRK06724 hypothetical protein; Provisional 128 matched cddid_all.tbl CDD PRK06725 PRK06725 180672 PRK06725 acetolactate synthase large subunit. 570 matched cddid_all.tbl CDD PRK06728 PRK06728 136022 PRK06728 aspartate-semialdehyde dehydrogenase; Provisional 347 matched cddid_all.tbl CDD PRK06731 PRK06731 75717 flhF flagellar biosynthesis regulator FlhF; Validated 270 matched cddid_all.tbl CDD PRK06732 PRK06732 235856 PRK06732 phosphopantothenate--cysteine ligase; Validated 229 matched cddid_all.tbl CDD PRK06733 PRK06733 180674 PRK06733 hypothetical protein; Provisional 151 matched cddid_all.tbl CDD PRK06737 PRK06737 180675 PRK06737 ACT domain-containing protein. 76 matched cddid_all.tbl CDD PRK06739 PRK06739 180676 PRK06739 pyruvate kinase; Validated 352 matched cddid_all.tbl CDD PRK06740 PRK06740 180677 PRK06740 histidinol phosphate phosphatase domain-containing protein. 331 matched cddid_all.tbl CDD PRK06742 PRK06742 102525 PRK06742 flagellar motor protein MotS; Reviewed 225 matched cddid_all.tbl CDD PRK06743 PRK06743 136027 PRK06743 flagellar motor protein MotP; Reviewed 254 matched cddid_all.tbl CDD PRK06746 PRK06746 75726 PRK06746 peptide chain release factor 2; Provisional 326 matched cddid_all.tbl CDD PRK06748 PRK06748 180678 PRK06748 hypothetical protein; Validated 83 matched cddid_all.tbl CDD PRK06749 PRK06749 168658 PRK06749 replicative DNA helicase; Provisional 428 matched cddid_all.tbl CDD PRK06751 PRK06751 168659 PRK06751 single-stranded DNA-binding protein; Provisional 173 matched cddid_all.tbl CDD PRK06752 PRK06752 168660 PRK06752 single-stranded DNA-binding protein; Validated 112 matched cddid_all.tbl CDD PRK06753 PRK06753 168661 PRK06753 hypothetical protein; Provisional 373 matched cddid_all.tbl CDD PRK06754 PRK06754 180679 mtnB methylthioribulose 1-phosphate dehydratase. 208 matched cddid_all.tbl CDD PRK06755 PRK06755 102532 PRK06755 hypothetical protein; Validated 209 matched cddid_all.tbl CDD PRK06756 PRK06756 168663 PRK06756 flavodoxin; Provisional 148 matched cddid_all.tbl CDD PRK06758 PRK06758 136035 PRK06758 hypothetical protein; Provisional 128 matched cddid_all.tbl CDD PRK06759 PRK06759 235857 PRK06759 RNA polymerase factor sigma-70; Validated 154 matched cddid_all.tbl CDD PRK06760 PRK06760 180681 PRK06760 hypothetical protein; Provisional 223 matched cddid_all.tbl CDD PRK06761 PRK06761 180682 PRK06761 hypothetical protein; Provisional 282 matched cddid_all.tbl CDD PRK06762 PRK06762 235858 PRK06762 hypothetical protein; Provisional 166 matched cddid_all.tbl CDD PRK06763 PRK06763 136040 PRK06763 F0F1 ATP synthase subunit alpha; Validated 213 matched cddid_all.tbl CDD PRK06764 PRK06764 102540 PRK06764 hypothetical protein; Provisional 105 matched cddid_all.tbl CDD PRK06765 PRK06765 235859 PRK06765 homoserine O-acetyltransferase; Provisional 389 matched cddid_all.tbl CDD PRK06767 PRK06767 180685 PRK06767 methionine gamma-lyase; Provisional 386 matched cddid_all.tbl CDD PRK06769 PRK06769 180686 PRK06769 HAD-IIIA family hydrolase. 173 matched cddid_all.tbl CDD PRK06770 PRK06770 180687 PRK06770 hypothetical protein; Provisional 180 matched cddid_all.tbl CDD PRK06771 PRK06771 180688 PRK06771 hypothetical protein; Provisional 93 matched cddid_all.tbl CDD PRK06772 PRK06772 102546 PRK06772 salicylate synthase. 434 matched cddid_all.tbl CDD PRK06774 PRK06774 180689 PRK06774 aminodeoxychorismate synthase component II. 191 matched cddid_all.tbl CDD PRK06777 PRK06777 180690 PRK06777 4-aminobutyrate--2-oxoglutarate transaminase. 421 matched cddid_all.tbl CDD PRK06778 PRK06778 235860 PRK06778 hypothetical protein; Validated 289 matched cddid_all.tbl CDD PRK06782 PRK06782 235861 PRK06782 flagellar motor switch protein; Reviewed 528 matched cddid_all.tbl CDD PRK06788 PRK06788 180693 PRK06788 flagellar motor switch protein; Validated 119 matched cddid_all.tbl CDD PRK06789 PRK06789 180694 PRK06789 flagellar motor switch protein; Validated 74 matched cddid_all.tbl CDD PRK06792 PRK06792 180695 flgD flagellar basal body rod modification protein; Validated 190 matched cddid_all.tbl CDD PRK06793 PRK06793 180696 fliI flagellar protein export ATPase FliI. 432 matched cddid_all.tbl CDD PRK06797 PRK06797 180697 flgB flagellar basal body rod protein FlgB; Reviewed 135 matched cddid_all.tbl CDD PRK06798 PRK06798 180698 fliD flagellar hook-associated protein 2. 440 matched cddid_all.tbl CDD PRK06799 PRK06799 180699 flgK flagellar hook-associated protein FlgK; Validated 431 matched cddid_all.tbl CDD PRK06800 PRK06800 180700 fliH flagellar assembly protein H; Validated 228 matched cddid_all.tbl CDD PRK06801 PRK06801 180701 PRK06801 ketose 1,6-bisphosphate aldolase. 286 matched cddid_all.tbl CDD PRK06802 PRK06802 180702 flgC flagellar basal body rod protein FlgC; Reviewed 141 matched cddid_all.tbl CDD PRK06803 PRK06803 235862 flgE flagellar basal body protein FlaE. 402 matched cddid_all.tbl CDD PRK06804 PRK06804 235863 flgA flagellar basal body P-ring formation protein FlgA. 261 matched cddid_all.tbl CDD PRK06806 PRK06806 180705 PRK06806 class II aldolase. 281 matched cddid_all.tbl CDD PRK06807 PRK06807 235864 PRK06807 3'-5' exonuclease. 313 matched cddid_all.tbl CDD PRK06811 PRK06811 180707 PRK06811 RNA polymerase factor sigma-70; Validated 189 matched cddid_all.tbl CDD PRK06813 PRK06813 168683 PRK06813 homoserine dehydrogenase; Validated 346 matched cddid_all.tbl CDD PRK06814 PRK06814 235865 PRK06814 acyl-[ACP]--phospholipid O-acyltransferase. 1140 matched cddid_all.tbl CDD PRK06815 PRK06815 180709 PRK06815 threonine/serine dehydratase. 317 matched cddid_all.tbl CDD PRK06816 PRK06816 235866 PRK06816 StlD/DarB family beta-ketosynthase. 378 matched cddid_all.tbl CDD PRK06819 PRK06819 235867 PRK06819 FliC/FljB family flagellin. 376 matched cddid_all.tbl CDD PRK06820 PRK06820 180712 PRK06820 EscN/YscN/HrcN family type III secretion system ATPase. 440 matched cddid_all.tbl CDD PRK06823 PRK06823 136070 PRK06823 ornithine cyclodeaminase family protein. 315 matched cddid_all.tbl CDD PRK06824 PRK06824 168689 PRK06824 translation initiation factor Sui1; Validated 118 matched cddid_all.tbl CDD PRK06826 PRK06826 235868 dnaE DNA polymerase III DnaE; Reviewed 1151 matched cddid_all.tbl CDD PRK06827 PRK06827 180714 PRK06827 phosphoribosylpyrophosphate synthetase; Provisional 382 matched cddid_all.tbl CDD PRK06828 PRK06828 180715 PRK06828 amidase; Provisional 491 matched cddid_all.tbl CDD PRK06830 PRK06830 235869 PRK06830 ATP-dependent 6-phosphofructokinase. 443 matched cddid_all.tbl CDD PRK06833 PRK06833 180717 PRK06833 L-fuculose-phosphate aldolase. 214 matched cddid_all.tbl CDD PRK06834 PRK06834 235870 PRK06834 hypothetical protein; Provisional 488 matched cddid_all.tbl CDD PRK06835 PRK06835 235871 PRK06835 DNA replication protein DnaC; Validated 329 matched cddid_all.tbl CDD PRK06836 PRK06836 180720 PRK06836 pyridoxal phosphate-dependent aminotransferase. 394 matched cddid_all.tbl CDD PRK06837 PRK06837 180721 PRK06837 ArgE/DapE family deacylase. 427 matched cddid_all.tbl CDD PRK06839 PRK06839 168698 PRK06839 o-succinylbenzoate--CoA ligase. 496 matched cddid_all.tbl CDD PRK06840 PRK06840 235872 PRK06840 3-oxoacyl-ACP synthase. 339 matched cddid_all.tbl CDD PRK06841 PRK06841 180723 PRK06841 short chain dehydrogenase; Provisional 255 matched cddid_all.tbl CDD PRK06842 PRK06842 180724 PRK06842 Fe-S-containing hydro-lyase. 185 matched cddid_all.tbl CDD PRK06843 PRK06843 180725 PRK06843 inosine 5-monophosphate dehydrogenase; Validated 404 matched cddid_all.tbl CDD PRK06846 PRK06846 235873 PRK06846 putative deaminase; Validated 410 matched cddid_all.tbl CDD PRK06847 PRK06847 235874 PRK06847 hypothetical protein; Provisional 375 matched cddid_all.tbl CDD PRK06848 PRK06848 235875 PRK06848 cytidine deaminase. 139 matched cddid_all.tbl CDD PRK06849 PRK06849 235876 PRK06849 hypothetical protein; Provisional 389 matched cddid_all.tbl CDD PRK06850 PRK06850 235877 PRK06850 hypothetical protein; Provisional 507 matched cddid_all.tbl CDD PRK06851 PRK06851 235878 PRK06851 hypothetical protein; Provisional 367 matched cddid_all.tbl CDD PRK06852 PRK06852 180731 PRK06852 aldolase; Validated 304 matched cddid_all.tbl CDD PRK06853 PRK06853 180732 PRK06853 indolepyruvate oxidoreductase subunit beta; Reviewed 197 matched cddid_all.tbl CDD PRK06854 PRK06854 235879 PRK06854 adenylyl-sulfate reductase subunit alpha. 608 matched cddid_all.tbl CDD PRK06855 PRK06855 180734 PRK06855 pyridoxal phosphate-dependent aminotransferase. 433 matched cddid_all.tbl CDD PRK06856 PRK06856 180735 PRK06856 DNA polymerase III subunit psi; Validated 128 matched cddid_all.tbl CDD PRK06860 PRK06860 235880 PRK06860 lipid A biosynthesis lauroyl acyltransferase; Provisional 309 matched cddid_all.tbl CDD PRK06863 PRK06863 136097 PRK06863 single-stranded DNA-binding protein; Provisional 168 matched cddid_all.tbl CDD PRK06871 PRK06871 180738 PRK06871 DNA polymerase III subunit delta'; Validated 325 matched cddid_all.tbl CDD PRK06876 PRK06876 180739 PRK06876 F0F1 ATP synthase subunit C; Validated 78 matched cddid_all.tbl CDD PRK06882 PRK06882 168717 PRK06882 acetolactate synthase 3 large subunit. 574 matched cddid_all.tbl CDD PRK06886 PRK06886 180740 PRK06886 hypothetical protein; Validated 329 matched cddid_all.tbl CDD PRK06895 PRK06895 235882 PRK06895 anthranilate synthase component II. 190 matched cddid_all.tbl CDD PRK06901 PRK06901 235883 PRK06901 oxidoreductase. 322 matched cddid_all.tbl CDD PRK06904 PRK06904 136106 PRK06904 replicative DNA helicase; Validated 472 matched cddid_all.tbl CDD PRK06911 PRK06911 180742 rpsN 30S ribosomal protein S14; Reviewed 100 matched cddid_all.tbl CDD PRK06914 PRK06914 180744 PRK06914 SDR family oxidoreductase. 280 matched cddid_all.tbl CDD PRK06915 PRK06915 180745 PRK06915 peptidase. 422 matched cddid_all.tbl CDD PRK06917 PRK06917 235884 PRK06917 aspartate aminotransferase family protein. 447 matched cddid_all.tbl CDD PRK06918 PRK06918 235885 PRK06918 4-aminobutyrate aminotransferase; Reviewed 451 matched cddid_all.tbl CDD PRK06920 PRK06920 180749 dnaE DNA polymerase III subunit alpha. 1107 matched cddid_all.tbl CDD PRK06921 PRK06921 180750 PRK06921 hypothetical protein; Provisional 266 matched cddid_all.tbl CDD PRK06922 PRK06922 180751 PRK06922 class I SAM-dependent methyltransferase. 677 matched cddid_all.tbl CDD PRK06923 PRK06923 235886 PRK06923 isochorismate synthase DhbC; Validated 399 matched cddid_all.tbl CDD PRK06924 PRK06924 180753 PRK06924 (S)-benzoin forming benzil reductase. 251 matched cddid_all.tbl CDD PRK06925 PRK06925 235887 PRK06925 flagellar motor protein MotB. 230 matched cddid_all.tbl CDD PRK06926 PRK06926 180755 PRK06926 flagellar motor protein MotP; Reviewed 271 matched cddid_all.tbl CDD PRK06928 PRK06928 235888 PRK06928 pyrroline-5-carboxylate reductase; Reviewed 277 matched cddid_all.tbl CDD PRK06930 PRK06930 180757 PRK06930 positive control sigma-like factor; Validated 170 matched cddid_all.tbl CDD PRK06931 PRK06931 235889 PRK06931 diaminobutyrate--2-oxoglutarate transaminase. 459 matched cddid_all.tbl CDD PRK06932 PRK06932 235890 PRK06932 2-hydroxyacid dehydrogenase. 314 matched cddid_all.tbl CDD PRK06933 PRK06933 235891 PRK06933 YscQ/HrcQ family type III secretion apparatus protein. 308 matched cddid_all.tbl CDD PRK06934 PRK06934 180760 PRK06934 flavodoxin; Provisional 221 matched cddid_all.tbl CDD PRK06935 PRK06935 180761 PRK06935 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD. 258 matched cddid_all.tbl CDD PRK06936 PRK06936 180762 PRK06936 EscN/YscN/HrcN family type III secretion system ATPase. 439 matched cddid_all.tbl CDD PRK06937 PRK06937 180763 PRK06937 HrpE/YscL family type III secretion apparatus protein. 204 matched cddid_all.tbl CDD PRK06938 PRK06938 235892 PRK06938 diaminobutyrate--2-oxoglutarate aminotransferase; Provisional 464 matched cddid_all.tbl CDD PRK06939 PRK06939 235893 PRK06939 2-amino-3-ketobutyrate coenzyme A ligase; Provisional 397 matched cddid_all.tbl CDD PRK06940 PRK06940 180766 PRK06940 short chain dehydrogenase; Provisional 275 matched cddid_all.tbl CDD PRK06945 PRK06945 235895 flgK flagellar hook-associated protein FlgK; Validated 651 matched cddid_all.tbl CDD PRK06946 PRK06946 180770 PRK06946 lipid A biosynthesis lauroyl acyltransferase; Provisional 293 matched cddid_all.tbl CDD PRK06947 PRK06947 180771 PRK06947 SDR family oxidoreductase. 248 matched cddid_all.tbl CDD PRK06948 PRK06948 180772 PRK06948 ribonucleotide reductase-like protein; Provisional 595 matched cddid_all.tbl CDD PRK06949 PRK06949 180773 PRK06949 SDR family oxidoreductase. 258 matched cddid_all.tbl CDD PRK06953 PRK06953 180774 PRK06953 SDR family oxidoreductase. 222 matched cddid_all.tbl CDD PRK06954 PRK06954 180775 PRK06954 acetyl-CoA C-acetyltransferase. 397 matched cddid_all.tbl CDD PRK06955 PRK06955 235896 PRK06955 biotin--[acetyl-CoA-carboxylase] ligase. 300 matched cddid_all.tbl CDD PRK06958 PRK06958 180777 PRK06958 single-stranded DNA-binding protein; Provisional 182 matched cddid_all.tbl CDD PRK06964 PRK06964 235898 PRK06964 DNA polymerase III subunit delta'; Validated 342 matched cddid_all.tbl CDD PRK06965 PRK06965 180780 PRK06965 acetolactate synthase 3 catalytic subunit; Validated 587 matched cddid_all.tbl CDD PRK06973 PRK06973 180781 PRK06973 nicotinate-nucleotide adenylyltransferase. 243 matched cddid_all.tbl CDD PRK06975 PRK06975 235899 PRK06975 bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase; Reviewed 656 matched cddid_all.tbl CDD PRK06986 PRK06986 235901 fliA flagellar biosynthesis sigma factor; Validated 236 matched cddid_all.tbl CDD PRK06988 PRK06988 235902 PRK06988 formyltransferase. 312 matched cddid_all.tbl CDD PRK06991 PRK06991 235903 PRK06991 electron transport complex subunit RsxB. 270 matched cddid_all.tbl CDD PRK06995 PRK06995 235904 flhF flagellar biosynthesis protein FlhF. 484 matched cddid_all.tbl CDD PRK06996 PRK06996 235905 PRK06996 UbiH/UbiF/VisC/COQ6 family ubiquinone biosynthesis hydroxylase. 398 matched cddid_all.tbl CDD PRK06997 PRK06997 180789 PRK06997 enoyl-[acyl-carrier-protein] reductase FabI. 260 matched cddid_all.tbl CDD PRK07003 PRK07003 235906 PRK07003 DNA polymerase III subunit gamma/tau. 830 matched cddid_all.tbl CDD PRK07004 PRK07004 235907 PRK07004 replicative DNA helicase; Provisional 460 matched cddid_all.tbl CDD PRK07006 PRK07006 180792 PRK07006 isocitrate dehydrogenase; Reviewed 409 matched cddid_all.tbl CDD PRK07008 PRK07008 235908 PRK07008 long-chain-fatty-acid--CoA ligase; Validated 539 matched cddid_all.tbl CDD PRK07018 PRK07018 180794 flgA flagellar basal body P-ring formation protein FlgA. 235 matched cddid_all.tbl CDD PRK07021 PRK07021 235909 fliL flagellar basal body-associated protein FliL; Reviewed 162 matched cddid_all.tbl CDD PRK07023 PRK07023 180796 PRK07023 SDR family oxidoreductase. 243 matched cddid_all.tbl CDD PRK07024 PRK07024 235910 PRK07024 SDR family oxidoreductase. 257 matched cddid_all.tbl CDD PRK07027 PRK07027 235911 PRK07027 cobalamin biosynthesis protein CbiG; Provisional 126 matched cddid_all.tbl CDD PRK07028 PRK07028 235912 PRK07028 bifunctional hexulose-6-phosphate synthase/ribonuclease regulator; Validated 430 matched cddid_all.tbl CDD PRK07030 PRK07030 180800 PRK07030 adenosylmethionine--8-amino-7-oxononanoate transaminase; Provisional 466 matched cddid_all.tbl CDD PRK07033 PRK07033 180801 PRK07033 DotU family type VI secretion system protein. 427 matched cddid_all.tbl CDD PRK07034 PRK07034 168775 PRK07034 hypothetical protein; Provisional 536 matched cddid_all.tbl CDD PRK07035 PRK07035 180802 PRK07035 SDR family oxidoreductase. 252 matched cddid_all.tbl CDD PRK07036 PRK07036 235913 PRK07036 aminotransferase. 466 matched cddid_all.tbl CDD PRK07037 PRK07037 180803 PRK07037 extracytoplasmic-function sigma-70 factor; Validated 163 matched cddid_all.tbl CDD PRK07041 PRK07041 235914 PRK07041 SDR family oxidoreductase. 230 matched cddid_all.tbl CDD PRK07042 PRK07042 235915 PRK07042 amidase; Provisional 464 matched cddid_all.tbl CDD PRK07044 PRK07044 235916 PRK07044 aldolase II superfamily protein; Provisional 252 matched cddid_all.tbl CDD PRK07045 PRK07045 136171 PRK07045 putative monooxygenase; Reviewed 388 matched cddid_all.tbl CDD PRK07046 PRK07046 235917 PRK07046 aminotransferase; Validated 453 matched cddid_all.tbl CDD PRK07048 PRK07048 235918 PRK07048 threo-3-hydroxy-L-aspartate ammonia-lyase. 321 matched cddid_all.tbl CDD PRK07049 PRK07049 180809 PRK07049 cystathionine gamma-synthase family protein. 427 matched cddid_all.tbl CDD PRK07050 PRK07050 180810 PRK07050 cystathionine beta-lyase; Provisional 394 matched cddid_all.tbl CDD PRK07051 PRK07051 180811 PRK07051 biotin carboxyl carrier domain-containing protein. 80 matched cddid_all.tbl CDD PRK07053 PRK07053 235919 PRK07053 glutamine amidotransferase; Provisional 234 matched cddid_all.tbl CDD PRK07054 PRK07054 235920 PRK07054 isochorismate synthase. 475 matched cddid_all.tbl CDD PRK07056 PRK07056 235921 PRK07056 amidase; Provisional 454 matched cddid_all.tbl CDD PRK07058 PRK07058 235922 PRK07058 acetate/propionate family kinase. 396 matched cddid_all.tbl CDD PRK07059 PRK07059 235923 PRK07059 Long-chain-fatty-acid--CoA ligase; Validated 557 matched cddid_all.tbl CDD PRK07060 PRK07060 180817 PRK07060 short chain dehydrogenase; Provisional 245 matched cddid_all.tbl CDD PRK07062 PRK07062 180818 PRK07062 SDR family oxidoreductase. 265 matched cddid_all.tbl CDD PRK07063 PRK07063 235924 PRK07063 SDR family oxidoreductase. 260 matched cddid_all.tbl CDD PRK07064 PRK07064 180820 PRK07064 thiamine pyrophosphate-binding protein. 544 matched cddid_all.tbl CDD PRK07066 PRK07066 168796 PRK07066 L-carnitine dehydrogenase. 321 matched cddid_all.tbl CDD PRK07067 PRK07067 235925 PRK07067 L-iditol 2-dehydrogenase. 257 matched cddid_all.tbl CDD PRK07069 PRK07069 180822 PRK07069 short chain dehydrogenase; Validated 251 matched cddid_all.tbl CDD PRK07074 PRK07074 180823 PRK07074 SDR family oxidoreductase. 257 matched cddid_all.tbl CDD PRK07075 PRK07075 136191 PRK07075 isochorismate lyase. 101 matched cddid_all.tbl CDD PRK07077 PRK07077 235926 PRK07077 phosphorylase. 238 matched cddid_all.tbl CDD PRK07078 PRK07078 235927 PRK07078 hypothetical protein; Validated 759 matched cddid_all.tbl CDD PRK07079 PRK07079 235928 PRK07079 hypothetical protein; Provisional 469 matched cddid_all.tbl CDD PRK07080 PRK07080 235929 PRK07080 amino acid--[acyl-carrier-protein] ligase. 317 matched cddid_all.tbl CDD PRK07081 PRK07081 180828 PRK07081 acyl carrier protein; Provisional 83 matched cddid_all.tbl CDD PRK07084 PRK07084 180829 PRK07084 class II fructose-1,6-bisphosphate aldolase. 321 matched cddid_all.tbl CDD PRK07085 PRK07085 235930 PRK07085 diphosphate--fructose-6-phosphate 1-phosphotransferase; Provisional 555 matched cddid_all.tbl CDD PRK07088 PRK07088 180831 PRK07088 ribonucleoside-diphosphate reductase subunit alpha. 764 matched cddid_all.tbl CDD PRK07090 PRK07090 180832 PRK07090 class II aldolase/adducin domain protein; Provisional 260 matched cddid_all.tbl CDD PRK07092 PRK07092 235931 PRK07092 benzoylformate decarboxylase; Reviewed 530 matched cddid_all.tbl CDD PRK07093 PRK07093 235932 PRK07093 para-aminobenzoate synthase component I; Validated 323 matched cddid_all.tbl CDD PRK07097 PRK07097 235933 PRK07097 gluconate 5-dehydrogenase; Provisional 265 matched cddid_all.tbl CDD PRK07101 PRK07101 235934 PRK07101 hypothetical protein; Provisional 187 matched cddid_all.tbl CDD PRK07102 PRK07102 180838 PRK07102 SDR family oxidoreductase. 243 matched cddid_all.tbl CDD PRK07103 PRK07103 180839 PRK07103 polyketide beta-ketoacyl:acyl carrier protein synthase; Validated 410 matched cddid_all.tbl CDD PRK07105 PRK07105 180840 PRK07105 pyridoxamine kinase; Validated 284 matched cddid_all.tbl CDD PRK07106 PRK07106 180841 PRK07106 phosphoribosylaminoimidazolecarboxamide formyltransferase. 390 matched cddid_all.tbl CDD PRK07107 PRK07107 180842 PRK07107 IMP dehydrogenase. 502 matched cddid_all.tbl CDD PRK07108 PRK07108 180843 PRK07108 acetyl-CoA C-acyltransferase. 392 matched cddid_all.tbl CDD PRK07109 PRK07109 235935 PRK07109 short chain dehydrogenase; Provisional 334 matched cddid_all.tbl CDD PRK07110 PRK07110 235936 PRK07110 polyketide biosynthesis enoyl-CoA hydratase; Validated 249 matched cddid_all.tbl CDD PRK07111 PRK07111 235937 PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional 735 matched cddid_all.tbl CDD PRK07112 PRK07112 235938 PRK07112 enoyl-CoA hydratase/isomerase. 255 matched cddid_all.tbl CDD PRK07114 PRK07114 235939 PRK07114 bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase. 222 matched cddid_all.tbl CDD PRK07115 PRK07115 235940 PRK07115 AMP nucleosidase; Provisional 258 matched cddid_all.tbl CDD PRK07116 PRK07116 180850 PRK07116 flavodoxin; Provisional 160 matched cddid_all.tbl CDD PRK07117 PRK07117 180851 PRK07117 acyl carrier protein; Validated 79 matched cddid_all.tbl CDD PRK07118 PRK07118 235941 PRK07118 Fe-S cluster domain-containing protein. 280 matched cddid_all.tbl CDD PRK07119 PRK07119 235942 PRK07119 2-ketoisovalerate ferredoxin reductase; Validated 352 matched cddid_all.tbl CDD PRK07121 PRK07121 180854 PRK07121 FAD-binding protein. 492 matched cddid_all.tbl CDD PRK07122 PRK07122 168831 PRK07122 RNA polymerase sigma factor SigF; Reviewed 264 matched cddid_all.tbl CDD PRK07132 PRK07132 180855 PRK07132 DNA polymerase III subunit delta'; Validated 299 matched cddid_all.tbl CDD PRK07133 PRK07133 235943 PRK07133 DNA polymerase III subunits gamma and tau; Validated 725 matched cddid_all.tbl CDD PRK07135 PRK07135 235944 dnaE DNA polymerase III DnaE; Validated 973 matched cddid_all.tbl CDD PRK07139 PRK07139 235945 PRK07139 amidase; Provisional 439 matched cddid_all.tbl CDD PRK07143 PRK07143 235946 PRK07143 hypothetical protein; Provisional 279 matched cddid_all.tbl CDD PRK07152 PRK07152 235947 nadD nicotinate-nucleotide adenylyltransferase. 342 matched cddid_all.tbl CDD PRK07157 PRK07157 235948 PRK07157 acetate kinase; Provisional 400 matched cddid_all.tbl CDD PRK07159 PRK07159 235949 PRK07159 F0F1 ATP synthase subunit C; Validated 100 matched cddid_all.tbl CDD PRK07164 PRK07164 235950 PRK07164 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; Provisional 218 matched cddid_all.tbl CDD PRK07165 PRK07165 235951 PRK07165 ATP F0F1 synthase subunit alpha. 507 matched cddid_all.tbl CDD PRK07168 PRK07168 180864 PRK07168 uroporphyrin-III C-methyltransferase. 474 matched cddid_all.tbl CDD PRK07178 PRK07178 180865 PRK07178 acetyl-CoA carboxylase biotin carboxylase subunit. 472 matched cddid_all.tbl CDD PRK07179 PRK07179 180866 PRK07179 quorum-sensing autoinducer synthase. 407 matched cddid_all.tbl CDD PRK07182 PRK07182 75964 flgB flagellar basal body rod protein FlgB; Reviewed 148 matched cddid_all.tbl CDD PRK07188 PRK07188 235953 PRK07188 nicotinate phosphoribosyltransferase; Provisional 352 matched cddid_all.tbl CDD PRK07189 PRK07189 235954 PRK07189 malonate decarboxylase subunit beta; Reviewed 301 matched cddid_all.tbl CDD PRK07190 PRK07190 235955 PRK07190 FAD-binding protein. 487 matched cddid_all.tbl CDD PRK07191 PRK07191 180871 flgK flagellar hook-associated protein FlgK; Validated 456 matched cddid_all.tbl CDD PRK07192 PRK07192 235956 flgL flagellar hook-associated protein FlgL; Reviewed 305 matched cddid_all.tbl CDD PRK07194 PRK07194 235958 fliG flagellar motor switch protein G; Reviewed 334 matched cddid_all.tbl CDD PRK07196 PRK07196 180875 fliI flagellar protein export ATPase FliI. 434 matched cddid_all.tbl CDD PRK07198 PRK07198 235959 PRK07198 GTP cyclohydrolase II. 418 matched cddid_all.tbl CDD PRK07199 PRK07199 235960 PRK07199 ribose-phosphate diphosphokinase. 301 matched cddid_all.tbl CDD PRK07200 PRK07200 235961 PRK07200 aspartate/ornithine carbamoyltransferase family protein; Validated 395 matched cddid_all.tbl CDD PRK07201 PRK07201 235962 PRK07201 SDR family oxidoreductase. 657 matched cddid_all.tbl CDD PRK07203 PRK07203 235963 PRK07203 putative aminohydrolase SsnA. 442 matched cddid_all.tbl CDD PRK07204 PRK07204 235964 PRK07204 beta-ketoacyl-ACP synthase III. 329 matched cddid_all.tbl CDD PRK07205 PRK07205 235965 PRK07205 hypothetical protein; Provisional 444 matched cddid_all.tbl CDD PRK07206 PRK07206 180883 PRK07206 hypothetical protein; Provisional 416 matched cddid_all.tbl CDD PRK07207 PRK07207 235966 PRK07207 ribonucleoside-diphosphate reductase subunit alpha. 965 matched cddid_all.tbl CDD PRK07208 PRK07208 235967 PRK07208 hypothetical protein; Provisional 479 matched cddid_all.tbl CDD PRK07209 PRK07209 235968 PRK07209 ribonucleotide-diphosphate reductase subunit beta; Validated 369 matched cddid_all.tbl CDD PRK07211 PRK07211 180887 PRK07211 single-stranded DNA binding protein. 485 matched cddid_all.tbl CDD PRK07213 PRK07213 235969 PRK07213 chlorohydrolase; Provisional 375 matched cddid_all.tbl CDD PRK07217 PRK07217 235970 PRK07217 replication factor A; Reviewed 311 matched cddid_all.tbl CDD PRK07218 PRK07218 180890 PRK07218 Single-stranded DNA binding protein. 423 matched cddid_all.tbl CDD PRK07219 PRK07219 235971 PRK07219 DNA topoisomerase I; Validated 822 matched cddid_all.tbl CDD PRK07220 PRK07220 180892 PRK07220 DNA topoisomerase I; Validated 740 matched cddid_all.tbl CDD PRK07225 PRK07225 235972 PRK07225 DNA-directed RNA polymerase subunit B'; Validated 605 matched cddid_all.tbl CDD PRK07226 PRK07226 235973 PRK07226 fructose-bisphosphate aldolase; Provisional 267 matched cddid_all.tbl CDD PRK07228 PRK07228 180895 PRK07228 5'-deoxyadenosine deaminase. 445 matched cddid_all.tbl CDD PRK07229 PRK07229 235974 PRK07229 aconitate hydratase; Validated 646 matched cddid_all.tbl CDD PRK07231 PRK07231 235975 FabG-like SDR family oxidoreductase. 251 matched cddid_all.tbl CDD PRK07232 PRK07232 235976 PRK07232 bifunctional malic enzyme oxidoreductase/phosphotransacetylase; Reviewed 752 matched cddid_all.tbl CDD PRK07233 PRK07233 235977 PRK07233 hypothetical protein; Provisional 434 matched cddid_all.tbl CDD PRK07234 PRK07234 235978 PRK07234 putative monovalent cation/H+ antiporter subunit D; Reviewed 470 matched cddid_all.tbl CDD PRK07235 PRK07235 235979 PRK07235 amidase; Provisional 502 matched cddid_all.tbl CDD PRK07236 PRK07236 235980 PRK07236 hypothetical protein; Provisional 386 matched cddid_all.tbl CDD PRK07238 PRK07238 180903 PRK07238 bifunctional RNase H/acid phosphatase; Provisional 372 matched cddid_all.tbl CDD PRK07239 PRK07239 235981 PRK07239 bifunctional uroporphyrinogen-III synthetase/response regulator domain protein; Validated 381 matched cddid_all.tbl CDD PRK07246 PRK07246 180905 PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated 820 matched cddid_all.tbl CDD PRK07247 PRK07247 180906 PRK07247 3'-5' exonuclease. 195 matched cddid_all.tbl CDD PRK07248 PRK07248 168880 PRK07248 chorismate mutase. 87 matched cddid_all.tbl CDD PRK07251 PRK07251 180907 PRK07251 FAD-containing oxidoreductase. 438 matched cddid_all.tbl CDD PRK07252 PRK07252 180908 PRK07252 S1 RNA-binding domain-containing protein. 120 matched cddid_all.tbl CDD PRK07259 PRK07259 235982 PRK07259 dihydroorotate dehydrogenase. 301 matched cddid_all.tbl CDD PRK07260 PRK07260 180910 PRK07260 enoyl-CoA hydratase; Provisional 255 matched cddid_all.tbl CDD PRK07261 PRK07261 180911 PRK07261 DNA topology modulation protein. 171 matched cddid_all.tbl CDD PRK07269 PRK07269 235983 PRK07269 cystathionine gamma-synthase; Reviewed 364 matched cddid_all.tbl CDD PRK07274 PRK07274 180914 PRK07274 single-stranded DNA-binding protein; Provisional 131 matched cddid_all.tbl CDD PRK07275 PRK07275 180915 PRK07275 single-stranded DNA-binding protein; Provisional 162 matched cddid_all.tbl CDD PRK07276 PRK07276 180916 PRK07276 DNA polymerase III subunit delta'; Validated 290 matched cddid_all.tbl CDD PRK07279 PRK07279 180917 dnaE DNA polymerase III DnaE; Reviewed 1034 matched cddid_all.tbl CDD PRK07281 PRK07281 180918 PRK07281 methionyl aminopeptidase. 286 matched cddid_all.tbl CDD PRK07282 PRK07282 180919 PRK07282 acetolactate synthase large subunit. 566 matched cddid_all.tbl CDD PRK07283 PRK07283 180920 PRK07283 YlxQ-related RNA-binding protein. 98 matched cddid_all.tbl CDD PRK07308 PRK07308 180922 PRK07308 flavodoxin; Validated 146 matched cddid_all.tbl CDD PRK07309 PRK07309 235985 PRK07309 pyridoxal phosphate-dependent aminotransferase. 391 matched cddid_all.tbl CDD PRK07313 PRK07313 235986 PRK07313 phosphopantothenoylcysteine decarboxylase; Validated 182 matched cddid_all.tbl CDD PRK07314 PRK07314 235987 PRK07314 beta-ketoacyl-ACP synthase II. 411 matched cddid_all.tbl CDD PRK07315 PRK07315 180926 PRK07315 fructose-bisphosphate aldolase; Provisional 293 matched cddid_all.tbl CDD PRK07318 PRK07318 235988 PRK07318 dipeptidase PepV; Reviewed 466 matched cddid_all.tbl CDD PRK07322 PRK07322 180928 PRK07322 adenine phosphoribosyltransferase; Provisional 178 matched cddid_all.tbl CDD PRK07324 PRK07324 235989 PRK07324 transaminase; Validated 373 matched cddid_all.tbl CDD PRK07326 PRK07326 235990 PRK07326 SDR family oxidoreductase. 237 matched cddid_all.tbl CDD PRK07327 PRK07327 235991 PRK07327 enoyl-CoA hydratase/isomerase family protein. 268 matched cddid_all.tbl CDD PRK07328 PRK07328 235992 PRK07328 histidinol-phosphatase; Provisional 269 matched cddid_all.tbl CDD PRK07329 PRK07329 180933 PRK07329 hypothetical protein; Provisional 246 matched cddid_all.tbl CDD PRK07331 PRK07331 235993 PRK07331 cobalt transporter CbiM. 322 matched cddid_all.tbl CDD PRK07333 PRK07333 180935 PRK07333 ubiquinone biosynthesis hydroxylase. 403 matched cddid_all.tbl CDD PRK07334 PRK07334 235994 PRK07334 threonine dehydratase; Provisional 403 matched cddid_all.tbl CDD PRK07337 PRK07337 180937 PRK07337 pyridoxal phosphate-dependent aminotransferase. 388 matched cddid_all.tbl CDD PRK07338 PRK07338 235995 PRK07338 hydrolase. 402 matched cddid_all.tbl CDD PRK07340 PRK07340 235996 PRK07340 delta(1)-pyrroline-2-carboxylate reductase family protein. 304 matched cddid_all.tbl CDD PRK07342 PRK07342 235997 PRK07342 peptide chain release factor 2; Provisional 339 matched cddid_all.tbl CDD PRK07352 PRK07352 180941 PRK07352 F0F1 ATP synthase subunit B; Validated 174 matched cddid_all.tbl CDD PRK07353 PRK07353 235999 PRK07353 F0F1 ATP synthase subunit B'; Validated 140 matched cddid_all.tbl CDD PRK07354 PRK07354 180942 PRK07354 F0F1 ATP synthase subunit C; Validated 81 matched cddid_all.tbl CDD PRK07360 PRK07360 236000 PRK07360 FO synthase subunit 2; Reviewed 371 matched cddid_all.tbl CDD PRK07362 PRK07362 180944 PRK07362 NADP-dependent isocitrate dehydrogenase. 474 matched cddid_all.tbl CDD PRK07363 PRK07363 180945 PRK07363 NADH-quinone oxidoreductase subunit M. 501 matched cddid_all.tbl CDD PRK07364 PRK07364 236001 PRK07364 FAD-dependent hydroxylase. 415 matched cddid_all.tbl CDD PRK07366 PRK07366 180947 PRK07366 LL-diaminopimelate aminotransferase. 388 matched cddid_all.tbl CDD PRK07369 PRK07369 236002 PRK07369 dihydroorotase; Provisional 418 matched cddid_all.tbl CDD PRK07370 PRK07370 180949 PRK07370 enoyl-[acyl-carrier-protein] reductase FabI. 258 matched cddid_all.tbl CDD PRK07373 PRK07373 236003 PRK07373 DNA polymerase III subunit alpha; Reviewed 449 matched cddid_all.tbl CDD PRK07374 PRK07374 168927 dnaE DNA polymerase III subunit alpha; Validated 1170 matched cddid_all.tbl CDD PRK07375 PRK07375 236004 PRK07375 Na+/H+ antiporter subunit C. 112 matched cddid_all.tbl CDD PRK07376 PRK07376 236005 PRK07376 NADH-quinone oxidoreductase subunit L. 673 matched cddid_all.tbl CDD PRK07377 PRK07377 236006 PRK07377 hypothetical protein; Provisional 184 matched cddid_all.tbl CDD PRK07390 PRK07390 236008 PRK07390 NAD(P)H-quinone oxidoreductase subunit F; Validated 613 matched cddid_all.tbl CDD PRK07394 PRK07394 168934 PRK07394 hypothetical protein; Provisional 342 matched cddid_all.tbl CDD PRK07395 PRK07395 236010 PRK07395 L-aspartate oxidase; Provisional 553 matched cddid_all.tbl CDD PRK07396 PRK07396 180958 PRK07396 dihydroxynaphthoic acid synthetase; Validated 273 matched cddid_all.tbl CDD PRK07399 PRK07399 236011 PRK07399 DNA polymerase III subunit delta'; Validated 314 matched cddid_all.tbl CDD PRK07400 PRK07400 180960 PRK07400 30S ribosomal protein S1; Reviewed 318 matched cddid_all.tbl CDD PRK07402 PRK07402 180961 PRK07402 precorrin-6Y C5,15-methyltransferase subunit CbiT. 196 matched cddid_all.tbl CDD PRK07403 PRK07403 180962 PRK07403 type I glyceraldehyde-3-phosphate dehydrogenase. 337 matched cddid_all.tbl CDD PRK07405 PRK07405 180963 PRK07405 RNA polymerase sigma factor SigD; Validated 317 matched cddid_all.tbl CDD PRK07406 PRK07406 236012 PRK07406 RNA polymerase sigma factor RpoD; Validated 373 matched cddid_all.tbl CDD PRK07408 PRK07408 180965 PRK07408 RNA polymerase sigma factor SigF; Reviewed 256 matched cddid_all.tbl CDD PRK07411 PRK07411 180967 PRK07411 molybdopterin-synthase adenylyltransferase MoeB. 390 matched cddid_all.tbl CDD PRK07413 PRK07413 180968 PRK07413 cob(I)yrinic acid a,c-diamide adenosyltransferase. 382 matched cddid_all.tbl CDD PRK07414 PRK07414 168945 PRK07414 P-loop NTPase family protein. 178 matched cddid_all.tbl CDD PRK07415 PRK07415 180969 PRK07415 NAD(P)H-quinone oxidoreductase subunit H; Validated 394 matched cddid_all.tbl CDD PRK07417 PRK07417 180970 PRK07417 prephenate/arogenate dehydrogenase. 279 matched cddid_all.tbl CDD PRK07418 PRK07418 236014 PRK07418 acetolactate synthase large subunit. 616 matched cddid_all.tbl CDD PRK07419 PRK07419 236015 PRK07419 2-carboxy-1,4-naphthoquinone phytyltransferase. 304 matched cddid_all.tbl CDD PRK07424 PRK07424 236016 PRK07424 bifunctional sterol desaturase/short chain dehydrogenase; Validated 406 matched cddid_all.tbl CDD PRK07429 PRK07429 180975 PRK07429 phosphoribulokinase; Provisional 327 matched cddid_all.tbl CDD PRK07431 PRK07431 236018 PRK07431 aspartate kinase; Provisional 587 matched cddid_all.tbl CDD PRK07432 PRK07432 180977 PRK07432 S-methyl-5'-thioadenosine phosphorylase. 290 matched cddid_all.tbl CDD PRK07445 PRK07445 236019 PRK07445 O-succinylbenzoic acid--CoA ligase; Reviewed 452 matched cddid_all.tbl CDD PRK07451 PRK07451 236021 PRK07451 translation initiation factor. 115 matched cddid_all.tbl CDD PRK07454 PRK07454 180984 PRK07454 SDR family oxidoreductase. 241 matched cddid_all.tbl CDD PRK07455 PRK07455 180985 PRK07455 bifunctional 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxy-phosphogluconate aldolase. 187 matched cddid_all.tbl CDD PRK07459 PRK07459 180986 PRK07459 single-stranded DNA-binding protein; Provisional 121 matched cddid_all.tbl CDD PRK07468 PRK07468 180987 PRK07468 crotonase/enoyl-CoA hydratase family protein. 262 matched cddid_all.tbl CDD PRK07470 PRK07470 180988 PRK07470 acyl-CoA synthetase; Validated 528 matched cddid_all.tbl CDD PRK07471 PRK07471 236022 PRK07471 DNA polymerase III subunit delta'; Validated 365 matched cddid_all.tbl CDD PRK07473 PRK07473 168961 PRK07473 M20/M25/M40 family metallo-hydrolase. 376 matched cddid_all.tbl CDD PRK07474 PRK07474 236023 PRK07474 sulfur oxidation protein SoxY; Provisional 154 matched cddid_all.tbl CDD PRK07475 PRK07475 236024 PRK07475 hypothetical protein; Provisional 245 matched cddid_all.tbl CDD PRK07476 PRK07476 236025 eutB threonine dehydratase; Provisional 322 matched cddid_all.tbl CDD PRK07478 PRK07478 180993 PRK07478 short chain dehydrogenase; Provisional 254 matched cddid_all.tbl CDD PRK07480 PRK07480 180994 PRK07480 putative aminotransferase; Validated 456 matched cddid_all.tbl CDD PRK07481 PRK07481 168967 PRK07481 hypothetical protein; Provisional 449 matched cddid_all.tbl CDD PRK07482 PRK07482 236026 PRK07482 hypothetical protein; Provisional 461 matched cddid_all.tbl CDD PRK07483 PRK07483 236027 PRK07483 aspartate aminotransferase family protein. 443 matched cddid_all.tbl CDD PRK07486 PRK07486 236028 PRK07486 amidase; Provisional 484 matched cddid_all.tbl CDD PRK07487 PRK07487 236029 PRK07487 amidase; Provisional 469 matched cddid_all.tbl CDD PRK07488 PRK07488 236030 PRK07488 indoleacetamide hydrolase. 472 matched cddid_all.tbl CDD PRK07490 PRK07490 236031 PRK07490 hypothetical protein; Provisional 245 matched cddid_all.tbl CDD PRK07494 PRK07494 181001 PRK07494 UbiH/UbiF family hydroxylase. 388 matched cddid_all.tbl CDD PRK07495 PRK07495 236032 PRK07495 4-aminobutyrate--2-oxoglutarate transaminase. 425 matched cddid_all.tbl CDD PRK07500 PRK07500 236033 rpoH2 RNA polymerase factor sigma-32; Reviewed 289 matched cddid_all.tbl CDD PRK07502 PRK07502 236034 PRK07502 prephenate/arogenate dehydrogenase family protein. 307 matched cddid_all.tbl CDD PRK07503 PRK07503 181005 PRK07503 methionine gamma-lyase; Provisional 403 matched cddid_all.tbl CDD PRK07504 PRK07504 168979 PRK07504 O-succinylhomoserine sulfhydrylase; Reviewed 398 matched cddid_all.tbl CDD PRK07505 PRK07505 181006 PRK07505 hypothetical protein; Provisional 402 matched cddid_all.tbl CDD PRK07508 PRK07508 236035 PRK07508 aminodeoxychorismate synthase component I. 378 matched cddid_all.tbl CDD PRK07509 PRK07509 181008 PRK07509 crotonase/enoyl-CoA hydratase family protein. 262 matched cddid_all.tbl CDD PRK07511 PRK07511 181009 PRK07511 enoyl-CoA hydratase; Provisional 260 matched cddid_all.tbl CDD PRK07512 PRK07512 236036 PRK07512 L-aspartate oxidase; Provisional 513 matched cddid_all.tbl CDD PRK07514 PRK07514 181011 PRK07514 malonyl-CoA synthase; Validated 504 matched cddid_all.tbl CDD PRK07515 PRK07515 236037 PRK07515 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed 372 matched cddid_all.tbl CDD PRK07516 PRK07516 181013 PRK07516 thiolase domain-containing protein. 389 matched cddid_all.tbl CDD PRK07521 PRK07521 236038 flgK flagellar hook-associated protein FlgK; Validated 483 matched cddid_all.tbl CDD PRK07522 PRK07522 236039 PRK07522 acetylornithine deacetylase; Provisional 385 matched cddid_all.tbl CDD PRK07523 PRK07523 236040 PRK07523 gluconate 5-dehydrogenase; Provisional 255 matched cddid_all.tbl CDD PRK07524 PRK07524 236041 PRK07524 5-guanidino-2-oxopentanoate decarboxylase. 535 matched cddid_all.tbl CDD PRK07525 PRK07525 236042 PRK07525 sulfoacetaldehyde acetyltransferase; Validated 588 matched cddid_all.tbl CDD PRK07529 PRK07529 236043 PRK07529 AMP-binding domain protein; Validated 632 matched cddid_all.tbl CDD PRK07530 PRK07530 181018 PRK07530 3-hydroxybutyryl-CoA dehydrogenase; Validated 292 matched cddid_all.tbl CDD PRK07531 PRK07531 236044 PRK07531 carnitine 3-dehydrogenase. 495 matched cddid_all.tbl CDD PRK07533 PRK07533 181020 PRK07533 enoyl-[acyl-carrier-protein] reductase FabI. 258 matched cddid_all.tbl CDD PRK07534 PRK07534 236045 PRK07534 betaine--homocysteine S-methyltransferase. 336 matched cddid_all.tbl CDD PRK07535 PRK07535 181022 PRK07535 methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase; Validated 261 matched cddid_all.tbl CDD PRK07538 PRK07538 236046 PRK07538 hypothetical protein; Provisional 413 matched cddid_all.tbl CDD PRK07539 PRK07539 181024 PRK07539 NADH-quinone oxidoreductase subunit NuoE. 154 matched cddid_all.tbl CDD PRK07544 PRK07544 181025 PRK07544 branched-chain amino acid aminotransferase; Validated 292 matched cddid_all.tbl CDD PRK07546 PRK07546 169002 PRK07546 hypothetical protein; Provisional 209 matched cddid_all.tbl CDD PRK07550 PRK07550 181026 PRK07550 aminotransferase. 386 matched cddid_all.tbl CDD PRK07558 PRK07558 181027 PRK07558 F0F1 ATP synthase subunit C; Validated 74 matched cddid_all.tbl CDD PRK07559 PRK07559 181028 PRK07559 2'-deoxycytidine 5'-triphosphate deaminase; Provisional 365 matched cddid_all.tbl CDD PRK07560 PRK07560 236047 PRK07560 elongation factor EF-2; Reviewed 731 matched cddid_all.tbl CDD PRK07561 PRK07561 236048 PRK07561 DNA topoisomerase I subunit omega; Validated 859 matched cddid_all.tbl CDD PRK07562 PRK07562 236049 PRK07562 vitamin B12-dependent ribonucleotide reductase. 1220 matched cddid_all.tbl CDD PRK07564 PRK07564 236050 PRK07564 phosphoglucomutase; Validated 543 matched cddid_all.tbl CDD PRK07565 PRK07565 236051 PRK07565 dihydroorotate dehydrogenase-like protein. 334 matched cddid_all.tbl CDD PRK07566 PRK07566 236052 PRK07566 chlorophyll synthase ChlG. 314 matched cddid_all.tbl CDD PRK07567 PRK07567 181035 PRK07567 glutamine amidotransferase; Provisional 242 matched cddid_all.tbl CDD PRK07568 PRK07568 181036 PRK07568 pyridoxal phosphate-dependent aminotransferase. 397 matched cddid_all.tbl CDD PRK07569 PRK07569 181037 PRK07569 bidirectional hydrogenase complex protein HoxU; Validated 234 matched cddid_all.tbl CDD PRK07570 PRK07570 181038 PRK07570 succinate dehydrogenase/fumarate reductase iron-sulfur subunit; Validated 250 matched cddid_all.tbl CDD PRK07571 PRK07571 236053 PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed 169 matched cddid_all.tbl CDD PRK07572 PRK07572 181039 PRK07572 cytosine deaminase; Validated 426 matched cddid_all.tbl CDD PRK07573 PRK07573 236054 sdhA fumarate reductase/succinate dehydrogenase flavoprotein subunit. 640 matched cddid_all.tbl CDD PRK07574 PRK07574 181041 PRK07574 NAD-dependent formate dehydrogenase. 385 matched cddid_all.tbl CDD PRK07575 PRK07575 236055 PRK07575 dihydroorotase; Provisional 438 matched cddid_all.tbl CDD PRK07576 PRK07576 236056 PRK07576 short chain dehydrogenase; Provisional 264 matched cddid_all.tbl CDD PRK07577 PRK07577 181044 PRK07577 SDR family oxidoreductase. 234 matched cddid_all.tbl CDD PRK07578 PRK07578 236057 PRK07578 short chain dehydrogenase; Provisional 199 matched cddid_all.tbl CDD PRK07579 PRK07579 236058 PRK07579 dTDP-4-amino-4,6-dideoxyglucose formyltransferase. 245 matched cddid_all.tbl CDD PRK07580 PRK07580 236059 PRK07580 Mg-protoporphyrin IX methyl transferase; Validated 230 matched cddid_all.tbl CDD PRK07581 PRK07581 236060 PRK07581 hypothetical protein; Validated 339 matched cddid_all.tbl CDD PRK07582 PRK07582 236061 PRK07582 cystathionine gamma-lyase; Validated 366 matched cddid_all.tbl CDD PRK07583 PRK07583 236062 PRK07583 cytosine deaminase. 438 matched cddid_all.tbl CDD PRK07586 PRK07586 236063 PRK07586 acetolactate synthase large subunit. 514 matched cddid_all.tbl CDD PRK07588 PRK07588 169028 PRK07588 FAD-binding domain. 391 matched cddid_all.tbl CDD PRK07589 PRK07589 236064 PRK07589 ornithine cyclodeaminase; Validated 346 matched cddid_all.tbl CDD PRK07594 PRK07594 136438 PRK07594 EscN/YscN/HrcN family type III secretion system ATPase. 433 matched cddid_all.tbl CDD PRK07597 PRK07597 236066 secE preprotein translocase subunit SecE; Reviewed 64 matched cddid_all.tbl CDD PRK07598 PRK07598 236067 PRK07598 RNA polymerase sigma factor SigC; Validated 415 matched cddid_all.tbl CDD PRK07608 PRK07608 181057 PRK07608 UbiH/UbiF family hydroxylase. 388 matched cddid_all.tbl CDD PRK07609 PRK07609 181058 PRK07609 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated 339 matched cddid_all.tbl CDD PRK07627 PRK07627 181059 PRK07627 dihydroorotase; Provisional 425 matched cddid_all.tbl CDD PRK07630 PRK07630 236068 PRK07630 CobD/CbiB family protein; Provisional 312 matched cddid_all.tbl CDD PRK07636 PRK07636 236070 ligB ATP-dependent DNA ligase; Reviewed 275 matched cddid_all.tbl CDD PRK07638 PRK07638 236071 PRK07638 acyl-CoA synthetase; Validated 487 matched cddid_all.tbl CDD PRK07639 PRK07639 181065 PRK07639 petrobactin biosynthesis protein AsbD. 86 matched cddid_all.tbl CDD PRK07649 PRK07649 181066 PRK07649 aminodeoxychorismate/anthranilate synthase component II. 195 matched cddid_all.tbl CDD PRK07650 PRK07650 181067 PRK07650 4-amino-4-deoxychorismate lyase; Provisional 283 matched cddid_all.tbl CDD PRK07656 PRK07656 236072 PRK07656 long-chain-fatty-acid--CoA ligase; Validated 513 matched cddid_all.tbl CDD PRK07657 PRK07657 181069 PRK07657 enoyl-CoA hydratase; Provisional 260 matched cddid_all.tbl CDD PRK07658 PRK07658 181070 PRK07658 enoyl-CoA hydratase; Provisional 257 matched cddid_all.tbl CDD PRK07659 PRK07659 236073 PRK07659 enoyl-CoA hydratase; Provisional 260 matched cddid_all.tbl CDD PRK07661 PRK07661 181072 PRK07661 acetyl-CoA C-acetyltransferase. 391 matched cddid_all.tbl CDD PRK07666 PRK07666 236074 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional 239 matched cddid_all.tbl CDD PRK07667 PRK07667 169051 PRK07667 uridine kinase; Provisional 193 matched cddid_all.tbl CDD PRK07668 PRK07668 181074 PRK07668 hypothetical protein; Validated 254 matched cddid_all.tbl CDD PRK07670 PRK07670 181075 PRK07670 FliA/WhiG family RNA polymerase sigma factor. 251 matched cddid_all.tbl CDD PRK07671 PRK07671 181076 PRK07671 bifunctional cystathionine gamma-lyase/homocysteine desulfhydrase. 377 matched cddid_all.tbl CDD PRK07677 PRK07677 181077 PRK07677 short chain dehydrogenase; Provisional 252 matched cddid_all.tbl CDD PRK07678 PRK07678 181078 PRK07678 aminotransferase; Validated 451 matched cddid_all.tbl CDD PRK07679 PRK07679 181079 PRK07679 pyrroline-5-carboxylate reductase; Reviewed 279 matched cddid_all.tbl CDD PRK07680 PRK07680 181080 PRK07680 late competence protein ComER; Validated 273 matched cddid_all.tbl CDD PRK07681 PRK07681 181081 PRK07681 LL-diaminopimelate aminotransferase. 399 matched cddid_all.tbl CDD PRK07682 PRK07682 181082 PRK07682 aminotransferase. 378 matched cddid_all.tbl CDD PRK07683 PRK07683 236075 PRK07683 aminotransferase A; Validated 387 matched cddid_all.tbl CDD PRK07688 PRK07688 181084 PRK07688 thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated 339 matched cddid_all.tbl CDD PRK07691 PRK07691 181085 PRK07691 putative monovalent cation/H+ antiporter subunit D; Reviewed 496 matched cddid_all.tbl CDD PRK07695 PRK07695 181086 PRK07695 thiazole tautomerase TenI. 201 matched cddid_all.tbl CDD PRK07701 PRK07701 181087 flgL flagellar hook-associated protein FlgL; Validated 298 matched cddid_all.tbl CDD PRK07708 PRK07708 181088 PRK07708 hypothetical protein; Validated 219 matched cddid_all.tbl CDD PRK07709 PRK07709 169068 PRK07709 fructose-bisphosphate aldolase; Provisional 285 matched cddid_all.tbl CDD PRK07710 PRK07710 236076 PRK07710 acetolactate synthase large subunit. 571 matched cddid_all.tbl CDD PRK07714 PRK07714 236077 PRK07714 YlxQ family RNA-binding protein. 100 matched cddid_all.tbl CDD PRK07718 PRK07718 181090 fliL flagellar basal body-associated protein FliL; Reviewed 142 matched cddid_all.tbl CDD PRK07720 PRK07720 181091 fliJ flagellar biosynthesis chaperone FliJ. 146 matched cddid_all.tbl CDD PRK07721 PRK07721 181092 fliI flagellar protein export ATPase FliI. 438 matched cddid_all.tbl CDD PRK07726 PRK07726 236078 PRK07726 DNA topoisomerase 3. 658 matched cddid_all.tbl CDD PRK07729 PRK07729 236079 PRK07729 glyceraldehyde-3-phosphate dehydrogenase; Validated 343 matched cddid_all.tbl CDD PRK07734 PRK07734 236080 motB flagellar motor protein MotB; Reviewed 259 matched cddid_all.tbl CDD PRK07735 PRK07735 236081 PRK07735 NADH-quinone oxidoreductase subunit C. 430 matched cddid_all.tbl CDD PRK07737 PRK07737 236082 fliD flagellar hook-associated protein 2. 501 matched cddid_all.tbl CDD PRK07738 PRK07738 236083 PRK07738 flagellar protein FlaG; Provisional 117 matched cddid_all.tbl CDD PRK07739 PRK07739 236084 flgK flagellar hook-associated protein FlgK; Validated 507 matched cddid_all.tbl CDD PRK07740 PRK07740 236085 PRK07740 hypothetical protein; Provisional 244 matched cddid_all.tbl CDD PRK07742 PRK07742 236086 PRK07742 phosphate butyryltransferase; Validated 299 matched cddid_all.tbl CDD PRK07748 PRK07748 236087 PRK07748 3'-5' exonuclease KapD. 207 matched cddid_all.tbl CDD PRK07756 PRK07756 169084 PRK07756 NADH-quinone oxidoreductase subunit A. 122 matched cddid_all.tbl CDD PRK07757 PRK07757 236088 PRK07757 N-acetyltransferase. 152 matched cddid_all.tbl CDD PRK07758 PRK07758 181104 PRK07758 hypothetical protein; Provisional 95 matched cddid_all.tbl CDD PRK07764 PRK07764 236090 PRK07764 DNA polymerase III subunits gamma and tau; Validated 824 matched cddid_all.tbl CDD PRK07765 PRK07765 181107 PRK07765 aminodeoxychorismate/anthranilate synthase component II. 214 matched cddid_all.tbl CDD PRK07768 PRK07768 236091 PRK07768 long-chain-fatty-acid--CoA ligase; Validated 545 matched cddid_all.tbl CDD PRK07769 PRK07769 181109 PRK07769 long-chain-fatty-acid--CoA ligase; Validated 631 matched cddid_all.tbl CDD PRK07772 PRK07772 236092 PRK07772 single-stranded DNA-binding protein; Provisional 186 matched cddid_all.tbl CDD PRK07773 PRK07773 236093 PRK07773 replicative DNA helicase; Validated 886 matched cddid_all.tbl CDD PRK07774 PRK07774 236094 PRK07774 SDR family oxidoreductase. 250 matched cddid_all.tbl CDD PRK07775 PRK07775 181113 PRK07775 SDR family oxidoreductase. 274 matched cddid_all.tbl CDD PRK07777 PRK07777 236095 PRK07777 putative succinyldiaminopimelate transaminase DapC. 387 matched cddid_all.tbl CDD PRK07785 PRK07785 181115 PRK07785 NADH dehydrogenase subunit C; Provisional 235 matched cddid_all.tbl CDD PRK07786 PRK07786 169098 PRK07786 long-chain-fatty-acid--CoA ligase; Validated 542 matched cddid_all.tbl CDD PRK07787 PRK07787 236096 PRK07787 acyl-CoA synthetase; Validated 471 matched cddid_all.tbl CDD PRK07788 PRK07788 236097 PRK07788 acyl-CoA synthetase; Validated 549 matched cddid_all.tbl CDD PRK07789 PRK07789 236098 PRK07789 acetolactate synthase 1 catalytic subunit; Validated 612 matched cddid_all.tbl CDD PRK07791 PRK07791 236099 PRK07791 short chain dehydrogenase; Provisional 286 matched cddid_all.tbl CDD PRK07792 PRK07792 181120 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional 306 matched cddid_all.tbl CDD PRK07798 PRK07798 236100 PRK07798 acyl-CoA synthetase; Validated 533 matched cddid_all.tbl CDD PRK07799 PRK07799 181122 PRK07799 crotonase/enoyl-CoA hydratase family protein. 263 matched cddid_all.tbl CDD PRK07801 PRK07801 181123 PRK07801 acetyl-CoA C-acetyltransferase. 382 matched cddid_all.tbl CDD PRK07803 PRK07803 236101 sdhA succinate dehydrogenase flavoprotein subunit; Reviewed 626 matched cddid_all.tbl CDD PRK07804 PRK07804 236102 PRK07804 L-aspartate oxidase; Provisional 541 matched cddid_all.tbl CDD PRK07806 PRK07806 181126 PRK07806 SDR family oxidoreductase. 248 matched cddid_all.tbl CDD PRK07807 PRK07807 181127 PRK07807 GuaB1 family IMP dehydrogenase-related protein. 479 matched cddid_all.tbl CDD PRK07810 PRK07810 236103 PRK07810 O-succinylhomoserine sulfhydrylase; Provisional 403 matched cddid_all.tbl CDD PRK07811 PRK07811 236104 PRK07811 cystathionine gamma-synthase; Provisional 388 matched cddid_all.tbl CDD PRK07812 PRK07812 236105 PRK07812 O-acetylhomoserine aminocarboxypropyltransferase; Validated 436 matched cddid_all.tbl CDD PRK07814 PRK07814 181131 PRK07814 SDR family oxidoreductase. 263 matched cddid_all.tbl CDD PRK07819 PRK07819 181133 PRK07819 3-hydroxybutyryl-CoA dehydrogenase; Validated 286 matched cddid_all.tbl CDD PRK07823 PRK07823 236107 PRK07823 S-methyl-5'-thioadenosine phosphorylase. 264 matched cddid_all.tbl CDD PRK07824 PRK07824 236108 PRK07824 o-succinylbenzoate--CoA ligase. 358 matched cddid_all.tbl CDD PRK07825 PRK07825 181136 PRK07825 short chain dehydrogenase; Provisional 273 matched cddid_all.tbl CDD PRK07827 PRK07827 236109 PRK07827 enoyl-CoA hydratase family protein. 260 matched cddid_all.tbl CDD PRK07831 PRK07831 236110 PRK07831 SDR family oxidoreductase. 262 matched cddid_all.tbl CDD PRK07832 PRK07832 181139 PRK07832 SDR family oxidoreductase. 272 matched cddid_all.tbl CDD PRK07843 PRK07843 236111 PRK07843 3-oxosteroid 1-dehydrogenase. 557 matched cddid_all.tbl CDD PRK07845 PRK07845 236112 PRK07845 flavoprotein disulfide reductase; Reviewed 466 matched cddid_all.tbl CDD PRK07846 PRK07846 181142 PRK07846 mycothione reductase; Reviewed 451 matched cddid_all.tbl CDD PRK07849 PRK07849 236114 PRK07849 aminodeoxychorismate lyase. 292 matched cddid_all.tbl CDD PRK07850 PRK07850 181145 PRK07850 steroid 3-ketoacyl-CoA thiolase. 387 matched cddid_all.tbl CDD PRK07851 PRK07851 181146 PRK07851 acetyl-CoA C-acetyltransferase. 406 matched cddid_all.tbl CDD PRK07854 PRK07854 236115 PRK07854 enoyl-CoA hydratase; Provisional 243 matched cddid_all.tbl CDD PRK07855 PRK07855 181147 PRK07855 lipid-transfer protein; Provisional 386 matched cddid_all.tbl CDD PRK07856 PRK07856 236116 PRK07856 SDR family oxidoreductase. 252 matched cddid_all.tbl CDD PRK07857 PRK07857 236117 PRK07857 chorismate mutase. 106 matched cddid_all.tbl CDD PRK07860 PRK07860 236118 PRK07860 NADH dehydrogenase subunit G; Validated 797 matched cddid_all.tbl CDD PRK07867 PRK07867 236120 PRK07867 acyl-CoA synthetase; Validated 529 matched cddid_all.tbl CDD PRK07868 PRK07868 236121 PRK07868 acyl-CoA synthetase; Validated 994 matched cddid_all.tbl CDD PRK07869 PRK07869 181154 PRK07869 amidase; Provisional 468 matched cddid_all.tbl CDD PRK07874 PRK07874 169138 PRK07874 ATP synthase F0 subunit C. 80 matched cddid_all.tbl CDD PRK07877 PRK07877 236122 PRK07877 Rv1355c family protein. 722 matched cddid_all.tbl CDD PRK07878 PRK07878 181156 PRK07878 molybdopterin biosynthesis-like protein MoeZ; Validated 392 matched cddid_all.tbl CDD PRK07883 PRK07883 236123 PRK07883 DEDD exonuclease domain-containing protein. 557 matched cddid_all.tbl CDD PRK07889 PRK07889 236124 PRK07889 enoyl-[acyl-carrier-protein] reductase FabI. 256 matched cddid_all.tbl CDD PRK07890 PRK07890 181159 PRK07890 short chain dehydrogenase; Provisional 258 matched cddid_all.tbl CDD PRK07899 PRK07899 236126 rpsA 30S ribosomal protein S1; Reviewed 486 matched cddid_all.tbl CDD PRK07904 PRK07904 181162 PRK07904 decaprenylphospho-beta-D-erythro-pentofuranosid-2-ulose 2-reductase. 253 matched cddid_all.tbl CDD PRK07906 PRK07906 181163 PRK07906 hypothetical protein; Provisional 426 matched cddid_all.tbl CDD PRK07907 PRK07907 236127 PRK07907 hypothetical protein; Provisional 449 matched cddid_all.tbl CDD PRK07908 PRK07908 236128 PRK07908 threonine-phosphate decarboxylase. 349 matched cddid_all.tbl CDD PRK07910 PRK07910 236129 PRK07910 beta-ketoacyl-ACP synthase. 418 matched cddid_all.tbl CDD PRK07912 PRK07912 169151 PRK07912 salicylate synthase. 449 matched cddid_all.tbl CDD PRK07914 PRK07914 236130 PRK07914 hypothetical protein; Reviewed 320 matched cddid_all.tbl CDD PRK07920 PRK07920 236131 PRK07920 lipid A biosynthesis lauroyl acyltransferase; Provisional 298 matched cddid_all.tbl CDD PRK07921 PRK07921 181169 PRK07921 RNA polymerase sigma factor SigB; Reviewed 324 matched cddid_all.tbl CDD PRK07922 PRK07922 236132 PRK07922 amino-acid N-acetyltransferase. 169 matched cddid_all.tbl CDD PRK07928 PRK07928 181171 PRK07928 NADH dehydrogenase subunit A; Validated 119 matched cddid_all.tbl CDD PRK07933 PRK07933 236133 PRK07933 dTMP kinase. 213 matched cddid_all.tbl CDD PRK07937 PRK07937 181173 PRK07937 lipid-transfer protein; Provisional 352 matched cddid_all.tbl CDD PRK07938 PRK07938 181174 PRK07938 enoyl-CoA hydratase family protein. 249 matched cddid_all.tbl CDD PRK07940 PRK07940 236134 PRK07940 DNA polymerase III subunit delta'; Validated 394 matched cddid_all.tbl CDD PRK07942 PRK07942 181176 PRK07942 DNA polymerase III subunit epsilon; Provisional 232 matched cddid_all.tbl CDD PRK07945 PRK07945 236135 PRK07945 PHP domain-containing protein. 335 matched cddid_all.tbl CDD PRK07946 PRK07946 236136 PRK07946 putative monovalent cation/H+ antiporter subunit C; Reviewed 163 matched cddid_all.tbl CDD PRK07948 PRK07948 181179 PRK07948 putative monovalent cation/H+ antiporter subunit F; Reviewed 86 matched cddid_all.tbl CDD PRK07952 PRK07952 181180 PRK07952 DNA replication protein DnaC; Validated 244 matched cddid_all.tbl CDD PRK07956 PRK07956 236137 ligA NAD-dependent DNA ligase LigA; Validated 665 matched cddid_all.tbl CDD PRK07960 PRK07960 181182 fliI flagellum-specific ATP synthase FliI. 455 matched cddid_all.tbl CDD PRK07963 PRK07963 181183 fliN flagellar motor switch protein FliN; Validated 137 matched cddid_all.tbl CDD PRK07967 PRK07967 181184 PRK07967 beta-ketoacyl-ACP synthase I. 406 matched cddid_all.tbl CDD PRK07979 PRK07979 181185 PRK07979 acetolactate synthase 3 large subunit. 574 matched cddid_all.tbl CDD PRK07983 PRK07983 181186 PRK07983 exodeoxyribonuclease X; Provisional 219 matched cddid_all.tbl CDD PRK07984 PRK07984 181187 PRK07984 enoyl-ACP reductase FabI. 262 matched cddid_all.tbl CDD PRK07985 PRK07985 181188 PRK07985 SDR family oxidoreductase. 294 matched cddid_all.tbl CDD PRK07986 PRK07986 181189 PRK07986 adenosylmethionine--8-amino-7-oxononanoate transaminase; Validated 428 matched cddid_all.tbl CDD PRK07993 PRK07993 181190 PRK07993 DNA polymerase III subunit delta'; Validated 334 matched cddid_all.tbl CDD PRK07994 PRK07994 236138 PRK07994 DNA polymerase III subunits gamma and tau; Validated 647 matched cddid_all.tbl CDD PRK07998 PRK07998 181192 gatY class II aldolase. 283 matched cddid_all.tbl CDD PRK08005 PRK08005 169179 PRK08005 ribulose-phosphate 3 epimerase family protein. 210 matched cddid_all.tbl CDD PRK08006 PRK08006 181193 PRK08006 replicative DNA helicase DnaB. 471 matched cddid_all.tbl CDD PRK08007 PRK08007 181194 PRK08007 aminodeoxychorismate synthase component 2. 187 matched cddid_all.tbl CDD PRK08008 PRK08008 181195 caiC putative crotonobetaine/carnitine-CoA ligase; Validated 517 matched cddid_all.tbl CDD PRK08010 PRK08010 181196 PRK08010 pyridine nucleotide-disulfide oxidoreductase; Provisional 441 matched cddid_all.tbl CDD PRK08013 PRK08013 236139 PRK08013 oxidoreductase; Provisional 400 matched cddid_all.tbl CDD PRK08017 PRK08017 181198 PRK08017 SDR family oxidoreductase. 256 matched cddid_all.tbl CDD PRK08020 PRK08020 181199 ubiF 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Reviewed 391 matched cddid_all.tbl CDD PRK08025 PRK08025 181200 PRK08025 kdo(2)-lipid IV(A) palmitoleoyltransferase. 305 matched cddid_all.tbl CDD PRK08026 PRK08026 236140 PRK08026 FliC/FljB family flagellin. 529 matched cddid_all.tbl CDD PRK08027 PRK08027 181202 flgL flagellar hook-filament junction protein FlgL. 317 matched cddid_all.tbl CDD PRK08032 PRK08032 236141 fliD flagellar capping protein; Reviewed 462 matched cddid_all.tbl CDD PRK08035 PRK08035 181204 PRK08035 YscQ/HrcQ family type III secretion apparatus protein. 323 matched cddid_all.tbl CDD PRK08040 PRK08040 181205 PRK08040 putative semialdehyde dehydrogenase; Provisional 336 matched cddid_all.tbl CDD PRK08042 PRK08042 181206 PRK08042 formate hydrogenlyase subunit 3; Reviewed 593 matched cddid_all.tbl CDD PRK08043 PRK08043 181207 PRK08043 bifunctional acyl-ACP--phospholipid O-acyltransferase/long-chain-fatty-acid--ACP ligase. 718 matched cddid_all.tbl CDD PRK08044 PRK08044 169193 PRK08044 allantoinase AllB. 449 matched cddid_all.tbl CDD PRK08045 PRK08045 169194 PRK08045 cystathionine gamma-synthase; Provisional 386 matched cddid_all.tbl CDD PRK08049 PRK08049 181208 PRK08049 F0F1 ATP synthase subunit I; Validated 124 matched cddid_all.tbl CDD PRK08051 PRK08051 236142 fre FMN reductase; Validated 232 matched cddid_all.tbl CDD PRK08055 PRK08055 236143 PRK08055 chorismate mutase; Provisional 181 matched cddid_all.tbl CDD PRK08057 PRK08057 236144 PRK08057 cobalt-precorrin-6x reductase; Reviewed 248 matched cddid_all.tbl CDD PRK08058 PRK08058 181214 PRK08058 DNA polymerase III subunit delta'; Validated 329 matched cddid_all.tbl CDD PRK08059 PRK08059 181215 PRK08059 general stress protein 13; Validated 123 matched cddid_all.tbl CDD PRK08061 PRK08061 181216 rpsN type Z 30S ribosomal protein S14. 61 matched cddid_all.tbl CDD PRK08063 PRK08063 236145 PRK08063 enoyl-[acyl-carrier-protein] reductase FabL. 250 matched cddid_all.tbl CDD PRK08064 PRK08064 236146 PRK08064 cystathionine beta-lyase MetC. 390 matched cddid_all.tbl CDD PRK08068 PRK08068 181219 PRK08068 transaminase; Reviewed 389 matched cddid_all.tbl CDD PRK08071 PRK08071 236147 PRK08071 L-aspartate oxidase; Provisional 510 matched cddid_all.tbl CDD PRK08073 PRK08073 181222 flgL flagellar hook-associated protein 3. 287 matched cddid_all.tbl CDD PRK08074 PRK08074 236148 PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated 928 matched cddid_all.tbl CDD PRK08084 PRK08084 181224 PRK08084 DnaA inactivator Hda. 235 matched cddid_all.tbl CDD PRK08085 PRK08085 181225 PRK08085 gluconate 5-dehydrogenase; Provisional 254 matched cddid_all.tbl CDD PRK08087 PRK08087 181226 PRK08087 L-fuculose-phosphate aldolase. 215 matched cddid_all.tbl CDD PRK08088 PRK08088 236149 PRK08088 4-aminobutyrate--2-oxoglutarate transaminase. 425 matched cddid_all.tbl CDD PRK08091 PRK08091 169215 PRK08091 ribulose-phosphate 3-epimerase; Validated 228 matched cddid_all.tbl CDD PRK08097 PRK08097 236150 ligB NAD-dependent DNA ligase LigB. 562 matched cddid_all.tbl CDD PRK08099 PRK08099 236151 PRK08099 multifunctional transcriptional regulator/nicotinamide-nucleotide adenylyltransferase/ribosylnicotinamide kinase NadR. 399 matched cddid_all.tbl CDD PRK08105 PRK08105 181230 PRK08105 flavodoxin; Provisional 149 matched cddid_all.tbl CDD PRK08114 PRK08114 181231 PRK08114 cystathionine beta-lyase; Provisional 395 matched cddid_all.tbl CDD PRK08115 PRK08115 236152 PRK08115 vitamin B12-dependent ribonucleotide reductase. 858 matched cddid_all.tbl CDD PRK08116 PRK08116 236153 PRK08116 hypothetical protein; Validated 268 matched cddid_all.tbl CDD PRK08117 PRK08117 181234 PRK08117 aspartate aminotransferase family protein. 433 matched cddid_all.tbl CDD PRK08118 PRK08118 181235 PRK08118 DNA topology modulation protein. 167 matched cddid_all.tbl CDD PRK08119 PRK08119 236154 PRK08119 flagellar motor switch protein; Validated 382 matched cddid_all.tbl CDD PRK08123 PRK08123 236155 PRK08123 histidinol-phosphatase HisJ. 270 matched cddid_all.tbl CDD PRK08124 PRK08124 181238 PRK08124 flagellar motor protein MotA; Validated 263 matched cddid_all.tbl CDD PRK08125 PRK08125 236156 PRK08125 bifunctional UDP-4-amino-4-deoxy-L-arabinose formyltransferase/UDP-glucuronic acid oxidase ArnA. 660 matched cddid_all.tbl CDD PRK08126 PRK08126 236157 PRK08126 hypothetical protein; Provisional 432 matched cddid_all.tbl CDD PRK08130 PRK08130 181241 PRK08130 putative aldolase; Validated 213 matched cddid_all.tbl CDD PRK08131 PRK08131 181242 PRK08131 3-oxoadipyl-CoA thiolase. 401 matched cddid_all.tbl CDD PRK08132 PRK08132 236158 PRK08132 FAD-dependent oxidoreductase; Provisional 547 matched cddid_all.tbl CDD PRK08133 PRK08133 181244 PRK08133 O-succinylhomoserine sulfhydrylase; Validated 390 matched cddid_all.tbl CDD PRK08134 PRK08134 236159 PRK08134 O-acetylhomoserine aminocarboxypropyltransferase; Validated 433 matched cddid_all.tbl CDD PRK08136 PRK08136 236160 PRK08136 glycosyl transferase family protein; Provisional 317 matched cddid_all.tbl CDD PRK08137 PRK08137 236161 PRK08137 amidase; Provisional 497 matched cddid_all.tbl CDD PRK08138 PRK08138 236162 PRK08138 enoyl-CoA hydratase; Provisional 261 matched cddid_all.tbl CDD PRK08139 PRK08139 181249 PRK08139 enoyl-CoA hydratase; Validated 266 matched cddid_all.tbl CDD PRK08140 PRK08140 236163 PRK08140 enoyl-CoA hydratase; Provisional 262 matched cddid_all.tbl CDD PRK08142 PRK08142 236164 PRK08142 thiolase domain-containing protein. 388 matched cddid_all.tbl CDD PRK08147 PRK08147 236165 flgK flagellar hook-associated protein FlgK; Validated 547 matched cddid_all.tbl CDD PRK08149 PRK08149 236166 PRK08149 FliI/YscN family ATPase. 428 matched cddid_all.tbl CDD PRK08150 PRK08150 181254 PRK08150 crotonase/enoyl-CoA hydratase family protein. 255 matched cddid_all.tbl CDD PRK08153 PRK08153 181255 PRK08153 pyridoxal phosphate-dependent aminotransferase. 369 matched cddid_all.tbl CDD PRK08154 PRK08154 236167 PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed 309 matched cddid_all.tbl CDD PRK08155 PRK08155 181257 PRK08155 acetolactate synthase large subunit. 564 matched cddid_all.tbl CDD PRK08156 PRK08156 236168 PRK08156 EscU/YscU/HrcU family type III secretion system export apparatus switch protein. 361 matched cddid_all.tbl CDD PRK08158 PRK08158 181259 PRK08158 YscQ/HrcQ family type III secretion apparatus protein. 303 matched cddid_all.tbl CDD PRK08159 PRK08159 181260 PRK08159 enoyl-[acyl-carrier-protein] reductase FabI. 272 matched cddid_all.tbl CDD PRK08162 PRK08162 236169 PRK08162 acyl-CoA synthetase; Validated 545 matched cddid_all.tbl CDD PRK08163 PRK08163 181262 PRK08163 3-hydroxybenzoate 6-monooxygenase. 396 matched cddid_all.tbl CDD PRK08168 PRK08168 236171 PRK08168 NADH-quinone oxidoreductase subunit L. 516 matched cddid_all.tbl CDD PRK08170 PRK08170 181265 PRK08170 acetyl-CoA C-acetyltransferase. 426 matched cddid_all.tbl CDD PRK08172 PRK08172 181266 PRK08172 acyl carrier protein. 82 matched cddid_all.tbl CDD PRK08173 PRK08173 236172 PRK08173 DNA topoisomerase III; Validated 862 matched cddid_all.tbl CDD PRK08175 PRK08175 181268 PRK08175 aminotransferase; Validated 395 matched cddid_all.tbl CDD PRK08176 PRK08176 181269 pdxK pyridoxine/pyridoxal/pyridoxamine kinase. 281 matched cddid_all.tbl CDD PRK08177 PRK08177 236173 PRK08177 SDR family oxidoreductase. 225 matched cddid_all.tbl CDD PRK08178 PRK08178 236174 PRK08178 acetolactate synthase 1 small subunit. 96 matched cddid_all.tbl CDD PRK08180 PRK08180 236175 PRK08180 feruloyl-CoA synthase; Reviewed 614 matched cddid_all.tbl CDD PRK08181 PRK08181 136670 PRK08181 transposase; Validated 269 matched cddid_all.tbl CDD PRK08182 PRK08182 169261 PRK08182 single-stranded DNA-binding protein; Provisional 148 matched cddid_all.tbl CDD PRK08183 PRK08183 236176 PRK08183 NADH:ubiquinone oxidoreductase subunit NDUFA12. 133 matched cddid_all.tbl CDD PRK08185 PRK08185 181275 PRK08185 hypothetical protein; Provisional 283 matched cddid_all.tbl CDD PRK08186 PRK08186 236177 PRK08186 allophanate hydrolase; Provisional 600 matched cddid_all.tbl CDD PRK08187 PRK08187 236178 PRK08187 pyruvate kinase; Validated 493 matched cddid_all.tbl CDD PRK08190 PRK08190 236180 PRK08190 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated 466 matched cddid_all.tbl CDD PRK08192 PRK08192 169269 PRK08192 aspartate carbamoyltransferase; Provisional 338 matched cddid_all.tbl CDD PRK08193 PRK08193 236181 araD L-ribulose-5-phosphate 4-epimerase AraD. 231 matched cddid_all.tbl CDD PRK08194 PRK08194 181281 PRK08194 tartrate dehydrogenase; Provisional 352 matched cddid_all.tbl CDD PRK08195 PRK08195 181282 PRK08195 4-hyroxy-2-oxovalerate/4-hydroxy-2-oxopentanoic acid aldolase,; Validated 337 matched cddid_all.tbl CDD PRK08197 PRK08197 181283 PRK08197 threonine synthase; Validated 394 matched cddid_all.tbl CDD PRK08199 PRK08199 181285 PRK08199 thiamine pyrophosphate protein; Validated 557 matched cddid_all.tbl CDD PRK08201 PRK08201 169276 PRK08201 dipeptidase. 456 matched cddid_all.tbl CDD PRK08202 PRK08202 236183 PRK08202 purine nucleoside phosphorylase; Provisional 272 matched cddid_all.tbl CDD PRK08203 PRK08203 236184 PRK08203 hydroxydechloroatrazine ethylaminohydrolase; Reviewed 451 matched cddid_all.tbl CDD PRK08204 PRK08204 181288 PRK08204 hypothetical protein; Provisional 449 matched cddid_all.tbl CDD PRK08206 PRK08206 236186 PRK08206 diaminopropionate ammonia-lyase; Provisional 399 matched cddid_all.tbl CDD PRK08207 PRK08207 236187 PRK08207 coproporphyrinogen III oxidase; Provisional 488 matched cddid_all.tbl CDD PRK08208 PRK08208 181292 PRK08208 coproporphyrinogen III oxidase family protein. 430 matched cddid_all.tbl CDD PRK08210 PRK08210 236188 PRK08210 aspartate kinase I; Reviewed 403 matched cddid_all.tbl CDD PRK08213 PRK08213 181295 PRK08213 gluconate 5-dehydrogenase; Provisional 259 matched cddid_all.tbl CDD PRK08215 PRK08215 181296 PRK08215 RNA polymerase sporulation sigma factor SigG. 258 matched cddid_all.tbl CDD PRK08217 PRK08217 181297 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional 253 matched cddid_all.tbl CDD PRK08219 PRK08219 181298 PRK08219 SDR family oxidoreductase. 227 matched cddid_all.tbl CDD PRK08220 PRK08220 236190 PRK08220 2,3-dihydroxybenzoate-2,3-dehydrogenase; Validated 252 matched cddid_all.tbl CDD PRK08222 PRK08222 181301 PRK08222 hydrogenase 4 subunit H; Validated 181 matched cddid_all.tbl CDD PRK08223 PRK08223 181302 PRK08223 hypothetical protein; Validated 287 matched cddid_all.tbl CDD PRK08224 PRK08224 236191 ligC ATP-dependent DNA ligase; Reviewed 350 matched cddid_all.tbl CDD PRK08225 PRK08225 181304 PRK08225 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit; Validated 70 matched cddid_all.tbl CDD PRK08226 PRK08226 181305 PRK08226 SDR family oxidoreductase UcpA. 263 matched cddid_all.tbl CDD PRK08227 PRK08227 181306 PRK08227 3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase. 264 matched cddid_all.tbl CDD PRK08228 PRK08228 236192 PRK08228 L(+)-tartrate dehydratase subunit beta; Validated 204 matched cddid_all.tbl CDD PRK08229 PRK08229 236193 PRK08229 2-dehydropantoate 2-reductase; Provisional 341 matched cddid_all.tbl CDD PRK08230 PRK08230 181309 PRK08230 tartrate dehydratase subunit alpha; Validated 299 matched cddid_all.tbl CDD PRK08233 PRK08233 181310 PRK08233 hypothetical protein; Provisional 182 matched cddid_all.tbl CDD PRK08235 PRK08235 181311 PRK08235 acetyl-CoA C-acetyltransferase. 393 matched cddid_all.tbl CDD PRK08236 PRK08236 236194 PRK08236 hypothetical protein; Provisional 212 matched cddid_all.tbl CDD PRK08238 PRK08238 236195 PRK08238 UbiA family prenyltransferase. 479 matched cddid_all.tbl CDD PRK08241 PRK08241 236196 PRK08241 RNA polymerase subunit sigma-70. 339 matched cddid_all.tbl CDD PRK08242 PRK08242 236197 PRK08242 acetyl-CoA C-acetyltransferase. 402 matched cddid_all.tbl CDD PRK08243 PRK08243 236198 PRK08243 4-hydroxybenzoate 3-monooxygenase; Validated 392 matched cddid_all.tbl CDD PRK08244 PRK08244 236199 PRK08244 monooxygenase. 493 matched cddid_all.tbl CDD PRK08245 PRK08245 236200 PRK08245 hypothetical protein; Validated 240 matched cddid_all.tbl CDD PRK08246 PRK08246 181319 PRK08246 serine/threonine dehydratase. 310 matched cddid_all.tbl CDD PRK08247 PRK08247 181320 PRK08247 methionine biosynthesis PLP-dependent protein. 366 matched cddid_all.tbl CDD PRK08248 PRK08248 236201 PRK08248 homocysteine synthase. 431 matched cddid_all.tbl CDD PRK08249 PRK08249 236202 PRK08249 cystathionine gamma-synthase family protein. 398 matched cddid_all.tbl CDD PRK08250 PRK08250 181323 PRK08250 glutamine amidotransferase; Provisional 235 matched cddid_all.tbl CDD PRK08251 PRK08251 181324 PRK08251 SDR family oxidoreductase. 248 matched cddid_all.tbl CDD PRK08252 PRK08252 181325 PRK08252 crotonase/enoyl-CoA hydratase family protein. 254 matched cddid_all.tbl CDD PRK08255 PRK08255 236203 PRK08255 bifunctional salicylyl-CoA 5-hydroxylase/oxidoreductase. 765 matched cddid_all.tbl CDD PRK08256 PRK08256 181327 PRK08256 lipid-transfer protein; Provisional 391 matched cddid_all.tbl CDD PRK08257 PRK08257 236204 PRK08257 acetyl-CoA acetyltransferase; Validated 498 matched cddid_all.tbl CDD PRK08258 PRK08258 181329 PRK08258 enoyl-CoA hydratase family protein. 277 matched cddid_all.tbl CDD PRK08259 PRK08259 236205 PRK08259 crotonase/enoyl-CoA hydratase family protein. 254 matched cddid_all.tbl CDD PRK08260 PRK08260 236206 PRK08260 enoyl-CoA hydratase; Provisional 296 matched cddid_all.tbl CDD PRK08261 PRK08261 236207 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional 450 matched cddid_all.tbl CDD PRK08262 PRK08262 236208 PRK08262 M20 family peptidase. 486 matched cddid_all.tbl CDD PRK08263 PRK08263 181334 PRK08263 short chain dehydrogenase; Provisional 275 matched cddid_all.tbl CDD PRK08264 PRK08264 181335 PRK08264 SDR family oxidoreductase. 238 matched cddid_all.tbl CDD PRK08265 PRK08265 236209 PRK08265 short chain dehydrogenase; Provisional 261 matched cddid_all.tbl CDD PRK08266 PRK08266 181337 PRK08266 hypothetical protein; Provisional 542 matched cddid_all.tbl CDD PRK08267 PRK08267 236210 PRK08267 SDR family oxidoreductase. 260 matched cddid_all.tbl CDD PRK08268 PRK08268 236211 PRK08268 3-hydroxy-acyl-CoA dehydrogenase; Validated 507 matched cddid_all.tbl CDD PRK08269 PRK08269 181340 PRK08269 3-hydroxybutyryl-CoA dehydrogenase; Validated 314 matched cddid_all.tbl CDD PRK08270 PRK08270 236212 PRK08270 ribonucleoside triphosphate reductase. 656 matched cddid_all.tbl CDD PRK08271 PRK08271 181342 PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional 623 matched cddid_all.tbl CDD PRK08272 PRK08272 236213 PRK08272 crotonase/enoyl-CoA hydratase family protein. 302 matched cddid_all.tbl CDD PRK08273 PRK08273 181344 PRK08273 thiamine pyrophosphate protein; Provisional 597 matched cddid_all.tbl CDD PRK08274 PRK08274 236214 PRK08274 FAD-dependent tricarballylate dehydrogenase TcuA. 466 matched cddid_all.tbl CDD PRK08275 PRK08275 181346 PRK08275 putative oxidoreductase; Provisional 554 matched cddid_all.tbl CDD PRK08276 PRK08276 236215 PRK08276 long-chain-fatty-acid--CoA ligase; Validated 502 matched cddid_all.tbl CDD PRK08277 PRK08277 236216 PRK08277 D-mannonate oxidoreductase; Provisional 278 matched cddid_all.tbl CDD PRK08278 PRK08278 181349 PRK08278 SDR family oxidoreductase. 273 matched cddid_all.tbl CDD PRK08279 PRK08279 236217 PRK08279 long-chain-acyl-CoA synthetase; Validated 600 matched cddid_all.tbl CDD PRK08285 PRK08285 181352 cobH precorrin-8X methylmutase; Reviewed 208 matched cddid_all.tbl CDD PRK08286 PRK08286 181353 cbiC cobalt-precorrin-8 methylmutase. 214 matched cddid_all.tbl CDD PRK08287 PRK08287 181354 PRK08287 decarboxylating cobalt-precorrin-6B (C(15))-methyltransferase. 187 matched cddid_all.tbl CDD PRK08289 PRK08289 236219 PRK08289 glyceraldehyde-3-phosphate dehydrogenase; Reviewed 477 matched cddid_all.tbl CDD PRK08290 PRK08290 236220 PRK08290 enoyl-CoA hydratase; Provisional 288 matched cddid_all.tbl CDD PRK08291 PRK08291 236221 PRK08291 cyclodeaminase. 330 matched cddid_all.tbl CDD PRK08292 PRK08292 236222 PRK08292 AMP nucleosidase; Provisional 489 matched cddid_all.tbl CDD PRK08293 PRK08293 181359 PRK08293 3-hydroxyacyl-CoA dehydrogenase. 287 matched cddid_all.tbl CDD PRK08294 PRK08294 236223 PRK08294 phenol 2-monooxygenase; Provisional 634 matched cddid_all.tbl CDD PRK08295 PRK08295 181361 PRK08295 RNA polymerase sporulation sigma factor SigH. 208 matched cddid_all.tbl CDD PRK08296 PRK08296 181362 PRK08296 hypothetical protein; Provisional 603 matched cddid_all.tbl CDD PRK08298 PRK08298 236225 PRK08298 cytidine deaminase; Validated 136 matched cddid_all.tbl CDD PRK08299 PRK08299 236226 PRK08299 NADP-dependent isocitrate dehydrogenase. 402 matched cddid_all.tbl CDD PRK08300 PRK08300 236227 PRK08300 acetaldehyde dehydrogenase; Validated 302 matched cddid_all.tbl CDD PRK08301 PRK08301 236228 PRK08301 RNA polymerase sporulation sigma factor SigE. 234 matched cddid_all.tbl CDD PRK08303 PRK08303 236229 PRK08303 short chain dehydrogenase; Provisional 305 matched cddid_all.tbl CDD PRK08304 PRK08304 236230 PRK08304 stage V sporulation protein AD; Validated 337 matched cddid_all.tbl CDD PRK08305 PRK08305 181370 spoVFB dipicolinate synthase subunit B; Reviewed 196 matched cddid_all.tbl CDD PRK08306 PRK08306 181371 PRK08306 dipicolinate synthase subunit DpsA. 296 matched cddid_all.tbl CDD PRK08307 PRK08307 181372 PRK08307 stage III sporulation protein SpoAB; Provisional 171 matched cddid_all.tbl CDD PRK08308 PRK08308 236231 PRK08308 acyl-CoA synthetase; Validated 414 matched cddid_all.tbl CDD PRK08309 PRK08309 236232 PRK08309 short chain dehydrogenase; Provisional 177 matched cddid_all.tbl CDD PRK08310 PRK08310 181375 PRK08310 amidase; Provisional 395 matched cddid_all.tbl CDD PRK08311 PRK08311 236233 PRK08311 RNA polymerase sigma factor SigI. 237 matched cddid_all.tbl CDD PRK08312 PRK08312 236234 PRK08312 indolepyruvate oxidoreductase subunit beta family protein. 510 matched cddid_all.tbl CDD PRK08313 PRK08313 181378 PRK08313 thiolase domain-containing protein. 386 matched cddid_all.tbl CDD PRK08314 PRK08314 236235 PRK08314 long-chain-fatty-acid--CoA ligase; Validated 546 matched cddid_all.tbl CDD PRK08315 PRK08315 236236 PRK08315 AMP-binding domain protein; Validated 559 matched cddid_all.tbl CDD PRK08316 PRK08316 181381 PRK08316 acyl-CoA synthetase; Validated 523 matched cddid_all.tbl CDD PRK08317 PRK08317 181382 PRK08317 hypothetical protein; Provisional 241 matched cddid_all.tbl CDD PRK08318 PRK08318 236237 PRK08318 NAD-dependent dihydropyrimidine dehydrogenase subunit PreA. 420 matched cddid_all.tbl CDD PRK08319 PRK08319 181384 PRK08319 energy-coupling factor ABC transporter permease. 224 matched cddid_all.tbl CDD PRK08320 PRK08320 236238 PRK08320 branched-chain amino acid aminotransferase; Reviewed 288 matched cddid_all.tbl CDD PRK08321 PRK08321 181386 PRK08321 1,4-dihydroxy-2-naphthoyl-CoA synthase. 302 matched cddid_all.tbl CDD PRK08322 PRK08322 236239 PRK08322 acetolactate synthase large subunit. 547 matched cddid_all.tbl CDD PRK08323 PRK08323 236240 PRK08323 phenylhydantoinase; Validated 459 matched cddid_all.tbl CDD PRK08324 PRK08324 236241 PRK08324 bifunctional aldolase/short-chain dehydrogenase. 681 matched cddid_all.tbl CDD PRK08326 PRK08326 236242 PRK08326 R2-like ligand-binding oxidase. 311 matched cddid_all.tbl CDD PRK08327 PRK08327 236243 PRK08327 thiamine pyrophosphate-requiring protein. 569 matched cddid_all.tbl CDD PRK08328 PRK08328 169382 PRK08328 hypothetical protein; Provisional 231 matched cddid_all.tbl CDD PRK08329 PRK08329 236244 PRK08329 threonine synthase; Validated 347 matched cddid_all.tbl CDD PRK08330 PRK08330 169384 PRK08330 biotin--protein ligase; Provisional 236 matched cddid_all.tbl CDD PRK08332 PRK08332 181392 PRK08332 vitamin B12-dependent ribonucleotide reductase. 1740 matched cddid_all.tbl CDD PRK08333 PRK08333 181393 PRK08333 aldolase. 184 matched cddid_all.tbl CDD PRK08334 PRK08334 169386 PRK08334 S-methyl-5-thioribose-1-phosphate isomerase. 356 matched cddid_all.tbl CDD PRK08335 PRK08335 169387 PRK08335 translation initiation factor IF-2B subunit alpha; Validated 275 matched cddid_all.tbl CDD PRK08338 PRK08338 181394 PRK08338 2-oxoacid:ferredoxin oxidoreductase subunit gamma. 170 matched cddid_all.tbl CDD PRK08339 PRK08339 169389 PRK08339 short chain dehydrogenase; Provisional 263 matched cddid_all.tbl CDD PRK08340 PRK08340 169390 PRK08340 SDR family oxidoreductase. 259 matched cddid_all.tbl CDD PRK08343 PRK08343 236245 secD preprotein translocase subunit SecD; Reviewed 417 matched cddid_all.tbl CDD PRK08344 PRK08344 236246 PRK08344 V-type ATP synthase subunit K; Validated 157 matched cddid_all.tbl CDD PRK08345 PRK08345 236247 PRK08345 cytochrome-c3 hydrogenase subunit gamma; Provisional 289 matched cddid_all.tbl CDD PRK08348 PRK08348 181399 PRK08348 NADH-plastoquinone oxidoreductase subunit; Provisional 120 matched cddid_all.tbl CDD PRK08349 PRK08349 169396 PRK08349 hypothetical protein; Validated 198 matched cddid_all.tbl CDD PRK08350 PRK08350 169397 PRK08350 hypothetical protein; Provisional 341 matched cddid_all.tbl CDD PRK08351 PRK08351 181400 PRK08351 DNA-directed RNA polymerase subunit E''; Validated 61 matched cddid_all.tbl CDD PRK08354 PRK08354 169399 PRK08354 putative aminotransferase; Provisional 311 matched cddid_all.tbl CDD PRK08356 PRK08356 169400 PRK08356 hypothetical protein; Provisional 195 matched cddid_all.tbl CDD PRK08360 PRK08360 181401 PRK08360 aspartate aminotransferase family protein. 443 matched cddid_all.tbl CDD PRK08361 PRK08361 236248 PRK08361 aspartate aminotransferase; Provisional 391 matched cddid_all.tbl CDD PRK08363 PRK08363 181402 PRK08363 alanine aminotransferase; Validated 398 matched cddid_all.tbl CDD PRK08364 PRK08364 236249 PRK08364 sulfur carrier protein ThiS; Provisional 70 matched cddid_all.tbl CDD PRK08366 PRK08366 169406 vorA 2-ketoisovalerate ferredoxin oxidoreductase subunit alpha; Reviewed 390 matched cddid_all.tbl CDD PRK08367 PRK08367 181403 porA pyruvate ferredoxin oxidoreductase subunit alpha; Reviewed 394 matched cddid_all.tbl CDD PRK08373 PRK08373 236250 PRK08373 aspartate kinase; Validated 341 matched cddid_all.tbl CDD PRK08374 PRK08374 169409 PRK08374 homoserine dehydrogenase; Provisional 336 matched cddid_all.tbl CDD PRK08375 PRK08375 236251 PRK08375 putative monovalent cation/H+ antiporter subunit D; Reviewed 487 matched cddid_all.tbl CDD PRK08376 PRK08376 236252 PRK08376 putative monovalent cation/H+ antiporter subunit D; Reviewed 521 matched cddid_all.tbl CDD PRK08377 PRK08377 181406 PRK08377 NADH dehydrogenase subunit N; Validated 494 matched cddid_all.tbl CDD PRK08378 PRK08378 236253 PRK08378 hypothetical protein; Provisional 93 matched cddid_all.tbl CDD PRK08381 PRK08381 169414 PRK08381 putative monovalent cation/H+ antiporter subunit F; Reviewed 87 matched cddid_all.tbl CDD PRK08382 PRK08382 169415 PRK08382 putative monovalent cation/H+ antiporter subunit E; Reviewed 201 matched cddid_all.tbl CDD PRK08383 PRK08383 181407 PRK08383 putative monovalent cation/H+ antiporter subunit E; Reviewed 168 matched cddid_all.tbl CDD PRK08386 PRK08386 236256 PRK08386 putative monovalent cation/H+ antiporter subunit B; Reviewed 151 matched cddid_all.tbl CDD PRK08387 PRK08387 169420 PRK08387 putative monovalent cation/H+ antiporter subunit B; Reviewed 131 matched cddid_all.tbl CDD PRK08388 PRK08388 236257 PRK08388 putative monovalent cation/H+ antiporter subunit C; Reviewed 119 matched cddid_all.tbl CDD PRK08389 PRK08389 236258 PRK08389 putative monovalent cation/H+ antiporter subunit C; Reviewed 114 matched cddid_all.tbl CDD PRK08392 PRK08392 169423 PRK08392 hypothetical protein; Provisional 215 matched cddid_all.tbl CDD PRK08393 PRK08393 181411 PRK08393 N-ethylammeline chlorohydrolase; Provisional 424 matched cddid_all.tbl CDD PRK08395 PRK08395 169425 PRK08395 fumarate hydratase; Provisional 162 matched cddid_all.tbl CDD PRK08401 PRK08401 236259 PRK08401 L-aspartate oxidase; Provisional 466 matched cddid_all.tbl CDD PRK08402 PRK08402 169427 PRK08402 replication factor A; Reviewed 355 matched cddid_all.tbl CDD PRK08404 PRK08404 169428 PRK08404 V-type ATP synthase subunit H; Validated 103 matched cddid_all.tbl CDD PRK08406 PRK08406 181413 PRK08406 transcription elongation factor NusA-like protein; Validated 140 matched cddid_all.tbl CDD PRK08410 PRK08410 181414 PRK08410 D-2-hydroxyacid dehydrogenase. 311 matched cddid_all.tbl CDD PRK08411 PRK08411 236260 PRK08411 flagellin; Reviewed 572 matched cddid_all.tbl CDD PRK08412 PRK08412 236261 flgL flagellar hook-associated protein FlgL; Validated 827 matched cddid_all.tbl CDD PRK08415 PRK08415 181416 PRK08415 enoyl-[acyl-carrier-protein] reductase FabI. 274 matched cddid_all.tbl CDD PRK08416 PRK08416 181417 PRK08416 enoyl-ACP reductase. 260 matched cddid_all.tbl CDD PRK08417 PRK08417 236262 PRK08417 metal-dependent hydrolase. 386 matched cddid_all.tbl CDD PRK08418 PRK08418 181419 PRK08418 metal-dependent hydrolase. 408 matched cddid_all.tbl CDD PRK08419 PRK08419 181420 PRK08419 lipid A biosynthesis lauroyl acyltransferase; Reviewed 298 matched cddid_all.tbl CDD PRK08425 PRK08425 236263 flgE flagellar hook protein FlgE; Validated 731 matched cddid_all.tbl CDD PRK08432 PRK08432 236264 PRK08432 flagellar motor switch protein FliY; Validated 283 matched cddid_all.tbl CDD PRK08433 PRK08433 181423 PRK08433 flagellar motor switch protein FliN. 111 matched cddid_all.tbl CDD PRK08439 PRK08439 236265 PRK08439 3-oxoacyl-(acyl carrier protein) synthase II; Reviewed 406 matched cddid_all.tbl CDD PRK08441 PRK08441 181425 oorC 2-oxoglutarate-acceptor oxidoreductase subunit OorC; Reviewed 183 matched cddid_all.tbl CDD PRK08444 PRK08444 181426 PRK08444 aminofutalosine synthase MqnE. 353 matched cddid_all.tbl CDD PRK08445 PRK08445 181427 PRK08445 dehypoxanthine futalosine cyclase. 348 matched cddid_all.tbl CDD PRK08447 PRK08447 236266 PRK08447 ribonucleoside-diphosphate reductase subunit alpha. 789 matched cddid_all.tbl CDD PRK08451 PRK08451 236267 PRK08451 DNA polymerase III subunits gamma and tau; Validated 535 matched cddid_all.tbl CDD PRK08452 PRK08452 236268 PRK08452 flagellar protein FlaG; Provisional 124 matched cddid_all.tbl CDD PRK08453 PRK08453 181432 fliD flagellar filament capping protein FliD. 673 matched cddid_all.tbl CDD PRK08455 PRK08455 181433 fliL flagellar basal body-associated protein FliL; Reviewed 182 matched cddid_all.tbl CDD PRK08456 PRK08456 181434 PRK08456 flagellar motor protein MotA; Validated 257 matched cddid_all.tbl CDD PRK08457 PRK08457 181435 motB flagellar motor protein MotB; Reviewed 257 matched cddid_all.tbl CDD PRK08462 PRK08462 236269 PRK08462 acetyl-CoA carboxylase biotin carboxylase subunit. 445 matched cddid_all.tbl CDD PRK08463 PRK08463 169452 PRK08463 acetyl-CoA carboxylase subunit A; Validated 478 matched cddid_all.tbl CDD PRK08471 PRK08471 236270 flgK flagellar hook-associated protein FlgK; Validated 613 matched cddid_all.tbl CDD PRK08472 PRK08472 181439 fliI flagellar protein export ATPase FliI. 434 matched cddid_all.tbl CDD PRK08474 PRK08474 236271 PRK08474 F0F1 ATP synthase subunit delta; Validated 176 matched cddid_all.tbl CDD PRK08475 PRK08475 236272 PRK08475 F0F1 ATP synthase subunit B; Validated 167 matched cddid_all.tbl CDD PRK08476 PRK08476 181442 PRK08476 F0F1 ATP synthase subunit B'; Validated 141 matched cddid_all.tbl CDD PRK08477 PRK08477 236273 PRK08477 biotin--[acetyl-CoA-carboxylase] ligase. 211 matched cddid_all.tbl CDD PRK08482 PRK08482 181444 PRK08482 F0F1 ATP synthase subunit C; Validated 105 matched cddid_all.tbl CDD PRK08485 PRK08485 236274 PRK08485 DNA polymerase III subunit delta'; Validated 206 matched cddid_all.tbl CDD PRK08486 PRK08486 236275 PRK08486 single-stranded DNA-binding protein; Provisional 182 matched cddid_all.tbl CDD PRK08487 PRK08487 236276 PRK08487 DNA polymerase III subunit delta; Validated 328 matched cddid_all.tbl CDD PRK08489 PRK08489 181448 PRK08489 NAD(P)H-quinone oxidoreductase subunit 3. 129 matched cddid_all.tbl CDD PRK08491 PRK08491 181449 PRK08491 NADH-quinone oxidoreductase subunit C. 263 matched cddid_all.tbl CDD PRK08493 PRK08493 236277 PRK08493 NADH-quinone oxidoreductase subunit G. 819 matched cddid_all.tbl CDD PRK08506 PRK08506 236278 PRK08506 replicative DNA helicase; Provisional 472 matched cddid_all.tbl CDD PRK08507 PRK08507 181452 PRK08507 prephenate dehydrogenase; Validated 275 matched cddid_all.tbl CDD PRK08508 PRK08508 236279 PRK08508 biotin synthase; Provisional 279 matched cddid_all.tbl CDD PRK08515 PRK08515 236280 flgA flagellar basal body P-ring formation protein FlgA. 222 matched cddid_all.tbl CDD PRK08517 PRK08517 236281 PRK08517 3'-5' exonuclease. 257 matched cddid_all.tbl CDD PRK08527 PRK08527 181458 PRK08527 acetolactate synthase large subunit. 563 matched cddid_all.tbl CDD PRK08533 PRK08533 181459 PRK08533 flagellar accessory protein FlaH; Reviewed 230 matched cddid_all.tbl CDD PRK08534 PRK08534 181460 PRK08534 pyruvate ferredoxin oxidoreductase subunit gamma; Reviewed 181 matched cddid_all.tbl CDD PRK08535 PRK08535 236282 PRK08535 ribose 1,5-bisphosphate isomerase. 310 matched cddid_all.tbl CDD PRK08537 PRK08537 181462 PRK08537 2-oxoacid:ferredoxin oxidoreductase subunit gamma. 177 matched cddid_all.tbl CDD PRK08541 PRK08541 236284 PRK08541 flagellin; Validated 211 matched cddid_all.tbl CDD PRK08554 PRK08554 236285 PRK08554 peptidase; Reviewed 438 matched cddid_all.tbl CDD PRK08557 PRK08557 181465 PRK08557 hypothetical protein; Provisional 417 matched cddid_all.tbl CDD PRK08558 PRK08558 181466 PRK08558 adenine phosphoribosyltransferase; Provisional 238 matched cddid_all.tbl CDD PRK08559 PRK08559 181467 nusG transcription antitermination protein NusG; Validated 153 matched cddid_all.tbl CDD PRK08560 PRK08560 236286 PRK08560 tyrosyl-tRNA synthetase; Validated 329 matched cddid_all.tbl CDD PRK08561 PRK08561 236287 rps15p 30S ribosomal protein S15P; Reviewed 151 matched cddid_all.tbl CDD PRK08562 PRK08562 236288 rpl32e 50S ribosomal protein L32e; Validated 125 matched cddid_all.tbl CDD PRK08563 PRK08563 236289 PRK08563 DNA-directed RNA polymerase subunit E'; Provisional 187 matched cddid_all.tbl CDD PRK08564 PRK08564 236290 PRK08564 S-methyl-5'-thioadenosine phosphorylase. 267 matched cddid_all.tbl CDD PRK08565 PRK08565 236291 PRK08565 DNA-directed RNA polymerase subunit B; Provisional 1103 matched cddid_all.tbl CDD PRK08566 PRK08566 236292 PRK08566 DNA-directed RNA polymerase subunit A'; Validated 882 matched cddid_all.tbl CDD PRK08568 PRK08568 236293 PRK08568 preprotein translocase subunit SecY; Reviewed 462 matched cddid_all.tbl CDD PRK08569 PRK08569 236294 rpl18p 50S ribosomal protein L18P; Reviewed 193 matched cddid_all.tbl CDD PRK08570 PRK08570 236295 rpl19e 50S ribosomal protein L19e; Reviewed 150 matched cddid_all.tbl CDD PRK08571 PRK08571 181478 rpl14p 50S ribosomal protein L14P; Reviewed 132 matched cddid_all.tbl CDD PRK08572 PRK08572 236296 rps17p 30S ribosomal protein S17P; Reviewed 108 matched cddid_all.tbl CDD PRK08573 PRK08573 236297 PRK08573 bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase. 448 matched cddid_all.tbl CDD PRK08574 PRK08574 236298 PRK08574 cystathionine gamma-synthase family protein. 385 matched cddid_all.tbl CDD PRK08575 PRK08575 236299 PRK08575 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase; Provisional 326 matched cddid_all.tbl CDD PRK08576 PRK08576 236300 PRK08576 hypothetical protein; Provisional 438 matched cddid_all.tbl CDD PRK08577 PRK08577 236301 PRK08577 hypothetical protein; Provisional 136 matched cddid_all.tbl CDD PRK08578 PRK08578 236302 PRK08578 preprotein translocase subunit SecF; Reviewed 292 matched cddid_all.tbl CDD PRK08579 PRK08579 236303 PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional 625 matched cddid_all.tbl CDD PRK08581 PRK08581 236304 PRK08581 amidase domain-containing protein. 619 matched cddid_all.tbl CDD PRK08582 PRK08582 236305 PRK08582 RNA-binding protein S1. 139 matched cddid_all.tbl CDD PRK08583 PRK08583 236306 PRK08583 RNA polymerase sigma factor SigB; Validated 257 matched cddid_all.tbl CDD PRK08588 PRK08588 181490 PRK08588 succinyl-diaminopimelate desuccinylase; Reviewed 377 matched cddid_all.tbl CDD PRK08589 PRK08589 181491 PRK08589 SDR family oxidoreductase. 272 matched cddid_all.tbl CDD PRK08591 PRK08591 236307 PRK08591 acetyl-CoA carboxylase biotin carboxylase subunit; Validated 451 matched cddid_all.tbl CDD PRK08593 PRK08593 181493 PRK08593 aspartate aminotransferase family protein. 445 matched cddid_all.tbl CDD PRK08594 PRK08594 236308 PRK08594 enoyl-[acyl-carrier-protein] reductase FabI. 257 matched cddid_all.tbl CDD PRK08596 PRK08596 181495 PRK08596 acetylornithine deacetylase; Validated 421 matched cddid_all.tbl CDD PRK08600 PRK08600 181497 PRK08600 putative monovalent cation/H+ antiporter subunit C; Reviewed 113 matched cddid_all.tbl CDD PRK08601 PRK08601 236310 PRK08601 NADH dehydrogenase subunit 5; Validated 509 matched cddid_all.tbl CDD PRK08605 PRK08605 181499 PRK08605 D-lactate dehydrogenase; Validated 332 matched cddid_all.tbl CDD PRK08609 PRK08609 236311 PRK08609 DNA polymerase/3'-5' exonuclease PolX. 570 matched cddid_all.tbl CDD PRK08610 PRK08610 181501 PRK08610 fructose-bisphosphate aldolase; Reviewed 286 matched cddid_all.tbl CDD PRK08611 PRK08611 181502 PRK08611 pyruvate oxidase; Provisional 576 matched cddid_all.tbl CDD PRK08617 PRK08617 236312 PRK08617 acetolactate synthase AlsS. 552 matched cddid_all.tbl CDD PRK08618 PRK08618 236313 PRK08618 ornithine cyclodeaminase family protein. 325 matched cddid_all.tbl CDD PRK08621 PRK08621 181505 PRK08621 galactose-6-phosphate isomerase subunit LacA; Reviewed 142 matched cddid_all.tbl CDD PRK08622 PRK08622 181506 PRK08622 galactose-6-phosphate isomerase subunit LacB; Reviewed 171 matched cddid_all.tbl CDD PRK08624 PRK08624 236314 PRK08624 hypothetical protein; Provisional 373 matched cddid_all.tbl CDD PRK08626 PRK08626 181507 PRK08626 fumarate reductase flavoprotein subunit; Provisional 657 matched cddid_all.tbl CDD PRK08628 PRK08628 181508 PRK08628 SDR family oxidoreductase. 258 matched cddid_all.tbl CDD PRK08629 PRK08629 181509 PRK08629 coproporphyrinogen III oxidase family protein. 433 matched cddid_all.tbl CDD PRK08633 PRK08633 236315 PRK08633 2-acyl-glycerophospho-ethanolamine acyltransferase; Validated 1146 matched cddid_all.tbl CDD PRK08636 PRK08636 236316 PRK08636 LL-diaminopimelate aminotransferase. 403 matched cddid_all.tbl CDD PRK08637 PRK08637 181512 PRK08637 hypothetical protein; Provisional 388 matched cddid_all.tbl CDD PRK08638 PRK08638 236317 PRK08638 bifunctional threonine ammonia-lyase/L-serine ammonia-lyase TdcB. 333 matched cddid_all.tbl CDD PRK08639 PRK08639 236318 PRK08639 threonine dehydratase; Validated 420 matched cddid_all.tbl CDD PRK08640 PRK08640 181515 sdhB succinate dehydrogenase iron-sulfur subunit; Reviewed 249 matched cddid_all.tbl CDD PRK08641 PRK08641 236319 sdhA succinate dehydrogenase flavoprotein subunit; Reviewed 589 matched cddid_all.tbl CDD PRK08642 PRK08642 181517 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional 253 matched cddid_all.tbl CDD PRK08643 PRK08643 181518 PRK08643 (S)-acetoin forming diacetyl reductase. 256 matched cddid_all.tbl CDD PRK08644 PRK08644 236320 PRK08644 sulfur carrier protein ThiS adenylyltransferase ThiF. 212 matched cddid_all.tbl CDD PRK08645 PRK08645 236321 PRK08645 bifunctional homocysteine S-methyltransferase/5,10-methylenetetrahydrofolate reductase protein; Reviewed 612 matched cddid_all.tbl CDD PRK08651 PRK08651 236323 PRK08651 succinyl-diaminopimelate desuccinylase; Reviewed 394 matched cddid_all.tbl CDD PRK08652 PRK08652 236324 PRK08652 acetylornithine deacetylase; Provisional 347 matched cddid_all.tbl CDD PRK08654 PRK08654 236325 PRK08654 acetyl-CoA carboxylase biotin carboxylase subunit. 499 matched cddid_all.tbl CDD PRK08655 PRK08655 236326 PRK08655 prephenate dehydrogenase; Provisional 437 matched cddid_all.tbl CDD PRK08659 PRK08659 181526 PRK08659 2-oxoacid:acceptor oxidoreductase subunit alpha. 376 matched cddid_all.tbl CDD PRK08660 PRK08660 181527 PRK08660 aldolase. 181 matched cddid_all.tbl CDD PRK08662 PRK08662 236328 PRK08662 nicotinate phosphoribosyltransferase; Reviewed 343 matched cddid_all.tbl CDD PRK08664 PRK08664 236329 PRK08664 aspartate-semialdehyde dehydrogenase; Reviewed 349 matched cddid_all.tbl CDD PRK08665 PRK08665 236330 PRK08665 vitamin B12-dependent ribonucleotide reductase. 752 matched cddid_all.tbl CDD PRK08666 PRK08666 169548 PRK08666 5'-methylthioadenosine phosphorylase; Validated 261 matched cddid_all.tbl CDD PRK08667 PRK08667 236331 PRK08667 hydrogenase membrane subunit; Validated 644 matched cddid_all.tbl CDD PRK08668 PRK08668 236332 PRK08668 NADH dehydrogenase subunit M; Validated 610 matched cddid_all.tbl CDD PRK08673 PRK08673 181535 PRK08673 3-deoxy-7-phosphoheptulonate synthase; Reviewed 335 matched cddid_all.tbl CDD PRK08674 PRK08674 181536 PRK08674 bifunctional phosphoglucose/phosphomannose isomerase; Validated 337 matched cddid_all.tbl CDD PRK08676 PRK08676 181537 PRK08676 hydrogenase membrane subunit; Validated 485 matched cddid_all.tbl CDD PRK08690 PRK08690 169553 PRK08690 enoyl-[acyl-carrier-protein] reductase FabI. 261 matched cddid_all.tbl CDD PRK08691 PRK08691 236333 PRK08691 DNA polymerase III subunits gamma and tau; Validated 709 matched cddid_all.tbl CDD PRK08699 PRK08699 181538 PRK08699 DNA polymerase III subunit delta'; Validated 325 matched cddid_all.tbl CDD PRK08703 PRK08703 169556 PRK08703 SDR family oxidoreductase. 239 matched cddid_all.tbl CDD PRK08706 PRK08706 169557 PRK08706 lipid A biosynthesis lauroyl acyltransferase; Provisional 289 matched cddid_all.tbl CDD PRK08719 PRK08719 236334 PRK08719 ribonuclease H; Reviewed 147 matched cddid_all.tbl CDD PRK08722 PRK08722 181539 PRK08722 beta-ketoacyl-ACP synthase II. 414 matched cddid_all.tbl CDD PRK08724 PRK08724 236335 fliD flagellar filament capping protein FliD. 673 matched cddid_all.tbl CDD PRK08733 PRK08733 181542 PRK08733 LpxL/LpxP family Kdo(2)-lipid IV(A) lauroyl/palmitoleoyl acyltransferase. 306 matched cddid_all.tbl CDD PRK08734 PRK08734 181543 PRK08734 lauroyl acyltransferase. 305 matched cddid_all.tbl CDD PRK08737 PRK08737 181544 PRK08737 acetylornithine deacetylase; Provisional 364 matched cddid_all.tbl CDD PRK08751 PRK08751 181546 PRK08751 long-chain fatty acid--CoA ligase. 560 matched cddid_all.tbl CDD PRK08760 PRK08760 181547 PRK08760 replicative DNA helicase; Provisional 476 matched cddid_all.tbl CDD PRK08762 PRK08762 236337 PRK08762 molybdopterin-synthase adenylyltransferase MoeB. 376 matched cddid_all.tbl CDD PRK08763 PRK08763 181549 PRK08763 single-stranded DNA-binding protein; Provisional 164 matched cddid_all.tbl CDD PRK08764 PRK08764 181550 PRK08764 Rnf electron transport complex subunit RnfB. 135 matched cddid_all.tbl CDD PRK08769 PRK08769 181551 PRK08769 DNA polymerase III subunit delta'; Validated 319 matched cddid_all.tbl CDD PRK08773 PRK08773 181552 PRK08773 UbiH/UbiF family hydroxylase. 392 matched cddid_all.tbl CDD PRK08775 PRK08775 181553 PRK08775 homoserine O-succinyltransferase. 343 matched cddid_all.tbl CDD PRK08776 PRK08776 181554 PRK08776 O-succinylhomoserine (thiol)-lyase. 405 matched cddid_all.tbl CDD PRK08780 PRK08780 181555 PRK08780 DNA topoisomerase I; Provisional 780 matched cddid_all.tbl CDD PRK08787 PRK08787 136970 PRK08787 peptide chain release factor 2; Provisional 313 matched cddid_all.tbl CDD PRK08788 PRK08788 236338 PRK08788 enoyl-CoA hydratase; Validated 287 matched cddid_all.tbl CDD PRK08808 PRK08808 181557 PRK08808 type II secretion system protein J. 211 matched cddid_all.tbl CDD PRK08811 PRK08811 181558 PRK08811 uroporphyrinogen-III synthase; Validated 266 matched cddid_all.tbl CDD PRK08813 PRK08813 236339 PRK08813 threonine dehydratase; Provisional 349 matched cddid_all.tbl CDD PRK08815 PRK08815 236340 PRK08815 GTP cyclohydrolase II RibA. 375 matched cddid_all.tbl CDD PRK08818 PRK08818 181561 PRK08818 prephenate dehydrogenase; Provisional 370 matched cddid_all.tbl CDD PRK08840 PRK08840 181562 PRK08840 replicative DNA helicase; Provisional 464 matched cddid_all.tbl CDD PRK08841 PRK08841 181563 PRK08841 aspartate kinase; Validated 392 matched cddid_all.tbl CDD PRK08849 PRK08849 181564 PRK08849 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase; Provisional 384 matched cddid_all.tbl CDD PRK08850 PRK08850 236341 PRK08850 2-octaprenyl-6-methoxyphenol hydroxylase; Validated 405 matched cddid_all.tbl CDD PRK08857 PRK08857 181566 PRK08857 aminodeoxychorismate/anthranilate synthase component II. 193 matched cddid_all.tbl CDD PRK08861 PRK08861 181567 PRK08861 O-succinylhomoserine (thiol)-lyase. 388 matched cddid_all.tbl CDD PRK08862 PRK08862 236342 PRK08862 SDR family oxidoreductase. 227 matched cddid_all.tbl CDD PRK08868 PRK08868 236343 PRK08868 flagellar protein FlaG; Provisional 144 matched cddid_all.tbl CDD PRK08869 PRK08869 236344 PRK08869 polar flagellin E. 376 matched cddid_all.tbl CDD PRK08870 PRK08870 236345 flgL flagellar hook-associated protein FlgL; Reviewed 404 matched cddid_all.tbl CDD PRK08871 PRK08871 181572 flgK flagellar hook-associated protein FlgK; Validated 626 matched cddid_all.tbl CDD PRK08878 PRK08878 181573 PRK08878 cobalamin biosynthesis family protein. 317 matched cddid_all.tbl CDD PRK08881 PRK08881 181574 rpsN 30S ribosomal protein S14; Reviewed 101 matched cddid_all.tbl CDD PRK08887 PRK08887 181576 PRK08887 nicotinate-nicotinamide nucleotide adenylyltransferase. 174 matched cddid_all.tbl CDD PRK08903 PRK08903 236347 PRK08903 DnaA regulatory inactivator Hda; Validated 227 matched cddid_all.tbl CDD PRK08905 PRK08905 236348 PRK08905 lysophospholipid acyltransferase family protein. 289 matched cddid_all.tbl CDD PRK08912 PRK08912 181580 PRK08912 aminotransferase. 387 matched cddid_all.tbl CDD PRK08913 PRK08913 236349 flgL flagellin. 301 matched cddid_all.tbl CDD PRK08916 PRK08916 236350 PRK08916 flagellar motor switch protein FliN. 116 matched cddid_all.tbl CDD PRK08927 PRK08927 236351 fliI flagellar protein export ATPase FliI. 442 matched cddid_all.tbl CDD PRK08931 PRK08931 181584 PRK08931 S-methyl-5'-thioadenosine phosphorylase. 289 matched cddid_all.tbl CDD PRK08936 PRK08936 181585 PRK08936 glucose-1-dehydrogenase; Provisional 261 matched cddid_all.tbl CDD PRK08937 PRK08937 236352 PRK08937 adenylosuccinate lyase; Provisional 216 matched cddid_all.tbl CDD PRK08939 PRK08939 236353 PRK08939 primosomal protein DnaI; Reviewed 306 matched cddid_all.tbl CDD PRK08942 PRK08942 236354 PRK08942 D-glycero-beta-D-manno-heptose 1,7-bisphosphate 7-phosphatase. 181 matched cddid_all.tbl CDD PRK08943 PRK08943 236355 PRK08943 lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase; Validated 314 matched cddid_all.tbl CDD PRK08944 PRK08944 236356 motB flagellar motor protein MotB; Reviewed 302 matched cddid_all.tbl CDD PRK08945 PRK08945 236357 PRK08945 putative oxoacyl-(acyl carrier protein) reductase; Provisional 247 matched cddid_all.tbl CDD PRK08947 PRK08947 181592 fadA 3-ketoacyl-CoA thiolase; Reviewed 387 matched cddid_all.tbl CDD PRK08951 PRK08951 181593 PRK08951 malate synthase; Provisional 190 matched cddid_all.tbl CDD PRK08955 PRK08955 169599 PRK08955 glyceraldehyde-3-phosphate dehydrogenase; Validated 334 matched cddid_all.tbl CDD PRK08960 PRK08960 181595 PRK08960 pyridoxal phosphate-dependent aminotransferase. 387 matched cddid_all.tbl CDD PRK08961 PRK08961 236358 PRK08961 bifunctional aspartate kinase/diaminopimelate decarboxylase. 861 matched cddid_all.tbl CDD PRK08963 PRK08963 181597 fadI 3-ketoacyl-CoA thiolase; Reviewed 428 matched cddid_all.tbl CDD PRK08965 PRK08965 181598 PRK08965 putative monovalent cation/H+ antiporter subunit E; Reviewed 162 matched cddid_all.tbl CDD PRK08972 PRK08972 181599 fliI flagellar protein export ATPase FliI. 444 matched cddid_all.tbl CDD PRK08974 PRK08974 236359 PRK08974 long-chain-fatty-acid--CoA ligase FadD. 560 matched cddid_all.tbl CDD PRK08978 PRK08978 181601 PRK08978 acetolactate synthase 2 catalytic subunit; Reviewed 548 matched cddid_all.tbl CDD PRK08979 PRK08979 181602 PRK08979 acetolactate synthase 3 large subunit. 572 matched cddid_all.tbl CDD PRK08983 PRK08983 236360 fliN flagellar motor switch protein FliN. 127 matched cddid_all.tbl CDD PRK08990 PRK08990 181604 PRK08990 flagellar motor protein PomA; Reviewed 254 matched cddid_all.tbl CDD PRK08993 PRK08993 181605 PRK08993 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD. 253 matched cddid_all.tbl CDD PRK08997 PRK08997 181606 PRK08997 isocitrate dehydrogenase; Provisional 334 matched cddid_all.tbl CDD PRK08999 PRK08999 236361 PRK08999 Nudix family hydrolase. 312 matched cddid_all.tbl CDD PRK09004 PRK09004 181608 PRK09004 FMN-binding protein MioC; Provisional 146 matched cddid_all.tbl CDD PRK09009 PRK09009 181609 PRK09009 SDR family oxidoreductase. 235 matched cddid_all.tbl CDD PRK09010 PRK09010 236362 PRK09010 single-stranded DNA-binding protein; Provisional 177 matched cddid_all.tbl CDD PRK09014 PRK09014 181611 rfaH transcription/translation regulatory transformer protein RfaH. 162 matched cddid_all.tbl CDD PRK09019 PRK09019 181613 PRK09019 stress response translation initiation inhibitor YciH. 108 matched cddid_all.tbl CDD PRK09027 PRK09027 181614 PRK09027 cytidine deaminase; Provisional 295 matched cddid_all.tbl CDD PRK09028 PRK09028 181615 PRK09028 cystathionine beta-lyase; Provisional 394 matched cddid_all.tbl CDD PRK09029 PRK09029 236363 PRK09029 O-succinylbenzoic acid--CoA ligase; Provisional 458 matched cddid_all.tbl CDD PRK09034 PRK09034 236364 PRK09034 aspartate kinase; Reviewed 454 matched cddid_all.tbl CDD PRK09038 PRK09038 181618 PRK09038 flagellar motor protein MotD; Reviewed 281 matched cddid_all.tbl CDD PRK09039 PRK09039 181619 PRK09039 peptidoglycan -binding protein. 343 matched cddid_all.tbl CDD PRK09040 PRK09040 181620 PRK09040 hypothetical protein; Provisional 214 matched cddid_all.tbl CDD PRK09041 PRK09041 236365 motB motility protein MotB. 317 matched cddid_all.tbl CDD PRK09045 PRK09045 236366 PRK09045 TRZ/ATZ family hydrolase. 443 matched cddid_all.tbl CDD PRK09047 PRK09047 236367 PRK09047 RNA polymerase factor sigma-70; Validated 161 matched cddid_all.tbl CDD PRK09050 PRK09050 181624 PRK09050 beta-ketoadipyl CoA thiolase; Validated 401 matched cddid_all.tbl CDD PRK09051 PRK09051 181625 PRK09051 beta-ketothiolase BktB. 394 matched cddid_all.tbl CDD PRK09052 PRK09052 181626 PRK09052 acetyl-CoA C-acyltransferase. 399 matched cddid_all.tbl CDD PRK09053 PRK09053 181627 PRK09053 3-carboxy-cis,cis-muconate cycloisomerase; Provisional 452 matched cddid_all.tbl CDD PRK09059 PRK09059 181631 PRK09059 dihydroorotase; Validated 429 matched cddid_all.tbl CDD PRK09060 PRK09060 181632 PRK09060 dihydroorotase; Validated 444 matched cddid_all.tbl CDD PRK09061 PRK09061 236369 PRK09061 D-glutamate deacylase; Validated 509 matched cddid_all.tbl CDD PRK09065 PRK09065 181635 PRK09065 glutamine amidotransferase; Provisional 237 matched cddid_all.tbl CDD PRK09070 PRK09070 236371 PRK09070 aminodeoxychorismate synthase component I. 447 matched cddid_all.tbl CDD PRK09071 PRK09071 181637 PRK09071 glycosyl transferase family protein. 323 matched cddid_all.tbl CDD PRK09072 PRK09072 236372 PRK09072 SDR family oxidoreductase. 263 matched cddid_all.tbl CDD PRK09076 PRK09076 236373 PRK09076 enoyl-CoA hydratase; Provisional 258 matched cddid_all.tbl CDD PRK09077 PRK09077 236374 PRK09077 L-aspartate oxidase; Provisional 536 matched cddid_all.tbl CDD PRK09082 PRK09082 181642 PRK09082 methionine aminotransferase; Validated 386 matched cddid_all.tbl CDD PRK09084 PRK09084 236376 PRK09084 aspartate kinase III; Validated 448 matched cddid_all.tbl CDD PRK09087 PRK09087 169652 PRK09087 hypothetical protein; Validated 226 matched cddid_all.tbl CDD PRK09088 PRK09088 181644 PRK09088 acyl-CoA synthetase; Validated 488 matched cddid_all.tbl CDD PRK09094 PRK09094 236377 PRK09094 putative monovalent cation/H+ antiporter subunit C; Reviewed 114 matched cddid_all.tbl CDD PRK09098 PRK09098 181646 PRK09098 HrpE/YscL family type III secretion apparatus protein. 233 matched cddid_all.tbl CDD PRK09099 PRK09099 169656 PRK09099 type III secretion system ATPase; Provisional 441 matched cddid_all.tbl CDD PRK09101 PRK09101 181647 nrdB ribonucleotide-diphosphate reductase subunit beta; Reviewed 376 matched cddid_all.tbl CDD PRK09102 PRK09102 236378 PRK09102 ribonucleoside-diphosphate reductase subunit alpha. 601 matched cddid_all.tbl CDD PRK09103 PRK09103 181649 PRK09103 ribonucleoside-diphosphate reductase subunit alpha. 758 matched cddid_all.tbl CDD PRK09104 PRK09104 236379 PRK09104 hypothetical protein; Validated 464 matched cddid_all.tbl CDD PRK09105 PRK09105 181651 PRK09105 pyridoxal phosphate-dependent aminotransferase. 370 matched cddid_all.tbl CDD PRK09107 PRK09107 236380 PRK09107 acetolactate synthase 3 catalytic subunit; Validated 595 matched cddid_all.tbl CDD PRK09109 PRK09109 181654 motC flagellar motor protein; Reviewed 246 matched cddid_all.tbl CDD PRK09110 PRK09110 181655 PRK09110 flagellar motor stator protein MotA. 283 matched cddid_all.tbl CDD PRK09111 PRK09111 236382 PRK09111 DNA polymerase III subunits gamma and tau; Validated 598 matched cddid_all.tbl CDD PRK09112 PRK09112 169667 PRK09112 DNA polymerase III subunit delta'; Validated 351 matched cddid_all.tbl CDD PRK09116 PRK09116 181657 PRK09116 beta-ketoacyl-ACP synthase. 405 matched cddid_all.tbl CDD PRK09120 PRK09120 236383 PRK09120 p-hydroxycinnamoyl CoA hydratase/lyase; Validated 275 matched cddid_all.tbl CDD PRK09121 PRK09121 181659 PRK09121 methionine synthase. 339 matched cddid_all.tbl CDD PRK09124 PRK09124 181661 PRK09124 ubiquinone-dependent pyruvate dehydrogenase. 574 matched cddid_all.tbl CDD PRK09125 PRK09125 181662 PRK09125 DNA ligase; Provisional 282 matched cddid_all.tbl CDD PRK09126 PRK09126 236385 PRK09126 FAD-dependent hydroxylase. 392 matched cddid_all.tbl CDD PRK09133 PRK09133 236388 PRK09133 hypothetical protein; Provisional 472 matched cddid_all.tbl CDD PRK09134 PRK09134 236389 PRK09134 SDR family oxidoreductase. 258 matched cddid_all.tbl CDD PRK09135 PRK09135 181668 PRK09135 pteridine reductase; Provisional 249 matched cddid_all.tbl CDD PRK09136 PRK09136 236390 PRK09136 S-methyl-5'-thioinosine phosphorylase. 245 matched cddid_all.tbl CDD PRK09140 PRK09140 181670 PRK09140 2-dehydro-3-deoxy-6-phosphogalactonate aldolase; Reviewed 206 matched cddid_all.tbl CDD PRK09145 PRK09145 236391 PRK09145 3'-5' exonuclease. 202 matched cddid_all.tbl CDD PRK09146 PRK09146 236392 PRK09146 DNA polymerase III subunit epsilon; Validated 239 matched cddid_all.tbl CDD PRK09147 PRK09147 236393 PRK09147 succinyldiaminopimelate transaminase; Provisional 396 matched cddid_all.tbl CDD PRK09148 PRK09148 181674 PRK09148 LL-diaminopimelate aminotransferase. 405 matched cddid_all.tbl CDD PRK09162 PRK09162 181675 PRK09162 hypoxanthine-guanine phosphoribosyltransferase; Provisional 181 matched cddid_all.tbl CDD PRK09165 PRK09165 181676 PRK09165 replicative DNA helicase; Provisional 497 matched cddid_all.tbl CDD PRK09169 PRK09169 236394 PRK09169 hypothetical protein; Validated 2316 matched cddid_all.tbl CDD PRK09173 PRK09173 169691 PRK09173 F0F1 ATP synthase subunit B; Validated 159 matched cddid_all.tbl CDD PRK09174 PRK09174 169692 PRK09174 F0F1 ATP synthase subunit B. 204 matched cddid_all.tbl CDD PRK09177 PRK09177 236395 PRK09177 xanthine-guanine phosphoribosyltransferase; Validated 156 matched cddid_all.tbl CDD PRK09181 PRK09181 236396 PRK09181 aspartate kinase; Validated 475 matched cddid_all.tbl CDD PRK09182 PRK09182 236397 PRK09182 DNA polymerase III subunit epsilon; Validated 294 matched cddid_all.tbl CDD PRK09183 PRK09183 181681 PRK09183 transposase/IS protein; Provisional 259 matched cddid_all.tbl CDD PRK09184 PRK09184 181682 PRK09184 acyl carrier protein; Provisional 89 matched cddid_all.tbl CDD PRK09185 PRK09185 236398 PRK09185 beta-ketoacyl-ACP synthase. 392 matched cddid_all.tbl CDD PRK09186 PRK09186 236399 PRK09186 flagellin modification protein A; Provisional 256 matched cddid_all.tbl CDD PRK09188 PRK09188 236400 PRK09188 serine/threonine protein kinase; Provisional 365 matched cddid_all.tbl CDD PRK09189 PRK09189 169701 PRK09189 uroporphyrinogen-III synthase; Validated 240 matched cddid_all.tbl CDD PRK09190 PRK09190 236401 PRK09190 RNA-binding protein. 220 matched cddid_all.tbl CDD PRK09191 PRK09191 236402 PRK09191 two-component response regulator; Provisional 261 matched cddid_all.tbl CDD PRK09192 PRK09192 236403 PRK09192 fatty acyl-AMP ligase. 579 matched cddid_all.tbl CDD PRK09193 PRK09193 236404 PRK09193 indolepyruvate ferredoxin oxidoreductase; Validated 1165 matched cddid_all.tbl CDD PRK09194 PRK09194 236405 PRK09194 prolyl-tRNA synthetase; Provisional 565 matched cddid_all.tbl CDD PRK09195 PRK09195 181690 gatY tagatose-bisphosphate aldolase; Reviewed 284 matched cddid_all.tbl CDD PRK09196 PRK09196 181691 PRK09196 fructose-bisphosphate aldolase class II. 347 matched cddid_all.tbl CDD PRK09197 PRK09197 236406 PRK09197 fructose-bisphosphate aldolase; Provisional 350 matched cddid_all.tbl CDD PRK09198 PRK09198 236407 PRK09198 putative nicotinate phosphoribosyltransferase; Provisional 463 matched cddid_all.tbl CDD PRK09200 PRK09200 236408 PRK09200 preprotein translocase subunit SecA; Reviewed 790 matched cddid_all.tbl CDD PRK09201 PRK09201 236409 PRK09201 AtzE family amidohydrolase. 465 matched cddid_all.tbl CDD PRK09202 PRK09202 236410 nusA transcription elongation factor NusA; Validated 470 matched cddid_all.tbl CDD PRK09206 PRK09206 181699 PRK09206 pyruvate kinase PykF. 470 matched cddid_all.tbl CDD PRK09209 PRK09209 181700 PRK09209 ribonucleoside-diphosphate reductase subunit alpha. 761 matched cddid_all.tbl CDD PRK09210 PRK09210 236413 PRK09210 RNA polymerase sigma factor RpoD; Validated 367 matched cddid_all.tbl CDD PRK09212 PRK09212 169719 PRK09212 pyruvate dehydrogenase subunit beta; Validated 327 matched cddid_all.tbl CDD PRK09218 PRK09218 181704 PRK09218 peptide deformylase; Validated 136 matched cddid_all.tbl CDD PRK09219 PRK09219 181705 PRK09219 xanthine phosphoribosyltransferase; Validated 189 matched cddid_all.tbl CDD PRK09220 PRK09220 236415 PRK09220 methylthioribulose 1-phosphate dehydratase. 204 matched cddid_all.tbl CDD PRK09221 PRK09221 181707 PRK09221 beta alanine--pyruvate transaminase; Provisional 445 matched cddid_all.tbl CDD PRK09222 PRK09222 236416 PRK09222 NADP-dependent isocitrate dehydrogenase. 482 matched cddid_all.tbl CDD PRK09224 PRK09224 236417 PRK09224 threonine ammonia-lyase IlvA. 504 matched cddid_all.tbl CDD PRK09228 PRK09228 236419 PRK09228 guanine deaminase; Provisional 433 matched cddid_all.tbl CDD PRK09229 PRK09229 236420 PRK09229 N-formimino-L-glutamate deiminase; Validated 456 matched cddid_all.tbl CDD PRK09230 PRK09230 181713 PRK09230 cytosine deaminase; Provisional 426 matched cddid_all.tbl CDD PRK09231 PRK09231 236421 PRK09231 fumarate reductase flavoprotein subunit; Validated 582 matched cddid_all.tbl CDD PRK09234 PRK09234 236422 fbiC FO synthase; Reviewed 843 matched cddid_all.tbl CDD PRK09236 PRK09236 181716 PRK09236 dihydroorotase; Reviewed 444 matched cddid_all.tbl CDD PRK09237 PRK09237 236423 PRK09237 amidohydrolase/deacetylase family metallohydrolase. 380 matched cddid_all.tbl CDD PRK09238 PRK09238 236424 PRK09238 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase; Validated 835 matched cddid_all.tbl CDD PRK09239 PRK09239 181719 PRK09239 chorismate mutase; Provisional 104 matched cddid_all.tbl CDD PRK09242 PRK09242 181721 PRK09242 SDR family oxidoreductase. 257 matched cddid_all.tbl CDD PRK09243 PRK09243 236426 PRK09243 nicotinate phosphoribosyltransferase; Validated 464 matched cddid_all.tbl CDD PRK09245 PRK09245 181723 PRK09245 crotonase/enoyl-CoA hydratase family protein. 266 matched cddid_all.tbl CDD PRK09247 PRK09247 236428 PRK09247 ATP-dependent DNA ligase; Validated 539 matched cddid_all.tbl CDD PRK09248 PRK09248 236429 PRK09248 putative hydrolase; Validated 246 matched cddid_all.tbl CDD PRK09250 PRK09250 236431 PRK09250 class I fructose-bisphosphate aldolase. 348 matched cddid_all.tbl CDD PRK09256 PRK09256 181730 PRK09256 aminoacyl-tRNA hydrolase. 138 matched cddid_all.tbl CDD PRK09257 PRK09257 181731 PRK09257 aromatic amino acid transaminase. 396 matched cddid_all.tbl CDD PRK09258 PRK09258 181732 PRK09258 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed 338 matched cddid_all.tbl CDD PRK09259 PRK09259 236433 PRK09259 putative oxalyl-CoA decarboxylase; Validated 569 matched cddid_all.tbl CDD PRK09260 PRK09260 236434 PRK09260 3-hydroxyacyl-CoA dehydrogenase. 288 matched cddid_all.tbl CDD PRK09261 PRK09261 236435 PRK09261 phospho-2-dehydro-3-deoxyheptonate aldolase; Validated 349 matched cddid_all.tbl CDD PRK09262 PRK09262 181735 PRK09262 hypothetical protein; Provisional 225 matched cddid_all.tbl CDD PRK09263 PRK09263 236436 PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional 711 matched cddid_all.tbl CDD PRK09264 PRK09264 236437 PRK09264 diaminobutyrate--2-oxoglutarate transaminase. 425 matched cddid_all.tbl CDD PRK09265 PRK09265 181738 PRK09265 aminotransferase AlaT; Validated 404 matched cddid_all.tbl CDD PRK09266 PRK09266 236438 PRK09266 hypothetical protein; Provisional 266 matched cddid_all.tbl CDD PRK09267 PRK09267 236439 PRK09267 flavodoxin FldA; Validated 169 matched cddid_all.tbl CDD PRK09268 PRK09268 236440 PRK09268 acetyl-CoA C-acetyltransferase. 427 matched cddid_all.tbl CDD PRK09269 PRK09269 236441 PRK09269 chorismate mutase; Provisional 193 matched cddid_all.tbl CDD PRK09270 PRK09270 236442 PRK09270 nucleoside triphosphate hydrolase domain-containing protein; Reviewed 229 matched cddid_all.tbl CDD PRK09271 PRK09271 181744 PRK09271 flavodoxin; Provisional 160 matched cddid_all.tbl CDD PRK09272 PRK09272 181745 PRK09272 hypothetical protein; Provisional 109 matched cddid_all.tbl CDD PRK09273 PRK09273 181746 PRK09273 hypothetical protein; Provisional 211 matched cddid_all.tbl CDD PRK09274 PRK09274 236443 PRK09274 peptide synthase; Provisional 552 matched cddid_all.tbl CDD PRK09275 PRK09275 236444 PRK09275 bifunctional aspartate transaminase/aspartate 4-decarboxylase. 527 matched cddid_all.tbl CDD PRK09276 PRK09276 181749 PRK09276 LL-diaminopimelate aminotransferase; Provisional 385 matched cddid_all.tbl CDD PRK09277 PRK09277 236445 PRK09277 aconitate hydratase AcnA. 888 matched cddid_all.tbl CDD PRK09281 PRK09281 236448 PRK09281 F0F1 ATP synthase subunit alpha; Validated 502 matched cddid_all.tbl CDD PRK09282 PRK09282 236449 PRK09282 pyruvate carboxylase subunit B; Validated 592 matched cddid_all.tbl CDD PRK09283 PRK09283 236450 PRK09283 porphobilinogen synthase. 323 matched cddid_all.tbl CDD PRK09284 PRK09284 236451 PRK09284 thiamine biosynthesis protein ThiC; Provisional 607 matched cddid_all.tbl CDD PRK09285 PRK09285 236452 PRK09285 adenylosuccinate lyase; Provisional 456 matched cddid_all.tbl CDD PRK09287 PRK09287 236453 PRK09287 NADP-dependent phosphogluconate dehydrogenase. 459 matched cddid_all.tbl CDD PRK09288 PRK09288 236454 purT formate-dependent phosphoribosylglycinamide formyltransferase. 395 matched cddid_all.tbl CDD PRK09289 PRK09289 236455 PRK09289 riboflavin synthase. 194 matched cddid_all.tbl CDD PRK09290 PRK09290 236456 PRK09290 allantoate amidohydrolase; Reviewed 413 matched cddid_all.tbl CDD PRK09291 PRK09291 181762 PRK09291 SDR family oxidoreductase. 257 matched cddid_all.tbl CDD PRK09292 PRK09292 236457 PRK09292 Na(+)-translocating NADH-quinone reductase subunit D; Validated 209 matched cddid_all.tbl CDD PRK09293 PRK09293 236458 PRK09293 class 1 fructose-bisphosphatase. 327 matched cddid_all.tbl CDD PRK09294 PRK09294 181765 PRK09294 phthiocerol/phthiodiolone dimycocerosyl transferase. 416 matched cddid_all.tbl CDD PRK09295 PRK09295 181766 PRK09295 cysteine desulfurase SufS. 406 matched cddid_all.tbl CDD PRK09296 PRK09296 181767 PRK09296 cysteine desulfuration protein SufE. 138 matched cddid_all.tbl CDD PRK09300 PRK09300 236460 PRK09300 tRNA splicing endonuclease; Reviewed 330 matched cddid_all.tbl CDD PRK09301 PRK09301 181770 PRK09301 circadian clock protein KaiB; Provisional 103 matched cddid_all.tbl CDD PRK09302 PRK09302 236461 PRK09302 circadian clock protein KaiC; Reviewed 509 matched cddid_all.tbl CDD PRK09303 PRK09303 236462 PRK09303 histidine kinase. 380 matched cddid_all.tbl CDD PRK09304 PRK09304 236463 PRK09304 arginine exporter ArgO. 207 matched cddid_all.tbl CDD PRK09310 PRK09310 137204 aroDE bifunctional 3-dehydroquinate dehydratase/shikimate dehydrogenase. 477 matched cddid_all.tbl CDD PRK09311 PRK09311 181774 PRK09311 bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II. 402 matched cddid_all.tbl CDD PRK09314 PRK09314 181775 PRK09314 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II. 339 matched cddid_all.tbl CDD PRK09318 PRK09318 236464 PRK09318 bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II. 387 matched cddid_all.tbl CDD PRK09319 PRK09319 236465 PRK09319 bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase RibB/GTP cyclohydrolase II RibA. 555 matched cddid_all.tbl CDD PRK09325 PRK09325 236466 PRK09325 coenzyme F420-reducing hydrogenase subunit beta; Validated 282 matched cddid_all.tbl CDD PRK09326 PRK09326 181779 PRK09326 F420H2 dehydrogenase subunit F; Provisional 341 matched cddid_all.tbl CDD PRK09328 PRK09328 236467 PRK09328 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional 275 matched cddid_all.tbl CDD PRK09331 PRK09331 236469 PRK09331 Sep-tRNA:Cys-tRNA synthetase; Provisional 387 matched cddid_all.tbl CDD PRK09333 PRK09333 236470 PRK09333 30S ribosomal protein S19e; Provisional 150 matched cddid_all.tbl CDD PRK09334 PRK09334 181784 PRK09334 30S ribosomal protein S25e; Provisional 86 matched cddid_all.tbl CDD PRK09335 PRK09335 181785 PRK09335 30S ribosomal protein S26e; Provisional 95 matched cddid_all.tbl CDD PRK09336 PRK09336 181786 PRK09336 30S ribosomal protein S30e; Provisional 50 matched cddid_all.tbl CDD PRK09343 PRK09343 181787 PRK09343 prefoldin subunit beta; Provisional 121 matched cddid_all.tbl CDD PRK09344 PRK09344 236471 PRK09344 phosphoenolpyruvate carboxykinase. 526 matched cddid_all.tbl CDD PRK09347 PRK09347 236472 folE GTP cyclohydrolase I; Provisional 188 matched cddid_all.tbl CDD PRK09348 PRK09348 236473 glyQ glycyl-tRNA synthetase subunit alpha; Validated 283 matched cddid_all.tbl CDD PRK09350 PRK09350 236474 PRK09350 elongation factor P--(R)-beta-lysine ligase. 306 matched cddid_all.tbl CDD PRK09352 PRK09352 236475 PRK09352 beta-ketoacyl-ACP synthase 3. 319 matched cddid_all.tbl CDD PRK09354 PRK09354 236476 recA recombinase A; Provisional 349 matched cddid_all.tbl CDD PRK09355 PRK09355 236477 PRK09355 hydroxyethylthiazole kinase; Validated 263 matched cddid_all.tbl CDD PRK09357 PRK09357 236479 pyrC dihydroorotase; Validated 423 matched cddid_all.tbl CDD PRK09358 PRK09358 236480 PRK09358 adenosine deaminase; Provisional 340 matched cddid_all.tbl CDD PRK09360 PRK09360 236481 lamB maltoporin LamB. 415 matched cddid_all.tbl CDD PRK09361 PRK09361 236482 radB DNA repair and recombination protein RadB; Provisional 225 matched cddid_all.tbl CDD PRK09362 PRK09362 181800 PRK09362 phosphoribosylaminoimidazole-succinocarboxamide synthase; Reviewed 238 matched cddid_all.tbl CDD PRK09364 PRK09364 236483 moaC cyclic pyranopterin monophosphate synthase MoaC. 159 matched cddid_all.tbl CDD PRK09367 PRK09367 236484 PRK09367 histidine ammonia-lyase; Provisional 500 matched cddid_all.tbl CDD PRK09368 PRK09368 236485 PRK09368 gas vesicle structural protein GvpA. 140 matched cddid_all.tbl CDD PRK09369 PRK09369 236486 PRK09369 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Validated 417 matched cddid_all.tbl CDD PRK09371 PRK09371 181805 PRK09371 gas vesicle structural protein GvpA. 68 matched cddid_all.tbl CDD PRK09372 PRK09372 236487 PRK09372 ribonuclease E inhibitor RraA. 159 matched cddid_all.tbl CDD PRK09375 PRK09375 236489 PRK09375 quinolinate synthase NadA. 319 matched cddid_all.tbl CDD PRK09376 PRK09376 236490 rho transcription termination factor Rho; Provisional 416 matched cddid_all.tbl CDD PRK09379 PRK09379 181811 PRK09379 LytR family transcriptional regulator. 303 matched cddid_all.tbl CDD PRK09381 PRK09381 181812 trxA thioredoxin TrxA. 109 matched cddid_all.tbl CDD PRK09382 PRK09382 236492 ispDF bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional 378 matched cddid_all.tbl CDD PRK09389 PRK09389 236493 PRK09389 (R)-citramalate synthase; Provisional 488 matched cddid_all.tbl CDD PRK09390 PRK09390 181815 fixJ response regulator FixJ; Provisional 202 matched cddid_all.tbl CDD PRK09391 PRK09391 236494 fixK transcriptional regulator FixK; Provisional 230 matched cddid_all.tbl CDD PRK09392 PRK09392 181817 ftrB transcriptional activator FtrB; Provisional 236 matched cddid_all.tbl CDD PRK09393 PRK09393 181818 ftrA transcriptional activator FtrA; Provisional 322 matched cddid_all.tbl CDD PRK09395 PRK09395 236495 actP cation/acetate symporter ActP. 551 matched cddid_all.tbl CDD PRK09398 PRK09398 236496 sspN acid-soluble spore protein N; Provisional 47 matched cddid_all.tbl CDD PRK09399 PRK09399 181821 sspP small acid-soluble spore protein P. 48 matched cddid_all.tbl CDD PRK09400 PRK09400 236497 secE preprotein translocase subunit SecE; Reviewed 61 matched cddid_all.tbl CDD PRK09404 PRK09404 236499 sucA 2-oxoglutarate dehydrogenase E1 component; Reviewed 924 matched cddid_all.tbl CDD PRK09405 PRK09405 236500 aceE pyruvate dehydrogenase subunit E1; Reviewed 891 matched cddid_all.tbl CDD PRK09406 PRK09406 181826 gabD1 succinic semialdehyde dehydrogenase; Reviewed 457 matched cddid_all.tbl CDD PRK09407 PRK09407 236501 gabD2 succinic semialdehyde dehydrogenase; Reviewed 524 matched cddid_all.tbl CDD PRK09408 PRK09408 181828 ompX outer membrane protein OmpX. 171 matched cddid_all.tbl CDD PRK09409 PRK09409 181829 PRK09409 IS2 transposase TnpB; Reviewed 301 matched cddid_all.tbl CDD PRK09410 PRK09410 236502 ulaA PTS system ascorbate-specific transporter subunit IIC; Reviewed 452 matched cddid_all.tbl CDD PRK09411 PRK09411 181831 PRK09411 carbamate kinase; Reviewed 297 matched cddid_all.tbl CDD PRK09412 PRK09412 236503 PRK09412 anaerobic C4-dicarboxylate transporter; Reviewed 433 matched cddid_all.tbl CDD PRK09413 PRK09413 181833 PRK09413 IS2 repressor TnpA; Reviewed 121 matched cddid_all.tbl CDD PRK09414 PRK09414 181834 PRK09414 NADP-specific glutamate dehydrogenase. 445 matched cddid_all.tbl CDD PRK09415 PRK09415 181835 PRK09415 RNA polymerase factor sigma C; Reviewed 179 matched cddid_all.tbl CDD PRK09416 PRK09416 181836 lstR PadR family transcriptional regulator. 135 matched cddid_all.tbl CDD PRK09417 PRK09417 181837 mogA molybdenum cofactor biosynthesis protein MogA; Provisional 193 matched cddid_all.tbl CDD PRK09418 PRK09418 236504 PRK09418 bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase. 780 matched cddid_all.tbl CDD PRK09419 PRK09419 236505 PRK09419 multifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase/5'-nucleotidase. 1163 matched cddid_all.tbl CDD PRK09420 PRK09420 236506 cpdB bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase. 649 matched cddid_all.tbl CDD PRK09421 PRK09421 181841 modB molybdate ABC transporter permease subunit. 229 matched cddid_all.tbl CDD PRK09422 PRK09422 181842 PRK09422 ethanol-active dehydrogenase/acetaldehyde-active reductase; Provisional 338 matched cddid_all.tbl CDD PRK09423 PRK09423 181843 gldA glycerol dehydrogenase; Provisional 366 matched cddid_all.tbl CDD PRK09424 PRK09424 236507 pntA Re/Si-specific NAD(P)(+) transhydrogenase subunit alpha. 509 matched cddid_all.tbl CDD PRK09425 PRK09425 181845 prpD bifunctional 2-methylcitrate dehydratase/aconitate hydratase. 480 matched cddid_all.tbl CDD PRK09426 PRK09426 236508 PRK09426 methylmalonyl-CoA mutase; Reviewed 714 matched cddid_all.tbl CDD PRK09427 PRK09427 236509 PRK09427 bifunctional indole-3-glycerol-phosphate synthase TrpC/phosphoribosylanthranilate isomerase TrpF. 454 matched cddid_all.tbl CDD PRK09428 PRK09428 236510 pssA CDP-diacylglycerol--serine O-phosphatidyltransferase. 451 matched cddid_all.tbl CDD PRK09429 PRK09429 236511 mepA penicillin-insensitive murein endopeptidase; Reviewed 275 matched cddid_all.tbl CDD PRK09430 PRK09430 236512 djlA co-chaperone DjlA. 267 matched cddid_all.tbl CDD PRK09431 PRK09431 236513 asnB asparagine synthetase B; Provisional 554 matched cddid_all.tbl CDD PRK09432 PRK09432 181852 metF methylenetetrahydrofolate reductase. 296 matched cddid_all.tbl CDD PRK09433 PRK09433 181853 thiP thiamine transporter membrane protein; Reviewed 525 matched cddid_all.tbl CDD PRK09434 PRK09434 236514 PRK09434 aminoimidazole riboside kinase; Provisional 304 matched cddid_all.tbl CDD PRK09435 PRK09435 236515 PRK09435 methylmalonyl Co-A mutase-associated GTPase MeaB. 332 matched cddid_all.tbl CDD PRK09436 PRK09436 181856 thrA bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional 819 matched cddid_all.tbl CDD PRK09437 PRK09437 181857 bcp thioredoxin-dependent thiol peroxidase; Reviewed 154 matched cddid_all.tbl CDD PRK09438 PRK09438 236516 nudB dihydroneopterin triphosphate pyrophosphatase; Provisional 148 matched cddid_all.tbl CDD PRK09439 PRK09439 181859 PRK09439 PTS system glucose-specific transporter subunit; Provisional 169 matched cddid_all.tbl CDD PRK09440 PRK09440 236517 avtA valine--pyruvate transaminase; Provisional 416 matched cddid_all.tbl CDD PRK09441 PRK09441 236518 PRK09441 cytoplasmic alpha-amylase; Reviewed 479 matched cddid_all.tbl CDD PRK09444 PRK09444 236520 pntB Re/Si-specific NAD(P)(+) transhydrogenase subunit beta. 462 matched cddid_all.tbl CDD PRK09448 PRK09448 236521 PRK09448 DNA starvation/stationary phase protection protein Dps; Provisional 162 matched cddid_all.tbl CDD PRK09449 PRK09449 181865 PRK09449 dUMP phosphatase; Provisional 224 matched cddid_all.tbl CDD PRK09450 PRK09450 236522 cyaA class I adenylate cyclase. 830 matched cddid_all.tbl CDD PRK09451 PRK09451 181867 glmU bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU. 456 matched cddid_all.tbl CDD PRK09452 PRK09452 236523 potA spermidine/putrescine ABC transporter ATP-binding protein PotA. 375 matched cddid_all.tbl CDD PRK09453 PRK09453 181869 PRK09453 phosphodiesterase; Provisional 182 matched cddid_all.tbl CDD PRK09454 PRK09454 236524 ugpQ cytoplasmic glycerophosphodiester phosphodiesterase; Provisional 249 matched cddid_all.tbl CDD PRK09455 PRK09455 236525 rseB anti-sigma E factor; Provisional 319 matched cddid_all.tbl CDD PRK09456 PRK09456 181872 PRK09456 ?-D-glucose-1-phosphatase; Provisional 199 matched cddid_all.tbl CDD PRK09457 PRK09457 181873 astD succinylglutamic semialdehyde dehydrogenase; Reviewed 487 matched cddid_all.tbl CDD PRK09458 PRK09458 236526 pspB envelope stress response membrane protein PspB. 75 matched cddid_all.tbl CDD PRK09461 PRK09461 181876 ansA cytoplasmic asparaginase I; Provisional 335 matched cddid_all.tbl CDD PRK09462 PRK09462 236527 fur ferric uptake regulator; Provisional 148 matched cddid_all.tbl CDD PRK09463 PRK09463 236528 fadE acyl-CoA dehydrogenase; Reviewed 777 matched cddid_all.tbl CDD PRK09464 PRK09464 181879 pdhR pyruvate dehydrogenase complex transcriptional repressor PdhR. 254 matched cddid_all.tbl CDD PRK09465 PRK09465 236529 tolC outer membrane channel protein; Reviewed 446 matched cddid_all.tbl CDD PRK09466 PRK09466 236530 metL bifunctional aspartate kinase II/homoserine dehydrogenase II; Provisional 810 matched cddid_all.tbl CDD PRK09467 PRK09467 236531 envZ osmolarity sensor protein; Provisional 435 matched cddid_all.tbl CDD PRK09468 PRK09468 181883 ompR osmolarity response regulator; Provisional 239 matched cddid_all.tbl CDD PRK09469 PRK09469 181884 glnA glutamate--ammonia ligase. 469 matched cddid_all.tbl CDD PRK09470 PRK09470 236532 cpxA envelope stress sensor histidine kinase CpxA. 461 matched cddid_all.tbl CDD PRK09471 PRK09471 181886 oppB oligopeptide ABC transporter permease OppB. 306 matched cddid_all.tbl CDD PRK09472 PRK09472 181887 ftsA cell division protein FtsA; Reviewed 420 matched cddid_all.tbl CDD PRK09473 PRK09473 181888 oppD oligopeptide transporter ATP-binding component; Provisional 330 matched cddid_all.tbl CDD PRK09474 PRK09474 236533 malE maltose/maltodextrin ABC transporter substrate-binding protein MalE. 396 matched cddid_all.tbl CDD PRK09476 PRK09476 236534 napG quinol dehydrogenase periplasmic component; Provisional 254 matched cddid_all.tbl CDD PRK09477 PRK09477 236535 napH quinol dehydrogenase membrane component; Provisional 271 matched cddid_all.tbl CDD PRK09478 PRK09478 181892 mglC galactose/methyl galactoside ABC transporter permease MglC. 336 matched cddid_all.tbl CDD PRK09479 PRK09479 236536 glpX fructose 1,6-bisphosphatase II; Reviewed 319 matched cddid_all.tbl CDD PRK09480 PRK09480 181894 slmA division inhibitor protein; Provisional 194 matched cddid_all.tbl CDD PRK09481 PRK09481 236537 sspA stringent starvation protein A; Provisional 211 matched cddid_all.tbl CDD PRK09482 PRK09482 181896 PRK09482 flap endonuclease-like protein; Provisional 256 matched cddid_all.tbl CDD PRK09483 PRK09483 236538 PRK09483 response regulator; Provisional 217 matched cddid_all.tbl CDD PRK09484 PRK09484 181898 PRK09484 3-deoxy-manno-octulosonate-8-phosphatase KdsC. 183 matched cddid_all.tbl CDD PRK09485 PRK09485 181899 mmuM homocysteine methyltransferase; Provisional 304 matched cddid_all.tbl CDD PRK09487 PRK09487 181900 sdhC succinate dehydrogenase cytochrome b556 subunit. 129 matched cddid_all.tbl CDD PRK09488 PRK09488 181901 sdhD succinate dehydrogenase membrane anchor subunit. 115 matched cddid_all.tbl CDD PRK09489 PRK09489 181902 rsmC 16S rRNA (guanine(1207)-N(2))-methyltransferase RsmC. 342 matched cddid_all.tbl CDD PRK09490 PRK09490 236539 metH B12-dependent methionine synthase; Provisional 1229 matched cddid_all.tbl CDD PRK09491 PRK09491 181904 rimI ribosomal-protein-alanine N-acetyltransferase; Provisional 146 matched cddid_all.tbl CDD PRK09493 PRK09493 181906 glnQ glutamine ABC transporter ATP-binding protein GlnQ. 240 matched cddid_all.tbl CDD PRK09494 PRK09494 181907 glnP glutamine ABC transporter permease protein; Reviewed 219 matched cddid_all.tbl CDD PRK09495 PRK09495 236540 glnH glutamine ABC transporter periplasmic protein; Reviewed 247 matched cddid_all.tbl CDD PRK09496 PRK09496 236541 trkA Trk system potassium transporter TrkA. 453 matched cddid_all.tbl CDD PRK09497 PRK09497 181910 potB spermidine/putrescine ABC transporter membrane protein; Reviewed 285 matched cddid_all.tbl CDD PRK09498 PRK09498 181911 sifA type III secretion system effector SifA. 336 matched cddid_all.tbl CDD PRK09499 PRK09499 137339 sifB type III secretion system effector SifB. 316 matched cddid_all.tbl CDD PRK09500 PRK09500 236542 potC spermidine/putrescine ABC transporter membrane protein; Reviewed 256 matched cddid_all.tbl CDD PRK09501 PRK09501 181913 potD spermidine/putrescine ABC transporter periplasmic substrate-binding protein; Reviewed 348 matched cddid_all.tbl CDD PRK09502 PRK09502 181914 iscA iron-sulfur cluster assembly protein IscA. 107 matched cddid_all.tbl CDD PRK09504 PRK09504 181915 sufA iron-sulfur cluster assembly scaffold protein; Provisional 122 matched cddid_all.tbl CDD PRK09505 PRK09505 236543 malS alpha-amylase; Reviewed 683 matched cddid_all.tbl CDD PRK09506 PRK09506 236544 mrcB bifunctional glycosyl transferase/transpeptidase; Reviewed 830 matched cddid_all.tbl CDD PRK09507 PRK09507 169931 cspE cold shock-like protein CspE. 69 matched cddid_all.tbl CDD PRK09508 PRK09508 181918 leuO leucine transcriptional activator; Reviewed 314 matched cddid_all.tbl CDD PRK09509 PRK09509 181919 fieF CDF family cation-efflux pump FieF. 299 matched cddid_all.tbl CDD PRK09510 PRK09510 236545 tolA cell envelope integrity inner membrane protein TolA; Provisional 387 matched cddid_all.tbl CDD PRK09511 PRK09511 181921 nirD nitrite reductase small subunit NirD. 108 matched cddid_all.tbl CDD PRK09512 PRK09512 181922 rbsC ribose ABC transporter permease protein; Reviewed 320 matched cddid_all.tbl CDD PRK09513 PRK09513 181923 fruK 1-phosphofructokinase; Provisional 312 matched cddid_all.tbl CDD PRK09514 PRK09514 181924 zntR Zn(2+)-responsive transcriptional regulator. 140 matched cddid_all.tbl CDD PRK09517 PRK09517 169939 PRK09517 multifunctional thiamine-phosphate pyrophosphorylase/synthase/phosphomethylpyrimidine kinase; Provisional 755 matched cddid_all.tbl CDD PRK09518 PRK09518 236546 PRK09518 bifunctional cytidylate kinase/GTPase Der; Reviewed 712 matched cddid_all.tbl CDD PRK09519 PRK09519 77219 recA intein-containing recombinase RecA. 790 matched cddid_all.tbl CDD PRK09521 PRK09521 236547 PRK09521 exosome complex RNA-binding protein Csl4; Provisional 189 matched cddid_all.tbl CDD PRK09522 PRK09522 181927 PRK09522 bifunctional anthranilate synthase glutamate amidotransferase component TrpG/anthranilate phosphoribosyltransferase TrpD. 531 matched cddid_all.tbl CDD PRK09525 PRK09525 236548 lacZ beta-galactosidase. 1027 matched cddid_all.tbl CDD PRK09526 PRK09526 181929 lacI lac repressor; Reviewed 342 matched cddid_all.tbl CDD PRK09527 PRK09527 181930 lacA galactoside O-acetyltransferase; Reviewed 203 matched cddid_all.tbl CDD PRK09528 PRK09528 236549 lacY galactoside permease; Reviewed 420 matched cddid_all.tbl CDD PRK09529 PRK09529 236550 PRK09529 bifunctional acetyl-CoA decarbonylase/synthase complex subunit alpha/beta; Reviewed 711 matched cddid_all.tbl CDD PRK09532 PRK09532 181933 PRK09532 DNA polymerase III subunit alpha; Reviewed 874 matched cddid_all.tbl CDD PRK09533 PRK09533 236551 PRK09533 bifunctional transaldolase/phosoglucose isomerase; Validated 948 matched cddid_all.tbl CDD PRK09534 PRK09534 236552 btuF corrinoid ABC transporter substrate-binding protein; Reviewed 359 matched cddid_all.tbl CDD PRK09535 PRK09535 236553 btuC cobalamin ABC transporter permease BtuC. 366 matched cddid_all.tbl CDD PRK09536 PRK09536 236554 btuD corrinoid ABC transporter ATPase; Reviewed 402 matched cddid_all.tbl CDD PRK09537 PRK09537 236555 pylS pyrrolysine--tRNA(Pyl) ligase. 417 matched cddid_all.tbl CDD PRK09539 PRK09539 236556 PRK09539 tRNA-splicing endonuclease subunit beta; Reviewed 124 matched cddid_all.tbl CDD PRK09541 PRK09541 137367 emrE EmrE family multidrug efflux SMR transporter. 110 matched cddid_all.tbl CDD PRK09542 PRK09542 236557 manB phosphomannomutase/phosphoglucomutase; Reviewed 445 matched cddid_all.tbl CDD PRK09543 PRK09543 181938 znuB zinc ABC transporter permease subunit ZnuB. 261 matched cddid_all.tbl CDD PRK09544 PRK09544 181939 znuC high-affinity zinc transporter ATPase; Reviewed 251 matched cddid_all.tbl CDD PRK09545 PRK09545 236558 znuA zinc ABC transporter substrate-binding protein ZnuA. 311 matched cddid_all.tbl CDD PRK09546 PRK09546 181941 zntB zinc transporter ZntB. 324 matched cddid_all.tbl CDD PRK09547 PRK09547 181942 nhaB sodium/proton antiporter NhaB. 513 matched cddid_all.tbl CDD PRK09548 PRK09548 236559 PRK09548 PTS ascorbate-specific subunit IIBC. 602 matched cddid_all.tbl CDD PRK09549 PRK09549 236560 mtnW 2,3-diketo-5-methylthiopentyl-1-phosphate enolase; Reviewed 407 matched cddid_all.tbl CDD PRK09552 PRK09552 236562 mtnX 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase; Reviewed 219 matched cddid_all.tbl CDD PRK09553 PRK09553 181947 tauD taurine dioxygenase; Reviewed 277 matched cddid_all.tbl CDD PRK09554 PRK09554 236563 feoB Fe(2+) transporter permease subunit FeoB. 772 matched cddid_all.tbl CDD PRK09555 PRK09555 181949 feoA ferrous iron transporter A. 74 matched cddid_all.tbl CDD PRK09556 PRK09556 236564 uhpT hexose-6-phosphate:phosphate antiporter. 467 matched cddid_all.tbl CDD PRK09557 PRK09557 236565 PRK09557 fructokinase; Reviewed 301 matched cddid_all.tbl CDD PRK09558 PRK09558 236566 ushA bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor; Reviewed 551 matched cddid_all.tbl CDD PRK09559 PRK09559 236567 PRK09559 putative global regulator; Reviewed 327 matched cddid_all.tbl CDD PRK09560 PRK09560 236568 nhaA pH-dependent sodium/proton antiporter; Reviewed 389 matched cddid_all.tbl CDD PRK09561 PRK09561 181955 nhaA sodium/proton antiporter NhaA. 388 matched cddid_all.tbl CDD PRK09562 PRK09562 236569 mazG nucleoside triphosphate pyrophosphohydrolase; Reviewed 262 matched cddid_all.tbl CDD PRK09564 PRK09564 181958 PRK09564 coenzyme A disulfide reductase; Reviewed 444 matched cddid_all.tbl CDD PRK09565 PRK09565 236571 PRK09565 heme-binding protein. 533 matched cddid_all.tbl CDD PRK09566 PRK09566 236572 nirA ferredoxin-nitrite reductase; Reviewed 513 matched cddid_all.tbl CDD PRK09567 PRK09567 236573 nirA NirA family protein. 593 matched cddid_all.tbl CDD PRK09568 PRK09568 236574 PRK09568 DNA primase regulatory subunit PriL. 306 matched cddid_all.tbl CDD PRK09569 PRK09569 181961 PRK09569 citrate (Si)-synthase. 437 matched cddid_all.tbl CDD PRK09570 PRK09570 236575 rpoH DNA-directed RNA polymerase subunit H; Reviewed 79 matched cddid_all.tbl CDD PRK09573 PRK09573 181963 PRK09573 (S)-2,3-di-O-geranylgeranylglyceryl phosphate synthase; Reviewed 279 matched cddid_all.tbl CDD PRK09575 PRK09575 236576 vmrA MATE family efflux transporter. 453 matched cddid_all.tbl CDD PRK09577 PRK09577 169981 PRK09577 multidrug efflux RND transporter permease subunit. 1032 matched cddid_all.tbl CDD PRK09578 PRK09578 169982 PRK09578 MexX/AxyX family multidrug efflux RND transporter periplasmic adaptor subunit. 385 matched cddid_all.tbl CDD PRK09579 PRK09579 169983 PRK09579 multidrug efflux RND transporter permease subunit. 1017 matched cddid_all.tbl CDD PRK09580 PRK09580 181965 sufC cysteine desulfurase ATPase component; Reviewed 248 matched cddid_all.tbl CDD PRK09581 PRK09581 236577 pleD response regulator PleD; Reviewed 457 matched cddid_all.tbl CDD PRK09582 PRK09582 181967 chaB putative cation transport regulator ChaB. 76 matched cddid_all.tbl CDD PRK09583 PRK09583 236578 PRK09583 mycothiol-dependent maleylpyruvate isomerase; Reviewed 241 matched cddid_all.tbl CDD PRK09584 PRK09584 181969 tppB dipeptide/tripeptide permease DtpA. 500 matched cddid_all.tbl CDD PRK09585 PRK09585 236579 anmK anhydro-N-acetylmuramic acid kinase; Reviewed 365 matched cddid_all.tbl CDD PRK09586 PRK09586 181971 murP PTS system N-acetylmuramic acid transporter subunits EIIBC; Reviewed 476 matched cddid_all.tbl CDD PRK09588 PRK09588 181972 PRK09588 hypothetical protein; Reviewed 376 matched cddid_all.tbl CDD PRK09589 PRK09589 181973 celA 6-phospho-beta-glucosidase; Reviewed 476 matched cddid_all.tbl CDD PRK09590 PRK09590 181974 celB PTS cellobiose transporter subunit IIB. 104 matched cddid_all.tbl CDD PRK09591 PRK09591 181975 celC PTS cellobiose transporter subunit IIA. 104 matched cddid_all.tbl CDD PRK09592 PRK09592 181976 celD PTS cellobiose transporter subunit IIC. 449 matched cddid_all.tbl CDD PRK09593 PRK09593 236580 arb 6-phospho-beta-glucosidase; Reviewed 478 matched cddid_all.tbl CDD PRK09597 PRK09597 181978 PRK09597 lipid A 1-phosphatase LpxE. 190 matched cddid_all.tbl CDD PRK09598 PRK09598 236581 PRK09598 phosphoethanolamine--lipid A transferase EptA. 522 matched cddid_all.tbl CDD PRK09599 PRK09599 236582 PRK09599 NADP-dependent phosphogluconate dehydrogenase. 301 matched cddid_all.tbl CDD PRK09602 PRK09602 236584 PRK09602 translation-associated GTPase; Reviewed 396 matched cddid_all.tbl CDD PRK09603 PRK09603 181983 PRK09603 DNA-directed RNA polymerase subunit beta/beta'. 2890 matched cddid_all.tbl CDD PRK09604 PRK09604 236585 PRK09604 tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex transferase subunit TsaD. 332 matched cddid_all.tbl CDD PRK09605 PRK09605 236586 PRK09605 bifunctional N(6)-L-threonylcarbamoyladenine synthase/serine/threonine protein kinase. 535 matched cddid_all.tbl CDD PRK09606 PRK09606 236587 PRK09606 DNA-directed RNA polymerase subunit B''; Validated 494 matched cddid_all.tbl CDD PRK09607 PRK09607 236588 rps11p 30S ribosomal protein S11P; Reviewed 132 matched cddid_all.tbl CDD PRK09609 PRK09609 181988 PRK09609 hypothetical protein; Provisional 312 matched cddid_all.tbl CDD PRK09612 PRK09612 236589 rpl2p 50S ribosomal protein L2P; Validated 238 matched cddid_all.tbl CDD PRK09614 PRK09614 236591 nrdF ribonucleotide-diphosphate reductase subunit beta; Reviewed 324 matched cddid_all.tbl CDD PRK09615 PRK09615 181992 ggt gamma-glutamyltranspeptidase; Reviewed 581 matched cddid_all.tbl CDD PRK09617 PRK09617 236593 PRK09617 type III secretion system protein; Reviewed 243 matched cddid_all.tbl CDD PRK09618 PRK09618 236594 flgD flagellar hook assembly protein FlgD. 142 matched cddid_all.tbl CDD PRK09619 PRK09619 181996 flgD flagellar hook assembly protein FlgD. 218 matched cddid_all.tbl CDD PRK09620 PRK09620 181997 PRK09620 hypothetical protein; Provisional 229 matched cddid_all.tbl CDD PRK09621 PRK09621 236595 PRK09621 ATP synthase subunit C. 141 matched cddid_all.tbl CDD PRK09622 PRK09622 181999 porA 2-oxoacid:ferredoxin oxidoreductase subunit alpha. 407 matched cddid_all.tbl CDD PRK09623 PRK09623 170016 vorD 3-methyl-2-oxobutanoate dehydrogenase subunit delta. 105 matched cddid_all.tbl CDD PRK09624 PRK09624 170017 porD pyruvate ferredoxin oxidoreductase subunit delta; Reviewed 105 matched cddid_all.tbl CDD PRK09625 PRK09625 236596 porD pyruvate flavodoxin oxidoreductase subunit delta; Reviewed 133 matched cddid_all.tbl CDD PRK09626 PRK09626 236597 oorD 2-oxoglutarate-acceptor oxidoreductase subunit OorD; Reviewed 103 matched cddid_all.tbl CDD PRK09627 PRK09627 182002 oorA 2-oxoglutarate synthase subunit alpha. 375 matched cddid_all.tbl CDD PRK09628 PRK09628 182003 oorB 2-oxoglutarate ferredoxin oxidoreductase subunit beta. 277 matched cddid_all.tbl CDD PRK09629 PRK09629 104071 PRK09629 bifunctional thiosulfate sulfurtransferase/phosphatidylserine decarboxylase; Provisional 610 matched cddid_all.tbl CDD PRK09630 PRK09630 170022 PRK09630 DNA topoisomerase IV subunit A; Provisional 479 matched cddid_all.tbl CDD PRK09631 PRK09631 236598 PRK09631 DNA topoisomerase IV subunit A; Provisional 635 matched cddid_all.tbl CDD PRK09632 PRK09632 236599 PRK09632 ATP-dependent DNA ligase; Reviewed 764 matched cddid_all.tbl CDD PRK09633 PRK09633 182006 ligD DNA ligase D. 610 matched cddid_all.tbl CDD PRK09635 PRK09635 182008 sigI RNA polymerase sigma factor SigI; Provisional 290 matched cddid_all.tbl CDD PRK09636 PRK09636 236600 PRK09636 RNA polymerase sigma factor SigJ; Provisional 293 matched cddid_all.tbl CDD PRK09637 PRK09637 236601 PRK09637 RNA polymerase sigma factor SigZ; Provisional 181 matched cddid_all.tbl CDD PRK09638 PRK09638 182010 PRK09638 RNA polymerase sigma factor SigY; Reviewed 176 matched cddid_all.tbl CDD PRK09639 PRK09639 236602 PRK09639 RNA polymerase sigma factor SigX; Provisional 166 matched cddid_all.tbl CDD PRK09640 PRK09640 236603 PRK09640 RNA polymerase sigma factor SigX; Reviewed 188 matched cddid_all.tbl CDD PRK09641 PRK09641 182012 PRK09641 RNA polymerase sigma factor SigW; Provisional 187 matched cddid_all.tbl CDD PRK09642 PRK09642 170031 PRK09642 RNA polymerase sigma factor. 160 matched cddid_all.tbl CDD PRK09643 PRK09643 236604 PRK09643 RNA polymerase sigma factor SigM; Reviewed 192 matched cddid_all.tbl CDD PRK09644 PRK09644 170033 PRK09644 RNA polymerase sigma factor SigM; Provisional 165 matched cddid_all.tbl CDD PRK09645 PRK09645 236605 PRK09645 ECF RNA polymerase sigma factor SigL. 173 matched cddid_all.tbl CDD PRK09646 PRK09646 182015 PRK09646 ECF RNA polymerase sigma factor SigK. 194 matched cddid_all.tbl CDD PRK09647 PRK09647 236606 PRK09647 RNA polymerase sigma factor SigE; Reviewed 203 matched cddid_all.tbl CDD PRK09648 PRK09648 236607 PRK09648 RNA polymerase sigma factor ShbA. 189 matched cddid_all.tbl CDD PRK09649 PRK09649 137458 PRK09649 RNA polymerase sigma factor SigC; Reviewed 185 matched cddid_all.tbl CDD PRK09651 PRK09651 182018 PRK09651 RNA polymerase sigma factor FecI; Provisional 172 matched cddid_all.tbl CDD PRK09652 PRK09652 236608 PRK09652 RNA polymerase sigma factor RpoE; Provisional 182 matched cddid_all.tbl CDD PRK09653 PRK09653 236609 eutD phosphotransacetylase. 324 matched cddid_all.tbl CDD PRK09662 PRK09662 182021 PRK09662 GspL-like protein; Provisional 286 matched cddid_all.tbl CDD PRK09664 PRK09664 182022 PRK09664 low affinity tryptophan permease TnaB. 415 matched cddid_all.tbl CDD PRK09665 PRK09665 182023 PRK09665 PTS galactitol transporter subunit IIA. 150 matched cddid_all.tbl CDD PRK09669 PRK09669 236610 PRK09669 putative symporter YagG; Provisional 444 matched cddid_all.tbl CDD PRK09672 PRK09672 236611 PRK09672 phage exclusion protein Lit; Provisional 305 matched cddid_all.tbl CDD PRK09674 PRK09674 182026 PRK09674 enoyl-CoA hydratase-isomerase; Provisional 255 matched cddid_all.tbl CDD PRK09677 PRK09677 137467 PRK09677 putative lipopolysaccharide biosynthesis O-acetyl transferase WbbJ; Provisional 192 matched cddid_all.tbl CDD PRK09678 PRK09678 137468 PRK09678 DNA-binding transcriptional regulator; Provisional 72 matched cddid_all.tbl CDD PRK09681 PRK09681 182027 PRK09681 putative type II secretion protein GspC; Provisional 276 matched cddid_all.tbl CDD PRK09685 PRK09685 236612 PRK09685 DNA-binding transcriptional activator FeaR; Provisional 302 matched cddid_all.tbl CDD PRK09687 PRK09687 170047 PRK09687 putative lyase; Provisional 280 matched cddid_all.tbl CDD PRK09689 PRK09689 182029 PRK09689 prophage protein NinE; Provisional 56 matched cddid_all.tbl CDD PRK09692 PRK09692 170049 PRK09692 integrase; Provisional 413 matched cddid_all.tbl CDD PRK09693 PRK09693 236613 PRK09693 Cascade antiviral complex protein; Validated 489 matched cddid_all.tbl CDD PRK09694 PRK09694 182031 PRK09694 CRISPR-associated helicase/endonuclease Cas3. 878 matched cddid_all.tbl CDD PRK09695 PRK09695 182032 PRK09695 glycolate permease GlcA. 560 matched cddid_all.tbl CDD PRK09697 PRK09697 182033 PRK09697 putative general secretion pathway protein GspB. 139 matched cddid_all.tbl CDD PRK09698 PRK09698 182034 PRK09698 D-allose kinase; Provisional 302 matched cddid_all.tbl CDD PRK09699 PRK09699 182035 PRK09699 D-allose ABC transporter permease. 312 matched cddid_all.tbl CDD PRK09700 PRK09700 182036 PRK09700 D-allose ABC transporter ATP-binding protein AlsA. 510 matched cddid_all.tbl CDD PRK09701 PRK09701 182037 PRK09701 D-allose transporter substrate-binding protein. 311 matched cddid_all.tbl CDD PRK09702 PRK09702 77355 PRK09702 PTS sugar transporter subunit IIB. 161 matched cddid_all.tbl CDD PRK09705 PRK09705 236614 cynX putative cyanate transporter; Provisional 393 matched cddid_all.tbl CDD PRK09706 PRK09706 182039 PRK09706 transcriptional repressor DicA; Reviewed 135 matched cddid_all.tbl CDD PRK09709 PRK09709 236615 PRK09709 exodeoxyribonuclease VIII. 877 matched cddid_all.tbl CDD PRK09710 PRK09710 182042 lar type I toxin-antitoxin system endodeoxyribonuclease toxin RalR. 64 matched cddid_all.tbl CDD PRK09713 PRK09713 137485 focB formate transporter. 282 matched cddid_all.tbl CDD PRK09716 PRK09716 182043 PRK09716 YhaC family protein. 395 matched cddid_all.tbl CDD PRK09717 PRK09717 182044 PRK09717 stationary phase growth adaptation protein; Provisional 179 matched cddid_all.tbl CDD PRK09718 PRK09718 182045 PRK09718 SopA family protein. 512 matched cddid_all.tbl CDD PRK09719 PRK09719 182046 PRK09719 hypothetical protein; Provisional 89 matched cddid_all.tbl CDD PRK09720 PRK09720 182047 cybC cytochrome b562; Provisional 100 matched cddid_all.tbl CDD PRK09722 PRK09722 236616 PRK09722 allulose-6-phosphate 3-epimerase; Provisional 229 matched cddid_all.tbl CDD PRK09723 PRK09723 236617 PRK09723 fimbrial-like adhesin. 421 matched cddid_all.tbl CDD PRK09726 PRK09726 182049 PRK09726 type II toxin-antitoxin system antitoxin HipB. 88 matched cddid_all.tbl CDD PRK09727 PRK09727 137493 PRK09727 his operon leader peptide; Provisional 16 matched cddid_all.tbl CDD PRK09729 PRK09729 182050 PRK09729 hypothetical protein; Provisional 68 matched cddid_all.tbl CDD PRK09730 PRK09730 182051 PRK09730 SDR family oxidoreductase. 247 matched cddid_all.tbl CDD PRK09731 PRK09731 182052 PRK09731 type II secretion system protein. 178 matched cddid_all.tbl CDD PRK09732 PRK09732 170072 PRK09732 hypothetical protein; Provisional 134 matched cddid_all.tbl CDD PRK09733 PRK09733 182053 PRK09733 fimbrial-like protein. 181 matched cddid_all.tbl CDD PRK09736 PRK09736 236618 PRK09736 5-methylcytosine-specific restriction enzyme subunit McrC; Provisional 352 matched cddid_all.tbl CDD PRK09737 PRK09737 236619 PRK09737 type I restriction-modification system specificity subunit. 461 matched cddid_all.tbl CDD PRK09738 PRK09738 182055 PRK09738 small toxic polypeptide; Provisional 52 matched cddid_all.tbl CDD PRK09739 PRK09739 236620 PRK09739 NAD(P)H oxidoreductase. 199 matched cddid_all.tbl CDD PRK09741 PRK09741 182057 PRK09741 hypothetical protein; Provisional 148 matched cddid_all.tbl CDD PRK09744 PRK09744 137503 PRK09744 DNA-binding transcriptional regulator DicC; Provisional 75 matched cddid_all.tbl CDD PRK09750 PRK09750 182058 PRK09750 hypothetical protein; Provisional 64 matched cddid_all.tbl CDD PRK09751 PRK09751 137505 PRK09751 putative ATP-dependent helicase Lhr; Provisional 1490 matched cddid_all.tbl CDD PRK09752 PRK09752 182059 PRK09752 AIDA-I family autotransporter YfaL. 1250 matched cddid_all.tbl CDD PRK09754 PRK09754 170080 PRK09754 phenylpropionate dioxygenase ferredoxin reductase subunit; Provisional 396 matched cddid_all.tbl CDD PRK09755 PRK09755 182060 PRK09755 ABC transporter substrate-binding protein. 535 matched cddid_all.tbl CDD PRK09756 PRK09756 182061 PRK09756 PTS N-acetylgalactosamine transporter subunit IIB. 158 matched cddid_all.tbl CDD PRK09757 PRK09757 236621 PRK09757 PTS N-acetylgalactosamine transporter subunit IIC. 267 matched cddid_all.tbl CDD PRK09759 PRK09759 182063 PRK09759 type I toxin-antitoxin system toxin HokA. 50 matched cddid_all.tbl CDD PRK09762 PRK09762 182064 PRK09762 galactosamine-6-phosphate isomerase; Provisional 232 matched cddid_all.tbl CDD PRK09764 PRK09764 182065 PRK09764 GntR family transcriptional regulator. 240 matched cddid_all.tbl CDD PRK09765 PRK09765 182066 PRK09765 PTS system 2-O-a-mannosyl-D-glycerate specific transporter subunit IIABC; Provisional 631 matched cddid_all.tbl CDD PRK09767 PRK09767 182067 PRK09767 DUF559 domain-containing protein. 117 matched cddid_all.tbl CDD PRK09772 PRK09772 170086 PRK09772 transcriptional antiterminator BglG; Provisional 278 matched cddid_all.tbl CDD PRK09774 PRK09774 236622 PRK09774 fec operon regulator FecR; Reviewed 319 matched cddid_all.tbl CDD PRK09775 PRK09775 236623 PRK09775 type II toxin-antitoxin system HipA family toxin YjjJ. 442 matched cddid_all.tbl CDD PRK09776 PRK09776 182070 PRK09776 putative diguanylate cyclase; Provisional 1092 matched cddid_all.tbl CDD PRK09777 PRK09777 182071 fecD Fe(3+) dicitrate ABC transporter permease subunit FecD. 318 matched cddid_all.tbl CDD PRK09778 PRK09778 170091 PRK09778 type I toxin-antitoxin system antitoxin YafN. 97 matched cddid_all.tbl CDD PRK09781 PRK09781 170092 PRK09781 hypothetical protein; Provisional 181 matched cddid_all.tbl CDD PRK09782 PRK09782 236624 PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional 987 matched cddid_all.tbl CDD PRK09783 PRK09783 236625 PRK09783 copper/silver efflux system membrane fusion protein CusB; Provisional 409 matched cddid_all.tbl CDD PRK09784 PRK09784 182074 PRK09784 YccE family protein. 417 matched cddid_all.tbl CDD PRK09786 PRK09786 182075 PRK09786 endodeoxyribonuclease RUS; Reviewed 120 matched cddid_all.tbl CDD PRK09790 PRK09790 182076 PRK09790 hypothetical protein; Reviewed 91 matched cddid_all.tbl CDD PRK09791 PRK09791 182077 PRK09791 LysR family transcriptional regulator. 302 matched cddid_all.tbl CDD PRK09792 PRK09792 182078 PRK09792 4-aminobutyrate transaminase; Provisional 421 matched cddid_all.tbl CDD PRK09793 PRK09793 182079 PRK09793 methyl-accepting chemotaxis protein IV. 533 matched cddid_all.tbl CDD PRK09795 PRK09795 182080 PRK09795 aminopeptidase; Provisional 361 matched cddid_all.tbl CDD PRK09796 PRK09796 182081 PRK09796 PTS system cellobiose/arbutin/salicin-specific transporter subunits IIBC; Provisional 472 matched cddid_all.tbl CDD PRK09798 PRK09798 182082 PRK09798 MazF-MazE toxin-antitoxin system antitoxin MazE. 82 matched cddid_all.tbl CDD PRK09800 PRK09800 182084 PRK09800 putative hypoxanthine oxidase; Provisional 956 matched cddid_all.tbl CDD PRK09801 PRK09801 182085 PRK09801 LysR family transcriptional regulator. 310 matched cddid_all.tbl CDD PRK09802 PRK09802 182086 PRK09802 DeoR family transcriptional regulator. 269 matched cddid_all.tbl CDD PRK09804 PRK09804 182087 PRK09804 C4-dicarboxylate transporter DcuC. 455 matched cddid_all.tbl CDD PRK09806 PRK09806 77417 PRK09806 tryptophanase leader peptide; Provisional 24 matched cddid_all.tbl CDD PRK09807 PRK09807 182088 PRK09807 hypothetical protein; Provisional 161 matched cddid_all.tbl CDD PRK09810 PRK09810 137533 PRK09810 lipoprotein antitoxin entericidin A. 41 matched cddid_all.tbl CDD PRK09812 PRK09812 182089 PRK09812 type II toxin-antitoxin system ChpB family toxin. 116 matched cddid_all.tbl CDD PRK09813 PRK09813 182090 PRK09813 fructoselysine 6-kinase; Provisional 260 matched cddid_all.tbl CDD PRK09814 PRK09814 236626 PRK09814 sugar transferase. 333 matched cddid_all.tbl CDD PRK09816 PRK09816 77423 thrL thr operon leader peptide; Provisional 21 matched cddid_all.tbl CDD PRK09818 PRK09818 182092 PRK09818 kinase inhibitor. 183 matched cddid_all.tbl CDD PRK09819 PRK09819 182093 PRK09819 mannosylglycerate hydrolase. 875 matched cddid_all.tbl CDD PRK09821 PRK09821 182094 PRK09821 putative transporter; Provisional 454 matched cddid_all.tbl CDD PRK09822 PRK09822 182095 PRK09822 lipopolysaccharide core biosynthesis protein; Provisional 269 matched cddid_all.tbl CDD PRK09823 PRK09823 170114 PRK09823 putative inner membrane protein; Provisional 160 matched cddid_all.tbl CDD PRK09824 PRK09824 236627 PRK09824 PTS system beta-glucoside-specific transporter subunits IIABC; Provisional 627 matched cddid_all.tbl CDD PRK09825 PRK09825 182097 idnK gluconokinase. 176 matched cddid_all.tbl CDD PRK09828 PRK09828 182098 PRK09828 putative fimbrial outer membrane usher protein; Provisional 865 matched cddid_all.tbl CDD PRK09831 PRK09831 182099 PRK09831 GNAT family N-acetyltransferase. 147 matched cddid_all.tbl CDD PRK09834 PRK09834 182100 PRK09834 DNA-binding transcriptional regulator. 263 matched cddid_all.tbl CDD PRK09835 PRK09835 182101 PRK09835 Cu(+)/Ag(+) sensor histidine kinase. 482 matched cddid_all.tbl CDD PRK09836 PRK09836 182102 PRK09836 DNA-binding transcriptional activator CusR; Provisional 227 matched cddid_all.tbl CDD PRK09837 PRK09837 182103 PRK09837 Cu(I)/Ag(I) efflux RND transporter outer membrane protein. 461 matched cddid_all.tbl CDD PRK09838 PRK09838 182104 PRK09838 periplasmic copper-binding protein; Provisional 115 matched cddid_all.tbl CDD PRK09840 PRK09840 182105 PRK09840 catecholate siderophore receptor Fiu; Provisional 761 matched cddid_all.tbl CDD PRK09841 PRK09841 182106 PRK09841 tyrosine-protein kinase. 726 matched cddid_all.tbl CDD PRK09846 PRK09846 236628 recT recombination protein RecT. 266 matched cddid_all.tbl CDD PRK09847 PRK09847 182108 PRK09847 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase; Provisional 494 matched cddid_all.tbl CDD PRK09848 PRK09848 182109 PRK09848 glucuronide transporter; Provisional 448 matched cddid_all.tbl CDD PRK09849 PRK09849 236629 PRK09849 putative oxidoreductase; Provisional 702 matched cddid_all.tbl CDD PRK09850 PRK09850 182111 PRK09850 pseudouridine kinase; Provisional 313 matched cddid_all.tbl CDD PRK09852 PRK09852 182112 PRK09852 cryptic 6-phospho-beta-glucosidase; Provisional 474 matched cddid_all.tbl CDD PRK09854 PRK09854 182114 cmtB PTS mannitol transporter subunit IIA. 147 matched cddid_all.tbl CDD PRK09855 PRK09855 182115 PRK09855 PTS N-acetylgalactosamine transporter subunit IID. 263 matched cddid_all.tbl CDD PRK09856 PRK09856 182116 PRK09856 fructoselysine 3-epimerase; Provisional 275 matched cddid_all.tbl CDD PRK09857 PRK09857 182117 PRK09857 recombination-promoting nuclease RpnA. 292 matched cddid_all.tbl CDD PRK09859 PRK09859 137559 PRK09859 multidrug transporter subunit MdtE. 385 matched cddid_all.tbl CDD PRK09860 PRK09860 182118 PRK09860 putative alcohol dehydrogenase; Provisional 383 matched cddid_all.tbl CDD PRK09861 PRK09861 182119 PRK09861 lipoprotein NlpA. 272 matched cddid_all.tbl CDD PRK09862 PRK09862 182120 PRK09862 ATP-dependent protease. 506 matched cddid_all.tbl CDD PRK09863 PRK09863 182121 PRK09863 putative frv operon regulatory protein; Provisional 584 matched cddid_all.tbl CDD PRK09864 PRK09864 182122 PRK09864 aminopeptidase. 356 matched cddid_all.tbl CDD PRK09866 PRK09866 182123 PRK09866 clamp-binding protein CrfC. 741 matched cddid_all.tbl CDD PRK09867 PRK09867 182124 PRK09867 hypothetical protein; Provisional 209 matched cddid_all.tbl CDD PRK09870 PRK09870 182125 PRK09870 tyrosine recombinase; Provisional 200 matched cddid_all.tbl CDD PRK09871 PRK09871 182126 PRK09871 tyrosine recombinase; Provisional 198 matched cddid_all.tbl CDD PRK09874 PRK09874 182127 PRK09874 multidrug efflux MFS transporter MdtG. 408 matched cddid_all.tbl CDD PRK09875 PRK09875 182128 PRK09875 phosphotriesterase-related protein. 292 matched cddid_all.tbl CDD PRK09877 PRK09877 182129 PRK09877 2,3-diketo-L-gulonate TRAP transporter small permease protein YiaM; Provisional 157 matched cddid_all.tbl CDD PRK09880 PRK09880 182130 PRK09880 L-idonate 5-dehydrogenase; Provisional 343 matched cddid_all.tbl CDD PRK09881 PRK09881 182131 PRK09881 D,D-dipeptide ABC transporter permease. 296 matched cddid_all.tbl CDD PRK09885 PRK09885 236631 PRK09885 type II toxin-antitoxin system YafO family toxin. 132 matched cddid_all.tbl CDD PRK09890 PRK09890 77467 PRK09890 cold shock protein CspG; Provisional 70 matched cddid_all.tbl CDD PRK09891 PRK09891 170147 PRK09891 protein YmcE. 76 matched cddid_all.tbl CDD PRK09894 PRK09894 182133 PRK09894 diguanylate cyclase; Provisional 296 matched cddid_all.tbl CDD PRK09897 PRK09897 182134 PRK09897 FAD-NAD(P)-binding protein. 534 matched cddid_all.tbl CDD PRK09898 PRK09898 182135 PRK09898 ferredoxin-like protein. 208 matched cddid_all.tbl CDD PRK09902 PRK09902 182136 PRK09902 lipopolysaccharide kinase InaA. 216 matched cddid_all.tbl CDD PRK09903 PRK09903 104216 PRK09903 transporter YfdV. 314 matched cddid_all.tbl CDD PRK09906 PRK09906 182137 PRK09906 DNA-binding transcriptional regulator HcaR; Provisional 296 matched cddid_all.tbl CDD PRK09907 PRK09907 182138 PRK09907 endoribonuclease MazF. 111 matched cddid_all.tbl CDD PRK09908 PRK09908 182139 PRK09908 xanthine dehydrogenase iron sulfur-binding subunit XdhC. 159 matched cddid_all.tbl CDD PRK09912 PRK09912 182140 PRK09912 L-glyceraldehyde 3-phosphate reductase; Provisional 346 matched cddid_all.tbl CDD PRK09913 PRK09913 182141 PRK09913 PTS fructose transporter subunit IIA. 148 matched cddid_all.tbl CDD PRK09915 PRK09915 182142 PRK09915 MdtP family multidrug efflux transporter outer membrane subunit. 488 matched cddid_all.tbl CDD PRK09917 PRK09917 182143 PRK09917 threonine/serine exporter. 157 matched cddid_all.tbl CDD PRK09918 PRK09918 236632 PRK09918 putative fimbrial chaperone protein; Provisional 230 matched cddid_all.tbl CDD PRK09919 PRK09919 236633 PRK09919 anti-adapter protein IraM; Provisional 114 matched cddid_all.tbl CDD PRK09920 PRK09920 182146 PRK09920 acetyl-CoA:acetoacetyl-CoA transferase subunit alpha; Provisional 219 matched cddid_all.tbl CDD PRK09921 PRK09921 182147 PRK09921 permease DsdX; Provisional 445 matched cddid_all.tbl CDD PRK09922 PRK09922 182148 PRK09922 lipopolysaccharide 1,6-galactosyltransferase. 359 matched cddid_all.tbl CDD PRK09925 PRK09925 137592 PRK09925 leu operon leader peptide; Provisional 28 matched cddid_all.tbl CDD PRK09926 PRK09926 236634 PRK09926 fimbrial chaperone. 246 matched cddid_all.tbl CDD PRK09928 PRK09928 236635 PRK09928 choline transport protein BetT; Provisional 679 matched cddid_all.tbl CDD PRK09929 PRK09929 182151 PRK09929 hypothetical protein; Provisional 91 matched cddid_all.tbl CDD PRK09932 PRK09932 182152 PRK09932 glycerate 3-kinase. 381 matched cddid_all.tbl CDD PRK09934 PRK09934 182153 PRK09934 fimbriae assembly protein. 171 matched cddid_all.tbl CDD PRK09935 PRK09935 182154 PRK09935 fimbriae biosynthesis transcriptional regulator FimZ. 210 matched cddid_all.tbl CDD PRK09936 PRK09936 182155 PRK09936 DUF4434 family protein. 296 matched cddid_all.tbl CDD PRK09937 PRK09937 77494 PRK09937 cold shock-like protein CspD. 74 matched cddid_all.tbl CDD PRK09939 PRK09939 182156 PRK09939 acid resistance putative oxidoreductase YdeP. 759 matched cddid_all.tbl CDD PRK09940 PRK09940 182157 PRK09940 transcriptional regulator YdeO; Provisional 253 matched cddid_all.tbl CDD PRK09943 PRK09943 182158 PRK09943 HTH-type transcriptional regulator PuuR. 185 matched cddid_all.tbl CDD PRK09945 PRK09945 137602 PRK09945 hypothetical protein; Provisional 418 matched cddid_all.tbl CDD PRK09946 PRK09946 182159 PRK09946 hypothetical protein; Provisional 270 matched cddid_all.tbl CDD PRK09947 PRK09947 182160 PRK09947 YdhW family putative oxidoreductase system protein. 215 matched cddid_all.tbl CDD PRK09950 PRK09950 236636 PRK09950 putative transporter; Provisional 506 matched cddid_all.tbl CDD PRK09951 PRK09951 182162 PRK09951 hypothetical protein; Provisional 222 matched cddid_all.tbl CDD PRK09952 PRK09952 182163 PRK09952 shikimate transporter; Provisional 438 matched cddid_all.tbl CDD PRK09954 PRK09954 182165 PRK09954 sugar kinase. 362 matched cddid_all.tbl CDD PRK09955 PRK09955 182166 rihB ribosylpyrimidine nucleosidase. 313 matched cddid_all.tbl CDD PRK09956 PRK09956 182167 PRK09956 ISNCY family transposase. 308 matched cddid_all.tbl CDD PRK09958 PRK09958 182168 PRK09958 acid-sensing system DNA-binding response regulator EvgA. 204 matched cddid_all.tbl CDD PRK09959 PRK09959 182169 PRK09959 acid-sensing system histidine kinase EvgS. 1197 matched cddid_all.tbl CDD PRK09961 PRK09961 182170 PRK09961 aminopeptidase. 344 matched cddid_all.tbl CDD PRK09965 PRK09965 170182 PRK09965 3-phenylpropionate dioxygenase ferredoxin subunit; Provisional 106 matched cddid_all.tbl CDD PRK09966 PRK09966 182171 PRK09966 diguanylate cyclase DgcN. 407 matched cddid_all.tbl CDD PRK09967 PRK09967 182172 PRK09967 OmpA family protein. 160 matched cddid_all.tbl CDD PRK09968 PRK09968 182173 PRK09968 protein-serine/threonine phosphatase. 218 matched cddid_all.tbl CDD PRK09970 PRK09970 236637 PRK09970 xanthine dehydrogenase subunit XdhA; Provisional 759 matched cddid_all.tbl CDD PRK09971 PRK09971 182175 PRK09971 xanthine dehydrogenase subunit XdhB; Provisional 291 matched cddid_all.tbl CDD PRK09973 PRK09973 170188 PRK09973 lipoprotein YqhH. 85 matched cddid_all.tbl CDD PRK09974 PRK09974 236638 PRK09974 type II toxin-antitoxin system PrlF family antitoxin. 111 matched cddid_all.tbl CDD PRK09975 PRK09975 182177 PRK09975 DNA-binding transcriptional regulator EnvR; Provisional 213 matched cddid_all.tbl CDD PRK09977 PRK09977 182178 PRK09977 MgtC/SapB family protein. 215 matched cddid_all.tbl CDD PRK09978 PRK09978 137624 PRK09978 DNA-binding transcriptional regulator GadX; Provisional 274 matched cddid_all.tbl CDD PRK09979 PRK09979 77522 PRK09979 rho operon leader peptide rhoL. 33 matched cddid_all.tbl CDD PRK09980 PRK09980 182179 ompL porin OmpL. 230 matched cddid_all.tbl CDD PRK09981 PRK09981 182180 PRK09981 DUF406 domain-containing protein. 99 matched cddid_all.tbl CDD PRK09982 PRK09982 137627 PRK09982 universal stress protein UspD; Provisional 142 matched cddid_all.tbl CDD PRK09983 PRK09983 182181 pflD putative formate acetyltransferase 2; Provisional 765 matched cddid_all.tbl CDD PRK09984 PRK09984 182182 PRK09984 phosphonate ABC transporter ATP-binding protein. 262 matched cddid_all.tbl CDD PRK09986 PRK09986 182183 PRK09986 LysR family transcriptional regulator. 294 matched cddid_all.tbl CDD PRK09987 PRK09987 182184 PRK09987 dTDP-4-dehydrorhamnose reductase; Provisional 299 matched cddid_all.tbl CDD PRK09989 PRK09989 182185 PRK09989 HPr family phosphocarrier protein. 258 matched cddid_all.tbl CDD PRK09990 PRK09990 182186 PRK09990 DNA-binding transcriptional regulator GlcC; Provisional 251 matched cddid_all.tbl CDD PRK09993 PRK09993 182187 PRK09993 C-lysozyme inhibitor; Provisional 153 matched cddid_all.tbl CDD PRK09997 PRK09997 182188 PRK09997 hydroxypyruvate isomerase; Provisional 258 matched cddid_all.tbl CDD PRK10001 PRK10001 182189 PRK10001 serine-type D-Ala-D-Ala carboxypeptidase. 400 matched cddid_all.tbl CDD PRK10002 PRK10002 236639 PRK10002 porin OmpF. 362 matched cddid_all.tbl CDD PRK10003 PRK10003 236640 PRK10003 ferric-rhodotorulic acid outer membrane transporter; Provisional 729 matched cddid_all.tbl CDD PRK10005 PRK10005 182192 PRK10005 dihydroxyacetone kinase ADP-binding subunit DhaL. 210 matched cddid_all.tbl CDD PRK10014 PRK10014 182193 PRK10014 DNA-binding transcriptional repressor MalI; Provisional 342 matched cddid_all.tbl CDD PRK10015 PRK10015 182194 PRK10015 oxidoreductase; Provisional 429 matched cddid_all.tbl CDD PRK10016 PRK10016 182195 PRK10016 DNA gyrase inhibitor SbmC. 156 matched cddid_all.tbl CDD PRK10017 PRK10017 182196 PRK10017 colanic acid biosynthesis protein; Provisional 426 matched cddid_all.tbl CDD PRK10018 PRK10018 182197 PRK10018 colanic acid biosynthesis glycosyltransferase WcaA. 279 matched cddid_all.tbl CDD PRK10019 PRK10019 236641 PRK10019 nickel/cobalt efflux transporter RcnA. 279 matched cddid_all.tbl CDD PRK10022 PRK10022 182199 PRK10022 putative DNA-binding transcriptional regulator; Provisional 167 matched cddid_all.tbl CDD PRK10026 PRK10026 182200 PRK10026 arsenate reductase (glutaredoxin). 141 matched cddid_all.tbl CDD PRK10027 PRK10027 182201 PRK10027 cryptic adenine deaminase; Provisional 588 matched cddid_all.tbl CDD PRK10030 PRK10030 236642 PRK10030 YiiX family permuted papain-like enzyme. 197 matched cddid_all.tbl CDD PRK10034 PRK10034 182203 PRK10034 gluconate transporter GntP. 447 matched cddid_all.tbl CDD PRK10037 PRK10037 182204 PRK10037 cellulose biosynthesis protein BcsQ. 250 matched cddid_all.tbl CDD PRK10039 PRK10039 170217 PRK10039 hypothetical protein; Provisional 127 matched cddid_all.tbl CDD PRK10040 PRK10040 182205 PRK10040 hypothetical protein; Provisional 52 matched cddid_all.tbl CDD PRK10044 PRK10044 236643 PRK10044 ferrichrome outer membrane transporter; Provisional 727 matched cddid_all.tbl CDD PRK10045 PRK10045 182207 PRK10045 ACP phosphodiesterase. 193 matched cddid_all.tbl CDD PRK10046 PRK10046 182208 dpiA two-component response regulator DpiA; Provisional 225 matched cddid_all.tbl CDD PRK10049 PRK10049 236644 pgaA outer membrane protein PgaA; Provisional 765 matched cddid_all.tbl CDD PRK10050 PRK10050 182210 PRK10050 curli production assembly/transport protein CsgF. 138 matched cddid_all.tbl CDD PRK10051 PRK10051 182211 csgA major curlin subunit CsgA. 151 matched cddid_all.tbl CDD PRK10053 PRK10053 182212 PRK10053 YdeI family stress tolerance OB fold protein. 130 matched cddid_all.tbl CDD PRK10054 PRK10054 182213 PRK10054 efflux MFS transporter YdeE. 395 matched cddid_all.tbl CDD PRK10057 PRK10057 182214 rpsV stationary-phase-induced ribosome-associated protein. 44 matched cddid_all.tbl CDD PRK10060 PRK10060 236645 PRK10060 cyclic di-GMP phosphodiesterase. 663 matched cddid_all.tbl CDD PRK10061 PRK10061 182216 PRK10061 DNA damage-inducible protein YebG; Provisional 96 matched cddid_all.tbl CDD PRK10062 PRK10062 182217 PRK10062 hypothetical protein; Provisional 303 matched cddid_all.tbl CDD PRK10064 PRK10064 236646 PRK10064 catecholate siderophore receptor CirA; Provisional 663 matched cddid_all.tbl CDD PRK10069 PRK10069 236647 PRK10069 3-phenylpropionate/cinnamic acid dioxygenase subunit beta. 183 matched cddid_all.tbl CDD PRK10070 PRK10070 182221 PRK10070 proline/glycine betaine ABC transporter ATP-binding protein ProV. 400 matched cddid_all.tbl CDD PRK10072 PRK10072 182222 PRK10072 HTH-type transcriptional regulator. 96 matched cddid_all.tbl CDD PRK10073 PRK10073 182223 PRK10073 putative glycosyl transferase; Provisional 328 matched cddid_all.tbl CDD PRK10076 PRK10076 182224 PRK10076 pyruvate formate lyase II activase; Provisional 213 matched cddid_all.tbl CDD PRK10077 PRK10077 182225 xylE D-xylose transporter XylE; Provisional 479 matched cddid_all.tbl CDD PRK10078 PRK10078 236648 PRK10078 ribose 1,5-bisphosphokinase; Provisional 186 matched cddid_all.tbl CDD PRK10079 PRK10079 182227 PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional 241 matched cddid_all.tbl CDD PRK10081 PRK10081 170240 PRK10081 lipoprotein toxin entericidin B. 48 matched cddid_all.tbl CDD PRK10082 PRK10082 182228 PRK10082 hypochlorite stress DNA-binding transcriptional regulator HypT. 303 matched cddid_all.tbl CDD PRK10083 PRK10083 182229 PRK10083 putative oxidoreductase; Provisional 339 matched cddid_all.tbl CDD PRK10084 PRK10084 236649 PRK10084 dTDP-glucose 4,6 dehydratase; Provisional 352 matched cddid_all.tbl CDD PRK10086 PRK10086 182231 PRK10086 DNA-binding transcriptional regulator DsdC. 311 matched cddid_all.tbl CDD PRK10089 PRK10089 182232 PRK10089 chaperone CsaA. 112 matched cddid_all.tbl CDD PRK10090 PRK10090 182233 PRK10090 aldehyde dehydrogenase A; Provisional 409 matched cddid_all.tbl CDD PRK10091 PRK10091 182234 PRK10091 MFS transport protein AraJ; Provisional 382 matched cddid_all.tbl CDD PRK10092 PRK10092 182235 PRK10092 maltose O-acetyltransferase; Provisional 183 matched cddid_all.tbl CDD PRK10093 PRK10093 182236 PRK10093 primosomal replication protein N''; Provisional 171 matched cddid_all.tbl CDD PRK10094 PRK10094 182237 PRK10094 HTH-type transcriptional activator AllS. 308 matched cddid_all.tbl CDD PRK10095 PRK10095 236650 PRK10095 ribonuclease I; Provisional 268 matched cddid_all.tbl CDD PRK10096 PRK10096 182239 citG triphosphoribosyl-dephospho-CoA synthase; Provisional 292 matched cddid_all.tbl CDD PRK10098 PRK10098 182240 PRK10098 putative dehydrogenase; Provisional 350 matched cddid_all.tbl CDD PRK10100 PRK10100 182241 PRK10100 transcriptional regulator CsgD. 216 matched cddid_all.tbl CDD PRK10101 PRK10101 182242 csgB curlin minor subunit CsgB; Provisional 151 matched cddid_all.tbl CDD PRK10102 PRK10102 182243 csgC curli assembly protein CsgC; Provisional 110 matched cddid_all.tbl CDD PRK10106 PRK10106 236651 PRK10106 multiple antibiotic resistance protein MarB. 65 matched cddid_all.tbl CDD PRK10110 PRK10110 182245 PRK10110 PTS maltose transporter subunit IICB. 530 matched cddid_all.tbl CDD PRK10113 PRK10113 182246 PRK10113 cell division activator CedA. 80 matched cddid_all.tbl CDD PRK10115 PRK10115 182247 PRK10115 protease 2; Provisional 686 matched cddid_all.tbl CDD PRK10116 PRK10116 182248 PRK10116 universal stress protein UspC; Provisional 142 matched cddid_all.tbl CDD PRK10117 PRK10117 182249 PRK10117 trehalose-6-phosphate synthase; Provisional 474 matched cddid_all.tbl CDD PRK10118 PRK10118 236652 PRK10118 flagellar hook length control protein FliK. 408 matched cddid_all.tbl CDD PRK10119 PRK10119 182251 PRK10119 putative hydrolase; Provisional 231 matched cddid_all.tbl CDD PRK10122 PRK10122 182252 PRK10122 UTP--glucose-1-phosphate uridylyltransferase GalF. 297 matched cddid_all.tbl CDD PRK10123 PRK10123 182253 wcaM putative colanic acid biosynthesis protein; Provisional 464 matched cddid_all.tbl CDD PRK10124 PRK10124 182254 PRK10124 putative UDP-glucose lipid carrier transferase; Provisional 463 matched cddid_all.tbl CDD PRK10126 PRK10126 182256 PRK10126 low molecular weight protein-tyrosine-phosphatase Wzb. 147 matched cddid_all.tbl CDD PRK10128 PRK10128 182257 PRK10128 2-keto-3-deoxy-L-rhamnonate aldolase; Provisional 267 matched cddid_all.tbl CDD PRK10130 PRK10130 182258 PRK10130 HTH-type transcriptional regulator EutR. 350 matched cddid_all.tbl CDD PRK10132 PRK10132 182259 PRK10132 hypothetical protein; Provisional 108 matched cddid_all.tbl CDD PRK10133 PRK10133 182260 PRK10133 L-fucose:H+ symporter permease. 438 matched cddid_all.tbl CDD PRK10137 PRK10137 236653 PRK10137 alpha-glucosidase; Provisional 786 matched cddid_all.tbl CDD PRK10139 PRK10139 182262 PRK10139 serine endoprotease DegQ. 455 matched cddid_all.tbl CDD PRK10140 PRK10140 182263 PRK10140 N-acetyltransferase. 162 matched cddid_all.tbl CDD PRK10141 PRK10141 236654 PRK10141 DNA-binding transcriptional repressor ArsR; Provisional 117 matched cddid_all.tbl CDD PRK10146 PRK10146 182266 PRK10146 aminoalkylphosphonate N-acetyltransferase. 144 matched cddid_all.tbl CDD PRK10147 PRK10147 236655 phnH phosphonate C-P lyase system protein PhnH. 196 matched cddid_all.tbl CDD PRK10148 PRK10148 236656 PRK10148 VOC family metalloprotein YjdN. 147 matched cddid_all.tbl CDD PRK10150 PRK10150 236657 PRK10150 beta-D-glucuronidase; Provisional 604 matched cddid_all.tbl CDD PRK10151 PRK10151 182270 PRK10151 50S ribosomal protein L7/L12-serine acetyltransferase. 179 matched cddid_all.tbl CDD PRK10153 PRK10153 236658 PRK10153 DNA-binding transcriptional activator CadC; Provisional 517 matched cddid_all.tbl CDD PRK10154 PRK10154 182272 PRK10154 DUF2541 family protein. 134 matched cddid_all.tbl CDD PRK10157 PRK10157 182273 PRK10157 putative oxidoreductase FixC; Provisional 428 matched cddid_all.tbl CDD PRK10158 PRK10158 236659 PRK10158 bifunctional tRNA pseudouridine(32) synthase/23S rRNA pseudouridine(746) synthase RluA. 219 matched cddid_all.tbl CDD PRK10159 PRK10159 182275 PRK10159 phosphoporin PhoE. 351 matched cddid_all.tbl CDD PRK10160 PRK10160 182276 PRK10160 taurine ABC transporter permease TauC. 275 matched cddid_all.tbl CDD PRK10161 PRK10161 182277 PRK10161 phosphate response regulator transcription factor PhoB. 229 matched cddid_all.tbl CDD PRK10162 PRK10162 236660 PRK10162 acetyl esterase. 318 matched cddid_all.tbl CDD PRK10163 PRK10163 182279 PRK10163 HTH-type transcriptional repressor AllR. 271 matched cddid_all.tbl CDD PRK10167 PRK10167 182280 PRK10167 hypothetical protein; Provisional 169 matched cddid_all.tbl CDD PRK10170 PRK10170 182281 PRK10170 Ni/Fe-hydrogenase large subunit. 597 matched cddid_all.tbl CDD PRK10171 PRK10171 182282 PRK10171 Ni/Fe-hydrogenase b-type cytochrome subunit. 235 matched cddid_all.tbl CDD PRK10172 PRK10172 182283 PRK10172 AppA family phytase/histidine-type acid phosphatase. 436 matched cddid_all.tbl CDD PRK10173 PRK10173 182284 PRK10173 glucose-1-phosphatase/inositol phosphatase; Provisional 413 matched cddid_all.tbl CDD PRK10174 PRK10174 182285 PRK10174 hypothetical protein; Provisional 75 matched cddid_all.tbl CDD PRK10175 PRK10175 182286 PRK10175 YceK/YidQ family lipoprotein. 75 matched cddid_all.tbl CDD PRK10177 PRK10177 236661 PRK10177 YchO/YchP family invasin. 465 matched cddid_all.tbl CDD PRK10178 PRK10178 236662 PRK10178 D-alanyl-D-alanine dipeptidase; Provisional 184 matched cddid_all.tbl CDD PRK10179 PRK10179 182289 PRK10179 formate dehydrogenase-N subunit gamma; Provisional 217 matched cddid_all.tbl CDD PRK10183 PRK10183 182290 PRK10183 hypothetical protein; Provisional 56 matched cddid_all.tbl CDD PRK10187 PRK10187 182291 PRK10187 trehalose-6-phosphate phosphatase; Provisional 266 matched cddid_all.tbl CDD PRK10188 PRK10188 182292 PRK10188 transcriptional regulator SdiA. 240 matched cddid_all.tbl CDD PRK10189 PRK10189 182293 PRK10189 EmmdR/YeeO family multidrug/toxin efflux MATE transporter. 478 matched cddid_all.tbl CDD PRK10190 PRK10190 182294 PRK10190 L,D-transpeptidase; Provisional 310 matched cddid_all.tbl CDD PRK10191 PRK10191 182295 PRK10191 putative acyl transferase; Provisional 146 matched cddid_all.tbl CDD PRK10194 PRK10194 182296 PRK10194 ferredoxin-type protein NapF. 163 matched cddid_all.tbl CDD PRK10197 PRK10197 182297 PRK10197 GABA permease. 446 matched cddid_all.tbl CDD PRK10198 PRK10198 182298 PRK10198 formate hydrogenlyase regulator HycA. 152 matched cddid_all.tbl CDD PRK10199 PRK10199 182299 PRK10199 alkaline phosphatase isozyme conversion aminopeptidase; Provisional 346 matched cddid_all.tbl CDD PRK10200 PRK10200 182300 PRK10200 putative racemase; Provisional 230 matched cddid_all.tbl CDD PRK10201 PRK10201 182301 PRK10201 G/U mismatch-specific DNA glycosylase. 168 matched cddid_all.tbl CDD PRK10202 PRK10202 182302 ebgC beta-galactosidase subunit beta. 149 matched cddid_all.tbl CDD PRK10203 PRK10203 182303 PRK10203 hypothetical protein; Provisional 122 matched cddid_all.tbl CDD PRK10204 PRK10204 182304 PRK10204 hypothetical protein; Provisional 55 matched cddid_all.tbl CDD PRK10206 PRK10206 182305 PRK10206 putative oxidoreductase; Provisional 344 matched cddid_all.tbl CDD PRK10207 PRK10207 182306 PRK10207 dipeptide/tripeptide permease DtpB. 489 matched cddid_all.tbl CDD PRK10208 PRK10208 182307 PRK10208 acid-activated periplasmic chaperone HdeA. 114 matched cddid_all.tbl CDD PRK10209 PRK10209 182308 PRK10209 HdeD family acid-resistance protein. 190 matched cddid_all.tbl CDD PRK10213 PRK10213 182309 nepI purine ribonucleoside efflux pump NepI. 394 matched cddid_all.tbl CDD PRK10214 PRK10214 182310 PRK10214 ilvB operon leader peptide IvbL. 32 matched cddid_all.tbl CDD PRK10215 PRK10215 236663 PRK10215 hypothetical protein; Provisional 218 matched cddid_all.tbl CDD PRK10216 PRK10216 182312 PRK10216 HTH-type transcriptional regulator YidZ. 319 matched cddid_all.tbl CDD PRK10217 PRK10217 182313 PRK10217 dTDP-glucose 4,6-dehydratase; Provisional 355 matched cddid_all.tbl CDD PRK10218 PRK10218 104396 PRK10218 translational GTPase TypA. 607 matched cddid_all.tbl CDD PRK10219 PRK10219 182314 PRK10219 superoxide response transcriptional regulator SoxS. 107 matched cddid_all.tbl CDD PRK10220 PRK10220 182315 PRK10220 phnA family protein. 111 matched cddid_all.tbl CDD PRK10222 PRK10222 182316 PRK10222 PTS ascorbate transporter subunit IIB. 85 matched cddid_all.tbl CDD PRK10224 PRK10224 236664 PRK10224 pyr operon leader peptide. 44 matched cddid_all.tbl CDD PRK10225 PRK10225 182318 PRK10225 Uxu operon transcriptional regulator. 257 matched cddid_all.tbl CDD PRK10226 PRK10226 182319 PRK10226 isoaspartyl peptidase; Provisional 313 matched cddid_all.tbl CDD PRK10227 PRK10227 182320 PRK10227 HTH-type transcriptional regulator CueR. 135 matched cddid_all.tbl CDD PRK10229 PRK10229 236665 PRK10229 threonine efflux system; Provisional 206 matched cddid_all.tbl CDD PRK10234 PRK10234 182322 PRK10234 transcriptional regulator GutM. 118 matched cddid_all.tbl CDD PRK10236 PRK10236 182323 PRK10236 acidic protein MsyB. 237 matched cddid_all.tbl CDD PRK10238 PRK10238 182324 PRK10238 aromatic amino acid transporter AroP. 456 matched cddid_all.tbl CDD PRK10239 PRK10239 182325 PRK10239 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase. 159 matched cddid_all.tbl CDD PRK10240 PRK10240 182326 PRK10240 (2E,6E)-farnesyl-diphosphate-specific ditrans,polycis-undecaprenyl-diphosphate synthase. 229 matched cddid_all.tbl CDD PRK10241 PRK10241 182327 PRK10241 hydroxyacylglutathione hydrolase; Provisional 251 matched cddid_all.tbl CDD PRK10244 PRK10244 236666 PRK10244 anti-adapter protein IraP. 88 matched cddid_all.tbl CDD PRK10245 PRK10245 182329 adrA diguanylate cyclase AdrA; Provisional 366 matched cddid_all.tbl CDD PRK10246 PRK10246 182330 PRK10246 exonuclease subunit SbcC; Provisional 1047 matched cddid_all.tbl CDD PRK10247 PRK10247 182331 PRK10247 putative ABC transporter ATP-binding protein YbbL; Provisional 225 matched cddid_all.tbl CDD PRK10249 PRK10249 236667 PRK10249 phenylalanine transporter; Provisional 458 matched cddid_all.tbl CDD PRK10250 PRK10250 182333 PRK10250 MmcQ/YjbR family DNA-binding protein. 122 matched cddid_all.tbl CDD PRK10251 PRK10251 182334 PRK10251 enterobactin synthase subunit EntD. 207 matched cddid_all.tbl CDD PRK10252 PRK10252 236668 entF enterobactin non-ribosomal peptide synthetase EntF. 1296 matched cddid_all.tbl CDD PRK10253 PRK10253 182336 PRK10253 iron-enterobactin ABC transporter ATP-binding protein. 265 matched cddid_all.tbl CDD PRK10254 PRK10254 182337 PRK10254 proofreading thioesterase EntH. 137 matched cddid_all.tbl CDD PRK10255 PRK10255 182338 PRK10255 PTS system N-acetyl glucosamine specific transporter subunits IIABC; Provisional 648 matched cddid_all.tbl CDD PRK10257 PRK10257 182339 PRK10257 putative kinase inhibitor protein; Provisional 158 matched cddid_all.tbl CDD PRK10258 PRK10258 182340 PRK10258 biotin biosynthesis protein BioC; Provisional 251 matched cddid_all.tbl CDD PRK10259 PRK10259 137782 PRK10259 hypothetical protein; Provisional 86 matched cddid_all.tbl CDD PRK10260 PRK10260 182341 PRK10260 L,D-transpeptidase; Provisional 306 matched cddid_all.tbl CDD PRK10261 PRK10261 182342 PRK10261 glutathione transporter ATP-binding protein; Provisional 623 matched cddid_all.tbl CDD PRK10262 PRK10262 182343 PRK10262 thioredoxin reductase; Provisional 321 matched cddid_all.tbl CDD PRK10263 PRK10263 236669 PRK10263 DNA translocase FtsK; Provisional 1355 matched cddid_all.tbl CDD PRK10264 PRK10264 182345 PRK10264 hydrogenase 1 maturation protease; Provisional 195 matched cddid_all.tbl CDD PRK10265 PRK10265 182346 PRK10265 chaperone modulator CbpM. 101 matched cddid_all.tbl CDD PRK10266 PRK10266 182347 PRK10266 curved DNA-binding protein. 306 matched cddid_all.tbl CDD PRK10270 PRK10270 182348 PRK10270 putative aminodeoxychorismate lyase; Provisional 340 matched cddid_all.tbl CDD PRK10271 PRK10271 182349 thiK thiamine kinase; Provisional 188 matched cddid_all.tbl CDD PRK10276 PRK10276 182350 PRK10276 translesion error-prone DNA polymerase V autoproteolytic subunit. 139 matched cddid_all.tbl CDD PRK10278 PRK10278 182351 PRK10278 SirB family protein. 130 matched cddid_all.tbl CDD PRK10279 PRK10279 182352 PRK10279 patatin-like phospholipase RssA. 300 matched cddid_all.tbl CDD PRK10280 PRK10280 182353 PRK10280 peptidyl-dipeptidase Dcp. 681 matched cddid_all.tbl CDD PRK10281 PRK10281 182354 PRK10281 PhzF family isomerase. 299 matched cddid_all.tbl CDD PRK10286 PRK10286 182355 PRK10286 methylated-DNA--[protein]-cysteine S-methyltransferase. 171 matched cddid_all.tbl CDD PRK10287 PRK10287 182356 PRK10287 thiosulfate:cyanide sulfurtransferase; Provisional 104 matched cddid_all.tbl CDD PRK10290 PRK10290 182357 PRK10290 superoxide dismutase [Cu-Zn] SodC2. 173 matched cddid_all.tbl CDD PRK10291 PRK10291 182358 PRK10291 glyoxalase I; Provisional 129 matched cddid_all.tbl CDD PRK10292 PRK10292 182359 PRK10292 fumarate hydratase FumD. 69 matched cddid_all.tbl CDD PRK10293 PRK10293 182360 PRK10293 1,4-dihydroxy-2-naphthoyl-CoA hydrolase. 136 matched cddid_all.tbl CDD PRK10294 PRK10294 182361 PRK10294 6-phosphofructokinase 2; Provisional 309 matched cddid_all.tbl CDD PRK10296 PRK10296 182362 PRK10296 DNA-binding transcriptional regulator ChbR; Provisional 278 matched cddid_all.tbl CDD PRK10297 PRK10297 182363 PRK10297 PTS system N,N'-diacetylchitobiose-specific transporter subunit IIC; Provisional 452 matched cddid_all.tbl CDD PRK10299 PRK10299 182364 PRK10299 PhoP/PhoQ regulator MgrB. 47 matched cddid_all.tbl CDD PRK10301 PRK10301 182365 PRK10301 CopC domain-containing protein YobA. 124 matched cddid_all.tbl CDD PRK10302 PRK10302 182366 PRK10302 hypothetical protein; Provisional 272 matched cddid_all.tbl CDD PRK10304 PRK10304 182367 PRK10304 non-heme ferritin. 165 matched cddid_all.tbl CDD PRK10306 PRK10306 182368 PRK10306 zinc/cadmium-binding protein; Provisional 216 matched cddid_all.tbl CDD PRK10307 PRK10307 236670 PRK10307 colanic acid biosynthesis glycosyltransferase WcaI. 412 matched cddid_all.tbl CDD PRK10308 PRK10308 236671 PRK10308 3-methyl-adenine DNA glycosylase II; Provisional 283 matched cddid_all.tbl CDD PRK10309 PRK10309 182371 PRK10309 galactitol-1-phosphate 5-dehydrogenase. 347 matched cddid_all.tbl CDD PRK10310 PRK10310 182372 PRK10310 PTS galactitol transporter subunit IIB. 94 matched cddid_all.tbl CDD PRK10314 PRK10314 182373 PRK10314 GNAT family N-acetyltransferase. 153 matched cddid_all.tbl CDD PRK10316 PRK10316 182374 PRK10316 hypothetical protein; Provisional 209 matched cddid_all.tbl CDD PRK10318 PRK10318 236672 PRK10318 hypothetical protein; Provisional 121 matched cddid_all.tbl CDD PRK10319 PRK10319 182376 PRK10319 N-acetylmuramoyl-L-alanine amidase AmiA. 287 matched cddid_all.tbl CDD PRK10323 PRK10323 182377 PRK10323 cysteine/O-acetylserine transporter. 195 matched cddid_all.tbl CDD PRK10324 PRK10324 182378 PRK10324 ribosome-associated translation inhibitor RaiA. 113 matched cddid_all.tbl CDD PRK10325 PRK10325 182379 PRK10325 heat shock protein GrpE; Provisional 197 matched cddid_all.tbl CDD PRK10328 PRK10328 182380 PRK10328 DNA-binding protein StpA. 134 matched cddid_all.tbl CDD PRK10329 PRK10329 182381 PRK10329 glutaredoxin-like protein NrdH. 81 matched cddid_all.tbl CDD PRK10330 PRK10330 182382 PRK10330 electron transport protein HydN. 181 matched cddid_all.tbl CDD PRK10331 PRK10331 182383 PRK10331 L-fuculokinase; Provisional 470 matched cddid_all.tbl CDD PRK10332 PRK10332 182384 PRK10332 prepilin-type N-terminal cleavage/methylation domain-containing protein. 107 matched cddid_all.tbl CDD PRK10333 PRK10333 182385 PRK10333 5-formyltetrahydrofolate cyclo-ligase family protein; Provisional 182 matched cddid_all.tbl CDD PRK10334 PRK10334 182386 PRK10334 small-conductance mechanosensitive channel MscS. 286 matched cddid_all.tbl CDD PRK10336 PRK10336 182387 PRK10336 two-component system response regulator QseB. 219 matched cddid_all.tbl CDD PRK10337 PRK10337 182388 PRK10337 sensor protein QseC; Provisional 449 matched cddid_all.tbl CDD PRK10339 PRK10339 182389 PRK10339 DNA-binding transcriptional repressor EbgR; Provisional 327 matched cddid_all.tbl CDD PRK10340 PRK10340 236673 ebgA cryptic beta-D-galactosidase subunit alpha; Reviewed 1021 matched cddid_all.tbl CDD PRK10341 PRK10341 182391 PRK10341 transcriptional regulator TdcA. 312 matched cddid_all.tbl CDD PRK10342 PRK10342 182392 PRK10342 glycerate kinase I; Provisional 381 matched cddid_all.tbl CDD PRK10343 PRK10343 182393 PRK10343 ribosome assembly RNA-binding protein YhbY. 97 matched cddid_all.tbl CDD PRK10344 PRK10344 182394 PRK10344 DNA-binding transcriptional regulator SfsB. 92 matched cddid_all.tbl CDD PRK10345 PRK10345 182395 PRK10345 PhoP regulatory network protein YrbL. 210 matched cddid_all.tbl CDD PRK10347 PRK10347 182396 PRK10347 putative adenosine monophosphate-protein transferase Fic. 200 matched cddid_all.tbl CDD PRK10348 PRK10348 182397 PRK10348 ribosome-associated heat shock protein Hsp15; Provisional 133 matched cddid_all.tbl CDD PRK10349 PRK10349 137836 PRK10349 pimeloyl-ACP methyl ester esterase BioH. 256 matched cddid_all.tbl CDD PRK10350 PRK10350 182398 PRK10350 DUF2756 family protein. 145 matched cddid_all.tbl CDD PRK10351 PRK10351 182399 PRK10351 4'-phosphopantetheinyl transferase AcpT. 187 matched cddid_all.tbl CDD PRK10352 PRK10352 182400 PRK10352 nickel transporter permease NikB; Provisional 314 matched cddid_all.tbl CDD PRK10353 PRK10353 182401 PRK10353 DNA-3-methyladenine glycosylase I. 187 matched cddid_all.tbl CDD PRK10354 PRK10354 182402 PRK10354 RNA chaperone/antiterminator CspA. 70 matched cddid_all.tbl CDD PRK10355 PRK10355 182403 xylF D-xylose ABC transporter substrate-binding protein. 330 matched cddid_all.tbl CDD PRK10356 PRK10356 182404 PRK10356 protein bax. 274 matched cddid_all.tbl CDD PRK10357 PRK10357 182405 PRK10357 putative glutathione S-transferase; Provisional 202 matched cddid_all.tbl CDD PRK10358 PRK10358 182406 PRK10358 tRNA (uridine(34)/cytosine(34)/5-carboxymethylaminomethyluridine(34)-2'-O)-methyltransferase TrmL. 157 matched cddid_all.tbl CDD PRK10359 PRK10359 182407 PRK10359 lipopolysaccharide core heptose(II) kinase RfaY. 232 matched cddid_all.tbl CDD PRK10360 PRK10360 182408 PRK10360 transcriptional regulator UhpA. 196 matched cddid_all.tbl CDD PRK10361 PRK10361 182409 PRK10361 DNA recombination protein RmuC; Provisional 475 matched cddid_all.tbl CDD PRK10363 PRK10363 182410 cpxP cell-envelope stress modulator CpxP. 166 matched cddid_all.tbl CDD PRK10364 PRK10364 236674 PRK10364 two-component system sensor histidine kinase ZraS. 457 matched cddid_all.tbl CDD PRK10365 PRK10365 182412 PRK10365 sigma-54-dependent response regulator transcription factor ZraR. 441 matched cddid_all.tbl CDD PRK10367 PRK10367 182413 PRK10367 DNA-damage-inducible SOS response protein; Provisional 441 matched cddid_all.tbl CDD PRK10369 PRK10369 236675 PRK10369 heme lyase subunit NrfE; Provisional 571 matched cddid_all.tbl CDD PRK10370 PRK10370 182415 PRK10370 formate-dependent nitrite reductase complex subunit NrfG; Provisional 198 matched cddid_all.tbl CDD PRK10371 PRK10371 182416 PRK10371 transcriptional regulator MelR. 302 matched cddid_all.tbl CDD PRK10372 PRK10372 182417 PRK10372 PTS ascorbate transporter subunit IIA. 154 matched cddid_all.tbl CDD PRK10376 PRK10376 236676 PRK10376 putative oxidoreductase; Provisional 290 matched cddid_all.tbl CDD PRK10377 PRK10377 182419 PRK10377 PTS glucitol/sorbitol transporter subunit IIA. 120 matched cddid_all.tbl CDD PRK10378 PRK10378 236677 PRK10378 inactive ferrous ion transporter periplasmic protein EfeO; Provisional 375 matched cddid_all.tbl CDD PRK10380 PRK10380 182421 PRK10380 hypothetical protein; Provisional 63 matched cddid_all.tbl CDD PRK10381 PRK10381 182422 PRK10381 LPS O-antigen length regulator; Provisional 377 matched cddid_all.tbl CDD PRK10382 PRK10382 182423 PRK10382 alkyl hydroperoxide reductase subunit C; Provisional 187 matched cddid_all.tbl CDD PRK10386 PRK10386 236678 PRK10386 curli production assembly/transport protein CsgE. 130 matched cddid_all.tbl CDD PRK10387 PRK10387 236679 PRK10387 glutaredoxin 2; Provisional 210 matched cddid_all.tbl CDD PRK10391 PRK10391 182426 PRK10391 transcription modulator YdgT. 71 matched cddid_all.tbl CDD PRK10396 PRK10396 236680 PRK10396 hypothetical protein; Provisional 221 matched cddid_all.tbl CDD PRK10397 PRK10397 182428 PRK10397 lipoprotein; Provisional 137 matched cddid_all.tbl CDD PRK10401 PRK10401 236681 PRK10401 HTH-type transcriptional regulator GalS. 346 matched cddid_all.tbl CDD PRK10402 PRK10402 236682 PRK10402 DNA-binding transcriptional activator YeiL; Provisional 226 matched cddid_all.tbl CDD PRK10403 PRK10403 182431 PRK10403 nitrate/nitrite response regulator protein NarP. 215 matched cddid_all.tbl CDD PRK10404 PRK10404 182432 PRK10404 stress response protein ElaB. 101 matched cddid_all.tbl CDD PRK10406 PRK10406 182433 PRK10406 alpha-ketoglutarate transporter; Provisional 432 matched cddid_all.tbl CDD PRK10408 PRK10408 182434 PRK10408 L-valine transporter subunit YgaH. 111 matched cddid_all.tbl CDD PRK10409 PRK10409 182435 PRK10409 HypC/HybG/HupF family hydrogenase formation chaperone. 90 matched cddid_all.tbl CDD PRK10410 PRK10410 236683 PRK10410 nitrous oxide-stimulated promoter family protein. 100 matched cddid_all.tbl CDD PRK10411 PRK10411 236684 PRK10411 L-fucose operon activator. 240 matched cddid_all.tbl CDD PRK10413 PRK10413 182438 PRK10413 hydrogenase maturation factor HybG. 82 matched cddid_all.tbl CDD PRK10414 PRK10414 236685 PRK10414 biopolymer transporter ExbB. 244 matched cddid_all.tbl CDD PRK10415 PRK10415 182440 PRK10415 tRNA-dihydrouridine synthase B; Provisional 321 matched cddid_all.tbl CDD PRK10416 PRK10416 236686 PRK10416 signal recognition particle-docking protein FtsY; Provisional 318 matched cddid_all.tbl CDD PRK10417 PRK10417 236687 nikC nickel transporter permease NikC; Provisional 272 matched cddid_all.tbl CDD PRK10418 PRK10418 236688 nikD nickel transporter ATP-binding protein NikD; Provisional 254 matched cddid_all.tbl CDD PRK10419 PRK10419 236689 nikE nickel ABC transporter ATP-binding protein NikE. 268 matched cddid_all.tbl CDD PRK10420 PRK10420 182445 PRK10420 L-lactate permease; Provisional 551 matched cddid_all.tbl CDD PRK10421 PRK10421 236690 PRK10421 DNA-binding transcriptional repressor LldR; Provisional 253 matched cddid_all.tbl CDD PRK10422 PRK10422 182447 PRK10422 lipopolysaccharide core biosynthesis protein; Provisional 352 matched cddid_all.tbl CDD PRK10423 PRK10423 182448 PRK10423 transcriptional repressor RbsR; Provisional 327 matched cddid_all.tbl CDD PRK10424 PRK10424 170429 PRK10424 ilv operon leader peptide. 32 matched cddid_all.tbl CDD PRK10425 PRK10425 182449 PRK10425 3'-5' ssDNA/RNA exonuclease TatD. 258 matched cddid_all.tbl CDD PRK10426 PRK10426 236691 PRK10426 alpha-glucosidase; Provisional 635 matched cddid_all.tbl CDD PRK10427 PRK10427 182451 PRK10427 PTS fructose-like transporter subunit IIB. 114 matched cddid_all.tbl CDD PRK10428 PRK10428 182452 PRK10428 hypothetical protein; Provisional 69 matched cddid_all.tbl CDD PRK10429 PRK10429 182453 PRK10429 melibiose:sodium transporter MelB. 473 matched cddid_all.tbl CDD PRK10430 PRK10430 182454 PRK10430 two-component system response regulator DcuR. 239 matched cddid_all.tbl CDD PRK10431 PRK10431 236692 PRK10431 N-acetylmuramoyl-l-alanine amidase II; Provisional 445 matched cddid_all.tbl CDD PRK10433 PRK10433 236693 PRK10433 putative RNA methyltransferase; Provisional 228 matched cddid_all.tbl CDD PRK10434 PRK10434 182457 srlR DNA-binding transcriptional repressor. 256 matched cddid_all.tbl CDD PRK10435 PRK10435 182458 cadB cadaverine/lysine antiporter. 435 matched cddid_all.tbl CDD PRK10436 PRK10436 236694 PRK10436 hypothetical protein; Provisional 462 matched cddid_all.tbl CDD PRK10437 PRK10437 182460 PRK10437 carbonic anhydrase; Provisional 220 matched cddid_all.tbl CDD PRK10438 PRK10438 182461 PRK10438 C-N hydrolase family amidase; Provisional 256 matched cddid_all.tbl CDD PRK10439 PRK10439 236695 PRK10439 enterobactin/ferric enterobactin esterase; Provisional 411 matched cddid_all.tbl CDD PRK10440 PRK10440 182463 PRK10440 iron-enterobactin ABC transporter permease. 330 matched cddid_all.tbl CDD PRK10441 PRK10441 182464 PRK10441 Fe(3+)-siderophore ABC transporter permease. 335 matched cddid_all.tbl CDD PRK10443 PRK10443 182465 rihA ribonucleoside hydrolase 1; Provisional 311 matched cddid_all.tbl CDD PRK10444 PRK10444 182466 PRK10444 HAD-IIA family hydrolase. 248 matched cddid_all.tbl CDD PRK10445 PRK10445 182467 PRK10445 endonuclease VIII; Provisional 263 matched cddid_all.tbl CDD PRK10446 PRK10446 182468 PRK10446 30S ribosomal protein S6--L-glutamate ligase. 300 matched cddid_all.tbl CDD PRK10447 PRK10447 182469 PRK10447 FtsH protease modulator YccA. 219 matched cddid_all.tbl CDD PRK10449 PRK10449 182470 PRK10449 heat shock protein HslJ. 140 matched cddid_all.tbl CDD PRK10452 PRK10452 182471 PRK10452 multidrug/spermidine efflux SMR transporter subunit MdtJ. 120 matched cddid_all.tbl CDD PRK10454 PRK10454 182472 PRK10454 PTS N,N'-diacetylchitobiose transporter subunit IIA. 115 matched cddid_all.tbl CDD PRK10455 PRK10455 182473 PRK10455 periplasmic protein; Reviewed 161 matched cddid_all.tbl CDD PRK10456 PRK10456 182474 PRK10456 arginine succinyltransferase; Provisional 344 matched cddid_all.tbl CDD PRK10457 PRK10457 182475 PRK10457 hypothetical protein; Provisional 82 matched cddid_all.tbl CDD PRK10458 PRK10458 236696 PRK10458 DNA cytosine methylase; Provisional 467 matched cddid_all.tbl CDD PRK10459 PRK10459 236697 PRK10459 MOP flippase family protein. 492 matched cddid_all.tbl CDD PRK10461 PRK10461 182478 PRK10461 thiamine biosynthesis lipoprotein ApbE; Provisional 350 matched cddid_all.tbl CDD PRK10463 PRK10463 182479 PRK10463 hydrogenase nickel incorporation protein HypB; Provisional 290 matched cddid_all.tbl CDD PRK10465 PRK10465 182480 PRK10465 hydrogenase-2 assembly chaperone. 159 matched cddid_all.tbl CDD PRK10466 PRK10466 182481 hybD HyaD/HybD family hydrogenase maturation endopeptidase. 164 matched cddid_all.tbl CDD PRK10467 PRK10467 182482 PRK10467 hydrogenase 2 large subunit; Provisional 567 matched cddid_all.tbl CDD PRK10468 PRK10468 182483 PRK10468 hydrogenase 2 small subunit; Provisional 371 matched cddid_all.tbl CDD PRK10470 PRK10470 182484 PRK10470 ribosome hibernation promoting factor. 95 matched cddid_all.tbl CDD PRK10472 PRK10472 182485 PRK10472 low affinity gluconate transporter; Provisional 445 matched cddid_all.tbl CDD PRK10473 PRK10473 182486 PRK10473 MdtL family multidrug efflux MFS transporter. 392 matched cddid_all.tbl CDD PRK10474 PRK10474 170468 PRK10474 PTS fructose-like transporter subunit IIB. 88 matched cddid_all.tbl CDD PRK10475 PRK10475 236698 PRK10475 23S rRNA pseudouridine(2604) synthase RluF. 290 matched cddid_all.tbl CDD PRK10476 PRK10476 182488 PRK10476 multidrug transporter subunit MdtN. 346 matched cddid_all.tbl CDD PRK10477 PRK10477 182489 PRK10477 outer membrane lipoprotein Blc; Provisional 177 matched cddid_all.tbl CDD PRK10478 PRK10478 182490 PRK10478 PTS fructose transporter subunit EIIC. 359 matched cddid_all.tbl CDD PRK10481 PRK10481 182491 PRK10481 hypothetical protein; Provisional 224 matched cddid_all.tbl CDD PRK10483 PRK10483 182492 PRK10483 tryptophan permease; Provisional 414 matched cddid_all.tbl CDD PRK10484 PRK10484 236699 PRK10484 putative transporter; Provisional 523 matched cddid_all.tbl CDD PRK10486 PRK10486 182494 PRK10486 (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase. 96 matched cddid_all.tbl CDD PRK10489 PRK10489 236700 PRK10489 enterobactin transporter EntS. 417 matched cddid_all.tbl CDD PRK10490 PRK10490 236701 PRK10490 sensor protein KdpD; Provisional 895 matched cddid_all.tbl CDD PRK10494 PRK10494 236702 PRK10494 envelope biogenesis factor ElyC. 259 matched cddid_all.tbl CDD PRK10497 PRK10497 182498 PRK10497 phage shock protein PspD. 73 matched cddid_all.tbl CDD PRK10499 PRK10499 182499 PRK10499 PTS sugar transporter subunit IIB. 106 matched cddid_all.tbl CDD PRK10502 PRK10502 236703 PRK10502 putative acyl transferase; Provisional 182 matched cddid_all.tbl CDD PRK10503 PRK10503 182501 PRK10503 MdtB/MuxB family multidrug efflux RND transporter permease subunit. 1040 matched cddid_all.tbl CDD PRK10504 PRK10504 182502 PRK10504 putative transporter; Provisional 471 matched cddid_all.tbl CDD PRK10506 PRK10506 236704 PRK10506 prepilin peptidase-dependent protein. 162 matched cddid_all.tbl CDD PRK10507 PRK10507 182504 PRK10507 bifunctional glutathionylspermidine amidase/glutathionylspermidine synthetase; Provisional 619 matched cddid_all.tbl CDD PRK10508 PRK10508 182505 PRK10508 luciferase-like monooxygenase. 333 matched cddid_all.tbl CDD PRK10509 PRK10509 182506 PRK10509 bacterioferritin-associated ferredoxin; Provisional 64 matched cddid_all.tbl CDD PRK10510 PRK10510 182507 PRK10510 OmpA family lipoprotein. 219 matched cddid_all.tbl CDD PRK10512 PRK10512 182508 PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional 614 matched cddid_all.tbl CDD PRK10513 PRK10513 182509 PRK10513 sugar phosphate phosphatase; Provisional 270 matched cddid_all.tbl CDD PRK10514 PRK10514 182510 PRK10514 putative acetyltransferase; Provisional 145 matched cddid_all.tbl CDD PRK10515 PRK10515 170492 PRK10515 hypothetical protein; Provisional 90 matched cddid_all.tbl CDD PRK10517 PRK10517 236705 PRK10517 magnesium-transporting P-type ATPase MgtA. 902 matched cddid_all.tbl CDD PRK10518 PRK10518 236706 PRK10518 alkaline phosphatase; Provisional 476 matched cddid_all.tbl CDD PRK10519 PRK10519 182513 PRK10519 hypothetical protein; Provisional 151 matched cddid_all.tbl CDD PRK10520 PRK10520 182514 rhtB homoserine/homoserine lactone efflux protein; Provisional 205 matched cddid_all.tbl CDD PRK10522 PRK10522 236707 PRK10522 multidrug transporter membrane component/ATP-binding component; Provisional 547 matched cddid_all.tbl CDD PRK10523 PRK10523 236708 PRK10523 envelope stress response activation lipoprotein NlpE. 234 matched cddid_all.tbl CDD PRK10524 PRK10524 182517 prpE propionyl-CoA synthetase; Provisional 629 matched cddid_all.tbl CDD PRK10525 PRK10525 182518 PRK10525 cytochrome o ubiquinol oxidase subunit II; Provisional 315 matched cddid_all.tbl CDD PRK10526 PRK10526 182519 PRK10526 acyl-CoA thioesterase II; Provisional 286 matched cddid_all.tbl CDD PRK10527 PRK10527 182520 PRK10527 DUF454 family protein. 125 matched cddid_all.tbl CDD PRK10528 PRK10528 182521 PRK10528 multifunctional acyl-CoA thioesterase I and protease I and lysophospholipase L1; Provisional 191 matched cddid_all.tbl CDD PRK10529 PRK10529 182522 PRK10529 DNA-binding transcriptional activator KdpE; Provisional 225 matched cddid_all.tbl CDD PRK10530 PRK10530 182523 PRK10530 pyridoxal phosphate (PLP) phosphatase; Provisional 272 matched cddid_all.tbl CDD PRK10531 PRK10531 236709 PRK10531 putative acyl-CoA thioester hydrolase. 422 matched cddid_all.tbl CDD PRK10532 PRK10532 182525 PRK10532 threonine and homoserine efflux system; Provisional 293 matched cddid_all.tbl CDD PRK10533 PRK10533 182526 PRK10533 putative lipoprotein; Provisional 171 matched cddid_all.tbl CDD PRK10534 PRK10534 236710 PRK10534 L-threonine aldolase; Provisional 333 matched cddid_all.tbl CDD PRK10535 PRK10535 182528 PRK10535 macrolide ABC transporter ATP-binding protein/permease MacB. 648 matched cddid_all.tbl CDD PRK10536 PRK10536 182529 PRK10536 phosphate starvation-inducible protein PhoH. 262 matched cddid_all.tbl CDD PRK10537 PRK10537 236711 PRK10537 voltage-gated potassium channel protein. 393 matched cddid_all.tbl CDD PRK10538 PRK10538 182531 PRK10538 bifunctional NADP-dependent 3-hydroxy acid dehydrogenase/3-hydroxypropionate dehydrogenase YdfG. 248 matched cddid_all.tbl CDD PRK10540 PRK10540 182532 PRK10540 osmotically-inducible lipoprotein OsmB. 72 matched cddid_all.tbl CDD PRK10542 PRK10542 182533 PRK10542 glutathionine S-transferase; Provisional 201 matched cddid_all.tbl CDD PRK10543 PRK10543 182534 PRK10543 superoxide dismutase [Fe]. 193 matched cddid_all.tbl CDD PRK10545 PRK10545 182535 PRK10545 excinuclease Cho. 286 matched cddid_all.tbl CDD PRK10546 PRK10546 182536 PRK10546 pyrimidine (deoxy)nucleoside triphosphate diphosphatase. 135 matched cddid_all.tbl CDD PRK10547 PRK10547 236712 PRK10547 chemotaxis protein CheA; Provisional 670 matched cddid_all.tbl CDD PRK10548 PRK10548 182538 PRK10548 flagella biosynthesis regulatory protein FliT. 121 matched cddid_all.tbl CDD PRK10549 PRK10549 182539 PRK10549 two-component system sensor histidine kinase BaeS. 466 matched cddid_all.tbl CDD PRK10550 PRK10550 236713 PRK10550 tRNA dihydrouridine(16) synthase DusC. 312 matched cddid_all.tbl CDD PRK10551 PRK10551 182541 PRK10551 cyclic di-GMP phosphodiesterase. 518 matched cddid_all.tbl CDD PRK10553 PRK10553 182542 PRK10553 chaperone NapD. 87 matched cddid_all.tbl CDD PRK10554 PRK10554 182543 PRK10554 outer membrane porin protein C; Provisional 355 matched cddid_all.tbl CDD PRK10555 PRK10555 182544 PRK10555 multidrug efflux RND transporter permease AcrD. 1037 matched cddid_all.tbl CDD PRK10556 PRK10556 182545 PRK10556 hypothetical protein; Provisional 111 matched cddid_all.tbl CDD PRK10557 PRK10557 236714 PRK10557 prepilin peptidase-dependent protein. 192 matched cddid_all.tbl CDD PRK10558 PRK10558 182547 PRK10558 alpha-dehydro-beta-deoxy-D-glucarate aldolase; Provisional 256 matched cddid_all.tbl CDD PRK10559 PRK10559 182548 PRK10559 p-hydroxybenzoic acid efflux pump subunit AaeA. 310 matched cddid_all.tbl CDD PRK10560 PRK10560 182549 hofQ outer membrane porin HofQ; Provisional 386 matched cddid_all.tbl CDD PRK10561 PRK10561 182550 PRK10561 sn-glycerol-3-phosphate ABC transporter permease UgpA. 280 matched cddid_all.tbl CDD PRK10562 PRK10562 236715 PRK10562 putative acetyltransferase; Provisional 145 matched cddid_all.tbl CDD PRK10563 PRK10563 182552 PRK10563 6-phosphogluconate phosphatase; Provisional 221 matched cddid_all.tbl CDD PRK10564 PRK10564 236716 PRK10564 maltose operon protein MalM. 303 matched cddid_all.tbl CDD PRK10565 PRK10565 182554 PRK10565 putative carbohydrate kinase; Provisional 508 matched cddid_all.tbl CDD PRK10566 PRK10566 182555 PRK10566 esterase; Provisional 249 matched cddid_all.tbl CDD PRK10568 PRK10568 182556 PRK10568 molecular chaperone OsmY. 203 matched cddid_all.tbl CDD PRK10569 PRK10569 182557 PRK10569 NAD(P)H-dependent FMN reductase; Provisional 191 matched cddid_all.tbl CDD PRK10572 PRK10572 236717 PRK10572 arabinose operon transcriptional regulator AraC. 290 matched cddid_all.tbl CDD PRK10573 PRK10573 182559 PRK10573 protein transport protein HofC. 399 matched cddid_all.tbl CDD PRK10574 PRK10574 236718 PRK10574 putative major pilin subunit; Provisional 146 matched cddid_all.tbl CDD PRK10575 PRK10575 182561 PRK10575 Fe3+-hydroxamate ABC transporter ATP-binding protein FhuC. 265 matched cddid_all.tbl CDD PRK10576 PRK10576 236719 PRK10576 Fe(3+)-hydroxamate ABC transporter substrate-binding protein FhuD. 292 matched cddid_all.tbl CDD PRK10577 PRK10577 236720 PRK10577 Fe(3+)-hydroxamate ABC transporter permease FhuB. 668 matched cddid_all.tbl CDD PRK10578 PRK10578 182564 PRK10578 hypothetical protein; Provisional 207 matched cddid_all.tbl CDD PRK10579 PRK10579 182565 PRK10579 pyrimidine/purine nucleoside phosphorylase. 94 matched cddid_all.tbl CDD PRK10580 PRK10580 182566 proY putative proline-specific permease; Provisional 457 matched cddid_all.tbl CDD PRK10581 PRK10581 182567 PRK10581 (2E,6E)-farnesyl diphosphate synthase. 299 matched cddid_all.tbl CDD PRK10582 PRK10582 182568 PRK10582 cytochrome o ubiquinol oxidase subunit IV; Provisional 109 matched cddid_all.tbl CDD PRK10584 PRK10584 182569 PRK10584 putative ABC transporter ATP-binding protein YbbA; Provisional 228 matched cddid_all.tbl CDD PRK10586 PRK10586 182570 PRK10586 putative oxidoreductase; Provisional 362 matched cddid_all.tbl CDD PRK10588 PRK10588 236721 PRK10588 hypothetical protein; Provisional 97 matched cddid_all.tbl CDD PRK10590 PRK10590 236722 PRK10590 ATP-dependent RNA helicase RhlE; Provisional 456 matched cddid_all.tbl CDD PRK10591 PRK10591 182573 PRK10591 hypothetical protein; Provisional 92 matched cddid_all.tbl CDD PRK10592 PRK10592 182574 PRK10592 putrescine transporter subunit: membrane component of ABC superfamily; Provisional 281 matched cddid_all.tbl CDD PRK10593 PRK10593 182575 PRK10593 hypothetical protein; Provisional 297 matched cddid_all.tbl CDD PRK10594 PRK10594 236723 PRK10594 murein L,D-transpeptidase; Provisional 608 matched cddid_all.tbl CDD PRK10595 PRK10595 182577 PRK10595 cell division inhibitor SulA. 164 matched cddid_all.tbl CDD PRK10597 PRK10597 182578 PRK10597 DNA damage-inducible protein I; Provisional 81 matched cddid_all.tbl CDD PRK10598 PRK10598 182579 PRK10598 lipoprotein; Provisional 186 matched cddid_all.tbl CDD PRK10599 PRK10599 182580 PRK10599 sodium-potassium/proton antiporter ChaA. 366 matched cddid_all.tbl CDD PRK10600 PRK10600 182581 PRK10600 nitrate/nitrite two-component system sensor histidine kinase NarX. 569 matched cddid_all.tbl CDD PRK10602 PRK10602 182582 PRK10602 murein tripeptide amidase MpaA. 237 matched cddid_all.tbl CDD PRK10604 PRK10604 236724 PRK10604 sensor protein RstB; Provisional 433 matched cddid_all.tbl CDD PRK10605 PRK10605 182584 PRK10605 N-ethylmaleimide reductase; Provisional 362 matched cddid_all.tbl CDD PRK10606 PRK10606 182585 btuE putative glutathione peroxidase; Provisional 183 matched cddid_all.tbl CDD PRK10610 PRK10610 170568 PRK10610 chemotaxis protein CheY. 129 matched cddid_all.tbl CDD PRK10611 PRK10611 236725 PRK10611 protein-glutamate O-methyltransferase CheR. 287 matched cddid_all.tbl CDD PRK10612 PRK10612 182587 PRK10612 chemotaxis protein CheW. 167 matched cddid_all.tbl CDD PRK10613 PRK10613 182588 PRK10613 DUF2594 family protein. 74 matched cddid_all.tbl CDD PRK10614 PRK10614 182589 PRK10614 multidrug efflux system subunit MdtC; Provisional 1025 matched cddid_all.tbl CDD PRK10617 PRK10617 182590 PRK10617 cytochrome c-type protein NapC; Provisional 200 matched cddid_all.tbl CDD PRK10618 PRK10618 236726 PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional 894 matched cddid_all.tbl CDD PRK10619 PRK10619 182592 PRK10619 histidine ABC transporter ATP-binding protein HisP. 257 matched cddid_all.tbl CDD PRK10621 PRK10621 182593 PRK10621 hypothetical protein; Provisional 266 matched cddid_all.tbl CDD PRK10622 PRK10622 182594 pheA bifunctional chorismate mutase/prephenate dehydratase; Provisional 386 matched cddid_all.tbl CDD PRK10624 PRK10624 182595 PRK10624 L-1,2-propanediol oxidoreductase; Provisional 382 matched cddid_all.tbl CDD PRK10625 PRK10625 236727 tas putative aldo-keto reductase; Provisional 346 matched cddid_all.tbl CDD PRK10626 PRK10626 182597 PRK10626 hypothetical protein; Provisional 239 matched cddid_all.tbl CDD PRK10628 PRK10628 182598 PRK10628 LigB family dioxygenase; Provisional 246 matched cddid_all.tbl CDD PRK10629 PRK10629 236728 PRK10629 EnvZ/OmpR regulon moderator MzrA. 127 matched cddid_all.tbl CDD PRK10631 PRK10631 182600 PRK10631 p-hydroxybenzoic acid efflux subunit AaeB; Provisional 652 matched cddid_all.tbl CDD PRK10632 PRK10632 182601 PRK10632 HTH-type transcriptional activator AaeR. 309 matched cddid_all.tbl CDD PRK10633 PRK10633 182602 PRK10633 hypothetical protein; Provisional 80 matched cddid_all.tbl CDD PRK10634 PRK10634 182603 PRK10634 L-threonylcarbamoyladenylate synthase type 1 TsaC. 190 matched cddid_all.tbl CDD PRK10635 PRK10635 182604 PRK10635 bacterioferritin; Provisional 158 matched cddid_all.tbl CDD PRK10636 PRK10636 236729 PRK10636 putative ABC transporter ATP-binding protein; Provisional 638 matched cddid_all.tbl CDD PRK10637 PRK10637 182606 cysG siroheme synthase CysG. 457 matched cddid_all.tbl CDD PRK10638 PRK10638 182607 PRK10638 glutaredoxin 3; Provisional 83 matched cddid_all.tbl CDD PRK10639 PRK10639 182608 PRK10639 formate dehydrogenase cytochrome b556 subunit. 211 matched cddid_all.tbl CDD PRK10640 PRK10640 182609 rhaB rhamnulokinase; Provisional 471 matched cddid_all.tbl CDD PRK10641 PRK10641 236730 btuB TonB-dependent vitamin B12 receptor BtuB. 614 matched cddid_all.tbl CDD PRK10642 PRK10642 182611 PRK10642 proline/glycine betaine transporter ProP. 490 matched cddid_all.tbl CDD PRK10643 PRK10643 182612 PRK10643 two-component system response regulator PmrA. 222 matched cddid_all.tbl CDD PRK10644 PRK10644 182613 PRK10644 arginine/agmatine antiporter. 445 matched cddid_all.tbl CDD PRK10645 PRK10645 182614 PRK10645 divalent cation tolerance protein CutA. 112 matched cddid_all.tbl CDD PRK10646 PRK10646 182615 PRK10646 tRNA (adenosine(37)-N6)-threonylcarbamoyltransferase complex ATPase subunit type 1 TsaE. 153 matched cddid_all.tbl CDD PRK10647 PRK10647 182616 PRK10647 ferric iron reductase involved in ferric hydroximate transport; Provisional 262 matched cddid_all.tbl CDD PRK10649 PRK10649 182617 PRK10649 phosphoethanolamine transferase CptA. 577 matched cddid_all.tbl CDD PRK10650 PRK10650 182618 PRK10650 multidrug/spermidine efflux SMR transporter subunit MdtI. 109 matched cddid_all.tbl CDD PRK10651 PRK10651 182619 PRK10651 transcriptional regulator NarL; Provisional 216 matched cddid_all.tbl CDD PRK10653 PRK10653 182620 PRK10653 ribose ABC transporter substrate-binding protein RbsB. 295 matched cddid_all.tbl CDD PRK10654 PRK10654 182621 dcuC C4-dicarboxylate transporter DcuC; Provisional 455 matched cddid_all.tbl CDD PRK10655 PRK10655 182622 potE putrescine transporter; Provisional 438 matched cddid_all.tbl CDD PRK10658 PRK10658 236731 PRK10658 putative alpha-glucosidase; Provisional 665 matched cddid_all.tbl CDD PRK10659 PRK10659 182625 PRK10659 acetate uptake transporter. 188 matched cddid_all.tbl CDD PRK10660 PRK10660 182626 tilS tRNA(Ile)-lysidine synthetase; Provisional 436 matched cddid_all.tbl CDD PRK10662 PRK10662 236732 PRK10662 beta-lactam binding protein AmpH; Provisional 378 matched cddid_all.tbl CDD PRK10663 PRK10663 182628 PRK10663 cytochrome o ubiquinol oxidase subunit III; Provisional 204 matched cddid_all.tbl CDD PRK10664 PRK10664 170612 PRK10664 DNA-binding protein HU-beta. 90 matched cddid_all.tbl CDD PRK10665 PRK10665 182629 PRK10665 P-II family nitrogen regulator. 112 matched cddid_all.tbl CDD PRK10666 PRK10666 182630 PRK10666 ammonium transporter AmtB. 428 matched cddid_all.tbl CDD PRK10667 PRK10667 182631 PRK10667 Hha toxicity modulator TomB. 122 matched cddid_all.tbl CDD PRK10668 PRK10668 182632 PRK10668 DNA-binding transcriptional repressor AcrR; Provisional 215 matched cddid_all.tbl CDD PRK10669 PRK10669 182633 PRK10669 putative cation:proton antiport protein; Provisional 558 matched cddid_all.tbl CDD PRK10670 PRK10670 182634 PRK10670 Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK. 159 matched cddid_all.tbl CDD PRK10671 PRK10671 182635 copA copper-exporting P-type ATPase CopA. 834 matched cddid_all.tbl CDD PRK10672 PRK10672 236733 PRK10672 endolytic peptidoglycan transglycosylase RlpA. 361 matched cddid_all.tbl CDD PRK10673 PRK10673 182637 PRK10673 esterase. 255 matched cddid_all.tbl CDD PRK10674 PRK10674 236734 PRK10674 deoxyribodipyrimidine photolyase; Provisional 472 matched cddid_all.tbl CDD PRK10675 PRK10675 182639 PRK10675 UDP-galactose-4-epimerase; Provisional 338 matched cddid_all.tbl CDD PRK10676 PRK10676 182640 PRK10676 DNA-binding transcriptional regulator ModE; Provisional 263 matched cddid_all.tbl CDD PRK10677 PRK10677 182641 modA molybdate transporter periplasmic protein; Provisional 257 matched cddid_all.tbl CDD PRK10678 PRK10678 182642 moaE molybdopterin synthase catalytic subunit MoaE. 150 matched cddid_all.tbl CDD PRK10680 PRK10680 182643 PRK10680 molybdopterin biosynthesis protein MoeA; Provisional 411 matched cddid_all.tbl CDD PRK10681 PRK10681 182644 PRK10681 DNA-binding transcriptional repressor DeoR; Provisional 252 matched cddid_all.tbl CDD PRK10682 PRK10682 182645 PRK10682 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional 370 matched cddid_all.tbl CDD PRK10683 PRK10683 182646 PRK10683 putrescine transporter subunit: membrane component of ABC superfamily; Provisional 317 matched cddid_all.tbl CDD PRK10684 PRK10684 236735 PRK10684 HCP oxidoreductase, NADH-dependent; Provisional 332 matched cddid_all.tbl CDD PRK10687 PRK10687 182648 PRK10687 purine nucleoside phosphoramidase; Provisional 119 matched cddid_all.tbl CDD PRK10689 PRK10689 182649 PRK10689 transcription-repair coupling factor; Provisional 1147 matched cddid_all.tbl CDD PRK10691 PRK10691 182650 PRK10691 fumarylacetoacetate hydrolase family protein. 219 matched cddid_all.tbl CDD PRK10692 PRK10692 182651 PRK10692 stress response protein YchH. 92 matched cddid_all.tbl CDD PRK10693 PRK10693 182652 PRK10693 two-component system response regulator RssB. 303 matched cddid_all.tbl CDD PRK10694 PRK10694 236736 PRK10694 acyl-CoA thioester hydrolase YciA. 133 matched cddid_all.tbl CDD PRK10695 PRK10695 182654 PRK10695 YdbH family protein. 859 matched cddid_all.tbl CDD PRK10696 PRK10696 236737 PRK10696 tRNA 2-thiocytidine biosynthesis protein TtcA; Provisional 258 matched cddid_all.tbl CDD PRK10697 PRK10697 182656 PRK10697 envelope stress response membrane protein PspC. 118 matched cddid_all.tbl CDD PRK10698 PRK10698 182657 PRK10698 phage shock protein PspA; Provisional 222 matched cddid_all.tbl CDD PRK10699 PRK10699 182658 PRK10699 phosphatidylglycerophosphatase B; Provisional 244 matched cddid_all.tbl CDD PRK10700 PRK10700 182659 PRK10700 23S rRNA pseudouridine(2605) synthase RluB. 289 matched cddid_all.tbl CDD PRK10701 PRK10701 236738 PRK10701 DNA-binding transcriptional regulator RstA; Provisional 240 matched cddid_all.tbl CDD PRK10702 PRK10702 182661 PRK10702 endonuclease III; Provisional 211 matched cddid_all.tbl CDD PRK10703 PRK10703 236739 PRK10703 HTH-type transcriptional repressor PurR. 341 matched cddid_all.tbl CDD PRK10707 PRK10707 182663 PRK10707 putative NUDIX hydrolase; Provisional 190 matched cddid_all.tbl CDD PRK10708 PRK10708 182664 PRK10708 protein DsrB. 62 matched cddid_all.tbl CDD PRK10710 PRK10710 182665 PRK10710 DNA-binding transcriptional regulator BaeR; Provisional 240 matched cddid_all.tbl CDD PRK10711 PRK10711 182666 PRK10711 hypothetical protein; Provisional 231 matched cddid_all.tbl CDD PRK10712 PRK10712 236740 PRK10712 PTS system fructose-specific transporter subunits IIBC; Provisional 563 matched cddid_all.tbl CDD PRK10713 PRK10713 182668 PRK10713 2Fe-2S ferredoxin-like protein. 84 matched cddid_all.tbl CDD PRK10714 PRK10714 182669 PRK10714 undecaprenyl phosphate 4-deoxy-4-formamido-L-arabinose transferase; Provisional 325 matched cddid_all.tbl CDD PRK10715 PRK10715 182670 flk flagella biosynthesis regulator Flk. 335 matched cddid_all.tbl CDD PRK10716 PRK10716 236741 PRK10716 long-chain fatty acid transporter FadL. 435 matched cddid_all.tbl CDD PRK10717 PRK10717 182672 PRK10717 cysteine synthase A; Provisional 330 matched cddid_all.tbl CDD PRK10718 PRK10718 236742 PRK10718 RpoE-regulated lipoprotein; Provisional 191 matched cddid_all.tbl CDD PRK10719 PRK10719 236743 eutA ethanolamine ammonia-lyase reactivating factor EutA. 475 matched cddid_all.tbl CDD PRK10720 PRK10720 236744 PRK10720 uracil transporter; Provisional 428 matched cddid_all.tbl CDD PRK10721 PRK10721 170660 PRK10721 hypothetical protein; Provisional 66 matched cddid_all.tbl CDD PRK10722 PRK10722 236745 PRK10722 two-component system QseEF-associated lipoprotein QseG. 247 matched cddid_all.tbl CDD PRK10723 PRK10723 182677 PRK10723 polyphenol oxidase. 243 matched cddid_all.tbl CDD PRK10724 PRK10724 182678 PRK10724 type II toxin-antitoxin system RatA family toxin. 158 matched cddid_all.tbl CDD PRK10725 PRK10725 182679 PRK10725 fructose-1-phosphate/6-phosphogluconate phosphatase. 188 matched cddid_all.tbl CDD PRK10726 PRK10726 236746 PRK10726 DUF3561 family protein. 105 matched cddid_all.tbl CDD PRK10727 PRK10727 182681 PRK10727 HTH-type transcriptional regulator GalR. 343 matched cddid_all.tbl CDD PRK10729 PRK10729 182682 nudF ADP-ribose pyrophosphatase NudF; Provisional 202 matched cddid_all.tbl CDD PRK10733 PRK10733 182683 hflB ATP-dependent zinc metalloprotease FtsH. 644 matched cddid_all.tbl CDD PRK10734 PRK10734 182684 PRK10734 putative calcium/sodium:proton antiporter; Provisional 325 matched cddid_all.tbl CDD PRK10735 PRK10735 182685 tldD protease TldD; Provisional 481 matched cddid_all.tbl CDD PRK10736 PRK10736 236747 PRK10736 DNA-protecting protein DprA. 374 matched cddid_all.tbl CDD PRK10737 PRK10737 236748 PRK10737 peptidylprolyl isomerase. 196 matched cddid_all.tbl CDD PRK10738 PRK10738 182688 PRK10738 OsmC family protein. 134 matched cddid_all.tbl CDD PRK10739 PRK10739 170674 PRK10739 YhgN family NAAT transporter. 197 matched cddid_all.tbl CDD PRK10740 PRK10740 182689 PRK10740 high-affinity branched-chain amino acid ABC transporter permease LivH. 308 matched cddid_all.tbl CDD PRK10742 PRK10742 236749 PRK10742 16S rRNA (guanine(1516)-N(2))-methyltransferase RsmJ. 250 matched cddid_all.tbl CDD PRK10743 PRK10743 182691 PRK10743 heat shock chaperone IbpA. 137 matched cddid_all.tbl CDD PRK10745 PRK10745 182693 trkD low affinity potassium transporter Kup. 622 matched cddid_all.tbl CDD PRK10746 PRK10746 182694 PRK10746 putative transport protein YifK; Provisional 461 matched cddid_all.tbl CDD PRK10747 PRK10747 182695 PRK10747 putative protoheme IX biogenesis protein; Provisional 398 matched cddid_all.tbl CDD PRK10748 PRK10748 182696 PRK10748 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase YigB. 238 matched cddid_all.tbl CDD PRK10749 PRK10749 182697 PRK10749 lysophospholipase L2; Provisional 330 matched cddid_all.tbl CDD PRK10750 PRK10750 182698 PRK10750 Trk system potassium transporter TrkH. 483 matched cddid_all.tbl CDD PRK10751 PRK10751 236750 PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional 173 matched cddid_all.tbl CDD PRK10752 PRK10752 182700 PRK10752 sulfate ABC transporter substrate-binding protein. 329 matched cddid_all.tbl CDD PRK10753 PRK10753 138142 PRK10753 DNA-binding protein HU-alpha. 90 matched cddid_all.tbl CDD PRK10754 PRK10754 182701 PRK10754 NADPH:quinone reductase. 327 matched cddid_all.tbl CDD PRK10755 PRK10755 236751 PRK10755 two-component system sensor histidine kinase PmrB. 356 matched cddid_all.tbl CDD PRK10756 PRK10756 236752 PRK10756 protein CreA. 157 matched cddid_all.tbl CDD PRK10757 PRK10757 236753 PRK10757 inositol-1-monophosphatase. 267 matched cddid_all.tbl CDD PRK10759 PRK10759 182705 PRK10759 YfiM family lipoprotein. 106 matched cddid_all.tbl CDD PRK10760 PRK10760 236754 PRK10760 murein hydrolase B; Provisional 359 matched cddid_all.tbl CDD PRK10762 PRK10762 236755 PRK10762 D-ribose transporter ATP binding protein; Provisional 501 matched cddid_all.tbl CDD PRK10763 PRK10763 182708 PRK10763 phospholipase A; Provisional 289 matched cddid_all.tbl CDD PRK10764 PRK10764 236756 PRK10764 potassium-tellurite ethidium and proflavin transporter; Provisional 324 matched cddid_all.tbl CDD PRK10765 PRK10765 182710 PRK10765 oxygen-insensitive NADPH nitroreductase. 240 matched cddid_all.tbl CDD PRK10766 PRK10766 182711 PRK10766 two-component system response regulator TorR. 221 matched cddid_all.tbl CDD PRK10767 PRK10767 236757 PRK10767 chaperone protein DnaJ; Provisional 371 matched cddid_all.tbl CDD PRK10768 PRK10768 182713 PRK10768 ribonucleoside hydrolase RihC; Provisional 304 matched cddid_all.tbl CDD PRK10769 PRK10769 182714 folA type 3 dihydrofolate reductase. 159 matched cddid_all.tbl CDD PRK10770 PRK10770 236758 PRK10770 peptidyl-prolyl cis-trans isomerase SurA; Provisional 413 matched cddid_all.tbl CDD PRK10771 PRK10771 182716 thiQ thiamine ABC transporter ATP-binding protein ThiQ. 232 matched cddid_all.tbl CDD PRK10772 PRK10772 182717 PRK10772 cell division protein FtsL; Provisional 108 matched cddid_all.tbl CDD PRK10773 PRK10773 182718 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed 453 matched cddid_all.tbl CDD PRK10774 PRK10774 182719 PRK10774 cell division protein FtsW; Provisional 404 matched cddid_all.tbl CDD PRK10775 PRK10775 182720 PRK10775 cell division protein FtsQ; Provisional 276 matched cddid_all.tbl CDD PRK10776 PRK10776 182721 PRK10776 8-oxo-dGTP diphosphatase MutT. 129 matched cddid_all.tbl CDD PRK10778 PRK10778 182722 dksA RNA polymerase-binding protein DksA. 151 matched cddid_all.tbl CDD PRK10779 PRK10779 182723 PRK10779 sigma E protease regulator RseP. 449 matched cddid_all.tbl CDD PRK10780 PRK10780 182724 PRK10780 molecular chaperone Skp. 165 matched cddid_all.tbl CDD PRK10781 PRK10781 182725 rcsF Rcs stress response system protein RcsF. 133 matched cddid_all.tbl CDD PRK10782 PRK10782 182726 PRK10782 D-methionine ABC transporter permease MetI. 217 matched cddid_all.tbl CDD PRK10783 PRK10783 182727 mltD membrane-bound lytic murein transglycosylase D; Provisional 456 matched cddid_all.tbl CDD PRK10785 PRK10785 236759 PRK10785 maltodextrin glucosidase; Provisional 598 matched cddid_all.tbl CDD PRK10786 PRK10786 182729 ribD bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD. 367 matched cddid_all.tbl CDD PRK10787 PRK10787 182730 PRK10787 DNA-binding ATP-dependent protease La; Provisional 784 matched cddid_all.tbl CDD PRK10788 PRK10788 182731 PRK10788 periplasmic folding chaperone; Provisional 623 matched cddid_all.tbl CDD PRK10789 PRK10789 182732 PRK10789 SmdA family multidrug ABC transporter permease/ATP-binding protein. 569 matched cddid_all.tbl CDD PRK10790 PRK10790 182733 PRK10790 SmdB family multidrug efflux ABC transporter permease/ATP-binding protein. 592 matched cddid_all.tbl CDD PRK10791 PRK10791 182734 PRK10791 peptidylprolyl isomerase B. 164 matched cddid_all.tbl CDD PRK10792 PRK10792 236760 PRK10792 bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD. 285 matched cddid_all.tbl CDD PRK10793 PRK10793 182736 PRK10793 D-alanyl-D-alanine carboxypeptidase fraction A; Provisional 403 matched cddid_all.tbl CDD PRK10794 PRK10794 182737 PRK10794 rod shape-determining protein RodA. 370 matched cddid_all.tbl CDD PRK10795 PRK10795 236761 PRK10795 penicillin-binding protein 2; Provisional 634 matched cddid_all.tbl CDD PRK10796 PRK10796 236762 PRK10796 LPS-assembly lipoprotein RlpB; Provisional 188 matched cddid_all.tbl CDD PRK10797 PRK10797 236763 PRK10797 glutamate and aspartate transporter subunit; Provisional 302 matched cddid_all.tbl CDD PRK10799 PRK10799 182741 PRK10799 type 2 GTP cyclohydrolase I. 247 matched cddid_all.tbl CDD PRK10800 PRK10800 182742 PRK10800 acyl-CoA thioesterase YbgC; Provisional 130 matched cddid_all.tbl CDD PRK10801 PRK10801 182743 PRK10801 Tol-Pal system protein TolQ. 227 matched cddid_all.tbl CDD PRK10802 PRK10802 182744 PRK10802 peptidoglycan-associated lipoprotein Pal. 173 matched cddid_all.tbl CDD PRK10803 PRK10803 182745 PRK10803 tol-pal system protein YbgF; Provisional 263 matched cddid_all.tbl CDD PRK10805 PRK10805 182746 PRK10805 formate transporter; Provisional 285 matched cddid_all.tbl CDD PRK10807 PRK10807 182747 PRK10807 intermembrane transport protein PqiB. 547 matched cddid_all.tbl CDD PRK10808 PRK10808 236764 PRK10808 outer membrane protein A; Reviewed 351 matched cddid_all.tbl CDD PRK10809 PRK10809 182749 PRK10809 30S ribosomal protein S5 alanine N-acetyltransferase. 194 matched cddid_all.tbl CDD PRK10810 PRK10810 236765 PRK10810 anti-sigma-28 factor FlgM. 98 matched cddid_all.tbl CDD PRK10811 PRK10811 236766 rne ribonuclease E; Reviewed 1068 matched cddid_all.tbl CDD PRK10812 PRK10812 236767 PRK10812 putative DNAse; Provisional 265 matched cddid_all.tbl CDD PRK10814 PRK10814 182753 PRK10814 lipoprotein-releasing ABC transporter permease subunit LolC. 399 matched cddid_all.tbl CDD PRK10815 PRK10815 182754 PRK10815 two-component system sensor histidine kinase PhoQ. 485 matched cddid_all.tbl CDD PRK10816 PRK10816 182755 PRK10816 two-component system response regulator PhoP. 223 matched cddid_all.tbl CDD PRK10818 PRK10818 182756 PRK10818 septum site-determining protein MinD. 270 matched cddid_all.tbl CDD PRK10819 PRK10819 236768 PRK10819 transport protein TonB; Provisional 246 matched cddid_all.tbl CDD PRK10820 PRK10820 236769 PRK10820 transcriptional regulator TyrR. 520 matched cddid_all.tbl CDD PRK10824 PRK10824 182759 PRK10824 Grx4 family monothiol glutaredoxin. 115 matched cddid_all.tbl CDD PRK10826 PRK10826 236770 PRK10826 hexitol phosphatase HxpB. 222 matched cddid_all.tbl CDD PRK10828 PRK10828 182761 PRK10828 putative oxidoreductase; Provisional 183 matched cddid_all.tbl CDD PRK10829 PRK10829 236771 PRK10829 ribonuclease D; Provisional 373 matched cddid_all.tbl CDD PRK10832 PRK10832 182763 PRK10832 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase. 182 matched cddid_all.tbl CDD PRK10833 PRK10833 236772 PRK10833 putative assembly protein; Provisional 617 matched cddid_all.tbl CDD PRK10834 PRK10834 182765 PRK10834 outer membrane permeability protein SanA. 239 matched cddid_all.tbl CDD PRK10835 PRK10835 182766 PRK10835 hypothetical protein; Provisional 373 matched cddid_all.tbl CDD PRK10836 PRK10836 182767 PRK10836 lysine transporter; Provisional 489 matched cddid_all.tbl CDD PRK10837 PRK10837 182768 PRK10837 putative DNA-binding transcriptional regulator; Provisional 290 matched cddid_all.tbl CDD PRK10838 PRK10838 236773 spr bifunctional murein DD-endopeptidase/murein LD-carboxypeptidase. 190 matched cddid_all.tbl CDD PRK10839 PRK10839 236774 PRK10839 16S rRNA pseudouridine(516) synthase RsuA. 232 matched cddid_all.tbl CDD PRK10840 PRK10840 182771 PRK10840 transcriptional regulator RcsB; Provisional 216 matched cddid_all.tbl CDD PRK10841 PRK10841 182772 PRK10841 two-component system sensor histidine kinase RcsC. 924 matched cddid_all.tbl CDD PRK10845 PRK10845 182773 PRK10845 colicin V production protein; Provisional 162 matched cddid_all.tbl CDD PRK10846 PRK10846 182774 PRK10846 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional 416 matched cddid_all.tbl CDD PRK10847 PRK10847 182775 PRK10847 DedA family protein. 219 matched cddid_all.tbl CDD PRK10850 PRK10850 182777 PRK10850 phosphocarrier protein Hpr. 85 matched cddid_all.tbl CDD PRK10851 PRK10851 182778 PRK10851 sulfate/thiosulfate ABC transporter ATP-binding protein CysA. 353 matched cddid_all.tbl CDD PRK10852 PRK10852 236775 PRK10852 thiosulfate ABC transporter substrate-binding protein CysP. 338 matched cddid_all.tbl CDD PRK10853 PRK10853 182780 PRK10853 putative reductase; Provisional 118 matched cddid_all.tbl CDD PRK10854 PRK10854 182781 PRK10854 exopolyphosphatase; Provisional 513 matched cddid_all.tbl CDD PRK10856 PRK10856 236776 PRK10856 cytoskeleton protein RodZ. 331 matched cddid_all.tbl CDD PRK10857 PRK10857 236777 PRK10857 Fe-S cluster assembly transcriptional regulator IscR. 164 matched cddid_all.tbl CDD PRK10858 PRK10858 182784 PRK10858 nitrogen regulatory protein P-II. 112 matched cddid_all.tbl CDD PRK10859 PRK10859 236778 PRK10859 membrane-bound lytic murein transglycosylase MltF. 482 matched cddid_all.tbl CDD PRK10860 PRK10860 182786 PRK10860 tRNA-specific adenosine deaminase; Provisional 172 matched cddid_all.tbl CDD PRK10861 PRK10861 182787 PRK10861 signal peptidase I. 324 matched cddid_all.tbl CDD PRK10862 PRK10862 182788 PRK10862 SoxR-reducing system protein RseC. 154 matched cddid_all.tbl CDD PRK10863 PRK10863 182789 PRK10863 anti-sigma-E factor RseA. 216 matched cddid_all.tbl CDD PRK10864 PRK10864 236779 PRK10864 putative methyltransferase; Provisional 346 matched cddid_all.tbl CDD PRK10865 PRK10865 182791 PRK10865 ATP-dependent chaperone ClpB. 857 matched cddid_all.tbl CDD PRK10866 PRK10866 182792 PRK10866 outer membrane protein assembly factor BamD. 243 matched cddid_all.tbl CDD PRK10869 PRK10869 236781 PRK10869 recombination and repair protein; Provisional 553 matched cddid_all.tbl CDD PRK10870 PRK10870 182795 PRK10870 transcriptional repressor MprA; Provisional 176 matched cddid_all.tbl CDD PRK10871 PRK10871 236782 nlpD murein hydrolase activator NlpD. 319 matched cddid_all.tbl CDD PRK10872 PRK10872 182797 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional 743 matched cddid_all.tbl CDD PRK10873 PRK10873 182798 PRK10873 hypothetical protein; Provisional 131 matched cddid_all.tbl CDD PRK10874 PRK10874 182799 PRK10874 cysteine desulfurase CsdA. 401 matched cddid_all.tbl CDD PRK10875 PRK10875 236783 recD exodeoxyribonuclease V subunit alpha. 615 matched cddid_all.tbl CDD PRK10876 PRK10876 236784 recB exonuclease V subunit beta; Provisional 1181 matched cddid_all.tbl CDD PRK10877 PRK10877 182802 PRK10877 protein disulfide isomerase II DsbC; Provisional 232 matched cddid_all.tbl CDD PRK10878 PRK10878 182803 PRK10878 FAD assembly factor SdhE. 72 matched cddid_all.tbl CDD PRK10879 PRK10879 182804 PRK10879 proline aminopeptidase P II; Provisional 438 matched cddid_all.tbl CDD PRK10880 PRK10880 182805 PRK10880 adenine DNA glycosylase. 350 matched cddid_all.tbl CDD PRK10881 PRK10881 236785 PRK10881 Ni/Fe-hydrogenase cytochrome b subunit. 394 matched cddid_all.tbl CDD PRK10882 PRK10882 236786 PRK10882 hydrogenase 2 operon protein HybA. 328 matched cddid_all.tbl CDD PRK10883 PRK10883 182808 PRK10883 FtsI repressor; Provisional 471 matched cddid_all.tbl CDD PRK10884 PRK10884 182809 PRK10884 SH3 domain-containing protein; Provisional 206 matched cddid_all.tbl CDD PRK10885 PRK10885 182810 cca multifunctional CCA addition/repair protein. 409 matched cddid_all.tbl CDD PRK10886 PRK10886 182811 PRK10886 DnaA initiator-associating protein DiaA; Provisional 196 matched cddid_all.tbl CDD PRK10887 PRK10887 236787 glmM phosphoglucosamine mutase; Provisional 443 matched cddid_all.tbl CDD PRK10888 PRK10888 182813 PRK10888 octaprenyl diphosphate synthase; Provisional 323 matched cddid_all.tbl CDD PRK10892 PRK10892 182814 PRK10892 arabinose-5-phosphate isomerase KdsD. 326 matched cddid_all.tbl CDD PRK10893 PRK10893 236788 PRK10893 LPS export ABC transporter periplasmic protein LptC. 192 matched cddid_all.tbl CDD PRK10894 PRK10894 182816 PRK10894 lipopolysaccharide ABC transporter substrate-binding protein LptA. 180 matched cddid_all.tbl CDD PRK10895 PRK10895 182817 PRK10895 lipopolysaccharide ABC transporter ATP-binding protein; Provisional 241 matched cddid_all.tbl CDD PRK10896 PRK10896 182818 PRK10896 PTS IIA-like nitrogen regulatory protein PtsN. 154 matched cddid_all.tbl CDD PRK10897 PRK10897 182819 PRK10897 PTS phosphocarrier protein NPr. 90 matched cddid_all.tbl CDD PRK10898 PRK10898 182820 PRK10898 serine endoprotease DegS. 353 matched cddid_all.tbl CDD PRK10899 PRK10899 236789 PRK10899 AsmA2 domain-containing protein. 1022 matched cddid_all.tbl CDD PRK10901 PRK10901 236790 PRK10901 16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB. 427 matched cddid_all.tbl CDD PRK10902 PRK10902 236791 PRK10902 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional 269 matched cddid_all.tbl CDD PRK10903 PRK10903 182824 PRK10903 peptidylprolyl isomerase A. 190 matched cddid_all.tbl CDD PRK10904 PRK10904 182825 PRK10904 adenine-specific DNA-methyltransferase. 271 matched cddid_all.tbl CDD PRK10905 PRK10905 236792 PRK10905 cell division protein DamX; Validated 328 matched cddid_all.tbl CDD PRK10906 PRK10906 182827 PRK10906 DeoR/GlpR family transcriptional regulator. 252 matched cddid_all.tbl CDD PRK10907 PRK10907 182828 PRK10907 intramembrane serine protease GlpG; Provisional 276 matched cddid_all.tbl CDD PRK10908 PRK10908 182829 PRK10908 cell division ATP-binding protein FtsE. 222 matched cddid_all.tbl CDD PRK10909 PRK10909 236793 rsmD 16S rRNA m(2)G966-methyltransferase; Provisional 199 matched cddid_all.tbl CDD PRK10910 PRK10910 182831 PRK10910 DUF1145 family protein. 89 matched cddid_all.tbl CDD PRK10911 PRK10911 182832 PRK10911 oligopeptidase A; Provisional 680 matched cddid_all.tbl CDD PRK10913 PRK10913 182833 PRK10913 dipeptide ABC transporter permease DppC. 300 matched cddid_all.tbl CDD PRK10914 PRK10914 182834 PRK10914 dipeptide ABC transporter permease DppB. 339 matched cddid_all.tbl CDD PRK10916 PRK10916 182835 PRK10916 ADP-heptose--LPS heptosyltransferase RfaF. 348 matched cddid_all.tbl CDD PRK10917 PRK10917 236794 PRK10917 ATP-dependent DNA helicase RecG; Provisional 681 matched cddid_all.tbl CDD PRK10918 PRK10918 182837 PRK10918 phosphate ABC transporter substrate-binding protein PstS. 346 matched cddid_all.tbl CDD PRK10919 PRK10919 182838 PRK10919 ATP-dependent DNA helicase Rep; Provisional 672 matched cddid_all.tbl CDD PRK10920 PRK10920 236795 PRK10920 putative uroporphyrinogen III C-methyltransferase; Provisional 390 matched cddid_all.tbl CDD PRK10921 PRK10921 182840 PRK10921 Sec-independent protein translocase subunit TatC. 258 matched cddid_all.tbl CDD PRK10922 PRK10922 236796 PRK10922 4-hydroxy-3-polyprenylbenzoate decarboxylase. 497 matched cddid_all.tbl CDD PRK10923 PRK10923 182842 glnG nitrogen regulation protein NR(I); Provisional 469 matched cddid_all.tbl CDD PRK10925 PRK10925 182843 PRK10925 superoxide dismutase [Mn]. 206 matched cddid_all.tbl CDD PRK10926 PRK10926 182844 PRK10926 ferredoxin-NADP reductase; Provisional 248 matched cddid_all.tbl CDD PRK10927 PRK10927 236797 PRK10927 cell division protein FtsN. 319 matched cddid_all.tbl CDD PRK10929 PRK10929 236798 PRK10929 putative mechanosensitive channel protein; Provisional 1109 matched cddid_all.tbl CDD PRK10930 PRK10930 236799 PRK10930 FtsH protease activity modulator HflK. 419 matched cddid_all.tbl CDD PRK10931 PRK10931 182848 PRK10931 adenosine-3'(2'),5'-bisphosphate nucleotidase; Provisional 246 matched cddid_all.tbl CDD PRK10933 PRK10933 182849 PRK10933 trehalose-6-phosphate hydrolase; Provisional 551 matched cddid_all.tbl CDD PRK10935 PRK10935 236800 PRK10935 nitrate/nitrite two-component system sensor histidine kinase NarQ. 565 matched cddid_all.tbl CDD PRK10936 PRK10936 236801 PRK10936 TMAO reductase system periplasmic protein TorT; Provisional 343 matched cddid_all.tbl CDD PRK10938 PRK10938 182852 PRK10938 putative molybdenum transport ATP-binding protein ModF; Provisional 490 matched cddid_all.tbl CDD PRK10939 PRK10939 182853 PRK10939 autoinducer-2 (AI-2) kinase; Provisional 520 matched cddid_all.tbl CDD PRK10941 PRK10941 182854 PRK10941 tetratricopeptide repeat-containing protein. 269 matched cddid_all.tbl CDD PRK10942 PRK10942 236802 PRK10942 serine endoprotease DegP. 473 matched cddid_all.tbl CDD PRK10943 PRK10943 170841 PRK10943 cold shock-like protein CspC; Provisional 69 matched cddid_all.tbl CDD PRK10945 PRK10945 182856 PRK10945 hemolysin expression modulator Hha. 72 matched cddid_all.tbl CDD PRK10946 PRK10946 236803 entE (2,3-dihydroxybenzoyl)adenylate synthase. 536 matched cddid_all.tbl CDD PRK10947 PRK10947 182858 PRK10947 DNA-binding transcriptional regulator H-NS. 135 matched cddid_all.tbl CDD PRK10948 PRK10948 236804 PRK10948 Fe-S cluster assembly protein SufD. 424 matched cddid_all.tbl CDD PRK10949 PRK10949 182860 PRK10949 signal peptide peptidase SppA. 618 matched cddid_all.tbl CDD PRK10952 PRK10952 236805 PRK10952 proline/glycine betaine ABC transporter permease ProW. 355 matched cddid_all.tbl CDD PRK10953 PRK10953 182862 cysJ NADPH-dependent assimilatory sulfite reductase flavoprotein subunit. 600 matched cddid_all.tbl CDD PRK10954 PRK10954 182863 PRK10954 thiol:disulfide interchange protein DsbA. 207 matched cddid_all.tbl CDD PRK10955 PRK10955 182864 PRK10955 envelope stress response regulator transcription factor CpxR. 232 matched cddid_all.tbl CDD PRK10957 PRK10957 236806 PRK10957 iron-enterobactin transporter periplasmic binding protein; Provisional 317 matched cddid_all.tbl CDD PRK10958 PRK10958 236807 PRK10958 leucine export protein LeuE; Provisional 212 matched cddid_all.tbl CDD PRK10959 PRK10959 182867 PRK10959 outer membrane protein W; Provisional 212 matched cddid_all.tbl CDD PRK10963 PRK10963 236808 PRK10963 hypothetical protein; Provisional 223 matched cddid_all.tbl CDD PRK10964 PRK10964 236809 PRK10964 lipopolysaccharide heptosyltransferase RfaC. 322 matched cddid_all.tbl CDD PRK10965 PRK10965 236810 PRK10965 multicopper oxidase; Provisional 523 matched cddid_all.tbl CDD PRK10966 PRK10966 182871 PRK10966 exonuclease subunit SbcD; Provisional 407 matched cddid_all.tbl CDD PRK10969 PRK10969 182872 PRK10969 DNA polymerase III subunit theta; Reviewed 75 matched cddid_all.tbl CDD PRK10971 PRK10971 182873 PRK10971 sulfate/thiosulfate ABC transporter permease CysT. 277 matched cddid_all.tbl CDD PRK10972 PRK10972 182874 PRK10972 cell division protein ZapA. 109 matched cddid_all.tbl CDD PRK10973 PRK10973 182875 PRK10973 sn-glycerol-3-phosphate ABC transporter permease UgpE. 281 matched cddid_all.tbl CDD PRK10974 PRK10974 182876 PRK10974 sn-glycerol-3-phosphate ABC transporter substrate-binding protein UgpB. 438 matched cddid_all.tbl CDD PRK10975 PRK10975 182877 PRK10975 dTDP-4-amino-4,6-dideoxy-D-galactose acyltransferase. 194 matched cddid_all.tbl CDD PRK10976 PRK10976 182878 PRK10976 putative hydrolase; Provisional 266 matched cddid_all.tbl CDD PRK10982 PRK10982 182880 PRK10982 galactose/methyl galaxtoside transporter ATP-binding protein; Provisional 491 matched cddid_all.tbl CDD PRK10983 PRK10983 182881 PRK10983 AI-2E family transporter YdiK. 368 matched cddid_all.tbl CDD PRK10984 PRK10984 182882 PRK10984 sigma factor-binding protein Crl. 127 matched cddid_all.tbl CDD PRK10985 PRK10985 182883 PRK10985 putative hydrolase; Provisional 324 matched cddid_all.tbl CDD PRK10987 PRK10987 236811 PRK10987 beta-lactamase regulator AmpE. 284 matched cddid_all.tbl CDD PRK10991 PRK10991 182885 fucI L-fucose isomerase; Provisional 588 matched cddid_all.tbl CDD PRK10992 PRK10992 236812 PRK10992 iron-sulfur cluster repair protein YtfE. 220 matched cddid_all.tbl CDD PRK10993 PRK10993 236813 PRK10993 omptin family outer membrane protease. 314 matched cddid_all.tbl CDD PRK10995 PRK10995 236814 PRK10995 MarC family NAAT transporter. 221 matched cddid_all.tbl CDD PRK10996 PRK10996 182889 PRK10996 thioredoxin 2; Provisional 139 matched cddid_all.tbl CDD PRK10997 PRK10997 236815 yieM ATPase RavA stimulator ViaA. 487 matched cddid_all.tbl CDD PRK10998 PRK10998 182891 malG maltose ABC transporter permease MalG. 296 matched cddid_all.tbl CDD PRK10999 PRK10999 236816 malF maltose ABC transporter permease MalF. 520 matched cddid_all.tbl CDD PRK11000 PRK11000 182893 PRK11000 maltose/maltodextrin ABC transporter ATP-binding protein MalK. 369 matched cddid_all.tbl CDD PRK11001 PRK11001 236817 mtlR MltR family transcriptional regulator. 171 matched cddid_all.tbl CDD PRK11006 PRK11006 182895 phoR phosphate regulon sensor histidine kinase PhoR. 430 matched cddid_all.tbl CDD PRK11007 PRK11007 182896 PRK11007 PTS system trehalose(maltose)-specific transporter subunits IIBC; Provisional 473 matched cddid_all.tbl CDD PRK11010 PRK11010 182898 ampG muropeptide MFS transporter AmpG. 491 matched cddid_all.tbl CDD PRK11013 PRK11013 236819 PRK11013 DNA-binding transcriptional regulator LysR; Provisional 309 matched cddid_all.tbl CDD PRK11014 PRK11014 236820 PRK11014 HTH-type transcriptional repressor NsrR. 141 matched cddid_all.tbl CDD PRK11017 PRK11017 236821 codB cytosine permease; Provisional 404 matched cddid_all.tbl CDD PRK11018 PRK11018 236822 PRK11018 putative sulfurtransferase YedF. 78 matched cddid_all.tbl CDD PRK11019 PRK11019 182903 PRK11019 DksA/TraR family C4-type zinc finger protein. 88 matched cddid_all.tbl CDD PRK11020 PRK11020 182904 PRK11020 YibL family ribosome-associated protein. 118 matched cddid_all.tbl CDD PRK11021 PRK11021 236823 PRK11021 putative transporter; Provisional 410 matched cddid_all.tbl CDD PRK11022 PRK11022 182906 dppD dipeptide transporter ATP-binding subunit; Provisional 326 matched cddid_all.tbl CDD PRK11023 PRK11023 182907 PRK11023 divisome-associated lipoprotein YraP. 191 matched cddid_all.tbl CDD PRK11024 PRK11024 236824 PRK11024 colicin uptake protein TolR; Provisional 141 matched cddid_all.tbl CDD PRK11025 PRK11025 182909 PRK11025 23S rRNA pseudouridine(955/2504/2580) synthase RluC. 317 matched cddid_all.tbl CDD PRK11026 PRK11026 182910 ftsX putative protein insertion permease FtsX. FtsX is an integral membrane protein encoded in the same operon as signal recognition particle docking protein FtsY and FtsE. It belongs to a family of predicted permeases and may play a role in the insertion of proteins required for potassium transport, cell division, and other activities. FtsE is a hydrophilic nucleotide-binding protein that associates with the inner membrane by means of association with FtsX. [Cellular processes, Cell division, Protein fate, Protein and peptide secretion and trafficking] 309 matched cddid_all.tbl CDD PRK11027 PRK11027 236825 PRK11027 hypothetical protein; Provisional 112 matched cddid_all.tbl CDD PRK11028 PRK11028 182912 PRK11028 6-phosphogluconolactonase; Provisional 330 matched cddid_all.tbl CDD PRK11029 PRK11029 182913 PRK11029 protease modulator HflC. 334 matched cddid_all.tbl CDD PRK11031 PRK11031 236826 PRK11031 guanosine-5'-triphosphate,3'-diphosphate diphosphatase. 496 matched cddid_all.tbl CDD PRK11032 PRK11032 182915 PRK11032 zinc ribbon-containing protein. 160 matched cddid_all.tbl CDD PRK11033 PRK11033 236827 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional 741 matched cddid_all.tbl CDD PRK11034 PRK11034 236828 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional 758 matched cddid_all.tbl CDD PRK11036 PRK11036 182918 PRK11036 tRNA uridine 5-oxyacetic acid(34) methyltransferase CmoM. 255 matched cddid_all.tbl CDD PRK11037 PRK11037 182919 PRK11037 hypothetical protein; Provisional 83 matched cddid_all.tbl CDD PRK11038 PRK11038 182920 PRK11038 hypothetical protein; Provisional 47 matched cddid_all.tbl CDD PRK11039 PRK11039 182921 PRK11039 DUF1249 family protein. 140 matched cddid_all.tbl CDD PRK11040 PRK11040 182922 PRK11040 peptidase PmbA; Provisional 446 matched cddid_all.tbl CDD PRK11041 PRK11041 182923 PRK11041 DNA-binding transcriptional regulator CytR; Provisional 309 matched cddid_all.tbl CDD PRK11043 PRK11043 182924 PRK11043 Bcr/CflA family multidrug efflux MFS transporter. 401 matched cddid_all.tbl CDD PRK11045 PRK11045 236829 pagP lipid IV(A) palmitoyltransferase PagP. 184 matched cddid_all.tbl CDD PRK11049 PRK11049 236830 PRK11049 D-alanine/D-serine/glycine permease; Provisional 469 matched cddid_all.tbl CDD PRK11050 PRK11050 182927 PRK11050 manganese-binding transcriptional regulator MntR. 152 matched cddid_all.tbl CDD PRK11052 PRK11052 236831 malQ 4-alpha-glucanotransferase; Provisional 695 matched cddid_all.tbl CDD PRK11053 PRK11053 182929 PRK11053 oxygen-insensitive NAD(P)H nitroreductase. 217 matched cddid_all.tbl CDD PRK11054 PRK11054 182930 helD DNA helicase IV; Provisional 684 matched cddid_all.tbl CDD PRK11055 PRK11055 182931 galM galactose-1-epimerase; Provisional 342 matched cddid_all.tbl CDD PRK11056 PRK11056 236832 PRK11056 YijD family membrane protein. 120 matched cddid_all.tbl CDD PRK11057 PRK11057 182933 PRK11057 ATP-dependent DNA helicase RecQ; Provisional 607 matched cddid_all.tbl CDD PRK11058 PRK11058 182934 PRK11058 GTPase HflX; Provisional 426 matched cddid_all.tbl CDD PRK11059 PRK11059 236833 PRK11059 regulatory protein CsrD; Provisional 640 matched cddid_all.tbl CDD PRK11060 PRK11060 182936 PRK11060 rod shape-determining protein MreD; Provisional 162 matched cddid_all.tbl CDD PRK11061 PRK11061 182937 PRK11061 phosphoenolpyruvate--protein phosphotransferase. 748 matched cddid_all.tbl CDD PRK11062 PRK11062 182938 nhaR transcriptional activator NhaR; Provisional 296 matched cddid_all.tbl CDD PRK11063 PRK11063 182939 metQ D-methionine ABC transporter substrate-binding protein MetQ. 271 matched cddid_all.tbl CDD PRK11064 PRK11064 182940 wecC UDP-N-acetyl-D-mannosamine dehydrogenase; Provisional 415 matched cddid_all.tbl CDD PRK11067 PRK11067 236834 PRK11067 outer membrane protein assembly factor YaeT; Provisional 803 matched cddid_all.tbl CDD PRK11068 PRK11068 182942 PRK11068 phosphatidylglycerophosphatase A; Provisional 164 matched cddid_all.tbl CDD PRK11069 PRK11069 236835 recC exodeoxyribonuclease V subunit gamma. 1122 matched cddid_all.tbl CDD PRK11070 PRK11070 182944 PRK11070 single-stranded-DNA-specific exonuclease RecJ. 575 matched cddid_all.tbl CDD PRK11071 PRK11071 182945 PRK11071 esterase YqiA; Provisional 190 matched cddid_all.tbl CDD PRK11072 PRK11072 236836 PRK11072 bifunctional [glutamate--ammonia ligase]-adenylyl-L-tyrosine phosphorylase/[glutamate--ammonia-ligase] adenylyltransferase. 943 matched cddid_all.tbl CDD PRK11073 PRK11073 182947 glnL nitrogen regulation protein NR(II). 348 matched cddid_all.tbl CDD PRK11074 PRK11074 182948 PRK11074 putative DNA-binding transcriptional regulator; Provisional 300 matched cddid_all.tbl CDD PRK11081 PRK11081 236837 PRK11081 tRNA guanosine-2'-O-methyltransferase; Provisional 229 matched cddid_all.tbl CDD PRK11083 PRK11083 236838 PRK11083 DNA-binding response regulator CreB; Provisional 228 matched cddid_all.tbl CDD PRK11085 PRK11085 182951 PRK11085 magnesium/cobalt transporter CorA. 316 matched cddid_all.tbl CDD PRK11086 PRK11086 236839 PRK11086 sensory histidine kinase DcuS; Provisional 542 matched cddid_all.tbl CDD PRK11087 PRK11087 236840 PRK11087 oxidative stress defense protein; Provisional 231 matched cddid_all.tbl CDD PRK11088 PRK11088 236841 rrmA 23S rRNA methyltransferase A; Provisional 272 matched cddid_all.tbl CDD PRK11089 PRK11089 182955 PRK11089 PTS system glucose-specific transporter subunits IIBC; Provisional 477 matched cddid_all.tbl CDD PRK11091 PRK11091 236842 PRK11091 aerobic respiration control sensor protein ArcB; Provisional 779 matched cddid_all.tbl CDD PRK11092 PRK11092 236843 PRK11092 bifunctional GTP diphosphokinase/guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase. 702 matched cddid_all.tbl CDD PRK11096 PRK11096 182958 ansB L-asparaginase II; Provisional 347 matched cddid_all.tbl CDD PRK11097 PRK11097 236844 PRK11097 cellulase. 376 matched cddid_all.tbl CDD PRK11098 PRK11098 182960 PRK11098 peptide antibiotic transporter SbmA. 409 matched cddid_all.tbl CDD PRK11099 PRK11099 236845 PRK11099 putative inner membrane protein; Provisional 399 matched cddid_all.tbl CDD PRK11100 PRK11100 236846 PRK11100 sensory histidine kinase CreC; Provisional 475 matched cddid_all.tbl CDD PRK11101 PRK11101 236847 glpA anaerobic glycerol-3-phosphate dehydrogenase subunit A. 546 matched cddid_all.tbl CDD PRK11102 PRK11102 182964 PRK11102 Bcr/CflA family multidrug efflux MFS transporter. 377 matched cddid_all.tbl CDD PRK11103 PRK11103 182965 PRK11103 PTS mannose transporter subunit IID. 282 matched cddid_all.tbl CDD PRK11104 PRK11104 182966 hemG menaquinone-dependent protoporphyrinogen IX dehydrogenase. 177 matched cddid_all.tbl CDD PRK11106 PRK11106 182967 PRK11106 queuosine biosynthesis protein QueC; Provisional 231 matched cddid_all.tbl CDD PRK11107 PRK11107 236848 PRK11107 hybrid sensory histidine kinase BarA; Provisional 919 matched cddid_all.tbl CDD PRK11109 PRK11109 236849 PRK11109 fused PTS fructose transporter subunit IIA/HPr protein. 375 matched cddid_all.tbl CDD PRK11111 PRK11111 236850 PRK11111 YchE family NAAT transporter. 214 matched cddid_all.tbl CDD PRK11112 PRK11112 182971 PRK11112 tRNA pseudouridine synthase C; Provisional 257 matched cddid_all.tbl CDD PRK11113 PRK11113 182972 PRK11113 D-alanyl-D-alanine carboxypeptidase/endopeptidase; Provisional 477 matched cddid_all.tbl CDD PRK11114 PRK11114 236851 PRK11114 cellulose biosynthesis cyclic di-GMP-binding regulatory protein BcsB. 756 matched cddid_all.tbl CDD PRK11115 PRK11115 182974 PRK11115 phosphate signaling complex protein PhoU. 236 matched cddid_all.tbl CDD PRK11118 PRK11118 182975 PRK11118 putative monooxygenase; Provisional 100 matched cddid_all.tbl CDD PRK11119 PRK11119 236852 proX proline/glycine betaine ABC transporter substrate-binding protein ProX. 331 matched cddid_all.tbl CDD PRK11121 PRK11121 236853 nrdG anaerobic ribonucleoside-triphosphate reductase-activating protein. 154 matched cddid_all.tbl CDD PRK11122 PRK11122 182978 artM arginine ABC transporter permease ArtM. 222 matched cddid_all.tbl CDD PRK11123 PRK11123 182979 PRK11123 arginine ABC transporter permease ArtQ. 238 matched cddid_all.tbl CDD PRK11124 PRK11124 182980 artP arginine transporter ATP-binding subunit; Provisional 242 matched cddid_all.tbl CDD PRK11125 PRK11125 236854 nrfA ammonia-forming cytochrome c nitrite reductase. 480 matched cddid_all.tbl CDD PRK11126 PRK11126 236855 PRK11126 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase; Provisional 242 matched cddid_all.tbl CDD PRK11127 PRK11127 182983 PRK11127 autonomous glycyl radical cofactor GrcA; Provisional 127 matched cddid_all.tbl CDD PRK11128 PRK11128 236856 PRK11128 3-phenylpropionate MFS transporter. 382 matched cddid_all.tbl CDD PRK11130 PRK11130 182985 moaD molybdopterin synthase small subunit; Provisional 81 matched cddid_all.tbl CDD PRK11131 PRK11131 182986 PRK11131 ATP-dependent RNA helicase HrpA; Provisional 1294 matched cddid_all.tbl CDD PRK11132 PRK11132 182987 cysE serine acetyltransferase; Provisional 273 matched cddid_all.tbl CDD PRK11133 PRK11133 182988 serB phosphoserine phosphatase; Provisional 322 matched cddid_all.tbl CDD PRK11138 PRK11138 236857 PRK11138 outer membrane biogenesis protein BamB; Provisional 394 matched cddid_all.tbl CDD PRK11139 PRK11139 182990 PRK11139 DNA-binding transcriptional activator GcvA; Provisional 297 matched cddid_all.tbl CDD PRK11142 PRK11142 236858 PRK11142 ribokinase; Provisional 306 matched cddid_all.tbl CDD PRK11143 PRK11143 236859 glpQ glycerophosphodiester phosphodiesterase; Provisional 355 matched cddid_all.tbl CDD PRK11144 PRK11144 182993 modC molybdenum ABC transporter ATP-binding protein ModC. 352 matched cddid_all.tbl CDD PRK11145 PRK11145 182994 pflA pyruvate formate lyase 1-activating protein. 246 matched cddid_all.tbl CDD PRK11146 PRK11146 236860 PRK11146 lipoprotein-releasing ABC transporter permease subunit LolE. 412 matched cddid_all.tbl CDD PRK11147 PRK11147 236861 PRK11147 ABC transporter ATPase component; Reviewed 635 matched cddid_all.tbl CDD PRK11148 PRK11148 182997 PRK11148 cyclic 3',5'-adenosine monophosphate phosphodiesterase; Provisional 275 matched cddid_all.tbl CDD PRK11150 PRK11150 182998 rfaD ADP-L-glycero-D-mannoheptose-6-epimerase; Provisional 308 matched cddid_all.tbl CDD PRK11151 PRK11151 182999 PRK11151 DNA-binding transcriptional regulator OxyR; Provisional 305 matched cddid_all.tbl CDD PRK11152 PRK11152 236862 ilvM acetolactate synthase 2 small subunit. 76 matched cddid_all.tbl CDD PRK11153 PRK11153 236863 metN DL-methionine transporter ATP-binding subunit; Provisional 343 matched cddid_all.tbl CDD PRK11154 PRK11154 236864 fadJ fatty acid oxidation complex subunit alpha FadJ. 708 matched cddid_all.tbl CDD PRK11160 PRK11160 236865 PRK11160 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed 574 matched cddid_all.tbl CDD PRK11161 PRK11161 183004 PRK11161 fumarate/nitrate reduction transcriptional regulator Fnr. 235 matched cddid_all.tbl CDD PRK11162 PRK11162 236866 mltA murein transglycosylase A; Provisional 355 matched cddid_all.tbl CDD PRK11166 PRK11166 236868 PRK11166 chemotaxis regulator CheZ; Provisional 214 matched cddid_all.tbl CDD PRK11168 PRK11168 236869 glpC anaerobic glycerol-3-phosphate dehydrogenase subunit C. 396 matched cddid_all.tbl CDD PRK11169 PRK11169 183009 PRK11169 leucine-responsive transcriptional regulator Lrp. 164 matched cddid_all.tbl CDD PRK11170 PRK11170 183010 nagA N-acetylglucosamine-6-phosphate deacetylase; Provisional 382 matched cddid_all.tbl CDD PRK11171 PRK11171 183011 PRK11171 (S)-ureidoglycine aminohydrolase. 266 matched cddid_all.tbl CDD PRK11172 PRK11172 183012 dkgB 2,5-didehydrogluconate reductase DkgB. 267 matched cddid_all.tbl CDD PRK11173 PRK11173 183013 PRK11173 two-component response regulator; Provisional 237 matched cddid_all.tbl CDD PRK11174 PRK11174 236870 PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed 588 matched cddid_all.tbl CDD PRK11175 PRK11175 236871 PRK11175 universal stress protein UspE; Provisional 305 matched cddid_all.tbl CDD PRK11176 PRK11176 183016 PRK11176 lipid A ABC transporter ATP-binding protein/permease MsbA. 582 matched cddid_all.tbl CDD PRK11177 PRK11177 183017 PRK11177 phosphoenolpyruvate-protein phosphotransferase PtsI. 575 matched cddid_all.tbl CDD PRK11178 PRK11178 183018 PRK11178 uridine phosphorylase; Provisional 251 matched cddid_all.tbl CDD PRK11179 PRK11179 183019 PRK11179 DNA-binding transcriptional regulator AsnC; Provisional 153 matched cddid_all.tbl CDD PRK11180 PRK11180 183020 rluD 23S rRNA pseudouridine(1911/1915/1917) synthase RluD. 325 matched cddid_all.tbl CDD PRK11181 PRK11181 183021 PRK11181 23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB. 244 matched cddid_all.tbl CDD PRK11183 PRK11183 236872 PRK11183 D-lactate dehydrogenase; Provisional 564 matched cddid_all.tbl CDD PRK11186 PRK11186 236873 PRK11186 carboxy terminal-processing peptidase. 667 matched cddid_all.tbl CDD PRK11187 PRK11187 236874 PRK11187 replication initiation negative regulator SeqA. 182 matched cddid_all.tbl CDD PRK11188 PRK11188 183025 rrmJ 23S rRNA (uridine(2552)-2'-O)-methyltransferase RlmE. 209 matched cddid_all.tbl CDD PRK11189 PRK11189 236875 PRK11189 lipoprotein NlpI; Provisional 296 matched cddid_all.tbl CDD PRK11190 PRK11190 183027 PRK11190 iron-sulfur cluster biogenesis protein NfuA. 192 matched cddid_all.tbl CDD PRK11191 PRK11191 236876 PRK11191 ribonuclease E inhibitor RraB. 138 matched cddid_all.tbl CDD PRK11192 PRK11192 236877 PRK11192 ATP-dependent RNA helicase SrmB; Provisional 434 matched cddid_all.tbl CDD PRK11193 PRK11193 236878 PRK11193 23S rRNA accumulation protein YceD. 172 matched cddid_all.tbl CDD PRK11194 PRK11194 183031 PRK11194 ribosomal RNA large subunit methyltransferase N; Provisional 372 matched cddid_all.tbl CDD PRK11195 PRK11195 236879 PRK11195 lysophospholipid transporter LplT; Provisional 393 matched cddid_all.tbl CDD PRK11197 PRK11197 183033 lldD L-lactate dehydrogenase; Provisional 381 matched cddid_all.tbl CDD PRK11198 PRK11198 236880 PRK11198 LysM domain/BON superfamily protein; Provisional 147 matched cddid_all.tbl CDD PRK11199 PRK11199 183035 tyrA bifunctional chorismate mutase/prephenate dehydrogenase; Provisional 374 matched cddid_all.tbl CDD PRK11200 PRK11200 183036 grxA glutaredoxin 1; Provisional 85 matched cddid_all.tbl CDD PRK11202 PRK11202 236881 PRK11202 HTH-type transcriptional repressor FabR. 203 matched cddid_all.tbl CDD PRK11207 PRK11207 183040 PRK11207 tellurite resistance methyltransferase TehB. 197 matched cddid_all.tbl CDD PRK11212 PRK11212 183041 PRK11212 7-cyano-7-deazaguanine/7-aminomethyl-7-deazaguanine transporter. 210 matched cddid_all.tbl CDD PRK11228 PRK11228 183042 fecC iron-dicitrate ABC transporter permease FecC. 323 matched cddid_all.tbl CDD PRK11230 PRK11230 183043 PRK11230 glycolate oxidase subunit GlcD; Provisional 499 matched cddid_all.tbl CDD PRK11231 PRK11231 183044 fecE Fe(3+) dicitrate ABC transporter ATP-binding protein FecE. 255 matched cddid_all.tbl CDD PRK11233 PRK11233 183045 PRK11233 nitrogen assimilation transcriptional regulator; Provisional 305 matched cddid_all.tbl CDD PRK11234 PRK11234 236884 nfrB phage adsorption protein NrfB. 727 matched cddid_all.tbl CDD PRK11235 PRK11235 183047 PRK11235 type II toxin-antitoxin system RelB/DinJ family antitoxin. 80 matched cddid_all.tbl CDD PRK11239 PRK11239 183048 PRK11239 hypothetical protein; Provisional 215 matched cddid_all.tbl CDD PRK11240 PRK11240 183049 PRK11240 penicillin-binding protein 1C; Provisional 772 matched cddid_all.tbl CDD PRK11241 PRK11241 183050 gabD NADP-dependent succinate-semialdehyde dehydrogenase I. 482 matched cddid_all.tbl CDD PRK11242 PRK11242 183051 PRK11242 DNA-binding transcriptional regulator CynR; Provisional 296 matched cddid_all.tbl CDD PRK11245 PRK11245 183053 folX dihydroneopterin triphosphate 2'-epimerase. 120 matched cddid_all.tbl CDD PRK11246 PRK11246 236885 PRK11246 YtjB family periplasmic protein. 218 matched cddid_all.tbl CDD PRK11247 PRK11247 183055 ssuB aliphatic sulfonates transport ATP-binding subunit; Provisional 257 matched cddid_all.tbl CDD PRK11248 PRK11248 183056 tauB taurine ABC transporter ATP-binding subunit. 255 matched cddid_all.tbl CDD PRK11249 PRK11249 236886 katE hydroperoxidase II; Provisional 752 matched cddid_all.tbl CDD PRK11251 PRK11251 183058 PRK11251 osmotically-inducible lipoprotein OsmE. 109 matched cddid_all.tbl CDD PRK11253 PRK11253 183059 ldcA L,D-carboxypeptidase A; Provisional 305 matched cddid_all.tbl CDD PRK11259 PRK11259 236887 solA N-methyl-L-tryptophan oxidase. 376 matched cddid_all.tbl CDD PRK11260 PRK11260 183061 PRK11260 cystine ABC transporter substrate-binding protein. 266 matched cddid_all.tbl CDD PRK11263 PRK11263 236888 PRK11263 cardiolipin synthase ClsB. 411 matched cddid_all.tbl CDD PRK11264 PRK11264 183063 PRK11264 putative amino-acid ABC transporter ATP-binding protein YecC; Provisional 250 matched cddid_all.tbl CDD PRK11267 PRK11267 183064 PRK11267 biopolymer transport protein ExbD; Provisional 141 matched cddid_all.tbl CDD PRK11268 PRK11268 183065 pstA phosphate ABC transporter permease PstA. 295 matched cddid_all.tbl CDD PRK11269 PRK11269 183066 PRK11269 glyoxylate carboligase; Provisional 591 matched cddid_all.tbl CDD PRK11272 PRK11272 183067 PRK11272 putative DMT superfamily transporter inner membrane protein; Provisional 292 matched cddid_all.tbl CDD PRK11273 PRK11273 236889 glpT glycerol-3-phosphate transporter. 452 matched cddid_all.tbl CDD PRK11274 PRK11274 236890 glcF glycolate oxidase subunit GlcF. 407 matched cddid_all.tbl CDD PRK11275 PRK11275 183070 pstC phosphate ABC transporter permease PstC. 319 matched cddid_all.tbl CDD PRK11278 PRK11278 236891 PRK11278 NADH-quinone oxidoreductase subunit NuoF. 448 matched cddid_all.tbl CDD PRK11280 PRK11280 183072 PRK11280 hypothetical protein; Provisional 170 matched cddid_all.tbl CDD PRK11281 PRK11281 236892 PRK11281 mechanosensitive channel MscK. 1113 matched cddid_all.tbl CDD PRK11282 PRK11282 236893 glcE glycolate oxidase FAD binding subunit; Provisional 352 matched cddid_all.tbl CDD PRK11283 PRK11283 183075 gltP glutamate/aspartate:proton symporter; Provisional 437 matched cddid_all.tbl CDD PRK11285 PRK11285 183076 araH L-arabinose transporter permease protein; Provisional 333 matched cddid_all.tbl CDD PRK11288 PRK11288 183077 araG L-arabinose ABC transporter ATP-binding protein AraG. 501 matched cddid_all.tbl CDD PRK11289 PRK11289 236894 ampC beta-lactamase/D-alanine carboxypeptidase; Provisional 384 matched cddid_all.tbl CDD PRK11295 PRK11295 236895 PRK11295 HNH nuclease family protein. 113 matched cddid_all.tbl CDD PRK11300 PRK11300 183080 livG leucine/isoleucine/valine transporter ATP-binding subunit; Provisional 255 matched cddid_all.tbl CDD PRK11301 PRK11301 236896 livM leucine/isoleucine/valine transporter permease subunit; Provisional 419 matched cddid_all.tbl CDD PRK11302 PRK11302 183082 PRK11302 DNA-binding transcriptional regulator HexR; Provisional 284 matched cddid_all.tbl CDD PRK11303 PRK11303 236897 PRK11303 catabolite repressor/activator. 328 matched cddid_all.tbl CDD PRK11308 PRK11308 236898 dppF dipeptide transporter ATP-binding subunit; Provisional 327 matched cddid_all.tbl CDD PRK11316 PRK11316 183085 PRK11316 bifunctional D-glycero-beta-D-manno-heptose-7-phosphate kinase/D-glycero-beta-D-manno-heptose 1-phosphate adenylyltransferase HldE. 473 matched cddid_all.tbl CDD PRK11320 PRK11320 183086 prpB 2-methylisocitrate lyase; Provisional 292 matched cddid_all.tbl CDD PRK11331 PRK11331 183088 PRK11331 5-methylcytosine-specific restriction enzyme subunit McrB; Provisional 459 matched cddid_all.tbl CDD PRK11337 PRK11337 183089 PRK11337 MurR/RpiR family transcriptional regulator. 292 matched cddid_all.tbl CDD PRK11339 PRK11339 183090 abgT putative aminobenzoyl-glutamate transporter; Provisional 508 matched cddid_all.tbl CDD PRK11340 PRK11340 236899 PRK11340 phosphodiesterase YaeI; Provisional 271 matched cddid_all.tbl CDD PRK11342 PRK11342 183092 mhpD 2-keto-4-pentenoate hydratase; Provisional 262 matched cddid_all.tbl CDD PRK11346 PRK11346 183093 PRK11346 hypothetical protein; Provisional 285 matched cddid_all.tbl CDD PRK11347 PRK11347 183094 PRK11347 antitoxin ChpS; Provisional 83 matched cddid_all.tbl CDD PRK11352 PRK11352 183095 PRK11352 formaldehyde-responsive transcriptional repressor FrmR. 91 matched cddid_all.tbl CDD PRK11354 PRK11354 236900 kil FtsZ inhibitor protein; Reviewed 73 matched cddid_all.tbl CDD PRK11357 PRK11357 183096 frlA amino acid permease. 445 matched cddid_all.tbl CDD PRK11359 PRK11359 183097 PRK11359 cyclic-di-GMP phosphodiesterase; Provisional 799 matched cddid_all.tbl CDD PRK11360 PRK11360 236901 PRK11360 two-component system sensor histidine kinase AtoS. 607 matched cddid_all.tbl CDD PRK11361 PRK11361 183099 PRK11361 acetoacetate metabolism transcriptional regulator AtoC. 457 matched cddid_all.tbl CDD PRK11365 PRK11365 183100 ssuC aliphatic sulfonate ABC transporter permease SsuC. 263 matched cddid_all.tbl CDD PRK11366 PRK11366 183101 puuD gamma-glutamyl-gamma-aminobutyrate hydrolase; Provisional 254 matched cddid_all.tbl CDD PRK11367 PRK11367 183102 PRK11367 hypothetical protein; Provisional 476 matched cddid_all.tbl CDD PRK11370 PRK11370 183103 PRK11370 YciI family protein. 99 matched cddid_all.tbl CDD PRK11371 PRK11371 183104 PRK11371 hypothetical protein; Provisional 126 matched cddid_all.tbl CDD PRK11372 PRK11372 236902 PRK11372 C-type lysozyme inhibitor. 109 matched cddid_all.tbl CDD PRK11375 PRK11375 183106 PRK11375 putative allantoin permease. 484 matched cddid_all.tbl CDD PRK11376 PRK11376 183107 hlyE hemolysin HlyE. 303 matched cddid_all.tbl CDD PRK11377 PRK11377 183108 PRK11377 dihydroxyacetone kinase subunit M; Provisional 473 matched cddid_all.tbl CDD PRK11379 PRK11379 183109 PRK11379 putative outer membrane porin protein; Provisional 417 matched cddid_all.tbl CDD PRK11380 PRK11380 236903 PRK11380 hypothetical protein; Provisional 353 matched cddid_all.tbl CDD PRK11382 PRK11382 183111 frlB fructoselysine 6-phosphate deglycase. 340 matched cddid_all.tbl CDD PRK11383 PRK11383 105206 PRK11383 YiaB family inner membrane protein. 145 matched cddid_all.tbl CDD PRK11385 PRK11385 183112 PRK11385 fimbrial chaperone. 236 matched cddid_all.tbl CDD PRK11387 PRK11387 236904 PRK11387 S-methylmethionine permease. 471 matched cddid_all.tbl CDD PRK11388 PRK11388 183114 PRK11388 DNA-binding transcriptional regulator DhaR; Provisional 638 matched cddid_all.tbl CDD PRK11391 PRK11391 138553 etp phosphotyrosine-protein phosphatase; Provisional 144 matched cddid_all.tbl CDD PRK11394 PRK11394 183115 PRK11394 23S rRNA pseudouridine(2457) synthase RluE. 217 matched cddid_all.tbl CDD PRK11396 PRK11396 236905 PRK11396 environmental stress-induced protein Ves. 191 matched cddid_all.tbl CDD PRK11397 PRK11397 183117 dacD serine-type D-Ala-D-Ala carboxypeptidase DacD. 388 matched cddid_all.tbl CDD PRK11401 PRK11401 105214 PRK11401 enamine/imine deaminase. 129 matched cddid_all.tbl CDD PRK11402 PRK11402 183118 PRK11402 transcriptional regulator PhoB. 241 matched cddid_all.tbl CDD PRK11403 PRK11403 183119 PRK11403 hypothetical protein; Provisional 113 matched cddid_all.tbl CDD PRK11404 PRK11404 183120 PRK11404 PTS fructose-like transporter subunit IIBC. 482 matched cddid_all.tbl CDD PRK11408 PRK11408 236906 PRK11408 hypothetical protein; Provisional 145 matched cddid_all.tbl CDD PRK11409 PRK11409 171099 PRK11409 YoeB-YefM toxin-antitoxin system antitoxin YefM. 83 matched cddid_all.tbl CDD PRK11410 PRK11410 236907 PRK11410 hypothetical protein; Provisional 561 matched cddid_all.tbl CDD PRK11411 PRK11411 183123 fecB iron-dicitrate transporter substrate-binding subunit; Provisional 303 matched cddid_all.tbl CDD PRK11412 PRK11412 183124 PRK11412 uracil/xanthine transporter. 433 matched cddid_all.tbl CDD PRK11413 PRK11413 183125 PRK11413 putative hydratase; Provisional 751 matched cddid_all.tbl CDD PRK11414 PRK11414 183126 PRK11414 GntR family transcriptional regulator. 221 matched cddid_all.tbl CDD PRK11415 PRK11415 183127 PRK11415 hypothetical protein; Provisional 74 matched cddid_all.tbl CDD PRK11423 PRK11423 236908 PRK11423 methylmalonyl-CoA decarboxylase; Provisional 261 matched cddid_all.tbl CDD PRK11424 PRK11424 236909 PRK11424 DNA-binding transcriptional activator TdcR; Provisional 114 matched cddid_all.tbl CDD PRK11425 PRK11425 183129 PRK11425 PTS N-acetylgalactosamine transporter subunit IIB. 157 matched cddid_all.tbl CDD PRK11426 PRK11426 183130 PRK11426 hypothetical protein; Provisional 132 matched cddid_all.tbl CDD PRK11427 PRK11427 183131 PRK11427 multidrug efflux transporter permease subunit MdtO. 683 matched cddid_all.tbl CDD PRK11430 PRK11430 183132 PRK11430 putative CoA-transferase; Provisional 381 matched cddid_all.tbl CDD PRK11431 PRK11431 171110 PRK11431 quaternary ammonium compound efflux SMR transporter SugE. 105 matched cddid_all.tbl CDD PRK11432 PRK11432 183133 fbpC ferric ABC transporter ATP-binding protein. 351 matched cddid_all.tbl CDD PRK11433 PRK11433 236910 PRK11433 aldehyde oxidoreductase 2Fe-2S subunit; Provisional 217 matched cddid_all.tbl CDD PRK11436 PRK11436 183135 PRK11436 biofilm-dependent modulation protein; Provisional 71 matched cddid_all.tbl CDD PRK11439 PRK11439 236911 pphA protein-serine/threonine phosphatase. 218 matched cddid_all.tbl CDD PRK11440 PRK11440 183137 PRK11440 putative hydrolase; Provisional 188 matched cddid_all.tbl CDD PRK11443 PRK11443 183138 PRK11443 lipoprotein; Provisional 124 matched cddid_all.tbl CDD PRK11445 PRK11445 183139 PRK11445 FAD-binding protein. 351 matched cddid_all.tbl CDD PRK11447 PRK11447 183140 PRK11447 cellulose synthase subunit BcsC; Provisional 1157 matched cddid_all.tbl CDD PRK11448 PRK11448 236912 hsdR type I restriction enzyme EcoKI subunit R; Provisional 1123 matched cddid_all.tbl CDD PRK11449 PRK11449 171118 PRK11449 metal-dependent hydrolase. 258 matched cddid_all.tbl CDD PRK11453 PRK11453 183142 PRK11453 O-acetylserine/cysteine exporter. 299 matched cddid_all.tbl CDD PRK11459 PRK11459 183143 PRK11459 multidrug resistance outer membrane protein MdtQ; Provisional 478 matched cddid_all.tbl CDD PRK11460 PRK11460 183144 PRK11460 putative hydrolase; Provisional 232 matched cddid_all.tbl CDD PRK11462 PRK11462 183145 PRK11462 putative transporter; Provisional 460 matched cddid_all.tbl CDD PRK11463 PRK11463 236913 fxsA phage T7 F exclusion suppressor FxsA; Reviewed 148 matched cddid_all.tbl CDD PRK11465 PRK11465 183147 PRK11465 putative mechanosensitive channel protein; Provisional 741 matched cddid_all.tbl CDD PRK11466 PRK11466 236914 PRK11466 hybrid sensory histidine kinase TorS; Provisional 914 matched cddid_all.tbl CDD PRK11467 PRK11467 183149 PRK11467 secY/secA suppressor protein; Provisional 124 matched cddid_all.tbl CDD PRK11468 PRK11468 183150 PRK11468 dihydroxyacetone kinase subunit DhaK; Provisional 356 matched cddid_all.tbl CDD PRK11469 PRK11469 183151 PRK11469 manganese efflux pump MntP. 188 matched cddid_all.tbl CDD PRK11470 PRK11470 183152 PRK11470 YebB family permuted papain-like enzyme. 200 matched cddid_all.tbl CDD PRK11475 PRK11475 236915 PRK11475 DNA-binding transcriptional activator BglJ; Provisional 207 matched cddid_all.tbl CDD PRK11476 PRK11476 183154 PRK11476 carnitine metabolism transcriptional regulator CaiF. 113 matched cddid_all.tbl CDD PRK11477 PRK11477 183155 PRK11477 CdaR family transcriptional regulator. 385 matched cddid_all.tbl CDD PRK11478 PRK11478 183156 PRK11478 VOC family protein. 129 matched cddid_all.tbl CDD PRK11479 PRK11479 183157 PRK11479 YaeF family permuted papain-like enzyme. 274 matched cddid_all.tbl CDD PRK11480 PRK11480 183158 tauA taurine transporter substrate binding subunit; Provisional 320 matched cddid_all.tbl CDD PRK11482 PRK11482 183159 PRK11482 DNA-binding transcriptional regulator. 317 matched cddid_all.tbl CDD PRK11486 PRK11486 183160 PRK11486 flagellar type III secretion system protein FliO. 124 matched cddid_all.tbl CDD PRK11492 PRK11492 236916 hyfE hydrogenase 4 membrane subunit; Provisional 216 matched cddid_all.tbl CDD PRK11493 PRK11493 236917 sseA 3-mercaptopyruvate sulfurtransferase; Provisional 281 matched cddid_all.tbl CDD PRK11498 PRK11498 236918 bcsA cellulose synthase catalytic subunit; Provisional 852 matched cddid_all.tbl CDD PRK11504 PRK11504 236919 tynA primary-amine oxidase. 647 matched cddid_all.tbl CDD PRK11505 PRK11505 183165 PRK11505 phosphate starvation-inducible protein PsiF. 106 matched cddid_all.tbl CDD PRK11507 PRK11507 183166 PRK11507 ribosome-associated protein YbcJ. 70 matched cddid_all.tbl CDD PRK11508 PRK11508 183167 PRK11508 sulfurtransferase TusE. 109 matched cddid_all.tbl CDD PRK11509 PRK11509 183168 PRK11509 hydrogenase-1 operon protein HyaE; Provisional 132 matched cddid_all.tbl CDD PRK11511 PRK11511 236920 PRK11511 MDR efflux pump AcrAB transcriptional activator MarA. 127 matched cddid_all.tbl CDD PRK11512 PRK11512 183170 PRK11512 multiple antibiotic resistance transcriptional regulator MarR. 144 matched cddid_all.tbl CDD PRK11513 PRK11513 236921 PRK11513 cytochrome b561; Provisional 176 matched cddid_all.tbl CDD PRK11517 PRK11517 183172 PRK11517 DNA-binding response regulator HprR. 223 matched cddid_all.tbl CDD PRK11519 PRK11519 183173 PRK11519 tyrosine-protein kinase Wzc. 719 matched cddid_all.tbl CDD PRK11521 PRK11521 183174 PRK11521 DUF2509 family protein. 124 matched cddid_all.tbl CDD PRK11522 PRK11522 183175 PRK11522 putrescine--2-oxoglutarate aminotransferase; Provisional 459 matched cddid_all.tbl CDD PRK11523 PRK11523 183176 PRK11523 transcriptional regulator ExuR. 253 matched cddid_all.tbl CDD PRK11524 PRK11524 183177 PRK11524 adenine-specific DNA-methyltransferase. 284 matched cddid_all.tbl CDD PRK11525 PRK11525 183178 dinD DNA-damage-inducible protein D; Provisional 279 matched cddid_all.tbl CDD PRK11528 PRK11528 236922 PRK11528 hypothetical protein; Provisional 254 matched cddid_all.tbl CDD PRK11530 PRK11530 236923 PRK11530 hypothetical protein; Provisional 183 matched cddid_all.tbl CDD PRK11534 PRK11534 183181 PRK11534 DNA-binding transcriptional regulator CsiR; Provisional 224 matched cddid_all.tbl CDD PRK11536 PRK11536 183182 PRK11536 6-N-hydroxylaminopurine resistance protein; Provisional 223 matched cddid_all.tbl CDD PRK11537 PRK11537 183183 PRK11537 putative GTP-binding protein YjiA; Provisional 318 matched cddid_all.tbl CDD PRK11538 PRK11538 183184 PRK11538 ribosome silencing factor. 105 matched cddid_all.tbl CDD PRK11539 PRK11539 236924 PRK11539 ComEC family competence protein; Provisional 755 matched cddid_all.tbl CDD PRK11543 PRK11543 183186 gutQ arabinose-5-phosphate isomerase GutQ. 321 matched cddid_all.tbl CDD PRK11545 PRK11545 236926 gntK gluconokinase. 163 matched cddid_all.tbl CDD PRK11546 PRK11546 183189 zraP zinc resistance sensor/chaperone ZraP. 143 matched cddid_all.tbl CDD PRK11548 PRK11548 183190 PRK11548 outer membrane protein assembly factor BamE. 113 matched cddid_all.tbl CDD PRK11551 PRK11551 236927 PRK11551 putative 3-hydroxyphenylpropionic transporter MhpT; Provisional 406 matched cddid_all.tbl CDD PRK11552 PRK11552 236928 PRK11552 putative DNA-binding transcriptional regulator; Provisional 225 matched cddid_all.tbl CDD PRK11553 PRK11553 236929 PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional 314 matched cddid_all.tbl CDD PRK11556 PRK11556 183194 PRK11556 MdtA/MuxA family multidrug efflux RND transporter periplasmic adaptor subunit. 415 matched cddid_all.tbl CDD PRK11557 PRK11557 183195 PRK11557 MurR/RpiR family transcriptional regulator. 278 matched cddid_all.tbl CDD PRK11558 PRK11558 236930 PRK11558 putative ssRNA endonuclease; Provisional 97 matched cddid_all.tbl CDD PRK11559 PRK11559 183197 garR tartronate semialdehyde reductase; Provisional 296 matched cddid_all.tbl CDD PRK11560 PRK11560 183198 PRK11560 kdo(2)-lipid A phosphoethanolamine 7''-transferase. 558 matched cddid_all.tbl CDD PRK11561 PRK11561 183199 PRK11561 isovaleryl CoA dehydrogenase; Provisional 538 matched cddid_all.tbl CDD PRK11562 PRK11562 183200 PRK11562 nitrite transporter NirC; Provisional 268 matched cddid_all.tbl CDD PRK11564 PRK11564 236932 PRK11564 stationary phase inducible protein CsiE; Provisional 426 matched cddid_all.tbl CDD PRK11565 PRK11565 183203 dkgA 2,5-didehydrogluconate reductase DkgA. 275 matched cddid_all.tbl CDD PRK11566 PRK11566 183204 hdeB acid-activated periplasmic chaperone HdeB. 102 matched cddid_all.tbl CDD PRK11568 PRK11568 183205 PRK11568 IMPACT family protein. 204 matched cddid_all.tbl CDD PRK11569 PRK11569 183206 PRK11569 glyoxylate bypass operon transcriptional repressor IclR. 274 matched cddid_all.tbl CDD PRK11570 PRK11570 183207 PRK11570 peptidyl-prolyl cis-trans isomerase; Provisional 206 matched cddid_all.tbl CDD PRK11572 PRK11572 183208 PRK11572 copper homeostasis protein CutC; Provisional 248 matched cddid_all.tbl CDD PRK11573 PRK11573 236933 PRK11573 hypothetical protein; Provisional 413 matched cddid_all.tbl CDD PRK11574 PRK11574 183210 PRK11574 protein deglycase YajL. 196 matched cddid_all.tbl CDD PRK11578 PRK11578 183211 PRK11578 macrolide transporter subunit MacA; Provisional 370 matched cddid_all.tbl CDD PRK11579 PRK11579 183212 PRK11579 putative oxidoreductase; Provisional 346 matched cddid_all.tbl CDD PRK11582 PRK11582 183213 PRK11582 flagella biosynthesis regulatory protein FliZ. 169 matched cddid_all.tbl CDD PRK11586 PRK11586 183214 napB nitrate reductase cytochrome c-type subunit. 149 matched cddid_all.tbl CDD PRK11587 PRK11587 183215 PRK11587 putative phosphatase; Provisional 218 matched cddid_all.tbl CDD PRK11588 PRK11588 236934 PRK11588 putative basic amino acid antiporter YfcC. 506 matched cddid_all.tbl CDD PRK11589 PRK11589 236935 gcvR glycine cleavage system transcriptional repressor; Provisional 190 matched cddid_all.tbl CDD PRK11593 PRK11593 183219 folB bifunctional dihydroneopterin aldolase/7,8-dihydroneopterin epimerase. 119 matched cddid_all.tbl CDD PRK11594 PRK11594 183220 PRK11594 efflux system membrane protein; Provisional 67 matched cddid_all.tbl CDD PRK11595 PRK11595 183221 PRK11595 DNA utilization protein GntX; Provisional 227 matched cddid_all.tbl CDD PRK11596 PRK11596 183222 PRK11596 cyclic-di-GMP phosphodiesterase; Provisional 255 matched cddid_all.tbl CDD PRK11597 PRK11597 183223 PRK11597 heat shock chaperone IbpB; Provisional 142 matched cddid_all.tbl CDD PRK11598 PRK11598 183224 PRK11598 putative metal dependent hydrolase; Provisional 545 matched cddid_all.tbl CDD PRK11602 PRK11602 183225 cysW sulfate/thiosulfate ABC transporter permease CysW. 283 matched cddid_all.tbl CDD PRK11607 PRK11607 183226 potG putrescine ABC transporter ATP-binding subunit PotG. 377 matched cddid_all.tbl CDD PRK11608 PRK11608 236936 pspF phage shock protein operon transcriptional activator; Provisional 326 matched cddid_all.tbl CDD PRK11609 PRK11609 183228 PRK11609 bifunctional nicotinamidase/pyrazinamidase. 212 matched cddid_all.tbl CDD PRK11611 PRK11611 183229 PRK11611 enhanced serine sensitivity protein SseB; Provisional 246 matched cddid_all.tbl CDD PRK11613 PRK11613 183230 folP dihydropteroate synthase; Provisional 282 matched cddid_all.tbl CDD PRK11614 PRK11614 183231 livF high-affinity branched-chain amino acid ABC transporter ATP-binding protein LivF. 237 matched cddid_all.tbl CDD PRK11615 PRK11615 183232 PRK11615 hypothetical protein; Provisional 185 matched cddid_all.tbl CDD PRK11616 PRK11616 183233 PRK11616 hypothetical protein; Provisional 109 matched cddid_all.tbl CDD PRK11617 PRK11617 236937 PRK11617 deoxyribonuclease V. 224 matched cddid_all.tbl CDD PRK11618 PRK11618 183235 PRK11618 inner membrane ABC transporter permease protein YjfF; Provisional 317 matched cddid_all.tbl CDD PRK11619 PRK11619 183236 PRK11619 lytic murein transglycosylase; Provisional 644 matched cddid_all.tbl CDD PRK11621 PRK11621 236938 PRK11621 Tat proofreading chaperone DmsD. 204 matched cddid_all.tbl CDD PRK11622 PRK11622 183238 PRK11622 ABC transporter substrate-binding protein. 401 matched cddid_all.tbl CDD PRK11623 PRK11623 236939 pcnB poly(A) polymerase I; Provisional 472 matched cddid_all.tbl CDD PRK11624 PRK11624 183240 cdsA phosphatidate cytidylyltransferase. 285 matched cddid_all.tbl CDD PRK11625 PRK11625 183241 PRK11625 Rho-binding antiterminator; Provisional 84 matched cddid_all.tbl CDD PRK11627 PRK11627 183242 PRK11627 hypothetical protein; Provisional 192 matched cddid_all.tbl CDD PRK11628 PRK11628 183243 PRK11628 transcriptional regulator BolA; Provisional 105 matched cddid_all.tbl CDD PRK11629 PRK11629 183244 lolD lipoprotein-releasing ABC transporter ATP-binding protein LolD. 233 matched cddid_all.tbl CDD PRK11630 PRK11630 183245 PRK11630 threonylcarbamoyl-AMP synthase. 206 matched cddid_all.tbl CDD PRK11633 PRK11633 236940 PRK11633 cell division protein DedD; Provisional 226 matched cddid_all.tbl CDD PRK11634 PRK11634 236941 PRK11634 ATP-dependent RNA helicase DeaD; Provisional 629 matched cddid_all.tbl CDD PRK11636 PRK11636 183248 mrcA penicillin-binding protein 1a; Provisional 850 matched cddid_all.tbl CDD PRK11637 PRK11637 236942 PRK11637 AmiB activator; Provisional 428 matched cddid_all.tbl CDD PRK11638 PRK11638 236943 PRK11638 ECA polysaccharide chain length modulation protein. 342 matched cddid_all.tbl CDD PRK11639 PRK11639 183251 PRK11639 zinc uptake transcriptional repressor Zur. 169 matched cddid_all.tbl CDD PRK11640 PRK11640 183252 PRK11640 putative transcriptional regulator; Provisional 191 matched cddid_all.tbl CDD PRK11642 PRK11642 236944 PRK11642 ribonuclease R. 813 matched cddid_all.tbl CDD PRK11644 PRK11644 236945 PRK11644 signal transduction histidine-protein kinase/phosphatase UhpB. 495 matched cddid_all.tbl CDD PRK11646 PRK11646 183255 PRK11646 multidrug efflux MFS transporter MdtH. 400 matched cddid_all.tbl CDD PRK11648 PRK11648 183256 PRK11648 metal-dependent hydrolase. 195 matched cddid_all.tbl CDD PRK11649 PRK11649 236946 PRK11649 putative peptidase; Provisional 439 matched cddid_all.tbl CDD PRK11650 PRK11650 236947 ugpC sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC. 356 matched cddid_all.tbl CDD PRK11652 PRK11652 183259 emrD multidrug transporter EmrD. 394 matched cddid_all.tbl CDD PRK11653 PRK11653 236948 PRK11653 DUF1190 family protein. 225 matched cddid_all.tbl CDD PRK11655 PRK11655 236949 ubiC chorismate pyruvate lyase; Provisional 169 matched cddid_all.tbl CDD PRK11657 PRK11657 183262 dsbG disulfide isomerase/thiol-disulfide oxidase; Provisional 251 matched cddid_all.tbl CDD PRK11658 PRK11658 183263 PRK11658 UDP-4-amino-4-deoxy-L-arabinose aminotransferase. 379 matched cddid_all.tbl CDD PRK11659 PRK11659 183264 PRK11659 cytochrome c nitrite reductase pentaheme subunit; Provisional 183 matched cddid_all.tbl CDD PRK11660 PRK11660 183265 PRK11660 putative transporter; Provisional 568 matched cddid_all.tbl CDD PRK11663 PRK11663 183266 PRK11663 glucose-6-phosphate receptor/MFS transporter UhpC. 434 matched cddid_all.tbl CDD PRK11664 PRK11664 236950 PRK11664 ATP-dependent RNA helicase HrpB; Provisional 812 matched cddid_all.tbl CDD PRK11667 PRK11667 236951 PRK11667 hypothetical protein; Provisional 163 matched cddid_all.tbl CDD PRK11669 PRK11669 236952 pbpG D-alanyl-D-alanine endopeptidase; Provisional 306 matched cddid_all.tbl CDD PRK11670 PRK11670 183270 PRK11670 iron-sulfur cluster carrier protein ApbC. 369 matched cddid_all.tbl CDD PRK11671 PRK11671 183271 mltC membrane-bound lytic murein transglycosylase MltC. 359 matched cddid_all.tbl CDD PRK11675 PRK11675 183272 PRK11675 LexA regulated protein; Provisional 90 matched cddid_all.tbl CDD PRK11677 PRK11677 236953 PRK11677 DUF1043 family protein. 134 matched cddid_all.tbl CDD PRK11678 PRK11678 236954 PRK11678 putative chaperone; Provisional 450 matched cddid_all.tbl CDD PRK11679 PRK11679 236955 PRK11679 outer membrane protein assembly factor BamC. 346 matched cddid_all.tbl CDD PRK11688 PRK11688 183276 PRK11688 thioesterase family protein. 154 matched cddid_all.tbl CDD PRK11689 PRK11689 183277 PRK11689 aromatic amino acid efflux DMT transporter YddG. 295 matched cddid_all.tbl CDD PRK11697 PRK11697 236956 PRK11697 two-component system response regulator BtsR. 238 matched cddid_all.tbl CDD PRK11700 PRK11700 236957 PRK11700 VOC family protein. 187 matched cddid_all.tbl CDD PRK11701 PRK11701 183280 phnK phosphonate C-P lyase system protein PhnK; Provisional 258 matched cddid_all.tbl CDD PRK11702 PRK11702 183281 PRK11702 hypothetical protein; Provisional 108 matched cddid_all.tbl CDD PRK11705 PRK11705 183282 PRK11705 cyclopropane fatty acyl phospholipid synthase. 383 matched cddid_all.tbl CDD PRK11706 PRK11706 183283 PRK11706 TDP-4-oxo-6-deoxy-D-glucose transaminase; Provisional 375 matched cddid_all.tbl CDD PRK11709 PRK11709 236958 PRK11709 putative L-ascorbate 6-phosphate lactonase; Provisional 355 matched cddid_all.tbl CDD PRK11712 PRK11712 183285 PRK11712 ribonuclease G; Provisional 489 matched cddid_all.tbl CDD PRK11713 PRK11713 236959 PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional 234 matched cddid_all.tbl CDD PRK11715 PRK11715 236960 PRK11715 cell envelope integrity protein CreD. 436 matched cddid_all.tbl CDD PRK11716 PRK11716 236961 PRK11716 HTH-type transcriptional activator IlvY. 269 matched cddid_all.tbl CDD PRK11718 PRK11718 236962 PRK11718 sigma D regulator. 161 matched cddid_all.tbl CDD PRK11720 PRK11720 236963 PRK11720 UDP-glucose--hexose-1-phosphate uridylyltransferase. 346 matched cddid_all.tbl CDD PRK11727 PRK11727 236964 PRK11727 23S rRNA (adenine(1618)-N(6))-methyltransferase RlmF. 321 matched cddid_all.tbl CDD PRK11728 PRK11728 183292 PRK11728 L-2-hydroxyglutarate oxidase. 393 matched cddid_all.tbl CDD PRK11730 PRK11730 183293 fadB fatty acid oxidation complex subunit alpha FadB. 715 matched cddid_all.tbl CDD PRK11742 PRK11742 236965 PRK11742 bifunctional NADH:ubiquinone oxidoreductase subunit C/D; Provisional 575 matched cddid_all.tbl CDD PRK11747 PRK11747 236966 dinG ATP-dependent DNA helicase DinG; Provisional 697 matched cddid_all.tbl CDD PRK11749 PRK11749 236967 PRK11749 dihydropyrimidine dehydrogenase subunit A; Provisional 457 matched cddid_all.tbl CDD PRK11750 PRK11750 236968 gltB glutamate synthase subunit alpha; Provisional 1485 matched cddid_all.tbl CDD PRK11752 PRK11752 183298 PRK11752 putative S-transferase; Provisional 264 matched cddid_all.tbl CDD PRK11753 PRK11753 236969 PRK11753 cAMP-activated global transcriptional regulator CRP. 211 matched cddid_all.tbl CDD PRK11756 PRK11756 236970 PRK11756 exonuclease III; Provisional 268 matched cddid_all.tbl CDD PRK11760 PRK11760 236971 PRK11760 putative 23S rRNA C2498 ribose 2'-O-ribose methyltransferase; Provisional 357 matched cddid_all.tbl CDD PRK11761 PRK11761 236972 cysM cysteine synthase CysM. 296 matched cddid_all.tbl CDD PRK11762 PRK11762 183303 nudE adenosine nucleotide hydrolase NudE; Provisional 185 matched cddid_all.tbl CDD PRK11767 PRK11767 236973 PRK11767 SpoVR family protein; Provisional 498 matched cddid_all.tbl CDD PRK11768 PRK11768 236974 PRK11768 serine/threonine protein kinase. 325 matched cddid_all.tbl CDD PRK11770 PRK11770 236975 PRK11770 YccF domain-containing protein. 135 matched cddid_all.tbl CDD PRK11773 PRK11773 236976 uvrD DNA-dependent helicase II; Provisional 721 matched cddid_all.tbl CDD PRK11776 PRK11776 236977 PRK11776 ATP-dependent RNA helicase DbpA; Provisional 460 matched cddid_all.tbl CDD PRK11778 PRK11778 236978 PRK11778 putative inner membrane peptidase; Provisional 330 matched cddid_all.tbl CDD PRK11779 PRK11779 236979 sbcB exonuclease I; Provisional 476 matched cddid_all.tbl CDD PRK11780 PRK11780 236980 PRK11780 isoprenoid biosynthesis glyoxalase ElbB. 217 matched cddid_all.tbl CDD PRK11783 PRK11783 236981 rlmL bifunctional 23S rRNA (guanine(2069)-N(7))-methyltransferase RlmK/23S rRNA (guanine(2445)-N(2))-methyltransferase RlmL. 702 matched cddid_all.tbl CDD PRK11784 PRK11784 236982 PRK11784 tRNA 2-selenouridine synthase; Provisional 345 matched cddid_all.tbl CDD PRK11788 PRK11788 236983 PRK11788 tetratricopeptide repeat protein; Provisional 389 matched cddid_all.tbl CDD PRK11789 PRK11789 236984 PRK11789 1,6-anhydro-N-acetylmuramyl-L-alanine amidase AmpD. 185 matched cddid_all.tbl CDD PRK11790 PRK11790 236985 PRK11790 phosphoglycerate dehydrogenase. 409 matched cddid_all.tbl CDD PRK11792 PRK11792 236986 queF 7-cyano-7-deazaguanine reductase; Provisional 273 matched cddid_all.tbl CDD PRK11797 PRK11797 183318 PRK11797 D-ribose pyranase; Provisional 139 matched cddid_all.tbl CDD PRK11798 PRK11798 236987 PRK11798 ClpXP protease specificity-enhancing factor; Provisional 138 matched cddid_all.tbl CDD PRK11809 PRK11809 236989 putA trifunctional transcriptional regulator/proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed 1318 matched cddid_all.tbl CDD PRK11814 PRK11814 236990 PRK11814 cysteine desulfurase activator complex subunit SufB; Provisional 486 matched cddid_all.tbl CDD PRK11815 PRK11815 236991 PRK11815 tRNA dihydrouridine(20/20a) synthase DusA. 333 matched cddid_all.tbl CDD PRK11819 PRK11819 236992 PRK11819 putative ABC transporter ATP-binding protein; Reviewed 556 matched cddid_all.tbl CDD PRK11824 PRK11824 236995 PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional 693 matched cddid_all.tbl CDD PRK11827 PRK11827 183328 PRK11827 protein YcaR. 60 matched cddid_all.tbl CDD PRK11829 PRK11829 183329 PRK11829 biofilm formation regulator HmsP; Provisional 660 matched cddid_all.tbl CDD PRK11830 PRK11830 236996 dapD 2,3,4,5-tetrahydropyridine-2,6-carboxylate N-succinyltransferase; Provisional 272 matched cddid_all.tbl CDD PRK11831 PRK11831 236997 PRK11831 phospholipid ABC transporter ATP-binding protein MlaF. 269 matched cddid_all.tbl CDD PRK11832 PRK11832 183332 PRK11832 hydrogen peroxide resistance inhibitor IprA. 207 matched cddid_all.tbl CDD PRK11835 PRK11835 183333 PRK11835 hypothetical protein; Provisional 114 matched cddid_all.tbl CDD PRK11836 PRK11836 183334 PRK11836 deubiquitinase; Provisional 403 matched cddid_all.tbl CDD PRK11837 PRK11837 183335 PRK11837 undecaprenyl pyrophosphate phosphatase; Provisional 202 matched cddid_all.tbl CDD PRK11840 PRK11840 236998 PRK11840 bifunctional sulfur carrier protein/thiazole synthase protein; Provisional 326 matched cddid_all.tbl CDD PRK11854 PRK11854 236999 aceF pyruvate dehydrogenase dihydrolipoyltransacetylase; Validated 633 matched cddid_all.tbl CDD PRK11855 PRK11855 237000 PRK11855 dihydrolipoamide acetyltransferase; Reviewed 547 matched cddid_all.tbl CDD PRK11856 PRK11856 237001 PRK11856 branched-chain alpha-keto acid dehydrogenase subunit E2; Reviewed 411 matched cddid_all.tbl CDD PRK11857 PRK11857 237002 PRK11857 dihydrolipoamide acetyltransferase; Reviewed 306 matched cddid_all.tbl CDD PRK11858 PRK11858 183341 aksA trans-homoaconitate synthase; Reviewed 378 matched cddid_all.tbl CDD PRK11860 PRK11860 237003 PRK11860 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidylate kinase. 661 matched cddid_all.tbl CDD PRK11861 PRK11861 183343 PRK11861 bifunctional prephenate dehydrogenase/3-phosphoshikimate 1-carboxyvinyltransferase; Provisional 673 matched cddid_all.tbl CDD PRK11864 PRK11864 237005 PRK11864 3-methyl-2-oxobutanoate dehydrogenase subunit beta. 300 matched cddid_all.tbl CDD PRK11865 PRK11865 183346 PRK11865 pyruvate synthase subunit beta. 299 matched cddid_all.tbl CDD PRK11866 PRK11866 183347 PRK11866 2-oxoacid ferredoxin oxidoreductase subunit beta; Provisional 279 matched cddid_all.tbl CDD PRK11867 PRK11867 237006 PRK11867 2-oxoglutarate ferredoxin oxidoreductase subunit beta; Reviewed 286 matched cddid_all.tbl CDD PRK11869 PRK11869 183349 PRK11869 2-oxoacid ferredoxin oxidoreductase subunit beta; Provisional 280 matched cddid_all.tbl CDD PRK11872 PRK11872 183350 antC anthranilate 1,2-dioxygenase electron transfer component AntC. 340 matched cddid_all.tbl CDD PRK11873 PRK11873 237007 arsM arsenite methyltransferase. 272 matched cddid_all.tbl CDD PRK11874 PRK11874 183352 petL cytochrome b6-f complex subunit PetL; Reviewed 30 matched cddid_all.tbl CDD PRK11875 PRK11875 183353 psbT photosystem II reaction center protein T; Reviewed 31 matched cddid_all.tbl CDD PRK11876 PRK11876 183354 petM cytochrome b6-f complex subunit PetM; Reviewed 32 matched cddid_all.tbl CDD PRK11877 PRK11877 183355 psaI photosystem I reaction center subunit VIII; Reviewed 38 matched cddid_all.tbl CDD PRK11878 PRK11878 183356 psaM photosystem I reaction center subunit XII; Reviewed 34 matched cddid_all.tbl CDD PRK11880 PRK11880 237008 PRK11880 pyrroline-5-carboxylate reductase; Reviewed 267 matched cddid_all.tbl CDD PRK11883 PRK11883 237009 PRK11883 protoporphyrinogen oxidase; Reviewed 451 matched cddid_all.tbl CDD PRK11886 PRK11886 237010 PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA. 319 matched cddid_all.tbl CDD PRK11889 PRK11889 183360 flhF flagellar biosynthesis protein FlhF. 436 matched cddid_all.tbl CDD PRK11890 PRK11890 183361 PRK11890 phosphate acetyltransferase; Provisional 312 matched cddid_all.tbl CDD PRK11891 PRK11891 183362 PRK11891 aspartate carbamoyltransferase; Provisional 429 matched cddid_all.tbl CDD PRK11892 PRK11892 237011 PRK11892 pyruvate dehydrogenase subunit beta; Provisional 464 matched cddid_all.tbl CDD PRK11893 PRK11893 237012 PRK11893 methionyl-tRNA synthetase; Reviewed 511 matched cddid_all.tbl CDD PRK11895 PRK11895 183365 ilvH acetolactate synthase 3 regulatory subunit; Reviewed 161 matched cddid_all.tbl CDD PRK11898 PRK11898 237013 PRK11898 prephenate dehydratase; Provisional 283 matched cddid_all.tbl CDD PRK11899 PRK11899 237014 PRK11899 prephenate dehydratase; Provisional 279 matched cddid_all.tbl CDD PRK11901 PRK11901 237015 PRK11901 hypothetical protein; Reviewed 327 matched cddid_all.tbl CDD PRK11902 PRK11902 183369 ampG muropeptide transporter; Reviewed 402 matched cddid_all.tbl CDD PRK11903 PRK11903 237016 PRK11903 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase. 521 matched cddid_all.tbl CDD PRK11904 PRK11904 237017 PRK11904 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA. 1038 matched cddid_all.tbl CDD PRK11905 PRK11905 237018 PRK11905 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase; Reviewed 1208 matched cddid_all.tbl CDD PRK11906 PRK11906 183373 PRK11906 HilA family transcriptional regulator YgeH. 458 matched cddid_all.tbl CDD PRK11907 PRK11907 237019 PRK11907 bifunctional 2',3'-cyclic-nucleotide 2'-phosphodiesterase/3'-nucleotidase. 814 matched cddid_all.tbl CDD PRK11908 PRK11908 183375 PRK11908 bifunctional UDP-4-keto-pentose/UDP-xylose synthase. 347 matched cddid_all.tbl CDD PRK11909 PRK11909 183376 PRK11909 cobalt transporter CbiM. 230 matched cddid_all.tbl CDD PRK11910 PRK11910 183377 PRK11910 amidase; Provisional 615 matched cddid_all.tbl CDD PRK11911 PRK11911 138812 flgD flagellar basal body rod modification protein; Provisional 140 matched cddid_all.tbl CDD PRK11913 PRK11913 237020 phhA phenylalanine 4-monooxygenase; Reviewed 275 matched cddid_all.tbl CDD PRK11914 PRK11914 237021 PRK11914 diacylglycerol kinase; Reviewed 306 matched cddid_all.tbl CDD PRK11915 PRK11915 237022 PRK11915 lysophospholipid acyltransferase. 621 matched cddid_all.tbl CDD PRK11916 PRK11916 183380 PRK11916 electron transfer flavoprotein subunit alpha. 312 matched cddid_all.tbl CDD PRK11917 PRK11917 183381 PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed 259 matched cddid_all.tbl CDD PRK11920 PRK11920 171344 rirA iron-responsive transcriptional regulator RirA. 153 matched cddid_all.tbl CDD PRK11921 PRK11921 237023 PRK11921 anaerobic nitric oxide reductase flavorubredoxin. 394 matched cddid_all.tbl CDD PRK11922 PRK11922 237024 PRK11922 RNA polymerase sigma factor; Provisional 231 matched cddid_all.tbl CDD PRK11923 PRK11923 171347 algU RNA polymerase sigma factor AlgU; Provisional 193 matched cddid_all.tbl CDD PRK11924 PRK11924 183384 PRK11924 RNA polymerase sigma factor; Provisional 179 matched cddid_all.tbl CDD PRK11929 PRK11929 237025 PRK11929 bifunctional UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase MurE/UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase MurF. 958 matched cddid_all.tbl CDD PRK11930 PRK11930 237026 PRK11930 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional 822 matched cddid_all.tbl CDD PRK11933 PRK11933 183387 yebU rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed 470 matched cddid_all.tbl CDD PRK12266 PRK12266 237027 glpD glycerol-3-phosphate dehydrogenase; Reviewed 508 matched cddid_all.tbl CDD PRK12267 PRK12267 237028 PRK12267 methionyl-tRNA synthetase; Reviewed 648 matched cddid_all.tbl CDD PRK12269 PRK12269 105491 PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional 863 matched cddid_all.tbl CDD PRK12270 PRK12270 237030 kgd multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit. 1228 matched cddid_all.tbl CDD PRK12273 PRK12273 237031 aspA aspartate ammonia-lyase; Provisional 472 matched cddid_all.tbl CDD PRK12274 PRK12274 237032 PRK12274 serine/threonine protein kinase; Provisional 218 matched cddid_all.tbl CDD PRK12275 PRK12275 183395 PRK12275 hypothetical protein; Reviewed 116 matched cddid_all.tbl CDD PRK12276 PRK12276 237033 PRK12276 putative heme peroxidase; Provisional 248 matched cddid_all.tbl CDD PRK12277 PRK12277 183397 PRK12277 50S ribosomal protein L13e; Provisional 83 matched cddid_all.tbl CDD PRK12278 PRK12278 237034 PRK12278 50S ribosomal protein L21. 221 matched cddid_all.tbl CDD PRK12279 PRK12279 138835 PRK12279 50S ribosomal protein L22/unknown domain fusion protein; Provisional 311 matched cddid_all.tbl CDD PRK12280 PRK12280 237035 rplW 50S ribosomal protein L23; Reviewed 158 matched cddid_all.tbl CDD PRK12281 PRK12281 183399 rplX 50S ribosomal protein L24; Reviewed 76 matched cddid_all.tbl CDD PRK12282 PRK12282 183400 PRK12282 tryptophanyl-tRNA synthetase II; Reviewed 333 matched cddid_all.tbl CDD PRK12283 PRK12283 183401 PRK12283 tryptophanyl-tRNA synthetase; Reviewed 398 matched cddid_all.tbl CDD PRK12284 PRK12284 237036 PRK12284 tryptophanyl-tRNA synthetase; Reviewed 431 matched cddid_all.tbl CDD PRK12285 PRK12285 237037 PRK12285 tryptophanyl-tRNA synthetase; Reviewed 368 matched cddid_all.tbl CDD PRK12287 PRK12287 183405 tqsA pheromone autoinducer 2 transporter; Reviewed 344 matched cddid_all.tbl CDD PRK12288 PRK12288 237039 PRK12288 small ribosomal subunit biogenesis GTPase RsgA. 347 matched cddid_all.tbl CDD PRK12289 PRK12289 237040 PRK12289 small ribosomal subunit biogenesis GTPase RsgA. 352 matched cddid_all.tbl CDD PRK12290 PRK12290 237041 thiE thiamine phosphate synthase. 437 matched cddid_all.tbl CDD PRK12291 PRK12291 237042 PRK12291 apolipoprotein N-acyltransferase; Reviewed 418 matched cddid_all.tbl CDD PRK12292 PRK12292 237043 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional 391 matched cddid_all.tbl CDD PRK12293 PRK12293 183411 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional 281 matched cddid_all.tbl CDD PRK12294 PRK12294 237044 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional 272 matched cddid_all.tbl CDD PRK12295 PRK12295 183413 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional 373 matched cddid_all.tbl CDD PRK12296 PRK12296 237045 obgE GTPase CgtA; Reviewed 500 matched cddid_all.tbl CDD PRK12297 PRK12297 237046 obgE GTPase CgtA; Reviewed 424 matched cddid_all.tbl CDD PRK12298 PRK12298 237047 obgE GTPase CgtA; Reviewed 390 matched cddid_all.tbl CDD PRK12299 PRK12299 237048 obgE GTPase CgtA; Reviewed 335 matched cddid_all.tbl CDD PRK12300 PRK12300 237049 leuS leucyl-tRNA synthetase; Reviewed 897 matched cddid_all.tbl CDD PRK12301 PRK12301 183419 bssS biofilm formation regulator BssS. 84 matched cddid_all.tbl CDD PRK12302 PRK12302 183420 bssR biofilm formation regulator BssR. 127 matched cddid_all.tbl CDD PRK12303 PRK12303 183421 PRK12303 tumor necrosis factor alpha-inducing protein; Reviewed 192 matched cddid_all.tbl CDD PRK12307 PRK12307 237051 PRK12307 MFS transporter. 426 matched cddid_all.tbl CDD PRK12308 PRK12308 183425 PRK12308 argininosuccinate lyase. 614 matched cddid_all.tbl CDD PRK12309 PRK12309 183426 PRK12309 transaldolase. 391 matched cddid_all.tbl CDD PRK12310 PRK12310 183427 PRK12310 hydroxylamine reductase; Provisional 433 matched cddid_all.tbl CDD PRK12311 PRK12311 183428 rpsB 30S ribosomal protein S2. 326 matched cddid_all.tbl CDD PRK12313 PRK12313 237052 PRK12313 1,4-alpha-glucan branching protein GlgB. 633 matched cddid_all.tbl CDD PRK12314 PRK12314 183430 PRK12314 gamma-glutamyl kinase; Provisional 266 matched cddid_all.tbl CDD PRK12315 PRK12315 237053 PRK12315 1-deoxy-D-xylulose-5-phosphate synthase; Provisional 581 matched cddid_all.tbl CDD PRK12316 PRK12316 237054 PRK12316 peptide synthase; Provisional 5163 matched cddid_all.tbl CDD PRK12317 PRK12317 237055 PRK12317 elongation factor 1-alpha; Reviewed 425 matched cddid_all.tbl CDD PRK12318 PRK12318 183434 PRK12318 methionyl aminopeptidase. 291 matched cddid_all.tbl CDD PRK12319 PRK12319 183435 PRK12319 acetyl-CoA carboxylase subunit alpha; Provisional 256 matched cddid_all.tbl CDD PRK12320 PRK12320 138873 PRK12320 hypothetical protein; Provisional 699 matched cddid_all.tbl CDD PRK12321 PRK12321 237056 cobN cobaltochelatase subunit CobN; Reviewed 1100 matched cddid_all.tbl CDD PRK12322 PRK12322 183437 PRK12322 NADH-quinone oxidoreductase subunit D. 366 matched cddid_all.tbl CDD PRK12323 PRK12323 237057 PRK12323 DNA polymerase III subunit gamma/tau. 700 matched cddid_all.tbl CDD PRK12324 PRK12324 237058 PRK12324 decaprenyl-phosphate phosphoribosyltransferase. 295 matched cddid_all.tbl CDD PRK12325 PRK12325 237059 PRK12325 prolyl-tRNA synthetase; Provisional 439 matched cddid_all.tbl CDD PRK12330 PRK12330 183445 PRK12330 methylmalonyl-CoA carboxytransferase subunit 5S. 499 matched cddid_all.tbl CDD PRK12331 PRK12331 183446 PRK12331 oxaloacetate decarboxylase subunit alpha. 448 matched cddid_all.tbl CDD PRK12332 PRK12332 183447 tsf elongation factor Ts; Reviewed 198 matched cddid_all.tbl CDD PRK12333 PRK12333 237064 PRK12333 nucleoside triphosphate pyrophosphohydrolase; Reviewed 204 matched cddid_all.tbl CDD PRK12334 PRK12334 237065 PRK12334 nucleoside triphosphate pyrophosphohydrolase; Reviewed 277 matched cddid_all.tbl CDD PRK12335 PRK12335 183450 PRK12335 tellurite resistance protein TehB; Provisional 287 matched cddid_all.tbl CDD PRK12336 PRK12336 183451 PRK12336 translation initiation factor IF-2 subunit beta; Provisional 201 matched cddid_all.tbl CDD PRK12337 PRK12337 183452 PRK12337 2-phosphoglycerate kinase; Provisional 475 matched cddid_all.tbl CDD PRK12338 PRK12338 237066 PRK12338 hypothetical protein; Provisional 319 matched cddid_all.tbl CDD PRK12339 PRK12339 105560 PRK12339 mevalonate-3-phosphate 5-kinase. 197 matched cddid_all.tbl CDD PRK12341 PRK12341 183454 PRK12341 acyl-CoA dehydrogenase. 381 matched cddid_all.tbl CDD PRK12342 PRK12342 183455 PRK12342 electron transfer flavoprotein. 254 matched cddid_all.tbl CDD PRK12343 PRK12343 237067 PRK12343 cyclic pyranopterin monophosphate synthase MoaC. 151 matched cddid_all.tbl CDD PRK12344 PRK12344 237068 PRK12344 putative alpha-isopropylmalate/homocitrate synthase family transferase; Provisional 524 matched cddid_all.tbl CDD PRK12346 PRK12346 183458 PRK12346 transaldolase A; Provisional 316 matched cddid_all.tbl CDD PRK12347 PRK12347 183459 sgbE L-ribulose-5-phosphate 4-epimerase; Reviewed 231 matched cddid_all.tbl CDD PRK12348 PRK12348 183460 sgaE L-ribulose-5-phosphate 4-epimerase; Reviewed 228 matched cddid_all.tbl CDD PRK12349 PRK12349 237069 PRK12349 citrate synthase. 369 matched cddid_all.tbl CDD PRK12350 PRK12350 237070 PRK12350 citrate synthase 2; Provisional 353 matched cddid_all.tbl CDD PRK12351 PRK12351 183463 PRK12351 methylcitrate synthase; Provisional 378 matched cddid_all.tbl CDD PRK12352 PRK12352 183464 PRK12352 putative carbamate kinase; Reviewed 316 matched cddid_all.tbl CDD PRK12353 PRK12353 237071 PRK12353 putative amino acid kinase; Reviewed 314 matched cddid_all.tbl CDD PRK12354 PRK12354 183466 PRK12354 carbamate kinase; Reviewed 307 matched cddid_all.tbl CDD PRK12355 PRK12355 237072 PRK12355 type-F conjugative transfer system mating-pair stabilization protein TraN. 558 matched cddid_all.tbl CDD PRK12356 PRK12356 237073 PRK12356 glutaminase; Reviewed 319 matched cddid_all.tbl CDD PRK12357 PRK12357 237074 PRK12357 glutaminase; Reviewed 326 matched cddid_all.tbl CDD PRK12358 PRK12358 183470 PRK12358 glucosamine-6-phosphate deaminase. 239 matched cddid_all.tbl CDD PRK12359 PRK12359 183471 PRK12359 flavodoxin FldB; Provisional 172 matched cddid_all.tbl CDD PRK12360 PRK12360 237075 PRK12360 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional 281 matched cddid_all.tbl CDD PRK12361 PRK12361 183473 PRK12361 hypothetical protein; Provisional 547 matched cddid_all.tbl CDD PRK12363 PRK12363 171438 PRK12363 phosphoglycerol transferase I; Provisional 703 matched cddid_all.tbl CDD PRK12364 PRK12364 237077 PRK12364 ribonucleoside-diphosphate reductase subunit alpha. 842 matched cddid_all.tbl CDD PRK12365 PRK12365 171440 PRK12365 ribonucleoside-diphosphate reductase subunit alpha. 1046 matched cddid_all.tbl CDD PRK12366 PRK12366 237078 PRK12366 replication factor A; Reviewed 637 matched cddid_all.tbl CDD PRK12367 PRK12367 237079 PRK12367 short chain dehydrogenase; Provisional 245 matched cddid_all.tbl CDD PRK12369 PRK12369 171443 PRK12369 putative transporter; Reviewed 326 matched cddid_all.tbl CDD PRK12370 PRK12370 237080 PRK12370 HilA/EilA family virulence transcriptional regulator. 553 matched cddid_all.tbl CDD PRK12373 PRK12373 237082 PRK12373 NADH-quinone oxidoreductase subunit E. 400 matched cddid_all.tbl CDD PRK12377 PRK12377 183482 PRK12377 putative replication protein; Provisional 248 matched cddid_all.tbl CDD PRK12378 PRK12378 237084 PRK12378 YebC/PmpR family DNA-binding transcriptional regulator. 235 matched cddid_all.tbl CDD PRK12379 PRK12379 183484 PRK12379 propionate kinase. 396 matched cddid_all.tbl CDD PRK12380 PRK12380 183485 PRK12380 hydrogenase/urease nickel incorporation protein. 113 matched cddid_all.tbl CDD PRK12381 PRK12381 183486 PRK12381 bifunctional succinylornithine transaminase/acetylornithine transaminase; Provisional 406 matched cddid_all.tbl CDD PRK12382 PRK12382 183487 PRK12382 putative transporter; Provisional 392 matched cddid_all.tbl CDD PRK12383 PRK12383 237085 PRK12383 putative mutase; Provisional 406 matched cddid_all.tbl CDD PRK12384 PRK12384 183489 PRK12384 sorbitol-6-phosphate dehydrogenase; Provisional 259 matched cddid_all.tbl CDD PRK12385 PRK12385 183490 PRK12385 succinate dehydrogenase/fumarate reductase iron-sulfur subunit. 244 matched cddid_all.tbl CDD PRK12386 PRK12386 237086 PRK12386 fumarate reductase iron-sulfur subunit; Provisional 251 matched cddid_all.tbl CDD PRK12387 PRK12387 183492 PRK12387 formate hydrogenlyase complex iron-sulfur subunit; Provisional 180 matched cddid_all.tbl CDD PRK12388 PRK12388 171459 PRK12388 class II fructose-bisphosphatase. 321 matched cddid_all.tbl CDD PRK12389 PRK12389 183493 PRK12389 glutamate-1-semialdehyde aminotransferase; Provisional 428 matched cddid_all.tbl CDD PRK12390 PRK12390 183494 PRK12390 1-aminocyclopropane-1-carboxylate deaminase; Provisional 337 matched cddid_all.tbl CDD PRK12391 PRK12391 237087 PRK12391 TrpB-like pyridoxal phosphate-dependent enzyme. 427 matched cddid_all.tbl CDD PRK12392 PRK12392 171463 PRK12392 bacteriochlorophyll c synthase; Provisional 331 matched cddid_all.tbl CDD PRK12393 PRK12393 237088 PRK12393 amidohydrolase; Provisional 457 matched cddid_all.tbl CDD PRK12394 PRK12394 183497 PRK12394 metallo-dependent hydrolase. 379 matched cddid_all.tbl CDD PRK12395 PRK12395 183498 PRK12395 maltoporin; Provisional 419 matched cddid_all.tbl CDD PRK12397 PRK12397 183500 PRK12397 acetate/propionate family kinase. 404 matched cddid_all.tbl CDD PRK12398 PRK12398 237089 PRK12398 pyruvoyl-dependent arginine decarboxylase; Provisional 162 matched cddid_all.tbl CDD PRK12399 PRK12399 183502 PRK12399 tagatose 1,6-diphosphate aldolase; Reviewed 324 matched cddid_all.tbl CDD PRK12400 PRK12400 171470 PRK12400 D-amino acid aminotransferase; Reviewed 290 matched cddid_all.tbl CDD PRK12402 PRK12402 237090 PRK12402 replication factor C small subunit 2; Reviewed 337 matched cddid_all.tbl CDD PRK12403 PRK12403 171472 PRK12403 aspartate aminotransferase family protein. 460 matched cddid_all.tbl CDD PRK12404 PRK12404 183504 PRK12404 stage V sporulation protein AD; Provisional 334 matched cddid_all.tbl CDD PRK12405 PRK12405 237091 PRK12405 electron transport complex RsxE subunit; Provisional 231 matched cddid_all.tbl CDD PRK12406 PRK12406 183506 PRK12406 long-chain-fatty-acid--CoA ligase; Provisional 509 matched cddid_all.tbl CDD PRK12407 PRK12407 183507 flgH flagellar basal body L-ring protein FlgH. 221 matched cddid_all.tbl CDD PRK12408 PRK12408 237092 PRK12408 glucokinase; Provisional 336 matched cddid_all.tbl CDD PRK12409 PRK12409 237093 PRK12409 D-amino acid dehydrogenase small subunit; Provisional 410 matched cddid_all.tbl CDD PRK12411 PRK12411 183511 PRK12411 cytidine deaminase; Provisional 132 matched cddid_all.tbl CDD PRK12412 PRK12412 183512 PRK12412 bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase. 268 matched cddid_all.tbl CDD PRK12413 PRK12413 183513 PRK12413 bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase. 253 matched cddid_all.tbl CDD PRK12414 PRK12414 183514 PRK12414 putative aminotransferase; Provisional 384 matched cddid_all.tbl CDD PRK12415 PRK12415 183515 PRK12415 fructose-bisphosphatase class II. 322 matched cddid_all.tbl CDD PRK12416 PRK12416 183516 PRK12416 protoporphyrinogen oxidase; Provisional 463 matched cddid_all.tbl CDD PRK12417 PRK12417 237095 secY preprotein translocase subunit SecY; Reviewed 404 matched cddid_all.tbl CDD PRK12418 PRK12418 183518 PRK12418 cysteinyl-tRNA synthetase; Provisional 384 matched cddid_all.tbl CDD PRK12419 PRK12419 237096 PRK12419 6,7-dimethyl-8-ribityllumazine synthase. 158 matched cddid_all.tbl CDD PRK12420 PRK12420 237097 PRK12420 histidyl-tRNA synthetase; Provisional 423 matched cddid_all.tbl CDD PRK12421 PRK12421 237098 PRK12421 ATP phosphoribosyltransferase regulatory subunit; Provisional 392 matched cddid_all.tbl CDD PRK12422 PRK12422 183521 PRK12422 chromosomal replication initiator protein DnaA. 445 matched cddid_all.tbl CDD PRK12425 PRK12425 171490 PRK12425 class II fumarate hydratase. 464 matched cddid_all.tbl CDD PRK12426 PRK12426 183522 PRK12426 elongation factor P; Provisional 185 matched cddid_all.tbl CDD PRK12427 PRK12427 183523 PRK12427 FliA/WhiG family RNA polymerase sigma factor. 231 matched cddid_all.tbl CDD PRK12428 PRK12428 237099 PRK12428 coniferyl-alcohol dehydrogenase. 241 matched cddid_all.tbl CDD PRK12429 PRK12429 237100 PRK12429 3-hydroxybutyrate dehydrogenase; Provisional 258 matched cddid_all.tbl CDD PRK12430 PRK12430 237101 PRK12430 putative bifunctional flagellar biosynthesis protein FliO/FliP; Provisional 379 matched cddid_all.tbl CDD PRK12435 PRK12435 183526 PRK12435 ferrochelatase; Provisional 311 matched cddid_all.tbl CDD PRK12436 PRK12436 171497 PRK12436 UDP-N-acetylmuramate dehydrogenase. 305 matched cddid_all.tbl CDD PRK12437 PRK12437 183527 PRK12437 prolipoprotein diacylglyceryl transferase; Reviewed 269 matched cddid_all.tbl CDD PRK12438 PRK12438 171499 PRK12438 hypothetical protein; Provisional 991 matched cddid_all.tbl CDD PRK12439 PRK12439 171500 PRK12439 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Provisional 341 matched cddid_all.tbl CDD PRK12440 PRK12440 183528 PRK12440 acetate/propionate family kinase. 397 matched cddid_all.tbl CDD PRK12444 PRK12444 183530 PRK12444 threonyl-tRNA synthetase; Reviewed 639 matched cddid_all.tbl CDD PRK12445 PRK12445 171504 PRK12445 lysyl-tRNA synthetase; Reviewed 505 matched cddid_all.tbl CDD PRK12446 PRK12446 171505 PRK12446 undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase; Reviewed 352 matched cddid_all.tbl CDD PRK12447 PRK12447 237103 PRK12447 histidinol dehydrogenase; Reviewed 426 matched cddid_all.tbl CDD PRK12448 PRK12448 237104 PRK12448 dihydroxy-acid dehydratase; Provisional 615 matched cddid_all.tbl CDD PRK12449 PRK12449 183533 PRK12449 acyl carrier protein; Provisional 80 matched cddid_all.tbl CDD PRK12450 PRK12450 138982 PRK12450 foldase protein PrsA; Reviewed 309 matched cddid_all.tbl CDD PRK12452 PRK12452 171510 PRK12452 cardiolipin synthase. 509 matched cddid_all.tbl CDD PRK12454 PRK12454 183535 PRK12454 carbamate kinase-like carbamoyl phosphate synthetase; Reviewed 313 matched cddid_all.tbl CDD PRK12456 PRK12456 84141 PRK12456 Na(+)-translocating NADH-quinone reductase subunit E; Provisional 199 matched cddid_all.tbl CDD PRK12457 PRK12457 237105 PRK12457 3-deoxy-8-phosphooctulonate synthase. 281 matched cddid_all.tbl CDD PRK12458 PRK12458 183536 PRK12458 glutathione synthetase; Provisional 338 matched cddid_all.tbl CDD PRK12460 PRK12460 183538 PRK12460 2-keto-3-deoxygluconate permease; Provisional 312 matched cddid_all.tbl CDD PRK12461 PRK12461 183539 PRK12461 UDP-N-acetylglucosamine acyltransferase; Provisional 255 matched cddid_all.tbl CDD PRK12462 PRK12462 183540 PRK12462 phosphoserine aminotransferase; Provisional 364 matched cddid_all.tbl CDD PRK12463 PRK12463 171518 PRK12463 chorismate synthase; Reviewed 390 matched cddid_all.tbl CDD PRK12464 PRK12464 237107 PRK12464 1-deoxy-D-xylulose 5-phosphate reductoisomerase; Provisional 383 matched cddid_all.tbl CDD PRK12465 PRK12465 183542 PRK12465 xylose isomerase; Provisional 445 matched cddid_all.tbl CDD PRK12466 PRK12466 183543 PRK12466 3-isopropylmalate dehydratase large subunit. 471 matched cddid_all.tbl CDD PRK12467 PRK12467 237108 PRK12467 peptide synthase; Provisional 3956 matched cddid_all.tbl CDD PRK12468 PRK12468 171522 flhB flagellar biosynthesis protein FlhB; Reviewed 386 matched cddid_all.tbl CDD PRK12469 PRK12469 237109 PRK12469 RNA polymerase factor sigma-54; Provisional 481 matched cddid_all.tbl CDD PRK12470 PRK12470 171524 PRK12470 amidase; Provisional 462 matched cddid_all.tbl CDD PRK12472 PRK12472 237110 PRK12472 hypothetical protein; Provisional 508 matched cddid_all.tbl CDD PRK12473 PRK12473 183546 PRK12473 hypothetical protein; Provisional 198 matched cddid_all.tbl CDD PRK12474 PRK12474 139002 PRK12474 hypothetical protein; Provisional 518 matched cddid_all.tbl CDD PRK12475 PRK12475 183547 PRK12475 thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional 338 matched cddid_all.tbl CDD PRK12476 PRK12476 171527 PRK12476 putative fatty-acid--CoA ligase; Provisional 612 matched cddid_all.tbl CDD PRK12478 PRK12478 183548 PRK12478 crotonase/enoyl-CoA hydratase family protein. 298 matched cddid_all.tbl CDD PRK12479 PRK12479 183549 PRK12479 branched-chain-amino-acid transaminase. 299 matched cddid_all.tbl CDD PRK12480 PRK12480 183550 PRK12480 D-lactate dehydrogenase; Provisional 330 matched cddid_all.tbl CDD PRK12481 PRK12481 171531 PRK12481 2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD. 251 matched cddid_all.tbl CDD PRK12482 PRK12482 171532 PRK12482 flagellar motor stator protein MotA. 287 matched cddid_all.tbl CDD PRK12483 PRK12483 237111 PRK12483 threonine dehydratase; Reviewed 521 matched cddid_all.tbl CDD PRK12484 PRK12484 237112 PRK12484 nicotinate phosphoribosyltransferase; Provisional 443 matched cddid_all.tbl CDD PRK12485 PRK12485 171535 PRK12485 bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II. 369 matched cddid_all.tbl CDD PRK12486 PRK12486 237113 dmdA dimethylsulfoniopropionate demethylase. 368 matched cddid_all.tbl CDD PRK12487 PRK12487 183553 PRK12487 putative 4-hydroxy-4-methyl-2-oxoglutarate aldolase. 163 matched cddid_all.tbl CDD PRK12488 PRK12488 237114 PRK12488 cation/acetate symporter. 549 matched cddid_all.tbl CDD PRK12489 PRK12489 237115 PRK12489 anaerobic C4-dicarboxylate transporter; Reviewed 443 matched cddid_all.tbl CDD PRK12492 PRK12492 171539 PRK12492 long-chain-fatty-acid--CoA ligase; Provisional 562 matched cddid_all.tbl CDD PRK12493 PRK12493 237117 PRK12493 magnesium chelatase subunit H; Provisional 1310 matched cddid_all.tbl CDD PRK12494 PRK12494 183557 PRK12494 NAD(P)H-quinone oxidoreductase subunit J. 172 matched cddid_all.tbl CDD PRK12495 PRK12495 183558 PRK12495 hypothetical protein; Provisional 226 matched cddid_all.tbl CDD PRK12496 PRK12496 237118 PRK12496 hypothetical protein; Provisional 164 matched cddid_all.tbl CDD PRK12497 PRK12497 237119 PRK12497 YraN family protein. 119 matched cddid_all.tbl CDD PRK12504 PRK12504 183561 PRK12504 DUF4040 domain-containing protein. 178 matched cddid_all.tbl CDD PRK12505 PRK12505 237120 PRK12505 putative monovalent cation/H+ antiporter subunit B; Reviewed 159 matched cddid_all.tbl CDD PRK12507 PRK12507 237121 PRK12507 putative monovalent cation/H+ antiporter subunit B; Reviewed 332 matched cddid_all.tbl CDD PRK12508 PRK12508 183563 PRK12508 Na(+)/H(+) antiporter subunit B. 139 matched cddid_all.tbl CDD PRK12509 PRK12509 237122 PRK12509 Na+/H+ antiporter subunit B. 137 matched cddid_all.tbl CDD PRK12511 PRK12511 237123 PRK12511 RNA polymerase sigma factor; Provisional 182 matched cddid_all.tbl CDD PRK12512 PRK12512 171551 PRK12512 RNA polymerase sigma factor; Provisional 184 matched cddid_all.tbl CDD PRK12513 PRK12513 183566 PRK12513 RNA polymerase sigma factor; Provisional 194 matched cddid_all.tbl CDD PRK12514 PRK12514 105710 PRK12514 RNA polymerase sigma factor; Provisional 179 matched cddid_all.tbl CDD PRK12515 PRK12515 183567 PRK12515 RNA polymerase sigma factor; Provisional 189 matched cddid_all.tbl CDD PRK12516 PRK12516 183568 PRK12516 RNA polymerase sigma factor; Provisional 187 matched cddid_all.tbl CDD PRK12517 PRK12517 183569 PRK12517 RNA polymerase sigma factor; Provisional 188 matched cddid_all.tbl CDD PRK12518 PRK12518 237124 PRK12518 RNA polymerase sigma factor; Provisional 175 matched cddid_all.tbl CDD PRK12519 PRK12519 237125 PRK12519 RNA polymerase sigma factor; Provisional 194 matched cddid_all.tbl CDD PRK12520 PRK12520 237126 PRK12520 RNA polymerase sigma factor; Provisional 191 matched cddid_all.tbl CDD PRK12522 PRK12522 183571 PRK12522 RNA polymerase sigma factor; Provisional 173 matched cddid_all.tbl CDD PRK12523 PRK12523 183572 PRK12523 RNA polymerase sigma factor; Reviewed 172 matched cddid_all.tbl CDD PRK12524 PRK12524 183573 PRK12524 RNA polymerase sigma factor; Provisional 196 matched cddid_all.tbl CDD PRK12525 PRK12525 139037 PRK12525 RNA polymerase sigma factor; Provisional 168 matched cddid_all.tbl CDD PRK12526 PRK12526 237127 PRK12526 RNA polymerase sigma factor; Provisional 206 matched cddid_all.tbl CDD PRK12527 PRK12527 171560 PRK12527 RNA polymerase sigma factor; Reviewed 159 matched cddid_all.tbl CDD PRK12528 PRK12528 171561 PRK12528 RNA polymerase sigma factor; Provisional 161 matched cddid_all.tbl CDD PRK12529 PRK12529 183574 PRK12529 RNA polymerase sigma factor; Provisional 178 matched cddid_all.tbl CDD PRK12530 PRK12530 237128 PRK12530 RNA polymerase sigma factor; Provisional 189 matched cddid_all.tbl CDD PRK12531 PRK12531 105726 PRK12531 RNA polymerase sigma factor; Provisional 194 matched cddid_all.tbl CDD PRK12532 PRK12532 171564 PRK12532 RNA polymerase sigma factor; Provisional 195 matched cddid_all.tbl CDD PRK12533 PRK12533 237129 PRK12533 RNA polymerase sigma factor; Provisional 216 matched cddid_all.tbl CDD PRK12534 PRK12534 183576 PRK12534 RNA polymerase sigma factor; Provisional 187 matched cddid_all.tbl CDD PRK12535 PRK12535 237130 PRK12535 RNA polymerase sigma factor; Provisional 196 matched cddid_all.tbl CDD PRK12536 PRK12536 237131 PRK12536 RNA polymerase sigma factor; Provisional 181 matched cddid_all.tbl CDD PRK12537 PRK12537 171568 PRK12537 RNA polymerase sigma factor; Provisional 182 matched cddid_all.tbl CDD PRK12538 PRK12538 139048 PRK12538 RNA polymerase sigma factor; Provisional 233 matched cddid_all.tbl CDD PRK12539 PRK12539 237132 PRK12539 RNA polymerase sigma factor SigF. 184 matched cddid_all.tbl CDD PRK12540 PRK12540 183579 PRK12540 RNA polymerase sigma factor; Provisional 182 matched cddid_all.tbl CDD PRK12541 PRK12541 183580 PRK12541 RNA polymerase sigma factor; Provisional 161 matched cddid_all.tbl CDD PRK12542 PRK12542 183581 PRK12542 RNA polymerase sigma factor; Provisional 185 matched cddid_all.tbl CDD PRK12543 PRK12543 183582 PRK12543 RNA polymerase sigma factor; Provisional 179 matched cddid_all.tbl CDD PRK12544 PRK12544 183583 PRK12544 RNA polymerase factor sigma-70. 206 matched cddid_all.tbl CDD PRK12545 PRK12545 183584 PRK12545 RNA polymerase factor sigma-70. 201 matched cddid_all.tbl CDD PRK12546 PRK12546 139055 PRK12546 RNA polymerase sigma factor; Provisional 188 matched cddid_all.tbl CDD PRK12547 PRK12547 139056 PRK12547 RNA polymerase sigma factor; Provisional 164 matched cddid_all.tbl CDD PRK12548 PRK12548 183585 PRK12548 shikimate dehydrogenase. 289 matched cddid_all.tbl CDD PRK12549 PRK12549 183586 PRK12549 shikimate 5-dehydrogenase; Reviewed 284 matched cddid_all.tbl CDD PRK12550 PRK12550 183587 PRK12550 shikimate 5-dehydrogenase; Reviewed 272 matched cddid_all.tbl CDD PRK12551 PRK12551 139060 PRK12551 ATP-dependent Clp protease proteolytic subunit; Reviewed 196 matched cddid_all.tbl CDD PRK12552 PRK12552 183588 PRK12552 ATP-dependent Clp protease proteolytic subunit. 222 matched cddid_all.tbl CDD PRK12553 PRK12553 237133 PRK12553 ATP-dependent Clp protease proteolytic subunit; Reviewed 207 matched cddid_all.tbl CDD PRK12554 PRK12554 237134 PRK12554 undecaprenyl pyrophosphate phosphatase; Reviewed 276 matched cddid_all.tbl CDD PRK12555 PRK12555 237135 PRK12555 chemotaxis-specific protein-glutamate methyltransferase CheB. 337 matched cddid_all.tbl CDD PRK12556 PRK12556 183592 PRK12556 tryptophanyl-tRNA synthetase; Provisional 332 matched cddid_all.tbl CDD PRK12557 PRK12557 237136 PRK12557 H(2)-dependent methylenetetrahydromethanopterin dehydrogenase-related protein; Provisional 342 matched cddid_all.tbl CDD PRK12559 PRK12559 79035 PRK12559 transcriptional regulator Spx; Provisional 131 matched cddid_all.tbl CDD PRK12560 PRK12560 183595 PRK12560 adenine phosphoribosyltransferase; Provisional 187 matched cddid_all.tbl CDD PRK12561 PRK12561 237137 PRK12561 NAD(P)H-quinone oxidoreductase subunit 4; Provisional 504 matched cddid_all.tbl CDD PRK12562 PRK12562 105755 PRK12562 ornithine carbamoyltransferase subunit F; Provisional 334 matched cddid_all.tbl CDD PRK12563 PRK12563 237138 PRK12563 sulfate adenylyltransferase subunit CysD. 312 matched cddid_all.tbl CDD PRK12564 PRK12564 237139 PRK12564 carbamoyl-phosphate synthase small subunit. 360 matched cddid_all.tbl CDD PRK12567 PRK12567 237140 PRK12567 putative monovalent cation/H+ antiporter subunit B; Reviewed 218 matched cddid_all.tbl CDD PRK12568 PRK12568 139075 PRK12568 glycogen branching enzyme; Provisional 730 matched cddid_all.tbl CDD PRK12569 PRK12569 237141 PRK12569 hypothetical protein; Provisional 245 matched cddid_all.tbl CDD PRK12570 PRK12570 237142 PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed 296 matched cddid_all.tbl CDD PRK12571 PRK12571 183601 PRK12571 1-deoxy-D-xylulose-5-phosphate synthase; Provisional 641 matched cddid_all.tbl CDD PRK12573 PRK12573 183602 PRK12573 Na(+)/H(+) antiporter subunit B. 140 matched cddid_all.tbl CDD PRK12574 PRK12574 183603 PRK12574 monovalent cation/H+ antiporter subunit B. 141 matched cddid_all.tbl CDD PRK12575 PRK12575 171592 PRK12575 succinate dehydrogenase/fumarate reductase iron-sulfur subunit. 235 matched cddid_all.tbl CDD PRK12576 PRK12576 237143 PRK12576 succinate dehydrogenase/fumarate reductase iron-sulfur subunit. 279 matched cddid_all.tbl CDD PRK12577 PRK12577 183605 PRK12577 succinate dehydrogenase/fumarate reductase iron-sulfur subunit. 329 matched cddid_all.tbl CDD PRK12578 PRK12578 183606 PRK12578 thiolase domain-containing protein. 385 matched cddid_all.tbl CDD PRK12579 PRK12579 183607 PRK12579 putative monovalent cation/H+ antiporter subunit B; Reviewed 258 matched cddid_all.tbl CDD PRK12580 PRK12580 79055 PRK12580 omptin family plasminogen activator Pla. 312 matched cddid_all.tbl CDD PRK12581 PRK12581 79056 PRK12581 oxaloacetate decarboxylase; Provisional 468 matched cddid_all.tbl CDD PRK12582 PRK12582 237144 PRK12582 acyl-CoA synthetase; Provisional 624 matched cddid_all.tbl CDD PRK12583 PRK12583 237145 PRK12583 acyl-CoA synthetase; Provisional 558 matched cddid_all.tbl CDD PRK12584 PRK12584 237146 PRK12584 flagellin A; Reviewed 510 matched cddid_all.tbl CDD PRK12585 PRK12585 183610 PRK12585 putative monovalent cation/H+ antiporter subunit G; Reviewed 197 matched cddid_all.tbl CDD PRK12586 PRK12586 237147 PRK12586 Na+/H+ antiporter subunit G. 145 matched cddid_all.tbl CDD PRK12587 PRK12587 183612 PRK12587 putative monovalent cation/H+ antiporter subunit G; Reviewed 118 matched cddid_all.tbl CDD PRK12592 PRK12592 183613 PRK12592 putative monovalent cation/H+ antiporter subunit G; Reviewed 126 matched cddid_all.tbl CDD PRK12595 PRK12595 183614 PRK12595 bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase; Reviewed 360 matched cddid_all.tbl CDD PRK12596 PRK12596 105779 PRK12596 putative monovalent cation/H+ antiporter subunit E; Reviewed 171 matched cddid_all.tbl CDD PRK12599 PRK12599 237148 PRK12599 putative monovalent cation/H+ antiporter subunit F; Reviewed 91 matched cddid_all.tbl CDD PRK12600 PRK12600 183617 PRK12600 Na(+)/H(+) antiporter subunit F1. 94 matched cddid_all.tbl CDD PRK12603 PRK12603 183618 PRK12603 putative monovalent cation/H+ antiporter subunit F; Reviewed 86 matched cddid_all.tbl CDD PRK12604 PRK12604 183619 PRK12604 putative monovalent cation/H+ antiporter subunit F; Reviewed 84 matched cddid_all.tbl CDD PRK12606 PRK12606 237149 PRK12606 GTP cyclohydrolase I; Reviewed 201 matched cddid_all.tbl CDD PRK12607 PRK12607 183621 PRK12607 phosphoribosylaminoimidazole-succinocarboxamide synthase; Provisional 313 matched cddid_all.tbl CDD PRK12608 PRK12608 237150 PRK12608 transcription termination factor Rho; Provisional 380 matched cddid_all.tbl CDD PRK12612 PRK12612 237151 PRK12612 putative monovalent cation/H+ antiporter subunit F; Reviewed 87 matched cddid_all.tbl CDD PRK12613 PRK12613 171609 PRK12613 galactose-6-phosphate isomerase subunit LacA; Provisional 141 matched cddid_all.tbl CDD PRK12615 PRK12615 171610 PRK12615 galactose-6-phosphate isomerase subunit LacB; Reviewed 171 matched cddid_all.tbl CDD PRK12616 PRK12616 183624 PRK12616 bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase. 270 matched cddid_all.tbl CDD PRK12617 PRK12617 183625 flgA flagellar basal body P-ring formation protein FlgA. 214 matched cddid_all.tbl CDD PRK12618 PRK12618 183626 flgA flagellar basal body P-ring formation protein FlgA. 141 matched cddid_all.tbl CDD PRK12619 PRK12619 183627 flgB flagellar basal body rod protein FlgB; Provisional 130 matched cddid_all.tbl CDD PRK12620 PRK12620 183628 flgB flagellar basal body rod protein FlgB; Provisional 132 matched cddid_all.tbl CDD PRK12621 PRK12621 171613 flgB flagellar basal body rod protein FlgB; Provisional 136 matched cddid_all.tbl CDD PRK12622 PRK12622 183629 flgB flagellar basal body rod protein FlgB; Provisional 135 matched cddid_all.tbl CDD PRK12623 PRK12623 183630 flgB flagellar basal body rod protein FlgB; Provisional 131 matched cddid_all.tbl CDD PRK12624 PRK12624 139107 flgB flagellar basal body rod protein FlgB; Provisional 143 matched cddid_all.tbl CDD PRK12626 PRK12626 183632 flgB flagellar basal body rod protein FlgB; Provisional 162 matched cddid_all.tbl CDD PRK12627 PRK12627 237152 flgB FlgB family protein. 128 matched cddid_all.tbl CDD PRK12628 PRK12628 79089 flgC flagellar basal body rod protein FlgC; Provisional 140 matched cddid_all.tbl CDD PRK12629 PRK12629 183634 flgC flagellar basal body rod protein FlgC; Provisional 135 matched cddid_all.tbl CDD PRK12630 PRK12630 183635 flgC flagellar basal body rod protein FlgC; Provisional 143 matched cddid_all.tbl CDD PRK12631 PRK12631 183636 flgC flagellar basal body rod protein FlgC; Provisional 138 matched cddid_all.tbl CDD PRK12632 PRK12632 183637 flgC flagellar basal body rod protein FlgC; Provisional 130 matched cddid_all.tbl CDD PRK12633 PRK12633 183638 flgD flagellar basal body rod modification protein; Provisional 230 matched cddid_all.tbl CDD PRK12634 PRK12634 183639 flgD flagellar basal body rod modification protein; Reviewed 221 matched cddid_all.tbl CDD PRK12636 PRK12636 183640 flgG flagellar basal body rod protein FlgG; Provisional 263 matched cddid_all.tbl CDD PRK12637 PRK12637 183641 flgE flagellar hook protein FlgE; Provisional 473 matched cddid_all.tbl CDD PRK12640 PRK12640 183642 flgF flagellar basal body rod protein FlgF; Reviewed 246 matched cddid_all.tbl CDD PRK12641 PRK12641 105809 flgF flagellar basal-body rod protein FlgF. 252 matched cddid_all.tbl CDD PRK12642 PRK12642 237153 flgF flagellar basal-body rod protein FlgF. 241 matched cddid_all.tbl CDD PRK12643 PRK12643 139117 flgF flagellar basal body rod protein FlgF; Reviewed 209 matched cddid_all.tbl CDD PRK12644 PRK12644 237154 PRK12644 putative monovalent cation/H+ antiporter subunit A; Reviewed 965 matched cddid_all.tbl CDD PRK12645 PRK12645 237155 PRK12645 monovalent cation/H+ antiporter subunit A; Reviewed 800 matched cddid_all.tbl CDD PRK12646 PRK12646 183646 PRK12646 DUF4040 family protein. 800 matched cddid_all.tbl CDD PRK12647 PRK12647 237156 PRK12647 putative monovalent cation/H+ antiporter subunit A; Reviewed 761 matched cddid_all.tbl CDD PRK12648 PRK12648 237157 PRK12648 putative monovalent cation/H+ antiporter subunit A; Reviewed 948 matched cddid_all.tbl CDD PRK12649 PRK12649 183649 PRK12649 putative monovalent cation/H+ antiporter subunit A; Reviewed 789 matched cddid_all.tbl CDD PRK12650 PRK12650 237158 PRK12650 DUF4040 family protein. 962 matched cddid_all.tbl CDD PRK12651 PRK12651 237159 PRK12651 Na+/H+ antiporter subunit E. 158 matched cddid_all.tbl CDD PRK12652 PRK12652 237160 PRK12652 monovalent cation/H+ antiporter subunit E. 357 matched cddid_all.tbl CDD PRK12653 PRK12653 183653 PRK12653 fructose-6-phosphate aldolase; Reviewed 220 matched cddid_all.tbl CDD PRK12654 PRK12654 237161 PRK12654 monovalent cation/H+ antiporter subunit E. 151 matched cddid_all.tbl CDD PRK12656 PRK12656 183656 PRK12656 fructose-6-phosphate aldolase; Reviewed 222 matched cddid_all.tbl CDD PRK12657 PRK12657 183657 PRK12657 putative monovalent cation/H+ antiporter subunit F; Reviewed 100 matched cddid_all.tbl CDD PRK12658 PRK12658 183658 PRK12658 Na+/H+ antiporter subunit C. 125 matched cddid_all.tbl CDD PRK12659 PRK12659 183659 PRK12659 Na+/H+ antiporter subunit C. 117 matched cddid_all.tbl CDD PRK12660 PRK12660 183660 PRK12660 putative monovalent cation/H+ antiporter subunit C; Reviewed 114 matched cddid_all.tbl CDD PRK12661 PRK12661 237162 PRK12661 putative monovalent cation/H+ antiporter subunit C; Reviewed 140 matched cddid_all.tbl CDD PRK12662 PRK12662 183662 PRK12662 putative monovalent cation/H+ antiporter subunit D; Reviewed 492 matched cddid_all.tbl CDD PRK12663 PRK12663 237163 PRK12663 Na+/H+ antiporter subunit D. 497 matched cddid_all.tbl CDD PRK12664 PRK12664 237164 PRK12664 putative monovalent cation/H+ antiporter subunit D; Reviewed 527 matched cddid_all.tbl CDD PRK12665 PRK12665 237165 PRK12665 putative monovalent cation/H+ antiporter subunit D; Reviewed 521 matched cddid_all.tbl CDD PRK12666 PRK12666 237166 PRK12666 putative monovalent cation/H+ antiporter subunit D; Reviewed 528 matched cddid_all.tbl CDD PRK12667 PRK12667 237167 PRK12667 putative monovalent cation/H+ antiporter subunit D; Reviewed 520 matched cddid_all.tbl CDD PRK12668 PRK12668 237168 PRK12668 Na(+)/H(+) antiporter subunit D. 581 matched cddid_all.tbl CDD PRK12670 PRK12670 183669 PRK12670 putative monovalent cation/H+ antiporter subunit G; Reviewed 99 matched cddid_all.tbl CDD PRK12671 PRK12671 183670 PRK12671 putative monovalent cation/H+ antiporter subunit G; Reviewed 120 matched cddid_all.tbl CDD PRK12672 PRK12672 183671 PRK12672 putative monovalent cation/H+ antiporter subunit G; Reviewed 118 matched cddid_all.tbl CDD PRK12674 PRK12674 237169 PRK12674 putative monovalent cation/H+ antiporter subunit G; Reviewed 99 matched cddid_all.tbl CDD PRK12675 PRK12675 171652 PRK12675 putative monovalent cation/H+ antiporter subunit G; Reviewed 104 matched cddid_all.tbl CDD PRK12676 PRK12676 183673 PRK12676 bifunctional fructose-bisphosphatase/inositol-phosphate phosphatase. 263 matched cddid_all.tbl CDD PRK12678 PRK12678 237171 PRK12678 transcription termination factor Rho; Provisional 672 matched cddid_all.tbl CDD PRK12679 PRK12679 183676 cbl HTH-type transcriptional regulator Cbl. 316 matched cddid_all.tbl CDD PRK12680 PRK12680 183677 PRK12680 LysR family transcriptional regulator. 327 matched cddid_all.tbl CDD PRK12681 PRK12681 183678 cysB HTH-type transcriptional regulator CysB. 324 matched cddid_all.tbl CDD PRK12682 PRK12682 183679 PRK12682 transcriptional regulator CysB-like protein; Reviewed 309 matched cddid_all.tbl CDD PRK12683 PRK12683 237172 PRK12683 transcriptional regulator CysB-like protein; Reviewed 309 matched cddid_all.tbl CDD PRK12684 PRK12684 237173 PRK12684 CysB family HTH-type transcriptional regulator. 313 matched cddid_all.tbl CDD PRK12685 PRK12685 183682 flgB flagellar basal body rod protein FlgB; Reviewed 116 matched cddid_all.tbl CDD PRK12686 PRK12686 183683 PRK12686 carbamate kinase; Reviewed 312 matched cddid_all.tbl CDD PRK12687 PRK12687 105853 PRK12687 flagellin; Reviewed 311 matched cddid_all.tbl CDD PRK12688 PRK12688 171664 PRK12688 flagellin; Reviewed 751 matched cddid_all.tbl CDD PRK12689 PRK12689 183684 flgF flagellar basal-body rod protein FlgF. 253 matched cddid_all.tbl CDD PRK12690 PRK12690 183685 flgF flagellar hook-basal body complex protein. 238 matched cddid_all.tbl CDD PRK12692 PRK12692 139158 flgG flagellar basal body rod protein FlgG; Reviewed 262 matched cddid_all.tbl CDD PRK12693 PRK12693 183687 flgG flagellar basal body rod protein FlgG; Provisional 261 matched cddid_all.tbl CDD PRK12696 PRK12696 237174 flgH flagellar basal body L-ring protein; Reviewed 236 matched cddid_all.tbl CDD PRK12697 PRK12697 237175 flgH flagellar basal body L-ring protein FlgH. 226 matched cddid_all.tbl CDD PRK12698 PRK12698 183690 flgH flagellar basal body L-ring protein FlgH. 224 matched cddid_all.tbl CDD PRK12699 PRK12699 105864 flgH flagellar basal body L-ring protein; Reviewed 246 matched cddid_all.tbl CDD PRK12700 PRK12700 139164 flgH flagellar basal body L-ring protein; Reviewed 230 matched cddid_all.tbl CDD PRK12701 PRK12701 183691 flgH flagellar basal body L-ring protein; Reviewed 230 matched cddid_all.tbl CDD PRK12702 PRK12702 105866 PRK12702 mannosyl-3-phosphoglycerate phosphatase; Reviewed 302 matched cddid_all.tbl CDD PRK12703 PRK12703 237176 PRK12703 tRNA 2'-O-methylase; Reviewed 339 matched cddid_all.tbl CDD PRK12704 PRK12704 237177 PRK12704 phosphodiesterase; Provisional 520 matched cddid_all.tbl CDD PRK12705 PRK12705 237178 PRK12705 hypothetical protein; Provisional 508 matched cddid_all.tbl CDD PRK12706 PRK12706 183694 flgI flagellar basal body P-ring protein; Provisional 328 matched cddid_all.tbl CDD PRK12708 PRK12708 139168 flgJ peptidoglycan hydrolase; Reviewed 134 matched cddid_all.tbl CDD PRK12709 PRK12709 237179 flgJ flagellar rod assembly protein/muramidase FlgJ; Provisional 320 matched cddid_all.tbl CDD PRK12710 PRK12710 139170 flgJ flagellar rod assembly protein/muramidase FlgJ; Provisional 291 matched cddid_all.tbl CDD PRK12711 PRK12711 237180 flgJ flagellar assembly peptidoglycan hydrolase FlgJ. 392 matched cddid_all.tbl CDD PRK12712 PRK12712 139172 flgJ flagellar rod assembly protein/muramidase FlgJ; Provisional 344 matched cddid_all.tbl CDD PRK12713 PRK12713 139173 flgJ flagellar rod assembly protein/muramidase FlgJ; Provisional 339 matched cddid_all.tbl CDD PRK12714 PRK12714 183697 flgK flagellar hook-associated protein FlgK; Provisional 624 matched cddid_all.tbl CDD PRK12715 PRK12715 183698 flgK flagellar hook-associated protein FlgK; Provisional 649 matched cddid_all.tbl CDD PRK12717 PRK12717 171679 flgL flagellar hook-associated protein 3. 523 matched cddid_all.tbl CDD PRK12718 PRK12718 79176 flgL flagellar hook-associated protein FlgL; Provisional 510 matched cddid_all.tbl CDD PRK12720 PRK12720 183699 PRK12720 EscV/YscV/HrcV family type III secretion system export apparatus protein. 675 matched cddid_all.tbl CDD PRK12721 PRK12721 183700 PRK12721 EscU/YscU/HrcU family type III secretion system export apparatus switch protein. 349 matched cddid_all.tbl CDD PRK12722 PRK12722 237181 PRK12722 flagellar transcriptional regulator FlhC. 187 matched cddid_all.tbl CDD PRK12723 PRK12723 183702 PRK12723 flagellar biosynthesis regulator FlhF; Provisional 388 matched cddid_all.tbl CDD PRK12724 PRK12724 183703 PRK12724 flagellar biosynthesis regulator FlhF; Provisional 432 matched cddid_all.tbl CDD PRK12726 PRK12726 183704 PRK12726 flagellar biosynthesis regulator FlhF; Provisional 407 matched cddid_all.tbl CDD PRK12727 PRK12727 237182 PRK12727 flagellar biosynthesis protein FlhF. 559 matched cddid_all.tbl CDD PRK12728 PRK12728 237183 fliE flagellar hook-basal body protein FliE; Provisional 102 matched cddid_all.tbl CDD PRK12729 PRK12729 183707 fliE flagellar hook-basal body protein FliE; Provisional 127 matched cddid_all.tbl CDD PRK12735 PRK12735 183708 PRK12735 elongation factor Tu; Reviewed 396 matched cddid_all.tbl CDD PRK12736 PRK12736 237184 PRK12736 elongation factor Tu; Reviewed 394 matched cddid_all.tbl CDD PRK12737 PRK12737 183710 gatY tagatose-bisphosphate aldolase subunit GatY. 284 matched cddid_all.tbl CDD PRK12738 PRK12738 183711 kbaY tagatose-bisphosphate aldolase subunit KbaY. 286 matched cddid_all.tbl CDD PRK12740 PRK12740 237186 PRK12740 elongation factor G-like protein EF-G2. 668 matched cddid_all.tbl CDD PRK12742 PRK12742 183714 PRK12742 SDR family oxidoreductase. 237 matched cddid_all.tbl CDD PRK12743 PRK12743 237187 PRK12743 SDR family oxidoreductase. 256 matched cddid_all.tbl CDD PRK12744 PRK12744 183716 PRK12744 SDR family oxidoreductase. 257 matched cddid_all.tbl CDD PRK12745 PRK12745 237188 PRK12745 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional 256 matched cddid_all.tbl CDD PRK12746 PRK12746 183718 PRK12746 SDR family oxidoreductase. 254 matched cddid_all.tbl CDD PRK12747 PRK12747 183719 PRK12747 short chain dehydrogenase; Provisional 252 matched cddid_all.tbl CDD PRK12748 PRK12748 237189 PRK12748 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional 256 matched cddid_all.tbl CDD PRK12749 PRK12749 183721 PRK12749 quinate/shikimate dehydrogenase; Reviewed 288 matched cddid_all.tbl CDD PRK12750 PRK12750 183722 cpxP periplasmic repressor CpxP; Reviewed 170 matched cddid_all.tbl CDD PRK12751 PRK12751 171704 cpxP periplasmic stress adaptor protein CpxP; Reviewed 162 matched cddid_all.tbl CDD PRK12755 PRK12755 237190 PRK12755 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional 353 matched cddid_all.tbl CDD PRK12756 PRK12756 183726 PRK12756 Trp-sensitive 3-deoxy-7-phosphoheptulonate synthase AroH. 348 matched cddid_all.tbl CDD PRK12757 PRK12757 237191 PRK12757 cell division protein FtsN; Provisional 256 matched cddid_all.tbl CDD PRK12758 PRK12758 237192 PRK12758 DNA gyrase/topoisomerase IV subunit A. 869 matched cddid_all.tbl CDD PRK12759 PRK12759 139206 PRK12759 bifunctional gluaredoxin/ribonucleoside-diphosphate reductase subunit beta; Provisional 410 matched cddid_all.tbl CDD PRK12764 PRK12764 237193 PRK12764 fumarylacetoacetate hydrolase family protein. 500 matched cddid_all.tbl CDD PRK12765 PRK12765 237194 PRK12765 flagellar filament capping protein FliD. 595 matched cddid_all.tbl CDD PRK12766 PRK12766 183731 PRK12766 50S ribosomal protein L32e; Provisional 232 matched cddid_all.tbl CDD PRK12767 PRK12767 237195 PRK12767 carbamoyl phosphate synthase-like protein; Provisional 326 matched cddid_all.tbl CDD PRK12768 PRK12768 237196 PRK12768 sulfate transporter family protein. 240 matched cddid_all.tbl CDD PRK12769 PRK12769 183733 PRK12769 putative oxidoreductase Fe-S binding subunit; Reviewed 654 matched cddid_all.tbl CDD PRK12770 PRK12770 237197 PRK12770 putative glutamate synthase subunit beta; Provisional 352 matched cddid_all.tbl CDD PRK12771 PRK12771 237198 PRK12771 putative glutamate synthase (NADPH) small subunit; Provisional 564 matched cddid_all.tbl CDD PRK12772 PRK12772 237199 PRK12772 fused FliR family export protein/FlhB family type III secretion system protein. 609 matched cddid_all.tbl CDD PRK12773 PRK12773 183737 flhB flagellar biosynthesis protein FlhB; Reviewed 646 matched cddid_all.tbl CDD PRK12775 PRK12775 183738 PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional 1006 matched cddid_all.tbl CDD PRK12778 PRK12778 237200 PRK12778 bifunctional dihydroorotate dehydrogenase B NAD binding subunit/NADPH-dependent glutamate synthase. 752 matched cddid_all.tbl CDD PRK12779 PRK12779 183740 PRK12779 putative bifunctional glutamate synthase subunit beta/2-polyprenylphenol hydroxylase; Provisional 944 matched cddid_all.tbl CDD PRK12780 PRK12780 183741 fliR flagellar biosynthesis protein FliR; Reviewed 251 matched cddid_all.tbl CDD PRK12781 PRK12781 139219 fliQ flagellar biosynthetic protein FliQ. 88 matched cddid_all.tbl CDD PRK12782 PRK12782 139220 flgC flagellar basal body rod protein FlgC; Reviewed 138 matched cddid_all.tbl CDD PRK12783 PRK12783 171720 fliP flagellar biosynthesis protein FliP; Reviewed 255 matched cddid_all.tbl CDD PRK12784 PRK12784 183742 PRK12784 hypothetical protein; Provisional 84 matched cddid_all.tbl CDD PRK12785 PRK12785 183743 fliL flagellar basal body-associated protein FliL; Reviewed 166 matched cddid_all.tbl CDD PRK12786 PRK12786 237201 flgA flagellar basal body P-ring formation protein FlgA. 338 matched cddid_all.tbl CDD PRK12787 PRK12787 183745 fliX flagellar assembly regulator FliX; Reviewed 138 matched cddid_all.tbl CDD PRK12788 PRK12788 237202 flgH flagellar basal body L-ring protein FlgH. 234 matched cddid_all.tbl CDD PRK12789 PRK12789 183746 flgI flagellar basal body P-ring protein FlgI. 367 matched cddid_all.tbl CDD PRK12790 PRK12790 237203 PRK12790 flagellar rod assembly protein FlgJ. 115 matched cddid_all.tbl CDD PRK12791 PRK12791 237204 flbT flagellar biosynthesis repressor FlbT; Reviewed 131 matched cddid_all.tbl CDD PRK12792 PRK12792 237205 flhA flagellar biosynthesis protein FlhA; Reviewed 694 matched cddid_all.tbl CDD PRK12793 PRK12793 237206 flaF flagellar biosynthesis regulator FlaF. 115 matched cddid_all.tbl CDD PRK12794 PRK12794 237207 flaF flagellar biosynthesis regulatory protein FlaF; Reviewed 122 matched cddid_all.tbl CDD PRK12795 PRK12795 237208 fliM flagellar motor switch protein FliM; Reviewed 388 matched cddid_all.tbl CDD PRK12796 PRK12796 237209 spaP EscR/YscR/HrcR family type III secretion system export apparatus protein. 221 matched cddid_all.tbl CDD PRK12797 PRK12797 237210 PRK12797 type III secretion system protein YscR; Provisional 213 matched cddid_all.tbl CDD PRK12798 PRK12798 237211 PRK12798 chemotaxis protein; Reviewed 421 matched cddid_all.tbl CDD PRK12799 PRK12799 183756 motB flagellar motor protein MotB; Reviewed 421 matched cddid_all.tbl CDD PRK12802 PRK12802 139237 PRK12802 flagellin; Provisional 282 matched cddid_all.tbl CDD PRK12803 PRK12803 183758 PRK12803 flagellin; Provisional 335 matched cddid_all.tbl CDD PRK12804 PRK12804 183759 PRK12804 flagellin; Provisional 301 matched cddid_all.tbl CDD PRK12805 PRK12805 183760 PRK12805 FliC/FljB family flagellin. 287 matched cddid_all.tbl CDD PRK12806 PRK12806 183761 PRK12806 flagellin; Provisional 475 matched cddid_all.tbl CDD PRK12807 PRK12807 171737 PRK12807 flagellin; Provisional 287 matched cddid_all.tbl CDD PRK12808 PRK12808 237212 PRK12808 flagellin; Provisional 476 matched cddid_all.tbl CDD PRK12809 PRK12809 183762 PRK12809 putative oxidoreductase Fe-S binding subunit; Reviewed 639 matched cddid_all.tbl CDD PRK12810 PRK12810 237213 gltD glutamate synthase subunit beta; Reviewed 471 matched cddid_all.tbl CDD PRK12812 PRK12812 139245 flgD flagellar basal body rod modification protein; Reviewed 259 matched cddid_all.tbl CDD PRK12813 PRK12813 237214 flgD flagellar basal body rod modification protein; Reviewed 223 matched cddid_all.tbl CDD PRK12814 PRK12814 139246 PRK12814 putative NADPH-dependent glutamate synthase small subunit; Provisional 652 matched cddid_all.tbl CDD PRK12815 PRK12815 237215 carB carbamoyl phosphate synthase large subunit; Reviewed 1068 matched cddid_all.tbl CDD PRK12816 PRK12816 183766 flgG flagellar basal body rod protein FlgG; Reviewed 264 matched cddid_all.tbl CDD PRK12817 PRK12817 183767 flgG flagellar basal body rod protein FlgG; Reviewed 260 matched cddid_all.tbl CDD PRK12818 PRK12818 183768 flgG flagellar basal body rod protein FlgG; Reviewed 256 matched cddid_all.tbl CDD PRK12819 PRK12819 183769 flgG flagellar basal-body rod protein FlgG. 257 matched cddid_all.tbl CDD PRK12820 PRK12820 105955 PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional 706 matched cddid_all.tbl CDD PRK12821 PRK12821 237216 PRK12821 aspartyl/glutamyl-tRNA amidotransferase subunit C-like protein; Provisional 477 matched cddid_all.tbl CDD PRK12822 PRK12822 237217 PRK12822 phospho-2-dehydro-3-deoxyheptonate aldolase; Provisional 356 matched cddid_all.tbl CDD PRK12823 PRK12823 183772 benD 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase; Provisional 260 matched cddid_all.tbl CDD PRK12824 PRK12824 183773 PRK12824 3-oxoacyl-ACP reductase. 245 matched cddid_all.tbl CDD PRK12825 PRK12825 237218 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional 249 matched cddid_all.tbl CDD PRK12826 PRK12826 183775 PRK12826 SDR family oxidoreductase. 251 matched cddid_all.tbl CDD PRK12827 PRK12827 237219 PRK12827 short chain dehydrogenase; Provisional 249 matched cddid_all.tbl CDD PRK12828 PRK12828 237220 PRK12828 short chain dehydrogenase; Provisional 239 matched cddid_all.tbl CDD PRK12829 PRK12829 183778 PRK12829 short chain dehydrogenase; Provisional 264 matched cddid_all.tbl CDD PRK12830 PRK12830 183779 PRK12830 UDP-N-acetylglucosamine 1-carboxyvinyltransferase; Reviewed 417 matched cddid_all.tbl CDD PRK12831 PRK12831 183780 PRK12831 putative oxidoreductase; Provisional 464 matched cddid_all.tbl CDD PRK12833 PRK12833 183781 PRK12833 acetyl-CoA carboxylase biotin carboxylase subunit; Provisional 467 matched cddid_all.tbl CDD PRK12834 PRK12834 183782 PRK12834 putative FAD-binding dehydrogenase; Reviewed 549 matched cddid_all.tbl CDD PRK12835 PRK12835 237221 PRK12835 3-ketosteroid-delta-1-dehydrogenase; Reviewed 584 matched cddid_all.tbl CDD PRK12837 PRK12837 237222 PRK12837 FAD-binding protein. 513 matched cddid_all.tbl CDD PRK12838 PRK12838 183784 PRK12838 carbamoyl phosphate synthase small subunit; Reviewed 354 matched cddid_all.tbl CDD PRK12839 PRK12839 237223 PRK12839 FAD-dependent oxidoreductase. 572 matched cddid_all.tbl CDD PRK12842 PRK12842 237224 PRK12842 putative succinate dehydrogenase; Reviewed 574 matched cddid_all.tbl CDD PRK12843 PRK12843 237225 PRK12843 FAD-dependent oxidoreductase. 578 matched cddid_all.tbl CDD PRK12844 PRK12844 183787 PRK12844 3-ketosteroid-delta-1-dehydrogenase; Reviewed 557 matched cddid_all.tbl CDD PRK12845 PRK12845 237226 PRK12845 3-ketosteroid-delta-1-dehydrogenase; Reviewed 564 matched cddid_all.tbl CDD PRK12846 PRK12846 237227 PRK12846 peptide deformylase; Reviewed 165 matched cddid_all.tbl CDD PRK12849 PRK12849 237230 groEL chaperonin GroEL; Reviewed 542 matched cddid_all.tbl CDD PRK12850 PRK12850 237231 groEL chaperonin GroEL; Reviewed 544 matched cddid_all.tbl CDD PRK12851 PRK12851 171770 groEL chaperonin GroEL; Reviewed 541 matched cddid_all.tbl CDD PRK12852 PRK12852 237232 groEL chaperonin GroEL; Reviewed 545 matched cddid_all.tbl CDD PRK12853 PRK12853 237233 PRK12853 glucose-6-phosphate dehydrogenase. 482 matched cddid_all.tbl CDD PRK12854 PRK12854 237234 PRK12854 glucose-6-phosphate 1-dehydrogenase; Provisional 484 matched cddid_all.tbl CDD PRK12855 PRK12855 171774 PRK12855 hypothetical protein; Provisional 103 matched cddid_all.tbl CDD PRK12856 PRK12856 105987 PRK12856 hypothetical protein; Provisional 103 matched cddid_all.tbl CDD PRK12857 PRK12857 237235 PRK12857 class II fructose-1,6-bisphosphate aldolase. 284 matched cddid_all.tbl CDD PRK12858 PRK12858 237236 PRK12858 tagatose 1,6-diphosphate aldolase; Reviewed 340 matched cddid_all.tbl CDD PRK12859 PRK12859 183797 PRK12859 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional 256 matched cddid_all.tbl CDD PRK12860 PRK12860 237237 PRK12860 flagellar transcriptional regulator FlhC. 189 matched cddid_all.tbl CDD PRK12861 PRK12861 183798 PRK12861 malic enzyme; Reviewed 764 matched cddid_all.tbl CDD PRK12862 PRK12862 183799 PRK12862 malic enzyme; Reviewed 763 matched cddid_all.tbl CDD PRK12863 PRK12863 183800 PRK12863 YciI-like protein; Reviewed 94 matched cddid_all.tbl CDD PRK12864 PRK12864 183801 PRK12864 YciI-like protein; Reviewed 89 matched cddid_all.tbl CDD PRK12865 PRK12865 171782 PRK12865 YciI-like protein; Reviewed 97 matched cddid_all.tbl CDD PRK12866 PRK12866 237238 PRK12866 YciI-like protein; Reviewed 97 matched cddid_all.tbl CDD PRK12871 PRK12871 106000 ubiA prenyltransferase; Reviewed 297 matched cddid_all.tbl CDD PRK12872 PRK12872 237241 ubiA prenyltransferase; Reviewed 285 matched cddid_all.tbl CDD PRK12873 PRK12873 171787 ubiA 4-hydroxybenzoate polyprenyltransferase. 294 matched cddid_all.tbl CDD PRK12874 PRK12874 237242 ubiA 4-hydroxybenzoate polyprenyltransferase. 291 matched cddid_all.tbl CDD PRK12875 PRK12875 237243 ubiA prenyltransferase; Reviewed 282 matched cddid_all.tbl CDD PRK12876 PRK12876 237244 ubiA prenyltransferase; Reviewed 300 matched cddid_all.tbl CDD PRK12879 PRK12879 237245 PRK12879 3-oxoacyl-(acyl carrier protein) synthase III; Reviewed 325 matched cddid_all.tbl CDD PRK12880 PRK12880 171793 PRK12880 beta-ketoacyl-ACP synthase III. 353 matched cddid_all.tbl CDD PRK12881 PRK12881 237246 acnA aconitate hydratase AcnA. 889 matched cddid_all.tbl CDD PRK12882 PRK12882 183811 ubiA prenyltransferase; Reviewed 276 matched cddid_all.tbl CDD PRK12883 PRK12883 171796 ubiA prenyltransferase UbiA-like protein; Reviewed 277 matched cddid_all.tbl CDD PRK12884 PRK12884 183812 ubiA prenyltransferase; Reviewed 279 matched cddid_all.tbl CDD PRK12886 PRK12886 237247 ubiA prenyltransferase; Reviewed 291 matched cddid_all.tbl CDD PRK12887 PRK12887 183813 ubiA tocopherol phytyltransferase; Reviewed 308 matched cddid_all.tbl CDD PRK12888 PRK12888 183814 ubiA 4-hydroxybenzoate octaprenyltransferase. 284 matched cddid_all.tbl CDD PRK12890 PRK12890 237248 PRK12890 allantoate amidohydrolase; Reviewed 414 matched cddid_all.tbl CDD PRK12891 PRK12891 237249 PRK12891 allantoate amidohydrolase; Reviewed 414 matched cddid_all.tbl CDD PRK12892 PRK12892 183817 PRK12892 allantoate amidohydrolase; Reviewed 412 matched cddid_all.tbl CDD PRK12893 PRK12893 237250 PRK12893 Zn-dependent hydrolase. 412 matched cddid_all.tbl CDD PRK12895 PRK12895 237251 ubiA prenyltransferase; Reviewed 286 matched cddid_all.tbl CDD PRK12896 PRK12896 237252 PRK12896 methionine aminopeptidase; Reviewed 255 matched cddid_all.tbl CDD PRK12897 PRK12897 171806 PRK12897 type I methionyl aminopeptidase. 248 matched cddid_all.tbl CDD PRK12898 PRK12898 237253 secA preprotein translocase subunit SecA; Reviewed 656 matched cddid_all.tbl CDD PRK12901 PRK12901 237256 secA preprotein translocase subunit SecA; Reviewed 1112 matched cddid_all.tbl CDD PRK12903 PRK12903 237258 secA preprotein translocase subunit SecA; Reviewed 925 matched cddid_all.tbl CDD PRK12904 PRK12904 237259 PRK12904 preprotein translocase subunit SecA; Reviewed 830 matched cddid_all.tbl CDD PRK12906 PRK12906 237260 secA preprotein translocase subunit SecA; Reviewed 796 matched cddid_all.tbl CDD PRK12911 PRK12911 171815 PRK12911 bifunctional preprotein translocase subunit SecD/SecF; Reviewed 1403 matched cddid_all.tbl CDD PRK12921 PRK12921 183829 PRK12921 oxidoreductase. 305 matched cddid_all.tbl CDD PRK12928 PRK12928 237261 PRK12928 lipoyl synthase; Provisional 290 matched cddid_all.tbl CDD PRK12933 PRK12933 183831 secD protein translocase subunit SecD. 604 matched cddid_all.tbl CDD PRK12935 PRK12935 183832 PRK12935 acetoacetyl-CoA reductase; Provisional 247 matched cddid_all.tbl CDD PRK12936 PRK12936 171820 PRK12936 3-ketoacyl-(acyl-carrier-protein) reductase NodG; Reviewed 245 matched cddid_all.tbl CDD PRK12937 PRK12937 171821 PRK12937 short chain dehydrogenase; Provisional 245 matched cddid_all.tbl CDD PRK12938 PRK12938 171822 PRK12938 3-ketoacyl-ACP reductase. 246 matched cddid_all.tbl CDD PRK12939 PRK12939 183833 PRK12939 short chain dehydrogenase; Provisional 250 matched cddid_all.tbl CDD PRK12996 PRK12996 171824 ulaA PTS ascorbate transporter subunit IIC. 463 matched cddid_all.tbl CDD PRK12997 PRK12997 237262 PRK12997 PTS sugar transporter subunit IIC. 466 matched cddid_all.tbl CDD PRK12999 PRK12999 237263 PRK12999 pyruvate carboxylase; Reviewed 1146 matched cddid_all.tbl CDD PRK13004 PRK13004 183836 PRK13004 YgeY family selenium metabolism-linked hydrolase. 399 matched cddid_all.tbl CDD PRK13009 PRK13009 237265 PRK13009 succinyl-diaminopimelate desuccinylase; Reviewed 375 matched cddid_all.tbl CDD PRK13010 PRK13010 139334 purU formyltetrahydrofolate deformylase; Reviewed 289 matched cddid_all.tbl CDD PRK13011 PRK13011 237266 PRK13011 formyltetrahydrofolate deformylase; Reviewed 286 matched cddid_all.tbl CDD PRK13012 PRK13012 237267 PRK13012 2-oxoacid dehydrogenase subunit E1; Provisional 896 matched cddid_all.tbl CDD PRK13013 PRK13013 237268 PRK13013 acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase family protein. 427 matched cddid_all.tbl CDD PRK13014 PRK13014 237269 PRK13014 methionine sulfoxide reductase A; Provisional 186 matched cddid_all.tbl CDD PRK13015 PRK13015 237270 PRK13015 3-dehydroquinate dehydratase; Reviewed 146 matched cddid_all.tbl CDD PRK13016 PRK13016 237271 PRK13016 dihydroxy-acid dehydratase; Provisional 577 matched cddid_all.tbl CDD PRK13017 PRK13017 237272 PRK13017 dihydroxy-acid dehydratase; Provisional 596 matched cddid_all.tbl CDD PRK13018 PRK13018 237273 PRK13018 cell division protein FtsZ; Provisional 378 matched cddid_all.tbl CDD PRK13019 PRK13019 183845 clpS ATP-dependent Clp protease adapter ClpS. 94 matched cddid_all.tbl CDD PRK13020 PRK13020 183846 PRK13020 riboflavin synthase subunit alpha; Provisional 206 matched cddid_all.tbl CDD PRK13021 PRK13021 237274 secF preprotein translocase subunit SecF; Reviewed 297 matched cddid_all.tbl CDD PRK13023 PRK13023 171842 PRK13023 protein translocase subunit SecDF. 758 matched cddid_all.tbl CDD PRK13024 PRK13024 237276 PRK13024 bifunctional preprotein translocase subunit SecD/SecF; Reviewed 755 matched cddid_all.tbl CDD PRK13026 PRK13026 237277 PRK13026 acyl-CoA dehydrogenase; Reviewed 774 matched cddid_all.tbl CDD PRK13027 PRK13027 183850 PRK13027 C4-dicarboxylate transporter DctA; Reviewed 421 matched cddid_all.tbl CDD PRK13028 PRK13028 183851 PRK13028 tryptophan synthase subunit beta; Provisional 402 matched cddid_all.tbl CDD PRK13029 PRK13029 237278 PRK13029 indolepyruvate ferredoxin oxidoreductase family protein. 1186 matched cddid_all.tbl CDD PRK13030 PRK13030 237279 PRK13030 indolepyruvate ferredoxin oxidoreductase family protein. 1159 matched cddid_all.tbl CDD PRK13031 PRK13031 106068 PRK13031 preprotein translocase subunit SecB; Provisional 149 matched cddid_all.tbl CDD PRK13032 PRK13032 171848 PRK13032 chemotaxis-inhibiting protein CHIPS; Reviewed 149 matched cddid_all.tbl CDD PRK13033 PRK13033 171849 PRK13033 formyl peptide receptor-like 1 inhibitory protein; Reviewed 133 matched cddid_all.tbl CDD PRK13034 PRK13034 237280 PRK13034 serine hydroxymethyltransferase; Reviewed 416 matched cddid_all.tbl CDD PRK13035 PRK13035 171851 PRK13035 superantigen-like protein SSL5; Reviewed. 234 matched cddid_all.tbl CDD PRK13036 PRK13036 171852 PRK13036 superantigen-like protein SSL11; Reviewed. 227 matched cddid_all.tbl CDD PRK13037 PRK13037 106074 PRK13037 superantigen-like protein SSL1; Reviewed. 226 matched cddid_all.tbl CDD PRK13038 PRK13038 171853 PRK13038 superantigen-like protein SSL10; Reviewed. 227 matched cddid_all.tbl CDD PRK13039 PRK13039 171854 PRK13039 superantigen-like protein SSL8; Reviewed. 232 matched cddid_all.tbl CDD PRK13040 PRK13040 106077 PRK13040 superantigen-like protein SSL6; Reviewed. 231 matched cddid_all.tbl CDD PRK13041 PRK13041 106078 PRK13041 superantigen-like protein SSL2; Reviewed. 231 matched cddid_all.tbl CDD PRK13042 PRK13042 183854 PRK13042 superantigen-like protein SSL4; Reviewed. 291 matched cddid_all.tbl CDD PRK13043 PRK13043 171855 PRK13043 superantigen-like protein SSL14; Reviewed. 241 matched cddid_all.tbl CDD PRK13054 PRK13054 237281 PRK13054 lipid kinase; Reviewed 300 matched cddid_all.tbl CDD PRK13055 PRK13055 237282 PRK13055 putative lipid kinase; Reviewed 334 matched cddid_all.tbl CDD PRK13057 PRK13057 183857 PRK13057 lipid kinase. 287 matched cddid_all.tbl CDD PRK13059 PRK13059 183858 PRK13059 putative lipid kinase; Reviewed 295 matched cddid_all.tbl CDD PRK13105 PRK13105 183861 ubiA prenyltransferase; Reviewed 282 matched cddid_all.tbl CDD PRK13106 PRK13106 237283 ubiA prenyltransferase; Reviewed 300 matched cddid_all.tbl CDD PRK13108 PRK13108 237284 PRK13108 prolipoprotein diacylglyceryl transferase; Reviewed 460 matched cddid_all.tbl CDD PRK13109 PRK13109 183864 flhB flagellar biosynthesis protein FlhB; Reviewed 358 matched cddid_all.tbl CDD PRK13111 PRK13111 237285 trpA tryptophan synthase subunit alpha; Provisional 258 matched cddid_all.tbl CDD PRK13125 PRK13125 237286 trpA tryptophan synthase subunit alpha; Provisional 244 matched cddid_all.tbl CDD PRK13128 PRK13128 171868 PRK13128 D-aminopeptidase; Reviewed 518 matched cddid_all.tbl CDD PRK13130 PRK13130 237287 PRK13130 RNA-protein complex protein Nop10. 56 matched cddid_all.tbl CDD PRK13141 PRK13141 237288 hisH imidazole glycerol phosphate synthase subunit HisH; Provisional 205 matched cddid_all.tbl CDD PRK13142 PRK13142 171871 hisH imidazole glycerol phosphate synthase subunit HisH; Provisional 192 matched cddid_all.tbl CDD PRK13143 PRK13143 237289 hisH imidazole glycerol phosphate synthase subunit HisH; Provisional 200 matched cddid_all.tbl CDD PRK13145 PRK13145 183870 araD L-ribulose-5-phosphate 4-epimerase; Provisional 234 matched cddid_all.tbl CDD PRK13146 PRK13146 237290 hisH imidazole glycerol phosphate synthase subunit HisH; Provisional 209 matched cddid_all.tbl CDD PRK13149 PRK13149 183872 PRK13149 H/ACA RNA-protein complex component Gar1; Reviewed 73 matched cddid_all.tbl CDD PRK13150 PRK13150 139376 PRK13150 cytochrome c maturation protein CcmE. 159 matched cddid_all.tbl CDD PRK13152 PRK13152 171876 hisH imidazole glycerol phosphate synthase subunit HisH; Provisional 201 matched cddid_all.tbl CDD PRK13159 PRK13159 183873 PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed 155 matched cddid_all.tbl CDD PRK13165 PRK13165 183874 PRK13165 cytochrome c maturation protein CcmE. 160 matched cddid_all.tbl CDD PRK13168 PRK13168 237291 rumA 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD. 443 matched cddid_all.tbl CDD PRK13169 PRK13169 183876 PRK13169 DNA replication initiation control protein YabA. 110 matched cddid_all.tbl CDD PRK13170 PRK13170 183877 hisH imidazole glycerol phosphate synthase subunit HisH; Provisional 196 matched cddid_all.tbl CDD PRK13181 PRK13181 183878 hisH imidazole glycerol phosphate synthase subunit HisH; Provisional 199 matched cddid_all.tbl CDD PRK13182 PRK13182 237292 racA chromosome-anchoring protein RacA. 175 matched cddid_all.tbl CDD PRK13183 PRK13183 171884 psbN photosystem II reaction center protein PsbN. 46 matched cddid_all.tbl CDD PRK13184 PRK13184 183880 pknD serine/threonine-protein kinase PknD. 932 matched cddid_all.tbl CDD PRK13185 PRK13185 237293 chlL protochlorophyllide reductase iron-sulfur ATP-binding protein; Provisional 270 matched cddid_all.tbl CDD PRK13187 PRK13187 237295 PRK13187 UDP-3-O-acyl N-acetylglycosamine deacetylase. 304 matched cddid_all.tbl CDD PRK13188 PRK13188 237296 PRK13188 bifunctional UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase/(3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase; Reviewed 464 matched cddid_all.tbl CDD PRK13189 PRK13189 237297 PRK13189 peroxiredoxin; Provisional 222 matched cddid_all.tbl CDD PRK13190 PRK13190 106159 PRK13190 putative peroxiredoxin; Provisional 202 matched cddid_all.tbl CDD PRK13191 PRK13191 183885 PRK13191 putative peroxiredoxin; Provisional 215 matched cddid_all.tbl CDD PRK13192 PRK13192 183886 PRK13192 bifunctional urease subunit gamma/beta; Reviewed 208 matched cddid_all.tbl CDD PRK13193 PRK13193 237298 PRK13193 pyroglutamyl-peptidase I. 209 matched cddid_all.tbl CDD PRK13194 PRK13194 183887 PRK13194 pyrrolidone-carboxylate peptidase; Provisional 208 matched cddid_all.tbl CDD PRK13195 PRK13195 171894 PRK13195 pyrrolidone-carboxylate peptidase; Provisional 222 matched cddid_all.tbl CDD PRK13196 PRK13196 171895 PRK13196 pyroglutamyl-peptidase I. 211 matched cddid_all.tbl CDD PRK13197 PRK13197 237299 PRK13197 pyrrolidone-carboxylate peptidase; Provisional 215 matched cddid_all.tbl CDD PRK13198 PRK13198 171897 ureB urease subunit beta; Reviewed 158 matched cddid_all.tbl CDD PRK13201 PRK13201 237302 ureB urease subunit beta; Reviewed 136 matched cddid_all.tbl CDD PRK13202 PRK13202 106171 ureB urease subunit beta; Reviewed 104 matched cddid_all.tbl CDD PRK13203 PRK13203 237303 ureB urease subunit beta; Reviewed 102 matched cddid_all.tbl CDD PRK13204 PRK13204 171902 ureB urease subunit beta; Reviewed 159 matched cddid_all.tbl CDD PRK13205 PRK13205 106174 ureB urease subunit beta; Reviewed 162 matched cddid_all.tbl CDD PRK13206 PRK13206 237304 ureC urease subunit alpha; Reviewed 573 matched cddid_all.tbl CDD PRK13207 PRK13207 237305 ureC urease subunit alpha; Reviewed 568 matched cddid_all.tbl CDD PRK13208 PRK13208 237306 valS valyl-tRNA synthetase; Reviewed 800 matched cddid_all.tbl CDD PRK13209 PRK13209 237307 PRK13209 L-ribulose-5-phosphate 3-epimerase. 283 matched cddid_all.tbl CDD PRK13210 PRK13210 237308 PRK13210 L-ribulose-5-phosphate 3-epimerase. 284 matched cddid_all.tbl CDD PRK13211 PRK13211 237309 PRK13211 N-acetylglucosamine-binding protein GbpA. 478 matched cddid_all.tbl CDD PRK13213 PRK13213 106181 araD L-ribulose-5-phosphate 4-epimerase; Reviewed 231 matched cddid_all.tbl CDD PRK13216 PRK13216 183900 PRK13216 photosystem I reaction center subunit X-like protein; Reviewed 91 matched cddid_all.tbl CDD PRK13222 PRK13222 237310 PRK13222 N-acetylmuramic acid 6-phosphate phosphatase MupP. 226 matched cddid_all.tbl CDD PRK13223 PRK13223 171912 PRK13223 phosphoglycolate phosphatase; Provisional 272 matched cddid_all.tbl CDD PRK13225 PRK13225 106187 PRK13225 phosphoglycolate phosphatase; Provisional 273 matched cddid_all.tbl CDD PRK13226 PRK13226 237311 PRK13226 phosphoglycolate phosphatase; Provisional 229 matched cddid_all.tbl CDD PRK13230 PRK13230 183903 PRK13230 nitrogenase reductase-like protein; Reviewed 279 matched cddid_all.tbl CDD PRK13231 PRK13231 183904 PRK13231 nitrogenase reductase-like protein; Reviewed 264 matched cddid_all.tbl CDD PRK13233 PRK13233 183905 nifH nitrogenase iron protein. 275 matched cddid_all.tbl CDD PRK13238 PRK13238 237314 tnaA tryptophanase. 460 matched cddid_all.tbl CDD PRK13239 PRK13239 183911 PRK13239 alkylmercury lyase MerB. 206 matched cddid_all.tbl CDD PRK13240 PRK13240 183912 pbsY photosystem II protein Y; Reviewed 40 matched cddid_all.tbl CDD PRK13241 PRK13241 183913 ureA urease subunit gamma; Provisional 100 matched cddid_all.tbl CDD PRK13242 PRK13242 139420 ureA urease subunit gamma; Provisional 100 matched cddid_all.tbl CDD PRK13243 PRK13243 183914 PRK13243 glyoxylate reductase; Reviewed 333 matched cddid_all.tbl CDD PRK13244 PRK13244 183915 PRK13244 protease inhibitor. 145 matched cddid_all.tbl CDD PRK13245 PRK13245 183916 hetR heterocyst differentiation control protein; Reviewed 299 matched cddid_all.tbl CDD PRK13246 PRK13246 106208 PRK13246 15,16-dihydrobiliverdin:ferredoxin oxidoreductase. 236 matched cddid_all.tbl CDD PRK13247 PRK13247 237315 PRK13247 15,16-dihydrobiliverdin:ferredoxin oxidoreductase. 238 matched cddid_all.tbl CDD PRK13248 PRK13248 139425 PRK13248 phycoerythrobilin:ferredoxin oxidoreductase; Provisional 253 matched cddid_all.tbl CDD PRK13249 PRK13249 139426 PRK13249 phycoerythrobilin:ferredoxin oxidoreductase; Provisional 257 matched cddid_all.tbl CDD PRK13250 PRK13250 139427 PRK13250 phycoerythrobilin:ferredoxin oxidoreductase; Provisional 248 matched cddid_all.tbl CDD PRK13251 PRK13251 183917 PRK13251 trp RNA-binding attenuation protein MtrB. 75 matched cddid_all.tbl CDD PRK13252 PRK13252 183918 PRK13252 betaine aldehyde dehydrogenase; Provisional 488 matched cddid_all.tbl CDD PRK13253 PRK13253 237316 PRK13253 citrate lyase subunit gamma; Provisional 92 matched cddid_all.tbl CDD PRK13254 PRK13254 237317 PRK13254 cytochrome c maturation protein CcmE. 148 matched cddid_all.tbl CDD PRK13255 PRK13255 183921 PRK13255 thiopurine S-methyltransferase; Reviewed 218 matched cddid_all.tbl CDD PRK13256 PRK13256 237318 PRK13256 thiopurine S-methyltransferase; Reviewed 226 matched cddid_all.tbl CDD PRK13259 PRK13259 237321 PRK13259 septation regulator SpoVG. 94 matched cddid_all.tbl CDD PRK13260 PRK13260 183926 PRK13260 2,3-diketo-L-gulonate reductase; Provisional 332 matched cddid_all.tbl CDD PRK13261 PRK13261 237322 ureE urease accessory protein UreE; Provisional 159 matched cddid_all.tbl CDD PRK13262 PRK13262 183928 ureE urease accessory protein UreE; Provisional 231 matched cddid_all.tbl CDD PRK13263 PRK13263 237323 ureE urease accessory protein UreE; Provisional 206 matched cddid_all.tbl CDD PRK13264 PRK13264 183930 PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional 177 matched cddid_all.tbl CDD PRK13265 PRK13265 183931 PRK13265 glycine/sarcosine/betaine reductase complex protein A; Reviewed 154 matched cddid_all.tbl CDD PRK13267 PRK13267 237325 PRK13267 archaemetzincin-like protein; Reviewed 179 matched cddid_all.tbl CDD PRK13270 PRK13270 183934 treF alpha,alpha-trehalase TreF. 549 matched cddid_all.tbl CDD PRK13271 PRK13271 237326 treA alpha,alpha-trehalase TreA. 569 matched cddid_all.tbl CDD PRK13272 PRK13272 183936 treA alpha,alpha-trehalase TreA. 542 matched cddid_all.tbl CDD PRK13273 PRK13273 237327 mdoD glucan biosynthesis protein D; Provisional 476 matched cddid_all.tbl CDD PRK13274 PRK13274 237328 mdoG glucan biosynthesis protein G; Provisional 516 matched cddid_all.tbl CDD PRK13275 PRK13275 183939 mtrF tetrahydromethanopterin S-methyltransferase subunit F; Provisional 67 matched cddid_all.tbl CDD PRK13276 PRK13276 183940 PRK13276 iron-sulfur cluster repair di-iron protein ScdA. 224 matched cddid_all.tbl CDD PRK13277 PRK13277 183941 PRK13277 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase-like protein; Provisional 366 matched cddid_all.tbl CDD PRK13278 PRK13278 237329 purP formate--phosphoribosylaminoimidazolecarboxamide ligase. 358 matched cddid_all.tbl CDD PRK13279 PRK13279 237330 arnT lipid IV(A) 4-amino-4-deoxy-L-arabinosyltransferase. 552 matched cddid_all.tbl CDD PRK13280 PRK13280 237331 PRK13280 N-glycosylase/DNA lyase; Provisional 269 matched cddid_all.tbl CDD PRK13281 PRK13281 237332 PRK13281 N-succinylarginine dihydrolase. 442 matched cddid_all.tbl CDD PRK13282 PRK13282 183946 PRK13282 flagellar assembly protein FliW; Provisional 128 matched cddid_all.tbl CDD PRK13283 PRK13283 183947 PRK13283 flagellar assembly protein FliW; Provisional 134 matched cddid_all.tbl CDD PRK13284 PRK13284 237333 PRK13284 flagellar assembly protein FliW; Provisional 145 matched cddid_all.tbl CDD PRK13285 PRK13285 237334 PRK13285 flagellar assembly protein FliW; Provisional 148 matched cddid_all.tbl CDD PRK13286 PRK13286 237335 amiE aliphatic amidase. 345 matched cddid_all.tbl CDD PRK13287 PRK13287 183950 amiF formamidase; Provisional 333 matched cddid_all.tbl CDD PRK13288 PRK13288 237336 PRK13288 pyrophosphatase PpaX; Provisional 214 matched cddid_all.tbl CDD PRK13289 PRK13289 237337 PRK13289 NO-inducible flavohemoprotein. 399 matched cddid_all.tbl CDD PRK13290 PRK13290 183953 ectC L-ectoine synthase; Reviewed 125 matched cddid_all.tbl CDD PRK13291 PRK13291 183954 PRK13291 putative metal-dependent hydrolase. 173 matched cddid_all.tbl CDD PRK13292 PRK13292 183955 PRK13292 NADH-quinone oxidoreductase subunit B/C/D. 788 matched cddid_all.tbl CDD PRK13293 PRK13293 183956 PRK13293 F420-0--gamma-glutamyl ligase; Reviewed 245 matched cddid_all.tbl CDD PRK13294 PRK13294 183957 PRK13294 F420-0--gamma-glutamyl ligase; Provisional 448 matched cddid_all.tbl CDD PRK13295 PRK13295 171961 PRK13295 cyclohexanecarboxylate-CoA ligase; Reviewed 547 matched cddid_all.tbl CDD PRK13296 PRK13296 106256 PRK13296 CCA tRNA nucleotidyltransferase. 360 matched cddid_all.tbl CDD PRK13297 PRK13297 139469 PRK13297 tRNA CCA-pyrophosphorylase; Provisional 364 matched cddid_all.tbl CDD PRK13298 PRK13298 237338 PRK13298 tRNA CCA-pyrophosphorylase; Provisional 417 matched cddid_all.tbl CDD PRK13299 PRK13299 237339 PRK13299 tRNA CCA-pyrophosphorylase; Provisional 394 matched cddid_all.tbl CDD PRK13300 PRK13300 237340 PRK13300 CCA tRNA nucleotidyltransferase. 447 matched cddid_all.tbl CDD PRK13301 PRK13301 106261 PRK13301 putative L-aspartate dehydrogenase; Provisional 267 matched cddid_all.tbl CDD PRK13302 PRK13302 237341 PRK13302 aspartate dehydrogenase. 271 matched cddid_all.tbl CDD PRK13303 PRK13303 237342 PRK13303 aspartate dehydrogenase. 265 matched cddid_all.tbl CDD PRK13304 PRK13304 237343 PRK13304 aspartate dehydrogenase. 265 matched cddid_all.tbl CDD PRK13305 PRK13305 183962 sgbH 3-keto-L-gulonate-6-phosphate decarboxylase UlaD. 218 matched cddid_all.tbl CDD PRK13306 PRK13306 237344 ulaD 3-dehydro-L-gulonate-6-phosphate decarboxylase. 216 matched cddid_all.tbl CDD PRK13307 PRK13307 183964 PRK13307 bifunctional 5,6,7,8-tetrahydromethanopterin hydro-lyase/3-hexulose-6-phosphate synthase. 391 matched cddid_all.tbl CDD PRK13308 PRK13308 183965 ureC urease subunit alpha; Reviewed 569 matched cddid_all.tbl CDD PRK13309 PRK13309 183966 ureC urease subunit alpha; Reviewed 572 matched cddid_all.tbl CDD PRK13310 PRK13310 183967 PRK13310 N-acetyl-D-glucosamine kinase; Provisional 303 matched cddid_all.tbl CDD PRK13311 PRK13311 106271 PRK13311 N-acetyl-D-glucosamine kinase; Provisional 256 matched cddid_all.tbl CDD PRK13312 PRK13312 139480 PRK13312 staphylobilin-forming heme oxygenase IsdG. 107 matched cddid_all.tbl CDD PRK13313 PRK13313 183968 PRK13313 staphylobilin-forming heme oxygenase IsdI. 108 matched cddid_all.tbl CDD PRK13314 PRK13314 183969 PRK13314 heme oxygenase. 107 matched cddid_all.tbl CDD PRK13315 PRK13315 237345 PRK13315 heme oxygenase. 107 matched cddid_all.tbl CDD PRK13316 PRK13316 183970 PRK13316 heme oxygenase IsdG. 121 matched cddid_all.tbl CDD PRK13317 PRK13317 237346 PRK13317 pantothenate kinase; Provisional 277 matched cddid_all.tbl CDD PRK13318 PRK13318 237347 PRK13318 type III pantothenate kinase. 258 matched cddid_all.tbl CDD PRK13320 PRK13320 237348 PRK13320 type III pantothenate kinase. 244 matched cddid_all.tbl CDD PRK13321 PRK13321 237349 PRK13321 type III pantothenate kinase. 256 matched cddid_all.tbl CDD PRK13322 PRK13322 237350 PRK13322 pantothenate kinase; Reviewed 246 matched cddid_all.tbl CDD PRK13324 PRK13324 106284 PRK13324 type III pantothenate kinase. 258 matched cddid_all.tbl CDD PRK13325 PRK13325 183976 PRK13325 bifunctional biotin--[acetyl-CoA-carboxylase] ligase/type III pantothenate kinase. 592 matched cddid_all.tbl CDD PRK13326 PRK13326 237351 PRK13326 type III pantothenate kinase. 262 matched cddid_all.tbl CDD PRK13327 PRK13327 183977 PRK13327 type III pantothenate kinase. 242 matched cddid_all.tbl CDD PRK13328 PRK13328 237352 PRK13328 type III pantothenate kinase. 255 matched cddid_all.tbl CDD PRK13329 PRK13329 183979 PRK13329 pantothenate kinase; Reviewed 249 matched cddid_all.tbl CDD PRK13331 PRK13331 237353 PRK13331 pantothenate kinase; Reviewed 251 matched cddid_all.tbl CDD PRK13333 PRK13333 183981 PRK13333 type III pantothenate kinase. 206 matched cddid_all.tbl CDD PRK13335 PRK13335 139494 PRK13335 superantigen-like protein SSL3; Reviewed. 356 matched cddid_all.tbl CDD PRK13337 PRK13337 183982 PRK13337 putative lipid kinase; Reviewed 304 matched cddid_all.tbl CDD PRK13339 PRK13339 183983 PRK13339 malate:quinone oxidoreductase; Reviewed 497 matched cddid_all.tbl CDD PRK13340 PRK13340 183984 PRK13340 alanine racemase; Reviewed 406 matched cddid_all.tbl CDD PRK13341 PRK13341 237354 PRK13341 AAA family ATPase. 725 matched cddid_all.tbl CDD PRK13342 PRK13342 237355 PRK13342 recombination factor protein RarA; Reviewed 413 matched cddid_all.tbl CDD PRK13343 PRK13343 183987 PRK13343 F0F1 ATP synthase subunit alpha; Provisional 502 matched cddid_all.tbl CDD PRK13344 PRK13344 183988 spxA transcriptional regulator Spx; Reviewed 132 matched cddid_all.tbl CDD PRK13345 PRK13345 106303 PRK13345 superantigen-like protein SSL9; Reviewed. 232 matched cddid_all.tbl CDD PRK13346 PRK13346 106304 PRK13346 superantigen-like protein SSL7; Reviewed. 231 matched cddid_all.tbl CDD PRK13347 PRK13347 237356 PRK13347 coproporphyrinogen III oxidase; Provisional 453 matched cddid_all.tbl CDD PRK13348 PRK13348 237357 PRK13348 HTH-type transcriptional regulator ArgP. 294 matched cddid_all.tbl CDD PRK13349 PRK13349 106307 PRK13349 superantigen-like protein SSL13; Reviewed. 241 matched cddid_all.tbl CDD PRK13350 PRK13350 171995 PRK13350 superantigen-like protein SSL12; Reviewed. 238 matched cddid_all.tbl CDD PRK13351 PRK13351 237358 PRK13351 elongation factor G-like protein. 687 matched cddid_all.tbl CDD PRK13352 PRK13352 237359 PRK13352 phosphomethylpyrimidine synthase ThiC. 431 matched cddid_all.tbl CDD PRK13353 PRK13353 183992 PRK13353 aspartate ammonia-lyase; Provisional 473 matched cddid_all.tbl CDD PRK13354 PRK13354 237360 PRK13354 tyrosyl-tRNA synthetase; Provisional 410 matched cddid_all.tbl CDD PRK13355 PRK13355 237361 PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional 517 matched cddid_all.tbl CDD PRK13356 PRK13356 237362 PRK13356 branched-chain amino acid aminotransferase. 286 matched cddid_all.tbl CDD PRK13357 PRK13357 237363 PRK13357 branched-chain amino acid aminotransferase; Provisional 356 matched cddid_all.tbl CDD PRK13358 PRK13358 183997 PRK13358 protocatechuate 4,5-dioxygenase subunit beta; Provisional 269 matched cddid_all.tbl CDD PRK13360 PRK13360 183999 PRK13360 omega amino acid--pyruvate transaminase; Provisional 442 matched cddid_all.tbl CDD PRK13363 PRK13363 184002 PRK13363 protocatechuate 4,5-dioxygenase subunit beta; Provisional 335 matched cddid_all.tbl CDD PRK13364 PRK13364 184003 PRK13364 protocatechuate 4,5-dioxygenase subunit beta; Provisional 278 matched cddid_all.tbl CDD PRK13365 PRK13365 184004 PRK13365 protocatechuate 4,5-dioxygenase subunit beta; Provisional 279 matched cddid_all.tbl CDD PRK13366 PRK13366 184005 PRK13366 protocatechuate 4,5-dioxygenase subunit beta; Provisional 284 matched cddid_all.tbl CDD PRK13367 PRK13367 184006 PRK13367 gallate dioxygenase. 420 matched cddid_all.tbl CDD PRK13368 PRK13368 184007 PRK13368 3-deoxy-manno-octulosonate cytidylyltransferase; Provisional 238 matched cddid_all.tbl CDD PRK13369 PRK13369 237365 PRK13369 glycerol-3-phosphate dehydrogenase; Provisional 502 matched cddid_all.tbl CDD PRK13370 PRK13370 237366 mhpB 3-carboxyethylcatechol 2,3-dioxygenase. 313 matched cddid_all.tbl CDD PRK13371 PRK13371 237367 PRK13371 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional 387 matched cddid_all.tbl CDD PRK13372 PRK13372 106330 pcmA protocatechuate 4,5-dioxygenase subunit alpha/beta. 444 matched cddid_all.tbl CDD PRK13373 PRK13373 106331 PRK13373 putative dioxygenase; Provisional 344 matched cddid_all.tbl CDD PRK13374 PRK13374 237368 PRK13374 DeoD-type purine-nucleoside phosphorylase. 233 matched cddid_all.tbl CDD PRK13375 PRK13375 172015 pimE mannosyltransferase; Provisional 409 matched cddid_all.tbl CDD PRK13376 PRK13376 237369 pyrB bifunctional aspartate carbamoyltransferase catalytic subunit/aspartate carbamoyltransferase regulatory subunit; Provisional 525 matched cddid_all.tbl CDD PRK13377 PRK13377 184013 PRK13377 protocatechuate 4,5-dioxygenase subunit alpha; Provisional 129 matched cddid_all.tbl CDD PRK13378 PRK13378 139527 PRK13378 protocatechuate 4,5-dioxygenase subunit alpha; Provisional 117 matched cddid_all.tbl CDD PRK13379 PRK13379 184014 PRK13379 protocatechuate 4,5-dioxygenase subunit alpha; Provisional 119 matched cddid_all.tbl CDD PRK13380 PRK13380 237370 PRK13380 glycine cleavage system protein H; Provisional 144 matched cddid_all.tbl CDD PRK13381 PRK13381 237371 PRK13381 peptidase T; Provisional 404 matched cddid_all.tbl CDD PRK13382 PRK13382 172019 PRK13382 bile acid CoA ligase. 537 matched cddid_all.tbl CDD PRK13383 PRK13383 139531 PRK13383 acyl-CoA synthetase; Provisional 516 matched cddid_all.tbl CDD PRK13384 PRK13384 172020 PRK13384 porphobilinogen synthase. 322 matched cddid_all.tbl CDD PRK13385 PRK13385 184017 PRK13385 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase; Provisional 230 matched cddid_all.tbl CDD PRK13386 PRK13386 237372 fliH flagellar assembly protein H; Provisional 236 matched cddid_all.tbl CDD PRK13387 PRK13387 237373 PRK13387 1,4-dihydroxy-2-naphthoate octaprenyltransferase; Provisional 317 matched cddid_all.tbl CDD PRK13388 PRK13388 237374 PRK13388 acyl-CoA synthetase; Provisional 540 matched cddid_all.tbl CDD PRK13389 PRK13389 184021 PRK13389 UTP--glucose-1-phosphate uridylyltransferase GalU. 302 matched cddid_all.tbl CDD PRK13390 PRK13390 139538 PRK13390 acyl-CoA synthetase; Provisional 501 matched cddid_all.tbl CDD PRK13391 PRK13391 184022 PRK13391 acyl-CoA synthetase; Provisional 511 matched cddid_all.tbl CDD PRK13392 PRK13392 184023 PRK13392 5-aminolevulinate synthase; Provisional 410 matched cddid_all.tbl CDD PRK13394 PRK13394 184025 PRK13394 3-hydroxybutyrate dehydrogenase; Provisional 262 matched cddid_all.tbl CDD PRK13395 PRK13395 237375 PRK13395 ureidoglycolate lyase. 171 matched cddid_all.tbl CDD PRK13396 PRK13396 237376 PRK13396 3-deoxy-7-phosphoheptulonate synthase; Provisional 352 matched cddid_all.tbl CDD PRK13399 PRK13399 184029 PRK13399 fructose-bisphosphate aldolase class II. 347 matched cddid_all.tbl CDD PRK13403 PRK13403 106361 PRK13403 ketol-acid reductoisomerase; Provisional 335 matched cddid_all.tbl CDD PRK13404 PRK13404 184033 PRK13404 dihydropyrimidinase; Provisional 477 matched cddid_all.tbl CDD PRK13405 PRK13405 237377 bchH magnesium chelatase subunit H; Provisional 1209 matched cddid_all.tbl CDD PRK13406 PRK13406 237378 bchD magnesium chelatase subunit D; Provisional 584 matched cddid_all.tbl CDD PRK13409 PRK13409 184037 PRK13409 ribosome biogenesis/translation initiation ATPase RLI. 590 matched cddid_all.tbl CDD PRK13410 PRK13410 184038 PRK13410 molecular chaperone DnaK; Provisional 668 matched cddid_all.tbl CDD PRK13411 PRK13411 184039 PRK13411 molecular chaperone DnaK; Provisional 653 matched cddid_all.tbl CDD PRK13412 PRK13412 237379 fkp bifunctional fucokinase/L-fucose-1-P-guanylyltransferase; Provisional 974 matched cddid_all.tbl CDD PRK13413 PRK13413 184041 mpi master DNA invertase Mpi family serine-type recombinase. 200 matched cddid_all.tbl CDD PRK13414 PRK13414 139556 PRK13414 flagellar biosynthesis protein FliZ; Provisional 209 matched cddid_all.tbl CDD PRK13415 PRK13415 184042 PRK13415 flagella biosynthesis protein FliZ; Provisional 219 matched cddid_all.tbl CDD PRK13417 PRK13417 237380 PRK13417 F0F1 ATP synthase subunit A; Provisional 352 matched cddid_all.tbl CDD PRK13419 PRK13419 237381 PRK13419 F0F1 ATP synthase subunit A; Provisional 342 matched cddid_all.tbl CDD PRK13420 PRK13420 237382 PRK13420 F0F1 ATP synthase subunit A; Provisional 226 matched cddid_all.tbl CDD PRK13421 PRK13421 237383 PRK13421 F0F1 ATP synthase subunit A; Provisional 223 matched cddid_all.tbl CDD PRK13422 PRK13422 184046 PRK13422 F0F1 ATP synthase subunit gamma; Provisional 298 matched cddid_all.tbl CDD PRK13423 PRK13423 237384 PRK13423 F0F1 ATP synthase subunit gamma; Provisional 288 matched cddid_all.tbl CDD PRK13424 PRK13424 172047 PRK13424 F0F1 ATP synthase subunit gamma; Provisional 291 matched cddid_all.tbl CDD PRK13425 PRK13425 139564 PRK13425 F0F1 ATP synthase subunit gamma; Provisional 291 matched cddid_all.tbl CDD PRK13426 PRK13426 237385 PRK13426 F0F1 ATP synthase subunit gamma; Provisional 291 matched cddid_all.tbl CDD PRK13427 PRK13427 172049 PRK13427 F0F1 ATP synthase subunit gamma; Provisional 289 matched cddid_all.tbl CDD PRK13428 PRK13428 184048 PRK13428 F0F1 ATP synthase subunit delta; Provisional 445 matched cddid_all.tbl CDD PRK13429 PRK13429 237386 PRK13429 F0F1 ATP synthase subunit delta; Provisional 181 matched cddid_all.tbl CDD PRK13430 PRK13430 237387 PRK13430 F0F1 ATP synthase subunit delta; Provisional 271 matched cddid_all.tbl CDD PRK13431 PRK13431 184051 PRK13431 F0F1 ATP synthase subunit delta; Provisional 180 matched cddid_all.tbl CDD PRK13434 PRK13434 139571 PRK13434 F0F1 ATP synthase subunit delta; Provisional 184 matched cddid_all.tbl CDD PRK13435 PRK13435 184052 PRK13435 response regulator; Provisional 145 matched cddid_all.tbl CDD PRK13436 PRK13436 184053 PRK13436 F0F1 ATP synthase subunit delta; Provisional 179 matched cddid_all.tbl CDD PRK13441 PRK13441 184054 PRK13441 F0F1 ATP synthase subunit delta; Provisional 180 matched cddid_all.tbl CDD PRK13442 PRK13442 184055 atpC F0F1 ATP synthase subunit epsilon; Provisional 89 matched cddid_all.tbl CDD PRK13443 PRK13443 237388 atpC F0F1 ATP synthase subunit epsilon; Provisional 136 matched cddid_all.tbl CDD PRK13444 PRK13444 139576 atpC F0F1 ATP synthase subunit epsilon; Provisional 127 matched cddid_all.tbl CDD PRK13446 PRK13446 184056 atpC F0F1 ATP synthase subunit epsilon; Provisional 136 matched cddid_all.tbl CDD PRK13447 PRK13447 184057 PRK13447 F0F1 ATP synthase subunit epsilon; Provisional 136 matched cddid_all.tbl CDD PRK13448 PRK13448 139579 atpC F0F1 ATP synthase subunit epsilon; Provisional 135 matched cddid_all.tbl CDD PRK13449 PRK13449 184058 atpC ATP synthase F1 subunit epsilon. 88 matched cddid_all.tbl CDD PRK13450 PRK13450 184059 atpC F0F1 ATP synthase subunit epsilon; Provisional 132 matched cddid_all.tbl CDD PRK13451 PRK13451 172059 atpC F0F1 ATP synthase subunit epsilon; Provisional 101 matched cddid_all.tbl CDD PRK13452 PRK13452 106409 atpC F0F1 ATP synthase subunit epsilon; Provisional 145 matched cddid_all.tbl CDD PRK13453 PRK13453 184060 PRK13453 F0F1 ATP synthase subunit B; Provisional 173 matched cddid_all.tbl CDD PRK13454 PRK13454 184061 PRK13454 F0F1 ATP synthase subunit B'; Provisional 181 matched cddid_all.tbl CDD PRK13455 PRK13455 184062 PRK13455 F0F1 ATP synthase subunit B; Provisional 184 matched cddid_all.tbl CDD PRK13456 PRK13456 237389 PRK13456 DNA protection protein DPS; Provisional 186 matched cddid_all.tbl CDD PRK13460 PRK13460 139585 PRK13460 F0F1 ATP synthase subunit B; Provisional 173 matched cddid_all.tbl CDD PRK13461 PRK13461 184064 PRK13461 F0F1 ATP synthase subunit B; Provisional 159 matched cddid_all.tbl CDD PRK13462 PRK13462 139587 PRK13462 acid phosphatase; Provisional 203 matched cddid_all.tbl CDD PRK13463 PRK13463 172065 PRK13463 phosphoserine phosphatase 1. 203 matched cddid_all.tbl CDD PRK13464 PRK13464 184065 PRK13464 F0F1 ATP synthase subunit B. 101 matched cddid_all.tbl CDD PRK13466 PRK13466 172066 PRK13466 F0F1 ATP synthase subunit C; Provisional 66 matched cddid_all.tbl CDD PRK13467 PRK13467 237390 PRK13467 F0F1 ATP synthase subunit C; Provisional 66 matched cddid_all.tbl CDD PRK13468 PRK13468 184067 PRK13468 F0F1 ATP synthase subunit C; Provisional 82 matched cddid_all.tbl CDD PRK13469 PRK13469 184068 PRK13469 F0F1 ATP synthase subunit C; Provisional 79 matched cddid_all.tbl CDD PRK13471 PRK13471 184069 PRK13471 F0F1 ATP synthase subunit C; Provisional 85 matched cddid_all.tbl CDD PRK13473 PRK13473 237391 PRK13473 aminobutyraldehyde dehydrogenase. 475 matched cddid_all.tbl CDD PRK13474 PRK13474 237392 PRK13474 cytochrome b6-f complex iron-sulfur subunit; Provisional 178 matched cddid_all.tbl CDD PRK13475 PRK13475 184072 PRK13475 ribulose-bisphosphate carboxylase. 443 matched cddid_all.tbl CDD PRK13477 PRK13477 237393 PRK13477 bifunctional pantoate--beta-alanine ligase/(d)CMP kinase. 512 matched cddid_all.tbl CDD PRK13478 PRK13478 184075 PRK13478 phosphonoacetaldehyde hydrolase; Provisional 267 matched cddid_all.tbl CDD PRK13479 PRK13479 184076 PRK13479 2-aminoethylphosphonate--pyruvate transaminase; Provisional 368 matched cddid_all.tbl CDD PRK13480 PRK13480 237394 PRK13480 3'-5' exoribonuclease YhaM; Provisional 314 matched cddid_all.tbl CDD PRK13481 PRK13481 184078 PRK13481 glycosyltransferase; Provisional 232 matched cddid_all.tbl CDD PRK13482 PRK13482 237395 PRK13482 DNA integrity scanning protein DisA; Provisional 352 matched cddid_all.tbl CDD PRK13483 PRK13483 184080 PRK13483 ligand-gated channel protein. 660 matched cddid_all.tbl CDD PRK13484 PRK13484 139605 PRK13484 IreA family TonB-dependent siderophore receptor. 682 matched cddid_all.tbl CDD PRK13486 PRK13486 139606 PRK13486 TonB-dependent receptor. 696 matched cddid_all.tbl CDD PRK13487 PRK13487 237396 PRK13487 chemoreceptor glutamine deamidase CheD; Provisional 201 matched cddid_all.tbl CDD PRK13488 PRK13488 237397 PRK13488 chemoreceptor glutamine deamidase CheD; Provisional 157 matched cddid_all.tbl CDD PRK13489 PRK13489 237398 PRK13489 chemoreceptor glutamine deamidase CheD; Provisional 233 matched cddid_all.tbl CDD PRK13490 PRK13490 184084 PRK13490 chemoreceptor glutamine deamidase CheD; Provisional 162 matched cddid_all.tbl CDD PRK13491 PRK13491 184085 PRK13491 chemoreceptor glutamine deamidase CheD; Provisional 199 matched cddid_all.tbl CDD PRK13493 PRK13493 184086 PRK13493 chemoreceptor glutamine deamidase CheD; Provisional 213 matched cddid_all.tbl CDD PRK13494 PRK13494 184087 PRK13494 chemoreceptor glutamine deamidase CheD; Provisional 163 matched cddid_all.tbl CDD PRK13495 PRK13495 184088 PRK13495 chemoreceptor glutamine deamidase CheD; Provisional 159 matched cddid_all.tbl CDD PRK13497 PRK13497 237399 PRK13497 chemoreceptor glutamine deamidase CheD; Provisional 184 matched cddid_all.tbl CDD PRK13498 PRK13498 237400 PRK13498 chemoreceptor glutamine deamidase CheD; Provisional 167 matched cddid_all.tbl CDD PRK13499 PRK13499 237401 PRK13499 L-rhamnose/proton symporter RhaT. 345 matched cddid_all.tbl CDD PRK13500 PRK13500 184091 PRK13500 HTH-type transcriptional activator RhaR. 312 matched cddid_all.tbl CDD PRK13501 PRK13501 184092 PRK13501 HTH-type transcriptional activator RhaR. 290 matched cddid_all.tbl CDD PRK13502 PRK13502 184093 PRK13502 HTH-type transcriptional activator RhaR. 282 matched cddid_all.tbl CDD PRK13503 PRK13503 184094 PRK13503 HTH-type transcriptional activator RhaS. 278 matched cddid_all.tbl CDD PRK13504 PRK13504 237402 PRK13504 NADPH-dependent assimilatory sulfite reductase hemoprotein subunit. 569 matched cddid_all.tbl CDD PRK13505 PRK13505 237403 PRK13505 formate--tetrahydrofolate ligase; Provisional 557 matched cddid_all.tbl CDD PRK13506 PRK13506 237404 PRK13506 formate--tetrahydrofolate ligase; Provisional 578 matched cddid_all.tbl CDD PRK13507 PRK13507 184098 PRK13507 formate--tetrahydrofolate ligase; Provisional 587 matched cddid_all.tbl CDD PRK13508 PRK13508 237405 PRK13508 tagatose-6-phosphate kinase; Provisional 309 matched cddid_all.tbl CDD PRK13509 PRK13509 184100 PRK13509 HTH-type transcriptional regulator UlaR. 251 matched cddid_all.tbl CDD PRK13510 PRK13510 184101 PRK13510 sulfurtransferase complex subunit TusB. 95 matched cddid_all.tbl CDD PRK13511 PRK13511 184102 PRK13511 6-phospho-beta-galactosidase; Provisional 469 matched cddid_all.tbl CDD PRK13512 PRK13512 184103 PRK13512 coenzyme A disulfide reductase; Provisional 438 matched cddid_all.tbl CDD PRK13513 PRK13513 184104 PRK13513 ligand-gated channel protein. 659 matched cddid_all.tbl CDD PRK13515 PRK13515 237406 PRK13515 carboxylate-amine ligase; Provisional 371 matched cddid_all.tbl CDD PRK13516 PRK13516 237407 PRK13516 gamma-glutamyl:cysteine ligase; Provisional 373 matched cddid_all.tbl CDD PRK13517 PRK13517 237408 PRK13517 glutamate--cysteine ligase. 373 matched cddid_all.tbl CDD PRK13518 PRK13518 184108 PRK13518 glutamate--cysteine ligase. 357 matched cddid_all.tbl CDD PRK13523 PRK13523 184110 PRK13523 NADPH dehydrogenase NamA; Provisional 337 matched cddid_all.tbl CDD PRK13524 PRK13524 237410 PRK13524 FepA family TonB-dependent siderophore receptor. 744 matched cddid_all.tbl CDD PRK13525 PRK13525 237411 PRK13525 pyridoxal 5'-phosphate synthase glutaminase subunit PdxT. 189 matched cddid_all.tbl CDD PRK13526 PRK13526 184113 PRK13526 glutamine amidotransferase subunit PdxT; Provisional 179 matched cddid_all.tbl CDD PRK13527 PRK13527 237412 PRK13527 glutamine amidotransferase subunit PdxT; Provisional 200 matched cddid_all.tbl CDD PRK13528 PRK13528 237413 PRK13528 outer membrane receptor FepA; Provisional 727 matched cddid_all.tbl CDD PRK13529 PRK13529 237414 PRK13529 oxaloacetate-decarboxylating malate dehydrogenase. 563 matched cddid_all.tbl CDD PRK13530 PRK13530 237415 PRK13530 arsenate reductase (thioredoxin). 133 matched cddid_all.tbl CDD PRK13531 PRK13531 184118 PRK13531 regulatory ATPase RavA; Provisional 498 matched cddid_all.tbl CDD PRK13532 PRK13532 237416 PRK13532 nitrate reductase catalytic subunit NapA. 830 matched cddid_all.tbl CDD PRK13535 PRK13535 184122 PRK13535 erythrose 4-phosphate dehydrogenase; Provisional 336 matched cddid_all.tbl CDD PRK13536 PRK13536 237419 PRK13536 nodulation factor ABC transporter ATP-binding protein NodI. 340 matched cddid_all.tbl CDD PRK13537 PRK13537 237420 PRK13537 nodulation factor ABC transporter ATP-binding protein NodI. 306 matched cddid_all.tbl CDD PRK13538 PRK13538 184125 PRK13538 cytochrome c biogenesis heme-transporting ATPase CcmA. 204 matched cddid_all.tbl CDD PRK13539 PRK13539 237421 PRK13539 cytochrome c biogenesis protein CcmA; Provisional 207 matched cddid_all.tbl CDD PRK13540 PRK13540 184127 PRK13540 cytochrome c biogenesis protein CcmA; Provisional 200 matched cddid_all.tbl CDD PRK13541 PRK13541 184128 PRK13541 cytochrome c biogenesis protein CcmA; Provisional 195 matched cddid_all.tbl CDD PRK13543 PRK13543 184129 PRK13543 heme ABC exporter ATP-binding protein CcmA. 214 matched cddid_all.tbl CDD PRK13545 PRK13545 184130 tagH teichoic acids export protein ATP-binding subunit; Provisional 549 matched cddid_all.tbl CDD PRK13546 PRK13546 184131 PRK13546 teichoic acids export ABC transporter ATP-binding subunit TagH. 264 matched cddid_all.tbl CDD PRK13547 PRK13547 184132 hmuV heme ABC transporter ATP-binding protein. 272 matched cddid_all.tbl CDD PRK13548 PRK13548 237422 hmuV hemin importer ATP-binding subunit; Provisional 258 matched cddid_all.tbl CDD PRK13549 PRK13549 184134 PRK13549 xylose transporter ATP-binding subunit; Provisional 506 matched cddid_all.tbl CDD PRK13551 PRK13551 184135 PRK13551 agmatine deiminase; Provisional 362 matched cddid_all.tbl CDD PRK13552 PRK13552 184136 frdB fumarate reductase iron-sulfur subunit; Provisional 239 matched cddid_all.tbl CDD PRK13553 PRK13553 237423 PRK13553 fumarate reductase cytochrome b subunit. 258 matched cddid_all.tbl CDD PRK13554 PRK13554 237424 PRK13554 fumarate reductase cytochrome b-556 subunit; Provisional 241 matched cddid_all.tbl CDD PRK13555 PRK13555 184139 PRK13555 FMN-dependent NADH-azoreductase. 208 matched cddid_all.tbl CDD PRK13556 PRK13556 184140 PRK13556 FMN-dependent NADH-azoreductase. 208 matched cddid_all.tbl CDD PRK13557 PRK13557 237425 PRK13557 histidine kinase; Provisional 540 matched cddid_all.tbl CDD PRK13558 PRK13558 237426 PRK13558 bacterio-opsin activator; Provisional 665 matched cddid_all.tbl CDD PRK13559 PRK13559 237427 PRK13559 hypothetical protein; Provisional 361 matched cddid_all.tbl CDD PRK13560 PRK13560 106506 PRK13560 hypothetical protein; Provisional 807 matched cddid_all.tbl CDD PRK13561 PRK13561 184143 PRK13561 putative diguanylate cyclase; Provisional 651 matched cddid_all.tbl CDD PRK13562 PRK13562 184144 PRK13562 ACT domain-containing protein. 84 matched cddid_all.tbl CDD PRK13564 PRK13564 237428 PRK13564 anthranilate synthase component 1. 520 matched cddid_all.tbl CDD PRK13566 PRK13566 237429 PRK13566 anthranilate synthase component I. 720 matched cddid_all.tbl CDD PRK13567 PRK13567 184148 PRK13567 anthranilate synthase component I; Provisional 468 matched cddid_all.tbl CDD PRK13568 PRK13568 237430 hofQ DNA uptake porin HofQ. 381 matched cddid_all.tbl CDD PRK13571 PRK13571 184152 PRK13571 anthranilate synthase component I; Provisional 506 matched cddid_all.tbl CDD PRK13572 PRK13572 237432 PRK13572 anthranilate synthase component I; Provisional 435 matched cddid_all.tbl CDD PRK13574 PRK13574 184155 PRK13574 anthranilate synthase component I; Provisional 420 matched cddid_all.tbl CDD PRK13576 PRK13576 237433 PRK13576 type I 3-dehydroquinate dehydratase. 216 matched cddid_all.tbl CDD PRK13577 PRK13577 184158 PRK13577 diaminopimelate epimerase; Provisional 281 matched cddid_all.tbl CDD PRK13578 PRK13578 237434 PRK13578 ornithine decarboxylase; Provisional 720 matched cddid_all.tbl CDD PRK13579 PRK13579 237435 gcvT glycine cleavage system aminomethyltransferase GcvT. 370 matched cddid_all.tbl CDD PRK13580 PRK13580 184161 PRK13580 glycine hydroxymethyltransferase. 493 matched cddid_all.tbl CDD PRK13582 PRK13582 237437 thrH bifunctional phosphoserine phosphatase/homoserine phosphotransferase ThrH. 205 matched cddid_all.tbl CDD PRK13585 PRK13585 184165 PRK13585 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase. 241 matched cddid_all.tbl CDD PRK13586 PRK13586 237439 PRK13586 1-(5-phosphoribosyl)-5- ((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase. 232 matched cddid_all.tbl CDD PRK13587 PRK13587 172156 PRK13587 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Provisional 234 matched cddid_all.tbl CDD PRK13588 PRK13588 237440 PRK13588 flagellin B; Provisional 514 matched cddid_all.tbl CDD PRK13589 PRK13589 172158 PRK13589 flagellin A. 576 matched cddid_all.tbl CDD PRK13590 PRK13590 184168 PRK13590 putative bifunctional OHCU decarboxylase/allantoate amidohydrolase; Provisional 591 matched cddid_all.tbl CDD PRK13591 PRK13591 184169 ubiA prenyltransferase; Provisional 307 matched cddid_all.tbl CDD PRK13592 PRK13592 139690 ubiA prenyltransferase; Provisional 299 matched cddid_all.tbl CDD PRK13595 PRK13595 172161 ubiA prenyltransferase; Provisional 292 matched cddid_all.tbl CDD PRK13596 PRK13596 237441 PRK13596 NADH-quinone oxidoreductase subunit NuoF. 433 matched cddid_all.tbl CDD PRK13598 PRK13598 184171 hisB imidazoleglycerol-phosphate dehydratase; Provisional 193 matched cddid_all.tbl CDD PRK13599 PRK13599 106544 PRK13599 peroxiredoxin. 215 matched cddid_all.tbl CDD PRK13600 PRK13600 184172 PRK13600 putative ribosomal protein L7Ae-like; Provisional 84 matched cddid_all.tbl CDD PRK13601 PRK13601 184173 PRK13601 putative L7Ae-like ribosomal protein; Provisional 82 matched cddid_all.tbl CDD PRK13602 PRK13602 184174 PRK13602 50S ribosomal protein L7ae-like protein. 82 matched cddid_all.tbl CDD PRK13603 PRK13603 172166 PRK13603 fumarate reductase subunit C; Provisional 126 matched cddid_all.tbl CDD PRK13604 PRK13604 184175 luxD acyl transferase; Provisional 307 matched cddid_all.tbl CDD PRK13605 PRK13605 237442 PRK13605 endoribonuclease SymE; Provisional 113 matched cddid_all.tbl CDD PRK13607 PRK13607 237444 PRK13607 proline dipeptidase; Provisional 443 matched cddid_all.tbl CDD PRK13608 PRK13608 184179 PRK13608 diacylglycerol glucosyltransferase; Provisional 391 matched cddid_all.tbl CDD PRK13609 PRK13609 237445 PRK13609 diacylglycerol glucosyltransferase; Provisional 380 matched cddid_all.tbl CDD PRK13610 PRK13610 139699 PRK13610 photosystem II reaction center protein Psb28; Provisional 113 matched cddid_all.tbl CDD PRK13611 PRK13611 106556 PRK13611 photosystem II reaction center protein Psb28; Provisional 104 matched cddid_all.tbl CDD PRK13612 PRK13612 237446 PRK13612 photosystem II reaction center protein Psb28; Provisional 113 matched cddid_all.tbl CDD PRK13613 PRK13613 237447 PRK13613 lipoprotein LpqB; Provisional 599 matched cddid_all.tbl CDD PRK13614 PRK13614 237448 PRK13614 lipoprotein LpqB; Provisional 573 matched cddid_all.tbl CDD PRK13615 PRK13615 184183 PRK13615 lipoprotein LpqB; Provisional 557 matched cddid_all.tbl CDD PRK13616 PRK13616 237449 PRK13616 MtrAB system accessory protein LpqB. 591 matched cddid_all.tbl CDD PRK13620 PRK13620 139707 psbV cytochrome c-550; Provisional 215 matched cddid_all.tbl CDD PRK13621 PRK13621 237450 psbV cytochrome c-550; Provisional 170 matched cddid_all.tbl CDD PRK13623 PRK13623 184186 PRK13623 iron-sulfur cluster insertion protein ErpA; Provisional 115 matched cddid_all.tbl CDD PRK13625 PRK13625 184187 PRK13625 bis(5'-nucleosyl)-tetraphosphatase PrpE; Provisional 245 matched cddid_all.tbl CDD PRK13626 PRK13626 184188 PRK13626 HTH-type transcriptional regulator SgrR. 552 matched cddid_all.tbl CDD PRK13627 PRK13627 184189 PRK13627 carnitine operon protein CaiE; Provisional 196 matched cddid_all.tbl CDD PRK13628 PRK13628 184190 PRK13628 serine/threonine transporter SstT; Provisional 402 matched cddid_all.tbl CDD PRK13629 PRK13629 184191 PRK13629 threonine/serine transporter TdcC; Provisional 443 matched cddid_all.tbl CDD PRK13631 PRK13631 237451 cbiO cobalt transporter ATP-binding subunit; Provisional 320 matched cddid_all.tbl CDD PRK13632 PRK13632 237452 cbiO cobalt transporter ATP-binding subunit; Provisional 271 matched cddid_all.tbl CDD PRK13633 PRK13633 237453 PRK13633 energy-coupling factor transporter ATPase. 280 matched cddid_all.tbl CDD PRK13634 PRK13634 237454 cbiO cobalt transporter ATP-binding subunit; Provisional 290 matched cddid_all.tbl CDD PRK13635 PRK13635 184195 cbiO energy-coupling factor ABC transporter ATP-binding protein. 279 matched cddid_all.tbl CDD PRK13636 PRK13636 184196 cbiO cobalt transporter ATP-binding subunit; Provisional 283 matched cddid_all.tbl CDD PRK13637 PRK13637 237455 cbiO energy-coupling factor transporter ATPase. 287 matched cddid_all.tbl CDD PRK13638 PRK13638 184198 cbiO energy-coupling factor ABC transporter ATP-binding protein. 271 matched cddid_all.tbl CDD PRK13639 PRK13639 184199 cbiO cobalt transporter ATP-binding subunit; Provisional 275 matched cddid_all.tbl CDD PRK13640 PRK13640 184200 cbiO energy-coupling factor transporter ATPase. 282 matched cddid_all.tbl CDD PRK13641 PRK13641 237456 cbiO energy-coupling factor transporter ATPase. 287 matched cddid_all.tbl CDD PRK13642 PRK13642 184202 cbiO energy-coupling factor transporter ATPase. 277 matched cddid_all.tbl CDD PRK13643 PRK13643 184203 cbiO energy-coupling factor transporter ATPase. 288 matched cddid_all.tbl CDD PRK13644 PRK13644 106587 cbiO energy-coupling factor transporter ATPase. 274 matched cddid_all.tbl CDD PRK13645 PRK13645 184204 cbiO energy-coupling factor transporter ATPase. 289 matched cddid_all.tbl CDD PRK13646 PRK13646 184205 cbiO energy-coupling factor transporter ATPase. 286 matched cddid_all.tbl CDD PRK13647 PRK13647 237457 cbiO cobalt transporter ATP-binding subunit; Provisional 274 matched cddid_all.tbl CDD PRK13648 PRK13648 184207 cbiO cobalt transporter ATP-binding subunit; Provisional 269 matched cddid_all.tbl CDD PRK13649 PRK13649 184208 cbiO energy-coupling factor transporter ATPase. 280 matched cddid_all.tbl CDD PRK13650 PRK13650 184209 cbiO energy-coupling factor transporter ATPase. 279 matched cddid_all.tbl CDD PRK13651 PRK13651 184210 PRK13651 cobalt transporter ATP-binding subunit; Provisional 305 matched cddid_all.tbl CDD PRK13652 PRK13652 172200 cbiO cobalt transporter ATP-binding subunit; Provisional 277 matched cddid_all.tbl CDD PRK13654 PRK13654 237458 PRK13654 magnesium-protoporphyrin IX monomethyl ester cyclase; Provisional 355 matched cddid_all.tbl CDD PRK13655 PRK13655 237459 PRK13655 phosphoenolpyruvate carboxylase; Provisional 494 matched cddid_all.tbl CDD PRK13656 PRK13656 237460 PRK13656 enoyl-[acyl-carrier-protein] reductase FabV. 398 matched cddid_all.tbl CDD PRK13657 PRK13657 184214 PRK13657 glucan ABC transporter ATP-binding protein/ permease. 588 matched cddid_all.tbl CDD PRK13658 PRK13658 184215 PRK13658 hypothetical protein; Provisional 59 matched cddid_all.tbl CDD PRK13659 PRK13659 184216 PRK13659 DUF1283 family protein. 103 matched cddid_all.tbl CDD PRK13660 PRK13660 237461 PRK13660 hypothetical protein; Provisional 182 matched cddid_all.tbl CDD PRK13661 PRK13661 184218 PRK13661 ECF-type riboflavin transporter substrate-binding protein. 182 matched cddid_all.tbl CDD PRK13662 PRK13662 184219 PRK13662 hypothetical protein; Provisional 177 matched cddid_all.tbl CDD PRK13663 PRK13663 184220 PRK13663 hypothetical protein; Provisional 493 matched cddid_all.tbl CDD PRK13664 PRK13664 184221 PRK13664 hypothetical protein; Provisional 62 matched cddid_all.tbl CDD PRK13665 PRK13665 237462 PRK13665 hypothetical protein; Provisional 316 matched cddid_all.tbl CDD PRK13666 PRK13666 184223 PRK13666 hypothetical protein; Provisional 92 matched cddid_all.tbl CDD PRK13667 PRK13667 184224 PRK13667 hypothetical protein; Provisional 70 matched cddid_all.tbl CDD PRK13668 PRK13668 237463 PRK13668 hypothetical protein; Provisional 267 matched cddid_all.tbl CDD PRK13669 PRK13669 184226 PRK13669 hypothetical protein; Provisional 78 matched cddid_all.tbl CDD PRK13670 PRK13670 237464 PRK13670 nucleotidyltransferase. 388 matched cddid_all.tbl CDD PRK13671 PRK13671 184228 PRK13671 nucleotidyltransferase. 298 matched cddid_all.tbl CDD PRK13672 PRK13672 184229 PRK13672 hypothetical protein; Provisional 71 matched cddid_all.tbl CDD PRK13673 PRK13673 237465 PRK13673 hypothetical protein; Provisional 118 matched cddid_all.tbl CDD PRK13674 PRK13674 237466 PRK13674 GTP cyclohydrolase I FolE2. 271 matched cddid_all.tbl CDD PRK13675 PRK13675 184232 PRK13675 GTP cyclohydrolase; Provisional 308 matched cddid_all.tbl CDD PRK13676 PRK13676 237467 PRK13676 YlbF/YmcA family competence regulator. 114 matched cddid_all.tbl CDD PRK13677 PRK13677 184234 PRK13677 DUF3461 family protein. 125 matched cddid_all.tbl CDD PRK13678 PRK13678 184235 PRK13678 hypothetical protein; Provisional 95 matched cddid_all.tbl CDD PRK13679 PRK13679 184236 PRK13679 hypothetical protein; Provisional 168 matched cddid_all.tbl CDD PRK13680 PRK13680 184237 PRK13680 hypothetical protein; Provisional 117 matched cddid_all.tbl CDD PRK13681 PRK13681 184238 PRK13681 protein YohO. 35 matched cddid_all.tbl CDD PRK13682 PRK13682 184239 PRK13682 hypothetical protein; Provisional 51 matched cddid_all.tbl CDD PRK13683 PRK13683 184240 PRK13683 hypothetical protein; Provisional 87 matched cddid_all.tbl CDD PRK13684 PRK13684 237468 PRK13684 photosynthesis system II assembly factor Ycf48. 334 matched cddid_all.tbl CDD PRK13685 PRK13685 184242 PRK13685 hypothetical protein; Provisional 326 matched cddid_all.tbl CDD PRK13686 PRK13686 237469 PRK13686 photosystem II reaction center protein Ycf12. 43 matched cddid_all.tbl CDD PRK13687 PRK13687 184244 PRK13687 hypothetical protein; Provisional 85 matched cddid_all.tbl CDD PRK13688 PRK13688 237470 PRK13688 N-acetyltransferase. 156 matched cddid_all.tbl CDD PRK13689 PRK13689 237471 PRK13689 hypothetical protein; Provisional 75 matched cddid_all.tbl CDD PRK13691 PRK13691 139768 PRK13691 (3R)-hydroxyacyl-ACP dehydratase subunit HadC; Provisional 166 matched cddid_all.tbl CDD PRK13692 PRK13692 237473 PRK13692 (3R)-hydroxyacyl-ACP dehydratase subunit HadA; Provisional 159 matched cddid_all.tbl CDD PRK13693 PRK13693 184249 PRK13693 (3R)-hydroxyacyl-ACP dehydratase subunit HadB; Provisional 142 matched cddid_all.tbl CDD PRK13694 PRK13694 237474 PRK13694 hypothetical protein; Provisional 83 matched cddid_all.tbl CDD PRK13695 PRK13695 237475 PRK13695 NTPase. 174 matched cddid_all.tbl CDD PRK13696 PRK13696 237476 PRK13696 hypothetical protein; Provisional 62 matched cddid_all.tbl CDD PRK13697 PRK13697 184253 PRK13697 cytochrome c6; Provisional 111 matched cddid_all.tbl CDD PRK13698 PRK13698 184254 PRK13698 ParB/RepB/Spo0J family plasmid partition protein. 323 matched cddid_all.tbl CDD PRK13699 PRK13699 184255 PRK13699 putative methylase; Provisional 227 matched cddid_all.tbl CDD PRK13700 PRK13700 184256 PRK13700 conjugal transfer protein TraD; Provisional 732 matched cddid_all.tbl CDD PRK13701 PRK13701 237477 psiB conjugation system SOS inhibitor PsiB. 144 matched cddid_all.tbl CDD PRK13702 PRK13702 184258 PRK13702 replication regulatory protein RepA. 85 matched cddid_all.tbl CDD PRK13703 PRK13703 184259 PRK13703 conjugal pilus assembly protein TraF; Provisional 248 matched cddid_all.tbl CDD PRK13704 PRK13704 184260 PRK13704 plasmid SOS inhibition protein A; Provisional 240 matched cddid_all.tbl CDD PRK13705 PRK13705 184261 PRK13705 plasmid-partitioning protein SopA; Provisional 388 matched cddid_all.tbl CDD PRK13706 PRK13706 184262 PRK13706 conjugal transfer pilus acetylase TraX. 248 matched cddid_all.tbl CDD PRK13707 PRK13707 184263 PRK13707 type IV conjugative transfer system protein TraL. 101 matched cddid_all.tbl CDD PRK13708 PRK13708 184264 PRK13708 type II toxin-antitoxin system toxin CcdB. 101 matched cddid_all.tbl CDD PRK13709 PRK13709 237478 PRK13709 conjugal transfer nickase/helicase TraI; Provisional 1747 matched cddid_all.tbl CDD PRK13710 PRK13710 184266 PRK13710 type II toxin-antitoxin system antitoxin CcdA. 72 matched cddid_all.tbl CDD PRK13711 PRK13711 184267 PRK13711 P-type conjugative transfer protein TrbJ. 113 matched cddid_all.tbl CDD PRK13712 PRK13712 184268 PRK13712 conjugal transfer protein TrbA; Provisional 115 matched cddid_all.tbl CDD PRK13713 PRK13713 184269 PRK13713 relaxosome protein TraM. 118 matched cddid_all.tbl CDD PRK13715 PRK13715 184270 PRK13715 conjugal transfer protein TraR; Provisional 73 matched cddid_all.tbl CDD PRK13716 PRK13716 106657 PRK13716 RepA leader peptide Tap. 24 matched cddid_all.tbl CDD PRK13717 PRK13717 184271 PRK13717 type-F conjugative transfer system protein TrbI. 128 matched cddid_all.tbl CDD PRK13718 PRK13718 172260 PRK13718 conjugal transfer protein TrbE; Provisional 84 matched cddid_all.tbl CDD PRK13719 PRK13719 237479 PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional 217 matched cddid_all.tbl CDD PRK13720 PRK13720 172262 PRK13720 modulator of post-segregation killing protein; Provisional 70 matched cddid_all.tbl CDD PRK13721 PRK13721 237480 PRK13721 conjugal transfer ATP-binding protein TraC; Provisional 844 matched cddid_all.tbl CDD PRK13722 PRK13722 184274 PRK13722 lytic transglycosylase; Provisional 169 matched cddid_all.tbl CDD PRK13723 PRK13723 237481 PRK13723 conjugal transfer pilus assembly protein TraH; Provisional 451 matched cddid_all.tbl CDD PRK13724 PRK13724 237482 PRK13724 conjugal transfer protein TrbD; Provisional 65 matched cddid_all.tbl CDD PRK13725 PRK13725 184277 PRK13725 tRNA(fMet)-specific endonuclease VapC. 132 matched cddid_all.tbl CDD PRK13726 PRK13726 184278 PRK13726 type IV conjugative transfer system protein TraE. 188 matched cddid_all.tbl CDD PRK13727 PRK13727 237483 PRK13727 conjugal transfer pilin chaperone TraQ; Provisional 80 matched cddid_all.tbl CDD PRK13728 PRK13728 237484 PRK13728 conjugal transfer protein TrbB; Provisional 181 matched cddid_all.tbl CDD PRK13729 PRK13729 184281 PRK13729 conjugal transfer pilus assembly protein TraB; Provisional 475 matched cddid_all.tbl CDD PRK13730 PRK13730 184282 PRK13730 conjugal transfer pilus assembly protein TrbC; Provisional 212 matched cddid_all.tbl CDD PRK13731 PRK13731 184283 PRK13731 complement resistance protein TraT. 243 matched cddid_all.tbl CDD PRK13732 PRK13732 184284 PRK13732 single-stranded DNA-binding protein; Provisional 175 matched cddid_all.tbl CDD PRK13733 PRK13733 184285 PRK13733 conjugal transfer protein TraV; Provisional 171 matched cddid_all.tbl CDD PRK13734 PRK13734 237485 PRK13734 conjugal transfer pilin subunit TraA; Provisional 120 matched cddid_all.tbl CDD PRK13735 PRK13735 184287 PRK13735 conjugal transfer mating pair stabilization protein TraG; Provisional 942 matched cddid_all.tbl CDD PRK13736 PRK13736 237486 PRK13736 conjugal transfer protein TraK; Provisional 245 matched cddid_all.tbl CDD PRK13737 PRK13737 237487 PRK13737 conjugal transfer pilus assembly protein TraU; Provisional 330 matched cddid_all.tbl CDD PRK13738 PRK13738 184290 PRK13738 conjugal transfer pilus assembly protein TraW; Provisional 209 matched cddid_all.tbl CDD PRK13739 PRK13739 237488 PRK13739 conjugal transfer protein TraP; Provisional 198 matched cddid_all.tbl CDD PRK13740 PRK13740 184292 PRK13740 conjugal transfer relaxosome protein TraY. 70 matched cddid_all.tbl CDD PRK13741 PRK13741 172283 PRK13741 conjugal transfer protein TraS. 171 matched cddid_all.tbl CDD PRK13742 PRK13742 184293 PRK13742 replication initiation protein RepE. 245 matched cddid_all.tbl CDD PRK13743 PRK13743 184294 PRK13743 conjugal transfer protein TrbF; Provisional 141 matched cddid_all.tbl CDD PRK13744 PRK13744 139817 PRK13744 conjugal transfer protein TrbG; Provisional 83 matched cddid_all.tbl CDD PRK13745 PRK13745 237489 PRK13745 anaerobic sulfatase-maturation protein. 412 matched cddid_all.tbl CDD PRK13746 PRK13746 184296 PRK13746 aminoglycoside resistance protein; Provisional 262 matched cddid_all.tbl CDD PRK13747 PRK13747 184297 PRK13747 putative mercury resistance protein; Provisional 78 matched cddid_all.tbl CDD PRK13748 PRK13748 184298 PRK13748 putative mercuric reductase; Provisional 561 matched cddid_all.tbl CDD PRK13749 PRK13749 184299 PRK13749 HTH-type transcriptional regulator MerD. 121 matched cddid_all.tbl CDD PRK13750 PRK13750 184300 PRK13750 replication protein; Provisional 285 matched cddid_all.tbl CDD PRK13751 PRK13751 184301 PRK13751 putative mercuric transport protein; Provisional 116 matched cddid_all.tbl CDD PRK13752 PRK13752 184302 PRK13752 mercuric resistance operon transcriptional regulator MerR. 144 matched cddid_all.tbl CDD PRK13753 PRK13753 184303 PRK13753 dihydropteroate synthase; Provisional 279 matched cddid_all.tbl CDD PRK13754 PRK13754 184304 PRK13754 fertility inhibition protein FinO. 186 matched cddid_all.tbl CDD PRK13755 PRK13755 237490 PRK13755 organomercurial transporter MerC. 139 matched cddid_all.tbl CDD PRK13756 PRK13756 172294 PRK13756 TetR family transcriptional regulator. 205 matched cddid_all.tbl CDD PRK13757 PRK13757 172295 PRK13757 type A chloramphenicol O-acetyltransferase. 219 matched cddid_all.tbl CDD PRK13758 PRK13758 172296 PRK13758 anaerobic sulfatase-maturase; Provisional 370 matched cddid_all.tbl CDD PRK13759 PRK13759 237491 PRK13759 arylsulfatase; Provisional 485 matched cddid_all.tbl CDD PRK13761 PRK13761 184308 PRK13761 phosphopantothenate/pantothenate synthetase. 248 matched cddid_all.tbl CDD PRK13763 PRK13763 237494 PRK13763 putative RNA-processing protein; Provisional 180 matched cddid_all.tbl CDD PRK13764 PRK13764 184311 PRK13764 ATPase; Provisional 602 matched cddid_all.tbl CDD PRK13766 PRK13766 237496 PRK13766 Hef nuclease; Provisional 773 matched cddid_all.tbl CDD PRK13767 PRK13767 237497 PRK13767 ATP-dependent helicase; Provisional 876 matched cddid_all.tbl CDD PRK13768 PRK13768 237498 PRK13768 GTPase; Provisional 253 matched cddid_all.tbl CDD PRK13769 PRK13769 172307 PRK13769 histidinol dehydrogenase; Provisional 368 matched cddid_all.tbl CDD PRK13770 PRK13770 172308 PRK13770 histidinol dehydrogenase; Provisional 416 matched cddid_all.tbl CDD PRK13771 PRK13771 184316 PRK13771 putative alcohol dehydrogenase; Provisional 334 matched cddid_all.tbl CDD PRK13773 PRK13773 237499 PRK13773 formimidoylglutamase; Provisional 324 matched cddid_all.tbl CDD PRK13775 PRK13775 172313 PRK13775 formimidoylglutamase; Provisional 328 matched cddid_all.tbl CDD PRK13777 PRK13777 237501 PRK13777 HTH-type transcriptional regulator Hpr. 185 matched cddid_all.tbl CDD PRK13778 PRK13778 184320 paaA phenylacetate-CoA oxygenase subunit PaaA; Provisional 314 matched cddid_all.tbl CDD PRK13779 PRK13779 237502 PRK13779 bifunctional PTS system fructose-specific transporter subunit IIA/HPr protein; Provisional 503 matched cddid_all.tbl CDD PRK13780 PRK13780 237503 PRK13780 phosphocarrier protein HPr; Provisional 88 matched cddid_all.tbl CDD PRK13782 PRK13782 172320 PRK13782 HPr family phosphocarrier protein. 82 matched cddid_all.tbl CDD PRK13783 PRK13783 237505 PRK13783 adenylosuccinate synthetase; Provisional 404 matched cddid_all.tbl CDD PRK13784 PRK13784 172322 PRK13784 adenylosuccinate synthetase; Provisional 428 matched cddid_all.tbl CDD PRK13785 PRK13785 237506 PRK13785 adenylosuccinate synthetase; Provisional 454 matched cddid_all.tbl CDD PRK13786 PRK13786 184325 PRK13786 adenylosuccinate synthetase; Provisional 424 matched cddid_all.tbl CDD PRK13787 PRK13787 172324 PRK13787 adenylosuccinate synthetase; Provisional 423 matched cddid_all.tbl CDD PRK13788 PRK13788 184326 PRK13788 adenylosuccinate synthetase; Provisional 404 matched cddid_all.tbl CDD PRK13791 PRK13791 237508 PRK13791 c-type lysozyme inhibitor. 113 matched cddid_all.tbl CDD PRK13792 PRK13792 106733 PRK13792 lysozyme inhibitor; Provisional 127 matched cddid_all.tbl CDD PRK13793 PRK13793 184329 PRK13793 nicotinate-nicotinamide nucleotide adenylyltransferase. 196 matched cddid_all.tbl CDD PRK13794 PRK13794 237509 PRK13794 hypothetical protein; Provisional 479 matched cddid_all.tbl CDD PRK13795 PRK13795 237510 PRK13795 hypothetical protein; Provisional 636 matched cddid_all.tbl CDD PRK13797 PRK13797 106738 PRK13797 allantoicase. 516 matched cddid_all.tbl CDD PRK13798 PRK13798 184333 PRK13798 putative OHCU decarboxylase; Provisional 166 matched cddid_all.tbl CDD PRK13799 PRK13799 106740 PRK13799 unknown domain/N-carbamoyl-L-amino acid hydrolase fusion protein; Provisional 591 matched cddid_all.tbl CDD PRK13800 PRK13800 237512 PRK13800 fumarate reductase/succinate dehydrogenase flavoprotein subunit. 897 matched cddid_all.tbl CDD PRK13802 PRK13802 184335 PRK13802 bifunctional indole-3-glycerol phosphate synthase/tryptophan synthase subunit beta; Provisional 695 matched cddid_all.tbl CDD PRK13803 PRK13803 237513 PRK13803 bifunctional phosphoribosylanthranilate isomerase/tryptophan synthase subunit beta; Provisional 610 matched cddid_all.tbl CDD PRK13805 PRK13805 237515 PRK13805 bifunctional acetaldehyde-CoA/alcohol dehydrogenase; Provisional 862 matched cddid_all.tbl CDD PRK13806 PRK13806 237516 rpsA 30S ribosomal protein S1; Provisional 491 matched cddid_all.tbl CDD PRK13807 PRK13807 237517 PRK13807 maltose phosphorylase; Provisional 756 matched cddid_all.tbl CDD PRK13808 PRK13808 172341 PRK13808 adenylate kinase; Provisional 333 matched cddid_all.tbl CDD PRK13809 PRK13809 184340 PRK13809 orotate phosphoribosyltransferase; Provisional 206 matched cddid_all.tbl CDD PRK13813 PRK13813 237520 PRK13813 orotidine 5'-phosphate decarboxylase; Provisional 215 matched cddid_all.tbl CDD PRK13814 PRK13814 139876 pyrB aspartate carbamoyltransferase. 310 matched cddid_all.tbl CDD PRK13815 PRK13815 172345 PRK13815 ribosome-binding factor A; Provisional 122 matched cddid_all.tbl CDD PRK13816 PRK13816 184344 PRK13816 ribosome-binding factor A; Provisional 131 matched cddid_all.tbl CDD PRK13817 PRK13817 139879 PRK13817 ribosome-binding factor A; Provisional 119 matched cddid_all.tbl CDD PRK13818 PRK13818 184345 PRK13818 ribosome-binding factor A; Provisional 121 matched cddid_all.tbl CDD PRK13820 PRK13820 237521 PRK13820 argininosuccinate synthase; Provisional 394 matched cddid_all.tbl CDD PRK13821 PRK13821 184347 thyA thymidylate synthase; Provisional 323 matched cddid_all.tbl CDD PRK13822 PRK13822 237522 PRK13822 conjugal transfer coupling protein TraG; Provisional 641 matched cddid_all.tbl CDD PRK13823 PRK13823 184348 PRK13823 conjugal transfer protein TrbD; Provisional 94 matched cddid_all.tbl CDD PRK13824 PRK13824 184349 PRK13824 replication initiation protein RepC; Provisional 404 matched cddid_all.tbl CDD PRK13825 PRK13825 237523 PRK13825 conjugal transfer protein TraB; Provisional 388 matched cddid_all.tbl CDD PRK13826 PRK13826 237524 PRK13826 Dtr system oriT relaxase; Provisional 1102 matched cddid_all.tbl CDD PRK13828 PRK13828 184351 rimM 16S rRNA-processing protein RimM; Provisional 161 matched cddid_all.tbl CDD PRK13829 PRK13829 184352 rimM 16S rRNA-processing protein RimM; Provisional 162 matched cddid_all.tbl CDD PRK13830 PRK13830 237525 PRK13830 conjugal transfer protein TrbE; Provisional 818 matched cddid_all.tbl CDD PRK13831 PRK13831 172358 PRK13831 conjugal transfer protein TrbI; Provisional 432 matched cddid_all.tbl CDD PRK13832 PRK13832 184353 PRK13832 plasmid partitioning protein; Provisional 520 matched cddid_all.tbl CDD PRK13833 PRK13833 172360 PRK13833 conjugal transfer protein TrbB; Provisional 323 matched cddid_all.tbl CDD PRK13834 PRK13834 172361 PRK13834 putative autoinducer synthesis protein; Provisional 207 matched cddid_all.tbl CDD PRK13835 PRK13835 172362 PRK13835 conjugal transfer protein TrbH; Provisional 145 matched cddid_all.tbl CDD PRK13836 PRK13836 172363 PRK13836 conjugal transfer protein TrbF; Provisional 220 matched cddid_all.tbl CDD PRK13837 PRK13837 237526 PRK13837 two-component system VirA-like sensor kinase. 828 matched cddid_all.tbl CDD PRK13838 PRK13838 172365 PRK13838 conjugal transfer pilin processing protease TraF; Provisional 176 matched cddid_all.tbl CDD PRK13839 PRK13839 237527 PRK13839 conjugal transfer protein TrbG; Provisional 277 matched cddid_all.tbl CDD PRK13841 PRK13841 237529 PRK13841 conjugal transfer protein TrbL; Provisional 391 matched cddid_all.tbl CDD PRK13842 PRK13842 172369 PRK13842 conjugal transfer protein TrbJ; Provisional 267 matched cddid_all.tbl CDD PRK13843 PRK13843 237530 PRK13843 conjugal transfer protein TraH; Provisional 207 matched cddid_all.tbl CDD PRK13845 PRK13845 172371 PRK13845 putative glycerol-3-phosphate acyltransferase PlsX; Provisional 437 matched cddid_all.tbl CDD PRK13846 PRK13846 139906 PRK13846 phosphate acyltransferase PlsX. 316 matched cddid_all.tbl CDD PRK13847 PRK13847 172372 PRK13847 type IV conjugative transfer system coupling protein TraD. 71 matched cddid_all.tbl CDD PRK13848 PRK13848 172373 PRK13848 conjugal transfer protein TraC; Provisional 98 matched cddid_all.tbl CDD PRK13849 PRK13849 139909 PRK13849 conjugal transfer ATPase VirC1. 231 matched cddid_all.tbl CDD PRK13850 PRK13850 237531 PRK13850 type IV secretion system protein VirD4; Provisional 670 matched cddid_all.tbl CDD PRK13851 PRK13851 172375 PRK13851 type IV secretion system protein VirB11; Provisional 344 matched cddid_all.tbl CDD PRK13852 PRK13852 139912 PRK13852 type IV secretion system protein. 295 matched cddid_all.tbl CDD PRK13853 PRK13853 139913 PRK13853 type IV secretion system protein VirB4; Provisional 789 matched cddid_all.tbl CDD PRK13854 PRK13854 139914 PRK13854 type IV secretion system protein VirB3; Provisional 108 matched cddid_all.tbl CDD PRK13855 PRK13855 172376 PRK13855 type IV secretion system protein VirB10; Provisional 376 matched cddid_all.tbl CDD PRK13856 PRK13856 172377 PRK13856 two-component response regulator VirG; Provisional 241 matched cddid_all.tbl CDD PRK13857 PRK13857 172378 PRK13857 pilin major subunit VirB2. 120 matched cddid_all.tbl CDD PRK13858 PRK13858 237532 PRK13858 T-DNA border endonuclease VirD1. 147 matched cddid_all.tbl CDD PRK13859 PRK13859 172380 PRK13859 type IV secretion system lipoprotein VirB7; Provisional 55 matched cddid_all.tbl CDD PRK13860 PRK13860 172381 PRK13860 pilin minor subunit VirB5. 220 matched cddid_all.tbl CDD PRK13861 PRK13861 172382 PRK13861 type IV secretion system protein VirB9; Provisional 292 matched cddid_all.tbl CDD PRK13862 PRK13862 172383 PRK13862 conjugal transfer protein VirC2. 201 matched cddid_all.tbl CDD PRK13863 PRK13863 237533 PRK13863 T-DNA border endonuclease VirD2. 446 matched cddid_all.tbl CDD PRK13864 PRK13864 237534 PRK13864 type IV secretion system lytic transglycosylase VirB1; Provisional 245 matched cddid_all.tbl CDD PRK13865 PRK13865 172386 PRK13865 type IV secretion system protein VirB8; Provisional 229 matched cddid_all.tbl CDD PRK13866 PRK13866 172387 PRK13866 plasmid partitioning protein RepB; Provisional 336 matched cddid_all.tbl CDD PRK13867 PRK13867 172388 PRK13867 type IV secretion system effector chaperone VirE1. 65 matched cddid_all.tbl CDD PRK13868 PRK13868 237535 PRK13868 type IV secretion system single-stranded DNA binding effector VirE2. 556 matched cddid_all.tbl CDD PRK13869 PRK13869 139929 PRK13869 plasmid-partitioning protein RepA; Provisional 405 matched cddid_all.tbl CDD PRK13870 PRK13870 172390 PRK13870 transcriptional regulator TraR; Provisional 234 matched cddid_all.tbl CDD PRK13871 PRK13871 172391 PRK13871 conjugal transfer protein TrbC; Provisional 135 matched cddid_all.tbl CDD PRK13872 PRK13872 184356 PRK13872 conjugal transfer protein TrbF; Provisional 228 matched cddid_all.tbl CDD PRK13873 PRK13873 237536 PRK13873 conjugal transfer ATPase TrbE; Provisional 811 matched cddid_all.tbl CDD PRK13874 PRK13874 184358 PRK13874 conjugal transfer protein TrbJ; Provisional 230 matched cddid_all.tbl CDD PRK13875 PRK13875 237537 PRK13875 conjugal transfer protein TrbL; Provisional 440 matched cddid_all.tbl CDD PRK13876 PRK13876 237538 PRK13876 conjugal transfer coupling protein TraG; Provisional 663 matched cddid_all.tbl CDD PRK13877 PRK13877 184361 PRK13877 conjugal transfer transcriptional regulator TraJ. 114 matched cddid_all.tbl CDD PRK13878 PRK13878 237539 PRK13878 conjugal transfer relaxase TraI; Provisional 746 matched cddid_all.tbl CDD PRK13879 PRK13879 184363 PRK13879 P-type conjugative transfer protein TrbJ. 253 matched cddid_all.tbl CDD PRK13880 PRK13880 237540 PRK13880 conjugal transfer coupling protein TraG; Provisional 636 matched cddid_all.tbl CDD PRK13881 PRK13881 237541 PRK13881 conjugal transfer protein TrbI; Provisional 472 matched cddid_all.tbl CDD PRK13882 PRK13882 237542 PRK13882 conjugal transfer protein TrbP; Provisional 232 matched cddid_all.tbl CDD PRK13883 PRK13883 184367 PRK13883 conjugal transfer protein TrbH; Provisional 151 matched cddid_all.tbl CDD PRK13884 PRK13884 184368 PRK13884 conjugal transfer peptidase TraF; Provisional 178 matched cddid_all.tbl CDD PRK13885 PRK13885 237543 PRK13885 conjugal transfer protein TrbG; Provisional 299 matched cddid_all.tbl CDD PRK13886 PRK13886 184370 PRK13886 conjugal transfer protein TraL; Provisional 241 matched cddid_all.tbl CDD PRK13887 PRK13887 237544 PRK13887 conjugal transfer protein TrbF; Provisional 250 matched cddid_all.tbl CDD PRK13888 PRK13888 237545 PRK13888 conjugal transfer protein TrbN; Provisional 206 matched cddid_all.tbl CDD PRK13889 PRK13889 237546 PRK13889 conjugal transfer relaxase TraA; Provisional 988 matched cddid_all.tbl CDD PRK13890 PRK13890 237547 PRK13890 conjugal transfer protein TrbA; Provisional 120 matched cddid_all.tbl CDD PRK13891 PRK13891 184375 PRK13891 conjugal transfer protein TrbE; Provisional 852 matched cddid_all.tbl CDD PRK13892 PRK13892 184376 PRK13892 conjugal transfer protein TrbC; Provisional 134 matched cddid_all.tbl CDD PRK13893 PRK13893 237548 PRK13893 conjugal transfer protein TrbM; Provisional 193 matched cddid_all.tbl CDD PRK13894 PRK13894 184377 PRK13894 conjugal transfer ATPase TrbB; Provisional 319 matched cddid_all.tbl CDD PRK13895 PRK13895 184378 PRK13895 conjugal transfer protein TraM; Provisional 144 matched cddid_all.tbl CDD PRK13896 PRK13896 184379 PRK13896 cobyrinic acid a,c-diamide synthase; Provisional 433 matched cddid_all.tbl CDD PRK13897 PRK13897 237549 PRK13897 type IV secretion system component VirD4; Provisional 606 matched cddid_all.tbl CDD PRK13898 PRK13898 172418 PRK13898 type IV secretion system ATPase VirB4; Provisional 800 matched cddid_all.tbl CDD PRK13899 PRK13899 237550 PRK13899 type IV secretion system protein VirB3; Provisional 97 matched cddid_all.tbl CDD PRK13900 PRK13900 184381 PRK13900 type IV secretion system ATPase VirB11; Provisional 332 matched cddid_all.tbl CDD PRK13903 PRK13903 237552 murB UDP-N-acetylmuramate dehydrogenase. 363 matched cddid_all.tbl CDD PRK13904 PRK13904 184384 murB UDP-N-acetylmuramate dehydrogenase. 257 matched cddid_all.tbl CDD PRK13905 PRK13905 237553 murB UDP-N-acetylmuramate dehydrogenase. 298 matched cddid_all.tbl CDD PRK13906 PRK13906 184386 murB UDP-N-acetylmuramate dehydrogenase. 307 matched cddid_all.tbl CDD PRK13907 PRK13907 139967 rnhA ribonuclease H; Provisional 128 matched cddid_all.tbl CDD PRK13908 PRK13908 184387 PRK13908 recombination protein RecO. 204 matched cddid_all.tbl CDD PRK13909 PRK13909 237554 PRK13909 RecB-like helicase. 910 matched cddid_all.tbl CDD PRK13910 PRK13910 172427 PRK13910 DNA glycosylase MutY; Provisional 289 matched cddid_all.tbl CDD PRK13911 PRK13911 139971 PRK13911 exodeoxyribonuclease III; Provisional 250 matched cddid_all.tbl CDD PRK13912 PRK13912 184389 PRK13912 nuclease NucT; Provisional 177 matched cddid_all.tbl CDD PRK13913 PRK13913 184390 PRK13913 3-methyladenine DNA glycosylase; Provisional 218 matched cddid_all.tbl CDD PRK13914 PRK13914 237555 PRK13914 invasion associated endopeptidase. 481 matched cddid_all.tbl CDD PRK13915 PRK13915 237556 PRK13915 putative glucosyl-3-phosphoglycerate synthase; Provisional 306 matched cddid_all.tbl CDD PRK13916 PRK13916 139976 PRK13916 plasmid segregation protein ParR; Provisional 97 matched cddid_all.tbl CDD PRK13917 PRK13917 184393 PRK13917 plasmid segregation protein ParM; Provisional 344 matched cddid_all.tbl CDD PRK13918 PRK13918 237557 PRK13918 CRP/FNR family transcriptional regulator; Provisional 202 matched cddid_all.tbl CDD PRK13919 PRK13919 184395 PRK13919 putative RNA polymerase sigma E protein; Provisional 186 matched cddid_all.tbl CDD PRK13920 PRK13920 237558 PRK13920 putative anti-sigmaE protein; Provisional 206 matched cddid_all.tbl CDD PRK13921 PRK13921 237559 PRK13921 CRISPR-associated Cse2 family protein; Provisional 173 matched cddid_all.tbl CDD PRK13922 PRK13922 237560 PRK13922 rod shape-determining protein MreC; Provisional 276 matched cddid_all.tbl CDD PRK13923 PRK13923 237561 PRK13923 putative spore coat protein regulator protein YlbO; Provisional 170 matched cddid_all.tbl CDD PRK13925 PRK13925 184399 rnhB ribonuclease HII; Provisional 198 matched cddid_all.tbl CDD PRK13926 PRK13926 184400 PRK13926 ribonuclease HII; Provisional 207 matched cddid_all.tbl CDD PRK13927 PRK13927 237562 PRK13927 rod shape-determining protein MreB; Provisional 334 matched cddid_all.tbl CDD PRK13928 PRK13928 237563 PRK13928 rod shape-determining protein Mbl; Provisional 336 matched cddid_all.tbl CDD PRK13929 PRK13929 184403 PRK13929 rod-share determining protein MreBH; Provisional 335 matched cddid_all.tbl CDD PRK13930 PRK13930 237564 PRK13930 rod shape-determining protein MreB; Provisional 335 matched cddid_all.tbl CDD PRK13931 PRK13931 184405 PRK13931 5'/3'-nucleotidase SurE. 261 matched cddid_all.tbl CDD PRK13932 PRK13932 172445 PRK13932 stationary phase survival protein SurE; Provisional 257 matched cddid_all.tbl CDD PRK13933 PRK13933 184406 PRK13933 stationary phase survival protein SurE; Provisional 253 matched cddid_all.tbl CDD PRK13934 PRK13934 237565 PRK13934 stationary phase survival protein SurE; Provisional 266 matched cddid_all.tbl CDD PRK13935 PRK13935 237566 PRK13935 stationary phase survival protein SurE; Provisional 253 matched cddid_all.tbl CDD PRK13936 PRK13936 237567 PRK13936 phosphoheptose isomerase; Provisional 197 matched cddid_all.tbl CDD PRK13937 PRK13937 184408 PRK13937 phosphoheptose isomerase; Provisional 188 matched cddid_all.tbl CDD PRK13938 PRK13938 139997 PRK13938 phosphoheptose isomerase; Provisional 196 matched cddid_all.tbl CDD PRK13940 PRK13940 172450 PRK13940 glutamyl-tRNA reductase; Provisional 414 matched cddid_all.tbl CDD PRK13942 PRK13942 184409 PRK13942 protein-L-isoaspartate O-methyltransferase; Provisional 212 matched cddid_all.tbl CDD PRK13943 PRK13943 237568 PRK13943 protein-L-isoaspartate O-methyltransferase; Provisional 322 matched cddid_all.tbl CDD PRK13944 PRK13944 140001 PRK13944 protein-L-isoaspartate O-methyltransferase; Provisional 205 matched cddid_all.tbl CDD PRK13945 PRK13945 184410 PRK13945 formamidopyrimidine-DNA glycosylase; Provisional 282 matched cddid_all.tbl CDD PRK13946 PRK13946 184411 PRK13946 shikimate kinase; Provisional 184 matched cddid_all.tbl CDD PRK13947 PRK13947 184412 PRK13947 shikimate kinase; Provisional 171 matched cddid_all.tbl CDD PRK13948 PRK13948 184413 PRK13948 shikimate kinase; Provisional 182 matched cddid_all.tbl CDD PRK13949 PRK13949 140006 PRK13949 shikimate kinase; Provisional 169 matched cddid_all.tbl CDD PRK13951 PRK13951 172457 PRK13951 bifunctional shikimate kinase AroK/3-dehydroquinate synthase AroB. 488 matched cddid_all.tbl CDD PRK13952 PRK13952 237569 mscL large conductance mechanosensitive channel protein MscL. 142 matched cddid_all.tbl CDD PRK13953 PRK13953 184415 mscL large conductance mechanosensitive channel protein MscL. 125 matched cddid_all.tbl CDD PRK13954 PRK13954 172460 mscL large conductance mechanosensitive channel protein MscL. 119 matched cddid_all.tbl CDD PRK13955 PRK13955 184416 mscL large conductance mechanosensitive channel protein MscL. 130 matched cddid_all.tbl CDD PRK13956 PRK13956 184417 dut dUTP diphosphatase. 147 matched cddid_all.tbl CDD PRK13957 PRK13957 140013 PRK13957 indole-3-glycerol-phosphate synthase; Provisional 247 matched cddid_all.tbl CDD PRK13958 PRK13958 184418 PRK13958 N-(5'-phosphoribosyl)anthranilate isomerase; Provisional 207 matched cddid_all.tbl CDD PRK13959 PRK13959 237570 PRK13959 phosphoribosylaminoimidazole-succinocarboxamide synthase; Provisional 341 matched cddid_all.tbl CDD PRK13960 PRK13960 184420 PRK13960 phosphoribosylaminoimidazole-succinocarboxamide synthase; Provisional 367 matched cddid_all.tbl CDD PRK13961 PRK13961 237571 PRK13961 phosphoribosylaminoimidazole-succinocarboxamide synthase; Provisional 296 matched cddid_all.tbl CDD PRK13962 PRK13962 237572 PRK13962 bifunctional phosphoglycerate kinase/triosephosphate isomerase; Provisional 645 matched cddid_all.tbl CDD PRK13963 PRK13963 237573 PRK13963 rRNA maturation RNase YbeY. 258 matched cddid_all.tbl CDD PRK13965 PRK13965 184425 PRK13965 ribonucleotide-diphosphate reductase subunit beta; Provisional 335 matched cddid_all.tbl CDD PRK13966 PRK13966 140022 nrdF2 ribonucleotide-diphosphate reductase subunit beta; Provisional 324 matched cddid_all.tbl CDD PRK13967 PRK13967 140023 nrdF1 ribonucleotide-diphosphate reductase subunit beta; Provisional 322 matched cddid_all.tbl CDD PRK13968 PRK13968 184426 PRK13968 putative succinate semialdehyde dehydrogenase; Provisional 462 matched cddid_all.tbl CDD PRK13969 PRK13969 184427 PRK13969 proline racemase; Provisional 334 matched cddid_all.tbl CDD PRK13970 PRK13970 172473 PRK13970 4-hydroxyproline epimerase. 311 matched cddid_all.tbl CDD PRK13971 PRK13971 184428 PRK13971 4-hydroxyproline epimerase. 333 matched cddid_all.tbl CDD PRK13972 PRK13972 172475 PRK13972 GSH-dependent disulfide bond oxidoreductase; Provisional 215 matched cddid_all.tbl CDD PRK13977 PRK13977 237575 PRK13977 myosin-cross-reactive antigen; Provisional 576 matched cddid_all.tbl CDD PRK13978 PRK13978 184433 PRK13978 ribose 5-phosphate isomerase A. 228 matched cddid_all.tbl CDD PRK13979 PRK13979 237576 PRK13979 DNA topoisomerase IV subunit A; Provisional 957 matched cddid_all.tbl CDD PRK13980 PRK13980 184435 PRK13980 NAD synthetase; Provisional 265 matched cddid_all.tbl CDD PRK13981 PRK13981 237577 PRK13981 NAD synthetase; Provisional 540 matched cddid_all.tbl CDD PRK13982 PRK13982 172484 PRK13982 bifunctional SbtC-like/phosphopantothenoylcysteine decarboxylase/phosphopantothenate synthase; Provisional 475 matched cddid_all.tbl CDD PRK13983 PRK13983 237578 PRK13983 M20 family metallo-hydrolase. 400 matched cddid_all.tbl CDD PRK13984 PRK13984 172486 PRK13984 putative oxidoreductase; Provisional 604 matched cddid_all.tbl CDD PRK13985 PRK13985 184438 ureB urease subunit alpha. 568 matched cddid_all.tbl CDD PRK13986 PRK13986 184439 PRK13986 urease subunit beta. 225 matched cddid_all.tbl CDD PRK13987 PRK13987 237579 PRK13987 cell division topological specificity factor MinE; Provisional 91 matched cddid_all.tbl CDD PRK13988 PRK13988 184441 PRK13988 cell division topological specificity factor MinE; Provisional 97 matched cddid_all.tbl CDD PRK13989 PRK13989 184442 PRK13989 cell division topological specificity factor MinE; Provisional 84 matched cddid_all.tbl CDD PRK13990 PRK13990 172492 PRK13990 cell division topological specificity factor MinE; Provisional 90 matched cddid_all.tbl CDD PRK13991 PRK13991 172493 PRK13991 cell division topological specificity factor MinE; Provisional 87 matched cddid_all.tbl CDD PRK13992 PRK13992 237580 minC septum site-determining protein MinC. 205 matched cddid_all.tbl CDD PRK13994 PRK13994 237581 PRK13994 potassium-transporting ATPase subunit C; Provisional 222 matched cddid_all.tbl CDD PRK13995 PRK13995 184445 PRK13995 K(+)-transporting ATPase subunit C. 203 matched cddid_all.tbl CDD PRK13996 PRK13996 172497 PRK13996 potassium-transporting ATPase subunit C; Provisional 197 matched cddid_all.tbl CDD PRK13997 PRK13997 172498 PRK13997 K(+)-transporting ATPase subunit C. 193 matched cddid_all.tbl CDD PRK13998 PRK13998 172499 PRK13998 K(+)-transporting ATPase subunit C. 186 matched cddid_all.tbl CDD PRK13999 PRK13999 172500 PRK13999 K(+)-transporting ATPase subunit C. 201 matched cddid_all.tbl CDD PRK14000 PRK14000 184446 PRK14000 K(+)-transporting ATPase subunit C. 185 matched cddid_all.tbl CDD PRK14001 PRK14001 172502 PRK14001 K(+)-transporting ATPase subunit C. 189 matched cddid_all.tbl CDD PRK14002 PRK14002 172503 PRK14002 K(+)-transporting ATPase subunit C. 186 matched cddid_all.tbl CDD PRK14003 PRK14003 184447 PRK14003 K(+)-transporting ATPase subunit C. 194 matched cddid_all.tbl CDD PRK14004 PRK14004 172505 hisH imidazole glycerol phosphate synthase subunit HisH; Provisional 210 matched cddid_all.tbl CDD PRK14010 PRK14010 184448 PRK14010 K(+)-transporting ATPase subunit B. 673 matched cddid_all.tbl CDD PRK14012 PRK14012 184450 PRK14012 IscS subfamily cysteine desulfurase. 404 matched cddid_all.tbl CDD PRK14013 PRK14013 237583 PRK14013 hypothetical protein; Provisional 338 matched cddid_all.tbl CDD PRK14014 PRK14014 237584 PRK14014 putative acyltransferase; Provisional 301 matched cddid_all.tbl CDD PRK14015 PRK14015 237585 pepN aminopeptidase N; Provisional 875 matched cddid_all.tbl CDD PRK14016 PRK14016 237586 PRK14016 cyanophycin synthetase; Provisional 727 matched cddid_all.tbl CDD PRK14017 PRK14017 184455 PRK14017 galactonate dehydratase; Provisional 382 matched cddid_all.tbl CDD PRK14018 PRK14018 184456 PRK14018 bifunctional peptide-methionine (S)-S-oxide reductase MsrA/peptide-methionine (R)-S-oxide reductase MsrB. 521 matched cddid_all.tbl CDD PRK14019 PRK14019 237587 PRK14019 bifunctional 3,4-dihydroxy-2-butanone-4-phosphate synthase/GTP cyclohydrolase II. 367 matched cddid_all.tbl CDD PRK14021 PRK14021 184458 PRK14021 bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional 542 matched cddid_all.tbl CDD PRK14022 PRK14022 237588 PRK14022 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase. 481 matched cddid_all.tbl CDD PRK14023 PRK14023 184460 PRK14023 homoaconitate hydratase small subunit; Provisional 166 matched cddid_all.tbl CDD PRK14024 PRK14024 237589 PRK14024 phosphoribosyl isomerase A; Provisional 241 matched cddid_all.tbl CDD PRK14025 PRK14025 184462 PRK14025 multifunctional 3-isopropylmalate dehydrogenase/D-malate dehydrogenase; Provisional 330 matched cddid_all.tbl CDD PRK14027 PRK14027 172521 PRK14027 quinate/shikimate dehydrogenase (NAD+). 283 matched cddid_all.tbl CDD PRK14028 PRK14028 172522 PRK14028 pyruvate ferredoxin oxidoreductase subunit gamma/delta; Provisional 312 matched cddid_all.tbl CDD PRK14029 PRK14029 172523 PRK14029 pyruvate/ketoisovalerate ferredoxin oxidoreductase subunit gamma; Provisional 185 matched cddid_all.tbl CDD PRK14030 PRK14030 184463 PRK14030 glutamate dehydrogenase; Provisional 445 matched cddid_all.tbl CDD PRK14031 PRK14031 184464 PRK14031 NADP-specific glutamate dehydrogenase. 444 matched cddid_all.tbl CDD PRK14032 PRK14032 184465 PRK14032 citrate synthase; Provisional 447 matched cddid_all.tbl CDD PRK14033 PRK14033 237590 PRK14033 bifunctional 2-methylcitrate synthase/citrate synthase. 375 matched cddid_all.tbl CDD PRK14034 PRK14034 184467 PRK14034 citrate synthase; Provisional 372 matched cddid_all.tbl CDD PRK14035 PRK14035 184468 PRK14035 citrate synthase; Provisional 371 matched cddid_all.tbl CDD PRK14036 PRK14036 237591 PRK14036 citrate synthase; Provisional 377 matched cddid_all.tbl CDD PRK14037 PRK14037 184470 PRK14037 citrate synthase; Provisional 377 matched cddid_all.tbl CDD PRK14038 PRK14038 172532 PRK14038 ADP-specific glucokinase. 453 matched cddid_all.tbl CDD PRK14039 PRK14039 184471 PRK14039 ADP-dependent glucokinase; Provisional 453 matched cddid_all.tbl CDD PRK14040 PRK14040 237592 PRK14040 oxaloacetate decarboxylase subunit alpha. 593 matched cddid_all.tbl CDD PRK14041 PRK14041 237593 PRK14041 pyruvate carboxylase subunit B. 467 matched cddid_all.tbl CDD PRK14042 PRK14042 172536 PRK14042 pyruvate carboxylase subunit B; Provisional 596 matched cddid_all.tbl CDD PRK14045 PRK14045 172537 PRK14045 1-aminocyclopropane-1-carboxylate deaminase; Provisional 329 matched cddid_all.tbl CDD PRK14046 PRK14046 237594 PRK14046 malate--CoA ligase subunit beta; Provisional 392 matched cddid_all.tbl CDD PRK14048 PRK14048 172540 PRK14048 ferrichrome/ferrioxamine B periplasmic transporter; Provisional 374 matched cddid_all.tbl CDD PRK14049 PRK14049 172541 PRK14049 ferrioxamine B receptor precursor protein; Provisional 726 matched cddid_all.tbl CDD PRK14050 PRK14050 237595 PRK14050 TonB-dependent siderophore receptor. 728 matched cddid_all.tbl CDD PRK14051 PRK14051 184476 PRK14051 negative regulator GrlR; Provisional 123 matched cddid_all.tbl CDD PRK14052 PRK14052 184477 PRK14052 adenosine monophosphate-protein transferase vopS. 387 matched cddid_all.tbl CDD PRK14053 PRK14053 237596 PRK14053 methyltransferase; Provisional 194 matched cddid_all.tbl CDD PRK14055 PRK14055 172547 PRK14055 aromatic amino acid hydroxylase; Provisional 362 matched cddid_all.tbl CDD PRK14056 PRK14056 237598 PRK14056 aromatic amino acid hydroxylase. 578 matched cddid_all.tbl CDD PRK14057 PRK14057 172549 PRK14057 epimerase; Provisional 254 matched cddid_all.tbl CDD PRK14058 PRK14058 237599 PRK14058 [LysW]-aminoadipate/[LysW]-glutamate kinase. 268 matched cddid_all.tbl CDD PRK14059 PRK14059 184482 PRK14059 pyrimidine reductase family protein. 251 matched cddid_all.tbl CDD PRK14061 PRK14061 172552 PRK14061 unknown domain/lipoate-protein ligase A fusion protein; Provisional 562 matched cddid_all.tbl CDD PRK14063 PRK14063 184483 PRK14063 exodeoxyribonuclease VII small subunit; Provisional 76 matched cddid_all.tbl CDD PRK14064 PRK14064 172554 PRK14064 exodeoxyribonuclease VII small subunit; Provisional 75 matched cddid_all.tbl CDD PRK14065 PRK14065 184484 PRK14065 exodeoxyribonuclease VII small subunit; Provisional 86 matched cddid_all.tbl CDD PRK14066 PRK14066 172556 PRK14066 exodeoxyribonuclease VII small subunit; Provisional 75 matched cddid_all.tbl CDD PRK14067 PRK14067 172557 PRK14067 exodeoxyribonuclease VII small subunit; Provisional 80 matched cddid_all.tbl CDD PRK14068 PRK14068 184485 PRK14068 exodeoxyribonuclease VII small subunit; Provisional 76 matched cddid_all.tbl CDD PRK14069 PRK14069 172559 PRK14069 exodeoxyribonuclease VII small subunit; Provisional 95 matched cddid_all.tbl CDD PRK14070 PRK14070 184486 PRK14070 exodeoxyribonuclease VII small subunit; Provisional 69 matched cddid_all.tbl CDD PRK14071 PRK14071 184487 PRK14071 ATP-dependent 6-phosphofructokinase. 360 matched cddid_all.tbl CDD PRK14072 PRK14072 237600 PRK14072 diphosphate--fructose-6-phosphate 1-phosphotransferase. 416 matched cddid_all.tbl CDD PRK14075 PRK14075 184489 pnk NAD(+) kinase. 256 matched cddid_all.tbl CDD PRK14076 PRK14076 237601 pnk bifunctional NADP phosphatase/NAD kinase. 569 matched cddid_all.tbl CDD PRK14077 PRK14077 172567 pnk NAD(+) kinase. 287 matched cddid_all.tbl CDD PRK14079 PRK14079 184491 recF recombination protein F; Provisional 349 matched cddid_all.tbl CDD PRK14081 PRK14081 237602 PRK14081 triple tyrosine motif-containing protein; Provisional 667 matched cddid_all.tbl CDD PRK14082 PRK14082 184493 PRK14082 hypothetical protein; Provisional 65 matched cddid_all.tbl CDD PRK14083 PRK14083 237603 PRK14083 HSP90 family protein; Provisional 601 matched cddid_all.tbl CDD PRK14084 PRK14084 184495 PRK14084 DNA-binding response regulator. 246 matched cddid_all.tbl CDD PRK14086 PRK14086 237605 dnaA chromosomal replication initiator protein DnaA. 617 matched cddid_all.tbl CDD PRK14090 PRK14090 184499 PRK14090 phosphoribosylformylglycinamidine synthase subunit PurL. 601 matched cddid_all.tbl CDD PRK14091 PRK14091 237607 PRK14091 RNA chaperone Hfq. 165 matched cddid_all.tbl CDD PRK14092 PRK14092 172582 PRK14092 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase. 163 matched cddid_all.tbl CDD PRK14093 PRK14093 184501 PRK14093 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanine ligase; Provisional 479 matched cddid_all.tbl CDD PRK14094 PRK14094 172584 psbM photosystem II reaction center protein PsbM. 50 matched cddid_all.tbl CDD PRK14095 PRK14095 237608 pgi glucose-6-phosphate isomerase; Provisional 533 matched cddid_all.tbl CDD PRK14096 PRK14096 237609 pgi glucose-6-phosphate isomerase; Provisional 528 matched cddid_all.tbl CDD PRK14097 PRK14097 184504 pgi glucose-6-phosphate isomerase; Provisional 448 matched cddid_all.tbl CDD PRK14098 PRK14098 172588 PRK14098 starch synthase. 489 matched cddid_all.tbl CDD PRK14099 PRK14099 237610 PRK14099 glycogen synthase GlgA. 485 matched cddid_all.tbl CDD PRK14100 PRK14100 184506 PRK14100 2-phosphosulfolactate phosphatase; Provisional 237 matched cddid_all.tbl CDD PRK14101 PRK14101 184507 PRK14101 bifunctional transcriptional regulator/glucokinase. 638 matched cddid_all.tbl CDD PRK14102 PRK14102 184508 nifW nitrogenase-stabilizing/protective protein NifW. 105 matched cddid_all.tbl CDD PRK14103 PRK14103 184509 PRK14103 trans-aconitate 2-methyltransferase; Provisional 255 matched cddid_all.tbl CDD PRK14104 PRK14104 172594 PRK14104 chaperonin GroEL; Provisional 546 matched cddid_all.tbl CDD PRK14105 PRK14105 237611 PRK14105 selenide, water dikinase SelD. 345 matched cddid_all.tbl CDD PRK14106 PRK14106 184511 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional 450 matched cddid_all.tbl CDD PRK14108 PRK14108 237612 PRK14108 bifunctional [glutamine synthetase] adenylyltransferase/[glutamine synthetase]-adenylyl-L-tyrosine phosphorylase. 986 matched cddid_all.tbl CDD PRK14109 PRK14109 237613 PRK14109 bifunctional [glutamine synthetase] adenylyltransferase/[glutamine synthetase]-adenylyl-L-tyrosine phosphorylase. 1007 matched cddid_all.tbl CDD PRK14110 PRK14110 184514 PRK14110 F0F1 ATP synthase subunit gamma; Provisional 291 matched cddid_all.tbl CDD PRK14111 PRK14111 184515 PRK14111 F0F1 ATP synthase subunit gamma; Provisional 290 matched cddid_all.tbl CDD PRK14112 PRK14112 172602 PRK14112 urease accessory protein UreE; Provisional 149 matched cddid_all.tbl CDD PRK14113 PRK14113 237614 PRK14113 urease accessory protein UreE; Provisional 152 matched cddid_all.tbl CDD PRK14114 PRK14114 172604 PRK14114 1-(5-phosphoribosyl)-5- ((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase. 241 matched cddid_all.tbl CDD PRK14115 PRK14115 184516 gpmA 2,3-diphosphoglycerate-dependent phosphoglycerate mutase. 247 matched cddid_all.tbl CDD PRK14116 PRK14116 172606 gpmA 2,3-diphosphoglycerate-dependent phosphoglycerate mutase. 228 matched cddid_all.tbl CDD PRK14117 PRK14117 184517 gpmA phosphoglyceromutase; Provisional 230 matched cddid_all.tbl CDD PRK14118 PRK14118 172608 gpmA 2,3-diphosphoglycerate-dependent phosphoglycerate mutase. 227 matched cddid_all.tbl CDD PRK14119 PRK14119 184518 gpmA phosphoglyceromutase; Provisional 228 matched cddid_all.tbl CDD PRK14120 PRK14120 184519 gpmA phosphoglyceromutase; Provisional 249 matched cddid_all.tbl CDD PRK14121 PRK14121 237615 PRK14121 tRNA (guanine-N(7)-)-methyltransferase; Provisional 390 matched cddid_all.tbl CDD PRK14125 PRK14125 184523 PRK14125 cell division suppressor protein YneA; Provisional 103 matched cddid_all.tbl CDD PRK14126 PRK14126 172616 PRK14126 cell division protein ZapA; Provisional 85 matched cddid_all.tbl CDD PRK14127 PRK14127 237616 PRK14127 cell division regulator GpsB. 109 matched cddid_all.tbl CDD PRK14128 PRK14128 184525 iraD anti-adapter protein IraD. 69 matched cddid_all.tbl CDD PRK14129 PRK14129 184526 PRK14129 heat shock protein HspQ; Provisional 105 matched cddid_all.tbl CDD PRK14131 PRK14131 237617 PRK14131 N-acetylneuraminate epimerase. 376 matched cddid_all.tbl CDD PRK14132 PRK14132 237618 PRK14132 riboflavin kinase; Provisional 126 matched cddid_all.tbl CDD PRK14133 PRK14133 184529 PRK14133 DNA polymerase IV; Provisional 347 matched cddid_all.tbl CDD PRK14134 PRK14134 184530 recX recombination regulator RecX; Provisional 283 matched cddid_all.tbl CDD PRK14135 PRK14135 237619 recX recombination regulator RecX; Provisional 263 matched cddid_all.tbl CDD PRK14136 PRK14136 237620 recX recombination regulator RecX; Provisional 309 matched cddid_all.tbl CDD PRK14137 PRK14137 172626 recX recombination regulator RecX; Provisional 195 matched cddid_all.tbl CDD PRK14138 PRK14138 172627 PRK14138 NAD-dependent deacetylase; Provisional 244 matched cddid_all.tbl CDD PRK14139 PRK14139 237621 PRK14139 heat shock protein GrpE; Provisional 185 matched cddid_all.tbl CDD PRK14140 PRK14140 237622 PRK14140 heat shock protein GrpE; Provisional 191 matched cddid_all.tbl CDD PRK14141 PRK14141 172630 PRK14141 heat shock protein GrpE; Provisional 209 matched cddid_all.tbl CDD PRK14142 PRK14142 237623 PRK14142 heat shock protein GrpE; Provisional 223 matched cddid_all.tbl CDD PRK14143 PRK14143 237624 PRK14143 heat shock protein GrpE; Provisional 238 matched cddid_all.tbl CDD PRK14144 PRK14144 184535 PRK14144 heat shock protein GrpE; Provisional 199 matched cddid_all.tbl CDD PRK14145 PRK14145 184536 PRK14145 heat shock protein GrpE; Provisional 196 matched cddid_all.tbl CDD PRK14146 PRK14146 172635 PRK14146 heat shock protein GrpE; Provisional 215 matched cddid_all.tbl CDD PRK14147 PRK14147 237625 PRK14147 heat shock protein GrpE; Provisional 172 matched cddid_all.tbl CDD PRK14148 PRK14148 172637 PRK14148 heat shock protein GrpE; Provisional 195 matched cddid_all.tbl CDD PRK14149 PRK14149 184538 PRK14149 heat shock protein GrpE; Provisional 191 matched cddid_all.tbl CDD PRK14150 PRK14150 184539 PRK14150 heat shock protein GrpE; Provisional 193 matched cddid_all.tbl CDD PRK14151 PRK14151 172640 PRK14151 heat shock protein GrpE; Provisional 176 matched cddid_all.tbl CDD PRK14153 PRK14153 184540 PRK14153 heat shock protein GrpE; Provisional 194 matched cddid_all.tbl CDD PRK14154 PRK14154 237626 PRK14154 heat shock protein GrpE; Provisional 208 matched cddid_all.tbl CDD PRK14155 PRK14155 237627 PRK14155 heat shock protein GrpE; Provisional 208 matched cddid_all.tbl CDD PRK14156 PRK14156 237628 PRK14156 heat shock protein GrpE; Provisional 177 matched cddid_all.tbl CDD PRK14157 PRK14157 184543 PRK14157 heat shock protein GrpE; Provisional 227 matched cddid_all.tbl CDD PRK14158 PRK14158 172646 PRK14158 heat shock protein GrpE; Provisional 194 matched cddid_all.tbl CDD PRK14159 PRK14159 172647 PRK14159 heat shock protein GrpE; Provisional 176 matched cddid_all.tbl CDD PRK14160 PRK14160 237629 PRK14160 heat shock protein GrpE; Provisional 211 matched cddid_all.tbl CDD PRK14161 PRK14161 237630 PRK14161 heat shock protein GrpE; Provisional 178 matched cddid_all.tbl CDD PRK14162 PRK14162 237631 PRK14162 heat shock protein GrpE; Provisional 194 matched cddid_all.tbl CDD PRK14163 PRK14163 184546 PRK14163 heat shock protein GrpE; Provisional 214 matched cddid_all.tbl CDD PRK14164 PRK14164 237632 PRK14164 heat shock protein GrpE; Provisional 218 matched cddid_all.tbl CDD PRK14165 PRK14165 184548 PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional 217 matched cddid_all.tbl CDD PRK14166 PRK14166 172654 PRK14166 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional 282 matched cddid_all.tbl CDD PRK14167 PRK14167 184549 PRK14167 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional 297 matched cddid_all.tbl CDD PRK14168 PRK14168 237633 PRK14168 bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD. 297 matched cddid_all.tbl CDD PRK14169 PRK14169 184550 PRK14169 bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD. 282 matched cddid_all.tbl CDD PRK14170 PRK14170 172658 PRK14170 bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD. 284 matched cddid_all.tbl CDD PRK14171 PRK14171 172659 PRK14171 bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD. 288 matched cddid_all.tbl CDD PRK14172 PRK14172 172660 PRK14172 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional 278 matched cddid_all.tbl CDD PRK14173 PRK14173 184551 PRK14173 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional 287 matched cddid_all.tbl CDD PRK14174 PRK14174 172662 PRK14174 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional 295 matched cddid_all.tbl CDD PRK14175 PRK14175 184552 PRK14175 bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD. 286 matched cddid_all.tbl CDD PRK14176 PRK14176 184553 PRK14176 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional 287 matched cddid_all.tbl CDD PRK14177 PRK14177 172665 PRK14177 bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD. 284 matched cddid_all.tbl CDD PRK14178 PRK14178 172666 PRK14178 bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD. 279 matched cddid_all.tbl CDD PRK14179 PRK14179 237634 PRK14179 bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase. 284 matched cddid_all.tbl CDD PRK14180 PRK14180 172668 PRK14180 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional 282 matched cddid_all.tbl CDD PRK14181 PRK14181 172669 PRK14181 bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD. 287 matched cddid_all.tbl CDD PRK14182 PRK14182 172670 PRK14182 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional 282 matched cddid_all.tbl CDD PRK14183 PRK14183 184555 PRK14183 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional 281 matched cddid_all.tbl CDD PRK14184 PRK14184 237635 PRK14184 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional 286 matched cddid_all.tbl CDD PRK14185 PRK14185 184556 PRK14185 bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD. 293 matched cddid_all.tbl CDD PRK14186 PRK14186 237636 PRK14186 bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD. 297 matched cddid_all.tbl CDD PRK14187 PRK14187 172675 PRK14187 bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD. 294 matched cddid_all.tbl CDD PRK14188 PRK14188 184558 PRK14188 bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD. 296 matched cddid_all.tbl CDD PRK14189 PRK14189 184559 PRK14189 bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase. 285 matched cddid_all.tbl CDD PRK14190 PRK14190 184560 PRK14190 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional 284 matched cddid_all.tbl CDD PRK14191 PRK14191 172679 PRK14191 bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD. 285 matched cddid_all.tbl CDD PRK14192 PRK14192 184561 PRK14192 bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD. 283 matched cddid_all.tbl CDD PRK14193 PRK14193 237637 PRK14193 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional 284 matched cddid_all.tbl CDD PRK14194 PRK14194 172682 PRK14194 bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD. 301 matched cddid_all.tbl CDD PRK14195 PRK14195 184563 PRK14195 fluoride efflux transporter CrcB. 125 matched cddid_all.tbl CDD PRK14196 PRK14196 184564 PRK14196 fluoride efflux transporter CrcB. 127 matched cddid_all.tbl CDD PRK14197 PRK14197 172685 PRK14197 fluoride efflux transporter CrcB. 124 matched cddid_all.tbl CDD PRK14198 PRK14198 172686 PRK14198 fluoride efflux transporter CrcB. 124 matched cddid_all.tbl CDD PRK14199 PRK14199 172687 PRK14199 fluoride efflux transporter CrcB. 128 matched cddid_all.tbl CDD PRK14200 PRK14200 237638 PRK14200 fluoride efflux transporter CrcB. 127 matched cddid_all.tbl CDD PRK14201 PRK14201 184566 PRK14201 fluoride efflux transporter CrcB. 121 matched cddid_all.tbl CDD PRK14202 PRK14202 172690 PRK14202 fluoride efflux transporter CrcB. 128 matched cddid_all.tbl CDD PRK14203 PRK14203 237639 PRK14203 fluoride efflux transporter CrcB. 132 matched cddid_all.tbl CDD PRK14204 PRK14204 172692 PRK14204 fluoride efflux transporter CrcB. 127 matched cddid_all.tbl CDD PRK14205 PRK14205 172693 PRK14205 fluoride efflux transporter CrcB. 118 matched cddid_all.tbl CDD PRK14206 PRK14206 172694 PRK14206 fluoride efflux transporter CrcB. 127 matched cddid_all.tbl CDD PRK14207 PRK14207 172695 PRK14207 fluoride efflux transporter CrcB. 123 matched cddid_all.tbl CDD PRK14208 PRK14208 172696 PRK14208 fluoride efflux transporter CrcB. 126 matched cddid_all.tbl CDD PRK14209 PRK14209 237640 PRK14209 fluoride efflux transporter CrcB. 124 matched cddid_all.tbl CDD PRK14210 PRK14210 172698 PRK14210 fluoride efflux transporter CrcB. 127 matched cddid_all.tbl CDD PRK14211 PRK14211 172699 PRK14211 fluoride efflux transporter CrcB. 114 matched cddid_all.tbl CDD PRK14212 PRK14212 184569 PRK14212 fluoride efflux transporter CrcB. 128 matched cddid_all.tbl CDD PRK14213 PRK14213 184570 PRK14213 camphor resistance protein CrcB; Provisional 118 matched cddid_all.tbl CDD PRK14214 PRK14214 184571 PRK14214 fluoride efflux transporter CrcB. 118 matched cddid_all.tbl CDD PRK14215 PRK14215 172703 PRK14215 fluoride efflux transporter CrcB. 126 matched cddid_all.tbl CDD PRK14216 PRK14216 184572 PRK14216 fluoride efflux transporter CrcB. 132 matched cddid_all.tbl CDD PRK14217 PRK14217 172705 PRK14217 fluoride efflux transporter CrcB. 134 matched cddid_all.tbl CDD PRK14218 PRK14218 184573 PRK14218 fluoride efflux transporter CrcB. 133 matched cddid_all.tbl CDD PRK14219 PRK14219 172707 PRK14219 fluoride efflux transporter CrcB. 132 matched cddid_all.tbl CDD PRK14220 PRK14220 237641 PRK14220 fluoride efflux transporter CrcB. 120 matched cddid_all.tbl CDD PRK14221 PRK14221 184575 PRK14221 fluoride efflux transporter CrcB. 124 matched cddid_all.tbl CDD PRK14222 PRK14222 172710 PRK14222 fluoride efflux transporter CrcB. 124 matched cddid_all.tbl CDD PRK14223 PRK14223 184576 PRK14223 fluoride efflux transporter CrcB. 122 matched cddid_all.tbl CDD PRK14224 PRK14224 237642 PRK14224 fluoride efflux transporter CrcB. 126 matched cddid_all.tbl CDD PRK14225 PRK14225 172713 PRK14225 fluoride efflux transporter CrcB. 137 matched cddid_all.tbl CDD PRK14226 PRK14226 172714 PRK14226 fluoride efflux transporter CrcB. 130 matched cddid_all.tbl CDD PRK14227 PRK14227 172715 PRK14227 fluoride efflux transporter CrcB. 124 matched cddid_all.tbl CDD PRK14228 PRK14228 237643 PRK14228 fluoride efflux transporter CrcB. 122 matched cddid_all.tbl CDD PRK14229 PRK14229 172717 PRK14229 fluoride efflux transporter CrcB. 108 matched cddid_all.tbl CDD PRK14230 PRK14230 172718 PRK14230 camphor resistance protein CrcB; Provisional 119 matched cddid_all.tbl CDD PRK14231 PRK14231 184579 PRK14231 fluoride efflux transporter CrcB. 129 matched cddid_all.tbl CDD PRK14232 PRK14232 237644 PRK14232 fluoride efflux transporter CrcB. 120 matched cddid_all.tbl CDD PRK14233 PRK14233 172721 PRK14233 fluoride efflux transporter CrcB. 133 matched cddid_all.tbl CDD PRK14234 PRK14234 172722 PRK14234 fluoride efflux transporter CrcB. 124 matched cddid_all.tbl CDD PRK14239 PRK14239 184585 PRK14239 phosphate transporter ATP-binding protein; Provisional 252 matched cddid_all.tbl CDD PRK14243 PRK14243 184588 PRK14243 phosphate transporter ATP-binding protein; Provisional 264 matched cddid_all.tbl CDD PRK14246 PRK14246 172734 PRK14246 phosphate ABC transporter ATP-binding protein; Provisional 257 matched cddid_all.tbl CDD PRK14247 PRK14247 172735 PRK14247 phosphate ABC transporter ATP-binding protein; Provisional 250 matched cddid_all.tbl CDD PRK14258 PRK14258 184593 PRK14258 phosphate ABC transporter ATP-binding protein; Provisional 261 matched cddid_all.tbl CDD PRK14267 PRK14267 184596 PRK14267 phosphate ABC transporter ATP-binding protein; Provisional 253 matched cddid_all.tbl CDD PRK14271 PRK14271 172759 PRK14271 phosphate ABC transporter ATP-binding protein; Provisional 276 matched cddid_all.tbl CDD PRK14276 PRK14276 237653 PRK14276 chaperone protein DnaJ; Provisional 380 matched cddid_all.tbl CDD PRK14277 PRK14277 184599 PRK14277 chaperone protein DnaJ; Provisional 386 matched cddid_all.tbl CDD PRK14278 PRK14278 237654 PRK14278 chaperone protein DnaJ; Provisional 378 matched cddid_all.tbl CDD PRK14279 PRK14279 237655 PRK14279 molecular chaperone DnaJ. 392 matched cddid_all.tbl CDD PRK14280 PRK14280 237656 PRK14280 molecular chaperone DnaJ. 376 matched cddid_all.tbl CDD PRK14281 PRK14281 237657 PRK14281 chaperone protein DnaJ; Provisional 397 matched cddid_all.tbl CDD PRK14282 PRK14282 184603 PRK14282 chaperone protein DnaJ; Provisional 369 matched cddid_all.tbl CDD PRK14283 PRK14283 184604 PRK14283 chaperone protein DnaJ; Provisional 378 matched cddid_all.tbl CDD PRK14284 PRK14284 237658 PRK14284 chaperone protein DnaJ; Provisional 391 matched cddid_all.tbl CDD PRK14285 PRK14285 172773 PRK14285 chaperone protein DnaJ; Provisional 365 matched cddid_all.tbl CDD PRK14286 PRK14286 172774 PRK14286 chaperone protein DnaJ; Provisional 372 matched cddid_all.tbl CDD PRK14287 PRK14287 237659 PRK14287 chaperone protein DnaJ; Provisional 371 matched cddid_all.tbl CDD PRK14288 PRK14288 172776 PRK14288 molecular chaperone DnaJ. 369 matched cddid_all.tbl CDD PRK14289 PRK14289 237660 PRK14289 molecular chaperone DnaJ. 386 matched cddid_all.tbl CDD PRK14290 PRK14290 172778 PRK14290 chaperone protein DnaJ; Provisional 365 matched cddid_all.tbl CDD PRK14291 PRK14291 237661 PRK14291 chaperone protein DnaJ; Provisional 382 matched cddid_all.tbl CDD PRK14292 PRK14292 237662 PRK14292 chaperone protein DnaJ; Provisional 371 matched cddid_all.tbl CDD PRK14293 PRK14293 237663 PRK14293 molecular chaperone DnaJ. 374 matched cddid_all.tbl CDD PRK14294 PRK14294 237664 PRK14294 chaperone protein DnaJ; Provisional 366 matched cddid_all.tbl CDD PRK14295 PRK14295 237665 PRK14295 molecular chaperone DnaJ. 389 matched cddid_all.tbl CDD PRK14296 PRK14296 237666 PRK14296 chaperone protein DnaJ; Provisional 372 matched cddid_all.tbl CDD PRK14297 PRK14297 184611 PRK14297 molecular chaperone DnaJ. 380 matched cddid_all.tbl CDD PRK14298 PRK14298 184612 PRK14298 chaperone protein DnaJ; Provisional 377 matched cddid_all.tbl CDD PRK14299 PRK14299 237667 PRK14299 chaperone protein DnaJ; Provisional 291 matched cddid_all.tbl CDD PRK14300 PRK14300 172788 PRK14300 chaperone protein DnaJ; Provisional 372 matched cddid_all.tbl CDD PRK14301 PRK14301 237668 PRK14301 chaperone protein DnaJ; Provisional 373 matched cddid_all.tbl CDD PRK14328 PRK14328 237675 PRK14328 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional 439 matched cddid_all.tbl CDD PRK14336 PRK14336 184632 PRK14336 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional 418 matched cddid_all.tbl CDD PRK14341 PRK14341 237680 PRK14341 lipoyl(octanoyl) transferase LipB. 213 matched cddid_all.tbl CDD PRK14342 PRK14342 237681 PRK14342 lipoyl(octanoyl) transferase LipB. 213 matched cddid_all.tbl CDD PRK14343 PRK14343 237682 PRK14343 lipoyl(octanoyl) transferase LipB. 235 matched cddid_all.tbl CDD PRK14344 PRK14344 237683 PRK14344 lipoyl(octanoyl) transferase LipB. 223 matched cddid_all.tbl CDD PRK14345 PRK14345 184638 PRK14345 lipoyl(octanoyl) transferase LipB. 234 matched cddid_all.tbl CDD PRK14346 PRK14346 237684 PRK14346 lipoyl(octanoyl) transferase LipB. 230 matched cddid_all.tbl CDD PRK14347 PRK14347 172823 PRK14347 lipoyl(octanoyl) transferase LipB. 209 matched cddid_all.tbl CDD PRK14348 PRK14348 172824 PRK14348 lipoyl(octanoyl) transferase LipB. 221 matched cddid_all.tbl CDD PRK14349 PRK14349 172825 PRK14349 lipoyl(octanoyl) transferase LipB. 220 matched cddid_all.tbl CDD PRK14350 PRK14350 172826 ligA NAD-dependent DNA ligase LigA; Provisional 669 matched cddid_all.tbl CDD PRK14351 PRK14351 184640 ligA NAD-dependent DNA ligase LigA; Provisional 689 matched cddid_all.tbl CDD PRK14352 PRK14352 184641 glmU bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU. 482 matched cddid_all.tbl CDD PRK14353 PRK14353 184642 glmU bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU. 446 matched cddid_all.tbl CDD PRK14354 PRK14354 184643 glmU bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU. 458 matched cddid_all.tbl CDD PRK14355 PRK14355 237685 glmU bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU. 459 matched cddid_all.tbl CDD PRK14356 PRK14356 237686 glmU bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU. 456 matched cddid_all.tbl CDD PRK14357 PRK14357 237687 glmU bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU. 448 matched cddid_all.tbl CDD PRK14358 PRK14358 237688 glmU bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/glucosamine-1-phosphate acetyltransferase; Provisional 481 matched cddid_all.tbl CDD PRK14359 PRK14359 237689 glmU bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU. 430 matched cddid_all.tbl CDD PRK14360 PRK14360 184646 glmU bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU. 450 matched cddid_all.tbl CDD PRK14361 PRK14361 172837 PRK14361 Maf-like protein; Provisional 187 matched cddid_all.tbl CDD PRK14362 PRK14362 172838 PRK14362 Maf-like protein; Provisional 207 matched cddid_all.tbl CDD PRK14363 PRK14363 184647 PRK14363 Maf-like protein; Provisional 204 matched cddid_all.tbl CDD PRK14364 PRK14364 184648 PRK14364 Maf-like protein; Provisional 181 matched cddid_all.tbl CDD PRK14365 PRK14365 237690 PRK14365 Maf-like protein; Provisional 197 matched cddid_all.tbl CDD PRK14366 PRK14366 237691 PRK14366 Maf-like protein; Provisional 195 matched cddid_all.tbl CDD PRK14367 PRK14367 237692 PRK14367 Maf-like protein; Provisional 202 matched cddid_all.tbl CDD PRK14368 PRK14368 237693 PRK14368 Maf-like protein; Provisional 193 matched cddid_all.tbl CDD PRK14369 PRK14369 184650 PRK14369 membrane protein insertion efficiency factor YidD. 119 matched cddid_all.tbl CDD PRK14370 PRK14370 184651 PRK14370 hypothetical protein; Provisional 120 matched cddid_all.tbl CDD PRK14371 PRK14371 172847 PRK14371 hypothetical protein; Provisional 81 matched cddid_all.tbl CDD PRK14372 PRK14372 172848 PRK14372 membrane protein insertion efficiency factor YidD. 97 matched cddid_all.tbl CDD PRK14373 PRK14373 172849 PRK14373 hypothetical protein; Provisional 73 matched cddid_all.tbl CDD PRK14374 PRK14374 237694 PRK14374 membrane protein insertion efficiency factor YidD. 118 matched cddid_all.tbl CDD PRK14375 PRK14375 172851 PRK14375 membrane protein insertion efficiency factor YidD. 70 matched cddid_all.tbl CDD PRK14376 PRK14376 237695 PRK14376 membrane protein insertion efficiency factor YidD. 176 matched cddid_all.tbl CDD PRK14377 PRK14377 172853 PRK14377 membrane protein insertion efficiency factor YidD. 104 matched cddid_all.tbl CDD PRK14378 PRK14378 237696 PRK14378 membrane protein insertion efficiency factor YidD. 103 matched cddid_all.tbl CDD PRK14379 PRK14379 237697 PRK14379 membrane protein insertion efficiency factor YidD. 95 matched cddid_all.tbl CDD PRK14380 PRK14380 184654 PRK14380 hypothetical protein; Provisional 81 matched cddid_all.tbl CDD PRK14381 PRK14381 172857 PRK14381 membrane protein insertion efficiency factor YidD. 103 matched cddid_all.tbl CDD PRK14382 PRK14382 172858 PRK14382 hypothetical protein; Provisional 68 matched cddid_all.tbl CDD PRK14383 PRK14383 237698 PRK14383 membrane protein insertion efficiency factor YidD. 84 matched cddid_all.tbl CDD PRK14384 PRK14384 172860 PRK14384 hypothetical protein; Provisional 56 matched cddid_all.tbl CDD PRK14385 PRK14385 172861 PRK14385 membrane protein insertion efficiency factor YidD. 96 matched cddid_all.tbl CDD PRK14386 PRK14386 172862 PRK14386 membrane protein insertion efficiency factor YidD. 106 matched cddid_all.tbl CDD PRK14387 PRK14387 184655 PRK14387 membrane protein insertion efficiency factor YidD. 84 matched cddid_all.tbl CDD PRK14388 PRK14388 172864 PRK14388 membrane protein insertion efficiency factor YidD. 82 matched cddid_all.tbl CDD PRK14389 PRK14389 184656 PRK14389 membrane protein insertion efficiency factor YidD. 98 matched cddid_all.tbl CDD PRK14390 PRK14390 172866 PRK14390 hypothetical protein; Provisional 63 matched cddid_all.tbl CDD PRK14391 PRK14391 172867 PRK14391 membrane protein insertion efficiency factor YidD. 84 matched cddid_all.tbl CDD PRK14397 PRK14397 237700 PRK14397 membrane protein; Provisional 222 matched cddid_all.tbl CDD PRK14399 PRK14399 237702 PRK14399 membrane protein; Provisional 258 matched cddid_all.tbl CDD PRK14401 PRK14401 184658 PRK14401 membrane protein; Provisional 187 matched cddid_all.tbl CDD PRK14405 PRK14405 237706 PRK14405 membrane protein; Provisional 202 matched cddid_all.tbl CDD PRK14411 PRK14411 184663 PRK14411 membrane protein; Provisional 204 matched cddid_all.tbl CDD PRK14414 PRK14414 184665 PRK14414 glycerol-3-phosphate acyltransferase. 210 matched cddid_all.tbl CDD PRK14416 PRK14416 184667 PRK14416 membrane protein; Provisional 200 matched cddid_all.tbl CDD PRK14417 PRK14417 184668 PRK14417 membrane protein; Provisional 232 matched cddid_all.tbl CDD PRK14419 PRK14419 237709 PRK14419 membrane protein; Provisional 199 matched cddid_all.tbl CDD PRK14420 PRK14420 237710 PRK14420 acylphosphatase; Provisional 91 matched cddid_all.tbl CDD PRK14421 PRK14421 237711 PRK14421 acylphosphatase; Provisional 99 matched cddid_all.tbl CDD PRK14422 PRK14422 237712 PRK14422 acylphosphatase; Provisional 93 matched cddid_all.tbl CDD PRK14423 PRK14423 237713 PRK14423 acylphosphatase; Provisional 92 matched cddid_all.tbl CDD PRK14424 PRK14424 184674 PRK14424 acylphosphatase; Provisional 94 matched cddid_all.tbl CDD PRK14425 PRK14425 172901 PRK14425 acylphosphatase; Provisional 94 matched cddid_all.tbl CDD PRK14426 PRK14426 184675 PRK14426 acylphosphatase; Provisional 92 matched cddid_all.tbl CDD PRK14427 PRK14427 172903 PRK14427 acylphosphatase; Provisional 94 matched cddid_all.tbl CDD PRK14428 PRK14428 172904 PRK14428 acylphosphatase; Provisional 97 matched cddid_all.tbl CDD PRK14429 PRK14429 184676 PRK14429 acylphosphatase; Provisional 90 matched cddid_all.tbl CDD PRK14430 PRK14430 172906 PRK14430 acylphosphatase; Provisional 92 matched cddid_all.tbl CDD PRK14431 PRK14431 184677 PRK14431 acylphosphatase; Provisional 89 matched cddid_all.tbl CDD PRK14432 PRK14432 184678 PRK14432 acylphosphatase; Provisional 93 matched cddid_all.tbl CDD PRK14433 PRK14433 184679 PRK14433 acylphosphatase; Provisional 87 matched cddid_all.tbl CDD PRK14434 PRK14434 184680 PRK14434 acylphosphatase; Provisional 92 matched cddid_all.tbl CDD PRK14435 PRK14435 184681 PRK14435 acylphosphatase; Provisional 90 matched cddid_all.tbl CDD PRK14436 PRK14436 172912 PRK14436 acylphosphatase; Provisional 91 matched cddid_all.tbl CDD PRK14437 PRK14437 172913 PRK14437 acylphosphatase; Provisional 109 matched cddid_all.tbl CDD PRK14438 PRK14438 172914 PRK14438 acylphosphatase; Provisional 91 matched cddid_all.tbl CDD PRK14439 PRK14439 237714 PRK14439 acylphosphatase; Provisional 163 matched cddid_all.tbl CDD PRK14440 PRK14440 172916 PRK14440 acylphosphatase; Provisional 90 matched cddid_all.tbl CDD PRK14441 PRK14441 172917 PRK14441 acylphosphatase; Provisional 93 matched cddid_all.tbl CDD PRK14442 PRK14442 172918 PRK14442 acylphosphatase; Provisional 91 matched cddid_all.tbl CDD PRK14443 PRK14443 172919 PRK14443 acylphosphatase; Provisional 93 matched cddid_all.tbl CDD PRK14444 PRK14444 172920 PRK14444 acylphosphatase; Provisional 92 matched cddid_all.tbl CDD PRK14445 PRK14445 172921 PRK14445 acylphosphatase; Provisional 91 matched cddid_all.tbl CDD PRK14446 PRK14446 172922 PRK14446 acylphosphatase; Provisional 88 matched cddid_all.tbl CDD PRK14447 PRK14447 172923 PRK14447 acylphosphatase; Provisional 95 matched cddid_all.tbl CDD PRK14448 PRK14448 172924 PRK14448 acylphosphatase; Provisional 90 matched cddid_all.tbl CDD PRK14449 PRK14449 184682 PRK14449 acylphosphatase; Provisional 90 matched cddid_all.tbl CDD PRK14450 PRK14450 184683 PRK14450 acylphosphatase; Provisional 91 matched cddid_all.tbl CDD PRK14451 PRK14451 237715 PRK14451 acylphosphatase; Provisional 89 matched cddid_all.tbl CDD PRK14452 PRK14452 237716 PRK14452 acylphosphatase; Provisional 107 matched cddid_all.tbl CDD PRK14453 PRK14453 184685 PRK14453 chloramphenicol/florfenicol resistance protein; Provisional 347 matched cddid_all.tbl CDD PRK14461 PRK14461 237718 PRK14461 ribosomal RNA large subunit methyltransferase N; Provisional 371 matched cddid_all.tbl CDD PRK14464 PRK14464 184691 PRK14464 RNA methyltransferase. 344 matched cddid_all.tbl CDD PRK14470 PRK14470 172945 PRK14470 ribosomal RNA large subunit methyltransferase N; Provisional 336 matched cddid_all.tbl CDD PRK14471 PRK14471 184695 PRK14471 F0F1 ATP synthase subunit B; Provisional 164 matched cddid_all.tbl CDD PRK14472 PRK14472 172947 PRK14472 F0F1 ATP synthase subunit B; Provisional 175 matched cddid_all.tbl CDD PRK14473 PRK14473 172948 PRK14473 F0F1 ATP synthase subunit B; Provisional 164 matched cddid_all.tbl CDD PRK14474 PRK14474 184696 PRK14474 F0F1 ATP synthase subunit B; Provisional 250 matched cddid_all.tbl CDD PRK14475 PRK14475 184697 PRK14475 F0F1 ATP synthase subunit B; Provisional 167 matched cddid_all.tbl CDD PRK14477 PRK14477 172952 PRK14477 bifunctional nitrogenase molybdenum-cofactor biosynthesis protein NifE/NifN; Provisional 917 matched cddid_all.tbl CDD PRK14479 PRK14479 237723 PRK14479 dihydroxyacetone kinase; Provisional 568 matched cddid_all.tbl CDD PRK14481 PRK14481 237724 PRK14481 dihydroxyacetone kinase subunit DhaK; Provisional 331 matched cddid_all.tbl CDD PRK14483 PRK14483 172956 PRK14483 DhaKLM operon coactivator DhaQ; Provisional 329 matched cddid_all.tbl CDD PRK14484 PRK14484 184702 PRK14484 phosphotransferase mannnose-specific family component IIA; Provisional 124 matched cddid_all.tbl CDD PRK14485 PRK14485 184703 PRK14485 putative bifunctional cbb3-type cytochrome c oxidase subunit I/II; Provisional 712 matched cddid_all.tbl CDD PRK14486 PRK14486 184704 PRK14486 putative bifunctional cbb3-type cytochrome c oxidase subunit II/cytochrome c; Provisional 294 matched cddid_all.tbl CDD PRK14487 PRK14487 237725 PRK14487 cbb3-type cytochrome c oxidase subunit II; Provisional 217 matched cddid_all.tbl CDD PRK14488 PRK14488 237726 PRK14488 cbb3-type cytochrome c oxidase subunit I; Provisional 473 matched cddid_all.tbl CDD PRK14489 PRK14489 237727 PRK14489 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobA/MobB; Provisional 366 matched cddid_all.tbl CDD PRK14490 PRK14490 237728 PRK14490 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MobA; Provisional 369 matched cddid_all.tbl CDD PRK14491 PRK14491 237729 PRK14491 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoeA; Provisional 597 matched cddid_all.tbl CDD PRK14493 PRK14493 237730 PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional 274 matched cddid_all.tbl CDD PRK14494 PRK14494 237731 PRK14494 putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein protein; Provisional 229 matched cddid_all.tbl CDD PRK14495 PRK14495 172967 PRK14495 putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/unknown domain fusion protein; Provisional 452 matched cddid_all.tbl CDD PRK14497 PRK14497 172968 PRK14497 putative molybdopterin biosynthesis protein MoeA/unknown domain fusion protein; Provisional 546 matched cddid_all.tbl CDD PRK14498 PRK14498 237732 PRK14498 putative molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein; Provisional 633 matched cddid_all.tbl CDD PRK14499 PRK14499 237733 PRK14499 cyclic pyranopterin monophosphate synthase MoaC/MOSC-domain-containing protein. 308 matched cddid_all.tbl CDD PRK14500 PRK14500 237734 PRK14500 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MoaC/MobA; Provisional 346 matched cddid_all.tbl CDD PRK14501 PRK14501 184712 PRK14501 putative bifunctional trehalose-6-phosphate synthase/HAD hydrolase subfamily IIB; Provisional 726 matched cddid_all.tbl CDD PRK14502 PRK14502 184713 PRK14502 bifunctional mannosyl-3-phosphoglycerate synthase/mannosyl-3 phosphoglycerate phosphatase; Provisional 694 matched cddid_all.tbl CDD PRK14505 PRK14505 172976 PRK14505 bifunctional photosynthetic reaction center subunit L/M; Provisional 643 matched cddid_all.tbl CDD PRK14507 PRK14507 237737 PRK14507 malto-oligosyltrehalose synthase. 1693 matched cddid_all.tbl CDD PRK14508 PRK14508 237738 PRK14508 4-alpha-glucanotransferase; Provisional 497 matched cddid_all.tbl CDD PRK14510 PRK14510 237739 PRK14510 bifunctional glycogen debranching protein GlgX/4-alpha-glucanotransferase. 1221 matched cddid_all.tbl CDD PRK14511 PRK14511 237740 PRK14511 malto-oligosyltrehalose synthase. 879 matched cddid_all.tbl CDD PRK14512 PRK14512 237741 PRK14512 ATP-dependent Clp protease proteolytic subunit; Provisional 197 matched cddid_all.tbl CDD PRK14513 PRK14513 237742 PRK14513 ATP-dependent Clp protease proteolytic subunit; Provisional 201 matched cddid_all.tbl CDD PRK14514 PRK14514 184722 PRK14514 ATP-dependent Clp endopeptidase proteolytic subunit ClpP. 221 matched cddid_all.tbl CDD PRK14515 PRK14515 237743 PRK14515 aspartate ammonia-lyase; Provisional 479 matched cddid_all.tbl CDD PRK14520 PRK14520 184724 rpsP 30S ribosomal protein S16; Provisional 155 matched cddid_all.tbl CDD PRK14521 PRK14521 237744 rpsP 30S ribosomal protein S16; Provisional 186 matched cddid_all.tbl CDD PRK14522 PRK14522 172988 rpsP 30S ribosomal protein S16; Provisional 116 matched cddid_all.tbl CDD PRK14526 PRK14526 172992 PRK14526 adenylate kinase; Provisional 211 matched cddid_all.tbl CDD PRK14527 PRK14527 237745 PRK14527 adenylate kinase; Provisional 191 matched cddid_all.tbl CDD PRK14528 PRK14528 172994 PRK14528 adenylate kinase; Provisional 186 matched cddid_all.tbl CDD PRK14529 PRK14529 237746 PRK14529 adenylate kinase; Provisional 223 matched cddid_all.tbl CDD PRK14530 PRK14530 237747 PRK14530 adenylate kinase; Provisional 215 matched cddid_all.tbl CDD PRK14531 PRK14531 172997 PRK14531 adenylate kinase; Provisional 183 matched cddid_all.tbl CDD PRK14532 PRK14532 184729 PRK14532 adenylate kinase; Provisional 188 matched cddid_all.tbl CDD PRK14533 PRK14533 184730 groES co-chaperonin GroES; Provisional 91 matched cddid_all.tbl CDD PRK14534 PRK14534 173000 cysS cysteinyl-tRNA synthetase; Provisional 481 matched cddid_all.tbl CDD PRK14535 PRK14535 173001 cysS cysteinyl-tRNA synthetase; Provisional 699 matched cddid_all.tbl CDD PRK14536 PRK14536 184731 cysS cysteinyl-tRNA synthetase; Provisional 490 matched cddid_all.tbl CDD PRK14537 PRK14537 237748 PRK14537 50S ribosomal protein L20/unknown domain fusion protein; Provisional 230 matched cddid_all.tbl CDD PRK14538 PRK14538 173004 PRK14538 putative bifunctional signaling protein/50S ribosomal protein L9; Provisional 838 matched cddid_all.tbl CDD PRK14539 PRK14539 184732 PRK14539 50S ribosomal protein L11/unknown domain fusion protein; Provisional 196 matched cddid_all.tbl CDD PRK14540 PRK14540 184733 PRK14540 nucleoside diphosphate kinase; Provisional 134 matched cddid_all.tbl CDD PRK14541 PRK14541 173007 PRK14541 nucleoside diphosphate kinase; Provisional 140 matched cddid_all.tbl CDD PRK14542 PRK14542 173008 PRK14542 nucleoside diphosphate kinase; Provisional 137 matched cddid_all.tbl CDD PRK14543 PRK14543 237749 PRK14543 nucleoside diphosphate kinase; Provisional 169 matched cddid_all.tbl CDD PRK14544 PRK14544 173010 PRK14544 nucleoside diphosphate kinase; Provisional 183 matched cddid_all.tbl CDD PRK14545 PRK14545 184734 PRK14545 nucleoside diphosphate kinase; Provisional 139 matched cddid_all.tbl CDD PRK14548 PRK14548 237750 PRK14548 50S ribosomal protein L23P; Provisional 84 matched cddid_all.tbl CDD PRK14549 PRK14549 237751 PRK14549 50S ribosomal protein L29P; Provisional 69 matched cddid_all.tbl CDD PRK14550 PRK14550 173015 rnhB ribonuclease HII; Provisional 204 matched cddid_all.tbl CDD PRK14552 PRK14552 237753 PRK14552 C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional 414 matched cddid_all.tbl CDD PRK14553 PRK14553 184740 PRK14553 ribosomal-processing cysteine protease Prp. 108 matched cddid_all.tbl CDD PRK14554 PRK14554 237754 PRK14554 tRNA pseudouridine(54/55) synthase Pus10. 422 matched cddid_all.tbl CDD PRK14555 PRK14555 237755 PRK14555 RNA-binding protein. 145 matched cddid_all.tbl CDD PRK14559 PRK14559 237756 PRK14559 serine/threonine phosphatase. 645 matched cddid_all.tbl CDD PRK14560 PRK14560 237757 PRK14560 putative RNA-binding protein; Provisional 160 matched cddid_all.tbl CDD PRK14561 PRK14561 184745 PRK14561 hypothetical protein; Provisional 194 matched cddid_all.tbl CDD PRK14562 PRK14562 184746 PRK14562 haloacid dehalogenase superfamily protein; Provisional 204 matched cddid_all.tbl CDD PRK14563 PRK14563 184747 PRK14563 ribosome modulation factor; Provisional 55 matched cddid_all.tbl CDD PRK14565 PRK14565 237758 PRK14565 triosephosphate isomerase; Provisional 237 matched cddid_all.tbl CDD PRK14569 PRK14569 173033 PRK14569 D-alanyl-alanine synthetase A; Provisional 296 matched cddid_all.tbl CDD PRK14570 PRK14570 173034 PRK14570 D-alanyl-alanine synthetase A; Provisional 364 matched cddid_all.tbl CDD PRK14571 PRK14571 184751 PRK14571 D-alanyl-alanine synthetase A; Provisional 299 matched cddid_all.tbl CDD PRK14572 PRK14572 173036 PRK14572 D-alanyl-alanine synthetase A; Provisional 347 matched cddid_all.tbl CDD PRK14573 PRK14573 184752 PRK14573 bifunctional UDP-N-acetylmuramate--L-alanine ligase/D-alanine--D-alanine ligase. 809 matched cddid_all.tbl CDD PRK14574 PRK14574 173038 hmsH poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA. 822 matched cddid_all.tbl CDD PRK14575 PRK14575 173039 PRK14575 putative peptidase; Provisional 406 matched cddid_all.tbl CDD PRK14576 PRK14576 173040 PRK14576 putative endopeptidase; Provisional 405 matched cddid_all.tbl CDD PRK14578 PRK14578 173042 PRK14578 elongation factor P; Provisional 187 matched cddid_all.tbl CDD PRK14581 PRK14581 184753 hmsF outer membrane N-deacetylase; Provisional 672 matched cddid_all.tbl CDD PRK14582 PRK14582 184754 pgaB poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB. 671 matched cddid_all.tbl CDD PRK14584 PRK14584 184756 hmsS hemin storage system protein; Provisional 153 matched cddid_all.tbl CDD PRK14585 PRK14585 173049 pgaD putative PGA biosynthesis protein; Provisional 137 matched cddid_all.tbl CDD PRK14587 PRK14587 173051 PRK14587 tRNA pseudouridine synthase ACD; Provisional 256 matched cddid_all.tbl CDD PRK14590 PRK14590 173054 rimM 16S rRNA-processing protein RimM; Provisional 171 matched cddid_all.tbl CDD PRK14591 PRK14591 173055 rimM 16S rRNA-processing protein RimM; Provisional 169 matched cddid_all.tbl CDD PRK14592 PRK14592 173056 rimM 16S rRNA-processing protein RimM; Provisional 165 matched cddid_all.tbl CDD PRK14593 PRK14593 237760 rimM ribosome maturation factor RimM. 184 matched cddid_all.tbl CDD PRK14594 PRK14594 173058 rimM 16S rRNA-processing protein RimM; Provisional 166 matched cddid_all.tbl CDD PRK14595 PRK14595 184757 PRK14595 peptide deformylase; Provisional 162 matched cddid_all.tbl CDD PRK14599 PRK14599 173063 trmD tRNA (guanine-N(1)-)-methyltransferase/unknown domain fusion protein; Provisional 222 matched cddid_all.tbl CDD PRK14600 PRK14600 173064 ruvA Holliday junction branch migration protein RuvA. 186 matched cddid_all.tbl CDD PRK14607 PRK14607 237764 PRK14607 bifunctional anthranilate synthase component II/anthranilate phosphoribosyltransferase. 534 matched cddid_all.tbl CDD PRK14608 PRK14608 237765 PRK14608 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; Provisional 290 matched cddid_all.tbl CDD PRK14611 PRK14611 184767 PRK14611 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase. 275 matched cddid_all.tbl CDD PRK14613 PRK14613 173077 PRK14613 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase. 297 matched cddid_all.tbl CDD PRK14618 PRK14618 237770 PRK14618 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Provisional 328 matched cddid_all.tbl CDD PRK14619 PRK14619 237771 PRK14619 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Provisional 308 matched cddid_all.tbl CDD PRK14620 PRK14620 173083 PRK14620 NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Provisional 326 matched cddid_all.tbl CDD PRK14625 PRK14625 184772 PRK14625 hypothetical protein; Provisional 109 matched cddid_all.tbl CDD PRK14630 PRK14630 173093 PRK14630 ribosome maturation factor RimP. 143 matched cddid_all.tbl CDD PRK14631 PRK14631 237772 PRK14631 ribosome maturation factor RimP. 174 matched cddid_all.tbl CDD PRK14632 PRK14632 173095 PRK14632 ribosome maturation factor RimP. 172 matched cddid_all.tbl CDD PRK14633 PRK14633 173096 PRK14633 ribosome maturation factor RimP. 150 matched cddid_all.tbl CDD PRK14634 PRK14634 173097 PRK14634 ribosome maturation factor RimP. 155 matched cddid_all.tbl CDD PRK14635 PRK14635 184774 PRK14635 ribosome maturation factor RimP. 162 matched cddid_all.tbl CDD PRK14636 PRK14636 237773 PRK14636 ribosome maturation protein RimP. 176 matched cddid_all.tbl CDD PRK14637 PRK14637 237774 PRK14637 ribosome maturation factor RimP. 151 matched cddid_all.tbl CDD PRK14638 PRK14638 184777 PRK14638 ribosome maturation factor RimP. 150 matched cddid_all.tbl CDD PRK14639 PRK14639 173102 PRK14639 ribosome maturation factor RimP. 140 matched cddid_all.tbl CDD PRK14640 PRK14640 173103 PRK14640 hypothetical protein; Provisional 152 matched cddid_all.tbl CDD PRK14641 PRK14641 173104 PRK14641 ribosome maturation factor RimP. 173 matched cddid_all.tbl CDD PRK14642 PRK14642 237775 PRK14642 ribosome maturation factor RimP. 197 matched cddid_all.tbl CDD PRK14643 PRK14643 173106 PRK14643 ribosome maturation factor RimP. 164 matched cddid_all.tbl CDD PRK14644 PRK14644 184779 PRK14644 hypothetical protein; Provisional 136 matched cddid_all.tbl CDD PRK14645 PRK14645 184780 PRK14645 ribosome maturation factor RimP. 154 matched cddid_all.tbl CDD PRK14646 PRK14646 173109 PRK14646 ribosome maturation factor RimP. 155 matched cddid_all.tbl CDD PRK14647 PRK14647 173110 PRK14647 ribosome maturation factor RimP. 159 matched cddid_all.tbl CDD PRK14648 PRK14648 173111 PRK14648 UDP-N-acetylmuramate dehydrogenase. 354 matched cddid_all.tbl CDD PRK14649 PRK14649 173112 PRK14649 UDP-N-acetylmuramate dehydrogenase. 295 matched cddid_all.tbl CDD PRK14650 PRK14650 173113 PRK14650 UDP-N-acetylmuramate dehydrogenase. 302 matched cddid_all.tbl CDD PRK14651 PRK14651 237776 PRK14651 UDP-N-acetylmuramate dehydrogenase. 273 matched cddid_all.tbl CDD PRK14652 PRK14652 237777 PRK14652 UDP-N-acetylmuramate dehydrogenase. 302 matched cddid_all.tbl CDD PRK14653 PRK14653 237778 PRK14653 UDP-N-acetylmuramate dehydrogenase. 297 matched cddid_all.tbl CDD PRK14656 PRK14656 237779 acpS holo-[acyl-carrier-protein] synthase. 126 matched cddid_all.tbl CDD PRK14657 PRK14657 173120 acpS holo-[acyl-carrier-protein] synthase. 123 matched cddid_all.tbl CDD PRK14658 PRK14658 173121 acpS holo-ACP synthase. 115 matched cddid_all.tbl CDD PRK14659 PRK14659 237780 acpS holo-[acyl-carrier-protein] synthase. 122 matched cddid_all.tbl CDD PRK14660 PRK14660 173123 acpS holo-[acyl-carrier-protein] synthase. 125 matched cddid_all.tbl CDD PRK14661 PRK14661 184782 acpS holo-[acyl-carrier-protein] synthase. 169 matched cddid_all.tbl CDD PRK14662 PRK14662 184783 acpS 4'-phosphopantetheinyl transferase; Provisional 120 matched cddid_all.tbl CDD PRK14663 PRK14663 237781 acpS holo-[acyl-carrier-protein] synthase. 116 matched cddid_all.tbl CDD PRK14664 PRK14664 173127 PRK14664 tRNA-specific 2-thiouridylase MnmA; Provisional 362 matched cddid_all.tbl CDD PRK14665 PRK14665 173128 mnmA tRNA-specific 2-thiouridylase MnmA; Provisional 360 matched cddid_all.tbl CDD PRK14666 PRK14666 237782 uvrC excinuclease ABC subunit C; Provisional 694 matched cddid_all.tbl CDD PRK14667 PRK14667 237783 uvrC excinuclease ABC subunit C; Provisional 567 matched cddid_all.tbl CDD PRK14668 PRK14668 184785 uvrC excinuclease ABC subunit C; Provisional 577 matched cddid_all.tbl CDD PRK14669 PRK14669 237784 uvrC excinuclease ABC subunit C; Provisional 624 matched cddid_all.tbl CDD PRK14670 PRK14670 173133 uvrC excinuclease ABC subunit C; Provisional 574 matched cddid_all.tbl CDD PRK14672 PRK14672 173135 uvrC excinuclease ABC subunit C; Provisional 691 matched cddid_all.tbl CDD PRK14673 PRK14673 237786 PRK14673 hypothetical protein; Provisional 137 matched cddid_all.tbl CDD PRK14674 PRK14674 184788 PRK14674 hypothetical protein; Provisional 133 matched cddid_all.tbl CDD PRK14675 PRK14675 173138 PRK14675 hypothetical protein; Provisional 125 matched cddid_all.tbl CDD PRK14676 PRK14676 173139 PRK14676 hypothetical protein; Provisional 117 matched cddid_all.tbl CDD PRK14677 PRK14677 184789 PRK14677 hypothetical protein; Provisional 107 matched cddid_all.tbl CDD PRK14678 PRK14678 173141 PRK14678 hypothetical protein; Provisional 120 matched cddid_all.tbl CDD PRK14679 PRK14679 173142 PRK14679 hypothetical protein; Provisional 128 matched cddid_all.tbl CDD PRK14680 PRK14680 173143 PRK14680 hypothetical protein; Provisional 134 matched cddid_all.tbl CDD PRK14681 PRK14681 237787 PRK14681 hypothetical protein; Provisional 158 matched cddid_all.tbl CDD PRK14682 PRK14682 173145 PRK14682 hypothetical protein; Provisional 117 matched cddid_all.tbl CDD PRK14683 PRK14683 173146 PRK14683 hypothetical protein; Provisional 122 matched cddid_all.tbl CDD PRK14684 PRK14684 173147 PRK14684 hypothetical protein; Provisional 120 matched cddid_all.tbl CDD PRK14685 PRK14685 173148 PRK14685 hypothetical protein; Provisional 177 matched cddid_all.tbl CDD PRK14686 PRK14686 184791 PRK14686 hypothetical protein; Provisional 119 matched cddid_all.tbl CDD PRK14687 PRK14687 237788 PRK14687 hypothetical protein; Provisional 173 matched cddid_all.tbl CDD PRK14688 PRK14688 184792 PRK14688 hypothetical protein; Provisional 121 matched cddid_all.tbl CDD PRK14689 PRK14689 173152 PRK14689 hypothetical protein; Provisional 124 matched cddid_all.tbl CDD PRK14690 PRK14690 237789 PRK14690 molybdopterin biosynthesis protein MoeA; Provisional 419 matched cddid_all.tbl CDD PRK14691 PRK14691 173154 PRK14691 3-oxoacyl-(acyl carrier protein) synthase II; Provisional 342 matched cddid_all.tbl CDD PRK14692 PRK14692 173155 PRK14692 flagellar hook-associated protein FlgL. 749 matched cddid_all.tbl CDD PRK14693 PRK14693 173156 PRK14693 hypothetical protein; Provisional 552 matched cddid_all.tbl CDD PRK14695 PRK14695 173158 PRK14695 serine/threonine transporter SstT; Provisional 319 matched cddid_all.tbl CDD PRK14696 PRK14696 184793 tynA primary-amine oxidase. 721 matched cddid_all.tbl CDD PRK14697 PRK14697 184794 PRK14697 bifunctional 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase/phosphatase; Provisional 233 matched cddid_all.tbl CDD PRK14698 PRK14698 184795 PRK14698 V-type ATP synthase subunit A; Provisional 1017 matched cddid_all.tbl CDD PRK14699 PRK14699 173162 PRK14699 replication factor A; Provisional 484 matched cddid_all.tbl CDD PRK14700 PRK14700 173163 PRK14700 recombination factor protein RarA; Provisional 300 matched cddid_all.tbl CDD PRK14702 PRK14702 237792 PRK14702 insertion element IS2 transposase InsD; Provisional 262 matched cddid_all.tbl CDD PRK14703 PRK14703 237793 PRK14703 glutaminyl-tRNA synthetase/YqeY domain fusion protein; Provisional 771 matched cddid_all.tbl CDD PRK14704 PRK14704 184798 PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional 618 matched cddid_all.tbl CDD PRK14705 PRK14705 237794 PRK14705 glycogen branching enzyme; Provisional 1224 matched cddid_all.tbl CDD PRK14706 PRK14706 237795 PRK14706 glycogen branching enzyme; Provisional 639 matched cddid_all.tbl CDD PRK14707 PRK14707 173170 PRK14707 hypothetical protein; Provisional 2710 matched cddid_all.tbl CDD PRK14708 PRK14708 173171 PRK14708 flagellin; Provisional 888 matched cddid_all.tbl CDD PRK14709 PRK14709 173172 PRK14709 hypothetical protein; Provisional 469 matched cddid_all.tbl CDD PRK14710 PRK14710 173173 PRK14710 hypothetical protein; Provisional 86 matched cddid_all.tbl CDD PRK14711 PRK14711 173174 ureE urease accessory protein UreE; Provisional 191 matched cddid_all.tbl CDD PRK14712 PRK14712 237796 PRK14712 conjugal transfer nickase/helicase TraI; Provisional 1623 matched cddid_all.tbl CDD PRK14713 PRK14713 237797 PRK14713 bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase. 530 matched cddid_all.tbl CDD PRK14714 PRK14714 237798 PRK14714 DNA-directed DNA polymerase II large subunit. 1337 matched cddid_all.tbl CDD PRK14715 PRK14715 237799 PRK14715 DNA-directed DNA polymerase II large subunit. 1627 matched cddid_all.tbl CDD PRK14716 PRK14716 237800 PRK14716 glycosyl transferase family protein. 504 matched cddid_all.tbl CDD PRK14717 PRK14717 184803 PRK14717 putative glycine/sarcosine/betaine reductase complex protein A; Provisional 107 matched cddid_all.tbl CDD PRK14719 PRK14719 237801 PRK14719 bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional 360 matched cddid_all.tbl CDD PRK14720 PRK14720 184804 PRK14720 transcription elongation factor GreA. 906 matched cddid_all.tbl CDD PRK14721 PRK14721 173184 flhF flagellar biosynthesis regulator FlhF; Provisional 420 matched cddid_all.tbl CDD PRK14722 PRK14722 173185 flhF flagellar biosynthesis regulator FlhF; Provisional 374 matched cddid_all.tbl CDD PRK14723 PRK14723 237802 flhF flagellar biosynthesis regulator FlhF; Provisional 767 matched cddid_all.tbl CDD PRK14724 PRK14724 237803 PRK14724 DNA topoisomerase III; Provisional 987 matched cddid_all.tbl CDD PRK14725 PRK14725 237804 PRK14725 pyruvate kinase; Provisional 608 matched cddid_all.tbl CDD PRK14726 PRK14726 237805 PRK14726 protein translocase subunit SecDF. 855 matched cddid_all.tbl CDD PRK14734 PRK14734 237808 coaE dephospho-CoA kinase; Provisional 200 matched cddid_all.tbl CDD PRK14735 PRK14735 173197 atpC F0F1 ATP synthase subunit epsilon; Provisional 139 matched cddid_all.tbl CDD PRK14736 PRK14736 173198 atpC F0F1 ATP synthase subunit epsilon; Provisional 133 matched cddid_all.tbl CDD PRK14737 PRK14737 173199 gmk guanylate kinase; Provisional 186 matched cddid_all.tbl CDD PRK14738 PRK14738 237809 gmk guanylate kinase; Provisional 206 matched cddid_all.tbl CDD PRK14740 PRK14740 173201 kdbF K(+)-transporting ATPase subunit F. 29 matched cddid_all.tbl CDD PRK14741 PRK14741 173202 spoVM stage V sporulation protein SpoVM. 26 matched cddid_all.tbl CDD PRK14742 PRK14742 173203 thrL thr operon leader peptide; Provisional 28 matched cddid_all.tbl CDD PRK14743 PRK14743 173204 thrL thr operon leader peptide; Provisional 22 matched cddid_all.tbl CDD PRK14744 PRK14744 173205 PRK14744 leu operon leader peptide; Provisional 28 matched cddid_all.tbl CDD PRK14745 PRK14745 173206 PRK14745 RepA leader peptide Tap; Provisional 25 matched cddid_all.tbl CDD PRK14746 PRK14746 173207 PRK14746 RepA leader peptide Tap; Provisional 24 matched cddid_all.tbl CDD PRK14747 PRK14747 184810 PRK14747 cytochrome b6-f complex subunit PetN; Provisional 29 matched cddid_all.tbl CDD PRK14748 PRK14748 173209 kdpF K(+)-transporting ATPase subunit F. 29 matched cddid_all.tbl CDD PRK14749 PRK14749 173210 PRK14749 cytochrome bd-II oxidase subunit CbdX. 30 matched cddid_all.tbl CDD PRK14750 PRK14750 173211 kdpF K(+)-transporting ATPase subunit F. 29 matched cddid_all.tbl CDD PRK14751 PRK14751 173212 PRK14751 tetracycline resistance determinant leader peptide; Provisional 28 matched cddid_all.tbl CDD PRK14752 PRK14752 173213 PRK14752 delta-lysin family phenol-soluble modulin. 44 matched cddid_all.tbl CDD PRK14753 PRK14753 184811 PRK14753 30S ribosomal protein Thx; Provisional 27 matched cddid_all.tbl CDD PRK14754 PRK14754 173215 PRK14754 toxic peptide TisB; Provisional 29 matched cddid_all.tbl CDD PRK14755 PRK14755 173216 PRK14755 transcriptional regulatory protein PufK; Provisional 20 matched cddid_all.tbl CDD PRK14756 PRK14756 341227 small_mem_YnhF YnhF family membrane protein; Validated. 29 matched cddid_all.tbl CDD PRK14757 PRK14757 173218 PRK14757 putative protamine-like protein; Provisional 29 matched cddid_all.tbl CDD PRK14758 PRK14758 173219 PRK14758 hypothetical protein; Provisional 27 matched cddid_all.tbl CDD PRK14759 PRK14759 173220 PRK14759 K(+)-transporting ATPase subunit F. 29 matched cddid_all.tbl CDD PRK14760 PRK14760 173221 PRK14760 protein YoaJ. 24 matched cddid_all.tbl CDD PRK14761 PRK14761 173222 PRK14761 fur leader peptide. 28 matched cddid_all.tbl CDD PRK14762 PRK14762 173223 PRK14762 protein YohP. 27 matched cddid_all.tbl CDD PRK14763 PRK14763 184813 PRK14763 pyrroloquinoline quinone precursor peptide PqqA. 23 matched cddid_all.tbl CDD PRK14766 PRK14766 173227 PRK14766 lipoprotein signal peptidase; Provisional 201 matched cddid_all.tbl CDD PRK14767 PRK14767 237811 PRK14767 lipoprotein signal peptidase; Provisional 174 matched cddid_all.tbl CDD PRK14768 PRK14768 173229 PRK14768 lipoprotein signal peptidase; Provisional 148 matched cddid_all.tbl CDD PRK14769 PRK14769 173230 PRK14769 lipoprotein signal peptidase; Provisional 156 matched cddid_all.tbl CDD PRK14770 PRK14770 173231 PRK14770 lipoprotein signal peptidase; Provisional 167 matched cddid_all.tbl CDD PRK14771 PRK14771 184816 PRK14771 lipoprotein signal peptidase; Provisional 165 matched cddid_all.tbl CDD PRK14772 PRK14772 237812 PRK14772 lipoprotein signal peptidase; Provisional 190 matched cddid_all.tbl CDD PRK14773 PRK14773 173234 PRK14773 lipoprotein signal peptidase; Provisional 192 matched cddid_all.tbl CDD PRK14774 PRK14774 173235 PRK14774 lipoprotein signal peptidase; Provisional 185 matched cddid_all.tbl CDD PRK14775 PRK14775 237813 PRK14775 lipoprotein signal peptidase; Provisional 170 matched cddid_all.tbl CDD PRK14776 PRK14776 173237 PRK14776 lipoprotein signal peptidase; Provisional 170 matched cddid_all.tbl CDD PRK14777 PRK14777 237814 PRK14777 lipoprotein signal peptidase; Provisional 184 matched cddid_all.tbl CDD PRK14778 PRK14778 173239 PRK14778 lipoprotein signal peptidase; Provisional 186 matched cddid_all.tbl CDD PRK14779 PRK14779 184818 PRK14779 lipoprotein signal peptidase; Provisional 159 matched cddid_all.tbl CDD PRK14780 PRK14780 173241 PRK14780 lipoprotein signal peptidase; Provisional 263 matched cddid_all.tbl CDD PRK14781 PRK14781 237815 PRK14781 lipoprotein signal peptidase; Provisional 153 matched cddid_all.tbl CDD PRK14783 PRK14783 173244 PRK14783 lipoprotein signal peptidase; Provisional 182 matched cddid_all.tbl CDD PRK14784 PRK14784 184819 PRK14784 lipoprotein signal peptidase; Provisional 160 matched cddid_all.tbl CDD PRK14785 PRK14785 184820 PRK14785 lipoprotein signal peptidase; Provisional 171 matched cddid_all.tbl CDD PRK14786 PRK14786 173247 PRK14786 lipoprotein signal peptidase; Provisional 154 matched cddid_all.tbl CDD PRK14787 PRK14787 173248 PRK14787 lipoprotein signal peptidase; Provisional 159 matched cddid_all.tbl CDD PRK14788 PRK14788 237816 PRK14788 lipoprotein signal peptidase; Provisional 200 matched cddid_all.tbl CDD PRK14789 PRK14789 173250 PRK14789 lipoprotein signal peptidase; Provisional 191 matched cddid_all.tbl CDD PRK14790 PRK14790 173251 PRK14790 lipoprotein signal peptidase; Provisional 169 matched cddid_all.tbl CDD PRK14791 PRK14791 237817 PRK14791 lipoprotein signal peptidase; Provisional 146 matched cddid_all.tbl CDD PRK14804 PRK14804 173265 PRK14804 ornithine carbamoyltransferase; Provisional 311 matched cddid_all.tbl CDD PRK14805 PRK14805 237819 PRK14805 ornithine carbamoyltransferase; Provisional 302 matched cddid_all.tbl CDD PRK14806 PRK14806 237820 PRK14806 bifunctional cyclohexadienyl dehydrogenase/ 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional 735 matched cddid_all.tbl CDD PRK14810 PRK14810 173271 PRK14810 formamidopyrimidine-DNA glycosylase; Provisional 272 matched cddid_all.tbl CDD PRK14811 PRK14811 184831 PRK14811 formamidopyrimidine-DNA glycosylase; Provisional 269 matched cddid_all.tbl CDD PRK14812 PRK14812 173273 PRK14812 hypothetical protein; Provisional 119 matched cddid_all.tbl CDD PRK14813 PRK14813 173274 PRK14813 NADH dehydrogenase subunit B; Provisional 189 matched cddid_all.tbl CDD PRK14814 PRK14814 173275 PRK14814 NADH dehydrogenase subunit B; Provisional 186 matched cddid_all.tbl CDD PRK14815 PRK14815 237821 PRK14815 NADH dehydrogenase subunit B; Provisional 183 matched cddid_all.tbl CDD PRK14816 PRK14816 173277 PRK14816 NADH-quinone oxidoreductase subunit B. 182 matched cddid_all.tbl CDD PRK14817 PRK14817 173278 PRK14817 NADH-quinone oxidoreductase subunit B. 181 matched cddid_all.tbl CDD PRK14818 PRK14818 173279 PRK14818 NADH dehydrogenase subunit B; Provisional 173 matched cddid_all.tbl CDD PRK14819 PRK14819 237822 PRK14819 NADH-quinone oxidoreductase subunit B. 264 matched cddid_all.tbl CDD PRK14820 PRK14820 184833 PRK14820 NADH-quinone oxidoreductase subunit B. 180 matched cddid_all.tbl CDD PRK14821 PRK14821 184834 PRK14821 XTP/dITP diphosphatase. 184 matched cddid_all.tbl CDD PRK14822 PRK14822 184835 PRK14822 XTP/dITP diphosphatase. 200 matched cddid_all.tbl CDD PRK14823 PRK14823 237823 PRK14823 putative deoxyribonucleoside-triphosphatase; Provisional 191 matched cddid_all.tbl CDD PRK14824 PRK14824 237824 PRK14824 putative deoxyribonucleotide triphosphate pyrophosphatase; Provisional 201 matched cddid_all.tbl CDD PRK14825 PRK14825 173286 PRK14825 putative deoxyribonucleotide triphosphate pyrophosphatase; Provisional 199 matched cddid_all.tbl CDD PRK14826 PRK14826 173287 PRK14826 putative deoxyribonucleotide triphosphate pyrophosphatase; Provisional 222 matched cddid_all.tbl CDD PRK14827 PRK14827 173288 PRK14827 undecaprenyl pyrophosphate synthase; Provisional 296 matched cddid_all.tbl CDD PRK14828 PRK14828 237825 PRK14828 undecaprenyl pyrophosphate synthase; Provisional 256 matched cddid_all.tbl CDD PRK14829 PRK14829 237826 PRK14829 undecaprenyl pyrophosphate synthase; Provisional 243 matched cddid_all.tbl CDD PRK14830 PRK14830 184840 PRK14830 undecaprenyl pyrophosphate synthase; Provisional 251 matched cddid_all.tbl CDD PRK14831 PRK14831 184841 PRK14831 undecaprenyl pyrophosphate synthase; Provisional 249 matched cddid_all.tbl CDD PRK14832 PRK14832 237827 PRK14832 undecaprenyl pyrophosphate synthase; Provisional 253 matched cddid_all.tbl CDD PRK14833 PRK14833 237828 PRK14833 di-trans,poly-cis-decaprenylcistransferase. 233 matched cddid_all.tbl CDD PRK14834 PRK14834 237829 PRK14834 isoprenyl transferase. 249 matched cddid_all.tbl CDD PRK14835 PRK14835 237830 PRK14835 isoprenyl transferase. 275 matched cddid_all.tbl CDD PRK14836 PRK14836 237831 PRK14836 undecaprenyl pyrophosphate synthase; Provisional 253 matched cddid_all.tbl CDD PRK14837 PRK14837 173298 PRK14837 undecaprenyl pyrophosphate synthase; Provisional 230 matched cddid_all.tbl CDD PRK14838 PRK14838 184846 PRK14838 isoprenyl transferase. 242 matched cddid_all.tbl CDD PRK14839 PRK14839 237832 PRK14839 di-trans,poly-cis-decaprenylcistransferase. 239 matched cddid_all.tbl CDD PRK14840 PRK14840 173301 PRK14840 undecaprenyl pyrophosphate synthase; Provisional 250 matched cddid_all.tbl CDD PRK14841 PRK14841 173302 PRK14841 undecaprenyl pyrophosphate synthase; Provisional 233 matched cddid_all.tbl CDD PRK14842 PRK14842 173303 PRK14842 undecaprenyl pyrophosphate synthase; Provisional 241 matched cddid_all.tbl CDD PRK14843 PRK14843 184847 PRK14843 dihydrolipoamide acetyltransferase; Provisional 347 matched cddid_all.tbl CDD PRK14844 PRK14844 173305 PRK14844 DNA-directed RNA polymerase subunit beta/beta'. 2836 matched cddid_all.tbl CDD PRK14845 PRK14845 237833 PRK14845 translation initiation factor IF-2; Provisional 1049 matched cddid_all.tbl CDD PRK14846 PRK14846 237834 truB tRNA pseudouridine synthase B; Provisional 345 matched cddid_all.tbl CDD PRK14847 PRK14847 184849 PRK14847 2-isopropylmalate synthase. 333 matched cddid_all.tbl CDD PRK14848 PRK14848 184850 PRK14848 type III secretion system effector deubiquitinase SseL. 317 matched cddid_all.tbl CDD PRK14849 PRK14849 184851 PRK14849 autotransporter barrel domain-containing lipoprotein. 1806 matched cddid_all.tbl CDD PRK14850 PRK14850 237835 PRK14850 penicillin-binding protein 1b; Provisional 764 matched cddid_all.tbl CDD PRK14851 PRK14851 184853 PRK14851 hypothetical protein; Provisional 679 matched cddid_all.tbl CDD PRK14852 PRK14852 184854 PRK14852 hypothetical protein; Provisional 989 matched cddid_all.tbl CDD PRK14854 PRK14854 184856 nhaA pH-dependent sodium/proton antiporter; Provisional 383 matched cddid_all.tbl CDD PRK14855 PRK14855 237836 nhaA pH-dependent sodium/proton antiporter; Provisional 423 matched cddid_all.tbl CDD PRK14856 PRK14856 184858 nhaA sodium/proton antiporter NhaA. 438 matched cddid_all.tbl CDD PRK14857 PRK14857 184859 tatA TatA/E family twin arginine-targeting protein translocase. 90 matched cddid_all.tbl CDD PRK14858 PRK14858 184860 tatA twin arginine translocase protein A; Provisional 108 matched cddid_all.tbl CDD PRK14859 PRK14859 184861 tatA twin arginine translocase protein A; Provisional 63 matched cddid_all.tbl CDD PRK14860 PRK14860 184862 tatA twin arginine translocase protein A; Provisional 64 matched cddid_all.tbl CDD PRK14861 PRK14861 237837 tatA twin arginine translocase protein A; Provisional 61 matched cddid_all.tbl CDD PRK14863 PRK14863 184865 PRK14863 bifunctional regulator KidO; Provisional 292 matched cddid_all.tbl CDD PRK14864 PRK14864 184866 PRK14864 biofilm peroxide resistance protein BsmA. 104 matched cddid_all.tbl CDD PRK14866 PRK14866 237840 PRK14866 hypothetical protein; Provisional 451 matched cddid_all.tbl CDD PRK14867 PRK14867 237841 PRK14867 DNA topoisomerase VI subunit B; Provisional 659 matched cddid_all.tbl CDD PRK14868 PRK14868 237842 PRK14868 DNA topoisomerase VI subunit B; Provisional 795 matched cddid_all.tbl CDD PRK14869 PRK14869 237843 PRK14869 putative manganese-dependent inorganic diphosphatase. 546 matched cddid_all.tbl CDD PRK14872 PRK14872 184872 PRK14872 rod shape-determining protein MreC; Provisional 337 matched cddid_all.tbl CDD PRK14873 PRK14873 237844 PRK14873 primosomal protein N'. 665 matched cddid_all.tbl CDD PRK14874 PRK14874 237845 PRK14874 aspartate-semialdehyde dehydrogenase; Provisional 334 matched cddid_all.tbl CDD PRK14875 PRK14875 184875 PRK14875 acetoin dehydrogenase E2 subunit dihydrolipoyllysine-residue acetyltransferase; Provisional 371 matched cddid_all.tbl CDD PRK14876 PRK14876 237846 PRK14876 conjugal transfer mating pair stabilization protein TraN; Provisional 928 matched cddid_all.tbl CDD PRK14877 PRK14877 184877 PRK14877 conjugal transfer mating pair stabilization protein TraN; Provisional 1062 matched cddid_all.tbl CDD PRK14878 PRK14878 184878 PRK14878 UGMP family protein; Provisional 323 matched cddid_all.tbl CDD PRK14879 PRK14879 237847 PRK14879 Kae1-associated kinase Bud32. 211 matched cddid_all.tbl CDD PRK14886 PRK14886 237848 PRK14886 KEOPS complex subunit Cgi121. 167 matched cddid_all.tbl CDD PRK14887 PRK14887 237849 PRK14887 KEOPS complex Pcc1-like subunit; Provisional 84 matched cddid_all.tbl CDD PRK14888 PRK14888 237850 PRK14888 KEOPS complex Pcc1-like subunit; Provisional 59 matched cddid_all.tbl CDD PRK14889 PRK14889 184883 PRK14889 VKOR family protein; Provisional 143 matched cddid_all.tbl CDD PRK14890 PRK14890 184884 PRK14890 putative Zn-ribbon RNA-binding protein; Provisional 59 matched cddid_all.tbl CDD PRK14891 PRK14891 184885 PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional 131 matched cddid_all.tbl CDD PRK14892 PRK14892 184886 PRK14892 putative transcription elongation factor Elf1; Provisional 99 matched cddid_all.tbl CDD PRK14893 PRK14893 184887 PRK14893 V-type ATP synthase subunit K; Provisional 161 matched cddid_all.tbl CDD PRK14894 PRK14894 237851 PRK14894 glycyl-tRNA synthetase; Provisional 539 matched cddid_all.tbl CDD PRK14896 PRK14896 237852 ksgA 16S ribosomal RNA methyltransferase A. 258 matched cddid_all.tbl CDD PRK14897 PRK14897 237853 PRK14897 unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional 509 matched cddid_all.tbl CDD PRK14898 PRK14898 237854 PRK14898 DNA-directed RNA polymerase subunit A''; Provisional 858 matched cddid_all.tbl CDD PRK14900 PRK14900 237855 valS valyl-tRNA synthetase; Provisional 1052 matched cddid_all.tbl CDD PRK14901 PRK14901 237856 PRK14901 16S rRNA methyltransferase B; Provisional 434 matched cddid_all.tbl CDD PRK14902 PRK14902 237857 PRK14902 16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB. 444 matched cddid_all.tbl CDD PRK14903 PRK14903 184896 PRK14903 16S rRNA methyltransferase B; Provisional 431 matched cddid_all.tbl CDD PRK14904 PRK14904 237858 PRK14904 16S rRNA methyltransferase B; Provisional 445 matched cddid_all.tbl CDD PRK14905 PRK14905 184898 PRK14905 triosephosphate isomerase/PTS system glucose/sucrose-specific transporter subunit IIB; Provisional 355 matched cddid_all.tbl CDD PRK14906 PRK14906 184899 PRK14906 DNA-directed RNA polymerase subunit beta'. 1460 matched cddid_all.tbl CDD PRK14907 PRK14907 184900 rplD 50S ribosomal protein L4; Provisional 295 matched cddid_all.tbl CDD PRK14908 PRK14908 237859 PRK14908 glycine--tRNA ligase. 1000 matched cddid_all.tbl CDD PRK14938 PRK14938 184902 PRK14938 Ser-tRNA(Thr) hydrolase; Provisional 387 matched cddid_all.tbl CDD PRK14939 PRK14939 237860 gyrB DNA gyrase subunit B; Provisional 756 matched cddid_all.tbl CDD PRK14946 PRK14946 184910 PRK14946 DNA polymerase III subunit beta; Provisional 366 matched cddid_all.tbl CDD PRK14948 PRK14948 237862 PRK14948 DNA polymerase III subunit gamma/tau. 620 matched cddid_all.tbl CDD PRK14949 PRK14949 237863 PRK14949 DNA polymerase III subunits gamma and tau; Provisional 944 matched cddid_all.tbl CDD PRK14950 PRK14950 237864 PRK14950 DNA polymerase III subunits gamma and tau; Provisional 585 matched cddid_all.tbl CDD PRK14951 PRK14951 237865 PRK14951 DNA polymerase III subunits gamma and tau; Provisional 618 matched cddid_all.tbl CDD PRK14952 PRK14952 237866 PRK14952 DNA polymerase III subunits gamma/tau. 584 matched cddid_all.tbl CDD PRK14953 PRK14953 237867 PRK14953 DNA polymerase III subunits gamma and tau; Provisional 486 matched cddid_all.tbl CDD PRK14954 PRK14954 184918 PRK14954 DNA polymerase III subunits gamma and tau; Provisional 620 matched cddid_all.tbl CDD PRK14955 PRK14955 184919 PRK14955 DNA polymerase III subunits gamma and tau; Provisional 397 matched cddid_all.tbl CDD PRK14956 PRK14956 184920 PRK14956 DNA polymerase III subunits gamma and tau; Provisional 484 matched cddid_all.tbl CDD PRK14957 PRK14957 184921 PRK14957 DNA polymerase III subunits gamma and tau; Provisional 546 matched cddid_all.tbl CDD PRK14958 PRK14958 184922 PRK14958 DNA polymerase III subunits gamma and tau; Provisional 509 matched cddid_all.tbl CDD PRK14959 PRK14959 184923 PRK14959 DNA polymerase III subunits gamma and tau; Provisional 624 matched cddid_all.tbl CDD PRK14960 PRK14960 237868 PRK14960 DNA polymerase III subunit gamma/tau. 702 matched cddid_all.tbl CDD PRK14961 PRK14961 184925 PRK14961 DNA polymerase III subunits gamma and tau; Provisional 363 matched cddid_all.tbl CDD PRK14962 PRK14962 237869 PRK14962 DNA polymerase III subunits gamma and tau; Provisional 472 matched cddid_all.tbl CDD PRK14963 PRK14963 184927 PRK14963 DNA polymerase III subunits gamma and tau; Provisional 504 matched cddid_all.tbl CDD PRK14964 PRK14964 237870 PRK14964 DNA polymerase III subunits gamma and tau; Provisional 491 matched cddid_all.tbl CDD PRK14965 PRK14965 237871 PRK14965 DNA polymerase III subunits gamma and tau; Provisional 576 matched cddid_all.tbl CDD PRK14966 PRK14966 184930 PRK14966 unknown domain/N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase fusion protein; Provisional 423 matched cddid_all.tbl CDD PRK14967 PRK14967 184931 PRK14967 putative methyltransferase; Provisional 223 matched cddid_all.tbl CDD PRK14968 PRK14968 237872 PRK14968 putative methyltransferase; Provisional 188 matched cddid_all.tbl CDD PRK14969 PRK14969 237873 PRK14969 DNA polymerase III subunits gamma and tau; Provisional 527 matched cddid_all.tbl CDD PRK14970 PRK14970 184934 PRK14970 DNA polymerase III subunits gamma and tau; Provisional 367 matched cddid_all.tbl CDD PRK14971 PRK14971 237874 PRK14971 DNA polymerase III subunit gamma/tau. 614 matched cddid_all.tbl CDD PRK14973 PRK14973 184936 PRK14973 DNA topoisomerase I; Provisional 936 matched cddid_all.tbl CDD PRK14974 PRK14974 237875 PRK14974 signal recognition particle-docking protein FtsY. 336 matched cddid_all.tbl CDD PRK14975 PRK14975 237876 PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional 553 matched cddid_all.tbl CDD PRK14976 PRK14976 237877 PRK14976 5'-3' exonuclease; Provisional 281 matched cddid_all.tbl CDD PRK14977 PRK14977 184940 PRK14977 bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional 1321 matched cddid_all.tbl CDD PRK14979 PRK14979 237878 PRK14979 DNA-directed RNA polymerase subunit D; Provisional 195 matched cddid_all.tbl CDD PRK14980 PRK14980 184942 PRK14980 DNA-directed RNA polymerase subunit G; Provisional 127 matched cddid_all.tbl CDD PRK14981 PRK14981 184943 PRK14981 RNA polymerase Rpb4 family protein. 112 matched cddid_all.tbl CDD PRK14984 PRK14984 237880 PRK14984 gluconate transporter. 438 matched cddid_all.tbl CDD PRK14985 PRK14985 237881 PRK14985 maltodextrin phosphorylase; Provisional 798 matched cddid_all.tbl CDD PRK14986 PRK14986 184948 PRK14986 glycogen phosphorylase; Provisional 815 matched cddid_all.tbl CDD PRK14987 PRK14987 184949 PRK14987 HTH-type transcriptional regulator GntR. 331 matched cddid_all.tbl CDD PRK14988 PRK14988 237882 PRK14988 GMP/IMP nucleotidase; Provisional 224 matched cddid_all.tbl CDD PRK14989 PRK14989 184951 PRK14989 nitrite reductase subunit NirD; Provisional 847 matched cddid_all.tbl CDD PRK14990 PRK14990 184952 PRK14990 anaerobic dimethyl sulfoxide reductase subunit A; Provisional 814 matched cddid_all.tbl CDD PRK14991 PRK14991 237883 PRK14991 tetrathionate reductase subunit TtrA. 1031 matched cddid_all.tbl CDD PRK14992 PRK14992 184954 PRK14992 tetrathionate reductase subunit TtrC. 335 matched cddid_all.tbl CDD PRK14993 PRK14993 184955 PRK14993 tetrathionate reductase subunit TtrB. 244 matched cddid_all.tbl CDD PRK14994 PRK14994 184956 PRK14994 SAM-dependent 16S ribosomal RNA C1402 ribose 2'-O-methyltransferase; Provisional 287 matched cddid_all.tbl CDD PRK14995 PRK14995 184957 PRK14995 SmvA family efflux MFS transporter. 495 matched cddid_all.tbl CDD PRK14996 PRK14996 184958 PRK14996 TetR family transcriptional regulator; Provisional 192 matched cddid_all.tbl CDD PRK14997 PRK14997 184959 PRK14997 LysR family transcriptional regulator; Provisional 301 matched cddid_all.tbl CDD PRK14998 PRK14998 184960 PRK14998 cold shock-like protein CspD; Provisional 73 matched cddid_all.tbl CDD PRK14999 PRK14999 184961 PRK14999 histidine utilization repressor; Provisional 241 matched cddid_all.tbl CDD PRK15000 PRK15000 184962 PRK15000 peroxiredoxin C. 200 matched cddid_all.tbl CDD PRK15001 PRK15001 184963 PRK15001 23S rRNA (guanine(1835)-N(2))-methyltransferase RlmG. 378 matched cddid_all.tbl CDD PRK15002 PRK15002 184964 PRK15002 redox-sensitive transcriptional activator SoxR. 154 matched cddid_all.tbl CDD PRK15003 PRK15003 184965 PRK15003 cytochrome d ubiquinol oxidase subunit II. 379 matched cddid_all.tbl CDD PRK15004 PRK15004 184966 PRK15004 adenosylcobalamin/alpha-ribazole phosphatase. 199 matched cddid_all.tbl CDD PRK15005 PRK15005 184967 PRK15005 universal stress protein UspF. 144 matched cddid_all.tbl CDD PRK15006 PRK15006 184968 PRK15006 thiosulfate reductase cytochrome B subunit; Provisional 261 matched cddid_all.tbl CDD PRK15007 PRK15007 184969 PRK15007 arginine ABC transporter substrate-binding protein. 243 matched cddid_all.tbl CDD PRK15008 PRK15008 184970 PRK15008 HTH-type transcriptional regulator RutR; Provisional 212 matched cddid_all.tbl CDD PRK15009 PRK15009 184971 PRK15009 GDP-mannose pyrophosphatase NudK; Provisional 191 matched cddid_all.tbl CDD PRK15010 PRK15010 184972 PRK15010 lysine/arginine/ornithine ABC transporter substrate-binding protein ArgT. 260 matched cddid_all.tbl CDD PRK15011 PRK15011 184973 PRK15011 sugar efflux transporter SetB. 393 matched cddid_all.tbl CDD PRK15012 PRK15012 184974 PRK15012 menaquinone-specific isochorismate synthase; Provisional 431 matched cddid_all.tbl CDD PRK15014 PRK15014 184975 PRK15014 6-phospho-beta-glucosidase BglA; Provisional 477 matched cddid_all.tbl CDD PRK15015 PRK15015 184976 PRK15015 carbon starvation protein CstA. 701 matched cddid_all.tbl CDD PRK15016 PRK15016 184977 PRK15016 isochorismate synthase EntC; Provisional 391 matched cddid_all.tbl CDD PRK15017 PRK15017 184978 PRK15017 cytochrome o ubiquinol oxidase subunit I; Provisional 663 matched cddid_all.tbl CDD PRK15018 PRK15018 184979 PRK15018 1-acyl-sn-glycerol-3-phosphate acyltransferase; Provisional 245 matched cddid_all.tbl CDD PRK15019 PRK15019 184980 PRK15019 cysteine desulfurase sulfur acceptor subunit CsdE. 147 matched cddid_all.tbl CDD PRK15020 PRK15020 237884 PRK15020 ethanolamine utilization cob(I)yrinic acid a,c-diamide adenosyltransferase EutT. 267 matched cddid_all.tbl CDD PRK15021 PRK15021 184982 PRK15021 microcin C ABC transporter permease; Provisional 341 matched cddid_all.tbl CDD PRK15022 PRK15022 184983 PRK15022 non-heme ferritin-like protein. 167 matched cddid_all.tbl CDD PRK15023 PRK15023 184984 PRK15023 L-serine deaminase; Provisional 454 matched cddid_all.tbl CDD PRK15025 PRK15025 184985 PRK15025 ureidoglycolate dehydrogenase; Provisional 349 matched cddid_all.tbl CDD PRK15026 PRK15026 184986 PRK15026 aminoacyl-histidine dipeptidase; Provisional 485 matched cddid_all.tbl CDD PRK15027 PRK15027 184987 PRK15027 xylulokinase; Provisional 484 matched cddid_all.tbl CDD PRK15028 PRK15028 184988 PRK15028 cytochrome d ubiquinol oxidase subunit II. 378 matched cddid_all.tbl CDD PRK15029 PRK15029 184989 PRK15029 arginine decarboxylase; Provisional 755 matched cddid_all.tbl CDD PRK15030 PRK15030 184990 PRK15030 multidrug efflux RND transporter periplasmic adaptor subunit AcrA. 397 matched cddid_all.tbl CDD PRK15031 PRK15031 184991 PRK15031 5-carboxymethyl-2-hydroxymuconate Delta-isomerase. 126 matched cddid_all.tbl CDD PRK15032 PRK15032 184992 PRK15032 pentaheme c-type cytochrome TorC. 390 matched cddid_all.tbl CDD PRK15033 PRK15033 237885 PRK15033 tricarballylate utilization 4Fe-4S protein TcuB. 389 matched cddid_all.tbl CDD PRK15034 PRK15034 184994 PRK15034 nitrate/nitrite transport protein NarU; Provisional 462 matched cddid_all.tbl CDD PRK15035 PRK15035 184995 PRK15035 cytochrome bd-II oxidase subunit 1; Provisional 514 matched cddid_all.tbl CDD PRK15036 PRK15036 184996 PRK15036 hydroxyisourate hydrolase; Provisional 137 matched cddid_all.tbl CDD PRK15037 PRK15037 184997 PRK15037 D-mannonate oxidoreductase; Provisional 486 matched cddid_all.tbl CDD PRK15038 PRK15038 184998 PRK15038 autoinducer 2 ABC transporter permease LsrD. 330 matched cddid_all.tbl CDD PRK15039 PRK15039 184999 PRK15039 Ni(II)/Co(II)-binding transcriptional repressor RcnR. 90 matched cddid_all.tbl CDD PRK15040 PRK15040 185000 PRK15040 L-serine ammonia-lyase. 454 matched cddid_all.tbl CDD PRK15041 PRK15041 185001 PRK15041 methyl-accepting chemotaxis protein. 554 matched cddid_all.tbl CDD PRK15042 PRK15042 237886 pduD propanediol/glycerol family dehydratase medium subunit. 219 matched cddid_all.tbl CDD PRK15043 PRK15043 185003 PRK15043 HTH-type transcriptional regulator MlrA. 243 matched cddid_all.tbl CDD PRK15044 PRK15044 185004 PRK15044 transcriptional regulator SirC; Provisional 295 matched cddid_all.tbl CDD PRK15045 PRK15045 185005 PRK15045 cellulose biosynthesis protein BcsE; Provisional 519 matched cddid_all.tbl CDD PRK15046 PRK15046 237887 PRK15046 2-aminoethylphosphonate ABC transporter substrate-binding protein; Provisional 349 matched cddid_all.tbl CDD PRK15047 PRK15047 185007 PRK15047 N-hydroxyarylamine O-acetyltransferase; Provisional 281 matched cddid_all.tbl CDD PRK15048 PRK15048 185008 PRK15048 methyl-accepting chemotaxis protein II; Provisional 553 matched cddid_all.tbl CDD PRK15049 PRK15049 185009 PRK15049 L-asparagine permease. 499 matched cddid_all.tbl CDD PRK15050 PRK15050 237888 PRK15050 2-aminoethylphosphonate transport system permease PhnU; Provisional 296 matched cddid_all.tbl CDD PRK15051 PRK15051 185011 PRK15051 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol flippase subunit ArnE; Provisional 111 matched cddid_all.tbl CDD PRK15052 PRK15052 237889 PRK15052 tagatose-bisphosphate aldolase subunit GatZ. 421 matched cddid_all.tbl CDD PRK15053 PRK15053 185013 dpiB sensor histidine kinase DpiB; Provisional 545 matched cddid_all.tbl CDD PRK15054 PRK15054 185014 PRK15054 nitrate reductase molybdenum cofactor assembly chaperone. 231 matched cddid_all.tbl CDD PRK15056 PRK15056 185016 PRK15056 manganese/iron ABC transporter ATP-binding protein. 272 matched cddid_all.tbl CDD PRK15057 PRK15057 185017 PRK15057 UDP-glucose 6-dehydrogenase; Provisional 388 matched cddid_all.tbl CDD PRK15058 PRK15058 185018 PRK15058 cytochrome b562; Provisional 128 matched cddid_all.tbl CDD PRK15059 PRK15059 185019 PRK15059 2-hydroxy-3-oxopropionate reductase. 292 matched cddid_all.tbl CDD PRK15060 PRK15060 185020 PRK15060 2,3-diketo-L-gulonate transporter large permease YiaN. 425 matched cddid_all.tbl CDD PRK15061 PRK15061 237891 PRK15061 catalase/peroxidase. 726 matched cddid_all.tbl CDD PRK15063 PRK15063 237893 PRK15063 isocitrate lyase; Provisional 428 matched cddid_all.tbl CDD PRK15064 PRK15064 237894 PRK15064 ABC transporter ATP-binding protein; Provisional 530 matched cddid_all.tbl CDD PRK15065 PRK15065 237895 PRK15065 mannose/fructose/sorbose family PTS transporter subunit IIC. 262 matched cddid_all.tbl CDD PRK15066 PRK15066 237896 PRK15066 inner membrane transport permease; Provisional 257 matched cddid_all.tbl CDD PRK15067 PRK15067 237897 PRK15067 ethanolamine ammonia-lyase subunit EutB. 461 matched cddid_all.tbl CDD PRK15068 PRK15068 237898 PRK15068 tRNA 5-methoxyuridine(34)/uridine 5-oxyacetic acid(34) synthase CmoB. 322 matched cddid_all.tbl CDD PRK15069 PRK15069 185029 PRK15069 histidine ABC transporter permease HisM. 234 matched cddid_all.tbl CDD PRK15070 PRK15070 237899 PRK15070 phosphate propanoyltransferase. 211 matched cddid_all.tbl CDD PRK15072 PRK15072 237901 PRK15072 D-galactonate dehydratase family protein. 404 matched cddid_all.tbl CDD PRK15074 PRK15074 185033 PRK15074 inosine/guanosine kinase; Provisional 434 matched cddid_all.tbl CDD PRK15075 PRK15075 237902 PRK15075 tricarballylate/proton symporter TcuC. 434 matched cddid_all.tbl CDD PRK15076 PRK15076 185035 PRK15076 alpha-galactosidase; Provisional 431 matched cddid_all.tbl CDD PRK15078 PRK15078 237903 PRK15078 polysaccharide export protein Wza; Provisional 379 matched cddid_all.tbl CDD PRK15079 PRK15079 185037 PRK15079 oligopeptide ABC transporter ATP-binding protein OppF; Provisional 331 matched cddid_all.tbl CDD PRK15080 PRK15080 237904 PRK15080 ethanolamine utilization protein EutJ; Provisional 267 matched cddid_all.tbl CDD PRK15081 PRK15081 185039 PRK15081 glutathione ABC transporter permease GsiC; Provisional 306 matched cddid_all.tbl CDD PRK15082 PRK15082 185040 PRK15082 glutathione ABC transporter permease GsiD; Provisional 301 matched cddid_all.tbl CDD PRK15083 PRK15083 237905 PRK15083 PTS system mannitol-specific transporter subunit IICBA; Provisional 639 matched cddid_all.tbl CDD PRK15084 PRK15084 185042 PRK15084 formate hydrogenlyase maturation protein HycH; Provisional 133 matched cddid_all.tbl CDD PRK15086 PRK15086 237906 PRK15086 ethanolamine utilization protein EutH; Provisional 372 matched cddid_all.tbl CDD PRK15087 PRK15087 185044 PRK15087 hemolysin; Provisional 219 matched cddid_all.tbl CDD PRK15088 PRK15088 185045 PRK15088 PTS system mannose-specific transporter subunits IIAB; Provisional 322 matched cddid_all.tbl CDD PRK15090 PRK15090 185046 PRK15090 DNA-binding transcriptional regulator KdgR; Provisional 257 matched cddid_all.tbl CDD PRK15091 PRK15091 185047 PRK15091 phospholipid-binding lipoprotein MlaA. 251 matched cddid_all.tbl CDD PRK15092 PRK15092 237907 PRK15092 DNA-binding transcriptional repressor LrhA; Provisional 310 matched cddid_all.tbl CDD PRK15093 PRK15093 185049 PRK15093 peptide ABC transporter ATP-binding protein SapD. 330 matched cddid_all.tbl CDD PRK15094 PRK15094 185050 PRK15094 magnesium/cobalt transporter CorC. 292 matched cddid_all.tbl CDD PRK15095 PRK15095 237908 PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional 156 matched cddid_all.tbl CDD PRK15097 PRK15097 185052 PRK15097 cytochrome bd-I ubiquinol oxidase subunit CydA. 522 matched cddid_all.tbl CDD PRK15098 PRK15098 185053 PRK15098 beta-glucosidase BglX. 765 matched cddid_all.tbl CDD PRK15099 PRK15099 185054 PRK15099 lipid III flippase WzxE. 416 matched cddid_all.tbl CDD PRK15100 PRK15100 185055 PRK15100 cystine ABC transporter permease. 220 matched cddid_all.tbl CDD PRK15101 PRK15101 185056 PRK15101 protease3; Provisional 961 matched cddid_all.tbl CDD PRK15102 PRK15102 237909 PRK15102 trimethylamine-N-oxide reductase TorA. 825 matched cddid_all.tbl CDD PRK15103 PRK15103 237910 PRK15103 membrane integrity-associated transporter subunit PqiA. 419 matched cddid_all.tbl CDD PRK15104 PRK15104 185059 PRK15104 oligopeptide ABC transporter substrate-binding protein OppA; Provisional 543 matched cddid_all.tbl CDD PRK15105 PRK15105 185060 PRK15105 peptidoglycan synthase FtsI; Provisional 578 matched cddid_all.tbl CDD PRK15106 PRK15106 237911 PRK15106 nucleoside-specific channel-forming protein Tsx; Provisional 289 matched cddid_all.tbl CDD PRK15107 PRK15107 185062 PRK15107 glutamate/aspartate ABC transporter permease GltK. 224 matched cddid_all.tbl CDD PRK15109 PRK15109 185064 PRK15109 antimicrobial peptide ABC transporter periplasmic binding protein SapA; Provisional 547 matched cddid_all.tbl CDD PRK15110 PRK15110 185065 PRK15110 peptide ABC transporter permease SapB. 321 matched cddid_all.tbl CDD PRK15111 PRK15111 185066 PRK15111 peptide ABC transporter permease SapC. 296 matched cddid_all.tbl CDD PRK15112 PRK15112 185067 PRK15112 peptide ABC transporter ATP-binding protein SapF. 267 matched cddid_all.tbl CDD PRK15113 PRK15113 185068 PRK15113 glutathione transferase. 214 matched cddid_all.tbl CDD PRK15114 PRK15114 185069 PRK15114 tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ; Provisional 245 matched cddid_all.tbl CDD PRK15115 PRK15115 185070 PRK15115 response regulator GlrR; Provisional 444 matched cddid_all.tbl CDD PRK15116 PRK15116 185071 PRK15116 sulfur acceptor protein CsdL; Provisional 268 matched cddid_all.tbl CDD PRK15117 PRK15117 237912 PRK15117 phospholipid-binding protein MlaC. 211 matched cddid_all.tbl CDD PRK15118 PRK15118 185073 PRK15118 universal stress protein UspA. 144 matched cddid_all.tbl CDD PRK15121 PRK15121 185076 PRK15121 MDR efflux pump AcrAB transcriptional activator RobA. 289 matched cddid_all.tbl CDD PRK15122 PRK15122 237914 PRK15122 magnesium-transporting ATPase; Provisional 903 matched cddid_all.tbl CDD PRK15123 PRK15123 237915 PRK15123 lipopolysaccharide core heptose(I) kinase RfaP; Provisional 268 matched cddid_all.tbl CDD PRK15124 PRK15124 185079 PRK15124 RNA 2',3'-cyclic phosphodiesterase. 176 matched cddid_all.tbl CDD PRK15126 PRK15126 185080 PRK15126 HMP-PP phosphatase. 272 matched cddid_all.tbl CDD PRK15127 PRK15127 185081 PRK15127 multidrug efflux RND transporter permease subunit AcrB. 1049 matched cddid_all.tbl CDD PRK15128 PRK15128 185082 PRK15128 23S rRNA (cytosine(1962)-C(5))-methyltransferase RlmI. 396 matched cddid_all.tbl CDD PRK15129 PRK15129 185083 PRK15129 L-Ala-D/L-Glu epimerase; Provisional 321 matched cddid_all.tbl CDD PRK15130 PRK15130 237916 PRK15130 spermidine N1-acetyltransferase; Provisional 186 matched cddid_all.tbl CDD PRK15131 PRK15131 185085 PRK15131 mannose-6-phosphate isomerase; Provisional 389 matched cddid_all.tbl CDD PRK15132 PRK15132 185086 PRK15132 tyrosine transporter TyrP; Provisional 403 matched cddid_all.tbl CDD PRK15133 PRK15133 185087 PRK15133 microcin C ABC transporter permease YejB; Provisional 364 matched cddid_all.tbl CDD PRK15134 PRK15134 237917 PRK15134 microcin C ABC transporter ATP-binding protein YejF; Provisional 529 matched cddid_all.tbl CDD PRK15135 PRK15135 185089 PRK15135 histidine ABC transporter permease HisQ. 228 matched cddid_all.tbl CDD PRK15136 PRK15136 185090 PRK15136 multidrug efflux MFS transporter periplasmic adaptor subunit EmrA. 390 matched cddid_all.tbl CDD PRK15137 PRK15137 185091 PRK15137 DNA-specific endonuclease I; Provisional 235 matched cddid_all.tbl CDD PRK15138 PRK15138 185092 PRK15138 alcohol dehydrogenase. 387 matched cddid_all.tbl CDD PRK15171 PRK15171 185093 PRK15171 lipopolysaccharide 3-alpha-galactosyltransferase. 334 matched cddid_all.tbl CDD PRK15172 PRK15172 237918 PRK15172 aldose-1-epimerase. 300 matched cddid_all.tbl CDD PRK15173 PRK15173 185095 PRK15173 peptidase; Provisional 323 matched cddid_all.tbl CDD PRK15174 PRK15174 185096 PRK15174 Vi polysaccharide transport protein VexE. 656 matched cddid_all.tbl CDD PRK15175 PRK15175 185097 PRK15175 Vi polysaccharide ABC transporter protein VexA. 355 matched cddid_all.tbl CDD PRK15176 PRK15176 185098 PRK15176 Vi polysaccharide ABC transporter inner membrane protein VexB. 264 matched cddid_all.tbl CDD PRK15177 PRK15177 185099 PRK15177 Vi polysaccharide ABC transporter ATP-binding protein VexC. 213 matched cddid_all.tbl CDD PRK15178 PRK15178 185100 PRK15178 Vi polysaccharide ABC transporter inner membrane protein VexD. 434 matched cddid_all.tbl CDD PRK15179 PRK15179 185101 PRK15179 Vi polysaccharide biosynthesis protein TviE; Provisional 694 matched cddid_all.tbl CDD PRK15180 PRK15180 185102 PRK15180 Vi polysaccharide biosynthesis protein TviD; Provisional 831 matched cddid_all.tbl CDD PRK15181 PRK15181 185103 PRK15181 Vi polysaccharide biosynthesis UDP-N-acetylglucosaminuronic acid C-4 epimerase TviC. 348 matched cddid_all.tbl CDD PRK15182 PRK15182 185104 PRK15182 Vi polysaccharide biosynthesis UDP-N-acetylglucosamine C-6 dehydrogenase TviB. 425 matched cddid_all.tbl CDD PRK15183 PRK15183 185105 PRK15183 Vi polysaccharide biosynthesis regulator TviA. 143 matched cddid_all.tbl CDD PRK15184 PRK15184 185106 PRK15184 curli production assembly/transport protein CsgG; Provisional 277 matched cddid_all.tbl CDD PRK15185 PRK15185 185107 PRK15185 transcriptional regulator HilD; Provisional 309 matched cddid_all.tbl CDD PRK15186 PRK15186 185108 PRK15186 AraC family transcriptional regulator; Provisional 291 matched cddid_all.tbl CDD PRK15187 PRK15187 185109 PRK15187 fimbrial protein BcfA; Provisional 180 matched cddid_all.tbl CDD PRK15188 PRK15188 185110 PRK15188 fimbrial chaperone protein BcfB; Provisional 228 matched cddid_all.tbl CDD PRK15189 PRK15189 185111 PRK15189 fimbrial protein BcfD; Provisional 335 matched cddid_all.tbl CDD PRK15190 PRK15190 185112 PRK15190 fimbrial protein BcfE; Provisional 181 matched cddid_all.tbl CDD PRK15191 PRK15191 185113 PRK15191 fimbrial protein BcfF; Provisional 172 matched cddid_all.tbl CDD PRK15192 PRK15192 185114 PRK15192 pili/flagellar-assembly chaperone. 234 matched cddid_all.tbl CDD PRK15193 PRK15193 237919 PRK15193 outer membrane usher protein; Provisional 876 matched cddid_all.tbl CDD PRK15194 PRK15194 237920 PRK15194 type 1 fimbrial protein subunit FimA. 185 matched cddid_all.tbl CDD PRK15195 PRK15195 185117 PRK15195 molecular chaperone FimC. 229 matched cddid_all.tbl CDD PRK15196 PRK15196 185118 PRK15196 type III secretion system effector PipB2. 350 matched cddid_all.tbl CDD PRK15197 PRK15197 185119 PRK15197 type III secretion system effector PipB. 291 matched cddid_all.tbl CDD PRK15198 PRK15198 185120 PRK15198 outer membrane usher protein FimD. 860 matched cddid_all.tbl CDD PRK15199 PRK15199 237921 fimH type 1 fimbrin D-mannose specific adhesin FimH. 335 matched cddid_all.tbl CDD PRK15200 PRK15200 185122 PRK15200 type 1 fimbrial protein subunit FimI. 177 matched cddid_all.tbl CDD PRK15201 PRK15201 185123 PRK15201 fimbriae biosynthesis transcriptional regulator FimW. 198 matched cddid_all.tbl CDD PRK15202 PRK15202 237922 PRK15202 type III secretion system chaperone. 117 matched cddid_all.tbl CDD PRK15203 PRK15203 185125 PRK15203 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase; Provisional 429 matched cddid_all.tbl CDD PRK15204 PRK15204 185126 PRK15204 undecaprenyl-phosphate galactose phosphotransferase; Provisional 476 matched cddid_all.tbl CDD PRK15205 PRK15205 237923 PRK15205 long polar fimbrial protein LpfE; Provisional 176 matched cddid_all.tbl CDD PRK15206 PRK15206 237924 PRK15206 long polar fimbrial protein LpfD; Provisional 359 matched cddid_all.tbl CDD PRK15207 PRK15207 185129 PRK15207 outer membrane usher protein LpfC. 842 matched cddid_all.tbl CDD PRK15208 PRK15208 237925 PRK15208 molecular chaperone LpfB. 228 matched cddid_all.tbl CDD PRK15209 PRK15209 185131 PRK15209 long polar fimbrial protein LpfA; Provisional 174 matched cddid_all.tbl CDD PRK15210 PRK15210 185132 PRK15210 fimbrial protein. 194 matched cddid_all.tbl CDD PRK15211 PRK15211 185133 PRK15211 fimbrial chaperone. 229 matched cddid_all.tbl CDD PRK15212 PRK15212 185134 PRK15212 virulence protein SpvA; Provisional 255 matched cddid_all.tbl CDD PRK15213 PRK15213 237926 PRK15213 outer membrane usher protein PefC. 797 matched cddid_all.tbl CDD PRK15214 PRK15214 185136 PRK15214 fimbrial protein PefA; Provisional 172 matched cddid_all.tbl CDD PRK15215 PRK15215 185137 PRK15215 fimbriae biosynthesis regulatory protein; Provisional 100 matched cddid_all.tbl CDD PRK15216 PRK15216 185138 PRK15216 putative fimbrial biosynthesis regulatory protein; Provisional 340 matched cddid_all.tbl CDD PRK15217 PRK15217 185139 PRK15217 fimbrial outer membrane usher protein; Provisional 826 matched cddid_all.tbl CDD PRK15218 PRK15218 185140 PRK15218 fimbrial assembly chaperone. 226 matched cddid_all.tbl CDD PRK15219 PRK15219 237927 PRK15219 carbonic anhydrase; Provisional 245 matched cddid_all.tbl CDD PRK15220 PRK15220 237928 PRK15220 fimbrial protein YehD. 178 matched cddid_all.tbl CDD PRK15221 PRK15221 185143 PRK15221 Saf-pilin pilus formation protein SafA; Provisional 165 matched cddid_all.tbl CDD PRK15222 PRK15222 185144 PRK15222 putative pilin structural protein SafD; Provisional 156 matched cddid_all.tbl CDD PRK15223 PRK15223 185145 PRK15223 fimbrial biogenesis outer membrane usher protein. 836 matched cddid_all.tbl CDD PRK15224 PRK15224 185146 PRK15224 pili assembly chaperone PapD. 237 matched cddid_all.tbl CDD PRK15228 PRK15228 185147 PRK15228 fimbrial protein SefA; Provisional 165 matched cddid_all.tbl CDD PRK15231 PRK15231 185148 PRK15231 fimbrial adhesin protein SefD; Provisional 150 matched cddid_all.tbl CDD PRK15233 PRK15233 185149 PRK15233 fimbrial chaperone SefB. 246 matched cddid_all.tbl CDD PRK15235 PRK15235 185150 PRK15235 outer membrane fimbrial usher protein SefC; Provisional 814 matched cddid_all.tbl CDD PRK15238 PRK15238 237929 PRK15238 inner membrane transporter YjeM; Provisional 496 matched cddid_all.tbl CDD PRK15239 PRK15239 185152 PRK15239 putative fimbrial protein StaA; Provisional 197 matched cddid_all.tbl CDD PRK15240 PRK15240 185153 PRK15240 resistance to complement killing; Provisional 185 matched cddid_all.tbl CDD PRK15241 PRK15241 185154 PRK15241 putative fimbrial protein StaD; Provisional 188 matched cddid_all.tbl CDD PRK15243 PRK15243 185155 PRK15243 virulence genes transcriptional activator SpvR. 297 matched cddid_all.tbl CDD PRK15244 PRK15244 185156 PRK15244 type III secretion system effector NAD(+)--protein-arginine ADP-ribosyltransferase SpvB. 591 matched cddid_all.tbl CDD PRK15245 PRK15245 185157 PRK15245 type III secretion system effector phosphothreonine lyase. 241 matched cddid_all.tbl CDD PRK15246 PRK15246 185158 PRK15246 fimbrial assembly chaperone. 233 matched cddid_all.tbl CDD PRK15247 PRK15247 185159 PRK15247 fimbrial usher protein StbD. 441 matched cddid_all.tbl CDD PRK15248 PRK15248 185160 PRK15248 fimbrial outer membrane usher protein. 853 matched cddid_all.tbl CDD PRK15249 PRK15249 237930 PRK15249 fimbrial chaperone. 253 matched cddid_all.tbl CDD PRK15250 PRK15250 185162 PRK15250 type III secretion system effector cysteine hydrolase SpvD. 216 matched cddid_all.tbl CDD PRK15251 PRK15251 237931 PRK15251 cytolethal distending toxin subunit B family protein. 271 matched cddid_all.tbl CDD PRK15252 PRK15252 237932 PRK15252 putative fimbrial-like adhesin protein. 344 matched cddid_all.tbl CDD PRK15253 PRK15253 185165 PRK15253 putative fimbrial assembly chaperone protein StcB; Provisional 242 matched cddid_all.tbl CDD PRK15254 PRK15254 185166 PRK15254 fimbrial chaperone protein StdC; Provisional 239 matched cddid_all.tbl CDD PRK15255 PRK15255 185167 PRK15255 fimbrial outer membrane usher protein StdB; Provisional 829 matched cddid_all.tbl CDD PRK15260 PRK15260 185168 PRK15260 fimbrial protein SteF; Provisional 178 matched cddid_all.tbl CDD PRK15261 PRK15261 185169 PRK15261 fimbrial protein SteA; Provisional 195 matched cddid_all.tbl CDD PRK15262 PRK15262 237933 PRK15262 putative fimbrial protein StaF; Provisional 197 matched cddid_all.tbl CDD PRK15263 PRK15263 185171 PRK15263 fimbrial-like protein. 196 matched cddid_all.tbl CDD PRK15265 PRK15265 185172 PRK15265 subtilase cytotoxin subunit B-like protein; Provisional 134 matched cddid_all.tbl CDD PRK15266 PRK15266 185173 PRK15266 subtilase cytotoxin subunit B; Provisional 135 matched cddid_all.tbl CDD PRK15267 PRK15267 185174 PRK15267 subtilase cytotoxin subunit B-like protein; Provisional 141 matched cddid_all.tbl CDD PRK15272 PRK15272 185175 PRK15272 pertussis-like toxin subunit ArtA. 242 matched cddid_all.tbl CDD PRK15273 PRK15273 185176 PRK15273 fimbrial biogenesis outer membrane usher protein. 881 matched cddid_all.tbl CDD PRK15274 PRK15274 185177 PRK15274 putative periplasmic fimbrial chaperone protein SteC; Provisional 257 matched cddid_all.tbl CDD PRK15275 PRK15275 185178 PRK15275 putative fimbrial protein SteD; Provisional 166 matched cddid_all.tbl CDD PRK15276 PRK15276 185179 PRK15276 putative fimbrial subunit SteE; Provisional 153 matched cddid_all.tbl CDD PRK15278 PRK15278 185180 PRK15278 type III secretion protein BopE; Provisional 261 matched cddid_all.tbl CDD PRK15279 PRK15279 185181 PRK15279 type III secretion system guanine nucleotide exchange factor SopE. 240 matched cddid_all.tbl CDD PRK15280 PRK15280 185182 PRK15280 type III secretion system guanine nucleotide exchange factor SopE2. 240 matched cddid_all.tbl CDD PRK15283 PRK15283 185183 PRK15283 fimbrial major subunit StfA. 186 matched cddid_all.tbl CDD PRK15284 PRK15284 185184 PRK15284 putative fimbrial outer membrane usher protein StfC; Provisional 881 matched cddid_all.tbl CDD PRK15285 PRK15285 185185 PRK15285 fimbrial chaperone StfD. 250 matched cddid_all.tbl CDD PRK15286 PRK15286 185186 PRK15286 putative minor fimbrial subunit StfE; Provisional 170 matched cddid_all.tbl CDD PRK15287 PRK15287 185187 PRK15287 fimbrial minor subunit StfF. 158 matched cddid_all.tbl CDD PRK15288 PRK15288 185188 PRK15288 putative minor fimbrial subunit StfG; Provisional 176 matched cddid_all.tbl CDD PRK15289 PRK15289 185189 lpfA fimbrial protein; Provisional 190 matched cddid_all.tbl CDD PRK15290 PRK15290 237934 lfpB fimbrial chaperone. 243 matched cddid_all.tbl CDD PRK15291 PRK15291 185191 PRK15291 fimbrial protein StgD; Provisional 355 matched cddid_all.tbl CDD PRK15292 PRK15292 237935 PRK15292 type 1 fimbrial protein. 365 matched cddid_all.tbl CDD PRK15293 PRK15293 185193 PRK15293 fimbrial protein SthD. 185 matched cddid_all.tbl CDD PRK15294 PRK15294 185194 PRK15294 fimbrial outer membrane usher protein. 845 matched cddid_all.tbl CDD PRK15295 PRK15295 237936 PRK15295 fimbrial assembly chaperone. 226 matched cddid_all.tbl CDD PRK15296 PRK15296 185196 PRK15296 fimbrial protein SthA. 181 matched cddid_all.tbl CDD PRK15297 PRK15297 185197 PRK15297 fimbrial protein. 359 matched cddid_all.tbl CDD PRK15298 PRK15298 185198 PRK15298 fimbrial outer membrane usher protein. 848 matched cddid_all.tbl CDD PRK15299 PRK15299 185199 PRK15299 fimbrial chaperone protein StiB; Provisional 227 matched cddid_all.tbl CDD PRK15300 PRK15300 185200 PRK15300 fimbrial protein StiA; Provisional 179 matched cddid_all.tbl CDD PRK15301 PRK15301 185201 PRK15301 hypothetical protein; Provisional 186 matched cddid_all.tbl CDD PRK15302 PRK15302 185202 PRK15302 hypothetical protein; Provisional 229 matched cddid_all.tbl CDD PRK15303 PRK15303 185203 PRK15303 hypothetical protein; Provisional 229 matched cddid_all.tbl CDD PRK15304 PRK15304 237937 PRK15304 putative fimbrial outer membrane usher protein; Provisional 801 matched cddid_all.tbl CDD PRK15305 PRK15305 185205 PRK15305 fimbrial protein StkG. 353 matched cddid_all.tbl CDD PRK15306 PRK15306 237938 PRK15306 fimbrial protein. 190 matched cddid_all.tbl CDD PRK15307 PRK15307 185207 PRK15307 major fimbrial protein StkA; Provisional 201 matched cddid_all.tbl CDD PRK15308 PRK15308 237939 PRK15308 fimbrial protein TcfA. 234 matched cddid_all.tbl CDD PRK15309 PRK15309 185209 PRK15309 fimbrial protein TcfB. 191 matched cddid_all.tbl CDD PRK15310 PRK15310 185210 PRK15310 fimbrial outer membrane usher protein TcfC; Provisional 895 matched cddid_all.tbl CDD PRK15311 PRK15311 185211 PRK15311 fimbrial protein TcfD. 359 matched cddid_all.tbl CDD PRK15312 PRK15312 185212 PRK15312 antimicrobial resistance protein Mig-14; Provisional 298 matched cddid_all.tbl CDD PRK15313 PRK15313 237940 PRK15313 intestinal colonization autotransporter adhesin MisL. 955 matched cddid_all.tbl CDD PRK15314 PRK15314 185214 PRK15314 outer membrane protein RatB; Provisional 2435 matched cddid_all.tbl CDD PRK15315 PRK15315 237941 PRK15315 outer membrane protein RatA; Provisional 1865 matched cddid_all.tbl CDD PRK15316 PRK15316 185216 PRK15316 RatA-like protein; Provisional 2683 matched cddid_all.tbl CDD PRK15317 PRK15317 237942 PRK15317 alkyl hydroperoxide reductase subunit F; Provisional 517 matched cddid_all.tbl CDD PRK15318 PRK15318 237943 PRK15318 intimin-like protein SinH; Provisional 730 matched cddid_all.tbl CDD PRK15319 PRK15319 185219 PRK15319 fibronectin-binding autotransporter adhesin ShdA. 2039 matched cddid_all.tbl CDD PRK15320 PRK15320 185220 PRK15320 transcriptional activator SprB; Provisional 251 matched cddid_all.tbl CDD PRK15321 PRK15321 185221 PRK15321 type III secretion system effector protein OrgC. 120 matched cddid_all.tbl CDD PRK15322 PRK15322 185222 PRK15322 oxygen-regulated invasion protein OrgB. 210 matched cddid_all.tbl CDD PRK15323 PRK15323 185223 PRK15323 oxygen-regulated invasion protein OrgA. 167 matched cddid_all.tbl CDD PRK15324 PRK15324 185224 PRK15324 EscJ/YscJ/HrcJ family type III secretion inner membrane ring protein. 252 matched cddid_all.tbl CDD PRK15325 PRK15325 185225 PRK15325 type III secretion system inner rod protein PrgJ. 80 matched cddid_all.tbl CDD PRK15326 PRK15326 185226 PRK15326 type III secretion system needle complex protein. 80 matched cddid_all.tbl CDD PRK15327 PRK15327 237944 PRK15327 PrgH/EprH family type III secretion inner membrane ring protein. 393 matched cddid_all.tbl CDD PRK15328 PRK15328 185228 PRK15328 type III secretion system invasion protein IagB. 160 matched cddid_all.tbl CDD PRK15329 PRK15329 237945 PRK15329 chaperone SicP. 138 matched cddid_all.tbl CDD PRK15330 PRK15330 185230 PRK15330 type III secretion system needle tip protein SipD. 343 matched cddid_all.tbl CDD PRK15331 PRK15331 185231 PRK15331 type III secretion system translocator chaperone SicA. 165 matched cddid_all.tbl CDD PRK15332 PRK15332 185232 PRK15332 SpaR/YscT/HrcT type III secretion system export apparatus protein. 263 matched cddid_all.tbl CDD PRK15333 PRK15333 185233 PRK15333 EscS/YscS/HrcS family type III secretion system export apparatus protein. 86 matched cddid_all.tbl CDD PRK15334 PRK15334 185234 PRK15334 type III secretion system protein SpaN. 336 matched cddid_all.tbl CDD PRK15335 PRK15335 185235 PRK15335 type III secretion system protein SpaM; Provisional 147 matched cddid_all.tbl CDD PRK15336 PRK15336 185236 PRK15336 type III secretion system chaperone SpaK; Provisional 135 matched cddid_all.tbl CDD PRK15337 PRK15337 237946 PRK15337 EscV/YscV/HrcV family type III secretion system export apparatus protein. 686 matched cddid_all.tbl CDD PRK15338 PRK15338 237947 PRK15338 YopN/LcrE/InvE/MxiC type III secretion system gatekeeper. 372 matched cddid_all.tbl CDD PRK15339 PRK15339 237948 PRK15339 EscC/YscC/HrcC family type III secretion system outer membrane ring protein. 559 matched cddid_all.tbl CDD PRK15340 PRK15340 185240 PRK15340 AraC family transcriptional regulator InvF. 216 matched cddid_all.tbl CDD PRK15341 PRK15341 185241 PRK15341 type III secretion system invasion lipoprotein InvH. 147 matched cddid_all.tbl CDD PRK15344 PRK15344 185242 PRK15344 type III secretion system needle protein SsaG; Provisional 71 matched cddid_all.tbl CDD PRK15345 PRK15345 237949 PRK15345 SepL/TyeA/HrpJ family type III secretion system protein. 326 matched cddid_all.tbl CDD PRK15346 PRK15346 237950 PRK15346 EscC/YscC/HrcC family type III secretion system outer membrane ring protein. 499 matched cddid_all.tbl CDD PRK15347 PRK15347 237951 PRK15347 two component system sensor kinase. 921 matched cddid_all.tbl CDD PRK15348 PRK15348 185246 PRK15348 EscJ/YscJ/HrcJ family type III secretion inner membrane ring protein SsaJ. 249 matched cddid_all.tbl CDD PRK15349 PRK15349 185247 PRK15349 EscT/YscT/HrcT family type III secretion system export apparatus protein. 259 matched cddid_all.tbl CDD PRK15350 PRK15350 185248 PRK15350 EscS/YscS/HrcS family type III secretion system export apparatus protein. 88 matched cddid_all.tbl CDD PRK15351 PRK15351 185249 PRK15351 type III secretion system apparatus protein SsaP. 124 matched cddid_all.tbl CDD PRK15352 PRK15352 185250 PRK15352 type III secretion system apparatus protein SsaO. 125 matched cddid_all.tbl CDD PRK15353 PRK15353 185251 PRK15353 type III secretion system apparatus protein. 122 matched cddid_all.tbl CDD PRK15354 PRK15354 185252 PRK15354 type III secretion system apparatus protein SsaK. 224 matched cddid_all.tbl CDD PRK15355 PRK15355 185253 PRK15355 type III secretion system protein SsaI; Provisional 82 matched cddid_all.tbl CDD PRK15356 PRK15356 185254 PRK15356 type III secretion system protein SsaH; Provisional 75 matched cddid_all.tbl CDD PRK15357 PRK15357 185255 PRK15357 pathogenicity island 2 effector protein SseG; Provisional 229 matched cddid_all.tbl CDD PRK15358 PRK15358 185256 PRK15358 type III secretion systems effector SseF. 239 matched cddid_all.tbl CDD PRK15359 PRK15359 185257 PRK15359 type III secretion system chaperone protein SscB; Provisional 144 matched cddid_all.tbl CDD PRK15360 PRK15360 185258 PRK15360 pathogenicity island 2 effector protein SseE; Provisional 137 matched cddid_all.tbl CDD PRK15361 PRK15361 185259 PRK15361 type III secretion system translocon protein SseD. 195 matched cddid_all.tbl CDD PRK15362 PRK15362 237952 PRK15362 type III secretion system translocon protein. 473 matched cddid_all.tbl CDD PRK15363 PRK15363 185261 PRK15363 CesD/SycD/LcrH family type III secretion system chaperone SscA. 157 matched cddid_all.tbl CDD PRK15364 PRK15364 185262 PRK15364 type III secretion system translocon protein SseB. 196 matched cddid_all.tbl CDD PRK15365 PRK15365 185263 PRK15365 type III secretion system chaperone SseA; Provisional 107 matched cddid_all.tbl CDD PRK15366 PRK15366 185264 PRK15366 type III secretion system chaperone SsaE; Provisional 80 matched cddid_all.tbl CDD PRK15367 PRK15367 185265 PRK15367 EscD/YscD/HrpQ family type III secretion system inner membrane ring protein. 395 matched cddid_all.tbl CDD PRK15368 PRK15368 185266 PRK15368 type III secretion system protein SpiC. 127 matched cddid_all.tbl CDD PRK15369 PRK15369 185267 PRK15369 two component system response regulator. 211 matched cddid_all.tbl CDD PRK15370 PRK15370 185268 PRK15370 type III secretion system effector E3 ubiquitin transferase SlrP. 754 matched cddid_all.tbl CDD PRK15371 PRK15371 185269 PRK15371 YopJ family type III secretion system effector serine/threonine acetyltransferase. 287 matched cddid_all.tbl CDD PRK15372 PRK15372 185270 PRK15372 type III secretion system effector SseI. 292 matched cddid_all.tbl CDD PRK15373 PRK15373 185271 PRK15373 IpaC/SipC family type III secretion system needle tip complex protein. 411 matched cddid_all.tbl CDD PRK15374 PRK15374 185272 PRK15374 type III secretion system needle tip complex protein SipB. 593 matched cddid_all.tbl CDD PRK15375 PRK15375 185273 PRK15375 type III secretion system effector GTPase-activating protein SptP. 535 matched cddid_all.tbl CDD PRK15376 PRK15376 185274 PRK15376 type III secretion system effector SipA. 670 matched cddid_all.tbl CDD PRK15377 PRK15377 185275 PRK15377 type III secretion system effector HECT-type E3 ubiquitin transferase. 782 matched cddid_all.tbl CDD PRK15378 PRK15378 237953 PRK15378 type III secretion system effector inositol phosphate phosphatase. 564 matched cddid_all.tbl CDD PRK15379 PRK15379 185277 PRK15379 type III secretion system effector SopD. 317 matched cddid_all.tbl CDD PRK15380 PRK15380 185278 PRK15380 type III secretion system effector SopD2. 319 matched cddid_all.tbl CDD PRK15381 PRK15381 185279 PRK15381 type III secretion system effector. 408 matched cddid_all.tbl CDD PRK15382 PRK15382 185280 PRK15382 NleB family type III secretion system effector arginine glycosyltransferase. 326 matched cddid_all.tbl CDD PRK15383 PRK15383 185281 PRK15383 type III secretion system effector arginine glycosyltransferase. 335 matched cddid_all.tbl CDD PRK15384 PRK15384 185282 PRK15384 type III secretion system effector arginine glycosyltransferase SseK1. 336 matched cddid_all.tbl CDD PRK15385 PRK15385 185283 PRK15385 MgtC family protein. 225 matched cddid_all.tbl CDD PRK15386 PRK15386 237954 PRK15386 type III secretion effector GogB. 426 matched cddid_all.tbl CDD PRK15387 PRK15387 185285 PRK15387 type III secretion system effector E3 ubiquitin transferase SspH2. 788 matched cddid_all.tbl CDD PRK15388 PRK15388 185286 PRK15388 superoxide dismutase [Cu-Zn]. 177 matched cddid_all.tbl CDD PRK15389 PRK15389 237955 PRK15389 fumarate hydratase; Provisional 536 matched cddid_all.tbl CDD PRK15390 PRK15390 185288 PRK15390 fumarate hydratase FumA; Provisional 548 matched cddid_all.tbl CDD PRK15391 PRK15391 185289 PRK15391 class I fumarate hydratase. 548 matched cddid_all.tbl CDD PRK15392 PRK15392 185290 PRK15392 class I fumarate hydratase. 550 matched cddid_all.tbl CDD PRK15393 PRK15393 185291 PRK15393 NUDIX hydrolase YfcD; Provisional 180 matched cddid_all.tbl CDD PRK15394 PRK15394 185292 PRK15394 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD; Provisional 296 matched cddid_all.tbl CDD PRK15395 PRK15395 185293 PRK15395 galactose/glucose ABC transporter substrate-binding protein MglB. 330 matched cddid_all.tbl CDD PRK15396 PRK15396 185294 PRK15396 major outer membrane lipoprotein. 78 matched cddid_all.tbl CDD PRK15397 PRK15397 185295 PRK15397 nicotinamide riboside transporter PnuC; Provisional 239 matched cddid_all.tbl CDD PRK15398 PRK15398 237956 PRK15398 aldehyde dehydrogenase. 465 matched cddid_all.tbl CDD PRK15399 PRK15399 185297 PRK15399 lysine decarboxylase. 713 matched cddid_all.tbl CDD PRK15400 PRK15400 185298 PRK15400 lysine decarboxylase. 714 matched cddid_all.tbl CDD PRK15401 PRK15401 237957 PRK15401 DNA oxidative demethylase AlkB. 213 matched cddid_all.tbl CDD PRK15402 PRK15402 185300 PRK15402 MdfA family multidrug efflux MFS transporter. 406 matched cddid_all.tbl CDD PRK15403 PRK15403 237958 PRK15403 multidrug efflux MFS transporter MdtM. 413 matched cddid_all.tbl CDD PRK15404 PRK15404 237959 PRK15404 high-affinity branched-chain amino acid ABC transporter substrate-binding protein. 369 matched cddid_all.tbl CDD PRK15405 PRK15405 185303 PRK15405 ethanolamine utilization microcompartment protein EutL. 217 matched cddid_all.tbl CDD PRK15406 PRK15406 185304 PRK15406 oligopeptide ABC transporter permease OppC; Provisional 302 matched cddid_all.tbl CDD PRK15407 PRK15407 237960 PRK15407 lipopolysaccharide biosynthesis protein RfbH; Provisional 438 matched cddid_all.tbl CDD PRK15408 PRK15408 237961 PRK15408 autoinducer 2 ABC transporter substrate-binding protein LsrB. 336 matched cddid_all.tbl CDD PRK15409 PRK15409 185307 PRK15409 glyoxylate/hydroxypyruvate reductase GhrB. 323 matched cddid_all.tbl CDD PRK15410 PRK15410 185308 PRK15410 DgsA anti-repressor MtfA; Provisional 260 matched cddid_all.tbl CDD PRK15411 PRK15411 185309 rcsA transcriptional regulator RcsA. 207 matched cddid_all.tbl CDD PRK15412 PRK15412 185310 PRK15412 thiol:disulfide interchange protein DsbE; Provisional 185 matched cddid_all.tbl CDD PRK15413 PRK15413 185311 PRK15413 glutathione ABC transporter substrate-binding protein GsiB; Provisional 512 matched cddid_all.tbl CDD PRK15414 PRK15414 185312 PRK15414 phosphomannomutase. 456 matched cddid_all.tbl CDD PRK15415 PRK15415 185313 PRK15415 propanediol utilization microcompartment protein PduB. 266 matched cddid_all.tbl CDD PRK15416 PRK15416 185314 PRK15416 lipopolysaccharide core heptose(II)-phosphate phosphatase; Provisional 201 matched cddid_all.tbl CDD PRK15417 PRK15417 185315 PRK15417 integron integrase. 337 matched cddid_all.tbl CDD PRK15418 PRK15418 237962 PRK15418 transcriptional regulator LsrR; Provisional 318 matched cddid_all.tbl CDD PRK15419 PRK15419 185317 PRK15419 sodium/proline symporter PutP. 502 matched cddid_all.tbl CDD PRK15420 PRK15420 185318 fucU L-fucose mutarotase; Provisional 140 matched cddid_all.tbl CDD PRK15421 PRK15421 185319 PRK15421 HTH-type transcriptional regulator MetR. 317 matched cddid_all.tbl CDD PRK15422 PRK15422 185320 PRK15422 septal ring assembly protein ZapB; Provisional 79 matched cddid_all.tbl CDD PRK15423 PRK15423 185321 PRK15423 hypoxanthine phosphoribosyltransferase; Provisional 178 matched cddid_all.tbl CDD PRK15424 PRK15424 237963 PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional 538 matched cddid_all.tbl CDD PRK15425 PRK15425 185323 gapA glyceraldehyde-3-phosphate dehydrogenase. 331 matched cddid_all.tbl CDD PRK15426 PRK15426 237964 PRK15426 cellulose biosynthesis regulator YedQ. 570 matched cddid_all.tbl CDD PRK15428 PRK15428 185326 PRK15428 putative propanediol utilization protein PduM; Provisional 163 matched cddid_all.tbl CDD PRK15429 PRK15429 237965 PRK15429 formate hydrogenlyase transcriptional activator FlhA. 686 matched cddid_all.tbl CDD PRK15430 PRK15430 185328 PRK15430 EamA family transporter RarD. 296 matched cddid_all.tbl CDD PRK15431 PRK15431 185329 PRK15431 [Fe-S]-dependent transcriptional repressor FeoC. 78 matched cddid_all.tbl CDD PRK15432 PRK15432 185330 PRK15432 autoinducer 2 ABC transporter permease LsrC; Provisional 344 matched cddid_all.tbl CDD PRK15433 PRK15433 185331 PRK15433 branched-chain amino acid transporter carrier protein BrnQ. 439 matched cddid_all.tbl CDD PRK15434 PRK15434 237966 PRK15434 GDP-mannose mannosyl hydrolase. 159 matched cddid_all.tbl CDD PRK15435 PRK15435 185333 PRK15435 bifunctional DNA-binding transcriptional regulator/O6-methylguanine-DNA methyltransferase Ada. 353 matched cddid_all.tbl CDD PRK15437 PRK15437 185334 PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional 259 matched cddid_all.tbl CDD PRK15438 PRK15438 185335 PRK15438 erythronate-4-phosphate dehydrogenase PdxB; Provisional 378 matched cddid_all.tbl CDD PRK15439 PRK15439 185336 PRK15439 autoinducer 2 ABC transporter ATP-binding protein LsrA; Provisional 510 matched cddid_all.tbl CDD PRK15440 PRK15440 185337 PRK15440 L-rhamnonate dehydratase; Provisional 394 matched cddid_all.tbl CDD PRK15441 PRK15441 185338 PRK15441 peptidyl-prolyl cis-trans isomerase C; Provisional 93 matched cddid_all.tbl CDD PRK15442 PRK15442 185339 PRK15442 beta-lactamase TEM; Provisional 284 matched cddid_all.tbl CDD PRK15443 PRK15443 185340 pduE diol dehydratase small subunit. 138 matched cddid_all.tbl CDD PRK15444 PRK15444 185341 pduC propanediol/glycerol family dehydratase large subunit. 554 matched cddid_all.tbl CDD PRK15445 PRK15445 185342 PRK15445 arsenical efflux pump membrane protein ArsB. 427 matched cddid_all.tbl CDD PRK15446 PRK15446 237967 PRK15446 phosphonate metabolism protein PhnM; Provisional 383 matched cddid_all.tbl CDD PRK15447 PRK15447 237968 PRK15447 putative protease; Provisional 301 matched cddid_all.tbl CDD PRK15448 PRK15448 185345 PRK15448 ethanolamine utilization microcompartment protein EutN. 95 matched cddid_all.tbl CDD PRK15449 PRK15449 185346 PRK15449 ferredoxin-like protein FixX; Provisional 95 matched cddid_all.tbl CDD PRK15450 PRK15450 185347 PRK15450 signal transduction protein PmrD; Provisional 85 matched cddid_all.tbl CDD PRK15451 PRK15451 185348 PRK15451 carboxy-S-adenosyl-L-methionine synthase CmoA. 247 matched cddid_all.tbl CDD PRK15452 PRK15452 237969 PRK15452 putative protease; Provisional 443 matched cddid_all.tbl CDD PRK15453 PRK15453 237970 PRK15453 phosphoribulokinase; Provisional 290 matched cddid_all.tbl CDD PRK15454 PRK15454 185351 PRK15454 ethanolamine utilization ethanol dehydrogenase EutG. 395 matched cddid_all.tbl CDD PRK15455 PRK15455 185352 PRK15455 PrkA family serine protein kinase; Provisional 644 matched cddid_all.tbl CDD PRK15456 PRK15456 185353 PRK15456 universal stress protein UspG; Provisional 142 matched cddid_all.tbl CDD PRK15457 PRK15457 185354 PRK15457 ethanolamine utilization acetate kinase EutQ. 233 matched cddid_all.tbl CDD PRK15458 PRK15458 185355 PRK15458 tagatose 6-phosphate aldolase subunit KbaZ; Provisional 426 matched cddid_all.tbl CDD PRK15459 PRK15459 185356 PRK15459 flagella biosynthesis chaperone FlgN. 140 matched cddid_all.tbl CDD PRK15460 PRK15460 185357 cpsB mannose-1-phosphate guanyltransferase; Provisional 478 matched cddid_all.tbl CDD PRK15461 PRK15461 185358 PRK15461 sulfolactaldehyde 3-reductase. 296 matched cddid_all.tbl CDD PRK15462 PRK15462 237971 PRK15462 dipeptide permease. 493 matched cddid_all.tbl CDD PRK15463 PRK15463 185360 PRK15463 cold shock-like protein CspF; Provisional 70 matched cddid_all.tbl CDD PRK15464 PRK15464 185361 PRK15464 cold shock-like protein CspH; Provisional 70 matched cddid_all.tbl CDD PRK15465 PRK15465 185362 pabB aminodeoxychorismate synthase component 1. 453 matched cddid_all.tbl CDD PRK15466 PRK15466 185363 PRK15466 ethanolamine utilization microcompartment protein EutK. 166 matched cddid_all.tbl CDD PRK15467 PRK15467 185364 PRK15467 ethanolamine utilization acetate kinase EutP. 158 matched cddid_all.tbl CDD PRK15468 PRK15468 185365 PRK15468 ethanolamine utilization microcompartment protein EutS. 111 matched cddid_all.tbl CDD PRK15469 PRK15469 185366 ghrA glyoxylate/hydroxypyruvate reductase GhrA. 312 matched cddid_all.tbl CDD PRK15470 PRK15470 185367 emtA membrane-bound lytic murein transglycosylase EmtA. 203 matched cddid_all.tbl CDD PRK15471 PRK15471 185368 PRK15471 chain length determinant protein WzzB; Provisional 325 matched cddid_all.tbl CDD PRK15472 PRK15472 185369 PRK15472 nucleoside triphosphatase NudI; Provisional 141 matched cddid_all.tbl CDD PRK15473 PRK15473 185370 cbiF cobalt-precorrin-4 methyltransferase. 257 matched cddid_all.tbl CDD PRK15474 PRK15474 185371 PRK15474 ethanolamine utilization microcompartment protein EutM. 97 matched cddid_all.tbl CDD PRK15475 PRK15475 185372 PRK15475 oxaloacetate decarboxylase subunit beta; Provisional 433 matched cddid_all.tbl CDD PRK15476 PRK15476 185373 PRK15476 oxaloacetate decarboxylase subunit beta; Provisional 433 matched cddid_all.tbl CDD PRK15477 PRK15477 185374 PRK15477 oxaloacetate decarboxylase subunit beta; Provisional 433 matched cddid_all.tbl CDD PRK15478 PRK15478 185375 cbiH precorrin-3B C(17)-methyltransferase. 241 matched cddid_all.tbl CDD PRK15479 PRK15479 185376 PRK15479 transcriptional regulator TctD. 221 matched cddid_all.tbl CDD PRK15480 PRK15480 185377 PRK15480 glucose-1-phosphate thymidylyltransferase RfbA; Provisional 292 matched cddid_all.tbl CDD PRK15481 PRK15481 185378 PRK15481 transcriptional regulatory protein PtsJ; Provisional 431 matched cddid_all.tbl CDD PRK15482 PRK15482 185379 PRK15482 HTH-type transcriptional regulator MurR. 285 matched cddid_all.tbl CDD PRK15483 PRK15483 237972 PRK15483 type III restriction-modification system endonuclease. 986 matched cddid_all.tbl CDD PRK15484 PRK15484 185381 PRK15484 lipopolysaccharide N-acetylglucosaminyltransferase. 380 matched cddid_all.tbl CDD PRK15485 PRK15485 185382 PRK15485 energy-coupling factor ABC transporter transmembrane protein. 225 matched cddid_all.tbl CDD PRK15486 PRK15486 185383 hpaC 4-hydroxyphenylacetate 3-monooxygenase reductase subunit; Provisional 170 matched cddid_all.tbl CDD PRK15487 PRK15487 185384 PRK15487 O-antigen ligase RfaL; Provisional 400 matched cddid_all.tbl CDD PRK15488 PRK15488 237973 PRK15488 thiosulfate reductase PhsA; Provisional 759 matched cddid_all.tbl CDD PRK15489 PRK15489 237974 nfrB glycosyl transferase family protein. 703 matched cddid_all.tbl CDD PRK15490 PRK15490 185387 PRK15490 Vi polysaccharide biosynthesis glycosyltransferase TviE. 578 matched cddid_all.tbl CDD PRK15491 PRK15491 185388 PRK15491 replication factor A; Provisional 374 matched cddid_all.tbl CDD PRK15492 PRK15492 185389 PRK15492 triosephosphate isomerase; Provisional 260 matched cddid_all.tbl CDD PRK15493 PRK15493 185390 PRK15493 bifunctional S-methyl-5'-thioadenosine deaminase/S-adenosylhomocysteine deaminase. 435 matched cddid_all.tbl CDD PTZ00004 PTZ00004 240225 PTZ00004 actin-2; Provisional 378 matched cddid_all.tbl CDD PTZ00005 PTZ00005 173310 PTZ00005 phosphoglycerate kinase; Provisional 417 matched cddid_all.tbl CDD PTZ00007 PTZ00007 240226 PTZ00007 (NAP-L) nucleosome assembly protein -L; Provisional 337 matched cddid_all.tbl CDD PTZ00008 PTZ00008 185394 PTZ00008 (NAP-S) nucleosome assembly protein-S; Provisional 185 matched cddid_all.tbl CDD PTZ00009 PTZ00009 240227 PTZ00009 heat shock 70 kDa protein; Provisional 653 matched cddid_all.tbl CDD PTZ00010 PTZ00010 240228 PTZ00010 tubulin beta chain; Provisional 445 matched cddid_all.tbl CDD PTZ00013 PTZ00013 140051 PTZ00013 plasmepsin 4 (PM4); Provisional 450 matched cddid_all.tbl CDD PTZ00014 PTZ00014 240229 PTZ00014 myosin-A; Provisional 821 matched cddid_all.tbl CDD PTZ00015 PTZ00015 185397 PTZ00015 histone H4; Provisional 102 matched cddid_all.tbl CDD PTZ00016 PTZ00016 240230 PTZ00016 aquaglyceroporin; Provisional 294 matched cddid_all.tbl CDD PTZ00017 PTZ00017 185399 PTZ00017 histone H2A; Provisional 134 matched cddid_all.tbl CDD PTZ00018 PTZ00018 185400 PTZ00018 histone H3; Provisional 136 matched cddid_all.tbl CDD PTZ00019 PTZ00019 240231 PTZ00019 fructose-bisphosphate aldolase; Provisional 355 matched cddid_all.tbl CDD PTZ00021 PTZ00021 240232 PTZ00021 falcipain-2; Provisional 489 matched cddid_all.tbl CDD PTZ00023 PTZ00023 173322 PTZ00023 glyceraldehyde-3-phosphate dehydrogenase; Provisional 337 matched cddid_all.tbl CDD PTZ00024 PTZ00024 240233 PTZ00024 cyclin-dependent protein kinase; Provisional 335 matched cddid_all.tbl CDD PTZ00026 PTZ00026 185402 PTZ00026 60S ribosomal protein L15; Provisional 204 matched cddid_all.tbl CDD PTZ00027 PTZ00027 240234 PTZ00027 60S ribosomal protein L6; Provisional 190 matched cddid_all.tbl CDD PTZ00028 PTZ00028 185404 PTZ00028 40S ribosomal protein S6e; Provisional 218 matched cddid_all.tbl CDD PTZ00029 PTZ00029 185405 PTZ00029 60S ribosomal protein L10a; Provisional 216 matched cddid_all.tbl CDD PTZ00030 PTZ00030 185406 PTZ00030 60S ribosomal protein L20; Provisional 121 matched cddid_all.tbl CDD PTZ00031 PTZ00031 173329 PTZ00031 ribosomal protein L2; Provisional 317 matched cddid_all.tbl CDD PTZ00032 PTZ00032 240235 PTZ00032 60S ribosomal protein L18; Provisional 211 matched cddid_all.tbl CDD PTZ00033 PTZ00033 140068 PTZ00033 60S ribosomal protein L24; Provisional 125 matched cddid_all.tbl CDD PTZ00034 PTZ00034 173331 PTZ00034 40S ribosomal protein S10; Provisional 124 matched cddid_all.tbl CDD PTZ00035 PTZ00035 185407 PTZ00035 Rad51 protein; Provisional 337 matched cddid_all.tbl CDD PTZ00036 PTZ00036 173333 PTZ00036 glycogen synthase kinase; Provisional 440 matched cddid_all.tbl CDD PTZ00037 PTZ00037 240236 PTZ00037 DnaJ_C chaperone protein; Provisional 421 matched cddid_all.tbl CDD PTZ00038 PTZ00038 240237 PTZ00038 ferredoxin; Provisional 191 matched cddid_all.tbl CDD PTZ00039 PTZ00039 173336 PTZ00039 40S ribosomal protein S20; Provisional 115 matched cddid_all.tbl CDD PTZ00040 PTZ00040 240238 PTZ00040 translation initiation factor E4; Provisional 233 matched cddid_all.tbl CDD PTZ00041 PTZ00041 240239 PTZ00041 60S ribosomal protein L35a; Provisional 120 matched cddid_all.tbl CDD PTZ00043 PTZ00043 240240 PTZ00043 cytochrome c oxidase subunit; Provisional 268 matched cddid_all.tbl CDD PTZ00044 PTZ00044 185411 PTZ00044 ubiquitin; Provisional 76 matched cddid_all.tbl CDD PTZ00045 PTZ00045 240241 PTZ00045 apical membrane antigen 1; Provisional 595 matched cddid_all.tbl CDD PTZ00046 PTZ00046 240242 PTZ00046 rifin; Provisional 358 matched cddid_all.tbl CDD PTZ00047 PTZ00047 240243 PTZ00047 cytochrome c oxidase subunit II; Provisional 162 matched cddid_all.tbl CDD PTZ00048 PTZ00048 185414 PTZ00048 cytochrome c; Provisional 115 matched cddid_all.tbl CDD PTZ00049 PTZ00049 240244 PTZ00049 cathepsin C-like protein; Provisional 693 matched cddid_all.tbl CDD PTZ00050 PTZ00050 240245 PTZ00050 3-oxoacyl-acyl carrier protein synthase; Provisional 421 matched cddid_all.tbl CDD PTZ00051 PTZ00051 173347 PTZ00051 thioredoxin; Provisional 98 matched cddid_all.tbl CDD PTZ00052 PTZ00052 185416 PTZ00052 thioredoxin reductase; Provisional 499 matched cddid_all.tbl CDD PTZ00053 PTZ00053 240246 PTZ00053 methionine aminopeptidase 2; Provisional 470 matched cddid_all.tbl CDD PTZ00054 PTZ00054 185418 PTZ00054 60S ribosomal protein L23; Provisional 139 matched cddid_all.tbl CDD PTZ00055 PTZ00055 240247 PTZ00055 glutathione synthetase; Provisional 619 matched cddid_all.tbl CDD PTZ00056 PTZ00056 240248 PTZ00056 glutathione peroxidase; Provisional 199 matched cddid_all.tbl CDD PTZ00057 PTZ00057 173353 PTZ00057 glutathione s-transferase; Provisional 205 matched cddid_all.tbl CDD PTZ00058 PTZ00058 185420 PTZ00058 glutathione reductase; Provisional 561 matched cddid_all.tbl CDD PTZ00059 PTZ00059 185421 PTZ00059 dynein light chain; Provisional 90 matched cddid_all.tbl CDD PTZ00060 PTZ00060 240249 PTZ00060 cyclophilin; Provisional 183 matched cddid_all.tbl CDD PTZ00061 PTZ00061 173356 PTZ00061 DNA-directed RNA polymerase; Provisional 205 matched cddid_all.tbl CDD PTZ00062 PTZ00062 240250 PTZ00062 glutaredoxin; Provisional 204 matched cddid_all.tbl CDD PTZ00063 PTZ00063 240251 PTZ00063 histone deacetylase; Provisional 436 matched cddid_all.tbl CDD PTZ00064 PTZ00064 173359 PTZ00064 histone acetyltransferase; Provisional 552 matched cddid_all.tbl CDD PTZ00065 PTZ00065 240252 PTZ00065 60S ribosomal protein L14; Provisional 130 matched cddid_all.tbl CDD PTZ00066 PTZ00066 173361 PTZ00066 pyruvate kinase; Provisional 513 matched cddid_all.tbl CDD PTZ00067 PTZ00067 185422 PTZ00067 40S ribosomal S23; Provisional 143 matched cddid_all.tbl CDD PTZ00068 PTZ00068 240253 PTZ00068 60S ribosomal protein L13a; Provisional 202 matched cddid_all.tbl CDD PTZ00069 PTZ00069 240254 PTZ00069 60S ribosomal protein L5; Provisional 300 matched cddid_all.tbl CDD PTZ00070 PTZ00070 240255 PTZ00070 40S ribosomal protein S2; Provisional 257 matched cddid_all.tbl CDD PTZ00071 PTZ00071 240256 PTZ00071 40S ribosomal protein S24; Provisional 132 matched cddid_all.tbl CDD PTZ00072 PTZ00072 185427 PTZ00072 40S ribosomal protein S13; Provisional 148 matched cddid_all.tbl CDD PTZ00073 PTZ00073 240257 PTZ00073 60S ribosomal protein L37; Provisional 91 matched cddid_all.tbl CDD PTZ00074 PTZ00074 185429 PTZ00074 60S ribosomal protein L34; Provisional 135 matched cddid_all.tbl CDD PTZ00075 PTZ00075 240258 PTZ00075 Adenosylhomocysteinase; Provisional 476 matched cddid_all.tbl CDD PTZ00076 PTZ00076 173371 PTZ00076 60S ribosomal protein L17; Provisional 253 matched cddid_all.tbl CDD PTZ00077 PTZ00077 185431 PTZ00077 asparagine synthetase-like protein; Provisional 586 matched cddid_all.tbl CDD PTZ00078 PTZ00078 185432 PTZ00078 Superoxide dismutase [Fe]; Provisional 193 matched cddid_all.tbl CDD PTZ00079 PTZ00079 185433 PTZ00079 NADP-specific glutamate dehydrogenase; Provisional 454 matched cddid_all.tbl CDD PTZ00081 PTZ00081 240259 PTZ00081 enolase; Provisional 439 matched cddid_all.tbl CDD PTZ00082 PTZ00082 173376 PTZ00082 L-lactate dehydrogenase; Provisional 321 matched cddid_all.tbl CDD PTZ00083 PTZ00083 185434 PTZ00083 40S ribosomal protein S27; Provisional 85 matched cddid_all.tbl CDD PTZ00084 PTZ00084 240260 PTZ00084 40S ribosomal protein S3; Provisional 220 matched cddid_all.tbl CDD PTZ00085 PTZ00085 240261 PTZ00085 40S ribosomal protein S28; Provisional 73 matched cddid_all.tbl CDD PTZ00086 PTZ00086 185437 PTZ00086 40S ribosomal protein S16; Provisional 147 matched cddid_all.tbl CDD PTZ00087 PTZ00087 185438 PTZ00087 thrombosponding-related protein; Provisional 340 matched cddid_all.tbl CDD PTZ00088 PTZ00088 240262 PTZ00088 adenylate kinase 1; Provisional 229 matched cddid_all.tbl CDD PTZ00089 PTZ00089 173383 PTZ00089 transketolase; Provisional 661 matched cddid_all.tbl CDD PTZ00090 PTZ00090 173384 PTZ00090 40S ribosomal protein S11; Provisional 233 matched cddid_all.tbl CDD PTZ00091 PTZ00091 185439 PTZ00091 40S ribosomal protein S5; Provisional 193 matched cddid_all.tbl CDD PTZ00092 PTZ00092 240263 PTZ00092 aconitate hydratase-like protein; Provisional 898 matched cddid_all.tbl CDD PTZ00093 PTZ00093 173387 PTZ00093 nucleoside diphosphate kinase, cytosolic; Provisional 149 matched cddid_all.tbl CDD PTZ00094 PTZ00094 240264 PTZ00094 serine hydroxymethyltransferase; Provisional 452 matched cddid_all.tbl CDD PTZ00095 PTZ00095 140127 PTZ00095 40S ribosomal protein S19; Provisional 169 matched cddid_all.tbl CDD PTZ00096 PTZ00096 185442 PTZ00096 40S ribosomal protein S15; Provisional 143 matched cddid_all.tbl CDD PTZ00097 PTZ00097 185443 PTZ00097 60S ribosomal protein L19; Provisional 175 matched cddid_all.tbl CDD PTZ00098 PTZ00098 173391 PTZ00098 phosphoethanolamine N-methyltransferase; Provisional 263 matched cddid_all.tbl CDD PTZ00099 PTZ00099 185444 PTZ00099 rab6; Provisional 176 matched cddid_all.tbl CDD PTZ00100 PTZ00100 240265 PTZ00100 DnaJ chaperone protein; Provisional 116 matched cddid_all.tbl CDD PTZ00101 PTZ00101 185445 PTZ00101 rhomboid-1 protease; Provisional 278 matched cddid_all.tbl CDD PTZ00102 PTZ00102 240266 PTZ00102 disulphide isomerase; Provisional 477 matched cddid_all.tbl CDD PTZ00103 PTZ00103 240267 PTZ00103 60S ribosomal protein L3; Provisional 390 matched cddid_all.tbl CDD PTZ00104 PTZ00104 240268 PTZ00104 S-adenosylmethionine synthase; Provisional 398 matched cddid_all.tbl CDD PTZ00105 PTZ00105 240269 PTZ00105 60S ribosomal protein L12; Provisional 140 matched cddid_all.tbl CDD PTZ00106 PTZ00106 185450 PTZ00106 60S ribosomal protein L30; Provisional 108 matched cddid_all.tbl CDD PTZ00107 PTZ00107 240270 PTZ00107 hexokinase; Provisional 464 matched cddid_all.tbl CDD PTZ00108 PTZ00108 240271 PTZ00108 DNA topoisomerase 2-like protein; Provisional 1388 matched cddid_all.tbl CDD PTZ00109 PTZ00109 240272 PTZ00109 DNA gyrase subunit b; Provisional 903 matched cddid_all.tbl CDD PTZ00110 PTZ00110 240273 PTZ00110 helicase; Provisional 545 matched cddid_all.tbl CDD PTZ00111 PTZ00111 173403 PTZ00111 DNA replication licensing factor MCM4; Provisional 915 matched cddid_all.tbl CDD PTZ00112 PTZ00112 240274 PTZ00112 origin recognition complex 1 protein; Provisional 1164 matched cddid_all.tbl CDD PTZ00113 PTZ00113 240275 PTZ00113 proliferating cell nuclear antigen; Provisional 275 matched cddid_all.tbl CDD PTZ00114 PTZ00114 185455 PTZ00114 Heat shock protein 60; Provisional 555 matched cddid_all.tbl CDD PTZ00115 PTZ00115 240276 PTZ00115 40S ribosomal protein S12; Provisional 290 matched cddid_all.tbl CDD PTZ00116 PTZ00116 173408 PTZ00116 signal peptidase; Provisional 185 matched cddid_all.tbl CDD PTZ00117 PTZ00117 173409 PTZ00117 malate dehydrogenase; Provisional 319 matched cddid_all.tbl CDD PTZ00118 PTZ00118 240277 PTZ00118 40S ribosomal protein S4; Provisional 262 matched cddid_all.tbl CDD PTZ00119 PTZ00119 240278 PTZ00119 40S ribosomal protein S15; Provisional 302 matched cddid_all.tbl CDD PTZ00120 PTZ00120 185458 PTZ00120 D-tyrosyl-tRNA(Tyr) deacylase; Provisional 154 matched cddid_all.tbl CDD PTZ00121 PTZ00121 173412 PTZ00121 MAEBL; Provisional 2084 matched cddid_all.tbl CDD PTZ00122 PTZ00122 240279 PTZ00122 phosphoglycerate mutase; Provisional 299 matched cddid_all.tbl CDD PTZ00123 PTZ00123 240280 PTZ00123 phosphoglycerate mutase like-protein; Provisional 236 matched cddid_all.tbl CDD PTZ00124 PTZ00124 173415 PTZ00124 adenosine deaminase; Provisional 362 matched cddid_all.tbl CDD PTZ00125 PTZ00125 240281 PTZ00125 ornithine aminotransferase-like protein; Provisional 400 matched cddid_all.tbl CDD PTZ00126 PTZ00126 240282 PTZ00126 tyrosyl-tRNA synthetase; Provisional 383 matched cddid_all.tbl CDD PTZ00127 PTZ00127 240283 PTZ00127 cytochrome c oxidase assembly protein; Provisional 403 matched cddid_all.tbl CDD PTZ00128 PTZ00128 185464 PTZ00128 cytochrome c oxidase assembly protein-like; Provisional 232 matched cddid_all.tbl CDD PTZ00129 PTZ00129 185465 PTZ00129 40S ribosomal protein S14; Provisional 149 matched cddid_all.tbl CDD PTZ00130 PTZ00130 185466 PTZ00130 heat shock protein 90; Provisional 814 matched cddid_all.tbl CDD PTZ00131 PTZ00131 185467 PTZ00131 glycophorin-binding protein; Provisional 413 matched cddid_all.tbl CDD PTZ00132 PTZ00132 240284 PTZ00132 GTP-binding nuclear protein Ran; Provisional 215 matched cddid_all.tbl CDD PTZ00133 PTZ00133 173423 PTZ00133 ADP-ribosylation factor; Provisional 182 matched cddid_all.tbl CDD PTZ00134 PTZ00134 185469 PTZ00134 40S ribosomal protein S18; Provisional 154 matched cddid_all.tbl CDD PTZ00135 PTZ00135 240285 PTZ00135 60S acidic ribosomal protein P0; Provisional 310 matched cddid_all.tbl CDD PTZ00136 PTZ00136 185471 PTZ00136 eukaryotic translation initiation factor 6-like protein; Provisional 247 matched cddid_all.tbl CDD PTZ00137 PTZ00137 173427 PTZ00137 2-Cys peroxiredoxin; Provisional 261 matched cddid_all.tbl CDD PTZ00138 PTZ00138 185472 PTZ00138 small nuclear ribonucleoprotein; Provisional 89 matched cddid_all.tbl CDD PTZ00139 PTZ00139 240286 PTZ00139 Succinate dehydrogenase [ubiquinone] flavoprotein subunit; Provisional 617 matched cddid_all.tbl CDD PTZ00140 PTZ00140 173430 PTZ00140 sexual stage antigen s45/48; Provisional 447 matched cddid_all.tbl CDD PTZ00141 PTZ00141 185474 PTZ00141 elongation factor 1- alpha; Provisional 446 matched cddid_all.tbl CDD PTZ00142 PTZ00142 240287 PTZ00142 6-phosphogluconate dehydrogenase; Provisional 470 matched cddid_all.tbl CDD PTZ00143 PTZ00143 240288 PTZ00143 deoxyuridine 5'-triphosphate nucleotidohydrolase; Provisional 155 matched cddid_all.tbl CDD PTZ00144 PTZ00144 240289 PTZ00144 dihydrolipoamide succinyltransferase; Provisional 418 matched cddid_all.tbl CDD PTZ00145 PTZ00145 240290 PTZ00145 phosphoribosylpyrophosphate synthetase; Provisional 439 matched cddid_all.tbl CDD PTZ00146 PTZ00146 240291 PTZ00146 fibrillarin; Provisional 293 matched cddid_all.tbl CDD PTZ00147 PTZ00147 140176 PTZ00147 plasmepsin-1; Provisional 453 matched cddid_all.tbl CDD PTZ00148 PTZ00148 240292 PTZ00148 40S ribosomal protein S8; Provisional 205 matched cddid_all.tbl CDD PTZ00149 PTZ00149 240293 PTZ00149 hypoxanthine phosphoribosyltransferase; Provisional 241 matched cddid_all.tbl CDD PTZ00150 PTZ00150 240294 PTZ00150 phosphoglucomutase-2-like protein; Provisional 584 matched cddid_all.tbl CDD PTZ00151 PTZ00151 173440 PTZ00151 translationally controlled tumor-like protein; Provisional 172 matched cddid_all.tbl CDD PTZ00152 PTZ00152 173441 PTZ00152 cofilin/actin-depolymerizing factor 1-like protein; Provisional 122 matched cddid_all.tbl CDD PTZ00153 PTZ00153 173442 PTZ00153 lipoamide dehydrogenase; Provisional 659 matched cddid_all.tbl CDD PTZ00154 PTZ00154 240295 PTZ00154 40S ribosomal protein S17; Provisional 134 matched cddid_all.tbl CDD PTZ00155 PTZ00155 185484 PTZ00155 40S ribosomal protein S9; Provisional 181 matched cddid_all.tbl CDD PTZ00156 PTZ00156 185485 PTZ00156 60S ribosomal protein L11; Provisional 172 matched cddid_all.tbl CDD PTZ00157 PTZ00157 240296 PTZ00157 60S ribosomal protein L36a; Provisional 84 matched cddid_all.tbl CDD PTZ00158 PTZ00158 185487 PTZ00158 40S ribosomal protein S15A; Provisional 130 matched cddid_all.tbl CDD PTZ00159 PTZ00159 240297 PTZ00159 60S ribosomal protein L32; Provisional 133 matched cddid_all.tbl CDD PTZ00160 PTZ00160 185489 PTZ00160 60S ribosomal protein L27a; Provisional 147 matched cddid_all.tbl CDD PTZ00162 PTZ00162 240298 PTZ00162 DNA-directed RNA polymerase II subunit 7; Provisional 176 matched cddid_all.tbl CDD PTZ00163 PTZ00163 185490 PTZ00163 hypothetical protein; Provisional 230 matched cddid_all.tbl CDD PTZ00164 PTZ00164 240299 PTZ00164 bifunctional dihydrofolate reductase-thymidylate synthase; Provisional 514 matched cddid_all.tbl CDD PTZ00165 PTZ00165 240300 PTZ00165 aspartyl protease; Provisional 482 matched cddid_all.tbl CDD PTZ00166 PTZ00166 240301 PTZ00166 DNA polymerase delta catalytic subunit; Provisional 1054 matched cddid_all.tbl CDD PTZ00167 PTZ00167 185493 PTZ00167 RNA polymerase subunit 8c; Provisional 144 matched cddid_all.tbl CDD PTZ00168 PTZ00168 185494 PTZ00168 mitochondrial carrier protein; Provisional 259 matched cddid_all.tbl CDD PTZ00169 PTZ00169 240302 PTZ00169 ADP/ATP transporter on adenylate translocase; Provisional 300 matched cddid_all.tbl CDD PTZ00170 PTZ00170 240303 PTZ00170 D-ribulose-5-phosphate 3-epimerase; Provisional 228 matched cddid_all.tbl CDD PTZ00171 PTZ00171 240304 PTZ00171 acyl carrier protein; Provisional 148 matched cddid_all.tbl CDD PTZ00172 PTZ00172 185497 PTZ00172 40S ribosomal protein S26; Provisional 108 matched cddid_all.tbl CDD PTZ00173 PTZ00173 185498 PTZ00173 60S ribosomal protein L10; Provisional 213 matched cddid_all.tbl CDD PTZ00174 PTZ00174 240305 PTZ00174 phosphomannomutase; Provisional 247 matched cddid_all.tbl CDD PTZ00175 PTZ00175 185500 PTZ00175 diphthine synthase; Provisional 270 matched cddid_all.tbl CDD PTZ00176 PTZ00176 140204 PTZ00176 erythrocyte membrane protein 1 (PfEMP1); Provisional 1317 matched cddid_all.tbl CDD PTZ00178 PTZ00178 240306 PTZ00178 60S ribosomal protein L17; Provisional 181 matched cddid_all.tbl CDD PTZ00179 PTZ00179 140206 PTZ00179 60S ribosomal protein L9; Provisional 189 matched cddid_all.tbl CDD PTZ00180 PTZ00180 173464 PTZ00180 60S ribosomal protein L8; Provisional 260 matched cddid_all.tbl CDD PTZ00181 PTZ00181 140208 PTZ00181 60S ribosomal protein L38; Provisional 82 matched cddid_all.tbl CDD PTZ00182 PTZ00182 185502 PTZ00182 3-methyl-2-oxobutanate dehydrogenase; Provisional 355 matched cddid_all.tbl CDD PTZ00183 PTZ00183 185503 PTZ00183 centrin; Provisional 158 matched cddid_all.tbl CDD PTZ00184 PTZ00184 185504 PTZ00184 calmodulin; Provisional 149 matched cddid_all.tbl CDD PTZ00185 PTZ00185 140212 PTZ00185 ATPase alpha subunit; Provisional 574 matched cddid_all.tbl CDD PTZ00186 PTZ00186 140213 PTZ00186 heat shock 70 kDa precursor protein; Provisional 657 matched cddid_all.tbl CDD PTZ00187 PTZ00187 240307 PTZ00187 succinyl-CoA synthetase alpha subunit; Provisional 317 matched cddid_all.tbl CDD PTZ00188 PTZ00188 240308 PTZ00188 adrenodoxin reductase; Provisional 506 matched cddid_all.tbl CDD PTZ00189 PTZ00189 240309 PTZ00189 60S ribosomal protein L21; Provisional 160 matched cddid_all.tbl CDD PTZ00190 PTZ00190 140217 PTZ00190 60S ribosomal protein L29; Provisional 70 matched cddid_all.tbl CDD PTZ00191 PTZ00191 185507 PTZ00191 60S ribosomal protein L23a; Provisional 145 matched cddid_all.tbl CDD PTZ00192 PTZ00192 173472 PTZ00192 60S ribosomal protein L13; Provisional 218 matched cddid_all.tbl CDD PTZ00193 PTZ00193 140220 PTZ00193 60S ribosomal protein L31; Provisional 188 matched cddid_all.tbl CDD PTZ00194 PTZ00194 185508 PTZ00194 60S ribosomal protein L26; Provisional 143 matched cddid_all.tbl CDD PTZ00195 PTZ00195 140222 PTZ00195 60S ribosomal protein L18; Provisional 198 matched cddid_all.tbl CDD PTZ00196 PTZ00196 185509 PTZ00196 60S ribosomal protein L36; Provisional 98 matched cddid_all.tbl CDD PTZ00197 PTZ00197 185510 PTZ00197 60S ribosomal protein L28; Provisional 146 matched cddid_all.tbl CDD PTZ00198 PTZ00198 173474 PTZ00198 60S ribosomal protein L22; Provisional 122 matched cddid_all.tbl CDD PTZ00199 PTZ00199 185511 PTZ00199 high mobility group protein; Provisional 94 matched cddid_all.tbl CDD PTZ00200 PTZ00200 240310 PTZ00200 cysteine proteinase; Provisional 448 matched cddid_all.tbl CDD PTZ00201 PTZ00201 240311 PTZ00201 amastin surface glycoprotein; Provisional 192 matched cddid_all.tbl CDD PTZ00202 PTZ00202 240312 PTZ00202 tuzin; Provisional 550 matched cddid_all.tbl CDD PTZ00203 PTZ00203 185513 PTZ00203 cathepsin L protease; Provisional 348 matched cddid_all.tbl CDD PTZ00204 PTZ00204 140231 PTZ00204 hypothetical protein; Provisional 120 matched cddid_all.tbl CDD PTZ00205 PTZ00205 140232 PTZ00205 DNA polymerase kappa; Provisional 571 matched cddid_all.tbl CDD PTZ00206 PTZ00206 240313 PTZ00206 amino acid transporter; Provisional 467 matched cddid_all.tbl CDD PTZ00207 PTZ00207 140234 PTZ00207 hypothetical protein; Provisional 591 matched cddid_all.tbl CDD PTZ00208 PTZ00208 240314 PTZ00208 65 kDa invariant surface glycoprotein; Provisional 436 matched cddid_all.tbl CDD PTZ00209 PTZ00209 140236 PTZ00209 retrotransposon hot spot protein; Provisional 693 matched cddid_all.tbl CDD PTZ00210 PTZ00210 140237 PTZ00210 UDP-GlcNAc-dependent glycosyltransferase; Provisional 382 matched cddid_all.tbl CDD PTZ00211 PTZ00211 240315 PTZ00211 ribonucleoside-diphosphate reductase small subunit; Provisional 330 matched cddid_all.tbl CDD PTZ00212 PTZ00212 185514 PTZ00212 T-complex protein 1 subunit beta; Provisional 533 matched cddid_all.tbl CDD PTZ00213 PTZ00213 185515 PTZ00213 asparagine synthetase A; Provisional 348 matched cddid_all.tbl CDD PTZ00214 PTZ00214 173479 PTZ00214 high cysteine membrane protein Group 4; Provisional 800 matched cddid_all.tbl CDD PTZ00215 PTZ00215 185516 PTZ00215 ribose 5-phosphate isomerase; Provisional 151 matched cddid_all.tbl CDD PTZ00216 PTZ00216 240316 PTZ00216 acyl-CoA synthetase; Provisional 700 matched cddid_all.tbl CDD PTZ00217 PTZ00217 240317 PTZ00217 flap endonuclease-1; Provisional 393 matched cddid_all.tbl CDD PTZ00218 PTZ00218 185518 PTZ00218 40S ribosomal protein S29; Provisional 54 matched cddid_all.tbl CDD PTZ00219 PTZ00219 185519 PTZ00219 Sec61 alpha subunit; Provisional 474 matched cddid_all.tbl CDD PTZ00220 PTZ00220 173484 PTZ00220 Activator of HSP-90 ATPase; Provisional 132 matched cddid_all.tbl CDD PTZ00221 PTZ00221 140248 PTZ00221 cyclophilin; Provisional 249 matched cddid_all.tbl CDD PTZ00222 PTZ00222 140249 PTZ00222 60S ribosomal protein L7a; Provisional 263 matched cddid_all.tbl CDD PTZ00223 PTZ00223 140250 PTZ00223 40S ribosomal protein S4; Provisional 273 matched cddid_all.tbl CDD PTZ00224 PTZ00224 240318 PTZ00224 protein phosphatase 2C; Provisional 381 matched cddid_all.tbl CDD PTZ00225 PTZ00225 140252 PTZ00225 60S ribosomal protein L10a; Provisional 214 matched cddid_all.tbl CDD PTZ00226 PTZ00226 240319 PTZ00226 fumarate hydratase; Provisional 570 matched cddid_all.tbl CDD PTZ00227 PTZ00227 140254 PTZ00227 variable surface protein Vir14; Provisional 418 matched cddid_all.tbl CDD PTZ00228 PTZ00228 240320 PTZ00228 variable surface protein Vir21; Provisional 350 matched cddid_all.tbl CDD PTZ00229 PTZ00229 140256 PTZ00229 variable surface protein Vir30; Provisional 317 matched cddid_all.tbl CDD PTZ00230 PTZ00230 240321 PTZ00230 variable surface protein Vir7; Provisional 364 matched cddid_all.tbl CDD PTZ00231 PTZ00231 140258 PTZ00231 variable surface protein Vir17; Provisional 385 matched cddid_all.tbl CDD PTZ00232 PTZ00232 240322 PTZ00232 variable surface protein Vir27; Provisional 363 matched cddid_all.tbl CDD PTZ00233 PTZ00233 240323 PTZ00233 variable surface protein Vir18; Provisional 509 matched cddid_all.tbl CDD PTZ00234 PTZ00234 240324 PTZ00234 variable surface protein Vir12; Provisional 433 matched cddid_all.tbl CDD PTZ00235 PTZ00235 185521 PTZ00235 DNA polymerase epsilon subunit B; Provisional 291 matched cddid_all.tbl CDD PTZ00236 PTZ00236 173487 PTZ00236 mitochondrial import inner membrane translocase subunit tim17; Provisional 164 matched cddid_all.tbl CDD PTZ00237 PTZ00237 240325 PTZ00237 acetyl-CoA synthetase; Provisional 647 matched cddid_all.tbl CDD PTZ00238 PTZ00238 140265 PTZ00238 expression site-associated gene (ESAG); Provisional 326 matched cddid_all.tbl CDD PTZ00239 PTZ00239 173488 PTZ00239 serine/threonine protein phosphatase 2A; Provisional 303 matched cddid_all.tbl CDD PTZ00240 PTZ00240 140267 PTZ00240 60S ribosomal protein P0; Provisional 323 matched cddid_all.tbl CDD PTZ00241 PTZ00241 240326 PTZ00241 40S ribosomal protein S11; Provisional 158 matched cddid_all.tbl CDD PTZ00242 PTZ00242 185524 PTZ00242 protein tyrosine phosphatase; Provisional 166 matched cddid_all.tbl CDD PTZ00243 PTZ00243 240327 PTZ00243 ABC transporter; Provisional 1560 matched cddid_all.tbl CDD PTZ00244 PTZ00244 140271 PTZ00244 serine/threonine-protein phosphatase PP1; Provisional 294 matched cddid_all.tbl CDD PTZ00245 PTZ00245 140272 PTZ00245 ubiquitin activating enzyme; Provisional 287 matched cddid_all.tbl CDD PTZ00246 PTZ00246 173491 PTZ00246 proteasome subunit alpha; Provisional 253 matched cddid_all.tbl CDD PTZ00247 PTZ00247 240328 PTZ00247 adenosine kinase; Provisional 345 matched cddid_all.tbl CDD PTZ00248 PTZ00248 240329 PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional 319 matched cddid_all.tbl CDD PTZ00249 PTZ00249 140276 PTZ00249 variable surface protein Vir28; Provisional 516 matched cddid_all.tbl CDD PTZ00250 PTZ00250 140277 PTZ00250 variable surface protein Vir23; Provisional 350 matched cddid_all.tbl CDD PTZ00251 PTZ00251 140278 PTZ00251 fatty acid elongase; Provisional 272 matched cddid_all.tbl CDD PTZ00252 PTZ00252 240330 PTZ00252 histone H2A; Provisional 134 matched cddid_all.tbl CDD PTZ00253 PTZ00253 140280 PTZ00253 tryparedoxin peroxidase; Provisional 199 matched cddid_all.tbl CDD PTZ00254 PTZ00254 240331 PTZ00254 40S ribosomal protein SA; Provisional 249 matched cddid_all.tbl CDD PTZ00255 PTZ00255 240332 PTZ00255 60S ribosomal protein L37a; Provisional 90 matched cddid_all.tbl CDD PTZ00256 PTZ00256 173495 PTZ00256 glutathione peroxidase; Provisional 183 matched cddid_all.tbl CDD PTZ00257 PTZ00257 240333 PTZ00257 Glycoprotein GP63 (leishmanolysin); Provisional 622 matched cddid_all.tbl CDD PTZ00258 PTZ00258 240334 PTZ00258 GTP-binding protein; Provisional 390 matched cddid_all.tbl CDD PTZ00259 PTZ00259 240335 PTZ00259 endonuclease G; Provisional 434 matched cddid_all.tbl CDD PTZ00260 PTZ00260 240336 PTZ00260 dolichyl-phosphate beta-glucosyltransferase; Provisional 333 matched cddid_all.tbl CDD PTZ00261 PTZ00261 240337 PTZ00261 acyltransferase; Provisional 355 matched cddid_all.tbl CDD PTZ00262 PTZ00262 240338 PTZ00262 subtilisin-like protease; Provisional 639 matched cddid_all.tbl CDD PTZ00263 PTZ00263 140289 PTZ00263 protein kinase A catalytic subunit; Provisional 329 matched cddid_all.tbl CDD PTZ00264 PTZ00264 173500 PTZ00264 circumsporozoite-related antigen; Provisional 148 matched cddid_all.tbl CDD PTZ00265 PTZ00265 240339 PTZ00265 multidrug resistance protein (mdr1); Provisional 1466 matched cddid_all.tbl CDD PTZ00266 PTZ00266 173502 PTZ00266 NIMA-related protein kinase; Provisional 1021 matched cddid_all.tbl CDD PTZ00267 PTZ00267 140293 PTZ00267 NIMA-related protein kinase; Provisional 478 matched cddid_all.tbl CDD PTZ00268 PTZ00268 140294 PTZ00268 glycosylphosphatidylinositol-specific phospholipase C; Provisional 380 matched cddid_all.tbl CDD PTZ00269 PTZ00269 140295 PTZ00269 variant surface glycoprotein; Provisional 472 matched cddid_all.tbl CDD PTZ00270 PTZ00270 240340 PTZ00270 variable surface protein Vir32; Provisional 333 matched cddid_all.tbl CDD PTZ00271 PTZ00271 140297 PTZ00271 hypoxanthine-guanine phosphoribosyltransferase; Provisional 211 matched cddid_all.tbl CDD PTZ00272 PTZ00272 240341 PTZ00272 heat shock protein 83 kDa (Hsp83); Provisional 701 matched cddid_all.tbl CDD PTZ00273 PTZ00273 140299 PTZ00273 oxidase reductase; Provisional 320 matched cddid_all.tbl CDD PTZ00274 PTZ00274 140300 PTZ00274 cytochrome b5 reductase; Provisional 325 matched cddid_all.tbl CDD PTZ00275 PTZ00275 185536 PTZ00275 biotin-acetyl-CoA-carboxylase ligase; Provisional 285 matched cddid_all.tbl CDD PTZ00276 PTZ00276 140302 PTZ00276 biotin/lipoate protein ligase; Provisional 245 matched cddid_all.tbl CDD PTZ00278 PTZ00278 240342 PTZ00278 ARP2/3 complex subunit; Provisional 174 matched cddid_all.tbl CDD PTZ00280 PTZ00280 240343 PTZ00280 Actin-related protein 3; Provisional 414 matched cddid_all.tbl CDD PTZ00281 PTZ00281 173506 PTZ00281 actin; Provisional 376 matched cddid_all.tbl CDD PTZ00283 PTZ00283 240344 PTZ00283 serine/threonine protein kinase; Provisional 496 matched cddid_all.tbl CDD PTZ00284 PTZ00284 140307 PTZ00284 protein kinase; Provisional 467 matched cddid_all.tbl CDD PTZ00285 PTZ00285 140308 PTZ00285 glucosamine-6-phosphate isomerase; Provisional 253 matched cddid_all.tbl CDD PTZ00286 PTZ00286 185539 PTZ00286 6-phospho-1-fructokinase; Provisional 459 matched cddid_all.tbl CDD PTZ00287 PTZ00287 240345 PTZ00287 6-phosphofructokinase; Provisional 1419 matched cddid_all.tbl CDD PTZ00288 PTZ00288 240346 PTZ00288 glucokinase 1; Provisional 405 matched cddid_all.tbl CDD PTZ00290 PTZ00290 240347 PTZ00290 galactokinase; Provisional 468 matched cddid_all.tbl CDD PTZ00292 PTZ00292 185541 PTZ00292 ribokinase; Provisional 326 matched cddid_all.tbl CDD PTZ00293 PTZ00293 185542 PTZ00293 thymidine kinase; Provisional 211 matched cddid_all.tbl CDD PTZ00294 PTZ00294 240348 PTZ00294 glycerol kinase-like protein; Provisional 504 matched cddid_all.tbl CDD PTZ00295 PTZ00295 240349 PTZ00295 glucosamine-fructose-6-phosphate aminotransferase; Provisional 640 matched cddid_all.tbl CDD PTZ00296 PTZ00296 240350 PTZ00296 choline kinase; Provisional 442 matched cddid_all.tbl CDD PTZ00297 PTZ00297 140318 PTZ00297 pantothenate kinase; Provisional 1452 matched cddid_all.tbl CDD PTZ00298 PTZ00298 240351 PTZ00298 mevalonate kinase; Provisional 328 matched cddid_all.tbl CDD PTZ00299 PTZ00299 140320 PTZ00299 homoserine kinase; Provisional 336 matched cddid_all.tbl CDD PTZ00300 PTZ00300 140321 PTZ00300 pyruvate kinase; Provisional 454 matched cddid_all.tbl CDD PTZ00301 PTZ00301 140322 PTZ00301 uridine kinase; Provisional 210 matched cddid_all.tbl CDD PTZ00302 PTZ00302 240352 PTZ00302 N-acetylglucosamine-phosphate mutase; Provisional 585 matched cddid_all.tbl CDD PTZ00303 PTZ00303 140324 PTZ00303 phosphatidylinositol kinase; Provisional 1374 matched cddid_all.tbl CDD PTZ00304 PTZ00304 185547 PTZ00304 NADH dehydrogenase [ubiquinone] flavoprotein 1; Provisional 461 matched cddid_all.tbl CDD PTZ00305 PTZ00305 140326 PTZ00305 NADH:ubiquinone oxidoreductase; Provisional 297 matched cddid_all.tbl CDD PTZ00306 PTZ00306 140327 PTZ00306 NADH-dependent fumarate reductase; Provisional 1167 matched cddid_all.tbl CDD PTZ00307 PTZ00307 140328 PTZ00307 ethanolamine phosphotransferase; Provisional 417 matched cddid_all.tbl CDD PTZ00308 PTZ00308 140329 PTZ00308 ethanolamine-phosphate cytidylyltransferase; Provisional 353 matched cddid_all.tbl CDD PTZ00309 PTZ00309 240353 PTZ00309 glucose-6-phosphate 1-dehydrogenase; Provisional 542 matched cddid_all.tbl CDD PTZ00310 PTZ00310 240354 PTZ00310 AMP deaminase; Provisional 1453 matched cddid_all.tbl CDD PTZ00311 PTZ00311 185549 PTZ00311 phosphoenolpyruvate carboxykinase; Provisional 561 matched cddid_all.tbl CDD PTZ00312 PTZ00312 140333 PTZ00312 inositol-1,4,5-triphosphate 5-phosphatase; Provisional 356 matched cddid_all.tbl CDD PTZ00313 PTZ00313 140334 PTZ00313 inosine-adenosine-guanosine-nucleoside hydrolase; Provisional 326 matched cddid_all.tbl CDD PTZ00314 PTZ00314 240355 PTZ00314 inosine-5'-monophosphate dehydrogenase; Provisional 495 matched cddid_all.tbl CDD PTZ00315 PTZ00315 240356 PTZ00315 2'-phosphotransferase; Provisional 582 matched cddid_all.tbl CDD PTZ00316 PTZ00316 140337 PTZ00316 profilin; Provisional 150 matched cddid_all.tbl CDD PTZ00317 PTZ00317 240357 PTZ00317 NADP-dependent malic enzyme; Provisional 559 matched cddid_all.tbl CDD PTZ00318 PTZ00318 185553 PTZ00318 NADH dehydrogenase-like protein; Provisional 424 matched cddid_all.tbl CDD PTZ00319 PTZ00319 173521 PTZ00319 NADH-cytochrome B5 reductase; Provisional 300 matched cddid_all.tbl CDD PTZ00320 PTZ00320 140341 PTZ00320 ribosomal protein L14; Provisional 188 matched cddid_all.tbl CDD PTZ00321 PTZ00321 240358 PTZ00321 ribosomal protein L11; Provisional 342 matched cddid_all.tbl CDD PTZ00322 PTZ00322 140343 PTZ00322 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase; Provisional 664 matched cddid_all.tbl CDD PTZ00323 PTZ00323 185554 PTZ00323 NAD+ synthase; Provisional 294 matched cddid_all.tbl CDD PTZ00324 PTZ00324 240359 PTZ00324 glutamate dehydrogenase 2; Provisional 1002 matched cddid_all.tbl CDD PTZ00325 PTZ00325 240360 PTZ00325 malate dehydrogenase; Provisional 321 matched cddid_all.tbl CDD PTZ00326 PTZ00326 240361 PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional 494 matched cddid_all.tbl CDD PTZ00327 PTZ00327 240362 PTZ00327 eukaryotic translation initiation factor 2 gamma subunit; Provisional 460 matched cddid_all.tbl CDD PTZ00328 PTZ00328 140349 PTZ00328 eukaryotic initiation factor 5a; Provisional 166 matched cddid_all.tbl CDD PTZ00329 PTZ00329 185558 PTZ00329 eukaryotic translation initiation factor 1A; Provisional 155 matched cddid_all.tbl CDD PTZ00330 PTZ00330 140351 PTZ00330 acetyltransferase; Provisional 147 matched cddid_all.tbl CDD PTZ00331 PTZ00331 240363 PTZ00331 alpha/beta hydrolase; Provisional 212 matched cddid_all.tbl CDD PTZ00332 PTZ00332 240364 PTZ00332 paraflagellar rod protein; Provisional 589 matched cddid_all.tbl CDD PTZ00333 PTZ00333 240365 PTZ00333 triosephosphate isomerase; Provisional 255 matched cddid_all.tbl CDD PTZ00334 PTZ00334 240366 PTZ00334 trans-sialidase; Provisional 780 matched cddid_all.tbl CDD PTZ00335 PTZ00335 185562 PTZ00335 tubulin alpha chain; Provisional 448 matched cddid_all.tbl CDD PTZ00337 PTZ00337 185563 PTZ00337 surface protease GP63; Provisional 567 matched cddid_all.tbl CDD PTZ00338 PTZ00338 240367 PTZ00338 dimethyladenosine transferase-like protein; Provisional 294 matched cddid_all.tbl CDD PTZ00339 PTZ00339 240368 PTZ00339 UDP-N-acetylglucosamine pyrophosphorylase; Provisional 482 matched cddid_all.tbl CDD PTZ00340 PTZ00340 240369 PTZ00340 O-sialoglycoprotein endopeptidase-like protein; Provisional 345 matched cddid_all.tbl CDD PTZ00341 PTZ00341 173534 PTZ00341 Ring-infected erythrocyte surface antigen; Provisional 1136 matched cddid_all.tbl CDD PTZ00342 PTZ00342 240370 PTZ00342 acyl-CoA synthetase; Provisional 746 matched cddid_all.tbl CDD PTZ00343 PTZ00343 240371 PTZ00343 triose or hexose phosphate/phosphate translocator; Provisional 350 matched cddid_all.tbl CDD PTZ00344 PTZ00344 240372 PTZ00344 pyridoxal kinase; Provisional 296 matched cddid_all.tbl CDD PTZ00345 PTZ00345 240373 PTZ00345 glycerol-3-phosphate dehydrogenase; Provisional 365 matched cddid_all.tbl CDD PTZ00346 PTZ00346 240374 PTZ00346 histone deacetylase; Provisional 429 matched cddid_all.tbl CDD PTZ00347 PTZ00347 240375 PTZ00347 phosphomethylpyrimidine kinase; Provisional 504 matched cddid_all.tbl CDD PTZ00348 PTZ00348 173541 PTZ00348 tyrosyl-tRNA synthetase; Provisional 682 matched cddid_all.tbl CDD PTZ00349 PTZ00349 185571 PTZ00349 dehydrodolichyl diphosphate synthetase; Provisional 322 matched cddid_all.tbl CDD PTZ00350 PTZ00350 240376 PTZ00350 adenylosuccinate synthetase; Provisional 436 matched cddid_all.tbl CDD PTZ00351 PTZ00351 173544 PTZ00351 adenylosuccinate synthetase; Provisional 710 matched cddid_all.tbl CDD PTZ00352 PTZ00352 240377 PTZ00352 60S ribosomal protein L13; Provisional 212 matched cddid_all.tbl CDD PTZ00353 PTZ00353 173546 PTZ00353 glycosomal glyceraldehyde-3-phosphate dehydrogenase; Provisional 342 matched cddid_all.tbl CDD PTZ00354 PTZ00354 173547 PTZ00354 alcohol dehydrogenase; Provisional 334 matched cddid_all.tbl CDD PTZ00355 PTZ00355 173548 PTZ00355 Rhoptry-associated protein 2; Provisional 400 matched cddid_all.tbl CDD PTZ00356 PTZ00356 185573 PTZ00356 peptidyl-prolyl cis-trans isomerase (PPIase); Provisional 115 matched cddid_all.tbl CDD PTZ00357 PTZ00357 173550 PTZ00357 methyltransferase; Provisional 1072 matched cddid_all.tbl CDD PTZ00358 PTZ00358 240378 PTZ00358 hypothetical protein; Provisional 367 matched cddid_all.tbl CDD PTZ00359 PTZ00359 173552 PTZ00359 hypothetical protein; Provisional 443 matched cddid_all.tbl CDD PTZ00360 PTZ00360 240379 PTZ00360 sexual stage antigen; Provisional 543 matched cddid_all.tbl CDD PTZ00361 PTZ00361 185575 PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional 438 matched cddid_all.tbl CDD PTZ00362 PTZ00362 240380 PTZ00362 hypothetical protein; Provisional 479 matched cddid_all.tbl CDD PTZ00363 PTZ00363 185577 PTZ00363 rab-GDP dissociation inhibitor; Provisional 443 matched cddid_all.tbl CDD PTZ00364 PTZ00364 240381 PTZ00364 dipeptidyl-peptidase I precursor; Provisional 548 matched cddid_all.tbl CDD PTZ00365 PTZ00365 240382 PTZ00365 60S ribosomal protein L7Ae-like; Provisional 266 matched cddid_all.tbl CDD PTZ00366 PTZ00366 240383 PTZ00366 Surface antigen (SAG) superfamily; Provisional 392 matched cddid_all.tbl CDD PTZ00367 PTZ00367 240384 PTZ00367 squalene epoxidase; Provisional 567 matched cddid_all.tbl CDD PTZ00368 PTZ00368 173561 PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional 148 matched cddid_all.tbl CDD PTZ00369 PTZ00369 240385 PTZ00369 Ras-like protein; Provisional 189 matched cddid_all.tbl CDD PTZ00370 PTZ00370 240386 PTZ00370 STEVOR; Provisional 296 matched cddid_all.tbl CDD PTZ00371 PTZ00371 240387 PTZ00371 aspartyl aminopeptidase; Provisional 465 matched cddid_all.tbl CDD PTZ00372 PTZ00372 240388 PTZ00372 endonuclease 4-like protein; Provisional 413 matched cddid_all.tbl CDD PTZ00373 PTZ00373 185582 PTZ00373 60S Acidic ribosomal protein P2; Provisional 112 matched cddid_all.tbl CDD PTZ00374 PTZ00374 240389 PTZ00374 dihydroxyacetone phosphate acyltransferase; Provisional 1108 matched cddid_all.tbl CDD PTZ00375 PTZ00375 185583 PTZ00375 dihydroxyacetone kinase-like protein; Provisional 584 matched cddid_all.tbl CDD PTZ00376 PTZ00376 240390 PTZ00376 aspartate aminotransferase; Provisional 404 matched cddid_all.tbl CDD PTZ00377 PTZ00377 240391 PTZ00377 alanine aminotransferase; Provisional 481 matched cddid_all.tbl CDD PTZ00378 PTZ00378 173571 PTZ00378 hypothetical protein; Provisional 518 matched cddid_all.tbl CDD PTZ00380 PTZ00380 173572 PTZ00380 microtubule-associated protein (MAP); Provisional 121 matched cddid_all.tbl CDD PTZ00381 PTZ00381 240392 PTZ00381 aldehyde dehydrogenase family protein; Provisional 493 matched cddid_all.tbl CDD PTZ00382 PTZ00382 173574 PTZ00382 Variant-specific surface protein (VSP); Provisional 96 matched cddid_all.tbl CDD PTZ00383 PTZ00383 240393 PTZ00383 malate:quinone oxidoreductase; Provisional 497 matched cddid_all.tbl CDD PTZ00384 PTZ00384 173576 PTZ00384 choline kinase; Provisional 383 matched cddid_all.tbl CDD PTZ00385 PTZ00385 185588 PTZ00385 lysyl-tRNA synthetase; Provisional 659 matched cddid_all.tbl CDD PTZ00386 PTZ00386 240394 PTZ00386 formyl tetrahydrofolate synthetase; Provisional 625 matched cddid_all.tbl CDD PTZ00387 PTZ00387 240395 PTZ00387 epsilon tubulin; Provisional 465 matched cddid_all.tbl CDD PTZ00388 PTZ00388 240396 PTZ00388 40S ribosomal protein S8-like; Provisional 223 matched cddid_all.tbl CDD PTZ00389 PTZ00389 185592 PTZ00389 40S ribosomal protein S7; Provisional 184 matched cddid_all.tbl CDD PTZ00390 PTZ00390 240397 PTZ00390 ubiquitin-conjugating enzyme; Provisional 152 matched cddid_all.tbl CDD PTZ00391 PTZ00391 240398 PTZ00391 transport protein particle component (TRAPP) superfamily; Provisional 168 matched cddid_all.tbl CDD PTZ00393 PTZ00393 240399 PTZ00393 protein tyrosine phosphatase; Provisional 241 matched cddid_all.tbl CDD PTZ00394 PTZ00394 173585 PTZ00394 glucosamine-fructose-6-phosphate aminotransferase; Provisional 670 matched cddid_all.tbl CDD PTZ00395 PTZ00395 185594 PTZ00395 Sec24-related protein; Provisional 1560 matched cddid_all.tbl CDD PTZ00396 PTZ00396 240400 PTZ00396 Casein kinase II subunit beta; Provisional 251 matched cddid_all.tbl CDD PTZ00397 PTZ00397 240401 PTZ00397 macrophage migration inhibition factor-like protein; Provisional 116 matched cddid_all.tbl CDD PTZ00398 PTZ00398 173589 PTZ00398 phosphoenolpyruvate carboxylase; Provisional 974 matched cddid_all.tbl CDD PTZ00399 PTZ00399 240402 PTZ00399 cysteinyl-tRNA-synthetase; Provisional 651 matched cddid_all.tbl CDD PTZ00400 PTZ00400 240403 PTZ00400 DnaK-type molecular chaperone; Provisional 663 matched cddid_all.tbl CDD PTZ00401 PTZ00401 173592 PTZ00401 aspartyl-tRNA synthetase; Provisional 550 matched cddid_all.tbl CDD PTZ00402 PTZ00402 240404 PTZ00402 glutamyl-tRNA synthetase; Provisional 601 matched cddid_all.tbl CDD PTZ00403 PTZ00403 173594 PTZ00403 phosphatidylserine decarboxylase; Provisional 353 matched cddid_all.tbl CDD PTZ00404 PTZ00404 173595 PTZ00404 cytochrome P450; Provisional 482 matched cddid_all.tbl CDD PTZ00405 PTZ00405 173596 PTZ00405 cytochrome c; Provisional 114 matched cddid_all.tbl CDD PTZ00407 PTZ00407 173597 PTZ00407 DNA topoisomerase IA; Provisional 805 matched cddid_all.tbl CDD PTZ00408 PTZ00408 240405 PTZ00408 NAD-dependent deacetylase; Provisional 242 matched cddid_all.tbl CDD PTZ00409 PTZ00409 173599 PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional 271 matched cddid_all.tbl CDD PTZ00410 PTZ00410 185600 PTZ00410 NAD-dependent SIR2; Provisional 349 matched cddid_all.tbl CDD PTZ00411 PTZ00411 240406 PTZ00411 transaldolase-like protein; Provisional 333 matched cddid_all.tbl CDD PTZ00412 PTZ00412 240407 PTZ00412 leucyl aminopeptidase; Provisional 569 matched cddid_all.tbl CDD PTZ00413 PTZ00413 240408 PTZ00413 lipoate synthase; Provisional 398 matched cddid_all.tbl CDD PTZ00414 PTZ00414 173604 PTZ00414 10 kDa heat shock protein; Provisional 100 matched cddid_all.tbl CDD PTZ00415 PTZ00415 185603 PTZ00415 transmission-blocking target antigen s230; Provisional 2849 matched cddid_all.tbl CDD PTZ00416 PTZ00416 240409 PTZ00416 elongation factor 2; Provisional 836 matched cddid_all.tbl CDD PTZ00417 PTZ00417 173607 PTZ00417 lysine-tRNA ligase; Provisional 585 matched cddid_all.tbl CDD PTZ00418 PTZ00418 240410 PTZ00418 Poly(A) polymerase; Provisional 593 matched cddid_all.tbl CDD PTZ00419 PTZ00419 240411 PTZ00419 valyl-tRNA synthetase-like protein; Provisional 995 matched cddid_all.tbl CDD PTZ00420 PTZ00420 240412 PTZ00420 coronin; Provisional 568 matched cddid_all.tbl CDD PTZ00421 PTZ00421 173611 PTZ00421 coronin; Provisional 493 matched cddid_all.tbl CDD PTZ00422 PTZ00422 185607 PTZ00422 glideosome-associated protein 50; Provisional 394 matched cddid_all.tbl CDD PTZ00423 PTZ00423 240413 PTZ00423 glideosome-associated protein 45; Provisional 193 matched cddid_all.tbl CDD PTZ00424 PTZ00424 185609 PTZ00424 helicase 45; Provisional 401 matched cddid_all.tbl CDD PTZ00425 PTZ00425 240414 PTZ00425 asparagine-tRNA ligase; Provisional 586 matched cddid_all.tbl CDD PTZ00426 PTZ00426 173616 PTZ00426 cAMP-dependent protein kinase catalytic subunit; Provisional 340 matched cddid_all.tbl CDD PTZ00427 PTZ00427 173617 PTZ00427 isoleucine-tRNA ligase, putative; Provisional 1205 matched cddid_all.tbl CDD PTZ00428 PTZ00428 185611 PTZ00428 60S ribosomal protein L4; Provisional 381 matched cddid_all.tbl CDD PTZ00429 PTZ00429 240415 PTZ00429 beta-adaptin; Provisional 746 matched cddid_all.tbl CDD PTZ00430 PTZ00430 185612 PTZ00430 glucose-6-phosphate isomerase; Provisional 552 matched cddid_all.tbl CDD PTZ00431 PTZ00431 173621 PTZ00431 pyrroline carboxylate reductase; Provisional 260 matched cddid_all.tbl CDD PTZ00432 PTZ00432 240416 PTZ00432 falcilysin; Provisional 1119 matched cddid_all.tbl CDD PTZ00433 PTZ00433 185613 PTZ00433 tyrosine aminotransferase; Provisional 412 matched cddid_all.tbl CDD PTZ00434 PTZ00434 185614 PTZ00434 cytosolic glyceraldehyde 3-phosphate dehydrogenase; Provisional 361 matched cddid_all.tbl CDD PTZ00435 PTZ00435 240417 PTZ00435 isocitrate dehydrogenase; Provisional 413 matched cddid_all.tbl CDD PTZ00436 PTZ00436 185616 PTZ00436 60S ribosomal protein L19-like protein; Provisional 357 matched cddid_all.tbl CDD PTZ00437 PTZ00437 240418 PTZ00437 glutaminyl-tRNA synthetase; Provisional 574 matched cddid_all.tbl CDD PTZ00438 PTZ00438 185618 PTZ00438 gamete antigen 27/25-like protein; Provisional 374 matched cddid_all.tbl CDD PTZ00440 PTZ00440 240419 PTZ00440 reticulocyte binding protein 2-like protein; Provisional 2722 matched cddid_all.tbl CDD PTZ00441 PTZ00441 240420 PTZ00441 sporozoite surface protein 2 (SSP2); Provisional 576 matched cddid_all.tbl CDD PTZ00442 PTZ00442 185621 PTZ00442 sexual stage antigen s48/45-like protein; Provisional 347 matched cddid_all.tbl CDD PTZ00443 PTZ00443 185622 PTZ00443 Thioredoxin domain-containing protein; Provisional 224 matched cddid_all.tbl CDD PTZ00444 PTZ00444 185623 PTZ00444 hypothetical protein; Provisional 184 matched cddid_all.tbl CDD PTZ00445 PTZ00445 240421 PTZ00445 p36-lilke protein; Provisional 219 matched cddid_all.tbl CDD PTZ00446 PTZ00446 240422 PTZ00446 vacuolar sorting protein SNF7-like; Provisional 191 matched cddid_all.tbl CDD PTZ00447 PTZ00447 185626 PTZ00447 apical membrane antigen 1-like protein; Provisional 508 matched cddid_all.tbl CDD PTZ00448 PTZ00448 185627 PTZ00448 hypothetical protein; Provisional 373 matched cddid_all.tbl CDD PTZ00449 PTZ00449 185628 PTZ00449 104 kDa microneme/rhoptry antigen; Provisional 943 matched cddid_all.tbl CDD PTZ00450 PTZ00450 185629 PTZ00450 macrophage migration inhibitory factor-like protein; Provisional 113 matched cddid_all.tbl CDD PTZ00451 PTZ00451 185630 PTZ00451 dephospho-CoA kinase; Provisional 244 matched cddid_all.tbl CDD PTZ00452 PTZ00452 185631 PTZ00452 actin; Provisional 375 matched cddid_all.tbl CDD PTZ00453 PTZ00453 185632 PTZ00453 cyclin-dependent kinase; Provisional 96 matched cddid_all.tbl CDD PTZ00454 PTZ00454 240423 PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional 398 matched cddid_all.tbl CDD PTZ00455 PTZ00455 240424 PTZ00455 3-ketoacyl-CoA thiolase; Provisional 438 matched cddid_all.tbl CDD PTZ00456 PTZ00456 185635 PTZ00456 acyl-CoA dehydrogenase; Provisional 622 matched cddid_all.tbl CDD PTZ00457 PTZ00457 185636 PTZ00457 acyl-CoA dehydrogenase; Provisional 520 matched cddid_all.tbl CDD PTZ00458 PTZ00458 185637 PTZ00458 acyl CoA binding protein; Provisional 90 matched cddid_all.tbl CDD PTZ00459 PTZ00459 185638 PTZ00459 mucin-associated surface protein (MASP); Provisional 291 matched cddid_all.tbl CDD PTZ00460 PTZ00460 185639 PTZ00460 acyl-CoA dehydrogenase; Provisional 646 matched cddid_all.tbl CDD PTZ00461 PTZ00461 185640 PTZ00461 isovaleryl-CoA dehydrogenase; Provisional 410 matched cddid_all.tbl CDD PTZ00462 PTZ00462 185641 PTZ00462 Serine-repeat antigen protein; Provisional 1004 matched cddid_all.tbl CDD PTZ00463 PTZ00463 185642 PTZ00463 histone H2B; Provisional 117 matched cddid_all.tbl CDD PTZ00464 PTZ00464 240425 PTZ00464 SNF-7-like protein; Provisional 211 matched cddid_all.tbl CDD PTZ00465 PTZ00465 185644 PTZ00465 rhoptry-associated protein 1 (RAP-1); Provisional 565 matched cddid_all.tbl CDD PTZ00466 PTZ00466 240426 PTZ00466 actin-like protein; Provisional 380 matched cddid_all.tbl CDD PTZ00467 PTZ00467 185646 PTZ00467 40S ribosomal protein S30; Provisional 66 matched cddid_all.tbl CDD PTZ00468 PTZ00468 185647 PTZ00468 phosphofructokinase family protein; Provisional 1328 matched cddid_all.tbl CDD PTZ00469 PTZ00469 185648 PTZ00469 60S ribosomal subunit protein L18; Provisional 187 matched cddid_all.tbl CDD PTZ00470 PTZ00470 240427 PTZ00470 glycoside hydrolase family 47 protein; Provisional 522 matched cddid_all.tbl CDD PTZ00471 PTZ00471 240428 PTZ00471 60S ribosomal protein L27; Provisional 134 matched cddid_all.tbl CDD PTZ00472 PTZ00472 240429 PTZ00472 serine carboxypeptidase (CBP1); Provisional 462 matched cddid_all.tbl CDD PTZ00473 PTZ00473 240430 PTZ00473 Plasmodium Vir superfamily; Provisional 420 matched cddid_all.tbl CDD PTZ00474 PTZ00474 240431 PTZ00474 tryptophan/threonine-rich antigen superfamily; Provisional 316 matched cddid_all.tbl CDD PTZ00475 PTZ00475 185654 PTZ00475 RESA-like protein; Provisional 282 matched cddid_all.tbl CDD PTZ00477 PTZ00477 240432 PTZ00477 rhoptry-associated protein; Provisional 524 matched cddid_all.tbl CDD PTZ00478 PTZ00478 185656 PTZ00478 Sec superfamily; Provisional 81 matched cddid_all.tbl CDD PTZ00479 PTZ00479 185657 PTZ00479 RAP Superfamily; Provisional 435 matched cddid_all.tbl CDD PTZ00480 PTZ00480 185658 PTZ00480 serine/threonine-protein phosphatase; Provisional 320 matched cddid_all.tbl CDD PTZ00481 PTZ00481 185659 PTZ00481 Membrane attack complex/ Perforin (MACPF) Superfamily; Provisional 524 matched cddid_all.tbl CDD PTZ00482 PTZ00482 240433 PTZ00482 membrane-attack complex/perforin (MACPF) Superfamily; Provisional 844 matched cddid_all.tbl CDD PTZ00483 PTZ00483 185661 PTZ00483 proliferating cell nuclear antigen; Provisional 264 matched cddid_all.tbl CDD PTZ00484 PTZ00484 240434 PTZ00484 GTP cyclohydrolase I; Provisional 259 matched cddid_all.tbl CDD PTZ00485 PTZ00485 240435 PTZ00485 aldolase 1-epimerase; Provisional 376 matched cddid_all.tbl CDD PTZ00486 PTZ00486 240436 PTZ00486 apyrase Superfamily; Provisional 352 matched cddid_all.tbl CDD PTZ00487 PTZ00487 240437 PTZ00487 ceramidase; Provisional 715 matched cddid_all.tbl CDD PTZ00488 PTZ00488 185666 PTZ00488 Proteasome subunit beta type-5; Provisional 247 matched cddid_all.tbl CDD PTZ00489 PTZ00489 240438 PTZ00489 glutamate 5-kinase; Provisional 264 matched cddid_all.tbl CDD PTZ00490 PTZ00490 185668 PTZ00490 Ferredoxin superfamily; Provisional 143 matched cddid_all.tbl CDD PTZ00491 PTZ00491 240439 PTZ00491 major vault protein; Provisional 850 matched cddid_all.tbl CDD PTZ00493 PTZ00493 240440 PTZ00493 phosphomethylpyrimidine kinase; Provisional 321 matched cddid_all.tbl CDD PTZ00494 PTZ00494 185671 PTZ00494 tuzin-like protein; Provisional 664 matched cddid_all.tbl CDD TIGR00001 TIGR00001 272847 rpmI_bact ribosomal protein L35. This ribosomal protein is found in bacteria and organelles only. It is not closely related to any eukaryotic or archaeal ribosomal protein. [Protein synthesis, Ribosomal proteins: synthesis and modification] 63 matched cddid_all.tbl CDD TIGR00002 TIGR00002 272848 S16 ribosomal protein S16. This model describes ribosomal S16 of bacteria and organelles. [Protein synthesis, Ribosomal proteins: synthesis and modification] 78 matched cddid_all.tbl CDD TIGR00003 TIGR00003 188014 TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases. [Transport and binding proteins, Cations and iron carrying compounds] 66 matched cddid_all.tbl CDD TIGR00004 TIGR00004 129116 TIGR00004 reactive intermediate/imine deaminase. This protein was described initially as an inhibitor of protein synthesis intiation, then as an endoribonuclease active on single-stranded mRNA, endoribonuclease L-PSP. Members of this family, conserved in all domains of life and often with several members per bacterial genome, appear to catalyze a reaction that minimizes toxic by-products from reactions catalyzed by pyridoxal phosphate-dependent enzymes. [Cellular processes, Other] 124 matched cddid_all.tbl CDD TIGR00005 TIGR00005 161659 rluA_subfam pseudouridine synthase, RluA family. In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli outside this family, TruC (SP|Q46918), modifies uracil-65 in transfer RNAs to pseudouridine. [Protein synthesis, tRNA and rRNA base modification] 299 matched cddid_all.tbl CDD TIGR00006 TIGR00006 272849 TIGR00006 16S rRNA (cytosine(1402)-N(4))-methyltransferase. This model describes RsmH, a 16S rRNA methyltransferase. Previously, this gene was designated MraW, known to be essential in E. coli and widely conserved in bacteria. [Protein synthesis, tRNA and rRNA base modification] 307 matched cddid_all.tbl CDD TIGR00007 TIGR00007 272850 TIGR00007 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase. This protein family consists of HisA, phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase, the enzyme catalyzing the fourth step in histidine biosynthesis. It is closely related to the enzyme HisF for the sixth step. Examples of this enzyme in Actinobacteria have been found to be bifunctional, also possessing phosphoribosylanthranilate isomerase activity; the trusted cutoff here has now been raised to 275.0 to exclude the bifunctional group, now represented by model TIGR01919. HisA from Lactococcus lactis was reported to be inactive (MEDLINE:93322317). [Amino acid biosynthesis, Histidine family] 230 matched cddid_all.tbl CDD TIGR00008 TIGR00008 188015 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575). [Protein synthesis, Translation factors] 69 matched cddid_all.tbl CDD TIGR00009 TIGR00009 272851 L28 ribosomal protein L28. This model describes bacterial and chloroplast forms of the 50S ribosomal protein L28, a polypeptide about 60 amino acids in length. Mitochondrial homologs differ substantially in architecture (e.g. SP|P36525 from Saccharomyces cerevisiae, which is 258 amino acids long) and are not included. [Protein synthesis, Ribosomal proteins: synthesis and modification] 56 matched cddid_all.tbl CDD TIGR00010 TIGR00010 272852 TIGR00010 hydrolase, TatD family. PSI-BLAST, starting with a urease alpha subunit, finds a large superfamily of proteins, including a number of different enzymes that act as hydrolases at C-N bonds other than peptide bonds (EC 3.5.-.-), many uncharacterized proteins, and the members of this family. Several genomes have multiple paralogs related to this family. However, a set of 17 proteins can be found, one each from 17 of the first 20 genomes, such that each member forms a bidirectional best hit across genomes with all other members of the set. This core set (and one other near-perfect member), but not the other paralogs, form the seed for this model. Additionally, members of the seed alignment and all trusted hits, but not all paralogs, have a conserved motif DxHxH near the amino end. The member from E. coli was recently shown to have DNase activity. [Unknown function, Enzymes of unknown specificity] 252 matched cddid_all.tbl CDD TIGR00011 TIGR00011 272853 YbaK_EbsC Cys-tRNA(Pro) deacylase. This model represents the YbaK family, bacterial proteins whose full length sequence is homologous to an insertion domain in proline--tRNA ligases. The domain deacylates mischarged tRNAs. The YbaK protein of Haemophilus influenzae (HI1434) likewise deacylates Ala-tRNA(Pro), but not the correctly charged Pro-tRNA(Pro). A crystallographic study of HI1434 suggests a nucleotide binding function. Previously, a member of this family was described as EbsC and was thought to be involved in cell wall metabolism. [Protein synthesis, tRNA aminoacylation] 152 matched cddid_all.tbl CDD TIGR00012 TIGR00012 272854 L29 ribosomal protein L29. This model describes a ribosomal large subunit protein, called L29 in prokaryotic (50S) large subunits and L35 in eukaryotic (60S) large subunits. [Protein synthesis, Ribosomal proteins: synthesis and modification] 55 matched cddid_all.tbl CDD TIGR00013 TIGR00013 129125 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function. [Energy metabolism, Other] 63 matched cddid_all.tbl CDD TIGR00014 TIGR00014 272855 arsC arsenate reductase (glutaredoxin). This model describes a distinct clade, including ArsC itself, of the broader ArsC family described by Pfam pfam03960. This clade is almost completely restricted to the Proteobacteria. An anion-translocating ATPase has been identified as the product of the arsenical resistance operon of resistance plasmid R773. When expressed in Escherichia coli this ATP-driven oxyanion pump catalyses extrusion of the oxyanions arsenite, antimonite and arsenate. The pump is composed of two polypeptides, the products of the arsA and arsB genes. The pump alone produces resistance to arsenite and antimonite. This protein, ArsC, catalyzes the reduction of arsenate to arsenite, and thus extends resistance to include arsenate. [Cellular processes, Detoxification] 114 matched cddid_all.tbl CDD TIGR00016 TIGR00016 272856 ackA acetate kinase. Acetate kinase is involved in the activation of acetate to acetyl CoA and in the secretion of acetate. It catalyzes the reaction ATP + acetate = ADP + acetyl phosphate. Some members of this family have been shown to act on propionate as well as acetate. An example of a propionate/acetate kinase is TdcD of E. coli (SP|P11868), an enzyme of an anaerobic pathway of threonine catabolism. It is not known how many members of this family act on additional substrates besides acetate. [Energy metabolism, Fermentation] 404 matched cddid_all.tbl CDD TIGR00017 TIGR00017 129128 cmk cytidylate kinase. This family consists of cytidylate kinase, which catalyzes the phosphorylation of cytidine 5-monophosphate (dCMP) to cytidine 5 -diphosphate (dCDP) in the presence of ATP or GTP. UMP and dCMP can also act as acceptors. [Purines, pyrimidines, nucleosides, and nucleotides, Nucleotide and nucleoside interconversions] 217 matched cddid_all.tbl CDD TIGR00018 TIGR00018 272857 panC pantoate--beta-alanine ligase. This family is pantoate--beta-alanine ligase, the last enzyme of pantothenate biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pantothenate and coenzyme A] 282 matched cddid_all.tbl CDD TIGR00019 TIGR00019 129130 prfA peptide chain release factor 1. This model describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognize and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cutoff for this model. RF-1 does not have a translational frameshift. [Protein synthesis, Translation factors] 360 matched cddid_all.tbl CDD TIGR00020 TIGR00020 272858 prfB "peptide chain release factor 2. In many but not all taxa, there is a conserved real translational frameshift at a TGA codon. RF-2 helps terminate translation at TGA codons and can therefore regulate its own production by readthrough when RF-2 is insufficient. There is a Pfam model called ""RF-1"" for the superfamily of RF-1, RF-2, mitochondrial, RF-H, etc. [Protein synthesis, Translation factors]" 364 matched cddid_all.tbl CDD TIGR00021 TIGR00021 272859 rpiA ribose 5-phosphate isomerase. This model describes ribose 5-phosphate isomerase, an enzyme of the non-oxidative branch of the pentose phosphate pathway. [Energy metabolism, Pentose phosphate pathway] 218 matched cddid_all.tbl CDD TIGR00022 TIGR00022 129133 TIGR00022 YhcH/YjgK/YiaL family protein. This family consists of conserved hypothetical proteins, about 150 amino acids in length. Members with limited information include YhcH, a possible sugar isomerase of sialic acid catabolism, and YjgK. [Unknown function, General] 142 matched cddid_all.tbl CDD TIGR00023 TIGR00023 272860 TIGR00023 acyl-phosphate glycerol 3-phosphate acyltransferase. This model represents the full length of acylphosphate:glycerol 3-phosphate acyltransferase, and integral membrane protein about 200 amino acids in length, called PlsY in Streptococcus pneumoniae, YneS in Bacillus subtilis, and YgiH in E. coli. It is found in a single copy in a large number of bacteria, including the Mycoplasmas but not Mycobacteria or spirochetes, for example. Its partner is PlsX (see TIGR00182), and the pair can replace PlsB for synthesizing 1-acylglycerol-3-phosphate. [Fatty acid and phospholipid metabolism, Biosynthesis] 196 matched cddid_all.tbl CDD TIGR00024 TIGR00024 129135 SbcD_rel_arch putative phosphoesterase, SbcD/Mre11-related. Members of this uncharacterized family share a motif approximating DXH(X25)GDXXD(X25)GNHD as found in several phosphoesterases, including the nucleases SbcD and Mre11. SbcD is a subunit of the SbcCD nuclease of E. coli that can cleave DNA hairpins to unblock stalled DNA replication. All members of this family are archaeal. [Unknown function, Enzymes of unknown specificity] 225 matched cddid_all.tbl CDD TIGR00025 TIGR00025 272861 Mtu_efflux ABC transporter efflux protein, DrrB family. The seed members for this model are a paralogous family of Mycobacterium tuberculosis. Nearly all proteins scoring above the noise cutoff are from high-GC Gram-positive organisms. The members of this paralogous family of efflux proteins are all found in operons with ATP-binding chain partners. They are related to a putative daunorubicin resistance efflux protein of Streptomyces peucetius. This model represents a branch of a larger superfamily that also includes NodJ, a part of the NodIJ pair of nodulation-triggering signal efflux proteins. The members of this branch may all act in antibiotic resistance. 232 matched cddid_all.tbl CDD TIGR00026 TIGR00026 211538 hi_GC_TIGR00026 deazaflavin-dependent oxidoreductase, nitroreductase family. This model represents a family of proteins found in paralogous families in the genera Mycobacterium and Streptomyces. Seven members are in Mycobacterium tuberculosis. Member protein Rv3547 has been characterized as a deazaflavin-dependent nitroreductase. [Unknown function, Enzymes of unknown specificity] 113 matched cddid_all.tbl CDD TIGR00027 TIGR00027 272862 mthyl_TIGR00027 methyltransferase, TIGR00027 family. This model represents a set of probable methyltransferases, about 300 amino acids long, with essentially full length homology. Members share an N-terminal region described by Pfam model pfam02409. Included are a paralogous family of 12 proteins in Mycobacterium tuberculosis, plus close homologs in related species, a family of 8 in the archaeon Methanosarcina acetivorans, and small numbers of members in other species, including plants. [Unknown function, Enzymes of unknown specificity] 260 matched cddid_all.tbl CDD TIGR00028 TIGR00028 272863 Mtu_PIN_fam toxin-antitoxin system PIN domain toxin. Members of this protein consist almost entirely of a PIN (PilT N terminus) domain (see pfam01850). This family was originally defined a set of twelve closely related paralogs found in Mycobacterium tuberculosis, but additional members are found now Synechococcus sp. WH8102, etc. Inspection of genomic regions suggests these represent toxin components of toxin-antitoxin regions, potentially important to creating dormant persister cells. 142 matched cddid_all.tbl CDD TIGR00029 TIGR00029 211539 S20 ribosomal protein S20. This family consists of bacterial (and chloroplast) examples of the bacteria ribosomal small subunit protein S20. [Protein synthesis, Ribosomal proteins: synthesis and modification] 87 matched cddid_all.tbl CDD TIGR00030 TIGR00030 129141 S21p ribosomal protein S21. This model describes bacterial ribosomal protein S21 and most mitochondrial and chloroplast equivalents. [Protein synthesis, Ribosomal proteins: synthesis and modification] 58 matched cddid_all.tbl CDD TIGR00031 TIGR00031 272864 UDP-GALP_mutase UDP-galactopyranose mutase. This enzyme is involved in the conversion of UDP-GALP into UDP-GALF through a 2-keto intermediate. It contains FAD as a cofactor. The gene is known as glf, ceoA, and rfbD. It is known experimentally in E. coli, Mycobacterium tuberculosis, and Klebsiella pneumoniae. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 377 matched cddid_all.tbl CDD TIGR00032 TIGR00032 199987 argG argininosuccinate synthase. argG in bacteria, ARG1 in Saccharomyces cerevisiae. There is a very unusual clustering in the alignment, with a deep split between one cohort of E. coli, H. influenzae, and Streptomyces, and the other cohort of eukaryotes, archaea, and the rest of the eubacteria. [Amino acid biosynthesis, Glutamate family] 394 matched cddid_all.tbl CDD TIGR00033 TIGR00033 272865 aroC chorismate synthase. Homotetramer (noted in E.coli) suggests reason for good conservation. [Amino acid biosynthesis, Aromatic amino acid family] 351 matched cddid_all.tbl CDD TIGR00034 TIGR00034 129145 aroFGH phospho-2-dehydro-3-deoxyheptonate aldolase. [Amino acid biosynthesis, Aromatic amino acid family] 344 matched cddid_all.tbl CDD TIGR00035 TIGR00035 213495 asp_race aspartate racemase. Asparate racemases and some close homologs of unknown function are related to the more common glutamate racemases, but form a distinct evolutionary branch. This model identifies members of the aspartate racemase-related subset of amino acid racemases. [Energy metabolism, Amino acids and amines] 229 matched cddid_all.tbl CDD TIGR00036 TIGR00036 129147 dapB 4-hydroxy-tetrahydrodipicolinate reductase. [Amino acid biosynthesis, Aspartate family] 266 matched cddid_all.tbl CDD TIGR00037 TIGR00037 272866 eIF_5A translation elongation factor IF5A. Recent work (2009) changed the view of eIF5A in eukaryotes and aIF5A in archaea, hypusine-containing proteins, from translation initiation factor to translation elongation factor. [Protein synthesis, Translation factors] 130 matched cddid_all.tbl CDD TIGR00038 TIGR00038 272867 efp translation elongation factor P. function: involved in peptide bond synthesis. stimulate efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase (by similarity). The trusted cutoff of this model is set high enough to exclude members of TIGR02178, an EFP-like protein of certain Gammaproteobacteria. [Protein synthesis, Translation factors] 184 matched cddid_all.tbl CDD TIGR00039 TIGR00039 272868 6PTHBS 6-pyruvoyl tetrahydropterin synthase/QueD family protein. This model has been downgraded from hypothetical_equivalog to subfamily. The animal enzymes are known to be 6-pyruvoyl tetrahydropterin synthase. The function of the bacterial branch of the sequence lineage had been thought to be the same, but many are now taken to be QueD, and enzyme of queuosine biosynthesis. Queuosine is a hypermodified base in the wobble position of some tRNAs in most species. A new model is built to be the QueD equivalog model. [Protein synthesis, tRNA and rRNA base modification] 124 matched cddid_all.tbl CDD TIGR00040 TIGR00040 272869 yfcE phosphoesterase, MJ0936 family. Members of this largely uncharacterized family share a motif approximating DXH(X25)GDXXD(X25)GNHD as found in several phosphoesterases, including the nucleases SbcD and Mre11, and a family of uncharacterized archaeal putative phosphoesterases described by TIGR00024. In this family, the His residue in GNHD portion of the motif is not conserved. The member MJ0936, one of two from Methanococcus jannaschii, was shown () to act on model phosphodiesterase substrates; a divalent cation was required. [Unknown function, Enzymes of unknown specificity] 158 matched cddid_all.tbl CDD TIGR00041 TIGR00041 161676 DTMP_kinase dTMP kinase. Function: phosphorylation of DTMP to form DTDP in both de novo and salvage pathways of DTTP synthesis. Catalytic activity: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate. [Purines, pyrimidines, nucleosides, and nucleotides, Nucleotide and nucleoside interconversions] 195 matched cddid_all.tbl CDD TIGR00042 TIGR00042 272870 TIGR00042 non-canonical purine NTP pyrophosphatase, RdgB/HAM1 family. Saccharomyces cerevisiae HAM1 protects against the mutagenic effects of the base analog 6-N-hydroxylaminopurine, which can be a natural product of monooxygenase activity on adenine. Methanococcus jannaschii MJ0226 and E. coli RdgB are also characterized as pyrophosphatases active against non-standard purines NTPs. E. coli RdgB appears to act by intercepting non-canonical deoxyribonucleotide triphosphates from replication precursor pools. [DNA metabolism, DNA replication, recombination, and repair] 184 matched cddid_all.tbl CDD TIGR00043 TIGR00043 272871 TIGR00043 rRNA maturation RNase YbeY. This metalloprotein family is represented by a single member sequence only in nearly every bacterium. Crystallography demonstrated metal-binding activity, possibly to nickel. It is a predicted to be a metallohydrolase, and more recently it was shown that mutants have a ribosomal RNA processing defect. [Protein synthesis, Other] 110 matched cddid_all.tbl CDD TIGR00044 TIGR00044 129155 TIGR00044 pyridoxal phosphate enzyme, YggS family. Members of this protein family include YggS from Escherichia coli and YBL036C, an uncharacterized pyridoxal protein of Saccharomyces cerevisiae. [Unknown function, Enzymes of unknown specificity] 229 matched cddid_all.tbl CDD TIGR00045 TIGR00045 272872 TIGR00045 glycerate kinase. The only characterized member of this family so far is the glycerate kinase GlxK (EC 2.7.1.31) of E. coli. This enzyme acts after glyoxylate carboligase and 2-hydroxy-3-oxopropionate reductase (tartronate semialdehyde reductase) in the conversion of glyoxylate to 3-phosphoglycerate (the D-glycerate pathway) as a part of allantoin degradation. [Energy metabolism, Other] 375 matched cddid_all.tbl CDD TIGR00046 TIGR00046 272873 TIGR00046 RNA methyltransferase, RsmE family. Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA. [Protein synthesis, tRNA and rRNA base modification] 240 matched cddid_all.tbl CDD TIGR00048 TIGR00048 272874 rRNA_mod_RlmN 23S rRNA (adenine(2503)-C(2))-methyltransferase. Members of this family are RlmN, a 23S rRNA m2A2503 methyltransferase in the radical SAM enzyme family. Closely related is Cfr, a Staphylococcus sciuri plasmid-borne homolog to this family, Cfr, has been identified as essential to transferrable resistance to chloramphenicol and florfenicol. Cfr methylates 23S RNA at a different site. [Protein synthesis, tRNA and rRNA base modification] 355 matched cddid_all.tbl CDD TIGR00049 TIGR00049 272875 TIGR00049 Iron-sulfur cluster assembly accessory protein. Proteins in this subfamily appear to be associated with the process of FeS-cluster assembly. The HesB proteins are associated with the nif gene cluster and the Rhizobium gene IscN has been shown to be required for nitrogen fixation. Nitrogenase includes multiple FeS clusters and many genes for their assembly. The E. coli SufA protein is associated with SufS, a NifS homolog and SufD which are involved in the FeS cluster assembly of the FhnF protein. The Azotobacter protein IscA (homologs of which are also found in E.coli) is associated which IscS, another NifS homolog and IscU, a nifU homolog as well as other factors consistent with a role in FeS cluster chemistry. A homolog from Geobacter contains a selenocysteine in place of an otherwise invariant cysteine, further suggesting a role in redox chemistry. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 105 matched cddid_all.tbl CDD TIGR00050 TIGR00050 272876 rRNA_methyl_1 RNA methyltransferase, TrmH family, group 1. This is part of the trmH (spoU) family of S-adenosyl-L-methionine (AdoMet)-dependent methyltransferases, and is now characterized, in E. coli, as a tRNA:Cm32/Um32 methyltransferase. It may be named TrMet(Xm32), or TrmJ, according to the nomenclature style chosen [Protein synthesis, tRNA and rRNA base modification] 233 matched cddid_all.tbl CDD TIGR00051 TIGR00051 129161 TIGR00051 acyl-CoA thioester hydrolase, YbgC/YbaW family. This model describes a subset of related acyl-CoA thioesterases that include several at least partially characterized proteins. YbgC is an acyl-CoA thioesterase associated with the Tol-Pal system. YbaW is part of the FadM regulon. [Unknown function, General] 117 matched cddid_all.tbl CDD TIGR00052 TIGR00052 129162 TIGR00052 nudix-type nucleoside diphosphatase, YffH/AdpP family. Members of this family include proteins of about 200 amino acids, including the recently characterized nudix hydrolase YffH, shows to be highly active as a GDP-mannose pyrophosphatase. It also includes the C-terminal half of a 361-amino acid protein, TrgB from Rhodobacter sphaeroides, shown experimentally to help confer tellurite resistance. This model also hits a region near the C-terminus of a 1092-amino acid protein of C. elegans. [Unknown function, Enzymes of unknown specificity] 185 matched cddid_all.tbl CDD TIGR00053 TIGR00053 272877 TIGR00053 addiction module toxin component, YafQ family. This model represents a cluster of eubacterial proteins and a cluster of archaeal proteins, all of which are uncharacterized, from 85 to 102 residues in length, and similar in sequence. These include YafQ, a ribosome-associated endoribonuclease that serves as part of a toxin-antitoxin system, for which DinJ is the antidote component. [Cellular processes, Adaptations to atypical conditions] 90 matched cddid_all.tbl CDD TIGR00054 TIGR00054 272878 TIGR00054 RIP metalloprotease RseP. Members of this nearly universal bacterial protein family are regulated intramembrane proteolysis (RIP) proteases. Older and synonymous gene symbols include yaeL in E. coli, mmpA in Caulobacter crescentus, etc. This family includes a region that hits the PDZ domain, found in a number of proteins targeted to the membrane by binding to a peptide ligand. The N-terminal region of this family contains a perfectly conserved motif HEXGH as found in a number of metalloproteinases, where the Glu is the active site and the His residues coordinate the metal cation. Membership in this family is determined by a match to the full length of the seed alignment; the model also detects fragments as well matches a number of members of the PEPTIDASE FAMILY S2C. The region of match appears not to overlap the active site domain. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 419 matched cddid_all.tbl CDD TIGR00055 TIGR00055 129165 uppS undecaprenyl diphosphate synthase. This enzyme builds undecaprenyl diphosphate, a molecule that in bacteria is used a carrier in synthesizing cell wall components. Alternate name: undecaprenyl pyrophosphate synthetase. Activity has been demonstrated experimentally for members of this family from Micrococcus luteus, E. coli, Haemophilus influenzae, and Streptococcus pneumoniae. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 226 matched cddid_all.tbl CDD TIGR00056 TIGR00056 129166 TIGR00056 ABC transport permease subunit. This model describes a subfamily of ABC transporter permease subunits. One member of this family has been associated with the toluene tolerance phenotype of Pseudomonas putida, another with L-glutamate transport, another with maintenance of lipid asymmetry. Many bacterial species have one or two members. The Mycobacteria have large paralogous families included in the DUF140 family but excluded from this subfamily on based on extreme divergence at the amino end and on phylogenetic and UPGMA trees on the more conserved regions. [Hypothetical proteins, Conserved] 259 matched cddid_all.tbl CDD TIGR00057 TIGR00057 272879 TIGR00057 tRNA threonylcarbamoyl adenosine modification protein, Sua5/YciO/YrdC/YwlC family. Has paralogs, but YrdC called a tRNA modification protein. Ref 2 authors say probably heteromultimeric complex. Paralogs may mean its does the final binding to the tRNA. [Protein synthesis, tRNA and rRNA base modification] 201 matched cddid_all.tbl CDD TIGR00058 TIGR00058 129168 Hemerythrin hemerythrin family non-heme iron protein. This family includes oxygen carrier proteins of various oligomeric states from the vascular fluid (hemerythrin) and muscle (myohemerythrin) of some marine invertebrates. Each unit binds 2 non-heme Fe using 5 H, one E and one D. One member of this family,from the sandworm Nereis diversicolor, is an unusual (non-metallothionein) cadmium-binding protein. Homologous proteins, excluded from this narrowly defined family, are found in archaea and bacteria (see pfam01814). 115 matched cddid_all.tbl CDD TIGR00059 TIGR00059 272880 L17 ribosomal protein L17. Eubacterial and mitochondrial. The mitochondrial form, from yeast, contains an additional 110 amino acids C-terminal to the region found by this model. [Protein synthesis, Ribosomal proteins: synthesis and modification] 111 matched cddid_all.tbl CDD TIGR00060 TIGR00060 272881 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model. [Protein synthesis, Ribosomal proteins: synthesis and modification] 114 matched cddid_all.tbl CDD TIGR00061 TIGR00061 129171 L21 ribosomal protein L21. Eubacterial and chloroplast. [Protein synthesis, Ribosomal proteins: synthesis and modification] 101 matched cddid_all.tbl CDD TIGR00062 TIGR00062 272882 L27 ribosomal protein L27. Eubacterial, chloroplast, and mitochondrial. Mitochondrial members have an additional C-terminal domain. [Protein synthesis, Ribosomal proteins: synthesis and modification] 84 matched cddid_all.tbl CDD TIGR00063 TIGR00063 129173 folE GTP cyclohydrolase I. alternate names: Punch (Drosophila),GTP cyclohydrolase I (EC 3.5.4.16) catalyzes the biosynthesis of formic acid and dihydroneopterin triphosphate from GTP. This reaction is the first step in the biosynthesis of tetrahydrofolate in prokaryotes, of tetrahydrobiopterin in vertebrates, and of pteridine-containing pigments in insects. [Biosynthesis of cofactors, prosthetic groups, and carriers, Folic acid] 180 matched cddid_all.tbl CDD TIGR00064 TIGR00064 272883 ftsY signal recognition particle-docking protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In E.coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein. [Protein fate, Protein and peptide secretion and trafficking] 277 matched cddid_all.tbl CDD TIGR00065 TIGR00065 272884 ftsZ cell division protein FtsZ. This family consists of cell division protein FtsZ, a GTPase found in bacteria, the chloroplast of plants, and in archaebacteria. Structurally similar to tubulin, FtsZ undergoes GTP-dependent polymerization into filaments that form a cytoskeleton involved in septum synthesis. [Cellular processes, Cell division] 349 matched cddid_all.tbl CDD TIGR00066 TIGR00066 129176 g_glut_trans gamma-glutamyltranspeptidase. Also called gamma-glutamyltranspeptidase (ggt). Some members of this family have antibiotic synthesis or resistance activities. In the case of a cephalosporin acylase from Pseudomonas sp., the enzyme was shown to retain some gamma-glutamyltranspeptidase activity. Other, more distantly related proteins have ggt-related activities and score below the trusted cutoff. [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 516 matched cddid_all.tbl CDD TIGR00067 TIGR00067 272885 glut_race glutamate racemase. This family consists of glutamate racemase, a protein required for making the UDP-N-acetylmuramoyl-pentapeptide used as a precursor in bacterial peptidoglycan biosynthesis. The most closely related proteins differing in function are aspartate racemases. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 251 matched cddid_all.tbl CDD TIGR00068 TIGR00068 272886 glyox_I lactoylglutathione lyase. Lactoylglutathione lyase is also known as aldoketomutase and glyoxalase I. Glyoxylase I is a homodimer in many species. In some eukaryotes, including yeasts and plants, the orthologous protein carries a tandem duplication, is twice as long, and hits this model twice. [Central intermediary metabolism, Amino sugars, Energy metabolism, Other] 150 matched cddid_all.tbl CDD TIGR00069 TIGR00069 272887 hisD histidinol dehydrogenase. This model describes a polypeptide sequence catalyzing the final step in histidine biosynthesis, found sometimes as an independent protein and sometimes as a part of a multifunctional protein. [Amino acid biosynthesis, Histidine family] 393 matched cddid_all.tbl CDD TIGR00070 TIGR00070 272888 hisG ATP phosphoribosyltransferase. Members of this family from B. subtilis, Aquifex aeolicus, and Synechocystis PCC6803 (and related taxa) lack the C-terminal third of the sequence. The sole homolog from Archaeoglobus fulgidus lacks the N-terminal 50 residues (as reported) and is otherwise atypical of the rest of the family. This model excludes the C-terminal extension. [Amino acid biosynthesis, Histidine family] 183 matched cddid_all.tbl CDD TIGR00071 TIGR00071 272889 hisT_truA tRNA pseudouridine(38-40) synthase. Members of this family are the tRNA modification enzyme TruA, tRNA pseudouridine(38-40) synthase. In a few species (e.g. Bacillus anthracis), TruA is represented by two paralogs. [Protein synthesis, tRNA and rRNA base modification] 227 matched cddid_all.tbl CDD TIGR00072 TIGR00072 272890 hydrog_prot hydrogenase maturation protease. HycI and HoxM are well-characterized as responsible for C-terminal protease activity on their respective hydrogenase large chains. A large number of homologous proteins appear responsible for the maturation of various forms of hydrogenase. 145 matched cddid_all.tbl CDD TIGR00073 TIGR00073 272891 hypB hydrogenase accessory protein HypB. A GTP hydrolase for assembly of nickel metallocenter of hydrogenase. A similar protein, ureG, is an accessory protein for urease, which also uses nickel. hits scoring 75 and above are safe as orthologs. [SS 1/05/04 I changed the role_ID and process GO from protein folding to to protein modification, since a protein folding role has not been established, but HypB is implicated in insertion of nickel into the large subunit of NiFe hydrogenases.] [Protein fate, Protein modification and repair] 208 matched cddid_all.tbl CDD TIGR00074 TIGR00074 129184 hypC_hupF hydrogenase assembly chaperone HypC/HupF. This protein is suggested by act as a chaperone for a hydrogenase large subunit, holding the precursor form before metallocenter nickel incorporation. [SS 12/31/03] More recently proposed additional function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. . Added metallochaperone and protein mod GO terms. [Protein fate, Protein folding and stabilization, Protein fate, Protein modification and repair] 76 matched cddid_all.tbl CDD TIGR00075 TIGR00075 272892 hypD hydrogenase expression/formation protein HypD. HypD is involved in the hyp operon which is needed for the activity of the three hydrogenase isoenzymes in Escherichia coli. HypD is one of the genes needed for formation of these enzymes. This protein has been found in gram-negative and gram-positive bacteria and Archaea. [Protein fate, Protein modification and repair] 369 matched cddid_all.tbl CDD TIGR00077 TIGR00077 272893 lspA lipoprotein signal peptidase. Alternate name: lipoprotein signal peptidase [Protein fate, Protein and peptide secretion and trafficking] 166 matched cddid_all.tbl CDD TIGR00078 TIGR00078 272894 nadC nicotinate-nucleotide pyrophosphorylase. Synonym: quinolinate phosphoribosyltransferase (decarboxylating) [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridine nucleotides] 265 matched cddid_all.tbl CDD TIGR00079 TIGR00079 272895 pept_deformyl peptide deformylase. Peptide deformylase (EC 3.5.1.88), also called polypeptide deformylase, is a metalloenzyme that uses water to release formate from the N-terminal formyl-L-methionine of bacterial and chloroplast peptides. This enzyme should not be confused with formylmethionine deformylase (EC 3.5.1.31) which is active on free N-formyl methionine and has been reported from rat intestine. [Protein fate, Protein modification and repair] 161 matched cddid_all.tbl CDD TIGR00080 TIGR00080 272896 pimt protein-L-isoaspartate(D-aspartate) O-methyltransferase. This is an all-kingdom (but not all species) full-length ortholog enzyme for repairing aging proteins. Among the prokaryotes, the gene name is pcm. Among eukaryotes, pimt. [Protein fate, Protein modification and repair] 215 matched cddid_all.tbl CDD TIGR00081 TIGR00081 272897 purC phosphoribosylaminoimidazole-succinocarboxamide synthase. Alternate name: SAICAR synthetase purine de novo biosynthesis. E.coli example noted as homotrimer. Check length. Longer versions may be multifunctional enzymes. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 237 matched cddid_all.tbl CDD TIGR00082 TIGR00082 129191 rbfA ribosome-binding factor A. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Essential for efficient processing of 16S rRNA. May interact with the 5'terminal helix region of 16S rRNA. Mutants lacking rbfA have a cold-sensitive phenotype. [Transcription, RNA processing] 114 matched cddid_all.tbl CDD TIGR00083 TIGR00083 272898 ribF riboflavin kinase/FMN adenylyltransferase. multifunctional enzyme: riboflavin kinase (EC 2.7.1.26) (flavokinase) / FMN adenylyltransferase (EC 2.7.7.2) (FAD pyrophosphorylase) (FAD synthetase). [Biosynthesis of cofactors, prosthetic groups, and carriers, Riboflavin, FMN, and FAD] 288 matched cddid_all.tbl CDD TIGR00084 TIGR00084 129193 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions. [DNA metabolism, DNA replication, recombination, and repair] 191 matched cddid_all.tbl CDD TIGR00086 TIGR00086 129194 smpB SsrA-binding protein. This model describes the SsrA-binding protein, also called tmRNA binding protein, small protein B, and SmpB. The small, stable RNA SsrA (also called tmRNA or 10Sa RNA) recognizes stalled ribosomes such as occur during translation from message that lacks a stop codon. It becomes charged with Ala like a tRNA, then acts as mRNA to resume translation started with the defective mRNA. The short C-terminal peptide tag added by the SsrA system marks the abortively translated protein for degradation. SmpB binds SsrA after its aminoacylation but before the coupling of the Ala to the nascent polypeptide chain and is an essential part of the SsrA peptide tagging system. SmpB has been associated with the survival of bacterial pathogens in conditions of stress. It is universal in the first 100 sequenced bacterial genomes. [Protein synthesis, Other] 144 matched cddid_all.tbl CDD TIGR00087 TIGR00087 272899 surE 5'/3'-nucleotidase SurE. This protein family originally was named SurE because of its role in stationary phase survivalin Escherichia coli. In E. coli, surE is next to pcm, an L-isoaspartyl protein repair methyltransferase that is also required for stationary phase survival. Recent work () shows that viewing SurE as an acid phosphatase (3.1.3.2) is not accurate. Rather, SurE in E. coli, Thermotoga maritima, and Pyrobaculum aerophilum acts strictly on nucleoside 5'- and 3'-monophosphates. E. coli SurE is Recommended cutoffs are 15 for homology, 40 for probable orthology, and 200 for orthology with full-length homology. [Cellular processes, Adaptations to atypical conditions] 247 matched cddid_all.tbl CDD TIGR00088 TIGR00088 129196 trmD tRNA (guanine-N1)-methyltransferase. This model is specfic for the tRNA modification enzyme tRNA (guanine-N1)-methyltransferase (trmD). This enzyme methylates guanosime-37 in a number of tRNAs.The enzyme's catalytic activity is as follows: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N1-methylguanine. [Protein synthesis, tRNA and rRNA base modification] 233 matched cddid_all.tbl CDD TIGR00089 TIGR00089 272900 TIGR00089 radical SAM methylthiotransferase, MiaB/RimO family. This subfamily contains the tRNA-i(6)A37 modification enzyme, MiaB (TIGR01574). The phylogenetic tree indicates 4 distinct clades, one of which corresponds to MiaB. The other three clades are modelled by hypothetical equivalogs (TIGR01125, TIGR01579 and TIGR01578). Together, the four models hit every sequence hit by the subfamily model without any overlap between them. This subfamily is aparrently a part of a larger superfamily of enzymes utilizing both a 4Fe4S cluster and S-adenosyl methionine (SAM) to initiate radical reactions. MiaB acts on a particular isoprenylated Adenine base of certain tRNAs causing thiolation at an aromatic carbon, and probably also transferring a methyl grouyp from SAM to the thiol. The particular substrate of the three other clades is unknown but may be very closely related. 429 matched cddid_all.tbl CDD TIGR00090 TIGR00090 272901 rsfS_iojap_ybeB ribosome silencing factor RsfS/YbeB/iojap. This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes RsfS(YbeB) from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. The conserved function of this protein is to silence ribosomes by binding the ribosomal large subunit and impairing joining with the small subunit in response to nutrient stress. Note that RsfS (starvation) is an author-endorsed change from the published symbol RsfA, which conflicted with previously published gene symbols. [Protein synthesis, Translation factors] 99 matched cddid_all.tbl CDD TIGR00091 TIGR00091 161703 TIGR00091 tRNA (guanine-N(7)-)-methyltransferase. This predicted S-adenosylmethionine-dependent methyltransferase is found in a single copy in most Bacteria. It is also found, with a short amino-terminal extension in eukaryotes. Its function is unknown. In E. coli, this protein flanks the DNA repair protein MutY, also called micA. [Protein synthesis, tRNA and rRNA base modification] 194 matched cddid_all.tbl CDD TIGR00092 TIGR00092 129200 TIGR00092 GTP-binding protein YchF. This predicted GTP-binding protein is found in a single copy in every complete bacterial genome, and is found in Eukaryotes. A more distantly related protein, separated from this model, is found in the archaea. It is known to bind GTP and double-stranded nucleic acid. It is suggested to belong to a nucleoprotein complex and act as a translation factor. [Unknown function, General] 368 matched cddid_all.tbl CDD TIGR00093 TIGR00093 272902 TIGR00093 pseudouridine synthase. This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc. [Protein synthesis, tRNA and rRNA base modification] 128 matched cddid_all.tbl CDD TIGR00094 TIGR00094 272903 tRNA_TruD_broad tRNA pseudouridine synthase, TruD family. an EGAD loading error caused one member to be called surE, but that's an adjacent gene. MJ11364 is a strong partial match from 50 to 230 aa. [Protein synthesis, tRNA and rRNA base modification] 387 matched cddid_all.tbl CDD TIGR00095 TIGR00095 188022 TIGR00095 16S rRNA (guanine(966)-N(2))-methyltransferase RsmD. This model represents a family of uncharacterized bacterial proteins. Members are present in nearly every complete bacterial genome, always in a single copy. PSI-BLAST analysis shows homology to several families of SAM-dependent methyltransferases, including ribosomal RNA adenine dimethylases. [Protein synthesis, tRNA and rRNA base modification] 190 matched cddid_all.tbl CDD TIGR00096 TIGR00096 129204 TIGR00096 16S rRNA (cytidine(1402)-2'-O)-methyltransferase. This protein, previously known as YraL, is RsmI, one of a pair of genes involved in a unique dimethyl modification of a cytidine in 16S rRNA. See pfam00590 (tetrapyrrole methylase), which demonstrates homology between this family and other members, including several methylases for the tetrapyrrole class of compound, as well as the enzyme diphthine synthase. [Protein synthesis, tRNA and rRNA base modification] 276 matched cddid_all.tbl CDD TIGR00097 TIGR00097 272904 HMP-P_kinase hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase. This model represents a bifunctional enzyme, phosphomethylpyrimidine kinase (EC 2.7.4.7)/Hydroxymethylpyrimidine kinase (EC 2.7.1.49), the ThiD/J protein of thiamine biosynthesis. The protein is commonly observed within operons containing other thiamine biosynthesis genes. Numerous examples are fusion proteins with other thiamine-biosynthetic domains. Saccaromyces has three recent paralogs, two of which are isofunctional and score above the trusted cutoff. The third shows a longer branch length in a phylogenetic tree and scores below the trusted cutoff, as do putative second copies in a number of species. [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine] 254 matched cddid_all.tbl CDD TIGR00099 TIGR00099 272905 Cof-subfamily "Cof subfamily of IIB subfamily of haloacid dehalogenase superfamily. This subfamily of sequences falls within the Class-IIB subfamily (TIGR01484) of the Haloacid Dehalogenase superfamily of aspartate-nucleophile hydrolases. The use of the name ""Cof"" as an identifier here is arbitrary and refers to the E. coli Cof protein. This subfamily is notable for the large number of recent paralogs in many species. Listeria, for instance, has 12, Clostridium, Lactococcus and Streptococcus pneumoniae have 8 each, Enterococcus and Salmonella have 7 each, and Bacillus subtilus, Mycoplasma, Staphylococcus and E. coli have 6 each. This high degree of gene duplication is limited to the gamma proteobacteria and low-GC gram positive lineages. The profusion of genes in this subfamily is not coupled with a high degree of divergence, so it is impossible to determine an accurate phylogeny at the equivalog level. Considering the relationship of this subfamily to the other known members of the HAD-IIB subfamily (TIGR01484), sucrose and trehalose phosphatases and phosphomannomutase, it seems a reasonable hypothesis that these enzymes act on phosphorylated sugars. Possibly the diversification of genes in this subfamily represents the diverse sugars and polysaccharides that various bacteria find in their biological niches. The members of this subfamily are restricted almost exclusively to bacteria (one sequences from S. pombe scores above trusted, while another is between trusted and noise). It is notable that no archaea are found in this group, the closest relations to the archaea found here being two Deinococcus sequences. [Unknown function, Enzymes of unknown specificity]" 256 matched cddid_all.tbl CDD TIGR00100 TIGR00100 272906 hypA hydrogenase nickel insertion protein HypA. CXXC-~12X-CXXC and genetically seems a regulatory protein. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes. [Protein fate, Protein modification and repair] 115 matched cddid_all.tbl CDD TIGR00101 TIGR00101 129208 ureG urease accessory protein UreG. This model represents UreG, a GTP hydrolase that acts in the assembly of the nickel metallocenter of urease. It is found only in urease-positive species, although some urease-positive species (e.g. Bacillus subtilis) lack this protein. A similar protein, hypB, is an accessory protein for expression of hydrogenase, which also uses nickel. [Central intermediary metabolism, Nitrogen metabolism] 199 matched cddid_all.tbl CDD TIGR00103 TIGR00103 211546 DNA_YbaB_EbfC DNA-binding protein, YbaB/EbfC family. The function of this protein is unknown, but it has been expressed and crystallized. Its gene nearly always occurs next to recR and/or dnaX. It is restricted to Bacteria and the plant Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A member is present even in the minimal gene complement of Mycoplasm genitalium. [Unknown function, General] 101 matched cddid_all.tbl CDD TIGR00104 TIGR00104 129210 tRNA_TsaA tRNA-Thr(GGU) m(6)t(6)A37 methyltransferase TsaA. This protein has been characterized by crystallography in complex with S-Adenosylmethionine, making it a probable S-adenosylmethionine-dependent methyltransferase. Analysis in EcoGene links this protein to the enzyme characterization mapped to the tsaA gene in Escherichia coli. [Unknown function, Enzymes of unknown specificity] 142 matched cddid_all.tbl CDD TIGR00105 TIGR00105 272907 L31 ribosomal protein L31. This family consists exclusively of bacterial (and organellar) 50S ribosomal protein L31. In some species, such as Bacillus subtilis, this protein exists in two forms (RpmE and YtiA), one of which (RpmE) contains a pair of motifs, CXC and CXXC, for binding zinc. [Protein synthesis, Ribosomal proteins: synthesis and modification] 68 matched cddid_all.tbl CDD TIGR00106 TIGR00106 272908 TIGR00106 uncharacterized protein, MTH1187 family. This protein has been crystallized in both Methanobacterium thermoautotrophicum and yeast, but its function remains unknown. Both crystal structures showed sulfate ions bound at the interface of two dimers to form a tetramer. [Unknown function, General] 97 matched cddid_all.tbl CDD TIGR00107 TIGR00107 188024 deoD purine-nucleoside phosphorylase, family 1 (deoD). Purine nucleoside phosphorylase (also called inosine phosphorylase) is a purine salvage enzyme. Purine nucleosides, such as guanosine, inosine, or xanthosine, plus orthophosphate, can be converted to their respective purine bases (guanine, hypoxanthine, or xanthine) plus ribose-1-phosphate. This family of purine nucleoside phosphorylase is restricted to the bacteria. [Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides] 232 matched cddid_all.tbl CDD TIGR00109 TIGR00109 272909 hemH ferrochelatase. Human ferrochelatase, found at the mitochondrial inner membrane inner surface, was shown in an active recombinant form to be a homodimer. This contrasts to an earlier finding by gel filtration that overexpressed E. coli ferrochelatase runs as a monomer. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 322 matched cddid_all.tbl CDD TIGR00110 TIGR00110 272910 ilvD dihydroxy-acid dehydratase. This protein, dihydroxy-acid dehydratase, catalyzes the fourth step in valine and isoleucine biosynthesis. It contains a catalytically essential [4Fe-4S] cluster This model generates scores of up to 150 bits vs. 6-phosphogluconate dehydratase, a homologous enzyme. [Amino acid biosynthesis, Pyruvate family] 535 matched cddid_all.tbl CDD TIGR00111 TIGR00111 129217 pelota mRNA surveillance protein pelota. This model describes the Drosophila protein Pelota, the budding yeast protein DOM34 which it can replace, and a set of closely related archaeal proteins. Members contain a proposed RNA binding motif. The meiotic defect in pelota mutants may be a complex result of a protein translation defect, as suggested in yeast by ribosomal protein RPS30A being a multicopy suppressor and by an altered polyribosome profile in DOM34 mutants rescued by RPS30A. This family is homologous to a family of peptide chain release factors. Pelota is proposed to act in protein translation. [Protein synthesis, Translation factors] 351 matched cddid_all.tbl CDD TIGR00112 TIGR00112 272911 proC pyrroline-5-carboxylate reductase. This enzyme catalyzes the final step in proline biosynthesis. Among the four paralogs in Bacillus subtilis (proG, proH, proI, and comER), ComER is the most divergent and does not prevent proline auxotrophy from mutation of the other three. It is excluded from the seed and scores between the trusted and noise cutoffs. [Amino acid biosynthesis, Glutamate family] 245 matched cddid_all.tbl CDD TIGR00113 TIGR00113 272912 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase. This model describes the enzyme for S-adenosylmethionine:tRNA ribosyltransferase-isomerase (QueA). QueA synthesizes Queuosine which is usually in the first position of the anticodon of tRNAs specific for asparagine, aspartate, histidine, and tyrosine. [Protein synthesis, tRNA and rRNA base modification] 344 matched cddid_all.tbl CDD TIGR00114 TIGR00114 211550 lumazine-synth 6,7-dimethyl-8-ribityllumazine synthase. This enzyme catalyzes the cyclo-ligation of 3,4-dihydroxy-2-butanone-4-P and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione to form 6,7-dimethyl-8-ribityllumazine, the immediate precursor of riboflavin. Sometimes referred to as riboflavin synthase, beta subunit, this should not be confused with the alpha subunit which carries out the subsequent reaction. Archaeal members of this family are considered putative, although included in the seed and scoring above the trusted cutoff. [Biosynthesis of cofactors, prosthetic groups, and carriers, Riboflavin, FMN, and FAD] 138 matched cddid_all.tbl CDD TIGR00115 TIGR00115 272913 tig trigger factor. Trigger factor is a ribosome-associated molecular chaperone and is the first chaperone to interact with nascent polypeptide. Trigger factor can bind at the same time as the signal recognition particle (SRP), but is excluded by the SRP receptor (FtsY). The central domain of trigger factor has peptidyl-prolyl cis/trans isomerase activity. This protein is found in a single copy in virtually every bacterial genome. [Protein fate, Protein folding and stabilization] 410 matched cddid_all.tbl CDD TIGR00116 TIGR00116 272914 tsf translation elongation factor Ts. Translational elongation factor Ts (EF-Ts) catalyzes the exchange of GTP for the GDP of the EF-Tu.GDP complex as part of the cycle of translation elongation. This protein is found in Bacteria, mitochondria, and chloroplasts. [Protein synthesis, Translation factors] 291 matched cddid_all.tbl CDD TIGR00117 TIGR00117 129223 acnB aconitate hydratase 2. Aconitate hydratase (aconitase) is an enzyme of the TCA cycle. This model describes aconitase 2, AcnB, which has weak similarity to aconitase 1. It is found almost exclusively in the Proteobacteria. [Energy metabolism, TCA cycle] 844 matched cddid_all.tbl CDD TIGR00118 TIGR00118 272915 acolac_lg acetolactate synthase, large subunit, biosynthetic type. Two groups of proteins form acetolactate from two molecules of pyruvate. The type of acetolactate synthase described in this model also catalyzes the formation of acetohydroxybutyrate from pyruvate and 2-oxobutyrate, an early step in the branched chain amino acid biosynthesis; it is therefore also termed acetohydroxyacid synthase. In bacteria, this catalytic chain is associated with a smaller regulatory chain in an alpha2/beta2 heterotetramer. Acetolactate synthase is a thiamine pyrophosphate enzyme. In this type, FAD and Mg++ are also found. Several isozymes of this enzyme are found in E. coli K12, one of which contains a frameshift in the large subunit gene and is not expressed. [Amino acid biosynthesis, Pyruvate family] 558 matched cddid_all.tbl CDD TIGR00119 TIGR00119 272916 acolac_sm acetolactate synthase, small subunit. Acetolactate synthase is a heterodimeric thiamine pyrophosphate enzyme with large and small subunits. One of the three isozymes in E. coli K12 contains a frameshift in the large subunit gene and is not expressed. acetohydroxyacid synthase is a synonym. [Amino acid biosynthesis, Pyruvate family] 157 matched cddid_all.tbl CDD TIGR00120 TIGR00120 161718 ArgJ glutamate N-acetyltransferase/amino-acid acetyltransferase. This enzyme can acetylate Glu to N-acetyl-Glu by deacetylating N-2-acetyl-ornithine into ornithine; the two halves of this reaction represent the first and fifth steps in the synthesis of Arg (or citrulline) from Glu by way of ornithine (EC 2.3.1.35). In Bacillus stearothermophilus, but not in Thermus thermophilus HB27, the enzyme is bifunctional and can also use acetyl-CoA to acetylate Glu (EC 2.3.1.1). [Amino acid biosynthesis, Glutamate family] 404 matched cddid_all.tbl CDD TIGR00121 TIGR00121 272917 birA_ligase birA, biotin-[acetyl-CoA-carboxylase] ligase region. This model represents the biotin--acetyl-CoA-carboxylase ligase region of biotin--acetyl-CoA-carboxylase ligase. In Escherichia coli and some other species, this enzyme is part of a bifunction protein BirA that includes a small, N-terminal biotin operon repressor domain. Proteins identified by this model should not be called bifunctional unless they are also identified by birA_repr_reg (TIGR00122). The protein name suggests that this enzyme transfers biotin only to acetyl-CoA-carboxylase but it also transfers the biotin moiety to other proteins. The apparent orthologs among the eukaryotes are larger proteins that contain a single copy of this domain. [Protein fate, Protein modification and repair] 237 matched cddid_all.tbl CDD TIGR00122 TIGR00122 272918 birA_repr_reg BirA biotin operon repressor domain. This model represents the amino-terminal helix-turn-helix repressor region of the biotin--acetyl-CoA-carboxylase ligase/biotin operon repressor bifunctional protein BirA. In many species, the biotin--acetyl-CoA-carboxylase ligase ortholog lacks this DNA-binding repressor region and therefore is not equivalent to the well-characterized BirA of E. coli. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value. [Regulatory functions, DNA interactions] 69 matched cddid_all.tbl CDD TIGR00123 TIGR00123 272919 cbiM cobalamin biosynthesis protein CbiM. A cutoff of 200 bits for trusted orthologs of cbiM is suggested. Scores lower than 200 but higher than 20 may be considered sufficient to call a protein cobalamin biosynthesis protein CbiM-related.The seed alignment for this model is a cluster of very closely related proteins from Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, Methanococcus jannaschii, and Salmonella typhimurium, each of which has greater than 50% identity to all the others. The ortholog from Salmonella is the source of the gene symbol cbiM for this set.In Methanobacterium thermoautotrophicum, Archaeoglobus fulgidus, and Methanococcus jannaschii, a second homolog of cbiM is also found. These cbiM-related proteins appear to represent a distinct but less well-conserved orthologous group. Still more distant homologs include sll0383 from Synechocystis sp. and HI1621 from Haemophilus influenzae; the latter protein, from a species that does not synthesize cobalamin, is the most divergent member of the group. The functions of and relationships among the set of proteins homologous to cbiM have not been determined. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 214 matched cddid_all.tbl CDD TIGR00124 TIGR00124 129230 cit_ly_ligase [citrate (pro-3S)-lyase] ligase. ATP is cleaved to AMP and pyrophosphate during the reaction. The carboxyl end is homologous to a number of cytidyltransferases that also release pyrophosphate. [Energy metabolism, Fermentation, Protein fate, Protein modification and repair] 332 matched cddid_all.tbl CDD TIGR00125 TIGR00125 272920 cyt_tran_rel cytidyltransferase-like domain. Protein families that contain at least one copy of this domain include citrate lyase ligase, pantoate-beta-alanine ligase, glycerol-3-phosphate cytidyltransferase, ADP-heptose synthase, phosphocholine cytidylyltransferase, lipopolysaccharide core biosynthesis protein KdtB, the bifunctional protein NadR, and a number whose function is unknown. Many of these proteins are known to use CTP or ATP and release pyrophosphate. 66 matched cddid_all.tbl CDD TIGR00126 TIGR00126 272921 deoC deoxyribose-phosphate aldolase. Deoxyribose-phosphate aldolase is involved in the catabolism of nucleotides and deoxyriibonucleotides. The catalytic process is as follows: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde. It is found in both gram-postive and gram-negative bacteria. [Purines, pyrimidines, nucleosides, and nucleotides, Other, Energy metabolism, Other] 211 matched cddid_all.tbl CDD TIGR00127 TIGR00127 129233 nadp_idh_euk isocitrate dehydrogenase, NADP-dependent, eukaryotic type. This model describes a eukaryotic, NADP-dependent form of isocitrate dehydrogenase. These eukaryotic enzymes differ considerably from a fairly tight cluster that includes all other related isocitrate dehydrogenases, 3-isopropylmalate dehydrogenases, and tartrate dehydrogenases. Several NAD- or NADP-dependent dehydrogenases, including 3-isopropylmalate dehydrogenase, tartrate dehydrogenase, and the multimeric forms of isocitrate dehydrogenase, share a nucleotide binding domain unrelated to that of lactate dehydrogenase and its homologs. These enzymes dehydrogenate their substates at a H-C-OH site adjacent to a H-C-COOH site; the latter carbon, now adjacent to a carbonyl group, readily decarboxylates. This model does not discriminate cytosolic, mitochondrial, and chloroplast proteins. However, the model starts very near the amino end of the cytosolic form; the finding of additional amino-terminal sequence may indicate a transit peptide. [Energy metabolism, TCA cycle] 409 matched cddid_all.tbl CDD TIGR00128 TIGR00128 272922 fabD malonyl CoA-acyl carrier protein transacylase. This enzyme of fatty acid biosynthesis transfers the malonyl moeity from coenzyme A to acyl-carrier protein. The seed alignment for this family of proteins contains a single member each from a number of bacterial species but also an additional pair of closely related, uncharacterized proteins from B. subtilis, one of which has a long C-terminal extension. [Fatty acid and phospholipid metabolism, Biosynthesis] 290 matched cddid_all.tbl CDD TIGR00129 TIGR00129 272923 fdhD_narQ formate dehydrogenase family accessory protein FdhD. FdhD in E. coli and NarQ in B. subtilis are required for the activity of formate dehydrogenase. The gene name in B. subtilis reflects the requirement of the neighboring gene narA for nitrate assimilation, for which NarQ is not required. In some species, the gene is associated not with a known formate dehydrogenase but with a related putative molybdopterin-binding oxidoreductase. A reasonable hypothesis is that this protein helps prepare a required cofactor for assembly into the holoenzyme. [Energy metabolism, Anaerobic, Energy metabolism, Electron transport] 237 matched cddid_all.tbl CDD TIGR00130 TIGR00130 161726 frhD coenzyme F420-reducing hydrogenase delta subunit (putative coenzyme F420 hydrogenase processing subunit). FrhD is not part of the active FRH heterotrimer, but is probably a protease required for maturation. Alternative name: 8-hydroxy-5-deazaflavin (F420) reducing hydrogenase (FRH) subunit delta. [Protein fate, Protein modification and repair] 153 matched cddid_all.tbl CDD TIGR00131 TIGR00131 272924 gal_kin galactokinase. Galactokinase is a member of the GHMP kinases (Galactokinase, Homoserine kinase, Mevalonate kinase, Phosphomevalonate kinase) and shares with them an amino-terminal domain probably related to ATP binding.The galactokinases found by this model are divided into two sets. Prokaryotic forms are generally shorter. The eukaryotic forms are longer because of additional central regions and in some cases are known to be bifunctional, with regulatory activities that are independent of galactokinase activity. [Energy metabolism, Sugars] 386 matched cddid_all.tbl CDD TIGR00132 TIGR00132 272925 gatA aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit. In many species, Gln--tRNA ligase is missing. tRNA(Gln) is misacylated with Glu after which a heterotrimeric amidotransferase converts Glu to Gln. This model represents the amidase chain of that heterotrimer, encoded by the gatA gene. In the Archaea, Asn--tRNA ligase is also missing. This amidase subunit may also function in the conversion of Asp-tRNA(Asn) to Asn-tRNA(Asn), presumably with a different recognition unit to replace gatB. Both Methanococcus jannaschii and Methanobacterium thermoautotrophicum have both authentic gatB and a gatB-related gene, but only one gene like gatA. It has been shown that gatA can be expressed only when gatC is also expressed. In most species expressing the amidotransferase, the gatC ortholog is about 90 residues in length, but in Mycoplasma genitalium and Mycoplasma pneumoniae the gatC equivalent is as the C-terminal domain of a much longer protein. Not surprisingly, the Mycoplasmas also represent the most atypical lineage of gatA orthology. This orthology group is more narrowly defined here than in Proc Natl Acad Aci USA 94, 11819-11826 (1997). In particular, a Rhodococcus homolog found in association with nitrile hydratase genes and described as an enantiomer-selective amidase active on several 2-aryl propionamides, is excluded here. It is likely, however, that the amidase subunit GatA is not exclusively a part of the Glu-tRNA(Gln) amidotransferase heterotrimer and restricted to that function in all species. [Protein synthesis, tRNA aminoacylation] 460 matched cddid_all.tbl CDD TIGR00133 TIGR00133 272926 gatB aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit. The heterotrimer GatABC is responsible for transferring the NH2 group that converts Glu to Gln, or Asp to Asn after the Glu or Asp has been ligated to the tRNA for Gln or Asn, respectively. In Lactobacillus, GatABC is responsible only for tRNA(Gln). In the Archaea, GatABC is responsible only for tRNA(Asn), while GatDE is responsible for tRNA(Gln). In lineages that include Thermus, Chlamydia, or Acidithiobacillus, the GatABC complex catalyzes both. [Protein synthesis, tRNA aminoacylation] 478 matched cddid_all.tbl CDD TIGR00134 TIGR00134 213509 gatE_arch glutamyl-tRNA(Gln) amidotransferase, subunit E. This peptide is found only in the Archaea. It is paralogous to the gatB-encoded subunit of Glu-tRNA(Gln) amidotransferase. The GatABC system operates in many bacteria to convert Glu-tRNA(Gln) into Gln-tRNA(Gln). However, the homologous system in archaea instead converts Asp-tRNA(Asn) to Asn-tRNA(Asn). Glu-tRNA(Gln) is converted to Gln-tRNA(Gln) by a heterodimeric amidotransferase of GatE (this protein) and GatD. The Archaea have an Asp-tRNA(Asn) amidotransferase instead of an Asp--tRNA ligase, but the genes have not been identified. It is likely that this protein replaces gatB in Asp-tRNA(Asn) amidotransferase but that both enzymes share gatA. [Protein synthesis, tRNA aminoacylation] 620 matched cddid_all.tbl CDD TIGR00135 TIGR00135 129241 gatC aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C subunit. Archaea, organelles, and many bacteria charge Gln-tRNA by first misacylating it with Glu and then amidating Glu to Gln. This small protein is part of the amidotransferase heterotrimer and appears to be important to the stability of the amidase subunit encode by gatA, but its function may not be required in every organism that expresses gatA and gatB. The seed alignment for this model does not include any eukaryotic sequence and is not guaranteed to find eukaryotic examples, although it does find some. Saccharomyces cerevisiae, which expresses the amidotransferase for mitochondrial protein translation, seems to lack a gatC ortholog. This model has been revised to remove the candidate sequence from Methanococcus jannaschii, now part of a related model. [Protein synthesis, tRNA aminoacylation] 93 matched cddid_all.tbl CDD TIGR00136 TIGR00136 272927 gidA glucose-inhibited division protein A. GidA, the longer of two forms of GidA-related proteins, appears to be present in all complete eubacterial genomes so far, as well as Saccharomyces cerevisiae. A subset of these organisms have a closely related protein. GidA is absent in the Archaea. It appears to act with MnmE, in an alpha2/beta2 heterotetramer, in the 5-carboxymethylaminomethyl modification of uridine 34 in certain tRNAs. The shorter, related protein, previously called gid or gidA(S), is now called TrmFO (see model TIGR00137). [Protein synthesis, tRNA and rRNA base modification] 616 matched cddid_all.tbl CDD TIGR00137 TIGR00137 129243 gid_trmFO tRNA:m(5)U-54 methyltransferase. This model represents an orthologous set of proteins present in relatively few bacteria but very tightly conserved where it occurs. It is closely related to gidA (glucose-inhibited division protein A), which appears to be present in all complete eubacterial genomes so far and in Saccharomyces cerevisiae. It was designated gid but is now recognized as a tRNA:m(5)U-54 methyltransferase and is now designated trmFO. [Protein synthesis, tRNA and rRNA base modification] 433 matched cddid_all.tbl CDD TIGR00138 TIGR00138 272928 rsmG_gidB 16S rRNA (guanine(527)-N(7))-methyltransferase RsmG. RsmG was previously called GidB (glucose-inhibited division protein B). It is present and a single copy in nearly all complete eubacterial genomes. It is missing only from some obligate intracellular species of various lineages (Chlamydiae, Ehrlichia, Wolbachia, Anaplasma, Buchnera, etc.). RsmG shows a methytransferase fold in its the crystal structure, and acts as a 7-methylguanosine (m(7)G) methyltransferase, apparently specific to 16S rRNA. [Protein synthesis, tRNA and rRNA base modification] 181 matched cddid_all.tbl CDD TIGR00139 TIGR00139 129245 h_aconitase homoaconitase. Homoaconitase is known only as a fungal enzyme from two species, where it is part of an unusual lysine biosynthesis pathway. Because this model is based on just two sequences from a narrow taxonomic range, it may not recognize distant orthologs, should any exist. Homoaconitase, aconitase, and 3-isopropylmalate dehydratase have similar overall structures, but 3-isopropylmalate dehydratase is split into large (leuC) and small (leuD) chains in eubacteria. Several pairs of archaeal proteins resemble leuC and leuD over their lengths but are even closer to the respective domains of homoaconitase, and their identity is uncertain. [Amino acid biosynthesis, Aspartate family] 712 matched cddid_all.tbl CDD TIGR00140 TIGR00140 129246 hupD hydrogenase expression/formation protein. valid names: hupD, hynC, hoxM. C at 64 and 67 are believed to be metal binding. Postulated to be involved in processing or hydrogenase. Superfamily suggests that it is a peptidase/protease. [Protein fate, Protein modification and repair] 134 matched cddid_all.tbl CDD TIGR00142 TIGR00142 129247 hycI hydrogenase maturation protease HycI. Hydrogenase maturation protease is a protease that is involved in the C-terminal processing of HycE,the large subunit of hydrogenase 3 from E.Coli. This protein seems to be found in E.Coli and in Archaea. [Protein fate, Protein modification and repair] 146 matched cddid_all.tbl CDD TIGR00143 TIGR00143 272929 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression. [Protein fate, Protein modification and repair] 711 matched cddid_all.tbl CDD TIGR00144 TIGR00144 129249 beta_RFAP_syn beta-RFAP synthase. This protein family contains several archaeal examples of beta-ribofuranosylaminobenzene 5-prime-phosphate synthase (beta-RFAP synthase), an enzyme involved in methanopterin biosynthesis. In some species, two members of this family are found. It is unclear whether both act as beta-RFAP synthase. This family is related to the GHMP kinases (Galactokinase, Homoserine kinase, Mevalonate kinase, Phosphomevalonate kinase). Members are found so far only in the Archaea and in Methylobacterium extorquens. [Unknown function, Enzymes of unknown specificity] 324 matched cddid_all.tbl CDD TIGR00145 TIGR00145 272930 TIGR00145 FTR1 family protein. A characterized member from yeast acts as oxidase-coupled high affinity iron transporter. Note that the apparent member from E. coli K12-MG1655 has a frameshift by homology with member sequences from other species. [Unknown function, General] 283 matched cddid_all.tbl CDD TIGR00147 TIGR00147 161732 TIGR00147 lipid kinase, YegS/Rv2252/BmrU family. The E. coli member of this family, YegS has been purified and shown to have phosphatidylglycerol kinase activity. The member from M. tuberculosis, Rv2252, has diacylglycerol kinase activity. BmrU from B. subtilis is in an operon with multidrug efflux transporter Bmr, but is uncharacterized. [Unknown function, Enzymes of unknown specificity] 293 matched cddid_all.tbl CDD TIGR00148 TIGR00148 129252 TIGR00148 UbiD family decarboxylase. The member of this family in E. coli is UbiD, 3-octaprenyl-4-hydroxybenzoate carboxy-lyase. The family described by this model, however, is broad enough that it is likely to contain several different decarboxylases. Found in bacteria, archaea, and yeast, with two members in A. fulgidus. No homologs were detected besides those classified as orthologs. The member from H. pylori has a C-terminal extension of just over 100 residues that is shared in part by the Aquifex aeolicus homolog. [Unknown function, General] 438 matched cddid_all.tbl CDD TIGR00149 TIGR00149 129253 TIGR00149_YjbQ secondary thiamine-phosphate synthase enzyme. Members of this protein family have been studied extensively by crystallography. Members from several different species have been shown to have sufficient thiamin phosphate synthase activity (EC 2.5.1.3) to complement thiE mutants. However, it is presumed that this is a secondary activity, and the primary function of this enzyme remains unknown. [Unknown function, Enzymes of unknown specificity] 132 matched cddid_all.tbl CDD TIGR00150 TIGR00150 129254 T6A_YjeE tRNA threonylcarbamoyl adenosine modification protein YjeE. This protein family belongs to a four-gene system responsible for the threonylcarbamoyl adenosine (t6A) tRNA modification. Members of this family have a conserved nucleotide-binding motif GXXGXGKT and a nucleotide-binding fold. Member protein YjeE of Haemophilus influenzae (HI0065) was shown to have (weak) ATPase activity. [Protein synthesis, tRNA and rRNA base modification] 133 matched cddid_all.tbl CDD TIGR00151 TIGR00151 129255 ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. Members of this protein family are 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, the IspF protein of the deoxyxylulose (non-mevalonate) pathway of IPP biosynthesis. This protein occurs as an IspDF bifunctional fusion protein in about 20 percent of bacterial genomes. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 155 matched cddid_all.tbl CDD TIGR00152 TIGR00152 272931 TIGR00152 dephospho-CoA kinase. This model produces scores in the range of 0-25 bits against adenylate, guanylate, uridine, and thymidylate kinases. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pantothenate and coenzyme A] 190 matched cddid_all.tbl CDD TIGR00153 TIGR00153 272932 TIGR00153 TIGR00153 family protein. An apparent homolog with a suggested function is Pit accessory protein from Sinorhizobium meliloti, which may be involved in phosphate (Pi) transport. [Hypothetical proteins, Conserved] 216 matched cddid_all.tbl CDD TIGR00154 TIGR00154 188029 ispE 4-diphosphocytidyl-2C-methyl-D-erythritol kinase. Members of this family of GHMP kinases were previously designated as conserved hypothetical protein YchB or as isopentenyl monophosphate kinase. It is now known, in tomato and E. coli, to encode 4-diphosphocytidyl-2C-methyl-D-erythritol kinase, an enzyme of the deoxyxylulose phosphate pathway of terpenoid biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 294 matched cddid_all.tbl CDD TIGR00155 TIGR00155 272933 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A. [Unknown function, General] 403 matched cddid_all.tbl CDD TIGR00156 TIGR00156 129260 TIGR00156 TIGR00156 family protein. As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae. [Hypothetical proteins, Conserved] 126 matched cddid_all.tbl CDD TIGR00157 TIGR00157 272934 TIGR00157 ribosome small subunit-dependent GTPase A. Members of this protein were designated YjeQ and are now designated RsgA (ribosome small subunit-dependent GTPase A). The strongest motif in the alignment of these proteins is GXSGVGKS[ST], a classic P-loop for nucleotide binding. This protein has been shown to cleave GTP and remain bound to GDP. A role as a regulator of translation has been suggested. The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option). [Protein synthesis, Translation factors] 245 matched cddid_all.tbl CDD TIGR00158 TIGR00158 129262 L9 ribosomal protein L9. Ribosomal protein L9 appears to be universal in, but restricted to, eubacteria and chloroplast. [Protein synthesis, Ribosomal proteins: synthesis and modification] 148 matched cddid_all.tbl CDD TIGR00159 TIGR00159 129263 TIGR00159 TIGR00159 family protein. These proteins have no detectable global or local homology to any protein of known function. Members are restricted to the bacteria and found broadly in lineages other than the Proteobacteria. [Hypothetical proteins, Conserved] 211 matched cddid_all.tbl CDD TIGR00160 TIGR00160 272935 MGSA methylglyoxal synthase. Methylglyoxal synthase (MGS) generates methylglyoxal (MG), a toxic metabolite (that may also be a regulatory metabolite and) that is detoxified, prinicipally, through a pathway involving glutathione and glyoxylase I. Totemeyer et al. propose that, during a loss of control over carbon flux, with accumulation of phosphorylated sugars and depletion of phosphate, as might happen during a rapid shift to a richer medium, MGS aids the cell by converting some dihydroxyacetone phosphate (DHAP) to MG and phosphate. This is therefore an alternative to triosephosphate isomerase and the remainder of the glycolytic pathway for the disposal of DHAP during the stress of a sudden increase in available sugars. [Energy metabolism, Other] 143 matched cddid_all.tbl CDD TIGR00161 TIGR00161 129265 TIGR00161 TIGR00161 family protein. This model represents one out of two closely related ortholgous sets of proteins that, so far, are found only in the Archaea. This ortholog set includes MJ0106 from Methanococcus jannaschii and AF1251 from Archaeoglobus fulgidus, but not MJ1210 or AF0525. [Hypothetical proteins, Conserved] 238 matched cddid_all.tbl CDD TIGR00162 TIGR00162 129266 TIGR00162 TIGR00162 family protein. This model represents one out of two closely related ortholgous sets of proteins that, so far, are found only in but are universal among the Archaea. This ortholog set includes MJ1210 from Methanococcus jannaschii and AF0525 from Archaeoglobus fulgidus while excluding MJ0106 and AF1251. [Hypothetical proteins, Conserved] 188 matched cddid_all.tbl CDD TIGR00163 TIGR00163 272936 PS_decarb phosphatidylserine decarboxylase precursor. Phosphatidylserine decarboxylase is synthesized as a single chain precursor. Generation of the pyruvoyl active site from a Ser is coupled to cleavage of a Gly-Ser bond between the larger (beta) and smaller (alpha chains). It is an integral membrane protein. A closely related family, possibly also active as phosphatidylserine decarboxylase, falls under model TIGR00164. [Fatty acid and phospholipid metabolism, Biosynthesis] 238 matched cddid_all.tbl CDD TIGR00164 TIGR00164 129268 PS_decarb_rel phosphatidylserine decarboxylase precursor-related protein. Phosphatidylserine decarboxylase is synthesized as a single chain precursor. Generation of the pyruvoyl active site from a Ser is coupled to cleavage of a Gly-Ser bond between the larger (beta) and smaller (alpha chains). It is an integral membrane protein. This protein has many regions of homology to known phosphatidylserine decarboxylases, including the Gly-Ser motif for chain cleavage and active site generation, but has a shorter amino end and a number of deletions along the length of the alignment to the phosphatidylserine decarboxylases. It is unclear whether this protein is a form of phosphatidylserine decarboxylase or is a related enzyme. It is found in Neisseria gonorrhoeae, Mycobacterium tuberculosis, and several archaeal species, all of which lack known phosphatidylserine decarboxylase. [Unknown function, General] 189 matched cddid_all.tbl CDD TIGR00165 TIGR00165 272937 S18 ribosomal protein S18. This ribosomal small subunit protein is found in all eubacteria so far, as well as in chloroplasts. YER050C from Saccharomyces cerevisiae and a related protein from Caenorhabditis elegans appear to be homologous and may represent mitochondrial forms. The trusted cutoff is set high enough that these two candidate S18 proteins are not categorized automatically. [Protein synthesis, Ribosomal proteins: synthesis and modification] 70 matched cddid_all.tbl CDD TIGR00166 TIGR00166 129270 S6 ribosomal protein S6. The ribosomal protein S6 ortholog family, including yeast MRP17, shows more than two-fold length variation from 95 residues in Bacillus subtilis to 215 in Mycoplasma pneumoniae. This length variation comes primarily from poorly conserved C-terminal extensions that are particularly long in the Mycoplasmas. MRP17 protein is a component of the small ribosomal subunit in mitochondria, and is shown here to be an ortholog of S6. [Protein synthesis, Ribosomal proteins: synthesis and modification] 93 matched cddid_all.tbl CDD TIGR00167 TIGR00167 272938 cbbA ketose-bisphosphate aldolase. This model is under revision. Proteins found by this model include fructose-bisphosphate and tagatose-bisphosphate aldolase. [Energy metabolism, Glycolysis/gluconeogenesis] 288 matched cddid_all.tbl CDD TIGR00168 TIGR00168 129272 infC translation initiation factor IF-3. infC uses abnormal initiation codons such as AUA, AUC, and CUG which render its expression particularly sensitive to excess of its gene product IF-3 thereby regulating its own expression [Protein synthesis, Translation factors] 165 matched cddid_all.tbl CDD TIGR00169 TIGR00169 272939 leuB 3-isopropylmalate dehydrogenase. Several NAD- or NADP-dependent dehydrogenases, including 3-isopropylmalate dehydrogenase, tartrate dehydrogenase, and the dimeric forms of isocitrate dehydrogenase, share a nucleotide binding domain unrelated to that of lactate dehydrogenase and its homologs. These enzymes dehydrogenate their substates at a H-C-OH site adjacent to a H-C-COOH site; the latter carbon, now adjacent to a carbonyl group, readily decarboxylates.Among these decarboxylating dehydrogenases of hydroxyacids, overall sequence homology indicates evolutionary history rather than actual substrate or cofactor specifity, which may be toggled experimentally by replacement of just a few amino acids. 3-isopropylmalate dehydrogenase is an NAD-dependent enzyme and should have a sequence resembling HGSAPDI around residue 340. The subtrate binding loop should include a sequence resembling E[KQR]X(0,1)LLXXR around residue 115. Other contacts of importance are known from crystallography but not detailed here.This model will not find all isopropylmalate dehydrogenases; the enzyme from Sulfolobus sp. strain 7 is more similar to mitochondrial NAD-dependent isocitrate dehydrogenases than to other known isopropylmalate dehydrogenases and was omitted to improve the specificity of the model. It scores below the cutoff and below some enzymes known not to be isopropylmalate dehydrogenase. [Amino acid biosynthesis, Pyruvate family] 346 matched cddid_all.tbl CDD TIGR00170 TIGR00170 272940 leuC 3-isopropylmalate dehydratase, large subunit. Members of this family are 3-isopropylmalate dehydratase, large subunit, or the large subunit domain of single-chain forms. Homoaconitase, aconitase, and 3-isopropylmalate dehydratase have similar overall structures. All are dehydratases (EC 4.2.1.-) and bind a Fe-4S iron-sulfur cluster. 3-isopropylmalate dehydratase is split into large (leuC) and small (leuD) chains in eubacteria. Several pairs of archaeal proteins resemble the leuC and leuD pair in length and sequence but even more closely resemble the respective domains of homoaconitase, and their identity is uncertain. These homologs are now described by a separate model of subfamily (rather than equivalog) homology type, and the priors and cutoffs for this model have been changed to focus this equivalog family more narrowly. [Amino acid biosynthesis, Pyruvate family] 465 matched cddid_all.tbl CDD TIGR00171 TIGR00171 129275 leuD 3-isopropylmalate dehydratase, small subunit. Homoaconitase, aconitase, and 3-isopropylmalate dehydratase have similar overall structures. All are dehydratases (EC 4.2.1.-) and bind a Fe-4S iron-sulfur cluster. 3-isopropylmalate dehydratase is split into large (leuC) and small (leuD) chains in eubacteria. Several pairs of archaeal proteins resemble the leuC and leuD pair in length and sequence but even more closely resemble the respective domains of homoaconitase, and their identity is uncertain. The candidate archaeal leuD proteins are not included in the seed alignment for this model and score below the trusted cutoff. [Amino acid biosynthesis, Pyruvate family] 188 matched cddid_all.tbl CDD TIGR00172 TIGR00172 129276 maf MAF protein. This nonessential gene causes inhibition of septation when overexpressed. A member of the family is found in the Archaeon Pyrococcus horikoshii and another in the round worm Caenorhabditis elegans. [Cellular processes, Cell division] 183 matched cddid_all.tbl CDD TIGR00173 TIGR00173 272941 menD 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase. MenD was thought until recently to act as SHCHC synthase, but has recently been shown to act instead as SEPHCHC synthase. Conversion of SEPHCHC into SHCHC and pyruvate may occur spontaneously but is catalyzed efficiently, at least in some organisms, by MenH (see TIGR03695). 2-oxoglutarate decarboxylase/SHCHC synthase (menD) is a thiamine pyrophosphate enzyme involved in menaquinone biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 432 matched cddid_all.tbl CDD TIGR00174 TIGR00174 213512 miaA tRNA dimethylallyltransferase. Alternate names include delta(2)-isopentenylpyrophosphate transferase, IPP transferase, 2-methylthio-N6-isopentyladenosine tRNA modification enzyme. Catalyzes the first step in the modification of an adenosine near the anticodon to 2-methylthio-N6-isopentyladenosine. Understanding of substrate specificity has changed. [Protein synthesis, tRNA and rRNA base modification] 287 matched cddid_all.tbl CDD TIGR00175 TIGR00175 272942 mito_nad_idh isocitrate dehydrogenase, NAD-dependent, mitochondrial type. Several NAD- or NADP-dependent dehydrogenases, including 3-isopropylmalate dehydrogenase, tartrate dehydrogenase, and the multimeric forms of isocitrate dehydrogenase, share a nucleotide binding domain unrelated to that of lactate dehydrogenase and its homologs. These enzymes dehydrogenate their substates at a H-C-OH site adjacent to a H-C-COOH site; the latter carbon, now adjacent to a carbonyl group, readily decarboxylates. Mitochondrial NAD-dependent isocitrate dehydrogenases (IDH) resemble prokaryotic NADP-dependent IDH and 3-isopropylmalate dehydrogenase (an NAD-dependent enzyme) more closely than they resemble eukaryotic NADP-dependent IDH. The mitochondrial NAD-dependent isocitrate dehydrogenase is believed to be an alpha(2)-beta-gamma heterotetramer. All subunits are homologous and found by this model. The NADP-dependent IDH of Thermus aquaticus thermophilus strain HB8 resembles these NAD-dependent IDH, except for the residues involved in cofactor specificity, much more closely than it resembles other prokaryotic NADP-dependent IDH, including that of Thermus aquaticus strain YT1. [Energy metabolism, TCA cycle] 333 matched cddid_all.tbl CDD TIGR00176 TIGR00176 272943 mobB molybdopterin-guanine dinucleotide biosynthesis protein MobB. This molybdenum cofactor biosynthesis enzyme is similar to the urease accessory protein UreG and to the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocenters of their respective target enzymes. [Biosynthesis of cofactors, prosthetic groups, and carriers, Molybdopterin] 155 matched cddid_all.tbl CDD TIGR00177 TIGR00177 272944 molyb_syn molybdenum cofactor synthesis domain. The Drosophila protein cinnamon, the Arabidopsis protein cnx1, and rat protein gephyrin each have one domain like MoeA and one like MoaB and Mog. These domains are, however, distantly related to each other, as captured by this model. Gephyrin is unusual in that it seems to be a tubulin-binding neuroprotein involved in the clustering of both blycine receptors and GABA receptors, rather than a protein of molybdenum cofactor biosynthesis. 148 matched cddid_all.tbl CDD TIGR00178 TIGR00178 129282 monomer_idh isocitrate dehydrogenase, NADP-dependent, monomeric type. The monomeric type of isocitrate dehydrogenase has been found so far in a small number of species, including Azotobacter vinelandii, Corynebacterium glutamicum, Rhodomicrobium vannielii, and Neisseria meningitidis. It is NADP-specific. [Energy metabolism, TCA cycle] 741 matched cddid_all.tbl CDD TIGR00179 TIGR00179 272945 murB UDP-N-acetylenolpyruvoylglucosamine reductase. This model describes MurB, UDP-N-acetylenolpyruvoylglucosamine reductase, which is also called UDP-N-acetylmuramate dehydrogenase. It is part of the pathway for the biosynthesis of the UDP-N-acetylmuramoyl-pentapeptide that is a precursor of bacterial peptidoglycan. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 284 matched cddid_all.tbl CDD TIGR00180 TIGR00180 272946 parB_part ParB/RepB/Spo0J family partition protein. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction. 187 matched cddid_all.tbl CDD TIGR00181 TIGR00181 272947 pepF oligoendopeptidase F. This family represents the oligoendopeptidase F clade of the family of larger M3 or thimet (for thiol-dependent metallopeptidase) oligopeptidase family. Lactococcus lactis PepF hydrolyzed peptides of 7 and 17 amino acids with fairly broad specificity. The homolog of lactococcal PepF in group B Streptococcus was named PepB (, with the name difference reflecting a difference in species of origin rather activity; substrate profiles were quite similar. Differences in substrate specificity should be expected in other species. The gene is duplicated in Lactococcus lactis on the plasmid that bears it. A shortened second copy is found in Bacillus subtilis. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 591 matched cddid_all.tbl CDD TIGR00182 TIGR00182 129286 plsX fatty acid/phospholipid synthesis protein PlsX. This protein of fatty acid/phospholipid biosynthesis, called PlsX after the member in Streptococcus pneumoniae, is proposed to be a phosphate acyltransferase that partners with PlsY (TIGR00023) in a two-step 1-acylglycerol-3-phosphate biosynthesis pathway alternative to the one-step PlsB (EC 2.3.1.15) pathway. [Fatty acid and phospholipid metabolism, Biosynthesis] 322 matched cddid_all.tbl CDD TIGR00183 TIGR00183 272948 prok_nadp_idh isocitrate dehydrogenase, NADP-dependent, prokaryotic type. Several NAD- or NADP-dependent dehydrogenases, including 3-isopropylmalate dehydrogenase, tartrate dehydrogenase, and the multimeric forms of isocitrate dehydrogenase, share a nucleotide binding domain unrelated to that of lactate dehydrogenase and its homologs. These enzymes dehydrogenate their substates at a H-C-OH site adjacent to a H-C-COOH site; Prokaryotic NADP-dependent isocitrate dehydrogenases resemble their NAD-dependent counterparts and 3-isopropylmalate dehydrogenase (an NAD-dependent enzyme) more closely than they resemble eukaryotic NADP-dependent isocitrate dehydrogenases. [Energy metabolism, TCA cycle] 416 matched cddid_all.tbl CDD TIGR00184 TIGR00184 272949 purA adenylosuccinate synthase. Alternate name IMP--aspartate ligase. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 425 matched cddid_all.tbl CDD TIGR00185 TIGR00185 211559 tRNA_yibK_trmL tRNA (cytidine(34)-2'-O)-methyltransferase. TrmL (previously YibK) is responsible for 2'-O-methylation at tRNA(Leu) position 34. [Protein synthesis, tRNA and rRNA base modification] 153 matched cddid_all.tbl CDD TIGR00186 TIGR00186 129290 rRNA_methyl_3 rRNA methylase, putative, group 3. this is part of the trmH (spoU) family of rRNA methylases [Protein synthesis, tRNA and rRNA base modification] 237 matched cddid_all.tbl CDD TIGR00187 TIGR00187 272950 ribE riboflavin synthase, alpha subunit. This protein family consists almost entirely of two lumazine-binding domains, described in the family Lum_binding from Pfam. The model generates lower scores against other proteins that also have two lumazine-binding domains, including some involved in bioluminescence.The name ribE was selected, from among alternatives including ribB and ribC, to match the usage in EcoCyc. [Biosynthesis of cofactors, prosthetic groups, and carriers, Riboflavin, FMN, and FAD] 200 matched cddid_all.tbl CDD TIGR00188 TIGR00188 211560 rnpA ribonuclease P protein component, eubacterial. This peptide is the protein component of a ribonucleoprotein that cleaves the leader sequence from each tRNA precursor to leave the mature 5'-terminus. The catalytic site is in the RNA component, M1 RNA. The yeast mitochondrial RNase P protein component gene RPM2 has no obvious sequence similarity to rnpA, but resembles eukaryotic nuclear RNase P instead. [Transcription, RNA processing] 111 matched cddid_all.tbl CDD TIGR00189 TIGR00189 272951 tesB acyl-CoA thioesterase II. Function: hydrolyzes a broad range of acyl-CoA thioesters. Physiological function is not known. Subunit: homotetramer. [Fatty acid and phospholipid metabolism, Biosynthesis] 271 matched cddid_all.tbl CDD TIGR00190 TIGR00190 129294 thiC phosphomethylpyrimidine synthase. The thiC ortholog is designated thiA in Bacillus subtilis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine] 423 matched cddid_all.tbl CDD TIGR00191 TIGR00191 129295 thrB homoserine kinase. Homoserine kinase is part of the threonine biosynthetic pathway.Homoserine kinase is a member of the GHMP kinases (Galactokinase, Homoserine kinase, Mevalonate kinase, Phosphomevalonate kinase) and shares with them an amino-terminal domain probably related to ATP binding.P.aeruginosa homoserine kinase seems not to be homologous (see PROSITE:PDOC0054) [Amino acid biosynthesis, Aspartate family] 302 matched cddid_all.tbl CDD TIGR00192 TIGR00192 129296 urease_beta urease, beta subunit. In a number of species, including B.subtilis, Synechocystis, and Haemophilus influenzae, urease subunits beta and gamma are encoded as separate polypeptides. In Helicobacter pylori UreA and in the fission yeast Schizosaccharomyces pombe, beta subunit-like sequence follows gamma subunit-like sequence in a single chain; the fission yeast protein contains additional C-terminal regions. [Central intermediary metabolism, Nitrogen metabolism] 101 matched cddid_all.tbl CDD TIGR00193 TIGR00193 272952 urease_gam urease, gamma subunit. In a number of species, including B.subtilis, Synechocystis, and Haemophilus influenzae, urease subunits beta and gamma are encoded as separate polypeptides. In Helicobacter pylori UreA and in the fission yeast Schizosaccharomyces pombe, beta subunit-like sequence follows gamma subunit-like sequence in a single chain; the fission yeast protein contains additional C-terminal regions. Nomenclature for the various subunits of urease in Helicobacter differs from nomenclature in most other species. [Central intermediary metabolism, Nitrogen metabolism] 102 matched cddid_all.tbl CDD TIGR00194 TIGR00194 272953 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments. [DNA metabolism, DNA replication, recombination, and repair] 574 matched cddid_all.tbl CDD TIGR00195 TIGR00195 272954 exoDNase_III exodeoxyribonuclease III. The model brings in reverse transcriptases at scores below 50, model also contains eukaryotic apurinic/apyrimidinic endonucleases which group in the same family [DNA metabolism, DNA replication, recombination, and repair] 254 matched cddid_all.tbl CDD TIGR00196 TIGR00196 272955 yjeF_cterm yjeF C-terminal region, hydroxyethylthiazole kinase-related. E. coli yjeF has full-length orthologs in a number of species, all of unknown function. However, yeast YNL200C is homologous and corresponds to the N-terminal region while yeast YKL151C and B. subtilis yxkO correspond to this C-terminal region only. The present model may hit hydroxyethylthiazole kinase, an enzyme associated with thiamine biosynthesis. [Unknown function, General] 270 matched cddid_all.tbl CDD TIGR00197 TIGR00197 272956 yjeF_nterm yjeF N-terminal region. The protein region corresponding to this model shows no clear homology to any protein of known function. This model is built on yeast protein YNL200C and the N-terminal regions of E. coli yjeF and its orthologs in various species. The C-terminal region of yjeF and its orthologs shows similarity to hydroxyethylthiazole kinase (thiM) and other enzymes involved in thiamine biosynthesis. Yeast YKL151C and B. subtilis yxkO match the yjeF C-terminal domain but lack this region. [Unknown function, General] 205 matched cddid_all.tbl CDD TIGR00198 TIGR00198 272957 cat_per_HPI catalase/peroxidase HPI. As catalase, this enzyme catalyzes the dismutation of two molecules of hydrogen peroxide to dioxygen and two molecules of water. As a peroxidase, it uses hydrogen peroxide to oxidize donor compounds and produce water. KatG from E. coli is a homotetramer with two non-covalently associated iron protoheme IX groups per tetramer, but the ortholog from Synechococcus sp. is a homodimer with one protoheme. Important sites (numbered according to E. coli KatG) include heme ligands His-106 and His-267 and active site Trp-318. Note that the translation PID:g296476 from accession X71420 from Rhodobacter capsulatus B10 contains extensive frameshift differences from the rest of the orthologous family. [Cellular processes, Detoxification] 716 matched cddid_all.tbl CDD TIGR00199 TIGR00199 129303 PncC_domain amidohydrolase, PncC family. CinA is a DNA damage- or competence-inducible protein that is polycistronic with recA in a number of species. Several bacterial species have a protein consisting largely of the C-terminal domain of CinA but lacking the N-terminal domain, including nicotinamide mononucleotide (NMN) deamidase (3.5.1.42) proteins PncC in Shewanella oneidensis and ygaD in E. coli. [DNA metabolism, DNA replication, recombination, and repair] 146 matched cddid_all.tbl CDD TIGR00200 TIGR00200 161761 cinA_nterm competence/damage-inducible protein CinA N-terminal domain. cinA is a DNA damage- or competence-inducible protein that is polycistronic with recA in a number of species [DNA metabolism, DNA replication, recombination, and repair] 413 matched cddid_all.tbl CDD TIGR00201 TIGR00201 272958 comF comF family protein. This protein is found in species that do (Bacillus subtilis, Haemophilus influenzae) or do not (E. coli, Borrelia burgdorferi) have described systems for natural transformation with exogenous DNA. It is involved in competence for transformation in Bacillus subtilis. [Cellular processes, DNA transformation] 190 matched cddid_all.tbl CDD TIGR00202 TIGR00202 272959 csrA carbon storage regulator (csrA). Modulates the expression of genes in the glycogen biosynthesis and gluconeogenesis pathways by accelerating the 5'-to-3' degradation of these transcripts through selective RNA binding. The N-terminal end of the sequence (AA 11-45) contains the KH motif which is characteristic of a set of RNA-binding proteins. [Energy metabolism, Glycolysis/gluconeogenesis, Regulatory functions, RNA interactions] 69 matched cddid_all.tbl CDD TIGR00203 TIGR00203 129307 cydB cytochrome d oxidase, subunit II (cydB). part of a two component cytochrome D terminal complex. Terminal reaction in the aerobic respiratory chain. [Energy metabolism, Electron transport] 378 matched cddid_all.tbl CDD TIGR00204 TIGR00204 129308 dxs 1-deoxy-D-xylulose-5-phosphate synthase. DXP synthase is a thiamine diphosphate-dependent enzyme related to transketolase and the pyruvate dehydrogenase E1-beta subunit. By an acyloin condensation of pyruvate with glyceraldehyde 3-phosphate, it produces 1-deoxy-D-xylulose 5-phosphate, a precursor of thiamine diphosphate (TPP), pyridoxal phosphate, and the isoprenoid building block isopentenyl diphosphate (IPP). [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridoxine, Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine] 617 matched cddid_all.tbl CDD TIGR00205 TIGR00205 272960 fliE flagellar hook-basal body complex protein FliE. fliE is a component of the flagellar hook-basal body complex located possibly at (MS-ring)-rod junction. [Cellular processes, Chemotaxis and motility] 108 matched cddid_all.tbl CDD TIGR00206 TIGR00206 129310 fliF flagellar basal-body M-ring protein/flagellar hook-basal body protein (fliF). Component of the M (cytoplasmic associated) ring, one of four rings (L,P,S,M) which make up the flagellar hook-basal body which is a major portion of the flagellar organelle. Although the basic structure of the flagella appears to be similar for all bacteria, additional rings and structures surrounding the basal body have been observed for some bacteria (eg Vibrio cholerae and Treponema pallidum). [Cellular processes, Chemotaxis and motility] 555 matched cddid_all.tbl CDD TIGR00207 TIGR00207 272961 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family. [Cellular processes, Chemotaxis and motility] 338 matched cddid_all.tbl CDD TIGR00208 TIGR00208 188033 fliS flagellar biosynthetic protein FliS. The function of this protein in flagellar biosynthesis is unknown, but appears to be regulatory. The member of this family in Vibrio parahaemolyticus is designated FlaJ (creating a synonym for FliS) and was shown essential for flagellin biosynthesis. [Cellular processes, Chemotaxis and motility] 124 matched cddid_all.tbl CDD TIGR00209 TIGR00209 129313 galT_1 galactose-1-phosphate uridylyltransferase, family 1. This enzyme is involved in glucose and galactose interconversion. This model describes one of two extremely distantly related branches of the model pfam01087. [Energy metabolism, Sugars] 347 matched cddid_all.tbl CDD TIGR00210 TIGR00210 129314 gltS sodium--glutamate symport carrier (gltS). [Transport and binding proteins, Amino acids, peptides and amines] 398 matched cddid_all.tbl CDD TIGR00211 TIGR00211 272962 glyS glycyl-tRNA synthetase, tetrameric type, beta subunit. The glycyl-tRNA synthetases differ even among the eubacteria in oligomeric structure. In Escherichia coli and most others, it is a heterodimer of two alpha chains and two beta chains, encoded by tandem genes. The genes are similar, but fused, in Chlamydia trachomatis. By contrast, the glycyl-tRNA synthetases of Thermus thermophilus and of archaea and eukaryotes differ considerably; they are homodimeric, mutually similar, and not detected by this model. [Protein synthesis, tRNA aminoacylation] 691 matched cddid_all.tbl CDD TIGR00212 TIGR00212 272963 hemC hydroxymethylbilane synthase. Alternate name hydroxymethylbilane synthase Biosynthesis of cofactors, prosthetic groups, and carriers: Heme and porphyrin [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 292 matched cddid_all.tbl CDD TIGR00213 TIGR00213 129317 GmhB_yaeD D,D-heptose 1,7-bisphosphate phosphatase. This family of proteins formerly designated yaeD resembles the histidinol phosphatase domain of the bifunctional protein HisB. The member from E. coli has been characterized as D,D-heptose 1,7-bisphosphate phosphatase, GmhB, involved in inner core LPS assembly (). [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 176 matched cddid_all.tbl CDD TIGR00214 TIGR00214 272964 lipB lipoate-protein ligase B. Involved in lipoate biosynthesis as the main determinant of the lipoyl-protein ligase activity required for lipoylation of enzymes such as alpha-ketoacid dehydrogenases. Involved in activation and re-activation (following denaturation) of lipoyl-protein ligases (calcium ion-dependant process). [Protein fate, Protein modification and repair] 184 matched cddid_all.tbl CDD TIGR00215 TIGR00215 129319 lpxB lipid-A-disaccharide synthase. Lipid-A precursor biosynthesis producing lipid A disaccharide in a condensation reaction. transcribed as part of an operon including lpxA [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 385 matched cddid_all.tbl CDD TIGR00216 TIGR00216 272965 ispH_lytB (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming). The IspH protein (previously designated LytB) has now been recognized as the last enzyme in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Escherichia coli LytB protein had been found to regulate the activity of RelA (guanosine 3',5'-bispyrophosphate synthetase I), which in turn controls the level of a regulatory metabolite. It is involved in penicillin tolerance and the stringent response. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 282 matched cddid_all.tbl CDD TIGR00217 TIGR00217 129321 malQ 4-alpha-glucanotransferase. This enzyme is known as amylomaltase and disproportionating enzyme. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 513 matched cddid_all.tbl CDD TIGR00218 TIGR00218 272966 manA mannose-6-phosphate isomerase, class I. The names phosphomannose isomerase and mannose-6-phosphate isomerase are synonomous. This family contains two rather deeply branched groups. One group contains an experimentally determined phosphomannose isomerase of Streptococcus mutans as well as three uncharacterized paralogous proteins of Bacillus subtilis, all at more than 50 % identity to each other, plus a more distant homolog from Archaeoglobus fulgidus. The other group contains members from E. coli, budding yeast, Borrelia burgdorferi, etc. [Energy metabolism, Sugars] 302 matched cddid_all.tbl CDD TIGR00219 TIGR00219 129323 mreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 283 matched cddid_all.tbl CDD TIGR00220 TIGR00220 272967 mscL large conductance mechanosensitive channel protein. Protein encodes a channel which opens in response to a membrane stretch force. Probably serves as an osmotic gauge. Carboxy terminus tends to be more divergent across species with a high degree of sequence conservation found at the N-terminus. [Cellular processes, Adaptations to atypical conditions] 127 matched cddid_all.tbl CDD TIGR00221 TIGR00221 272968 nagA N-acetylglucosamine-6-phosphate deacetylase. [Central intermediary metabolism, Amino sugars] 380 matched cddid_all.tbl CDD TIGR00222 TIGR00222 272969 panB 3-methyl-2-oxobutanoate hydroxymethyltransferase. Members of this family are 3-methyl-2-oxobutanoate hydroxymethyltransferase, the first enzyme of the pantothenate biosynthesis pathway. An alternate name is ketopantoate hydroxymethyltransferase. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pantothenate and coenzyme A] 263 matched cddid_all.tbl CDD TIGR00223 TIGR00223 129327 panD L-aspartate-alpha-decarboxylase. Members of this family are aspartate 1-decarboxylase, the enzyme that makes beta-alanine and C02 from aspartate. Beta-alanine is then used to make the vitamin pantothenate, from which coenzyme A is made. Aspartate 1-decarboxylase is synthesized as a proenzyme, then cleaved to an alpha (C-terminal) and beta (N-terminal) subunit with a pyruvoyl group. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pantothenate and coenzyme A] 126 matched cddid_all.tbl CDD TIGR00224 TIGR00224 161774 pckA phosphoenolpyruvate carboxykinase (ATP). Involved in the gluconeogenesis pathway. It converts oxaloacetic acid to phosphoenolpyruvate using ATP. Enzyme is a monomer. The reaction is also catalysed by phosphoenolpyruvate carboxykinase (GTP) (EC 4.1.1.32) using GTP instead of ATP, described in PROSITE:PDOC00421 [Energy metabolism, Glycolysis/gluconeogenesis] 532 matched cddid_all.tbl CDD TIGR00225 TIGR00225 272970 prc C-terminal peptidase (prc). A C-terminal peptidase with different substrates in different species including processing of D1 protein of the photosystem II reaction center in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein in E.coli E.coli and H influenza have the most distal branch of the tree and their proteins have an N-terminal 200 amino acids that show no homology to other proteins in the database. [Protein fate, Degradation of proteins, peptides, and glycopeptides, Protein fate, Protein modification and repair] 334 matched cddid_all.tbl CDD TIGR00227 TIGR00227 129330 ribD_Cterm riboflavin-specific deaminase C-terminal domain. Eubacterial riboflavin-specific deaminases have a zinc-binding domain recognized by the dCMP_cyt_deam model toward the N-terminus and this domain toward the C-terminus. Yeast HTP reductase, a riboflavin-biosynthetic enzyme, and several archaeal proteins believed related to riboflavin biosynthesis consist only of this domain and lack the dCMP_cyt_deam domain. 216 matched cddid_all.tbl CDD TIGR00228 TIGR00228 129331 ruvC crossover junction endodeoxyribonuclease RuvC. Endonuclease that resolves Holliday junction intermediates in genetic recombination. The active form of the protein is a dimer. Structure studies reveals that the catalytic center, comprised of four acidic residues, lies at the bottom of a cleft that fits a DNA duplex. The model hits a single Synechocystis PCC6803 protein at a score of 30, below the trusted cutoff, that appears orthologous and may act as authentic RuvC. [DNA metabolism, DNA replication, recombination, and repair] 156 matched cddid_all.tbl CDD TIGR00229 TIGR00229 272971 sensory_box PAS domain S-box. The PAS domain was previously described. This sensory box, or S-box domain occupies the central portion of the PAS domain but is more widely distributed. It is often tandemly repeated. Known prosthetic groups bound in the S-box domain include heme in the oxygen sensor FixL, FAD in the redox potential sensor NifL, and a 4-hydroxycinnamyl chromophore in photoactive yellow protein. Proteins containing the domain often contain other regulatory domains such as response regulator or sensor histidine kinase domains. Other S-box proteins include phytochromes and the aryl hydrocarbon receptor nuclear translocator. [Regulatory functions, Small molecule interactions] 124 matched cddid_all.tbl CDD TIGR00230 TIGR00230 272972 sfsA sugar fermentation stimulation protein. probable regulatory factor involved in maltose metabolism contains a putative DNA binding domain. Isolated as a gene which enabled E.coli strain MK2001 to use maltose. [Energy metabolism, Sugars, Regulatory functions, Other] 234 matched cddid_all.tbl CDD TIGR00231 TIGR00231 272973 small_GTP small GTP-binding protein domain. Proteins with a small GTP-binding domain recognized by this model include Ras, RhoA, Rab11, translation elongation factor G, translation initiation factor IF-2, tetratcycline resistance protein TetM, CDC42, Era, ADP-ribosylation factors, tdhF, and many others. In some proteins the domain occurs more than once.This model recognizes a large number of small GTP-binding proteins and related domains in larger proteins. Note that the alpha chains of heterotrimeric G proteins are larger proteins in which the NKXD motif is separated from the GxxxxGK[ST] motif (P-loop) by a long insert and are not easily detected by this model. [Unknown function, General] 162 matched cddid_all.tbl CDD TIGR00232 TIGR00232 272974 tktlase_bact transketolase, bacterial and yeast. This model is designed to capture orthologs of bacterial transketolases. The group includes two from the yeast Saccharomyces cerevisiae but excludes dihydroxyactetone synthases (formaldehyde transketolases) from various yeasts and the even more distant mammalian transketolases. Among the family of thiamine diphosphate-dependent enzymes that includes transketolases, dihydroxyacetone synthases, pyruvate dehydrogenase E1-beta subunits, and deoxyxylulose-5-phosphate synthases, mammalian and bacterial transketolases seem not to be orthologous. [Energy metabolism, Pentose phosphate pathway] 653 matched cddid_all.tbl CDD TIGR00233 TIGR00233 272975 trpS tryptophanyl-tRNA synthetase. This model represents tryptophanyl-tRNA synthetase. Some members of the family have a pfam00458 domain amino-terminal to the region described by this model. [Protein synthesis, tRNA aminoacylation] 327 matched cddid_all.tbl CDD TIGR00234 TIGR00234 272976 tyrS tyrosyl-tRNA synthetase. This tyrosyl-tRNA synthetase model starts picking up tryptophanyl-tRNA synthetases at scores of 0 and below. The proteins found by this model have a deep split between two groups. One group contains bacterial and organellar eukaryotic examples. The other contains archaeal and cytosolic eukaryotic examples. [Protein synthesis, tRNA aminoacylation] 378 matched cddid_all.tbl CDD TIGR00235 TIGR00235 272977 udk uridine kinase. Model contains a number of longer eukaryotic proteins and starts bringing in phosphoribulokinase hits at scores of 160 and below [Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides] 207 matched cddid_all.tbl CDD TIGR00236 TIGR00236 272978 wecB UDP-N-acetylglucosamine 2-epimerase. This cytosolic enzyme converts UDP-N-acetyl-D-glucosamine to UDP-N-acetyl-D-mannosamine. In E. coli, this is the first step in the pathway of enterobacterial common antigen biosynthesis.Members of this orthology group have many gene symbols, often reflecting the overall activity of the pathway and/or operon that includes it. Symbols include epsC (exopolysaccharide C) in Burkholderia solanacerum, cap8P (type 8 capsule P) in Staphylococcus aureus, and nfrC in an older designation based on the effects of deletion on phage N4 adsorption. Epimerase activity was also demonstrated in a bifunctional rat enzyme, for which the N-terminal domain appears to be orthologous. The set of proteins found above the suggested cutoff includes E. coli WecB in one of two deeply branched clusters and the rat UDP-N-acetylglucosamine 2-epimerase domain in the other. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 365 matched cddid_all.tbl CDD TIGR00237 TIGR00237 272979 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'->3' or 3'->5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits. [DNA metabolism, Degradation of DNA] 389 matched cddid_all.tbl CDD TIGR00238 TIGR00238 272980 TIGR00238 KamA family protein. This model represents essentially the whole of E. coli YjeK and of some of its apparent orthologs. YodO in Bacillus subtilis, a family member which is longer protein by an additional 100 residues, is characterized as a lysine 2,3-aminomutase with iron, sulphide and pyridoxal 5'-phosphate groups. The homolog MJ0634 from M. jannaschii is preceded by nearly 200 C-terminal residues. This family shows similarity to molybdenum cofactor biosynthesis protein MoaA and related proteins. Note that the E. coli homolog was expressed in E. coli and purified and found not to display display lysine 2,3-aminomutase activity. Active site residues are found in 100 residue extension in B. subtilis. Name changed to KamA family protein. [Cellular processes, Adaptations to atypical conditions] 331 matched cddid_all.tbl CDD TIGR00239 TIGR00239 161785 2oxo_dh_E1 2-oxoglutarate dehydrogenase, E1 component. The 2-oxoglutarate dehydrogenase complex consists of this thiamine pyrophosphate-binding subunit (E1), dihydrolipoamide succinyltransferase (E2), and lipoamide dehydrogenase (E3). The E1 ortholog from Corynebacterium glutamicum is unusual in having an N-terminal extension that resembles the dihydrolipoamide succinyltransferase (E2) component of 2-oxoglutarate dehydrogenase. [Energy metabolism, TCA cycle] 929 matched cddid_all.tbl CDD TIGR00240 TIGR00240 272981 ATCase_reg aspartate carbamoyltransferase, regulatory subunit. The presence of this regulatory subunit allows feedback inhibition by CTP on aspartate carbamoyltransferase, the first step in the synthesis of CTP from aspartate. In many species, this regulatory subunit is not present. In Thermotoga maritima, the catalytic and regulatory subunits are encoded by a fused gene and the regulatory region has enough sequence differences to score below the trusted cutoff. [Purines, pyrimidines, nucleosides, and nucleotides, Pyrimidine ribonucleotide biosynthesis] 150 matched cddid_all.tbl CDD TIGR00241 TIGR00241 129344 CoA_E_activ CoA-substrate-specific enzyme activase, putative. This domain is found in a set of closely related proteins including the (R)-2-hydroxyglutaryl-CoA dehydratase activase of Acidaminococcus fermentans, in longer proteins from M. jannaschii and M. thermoautotrophicum that share an additional N-terminal domain, in a protein described as a subunit of the benzoyl-CoA reductase of Rhodopseudomonas palustris, and in two repeats of an uncharacterized protein of Aquifex aeolicus.This domain may be involved in generating or regenerating the active sites of enzymes related to (R)-2-hydroxyglutaryl-CoA dehydratase and benzoyl-CoA reductase. 248 matched cddid_all.tbl CDD TIGR00242 TIGR00242 129345 TIGR00242 division/cell wall cluster transcriptional repressor MraZ. Members of this family contain two tandem copies of a domain described by pfam02381. This protein often is found with other genes of the dcw (division cell wall) gene cluster, including mraW, ftsI, murE, murF, ftsW, murG, etc. Recent work shows MraW in E. coli binds an upstream region with three tandem GTGGG repeats separated by 5bp spacers. We find similar sites in other species. [Cellular processes, Cell division, Regulatory functions, DNA interactions] 142 matched cddid_all.tbl CDD TIGR00243 TIGR00243 161787 Dxr 1-deoxy-D-xylulose 5-phosphate reductoisomerase. 1-deoxy-D-xylulose 5-phosphate is converted to 2-C-methyl-D-erythritol 4-phosphate in the presence of NADPH. It is involved in the synthesis of isopentenyl diphosphate (IPP), a basic building block in isoprenoid, thiamin, and pyridoxal biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 389 matched cddid_all.tbl CDD TIGR00244 TIGR00244 129347 TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (pfam03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes. [Regulatory functions, DNA interactions] 147 matched cddid_all.tbl CDD TIGR00245 TIGR00245 272982 TIGR00245 TIGR00245 family protein. [Hypothetical proteins, Conserved] 248 matched cddid_all.tbl CDD TIGR00246 TIGR00246 129349 tRNA_RlmH_YbeA rRNA large subunit m3Psi methyltransferase RlmH. This protein, in the SPOUT methyltransferase family, previously designated YbeA in E. coli, was shown to be responsible for a further modification, a methylation, to a pseudouridine base in ribosomal large subunit RNA. [Protein synthesis, tRNA and rRNA base modification] 153 matched cddid_all.tbl CDD TIGR00247 TIGR00247 272983 TIGR00247 conserved hypothetical protein, YceG family. This uncharacterized protein family, found in three of four microbial genomes, virtually always once per genome, includes YceG from Escherichia coli. This protein is encoded next to PabC, 4-amino-4-deoxychorismate lyase, in E. coli and numerous other proteobacteria, but that proximity is not conserved in other lineages. Numerous members of this family have been misannotated as aminodeoxychorismate lyase, apparently because of promiximty to PabC. [Hypothetical proteins, Conserved] 342 matched cddid_all.tbl CDD TIGR00249 TIGR00249 129351 sixA phosphohistidine phosphatase SixA. [Regulatory functions, Protein interactions] 152 matched cddid_all.tbl CDD TIGR00250 TIGR00250 129352 RNAse_H_YqgF putative transcription antitermination factor YqgF. This protein family, which exhibits an RNAse H fold in crystal structure, has been proposed as a putative Holliday junction resolvase, an alternate to RuvC. [Unknown function, General] 130 matched cddid_all.tbl CDD TIGR00251 TIGR00251 129353 TIGR00251 TIGR00251 family protein. [Hypothetical proteins, Conserved] 87 matched cddid_all.tbl CDD TIGR00252 TIGR00252 129354 TIGR00252 TIGR00252 family protein. the scores for Mycobacterium tuberculosis and Treponema pallidum are low considering the alignment [Hypothetical proteins, Conserved] 119 matched cddid_all.tbl CDD TIGR00253 TIGR00253 129355 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins. [Unknown function, General] 95 matched cddid_all.tbl CDD TIGR00254 TIGR00254 272984 GGDEF diguanylate cyclase (GGDEF) domain. The GGDEF domain is named for the motif GG[DE]EF shared by many proteins carrying the domain. There is evidence that the domain has diguanylate cyclase activity. Several proteins carrying this domain also carry domains with functions relating to environmental sensing. These include PleD, a response regulator protein involved in the swarmer-to-stalked cell transition in Caulobacter crescentus, and FixL, a heme-containing oxygen sensor protein. [Regulatory functions, Small molecule interactions, Signal transduction, Other] 165 matched cddid_all.tbl CDD TIGR00255 TIGR00255 129357 TIGR00255 TIGR00255 family protein. The apparent ortholog from Aquifex aeolicus as reported is split into two consecutive reading frames. [Hypothetical proteins, Conserved] 291 matched cddid_all.tbl CDD TIGR00256 TIGR00256 129358 TIGR00256 D-tyrosyl-tRNA(Tyr) deacylase. This homodimeric enzyme appears able to cleave any D-amino acid (and glycine, which does not have distinct D/L forms) from charged tRNA. The name reflects characterization with respect to D-Tyr on tRNA(Tyr) as established in the literature, but substrate specificity seems much broader. [Protein synthesis, tRNA aminoacylation] 145 matched cddid_all.tbl CDD TIGR00257 TIGR00257 129359 IMPACT_YIGZ uncharacterized protein, YigZ family. This uncharacterized protein family includes YigZ, which has been crystallized, from E. coli. YigZ is homologous to the protein product of the mouse IMPACT gene. Crystallography shows a two-domain stucture, and the C-terminal domain is suggested to bind nucleic acids. The function is unknown. Note that the ortholog from E. coli was shown fused to the pepQ gene in GenBank entry X54687. This caused occasional misidentification of this protein as pepQ; this family is found in a number of species that lack pepQ. [Unknown function, General] 204 matched cddid_all.tbl CDD TIGR00258 TIGR00258 272985 TIGR00258 inosine/xanthosine triphosphatase. [Purines, pyrimidines, nucleosides, and nucleotides, Other] 163 matched cddid_all.tbl CDD TIGR00259 TIGR00259 129361 thylakoid_BtpA membrane complex biogenesis protein, BtpA family. Members of this family are found in C. elegans, Synechocystis sp., E. coli, and several of the Archaea. Members in Cyanobacteria have been shown to play a role in protein complex biogenesis, and designated BtpA (biogenesis of thylakoid protein). Homologs in non-photosynthetic species, where thylakoid intracytoplasmic membranes are lacking, are likely to act elsewhere in membrane protein biogenesis. [Protein fate, Protein folding and stabilization] 257 matched cddid_all.tbl CDD TIGR00260 TIGR00260 272986 thrC threonine synthase. Involved in threonine biosynthesis it catalyses the reaction O-PHOSPHO-L-HOMOSERINE + H(2)O = L-THREONINE + ORTHOPHOSPHATE using pyridoxal phosphate as a cofactor. the enzyme is distantly related to the serine/threonine dehydratases which are also pyridoxal-phosphate dependent enzymes. the pyridoxal-phosphate binding site is a Lys (K) residues present at residue 70 of the model. [Amino acid biosynthesis, Aspartate family] 327 matched cddid_all.tbl CDD TIGR00261 TIGR00261 129363 traB pheromone shutdown-related protein TraB. traB is a plasmid encoded gene that functions in the shutdown of the peptide sex pheromone cPD1 which is produced by the plasmid free recipient cell prior to conjugative transfer in Enterococcus faecalis. Once the recipient acquires the plasmid, production of cPD1 is shut down. The gene product may play another role in the other species in the family. [Unknown function, General] 380 matched cddid_all.tbl CDD TIGR00262 TIGR00262 161792 trpA tryptophan synthase, alpha subunit. Tryptophan synthase catalyzes the last step in the biosynthesis of tryptophan. The alpha chain is responsible for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate. In bacteria and plants each domain is found on a separate subunit (alpha and beta chains), while in fungi the two domains are fused together on a single multifunctional protein. The signature pattern for trpA contains three conserved acidic residues. [LIVM]-E-[LIVM]-G-x(2)-[FYC]-[ST]-[DE]-[PA]-[LIVMY]-[AGLI]-[DE]-G and this is located between residues 43-58 of the model. The Sulfolobus solfataricus trpA is known to be quite divergent from other known trpA sequences. [Amino acid biosynthesis, Aromatic amino acid family] 256 matched cddid_all.tbl CDD TIGR00263 TIGR00263 272987 trpB tryptophan synthase, beta subunit. Tryptophan synthase catalyzes the last step in the biosynthesis of tryptophan. the beta chain contains the functional domain for or the synthesis of tryptophan from indole and serine. The enzyme requires pyridoxal-phosphate as a cofactor. The pyridoxal-P attachment site is contained within the conserved region [LIVM]-x-H-x-G-[STA]-H-K-x-N] [K is the pyridoxal-P attachment site] which is present between residues 90-100 of the model. [Amino acid biosynthesis, Aromatic amino acid family] 385 matched cddid_all.tbl CDD TIGR00264 TIGR00264 272988 TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator. [Unknown function, General] 116 matched cddid_all.tbl CDD TIGR00266 TIGR00266 272989 TIGR00266 TIGR00266 family protein. [Hypothetical proteins, Conserved] 222 matched cddid_all.tbl CDD TIGR00267 TIGR00267 129368 TIGR00267 TIGR00267 family protein. This family of uncharacterized proteins shows a low level of similarity (possibly meaningful) to the predicted membrane protein YLR220W, which is involved in calcium homeostatis. It shows no similarity to any other characterized protein.This family is represented in three of the first four completed archaeal genomes, with two members in A. fulgidus. [Hypothetical proteins, Conserved] 169 matched cddid_all.tbl CDD TIGR00268 TIGR00268 129369 TIGR00268 TIGR00268 family protein. The N-terminal region of the model shows similarity to Argininosuccinate synthase proteins using PSI-blast and using the recognize protein identification server. [Hypothetical proteins, Conserved] 252 matched cddid_all.tbl CDD TIGR00269 TIGR00269 129370 TIGR00269 TIGR00269 family protein. [Hypothetical proteins, Conserved] 104 matched cddid_all.tbl CDD TIGR00270 TIGR00270 129371 TIGR00270 TIGR00270 family protein. [Hypothetical proteins, Conserved] 154 matched cddid_all.tbl CDD TIGR00271 TIGR00271 129372 TIGR00271 uncharacterized hydrophobic domain. This domain is in a family of archaeal proteins that includes AF0785 of Archaeoglobus fulgidus and in several eubacterial proteins, including the much longer protein sll1151 from Synechocystis PCC6803. 175 matched cddid_all.tbl CDD TIGR00272 TIGR00272 272990 DPH2 diphthamide biosynthesis protein 2. This protein has been shown in Saccharomyces cerevisiae to be one of several required for the modification of a particular histidine residue of translation elongation factor 2 to diphthamide. This modified site can then become the target for ADP-ribosylation by diphtheria toxin. [Protein fate, Protein modification and repair] 496 matched cddid_all.tbl CDD TIGR00273 TIGR00273 129374 TIGR00273 iron-sulfur cluster-binding protein. Members of this family have a perfect 4Fe-4S binding motif C-x(2)-C-x(2)-C-x(3)-CP followed by either a perfect or imperfect (the first Cys replaced by Ser) second copy. Members probably bind two 4fe-4S iron-sulfur clusters. [Energy metabolism, Electron transport] 432 matched cddid_all.tbl CDD TIGR00274 TIGR00274 272991 TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 291 matched cddid_all.tbl CDD TIGR00275 TIGR00275 272992 TIGR00275 flavoprotein, HI0933 family. The model when searched with a partial length search brings in proteins with a dinucleotide-binding motif (Rossman fold) over the initial 40 residues of the model, including oxidoreductases and dehydrogenases. Partially characterized members include an FAD-binding protein from Bacillus cereus and flavoprotein HI0933 from Haemophilus influenzae. [Unknown function, Enzymes of unknown specificity] 400 matched cddid_all.tbl CDD TIGR00276 TIGR00276 272993 TIGR00276 epoxyqueuosine reductase. This model was rebuilt to exclude archaeal homologs, now that there is new information that bacterial members are epoxyqueuosine reductase, QueG, involved in queuosine biosynthesis for tRNA maturation. [Protein synthesis, tRNA and rRNA base modification] 337 matched cddid_all.tbl CDD TIGR00277 TIGR00277 272994 HDIG HDIG domain. This domain is found in a few known nucleotidyltransferes and in a large number of uncharacterized proteins. It contains four widely separated His residues, the second of which is part of an invariant dipeptide His-Asp in a region matched approximately by the motif HDIG. This model may annotate homologous domains in which one or more of the His residues is conserved but misaligned, and some probable false-positive hits. 80 matched cddid_all.tbl CDD TIGR00278 TIGR00278 272995 TIGR00278 putative membrane protein insertion efficiency factor. This model describes a family, YidD, of small, non-essential proteins now suggested to improve YidC-dependent inner membrane protein insertion. A related protein is found in the temperature phage HP1 of Haemophilus influenzae. Annotation of some members of this family as hemolysins appears to represent propagation from an unpublished GenBank submission, L36462, attributed to Aeromonas hydrophila but a close match to E. coli. [Hypothetical proteins, Conserved] 75 matched cddid_all.tbl CDD TIGR00279 TIGR00279 129380 uL16_euk_arch ribosomal protein uL16(L10.e), eukarotic/archaeal form. This model finds the archaeal and eukaryotic forms of ribosomal protein uL16, previously L10.e. The protein is encoded by multiple loci in some eukaryotes and has been assigned a number of extra-ribosomal functions, some of which will require re-evaluation in the context of identification as a ribosomal protein. L10.e is distantly related to eubacterial ribosomal protein L16. [Protein synthesis, Ribosomal proteins: synthesis and modification] 172 matched cddid_all.tbl CDD TIGR00280 TIGR00280 272996 eL43_euk_arch ribosomal protein eL43. This model finds eukaryotic ribosomal protein eL43 (previously L37a) and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a. [Protein synthesis, Ribosomal proteins: synthesis and modification] 92 matched cddid_all.tbl CDD TIGR00281 TIGR00281 213521 TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] 186 matched cddid_all.tbl CDD TIGR00282 TIGR00282 161802 TIGR00282 metallophosphoesterase, MG_246/BB_0505 family. A member of this family from Mycoplasma Pneumoniae has been crystallized and described as a novel phosphatase. [Unknown function, Enzymes of unknown specificity] 266 matched cddid_all.tbl CDD TIGR00283 TIGR00283 161803 arch_pth2 peptidyl-tRNA hydrolase. This model describes an archaeal/eukaryotic form of peptidyl-tRNA hydrolase. Most bacterial forms are described by TIGR00447. [Protein synthesis, Other] 115 matched cddid_all.tbl CDD TIGR00284 TIGR00284 272997 TIGR00284 dihydropteroate synthase-related protein. This protein has been found so far only in the Archaea, and in particular in those archaea that lack a bacterial-type dihydropteroate synthase. The central region of this protein shows considerable homology to the amino-terminal half of dihydropteroate synthases, while the carboxyl-terminal region shows homology to the small, uncharacterized protein slr0651 of Synechocystis PCC6803. [Unknown function, General] 499 matched cddid_all.tbl CDD TIGR00285 TIGR00285 129386 TIGR00285 DNA-binding protein Alba. Alba has been shown to bind DNA and affect DNA supercoiling in a temperature dependent manner. It is regulated by acetylation (alba = acetylation lowers binding affinity) by the Sir2 protein. Alba is proposed to play a role in establishment or maintenace of chromatin architecture and thereby in transcription repression. This protein appears so far only in the Archaea, but may be universal there. There is a single member in three of the first four completed archaeal genomes, and a second copy in A. fulgidus. In Sulfolobus shibatae there is a tandem second copy that is poorly conserved and scores below the trusted cutoff; all other members of the family are conserved at greater than 50 % pairwise identity. [DNA metabolism, Chromosome-associated proteins] 87 matched cddid_all.tbl CDD TIGR00286 TIGR00286 211565 TIGR00286 arginine decarboxylase, pyruvoyl-dependent. The three copies present in Archeoglobus fulgidus, one of which is only half-length and excluded from the seed alignment, are very closely related and clearly arose by duplication after the separation from well-studied species. The other completed archaeal genomes each contain a single copy. The lone, weak (below trusted cutoff) hit to a non-archaeal sequence is to an uncharacterized protein of Chlamydia, with the greatest similarity in the amino-terminal half of the model. [Central intermediary metabolism, Polyamine biosynthesis, Energy metabolism, Amino acids and amines] 152 matched cddid_all.tbl CDD TIGR00287 TIGR00287 272998 cas1 CRISPR-associated endonuclease Cas1. This model identifies CRISPR-associated protein Cas1, the most universal CRISPR system protein. CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, a system for heritable host defense by prokaryotic cells against phage and other foreign DNA. Cas1 is a metal-dependent DNA-specific endonuclease. 323 matched cddid_all.tbl CDD TIGR00288 TIGR00288 272999 TIGR00288 TIGR00288 family protein. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized. [Hypothetical proteins, Conserved] 160 matched cddid_all.tbl CDD TIGR00289 TIGR00289 129390 TIGR00289 TIGR00289 family protein. Homologous proteins related to MJ0570 of Methanococcus jannaschii include both the apparent orthologs found by this model above the trusted cutoff, the much longer protein YLR143W from Saccharomyces cerevisiae, and second homologous proteins from Archaeoglobus fulgidus and Pyrococcus horikoshii that appear to represent a second orthologous group. [Hypothetical proteins, Conserved] 222 matched cddid_all.tbl CDD TIGR00290 TIGR00290 273000 MJ0570_dom MJ0570-related uncharacterized domain. Proteins with this uncharacterized domain include two apparent ortholog families in the Archaea, one of which is universal among the first four completed archaeal genomes, and YLR143W, a much longer protein from Saccharomyces cerevisiae. The domain comprises the full length of the archaeal proteins and the first third of the yeast protein. 223 matched cddid_all.tbl CDD TIGR00291 TIGR00291 129392 RNA_SBDS rRNA metabolism protein, SBDS family. This protein family, possibly universal in both archaea and eukaryotes, appears to be involved in (ribosomal) RNA metabolism. Mutations in the human ortholog are associated with Shwachman-Bodian-Diamond syndrome. [Protein synthesis, Other] 231 matched cddid_all.tbl CDD TIGR00292 TIGR00292 273001 TIGR00292 thiazole biosynthesis enzyme. This enzyme is involved in the biosynthesis of the thiamine precursor thiazole, and is repressed by thiamine. This family includes c-thi1, a Citrus gene induced during natural and ethylene induced fruit maturation and is highly homologous to plant and yeast thi genes involved in thiamine biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine] 254 matched cddid_all.tbl CDD TIGR00293 TIGR00293 129394 TIGR00293 prefoldin, archaeal alpha subunit/eukaryotic subunit 5. Members of this protein family, rich in coiled coil regions, are molecular chaperones in the class of the prefoldin (GimC) alpha subunit. Prefoldin is a hexamer of two alpha and four beta subunits. This protein appears universal in the archaea but is restricted to Aquifex aeolicus among bacteria so far. Eukaryotes have several related proteins; only prefoldin subunit 5, which appeared the most similar to archaeal prefoldin alpha, is included in this model. This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and the model may have a significant number of hits to proteins that contain coiled coil regions. [Protein fate, Protein folding and stabilization] 126 matched cddid_all.tbl CDD TIGR00294 TIGR00294 129395 TIGR00294 GTP cyclohydrolase, MptA/FolE2 family. This family includes type I GTP cyclohydrolases involved in methanopterin in archaea (MptA) and de novo tetrahydrofolate biosynthesis in bacteria (FolE2). [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 308 matched cddid_all.tbl CDD TIGR00295 TIGR00295 129396 TIGR00295 TIGR00295 family protein. This set of orthologs is narrowly defined, comprising proteins found in three Archaea but not in Pyrococcus horikoshii. The closest homologs are other archaeal proteins that appear to be represent distinct orthologous clusters. [Hypothetical proteins, Conserved] 164 matched cddid_all.tbl CDD TIGR00296 TIGR00296 273002 TIGR00296 uncharacterized protein, PH0010 family. Members of this functionally uncharacterized protein family have been crystallized from Pyrococcus Horikoshii, Methanosarcina Mazei, and Sulfolobus Tokodaii. [Unknown function, General] 200 matched cddid_all.tbl CDD TIGR00297 TIGR00297 213522 TIGR00297 TIGR00297 family protein. [Hypothetical proteins, Conserved] 237 matched cddid_all.tbl CDD TIGR00298 TIGR00298 273003 TIGR00298 2-phosphosulfolactate phosphatase. 2-phosphosulfolactate phosphatase catalyzes the sulfonation of phosphoenolpyruvate to form 2-phospho-3-sulfolactate, the second step in coenzyme M biosynthesis. Coenzyme M is the terminal methyl carrier in methanogenesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Energy metabolism, Methanogenesis] 216 matched cddid_all.tbl CDD TIGR00299 TIGR00299 129400 TIGR00299 TIGR00299 family protein. Members of this family are found in the Archaea and in several different bacteria lineages. The function in unknown and the genomic context is not well conserved. [Hypothetical proteins, Conserved] 382 matched cddid_all.tbl CDD TIGR00300 TIGR00300 129401 TIGR00300 TIGR00300 family protein. All members of the family come from genome projects. A partial length search brings in two plant lysine-ketoglutarate reductase/saccharopine dehydrogenase bifunctional enzymes hitting the N-terminal region of the family. [Hypothetical proteins, Conserved] 407 matched cddid_all.tbl CDD TIGR00302 TIGR00302 129402 TIGR00302 phosphoribosylformylglycinamidine synthase, purS protein. In species such as Bacillus subtilis in which FGAM synthetase is split into two ORFs purL and purQ, this small protein, previously called yexA, is required for FGAM synthetase activity. Although the article does not make it clear whether this is a subunit or an accessory protein, it is encoded as part of the operon, which suggests stochiometric amounts, = subunit. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 80 matched cddid_all.tbl CDD TIGR00303 TIGR00303 273004 TIGR00303 TIGR00303 family protein. All current members of the family are from genome projects. [Hypothetical proteins, Conserved] 331 matched cddid_all.tbl CDD TIGR00304 TIGR00304 213523 TIGR00304 TIGR00304 family protein. The member of this family from Pyrococcus horikoshii scores only 13.91 bits, largely because it is at least 15 residues shorter than other members of this family of small proteins and is penalized for not matching to the N-terminal section of the model. Cutoff scores are set so this hit is between noise and trusted cutoffs. [Hypothetical proteins, Conserved] 77 matched cddid_all.tbl CDD TIGR00305 TIGR00305 129405 TIGR00305 putative toxin-antitoxin system toxin component, PIN family. This uncharacterized protein family, part of the PIN domain superfamily, is restricted to bacteria and archaea. A comprehensive in silico study of toxin-antitoxin systems by Makarova, et al. (2009) finds evidence this family represents the toxin-like component of one class of type 2 toxin-antitoxin systems. [Cellular processes, Other, Transcription, Degradation of RNA] 114 matched cddid_all.tbl CDD TIGR00306 TIGR00306 273005 apgM phosphoglycerate mutase (2,3-diphosphoglycerate-independent), archaeal form. Experimentally characterized in archaea as 2,3-bisphosphoglycerate-independent phosphoglycerate mutase. This model describes a set of proteins in the Archaea (two each in Methanococcus jannaschii, Methanobacterium thermoautotrophicum, and Archaeoglobus fulgidus) and in Aquifex aeolicus (1 member). [Energy metabolism, Glycolysis/gluconeogenesis] 396 matched cddid_all.tbl CDD TIGR00307 TIGR00307 129407 eS8 ribosomal protein eS8. Archaeal and eukaryotic ribosomal protein S8. This model could easily have been split into two models, one for eukaryotic S8 and one for archaeal S8; eukaryotic forms invariably have in insert of about 80 residues that archaeal forms of S8 do not. [Protein synthesis, Ribosomal proteins: synthesis and modification] 127 matched cddid_all.tbl CDD TIGR00308 TIGR00308 273006 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes. [Protein synthesis, tRNA and rRNA base modification] 374 matched cddid_all.tbl CDD TIGR00309 TIGR00309 129409 V_ATPase_subD H(+)-transporting ATP synthase, vacuolar type, subunit D. Although this ATPase can run backwards, using a proton gradient to synthesize ATP, the primary biological role is to acidify some compartment, such as yeast vacuole (a lysosomal homolog) or the interior of a prokaryote. [Transport and binding proteins, Cations and iron carrying compounds] 209 matched cddid_all.tbl CDD TIGR00310 TIGR00310 273007 ZPR1_znf ZPR1 zinc finger domain. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction. 192 matched cddid_all.tbl CDD TIGR00311 TIGR00311 129411 aIF-2beta translation initiation factor aIF-2, beta subunit, putative. The trusted cutoff is set high enough to select only archaeal members. The suggested cutoff is set to include most eukaryotic members but largely exclude the related eIF-5. [Protein synthesis, Translation factors] 133 matched cddid_all.tbl CDD TIGR00312 TIGR00312 273008 cbiD cobalamin biosynthesis protein CbiD. This protein has been shown by cloning into E. coli to be required for cobalamin biosynthesis. role_id [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 347 matched cddid_all.tbl CDD TIGR00313 TIGR00313 129413 cobQ cobyric acid synthase CobQ. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 475 matched cddid_all.tbl CDD TIGR00314 TIGR00314 129414 cdhA CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit. Acetyl-CoA decarbonylase/synthase (ACDS) is a multienzyme complex. Carbon monoxide dehydrogenase is a synonym. The ACDS complex carries out an unusual reaction involving the reversible cleavage and synthesis of acetyl-CoA in methanogens. The model contains the prosite signature for 4Fe-4S ferredoxins [C-x(2)-C-x(2)-C-x(3)-C-[PEG]] between residues 448-462 of the model. [Energy metabolism, Chemoautotrophy] 784 matched cddid_all.tbl CDD TIGR00315 TIGR00315 273009 cdhB CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit. Nomenclature follows the description for Methanosarcina thermophila. The complex is also found in Archaeoglobus fulgidus, not considered a methanogen, but is otherwise generally associated with methanogenesis. [Energy metabolism, Chemoautotrophy] 165 matched cddid_all.tbl CDD TIGR00316 TIGR00316 129416 cdhC CO dehydrogenase/CO-methylating acetyl-CoA synthase complex, beta subunit. Nomenclature follows the description for Methanosarcina thermophila. The CO-methylating acetyl-CoA synthase is considered the defining enzyme of the Wood-Ljungdahl pathway, used for acetate catabolism by sulfate reducing bacteria but for acetate biosynthesis by acetogenic bacteria such as oorella thermoacetica (f. Clostridium thermoaceticum). [Energy metabolism, Chemoautotrophy] 458 matched cddid_all.tbl CDD TIGR00317 TIGR00317 213524 cobS cobalamin 5'-phosphate synthase/cobalamin synthase. cobS is involved with cobalamin biosynthesis in part III of colbalmin biosynthesis. The enzyme catyalzes the reactions adenosylcobinamide-GDP + alpha-ribazole-5'-P = adenosylcobalamin-5'-phosphate + GMP and adenosylcobinamide-GDP + alpha-ribazole = adenosylcobalamin + GMP. The protein product is associated with a large complex of proteins and is induced by cobinamide. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 241 matched cddid_all.tbl CDD TIGR00318 TIGR00318 273010 cyaB adenylyl cyclase CyaB, putative. The protein CyaB from Aeromonas hydrophila is a second adenylyl cyclase from that species, as demonstrated by complementation in E. coli and by assay of the enzymatic properties of purified recombinant protein. It has no detectable homology to any other protein of known function, and has several unusual properties, including an optimal temperature of 65 degrees and an optimal pH of 9.5. A cluster of uncharaterized archaeal homologs may be orthologous and serve (under certain circumstances) to produce the regulatory metabolite cyclic AMP (cAMP). [Regulatory functions, Small molecule interactions] 174 matched cddid_all.tbl CDD TIGR00319 TIGR00319 200008 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-heme iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-heme iron protein with 2 Fe atoms per monomer in different oxidation states.This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin.Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain. [Energy metabolism, Electron transport] 33 matched cddid_all.tbl CDD TIGR00320 TIGR00320 273011 dfx_rbo desulfoferrodoxin. The short N-terminal domain contains four conserved Cys for binding of a ferric iron atom, and is homologous to the small protein desulforedoxin; this domain may also be responsible for dimerization. The remainder of the molecule binds a ferrous iron atom and is similar to neelaredoxin, a monomeric blue non-heme iron protein. The homolog from Treponema pallidum scores between the trusted cutoff for orthology and the noise cutoff. Although essentially a full length homolog, it lacks three of the four Cys residues in the N-terminal domain; the domain may have lost ferric binding ability but may have some conserved structural role such as dimerization, or some new function. This protein is described in some articles as rubredoxin oxidoreductase (rbo), and its gene shares an operon with the rubredoxin gene in Desulfovibrio vulgaris Hildenborough. [Energy metabolism, Electron transport] 125 matched cddid_all.tbl CDD TIGR00321 TIGR00321 273012 dhys deoxyhypusine synthase. Deoxyhypusine synthase is responsible for the first step in creating hypusine. Hypusine is a modified amino acid found in eukaryotes and in archaea in their respective forms of initiation factor 5A. Its presence is confirmed in archaeal genera Pyrococcus (), Sulfolobus, Halobacterium, and Haloferax (), but in an older report was not detected in Methanococcus voltae (J Biol Chem 1987 Dec 5;262(34):16585-9). This family of apparent orthologs has an unusual UPGMA difference tree, in which the members from the archaea M. jannaschii and P. horikoshii cluster with the known eukaryotic deoxyhypusine synthases. Separated by a fairly deep branch, although still strongly related, is a small cluster of proteins from Methanobacterium thermoautotrophicum and Archeoglobus fulgidus, the latter of which has two. [Protein fate, Protein modification and repair] 301 matched cddid_all.tbl CDD TIGR00322 TIGR00322 273013 diphth2_R diphthamide biosynthesis enzyme Dph1/Dph2 domain. Archaea and Eukaryotes, but not Eubacteria, share the property of having a covalently modified residue, 2'-[3-carboxamido-3-(trimethylammonio)propyl]histidine, as a part of a cytosolic protein. The modified His, termed diphthamide, is part of translation elongation factor EF-2 and is the site for ADP-ribosylation by diphtheria toxin. This model includes both Dph1 and Dph2 from Saccharomyces cerevisiae, although only Dph2 is found in the Archaea (see TIGR03682). Dph2 has been shown to act analogously to the radical SAM (rSAM) family (pfam04055), with 4Fe-4S-assisted cleavage of S-adenosylmethionine to create a free radical, but a different organic radical than in rSAM. 318 matched cddid_all.tbl CDD TIGR00323 TIGR00323 211569 eIF-6 translation initiation factor eIF-6, putative. This model finds translation initiation factor eIF-6 of eukaryotes, which is a ribosome dissociation factor. It also finds a set of apparent archaeal orthologs, slightly shorter proteins not yet shown to act as initiation factors; these probably should be designated as translation initiation factor aIF-6, putative. [Protein synthesis, Translation factors] 216 matched cddid_all.tbl CDD TIGR00324 TIGR00324 129424 endA tRNA-intron lyase. The enzyme catalyses the endonucleolytic cleavage of pre tRNA at the 5' and 3' splice sites to release the intron and produces two half tRNA molecules bearing 5' hydroxyl and 2', 3'-cyclic phosphate termini. The genes are homologous in Eucarya and Archea. The two yeast genes have been functionally studied and are two subunits of a heterotetramer enzyme in yeast the other two subunits of which have no known homologs. [Transcription, RNA processing] 170 matched cddid_all.tbl CDD TIGR00325 TIGR00325 273014 lpxC UDP-3-0-acyl N-acetylglucosamine deacetylase. UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc deacetylase from E. coli , LpxC, was previously designated EnvA. This enzyme is involved in lipid-A precursor biosynthesis. It is essential for cell viability. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 297 matched cddid_all.tbl CDD TIGR00326 TIGR00326 273015 eubact_ribD riboflavin biosynthesis protein RibD. This model describes the ribD protein as found in Escherichia coli. The N-terminal domain includes the conserved zinc-binding site region captured in the model dCMP_cyt_deam and shared by proteins such as cytosine deaminase, mammalian apolipoprotein B mRNA editing protein, blasticidin-S deaminase, and Bacillus subtilis competence protein comEB. The C-terminal domain is homologous to the full length of yeast HTP reductase, a protein required for riboflavin biosynthesis. A number of archaeal proteins believed related to riboflavin biosynthesis contain only this C-terminal domain and are not found as full-length matches to this model. [Biosynthesis of cofactors, prosthetic groups, and carriers, Riboflavin, FMN, and FAD] 344 matched cddid_all.tbl CDD TIGR00327 TIGR00327 273016 secE_euk_arch protein translocase SEC61 complex gamma subunit, archaeal and eukaryotic. This model describes archaeal SEC61-like and eukaryotic SEC61 but not bacterial secE proteins, for which a Pfam pfam00584 (SecE) has been created. [Protein fate, Protein and peptide secretion and trafficking] 61 matched cddid_all.tbl CDD TIGR00328 TIGR00328 129428 flhB flagellar biosynthetic protein FlhB. FlhB and its functionally equivalent orthologs, from among a larger superfamily of proteins involved in type III protein export systems, are specifically involved in flagellar protein export. The seed members are restricted and the trusted cutoff is set high such that the proteins gathered by this model play roles specifically related to flagellar structures. Full-length homologs scoring below the trusted cutoff are involved in peptide export but not necessarily in the creation of flagella. [Cellular processes, Chemotaxis and motility] 347 matched cddid_all.tbl CDD TIGR00329 TIGR00329 129429 gcp_kae1 metallohydrolase, glycoprotease/Kae1 family. This subfamily includes the well-studied secreted O-sialoglycoprotein endopeptidase (glycoprotease, EC 3.4.24.57) of Pasteurella haemolytica, a pathogen. A member from Riemerella anatipestifer, associated with cohemolysin activity, likewise is exported without benefit of a classical signal peptide and shows glycoprotease activity on the test substrate glycophorin. However, archaeal members of this subfamily show unrelated activities as demonstrated in Pyrococcus abyssi: DNA binding, iron binding, apurinic endonuclease activity, genomic association with a kinase domain, and no glycoprotease activity. This family thus pulls together a set of proteins as a homology group that appears to be near-universal in life, yet heterogeneous in assayed function between bacteria and archaea. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 305 matched cddid_all.tbl CDD TIGR00330 TIGR00330 129430 glpX fructose-1,6-bisphosphatase, class II. This model represents GlpX, one of three classes of bacterial fructose-1,6-bisphosphatases. This form is homodimeric and Mn2+-dependent, and only very distantly related to the class I fructose-1,6-bisphosphatase, the product of the fbp gene, which is homotetrameric and Mg2+-dependent. A third class is found as one of two types in Bacillus subtilis. In E. coli, GlpX is found in the glpFKX operon together with a glycerol update protein and glycerol kinase. [Energy metabolism, Pentose phosphate pathway] 321 matched cddid_all.tbl CDD TIGR00331 TIGR00331 273017 hrcA heat shock gene repressor HrcA. HrcA represses the class I heat shock operons groE and dnaK; overproduction prevents induction of these operons by heat shock while deletion allows constitutive expression even at low temperatures. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene. [Regulatory functions, DNA interactions] 337 matched cddid_all.tbl CDD TIGR00332 TIGR00332 273018 neela_ferrous desulfoferrodoxin ferrous iron-binding domain. This domain comprises essentially the full length of neelaredoxin, a monomeric, blue, non-heme iron protein of Desulfovibrio gigas said to bind two iron atoms per monomer with identical spectral properties. Neelaredoxin was shown recently to have significant superoxide dismutase activity. This domain is also found (in a form in which the distance between the motifs H[HWYF]IXW and CN[IL]HGXW is somewhat shorter) as the C-terminal domain of desulfoferrodoxin, which is said to bind a single ferrous iron atom.The N-terminal domain of desulfoferrodoxin is described in a separate model, dfx_rbo (TIGR00320). [Energy metabolism, Electron transport] 106 matched cddid_all.tbl CDD TIGR00333 TIGR00333 188042 nrdI ribonucleoside-diphosphate reductase 2, operon protein nrdI. Ribonucleotide reductases (RNRs) are enzymes that provide the precursors of DNA synthesis. The three characterized classes of RNRs differ by their metal cofactor and their stable organic radical. The exact function of nrdI within the ribonucleotide reductases has not yet been fully characterised. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism] 127 matched cddid_all.tbl CDD TIGR00334 TIGR00334 273019 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases. [Transcription, RNA processing] 174 matched cddid_all.tbl CDD TIGR00335 TIGR00335 273020 primase_sml DNA primase, eukaryotic-type, small subunit, putative. Archaeal members differ substantially from eukaryotic members and should be considered putative pending experimental evidence. The protein is universal and single copy among completed archaeal and eukarotic genomes to date. DNA primase creates RNA primers needed for DNA replication.This model is named putative because the assignment is putative for archaeal proteins. Eukaryotic proteins scoring above the trusted cutoff can be considered authentic. [DNA metabolism, DNA replication, recombination, and repair] 297 matched cddid_all.tbl CDD TIGR00336 TIGR00336 129436 pyrE orotate phosphoribosyltransferase. Orotate phosphoribosyltransferase (OPRTase) is involved in the biosynthesis of pyrimidine nucleotides. Alpha-D-ribosyldiphosphate 5-phosphate (PRPP) and orotate are utilized to form pyrophosphate and orotidine 5'-monophosphate (OMP) in the presence of divalent cations, preferably Mg2+. In a number of eukaryotes, this protein is fused to a domain that catalyses the reaction (EC 4.1.1.23). The combined activity of EC 2.4.2.10 and EC 4.1.1.23 is termed uridine 5'-monophosphate synthase. The conserved Lys (K) residue at position 101 of the seed alignment has been proposed as the active site for the enzyme. [Purines, pyrimidines, nucleosides, and nucleotides, Pyrimidine ribonucleotide biosynthesis] 173 matched cddid_all.tbl CDD TIGR00337 TIGR00337 273021 PyrG CTP synthase. CTP synthase is involved in pyrimidine ribonucleotide/ribonucleoside metabolism. The enzyme catalyzes the reaction L-glutamine + H2O + UTP + ATP = CTP + phosphate + ADP + L-glutamate. The enzyme exists as a dimer of identical chains that aggregates as a tetramer. This gene has been found circa 500 bp 5' upstream of enolase in both beta (Nitrosomonas europaea) and gamma (E.coli) subdivisions of proteobacterium (FEMS Microbiol Lett 1998 Aug 1;165(1):153-7). [Purines, pyrimidines, nucleosides, and nucleotides, Pyrimidine ribonucleotide biosynthesis] 525 matched cddid_all.tbl CDD TIGR00338 TIGR00338 273022 serB phosphoserine phosphatase SerB. Phosphoserine phosphatase catalyzes the reaction 3-phospho-serine + H2O = L-serine + phosphate. It catalyzes the last of three steps in the biosynthesis of serine from D-3-phosphoglycerate. Note that this enzyme acts on free phosphoserine, not on phosphoserine residues of phosphoproteins. [Amino acid biosynthesis, Serine family] 219 matched cddid_all.tbl CDD TIGR00339 TIGR00339 273023 sopT ATP sulphurylase. This enzyme forms adenosine 5'-phosphosulfate (APS) from ATP and free sulfate, the first step in the formation of the activated sulfate donor 3'-phosphoadenylylsulfate (PAPS). In some cases, it is found in a bifunctional protein in which the other domain, APS kinase, catalyzes the second and final step, the phosphorylation of APS to PAPS; the combined ATP sulfurylase/APS kinase may be called PAPS synthase. Members of this family also include the dissimilatory sulfate adenylyltransferase (sat) of the sulfate reducer Archaeoglobus fulgidus. [Central intermediary metabolism, Sulfur metabolism] 383 matched cddid_all.tbl CDD TIGR00340 TIGR00340 129440 zpr1_rel ZPR1-related zinc finger protein. This model describes a strictly archaeal family homologous to the domain duplicated in the eukaryotic zinc-binding protein ZPR1. ZPR1 was shown experimentally to bind approximately two moles of zinc; each copy of the domain contains a putative zinc finger of the form CXXCX(25)CXXC. ZPR1 binds the tyrosine kinase domain of epidermal growth factor receptor, but is displaced by receptor activation and autophosphorylation after which it redistributes in part to the nucleus. The proteins described by this model by analogy may be suggested to play a role in signal transduction. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1. [Unknown function, General] 163 matched cddid_all.tbl CDD TIGR00341 TIGR00341 273024 TIGR00341 TIGR00341 family protein. This conserved hypothetical protein is found so far only in three archaeal genomes and in Streptomyces coelicolor. It shares a hydrophobic uncharacterized domain (see TIGR00271) of about 180 residues with several eubacterial proteins, including the much longer protein sll1151 of Synechocystis PCC6803. [Hypothetical proteins, Conserved] 325 matched cddid_all.tbl CDD TIGR00342 TIGR00342 273025 TIGR00342 "tRNA sulfurtransferase ThiI. Members of this protein family are ""ThiI"", a sulfurtransferase involved in 4-thiouridine modification of tRNA. This protein often is bifunctional, with genetically separable activities, where the C-terminal rhodanese-like domain (residues 385 to 482 in E. coli ThiI), a domain not included in this model, is sufficient to synthesize the thiazole moiety of thiamine (see TIGR04271). Note that ThiI, because of its role in tRNA modification, may occur in species (such as Mycoplasma genitalium) that lack de novo thiamine biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine, Protein synthesis, tRNA and rRNA base modification]" 371 matched cddid_all.tbl CDD TIGR00343 TIGR00343 129443 TIGR00343 pyridoxal 5'-phosphate synthase, synthase subunit Pdx1. This protein had been believed to be a singlet oxygen resistance protein. Subsequent work showed that it is a protein of pyridoxine (vitamin B6) biosynthesis, and that pyridoxine quenches the highly toxic singlet form of oxygen produced by light in the presence of certain chemicals. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridoxine] 287 matched cddid_all.tbl CDD TIGR00344 TIGR00344 273026 alaS alanine--tRNA ligase. The model describes alanine--tRNA ligase. This enzyme catalyzes the reaction (tRNAala + L-alanine + ATP = L-alanyl-tRNAala + pyrophosphate + AMP). [Protein synthesis, tRNA aminoacylation] 845 matched cddid_all.tbl CDD TIGR00345 TIGR00345 273027 GET3_arsA_TRC40 transport-energizing ATPase, TRC40/GET3/ArsA family. Members of this family are ATPases that energize transport, although with different partner proteins for different functions. Recent findings show that TRC40 (GET3 in yeast) in involved in the insertion of tail-anchored membrane proteins in eukaryotes. A similar function is expected for members of this family in archaea. However, the earliest discovery of a function for this protein family is ArsA, an arsenic resistance protein that partners with ArsB (see pfam02040) for As(III) efflux. [Hypothetical proteins, Conserved] 284 matched cddid_all.tbl CDD TIGR00346 TIGR00346 129446 azlC 4-azaleucine resistance probable transporter AzlC. Overexpression of this gene results in resistance to a leucine analog, 4-azaleucine. The protein has 5 potential transmembrane motifs. It has been inferred, but not experimentally demonstrated, to be part of a branched-chain amino acid transport system. Commonly found in association with azlD. [Transport and binding proteins, Amino acids, peptides and amines] 221 matched cddid_all.tbl CDD TIGR00347 TIGR00347 129447 bioD dethiobiotin synthase. Dethiobiotin synthase is involved in biotin biosynthesis and catalyses the reaction (CO2 + 7,8-diaminononanoate + ATP = dethiobiotin + phosphate + ADP). The enzyme binds ATP (see motif in first 12 residues of the SEED alignment) and requires magnesium as a co-factor. [Biosynthesis of cofactors, prosthetic groups, and carriers, Biotin] 166 matched cddid_all.tbl CDD TIGR00348 TIGR00348 273028 hsdR type I site-specific deoxyribonuclease, HsdR family. This gene is part of the type I restriction and modification system which is composed of three polypeptides R (restriction endonuclease), M (modification) and S (specificity). This group of enzymes recognize specific short DNA sequences and have an absolute requirement for ATP (or dATP) and S-adenosyl-L-methionine. They also catalyse the reactions of EC 2.1.1.72 and EC 2.1.1.73, with similar site specificity.(J. Mol. Biol. 271 (3), 342-348 (1997)). Members of this family are assumed to differ from each other in DNA site specificity. [DNA metabolism, Restriction/modification] 667 matched cddid_all.tbl CDD TIGR00350 TIGR00350 273029 lytR_cpsA_psr cell envelope-related function transcriptional attenuator common domain. This model describes a domain of unknown function that is found in the predicted extracellular domain of a number of putative membrane-bound proteins. One of these is proteins psr, described as a penicillin binding protein 5 (PDP-5) synthesis repressor. Another is Bacillus subtilis LytR, described as a transcriptional attenuator of itself and the LytABC operon, where LytC is N-acetylmuramoyl-L-alanine amidase. A third is CpsA, a putative regulatory protein involved in exocellular polysaccharide biosynthesis. Besides the region of strong similarily represented by this model, these proteins share the property of having a short putative N-terminal cytoplasmic domain and transmembrane domain forming a signal-anchor. [Regulatory functions, Other] 152 matched cddid_all.tbl CDD TIGR00351 TIGR00351 273030 narI respiratory nitrate reductase, gamma subunit. Involved in anerobic respiration the gene product catalyzes the reaction (reduced acceptor + NO3- = Acceptor + nitrite). Another possible role_id for this gene product is in nitrogen fixation (Role_id:160). [Energy metabolism, Anaerobic] 224 matched cddid_all.tbl CDD TIGR00353 TIGR00353 129451 nrfE c-type cytochrome biogenesis protein CcmF. The product of this gene is required for the biogenesis of C-type cytochromes. This gene is thought to have eleven transmembrane helices. Disruption of this gene in Paracoccus denitrificans, encoding a putative transporter, results in formation of an unstable apocytochrome c and deficiency in siderophore production. [Energy metabolism, Electron transport] 576 matched cddid_all.tbl CDD TIGR00354 TIGR00354 273031 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. [DNA metabolism, DNA replication, recombination, and repair] 1095 matched cddid_all.tbl CDD TIGR00355 TIGR00355 273032 purH phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase. PurH is bifunctional: IMP cyclohydrolase (EC 3.5.4.10); phosphoribosylaminoimidazolecarboxamide formyltransferase (EC 2.1.2.3) Involved in purine ribonucleotide biosynthesis. The IMP cyclohydrolase activity is in the N-terminal region. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 511 matched cddid_all.tbl CDD TIGR00357 TIGR00357 129454 TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested. [Protein fate, Protein modification and repair, Cellular processes, Adaptations to atypical conditions] 134 matched cddid_all.tbl CDD TIGR00358 TIGR00358 273033 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases. [Transcription, Degradation of RNA] 654 matched cddid_all.tbl CDD TIGR00359 TIGR00359 273034 cello_pts_IIC phosphotransferase system, cellobiose specific, IIC component. The family consists of the cellobiose specific form of the phosphotransferase system (PTS), IIC component. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids, Signal transduction, PTS] 423 matched cddid_all.tbl CDD TIGR00360 TIGR00360 273035 ComEC_N-term ComEC/Rec2-related protein. The related model ComEC_Rec2 (TIGR00361) describes a set of proteins of ~ 700-800 residues, one each from a number of different species, of which most can become competent for natural transformation with exogenous DNA. The best-studied examples are ComEC from Bacillus subtilis and Rec-2 from Haemophilus influenzae, where the protein appears to form part of the DNA import structure. This model represents a region found in full-length ComEC/Rec2 and shorter homologs of unknown function from large number of additional bacterial species, most of which are not known to become competent for transformation (an exception is Helicobacter pylori). [Unknown function, General] 171 matched cddid_all.tbl CDD TIGR00361 TIGR00361 273036 ComEC_Rec2 DNA internalization-related competence protein ComEC/Rec2. Apparant orthologs are found in 5 species so far (Haemophilus influenzae, Escherichia coli, Bacillus subtilis, Neisseria gonorrhoeae, Streptococcus pneumoniae), of which all but E. coli are model systems for the study of competence for natural transformation. This protein is a predicted multiple membrane-spanning protein likely to be involved in DNA internalization. In a large number of bacterial species not known to exhibit competence, this protein is replaced by a half-length N-terminal homolog of unknown function, modelled by the related model ComEC_N-term. The role for this protein in species that are not naturally transformable is unknown. [Cellular processes, DNA transformation] 662 matched cddid_all.tbl CDD TIGR00362 TIGR00362 273037 DnaA chromosomal replication initiator protein DnaA. DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006). [DNA metabolism, DNA replication, recombination, and repair] 437 matched cddid_all.tbl CDD TIGR00363 TIGR00363 129460 TIGR00363 lipoprotein, YaeC family. This family of putative lipoproteins contains a consensus site for lipoprotein signal sequence cleavage. Included in this family is the E. coli hypothetical protein yaeC. About half of the proteins between the noise and trusted cutoffs contain the consensus lipoprotein signature and may belong to this family. [Cell envelope, Other] 258 matched cddid_all.tbl CDD TIGR00364 TIGR00364 129461 TIGR00364 queuosine biosynthesis protein QueC. Members of this protein family are QueC, involved in synthesizing pre-Q0 from GTP en route to tRNA modification with queuosine. This protein family is represented by a single member in nearly every completed large (> 1000 genes) prokaryotic genome. In Rhizobium meliloti, the gene was designated exsB, possibly because of polar effects on exsA expression in a shared polycistronic mRNA. In Arthrobacter viscosus, the homologous gene was designated ALU1 and was associated with an aluminum tolerance phenotype. [Unknown function, General] 201 matched cddid_all.tbl CDD TIGR00365 TIGR00365 188046 TIGR00365 monothiol glutaredoxin, Grx4 family. The gene for the member of this glutaredoxin family in E. coli, originally designated ydhD, is now designated grxD. Its protein, Grx4, is a monothiol glutaredoxin similar to Grx5 of yeast, which is involved in iron-sulfur cluster formation. [Energy metabolism, Electron transport] 97 matched cddid_all.tbl CDD TIGR00366 TIGR00366 273038 TIGR00366 TIGR00366 family protein. [Hypothetical proteins, Conserved] 438 matched cddid_all.tbl CDD TIGR00367 TIGR00367 273039 TIGR00367 K+-dependent Na+/Ca+ exchanger related-protein. This model models a family of bacterial and archaeal proteins that is homologous, except for lacking a central region of ~ 250 amino acids and an N-terminal region of > 100 residues, to a functionally proven potassium-dependent sodium-calcium exchanger of the rat. [Unknown function, General] 307 matched cddid_all.tbl CDD TIGR00368 TIGR00368 129465 TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain. [Unknown function, General] 499 matched cddid_all.tbl CDD TIGR00369 TIGR00369 161843 unchar_dom_1 uncharacterized domain 1. Most proteins containing this domain consist almost entirely of a single copy of this domain. A protein from C. elegans consists of two tandem copies of the domain. The domain is also found as the N-terminal region of an apparent initiation factor eIF-2B alpha subunit of Aquifex aeolicus. The function of the domain is unknown. 117 matched cddid_all.tbl CDD TIGR00370 TIGR00370 129467 TIGR00370 sensor histidine kinase inhibitor, KipI family. [Hypothetical proteins, Conserved] 202 matched cddid_all.tbl CDD TIGR00372 TIGR00372 273040 cas4 CRISPR-associated protein Cas4. This model represents a family of proteins associated with CRISPR repeats in a wide set of prokaryotic genomes. This scope of this model has been broadened since it was first built to describe an archaeal subset only. The function of the protein is undefined. Distantly related proteins, excluded from this model, include ORFs from Mycobacteriophage D29 and Sulfolobus islandicus filamentous virus and a region of the Schizosaccharomyces pombe DNA replication helicase Dna2p. 178 matched cddid_all.tbl CDD TIGR00373 TIGR00373 129469 TIGR00373 transcription factor E. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain. [Transcription, Transcription factors] 158 matched cddid_all.tbl CDD TIGR00374 TIGR00374 129470 TIGR00374 conserved hypothetical protein. This model is built on a superfamily of proteins in the Archaea and in Aquifex aeolicus. The authenticity of homology can be seen in the presence of motifs in the alignment that include residues relatively rare among these sequences, even though the alignment includes long regions of low-complexity hydrophobic sequences. One apparent fusion protein contains a Glycos_transf_2 region in the N-terminal half of the protein and a region homologous to this superfamily in the C-terminal region. [Unknown function, General] 319 matched cddid_all.tbl CDD TIGR00375 TIGR00375 161657 TIGR00375 TIGR00375 family protein. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology. [Hypothetical proteins, Conserved] 374 matched cddid_all.tbl CDD TIGR00376 TIGR00376 273041 TIGR00376 DNA helicase, putative. The gene product may represent a DNA helicase. Eukaryotic members of this family have been characterized as binding certain single-stranded G-rich DNA sequences (GGGGT and GGGCT). A number of related proteins are characterized as helicases. [DNA metabolism, DNA replication, recombination, and repair] 636 matched cddid_all.tbl CDD TIGR00377 TIGR00377 273042 ant_ant_sig anti-anti-sigma factor. This superfamily includes small (105-125 residue) proteins related to SpoIIAA of Bacillus subtilis, an anti-anti-sigma factor. SpoIIAA can bind to and inhibit the anti-sigma F factor SpoIIAB. Also, it can be phosphorylated by SpoIIAB on a Ser residue at position 59 of the seed alignment. A similar arrangement is inferred for RsbV, an anti-anti-sigma factor for sigma B. This Ser is fairly well conserved within a motif resembling MXS[STA]G[VIL]X[VIL][VILF] among homologous known or predicted anti-anti-sigma factors. Regions similar to SpoIIAA and apparently homologous, but differing considerably near the phosphorlated Ser of SpoIIAA, appear in a single copy in several longer proteins. [Regulatory functions, Protein interactions] 108 matched cddid_all.tbl CDD TIGR00378 TIGR00378 273043 cax calcium/proton exchanger (cax). [Transport and binding proteins, Cations and iron carrying compounds] 349 matched cddid_all.tbl CDD TIGR00379 TIGR00379 273044 cobB cobyrinic acid a,c-diamide synthase. This model describes cobyrinic acid a,c-diamide synthase, the cobB (cbiA in Salmonella) protein of cobalamin biosynthesis. It is responsible for the amidation of carboxylic groups at positions A and C of either cobyrinic acid or hydrogenobrynic acid. NH(2) groups are provided by glutamine and one molecule of ATP hydrogenolyzed for each amidation. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 449 matched cddid_all.tbl CDD TIGR00380 TIGR00380 273045 cobD cobalamin biosynthesis protein CobD. This protein is involved in cobalamin (vitamin B12) biosynthesis and porphyrin biosynthesis. It converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group. It is part of the cob operon. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 305 matched cddid_all.tbl CDD TIGR00381 TIGR00381 273046 cdhD CO dehydrogenase/acetyl-CoA synthase, delta subunit. This is the small subunit of a heterodimer which catalyzes the reaction CO + H2O + Acceptor = CO2 + Reduced acceptor and is involved in the synthesis of acetyl-CoA from CO2 and H2. [Energy metabolism, Chemoautotrophy] 389 matched cddid_all.tbl CDD TIGR00382 TIGR00382 273047 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction. [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides] 413 matched cddid_all.tbl CDD TIGR00383 TIGR00383 273048 corA magnesium Mg(2+) and cobalt Co(2+) transport protein (corA). The article in Microb Comp Genomics 1998;3(3):151-69 discusses this family and suggests that some members may have functions other than Mg2+ transport. [Transport and binding proteins, Cations and iron carrying compounds] 318 matched cddid_all.tbl CDD TIGR00384 TIGR00384 273049 dhsB succinate dehydrogenase and fumarate reductase iron-sulfur protein. Succinate dehydrogenase and fumarate reductase are reverse directions of the same enzymatic interconversion, succinate + FAD+ = fumarate + FADH2 (EC 1.3.11.1). In E. coli, the forward and reverse reactions are catalyzed by distinct complexes: fumarate reductase operates under anaerobic conditions and succinate dehydrogenase operates under aerobic conditions. This model also describes a region of the B subunit of a cytosolic archaeal fumarate reductase. [Energy metabolism, Aerobic, Energy metabolism, Anaerobic, Energy metabolism, TCA cycle] 220 matched cddid_all.tbl CDD TIGR00385 TIGR00385 129481 dsbE periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily. Involved in the biogenesis of c-type cytochromes as well as in disulfide bond formation in some periplasmic proteins. [Protein fate, Protein folding and stabilization] 173 matched cddid_all.tbl CDD TIGR00387 TIGR00387 273050 glcD glycolate oxidase, subunit GlcD. This protein, the glycolate oxidase GlcD subunit, is similar in sequence to that of several D-lactate dehydrogenases, including that of E. coli. The glycolate oxidase has been found to have some D-lactate dehydrogenase activity. [Energy metabolism, Other] 413 matched cddid_all.tbl CDD TIGR00388 TIGR00388 129483 glyQ glycyl-tRNA synthetase, tetrameric type, alpha subunit. This tetrameric form of glycyl-tRNA synthetase (2 alpha, 2 beta) is found in the majority of completed eubacterial genomes, with the two genes fused in a few species. A substantially different homodimeric form (not recognized by this model) replaces this form in the Archaea, animals, yeasts, and some eubacteria. [Protein synthesis, tRNA aminoacylation] 293 matched cddid_all.tbl CDD TIGR00389 TIGR00389 273051 glyS_dimeric glycyl-tRNA synthetase, dimeric type. This model describes a glycyl-tRNA synthetase distinct from the two alpha and two beta chains of the tetrameric E. coli glycyl-tRNA synthetase. This enzyme is a homodimeric class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes His, Ser, Pro, and this set of glycyl-tRNA synthetases. [Protein synthesis, tRNA aminoacylation] 551 matched cddid_all.tbl CDD TIGR00390 TIGR00390 273052 hslU ATP-dependent protease HslVU, ATPase subunit. This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment) is Ser in other members of the seed alignment. [Protein fate, Protein folding and stabilization] 441 matched cddid_all.tbl CDD TIGR00391 TIGR00391 273053 hydA hydrogenase (NiFe) small subunit (hydA). Called (hupA/hydA/hupS/hoxK/vhtG) Involved in hydrogenase reactions performing different specific functions in different species eg (EC 1.12.2.1) in Desulfovibrio gigas,(EC 1.12.99.3) in Wolinella succinogenes and (EC 1.18.99.1) in E.coli and a number of other species and (EC 1.12.99.-) in the archea. [Energy metabolism, Electron transport] 365 matched cddid_all.tbl CDD TIGR00392 TIGR00392 273054 ileS isoleucyl-tRNA synthetase. The isoleucyl tRNA synthetase (IleS) is a class I amino acyl-tRNA ligase and is particularly closely related to the valyl tRNA synthetase. This model may recognize IleS from every species, including eukaryotic cytosolic and mitochondrial forms. [Protein synthesis, tRNA aminoacylation] 861 matched cddid_all.tbl CDD TIGR00393 TIGR00393 129488 kpsF KpsF/GutQ family protein. This model describes a number of closely related proteins with the phosphosugar-binding domain SIS (Sugar ISomerase) followed by two copies of the CBS (named after Cystathionine Beta Synthase) domain. One is GutQ, a protein of the glucitol operon. Another is KpsF, a virulence factor involved in capsular polysialic acid biosynthesis in some pathogenic strains of E. coli. [Energy metabolism, Sugars] 268 matched cddid_all.tbl CDD TIGR00394 TIGR00394 273055 lac_pts_IIC phosphotransferase system, lactose specific, IIC component. This family of proteins models the IIC domain of the phosphotransferase system (PTS) for lactose. The IIC domain catalyzes the transfer of a phosphoryl group from the IIB domain to lactose. When the IIC component and IIB components are in the same polypeptide chain they are designated IIBC. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids, Signal transduction, PTS] 412 matched cddid_all.tbl CDD TIGR00395 TIGR00395 273056 leuS_arch leucyl-tRNA synthetase, archaeal and cytosolic family. The leucyl-tRNA synthetases belong to two families so broadly different that they are represented by separate models. This model includes both archaeal and cytosolic eukaryotic leucyl-tRNA synthetases; the eubacterial and mitochondrial forms differ so substantially that some other tRNA ligases score higher by this model than does any eubacterial LeuS. [Protein synthesis, tRNA aminoacylation] 938 matched cddid_all.tbl CDD TIGR00396 TIGR00396 273057 leuS_bact leucyl-tRNA synthetase, eubacterial and mitochondrial family. The leucyl-tRNA synthetases belong to two families so broadly different that they are represented by separate models. This model includes both eubacterial and mitochondrial leucyl-tRNA synthetases. It generates higher scores for some valyl-tRNA synthetases than for any archaeal or eukaryotic cytosolic leucyl-tRNA synthetase. Note that the enzyme from Aquifex aeolicus is split into alpha and beta chains; neither chain is long enough to score above the trusted cutoff, but the alpha chain scores well above the noise cutoff. The beta chain must be found by a model and search designed for partial length matches. [Protein synthesis, tRNA aminoacylation] 842 matched cddid_all.tbl CDD TIGR00397 TIGR00397 129492 mauM_napG MauM/NapG family ferredoxin-type protein. MauM is involved in methylamine utilization. NapG is associated with nitrate reductase activity. The two proteins are highly similar. [Energy metabolism, Electron transport] 213 matched cddid_all.tbl CDD TIGR00398 TIGR00398 273058 metG methionine--tRNA ligase. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (small) subunit; this model does not include the C-terminal region corresponding to the beta chain. [Protein synthesis, tRNA aminoacylation] 530 matched cddid_all.tbl CDD TIGR00399 TIGR00399 273059 metG_C_term methionyl-tRNA synthetase C-terminal region/beta chain. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model describes a region of the methionyl-tRNA synthetase that is present at the C-terminus of MetG in some species (E. coli, B. subtilis, Thermotoga maritima, Methanobacterium thermoautotrophicum), and as a separate beta chain in Aquifex aeolicus. It is absent in a number of other species (e.g. Mycoplasma genitalium, Mycobacterium tuberculosis), while Pyrococcus horikoshii has both a full length MetG and a second protein homologous to the beta chain only. Proteins hit by this model should be called methionyl-tRNA synthetase beta chain if and only if the model metG hits a separate protein not also hit by this model. [Protein synthesis, tRNA aminoacylation] 137 matched cddid_all.tbl CDD TIGR00400 TIGR00400 129495 mgtE Mg2+ transporter (mgtE). This family of prokaryotic proteins models a class of Mg++ transporter first described in Bacillus firmus. May form a homodimer. [Transport and binding proteins, Cations and iron carrying compounds] 449 matched cddid_all.tbl CDD TIGR00401 TIGR00401 129496 msrA methionine-S-sulfoxide reductase. This model describes peptide methionine sulfoxide reductase (MsrA), a repair enzyme for proteins that have been inactivated by oxidation. The enzyme from E. coli is coextensive with this model and has enzymatic activity. However, in all completed genomes in which this module is present, a second protein module, described in TIGR00357, is also found, and in several cases as part of the same polypeptide chain: N-terminal to this module in Helicobacter pylori and Haemophilus influenzae (as in PilB of Neisseria gonorrhoeae) but C-terminal to it in Treponema pallidum. PilB, containing both domains, has been shown to be important for the expression of adhesins in certain pathogens. [Protein fate, Protein modification and repair, Cellular processes, Adaptations to atypical conditions] 149 matched cddid_all.tbl CDD TIGR00402 TIGR00402 273060 napF ferredoxin-type protein NapF. The gene codes for a ferredoxin-type cytosolic protein, NapF, of the periplasmic nitrate reductase system, as in Escherichia coli. NapF interacts with the catalytic subunit, NapA, and may be an accessory protein for NapA maturation. [Energy metabolism, Electron transport] 101 matched cddid_all.tbl CDD TIGR00403 TIGR00403 129498 ndhI NADH-plastoquinone oxidoreductase subunit I protein. [Energy metabolism, Electron transport] 183 matched cddid_all.tbl CDD TIGR00405 TIGR00405 129499 KOW_elon_Spt5 transcription elongation factor Spt5. This protein contains a KOW domain, shared by bacterial NusG and the uL24 (previously L24p/L26e) family of ribosomal proteins. The most recent papers and crystal structures make this a transcription elongation factor rather than a ribosomal protein. 145 matched cddid_all.tbl CDD TIGR00406 TIGR00406 273061 prmA ribosomal protein L11 methyltransferase. Ribosomal protein L11 methyltransferase is an S-adenosyl-L-methionine-dependent methyltransferase required for the modification of ribosomal protein L11. This protein is found in bacteria and (with a probable transit peptide) in Arabidopsis. [Protein synthesis, Ribosomal proteins: synthesis and modification] 288 matched cddid_all.tbl CDD TIGR00407 TIGR00407 161862 proA gamma-glutamyl phosphate reductase. The related model TIGR01092 describes a full-length fusion protein delta l-pyrroline-5-carboxylate synthetase that includes a gamma-glutamyl phosphate reductase region as described by this model. Alternate name: glutamate-5-semialdehyde dehydrogenase. The prosite motif begins at residue 332 of the seed alignment although not all of the members of the family exactly obey the motif. [Amino acid biosynthesis, Glutamate family] 398 matched cddid_all.tbl CDD TIGR00408 TIGR00408 273062 proS_fam_I prolyl-tRNA synthetase, family I. Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent families. This family includes the archaeal enzyme, the Pro-specific domain of a human multifunctional tRNA ligase, and the enzyme from the spirochete Borrelia burgdorferi. The other family includes enzymes from Escherichia coli, Bacillus subtilis, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae. [Protein synthesis, tRNA aminoacylation] 472 matched cddid_all.tbl CDD TIGR00409 TIGR00409 273063 proS_fam_II prolyl-tRNA synthetase, family II. Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent groups. This group includes enzymes from Escherichia coli, Bacillus subtilis, Aquifex aeolicus, the spirochete Treponema pallidum, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae. The other group includes the Pro-specific domain of a human multifunctional tRNA ligase and the prolyl-tRNA synthetases from the Archaea, the Mycoplasmas, and the spirochete Borrelia burgdorferi. [Protein synthesis, tRNA aminoacylation] 568 matched cddid_all.tbl CDD TIGR00410 TIGR00410 273064 lacE PTS system, lactose/cellobiose family IIC component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. This family of proteins consists of both the cellobiose specific and the lactose specific forms of the phosphotransferase system (PTS) IIC component. The IIC domain catalyzes the transfer of a phosphoryl group from the IIB domain to the substrate. When the IIC component and IIB components are in the same polypeptide chain they are designated IIBC. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids, Signal transduction, PTS] 423 matched cddid_all.tbl CDD TIGR00411 TIGR00411 129505 redox_disulf_1 small redox-active disulfide protein 1. This protein is homologous to a family of proteins that includes thioredoxins, glutaredoxins, protein-disulfide isomerases, and others, some of which have several such domains. The sequence of this protein at the redox-active disufide site, CPYC, matches glutaredoxins rather than thioredoxins, although its overall sequence seems closer to thioredoxins. It is suggested to be a ribonucleotide-reducing system component distinct from thioredoxin or glutaredoxin. [Unknown function, General] 82 matched cddid_all.tbl CDD TIGR00412 TIGR00412 129506 redox_disulf_2 small redox-active disulfide protein 2. This small protein is found in three archaeal species so far (Methanococcus jannaschii, Archeoglobus fulgidus, and Methanobacterium thermoautotrophicum) as well as in Anabaena PCC7120. It is homologous to thioredoxins, glutaredoxins, and protein disulfide isomerases, and shares with them a redox-active disulfide. The redox active disulfide region CXXC motif resembles neither thioredoxin nor glutaredoxin. A closely related protein found in the same three Archaea, described by redox_disulf_1, has a glutaredoxin-like CP[YH]C sequence; it has been characterized in functional assays as redox-active but unlikely to be a thioredoxin or glutaredoxin. [Unknown function, General] 76 matched cddid_all.tbl CDD TIGR00413 TIGR00413 273065 rlpA rare lipoprotein A. This is a family of prokaryotic proteins with unknown function. Lipoprotein annotation based on the presence of consensus lipoprotein signal sequence. Included in this family is the E. coli putative lipoprotein rlpA. [Cell envelope, Other] 208 matched cddid_all.tbl CDD TIGR00414 TIGR00414 273066 serS seryl-tRNA synthetase. This model represents the seryl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. The seryl-tRNA synthetases of two archaeal species, Methanococcus jannaschii and Methanobacterium thermoautotrophicum, differ considerably and are included in a different model. [Protein synthesis, tRNA aminoacylation] 418 matched cddid_all.tbl CDD TIGR00415 TIGR00415 129509 serS_MJ seryl-tRNA synthetase, Methanococcus jannaschii family. The seryl-tRNA synthetases from a few of the Archaea, represented by this model, are very different from the set of mutually more closely related seryl-tRNA synthetases from Eubacteria, Eukaryotes, and other Archaea. Although distantly homologous, the present set differs enough not to be recognized by the pfam model tRNA-synt_2b that recognizes the remainder of seryl-tRNA synthetases among oither class II amino-acyl tRNA synthetases. [Protein synthesis, tRNA aminoacylation] 520 matched cddid_all.tbl CDD TIGR00416 TIGR00416 273067 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus (SP:P45266) and in Listeria monocytogenes (SP:Q48761) . for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)). [DNA metabolism, DNA replication, recombination, and repair] 454 matched cddid_all.tbl CDD TIGR00417 TIGR00417 188048 speE spermidine synthase. the SpeE subunit of spermidine synthase catalysesthe reaction (putrescine + S-adenosylmethioninamine = spermidine + 5'-methylthioadenosine) and is involved in polyamine biosynthesis and in the biosynthesis of spermidine from arganine. The region between residues 77 and 120 of the seed alignment is thought to be involved in binding to decarboxylated SAM. [Central intermediary metabolism, Polyamine biosynthesis] 271 matched cddid_all.tbl CDD TIGR00418 TIGR00418 273068 thrS threonyl-tRNA synthetase. This model represents the threonyl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. Note that B. subtilis has closely related isozymes thrS and thrZ. The N-terminal regions are quite dissimilar between archaeal and eubacterial forms, while some eukaryotic forms are missing sequence there altogether. . [Protein synthesis, tRNA aminoacylation] 563 matched cddid_all.tbl CDD TIGR00419 TIGR00419 129513 tim triosephosphate isomerase. Triosephosphate isomerase (tim/TPIA) is the glycolytic enzyme that catalyzes the reversible interconversion of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. The active site of the enzyme is located between residues 240-258 of the model ([AV]-Y-E-P-[LIVM]-W-[SA]-I-G-T-[GK]) with E being the active site residue. There is a slight deviation from this sequence within the archeal members of this family. [Energy metabolism, Glycolysis/gluconeogenesis] 205 matched cddid_all.tbl CDD TIGR00420 TIGR00420 273069 trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase. tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (trmU, asuE, or mnmA) is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine (mnm5s2U34) present in the wobble position of some tRNAs. This enzyme appears not to occur in the Archaea. [Protein synthesis, tRNA and rRNA base modification] 352 matched cddid_all.tbl CDD TIGR00421 TIGR00421 129515 ubiX_pad UbiX family flavin prenyltransferase. UbiX partners with UbiD for decarboxylation of the 3-octaprenyl-4-hydroxybenzoate precursor during ubiquinone biosynthesis, but the role of UbiX is as a flavin prenyltransferase that provides a cofactor UbiD requires.In E.coli, the protein UbiX (3-octaprenyl-4-hydroxybenzoate carboxy-lyase) has been shown to be involved in the third step of ubiquinone biosynthesis, the reaction [3-octaprenyl-4-hydroxybenzoate = 2-octaprenylphenol + CO2]. The knockout of the homologous protein in yeast confers sensitivity to phenylacrylic acid. Members are not restricted to ubiquinone-synthesizing species. This family represents a distinct clade within the flavoprotein family of pfam02441. 181 matched cddid_all.tbl CDD TIGR00422 TIGR00422 273070 valS valyl-tRNA synthetase. The valyl-tRNA synthetase (ValS) is a class I amino acyl-tRNA ligase and is particularly closely related to the isoleucyl tRNA synthetase. [Protein synthesis, tRNA aminoacylation] 861 matched cddid_all.tbl CDD TIGR00423 TIGR00423 273071 TIGR00423 radical SAM domain protein, CofH subfamily. This protein family includes the CofH protein of coenzyme F(420) biosynthesis from Methanocaldococcus jannaschii, but appears to hit genomes more broadly than just the subset that make coenzyme F(420), so that narrower group is being built as a separate family. [Hypothetical proteins, Conserved] 309 matched cddid_all.tbl CDD TIGR00424 TIGR00424 273072 APS_reduc 5'-adenylylsulfate reductase, thioredoxin-independent. This enzyme, involved in the assimilation of inorganic sulfate, is closely related to the thioredoxin-dependent PAPS reductase of Bacteria (CysH) and Saccharomyces cerevisiae. However, it has its own C-terminal thioredoxin-like domain and is not thioredoxin-dependent. Also, it has a substrate preference for 5'-adenylylsulfate (APS) over 3'-phosphoadenylylsulfate (PAPS) so the pathway does not require an APS kinase (CysC) to convert APS to PAPS. Arabidopsis thaliana appears to have three isozymes, all able to complement E. coli CysH mutants (even in backgrounds lacking thioredoxin or APS kinase) but likely localized to different compartments in Arabidopsis. [Central intermediary metabolism, Sulfur metabolism] 463 matched cddid_all.tbl CDD TIGR00425 TIGR00425 273073 CBF5 rRNA pseudouridine synthase, putative. This family, found in archaea and eukaryotes, includes the only archaeal proteins markedly similar to bacterial TruB, the tRNA pseudouridine 55 synthase. However, among two related yeast proteins, the archaeal set matches yeast YLR175w far better than YNL292w. The first, termed centromere/microtubule binding protein 5 (CBF5), is an apparent rRNA pseudouridine synthase, while the second is the exclusive tRNA pseudouridine 55 synthase for both cytosolic and mitochondrial compartments. It is unclear whether archaeal proteins found by this model modify tRNA, rRNA, or both. [Protein synthesis, tRNA and rRNA base modification] 322 matched cddid_all.tbl CDD TIGR00426 TIGR00426 129520 TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model. [Cellular processes, DNA transformation] 69 matched cddid_all.tbl CDD TIGR00427 TIGR00427 129521 TIGR00427 membrane protein, MarC family. MarC is a protein that spans the plasma membrane multiple times and once was thought to be a multiple antibiotic resistance protein. The function for this family is unknown. [Unknown function, General] 201 matched cddid_all.tbl CDD TIGR00430 TIGR00430 129522 Q_tRNA_tgt tRNA-guanine transglycosylase. This tRNA-guanine transglycosylase (tgt) catalyzes an exchange for the guanine base at position 34 of many tRNAs; this nucleotide is subsequently modified to queuosine. The Archaea have a closely related enzyme that catalyzes a base exchange for guanine at position 15 in some tRNAs, a site that is subsequently converted to the archaeal-specific modified base archaeosine (7-formamidino-7-deazaguanosine), while Archaeoglobus fulgidus has both enzymes. [Protein synthesis, tRNA and rRNA base modification] 368 matched cddid_all.tbl CDD TIGR00431 TIGR00431 129523 TruB tRNA pseudouridine(55) synthase. TruB, the tRNA pseudouridine 55 synthase, converts uracil to pseudouridine in the T loop of most tRNAs in all three domains of life. This model is built on a seed alignment of bacterial proteins only. Saccharomyces cerevisiae protein YNL292w (Pus4) has been shown to be the pseudouridine 55 synthase of both cytosolic and mitochondrial compartments, active at no other position on tRNA and the only enzyme active at that position in the species. A distinct yeast protein YLR175w, (centromere/microtubule-binding protein CBF5) is an rRNA pseudouridine synthase, and the archaeal set is much more similar to CBF5 than to Pus4. It is unclear whether the archaeal proteins found by this model are tRNA pseudouridine 55 synthases like TruB, rRNA pseudouridine synthases like CBF5, or (as suggested by the absence of paralogs in the Archaea) both. CBF5 likely has additional, eukaryotic-specific functions. The trusted cutoff is set above the scores for the archaeal homologs of unknown function, so yeast Pus4p scores between trusted and noise. [Protein synthesis, tRNA and rRNA base modification] 209 matched cddid_all.tbl CDD TIGR00432 TIGR00432 273074 arcsn_tRNA_tgt tRNA-guanine(15) transglycosylase. This tRNA-guanine transglycosylase (tgt) differs from the tgt of E. coli and other Bacteria in the site of action and the modification that results. It exchanges 7-cyano-7-deazaguanine (preQ0) with guanine at position 15 of archaeal tRNA; this nucleotide is subsequently converted to archaeosine, found exclusively in the Archaea. This enzyme from Haloferax volcanii has been purified, characterized, and partially sequenced and is the basis for identifying this family. In contrast, bacterial tgt (TIGR00430) catalyzes the exchange of preQ0 or preQ1 for the guanine base at position 34; this nucleotide is subsequently modified to queuosine. Archeoglobus fulgidus has both enzymes, while some other Archaea have just this one. [Protein synthesis, tRNA and rRNA base modification] 540 matched cddid_all.tbl CDD TIGR00433 TIGR00433 273075 bioB biotin synthase. Catalyzes the last step of the biotin biosynthesis pathway. All members of the seed alignment are in the immediate gene neighborhood of a bioA gene. [Biosynthesis of cofactors, prosthetic groups, and carriers, Biotin] 296 matched cddid_all.tbl CDD TIGR00434 TIGR00434 129526 cysH phosophoadenylyl-sulfate reductase (thioredoxin). This enzyme, involved in the assimilation of inorganic sulfate, is designated cysH in Bacteria and MET16 in Saccharomyces cerevisiae. Synonyms include phosphoadenosine phosphosulfate reductase, PAPS reductase, and PAPS reductase, thioredoxin-dependent. In a reaction requiring reduced thioredoxin and NADPH, it converts 3(prime)-phosphoadenylylsulfate (PAPS) to sulfite and adenosine 3(prime),5(prime) diphosphate (PAP). A related family of plant enzymes, scoring below the trusted cutoff, differs in having a thioredoxin-like C-terminal domain, not requiring thioredoxin, and in having a preference for 5(prime)-adenylylsulfate (APS) over PAPS. [Central intermediary metabolism, Sulfur metabolism] 212 matched cddid_all.tbl CDD TIGR00435 TIGR00435 273076 cysS cysteinyl-tRNA synthetase. This model finds the cysteinyl-tRNA synthetase from most but not from all species. The enzyme from one archaeal species, Archaeoglobus fulgidus, is found but the equivalent enzymes from some other Archaea, including Methanococcus jannaschii, are not found, although biochemical evidence suggests that tRNA(Cys) in these species are charged directly with Cys rather than through a misacylation and correction pathway as for tRNA(Gln). [Protein synthesis, tRNA aminoacylation] 464 matched cddid_all.tbl CDD TIGR00436 TIGR00436 129528 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein. [Protein synthesis, Other] 270 matched cddid_all.tbl CDD TIGR00437 TIGR00437 273077 feoB ferrous iron transporter FeoB. FeoB (773 amino acids in E. coli), a cytoplasmic membrane protein required for iron(II) update, is encoded in an operon with FeoA (75 amino acids), which is also required, and is regulated by Fur. There appear to be two copies in Archaeoglobus fulgidus and Clostridium acetobutylicum. [Transport and binding proteins, Cations and iron carrying compounds] 591 matched cddid_all.tbl CDD TIGR00438 TIGR00438 273078 rrmJ cell division protein FtsJ. Methylates the 23S rRNA. Previously known as cell division protein ftsJ.// Trusted cutoff too high? [SS 10/1/04] [Protein synthesis, tRNA and rRNA base modification] 188 matched cddid_all.tbl CDD TIGR00439 TIGR00439 129531 ftsX putative protein insertion permease FtsX. FtsX is an integral membrane protein encoded in the same operon as signal recognition particle docking protein FtsY and FtsE. It belongs to a family of predicted permeases and may play a role in the insertion of proteins required for potassium transport, cell division, and other activities. FtsE is a hydrophilic nucleotide-binding protein that associates with the inner membrane by means of association with FtsX. [Cellular processes, Cell division, Protein fate, Protein and peptide secretion and trafficking] 309 matched cddid_all.tbl CDD TIGR00440 TIGR00440 273079 glnS glutaminyl-tRNA synthetase. This protein is a relatively rare aminoacyl-tRNA synthetase, found in the cytosolic compartment of eukaryotes, in E. coli and a number of other Gram-negative Bacteria, and in Deinococcus radiodurans. In contrast, the pathway to Gln-tRNA in mitochondria, Archaea, Gram-positive Bacteria, and a number of other lineages is by misacylation with Glu followed by transamidation to correct the aminoacylation to Gln. This enzyme is a class I tRNA synthetase (hit by the pfam model tRNA-synt_1c) and is quite closely related to glutamyl-tRNA synthetases. [Protein synthesis, tRNA aminoacylation] 522 matched cddid_all.tbl CDD TIGR00441 TIGR00441 129533 gmhA phosphoheptose isomerase. This model describes phosphoheptose isomerase. Because a closely related paralo in Escherichia coli differs in function (DnaA initiator-associating protein diaA), this model has been rebuilt with a high stringency, and is likely to miss many true examples for phosphoheptose isomerase. Involved in lipopolysaccharide biosynthesis it may have a role in virulence in Haemophilus ducreyi. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 154 matched cddid_all.tbl CDD TIGR00442 TIGR00442 273080 hisS histidyl-tRNA synthetase. This model finds a histidyl-tRNA synthetase in every completed genome. Apparent second copies from Bacillus subtilis, Synechocystis sp., and Aquifex aeolicus are slightly shorter, more closely related to each other than to other hisS proteins, and actually serve as regulatory subunits for an enzyme of histidine biosynthesis. They were excluded from the seed alignment and score much lower than do single copy histidyl-tRNA synthetases of other genomes not included in the seed alignment. These putative second copies of HisS score below the trusted cutoff. The regulatory protein kinase GCN2 of Saccharomyces cerevisiae (YDR283c), and related proteins from other species designated eIF-2 alpha kinase, have a domain closely related to histidyl-tRNA synthetase that may serve to detect and respond to uncharged tRNA(his), an indicator of amino acid starvation; these regulatory proteins are not orthologous and so score below the noise cutoff. [Protein synthesis, tRNA aminoacylation] 404 matched cddid_all.tbl CDD TIGR00443 TIGR00443 273081 hisZ_biosyn_reg ATP phosphoribosyltransferase, regulatory subunit. Apparant second copies of histidyl-tRNA synthetase, found in Bacillus subtilis, Synechocystis sp., Aquifex aeolicus, and others, are in fact a regulatory subunit of ATP phosphoribosyltransferase, and usually encoded by a gene adjacent to that encoding the catalytic subunit. [Amino acid biosynthesis, Histidine family] 313 matched cddid_all.tbl CDD TIGR00444 TIGR00444 273082 mazG MazG family protein. This family of prokaryotic proteins has no known function. It includes the uncharacterized protein MazG in E. coli. [Unknown function, General] 248 matched cddid_all.tbl CDD TIGR00445 TIGR00445 161884 mraY phospho-N-acetylmuramoyl-pentapeptide-transferase. Involved in peptidoglycan biosynthesis, the enzyme catalyzes the first of the lipid cycle reactions. Also known as Muramoyl-Pentapeptide Transferase (murX). [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 321 matched cddid_all.tbl CDD TIGR00446 TIGR00446 188051 nop2p NOL1/NOP2/sun family putative RNA methylase. [Protein synthesis, tRNA and rRNA base modification] 264 matched cddid_all.tbl CDD TIGR00447 TIGR00447 213531 pth aminoacyl-tRNA hydrolase. The natural substrate for this enzyme may be peptidyl-tRNAs that drop off the ribosome during protein synthesis. Peptidyl-tRNA hydrolase is a bacterial protein; YHR189W from Saccharomyces cerevisiae appears to be orthologous and likely has the same function. [Protein synthesis, Other] 188 matched cddid_all.tbl CDD TIGR00448 TIGR00448 129540 rpoE DNA-directed RNA polymerase (rpoE), archaeal and eukaryotic form. This family seems to be confined to the archea and eukaryotic taxa and are quite dissimilar to E.coli rpoE. [Transcription, DNA-dependent RNA polymerase] 179 matched cddid_all.tbl CDD TIGR00449 TIGR00449 129541 tgt_general tRNA-guanine family transglycosylase. Different tRNA-guanine transglycosylases catalyze different tRNA base modifications. Two guanine base substitutions by different enzymes described by the model are involved in generating queuosine at position 34 in bacterial tRNAs and archaeosine at position 15 in archaeal tRNAs. This model is designed for fragment searching, so the superfamily is used loosely. [Protein synthesis, tRNA and rRNA base modification] 367 matched cddid_all.tbl CDD TIGR00450 TIGR00450 273083 mnmE_trmE_thdF tRNA modification GTPase TrmE. TrmE, also called MnmE and previously designated ThdF (thiophene and furan oxidation protein), is a GTPase involved in tRNA modification to create 5-methylaminomethyl-2-thiouridine in the wobble position of some tRNAs. This protein and GidA form an alpha2/beta2 heterotetramer. [Protein synthesis, tRNA and rRNA base modification] 442 matched cddid_all.tbl CDD TIGR00451 TIGR00451 129543 unchar_dom_2 uncharacterized domain 2. This uncharacterized domain is found a number of enzymes and uncharacterized proteins, often at the C-terminus. It is found in some but not all members of a family of related tRNA-guanine transglycosylases (tgt), which exchange a guanine base for some modified base without breaking the phosphodiester backbone of the tRNA. It is also found in rRNA pseudouridine synthase, another enzyme of RNA base modification not otherwise homologous to tgt. It is found, again at the C-terminus, in two putative glutamate 5-kinases. It is also found in a family of small, uncharacterized archaeal proteins consisting mostly of this domain. 107 matched cddid_all.tbl CDD TIGR00452 TIGR00452 273084 TIGR00452 tRNA (mo5U34)-methyltransferase. This model describes CmoB, the enzyme tRNA (mo5U34)-methyltransferase involved in tRNA wobble base modification. [Unknown function, Enzymes of unknown specificity] 316 matched cddid_all.tbl CDD TIGR00453 TIGR00453 213532 ispD 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase. Members of this protein family are 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, the IspD protein of the deoxyxylulose pathway of IPP biosynthesis. In about twenty percent of bacterial genomes, this protein occurs as IspDF, a bifunctional fusion protein. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 217 matched cddid_all.tbl CDD TIGR00454 TIGR00454 200016 TIGR00454 TIGR00454 family protein. At this time this gene appears to be present only in Archea [Hypothetical proteins, Conserved] 175 matched cddid_all.tbl CDD TIGR00455 TIGR00455 129547 apsK adenylyl-sulfate kinase. This protein, adenylylsulfate kinase, is often found as a fusion protein with sulfate adenylyltransferase. Important residue (active site in E.coli) is residue 100 of the seed alignment. [Central intermediary metabolism, Sulfur metabolism] 184 matched cddid_all.tbl CDD TIGR00456 TIGR00456 273085 argS arginyl-tRNA synthetase. This model recognizes arginyl-tRNA synthetase in every completed genome to date. An interesting feature of the alignment of all arginyl-tRNA synthetases is a fairly deep split between two families. One family includes archaeal, eukaryotic and organellar, spirochete, E. coli, and Synechocystis sp. The second, sharing a deletion of about 25 residues in the central region relative to the first, includes Bacillus subtilis, Aquifex aeolicus, the Mycoplasmas and Mycobacteria, and the Gram-negative bacterium Helicobacter pylori. [Protein synthesis, tRNA aminoacylation] 563 matched cddid_all.tbl CDD TIGR00457 TIGR00457 273086 asnS asparaginyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn. [Protein synthesis, tRNA aminoacylation] 453 matched cddid_all.tbl CDD TIGR00458 TIGR00458 273087 aspS_nondisc nondiscriminating aspartyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). [Protein synthesis, tRNA aminoacylation] 428 matched cddid_all.tbl CDD TIGR00459 TIGR00459 211576 aspS_bact aspartyl-tRNA synthetase, bacterial type. Asparate--tRNA ligases in this family may be discriminating (6.1.1.12) or nondiscriminating (6.1.1.23). In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_bact, represents aspartyl-tRNA synthetases from the Bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). This model generates very low scores for the archaeal type of aspS and for asnS; scores between the trusted and noise cutoffs represent fragmentary sequences. [Protein synthesis, tRNA aminoacylation] 583 matched cddid_all.tbl CDD TIGR00460 TIGR00460 273088 fmt methionyl-tRNA formyltransferase. The top-scoring characterized proteins other than methionyl-tRNA formyltransferase (fmt) itself are formyltetrahydrofolate dehydrogenases. The mitochondrial methionyl-tRNA formyltransferases are so divergent that, in a multiple alignment of bacterial fmt, mitochondrial fmt, and formyltetrahydrofolate dehydrogenases, the mitochondrial fmt appears the most different. However, because both bacterial and mitochondrial fmt are included in the seed alignment, all credible fmt sequences score higher than any non-fmt sequence. This enzyme modifies Met on initiator tRNA to f-Met. [Protein synthesis, tRNA aminoacylation] 313 matched cddid_all.tbl CDD TIGR00461 TIGR00461 273089 gcvP glycine dehydrogenase (decarboxylating). This apparently ubiquitous enzyme is found in bacterial, mammalian and plant sources. The enzyme catalyzes the reaction: GLYCINE + LIPOYLPROTEIN = S-AMINOMETHYL-DIHYDROLIPOYLPROTEIN + CO2. It is part of the glycine decarboxylase multienzyme complex (GDC) consisting of four proteins P, H, L and T. Active site in E.coli is located as the (K) residues at position 713 of the SEED alignment. [Energy metabolism, Amino acids and amines] 939 matched cddid_all.tbl CDD TIGR00462 TIGR00462 273090 genX EF-P lysine aminoacylase GenX. Many Gram-negative bacteria have a protein closely homologous to the C-terminal region of lysyl-tRNA synthetase (LysS). Multiple sequence alignment of these proteins with the homologous regions of collected LysS proteins shows that these proteins form a distinct set rather than just similar truncations of LysS. The protein is termed GenX after its designation in E. coli. Interestingly, genX often is located near a homolog of lysine-2,3-aminomutase. Its function is unknown. [Unknown function, General] 290 matched cddid_all.tbl CDD TIGR00463 TIGR00463 273091 gltX_arch glutamyl-tRNA synthetase, archaeal and eukaryotic family. The glutamyl-tRNA synthetases of the eukaryotic cytosol and of the Archaea are more similar to glutaminyl-tRNA synthetases than to bacterial glutamyl-tRNA synthetases. This model models just the eukaryotic cytosolic and archaeal forms of the enzyme. In some eukaryotes, the glutamyl-tRNA synthetase is part of a longer, multifunctional aminoacyl-tRNA ligase. In many species, the charging of tRNA(gln) proceeds first through misacylation with Glu and then transamidation. For this reason, glutamyl-tRNA synthetases, including all known archaeal enzymes (as of 2010) may act on both tRNA(gln) and tRNA(glu). [Protein synthesis, tRNA aminoacylation] 556 matched cddid_all.tbl CDD TIGR00464 TIGR00464 273092 gltX_bact glutamyl-tRNA synthetase, bacterial family. The glutamyl-tRNA synthetases of the eukaryotic cytosol and of the Archaea are more similar to glutaminyl-tRNA synthetases than to bacterial glutamyl-tRNA synthetases. This model models just the bacterial and mitochondrial forms of the enzyme. In many species, the charging of tRNA(gln) proceeds first through misacylation with Glu and then transamidation. For this reason, glutamyl-tRNA synthetases may act on both tRNA(gln) and tRNA(glu). This model is highly specific. Proteins with positive scores below the trusted cutoff may be fragments rather than full-length sequences. [Protein synthesis, tRNA aminoacylation] 470 matched cddid_all.tbl CDD TIGR00465 TIGR00465 273093 ilvC ketol-acid reductoisomerase. This is the second enzyme in the parallel isoleucine-valine biosynthetic pathway [Amino acid biosynthesis, Pyruvate family] 314 matched cddid_all.tbl CDD TIGR00466 TIGR00466 129558 kdsB 3-deoxy-D-manno-octulosonate cytidylyltransferase. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 238 matched cddid_all.tbl CDD TIGR00467 TIGR00467 273094 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set. [Protein synthesis, tRNA aminoacylation] 515 matched cddid_all.tbl CDD TIGR00468 TIGR00468 273095 pheS phenylalanyl-tRNA synthetase, alpha subunit. Most phenylalanyl-tRNA synthetases are heterodimeric, with 2 alpha (pheS) and 2 beta (pheT) subunits. This model describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this model. An interesting feature of the alignment of all sequences captured by this model is a deep split between non-spirochete bacterial examples and all other examples; supporting this split is a relative deletion of about 50 residues in the former set between two motifs well conserved throughout the alignment. [Protein synthesis, tRNA aminoacylation] 293 matched cddid_all.tbl CDD TIGR00469 TIGR00469 129561 pheS_mito phenylalanyl-tRNA synthetase, mitochondrial. Unlike all other known phenylalanyl-tRNA synthetases, the mitochondrial form demonstrated from yeast is monomeric. It is similar to but longer than the alpha subunit (PheS) of the alpha 2 beta 2 form found in Bacteria, Archaea, and eukaryotes, and shares the characteristic motifs of class II aminoacyl-tRNA ligases. This model models the experimental example from Saccharomyces cerevisiae (designated MSF1) and its orthologs from other eukaryotic species. [Protein synthesis, tRNA aminoacylation] 460 matched cddid_all.tbl CDD TIGR00470 TIGR00470 129562 sepS O-phosphoserine--tRNA ligase. This family of archaeal proteins resembles known phenylalanyl-tRNA synthetase alpha chains. Recently, it was shown to act in a proposed pathway of tRNA(Cys) indirect aminoacylation, resulting in Cys biosynthesis from O-phosphoserine, in certain archaea. It charges tRNA(Cys) with O-phosphoserine. The pscS gene product converts the phosphoserine to Cys. [Amino acid biosynthesis, Serine family, Protein synthesis, tRNA aminoacylation] 533 matched cddid_all.tbl CDD TIGR00471 TIGR00471 273096 pheT_arch phenylalanyl-tRNA synthetase, beta subunit. Every known example of the phenylalanyl-tRNA synthetase, except the monomeric form of mitochondrial, is an alpha 2 beta 2 heterotetramer. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps. This model represents the subfamily that includes the beta subunit from eukaryotic cytosol, the Archaea, and spirochetes. [Protein synthesis, tRNA aminoacylation] 551 matched cddid_all.tbl CDD TIGR00472 TIGR00472 273097 pheT_bact phenylalanyl-tRNA synthetase, beta subunit, non-spirochete bacterial. Every known example of the phenylalanyl-tRNA synthetase, except the monomeric form of mitochondrial, is an alpha 2 beta 2 heterotetramer. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps. This model represents the subfamily that includes the beta subunit from Bacteria other than spirochetes, as well as a chloroplast-encoded form from Porphyra purpurea. The chloroplast-derived sequence is considerably shorter at the amino end. [Protein synthesis, tRNA aminoacylation] 797 matched cddid_all.tbl CDD TIGR00473 TIGR00473 273098 pssA CDP-diacylglycerol--serine O-phosphatidyltransferase. This enzyme, CDP-diacylglycerol--serine O-phosphatidyltransferase, is involved in phospholipid biosynthesis catalyzing the reaction CDP-diacylglycerol + L-serine = CMP + L-1-phosphatidylserine. Members of this family do not bear any significant sequence similarity to the corresponding E.coli protein. [Fatty acid and phospholipid metabolism, Biosynthesis] 151 matched cddid_all.tbl CDD TIGR00474 TIGR00474 273099 selA L-seryl-tRNA(Sec) selenium transferase. In bacteria, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes SelA. This model excludes homologs that appear to differ in function from Frankia alni, Helicobacter pylori, Methanococcus jannaschii and other archaea, and so on. [Protein synthesis, tRNA aminoacylation] 454 matched cddid_all.tbl CDD TIGR00475 TIGR00475 129567 selB selenocysteine-specific elongation factor SelB. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes. [Protein synthesis, Translation factors] 581 matched cddid_all.tbl CDD TIGR00476 TIGR00476 273100 selD selenium donor protein. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes SelD, known as selenophosphate synthetase, selenium donor protein, and selenide,water dikinase. SelD provides reduced selenium for the selenium transferase SelA. This protein itself contains selenocysteine in many species; any sequence scoring well but not aligning to the beginning of the model is likely to have a selenocysteine residue incorrectly interpreted as a stop codon upstream of the given sequence. The SelD protein also provides selenophosphate for the enzyme tRNA 2-selenouridine synthase, which catalyzes a tRNA base modification. It also contributes to selenium incorporation by selenium-dependent molybdenum hydroxylases (SDMH), in genomes with the marker TIGR03309. All genomes with SelD should make selenocysteine, selenouridine, SDMH, or some combination. 301 matched cddid_all.tbl CDD TIGR00477 TIGR00477 188054 tehB tellurite resistance protein TehB. Part of a tellurite-reducing operon tehA and tehB [Cellular processes, Toxin production and resistance] 195 matched cddid_all.tbl CDD TIGR00478 TIGR00478 129570 tly TlyA family rRNA methyltransferase/putative hemolysin. Members of this family include TlyA from Mycobacterium tuberculosis, an rRNA methylase whose modifications are necessary to confer sensitivity to ribosome-targeting antibiotics capreomycin and viomycin. Homology supports identification as a methyltransferase. However, a parallel literature persists in calling some members hemolysins. Hemolysins are exotoxins that attack blood cell membranes and cause cell rupture, often by forming a pore in the membrane. A recent study (2013) on SCO1782 from Streptomyces coelicolor shows hemolysin activity as earlier described for a homolog from the spirochete Serpula (Treponema) hyodysenteriae and one from Mycobacterium tuberculosis. [Unknown function, General] 228 matched cddid_all.tbl CDD TIGR00479 TIGR00479 129571 rumA 23S rRNA (uracil-5-)-methyltransferase RumA. This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA. [Protein synthesis, tRNA and rRNA base modification] 431 matched cddid_all.tbl CDD TIGR00481 TIGR00481 129572 TIGR00481 Raf kinase inhibitor-like protein, YbhB/YbcL family. [Unknown function, General] 141 matched cddid_all.tbl CDD TIGR00482 TIGR00482 273101 TIGR00482 nicotinate (nicotinamide) nucleotide adenylyltransferase. This model represents the predominant bacterial/eukaryotic adenylyltransferase for nicotinamide-nucleotide, its deamido form nicotinate nucleotide, or both. The first activity, nicotinamide-nucleotide adenylyltransferase (EC 2.7.7.1), synthesizes NAD by the salvage pathway, while the second, nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18) synthesizes the immediate precursor of NAD by the de novo pathway. In E. coli, NadD activity is biased toward the de novo pathway while salvage activity is channeled through the multifunctional NadR protein, but this division of labor may be exceptional. The given name of this model, nicotinate (nicotinamide) nucleotide adenylyltransferase, reflects the lack of absolute specificity with respect to substrate amidation state in most species. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridine nucleotides] 193 matched cddid_all.tbl CDD TIGR00483 TIGR00483 129574 EF-1_alpha translation elongation factor EF-1 alpha. This model represents the counterpart of bacterial EF-Tu for the Archaea (aEF-1 alpha) and Eukaryotes (eEF-1 alpha). The trusted cutoff is set fairly high so that incomplete sequences will score between suggested and trusted cutoff levels. [Protein synthesis, Translation factors] 426 matched cddid_all.tbl CDD TIGR00484 TIGR00484 129575 EF-G translation elongation factor EF-G. After peptide bond formation, this elongation factor of bacteria and organelles catalyzes the translocation of the tRNA-mRNA complex, with its attached nascent polypeptide chain, from the A-site to the P-site of the ribosome. Every completed bacterial genome has at least one copy, but some species have additional EF-G-like proteins. The closest homolog to canonical (e.g. E. coli) EF-G in the spirochetes clusters as if it is derived from mitochondrial forms, while a more distant second copy is also present. Synechocystis PCC6803 has a few proteins more closely related to EF-G than to any other characterized protein. Two of these resemble E. coli EF-G more closely than does the best match from the spirochetes; it may be that both function as authentic EF-G. [Protein synthesis, Translation factors] 689 matched cddid_all.tbl CDD TIGR00485 TIGR00485 129576 EF-Tu translation elongation factor TU. This model models orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts, one of several GTP-binding translation factors found by the more general pfam model GTP_EFTU. The eukaryotic conterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this model. EF-Tu is one of the most abundant proteins in bacteria, as well as one of the most highly conserved, and in a number of species the gene is duplicated with identical function. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors. Transfer RNA is carried to the ribosome in these complexes for protein translation. [Protein synthesis, Translation factors] 394 matched cddid_all.tbl CDD TIGR00486 TIGR00486 213534 YbgI_SA1388 dinuclear metal center protein, YbgI/SA1388 family. The characterization of this family of uncharacterized proteins as orthologous is tentative. Members are found in all three domains of life. Several members (from Bacillus subtilis, Listeria monocytogenes, and Mycobacterium tuberculosis - all classified as Firmicutes within the Eubacteria) share a long insert relative to other members. [Unknown function, General] 249 matched cddid_all.tbl CDD TIGR00487 TIGR00487 273102 IF-2 translation initiation factor IF-2. This model discriminates eubacterial (and mitochondrial) translation initiation factor 2 (IF-2), encoded by the infB gene in bacteria, from similar proteins in the Archaea and Eukaryotes. In the bacteria and in organelles, the initiator tRNA is charged with N-formyl-Met instead of Met. This translation factor acts in delivering the initator tRNA to the ribosome. It is one of a number of GTP-binding translation factors recognized by the pfam model GTP_EFTU. [Protein synthesis, Translation factors] 587 matched cddid_all.tbl CDD TIGR00488 TIGR00488 273103 TIGR00488 putative HD superfamily hydrolase of NAD metabolism. The function of this protein family is unknown. Members of this family of uncharacterized proteins from the Mycoplasmas are longer at the amino end, fused to a region of nicotinamide nucleotide adenylyltransferase, an NAD salvage biosynthesis enzyme. Members are putative metal-dependent phosphohydrolases for NAD metabolism. [Unknown function, Enzymes of unknown specificity] 158 matched cddid_all.tbl CDD TIGR00489 TIGR00489 129580 aEF-1_beta translation elongation factor aEF-1 beta. This model describes the archaeal translation elongation factor aEF-1 beta. The member from Sulfolobus solfataricus was demonstrated experimentally. It is a dimer that catalyzes the exchange of GDP for GTP on aEF-1 alpha. [Protein synthesis, Translation factors] 88 matched cddid_all.tbl CDD TIGR00490 TIGR00490 129581 aEF-2 translation elongation factor aEF-2. This model represents archaeal elongation factor 2, a protein more similar to eukaryotic EF-2 than to bacterial EF-G, both in sequence similarity and in sharing with eukaryotes the property of having a diphthamide (modified His) residue at a conserved position. The diphthamide can be ADP-ribosylated by diphtheria toxin in the presence of NAD. [Protein synthesis, Translation factors] 720 matched cddid_all.tbl CDD TIGR00491 TIGR00491 273104 aIF-2 translation initiation factor aIF-2/yIF-2. This model describes archaeal and eukaryotic orthologs of bacterial IF-2. Like IF-2, it helps convey the initiator tRNA to the ribosome, although the initiator is N-formyl-Met in bacteria and Met here. This protein is not closely related to the subunits of eIF-2 of eukaryotes, which is also involved in the initiation of translation. The aIF-2 of Methanococcus jannaschii contains a large intein interrupting a region of very strongly conserved sequence very near the amino end; the alignment generated by this model does not correctly align the sequences from Methanococcus jannaschii and Pyrococcus horikoshii in this region. [Protein synthesis, Translation factors] 591 matched cddid_all.tbl CDD TIGR00492 TIGR00492 129583 alr alanine racemase. This enzyme interconverts L-alanine and D-alanine. Its primary function is to generate D-alanine for cell wall formation. With D-alanine-D-alanine ligase, it makes up the D-alanine branch of the peptidoglycan biosynthetic route. It is a monomer with one pyridoxal phosphate per subunit. In E. coli, the ortholog is duplicated so that a second isozyme, DadX, is present. DadX, a paralog of the biosynthetic Alr, is induced by D- or L-alanine and is involved in catabolism. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 367 matched cddid_all.tbl CDD TIGR00493 TIGR00493 188055 clpP ATP-dependent Clp endopeptidase, proteolytic subunit ClpP. This model for the proteolytic subunit ClpP has been rebuilt to a higher stringency. In every bacterial genome with the ClpXP machine, a ClpP protein will be found that scores well with this model. In general, this ClpP member will be encoded adjacent to the clpX gene, as were all examples used in the seed alignment. A large fraction of genomes have one or more additional ClpP paralogs, sometimes encoded nearby and sometimes elsewhere. The stringency of the trusted cutoff used here excludes the more divergent ClpP paralogs from being called authentic ClpP by this model. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 192 matched cddid_all.tbl CDD TIGR00494 TIGR00494 129585 crcB protein CrcB. The role of this protein is uncharacterized, but phenotypes associated with overproduction include resistance to camphor, suppression of a mukB chromosomal partition mutant, and chromosome condensation, together suggesting a function related to chromosome folding. [Unknown function, General] 117 matched cddid_all.tbl CDD TIGR00495 TIGR00495 273105 crvDNA_42K 42K curved DNA binding protein. Proteins identified by this model have been identified in a number of species as a nuclear (but not nucleolar) protein with a cell cycle dependence. Various names given to members of this family have included cell cycle protein p38-2G4, DNA-binding protein GBP16, and proliferation-associated protein 1. This protein is closely related to methionine aminopeptidase, a cobolt-binding protein. [Unknown function, General] 390 matched cddid_all.tbl CDD TIGR00496 TIGR00496 129587 frr ribosome recycling factor. This model finds only eubacterial proteins. Mitochondrial and/or chloroplast forms might be expected but are not currently known. This protein was previously called ribosome releasing factor. By releasing ribosomes from mRNA at the end of protein biosynthesis, it prevents inappropriate translation from 3-prime regions of the mRNA and frees the ribosome for new rounds of translation. EGAD|53116|YHR038W is part of the frr superfamily. [Protein synthesis, Translation factors] 176 matched cddid_all.tbl CDD TIGR00497 TIGR00497 211578 hsdM type I restriction system adenine methylase (hsdM). Function: methylation of specific adenine residues; required for both restriction and modification activities. The ECOR124/3 I enzyme recognizes 5'GAA(N7)RTCG. for E.coli see (J. Mol. Biol. 257: 960-969 (1996)). [DNA metabolism, Restriction/modification] 501 matched cddid_all.tbl CDD TIGR00498 TIGR00498 273106 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA. [DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions] 199 matched cddid_all.tbl CDD TIGR00499 TIGR00499 273107 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms. [Protein synthesis, tRNA aminoacylation] 493 matched cddid_all.tbl CDD TIGR00500 TIGR00500 129591 met_pdase_I methionine aminopeptidase, type I. Methionine aminopeptidase is a cobalt-binding enzyme. Bacterial and organellar examples (type I) differ from eukaroytic and archaeal (type II) examples in lacking a region of approximately 60 amino acids between the 4th and 5th cobalt-binding ligands. This model describes type I. The role of this protein in general is to produce the mature form of cytosolic proteins by removing the N-terminal methionine. [Protein fate, Protein modification and repair] 247 matched cddid_all.tbl CDD TIGR00501 TIGR00501 129592 met_pdase_II methionine aminopeptidase, type II. Methionine aminopeptidase (map) is a cobalt-binding enzyme. Bacterial and organellar examples (type I) differ from eukaroytic and archaeal (type II) examples in lacking a region of approximately 60 amino acids between the 4th and 5th cobalt-binding ligands. The role of this protein in general is to produce the mature amino end of cytosolic proteins by removing the N-terminal methionine. This model describes type II, among which the eukaryotic members typically have an N-terminal extension not present in archaeal members. It can act cotranslationally. The enzyme from rat has been shown to associate with translation initiation factor 2 (IF-2) and may have a role in translational regulation. [Protein fate, Protein modification and repair] 295 matched cddid_all.tbl CDD TIGR00502 TIGR00502 129593 nagB glucosamine-6-phosphate isomerase. The set of proteins recognized by this model includes a closely related pair from Bacillus subtilis, one of which is uncharacterized but included as a member of the orthologous set. [Central intermediary metabolism, Amino sugars] 259 matched cddid_all.tbl CDD TIGR00503 TIGR00503 129594 prfC peptide chain release factor 3. This translation releasing factor, RF-3 (prfC) was originally described as stop codon-independent, in contrast to peptide chain release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and RF-2 are closely related to each other, while RF-3 is similar to elongation factors EF-Tu and EF-G; RF-1 is active at UAA and UAG and RF-2 is active at UAA and UGA. More recently, RF-3 was shown to be active primarily at UGA stop codons in E. coli. All bacteria and organelles have RF-1. The Mycoplasmas and organelles, which translate UGA as Trp rather than as a stop codon, lack RF-2. RF-3, in contrast, seems to be rare among bacteria and is found so far only in Escherichia coli and some other gamma subdivision Proteobacteria, in Synechocystis PCC6803, and in Staphylococcus aureus. [Protein synthesis, Translation factors] 527 matched cddid_all.tbl CDD TIGR00504 TIGR00504 129595 pyro_pdase pyroglutamyl-peptidase I. Alternate names include pyroglutamate aminopeptidase, pyrrolidone-carboxylate peptidase, and 5-oxoprolyl-peptidase. It removes pyroglutamate (pyrrolidone-carboxylate, a modified glutamine) that can otherwise block hydrolysis of a polypeptide at the amino end, and so can be extremely useful in the biochemical studies of proteins. The biological role in the various species in which it is found is not fully understood. The enzyme appears to be a homodimer. It does not closely resemble any other peptidases. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 212 matched cddid_all.tbl CDD TIGR00505 TIGR00505 129596 ribA GTP cyclohydrolase II. Several members of the family are bifunctional, involving both ribA and ribB function. In these cases, ribA tends to be on the C-terminal end of the protein and ribB tends to be on the N-terminal. The function of archaeal members of the family has not been demonstrated and is assigned tentatively. [Biosynthesis of cofactors, prosthetic groups, and carriers, Riboflavin, FMN, and FAD] 191 matched cddid_all.tbl CDD TIGR00506 TIGR00506 273108 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase. Several members of the family are bifunctional, involving both ribA and ribB function. In these cases, ribA tends to be on the C-terminal end of the protein and ribB tends to be on the N-terminal. [Biosynthesis of cofactors, prosthetic groups, and carriers, Riboflavin, FMN, and FAD] 199 matched cddid_all.tbl CDD TIGR00507 TIGR00507 161904 aroE shikimate dehydrogenase. This model finds proteins from prokaryotes and functionally equivalent domains from larger, multifunctional proteins of fungi and plants. Below the trusted cutoff of 180, but above the noise cutoff of 20, are the putative shikimate dehydrogenases of Thermotoga maritima and Mycobacterium tuberculosis, and uncharacterized paralogs of shikimate dehydrogenase from E. coli and H. influenzae. The related enzyme quinate 5-dehydrogenase scores below the noise cutoff. A neighbor-joining tree, constructed with quinate 5-dehydrogenases as the outgroup, shows the Clamydial homolog as clustering among the shikimate dehydrogenases, although the sequence is unusual in the degree of sequence divergence and the presence of an additional N-terminal domain. [Amino acid biosynthesis, Aromatic amino acid family] 270 matched cddid_all.tbl CDD TIGR00508 TIGR00508 273109 bioA adenosylmethionine-8-amino-7-oxononanoate transaminase. All members of the seed alignment have been demonstrated experimentally to act as EC 2.6.1.62, an enzyme in the biotin biosynthetic pathway. Alternate names include 7,8-diaminopelargonic acid aminotransferase, DAPA aminotransferase, and adenosylmethionine-8-amino-7-oxononanoate aminotransferase. The gene symbol is bioA in E. coli and BIO3 in S. cerevisiae. [Biosynthesis of cofactors, prosthetic groups, and carriers, Biotin] 421 matched cddid_all.tbl CDD TIGR00509 TIGR00509 273110 bisC_fam molybdopterin guanine dinucleotide-containing S/N-oxide reductases. This enzyme family shares sequence similarity and a requirement for a molydenum cofactor as the only prosthetic group. The form of the cofactor is a single molybdenum atom coordinated by two molybdopterin guanine dinucleotide molecules. Members of the family include biotin sulfoxide reductase, dimethylsulfoxide reductase, and trimethylamine-N-oxide reductase, although a single member may show all those activities and related activities; it may not be possible to resolve the primary function for members of this family by sequence comparison alone. A number of similar molybdoproteins in which the N-terminal region contains a CXXXC motif and may bind an iron-sulfur cluster are excluded from this set, including formate dehydrogenases and nitrate reductases. Also excluded is the A chain of a heteromeric, anaerobic DMSO reductase, which also contains the CXXXC motif. 770 matched cddid_all.tbl CDD TIGR00510 TIGR00510 273111 lipA lipoate synthase. This enzyme is an iron-sulfur protein. It is localized to mitochondria in yeast and Arabidopsis. It generates lipoic acid, a thiol antioxidant that is linked to a specific Lys as prosthetic group for the pyruvate and alpha-ketoglutarate dehydrogenase complexes and the glycine-cleavage system. The family shows strong sequence conservation. [Biosynthesis of cofactors, prosthetic groups, and carriers, Lipoate] 302 matched cddid_all.tbl CDD TIGR00511 TIGR00511 188057 ribulose_e2b2 ribose-1,5-bisphosphate isomerase, e2b2 family. The delineation of this family was based originally, in part, on a discussion and neighbor-joining phylogenetic study by Kyrpides and Woese of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. Recently, Sato, et al. assigned the function ribulose-1,5 bisphosphate isomerase. [Energy metabolism, Other] 301 matched cddid_all.tbl CDD TIGR00512 TIGR00512 273112 salvage_mtnA S-methyl-5-thioribose-1-phosphate isomerase. The delineation of this family was based in part on a discussion and neighbor-joining phylogenetic study, by Kyrpides and Woese, of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. This clade is now recognized to include the methionine salvage pathway enzyme MtnA. [Amino acid biosynthesis, Aspartate family] 335 matched cddid_all.tbl CDD TIGR00513 TIGR00513 273113 accA acetyl-CoA carboxylase, carboxyl transferase, alpha subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the alpha chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta. [Fatty acid and phospholipid metabolism, Biosynthesis] 316 matched cddid_all.tbl CDD TIGR00514 TIGR00514 129605 accC acetyl-CoA carboxylase, biotin carboxylase subunit. This model represents the biotin carboxylase subunit found usually as a component of acetyl-CoA carboxylase. Acetyl-CoA carboxylase is designated EC 6.4.1.2 and this component, biotin carboxylase, has its own designation, EC 6.3.4.14. Homologous domains are found in eukaryotic forms of acetyl-CoA carboxylase and in a number of other carboxylases (e.g. pyruvate carboxylase), but seed members and trusted cutoff are selected so as to exclude these. In some systems, the biotin carboxyl carrier protein and this protein (biotin carboxylase) may be shared by different carboxyltransferases. However, this model is not intended to identify the biotin carboxylase domain of propionyl-coA carboxylase. The model should hit the full length of proteins, except for chloroplast transit peptides in plants. If it hits a domain only of a longer protein, there may be a problem with the identification. [Fatty acid and phospholipid metabolism, Biosynthesis] 449 matched cddid_all.tbl CDD TIGR00515 TIGR00515 129606 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta. [Fatty acid and phospholipid metabolism, Biosynthesis] 285 matched cddid_all.tbl CDD TIGR00516 TIGR00516 273114 acpS holo-[acyl-carrier-protein] synthase. Formerly dpj. This enzyme adds the prosthetic group, phosphopantethiene, to the acyl carrier protein (ACP) apo-enzyme to generate the holo-enzyme. Related phosphopantethiene--protein transferases also exist. There is an orthologous domain in eukaryotic proteins. [Fatty acid and phospholipid metabolism, Biosynthesis] 121 matched cddid_all.tbl CDD TIGR00517 TIGR00517 213536 acyl_carrier acyl carrier protein. This small protein has phosphopantetheine covalently bound to a Ser residue. It acts as a carrier of the growing fatty acid chain, which is bound to the prosthetic group, during fatty acid biosynthesis. Homologous phosphopantetheine-binding domains are found in longer proteins. Acyl carrier proteins scoring above the noise cutoff but below the trusted cutoff may be specialized versions. These include those involved in mycolic acid biosynthesis in the Mycobacteria, lipid A biosynthesis in Rhizobium, actinorhodin polyketide synthesis in Streptomyces coelicolor, etc. This protein is not found in the Archaea.Gene name acpP.S (Ser) at position 37 in the seed alignment, in the motif DSLD, is the phosphopantetheine attachment site. [Fatty acid and phospholipid metabolism, Biosynthesis] 77 matched cddid_all.tbl CDD TIGR00518 TIGR00518 129609 alaDH alanine dehydrogenase. The family of known L-alanine dehydrogenases (EC 1.4.1.1) includes representatives from the Proteobacteria, Firmicutes, Cyanobacteria, and Actinobacteria, all with about 50 % identity or better. An outlier to this group in both sequence and gap pattern is the homolog from Helicobacter pylori, an epsilon division Proteobacteria, which must be considered a putative alanine dehydrogenase. In Mycobacterium smegmatis and M. tuberculosis, the enzyme doubles as a glycine dehydrogenase (1.4.1.10), running in the reverse direction (glyoxylate amination to glycine, with conversion of NADH to NAD+). Related proteins include saccharopine dehydrogenase and the N-terminal half of the NAD(P) transhydrogenase alpha subunit. All of these related proteins bind NAD and/or NADP. [Energy metabolism, Amino acids and amines] 370 matched cddid_all.tbl CDD TIGR00519 TIGR00519 129610 asnASE_I L-asparaginase, type I. Two related families of asparaginase are designated type I and type II according to the terminology in E. coli, which has both: L-asparaginase I is a low-affinity enzyme found in the cytoplasm, while L-asparaginase II is a high-affinity secreted enzyme synthesized with a cleavable signal sequence. This model describes L-asparaginases related to type I of E. coli. Archaeal putative asparaginases are of this type but contain an extra ~ 80 residues in a conserved N-terminal region. These archaeal homologs are included in this model. 336 matched cddid_all.tbl CDD TIGR00520 TIGR00520 273115 asnASE_II L-asparaginase, type II. Two related families of asparaginase (L-asparagine amidohydrolase, EC 3.5.1.1) are designated type I and type II according to the terminology in E. coli, which has both: L-asparaginase I is a low-affinity enzyme found in the cytoplasm, while L-asparaginase II is a high-affinity periplasmic enzyme synthesized with a cleavable signal sequence. This model describes L-asparaginases related to type II of E. coli. Both the cytoplasmic and the cell wall asparaginases of Saccharomyces cerevisiae belong to this set. Members of this set from Acinetobacter glutaminasificans and Pseudomonas fluorescens are described as having both glutaminase and asparaginase activitities. All members are homotetrameric. [Energy metabolism, Amino acids and amines] 349 matched cddid_all.tbl CDD TIGR00521 TIGR00521 273116 coaBC_dfp phosphopantothenoylcysteine decarboxylase / phosphopantothenate--cysteine ligase. This model represents a bifunctional enzyme that catalyzes the second and third steps (cysteine ligation, EC 6.3.2.5, and decarboxylation, EC 4.1.1.36) in the biosynthesis of coenzyme A (CoA) from pantothenate in bacteria. In early descriptions of this flavoprotein, a ts mutation in one region of the protein appeared to cause a defect in DNA metaobolism rather than an increased need for the pantothenate precursor beta-alanine. This protein was then called dfp, for DNA/pantothenate metabolism flavoprotein. The authors responsible for detecting phosphopantothenate--cysteine ligase activity suggest renaming this bifunctional protein coaBC for its role in CoA biosynthesis. This enzyme contains the FMN cofactor, but no FAD or pyruvoyl group. The amino-terminal region contains the phosphopantothenoylcysteine decarboxylase activity. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pantothenate and coenzyme A] 391 matched cddid_all.tbl CDD TIGR00522 TIGR00522 273117 dph5 diphthine synthase. Alternate name: diphthamide biosynthesis S-adenosylmethionine-dependent methyltransferase. This protein participates in the modification of a specific His of elongation factor 2 of eukarotes and Archaea to diphthamide. The protein was characterized in Saccharomyces cerevisiae and designated DPH5. [Protein fate, Protein modification and repair] 257 matched cddid_all.tbl CDD TIGR00523 TIGR00523 273118 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C [Protein synthesis, Translation factors] 98 matched cddid_all.tbl CDD TIGR00524 TIGR00524 273119 eIF-2B_rel eIF-2B alpha/beta/delta-related uncharacterized proteins. This model, eIF-2B_rel, describes half of a superfamily, where the other half consists of eukaryotic translation initiation factor 2B (eIF-2B) subunits alpha, beta, and delta. It is unclear whether the eIF-2B_rel set is monophyletic, or whether they are all more closely related to each other than to any eIF-2B subunit because the eIF-2B clade is highly derived. Members of this branch of the family are all uncharacterized with respect to function and are found in the Archaea, Bacteria, and Eukarya, although a number are described as putative translation intiation factor components. Proteins found by eIF-2B_rel include at least three clades, including a set of uncharacterized eukaryotic proteins, a set found in some but not all Archaea, and a set universal so far among the Archaea and closely related to several uncharacterized bacterial proteins. [Unknown function, General] 303 matched cddid_all.tbl CDD TIGR00525 TIGR00525 213537 folB dihydroneopterin aldolase. This model describes a bacterial dihydroneopterin aldolase, shown to form homo-octamers in E. coli. The equivalent activity is catalyzed by domains of larger folate biosynthesis proteins in other systems. The closely related parologous enzyme in E. coli, dihydroneopterin triphosphate epimerase, which is also homo-octameric, and dihydroneopterin aldolase domains of larger proteins, score below the trusted cutoff but may score well above the noise cutoff. [Biosynthesis of cofactors, prosthetic groups, and carriers, Folic acid] 116 matched cddid_all.tbl CDD TIGR00526 TIGR00526 273120 folB_dom FolB domain. Two paralogous genes of E. coli, folB (dihydroneopterin aldolase) and folX (d-erythro-7,8-dihydroneopterin triphosphate epimerase) are homologous to each other and homo-octameric. In Pneumocystis carinii, a multifunctional enzyme of folate synthesis has an N-terminal region active as dihydroneopterin aldolase. This region consists of two tandem sequences each homologous to folB and forms tetramers. 118 matched cddid_all.tbl CDD TIGR00527 TIGR00527 200024 gcvH glycine cleavage system H protein. This model represents the glycine cleavage system H protein, which shuttles the methylamine group of glycine from the P protein to the T protein. The mature protein is about 130 residues long and contains a lipoyl group covalently bound to a conserved Lys residue. The genome of Aquifex aeolicus contains one protein scoring above the trusted cutoff and clustering with other bacterial H proteins, and four more proteins clustering together and scoring below the trusted cutoff; it seems doubtful that all of these homologs are authentic H protein. The Chlamydial homolog of H protein is nearly as divergent as the Aquifex outgroup, is not accompanied by P and T proteins, is not included in the seed alignment, and consequently also scores below the trusted cutoff. [Energy metabolism, Amino acids and amines] 128 matched cddid_all.tbl CDD TIGR00528 TIGR00528 273121 gcvT glycine cleavage system T protein. The glycine cleavage system T protein (GcvT) is also known as aminomethyltransferase (EC 2.1.2.10). It works with the H protein (GcvH), the P protein (GcvP), and lipoamide dehydrogenase. The reported sequence of the member from Aquifex aeolicus starts about 50 residues downstream of the start of other members of the family (perhaps in error); it scores below the trusted cutoff. Eukaryotic forms are mitochondrial and have an N-terminal transit peptide. [Energy metabolism, Amino acids and amines] 362 matched cddid_all.tbl CDD TIGR00529 TIGR00529 273122 AF0261 integral membrane protein, TIGR00529 family. This protein is predicted to have 10 transmembrane regions. Members of this family are found so far in the Archaea (Archaeoglobus fulgidus and Pyrococcus horikoshii) and in a bacterial thermophile, Thermotoga maritima. In Pyrococcus, the gene is located between nadA and nadB, two components of an enzyme involved in de novo synthesis of NAD. By PSI-BLAST, this family shows similarity (but not necessarily homology) to gluconate permease and other transport proteins. [Hypothetical proteins, Conserved] 387 matched cddid_all.tbl CDD TIGR00530 TIGR00530 129621 AGP_acyltrn 1-acyl-sn-glycerol-3-phosphate acyltransferases. This model describes the core homologous region of a collection of related proteins, several of which are known to act as 1-acyl-sn-glycerol-3-phosphate acyltransferases (EC 2.3.1.51). Proteins scoring above the trusted cutoff are likely to have the same general activity. However, there is variation among characterized members as to whether the acyl group can be donated by acyl carrier protein or coenzyme A, and in the length and saturation of the donated acyl group. 1-acyl-sn-glycerol-3-phosphate acyltransferase is also called 1-AGP acyltransferase, lysophosphatidic acid acyltransferase, and LPA acyltransferase. [Fatty acid and phospholipid metabolism, Biosynthesis] 130 matched cddid_all.tbl CDD TIGR00531 TIGR00531 273123 BCCP acetyl-CoA carboxylase, biotin carboxyl carrier protein. This model is designed to identify biotin carboxyl carrier protein as a peptide of acetyl-CoA carboxylase. Scoring below the trusted cutoff is a related protein encoded in a region associated with polyketide synthesis in the prokaryote Saccharopolyspora hirsuta, and a reported chloroplast-encoded biotin carboxyl carrier protein that may be highly derived from the last common ancestral sequence. Scoring below the noise cutoff are biotin carboxyl carrier domains of other enzymes such as pyruvate carboxylase.The gene name is accB or fabE. [Fatty acid and phospholipid metabolism, Biosynthesis] 155 matched cddid_all.tbl CDD TIGR00532 TIGR00532 129623 HMG_CoA_R_NAD hydroxymethylglutaryl-CoA reductase, degradative. Most known examples of hydroxymethylglutaryl-CoA reductase are NADP-dependent (EC 1.1.1.34) from eukaryotes and archaea, involved in the biosynthesis of mevalonate from 3-hydroxy-3-methylglutaryl-CoA. This model, in contrast, is built from the two examples in completed genomes of sequences closely related to the degradative, NAD-dependent hydroxymethylglutaryl-CoA reductase of Pseudomonas mevalonii, a bacterium that can use mevalonate as its sole carbon source. [Energy metabolism, Other] 393 matched cddid_all.tbl CDD TIGR00533 TIGR00533 129624 HMG_CoA_R_NADP 3-hydroxy-3-methylglutaryl Coenzyme A reductase, hydroxymethylglutaryl-CoA reductase (NADP). This model represents archaeal examples of the enzyme hydroxymethylglutaryl-CoA reductase (NADP) (EC 1.1.1.34) and the catalytic domain of eukaryotic examples, which also contain a hydrophobic N-terminal domain. This enzyme synthesizes mevalonate, a precursor of isopentenyl pyrophosphate (IPP), a building block for the synthesis of cholesterol, isoprenoids, and other molecules. A related hydroxymethylglutaryl-CoA reductase, typified by an example from Pseudomonas mevalonii, is NAD-dependent and catabolic. [Central intermediary metabolism, Other] 402 matched cddid_all.tbl CDD TIGR00534 TIGR00534 213538 OpcA glucose-6-phosphate dehydrogenase assembly protein OpcA. The opcA gene is found immediately downstream of zwf, the glucose-6-phosphate dehydrogenase (G6PDH) gene, in a number of species, including Mycobacterium tuberculosis, Streptomyces coelicolor, Nostoc punctiforme, and Synechococcus sp. PCC 7942. In the latter, disruption of opcA was shown to block assembly of G6PDH into active oligomeric forms. [Protein fate, Protein folding and stabilization] 311 matched cddid_all.tbl CDD TIGR00535 TIGR00535 273124 SAM_DCase S-adenosylmethionine decarboxylase proenzyme, eukaryotic form. This enzyme is a key regulatory enzyme of the polyamine synthetic pathway. This protein is a pyruvoyl-dependent enzyme. The proenzyme is cleaved at a Ser residue that becomes a pyruvoyl group active site. [Central intermediary metabolism, Polyamine biosynthesis] 334 matched cddid_all.tbl CDD TIGR00536 TIGR00536 273125 hemK_fam HemK family putative methylases. The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase. Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. Both E. coli and H. influenzae have two members rather than one. The members from the Mycoplasmas have an additional C-terminal domain. [Protein fate, Protein modification and repair] 284 matched cddid_all.tbl CDD TIGR00537 TIGR00537 129628 hemK_rel_arch HemK-related putative methylase. The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase. Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. This model represents an archaeal and eukaryotic protein family that lacks an N-terminal domain found in HemK and its eubacterial homologs. It is found in a single copy in the first six completed archaeal and eukaryotic genomes. [Unknown function, Enzymes of unknown specificity] 179 matched cddid_all.tbl CDD TIGR00538 TIGR00538 129629 hemN oxygen-independent coproporphyrinogen III oxidase. This model represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. Several species, including E. coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterized protein. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 455 matched cddid_all.tbl CDD TIGR00539 TIGR00539 129630 hemN_rel putative oxygen-independent coproporphyrinogen III oxidase. Experimentally determined examples of oxygen-independent coproporphyrinogen III oxidase, an enzyme that replaces HemF function under anaerobic conditions, belong to a family of proteins described by the model hemN. This model, hemN_rel, models a closely related protein, shorter at the amino end and lacking the region containing the motif PYRT[SC]YP found in members of the hemN family. Several species, including E. coli, Helicobacter pylori, Aquifex aeolicus, and Chlamydia trachomatis, have members of both this family and the E. coli hemN family. The member of this family from Bacillus subtilis was shown to complement an hemF/hemN double mutant of Salmonella typimurium and to prevent accumulation of coproporphyrinogen III under anaerobic conditions, but the exact role of this protein is still uncertain. It is found in a number of species that do not synthesize heme de novo. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 360 matched cddid_all.tbl CDD TIGR00540 TIGR00540 273126 TPR_hemY_coli heme biosynthesis-associated TPR protein. Members of this protein family are uncharacterized tetratricopeptide repeat (TPR) proteins invariably found in heme biosynthesis gene clusters. The absence of any invariant residues other than Ala argues against this protein serving as an enzyme per se. The gene symbol hemY assigned in E. coli is unfortunate in that an unrelated protein, protoporphyrinogen oxidase (HemG in E. coli) is designated HemY in Bacillus subtilis. [Unknown function, General] 367 matched cddid_all.tbl CDD TIGR00541 TIGR00541 129632 hisDCase_pyru histidine decarboxylase, pyruvoyl type. This enzyme converts histadine to histamine in a single step by catalyzing the release of CO2. This type is synthesized as an inactive single chain precursor, then cleaved into two chains. The Ser at the new N-terminus at the cleavage site is converted to a pyruvoyl group essential for activity. This type of histidine decarboxylase appears is known so far only in some Gram-positive bacteria, where it may play a role in amino acid catabolism. There is also a pyridoxal phosphate type histidine decarboxylase, as found in human, where histamine is a biologically active amine. [Energy metabolism, Amino acids and amines] 310 matched cddid_all.tbl CDD TIGR00542 TIGR00542 129633 hxl6Piso_put hexulose-6-phosphate isomerase, putative. This family shows similarity by PSI-BLAST to other isomerases. Putative identification as hexulose-6-phosphate isomerase is reported in Swiss-Prot, attributing a discussion in Genome Sci. Technol. 1:53-75(1996). This family is conserved at better than 40 % identity among the four known examples from three species: Escherichia coli (SgbU and SgaU), Haemophilus influenzae, and Mycoplasma pneumoniae. The rarity of the family, high level of conservation, and proposed catabolic role suggests lateral transfer may be a part of the evolutionary history of this protein. [Energy metabolism, Sugars] 279 matched cddid_all.tbl CDD TIGR00543 TIGR00543 273127 isochor_syn isochorismate synthases. This enzyme interconverts chorismate and isochorismate. In E. coli, different loci encode isochorismate synthases for the pathways of menaquinone biosynthesis and enterobactin biosynthesis (via salicilate) and fail to complement each other. Among isochorismate synthases, the N-terminal domain is poorly conserved. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 351 matched cddid_all.tbl CDD TIGR00544 TIGR00544 273128 lgt prolipoprotein diacylglyceryl transferase. The conversion of lipoprotein precursors into lipoproteins consists of three steps. First, the enzyme described by this model transfers a diacylglyceryl moiety from phosphatidylglycerol to the side chain of a Cys that will become the new N-terminus. Second, the signal peptide is removed by signal peptidase II. Finally, the free amino group of the new N-terminal Cys is acylated by apolipoprotein N-acyltransferase. [Protein fate, Protein modification and repair] 277 matched cddid_all.tbl CDD TIGR00545 TIGR00545 161920 lipoyltrans lipoyltransferase and lipoate-protein ligase. One member of this group of proteins is bovine lipoyltransferase, which transfers the lipoyl group from lipoyl-AMP to the specific Lys of lipoate-dependent enzymes. However, it does not first activate lipoic acid with ATP to create lipoyl-AMP and pyrophosphate. Another member of this group, lipoate-protein ligase A from E. coli, catalyzes both the activation and the transfer of lipoate. Homology between the two is full-length, except for the bovine mitochondrial targeting signal, but is strongest toward the N-terminus. [Protein fate, Protein modification and repair] 324 matched cddid_all.tbl CDD TIGR00546 TIGR00546 273129 lnt "apolipoprotein N-acyltransferase. This enzyme transfers the acyl group to lipoproteins in the lgt/lsp/lnt system which is found broadly in bacteria but not in archaea. This model represents one component of the ""lipoprotein lgt/lsp/lnt system"" genome property. [Protein fate, Protein modification and repair]" 391 matched cddid_all.tbl CDD TIGR00547 TIGR00547 129638 lolA periplasmic chaperone LolA. This protein, LolA, is known so far only in the gamma and beta subdivisions of the Proteobacteria. The E. coli major outer lipoprotein (Lpp) of E. coli is released from the inner membrane as a complex with this chaperone in an energy-requiring process, and is then delivered to LolB for insertion into the outer membrane. LolA is involved in the delivery of lipoproteins generally, rather than just Lpp, and is an essential protein in E. coli, unlike Lpp itself. [Protein fate, Protein and peptide secretion and trafficking] 204 matched cddid_all.tbl CDD TIGR00548 TIGR00548 129639 lolB outer membrane lipoprotein LolB. This protein, LolB, is known so far only in the gamma and beta subdivisions of the Proteobacteria. It is a processed, lipid-modified outer membrane protein. It is required in E. coli for insertion of the major outer lipoprotein (Lpp) into the outer membrane. Lpp is transferred to LolB from the carrier protein LolA in the periplasm. Previously, this protein was thought to play in role in 5-aminolevulinic acid synthesis and was designated HemM. [Protein fate, Protein and peptide secretion and trafficking] 202 matched cddid_all.tbl CDD TIGR00549 TIGR00549 273130 mevalon_kin mevalonate kinase. This model represents mevalonate kinase, the third step in the mevalonate pathway of isopentanyl pyrophosphate (IPP) biosynthesis. IPP is a common intermediate for a number of pathways including cholesterol biosynthesis. This model covers enzymes from eukaryotes, archaea and bacteria. The related enzyme from the same pathway, phosphmevalonate kinase, serves as an outgroup for this clade. Paracoccus exhibits two genes within the phosphomevalonate/mevalonate kinase family, one of which falls between trusted and noise cutoffs of this model. The degree of divergence is high, but if the trees created from this model are correct, the proper names of these genes have been swapped. [Central intermediary metabolism, Other] 273 matched cddid_all.tbl CDD TIGR00550 TIGR00550 129641 nadA quinolinate synthetase complex, A subunit. This protein, termed NadA, plays a role in the synthesis of pyridine, a precursor to NAD. The quinolinate synthetase complex consists of A protein (this protein) and B protein. B protein converts L-aspartate to iminoaspartate, an unstable reaction product which in the absence of A protein is spontaneously hydrolyzed to form oxaloacetate. The A protein, NadA, converts iminoaspartate to quinolate. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridine nucleotides] 310 matched cddid_all.tbl CDD TIGR00551 TIGR00551 273131 nadB L-aspartate oxidase. L-aspartate oxidase is the B protein, NadB, of the quinolinate synthetase complex. Quinolinate synthetase makes a precursor of the pyridine nucleotide portion of NAD. This model identifies proteins that cluster as L-aspartate oxidase (a flavoprotein difficult to separate from the set of closely related flavoprotein subunits of succinate dehydrogenase and fumarate reductase) by both UPGMA and neighbor-joining trees. The most distant protein accepted as an L-aspartate oxidase (NadB), that from Pyrococcus horikoshii, not only clusters with other NadB but is just one gene away from NadA. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridine nucleotides] 489 matched cddid_all.tbl CDD TIGR00552 TIGR00552 273132 nadE NAD+ synthetase. NAD+ synthetase is a nearly ubiquitous enzyme for the final step in the biosynthesis of the essensial cofactor NAD. The member of this family from Bacillus subtilis is a strictly NH(3)-dependent NAD(+) synthetase of 272 amino acids. Proteins consisting only of the domain modeled here may be named as NH3-dependent NAD+ synthetase. Amidotransferase activity may reside in a separate protein, or not be present. Some other members of the family, such as from Mycobacterium tuberculosis, are considerably longer, contain an apparent amidotransferase domain, and show glutamine-dependent as well as NH(3)-dependent activity. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridine nucleotides] 250 matched cddid_all.tbl CDD TIGR00553 TIGR00553 273133 pabB aminodeoxychorismate synthase, component I, bacterial clade. Members of this family, aminodeoxychorismate synthase, component I (PabB), were designated para-aminobenzoate synthase component I until it was recognized that PabC, a lyase, completes the pathway of PABA synthesis. This family is closely related to anthranilate synthase component I (trpE), and both act on chorismate. The clade of PabB enzymes represented by this model includes sequences from Gram-positive and alpha and gamma Proteobacteria as well as Chlorobium, Nostoc, Fusobacterium and Arabidopsis. A closely related clade of fungal PabB enzymes is identified by TIGR01823, while another bacterial clade of potential PabB enzymes is more closely related to TrpE (TIGR01824). [Biosynthesis of cofactors, prosthetic groups, and carriers, Folic acid] 328 matched cddid_all.tbl CDD TIGR00554 TIGR00554 273134 panK_bact pantothenate kinase, bacterial type. Shown to be a homodimer in E. coli. This enzyme catalyzes the rate-limiting step in the biosynthesis of coenzyme A. It is very well conserved from E. coli to B. subtilis, but differs considerably from known eukaryotic forms, described in a separate model. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pantothenate and coenzyme A] 290 matched cddid_all.tbl CDD TIGR00555 TIGR00555 273135 panK_eukar pantothenate kinase, eukaryotic/staphyloccocal type. This model describes a eukaryotic form of pantothenate kinase, characterized from the fungus Aspergillus nidulans and with similar forms known in several other eukaryotes. It also includes forms from several Gram-positive bacteria suggested to have originated from the eukaryotic form by lateral transfer. It differs in a number of biochemical properties (such as inhibition by acetyl-CoA) from most bacterial CoaA and lacks sequence similarity. This enzyme is the key regulatory step in the biosynthesis of coenzyme A (CoA). [Biosynthesis of cofactors, prosthetic groups, and carriers, Pantothenate and coenzyme A] 296 matched cddid_all.tbl CDD TIGR00556 TIGR00556 273136 pantethn_trn phosphopantetheine--protein transferase domain. This model models a domain active in transferring the phophopantetheine prosthetic group to its attachment site on enzymes and carrier proteins. Many members of this family are small proteins that act on the acyl carrier protein involved in fatty acid biosynthesis. Some members are domains of larger proteins involved specialized pathways for the synthesis of unusual molecules including polyketides, atypical fatty acids, and antibiotics. [Protein fate, Protein modification and repair] 128 matched cddid_all.tbl CDD TIGR00557 TIGR00557 273137 pdxA 4-hydroxythreonine-4-phosphate dehydrogenase. This model represents PdxA, an NAD+-dependent 4-hydroxythreonine 4-phosphate dehydrogenase (EC 1.1.1.262) active in pyridoxal phosphate biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridoxine] 320 matched cddid_all.tbl CDD TIGR00558 TIGR00558 273138 pdxH pyridoxamine-phosphate oxidase. This model is similar to Pyridox_oxidase from Pfam but is designed to find only true pyridoxamine-phosphate oxidase and to ignore the related protein PhzG involved in phenazine biosynthesis. This protein from E. coli was characterized as a homodimer with two FMN per dimer. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridoxine] 190 matched cddid_all.tbl CDD TIGR00559 TIGR00559 188064 pdxJ pyridoxine 5'-phosphate synthase. PdxJ is required in the biosynthesis of pyridoxine (vitamin B6), a precursor to the enzyme cofactor pyridoxal phosphate. ECOCYC describes the predicted reaction equation as 1-amino-propan-2-one-3-phosphate + deoxyxylulose-5-phosphate = pyridoxine-5'-phosphate. The product of that reaction is oxidized by PdxH to pyridoxal 5'-phosphate. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridoxine] 236 matched cddid_all.tbl CDD TIGR00560 TIGR00560 273139 pgsA CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase. Alternate names: phosphatidylglycerophosphate synthase; glycerophosphate phosphatidyltransferase; PGP synthase. A number of related enzymes are quite similar in both sequence and catalytic activity, including Saccharamyces cerevisiae YDL142c, now known to be a cardiolipin synthase. There may be problems with incorrect transitive annotation of near homologs as authentic CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase. [Fatty acid and phospholipid metabolism, Biosynthesis] 182 matched cddid_all.tbl CDD TIGR00561 TIGR00561 273140 pntA NAD(P) transhydrogenase, alpha subunit. This integral membrane protein is the alpha subunit of alpha 2 beta 2 tetramer that couples the proton transport across the membrane to the reversible transfer of hydride ion equivalents between NAD and NADP. An alternate name is pyridine nucleotide transhydrogenase alpha subunit. The N-terminal region is homologous to alanine dehydrogenase. In some species, such as Rhodospirillum rubrum, the alpha chain is replaced by two shorter chains, both with some homology to the full-length alpha chain modeled here. These score below the trusted cutoff. [Energy metabolism, Electron transport] 512 matched cddid_all.tbl CDD TIGR00562 TIGR00562 213540 proto_IX_ox protoporphyrinogen oxidase. This enzyme oxidizes protoporphyrinogen IX to protoporphyrin IX, a precursor of heme and chlorophyll. Bacillus subtilis HemY also has coproporphyrinogen III to coproporphyrin III oxidase activity in a heterologous expression system, although the role for this activity in vivo is unclear. This protein is a flavoprotein and has a beta-alpha-beta dinucleotide binding motif near the amino end. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 462 matched cddid_all.tbl CDD TIGR00563 TIGR00563 273141 rsmB 16S rRNA (cytosine(967)-C(5))-methyltransferase. This protein is also known as sun protein. The reading frame was originally interpreted as two reading frames, fmu and fmv. The recombinant protein from E. coli was shown to methylate only C967 of small subunit (16S) ribosomal RNA and to produce only m5C at that position. The seed alignment is built from bacterial sequences only. Eukaryotic homologs include Nop2, a protein required for processing pre-rRNA, that is likely also a rRNA methyltransferase, although the fine specificity may differ. Cutoff scores are set to avoid treating archaeal and eukaroytic homologs automatically as functionally equivalent, although they may have very similar roles. [Protein synthesis, tRNA and rRNA base modification] 426 matched cddid_all.tbl CDD TIGR00564 TIGR00564 273142 trpE_most anthranilate synthase component I, non-proteobacterial lineages. This enzyme resembles some other chorismate-binding enzymes, including para-aminobenzoate synthase (pabB) and isochorismate synthase. There is a fairly deep split between two sets, seen in the pattern of gaps as well as in amino acid sequence differences. Archaeal enzymes have been excluded from this model (and are now found in TIGR01820) as have a clade of enzymes which constitute a TrpE paralog which may have PabB activity (TIGR01824). This allows the B. subtilus paralog which has been shown to have PabB activity to score below trusted to this model. This model contains sequences from gram-positive bacteria, certain proteobacteria, cyanobacteria, plants, fungi and assorted other bacteria.A second family of TrpE enzymes is modelled by TIGR00565. The breaking of the TrpE family into these diverse models allows for the separation of the models for the related enzyme, PabB. [Amino acid biosynthesis, Aromatic amino acid family] 454 matched cddid_all.tbl CDD TIGR00565 TIGR00565 273143 trpE_proteo anthranilate synthase component I, proteobacterial subset. This enzyme resembles some other chorismate-binding enzymes, including para-aminobenzoate synthase (pabB) and isochorismate synthase. There is a fairly deep split between two sets, seen in the pattern of gaps as well as in amino acid sequence differences. This group includes proteobacteria such as E. coli and Helicobacter pylori but also the gram-positive organism Corynebacterium glutamicum. The second group includes eukaryotes, archaea, and most other bacterial lineages; sequences from the second group may resemble pabB more closely than other trpE from this group. [Amino acid biosynthesis, Aromatic amino acid family] 498 matched cddid_all.tbl CDD TIGR00566 TIGR00566 273144 trpG_papA glutamine amidotransferase of anthranilate synthase or aminodeoxychorismate synthase. This model describes the glutamine amidotransferase domain or peptide of the tryptophan-biosynthetic pathway enzyme anthranilate synthase or of the folate biosynthetic pathway enzyme para-aminobenzoate synthase. In at least one case, a single polypeptide from Bacillus subtilis was shown to have both functions. This model covers a subset of the sequences described by the Pfam model GATase. 188 matched cddid_all.tbl CDD TIGR00567 TIGR00567 273145 3mg DNA-3-methyladenine glycosylase. This families are based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). All proteins in this family for which the function is known are involved in the base excision repair of alkylation damage to DNA. The exact specificty of the type of alkylation damage repaired by each of these varies somewhat between species. Substrates include 3-methyl adenine, 7-methyl-guanaine, and 3-methyl-guanine. [DNA metabolism, DNA replication, recombination, and repair] 192 matched cddid_all.tbl CDD TIGR00568 TIGR00568 129659 alkb DNA alkylation damage repair protein AlkB. Proteins in this family have an as of yet undetermined function in the repair of alkylation damage to DNA. Alignment and family designation based on phylogenomic analysis of Jonathan A. Eisen (PhD Thesis, Stanford University, 1999). [DNA metabolism, DNA replication, recombination, and repair] 169 matched cddid_all.tbl CDD TIGR00569 TIGR00569 129660 ccl1 cyclin ccl1. All proteins in this family for which functions are known are cyclins that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, StanfordUniversity). [DNA metabolism, DNA replication, recombination, and repair] 305 matched cddid_all.tbl CDD TIGR00570 TIGR00570 129661 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 309 matched cddid_all.tbl CDD TIGR00571 TIGR00571 273146 dam DNA adenine methylase (dam). All proteins in this family for which functions are known are DNA-adenine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The DNA adenine methylase (dam) of E. coli and related species is instrumental in distinguishing the newly synthesized strand during DNA replication for methylation-directed mismatch repair. This family includes several phage methylases and a number of different restriction enzyme chromosomal site-specific modification systems. [DNA metabolism, DNA replication, recombination, and repair] 267 matched cddid_all.tbl CDD TIGR00573 TIGR00573 129663 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, Degradation of DNA] 217 matched cddid_all.tbl CDD TIGR00574 TIGR00574 273147 dnl1 DNA ligase I, ATP-dependent (dnl1). All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 514 matched cddid_all.tbl CDD TIGR00575 TIGR00575 273148 dnlj DNA ligase, NAD-dependent. All proteins in this family with known functions are NAD-dependent DNA ligases. Functions of these proteins include DNA repair, DNA replication, and DNA recombination. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed. [DNA metabolism, DNA replication, recombination, and repair] 652 matched cddid_all.tbl CDD TIGR00576 TIGR00576 273149 dut deoxyuridine 5'-triphosphate nucleotidohydrolase (dut). The main function of these proteins is in maintaining the levels of dUTP in the cell to prevent dUTP incorporation into DNA during DNA replication. Pol proteins in viruses are very similar to this protein family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Changed role from 132 to 123. RTD [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism] 142 matched cddid_all.tbl CDD TIGR00577 TIGR00577 273150 fpg DNA-formamidopyrimidine glycosylase. All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 272 matched cddid_all.tbl CDD TIGR00578 TIGR00578 273151 ku70 ATP-dependent DNA helicase II, 70 kDa subunit (ku70). Proteins in this family are involved in non-homologous end joining, a process used for the repair of double stranded DNA breaks. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Cutoff does not detect the putative ku70 homologs in yeast. [DNA metabolism, DNA replication, recombination, and repair] 586 matched cddid_all.tbl CDD TIGR00580 TIGR00580 273152 mfd transcription-repair coupling factor (mfd). All proteins in this family for which functions are known are DNA-dependent ATPases that function in the process of transcription-coupled DNA repair in which the repair of the transcribed strand of actively transcribed genes is repaired at a higher rate than the repair of non-transcribed regions of the genome and than the non-transcribed strand of the same gene. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is closely related to the RecG and UvrB families. [DNA metabolism, DNA replication, recombination, and repair] 926 matched cddid_all.tbl CDD TIGR00581 TIGR00581 129670 moaC molybdenum cofactor biosynthesis protein MoaC. MoaC catalyzes an early step in molybdenum cofactor biosynthesis in E. coli. The Arabidopsis homolog Cnx3 complements MoaC deficiency in E. coli. Eukarotic members of this family branch within the bacterial branch, with the archaeal members as an apparent outgroup. This protein is absent in a number of the pathogens with smaller genomes, including Mycoplasmas, Chlamydias, and spirochetes, but is found in most other complete genomes to date. The homolog form Synechocystis sp. is fused to a MobA-homologous region and is an outlier to all other bacterial forms by both neighbor-joining and UPGMA analyses. Members of this family are well-conserved. The seed for this model excludes both archaeal sequences and the most divergent bacterial sequences, but still finds all candidate MoaC sequences easily between trusted and noise cutoffs. We suggest that sequences branching outside the set that contains all seed members be regarded only as putative functional equivalents of MoaC unless and until a member of the archaeal outgroup is shown to have equivalent function. [Biosynthesis of cofactors, prosthetic groups, and carriers, Molybdopterin] 147 matched cddid_all.tbl CDD TIGR00583 TIGR00583 273153 mre11 DNA repair protein (mre11). All proteins in this family for which functions are known are subunits of a nuclease complex made up of multiple proteins including MRE11 and RAD50 homologs. The functions of this nuclease complex include recombinational repair and non-homolgous end joining. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The proteins in this family are distantly related to proteins in the SbcCD complex of bacteria. [DNA metabolism, DNA replication, recombination, and repair] 405 matched cddid_all.tbl CDD TIGR00584 TIGR00584 273154 mug mismatch-specific thymine-DNA glycosylate (mug). All proteins in this family for whcih functions are known are G-T or G-U mismatch glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Used 2pf model. [DNA metabolism, DNA replication, recombination, and repair] 328 matched cddid_all.tbl CDD TIGR00585 TIGR00585 273155 mutl DNA mismatch repair protein MutL. All proteins in this family for which the functions are known are involved in the process of generalized mismatch repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 312 matched cddid_all.tbl CDD TIGR00586 TIGR00586 200031 mutt mutator mutT protein. All proteins in this family for which functions are known are involved in repairing oxidative damage to dGTP (they are 8-oxo-dGTPases). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Lowering the threshold picks up members of MutT superfamily well. [DNA metabolism, DNA replication, recombination, and repair] 128 matched cddid_all.tbl CDD TIGR00587 TIGR00587 273156 nfo apurinic endonuclease (APN1). All proteins in this family for which functions are known are 5' AP endonculeases that are used in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 274 matched cddid_all.tbl CDD TIGR00588 TIGR00588 211589 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily. [DNA metabolism, DNA replication, recombination, and repair] 310 matched cddid_all.tbl CDD TIGR00589 TIGR00589 273157 ogt O-6-methylguanine DNA methyltransferase. All proteins in this family for which functions are known are involved alkyl-DNA transferases which remove alkyl groups from DNA as part of alkylation DNA repair. Some of the proteins in this family are also transcription regulators and have a distinct transcription regulatory domain. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 80 matched cddid_all.tbl CDD TIGR00590 TIGR00590 273158 pcna proliferating cell nuclear antigen (pcna). All proteins in this family for which functions are known form sliding DNA clamps that are used in DNA replication processes. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 259 matched cddid_all.tbl CDD TIGR00591 TIGR00591 129679 phr2 photolyase PhrII. All proteins in this family for which functions are known are DNA-photolyases used for the direct repair of UV irradiation induced DNA damage. Some repair 6-4 photoproducts while others repair cyclobutane pyrimidine dimers. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 454 matched cddid_all.tbl CDD TIGR00592 TIGR00592 273159 pol2 DNA polymerase (pol2). All proteins in this superfamily for which functions are known are DNA polymerases.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 1172 matched cddid_all.tbl CDD TIGR00593 TIGR00593 273160 pola DNA polymerase I. All proteins in this family for which functions are known are DNA polymerases Many also have an exonuclease motif. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 887 matched cddid_all.tbl CDD TIGR00594 TIGR00594 273161 polc DNA-directed DNA polymerase III (polc). All proteins in this family for which functions are known are DNA polymerases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 1022 matched cddid_all.tbl CDD TIGR00595 TIGR00595 273162 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 505 matched cddid_all.tbl CDD TIGR00596 TIGR00596 273163 rad1 DNA repair protein (rad1). All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombinational repair in some species. Most Archaeal species also have homologs of these genes, but the function of these Archaeal genes is not known, so we have set our cutoff to only pick up the eukaryotic genes.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit [DNA metabolism, DNA replication, recombination, and repair] 814 matched cddid_all.tbl CDD TIGR00597 TIGR00597 129685 rad10 DNA repair protein rad10. All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 112 matched cddid_all.tbl CDD TIGR00598 TIGR00598 273164 rad14 DNA repair protein. All proteins in this family for which functions are known are used for the recognition of DNA damage as part of nucleotide excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 172 matched cddid_all.tbl CDD TIGR00599 TIGR00599 273165 rad18 DNA repair protein rad18. All proteins in this family for which functions are known are involved in nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 397 matched cddid_all.tbl CDD TIGR00600 TIGR00600 273166 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 1034 matched cddid_all.tbl CDD TIGR00601 TIGR00601 273167 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 378 matched cddid_all.tbl CDD TIGR00602 TIGR00602 129690 rad24 checkpoint protein rad24. All proteins in this family for which functions are known are involved in DNA damage tolerance (likely cell cycle checkpoints).This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 637 matched cddid_all.tbl CDD TIGR00603 TIGR00603 273168 rad25 DNA repair helicase rad25. All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 732 matched cddid_all.tbl CDD TIGR00604 TIGR00604 273169 rad3 DNA repair helicase (rad3). All proteins in this family for which funcitons are known are DNA-DNA helicases that funciton in the initiation of transcription and nucleotide excision repair as part of the TFIIH complex. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 705 matched cddid_all.tbl CDD TIGR00605 TIGR00605 273170 rad4 DNA repair protein rad4. All proteins in this family for which functions are known are involved in targeting nucleotide excision repair to specific regions of the genome.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 713 matched cddid_all.tbl CDD TIGR00606 TIGR00606 129694 rad50 rad50. All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). 1311 matched cddid_all.tbl CDD TIGR00607 TIGR00607 129695 rad52 recombination protein rad52. All proteins in this family for which functions are known are involved in recombination and recombination repair. Their exact biochemical activity is not yet known.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 161 matched cddid_all.tbl CDD TIGR00608 TIGR00608 273171 radc DNA repair protein radc. The genes in this family for which the functions are known have an as yet porrly defined role in determining sensitivity to DNA damaging agents such as UV irradiation. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 218 matched cddid_all.tbl CDD TIGR00609 TIGR00609 273172 recB exodeoxyribonuclease V, beta subunit. The RecBCD holoenzyme is a multifunctional nuclease with potent ATP-dependent exodeoxyribonuclease activity. Ejection of RecD, as occurs at chi recombinational hotspots, cripples exonuclease activity in favor of recombinagenic helicase activity. All proteins in this family for which functions are known are DNA-DNA helicases that are used as part of an exonuclease-helicase complex (made up of RecBCD homologs) that function to generate substrates for the initiation of recombination and recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 1087 matched cddid_all.tbl CDD TIGR00611 TIGR00611 273173 recf recF protein. All proteins in this family for which functions are known are DNA binding proteins that assist the filamentation of RecA onto DNA for the initiation of recombination or recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 365 matched cddid_all.tbl CDD TIGR00612 TIGR00612 273174 ispG_gcpE 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase. This protein of previously unknown biochemical function has now been identified as an enzyme of the non-mevalonate pathway of IPP biosynthesis. Chlamydial members of the family have a long insert. The family is largely restricted to Bacteria, where it is widely but not universally distributed. No homology can be detected between the GcpE family and other proteins. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 346 matched cddid_all.tbl CDD TIGR00613 TIGR00613 273175 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair. [DNA metabolism, DNA replication, recombination, and repair] 241 matched cddid_all.tbl CDD TIGR00614 TIGR00614 129701 recQ_fam ATP-dependent DNA helicase, RecQ family. All proteins in this family for which functions are known are 3'-5' DNA-DNA helicases. These proteins are used for recombination, recombinational repair, and possibly maintenance of chromosome stability. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 470 matched cddid_all.tbl CDD TIGR00615 TIGR00615 273176 recR recombination protein RecR. All proteins in this family for which functions are known are involved in the initiation of recombination and recombinational repair. RecF is also required. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 195 matched cddid_all.tbl CDD TIGR00616 TIGR00616 129703 rect recombinase, phage RecT family. All proteins in this family for which functions are known bind ssDNA and are involved in the the pairing of homologous DNA This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). RecT and homologs are found in prophage regions of bacterial genomes. RecT works with a partner protein, RecE. [DNA metabolism, DNA replication, recombination, and repair, Mobile and extrachromosomal element functions, Prophage functions] 241 matched cddid_all.tbl CDD TIGR00617 TIGR00617 273177 rpa1 replication factor-a protein 1 (rpa1). All proteins in this family for which functions are known are part of a multiprotein complex made up of homologs of RPA1, RPA2 and RPA3 that bind ssDNA and function in the recognition of DNA damage for nucleotide excision repairThis family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 608 matched cddid_all.tbl CDD TIGR00618 TIGR00618 129705 sbcc exonuclease SbcC. All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 1042 matched cddid_all.tbl CDD TIGR00619 TIGR00619 273178 sbcd exonuclease SbcD. All proteins in this family for which functions are known are double-stranded DNA exonuclease (as part of a complex with SbcC homologs). This complex functions in the initiation of recombination and recombinational repair and is particularly important in regulating the stability of DNA sections that can form secondary structures. This family is likely homologous to the MRE11 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 253 matched cddid_all.tbl CDD TIGR00621 TIGR00621 273179 ssb single stranded DNA-binding protein (ssb). All proteins in this family for which functions are known are single-stranded DNA binding proteins that function in many processes including transcription, repair, replication and recombination. Members encoded between genes for ribosomal proteins S6 and S18 should be annotated as primosomal protein N (PriB). Forms in gamma-protoeobacteria are much shorter and poorly recognized by this model. Additional members of this family include phage proteins. Eukaryotic members are organellar proteins. [DNA metabolism, DNA replication, recombination, and repair] 164 matched cddid_all.tbl CDD TIGR00622 TIGR00622 129709 ssl1 transcription factor ssl1. All proteins in this family for which functions are known are components of the TFIIH complex which is involved in the initiaiton of transcription and nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 112 matched cddid_all.tbl CDD TIGR00623 TIGR00623 129710 sula cell division inhibitor SulA. All proteins in this family for which the functions are known are cell division inhibitors. In E. coli, SulA is one of the SOS regulated genes. [DNA metabolism, DNA replication, recombination, and repair] 168 matched cddid_all.tbl CDD TIGR00624 TIGR00624 129711 tag DNA-3-methyladenine glycosylase I. All proteins in this family are alkylation DNA glycosylases that function in base excision repair This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 179 matched cddid_all.tbl CDD TIGR00625 TIGR00625 273180 tfb2 Transcription factor tfb2. All proteins in this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 448 matched cddid_all.tbl CDD TIGR00627 TIGR00627 273181 tfb4 transcription factor tfb4. All proteins in this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 279 matched cddid_all.tbl CDD TIGR00628 TIGR00628 273182 ung uracil-DNA glycosylase. All proteins in this family for which functions are known are uracil-DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 211 matched cddid_all.tbl CDD TIGR00629 TIGR00629 273183 uvde UV damage endonuclease UvdE. All proteins in this family for which functions are known are UV dimer endonucleases that function in an alternative nucleotide excision repair process. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 312 matched cddid_all.tbl CDD TIGR00630 TIGR00630 273184 uvra excinuclease ABC, A subunit. This family is a member of the ABC transporter superfamily of proteins of which all members for which functions are known except the UvrA proteins are involved in the transport of material through membranes. UvrA orthologs are involved in the recognition of DNA damage as a step in nucleotide excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 925 matched cddid_all.tbl CDD TIGR00631 TIGR00631 273185 uvrb excinuclease ABC, B subunit. All proteins in this family for wich functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair] 655 matched cddid_all.tbl CDD TIGR00632 TIGR00632 211591 vsr DNA mismatch endonuclease Vsr. All proteins in this family for which functions are known are G:T mismatch endonucleases that function in a specialized mismatch repair process used usually to repair G:T mismatches in specific sections of the genome. This family was based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Members of this family typically are found near to a DNA cytosine methyltransferase. [DNA metabolism, DNA replication, recombination, and repair] 117 matched cddid_all.tbl CDD TIGR00633 TIGR00633 273186 xth exodeoxyribonuclease III (xth). All proteins in this family for which functions are known are 5' AP endonucleases that funciton in base excision repair and the repair of abasic sites in DNA.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 254 matched cddid_all.tbl CDD TIGR00634 TIGR00634 273187 recN DNA repair protein RecN. All proteins in this family for which functions are known are ATP binding proteins involved in the initiation of recombination and recombinational repair. [DNA metabolism, DNA replication, recombination, and repair] 563 matched cddid_all.tbl CDD TIGR00635 TIGR00635 129721 ruvB Holliday junction DNA helicase, RuvB subunit. All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions. [DNA metabolism, DNA replication, recombination, and repair] 305 matched cddid_all.tbl CDD TIGR00636 TIGR00636 213544 PduO_Nterm ATP:cob(I)alamin adenosyltransferase. This model represents as ATP:cob(I)alamin adenosyltransferase family corresponding to the N-terminal half of Salmonella PduO, a 1,2-propanediol utilization protein that probably is bifunctional. PduO represents one of at least three families of ATP:corrinoid adenosyltransferase: others are CobA (which partially complements PduO) and EutT. It was not clear originally whether ATP:cob(I)alamin adenosyltransferase activity resides in the N-terminal region of PduO, modeled here, but this has now become clear from the characterization of MeaD from Methylobacterium extorquens. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 171 matched cddid_all.tbl CDD TIGR00637 TIGR00637 273188 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins. [Regulatory functions, Other] 99 matched cddid_all.tbl CDD TIGR00638 TIGR00638 273189 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins. [Transport and binding proteins, Anions] 69 matched cddid_all.tbl CDD TIGR00639 TIGR00639 161973 PurN phosphoribosylglycinamide formyltransferase, formyltetrahydrofolate-dependent. This model describes phosphoribosylglycinamide formyltransferase (GAR transformylase), one of several proteins in formyl_transf (pfam00551). This enzyme uses formyl tetrahydrofolate as a formyl group donor to produce 5'-phosphoribosyl-N-formylglycinamide. PurT, a different GAR transformylase, uses ATP and formate rather than formyl tetrahydrofolate. Experimental proof includes complementation of E. coli purN mutants by orthologs from vertebrates (where it is a domain of a multifunctional protein), Bacillus subtilis, and Arabidopsis. No archaeal example was detected. In phylogenetic analyses, the member from Saccharomyces cerevisiae shows a long branch length but membership in the family, while the formyltetrahydrofolate deformylases form a closely related outgroup. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 190 matched cddid_all.tbl CDD TIGR00640 TIGR00640 129726 acid_CoA_mut_C methylmalonyl-CoA mutase C-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 and AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the C-terminal domain subfamily. In a neighbor-joining tree (methylaspartate mutase S chain as the outgroup), AF2219 branches with a coenzyme B12-dependent enzyme known not to be 5.4.99.2. 132 matched cddid_all.tbl CDD TIGR00641 TIGR00641 273190 acid_CoA_mut_N methylmalonyl-CoA mutase N-terminal domain. Methylmalonyl-CoA mutase (EC 5.4.99.2) catalyzes a reversible isomerization between L-methylmalonyl-CoA and succinyl-CoA. The enzyme uses an adenosylcobalamin cofactor. It may be a homodimer, as in mitochondrion, or a heterodimer with partially homologous beta chain that does not bind the adenosylcobalamin cofactor, as in Propionibacterium freudenreichii. The most similar archaeal sequences are separate chains, such as AF2215 abd AF2219 of Archaeoglobus fulgidus, that correspond roughly to the first 500 and last 130 residues, respectively of known methylmalonyl-CoA mutases. This model describes the N-terminal domain subfamily. In a neighbor-joining tree, AF2215 branches with a bacterial isobutyryl-CoA mutase, which is also the same length. Scoring between the noise and trusted cutoffs are the non-catalytic, partially homologous beta chains from certain heterodimeric examples of 5.4.99.2. 526 matched cddid_all.tbl CDD TIGR00642 TIGR00642 273191 mmCoA_mut_beta methylmalonyl-CoA mutase, heterodimeric type, beta chain. The adenosylcobalamin-binding, catalytic chain of methylmalonyl-CoA mutase may form homodimers, as in mitochondrion and E. coli, or heterodimers with a shorter, homologous chain that does not bind adenosylcobalamin. This model describes this non-catalytic beta chain, as found in the enzyme from Propionibacterium freudenreichii, for which the 3-dimensional structure has been solved. [Central intermediary metabolism, Other] 619 matched cddid_all.tbl CDD TIGR00643 TIGR00643 273192 recG ATP-dependent DNA helicase RecG. [DNA metabolism, DNA replication, recombination, and repair] 630 matched cddid_all.tbl CDD TIGR00644 TIGR00644 273193 recJ single-stranded-DNA-specific exonuclease RecJ. All proteins in this family are 5'-3' single-strand DNA exonucleases. These proteins are used in some aspects of mismatch repair, recombination, and recombinational repair. [DNA metabolism, DNA replication, recombination, and repair] 539 matched cddid_all.tbl CDD TIGR00645 TIGR00645 129731 HI0507 TIGR00645 family protein. This conserved hypothetical protein with four predicted transmembrane regions is found in E. coli, Haemophilus influenzae, and Helicobacter pylori, among completed genomes. A similar protein from Aquifex aeolicus appears to share a central region of homology and a similar overall arrangement of hydrophobic stretches, and forms a bidirectional best hit with several members of the seed alignment. However, it is uncertain whether the observed similarity represents full-length homology and/or equivalent function, and so it is excluded from the seed and scores below the trusted cutoff. [Hypothetical proteins, Conserved] 167 matched cddid_all.tbl CDD TIGR00646 TIGR00646 129732 MG010 DNA primase-related protein. The DNA primase DnaG of E. coli and its apparent orthologs in other eubacterial species are approximately 600 residues in length. Within this set, a conspicuous outlier in percent identity, as seen in a UPGMA difference tree, is the branch containing the Mycoplasmas. This lineage is also unique in containing the small, DNA primase-related protein modelled here, which is homologous to the central third of DNA primase. Several small regions of sequence similarity specifically to Mycoplasma sequences rather than to all DnaG homologs suggests that the divergence of this protein from DnaG post-dated the separation of bacterial lineages. The function of this DNA primase-related protein is unknown. [Unknown function, General] 218 matched cddid_all.tbl CDD TIGR00647 TIGR00647 273194 DNA_bind_WhiA DNA-binding protein WhiA. This family describes a DNA-binding protein widely conserved in Gram-positive bacteria, and occasionally occurring elsewhere, such as in Thermotoga. It is associated with cell division, and in sporulating organisms with sporulation. [Cellular processes, Cell division] 304 matched cddid_all.tbl CDD TIGR00648 TIGR00648 129734 recU recombination protein U. The Bacillus protein has been shown to be required for DNA recombination and repair. RJD 11/20/00 [DNA metabolism, DNA replication, recombination, and repair] 169 matched cddid_all.tbl CDD TIGR00649 TIGR00649 273195 MG423 beta-CASP ribonuclease, RNase J family. This family of metalloenzymes includes RNase J1 and RNase J2, involved in mRNA degradation in a wide range of organism. [Transcription, Degradation of RNA] 422 matched cddid_all.tbl CDD TIGR00651 TIGR00651 273196 pta phosphate acetyltransferase. Alternate name: phosphotransacetylase Model contains a gene from E.coli coding for ethanolamine utilization protein (euti) and also contains similarity to malate oxidoreductases [Central intermediary metabolism, Other, Energy metabolism, Fermentation] 303 matched cddid_all.tbl CDD TIGR00652 TIGR00652 273197 DapF diaminopimelate epimerase. [Amino acid biosynthesis, Aspartate family] 267 matched cddid_all.tbl CDD TIGR00653 TIGR00653 273198 GlnA glutamine synthetase, type I. Alternate name: glutamate--ammonia ligase. This model represents the dodecameric form, which can be subdivided into 1-alpha and 1-beta forms. The phylogeny of the 1-alpha and 1-beta forms appears polyphyletic. E. coli, Synechocystis PCC6803, Aquifex aeolicus, and the crenarcheon Sulfolobus acidocaldarius have form 1-beta, while Bacillus subtilis, Thermotoga maritima, and various euryarchaea has form 1-alpha. The 1-beta dodecamer from the crenarcheon Sulfolobus acidocaldarius differs from that in E. coli in that it is not regulated by adenylylation. [Amino acid biosynthesis, Glutamate family] 459 matched cddid_all.tbl CDD TIGR00654 TIGR00654 129739 PhzF_family phenazine biosynthesis protein PhzF family. Members of this family show a distant global similarity to diaminopimelate epimerases, which can be taken as the outgroup. One member of this family has been shown to act as an enzyme in the biosynthesis of the antibiotic phenazine in Pseudomonas aureofaciens. The function in other species is unclear. [Cellular processes, Toxin production and resistance] 297 matched cddid_all.tbl CDD TIGR00655 TIGR00655 273199 PurU formyltetrahydrofolate deformylase. This model describes formyltetrahydrofolate deformylases. The enzyme is a homohexamer. Sequences from a related enzyme formyl tetrahydrofolate-specific enzyme, phosphoribosylglycinamide formyltransferase, serve as an outgroup for phylogenetic analysis. Putative members of this family, scoring below the trusted cutoff, include a sequence from Rhodobacter capsulatus that lacks an otherwise conserved C-terminal region. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 280 matched cddid_all.tbl CDD TIGR00656 TIGR00656 273200 asp_kin_monofn aspartate kinase, monofunctional class. This model describes a subclass of aspartate kinases. These are mostly Lys-sensitive and not fused to homoserine dehydrogenase, unlike some Thr-sensitive and Met-sensitive forms. Homoserine dehydrogenase is part of Thr and Met but not Lys biosynthetic pathways. Aspartate kinase catalyzes a first step in the biosynthesis from Asp of Lys (and its precursor diaminopimelate), Met, and Thr. In E. coli, a distinct isozyme is inhibited by each of the three amino acid products. The Met-sensitive (I) and Thr-sensitive (II) forms are bifunctional enzymes fused to homoserine dehydrogenases and form homotetramers, while the Lys-sensitive form (III) is a monofunctional homodimer. The Lys-sensitive enzyme of Bacillus subtilis resembles the E. coli form but is an alpha 2/beta 2 heterotetramer, where the beta subunit is translated from an in-phase alternative initiator at Met-246. The protein slr0657 from Synechocystis PCC6803 is extended by a duplication of the C-terminal region corresponding to the beta chain. Incorporation of a second copy of the C-terminal domain may be quite common in this subgroup of aspartokinases. [Amino acid biosynthesis, Aspartate family] 400 matched cddid_all.tbl CDD TIGR00657 TIGR00657 273201 asp_kinases aspartate kinase. Aspartate kinase catalyzes a first step in the biosynthesis from Asp of Lys (and its precursor diaminopimelate), Met, and Thr. In E. coli, a distinct isozyme is inhibited by each of the three amino acid products. The Met-sensitive (I) and Thr-sensitive (II) forms are bifunctional enzymes fused to homoserine dehydrogenases and form homotetramers, while the Lys-sensitive form (III) is a monofunctional homodimer.The Lys-sensitive enzyme of Bacillus subtilis resembles the E. coli form but is an alpha 2/beta 2 heterotetramer, where the beta subunit is translated from an in-phase alternative initiator at Met-246. This may be a feature of a number of closely related forms, including a paralog from B. subtilis. [Amino acid biosynthesis, Aspartate family] 441 matched cddid_all.tbl CDD TIGR00658 TIGR00658 129743 orni_carb_tr ornithine carbamoyltransferase. This family of ornithine carbamoyltransferases (OTCase) is in a superfamily with the related enzyme aspartate carbamoyltransferase. Most known examples are anabolic, playing a role in arginine biosynthesis, but some are catabolic. Most OTCases are homotrimers, but the homotrimers are organized into dodecamers built from four trimers in at least two species; the catabolic OTCase of Pseudomonas aeruginosa is allosterically regulated, while OTCase of the extreme thermophile Pyrococcus furiosus shows both allostery and thermophily. [Amino acid biosynthesis, Glutamate family] 304 matched cddid_all.tbl CDD TIGR00659 TIGR00659 273202 TIGR00659 TIGR00659 family protein. Members of this small but broadly distibuted (Gram-positive, Gram-negative, and Archaeal) family appear to have multiple transmembrane segments. The function is unknown. A homolog, LrgB of Staphylococcus aureus, in the same small superfamily but in an outgroup to this subfamily, is regulated by LytSR and is suggested to act as a murein hydrolase. Of the three paralogous proteins in B. subtilis, one is a full length member of this family, one lacks the C-terminal 60 residues and has an additional 128 N-terminal residues but branches within the family in a phylogenetic tree, and one is closely related to LrgB and part of the outgroup. [Hypothetical proteins, Conserved] 226 matched cddid_all.tbl CDD TIGR00661 TIGR00661 273203 MJ1255 conserved hypothetical protein. This model represents nearly the full length of MJ1255 from Methanococcus jannaschii and of an unpublished protein from Vibrio cholerae, as well as the C-terminal half of a protein from Methanobacterium thermoautotrophicum. A small region (~50 amino acids) within the domain appears related to a family of sugar transferases. [Hypothetical proteins, Conserved] 321 matched cddid_all.tbl CDD TIGR00663 TIGR00663 273204 dnan DNA polymerase III, beta subunit. All proteins in this family for which functions are known are components of the DNA polymerase III complex (beta subunit). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 367 matched cddid_all.tbl CDD TIGR00664 TIGR00664 273205 DNA_III_psi DNA polymerase III, psi subunit. This small subunit of the DNA polymerase III holoenzyme in E. coli and related species appearsto have a narrow taxonomic distribution. It is not found so far outside the gamma subdivision proteobacteria. [DNA metabolism, DNA replication, recombination, and repair] 124 matched cddid_all.tbl CDD TIGR00665 TIGR00665 273206 DnaB replicative DNA helicase. This model describes the helicase DnaB, a homohexameric protein required for DNA replication. The homohexamer can form a ring around a single strand of DNA near a replication fork. An intein of > 400 residues is found at a conserved location in DnaB of Synechocystis PCC6803, Rhodothermus marinus (both experimentally confirmed), and Mycobacterium tuberculosis. The intein removes itself by a self-splicing reaction. The seed alignment contains inteins so that the model built from the seed alignment will model a low cost at common intein insertion sites. [DNA metabolism, DNA replication, recombination, and repair] 432 matched cddid_all.tbl CDD TIGR00666 TIGR00666 200042 PBP4 D-alanyl-D-alanine carboxypeptidase, serine-type, PBP4 family. In E. coli, this protein is known as penicillin binding protein 4 (dacB). A signal sequence is cleaved from a precursor form. The protein is described as periplasmic in E. coli (Gram-negative) and extracellular in Actinomadura R39 (Gram-positive). Unlike some other proteins with similar activity, it does not form transpeptidation. It is not essential for viability. This family is related to class A beta-lactamases. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 333 matched cddid_all.tbl CDD TIGR00667 TIGR00667 273207 aat leucyl/phenylalanyl-tRNA--protein transferase. The N-terminal residue controls the biological half-life of many proteins via the N-end rule pathway. This enzyme transfers a Leu or Phe to the amino end of certain proteins to enable degradation. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 185 matched cddid_all.tbl CDD TIGR00668 TIGR00668 273208 apaH "bis(5'-nucleosyl)-tetraphosphatase (symmetrical). Diadenosine 5',5""'-P1,P4-tetraphosphate (Ap4A) is a regulatory metabolite of stress conditions. It is hydrolyzed to two ADP by this enzyme. Alternate names include diadenosine-tetraphosphatase and Ap4A hydrolase. [Cellular processes, Adaptations to atypical conditions]" 279 matched cddid_all.tbl CDD TIGR00669 TIGR00669 129752 asnA aspartate--ammonia ligase, AsnA-type. This model represents one of two non-homologous forms of aspartate--ammonia ligase (asparagine synthetase) found in E. coli. This type is also found in Haemophilus influenzae, Treponema pallidum and Lactobacillus delbrueckii, but appears to have a very limited distribution. The fact that the protein from the H. influenzae is more than 70 % identical to that from the spirochete Treponema pallidum, but less than 65 % identical to that from the closely related E. coli, strongly suggests lateral transfer. [Amino acid biosynthesis, Aspartate family] 330 matched cddid_all.tbl CDD TIGR00670 TIGR00670 273209 asp_carb_tr aspartate carbamoyltransferase. Aspartate transcarbamylase (ATCase) is an alternate name.PyrB encodes the catalytic chain of aspartate carbamoyltransferase, an enzyme of pyrimidine biosynthesis, which organizes into trimers. In some species, including E. coli and the Archaea but excluding Bacillus subtilis, a regulatory subunit PyrI is also present in an allosterically regulated hexameric holoenzyme. Several molecular weight classes of ATCase are described in MEDLINE:96303527 and often vary within taxa. PyrB and PyrI are fused in Thermotoga maritima.Ornithine carbamoyltransferases are in the same superfamily and form an outgroup. [Purines, pyrimidines, nucleosides, and nucleotides, Pyrimidine ribonucleotide biosynthesis] 301 matched cddid_all.tbl CDD TIGR00671 TIGR00671 273210 baf pantothenate kinase, type III. This model describes a family of proteins found in a single copy in at least ten different early completed bacterial genomes. The only characterized member of the family is Bvg accessory factor (Baf), a protein required, in addition to the regulatory operon bvgAS, for heterologous transcription of the Bordetella pertussis toxin operon (ptx) in E. coli. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pantothenate and coenzyme A] 243 matched cddid_all.tbl CDD TIGR00672 TIGR00672 129755 cdh CDP-diacylglycerol diphosphatase, bacterial type. This model finds only bacterial examples of CDP-diacylglycerol pyrophosphatase. The member from Mycobacterium tuberculosis, the only non-proteobacterial example, is only tentatively identified and scores below the trusted cutoff. No homology is detected to functionally similar mammalian enzymes. Alternate names for this enzyme include CDP-diglyceride hydrolase and CDP-diacylglycerol hydrolase. [Fatty acid and phospholipid metabolism, Biosynthesis] 250 matched cddid_all.tbl CDD TIGR00673 TIGR00673 213549 cynS cyanase. Alternate names include cyanate C-N-lyase, cyanate hydratase, and cyanate hydrolase. [Cellular processes, Detoxification] 150 matched cddid_all.tbl CDD TIGR00674 TIGR00674 129757 dapA 4-hydroxy-tetrahydrodipicolinate synthase. Members of this family are 4-hydroxy-tetrahydrodipicolinate synthase, previously (incorrectly) called dihydrodipicolinate synthase. It is a homotetrameric enzyme of lysine biosynthesis. E. coli has several paralogs closely related to dihydrodipicoline synthase (DapA), as well as the more distant N-acetylneuraminate lyase. In Pyrococcus horikoshii, the bidirectional best hit with E. coli is to an uncharacterized paralog of DapA, not DapA itself, and it is omitted from the seed. The putative members from the Chlamydias (pathogens with a parasitic metabolism) are easily the most divergent members of the multiple alignment. [Amino acid biosynthesis, Aspartate family] 285 matched cddid_all.tbl CDD TIGR00675 TIGR00675 273211 dcm DNA-methyltransferase (dcm). All proteins in this family for which functions are known are DNA-cytosine methyltransferases. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] 315 matched cddid_all.tbl CDD TIGR00676 TIGR00676 273212 fadh2 5,10-methylenetetrahydrofolate reductase, prokaryotic form. The enzyme activities methylenetetrahydrofolate reductase (EC 1.5.1.20) and 5,10-methylenetetrahydrofolate reductase (FADH) (EC 1.7.99.5) differ in that 1.5.1.20 (assigned in many eukaryotes) is defined to use NADP+ as an acceptor, while 1.7.99.5 (assigned in many bacteria) is flexible with respect to the acceptor; both convert 5-methyltetrahydrofolate to 5,10-methylenetetrahydrofolate. From a larger set of proteins assigned as 1.5.1.20 and 1.7.99.5, this model describes the subset of proteins found in bacteria, and currently designated 1.7.99.5. This protein is an FAD-containing flavoprotein. [Amino acid biosynthesis, Aspartate family] 272 matched cddid_all.tbl CDD TIGR00677 TIGR00677 129760 fadh2_euk methylenetetrahydrofolate reductase, eukaryotic type. The enzyme activities methylenetetrahydrofolate reductase (EC 1.5.1.20) and 5,10-methylenetetrahydrofolate reductase (FADH) (EC 1.7.99.5) differ in that 1.5.1.20 (assigned in many eukaryotes) is defined to use NADP+ as an acceptor, while 1.7.99.5 (assigned in many bacteria) is flexible with respect to the acceptor; both convert 5-methyltetrahydrofolate to 5,10-methylenetetrahydrofolate. From a larger set of proteins assigned as 1.5.1.20 and 1.7.99.5, this model describes the subset of proteins found in eukaryotes and designated 1.5.1.20. This protein is an FAD-containing flavoprotein. [Biosynthesis of cofactors, prosthetic groups, and carriers, Folic acid] 281 matched cddid_all.tbl CDD TIGR00678 TIGR00678 273213 holB DNA polymerase III, delta' subunit. This model describes the N-terminal half of the delta' subunit of DNA polymerase III. Delta' is homologous to the gamma and tau subunits, which form an outgroup for phylogenetic comparison. The gamma/tau branch of the tree is much more tighly conserved than the delta' branch, and some members of that branch score more highly against this model than some proteins classisified as delta'. The noise cutoff is set to detect weakly scoring delta' subunits rather than to exclude gamma/tau subunits. At position 126-127 of the seed alignment, this family lacks the HM motif of gamma/tau; at 132 it has a near-invariant A vs. an invariant F in gamma/tau. [DNA metabolism, DNA replication, recombination, and repair] 188 matched cddid_all.tbl CDD TIGR00679 TIGR00679 273214 hpr-ser Hpr(Ser) kinase/phosphatase. Members of this family are the bifunctional enzyme, HPr kinase/phosphatase. All members of the seed alignment (n=57) have a gene tightly clustered with a gene for the phospocarrier protein HPr, its target. [Regulatory functions, Protein interactions, Signal transduction, PTS] 300 matched cddid_all.tbl CDD TIGR00680 TIGR00680 273215 kdpA K+-transporting ATPase, KdpA. Kdp is a high affinity ATP-driven K+ transport system in Escherichia coli. It is composed of three membrane-bound subunits, KdpA, KdpB and KdpC and one small peptide, KdpF. KdpA is the K+-transporting subunit of this complex. During assembly of the complex, KdpA and KdpC bind to each other. This interaction is thought to stabilize the complex [medline:9858692]. Data indicates that KdpC might connect the KdpA, the K+-transporting subunit, to KdpB, the ATP-hydrolyzing (energy providing) subunit [medline:9858692]. [Transport and binding proteins, Cations and iron carrying compounds] 563 matched cddid_all.tbl CDD TIGR00681 TIGR00681 129764 kdpC K+-transporting ATPase, C subunit. This chain has a single predicted transmembrane region near the amino end. It is part of a K+-transport ATPase that contains two other membrane-bound subunits, KdpA and KdpB, and a small subunit KdpF. KdpA is the K+-translocating subunit, KdpB the ATP-hydrolyzing subunit. During assembly of the complex, KdpA and KdpC bind to each other. This interaction is thought to stabilize the complex [MEDLINE:9858692]. Data indicates that KdpC might connect the KdpA, the K+-transporting subunit, to KdpB, the ATP-hydrolyzing (energy providing) subunit [MEDLINE:9858692]. [Transport and binding proteins, Cations and iron carrying compounds] 187 matched cddid_all.tbl CDD TIGR00682 TIGR00682 273216 lpxK tetraacyldisaccharide 4'-kinase. Also called lipid-A 4'-kinase. This essential gene encodes an enzyme in the pathway of lipid A biosynthesis in Gram-negative organisms. A single copy of this protein is found in Gram-negative bacteria. PSI-BLAST converges on this set of apparent orthologs without identifying any other homologs. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 311 matched cddid_all.tbl CDD TIGR00683 TIGR00683 273217 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides, Central intermediary metabolism, Amino sugars] 293 matched cddid_all.tbl CDD TIGR00684 TIGR00684 273218 narJ nitrate reductase molybdenum cofactor assembly chaperone. This protein is termed NarJ in most species that have a single copy, and has been called the delta subunit of nitrate reductase. However, although it is required for correct assembly of active enzyme, it dissociates and is not part of the enzyme. Two hits to this model are found each in E. coli and in Mycobacterium tuberculosis, but in each case duplication to create paralogs appears to be recent. The NarX protein of Mycobacterium tuberculosis includes one of these paralogs as a domain, fused to structural domains of nitrate reductases before and after the NarJ-homologous region. [Protein fate, Protein folding and stabilization] 152 matched cddid_all.tbl CDD TIGR00685 TIGR00685 273219 T6PP trehalose-phosphatase. Trehalose, a neutral disaccharide of two glucose residues, is an important osmolyte for dessication and/or salt tolerance in a number of prokaryotic and eukaryotic species, including E. coli, Saccharomyces cerevisiae, and Arabidopsis thaliana. Many bacteria also utilize trehalose in the synthesis of trehalolipids, specialized cell wall constituents believed to be involved in the uptake of hydrophobic substances. Trehalose dimycolate (TDM, cord factor) and related substances are important constituents of the mycobacterial waxy coat and responsible for various clinically important immunological interactions with host organism. This enzyme, trehalose-phosphatase, removes a phosphate group in the final step of trehalose biosynthesis. The trehalose-phosphatase from Saccharomyces cerevisiae is fused to the synthase. At least 18 distinct sequences from Arabidopsis have been identified, roughly half of these are of the fungal type, with a fused synthase and half are like the bacterial members having only the phosphatase domain. It has been suggested that trehalose is being used in Arabidopsis as a regulatory molecule in development and possibly other processes. [Cellular processes, Adaptations to atypical conditions] 244 matched cddid_all.tbl CDD TIGR00686 TIGR00686 273220 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997). [Unknown function, General] 109 matched cddid_all.tbl CDD TIGR00687 TIGR00687 273221 pyridox_kin pyridoxal kinase. E. coli has an enzyme PdxK that acts in vitro as a pyridoxine/pyridoxal/pyridoxamine kinase, but mutants lacking PdxK activity retain a specific pyridoxal kinase, PdxY. PdxY acts in the salvage pathway of pyridoxal 5'-phosphate biosynthesis. Mammalian forms of pyridoxal kinase are more similar to PdxY than to PdxK. The PdxK isozyme is omitted from the seed alignment but scores above the trusted cutoff.ThiD and related proteins form an outgroup. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridoxine] 287 matched cddid_all.tbl CDD TIGR00688 TIGR00688 129771 rarD rarD protein. This uncharacterized protein is predicted to have many membrane-spanning domains. [Transport and binding proteins, Unknown substrate] 256 matched cddid_all.tbl CDD TIGR00689 TIGR00689 129772 rpiB_lacA_lacB sugar-phosphate isomerase, RpiB/LacA/LacB family. Proteins of known function in this family act as sugar (pentose and/or hexose)-phosphate isomerases, including the LacA and LacB subunits of galactose-6-phosphate isomerases from Gram-positive bacteria and RpiB. RpiB is the second ribose phosphate isomerase of E. coli. It lacks homology to RpiA, its inducer is unknown (but is not ribose), and it can be replaced by the homologous galactose-6-phosphate isomerase of Streptococcus mutans, all of which suggests that the ribose phosphate isomerase activity of RpiB is a secondary function. On the other hand, there appear to be a significant number of species which contain rpiB, lack rpiA and seem to require rpi activity in order to complete the pentose phosphate pathway. 144 matched cddid_all.tbl CDD TIGR00690 TIGR00690 188073 rpoZ DNA-directed RNA polymerase, omega subunit. This small component of highly purified E. coli RNA polymerase is not required for transcription, but acts in assembly and is present in stochiometric amounts. The trusted cutoff excludes archaeal homologs but captures some organellar sequences. [Transcription, DNA-dependent RNA polymerase] 60 matched cddid_all.tbl CDD TIGR00691 TIGR00691 213552 spoT_relA (p)ppGpp synthetase, RelA/SpoT family. The functions of E. coli RelA and SpoT differ somewhat. RelA (EC 2.7.6.5) produces pppGpp (or ppGpp) from ATP and GTP (or GDP). SpoT (EC 3.1.7.2) degrades ppGpp, but may also act as a secondary ppGpp synthetase. The two proteins are strongly similar. In many species, a single homolog to SpoT and RelA appears reponsible for both ppGpp synthesis and ppGpp degradation. (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species. [Cellular processes, Adaptations to atypical conditions] 683 matched cddid_all.tbl CDD TIGR00692 TIGR00692 129775 tdh L-threonine 3-dehydrogenase. This protein is a tetrameric, zinc-binding, NAD-dependent enzyme of threonine catabolism. Closely related proteins include sorbitol dehydrogenase, xylitol dehydrogenase, and benzyl alcohol dehydrogenase. Eukaryotic examples of this enzyme have been demonstrated experimentally but do not appear in database search results.E. coli His-90 modulates substrate specificity and is believed part of the active site. [Energy metabolism, Amino acids and amines] 340 matched cddid_all.tbl CDD TIGR00693 TIGR00693 273222 thiE thiamine-phosphate diphosphorylase. This model represents the thiamine-phosphate pyrophosphorylase, ThiE, of a number of bacteria, and N-terminal domains of bifunctional thiamine proteins of Saccharomyces cerevisiae and Schizosaccharomyces pombe, in which the C-terminal domain corresponds to the bacterial hydroxyethylthiazole kinase (EC 2.7.1.50), ThiM. This model includes ThiE from Bacillus subtilis but excludes its paralog, the regulatory protein TenI (SP:P25053), and neighbors of TenI. [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine] 196 matched cddid_all.tbl CDD TIGR00694 TIGR00694 188074 thiM hydroxyethylthiazole kinase. This model represents the hydoxyethylthiazole kinase, ThiM, of a number of bacteria, and C-terminal domains of bifunctional thiamine biosynthesis proteins of Saccharomyces cerevisiae and Schizosaccharomyces pombe, in which the N-terminal domain corresponds to the bacterial thiamine-phosphate pyrophosphorylase (EC 2.5.1.3), ThiE. [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine] 249 matched cddid_all.tbl CDD TIGR00695 TIGR00695 129778 uxuA mannonate dehydratase. This Fe2+-requiring enzyme plays a role in D-glucuronate catabolism in Escherichia coli. Mannonate dehydratase converts D-mannonate to 2-dehydro-3-deoxy-D-gluconate. An apparent equivalog is found in a glucuronate utilization operon in Bacillus stearothermophilus T-6. [Energy metabolism, Sugars] 394 matched cddid_all.tbl CDD TIGR00696 TIGR00696 129779 wecG_tagA_cpsF bacterial polymer biosynthesis proteins, WecB/TagA/CpsF family. The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 177 matched cddid_all.tbl CDD TIGR00697 TIGR00697 129780 TIGR00697 conserved hypothetical integral membrane protein. All known members of this family are proteins or 210-250 amino acids in length. Conserved regions of hydrophobicity suggest that all members of the family are integral membrane proteins. [Hypothetical proteins, Conserved] 202 matched cddid_all.tbl CDD TIGR00698 TIGR00698 129781 TIGR00698 conserved hypothetical integral membrane protein. Members of this family are found so far only in one archaeal species, Archaeoglobus fulgidus, and in two related bacterial species, Haemophilus influenzae and Escherichia coli. It has 9 GES predicted transmembrane regions at conserved locations in all members. These proteins have a molecular weight of approximately 35 to 38 kDa. [Hypothetical proteins, Conserved] 335 matched cddid_all.tbl CDD TIGR00699 TIGR00699 129782 GABAtrns_euk 4-aminobutyrate aminotransferase, eukaryotic type. This enzyme is a class III pyridoxal-phosphate-dependent aminotransferase. This model describes known eukaryotic examples of the enzyme. The degree of sequence difference between this set and known bacterial examples is greater than the distance between either set the most similar enzyme with distinct function, and so separate models are built for prokaryotic and eukaryotic sets. Alternate names include GABA transaminase, gamma-amino-N-butyrate transaminase, and beta-alanine--oxoglutarate aminotransferase. [Central intermediary metabolism, Other] 464 matched cddid_all.tbl CDD TIGR00700 TIGR00700 129783 GABAtrnsam 4-aminobutyrate aminotransferase, prokaryotic type. This enzyme is a class III pyridoxal-phosphate-dependent aminotransferase. This model describes known bacterial examples of the enzyme. The best archaeal matches are presumed but not trusted to have the equivalent function. The degree of sequence difference between this set and known eukaryotic (mitochondrial) examples is greater than the distance to some proteins known to have different functions, and so separate models are built for prokaryotic and eukaryotic sets. E. coli has two isozymes. Alternate names include GABA transaminase, gamma-amino-N-butyrate transaminase, and beta-alanine--oxoglutarate aminotransferase. [Central intermediary metabolism, Other] 420 matched cddid_all.tbl CDD TIGR00701 TIGR00701 273223 TIGR00701 TIGR00701 family protein. It appears this conserved hypothetical integral membrane protein is found only in gram negative bacteria. Completed genomes that include a member of this family include Rickettsia prowazekii, Synechocystis sp. PCC6803, and Helicobacter pylori. These proteins have 3 (Helicobacter pylori) to 5 (Synechocystis sp. PCC 6803) GES predicted transmembrane regions. Most members have 4 GES predicted transmembrane regions. [Hypothetical proteins, Conserved] 142 matched cddid_all.tbl CDD TIGR00702 TIGR00702 273224 TIGR00702 YcaO-type kinase domain. This protein family includes YcaO and homologs that can phosphorylate a peptide amide backbone (rather than side chains), as during heterocycle-forming modifications during maturation of the TOMM class (Thiazole/Oxazole-Modified Microcins) of bacteriocins. However, YcaO domain proteins also occur in contexts that do not suggest peptide modification. [Hypothetical proteins, Conserved] 377 matched cddid_all.tbl CDD TIGR00703 TIGR00703 129786 TIGR00703 TIGR00703 family protein. The function of this family is unknown. These proteins are from 222 to 233 residues in length, lack hydrophobic stretches, and are found so far only in thermophiles. [Hypothetical proteins, Conserved] 223 matched cddid_all.tbl CDD TIGR00704 TIGR00704 273225 NaPi_cotrn_rel Na/Pi-cotransporter. This model describes essentially the full length of an uncharacterized protein from Bacillus subtilis and correponding lengths of longer proteins from E. coli and Treponema pallidum. PSI-BLAST analysis converges to demonstrate homology to one other group of proteins, type II sodium/phosphate (Na/Pi) cotransporters. A well-conserved repeated domain in this family, approximately 60 residues in length, is also repeated in the Na/Pi cotransporters, although with greater spacing between the repeats. The two families share additional homology in the region after the first repeat, share the properly of having extensive hydrophobic regions, and may be similar in function. [Transport and binding proteins, Cations and iron carrying compounds] 308 matched cddid_all.tbl CDD TIGR00705 TIGR00705 273226 SppA_67K signal peptide peptidase SppA, 67K type. This model represents the signal peptide peptidase A (SppA, protease IV) as found in E. coli, Treponema pallidum, Mycobacterium leprae, and several other species, in which it has a molecular mass around 67 kDa and a duplication such that the N-terminal half shares extensive homology with the C-terminal half. This enzyme was shown in E. coli to form homotetramers. E. coli SohB, which is most closely homologous to the C-terminal duplication of SppA, is predicted to perform a similar function of small peptide degradation, but in the periplasm. Many prokaryotes have a single SppA/SohB homolog that may perform the function of either or both. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 584 matched cddid_all.tbl CDD TIGR00706 TIGR00706 273227 SppA_dom signal peptide peptidase SppA, 36K type. The related but duplicated, double-length protein SppA (protease IV) of E. coli was shown experimentally to degrade signal peptides as are released by protein processing and secretion. This protein shows stronger homology to the C-terminal region of SppA than to the N-terminal domain or to the related putative protease SuhB. The member of this family from Bacillus subtilis was shown to have properties consistent with a role in degrading signal peptides after cleavage from precursor proteins, although it was not demonstrated conclusively. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 208 matched cddid_all.tbl CDD TIGR00707 TIGR00707 273228 argD transaminase, acetylornithine/succinylornithine family. This family of proteins, for which ornithine aminotransferases form an outgroup, consists mostly of proteins designated acetylornithine aminotransferase. However, the two very closely related members from E. coli are assigned different enzymatic activities. One is acetylornithine aminotransferase (EC 2.6.1.11), ArgD, an enzyme of arginine biosynthesis, while another is succinylornithine aminotransferase, an enzyme of the arginine succinyltransferase pathway, an ammonia-generating pathway of arginine catabolism (See MEDLINE:98361920). Members of this family may also act on ornithine, like ornithine aminotransferase (EC 2.6.1.13) (see MEDLINE:90337349) and on succinyldiaminopimelate, like N-succinyldiaminopmelate-aminotransferase (EC 2.6.1.17, DapC, an enzyme of lysine biosynthesis) (see MEDLINE:99175097) 379 matched cddid_all.tbl CDD TIGR00708 TIGR00708 129791 cobA cob(I)alamin adenosyltransferase. Alternate name: corrinoid adenosyltransferase. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 173 matched cddid_all.tbl CDD TIGR00709 TIGR00709 129792 dat 2,4-diaminobutyrate 4-transaminases. This family consists of L-diaminobutyric acid transaminases. This general designation covers both 2.6.1.76 (diaminobutyrate-2-oxoglutarate transaminase, which uses glutamate as the amino donor in DABA biosynthesis), and 2.6.1.46 (diaminobutyrate--pyruvate transaminase, which uses alanine as the amino donor). Most members with known function are 2.6.1.76, and at least some annotations as 2.6.1.46 in current databases at time of model revision are incorrect. A distinct branch of this family contains examples of 2.6.1.76 nearly all of which are involved in ectoine biosynthesis. A related enzyme is 4-aminobutyrate aminotransferase (EC 2.6.1.19), also called GABA transaminase. These enzymes all are pyridoxal phosphate-containing class III aminotransferase. [Central intermediary metabolism, Other] 442 matched cddid_all.tbl CDD TIGR00710 TIGR00710 273229 efflux_Bcr_CflA drug resistance transporter, Bcr/CflA subfamily. This subfamily of drug efflux proteins, a part of the major faciliator family, is predicted to have 12 membrane-spanning regions. Members with known activity include Bcr (bicyclomycin resistance protein) in E. coli, Flor (chloramphenicol and florfenicol resistance) in Salmonella typhimurium DT104, and CmlA (chloramphenicol resistance) in Pseudomonas sp. plasmid R1033. 385 matched cddid_all.tbl CDD TIGR00711 TIGR00711 129794 efflux_EmrB drug resistance transporter, EmrB/QacA subfamily. This subfamily of drug efflux proteins, a part of the major faciliator family, is predicted to have 14 potential membrane-spanning regions. Members with known activities include EmrB (multiple drug resistance efflux pump) in E. coli, FarB (antibacterial fatty acid resistance) in Neisseria gonorrhoeae, TcmA (tetracenomycin C resistance) in Streptomyces glaucescens, etc. In most cases, the efflux pump is described as having a second component encoded in the same operon, such as EmrA of E. coli. [Cellular processes, Toxin production and resistance, Transport and binding proteins, Other] 485 matched cddid_all.tbl CDD TIGR00712 TIGR00712 129795 glpT glycerol-3-phosphate transporter. This model describes a very hydrophobic protein, predicted to span the membrane at least 8 times. The two members confirmed experimentally as glycerol-3-phosphate transporters, from E. coli and B. subtilis, share more than 50 % amino acid identity. Proteins of the hexose phosphate and phosphoglycerate transport systems are also quite similar. [Transport and binding proteins, Other] 438 matched cddid_all.tbl CDD TIGR00713 TIGR00713 273230 hemL glutamate-1-semialdehyde-2,1-aminomutase. This enzyme, glutamate-1-semialdehyde-2,1-aminomutase (glutamate-1-semialdehyde aminotransferase, GSA aminotransferase), contains a pyridoxal phosphate attached at a Lys residue at position 283 of the seed alignment. It is in the family of class III aminotransferases. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 423 matched cddid_all.tbl CDD TIGR00714 TIGR00714 211601 hscB Fe-S protein assembly co-chaperone HscB. This model describes the small subunit, Hsc20 (20K heat shock cognate protein) of a pair of proteins Hsc66-Hsc20, related to the DnaK-DnaJ heat shock proteins, which also serve as molecular chaperones. Hsc20, unlike DnaJ, appears not to have chaperone activity on its own, but to act solely as a regulatory subunit for Hsc66 (i.e., to be a co-chaperone). The gene for Hsc20 in E. coli, hscB, is not induced by heat shock. [Protein fate, Protein folding and stabilization] 155 matched cddid_all.tbl CDD TIGR00715 TIGR00715 273231 precor6x_red precorrin-6x reductase. This enzyme catalyzes a step in cobalamin biosynthesis. It has been identified experimentally in Pseudomonas denitrificans and has been shown to be part of cobalamin biosynthetic operons in several other species. This enzyme was found to be a monomer by gel filtration. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 256 matched cddid_all.tbl CDD TIGR00716 TIGR00716 129799 rnhC ribonuclease HIII. This enzyme cleaves RNA from DNA-RNA hybrids. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other. The only RNase H homolog in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This model describes bacterial RNase III. [DNA metabolism, DNA replication, recombination, and repair] 284 matched cddid_all.tbl CDD TIGR00717 TIGR00717 273232 rpsA ribosomal protein S1. This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned. [Protein synthesis, Ribosomal proteins: synthesis and modification] 516 matched cddid_all.tbl CDD TIGR00718 TIGR00718 129801 sda_alpha L-serine dehydratase, iron-sulfur-dependent, alpha subunit. This enzyme is also called serine deaminase. L-serine dehydratase converts serine into pyruvate in the gluconeogenesis pathway from serine. This model describes the alpha chain of an iron-sulfur-dependent L-serine dehydratase, found in Bacillus subtilis. A fairly deep split in a UPGMA tree separates members of this family of alpha chains from the homologous region of single chain forms such as found in Escherichia coli. This family of enzymes is not homologous to the pyridoxal phosphate-dependent threonine deaminases and eukaryotic serine deaminases. [Energy metabolism, Amino acids and amines, Energy metabolism, Glycolysis/gluconeogenesis] 294 matched cddid_all.tbl CDD TIGR00719 TIGR00719 129802 sda_beta L-serine dehydratase, iron-sulfur-dependent, beta subunit. This enzyme is also called serine deaminase. This model describes the beta chain of an iron-sulfur-dependent L-serine dehydratase, as in Bacillus subtilis. A fairly deep split in a UPGMA tree separates members of this family of beta chains from the homologous region of single chain forms such as found in E. coli. This family of enzymes is not homologous to the pyridoxal phosphate-dependent threonine deaminases and eukaryotic serine deaminases. [Energy metabolism, Amino acids and amines, Energy metabolism, Glycolysis/gluconeogenesis] 208 matched cddid_all.tbl CDD TIGR00720 TIGR00720 273233 sda_mono L-serine dehydratase, iron-sulfur-dependent, single chain form. This enzyme is also called serine deaminase and L-serine dehydratase 1. L-serine ammonia-lyase converts serine into pyruvate in the gluconeogenesis pathway from serine. This enzyme is comprised of a single chain in Escherichia coli, Mycobacterium tuberculosis, and several other species, but has separate alpha and beta chains in Bacillus subtilis and related species. The beta and alpha chains are homologous to the N-terminal and C-terminal regions, respectively, but are rather deeply branched in a UPGMA tree. This enzyme requires iron and dithiothreitol for activation in vitro, and is a predicted 4Fe-4S protein. Escherichia coli Pseudomonas aeruginosa have two copies of this protein. [Energy metabolism, Amino acids and amines, Energy metabolism, Glycolysis/gluconeogenesis] 450 matched cddid_all.tbl CDD TIGR00721 TIGR00721 129804 tfx DNA-binding protein, Tfx family. PSI-BLAST starting with one member of this family converges with significant hits only to other members of the family, which is restricted to the Archaea. Homology is strongest in the helix-turn-helix-containing N-terminal region. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter. [Regulatory functions, DNA interactions] 137 matched cddid_all.tbl CDD TIGR00722 TIGR00722 273234 ttdA_fumA_fumB hydro-lyases, Fe-S type, tartrate/fumarate subfamily, alpha region. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase (see PROSITE:PDOC00147). This model represents a subset of closely related proteins or modules, including the E. coli tartrate dehydratase alpha chain and the N-terminal region of the class I fumarase (where the C-terminal region is homologous to the tartrate dehydratase beta chain). The activity of archaeal proteins in this subfamily has not been established. 273 matched cddid_all.tbl CDD TIGR00723 TIGR00723 129806 ttdB_fumA_fumB hydro-lyases, Fe-S type, tartrate/fumarate subfamily, beta region. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase (see PROSITE:PDOC00147). This model represents a subset of closely related proteins or modules, including the E. coli tartrate dehydratase beta chain and the C-terminal region of the class I fumarase (where the N-terminal region is homologous to the tartrate dehydratase alpha chain). The activity of archaeal proteins in this subfamily has not been established. 168 matched cddid_all.tbl CDD TIGR00724 TIGR00724 129807 urea_amlyse_rel biotin-dependent carboxylase uncharacterized domain. Urea amidolyase of Saccharomyces cerevisiae is a 1835 amino acid protein with an amidase domain, a biotin/lipoyl cofactor attachment domain, a carbamoyl-phosphate synthase L chain-like domain, and uncharacterized regions. It has both urea carboxylase and allophanate hydrolase activities. This model models a domain that represents uncharacterized prokaryotic proteins of about 300 amino acids, regions of prokaryotic urea carboxylase and of the urea carboxylase region of yeast urea amidolyase, and regions of other biotin-containing proteins. [Unknown function, General] 314 matched cddid_all.tbl CDD TIGR00725 TIGR00725 129808 TIGR00725 TIGR00725 family protein. This model represents one branch of a subfamily of uncharacterized proteins. Both PSI-BLAST and weak hits by this model show a low level of similarity and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting the branches may have distinct functions. This family is one of several families within the scope of pfam03641, several members of which are annotated as lysine decarboxylases. That larger family, and the branch described by this model, have a well-conserved motif PGGXGTXXE. [Hypothetical proteins, Conserved] 159 matched cddid_all.tbl CDD TIGR00726 TIGR00726 273235 TIGR00726 YfiH family protein. PSI-BLAST converges on members of this family of uncharacterized bacterial proteins and shows no significant similarity to any characterized protein. No completed genome to date has two members. Members of the family have been crystallized but the function is unknown. [Unknown function, General] 221 matched cddid_all.tbl CDD TIGR00727 TIGR00727 129810 ISP4_OPT small oligopeptide transporter, OPT family. This model represents a family of transporters of small oligopeptides, demonstrated experimentally in three different species of yeast. A set of related proteins from the plant Arabidopsis thaliana forms an outgroup to the yeast set by neighbor joining analysis but is remarkably well conserved and is predicted here to have equivalent function. [Transport and binding proteins, Amino acids, peptides and amines] 681 matched cddid_all.tbl CDD TIGR00728 TIGR00728 273236 OPT_sfam oligopeptide transporter, OPT superfamily. This superfamily has two main branches. One branch contains a tetrapeptide transporter demonstrated experimentally in three different species of yeast. The other family contains EspB of Myxococcus xanthus, a protein required for normal rather than delayed sporulation after cellular aggregation; its role is unknown but is compatible with transport of a signalling molecule. Homology between the two branches of the superfamily is seen most easily at the ends of the protein. The central regions are poorly conserved within each branch and may not be homologous between branches. 657 matched cddid_all.tbl CDD TIGR00729 TIGR00729 129812 TIGR00729 ribonuclease H, mammalian HI/archaeal HII subfamily. This enzyme cleaves RNA from DNA-RNA hybrids. Archaeal members of this subfamily of RNase H are designated RNase HII and one has been shown to be active as a monomer. A member from Homo sapiens was characterized as RNase HI, large subunit. [DNA metabolism, DNA replication, recombination, and repair] 206 matched cddid_all.tbl CDD TIGR00730 TIGR00730 129813 TIGR00730 TIGR00730 family protein. This model represents one branch of a subfamily of proteins of unknown function. Both PSI-BLAST and weak hits by this model show a low level of similarity to and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting that the branches may have distinct functions. [Hypothetical proteins, Conserved] 178 matched cddid_all.tbl CDD TIGR00731 TIGR00731 273237 bL25_bact_ctc ribosomal protein bL25, Ctc-form. This model models a family of proteins with full-length homology to the general stress protein Ctc of Bacillus subtilis, a mesophile, and ribosomal protein TL5 of Thermus thermophilus, a thermophile. Ribosomal protein L25 of Escherichia coli and H. influenzae appear to be orthologous but consist only of the N-terminal half of Ctc and TL5. Both short (L25-like) and full-length (CTC-like) members of this family bind the E-loop of bacterial 5S rRNA. This protein appears to be restricted to bacteria and organelles, and consists of at most one copy per prokaryotic genome.Ctc of Bacillus subtilis has now been localized to ribosomes and can be viewed as the long form, or Ctc form, of L25. The C-terminal domain of sll1824, an apparent L25 of Synechocystis PCC6803, matches the N-terminal domain of this family. Examples of L25 and Ctc are not separated by a UPGMA tree built on the region of shared homology. [Protein synthesis, Ribosomal proteins: synthesis and modification] 176 matched cddid_all.tbl CDD TIGR00732 TIGR00732 273238 dprA DNA protecting protein DprA. Disruption of this gene in both Haemophilus influenzae and Helicobacter pylori drastically reduces the efficiency of transformation with exogenous DNA, but with different levels of effect on chromosomal (linear) and plasmid (circular) DNA. This difference suggests the DprA is not active in recombination, and it has been shown not to affect DNA binding, leaving the intermediate step in natural transformation, DNA processing. In Strep. pneumoniae, inactivation of dprA had no effect on the uptake of DNA. All of these data indicated that DprA is required at a later stage in transformation. Subsequently DprA and RecA were both shown in S. pneumoniae to be required to protect incoming ssDNA from immediate degradation. Role of DprA in non-transformable species is not known. The gene symbol smf was assigned in E. coli, but without assignment of function. [Cellular processes, DNA transformation] 220 matched cddid_all.tbl CDD TIGR00733 TIGR00733 273239 TIGR00733 putative oligopeptide transporter, OPT family. This protein represents a small family of integral membrane proteins from Gram-negative bacteria, a Gram-positive bacteria, and an archaeal species. Members of this family contain 15 to 18 GES predicted transmembrane regions, and this family has extensive homology to a family of yeast tetrapeptide transporters, including isp4 (Schizosaccharomyces pombe) and Opt1 (Candida albicans). EspB, an apparent equivalog from Myxococcus xanthus, shares an operon with a two component system regulatory protein, and is required for the normal timing of sporulation after the aggregation of cells. This is consistent with a role in transporting oligopeptides as signals across the membrane. [Transport and binding proteins, Amino acids, peptides and amines] 591 matched cddid_all.tbl CDD TIGR00734 TIGR00734 273240 hisAF_rel hisA/hisF family protein. This model models a family of proteins found so far in three archaeal species: Methanobacterium thermoautotrophicum, Methanococcus jannaschii, and Archaeoglobus fulgidus. This protein is homologous to phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (HisA) and, with lower similarity, to the cyclase HisF, both of which are enzymes of histidine biosynthesis. Each species with this protein also encodes HisA. The function of this protein is unknown. [Unknown function, General] 221 matched cddid_all.tbl CDD TIGR00735 TIGR00735 273241 hisF imidazoleglycerol phosphate synthase, cyclase subunit. [Amino acid biosynthesis, Histidine family] 254 matched cddid_all.tbl CDD TIGR00736 TIGR00736 129819 nifR3_rel_arch TIM-barrel protein, putative. Members of this family show a distant relationship by PSI-BLAST to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. At least two closely related but well-separable families among the bacteria, the nifR3/yhdG family and the yjbN family, share a more distant relationship to this family of shorter, exclusively archaeal proteins. [Unknown function, General] 231 matched cddid_all.tbl CDD TIGR00737 TIGR00737 129820 nifR3_yhdG putative TIM-barrel protein, nifR3 family. This model represents one branch of COG0042 (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family). This branch includes NifR3 itself, from Rhodobacter capsulatus. It excludes a broadly distributed but more sparsely populated subfamily that contains sll0926 from Synechocystis PCC6803, HI0634 from Haemophilus influenzae, and BB0225 from Borrelia burgdorferi. It also excludes a shorter and more distant archaeal subfamily.The function of nifR3, a member of this family, is unknown, but it is found in an operon with nitrogen-sensing two component regulators in Rhodobacter capsulatus.Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. [Unknown function, General] 319 matched cddid_all.tbl CDD TIGR00738 TIGR00738 273242 rrf2_super Rrf2 family protein. This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency. [Unknown function, General] 132 matched cddid_all.tbl CDD TIGR00739 TIGR00739 273243 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas. [Protein fate, Protein and peptide secretion and trafficking] 84 matched cddid_all.tbl CDD TIGR00740 TIGR00740 273244 TIGR00740 tRNA (cmo5U34)-methyltransferase. This tRNA methyltransferase is involved, together with cmoB, in preparing the uridine-5-oxyacetic acid (cmo5U) at position 34. [Unknown function, Enzymes of unknown specificity] 239 matched cddid_all.tbl CDD TIGR00741 TIGR00741 129824 yfiA ribosomal subunit interface protein. This model includes a small protein encoded by one of two genes, both downstream of the gene rpoN for sigma 54, whose deletion leads to increased expression from sigma 54-dependent promoters. It also includes the N-terminal half of a light-repressed protein LtrA of Synechococcus PCC 7002 and the N-terminal region (after removal of the transit peptide) of a larger plastid-specific ribosomal protein of spinach. The member of this family from E. coli is now recognized as a protein at the interace between ribosomal large and small subunits, with about 1/3 as many copies per cell as the number of ribosomes. [Protein synthesis, Translation factors] 95 matched cddid_all.tbl CDD TIGR00742 TIGR00742 129825 yjbN tRNA dihydrouridine synthase A. This model represents one branch of COG0042 (Predicted TIM-barrel enzymes, possibly dehydrogenases, nifR3 family). It represents a distinct subset by a set of shared unique motifs, a conserved pattern of insertions/deletions relative to other nifR3 homologs, and by subclustering based on cross-genome bidirectional best hits. Members are found in species as diverse as the proteobacteria, a spirochete, a cyanobacterium, and Deinococcus radiodurans. NifR3 itself, a protein of unknown function associated with nitrogen regulation in Rhodobacter capsulatus, is not a member of this branch. Members of this family show a distant relationship to alpha/beta (TIM) barrel enzymes such as dihydroorotate dehydrogenase and glycolate oxidase. [Protein synthesis, tRNA and rRNA base modification] 318 matched cddid_all.tbl CDD TIGR00743 TIGR00743 273245 TIGR00743 conserved hypothetical protein. These small proteins are approximately 100 amino acids in length and appear to be found only in gamma proteobacteria. The function of this protein family is unknown. [Hypothetical proteins, Conserved] 95 matched cddid_all.tbl CDD TIGR00744 TIGR00744 273246 ROK_glcA_fam ROK family protein (putative glucokinase). This model models one branch of the ROK superfamily of proteins. The three members of the seed alignment for this model all have experimental evidence for activity as glucokinase, but the set of related proteins is crowded with paralogs of different or unknown function. Proteins scoring above the trusted_cutoff will show strong similarity to at least one known glucokinase and may be designated as putative glucokinases. However, definitive identification of glucokinases should be done only with extreme caution. [Unknown function, General] 318 matched cddid_all.tbl CDD TIGR00745 TIGR00745 273247 apbA_panE 2-dehydropantoate 2-reductase. This model describes enzymes that perform as 2-dehydropantoate 2-reductase, one of four enzymes required for the de novo biosynthesis of pantothenate (vitamin B5) from Asp and 2-oxoisovalerate. Although few members of the seed alignment are characterized experimentally, nearly all from complete genomes are found in a genome-wide (but not local) context of all three other pantothenate-biosynthetic enzymes (TIGR00222, TIGR00018, TIGR00223). The gene encoding this enzyme is designated apbA in Salmonella typhimurium and panE in Escherichia coli; this protein functions as a monomer and functions in the alternative pyrimidine biosynthetic, or APB, pathway, used to synthesize the pyrimidine moiety of thiamine. Note, synthesis of the pyrimidine moiety of thiamine occurs either via the first five steps in de novo purine biosynthesis, which uses the pur gene products, or through the APB pathway. Note that this family includes both NADH and NADPH-dependent enzymes, and enzymes with broad specificity, such as a D-mandelate dehydrogease that is also a 2-dehydropantoate 2-reductase. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pantothenate and coenzyme A] 293 matched cddid_all.tbl CDD TIGR00746 TIGR00746 273248 arcC carbamate kinase. In most species, carbamate kinase works in arginine catabolism and consumes carbamoyl phosphate to convert ADP into ATP. In the pathway in Pyrococcus furiosus, the enzyme acts instead to generate carbamoyl phosphate.The seed alignment for this model includes experimentally confirmed examples from a set of phylogenetically distinct species. In a neighbor-joining tree constructed from an alignment of candidate carbamate kinases and several acetylglutamate kinases, the latter group forms a clear outgroup which roots the tree of carbamate kinase-like proteins. This analysis suggests that in E. coli, the ArcC paralog YqeA may be a second isozyme, while the paralog YahI branches as an outlier and is less likely to be an authentic carbamate kinase. The homolog from Mycoplasma pneumoniae likewise branches outside the set containing known carbamate kinases and also scores below the trusted cutoff. [Energy metabolism, Amino acids and amines] 310 matched cddid_all.tbl CDD TIGR00747 TIGR00747 273249 fabH 3-oxoacyl-(acyl-carrier-protein) synthase III. FabH in general initiate elongation in type II fatty acid synthase systems found in bacteria and plants. The two members of this subfamily from Bacillus subtilis differ from each other, and from FabH from E. coli, in acyl group specificity. Active site residues include Cys112, His244 and Asn274 of E. coli FabH. Cys-112 is the site of acyl group attachment. [Fatty acid and phospholipid metabolism, Biosynthesis] 318 matched cddid_all.tbl CDD TIGR00748 TIGR00748 273250 HMG_CoA_syn_Arc hydroxymethylglutaryl-CoA synthase, putative. This family of archaeal proteins shows considerable homology and identical active site residues to the bacterial hydroxymethylglutaryl-CoA synthase (HMG-CoA synthase, modeled by TIGR01835) which is the second step in the mevalonate pathway of IPP biosynthesis. An enzyme from Pseudomonas fluorescens involved in the biosynthesis of the polyketide diacetyl-phloroglucinol is more closely related, but lacks the active site residues. In each of the genomes containing a member of this family there is no other recognized HMG-CoA synthase, although other elements of the mevalonate pathway are in evidence. The only archaeon currently sequenced which lacks a homolog in this pathway is Halobacterium, which _does_ contain a separate HMG-CoA synthase. Thus, although there is no experimental evidence supporting this name, the bioinformatics-based conclusion appears to be sound. [Fatty acid and phospholipid metabolism, Biosynthesis] 347 matched cddid_all.tbl CDD TIGR00749 TIGR00749 129832 glk glucokinase, proteobacterial type. This model represents glucokinase of E. coli and close homologs, mostly from other proteobacteria, presumed to have equivalent function. This glucokinase is more closely related to a number of uncharacterized paralogs than to the glucokinase glcK (fromerly yqgR) of Bacillus subtilis and its closest homologs, so the two sets are represented by separate models. [Energy metabolism, Glycolysis/gluconeogenesis] 316 matched cddid_all.tbl CDD TIGR00750 TIGR00750 129833 lao LAO/AO transport system ATPase. In E. coli, mutation of this kinase blocks phosphorylation of two transporter system periplasmic binding proteins and consequently inhibits those transporters. This kinase is also found in Gram-positive bacteria, archaea, and the roundworm C. elegans. It may have a more general, but still unknown function. Mutations have also been found that do not phosphorylate the periplasmic binding proteins, yet still allow transport. The ATPase activity of this protein seems to be necessary, however. [Transport and binding proteins, Amino acids, peptides and amines, Regulatory functions, Protein interactions] 300 matched cddid_all.tbl CDD TIGR00751 TIGR00751 129834 menA 1,4-dihydroxy-2-naphthoate octaprenyltransferase. This membrane-associated enzyme converts 1,4-dihydroxy-2-naphthoic acid (DHNA) to demethylmenaquinone, a step in menaquinone biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 284 matched cddid_all.tbl CDD TIGR00752 TIGR00752 273251 slp outer membrane lipoprotein, Slp family. Slp superfamily members are present in the Gram-negative gamma proteobacteria Escherichia coli, which also contains a close paralog, Haemophilus influenzae and Pasteurella multocida and Vibrio cholera. The known members of the family to date share a motif LX[GA]C near the N-terminus, which is compatible with the possibility that the protein is modified into a lipoprotein with Cys as the new N-terminus. Slp from Escherichia coli is known to be a lipoprotein of the outer membrane and to be expressed in response to carbon starvation. [Cell envelope, Other] 182 matched cddid_all.tbl CDD TIGR00753 TIGR00753 129836 undec_PP_bacA undecaprenyl-diphosphatase UppP. This is a family of small, highly hydrophobic proteins. Overexpression of this protein in Escherichia coli is associated with bacitracin resistance, and the protein was originally proposed to be an undecaprenol kinase and called bacA. It is now known to be an undecaprenyl pyrophosphate phosphatase (EC 3.6.1.27) and is renamed UppP. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 255 matched cddid_all.tbl CDD TIGR00754 TIGR00754 162022 bfr bacterioferritin. Bacterioferritin, predominantly an iron-storage protein restricted to Bacteria, has also been designated cytochrome b1 and cytochrome b-557.Bacterioferritin is a homomultimer most species. In Neisseria gonorrhoeae, Synechocystis PCC6803, Magnetospirillum magnetotacticum, and Pseudomonas aeruginosa, two types of subunit are found in a heteromultimeric complex, with each species having one member of each type. At present, both types of subunit are including in this single model. [Transport and binding proteins, Cations and iron carrying compounds] 157 matched cddid_all.tbl CDD TIGR00755 TIGR00755 273252 ksgA ribosomal RNA small subunit methyltransferase A. In both E. coli and Saccharomyces cerevisiae, this protein is responsible for the dimethylation of two adjacent adenosine residues in a conserved hairpin of 16S rRNA in bacteria, 18S rRNA in eukaryotes. This adjacent dimethylation is the only rRNA modification shared by bacteria and eukaryotes. A single member of this family is present in each of the first 20 completed microbial genomes. This protein is essential in yeast, but not in E. coli, where its deletion leads to resistance to the antibiotic kasugamycin. Alternate name: S-adenosylmethionine--6-N',N'-adenosyl (rRNA) dimethyltransferase [Protein synthesis, tRNA and rRNA base modification] 254 matched cddid_all.tbl CDD TIGR00756 TIGR00756 273253 PPR pentatricopeptide repeat domain (PPR motif). This model describes a domain called the PPR motif, or pentatricopeptide repeat. Its consensus sequence is 35 positions long and typically is found in four or more tandem copies. This family is strongly represented in plant proteins, particularly those sorted to chloroplasts or mitochondria. The pfam01535, domain of unknown function DUF17, consists of 6 copies of this repeat. This family has a similar consensus to the TPR domain (tetratricopeptide), pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR. 35 matched cddid_all.tbl CDD TIGR00757 TIGR00757 273254 RNaseEG ribonuclease, Rne/Rng family. This model describes ribonuclease G (formerly CafA, cytoplasmic axial filament protein A), the N-terminal domain of ribonuclease E in which ribonuclease activity resides, and related proteins. In E. coli, both RNase E and RNase G have been shown to play a role in the maturation of the 5' end of 16S RNA. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome. [Transcription, Degradation of RNA] 414 matched cddid_all.tbl CDD TIGR00758 TIGR00758 129841 UDG_fam4 uracil-DNA glycosylase, family 4. This well-conserved family of proteins is about 200 residues in length and homologous to the N-terminus of the DNA polymerase of phage SPO1 of Bacillus subtilis. The member from Thermus thermophilus HB8 is known to act as uracil-DNA glycosylase, an enzyme of DNA base excision repair. Its appearance as a domain of phage DNA polymerases could be consistent with uracil-DNA glycosylase activity. [DNA metabolism, DNA replication, recombination, and repair] 173 matched cddid_all.tbl CDD TIGR00759 TIGR00759 273255 aceE pyruvate dehydrogenase E1 component, homodimeric type. Most members of this family are pyruvate dehydrogenase complex, E1 component. Note: this family was classified as subfamily rather than equivalog because it includes a counterexample from Pseudomonas putida, MdeB, that is active as an E1 component of an alpha-ketoglutarate dehydrogenase complex rather than a pyruvate dehydrogase complex. The second pyruvate dehydrogenase complex E1 protein from Alcaligenes eutrophus, PdhE, complements an aceE mutant of E. coli but is not part of a pyruvate dehydrogenase complex operon, is more similar to the Pseudomonas putida MdeB than to E. coli AceE, and may have also have a different primary specificity. 885 matched cddid_all.tbl CDD TIGR00760 TIGR00760 129843 araD L-ribulose-5-phosphate 4-epimerase. E. coli has two genes, sgaE and sgbE (YiaS), that are very close homologs of araD, the established L-ribulose-5-phosphate 4-epimerase of E. coli. SgbE, part of an operon for L-xylulose metabolism, also has L-ribulose-5-phosphate 4-epimerase activity; L-xylulose-5-phosphate may be converted into L-ribulose-5-phosphate by another product of that operon. The homolog to this family from Mycobacterium smegmatis is flanked by putative araB and araA genes, consistent with it also being araD. [Energy metabolism, Sugars] 231 matched cddid_all.tbl CDD TIGR00761 TIGR00761 273256 argB "acetylglutamate kinase. This model describes N-acetylglutamate kinases (ArgB) of many prokaryotes and the N-acetylglutamate kinase domains of multifunctional proteins from yeasts. This enzyme is the second step in the ""acetylated"" ornithine biosynthesis pathway. A related group of enzymes representing the first step of the pathway contain a homologous domain and are excluded from this model. [Amino acid biosynthesis, Glutamate family]" 231 matched cddid_all.tbl CDD TIGR00762 TIGR00762 273257 DegV EDD domain protein, DegV family. This family of proteins is related to DegV of Bacillus subtilis and includes paralogous sets in several species (B. subtilis, Deinococcus radiodurans, Mycoplasma pneumoniae) that are closer in percent identity to each than to most homologs from other species. This suggests both recent paralogy and diversity of function. DegV itself is encoded immediately downstream of DegU, a transcriptional regulator of degradation, but is itself uncharacterized. Crystallography suggested a lipid-binding site, while comparison of the crystal structure to dihydroxyacetone kinase and to a mannose transporter EIIA domain suggests a conserved domain, EDD, with phosphotransferase activity. [Unknown function, General] 275 matched cddid_all.tbl CDD TIGR00763 TIGR00763 273258 lon endopeptidase La. This protein, the ATP-dependent serine endopeptidase La, is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 775 matched cddid_all.tbl CDD TIGR00764 TIGR00764 273259 lon_rel lon-related putative ATP-dependent protease. This model represents a set of proteins with extensive C-terminal homology to the ATP-dependent protease La, product of the lon gene of E. coli. The model is based on a seed alignment containing only archaeal members, but several bacterial proteins match the model well. Because several species, including Thermotoga maritima and Treponema pallidum, contain both a close homolog of the lon protease and nearly full-length homolog of the members of this family, we suggest there may also be a functional division between the two families. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 608 matched cddid_all.tbl CDD TIGR00765 TIGR00765 273260 yihY_not_rbn YihY family inner membrane protein. Initial identification of members of this protein family was based on characterization of the yihY gene product as ribonuclease BN in Escherichia coli. This identification has been withdrawn, as the group now finds the homolog in E. coli of RNase Z is the true ribonuclease BN rather than a strict functional equivalent of RNase Z. Members of this subfamily include the largely uncharacterized BrkB (Bordetella resist killing by serum B) from Bordetella pertussis. Some members have an additional C-terminal domain. Paralogs from E. coli (yhjD) and Mycobactrium tuberculosis (Rv3335c) are part of a smaller, related subfamily that form their own cluster. [Unknown function, General] 259 matched cddid_all.tbl CDD TIGR00766 TIGR00766 188082 TIGR00766 inner membrane protein YhjD. This family, including YhjD in E. coli, is a conserved inner membrane protein homologous YihY, which in turn was incorrectly assigned to be ribonuclease BN. This, any suggestion this family is similar to ribonucleases should be removed. [Transcription, Degradation of RNA] 263 matched cddid_all.tbl CDD TIGR00767 TIGR00767 162030 rho transcription termination factor Rho. This RNA helicase, the transcription termination factor Rho, occurs in nearly all bacteria but is missing from the Cyanobacteria, the Mollicutes (Mycoplasmas), and various Lactobacillales including Streptococcus. It is also missing, of course, from the Archaea, which also lack Nus factors. Members of this family from Micrococcus luteus, Mycobacterium tuberculosis, and related species have a related but highly variable long, highly charged insert near the amino end. Members of this family differ in the specificity of RNA binding. [Transcription, Transcription factors] 415 matched cddid_all.tbl CDD TIGR00768 TIGR00768 273261 rimK_fam alpha-L-glutamate ligase, RimK family. This family, related to bacterial glutathione synthetases, contains at least three different alpha-L-glutamate ligases. One is RimK, as in E. coli, which adds additional Glu residues to the native Glu-Glu C-terminus of ribosomal protein S6, but not to Lys-Glu mutants. Most species with a member of this subfamily lack an S6 homolog ending in Glu-Glu, however. Members in Methanococcus jannaschii act instead as a tetrahydromethanopterin:alpha-l-glutamate ligase (MJ0620) and a gamma-F420-2:alpha-l-glutamate ligase (MJ1001). 276 matched cddid_all.tbl CDD TIGR00769 TIGR00769 273262 AAA ADP/ATP carrier protein family. These proteins are members of the ATP:ADP Antiporter (AAA) Family (TC 2.A.12), which consists of nucleotide transporters that have 12 GES predicted transmembrane regions. One protein from Rickettsia prowazekii functions to take up ATP from the eukaryotic cell cytoplasm into the bacterium in exchange for ADP. Five AAA family paralogues are encoded within the genome of R. prowazekii. This organism transports UMP and GMP but not CMP, and it seems likely that one or more of the AAA family paralogues are responsible. The genome of Chlamydia trachomatis encodes two AAA family members, Npt1 and Npt2, which catalyse ATP/ADP exchange and GTP, CTP, ATP and UTP uptake probably employing a proton symport mechanism. Two homologous adenylate translocators of Arabidopsis thaliana are postulated to be localized to the intracellular plastid membrane where they function as ATP importers. [Transport and binding proteins, Nucleosides, purines and pyrimidines] 472 matched cddid_all.tbl CDD TIGR00770 TIGR00770 273263 Dcu anaerobic c4-dicarboxylate membrane transporter family protein. These proteins are members of th C4-Dicarboxylate Uptake (Dcu) Family (TC 2.A.13). Most proteins in this family have 12 GES predicted transmembrane regions; however one member has 10 experimentally determined transmembrane regions with both the N- and C-termini localized to the periplasm. The two Escherichia coli proteins, DcuA and DcuB, transport aspartate, malate, fumarate and succinate, and function as antiporters with any two of these substrates. Since DcuA is encoded in an operon with the gene for aspartase, and DcuB is encoded in an operon with the gene for fumarase, their physiological functions may be to catalyze aspartate:fumarate and fumarate:malate exchange during the anaerobic utilization of aspartate and fumarate, respectively. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 430 matched cddid_all.tbl CDD TIGR00771 TIGR00771 129854 DcuC c4-dicarboxylate anaerobic carrier family protein. These proteins are members of the C4-dicarboxylate Uptake C (DcuC) Family (TC 2.A.61). The only functionally characterized member of this family is the anaerobic C4-dicarboxylate transporter (DcuC) of Escherichia coli. DcuC has 12 GES predicted transmembrane regions, is induced only under anaerobic conditions, and is not repressed by glucose. It may therefore function as a succinate efflux system during anaerobic glucose fermentation. However, when overexpressed, it can replace either DcuA or DcuB in catalyzing fumarate-succinate exchange and fumarate uptake. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 388 matched cddid_all.tbl CDD TIGR00773 TIGR00773 273264 NhaA Na+/H+ antiporter NhaA. These proteins are members of the NhaA Na+:H+ Antiporter (NhaA) Family (TC. 2.A.33). The Escherichia coli NhaA protein probably functions in the regulation of the internal pH when the external pH is alkaline. It also uses the H+ gradient to expel Na+ from the cell. Its activity is highly pH dependent. Only the E. coli protein is functionally and structurally well characterized. [Transport and binding proteins, Cations and iron carrying compounds] 373 matched cddid_all.tbl CDD TIGR00774 TIGR00774 129856 NhaB Na+/H+ antiporter NhaB. These proteins are members of the NhaB Na+:H+ Antiporter (NhaB) Family (TC 2.A.34). The only characterised member of this family is the Escherichia coli NhaB protein, which has 12 GES predicted transmembrane regions, and catalyses sodium/proton exchange. Unlike NhaA this activity is not pH dependent. [Transport and binding proteins, Cations and iron carrying compounds] 515 matched cddid_all.tbl CDD TIGR00775 TIGR00775 129857 NhaD Na+/H+ antiporter, NhaD family. These proteins are members of the NhaD Na+:H+ Antiporter (NhaD) Family (TC 2.A.62). A single member of the NhaD family has been characterized. This protein is the NhaD protein of Vibrio parahaemolyticus which has 12 GES predicted transmembrane regions. It has been shown to catalyze Na+/H+ antiport, but Li+ can also be a substrate. [Transport and binding proteins, Cations and iron carrying compounds] 420 matched cddid_all.tbl CDD TIGR00776 TIGR00776 273265 RhaT RhaT L-rhamnose-proton symporter family protein. These proteins are members of the L-Rhamnose Symporter (RhaT) Family (TC 2.A.7). This family includes two characterized members, both of which function as L-rhamnose:H+ symporters and have 10 GES predicted transmembrane domains. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 290 matched cddid_all.tbl CDD TIGR00777 TIGR00777 129859 ahpD alkylhydroperoxidase, AhpD family. Members of this family are alkylhydroperoxidases, which catalyze the reduction of peroxides to their corresponding alcohols via oxidation of cysteine residues. In these alkylhydroperoxidases, the cysteines are located in a conserved -CXXC- motif located towards the COOH terminus. In Mycobacterium tuberculosis, two non-homologous alkylhydroperoxidases, AhpD and AhpC, are found in the same operon. [Cellular processes, Detoxification] 177 matched cddid_all.tbl CDD TIGR00778 TIGR00778 273266 ahpD_dom alkylhydroperoxidase AhpD family core domain. This model represents a 51-residue core region of homology among a family of mostly uncharacterized proteins of 110 to 227 amino acids. Most members of this family contain the motif EXXXXXX[SA]XXXXXC[VIL]XCXXXH. Members of the family include the alkylhydroperoxidase AhpD of Mycobacterium tuberculosis, a macrophage infectivity potentiator peptide of Legionella pneumophila, and an uncharacterized peptide in the tetrachloroethene reductive dehalogenase operon of Dehalospirillum multivorans. We suggest that many peptides containing this domain may have alkylhydroperoxidase or related antioxidant activity. [Unknown function, General] 50 matched cddid_all.tbl CDD TIGR00779 TIGR00779 129861 cad cadmium resistance transporter (or sequestration) family protein. These proteins are members of the Cadmium Resistance (CadD) Family (TC 2.A.77). To date, this family of proteins has only been found in Gram-positive bacteria. The CadD family includes several closely related Staphylococcal proteins reported to function in cadmium resistance. Members are predicted to span the membrane five times; the mechanism of resistance is believed to be export but has also been suggested to be binding and sequestration in the membrane. Closely related but outside the scope of this model is another staphylococcal protein that has been reported to possibly function in quaternary ammonium ion export. Still more distant are other members of the broader LysE family (see Vrljic. et al, ). [Transport and binding proteins, Amino acids, peptides and amines] 193 matched cddid_all.tbl CDD TIGR00780 TIGR00780 129862 ccoN cytochrome c oxidase, cbb3-type, subunit I. This model represents the largest subunit, I, of the ccb3-type cytochrome c oxidase, with two protohemes and copper. It shows strong homology to subunits of other types of cytochrome oxidases. Species with this type, all from the Proteobacteria so far, include Neisseria meningitidis, Helicobacter pylori, Campylobacter jejuni, Rhodobacter sphaeroides, Rhizobium leguminosarum, and others. Gene symbols ccoN and fixN are synonymous. [Energy metabolism, Electron transport] 474 matched cddid_all.tbl CDD TIGR00781 TIGR00781 129863 ccoO cytochrome c oxidase, cbb3-type, subunit II. This model describes the monoheme subunit of the cbb3-type cytochrome oxidase, found in a subset of Proteobacterial species. Species having this protein also have CcoN (subunit I, containing copper and two heme groups), CcoP (subunit III, containing two hemes), and CcoQ (essential for incorporation of the prosthetic groups). [Energy metabolism, Electron transport] 232 matched cddid_all.tbl CDD TIGR00782 TIGR00782 129864 ccoP cytochrome c oxidase, cbb3-type, subunit III. This model describes a di-heme subunit of approximately 26 kDa of the cbb3 type copper and heme-containing cytochrome oxidase. [Energy metabolism, Electron transport] 285 matched cddid_all.tbl CDD TIGR00783 TIGR00783 129865 ccs citrate carrier protein, CCS family. These proteins are members of the Citrate:Cation Symporter (CCS) Family (TC 2.A.24). These proteins have 12 GES predicted transmembrane regions. Most members of the CCS family catalyze citrate uptake with either Na+ or H+ as the cotransported cation. However, one member is specific for L-malate and probably functions by a proton symport mechanism. [Unclassified, Role category not yet assigned] 347 matched cddid_all.tbl CDD TIGR00784 TIGR00784 162036 citMHS citrate transporter, CitMHS family. This family includes two characterized citrate/proton symporters from Bacillus subtilis. CitM transports citrate complexed to Mg2+, while the CitH apparently transports citrate without Mg2+. The family also includes uncharacterized transporters, including a third paralog in Bacillus subtilis. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 431 matched cddid_all.tbl CDD TIGR00785 TIGR00785 273267 dass anion transporter. The Divalent Anion:Na+ Symporter (DASS) Family (TC 2.A.47) Functionally characterized proteins of the DASS family transport (1) organic di- and tricarboxylates of the Krebs Cycle as well as dicarboxylate amino acid, (2) inorganic sulfate and (3) phosphate. The animal NaDC-1 cotransport 3 Na+ with each dicarboxylate. Protonated tricarboxylates are also cotransported with 3Na+. [Transport and binding proteins, Anions, Transport and binding proteins, Cations and iron carrying compounds] 444 matched cddid_all.tbl CDD TIGR00786 TIGR00786 129868 dctM TRAP transporter, DctM subunit. The Tripartite ATP-independent Periplasmic Transporter (TRAP-T) Family (TC 2.A.56)- DctM subunit TRAP-T family permeases generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-postive bacteria and archaea. Only one member of the family has been both sequenced and functionally characterized. This system is the DctPQM system of Rhodobacter capsulatus (Forward et al., 1997). DctP is a periplasmic dicarboxylate (malate, fumarate, succinate) binding receptor that is biochemically well-characterized. DctQ is an integral cytoplasmic membrane protein with 4 putative transmembrane a-helical spanners (TMSs). DctM is a second integral cytoplasmic membrane protein with 12 putative TMSs. These proteins have been shown to be both necessary and sufficient for the proton motive force-dependent uptake of dicarboxylates into R. capsulatus. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 405 matched cddid_all.tbl CDD TIGR00787 TIGR00787 129869 dctP tripartite ATP-independent periplasmic transporter solute receptor, DctP family. TRAP-T (Tripartite ATP-independent Periplasmic Transporter) family proteins generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-postive bacteria and archaea. The best characterized example is the DctPQM system of Rhodobacter capsulatus, a C4 dicarboxylate (malate, fumarate, succinate) transporter. This model represents the DctP family, one of at least three major families of extracytoplasmic solute receptor for TRAP family transporters. Other are the SnoM family (see pfam03480) and TAXI (TRAP-associated extracytoplasmic immunogenic) family. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 257 matched cddid_all.tbl CDD TIGR00788 TIGR00788 273268 fbt folate/biopterin transporter. The Folate-Biopterin Transporter (FBT) Family (TC 2.A.71)The only functionally characterized members of the family are from protozoa and include FT1, the major folate transporter in Leishmania, and BT1, the Leishmania biopterin/folate transporter. A related protein in Trypanosoma brucei, ESAGIO, shows weak folate/biopterin transport activity. [Cell envelope, Other] 468 matched cddid_all.tbl CDD TIGR00789 TIGR00789 129871 flhB_rel flhB C-terminus-related protein. This model describes a short protein (80-93 residues) homologous to the C-terminus of the flagellar biosynthetic protein FlhB. It is found so far only in species that also have FlhB. In a phylogenetic tree based on alignment of both this family and the homologous region of FlhB and its homologs, the members of this family form a monophyletic set. [Unknown function, General] 82 matched cddid_all.tbl CDD TIGR00790 TIGR00790 273269 fnt formate/nitrite transporter. The Formate-Nitrite Transporter (FNT) Family (TC 2.A.44)The prokaryotic proteins of the FNT family probably function in the transport of the structurally related compounds, formate and nitrite. The homologous yeast protein may function as a short chain aliphatic carboxylate H+ symporter,transporting formate, acetate and propionate, and functioning primarily as an acetate uptake permease. The putative formate efflux transporters (FocA) of bacteria associated with pyruvate-formate lyase (pfl) comprise cluster I; the putative formate uptake permeases (FdhC) of bacteria and archaea associated with formate dehydrogenase comprise cluster II; the putative nitrite uptake permeases (NirC) of bacteria comprise cluster III, and the single yeast protein, the putative acetate:H+ symporter alone comprises cluster IV. The energy coupling mechanisms for proteins of the FNT family have not been extensively characterized. HCO2 -, CH3CO2 - and NO2 - uptakes are probably coupled to H+symport. HCO2 - efflux may be driven by the membrane potential by a uniport mechanism or by H+ antiport. [Transport and binding proteins, Anions] 239 matched cddid_all.tbl CDD TIGR00791 TIGR00791 129873 gntP gluconate transporter. This family includes known gluconate transporters of E. coli and Bacillus species as well as an idonate transporter from E. coli. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 440 matched cddid_all.tbl CDD TIGR00792 TIGR00792 273270 gph sugar (Glycoside-Pentoside-Hexuronide) transporter. The Glycoside-Pentoside-Hexuronide (GPH):Cation Symporter Family (TC 2.A.2) GPH:cation symporters catalyze uptake of sugars in symport with a monovalent cation (H+ or Na+). Members of this family includes transporters for melibiose, lactose, raffinose, glucuronides, pentosides and isoprimeverose. Mutants of two groups of these symporters (the melibiose permeases of enteric bacteria, and the lactose permease of Streptococcus thermophilus) have been isolated in which altered cation specificity is observed or in which sugar transport is uncoupled from cation symport (i.e., uniport is catalyzed). The various members of the family can use Na+, H+ or Li, Na+ or Li+, H+ or Li+, or only H+ as the symported cation. All of these proteins possess twelve putative transmembrane a-helical spanners. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 437 matched cddid_all.tbl CDD TIGR00793 TIGR00793 273271 kdgT 2-keto-3-deoxygluconate transporter. This family includes the characterized 2-Keto-3-Deoxygluconate transporters from Bacillus subtilis and Erwinia chrysanthemi. There are homologs of this protein found in both gram-positive and gram-negative bacteria. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 314 matched cddid_all.tbl CDD TIGR00794 TIGR00794 129876 kup potassium uptake protein. Proteins of the KUP family include the KUP (TrkD) protein of E. coli, a partially sequenced ORF from Lactococcus lactis, high affinity K+ uptake systems (Hak1) of the yeast Debaryomyces occidentalis as well as the fungus, Neurospora crassa, and several homologues in plants. While the E. coli KUP protein is assumed to be a secondary transporter, and uptake is blocked by protonophores such as CCCP (but not arsenate), the energy coupling mechanism has not been defined. However, the N. crassa protein has been shown to be a K+:H+ symporter, establishing that the KUP family consists of secondary carriers. The plant high affinity (20mM) K+ transporter can complement K+ uptake defects in E. coli. [Transport and binding proteins, Cations and iron carrying compounds] 688 matched cddid_all.tbl CDD TIGR00795 TIGR00795 162041 lctP L-lactate transport. The Lactate Permease (LctP) Family (TC 2.A.14) The only characterized member of this family, from E. coli, appears to catalyze lactate:H+ uptake. Members of this family have 12 probable TMS. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 530 matched cddid_all.tbl CDD TIGR00796 TIGR00796 273272 livcs branched-chain amino acid uptake carrier. The Branched Chain Amino Acid:Cation Symporter (LIVCS) Family (TC 2.A.26) Characterized members of this family transport all three of the branched chain aliphatic amino acids (leucine (L), isoleucine (I) and valine (V)). They function by a Na+ or H+ symport mechanism and display 12 putative transmembrane helical spanners. [Transport and binding proteins, Amino acids, peptides and amines] 378 matched cddid_all.tbl CDD TIGR00797 TIGR00797 273273 matE putative efflux protein, MATE family. The Multi Antimicrobial Extrusion (MATE) Family (TC 2.A.66) The MATE family consists of probable efflux proteins including a functionally characterized multi drug efflux system from Vibrio parahaemolyticus, a putative ethionine resistance protein of Saccharomyces cerevisiae, and the functionally uncharacterized DNA damage-inducible protein F (DinF) of E. coli. These proteins have 12 probable TMS. [Transport and binding proteins, Other] 342 matched cddid_all.tbl CDD TIGR00798 TIGR00798 129880 mtc tricarboxylate carrier. The MTC family consists of a limited number of homologues, all from eukaryotes. A single member of the family has been functionally characterized, the tricarboxylate carrier from rat liver mitochondria. The rat liver mitochondrial tricarboxylate carrier has been reported to transport citrate, cis-aconitate, threo-D-isocitrate, D- and L-tartrate, malate, succinate and phosphoenolpyruvate. It presumably functions by a proton symport mechanism. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 318 matched cddid_all.tbl CDD TIGR00799 TIGR00799 273274 mtp Golgi 4-transmembrane spanning transporter. The proteins of the MET family have 4 TMS regions and are located in late endosomal or lysosomal membranes. Substrates of the mouse MTP transporter include thymidine, both nucleoside and nucleobase analogues, antibiotics, anthracyclines, ionophores and steroid hormones. MET transporters may be involved in the subcellular compartmentation of steroid hormones and other compounds.Drug sensitivity by mouse MET was regulated by compounds that inhibit lysosomal function, interface with intracellular cholesterol transport, or modulate the multidrug resistance phenotype of mammalian cells. Thus, MET family members may compartmentalize diverse hydrophobic molecules, thereby affecting cellular drug sensitivity,nucleoside/nucleobase availability and steroid hormone responses. [Transport and binding proteins, Unknown substrate] 258 matched cddid_all.tbl CDD TIGR00800 TIGR00800 273275 ncs1 NCS1 nucleoside transporter family. The Nucleobase:Cation Symporter-1 (NCS1) Family (TC 2.A.39) The NCS1 family consists of bacterial and yeast transporters for nucleobases including purines and pyrimidines. Members of this family possess twelve putative transmembrane a-helical spanners (TMSs). At least some of them have been shown to function in uptake by substrate:H+ symport mechanism. [Transport and binding proteins, Nucleosides, purines and pyrimidines] 442 matched cddid_all.tbl CDD TIGR00801 TIGR00801 273276 ncs2 uracil-xanthine permease. The Nucleobase:Cation Symporter-2 (NCS2) Family (TC 2.A.40) Most of the functionally characterized members of the NCS2 family are transporters specific for nucleobases including both purines and pyrimidines. However, two closely related rat members of the family, SVCT1 and SVCT2, localized to different tissues of the body, cotransport L-ascorbate and Na+ with a high degree of specificity and high affinity for the vitamin. The NCS2 family appears to be distantly related to the NCS1 family (TC #2.A.39). [Transport and binding proteins, Nucleosides, purines and pyrimidines] 412 matched cddid_all.tbl CDD TIGR00802 TIGR00802 273277 nico high-affinity nickel-transporter, HoxN/HupN/NixA family. This family is found in both Gram-negative and Gram-positive bacteria. The functionally characterized members of the family catalyze uptake of either Ni2+ or Co2+ in a proton motive force-dependent process. Topological analyses with the HoxN Ni2+ transporter of Ralstonia eutropha (Alcaligenes eutrophus) suggest that it possesses 8 TMSs with its N- and C-termini in the cytoplasm. [Transport and binding proteins, Cations and iron carrying compounds] 280 matched cddid_all.tbl CDD TIGR00803 TIGR00803 129885 nst UDP-galactose transporter. The 10-12 TMS Nucleotide Sugar Transporters (TC 2.A.7.10)Nucleotide-sugar transporters (NSTs) are found in the Golgi apparatus and the endoplasmic reticulum of eukaryotic cells. Members of the family have been sequenced from yeast, protozoans and animals. Animals such as C. elegans possess many of these transporters. Humans have at least two closely related isoforms of the UDP-galactose:UMP exchange transporter.NSTs generally appear to function by antiport mechanisms, exchanging a nucleotide-sugar for a nucleotide. Thus, CMP-sialic acid is exchanged for CMP; GDP-mannose is preferentially exchanged for GMP, and UDP-galactose and UDP-N-acetylglucosamine are exchanged for UMP (or possibly UDP). Other nucleotide sugars (e.g., GDP-fucose, UDP-xylose, UDP-glucose, UDP-N-acetylgalactosamine, etc.) may also be transported in exchange for various nucleotides, but their transporters have not been molecularly characterized. Each compound appears to be translocated by its own transport protein. Transport allows the compound, synthesized in the cytoplasm, to be exported to the lumen of the Golgi apparatus or the endoplasmic reticulum where it is used for the synthesis of glycoproteins and glycolipids. 222 matched cddid_all.tbl CDD TIGR00804 TIGR00804 273278 nupC nucleoside transporter. The Concentrative Nucleoside Transporter (CNT) Family (TC 2.A.41) Members of the CNT family mediate nucleoside uptake. In bacteria they are energized by H+ symport, but in mammals they are energized by Na+ symport. The different transporters exhibit differing specificities for nucleosides. The E. coli NupC permease transports all nucleosides (both ribo- and deoxyribonucleosides) except hypoxanthine and guanine nucleosides. The B. subtilis NupC is specific for pyrimidine nucleosides (cytidine and uridine and the corresponding deoxyribonucleosides). The mammalian permease members of the CNT family also exhibit differing specificities. Thus, rats possess at least two NupC homologues, one specific for both purine and pyrimidine nucleosides and one specific for purine nucleosides. At least three paralogues have been characterized from humans. One human homologue(CNT1) transports pyrimidine nucleosides and adenosine, but deoxyadenosine and guanosine are poor substrates of this permease. Another (CNT2) is selective for purine nucleosides. Alteration of just a few amino acyl residues in TMSs 7 and 8 interconverts their specificities. [Transport and binding proteins, Nucleosides, purines and pyrimidines] 401 matched cddid_all.tbl CDD TIGR00805 TIGR00805 273279 oat sodium-independent organic anion transporter. The Organo Anion Transporter (OAT) Family (TC 2.A.60)Proteins of the OAT family catalyze the Na+-independent facilitated transport of organic anions such as bromosulfobromophthalein and prostaglandins as well as conjugated and unconjugated bile acids (taurocholate and cholate, respectively). These transporters have been characterized in mammals, but homologues are present in C. elegans and A. thaliana. Some of the mammalian proteins exhibit a high degree of tissue specificity. For example, the rat OAT is found at high levels in liver and kidney and at lower levels in other tissues. These proteins possess 10-12 putative a-helical transmembrane spanners. They may catalyze electrogenic anion uniport or anion exchange. 632 matched cddid_all.tbl CDD TIGR00806 TIGR00806 129888 rfc RFC reduced folate carrier. The Reduced Folate Carrier (RFC) Family (TC 2.A.48) Members of the RFC family mediate the uptake of folate, reduce folate, derivatives of reduced folate and the drug, methotrexate. Proteins of the RFC family are so-far restricted to animals. RFC proteins possess 12 putative transmembrane a-helical spanners (TMSs) and evidence for a 12 TMS topology has been published for the human RFC. The RFC transporters appear to transport reduced folate by an energy-dependent, pH-dependent, Na+-independent mechanism. Folate:H+ symport, folate:OH- antiport and folate:anion antiport mechanisms have been proposed, but the energetic mechanism is not well defined. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 511 matched cddid_all.tbl CDD TIGR00807 TIGR00807 129889 malonate_madL malonate transporter, MadL subunit. The MSS family includes the monobasic malonate:Na+ symporter of Malonomonas rubra. It consists of two integral membrane proteins, MadL and MadM. The transporter is believed to catalyze the electroneutral reversible uptake of H+-malonate with one Na+, and both subunits have been shown to be essential for activity. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 125 matched cddid_all.tbl CDD TIGR00808 TIGR00808 129890 malonate_madM malonate transporter, MadM subunit. The MSS family includes the monobasic malonate:Na+ symporter of Malonomonas rubra. It consists of two integral membrane proteins, MadL and MadM.The transporter is believed to catalyze the electroneutral reversible uptake of H+-malonate with one Na+, and both subunits have been shown to be essential for activity. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 254 matched cddid_all.tbl CDD TIGR00809 TIGR00809 213561 secB protein-export chaperone SecB. This protein acts as an export-specific cytosolic chaperone. It binds the mature region of pre-proteins destined for secretion, prevents aggregation, and delivers them to SecA. This protein is tetrameric in E. coli. The archaeal Methanococcus jannaschii homolog MJ0357 has been shown () to share many properties, including chaperone-like activity, and scores between trusted and noise. [Protein fate, Protein and peptide secretion and trafficking] 140 matched cddid_all.tbl CDD TIGR00810 TIGR00810 273280 secG protein translocase, SecG subunit. This family of proteins forms a complex with SecY and SecE. SecA then recruits the SecYEG complex to form an active protein translocation channel. [Protein fate, Protein and peptide secretion and trafficking] 73 matched cddid_all.tbl CDD TIGR00811 TIGR00811 273281 sit "silicon transporter. Marine diatoms such as Cylindrotheca fusiformis encode at least six silicon transport protein homologues which exhibit similar size and topology. One characterized member of the family (Sit1) functions in the energy-dependent uptake of either Silicic acid [Si(OH)4] or Silicate [Si(OH)3O-] by a Na+ symport mechanism. The system is found in marine diatoms which make their ""glass houses"" out of silicon. [Transport and binding proteins, Other]" 545 matched cddid_all.tbl CDD TIGR00813 TIGR00813 273282 sss transporter, SSS family. The Solute:Sodium Symporter (SSS) Family (TC 2.A.21) Members of the SSS family catalyze solute:Na+ symport. The solutes transported may be sugars, amino acids, nucleosides, inositols, vitamins, urea or anions, depending on the system. Members of the SSS family have been identified in bacteria, archaea and animals, and all functionally well characterized members catalyze solute uptake via Na+ symport. Proteins of the SSS generally share a core of 13 TMSs, but different members of the family may have different numbers of TMSs. A 13 TMS topology with a periplasmic N-terminus and a cytoplasmic C-terminus has been experimentally determined for the proline:Na+ symporter, PutP, of E. coli. [Transport and binding proteins, Cations and iron carrying compounds] 407 matched cddid_all.tbl CDD TIGR00814 TIGR00814 273283 stp serine transporter. The Hydroxy/Aromatic Amino Acid Permease (HAAAP) Family- serine/threonine subfamily (TC 2.A.42.2) The HAAAP family includes well characterized aromatic amino acid:H+ symport permeases and hydroxy amino acid permeases. This subfamily is specific for hydroxy amino acid transporters and includes the serine permease, SdaC, of E. coli, and the threonine permease, TdcC, of E. coli.//added GO terms, none avaialbelf or ser/thr specifically [SS 2/6/05] [Transport and binding proteins, Amino acids, peptides and amines] 397 matched cddid_all.tbl CDD TIGR00815 TIGR00815 273284 sulP "high affinity sulphate transporter 1. The SulP family is a large and ubiquitous family with over 30 sequenced members derived from bacteria, fungi, plants and animals. Many organisms including Bacillus subtilis, Synechocystis sp, Saccharomyces cerevisiae, Arabidopsis thaliana and Caenorhabditis elegans possess multiple SulP family paralogues. Many of these proteins are functionally characterized, and all are sulfate uptake transporters. Some transport their substrate with high affinities, while others transport it with relatively low affinities. Most function by SO42- :H+symport, but SO42- :HCO3- antiport has been reported for the rat protein (spP45380). The bacterial proteins vary in size from 434 residues to 566 residues with one exception, a Mycobacterium tuberculosis protein with 784 residues. The eukaryotic proteins vary in size from 611 residues to 893 residues with one exception, a protein designated ""early nodulin 70 protein"" from Glycine max which is reported to be of 485 residues. Thus, the eukaryotic proteins are almost without exception larger than the prokaryotic proteins. These proteins exhibit 10-13 putative transmembrane a-helical spanners (TMSs) depending on the protein. The phylogenetic tree for the SulP family reveals five principal branches. Three of these are bacterial specific as follows: one bears a single protein from M. tuberculosis; a second bears two proteins, one from M. tuberculosis, the other from Synechocystis sp, and the third bears all remaining prokaryotic proteins. The remaining two clusters bear only eukaryotic proteins with the animal proteins all localized to one branch and the plant and fungal proteins localized to the other. The generalized transport reactions catalyzed by SulP family proteins are: (1) SO42- (out) + nH+ (out) --> SO42- (in) + nH+ (in). (2) SO42- (out) + nHCO3- (in) SO42- (in) + nHCO3- (out). [Transport and binding proteins, Anions]" 552 matched cddid_all.tbl CDD TIGR00816 TIGR00816 273285 tdt C4-dicarboxylate transporter/malic acid transport protein. The Tellurite-Resistance/Dicarboxylate Transporter (TDT) Family (TC 2.A.16)Two members of the TDT family have been functionally characterized. One is the TehA protein of E. coli which has been implicated in resistance to tellurite; the other is the Mae1 protein of S. pombe which functions in the uptake of malate and other dicarboxylates by a proton symportmechanism. These proteins exhibit 10 putative transmembrane a-helicalspanners (TMSs). [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 320 matched cddid_all.tbl CDD TIGR00817 TIGR00817 129898 tpt Tpt phosphate/phosphoenolpyruvate translocator. The 6-8 TMS Triose-phosphate Transporter (TPT) Family (TC 2.A.7.9)Functionally characterized members of the TPT family are derived from the inner envelope membranes of chloroplasts and nongreen plastids of plants. However,homologues are also present in yeast. Saccharomyces cerevisiae has three functionally uncharacterized TPT paralogues encoded within its genome. Under normal physiologicalconditions, chloroplast TPTs mediate a strict antiport of substrates, frequently exchanging an organic three carbon compound phosphate ester for inorganic phosphate (Pi).Normally, a triose-phosphate, 3-phosphoglycerate, or another phosphorylated C3 compound made in the chloroplast during photosynthesis, exits the organelle into thecytoplasm of the plant cell in exchange for Pi. However, experiments with reconstituted translocator in artificial membranes indicate that transport can also occur by achannel-like uniport mechanism with up to 10-fold higher transport rates. Channel opening may be induced by a membrane potential of large magnitude and/or by high substrateconcentrations. Nongreen plastid and chloroplast carriers, such as those from maize endosperm and root membranes, mediate transport of C3 compounds phosphorylated atcarbon atom 2, particularly phosphenolpyruvate, in exchange for Pi. These are the phosphoenolpyruvate:Pi antiporters (PPT). Glucose-6-P has also been shown to be asubstrate of some plastid translocators (GPT). The three types of proteins (TPT, PPT and GPT) are divergent in sequence as well as substrate specificity, but their substratespecificities overlap. [Hypothetical proteins, Conserved] 302 matched cddid_all.tbl CDD TIGR00819 TIGR00819 273286 ydaH p-Aminobenzoyl-glutamate transporter family. The p-Aminobenzoyl-glutamate transporter family includes two transporters, the AbgT (YdaH) protein of E. coli and MtrF of Neisseria gonorrhoea. AbgT is apparently cryptic in wild type cells, but when expressed on a high copy number plasmid, or when expressed at higher levels due to mutation, it allows utilization of p-aminobenzoyl-glutamate as a source of p-aminobenzoate for p-aminobenzoate auxotrophs. p-Aminobenzoate is a constituent of and a precursor for the biosynthesis of folic acid. [Hypothetical proteins, Conserved] 524 matched cddid_all.tbl CDD TIGR00820 TIGR00820 273287 zip ZIP zinc/iron transport family. The Zinc (Zn2+)-Iron (Fe2+) Permease (ZIP) Family (TC 2.A.5)Members of the ZIP family consist of proteins with eight putative transmembrane spanners. They are derived from animals, plants and yeast. Theycomprise a diverse family, with several paralogues in any one organism (e.g., at least five in Caenorabditis elegans, at least five in Arabidopsis thaliana and two inSaccharomyces cervisiae. The two S. cerevisiae proteins, Zrt1 and Zrt2, both probably transport Zn2+ with high specificity, but Zrt1 transports Zn2+ with ten-fold higher affinitythan Zrt2. Some members of the ZIP family have been shown to transport Zn2+ while others transport Fe2+, and at least one transports a range of metal ions. The energy source fortransport has not been characterized, but these systems probably function as secondary carriers. [Transport and binding proteins, Cations and iron carrying compounds] 324 matched cddid_all.tbl CDD TIGR00821 TIGR00821 129901 EII-GUT PTS system, glucitol/sorbitol-specific, IIC component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Gut family consists only of glucitol-specific transporters, but these occur both in Gram-negative and Gram-positive bacteria.E. coli consists of IIA protein, a IIC protein and a IIBC protein. This family is specific for the IIC component. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids, Signal transduction, PTS] 181 matched cddid_all.tbl CDD TIGR00822 TIGR00822 129902 EII-Sor PTS system, mannose/fructose/sorbose family, IIC component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Man (PTS splinter group) family is unique in several respects among PTS permease families. It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine,N-acetylglucosamine, and other sugars. Other members of this family can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the sorbose-specific IIC subunits of this family of PTS transporters. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids, Signal transduction, PTS] 265 matched cddid_all.tbl CDD TIGR00823 TIGR00823 129903 EIIA-LAC phosphotransferase system enzyme II, lactose-specific, factor III. The PTS Lactose-N,N?-Diacetylchitobiose-b-glucoside (Lac) Family (TC 4.A.3)Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Lac family includes several sequenced lactose (b-galactoside) permeases of Gram-positive bacteria as well as the E. coli N,N?-diacetylchitobiose (Chb)permease which can transport aromatic b-glucosides and cellobiose as well as the chitin disaccharide, Chb, but only Chb induces expression of the chboperon. While the Lac permeases consist of two polypeptide chains (IIA and IICB), the Chb permease of E. coli consists of three (IIA, IIB and IIC). In B. subtilis, a PTS permease similar to the Chb permease of E. coli is believed to transport lichenan (a b-1,3;1,4 glucan) degradation products, oligosaccharides of 2-4 glucose units. This model is specific for the IIA subunit of the Lac PTS family. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 99 matched cddid_all.tbl CDD TIGR00824 TIGR00824 129904 EIIA-man PTS system, mannose/fructose/sorbose family, IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIA components. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids, Signal transduction, PTS] 116 matched cddid_all.tbl CDD TIGR00825 TIGR00825 129905 EIIBC-GUT PTS system, glucitol/sorbitol-specific, IIBC component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Gut family consists only of glucitol-specific permeases, but these occur both in Gram-negative and Gram-positive bacteria.E. coli consists of IIA protein, a IIC protein and a IIBC protein. This family is specific for the IIBC component. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids, Signal transduction, PTS] 331 matched cddid_all.tbl CDD TIGR00826 TIGR00826 273288 EIIB_glc PTS system, glucose-like IIB component. The PTS Glucose-Glucoside (Glc) Family (TC 4.A.1) Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Glc family includes permeases specific for glucose, N-acetylglucosamine and a large variety of a- and b-glucosides. However, not all b-glucoside PTS permeases are in this class, as the cellobiose (Cel) b-glucoside PTS permease is in the Lac family (TC #4.A.3). These permeases show limited sequence similarity with members of the Fru family (TC #4.A.2). Several of the E. coli PTS permeases in the Glc family lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). Most of these permeases have the B and C domains linked together in a single polypeptide chain, and a cysteyl residue in the IIB domain is phosphorylated by direct phosphoryl transfer from IIAglc(his~P). Those permeases which lack a IIA domain include the maltose (Mal), arbutin-salicin-cellobiose (ASC), trehalose (Tre), putative glucoside (Glv) and sucrose (Scr) permeases of E. coli . Most, but not all Scr permeases of other bacteria also lack a IIA domain. This model is specific for the IIB domain of the Glc family PTS transporters. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids, Signal transduction, PTS] 88 matched cddid_all.tbl CDD TIGR00827 TIGR00827 129907 EIIC-GAT PTS system, galactitol-specific IIC component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The only characterized member of this family of PTS transporters is the E. coli galactitol transporter. Gat family PTS systems typically have 3 components: IIA, IIB and IIC. This family is specific for the IIC component of the PTS Gat family. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids, Signal transduction, PTS] 407 matched cddid_all.tbl CDD TIGR00828 TIGR00828 129908 EIID-AGA PTS system, mannose/fructose/sorbose family, IID component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Man family is unique in several respects among PTS permease families.It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine,N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IID subunits of this family of PTS transporters. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids, Signal transduction, PTS] 271 matched cddid_all.tbl CDD TIGR00829 TIGR00829 129909 FRU PTS system, fructose-specific, IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Fru family is a large and complex family which includes several sequenced fructose and mannitol-specific permeases as well as several PTS components of unknown specificities. The fructose components of this family phosphorylate fructose on the 1-position. The Fru family PTS systems typically have 3 domains, IIA, IIB and IIC, which may be found as 1 or more proteins. The fructose and mannitol transporters form separate phylogenetic clusters in this family. This family is specific for the IIB domain of the fructose PTS transporters. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids, Signal transduction, PTS] 85 matched cddid_all.tbl CDD TIGR00830 TIGR00830 273289 PTBA PTS system, glucose subfamily, IIA component. These are part of the The PTS Glucose-Glucoside (Glc) SuperFamily. The Glc family includes permeases specific for glucose, N-acetylglucosamine and a large variety of a- and b-glucosides. However, not all b-glucoside PTS permeases are in this class, as the cellobiose (Cel) b-glucoside PTS permease is in the Lac family (TC #4.A.3). The IIA, IIB and IIC domains of all of the permeases listed below are demonstrably homologous. These permeases show limited sequence similarity with members of the Fru family (TC #4.A.2). Several of the PTS permeases in the Glc family lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). Most of these permeases have the B and C domains linked together in a single polypeptide chain, and a cysteyl residue in the IIB domain is phosphorylated by direct phosphoryl transfer from IIAglc(his~P). Those permeases which lack a IIA domain include the maltose (Mal), arbutin-salicin-cellobiose (ASC), trehalose (Tre), putative glucoside (Glv) and sucrose (Scr) permeases of E. coli . Most, but not all Scr permeases of other bacteria also lack a IIA domain. The three-dimensional structures of the IIA and IIB domains of the E. coli glucose permease have been elucidated. IIAglchas a complex b-sandwich structure while IIBglc is a split ab-sandwich with a topology unrelated to the split ab-sandwich structure of HPr. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids, Signal transduction, PTS] 121 matched cddid_all.tbl CDD TIGR00831 TIGR00831 129911 a_cpa1 Na+/H+ antiporter, bacterial form. The Monovalent Cation:Proton Antiporter-1 (CPA1) Family (TC 2.A.36) The CPA1 family is a large family of proteins derived from Gram-positive and Gram-negative bacteria, blue green bacteria, yeast, plants and animals. Transporters from eukaryotes have been functionally characterized, and all of these catalyze Na+:H+ exchange. Their primary physiological functions may be in (1) cytoplasmic pH regulation, extruding the H+ generated during metabolism, and (2) salt tolerance (in plants), due to Na+ uptake into vacuoles. This model is specific for the bacterial members of this family. [Transport and binding proteins, Cations and iron carrying compounds] 525 matched cddid_all.tbl CDD TIGR00832 TIGR00832 213563 acr3 arsenical-resistance protein. The Arsenical Resistance-3 (ACR3) Family (TC 2.A.59) The first protein of the ACR3 family functionally characterized was the ACR3 protein of Saccharomyces cerevisiae. It is present in the yeast plasma membrane and pumps arsenite out of the cell in response to the pmf. Similar proteins are found in bacteria, often as part of a four gene operon with an regulatory protein ArsR, a protein of unknown function ArsH, and an arsenate reductase that converts arsenate to arsenite to facilitate transport. [Cellular processes, Detoxification, Transport and binding proteins, Anions] 328 matched cddid_all.tbl CDD TIGR00833 TIGR00833 129913 actII Transport protein. The Resistance-Nodulation-Cell Division (RND) Superfamily- MmpL sub family (TC 2.A.6.5)Characterized members of the RND superfamily all probably catalyze substrate efflux via an H+ antiport mechanism. These proteins are found ubiquitously in bacteria, archaea and eukaryotes. This sub-family includes the S. coelicolor ActII3 protein, which may play a role in drug resistance, and the M. tuberculosis MmpL7 protein, which catalyzes export of an outer membrane lipid, phthiocerol dimycocerosate. [Transport and binding proteins, Unknown substrate] 910 matched cddid_all.tbl CDD TIGR00834 TIGR00834 273290 ae anion exchange protein. The Anion Exchanger (AE) Family (TC 2.A.31)Characterized protein members of the AE family are found only in animals.They preferentially catalyze anion exchange (antiport) reactions, typically acting as HCO3-:Cl- antiporters, but also transporting a range of other inorganic and organic anions. Additionally, renal Na+:HCO3- cotransporters have been found to be members of the AE family. They catalyze the reabsorption of HCO3- in the renal proximal tubule. [Transport and binding proteins, Anions] 900 matched cddid_all.tbl CDD TIGR00835 TIGR00835 273291 agcS amino acid carrier protein. The Alanine or Glycine: Cation Symporter (AGCS) Family (TC 2.A.25) Members of the AGCS family transport alanine and/or glycine in symport with Na+ and or H+. 425 matched cddid_all.tbl CDD TIGR00836 TIGR00836 273292 amt ammonium transporter. The Ammonium Transporter (Amt) Family (TC 2.A.49) All functionally characterized members of the Amt family are ammonia or ammonium uptake transporters. Some, but not others, also transport methylammonium. The mechanism of energy coupling, if any, to methyl-NH2 or NH3 uptake by the AmtB protein of E. coli is not entirely clear. NH4+ uniport driven by the pmf, energy independent NH3 facilitation, and NH4+/K+ antiport have been proposed as possible transport mechanisms. In Corynebacterium glutamicum and Arabidopsis thaliana, uptake via the Amt1 homologues of AmtB has been reported to be driven by the pmf. [Transport and binding proteins, Cations and iron carrying compounds] 403 matched cddid_all.tbl CDD TIGR00837 TIGR00837 273293 araaP aromatic amino acid transport protein. The Hydroxy/Aromatic Amino Acid Permease (HAAAP) Family- tyrosine/tryptophan subfamily (TC 2.A.42.1) The HAAAP family includes well characterized aromatic amino acid:H+ symport permeases and hydroxy amino acid permeases. This subfamily is specific for aromatic amino acid transporters and includes the tyrosine permease, TyrP, of E. coli, and the tryptophan transporters TnaB and Mtr of E. coli. [Transport and binding proteins, Amino acids, peptides and amines] 381 matched cddid_all.tbl CDD TIGR00838 TIGR00838 129918 argH argininosuccinate lyase. This model describes argininosuccinate lyase, but may include examples of avian delta crystallins, in which argininosuccinate lyase activity may or may not be present and the biological role is to provide the optically clear cellular protein of the eye lens. [Amino acid biosynthesis, Glutamate family] 455 matched cddid_all.tbl CDD TIGR00839 TIGR00839 213564 aspA aspartate ammonia-lyase. This enzyme, aspartate ammonia-lyase, shows local homology to a number of other lyases, as modeled by pfam00206. Fumarate hydratase scores as high as 570 bits against this model. [Energy metabolism, Amino acids and amines] 468 matched cddid_all.tbl CDD TIGR00840 TIGR00840 273294 b_cpa1 sodium/hydrogen exchanger 3. The Monovalent Cation:Proton Antiporter-1 (CPA1) Family (TC 2.A.36)The CPA1 family is a large family of proteins derived from Gram-positive and Gram-negative bacteria, blue green bacteria, yeast, plants and animals.Transporters from eukaryotes have been functionally characterized, and all of these catalyze Na+:H+ exchange. Their primary physiological functions may be in(1) cytoplasmic pH regulation, extruding the H+ generated during metabolism, and (2) salt tolerance (in plants), due to Na+ uptake into vacuoles.This model is specific for the eukaryotic members members of this family. [Transport and binding proteins, Cations and iron carrying compounds] 559 matched cddid_all.tbl CDD TIGR00841 TIGR00841 188087 bass bile acid transporter. The Bile Acid:Na+ Symporter (BASS) Family (TC 2.A.28) Functionally characterized members of the BASS family catalyze Na+:bile acid symport. These systems have been identified in intestinal, liver and kidney tissues of animals. These symporters exhibit broad specificity, taking up a variety of non bile organic compounds as well as taurocholate and other bile salts. Functionally uncharacterised homologues are found in plants, yeast, archaea and bacteria. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 286 matched cddid_all.tbl CDD TIGR00842 TIGR00842 213565 bcct choline/carnitine/betaine transport. The Betaine/Carnitine/Choline Transporter (BCCT) Family (TC 2.A.15) Proteins of the BCCT family share the common functional feature of transporting molecules with a quaternary ammonium group [R-N+(CH3)3]. The BCCT family includes transporters for carnitine, choline and glycine betaine. BCCT transporters have 12 putative TMS, and are energized by pmf-driven proton symport. Some of these permeases exhibit osmosensory and osmoregulatory properties inherent to their polypeptide chains. [Transport and binding proteins, Other] 452 matched cddid_all.tbl CDD TIGR00843 TIGR00843 129923 benE benzoate transporter. The benzoate transporter family contains only a single characterised member, the benzoate transporter of Acinetobacter calcoaceticus, which functions as a benzoate/proton symporter. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 395 matched cddid_all.tbl CDD TIGR00844 TIGR00844 273295 c_cpa1 na(+)/h(+) antiporter. The Monovalent Cation:Proton Antiporter-1 (CPA1) Family (TC 2.A.36) The CPA1 family is a large family of proteins derived from Gram-positive and Gram-negative bacteria, blue green bacteria, yeast, plants and animals. Transporters from eukaryotes have been functionally characterized, and all of these catalyze Na+:H+ exchange. Their primary physiological functions may be in (1) cytoplasmic pH regulation, extruding the H+ generated during metabolism, and (2) salt tolerance (in plants), due to Na+ uptake into vacuoles. This model is specific for the fungal members of this family. [Transport and binding proteins, Cations and iron carrying compounds] 810 matched cddid_all.tbl CDD TIGR00845 TIGR00845 273296 caca sodium/calcium exchanger 1. The Ca2+:Cation Antiporter (CaCA) Family (TC 2.A.19)Proteins of the CaCA family are found ubiquitously, having been identified in animals, plants, yeast, archaea and widely divergent bacteria.All of the characterized animal proteins catalyze Ca2+:Na+ exchange although some also transport K+. The NCX1 plasma membrane protein exchanges 3 Na+ for 1 Ca2+. The E. coli ChaA protein catalyzes Ca2+:H+ antiport but may also catalyze Na+:H+ antiport. All remaining well-characterized members of the family catalyze Ca2+:H+ exchange.This model is specific for the eukaryotic sodium ion/calcium ion exchangers of the Caca family [Transport and binding proteins, Other] 928 matched cddid_all.tbl CDD TIGR00846 TIGR00846 273297 caca2 calcium/proton exchanger. The Ca2+:Cation Antiporter (CaCA) Family (TC 2.A.19)Proteins of the CaCA family are found ubiquitously, having been identified in animals, plants, yeast, archaea and widely divergent bacteria.All of the characterized animal proteins catalyze Ca2+:Na+ exchange although some also transport K+. The NCX1 plasma membrane protein exchanges 3 Na+ for 1 Ca2+. The E. coli ChaA protein catalyzes Ca2+:H+ antiport but may also catalyze Na+:H+ antiport. All remaining well-characterized members of the family catalyze Ca2+:H+ exchange.This model is generated from the calcium ion/proton exchangers of the CacA family. [Transport and binding proteins, Cations and iron carrying compounds] 363 matched cddid_all.tbl CDD TIGR00847 TIGR00847 129927 ccoS cytochrome oxidase maturation protein, cbb3-type. CcoS from Rhodobacter capsulatus has been shown essential for incorporation of redox-active prosthetic groups (heme, Cu) into cytochrome cbb(3) oxidase. FixS of Bradyrhizobium japonicum appears to have the same function. Members of this family are found so far in organisms with a cbb3-type cytochrome oxidase, including Neisseria meningitidis, Helicobacter pylori, Campylobacter jejuni, Caulobacter crescentus, Bradyrhizobium japonicum, and Rhodobacter capsulatus. [Energy metabolism, Electron transport, Protein fate, Protein modification and repair] 51 matched cddid_all.tbl CDD TIGR00848 TIGR00848 273298 fruA PTS system, fructose subfamily, IIA component. 4.A.2 The PTS Fructose-Mannitol (Fru) Family Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Fru family is a large and complex family which includes several sequenced fructose and mannitol-specific permeases as well as several putative PTS permeases of unknown specificities. The fructose permeases of this family phosphorylate fructose on the 1-position. Those of family 4.6 phosphorylate fructose on the 6-position. The Fru family PTS systems typically have 3 domains, IIA, IIB and IIC, which may be found as 1 or more proteins. The fructose and mannitol transporters form separate phylogenetic clusters in this family. This model is specific for the IIA domain of the fructose PTS transporters. Also similar to the Enzyme IIA Fru subunits of the PTS, but included in TIGR01419 rather than this model, is enzyme IIA Ntr (nitrogen), also called PtsN, found in E. coli and other organisms, which may play a solely regulatory role. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids, Signal transduction, PTS] 129 matched cddid_all.tbl CDD TIGR00849 TIGR00849 129929 gutA PTS system, glucitol/sorbitol-specific IIA component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. This family consists only of glucitol-specific transporters, and occur both in Gram-negative and Gram-positive bacteria.The system in E.Coli consists of a IIA protein, and a IIBC protein. This family is specific for the IIA component. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids, Signal transduction, PTS] 121 matched cddid_all.tbl CDD TIGR00851 TIGR00851 129930 mtlA PTS system, mannitol-specific IIC component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Fru family is a large and complex family which includes several sequenced fructose and mannitol-specific permeases as well as several putative PTS permeases of unknown specificities.The Fru family PTS systems typically have 3 domains, IIA, IIB and IIC, which may be found as 1 or more proteins. The fructose and mannitol transporters form separate phylogenetic clusters in this family. This family is specific for the IIC domain of the mannitol PTS transporters. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids, Signal transduction, PTS] 338 matched cddid_all.tbl CDD TIGR00852 TIGR00852 273299 pts-Glc PTS system, maltose and glucose-specific subfamily, IIC component. The PTS Glucose-Glucoside (Glc) Family (TC 4.A.1) Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains. The Glc family includes permeases specific for glucose, N-acetylglucosamine and a large variety of a- and b-glucosides. However, not all b-glucoside PTS permeases are in this class, as the cellobiose (Cel) b-glucoside PTS permease is in the Lac family (TC #4.A.3). These permeases show limited sequence similarity with members of the Fru family (TC #4.A.2). Several of the E. coli PTS permeases in the Glc family lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). Most of these permeases have the B and C domains linked together in a single polypeptide chain, and a cysteyl residue in the IIB domain is phosphorylated by direct phosphoryl transfer from IIAglc(his~P). Those permeases which lack a IIA domain include the maltose (Mal), arbutin-salicin-cellobiose (ASC), trehalose (Tre), putative glucoside (Glv) and sucrose (Scr) permeases of E. coli . Most, but not all Scr permeases of other bacteria also lack a IIA domain. This model is specific for the IIC domain of the Glc family PTS transporters. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids, Signal transduction, PTS] 289 matched cddid_all.tbl CDD TIGR00853 TIGR00853 273300 pts-lac PTS system, lactose/cellobiose family IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Lac family includes several sequenced lactose (b-galactoside) permeases of Gram-positive bacteria as well as those in E. coli. While the Lac family usually consists of two polypeptide components IIA and IICB, the Chb permease of E. coli consists of three IIA, IIB and IIC. This family is specific for the IIB subunit of the Lac PTS family. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids, Signal transduction, PTS] 95 matched cddid_all.tbl CDD TIGR00854 TIGR00854 129933 pts-sorbose PTS system, mannose/fructose/sorbose family, IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families.It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIB components of this family of PTS transporters. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids, Signal transduction, PTS] 151 matched cddid_all.tbl CDD TIGR00855 TIGR00855 273301 L12 ribosomal protein L7/L12. Ribosomal proteins L7 and L12 are synonymous except for post-translational modification of the N-terminal amino acid. THis model resembles pfam00542 but matches the full length of prokaryotic and organellar proteins rather than just the C-terminus. [Protein synthesis, Ribosomal proteins: synthesis and modification] 123 matched cddid_all.tbl CDD TIGR00856 TIGR00856 129935 pyrC_dimer dihydroorotase, homodimeric type. This homodimeric form of dihydroorotase is less common in microbial genomes than a related dihydroorotase that appears in a complex with aspartyltranscarbamoylase or as a homologous domain in multifunctional proteins of pyrimidine biosynthesis in higher eukaryotes. [Purines, pyrimidines, nucleosides, and nucleotides, Pyrimidine ribonucleotide biosynthesis] 341 matched cddid_all.tbl CDD TIGR00857 TIGR00857 273302 pyrC_multi dihydroorotase, multifunctional complex type. In contrast to the homodimeric type of dihydroorotase found in E. coli, this class tends to appear in a large, multifunctional complex with aspartate transcarbamoylase. Homologous domains appear in multifunctional proteins of higher eukaryotes. In some species, including Pseudomonas putida and P. aeruginosa, this protein is inactive but is required as a non-catalytic subunit of aspartate transcarbamoylase (ATCase). In these species, a second, active dihydroorotase is also present. The seed for this model does not include any example of the dihydroorotase domain of eukaryotic multidomain pyrimidine synthesis proteins. All proteins described by this model should represent active and inactive dihydroorotase per se and functionally equivalent domains of multifunctional proteins from higher eukaryotes, but exclude related proteins such as allantoinase. [Purines, pyrimidines, nucleosides, and nucleotides, Pyrimidine ribonucleotide biosynthesis] 411 matched cddid_all.tbl CDD TIGR00858 TIGR00858 273303 bioF 8-amino-7-oxononanoate synthase. 7-keto-8-aminopelargonic acid synthetase is an alternate name. This model represents 8-amino-7-oxononanoate synthase, the BioF protein of biotin biosynthesis. This model is based on a careful phylogenetic analysis to separate members of this family from 2-amino-3-ketobutyrate and other related pyridoxal phosphate-dependent enzymes. In several species, including Staphylococcus and Coxiella, a candidate 8-amino-7-oxononanoate synthase is confirmed by location in the midst of a biotin biosynthesis operon but scores below the trusted cutoff of this model. [Biosynthesis of cofactors, prosthetic groups, and carriers, Biotin] 360 matched cddid_all.tbl CDD TIGR00859 TIGR00859 273304 ENaC sodium channel transporter. The Epithelial Na+ Channel (ENaC) Family (TC 1.A.06)The ENaC family consists of sodium channels from animals and has no recognizable homologues in other eukaryotes or bacteria. The vertebrate ENaC proteins from epithelial cells cluster tightly together on the phylogenetic tree: voltage-insensitive ENaC homologues are also found in the brain. Eleven sequenced C. elegans proteins, including the degenerins, are distantly related to the vertebrate proteins as well as to each other. At least some ofthese proteins form part of a mechano-transducing complex for touch sensitivity. Other members of the ENaC family, the acid-sensing ion channels, ASIC1-3,are homo- or hetero-oligomeric neuronal H+-gated channels that mediate pain sensation in response to tissue acidosis. The homologous Helix aspersa(FMRF-amide)-activated Na+ channel is the first peptide neurotransmitter-gated ionotropic receptor to be sequenced.Mammalian ENaC is important for the maintenance of Na+ balance and the regulation of blood pressure. Three homologous ENaC subunits, a, b and g, havebeen shown to assemble to form the highly Na+-selective channel.This model is designed from the vertebrate members of the ENaC family. [Transport and binding proteins, Cations and iron carrying compounds] 595 matched cddid_all.tbl CDD TIGR00860 TIGR00860 273305 LIC Cation transporter family protein. The Ligand-gated Ion Channel (LIC) Family of Neurotransmitter Receptors TC 1.A.9)Members of the LIC family of ionotropic neurotransmitter receptors are found only in vertebrate and invertebrate animals. They exhibit receptor specificity for (1)acetylcholine, (2) serotonin, (3) glycine, (4) glutamate and (5) g-aminobutyric acid (GABA). All of these receptor channels are probably hetero- orhomopentameric. The best characterized are the nicotinic acetyl-choline receptors which are pentameric channels of a2bgd subunit composition. All subunits arehomologous. The three dimensional structures of the protein complex in both the open and closed configurations have been solved at 0.9 nm resolution.The channel protein complexes of the LIC family preferentially transport cations or anions depending on the channel (e.g., the acetylcholine receptors are cationselective while glycine receptors are anion selective). [Transport and binding proteins, Cations and iron carrying compounds] 459 matched cddid_all.tbl CDD TIGR00861 TIGR00861 273306 MIP MIP family channel proteins. 1.A.8 The Major Intrinsic Protein (MIP) FamilyThe MIP family is large and diverse, possessing over 100 members that all form transmembrane channels. These channel proteins function in water, smallcarbohydrate (e.g., glycerol), urea, NH3, CO2 and possibly ion transport by an energy independent mechanism. They are found ubiquitously in bacteria, archaeaand eukaryotes. The MIP family contains two major groups of channels: aquaporins and glycerol facilitators.The known aquaporins cluster loosely together as do the known glycerol facilitators. MIP family proteins are believed to form aqueous pores that selectively allow passive transport of their solute(s) across the membrane with minimal apparent recognition. Aquaporins selectively transport water (but not glycerol) while glycerol facilitators selectively transport glycerol but not water. Some aquaporins can transport NH3 and CO2. Glycerol facilitators function as solute nonspecific channels, and may transport glycerol, dihydroxyacetone, propanediol, urea and other small neutral molecules in physiologically importantprocesses. Some members of the family, including the yeast FPS protein (TC #1.A.8.5.1) and tobacco NtTIPA may transport both water and small solutes. [Transport and binding proteins, Unknown substrate] 216 matched cddid_all.tbl CDD TIGR00862 TIGR00862 129941 O-ClC intracellular chloride channel protein. The Organellar Chloride Channel (O-ClC) Family (TC 1.A.12) Proteins of the O-ClC family are voltage-sensitive chloride channels found in intracellular membranes but not the plasma membranes of animal cells. They are found in human nuclear membranes, and the bovine protein targets to the microsomes, but not the plasma membrane, when expressed in Xenopus laevis oocytes. These proteins are thought to function in the regulation of the membrane potential and in transepithelial ion absorption and secretion in the kidney. [Transport and binding proteins, Anions] 236 matched cddid_all.tbl CDD TIGR00863 TIGR00863 273307 P2X cation transporter protein. ATP-gated Cation Channel (ACC) Family (TC 1.A.7)Members of the ACC family (also called P2X receptors) respond to ATP, a functional neurotransmitter released by exocytosis from many types of neurons.These channels, which function at neuron-neuron and neuron-smooth muscle junctions, may play roles in the control of blood pressure and pain sensation. They may also function in lymphocyte and plateletphysiology. They are found only in animals.ACC channels are probably hetero- or homomultimers and transport small monovalent cations (Me+). Some also transport Ca2+; a few also transport small metabolites. [Transport and binding proteins, Cations and iron carrying compounds] 372 matched cddid_all.tbl CDD TIGR00864 TIGR00864 188093 PCC polycystin cation channel protein. The Polycystin Cation Channel (PCC) Family (TC 1.A.5) Polycystin is a huge protein of 4303aas. Its repeated leucine-rich (LRR) segment is found in many proteins. It contains 16 polycystic kidney disease (PKD) domains, one LDL-receptor class A domain, one C-type lectin family domain, and 16-18 putative TMSs in positions between residues 2200 and 4100. Polycystin-L has been shown to be a cation (Na+, K+ and Ca2+) channel that is activated by Ca2+. Two members of the PCC family (polycystin 1 and 2) are mutated in autosomal dominant polycystic kidney disease, and polycystin-L is deleted in mice with renal and retinal defects. Note: this model is restricted to the amino half. 2740 matched cddid_all.tbl CDD TIGR00865 TIGR00865 273308 bcl-2 apoptosis regulator. The Bcl-2 (Bcl-2) Family (TC 1.A.21) The Bcl-2 family consists of the apoptosis regulator, Bcl-X, and its homologues. Bcl-X is a dominant regulator of programmed cell death in mammalian cells. The long form (Bcl-X(L)) displays cell death repressor activity, but the short isoform (Bcl-X(S)) and the b-isoform (Bcl-Xb) promote cell death. Bcl-X(L), Bcl-X(S) and Bcl-Xb are three isoforms derived by alternative RNA splicing. Bcl-X(S) forms heterodimers with Bcl-2. Homologues of Bcl-X include the Bax (rat; 192 aas; spQ63690) and Bak (mouse; 208 aas; spO08734) proteins which also influence apoptosis. Using isolated mitochondria, recombinant Bax and Bak have been shown to induce Dy loss, swelling and cytochrome c release. All of these changes are dependent on Ca2+ and are prevented by cyclosporin A and bongkrekic acid, both of which are known to close permeability transition pores (megachannels). Coimmimoprecipitation studies revealed that Bax and Bak interact with VDAC to form permeability transition pores. Thus, even though they can form channels in artificial membranes at acidic pH, proapoptotic Bcl-2 family proteins (including Bax and Bak) probably induce the mitochondrial permeability transition and cytochrome c release by interacting with permeability transition pores, the most important component for pore fomation of which is VDAC. [Regulatory functions, Other] 213 matched cddid_all.tbl CDD TIGR00867 TIGR00867 273309 deg-1 degenerin. The Epithelial Na+ Channel (ENaC) Family (TC 1.A.06)The ENaC family consists of sodium channels from animals and has no recognizable homologues in other eukaryotes or bacteria. The vertebrate ENaC proteins from epithelial cells cluster tightly together on the phylogenetic tree: voltage-insensitive ENaC homologues are also found in the brain. Eleven sequenced C. elegans proteins, including the degenerins, are distantly related to the vertebrate proteins as well as to each other. At least some ofthese proteins form part of a mechano-transducing complex for touch sensitivity. Other members of the ENaC family, the acid-sensing ion channels, ASIC1-3,are homo- or hetero-oligomeric neuronal H+-gated channels that mediate pain sensation in response to tissue acidosis. The homologous Helix aspersa(FMRF-amide)-activated Na+ channel is the first peptide neurotransmitter-gated ionotropic receptor to be sequenced.Mammalian ENaC is important for the maintenance of Na+ balance and the regulation of blood pressure. Three homologous ENaC subunits, a, b and g, havebeen shown to assemble to form the highly Na+-selective channel.This model is designed from the invertebrate members of the ENaC family. [Transport and binding proteins, Cations and iron carrying compounds] 600 matched cddid_all.tbl CDD TIGR00868 TIGR00868 129946 hCaCC calcium-activated chloride channel protein 1. The Epithelial Chloride Channel (E-ClC) Family (TC 1.A.13). Mammals have multiple isoforms of epithelial chloride channel proteins. The first member of this family to be characterized was a respiratory epithelium, Ca 2+-regulated, chloride channel protein isolated from bovine tracheal apical membranes. It was biochemically characterized as a 140 kDa complex. The purified complex when reconstituted in a planar lipid bilayer behaved as an anion-selective channel. It was regulated by Ca 2+ via a calmodulin kinase II-dependent mechanism. When the cRNA was injected into Xenopus oocytes, an outward rectifying, DIDS-sensitive, anion conductance was measured. A related gene, Lu-ECAM, was cloned from the bovine aortic endothelial cell line, BAEC. It is expressed in the lung and spleen but not in the trachea. Homologues are found in several mammals, and at least three paralogues(hCaCC-1-3) are present in humans, each with different tissue distributions. [Transport and binding proteins, Anions] 863 matched cddid_all.tbl CDD TIGR00869 TIGR00869 273310 sec62 protein translocation protein, Sec62 family. Members of the NSCC2 family have been sequenced from various yeast, fungal and animals species including Saccharomyces cerevisiae, Drosophila melanogaster and Homo sapiens. These proteins are the Sec62 proteins, believed to be associated with the Sec61 and Sec63 constituents of the general protein secretary systems of yeast microsomes. They are also the non-selective cation (NS) channels of the mammalian cytoplasmic membrane. The yeast Sec62 protein has been shown to be essential for cell growth. The mammalian NS channel proteins has been implicated in platelet derived growth factor(PGDF) dependent single channel current in fibroblasts. These channels are essentially closed in serum deprived tissue-culture cells and are specifically opened by exposure to PDGF. These channels are reported to exhibit equal selectivity for Na+, K+ and Cs+ with low permeability to Ca2+, and no permeability to anions. [Transport and binding proteins, Amino acids, peptides and amines] 232 matched cddid_all.tbl CDD TIGR00870 TIGR00870 273311 trp transient-receptor-potential calcium channel protein. The Transient Receptor Potential Ca2+ Channel (TRP-CC) Family (TC. 1.A.4)The TRP-CC family has also been called the store-operated calcium channel (SOC) family. The prototypical members include the Drosophila retinal proteinsTRP and TRPL (Montell and Rubin, 1989; Hardie and Minke, 1993). SOC members of the family mediate the entry of extracellular Ca2+ into cells in responseto depletion of intracellular Ca2+ stores (Clapham, 1996) and agonist stimulated production of inositol-1,4,5 trisphosphate (IP3). One member of the TRP-CCfamily, mammalian Htrp3, has been shown to form a tight complex with the IP3 receptor (TC #1.A.3.2.1). This interaction is apparently required for IP3 tostimulate Ca2+ release via Htrp3. The vanilloid receptor subtype 1 (VR1), which is the receptor for capsaicin (the ?hot? ingredient in chili peppers) and servesas a heat-activated ion channel in the pain pathway (Caterina et al., 1997), is also a member of this family. The stretch-inhibitable non-selective cation channel(SIC) is identical to the vanilloid receptor throughout all of its first 700 residues, but it exhibits a different sequence in its last 100 residues. VR1 and SICtransport monovalent cations as well as Ca2+. VR1 is about 10x more permeable to Ca2+ than to monovalent ions. Ca2+ overload probably causes cell deathafter chronic exposure to capsaicin. (McCleskey and Gold, 1999). [Transport and binding proteins, Cations and iron carrying compounds] 743 matched cddid_all.tbl CDD TIGR00871 TIGR00871 273312 zwf glucose-6-phosphate 1-dehydrogenase. This enzyme (EC 1.1.1.49) acts on glucose 6-phospate and reduces NADP(+). An alternate name appearing in the literature for the human enzyme, based on a slower activity with beta-D-glucose, is glucose 1-dehydrogenase (EC 1.1.1.47), but that name more properly describes a subfamily of the short chain dehydrogenases/reductases family. This is a well-studied enzyme family, with sequences available from well over 50 species. The trusted cutoff is set above the score for the Drosophila melanogaster CG7140 gene product, a homolog of unknown function. G6PD homologs from the bacteria Aquifex aeolicus and Helicobacter pylori lack several motifs well conserved most other members, were omitted from the seed alignment, and score well below the trusted cutoff. [Energy metabolism, Pentose phosphate pathway] 487 matched cddid_all.tbl CDD TIGR00872 TIGR00872 273313 gnd_rel 6-phosphogluconate dehydrogenase (decarboxylating). This family resembles a larger family (gnd) of bacterial and eukaryotic 6-phosphogluconate dehydrogenases but differs from it by a deep split in a UPGMA similarity clustering tree and the lack of a central region of about 140 residues. Among complete genomes, it is found is found in Bacillus subtilis and Mycobacterium tuberculosis, both of which also contain gnd, and in Aquifex aeolicus. The protein from Methylobacillus flagellatus KT has been characterized as a decarboxylating 6-phosphogluconate dehydrogenase as part of an unusual formaldehyde oxidation cycle. In some sequenced organisms members of this family are the sole 6-phosphogluconate dehydrogenase present and are probably active in the pentose phosphate cycle. [Energy metabolism, Pentose phosphate pathway] 298 matched cddid_all.tbl CDD TIGR00873 TIGR00873 273314 gnd 6-phosphogluconate dehydrogenase (decarboxylating). This model does not specify whether the cofactor is NADP only (EC 1.1.1.44), NAD only, or both. The model does not assign an EC number for that reason. [Energy metabolism, Pentose phosphate pathway] 467 matched cddid_all.tbl CDD TIGR00874 TIGR00874 162081 talAB transaldolase. This family includes the majority of known and predicted transaldolase sequences, including E. coli TalA and TalB. It excluded two other families. The first includes E. coli transaldolase-like protein TalC. The second family includes the putative transaldolases of Helicobacter pylori and Mycobacterium tuberculosis. [Energy metabolism, Pentose phosphate pathway] 317 matched cddid_all.tbl CDD TIGR00875 TIGR00875 129953 fsa_talC_mipB fructose-6-phosphate aldolase, TalC/MipB family. This model represents a family that includes the E. coli transaldolase homologs TalC and MipB, both shown to be fructose-6-phosphate aldolases rather than transaldolases as previously thought. It is related to but distinct from the transaldolase family of E. coli TalA and TalB. The member from Bacillus subtilis becomes phosphorylated during early stationary phase but not during exponential growth. [Energy metabolism, Pentose phosphate pathway] 213 matched cddid_all.tbl CDD TIGR00876 TIGR00876 129954 tal_mycobact transaldolase, mycobacterial type. This model describes one of three related but easily separable famiiles of known and putative transaldolases. This family and the family typified by E. coli TalA and TalB both contain experimentally verified examples. [Energy metabolism, Pentose phosphate pathway] 350 matched cddid_all.tbl CDD TIGR00877 TIGR00877 273315 purD phosphoribosylamine--glycine ligase. Alternate name: glycinamide ribonucleotide synthetase (GARS). This enzyme appears as a monofunctional protein in prokaryotes but as part of a larger, multidomain protein in eukaryotes. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 422 matched cddid_all.tbl CDD TIGR00878 TIGR00878 273316 purM phosphoribosylaminoimidazole synthetase. Alternate name: phosphoribosylformylglycinamidine cyclo-ligase; AIRS; AIR synthase This enzyme is found as a homodimeric monofunctional protein in prokaryotes and as part of a larger, multifunctional protein, sometimes with two copies of this enzyme in tandem, in eukaryotes. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 332 matched cddid_all.tbl CDD TIGR00879 TIGR00879 273317 SP MFS transporter, sugar porter (SP) family. This model represent the sugar porter subfamily of the major facilitator superfamily (pfam00083) [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 481 matched cddid_all.tbl CDD TIGR00880 TIGR00880 273318 2_A_01_02 Multidrug resistance protein. 141 matched cddid_all.tbl CDD TIGR00881 TIGR00881 273319 2A0104 phosphoglycerate transporter family protein. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 379 matched cddid_all.tbl CDD TIGR00882 TIGR00882 211613 2A0105 oligosaccharide:H+ symporter. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 396 matched cddid_all.tbl CDD TIGR00883 TIGR00883 273320 2A0106 metabolite-proton symporter. This model represents the metabolite:H+ symport subfamily of the major facilitator superfamily (pfam00083), including citrate-H+ symporters, dicarboxylate:H+ symporters, the proline/glycine-betaine transporter ProP, etc. [Transport and binding proteins, Unknown substrate] 394 matched cddid_all.tbl CDD TIGR00884 TIGR00884 273321 guaA_Cterm GMP synthase (glutamine-hydrolyzing), C-terminal domain or B subunit. This protein of purine de novo biosynthesis is well-conserved. However, it appears to split into two separate polypeptide chains in most of the Archaea. This C-terminal region would be the larger subunit [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 311 matched cddid_all.tbl CDD TIGR00885 TIGR00885 211614 fucP L-fucose:H+ symporter permease. This family describes the L-fucose permease in bacteria. L-fucose(6-deoxy-L-galactose) is a monosaccharide found in glycoproteins and cell wall polysaccharides. L-fucose is used in bacteria through an inducible pathway mediated by atleast four enzymes: a permease, isomerase, kinase and an aldolase which are encoded by fucP, fucI, fucK, fucA respectively. The fuc genes belong to a regulon comprising of four linked operons: fucO, fucA, fucPIK and fucR. The positive regulator is encoded by fucR, whose protein responds to fuculose-1-phosphate, which acts as an effector. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 408 matched cddid_all.tbl CDD TIGR00886 TIGR00886 273322 2A0108 nitrite extrusion protein (nitrite facilitator). [Transport and binding proteins, Anions] 354 matched cddid_all.tbl CDD TIGR00887 TIGR00887 129965 2A0109 phosphate:H+ symporter. This model represents the phosphate uptake symporter subfamily of the major facilitator superfamily (pfam00083). [Transport and binding proteins, Anions] 502 matched cddid_all.tbl CDD TIGR00888 TIGR00888 129966 guaA_Nterm GMP synthase (glutamine-hydrolyzing), N-terminal domain or A subunit. This protein of purine de novo biosynthesis is well-conserved. However, it appears to split into two separate polypeptide chains in most of the Archaea. This N-terminal region would be the smaller subunit. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 188 matched cddid_all.tbl CDD TIGR00889 TIGR00889 129967 2A0110 nucleoside transporter. This family of proteins transports nucleosides at a high affinity. The transport mechanism is driven by proton motive force. This family includes nucleoside permease NupG and xanthosine permease from E.Coli. [Transport and binding proteins, Nucleosides, purines and pyrimidines] 418 matched cddid_all.tbl CDD TIGR00890 TIGR00890 273323 2A0111 oxalate/formate antiporter family transporter. This subfamily belongs to the major facilitator family. Members include the oxalate/formate antiporter of Oxalobacter formigenes, where one substrate is decarboxylated in the cytosol into the other to consume a proton and drive an ion gradient. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 377 matched cddid_all.tbl CDD TIGR00891 TIGR00891 273324 2A0112 putative sialic acid transporter. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 405 matched cddid_all.tbl CDD TIGR00892 TIGR00892 273325 2A0113 monocarboxylate transporter 1. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 455 matched cddid_all.tbl CDD TIGR00893 TIGR00893 273326 2A0114 D-galactonate transporter. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 399 matched cddid_all.tbl CDD TIGR00894 TIGR00894 129972 2A0114euk Na(+)-dependent inorganic phosphate cotransporter. [Transport and binding proteins, Anions] 465 matched cddid_all.tbl CDD TIGR00895 TIGR00895 273327 2A0115 benzoate transport. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 398 matched cddid_all.tbl CDD TIGR00896 TIGR00896 129974 CynX cyanate transporter. This family of proteins is involved in active transport of cyanate. The cyanate transporter in E.Coli is used to transport cyanate into the cell so it can be metabolized into ammonia and bicarbonate. This process is used to overcome the toxicity of environmental cyanate. [Transport and binding proteins, Other] 355 matched cddid_all.tbl CDD TIGR00897 TIGR00897 162096 2A0118 polyol permease family. This family of proteins includes the ribitol and D-arabinitol transporters from Klebsiella pneumoniae and the alpha-ketoglutarate permease from Bacillus subtilis. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 402 matched cddid_all.tbl CDD TIGR00898 TIGR00898 273328 2A0119 cation transport protein. [Transport and binding proteins, Cations and iron carrying compounds] 505 matched cddid_all.tbl CDD TIGR00899 TIGR00899 129977 2A0120 sugar efflux transporter. This family of proteins is an efflux system for lactose, glucose, aromatic glucosides and galactosides, cellobiose, maltose, a-methyl glucoside and other sugar compounds. They are found in both gram-negative and gram-postitive bacteria. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 375 matched cddid_all.tbl CDD TIGR00900 TIGR00900 162098 2A0121 H+ Antiporter protein. [Transport and binding proteins, Cations and iron carrying compounds] 365 matched cddid_all.tbl CDD TIGR00901 TIGR00901 273329 2A0125 AmpG-like permease. [Cellular processes, Adaptations to atypical conditions] 356 matched cddid_all.tbl CDD TIGR00902 TIGR00902 129980 2A0127 phenyl proprionate permease family protein. This family of proteins is involved in the uptake of 3-phenylpropionic acid. This uptake mechanism is for the metabolism of phenylpropanoid compounds and plays an important role in the natural degradative cycle of these aromatic molecules. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 382 matched cddid_all.tbl CDD TIGR00903 TIGR00903 129981 2A0129 major facilitator 4 family protein. This family of proteins are uncharacterized proteins from archaea. This family includes proteins from Archaeoglobus fulgidus and Aeropyrum pernix. [Transport and binding proteins, Other] 368 matched cddid_all.tbl CDD TIGR00904 TIGR00904 129982 mreB cell shape determining protein, MreB/Mrl family. MreB (mecillinam resistance) in E. coli (also called envB) and the paralogous pair MreB and Mrl of Bacillus subtilis have all been shown to help determine cell shape. This protein is present in a wide variety of bacteria, including spirochetes, but is missing from the Mycoplasmas and from Gram-positive cocci. Most completed bacterial genomes have a single member of this family. In some species it is an essential gene. A close homolog is found in the Archaeon Methanobacterium thermoautotrophicum, and a more distant homolog in Archaeoglobus fulgidus. The family is related to cell division protein FtsA and heat shock protein DnaK. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 333 matched cddid_all.tbl CDD TIGR00905 TIGR00905 129983 2A0302 transporter, basic amino acid/polyamine antiporter (APA) family. This family includes several families of antiporters that, rather commonly, are encoded next to decarboxylases that convert one of the antiporter substrates into the other. This arrangement allows a cycle that can remove proteins from the cytoplasm and thereby protect against acidic conditions. [Transport and binding proteins, Amino acids, peptides and amines] 473 matched cddid_all.tbl CDD TIGR00906 TIGR00906 273330 2A0303 cationic amino acid transport permease. [Transport and binding proteins, Amino acids, peptides and amines] 557 matched cddid_all.tbl CDD TIGR00907 TIGR00907 273331 2A0304 amino acid permease (GABA permease). [Transport and binding proteins, Amino acids, peptides and amines] 482 matched cddid_all.tbl CDD TIGR00908 TIGR00908 129986 2A0305 ethanolamine permease. The three genes used as the seed for this model (from Burkholderia pseudomallei, Pseudomonas aeruginosa and Clostridium acetobutylicum are all adjacent to genes for the catabolism of ethanolamine. Most if not all of the hits to this model have a similar arrangement of genes. This group is a member of the Amino Acid-Polyamine-Organocation (APC) Superfamily. [Transport and binding proteins, Amino acids, peptides and amines] 442 matched cddid_all.tbl CDD TIGR00909 TIGR00909 129987 2A0306 amino acid transporter. [Transport and binding proteins, Amino acids, peptides and amines] 429 matched cddid_all.tbl CDD TIGR00910 TIGR00910 129988 2A0307_GadC glutamate:gamma-aminobutyrate antiporter. Lowered cutoffs from 1000/500 to 800/300, promoted from subfamily to equivalog, and put into a Genome Property DHH 9/1/2009 [Transport and binding proteins, Amino acids, peptides and amines] 507 matched cddid_all.tbl CDD TIGR00911 TIGR00911 273332 2A0308 L-type amino acid transporter. [Transport and binding proteins, Amino acids, peptides and amines] 501 matched cddid_all.tbl CDD TIGR00912 TIGR00912 273333 2A0309 spore germination protein (amino acid permease). This model describes spore germination protein GerKB and paralogs from Bacillus subtilis, Clostridium tetani, and other known or predicted endospore-forming members of the Firmicutes (low-GC Gram positive bacteria). Members show some similarity to amino acid permeases. [Transport and binding proteins, Amino acids, peptides and amines] 359 matched cddid_all.tbl CDD TIGR00913 TIGR00913 273334 2A0310 amino acid permease (yeast). [Transport and binding proteins, Amino acids, peptides and amines] 478 matched cddid_all.tbl CDD TIGR00914 TIGR00914 129992 2A0601 heavy metal efflux pump, CzcA family. This model represents a family of H+/heavy metal cation antiporters. This family is one of several subfamilies within the scope of pfam00873. [Cellular processes, Detoxification, Transport and binding proteins, Cations and iron carrying compounds] 1051 matched cddid_all.tbl CDD TIGR00915 TIGR00915 273335 2A0602 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family. Proteins scoring above the trusted cutoff (1000) form a tight clade within the RND (Resistance-Nodulation-Cell Division) superfamily. Proteins scoring greater than the noise cutoff (100) appear to form a larger clade, cleanly separated from more distant homologs that include cadmium/zinc/cobalt resistance transporters. This family is one of several subfamilies within the scope of pfam00873. [Cellular processes, Toxin production and resistance, Transport and binding proteins, Unknown substrate] 1044 matched cddid_all.tbl CDD TIGR00916 TIGR00916 273336 2A0604s01 protein-export membrane protein, SecD/SecF family. The SecA,SecB,SecD,SecE,SecF,SecG and SecY proteins form the protein translocation appartus in prokaryotes. This family is specific for the SecD and SecF proteins. [Protein fate, Protein and peptide secretion and trafficking] 192 matched cddid_all.tbl CDD TIGR00917 TIGR00917 273337 2A060601 Niemann-Pick C type protein family. The model describes Niemann-Pick C type protein in eukaryotes. The defective protein has been associated with Niemann-Pick disease which is described in humans as autosomal recessive lipidosis. It is characterized by the lysosomal accumulation of unestrified cholesterol. It is an integral membrane protein, which indicates that this protein is most likely involved in cholesterol transport or acts as some component of cholesterol homeostasis. [Transport and binding proteins, Other] 1205 matched cddid_all.tbl CDD TIGR00918 TIGR00918 273338 2A060602 The Eukaryotic (Putative) Sterol Transporter (EST) Family. 1145 matched cddid_all.tbl CDD TIGR00920 TIGR00920 273339 2A060605 3-hydroxy-3-methylglutaryl-coenzyme A reductase. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 886 matched cddid_all.tbl CDD TIGR00921 TIGR00921 273340 2A067 The (Largely Archaeal Putative) Hydrophobe/Amphiphile Efflux-3 (HAE3) Family. Characterized members of the RND superfamily all probably catalyze substrate efflux via an H+ antiport mechanism. These proteins are found ubiquitously in bacteria, archaea and eukaryotes. They fall into seven phylogenetic families, this family (2.A.6.7) consists of uncharacterised putative transporters, largely in the Archaea. [Transport and binding proteins, Unknown substrate] 719 matched cddid_all.tbl CDD TIGR00922 TIGR00922 273341 nusG transcription termination/antitermination factor NusG. NusG proteins are transcription factors which are aparrently universal in prokaryotes (archaea and eukaryotes have homologs that may have related functions). The essential components of these factors include an N-terminal RNP-like (ribonucleoprotein) domain and a C-terminal KOW motif (pfam00467) believed to be a nucleic acid binding domain. In E. coli, NusA has been shown to interact with RNA polymerase and termination factor Rho. This model covers a wide variety of bacterial species but excludes mycoplasmas which are covered by a separate model (TIGR01956).The function of all of these NusG proteins is likely to be the same at the level of interaction with RNA and other protein factors to affect termination; however different species may utilize NusG towards different processes and in combination with different suites of affector proteins.In E. coli, NusG promotes rho-dependent termination. It is an essential gene. In Streptomyces virginiae and related species, an additional N-terminal sequence is also present and is suggested to play a role in butyrolactone-mediated autoregulation. In Thermotoga maritima, NusG has a long insert, fails to substitute for E. coli NusG (with or without the long insert), is a large 0.7 % of total cellular protein, and has a general, sequence non-specific DNA and RNA binding activity that blocks ethidium staining, yet permits transcription.Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405). [Transcription, Transcription factors] 172 matched cddid_all.tbl CDD TIGR00924 TIGR00924 273342 yjdL_sub1_fam amino acid/peptide transporter (Peptide:H+ symporter), bacterial. The model describes proton-dependent oligopeptide transporters in bacteria. This model is restricted in its range in recognizing bacterial proton-dependent oligopeptide transporters, although they are found in yeast, plants and animals. They function by proton symport in a 1:1 stoichiometry, which is variable in different species. All of them are predicted to contain 12 transmembrane domains, for which limited experimental evidence exists. [Transport and binding proteins, Amino acids, peptides and amines] 475 matched cddid_all.tbl CDD TIGR00926 TIGR00926 273343 2A1704 Peptide:H+ symporter (also transports b-lactam antibiotics, the antitumor agent, bestatin, and various protease inhibitors). [Transport and binding proteins, Amino acids, peptides and amines] 654 matched cddid_all.tbl CDD TIGR00927 TIGR00927 273344 2A1904 K+-dependent Na+/Ca+ exchanger. [Transport and binding proteins, Cations and iron carrying compounds] 1096 matched cddid_all.tbl CDD TIGR00928 TIGR00928 273345 purB adenylosuccinate lyase. This family consists of adenylosuccinate lyase, the enzyme that catalyzes step 8 in the purine biosynthesis pathway for de novo synthesis of IMP and also the final reaction in the two-step sequence from IMP to AMP. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 435 matched cddid_all.tbl CDD TIGR00929 TIGR00929 273346 VirB4_CagE type IV secretion/conjugal transfer ATPase, VirB4 family. Type IV secretion systems are found in Gram-negative pathogens. They export proteins, DNA, or complexes in different systems and are related to plasmid conjugation systems. This model represents related ATPases that include VirB4 in Agrobacterium tumefaciens (DNA export) CagE in Helicobacter pylori (protein export) and plasmid TraB (conjugation). 785 matched cddid_all.tbl CDD TIGR00930 TIGR00930 273347 2a30 K-Cl cotransporter. [Transport and binding proteins, Other] 953 matched cddid_all.tbl CDD TIGR00931 TIGR00931 188097 antiport_nhaC Na+/H+ antiporter NhaC. A single member of the NhaC family, a protein from Bacillus firmus, has been functionally characterized.It is involved in pH homeostasis and sodium extrusion. Members of the NhaC family are found in both Gram-negative bacteria and Gram-positive bacteria. Intriguingly, archaeal homolog ArcD (just outside boundaries of family) has been identified as an arginine/ornithine antiporter. [Transport and binding proteins, Cations and iron carrying compounds] 454 matched cddid_all.tbl CDD TIGR00932 TIGR00932 273348 2a37 transporter, monovalent cation:proton antiporter-2 (CPA2) family. [Transport and binding proteins, Cations and iron carrying compounds] 273 matched cddid_all.tbl CDD TIGR00933 TIGR00933 273349 2a38 potassium uptake protein, TrkH family. The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. [Transport and binding proteins, Cations and iron carrying compounds] 391 matched cddid_all.tbl CDD TIGR00934 TIGR00934 130009 2a38euk potassium uptake protein, Trk family. The proteins of the Trk family are derived from Gram-negative and Gram-positive bacteria, yeast and wheat. The proteins of E. coli K12 TrkH and TrkG as well as several yeast proteins have been functionally characterized.The E. coli TrkH and TrkG proteins are complexed to two peripheral membrane proteins, TrkA, an NAD-binding protein, and TrkE, an ATP-binding protein. This complex forms the potassium uptake system. This family is specific for the eukaryotic Trk system. [Transport and binding proteins, Cations and iron carrying compounds] 800 matched cddid_all.tbl CDD TIGR00935 TIGR00935 213571 2a45 arsenite/antimonite efflux pump membrane protein. Members of this protein family are ArsB, a highly hydrophobic integral membrane protein involved in transport processes used to protect cells from arsenite (or antimonite). Members of the seed alignment were selected by adjacency to the ATPase subunit ArsA that energizes the transport. [Cellular processes, Detoxification, Transport and binding proteins, Other] 426 matched cddid_all.tbl CDD TIGR00936 TIGR00936 213572 ahcY adenosylhomocysteinase. This enzyme hydrolyzes adenosylhomocysteine as part of a cycle for the regeneration of the methyl donor S-adenosylmethionine. Species that lack this enzyme are likely to have adenosylhomocysteine nucleosidase (EC 3.2.2.9), an enzyme which also acts as 5'-methyladenosine nucleosidase (see TIGR01704). [Energy metabolism, Amino acids and amines] 407 matched cddid_all.tbl CDD TIGR00937 TIGR00937 273350 2A51 chromate transporter, chromate ion transporter (CHR) family. Members of this family probably act as chromate transporters, and are found in Pseudomonas aeruginosa, Alcaligenes eutrophus, Vibrio cholerae, Bacillus subtilis, Ochrobactrum tritici, cyanobacteria and archaea. The protein reduces chromate accumulation and is essential for chromate resistance. [Transport and binding proteins, Anions] 368 matched cddid_all.tbl CDD TIGR00938 TIGR00938 273351 thrB_alt homoserine kinase, Neisseria type. Homoserine kinase is required in the biosynthesis of threonine from aspartate.The member of this family from Pseudomonas aeruginosa was shown by direct assay and complementation to act specifically as a homoserine kinase. [Amino acid biosynthesis, Aspartate family] 307 matched cddid_all.tbl CDD TIGR00939 TIGR00939 273352 2a57 Equilibrative Nucleoside Transporter (ENT). [Transport and binding proteins, Nucleosides, purines and pyrimidines] 437 matched cddid_all.tbl CDD TIGR00940 TIGR00940 273353 2a6301s01 Tmonovalent cation:proton antiporter. This family of proteins constists of bacterial multicomponent K+:H+ and Na+:H+ antiporters. The best characterized systems are the PhaABCDEFG system of Rhizobium meliloti which functions in pH adaptation and as a K+ efflux system and the MnhABCDEFG system of Staphylococcus aureus which functions as a Na+:H+ antiporter. [Transport and binding proteins, Cations and iron carrying compounds] 793 matched cddid_all.tbl CDD TIGR00941 TIGR00941 273354 2a6301s03 Multicomponent Na+:H+ antiporter, MnhC subunit. [Transport and binding proteins, Cations and iron carrying compounds] 104 matched cddid_all.tbl CDD TIGR00942 TIGR00942 130017 2a6301s05 Monovalent Cation (K+ or Na+):Proton Antiporter-3 (CPA3) subfamily. [Transport and binding proteins, Cations and iron carrying compounds] 144 matched cddid_all.tbl CDD TIGR00943 TIGR00943 130018 2a6301s02 monovalent cation:proton antiporter. This family of proteins constists of bacterial multicomponent K+:H+ and Na+:H+ antiporters. The best characterized systems are the PhaABCDEFG system of Rhizobium meliloti which functions in pH adaptation and as a K+ efflux system and the MnhABCDEFG system of Staphylococcus aureus which functions as a Na+:H+ antiporter.This family is specific for the phaB and mnhB proteins. [Transport and binding proteins, Cations and iron carrying compounds] 107 matched cddid_all.tbl CDD TIGR00944 TIGR00944 130019 2a6301s04 Multicomponent K+:H+antiporter. [Transport and binding proteins, Cations and iron carrying compounds] 463 matched cddid_all.tbl CDD TIGR00945 TIGR00945 273355 tatC Twin arginine targeting (Tat) protein translocase TatC. This model represents the TatC translocase component of the Sec-independent protein translocation system. This system is responsible for translocation of folded proteins, often with bound cofactors across the periplasmic membrane. A related model (TIGR01912) represents the archaeal clade of this family. TatC is often found in a gene cluster with the two other components of the system, TatA/E (TIGR01411) and TatB (TIGR01410). A model also exists for the Twin-arginine signal sequence (TIGR01409). [Protein fate, Protein and peptide secretion and trafficking] 215 matched cddid_all.tbl CDD TIGR00946 TIGR00946 273356 2a69 he Auxin Efflux Carrier (AEC) Family. [Transport and binding proteins, Other] 321 matched cddid_all.tbl CDD TIGR00947 TIGR00947 273357 2A73 putative bicarbonate transporter, IctB family. This family of proteins is suggested to transport inorganic carbon (HCO3-), based on the phenotype of a mutant of IctB in Synechococcus sp. strain PCC 7942. Bicarbonate uptake is used by many photosynthetic organisms including cyanobacteria. These organisms are able to concentrate CO2/HCO3- against a greater than ten-fold concentration gradient. Cyanobacteria may have several such carriers operating with different efficiencies. Note that homology to various O-antigen ligases, with possible implications for mutant cell envelope structure, might allow alternatives to the interpretation of IctB as a bicarbonate transport protein. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 425 matched cddid_all.tbl CDD TIGR00948 TIGR00948 130023 2a75 L-lysine exporter. [Transport and binding proteins, Amino acids, peptides and amines] 177 matched cddid_all.tbl CDD TIGR00949 TIGR00949 273358 2A76 The Resistance to Homoserine/Threonine (RhtB) Family protein. [Transport and binding proteins, Amino acids, peptides and amines] 185 matched cddid_all.tbl CDD TIGR00950 TIGR00950 273359 2A78 Carboxylate/Amino Acid/Amine Transporter. [Transport and binding proteins, Amino acids, peptides and amines] 260 matched cddid_all.tbl CDD TIGR00951 TIGR00951 130026 2A43 Lysosomal Cystine Transporter. [Transport and binding proteins, Amino acids, peptides and amines] 220 matched cddid_all.tbl CDD TIGR00952 TIGR00952 130027 S15_bact ribosomal protein S15, bacterial/organelle. This model is built to recognize specifically bacterial, chloroplast, and mitochondrial ribosomal protein S15. The homologous proteins of Archaea and Eukarya are designated S13. [Protein synthesis, Ribosomal proteins: synthesis and modification] 86 matched cddid_all.tbl CDD TIGR00954 TIGR00954 273360 3a01203 Peroxysomal Fatty Acyl CoA Transporter (FAT) Family protein. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 659 matched cddid_all.tbl CDD TIGR00955 TIGR00955 273361 3a01204 The Eye Pigment Precursor Transporter (EPP) Family protein. [Transport and binding proteins, Other] 617 matched cddid_all.tbl CDD TIGR00956 TIGR00956 273362 3a01205 Pleiotropic Drug Resistance (PDR) Family protein. [Transport and binding proteins, Other] 1394 matched cddid_all.tbl CDD TIGR00957 TIGR00957 188098 MRP_assoc_pro multi drug resistance-associated protein (MRP). This model describes multi drug resistance-associated protein (MRP) in eukaryotes. The multidrug resistance-associated protein is an integral membrane protein that causes multidrug resistance when overexpressed in mammalian cells. It belongs to ABC transporter superfamily. The protein topology and function was experimentally demonstrated by epitope tagging and immunofluorescence. Insertion of tags in the critical regions associated with drug efflux, abrogated its function. The C-terminal domain seem to highly conserved. [Transport and binding proteins, Other] 1522 matched cddid_all.tbl CDD TIGR00958 TIGR00958 273363 3a01208 Conjugate Transporter-2 (CT2) Family protein. [Transport and binding proteins, Other] 711 matched cddid_all.tbl CDD TIGR00959 TIGR00959 273364 ffh signal recognition particle protein. This model represents Ffh (Fifty-Four Homolog), the protein component that forms the bacterial (and organellar) signal recognition particle together with a 4.5S RNA. Ffh is a GTPase homologous to eukaryotic SRP54 and also to the GTPase FtsY (TIGR00064) that is the receptor for the signal recognition particle. [Protein fate, Protein and peptide secretion and trafficking] 428 matched cddid_all.tbl CDD TIGR00962 TIGR00962 273365 atpA proton translocating ATP synthase, F1 alpha subunit. The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. The alpha-subunit contains a highly conserved adenine-specific noncatalytic nucleotide-binding domain. The conserved amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton translocating ATP synthase F1, alpha subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), B subunit. [Energy metabolism, ATP-proton motive force interconversion] 501 matched cddid_all.tbl CDD TIGR00963 TIGR00963 273366 secA preprotein translocase, SecA subunit. The proteins SecA-F and SecY, not all of which are necessary, comprise the standard prokaryotic protein translocation apparatus. Other, specialized translocation systems also exist but are not as broadly distributed. This model describes SecA, an essential member of the apparatus. This model excludes SecA2 of the accessory secretory system. [Protein fate, Protein and peptide secretion and trafficking] 742 matched cddid_all.tbl CDD TIGR00964 TIGR00964 273367 secE_bact preprotein translocase, SecE subunit, bacterial. This model represents exclusively the bacterial (and some organellar) SecE protein. SecE is part of the core heterotrimer, SecYEG, of the Sec preprotein translocase system. Other components are the ATPase SecA, a cytosolic chaperone SecB, and an accessory complex of SecDF and YajC. [Protein fate, Protein and peptide secretion and trafficking] 55 matched cddid_all.tbl CDD TIGR00965 TIGR00965 130038 dapD 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase. This enzyme is part of the diaminopimelate pathway of lysine biosynthesis. Alternate name: tetrahydrodipicolinate N-succinyltransferase. The closely related TabB protein of Pseudomonas syringae (pv. tabaci), SP|P31852|TABB_PSESZ, appears to act in the biosynthesis of tabtoxin rather than lysine. The trusted cutoff is set high enough to exclude this gene. Sequences below trusted also include a version of this enzyme which apparently utilize acetate rather than succinate (EC: 2.3.1.89). [Amino acid biosynthesis, Aspartate family] 269 matched cddid_all.tbl CDD TIGR00966 TIGR00966 273368 3a0501s07 protein-export membrane protein SecF. This bacterial protein is always found with the homologous protein-export membrane protein SecD. In numerous lineages, this protein occurs as a SecDF fusion protein. [Protein fate, Protein and peptide secretion and trafficking] 246 matched cddid_all.tbl CDD TIGR00967 TIGR00967 273369 3a0501s007 preprotein translocase, SecY subunit. Members of this protein family are the SecY component of the SecYEG translocon, or protein translocation pore, which is driven by the ATPase SecA. This model does not discriminate bacterial from archaeal forms. [Protein fate, Protein and peptide secretion and trafficking] 410 matched cddid_all.tbl CDD TIGR00968 TIGR00968 130041 3a0106s01 sulfate ABC transporter, ATP-binding protein. [Transport and binding proteins, Anions] 237 matched cddid_all.tbl CDD TIGR00969 TIGR00969 273370 3a0106s02 sulfate ABC transporter, permease protein. This model describes a subfamily of both CysT and CysW, paralogous and generally tandemly encoded permease proteins of the sulfate ABC transporter. [Transport and binding proteins, Anions] 271 matched cddid_all.tbl CDD TIGR00970 TIGR00970 273371 leuA_yeast 2-isopropylmalate synthase, yeast type. A larger family of homologous proteins includes homocitrate synthase, distinct lineages of 2-isopropylmalate synthase, several distinct, uncharacterized, orthologous sets in the Archaea, and other related enzymes. This model describes a family of 2-isopropylmalate synthases as found in yeasts and in a minority of studied bacteria. [Amino acid biosynthesis, Pyruvate family] 564 matched cddid_all.tbl CDD TIGR00971 TIGR00971 130044 3a0106s03 sulfate/thiosulfate-binding protein. This model describes binding proteins functionally associated with the sulfate ABC transporter. In the model bacterium E. coli, two different members work with the same transporter; mutation analysis says each enables the uptake of both sulfate and thiosulfate. In many species, a single binding protein is found, and may be referred to in general terms as a sulfate ABC transporter sulfate-binding protein. [Transport and binding proteins, Anions] 315 matched cddid_all.tbl CDD TIGR00972 TIGR00972 273372 3a0107s01c2 phosphate ABC transporter, ATP-binding protein. This model represents the ATP-binding protein of a family of ABC transporters for inorganic phosphate. In the model species Escherichia coli, a constitutive transporter for inorganic phosphate, with low affinity, is also present. The high affinity transporter that includes this polypeptide is induced when extracellular phosphate concentrations are low. The proteins most similar to the members of this family but not included appear to be amino acid transporters. [Transport and binding proteins, Anions] 247 matched cddid_all.tbl CDD TIGR00973 TIGR00973 130046 leuA_bact 2-isopropylmalate synthase, bacterial type. This is the first enzyme of leucine biosynthesis. A larger family of homologous proteins includes homocitrate synthase, distinct lineages of 2-isopropylmalate synthase, several distinct, uncharacterized, orthologous sets in the Archaea, and other related enzymes. This model describes a family of 2-isopropylmalate synthases found primarily in Bacteria. The homologous families in the Archaea may represent isozymes and/or related enzymes. [Amino acid biosynthesis, Pyruvate family] 494 matched cddid_all.tbl CDD TIGR00974 TIGR00974 273373 3a0107s02c phosphate ABC transporter, permease protein PstA. This model describes PtsA, one of a pair of permease proteins in the ABC (high affinity) phosphate transporter. In a number of species, this permease is fused with the PtsC protein (TIGR02138). In the model bacterium Escherichia coli, this transport system is induced when the concentration of extrallular inorganic phosphate is low. A constitutive, lower affinity transporter operates otherwise. [Transport and binding proteins, Anions] 271 matched cddid_all.tbl CDD TIGR00975 TIGR00975 273374 3a0107s03 phosphate ABC transporter, phosphate-binding protein. This family represents one type of (periplasmic, in Gram-negative bacteria) phosphate-binding protein found in phosphate ABC (ATP-binding cassette) transporters. This protein is accompanied, generally in the same operon, by an ATP binding protein and (usually) two permease proteins. [Transport and binding proteins, Anions] 313 matched cddid_all.tbl CDD TIGR00976 TIGR00976 273375 /NonD putative hydrolase, CocE/NonD family. This model represents a protein subfamily that includes the cocaine esterase CocE, several glutaryl-7-ACA acylases, and the putative diester hydrolase NonD of Streptomyces griseus (all hydrolases). This family shows extensive, low-level similarity to a family of xaa-pro dipeptidyl-peptidases, and local similarity by PSI-BLAST to many other hydrolases. [Unknown function, Enzymes of unknown specificity] 550 matched cddid_all.tbl CDD TIGR00977 TIGR00977 130050 citramal_synth citramalate synthase. This model includes GSU1798 and is now known to represent citramalate synthase. Members are related to 2-isopropylmalate synthases and homocitrate synthases but phylogenetically distinct. The role is isoleucine biosynthesis, the first dedicated step. [Unknown function, General] 526 matched cddid_all.tbl CDD TIGR00978 TIGR00978 273376 asd_EA aspartate-semialdehyde dehydrogenase (non-peptidoglycan organisms). Two closely related families of aspartate-semialdehyde dehydrogenase are found. They differ by a deep split in phylogenetic and percent identity trees and in gap patterns. Separate models are built for the two types in order to exclude the USG-1 protein, found in several species, which is specifically related to the Bacillus subtilis type of aspartate-semialdehyde dehydrogenase. Members of this type are found primarily in organisms that lack peptidoglycan. [Amino acid biosynthesis, Aspartate family] 341 matched cddid_all.tbl CDD TIGR00979 TIGR00979 130052 fumC_II fumarate hydratase, class II. Putative fumarases from several species (Mycobacterium tuberculosis, Streptomyces coelicolor, Pseudomonas aeruginosa) branch deeply, although within the same branch of a phylogenetic tree rooted by aspartate ammonia-lyase sequences, and score between the trusted and noise cutoffs. [Energy metabolism, TCA cycle] 458 matched cddid_all.tbl CDD TIGR00980 TIGR00980 130053 3a0801so1tim17 mitochondrial import inner membrane translocase subunit tim17. [Transport and binding proteins, Amino acids, peptides and amines] 170 matched cddid_all.tbl CDD TIGR00981 TIGR00981 130054 rpsL_bact ribosomal protein S12, bacterial/organelle. This model recognizes ribosomal protein S12 of Bacteria, mitochondria, and chloroplasts. The homologous ribosomal proteins of Archaea and Eukarya, termed S23 in Eukarya and S12 or S23 in Archaea, score below the trusted cutoff. [Protein synthesis, Ribosomal proteins: synthesis and modification] 124 matched cddid_all.tbl CDD TIGR00982 TIGR00982 273377 uS12_E_A ribosomal protein uS12, eukaryotic/archaeal form. This model represents eukaryotic and archaeal forms of ribosomal protein uS12. This protein was known previously as S23 in eukaryotes and as either S12 or S23 in the Archaea. [Protein synthesis, Ribosomal proteins: synthesis and modification] 139 matched cddid_all.tbl CDD TIGR00983 TIGR00983 130056 3a0801s02tim23 mitochondrial import inner membrane translocase subunit tim23. [Transport and binding proteins, Amino acids, peptides and amines] 149 matched cddid_all.tbl CDD TIGR00984 TIGR00984 130057 3a0801s03tim44 "mitochondrial import inner membrane, translocase subunit. The mitochondrial protein translocase (MPT) family, which brings nuclearly encoded preproteins into mitochondria, is very complex with 19 currently identified protein constituents.These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three ""motor"" proteins. This family is specific for the Tim proteins. [Transport and binding proteins, Amino acids, peptides and amines]" 378 matched cddid_all.tbl CDD TIGR00985 TIGR00985 273378 3a0801s04tom mitochondrial import receptor subunit translocase of outer membrane 20 kDa subunit. [Transport and binding proteins, Amino acids, peptides and amines] 148 matched cddid_all.tbl CDD TIGR00986 TIGR00986 273379 3a0801s05tom22 "mitochondrial import receptor subunit Tom22. The mitochondrial protein translocase (MPT) family, which brings nuclearly encoded preproteins into mitochondria, is very complex with 19 currently identified protein constituents.These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three ""motor"" proteins. This family is specific for the Tom22 proteins. [Transport and binding proteins, Amino acids, peptides and amines]" 145 matched cddid_all.tbl CDD TIGR00987 TIGR00987 130060 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU. [DNA metabolism, DNA replication, recombination, and repair] 96 matched cddid_all.tbl CDD TIGR00988 TIGR00988 130061 hip integration host factor, beta subunit. This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU. [DNA metabolism, DNA replication, recombination, and repair] 94 matched cddid_all.tbl CDD TIGR00989 TIGR00989 130062 3a0801s07tom40 "mitochondrial import receptor subunit Tom40. The mitochondrial protein translocase (MPT) family, which brings nuclearly encoded preproteins into mitochondria, is very complex with 19 currently identified protein constituents.These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three ""motor"" proteins. This family is specific for the Tom40 proteins. [Transport and binding proteins, Amino acids, peptides and amines]" 161 matched cddid_all.tbl CDD TIGR00990 TIGR00990 273380 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70). [Transport and binding proteins, Amino acids, peptides and amines] 615 matched cddid_all.tbl CDD TIGR00991 TIGR00991 130064 3a0901s02IAP34 GTP-binding protein (Chloroplast Envelope Protein Translocase). [Transport and binding proteins, Nucleosides, purines and pyrimidines] 313 matched cddid_all.tbl CDD TIGR00992 TIGR00992 130065 3a0901s03IAP75 chloroplast envelope protein translocase, IAP75 family. Two families of proteins are involved in the chloroplast envelope import appartus.They are the three proteins of the outer membrane (TOC) and four proteins in the inner membrane (TIC). This family is specific for the TOC IAP75 protein. [Transport and binding proteins, Amino acids, peptides and amines] 718 matched cddid_all.tbl CDD TIGR00993 TIGR00993 273381 3a0901s04IAP86 chloroplast protein import component Toc86/159, G and M domains. The long precursor of the 86K protein originally described is proposed to have three domains. The N-terminal A-domain is acidic, repetitive, weakly conserved, readily removed by proteolysis during chloroplast isolation, and not required for protein translocation. The other domains are designated G (GTPase) and M (membrane anchor); this family includes most of the G domain and all of M. [Transport and binding proteins, Amino acids, peptides and amines] 763 matched cddid_all.tbl CDD TIGR00994 TIGR00994 273382 3a0901s05TIC20 chloroplast protein import component, Tic20 family. Two families of proteins are involved in the chloroplast envelope import appartus.They are the three proteins of the outer membrane (TOC) and four proteins in the inner membrane (TIC). This family is specific for the Tic20 protein. [Transport and binding proteins, Amino acids, peptides and amines] 267 matched cddid_all.tbl CDD TIGR00995 TIGR00995 273383 3a0901s06TIC22 chloroplast protein import component, Tic22 family. Two families of proteins are involved in the chloroplast envelope import appartus.They are the three proteins of the outer membrane (TOC) and four proteins in the inner membrane (TIC). This family is specific for the Tic22 protein. [Transport and binding proteins, Amino acids, peptides and amines] 270 matched cddid_all.tbl CDD TIGR00996 TIGR00996 273384 Mtu_fam_mce virulence factor Mce family protein. Members of this paralogous family are found as six tandem homologous proteins in the same orientation per cassette, in four separate cassettes in Mycobacterium tuberculosis. The six members of each cassette represent six subfamilies. One subfamily includes the protein mce (mycobacterial cell entry), a virulence protein required for invasion of non-phagocytic cells. [Cellular processes, Pathogenesis] 291 matched cddid_all.tbl CDD TIGR00997 TIGR00997 130070 ispZ intracellular septation protein A. This partially characterized protein, whose absence can cause a cell division defect in an intracellularly replicating bacterium, is found only so far only in the Proteobacteria. [Cellular processes, Cell division] 178 matched cddid_all.tbl CDD TIGR00998 TIGR00998 273385 8a0101 efflux pump membrane protein (multidrug resistance protein A). [Transport and binding proteins, Other] 334 matched cddid_all.tbl CDD TIGR00999 TIGR00999 273386 8a0102 Membrane Fusion Protein cluster 2 (function with RND porters). [Transport and binding proteins, Other] 265 matched cddid_all.tbl CDD TIGR01000 TIGR01000 273387 bacteriocin_acc bacteriocin secretion accessory protein. This family represents an accessory protein that works with the bacteriocin maturation and ABC transport secretion protein described by TIGR01193. [Transport and binding proteins, Other] 457 matched cddid_all.tbl CDD TIGR01001 TIGR01001 130074 metA homoserine O-succinyltransferase. The apparent equivalog from Bacillus subtilis is broken into two tandem reading frames. [Amino acid biosynthesis, Aspartate family] 300 matched cddid_all.tbl CDD TIGR01002 TIGR01002 273388 hlyII beta-channel forming cytolysin. This family of cytolytic pore-forming proteins includes alpha toxin and leukocidin F and S subunits from Staphylococcus aureus, hemolysin II of Bacillus cereus, and related toxins. [Cellular processes, Toxin production and resistance] 312 matched cddid_all.tbl CDD TIGR01003 TIGR01003 273389 PTS_HPr_family Phosphotransferase System HPr (HPr) Family. The HPr family are bacterial proteins (or domains of proteins) which function in phosphoryl transfer system (PTS) systems. They include energy-coupling components which catalyze sugar uptake via a group translocation mechanism. The functions of most of these proteins are not known, but they presumably function in PTS-related regulatory capacities. All seed members are stand-alone HPr proteins, although the model also recognizes HPr domains of PTS fusion proteins. This family includes the related NPr protein. [Signal transduction, PTS] 82 matched cddid_all.tbl CDD TIGR01004 TIGR01004 273390 PulS_OutS lipoprotein, PulS/OutS family. This family comprises lipoproteins from four gamma proteobacterial species: PulS protein of Klebsiella pneumoniae, the OutS protein of Erwinia chrysanthemi and Pectobacterium chrysanthemi, and the functionally uncharacterized E. coli protein EtpO. PulS and OutS have been shown to interact with and facilitate insertion of secretins into the outer membrane, suggesting a chaperone-like, or piloting function for members of this family. [Transport and binding proteins, Amino acids, peptides and amines] 128 matched cddid_all.tbl CDD TIGR01005 TIGR01005 273391 eps_transp_fam exopolysaccharide transport protein family. The model describes the exopolysaccharide transport protein family in bacteria. The transport protein is part of a large genetic locus which is associated with exopolysaccharide (EPS) biosynthesis. Detailed molecular characterization and gene fusion analysis revealed atleast seven gene products are involved in the overall regulation, which among other things, include exopolysaccharide biosynthesis, property of conferring virulence and exopolysaccharide export. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 764 matched cddid_all.tbl CDD TIGR01006 TIGR01006 130079 polys_exp_MPA1 polysaccharide export protein, MPA1 family, Gram-positive type. This family contains members from Low GC Gram-positive bacteria; they are proposed to have a function in the export of complex polysaccharides. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 226 matched cddid_all.tbl CDD TIGR01007 TIGR01007 273392 eps_fam capsular exopolysaccharide family. This model describes the capsular exopolysaccharide proteins in bacteria. The exopolysaccharide gene cluster consists of several genes which encode a number of proteins which regulate the exoploysaccharide biosynthesis(EPS). Atleast 13 genes espA to espM in streptococcus species seem to direct the EPS proteins and all of which share high homology. Functional roles were characterized by gene disruption experiments which resulted in exopolysaccharide-deficient phenotypes. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 204 matched cddid_all.tbl CDD TIGR01008 TIGR01008 273393 uS3_euk_arch ribosomal protein uS3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly. [Protein synthesis, Ribosomal proteins: synthesis and modification] 195 matched cddid_all.tbl CDD TIGR01009 TIGR01009 130082 rpsC_bact ribosomal protein S3, bacterial type. This model describes the bacterial type of ribosomal protein S3. Chloroplast and mitochondrial forms have large, variable inserts between conserved N-terminal and C-terminal domains. This model recognizes all bacterial forms and many chloroplast forms above the trusted cutoff score. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea. [Protein synthesis, Ribosomal proteins: synthesis and modification] 211 matched cddid_all.tbl CDD TIGR01010 TIGR01010 130083 BexC_CtrB_KpsE polysaccharide export inner-membrane protein, BexC/CtrB/KpsE family. This family contains gamma proteobacterial proteins involved in capsule polysaccharide export. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 362 matched cddid_all.tbl CDD TIGR01011 TIGR01011 130084 rpsB_bact ribosomal protein S2, bacterial type. This model describes the bacterial, ribosomal, and chloroplast forms of ribosomal protein S2. TIGR01012 describes the archaeal and cytosolic forms. [Protein synthesis, Ribosomal proteins: synthesis and modification] 225 matched cddid_all.tbl CDD TIGR01012 TIGR01012 273394 uS2_euk_arch ribosomal protein uS2, eukaryotic/archaeal form. This model describes the ribosomal protein of the cytosol and of Archaea, homologous to S2 of bacteria. It is designated typically as Sa in eukaryotes and Sa or S2 in the archaea. TIGR01011 describes the related protein of organelles and bacteria. [Protein synthesis, Ribosomal proteins: synthesis and modification] 196 matched cddid_all.tbl CDD TIGR01013 TIGR01013 162157 2a58 Phosphate:Na+ Symporter (PNaS) Family. [Transport and binding proteins, Cations and iron carrying compounds] 456 matched cddid_all.tbl CDD TIGR01015 TIGR01015 273395 hmgA homogentisate 1,2-dioxygenase. Missing in human disease alkaptonuria. [Energy metabolism, Amino acids and amines] 429 matched cddid_all.tbl CDD TIGR01016 TIGR01016 273396 sucCoAbeta succinyl-CoA synthetase, beta subunit. This model is designated subfamily because it does not discriminate the ADP-forming enzyme ((EC 6.2.1.5) from the GDP_forming (EC 6.2.1.4) enzyme. The N-terminal half is described by the CoA-ligases model (pfam00549). The C-terminal half is described by the ATP-grasp model (pfam02222). This family contains a split seen both in a maximum parsimony tree (which ignores gaps) and in the gap pattern near position 85 of the seed alignment. Eukaryotic and most bacterial sequences are longer and contain a region similar to TXQTXXXG. Sequences from Deinococcus radiodurans, Mycobacterium tuberculosis, Streptomyces coelicolor, and the Archaea are 6 amino acids shorter in that region and contain a motif resembling [KR]G [Energy metabolism, TCA cycle] 386 matched cddid_all.tbl CDD TIGR01017 TIGR01017 200066 rpsD_bact ribosomal protein S4, bacterial/organelle type. This model finds organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4. [Protein synthesis, Ribosomal proteins: synthesis and modification] 200 matched cddid_all.tbl CDD TIGR01018 TIGR01018 273397 uS4_arch ribosomal protein uS4, eukaryotic/archaeal type. This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4. [Protein synthesis, Ribosomal proteins: synthesis and modification] 162 matched cddid_all.tbl CDD TIGR01019 TIGR01019 130091 sucCoAalpha succinyl-CoA synthetase, alpha subunit. This model describes succinyl-CoA synthetase alpha subunits but does not discriminate between GTP-specific and ATP-specific reactions. The model is designated as subfamily rather than equivalog for that reason. ATP citrate lyases appear to form an outgroup. [Energy metabolism, TCA cycle] 286 matched cddid_all.tbl CDD TIGR01020 TIGR01020 273398 uS5_euk_arch ribosomal protein uS5, eukaryotic/archaeal form. This model finds eukaryotic ribosomal protein uS5 (previously S2 in yeast and human) as well as archaeal ribosomal protein uS5. [Protein synthesis, Ribosomal proteins: synthesis and modification] 212 matched cddid_all.tbl CDD TIGR01021 TIGR01021 130093 rpsE_bact ribosomal protein S5, bacterial/organelle type. This model finds chloroplast ribosomal protein S5 as well as bacterial ribosomal protein S5. A candidate mitochondrial form (Saccharomyces cerevisiae YBR251W and its homolog) differs substantially and is not included in this model. [Protein synthesis, Ribosomal proteins: synthesis and modification] 154 matched cddid_all.tbl CDD TIGR01022 TIGR01022 130094 rpmJ_bact ribosomal protein L36, bacterial type. Proteins found by this model occur exclusively in bacteria and organelles. [Protein synthesis, Ribosomal proteins: synthesis and modification] 37 matched cddid_all.tbl CDD TIGR01023 TIGR01023 273399 rpmG_bact ribosomal protein L33, bacterial type. This model describes bacterial ribosomal protein L33 and its chloroplast and mitochondrial equivalents. [Protein synthesis, Ribosomal proteins: synthesis and modification] 54 matched cddid_all.tbl CDD TIGR01024 TIGR01024 130096 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs. [Protein synthesis, Ribosomal proteins: synthesis and modification] 113 matched cddid_all.tbl CDD TIGR01025 TIGR01025 273400 uS19_arch ribosomal protein uS19, eukaryotic/archaeal form. This model represents eukaryotic ribosomal protein uS19 (previously S15) and its archaeal equivalent. It excludes bacterial and organellar ribosomal protein S19. The nomenclature for the archaeal members is unresolved and given variously as S19 (after the more distant bacterial homologs) or S15. [Protein synthesis, Ribosomal proteins: synthesis and modification] 135 matched cddid_all.tbl CDD TIGR01026 TIGR01026 273401 fliI_yscN ATPase, FliI/YscN family. This family of ATPases demonstrates extensive homology with ATP synthase F1, beta subunit. It is a mixture of members with two different protein functions. The first group is exemplified by Salmonella typhimurium FliI protein. It is needed for flagellar assembly, its ATPase activity is required for flagellation, and it may be involved in a specialized protein export pathway that proceeds without signal peptide cleavage. The second group of proteins function in the export of virulence proteins; exemplified by Yersinia sp. YscN protein an ATPase involved in the type III secretory pathway for the antihost Yops proteins. [Energy metabolism, ATP-proton motive force interconversion] 440 matched cddid_all.tbl CDD TIGR01027 TIGR01027 162163 proB glutamate 5-kinase. Bacterial ProB proteins hit the full length of this model, but the ProB-like domain of delta 1-pyrroline-5-carboxylate synthetase does not hit the C-terminal 100 residues of this model. The noise cutoff is set low enough to hit delta 1-pyrroline-5-carboxylate synthetase and other partial matches to this family. [Amino acid biosynthesis, Glutamate family] 363 matched cddid_all.tbl CDD TIGR01028 TIGR01028 273402 uS7_euk_arch ribosomal protein uS7, eukaryotic/archaeal. This model describes the members from the eukaryotic cytosol and the Archaea of the family that includes ribosomal protein uS7 (previously S5 in yeast and human). A separate model describes bacterial and organellar S7. [Protein synthesis, Ribosomal proteins: synthesis and modification] 186 matched cddid_all.tbl CDD TIGR01029 TIGR01029 273403 rpsG_bact ribosomal protein S7, bacterial/organelle. This model describes the bacterial and organellar branch of the ribosomal protein S7 family (includes prokaroytic S7 and eukaryotic S5). The eukaryotic and archaeal branch is described by model TIGR01028. [Protein synthesis, Ribosomal proteins: synthesis and modification] 154 matched cddid_all.tbl CDD TIGR01030 TIGR01030 130102 rpmH_bact ribosomal protein L34, bacterial type. This model describes the bacterial protein L34 and its equivalents in organelles. [Protein synthesis, Ribosomal proteins: synthesis and modification] 44 matched cddid_all.tbl CDD TIGR01031 TIGR01031 273404 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus. [Protein synthesis, Ribosomal proteins: synthesis and modification] 55 matched cddid_all.tbl CDD TIGR01032 TIGR01032 130104 rplT_bact ribosomal protein L20. This model describes bacterial ribosomal protein L20 and its chloroplast equvalent. This protein binds directly to 23s ribosomal RNA and is necessary for the in vitro assembly process of the 50s ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit. GO process changed accordingly (SS 5/09/03) [Protein synthesis, Ribosomal proteins: synthesis and modification] 113 matched cddid_all.tbl CDD TIGR01033 TIGR01033 273405 TIGR01033 DNA-binding regulatory protein, YebC/PmpR family. This model describes a minimally characterized protein family, restricted to bacteria excepting for some eukaryotic sequences that have possible transit peptides. YebC from E. coli is crystallized, and PA0964 from Pseudomonas aeruginosa has been shown to be a sequence-specific DNA-binding regulatory protein. In silico analysis suggests a role in Holliday junction resolution. [Regulatory functions, DNA interactions] 238 matched cddid_all.tbl CDD TIGR01034 TIGR01034 273406 metK S-adenosylmethionine synthetase. Tandem isozymes of this S-adenosylmethionine synthetase in E. coli are designated MetK and MetX. [Central intermediary metabolism, Other] 377 matched cddid_all.tbl CDD TIGR01035 TIGR01035 273407 hemA glutamyl-tRNA reductase. This enzyme, together with glutamate-1-semialdehyde-2,1-aminomutase (TIGR00713), leads to the production of delta-amino-levulinic acid from Glu-tRNA. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 417 matched cddid_all.tbl CDD TIGR01036 TIGR01036 273408 pyrD_sub2 dihydroorotate dehydrogenase, subfamily 2. This model describes enzyme protein dihydroorotate dehydrogenase exclusively for subfamily 2. It includes members from bacteria, yeast, plants etc. The subfamilies 1 and 2 share extensive homology, particularly toward the C-terminus. This subfamily has a longer N-terminal region. [Purines, pyrimidines, nucleosides, and nucleotides, Pyrimidine ribonucleotide biosynthesis] 335 matched cddid_all.tbl CDD TIGR01037 TIGR01037 130109 pyrD_sub1_fam dihydroorotate dehydrogenase (subfamily 1) family protein. This family includes subfamily 1 dihydroorotate dehydrogenases while excluding the closely related subfamily 2 (TIGR01036). This family also includes a number of uncharacterized proteins and a domain of dihydropyrimidine dehydrogenase. The uncharacterized proteins might all be dihydroorotate dehydrogenase. 300 matched cddid_all.tbl CDD TIGR01038 TIGR01038 273409 uL22_arch_euk ribosomal protein uL22, eukaryotic/archaeal form. This model describes the ribosomal protein uL22 of the eukaryotic cytosol and of the Archaea, previously designated as L17, L22, and L23. The corresponding bacterial form of uL22 is described by a separate model. [Protein synthesis, Ribosomal proteins: synthesis and modification] 148 matched cddid_all.tbl CDD TIGR01039 TIGR01039 211621 atpD ATP synthase, F1 beta subunit. The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. Proton translocating ATP synthase, F1 beta subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), A subunit. [Energy metabolism, ATP-proton motive force interconversion] 461 matched cddid_all.tbl CDD TIGR01040 TIGR01040 273410 V-ATPase_V1_B V-type (H+)-ATPase V1, B subunit. This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase. [Transport and binding proteins, Cations and iron carrying compounds] 466 matched cddid_all.tbl CDD TIGR01041 TIGR01041 200071 ATP_syn_B_arch ATP synthase archaeal, B subunit. Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases. [Energy metabolism, ATP-proton motive force interconversion] 458 matched cddid_all.tbl CDD TIGR01042 TIGR01042 273411 V-ATPase_V1_A V-type (H+)-ATPase V1, A subunit. This models eukaryotic vacuolar (H+)-ATPase that is responsible for acidifying cellular compartments. This enzyme shares extensive sequence similarity with archaeal ATP synthase. [Transport and binding proteins, Cations and iron carrying compounds] 591 matched cddid_all.tbl CDD TIGR01043 TIGR01043 130115 ATP_syn_A_arch ATP synthase archaeal, A subunit. Archaeal ATP synthase shares extensive sequence similarity with eukaryotic and prokaryotic V-type (H+)-ATPases. [Energy metabolism, ATP-proton motive force interconversion] 578 matched cddid_all.tbl CDD TIGR01044 TIGR01044 130116 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22. [Protein synthesis, Ribosomal proteins: synthesis and modification] 103 matched cddid_all.tbl CDD TIGR01045 TIGR01045 273412 RPE1 Rickettsial palindromic element RPE1 domain. This model describes protein translations of the first family described, RPE1, of Rickettsia palindromic elements (RPE). In Rickettsia conorii, 19 copies are found within protein coding regions, where they encode an insert relative to homologs from other species but do not disrupt the reading frame. Insertion is always in the same reading frame. This model finds RPE-encoded regions in several Rickettsial species and, so far, no where else. 46 matched cddid_all.tbl CDD TIGR01046 TIGR01046 273413 uS10_euk_arch ribosomal protein uS10, eukaryotic/archaeal. This model describes the archaeal ribosomal protein uS10 and its equivalents (previously called S20) in eukaryotes. [Protein synthesis, Ribosomal proteins: synthesis and modification] 99 matched cddid_all.tbl CDD TIGR01047 TIGR01047 273414 nspC carboxynorspermidine decarboxylase. This protein is related to diaminopimelate decarboxylase. It is the last enzyme in norspermidine biosynthesis by an unusual pathway shown in Vibrio alginolyticus. [Central intermediary metabolism, Polyamine biosynthesis] 379 matched cddid_all.tbl CDD TIGR01048 TIGR01048 273415 lysA diaminopimelate decarboxylase. This family consists of diaminopimelate decarboxylase, an enzyme which catalyzes the conversion of diaminopimelic acid into lysine during the last step of lysine biosynthesis. [Amino acid biosynthesis, Aspartate family] 414 matched cddid_all.tbl CDD TIGR01049 TIGR01049 130121 rpsJ_bact ribosomal protein S10, bacterial/organelle. This model describes bacterial 30S ribosomal protein S10. In species that have a transcription antitermination complex, or N utilization substance, with NusA, NusB, NusG, and NusE, this ribosomal protein is responsible for NusE activity. Included in the family are one member each from Saccharomyces cerevisiae and Schizosaccharomyces pombe. These proteins lack an N-terminal mitochondrial transit peptide but contain additional sequence C-terminal to the ribosomal S10 protein region. [Protein synthesis, Ribosomal proteins: synthesis and modification] 99 matched cddid_all.tbl CDD TIGR01050 TIGR01050 130122 rpsS_bact ribosomal protein S19, bacterial/organelle. The homologous protein of the eukaryotic cytosol and of the Archaea may be designated S15 or S19. [Protein synthesis, Ribosomal proteins: synthesis and modification] 92 matched cddid_all.tbl CDD TIGR01051 TIGR01051 273416 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events. [DNA metabolism, DNA replication, recombination, and repair] 610 matched cddid_all.tbl CDD TIGR01052 TIGR01052 273417 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase). [DNA metabolism, DNA replication, recombination, and repair] 488 matched cddid_all.tbl CDD TIGR01053 TIGR01053 130125 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC 31 matched cddid_all.tbl CDD TIGR01054 TIGR01054 273418 rgy reverse gyrase. This model describes reverse gyrase, found in both archaeal and bacterial thermophiles. This enzyme, a fusion of a type I topoisomerase domain and a helicase domain, introduces positive supercoiling to increase the melting temperature of DNA double strands. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA. [DNA metabolism, DNA replication, recombination, and repair] 1171 matched cddid_all.tbl CDD TIGR01055 TIGR01055 130127 parE_Gneg DNA topoisomerase IV, B subunit, proteobacterial. Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason. This protein is active as an alpha(2)beta(2) heterotetramer. [DNA metabolism, DNA replication, recombination, and repair] 625 matched cddid_all.tbl CDD TIGR01056 TIGR01056 273419 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent. [DNA metabolism, DNA replication, recombination, and repair] 660 matched cddid_all.tbl CDD TIGR01057 TIGR01057 273420 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent. [DNA metabolism, DNA replication, recombination, and repair] 618 matched cddid_all.tbl CDD TIGR01058 TIGR01058 130130 parE_Gpos DNA topoisomerase IV, B subunit, Gram-positive. Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation step of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason. [DNA metabolism, DNA replication, recombination, and repair] 637 matched cddid_all.tbl CDD TIGR01059 TIGR01059 273421 gyrB DNA gyrase, B subunit. This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Proteins scoring above the noise cutoff for this model and below the trusted cutoff for topoisomerase IV models probably should be designated GyrB. [DNA metabolism, DNA replication, recombination, and repair] 654 matched cddid_all.tbl CDD TIGR01060 TIGR01060 213580 eno phosphopyruvate hydratase. Alternate name: enolase [Energy metabolism, Glycolysis/gluconeogenesis] 425 matched cddid_all.tbl CDD TIGR01061 TIGR01061 273422 parC_Gpos DNA topoisomerase IV, A subunit, Gram-positive. Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason. [DNA metabolism, DNA replication, recombination, and repair] 738 matched cddid_all.tbl CDD TIGR01062 TIGR01062 130134 parC_Gneg DNA topoisomerase IV, A subunit, proteobacterial. Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason. [DNA metabolism, DNA replication, recombination, and repair] 735 matched cddid_all.tbl CDD TIGR01063 TIGR01063 273423 gyrA DNA gyrase, A subunit. This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. [DNA metabolism, DNA replication, recombination, and repair] 800 matched cddid_all.tbl CDD TIGR01064 TIGR01064 273424 pyruv_kin pyruvate kinase. This enzyme is a homotetramer. Some forms are active only in the presence of fructose-1,6-bisphosphate or similar phosphorylated sugars. [Energy metabolism, Glycolysis/gluconeogenesis] 472 matched cddid_all.tbl CDD TIGR01065 TIGR01065 273425 hlyIII channel protein, hemolysin III family. This family includes proteins from pathogenic and non-pathogenic bacteria, Homo sapiens and Drosophila. In Bacillus cereus, a pathogen, it has been show to function as a channel-forming cytolysin. The human protein is expressed preferentially in mature macrophages, consistent with a role cytolytic role. 204 matched cddid_all.tbl CDD TIGR01066 TIGR01066 162186 rplM_bact ribosomal protein L13, bacterial type. This model distinguishes ribosomal protein L13 of bacteria and organelles from its eukarytotic and archaeal counterparts. [Protein synthesis, Ribosomal proteins: synthesis and modification] 140 matched cddid_all.tbl CDD TIGR01067 TIGR01067 273426 rplN_bact ribosomal protein L14, bacterial/organelle. This model distinguishes bacterial and most organellar examples of ribosomal protein L14 from all archaeal and eukaryotic forms. [Protein synthesis, Ribosomal proteins: synthesis and modification] 122 matched cddid_all.tbl CDD TIGR01068 TIGR01068 200072 thioredoxin thioredoxin. Several proteins, such as protein disulfide isomerase, have two or more copies of a domain closely related to thioredoxin. This model is designed to recognize authentic thioredoxin, a small protein that should be hit exactly once by this model. Any protein that hits once with a score greater than the second (per domain) trusted cutoff may be taken as thioredoxin. [Energy metabolism, Electron transport] 101 matched cddid_all.tbl CDD TIGR01069 TIGR01069 130141 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function. [DNA metabolism, Other] 771 matched cddid_all.tbl CDD TIGR01070 TIGR01070 273427 mutS1 DNA mismatch repair protein MutS. [DNA metabolism, DNA replication, recombination, and repair] 840 matched cddid_all.tbl CDD TIGR01071 TIGR01071 273428 rplO_bact ribosomal protein L15, bacterial/organelle. [Protein synthesis, Ribosomal proteins: synthesis and modification] 145 matched cddid_all.tbl CDD TIGR01072 TIGR01072 162190 murA UDP-N-acetylglucosamine 1-carboxyvinyltransferase. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 416 matched cddid_all.tbl CDD TIGR01073 TIGR01073 273429 pcrA ATP-dependent DNA helicase PcrA. Designed to identify pcrA members of the uvrD/rep subfamily. [DNA metabolism, DNA replication, recombination, and repair] 726 matched cddid_all.tbl CDD TIGR01074 TIGR01074 130146 rep ATP-dependent DNA helicase Rep. Designed to identify rep members of the uvrD/rep subfamily. [DNA metabolism, DNA replication, recombination, and repair] 664 matched cddid_all.tbl CDD TIGR01075 TIGR01075 130147 uvrD DNA helicase II. Designed to identify uvrD members of the uvrD/rep subfamily. [DNA metabolism, DNA replication, recombination, and repair] 715 matched cddid_all.tbl CDD TIGR01076 TIGR01076 130148 sortase_fam LPXTG-site transpeptidase (sortase) family protein. This family includes Staphylococcus aureus sortase, a transpeptidase that attaches surface proteins by the Thr of an LPXTG motif to the cell wall. It also includes a protein required for correct assembly of an LPXTG-containing fimbrial protein, a set of homologous proteins from Streptococcus pneumoniae, in which LPXTG proteins are common. However, related proteins are found in Bacillus subtilis and Methanobacterium thermoautotrophicum, in which LPXTG-mediated cell wall attachment is not known. [Cell envelope, Other, Protein fate, Protein and peptide secretion and trafficking] 136 matched cddid_all.tbl CDD TIGR01077 TIGR01077 162192 L13_A_E ribosomal protein uL13, archaeal/eukaryotic form. This model represents ribosomal protein of L13 from the Archaea and from the eukaryotic cytosol. Bacterial and organellar forms are represented by model TIGR01066. [Protein synthesis, Ribosomal proteins: synthesis and modification] 142 matched cddid_all.tbl CDD TIGR01078 TIGR01078 273430 arcA arginine deiminase. Arginine deiminase is the first enzyme of the arginine deiminase pathway of arginine degradation. [Energy metabolism, Amino acids and amines] 405 matched cddid_all.tbl CDD TIGR01079 TIGR01079 273431 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes. [Protein synthesis, Ribosomal proteins: synthesis and modification] 102 matched cddid_all.tbl CDD TIGR01080 TIGR01080 273432 rplX_A_E ribosomal protein uL24, archaeal/eukaryotic form. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by related model TIGR01079. [Protein synthesis, Ribosomal proteins: synthesis and modification] 114 matched cddid_all.tbl CDD TIGR01081 TIGR01081 130153 mpl UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase. Alternate name: murein tripeptide ligase [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 448 matched cddid_all.tbl CDD TIGR01082 TIGR01082 273433 murC UDP-N-acetylmuramate--L-alanine ligase. This model describes the MurC protein in bacterial peptidoglycan (murein) biosynthesis. In a few species (Mycobacterium leprae, the Chlamydia), the amino acid may be L-serine or glycine instead of L-alanine. A related protein, UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase (murein tripeptide ligase) is described by model TIGR01081. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 448 matched cddid_all.tbl CDD TIGR01083 TIGR01083 273434 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY. [DNA metabolism, DNA replication, recombination, and repair] 192 matched cddid_all.tbl CDD TIGR01084 TIGR01084 130156 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY. [DNA metabolism, DNA replication, recombination, and repair] 275 matched cddid_all.tbl CDD TIGR01085 TIGR01085 273435 murE UDP-N-acetylmuramyl-tripeptide synthetase. Most members of this family are EC 6.3.2.13, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase. An exception is Staphylococcus aureus, in which diaminopimelate is replaced by lysine in the peptidoglycan and MurE is EC 6.3.2.7. The Mycobacteria, part of the closest neighboring branch outside of the low-GC Gram-positive bacteria, use diaminopimelate. A close homolog, scoring just below the trusted cutoff, is found (with introns) in Arabidopsis thaliana. Its role is unknown. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 464 matched cddid_all.tbl CDD TIGR01086 TIGR01086 188107 fucA L-fuculose phosphate aldolase. Members of this family are L-fuculose phosphate aldolase from various Proteobacteria, encoded in fucose utilization operons. Homologs in other bacteria given similar annotation but scoring below the trusted cutoff may share extensive sequence similarity but are not experimenally characterized and are not found in apparent fucose utilization operons; we consider their annotation as L-fuculose phosphate aldolase to be tenuous. This model has been narrowed in scope from the previous version. [Energy metabolism, Sugars] 214 matched cddid_all.tbl CDD TIGR01087 TIGR01087 273436 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 433 matched cddid_all.tbl CDD TIGR01088 TIGR01088 130160 aroQ 3-dehydroquinate dehydratase, type II. This model specifies the type II enzyme. The type I enzyme, often found as part of a multifunctional protein, is described by TIGR01093. [Amino acid biosynthesis, Aromatic amino acid family] 141 matched cddid_all.tbl CDD TIGR01089 TIGR01089 130161 fucI L-fucose isomerase. This enzyme catalyzes the first step in fucose metabolism, and has been characterized in Escherichia coli and Bacteroides thetaiotaomicron. [Energy metabolism, Sugars] 587 matched cddid_all.tbl CDD TIGR01090 TIGR01090 273437 apt adenine phosphoribosyltransferase. A phylogenetic analysis suggested omitting the bi-directional best hit homologs from the spirochetes from the seed for this model and making only tentative predictions of adenine phosphoribosyltransferase function for this lineage. The trusted cutoff score is made high for this reason. Most proteins scoring between the trusted and noise cutoffs are likely to act as adenine phosphotransferase. [Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides] 169 matched cddid_all.tbl CDD TIGR01091 TIGR01091 273438 upp uracil phosphoribosyltransferase. A fairly deep split in phylogenetic and UPGMA trees separates this mostly prokaryotic set of uracil phosphoribosyltransferases from a mostly eukaryotic set that includes uracil phosphoribosyltransferase, uridine kinases, and other, uncharacterized proteins. [Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides] 207 matched cddid_all.tbl CDD TIGR01092 TIGR01092 130164 P5CS delta l-pyrroline-5-carboxylate synthetase. This protein contains a glutamate 5-kinase (ProB, EC 2.7.2.11) region followed by a gamma-glutamyl phosphate reductase (ProA, EC 1.2.1.41) region. [Amino acid biosynthesis, Glutamate family] 715 matched cddid_all.tbl CDD TIGR01093 TIGR01093 273439 aroD 3-dehydroquinate dehydratase, type I. This model detects 3-dehydroquinate dehydratase, type I, either as a monofunctional protein or as a domain of a larger, multifunctional protein. It is often found fused to shikimate 5-dehydrogenase (EC 1.1.1.25), and sometimes additional domains. Type II 3-dehydroquinate dehydratase, designated AroQ, is described by the model TIGR01088. [Amino acid biosynthesis, Aromatic amino acid family] 229 matched cddid_all.tbl CDD TIGR01096 TIGR01096 273440 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein. [Transport and binding proteins, Amino acids, peptides and amines] 250 matched cddid_all.tbl CDD TIGR01097 TIGR01097 273441 PhnE "phosphonate ABC transporter, permease protein PhnE. Phosphonates are a class of compound analogous to organic phosphates, but in which the C-O-P linkage is replaced by a direct, stable C-P bond. Some bacteria can utilize phosphonates as a source of phosphorus. This family consists of permease proteins of known or predicted phosphonate ABC transporters. Often this protein is found as a duplicated pair, occasionally as a fused pair. Certain ""second"" copies score in between the trusted and noise cutoff and should be considered true hits (by context). [Transport and binding proteins, Anions]" 250 matched cddid_all.tbl CDD TIGR01098 TIGR01098 273442 3A0109s03R phosphate/phosphite/phosphonate ABC transporter, periplasmic binding protein. Phosphonates are a varied class of phosphorus-containing organic compound in which a direct C-P bond is found, rather than a C-O-P linkage of the phosphorus through an oxygen atom. They may be toxic but also may be used as sources of phosphorus and energy by various bacteria. Phosphonate utilization systems typically are encoded in 14 or more genes, including a three gene ABC transporter. This family includes the periplasmic binding protein component of ABC transporters for phosphonates as well as other, related binding components for closely related substances such as phosphate and phosphite. A number of members of this family are found in genomic contexts with components of selenium metabolic processes suggestive of a role in selenate or other selenium-compound transport. A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system (GenProp0232) has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates. [Transport and binding proteins, Anions] 254 matched cddid_all.tbl CDD TIGR01099 TIGR01099 273443 galU UTP--glucose-1-phosphate uridylyltransferase. Built to distinquish between the highly similar genes galU and galF [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 260 matched cddid_all.tbl CDD TIGR01100 TIGR01100 130170 V_ATP_synt_C vacuolar ATP synthase 16 kDa proteolipid subunit. This model describes the vacuolar ATP synthase 16 kDa proteolipid subunit in eukaryotes and includes members from diverse groups e.g., fungi, plants, parasites etc. The principal role V-ATPases are the acidification of intracellular compartments of eukaryotic cells. [Transport and binding proteins, Cations and iron carrying compounds] 108 matched cddid_all.tbl CDD TIGR01101 TIGR01101 130171 V_ATP_synt_F vacuolar ATP synthase F subunit. This model describes the vacuolar ATP synthase F subunit (14 kDa subunit) in eukaryotes. In some archaeal species this protein subunit is referred as G subunit [Transport and binding proteins, Cations and iron carrying compounds] 115 matched cddid_all.tbl CDD TIGR01102 TIGR01102 130172 yscR type III secretion apparatus protein, YscR/HrcR family. This model identifies the generic virulence translocation proteins in bacteria. It derives its name:'Yop' from Yersinia enterocolitica species, where this virulence protein was identified. In bacterial pathogenesis, Yop effector proteins are translocated into the eukaryotic cells. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 202 matched cddid_all.tbl CDD TIGR01103 TIGR01103 211625 fliP flagellar biosynthetic protein FliP. This model describes bacterial flagellar biogenesis protein fliP, which is one of the genes in motility locus on the bacterial chromosome that is involved in structure and function of bacterial flagellum. It was demonstrated that mutants in fliP locus were non-flagellated and non-motile, while revertants were flagellated and motile. [Cellular processes, Chemotaxis and motility] 197 matched cddid_all.tbl CDD TIGR01104 TIGR01104 273444 V_PPase vacuolar-type H(+)-translocating pyrophosphatase. This model describes proton pyrophosphatases from eukaryotes (predominantly plants), archaea and bacteria. It is an integral membrane protein and is suggested to have about 15 membrane spanning domains. Proton translocating inorganic pyrophosphatase, like H(+)-ATPase, acidifies the vacuoles and is pivotal to the vacuolar secondary active transport systems in plants. [Transport and binding proteins, Cations and iron carrying compounds] 695 matched cddid_all.tbl CDD TIGR01105 TIGR01105 130175 galF UTP-glucose-1-phosphate uridylyltransferase, non-catalytic GalF subunit. GalF is a non-catalytic subunit of the UTP-glucose pyrophosphorylase modulating the enzyme activity to increase the formation of UDP-glucose [Regulatory functions, Protein interactions] 297 matched cddid_all.tbl CDD TIGR01106 TIGR01106 273445 ATPase-IIC_X-K sodium or proton efflux -- potassium uptake antiporter, P-type ATPase, alpha subunit. This model describes the P-type ATPases responsible for the exchange of either protons or sodium ions for potassium ions across the plasma membranes of eukaryotes. Unlike most other P-type ATPases, members of this subfamily require a beta subunit for activity. This model encompasses eukaryotes and consists of two functional types, a Na/K antiporter found widely distributed in eukaryotes and a H/K antiporter found only in vertebrates. The Na+ or H+/K+ antiporter P-type ATPases have been characterized as Type IIC based on a published phylogenetic analysis. Sequences from Blastocladiella emersonii (GP|6636502, GP|6636502 and PIR|T43025), C. elegans (GP|2315419, GP|6671808 and PIR|T31763) and Drosophila melanogaster (GP|7291424) score below trusted cutoff, apparently due to long branch length (excessive divergence from the last common ancestor) as evidenced by a phylogenetic tree. Experimental evidence is needed to determine whether these sequences represent ATPases with conserved function. Aside from fragments, other sequences between trusted and noise appear to be bacterial ATPases of unclear lineage, but most likely calcium pumps. [Energy metabolism, ATP-proton motive force interconversion] 997 matched cddid_all.tbl CDD TIGR01107 TIGR01107 273446 Na_K_ATPase_bet Sodium Potassium ATPase beta subunit. This model describes the Na+/K+ ATPase beta subunit in eukaryotes. Na+/K+ ATPase(also called Sodium-Potassium pump) is intimately associated with the plasma membrane. It couples the energy released by the hydrolysis of ATP to extrude 3 Na+ ions, with the concomitant uptake of 2K+ ions, against their ionic gradients. [Transport and binding proteins, Cations and iron carrying compounds] 290 matched cddid_all.tbl CDD TIGR01108 TIGR01108 273447 oadA oxaloacetate decarboxylase alpha subunit. This model describes the bacterial oxaloacetate decarboxylase alpha subunit and its equivalents in archaea. The oxaloacetate decarboxylase Na+ pump is the paradigm of the family of Na+ transport decarboxylases that present in bacteria and archaea. It a multi subunit enzyme consisting of a peripheral alpha-subunit and integral membrane subunits beta and gamma. The energy released by the decarboxylation reaction of oxaloacetate is coupled to Na+ ion pumping across the membrane. [Transport and binding proteins, Cations and iron carrying compounds, Energy metabolism, Other] 582 matched cddid_all.tbl CDD TIGR01109 TIGR01109 130179 Na_pump_decarbB sodium ion-translocating decarboxylase, beta subunit. This model describes the beta subunits of sodium pump decarboxylases that include oxaloacetate decarboxylase, methylmalonyl-CoA decarboxylase, and glutaconyl-CoA decarboxylase. Beta and gammma-subunits are integral membrane proteins, while alpha is membrane bound. Catalytically, the energy released by the decarboxylation reaction is coupled to the extrusion of Na+ ions across the membrane. [Transport and binding proteins, Cations and iron carrying compounds, Energy metabolism, Other] 354 matched cddid_all.tbl CDD TIGR01110 TIGR01110 273448 mdcA malonate decarboxylase, alpha subunit. This model describes malonate decarboxylase alpha subunit, from both the water-soluble form as found in Klebsiella pneumoniae and the form couple to sodium ion pumping in Malonomonas rubra. Malonate decarboxylase Na+ pump is the paradigm of the family of Na+ transport decarboxylases. Essentially, it couples the energy derived from decarboxylation of a carboxylic acid substrate to move Na+ ion across the bilayer. Functional malonate decarboylase is a multi subunit protein. The alpha subunit enzymatically performs the transfer of malonate (substrate) to an acyl carrier protein subunit for subsequent decarboxylation, hence the name: acetyl-S-acyl carrier protein:malonate carrier protein-SH transferase. [Transport and binding proteins, Cations and iron carrying compounds, Energy metabolism, Other] 543 matched cddid_all.tbl CDD TIGR01111 TIGR01111 130181 mtrA N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit A. This model describes N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit A in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase (encoded by subunit A) is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase. [Transport and binding proteins, Cations and iron carrying compounds] 238 matched cddid_all.tbl CDD TIGR01112 TIGR01112 273449 mtrD N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit D. This model describes N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit D in methanogenic archaea. This methyltranferase is membrane-associated enzyme complex that uses methy-transfer reaction to drive sodium-ion pump. Archaea domain, have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase. [Transport and binding proteins, Cations and iron carrying compounds, Energy metabolism, Methanogenesis] 223 matched cddid_all.tbl CDD TIGR01113 TIGR01113 130183 mtrE N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit E. This model describes N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit E in methanogenic archaea. This methyltranfersae is membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of methyl-coenzyme M by another enzyme methyl-coenzyme M reductase. [Transport and binding proteins, Cations and iron carrying compounds, Energy metabolism, Methanogenesis] 283 matched cddid_all.tbl CDD TIGR01114 TIGR01114 273450 mtrH N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit H. This model describes N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit H in methanogenic archaea. This methyltranfersae is membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of methyl-coenzyme M by another enzyme methyl-coenzyme M reductase. [Energy metabolism, Methanogenesis] 314 matched cddid_all.tbl CDD TIGR01115 TIGR01115 273451 pufM photosynthetic reaction center M subunit. This model decribes the photosynthetic reaction center M subunit in non-oxygenic photosynthetic bacteria. Reaction center is an integral membrane pigment-protein that carries out light-driven electron transfer reactions. At the core of reacion center is a collection light-harvesting cofactors and closely associated polypeptides. The core protein complex is made of L, M and H subunits. The common cofactors include bacterichlorophyll, bacteriopheophytins, ubiquinone and no-heme ferrous iron. The net result of electron tranfer reactions is the establishment of proton electrochemical gradient and production of reducing equivalents in form of NADH. Ultimately the process results in the reduction of C02 to carbohydrates(C6H12O6) In non-oxygenic organisms, the electron donor is some organic acid and not water. Much of our current functional understanding of photosynthesis comes from the structural determination, spectroscopic studies and mutational analysis on the reaction center of Rhodobacter sphaeroides. [Energy metabolism, Electron transport, Energy metabolism, Photosynthesis] 305 matched cddid_all.tbl CDD TIGR01116 TIGR01116 273452 ATPase-IIA1_Ca sarco/endoplasmic reticulum calcium-translocating P-type ATPase. This model describes the P-type ATPase responsible for translocating calcium ions across the endoplasmic reticulum membrane of eukaryotes, and is of particular importance in the sarcoplasmic reticulum of skeletal and cardiac muscle in vertebrates. These pumps transfer Ca2+ from the cytoplasm to the lumen of the endoplasmic reticulum. In humans and mice, at least, there are multiple isoforms of the SERCA pump with overlapping but not redundant functions. Defects in SERCA isoforms are associated with diseases in humans. The calcium P-type ATPases have been characterized as Type IIA based on a phylogenetic analysis which distinguishes this group from the Type IIB PMCA calcium pump modelled by TIGR01517. A separate analysis divides Type IIA into sub-types, SERCA and PMR1, the latter of which is modelled by TIGR01522. [Transport and binding proteins, Cations and iron carrying compounds] 917 matched cddid_all.tbl CDD TIGR01117 TIGR01117 130187 mmdA methylmalonyl-CoA decarboxylase alpha subunit. This model describes methymalonyl-CoA decarboxylase aplha subunit in archaea and bacteria. Metylmalonyl-CoA decarboxylase Na+ pump is a representative of a class of Na+ transport decarboxylases that couples the energy derived by decarboxylation of carboxylic acid substrates to drive the extrusion of Na+ ion across the membrane. [Energy metabolism, ATP-proton motive force interconversion, Energy metabolism, Fermentation, Transport and binding proteins, Cations and iron carrying compounds] 512 matched cddid_all.tbl CDD TIGR01118 TIGR01118 130188 lacA galactose-6-phosphate isomerase, LacA subunit. This family contains members from low GC gram-positive bacteria. Galactose-6-phosphate isomerase is involved in lactose catabolism by the tagatose-6-phosphate pathway. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 141 matched cddid_all.tbl CDD TIGR01119 TIGR01119 130189 lacB galactose-6-phosphate isomerase, LacB subunit. This family contains four members from low GC gram-positive bacteria. Galactose-6-phosphate isomerase is involved in lactose catabolism by the tagatose-6-phosphate pathway. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 171 matched cddid_all.tbl CDD TIGR01120 TIGR01120 130190 rpiB ribose 5-phosphate isomerase B. Involved in the non-oxidative branch of the pentose phospate pathway. [Energy metabolism, Pentose phosphate pathway] 143 matched cddid_all.tbl CDD TIGR01121 TIGR01121 130191 D_amino_aminoT D-amino acid aminotransferase. This enzyme is a homodimer. The pyridoxal phosphate attachment site is the Lys at position 146 of the seed alignment, in the motif Cys-Asp-Ile-Lys-Ser-Leu-Asn. Specificity is broad for various D-amino acids, and differs among members of the family; the family is designated equivalog, but with this caveat attached. [Energy metabolism, Amino acids and amines] 276 matched cddid_all.tbl CDD TIGR01122 TIGR01122 130192 ilvE_I branched-chain amino acid aminotransferase, group I. Among the class IV aminotransferases are two phylogenetically separable groups of branched-chain amino acid aminotransferase (IlvE). The last common ancestor of the two lineages appears also to have given rise to a family of D-amino acid aminotransferases (DAAT). This model represents the IlvE family more strongly similar to the DAAT family. [Amino acid biosynthesis, Pyruvate family] 298 matched cddid_all.tbl CDD TIGR01123 TIGR01123 233278 ilvE_II branched-chain amino acid aminotransferase, group II. Among the class IV aminotransferases are two phylogenetically separable groups of branched-chain amino acid aminotransferase (IlvE). The last common ancestor of the two lineages appears also to have given rise to a family of D-amino acid aminotransferases (DAAT). This model represents the IlvE family less similar to the DAAT family. [Amino acid biosynthesis, Pyruvate family] 313 matched cddid_all.tbl CDD TIGR01124 TIGR01124 130194 ilvA_2Cterm threonine ammonia-lyase, biosynthetic, long form. This model describes a form of threonine ammonia-lyase, a pyridoxal-phosphate dependent enzyme, with two copies of the threonine dehydratase C-terminal domain (pfam00585). Members with known function participate in isoleucine biosynthesis and are inhibited by isoleucine. Alternate name: threonine deaminase, threonine dehydratase. Forms scoring between the trusted and noise cutoff tend to branch with this subgroup of threonine ammonia-lyase phylogenetically but have only a single copy of the C-terminal domain. [Amino acid biosynthesis, Pyruvate family] 499 matched cddid_all.tbl CDD TIGR01125 TIGR01125 273453 TIGR01125 ribosomal protein S12 methylthiotransferase RimO. Members of this protein are the methylthiotransferase RimO, which modifies a conserved Asp residue in ribosomal protein S12. This clade of radical SAM family proteins is closely related to the tRNA modification bifunctional enzyme MiaB (see TIGR01574), and it catalyzes the same two types of reactions: a radical-mechanism sulfur insertion, and a methylation of the inserted sulfur. This clade spans alpha and gamma proteobacteria, cyano bacteria, Deinococcus, Porphyromonas, Aquifex, Helicobacter, Campylobacter, Thermotoga, Chlamydia, Streptococcus coelicolor and Clostridium, but does not include most other gram positive bacteria, archaea or eukaryotes. [Protein synthesis, Ribosomal proteins: synthesis and modification] 426 matched cddid_all.tbl CDD TIGR01126 TIGR01126 273454 pdi_dom protein disulfide-isomerase domain. This model describes a domain of eukaryotic protein disulfide isomerases, generally found in two copies. The high cutoff for total score reflects the expectation of finding both copies. The domain is similar to thioredoxin but the redox-active disulfide region motif is APWCGHCK. [Protein fate, Protein folding and stabilization] 102 matched cddid_all.tbl CDD TIGR01127 TIGR01127 130197 ilvA_1Cterm threonine ammonia-lyase, medium form. A form of threonine dehydratase with two copies of the C-terminal domain pfam00585 is described by TIGR01124. This model describes a phylogenetically distinct form with a single copy of pfam00585. This form branches with the catabolic threonine dehydratase of E. coli; many members are designated as catabolic for this reason. However, the catabolic form lacks any pfam00585 domain. Many members of this model are found in species with other Ile biosynthetic enzymes. [Amino acid biosynthesis, Pyruvate family] 380 matched cddid_all.tbl CDD TIGR01128 TIGR01128 273455 holA DNA polymerase III, delta subunit. DNA polymerase III delta (holA) and delta prime (holB) subunits are distinct proteins encoded by separate genes. The delta prime subunit (holB) exhibits sequence homology to the tau and gamma subunits (dnaX), but the delta subunit (holA) does not demonstrate this same homology with dnaX. The delta, delta prime, gamma, chi and psi subunits form the gamma complex subassembly of DNA polymerase III holoenzyme, which couples ATP to assemble the ring-shaped beta subunit around DNA forming a DNA sliding clamp. [DNA metabolism, DNA replication, recombination, and repair] 302 matched cddid_all.tbl CDD TIGR01129 TIGR01129 273456 secD protein-export membrane protein SecD. Members of this family are highly variable in length immediately after the well-conserved motif LGLGLXGG at the amino-terminal end of this model. Archaeal homologs are not included in the seed and score between the trusted and noise cutoffs. SecD from Mycobacterium tuberculosis has a long Pro-rich insert. [Protein fate, Protein and peptide secretion and trafficking] 397 matched cddid_all.tbl CDD TIGR01130 TIGR01130 273457 ER_PDI_fam protein disulfide isomerase, eukaryotic. This model represents eukaryotic protein disulfide isomerases retained in the endoplasmic reticulum (ER) and closely related forms. Some members have been assigned alternative or additional functions such as prolyl 4-hydroxylase and dolichyl-diphosphooligosaccharide-protein glycotransferase. Members of this family have at least two protein-disulfide domains, each similar to thioredoxin but with the redox-active disulfide in the motif PWCGHCK, and an ER retention signal at the extreme C-terminus (KDEL, HDEL, and similar motifs). 462 matched cddid_all.tbl CDD TIGR01131 TIGR01131 273458 ATP_synt_6_or_A ATP synthase subunit 6 (eukaryotes),also subunit A (prokaryotes). Bacterial forms should be designated ATP synthase, F0 subunit A; eukaryotic (chloroplast and mitochondrial) forms should be designated ATP synthase, F0 subunit 6. The F1/F0 ATP synthase is a multisubunit, membrane associated enzyme found in bacteria and mitochondria and chloroplast. This enzyme is principally involved in the synthesis of ATP from ADP and inorganic phosphate by coupling the energy derived from the proton electrochemical gradient across the biological membrane. A brief description of this multisubunit enzyme complex: F1 and F0 represent two major clusters of subunits. Individual subunits in each of these clusters are named differently in prokaryotes and in organelles e.g., mitochondria and chloroplast. The bacterial equivalent of subunit 6 is named subunit 'A'. It has been shown that proton is conducted though this subunit. Typically, deprotonation and reprotonation of the acidic amino acid side-chains are implicated in the process. [Energy metabolism, ATP-proton motive force interconversion] 226 matched cddid_all.tbl CDD TIGR01132 TIGR01132 273459 pgm phosphoglucomutase, alpha-D-glucose phosphate-specific. This enzyme interconverts alpha-D-glucose-1-P and alpha-D-glucose-6-P. [Energy metabolism, Sugars] 543 matched cddid_all.tbl CDD TIGR01133 TIGR01133 273460 murG undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase. RM 8449890 RT The final step of peptidoglycan subunit assembly in Escherichia coli occurs in the cytoplasm. RA Bupp K, van Heijenoort J. RL J Bacteriol 1993 Mar;175(6):1841-3 [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 348 matched cddid_all.tbl CDD TIGR01134 TIGR01134 273461 purF amidophosphoribosyltransferase. Alternate name: glutamine phosphoribosylpyrophosphate (PRPP) amidotransferase. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 442 matched cddid_all.tbl CDD TIGR01135 TIGR01135 273462 glmS glucosamine--fructose-6-phosphate aminotransferase (isomerizing). The member from Methanococcus jannaschii contains an intein. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan, Central intermediary metabolism, Amino sugars] 607 matched cddid_all.tbl CDD TIGR01136 TIGR01136 273463 cysKM cysteine synthase. This model discriminates cysteine synthases (EC 2.5.1.47) (both CysK and CysM) from cystathionine beta-synthase, a protein found primarily in eukaryotes and carrying a C-terminal CBS domain lacking from this protein. Bacterial proteins lacking the CBS domain but otherwise showing resemblamnce to cystathionine beta-synthases and considerable phylogenetic distance from known cysteine synthases were excluded from the seed and score below the trusted cutoff. [Amino acid biosynthesis, Serine family] 299 matched cddid_all.tbl CDD TIGR01137 TIGR01137 273464 cysta_beta cystathionine beta-synthase. Members of this family closely resemble cysteine synthase but contain an additional C-terminal CBS domain. The function of any bacterial member included in this family is proposed but not proven. [Amino acid biosynthesis, Serine family] 455 matched cddid_all.tbl CDD TIGR01138 TIGR01138 130208 cysM cysteine synthase B. CysM differs from CysK in that it can also use thiosulfate instead of sulfide, to produce cysteine thiosulfonate instead of cysteine. Alternate name: O-acetylserine (thiol)-lyase [Amino acid biosynthesis, Serine family] 290 matched cddid_all.tbl CDD TIGR01139 TIGR01139 273465 cysK cysteine synthase A. This model distinguishes cysteine synthase A (CysK) from cysteine synthase B (CysM). CysM differs in having a broader specificity that also allows the use of thiosulfate to produce cysteine thiosulfonate. [Amino acid biosynthesis, Serine family] 298 matched cddid_all.tbl CDD TIGR01140 TIGR01140 273466 L_thr_O3P_dcar L-threonine-O-3-phosphate decarboxylase. This family contains pyridoxal phosphate-binding class II aminotransferases (see pfamAM:pfam00222) closely related to, yet distinct from, histidinol-phosphate aminotransferase (HisC). It is found in cobalamin biosynthesis operons in Salmonella typhimurium and Bacillus halodurans (each of which also has HisC) and has been shown to have L-threonine-O-3-phosphate decarboxylase activity in Salmonella. Although the gene symbol cobD was assigned in Salmonella, cobD in other contexts refers to a different cobalamin biosynthesis enzyme, modeled by pfam03186 and called cbiB in Salmonella. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 330 matched cddid_all.tbl CDD TIGR01141 TIGR01141 273467 hisC histidinol-phosphate aminotransferase. Alternate names: histidinol-phosphate transaminase; imidazole acetol-phosphate transaminase Histidinol-phosphate aminotransferase is a pyridoxal-phosphate dependent enzyme. [Amino acid biosynthesis, Histidine family] 350 matched cddid_all.tbl CDD TIGR01142 TIGR01142 130212 purT phosphoribosylglycinamide formyltransferase 2. This enzyme is an alternative to PurN (TIGR00639) [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 380 matched cddid_all.tbl CDD TIGR01143 TIGR01143 273468 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase. This family consists of the strictly bacterial MurF gene of peptidoglycan biosynthesis. This enzyme is almost always UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanyl ligase, but in a few species, MurE adds lysine rather than diaminopimelate. This enzyme acts on the product from MurE activity, and so is also subfamily rather than equivalog. Staphylococcus aureus is an example of species in this MurF protein would differ. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 417 matched cddid_all.tbl CDD TIGR01144 TIGR01144 130214 ATP_synt_b ATP synthase, F0 subunit b. This model describes the F1/F0 ATP synthase b subunit in bacteria only. Scoring just below the trusted cutoff are the N-terminal domains of Mycobacterial b/delta fusion proteins and a subunit from an archaeon, Methanosarcina barkeri, in which the ATP synthase homolog differs in architecture and is not experimentally confirmed. This model helps resolve b from the related b' subunit. Within the family is an example from a sodium-translocating rather than proton-translocating ATP synthase. [Energy metabolism, ATP-proton motive force interconversion] 147 matched cddid_all.tbl CDD TIGR01145 TIGR01145 130215 ATP_synt_delta ATP synthase, F1 delta subunit. This model describes the ATP synthase delta subunit in bacteria, mitochondria, and chloroplasts. It is sometimes called OSCP for Oligomycin Sensitivity Conferring Protein. F1/F0-ATP synthase is a multisubunit, membrane associated enzyme found in bacteria and organelles of higher eukaryotes, namely, mitochondria and chloroplast. This enzyme is principally involved in the synthesis of ATP from ADP and inorganic phosphate by coupling the energy derived from the proton electrochemical gradient across the biological membrane. A brief description of this multisubunit enzyme complex: F1 and F0 represent two major clusters of subunits. Delta subunit belongs to the F1 cluster or sector and functionally implicated in the overall stability of the complex. Expression of truncated forms of this subunit results in low ATPase activity. [Energy metabolism, ATP-proton motive force interconversion] 172 matched cddid_all.tbl CDD TIGR01146 TIGR01146 273469 ATPsyn_F1gamma ATP synthase, F1 gamma subunit. This model describes the ATP synthase gamma subunit in bacteria and its equivalents in organelles, namely, mitochondria and chloroplast. F1/F0-ATP synthase is a multisubunit, membrane associated enzyme found in bacteria and organelles of higher eukaryotes, namely, mitochondria and chloroplast. This enzyme is principally involed in the synthesis of ATP from ADP and inorganic phosphate by coupling the energy derived from the proton electrochemical gradient across the biological membrane. A brief description of this multisubunit enzyme complex: F1 and F0 represent two major clusters of subunits. The gamma subunit is the part of F1 cluster. Surrounding the gamma subunit in a cylinder-like structure are three alpha and three subunits in an alternating fashion. This is the central catalytic unit whose different conformations permit the binding of ADP and inorganic phosphate and release of ATP. [Energy metabolism, ATP-proton motive force interconversion] 286 matched cddid_all.tbl CDD TIGR01147 TIGR01147 130217 V_ATP_synt_G vacuolar ATP synthase, subunit G. This model describes the vacuolar ATP synthase G subunit in eukaryotes and includes members from diverse groups e.g., fungi, plants, parasites etc. V-ATPases are multi-subunit enzymes composed of two functional domains: A transmembrane Vo domain and a peripheral catalytic domain V1. The G subunit is one of the subunits of the catalytic domain. V-ATPases are responsible for the acidification of endosomes and lysosomes, which are part of the central vacuolar system. [Energy metabolism, ATP-proton motive force interconversion] 113 matched cddid_all.tbl CDD TIGR01148 TIGR01148 130218 mtrC N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit C. This model describes N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit C in methanogenic archaea. This methyltranferase is membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase. [Energy metabolism, Other] 265 matched cddid_all.tbl CDD TIGR01149 TIGR01149 130219 mtrG N5-methyltetrahydromethanopterin:coenzyme M methyltransferase subunit G. This model describes N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranfersae is membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase. [Energy metabolism, Other] 70 matched cddid_all.tbl CDD TIGR01150 TIGR01150 273470 puhA photosynthetic reaction center, subunit H, bacterial. This model describes the photosynthetic reaction center H subunit in non-oxygenic photosynthetic bacteria. The reaction center is an integral membrane pigment-protein that carries out light-driven electron transfer reactions. At the core of reaction center is a collection light-harvesting cofactors and closely associated polypeptides. The core protein complex is made of L, M and H subunits. The common cofactors include bacterichlorophyll, bacteriopheophytins, ubiquinone and no-heme ferrous iron. The net result of electron tranfer reactions is the establishment of proton electrochemical gradient and production of reducing equivalents in the form of NADH. Ultimately, the process results in the reduction of C02 to carbohydrates(C6H12O6) In non-oxygenic organisms, the electron donor is an organic acid rather than water. Much of our current functional understanding of photosynthesis comes from the structural determination and spectroscopic studies on the reaction center of Rhodobacter sphaeroides. [Energy metabolism, Electron transport, Energy metabolism, Photosynthesis] 252 matched cddid_all.tbl CDD TIGR01151 TIGR01151 130221 psbA photosystem II, DI subunit (also called Q(B)). This model describes the Photosystem II, DI subunit (also called Q(B)) in bacterial and its equivalents in chloroplast of algae and higher plants. Photosystem II is many ways functionally equivalent to bacterial reaction center. At the core of Photosystem II are several light harvesting cofactors including plastoquinones, pheophytins, phyloquinones etc. These cofactors are intimately associated with the polypeptides, which principally including subunits DI, DII, Cyt.b, Cyt.f and iron-sulphur protein. Together they participate in the electron transfer reactions that lead to the net production of the reducting equivalents in the form of NADPH, which are used for reduction of CO2 to carbohydrates(C6H1206). Phosystem II operates during oxygenic photosynthesis and principal electron donor is H2O. Although no structural data is presently available, a huge body of literature exits that describes function using a variety of biochemical and biophysical techniques. [Energy metabolism, Electron transport, Energy metabolism, Photosynthesis] 360 matched cddid_all.tbl CDD TIGR01152 TIGR01152 130222 psbD Photosystem II, DII subunit (also called Q(A)). This model describes the Photosystem II, DII subunit (also called Q(A)) in bacterial and its equivalents in chloroplast of algae and higher plants. Photosystem II is in many ways functionally equivalent to bacterial reaction center. At the core of Photosystem II are several light harvesting cofactors including plastoquinones, pheophytins, phyloquinones etc. These cofactors are intimately associated with the polypeptides, which principally including subunits DI, DII, Cyt.b, Cyt.f and iron-sulphur protein. Together they participate in the electron transfer reactions that lead to the net production of the reducting equivalents in the form of NADPH, which are used for reduction of CO2 to carbohydrates(C6H1206). Phosystem II operates during oxygenic photosynthesis and principal electron donor is H2O. Although no high resolution X-ray structural data is presently available, recently a 3D structure of the supercomplex has been described by cryo-electron microscopy. Besides a huge body of literature exits that describes function using a variety of biochemical and biophysical techniques. [Energy metabolism, Electron transport, Energy metabolism, Photosynthesis] 352 matched cddid_all.tbl CDD TIGR01153 TIGR01153 213589 psbC photosystem II 44 kDa subunit reaction center protein (also called P6 protein, CP43), bacterial and chloroplast. This model describes the Photosystem II, 44kDa subunit (also called P6 protein, CP43) in bacterial and its equivalents in chloroplast of algae and higher plants. Photosystem II is in many ways functionally equivalent to bacterial reaction center. At the core of Photosystem II are several light harvesting cofactors including plastoquinones, pheophytins, phyloquinones etc. These cofactors are intimately associated with the polypeptides, which principally including subunits 44 kDa protein,DI, DII, Cyt.b, Cyt.f, iron-sulphur protein and others. Functinally 44 kDa subunit is imlicated in chlorophyll binding. Together they participate in the electron transfer reactions that lead to the net production of the reducting equivalents in the form of NADPH, which are used for reduction of CO2 to carbohydrates(C6H1206). Phosystem II operates during oxygenic photosynthesis and principal electron donor is H2O. Although no high resolution X-ray structural data is presently available, recently a 3D structure of the supercomplex has been described by cryo-electron microscopy. Besides a huge body of literature exits that describes function using a variety of biochemical and biophysical techniques. [Energy metabolism, Electron transport, Energy metabolism, Photosynthesis] 432 matched cddid_all.tbl CDD TIGR01156 TIGR01156 130224 cytb6/f_IV cytochrome b6/f complex subunit IV. This model describes the subunit IV of the cytochrome b6/f complex. The cyt b6/f complex is central to the functions of the oxygenic phosynthetic electron transport in cyanobacteria and its equivalents in algae and higher plants. Energetically, on the redox scale the cytb6/f complex is placed below the other components - Q(A); Q(B) of the photosystem II in the Z-scheme, along the pathway of the electron transport. The complex is made of the following subunits: cytochrome f; cytochrome b6; Rieske 2Fe-2S; and subunits IV; V; VI; VII. Subunit IV is one of the principal subunits for the binding of the redox prosthetic groups. Each monomer of the complex contains a molecule of chlorophyll a and beta-carotene. [Energy metabolism, Electron transport, Energy metabolism, Photosynthesis] 159 matched cddid_all.tbl CDD TIGR01157 TIGR01157 130225 pufL photosynthetic reaction center L subunit. This model describes the photosynthetic reaction center L subunit in non-oxygenic photosynthetic bacteria. Reaction center is an integral membrane pigment-protein that carries out light-driven electron transfer reactions. At the core of reaction center is a collection light-harvesting cofactors and closely associated polypeptides. The core protein complex is made of L, M and H subunits. The common cofactors include bacterichlorophyll, bacteriopheophytins, ubiquinone and no-heme ferrous iron. The net result of electron tranfer reactions is the establishment of proton electrochemical gradient and production of reducing equivalents in form of NADH. Ultimately the process results in the reduction of C02 to carbohydrates(C6H12O6) In non-oxygenic organisms, the electron donor is some organic acid and not water. Much of our current functional understanding of photosynthesis comes from the structural determination, spectroscopic studies and mutational analysis on the reaction center of Rhodobacter sphaeroides. [Energy metabolism, Electron transport, Energy metabolism, Photosynthesis] 239 matched cddid_all.tbl CDD TIGR01158 TIGR01158 273471 SUI1_rel translation initation factor SUI1, putative, prokaryotic. This family of archaeal and bacterial proteins is homologous to the eukaryotic translation intiation factor SUI1 involved in directing the ribosome to the proper start site of translation by functioning in concert with eIF-2 and the initiator tRNA-Met. [Protein synthesis, Translation factors] 101 matched cddid_all.tbl CDD TIGR01159 TIGR01159 273472 DRP1 density-regulated protein DRP1. This protein family shows weak but suggestive similarity to translation initiation factor SUI1 and its prokaryotic homologs. 173 matched cddid_all.tbl CDD TIGR01160 TIGR01160 130228 SUI1_MOF2 translation initiation factor SUI1, eukaryotic. Alternate name: MOF2. A similar protein family (see TIGRFAMs model TIGR01158) is found in prokaryotes. The human proteins complements a yeast SUI1 mutatation. [Protein synthesis, Translation factors] 110 matched cddid_all.tbl CDD TIGR01161 TIGR01161 273473 purK phosphoribosylaminoimidazole carboxylase, PurK protein. Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This model represents PurK, N5-carboxyaminoimidazole ribonucleotide synthetase, which hydrolyzes ATP and converts AIR to N5-CAIR. PurE converts N5-CAIR to CAIR. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 352 matched cddid_all.tbl CDD TIGR01162 TIGR01162 273474 purE phosphoribosylaminoimidazole carboxylase, PurE protein. Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. This model represents PurK, an N5-CAIR mutase. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 156 matched cddid_all.tbl CDD TIGR01163 TIGR01163 273475 rpe ribulose-phosphate 3-epimerase. This family consists of Ribulose-phosphate 3-epimerase, also known as pentose-5-phosphate 3-epimerase (PPE). PPE converts D-ribulose 5-phosphate into D-xylulose 5-phosphate in Calvin's reductive pentose phosphate cycle. It has been found in a wide range of bacteria, archebacteria, fungi and plants. [Energy metabolism, Pentose phosphate pathway] 210 matched cddid_all.tbl CDD TIGR01164 TIGR01164 273476 rplP_bact ribosomal protein L16, bacterial/organelle. This model describes bacterial and organellar ribosomal protein L16. The homologous protein of the eukaryotic cytosol is designated L10 [Protein synthesis, Ribosomal proteins: synthesis and modification] 125 matched cddid_all.tbl CDD TIGR01165 TIGR01165 273477 cbiN cobalt transport protein. This model describes the cobalt transporter in bacteria and its equivalents in archaea. It principally functions in the ion uptake mechanism. It is a multisubunit transporter with two integral membrane proteins and two closely associated cytoplasmic subunits. This transporter belongs to the ABC transporter superfamily (ATP stands for ATP Binding Cassette). This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux. [Transport and binding proteins, Cations and iron carrying compounds] 91 matched cddid_all.tbl CDD TIGR01166 TIGR01166 130234 cbiO cobalt transport protein ATP-binding subunit. This model describes the ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. The model is restricted to ATP subunit that is a part of the cobalt transporter, which belongs to the ABC transporter superfamily (ATP Binding Cassette). The model excludes ATP binding subunit that are associated with other transporters belonging to ABC transporter superfamily. This superfamily includes two groups, one which catalyze the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drive the both the process of uptake and efflux. [Transport and binding proteins, Cations and iron carrying compounds] 190 matched cddid_all.tbl CDD TIGR01167 TIGR01167 273478 LPXTG_anchor LPXTG-motif cell wall anchor domain. This model describes the LPXTG motif-containing region found at the C-terminus of many surface proteins of Streptococcus and Streptomyces species. Cleavage between the Thr and Gly by sortase or a related enzyme leads to covalent anchoring at the new C-terminal Thr to the cell wall. Hits that do not lie at the C-terminus or are not found in Gram-positive bacteria are probably false-positive. A common feature of this proteins containing this domain appears to be a high proportion of charged and zwitterionic residues immediatedly upstream of the LPXTG motif. This model differs from other descriptions of the LPXTG region by including a portion of that upstream charged region. [Cell envelope, Other] 34 matched cddid_all.tbl CDD TIGR01168 TIGR01168 273479 YSIRK_signal Gram-positive signal peptide, YSIRK family. Many surface proteins found in Streptococcus, Staphylococcus, and related lineages share apparently homologous signal sequences. A motif resembling [YF]SIRKxxxGxxS[VIA] appears at the start of the transmembrane domain. The GxxS motif appears perfectly conserved, suggesting a specific function and not just homology. There is a strong correlation between proteins carrying this region at the N-terminus and those carrying the Gram-positive anchor domain with the LPXTG sortase processing site at the C-terminus. 39 matched cddid_all.tbl CDD TIGR01169 TIGR01169 211630 rplA_bact ribosomal protein L1, bacterial/chloroplast. This model describes bacterial (and chloroplast) ribosomal protein L1. The apparent mitochondrial L1 is sufficiently diverged to be the subject of a separate model. [Protein synthesis, Ribosomal proteins: synthesis and modification] 227 matched cddid_all.tbl CDD TIGR01170 TIGR01170 273480 rplA_mito ribosomal protein uL1, mitochondrial. This model represents the mitochondrial homolog of bacterial ribosomal protein L1. Unlike chloroplast L1, this form was not sufficiently similar to bacterial forms to include in a single bacterial/organellar L1 model. [Protein synthesis, Ribosomal proteins: synthesis and modification] 141 matched cddid_all.tbl CDD TIGR01171 TIGR01171 273481 rplB_bact ribosomal protein L2, bacterial/organellar. This model distinguishes bacterial and organellar ribosomal protein L2 from its counterparts in the archaea nad in the eukaryotic cytosol. Plant mitochondrial examples tend to have long, variable inserts. [Protein synthesis, Ribosomal proteins: synthesis and modification] 273 matched cddid_all.tbl CDD TIGR01172 TIGR01172 200082 cysE serine O-acetyltransferase. Cysteine biosynthesis [Amino acid biosynthesis, Serine family] 162 matched cddid_all.tbl CDD TIGR01173 TIGR01173 273482 glmU UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase. This protein is a bifunctional enzyme, GlmU, which catalyzes last two reactions in the four-step pathway of UDP-N-acetylglucosamine biosynthesis from fructose-6-phosphate. Its reaction product is required from peptidoglycan biosynthesis, LPS biosynthesis in species with LPS, and certain other processes. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan, Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides, Central intermediary metabolism, Amino sugars] 451 matched cddid_all.tbl CDD TIGR01174 TIGR01174 273483 ftsA cell division protein FtsA. This bacterial cell division protein interacts with FtsZ, the bacterial homolog of tubulin. It is an ATP-binding protein and shows structural similarities to actin and heat shock cognate protein 70. [Cellular processes, Cell division] 371 matched cddid_all.tbl CDD TIGR01175 TIGR01175 273484 pilM type IV pilus assembly protein PilM. This protein is required for the assembly of the type IV fimbria in Pseudomonas aeruginosa responsible for twitching motility, and for a similar pilus-like structure in Synechocystis. It is also found in species such as Deinococcus described as having natural transformation (for which a type IV pilus-like structure is proposed) but not fimbria. 348 matched cddid_all.tbl CDD TIGR01176 TIGR01176 273485 fum_red_Fp fumarate reductase (quinol), flavoprotein subunit. The terms succinate dehydrogenase and fumarate reductase may be used interchangeably in certain systems. However, a number of species have distinct complexes, with the fumarate reductase active under anaerobic conditions. This model represents the fumarate reductase flavoprotein subunit from several such species in which a distinct succinate dehydrogenase is also found. Not all bona fide fumarate reductases will be found by this model. 580 matched cddid_all.tbl CDD TIGR01177 TIGR01177 273486 TIGR01177 putative methyltransferase, TIGR01177 family. This family of probable methyltransferases is found exclusively in the Archaea. [Hypothetical proteins, Conserved] 329 matched cddid_all.tbl CDD TIGR01178 TIGR01178 130246 ade adenine deaminase. The family described by this model includes an experimentally characterized adenine deaminase of Bacillus subtilis. It also include a member from Methanobacterium thermoautotrophicum, in which adenine deaminase activity has been detected. [Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides] 552 matched cddid_all.tbl CDD TIGR01179 TIGR01179 273487 galE UDP-glucose-4-epimerase GalE. Alternate name: UDPgalactose 4-epimerase This enzyme interconverts UDP-glucose and UDP-galactose. A set of related proteins, some of which are tentatively identified as UDP-glucose-4-epimerase in Thermotoga maritima, Bacillus halodurans, and several archaea, but deeply branched from this set and lacking experimental evidence, are excluded from this model and described by a separate model. [Energy metabolism, Sugars] 328 matched cddid_all.tbl CDD TIGR01180 TIGR01180 273488 aman2_put alpha-1,2-mannosidase, putative. The identification of members of this family as putative alpha-1,2-mannosidases is based on an unpublished characterization of the aman2 gene in Bacillus sp. M-90 by Maruyama,Y., Nakajima,M. and Nakajima,T. (Genbank accession BAA76709, pid g4587313). Most members of this family appear to have signal sequences. Members from the dental pathogen Porphyromonas gingivalis have been described as immunoreactive with periodontitis patient serum. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 750 matched cddid_all.tbl CDD TIGR01181 TIGR01181 273489 dTDP_gluc_dehyt dTDP-glucose 4,6-dehydratase. This protein is related to UDP-glucose 4-epimerase (GalE) and likewise has an NAD cofactor. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 317 matched cddid_all.tbl CDD TIGR01182 TIGR01182 273490 eda Entner-Doudoroff aldolase. 2-deydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) is an enzyme of the Entner-Doudoroff pathway. This aldolase has another function, 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) shown experimentally in Escherichia coli and Pseudomonas putida [Amino acid biosynthesis, Glutamate family, Energy metabolism, Entner-Doudoroff] 204 matched cddid_all.tbl CDD TIGR01183 TIGR01183 130251 ntrB nitrate ABC transporter, permease protein. This model describes the nitrate transport permease in bacteria. This is gene product of ntrB. The nitrate transport permease is the integral membrane component of the nitrate transport system and belongs to the ATP-binding cassette (ABC) superfamily. At least in photosynthetic bacteria nitrate assimilation is aided by other proteins derived from the operon which among others include products of ntrA, ntrB, ntrC, ntrD, narB. Functionally ntrC and ntrD resemble the ATP binding components of the binding protein-dependent transport systems. Mutational studies have shown that ntrB and ntrC are mandatory for nitrate accumulation. Nitrate reductase is encoded by narB. [Transport and binding proteins, Anions] 202 matched cddid_all.tbl CDD TIGR01184 TIGR01184 130252 ntrCD nitrate transport ATP-binding subunits C and D. This model describes the ATP binding subunits of nitrate transport in bacteria and archaea. This protein belongs to the ATP-binding cassette (ABC) superfamily. It is thought that the two subunits encoded by ntrC and ntrD form the binding surface for interaction with ATP. This model is restricted in identifying ATP binding subunit associated with the nitrate transport. Nitrate assimilation is aided by other proteins derived from the operon which among others include products of ntrA - a regulatory protein; ntrB - a hydropbobic transmembrane permease and narB - a reductase. [Transport and binding proteins, Anions, Transport and binding proteins, Other] 230 matched cddid_all.tbl CDD TIGR01185 TIGR01185 130253 devC DevC protein. This model describes a predicted membrane subunit, DevC, of an ABC transporter known so far from two species of cyanobacteria. Some experimental data from mutational analysis suggest that this protein along with DevA and DevB encoded in the same operon may be involved in the transport/export of glycolipids. [Transport and binding proteins, Other] 380 matched cddid_all.tbl CDD TIGR01186 TIGR01186 130254 proV glycine betaine/L-proline transport ATP binding subunit. This model describes the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. Functionally, this transport system is involved in osmoregulation. Under conditions of stress, the organism recruits these transport system to accumulate glycine betaine and other solutes which offer osmo-protection. It has been demonstrated that glycine betaine uptake is accompanied by symport with sodium ions. The locus has been named variously as proU or opuA. A gene library from L.lactis functionally complements an E.coli proU mutant. The comlementing locus is similar to a opuA locus in B.sutlis. This clarifies the differences in nomenclature. [Transport and binding proteins, Amino acids, peptides and amines] 363 matched cddid_all.tbl CDD TIGR01187 TIGR01187 162242 potA spermidine/putrescine ABC transporter ATP-binding subunit. This model describes spermidine/putrescine ABC transporter, ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. Polyamines like spermidine and putrescine play vital role in cell proliferation, differentiation, and ion homeostasis. The concentration of polyamines within the cell are regulated by biosynthesis, degradation and transport (uptake and efflux included). [Transport and binding proteins, Amino acids, peptides and amines] 325 matched cddid_all.tbl CDD TIGR01188 TIGR01188 130256 drrA daunorubicin resistance ABC transporter ATP-binding subunit. This model describes daunorubicin resistance ABC transporter, ATP binding subunit in bacteria and archaea. This model is restricted in its scope to preferentially recognize the ATP binding subunit associated with effux of the drug, daunorubicin. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. In eukaryotes proteins of similar function include p-gyco proteins, multidrug resistance protein etc. [Transport and binding proteins, Other] 302 matched cddid_all.tbl CDD TIGR01189 TIGR01189 273491 ccmA heme ABC exporter, ATP-binding protein CcmA. This model describes the cyt c biogenesis protein encoded by ccmA in bacteria. An exception is, an arabidopsis protein. Quite likely this is encoded by an organelle. Bacterial c-type cytocromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This cluster includes genes: ccmA;B;C;D;E;F;G and H. The posttranslational pathway includes the transport of heme moiety, the secretion of the apoprotein and the covalent attachment of the heme with the apoprotein. The proteins ccmA and B represent an ABC transporter; ccmC and D participate in heme transfer to ccmE, which function as a periplasmic heme chaperone. The presence of ccmF, G and H is suggested to be obligatory for the final functional assembly of cytochrome c. [Protein fate, Protein and peptide secretion and trafficking, Transport and binding proteins, Other] 198 matched cddid_all.tbl CDD TIGR01190 TIGR01190 200083 ccmB heme exporter protein CcmB. This model describes the cyt c biogenesis protein encoded by ccmB in bacteria. Bacterial c-type cytochromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This cluster includes genes: ccmA;B;C;D;E;F;G and H. The posttranslational pathway includes the transport of heme moiety, the secretion of the apoprotein and the covalent attachment of the heme with the apoprotein. The proteins ccmA and B represent an ABC transporter; ccmC and D participate in heme transfer to ccmE, which function as a periplasmic heme chaperone. The presence of ccmF, G and H is suggested to be obligatory for the final functional assembly of cytochrome C. [Protein fate, Protein and peptide secretion and trafficking, Transport and binding proteins, Other] 211 matched cddid_all.tbl CDD TIGR01191 TIGR01191 273492 ccmC heme exporter protein CcmC. This model describes the cyt c biogenesis protein encoded by ccmC in bacteria. It must be noted an arabidopsis, a tritcum and a piscum plant proteins were recognizable in the clade. Quite likely they are of organellar origin. Bacterial c-type cytocromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This cluster includes genes, ccmA;B;C;D;E;F;G and H. The posttranslational pathway includes the transport of heme moiety, the secretion of the apoprotein and the covalent attachment of the heme with the apoprotein. The proteins ccmA and B represent an ABC transporter; ccmC and D participate in the heme transfer to ccmE, which function as a periplasmic heme chaperone. The presence of ccmF, G and H is suggested to be obligatory for the final functional assembly of cytochrome c. [Protein fate, Protein and peptide secretion and trafficking, Transport and binding proteins, Other] 184 matched cddid_all.tbl CDD TIGR01192 TIGR01192 130260 chvA glucan exporter ATP-binding protein. This model describes glucan exporter ATP binding protein in bacteria. It belongs to the larger ABC transporter superfamily with the characteristic ATP binding motif. The In general, this protein is in some ways implicated in osmoregulation and suggested to participate in the export of glucan from the cytoplasm to periplasm. The cyclic beta-1,2-glucan in the bactrerial periplasmic space is suggested to confer the property of high osmolority. It has also been demonstrated that mutants in this loci have lost functions of virulence and motility. It is unclear as to how virulence and osmoadaptaion are related. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 585 matched cddid_all.tbl CDD TIGR01193 TIGR01193 130261 bacteriocin_ABC ABC-type bacteriocin transporter. This model describes ABC-type bacteriocin transporter. The amino terminal domain (pfam03412) processes the N-terminal leader peptide from the bacteriocin while C-terminal domains resemble ABC transporter membrane protein and ATP-binding cassette domain. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are usually encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc. [Protein fate, Protein and peptide secretion and trafficking, Protein fate, Protein modification and repair, Transport and binding proteins, Other] 708 matched cddid_all.tbl CDD TIGR01194 TIGR01194 130262 cyc_pep_trnsptr cyclic peptide transporter. This model describes cyclic peptide transporter in bacteria. Bacteria have elaborate pathways for the production of toxins and secondary metabolites. Many such compounds, including syringomycin and pyoverdine are synthesized on non-ribosomal templates consisting of a multienzyme complex. On several occasions the proteins of the complex and transporter protein are present on the same operon. Often times these compounds cross the biological membrane by specific transporters. Syringomycin is an amphipathic, cylclic lipodepsipeptide when inserted into host causes formation of channels, permeable to variety of cations. On the other hand, pyoverdine is a cyclic octa-peptidyl dihydroxyquinoline, which is efficient in sequestering iron for uptake. [Transport and binding proteins, Amino acids, peptides and amines, Transport and binding proteins, Other] 555 matched cddid_all.tbl CDD TIGR01195 TIGR01195 273493 oadG_fam sodium pump decarboxylases, gamma subunit. This model finds the subfamily of distantly related, low complexity, hydrophobic small subunits of several related sodium ion-pumping decarboxylases. These include oxaloacetate decarboxylase gamma subunit and methylmalonyl-CoA decarboxylase delta subunit. Most sequences scoring between the noise and trusted cutoffs are eukaryotic sodium channel proteins. 82 matched cddid_all.tbl CDD TIGR01196 TIGR01196 130264 edd 6-phosphogluconate dehydratase. A close homolog, designated MocB (mannityl opine catabolism), is found in a mannopine catabolism region of a plasmid of Agrobacterium tumefaciens. However, it is not essential for mannopine catabolism, branches within the cluster of 6-phosphogluconate dehydratases (with a short branch length) in a tree rooted by the presence of other dehydyatases. It may represent an authentic 6-phosphogluconate dehydratase, redundant with the chromosomal copy shown to exist in plasmid-cured strains. This model includes mocB above the trusted cutoff, although the designation is somewhat tenuous. [Energy metabolism, Entner-Doudoroff] 601 matched cddid_all.tbl CDD TIGR01197 TIGR01197 162246 nramp NRAMP (natural resistance-associated macrophage protein) metal ion transporters. This model describes the Nramp metal ion transporter family. Historically, in mammals these proteins have been functionally characterized as proteins involved in the host pathogen resistance, hence the name - NRAMP. At least two isoforms Nramp1 and Nramp2 have been identified. However the exact mechanism of pathogen resistance was unclear, until it was demonstrated by expression cloning and electrophysiological techniques that this protein was a metal ion transporter. It was also independently demonstrated that a microcytic anemia (mk) locus in mouse, encodes a metal ion transporter (DCT1 or Nramp2). The transporter has a broad range of substrate specificity that include Fe+2, Zn+2, Mn+2, Co+2, Cd+2, Cu+2, Ni+2 and Pb+2. The uptake of these metal ions is coupled to proton symport. Metal ions are essential cofactors in a number of biological process including, oxidative phosphorylation, gene regulation and metal ion homeostasis. Nramp1 could confer resistance to infection in one of the two ways. (1) The uptake of Fe+2 can produce toxic hydroxyl radicals via Fenton reaction killing the pathogens in phagosomes or (2) Deplete the metal ion pools in the phagosome and deprive the pathogens of metal ions, which is critical for its survival. [Transport and binding proteins, Cations and iron carrying compounds] 390 matched cddid_all.tbl CDD TIGR01198 TIGR01198 273494 pgl 6-phosphogluconolactonase. This enzyme of the pentose phosphate pathway is often found as a part of a multifunctional protein with [Energy metabolism, Pentose phosphate pathway] 233 matched cddid_all.tbl CDD TIGR01200 TIGR01200 273495 GLPGLI GLPGLI family protein. This protein family was first noted as a paralogous set in Porphyromonas gingivalis, but it is more widely distributed among the Bacteroidetes. The protein family is now renamed GLPGLI after its best-conserved motif. 226 matched cddid_all.tbl CDD TIGR01201 TIGR01201 273496 HU_rel DNA-binding protein, histone-like, putative. This model describes a set of proteins related to but longer than DNA-binding protein HU. Its distinctive domain architecture compared to HU and related histone-like DNA-binding proteins justifies the designation as superfamily. Members include, so far, one from Bacteroides fragilis, a gut bacterium, and ten from Porphyromonas gingivalis, an oral anaerobe. [DNA metabolism, Chromosome-associated proteins] 145 matched cddid_all.tbl CDD TIGR01202 TIGR01202 130269 bchC 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A dehydrogenase. [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll] 308 matched cddid_all.tbl CDD TIGR01203 TIGR01203 273497 HGPRTase hypoxanthine phosphoribosyltransferase. Alternate name: hypoxanthine-guanine phosphoribosyltransferase. Sequence differences as small as a single residue can affect whether members of this family act on hypoxanthine and guanine or hypoxanthine only. The designation of this model as equivalog reflects hypoxanthine specificity and does not reflect whether or not guanine can replace hypoxanthine. [Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides] 166 matched cddid_all.tbl CDD TIGR01204 TIGR01204 130271 bioW 6-carboxyhexanoate--CoA ligase. Alternate name: pimeloyl-CoA synthase. [Biosynthesis of cofactors, prosthetic groups, and carriers, Biotin] 232 matched cddid_all.tbl CDD TIGR01205 TIGR01205 273498 D_ala_D_alaTIGR D-alanine--D-alanine ligase. This model describes D-Ala--D-Ala ligase, an enzyme that makes a required precursor of the bacterial cell wall. It also describes some closely related proteins responsible for resistance to glycopeptide antibiotics such as vancomycin. The mechanism of glyopeptide antibiotic resistance involves the production of D-alanine-D-lactate (VanA and VanB families) or D-alanine-D-serine (VanC). The seed alignment contains only chromosomally encoded D-ala--D-ala ligases, but a number of antibiotic resistance proteins score above the trusted cutoff of this model. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 315 matched cddid_all.tbl CDD TIGR01206 TIGR01206 273499 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway. [Amino acid biosynthesis, Aspartate family] 54 matched cddid_all.tbl CDD TIGR01207 TIGR01207 130274 rmlA glucose-1-phosphate thymidylyltransferase, short form. Alternate name: dTDP-D-glucose synthase homotetramer This model describes a tightly conserved but broadly distributed subfamily (here designated as short form) of known and putative bacterial glucose-1-phosphate thymidylyltransferases. It is well characterized in several species as the first of four enzymes involved in the biosynthesis of dTDP-L-rhamnose, a cell wall constituent and a feedback inhibitor of the enzyme. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 286 matched cddid_all.tbl CDD TIGR01208 TIGR01208 273500 rmlA_long glucose-1-phosphate thymidylylransferase, long form. The family of known and putative glucose-1-phosphate thymidyltransferase (also called dTDP-glucose synthase) shows a deep split into a short form (see TIGR01207) and a long form described by this model. The homotetrameric short form is found in numerous bacterial species that incorporate dTDP-L-rhamnose, which it helps synthesize, into the cell wall. It is subject to feedback inhibition. This form, in contrast, is found in many species for which it serves as a sugar-activating enzyme for antibiotic biosynthesis and or other, unknown pathways, and in which dTDP-L-rhamnose is not necessarily produced. Alternate name: dTDP-D-glucose synthase 353 matched cddid_all.tbl CDD TIGR01209 TIGR01209 273501 TIGR01209 RNA ligase, Pab1020 family. Members of this family are found, so far, in a single copy per genome and largely in thermophiles, of which only Aquifex aeolicus is bacterial rather than archaeal. PSI-BLAST converges after a single iteration to the whole of this family and reveals no convincing similarity to any other protein. The member protein Pab1020 has been characterized as an RNA ligase with circularization activity. [Transcription, RNA processing] 374 matched cddid_all.tbl CDD TIGR01210 TIGR01210 273502 TIGR01210 radical SAM enzyme, TIGR01210 family. This family of exclusively archaeal radical SAM enzymes has no characterized close homologs. [Hypothetical proteins, Conserved] 313 matched cddid_all.tbl CDD TIGR01211 TIGR01211 273503 ELP3 radical SAM enzyme/protein acetyltransferase, ELP3 family. This family includes elongator complex protein 3 (ELP3) from eukaryotes and related proteins from other lineages. ELP3 is a component of the RNA polymerase II holoenzyme. It has an N-terminal radical SAM domain and C-terminal GNAT acetyltransferase domain. Members of this family are found in eukaryotes, archaea, and a few bacteria (e.g. Atopobium sp). The activity discovered first was an acetyltransferase modification at the N-termini of all four core histones, shown in vitro in eukaryotes. More recently, the radical SAM domain was shown to play a role in zygotic paternal genome demethylation. Family TIGR01212, widespread in prokaryotes, lacks the GNAT acetyltransferase domain but shares extensive sequence similarity with this family (TIGR01211). [Transcription, DNA-dependent RNA polymerase] 522 matched cddid_all.tbl CDD TIGR01212 TIGR01212 130279 TIGR01212 radical SAM protein, TIGR01212 family. Members of this family are apparent radical-SAM enzymes, related to the N-terminal region of the bifunctional ELP3, whose C-terminal region is part of the elongator complex and appears to acetylate histones and other proteins. ELP3 binds S-adenosylmethionine (SAM) and was recently shown to be involved in a DNA demethylation process in eukaryotes. Close sequence similarity of this family (with lacks the GNAT family acetyltransferase domain) to the ELP3 N-terminal region and a strong match to the pfam04055 support identification of this family as radical SAM despite the atypical spacing between first and second Cys residues in the 4Fe4S-binding motif. [Unknown function, Enzymes of unknown specificity] 302 matched cddid_all.tbl CDD TIGR01213 TIGR01213 273504 pseudo_Pus10arc tRNA pseudouridine(54/55) synthase. Members of this family show twilight-zone similarity to several predicted RNA pseudouridine synthases. All trusted members of this family are archaeal. Several eukaryotic homologs lack N-terminal homology including two CXXC motifs. [Hypothetical proteins, Conserved] 388 matched cddid_all.tbl CDD TIGR01214 TIGR01214 273505 rmlD dTDP-4-dehydrorhamnose reductase. This enzyme catalyzes the last of 4 steps in making dTDP-rhamnose, a precursor of LPS core antigen, O-antigen, etc. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 287 matched cddid_all.tbl CDD TIGR01215 TIGR01215 188120 minE cell division topological specificity factor MinE. This protein is involved in the process of cell division. This protein prevents the proteins MinC and MinD to inhibit cell division at internal sites, but allows inhibiton at polar sites. This allows for correct cell division at the proper sites. [Cellular processes, Cell division] 81 matched cddid_all.tbl CDD TIGR01216 TIGR01216 273506 ATP_synt_epsi ATP synthase, F1 epsilon subunit (delta in mitochondria). This model describes one of the five types of subunits in the F1 part of F1/F0 ATP synthases. Members of this family are designated epsilon in bacterial and chloroplast systems but designated delta in mitochondria, where the counterpart of the bacterial delta subunit is designated OSCP. In a few cases (Propionigenium modestum, Acetobacterium woodii) scoring above the trusted cutoff and designated here as exceptions, Na+ replaces H+ for translocation. [Energy metabolism, ATP-proton motive force interconversion] 130 matched cddid_all.tbl CDD TIGR01217 TIGR01217 273507 ac_ac_CoA_syn acetoacetyl-CoA synthase. This enzyme catalyzes the first step of the mevalonate pathway of IPP biosynthesis. Most bacteria do not use this pathway, but rather the deoxyxylulose pathway. [Central intermediary metabolism, Other] 652 matched cddid_all.tbl CDD TIGR01218 TIGR01218 273508 Gpos_tandem_5TM tandem five-transmembrane protein. Members of this family of proteins, with average length of 210, have no invariant residues but five predicted transmembrane segments. Strangely, most members occur in groups of consecutive paralogous genes. A striking example is a set of eleven encoded consecutively, head-to-tail, in Staphylococcus aureus strain COL. 207 matched cddid_all.tbl CDD TIGR01219 TIGR01219 273509 Pmev_kin_ERG8 phosphomevalonate kinase, ERG8-type, eukaryotic branch. This enzyme is part of the mevalonate pathway, one of two alternative pathways for the biosynthesis of IPP. In an example of nonorthologous gene displacement, two different types of phosphomevalonate kinase are found - the animal type and this ERG8 type. This model represents plant and fungal forms of the ERG8 type of phosphomevalonate kinase. [Central intermediary metabolism, Other] 454 matched cddid_all.tbl CDD TIGR01220 TIGR01220 130287 Pmev_kin_Gr_pos phosphomevalonate kinase, ERG8-type, Gram-positive branch. This enzyme is part of the mevalonate pathway, one of two alternative pathways for the biosynthesis of IPP. In an example of nonorthologous gene displacement, two different types of phosphomevalonate kinase are found - the animal type and this ERG8 type. This model represents the low GC Gram-positive organism forms of the ERG8 type of phosphomevalonate kinase. [Central intermediary metabolism, Other] 358 matched cddid_all.tbl CDD TIGR01221 TIGR01221 273510 rmlC dTDP-4-dehydrorhamnose 3,5-epimerase. This enzyme participates in the biosynthesis of dTDP-L-rhamnose, often as a precursor to LPS O-antigen [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 176 matched cddid_all.tbl CDD TIGR01222 TIGR01222 273511 minC septum site-determining protein MinC. The minC protein assists in correct placement of the septum for cell division by inhibiting septum formation at other sites. Homologs from Deinocoocus, Synechocystis PCC 6803, and Helicobacter pylori do not hit the full length of the model and score between the trusted and noise cutoffs. [Cellular processes, Cell division] 217 matched cddid_all.tbl CDD TIGR01223 TIGR01223 130290 Pmev_kin_anim phosphomevalonate kinase, animal type. This enzyme is part of the mevalonate pathway, one of two alternative pathways for the biosynthesis of IPP. In an example of nonorthologous gene displacement, two different types of phosphomevalonate kinase are found. One is this type, found in animals. The other is the ERG8 type, found in plants and fungi (TIGR01219) and in Gram-positive bacteria (TIGR01220). [Central intermediary metabolism, Other] 182 matched cddid_all.tbl CDD TIGR01224 TIGR01224 273512 hutI imidazolonepropionase. This enzyme catalyzes the third step in histidine degradation. [Energy metabolism, Amino acids and amines] 377 matched cddid_all.tbl CDD TIGR01225 TIGR01225 200086 hutH histidine ammonia-lyase. This enzyme deaminates histidine to urocanic acid, the first step in histidine degradation. It is closely related to phenylalanine ammonia-lyase. [Energy metabolism, Amino acids and amines] 506 matched cddid_all.tbl CDD TIGR01226 TIGR01226 130293 phe_am_lyase phenylalanine ammonia-lyase. Members of this subfamily of MIO prosthetic group enzymes are phenylalanine ammonia-lyases. They are found, so far, in plants and fungi. From phenylalanine, this enzyme yields cinnaminic acid, a precursor of many important plant compounds. This protein shows extensive homology to histidine ammonia-lyase, the first enzyme of a histidine degradation pathway. Note that members of this family from plant species that synthesize taxol are actually phenylalanine aminomutase, and are covered by exception model TIGR04473. 680 matched cddid_all.tbl CDD TIGR01227 TIGR01227 273513 hutG formimidoylglutamase. Formiminoglutamase, the fourth enzyme of histidine degradation, is similar to arginases and agmatinases. It is often encoded near other enzymes of the histidine degredation pathway: histidine ammonia-lyase, urocanate hydratase, and imidazolonepropionase. [Energy metabolism, Amino acids and amines] 307 matched cddid_all.tbl CDD TIGR01228 TIGR01228 130295 hutU urocanate hydratase. This model represents the second of four enzymes involved in the degradation of histidine to glutamate. [Energy metabolism, Amino acids and amines] 545 matched cddid_all.tbl CDD TIGR01229 TIGR01229 162262 rocF_arginase arginase. This model helps resolve arginases from known and putative agmatinases, formiminoglutamases, and other related proteins of unknown specifity. The pathway from arginine to the polyamine putrescine may procede by hydrolysis to remove urea (arginase) followed by decarboxylation (ornithine decarboxylase), or by decarboxylation first (arginine decarboxylase) followed by removal of urea (agmatinase). 300 matched cddid_all.tbl CDD TIGR01230 TIGR01230 273514 agmatinase agmatinase. Members of this family include known and predicted examples of agmatinase (agmatine ureohydrolase). The seed includes members of archaea, for which no definitive agmatinase sequence has yet been made available. However, archaeal sequences are phylogenetically close to the experimentally verified B. subtilis sequence. One species of Halobacterium has been demonstrated in vitro to produce agmatine from arginine, but no putrescine from ornithine, suggesting that arginine decarboxylase and agmatinase, rather than arginase and ornithine decarboxylase, lead from Arg to polyamine biosynthesis. Note: a history of early misannotation of members of this family is detailed in PUBMED:10931887. 275 matched cddid_all.tbl CDD TIGR01231 TIGR01231 273515 lacC tagatose-6-phosphate kinase. This enzyme is part of the tagatose-6-phosphate pathway of lactose degradation. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 310 matched cddid_all.tbl CDD TIGR01232 TIGR01232 130299 lacD tagatose 1,6-diphosphate aldolase. This family consists of Gram-positive proteins. Tagatose 1,6-diphosphate aldolase is part of the tagatose-6-phosphate pathway of galactose-6-phosphate degradation. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 325 matched cddid_all.tbl CDD TIGR01233 TIGR01233 273516 lacG 6-phospho-beta-galactosidase. This enzyme is part of the tagatose-6-phosphate pathway of galactose-6-phosphate degradation. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 467 matched cddid_all.tbl CDD TIGR01234 TIGR01234 130301 L-ribulokinase ribulokinase. This enzyme catalyzes the second step in arabinose catabolism. The most closely related protein subfamily outside the scope of this model includes ribitol kinase from E. coli. [Energy metabolism, Sugars] 536 matched cddid_all.tbl CDD TIGR01235 TIGR01235 130302 pyruv_carbox pyruvate carboxylase. This enzyme plays a role in gluconeogensis but not glycolysis. [Energy metabolism, Glycolysis/gluconeogenesis] 1143 matched cddid_all.tbl CDD TIGR01236 TIGR01236 273517 D1pyr5carbox1 delta-1-pyrroline-5-carboxylate dehydrogenase, group 1. This model represents one of two related branches of delta-1-pyrroline-5-carboxylate dehydrogenase. The two branches are not as closely related to each other as some aldehyde dehydrogenases are to this branch, and separate models are built for this reason. The enzyme is the second of two in the degradation of proline to glutamate. [Energy metabolism, Amino acids and amines] 532 matched cddid_all.tbl CDD TIGR01237 TIGR01237 200087 D1pyr5carbox2 delta-1-pyrroline-5-carboxylate dehydrogenase, group 2, putative. This enzyme is the second of two in the degradation of proline to glutamate. This model represents one of several related branches of delta-1-pyrroline-5-carboxylate dehydrogenase. Members of this branch may be associated with proline dehydrogenase (the other enzyme of the pathway from proline to glutamate) but have not been demonstrated experimentally. The branches are not as closely related to each other as some distinct aldehyde dehydrogenases are to some; separate models were built to let each model describe a set of equivalogs. [Energy metabolism, Amino acids and amines] 511 matched cddid_all.tbl CDD TIGR01238 TIGR01238 273518 D1pyr5carbox3 delta-1-pyrroline-5-carboxylate dehydrogenase (PutA C-terminal domain). This model represents one of several related branches of delta-1-pyrroline-5-carboxylate dehydrogenase. Members of this branch are the C-terminal domain of the PutA bifunctional proline dehydrogenase / delta-1-pyrroline-5-carboxylate dehydrogenase. [Energy metabolism, Amino acids and amines] 500 matched cddid_all.tbl CDD TIGR01239 TIGR01239 273519 galT_2 galactose-1-phosphate uridylyltransferase, family 2. This enzyme is involved in glucose and galactose interconversion. This model describes one of two extremely distantly related branches of the model pfam01087 from Pfam. [Energy metabolism, Sugars] 489 matched cddid_all.tbl CDD TIGR01240 TIGR01240 130307 mevDPdecarb diphosphomevalonate decarboxylase. This enzyme catalyzes the last step in the synthesis of isopentenyl diphosphate (IPP) in the mevalonate pathway. Alternate names: mevalonate diphosphate decarboxylase; pyrophosphomevalonate decarboxylase [Central intermediary metabolism, Other] 305 matched cddid_all.tbl CDD TIGR01241 TIGR01241 273520 FtsH_fam ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH. [Cellular processes, Cell division, Protein fate, Degradation of proteins, peptides, and glycopeptides] 495 matched cddid_all.tbl CDD TIGR01242 TIGR01242 130309 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal 364 matched cddid_all.tbl CDD TIGR01243 TIGR01243 273521 CDC48 AAA family ATPase, CDC48 subfamily. This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus. 733 matched cddid_all.tbl CDD TIGR01244 TIGR01244 130311 TIGR01244 TIGR01244 family protein. No member of this family is characterized. The member from Xylella fastidiosa is a longer protein with an N-terminal region described by this model, followed by a metallo-beta-lactamase family domain and an additional C-terminal region. Members scoring above the trusted cutoff are limited to the proteobacteria. [Hypothetical proteins, Conserved] 135 matched cddid_all.tbl CDD TIGR01245 TIGR01245 273522 trpD anthranilate phosphoribosyltransferase. In many widely different species, including E. coli, Thermotoga maritima, and Archaeoglobus fulgidus, this enzymatic domain (anthranilate phosphoribosyltransferase) is found C-terminal to glutamine amidotransferase; the fusion protein is designated anthranilate synthase component II (EC 4.1.3.27) [Amino acid biosynthesis, Aromatic amino acid family] 330 matched cddid_all.tbl CDD TIGR01246 TIGR01246 162269 dapE_proteo succinyl-diaminopimelate desuccinylase, proteobacterial clade. This model describes a proteobacterial subset of succinyl-diaminopimelate desuccinylases. An experimentally confirmed Gram-positive lineage succinyl-diaminopimelate desuccinylase has been described for Corynebacterium glutamicum (SP:Q59284), and a neighbor-joining tree shows the seed members, SP:Q59284, and putative archaeal members such as TrEMBL:O58003 in a single clade. However, the archaeal members differ substantially, share a number of motifs with acetylornithine deacetylases rather than succinyl-diaminopimelate desuccinylases, and are not taken as trusted examples of succinyl-diaminopimelate desuccinylases. This model is limited to proteobacterial members for this reason. [Amino acid biosynthesis, Aspartate family] 370 matched cddid_all.tbl CDD TIGR01247 TIGR01247 130314 drrB daunorubicin resistance ABC transporter membrane protein. This model describes daunorubicin resistance ABC transporter, membrane associated protein in bacteria and archaea. The protein associated with effux of the drug, daunorubicin. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. In eukaryotes proteins of similar function include p-gyco proteins, multidrug resistance protein etc. [Transport and binding proteins, Other] 236 matched cddid_all.tbl CDD TIGR01248 TIGR01248 130315 drrC daunorubicin resistance protein C. The model describes daunorubicin resistance protein C in bacteria. This protein confers the function of daunorubicin resistance. The protein seems to share strong sequence similarity to UvrA proteins, which are involved in excision repair of DNA. Disruption of drrC gene showed increased sensitivity upon exposure to duanorubicin. However it failed to complement uvrA mutants to exposure to UV irradiation. The mechanism on how it confers duanomycin resistance is unclear, but has been suggested to be different from DrrA and DrrB which are antiporters. [Unclassified, Role category not yet assigned] 152 matched cddid_all.tbl CDD TIGR01249 TIGR01249 130316 pro_imino_pep_1 proline iminopeptidase, Neisseria-type subfamily. This model represents one of two related families of proline iminopeptidase in the alpha/beta fold hydrolase family. The fine specificities of the various members, including both the range of short peptides from which proline can be removed and whether other amino acids such as alanine can be also removed, may vary among members. 306 matched cddid_all.tbl CDD TIGR01250 TIGR01250 188121 pro_imino_pep_2 proline-specific peptidase, Bacillus coagulans-type subfamily. This model describes a subfamily of the alpha/beta fold family of hydrolases. Characterized members include prolinases (Pro-Xaa dipeptidase, EC 3.4.13.8), prolyl aminopeptidases (EC 3.4.11.5), and a leucyl aminopeptidase 289 matched cddid_all.tbl CDD TIGR01251 TIGR01251 273523 ribP_PPkin ribose-phosphate pyrophosphokinase. Alternate name: phosphoribosylpyrophosphate synthetase In some systems, close homologs lacking enzymatic activity exist and perform regulatory functions. The model is designated subfamily rather than equivalog for this reason. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 308 matched cddid_all.tbl CDD TIGR01252 TIGR01252 273524 acetolac_decarb alpha-acetolactate decarboxylase. Puruvate can be fermented to 2,3-butanediol. It is first converted to alpha-acetolactate by alpha-acetolactate synthase, then decarboxylated to acetoin by this enzyme. Acetoin can be reduced in some species to 2,3-butanediol by acetoin reductase. [Energy metabolism, Fermentation] 232 matched cddid_all.tbl CDD TIGR01253 TIGR01253 130320 thiP thiamine ABC transporter, permease protein. The model describes thiamine ABC transporter, permease protein in bacteria. The protein belongs to the larger ABC transport system. It consists of atleast three components: the inner mebrane permease; thiamine binding protein; an ATP-binding subunit. It has been experimentally demonstrated that the mutants in the various steps in the de novo synthesis of the thiamine and the biologically active form, namely thiamine pyrophosphate can be exogenously supplemented with thiamine, thiamine monophosphate (TMP) or thiamine pyrophosphate (TPP). [Transport and binding proteins, Other] 519 matched cddid_all.tbl CDD TIGR01254 TIGR01254 130321 sfuA ABC transporter periplasmic binding protein, thiB subfamily. The model describes thiamine ABC transporter, periplasmic protein in bacteria and archae. The protein belongs to the larger ABC transport system. It consists of at least three components: the thiamine binding periplasmic protein; an inner membrane permease; an ATP-binding subunit. It has been experimentally demonstrated that the mutants in the various steps in the de novo synthesis of the thiamine and the biologically active form, namely thiamine pyrophosphate can be exogenously supplemented with thiamine, thiamine monophosphate (TMP) or thiamine pyrophosphate (TPP). [Transport and binding proteins, Other] 304 matched cddid_all.tbl CDD TIGR01255 TIGR01255 273525 pyr_form_ly_1 formate acetyltransferase 1. Alternate names: pyruvate formate-lyase; formate C-acetyltransferase This enzyme converts formate + acetyl-CoA into pyruvate + CoA. This model describes formate acetyltransferase 1. More distantly related putative formate acetyltransferases have also been identified, including formate acetyltransferase 2 from E. coli, which is excluded from this model. [Energy metabolism, Fermentation] 744 matched cddid_all.tbl CDD TIGR01256 TIGR01256 273526 modA molybdenum ABC transporter, periplasmic molybdate-binding protein. The model describes the molybdate ABC transporter periplasmic binding protein in bacteria and archae. Several of the periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. It has been shown experimentally by radioactive labeling that ModA represent hydrophylioc periplasmic-binding protein in gram-negative organisms and its counterpart in gram-positive organisms is a lipoprotein. The other components of the system include the ModB, an integral membrane protein and ModC the ATP-binding subunit. Invariably almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains. [Transport and binding proteins, Anions] 216 matched cddid_all.tbl CDD TIGR01257 TIGR01257 130324 rim_protein retinal-specific rim ABC transporter. This model describes the photoreceptor protein (rim protein) in eukaryotes. It is the member of ABC transporter superfamily. Rim protein is a membrane glycoprotein which is localized in the photoreceptor outer segment discs. Mutation/s in its genetic loci is implicated in the recessive Stargardt's disease. [Transport and binding proteins, Other] 2272 matched cddid_all.tbl CDD TIGR01258 TIGR01258 213596 pgm_1 phosphoglycerate mutase, BPG-dependent, family 1. Most members of this family are phosphoglycerate mutase (EC 5.4.2.1). This enzyme interconverts 2-phosphoglycerate and 3-phosphoglycerate. The enzyme is transiently phosphorylated on an active site histidine by 2,3-diphosphoglyerate, which is both substrate and product. Some members of this family have are phosphoglycerate mutase as a minor activity and act primarily as a bisphoglycerate mutase, interconverting 2,3-diphosphoglycerate and 1,3-diphosphoglycerate (EC 5.4.2.4). This model is designated as a subfamily for this reason. The second and third paralogs in S. cerevisiae are somewhat divergent and apparently inactive (see PUBMED:9544241) but are also part of this subfamily phylogenetically. 245 matched cddid_all.tbl CDD TIGR01259 TIGR01259 213597 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation. [Cellular processes, DNA transformation] 120 matched cddid_all.tbl CDD TIGR01260 TIGR01260 130327 ATP_synt_c ATP synthase, F0 subunit c. This model describes the subunit c in F1/F0-ATP synthase, a membrane associated multisubunit complex found in bacteria and organelles of higher eukaryotes, namely, mitochondria and chloroplast. This enzyme is principally involved in the synthesis of ATP from ADP and inorganic phosphate by coupling the energy derived from the proton electrochemical gradient across the biological membrane. A brief description of this multisubunit enzyme complex: F1 and F0 represent two major clusters of subunits. The functional role of subunit c, which is the part of F0 cluster, has been delineated in-vitro reconstitution experiments. Overall experimental proof exists that demonstrate the electrochemical gradient is converted into a rotational torque that leads to ATP synthesis. [Energy metabolism, ATP-proton motive force interconversion] 58 matched cddid_all.tbl CDD TIGR01261 TIGR01261 130328 hisB_Nterm histidinol-phosphatase. This model describes histidinol phosphatase. All known examples in the scope of this model are bifunctional proteins with a histidinol phosphatase domain followed by an imidazoleglycerol-phosphate dehydratase domain. These enzymatic domains catalyze the ninth and seventh steps, respectively, of histidine biosynthesis. [Amino acid biosynthesis, Histidine family] 161 matched cddid_all.tbl CDD TIGR01262 TIGR01262 273527 maiA maleylacetoacetate isomerase. Maleylacetoacetate isomerase is an enzyme of tyrosine and phenylalanine catabolism. It requires glutathione and belongs by homology to the zeta family of glutathione S-transferases. The enzyme (EC 5.2.1.2) is described as active also on maleylpyruvate, and the example from a Ralstonia sp. catabolic plasmid is described as a maleylpyruvate isomerase involved in gentisate catabolism. [Energy metabolism, Amino acids and amines] 210 matched cddid_all.tbl CDD TIGR01263 TIGR01263 273528 4HPPD 4-hydroxyphenylpyruvate dioxygenase. This protein oxidizes 4-hydroxyphenylpyruvate, a tyrosine and phenylalanine catabolite, to homogentisate. Homogentisate can undergo a further non-enzymatic oxidation and polymerization into brown pigments that protect some bacterial species from light. A similar process occurs spontaneously in blood and is hemolytic (see . In some bacterial species, this enzyme has been studied as a hemolysin. [Energy metabolism, Amino acids and amines] 352 matched cddid_all.tbl CDD TIGR01264 TIGR01264 273529 tyr_amTase_E tyrosine aminotransferase, eukaryotic. This model describes tyrosine aminotransferase as found in animals and Trypanosoma cruzi. It is the first enzyme of a pathway of tyrosine degradation via homogentisate. Several plant enzyme designated as probable tyrosine aminotransferases are very closely related to an experimentally demonstrated nicotianamine aminotransferase, an enzyme in a siderophore (iron uptake chelator) biosynthesis pathway. These plant sequences are excluded from the model seed and score between the trusted an noise cutoffs. [Energy metabolism, Amino acids and amines] 401 matched cddid_all.tbl CDD TIGR01265 TIGR01265 188123 tyr_nico_aTase tyrosine/nicotianamine family aminotransferase. This subfamily of pyridoxal phosphate-dependent enzymes includes known examples of both tyrosine aminotransferase from animals and nicotianamine aminotransferase from barley. 403 matched cddid_all.tbl CDD TIGR01266 TIGR01266 162276 fum_ac_acetase fumarylacetoacetase. This enzyme catalyzes the final step in the breakdown of tyrosine or phenylalanine to fumarate and acetoacetate. [Energy metabolism, Amino acids and amines] 415 matched cddid_all.tbl CDD TIGR01267 TIGR01267 130334 Phe4hydrox_mono phenylalanine-4-hydroxylase, monomeric form. This model describes the smaller, monomeric form of phenylalanine-4-hydroxylase, as found in a small number of Gram-negative bacteria. The enzyme irreversibly converts phenylalanine to tryosine and is known to be the rate-limiting step in phenylalanine catabolism in some systems. This family is of biopterin and metal-dependent hydroxylases is related to a family of longer, multimeric aromatic amino acid hydroxylases that have additional N-terminal regulatory sequences. These include tyrosine 3-monooxygenase, phenylalanine-4-hydroxylase, and tryptophan 5-monoxygenase. [Energy metabolism, Amino acids and amines] 248 matched cddid_all.tbl CDD TIGR01268 TIGR01268 130335 Phe4hydrox_tetr phenylalanine-4-hydroxylase, tetrameric form. This model describes the larger, tetrameric form of phenylalanine-4-hydroxylase, as found in metazoans. The enzyme irreversibly converts phenylalanine to tryosine and is known to be the rate-limiting step in phenylalanine catabolism in some systems. It is closely related to metazoan tyrosine 3-monooxygenase and tryptophan 5-monoxygenase, and more distantly to monomeric phenylalanine-4-hydroxylases of some Gram-negative bacteria. The member of this family from Drosophila has been described as having both phenylalanine-4-hydroxylase and tryptophan 5-monoxygenase activity (. However, a Drosophila member of the tryptophan 5-monoxygenase clade has subsequently been discovered. 436 matched cddid_all.tbl CDD TIGR01269 TIGR01269 130336 Tyr_3_monoox tyrosine 3-monooxygenase, tetrameric. This model describes tyrosine 3-monooxygenase, a member of the family of tetrameric, biopterin-dependent aromatic amino acid hydroxylases found in metazoans. It is closely related to tetrameric phenylalanine-4-hydroxylase and tryptophan 5-monooxygenase, and more distantly related to the monomeric phenylalanine-4-hydroxylase found in some Gram-negative bacteria. 457 matched cddid_all.tbl CDD TIGR01270 TIGR01270 130337 Trp_5_monoox tryptophan 5-monooxygenase, tetrameric. This model describes tryptophan 5-monooxygenase, a member of the family of tetrameric, biopterin-dependent aromatic amino acid hydroxylases found in metazoans. It is closely related to tetrameric phenylalanine-4-hydroxylase and tyrosine 3-monooxygenase, and more distantly related to the monomeric phenylalanine-4-hydroxylase found in some Gram-negative bacteria. [Energy metabolism, Amino acids and amines] 464 matched cddid_all.tbl CDD TIGR01271 TIGR01271 273530 CFTR_protein cystic fibrosis transmembrane conductor regulator (CFTR). The model describes the cystis fibrosis transmembrane conductor regulator (CFTR) in eukaryotes. The principal role of this protein is chloride ion conductance. The protein is predicted to consist of 12 transmembrane domains. Mutations or lesions in the genetic loci have been linked to the aetiology of asthma, bronchiectasis, chronic obstructive pulmonary disease etc. Disease-causing mutations have been studied by 36Cl efflux assays in vitro cell cultures and electrophysiology, all of which point to the impairment of chloride channel stability and not the biosynthetic processing per se. [Transport and binding proteins, Anions] 1490 matched cddid_all.tbl CDD TIGR01272 TIGR01272 273531 gluP glucose/galactose transporter. This model describes the glucose/galactose transporter in bacteria. This belongs to the larger facilitator superfamily. Disruption of the loci leads to the total loss of glucose or galactose uptake in E.coli. Putative transporters in other bacterial species were isolated by functional complementation, which restored it functional activity. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 310 matched cddid_all.tbl CDD TIGR01273 TIGR01273 273532 speA arginine decarboxylase, biosynthetic. Two alternative pathways can convert arginine to putrescine. One is decarboxylation by this enzyme followed by removal of the urea moeity by agmatinase. In the other, the ureohydrolase (arginase) acts first, followed by ornithine decarboxylase. This pathway leads to spermidine biosynthesis, hence the gene symbol speA. A distinct biodegradative form is also pyridoxal phosphate-dependent but is not similar in sequence. [Central intermediary metabolism, Polyamine biosynthesis] 624 matched cddid_all.tbl CDD TIGR01274 TIGR01274 130341 ACC_deam 1-aminocyclopropane-1-carboxylate deaminase. This pyridoxal phosphate-dependent enzyme degrades 1-aminocyclopropane-1-carboxylate, which in plants is a precursor of the ripening hormone ethylene, to ammonia and alpha-ketoglutarate. This model includes all members of this family for which function has been demonstrated experimentally, but excludes a closely related family often annotated as putative members of this family. [Central intermediary metabolism, Other] 337 matched cddid_all.tbl CDD TIGR01275 TIGR01275 273533 ACC_deam_rel pyridoxal phosphate-dependent enzymes, D-cysteine desulfhydrase family. This model represents a family of pyridoxal phosphate-dependent enzymes closely related to (and often designated as putative examples of) 1-aminocyclopropane-1-carboxylate deaminase. It appears that members of this family include both D-cysteine desulfhydrase (EC 4.4.1.15) and 1-aminocyclopropane-1-carboxylate deaminase (EC 3.5.99.7). 318 matched cddid_all.tbl CDD TIGR01276 TIGR01276 130343 thiB thiamine ABC transporter, periplasmic binding protein. This model finds the thiamine (and thiamine pyrophosphate) ABC transporter periplasmic binding protein ThiB in proteobacteria. Completed genomes having this protein (E. coli, Vibrio cholera, Haemophilus influenzae) also have the permease ThiP, described by TIGRFAMs equivalog model TIGR01253. [Transport and binding proteins, Other] 309 matched cddid_all.tbl CDD TIGR01277 TIGR01277 130344 thiQ thiamine ABC transporter, ATP-binding protein. This model describes the energy-transducing ATPase subunit ThiQ of the ThiBPQ thiamine (and thiamine pyrophosphate) ABC transporter in several Proteobacteria. This protein is found so far only in Proteobacteria, and is found in complete genomes only if the ThiB and ThiP subunits are also found. [Transport and binding proteins, Other] 213 matched cddid_all.tbl CDD TIGR01278 TIGR01278 273534 DPOR_BchB light-independent protochlorophyllide reductase, B subunit. Alternate name: dark protochlorophyllide reductase This enzyme describes the B subunit of the dark form protochlorophyllide reductase, a nitrogenase-like enzyme. This subunit shows homology to the nitrogenase molybdenum-iron protein. It catalyzes a step in bacteriochlorophyll biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll] 511 matched cddid_all.tbl CDD TIGR01279 TIGR01279 273535 DPOR_bchN light-independent protochlorophyllide reductase, N subunit. This enzyme describes the N subunit of the dark form protochlorophyllide reductase, a nitrogenase-like enzyme involved in bacteriochlorophyll biosynthesis. This subunit shows homology to the nitrogenase molybdenum-iron protein NifN. [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll] 407 matched cddid_all.tbl CDD TIGR01280 TIGR01280 273536 xseB exodeoxyribonuclease VII, small subunit. This protein is the small subunit for exodeoxyribonuclease VII. Exodeoxyribonuclease VII is made of a complex of four small subunits to one large subunit. The complex degrades single-stranded DNA into large acid-insoluble oligonucleotides. These nucleotides are then degraded further into acid-soluble oligonucleotides. [DNA metabolism, Degradation of DNA] 54 matched cddid_all.tbl CDD TIGR01281 TIGR01281 130348 DPOR_bchL light-independent protochlorophyllide reductase, iron-sulfur ATP-binding protein. The BchL peptide (ChlL in chloroplast and cyanobacteria) is an ATP-binding iron-sulfur protein of the dark form protochlorophyllide reductase, an enzyme similar to nitrogenase. This subunit resembles the nitrogenase NifH subunit. [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll] 268 matched cddid_all.tbl CDD TIGR01282 TIGR01282 162284 nifD nitrogenase molybdenum-iron protein alpha chain. Nitrogenase consists of alpha (NifD) and beta (NifK) subunits of the molybdenum-iron protein and an ATP-binding iron-sulfur protein (NifH). This model describes a large clade of NifD proteins, but excludes a lineage that contains putative NifD and NifD homologs from species with vanadium-dependent nitrogenases. [Central intermediary metabolism, Nitrogen fixation] 466 matched cddid_all.tbl CDD TIGR01283 TIGR01283 188126 nifE nitrogenase molybdenum-iron cofactor biosynthesis protein NifE. This protein is part of the NifEN complex involved in biosynthesis of the molybdenum-iron cofactor used by the homologous NifDK complex of nitrogenase. In a few species, the protein is found as a NifEN fusion protein. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Central intermediary metabolism, Nitrogen fixation] 453 matched cddid_all.tbl CDD TIGR01284 TIGR01284 188127 alt_nitrog_alph nitrogenase alpha chain. This model represents the alpha chains of various forms of the nitrogen-fixing enzyme nitrogenase: vanadium-iron, iron-iron, and molybdenum-iron. Most examples of NifD, the molybdenum-iron type nitrogenase alpha chain, are excluded from this model and described instead by equivalog model TIGR01282. It appears by phylogenetic and UPGMA trees that this model represents a distinct clade of NifD homologs, in which arose several molybdenum-independent forms. [Central intermediary metabolism, Nitrogen fixation] 457 matched cddid_all.tbl CDD TIGR01285 TIGR01285 273537 nifN nitrogenase molybdenum-iron cofactor biosynthesis protein NifN. This protein forms a complex with NifE, and appears as a NifEN in some species. NifEN is a required for producing the molybdenum-iron cofactor of molybdenum-requiring nitrogenases. NifN is closely related to the nitrogenase molybdenum-iron protein beta chain NifK. This model describes most examples of NifN but excludes some cases, such as the putative NifN of Chlorobium tepidum, for which a separate model may be created. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Central intermediary metabolism, Nitrogen fixation] 432 matched cddid_all.tbl CDD TIGR01286 TIGR01286 130353 nifK nitrogenase molybdenum-iron protein beta chain. This model represents the majority of known sequences of the nitrogenase molybdenum-iron protein beta subunit. A distinct clade in a phylogenetic tree contains molybdenum-iron, vanadium-iron, and iron-iron forms of nitrogenase beta subunit and is excluded from this model. Nitrogenase, also called dinitrogenase, is responsible for nitrogen fixation. Note: the trusted cutoff score has recently been lowered to include an additional family in which the beta subunit is shorter by about 50 amino acids at the N-terminus. In species with the shorter form of the beta subunit, the alpha subunit has a novel insert of similar length. [Central intermediary metabolism, Nitrogen fixation] 515 matched cddid_all.tbl CDD TIGR01287 TIGR01287 273538 nifH nitrogenase iron protein. This model describes nitrogenase (EC 1.18.6.1) iron protein, also called nitrogenase reductase or nitrogenase component II. This model includes molybdenum-iron nitrogenase reductase (nifH), vanadium-iron nitrogenase reductase (vnfH), and iron-iron nitrogenase reductase (anfH). The model excludes the homologous protein from the light-independent protochlorophyllide reductase. [Central intermediary metabolism, Nitrogen fixation] 275 matched cddid_all.tbl CDD TIGR01288 TIGR01288 130355 nodI ATP-binding ABC transporter family nodulation protein NodI. This protein is required for normal nodulation by nitrogen-fixing root nodule bacteria such as Mesorhizobium loti. It is a member of the family of ABC transporter ATP binding proteins and works with NodJ to export a nodulation signal molecule. This model does not recognize the highly divergent NodI from Azorhizobium caulinodans. [Cellular processes, Other, Transport and binding proteins, Other] 303 matched cddid_all.tbl CDD TIGR01289 TIGR01289 200089 LPOR light-dependent protochlorophyllide reductase. This model represents the light-dependent, NADPH-dependent form of protochlorophyllide reductase. It belongs to the short chain alcohol dehydrogenase family, in contrast to the nitrogenase-related light-independent form. [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll] 314 matched cddid_all.tbl CDD TIGR01290 TIGR01290 273539 nifB nitrogenase cofactor biosynthesis protein NifB. This model describes NifB, a protein required for the biosynthesis of the iron-molybdenum (or iron-vanadium) cofactor used by the nitrogen-fixing enzyme nitrogenase. NifB belongs to the radical SAM family, and the FeMo cluster biosynthesis process requires S-adenosylmethionine. Archaeal homologs lack the most C-terminal region and score between the trusted and noise cutoffs of this model. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Central intermediary metabolism, Nitrogen fixation] 442 matched cddid_all.tbl CDD TIGR01291 TIGR01291 130358 nodJ ABC-2 type transporter, NodJ family. Nearly all members of this subfamily are NodJ which, together with NodI (TIGR01288), acts to export a variety of modified carbohydrate molecules as signals to plant hosts to establish root nodules. The seed alignment includes a highly divergent member from Azorhizobium caulinodans that is, nonetheless, associated with nodulation. This model is designated as subfamily in part because not all sequences derived from the last common ancestral sequence of Rhizobium sp. and Azorhizobium caulinodans NodJ are necessarily nodulation proteins. [Cellular processes, Other, Transport and binding proteins, Other] 253 matched cddid_all.tbl CDD TIGR01292 TIGR01292 273540 TRX_reduct thioredoxin-disulfide reductase. This model describes thioredoxin-disulfide reductase, a member of the pyridine nucleotide-disulphide oxidoreductases (pfam00070). [Energy metabolism, Electron transport] 299 matched cddid_all.tbl CDD TIGR01293 TIGR01293 213602 Kv_beta voltage-dependent potassium channel beta subunit, animal. This model describes the conserved core region of the beta subunit of voltage-gated potassium (Kv) channels in animals. Amino-terminal regions differ substantially, in part by alternative splicing, and are not included in the model. Four beta subunits form a complex with four alpha subunit cytoplasmic (T1) regions, and the structure of the complex is solved. The beta subunit belongs to a family of NAD(P)H-dependent aldo-keto reductases, binds NADPH, and couples voltage-gated channel activity to the redox potential of the cell. Plant beta subunits and their closely related bacterial homologs (in Deinococcus radiudurans, Xylella fastidiosa, etc.) appear more closely related to each other than to animal forms. However, the bacterial species lack convincing counterparts the Kv alpha subunit and the Kv beta homolog may serve as an enzyme. Cutoffs are set for this model such that yeast and plant forms and bacterial close homologs score between trusted and noise cutoffs. 317 matched cddid_all.tbl CDD TIGR01294 TIGR01294 273541 P_lamban phospholamban. This model represents the short (52 residue) transmembrane phosphoprotein phospholamban. Phospholamban, in its unphosphorylated form, inhibits SERCA2, the cardiac sarcoplasmic reticulum Ca-ATPase. 52 matched cddid_all.tbl CDD TIGR01295 TIGR01295 273542 PedC_BrcD bacteriocin transport accessory protein, putative. This model describes a small family of proteins believed to aid in the export of various class II bacteriocins, which are ribosomally-synthesized, non-lantibiotic bacterial peptide antibiotics. Members of this family are found in operons for pediocin PA-1 from Pediococcus acidilactici and brochocin-C from Brochothrix campestris. 122 matched cddid_all.tbl CDD TIGR01296 TIGR01296 273543 asd_B aspartate-semialdehyde dehydrogenase (peptidoglycan organisms). Two closely related families of aspartate-semialdehyde dehydrogenase are found. They differ by a deep split in phylogenetic and percent identity trees and in gap patterns. This model represents a branch more closely related to the USG-1 protein than to the other aspartate-semialdehyde dehydrogenases represented in model TIGR00978. [Amino acid biosynthesis, Aspartate family] 338 matched cddid_all.tbl CDD TIGR01297 TIGR01297 273544 CDF cation diffusion facilitator family transporter. This model describes a broadly distributed family of transporters, a number of which have been shown to transport divalent cations of cobalt, cadmium and/or zinc. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence. [Transport and binding proteins, Cations and iron carrying compounds] 268 matched cddid_all.tbl CDD TIGR01298 TIGR01298 188129 RNaseT ribonuclease T. This model describes ribonuclease T, an enzyme found so far only in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases. [Transcription, RNA processing] 200 matched cddid_all.tbl CDD TIGR01299 TIGR01299 130366 synapt_SV2 synaptic vesicle protein SV2. This model describes a tightly conserved subfamily of the larger family of sugar (and other) transporters described by pfam00083. Members of this subfamily include closely related forms SV2A and SV2B of synaptic vesicle protein from vertebrates and a more distantly related homolog (below trusted cutoff) from Drosophila melanogaster. Members are predicted to have two sets of six transmembrane helices. 742 matched cddid_all.tbl CDD TIGR01300 TIGR01300 130367 CPA3_mnhG_phaG monovalent cation/proton antiporter, MnhG/PhaG subunit. This model represents a subfamily of small, transmembrane proteins believed to be components of Na+/H+ and K+/H+ antiporters. Members, including proteins designated MnhG from Staphylococcus aureus and PhaG from Rhizobium meliloti, show some similarity to chain L of the NADH dehydrogenase I, which also translocates protons. [Transport and binding proteins, Cations and iron carrying compounds] 97 matched cddid_all.tbl CDD TIGR01301 TIGR01301 273545 GPH_sucrose GPH family sucrose/H+ symporter. This model represents sucrose/proton symporters, found in plants, from the Glycoside-Pentoside-Hexuronide (GPH)/cation symporter family. These proteins are predicted to have 12 transmembrane domains. Members may export sucrose (e.g. SUT1, SUT4) from green parts to the phloem for long-distance transport or import sucrose (e.g SUT2) to sucrose sinks such as the tap root of the carrot. 477 matched cddid_all.tbl CDD TIGR01302 TIGR01302 273546 IMP_dehydrog inosine-5'-monophosphate dehydrogenase. This model describes IMP dehydrogenase, an enzyme of GMP biosynthesis. This form contains two CBS domains. This model describes a rather tightly conserved cluster of IMP dehydrogenase sequences, many of which are characterized. The model excludes two related families of proteins proposed also to be IMP dehydrogenases, but without characterized members. These are related families are the subject of separate models. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 450 matched cddid_all.tbl CDD TIGR01303 TIGR01303 130370 IMP_DH_rel_1 IMP dehydrogenase family protein. This model represents a family of proteins, often annotated as a putative IMP dehydrogenase, related to IMP dehydrogenase and GMP reductase and restricted to the high GC Gram-positive bacteria. All species in which a member is found so far (Corynebacterium glutamicum, Mycobacterium tuberculosis, Streptomyces coelicolor, etc.) also have IMP dehydrogenase as described by TIGRFAMs entry TIGR01302. [Unknown function, General] 475 matched cddid_all.tbl CDD TIGR01304 TIGR01304 273547 IMP_DH_rel_2 IMP dehydrogenase family protein. This model represents a family of proteins, often annotated as a putative IMP dehydrogenase, related to IMP dehydrogenase and GMP reductase. Most species with a member of this family belong to the high GC Gram-positive bacteria, and these also have the IMP dehydrogenase described by TIGRFAMs equivalog model TIGR01302. [Unknown function, General] 369 matched cddid_all.tbl CDD TIGR01305 TIGR01305 130372 GMP_reduct_1 guanosine monophosphate reductase, eukaryotic. A deep split separates two families of GMP reductase. This family includes both eukaryotic and some proteobacterial sequences, while the other family contains other bacterial sequences. [Purines, pyrimidines, nucleosides, and nucleotides, Nucleotide and nucleoside interconversions] 343 matched cddid_all.tbl CDD TIGR01306 TIGR01306 130373 GMP_reduct_2 guanosine monophosphate reductase, bacterial. A deep split separates two families of GMP reductase. The other (TIGR01305) is found in eukaryotic and some proteobacterial lineages, including E. coli, while this family is found in a variety of bacterial lineages. [Purines, pyrimidines, nucleosides, and nucleotides, Nucleotide and nucleoside interconversions] 321 matched cddid_all.tbl CDD TIGR01307 TIGR01307 130374 pgm_bpd_ind phosphoglycerate mutase (2,3-diphosphoglycerate-independent). This protein is about double in length of, and devoid of homology to the form of phosphoglycerate mutase that uses 2,3-bisphosphoglycerate as a cofactor. [Energy metabolism, Glycolysis/gluconeogenesis] 501 matched cddid_all.tbl CDD TIGR01308 TIGR01308 130375 rpmD_bact ribosomal protein L30, bacterial/organelle. This model describes bacterial (and organellar) 50S ribosomal protein L30. Homologous ribosomal proteins of the eukaryotic cytosol and of the archaea differ substantially in architecture, from bacterial L30 and also from each other, and are described by separate models. [Protein synthesis, Ribosomal proteins: synthesis and modification] 55 matched cddid_all.tbl CDD TIGR01309 TIGR01309 130376 uL30_arch 50S ribosomal protein uL30, archaeal form. This model represents the archaeal ribosomal protein similar to longer (~ 250 residue) eukaryotic 60S ribosomal protein L7 and to the much shorter (~ 60 residue) bacterial 50S ribosomal protein L30. Protein naming follows the SwissProt designation as L30P, while the gene symbol rpmD follows TIGR usage. [Protein synthesis, Ribosomal proteins: synthesis and modification] 152 matched cddid_all.tbl CDD TIGR01310 TIGR01310 273548 uL30_euk 60S ribosomal protein uL30, eukaryotic form. This model describes the eukaryotic 60S (cytosolic) ribosomal protein uL30 (previously L7) and paralogs that may or may not also be uL30. Human, Drosophila, and Arabidopsis all have both a typical L7 and an L7-related paralog. This family is designated subfamily rather than equivalog to reflect these uncharacterized paralogs. Members of this family average ~ 250 residues in length, somewhat longer than the archaeal L30P/L7E homolog (~ 155 residues) and much longer than the related bacterial/organellar form (~ 60 residues). 235 matched cddid_all.tbl CDD TIGR01311 TIGR01311 273549 glycerol_kin glycerol kinase. This model describes glycerol kinase, a member of the FGGY family of carbohydrate kinases. [Energy metabolism, Other] 493 matched cddid_all.tbl CDD TIGR01312 TIGR01312 273550 XylB D-xylulose kinase. This model describes D-xylulose kinases, a subfamily of the FGGY family of carbohydrate kinases. The member from Klebsiella pneumoniae, designated DalK (see , was annotated erroneously in GenBank as D-arabinitol kinase but is authentic D-xylulose kinase. D-xylulose kinase (XylB) generally is found with xylose isomerase (XylA) and acts in xylose utilization. [Energy metabolism, Sugars] 481 matched cddid_all.tbl CDD TIGR01313 TIGR01313 273551 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family. This model represents a subfamily of proteins that includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases. 163 matched cddid_all.tbl CDD TIGR01314 TIGR01314 130381 gntK_FGGY gluconate kinase, FGGY type. Gluconate is derived from glucose in two steps. This model describes one form of gluconate kinase, belonging to the FGGY family of carbohydrate kinases. Gluconate kinase phosphoryates gluconate for entry into the Entner-Douderoff pathway. [Energy metabolism, Sugars] 505 matched cddid_all.tbl CDD TIGR01315 TIGR01315 273552 5C_CHO_kinase FGGY-family pentulose kinase. This model represents a subfamily of the FGGY family of carbohydrate kinases. This subfamily is closely related to a set of ribulose kinases, and many members are designated ribitol kinase. However, the member from Klebsiella pneumoniae, from a ribitol catabolism operon, accepts D-ribulose and to a lesser extent D-arabinitol and ribitol (and JW Lengeler, personal communication); its annotation in GenBank as ribitol kinase is imprecise and may have affected public annotation of related proteins. 541 matched cddid_all.tbl CDD TIGR01316 TIGR01316 130383 gltA glutamate synthase (NADPH), homotetrameric. This protein is homologous to the small subunit of NADPH and NADH forms of glutamate synthase as found in eukaryotes and some bacteria. This protein is found in numerous species having no homolog of the glutamate synthase large subunit. The prototype of the family, from Pyrococcus sp. KOD1, was shown to be active as a homotetramer and to require NADPH. [Amino acid biosynthesis, Glutamate family] 449 matched cddid_all.tbl CDD TIGR01317 TIGR01317 162300 GOGAT_sm_gam glutamate synthases, NADH/NADPH, small subunit. This model represents one of three built for the NADPH-dependent or NADH-dependent glutamate synthase (EC 1.4.1.13 and 1.4.1.14, respectively) small subunit or homologous region. TIGR01316 describes a family in several archaeal and deeply branched bacterial lineages of a homotetrameric form for which there is no large subunit. Another model describes glutamate synthase small subunit from gamma and some alpha subdivision Proteobacteria plus paralogs of unknown function. This model describes the small subunit, or homologous region of longer forms proteins, of eukaryotes, Gram-positive bacteria, cyanobacteria, and some other lineages. All members with known function participate in NADH or NADPH-dependent reactions to interconvert between glutamine plus 2-oxoglutarate and two molecules of glutamate. 485 matched cddid_all.tbl CDD TIGR01318 TIGR01318 273553 gltD_gamma_fam glutamate synthase small subunit family protein, proteobacterial. This model represents one of three built for the NADPH-dependent or NADH-dependent glutamate synthase (EC 1.4.1.13 and 1.4.1.14, respectively) small subunit and homologs. TIGR01317 describes the small subunit (or equivalent region from longer forms) in eukaryotes, Gram-positive bacteria, and some other lineages, both NADH and NADPH-dependent. TIGR01316 describes a protein of similar length, from Archaea and a number of bacterial lineages, that forms glutamate synthase homotetramers without a large subunit. This model describes both glutatate synthase small subunit and closely related paralogs of unknown function from a number of gamma and alpha subdivision Proteobacteria, including E. coli. 467 matched cddid_all.tbl CDD TIGR01319 TIGR01319 130386 glmL_fam conserved hypothetical protein. This small family includes, so far, an uncharacterized protein from E. coli O157:H7 and GlmL from Clostridium tetanomorphum and Clostridium cochlearium. GlmL is located between the genes for the two subunits, epsilon (GlmE) and sigma (GlmS), of the coenzyme-B12-dependent glutamate mutase (methylaspartate mutase), the first enzyme in a pathway of glutamate fermentation. Members shows significant sequence similarity to the hydantoinase branch of the hydantoinase/oxoprolinase family (pfam01968). 463 matched cddid_all.tbl CDD TIGR01320 TIGR01320 130387 mal_quin_oxido malate:quinone-oxidoreductase. This membrane-associated enzyme is an alternative to the better-known NAD-dependent malate dehydrogenase as part of the TCA cycle. The reduction of a quinone rather than NAD+ makes the reaction essentially irreversible in the direction of malate oxidation to oxaloacetate. Both forms of malate dehydrogenase are active in E. coli; disruption of this form causes less phenotypic change. In some bacteria, this form is the only or the more important malate dehydrogenase. [Energy metabolism, TCA cycle] 483 matched cddid_all.tbl CDD TIGR01321 TIGR01321 130388 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis. [Amino acid biosynthesis, Aromatic amino acid family, Regulatory functions, DNA interactions] 94 matched cddid_all.tbl CDD TIGR01322 TIGR01322 273554 scrB_fam sucrose-6-phosphate hydrolase. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 445 matched cddid_all.tbl CDD TIGR01323 TIGR01323 188130 nitrile_alph nitrile hydratase, alpha subunit. This model describes both iron- and cobalt-containing nitrile hydratase alpha chains. It excludes the thiocyanate hydrolase gamma subunit of Thiobacillus thioparus, a sequence that appears to have evolved from within the family of nitrile hydratase alpha subunits but which differs by several indels and a more rapid accumulation of point mutations. [Energy metabolism, Amino acids and amines] 189 matched cddid_all.tbl CDD TIGR01324 TIGR01324 130391 cysta_beta_ly_B cystathionine beta-lyase, bacterial. This model represents cystathionine beta-lyase (alternate name: beta-cystathionase), one of several pyridoxal-dependent enzymes of cysteine, methionine, and homocysteine metabolism. This enzyme is involved in the biosynthesis of Met from Cys. [Amino acid biosynthesis, Aspartate family] 377 matched cddid_all.tbl CDD TIGR01325 TIGR01325 188131 O_suc_HS_sulf O-succinylhomoserine sulfhydrylase. This model describes O-succinylhomoserine sulfhydrylase, one of several related pyridoxal phosphate-dependent enzymes of cysteine and methionine metabolism. This enzyme is part of an alternative pathway of homocysteine biosynthesis, a step in methionine biosynthesis. [Amino acid biosynthesis, Aspartate family] 381 matched cddid_all.tbl CDD TIGR01326 TIGR01326 273555 OAH_OAS_sulfhy OAH/OAS sulfhydrylase. This model describes a distinct clade of the Cys/Met metabolism pyridoxal phosphate-dependent enzyme superfamily. Members include examples of OAH/OAS sulfhydrylase, an enzyme with activity both as O-acetylhomoserine (OAH) sulfhydrylase (EC 2.5.1.49) and O-acetylserine (OAS) sulphydrylase (EC 2.5.1.47). An alternate name for OAH sulfhydrylase is homocysteine synthase. This model is designated subfamily because it may or may not have both activities. [Amino acid biosynthesis, Aspartate family, Amino acid biosynthesis, Serine family] 418 matched cddid_all.tbl CDD TIGR01327 TIGR01327 273556 PGDH D-3-phosphoglycerate dehydrogenase. This model represents a long form of D-3-phosphoglycerate dehydrogenase, the serA gene of one pathway of serine biosynthesis. Shorter forms, scoring between trusted and noise cutoff, include SerA from E. coli. [Amino acid biosynthesis, Serine family] 525 matched cddid_all.tbl CDD TIGR01328 TIGR01328 130395 met_gam_lyase methionine gamma-lyase. This model describes a methionine gamma-lyase subset of a family of PLP-dependent trans-sulfuration enzymes. The member from the parasite Trichomonas vaginalis is described as catalyzing alpha gamma- and alpha-beta eliminations and gamma-replacement reactions on methionine, cysteine, and some derivatives. Likewise, the enzyme from Pseudomonas degrades cysteine as well as methionine. [Energy metabolism, Amino acids and amines] 391 matched cddid_all.tbl CDD TIGR01329 TIGR01329 273557 cysta_beta_ly_E cystathionine beta-lyase, eukaryotic. This model represents cystathionine beta-lyase (alternate name: beta-cystathionase), one of several pyridoxal-dependent enzymes of cysteine, methionine, and homocysteine metabolism. This enzyme is involved in the biosynthesis of Met from Cys. 378 matched cddid_all.tbl CDD TIGR01330 TIGR01330 273558 bisphos_HAL2 3'(2'),5'-bisphosphate nucleotidase, HAL2 family. Sulfate is incorporated into 3-phosphoadenylylsulfate, PAPS, for utilization in pathways such as methionine biosynthesis. Transfer of sulfate from PAPS to an acceptor leaves adenosine 3'-5'-bisphosphate, APS. This model describes a form found in plants of the enzyme 3'(2'),5'-bisphosphate nucleotidase, which removes the 3'-phosphate from APS to regenerate AMP and help drive the cycle. Sensitivity of this essential enzyme to sodium and other metal ions results is responsible for characterization of this enzyme as a salt tolerance protein. Some members of this family are active also as inositol 1-monophosphatase. 353 matched cddid_all.tbl CDD TIGR01331 TIGR01331 130398 bisphos_cysQ 3'(2'),5'-bisphosphate nucleotidase, bacterial. Sulfate is incorporated into 3-phosphoadenylylsulfate, PAPS, for utilization in pathways such as methionine biosynthesis. Transfer of sulfate from PAPS to an acceptor leaves adenosine 3'-5'-bisphosphate, APS. This model describes a form found in bacteria of the enzyme 3'(2'),5'-bisphosphate nucleotidase, which removes the 3'-phosphate from APS to regenerate AMP and help drive the cycle. [Central intermediary metabolism, Sulfur metabolism] 249 matched cddid_all.tbl CDD TIGR01332 TIGR01332 130399 cyt_b559_alpha cytochrome b559, alpha subunit. This model describes the alpha subunit of cytochrome b559, about 83 residues in length. The N-terminal half is homologous to the ~ 40-residue beta subunit. Cytochrome b559 is associated with photosystem II. Sequences scoring between trusted and noise cutoffs are fragments. [Energy metabolism, Photosynthesis] 80 matched cddid_all.tbl CDD TIGR01333 TIGR01333 130400 cyt_b559_beta cytochrome b559, beta subunit. This model describes the beta subunit of cytochrome b559, about 40 residues in length. It is homologous to the N-terminal half of the alpha subunit, a protein of about 83 residues. Cytochrome b559 is associated with photosystem II. [Energy metabolism, Photosynthesis] 43 matched cddid_all.tbl CDD TIGR01334 TIGR01334 130401 modD putative molybdenum utilization protein ModD. The gene modD for a member of this family is found with molybdenum transport genes modABC in Rhodobacter capsulatus. However, disruption of modD causes only a 4-fold (rather than 500-fold for modA, modB, modC) change in the external molybdenum concentration required to suppress an alternative nitrogenase. ModD proteins are highly similar to nicotinate-nucleotide pyrophosphorylase (also called quinolinate phosphoribosyltransferase). The function unknown. [Unknown function, General] 277 matched cddid_all.tbl CDD TIGR01335 TIGR01335 130402 psaA photosystem I core protein PsaA. The core proteins of photosystem I are PsaA and PsaB, homologous integral membrane proteins that form a heterodimer. The heterodimer binds the electron-donating chlorophyll dimer P700, as well as chlorophyll, phylloquinone, and 4FE-4S electron acceptors. This model describes PsaA only. [Energy metabolism, Photosynthesis] 752 matched cddid_all.tbl CDD TIGR01336 TIGR01336 130403 psaB photosystem I core protein PsaB. The core proteins of photosystem I are PsaA and PsaB, homologous integral membrane proteins that form a heterodimer. The heterodimer binds the electron-donating chlorophyll dimer P700, as well as chlorophyll, phylloquinone, and 4FE-4S electron acceptors. This model describes PsaB only. [Energy metabolism, Photosynthesis] 734 matched cddid_all.tbl CDD TIGR01337 TIGR01337 273559 apcB allophycocyanin, beta subunit. The alpha and beta subunits of allophycocyanin form heterodimers, six of which associate into larger aggregates as part of the phycobilisome, a light-harvesting complex of phycobiliproteins and linker proteins. This model describes allophycocyanin beta subunit. Other, homologous phyobiliproteins include allophycocyanin alpha chain and the phycocyanin and phycoerythrin alpha and beta chains. [Energy metabolism, Photosynthesis] 167 matched cddid_all.tbl CDD TIGR01338 TIGR01338 130405 phycocy_alpha phycocyanin, alpha subunit. This model describes the phycocyanin alpha subunit. Other, homologous phyobiliproteins of the phycobilisome include phycocyanin alpha chain and the allophycocyanin and phycoerythrin alpha and beta chains. This model excludes the closely related phycoerythrocyanin alpha subunit. [Energy metabolism, Photosynthesis] 161 matched cddid_all.tbl CDD TIGR01339 TIGR01339 273560 phycocy_beta phycocyanin, beta subunit. This model describes the phycocyanin beta subunit. Other, homologous phycobiliproteins of the phycobilisome include phycocyanin beta chain and the allophycocyanin and phycoerythrin alpha and beta chains. This model excludes the closely related phycoerythrocyanin beta subunit. [Energy metabolism, Photosynthesis] 171 matched cddid_all.tbl CDD TIGR01340 TIGR01340 273561 aconitase_mito aconitate hydratase, mitochondrial. This model represents mitochondrial forms of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. [Energy metabolism, TCA cycle] 745 matched cddid_all.tbl CDD TIGR01341 TIGR01341 273562 aconitase_1 aconitate hydratase 1. This model represents one form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It is found in bacteria, archaea, and eukaryotic cytosol. It has been shown to act also as an iron-responsive element binding protein in animals and may have the same role in other eukaryotes. [Energy metabolism, TCA cycle] 876 matched cddid_all.tbl CDD TIGR01342 TIGR01342 130409 acon_putative aconitate hydratase, putative, Aquifex type. This model represents a small family of proteins homologous (and likely functionally equivalent to) aconitase 1. Members are found, so far in the anaerobe Clostridium acetobutylicum, in the microaerophilic, early-branching bacterium Aquifex aeolicus, and in the halophilic archaeon Halobacterium sp. NRC-1. No member is experimentally characterized. [Energy metabolism, TCA cycle] 658 matched cddid_all.tbl CDD TIGR01343 TIGR01343 273563 hacA_fam homoaconitate hydratase family protein. This model represents a subfamily of proteins consisting of aconitase, homoaconitase, 3-isopropylmalate dehydratase, and uncharacterized proteins. The majority of the members of this family have been designated as 3-isopropylmalate dehydratase large subunit (LeuC) in microbial genome annotation, but the only characterized member is Thermus thermophilus homoaconitase, an enzyme of a non-aspartate pathway of Lys biosynthesis. 412 matched cddid_all.tbl CDD TIGR01344 TIGR01344 188132 malate_syn_A malate synthase A. This model represents plant malate synthase and one of two bacterial forms, designated malate synthase A. The distantly related malate synthase G is described by a separate model. This enzyme and isocitrate lyase are the two characteristic enzymes of the glyoxylate shunt. The shunt enables the cell to use acetyl-CoA to generate increased levels of TCA cycle intermediates for biosynthetic pathways such as gluconeogenesis. [Energy metabolism, TCA cycle] 511 matched cddid_all.tbl CDD TIGR01345 TIGR01345 130412 malate_syn_G malate synthase G. This model describes the G isozyme of malate synthase. Isocitrate synthase and malate synthase form the glyoxylate shunt, which generates additional TCA cycle intermediates. [Energy metabolism, TCA cycle] 721 matched cddid_all.tbl CDD TIGR01346 TIGR01346 273564 isocit_lyase isocitrate lyase. Isocitrate lyase and malate synthase are the enzymes of the glyoxylate shunt, a pathway associated with the TCA cycle. [Energy metabolism, TCA cycle] 527 matched cddid_all.tbl CDD TIGR01347 TIGR01347 273565 sucB 2-oxoglutarate dehydrogenase complex dihydrolipoamide succinyltransferase (E2 component). This model describes the TCA cycle 2-oxoglutarate system E2 component, dihydrolipoamide succinyltransferase. It is closely related to the pyruvate dehydrogenase E2 component, dihydrolipoamide acetyltransferase. The seed for this model includes mitochondrial and Gram-negative bacterial forms. Mycobacterial candidates are highly derived, differ in having and extra copy of the lipoyl-binding domain at the N-terminus. They score below the trusted cutoff, but above the noise cutoff and above all examples of dihydrolipoamide acetyltransferase. [Energy metabolism, TCA cycle] 403 matched cddid_all.tbl CDD TIGR01348 TIGR01348 273566 PDHac_trf_long pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form. This model describes a subset of pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase specifically close by both phylogenetic and per cent identity (UPGMA) trees. Members of this set include two or three copies of the lipoyl-binding domain. E. coli AceF is a member of this model, while mitochondrial and some other bacterial forms belong to a separate model. [Energy metabolism, Pyruvate dehydrogenase] 546 matched cddid_all.tbl CDD TIGR01349 TIGR01349 273567 PDHac_trf_mito pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form. This model represents one of several closely related clades of the dihydrolipoamide acetyltransferase subunit of the pyruvate dehydrogenase complex. It includes sequences from mitochondria and from alpha and beta branches of the proteobacteria, as well as from some other bacteria. Sequences from Gram-positive bacteria are not included. The non-enzymatic homolog protein X, which serves as an E3 component binding protein, falls within the clade phylogenetically but is rejected by its low score. [Energy metabolism, Pyruvate dehydrogenase] 436 matched cddid_all.tbl CDD TIGR01350 TIGR01350 273568 lipoamide_DH dihydrolipoamide dehydrogenase. This model describes dihydrolipoamide dehydrogenase, a flavoprotein that acts in a number of ways. It is the E3 component of dehydrogenase complexes for pyruvate, 2-oxoglutarate, 2-oxoisovalerate, and acetoin. It can also serve as the L protein of the glycine cleavage system. This family includes a few members known to have distinct functions (ferric leghemoglobin reductase and NADH:ferredoxin oxidoreductase) but that may be predicted by homology to act as dihydrolipoamide dehydrogenase as well. The motif GGXCXXXGCXP near the N-terminus contains a redox-active disulfide. 460 matched cddid_all.tbl CDD TIGR01351 TIGR01351 273569 adk adenylate kinase. Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is SP|Q9UIJ7, a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason. [Purines, pyrimidines, nucleosides, and nucleotides, Nucleotide and nucleoside interconversions] 210 matched cddid_all.tbl CDD TIGR01352 TIGR01352 273570 tonB_Cterm TonB family C-terminal domain. This model represents the C-terminal of TonB and is homologs. TonB is an energy-transducer for TonB-dependent receptors of Gram-negative bacteria. Most members are designated as TonB or TonB-related proteins, but a few represent the paralogous TolA protein. Several bacteria have up to four TonB paralogs. In nearly every case, a proline-rich repetive region is found N-terminal to this domain; these low-complexity regions are highly divergent and cannot readily be aligned. The region is suggested to help span the periplasm. [Transport and binding proteins, Cations and iron carrying compounds] 74 matched cddid_all.tbl CDD TIGR01353 TIGR01353 273571 dGTP_triPase deoxyguanosinetriphosphate triphosphohydrolase, putative. dGTP triphosphohydrolase (dgt) releases inorganic triphosphate, an unusual activity reaction product, from GTP. Its activity has been called limited to the Enterobacteriaceae, although homologous sequences are detected elsewhere. This finding casts doubt on whether the activity is shared in other species. In several of these other species, the homologous gene is found in an apparent operon with dnaG, the DNA primase gene. The enzyme from E. coli was shown to bind coopertatively to single stranded DNA. The biological role of dgt is unknown. [Purines, pyrimidines, nucleosides, and nucleotides, Nucleotide and nucleoside interconversions] 381 matched cddid_all.tbl CDD TIGR01354 TIGR01354 273572 cyt_deam_tetra cytidine deaminase, homotetrameric. This small, homotetrameric zinc metalloprotein is found in humans and most bacteria. A related, homodimeric form with a much larger subunit is found in E. coli and in Arabidopsis. Both types may act on deoxycytidine as well as cytidine. [Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides] 127 matched cddid_all.tbl CDD TIGR01355 TIGR01355 273573 cyt_deam_dimer cytidine deaminase, homodimeric. This homodimeric zinc metalloprotein is found in Arabidopis and some Proteobacteria. A related, homotetrameric form with a much smaller subunit is found most bacteria and in animals. Both types may act on deoxycytidine as well as cytidine. [Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides] 283 matched cddid_all.tbl CDD TIGR01356 TIGR01356 273574 aroA 3-phosphoshikimate 1-carboxyvinyltransferase. This model represents 3-phosphoshikimate-1-carboxyvinyltransferase (aroA), which catalyzes the sixth of seven steps in the shikimate pathway of the biosynthesis of chorimate. Chorismate is last common precursor of all three aromatic amino acids. Sequences scoring between the trusted and noise cutoffs include fragmentary and aberrant sequences in which generally well-conserved motifs are missing or altererd, but no example of a protein known to have a different function. [Amino acid biosynthesis, Aromatic amino acid family] 409 matched cddid_all.tbl CDD TIGR01357 TIGR01357 273575 aroB 3-dehydroquinate synthase. This model represents 3-dehydroquinate synthase, the enzyme catalyzing the second of seven steps in the shikimate pathway of chorismate biosynthesis. Chorismate is the last common intermediate in the biosynthesis of all three aromatic amino acids. [Amino acid biosynthesis, Aromatic amino acid family] 344 matched cddid_all.tbl CDD TIGR01358 TIGR01358 130425 DAHP_synth_II 3-deoxy-7-phosphoheptulonate synthase, class II. This model represents the class II family of 3-deoxy-7-phosphoheptulonate synthase, aka phospho-2-dehydro-3-deoxyheptonate aldolase, as found in plants and some bacteria. It shows some similarity to the class I family found in many bacteria. The enzyme catalyzes the first of 7 steps in the biosynthesis of chorismate, that last common precursor of all three aromatic amino acids. Homologs scoring between trusted and noise cutoff include proteins involved in antibiotic biosynthesis; one example is active as this enzyme, while another acts on an amino analog. [Amino acid biosynthesis, Aromatic amino acid family] 443 matched cddid_all.tbl CDD TIGR01359 TIGR01359 273576 UMP_CMP_kin_fam UMP-CMP kinase family. This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic. 185 matched cddid_all.tbl CDD TIGR01360 TIGR01360 130427 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily. Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351. 188 matched cddid_all.tbl CDD TIGR01361 TIGR01361 273577 DAHP_synth_Bsub 3-deoxy-7-phosphoheptulonate synthase. This model describes one of at least three types of phospho-2-dehydro-3-deoxyheptonate aldolase (DAHP synthase). This enzyme catalyzes the first of 7 steps in the biosynthesis of chorismate, that last common precursor of all three aromatic amino acids and of PABA, ubiquinone and menaquinone. Some members of this family, including an experimentally characterized member from Bacillus subtilis, are bifunctional, with a chorismate mutase domain N-terminal to this region. The member of this family from Synechocystis PCC 6803, CcmA, was shown to be essential for carboxysome formation. However, no other candidate for this enzyme is present in that species, chorismate biosynthesis does occur, other species having this protein lack carboxysomes but appear to make chorismate, and a requirement of CcmA for carboxysome formation does not prohibit a role in chorismate biosynthesis. [Amino acid biosynthesis, Aromatic amino acid family] 260 matched cddid_all.tbl CDD TIGR01362 TIGR01362 130429 KDO8P_synth 3-deoxy-8-phosphooctulonate synthase. This model describes 3-deoxy-8-phosphooctulonate synthase. Alternate names include 2-dehydro-3-deoxyphosphooctonate aldolase, 3-deoxy-d-manno-octulosonic acid 8-phosphate and KDO-8 phosphate synthetase. It catalyzes the aldol condensation of phosphoenolpyruvate with D-arabinose 5-phosphate: phosphoenolpyruvate + D-arabinose 5-phosphate + H2O = 2-dehydro-3-deoxy-D-octonate 8-phosphate + phosphate In Gram-negative bacteria, this is the first step in the biosynthesis of 3-deoxy-D-manno-octulosonate, part of the oligosaccharide core of lipopolysaccharide. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 258 matched cddid_all.tbl CDD TIGR01363 TIGR01363 273578 strep_his_triad streptococcal histidine triad protein. This model represents the N-terminal half of a family of Streptococcal proteins that contain a signal peptide and then up to five repeats of a region that includes a His-X-X-His-X-His (histidine triad) motif. Three repeats are found in the seed alignment. Additional copies in more poorly conserved regions may be detected. Members of this family from Streptococcus pneumoniae are suggested to cleave human C3, and the member PhpA has been shown in vaccine studies to be a protective antigen in mice. [Cellular processes, Pathogenesis] 348 matched cddid_all.tbl CDD TIGR01364 TIGR01364 130431 serC_1 phosphoserine aminotransferase. This model represents the common form of the phosphoserine aminotransferase SerC. The phosphoserine aminotransferase of the archaeon Methanosarcina barkeri and putative phosphoserine aminotransferase of Mycobacterium tuberculosis are represented by separate models. All are members of the class V aminotransferases (pfam00266). [Amino acid biosynthesis, Serine family] 349 matched cddid_all.tbl CDD TIGR01365 TIGR01365 130432 serC_2 phosphoserine aminotransferase, Methanosarcina type. This model represents a variant form of the serine biosynthesis enzyme phosphoserine aminotransferase, as found in a small number of distantly related species, including Caulobacter crescentus, Mesorhizobium loti, and the archaeon Methanosarcina barkeri. [Amino acid biosynthesis, Serine family] 374 matched cddid_all.tbl CDD TIGR01366 TIGR01366 130433 serC_3 phosphoserine aminotransferase, putative. This model represents a putative variant form of the serine biosynthesis enzyme phosphoserine aminotransferase, as found in Mycobacterium tuberculosis and related high-GC Gram-positive bacteria. [Amino acid biosynthesis, Serine family] 361 matched cddid_all.tbl CDD TIGR01367 TIGR01367 273579 pyrE_Therm orotate phosphoribosyltransferase, Thermus family. This model represents a distinct clade of orotate phosphoribosyltransferases. Members include the experimentally determined example from Thermus aquaticus and additional examples from Caulobacter crescentus, Helicobacter pylori, Mesorhizobium loti, and related species. [Purines, pyrimidines, nucleosides, and nucleotides, Pyrimidine ribonucleotide biosynthesis] 187 matched cddid_all.tbl CDD TIGR01368 TIGR01368 273580 CPSaseIIsmall carbamoyl-phosphate synthase, small subunit. This model represents the whole of the small chain of the glutamine-dependent form (EC 6.3.5.5) of carbamoyl phosphate synthase, CPSase II. The C-terminal domain has glutamine amidotransferase activity. Note that the sequence from the mammalian urea cycle form has lost the active site Cys, resulting in an ammonia-dependent form, CPSase I (EC 6.3.4.16). CPSases of pyrimidine biosynthesis, arginine biosynthesis, and the urea cycle may be encoded by one or by several genes, depending on the species. [Purines, pyrimidines, nucleosides, and nucleotides, Pyrimidine ribonucleotide biosynthesis] 357 matched cddid_all.tbl CDD TIGR01369 TIGR01369 273581 CPSaseII_lrg carbamoyl-phosphate synthase, large subunit. Carbamoyl-phosphate synthase (CPSase) catalyzes the first committed step in pyrimidine, arginine, and urea biosynthesis. In general, it is a glutamine-dependent enzyme, EC 6.3.5.5, termed CPSase II in eukaryotes. An exception is the mammalian mitochondrial urea-cycle form, CPSase I, in which the glutamine amidotransferase domain active site Cys on the small subunit has been lost, and the enzyme is ammonia-dependent. In both CPSase I and the closely related, glutamine-dependent CPSase III (allosterically activated by acetyl-glutamate) demonstrated in some other vertebrates, the small and large chain regions are fused in a single polypeptide chain. This model represents the large chain of glutamine-hydrolysing carbamoyl-phosphate synthases, or the corresponding regions of larger, multifunctional proteins, as found in all domains of life, and CPSase I forms are considered exceptions within the family. In several thermophilic species (Methanobacterium thermoautotrophicum, Methanococcus jannaschii, Aquifex aeolicus), the large subunit appears split, at different points, into two separate genes. [Purines, pyrimidines, nucleosides, and nucleotides, Pyrimidine ribonucleotide biosynthesis] 1050 matched cddid_all.tbl CDD TIGR01370 TIGR01370 273582 TIGR01370 "extracellular protein. Original assignment of this protein family as cysteinyl-tRNA synthetase is controversial, supported by but challenged by and by subsequent discovery of the actual mechanism for synthesizing Cys-tRNA in species where a direct Cys--tRNA ligase was not found. Lingering legacy annotations of members of this family probably should be removed. Evidence against the role includes a signal peptide. This family as been renamed ""extracellular protein"" to facilitate correction. Members of this family occur in Deinococcus radiodurans (bacterial) and Methanococcus jannaschii (archaeal). A number of homologous but more distantly related proteins are annotated as alpha-1,4 polygalactosaminidases. The function remains unknown. [Unknown function, General]" 315 matched cddid_all.tbl CDD TIGR01371 TIGR01371 273583 met_syn_B12ind 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase. This model describes the cobalamin-independent methionine synthase. A family of uncharacterized archaeal proteins is homologous to the C-terminal region of this family. That family is excluded from this model but, along with this family, belongs to pfam01717. [Amino acid biosynthesis, Aspartate family] 750 matched cddid_all.tbl CDD TIGR01372 TIGR01372 273584 soxA sarcosine oxidase, alpha subunit family, heterotetrameric form. This model describes the alpha subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Mesorhizobium loti and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members are share the same function. The model is designated as subfamily rather than equivalog for this reason.Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) forms [Energy metabolism, Amino acids and amines] 985 matched cddid_all.tbl CDD TIGR01373 TIGR01373 273585 soxB sarcosine oxidase, beta subunit family, heterotetrameric form. This model describes the beta subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Mesorhizobium loti and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members are share the same function. The model is designated as subfamily rather than equivalog for this reason. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) forms. [Energy metabolism, Amino acids and amines] 407 matched cddid_all.tbl CDD TIGR01374 TIGR01374 130441 soxD sarcosine oxidase, delta subunit family, heterotetrameric form. This model describes the delta subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Mesorhizobium loti and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members are share the same function. The model is designated as subfamily rather than equivalog for this reason. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) form [Energy metabolism, Amino acids and amines] 84 matched cddid_all.tbl CDD TIGR01375 TIGR01375 273586 soxG sarcosine oxidase, gamma subunit family, heterotetrameric form. This model describes the gamma subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Mesorhizobium loti and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members are share the same function. The model is designated as subfamily rather than equivalog for this reason. The gamma subunit is the most divergent between operons of the four subunits. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) forms. [Energy metabolism, Amino acids and amines] 152 matched cddid_all.tbl CDD TIGR01376 TIGR01376 273587 POMP_repeat Chlamydial polymorphic outer membrane protein repeat. This model represents a repeat region of about 27 residues that appears from twice to over twenty times in Chlamydial polymorphic outer membrane proteins (POMP). Characteristic motifs in the repeat are FXXN and GGAI. Except for a few apparently truncated examples, Chlamydial proteins have this repeat region if and only if they also have the autotransporter beta-domain (pfam03797) at the C-terminus, with Phe as the C-terminal residue. This repeat is observed, but is very rare, outside the Chlamydias. 27 matched cddid_all.tbl CDD TIGR01377 TIGR01377 130444 soxA_mon sarcosine oxidase, monomeric form. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) forms [Energy metabolism, Amino acids and amines] 380 matched cddid_all.tbl CDD TIGR01378 TIGR01378 273588 thi_PPkinase thiamine pyrophosphokinase. This model has been revised. Originally, it described strictly eukaryotic thiamine pyrophosphokinase. However, it is now expanded to include also homologous enzymes, apparently functionally equivalent, from species that rely on thiamine pyrophosphokinase rather than thiamine-monophosphate kinase (TIGR01379) to produce the active TPP cofactor. This includes the thiamine pyrophosphokinase from Bacillus subtilis, previously designated YloS. [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine] 205 matched cddid_all.tbl CDD TIGR01379 TIGR01379 273589 thiL thiamine-phosphate kinase. This model describes thiamine-monophosphate kinase, an enzyme that converts thiamine monophosphate into thiamine pyrophosphate (TPP, coenzyme B1), an enzyme cofactor. Thiamine monophosphate may be derived from de novo synthesis or from unphosphorylated thiamine, known as vitamin B1. Proteins scoring between the trusted and noise cutoff for this model include short forms from the Thermoplasmas (which lack the N-terminal region) and a highly derived form from Campylobacter jejuni. Eukaryotes lack this enzyme, and add pyrophosphate from ATP to unphosphorylated thiamine in a single step. [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine] 317 matched cddid_all.tbl CDD TIGR01380 TIGR01380 130447 glut_syn glutathione synthetase, prokaryotic. This model was built using glutathione synthetases found in Gram-negative bacteria. This gene does not appear to be present in genomes of Gram-positive bacteria. Glutathione synthetase has an ATP-binding domain in the COOH terminus and catalyzes the second step in the glutathione biosynthesis pathway: ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione. Glutathione is a tripeptide that functions as a reductant in many cellular reactions. [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 312 matched cddid_all.tbl CDD TIGR01381 TIGR01381 273590 E1_like_apg7 E1-like protein-activating enzyme Gsa7p/Apg7p. This model represents a family of eukaryotic proteins found in animals, plants, and yeasts, including Apg7p (YHR171W) from Saccharomyces cerevisiae and GSA7 from Pichia pastoris. Members are about 650 to 700 residues in length and include a central domain of about 150 residues shared with the ThiF/MoeB/HesA family of proteins. A low level of similarity to ubiquitin-activating enzyme E1 is described in a paper on peroxisome autophagy mediated by GSA7, and is the basis of the name ubiquitin activating enzyme E1-like protein. Members of the family appear to be involved in protein lipidation events analogous to ubiquitination and required for membrane fusion events during autophagy. 664 matched cddid_all.tbl CDD TIGR01382 TIGR01382 273591 PfpI intracellular protease, PfpI family. The member of this family from Pyrococcus horikoshii has been solved to 2 Angstrom resolution. It is an ATP-independent intracellular protease that crystallizes as a hexameric ring. Cys-101 is proposed as the active site residue in a catalytic triad with the adjacent His-102 and a Glu residue from an adjacent monomer. A member of this family from Bacillus subtilis, GSP18, has been shown to be expressed in response to several forms of stress. A role in the degradation of small peptides has been suggested. A closely related family consists of the thiamine biosynthesis protein ThiJ and its homologs. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 166 matched cddid_all.tbl CDD TIGR01383 TIGR01383 213612 not_thiJ DJ-1 family protein. This model represents the DJ-1 clade of the so-called ThiJ/PfpI family of proteins. PfpI, represented by a distinct model, is a putative intracellular cysteine protease. DJ-1 is described as an oncogene that acts cooperatively with H-Ras. Many members of the DJ-1 clade are annotated (apparently incorrectly) as ThiJ, a protein of thiamine biosynthesis. However, published reports of ThiJ activity and identification of a ThiJ/ThiD bifunctional protein describe an unrelated locus mapping near ThiM, rather than the DJ-1 homolog of E. coli. The ThiJ designation for this family may be spurious; the cited paper refers to a locus near thiD and thiM in E. coli, unlike the gene represented here. Current public annotation reflects ThiJ/ThiD bifunctional activity, apparently a property of ThiD and not of this locus. [Unknown function, General] 179 matched cddid_all.tbl CDD TIGR01384 TIGR01384 130451 TFS_arch transcription factor S, archaeal. This model describes archaeal transcription factor S, a protein related in size and sequence to certain eukaryotic RNA polymerase small subunits, and in sequence and function to the much larger eukaryotic transcription factor IIS (TFIIS). Although originally suggested to be a subunit of the archaeal RNA polymerase, it elutes separately from active polymerase in gel filtration experiments and acts, like TFIIs, as an induction factor for RNA cleavage by RNA polymerase. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae. [Transcription, Transcription factors] 104 matched cddid_all.tbl CDD TIGR01385 TIGR01385 273592 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end. 299 matched cddid_all.tbl CDD TIGR01386 TIGR01386 273593 cztS_silS_copS heavy metal sensor kinase. Members of this family contain a sensor histidine kinase domain (pfam00512) and a domain found in bacterial signal proteins (pfam00672). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. 457 matched cddid_all.tbl CDD TIGR01387 TIGR01387 130454 cztR_silR_copR heavy metal response regulator. Members of this family contain a response regulator receiver domain (pfam00072) and an associated transcriptional regulatory region (pfam00486). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system. [Regulatory functions, DNA interactions] 218 matched cddid_all.tbl CDD TIGR01388 TIGR01388 130455 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown. [Transcription, RNA processing] 367 matched cddid_all.tbl CDD TIGR01389 TIGR01389 273594 recQ ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ. [DNA metabolism, DNA replication, recombination, and repair] 591 matched cddid_all.tbl CDD TIGR01390 TIGR01390 130457 CycNucDiestase 2',3'-cyclic-nucleotide 2'-phosphodiesterase. 2',3'-cyclic-nucleotide 2'-phosphodiesterase is a bifunctional enzyme localized to the periplasm of Gram-negative bacteria. 2',3'-cyclic-nucleotide 2'-phosphodiesters are intermediates formed during the hydrolysis of RNA by the ribonuclease I, which is also found to the periplasm, and other enzymes of the RNAse T2 family. Bacteria are unable to transport 2',3'-cyclic-nucleotides into the cytoplasm. 2',3'-cyclic-nucleotide 2'-phosphodiesterase contains 2 active sites which catalyze the reactions that convert the 2',3'-cyclic-nucleotide into a 3'-nucleotide, which is then converted into nucleic acid and phosphate. Both final products can be transported into the cytoplasm. Thus, it has been suggested that 2',3'-cyclic-nucleotide 2'-phosphodiesterase has a 'scavenging' function. Experimental evidence indicates that 2',3'-cyclic-nucleotide 2'-phosphodiesterase enables Yersinia enterocolitica O:8 to grow on 2'3'-cAMP as a sole source of carbon and energy (). [Purines, pyrimidines, nucleosides, and nucleotides, Other] 626 matched cddid_all.tbl CDD TIGR01391 TIGR01391 273595 dnaG DNA primase, catalytic core. Members of this family are DNA primase, a ubiquitous bacteria protein. Most members of this family contain nearly two hundred additional residues C-terminal to the region represented here, but conservation between species is poor and the C-terminal region was not included in the seed alignment. This protein contains a CHC2 zinc finger (pfam01807) and a Toprim domain (pfam01751). [DNA metabolism, DNA replication, recombination, and repair] 415 matched cddid_all.tbl CDD TIGR01392 TIGR01392 273596 homoserO_Ac_trn homoserine O-acetyltransferase. This family describes homoserine-O-acetyltransferase, an enzyme of methionine biosynthesis. This model has been rebuilt to identify sequences more broadly, including a number of sequences suggested to be homoserine O-acetyltransferase based on proximity to other Met biosynthesis genes. [Amino acid biosynthesis, Aspartate family] 351 matched cddid_all.tbl CDD TIGR01393 TIGR01393 130460 lepA elongation factor 4. LepA (GUF1 in Saccaromyces), now called elongation factor 4, is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function is unknown. [Unknown function, General] 595 matched cddid_all.tbl CDD TIGR01394 TIGR01394 273597 TypA_BipA GTP-binding protein TypA/BipA. This bacterial (and Arabidopsis) protein, termed TypA or BipA, a GTP-binding protein, is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways, but the precise function is unknown. [Regulatory functions, Other, Cellular processes, Adaptations to atypical conditions, Protein synthesis, Translation factors] 594 matched cddid_all.tbl CDD TIGR01395 TIGR01395 130462 FlgC flagellar basal-body rod protein FlgC. This model represents FlgC, one of several components of bacterial flagella that share a domain described by pfam00460. FlgC is part of the basal body. [Cellular processes, Chemotaxis and motility] 135 matched cddid_all.tbl CDD TIGR01396 TIGR01396 273598 FlgB flagellar basal-body rod protein FlgB. This model represents FlgB, one of several components of bacterial flagella that share a domain described by pfam00460. FlgB is part of the basal body. [Cellular processes, Chemotaxis and motility] 131 matched cddid_all.tbl CDD TIGR01397 TIGR01397 130464 fliM_switch flagellar motor switch protein FliM. Members of this family are the flagellar motor switch protein FliM. The family excludes FliM homologs that lack an N-terminal region critical to interaction with phosphorylated CheY. One set lacking this N-terminal region is found in Rhizobium meliloti, in which the direction of flagellar rotation is not reversible (i.e. the FliM homolog does not act to reverse the motor direction), and in related species. Another is found in Buchnera, an obligate intracellular endosymbiont with genes for many of the components of the flagellar apparatus, but not, apparently, for flagellin iself. [Cellular processes, Chemotaxis and motility] 320 matched cddid_all.tbl CDD TIGR01398 TIGR01398 273599 FlhA flagellar biosynthesis protein FlhA. This model describes flagellar biosynthesis protein FlhA, one of a large number of genes associated with the biosynthesis of functional bacterial flagella. Homologs of many such proteins, including FlhA, function in type III protein secretion systems. A separate model describes InvA (Salmonella enterica), LcrD (Yersinia enterocolitica), HrcV (Xanthomonas), etc., all of which score below the noise cutoff for this model. [Cellular processes, Chemotaxis and motility] 678 matched cddid_all.tbl CDD TIGR01399 TIGR01399 273600 hrcV type III secretion protein, HrcV family. Members of this family are closely homologous to the flagellar biosynthesis protein FlhA (TIGR01398) and should all participate in type III secretion systems. Examples include InvA (Salmonella enterica), LcrD (Yersinia enterocolitica), HrcV (Xanthomonas), etc. Type III secretion systems resemble flagellar biogenesis systems, and may share the property of translocating special classes of peptides through the membrane. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 677 matched cddid_all.tbl CDD TIGR01400 TIGR01400 130467 fliR flagellar biosynthetic protein FliR. This model recognizes the FliR protein of bacterial flagellar biosynthesis. It distinguishes FliR from the homologous proteins bacterial type III protein secretion systems, known by names such as YopT, EscT, and HrcT. [Cellular processes, Chemotaxis and motility] 245 matched cddid_all.tbl CDD TIGR01401 TIGR01401 130468 fliR_like_III type III secretion protein SpaR/YscT/HrcT. This model represents members of bacterial type III secretion systems homologous to the flagellar biosynthetic protein FliR (TIGRFAMs:TIGR01400). [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 253 matched cddid_all.tbl CDD TIGR01402 TIGR01402 130469 fliQ flagellar biosynthetic protein FliQ. This model describes FliQ, a protein involved in biosynthesis of bacterial flagella. A related family of proteins, excluded from this model, participates in bacterial type III protein secretion systems. [Cellular processes, Chemotaxis and motility] 88 matched cddid_all.tbl CDD TIGR01403 TIGR01403 130470 fliQ_rel_III type III secretion protein, HrpO family. This model represents one of several families of proteins related to bacterial flagellar biosynthesis proteins and involved in bacterial type III protein secretion systems. This family is homologous to, but distinguished from, flagellar biosynthetic protein FliQ. This model may not identify all type III secretion system FliQ homologs. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 81 matched cddid_all.tbl CDD TIGR01404 TIGR01404 130471 FlhB_rel_III type III secretion protein, YscU/HrpY family. This model represents one of several families of proteins related to bacterial flagellar biosynthesis proteins and involved in bacterial type III protein secretion systems. This family is homologous to, but distinguished from, flagellar biosynthetic protein FlhB (TIGRFAMs model TIGR00328). This model may not identify all type III secretion system FlhB homologs. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 342 matched cddid_all.tbl CDD TIGR01405 TIGR01405 273601 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. This model describes a polypeptide chain of DNA polymerase III. Full-length homologs of this protein are restricted to the Gram-positive lineages, including the Mycoplasmas. This protein is designated alpha chain and given the gene symbol polC, but is not a full-length homolog of other polC genes. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model. [DNA metabolism, DNA replication, recombination, and repair] 1213 matched cddid_all.tbl CDD TIGR01406 TIGR01406 130473 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria. [DNA metabolism, DNA replication, recombination, and repair] 225 matched cddid_all.tbl CDD TIGR01407 TIGR01407 273602 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli. [DNA metabolism, DNA replication, recombination, and repair] 850 matched cddid_all.tbl CDD TIGR01408 TIGR01408 273603 Ube1 ubiquitin-activating enzyme E1. This model represents the full length, over a thousand amino acids, of a multicopy family of eukaryotic proteins, many of which are designated ubiquitin-activating enzyme E1. Members have two copies of the ThiF family domain (pfam00899), a repeat found in ubiquitin-activating proteins (pfam02134), and other regions. 1006 matched cddid_all.tbl CDD TIGR01409 TIGR01409 273604 TAT_signal_seq Tat (twin-arginine translocation) pathway signal sequence. Proteins assembled with various cofactors or by means of cytosolic molecular chaperones are poor candidates for translocation across the bacterial inner membrane by the standard general secretory (Sec) pathway. This model describes a family of predicted long, non-Sec signal sequences and signal-anchor sequences (uncleaved signal sequences). All contain an absolutely conserved pair of arginine residues, in a motif approximated by (S/T)-R-R-X-F-L-K, followed by a membrane-spanning hydrophobic region. Members with small amino acid side chains at the -1 and -3 positions from the C-terminus of the model should be predicted to be cleaved as are Sec pathway signal sequences. Members are almost exclusively bacterial, although archaeal sequences are also found. A large fraction of the members of this family may have bound redox-active cofactors. [Protein fate, Protein and peptide secretion and trafficking] 29 matched cddid_all.tbl CDD TIGR01410 TIGR01410 130477 tatB twin arginine-targeting protein translocase TatB. This model represents the TatB protein of a Sec-independent system for transporting folded proteins, often with a bound redox cofactor, across the bacterial inner membrane. TatC is the multiple membrane spanning component. TatB, like the related TatA/E proteins, appears to span the membrane one time. The tat system recognizes proteins with an elongated signal sequence containing a conserved R-R in a motif approximated by RRxFLK N-terminal to the transmembrane helix. TIGRFAMs model TIGR01409 describes this twin-Arg signal sequence. A similar system, termed Delta-pH-dependent transport, operates on chloroplast-encoded proteins. [Protein fate, Protein and peptide secretion and trafficking] 80 matched cddid_all.tbl CDD TIGR01411 TIGR01411 273605 tatAE twin arginine-targeting protein translocase, TatA/E family. This model distinguishes TatA/E from the related TatB, but does not distinguish TatA from TatE. The Tat (twin-arginine translocation) system is a Sec-independent exporter for folded proteins, often with a redox cofactor already bound, across the bacterial inner membrane. Functionally equivalent systems are found in the chloroplast and some in archaeal species. The signal peptide recognized by the Tat system is modeled by TIGR01409. [Protein fate, Protein and peptide secretion and trafficking] 47 matched cddid_all.tbl CDD TIGR01412 TIGR01412 273606 tat_substr_1 Tat-translocated enzyme. This model represents a small family of proteins with a typical Tat (twin-arginine translocation) signal sequence, suggesting that the family is exported in a folded state, perhaps with a bound redox cofactor. Members of this family show homology to Dyp, a dye-decolorizing peroxidase from Geotrichum candidum that lacks any typical heme-binding site. 414 matched cddid_all.tbl CDD TIGR01413 TIGR01413 273607 Dyp_perox_fam Dyp-type peroxidase family. A defined member of this superfamily is Dyp, a dye-decolorizing peroxidase that lacks a typical heme-binding region. A distinct, uncharacterized branch (TIGR01412) of this superfamily has a typical twin-arginine dependent signal sequence characteristic of exported proteins with bound redox cofactors. 308 matched cddid_all.tbl CDD TIGR01414 TIGR01414 273608 autotrans_barl outer membrane autotransporter barrel domain. A number of Gram-negative bacterial proteins, mostly found in pathogens and associated with virulence, contain a conserved C-terminal domain that integrates into the outer membrane and enables the N-terminal region to be delivered across the membrane. This C-terminal autotransporter domain is about 400 amino acids in length and includes the aromatic amino acid-rich OMP signal, typically ending with a Phe or Trp residue, at the extreme C-terminus. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 431 matched cddid_all.tbl CDD TIGR01415 TIGR01415 273609 trpB_rel pyridoxal-phosphate dependent TrpB-like enzyme. This model represents a family of pyridoxal-phosphate dependent enzyme (pfam00291) closely related to the beta subunit of tryptophan synthase (TIGR00263). However, the only case in which a member of this family replaces a member of TIGR00263 is in Sulfolobus species which contain two sequences which hit this model, one of which is proximal to the alpha subunit. In every other case so far, either the species appears not to make tryptophan (there is no trp synthase alpha subunit), or a trp synthase beta subunit matching TIGR00263 is also found. [Unknown function, Enzymes of unknown specificity] 419 matched cddid_all.tbl CDD TIGR01416 TIGR01416 273610 Rieske_proteo ubiquinol-cytochrome c reductase, iron-sulfur subunit. This model represents the Proteobacterial and mitochondrial type of the Rieske [2Fe-2S] iron-sulfur as found in ubiquinol-cytochrome c reductase. The model excludes the Rieske iron-sulfur protein as found in the cytochrome b6-f complex of the Cyanobacteria and chloroplasts. Most members of this family have a recognizable twin-arginine translocation (tat) signal sequence (DeltaPh-dependent translocation in chloroplast) for transport across the membrane with the 2Fe-2S group already bound. These signal sequences include a motif resembling RRxFLK before the transmembrane helix. [Energy metabolism, Electron transport] 174 matched cddid_all.tbl CDD TIGR01417 TIGR01417 273611 PTS_I_fam phosphoenolpyruvate-protein phosphotransferase. This model recognizes a distinct clade of phophoenolpyruvate (PEP)-dependent enzymes. Most members are known or deduced to function as the phosphoenolpyruvate-protein phosphotransferase (or enzyme I) of PTS sugar transport systems. However, some species with both a member of this family and a homolog of the phosphocarrier protein HPr lack a IIC component able to serve as a permease. An HPr homolog designated NPr has been implicated in the regulation of nitrogen assimilation, which demonstrates that not all phosphotransferase system components are associated directly with PTS transport. 565 matched cddid_all.tbl CDD TIGR01418 TIGR01418 273612 PEP_synth phosphoenolpyruvate synthase. Also called pyruvate,water dikinase and PEP synthase. The member from Methanococcus jannaschii contains a large intein. This enzyme generates phosphoenolpyruvate (PEP) from pyruvate, hydrolyzing ATP to AMP and releasing inorganic phosphate in the process. The enzyme shows extensive homology to other enzymes that use PEP as substrate or product. This enzyme may provide PEP for gluconeogenesis, for PTS-type carbohydrate transport systems, or for other processes. [Energy metabolism, Glycolysis/gluconeogenesis] 786 matched cddid_all.tbl CDD TIGR01419 TIGR01419 162350 nitro_reg_IIA PTS IIA-like nitrogen-regulatory protein PtsN. This model describes a full-length protein of about 160 residues closely related to the fructose-specific phosphotransferase (PTS) system IIA component. It is a regulatory protein found only in species with a phosphoenolpyruvate-protein phosphotransferase (enzyme I of PTS systems) and an HPr-like phosphocarrier protein, but not all species have a IIC-like permease. Members of this family are found in Proteobacteria, Chlamydia, and the spirochete Treponema pallidum. [Signal transduction, PTS] 145 matched cddid_all.tbl CDD TIGR01420 TIGR01420 273613 pilT_fam pilus retraction protein PilT. This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation. [Cell envelope, Surface structures, Cellular processes, Chemotaxis and motility] 343 matched cddid_all.tbl CDD TIGR01421 TIGR01421 273614 gluta_reduc_1 glutathione-disulfide reductase, animal/bacterial. The tripeptide glutathione is an important reductant, e.g., for maintaining the cellular thiol/disulfide status and for protecting against reactive oxygen species such as hydrogen peroxide. Glutathione-disulfide reductase regenerates reduced glutathione from oxidized glutathione (glutathione disulfide) + NADPH. This model represents one of two closely related subfamilies of glutathione-disulfide reductase. Both are closely related to trypanothione reductase, and separate models are built so each of the three can describe proteins with conserved function. This model describes glutathione-disulfide reductases of animals, yeast, and a number of animal-resident bacteria. [Energy metabolism, Electron transport] 450 matched cddid_all.tbl CDD TIGR01422 TIGR01422 188140 phosphonatase phosphonoacetaldehyde hydrolase. This enzyme catalyzes the cleavage of the carbon phosphorous bond of a phosphonate. The mechanism depends on the substrate having a carbonyl one carbon away from the cleavage position. This enzyme is a member of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases (pfam00702), and contains a modified version of the conserved catalytic motifs of that superfamily: the first motif is usually DxDx(T/V), here it is DxAxT, and in the third motif the normal conserved lysine is instead an arginine. Additionally, the enzyme contains a unique conserved catalytic lysine (B. cereus pos. 53) which is involved in the binding and activation of the substrate through the formation of a Schiff base. The substrate of this enzyme is the product of 2-aminoethylphosphonate (AEP) transaminase, phosphonoacetaldehyde. This degradation pathway for AEP may be related to its toxic properties which are utilized by microorganisms as a chemical warfare agent. [Central intermediary metabolism, Other] 253 matched cddid_all.tbl CDD TIGR01423 TIGR01423 200098 trypano_reduc trypanothione-disulfide reductase. Trypanothione, a glutathione-modified derivative of spermidine, is (in its reduced form) an important antioxidant found in trypanosomatids (Crithidia, Leishmania, Trypanosoma). This model describes trypanothione reductase, a possible antitrypanosomal drug target closely related to some forms of glutathione reductase. 486 matched cddid_all.tbl CDD TIGR01424 TIGR01424 213618 gluta_reduc_2 glutathione-disulfide reductase, plant. The tripeptide glutathione is an important reductant, e.g., for maintaining the cellular thiol/disulfide status and for protecting against reactive oxygen species such as hydrogen peroxide. Glutathione-disulfide reductase regenerates reduced glutathione from oxidized glutathione (glutathione disulfide) + NADPH. This model represents one of two closely related subfamilies of glutathione-disulfide reductase. Both are closely related to trypanothione reductase, and separate models are built so each of the three can describe proteins with conserved function. This model describes glutathione-disulfide reductases of plants and some bacteria, including cyanobacteria. [Energy metabolism, Electron transport] 446 matched cddid_all.tbl CDD TIGR01425 TIGR01425 273615 SRP54_euk signal recognition particle protein SRP54. This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model. 428 matched cddid_all.tbl CDD TIGR01426 TIGR01426 273616 MGT glycosyltransferase, MGT family. This model describes the MGT (macroside glycosyltransferase) subfamily of the UDP-glucuronosyltransferase family. Members include a number of glucosyl transferases for macrolide antibiotic inactivation, but also include transferases of glucose-related sugars for macrolide antibiotic production. [Cellular processes, Toxin production and resistance] 392 matched cddid_all.tbl CDD TIGR01427 TIGR01427 273617 PTS_IIC_fructo PTS system, fructose subfamily, IIC component. This model represents the IIC component, or IIC region of a IIABC or IIBC polypeptide of a phosphotransferase system for carbohydrate transport. Members of this family belong to the fructose-specific subfamily of the broader family (pfam02378) of PTS IIC proteins. Members should be found as part of the same chain or in the same operon as fructose family IIA (TIGR00848) and IIB (TIGR00829) protein regions. A number of bacterial species have members in two different branches of this subfamily, suggesting some diversity in substrate specificity of its members. 346 matched cddid_all.tbl CDD TIGR01428 TIGR01428 130495 HAD_type_II 2-haloalkanoic acid dehalogenase, type II. Catalyzes the hydrolytic dehalogenation of small L-2-haloalkanoic acids to yield the corresponding D-2-hydroxyalkanoic acids. Belongs to the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases (pfam00702), class (subfamily) I. Note that the Type I HAD enzymes have not yet been fully characterized, but clearly utilize a substantially different catalytic mechanism and are thus unlikely to be related. 198 matched cddid_all.tbl CDD TIGR01429 TIGR01429 273618 AMP_deaminase AMP deaminase. This model describes AMP deaminase, a large, well-conserved eukaryotic protein involved in energy metabolism. Most members of the family have an additional, poorly alignable region of 150 amino acids or more N-terminal to the region included in the model. 611 matched cddid_all.tbl CDD TIGR01430 TIGR01430 273619 aden_deam adenosine deaminase. This family includes the experimentally verified adenosine deaminases of mammals and E. coli. Other members of this family are predicted also to be adenosine deaminase, an enzyme of nucleotide degradation. This family is distantly related to AMP deaminase. 324 matched cddid_all.tbl CDD TIGR01431 TIGR01431 273620 adm_rel adenosine deaminase-related growth factor. Members of this family have been described as secreted proteins with growth factor activity and regions of adenosine deaminase homology in insects, mollusks, and vertebrates. 479 matched cddid_all.tbl CDD TIGR01432 TIGR01432 273621 QOXA cytochrome aa3 quinol oxidase, subunit II. This enzyme catalyzes the oxidation of quinol with the concomitant reduction of molecular oxygen to water. This acts as the terminal electron acceptor in the respiratory chain. This subunit contains two transmembrane helices and a large external domain responsible for the binding and oxidation of quinol. QuoX is (presently) only found in gram positive bacteria of the Bacillus/Staphylococcus group. Like CyoA, the ubiquinol oxidase found in proteobacteria, the residues responsible for the ligation of Cu(a) and cytochrome c (found in the related cyt. c oxidases) are absent. Unlike CyoA, QoxA is in complex with a subunit I which contains cytochromes a similar to the cyt. c oxidases (as opposed to cytochromes b). [Energy metabolism, Electron transport] 226 matched cddid_all.tbl CDD TIGR01433 TIGR01433 213620 CyoA cytochrome o ubiquinol oxidase subunit II. This enzyme catalyzes the oxidation of ubiquinol with the concomitant reduction of molecular oxygen to water. This acts as the terminal electron acceptor in the respiratory chain. Subunit II is responsible for binding and oxidation of the ubiquinone substrate. This sequence is closely related to QoxA, which oxidizes quinol in gram positive bacteria but which is in complex with subunits which utilize cytochromes a in the reduction of molecular oxygen. Slightly more distantly related is subunit II of cytochrome c oxidase which uses cyt. c as the oxidant. [Energy metabolism, Electron transport] 226 matched cddid_all.tbl CDD TIGR01434 TIGR01434 213621 glu_cys_ligase glutamate--cysteine ligase. Alternate name: gamma-glutamylcysteine synthetase. This model represents glutamate--cysteine ligase, and enzyme in the biosynthesis of glutathione (GSH). GSH is one of several low molecular weight cysteine derivatives that can serve to protect against oxidative damage and participate in a biosynthetic or detoxification reactions. [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 512 matched cddid_all.tbl CDD TIGR01435 TIGR01435 273622 glu_cys_lig_rel glutamate--cysteine ligase/glutathione synthase, Streptococcus agalactiae type. This model represents a bifunctional protein family for the biosynthesis of glutathione, and perhaps a range of related gamma-glutamyltripeptides of the form gamma-Glu-Cys-X(aa). The N-terminal region is similar to proteobacterial glutamate-cysteine ligase. The C-terminal region is homologous to cyanophycin synthetase of cyanobacteria and, more distantly, to D-alanine-D-alanine ligases. Members of this family are found in Listeria and Enterococcus, Gram-positive lineages in which glutathione is produced (see PUBMED:8606174), and in Pasteurella multocida, a Proteobacterium. In Clostridium acetobutylicum, adjacent genes include separate proteins rather than a fusion protein. [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 737 matched cddid_all.tbl CDD TIGR01436 TIGR01436 130503 glu_cys_lig_pln glutamate--cysteine ligase, plant type. This model represents one of two highly dissimilar forms of glutamate--cysteine ligase (gamma-glutamylcysteine synthetase), an enzyme of glutathione biosynthesis. The other type is modeled by TIGR01434. This type is found in plants (with a probable transit peptide), root nodule and other bacteria, but not E. coli and closely related species. [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 446 matched cddid_all.tbl CDD TIGR01437 TIGR01437 273623 selA_rel uncharacterized pyridoxal phosphate-dependent enzyme. This model describes a protein related to a number of pyridoxal phosphate-dependent enzymes, and in particular to selenocysteine synthase (SelA), which converts Ser to selenocysteine on its tRNA. While resembling SelA, this protein is found only in species that have a better candidate SelA or else lack the other genes (selB, selC, and selD) required for selenocysteine incorporation. [Unknown function, Enzymes of unknown specificity] 363 matched cddid_all.tbl CDD TIGR01438 TIGR01438 273624 TGR thioredoxin and glutathione reductase selenoprotein. This homodimeric, FAD-containing member of the pyridine nucleotide disulfide oxidoreductase family contains a C-terminal motif Cys-SeCys-Gly, where SeCys is selenocysteine encoded by TGA (in some sequence reports interpreted as a stop codon). In some members of this subfamily, Cys-SeCys-Gly is replaced by Cys-Cys-Gly. The reach of the selenium atom at the C-term arm of the protein is proposed to allow broad substrate specificity. 484 matched cddid_all.tbl CDD TIGR01439 TIGR01439 273625 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609. [Regulatory functions, DNA interactions] 43 matched cddid_all.tbl CDD TIGR01440 TIGR01440 130507 TIGR01440 TIGR01440 family protein. Members of this family are uncharacterized proteins of about 180 amino acids from the Bacillus/Clostridium group of Gram-positive bacteria, found in no more than one copy per genome. [Hypothetical proteins, Conserved] 172 matched cddid_all.tbl CDD TIGR01441 TIGR01441 273626 GPR GPR endopeptidase. This model describes a tetrameric protease that makes the rate-limiting first cut in the small, acid-soluble spore proteins (SASP) of Bacillus subtilis and related species. The enzyme lacks clear homology to other known proteases. It processes its own amino end before becoming active to cleave SASPs. [Protein fate, Degradation of proteins, peptides, and glycopeptides, Cellular processes, Sporulation and germination] 358 matched cddid_all.tbl CDD TIGR01442 TIGR01442 273627 SASP_gamma small, acid-soluble spore protein, gamma-type. This model represents a family of small, glutamine and asparagine-rich peptides that store amino acids in the spores of Bacillus subtilis and related bacteria. Most members of the family have two copies of the spore protease (GPR) cleavage motif, typically EFASE in this family, separating three low-complexity repeats. [Cellular processes, Sporulation and germination] 85 matched cddid_all.tbl CDD TIGR01443 TIGR01443 213622 intein_Cterm intein C-terminal splicing region. This model represents the well-conserved C-terminal region of a large number of inteins. It is based on interated search results, starting with a curated collection of intein N-terminal splicing regions from InBase, the New England Biolabs Intein Database, as presented on its web site. Inteins are regions encoded within proteins from which they remove themselves after translation in a self-splicing reaction, leaving the remainder of the coding region to form a complete, functional protein as if the intein were never there. Proteins with inteins include RecA, GyrA, ribonucleotide reductase, and others. Most inteins have a central region with putative endonuclease activity. 21 matched cddid_all.tbl CDD TIGR01444 TIGR01444 273628 fkbM_fam methyltransferase, FkbM family. Members of this family are characterized by two well-conserved short regions separated by a variable in both sequence and length. The first of the two regions is found in a large number of proteins outside this subfamily, a number of which have been characterized as methyltransferases. One member of the present family, FkbM, was shown to be required for a specific methylation in the biosynthesis of the immunosuppressant FK506 in Streptomyces strain MA6548. 143 matched cddid_all.tbl CDD TIGR01445 TIGR01445 273629 intein_Nterm intein N-terminal splicing region. This model is based on interated search results, starting with a curated collection of intein N-terminal splicing regions from InBase, the New England Biolabs Intein Database, as presented on its web site. It is designed to recognize inteins but not the related region of the sonic hedgehog protein. 81 matched cddid_all.tbl CDD TIGR01446 TIGR01446 273630 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria. [DNA metabolism, DNA replication, recombination, and repair, Mobile and extrachromosomal element functions, Prophage functions] 73 matched cddid_all.tbl CDD TIGR01447 TIGR01447 273631 recD exodeoxyribonuclease V, alpha subunit. This family describes the exodeoxyribonuclease V alpha subunit, RecD. RecD is part of a RecBCD complex. A related family in the Gram-positive bacteria separates in a phylogenetic tree, has an additional N-terminal extension of about 200 residues, and is not supported as a member of a RecBCD complex by neighboring genes. The related family is consequently described by a different model. [DNA metabolism, DNA replication, recombination, and repair] 582 matched cddid_all.tbl CDD TIGR01448 TIGR01448 273632 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. [Unknown function, Enzymes of unknown specificity] 720 matched cddid_all.tbl CDD TIGR01449 TIGR01449 130516 PGP_bact 2-phosphoglycolate phosphatase, prokaryotic. PGP is an essential enzyme in the glycolate salvage pathway in higher organisms (photorespiration in plants). Phosphoglycolate results from the oxidase activity of RubisCO in the Calvin cycle when concentrations of carbon dioxide are low relative to oxygen. In Ralstonia (Alcaligenes) eutropha and Rhodobacter sphaeroides, the PGP gene (CbbZ) is located on an operon along with other Calvin cycle enzymes including RubisCO. The only other pertinent experimental evidence concerns the gene from E. coli. The in vitro activity of the Ralstonia and Escherichia enzymes was determined with crude cell extracts of strains containing PGP on expression plasmids and compared to controls. In E. coli, however, there does not appear to be a functional Calvin cycle (RubisCO is absent), although the E. coli PGP gene (gph) is on the same operon (dam) with ribulose-5-phosphate-3-epimerase (rpe), a gene in the pentose-phosphate pathway (along with other, unrelated genes). The E. coli enzyme is not expressed under normal laboratory conditions; the pathway to which it belongs has not been determined. In fact, the possibility exists, although unlikely, that the E. coli enzyme and others within this equivalog have as their physiological substrate another, closely related molecule. The other seed chosen for this model, from Xylella fastidiosa has no experimental evidence, but is a plant pathogen and thus may obtain phosphoglycolate from its host. This model has been restricted to encompass only proteobacteria as no related PGP has been verified outside of this clade. Sequences from Aquifex aeolicus and Treponema pallidum fall between the trusted and noise cutoffs. Just below the noise cutoff is a gene which is part of the operon for the biosynthesis of the blue pigment, indigoidine, from Erwinia (Pectobacterium) chrysanthemi, a plant pathogen. It does not seem likely, considering the proposed biosynthetic mechanism, that the dephosphorylation of phosphoglycolate or a closely related compound is required. Possibly, this gene is fortuitously located in this operon, or has an indirect relationship to the necessity for the biosynthesis of this compound. Sequences from 11 species have been annotated as PGP or putative PGP but fall below the noise cutoff. None of these have experimental validation. This enzyme is a member of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolase enzymes (pfam00702). [Energy metabolism, Sugars] 213 matched cddid_all.tbl CDD TIGR01450 TIGR01450 273633 recC exodeoxyribonuclease V, gamma subunit. This model describes the gamma subunit of exodeoxyribonuclease V. Species containing this protein should also have the alpha (TIGR01447) and beta (TIGR00609) subunits. Candidates from Borrelia and from the Chlamydias differ dramatically and score between trusted and noise cutoffs. [DNA metabolism, DNA replication, recombination, and repair] 1060 matched cddid_all.tbl CDD TIGR01451 TIGR01451 273634 B_ant_repeat conserved repeat domain. This model represents the conserved region of about 53 amino acids shared between regions, usually repeated, of proteins from a small number of phylogenetically distant prokaryotes. Examples include a 132-residue region found repeated in three of the five longest proteins of Bacillus anthracis, a 131-residue repeat in a cell wall-anchored protein of Enterococcus faecalis, and a 120-residue repeat in Methanobacterium thermoautotrophicum. A similar region is found in some Chlamydial outer membrane proteins. 53 matched cddid_all.tbl CDD TIGR01452 TIGR01452 273635 PGP_euk phosphoglycolate/pyridoxal phosphate phosphatase family. PGP is an essential enzyme in the glycolate salvage pathway in higher organisms (photorespiration in plants). Phosphoglycolate results from the oxidase activity of RubisCO in the Calvin cycle when concentrations of carbon dioxide are low relative to oxygen. In mammals, PGP is found in many tissues, notably in red blood cells where P-glycolate is and important activator of the hydrolysis of 2,3-bisphosphoglycerate, a major modifier of the oxygen affinity of hemoglobin. Pyridoxal phosphate (PLP, Vitamin B6) phosphatase is involved in the degradation of PLP in mammals and is widely distributed in human tissues including erythrocyes. The enzymes described here are members of the Haloacid dehalogenase superfamily of hydrolase enzymes (pfam00702). Unlike the bacterial PGP equivalog (TIGR01449), which is a member of class (subfamily) I, these enzymes are members of class (subfamily) II. These two families have almost certainly arisen from convergent evolution (although these two ancestors may themselves have diverged from a more distant HAD superfamily progenitor). The primary seed sequence for this model comes from Chlamydomonas reinhardtii, a photosynthetic alga. The enzyme has been purified and characterized and these data are fully consistent with the assignment of function as a PGPase involved in photorespiration. The second seed, from Homo sapiens chromosome 22 has been characterized as a pyridoxal phosphatase. Biochemical characterization of partially purified PGP's from various tissues including red blood cells have been performed while one gene for PGP has been localized to chromosome 16p13.3. The sequence used here maps to chromosome 22. There is indeed a related gene on chromosome 16 (and it is expressed, since EST's are found) which shows 46% identity. The chromosome 16 gene is not in evidence in nraa but translated from the genomic sequence. The third seed, from C. elegans, is only supported by sequence similarity. This model is limited to eukaryotic species including S. pombe and S. cerevisiae, although several archaea score between the trusted and noise cutoffs. This model is closely related to a family of bacterial sequences including the E. coli NagD and B. subtilus AraL genes which are characterized by the ability to hydrolyze para-nitrophenylphosphate (pNPPases or NPPases). The chlamydomonas PGPase d 279 matched cddid_all.tbl CDD TIGR01453 TIGR01453 273636 grpIintron_endo group I intron endonuclease. This model represents one subfamily of endonucleases containing the endo/excinuclease amino terminal domain, pfam01541 at its amino end. A distinct subfamily includes excinuclease abc subunit c (uvrC). Members of pfam01541 are often termed GIY-YIG endonucleases after conserved motifs near the amino end. This subfamily in this model is found in open reading frames of group I introns in both phage and mitochondria. The closely related endonucleases of phage T4: segA, segB, segC, segD and segE, score below the trusted cutoff for the family. 214 matched cddid_all.tbl CDD TIGR01454 TIGR01454 130521 AHBA_synth_RP 3-amino-5-hydroxybenoic acid synthesis related protein. The enzymes in this equivalog are all located in the operons for the biosynthesis of 3-amino-5-hydroxybenoic acid (AHBA), which is a precursor of several antibiotics including ansatrienin, naphthomycin, rifamycin and mitomycin. The role that this enzyme plays in this biosynthesis has not been elucidated. This enzyme is a member of the Haloacid dehalogenase superfamily (pfam00702) of aspartate-nucleophile hydrolases. This enzyme is closely related to phosphoglycolate phosphatase (TIGR01449), but it is unclear what purpose a PGPase or PGPase-like activity would serve in these biosyntheses. This model is limited to the Gram positive Actinobacteria. The most closely related enzyme below the noise cutoff is IndB which is involved in the biosynthesis of Indigoidine in Pectobacterium (Erwinia) chrysanthemi, a gamma proteobacter. This enzyme is similarly related to PGP. In this case, too it is unclear what role would be be played by a PGPase activity. 205 matched cddid_all.tbl CDD TIGR01455 TIGR01455 130522 glmM phosphoglucosamine mutase. This model describes GlmM, phosphoglucosamine mutase, also designated in MrsA and YhbF E. coli, UreC in Helicobacter pylori, and femR315 or FemD in Staphlococcus aureus. It converts glucosamine-6-phosphate to glucosamine-1-phosphate as part of the pathway toward UDP-N-acetylglucosamine for peptidoglycan and lipopolysaccharides. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan, Central intermediary metabolism, Amino sugars] 443 matched cddid_all.tbl CDD TIGR01456 TIGR01456 200106 CECR5 "HAD-superfamily class IIA hydrolase, TIGR01456, CECR5. This hypothetical equivalog is a member of the Class IIA subfamily of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. The sequences modelled by this equivalog are all eukaryotes. One sequence (GP|13344995) is called ""Cat Eye Syndrome critical region protein 5"" (CECR5). This gene has been cloned from a pericentromere region of human chromosome 22 believed to be the location of the gene or genes responsible for Cat Eye Syndrome. This is one of a number of candidate genes. The Schizosaccharomyces pombe sequence (EGAD|138276) is annotated as ""phosphatidyl synthase,"" however this is due entirely to a C-terminal region of the protein (outside the region of similarity of this model) which is highly homologous to a family of CDP-alcohol phosphatidyltransferases. (Thus, the annotation of GP|4226073 from C. elegans as similar to phosphatidyl synthase, is a mistake as this gene does not contain the C-terminal portion). The physical connection of the phosphatidyl synthase and the HAD-superfamily hydrolase domain in S. pombe may, however, be an important clue to the substrate for the hydrolases in this equivalog." 321 matched cddid_all.tbl CDD TIGR01457 TIGR01457 130524 HAD-SF-IIA-hyp2 HAD-superfamily subfamily IIA hydrolase, TIGR01457. This hypothetical equivalog is a member of the Class IIA subfamily of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. The sequences modelled by this equivalog are all gram positive (low-GC) bacteria. Sequences found in this model are annotated variously as related to NagD or 4-nitrophenyl phosphatase, and this hypothetical equivalog, of all of those within the Class IIA subfamily, is most closely related to the E. coli NagD enzyme and the PGP_euk equivalog (TIGR01452). However, there is presently no evidence that this hypothetical equivalog has the same function of either those. [Unknown function, Enzymes of unknown specificity] 249 matched cddid_all.tbl CDD TIGR01458 TIGR01458 162372 HAD-SF-IIA-hyp3 "HAD-superfamily subfamily IIA hydrolase, TIGR01458. This hypothetical equivalog is a member of the IIA subfamily (TIGR01460) of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. One sequence (GP|10716807) has been annotated as a ""phospholysine phosphohistidine inorganic pyrophosphatase,"" probably in reference to studies on similarly described (but unsequenced) enzymes from bovine and rat tissues. However, the supporting information for this annotation has never been published. [Unknown function, Enzymes of unknown specificity]" 257 matched cddid_all.tbl CDD TIGR01459 TIGR01459 130526 HAD-SF-IIA-hyp4 "HAD-superfamily class IIA hydrolase, TIGR01459. This hypothetical equivalog is a member of the Class IIA subfamily of the haloacid dehalogenase superfamily of aspartate-nucleophile hydrolases. The sequences modelled by this equivalog are all gram negative and primarily alpha proteobacteria. Only one sequence hase been annotated as other than ""hypothetical."" That one, from Brucella, is annotated as related to NagD, but only by sequence similarity and should be treated with some skepticism. (See comments for Class IIA subfamily model)" 242 matched cddid_all.tbl CDD TIGR01460 TIGR01460 273637 HAD-SF-IIA "Haloacid Dehalogenase Superfamily Class (subfamily) IIA. This model represents one structural subclass of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs. The classes are defined based on the location and the observed or predicted fold of a so-called ""capping domain"", or the absence of such a domain. Class I consists of sequences in which the capping domain is found in between the first and second catalytic motifs. Class II consists of sequences in which the capping domain is found between the second and third motifs. Class III sequences have no capping domain in iether of these positions. The Class IIA capping domain is predicted by PSI-PRED to consist of a mixed alpha-beta fold with the basic pattern: Helix-Helix-Helix-Sheet-Helix-Loop-Sheet-Helix-Sheet-Helix. Presently, this subfamily encompasses a single equivalog model (TIGR01452) for the eukaryotic phosphoglycolate phosphatase, as well as four hypothetical equivalogs covering closely related sequences (TIGR01456 and TIGR01458 in eukaryotes, TIGR01457 in gram positive bacteria and TIGR01459 in gram negative bacteria). The Escherishia coli NagD gene and the Bacillus subtilus AraL gene are members of this subfamily but are not members of the any of the presently defined equivalogs within it. NagD is part of the NAG operon responsible for N-acetylglucosamine metabolism. The function of this gene is unknown. Genes from several organisms have been annotated as NagD, or NagD-like. However, without data on the presence of other members of this pathway, (such as in the case of Yersinia pestis) these assignments should not be given great weight. The AraL gene is similar: it is part of the L-arabinose operon, but the function is unknown. A gene from Halobacterium has been annotated as AraL, but no other Ara operon genes have been annotated. Many of the genes in this subfamily have been annotated as ""pNPPase"" ""4-nitrophenyl phosphatase"" or ""NPPase"". These all refer to the same activity versus a common lab test compound used to determine phosphatase activity. There is no evidence that this activity is physiologically relevant. [Unknown function, Enzymes of unknown specificity]" 236 matched cddid_all.tbl CDD TIGR01461 TIGR01461 130528 greB transcription elongation factor GreB. The GreA and GreB transcription elongation factors enable to continuation of RNA transcription past template-encoded arresting sites. Among the Proteobacteria, distinct clades of GreA and GreB are found. GreB differs functionally in that it releases larger oligonucleotides. This model describes proteobacterial GreB. [Transcription, Transcription factors] 156 matched cddid_all.tbl CDD TIGR01462 TIGR01462 273638 greA transcription elongation factor GreA. The GreA and GreB transcription elongation factors enable to continuation of RNA transcription past template-encoded arresting sites. Among the Proteobacteria, distinct clades of GreA and GreB are found. GreA differs functionally in that it releases smaller oligonucleotides. Because members of the family outside the Proteobacteria resemble GreA more closely than GreB, the GreB clade (TIGR01461) forms a plausible outgroup and the remainder of the GreA/B family, included in this model, is designated GreA. In the Chlamydias and some spirochetes, the region described by this model is found as the C-terminal region of a much larger protein. [Transcription, Transcription factors] 151 matched cddid_all.tbl CDD TIGR01463 TIGR01463 273639 mtaA_cmuA methyltransferase, MtaA/CmuA family. This subfamily is closely related to, yet is distinct from, uroporphyrinogen decarboxylase (EC 4.1.1.37). It includes two isozymes from Methanosarcina barkeri of methylcobalamin--coenzyme M methyltransferase. It also includes a chloromethane utilization protein, CmuA, which transfers the methyl group of chloromethane to a corrinoid protein. 336 matched cddid_all.tbl CDD TIGR01464 TIGR01464 273640 hemE uroporphyrinogen decarboxylase. This model represents uroporphyrinogen decarboxylase (HemE), which converts uroporphyrinogen III to coproporphyrinogen III. This step takes the pathway toward protoporphyrin IX, a common precursor of both heme and chlorophyll, rather than toward precorrin 2 and its products. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 338 matched cddid_all.tbl CDD TIGR01465 TIGR01465 200107 cobM_cbiF precorrin-4 C11-methyltransferase. This model represents precorrin-4 C11-methyltransferase, one of two methyltransferases commonly referred to as precorrin-3 methylase (the other is precorrin-3B C17-methyltransferase, EC 2.1.1.131). This enzyme participates in the pathway toward the biosynthesis of cobalamin and related products. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 247 matched cddid_all.tbl CDD TIGR01466 TIGR01466 273641 cobJ_cbiH precorrin-3B C17-methyltransferase. This model represents precorrin-3B C17-methyltransferase, one of two methyltransferases commonly referred to as precorrin-3 methylase (the other is precorrin-4 C11-methyltransferase, EC 2.1.1.133). This enzyme participates in the pathway toward the biosynthesis of cobalamin and related products. Members of this family may appear as fusion proteins with other enzymes of cobalamin biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 239 matched cddid_all.tbl CDD TIGR01467 TIGR01467 273642 cobI_cbiL precorrin-2 C(20)-methyltransferase. This model represents precorrin-2 C(20)-methyltransferase, one of several closely related S-adenosylmethionine-dependent methyltransferases involved in cobalamin (vitamin B12) biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 230 matched cddid_all.tbl CDD TIGR01469 TIGR01469 273643 cobA_cysG_Cterm uroporphyrin-III C-methyltransferase. This model represents enzymes, or enzyme domains, with uroporphyrin-III C-methyltransferase activity. This enzyme catalyzes the first step committed to the biosynthesis of either siroheme or cobalamin (vitamin B12) rather than protoheme (heme). Cobalamin contains cobalt while siroheme contains iron. Siroheme is a cofactor for nitrite and sulfite reductases and therefore plays a role in cysteine biosynthesis; many members of this family are CysG, siroheme synthase, with an additional N-terminal domain and with additional oxidation and iron insertion activities. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 236 matched cddid_all.tbl CDD TIGR01470 TIGR01470 130536 cysG_Nterm siroheme synthase, N-terminal domain. This model represents a subfamily of CysG N-terminal region-related sequences. All sequences in the seed alignment for this model are N-terminal regions of known or predicted siroheme synthases. The C-terminal region of each is uroporphyrin-III C-methyltransferase (EC 2.1.1.107), which catalyzes the first step committed to the biosynthesis of either siroheme or cobalamin (vitamin B12) rather than protoheme (heme). The region represented by this model completes the process of oxidation and iron insertion to yield siroheme. Siroheme is a cofactor for nitrite and sulfite reductases, so siroheme synthase is CysG of cysteine biosynthesis in some organisms. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 205 matched cddid_all.tbl CDD TIGR01472 TIGR01472 273644 gmd GDP-mannose 4,6-dehydratase. Alternate name: GDP-D-mannose dehydratase. This enzyme converts GDP-mannose to GDP-4-dehydro-6-deoxy-D-mannose, the first of three steps for the conversion of GDP-mannose to GDP-fucose in animals, plants, and bacteria. In bacteria, GDP-L-fucose acts as a precursor of surface antigens such as the extracellular polysaccharide colanic acid of E. coli. Excluded from this model are members of the clade that score poorly because of highly dervied (phylogenetically long-branch) sequences, e.g. Aneurinibacillus thermoaerophilus Gmd, described as a bifunctional GDP-mannose 4,6-dehydratase/GDP-6-deoxy-D-lyxo-4-hexulose reductase (PUBMED:11096116). [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 343 matched cddid_all.tbl CDD TIGR01473 TIGR01473 273645 cyoE_ctaB protoheme IX farnesyltransferase. This model describes protoheme IX farnesyltransferase, also called heme O synthase, an enzyme that creates an intermediate in the biosynthesis of heme A. Prior to the description of its enzymatic function, this protein was often called a cytochrome o ubiquinol oxidase assembly factor. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 280 matched cddid_all.tbl CDD TIGR01474 TIGR01474 130539 ubiA_proteo 4-hydroxybenzoate polyprenyl transferase, proteobacterial. This model represents a family of integral membrane proteins that condenses para-hydroxybenzoate with any of several polyprenyldiphosphates. Heterologous expression studies suggest that for, many but not all members, the activity seen (e.g. octaprenyltransferase in E. coli) reflects available host isoprenyl pools rather than enzyme specificity. A fairly deep split by both clustering (UPGMA) and phylogenetics (NJ tree) separates this group (mostly Proteobacterial and mitochondrial), with several characterized members, from another group (mostly archaeal and Gram-positive bacterial) lacking characterized members. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 281 matched cddid_all.tbl CDD TIGR01475 TIGR01475 273646 ubiA_other putative 4-hydroxybenzoate polyprenyltransferase. A fairly deep split separates this polyprenyltransferase subfamily from the set of mitochondrial and proteobacterial 4-hydroxybenzoate polyprenyltransferases, described in TIGR01474. Protoheme IX farnesyltransferase (heme O synthase) (TIGR01473) is more distantly related. Because no species appears to have both this protein and a member of TIGR01474, it is likely that this model represents 4-hydroxybenzoate polyprenyltransferase, a critical enzyme of ubiquinone biosynthesis, in the Archaea, Gram-positive bacteria, Aquifex aeolicus, the Chlamydias, etc. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 282 matched cddid_all.tbl CDD TIGR01476 TIGR01476 130541 chlor_syn_BchG bacteriochlorophyll/chlorophyll synthetase. This model describes a subfamily of a large family of polyprenyltransferases (pfam01040) that also includes 4-hydroxybenzoate octaprenyltransferase and protoheme IX farnesyltransferase (heme O synthase). Members of this family are found exclusively in photosynthetic organisms, including a single copy in Arabidopsis thaliana. [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll] 283 matched cddid_all.tbl CDD TIGR01477 TIGR01477 273647 RIFIN variant surface antigen, rifin family. This model represents the rifin branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of rifin sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 20 bits. 353 matched cddid_all.tbl CDD TIGR01478 TIGR01478 130543 STEVOR variant surface antigen, stevor family. This model represents the stevor branch of the rifin/stevor family (pfam02009) of predicted variant surface antigens as found in Plasmodium falciparum. This model is based on a set of stevor sequences kindly provided by Matt Berriman from the Sanger Center. This is a global model and assesses a penalty for incomplete sequence. Additional fragmentary sequences may be found with the fragment model and a cutoff of 8 bits. 295 matched cddid_all.tbl CDD TIGR01479 TIGR01479 273648 GMP_PMI mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase. This enzyme is known to be bifunctional, as both mannose-6-phosphate isomerase (EC 5.3.1.8) (PMI) and mannose-1-phosphate guanylyltransferase (EC 2.7.7.22) in Pseudomonas aeruginosa, Xanthomonas campestris, and Gluconacetobacter xylinus. The literature on the enzyme from E. coli attributes mannose-6-phosphate isomerase activity to an adjacent gene, but the present sequence has not been shown to lack the activity. The PMI domain is C-terminal. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 468 matched cddid_all.tbl CDD TIGR01480 TIGR01480 273649 copper_res_A copper-resistance protein, CopA family. This model represents the CopA copper resistance protein family. CopA is related to laccase (benzenediol:oxygen oxidoreductase) and L-ascorbate oxidase, both copper-containing enzymes. Most members have a typical TAT (twin-arginine translocation) signal sequence with an Arg-Arg pair. Twin-arginine translocation is observed for a large number of periplasmic proteins that cross the inner membrane with metal-containing cofactors already bound. The combination of copper-binding sites and TAT translocation motif suggests a mechansism of resistance by packaging and export. [Cellular processes, Detoxification, Transport and binding proteins, Cations and iron carrying compounds] 587 matched cddid_all.tbl CDD TIGR01481 TIGR01481 130546 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways. [Regulatory functions, DNA interactions] 329 matched cddid_all.tbl CDD TIGR01482 TIGR01482 273650 SPP-subfamily sucrose-phosphate phosphatase subfamily. This model includes both the members of the SPP equivalog model (TIGR01485), encompassing plants and cyanobacteria, as well as those archaeal sequences which are the closest relatives (TIGR01487). It remains to be shown whether these archaeal sequences catalyze the same reaction as SPP. 225 matched cddid_all.tbl CDD TIGR01484 TIGR01484 273651 HAD-SF-IIB "HAD-superfamily hydrolase, subfamily IIB. This subfamily falls within the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The Class II subfamilies are characterized by a domain that is located between the second and third conserved catalytic motifs of the superfamily domain. The IIB subfamily is distinguished from the IIA subfamily (TIGR01460) by homology and the predicted secondary structure of this domain by PSI-PRED. The IIB subfamily's Class II domain has the following predicted structure: Helix-Sheet-Sheet-(Helix or Sheet)-Helix-Sheet-(variable)-Helix-Sheet-Sheet. The IIB subfamily consists of Trehalose-6-phosphatase (TIGR00685), plant and cyanobacterial Sucrose-phosphatase and a closely related group of bacterial and archaeal sequences, eukaryotic phosphomannomutase (pfam03332), a large subfamily (""Cof-like hydrolases"", TIGR00099) containing many closely related bacterial sequences, a hypothetical equivalog containing the E. coli YedP protein, as well as two small clusters containing OMNI|TC0379 and OMNI|SA2196 whose relationship to the other groups is unclear. [Unknown function, Enzymes of unknown specificity]" 207 matched cddid_all.tbl CDD TIGR01485 TIGR01485 130549 SPP_plant-cyano "sucrose-6F-phosphate phosphohydrolase. This model describes the sucrose phosphate phosphohydrolase from plants and cyanobacteria (SPP). SPP is a member of the Class IIB subfamily (TIGR01484) of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. SPP catalyzes the final step in the biosynthesis of sucrose, a critically important molecule for plants. Sucrose phosphate synthase (SPS), the prior step in the biosynthesis of sucrose, contains a domain which exhibits considerable similarity to SPP albeit without conservation of the catalytic residues. The catalytic machinery of the synthase resides in another domain. It seems likely that the phosphatase-like domain is involved in substrate binding, possibly binding both substrates in a ""product-like"" orientation prior to ligation by the synthase catalytic domain." 249 matched cddid_all.tbl CDD TIGR01486 TIGR01486 130550 HAD-SF-IIB-MPGP mannosyl-3-phosphoglycerate phosphatase family. This small group of proteins is a member of the IIB subfamily (TIGR01484) of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. Several members of this family from thermophiles (and from Dehalococcoides ethenogenes) are now known to act as mannosyl-3-phosphoglycerate (MPG) phosphatase. In these cases, the enzyme acts after MPG synthase to make the compatible solute mannosylglycerate. We propose that other mesophilic members of this family do not act as mannosyl-3-phosphoglycerate phosphatase. A member of this family is found in Escherichia coli, which appears to lack MPG synthase. Mannosylglycerate is imported in E. coli by phosphoenolpyruvate-dependent transporter (), but it appears the phosphorylation is not on the glycerate moiety, that the phosphorylated import is degraded by an alpha-mannosidase from an adjacent gene, and that E. coli would have no pathway to obtain MPG. 256 matched cddid_all.tbl CDD TIGR01487 TIGR01487 273652 Pglycolate_arch phosphoglycolate phosphatase, TA0175-type. This group of Archaeal sequences, now known to be phosphoglycolate phosphatases, is most closely related to the sucrose-phosphate phosphatases from plants and cyanobacteria (TIGR01485). Together, these two models comprise a subfamily model (TIGR01482). TIGR01482, in turn, is a member of the IIB subfamily (TIGR01484) of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. 215 matched cddid_all.tbl CDD TIGR01488 TIGR01488 273653 HAD-SF-IB Haloacid Dehalogenase superfamily, subfamily IB, phosphoserine phosphatase-like. This model represents a subfamily of the Haloacid Dehalogenase superfamily of aspartate-nucleophile hydrolases. Subfamily IA, B, C and D are distinguished from the rest of the superfamily by the presence of a variable domain between the first and second conserved catalytic motifs. In subfamilies IA and IB, this domain consists of an alpha-helical bundle. It was necessary to model these two subfamilies separately, breaking them at a an apparent phylogenetic bifurcation, so that the resulting model(s) are not so broadly defined that members of subfamily III (which lack the variable domain) are included. Subfamily IA includes the enzyme phosphoserine phosphatase (TIGR00338) as well as three hypothetical equivalogs. Many members of these hypothetical equivalogs have been annotated as PSPase-like or PSPase-family proteins. In particular, the hypothetical equivalog which appears to be most closely related to PSPase contains only Archaea (while TIGR00338 contains only eukaryotes and bacteria) of which some are annotated as PSPases. Although this is a reasonable conjecture, none of these sequences has sufficient evidence for this assignment. If such should be found, this model should be retired while the PSPase model should be broadened to include these sequences. [Unknown function, Enzymes of unknown specificity] 177 matched cddid_all.tbl CDD TIGR01489 TIGR01489 213629 DKMTPPase-SF "2,3-diketo-5-methylthio-1-phosphopentane phosphatase. This phosphatase is a member of the IB subfamily (TIGR01488) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. With the exception of OMNI|NTL01BS01361 from B. subtilis and GP|15024582 from Clostridium acetabutylicum, the members of this group are all eukaryotic, spanning metazoa, plants and fungi. The B. subtilus gene (YkrX, renamed MtnX) is part of an operon for the conversion of methylthioribose (MTR) to methionine. It works with the enolase MtnW, a RuBisCO homolog. The combination of MtnW and MtnX achieves the same overall reaction as the enolase-phosphatase MtnC. The function of MtnX was shown by Ashida, et al. (2003) to be 2,3-diketo-5-methylthio-1-phosphopentane phosphatase, rather than 2,3-diketo-5-methylthio-1-phosphopentane phosphatase as proposed earlier. See the Genome Property for methionine salvage for more details. In eukaryotes, methionine salvage from methylthioadenosine also occurs. It seems reasonable that members of this family in eukaryotes fulfill a similar role as in Bacillus. A more specific, equivalog-level model is TIGR03333. Note that SP|P53981 from S. cerevisiae, a member of this family, is annotated as a ""probable membrane protein"" due to a predicted transmembrane helix. The region in question contains the second of the three conserved HAD superfamily catalytic motifs and thus, considering the fold of the HAD catalytic domain, is unlikely to be a transmembrane region in fact. [Central intermediary metabolism, Other]" 188 matched cddid_all.tbl CDD TIGR01490 TIGR01490 273654 HAD-SF-IB-hyp1 "HAD-superfamily subfamily IB hydrolase, TIGR01490. This hypothetical equivalog is a member of the IB subfamily (TIGR01488) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The sequences modelled here are all bacterial. The IB subfamily includes the enzyme phosphoserine phosphatase (TIGR00338). Due to this relationship, several of these sequences have been annotated as ""phosphoserine phosphatase related proteins,"" or ""Phosphoserine phosphatase-family enzymes."" There is presently no evidence that any of the enzymes in this model possess PSPase activity. OMNI|NTL01ML1250 is annotated as a ""possible transferase,"" however this is due to the C-terminal domain found on this sequence which is homologous to a group of glycerol-phosphate acyltransferases (between trusted and noise to TIGR00530). A subset of these sequences including OMNI|CC1962, the Caulobacter crescentus CicA protein cluster together and may represent a separate equivalog. [Unknown function, Enzymes of unknown specificity]" 202 matched cddid_all.tbl CDD TIGR01491 TIGR01491 273655 HAD-SF-IB-PSPlk HAD-superfamily, subfamily-IB PSPase-like hydrolase, archaeal. This hypothetical equivalog is a member of the IB subfamily (TIGR01488) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The sequences modelled here are all from archaeal species. The phylogenetically closest group of sequences to these are phosphoserine phosphatases (TIGR00338). There are no known archaeal phosphoserine phosphatases, and no archaea fall within TIGR00338. It is likely, then, that this model represents the archaeal branch of the PSPase equivalog. 201 matched cddid_all.tbl CDD TIGR01492 TIGR01492 130556 CPW_WPC Plasmodium falciparum CPW-WPC domain. This model represents a domain of about 61 residues in length with six well-conserved cysteine residues and six well-conserved aromatic sites. The domain can be found in tandem repeats, and is known so far only in Plasmodium falciparum. It is named for motifs of CPxxW and (less well conserved) WPC. 62 matched cddid_all.tbl CDD TIGR01493 TIGR01493 130557 HAD-SF-IA-v2 Haloacid dehalogenase superfamily, subfamily IA, variant 2 with 3rd motif like haloacid dehalogenase. This model represents part of one structural subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs. The subfamilies are defined based on the location and the observed or predicted fold of a so-called 'capping domain', or the absence of such a domain. Subfamily I consists of sequences in which the capping domain is found in between the first and second catalytic motifs. Subfamily II consists of sequences in which the capping domain is found between the second and third motifs. Subfamily III sequences have no capping domain in either of these positions. The Subfamily IA and IB capping domains are predicted by PSI-PRED to consist of an alpha helical bundle. Subfamily I encompasses such a wide region of sequence space (the sequences are highly divergent) that representing it with a single model is impossible, resulting in an overly broad description which allows in many unrelated sequences. Subfamily IA and IB are separated based on an aparrent phylogenetic bifurcation. Subfamily IA is still too broad to model, but cannot be further subdivided into large chunks based on phylogenetic trees. Of the three motifs defining the HAD superfamily, the third has three variant forms: (1) hhhhsDxxx(x)D, (2) hhhhssxxx(x)D and (3) hhhhDDxxx(x)s where _s_ refers to a small amino acid and _h_ to a hydrophobic one. All three of these variants are found in subfamily IA. Individual models were made based on seeds exhibiting only one of the variants each. Variant 2 (this model) is distinctive of the type II haloacid dehalogenases, and nearly all of the sequences are also part of the HAD, type II equivalog model (TIGR01428). These three variant models were created with the knowledge that there will be overlap among them - this is by design and serves the purpose of eliminating the overlap with models of more distantly related HAD subfamilies caused by an overly broad single model. 175 matched cddid_all.tbl CDD TIGR01494 TIGR01494 273656 ATPase_P-type ATPase, P-type (transporting), HAD superfamily, subfamily IC. The P-type ATPases are a large family of trans-membrane transporters acting on charged substances. The distinguishing feature of the family is the formation of a phosphorylated intermediate (aspartyl-phosphate) during the course of the reaction. Another common name for these enzymes is the E1-E2 ATPases based on the two isolable conformations: E1 (unphosphorylated) and E2 (phosphorylated). Generally, P-type ATPases consist of only a single subunit encompassing the ATPase and ion translocation pathway, however, in the case of the potassium (TIGR01497) and sodium/potassium (TIGR01106) varieties, these functions are split between two subunits. Additional small regulatory or stabilizing subunits may also exist in some forms. P-type ATPases are nearly ubiquitous in life and are found in numerous copies in higher organisms (at least 45 in Arabidopsis thaliana, for instance). Phylogenetic analyses have revealed that the P-type ATPase subfamily is divided up into groups based on substrate specificities and this is represented in the various subfamily and equivalog models that have been made: IA (K+) TIGR01497, IB (heavy metals) TIGR01525, IIA1 (SERCA-type Ca++) TIGR01116, IIA2 (PMR1-type Ca++) TIGR01522, IIB (PMCA-type Ca++) TIGR01517, IIC (Na+/K+, H+/K+ antiporters) TIGR01106, IID (fungal-type Na+ and K+) TIGR01523, IIIA (H+) TIGR01647, IIIB (Mg++) TIGR01524, IV (phospholipid, flippase) TIGR01652 and V (unknown specificity) TIGR01657. The crystal structure of one calcium-pumping ATPase and an analysis of the fold of the catalytic domain of the P-type ATPases have been published. These reveal that the catalytic core of these enzymes is a haloacid dehalogenase(HAD)-type aspartate-nucleophile hydrolase. The location of the ATP-binding loop in between the first and second HAD conserved catalytic motifs defines these enzymes as members of subfamily I of the HAD superfamily (see also TIGR01493, TIGR01509, TIGR01549, TIGR01544 and TIGR01545). Based on these classifications, the P-type ATPase _superfamily_ corresponds to the IC subfamily of the HAD superfamily. 545 matched cddid_all.tbl CDD TIGR01495 TIGR01495 130559 ETRAMP Plasmodium ring stage membrane protein ETRAMP. This model describes a family of proteins from the malaria parasite Plasmodium falciparum, several of which have been shown to be expressed specifically in the ring stage as well as the rident parasite Plasmodium yoelii. A homolog from Plasmodium chabaudi was localized to the parasitophorous vacuole membrane. Members have an initial hydrophobic, Phe/Tyr-rich stretch long enough to span the membrane, a highly charged region rich in Lys, a second putative transmembrane region, and a second highly charged, low complexity sequence region. Some members have up to 100 residues of additional C-terminal sequence. These genes have been shown to be found in the sub-telomeric regions of both P. falciparum and P. yoelii chromosomes 85 matched cddid_all.tbl CDD TIGR01496 TIGR01496 273657 DHPS dihydropteroate synthase. This model represents dihydropteroate synthase, the enzyme that catalyzes the second to last step in folic acid biosynthesis. The gene is usually designated folP (folic acid biosynthsis) or sul (sulfanilamide resistance). This model represents one branch of the family of pterin-binding enzymes (pfam00809) and of a cluster of dihydropteroate synthase and related enzymes (COG0294). Other members of pfam00809 and COG0294 are represented by model TIGR00284. [Biosynthesis of cofactors, prosthetic groups, and carriers, Folic acid] 257 matched cddid_all.tbl CDD TIGR01497 TIGR01497 130561 kdpB K+-transporting ATPase, B subunit. This model describes the P-type ATPase subunit of the complex responsible for translocating potassium ions across biological membranes in microbes. In E. coli and other species, this complex consists of the proteins KdpA, KdpB, KdpC and KdpF. KdpB is the ATPase subunit, while KdpA is the potassium-ion translocating subunit. The function of KdpC is unclear, although cit has been suggested to couple the ATPase subunit to the ion-translocating subunit, while KdpF serves to stabilize the complex. The potassium P-type ATPases have been characterized as Type IA based on a phylogenetic analysis which places this clade closest to the heavy-metal translocating ATPases (Type IB). Others place this clade closer to the Na+/K+ antiporter type (Type IIC) based on physical characteristics. This model is very clear-cut, with a strong break between trusted hits and noise. All members of the seed alignment, from Clostridium, Anabaena and E. coli are in the characterized table. One sequence above trusted, OMNI|NTL01TA01282, is apparently mis-annotated in the primary literature, but properly annotated by TIGR. [Transport and binding proteins, Cations and iron carrying compounds] 675 matched cddid_all.tbl CDD TIGR01498 TIGR01498 273658 folK 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase. This model describes the folate biosynthesis enzyme 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase. Alternate names include 6-hydroxymethyl-7,8-dihydropterin diphosphokinase and 7,8-dihydro-6-hydroxymethylpterin pyrophosphokinase (HPPK). The extreme C-terminal region, of typically eight to thirty residues, is not included in the model. This enzyme may be found as a fusion protein with other enzymes of folate biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Folic acid] 129 matched cddid_all.tbl CDD TIGR01499 TIGR01499 273659 folC folylpolyglutamate synthase/dihydrofolate synthase. This model represents the FolC family of folate pathway proteins. Most examples are bifunctional, active as both folylpolyglutamate synthetase (EC 6.3.2.17) and dihydrofolate synthetase (EC 6.3.2.12). The two activities are similar - ATP + glutamate + dihydropteroate or tetrahydrofolyl-[Glu](n) = ADP + orthophosphate + dihydrofolate or tetrahydrofolyl-[Glu](n+1). A mutation study of the FolC gene of E. coli suggests that both activities belong to the same active site. Because some examples are monofunctional (and these cannot be separated phylogenetically), the model is treated as subfamily, not equivalog. [Biosynthesis of cofactors, prosthetic groups, and carriers, Folic acid] 397 matched cddid_all.tbl CDD TIGR01500 TIGR01500 273660 sepiapter_red sepiapterin reductase. This model describes sepiapterin reductase, a member of the short chain dehydrogenase/reductase family. The enzyme catalyzes the last step in the biosynthesis of tetrahydrobiopterin. A similar enzyme in Bacillus cereus was isolated for its ability to convert benzil to (S)-benzoin, a property sepiapterin reductase also shares. Cutoff scores for this model are set such that benzil reductase scores between trusted and noise cutoffs. 256 matched cddid_all.tbl CDD TIGR01501 TIGR01501 130565 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation. [Energy metabolism, Amino acids and amines, Energy metabolism, Fermentation] 134 matched cddid_all.tbl CDD TIGR01502 TIGR01502 213632 B_methylAsp_ase methylaspartate ammonia-lyase. This model describes methylaspartate ammonia-lyase, also called beta-methylaspartase (EC 4.3.1.2). It follows methylaspartate mutase (composed of S and E subunits) in one of several possible pathways of glutamate fermentation. [Energy metabolism, Amino acids and amines, Energy metabolism, Fermentation] 408 matched cddid_all.tbl CDD TIGR01503 TIGR01503 130567 MthylAspMut_E methylaspartate mutase, E subunit. This model represents the E (epsilon) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation. [Energy metabolism, Amino acids and amines, Energy metabolism, Fermentation] 480 matched cddid_all.tbl CDD TIGR01504 TIGR01504 213633 glyox_carbo_lig glyoxylate carboligase. Glyoxylate carboligase, also called tartronate-semialdehyde synthase, releases CO2 while synthesizing a single molecule of tartronate semialdehyde from two molecules of glyoxylate. It is a thiamine pyrophosphate-dependent enzyme, closely related in sequence to the large subunit of acetolactate synthase. In the D-glycerate pathway, part of allantoin degradation in the Enterobacteriaceae, tartronate semialdehyde is converted to D-glycerate and then 3-phosphoglycerate, a product of glycolysis and entry point in the general metabolism. 588 matched cddid_all.tbl CDD TIGR01505 TIGR01505 130569 tartro_sem_red 2-hydroxy-3-oxopropionate reductase. This model represents 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60), also called tartronate semialdehyde reductase. It follows glyoxylate carboligase and precedes glycerate kinase in D-glycerate pathway of glyoxylate degradation. The eventual product, 3-phosphoglycerate, is an intermediate of glycolysis and is readily metabolized. Tartronic semialdehyde, the substrate of this enzyme, may also come from other pathways, such as D-glucarate catabolism. 291 matched cddid_all.tbl CDD TIGR01506 TIGR01506 130570 ribC_arch riboflavin synthase. This archaeal protein catalyzes the same reaction, the final step in riboflavin biosynthesis, as bacterial riboflavin biosynthesis alpha chain. However, it is more similar in sequence to 6,7-dimethyl-8-ribityllumazine synthase, which catalyzes the previous reaction and which (in bacteria) is called the riboflavin synthase beta chain. [Biosynthesis of cofactors, prosthetic groups, and carriers, Riboflavin, FMN, and FAD] 151 matched cddid_all.tbl CDD TIGR01507 TIGR01507 273661 hopene_cyclase squalene-hopene cyclase. SHC is an essential prokaryotic gene in hopanoid (triterpenoid) biosynthesis. Squalene hopene cyclase, an integral membrane protein, directly cyclizes squalene into hopanoid products. [Fatty acid and phospholipid metabolism, Other] 635 matched cddid_all.tbl CDD TIGR01508 TIGR01508 130572 rib_reduct_arch 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine 1'-reductase, archaeal. This model represents a specific reductase of riboflavin biosynthesis in the Archaea, diaminohydroxyphosphoribosylaminopyrimidine reductase. It should not be confused with bacterial 5-amino-6-(5-phosphoribosylamino)uracil reductase. The intermediate 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine in riboflavin biosynthesis is reduced first, and then deaminated, in both Archaea and Fungi, opposite the order in Bacteria. The subsequent deaminase is not presently known and is not closely homologous to the deaminase domain (3.5.4.26) fused to the reductase domain (1.1.1.193) similar to this protein but found in most bacteria. 210 matched cddid_all.tbl CDD TIGR01509 TIGR01509 273662 HAD-SF-IA-v3 "haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or ED. This model represents part of one structural subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs. The subfamilies are defined based on the location and the observed or predicted fold of a so-called ""capping domain"", or the absence of such a domain. Subfamily I consists of sequences in which the capping domain is found in between the first and second catalytic motifs. Subfamily II consists of sequences in which the capping domain is found between the second and third motifs. Subfamily III sequences have no capping domain in either of these positions. The Subfamily IA and IB capping domains are predicted by PSI-PRED to consist of an alpha helical bundle. Subfamily I encompasses such a wide region of sequence space (the sequences are highly divergent) that representing it with a single model is impossible, resulting in an overly broad description which allows in many unrelated sequences. Subfamily IA and IB are separated based on an aparrent phylogenetic bifurcation. Subfamily IA is still too broad to model, but cannot be further subdivided into large chunks based on phylogenetic trees. Of the three motifs defining the HAD superfamily, the third has three variant forms: (1) hhhhsDxxx(x)D, (2) hhhhssxxx(x)D and (3) hhhhDDxxx(x)s where _s_ refers to a small amino acid and _h_ to a hydrophobic one. All three of these variants are found in subfamily IA. Individual models were made based on seeds exhibiting only one of the variants each. Variant 3 (this model) is found in the enzymes beta-phosphoglucomutase (TIGR01990) and deoxyglucose-6-phosphatase, while many other enzymes of subfamily IA exhibit this variant as well as variant 1 (TIGR01549). These three variant models were created with the knowledge that there will be overlap among them - this is by design and serves the purpose of eliminating the overlap with models of more distantly related HAD subfamilies caused by an overly broad single model. [Unknown function, Enzymes of unknown specificity]" 178 matched cddid_all.tbl CDD TIGR01510 TIGR01510 273663 coaD_prev_kdtB pantetheine-phosphate adenylyltransferase, bacterial. This model describes pantetheine-phosphate adenylyltransferase, the penultimate enzyme of coenzyme A (CoA) biosynthesis in bacteria. It does not show any strong homology to eukaryotic enzymes of coenzyme A biosynthesis. This protein was previously designated KdtB and postulated (because of cytidyltransferase homology and proximity to kdtA) to be an enzyme of LPS biosynthesis, a cytidyltransferase for 3-deoxy-D-manno-2-octulosonic acid. However, no activity toward that compound was found with either CTP or ATP. The phylogenetic distribution of this enzyme is more consistent with coenzyme A biosynthesis than with LPS biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pantothenate and coenzyme A] 155 matched cddid_all.tbl CDD TIGR01511 TIGR01511 273664 ATPase-IB1_Cu "copper-(or silver)-translocating P-type ATPase. This model describes the P-type ATPase primarily responsible for translocating copper ions accross biological membranes. These transporters are found in prokaryotes and eukaryotes. This model encompasses those species which pump copper ions out of cells or organelles (efflux pumps such as CopA of Escherichia coli) as well as those which pump the ion into cells or organelles either for the purpose of supporting life in extremely low-copper environments (for example CopA of Enterococcus hirae) or for the specific delivery of copper to a biological complex for which it is a necessary component (for example FixI of Bradyrhizobium japonicum, or CtaA and PacS of Synechocystis). The substrate specificity of these transporters may, to a varying degree, include silver ions (for example, CopA from Archaeoglobus fulgidus). Copper transporters from this family are well known as the genes which are mutated in two human disorders of copper metabolism, Wilson's and Menkes' diseases. The sequences contributing to the seed of this model are all experimentally characterized. The copper P-type ATPases have been characterized as Type IB based on a phylogenetic analysis which combines the copper-translocating ATPases with the cadmium-translocating species. This model and that describing the cadmium-ATPases (TIGR01512) are well separated, and thus we further type the copper-ATPases as IB1 (and the cadmium-ATPases as IB2). Several sequences which have not been characterized experimentally fall just below the cutoffs for both of these models (SP|Q9CCL1 from Mycobacterium leprae, GP|13816263 from Sulfolobus solfataricus, OMNI|NTL01CJ01098 from Campylobacter jejuni, OMNI|NTL01HS01687 from Halobacterium sp., GP|6899169 from Ureaplasma urealyticum and OMNI|HP1503 from Helicobacter pylori). Accession PIR|A29576 from Enterococcus faecalis scores very high against this model, but yet is annotated as an ""H+/K+ exchanging ATPase"". BLAST of this sequence does not hit anything else annotated in this way. This error may come from the characterization paper published in 1987. Accession GP|7415611 from Saccharomyces cerevisiae appears to be mis-annotated as a cadmium resistance protein. Accession OMNI|NTL01HS00542 from Halobacterium which scores above trusted for this model is annotated as ""molybdenum-binding protein"" although no evidence can be found for this classification. [Cellular processes, Detoxification, Transport and binding proteins, Cations and iron carrying compounds]" 562 matched cddid_all.tbl CDD TIGR01512 TIGR01512 273665 ATPase-IB2_Cd heavy metal-(Cd/Co/Hg/Pb/Zn)-translocating P-type ATPase. This model describes the P-type ATPase primarily responsible for translocating cadmium ions (and other closely-related divalent heavy metals such as cobalt, mercury, lead and zinc) across biological membranes. These transporters are found in prokaryotes and plants. Experimentally characterized members of the seed alignment include: SP|P37617 from E. coli, SP|Q10866 from Mycobacterium tuberculosis and SP|Q59998 from Synechocystis PCC6803. The cadmium P-type ATPases have been characterized as Type IB based on a phylogenetic analysis which combines the copper-translocating ATPases with the cadmium-translocating species. This model and that describing the copper-ATPases (TIGR01511) are well separated, and thus we further type the copper-ATPases as IB1 and the cadmium-ATPases as IB2. Several sequences which have not been characterized experimentally fall just below trusted cutoff for both of these models (SP|Q9CCL1 from Mycobacterium leprae, GP|13816263 from Sulfolobus solfataricus, OMNI|NTL01CJ01098 from Campylobacter jejuni, OMNI|NTL01HS01687 from Halobacterium sp., GP|6899169 from Ureaplasma urealyticum and OMNI|HP1503 from Helicobacter pylori). [Transport and binding proteins, Cations and iron carrying compounds] 550 matched cddid_all.tbl CDD TIGR01513 TIGR01513 273666 NAPRTase_put putative nicotinate phosphoribosyltransferase. A deep split separates two related families of proteins, one of which includes experimentally characterized examples of nicotinate phosphoribosyltransferase, an the first enzyme of NAD salvage biosynthesis. This model represents the other family. Members have a different (longer) spacing of several key motifs and have an additional C-terminal domain of up to 100 residues. One argument suggesting that this family represents the same enzyme is that no species has a member of both families. Another is that the gene encoding this protein is located near other NAD salvage biosynthesis genes in Nostoc and in at least four different Gram-positive bacteria. NAD and NADP are ubiquitous in life. Most members of this family are Gram-positive bacteria. An additional set of mutually closely related archaeal sequences score between the trusted and noise cutoffs. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridine nucleotides] 443 matched cddid_all.tbl CDD TIGR01514 TIGR01514 130578 NAPRTase nicotinate phosphoribosyltransferase. This model represents nicotinate phosphoribosyltransferase, the first enzyme in the salvage pathway of NAD biosynthesis from nicontinate (niacin). Members are primary proteobacterial but also include yeasts and Methanosarcina acetivorans. A related family, apparently non-overlapping in species distribution, is TIGR01513. Members of that family differ in substantially in sequence and have a long C-terminal extension missing from this family, but are proposed also to act as nicotinate phosphoribosyltransferase (see model TIGR01513). [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridine nucleotides] 394 matched cddid_all.tbl CDD TIGR01515 TIGR01515 273667 branching_enzym "alpha-1,4-glucan:alpha-1,4-glucan 6-glycosyltransferase. This model describes the glycogen branching enzymes which are responsible for the transfer of chains of approx. 7 alpha(1--4)-linked glucosyl residues to other similar chains (in new alpha(1--6) linkages) in the biosynthesis of glycogen. This enzyme is a member of the broader amylase family of starch hydrolases which fold as (beta/alpha)8 barrels, the so-called TIM-barrel structure. All of the sequences comprising the seed of this model have been experimentally characterized. This model encompasses both bacterial and eukaryotic species. No archaea have this enzyme, although Aquifex aolicus does. Two species, Bacillus thuringiensis and Clostridium perfringens have two sequences each which are annotated as amylases. These annotations are aparrently in error. GP|18143720 from C. perfringens, for instance, contains the note ""674 aa, similar to gp:A14658_1 amylase (1,4-alpha-glucan branching enzyme (EC 2.4.1.18) ) from Bacillus thuringiensis (648 aa); 51.1% identity in 632 aa overlap."" A branching enzyme from Porphyromonas gingivales, OMNI|PG1793, appears to be more closely related to the eukaryotic species (across a deep phylogenetic split) and may represent an instance of lateral transfer from this species' host. A sequence from Arabidopsis thaliana, GP|9294564, scores just above trusted, but appears either to contain corrupt sequence or, more likely, to be a pseudogene as some of the conserved catalytic residues common to the alpha amylase family are not conserved here. [Energy metabolism, Biosynthesis and degradation of polysaccharides]" 618 matched cddid_all.tbl CDD TIGR01517 TIGR01517 273668 ATPase-IIB_Ca plasma-membrane calcium-translocating P-type ATPase. This model describes the P-type ATPase responsible for translocating calcium ions across the plasma membrane of eukaryotes, out of the cell. In some organisms, this type of pump may also be found in vacuolar membranes. In humans and mice, at least, there are multiple isoforms of the PMCA pump with overlapping but not redundant functions. Accordingly, there are no human diseases linked to PMCA defects, although alterations of PMCA function do elicit physiological effects. The calcium P-type ATPases have been characterized as Type IIB based on a phylogenetic analysis which distinguishes this group from the Type IIA SERCA calcium pump. A separate analysis divides Type IIA into sub-types (SERCA and PMR1) which are represented by two corresponding models (TIGR01116 and TIGR01522). This model is well separated from those. 956 matched cddid_all.tbl CDD TIGR01518 TIGR01518 130581 g3p_cytidyltrns glycerol-3-phosphate cytidylyltransferase. This model describes glycerol-3-phosphate cytidyltransferase, also called CDP-glycerol pyrophosphorylase. A closely related protein assigned a different function experimentally is a human ethanolamine-phosphate cytidylyltransferase (EC 2.7.7.14). Glycerol-3-phosphate cytidyltransferase acts in pathways of teichoic acid biosynthesis. Teichoic acids are substituted polymers, linked by phosphodiester bonds, of glycerol, ribitol, etc. An example is poly(glycerol phosphate), the major teichoic acid of the Bacillus subtilis cell wall. Most but not all species encoding proteins in this family are Gram-positive bacteria. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 125 matched cddid_all.tbl CDD TIGR01519 TIGR01519 130582 plasmod_dom_1 Plasmodium falciparum uncharacterized domain. This model represents an uncharacterized domain present in roughly eight hypothetical proteins of the malaria parasite Plasmodium falciparum. 70 matched cddid_all.tbl CDD TIGR01520 TIGR01520 130583 FruBisAldo_II_A fructose-bisphosphate aldolase, class II, yeast/E. coli subtype. Members of this family are class II examples of the glycolytic enzyme fructose-bisphosphate aldolase (FBA). This model represents one of two deeply split, architecturally distinct clades of the family that includes class II fructose-bisphosphate aldolases, tagatose-bisphosphate aldolases, and related uncharacterized proteins. This family is well-conserved and includes characterized FBA from Saccharomyces cerevisiae, Escherichia coli, and Corynebacterium glutamicum. Proteins outside the scope of this model may also be designated as class II fructose-bisphosphate aldolases, but are well separated in an alignment-based phylogenetic tree. [Energy metabolism, Glycolysis/gluconeogenesis] 357 matched cddid_all.tbl CDD TIGR01521 TIGR01521 130584 FruBisAldo_II_B fructose-bisphosphate aldolase, class II, Calvin cycle subtype. Members of this family are class II examples of the enzyme fructose-bisphosphate aldolase, an enzyme both of glycolysis and (in the opposite direction) of the Calvin cycle of CO2 fixation. A deep split separates the tightly conserved yeast/E. coli/Mycobacterium subtype (all species lacking the Calvin cycle) represented by model TIGR01520 from a broader group of aldolases that includes both tagatose- and fructose-bisphosphate aldolases. This model represents a distinct, elongated, very well conserved subtype within the latter group. Most species with this aldolase subtype have the Calvin cycle. 347 matched cddid_all.tbl CDD TIGR01522 TIGR01522 130585 ATPase-IIA2_Ca golgi membrane calcium-translocating P-type ATPase. This model describes the P-type ATPase responsible for translocating calcium ions across the golgi membrane of fungi and animals, and is of particular importance in the sarcoplasmic reticulum of skeletal and cardiac muscle in vertebrates. The calcium P-type ATPases have been characterized as Type IIA based on a phylogenetic analysis which distinguishes this group from the Type IIB PMCA calcium pump modelled by TIGR01517. A separate analysis divides Type IIA into sub-types, SERCA and PMR1, the former of which is modelled by TIGR01116. 884 matched cddid_all.tbl CDD TIGR01523 TIGR01523 130586 ATPase-IID_K-Na potassium and/or sodium efflux P-type ATPase, fungal-type. Initially described as a calcium efflux ATPase, more recent work has shown that the S. pombe CTA3 gene is in fact a potassium ion efflux pump. This model describes the clade of fungal P-type ATPases responsible for potassium and sodium efflux. The degree to which these pumps show preference for sodium or potassium varies. This group of ATPases has been classified by phylogentic analysis as type IID. The Leishmania sequence (GP|3192903), which falls between trusted and noise in this model, may very well turn out to be an active potassium pump. 1053 matched cddid_all.tbl CDD TIGR01524 TIGR01524 130587 ATPase-IIIB_Mg magnesium-translocating P-type ATPase. This model describes the magnesium translocating P-type ATPase found in a limited number of bacterial species and best described in Salmonella typhimurium, which contains two isoforms. These transporters are active in low external Mg2+ concentrations and pump the ion into the cytoplasm. The magnesium ATPases have been classified as type IIIB by a phylogenetic analysis. [Transport and binding proteins, Cations and iron carrying compounds] 867 matched cddid_all.tbl CDD TIGR01525 TIGR01525 273669 ATPase-IB_hvy heavy metal translocating P-type ATPase. This model encompasses two equivalog models for the copper and cadmium-type heavy metal transporting P-type ATPases (TIGR01511 and TIGR01512) as well as those species which score ambiguously between both models. For more comments and references, see the files on TIGR01511 and 01512. 558 matched cddid_all.tbl CDD TIGR01526 TIGR01526 273670 nadR_NMN_Atrans nicotinamide-nucleotide adenylyltransferase, NadR type. The NadR protein of E. coli and closely related bacteria is both enzyme and regulatory protein. The first 60 or so amino acids, N-terminal to the region covered by this model, is a DNA-binding helix-turn-helix domain (pfam01381) responsible for repressing the nadAB genes of NAD de novo biosynthesis. The NadR homologs in Mycobacterium tuberculosis, Haemophilus influenzae, and others appear to lack the repressor domain. NadR has recently been shown to act as an enzyme of the salvage pathway of NAD biosynthesis, nicotinamide-nucleotide adenylyltransferase; members of this family are presumed to share this activity. E. coli NadR has also been found to regulate the import of its substrate, nicotinamide ribonucleotide, but it is not known if the other members of this model share that activity. 325 matched cddid_all.tbl CDD TIGR01527 TIGR01527 273671 arch_NMN_Atrans nicotinamide-nucleotide adenylyltransferase. This model describes a family of archaeal proteins with the activity of the NAD salvage biosynthesis enzyme nicotinamide-nucleotide adenylyltransferase (EC 2.7.7.1). In some cases, the enzyme was tested and found also to have the activity of nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18), an enzyme of NAD de novo biosynthesis, although with a higher Km. In some archaeal species, a lower-scoring paralog, uncharacterized with respect to activity, is also present. These score between trusted and noise cutoffs. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridine nucleotides] 165 matched cddid_all.tbl CDD TIGR01528 TIGR01528 273672 NMN_trans_PnuC nicotinamide mononucleotide transporter PnuC. The PnuC protein of E. coli is membrane protein responsible for nicotinamide mononucleotide transport, subject to regulation by interaction with the NadR (also called NadI) protein (see TIGR01526). This model defines a region corresponding to most of the length of PnuC, found primarily in pathogens. The extreme N- and C-terminal regions are poorly conserved and not included in the alignment and model. [Transport and binding proteins, Other, Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridine nucleotides] 189 matched cddid_all.tbl CDD TIGR01529 TIGR01529 130592 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs. [Amino acid biosynthesis, Glutamate family, Regulatory functions, DNA interactions] 146 matched cddid_all.tbl CDD TIGR01530 TIGR01530 211667 nadN NAD pyrophosphatase/5'-nucleotidase NadN. This model describes NadN of Haemophilus influenzae and a small number of close homologs in pathogenic, Gram-negative bacteria. NadN is a periplasmic enzyme that cleaves NAD (nicotinamide adenine dinucleotide) to NMN (nicotinamide mononucleotide) and AMP. The NMN must be converted by a 5'-nucleotidase to nicotinamide riboside for import. NadN belongs a large family of 5'-nucleotidases and has NMN 5'-nucleotidase activity for NMN, AMP, etc. [Transport and binding proteins, Other, Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridine nucleotides] 545 matched cddid_all.tbl CDD TIGR01531 TIGR01531 273673 glyc_debranch glycogen debranching enzymye. glycogen debranching enzyme possesses two different catalytic activities; oligo-1,4-->1,4-glucantransferase (EC 2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). Site directed mutagenesis studies in S. cerevisiae indicate that the transferase and glucosidase activities are independent and located in different regions of the polypeptide chain. Proteins in this model belong to the larger alpha-amylase family. The model covers eukaryotic proteins with a seed composed of human, nematode and yeast sequences. Yeast seed sequence is well characterized. The model is quite rigorous; either query sequence yields large bit score or it fails to hit the model altogether. There doesn't appear to be any middle ground. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 1464 matched cddid_all.tbl CDD TIGR01532 TIGR01532 130595 E4PD_g-proteo erythrose-4-phosphate dehydrogenase. This model represents the small clade of dehydrogenases in gamma-proteobacteria which utilize NAD+ to oxidize erythrose-4-phosphate (E4P) to 4-phospho-erythronate, a precursor for the de novo synthesis of pyridoxine via 4-hydroxythreonine and D-1-deoxyxylulose. This enzyme activity appears to have evolved from glyceraldehyde-3-phosphate dehydrogenase, whose substrate differs only in the lack of one carbon relative to E4P. Accordingly, this model is very close to the corresponding models for GAPDH, and those sequences which hit above trusted here invariably hit between trusted and noise to the GAPDH model (TIGR01534). Similarly, it may be found that there are species outside of the gamma proteobacteria which synthesize pyridoxine and have more than one aparrent GAPDH gene of which one may have E4PD activity - this may necessitate a readjustment of these models. Alternatively, some of the GAPDH enzymes may prove to be bifunctional in certain species. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridoxine] 325 matched cddid_all.tbl CDD TIGR01533 TIGR01533 273674 lipo_e_P4 5'-nucleotidase, lipoprotein e(P4) family. This model represents a set of bacterial lipoproteins belonging to a larger acid phosphatase family (pfam03767), which in turn belongs to the haloacid dehalogenase (HAD) superfamily of aspartate-dependent hydrolases. Members are found on the outer membrane of Gram-negative bacteria and the cytoplasmic membrane of Gram-positive bacteria. Most members have classic lipoprotein signal sequences. A critical role of this 5'-nucleotidase in Haemophilus influenzae is the degradation of external riboside in order to allow transport into the cell. An earlier suggested role in hemin transport is no longer current. This enzyme may also have other physiologically significant roles. [Transport and binding proteins, Other, Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridine nucleotides] 266 matched cddid_all.tbl CDD TIGR01534 TIGR01534 273675 GAPDH-I glyceraldehyde-3-phosphate dehydrogenase, type I. This model represents glyceraldehyde-3-phosphate dehydrogenase (GAPDH), the enzyme responsible for the interconversion of 1,3-diphosphoglycerate and glyceraldehyde-3-phosphate, a central step in glycolysis and gluconeogenesis. Forms exist which utilize NAD (EC 1.2.1.12), NADP (EC 1.2.1.13) or either (1.2.1.59). In some species, NAD- and NADP- utilizing forms exist, generally being responsible for reactions in the anabolic and catabolic directions respectively. Two Pfam models cover the two functional domains of this protein; pfam00044 represents the N-terminal NAD(P)-binding domain and pfam02800 represents the C-terminal catalytic domain. An additional form of gap gene is found in gamma proteobacteria and is responsible for the conversion of erythrose-4-phosphate (E4P) to 4-phospho-erythronate in the biosynthesis of pyridoxine. This pathway of pyridoxine biosynthesis appears to be limited, however, to a relatively small number of bacterial species although it is prevalent among the gamma-proteobacteria. This enzyme is described by TIGR001532. These sequences generally score between trusted and noise to this GAPDH model due to the close evolutionary relationship. There exists the possiblity that some forms of GAPDH may be bifunctional and act on E4P in species which make pyridoxine and via hydroxythreonine and lack a separate E4PDH enzyme (for instance, the GAPDH from Bacillus stearothermophilus has been shown to posess a limited E4PD activity as well as a robust GAPDH activity). There are a great number of sequences in the databases which score between trusted and noise to this model, nearly all of them due to fragmentary sequences. It seems that study of this gene has been carried out in many species utilizing PCR probes which exclude the extreme ends of the consenses used to define this model. The noise level is set relative not to E4PD, but the next closest outliers, the class II GAPDH's (found in archaea, TIGR01546) and aspartate semialdehyde dehydrogenase (ASADH, TIGR01296) both of which have highest-scoring hits around -225 to the prior model. [Energy metabolism, Glycolysis/gluconeogenesis] 326 matched cddid_all.tbl CDD TIGR01535 TIGR01535 130598 glucan_glucosid glucan 1,4-alpha-glucosidase. Glucan 1,4-alpha-glucosidase catalyzes the hydrolysis of terminal 1,4-linked alpha-D-glucose residues from non-reducing ends of polysaccharides, releasing a beta-D-glucose monomer. Some forms of this enzyme can hydrolyze terminal 1,6- and 1,3-alpha-D-glucosidic bonds in polysaccharides as well. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 648 matched cddid_all.tbl CDD TIGR01536 TIGR01536 273676 asn_synth_AEB asparagine synthase (glutamine-hydrolyzing). This model describes the glutamine-hydrolysing asparagine synthase. A poorly conserved C-terminal extension was removed from the model. Bacterial members of the family tend to have a long, poorly conserved insert lacking from archaeal and eukaryotic sequences. Multiple isozymes have been demonstrated, such as in Bacillus subtilis. Long-branch members of the phylogenetic tree (which typically were also second or third candidate members from their genomes) were removed from the seed alignment and score below trusted cutoff. [Amino acid biosynthesis, Aspartate family] 466 matched cddid_all.tbl CDD TIGR01537 TIGR01537 273677 portal_HK97 phage portal protein, HK97 family. This model represents one of several distantly related families of phage portal protein. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. It functions as a dodecamer of a single polypeptide of average mol. wt. of 40-90 KDa. [Mobile and extrachromosomal element functions, Prophage functions] 342 matched cddid_all.tbl CDD TIGR01538 TIGR01538 273678 portal_SPP1 phage portal protein, SPP1 family. This model represents one of several distantly related families of phage portal protein. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. It functions as a dodecamer of a single polypeptide of average mol. wt. of 40-90 KDa. [Mobile and extrachromosomal element functions, Prophage functions] 412 matched cddid_all.tbl CDD TIGR01539 TIGR01539 273679 portal_lambda phage portal protein, lambda family. This model represents one of several distantly related families of phage portal protein. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. It functions as a dodecamer of a single polypeptide of average mol. wt. of 40-90 KDa. [Mobile and extrachromosomal element functions, Prophage functions] 458 matched cddid_all.tbl CDD TIGR01540 TIGR01540 273680 portal_PBSX phage portal protein, PBSX family. This model represents one of several distantly related families of phage portal protein. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. It functions as a dodecamer of a single polypeptide of average mol. wt. of 40-90 KDa. This family shows clear homology to TIGR01537. The alignment for this group was trimmed of poorly alignable N-terminal sequence of about 50 residues and of C-terminal regions present in some but not all members of up 180 residues. [Mobile and extrachromosomal element functions, Prophage functions] 320 matched cddid_all.tbl CDD TIGR01541 TIGR01541 273681 tape_meas_lam_C phage tail tape measure protein, lambda family. This model represents a relatively well-conserved region near the C-terminus of the tape measure protein of a lambda and related phage. This protein, which controls phage tail length, is typically about 1000 residues in length. Both low-complexity sequence and insertion/deletion events appear common in this family. Mutational studies suggest a ruler or template role in the determination of phage tail length. Similar behavior is attributed to proteins from distantly related or unrelated families in other phage. [Mobile and extrachromosomal element functions, Prophage functions] 332 matched cddid_all.tbl CDD TIGR01542 TIGR01542 130605 A118_put_portal phage portal protein, putative, A118 family. This model represents a family of phage minor structural proteins. The protein is suggested to be the head-tail connector, or portal protein, on the basis of its position in the phage gene order, its presence in mature phage, its size, and its conservation across a number of complete genomes of tailed phage that lack other candidate portal proteins. Several other known portal protein families lack clear homology to this family and to each other. [Mobile and extrachromosomal element functions, Prophage functions] 476 matched cddid_all.tbl CDD TIGR01543 TIGR01543 273682 proheadase_HK97 phage prohead protease, HK97 family. This model describes the prohead protease of HK97 and related phage. It is generally encoded next to the gene for the capsid protein that it processes, and in some cases may be fused to it. This family does not show similarity to the prohead protease of phage T4 (see pfam03420). [Mobile and extrachromosomal element functions, Prophage functions, Protein fate, Other] 145 matched cddid_all.tbl CDD TIGR01544 TIGR01544 273683 HAD-SF-IE haloacid dehalogenase superfamily, subfamily IE hydrolase, TIGR01544. This model represents a small group of metazoan sequences. The sequences from mouse are annotated as Pyrimidine 5'-nucleotidases, aparrently in reference to HSPC233, the human homolog. However, no such annotation can currently be found for this gene. This group of sequences was found during searches for members of the haloacid dehalogenase (HAD) superfamily. All of the conserved catalytic motifs are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches (IA, TIGR01493, TIGR01509, TIGR01549; IB, TIGR01488; IC, TIGR01494; ID, TIGR01658; IF TIGR01545) of that subfamily as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB. 283 matched cddid_all.tbl CDD TIGR01545 TIGR01545 130608 YfhB_g-proteo haloacid dehalogenase superfamily, subfamily IF hydrolase, YfhB. This model describes a clade of sequences limited to the gamma proteobacteria. This group is a member of the haloacid dehalogenase (HAD) superfamily of aspartate-dependent hydrolases and all of the conserved catalytic motifs are present. Although structurally similar to subfamily IA in that the variable domain is predicted to consist of five consecutive alpha helices (by PSI-PRED), it is sufficiently divergent to warrant being regarded as a separate sub-family (IF). The gene name comes from the E. coli gene. There is currently no information regarding the function of this gene. 210 matched cddid_all.tbl CDD TIGR01546 TIGR01546 130609 GAPDH-II_archae glyceraldehyde-3-phosphate dehydrogenase, type II. This model describes the type II glyceraldehyde-3-phosphate dehydrogenases which are limited to archaea. These enzymes catalyze the interconversion of 1,3-diphosphoglycerate and glyceraldehyde-3-phosphate, a central step in glycolysis and gluconeogenesis. In archaea, either NAD or NADP may be utilized as the cofactor. The class I GAPDH's from bacteria and eukaryotes are covered by TIGR01534. All of the members of the seed are characterized. See, for instance. This model is very solid, there are no species falling between trusted and noise at this time. The closest relatives scoring in the noise are the class I GAPDH's. 333 matched cddid_all.tbl CDD TIGR01547 TIGR01547 273684 phage_term_2 phage terminase, large subunit, PBSX family. This model detects members of a highly divergent family of the large subunit of phage terminase. All members are encoded by phage genomes or within prophage regions of bacterial genomes. This is a distinct family from pfam03354. [Mobile and extrachromosomal element functions, Prophage functions] 394 matched cddid_all.tbl CDD TIGR01548 TIGR01548 273685 HAD-SF-IA-hyp1 "haloacid dehalogenase superfamily, subfamily IA hydrolase, TIGR01548. This model represents a small and phylogenetically curious clade of sequences. Sequences are found from Halobacterium (an archaeon), Nostoc and Synechococcus (cyanobacteria) and Phytophthora (a stramenophile eukaryote). These appear to be members of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases by general homology and the conservation of all of the recognized catalytic motifs. The variable domain is found in between motifs 1 and 2, indicating membership in subfamily I and phylogeny and prediction of the alpha helical nature of the variable domain (by PSI-PRED) indicate membership in subfamily IA. All but the Halobacterium sequence currently found are annotated as ""Imidazoleglycerol-phosphate dehydratase"", however, the source of the annotation could not be traced and significant homology could not be found between any of these sequences and known IGPD's." 197 matched cddid_all.tbl CDD TIGR01549 TIGR01549 273686 HAD-SF-IA-v1 "haloacid dehalogenase superfamily, subfamily IA, variant 1 with third motif having Dx(3-4)D or Dx(3-4)E. This model represents part of one structural subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs. The subfamilies are defined based on the location and the observed or predicted fold of a so-called ""capping domain"", or the absence of such a domain. Subfamily I consists of sequences in which the capping domain is found in between the first and second catalytic motifs. Subfamily II consists of sequences in which the capping domain is found between the second and third motifs. Subfamily III sequences have no capping domain in either of these positions.The Subfamily IA and IB capping domains are predicted by PSI-PRED to consist of an alpha helical bundle. Subfamily I encompasses such a wide region of sequence space (the sequences are highly divergent) that representing it with a single model is impossible, resulting in an overly broad description which allows in many unrelated sequences. Subfamily IA and IB are separated based on an aparrent phylogenetic bifurcation. Subfamily IA is still too broad to model, but cannot be further subdivided into large chunks based on phylogenetic trees. Of the three motifs defining the HAD superfamily, the third has three variant forms: (1) hhhhsDxxx(x)(D/E), (2) hhhhssxxx(x)D and (3) hhhhDDxxx(x)s where _s_ refers to a small amino acid and _h_ to a hydrophobic one. All three of these variants are found in subfamily IA. Individual models were made based on seeds exhibiting only one of the variants each. Variant 1 (this model) is found in the enzymes phosphoglycolate phosphatase (TIGR01449) and enolase-phosphatase. These three variant models (see also TIGR01493 and TIGR01509) were created withthe knowledge that there will be overlap among them - this is by design and serves the purpose of eliminating the overlap with models of more distantly relatedHAD subfamilies caused by an overly broad single model. [Unknown function, Enzymes of unknown specificity]" 164 matched cddid_all.tbl CDD TIGR01550 TIGR01550 273687 DOC_P1 death-on-curing family protein. The characterized member of this family is the death-on-curing (DOC) protein of phage P1. It is part of a two protein operon with prevents-host-death (phd) that forms an addiction module. DOC lacks homology to analogous addiction module post-segregational killing proteins involved in plasmid maintenance. These modules work as a combination of a long lived poison (e.g. this protein) and a more abundant but shorter lived antidote. Members of this family have a well-conserved central motif HxFx[ND][AG]NKR. A similar region, with K replaced by G, is found in the huntingtin interacting protein (HYPE) family. [Unknown function, General] 121 matched cddid_all.tbl CDD TIGR01551 TIGR01551 233464 major_capsid_P2 phage major capsid protein, P2 family. This model family represents the major capsid protein component of the heads (capsids) of bacteriophage P2 and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions] 327 matched cddid_all.tbl CDD TIGR01552 TIGR01552 273688 phd_fam prevent-host-death family protein. This model recognizes a region of about 55 amino acids toward the N-terminal end of bacterial proteins of about 85 amino acids in length. The best-characterized member is prevent-host-death (phd) of bacteriophage P1, the antidote partner of death-on-curing (doc) (TIGR01550) in an addiction module. Addiction modules prevent plasmid curing by killing the host cell as the longer-lived killing protein persists while the gene for the shorter-lived antidote is lost. Note, however, that relatively few members of this family appear to be plasmid or phage-encoded. Also, there is little overlap, except for phage P1 itself, of species with this family and with the doc family. [Cellular processes, Toxin production and resistance, Mobile and extrachromosomal element functions, Other] 52 matched cddid_all.tbl CDD TIGR01553 TIGR01553 273689 formate-DH-alph formate dehydrogenase-N alpha subunit. This model describes a subset of formate dehydrogenase alpha chains found mainly in proteobacteria but also in Aquifex. The alpha chain contains domains for molybdopterin dinucleotide binding and molybdopterin oxidoreductase (pfam01568 and pfam00384, respectively). The holo-enzyme also contains beta and gamma subunits of 32 and 20 kDa. The enzyme catalyzes the oxidation of formate (produced from pyruvate during anaerobic growth) to carbon dioxide with the concomitant release of two electrons and two protons. The electrons are utilized mainly in the nitrate respiration by nitrate reductase. In E. coli and Salmonella, there are two forms of the formate dehydrogenase, one induced by nitrate which is strictly anaerobic (fdn), and one incuced during the transition from aerobic to anaerobic growth (fdo). This subunit is one of only three proteins in E. coli which contain selenocysteine. This model is well-defined, with a large, unpopulated trusted/noise gap. [Energy metabolism, Anaerobic, Energy metabolism, Electron transport] 1009 matched cddid_all.tbl CDD TIGR01554 TIGR01554 273690 major_cap_HK97 phage major capsid protein, HK97 family. This model family represents the major capsid protein component of the heads (capsids) of bacteriophage HK97, phi-105, P27, and related phage. This model represents one of several analogous families lacking detectable sequence similarity. The gene encoding this component is typically located in an operon encoding the small and large terminase subunits, the portal protein and the prohead or maturation protease. [Mobile and extrachromosomal element functions, Prophage functions] 386 matched cddid_all.tbl CDD TIGR01555 TIGR01555 130618 phge_rel_HI1409 phage-related protein, HI1409 family. This model describes an uncharacterized family of proteins found in prophage regions of a number of bacterial genomes, including Haemophilus influenzae, Xylella fastidiosa, Salmonella typhi, and Enterococcus faecalis. Distantly related proteins can be found in the prophage-bearing plasmids of Borrelia burgdorferi. [Mobile and extrachromosomal element functions, Prophage functions] 404 matched cddid_all.tbl CDD TIGR01556 TIGR01556 130619 rhamnosyltran L-rhamnosyltransferase. This model subfamily is comprised of gamma proteobacteria whose proteins function as L-rhamnosyltransferases in the synthesis of their respective surface polysaccharides. Rhamnolipids are glycolipids containing mono- or di- L-rhamnose molecules. Rhamnolipid synthesis occurs by sequential glycosyltransferase reactions involving two distinct rhamnosyltransferase enzymes. In P.aeruginosa, the synthesis of mono-rhamnolipids is catalyzed by rhamnosyltransferase 1, and proceeds by a glycosyltransfer reaction catalyzed by rhamnosyltransferase 2 to yield di-rhamnolipids. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 281 matched cddid_all.tbl CDD TIGR01557 TIGR01557 130620 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif. 57 matched cddid_all.tbl CDD TIGR01558 TIGR01558 273691 sm_term_P27 phage terminase, small subunit, putative, P27 family. This model describes a distinct family of phage (and integrated prophage) putative terminase small subunit. Members tend to be adjacent to the phage terminase large subunit gene. [Mobile and extrachromosomal element functions, Prophage functions] 116 matched cddid_all.tbl CDD TIGR01559 TIGR01559 188157 squal_synth farnesyl-diphosphate farnesyltransferase. This model describes farnesyl-diphosphate farnesyltransferase, also known as squalene synthase, as found in eukaryotes. This family is related to phytoene synthases. Tentatively identified archaeal homologs (excluded from this model) lack the C-terminal predicted transmembrane region universally conserved among members of this family. 337 matched cddid_all.tbl CDD TIGR01560 TIGR01560 130623 put_DNA_pack uncharacterized phage protein (possible DNA packaging). This model describes a small (~ 100 amino acids) protein found in phage and in putative prophage regions of a number of bacterial genomes. Members have been annotated in some cases as a possible DNA packaging protein, but the source of this annotation was not traced during construction of this model. [Mobile and extrachromosomal element functions, Prophage functions] 91 matched cddid_all.tbl CDD TIGR01561 TIGR01561 130624 gde_arch glycogen debranching enzyme, archaeal type, putative. The seed for this model is composed of two uncharacterized archaeal proteins from Methanosarcina acetivorans and Sulfolobus solfataricus. Trusted cutoff is set so that essentially only archaeal members hit the model. The notable exceptions to archaeal membership are the Gram positive Clostridium perfringens which scores much better than some other archaea and the Cyanobacterium Nostoc sp. which scores just above the trusted cutoff. Noise cutoff is set to exclude the characterized eukaryotic glycogen debranching enzyme in S. cerevisiae. These cutoffs leave the prokaryotes Porphyromonas gingivalis and Deinococcus radiodurans below trusted but above noise. Multiple alignments including these last two species exhibit sequence divergence which may suggest a subtly different function for these prokaryotic proteins. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 575 matched cddid_all.tbl CDD TIGR01562 TIGR01562 130625 FdhE formate dehydrogenase accessory protein FdhE. This model describes an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulfur clusters and cytochrome b556, it is likely to have something to do with the insertion of cofactors. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553). 305 matched cddid_all.tbl CDD TIGR01563 TIGR01563 273692 gp16_SPP1 phage head-tail adaptor, putative, SPP1 family. This family describes a small protein of about 100 amino acids found in bacteriophage and in bacterial prophage regions. Examples include gp9 of phage HK022 and gp16 of phage SPP1. This minor structural protein is suggested to be a head-tail adaptor protein (although the source of this annotation was not traced during construction of this model). [Mobile and extrachromosomal element functions, Prophage functions] 101 matched cddid_all.tbl CDD TIGR01564 TIGR01564 273693 S_layer_MJ S-layer protein, MJ0822 family. This model represents one of several families of proteins associated with the formation of prokaryotic S-layers. Members of this family are found in archaeal species, including Pyrococcus horikoshii (split into two tandem reading frames), Methanococcus jannaschii, and related species. Some local similarity can be found to other S-layer protein families. [Cell envelope, Surface structures] 571 matched cddid_all.tbl CDD TIGR01565 TIGR01565 130628 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam00046. It is found in both C4 and C3 plants. 58 matched cddid_all.tbl CDD TIGR01566 TIGR01566 130629 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich dimerization domain. This model describes a 54-residue domain found in the N-terminal region of plant proteins, the vast majority of which contain a ZF-HD class homeobox domain toward the C-terminus. The region between the two domains typically is rich in low complexity sequence. The companion ZF-HD homeobox domain is described in model TIGR01565. 53 matched cddid_all.tbl CDD TIGR01567 TIGR01567 273694 S_layer_rel_Mac S-layer family duplication domain. This model represents a sequence region found tandemly duplicated in two proven archaeal S-layer glycoproteins, MA0829 from Methanosarcina acetivorans C2A and MM1976 from Methanosarcina mazei Go1, as well as in several paralogs of those L-layer proteins from both species. Members of the family show regions of local similarity to another known family of archaeal S-layer proteins described by model TIGR01564. Some members of this family, including the proven S-layer proteins, have the archaeosortase A target motif, PGF-CTERM (TIGR04126), at the protein C-terminus. [Cell envelope, Surface structures] 256 matched cddid_all.tbl CDD TIGR01568 TIGR01568 130631 A_thal_3678 uncharacterized plant-specific domain TIGR01568. This model describes an uncharacterized domain of about 70 residues found exclusively in plants, generally toward the C-terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana. Other regions of these proteins tend to consist largely of low-complexity sequence. 66 matched cddid_all.tbl CDD TIGR01569 TIGR01569 273695 A_tha_TIGR01569 plant integral membrane protein TIGR01569. This model describes a region of ~160 residues found exclusively in plant proteins, generally as the near complete length of the protein. At least 24 different members are found in Arabidopsis thaliana. Members have four predicted transmembrane regions, the last of which is preceded by an invariant CXXXXX[FY]C motif. The family is not functionally characterized. 154 matched cddid_all.tbl CDD TIGR01570 TIGR01570 273696 A_thal_3588 uncharacterized plant-specific domain TIGR01570. This model represents a region of about 170 amino acids found at the C-terminus of a family of plant proteins. These proteins typically have additional highly divergent N-terminal regions rich in low complexity sequence. PSI-BLAST reveals no clear similarity to any characterized protein. At least 12 distinct members are found in Arabidopsis thaliana. 161 matched cddid_all.tbl CDD TIGR01571 TIGR01571 273697 A_thal_Cys_rich uncharacterized Cys-rich domain. This model describes an uncharacterized domain of about 100 residues. It is common in plants but found also in Homo sapiens, Dictyostelium, and Leishmania; at least 12 distinct members are found in Arabidopsis. Most members of this family contain more than 10 per cent Cys, but no Cys residue is invariant across the family. 104 matched cddid_all.tbl CDD TIGR01572 TIGR01572 273698 A_thl_para_3677 Arabidopsis paralogous family TIGR01572. This model describes a paralogous family of hypothetical proteins in Arabidopsis thaliana. No homologs are detected from other species. Length heterogeneity within the family is attributable partly to a 21-residue repeat present in from zero to three tandem copies. The central region of the repeat resembles the pattern [VIF][FY][QK]GX[LM]P[DEK]XXXDDAL. 265 matched cddid_all.tbl CDD TIGR01573 TIGR01573 273699 cas2 CRISPR-associated endonuclease Cas2. This model describes most members of the family of Cas2, one of the first four protein families found to mark prokaryotic genomes that contain multiple CRISPR elements. CRISPR systems protect against invasive nucleic acid sequences, including phage. Cas2 proteins have been characterized as either endoribonuclease (for ssRNA) or endodeoxyribonuclease (for dsDNA), depending on the system to which the Cas2 belongs. CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeats. The cas genes usually are found near the repeats. A distinct branch of the Cas2 family shows a very low level of sequence identity and is modeled by TIGR01873 instead of by this model (TIGR01573). 95 matched cddid_all.tbl CDD TIGR01574 TIGR01574 273700 miaB-methiolase tRNA-N(6)-(isopentenyl)adenosine-37 thiotransferase enzyme MiaB. This model represents homologs of the MiaB enzyme responsible for the modification of the isopentenylated adenine-37 base of most bacterial and eukaryotic tRNAs that read codons beginning with uracil (all except tRNA(I,V) Ser). Adenine-37 is next to the anticodon on the 3' side in these tRNA's, and lack of modification at this site leads to an increased spontaneous mutation frequency. Isopentenylated A-37 is modified by methylthiolation at position 2, either by MiaB alone or in concert with a separate methylase yet to be discovered (MiaC?). MiaB contains a 4Fe-4S cluster which is labile under oxidizing conditions. Additionally, the sequence is homologous (via PSI-BLAST searches) to the biotin synthetase, BioB, which utilizes both an iron-sulfur cluster and S-adenosym methionine (SAM) to generate a radical which is responsible for initiating the insertion of sulfur into the substrate. It is reasonable to surmise that the methyl group of SAM becomes the methyl group of the product, but this has not been shown, and the possibility of a separate methylase exists. This equivalog is a member of a subfamily (TIGR00089) which contains several other hypothetical equivalogs which are all probably enzymes with similar function acting on different substrates. These enzymes contain a TRAM domain (pfam01938) which is believed to be responsible for binding to tRNAs. Hits to this model span all major groups of bacteria and eukaryotes, but not archaea, which are known to lack this particular tRNA modification. The enzyme from Thermotoga maritima has been cloned, expressed, spectroscopically characterized and shown to complement the E. coli MiaB enzyme. [Protein synthesis, tRNA and rRNA base modification] 438 matched cddid_all.tbl CDD TIGR01575 TIGR01575 273701 rimI ribosomal-protein-alanine acetyltransferase. Members of this model belong to the GCN5-related N-acetyltransferase (GNAT) superfamily. This model covers prokarotes and the archaea. The seed contains a characterized accession for Gram negative E. coli. An untraceable characterized accession (PIR|S66013) for Gram positive B. subtilis scores well (205.0) in the full alignment. Characterized members are lacking in the archaea. Noise cutoff (72.4) was set to exclude M. loti paralog of rimI. Trusted cutoff (80.0) was set at next highest scoring member in the mini-database. [Protein synthesis, Ribosomal proteins: synthesis and modification] 131 matched cddid_all.tbl CDD TIGR01577 TIGR01577 273702 oligosac_amyl oligosaccharide amylase. The name of this type of amylase is based on the characterization of an glucoamylase family enzyme from Thermoactinomyces vulgaris. The T. vulgaris enzyme was expressed in E. coli and, like other glucoamylases, it releases beta-D-glucose from starch. However, unlike previously characterized glucoamylases, this T. vulgaris amylase hydrolyzes maltooligosaccharides (maltotetraose, maltose) more efficiently than starch (1), indicating this enzyme belongs to a class of glucoamylase-type enzymes with oligosaccharide-metabolizing activity. 616 matched cddid_all.tbl CDD TIGR01578 TIGR01578 273703 MiaB-like-B MiaB-like tRNA modifying enzyme, archaeal-type. This clade of sequences is closely related to MiaB, a modifier of isopentenylated adenosine-37 of certain eukaryotic and bacterial tRNAs (see TIGR01574). Sequence alignments suggest that this equivalog performs the same chemical transformation as MiaB, perhaps on a different (or differently modified) tRNA base substrate. This clade is a member of a subfamily (TIGR00089) and spans the archaea and eukaryotes. The only archaeal miaB-like genes are in this clade, while eukaryotes have sequences described by this model as well as ones falling within the scope of the MiaB equivalog model. [Protein synthesis, tRNA and rRNA base modification] 420 matched cddid_all.tbl CDD TIGR01579 TIGR01579 273704 MiaB-like-C MiaB-like tRNA modifying enzyme. This clade of sequences is closely related to MiaB, a modifier of isopentenylated adenosine-37 of certain eukaryotic and bacterial tRNAs (see TIGR01574). Sequence alignments suggest that this equivalog performs the same chemical transformation as MiaB, perhaps on a different (or differently modified) tRNA base substrate. This clade is a member of a subfamily (TIGR00089) and spans low GC Gram positive bacteria, alpha and epsilon proteobacteria, Campylobacter, Porphyromonas, Aquifex, Thermotoga, Chlamydia, Treponema and Fusobacterium. [Protein synthesis, tRNA and rRNA base modification] 414 matched cddid_all.tbl CDD TIGR01580 TIGR01580 162434 narG respiratory nitrate reductase, alpha subunit. The Nitrate reductase enzyme complex allows bacteria to use nitrate as an electron acceptor during anaerobic growth. The enzyme complex consists of a tetramer that has an alpha, beta and 2 gamma subunits. The alpha and beta subunits have catalytic activity and the gamma subunits attach the enzyme to the membrane and is a b-type cytochrome that receives electrons from the quinone pool and transfers them to the beta subunit. This model is specific for the alpha subunit for nitrate reductase I (narG) and nitrate reductase II (narZ) for gram positive and gram negative bacteria.A few thermophiles and archaea also match the model The seed members used to make the model include Nitrate reductases from Pseudomonas fluorescens (GP:11344601), E.coli (SP:P09152) and B.subtilis (SP:P42175). All seed members are experimentally characterized. Some unpublished nitrate reductases, that are shorter sequences, and probably fragments fall in between the noise and trusted cutoffs. Pfam models pfam00384 (Molybdopterin oxidoreductase) and pfam01568(Molydopterin dinucleotide binding domain) will also match the nitrate reductase, alpha subunit. [Energy metabolism, Anaerobic] 1235 matched cddid_all.tbl CDD TIGR01581 TIGR01581 130643 Mo_ABC_porter NifC-like ABC-type porter. This model describes a clade of ABC porter genes with relatively weak homology compared to its neighbor clades, the molybdate (TIGR02141) and sulfate (TIGR00969) porters. Neighbor-Joining, PAM-distance phylogenetic trees support the separation of the clades in this way. Included in this group is a gene designated NifC in Clostridium pasturianum. It would be reasonable to presume that NifC acts as a molybdate porter since the most common form of nitrogenase is a molybdoenzyme. Several other sequences falling within the scope of this model are annotated as molybdate porters and one, from Halobacterium, is annotated as a sulfate porter. There is presently no experimental evidence to support annotations with this degree of specificity. 225 matched cddid_all.tbl CDD TIGR01582 TIGR01582 273705 FDH-beta formate dehydrogenase, beta subunit, Fe-S containing. This model represents the beta subunit of the gamma-proteobacterial formate dehydrogenase. This subunit contains four 4Fe-4S clusters and is involved in transmitting electrons from the alpha subunit (TIGR01553) at the periplasmic space to the gamma subunit which spans the cytoplasmic membrane. In addition to the gamma proteobacteria, a sequence from Aquifex aolicus falls within the scope of this model. This appears to be the case for the alpha, gamma and epsilon (accessory protein TIGR01562) chains as well. [Energy metabolism, Anaerobic, Energy metabolism, Electron transport] 283 matched cddid_all.tbl CDD TIGR01583 TIGR01583 130645 formate-DH-gamm formate dehydrogenase, gamma subunit. This model represents the gamma chain of the gamma proteobacteria (and Aquifex aolicus) formate dehydrogenase. This subunit is integral to the cytoplasmic membrane, consisting of 4 transmembrane helices, and receives electrons from the beta subunit. The entire E. coli formate dehydrogenase N (nitrate-inducible form) has been crystallized. The gamma subunit contains two cytochromes, heme b(P) and heme b(C) near the periplasmic and cytoplasmic sides of the membrane respectively. The electron acceptor quinone binds at the cytoplasmic heme histidine ligand. NiFe-hydrogenase and thiosulfate reductase contain homologous gamma subunits, and these can be found scoring in the noise of this model. [Energy metabolism, Anaerobic, Energy metabolism, Electron transport] 204 matched cddid_all.tbl CDD TIGR01584 TIGR01584 130646 citF citrate lyase, alpha subunit. This is a model of the alpha subunit of the holoenzyme citrate lyase (EC 4.1.3.6) composed of alpha (EC 2.8.3.10), beta (EC 4.1.3.34), and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The alpha subunit catalyzes the reaction Acetyl-CoA + citrate = acetate + (3S)-citryl-CoA. The seed contains an experimentally characterized member from Lactococcus lactis subsp. lactis. The model covers both Gram positive and Gram negative bacteria. It is quite robust with queries scoring either quite well or quite poorly against the model. There are currently no hits in between the noise cutoff and trusted cutoff. [Energy metabolism, Fermentation] 492 matched cddid_all.tbl CDD TIGR01586 TIGR01586 273706 yopT_cys_prot cysteine protease domain, YopT-type. The model represents a cysteine protease domain found in proteins of bacteria that include plant pathogens (Pseudomonas syringae), root nodule bacteria, and intracellular pathogens (e.g. Yersinia pestis, Haemophilus ducreyi, Pasteurella multocida, Chlamydia trachomatis) of animal hosts. The domain features a catalytic triad of Cys, His, and Asp. Sequences can be extremely divergent outside of a few well-conserved motifs, and additional members may exist that are detected by this model. YopT, a virulence effector protein of Yersinia pestis, cleaves and releases host cell Rho GTPases from the membrane, thereby disrupting the actin cytoskeleton. Members of the family from pathogenic bacteria are likely to be pathogenesis factors. [Cellular processes, Pathogenesis] 196 matched cddid_all.tbl CDD TIGR01587 TIGR01587 273707 cas3_core CRISPR-associated helicase Cas3. This model represents the highly conserved core region of an alignment of Cas3, a protein found in association with CRISPR repeat elements in a broad range of bacteria and archaea. Cas3 appears to be a helicase, with regions found by pfam00270 (DEAD/DEAH box helicase) and pfam00271 (Helicase conserved C-terminal domain). Some but not all members have an N-terminal HD domain region (pfam01966) that is not included within this model. 359 matched cddid_all.tbl CDD TIGR01588 TIGR01588 130649 citE citrate lyase, beta subunit. This is a model of the beta subunit of the holoenzyme citrate lyase (EC 4.1.3.6) composed of alpha (EC 2.8.3.10), beta (EC 4.1.3.34), and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The beta subunit catalyzes the reaction (3S)-citryl-CoA = acetyl-CoA + oxaloacetate. The seed contains an experimentally characterized member from Leuconostoc mesenteroides. The model covers a wide range of Gram positive bacteria. For Gram negative bacteria, it appears that only gamma proteobacteria hit this model. The model is quite robust with queries scoring either quite well or quite poorly against the model. There are currently no hits in-between the noise cutoff and trusted cutoff. [Energy metabolism, Fermentation] 288 matched cddid_all.tbl CDD TIGR01589 TIGR01589 130650 A_thal_3526 uncharacterized plant-specific domain TIGR01589. This model represents an uncharacterized plant-specific domain 57 residues in length. It is found toward the N-terminus of most proteins that contain it. Examples include at least 10 proteins from Arabidopsis thaliana and at least one from Oryza sativa. 57 matched cddid_all.tbl CDD TIGR01590 TIGR01590 130651 yir-bir-cir_Pla yir/bir/cir-family of variant antigens, Plasmodium-specific. This model represents a large paralogous family of variant antigens from several Plasmodium species (P. yoelii, P. berghei and P. chabaudi). The seed was generated from a list of ORF's in P. yoelii containing a paralagous domain as defined by an algorithm implemented at TIFR. The list was aligned and reduced to six sequences approximating the most divergent clades present in the data set. The model only hits genes previously characterized as yir, bir, or cir genes above the trusted cutoff. In between trusted and noise is one gene from P. vivax (vir25) which has been characterized as a distant relative of the yir/bir/cir family. The vir family appears to be present in 600-1000 copies per haploid genome and is preferentially located in the sub-telomeric regions of the chromosomes. The genomic data for yoelii is consistent with this observation. It is not believed that there are any orthologs of this family in P. falciparum. 199 matched cddid_all.tbl CDD TIGR01591 TIGR01591 130652 Fdh-alpha formate dehydrogenase, alpha subunit, archaeal-type. This model describes a subset of formate dehydrogenase alpha chains found mainly archaea but also in alpha and gamma proteobacteria and a small number of gram positive bacteria. The alpha chain contains domains for molybdopterin dinucleotide binding and molybdopterin oxidoreductase (pfam01568 and pfam00384, respectively). The holo-enzyme also contains beta and gamma subunits. The enzyme catalyzes the oxidation of formate (produced from pyruvate during anaerobic growth) to carbon dioxide with the concomitant release of two electrons and two protons. The enzyme's purpose is to allow growth on formate in some circumstances and, in the case of FdhH in gamma proteobacteria, to pass electrons to hydrogenase (by which process acid is neutralized). This model is well-defined, with only a single fragmentary sequence falling between trusted and noise. The alpha subunit of a version of nitrate reductase is closely related. 671 matched cddid_all.tbl CDD TIGR01592 TIGR01592 130653 holin_SPP1 holin, SPP1 family. This model represents one of more than 30 families of phage proteins, all lacking detectable homology with each other, known or believed to act as holins. Holins act in cell lysis by bacteriophage. Members of this family are found in phage PBSX and phage SPP1, among others. [Mobile and extrachromosomal element functions, Prophage functions] 75 matched cddid_all.tbl CDD TIGR01593 TIGR01593 273708 holin_tox_secr toxin secretion/phage lysis holin. This model describes one of the many mutally dissimilar families of holins, phage proteins that act together with lytic enzymes in bacterial lysis. This family includes, besides phage holins, the protein TcdE/UtxA involved in toxin secretion in Clostridium difficile and related species. [Protein fate, Protein and peptide secretion and trafficking, Mobile and extrachromosomal element functions, Prophage functions] 128 matched cddid_all.tbl CDD TIGR01594 TIGR01594 273709 holin_lambda phage holin, lambda family. This model represents one of a large number of mutally dissimilar families of phage holins. Holins act against the host cell membrane to allow lytic enzymes of the phage to reach the bacterial cell wall. This family includes the product of the S gene of phage lambda. [Mobile and extrachromosomal element functions, Prophage functions] 107 matched cddid_all.tbl CDD TIGR01595 TIGR01595 273710 cas_CT1132 CRISPR-associated protein, CT1132 family. This protein is found in at least five widely species that contain CRISPR loci. Four cas (CRISPR-associated) proteins that are widely distributed and found near the CRISPR repeats. This protein is found exclusively next to other cas proteins. Its function is unknown. 281 matched cddid_all.tbl CDD TIGR01596 TIGR01596 273711 cas3_HD CRISPR-associated endonuclease Cas3-HD. CRISPR/Cas systems are widespread, mobile systems for host defense against invasive elements such as phage. In these systems, Cas3 designates one of the core proteins shared widely by multiple types of CRISPR/Cas system. This model represents an HD-like endonuclease that occurs either separately or as the N-terminal region of Cas3, the helicase-containing CRISPR-associated protein. 176 matched cddid_all.tbl CDD TIGR01597 TIGR01597 130658 PYST-B Plasmodium yoelii subtelomeric family PYST-B. This model represents a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes. There are no obvious homologs to these genes in any other organism. 255 matched cddid_all.tbl CDD TIGR01598 TIGR01598 130659 holin_phiLC3 holin, phage phi LC3 family. Phage proteins for bacterial lysis typically include a membrane-disrupting protein, or holin, and one or more cell wall degrading enzymes that reach the cell wall because of holin action. Holins are found in a large number of mutually non-homologous families. [Mobile and extrachromosomal element functions, Prophage functions] 78 matched cddid_all.tbl CDD TIGR01599 TIGR01599 273712 PYST-A Plasmodium yoelii subtelomeric family PYST-A. This model represents a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes. Members of this family are expressed in both the Sporozoite and Gametozoite life stages. A single high-scoring gene was identified in the complete genome of P. falciparum as well as a single gene from P. chaboudi from GenBank which were included in the seed. There are no obvious homologs to these genes in any non-Plasmodium organism. These observations suggest an expansion of this family in yoelii from a common Plasmodium ancestor gene (present in a single copy in falciparum). 208 matched cddid_all.tbl CDD TIGR01600 TIGR01600 130661 phage_tail_L lambda-like phage minor tail protein L. This model detects members of the family of phage lambda minor tail protein L. This model was built as a fragment model to allow detection of fragmentary sequences, as might be found in cryptic prophage regions. [Mobile and extrachromosomal element functions, Prophage functions] 225 matched cddid_all.tbl CDD TIGR01601 TIGR01601 213640 PYST-C1 Plasmodium yoelii subtelomeric domain PYST-C1. This model represents the N-terminal domain of a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes. There are no obvious homologs to these genes in any other organism. The C-terminal portions of the genes which contain this domain are divergent and some contain other yoelii-specific paralogous domains such as PYST-C2 (TIGR01604). 82 matched cddid_all.tbl CDD TIGR01602 TIGR01602 130663 PY-rept-46 Plasmodium yoelii repeat of length 46. This repeat is found in only 2 genes in Plasmodium yoelii, in each of these genes it is repeated 9 times. It is found in no other organism. 46 matched cddid_all.tbl CDD TIGR01603 TIGR01603 273713 maj_tail_phi13 phage major tail protein, phi13 family. This model describes a set of proteins that share low levels of sequence similarity but similar lengths and similar patterns of charged, hydrophobic, and Gly/Pro residues. All members (except one attributed to mouse embryo cDNA) belong to phage of Gram-positive bacteria. Several are identified as phage major tail proteins. Some members of this family have additional C-terminal regions of about 100 residues not included in this model. [Mobile and extrachromosomal element functions, Prophage functions] 190 matched cddid_all.tbl CDD TIGR01604 TIGR01604 130665 PYST-C2 Plasmodium yoelii subtelomeric domain PYST-C2. This model represents a domain of a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes. There are no obvious homologs to these genes in any other organism. The genes found by this model often are associated with an N-terminal domain yoelii-specific domain such as PYST-C1 (TIGR01601). 150 matched cddid_all.tbl CDD TIGR01605 TIGR01605 130666 PYST-D Plasmodium yoelii subtelomeric family PYST-D. This model represents a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes. These genes are generally very short (ca. 50 residues). There are no obvious homologs to these genes in any other organism. 55 matched cddid_all.tbl CDD TIGR01606 TIGR01606 200119 holin_BlyA holin, BlyA family. This family represents a BlyA, a small holin found in Borrelia circular plasmids that prove to be temperate phage. This protein was previously proposed to be an hemolysin. BlyA is small (67 residues) and contains two largely hydrophobic helices and a highly charged C-terminus. [Mobile and extrachromosomal element functions, Prophage functions] 63 matched cddid_all.tbl CDD TIGR01607 TIGR01607 162444 PST-A Plasmodium subtelomeric family (PST-A). This model represents a paralogous family of genes in Plasmodium falciparum and Plasmodium yoelii, which are closely related to various phospholipases and lysophospholipases of plants as well as generally being related to the alpha/beta-fold superfamily of hydrolases. These genes are preferentially located in the subtelomeric regions of the chromosomes of both P. falciparum and P. yoelii. 332 matched cddid_all.tbl CDD TIGR01608 TIGR01608 130669 citD citrate lyase acyl carrier protein. This is a model of the acyl carrier protein (aka gamma subunit) of the holoenzyme citrate lyase (EC 4.1.3.6) composed of alpha (EC 2.8.3.10), beta (EC 4.1.3.34), and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The acyl carrier protein covalently binds the coenzyme of citrate lyase. The seed contains an experimentally characterized member from Leuconostoc mesenteroides. The model covers a wide range of Gram positive bacteria. For Gram negative bacteria, it appears that only gamma proteobacteria hit this model. The model is quite robust with queries scoring either quite well or quite poorly against the model. There are currently no hits in-between the noise cutoff and trusted cutoff. [Energy metabolism, Fermentation] 92 matched cddid_all.tbl CDD TIGR01609 TIGR01609 273714 PF_unchar_267 Plasmodium falciparum uncharacterized protein TIGR01609. This model represents a family of at least four proteins in Plasmodium falciparum. An interesting feature is five perfectly conserved Trp residues. 146 matched cddid_all.tbl CDD TIGR01610 TIGR01610 273715 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins. [DNA metabolism, DNA replication, recombination, and repair, Mobile and extrachromosomal element functions, Prophage functions] 95 matched cddid_all.tbl CDD TIGR01611 TIGR01611 130672 tail_tube phage contractile tail tube protein, P2 family. The tails of some phage are contractile. This model represents the tail tube, or tail core, protein of the contractile tail of phage P2, and homologous proteins from additional phage. [Mobile and extrachromosomal element functions, Prophage functions] 168 matched cddid_all.tbl CDD TIGR01612 TIGR01612 130673 235kDa-fam reticulocyte binding/rhoptry protein. This model represents a group of paralogous families in plasmodium species alternately annotated as reticulocyte binding protein, 235-kDa family protein and rhoptry protein. Rhoptry protein is localized on the cell surface and is extremely large (although apparently lacking in repeat structure) and is important for the process of invasion of the RBCs by the parasite. These proteins are found in P. falciparum, P. vivax and P. yoelii. 2757 matched cddid_all.tbl CDD TIGR01613 TIGR01613 273716 primase_Cterm phage/plasmid primase, P4 family, C-terminal domain. This model represents a clade within a larger family of proteins from viruses of bacteria and animals. Members of this family are found in phage and plasmids of bacteria and archaea only. The model describes a domain of about 300 residues, found generally toward the protein C-terminus. [DNA metabolism, DNA replication, recombination, and repair, Mobile and extrachromosomal element functions, Prophage functions] 304 matched cddid_all.tbl CDD TIGR01614 TIGR01614 273717 PME_inhib pectinesterase inhibitor domain. This model describes a plant domain of about 200 amino acids, characterized by four conserved Cys residues, shown in a pectinesterase inhibitor from Kiwi to form two disulfide bonds: first to second and third to fourth. Roughly half the members of this family have the region described by this model followed immediately by a pectinesterase domain, pfam01095. This suggests that the pairing of the enzymatic domain and its inhibitor reflects a conserved regulatory mechanism for this enzyme family. 178 matched cddid_all.tbl CDD TIGR01615 TIGR01615 273718 A_thal_3542 uncharacterized plant-specific domain TIGR01615. This model represents a domain found toward the C-terminus of a number of uncharacterized plant proteins. The domain is strongly conserved (greater than 30 % sequence identity between most pairs of members) but flanked by highly divergent regions including stretches of low-complexity sequence. 131 matched cddid_all.tbl CDD TIGR01616 TIGR01616 273719 nitro_assoc nitrogenase-associated protein. This model describes a small family of uncharacterized proteins found so far in alpha and gamma proteobacteria and in Nostoc sp. PCC 7120, a cyanobacterium. The gene for this protein is associated with nitrogenase genes. This family shows sequence similarity to TIGR00014, a glutaredoxin-dependent arsenate reductase that converts arsentate to arsenite for disposal. This family is one of several included in pfam03960. [Unknown function, General] 126 matched cddid_all.tbl CDD TIGR01617 TIGR01617 273720 arsC_related transcriptional regulator, Spx/MgsR family. This model represents a portion of the proteins within the larger set covered by pfam03960. That larger family includes a glutaredoxin-dependent arsenate reductase (TIGR00014). Characterized members of this family include Spx and MgsR from Bacillus subtili. Spx is a global regulator for response to thiol-specific oxidative stress. It interacts with RNA polymerase. MgsR (modulator of the general stress response, also called YqgZ) provides a second level of regulation for more than a third of the proteins in the B. subtilis general stress regulon controlled by Sigma-B. [Regulatory functions, DNA interactions] 117 matched cddid_all.tbl CDD TIGR01618 TIGR01618 130679 phage_P_loop phage nucleotide-binding protein. This model represents an uncharacterized family of proteins from a number of phage of Gram-positive bacteria. This protein contains a P-loop motif, G/A-X-X-G-X-G-K-T near its amino end. The function of this protein is unknown. [Mobile and extrachromosomal element functions, Prophage functions] 220 matched cddid_all.tbl CDD TIGR01619 TIGR01619 130680 hyp_HI0040 TIGR01619 family protein. This model represents a hypothetical equivalog of gamma proteobacteria, includes HI0040. These sequences do not have any similarity to known proteins by PSI-BLAST. 249 matched cddid_all.tbl CDD TIGR01620 TIGR01620 130681 hyp_HI0043 TIGR01620 family protein. This model includes putative membrane proteins from alpha and gamma proteobacteria, each making up their own clade. The two clades have less than 25% identity between them. We could not find support for the assignment to the sequence from Brucella (OMNI|NTL01BM0951) of being a GTP-binding protein. 289 matched cddid_all.tbl CDD TIGR01621 TIGR01621 130682 RluA-like pseudouridine synthase Rlu family protein, TIGR01621. This model represents a clade of sequences within the pseudouridine synthase superfamily (pfam00849). The superfamily includes E. coli proteins: RluA, RluB, RluC, RluD, and RsuA. The sequences modeled here are most closely related to RluA. Neisseria, among those species hitting this model, does not appear to have an RluA homolog. It is presumed that these sequences function as pseudouridine synthases, although perhaps with different specificity. [Protein synthesis, tRNA and rRNA base modification] 217 matched cddid_all.tbl CDD TIGR01622 TIGR01622 273721 SF-CC1 splicing factor, CC1-like family. This model represents a subfamily of RNA splicing factors including the Pad-1 protein (N. crassa), CAPER (M. musculus) and CC1.3 (H.sapiens). These proteins are characterized by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 H. sapiens paralogs, two) RNA recognition domains (rrm: pfam00706). These splicing factors are closely related to the U2AF splicing factor family (TIGR01642). A homologous gene from Plasmodium falciparum was identified in the course of the analysis of that genome at TIGR and was included in the seed. 494 matched cddid_all.tbl CDD TIGR01623 TIGR01623 130684 put_zinc_LRP1 putative zinc finger domain, LRP1 type. This model represents a putative zinc finger domain found in plants. Arabidopsis thaliana has at least 10 distinct members. Proteins containing this domain, including LRP1, generally share the same size, about 300 amino acids, and architecture. This 43-residue domain, and a more C-terminal companion domain of similar size, appear as tightly conserved islands of sequence similarity. The remainder consists largely of low-complexity sequence. Several animal proteins have regions with matching patterns of Cys, Gly, and His residues. These are not included in the model but score between trusted and noise cutoffs. 43 matched cddid_all.tbl CDD TIGR01624 TIGR01624 273722 LRP1_Cterm LRP1 C-terminal domain. This model represents a tightly conserved small domain found in LRP1 and related plant proteins. This family also contains a well-conserved putative zinc finger domain (TIGR01623). The rest of the sequence of most members consists of highly divergent, low-complexity sequence. 50 matched cddid_all.tbl CDD TIGR01625 TIGR01625 130686 YidE_YbjL_dupl AspT/YidE/YbjL antiporter duplication domain. This model represents a domain that is duplicated the aspartate-alanine antiporter AspT, as well as HI0035 of Haemophilus influenzae, YidE and YbjL of E. coli, and a number of other known or putative transporters. Member proteins may have 0, 1, or 2 copies of TrkA potassium uptake domain pfam02080 between the duplications. The domain contains several apparent transmembrane regions and is proposed here to act in transport. [Transport and binding proteins, Unknown substrate] 154 matched cddid_all.tbl CDD TIGR01626 TIGR01626 130687 ytfJ_HI0045 conserved hypothetical protein YtfJ-family, TIGR01626. This model represents sequences from gamma proteobacteria that are related to the E. coli protein, YtfJ. 184 matched cddid_all.tbl CDD TIGR01627 TIGR01627 130688 A_thal_3515 uncharacterized plant-specific domain TIGR01627. This model represents an uncharacterized domain found in both Arabidopsis thaliana (at least 10 copies) and Oryza sativa. Most member proteins have only a short stretch of sequence N-terminal to this domain, but one has a long N-terminal extension that includes a protein kinase domain (pfam00069). 225 matched cddid_all.tbl CDD TIGR01628 TIGR01628 130689 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family. These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range. 562 matched cddid_all.tbl CDD TIGR01629 TIGR01629 273723 rep_II_X phage/plasmid replication protein, gene II/X family. This model represents a family of phage and plasmid replication proteins. In bacteriophage IKe and related phage, the full-length protein is designated gene II protein. A much shorter protein of unknown function, translated from a conserved in-frame alternative initiator, is designated gene X protein. Members of this family also include plasmid replication proteins. This model is built as a fragment model to better detect translations from alternate intiators and other fragments relative to full length gene II protein. [Mobile and extrachromosomal element functions, Prophage functions, Mobile and extrachromosomal element functions, Plasmid functions] 345 matched cddid_all.tbl CDD TIGR01630 TIGR01630 130691 psiM2_ORF9 phage uncharacterized protein (putative large terminase), C-terminal domain. This model represents the C-terminal region of a set of phage proteins typically about 400-500 amino acids in length, although some members are considerably shorter. An article on Methanobacterium phage Psi-M2 ( calls the member from that phage, ORF9, a putative large terminase subunit, and ORF8 a candidate terminase small subunit. Most proteins in this family have an apparent P-loop nucleotide-binding sequence toward the N-terminus. [Mobile and extrachromosomal element functions, Prophage functions] 142 matched cddid_all.tbl CDD TIGR01631 TIGR01631 273724 Trypano_RHS trypanosome RHS (retrotransposon hot spot) family. This model describes full-length and part-length members of the RHS (retrotransposon hot spot) family in Trypanosoma brucei and Trypanosoma cruzi. Members of this family are frequently interrupted by non-LTR retrotransposons inserted at exactly the same relative position. 760 matched cddid_all.tbl CDD TIGR01632 TIGR01632 233500 L11_bact 50S ribosomal protein uL11, bacterial form. This model represents bacterial, chloroplast, and most mitochondrial forms of 50S ribosomal protein L11. [Protein synthesis, Ribosomal proteins: synthesis and modification] 140 matched cddid_all.tbl CDD TIGR01633 TIGR01633 188159 phi3626_gp14_N putative phage tail component, N-terminal domain. This model represents the best-conserved region of about 125 amino acids, toward the N-terminus, of a family of proteins from temperate phage of a number of Gram-positive bacteria. These phage proteins range in length from 230 to 525 amino acids. [Mobile and extrachromosomal element functions, Prophage functions] 124 matched cddid_all.tbl CDD TIGR01634 TIGR01634 130695 tail_P2_I phage tail protein, P2 protein I family. This model represents the family of phage P2 protein I and related tail proteins from a number of temperate phage of Gram-negative bacteria. This model is built as a fragment model and identifies some phage tail proteins with strong but local similarity to members of the seed alignment. [Mobile and extrachromosomal element functions, Prophage functions] 139 matched cddid_all.tbl CDD TIGR01635 TIGR01635 130696 tail_comp_S phage virion morphogenesis (putative tail completion) protein. This model describes protein S of phage P2, suggested experimentally to act in tail completion and stable head joining, and related proteins from a number of phage. [Mobile and extrachromosomal element functions, Prophage functions] 144 matched cddid_all.tbl CDD TIGR01636 TIGR01636 130697 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors. [Mobile and extrachromosomal element functions, Prophage functions, Regulatory functions, DNA interactions] 134 matched cddid_all.tbl CDD TIGR01637 TIGR01637 273725 phage_arpU phage transcriptional regulator, ArpU family. This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family. [Mobile and extrachromosomal element functions, Prophage functions, Regulatory functions, DNA interactions] 132 matched cddid_all.tbl CDD TIGR01638 TIGR01638 130699 Atha_cystat_rel Arabidopsis thaliana cystatin-related protein. This model represents a family similar in sequence and probably homologous to a large family of cysteine proteinase inhibitors, or cystatins, as described by pfam00031. Cystatins may help plants resist attack by insects. 92 matched cddid_all.tbl CDD TIGR01639 TIGR01639 130700 P_fal_TIGR01639 Plasmodium falciparum uncharacterized domain TIGR01639. This model represents a conserved sequence region of about 60 amino acids found in over 40 predicted proteins of Plasmodium falciparum. It is not found elsewhere, including closely related species such as Plasmodium yoelii. No member of this family is characterized. 61 matched cddid_all.tbl CDD TIGR01640 TIGR01640 273726 F_box_assoc_1 F-box protein interaction domain. This model describes a large family of plant domains, with several hundred members in Arabidopsis thaliana. Most examples are found C-terminal to an F-box (pfam00646), a 60 amino acid motif involved in ubiquitination of target proteins to mark them for degradation. Two-hybid experiments support the idea that most members are interchangeable F-box subunits of SCF E3 complexes. Some members have two copies of this domain. 230 matched cddid_all.tbl CDD TIGR01641 TIGR01641 213641 phageSPP1_gp7 phage putative head morphogenesis protein, SPP1 gp7 family. This model describes a region of about 110 amino acids found exclusively in phage-related proteins, internally or toward the C-terminus. One member, gp7 of phage SPP1, appears involved in head morphogenesis. [Mobile and extrachromosomal element functions, Prophage functions] 108 matched cddid_all.tbl CDD TIGR01642 TIGR01642 273727 U2AF_lg U2 snRNP auxilliary factor, large subunit, splicing factor. These splicing factors consist of an N-terminal arginine-rich low complexity domain followed by three tandem RNA recognition motifs (pfam00076). The well-characterized members of this family are auxilliary components of the U2 small nuclear ribonuclearprotein splicing factor (U2AF). These proteins are closely related to the CC1-like subfamily of splicing factors (TIGR01622). Members of this subfamily are found in plants, metazoa and fungi. 509 matched cddid_all.tbl CDD TIGR01643 TIGR01643 273728 YD_repeat_2x YD repeat (two copies). This model describes two tandem copies of a 21-residue extracellular repeat found in Gram-negative, Gram-positive, and animal proteins. The repeat is named for a YD dipeptide, the most strongly conserved motif of the repeat. These repeats appear in general to be involved in binding carbohydrate; the chicken teneurin-1 YD-repeat region has been shown to bind heparin. 42 matched cddid_all.tbl CDD TIGR01644 TIGR01644 273729 phage_P2_V phage baseplate assembly protein V. This model describes a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain. [Mobile and extrachromosomal element functions, Prophage functions] 190 matched cddid_all.tbl CDD TIGR01645 TIGR01645 130706 half-pint poly-U binding splicing factor, half-pint family. The proteins represented by this model contain three RNA recognition motifs (rrm: pfam00076) and have been characterized as poly-pyrimidine tract binding proteins associated with RNA splicing factors. In the case of PUF60 (GP|6176532), in complex with p54, and in the presence of U2AF, facilitates association of U2 snRNP with pre-mRNA. 612 matched cddid_all.tbl CDD TIGR01646 TIGR01646 273730 vgr_GE Rhs element Vgr protein. This model represents the Vgr family of proteins, associated with some classes of Rhs elements. This model does not include a large octapeptide repeat region, VGXXXXXX, found in the Vgr of Rhs classes G and E. 483 matched cddid_all.tbl CDD TIGR01647 TIGR01647 273731 ATPase-IIIA_H plasma-membrane proton-efflux P-type ATPase. This model describes the plasma membrane proton efflux P-type ATPase found in plants, fungi, protozoa, slime molds and archaea. The best studied representative is from yeast. 754 matched cddid_all.tbl CDD TIGR01648 TIGR01648 273732 hnRNP-R-Q heterogeneous nuclear ribonucleoprotein R, Q family. Sequences in this subfamily include the human heterogeneous nuclear ribonucleoproteins (hnRNP) R, Q, and APOBEC-1 complementation factor (aka APOBEC-1 stimulating protein). These proteins contain three RNA recognition domains (rrm: pfam00076) and a somewhat variable C-terminal domain. 578 matched cddid_all.tbl CDD TIGR01649 TIGR01649 273733 hnRNP-L_PTB hnRNP-L/PTB/hephaestus splicing factor family. Included in this family of heterogeneous ribonucleoproteins are PTB (polypyrimidine tract binding protein) and hnRNP-L. These proteins contain four RNA recognition motifs (rrm: pfam00067). 481 matched cddid_all.tbl CDD TIGR01650 TIGR01650 130711 PD_CobS cobaltochelatase, CobS subunit. This model describes Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in Pseudomonas denitrificans) and an anaerobic pathway (found in P. shermanii and Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation. There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction. Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobS in the aerobic pathway (P. denitrificans) is not a homolog of cobS in the anaerobic pathway (S. typhimurium). It should be noted that E. coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their Salmonella typhimurium homologs which function in the anaerobic cobalamin synthesis pathway. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobS gene product, which is a cobalt chelatase subunit, with a MW ~37 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobT (TIGR01651) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobS gene product, the P. denitrificans gene symbol is not used in the name of this model. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 327 matched cddid_all.tbl CDD TIGR01651 TIGR01651 130712 CobT cobaltochelatase, CobT subunit. This model describes Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit that functions in cobalamin biosynthesis. Cobalamin (vitamin B12) can be synthesized via several pathways, including an aerobic pathway (found in Pseudomonas denitrificans) and an anaerobic pathway (found in P. shermanii and Salmonella typhimurium). These pathways differ in the point of cobalt insertion during corrin ring formation. There are apparently a number of variations on these two pathways, where the major differences seem to be concerned with the process of ring contraction. Confusion regarding the functions of enzymes found in the aerobic vs. anaerobic pathways has arisen because nonhomologous genes in these different pathways were given the same gene symbols. Thus, cobT in the aerobic pathway (P. denitrificans) is not a homolog of cobT in the anaerobic pathway (S. typhimurium). It should be noted that E. coli synthesizes cobalamin only when it is supplied with the precursor cobinamide, which is a complex intermediate. Additionally, all E. coli cobalamin synthesis genes (cobU, cobS and cobT) were named after their Salmonella typhimurium homologs which function in the anaerobic cobalamin synthesis pathway. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 600 matched cddid_all.tbl CDD TIGR01652 TIGR01652 273734 ATPase-Plipid phospholipid-translocating P-type ATPase, flippase. This model describes the P-type ATPase responsible for transporting phospholipids from one leaflet of bilayer membranes to the other. These ATPases are found only in eukaryotes. 1057 matched cddid_all.tbl CDD TIGR01653 TIGR01653 273735 lactococcin_972 bacteriocin, lactococcin 972 family. This model represents bacteriocins related to lactococcin 972. Members tend to be found in association with a seven transmembrane putative immunity protein. [Cellular processes, Toxin production and resistance] 92 matched cddid_all.tbl CDD TIGR01654 TIGR01654 273736 bact_immun_7tm bacteriocin-associated integral membrane (putative immunity) protein. This model represents a family of integral membrane proteins, most of which are about 650 residues in size and predicted to span the membrane seven times. Nearly half of the members of this family are found in association with a member of the lactococcin 972 family of bacteriocins (TIGR01653). Others may be associated with uncharacterized proteins that may also act as bacteriocins. Although this protein is suggested to be an immunity protein, and the bacteriocin is suggested to be exported by a Sec-dependent process, the role of this protein is unclear. [Cellular processes, Toxin production and resistance] 679 matched cddid_all.tbl CDD TIGR01655 TIGR01655 130716 yxeA_fam conserved hypothetical protein TIGR01655. This model represents a family of small (about 115 amino acids) uncharacterized proteins with N-terminal signal sequences, found exclusively in Gram-positive organisms. Most genomes that have any members of this family have at least two members. [Hypothetical proteins, Conserved] 114 matched cddid_all.tbl CDD TIGR01656 TIGR01656 273737 Histidinol-ppas "histidinol-phosphate phosphatase family domain. This domain is found in authentic histidinol-phosphate phosphatases which are sometimes found as stand-alone entities and sometimes as fusions with imidazoleglycerol-phosphate dehydratase (TIGR01261). Additionally, a family of proteins including YaeD from E. coli (TIGR00213) and various other proteins are closely related but may not have the same substrate specificity. This domain is a member of the haloacid-dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. This superfamily is distinguished by the presence of three motifs: an N-terminal motif containing the nucleophilic aspartate, a central motif containing an conserved serine or threonine, and a C-terminal motif containing a conserved lysine (or arginine) and conserved aspartates. More specifically, the domian modelled here is a member of subfamily III of the HAD-superfamily by virtue of lacking a ""capping"" domain in either of the two common positions, between motifs 1 and 2, or between motifs 2 and 3." 147 matched cddid_all.tbl CDD TIGR01657 TIGR01657 273738 P-ATPase-V P-type ATPase of unknown pump specificity (type V). These P-type ATPases form a distinct clade but the substrate of their pumping activity has yet to be determined. This clade has been designated type V in. 1054 matched cddid_all.tbl CDD TIGR01658 TIGR01658 273739 EYA-cons_domain eyes absent protein conserved domain. This domain is common to all eyes absent (EYA) homologs. Metazoan EYA's also contain a variable N-terminal domain consisting largely of low-complexity sequences. 274 matched cddid_all.tbl CDD TIGR01659 TIGR01659 273740 sex-lethal sex-lethal family splicing factor. This model describes the sex-lethal family of splicing factors found in Dipteran insects. The sex-lethal phenotype, however, may be limited to the Melanogasters and closely related species. In Drosophila the protein acts as an inhibitor of splicing. This subfamily is most closely related to the ELAV/HUD subfamily of splicing factors (TIGR01661). 346 matched cddid_all.tbl CDD TIGR01660 TIGR01660 211677 narH nitrate reductase, beta subunit. The Nitrate reductase enzyme complex allows bacteria to use nitrate as an electron acceptor during anaerobic growth. The enzyme complex consists of a tetramer that has an alpha, beta and 2 gamma subunits. The alpha and beta subunits have catalytic activity and the gamma subunits attach the enzyme to the membrane and is a b-type cytochrome that receives electrons from the quinone pool and transfers them to the beta subunit. This model is specific for the beta subunit for nitrate reductase I (narH) and nitrate reductase II (narY) for gram positive and gram negative bacteria.A few thermophiles and archaea also match the model.The seed members used in this model are all experimentally characterized and include the following:SP:P11349, and SP:P19318, both E.Coli (NarH and NarY respectively), SP:P42176 from B. Subtilis, GP:11344602 from Psuedomonas fluorescens,GP:541762 from Paracoccus denitrificans, and GP:18413622 from Halomonas halodenitrificans. This model also matches Pfam pfam00037 for 4Fe-4S binding domain. [Energy metabolism, Anaerobic] 492 matched cddid_all.tbl CDD TIGR01661 TIGR01661 273741 ELAV_HUD_SF ELAV/HuD family splicing factor. This model describes the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human. ELAV stnds for the Drosophila Embryonic lethal abnormal visual protein. ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (TIGR01659). These proteins contain 3 RNA-recognition motifs (rrm: pfam00076). 352 matched cddid_all.tbl CDD TIGR01662 TIGR01662 273742 HAD-SF-IIIA HAD-superfamily hydrolase, subfamily IIIA. This subfamily falls within the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The Class III subfamilies are characterized by the lack of any domains located between either between the first and second conserved catalytic motifs (as in the Class I subfamilies, TIGR01493, TIGR01509, TIGR01488 and TIGR01494) or between the second and third conserved catalytic motifs (as in the Class II subfamilies, TIGR01460 and TIGR01484) of the superfamily domain. The IIIA subfamily contains five major clades: histidinol-phosphatase (TIGR01261) and histidinol-phosphatase-related protein (TIGR00213) which together form a subfamily (TIGR01656), DNA 3'-phosphatase (TIGR01663, TIGR01664), YqeG (TIGR01668) and YrbI (TIGR01670). In the case of histidinol phosphatase and PNK-3'-phosphatase, this model represents a domain of a bifunctional system. In the histidinol phosphatase HisB, a C-terminal domain is an imidazoleglycerol-phosphate dehydratase which catalyzes a related step in histidine biosynthesis. In PNK-3'-phosphatase, N- and C-terminal domains constitute the polynucleotide kinase and DNA-binding components of the enzyme. [Unknown function, Enzymes of unknown specificity] 135 matched cddid_all.tbl CDD TIGR01663 TIGR01663 130724 PNK-3'Pase polynucleotide 5'-kinase 3'-phosphatase. This model represents the metazoan 5'-polynucleotide-kinase-3'-phosphatase, PNKP, which is believed to be involved in repair of oxidative DNA damage. Removal of 3' phosphates is essential for the further processing of the break by DNA polymerases. The central phosphatase domain is a member of the IIIA subfamily (TIGR01662) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is replaced by a conserved arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Very close relatives of this domain are also found separate from the N- and C-terminal domains seen here, as in the 3'-phosphatase found in plants. The larger family of these domains is described by TIGR01664. Outside of the phosphatase domain is a P-loop ATP-binding motif associated with the kinase activity. The entry for the mouse homolog appears to be missing a large piece of sequence corresponding to the first conserved catalytic motif of the phosphatase domain as well as the conserved threonine of the second motif. Either this is a sequencing artifact or this may represent a pseudo- or non-functional gene. Note that the EC number for the kinase function is: 2.7.1.78 526 matched cddid_all.tbl CDD TIGR01664 TIGR01664 211680 DNA-3'-Pase DNA 3'-phosphatase. This model represents a family of proteins and protein domains which catalyze the dephosphorylation of DNA 3'-phosphates. It is believed that this activity is important for the repair of single-strand breaks in DNA caused by radiation or oxidative damage. This domain is often (TIGR01663), but not always linked to a DNA 5'-kinase domain. The central phosphatase domain is a member of the IIIA subfamily (TIGR01662) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. As is common in this superfamily, the enzyme is magnesium dependent. A difference between this enzyme and other HAD-superfamily phosphatases is in the third conserved catalytic motif which usually contains two conserved aspartate residues believed to be involved in binding the magnesium ion. Here, the second aspartate is usually replaced by an arginine residue which may indicate an interaction with the phosphate backbone of the substrate. Alternatively, there is an additional conserved aspartate downstream of the ususal site which may indicate slightly different fold in this region. 166 matched cddid_all.tbl CDD TIGR01665 TIGR01665 273743 put_anti_recept phage minor structural protein, N-terminal region. This model represents the conserved N-terminal region, typically from about residue 25 to about residue 350, of a family of uncharacterized phage proteins 500 to 1700 residues in length. [Mobile and extrachromosomal element functions, Prophage functions] 317 matched cddid_all.tbl CDD TIGR01666 TIGR01666 130727 YCCS TIGR01666 family membrane protein. This model represents a clade of sequences from gamma and beta proteobacteria. These proteins are >700 amino acids long and many have been annotated as putative membrane proteins. The gene from Salmonella has been annotated as a putative efflux transporter. The gene from E. coli has the name yccS. [Cell envelope, Other] 704 matched cddid_all.tbl CDD TIGR01667 TIGR01667 130728 YCCS_YHJK integral membrane protein, YccS/YhfK family. This model represents two clades of putative transmembrane proteins including the E. coli YccS and YhfK proteins. The YccS hypothetical equivalog (TIGR01666) is found in beta and gamma proteobacteria, while the smaller YhfK group is only found in E. coli, Salmonella and Yersinia. TMHMM on the 19 hits to this model shows a consensus of 11 transmembrane helices separated into two clusters, an N-terminal cluster of 6 and a central cluster of 5. This would indicate two non-membrane domains one on each side of the membrane 701 matched cddid_all.tbl CDD TIGR01668 TIGR01668 273744 YqeG_hyp_ppase HAD superfamily (subfamily IIIA) phosphatase, TIGR01668. This family of hypothetical proteins is a member of the IIIA subfamily of the haloacid dehalogenase (HAD) superfamily of hydrolases. All characterized members of this subfamily (TIGR01662) and most characterized members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs, all of which are found conserved here. This family consists of sequences from fungi, plants, cyanobacteria, gram-positive bacteria and Deinococcus. There is presently no characterization of any sequence in this family. 170 matched cddid_all.tbl CDD TIGR01669 TIGR01669 273745 phage_XkdX phage uncharacterized protein, XkdX family. This model represents a family of small (about 50 amino acid) phage proteins, found in at least 12 different phage and prophage regions of Gram-positive bacteria. In a number of these phage, the gene for this protein is found near the holin and endolysin genes. [Mobile and extrachromosomal element functions, Prophage functions] 45 matched cddid_all.tbl CDD TIGR01670 TIGR01670 130731 KdsC-phosphatas 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase, YrbI family. This family of proteins is a member of the IIIA subfamily of the haloacid dehalogenase (HAD) superfamily of hydrolases. All characterized members of this subfamily (TIGR01662) and most characterized members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs, all of which are found conserved here. One member of this family, the YrbI protein from H. influenzae has been cloned, expressed, purified and found to be an active 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase. Furthermore, its crystal structure has been determined. This family consists of sequences from beta, gamma and epsilon proteobacteria, Aquifex, Fusobacterium, Porphyromonas and Methanosarcina. The Methanosarcina sequence is distinctive in that it is linked to an N-terminal cytidylyltransferase domain (pfam02348) and is annotated as acylneuraminate cytidylyltransferase. This may give some clue as the function of these phosphatases. Several eukaryotic sequences scoring between trusted and noise are also closely related to this function such as the CMP-N-acetylneuraminic acid synthetase from mouse, but in these cases the phosphatase domain is clearly inactive as many of the active site residues are not conserved. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 154 matched cddid_all.tbl CDD TIGR01671 TIGR01671 273746 phage_TIGR01671 phage uncharacterized protein TIGR01671. This model represents an uncharacterized, well-conserved family of proteins found in bacteriophage and prophage regions of Gram-positive bacteria. [Mobile and extrachromosomal element functions, Prophage functions, Hypothetical proteins, Conserved] 151 matched cddid_all.tbl CDD TIGR01672 TIGR01672 273747 AphA "HAD superfamily (subfamily IIIB) phosphatase, TIGR01672. This family of proteins is a member of the IIIB subfamily (pfam02767) of the haloacid dehalogenase (HAD) superfamily of hydrolases. All characterized members of subfamily III and most characterized members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs, all of which are found conserved here. The AphA gene from E. coli has been characterized and shown to be an active phosphatase enzyme. This family has been previously described as the ""class B non-specific bacterial acid phosphatase"" (B-NSAP) family, where it is noted that the enzyme is secreted and has a broad substrate range. The possibility exists, however, that the enzyme is specific for an as yet undefined substrate. Supporting evidence for the inclusion in the HAD superfamily, whose phosphatase members are magnesium dependent, is the inhibition by EDTA and calcium ions, and stimulation by magnesium ion." 237 matched cddid_all.tbl CDD TIGR01673 TIGR01673 130734 holin_LLH phage holin, LL-H family. This model represents a putative phage holin from a number of phage and prophage regions of Gram-positive bacteria. Like other holins, it is small (about 100 amino acids) with stretches of hydrophobic sequence and is encoded adjacent to lytic enzymes. [Mobile and extrachromosomal element functions, Prophage functions] 108 matched cddid_all.tbl CDD TIGR01674 TIGR01674 273748 phage_lambda_G phage minor tail protein G. This model describes a family of bacteriophage proteins including G of phage lambda. This protein has been described as undergoing a translational frameshift at a Gly-Lys dipeptide near the C-terminus of protein G from phage lambda, with about 4 % efficiency, to produce tail assembly protein G-T. The Lys of the Gly-Lys pair is the conserved second-to-last residue of seed alignment for this family. [Mobile and extrachromosomal element functions, Prophage functions] 138 matched cddid_all.tbl CDD TIGR01675 TIGR01675 273749 plant-AP plant acid phosphatase. This model represents a family of acid phosphatase from plants which are most closely related to the (so called) class B non-specific acid phosphatase OlpA (TIGR01533, which is believed to be a 5'-nucleotide phosphatase) and somewhat more distantly to another class B phosphatase, AphA (TIGR01672). Together these three clades define a subfamily (pfam03767) which corresponds to the IIIB subfamily of the haloacid dehalogenase (HAD) superfamily of aspartate nucleophile hydrolases. It has been reported that the best substrate for this enzyme that could be found was purine 5'-nucleoside phosphates. This is in concordance with the assignment of the H. influenzae hel protein (from TIGR01533) as a 5'-nucleotidase, however there is presently no other evidence to support this specific function for these plant phosphatases. Many genes from this family have been annotated as vegetative storage proteins due to their close homology with these earlier-characterized gene products, which are highly expressed in leaves. There are significant differences however, including expression levels and distribution. The most important difference is the lack in authentic VSPs of the nucleophilic aspartate residue, which is instead replaced by serine, glycine or asparagine. Thus these proteins can not be expected to be active phosphatases. This issue was confused by the publication in 1992 of an article claiming activity for the Glycine max VSP. In 1994 this assertion was refuted by the separation of the activity from the VSP. This model explicitly excludes the VSPs which lack the nucleophilc aspartate. The possibility exists, however, that some members of this family may, while containing all of the conserved HAD-superfamily catalytic residues, lack activity and have a function related to the function of the VSPs rather than the acid phosphatases. 228 matched cddid_all.tbl CDD TIGR01676 TIGR01676 130737 GLDHase galactonolactone dehydrogenase. This model represents L-Galactono-gamma-lactone dehydrogenase (EC 1.3.2.3). This enzyme catalyzes the final step in ascorbic acid biosynthesis in higher plants. This protein is homologous to ascorbic acid biosynthesis enzymes of other species: L-gulono-gamma-lactone oxidase in rat and L-galactono-gamma-lactone oxidase in yeast. All three covalently bind the cofactor FAD. 541 matched cddid_all.tbl CDD TIGR01677 TIGR01677 273750 pln_FAD_oxido plant-specific FAD-dependent oxidoreductase. This model represents an uncharacterized plant-specific family of FAD-dependent oxidoreductases. At least seven distinct members are found in Arabidopsis thaliana. The family shows considerable sequence similarity to three different enzymes of ascorbic acid biosynthesis: L-galactono-1,4-lactone dehydrogenase (EC 1.3.2.3) from higher plants, D-arabinono-1,4-lactone oxidase (EC 1.1.3.37 from Saccharomyces cerevisiae, and L-gulonolactone oxidase (EC 1.1.3.8) from mouse, as well as to a bacterial sorbitol oxidase. The class of compound acted on by members of this family is unknown. 557 matched cddid_all.tbl CDD TIGR01678 TIGR01678 273751 FAD_lactone_ox sugar 1,4-lactone oxidases. This model represents a family of at least two different sugar 1,4 lactone oxidases, both involved in synthesizing ascorbic acid or a derivative. These include L-gulonolactone oxidase (EC 1.1.3.8) from rat and D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) from Saccharomyces cerevisiae. Members are proposed to have the cofactor FAD covalently bound at a site specified by Prosite motif PS00862; OX2_COVAL_FAD; 1. 438 matched cddid_all.tbl CDD TIGR01679 TIGR01679 130740 bact_FAD_ox FAD-linked oxidoreductase. This model represents a family of bacterial oxidoreductases with covalently linked FAD, closely related to two different eukaryotic oxidases, L-gulonolactone oxidase (EC 1.1.3.8) from rat and D-arabinono-1,4-lactone oxidase (EC 1.1.3.37) from Saccharomyces cerevisiae. 419 matched cddid_all.tbl CDD TIGR01680 TIGR01680 130741 Veg_Stor_Prot vegetative storage protein. The proteins represented by this model are close relatives of the plant acid phosphatases (TIGR01675), are limited to members of the Phaseoleae including Glycine max (soybean) and Phaseolus vulgaris (kidney bean). These proteins are highly expressed in the leaves of repeatedly depodded plants. VSP differs most strinkingly from the acid phosphatases in the lack of the conserved nucleophilic aspartate residue in the N-terminus, thus, they should be inactive as phosphatases. This issue was confused by the publication in 1992 of an article claiming activity for the Glycine max VSP. In 1994 this assertion was refuted by the separation of the activity from the VSP. 275 matched cddid_all.tbl CDD TIGR01681 TIGR01681 273752 HAD-SF-IIIC HAD-superfamily phosphatase, subfamily IIIC. This model represents the IIIC subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate nucleophile hydrolases. Subfamily III (also including IIIA - TIGR01662 and IIIB - pfam03767) contains sequences which do not contain either of the insert domains (between the 1st and 2nd conserved catalytic motifs, subfamily I - TIGR01493, TIGR01509, TIGR01549, TIGR01488, TIGR01494, TIGR01658, TIGR01544 and TIGR01545, or between the 2nd and 3rd, subfamily II - TIGR01460 and TIGR01484). Subfamily IIIC contains five relatively distantly related clades: a family of viral proteins (TIGR01684), a family of eukaryotic proteins called MDP-1 and a family of archaeal proteins most closely related to MDP-1 (TIGR01685), a family of bacteria including the Streptomyces FkbH protein (TIGR01686), and a small clade including the Pasteurella BcbF and EcbF proteins. The overall lack of species overlap among these clades may indicate a conserved function, but the degree of divergence between the clades and the differences in archetecture outside of the domain in some clades warns against such a conclusion. No member of this subfamily is characterized with respect to function, however the MDP-1 protein is a characterized phosphatase. All of the characterized enzymes within subfamily III are phosphatases, and all of the active site residues characteristic of HAD-superfamily phosphatases are present in subfamily IIIC. 128 matched cddid_all.tbl CDD TIGR01682 TIGR01682 273753 moaD molybdopterin converting factor, subunit 1, non-archaeal. This model describes MoaD. It excludes archaeal homologs, since many Archaea have two MoaD-like proteins, suggesting two different functions. pfam02597 describes both the thiamine biosynthesis protein ThiS and this protein, MoaD, a subunit (together with MoaE, pfam02391) of the molybdopterin converting factor. Both ThiS and MoaD are involved in sulfur transfer reactions. Distribution of this family appears limited to species that also have a member of pfam02391, but a number of Archaea have two different members, suggesting functionally distinct subtypes. The C-terminal Gly-Gly of this model is critical to function. [Biosynthesis of cofactors, prosthetic groups, and carriers, Molybdopterin] 80 matched cddid_all.tbl CDD TIGR01683 TIGR01683 273754 thiS thiamine biosynthesis protein ThiS. This model represents ThiS, a small, ubiquitin-like thiamine biosynthesis protein related to MoaD, a molybdenum cofactor biosynthesis protein. Both proteins are involved in sulfur transfer. ThiS has a conserved Gly-Gly C-terminus that is modified, in reactions requiring ThiI, ThiF, IscS, and a sulfur atom from Cys, into the thiocarboxylate that provides the sulfur for thiazole biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine] 64 matched cddid_all.tbl CDD TIGR01684 TIGR01684 273755 viral_ppase viral phosphatase. This model represents a family of viral proteins of unknown function. These proteins are members, however, of the IIIC (TIGR01681) subfamily of the haloacid dehalogenase (HAD) superfamily of aspartate nucleophile hydrolases. All characterized members of the III subfamilies (IIIA, TIGR01662; IIIB, pfam03767) are phosphatases, including MDP-1, a member of subfamily IIIC (TIGR01681). No member of this subfamily is characterized with respect to particular function. All of the active site residues characteristic of HAD-superfamily phosphatases are present in subfamily IIIC. These proteins also include an N-terminal domain (ca. 125 aas) that is unique to this clade. 301 matched cddid_all.tbl CDD TIGR01685 TIGR01685 273756 MDP-1 magnesium-dependent phosphatase-1. This model represents two closely related clades of sequences from eukaryotes and archaea. The mouse enzyme has been characterized as a phosphatase and has been positively identified as a member of the haloacid dehalogenase (HAD) superfamily by site-directed mutagenesis of the active site residues. 174 matched cddid_all.tbl CDD TIGR01686 TIGR01686 273757 FkbH "FkbH-like domain. This model describes a domain of a family of proteins of unknown overall function. One of these, however, is a modular polyketide synthase 4800 amino acids in length from Streptomyces avermilitis in which this domain is the C-terminal segment. By contrast, the FkbH protein from Streptomyces hygroscopicus aparently contains only this domain. The remaining members of the family all contain an additional N-terminal domain of between 200 and 275 amino acids which show less than 20% identity to one another. It seems likely then that these proteins are involved in disparate functions, probably the biosynthesis of different natural products. For instance, the FkbH gene is found in a gene cluster believed to be responsible for the biosynthesis of unususal ""PKS extender units"" in the ascomycin pathway. This domain is composed of two parts, the first of which is a member of subfamily IIIC (TIGR01681) of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. All of the characterized enzymes within subfamily III are phosphatases, and all of the active site residues characteristic of HAD-superfamily phosphatases are present in this domain. The C-terminal portion of this domain is unique to this family (by BLAST)." 320 matched cddid_all.tbl CDD TIGR01687 TIGR01687 273758 moaD_arch MoaD family protein, archaeal. Members of this family appear to be archaeal versions of MoaD, subunit 1 of molybdopterin converting factor. This model has been split from the bacterial/eukaryotic equivalog model TIGR01682 because the presence of two members of this family in a substantial number of archaeal species suggests that roles might not be interchangeable. [Biosynthesis of cofactors, prosthetic groups, and carriers, Molybdopterin] 88 matched cddid_all.tbl CDD TIGR01688 TIGR01688 130749 dltC D-alanine--poly(phosphoribitol) ligase, subunit 2. This protein is part of the teichoic acid operon in gram-positive organisms. Gram positive organisms incorporate teichoic acid in their cell walls, and in the fatty acid residues of the glycolipid component of the outer layer of the cytoplasmic membrane. This gene, dltC, encodes the alanyl carrier protein. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 73 matched cddid_all.tbl CDD TIGR01689 TIGR01689 273759 EcbF-BcbF capsule biosynthesis phosphatase. This model describes a small family of highly conserved proteins (>60% ID). Two of these, BcbF and EcbF of Pasteurella multocida are believed to be part of the capsule polysaccharide biosynthesis machinery because they are cotranscribed from a locus devoted to that purpose. In pasteurella there are six different variant capsules (A-F), and these proteins are found only in B and E. The other two species in which this gene is (currently) found are both also pathogenic. These proteins are also members of the IIIC (TIGR01681) subfamily of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. All of the characterized enzymes within subfamily III are phosphatases, and all of the active site residues characteristic of HAD-superfamily phosphatases are present in this subfamily. Due to the likelihood that the substrates of these enzymes are different depending on the nature of the particular polysaccharides associated with each species, this model has been classified as a subfamily despite the close homology. 126 matched cddid_all.tbl CDD TIGR01690 TIGR01690 162489 ICE_RAQPRD integrative conjugative element protein, RAQPRD family. This model represents a small family of proteins about 100 amino acids in length, including a predicted signal sequence and a perfectly conserved motif RAQPRD towards the C-terminus. Members are found in the Pseudomonas putida TOL plasmid pWW0 and in cryptic plasmid regions of Salmonella enterica subsp. enterica serovar Typhi and Pseudomonas syringae DC3000. The function is unknown. [Mobile and extrachromosomal element functions, Plasmid functions] 94 matched cddid_all.tbl CDD TIGR01691 TIGR01691 273760 enolase-ppase 2,3-diketo-5-methylthio-1-phosphopentane phosphatase. This enzyme is the enolase-phosphatase of methionine salvage, a pathway that regenerates methionine from methylthioadenosine (MTA). Adenosylmethionine (AdoMet) is a donor of different moieties for various processes, including methylation reactions. Use of AdoMet for spermidine biosynthesis, which leads to polyamine biosynthesis, leaves MTA as a by-product that must be cleared. In Bacillus subtilis and related species, this single protein is replaced by separate enzymes with enolase and phosphatase activities. [Central intermediary metabolism, Sulfur metabolism] 220 matched cddid_all.tbl CDD TIGR01692 TIGR01692 130753 HIBADH 3-hydroxyisobutyrate dehydrogenase. 3-hydroxyisobutyrate dehydrogenase is an enzyme that catalyzes the NAD+-dependent oxidation of 3-hydroxyisobutyrate to methylmalonate semialdehyde of the valine catabolism pathway. In Pseudomonas aeruginosa, 3-hydroxyisobutyrate dehydrogenase (mmsB) is co-induced with methylmalonate-semialdehyde dehydrogenase (mmsA) when grown on medium containing valine as the sole carbon source. The positive transcriptional regulator of this operon (mmsR) is located upstream of these genes and has been identified as a member of the XylS/AraC family of transcriptional regulators. 3-hydroxyisobutyrate dehydrogenase shares high sequence homology to the characterized 3-hydroxyisobutyrate dehydrogenase from rat liver with conservation of proposed NAD+ binding residues at the N-terminus (G-8,10,13,24 and D-31). This enzyme belongs to the 3-hydroxyacid dehydrogenase family, sharing a common evolutionary origin and enzymatic mechanism with 6-phosphogluconate. HIBADH exhibits sequence similarity to the NAD binding domain of 6-phosphogluconate dehydrogenase above trusted (pfam03446). [Energy metabolism, Amino acids and amines] 288 matched cddid_all.tbl CDD TIGR01693 TIGR01693 273761 UTase_glnD [Protein-PII] uridylyltransferase. This model describes GlnD, the uridylyltransferase/uridylyl-removing enzyme for the nitrogen regulatory protein PII. Not all homologs of PII share the property of uridylyltransferase modification on the characteristic Tyr residue (see Prosite pattern PS00496 and document PDOC00439), but the modification site is preserved in the PII homolog of all species with a member of this family. [Central intermediary metabolism, Nitrogen metabolism, Regulatory functions, Protein interactions] 850 matched cddid_all.tbl CDD TIGR01694 TIGR01694 273762 MTAP 5'-deoxy-5'-methylthioadenosine phosphorylase. This model represents the methylthioadenosine phosphorylase found in metazoa, cyanobacteria and a limited number of archaea such as Sulfolobus, Aeropyrum, Pyrobaculum, Pyrococcus, and Thermoplasma. This enzyme is responsible for the first step in the methionine salvage pathway after the transfer of the amino acid moiety from S-adenosylmethionine. The enzyme from human is well-characterized including a crystal structure. A misleading characterization is found for a Sulfolobus solfataricus enzyme, which is called a MTAP. In fact, as uncovered by the genome sequence of S. solfataricus, there are at least two nucleotide phosphorylases and the one found in the MTAP clade is not the one annotated as such. The sequence in this clade has not been isolated but is likely to be the authentic SsMTAP as it displays all of the conserved active site residues found in the human enzyme. This explains the finding that the characterized enzyme has greater efficiency towards the purines inosine, guanosine and adenosine over MTA. In fact, this mis-naming of this enzyme has been carried forward to several publications including a crystal stucture. In between the trusted and noise cutoffs are: 1) several archaeal sequences which appear to contain several residues characteristic of phosphorylases which act on guanosine or inosine (according to the crystal structure of MTAP and alignments). In any case, these residues are not conserved. 2) sequences from Mycobacterium tuberculosis and Streptomyces coelicolor which have better, although not perfect retention of the active site residues, but considering the general observation that bacteria utilize the MTA/SAH nucleotidase enzyme and a kinase to do this reaction, these have been excluded pending stronger evidence of their function, and 3) a sequence from Drosophila which appears to be a recent divergence (long branch in neighbor-joining trees) and lacks some of the conserved active site residues. [Central intermediary metabolism, Other, Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides] 241 matched cddid_all.tbl CDD TIGR01695 TIGR01695 273763 murJ_mviN murein biosynthesis integral membrane protein MurJ. This model represents MurJ (previously MviN), a family of integral membrane proteins predicted to have ten or more transmembrane regions. Members have been suggested to act as a lipid II flippase, translocated a precursor of murein. However, it appears FtsW has that activity. Flippase activity for MurJ has not been shown. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 502 matched cddid_all.tbl CDD TIGR01696 TIGR01696 162494 deoB phosphopentomutase. This protein is involved in the purine and pyrimidine salvage pathway. It catalyzes the conversion of D-ribose 1-phosphate to D-ribose 5-phosphate and the conversion of 2-deoxy-D-ribose 1-phosphate to 2-deoxy-D-ribose 5-phosphate. The seed members of this protein are characterized deoB proteins from E.Coli(SP:P07651) and Bacillus (SP:P46353). This model matches pfam01676 for Metalloenzyme superfamily. [Purines, pyrimidines, nucleosides, and nucleotides, Other] 381 matched cddid_all.tbl CDD TIGR01697 TIGR01697 130758 PNPH-PUNA-XAPA inosine/guanosine/xanthosine phosphorylase family. This model is a subset of the subfamily represented by pfam00896 (phosphorylase family 2). This model excludes the methylthioadenosine phosphorylases (MTAP, TIGR01684) which are believed toplay a specific role in the recycling of methionine from methylthioadenosine. In this subfamily is found three clades of purine phosphorylases based on a neighbor-joining tree using the MTAP family as an outgroup. The highest-branching clade (TIGR01698) consists of a group of sequences from both gram positive and gram negative bacteria which have been annotated as purine nucleotide phosphorylases but have not been further characterized as to substrate specificity. Of the two remaining clades, one is xanthosine phosphorylase (XAPA, TIGR01699), is limited to certain gamma proteobacteria and constitutes a special purine phosphorylase found in a specialized operon for xanthosine catabolism. The enzyme also acts on the same purines (inosine and guanosine) as the other characterized members of this subfamily, but is only induced when xanthosine must be degraded. The remaining and largest clade consists of purine nucleotide phosphorylases (PNPH, TIGR01700) from metazoa and bacteria which act primarily on guanosine and inosine (and do not act on adenosine). Sequences from Clostridium (GP:15025051) and Thermotoga (OMNI:TM1596) fall between these last two clades and are uncharacterized with respect to substrate range and operon. 248 matched cddid_all.tbl CDD TIGR01698 TIGR01698 130759 PUNP purine nucleotide phosphorylase. This clade of purine nucleotide phosphorylases has not been experimentally characterized but is assigned based on strong sequence homology. Closely related clades act on inosine and guanosine (PNPH, TIGR01700), and xanthosine, inosine and guanosine (XAPA, TIGR01699) neither of these will act on adenosine. A more distantly related clade (MTAP, TIGR01694) acts on methylthioadenosine. 237 matched cddid_all.tbl CDD TIGR01699 TIGR01699 130760 XAPA xanthosine phosphorylase. This model represents a small clade of purine nucleotide phosphorylases found in certain gamma proteobacteria. The gene is part of an operon for the degradation of xanthosine and is induced by xanthosine. The enzyme is also capable of acting on inosine and guanosine (but not adenosine) in a manner similar to those other phosphorylases to which it is closely related (TIGR01698, TIGR01700). 248 matched cddid_all.tbl CDD TIGR01700 TIGR01700 273764 PNPH purine nucleoside phosphorylase I, inosine and guanosine-specific. This model represents a family of bacterial and metazoan purine phosphorylases acting primarily on inosine and guanosine and not acting on adenosine. PNP-I refers to the nomenclature from Bacillus stearothermophilus where PHP-II refers to the nucleotidase acting on adenosine as the primary substrate.The bacterial enzymes (PUNA) are typified by the Bacilus PupG protein, which is involved in the metabolism of nucleosides as a carbon source.Several metazoan enzymes (PNPH) are well characterized including the human and bovine enzymes which have been crystallized. [Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides] 249 matched cddid_all.tbl CDD TIGR01701 TIGR01701 273765 Fdhalpha-like oxidoreductase alpha (molybdopterin) subunit. This model represents a well-defined clade of oxidoreductase alpha subunits most closely related to a group of formate dehydrogenases including the E. coli FdhH protein (TIGR01591). These alpha subunits contain a molybdopterin cofactor and generally associate with two other subunits which contain iron-sulfur clusters and cytochromes. The particular subunits with which this enzyme interacts and the substrate which is reduced is unknown at this time. In Ralstonia, the gene is associated with the cbb operon, but is not essential for CO2 fixation. 743 matched cddid_all.tbl CDD TIGR01702 TIGR01702 130763 CO_DH_cata carbon-monoxide dehydrogenase, catalytic subunit. This model represents the carbon-monoxide dehydrogenase catalytic subunit. This protein is related to prismane (also called hybrid cluster protein), a complex whose activity is not yet fully described; the two share similar sets of ligands to unusual metal-containing clusters. 621 matched cddid_all.tbl CDD TIGR01703 TIGR01703 130764 hybrid_clust hydroxylamine reductase. This model represents a family of proteins containing an unusual 4Fe-2S-2O hydrid cluster. Earlier reports had proposed a 6Fe-6S prismane cluster. This subfamily is heterogeneous with respect to the presence or absence of a region of about 100 amino acids not far from the N-terminus of the protein. Members have been described as monomeric. The general function is unknown, although members from E. coli and several other species have hydroxylamine reductase activity. Members are found in various bacteria, in Archaea, and in several parasitic eukaryotes: Giardia intestinalis, Trichomonas vaginalis, and Entamoeba histolytica. [Cellular processes, Detoxification, Energy metabolism, Amino acids and amines] 522 matched cddid_all.tbl CDD TIGR01704 TIGR01704 130765 MTA/SAH-Nsdase 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase. This model represents the enzyme 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase which acts on its two substrates at the same active site. This enzyme is involved in the recycling of the components of S-adenosylmethionine after it has donated one of its two non-ribose sulfur ligands to an acceptor. In the case of 5-methylthioadenosine this represents the first step of the methionine salvage pathway in bacteria. This enzyme is widely distributed in bacteria, especially those that lack adenosylhomocysteinase (EC 3.3.1.1). One clade of bacteria including Agrobacterium, Mesorhizobium, Sinorhizobium and Brucella includes sequences annotated as MTA/SAH nucleotidase, but differs significantly in homology and has no independent experimental evidence. There are homologs of this enzyme in plants, some of which score between trusted and noise cutoffs here, but there is no experimental evidence to validate this function at this time. [Central intermediary metabolism, Other, Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides] 228 matched cddid_all.tbl CDD TIGR01705 TIGR01705 130766 MTA/SAH-nuc-hyp 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase, putative. This model represents the enzyme 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase which acts on its two substrates at the same active site. This clade of sequences is sufficiently distinct from the characterized proteins, which form the seed of TIGR01704 as to cast some doubt on the accuracy of annotations based on sequence similarity alone. This enzyme is involved in the recycling of the components of S-adenosylmethionine after it has donated one of its two non-ribose sulfur ligands to an acceptor. In the case of 5'-methylthioadenosine this represents the first step of the methionine salvage pathway in bacteria. This enzyme is widely distributed in bacteria. 212 matched cddid_all.tbl CDD TIGR01706 TIGR01706 273766 NAPA periplasmic nitrate reductase, large subunit. This model represents the large subunit of a family of nitrate reductases found in proteobacteria which are localized to the periplasm. This subunit binds molybdopterin and contains a twin-arginine motif at the N-terminus. The protein associates with NapB, a soluble heme-containing protein and NapC, a membrane-bound cytochrome c. The periplasmic nitrate reductases are not involved in the assimilation of nitrogen, and are not directly involved in the formation of electrochemical gradients (i.e. respiration) either. Rather, the purpose of this enzyme is either dissimilatory (i.e. to dispose of excess reductive equivalents) or indirectly respiratory by virtue of the consumption of electrons derived from NADH via the proton translocating NADH dehydrogenase. The enzymes from Alicagenes eutrophus and Paracoccus pantotrophus have been characterized. In E. coli (as well as other organisms) this gene is part of a large nitrate reduction operon (napFDAGHBC). [Energy metabolism, Aerobic, Energy metabolism, Electron transport, Central intermediary metabolism, Nitrogen metabolism] 830 matched cddid_all.tbl CDD TIGR01707 TIGR01707 273767 gspI type II secretion system protein I. This model represents GspI, one of two proteins highly conserved at their N-termini and described by pfam02501 but easily separable phylogenetically. The other is GspJ. Both GspI and GspJ are proteins of the type II secretion pathway, or main terminal branch of the general secretion pathway. This pathway carries proteins across the outer membrane. Note that proteins of type II secretion are cryptic in E. coli K-12 - present but not yet demonstrated to act on any target. 101 matched cddid_all.tbl CDD TIGR01708 TIGR01708 130769 typeII_sec_gspH type II secretion system protein H. This model represents GspH, protein H of the main terminal branch of the general secretion pathway, also called type II secretion. It transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 143 matched cddid_all.tbl CDD TIGR01709 TIGR01709 273768 typeII_sec_gspL type II secretion system protein L. This model represents GspL, protein L of the main terminal branch of the general secretion pathway, also called type II secretion. It transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens. [Protein fate, Protein and peptide secretion and trafficking] 384 matched cddid_all.tbl CDD TIGR01710 TIGR01710 130771 typeII_sec_gspG type II secretion system protein G. This model represents GspG, protein G of the main terminal branch of the general secretion pathway, also called type II secretion. It transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 134 matched cddid_all.tbl CDD TIGR01711 TIGR01711 130772 gspJ type II secretion system protein J. This model represents GspJ, one of two proteins highly conserved at their N-termini and described by pfam02501 but easily separable phylogenetically. The other is GspI. Both GspI and GspJ are proteins of the type II secretion pathway, or main terminal branch of the general secretion pathway. This pathway carries proteins across the outer membrane. Note that proteins of type II secretion are cryptic in E. coli K-12 - present but not yet demonstrated to act on any target. 192 matched cddid_all.tbl CDD TIGR01712 TIGR01712 273769 phage_N6A_met phage N-6-adenine-methyltransferase. This model is a fragment-mode model for a phage-borne DNA N-6-adenine-methyltransferase. [Mobile and extrachromosomal element functions, Prophage functions, DNA metabolism, Restriction/modification] 166 matched cddid_all.tbl CDD TIGR01713 TIGR01713 273770 typeII_sec_gspC type II secretion system protein C. This model represents GspC, protein C of the main terminal branch of the general secretion pathway, also called type II secretion. This system transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens. [Protein fate, Protein and peptide secretion and trafficking] 259 matched cddid_all.tbl CDD TIGR01714 TIGR01714 130775 phage_rep_org_N phage replisome organizer, putative, N-terminal region. This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region. [Mobile and extrachromosomal element functions, Prophage functions] 119 matched cddid_all.tbl CDD TIGR01715 TIGR01715 273771 phage_lam_T phage tail assembly protein T. This model represents a translation of the T gene in phage lambda and related phage. A translational frameshift from the upstream gene G into the frame of T produces a minor protein gpG-T, essential in tail assembly but not found in the mature virion. [Mobile and extrachromosomal element functions, Prophage functions] 95 matched cddid_all.tbl CDD TIGR01716 TIGR01716 273772 RGG_Cterm transcriptional activator, Rgg/GadR/MutR family, C-terminal domain. This model describes the whole, except for a 60 residue N-terminal helix-turn-helix DNA-binding domain (pfam01381) of the family of proteins related to the transcriptional regulator Rgg, also called RopB. Rgg is required for secretion of several proteins, including a cysteine proteinase associated with virulence. GadR is a positive regulator of a glutamate-dependent acid resistance mechanism. MutR is a transcriptional activator for mutacin biosynthesis genes in Streptococcus mutans. This family appears restricted to the low-GC Gram-positive bacteria, including at least eight members in Lactococcus lactis. [Regulatory functions, DNA interactions] 220 matched cddid_all.tbl CDD TIGR01717 TIGR01717 273773 AMP-nucleosdse AMP nucleosidase. This model represents the AMP nucleosidase from proteobacteria but also including a sequence from Corynebacterium, a gram-positive organism. The species from E. coli has been most well studied. 477 matched cddid_all.tbl CDD TIGR01718 TIGR01718 130779 Uridine-psphlse uridine phosphorylase. This model represents a family of bacterial and archaeal uridine phosphorylases unrelated to the mammalian enzymes of the same name. The E. coli, Salmonella and Klebsiella genes have been characterized. Sequences from Clostridium, Streptomyces, Treponema, Halobacterium and Pyrobaculum were included above trusted on the basis of sequence homology and a PAM-based neighbor-joining tree. A clade including second sequences from Halobacterium and Vibrio was somewhat more distantly related and may represent a slightly different substrate specificity - these were placed below the noise cutoff. More distantly related is a clade of archaeal sequences which as related to the DeoD family of inosine phosphorylases (TIGR00107) as they are to these uridine phosphorylases. This clade includes a characterized protein from Sulfolobus solfataricus which has been mis-named as a methylthioadenosine phosphorylase, but which acts on inosine and guanosine - it is unclear whether uridine has been evaluated as a substrate. [Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides] 245 matched cddid_all.tbl CDD TIGR01719 TIGR01719 130780 euk_UDPppase uridine phosphorylase. This model represents a clade of mainly eucaryotic uridine phosphorylases. Genes from human and mouse have been characterized. This enzyme is a member of the PHP/UDP subfamily (pfam01048) and is closely related to the bacterial uridine (TIGR01718) and inosine (TIGR00107) phosphorylase equivalogs. In addition to the eukaryotes, a gene from Mycobacterium leprae is included in this equivalog and may have resulted from lateral gene transfer. [Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides] 287 matched cddid_all.tbl CDD TIGR01720 TIGR01720 273774 NRPS-para261 non-ribosomal peptide synthase domain TIGR01720. This domain appears to be located immediately downstream from a condensation domain (pfam00668), and is followed primarily by the end of the molecule or another condensation domain (in a few cases it is followed by pfam00501, an AMP-binding module). The converse is not true, pfam00668 domains are not always followed by this domain. This implicates this domain in possible post-condensation modification events. This model is 171 amino acids long and contains three very highly conserved regions. At the N-terminus is a nearly invariant lysine (position 11) followed by xxxRxxPxxGxGYG in which the proline and the first glycine are invariant. This is followed approximately 22 residues later by the motif FNYLG. Near the C-terminus of the domain is the sequence TxSD where the serine and aspartate are nearly invariant. 153 matched cddid_all.tbl CDD TIGR01721 TIGR01721 130782 AMN-like AMP nucleosidase, putative. The sequences in the clade represented by this model are most closely related to the AMP nucleosidase found in TIGR01717. These sequences are found only in Chlamydia and Porphyromonas and differ sufficiently from the characterized AMP nucleosidase to put some doubt on assignment of this name. 266 matched cddid_all.tbl CDD TIGR01722 TIGR01722 130783 MMSDH methylmalonic acid semialdehyde dehydrogenase. Involved in valine catabolism, methylmalonate-semialdehyde dehydrogenase catalyzes the irreversible NAD+- and CoA-dependent oxidative decarboxylation of methylmalonate semialdehyde to propionyl-CoA. Methylmalonate-semialdehyde dehydrogenase has been characterized in both prokaryotes and eukaryotes, functioning as a mammalian tetramer and a bacterial homodimer. Although similar in monomeric molecular mass and enzymatic activity, the N-terminal sequence in P.aeruginosa does not correspond with the N-terminal sequence predicted for rat liver. Sequence homology to a variety of prokaryotic and eukaryotic aldehyde dehydrogenases places MMSDH in the aldehyde dehydrogenase (NAD+) superfamily (pfam00171), making MMSDH's CoA requirement unique among known ALDHs. Methylmalonate semialdehyde dehydrogenase is closely related to betaine aldehyde dehydrogenase, 2-hydroxymuconic semialdehyde dehydrogenase, and class 1 and 2 aldehyde dehydrogenase. In Bacillus, a highly homologous protein to methylmalonic acid semialdehyde dehydrogenase, groups out from the main MMSDH clade with Listeria and Sulfolobus. This Bacillus protein has been suggested to be located in an iol operon and/or involved in myo-inositol catabolism, converting malonic semialdehyde to acetyl CoA ad CO2. The preceeding enzymes responsible for valine catabolism are present in Bacillus, Listeria, and Sulfolobus. [Energy metabolism, Amino acids and amines] 477 matched cddid_all.tbl CDD TIGR01723 TIGR01723 130784 hmd_TIGR 5,10-methenyltetrahydromethanopterin hydrogenase. This model represents a clade of authenticated coenzyme N(5),N(10)-methenyltetrahydromethanopterin reductases. This enzyme does not use F420. This enzyme acts in methanogenesis and as such is restricted to methanogenic archaeal species. This clade is one of two clades in pfam03201. [Energy metabolism, Methanogenesis] 340 matched cddid_all.tbl CDD TIGR01724 TIGR01724 130785 hmd_rel H2-forming N(5),N(10)-methenyltetrahydromethanopterin dehydrogenase-related protein. This model represents a sister clade to the authenticated coenzyme F420-dependent N(5),N(10)-methenyltetrahydromethanopterin reductase (HMD) of TIGR01723. Two members, designated HmdII and HmdIII, are found. Members are restricted to methanogens, but the function is unknown. [Unknown function, Enzymes of unknown specificity] 341 matched cddid_all.tbl CDD TIGR01725 TIGR01725 273775 phge_HK97_gp10 phage protein, HK97 gp10 family. This model represents an uncharacterized, highly divergent bacteriophage family. The family includes gp10 from HK022 and HK97. It appears related to TIGR01635, a phage morphogenesis family believed to be involved in tail completion. [Mobile and extrachromosomal element functions, Prophage functions] 119 matched cddid_all.tbl CDD TIGR01726 TIGR01726 130787 HEQRo_perm_3TM amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family. This model represents one of several classes of multiple membrane spanning regions found immediately N-terminal to the domain described by pfam00528, binding-protein-dependent transport systems inner membrane component. The region covered by this model generally is predicted to contain three transmembrane helices. Substrate specificities attributed to members of this family include histidine, arginine, glutamine, glutamate, and (in Agrobacterium) the opines octopine and nopaline. [Transport and binding proteins, Amino acids, peptides and amines] 99 matched cddid_all.tbl CDD TIGR01727 TIGR01727 213647 oligo_HPY oligopeptide/dipeptide ABC transporter, ATP-binding protein, C-terminal domain. This model represents a domain found in the C-terminal regions of oligopeptide ABC transporter ATP binding proteins, immediately following the ATP-binding domain (pfam00005). All characterized members appear able to be involved in the transport of oligopeptides or dipeptides. Some are important for sporulation or antibiotic resistance. Some dipeptide transporters also act on the heme precursor delta-aminolevulinic acid. [Transport and binding proteins, Amino acids, peptides and amines] 87 matched cddid_all.tbl CDD TIGR01728 TIGR01728 130789 SsuA_fam ABC transporter, substrate-binding protein, aliphatic sulfonates family. Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins. [Transport and binding proteins, Other] 288 matched cddid_all.tbl CDD TIGR01729 TIGR01729 130790 taurine_ABC_bnd taurine ABC transporter, periplasmic binding protein. This model identifies a cluster of ABC transporter periplasmic substrate binding proteins, apparently specific for taurine. Transport systems for taurine (NH2-CH2-CH2-SO3H), sulfonates, and sulfate esters import sulfur when sulfate levels are low. The most closely related proteins outside this family are putative aliphatic sulfonate binding proteins (TIGR01728). 300 matched cddid_all.tbl CDD TIGR01730 TIGR01730 273776 RND_mfp RND family efflux transporter, MFP subunit. This model represents the MFP (membrane fusion protein) component of the RND family of transporters. RND refers to Resistance, Nodulation, and cell Division. It is, in part, a subfamily of pfam00529 (Pfam release 7.5) but hits substantial numbers of proteins missed by that model. The related HlyD secretion protein, for which pfam00529 is named, is outside the scope of this model. Attributed functions imply outward transport. These functions include nodulation, acriflavin resistance, heavy metal efflux, and multidrug resistance proteins. Most members of this family are found in Gram-negative bacteria. The proposed function of MFP proteins is to bring the inner and outer membranes together and enable transport to the outside of the outer membrane. Note, however, that a few members of this family are found in Gram-positive bacteria, where there is no outer membrane. [Transport and binding proteins, Unknown substrate] 322 matched cddid_all.tbl CDD TIGR01731 TIGR01731 273777 fil_hemag_20aa adhesin HecA family 20-residue repeat (two copies). This model represents two copies of a 20-residue repeat found in Bordetella pertussis filamentous hemagglutinin family of adhesins. This family includes extremely long proteins from a number of plant and animal pathogens. 40 matched cddid_all.tbl CDD TIGR01732 TIGR01732 273778 tiny_TM_bacill conserved hypothetical tiny transmembrane protein. This model represents a family of hypothetical proteins, half of which are 40 residues or less in length. Members are found only in spore-forming species. A Gly-rich variable region is followed by a strongly conserved, highly hydrophobic region, predicted to form a transmembrane helix, ending with an invariant Gly. The consensus for this stretch is FALLVVFILLIIV. [Hypothetical proteins, Conserved] 26 matched cddid_all.tbl CDD TIGR01733 TIGR01733 273779 AA-adenyl-dom "amino acid adenylation domain. This model represents a domain responsible for the specific recognition of amino acids and activation as adenylyl amino acids. The reaction catalyzed is aa + ATP -> aa-AMP + PPi. These domains are usually found as components of multi-domain non-ribosomal peptide synthetases and are usually called ""A-domains"" in that context. A-domains are almost invariably followed by ""T-domains"" (thiolation domains, pfam00550) to which the amino acid adenylate is transferred as a thiol-ester to a bound pantetheine cofactor with the release of AMP (these are also called peptide carrier proteins, or PCPs. When the A-domain does not represent the first module (corresponding to the first amino acid in the product molecule) it is usually preceded by a ""C-domain"" (condensation domain, pfam00668) which catalyzes the ligation of two amino acid thiol-esters from neighboring modules. This domain is a subset of the AMP-binding domain found in Pfam (pfam00501) which also hits substrate--CoA ligases and luciferases. Sequences scoring in between trusted and noise for this model may be ambiguous as to whether they activate amino acids or other molecules lacking an alpha amino group." 409 matched cddid_all.tbl CDD TIGR01734 TIGR01734 273780 D-ala-DACP-lig D-alanine--poly(phosphoribitol) ligase, subunit 1. This model represents the enzyme (also called D-alanine-D-alanyl carrier protein ligase) which activates D-alanine as an adenylate via the reaction D-ala + ATP -> D-ala-AMP + PPi, and further catalyzes the condensation of the amino acid adenylate with the D-alanyl carrier protein (D-ala-ACP). The D-alanine is then further transferred to teichoic acid in the biosynthesis of lipoteichoic acid (LTA) and wall teichoic acid (WTA) in gram positive bacteria, both polysacchatides. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 502 matched cddid_all.tbl CDD TIGR01735 TIGR01735 188163 FGAM_synt phosphoribosylformylglycinamidine synthase, single chain form. This model represents a single-molecule form of phosphoribosylformylglycinamidine synthase, also called FGAM synthase, an enzyme of purine de novo biosynthesis. This form is found mostly in eukaryotes and Proteobacteria. In Bacillus subtilis PurL (FGAM synthase II) and PurQ (FGAM synthase I), homologous to different parts of this model, perform the equivalent function; the unrelated small protein PurS is also required and may be a third subunit. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 1310 matched cddid_all.tbl CDD TIGR01736 TIGR01736 273781 FGAM_synth_II phosphoribosylformylglycinamidine synthase II. Phosphoribosylformylglycinamidine synthase is a single, long polypeptide in most Proteobacteria and eukarotes. Three proteins are required in Bacillus subtilis and many other species. This is the longest of the three and is designated PurL, phosphoribosylformylglycinamidine synthase II, or FGAM synthase II. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 715 matched cddid_all.tbl CDD TIGR01737 TIGR01737 273782 FGAM_synth_I phosphoribosylformylglycinamidine synthase I. In some species, phosphoribosylformylglycinamidine synthase is composed of a single polypeptide chain. This model describes the PurQ protein of Bacillus subtilis (where PurL, PurQ, and PurS are required for phosphoribosylformylglycinamidine synthase activity) and functionally equivalent proteins from other bacteria and archaea. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 227 matched cddid_all.tbl CDD TIGR01738 TIGR01738 273783 bioH pimelyl-[acyl-carrier protein] methyl ester esterase. This CoA-binding enzyme is required for the production of pimeloyl-coenzyme A, the substrate of the BioF protein early in the biosynthesis of biotin. Its exact function is unknown, but is proposed in ref 2. This enzyme belongs to the alpha/beta hydrolase fold family (pfam00561). Members of this family are restricted to the Proteobacteria. [Biosynthesis of cofactors, prosthetic groups, and carriers, Biotin] 245 matched cddid_all.tbl CDD TIGR01739 TIGR01739 273784 tegu_FGAM_synt herpesvirus tegument protein/v-FGAM-synthase. This model describes a family of large proteins of herpesvirues. The protein is described variably as tegument protein or phosphoribosylformylglycinamidine synthase (FGAM-synthase). Most of the length of the protein shows homology to eukaryotic FGAM-synthase. Functional characterizations were not verified during construction of this model. 1202 matched cddid_all.tbl CDD TIGR01740 TIGR01740 273785 pyrF orotidine 5'-phosphate decarboxylase, subfamily 1. This model represents orotidine 5'-monophosphate decarboxylase, the PyrF protein of pyrimidine nucleotide biosynthesis. In many eukaryotes, the region hit by this model is part of a multifunctional protein. [Purines, pyrimidines, nucleosides, and nucleotides, Pyrimidine ribonucleotide biosynthesis] 214 matched cddid_all.tbl CDD TIGR01741 TIGR01741 130802 staph_tand_hypo conserved hypothetical protein. This model represents a tandem array of 10 proteins in Staphylococcus aureus and the C-terminal region of one protein each in Bacillus subtilis and Bacillus halodurans. 157 matched cddid_all.tbl CDD TIGR01742 TIGR01742 273786 SA_tandem_lipo Staphylococcus tandem lipoproteins. Members of this family are predicted lipoproteins (mostly), found in Staphylococcus aureus in several different tandem clusters in pathogenicity islands. Members are also found, clustered, in Staphylococcus epidermidis. 255 matched cddid_all.tbl CDD TIGR01743 TIGR01743 130804 purR_Bsub pur operon repressor, Bacillus subtilis type. This model represents the puring operon repressor PurR of low-GC Gram-positive bacteria. This homodimeric repressor contains a large region homologous to phosphoribosyltransferases and is inhibited by 5-phosphoribosyl 1-pyrophosphate. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis, Regulatory functions, DNA interactions] 268 matched cddid_all.tbl CDD TIGR01744 TIGR01744 130805 XPRTase xanthine phosphoribosyltransferase. This model represent a xanthine-specific phosphoribosyltransferase of Bacillus subtilis and closely related proteins from other species, mostly from other Gram-positive bacteria. The adjacent gene is a xanthine transporter; B. subtilis can import xanthine for the purine salvage pathway or for catabolism to obtain nitrogen. [Purines, pyrimidines, nucleosides, and nucleotides, Salvage of nucleosides and nucleotides] 191 matched cddid_all.tbl CDD TIGR01745 TIGR01745 130806 asd_gamma aspartate-semialdehyde dehydrogenase, gamma-proteobacterial. [Amino acid biosynthesis, Aspartate family] 366 matched cddid_all.tbl CDD TIGR01746 TIGR01746 273787 Thioester-redct thioester reductase domain. This model includes the terminal domain from the fungal alpha aminoadipate reductase enzyme (also known as aminoadipate semialdehyde dehydrogenase) which is involved in the biosynthesis of lysine, as well as the reductase-containing component of the myxochelin biosynthetic gene cluster, MxcG. The mechanism of reduction involves activation of the substrate by adenylation and transfer to a covalently-linked pantetheine cofactor as a thioester. This thioester is then reduced to give an aldehyde (thus releasing the product) and a regenerated pantetheine thiol. (In myxochelin biosynthesis this aldehyde is further reduced to an alcohol or converted to an amine by an aminotransferase.) This is a fundamentally different reaction than beta-ketoreductase domains of polyketide synthases which act at a carbonyl two carbons removed from the thioester and forms an alcohol as a product. This domain is invariably found at the C-terminus of the proteins which contain it (presumably because it results in the release of the product). The majority of hits to this model are non-ribosomal peptide synthetases in which this domain is similarly located proximal to a thiolation domain (pfam00550). In some cases this domain is found at the end of a polyketide synthetase enzyme, but is unlike ketoreductase domains which are found before the thiolase domains. Exceptions to this observed relationship with the thiolase domain include three proteins which consist of stand-alone reductase domains (GP|466833 from M. leprae, GP|435954 from Anabaena and OMNI|NTL02SC1199 from Strep. coelicolor) and one protein (OMNI|NTL01NS2636 from Nostoc) which contains N-terminal homology with a small group of hypothetical proteins but no evidence of a thiolation domain next to the putative reductase domain. Below the noise cutoff to this model are proteins containing more distantly related ketoreductase and dehydratase/epimerase domains. It has been suggested that a NADP-binding motif can be found in the N-terminal portion of this domain that may form a Rossman-type fold. 367 matched cddid_all.tbl CDD TIGR01747 TIGR01747 130808 diampropi_NH3ly diaminopropionate ammonia-lyase family. This small subfamily includes diaminopropionate ammonia-lyase from Salmonella typhimurium and a small number of close homologs, about 50 % identical in sequence. The enzyme is a pyridoxal phosphate-binding homodimer homologous to threonine dehydratase (threonine deaminase). [Energy metabolism, Other] 376 matched cddid_all.tbl CDD TIGR01748 TIGR01748 130809 rhaA L-rhamnose isomerase. This enzyme interconverts L-rhamnose and L-rhamnulose. In some species, including E. coli, this is the first step in rhamnose catabolism. Sequential steps are catalyzed by rhamnulose kinase (rhaB), then rhamnulose-1-phosphate aldolase (rhaD) to yield glycerone phosphate and (S)-lactaldehyde. Characterization of this family is based on members in E. coli and Salmonella. [Energy metabolism, Sugars] 414 matched cddid_all.tbl CDD TIGR01749 TIGR01749 130810 fabA beta-hydroxyacyl-[acyl carrier protein] dehydratase FabA. This enzyme, FabA, shows overlapping substrate specificity with FabZ with regard to chain length in fatty acid biosynthesis. It is commonly designated 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.60) as if it were specific for that chain length, but its specificity is broader; it is active even in the initiation of fatty acid biosynthesis. This enzyme can also isomerize trans-2-decenoyl-ACP to cis-3-decenoyl-ACP to bypass reduction by FabI and instead allow biosynthesis of unsaturated fatty acids. FabA cannot elongate unsaturated fatty acids. [Fatty acid and phospholipid metabolism, Biosynthesis] 169 matched cddid_all.tbl CDD TIGR01750 TIGR01750 130811 fabZ beta-hydroxyacyl-[acyl carrier protein] dehydratase FabZ. This enzyme, FabZ, shows overlapping substrate specificity with FabA with regard to chain length in fatty acid biosynthesis. FabZ works preferentially on shorter chains and is often designated (3R)-hydroxymyristoyl-[acyl carrier protein] dehydratase, although its actual specificity is broader. Unlike FabA, FabZ does not function as an isomerase and cannot initiate unsaturated fatty acid biosynthesis. However, only FabZ can act during the elongation of unsaturated fatty acid chains. [Fatty acid and phospholipid metabolism, Biosynthesis] 140 matched cddid_all.tbl CDD TIGR01751 TIGR01751 188164 crot-CoA-red crotonyl-CoA carboxylase/reductase. The enzyme represented by this model can convert crotonyl-CoA to butyryl-CoA (crotonyl-CoA reductase activity), but more importantly, in the presence of CO2, generates (2S)-ethylmalonyl-CoA. In serine cycle methylotrophic bacteria this enzyme is involved in the process of acetyl-CoA to glyoxylate. In other bacteria the enzyme is used to produce extender units for incorporation into polyketides such as tylosin from Streptomyces fradiae and coronatine from Pseudomonas syringae. 398 matched cddid_all.tbl CDD TIGR01752 TIGR01752 273788 flav_long flavodoxin, long chain. Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the long chain type, typical for nitrogen fixation but associated with pyruvate formate-lyase activation and cobalamin-dependent methionine synthase activity in E. coli. [Energy metabolism, Electron transport] 167 matched cddid_all.tbl CDD TIGR01753 TIGR01753 273789 flav_short flavodoxin, short chain. Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They can act in nitrogen fixation by nitrogenase, in sulfite reduction, and light-dependent NADP+ reduction in during photosynthesis, among other roles. This model describes the short chain type. Many of these are involved in sulfite reduction. [Energy metabolism, Electron transport] 140 matched cddid_all.tbl CDD TIGR01754 TIGR01754 130815 flav_RNR ribonucleotide reductase-associated flavodoxin, putative. This model represents a family of proteins found immediately downstream of ribonucleotide reductase genes in Xyella fastidiosa and some Gram-positive bacteria. It appears to be a highly divergent flavodoxin of the short chain type, more like the flavodoxins of the sulfate-reducing genus Desulfovibrio than like the NifF flavodoxins associated with nitrogen fixation. 140 matched cddid_all.tbl CDD TIGR01755 TIGR01755 130816 flav_wrbA NAD(P)H:quinone oxidoreductase, type IV. This model represents a protein, WrbA, related to and slightly larger than flavodoxin. It was just shown, in E. coli and Archaeoglobus fulgidus (and previously for some eukaryotic homologs) to act as fourth type of NAD(P)H:quinone oxidoreductase. In E. coli, this protein was earlier reported to be produced during stationary phase, bind to the trp repressor, and make trp operon repression more efficient. WrbA does not interact with the trp operator by itself. Members are found in species in which homologs of the E. coli trp operon repressor TrpR (SP:P03032) are not detected. [Energy metabolism, Electron transport] 197 matched cddid_all.tbl CDD TIGR01756 TIGR01756 130817 LDH_protist lactate dehydrogenase. This model represents a family of protist lactate dehydrogenases which have aparrently evolved from a recent protist malate dehydrogenase ancestor. Lactate dehydrogenase converts the hydroxyl at C-2 of lactate to a carbonyl in the product, pyruvate. The preference of this enzyme for NAD or NADP has not been determined. A critical residue in malate dehydrogenase, arginine-91 (T. vaginalis numbering) has been mutated to a leucine, eliminating the positive charge which complemeted the carboxylate in malate which is absent in lactate. Several other more subtle changes are proposed to make the active site smaller to accomadate the less bulky lactate molecule. 313 matched cddid_all.tbl CDD TIGR01757 TIGR01757 130818 Malate-DH_plant malate dehydrogenase, NADP-dependent. This model represents the NADP-dependent malate dehydrogenase found in plants, mosses and green algae and localized to the chloroplast. Malate dehydrogenase converts oxaloacetate into malate, a critical step in the C4 cycle which allows circumvention of the effects of photorespiration. Malate is subsequenctly transported from the chloroplast to the cytoplasm (and then to the bundle sheath cells in C4 plants). The plant and moss enzymes are light regulated via cysteine disulfide bonds. The enzyme from Sorghum has been crystallized. 387 matched cddid_all.tbl CDD TIGR01758 TIGR01758 130819 MDH_euk_cyt malate dehydrogenase, NAD-dependent. This model represents the NAD-dependent cytosolic malate dehydrogenase from eukaryotes. The enzyme from pig has been studied by X-ray crystallography 324 matched cddid_all.tbl CDD TIGR01759 TIGR01759 130820 MalateDH-SF1 malate dehydrogenase. This model represents a family of malate dehydrogenases in bacteria and eukaryotes which utilize either NAD or NADP depending on the species and context. MDH interconverts malate and oxaloacetate and is a part of the citric acid cycle as well as the C4 cycle in certain photosynthetic organisms. 323 matched cddid_all.tbl CDD TIGR01760 TIGR01760 273790 tape_meas_TP901 phage tail tape measure protein, TP901 family, core region. This model represents a reasonably well conserved core region of a family of phage tail proteins. The member from phage TP901-1 was characterized as a tail length tape measure protein in that a shortened form of the protein leads to phage with proportionately shorter tails. [Mobile and extrachromosomal element functions, Prophage functions] 350 matched cddid_all.tbl CDD TIGR01761 TIGR01761 273791 thiaz-red thiazolinyl imide reductase. This reductase is found associated with gene clusters for the biosynthesis of various non-ribosomal peptide derived natural products in which cysteine is cyclized to a thiazoline ring containing an imide double bond. Examples include yersiniabactin (irp3/YbtU, GP|21959262) and pyochelin (PchG, GP|4325022). 344 matched cddid_all.tbl CDD TIGR01762 TIGR01762 130823 chlorin-enz chlorinating enzyme. This model represents a a group of highly homologous enzymes related to dioxygenases which chlorinate amino acid methyl groups. BarB1 and BarB2 are proposed to trichlorinate one of the methyl groups of a leucine residue in the biosynthesis of barbamide in the cyanobacterium Lyngbya majuscula. SyrB2 is proposed to chlorinate the methyl group of threonine in the biosynthesis of syringomycin in Pseudomonas syringae. CmaB is proposed to chlorinate the beta-methyl group of alloisoleucine in the process of ring closure in the biosynthesis of coronamic acid, a component of coronatine also in Pseudomonas syringae. 288 matched cddid_all.tbl CDD TIGR01763 TIGR01763 273792 MalateDH_bact malate dehydrogenase, NAD-dependent. This enzyme converts malate into oxaloacetate in the citric acid cycle. The critical residues which discriminate malate dehydrogenase from lactate dehydrogenase have been characterized, and have been used to set the cutoffs for this model. Sequences showing [aflimv][ap]R[rk]pgM[st] and [ltv][ilm]gGhgd were kept above trusted, while those in which the capitalized residues in the patterns were found to be Q, E and E were kept below the noise cutoff. Some sequences in the grey zone have been annotated as malate dehydrogenases, but none have been characterized. Phylogenetically, a clade of sequences from eukaryotes such as Toxoplasma and Plasmodium which include a characterized lactate dehydrogenase and show abiguous critical residue patterns appears to be more closely related to these bacterial sequences than other eukaryotic sequences. These are relatively long branch and have been excluded from the model. All other sequences falling below trusted appear to be phylogenetically outside of the clade including the trusted hits. The annotation of Botryococcus braunii as lactate dehydrogenase appears top be in error. This was initially annotated as MDH by Swiss-Prot and then changed. The rationale for either of these annotations is not traceable. [Energy metabolism, TCA cycle] 305 matched cddid_all.tbl CDD TIGR01764 TIGR01764 200128 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376). [Unknown function, General] 49 matched cddid_all.tbl CDD TIGR01765 TIGR01765 130826 tspaseT_teng_N transposase, putative, N-terminal domain. This model represents the N-terminal region of a family of putative transposases found in the largest copy number in Thermoanaerobacter tengcongensis. The three homologs in Bacillus anthracis are each split into two ORFs and this model represents the upstream ORF. [Mobile and extrachromosomal element functions, Transposon functions] 73 matched cddid_all.tbl CDD TIGR01766 TIGR01766 273793 tspaseT_teng_C transposase, IS605 OrfB family, central region. This model represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by pfam01385, and other proteins. [Mobile and extrachromosomal element functions, Transposon functions] 82 matched cddid_all.tbl CDD TIGR01767 TIGR01767 130828 MTRK S-methyl-5-thioribose kinase. This enzyme, S-methyl-5-thioribose kinase (MtnK) is involved in the methionine salvage pathway in certain bacteria. 370 matched cddid_all.tbl CDD TIGR01768 TIGR01768 273794 GGGP-family geranylgeranylglyceryl phosphate synthase family protein. This model represents a family of sequences including geranylgeranylglyceryl phosphate synthase which catalyzes the first committed step in the synthesis of ether-linked membrane lipids in archaea. The clade of bacterial sequences may have the same function or a closely related function. This model supercedes TIGR00265, which has been retired. 223 matched cddid_all.tbl CDD TIGR01769 TIGR01769 130830 GGGP phosphoglycerol geranylgeranyltransferase. This model represents geranylgeranylglyceryl phosphate synthase which catalyzes the first committed step in the synthesis of ether-linked membrane lipids in archaea. The active enzyme is reported to be a homopentamer in Methanobacterium thermoautotrophicum but is reported to be a homodimer in Thermoplasma acidophilum. 205 matched cddid_all.tbl CDD TIGR01770 TIGR01770 273795 NDH_I_N proton-translocating NADH-quinone oxidoreductase, chain N. This model describes the 14th (based on E. coli) structural gene, N, of bacterial and chloroplast energy-transducing NADH (or NADPH) dehydrogenases. This model does not describe any subunit of the mitochondrial complex I (for which the subunit composition is very different), nor NADH dehydrogenases that are not coupled to ion transport. The Enzyme Commission designation 1.6.5.3, for NADH dehydrogenase (ubiquinone), is applied broadly, perhaps unfortunately, even if the quinone is menaquinone (Thermus, Mycobacterium) or plastoquinone (chloroplast). For chloroplast members, the name NADH-plastoquinone oxidoreductase is used for the complex and this protein is designated as subunit 2 or B. This model also includes a subunit of a related complex in the archaeal methanogen, Methanosarcina mazei, in which F420H2 replaces NADH and 2-hydroxyphenazine replaces the quinone. [Energy metabolism, Electron transport] 468 matched cddid_all.tbl CDD TIGR01771 TIGR01771 273796 L-LDH-NAD L-lactate dehydrogenase. This model represents the NAD-dependent L-lactate dehydrogenases from bacteria and eukaryotes. This enzyme function as as the final step in anaerobic glycolysis. Although lactate dehydrogenases have in some cases been mistaken for malate dehydrogenases due to the similarity of these two substrates and the apparent ease with which evolution can toggle these activities, critical residues have been identified which can discriminate between the two activities. At the time of the creation of this model no hits above the trusted cutoff contained critical residues typical of malate dehydrogenases. [Energy metabolism, Anaerobic, Energy metabolism, Glycolysis/gluconeogenesis] 299 matched cddid_all.tbl CDD TIGR01772 TIGR01772 130833 MDH_euk_gproteo malate dehydrogenase, NAD-dependent. This model represents the NAD-dependent malate dehydrogenase found in eukaryotes and certain gamma proteobacteria. The enzyme is involved in the citric acid cycle as well as the glyoxalate cycle. Several isoforms exidt in eukaryotes. In S. cereviseae, for example, there are cytoplasmic, mitochondrial and peroxisomal forms. Although malate dehydrogenases have in some cases been mistaken for lactate dehydrogenases due to the similarity of these two substrates and the apparent ease with which evolution can toggle these activities, critical residues have been identified which can discriminate between the two activities. At the time of the creation of this model no hits above the trusted cutoff contained critical residues typical of lactate dehydrogenases. [Energy metabolism, TCA cycle] 312 matched cddid_all.tbl CDD TIGR01773 TIGR01773 273797 GABAperm "gamma-aminobutyrate permease. GABA permease (gabP) catalyzes the translocation of 4-aminobutyrate (GABA) across the plasma membrane, with homologues expressed in Gram-negative and Gram-positive organisms. This permease is a highly hydrophobic transmembrane protein consisting of 12 transmembrane domains with hydrophilic N- and C-terminal ends. Induced by nitrogen-limited culture conditions in both Escherichia coli and Bacillus subtilis, gabP is an energy dependent transport system stimulated by membrane potential and has been observed adjacent and distant from other GABA degradation proteins. GabP is highly homologous to amino acid permeases from B. subtilis, E. coli, as well as to other members of the amino acid permease family (pfam00324). A member of the APC (amine-polyamine-choline) transporter superfamily, GABA permease possesses a ""consensus amphiphatic region"" (CAR) found to be evolutionarily conserved within this transport family. This amphiphatic region is located between helix 8 and cytoplasmic loop 8-9, forming a potential channel domain and suggested to play a significant role in ligand recognition and translocation. Unique to GABA permeases, a conserved cysteine residue (CYS-300, E.coli) located at the beginning of the amphiphatic domain, has been determined to be critical for catalytic specificity. [Transport and binding proteins, Amino acids, peptides and amines]" 452 matched cddid_all.tbl CDD TIGR01774 TIGR01774 273798 PFL2-3 glycyl radical enzyme, PFL2/glycerol dehydratase family. This family previously was designated pyruvate formate-lyase, but it now appears that members include the B12-independent glycerol dehydratase. Therefore, the functional definition of the family is being broadened. This family includes the PflF and PflD proteins of E. coli, described as isoforms of pyruvate-formate lyase found in a limited number additional species. PFL catalyzes the reaction pyruvate + CoA -> acetyl-CoA + formate, which is a step in the fermentation of glucose. 786 matched cddid_all.tbl CDD TIGR01776 TIGR01776 273799 TonB-tbp-lbp TonB-dependent lactoferrin and transferrin receptors. This family of TonB-dependent receptors are responsible for import of iron from the mammalian iron carriers lactoferrin and transferrin across the outer membrane. These receptors are found only in bacteria which can infect mammals such as Moraxella, Mannheimia, Neisseria, Actinobacillus, Pasteurella, Haemophilus and Histophilus species. [Transport and binding proteins, Cations and iron carrying compounds, Transport and binding proteins, Porins] 932 matched cddid_all.tbl CDD TIGR01777 TIGR01777 273800 yfcH TIGR01777 family protein. This model represents a clade of proteins of unknown function including the E. coli yfcH protein. [Hypothetical proteins, Conserved] 291 matched cddid_all.tbl CDD TIGR01778 TIGR01778 273801 TonB-copper TonB-dependent copper receptor. This model represents a family of proteobacterial TonB-dependent outer membrane receptor/transporters which bind and translocate copper ions. Two characterized members of this family exist, outer membrane protein C (OprC) from Pseudomonas aeruginosa and NosA from Pseudomonas stutzeri which is responsible for providing copper for the copper-containing N2O reducatse. [Transport and binding proteins, Cations and iron carrying compounds, Transport and binding proteins, Porins] 636 matched cddid_all.tbl CDD TIGR01779 TIGR01779 273802 TonB-B12 TonB-dependent vitamin B12 receptor. This model represents the TonB-dependent outer membrane receptor found in gamma proteobacteria responsible for translocating the cobalt-containing vitamin B12 (cobalamin). [Transport and binding proteins, Other, Transport and binding proteins, Porins] 614 matched cddid_all.tbl CDD TIGR01780 TIGR01780 188167 SSADH succinate-semialdehyde dehydrogenase. Succinic semialdehyde dehydrogenase is one of three enzymes constituting 4-aminobutyrate (GABA) degradation in both prokaryotes and eukaryotes, catalyzing the (NAD(P)+)-dependent catabolism reaction of succinic semialdehyde to succinate for metabolism by the citric acid cycle. The EC number depends on the cofactor: 1.2.1.24 for NAD only, 1.2.1.79 for NADP only, and 1.2.1.16 if both can be used. In Escherichia coli, succinic semialdehyde dehydrogenase is located in an unidirectionally transcribed gene cluster encoding enzymes for GABA degradation and is suggested to be cotranscribed with succinic semialdehyde transaminase from a common promoter upstream of SSADH. Similar gene arrangements can be found in characterized Ralstonia eutropha and the genome analysis of Bacillus subtilis. Prokaryotic succinic semialdehyde dehydrogenases (1.2.1.16) share high sequence homology to characterized succinic semialdehyde dehydrogenases from rat and human (1.2.1.24), exhibiting conservation of proposed cofactor binding residues, and putative active sites (G-237 & G-242, C-293 & G-259 respectively of rat SSADH). Eukaryotic SSADH enzymes exclusively utilize NAD+ as a cofactor, exhibiting little to no NADP+ activity. While a NADP+ preference has been detected in prokaryotes in addition to both NADP+- and NAD+-dependencies as in E.coli, Pseudomonas, and Klebsiella pneumoniae. The function of this alternative SSADH currently is unknown, but has been suggested to play a possible role in 4-hydroxyphenylacetic degradation. Just outside the scope of this model, are several sequences belonging to clades scoring between trusted and noise. These sequences may be actual SSADH enzymes, but lack sufficiently close characterized homologs to make a definitive assignment at this time. SSADH enzyme belongs to the aldehyde dehydrogenase family (pfam00171), sharing a common evolutionary origin and enzymatic mechanism with lactaldehyde dehydrogenase. Like in lactaldehyde dehydrogenase and succinate semialdehyde dehydrogenase, the mammalian catalytic glutamic acid and cysteine residues are conserved in all the enzymes of this family (PS00687, PS00070). [Central intermediary metabolism, Other] 448 matched cddid_all.tbl CDD TIGR01781 TIGR01781 273803 Trep_dent_lipo Treponema denticola clustered lipoprotein. This model represents a family of six predicted lipoproteins from a region of about 20 tandemly arranged genes in the Treponema denticola genome. Two other neighboring genes share the lipoprotein signal peptide region but do not show more extensive homology. The function of this locus is unknown. 412 matched cddid_all.tbl CDD TIGR01782 TIGR01782 273804 TonB-Xanth-Caul TonB-dependent receptor. This model represents a family of TonB-dependent outer-membrane receptors which are found mainly in Xanthomonas and Caulobacter. These appear to represent the expansion of a paralogous family in that the 22 X. axonopodis (21 in X. campestris) and 18 C. crescentus sequences are more closely related to each other than any of the many TonB-dependent receptors found in other species. In fact, the Crescentus and Xanthomonas sequences are inseparable on a phylogenetic tree using a PAM-weighted neighbor-joining method, indicating that one of the two genuses may have acquired this set of receptors from the other. The mechanism by which this family is shared between Xanthomonas, a gamma proteobacterial plant pathogen and Caulobacter, an alpha proteobacterial aquatic organism is unclear. [Transport and binding proteins, Porins] 845 matched cddid_all.tbl CDD TIGR01783 TIGR01783 273805 TonB-siderophor TonB-dependent siderophore receptor. This subfamily model encompasses a wide variety of TonB-dependent outer membrane siderophore receptors. It has no overlap with TonB receptors known to transport other substances, but is likely incomplete due to lack of characterizations. It is likely that genuine siderophore receptors will be identified which score below the noise cutoff to this model at which point the model should be updated. [Transport and binding proteins, Cations and iron carrying compounds, Transport and binding proteins, Porins] 651 matched cddid_all.tbl CDD TIGR01784 TIGR01784 273806 T_den_put_tspse conserved hypothetical protein (putative transposase or invertase). Several lines of evidence suggest that members of this family (loaded as a fragment mode model to find part-length matches) are associated with transposition, inversion, or recombination. Members are found in small numbers of genomes, but in large copy numbers in many of those species, including over 30 full length and fragmentary members in Treponema denticola. The strongest similarities are usually within rather than between species. PSI-BLAST shows similarity to proteins designated as possible transposases, DNA invertases (resolvases), and recombinases. In the oral pathogenic spirochete Treponema denticola, full-length members are often found near transporters or other membrane proteins. This family includes members of the putative transposase family pfam04754. 270 matched cddid_all.tbl CDD TIGR01785 TIGR01785 273807 TonB-hemin TonB-dependent heme/hemoglobin receptor family protein. This model represents the TonB-dependent outer membrane heme/hemoglobin receptor/transporter found in bacteria which live in contact with animals (which contain hemoglobin or other heme-bearing globins) or legumes (which contain leghemoglobin). Some species having hits to this model such as Nostoc, Caulobacter and Chlorobium do not have an obvious source of hemoglobin-like proteins in their biological niche and so the possibility exists that they act on some other substance. [Transport and binding proteins, Cations and iron carrying compounds, Transport and binding proteins, Porins] 665 matched cddid_all.tbl CDD TIGR01786 TIGR01786 273808 TonB-hemlactrns TonB-dependent hemoglobin/transferrin/lactoferrin receptor family protein. This model represents a family of TonB-dependent outer membrane receptor/transporters acting on iron-containing proteins such as hemoglobin, transferrin and lactoferrin. Two subfamily models with a narrower scope are contained within this model, the heme/hemoglobin receptor family protein model (TIGR01785) and the transferrin/lactoferrin receptor family model (TIGR01776). Accessions which score above trusted to this model while not scoring above trusted to the more specific models are most likely to be hemoglobin transporters. Nearly all of the species containing trusted hits to this model have access to hemoglobin, transferrin or lactoferrin or related proteins in their biological niche. [Transport and binding proteins, Cations and iron carrying compounds, Transport and binding proteins, Porins] 715 matched cddid_all.tbl CDD TIGR01787 TIGR01787 273809 squalene_cyclas squalene/oxidosqualene cyclases. This family of enzymes catalyzes the cyclization of the triterpenes squalene or 2-3-oxidosqualene to a variety of products including hopene, lanosterol, cycloartenol, amyrin, lupeol, and isomultiflorenol. 621 matched cddid_all.tbl CDD TIGR01788 TIGR01788 130848 Glu-decarb-GAD glutamate decarboxylase. This model represents the pyridoxal phosphate-dependent glutamate (alpha) decarboxylase found in bacteria (low and hi-GC gram positive, proteobacteria and cyanobacteria), plants, fungi and at least one archaon (Methanosarcina). The product of the enzyme is gamma-aminobutyrate (GABA). 431 matched cddid_all.tbl CDD TIGR01789 TIGR01789 130849 lycopene_cycl lycopene cyclase. This model represents a family of bacterial lycopene cyclases catalyzing the transformation of lycopene to carotene. These enzymes are found in a limited spectrum of alpha and gamma proteobacteria as well as Flavobacterium. 370 matched cddid_all.tbl CDD TIGR01790 TIGR01790 130850 carotene-cycl lycopene cyclase family protein. This family includes lycopene beta and epsilion cyclases (which form beta and delta carotene, respectively) from bacteria and plants as well as the plant capsanthin/capsorubin and neoxanthin cyclases which appear to have evolved from the plant lycopene cyclases. The plant lycopene epsilon cyclases also transform neurosporene to alpha zeacarotene. 388 matched cddid_all.tbl CDD TIGR01791 TIGR01791 130851 CM_archaeal chorismate mutase, archaeal type. This model represents a clade of archaeal chorismate mutases. Chorismate mutase catalyzes the conversion of chorismate into prephenate which is subsequently converted into either phenylalanine or tyrosine. In Sulfolobus this gene is found as a fusion with prephenate dehydrogenase (although the non-TIGR annotation contains a typographical error indicating it as a dehydratase OMNI|NTL02SS0274) which is the next enzyme in the tyrosine biosynthesis pathway. The Archaeoglobus gene contains an N-terminal prephenate dehydrogenase domain and a C-terminal prephenate dehydratase domain followed by a regulatory amino acid-binding ACT domain. The Thermoplasma volcanium gene is adjacent to prephenate dehydratase. [Amino acid biosynthesis, Aromatic amino acid family] 83 matched cddid_all.tbl CDD TIGR01792 TIGR01792 273810 urease_alph urease, alpha subunit. This model describes the urease alpha subunit UreC (designated beta or B chain, UreB in Helicobacter species). Accessory proteins for incorporation of the nickel cofactor are usually found in addition to the urease alpha, beta, and gamma subunits. The trusted cutoff is set above the scores of many reported fragments and of a putative second urease alpha chain in Streptomyces coelicolor. [Central intermediary metabolism, Nitrogen metabolism] 567 matched cddid_all.tbl CDD TIGR01793 TIGR01793 130853 cit_synth_euk citrate (Si)-synthase, eukaryotic. This model includes both mitochondrial and peroxisomal forms of citrate synthase. Citrate synthase is the entry point to the TCA cycle from acetyl-CoA. Peroxisomal forms, such as SP:P08679 from yeast (recognized by the C-terminal targeting motif SKL) act in the glyoxylate cycle. Eukaryotic homologs excluded by the high trusted cutoff of this model include a Tetrahymena thermophila citrate synthase that doubles as a filament protein, a putative citrate synthase from Plasmodium falciparum (no TCA cycle), and a methylcitrate synthase from Aspergillus nidulans. 427 matched cddid_all.tbl CDD TIGR01795 TIGR01795 130854 CM_mono_cladeE monofunctional chorismate mutase, alpha proteobacterial type. This model represents a small clade of monofunctional (non-fused) chorismate mutases spanning alpha proteobacteria and two actinobacter gram positive species. The alpha proteobacterial members are trusted because the pathways of CM are evident and there is only one plausible CM in the genome. In S. coelicolor, however, there is another aparrent monofunctional CM. [Amino acid biosynthesis, Aromatic amino acid family] 94 matched cddid_all.tbl CDD TIGR01796 TIGR01796 130855 CM_mono_aroH monofunctional chorismate mutase, gram positive type, clade 1. This model represents a family of monofunctional (non-fused) chorismate mutases from gram positive bacteria (Firmicutes) and cyanobacteria. Trusted members of the family are found in operons with other enzymes of the chorismate pathways, both up- and downstream of CM (Listeria, Bacillus, Oceanobacillus) or are the sole CM in the genome where the other members of the chorismate pathways are found elsewhere in the genome (Nostoc, Thermosynechococcus). [Amino acid biosynthesis, Aromatic amino acid family] 117 matched cddid_all.tbl CDD TIGR01797 TIGR01797 130856 CM_P_1 "chorismate mutase domain of proteobacterial P-protein, clade 1. This model represents the chorismate mutase domain of the gamma and beta proteobacterial ""P-protein"" which contains an N-terminal chorismate mutase domain and a C-terminal prephenate dehydratase domain. [Amino acid biosynthesis, Aromatic amino acid family]" 83 matched cddid_all.tbl CDD TIGR01798 TIGR01798 273811 cit_synth_I citrate synthase I (hexameric type). This model describes one of several distinct but closely homologous classes of citrate synthase, the protein that brings carbon (from acetyl-CoA) into the TCA cycle. This form, class I, is known to be hexameric and allosterically inhibited by NADH in Escherichia coli, Acinetobacter anitratum, Azotobacter vinelandii, Pseudomonas aeruginosa, etc. In most species with a class I citrate synthase, a dimeric class II isozyme is found. The class II enzyme may act primarily on propionyl-CoA to make 2-methylcitrate or be bifunctional, may be found among propionate utilization enzymes, and may be constitutive or induced by propionate. Some members of this model group as class I enzymes, and may be hexameric, but have shown regulatory properties more like class II enzymes. [Energy metabolism, TCA cycle] 412 matched cddid_all.tbl CDD TIGR01799 TIGR01799 130858 CM_T "chorismate mutase domain of T-protein. This model represents the chorismate mutase domain of the gamma proteobacterial ""T-protein"" which consists of an N-terminal chorismate mutase domain and a C-terminal prephenate dehydrogenase domain. [Amino acid biosynthesis, Aromatic amino acid family]" 83 matched cddid_all.tbl CDD TIGR01800 TIGR01800 130859 cit_synth_II 2-methylcitrate synthase/citrate synthase II. Members of this family are dimeric enzymes with activity as 2-methylcitrate synthase, citrate synthase, or both. Many Gram-negative species have a hexameric citrate synthase, termed citrate synthase I (TIGR01798). Members of this family (TIGR01800) appear as a second citrate synthase isozyme but typically are associated with propionate metabolism and synthesize 2-methylcitrate from propionyl-CoA; citrate synthase activity may be incidental. A number of species, including Thermoplasma acidophilum, Pyrococcus furiosus, and the Antarctic bacterium DS2-3R have a bifunctional member of this family as the only citrate synthase isozyme. 368 matched cddid_all.tbl CDD TIGR01801 TIGR01801 130860 CM_A chorismate mutase domain of gram positive AroA protein. This model represents a small clade of chorismate mutase domains N-terminally fused to the first enzyme in the chorismate pathway, 2-dehydro-3-deoxyphosphoheptanoate aldolase (DAHP synthetase, AroA) which are found in some gram positive species and Deinococcus. Only in Deinococcus, where this domain is the sole CM domain in the genome can a trusted assignment of function be made. In the other species there is at least one other trusted CM domain present. The similarity between the Deinococcus gene and the others in this clade is sufficiently strong (~44% identity), that the whole clade can be trusted to be functional. The possibility exists, however, that in the gram positive species the fusion to the first enzyme in the pathway has evolved a separate, regulatory role. [Amino acid biosynthesis, Aromatic amino acid family] 102 matched cddid_all.tbl CDD TIGR01802 TIGR01802 273812 CM_pl-yst monofunctional chorismate mutase, eukaryotic type. This model represents the plant and yeast (plastidic) chorismate mutase. These CM's are distinct from other forms by the presence of an extended regulatory domain. [Amino acid biosynthesis, Aromatic amino acid family] 246 matched cddid_all.tbl CDD TIGR01803 TIGR01803 130862 CM-like chorismate mutase related enzymes. This subfamily includes two enzymes which are variants on the mechanism of chorismate mutase and are likely to have evolved from an ancestral chorismate mutase enzyme. 4-amino-4-deoxy-chorismate mutase produces amino-deoxy-prephenate which is subsequently converted to para-dimethylamino-phenylalanine, a component of the natural product pristinamycin. Isochorismate-pyruvate lyase presumably catalyzes the same type of 2+2+2 cyclo-rearrangement as chorismate mutase, but acting on isochorismate, this results in two broken bonds instead of one broken and one made. The product of this reaction is salicylate (2-hydroxy-benzoate) which is also incorporated into various natural products. 82 matched cddid_all.tbl CDD TIGR01804 TIGR01804 200131 BADH betaine-aldehyde dehydrogenase. Under osmotic stress, betaine aldehyde dehydrogenase oxidizes glycine betaine aldehyde into the osmoprotectant glycine betaine, via the second of two oxidation steps from exogenously supplied choline or betaine aldehyde. This choline-glycine betaine synthesis pathway can be found in gram-positive and gram-negative bacteria. In Escherichia coli, betaine aldehyde dehydrogenase (betB) is osmotically co-induced with choline dehydrogenase (betA) in the presence of choline. These dehydrogenases are located in a betaine gene cluster with the upstream choline transporter (betT) and transcriptional regulator (betI). Similar to E.coli, betaine synthesis in Staphylococcus xylosus is also influenced by osmotic stress and the presence of choline with genes localized in a functionally equivalent gene cluster. Organization of the betaine gene cluster in Sinorhizobium meliloti and Bacillus subtilis differs from that of E.coli by the absence of upstream choline transporter and transcriptional regulator homologues. Additionally, B.subtilis co-expresses a type II alcohol dehydrogenase with betaine aldehyde dehydrogenase instead of choline dehydrogenase as in E.coli, St.xylosus, and Si.meliloti. Betaine aldehyde dehydrogenase is a member of the aldehyde dehydrogenase family (pfam00171). [Cellular processes, Adaptations to atypical conditions] 467 matched cddid_all.tbl CDD TIGR01805 TIGR01805 130864 CM_mono_grmpos monofunctional chorismate mutase, gram positive-type, clade 2. This model represents a clade of chorismate mutase proteins/domains from gram positive species. The sequence from Enterococcus is fused to the C-terminus of an aparrent acetyltransferase, and the seuence from Clostridium acetobutylicum (but not perfringens) is fused to the N-terminus of shikimate-5-dehydrogenase, another enzyme of the chorismate pathway. All the other members of this clade are mono-functional. Members of this clade from Streptococcus and Lactococcus have been found which represent the sole chorismate mutase domain in their respective genomes which also exhibit evidence of the enzymes of both the upstream and downstream branches of the chorismate pathways. [Amino acid biosynthesis, Aromatic amino acid family] 81 matched cddid_all.tbl CDD TIGR01806 TIGR01806 130865 CM_mono2 chorismate mutase, putative. This model represents a clade of probable chorismate mutases from alpha, beta and gamma proteobacteria as well as Mycobacterium tuberculosis and a clade of nematodes. Although the most likely function for the enzymes represented by this model is as a chorismate mutase, in no species are these enzymes the sole chorismate mutase in the genome. Also, in no case are these enzymes located in a region of the genome proximal to any other enzymes involved in chorismate pathways. Although the Pantoea enzyme has been shown to complement a CM-free mutant of E. coli, this was also shown to be the case with isochorismate-pyruvate lyase which only has a secondary (non-physiologically relevant) chorismate mutase activity. This enzyme is believed to be a homodimer and be localized to the periplasm. [Amino acid biosynthesis, Aromatic amino acid family] 114 matched cddid_all.tbl CDD TIGR01807 TIGR01807 130866 CM_P2 "chorismate mutase domain of proteobacterial P-protein, clade 2. This model represents one of two separate clades of the chorismate mutase domain of the gamma and beta and epsilon proteobacterial ""P-protein"" which contains an N-terminal chorismate mutase domain and a C-terminal prephenate dehydratase domain. It is also found in Aquifex aolicus. [Amino acid biosynthesis, Aromatic amino acid family]" 76 matched cddid_all.tbl CDD TIGR01808 TIGR01808 130867 CM_M_hiGC-arch monofunctional chorismate mutase, high GC gram positive type. This model represents the monofunctional chorismate mutase from high GC gram-positive bacteria and archaea. Trusted annotations from Corynebacterium and Pyrococcus are aparrently the sole chorismate mutase enzymes in their respective genomes. This is coupled with the presence in those genomes of the enzymes of the chorismate pathways both up- and downstream of chorismate mutase. [Amino acid biosynthesis, Aromatic amino acid family] 74 matched cddid_all.tbl CDD TIGR01809 TIGR01809 273813 Shik-DH-AROM shikimate-5-dehydrogenase, fungal AROM-type. This model represents a clade of shikimate-5-dehydrogenases found in Corynebacterium, Mycobacteria and fungi. The fungal sequences are pentafunctional proteins known as AroM which contain the central five seven steps in the chorismate biosynthesis pathway. The Corynebacterium and Mycobacterial sequences represent the sole shikimate-5-dehydrogenases in species which otherwise have every enzyme of the chorismate biosynthesis pathway. [Amino acid biosynthesis, Aromatic amino acid family] 282 matched cddid_all.tbl CDD TIGR01810 TIGR01810 273814 betA choline dehydrogenase. Choline dehydrogenase catalyzes the conversion of exogenously supplied choline into the intermediate glycine betaine aldehyde, as part of a two-step oxidative reaction leading to the formation of osmoprotectant betaine. This enzymatic system can be found in both gram-positive and gram-negative bacteria. As in Escherichia coli, Staphylococcus xylosus, and Sinorhizobium meliloti, this enzyme is found associated in a transciptionally co-induced gene cluster with betaine aldehyde dehydrogenase, the second catalytic enzyme in this reaction. Other gram-positive organisms have been shown to employ a different enzymatic system, utlizing a soluable choline oxidase or type III alcohol dehydrogenase instead of choline dehydrogenase. This enzyme is a member of the GMC oxidoreductase family (pfam00732 and pfam05199), sharing a common evoluntionary origin and enzymatic reaction with alcohol dehydrogenase. Outgrouping from this model, Caulobacter crescentus shares sequence homology with choline dehydrogenase, yet other genes participating in this enzymatic reaction have not currently been identified. [Cellular processes, Adaptations to atypical conditions] 532 matched cddid_all.tbl CDD TIGR01811 TIGR01811 130870 sdhA_Bsu succinate dehydrogenase or fumarate reductase, flavoprotein subunit, Bacillus subtilis subgroup. This model represents the succinate dehydrogenase flavoprotein subunit as found in the low-GC Gram-positive bacteria and a few other lineages. This enzyme may act in a complete or partial TCA cycle, or act in the opposite direction as fumarate reductase. In some but not all species, succinate dehydrogenase and fumarate reductase may be encoded as separate isozymes. [Energy metabolism, TCA cycle] 603 matched cddid_all.tbl CDD TIGR01812 TIGR01812 273815 sdhA_frdA_Gneg succinate dehydrogenase or fumarate reductase, flavoprotein subunitGram-negative/mitochondrial subgroup. This model represents the succinate dehydrogenase flavoprotein subunit as found in Gram-negative bacteria, mitochondria, and some Archaea. Mitochondrial forms interact with ubiquinone and are designated EC 1.3.5.1, but can be degraded to 1.3.99.1. Some isozymes in E. coli and other species run primarily in the opposite direction and are designated fumarate reductase. [Energy metabolism, Aerobic, Energy metabolism, Anaerobic, Energy metabolism, TCA cycle] 566 matched cddid_all.tbl CDD TIGR01813 TIGR01813 273816 flavo_cyto_c flavocytochrome c. This model describes a family of redox proteins related to the succinate dehydrogenases and fumarate reductases of E. coli, mitochondria, and other well-characterized systems. A member of this family from Shewanella frigidimarina NCIMB400 is characterized as a water-soluble periplasmic protein with four heme groups, a non-covalently bound FAD, and essentially unidirectional fumarate reductase activity. At least seven distinct members of this family are found in Shewanella oneidensis, a species able to use a wide variety of pathways for respiraton. [Energy metabolism, Electron transport] 439 matched cddid_all.tbl CDD TIGR01814 TIGR01814 130873 kynureninase kynureninase. This model describes kynureninase, a pyridoxal-phosphate enzyme. Kynurinine is a Trp breakdown product and a precursor for NAD. In Chlamydia psittaci, an obligate intracellular pathogen, kynureninase makes anthranilate, a Trp precursor, from kynurenine. This counters the tryptophan hydrolysis that occurs in the host cell in response to the pathogen. [Energy metabolism, Amino acids and amines] 406 matched cddid_all.tbl CDD TIGR01815 TIGR01815 130874 TrpE-clade3 anthranilate synthase, alpha proteobacterial clade. This model represents a small clade of anthranilate synthases from alpha proteobacteria and Nostoc (a cyanobacterium). This enzyme is the first step in the pathway for the biosynthesis of tryprophan from chorismate. [Amino acid biosynthesis, Aromatic amino acid family] 717 matched cddid_all.tbl CDD TIGR01816 TIGR01816 130875 sdhA_forward succinate dehydrogenase, flavoprotein subunit, E. coli/mitochondrial subgroup. Succinate dehydrogenase and fumarate reductase are homologous enzymes reversible in principle but favored under different circumstances. This model represents a narrowly defined clade of the succinate dehydrogenase flavoprotein subunit as found in mitochondria, in Rickettsia, in E. coli and other Proteobacteria, and in a few other lineages. However, this model excludes all known fumarate reductases. It also excludes putative succinate dehydrogenases that appear to diverged before the split between E. coli succinate dehydrogenase and fumarate reductase. [Energy metabolism, TCA cycle] 565 matched cddid_all.tbl CDD TIGR01817 TIGR01817 273817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms. [Central intermediary metabolism, Nitrogen fixation, Regulatory functions, DNA interactions] 534 matched cddid_all.tbl CDD TIGR01818 TIGR01818 273818 ntrC nitrogen regulation protein NR(I). This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc. [Central intermediary metabolism, Nitrogen metabolism, Regulatory functions, DNA interactions, Signal transduction, Two-component systems] 463 matched cddid_all.tbl CDD TIGR01819 TIGR01819 130878 F420_cofD 2-phospho-L-lactate transferase. This model represents LPPG:Fo 2-phospho-L-lactate transferase, which catalyses the fourth step in the biosynthesis of coenzyme F420, a flavin derivative found in methanogens, the Mycobacteria, and several other lineages. This enzyme is characterized so far in Methanococcus jannaschii but appears restricted to F420-containing species and is predicted to carry out the same function in these other species. The clade represented by this model is one of two major divisions of proteins in pfam01933. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 297 matched cddid_all.tbl CDD TIGR01820 TIGR01820 273819 TrpE-arch anthranilate synthase component I, archaeal clade. This model represents an archaeal clade of anthranilate synthase component I enzymes. This enzyme is responsible for the first step of tryptophan biosynthesis from chorismate. The Sulfolobus enzyme has been reported to be part of a gene cluster for Trp biosynthesis [Amino acid biosynthesis, Aromatic amino acid family] 435 matched cddid_all.tbl CDD TIGR01821 TIGR01821 273820 5aminolev_synth 5-aminolevulinic acid synthase. This model represents 5-aminolevulinic acid synthase, an enzyme for one of two routes to the heme precursor 5-aminolevulinate. The protein is a pyridoxal phosphate-dependent enzyme related to 2-amino-3-ketobutyrate CoA tranferase and 8-amino-7-oxononanoate synthase. This enzyme appears restricted to the alpha Proteobacteria and mitochondrial derivatives. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 402 matched cddid_all.tbl CDD TIGR01822 TIGR01822 130881 2am3keto_CoA glycine C-acetyltransferase. This model represents a narrowly defined clade of animal and bacterial (almost exclusively Proteobacterial) 2-amino-3-ketobutyrate--CoA ligase, now called glycine C-acetyltransferase. This enzyme can act in threonine catabolism. The closest homolog from Bacillus subtilis, and sequences like it, may be functionally equivalent but were not included in the model because of difficulty in finding reports of function. [Energy metabolism, Amino acids and amines] 393 matched cddid_all.tbl CDD TIGR01823 TIGR01823 273821 PabB-fungal aminodeoxychorismate synthase, fungal clade. This model represents the fungal clade of a para-aminobenzoate synthesis enzyme, aminodeoxychorismate synthase, which acts on chorismate in a pathway that yields PABA, a precursor of folate. 742 matched cddid_all.tbl CDD TIGR01824 TIGR01824 130883 PabB-clade2 aminodeoxychorismate synthase, component I, clade 2. This clade of sequences is more closely related to TrpE (anthranilate synthase, TIGR00564/TIGR01820/TIGR00565) than to the better characterized group of PabB enzymes (TIGR00553/TIGR01823). This clade includes one characterized enzyme from Lactococcus and the conserved function across the clade is supported by these pieces of evidence: 1) all genomes with a member in this clade also have a separate TrpE gene, 2) none of these genomes contain an aparrent PabB from any of the other PabB clades, 3) none of these sequences are found in a region of the genome in association with other Trp biosynthesis genes, 4) all of these genomes aparrently contain most if not all of the steps of the folate biosynthetic pathway (for which PABA is a precursor). Many of the sequences hit by this model are annotated as TrpE enzymes, however, we believe that all members of this clade are, in fact, PabB. The sequences from Bacillus halodurans and subtilus which score below the trusted cutoff for this model are also likely to be PabB enzymes, but are too closely related to TrpE to be separated at this time. 355 matched cddid_all.tbl CDD TIGR01825 TIGR01825 130884 gly_Cac_T_rel pyridoxal phosphate-dependent acyltransferase, putative. This model represents an enzyme subfamily related to three known enzymes; it appears closest to glycine C-acteyltransferase, shows no overlap with it in species distribution, and may share that function. The three closely related enzymes are glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase), 5-aminolevulinic acid synthase, and 8-amino-7-oxononanoate synthase. All transfer the R-group (acetyl, succinyl, or 6-carboxyhexanoyl) from coenzyme A to an amino acid (Gly, Gly, Ala, respectively), with release of CO2 for the latter two reactions. 385 matched cddid_all.tbl CDD TIGR01826 TIGR01826 211689 CofD_related conserved hypothetical protein, cofD-related. This model represents a subfamily of conserved hypothetical proteins that forms a sister group to the family of CofD, (TIGR01819), LPPG:Fo 2-phospho-L-lactate transferase, an enzyme of cytochrome F420 biosynthesis. Both this family and TIGR01819 are within the scope of the pfam01933. [Hypothetical proteins, Conserved] 310 matched cddid_all.tbl CDD TIGR01827 TIGR01827 130886 gatC_rel Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase, subunit C, putative. This model represents a family small family related to GatC, the third subunit of an enzyme for completing the charging of tRNA(Gln) by amidating the Glu-tRNA(Gln). The few known archaea that contain a member of this family appear to produce Asn-tRNA(Asn) by an analogous amidotransferase reaction. This protein is proposed to substitute for GatC in the charging of both tRNAs. 73 matched cddid_all.tbl CDD TIGR01828 TIGR01828 273822 pyru_phos_dikin pyruvate, phosphate dikinase. This model represents pyruvate,phosphate dikinase, also called pyruvate,orthophosphate dikinase. It is similar in sequence to other PEP-utilizing enzymes. [Energy metabolism, Other] 856 matched cddid_all.tbl CDD TIGR01829 TIGR01829 273823 AcAcCoA_reduct acetoacetyl-CoA reductase. This model represent acetoacetyl-CoA reductase, a member of the family short-chain-alcohol dehydrogenases. Note that, despite the precision implied by the enzyme name, the reaction of EC 1.1.1.36 is defined more generally as (R)-3-hydroxyacyl-CoA + NADP+ = 3-oxoacyl-CoA + NADPH. Members of this family may act in the biosynthesis of poly-beta-hydroxybutyrate (e.g. Rhizobium meliloti) and related poly-beta-hydroxyalkanoates. Note that the member of this family from Azospirillum brasilense, designated NodG, appears to lack acetoacetyl-CoA reductase activity and to act instead in the production of nodulation factor. This family is downgraded to subfamily for this NodG. Other proteins designated NodG, as from Rhizobium, belong to related but distinct protein families. 242 matched cddid_all.tbl CDD TIGR01830 TIGR01830 273824 3oxo_ACP_reduc 3-oxoacyl-(acyl-carrier-protein) reductase. This model represents 3-oxoacyl-[ACP] reductase, also called 3-ketoacyl-acyl carrier protein reductase, an enzyme of fatty acid biosynthesis. [Fatty acid and phospholipid metabolism, Biosynthesis] 239 matched cddid_all.tbl CDD TIGR01831 TIGR01831 273825 fabG_rel 3-oxoacyl-(acyl-carrier-protein) reductase, putative. This model represents a small, very well conserved family of proteins closely related to the FabG family, TIGR01830, and possibly equal in function. In all completed genomes with a member of this family, a FabG in TIGR01830 is also found. [Fatty acid and phospholipid metabolism, Biosynthesis] 239 matched cddid_all.tbl CDD TIGR01832 TIGR01832 188170 kduD 2-deoxy-D-gluconate 3-dehydrogenase. This model describes 2-deoxy-D-gluconate 3-dehydrogenase (also called 2-keto-3-deoxygluconate oxidoreductase), a member of the family of short-chain-alcohol dehydrogenases (pfam00106). This protein has been characterized in Erwinia chrysanthemi as an enzyme of pectin degradation. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 248 matched cddid_all.tbl CDD TIGR01833 TIGR01833 273826 HMG-CoA-S_euk 3-hydroxy-3-methylglutaryl-CoA-synthase, eukaryotic clade. Hydroxymethylglutaryl(HMG)-CoA synthase is the first step of isopentenyl pyrophosphate (IPP) biosynthesis via the mevalonate pathway. This pathway is found mainly in eukaryotes, but also in archaea and some bacteria. This model is specific for eukaryotes. 457 matched cddid_all.tbl CDD TIGR01834 TIGR01834 273827 PHA_synth_III_E poly(R)-hydroxyalkanoic acid synthase, class III, PhaE subunit. This model represents the PhaE subunit of the heterodimeric class (class III) of polymerase for poly(R)-hydroxyalkanoic acids (PHAs), carbon and energy storage polymers of many bacteria. The most common PHA is polyhydroxybutyrate but about 150 different constituent hydroxyalkanoic acids (HAs) have been identified in various species. This model must be designated subfamily to indicate the heterogeneity of PHAs. [Cellular processes, Adaptations to atypical conditions, Fatty acid and phospholipid metabolism, Biosynthesis] 320 matched cddid_all.tbl CDD TIGR01835 TIGR01835 213655 HMG-CoA-S_prok 3-hydroxy-3-methylglutaryl CoA synthase, prokaryotic clade. This clade of hydroxymethylglutaryl-CoA (HMG-CoA) synthases is found in a limited spectrum of mostly gram-positive bacteria which make isopentenyl pyrophosphate (IPP) via the mevalonate pathway. This pathway is found primarily in eukaryotes and archaea, but the bacterial homologs are distinct, having aparrently diverged after being laterally transferred from an early eukaryote. HMG-CoA synthase is the first step in the pathway and joins acetyl-CoA with acetoacetyl-CoA with the release of one molecule of CoA. The Borellia sequence may have resulted from a separate lateral transfer event. 379 matched cddid_all.tbl CDD TIGR01836 TIGR01836 130895 PHA_synth_III_C poly(R)-hydroxyalkanoic acid synthase, class III, PhaC subunit. This model represents the PhaC subunit of a heterodimeric form of polyhydroxyalkanoic acid (PHA) synthase. Excepting the PhaC of Bacillus megaterium (which needs PhaR), all members require PhaE (TIGR01834) for activity and are designated class III. This enzyme builds ester polymers for carbon and energy storage that accumulate in inclusions, and both this enzyme and the depolymerase associate with the inclusions. Class III enzymes polymerize short-chain-length hydroxyalkanoates. [Fatty acid and phospholipid metabolism, Biosynthesis] 350 matched cddid_all.tbl CDD TIGR01837 TIGR01837 130896 PHA_granule_1 poly(hydroxyalkanoate) granule-associated protein. This model describes a domain found in some proteins associated with polyhydroxyalkanoate (PHA) granules in a subset of species that have PHA inclusion granules. Included are two tandem proteins of Pseudomonas oleovorans, PhaI and PhaF, and their homologs in related species. PhaF proteins have a low-complexity C-terminal region with repeats similar to AAAKP. [Fatty acid and phospholipid metabolism, Biosynthesis] 118 matched cddid_all.tbl CDD TIGR01838 TIGR01838 213656 PHA_synth_I poly(R)-hydroxyalkanoic acid synthase, class I. This model represents the class I subfamily of poly(R)-hydroxyalkanoate synthases, which polymerizes hydroxyacyl-CoAs with three to five carbons in the hydroxyacyl backbone into aliphatic esters termed poly(R)-hydroxyalkanoic acids. These polymers accumulate as carbon and energy storage inclusions in many species and can amount to 90 percent of the dry weight of cell. [Fatty acid and phospholipid metabolism, Biosynthesis] 532 matched cddid_all.tbl CDD TIGR01839 TIGR01839 130898 PHA_synth_II poly(R)-hydroxyalkanoic acid synthase, class II. This model represents the class II subfamily of poly(R)-hydroxyalkanoate synthases, which polymerizes hydroxyacyl-CoAs, typically with six to fourteen carbons in the hydroxyacyl backbone into aliphatic esters termed poly(R)-hydroxyalkanoic acids. These polymers accumulate as carbon and energy storage inclusions in many species and can amount to 90 percent of the dry weight of cell. [Fatty acid and phospholipid metabolism, Biosynthesis] 560 matched cddid_all.tbl CDD TIGR01840 TIGR01840 273828 esterase_phb esterase, PHB depolymerase family. This model describes a subfamily among lipases of the ab-hydrolase family. This subfamily includes bacterial depolymerases for poly(3-hydroxybutyrate) (PHB) and related polyhydroxyalkanoates (PHA), as well as acetyl xylan esterases, feruloyl esterases, and others from fungi. [Fatty acid and phospholipid metabolism, Degradation] 212 matched cddid_all.tbl CDD TIGR01841 TIGR01841 130900 phasin phasin family protein. This model describes a family of small proteins found associated with inclusions in bacterial cells. Most associate with polyhydroxyalkanoate (PHA) inclusions, the most common of which consist of polyhydroxybutyrate (PHB). These are designated granule-associate proteins or phasins; the member from Rhodospirillum rubrum is an activator of polyhydroxybutyrate (PHB) degradation. However, the member from Magnetospirillum sp. AMB-1 is called a magnetic particle membrane-specific GTPase. 88 matched cddid_all.tbl CDD TIGR01842 TIGR01842 200134 type_I_sec_PrtD type I secretion system ABC transporter, PrtD family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. [Protein fate, Protein and peptide secretion and trafficking] 544 matched cddid_all.tbl CDD TIGR01843 TIGR01843 130902 type_I_hlyD type I secretion membrane fusion protein, HlyD family. Type I secretion is an ABC transport process that exports proteins, without cleavage of any signal sequence, from the cytosol to extracellular medium across both inner and outer membranes. The secretion signal is found in the C-terminus of the transported protein. This model represents the adaptor protein between the ATP-binding cassette (ABC) protein of the inner membrane and the outer membrane protein, and is called the membrane fusion protein. This model selects a subfamily closely related to HlyD; it is defined narrowly and excludes, for example, colicin V secretion protein CvaA and multidrug efflux proteins. [Protein fate, Protein and peptide secretion and trafficking] 423 matched cddid_all.tbl CDD TIGR01844 TIGR01844 273829 type_I_sec_TolC type I secretion outer membrane protein, TolC family. Members of this model are outer membrane proteins from the TolC subfamily within the RND (Resistance-Nodulation-cell Division) efflux systems. These proteins, unlike the NodT subfamily, appear not to be lipoproteins. All are believed to participate in type I protein secretion, an ABC transporter system for protein secretion without cleavage of a signal sequence, although they may, like TolC, participate also in the efflux of smaller molecules as well. This family includes the well-documented examples TolC (E. coli), PrtF (Erwinia), and AprF (Pseudomonas aeruginosa). [Protein fate, Protein and peptide secretion and trafficking, Transport and binding proteins, Porins] 415 matched cddid_all.tbl CDD TIGR01845 TIGR01845 273830 outer_NodT efflux transporter, outer membrane factor (OMF) lipoprotein, NodT family. Members of this model comprise a subfamily of the Outer Membrane Factor (TCDB 1.B.17) porins. OMF proteins operate in conjunction with a primary transporter of the RND, MFS, ABC, or PET systems, and a MFP (membrane fusion protein) to tranport substrates across membranes. The complex thus formed allows transport (export) of various solutes (heavy metal cations; drugs, oligosaccharides, proteins, etc.) across the two envelopes of the Gram-negative bacterial cell envelope in a single energy-coupled step. Current data suggest that the OMF (and not the MFP) is largely responsible for the formation of both the trans-outer membrane and trans-periplasmic channels. The roles played by the MFP have yet to be determined. [Cellular processes, Detoxification, Transport and binding proteins, Porins] 460 matched cddid_all.tbl CDD TIGR01846 TIGR01846 273831 type_I_sec_HlyB type I secretion system ABC transporter, HlyB family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. [Protein fate, Protein and peptide secretion and trafficking] 694 matched cddid_all.tbl CDD TIGR01847 TIGR01847 130906 bacteriocin_sig bacteriocin-type signal sequence. Bacteriocins are bacterial peptide products toxic to closely related bacteria. This model represents the N-terminal region up to the GG cleavage motif. Processing to remove this bacteriocin leader peptide occurs together with export by an ABC transporter. Note: because this model is so small (15 amino acids), it may have many spurious high-scoring matches to unrelated proteins, even with fairly stringent cutoff scores. The most likely true positives are small proteins of Gram-positive bacteria, matching regions that start within the first 15 amino acids, and encoded near bacteriocin transport family proteins (TIGR01000, TIGR01193). 15 matched cddid_all.tbl CDD TIGR01848 TIGR01848 130907 PHA_reg_PhaR polyhydroxyalkanoate synthesis repressor PhaR. Poly-B-hydroxyalkanoates are lipidlike carbon/energy storage polymers found in granular inclusions. PhaR is a regulatory protein found in general near other proteins associated with polyhydroxyalkanoate (PHA) granule biosynthesis and utilization. It is found to be a DNA-binding homotetramer that is also capable of binding short chain hydroxyalkanoic acids and PHA granules. PhaR may regulate the expression of itself, of the phasins that coat granules, and of enzymes that direct carbon flux into polymers stored in granules. The C-terminal region is poorly conserved in this family and is not part of this model.//GO terms added 12/6/04 [SS] [Fatty acid and phospholipid metabolism, Biosynthesis, Regulatory functions, DNA interactions] 107 matched cddid_all.tbl CDD TIGR01849 TIGR01849 130908 PHB_depoly_PhaZ polyhydroxyalkanoate depolymerase, intracellular. This model represents an intracellular depolymerase for polyhydroxyalkanoate (PHA), a carbon and energy storing polyester that accumulates in granules in many bacterial species when carbon sources are abundant but other nutrients are limiting. This family is named for PHAs generally, rather than polyhydroxybutyrate (PHB) specificially as in Ralstonia eutropha H16, to avoid overcalling chemical specificity in other species. Note that this family lacks the classic GXSXG lipase motif and instead shows weak similarity to some [Fatty acid and phospholipid metabolism, Degradation] 406 matched cddid_all.tbl CDD TIGR01850 TIGR01850 273832 argC N-acetyl-gamma-glutamyl-phosphate reductase, common form. This model represents the more common of two related families of N-acetyl-gamma-glutamyl-phosphate reductase, an enzyme catalyzing the third step or Arg biosynthesis from Glu. The two families differ by phylogeny, similarity clustering, and the gap architecture in a multiple sequence alignment. Bacterial members of this family tend to be found within Arg biosynthesis operons. [Amino acid biosynthesis, Glutamate family] 346 matched cddid_all.tbl CDD TIGR01851 TIGR01851 273833 argC_other N-acetyl-gamma-glutamyl-phosphate reductase, uncommon form. This model represents the less common of two related families of N-acetyl-gamma-glutamyl-phosphate reductase, an enzyme catalyzing the third step or Arg biosynthesis from Glu. The two families differ by phylogeny, similarity clustering, and gap architecture in a multiple sequence alignment. [Amino acid biosynthesis, Glutamate family] 310 matched cddid_all.tbl CDD TIGR01852 TIGR01852 188173 lipid_A_lpxA acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase. This model describes LpxA, an enzyme for the biosynthesis of lipid A, a component oflipopolysaccharide (LPS) in the outer membrane outer leaflet of most Gram-negative bacteria. Some differences are found between lipid A of different species, but this protein represents the first step (from UDP-N-acetyl-D-glucosamine) and appears to be conserved in function. Proteins from this family contain many copies of the bacterial transferase hexapeptide repeat (pfam00132). [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 254 matched cddid_all.tbl CDD TIGR01853 TIGR01853 273834 lipid_A_lpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase LpxD. This model describes LpxD, an enzyme for the biosynthesis of lipid A, a component oflipopolysaccharide (LPS) in the outer membrane outer leaflet of most Gram-negative bacteria. Some differences are found between lipid A of different species. This protein represents the third step from UDP-N-acetyl-D-glucosamine. The group added at this step generally is 14:0(3-OH) (myristate) but may vary; in Aquifex it appears to be 16:0(3-OH) (palmitate). [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 324 matched cddid_all.tbl CDD TIGR01854 TIGR01854 273835 lipid_A_lpxH UDP-2,3-diacylglucosamine diphosphatase. This model represents LpxH, UDP-2,3-diacylglucosamine hydrolase, and essential enzyme in E. coli that catalyzes the fourth step in lipid A biosynthesis. Note that Pseudomonas aeruginosa has both a member of this family that shares this function and a more distant homolog, designated LpxH2, that does not. Many species that produce lipid A lack an lpxH gene in this family; some of those species have an lpxH2 gene instead, although for which the function is unknown. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 231 matched cddid_all.tbl CDD TIGR01855 TIGR01855 273836 IMP_synth_hisH imidazole glycerol phosphate synthase, glutamine amidotransferase subunit. This model represents the glutamine amidotransferase subunit (or domain, in eukaryotic systems) of imidazole glycerol phosphate synthase. This subunit catalyzes step 5 of histidine biosynthesis from PRPP. The other subunit, the cyclase, catalyzes step 6. [Amino acid biosynthesis, Histidine family] 196 matched cddid_all.tbl CDD TIGR01856 TIGR01856 273837 hisJ_fam histidinol phosphate phosphatase, HisJ family. This model represents the histidinol phosphate phosphatase HisJ of Bacillus subtilis, and related proteins from a number of species within a larger family of phosphatases in the PHP hydrolase family. HisJ catalyzes the penultimate step of histidine biosynthesis but shows no homology to the functionally equivalent sequence in E. coli, a domain of the bifunctional HisB protein. Note, however, that many species have two members and that Clostridium perfringens, predicted not to make histidine, has five members of this family; this family is designated subfamily rather than equivalog to indicate that members may not all act as HisJ. 253 matched cddid_all.tbl CDD TIGR01857 TIGR01857 130916 FGAM-synthase phosphoribosylformylglycinamidine synthase, clade II. This model represents a single-molecule form of phosphoribosylformylglycinamidine synthase, also called FGAM synthase, an enzyme of purine de novo biosynthesis. This model represents a second clade of these enzymes found in Clostridia, Bifidobacteria and Streptococcus species. This enzyme performs the fourth step in IMP biosynthesis (the precursor of all purines) from PRPP. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 1239 matched cddid_all.tbl CDD TIGR01858 TIGR01858 130917 tag_bisphos_ald class II aldolase, tagatose bisphosphate family. This model describes tagatose-1,6-bisphosphate aldolases, and perhaps other closely related class II aldolases. This tetrameric, Zn2+-dependent enzyme is related to the class II fructose bisphosphate aldolase; fructose 1,6-bisphosphate and tagatose 1,6 bisphosphate differ only in chirality at C4. 282 matched cddid_all.tbl CDD TIGR01859 TIGR01859 130918 fruc_bis_ald_ fructose-1,6-bisphosphate aldolase, class II, various bacterial and amitochondriate protist. This model represents of one of several subtypes of the class II fructose-1,6-bisphosphate aldolase, an enzyme of glycolysis. The subtypes are split into several models to allow separation of a family of tagatose bisphosphate aldolases. This form is found in Gram-positive bacteria, a variety of Gram-negative, and in amitochondriate protists. The class II enzymes share homology with tagatose bisphosphate aldolase but not with class I aldolase. [Energy metabolism, Glycolysis/gluconeogenesis] 282 matched cddid_all.tbl CDD TIGR01860 TIGR01860 130919 VNFD nitrogenase vanadium-iron protein, alpha chain. This model represents the alpha chain of the vanadium-containing component of the vanadium-iron nitrogenase compound I. The complex also includes a second alpha chain, two beta chains and two delta chains. Compount I interacts with compound II also known as the iron-protein which transfers electrons to compound I where the catalysis occurs. [Central intermediary metabolism, Nitrogen fixation] 461 matched cddid_all.tbl CDD TIGR01861 TIGR01861 130920 ANFD nitrogenase iron-iron protein, alpha chain. This model represents the all-iron variant of the nitrogenase component I alpha chain. Molybdenum-iron and vanadium iron forms are also found. The complete complex contains two alpha chains, two beta chains and two delta chains. The component I associates with component II also known as the iron protein which serves to provide electrons for component I. [Central intermediary metabolism, Nitrogen fixation] 513 matched cddid_all.tbl CDD TIGR01862 TIGR01862 273838 N2-ase-Ialpha nitrogenase component I, alpha chain. This model represents the alpha chain of all three varieties (Mo-Fe, V-Fe, and Fe-Fe) of component I of nitrogenase. [Central intermediary metabolism, Nitrogen fixation] 443 matched cddid_all.tbl CDD TIGR01863 TIGR01863 273839 cas_Csd1 CRISPR-associated protein Cas8c/Csd1, subtype I-C/DVULG. CRISPR loci appear to be mobile elements with a wide host range. This model represents a protein that tends to be found near CRISPR repeats of the DVULG subtype of CRISPR/Cas locus. We designate this family Csd1 (CRISPR/Cas Subtype DVULG protein 1). The species range for this subtype, so far, is exclusively bacterial and mesophilic, although CRISPR loci in general are particularly common among archaea and thermophilic bacteria. In a few species (Xanthomonas axonopodis pv. citri str. 306 and Streptococcus mutans UA159), homology to this protein family is split across two tandem genes; the trusted cutoff to this family is set low enough to capture at least the longer of the two. 584 matched cddid_all.tbl CDD TIGR01865 TIGR01865 273840 cas_Csn1 CRISPR subtype II/NMENI RNA-guided endonuclease Cas9/Csn1. CRISPR loci appear to be mobile elements with a wide host range. This model represents a protein found only in CRISPR-containing species, near other CRISPR-associated proteins (cas), as part of the NMENI subtype of CRISPR/Cas locus. The species range so far for this protein is animal pathogens and commensals only. 805 matched cddid_all.tbl CDD TIGR01866 TIGR01866 273841 cas_Csn2 CRISPR type II-A/NMEMI-associated protein Csn2. CRISPR loci appear to be mobile elements with a wide host range. This model represents a protein found only in CRISPR-containing species, near other CRISPR-associated proteins (cas), as part of the NMENI subtype of CRISPR/Cas loci. The species range so far for this subtype is animal pathogens and commensals only. This protein is present in some but not all NMENI CRISPR/Cas loci. 222 matched cddid_all.tbl CDD TIGR01868 TIGR01868 273842 casD_Cas5e CRISPR-associated protein Cas5/CasD, subtype I-E/ECOLI. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family is part of the ECOLI subtype CRISPR/Cas locus, and now characterized as part of the CASCADE complex of that system. It shares a small N-terminal homology region with members of several other CRISPR/Cas subtypes, and we view the families that share this region as being Cas5. 216 matched cddid_all.tbl CDD TIGR01869 TIGR01869 273843 casC_Cse4 CRISPR-associated protein Cas7/Cse4/CasC, subtype I-E/ECOLI. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family is represented by CT1975 of Chlorobium tepidum and is part of the Ecoli subtype of CRISPR/Cas locis. It is designated Cse4, for CRISPR/Cas Subtype Ecoli protein 4. 325 matched cddid_all.tbl CDD TIGR01870 TIGR01870 273844 cas_TM1810_Csm2 CRISPR type III-A/MTUBE-associated protein Csm2. These proteins are found adjacent to a characteristic short, palidromic repeat cluster termed CRISPR, a probable mobile DNA element. This model represents the C-terminal domain of a minor family of CRISPR-associated protein from the Mtube subtype of CRISPR/Cas locus. The family is designated Csm2, for CRISPR/Cas Subtype Mtube Protein 2. 97 matched cddid_all.tbl CDD TIGR01873 TIGR01873 233610 cas_CT1978 CRISPR-associated endoribonuclease Cas2, subtype I-E/ECOLI. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model represents a minor branch of the Cas2 family of CRISPR-associated endonuclease, whereas most Cas2 proteins are modeled instead by TIGR01573. This form of Cas2 is characteristic for the Ecoli subtype of CRISPR/Cas locus. 87 matched cddid_all.tbl CDD TIGR01874 TIGR01874 273845 cas_cas5a CRISPR-associated protein Cas5, subtype I-A/APERN. This model represents a minor family of CRISPR-associated (Cas) protein. These proteins are found adjacent to a characteristic short, palidromic repeat cluster termed CRISPR, a probable mobile DNA element. This family belongs to a set of several Cas proteins, one each for a number of different CRISPR/Cas subtypes, that share a region of N-terminal sequence similarity modeled by TIGR02593. The family is designated Cas5a, for CRISPR-associated protein Cas5, Apern subtype. 172 matched cddid_all.tbl CDD TIGR01875 TIGR01875 273846 cas_MJ0381 CRISPR-associated autoregulator DevR family. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This model represents one such family, represented by MJ0381 of Methanococcus jannaschii. This family includes the DevR protein of Myxococcus xanthus, a protein whose expression appears to regulated through a number of means, including both location and autorepression; DevR mutants are incapable of fruiting body development. [Regulatory functions, DNA interactions, , ] 237 matched cddid_all.tbl CDD TIGR01876 TIGR01876 273847 cas_Cas5d CRISPR-associated protein Cas5, subtype I-C/DVULG. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This small Cas family is represented by CT1134 of Chlorobium tepidum. This family belongs to a set of several Cas protein families, one each for a number of different CRISPR/Cas subtypes, that share a region of N-terminal sequence similarity modeled by TIGR02593. This family represents the Dvulg subtype of CRISPR/Cas locus. 203 matched cddid_all.tbl CDD TIGR01877 TIGR01877 273848 cas_cas6 CRISPR-associated endoribonuclease Cas6. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This broadly distributed, highly divergent Cas family is now characterized as an endoribonuclease that generates guide RNAs for host defense against phage and other invaders. The family contains a C-terminal motif GXGXXXXXGXG, where the each X between two Gly is hydrophobic and the spacer XXXXX contains (usually) one Arg or Lys. The seed alignment for the current version of this model has gappy columns removed. Members of this protein family are found associated with several different CRISPR/cas system subtypes, and consequently we designate this family Cas6. 199 matched cddid_all.tbl CDD TIGR01878 TIGR01878 273849 cas_Csa5 CRISPR type I-A/APERN-associated protein Csa5. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model represents a minor family of Cas protein found in the (all archaeal) APERN subtype of CRISPR/Cas locus, so the family is designated Csa5, for CRISPR/Cas Subtype Protein 5. 97 matched cddid_all.tbl CDD TIGR01879 TIGR01879 200138 hydantase amidase, hydantoinase/carbamoylase family. Enzymes in this subfamily hydrolize the amide bonds of compounds containing carbamoyl groups or hydantoin rings. These enzymes are members of the broader family of amidases represented by pfam01546. 400 matched cddid_all.tbl CDD TIGR01880 TIGR01880 273850 Ac-peptdase-euk N-acyl-L-amino-acid amidohydrolase. This model represents a family of eukaryotic N-acyl-L-amino-acid amidohydrolases active on fatty acid and acetyl amides of L-amino acids. 400 matched cddid_all.tbl CDD TIGR01881 TIGR01881 273851 cas_Cmr5 CRISPR type III-B/RAMP module-associated protein Cmr5. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model family, represented by TM1791.1 of Thermotoga maritima, is found in both archaeal and bacterial species as part of the 6-gene CRISPR RAMP module. 127 matched cddid_all.tbl CDD TIGR01882 TIGR01882 130937 peptidase-T peptidase T. This model represents a tripeptide aminopeptidase known as Peptidase T, which has a substrate preference for hydrophobic peptides. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 410 matched cddid_all.tbl CDD TIGR01883 TIGR01883 162579 PepT-like peptidase T-like protein. This model represents a clade of enzymes closely related to Peptidase T, an aminotripeptidase found in bacteria. This clade consists of gram positive bacteria of which several additionally contain a Peptidase T gene. 361 matched cddid_all.tbl CDD TIGR01884 TIGR01884 273852 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity. [Regulatory functions, DNA interactions, , ] 203 matched cddid_all.tbl CDD TIGR01885 TIGR01885 273853 Orn_aminotrans ornithine aminotransferase. This model describes the final step in the biosynthesis of ornithine from glutamate via the non-acetylated pathway. Ornithine amino transferase takes L-glutamate 5-semialdehyde and makes it into ornithine, which is used in the urea cycle, as well as in the biosynthesis of arginine. This model includes low-GC bacteria and eukaryotic species. The genes from two species are annotated as putative acetylornithine aminotransferases - one from Porphyromonas gingivalis (OMNI|PG1271), and the other from Staphylococcus aureus (OMNI|SA0170). After homology searching using BLAST it was determined that these two sequences were most closely related to ornithine aminotransferases. This model's seed includes one characterized hit, from Bacillus subtilis (SP|P38021). 401 matched cddid_all.tbl CDD TIGR01886 TIGR01886 130941 dipeptidase dipeptidase PepV. This model represents a small clade of dipeptidase enzymes which are members of the larger M25 subfamily of metalloproteases. Two characterized enzymes are included in the seed. One, from Lactococcus lactis has been shown to act on a wide range of dipeptides, but not larger peptides. The enzyme from Lactobacillus delbrueckii was originally characterized as a Xaa-His dipeptidase, specifically a carnosinase (beta-Ala-His) by complementation of an E. coli mutant. Further study, including the crystallization of the enzyme, has shown it to also be a non-specific dipeptidase. This group also includes enzymes from Streptococcus and Enterococcus. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 466 matched cddid_all.tbl CDD TIGR01887 TIGR01887 273854 dipeptidaselike "dipeptidase, putative. This model represents a clade of probable zinc dipeptidases, closely related to the characterized non-specific dipeptidase, PepV. Many enzymes in this clade have been given names including the terms ""Xaa-His"" and ""carnosinase"" due to the early mis-characterization of the Lactobacillus delbrueckii PepV enzyme. These names are likely too specific." 447 matched cddid_all.tbl CDD TIGR01888 TIGR01888 273855 cas_cmr3 CRISPR type III-B/RAMP module-associated protein Cmr3. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This highly divergent family is found in at least ten different archaeal and bacterial species as part of the CRISPR RAMP modulue but is not a member of the RAMP superfamily itself. A typical example is TM1793 from Thermotoga maritima. 333 matched cddid_all.tbl CDD TIGR01889 TIGR01889 130944 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam01047. [Regulatory functions, DNA interactions] 109 matched cddid_all.tbl CDD TIGR01890 TIGR01890 273856 N-Ac-Glu-synth "amino-acid N-acetyltransferase. This model represents a clade of amino-acid N-acetyltransferases acting mainly on glutamate in the first step of the ""acetylated"" ornithine biosynthesis pathway. For this reason it is also called N-acetylglutamate synthase. The enzyme may also act on aspartate. [Amino acid biosynthesis, Glutamate family]" 429 matched cddid_all.tbl CDD TIGR01891 TIGR01891 273857 amidohydrolases amidohydrolase. This model represents a subfamily of amidohydrolases which are a subset of those sequences detected by pfam01546. Included within this group are hydrolases of hippurate (N-benzylglycine), indoleacetic acid (IAA) N-conjugates of amino acids, N-acetyl-L-amino acids and aminobenzoylglutamate. These hydrolases are of the carboxypeptidase-type, most likely utilizing a zinc ion in the active site. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 363 matched cddid_all.tbl CDD TIGR01892 TIGR01892 130947 AcOrn-deacetyl "acetylornithine deacetylase (ArgE). This model represents a clade of acetylornithine deacetylases from proteobacteria. This enzyme is the final step of the ""acetylated"" ornithine biosynthesis pathway. The enzyme is closely related to dapE, succinyl-diaminopimelate desuccinylase, and outside of this clade annotation is very inaccurate as to which function should be ascribed to genes. [Amino acid biosynthesis, Glutamate family]" 364 matched cddid_all.tbl CDD TIGR01893 TIGR01893 273858 aa-his-dipept Xaa-His dipeptidase. This model represents a clade of dipeptidase enzymes, many of which are specific for carnosine (beta-alanyl-histidine). This enzymes is found broadly in bacteria and at least one archaeon (Methanosarcina). In most species there is only one sequence hitting this model, while Bacteroides thetaiotaomicron, Chlorobium tepidum and Clostridium perfringens have two each and Fusobacterium nucleatum has three. These may indicate that there is a broader substrate range than just carnosine in these (and other) species. 8/19/03 GO terms added [SS] 477 matched cddid_all.tbl CDD TIGR01894 TIGR01894 273859 cas_TM1795_cmr1 CRISPR type III-B/RAMP module RAMP protein Cmr1. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model represents the region of stongest conservation, the N-terminal half, of one such family, represented by TM1795 from Thermotoga maritima. This protein is the first of a set of six genes, mostly from the RAMP superfamily, that we designated the CRISPR-associated RAMP module. 154 matched cddid_all.tbl CDD TIGR01895 TIGR01895 273860 cas_Cas5t CRISPR-associated protein Cas5, subtype I-B/TNEAP. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This family is represented by TM1800 from Thermotoga maritima. It is related to TIGR01868 (CRISPR-associated protein, CT1976 family). 215 matched cddid_all.tbl CDD TIGR01896 TIGR01896 273861 cas_AF1879 CRISPR-associated protein Cas4/Csa1, subtype I-A/APERN. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model describes a particularly strongly conserved family found so only in the APERN subtype of CRISPR/Cas loci and represented by AF1879 from Archaeoglobus fulgidus. This family has four perfectly preserved Cys residues. This subfamily is found in a CRISPR/Cas locus we designate APERN, so the family is designated Csa1, for CRISPR/Cas Subtype Protein 1. 271 matched cddid_all.tbl CDD TIGR01897 TIGR01897 273862 cas_MJ1666 CRISPR-associated protein, MJ1666 family. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model describes a Cas protein about 400 residues in length, found mostly in the Archaea but also in Aquifex. 410 matched cddid_all.tbl CDD TIGR01898 TIGR01898 213662 cas_TM1791_cmr6 CRISPR type III-B/RAMP module RAMP protein Cmr6. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This family, represented by TM1791 of Thermotoga maritima, is designated Cmr6 [sic], for CRISPR/Cas Ramp Module protein 6. This family is both closely related to and frequently encoded next to the TM1792 family of Cas proteins described by TIGR01867. The two proteins are fused in an example from Methanopyrus kandleri. 176 matched cddid_all.tbl CDD TIGR01899 TIGR01899 273863 cas_TM1807_csm5 CRISPR type III-A/MTUBE-associated RAMP protein Csm5. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. Members of this cas gene family are found in the mtube subtype of CRISPR/cas locus and designated Csm5, for CRISPR/cas Subtype Mtube, protein 5. 365 matched cddid_all.tbl CDD TIGR01900 TIGR01900 273864 dapE-gram_pos succinyl-diaminopimelate desuccinylase. This model represents a clade of succinyl-diaminopimelate desuccinylases from actinobacteria (high-GC gram positives), delta-proteobacteria and aquificales and is based on the characterization of the enzyme from Corynebacterium glutamicum. This enzyme is involved in the biosynthesis of lysine, and is related to the enzyme acetylornithine deacetylase and other amidases and peptidases found within pfam01546. Other sequences included in the seed of this model were assessed to confirm that 1) the related genes DapC (succinyl-diaminopimelate transaminase) and DapD (2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase) are also found in the genome, 2) each is found only once in those genomes, 3) the lysine biosynthesis pathway is complete and 4) the direct (TIGR03540 or TIGR03542) or acetylated (GenProp0787) aminotransferase pathways are absent in thes genomes. Additionally, a number of the seed members are observed adjacent to either DapC or DapD (often as a divergon with a putative promoter site between them. [Amino acid biosynthesis, Aspartate family] 351 matched cddid_all.tbl CDD TIGR01901 TIGR01901 273865 adhes_NPXG filamentous hemagglutinin family N-terminal domain. This model represents a conserved domain found near the N-terminus of a number of large, repetitive bacterial proteins, including many proteins of over 2500 amino acids. Members generally have a signal sequence, then an intervening region, then the region described by this model. Following this region, proteins typically have regions rich in repeats but may show no homology between the repeats of one member and the repeats of another. A number of the members of this family have been designated adhesins, filamentous haemagglutinins, heme/hemopexin-binding protein, etc. 79 matched cddid_all.tbl CDD TIGR01902 TIGR01902 130957 dapE-lys-deAc N-acetyl-ornithine/N-acetyl-lysine deacetylase. This clade of mainly archaeal and related bacterial species contains two characterized enzymes, an deacetylase with specificity for both N-acetyl-ornithine and N-acetyl-lysine from Thermus, which is found within a lysine biosynthesis operon, and a fusion protein with acetyl-glutamate kinase (an enzyme of ornithine biosynthesis) from Lactobacillus. It is possible that all of the sequences within this clade have dual specificity, or that a mix of specificities have evolved within this clade. 336 matched cddid_all.tbl CDD TIGR01903 TIGR01903 273866 cas5_csm4 CRISPR type III-A/MTUBE-associated RAMP protein Csm4. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. Members of this cas gene family are found in the mtube subtype of CRISPR/cas locus and designated Csm4, for CRISPR/cas Subtype Mtube, protein 4. 297 matched cddid_all.tbl CDD TIGR01904 TIGR01904 273867 GSu_C4xC__C2xCH Geobacter sulfurreducens CxxxxCH...CXXCH domain. This domain occurs from three to eight times in eight different proteins of Geobacter sulfurreducens. The final CXXCH motif matches ProSite motif PS00190, the cytochrome c family heme-binding site signature, suggesting 42 matched cddid_all.tbl CDD TIGR01905 TIGR01905 213663 paired_CXXCH_1 doubled CXXCH domain. This model represents a domain of about 41 amino acids that contains, among other motifs, two copies of the motif CXXCH associated with heme binding. Almost every member of this family has at least three copies of this domain (at least six copies of CXXCH) is predicted to be a high molecular weight c-type cytochrome. Members are found mostly in species of Shewanella, Geobacter, and Vibrio. 41 matched cddid_all.tbl CDD TIGR01906 TIGR01906 273868 integ_TIGR01906 integral membrane protein TIGR01906. This model represents a family of highly hydrophobic, uncharacterized predicted integral membrane proteins found almost entirely in low-GC Gram-positive bacteria, although a member is also found in the early-branching bacterium Aquifex aeolicus. 207 matched cddid_all.tbl CDD TIGR01907 TIGR01907 273869 casE_Cse3 CRISPR-associated protein Cas6/Cse3/CasE, subtype I-E/ECOLI. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model family, represented by CT1974 from Chlorobium tepidum, is found in the Ecoli subtype of CRISPR/Cas regions and is designated Cse3 (CRISPR/Cas Subtype Ecoli protein 3). The representative of this family from Thermus thermophilus HB8 (TTHB192) has been crystallized and found to have a structure consisting of two domains with opposing parallel beta-sheets known as a beta-sheet platform. This structure is similar to those found in the Sex-lethal protein and poly(A)-binding protein. This structure is consistent with an RNA-binding function. 206 matched cddid_all.tbl CDD TIGR01908 TIGR01908 162595 cas_CXXC_CXXC CRISPR-associated protein Cas8b1/Cst1, subtype I-B/TNEAP. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This (revised) model describes a conserved region from an otherwise highly divergent protein found in the Tneap subtype of CRISPR/Cas regions. This Cys-rich region features two motifs of CXXC. 309 matched cddid_all.tbl CDD TIGR01909 TIGR01909 213664 C_GCAxxG_C_C C_GCAxxG_C_C family probable redox protein. This model represents a putative redox-active protein of about 140 residues, with four perfectly conserved Cys residues. It includes a CGAXXG motif. Most members are found within one or two loci of transporter or oxidoreductase genes. A member from Geobacter sulfurreducens, located in a molybdenum transporter operon, has a TAT (twin-arginine translocation) signal sequence for Sec-independent transport across the plasma membrane, a hallmark of bound prosthetic groups such as FeS clusters. 120 matched cddid_all.tbl CDD TIGR01910 TIGR01910 273870 DapE-ArgE acetylornithine deacetylase or succinyl-diaminopimelate desuccinylase. This group of sequences contains annotations for both acetylornithine deacetylase and succinyl-diaminopimelate desuccinylase, but does not contain any members with experimental characterization. Bacillus, Staphylococcus and Sulfolobus species contain multiple hits to this subfamily and each may have a separate activity. Determining which is which must await further laboratory research. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 375 matched cddid_all.tbl CDD TIGR01911 TIGR01911 188182 HesB_rel_seleno HesB-like selenoprotein. This model represents a family of small proteins related to HesB and its close homologs, which are likely to be invovlved in iron-sulfur cluster assembly (See TIGR00049 and pfam01521). Several members are selenoproteins, with a TGA codon and Sec residue that aligns to the conserved Cys of the HesB domain. A variable Cys/Ser/Gly-rich C-terminal region is not included in the seed alignment and model. [Unknown function, General] 92 matched cddid_all.tbl CDD TIGR01912 TIGR01912 162597 TatC-Arch Twin arginine targeting (Tat) protein translocase TatC, Archaeal clade. This model represents the TatC translocase component of the Sec-independent protein translocation system. This system is responsible for translocation of folded proteins, often with bound cofactors across the periplasmic membrane. A related model (TIGR00945) represents the bacterial clade of this family. TatC is often found (in bacteria) in a gene cluster with the two other components of the system, TatA/E (TIGR01411) and TatB (TIGR01410). A model also exists for the Twin-arginine signal sequence (TIGR01409). 237 matched cddid_all.tbl CDD TIGR01913 TIGR01913 273871 bet_lambda phage recombination protein Bet. This model represents the phage recombination protein Bet from a number of phage, including phage lambda. All members of this family are found in phage genomes or in putative prophage regions of bacterial genomes. [Mobile and extrachromosomal element functions, Prophage functions] 180 matched cddid_all.tbl CDD TIGR01914 TIGR01914 273872 cas_Csa4 CRISPR-associated protein Cas8a2/Csa4, subtype I-A/APERN. CRISPR loci appear to be mobile elements with a wide host range. This model represents a protein that tends to be found near CRISPR repeats. The species range for this species, so far, is exclusively archaeal. It is found so far in only four different species, and includes two tandem genes in Pyrococcus furiosus DSM 3638. This subfamily is found in a CRISPR/Cas locus we designate APERN, so the family is designated Csa4, for CRISPR/Cas Subtype Protein 4. 354 matched cddid_all.tbl CDD TIGR01915 TIGR01915 273873 npdG NADPH-dependent F420 reductase. This model represents a subset of a parent family described by pfam03807. Unlike the parent family, members of this family are found only in species with evidence of coenzyme F420. All members of this family are believed to act as NADPH-dependent F420 reductase. [Energy metabolism, Electron transport] 219 matched cddid_all.tbl CDD TIGR01916 TIGR01916 273874 F420_cofE coenzyme F420-0:L-glutamate ligase. This model represents an enzyme of coenzyme F(420) biosynthesis, as catalyzed by MJ0768 of Methanococcus jannaschii and by the N-terminal half of FbiB of Mycobacterium bovis strain BCG. Note that only two glutamates are ligated in M. jannaschii, but five to six in the Mycobacterium lineage. In M. jannaschii, CofE catalyzes the GTP-dependent addition of two L-glutamates. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 243 matched cddid_all.tbl CDD TIGR01917 TIGR01917 130972 gly_red_sel_B glycine reductase, selenoprotein B. Glycine reductase is a complex with two selenoprotein subunits, A and B. This model represents the glycine reductase selenoprotein B. Closely related to it, but excluded from this model, are selenoprotein B subunits of betaine reductase and sarcosine reductase. All contain selenocysteine incorporated during translation at a specific UGA codon. 431 matched cddid_all.tbl CDD TIGR01918 TIGR01918 130973 various_sel_PB selenoprotein B, glycine/betaine/sarcosine/D-proline reductase family. This model represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. This model is built in fragment mode to assist in recognizing fragmentary translations. All members are expected to contain an internal TGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon. 431 matched cddid_all.tbl CDD TIGR01919 TIGR01919 273875 hisA-trpF 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase/N-(5'phosphoribosyl)anthranilate isomerase. This model represents a bifunctional protein posessing both hisA (1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase) and trpF (N-(5'phosphoribosyl)anthranilate isomerase) activities. Thus, it is involved in both the histidine and tryptophan biosynthetic pathways. Enzymes with this property have been described only in the Actinobacteria (High-GC gram-positive). The enzyme is closely related to the monofunctional HisA proteins (TIGR00007) and in Actinobacteria, the classical monofunctional TrpF is generally absent. 243 matched cddid_all.tbl CDD TIGR01920 TIGR01920 273876 Shik_kin_archae shikimate kinase. This model represents the shikimate kinase (SK) gene found in archaea which is only distantly related to homoserine kinase (thrB) and not atr all to the bacterial SK enzyme. The SK from M. janaschii has been overexpressed in E. coli and characterized. SK catalyzes the fifth step of the biosynthesis of chorismate from D-erythrose-4-phosphate and phosphoenolpyruvate. [Amino acid biosynthesis, Aromatic amino acid family] 261 matched cddid_all.tbl CDD TIGR01921 TIGR01921 273877 DAP-DH diaminopimelate dehydrogenase. This model represents the diaminopimelate dehydrogenase enzyme which provides an alternate (shortcut) route of lysine buiosynthesis in Corynebacterium, Bacterioides, Porphyromonas and scattered other species. The enzyme from Corynebacterium glutamicum has been crystallized and characterized. 324 matched cddid_all.tbl CDD TIGR01922 TIGR01922 273878 purO_arch IMP cyclohydrolase. This model represents IMP cyclohydrolase, the final step in the biosynthesis of inosine monophosphate (IMP) in archaea. In bacteria this step is catalyzed by a bifunctional enzyme (purH). 199 matched cddid_all.tbl CDD TIGR01923 TIGR01923 162605 menE O-succinylbenzoate-CoA ligase. This model represents an enzyme, O-succinylbenzoate-CoA ligase, which is involved in the fourth step of the menaquinone biosynthesis pathway. O-succinylbenzoate-CoA ligase, together with menB - naphtoate synthase, take 2-succinylbenzoate and convert it into 1,4-di-hydroxy-2- naphtoate. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 436 matched cddid_all.tbl CDD TIGR01924 TIGR01924 273879 rsbW_low_gc serine-protein kinase RsbW. This model describes the anti-sigma B factor also known as serine-protein kinase RsbW. Sigma B controls the general stress regulon in B subtilis and is activated by cell stresses such as stationary phase and heat shock. RsbW binds to sigma B and prevents formation of the transcription complex at the promoter. RsbV (anti-anti-sigma factor) binds to RsbW to inhibit association with sigma B, however RsbW can phosphorylate RsbV, causing disassociation of the RsbV/RsbW complex. Low ATP level or environmental stress causes the dephosphorylation of RsbV. 159 matched cddid_all.tbl CDD TIGR01925 TIGR01925 130980 spIIAB anti-sigma F factor. This model describes the SpoIIAB anti-sigma F factor. Sigma F regulates spore development in B subtilis. SpoIIAB binds to sigma F, preventing formation of the transcription complex at the promoter. SpoIIAA (anti-anti-sigma F factor) binds to SpoIIAB to inhibit association with sigma F, however SpoIIAB can phosphorylate SpoIIAA, causing disassociation of the SpoIIAA/B complex. The SpoIIE phosphatase dephosphorylates SpoIIAA. [Regulatory functions, Protein interactions, Cellular processes, Sporulation and germination] 137 matched cddid_all.tbl CDD TIGR01926 TIGR01926 130981 peroxid_rel uncharacterized peroxidase-related enzyme. This protein family with length of about 200 amino acids. One member, from Myxococcus xanthus, is a selenoprotein, with an otherwise conserved Cys replaced by Sec. This family is drawn narrowly enough to suggest that These proteins contain a domain described by TIGR00778, with a CxxCxxxHxxxxxxxG motif. Some members of that family are known to act as peroxidases or correlate with resistance to oxidative stress. 177 matched cddid_all.tbl CDD TIGR01927 TIGR01927 273880 menC_gamma/gm+ o-succinylbenzoate synthase. This model describes the enzyme o-succinylbenzoic acid synthetase (menC) that is involved in one of the steps of the menaquinone biosynthesis pathway. It takes SHCHC and makes it into 2-succinylbenzoate. Included in this model are gamma proteobacteria and archaea. Many of the com-names of the proteins identified by the model are identified as O-succinylbenzoyl-CoA synthase in error. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 307 matched cddid_all.tbl CDD TIGR01928 TIGR01928 213667 menC_lowGC/arch o-succinylbenzoate synthase. This model describes the enzyme o-succinylbenzoic acid synthetase (menC) that is involved in one of the steps of the menaquinone biosynthesis pathway. It takes SHCHC and makes it into 2-succinylbenzoate. Included in this model are low GC gram positive bacteria and archaea. Also included in the seed and in the model are enzymes with the com-name of N-acylamino acid racemase (or the more general term, racemase / racemase family), which refers to the enzyme's industrial application as racemases, and not to its biological function as o-succinylbenzoic acid synthetase. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 324 matched cddid_all.tbl CDD TIGR01929 TIGR01929 200143 menB naphthoate synthase (dihydroxynaphthoic acid synthetase). This model represents an enzyme, naphthoate synthase (dihydroxynaphthoic acid synthetase), which is involved in the fifth step of the menaquinone biosynthesis pathway. Together with o-succinylbenzoate-CoA ligase (menE: TIGR01923), this enzyme takes 2-succinylbenzoate and converts it into 1,4-di-hydroxy-2-naphthoate. Included above the trusted cutoff are two enzymes from Arabadopsis thaliana and one from Staphylococcus aureus which are identified as putative enoyl-CoA hydratase/isomerases. These enzymes group with the naphthoate synthases when building a tree and when doing BLAST searches. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 259 matched cddid_all.tbl CDD TIGR01930 TIGR01930 273881 AcCoA-C-Actrans "acetyl-CoA acetyltransferases. This model represents a large family of enzymes which catalyze the thiolysis of a linear fatty acid CoA (or acetoacetyl-CoA) using a second CoA molecule to produce acetyl-CoA and a CoA-ester product two carbons shorter (or, alternatively, the condensation of two molecules of acetyl-CoA to produce acetoacetyl-CoA and CoA). This enzyme is also known as ""thiolase"", ""3-ketoacyl-CoA thiolase"", ""beta-ketothiolase"" and ""Fatty oxidation complex beta subunit"". When catalyzing the degradative reaction on fatty acids the corresponding EC number is 2.3.1.16. The condensation reaction corresponds to 2.3.1.9. Note that the enzymes which catalyze the condensation are generally not involved in fatty acid biosynthesis, which is carried out by a decarboxylating condensation of acetyl and malonyl esters of acyl carrier proteins. Rather, this activity may produce acetoacetyl-CoA for pathways such as IPP biosynthesis in the absence of sufficient fatty acid oxidation. [Fatty acid and phospholipid metabolism, Other]" 385 matched cddid_all.tbl CDD TIGR01931 TIGR01931 273882 cysJ sulfite reductase [NADPH] flavoprotein, alpha-component. This model describes an NADPH-dependent sulfite reductase flavoprotein subunit. Most members of this family are found in Cys biosynthesis gene clusters. The closest homologs below the trusted cutoff are designated as subunits nitrate reductase. 597 matched cddid_all.tbl CDD TIGR01932 TIGR01932 273883 hflC HflC protein. HflK and HflC are paralogs encoded by tandem genes in Proteobacteria, spirochetes, and some other bacterial lineages. The HflKC complex is anchored in the membrane and exposed to the periplasm. The complex is not active as a protease, but rather binds to and appears to modulate the ATP-dependent protease FtsH. The overall function of HflKC is not fully described. [Protein fate, Degradation of proteins, peptides, and glycopeptides, Regulatory functions, Protein interactions] 317 matched cddid_all.tbl CDD TIGR01933 TIGR01933 130988 hflK HflK protein. HflK and HflC are paralogs encoded by tandem genes in Proteobacteria, spirochetes, and some other bacterial lineages. The HflKC complex is anchored in the membrane and exposed to the periplasm. The complex is not active as a protease, but rather binds to and appears to modulate the ATP-dependent protease FtsH. The overall function of HflKC is not fully described.//Regulation of FtsH by HflKC appears to be negative (SS 8/27/03] 261 matched cddid_all.tbl CDD TIGR01934 TIGR01934 273884 MenG_MenH_UbiE ubiquinone/menaquinone biosynthesis methyltransferases. This model represents a family of methyltransferases involved in the biosynthesis of menaquinone and ubiqinone. Some members such as the UbiE enzyme from E. coli are believed to act in both pathways, while others may act in only the menaquinone pathway. These methyltransferases are members of the UbiE/CoQ family of methyltransferases (pfam01209) which also contains ubiquinone methyltransferases and other methyltransferases. Members of this clade include a wide distribution of bacteria and eukaryotes, but no archaea. An outgroup for this clade is provided by the phosphatidylethanolamine methyltransferase (EC 2.1.1.17) from Rhodobacter sphaeroides. Note that a number of non-orthologous genes which are members of pfam03737 have been erroneously annotated as MenG methyltransferases. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 223 matched cddid_all.tbl CDD TIGR01935 TIGR01935 130990 NOT-MenG "RraA famliy. The E. coli member of this family has been characterized as a regulator of RNase E and its crystal structure has been analyzed. This model was initially classified as a ""hypothetical equivalog"" expressing the tentative hypothesis that all members might have the same function as the E. coli enzyme. Considering the second clade of enterobacterial sequences within this family, that appears to be less tenable. The function of these sequences outside of the narrow RraA equivalog model (TIGR02998) remains obscure. All of these were initially annotated as MenG, AKA S-adenosylmethionine: 2-demethylmenaquinone methyltransferase (EC 2.1.-.-). See the references characterizing this as a case of transitive annotation error in the case of the E. coli protein. [Unknown function, General]" 150 matched cddid_all.tbl CDD TIGR01936 TIGR01936 273885 nqrA NADH:ubiquinone oxidoreductase, Na(+)-translocating, A subunit. This model represents the NqrA subunit of the six-protein, Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria. This oxidoreductase complex functions primarily as a sodium ion pump. [Transport and binding proteins, Cations and iron carrying compounds] 447 matched cddid_all.tbl CDD TIGR01937 TIGR01937 130992 nqrB NADH:ubiquinone oxidoreductase, Na(+)-translocating, B subunit. This model represents the NqrB subunit of the six-protein, Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria. This oxidoreductase complex functions primarily as a sodium ion pump. [Transport and binding proteins, Cations and iron carrying compounds] 413 matched cddid_all.tbl CDD TIGR01938 TIGR01938 273886 nqrC NADH:ubiquinone oxidoreductase, Na(+)-translocating, C subunit. This model represents the NqrC subunit of the six-protein, Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria. This oxidoreductase complex functions primarily as a sodium ion pump. [Transport and binding proteins, Cations and iron carrying compounds] 251 matched cddid_all.tbl CDD TIGR01939 TIGR01939 130994 nqrD NADH:ubiquinone oxidoreductase, Na(+)-translocating, D subunit. This model represents the NqrD subunit of the six-protein, Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria. This oxidoreductase complex functions primarily as a sodium ion pump. [Transport and binding proteins, Cations and iron carrying compounds] 207 matched cddid_all.tbl CDD TIGR01940 TIGR01940 130995 nqrE NADH:ubiquinone oxidoreductase, Na(+)-translocating, E subunit. This model represents the NqrE subunit of the six-protein, Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria. This oxidoreductase complex functions primarily as a sodium ion pump. [Transport and binding proteins, Cations and iron carrying compounds] 200 matched cddid_all.tbl CDD TIGR01941 TIGR01941 130996 nqrF NADH:ubiquinone oxidoreductase, Na(+)-translocating, F subunit. This model represents the NqrF subunit of the six-protein, Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria. This oxidoreductase complex functions primarily as a sodium ion pump. [Transport and binding proteins, Cations and iron carrying compounds] 405 matched cddid_all.tbl CDD TIGR01942 TIGR01942 130997 pcnB poly(A) polymerase. This model describes the pcnB family of poly(A) polymerases (also known as plasmid copy number protein). These enzymes sequentially add adenosine nucleotides to the 3' end of RNAs, targeting them for degradation by the cell. This was originally described for anti-sense RNAs, but was later demonstrated for mRNAs as well. Members of this family are as yet limited to the gamma- and beta-proteobacteria, with putative members in the Chlamydiacae and spirochetes. This family has homology to tRNA nucleotidyltransferase (cca). 410 matched cddid_all.tbl CDD TIGR01943 TIGR01943 130998 rnfA electron transport complex, RnfABCDGE type, A subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the A subunit. [Energy metabolism, Electron transport] 190 matched cddid_all.tbl CDD TIGR01944 TIGR01944 273887 rnfB electron transport complex, RnfABCDGE type, B subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the B subunit. [Energy metabolism, Electron transport] 165 matched cddid_all.tbl CDD TIGR01945 TIGR01945 273888 rnfC electron transport complex, RnfABCDGE type, C subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the C subunit. [Energy metabolism, Electron transport] 435 matched cddid_all.tbl CDD TIGR01946 TIGR01946 131001 rnfD electron transport complex, RnfABCDGE type, D subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the A subunit. [Energy metabolism, Electron transport] 327 matched cddid_all.tbl CDD TIGR01947 TIGR01947 273889 rnfG electron transport complex, RnfABCDGE type, G subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the A subunit. [Energy metabolism, Electron transport] 186 matched cddid_all.tbl CDD TIGR01948 TIGR01948 162619 rnfE electron transport complex, RnfABCDGE type, E subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the E subunit. [Energy metabolism, Electron transport] 196 matched cddid_all.tbl CDD TIGR01949 TIGR01949 273890 AroFGH_arch predicted phospho-2-dehydro-3-deoxyheptonate aldolase. This model represents a clade of sequences related to fructose-bisphosphate aldolase (class I, included within pfam01791). The members of this clade appear to be phospho-2-dehydro-3-deoxyheptonate aldolases. This enzyme is the first step of the chorismate biosynthesis pathway. Evidence for this assignment is based on gene clustering and phylogenetic profiling. A group of species lack members of the three other types of phospho-2-dehydro-3-deoxyheptonate aldolase (represented by TIGR00034, TIGR01358 and TIGR01361), and also aparrently lack the well-known forms of step 2 (3-dehydroquinate synthase), but contain all other steps of the pathway: Desulfovibrio, Aquifex, Archaeoglobus, Halobacterium, Methanopyrus, Methanococcus and Methanobacterium. The clade of sequences represented here is limited strictly to this group of organisms. In Desulfovibrio, Aquifex, Archaeoglobus, Halobacterium and Methanosarcina the genes found by this model are clustered with other genes from the chorismate, phenylalanine, tyrosine and tryptophan biosynthesis pathways. In addition, these genes in Desulfovibrio, Archaeoglobus, Halobacterium, Methanosarcina and Methanopyrus are adjacent to a gene which hits pfam01959 which also has the property of having members only in those species which lack steps 1 and 2. Together these two genes appear to perform the synthesis of 3-dehydroquinate. It is presumed that the substrates and the chemical transformations involved are identical, but this has not yet been proven experimentally. 258 matched cddid_all.tbl CDD TIGR01950 TIGR01950 131005 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species. [Cellular processes, Detoxification, Regulatory functions, DNA interactions] 142 matched cddid_all.tbl CDD TIGR01951 TIGR01951 273891 nusB transcription antitermination factor NusB. A transcription antitermination complex active in many bacteria was designated N-utilization substance (Nus) in E. coli because of its interaction with phage lambda protein N. This model represents NusB. Other components are NusA and NusG. NusE is, in fact, ribosomal protein S10. [Transcription, Transcription factors] 129 matched cddid_all.tbl CDD TIGR01952 TIGR01952 273892 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea. 141 matched cddid_all.tbl CDD TIGR01953 TIGR01953 273893 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids. [Transcription, Transcription factors] 341 matched cddid_all.tbl CDD TIGR01954 TIGR01954 273894 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic. [Transcription, Transcription factors] 50 matched cddid_all.tbl CDD TIGR01955 TIGR01955 131010 RfaH transcription elongation factor/antiterminator RfaH. This model represents the transcription elongation factor/antiterminator, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes. [Transcription, Transcription factors] 159 matched cddid_all.tbl CDD TIGR01956 TIGR01956 273895 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member. 258 matched cddid_all.tbl CDD TIGR01957 TIGR01957 273896 nuoB_fam NADH-quinone oxidoreductase, B subunit. This model describes the B chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. The quinone is plastoquinone in Synechocystis (where the chain is designated K) and in chloroplast, where NADH may be replaced by NADPH. In the methanogenic archaeal genus Methanosarcina, NADH is replaced by F420H2. [Energy metabolism, Electron transport] 145 matched cddid_all.tbl CDD TIGR01958 TIGR01958 131013 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria. [Energy metabolism, Electron transport] 148 matched cddid_all.tbl CDD TIGR01959 TIGR01959 131014 nuoF_fam NADH-quinone oxidoreductase, F subunit. This model describes the F chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoF. This family does not have any members in chloroplast or cyanobacteria, where the quinone may be plastoquinone and NADH may be replaced by NADPH, nor in Methanosarcina, where NADH is replaced by F420H2. [Energy metabolism, Electron transport] 411 matched cddid_all.tbl CDD TIGR01960 TIGR01960 131015 ndhF3_CO2 NAD(P)H dehydrogenase, subunit NdhF3 family. This family represents a subfamily of NAD(P)H dehydrogenase subunit 5, or ndhF. It is restricted to two paralogs in each completed cyanobacterial genome, in which several subtypes of ndhF are found. Included in this family is NdhF3, shown to play a role in high-affinity CO2 uptake in Synechococcus sp. PCC7002. In all cases, neighboring genes include a paralog of ndhD but do include other NAD(P)H dehydrogenase subunits. Instead, genes related to C02 uptake tend to be found nearby. 606 matched cddid_all.tbl CDD TIGR01961 TIGR01961 273897 NuoC_fam NADH (or F420H2) dehydrogenase, subunit C. This model describes the C subunit of the NADH dehydrogenase complex I in bacteria, as well as many instances of the corresponding mitochondrial subunit (NADH dehydrogenase subunit 9) and of the F420H2 dehydrogenase in Methanosarcina. Complex I contains subunits designated A-N. This C subunit often occurs as a fusion protein with the D subunit. This model excludes the NAD(P)H and plastoquinone-dependent form of chloroplasts and [Energy metabolism, Electron transport] 121 matched cddid_all.tbl CDD TIGR01962 TIGR01962 273898 NuoD NADH dehydrogenase I, D subunit. This model recognizes specificially the D subunit of NADH dehydrogenase I complex. It excludes the related chain of NAD(P)H-quinone oxidoreductases from chloroplast and Synechocystis, where the quinone may be plastoquinone rather than ubiquinone. This subunit often appears as a C/D fusion. [Energy metabolism, Electron transport] 386 matched cddid_all.tbl CDD TIGR01963 TIGR01963 211705 PHB_DH 3-hydroxybutyrate dehydrogenase. This model represents a subfamily of the short chain dehydrogenases. Characterized members so far as 3-hydroxybutyrate dehydrogenases and are found in species that accumulate ester polmers called polyhydroxyalkanoic acids (PHAs) under certain conditions. Several members of the family are from species not known to accumulate PHAs, including Oceanobacillus iheyensis and Bacillus subtilis. However, polymer formation is not required for there be a role for 3-hydroxybutyrate dehydrogenase; it may be members of this family have the same function in those species. 255 matched cddid_all.tbl CDD TIGR01964 TIGR01964 213671 chpXY CO2 hydration protein. This small family of proteins includes paralogs ChpX and ChpY in Synechococcus sp. PCC7942 and other cyanobacteria, associated with distinct NAD(P)H dehydrogenase complexes. These proteins collectively enable light-dependent CO2 hydration and CO2 uptake; loss of both blocks growth at low CO2 concentrations. [Energy metabolism, Photosynthesis] 367 matched cddid_all.tbl CDD TIGR01965 TIGR01965 273899 VCBS_repeat VCBS repeat. This domain of about 100 residues is found multiple (up to 35) copies in long proteins from several species of Vibrio, Colwellia, Bradyrhizobium, and Shewanella (hence the name VCBS) and in smaller copy numbers in proteins from several other bacteria. The large protein size and repeat copy numbers, species distribution, and suggested activities of several member proteins suggests a role for this domain in adhesion. 99 matched cddid_all.tbl CDD TIGR01966 TIGR01966 131021 RNasePH ribonuclease PH. This bacterial enzyme, ribonuclease PH, performs the final 3'-trimming and modification of tRNA precursors. This model is restricted absolutely to bacteria. Related families outside the model include proteins described as probable exosome complex exonucleases (rRNA processing) and polyribonucleotide nucleotidyltransferases (mRNA degradation). The most divergent member within the family is RNase PH from Deinococcus radiodurans. [Transcription, RNA processing] 236 matched cddid_all.tbl CDD TIGR01967 TIGR01967 273900 DEAH_box_HrpA RNA helicase HrpA. This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. The HrpA/B homolog from Borrelia is 500 amino acids shorter but appears to be derived from HrpA rather than HrpB. [Unknown function, Enzymes of unknown specificity] 1283 matched cddid_all.tbl CDD TIGR01968 TIGR01968 131023 minD_bact septum site-determining protein MinD. This model describes the bacterial and chloroplast form of MinD, a multifunctional cell division protein that guides correct placement of the septum. The homologous archaeal MinD proteins, with many archaeal genomes having two or more forms, are described by a separate model. [Cellular processes, Cell division] 261 matched cddid_all.tbl CDD TIGR01969 TIGR01969 131024 minD_arch cell division ATPase MinD, archaeal. This model represents the archaeal branch of the MinD family. MinD, a weak ATPase, works in bacteria with MinC as a generalized cell division inhibitor and, through interaction with MinE, prevents septum placement inappropriate sites. Often several members of this family are found in archaeal genomes, and the function is uncharacterized. More distantly related proteins ParA chromosome partitioning proteins. The exact roles of the various archaeal MinD homologs are unknown. 251 matched cddid_all.tbl CDD TIGR01970 TIGR01970 273901 DEAH_box_HrpB ATP-dependent helicase HrpB. This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing. [Unknown function, Enzymes of unknown specificity] 819 matched cddid_all.tbl CDD TIGR01971 TIGR01971 273902 NuoI "NADH-quinone oxidoreductase, chain I. This model represents the I subunit (one of 14: A->N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This model excludes ""I"" subunits from the closely related F420H2 dehydrogenase and formate hydrogenlyase complexes. [Energy metabolism, Electron transport]" 122 matched cddid_all.tbl CDD TIGR01972 TIGR01972 273903 NDH_I_M proton-translocating NADH-quinone oxidoreductase, chain M. This model describes the 13th (based on E. coli) structural gene, M, of bacterial NADH dehydrogenase I, as well as chain 4 of the corresponding mitochondrial complex I and of the chloroplast NAD(P)H dehydrogenase complex. [Energy metabolism, Electron transport] 481 matched cddid_all.tbl CDD TIGR01973 TIGR01973 273904 NuoG NADH-quinone oxidoreductase, chain G. This model represents the G subunit (one of 14: A->N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This model excludes related subunits from formate dehydrogenase complexes. [Energy metabolism, Electron transport] 602 matched cddid_all.tbl CDD TIGR01974 TIGR01974 273905 NDH_I_L proton-translocating NADH-quinone oxidoreductase, chain L. This model describes the 12th (based on E. coli) structural gene, L, of bacterial NADH dehydrogenase I, as well as chain 5 of the corresponding mitochondrial complex I and subunit 5 (or F) of the chloroplast NAD(P)H-plastoquinone dehydrogenase complex. [Energy metabolism, Electron transport] 609 matched cddid_all.tbl CDD TIGR01975 TIGR01975 131030 isoAsp_dipep isoaspartyl dipeptidase IadA. The L-isoaspartyl derivative of Asp arises non-enzymatically over time as a form of protein damage. In this isomerization, the connectivity of the polypeptide changes to pass through the beta-carboxyl of the side chain. Much but not all of this damage can be repaired by protein-L-isoaspartate (D-aspartate) O-methyltransferase. This model describes the isoaspartyl dipeptidase IadA, apparently one of two such enzymes in E. coli, an enzyme that degrades isoaspartyl dipeptides and may unblock degradation of proteins that cannot be repaired. This model also describes closely related proteins from other species (e.g. Clostridium perfringens, Thermoanaerobacter tengcongensis) that we assume to be equivalent in function. This family shows homology to dihydroorotases. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 389 matched cddid_all.tbl CDD TIGR01976 TIGR01976 273906 am_tr_V_VC1184 cysteine desulfurase family protein, VC1184 subfamily. This model describes a subfamily of probable pyridoxal phosphate-dependent enzymes in the aminotransferase class V family (pfam00266). The most closely related characterized proteins are active as cysteine desulfurases, selenocysteine lyases, or both; some are involved in FeS cofactor biosynthesis and are designated NifS. An active site Cys residue present in those sequences, in motifs resembling GHHC or GSAC, is not found in this family. The function of members of this family is unknown, but seems unlike to be as an aminotransferase. [Unknown function, Enzymes of unknown specificity] 397 matched cddid_all.tbl CDD TIGR01977 TIGR01977 131032 am_tr_V_EF2568 cysteine desulfurase family protein. This model describes a subfamily of probable pyridoxal phosphate-dependent enzymes in the aminotransferase class V family. Related families contain members active as cysteine desulfurases, selenocysteine lyases, or both. The members of this family form a distinct clade and all are shorter at the N-terminus. The function of this subfamily is unknown. [Unknown function, Enzymes of unknown specificity] 376 matched cddid_all.tbl CDD TIGR01978 TIGR01978 273907 sufC FeS assembly ATPase SufC. SufC is part of the SUF system, shown in E. coli to consist of six proteins and believed to act in Fe-S cluster formation during oxidative stress. SufC forms a complex with SufB and SufD. SufC belongs to the ATP-binding cassette transporter family (pfam00005) but is no longer thought to be part of a transporter. The complex is reported as cytosolic () or associated with the membrane (). The SUF system also includes a cysteine desulfurase (SufS, enhanced by SufE) and a probable iron-sulfur cluster assembly scaffold protein, SufA. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 243 matched cddid_all.tbl CDD TIGR01979 TIGR01979 131034 sufS cysteine desulfurases, SufSfamily. This model represents a subfamily of NifS-related cysteine desulfurases involved in FeS cluster formation needed for nitrogen fixation among other vital functions. Many cysteine desulfurases are also active as selenocysteine lyase and/or cysteine sulfinate desulfinase. This subfamily is associated with the six-gene SUF system described in E. coli and Erwinia as an FeS cluster formation system during oxidative stress. The active site Cys is this subfamily resembles GHHC with one or both His conserved. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 403 matched cddid_all.tbl CDD TIGR01980 TIGR01980 131035 sufB FeS assembly protein SufB. This protein, SufB, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 448 matched cddid_all.tbl CDD TIGR01981 TIGR01981 273908 sufD FeS assembly protein SufD. This protein, SufD, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. SufB and SufD are homologous. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 275 matched cddid_all.tbl CDD TIGR01982 TIGR01982 273909 UbiB 2-polyprenylphenol 6-hydroxylase. This model represents the enzyme (UbiB) which catalyzes the first hydroxylation step in the ubiquinone biosynthetic pathway in bacteria. It is believed that the reaction is 2-polyprenylphenol -> 6-hydroxy-2-polyprenylphenol. This model finds hits primarily in the proteobacteria. The gene is also known as AarF in certain species. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 437 matched cddid_all.tbl CDD TIGR01983 TIGR01983 273910 UbiG ubiquinone biosynthesis O-methyltransferase. This model represents an O-methyltransferase believed to act at two points in the ubiquinone biosynthetic pathway in bacteria (UbiG) and fungi (COQ3). A separate methylase (MenG/UbiE) catalyzes the single C-methylation step. The most commonly used names for genes in this family do not indicate whether this gene is an O-methyl, or C-methyl transferase. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 224 matched cddid_all.tbl CDD TIGR01984 TIGR01984 273911 UbiH 2-polyprenyl-6-methoxyphenol 4-hydroxylase. This model represents the FAD-dependent monoxygenase responsible for the second hydroxylation step in the aerobic ubiquinone bioynthetic pathway. The scope of this model is limited to the proteobacteria. This family is closely related to the UbiF hydroxylase which catalyzes the final hydroxylation step. The enzyme has also been named VisB due to a mutant VISible light sensitive phenotype. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 382 matched cddid_all.tbl CDD TIGR01985 TIGR01985 131040 phasin_2 "phasin. This model represents a family of granule-associate proteins (phasins) which are part of the polyhydroxyalkanoate synthesis machinery. This family is based on a pair of characterized genes from Methylobacterium extorquens. Members of the seed for this model all contain the rest of the components believed to be essential for this system (see the ""polyhydroxyalkanoic acid synthesis"" property in the GenPropDB). Members of this family score below trusted to another phasin model, TIGR01841 and together may represent a subfamily or broader equivalog." 112 matched cddid_all.tbl CDD TIGR01986 TIGR01986 273912 glut_syn_euk glutathione synthetase, eukaryotic. This model represents the eukaryotic glutathione synthetase, which shows little resemblance to the analogous enzyme of Gram-negative bacteria (TIGR01380). In the Kinetoplastida, trypanothione replaces glutathione, but can be made from glutathione; a sequence from Leishmania is not included in the seed, is highly divergent, and therefore scores between the trusted and noise cutoffs. 472 matched cddid_all.tbl CDD TIGR01987 TIGR01987 131042 HI0074 nucleotidyltransferase substrate binding protein, HI0074 family. The member of this family from Haemophilus influenzae, HI0074, has been shown by crystal structure to resemble nucleotidyltransferase substrate binding proteins. It forms a complex with HI0073, encoded by the adjacent gene and containing a nucleotidyltransferase nucleotide binding domain (pfam01909). 123 matched cddid_all.tbl CDD TIGR01988 TIGR01988 273913 Ubi-OHases Ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family. This model represents a family of FAD-dependent hydroxylases (monooxygenases) which are all believed to act in the aerobic ubiquinone biosynthesis pathway. A separate set of hydroxylases, as yet undiscovered, are believed to be active under anaerobic conditions. In E. coli three enzyme activities have been described, UbiB (which acts first at position 6, see TIGR01982), UbiH (which acts at position 4) and UbiF (which acts at position 5). UbiH and UbiF are similar to one another and form the basis of this subfamily. Interestingly, E. coli contains another hydroxylase gene, called visC, that is highly similar to UbiF, adjacent to UbiH and, when mutated, results in a phenotype similar to that of UbiH (which has also been named visB). Several other species appear to have three homologs in this family, although they assort themselves differently on phylogenetic trees (e.g. Xylella and Mesorhizobium) making it difficult to ascribe a specific activity to each one. Eukaryotes appear to have only a single homolog in this subfamily (COQ6) which complements UbiH, but also possess a non-orthologous gene, COQ7 which complements UbiF. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 385 matched cddid_all.tbl CDD TIGR01989 TIGR01989 273914 COQ6 ubiquinone biosynthesis monooxygenase COQ6. This model represents the monooxygenase responsible for the 4-hydroxylateion of the phenol ring in the aerobic biosynthesis of ubiquinone 437 matched cddid_all.tbl CDD TIGR01990 TIGR01990 213672 bPGM beta-phosphoglucomutase. This model represents the beta-phosphoglucomutase enzyme which catalyzes the interconverison of beta-D-glucose-1-phosphate and beta-D-glucose-6-phosphate. The 6-phosphate is capable of non-enzymatic anomerization (alpha <-> beta) while the 1-phosphate is not. A separate enzyme is responsible for the isomerization of the alpha anomers. Beta-D-glucose-1-phosphate results from the phosphorylysis of maltose (2.4.1.8), trehalose (2.4.1.64) or trehalose-6-phosphate (2.4.1.216). Alternatively, these reactions can be run in the synthetic direction to create the disaccharides. All sequenced genomes which contain a member of this family also appear to contain at least one putative maltose or trehalose phosphorylase. Three species, Lactococcus, Enterococcus and Neisseria appear to contain a pair of paralogous beta-PGM's. Beta-phosphoglucomutase is a member of the haloacid dehalogenase superfamily of hydrolase enzymes. These enzymes are characterized by a series of three catalytic motifs positioned within an alpha-beta (Rossman) fold. beta-PGM contains an inserted alpha helical domain in between the first and second conserved motifs and thus is a member of subfamily IA of the superfamily. The third catalytic motif comes in three variants, the third of which, containing a conserved DD or ED, is the only one found here as well as in several other related enzymes (TIGR01509). The enzyme from L. lactis has been extensively characterized including a remarkable crystal structure which traps the pentacoordinate transition state. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 185 matched cddid_all.tbl CDD TIGR01991 TIGR01991 273915 HscA Fe-S protein assembly chaperone HscA. The Heat Shock Cognate proteins HscA and HscB act together as chaperones. HscA resembles DnaK but belongs in a separate clade. The apparent function is to aid assembly of iron-sulfur cluster proteins. Homologs from Buchnera and Wolbachia are clearly in the same clade but are highly derived and score lower than some examples of DnaK. [Protein fate, Protein folding and stabilization] 599 matched cddid_all.tbl CDD TIGR01992 TIGR01992 273916 PTS-IIBC-Tre PTS system, trehalose-specific IIBC component. This model represents the fused enzyme II B and C components of the trehalose-specific PTS sugar transporter system. Trehalose is converted to trehalose-6-phosphate in the process of translocation into the cell. These transporters lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). The exceptions to this rule are Staphylococci and Streptococci which contain their own A domain as a C-terminal fusion. This family is closely related to the sucrose transporting PTS IIBC enzymes and the B and C domains of each are described by subfamily-domain level TIGRFAMs models (TIGR00826 and TIGR00852, respectively). In E. coli, B. subtilis and P. fluorescens the presence of this gene is associated with the presence of trehalase which degrades T6P to glucose and glucose-6-P. Trehalose may also be transported (in Salmonella) via the mannose PTS or galactose permease systems, or (in Sinorhizobium, Thermococcus and Sulfolobus, for instance) by ABC transporters. 462 matched cddid_all.tbl CDD TIGR01993 TIGR01993 273917 Pyr-5-nucltdase pyrimidine 5'-nucleotidase. This family of proteins includes the SDT1/SSM1 gene from yeast which has been shown to code for a pyrimidine (UMP/CMP) 5'nucleotidase. The family spans plants, fungi and a small number of bacteria. These enzymes are members of the haloacid dehalogenase (HAD) superfamily of hydrolases, specifically the IA subfamily (variant 3, TIGR01509). 183 matched cddid_all.tbl CDD TIGR01994 TIGR01994 273918 SUF_scaf_2 SUF system FeS assembly protein, NifU family. Three iron-sulfur cluster assembly systems are known so far. ISC is broadly distributed while NIF tends to be associated with nitrogenase in nitrogen-fixing bacteria. The most recently described is SUF, believed to be important to maintain the function during aerobic stress of enzymes with labile Fe-S clusters. It is fairly widely distributed. This family represents one of two different proteins proposed to act as a scaffold on which the Fe-S cluster is built and from which it is transferred. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 137 matched cddid_all.tbl CDD TIGR01995 TIGR01995 273919 PTS-II-ABC-beta PTS system, beta-glucoside-specific IIABC component. This model represents a family of PTS enzyme II proteins in which all three domains are found in the same polypeptide chain and which appear to have a broad specificity for beta-glucosides including salicin (beta-D-glucose-1-salicylate) and arbutin (Hydroquinone-O-beta-D-glucopyranoside). These are distinct from the closely related sucrose-specific and trehalose-specific PTS transporters. 610 matched cddid_all.tbl CDD TIGR01996 TIGR01996 131051 PTS-II-BC-sucr PTS system, sucrose-specific IIBC component. This model represents the fused enzyme II B and C components of the sucrose-specific PTS sugar transporter system. Sucrose is converted to sucrose-6-phosphate in the process of translocation into the cell. Some of these transporters lack their own IIA domains and instead use the glucose IIA protein (IIAglc or Crr). The exceptions to this rule are Staphylococci, Streptococci, Lactococci, Lactobacilli, etc. which contain their own A domain as a C-terminal fusion. This family is closely related to the trehalose transporting PTS IIBC enzymes and the B and C domains of each are described by subfamily-domain level TIGRFAMs models (TIGR00826 and TIGR00852, respectively). 461 matched cddid_all.tbl CDD TIGR01997 TIGR01997 131052 sufA_proteo FeS assembly scaffold SufA. This model represents the SufA protein of the SUF system of iron-sulfur cluster biosynthesis. This system performs FeS biosynthesis even during oxidative stress and tends to be absent in obligate anaerobic and microaerophilic bacteria. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 107 matched cddid_all.tbl CDD TIGR01998 TIGR01998 273920 PTS-II-BC-nag "PTS system, N-acetylglucosamine-specific IIBC component. This model represents the combined B and C domains of the PTS transport system enzyme II specific for N-acetylglucosamine transport. Many of the genes in this family also include an A domain as part of the same polypeptide and thus should be given the name ""PTS system, N-acetylglucosamine-specific IIABC component"". This family is most closely related to the glucose-specific PTS enzymes. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids]" 475 matched cddid_all.tbl CDD TIGR01999 TIGR01999 188192 iscU FeS cluster assembly scaffold IscU. This model represents IscU, a homolog of the N-terminal region of NifU, an Fe-S cluster assembly protein found mostly in nitrogen-fixing bacteria. IscU is considered part of the IscSUA-hscAB-fdx system of Fe-S assembly, whereas NifU is found in nitrogenase-containing (nitrogen-fixing) species. A NifU-type protein is also found in Helicobacter and Campylobacter. IscU and NifU are considered scaffold proteins on which Fe-S clusters are assembled before transfer to apoproteins. This model excludes true NifU proteins as in Klebsiella pneumoniae and Anabaena sp. as well as archaeal homologs. It includes largely proteobacterial and eukaryotic forms. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 124 matched cddid_all.tbl CDD TIGR02000 TIGR02000 273921 NifU_proper Fe-S cluster assembly protein NifU. Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Central intermediary metabolism, Nitrogen fixation] 290 matched cddid_all.tbl CDD TIGR02001 TIGR02001 273922 gcw_chp conserved hypothetical protein, proteobacterial. This model represents a conserved hypothetical protein about 240 residues in length found so far in Proteobacteria including Shewanella oneidensis, Ralstonia solanacearum, and Colwellia psychrerythraea, usually as part of a paralogous family. The function is unknown. 243 matched cddid_all.tbl CDD TIGR02002 TIGR02002 273923 PTS-II-BC-glcB "PTS system, glucose-specific IIBC component. This model represents the combined B and C domains of the PTS transport system enzyme II specific for glucose transport. Many of the genes in this family also include an A domain as part of the same polypeptide and thus should be given the name ""PTS system, glucose-specific IIABC component"" while the B. subtilus enzyme also contains an enzyme III domain which appears to act independently of the enzyme II domains. This family is most closely related to the N-acetylglucosamine-specific PTS enzymes (TIGR01998). [Transport and binding proteins, Carbohydrates, organic alcohols, and acids]" 502 matched cddid_all.tbl CDD TIGR02003 TIGR02003 131058 PTS-II-BC-unk1 PTS system, IIBC component. This model represents a family of fused B and C components of PTS enzyme II. This clade is a member of a larger family which contains enzyme II's specific for a variety of sugars including glucose (TIGR02002) and N-acetylglucosamine (TIGR01998). None of the members of this clade have been experimentally characterized. This clade includes sequences from Streptococcus and Enterococcus which also include a C-terminal A domain as well as Bacillus and Clostridium which do not. In nearly all cases, these species also contain an authentic glucose-specific PTS transporter. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 548 matched cddid_all.tbl CDD TIGR02004 TIGR02004 273924 PTS-IIBC-malX PTS system, maltose and glucose-specific IIBC component. This model represents a family of PTS enzyme II fused B and C components including and most closely related to the MalX maltose and glucose-specific transporter of E. coli. A pair of paralogous genes from E. coli strain CFT073 score between trusted and noise and may have diverged sufficiently to have an altered substrate specificity. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 517 matched cddid_all.tbl CDD TIGR02005 TIGR02005 273925 PTS-IIBC-alpha PTS system, alpha-glucoside-specific IIBC component. This model represents a family of fused PTS enzyme II B and C domains. A gene from Clostridium has been partially characterized as a maltose transporter, while genes from Fusobacterium and Klebsiella have been proposed to transport the five non-standard isomers of sucrose. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 524 matched cddid_all.tbl CDD TIGR02006 TIGR02006 131061 IscS cysteine desulfurase IscS. This model represents IscS, one of several cysteine desulfurases from a larger protein family designated (misleadingly, in this case) class V aminotransferases. IscS is one of at least 6 enzymes characteristic of the IscSUA-hscAB-fsx system of iron-sulfur cluster assembly. Scoring almost as well as proteobacterial sequences included in the model are mitochondrial cysteine desulfurases, apparently from an analogous system in eukaryotes. The sulfur, taken from cysteine, may be used in other systems as well, such as tRNA base modification and biosynthesis of other cofactors. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Protein synthesis, tRNA and rRNA base modification] 402 matched cddid_all.tbl CDD TIGR02007 TIGR02007 131062 fdx_isc ferredoxin, 2Fe-2S type, ISC system. This family consists of proteobacterial ferredoxins associated with and essential to the ISC system of 2Fe-2S cluster assembly. This family is closely related to (but excludes) eukaryotic (mitochondrial) adrenodoxins, which are ferredoxins involved in electron transfer to P450 cytochromes. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 110 matched cddid_all.tbl CDD TIGR02008 TIGR02008 273926 fdx_plant ferredoxin [2Fe-2S]. This model represents single domain 2Fe-2S (also called plant type) ferredoxins. In general, these occur as a single domain proteins or with a chloroplast transit peptide. Species tend to be photosynthetic, but several forms may occur in one species and individually may not be associated with photocynthesis. Halobacterial forms differ somewhat in architecture; they score between trusted and noise cutoffs. Sequences scoring below the noise cutoff tend to be ferredoxin-related domains of larger proteins. 97 matched cddid_all.tbl CDD TIGR02009 TIGR02009 213673 PGMB-YQAB-SF "beta-phosphoglucomutase family hydrolase. This subfamily model groups together three clades: the characterized beta-phosphoglucomutases (including those from E.coli, B.subtilus and L.lactis, TIGR01990), a clade of putative bPGM's from mycobacteria and a clade including the uncharacterized E.coli and H.influenzae yqaB genes which may prove to be beta-mutases of a related 1-phosphosugar. All of these are members of the larger Haloacid dehalogenase (HAD) subfamily IA and include the ""variant 3"" glu-asp version of the third conserved HAD domain (TIGR01509)." 185 matched cddid_all.tbl CDD TIGR02010 TIGR02010 273927 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Regulatory functions, DNA interactions] 135 matched cddid_all.tbl CDD TIGR02011 TIGR02011 213674 IscA iron-sulfur cluster assembly protein IscA. This model represents the IscA component of the ISC system for iron-sulfur cluster assembly. The ISC system consists of IscRASU, HscAB and an Isc-specific ferredoxin. IscA previously was believed to act as a scaffold and now is seen as an iron donor protein. This clade is limited to the proteobacteria. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 105 matched cddid_all.tbl CDD TIGR02012 TIGR02012 162659 tigrfam_recA protein RecA. This model describes orthologs of the recA protein. RecA promotes hybridization of homolgous regions of DNA. A segment of ssDNA can be hybridized to another ssDNA region, or to a dsDNA region. ATP is hydrolyzed in the process. Part of the SOS respones, it is regulated by LexA via autocatalytic cleavage. [DNA metabolism, DNA replication, recombination, and repair] 321 matched cddid_all.tbl CDD TIGR02013 TIGR02013 273928 rpoB DNA-directed RNA polymerase, beta subunit. This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase] 1065 matched cddid_all.tbl CDD TIGR02014 TIGR02014 131069 BchZ chlorophyllide reductase subunit Z. This model represents the Z subunit of the three-subunit enzyme, (bacterio)chlorophyllide reductase. This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase. [Energy metabolism, Photosynthesis] 468 matched cddid_all.tbl CDD TIGR02015 TIGR02015 131070 BchY chlorophyllide reductase subunit Y. This model represents the Y subunit of the three-subunit enzyme, (bacterio)chlorophyllide reductase. This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase. [Energy metabolism, Photosynthesis] 422 matched cddid_all.tbl CDD TIGR02016 TIGR02016 273929 BchX "chlorophyllide reductase iron protein subunit X. This model represents the X subunit of the three-subunit enzyme, (bacterio)chlorophyllide reductase. This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase. This subunit is homologous to the nitrogenase component II, or ""iron"" protein. [Energy metabolism, Photosynthesis]" 296 matched cddid_all.tbl CDD TIGR02017 TIGR02017 131072 hutG_amidohyd N-formylglutamate amidohydrolase. In some species, histidine is converted to via urocanate and then formimino-L-glutamate to glutamate in four steps, where the fourth step is conversion of N-formimino-L-glutamate to L-glutamate and formamide. In others, that pathway from formimino-L-glutamate may differ, with the next enzyme being formiminoglutamate hydrolase (HutF) yielding N-formyl-L-glutamate. This model represents the enzyme N-formylglutamate deformylase, also called N-formylglutamate amidohydrolase, which then produces glutamate. [Energy metabolism, Amino acids and amines] 263 matched cddid_all.tbl CDD TIGR02018 TIGR02018 188194 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators. [Energy metabolism, Amino acids and amines, Regulatory functions, DNA interactions] 230 matched cddid_all.tbl CDD TIGR02019 TIGR02019 131074 BchJ "bacteriochlorophyll 4-vinyl reductase. This model represents the component of bacteriochlorophyll synthetase responsible for reduction of the B-ring pendant ethylene (4-vinyl) group. It appears that this step must precede the reduction of ring D, at least by the ""dark"" protochlorophyllide reductase enzymes BchN, BchB and BchL. This family appears to be present in photosynthetic bacteria except for the cyanobacterial clade. Cyanobacteria must use a non-orthologous gene to carry out this required step for the biosynthesis of both bacteriochlorophyll and chlorophyll. [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll]" 188 matched cddid_all.tbl CDD TIGR02020 TIGR02020 131075 BchF 2-vinyl bacteriochlorophyllide hydratase. This model represents the enzyme responsible for the first step in the modification of the ring A vinyl group of chlorophyllide a which (in part) distinguishes chlorophyll from bacteriochlorophyll. This enzyme is aparrently absent from cyanobacteria (which do not use bacteriochlorophyll). [Energy metabolism, Photosynthesis] 145 matched cddid_all.tbl CDD TIGR02021 TIGR02021 273930 BchM-ChlM magnesium protoporphyrin O-methyltransferase. This model represents the S-adenosylmethionine-dependent O-methyltransferase responsible for methylation of magnesium protoporphyrin IX. This step is essentiasl for the biosynthesis of both chlorophyll and bacteriochlorophyll. This model encompasses two closely related clades, from cyanobacteria (and plants) where it is called ChlM and other photosynthetic bacteria where it is known as BchM. [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll] 219 matched cddid_all.tbl CDD TIGR02022 TIGR02022 273931 hutF formiminoglutamate deiminase. In some species, histidine utilization goes via urocanate to glutamate in four step, the last being removal of formamide. This model describes an alternate fourth step, formiminoglutamate hydrolase, which leads to N-formyl-L-glutamate. This product may be acted on by formylglutamate amidohydrolase (TIGR02017) and bypass glutamate as a product during its degradation. Alternatively, removal of formate (by EC 3.5.1.68) would yield glutamate. [Energy metabolism, Amino acids and amines] 454 matched cddid_all.tbl CDD TIGR02023 TIGR02023 273932 BchP-ChlP geranylgeranyl reductase. This model represents a group of geranylgeranyl reductases specific for the biosyntheses of bacteriochlorophyll and chlorophyll. It is unclear whether the processes of isoprenoid ligation to the chlorin ring and reduction of the geranylgeranyl chain to a phytyl chain are necessarily ordered the same way in all species. [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll] 388 matched cddid_all.tbl CDD TIGR02024 TIGR02024 131079 FtcD glutamate formiminotransferase. This model represents the tetrahydrofolate (THF) dependent glutamate formiminotransferase involved in the histidine utilization pathway. This enzyme interconverts L-glutamate and N-formimino-L-glutamate. The enzyme is bifunctional as it also catalyzes the cyclodeaminase reaction on N-formimino-THF, converting it to 5,10-methenyl-THF and releasing ammonia - part of the process of regenerating THF. This model covers enzymes from metazoa as well as gram-positive bacteria and archaea. In humans, deficiency of this enzyme results in a disease phenotype. The crystal structure of the enzyme has been studied in the context of the catalytic mechanism. [Energy metabolism, Amino acids and amines] 298 matched cddid_all.tbl CDD TIGR02025 TIGR02025 273933 BchH magnesium chelatase, H subunit. This model represents the H subunit of the magnesium chelatase complex responsible for magnesium insertion into the protoporphyrin IX ring in the biosynthesis of both chlorophyll and bacteriochlorophyll. In chlorophyll-utilizing species, this gene is known as ChlH, while in bacteriochlorophyll-utilizing spoecies it is called BchH. Subunit H is the largest (~140kDa) of the three subunits (the others being BchD/ChlD and BchI/ChlI), and is known to bind protoporphyrin IX. Subunit H is homologous to the CobN subunit of cobaltochelatase and by anology with that enzyme, subunit H is believed to also bind the magnesium ion which is inserted into the ring. In conjunction with the hydrolysis of ATP by subunits I and D, a conformation change is believed to happen in subunit H causing the magnesium ion insertion into the distorted protoporphyrin ring. [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll] 1224 matched cddid_all.tbl CDD TIGR02026 TIGR02026 131081 BchE magnesium-protoporphyrin IX monomethyl ester anaerobic oxidative cyclase. This model represents the cobalamin-dependent oxidative cyclase, a radical SAM enzyme responsible for forming the distinctive E-ring of the chlorin ring system under anaerobic conditions. This step is essential in the biosynthesis of both bacteriochlorophyll and chlorophyll under anaerobic conditions (a separate enzyme, AcsF, acts under aerobic conditions). This model identifies two clades of sequences, one from photosynthetic, non-cyanobacterial bacteria and another including Synechocystis and several non-photosynthetic bacteria. The function of the Synechocystis gene is supported by gene clustering with other photosynthetic genes, so the purpose of the gene in the non-photosynthetic bacteria is uncertain. Note that homologs of this gene are not found in plants which rely solely on the aerobic cyclase. 497 matched cddid_all.tbl CDD TIGR02027 TIGR02027 273934 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins. [Transcription, DNA-dependent RNA polymerase] 297 matched cddid_all.tbl CDD TIGR02028 TIGR02028 131083 ChlP geranylgeranyl reductase. This model represents the reductase which acts reduces the geranylgeranyl group to the phytyl group in the side chain of chlorophyll. It is unclear whether the enzyme has a preference for acting before or after the attachment of the side chain to chlorophyllide a by chlorophyll synthase. This clade is restricted to plants and cyanobacteria to separate it from the homologues which act in the biosynthesis of bacteriochlorophyll. [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll] 398 matched cddid_all.tbl CDD TIGR02029 TIGR02029 131084 AcsF magnesium-protoporphyrin IX monomethyl ester aerobic oxidative cyclase. This model respresents the oxidative cyclase responsible for forming the distinctive E-ring of the chlorin ring system under aerobic conditions. This enzyme is believed to utilize a binuclear iron center and molecular oxygen. There are two isoforms of this enzyme in some plants and cyanobacterai which are differentially regulated based on the levels of copper and oxygen. This step is essential in the biosynthesis of both bacteriochlorophyll and chlorophyll under aerobic conditions (a separate enzyme, BchE, acts under anaerobic conditions). This enzyme is found in plants, cyanobacteria and other photosynthetic bacteria. [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll] 337 matched cddid_all.tbl CDD TIGR02030 TIGR02030 131085 BchI-ChlI magnesium chelatase ATPase subunit I. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll] 337 matched cddid_all.tbl CDD TIGR02031 TIGR02031 273935 BchD-ChlD magnesium chelatase ATPase subunit D. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea. [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll] 589 matched cddid_all.tbl CDD TIGR02032 TIGR02032 273936 GG-red-SF geranylgeranyl reductase family. This model represents a subfamily which includes geranylgeranyl reductases involved in chlorophyll and bacteriochlorophyll biosynthesis as well as other related enzymes which may also act on geranylgeranyl groups or related substrates. [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll] 295 matched cddid_all.tbl CDD TIGR02033 TIGR02033 273937 D-hydantoinase D-hydantoinase. This model represents the D-hydantoinase (dihydropyrimidinase) which primarily converts 5,6-dihydrouracil to 3-ureidopropanoate but also acts on dihydrothymine and hydantoin. The enzyme is a metalloenzyme. 454 matched cddid_all.tbl CDD TIGR02034 TIGR02034 213679 CysN sulfate adenylyltransferase, large subunit. Metabolic assimilation of sulfur from inorganic sulfate, requires sulfate activation by coupling to a nucleoside, for the production of high-energy nucleoside phosphosulfates. This pathway appears to be similar in all prokaryotic organisms. Activation is first achieved through sulfation of sulfate with ATP by sulfate adenylyltransferase (ATP sulfurylase) to produce 5'-phosphosulfate (APS), coupled by GTP hydrolysis. Subsequently, APS is phosphorylated by an APS kinase to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS). In Escherichia coli, ATP sulfurylase is a heterodimer composed of two subunits encoded by cysD and cysN, with APS kinase encoded by cysC. These genes are located in a unidirectionally transcribed gene cluster, and have been shown to be required for the synthesis of sulfur-containing amino acids. Homologous to this E.coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulfurase and APS kinase activity, yet are involved in Nod factor sulfation, and sulfation of other macromolecules. With members of the Rhizobiaceae family, nodQ often appears as a fusion of cysN (large subunit of ATP sulfurase) and cysC (APS kinase). [Central intermediary metabolism, Sulfur metabolism] 406 matched cddid_all.tbl CDD TIGR02035 TIGR02035 211710 D_Ser_am_lyase D-serine ammonia-lyase. This family consists of D-serine ammonia-lyase (EC 4.3.1.18), a pyridoxal-phosphate enzyme that converts D-serine to pyruvate and NH3. This enzyme is also called D-serine dehydratase and D-serine deaminase and was previously designated EC 4.2.1.14. It is homologous to an enzyme that acts on threonine and may itself act weakly on threonine. [Energy metabolism, Amino acids and amines] 431 matched cddid_all.tbl CDD TIGR02036 TIGR02036 131091 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea. [Regulatory functions, DNA interactions] 302 matched cddid_all.tbl CDD TIGR02037 TIGR02037 273938 degP_htrA_DO periplasmic serine protease, Do/DeqQ family. This family consists of a set proteins various designated DegP, heat shock protein HtrA, and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in E. coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens.// The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures. [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides] 428 matched cddid_all.tbl CDD TIGR02038 TIGR02038 273939 protease_degS periplasmic serine pepetdase DegS. This family consists of the periplasmic serine protease DegS (HhoB), a shorter paralog of protease DO (HtrA, DegP) and DegQ (HhoA). It is found in E. coli and several other Proteobacteria of the gamma subdivision. It contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress in the periplasm and partially degrade an inhibitor of sigma(E). [Protein fate, Degradation of proteins, peptides, and glycopeptides, Regulatory functions, Protein interactions] 351 matched cddid_all.tbl CDD TIGR02039 TIGR02039 131094 CysD sulfate adenylyltransferase, small subunit. Metabolic assimilation of sulfur from inorganic sulfate, requires sulfate activation by coupling to a nucleoside, for the production of high-energy nucleoside phosphosulfates. This pathway appears to be similar in all prokaryotic organisms. Activation is first achieved through sulfation of sulfate with ATP by sulfate adenylyltransferase (ATP sulfurylase) to produce 5'-phosphosulfate (APS), coupled by GTP hydrolysis. Subsequently, APS is phosphorylated by an APS kinase to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS). In Escherichia coli, ATP sulfurylase is a heterodimer composed of two subunits encoded by cysD and cysN, with APS kinase encoded by cysC. These genes are located in a unidirectionally transcribed gene cluster, and have been shown to be required for the synthesis of sulfur-containing amino acids. Homologous to this E.coli activation pathway are nodPQH gene products found among members of the Rhizobiaceae family. These gene products have been shown to exhibit ATP sulfurase and APS kinase activity, yet are involved in Nod factor sulfation, and sulfation of other macromolecules. [Central intermediary metabolism, Sulfur metabolism] 294 matched cddid_all.tbl CDD TIGR02040 TIGR02040 273940 PpsR-CrtJ "transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the ""fis"" type (pfam02954). [Energy metabolism, Photosynthesis, Regulatory functions, DNA interactions]" 442 matched cddid_all.tbl CDD TIGR02041 TIGR02041 273941 CysI sulfite reductase (NADPH) hemoprotein, beta-component. Sulfite reductase (NADPH) catalyzes a six electron reduction of sulfite to sulfide in prokaryotic organisms. It is a complex oligomeric enzyme composed of two different peptides with a subunit composition of alpha(8)-beta(4). The alpha component, encoded by cysJ, is a flavoprotein containing both FMN and FAD, while the beta component, encoded by cysI, is a siroheme, iron-sulfur protein. In Salmonella typhimurium and Escherichia coli, both the alpha and beta subunits of sulfite reductase are located in a unidirectional gene cluster along with phosphoadenosine phosphosulfate reductase, which catalyzes a two step reduction of PAPS to give free sulfite. In cyanobacteria and plant species, sulfite reductase ferredoxin (EC 1.8.7.1) catalyzes the reduction of sulfite to sulfide. [Central intermediary metabolism, Sulfur metabolism] 541 matched cddid_all.tbl CDD TIGR02042 TIGR02042 131097 sir ferredoxin-sulfite reductase. Distantly related to the iron-sulfur hemoprotein of sulfite reductase (NADPH) found in Proteobacteria and Eubacteria, sulfite reductase (ferredoxin) is a cyanobacterial and plant monomeric enzyme that also catalyzes the reduction of sulfite to sulfide. [Central intermediary metabolism, Sulfur metabolism] 577 matched cddid_all.tbl CDD TIGR02043 TIGR02043 131098 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix. [Regulatory functions, DNA interactions] 131 matched cddid_all.tbl CDD TIGR02044 TIGR02044 131099 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue. [Regulatory functions, DNA interactions] 127 matched cddid_all.tbl CDD TIGR02045 TIGR02045 131100 P_fruct_ADP ADP-specific phosphofructokinase. Phosphofructokinase is a key enzyme of glycolysis. The phosphate group donor for different subtypes of phosphofructokinase can be ATP, ADP, or pyrophosphate. This family consists of ADP-dependent phosphofructokinases. Members are more similar to ADP-dependent glucokinases (excluded from this family) than to other phosphofructokinases. [Energy metabolism, Glycolysis/gluconeogenesis] 446 matched cddid_all.tbl CDD TIGR02046 TIGR02046 131101 sdhC_b558_fam succinate dehydrogenase (or fumarate reductase) cytochrome b subunit, b558 family. This family consists of the succinate dehydrogenase subunit C of Bacillus subtilis, designated cytochrome b-558, and related sequences that include a fumarate reductase subunit C. This subfamily is only weakly similar to the main group of succinate dehydrogenase cytochrome b subunits described by pfam01127, so that some members score above the gathering threshold and some do not. [Energy metabolism, TCA cycle] 214 matched cddid_all.tbl CDD TIGR02047 TIGR02047 131102 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix. [Regulatory functions, DNA interactions] 127 matched cddid_all.tbl CDD TIGR02048 TIGR02048 131103 gshA_cyano glutamate--cysteine ligase, cyanobacterial, putative. This family consists of proteins believed (see Copley SD, Dhillon JK, 2002) to be the glutamate--cysteine ligases of several cyanobacteria, which are known to make glutathione. [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 376 matched cddid_all.tbl CDD TIGR02049 TIGR02049 273942 gshA_ferroox glutamate--cysteine ligase, T. ferrooxidans family. This family consists of a rare family of glutamate--cysteine ligases, demonstrated first in Thiobacillus ferrooxidans and present in a few other Proteobacteria. It is the first of two enzymes for glutathione biosynthesis. It is also called gamma-glutamylcysteine synthetase. [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 403 matched cddid_all.tbl CDD TIGR02050 TIGR02050 273943 gshA_cyan_rel carboxylate-amine ligase, YbdK family. This family represents a division of a larger family, the other branch of which is predicted to act as glutamate--cysteine ligase (the first of two enzymes in glutathione biosynthesis) in the cyanobacteria. Species containing this protein, however, are generally not believe to make glutathione, and the function is unknown. 287 matched cddid_all.tbl CDD TIGR02051 TIGR02051 131106 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix. [Cellular processes, Detoxification, Regulatory functions, DNA interactions] 124 matched cddid_all.tbl CDD TIGR02052 TIGR02052 131107 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403). [Cellular processes, Detoxification] 92 matched cddid_all.tbl CDD TIGR02053 TIGR02053 273944 MerA mercury(II) reductase. This model represents the mercuric reductase found in the mer operon for the detoxification of mercury compounds. MerA is a FAD-containing flavoprotein which reduces Hg(II) to Hg(0) utilizing NADPH. [Cellular processes, Detoxification] 463 matched cddid_all.tbl CDD TIGR02054 TIGR02054 131109 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon. [Cellular processes, Detoxification] 120 matched cddid_all.tbl CDD TIGR02055 TIGR02055 273945 APS_reductase thioredoxin-dependent adenylylsulfate APS reductase. This model describes recently identified adenosine 5'-phosphosulfate (APS) reductase activity found in sulfate-assimilatory prokaryotes, thus separating it from the traditionally described phosphoadenosine 5'-phosphosulfate (PAPS) reductases found in bacteria and fungi. Homologous to PAPS reductase in enterobacteria, cyanobacteria, and yeast, APS reductase here clusters with, and demonstrates greater homology to plant APS reductase. Additionally, the presence of two conserved C-terminal motifs (CCXXRKXXPL & SXGCXXCT) distinguishes APS substrate specificity and serves as a FeS cluster. [Central intermediary metabolism, Sulfur metabolism] 191 matched cddid_all.tbl CDD TIGR02056 TIGR02056 131111 ChlG chlorophyll synthase, ChlG. This model represents the strictly cyanobacterial and plant-specific chlorophyll synthase ChlG. ChlG is the enzyme (esterase) which attaches the side chain moiety onto chlorophyllide a. Both geranylgeranyl and phytyl pyrophosphates are substrates to varying degrees in enzymes from different sources. Thus, ChlG may act as the final or penultimate step in chlorophyll biosynthesis (along with the geranylgeranyl reductase, ChlP). [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll] 306 matched cddid_all.tbl CDD TIGR02057 TIGR02057 131112 PAPS_reductase phosphoadenosine phosphosulfate reductase, thioredoxin dependent. Requiring thioredoxin as an electron donor, phosphoadenosine phosphosulfate reductase catalyzes the reduction of 3'-phosphoadenylylsulfate (PAPS) to sulfite and phospho-adenosine-phosphate (PAP). Found in enterobacteria, cyanobacteria, and yeast, PAPS reductase is related to a group of plant (TIGR00424) and bacterial (TIGR02055) enzymes preferring 5'-adenylylsulfate (APS) over PAPS as a substrate for reduction to sulfite. [Central intermediary metabolism, Sulfur metabolism] 226 matched cddid_all.tbl CDD TIGR02058 TIGR02058 131113 lin0512_fam conserved hypothetical protein. This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a perfectly conserved motif GxGxDxHG near the N-terminus. [Hypothetical proteins, Conserved] 116 matched cddid_all.tbl CDD TIGR02059 TIGR02059 131114 swm_rep_I cyanobacterial long protein repeat. This domain appears in 29 copies in a large (>10000 amino protein in Synechococcus sp. WH8102 associated with a novel flagellar system, as one of three different repeats. Similar domains are found in two different large (<3500) proteins of Synechocystis PCC6803. 101 matched cddid_all.tbl CDD TIGR02060 TIGR02060 131115 aprB adenosine phosphosulphate reductase, beta subunit. During dissimilatory sulfate reduction and sulfur oxidation, adenylylsulfate (APS) reductase catalyzes reversibly the two-electron reduction of APS to sulfite and AMP. Found in several bacterial lineages and in Archaeoglobales, APS reductase is a heterodimer composed of an alpha subunit containing a noncovalently bound FAD, and a beta subunit containing two [4Fe-4S] clusters. Described by this model is the beta subunit of APS reductase, sharing common evolutionary origin with other iron-sulfur cluster-binding proteins. [Central intermediary metabolism, Sulfur metabolism] 132 matched cddid_all.tbl CDD TIGR02061 TIGR02061 273946 aprA adenosine phosphosulphate reductase, alpha subunit. During dissimilatory sulfate reduction or sulfur oxidation, adenylylsulfate (APS) reductase catalyzes reversibly the two-electron reduction of APS to sulfite and AMP. Found in several bacterial lineages and in Archaeoglobales, APS reductase is a heterodimer composed of an alpha subunit containing a noncovalently bound FAD, and a beta subunit containing two [4Fe-4S] clusters. Described by this model is the alpha subunit of APS reductase, sharing common evolutionary origin with fumarate reductase/succinate dehydrogenase flavoproteins. [Central intermediary metabolism, Sulfur metabolism] 614 matched cddid_all.tbl CDD TIGR02062 TIGR02062 131117 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing. [Transcription, Degradation of RNA] 639 matched cddid_all.tbl CDD TIGR02063 TIGR02063 273947 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans. [Transcription, Degradation of RNA] 709 matched cddid_all.tbl CDD TIGR02064 TIGR02064 273948 dsrA sulfite reductase, dissimilatory-type alpha subunit. Dissimilatory sulfite reductase catalyzes the six-electron reduction of sulfite to sulfide, as the terminal reaction in dissimilatory sulfate reduction. It remains unclear however, whether trithionate and thiosulfate serve as intermediate compounds to sulfide, or as end products of sulfite reduction. Sulfite reductase is a multisubunit enzyme composed of dimers of either alpha/beta or alpha/beta/gamma subunits, each containing a siroheme and iron sulfur cluster prosthetic center. Found in sulfate-reducing bacteria, these genes are commonly located in an unidirectional gene cluster. This model describes the alpha subunit of sulfite reductase. [Central intermediary metabolism, Sulfur metabolism] 402 matched cddid_all.tbl CDD TIGR02065 TIGR02065 131120 ECX1 archaeal exosome-like complex exonuclease 1. This family contains the archaeal protein orthologous to the eukaryotic exosome protein Rrp41. It is somewhat more distantly related to the bacterial protein ribonuclease PH. An exosome-like complex has been demonstrated experimentally for the Archaea in Sulfolobus solfataricus, so members of this family are designated exosome complex exonuclease 1, after usage in SwissProt. [Transcription, Degradation of RNA] 230 matched cddid_all.tbl CDD TIGR02066 TIGR02066 131121 dsrB sulfite reductase, dissimilatory-type beta subunit. Dissimilatory sulfite reductase catalyzes the six-electron reduction of sulfite to sulfide, as the terminal reaction in dissimilatory sulfate reduction. It remains unclear however, whether trithionate and thiosulfate serve as intermediate compounds to sulfide, or as end products of sulfite reduction. Sulfite reductase is a multisubunit enzyme composed of dimers of either alpha/beta or alpha/beta/gamma subunits, each containing a siroheme and iron sulfur cluster prosthetic center. Found in sulfate-reducing bacteria, these genes are commonly located in an unidirectional gene cluster. This model describes the beta subunit of sulfite reductase. [Central intermediary metabolism, Sulfur metabolism] 341 matched cddid_all.tbl CDD TIGR02067 TIGR02067 273949 his_9_HisN histidinol-phosphatase, inositol monophosphatase family. This subfamily belongs to the inositol monophosphatase family (pfam00459). The members of this family consist of no more than one per species and are found only in species in which histidine is synthesized de novo but no histidinol phosphatase can be found in either of the two described families (TIGR01261, TIGR01856). In at least one species, the member of this family is found near known histidine biosynthesis genes. The role as histidinol-phosphatase wsa first proven in Corynebacterium glutamicum. [Amino acid biosynthesis, Histidine family] 251 matched cddid_all.tbl CDD TIGR02068 TIGR02068 273950 cya_phycin_syn cyanophycin synthetase. Cyanophycin is an insoluble storage polymer for carbon, nitrogen, and energy, found in most Cyanobacteria. The polymer has a backbone of L-aspartic acid, with most Asp side chain carboxyl groups attached to L-arginine. The polymer is made by this enzyme, cyanophycin synthetase, and degraded by cyanophycinase. Heterologously expressed cyanophycin synthetase in E. coli produces a closely related, water-soluble polymer with some Arg replaced by Lys. It is unclear whether enzymes that produce soluble cyanophycin-like polymers in vivo in non-Cyanobacterial species should be designated as cyanophycin synthetase itself or as a related enzyme. This model makes the designation as cyanophycin synthetase. Cyanophycin synthesis is analogous to polyhydroxyalkanoic acid (PHA) biosynthesis, except that PHA polymers lack nitrogen and may be made under nitrogen-limiting conditions. [Cellular processes, Biosynthesis of natural products] 864 matched cddid_all.tbl CDD TIGR02069 TIGR02069 131124 cyanophycinase cyanophycinase. This model describes both cytosolic and extracellular cyanophycinases. The former are part of a system in many Cyanobacteria and a few other species of generating and later utilizing a storage polymer for nitrogen, carbon, and energy, called cyanophycin. The latter are found in species such as Pseudomonas anguilliseptica that can use external cyanophycin. The polymer has a backbone of L-aspartic acid, with most Asp side chain carboxyl groups attached to L-arginine. [Energy metabolism, Other] 250 matched cddid_all.tbl CDD TIGR02070 TIGR02070 273951 mono_pep_trsgly monofunctional biosynthetic peptidoglycan transglycosylase. This family is one of the transglycosylases involved in the late stages of peptidoglycan biosynthesis. Members tend to be small, about 240 amino acids in length, and consist almost entirely of a domain described by pfam00912 for transglycosylases. Species with this protein will have several other transglycosylases as well. All species with this protein are Proteobacteria that produce murein (peptidoglycan). [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 224 matched cddid_all.tbl CDD TIGR02071 TIGR02071 273952 PBP_1b penicillin-binding protein 1B. Bacterial that synthesize a cell wall of peptidoglycan (murein) generally have several transglycosylases and transpeptidases for the task. This family consists of a particular bifunctional transglycosylase/transpeptidase in E. coli and other Proteobacteria, designated penicillin-binding protein 1B. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 730 matched cddid_all.tbl CDD TIGR02072 TIGR02072 273953 BioC malonyl-acyl carrier protein O-methyltransferase BioC. This enzyme, which is found in biotin biosynthetic gene clusters in proteobacteria, firmicutes, green-sulfur bacteria, fusobacterium and bacteroides, carries out an enzymatic step prior to the formation of pimeloyl-CoA, namely O-methylation of the malonyl group preferentially while on acyl carrier protein. The enzyme is recognizable as a methyltransferase by homology. [Biosynthesis of cofactors, prosthetic groups, and carriers, Biotin] 240 matched cddid_all.tbl CDD TIGR02073 TIGR02073 273954 PBP_1c penicillin-binding protein 1C. This subfamily of the penicillin binding proteins includes the member from E. coli designated penicillin-binding protein 1C. Members have both transglycosylase and transpeptidase domains and are involved in forming cross-links in the late stages of peptidoglycan biosynthesis. All members of this subfamily are presumed to have the same basic function. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 727 matched cddid_all.tbl CDD TIGR02074 TIGR02074 273955 PBP_1a_fam penicillin-binding protein, 1A family. Bacterial that synthesize a cell wall of peptidoglycan (murein) generally have several transglycosylases and transpeptidases for the task. This family consists of bifunctional transglycosylase/transpeptidase penicillin-binding proteins (PBP). In the Proteobacteria, this family includes PBP 1A but not the paralogous PBP 1B (TIGR02071). This family also includes related proteins, often designated PBP 1A, from other bacterial lineages. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 531 matched cddid_all.tbl CDD TIGR02075 TIGR02075 213681 pyrH_bact uridylate kinase. This protein, also called UMP kinase, converts UMP to UDP by adding a phosphate from ATP. It is the first step in pyrimidine biosynthesis. GTP is an allosteric activator. In a large fraction of all bacterial genomes, the gene tends to be located immediately downstream of elongation factor Ts and upstream of ribosome recycling factor. A related protein family, believed to be equivalent in function and found in the archaea and in spirochetes, is described by a separate model, TIGR02076. [Purines, pyrimidines, nucleosides, and nucleotides, Nucleotide and nucleoside interconversions] 232 matched cddid_all.tbl CDD TIGR02076 TIGR02076 273956 pyrH_arch uridylate kinase, putative. This family consists of the archaeal and spirochete proteins most closely related to bacterial uridylate kinases (TIGR02075), an enzyme involved in pyrimidine biosynthesis. Members are likely, but not known, to be functionally equivalent to their bacterial counterparts. However, substantial sequence differences suggest that regulatory mechanisms may be different; the bacterial form is allosterically regulated by GTP. [Purines, pyrimidines, nucleosides, and nucleotides, Nucleotide and nucleoside interconversions] 221 matched cddid_all.tbl CDD TIGR02077 TIGR02077 200156 thr_lead_pep thr operon leader peptide. This family consists of examples of the threonine biosynthesis (thr) operon leader peptide, also called the thr operon attenuator. The small gene for this peptide is often missed in genome annotation. It should be looked for in genomes of the proteobacteria, immediately upstream of genes for threonine biosynthesis, typically aspartokinase I/homoserine dehydrogenase, homoserine kinase, and threonine synthase. Transcription of the rest of the Thr operon is attenuated (mostly turned off) unless the ribosome pauses during a stretch of the leader sequence rich in both Ile (made from Thr) and in Thr itself because of the scarcity of those amino acids at the time. The leader peptide itself, once made, may have no role other than to be degraded. Similar systems exist for some other amino acid biosynthetic operons, such as Trp. [Amino acid biosynthesis, Aspartate family] 24 matched cddid_all.tbl CDD TIGR02078 TIGR02078 131133 AspKin_pair Pyrococcus aspartate kinase subunit, putative. This family consists of proteins restricted to and found as paralogous pairs (typically close together) in species of Pyrococcus, a hyperthermophilic archaeal genus. Members are always found close to other genes of threonine biosynthesis and appear to represent the Pyrococcal form of aspartate kinase. Alignment to aspartokinase III from E. coli shows that 300 N-terminal and 20 C-terminal amino acids are homologous, but the form in Pyrococcus lacks ~ 100 amino acids in between. [Amino acid biosynthesis, Aspartate family] 327 matched cddid_all.tbl CDD TIGR02079 TIGR02079 273957 THD1 threonine dehydratase. This model represents threonine dehydratase, the first step in the pathway converting threonine into isoleucine. At least two other clades of biosynthetic threonine dehydratases have been characterized by models (TIGR01124 and TIGR01127). Those sequences described by this model are exclusively found in species containg the rest of the isoleucine pathway and which are generally lacking in members of the those other two clades of threonine dehydratases. Members of this clade are also often gene clustered with other elements of the isoleucine pathway. [Amino acid biosynthesis, Pyruvate family] 409 matched cddid_all.tbl CDD TIGR02080 TIGR02080 131135 O_succ_thio_ly O-succinylhomoserine (thiol)-lyase. This family consists of O-succinylhomoserine (thiol)-lyase, one of three different enzymes designated cystathionine gamma-synthase and involved in methionine biosynthesis. In all three cases, sulfur is added by transsulfuration from Cys to yield cystathionine rather than by a sulfhydrylation step that uses H2S directly and bypasses cystathionine. [Amino acid biosynthesis, Aspartate family] 382 matched cddid_all.tbl CDD TIGR02081 TIGR02081 273958 metW methionine biosynthesis protein MetW. This protein is found alongside MetX, of the enzyme that acylates homoserine as a first step toward methionine biosynthesis, in many species. It appears to act in methionine biosynthesis but is not fully characterized. [Amino acid biosynthesis, Aspartate family] 194 matched cddid_all.tbl CDD TIGR02082 TIGR02082 273959 metH 5-methyltetrahydrofolate--homocysteine methyltransferase. This family represents 5-methyltetrahydrofolate--homocysteine methyltransferase (EC 2.1.1.13), one of at least three different enzymes able to convert homocysteine to methionine by transferring a methyl group on to the sulfur atom. It is also called the vitamin B12(or cobalamine)-dependent methionine synthase. Other methionine synthases include 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase (MetE, EC 2.1.1.14, the cobalamin-independent methionine synthase) and betaine-homocysteine methyltransferase. [Amino acid biosynthesis, Aspartate family] 1181 matched cddid_all.tbl CDD TIGR02083 TIGR02083 131138 LEU2 3-isopropylmalate dehydratase, large subunit. Homoaconitase, aconitase, and 3-isopropylmalate dehydratase have similar overall structures. All are dehydratases (EC 4.2.1.-) and bind a Fe-4S iron-sulfur cluster. 3-isopropylmalate dehydratase is split into large (leuC) and small (leuD) chains in eubacteria. Several pairs of archaeal proteins resemble the leuC and leuD pair in length and sequence but even more closely resemble the respective domains of homoaconitase, and their identity is uncertain. These homologs are described by a separate model of subfamily (rather than equivalog) homology type (TIGR01343). This model along with TIGR00170 describe clades which consist only of LeuC sequences. Here, the genes from Pyrococcus furiosus, Clostridium acetobutylicum, Thermotoga maritima and others are gene clustered with related genes from the leucine biosynthesis pathway. [Amino acid biosynthesis, Pyruvate family] 419 matched cddid_all.tbl CDD TIGR02084 TIGR02084 131139 leud 3-isopropylmalate dehydratase, small subunit. Homoaconitase, aconitase, and 3-isopropylmalate dehydratase have similar overall structures. All are dehydratases (EC 4.2.1.-) and bind a Fe-4S iron-sulfur cluster. 3-isopropylmalate dehydratase is split into large (leuC) and small (leuD) chains in eubacteria. Several pairs of archaeal proteins resemble the leuC and leuD pair in length and sequence but even more closely resemble the respective domains of homoaconitase, and their identity is uncertain. The members of the seed for this model are those sequences which are gene clustered with other genes involved in leucine biosynthesis and include some archaea. [Amino acid biosynthesis, Pyruvate family] 156 matched cddid_all.tbl CDD TIGR02085 TIGR02085 131140 meth_trns_rumB 23S rRNA (uracil-5-)-methyltransferase RumB. This family consists of RNA methyltransferases designated RumB, formerly YbjF. Members act on 23S rRNA U747 and the equivalent position in other proteobacterial species. This family is homologous to the other 23S rRNA methyltransferase RumA and to the tRNA methyltransferase TrmA. [Protein synthesis, tRNA and rRNA base modification] 374 matched cddid_all.tbl CDD TIGR02086 TIGR02086 273960 IPMI_arch 3-isopropylmalate dehydratase, large subunit. This subfamily is a subset of the larger HacA family (Homoaconitate hydratase family, TIGR01343) and is most closely related to the 3-isopropylmalate dehydratase, large subunits which form TIGR00170. This subfamily includes the members of TIGR01343 which are gene clustered with other genes of leucine biosynthesis. The rest of the subfamily includes mainly archaeal species which exhibit two hits to this model. In these cases it is possible that one or the other of the hits does not have a 3-isopropylmalate dehydratase activity but rather one of the other related aconitase-like activities. 413 matched cddid_all.tbl CDD TIGR02087 TIGR02087 273961 LEUD_arch 3-isopropylmalate dehydratase, small subunit. This subfamily is most closely related to the 3-isopropylmalate dehydratase, small subunits which form TIGR00171. This subfamily includes the members of TIGR02084 which are gene clustered with other genes of leucine biosynthesis. The rest of the subfamily includes mainly archaeal species which exhibit two hits to this model. In these cases it is possible that one or the other of the hits does not have a 3-isopropylmalate dehydratase activity but rather one of the other related aconitase-like activities. 154 matched cddid_all.tbl CDD TIGR02088 TIGR02088 273962 LEU3_arch isopropylmalate/isohomocitrate dehydrogenases. This model represents a group of archaeal decarboxylating dehydrogenases which include the leucine biosynthesis enzyme 3-isopropylmalate dehydrogenase (LeuB, LEU3) and the methanogenic cofactor CoB biosynthesis enzyme isohomocitrate dehydrogenase (AksF). Both of these have been characterized in Methanococcus janaschii. Non-methanogenic archaea have only one hit to this model and presumably this is LeuB, although phylogenetic trees cannot establish which gene is which in the methanogens. The AksF gene is capable of acting on isohomocitrate, iso(homo)2-citrate and iso(homo)3-citrate in the successive elongation cycles of coenzyme B (7-mercaptoheptanoyl-threonine phosphate). This family is closely related to both the LeuB genes found in TIGR00169 and the mitochondrial eukaryotic isocitrate dehydratases found in TIGR00175. All of these are included within the broader subfamily model, pfam00180. 322 matched cddid_all.tbl CDD TIGR02089 TIGR02089 273963 TTC tartrate dehydrogenase. Tartrate dehydrogenase catalyzes the oxidation of both meso- and (+)-tartrate as well as a D-malate. These enzymes are closely related to the 3-isopropylmalate and isohomocitrate dehydrogenases found in TIGR00169 and TIGR02088, respectively. [Energy metabolism, Other] 352 matched cddid_all.tbl CDD TIGR02090 TIGR02090 273964 LEU1_arch isopropylmalate/citramalate/homocitrate synthases. Methanogenic archaea contain three closely related homologs of the 2-isopropylmalate synthases (LeuA) represented by TIGR00973. Two of these in Methanococcus janaschii (MJ1392 - CimA; MJ0503 - AksA) have been characterized as catalyzing alternative reactions leaving the third (MJ1195) as the presumptive LeuA enzyme. CimA is citramalate (2-methylmalate) synthase which condenses acetyl-CoA with pyruvate. This enzyme is believed to be involved in the biosynthesis of isoleucine in methanogens and possibly other species lacking threonine dehydratase. AksA is a homocitrate synthase which also produces (homo)2-citrate and (homo)3-citrate in the biosynthesis of Coenzyme B which is restricted solely to methanogenic archaea. Methanogens, then should and aparrently do contain all three of these enzymes. Unfortunately, phylogenetic trees do not resolve into three unambiguous clades, making assignment of function to particular genes problematic. Other archaea which lack a threonine dehydratase (mainly Euryarchaeota) should contain both a CimA and a LeuA gene. This is true of, for example, archaeoglobus fulgidis, but not for the Pyrococci which have none in this clade, but one in TIGR00973 and one in TIGRT00977 which may fulfill these roles. Other species which have only one hit to this model and lack threonine dehydratase are very likely LeuA enzymes. 363 matched cddid_all.tbl CDD TIGR02091 TIGR02091 273965 glgC glucose-1-phosphate adenylyltransferase. This enzyme, glucose-1-phosphate adenylyltransferase, is also called ADP-glucose pyrophosphorylase. The plant form is an alpha2,beta2 heterodimer, allosterically regulated in plants. Both subunits are homologous and included in this model. In bacteria, both homomeric forms of GlgC and more active heterodimers of GlgC and GlgD have been described. This model describes the GlgC subunit only. This enzyme appears in variants of glycogen synthesis pathways that use ADP-glucose, rather than UDP-glucose as in animals. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 361 matched cddid_all.tbl CDD TIGR02092 TIGR02092 273966 glgD glucose-1-phosphate adenylyltransferase, GlgD subunit. This family is GlgD, an apparent regulatory protein that appears in an alpha2/beta2 heterotetramer with GlgC (glucose-1-phosphate adenylyltransferase, TIGR02091) in a subset of bacteria that use GlgC for glycogen biosynthesis. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 369 matched cddid_all.tbl CDD TIGR02093 TIGR02093 273967 P_ylase glycogen/starch/alpha-glucan phosphorylases. This family consists of phosphorylases. Members use phosphate to break alpha 1,4 linkages between pairs of glucose residues at the end of long glucose polymers, releasing alpha-D-glucose 1-phosphate. The nomenclature convention is to preface the name according to the natural substrate, as in glycogen phosphorylase, starch phosphorylase, maltodextrin phosphorylase, etc. Name differences among these substrates reflect differences in patterns of branching with alpha 1,6 linkages. Members include allosterically regulated and unregulated forms. A related family, TIGR02094, contains examples known to act well on particularly small alpha 1,4 glucans, as may be found after import from exogenous sources. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 794 matched cddid_all.tbl CDD TIGR02094 TIGR02094 273968 more_P_ylases alpha-glucan phosphorylases. This family consists of known phosphorylases, and homologs believed to share the function of using inorganic phosphate to cleave an alpha 1,4 linkage between the terminal glucose residue and the rest of the polymer (maltodextrin, glycogen, etc.). The name of the glucose storage polymer substrate, and therefore the name of this enzyme, depends on the chain lengths and branching patterns. A number of the members of this family have been shown to operate on small maltodextrins, as may be obtained by utilization of exogenous sources. This family represents a distinct clade from the related family modeled by TIGR02093/pfam00343. 601 matched cddid_all.tbl CDD TIGR02095 TIGR02095 273969 glgA glycogen/starch synthase, ADP-glucose type. This family consists of glycogen (or starch) synthases that use ADP-glucose (EC 2.4.1.21), rather than UDP-glucose (EC 2.4.1.11) as in animals, as the glucose donor. This enzyme is found in bacteria and plants. Whether the name given is glycogen synthase or starch synthase depends on context, and therefore on substrate. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 473 matched cddid_all.tbl CDD TIGR02096 TIGR02096 273970 TIGR02096 conserved hypothetical protein, steroid delta-isomerase-related. This family of proteins about 135 amino acids in length largely restricted to the Proteobacteria. This family and a delta5-3-ketosteroid isomerase from Pseudomonas testosteroni appear homologous, especially toward their respective N-termini. Members, therefore, probably are enzymes. 129 matched cddid_all.tbl CDD TIGR02097 TIGR02097 131152 yccV hemimethylated DNA binding domain. This model describes the small protein from E. coli YccV and its homologs in other Proteobacteria. YccV is now described as a hemimethylated DNA binding protein. The model also describes a domain in longer eukaryotic proteins. 101 matched cddid_all.tbl CDD TIGR02098 TIGR02098 131153 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility. 38 matched cddid_all.tbl CDD TIGR02099 TIGR02099 273971 TIGR02099 TIGR02099 family protein. This model describes a family of long proteins, over 1250 amino acids in length and present in the Proteobacteria. The degree of sequence similarity is low between sequences from different genera. Apparent membrane-spanning regions at the N-terminus and C-terminus suggest the protein is inserted into (or exported through) the membrane. [Hypothetical proteins, Conserved] 1260 matched cddid_all.tbl CDD TIGR02100 TIGR02100 131155 glgX_debranch glycogen debranching enzyme GlgX. This family consists of the GlgX protein from the E. coli glycogen operon and probable equivalogs from other prokaryotic species. GlgX is not required for glycogen biosynthesis, but instead acts as a debranching enzyme for glycogen catabolism. This model distinguishes GlgX from pullanases and other related proteins that also operate on alpha-1,6-glycosidic linkages. In the wide band between the trusted and noise cutoffs are functionally similar enzymes, mostly from plants, that act similarly but usually are termed isoamylase. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 688 matched cddid_all.tbl CDD TIGR02101 TIGR02101 273972 IpaC_SipC type III secretion target, IpaC/SipC family. This model represents a family of proteins associated with bacterial type III secretion systems, which are injection machines for virulence factors into host cell cytoplasm. Characterized members of this protein family are known to be secreted and are described as invasins, including IpaC from Shigella flexneri (SP:P18012) and SipC from Salmonella typhimurium (GB:AAA75170.1). Members may be referred to as invasins, pathogenicity island effectors, and cell invasion proteins. [Cellular processes, Pathogenesis] 317 matched cddid_all.tbl CDD TIGR02102 TIGR02102 273973 pullulan_Gpos pullulanase, extracellular, Gram-positive. Pullulan is an unusual, industrially important polysaccharide in which short alpha-1,4 chains (maltotriose) are connected in alpha-1,6 linkages. Enzymes that cleave alpha-1,6 linkages in pullulan and release maltotriose are called pullulanases although pullulan itself may not be the natural substrate. In contrast, a glycogen debranching enzyme such GlgX, homologous to this family, can release glucose at alpha,1-6 linkages from glycogen first subjected to limit degradation by phosphorylase. Characterized members of this family include a surface-located pullulanase from Streptococcus pneumoniae () and an extracellular bifunctional amylase/pullulanase with C-terminal pullulanase activity (. 1111 matched cddid_all.tbl CDD TIGR02103 TIGR02103 273974 pullul_strch alpha-1,6-glucosidases, pullulanase-type. Members of this protein family include secreted (or membrane-anchored) pullulanases of Gram-negative bacteria and pullulanase-type starch debranching enzymes of plants. Both enzymes hydrolyze alpha-1,6 glycosidic linkages. Pullulan is an unusual, industrially important polysaccharide in which short alpha-1,4 chains (maltotriose) are connected in alpha-1,6 linkages. Enzymes that cleave alpha-1,6 linkages in pullulan and release maltotriose are called pullulanases although pullulan itself may not be the natural substrate. This family is closely homologous to, but architecturally different from, the Gram-positive pullulanases of Gram-positive bacteria (TIGR02102). [Energy metabolism, Biosynthesis and degradation of polysaccharides] 898 matched cddid_all.tbl CDD TIGR02104 TIGR02104 273975 pulA_typeI pullulanase, type I. Pullulan is an unusual, industrially important polysaccharide in which short alpha-1,4 chains (maltotriose) are connected in alpha-1,6 linkages. Enzymes that cleave alpha-1,6 linkages in pullulan and release maltotriose are called pullulanases although pullulan itself may not be the natural substrate. This family consists of pullulanases related to the subfamilies described in TIGR02102 and TIGR02103 but having a different domain architecture with shorter sequences. Members are called type I pullulanases. 605 matched cddid_all.tbl CDD TIGR02105 TIGR02105 131160 III_needle type III secretion apparatus needle protein. Type III secretion systems translocate proteins, usually virulence factors, out across both inner and outer membranes of certain Gram-negative bacteria and further across the plasma membrane and into the cytoplasm of the host cell. This protein, termed YscF in Yersinia, and EscF, PscF, EprI, etc. in other systems, forms the needle of the injection apparatus. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 72 matched cddid_all.tbl CDD TIGR02106 TIGR02106 211715 cyd_oper_ybgT cyd operon protein YbgT. This model describes a very small (as short as 33 amino acids) protein of unknown function, essentially always found in an operon with CydAB, subunits of the cytochrome d terminal oxidase. It begins with an aromatic motif MWYFXW and appears to contain a membrane-spanning helix. This protein appears to be restricted to the Proteobacteria and exist in a single copy only. We suggest it may be a membrane subunit of the terminal oxidase. The family is named after the E. coli member YbgT (SP|P56100). This model excludes the apparently related protein YccB (SP|P24244). [Energy metabolism, Electron transport] 30 matched cddid_all.tbl CDD TIGR02107 TIGR02107 273976 PQQ_syn_pqqA coenzyme PQQ precursor peptide PqqA. This model describes a very small protein, coenzyme PQQ biosynthesis protein A, which is smaller than 25 amino acids in many species. It is proposed to serve as a peptide precursor of coenzyme pyrrolo-quinoline-quinone (PQQ), with Glu and Tyr of a conserved motif Glu-Xxx-Xxx-Xxx-Tyr becoming part of the product. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 21 matched cddid_all.tbl CDD TIGR02108 TIGR02108 273977 PQQ_syn_pqqB coenzyme PQQ biosynthesis protein B. This model describes coenzyme PQQ biosynthesis protein B, a gene required for the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ). PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases. Note that this gene appears to be required for PQQ in biosynthesis in Methylobacterium extorquens (under the name pqqG) and in Klebiella pneumoniae but that the equivalent pqqV in Acinetobacter calcoaceticus is not necessary for heterologous expression of PQQ biosynthesis in E. coli. Based on this latter finding, it is suggested (Goosen, et al. 1989) that PqqB might be a transporter or a PQQ-dependent enzyme rather than a PQQ biosynthesis enzyme. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 302 matched cddid_all.tbl CDD TIGR02109 TIGR02109 162708 PQQ_syn_pqqE coenzyme PQQ biosynthesis enzyme PqqE. This model describes coenzyme PQQ biosynthesis protein E, a prototypical peptide-cyclizing radical SAM enzyme. It links a Tyr to a Glu as the first step in the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ) from the precursor peptide PqqA. PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 358 matched cddid_all.tbl CDD TIGR02110 TIGR02110 273978 PQQ_syn_pqqF coenzyme PQQ biosynthesis probable peptidase PqqF. In a subset of species that make coenzyme PQQ (pyrrolo-quinoline-quinone), this probable peptidase is found in the PQQ biosynthesis region and is thought to act as a protease on PqqA (TIGR02107), a probable peptide precursor of the coenzyme. PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 697 matched cddid_all.tbl CDD TIGR02111 TIGR02111 131166 PQQ_syn_pqqC coenzyme PQQ biosynthesis protein C. This model describes the coenzyme PQQ (pyrrolo-quinoline-quinone) biosynthesis protein PqqC.In contrast to the broader model pfam05312, this model does not include related proteins likely to be functionally distinct from PqqC, such as homologs found in the Chlamydias. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 239 matched cddid_all.tbl CDD TIGR02112 TIGR02112 131167 cyd_oper_ybgE cyd operon protein YbgE. This model describes a small protein of unknown function, about 100 amino acids in length, essentially always found in an operon with CydAB, subunits of the cytochrome d terminal oxidase. It appears to be an integral membrane protein. It is found so far only in the Proteobacteria. [Energy metabolism, Electron transport] 93 matched cddid_all.tbl CDD TIGR02113 TIGR02113 131168 coaC_strep phosphopantothenoylcysteine decarboxylase, streptococcal. In most bacteria, a single bifunctional protein catalyses phosphopantothenoylcysteine decarboxylase and phosphopantothenate--cysteine ligase activities, sequential steps in coenzyme A biosynthesis (see TIGR00521). These activities reside in separate proteins encoded by tandem genes in some bacterial lineages. This model describes proteins from the genera Streptococcus and Enterococcus homologous to the N-terminal region of TIGR00521, corresponding to phosphopantothenoylcysteine decarboxylase activity. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pantothenate and coenzyme A] 177 matched cddid_all.tbl CDD TIGR02114 TIGR02114 131169 coaB_strep phosphopantothenate--cysteine ligase, streptococcal. In most bacteria, a single bifunctional protein catalyses phosphopantothenoylcysteine decarboxylase and phosphopantothenate--cysteine ligase activities, sequential steps in coenzyme A biosynthesis (see TIGR00521). These activities reside in separate proteins encoded by tandem genes in some bacterial lineages. This model describes proteins from the genera Streptococcus and Enterococcus homologous to the C-terminal region of TIGR00521, corresponding to phosphopantothenate--cysteine ligase activity. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pantothenate and coenzyme A] 227 matched cddid_all.tbl CDD TIGR02115 TIGR02115 131170 potass_kdpF K+-transporting ATPase, KdpF subunit. This model describes a very small integral membrane peptide KdpF, a subunit of the K(+)-translocating Kdp complex. It is found upstream of the KdpA subunit (TIGR00680). Because of its very small size and highly hydrophobic character, it is sometimes missed in genome annotation. [Transport and binding proteins, Cations and iron carrying compounds] 24 matched cddid_all.tbl CDD TIGR02116 TIGR02116 131171 toxin_Txe_YoeB toxin-antitoxin system, toxin component, Txe/YoeB family. The Axe-Txe pair in Enterococcus faecium and the homologous YefM-YoeB pair in Escherichia coli have been shown to act as an antitoxin-toxin pair. This model describes the toxin component. Nearly every example found is next to an identifiable antitoxin, as indicated by match to models TIGR01552 and/or pfam02604. [Cellular processes, Toxin production and resistance, Mobile and extrachromosomal element functions, Other] 80 matched cddid_all.tbl CDD TIGR02117 TIGR02117 273979 chp_urease_rgn conserved hypothetical protein. This conserved hypothetical protein of unknown function is found in several Proteobacteria. Its function is unknown and its genome context is not well-conserved. It is found amid urease genes in at least one species. [Hypothetical proteins, Conserved] 208 matched cddid_all.tbl CDD TIGR02118 TIGR02118 131173 TIGR02118 conserved hypothetical protein. This model represents a small family of proteins of unknown function, each about 105 amino acids in length. Conserved sites in the multiple alignment include a pair of aromatic residues, a histidine, and an aspartate. [Hypothetical proteins, Conserved] 100 matched cddid_all.tbl CDD TIGR02119 TIGR02119 131174 panF sodium/pantothenate symporter. Pantothenate (vitamin B5) is a precursor of coenzyme A and is made from aspartate and 2-oxoisovalerate in most bacteria with completed genome sequences. However, some pathogens must import pantothenate. This model describes PanF, a sodium/pantothenate symporter, from a larger family of Sodium/substrate symporters (pfam00474). Several species that have this transporter appear to lack all enzymes of pantothenate biosynthesis, namely Haemophilus influenzae, Pasteurella multocida, Fusobacterium nucleatum, and Borrelia burgdorferi. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pantothenate and coenzyme A, Transport and binding proteins, Other] 471 matched cddid_all.tbl CDD TIGR02120 TIGR02120 273980 GspF "type II secretion system protein F. This membrane protein is a component of the terminal branch complex of the general secretion pathway (GSP), also known as the""Type II"" secretion pathway. The GSP transports proteins (generally virulence-associated cell wall hydrolases) across the outer membrase of the bacterial cell. Transport across the inner membrane is often, but not exclusively handled by the Sec system. This model was constructed from the broader subfamily model, pfam00482 which includes components of pilin complexes (PilC) as well as other related genes. GspF is nearly always gene clustered with other GSP subunits. Some genes from Xylella and Xanthomonas strains score below the trusted cutoff due to excessive divergence from the family such that a sequence from Deinococcus which does not appear to be GspF scores higher. [Protein fate, Protein and peptide secretion and trafficking]" 399 matched cddid_all.tbl CDD TIGR02121 TIGR02121 273981 Na_Pro_sym sodium/proline symporter. This family consists of the sodium/proline symporter (proline permease) from a number of Gram-negative and Gram-positive bacteria and from the archaeal genus Methanosarcina. Using the related pantothenate permease as an outgroup, candidate sequences from Bifidobacterium longum and several from archaea are found to be outside the clade defined by known proline permeases. These sequences, scoring between 570 and -40, define the range between trusted and noise cutoff scores. [Transport and binding proteins, Amino acids, peptides and amines] 487 matched cddid_all.tbl CDD TIGR02122 TIGR02122 273982 TRAP_TAXI TRAP transporter solute receptor, TAXI family. This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterized but, besides C4 dicarboxylates, may include mannitol and other compounds. [Transport and binding proteins, Unknown substrate] 320 matched cddid_all.tbl CDD TIGR02123 TIGR02123 273983 TRAP_fused TRAP transporter, 4TM/12TM fusion protein. In some species, the 12-transmembrane spanning and 4-transmembrane spanning components of tripartite ATP-independent periplasmic (TRAP)-type transporters are fused. This model describes such transporters, found in the Archaea and in Bacteria. [Transport and binding proteins, Unknown substrate] 614 matched cddid_all.tbl CDD TIGR02124 TIGR02124 273984 hypE hydrogenase expression/formation protein HypE. This family contains HypE (or HupE), a protein required for expression of catalytically active hydrogenase in many systems. It appears to be an accessory protein involved in maturation rather than a regulatory protein involved in expression. HypE shows considerable homology to the thiamine-monophosphate kinase ThiL (TIGR01379) and other enzymes. 320 matched cddid_all.tbl CDD TIGR02125 TIGR02125 273985 CytB-hydogenase Ni/Fe-hydrogenase, b-type cytochrome subunit. This model describes a family of cytochrome b proteins which appear to be specific for nickel-iron hydrogenase complexes. Every genome which contains a member of this family posesses a Ni/Fe hydrogenase according to Genome Properties (GenProp0177), and most are gene clustered with other hydrogenase components. Some Ni/Fe hydrogenase-containing species lack a member of this family but contain other CytB homologs (pfam01292) which may substitute for it. 211 matched cddid_all.tbl CDD TIGR02126 TIGR02126 273986 phgtail_TP901_1 phage major tail protein, TP901-1 family. This family includes the members of pfam06199 but is broader. Characterized members are major tail proteins from various phage, including lactococcal temperate bacteriophage TP901-1. [Mobile and extrachromosomal element functions, Prophage functions] 136 matched cddid_all.tbl CDD TIGR02127 TIGR02127 273987 pyrF_sub2 orotidine 5'-phosphate decarboxylase, subfamily 2. This model represents orotidine 5'-monophosphate decarboxylase, the PyrF protein of pyrimidine nucleotide biosynthesis. See TIGR01740 for a related but distinct subfamily of the same enzyme. [Purines, pyrimidines, nucleosides, and nucleotides, Pyrimidine ribonucleotide biosynthesis] 261 matched cddid_all.tbl CDD TIGR02128 TIGR02128 273988 G6PI_arch bifunctional phosphoglucose/phosphomannose isomerase. This bifunctional isomerase is a member of the larger PGI superfamily and only distantly related to other glucose-6-phosphate isomerases. The family is limited to the archaea. 308 matched cddid_all.tbl CDD TIGR02129 TIGR02129 162719 hisA_euk phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase, eukaryotic type. This enzyme acts in the biosynthesis of histidine and has been characterized in S. cerevisiae and Arabidopsis where it complements the E. coli HisA gene. In eukaryotes the gene is known as HIS6. In bacteria, this gene is found in Fibrobacter succinogenes, presumably due to lateral gene transfer from plants in the rumen gut. [Amino acid biosynthesis, Histidine family] 253 matched cddid_all.tbl CDD TIGR02130 TIGR02130 131185 dapB_plant dihydrodipicolinate reductase. This narrow family includes genes from Arabidopsis and Fibrobacter succinogenes (which probably recieved the gene from a plant via lateral gene transfer). The sequences are distantly related to the dihydrodipicolinate reductases from archaea. In Fibrobacter this gene is the only candidate DHPR in the genome. [Amino acid biosynthesis, Aspartate family] 275 matched cddid_all.tbl CDD TIGR02131 TIGR02131 131186 phaP_Bmeg polyhydroxyalkanoic acid inclusion protein PhaP. This model describes a protein found in polyhydroxyalkanoic acid (PHA) gene regions and incorporated into PHA inclusions in Bacillus cereus and Bacillus megaterium. The role of the protein may include amino acid storage (see McCool,G.J. and Cannon,M.C, 1999). 165 matched cddid_all.tbl CDD TIGR02132 TIGR02132 131187 phaR_Bmeg polyhydroxyalkanoic acid synthase, PhaR subunit. This model describes a protein, PhaR, localized to polyhydroxyalkanoic acid (PHA) inclusion granules in Bacillus cereus and related species. PhaR is required for PHA biosynthesis along with PhaC and may be a regulatory subunit. 189 matched cddid_all.tbl CDD TIGR02133 TIGR02133 273989 RPI_actino ribose 5-phosphate isomerase. This family is a member of the RpiB/LacA/LacB subfamily (TIGR00689) but lies outside the RpiB equivalog (TIGR01120) which is also a member of that subfamily. Ribose 5-phosphate isomerase is an essential enzyme of the pentose phosphate pathway; a pathway that appears to be present in the actinobacteria. The only candidates for ribose 5-phosphate isomerase in the Actinobacteria are members of this family. 148 matched cddid_all.tbl CDD TIGR02134 TIGR02134 131189 transald_staph transaldolase. This small family of proteins is a member of the transaldolase sybfamily represented by pfam00923. Coxiella and Staphylococcus lack members of the known transaldolase equivalog families and appear to require a transaldolase activity for completion of the pentose phosphate pathway. [Energy metabolism, Pentose phosphate pathway] 236 matched cddid_all.tbl CDD TIGR02135 TIGR02135 273990 phoU_full phosphate transport system regulatory protein PhoU. This model describes PhoU, a regulatory protein of unknown mechanism for high-affinity phosphate ABC transporter systems. The protein consists of two copies of the domain described by pfam01895. Deletion of PhoU activates constitutive expression of the phosphate ABC transporter and allows phosphate transport, but causes a growth defect and so likely has some second function. [Regulatory functions, Other, Transport and binding proteins, Anions] 212 matched cddid_all.tbl CDD TIGR02136 TIGR02136 273991 ptsS_2 phosphate binding protein. Members of this family are phosphate-binding proteins. Most are found in phosphate ABC-transporter operons, but some are found in phosphate regulatory operons. This model separates members of the current family from the phosphate ABC transporter phosphate binding protein described by TIGRFAMs model TIGR00975. [Transport and binding proteins, Anions] 287 matched cddid_all.tbl CDD TIGR02137 TIGR02137 162723 HSK-PSP phosphoserine phosphatase/homoserine phosphotransferase bifunctional protein. This protein is has been characterized as both a phosphoserine phosphatase and a phosphoserine:homoserine phosphotransferase. In Pseudomonas aeruginosa, where the characterization was done, a second phosphoserine phosphatase (SerB) and a second homoserine kinase (thrB) are found, but in Fibrobacter succinogenes neither are present. This enzyme is a member of the haloacid dehalogenase (HAD) superfamily, specifically part of subfamily IB by virtue of the presence of an alpha helical domain in between motifs I and II of the HAD domain. The closest homologs to this family are monofunctional phosphoserine phosphatases (TIGR00338). 203 matched cddid_all.tbl CDD TIGR02138 TIGR02138 273992 phosphate_pstC phosphate ABC transporter, permease protein PstC. The typical operon for the high affinity inorganic phosphate ABC transporter encodes an ATP-binding protein, a phosphate-binding protein, and two permease proteins. This family consists of one of the two permease proteins, PstC, which is homologous to PstA (TIGR00974). In the model bacterium Escherichia coli, this transport system is induced when the concentration of extrallular inorganic phosphate is low. A constitutive, lower affinity transporter operates otherwise. [Transport and binding proteins, Anions] 295 matched cddid_all.tbl CDD TIGR02139 TIGR02139 131194 permease_CysT sulfate ABC transporter, permease protein CysT. This model represents CysT, one of two homologous, tandem permeases in the sulfate ABC transporter system; the other is CysW (TIGR02140). The sulfate transporter has been described in E. coli as transporting sulfate, thiosulfate, selenate, and selenite. Sulfate transporters may also transport molybdate ion if a specific molybdate transporter is not present. [Transport and binding proteins, Anions] 265 matched cddid_all.tbl CDD TIGR02140 TIGR02140 162725 permease_CysW sulfate ABC transporter, permease protein CysW. This model represents CysW, one of two homologous, tandem permeases in the sulfate ABC transporter system; the other is CysT (TIGR02139). The sulfate transporter has been described in E. coli as transporting sulfate, thiosulfate, selenate, and selenite. Sulfate transporters may also transport molybdate ion if a specific molybdate transporter is not present. [Transport and binding proteins, Anions] 261 matched cddid_all.tbl CDD TIGR02141 TIGR02141 273993 modB_ABC molybdate ABC transporter, permease protein. This model describes the permease protein, ModB, of the molybdate ABC transporter. This system has been characterized in E. coli, Staphylococcus carnosus, Rhodobacter capsulatus and Azotobacter vinlandii. Molybdate is chemically similar to sulfate, thiosulfate, and selenate. These related substrates, and sometimes molybdate itself, can be transported by the homologous sulfate receptor. Some apparent molybdenum transport operons include a permease related to this ModB, although less similar than some sulfate permease proteins and not included in this model. [Transport and binding proteins, Anions] 208 matched cddid_all.tbl CDD TIGR02142 TIGR02142 131197 modC_ABC molybdenum ABC transporter, ATP-binding protein. This model represents the ATP-binding cassette (ABC) protein of the three subunit molybdate ABC transporter. The three proteins of this complex are homologous to proteins of the sulfate ABC transporter. Molybdenum may be used in nitrogenases of nitrogen-fixing bacteria and in molybdopterin cofactors. In some cases, molybdate may be transported by a sulfate transporter rather than by a specific molybdate transporter. [Transport and binding proteins, Anions] 354 matched cddid_all.tbl CDD TIGR02143 TIGR02143 131198 trmA_only tRNA (uracil(54)-C(5))-methyltransferase. This family consists exclusively of proteins believed to act as tRNA (uracil-5-)-methyltransferase. All members of far are proteobacterial. The seed alignment was taken directly from pfam05958 in Pfam 12.0, but higher cutoffs are used to select only functionally equivalent proteins. Homologous proteins excluded by the higher cutoff scores of this model include other uracil methyltransferases, such as RumA, active on rRNA. [Protein synthesis, tRNA and rRNA base modification] 353 matched cddid_all.tbl CDD TIGR02144 TIGR02144 273994 LysX_arch "Lysine biosynthesis enzyme LysX. The family of proteins found in this equivalog include the characterized LysX from Thermus thermophilus, which is part of a well-organized lysine biosynthesis gene cluster. LysX is believed to carry out an ATP-dependent acylation of the amino group of alpha-aminoadipate in the prokaryotic version of the fungal AAA lysine biosynthesis pathway. No species having a sequence in this equivalog contains the elements of the more common diaminopimelate lysine biosythesis pathway, and none has been shown to be a lysine auxotroph. These sequences have mainly recieved the name of the related enzyme, ""ribosomal protein S6 modification protein RimK"". RimK has been characterized in E. coli, and acts by ATP-dependent condensation of S6 with glutamate residues." 280 matched cddid_all.tbl CDD TIGR02145 TIGR02145 273995 Fib_succ_major Fibrobacter succinogenes major paralogous domain. This domain of about 175 to 200 amino acids is found, in from one to five copies, in over 50 proteins in Fibrobacter succinogenes S85, an obligate anaerobe of the rumen. Many members of this family have an apparent lipoprotein signal sequence. Conserved cysteine residues, suggestive of disulfide bond formation, are also consistent with an extracytoplasmic location for this domain. This domain can also be found in small numbers of proteins in Chlorobium tepidum and Bacteroides thetaiotaomicron. [Cell envelope, Other] 171 matched cddid_all.tbl CDD TIGR02146 TIGR02146 162728 LysS_fung_arch homocitrate synthase. This model includes the yeast LYS21 gene which carries out the first step of the alpha-aminoadipate (AAA) lysine biosynthesis pathway. A related pathway is found in Thermus thermophilus. This enzyme is closely related to 2-isopropylmalate synthase (LeuA) and citramalate synthase (CimA), both of which are present in the euryarchaeota. Some archaea have a separate homocitrate synthase (AksA) which also synthesizes longer homocitrate analogs. 344 matched cddid_all.tbl CDD TIGR02147 TIGR02147 273996 Fsuc_second TIGR02147 family protein. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85 and a smaller number in Bdellovibrio bacteriovorus HD100. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized. [Hypothetical proteins, Conserved] 271 matched cddid_all.tbl CDD TIGR02148 TIGR02148 162730 Fibro_Slime fibro-slime domain. This model represents a conserved region of about 90 amino acids, shared in at least 4 distinct large putative proteins from the slime mold Dictyostelium discoideum and 10 proteins from the rumen bacterium Fibrobacter succinogenes, and in no other species so far. We propose here the name fibro-slime domain 90 matched cddid_all.tbl CDD TIGR02149 TIGR02149 273997 glgA_Coryne glycogen synthase, Corynebacterium family. This model describes Corynebacterium glutamicum GlgA and closely related proteins in several other species. This enzyme is required for glycogen biosynthesis and appears to replace the distantly related TIGR02095 family of ADP-glucose type glycogen synthase in Corynebacterium glutamicum, Mycobacterium tuberculosis, Bifidobacterium longum, and Streptomyces coelicolor. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 388 matched cddid_all.tbl CDD TIGR02150 TIGR02150 273998 IPP_isom_1 isopentenyl-diphosphate delta-isomerase, type 1. This model represents type 1 of two non-homologous families of the enzyme isopentenyl-diphosphate delta-isomerase (IPP isomerase). IPP is an essential building block for many compounds, including enzyme cofactors, sterols, and prenyl groups. This inzyme interconverts isopentenyl diphosphate and dimethylallyl diphosphate. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 158 matched cddid_all.tbl CDD TIGR02151 TIGR02151 273999 IPP_isom_2 isopentenyl-diphosphate delta-isomerase, type 2. Isopentenyl-diphosphate delta-isomerase (IPP isomerase) interconverts isopentenyl diphosphate and dimethylallyl diphosphate. This model represents the type 2 enzyme. FMN, NADPH, and Mg2+ are required by this form, which lacks homology to the type 1 enzyme (TIGR02150). IPP is precursor to many compounds, including enzyme cofactors, sterols, and isoprenoids. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 333 matched cddid_all.tbl CDD TIGR02152 TIGR02152 274000 D_ribokin_bact ribokinase. This model describes ribokinase, an enzyme catalyzing the first step in ribose catabolism. The rbsK gene encoding ribokinase typically is found with ribose transport genes. Ribokinase belongs to the carbohydrate kinase pfkB family (pfam00294). In the wide gulf between the current trusted (360 bit) and noise (100 bit) cutoffs are a number of sequences, few of which are clustered with predicted ribose transport genes but many of which are currently annotated as if having ribokinase activity. Most likely some have this function and others do not. [Energy metabolism, Sugars] 293 matched cddid_all.tbl CDD TIGR02153 TIGR02153 274001 gatD_arch glutamyl-tRNA(Gln) amidotransferase, subunit D. This peptide is found only in the Archaea. It is part of a heterodimer, with GatE (TIGR00134), that acts as an amidotransferase on misacylated Glu-tRNA(Gln) to produce Gln-tRNA(Gln). The analogous amidotransferase found in bacteria is the GatABC system, although GatABC homologs in the Archaea appear to act instead on Asp-tRNA(Asn). [Protein synthesis, tRNA aminoacylation] 404 matched cddid_all.tbl CDD TIGR02154 TIGR02154 131209 PhoB phosphate regulon transcriptional regulatory protein PhoB. PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well. [Regulatory functions, DNA interactions, Signal transduction, Two-component systems] 226 matched cddid_all.tbl CDD TIGR02155 TIGR02155 131210 PA_CoA_ligase phenylacetate-CoA ligase. Phenylacetate-CoA ligase (PA-CoA ligase) catalyzes the first step in aromatic catabolism of phenylacetic acid (PA) into phenylacetyl-CoA (PA-CoA). Often located in a conserved gene cluster with enzymes involved in phenylacetic acid activation (paaG/H/I/J), phenylacetate-CoA ligase has been found among the proteobacteria as well as in gram positive prokaryotes. In the B-subclass proteobacterium Azoarcus evansii, phenylacetate-CoA ligase has been shown to be induced under aerobic and anaerobic growth conditions. It remains unclear however, whether this induction is due to the same enzyme or to another isoenzyme restricted to specific anaerobic growth conditions. [Energy metabolism, Other] 422 matched cddid_all.tbl CDD TIGR02156 TIGR02156 131211 PA_CoA_Oxy1 phenylacetate-CoA oxygenase, PaaG subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA. [Energy metabolism, Other] 289 matched cddid_all.tbl CDD TIGR02157 TIGR02157 274002 PA_CoA_Oxy2 phenylacetate-CoA oxygenase, PaaH subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA. [Energy metabolism, Other] 90 matched cddid_all.tbl CDD TIGR02158 TIGR02158 131213 PA_CoA_Oxy3 phenylacetate-CoA oxygenase, PaaI subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA. [Energy metabolism, Other] 237 matched cddid_all.tbl CDD TIGR02159 TIGR02159 131214 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA. [Energy metabolism, Other] 146 matched cddid_all.tbl CDD TIGR02160 TIGR02160 131215 PA_CoA_Oxy5 phenylacetate-CoA oxygenase/reductase, PaaK subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA. [Energy metabolism, Other] 352 matched cddid_all.tbl CDD TIGR02161 TIGR02161 131216 napC_nirT periplasmic nitrate (or nitrite) reductase c-type cytochrome, NapC/NirT family. Nearly every member of this subfamily is NapC, a predicted membrane-anchored four-heme c-type cytochrome that forms one component of the periplasmic nitrate reductase along with NapA, NapB, NapD, NapE, and NapF subunits. A single known exception at this time is NirT, which is instead a component of a nitrite reductase. This family excludes TorC subunits of trimethylamine N-oxide (TMAO) reductases. 185 matched cddid_all.tbl CDD TIGR02162 TIGR02162 274003 torC trimethylamine-N-oxide reductase c-type cytochrome TorC. This family includes consists of TorC, a pentahemic c-type cytochrome subunit of periplasmic reductases for trimethylamine-N-oxide (TMAO). The N-terminal half is closely related to tetrahemic NapC (or NirT) subunits of periplasmic nitrate (or nitrite) reductases; some species have both TMAO and nitrate reductase complexes. 386 matched cddid_all.tbl CDD TIGR02163 TIGR02163 274004 napH_ ferredoxin-type protein, NapH/MauN family. Most members of this family are the NapH protein, found next to NapG,in operons that encode the periplasmic nitrate reductase. Some species with this reductase lack NapC but accomplish electron transfer to NapAB in some other manner, likely to involve NapH, NapG, and/or some other protein. A few members of this protein are designated MauN and are found in methylamine utilization operons in species that appear to lack a periplasmic nitrate reductase. 255 matched cddid_all.tbl CDD TIGR02164 TIGR02164 131219 torA trimethylamine-N-oxide reductase TorA. This very narrowly defined family represents TorA, part of a family of related molybdoenzymes that include biotin sulfoxide reductases, dimethyl sulfoxide reductases, and at least two different subfamilies of trimethylamine-N-oxide reductases. A single enzyme from the larger family may have more than one activity. TorA typically is located in the periplasm, has a Tat (twin-arginine translocation)-dependent signal sequence, and is encoded in a torCAD operon. 822 matched cddid_all.tbl CDD TIGR02165 TIGR02165 274005 cas5_6_GSU0054 CRISPR-associated protein GSU0054/csb2, Dpsyc system. This model represents a CRISPR-associated protein from the Dpsyc subtype (a type I-C variant), named for Desulfotalea psychrophila LSv54. CRISPR systems confer resistance in prokaryotes to invasive DNA or RNA, including phage and plasmids. CRISPR-associated proteins typically are found near CRISPR repeats and other CRISPR-associated proteins, have low levels of sequence identify, have sequence relationships that suggest lateral transfer, and show some sequence similarity to DNA-active proteins such as helicases and repair proteins. 484 matched cddid_all.tbl CDD TIGR02166 TIGR02166 274006 dmsA_ynfE anaerobic dimethyl sulfoxide reductase, A subunit, DmsA/YnfE family. Members of this family include known and probable dimethyl sulfoxide reductase (DMSO reductase) A chains. In E. coli, dmsA encodes the canonical anaerobic DMSO reductase A chain. The paralog ynfE, as part of ynfFGH expressed from a multicopy plasmid, could complement a dmsABC deletion, suggesting a similar function and some overlap in specificity, although YnfE could not substitute for DmsA in a mixed complex. 797 matched cddid_all.tbl CDD TIGR02167 TIGR02167 274007 Liste_lipo_26 bacterial surface protein 26-residue repeat. This model describes a tandem peptide repeat sequence of 25 or 26 residues, found in predicted surface proteins (often lipoproteins) from Listeria monocytogenes, L. innocua, Enterococcus faecalis, Lactobacillus plantarum, Mycoplasma mycoides, Helicobacter hepaticus, and other species. 26 matched cddid_all.tbl CDD TIGR02168 TIGR02168 274008 SMC_prok_B chromosome segregation protein SMC, common bacterial type. SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] 1179 matched cddid_all.tbl CDD TIGR02169 TIGR02169 274009 SMC_prok_A chromosome segregation protein SMC, primarily archaeal type. SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] 1164 matched cddid_all.tbl CDD TIGR02170 TIGR02170 274010 thyX thymidylate synthase, flavin-dependent. Two forms of microbial thymidylate synthase are known: ThyA (2.1.1.45) and ThyX (2.1.1.148). This model describes ThyX, a homotetrameric flavoprotein. Both enzymes convert dUMP to dTMP. Under oxygen-limiting conditions, thyX can complement a thyA mutation. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism] 209 matched cddid_all.tbl CDD TIGR02171 TIGR02171 274011 Fb_sc_TIGR02171 Fibrobacter succinogenes paralogous family TIGR02171. This model describes a paralogous family of the rumen bacterium Fibrobacter succinogenes. Eleven members are found in Fibrobacter succinogenes S85, averaging over 900 amino acids in length. More than half are predicted lipoproteins. The function is unknown. 912 matched cddid_all.tbl CDD TIGR02172 TIGR02172 162743 Fb_sc_TIGR02172 Fibrobacter succinogenes paralogous family TIGR02172. This model describes a paralogous family of five proteins, likely to be enzymes, in the rumen bacterium Fibrobacter succinogenes S85. Members show homology to proteins described by pfam01636, a phosphotransferase enzyme family associated with resistance to aminoglycoside antibiotics. 226 matched cddid_all.tbl CDD TIGR02173 TIGR02173 274012 cyt_kin_arch cytidylate kinase, putative. Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017. 171 matched cddid_all.tbl CDD TIGR02174 TIGR02174 274013 CXXU_selWTH selT/selW/selH selenoprotein domain. This model represents a domain found in both bacteria and animals, including animal proteins SelT, SelW, and SelH, all of which are selenoproteins. In a CXXC motif near the N-terminus of the domain, selenocysteine may replace the second Cys. Proteins with this domain may include an insert of about 70 amino acids. This model is broader than the current SelW model pfam05169 in Pfam. 73 matched cddid_all.tbl CDD TIGR02175 TIGR02175 274014 PorC_KorC 2-oxoacid:acceptor oxidoreductase, gamma subunit, pyruvate/2-ketoisovalerate family. A number of anaerobic and microaerophilic species lack pyruvate dehydrogenase and have instead a four subunit, oxygen-sensitive pyruvate oxidoreductase, with either ferredoxins or flavodoxins (H. pylori) used as the acceptor. Several related four-subunit enzymes may exist in the same species. This model describes the gamma subunit. In Pyrococcus furious, enzymes active on pyruvate and 2-ketoisovalerate share a common gamma subunit. 177 matched cddid_all.tbl CDD TIGR02176 TIGR02176 131231 pyruv_ox_red pyruvate:ferredoxin (flavodoxin) oxidoreductase, homodimeric. This model represents a single chain form of pyruvate:ferredoxin (or flavodoxin) oxidoreductase. This enzyme may transfer electrons to nitrogenase in nitrogen-fixing species. Portions of this protein are homologous to gamma subunit of the four subunit pyruvate:ferredoxin (flavodoxin) oxidoreductase. 1165 matched cddid_all.tbl CDD TIGR02177 TIGR02177 274015 PorB_KorB 2-oxoacid:acceptor oxidoreductase, beta subunit, pyruvate/2-ketoisovalerate family. A number of anaerobic and microaerophilic species lack pyruvate dehydrogenase and have instead a four subunit, oxygen-sensitive pyruvate oxidoreductase, with either ferredoxins or flavodoxins used as the acceptor. Several related four-subunit enzymes may exist in the same species. This model describes a subfamily of beta subunits, representing mostly pyruvate and 2-ketoisovalerate specific enzymes. 287 matched cddid_all.tbl CDD TIGR02178 TIGR02178 131233 yeiP elongation factor P-like protein YeiP. This model represents the family of Escherichia coli protein YeiP, a close homolog of elongation factor P (TIGR00038) and probably itself a translation factor. Member of this family are found only in some Gammaproteobacteria, including E. coli and Vibrio cholerae. [Protein synthesis, Translation factors] 186 matched cddid_all.tbl CDD TIGR02179 TIGR02179 131234 PorD_KorD 2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family. A number of anaerobic and microaerophilic species lack pyruvate dehydrogenase and have instead a four subunit, oxygen-sensitive pyruvate oxidoreductase, with either ferredoxins or flavodoxins used as the acceptor. Several related four-subunit enzymes may exist in the same species. This model describes a subfamily of delta subunits, representing mostly pyruvate, 2-ketoisovalerate, and 2-oxoglutarate specific enzymes. The delta subunit is the smallest and resembles ferredoxins. 78 matched cddid_all.tbl CDD TIGR02180 TIGR02180 274016 GRX_euk Glutaredoxin. Glutaredoxins are thioltransferases (disulfide reductases) which utilize glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system. Glutaredoxins utilize the CXXC motif common to thioredoxins and are involved in multiple cellular processes including protection from redox stress, reduction of critical enzymes such as ribonucleotide reductase and the generation of reduced sulfur for iron sulfur cluster formation. Glutaredoxins are capable of reduction of mixed disulfides of glutathione as well as the formation of glutathione mixed disulfides. This model represents eukaryotic glutaredoxins and includes sequences from fungi, plants and metazoans as well as viruses. 83 matched cddid_all.tbl CDD TIGR02181 TIGR02181 274017 GRX_bact Glutaredoxin, GrxC family. Glutaredoxins are thioltransferases (disulfide reductases) which utilize glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system. Glutaredoxins utilize the CXXC motif common to thioredoxins and are involved in multiple cellular processes including protection from redox stress, reduction of critical enzymes such as ribonucleotide reductase and the generation of reduced sulfur for iron sulfur cluster formation. Glutaredoxins are capable of reduction of mixed disulfides of glutathione as well as the formation of glutathione mixed disulfides. This family of glutaredoxins includes the E. coli protein GrxC (Grx3) which appears to have a secondary role in reducing ribonucleotide reductase (in the absence of GrxA) possibly indicating a role in the reduction of other protein disulfides. [Energy metabolism, Electron transport] 79 matched cddid_all.tbl CDD TIGR02182 TIGR02182 274018 GRXB Glutaredoxin, GrxB family. Glutaredoxins are thioltransferases (disulfide reductases) which utilize glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system. Glutaredoxins utilize the CXXC motif common to thioredoxins and are involved in multiple cellular processes including protection from redox stress, reduction of critical enzymes such as ribonucleotide reductase and the generation of reduced sulfur for iron sulfur cluster formation. Glutaredoxins are capable of reduction of mixed disulfides of glutathione as well as the formation of glutathione mixed disulfides. This model includes the highly abundant E. coli GrxB (Grx2) glutaredoxin which is notably longer than either GrxA or GrxC. Unlike the other two E. coli glutaredoxins, GrxB appears to be unable to reduce ribonucleotide reductase, and may have more to do with resistance to redox stress. [Energy metabolism, Electron transport] 209 matched cddid_all.tbl CDD TIGR02183 TIGR02183 131238 GRXA Glutaredoxin, GrxA family. Glutaredoxins are thioltransferases (disulfide reductases) which utilize glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system. Glutaredoxins utilize the CXXC motif common to thioredoxins and are involved in multiple cellular processes including protection from redox stress, reduction of critical enzymes such as ribonucleotide reductase and the generation of reduced sulfur for iron sulfur cluster formation. Glutaredoxins are capable of reduction of mixed disulfides of glutathione as well as the formation of glutathione mixed disulfides. This model includes the E. coli glyutaredoxin GrxA which appears to have primary responsibility for the reduction of ribonucleotide reductase. 86 matched cddid_all.tbl CDD TIGR02184 TIGR02184 213689 Myco_arth_vir_N Mycoplasma virulence family signal region. This model represents the N-terminal region, including a probable signal sequence or signal anchor which in most instances has four consecutive Lys residues before the hydrophobic stretch, of a family of large, virulence-associated proteins in Mycoplasma arthritidis and smaller proteins in Mycoplasma capricolum. 33 matched cddid_all.tbl CDD TIGR02185 TIGR02185 274019 Trep_Strep putative ECF transporter S component, Trep_Strep family. This family consists of strongly hydrophobic proteins about 190 amino acids in length with a strongly basic motif near the C-terminus. If is found in rather few species, but in paralogous families of 12 members in the oral pathogenic spirochaete Treponema denticola and 2 in Streptococcus pneumoniae R6. [Transport and binding proteins, Unknown substrate] 189 matched cddid_all.tbl CDD TIGR02186 TIGR02186 274020 alph_Pro_TM conserved hypothetical protein. This family consists of predicted transmembrane proteins of about 270 amino acids. Members are found, so far, only among the Alphaproteobacteria and only once in each genome. 261 matched cddid_all.tbl CDD TIGR02187 TIGR02187 274021 GlrX_arch "Glutaredoxin-like domain protein. This family of archaeal proteins contains a C-terminal domain with homology to bacterial and eukaryotic glutaredoxins, including a CPYC motif. There is an N-terminal domain which has even more distant homology to glutaredoxins. The name ""glutaredoxin"" may be inappropriate in the sense of working in tandem with glutathione and glutathione reductase which may not be present in the archaea. The overall domain structure appears to be related to bacterial alkylhydroperoxide reductases, but the homology may be distant enough that the function of this family is wholly different." 215 matched cddid_all.tbl CDD TIGR02188 TIGR02188 274022 Ac_CoA_lig_AcsA acetate--CoA ligase. This model describes acetate-CoA ligase (EC 6.2.1.1), also called acetyl-CoA synthetase and acetyl-activating enzyme. It catalyzes the reaction ATP + acetate + CoA = AMP + diphosphate + acetyl-CoA and belongs to the family of AMP-binding enzymes described by pfam00501. 626 matched cddid_all.tbl CDD TIGR02189 TIGR02189 274023 GlrX-like_plant Glutaredoxin-like family. This family of glutaredoxin-like proteins is aparrently limited to plants. Multiple isoforms are found in A. thaliana and O.sativa. 99 matched cddid_all.tbl CDD TIGR02190 TIGR02190 131245 GlrX-dom Glutaredoxin-family domain. This C-terminal domain with homology to glutaredoxin is fused to an N-terminal peroxiredoxin-like domain. 79 matched cddid_all.tbl CDD TIGR02191 TIGR02191 274024 RNaseIII ribonuclease III, bacterial. This family consists of bacterial examples of ribonuclease III. This enzyme cleaves double-stranded rRNA. It is involved in processing ribosomal RNA precursors. It is found even in minimal genones such as Mycoplasma genitalium and Buchnera aphidicola, and in some cases has been shown to be an essential gene. These bacterial proteins contain a double-stranded RNA binding motif (pfam00035) and a ribonuclease III domain (pfam00636). Eukaryotic homologs tend to be much longer proteins with additional domains, localized to the nucleus, and not included in this family. [Transcription, RNA processing] 220 matched cddid_all.tbl CDD TIGR02192 TIGR02192 131247 HtrL_YibB protein YibB. The protein from this rare, uncharacterized protein family is designated HtrL or YibB in E. coli, where its gene is found in a region of LPS core biosynthesis genes. Homologs are found in Shigella flexneri, Campylobacter jejuni, and Caenorhabditis elegans only. The htrL gene may represent an insertion to the LPS core biosynthesis region, rather than an LPS biosynthetic protein. [Hypothetical proteins, Conserved] 270 matched cddid_all.tbl CDD TIGR02193 TIGR02193 274025 heptsyl_trn_I lipopolysaccharide heptosyltransferase I. This family consists of examples of ADP-heptose:LPS heptosyltransferase I, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 319 matched cddid_all.tbl CDD TIGR02194 TIGR02194 131249 GlrX_NrdH Glutaredoxin-like protein NrdH. NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterized by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase. 72 matched cddid_all.tbl CDD TIGR02195 TIGR02195 274026 heptsyl_trn_II lipopolysaccharide heptosyltransferase II. This family consists of examples of ADP-heptose:LPS heptosyltransferase II, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 334 matched cddid_all.tbl CDD TIGR02196 TIGR02196 274027 GlrX_YruB Glutaredoxin-like protein, YruB-family. This glutaredoxin-like protein family contains the conserved CxxC motif and includes the Clostridium pasteurianum protein YruB which has been cloned from a rubredoxin operon. Somewhat related to NrdH, it is unknown whether this protein actually interacts with glutathione/glutathione reducatase, or, like NrdH, some other reductant system. 74 matched cddid_all.tbl CDD TIGR02197 TIGR02197 274028 heptose_epim ADP-L-glycero-D-manno-heptose-6-epimerase. This family consists of examples of ADP-L-glycero-D-mannoheptose-6-epimerase, an enzyme involved in biosynthesis of the inner core of lipopolysaccharide (LPS) for Gram-negative bacteria. This enzyme is homologous to UDP-glucose 4-epimerase (TIGR01179) and belongs to the NAD dependent epimerase/dehydratase family (pfam01370). [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 314 matched cddid_all.tbl CDD TIGR02198 TIGR02198 274029 rfaE_dom_I rfaE bifunctional protein, domain I. RfaE is a protein involved in the biosynthesis of ADP-L-glycero-D-manno-heptose, a precursor for LPS inner core biosynthesis. RfaE is a bifunctional protein in E. coli, and separate proteins in some other genome. The longer, N-terminal domain I (this family) is suggested to act in D-glycero-D-manno-heptose 1-phosphate biosynthesis, while domain II (TIGR02199) adds ADP to yield ADP-D-glycero-D-manno-heptose. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 315 matched cddid_all.tbl CDD TIGR02199 TIGR02199 131254 rfaE_dom_II rfaE bifunctional protein, domain II. RfaE is a protein involved in the biosynthesis of ADP-L-glycero-D-manno-heptose, a precursor for LPS inner core biosynthesis. RfaE is a bifunctional protein in E. coli, and separate proteins in some other genome. Domain I (TIGR02198) is suggested to act in D-glycero-D-manno-heptose 1-phosphate biosynthesis, while domain II (this family) adds ADP to yield ADP-D-glycero-D-manno-heptose. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 144 matched cddid_all.tbl CDD TIGR02200 TIGR02200 131255 GlrX_actino Glutaredoxin-like protein. This family of glutaredoxin-like proteins is limited to the Actinobacteria and contains the conserved CxxC motif. 77 matched cddid_all.tbl CDD TIGR02201 TIGR02201 131256 heptsyl_trn_III lipopolysaccharide heptosyltransferase III, putative. This family consists of examples of the putative ADP-heptose:LPS heptosyltransferase III, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria. This enzyme may be less widely distributed than heptosyltransferases I and II. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 344 matched cddid_all.tbl CDD TIGR02202 TIGR02202 131257 Ehrlichia_rpt Ehrlichia chaffeensis immunodominant surface protein repeat. This model represents 77 residues of an 80 amino acid (240 nucleotide) tandem repeat, found in a variable number of copies in an immunodominant outer membrane protein of Ehrlichia chaffeensis, a tick-borne obligate intracellular pathogen. 77 matched cddid_all.tbl CDD TIGR02203 TIGR02203 131258 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA. This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides, Transport and binding proteins, Other] 571 matched cddid_all.tbl CDD TIGR02204 TIGR02204 131259 MsbA_rel ABC transporter, permease/ATP-binding protein. This protein is related to a Proteobacterial ATP transporter that exports lipid A and to eukaryotic P-glycoproteins. 576 matched cddid_all.tbl CDD TIGR02205 TIGR02205 274030 septum_zipA cell division protein ZipA. This model represents the full length of bacterial cell division protein ZipA. The N-terminal hydrophobic stretch is an uncleaved signal-anchor sequence. This is followed by an unconserved, variable length, low complexity region, and then a conserved C-terminal region of about 140 amino acids (see pfam04354) that interacts with the tubulin-like cell division protein FtsZ. [Cellular processes, Cell division] 284 matched cddid_all.tbl CDD TIGR02206 TIGR02206 131261 intg_mem_TP0381 conserved hypothetical integral membrane protein TIGR02206. This model represents a family of hydrophobic proteins with seven predicted transmembrane alpha helices. Members are found in Bacillus subtilis (ywaF), TP0381 from Treponema pallidum (TP0381), Streptococcus pyogenes, Rhodococcus erythropolis, etc. 222 matched cddid_all.tbl CDD TIGR02207 TIGR02207 274031 lipid_A_htrB lipid A biosynthesis lauroyl (or palmitoleoyl) acyltransferase. This model represents a narrow clade of acyltransferases, nearly all of which transfer a lauroyl group to KDO2-lipid IV-A, a lipid A precursor; these proteins are termed lipid A biosynthesis lauroyl acyltransferase, HtrB. An exception is a closely related paralog of E. coli HtrB, LpxP, which acts in cold shock conditions by transferring a palmitoleoyl rather than lauroyl group to the lipid A precursor. Members of this family are homologous to the family of acyltransferases responsible for the next step in lipid A biosynthesis. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 303 matched cddid_all.tbl CDD TIGR02208 TIGR02208 274032 lipid_A_msbB lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase. This family consists of MsbB in E. coli and closely related proteins in other species. MsbB is homologous to HtrB (TIGR02207) and acts immediately after it in the biosynthesis of KDO-2 lipid A (also called Re LPS and Re endotoxin). These two enzymes act after creation of KDO-2 lipid IV-A by addition of the KDO sugars. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 305 matched cddid_all.tbl CDD TIGR02209 TIGR02209 131264 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species. [Cellular processes, Cell division] 85 matched cddid_all.tbl CDD TIGR02210 TIGR02210 274033 rodA_shape rod shape-determining protein RodA. This protein is a member of the FtsW/RodA/SpoVE family (pfam01098). It is found only in species with rod (or spiral) shapes. In many species, mutation of rodA has been shown to correlate with loss of the normal rod shape. Note that RodA homologs are found, scoring below the cutoffs for this model, in a number of both rod-shaped and coccoid bacteria, including four proteins in Bacillus anthracis, for example. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan, Cellular processes, Cell division] 352 matched cddid_all.tbl CDD TIGR02211 TIGR02211 131266 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein. This model represents LolD, a member of the ABC transporter family (pfam00005). LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on whether the residue immediately following the new, modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. The top scoring proteins excluded by this model include homologs from the archaeal genus Methanosarcina. [Protein fate, Protein and peptide secretion and trafficking] 221 matched cddid_all.tbl CDD TIGR02212 TIGR02212 274034 lolCE lipoprotein releasing system, transmembrane protein, LolC/E family. This model describes the LolC protein, and its paralog LolE found in some species. These proteins are homologous to permease proteins of ABC transporters. In some species, two paralogs occur, designated LolC and LolE. In others, a single form is found and tends to be designated LolC. [Protein fate, Protein and peptide secretion and trafficking] 411 matched cddid_all.tbl CDD TIGR02213 TIGR02213 131268 lolE_release lipoprotein releasing system, transmembrane protein LolE. This protein is part of an unusual ABC transporter complex that releases lipoproteins from the periplasmic side of the bacterial inner membrane, rather than transport any substrate across the inner membrane. In some species, the permease-like transmembrane protein is represented by two paralogs, LolC and LolE, both in the LolCDE complex. This family consists of LolE, as found in E. coli and related species. [Protein fate, Protein and peptide secretion and trafficking] 411 matched cddid_all.tbl CDD TIGR02214 TIGR02214 131269 spoVD_pbp stage V sporulation protein D. This model describes the spoVD subfamily of homologs of the cell division protein FtsI, a penicillin binding protein. This subfamily is restricted to Bacillus subtilis and related Gram-positive species with known or suspected endospore formation capability. In these species, the functional equivalent of FtsI is desginated PBP-2B, a paralog of spoVD. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan, Cellular processes, Sporulation and germination] 636 matched cddid_all.tbl CDD TIGR02215 TIGR02215 274035 phage_chp_gp8 phage conserved hypothetical protein, phiE125 gp8 family. This model describes a family of proteins found exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus gene transfer agent, which packages DNA. Members of this family show some similarity to members of pfam05135, a putative DNA packaging protein family. [Mobile and extrachromosomal element functions, Prophage functions] 188 matched cddid_all.tbl CDD TIGR02216 TIGR02216 274036 phage_TIGR02216 phage conserved hypothetical protein. This model describes a family of proteins found exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus gene transfer agent, which packages DNA. [Mobile and extrachromosomal element functions, Prophage functions] 58 matched cddid_all.tbl CDD TIGR02217 TIGR02217 274037 chp_TIGR02217 TIGR02217 family protein. This model represents a family of conserved hypothetical proteins. It is usually (but not always) found in apparent phage-derived regions of bacterial chromosomes. [Mobile and extrachromosomal element functions, Prophage functions] 210 matched cddid_all.tbl CDD TIGR02218 TIGR02218 274038 phg_TIGR02218 phage conserved hypothetical protein BR0599. This model describes a family of proteins found almost exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus gene transfer agent, which packages DNA. An apparent exception is Wolbachia pipientis wMel, a bacterial endosymbiont of the fruit fly, which has several candidate phage-related genes physically separate from obvious prophage regions. [Mobile and extrachromosomal element functions, Prophage functions] 229 matched cddid_all.tbl CDD TIGR02219 TIGR02219 131274 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family. Members of this family show sequence similarity to members of the NlpC/P60 family described by pfam00877 and by Anantharaman and Aravind (). The NlpC/P60 family includes a number of characterized bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes. [Mobile and extrachromosomal element functions, Prophage functions] 134 matched cddid_all.tbl CDD TIGR02220 TIGR02220 274039 phg_TIGR02220 phage conserved hypothetical protein, C-terminal domain. This model represents the conserved C-terminal domain of a family of proteins found exclusively in bacteriophage and in bacterial prophage regions. The functions of this domain and the proteins containing it are unknown. [Mobile and extrachromosomal element functions, Prophage functions] 77 matched cddid_all.tbl CDD TIGR02221 TIGR02221 274040 cas_TM1812 CRISPR-associated protein, TM1812 family. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This family, represented by TM1812 of Thermotoga maritima, is found also in Vibrio vulnificus YJ016, Nitrosomonas europaea ATCC 19718, a large plasmid of Synechocystis sp. PCC 6803, and Fibrobacter succinogenes S85. 218 matched cddid_all.tbl CDD TIGR02222 TIGR02222 131277 chap_CsaA export-related chaperone protein CsaA. This model describes Bacillus subtilis CsaA, an export-related chaperone that interacts with the Sec system, and related proteins from a number of other bacteria and archaea. The crystal structure is known for the homodimer from Thermus thermophilus. [Protein fate, Protein folding and stabilization, Protein fate, Protein and peptide secretion and trafficking] 107 matched cddid_all.tbl CDD TIGR02223 TIGR02223 274041 ftsN cell division protein FtsN. FtsN is a poorly conserved protein active in cell division in a number of Proteobacteria. The N-terminal 30 residue region tends to by Lys/Arg-rich, and is followed by a membrane-spanning region. This is followed by an acidic low-complexity region of variable length and a well-conserved C-terminal domain of two tandem regions matched by pfam05036 (Sporulation related repeat), found in several cell division and sporulation proteins. The role of FtsN as a suppressor for other cell division mutations is poorly understood; it may involve cell wall hydrolysis. [Cellular processes, Cell division] 298 matched cddid_all.tbl CDD TIGR02224 TIGR02224 274042 recomb_XerC tyrosine recombinase XerC. The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerC, one of two closely related chromosomal proteins along with XerD (TIGR02225). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and homologs of XerC on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerC, as some apparent XerC examples score in the gray zone between trusted (450) and noise (410) cutoffs, along with some XerD examples. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair] 295 matched cddid_all.tbl CDD TIGR02225 TIGR02225 274043 recomb_XerD tyrosine recombinase XerD. The phage integrase family describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci. This model represents XerD, one of two closely related chromosomal proteins along with XerC (TIGR02224). XerC and XerD are site-specific recombinases which help resolve chromosome dimers to monomers for cell division after DNA replication. In species with a large chromosome and with homologs of XerD on other replicons, the chomosomal copy was preferred for building this model. This model does not detect all XerD, as some apparent XerD examples score below the trusted and noise cutoff scores. XerC and XerD interact with cell division protein FtsK. [DNA metabolism, DNA replication, recombination, and repair] 291 matched cddid_all.tbl CDD TIGR02226 TIGR02226 131281 two_anch N-terminal double-transmembrane domain. This model represents a prokaryotic N-terminal region of about 80 amino acids. The predicted membrane topology by TMHMM puts the N-terminus outside and spans the membrane twice, with a cytosolic region of about 25 amino acids between the two transmembrane regions. Member proteins tend to be between 600 and 1000 amino acids in length. [Hypothetical proteins, Domain] 82 matched cddid_all.tbl CDD TIGR02227 TIGR02227 274044 sigpep_I_bact signal peptidase I, bacterial type. This model represents signal peptidase I from most bacteria. Eukaryotic sequences are likely organellar. Several bacteria have multiple paralogs, but these represent isozymes of signal peptidase I. Virtually all known bacteria may be presumed to A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes. [Protein fate, Protein and peptide secretion and trafficking] 142 matched cddid_all.tbl CDD TIGR02228 TIGR02228 131283 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I. 158 matched cddid_all.tbl CDD TIGR02229 TIGR02229 131284 caa3_sub_IV caa(3)-type oxidase, subunit IV. This model represents a small set of proteins with weak similarity to the sequences in pfam03626, which describes the cytochrome C oxidase subunit IV. [Energy metabolism, Electron transport] 92 matched cddid_all.tbl CDD TIGR02230 TIGR02230 131285 ATPase_gene1 F0F1-ATPase subunit, putative. This model represents a protein found encoded in F1F0-ATPase operons in several genomes, including Methanosarcina barkeri (archaeal) and Chlorobium tepidum (bacterial). It is a small protein (about 100 amino acids) with long hydrophic stretches and is presumed to be a subunit of the enzyme. [Energy metabolism, ATP-proton motive force interconversion] 100 matched cddid_all.tbl CDD TIGR02231 TIGR02231 274045 TIGR02231 conserved hypothetical protein. This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown. 525 matched cddid_all.tbl CDD TIGR02232 TIGR02232 200169 myxo_disulf_rpt Myxococcus cysteine-rich repeat. This model represents a sequence region shared between several proteins of Myxococcus xanthus DK 1622 and some eukaryotic proteins that include human pappalysin-1 (SP|Q13219). The region of about 40 amino acids contains several conserved Cys residues presumed to form disulfide bonds. The region appears in up to 13 repeats in Myxococcus. 38 matched cddid_all.tbl CDD TIGR02234 TIGR02234 274046 trp_oprn_chp trp region conserved hypothetical membrane protein. Members of this family are predicted transmembrane proteins with four membrane-spanning helices. Members are found in the Actinobacteria (Mycobacterium, Corynebacterium, Streptomyces), always associated with genes for tryptophan biosynthesis. 202 matched cddid_all.tbl CDD TIGR02235 TIGR02235 131289 menA_cyano-plnt 1,4-dihydroxy-2-naphthoate phytyltransferase. This family of phytyltransferases, found in plants and cyanobacteria, are involved in the biosythesis of phylloquinone (Vitamin K1). Phylloquinone is a critical component of photosystem I. The closely related MenA enzyme from bacteria transfers a prenyl group (which only differs in the saturation of the isoprenyl groups) in the biosynthesis of menaquinone. Activity towards both substrates in certain organisms should be considered a possibility. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 285 matched cddid_all.tbl CDD TIGR02236 TIGR02236 131290 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein. [DNA metabolism, DNA replication, recombination, and repair] 310 matched cddid_all.tbl CDD TIGR02237 TIGR02237 274047 recomb_radB DNA repair and recombination protein RadB. This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and archaeal RadA (TIGR02236). 209 matched cddid_all.tbl CDD TIGR02238 TIGR02238 131292 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis. 313 matched cddid_all.tbl CDD TIGR02239 TIGR02239 274048 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012). 316 matched cddid_all.tbl CDD TIGR02240 TIGR02240 131294 PHA_depoly_arom poly(3-hydroxyalkanoate) depolymerase. This family consists of the polyhydroxyalkanoic acid (PHA) depolymerase of Pseudomonas oleovorans, Pseudomonas putida BM01, and related species. This enzyme is part of polyester storage and mobilization system as in many bacteria. However, species containing this enzyme are unusual in their capacity to produce aromatic polyesters when grown on carbon sources such as benzoic acid or phenylacetic acid. [Energy metabolism, Other] 276 matched cddid_all.tbl CDD TIGR02241 TIGR02241 274049 TIGR02241 conserved hypothetical phage tail region protein. This family consists of uncharacterized proteins. All members so far represent bacterial genes found in apparent phage or otherwisely laterally transferred regions of the chromosome. Tentatively identified neighboring proteins tend to be phage tail region proteins. In some species, including Photorhabdus luminescens TTO1, several members of this family may be encoded near each other. 140 matched cddid_all.tbl CDD TIGR02242 TIGR02242 274050 tail_TIGR02242 phage tail protein domain. This model describes a region of sequence similarity shared by a number of uncharacterized proteins in bacterial genomes, including Geobacter sulfurreducens PCA, Mesorhizobium loti, Streptomyces coelicolor A3(2), Gloeobacter violaceus PCC 7421, and Myxococcus xanthus. In all cases, the genomic region resembles a phage tail region, based on tentative identifications of neighboring genes. A region of this domain resembles a region of TIGR01634, another phage tail protein model. [Mobile and extrachromosomal element functions, Prophage functions] 130 matched cddid_all.tbl CDD TIGR02243 TIGR02243 274051 TIGR02243 putative baseplate assembly protein. This family consists of a large, conserved hypothetical protein in phage tail-like regions of at least six bacterial genomes: Gloeobacter violaceus PCC 7421, Geobacter sulfurreducens PCA, Streptomyces coelicolor A3(2), Streptomyces avermitilis MA-4680, Mesorhizobium loti, and Myxococcus xanthus. The C-terminal region is identified by the broader model pfam04865 as related to baseplate protein J from phage P2, but that relationship is not observed directly. [Mobile and extrachromosomal element functions, Prophage functions] 656 matched cddid_all.tbl CDD TIGR02244 TIGR02244 274052 HAD-IG-Ncltidse "HAD superfamily (subfamily IG) hydrolase, 5'-nucleotidase. This model includes a 5'-nucleotidase specific for purines (IMP and GMP). These enzymes are members of the Haloacid Dehalogenase (HAD) superfamily. HAD members are recognized by three short motifs {hhhhDxDx(T/V)}, {hhhh(T/S)}, and either {hhhh(D/E)(D/E)x(3-4)(G/N)} or {hhhh(G/N)(D/E)x(3-4)(D/E)} (where ""h"" stands for a hydrophobic residue). Crystal structures of many HAD enzymes has verified PSI-PRED predictions of secondary structural elements which show each of the ""hhhh"" sequences of the motifs as part of beta sheets. This subfamily of enzymes is part of ""Subfamily I"" of the HAD superfamily by virtue of a ""cap"" domain in between motifs 1 and 2. This subfamily's cap domain has a different predicted secondary structure than all other known HAD enzymes and thus has been designated ""subfamily IG"". This domain appears to consist of a mixed alpha/beta fold. A Pfam model (pfam05761) detects an identical range of sequences above the trusted cutoff, but does not model the N-terminal motif 1 region. A TIGRFAMs model (TIGR01993) represents a (putative) family of _pyrimidine_ 5'-nucleotidases which are also subfamily I HAD's, which should not be confused with the current model." 343 matched cddid_all.tbl CDD TIGR02245 TIGR02245 131299 HAD_IIID1 "HAD-superfamily subfamily IIID hydrolase, TIGR02245. This family of sequences appears to belong to the Haloacid Dehalogenase (HAD) superfamily of enzymes by virtue of the presence of three catalytic domains, in this case: LLVLD(ILV)D(YH)T, I(VMG)IWS, and (DN)(VC)K(PA)Lx{15-17}T(IL)(MH)(FV)DD(IL)(GRS)(RK)N. Since this family has no large ""cap"" domain between motifs 1 and 2 or between 2 and 3, it is formally a ""class III"" HAD." 195 matched cddid_all.tbl CDD TIGR02246 TIGR02246 274053 TIGR02246 conserved hypothetical protein. This family consists of uncharacterized proteins found in a number of genera and species, including Streptomyces, Xanthomonas, Oceanobacillus iheyensis, Caulobacter crescentus CB15, and Xylella fastidiosa. The function is unknown. 128 matched cddid_all.tbl CDD TIGR02247 TIGR02247 274054 HAD-1A3-hyp epoxide hydrolase N-terminal domain-like phosphatase. This model represents a small clade of sequences including C. elegans and mammalian sequences as well as a small number of bacteria. In eukaryotes, this domain exists as an N-terminal fusion to the soluble epoxide hydrolase enzyme and has recently been shown to be an active phosphatase, although the nature of the biological substrate is unclear. These appear to be members of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases by general homology and the conservation of all of the recognized catalytic motifs (although the first motif is unusual in the replacement of the more common aspartate with glycine...). The variable domain is found in between motifs 1 and 2, indicating membership in subfamily I and phylogeny and prediction of the alpha helical nature of the variable domain (by PSI-PRED) indicate membership in subfamily IA. 211 matched cddid_all.tbl CDD TIGR02248 TIGR02248 131302 mutH_TIGR DNA mismatch repair endonuclease MutH. This family consists exclusively of MutH, an endonuclease in some Proteobacteria that is activated by MutS1 and MutL for methylation-directed mismatch repair. [DNA metabolism, DNA replication, recombination, and repair] 217 matched cddid_all.tbl CDD TIGR02249 TIGR02249 131303 integrase_gron integron integrase. Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family (pfam00589) that also includes recombinases XerC (TIGR02224) and XerD (TIGR02225), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961. [DNA metabolism, DNA replication, recombination, and repair, Mobile and extrachromosomal element functions, Other] 315 matched cddid_all.tbl CDD TIGR02250 TIGR02250 131304 FCP1_euk "FCP1-like phosphatase, phosphatase domain. This model represents the phosphatase domain of the humanRNA polymerase II subunit A C-terminal domain phosphatase (FCP1) and closely related phosphatases from eukaryotes including plants, fungi, and slime mold. This domain is a member of the haloacid dehalogenase (HAD) superfamily by virtue of a conserved set of three catalytic motifs and a conserved fold as predicted by PSIPRED. The third motif in this family is distinctive (hhhhDDppphW). This domain is classified as a ""Class III"" HAD, since there is no large ""cap"" domain found between motifs 1 and 2 or motifs 2 and 3. This domain is related to domains found in the human NLI interacting factor-like phosphatases, and together both are detected by the pfam03031." 156 matched cddid_all.tbl CDD TIGR02251 TIGR02251 274055 HIF-SF_euk "Dullard-like phosphatase domain. This model represents the putative phosphatase domain of a family of eukaryotic proteins including ""Dullard"", and the NLI interacting factor (NIF)-like phosphatases. This domain is a member of the haloacid dehalogenase (HAD) superfamily by virtue of a conserved set of three catalytic motifs and a conserved fold as predicted by PSIPRED. The third motif in this family is distinctive (hhhhDNxPxxa) and aparrently lacking the last aspartate. This domain is classified as a ""Class III"" HAD, since there is no large ""cap"" domain found between motifs 1 and 2 or motifs 2 and 3. This domain is related to domains found in FCP1-like phosphatases (TIGR02250), and together both are detected by the pfam03031." 162 matched cddid_all.tbl CDD TIGR02252 TIGR02252 274056 DREG-2 "REG-2-like, HAD superfamily (subfamily IA) hydrolase. This family of proteins includes uncharacterized sequences from eukaryotes, cyanobacteria and Leptospira as well as the DREG-2 protein from Drosophila melanogaster which has been identified as a rhythmically (diurnally) regulated gene. This family is a member of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases. The superfamily is defined by the presence of three short catalytic motifs. The subfamilies are defined based on the location and the observed or predicted fold of a so-called 'capping domain', or the absence of such a domain. This family is a member of subfamily 1A in which the cap domain consists of a predicted alpha helical bundle found in between the first and second catalytic motifs. A distinctive feature of this family is a conserved tandem pair of tryptophan residues in the cap domain. The most divergent sequences included within the scope of this model are from plants and have ""FW"" at this position instead. Most likely, these sequences, like the vast majority of HAD sequences, represent phosphatase enzymes." 203 matched cddid_all.tbl CDD TIGR02253 TIGR02253 274057 CTE7 HAD superfamily (subfamily IA) hydrolase, TIGR02253. This family of sequences from archaea and metazoans includes the human uncharacterized protein CTE7. Pyrococcus species appear to have three different forms of this enzyme, so it is unclear whether all members of this family have the same function. This family is a member of the haloacid dehalogenase (HAD) superfamily of hydrolases which are characterized by three conserved sequence motifs. By virtue of an alpha helical domain in-between the first and second conserved motif, this family is a member of subfamily IA (TIGR01549). 221 matched cddid_all.tbl CDD TIGR02254 TIGR02254 162788 YjjG/YfnB noncanonical pyrimidine nucleotidase, YjjG family. This HAD superfamily includes including YjjG from E. coli and YfnB from B. subtilis. YjjG has been shown to act as a house-cleaning enzyme, cleaving nucleotides with non-canonical nucleotide bases. This family is a member of the haloacid dehalogenase (HAD) superfamily of hydrolases which are characterized by three conserved sequence motifs. By virtue of an alpha helical domain in-between the first and second conserved motif, this family is a member of subfamily IA (TIGR01549). 224 matched cddid_all.tbl CDD TIGR02256 TIGR02256 131309 ICE_VC0181 integrative and conjugative element protein, VC0181 family. This uncharacterized protein is found in several Proteobacteria, among them Rhizobium sp. NGR234, Vibrio cholerae, Myxococcus xanthus, and E. coli strain ECOR31. In the latter, it is part of an integrative and conjugative element that is readily induced to excise and circularize. 131 matched cddid_all.tbl CDD TIGR02257 TIGR02257 131310 cobalto_cobN cobaltochelatase, CobN subunit. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 1122 matched cddid_all.tbl CDD TIGR02258 TIGR02258 274058 2_5_ligase 2'-5' RNA ligase. This protein family consists of bacterial and archaeal proteins with two tandem copies of Pfam domain pfam02834. Members for which activity has been measured perform a reversible, ATP-independent 2'-5'-ligation of what is presumably a non-phyiological substrate: half-tRNA splice intermediates from an intron-containing yeast tRNA. The physiological substrate(s) in prokaryotes may include small 2'-5'-link-containing oligonucleotides, perhaps with regulatory or biosynthetic roles. [Transcription, RNA processing] 179 matched cddid_all.tbl CDD TIGR02259 TIGR02259 131312 benz_CoA_red_A benzoyl-CoA reductase, bcr type, subunit A. This model describes A, or gamma, subunit of the bcr type of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA. This family shows strong sequence similarity to the 2-hydroxyglutaryl-CoA dehydratase alpha chain and to subunits of different types of benzoyl-CoA reductase (such as the bzd type). 432 matched cddid_all.tbl CDD TIGR02260 TIGR02260 131313 benz_CoA_red_B benzoyl-CoA reductase, bcr type, subunit B. This model describes B, or beta, subunit of the bcr type of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA. 413 matched cddid_all.tbl CDD TIGR02261 TIGR02261 131314 benz_CoA_red_D benzoyl-CoA reductase, bcr type, subunit D. This model describes the D subunit of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA. This family shows sequence similarity to the A subunit (TIGR02259) and to the 2-hydroxyglutaryl-CoA dehydratase alpha chain. 262 matched cddid_all.tbl CDD TIGR02262 TIGR02262 274059 benz_CoA_lig benzoate-CoA ligase family. Characterized members of this protein family include benzoate-CoA ligase, 4-hydroxybenzoate-CoA ligase, 2-aminobenzoate-CoA ligase, etc. Members are related to fatty acid and acetate CoA ligases. 505 matched cddid_all.tbl CDD TIGR02263 TIGR02263 131316 benz_CoA_red_C benzoyl-CoA reductase, subunit C. This model describes C subunit of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA. This enzyme acts under anaerobic conditions. 380 matched cddid_all.tbl CDD TIGR02264 TIGR02264 131317 gmx_para_CXXCG Myxococcus xanthus double-CXXCG motif paralogous family. This family consists of at least 10 paralogous proteins from Myxococcus xanthus that lack detectable sequence similarity to any other protein family. An imperfectly conserved CXXCG motif, a probable binding site, appears twice in the multiple sequence alignment. 237 matched cddid_all.tbl CDD TIGR02265 TIGR02265 131318 Mxa_TIGR02265 Myxococcales-restricted protein, TIGR02265 family. This family consists of a set of at least 17 paralogous proteins in Myxococcus xanthus DK 1622. Members are about 200 amino acids in length. No other homologs are known; the function is unknown. 179 matched cddid_all.tbl CDD TIGR02266 TIGR02266 274060 gmx_TIGR02266 Myxococcus xanthus paralogous domain TIGR02266. This domain is related to Type IV pilus assembly protein PilZ (pfam07238). It is found in at least 12 copies in Myxococcus xanthus DK 1622. 96 matched cddid_all.tbl CDD TIGR02267 TIGR02267 131320 TIGR02267 DUSAM domain. This family consists of at least eight paralogs in Myxococcus xanthus and six in Stigmatella aurantiaca DW4/3-1, both members of Myxococcales order within the Deltaproteobacteria. The function is unknown. Some member proteins consist of two copies of the domain. This domain is hereby named DUSAM, DUplication in Stigmatella And Myxococcus. 123 matched cddid_all.tbl CDD TIGR02268 TIGR02268 131321 TIGR02268 Myxococcus xanthus paralogous family TIGR02268. This family consists of at least 8 paralogs in Myxococcus xanthus, a member of the Deltaproteobacteria. The function is unknown. 295 matched cddid_all.tbl CDD TIGR02269 TIGR02269 131322 TIGR02269 Myxococcus xanthus paralogous lipoprotein family TIGR02269. This family consists of at least 9 paralogs in Myxococcus xanthus, a member of the Deltaproteobacteria. One appears truncated toward the N-terminus; the others are predicted lipoproteins. The function is unknown. 211 matched cddid_all.tbl CDD TIGR02270 TIGR02270 131323 TIGR02270 conserved hypothetical protein. Members are found in Myxococcus xanthus (six members), Geobacter sulfurreducens, and Pseudomonas aeruginosa; a short protein homologous to the N-terminal region is found in Mesorhizobium loti. All sequence are from Proteobacteria. The function is unknown. [Hypothetical proteins, Conserved] 410 matched cddid_all.tbl CDD TIGR02271 TIGR02271 131324 TIGR02271 conserved domain. This model describes an uncharacterized domain, sometimes found in association with a PRC-barrel domain (pfam05239, which is also found in rRNA processing protein RimM and in a photosynthetic reaction center complex protein). This domain is found in proteins from Bacillus subtilis, Deinococcus radiodurans, Nostoc sp. PCC 7120, Myxococcus xanthus, and several other species. The function is not known. 115 matched cddid_all.tbl CDD TIGR02272 TIGR02272 131325 gentisate_1_2 gentisate 1,2-dioxygenase. This family consists of gentisate 1,2-dioxygenases. This ring-opening enzyme acts in salicylate degradation that goes via gentisate rather than via catechol. It converts gentisate to maleylpyruvate. Some putative gentisate 1,2-dioxygenases are excluded by a relatively high trusted cutoff score because they are too closely related to known examples of 1-hydroxy-2-naphthoate dioxygenase. Therefore some homologs may be bona fide gentisate 1,2-dioxygenases even if they score below the given cutoffs. 335 matched cddid_all.tbl CDD TIGR02273 TIGR02273 274061 16S_RimM 16S rRNA processing protein RimM. This family consists of the bacterial protein RimM (YfjA, 21K), a 30S ribosomal subunit-binding protein implicated in 16S ribsomal RNA processing. It has been partially characterized in Escherichia coli, is found with other translation-associated genes such as trmD. It is broadly distributed among bacteria, including some minimal genomes such the aphid endosymbiont Buchnera aphidicola. The protein contains a PRC-barrel domain that it shares with other protein families (pfam05239) and a unique domain (pfam01782). This model describes the full-length protein. A member from Arabidopsis (plant) has additional N-terminal sequence likely to represent a chloroplast transit peptide. [Transcription, RNA processing] 165 matched cddid_all.tbl CDD TIGR02274 TIGR02274 274062 dCTP_deam deoxycytidine triphosphate deaminase. Members of this family include the Escherichia coli monofunctional deoxycytidine triphosphate deaminase (dCTP deaminase) and a Methanocaldococcus jannaschii bifunctional dCTP deaminase (3.5.4.13)/dUTP diphosphatase (EC 3.6.1.23), which has the EC number 3.5.4.30 for the overall operation. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism] 179 matched cddid_all.tbl CDD TIGR02275 TIGR02275 274063 DHB_AMP_lig 2,3-dihydroxybenzoate-AMP ligase. Proteins in this family belong to the AMP-binding enzyme family (pfam00501). Members activate 2,3-dihydroxybenzoate (DHB) by ligation of AMP from ATP with the release of pyrophosphate; many are involved in synthesis of siderophores such as enterobactin, vibriobactin, vulnibactin, etc. The most closely related proteine believed to differ in function activates salicylate rather than DHB. [Transport and binding proteins, Cations and iron carrying compounds] 526 matched cddid_all.tbl CDD TIGR02276 TIGR02276 213697 beta_rpt_yvtn 40-residue YVTN family beta-propeller repeat. This repeat of about 40 amino acids is found in up to 14 copies per protein. Archaea Methanosarcina mazei and Methanosarcina acetivorans each have over 10 genes that encode tandem copies of this repeat, which is also found in other species. PSIPRED predicts with high confidence that each 40-residue repeats contains four beta strands. This model overlaps somewhat with the NHL repeat (pfam01436) and also shows sequence similarity to the WD domain, G-beta repeat (pfam00400). 42 matched cddid_all.tbl CDD TIGR02277 TIGR02277 274064 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription. [Regulatory functions, DNA interactions] 280 matched cddid_all.tbl CDD TIGR02278 TIGR02278 131331 PaaN-DH phenylacetic acid degradation protein paaN. This enzyme is proposed to act in the ring-opening step of phenylacetic acid degradation which follows ligation of the acid with coenzyme A (by PaaF) and hydroxylation by a multicomponent non-heme iron hydroxylase complex (PaaGHIJK). Gene symbols have been standardized in. This enzyme is related to aldehyde dehydrogenases and has domains which are members of the pfam00171 and pfam01575 families. This family includes paaN genes from Pseudomonas, Sinorhizobium, Rhodopseudomonas, Escherichia, Deinococcus and Corynebacterium. Another homology family (TIGR02288) includes several other species. 663 matched cddid_all.tbl CDD TIGR02279 TIGR02279 188207 PaaC-3OHAcCoADH 3-hydroxyacyl-CoA dehydrogenase PaaC. This 3-hydroxyacyl-CoA dehydrogenase is involved in the degradation of phenylacetic acid, presumably in steps following the opening of the phenyl ring. The sequences included in this model are all found in aparrent operons with other related genes such as paaA, paaB, paaD, paaE, paaF and paaN. Some genomes contain these other genes without an apparent paaC in the same operon - possibly in these cases a different dehydrogenase involved in fatty acid degradation may fill in the needed activity. This enzyme has domains which are members of the pfam02737 and pfam00725 families. 503 matched cddid_all.tbl CDD TIGR02280 TIGR02280 274065 PaaB1 phenylacetate degradation probable enoyl-CoA hydratase paaB. This family of proteins are found within apparent operons for the degradation of phenylacetic acid. These proteins contain the enoyl-CoA hydratase domain as detected by pfam00378. This activity is consistent with current hypotheses for the degradation pathway, which involve the ligation of phenylacetate with coenzyme A (paaF), hydroxylation (paaGHIJK), ring-opening (paaN) and degradation of the resulting fatty acid-like compound to a Krebs cycle intermediate (paaABCDE). 257 matched cddid_all.tbl CDD TIGR02281 TIGR02281 131334 clan_AA_DTGA clan AA aspartic protease, TIGR02281 family. This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix. Sequences in the seed alignment and those scoring above the trusted cutoff are Proteobacterial; homologs scroing between trusted and noise are found in Pyrobaculum aerophilum str. IM2 (archaeal), Pirellula sp. (Planctomycetes), and Nostoc sp. PCC 7120 (Cyanobacteria). [Protein fate, Degradation of proteins, peptides, and glycopeptides] 121 matched cddid_all.tbl CDD TIGR02282 TIGR02282 274066 MltB lytic murein transglycosylase B. This family consists of lytic murein transglycosylases (murein hydrolases) in the family of MltB, which is a membrane-bound lipoprotein in Escherichia coli. The N-terminal lipoprotein modification motif is conserved in about half the members of this family. The term Slt35 describes a naturally occurring soluble fragment of MltB. Members of this family never contain the putative peptidoglycan binding domain described by pfam01471, which is associated with several classes of bacterial cell wall lytic enzymes. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 290 matched cddid_all.tbl CDD TIGR02283 TIGR02283 274067 MltB_2 lytic murein transglycosylase. Members of this family are closely related to the MltB family lytic murein transglycosylases described by TIGR02282 and are likewise all proteobacterial, although that family and this one form clearly distinct clades. Several species have one member of each family. Many members of this family (unlike the MltB family) contain an additional C-terminal domain, a putative peptidoglycan binding domain (pfam01471), not included in region described by this model. Many sequences appear to contain N-terminal lipoprotein attachment sites, as does E. coli MltB in TIGR02282. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 300 matched cddid_all.tbl CDD TIGR02284 TIGR02284 131337 TIGR02284 conserved hypothetical protein. Members of this protein family are found mostly in the Proteobacteria, although one member is found in the the marine planctomycete Pirellula sp. strain 1. The function is unknown. 139 matched cddid_all.tbl CDD TIGR02285 TIGR02285 131338 TIGR02285 conserved hypothetical protein. Members of this family are found in several Proteobacteria, including Pseudomonas putida KT2440, Bdellovibrio bacteriovorus HD100 (three members), Aeromonas hydrophila, and Chromobacterium violaceum ATCC 12472. The function is unknown. [Hypothetical proteins, Conserved] 268 matched cddid_all.tbl CDD TIGR02286 TIGR02286 131339 PaaD phenylacetic acid degradation protein PaaD. This member of the domain family TIGR00369 (which is, in turn, a member of the pfam03061 thioesterase superfamily) is nearly always found adjacent to other genes of the phenylacetic acid degradation pathway. Its function is currently unknown, but a role as a thioesterase is not inconsistent with the proposed overall pathway. Sequences scoring between trusted and noise include those from archaea and other species not known to catabolize phenylacetic acid and which are not adjacent to other genes potentially involved with such a pathway. 114 matched cddid_all.tbl CDD TIGR02287 TIGR02287 131340 PaaY phenylacetic acid degradation protein PaaY. Members of this family are located next to other genes organized into apparent operons for phenylacetic acid degradation. PaaY is located near the end of these gene clusters and often next to PaaX, a transcriptional regulator. [Energy metabolism, Other] 192 matched cddid_all.tbl CDD TIGR02288 TIGR02288 131341 PaaN_2 phenylacetic acid degradation protein paaN. This enzyme is proposed to act in the ring-opening step of phenylacetic acid degradation which follows ligation of the acid with coenzyme A (by PaaF) and hydroxylation by a multicomponent non-heme iron hydroxylase complex (PaaGHIJK). Gene symbols have been standardized in. This enzyme is related to aldehyde dehydrogenases and has a domain which is a member of the pfam00171 family. This family includes sequences from Burkholderia, Bordetella, Streptomyces. Other PaaN enzymes are represented by a separate model, TIGR02278. 551 matched cddid_all.tbl CDD TIGR02289 TIGR02289 274068 M3_not_pepF oligoendopeptidase, M3 family. This family consists of probable oligoendopeptidases in the M3 family, related to lactococcal PepF and group B streptococcal PepB (TIGR00181) but in a distinct clade with considerable sequence differences. The likely substrate is small peptides and not whole proteins, as with PepF, but members are not characterized and the activity profile may differ. Several bacteria have both a member of this family and a member of the PepF family. 549 matched cddid_all.tbl CDD TIGR02290 TIGR02290 274069 M3_fam_3 oligoendopeptidase, pepF/M3 family. The M3 family of metallopeptidases contains several distinct clades. Oligoendopeptidase F as characterized in Lactococcus, the functionally equivalent oligoendopeptidase B of group B Streptococcus, and closely related sequences are described by TIGR00181. The present family is quite similar but forms a distinct clade, and a number of species have one member of each. A greater sequence difference separates members of TIGR02289, probable oligoendopeptidases of the M3 family that probably should not be designated PepF. 587 matched cddid_all.tbl CDD TIGR02291 TIGR02291 274070 rimK_rel_E_lig alpha-L-glutamate ligase-related protein. Members of this protein family contain a region of homology to the RimK family of alpha-L-glutamate ligases (TIGR00768), various members of which modify the Glu-Glu C-terminus of ribosomal protein S6, or tetrahydromethanopterin, or a form of coenzyme F420 derivative. Members of this family are found so far in various Vibrio and Pseudomonas species and some other gamma and beta Proteobacteria. The function is unknown. 317 matched cddid_all.tbl CDD TIGR02292 TIGR02292 274071 ygfB_yecA yecA family protein. This family resembles pfam03695 (version pfam03695.3), uncharacterised protein family UPF0149, but is broader in scope and includes additional proteins. It includes E. coli proteins YgfB and YecA. The function of this family of proteins is unknown. The crystal structure is known for the member from Haemophilus influenzae (Ygfb, HI0817). [Unknown function, General] 150 matched cddid_all.tbl CDD TIGR02293 TIGR02293 131346 TAS_TIGR02293 putative toxin-antitoxin system antitoxin component, TIGR02293 family. Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. This family was proposed by Makarova, et al. (2009) to be the antitoxin component of a new class of type 2 toxin-antitoxin system, or addiction module. [Cellular processes, Other] 133 matched cddid_all.tbl CDD TIGR02294 TIGR02294 274072 nickel_nikA nickel ABC transporter, nickel/metallophore periplasmic binding protein. Members of this family are periplasmic nickel-binding proteins of nickel ABC transporters. Most appear to be lipoproteins. This protein was previously (circa 2003) thought to mediate binding to nickel through water molecules, but is now thought to involve a chelating organic molecule, perhaps butane-1,2,4-tricarboxylate, acting as a metallophore. [Transport and binding proteins, Cations and iron carrying compounds] 500 matched cddid_all.tbl CDD TIGR02295 TIGR02295 213698 HpaD 3,4-dihydroxyphenylacetate 2,3-dioxygenase. This enzyme catalyzes the second step in the degradation of 4-hydroxyphenylacetate to succinate and pyruvate. 4-hydroxyphenylacetate arises from the degradation of tyrosine. The substrate, 3,4-dihydroxyphenylacetate (homoprotocatechuate) arises from the action of a hydroxylase on 4-hydroxyphenylacetate. The aromatic ring is opened by this dioxygenase exo to the 3,4-diol resulting in 2-hydroxy-5-carboxymethylmuconate semialdehyde. The enzyme from Bacillus brevis contains manganese. 294 matched cddid_all.tbl CDD TIGR02296 TIGR02296 131349 HpaC 4-hydroxyphenylacetate 3-monooxygenase, reductase component. This model identifies the reductase component (HpaC) of 4-hydroxyphenylacetate 3-monooxygenase. This enzyme catalyzes the first step (hydroxylation at the 3-position) in the degradation of 4-hydroxyphenylacetate to succinate and pyruvate. 4-hydroxyphenylacetate arises from the degradation of tyrosine. These reductases catalyze the reduction of free flavins by NADPH. The flavin is then utilized by the large subunit of the monooxygenase. 154 matched cddid_all.tbl CDD TIGR02297 TIGR02297 131350 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway. 287 matched cddid_all.tbl CDD TIGR02298 TIGR02298 131351 HpaD_Fe 3,4-dihydroxyphenylacetate 2,3-dioxygenase. This enzyme catalyzes the ring-opening step in the degradation of 4-hydroxyphenylacetate. 282 matched cddid_all.tbl CDD TIGR02299 TIGR02299 131352 HpaE 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase. This model represents the dehydrogenase responsible for the conversion of 5-carboxymethyl-2-hydroxymuconate semialdehyde to 5-carboxymethyl-2-hydroxymuconate (a tricarboxylic acid). This is the step in the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate following the oxidative opening of the aromatic ring. 488 matched cddid_all.tbl CDD TIGR02300 TIGR02300 131353 FYDLN_acid TIGR02300 family protein. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown. 129 matched cddid_all.tbl CDD TIGR02301 TIGR02301 131354 TIGR02301 TIGR02301 family protein. Members of this uncharacterized protein family are found in a number of alphaProteobacteria, including root nodule bacteria, Brucella suis, Caulobacter crescentus, and Rhodopseudomonas palustris. Conserved residues include two well-separated cysteines, suggesting a disulfide bond. The function is unknown. 121 matched cddid_all.tbl CDD TIGR02302 TIGR02302 274073 aProt_lowcomp TIGR02302 family protein. Members of this family are long (~850 residue) bacterial proteins from the alpha Proteobacteria. Each has 2-3 predicted transmembrane helices near the N-terminus and a long C-terminal region that includes stretches of Gln/Gly-rich low complexity sequence, predicted by TMHMM to be outside the membrane. In Bradyrhizobium japonicum, two tandem reading frames are together homologous the single members found in other species; the cutoffs scores are set low enough that the longer scores above the trusted cutoff and the shorter above the noise cutoff for this model. 851 matched cddid_all.tbl CDD TIGR02303 TIGR02303 131356 HpaG-C-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit. This model represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation. In E. coli and some other species this enzyme is encoded by a single polypeptide containing both this domain and the closely related N-terminal domain (TIGR02305). In other species such as Pasteurella multocida these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED). 245 matched cddid_all.tbl CDD TIGR02304 TIGR02304 274074 aden_form_hyp putative adenylate-forming enzyme. Members of this family form a distinct clade within a larger family of proteins that also includes coenzyme F390 synthetase, an enzyme known in Methanobacterium thermoautotrophicum and a few other methanogenic archaea. That enzyme adenylates coenzyme F420 to F390, a reversible process, during oxygen stress. Other informative homologies include domains of the non-ribosomal peptide synthetases involved in activation by adenylation. The family defined by this model is likely to be of an adenylate-forming enzyme related to but distinct from coenzyme F390 synthetase. 430 matched cddid_all.tbl CDD TIGR02305 TIGR02305 131358 HpaG-N-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, N-terminal subunit. This model represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation. In E. coli and some other species this enzyme is encoded by a single polypeptide containing both this domain and the closely related C-terminal domain (TIGR02303). In other species such as Pasteurella multocida these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED). 205 matched cddid_all.tbl CDD TIGR02306 TIGR02306 274075 RNA_lig_DRB0094 RNA ligase, DRB0094 family. The member of this family from Deinococcus radiodurans, a species that withstands and recovers from extensive radiation or dessication damage, is an apparent RNA ligase. It repairs RNA stand breaks in nicked DNA:RNA and RNA:RNA but not DNA:DNA duplexes. It has adenylyltransferase activity associated with the C-terminal domain. Related proteins also in this family are found in Streptomyces avermitilis MA-4680 and in bacteriophage 44RR2.8t. The phage example is unsurprising since one mechanism of host cell defense against phage is cleavage and inactivation of certain tRNA molecules. A fungal sequence from Neurospora crassa scores between trusted and noise cutofffs and may be similar in function. 341 matched cddid_all.tbl CDD TIGR02307 TIGR02307 274076 RNA_lig_RNL2 RNA ligase, Rnl2 family. Members of this family ligate (seal breaks in) RNA. Members so far include phage proteins that can counteract a host defense of cleavage of specific tRNA molecules, trypanosome ligases involved in RNA editing, but no prokaryotic host proteins . [Mobile and extrachromosomal element functions, Prophage functions, Transcription, RNA processing] 325 matched cddid_all.tbl CDD TIGR02308 TIGR02308 213699 RNA_lig_T4_1 RNA ligase, T4 RnlA family. Members of this family are phage proteins with ATP-dependent RNA ligase activity. Host defense to phage may include cleavage and inactivation of specific tRNA molecules; members of this family act to reverse this RNA damage. The enzyme is adenylated, transiently, on a Lys residue in a motif KXDGSL. [Mobile and extrachromosomal element functions, Prophage functions, Transcription, RNA processing] 374 matched cddid_all.tbl CDD TIGR02309 TIGR02309 131362 HpaB-1 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component. This gene for this monooxygenase is found within apparent operons for the degradation of 4-hydroxyphenylacetic acid in Deinococcus, Thermus and Oceanobacillus. Phylogenetic trees support inclusion of the Bacillus halodurans sequence above trusted although the complete 4-hydroxyphenylacetic acid degradation pathway may not exist in that organism. Generally, this enzyme acts with the assistance of a small flavin reductase domain protein (HpaC) to provide the cycle the flavin reductant for the reaction. This family of sequences is a member of a larger subfamily of monooxygenases (pfam03241). 477 matched cddid_all.tbl CDD TIGR02310 TIGR02310 213700 HpaB-2 4-hydroxyphenylacetate 3-monooxygenase, oxygenase component. This gene for this monooxygenase is found within apparent operons for the degradation of 4-hydroxyphenylacetic acid in Shigella, Photorhabdus and Pasteurella. The family represented by this model is narrowly limited to gammaproteobacteria to exclude other aromatic hydroxylases involved in various secondary metabolic pathways. Generally, this enzyme acts with the assistance of a small flavin reductase domain protein (HpaC) to provide the cycle the flavin reductant for the reaction. This family of sequences is a member of a larger subfamily of monooxygenases (pfam03241). 519 matched cddid_all.tbl CDD TIGR02311 TIGR02311 131364 HpaI 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents the aldolase which performs the final step unique to the 4-hydroxyphenylacetic acid catabolism pathway in which 2,4-dihydroxyhept-2-ene-1,7-dioic acid is split into pyruvate and succinate-semialdehyde. The gene for enzyme is generally found adjacent to other genes for this pathway organized into an operon. 249 matched cddid_all.tbl CDD TIGR02312 TIGR02312 131365 HpaH 2-oxo-hepta-3-ene-1,7-dioic acid hydratase. This model represents the enzyme which hydrates the double bond of 2-oxo-hepta-3-ene-1,7-dioic acid to form 4-hydroxy-2-oxo-heptane-1,7-dioic acid in the catabolism of 4-hydroxyphenylacetic acid. The gene for this enzyme is generally found adjacent to other genes of this pathway in an apparent operon. 267 matched cddid_all.tbl CDD TIGR02313 TIGR02313 131366 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism. 294 matched cddid_all.tbl CDD TIGR02314 TIGR02314 131367 ABC_MetN D-methionine ABC transporter, ATP-binding protein. Members of this family are the ATP-binding protein of the D-methionine ABC transporter complex. Known members belong to the Proteobacteria. 343 matched cddid_all.tbl CDD TIGR02315 TIGR02315 131368 ABC_phnC phosphonate ABC transporter, ATP-binding protein. Phosphonates are a class of phosphorus-containing organic compound with a stable direct C-P bond rather than a C-O-P linkage. A number of bacterial species have operons, typically about 14 genes in size, with genes for ATP-dependent transport of phosphonates, degradation, and regulation of the expression of the system. Members of this protein family are the ATP-binding cassette component of tripartite ABC transporters of phosphonates. [Transport and binding proteins, Anions] 243 matched cddid_all.tbl CDD TIGR02316 TIGR02316 131369 propion_prpE propionate--CoA ligase. This family contains one of three readily separable clades of proteins in the group of acetate and propionate--CoA ligases. Characterized members of this family act on propionate. From propionyl-CoA, there is a cyclic degradation pathway: it is ligated by PrpC to the TCA cycle intermediate oxaloacetate, acted upon further by PrpD and an aconitase, then cleaved by PrpB to pyruvate and the TCA cycle intermediate succinate. 628 matched cddid_all.tbl CDD TIGR02317 TIGR02317 131370 prpB methylisocitrate lyase. Members of this family are methylisocitrate lyase, also called (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate pyruvate-lyase. This enzyme acts in propionate metabolism. It cleaves a carbon-carbon bond to convert 2-methylisocitrate to pyruvate plus succinate. Some members of this family have been annotated, incorrectly it seems, as the related protein carboxyphosphoenolpyruvate phosphomutase, which is involved in synthesizing the antibiotic bialaphos in Streptomyces hygroscopicus. 285 matched cddid_all.tbl CDD TIGR02318 TIGR02318 131371 phosphono_phnM phosphonate metabolism protein PhnM. This family consists of proteins from in the PhnM family. PhnM is a a protein associated with phosphonate utilization in a number of bacterial species. In Pseudomonas stutzeri WM88, a protein that is part of a system for the oxidation of phosphites (another form of reduced phosphorous compound) scores between trusted and noise cutoffs. [Energy metabolism, Other] 376 matched cddid_all.tbl CDD TIGR02319 TIGR02319 131372 CPEP_Pphonmut carboxyvinyl-carboxyphosphonate phosphorylmutase. This family consists of carboxyvinyl-carboxyphosphonate phosphorylmutase (CPEP phosphonomutase), an unusual enzyme involved in the biosynthesis of the antibiotic bialaphos. So far, it is known only in that pathway and only in Streptomyces hygroscopicus. Some related proteins annotated as being functionally equivalent are likely misannotated examples of methylisocitrate lyase, an enzyme of priopionate utilization. 294 matched cddid_all.tbl CDD TIGR02320 TIGR02320 274077 PEP_mutase phosphoenolpyruvate mutase. This family consists of examples of phosphoenolpyruvate phosphomutase, an enzyme that creates a C-P bond as the first step in the biosynthesis of natural products including antibiotics like bialaphos and phosphonothricin in Streptomyces species, phosphonate-modified molecules such as the polysaccharide B of Bacteroides fragilis, the phosphonolipids of Tetrahymena pyroformis, the glycosylinositolphospholipids of Trypanosoma cruzi. This gene generally occurs in prokaryotic organisms adjacent to the gene for phosphonopyruvate decarboxylase (aepY). Since the PEP phosphomutase reaction favors the substrate PEP energetically, the decarboxylase is required to drive the reaction in the direction of phosphonate production. Most often an aminotansferase (aepZ) is also present which leads to the production of the most common phosphonate compound, 2-aminoethylphosphonate (AEP). A closely related enzyme, phosphonopyruvate hydrolase from Variovorax sp. Pal2, is excluded from this model. 284 matched cddid_all.tbl CDD TIGR02321 TIGR02321 131374 Pphn_pyruv_hyd phosphonopyruvate hydrolase. This family consists of phosphonopyruvate hydrolase, an enzyme closely related to phosphoenolpyruvate phosphomutase. It cleaves the direct C-P bond of phosphonopyruvate. The characterized example is from Variovorax sp. Pal2. 290 matched cddid_all.tbl CDD TIGR02322 TIGR02322 274078 phosphon_PhnN phosphonate metabolism protein/1,5-bisphosphokinase (PRPP-forming) PhnN. Members of this family resemble PhnN of phosphonate utilization operons, where different such operons confer the ability to use somewhat different profiles of C-P bond-containing compounds (see ), including phosphites as well as phosphonates. PhnN in E. coli shows considerable homology to guanylate kinases (EC 2.7.4.8), and has actually been shown to act as a ribose 1,5-bisphosphokinase (PRPP forming). This suggests an analogous kinase reaction for phosphonate metabolism, converting 5-phosphoalpha-1-(methylphosphono)ribose to methylphosphono-PRPP. [Central intermediary metabolism, Phosphorus compounds] 179 matched cddid_all.tbl CDD TIGR02323 TIGR02323 188208 CP_lyasePhnK phosphonate C-P lyase system protein PhnK. Members of this family are the PhnK protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated complex. This protein (PhnK) and the adjacent-encoded PhnL resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this complex rather than part of a transporter per se. [Central intermediary metabolism, Phosphorus compounds] 253 matched cddid_all.tbl CDD TIGR02324 TIGR02324 131377 CP_lyasePhnL phosphonate C-P lyase system protein PhnL. Members of this family are the PhnL protein of C-P lyase systems for utilization of phosphonates. These systems resemble phosphonatase-based systems in having a three component ABC transporter, where TIGR01097 is the permease, TIGR01098 is the phosphonates binding protein, and TIGR02315 is the ATP-binding cassette (ABC) protein. They differ, however, in having, typically, ten or more additional genes, many of which are believed to form a membrane-associated C-P lysase complex. This protein (PhnL) and the adjacent-encoded PhnK (TIGR02323) resemble transporter ATP-binding proteins but are suggested, based on mutatgenesis studies, to be part of this C-P lyase complex rather than part of a transporter per se. 224 matched cddid_all.tbl CDD TIGR02325 TIGR02325 131378 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond. [Transport and binding proteins, Anions, Regulatory functions, DNA interactions] 238 matched cddid_all.tbl CDD TIGR02326 TIGR02326 131379 transamin_PhnW 2-aminoethylphosphonate--pyruvate transaminase. Members of this family are 2-aminoethylphosphonate--pyruvate transaminase. This enzyme acts on the most common type of naturally occurring phosphonate. It interconverts 2-aminoethylphosphonate plus pyruvate with 2-phosphonoacetaldehyde plus alanine. The enzyme phosphonoacetaldehyde hydrolase (EC 3.11.1.1), usually encoded by an adjacent gene, then cleaves the C-P bond of phosphonoacetaldehyde, adding water to yield acetaldehyde plus inorganic phosphate. Species with this pathway generally have an identified phosphonate ABC transporter but do not also have the multisubunit C-P lysase complex as found in Escherichia coli. [Central intermediary metabolism, Phosphorus compounds] 363 matched cddid_all.tbl CDD TIGR02327 TIGR02327 131380 int_mem_ywzB conserved hypothetical integral membrane protein. Members of this protein family are small, typically about 80 residues in length, and are highly hydrophobic. The gene is found so far only in a subset of the Firmicutes in association with genes of the ATP synthase F1 complex or NADH-quinone oxidoreductase. This family includes ywzB from Bacillus subtilis; pfam06612 describes the same family as Protein of unknown function DUF1146. 68 matched cddid_all.tbl CDD TIGR02328 TIGR02328 131381 TIGR02328 conserved hypothetical protein. Members of this protein are found in a small number of taxonomically well separated species, yet are strongly conserved, suggesting lateral gene transfer. Members are found in Treponema denticola, Clostridium acetobutylicum, and several of the Firmicutes. The function of this protein is unknown. [Hypothetical proteins, Conserved] 120 matched cddid_all.tbl CDD TIGR02329 TIGR02329 274079 propionate_PrpR propionate catabolism operon regulatory protein PrpR. At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR. [Regulatory functions, DNA interactions] 526 matched cddid_all.tbl CDD TIGR02330 TIGR02330 131383 prpD 2-methylcitrate dehydratase. Members of this family are bacterial proteins known or predicted to act as 2-methylcitrate dehydratase, an enzyme involved in the methylcitrate cycle of propionate catabolism. A related clade of archaeal proteins that may or may not be functionally equivalent is reserved for a future model and is excluded from this family. The PrpD enzyme of E. coli is responsible for the minor aconitase activity (AcnC) not accounted for by AcnA and AcnB. 468 matched cddid_all.tbl CDD TIGR02331 TIGR02331 131384 rib_alpha Rib/alpha/Esp surface antigen repeat. Sequences in this family are tandem repeats of about 79 amino acids, present in up to 14 copies in a protein and highly identical, even at the DNA level, within each protein. Sequences with these repeats are found in the Rib and alpha surface antigens of group B Streptococcus, Esp of Enterococcus faecalis, and related proteins of Lactobacillus. The repeat lacks Cys residues. Most members of this protein family also have the cell wall anchor motif LPXTG shared by many staphyloccal and streptococcal surface antigens. 80 matched cddid_all.tbl CDD TIGR02332 TIGR02332 131385 HpaX 4-hydroxyphenylacetate permease. This protein is a part of the Major Facilitator Superfamily (pfam07690). Member of this family are found in a number of proteobacterial genomes, but only in the context of having genes for 4-hydroxyphenylacetate (4-HPA) degradation. The protein is characterized by Prieto, et al. ( as 4-hydroxyphenylacetate permease in E. coli, where 3-HPA and 3,4-dihydroxyphenylacetate are shown to competitively inhibit 4-HPA transport and therefore also interact specificially. 412 matched cddid_all.tbl CDD TIGR02333 TIGR02333 131386 2met_isocit_dHY 2-methylisocitrate dehydratase, Fe/S-dependent. Members of this family appear in an operon for the degradation of propionyl-CoA via 2-methylcitrate. This family is homologous to aconitases A and B and appears to act the part as 2-methylisocitrate dehydratase, the enzyme after PrpD and before PrpB. In Escherichia coli, which lacks a member of this family, 2-methylisocitrate dehydratase activity was traced to aconitase B (TIGR00117) (). 858 matched cddid_all.tbl CDD TIGR02334 TIGR02334 131387 prpF probable AcnD-accessory protein PrpF. The 2-methylcitrate cycle is one of at least five degradation pathways for propionate via propionyl-CoA. Degradation of propionate toward pyruvate consumes oxaloacetate and releases succinate. Oxidation of succinate back into oxaloacetate by the TCA cycle makes the 2-methylcitrate pathway a cycle. This family consists of PrpF, an incompletely characterized protein that appears to be an essential accessory protein for the Fe/S-dependent 2-methylisocitrate dehydratase AcnD (TIGR02333). This protein is related to but distinct from FldA (part of pfam04303), a putative fluorene degradation protein of Sphingomonas sp. LB126. [Energy metabolism, Fermentation] 390 matched cddid_all.tbl CDD TIGR02335 TIGR02335 131388 hydr_PhnA phosphonoacetate hydrolase. This family consists of examples of phosphonoacetate hydrolase, an enzyme specific for the cleavage of the C-P bond in phosphonoacetate. Phosphonates are organic compounds with a direct C-P bond that is far less labile that the C-O-P bonds of phosphate attachment sites. Phosphonates may be degraded for phosphorus and energy by broad spectrum C-P lyase encoded by large operon or by specific enzymes for some of the more common phosphonates in nature. This family represents an enzyme from the latter category. It may be found encoded near genes for phosphonate transport and for pther specific phosphonatases. 408 matched cddid_all.tbl CDD TIGR02336 TIGR02336 213701 TIGR02336 1,3-beta-galactosyl-N-acetylhexosamine phosphorylase. Members of this family are found in phylogenetically diverse bacteria, including Clostridium perfringens (in the Firmicutes), Bifidobacterium longum and Propionibacterium acnes (in the Actinobacteria), and Vibrio vulnificus (in the Proteobacteria), most of which occur as mammalian pathogens or commensals. The nominal activity, 1,3-beta-galactosyl-N-acetylhexosamine phosphorylase (EC 2.4.1.211), varies somewhat from instance to instance in relative rates for closely related substrates. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 719 matched cddid_all.tbl CDD TIGR02337 TIGR02337 188209 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate. 118 matched cddid_all.tbl CDD TIGR02338 TIGR02338 131391 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related. 110 matched cddid_all.tbl CDD TIGR02339 TIGR02339 274080 thermosome_arch thermosome, various subunits, archaeal. Thermosome is the name given to the archaeal rather than eukaryotic form of the group II chaperonin (counterpart to the group I chaperonin, GroEL/GroES, in bacterial), a torroidal, ATP-dependent molecular chaperone that assists in the folding or refolding of nascent or denatured proteins. Various homologous subunits, one to five per archaeal genome, may be designated alpha, beta, etc., but phylogenetic analysis does not show distinct alpha subunit and beta subunit lineages traceable to ancient paralogs. [Protein fate, Protein folding and stabilization] 519 matched cddid_all.tbl CDD TIGR02340 TIGR02340 274081 chap_CCT_alpha T-complex protein 1, alpha subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT alpha chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes. 536 matched cddid_all.tbl CDD TIGR02341 TIGR02341 274082 chap_CCT_beta T-complex protein 1, beta subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT beta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes. 519 matched cddid_all.tbl CDD TIGR02342 TIGR02342 274083 chap_CCT_delta T-complex protein 1, delta subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT delta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes. 517 matched cddid_all.tbl CDD TIGR02343 TIGR02343 274084 chap_CCT_epsi T-complex protein 1, epsilon subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT epsilon chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes. 532 matched cddid_all.tbl CDD TIGR02344 TIGR02344 274085 chap_CCT_gamma T-complex protein 1, gamma subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT gamma chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes. 524 matched cddid_all.tbl CDD TIGR02345 TIGR02345 274086 chap_CCT_eta T-complex protein 1, eta subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT eta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes. 523 matched cddid_all.tbl CDD TIGR02346 TIGR02346 274087 chap_CCT_theta T-complex protein 1, theta subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT alpha chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes. 531 matched cddid_all.tbl CDD TIGR02347 TIGR02347 274088 chap_CCT_zeta T-complex protein 1, zeta subunit. Members of this family, all eukaryotic, are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT zeta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes. 531 matched cddid_all.tbl CDD TIGR02348 TIGR02348 274089 GroEL chaperonin GroL. This family consists of GroEL, the larger subunit of the GroEL/GroES cytosolic chaperonin. It is found in bacteria, organelles derived from bacteria, and occasionally in the Archaea. The bacterial GroEL/GroES group I chaperonin is replaced a group II chaperonin, usually called the thermosome in the Archaeota and CCT (chaperone-containing TCP) in the Eukaryota. GroEL, thermosome subunits, and CCT subunits all fall under the scope of pfam00118. [Protein fate, Protein folding and stabilization] 524 matched cddid_all.tbl CDD TIGR02349 TIGR02349 274090 DnaJ_bact chaperone protein DnaJ. This model represents bacterial forms of DnaJ, part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes, typically not near DnaK and GrpE-like genes; most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family. 354 matched cddid_all.tbl CDD TIGR02350 TIGR02350 274091 prok_dnaK chaperone protein DnaK. Members of this family are the chaperone DnaK, of the DnaK-DnaJ-GrpE chaperone system. All members of the seed alignment were taken from completely sequenced bacterial or archaeal genomes and (except for Mycoplasma sequence) found clustered with other genes of this systems. This model excludes DnaK homologs that are not DnaK itself, such as the heat shock cognate protein HscA (TIGR01991). However, it is not designed to distinguish among DnaK paralogs in eukaryotes. Note that a number of dnaK genes have shadow ORFs in the same reverse (relative to dnaK) reading frame, a few of which have been assigned glutamate dehydrogenase activity. The significance of this observation is unclear; lengths of such shadow ORFs are highly variable as if the presumptive protein product is not conserved. [Protein fate, Protein folding and stabilization] 595 matched cddid_all.tbl CDD TIGR02351 TIGR02351 131404 thiH thiazole biosynthesis protein ThiH. Members this protein family are the ThiH protein of thiamine biosynthesis, a homolog of the BioB protein of biotin biosynthesis. Genes for the this protein generally are found in operons with other thiamin biosynthesis genes. [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine] 366 matched cddid_all.tbl CDD TIGR02352 TIGR02352 274092 thiamin_ThiO glycine oxidase ThiO. This family consists of the homotetrameric, FAD-dependent glycine oxidase ThiO, from species such as Bacillus subtilis that use glycine in thiamine biosynthesis. In general, members of this family will not be found in species such as E. coli that instead use tyrosine and the ThiH protein. [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine] 337 matched cddid_all.tbl CDD TIGR02353 TIGR02353 274093 NRPS_term_dom non-ribosomal peptide synthetase terminal domain of unknown function. This domain is found exclusively in non-ribosomal peptide synthetases and always as the final domain in the polypeptide. This domain is roughly 700 amino acids in size and is found in polypeptides roughly twice that size. 695 matched cddid_all.tbl CDD TIGR02354 TIGR02354 162819 thiF_fam2 thiamine biosynthesis protein ThiF, family 2. Members of the HesA/MoeB/ThiF family of proteins (pfam00899) include a number of members encoded in the midst of thiamine biosynthetic operons. This mix of known and putative ThiF proteins shows a deep split in phylogenetic trees, with one the E. coli ThiF and the E. coli MoeB proteins seemingly more closely related than E. coli ThiF and Campylobacter (for example) ThiF. This model represents the divergent clade of putative ThiF proteins such found in Campylobacter. [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine] 200 matched cddid_all.tbl CDD TIGR02355 TIGR02355 131408 moeB molybdopterin synthase sulfurylase MoeB. This model describes the molybdopterin biosynthesis protein MoeB in E. coli and related species. The enzyme covalently modifies the molybdopterin synthase MoaD by sulfurylation. This enzyme is closely related to ThiF, a thiamine biosynthesis enzyme that modifies ThiS by an analogous adenylation. Both MoeB and ThiF belong to the HesA/MoeB/ThiF family (pfam00899). [Biosynthesis of cofactors, prosthetic groups, and carriers, Molybdopterin] 240 matched cddid_all.tbl CDD TIGR02356 TIGR02356 274094 adenyl_thiF thiazole biosynthesis adenylyltransferase ThiF, E. coli subfamily. Members of the HesA/MoeB/ThiF family of proteins (pfam00899) include a number of members encoded in the midst of thiamine biosynthetic operons. This mix of known and putative ThiF proteins shows a deep split in phylogenetic trees, with the Escherichia. coli ThiF and the E. coli MoeB proteins seemingly more closely related than E. coli ThiF and Campylobacter (for example) ThiF. This model represents the more widely distributed clade of ThiF proteins such found in E. coli. [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine] 202 matched cddid_all.tbl CDD TIGR02357 TIGR02357 274095 ECF_ThiT_YuaJ energy-coupled thiamine transporter ThiT. Members of this protein family have been assigned as thiamine transporters by a phylogenomic analysis of families of genes regulated by the THI element, a broadly conserved RNA secondary structure element through which thiamine pyrophosphate (TPP) levels can regulate transcription of many genes related to thiamine transport, salvage, and de novo biosynthesis. Species with this protein always lack the ThiBPQ ABC transporter. In some species (e.g. Steptococcus mutans and Streptoccus pyogenes), yuaJ is the only THI-regulated gene. Evidence from Bacillus cereus indicated thiamine uptake is coupled to proton translocation. However, a more recent comprehensive study of energy-coupled factor (ECF) transport suggests this protein is the S (subtrate capture) component of an ECF system, meaning it is energized by ATP. Previously YuaJ, but renamed ThiT. [Transport and binding proteins, Other] 173 matched cddid_all.tbl CDD TIGR02358 TIGR02358 274096 thia_cytX putative hydroxymethylpyrimidine transporter CytX. On the basis of a phylogenomic study of thiamine biosythetic, salvage, and transporter genes and a highly conserved RNA element THI, this protein family has been identified as a probable transporter of hydroxymethylpyrimidine (HMP), the phosphorylated (by ThiD) form of which gets joined (by ThiE) to hydroxyethylthiazole phosphate to make thiamine phosphate. [Transport and binding proteins, Nucleosides, purines and pyrimidines, Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine] 386 matched cddid_all.tbl CDD TIGR02359 TIGR02359 131412 thiW energy coupling factor transporter S component ThiW. Levels of thiamine pyrophosphate (TPP) or thiamine regulate transcription or translation of a number of thiamine biosynthesis, salvage, or transport genes in a wide range of prokaryotes. The mechanism involves direct binding, with no protein involved,to a structural element called THI found in the untranslated upstream region of thiamine metabolism gene operons. This element is called a riboswitch and is seen also for other metabolites such as FMN and glycine. This protein family consists of proteins identified in operons controlled by the THI riboswitch and designated ThiW. The hydrophobic nature of this protein and reconstructed metabolic background suggests that this protein acts in transport of a thiazole precursor of thiamine. [Transport and binding proteins, Other, Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine] 160 matched cddid_all.tbl CDD TIGR02360 TIGR02360 131413 pbenz_hydroxyl 4-hydroxybenzoate 3-monooxygenase. Members of this family are the enzyme 4-hydroxybenzoate 3-monooxygenase, also called p-hydroxybenzoate hydroxylase. It converts 4-hydroxybenzoate + NADPH + molecular oxygen to protocatechuate + NADPH + water. It contains monooxygenase (pfam01360) and FAD binding (pfam01494) domains. Pathways that contain this enzyme include the protocatechuate 4,5-degradation pathway. [Energy metabolism, Other] 390 matched cddid_all.tbl CDD TIGR02361 TIGR02361 274097 dak_ATP dihydroxyacetone kinase, ATP-dependent. This family consists of examples of the form of dihydroxyacetone kinase (also called glycerone kinase) that uses ATP (2.7.1.29) as the phosphate donor, rather than a phosphoprotein as in E. coli. This form is composed of a single chain with separable domains homologous to the K and L subunits of the E. coli enzyme, and is found in yeasts and other eukaryotes and in some bacteria, including Citrobacter freundii. The member from tomato has been shown to phosphorylate dihydroxyacetone, 3,4-dihydroxy-2-butanone, and some other aldoses and ketoses (). 574 matched cddid_all.tbl CDD TIGR02362 TIGR02362 213706 dhaK1b probable dihydroxyacetone kinase DhaK1b subunit. Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated EC 2.7.1.29. By contract, E. coli and many other bacterial species have a multisubunit form with a phosphoprotein donor related to PTS transport proteins. This family represents a protein, unique to the Firmicutes (low GC Gram-positives), that appears to be a divergent second copy of the K subunit of that complex; its gene is always found in operons with the other three proteins of the complex. 326 matched cddid_all.tbl CDD TIGR02363 TIGR02363 274098 dhaK1 dihydroxyacetone kinase, DhaK subunit. Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated EC 2.7.1.29. By contract, E. coli and many other bacterial species have a multisubunit form (EC 2.7.1.-) with a phosphoprotein donor related to PTS transport proteins. This family represents the DhaK subunit of the latter type of dihydroxyacetone kinase, but it specifically excludes the DhaK paralog DhaK2 (TIGR02362) found in the same operon as DhaK and DhaK in the Firmicutes. 329 matched cddid_all.tbl CDD TIGR02364 TIGR02364 131417 dha_pts dihydroxyacetone kinase, phosphotransfer subunit. In E. coli and many other bacteria, unlike the yeasts and a few bacteria such as Citrobacter freundii, the dihydroxyacetone kinase (also called glycerone kinase) transfers a phosphate from a phosphoprotein rather than from ATP and contains multiple subunits. This protein, which resembles proteins of PTS transport systems, is found with its gene adjacent to 125 matched cddid_all.tbl CDD TIGR02365 TIGR02365 274099 dha_L_ycgS dihydroxyacetone kinase, phosphoprotein-dependent, L subunit. Two types of dihydroxyacetone kinase (glycerone kinase) are described. In yeast and a few bacteria, e.g. Citrobacter freundii, the enzyme is a single chain that uses ATP as phosphoryl donor and is designated EC 2.7.1.29. By contract, E. coli and many other bacterial species have a multisubunit form (EC 2.7.1.-) with a phosphoprotein donor related to PTS transport proteins. This family represents the subunit homologous to the E. coli YcgS subunit. 194 matched cddid_all.tbl CDD TIGR02366 TIGR02366 274100 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout. 176 matched cddid_all.tbl CDD TIGR02367 TIGR02367 188213 PylS_Cterm pyrrolysyl-tRNA synthetase, C-terminal region. PylS is the enzyme responsible for charging the pyrrolysine tRNA, PylT, by ligating a free molecule of pyrrolysine. Pyrrolysine is encoded at an in-frame UAG (amber) at least in several corrinoid-dependent methyltransferases of the archaeal genera Methanosarcina and Methanococcoides, such as trimethylamine methyltransferase. This protein occurs as a fusion protein in Methanosarcina but as split genes in Desulfitobacterium hafniense and other bacteria. [Protein synthesis, tRNA aminoacylation] 242 matched cddid_all.tbl CDD TIGR02368 TIGR02368 131421 dimeth_PyL dimethylamine:corrinoid methyltransferase. This family consists of dimethylamine methyltransferases from the genus Methanosarcina. It is found in three nearly identical copies in each of M. acetivorans, M. barkeri, and M. Mazei. It is one of a suite of three non-homologous enzymes with a critical UAG-encoded pyrrolysine residue in these species (along with trimethylamine methyltransferase and monomethylamine methyltransferase). It demethylates dimethylamine, leaving monomethylamine, and methylates the prosthetic group of the small corrinoid protein MtbC. The methyl group is then transferred by methylcorrinoid:coenzyme M methyltransferase to coenzyme M. Note that the pyrrolysine residue is variously translated as K or X, or as a stop codon that truncates the sequence. 466 matched cddid_all.tbl CDD TIGR02369 TIGR02369 131422 trimeth_pyl trimethylamine:corrinoid methyltransferase. This model represents a distinct subfamily of pfam06253. All members here are trimethylamine:corrinoid methyltransferases that contain a critical pyrrolysine residue incorporated during translation via a special tRNA for a TAG (amber) codon. Known members so far are from the genus Methanosarcina. It is one of a suite of three non-homologous enzymes with a critical UAG-encoded pyrrolysine residue in these species (along with dimethylamine methyltransferase and monomethylamine methyltransferase). It demethylates trimethylamine, leaving dimethylamine, and methylates the prosthetic group of its small cognate corrinoid protein, MttC. The methyl group is then transferred by methylcorrinoid:coenzyme M methyltransferase to coenzyme M. Note that the pyrrolysine residue is variously translated as K or X, or as a stop codon that truncates the sequence. 489 matched cddid_all.tbl CDD TIGR02370 TIGR02370 131423 pyl_corrinoid methyltransferase cognate corrinoid proteins, Methanosarcina family. This model describes a subfamily of the B12 binding domain (pfam02607, pfam02310) proteins. Members of the seed alignment include corrinoid proteins specific to four different, mutally non-homologous enzymes of the genus Methanosarcina. Three of the four cognate enzymes (trimethylamine, dimethylamine, and monomethylamine methyltransferases) all have the unusual, ribosomally incorporated amino acid pyrrolysine at the active site. All act in systems in which a methyl group is transferred to the corrinoid protein to create methylcobalamin, from which the methyl group is later transferred elsewhere. 197 matched cddid_all.tbl CDD TIGR02371 TIGR02371 131424 ala_DH_arch alanine dehydrogenase, Archaeoglobus fulgidus type. This enzyme, a homolog of bacterial ornithine cyclodeaminases and marsupial mu-crystallins, is a homodimeric, NAD-dependent alanine dehydrogenase found in Archaeoglobus fulgidus and several other Archaea. For a number of close homologs, scoring between trusted and noise cutoffs, it is not clear at present what is the enzymatic activity. 325 matched cddid_all.tbl CDD TIGR02372 TIGR02372 131425 4_coum_CoA_lig 4-coumarate--CoA ligase, photoactive yellow protein activation family. This model represents the 4-coumarate--CoA ligase associated with biosynthesis of the 4-hydroxy cinnamyl (also called 4-coumaroyl) chromophore covalently linked to a Cys residue in photoactive yellow protein of Rhodobacter spp. and 386 matched cddid_all.tbl CDD TIGR02373 TIGR02373 131426 photo_yellow photoactive yellow protein. Members of this family are photoactive yellow protein, a cytosolic, 14-kDa light-sensing protein which has a 4-hydroxycinnamyl (p-coumaric acid) chromophore covalently linked to a Cys residue. The enzyme 4-coumarate--CoA ligase as described by TIGR02372 is required for its biosynthesis. The modified Cys is in a PAS (pfam00989) domain, frequently found in signal transducing proteins. Members are known in alpha and gamma Proteobacteria that include Rhodobacter capsulatus, Halorhodospira halophila, Rhodospirillum centenum, etc. 124 matched cddid_all.tbl CDD TIGR02374 TIGR02374 162827 nitri_red_nirB nitrite reductase [NAD(P)H], large subunit. [Central intermediary metabolism, Nitrogen metabolism] 785 matched cddid_all.tbl CDD TIGR02375 TIGR02375 131428 pseudoazurin pseudoazurin. Pseudoazurin, also called cupredoxin, is a small, blue periplasmic protein with a single bound copper atom. Pseudoazurin is related plastocyanins. Several examples of pseudoazurin are encoded by a neighboring gene for, or have been shown to transfer electrons to, copper-containing nitrite reductases (TIGR02376) of the same species. [Energy metabolism, Electron transport] 116 matched cddid_all.tbl CDD TIGR02376 TIGR02376 131429 Cu_nitrite_red nitrite reductase, copper-containing. This family consists of copper-type nitrite reductase. It reduces nitrite to nitric oxide, the first step in denitrification. [Central intermediary metabolism, Nitrogen metabolism] 311 matched cddid_all.tbl CDD TIGR02377 TIGR02377 131430 MocE_fam_FeS Rieske [2Fe-2S] domain protein, MocE subfamily. This model describes a subfamily of the Rieske-like [2Fe-2S] family of ferredoxins that includes MocE, part of the rhizopine (3-O-methyl-scyllo-inosamine) catabolic cluster in Rhizobium. Members of this family are related to, yet distinct from, the small subunit of nitrite reductase [NAD(P)H]. 101 matched cddid_all.tbl CDD TIGR02378 TIGR02378 131431 nirD_assim_sml nitrite reductase [NAD(P)H], small subunit. This model describes NirD, the small subunit of nitrite reductase [NAD(P)H] (the assimilatory nitrite reductase), which associates with NirB, the large subunit (TIGR02374). In a few bacteria such as Klebsiella pneumoniae and in Fungi, the two regions are fused. [Central intermediary metabolism, Nitrogen metabolism] 105 matched cddid_all.tbl CDD TIGR02379 TIGR02379 131432 ECA_wecE TDP-4-keto-6-deoxy-D-glucose transaminase. This family consists of TDP-4-keto-6-deoxy-D-glucose transaminases, the WecE (formerly RffA) protein of enterobacterial common antigen (ECA) biosynthesis, from enterobacteria. It also includes closely matching sequence from species not expected to make ECA, but which contain other genes for the biosynthesis of TDP-4-keto-6-deoxy-D-Glc, an intermediate in the biosynthesis of other compounds as well and the substrate of WecA. This family belongs to the DegT/DnrJ/EryC1/StrS aminotransferase family (pfam01041). [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 376 matched cddid_all.tbl CDD TIGR02380 TIGR02380 131433 ECA_wecA undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphatetransferase. Members of this family are the WecA enzyme of enterobacterial common antigen biosynthesis, undecaprenyl-phosphate alpha-N-acetylglucosaminyl 1-phosphatetransferase. This family represents one narrow clade, and closely related sequences outside this clade may represent enzymes that catalyze the same specific reaction, but in the context of different pathways. A His-rich motif in a cytosolic loop of this integral membrane protein, shown critical to enzymatic activity for WecA is variously present or absent in the clade that includes Bacillus subtilis TagO teichoic acid biosynthesis enzyme, which may catalyze the same reaction as WecA. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 346 matched cddid_all.tbl CDD TIGR02381 TIGR02381 131434 cspD cold shock domain protein CspD. This model represents what appears to be a phylogenetically distinct clade, containing E. coli CspD (SP|P24245) and related proteobacterial proteins within the larger family of cold shock domain proteins described by pfam00313. The gene symbol cspD may have been used idependently for other subfamilies of cold shock domain proteins, such as for B. subtilis CspD. These proteins typically are shorter than 70 amino acids. In E. coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication. [DNA metabolism, DNA replication, recombination, and repair, Cellular processes, Adaptations to atypical conditions] 68 matched cddid_all.tbl CDD TIGR02382 TIGR02382 131435 wecD_rffC TDP-D-fucosamine acetyltransferase. This model represents the WecD protein (Formerly RffC) for the biosynthesis of enterobacterial common antigen (ECA), an outer leaflet, outer membrane glycolipid with a trisaccharide repeat unit. WecD is a member of the GNAT family of acetytransferases (pfam00583). [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 191 matched cddid_all.tbl CDD TIGR02383 TIGR02383 274101 Hfq RNA chaperone Hfq. This model represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory noncoding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see . The name hfq reflects phenomenology as a host factor for phage Q-beta RNA replication. [Regulatory functions, Other] 61 matched cddid_all.tbl CDD TIGR02384 TIGR02384 274102 RelB_DinJ addiction module antitoxin, RelB/DinJ family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. The resulting model appears to describe a narrower set of proteins than pfam04221, although many in the scope of this model are not obviously paired with toxin proteins. Several toxin/antitoxin pairs may occur in a single species. [Cellular processes, Toxin production and resistance, Mobile and extrachromosomal element functions, Other] 84 matched cddid_all.tbl CDD TIGR02385 TIGR02385 211740 RelE_StbE addiction module toxin, RelE/StbE family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all are found adjacent to RelB/DinJ family antitoxin genes (TIGR02384), as are most genes found by the resulting model. StbE from Morganella morganii plasmid R485 shows typical behaviour for an addiction module toxin. It cannot be cloned without its partner (the antitoxin), whereas its partner cannot confer plasmid stability without StbE. [Cellular processes, Toxin production and resistance, Mobile and extrachromosomal element functions, Other] 88 matched cddid_all.tbl CDD TIGR02386 TIGR02386 274103 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form. Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase] 1140 matched cddid_all.tbl CDD TIGR02387 TIGR02387 131440 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit. The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''. 619 matched cddid_all.tbl CDD TIGR02388 TIGR02388 274104 rpoC2_cyan DNA-directed RNA polymerase, beta'' subunit. The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase] 1227 matched cddid_all.tbl CDD TIGR02389 TIGR02389 274105 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase] 367 matched cddid_all.tbl CDD TIGR02390 TIGR02390 274106 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'. This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. 868 matched cddid_all.tbl CDD TIGR02391 TIGR02391 162834 hypoth_ymh TIGR02391 family protein. This family consists of a relatively rare (~ 8 occurrences per 200 genomes) prokaryotic protein family. Genes for members are appear to be associated variously with phage and plasmid regions, restriction system loci, transposons, and housekeeping genes. The function is unknown. [Hypothetical proteins, Domain] 125 matched cddid_all.tbl CDD TIGR02392 TIGR02392 274107 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors. [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors] 270 matched cddid_all.tbl CDD TIGR02393 TIGR02393 274108 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc. [Transcription, Transcription factors] 238 matched cddid_all.tbl CDD TIGR02394 TIGR02394 131447 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393). [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors] 285 matched cddid_all.tbl CDD TIGR02395 TIGR02395 274109 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., ). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations [Transcription, Transcription factors] 429 matched cddid_all.tbl CDD TIGR02396 TIGR02396 274110 diverge_rpsU rpsU-divergently transcribed protein. This uncharacterized protein is found in a number of Alphaproteobacteria and, with N-terminal regions long enough to be transit peptides, in eukaryotes. This phylogeny suggests mitochondrial derivation. In several Alphaproteobacteria, the gene for this protein is encoded divergently from rpsU, the gene for ribosomal protein S21. S21 is unusual in being encoded outside the usual long ribosomal protein operons, but rather in contexts that suggest regulation of the initiation of protein translation. [Unknown function, General] 185 matched cddid_all.tbl CDD TIGR02397 TIGR02397 274111 dnaX_nterm DNA polymerase III, subunit gamma and tau. This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis. [DNA metabolism, DNA replication, recombination, and repair] 355 matched cddid_all.tbl CDD TIGR02398 TIGR02398 131451 gluc_glyc_Psyn glucosylglycerol-phosphate synthase. Glucosylglycerol-phosphate synthase catalyzes the key step in the biosynthesis of the osmolyte glucosylglycerol. It is known in several cyanobacteria and in Pseudomonas anguilliseptica. The enzyme is closely related to the alpha,alpha-trehalose-phosphate synthase, likewise involved in osmolyte biosynthesis, of E. coli and many other bacteria. A close homolog from Xanthomonas campestris is excluded from this model and scores between trusted and noise. 487 matched cddid_all.tbl CDD TIGR02399 TIGR02399 131452 salt_tol_Pase glucosylglycerol 3-phosphatase. Proteins in this family are glucosylglycerol-phosphate phosphatase, with the gene symbol stpA (Salt Tolerance Protein A). A motif characteristic of acid phosphatases is found, but otherwise this family shows little sequence similarity to other phosphatases. This enzyme acts on the glucosylglycerol phosphate, product of glucosylglycerol phosphate synthase and immediate precursor of the osmoprotectant glucosylglycerol. 389 matched cddid_all.tbl CDD TIGR02400 TIGR02400 274112 trehalose_OtsA alpha,alpha-trehalose-phosphate synthase [UDP-forming]. This enzyme catalyzes the key, penultimate step in biosynthesis of trehalose, a compatible solute made as an osmoprotectant in some species in all three domains of life. The gene symbol OtsA stands for osmotically regulated trehalose synthesis A. Trehalose helps protect against both osmotic and thermal stresses, and is made from two glucose subunits. This model excludes glucosylglycerol-phosphate synthase, an enzyme of an analogous osmoprotectant system in many cyanobacterial strains. This model does not identify archaeal examples, as they are more divergent than glucosylglycerol-phosphate synthase. Sequences that score in the gray zone between the trusted and noise cutoffs include a number of yeast multidomain proteins in which the N-terminal domain may be functionally equivalent to this family. The gray zone also includes the OtsA of Cornyebacterium glutamicum (and related species), shown to be responsible for synthesis of only trace amounts of trehalose while the majority is synthesized by the TreYZ pathway; the significance of OtsA in this species is unclear (see Wolf, et al., ). [Cellular processes, Adaptations to atypical conditions] 456 matched cddid_all.tbl CDD TIGR02401 TIGR02401 274113 trehalose_TreY malto-oligosyltrehalose synthase. This enzyme, formally named (1->4)-alpha-D-glucan 1-alpha-D-glucosylmutase, is the TreY enzyme of the TreYZ pathway of trehalose biosynthesis, an alternative to the OtsAB pathway. Trehalose may be incorporated into more complex compounds but is best known as compatible solute. It is one of the most effective osmoprotectants, and unlike the various betaines does not require nitrogen for its synthesis. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 825 matched cddid_all.tbl CDD TIGR02402 TIGR02402 274114 trehalose_TreZ malto-oligosyltrehalose trehalohydrolase. Members of this family are the trehalose biosynthetic enzyme malto-oligosyltrehalose trehalohydrolase, formally known as 4-alpha-D-{(1->4)-alpha-D-glucano}trehalose trehalohydrolase (EC 3.2.1.141). It is the TreZ protein of the TreYZ pathway for trehalose biosynthesis, and alternative to the OtsAB system. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 544 matched cddid_all.tbl CDD TIGR02403 TIGR02403 274115 trehalose_treC alpha,alpha-phosphotrehalase. Trehalose is a glucose disaccharide that serves in many biological systems as a compatible solute for protection against hyperosmotic and thermal stress. This family describes trehalose-6-phosphate hydrolase, product of the treC (or treA) gene, which is often found together with a trehalose uptake transporter and a trehalose operon repressor. 543 matched cddid_all.tbl CDD TIGR02404 TIGR02404 274116 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli. [Regulatory functions, DNA interactions] 233 matched cddid_all.tbl CDD TIGR02405 TIGR02405 131458 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis [Regulatory functions, DNA interactions] 311 matched cddid_all.tbl CDD TIGR02406 TIGR02406 131459 ectoine_EctA diaminobutyrate acetyltransferase. This enzyme family is the EctA of ectoine biosynthesis. Ectoine is a compatible solute, analagous to trehalose, betaines, etc., found often in halotolerant organisms. EctA is L-2,4-diaminobutyric acid acetyltransferase, also called DABA acetyltransferase. [Cellular processes, Adaptations to atypical conditions] 157 matched cddid_all.tbl CDD TIGR02407 TIGR02407 274117 ectoine_ectB diaminobutyrate--2-oxoglutarate aminotransferase. Members of this family of class III pyridoxal-phosphate-dependent aminotransferases are diaminobutyrate--2-oxoglutarate aminotransferase (EC 2.6.1.76) that catalyze the first step in ectoine biosynthesis from L-aspartate beta-semialdehyde. This family is readily separated phylogenetically from enzymes with the same substrate and product but involved in other process such as siderophore (SP|Q9Z3R2) or 1,3-diaminopropane (SP|P44951) biosynthesis. The family TIGR00709 previously included both groups but has now been revised to exclude the ectoine biosynthesis proteins of this family. Ectoine is a compatible solute particularly effective in conferring salt tolerance. [Cellular processes, Adaptations to atypical conditions] 412 matched cddid_all.tbl CDD TIGR02408 TIGR02408 131461 ectoine_ThpD ectoine hydroxylase. Both ectoine and hydroxyectoine are compatible solvents that serve as protectants against osmotic and thermal stresses. A number of genomes synthesize ectoine. This enzyme allows conversion of ectoine to hydroxyectoine, which may be more effective for some purposes, and is found in a subset of ectoine-producing organisms. 277 matched cddid_all.tbl CDD TIGR02409 TIGR02409 274118 carnitine_bodg gamma-butyrobetaine hydroxylase. Members of this protein family are gamma-butyrobetaine hydroxylase, both bacterial and eukarytotic. This enzyme catalyzes the last step in the conversion of lysine to carnitine. Carnitine can serve as a compatible solvent in bacteria and also participates in fatty acid metabolism. 366 matched cddid_all.tbl CDD TIGR02410 TIGR02410 274119 carnitine_TMLD trimethyllysine dioxygenase. Members of this family with known function act as trimethyllysine dioxygenase, an enzyme in the pathway for carnitine biosynthesis from lysine. This enzyme is homologous to gamma-butyrobetaine,2-oxoglutarate dioxygenase, which catalyzes the last step in carnitine biosynthesis. Members of this family appear to be eukaryotic only. 362 matched cddid_all.tbl CDD TIGR02411 TIGR02411 274120 leuko_A4_hydro leukotriene A-4 hydrolase/aminopeptidase. Members of this family represent a distinctive subset within the zinc metallopeptidase family M1 (pfam01433). The majority of the members of pfam01433 are aminopeptidases, but the sequences in this family for which the function is known are leukotriene A-4 hydrolase. A dual epoxide hydrolase and aminopeptidase activity at the same active site is indicated. The physiological substrate for aminopeptidase activity is not known. 602 matched cddid_all.tbl CDD TIGR02412 TIGR02412 274121 pepN_strep_liv aminopeptidase N, Streptomyces lividans type. This family is a subset of the members of the zinc metallopeptidase family M1 (pfam01433), with a single member characterized in Streptomyces lividans 66 and designated aminopeptidase N. The spectrum of activity may differ somewhat from the aminopeptidase N clade of E. coli and most other Proteobacteria, well separated phylogenetically within the M1 family. The M1 family also includes leukotriene A-4 hydrolase/aminopeptidase (with a bifunctional active site). 831 matched cddid_all.tbl CDD TIGR02413 TIGR02413 131466 Bac_small_yrzI Bacillus tandem small hypothetical protein. Members of this family are very small proteins, about 47 residues each, in the genus Bacillus. Single members are found in Bacillus subtilis and Bacillus halodurans, but arrays of six in tandem in Bacillus cereus and Bacillus anthracis. An EIxxE motif present in most members of this family resembles cleavage sites by the germination protease GPR in a number small, acid-soluble spore proteins (SASP). A role in sporulation is possible. 46 matched cddid_all.tbl CDD TIGR02414 TIGR02414 274122 pepN_proteo aminopeptidase N, Escherichia coli type. The M1 family of zinc metallopeptidases contains a number of distinct, well-separated clades of proteins with aminopeptidase activity. Several are designated aminopeptidase N, EC 3.4.11.2, after the Escherichia coli enzyme, suggesting a similar activity profile (see SP|P04825 for a description of catalytic activity). This family consists of all aminopeptidases closely related to E. coli PepN and presumed to have similar (not identical) function. Nearly all are found in Proteobacteria, but members are found also in Cyanobacteria, plants, and apicomplexan parasites. This family differs greatly in sequence from the family of aminopeptidases typified by Streptomyces lividans PepN (TIGR02412), from the membrane bound aminopeptidase N family in animals, etc. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 863 matched cddid_all.tbl CDD TIGR02415 TIGR02415 131468 23BDH acetoin reductases. One member of this family, as characterized in Klebsiella terrigena, is described as able to interconvert acetoin + NADH with meso-2,3-butanediol + NAD(+). It is also called capable of irreversible reduction of diacetyl with NADH to acetoin. Blomqvist, et al. decline to specify either EC 1.1.1.4 which is (R,R)-butanediol dehydrogenase, or EC 1.1.1.5, which is acetoin dehydrogenase without a specified stereochemistry, for this enzyme. This enzyme is a homotetramer in the family of short chain dehydrogenases (pfam00106). Another member of this family, from Corynebacterium glutamicum, is called L-2,3-butanediol dehydrogenase (). [Energy metabolism, Fermentation] 254 matched cddid_all.tbl CDD TIGR02416 TIGR02416 131469 CO_dehy_Mo_lg carbon-monoxide dehydrogenase, large subunit. This model represents the large subunits of group of carbon-monoxide dehydrogenases that include molybdenum as part of the enzymatic cofactor. There are various forms of carbon-monoxide dehydrogenase; Salicibacter pomeroyi DSS-3, for example, has two forms. Note that, at least in some species, the active site Cys is modified with a selenium attached to (rather than replacing) the sulfur atom. This is termed selanylcysteine, and created post-translationally, in contrast to selenocysteine incorporation during translation as for many other selenoproteins. [Energy metabolism, Other] 770 matched cddid_all.tbl CDD TIGR02417 TIGR02417 131470 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer. [Regulatory functions, DNA interactions] 327 matched cddid_all.tbl CDD TIGR02418 TIGR02418 131471 acolac_catab acetolactate synthase, catabolic. Acetolactate synthase (EC 2.2.1.6) combines two molecules of pyruvate to yield 2-acetolactate with the release of CO2. This reaction may be involved in either valine biosynthesis (biosynthetic) or conversion of pyruvate to acetoin and possibly to 2,3-butanediol (catabolic). The biosynthetic type, described by TIGR00118, is also capable of forming acetohydroxybutyrate from pyruvate and 2-oxobutyrate for isoleucine biosynthesis. The family described here, part of the same larger family of thiamine pyrophosphate-dependent enzymes (pfam00205, pfam02776) is the catabolic form, generally found associated with in species with acetolactate decarboxylase and usually found in the same operon. The model may not encompass all catabolic acetolactate synthases, but rather one particular clade in the larger TPP-dependent enzyme family. [Energy metabolism, Fermentation] 539 matched cddid_all.tbl CDD TIGR02419 TIGR02419 274123 C4_traR_proteo phage/conjugal plasmid C-4 type zinc finger protein, TraR family. Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA. [Mobile and extrachromosomal element functions, Prophage functions] 63 matched cddid_all.tbl CDD TIGR02420 TIGR02420 274124 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage. [Transcription, Transcription factors, Regulatory functions, Small molecule interactions] 110 matched cddid_all.tbl CDD TIGR02421 TIGR02421 274125 QEGLA conserved hypothetical protein. Members of this family include a possible metal-binding motif HEXXXH and, nearby, a perfectly conserved motif QEGLA. All members belong to the Proteobacteria, including Agrobacterium tumefaciens and several species of Vibrio and Pseudomonas, and are found in only one copy per chromosome (Vibrio vulnificus, with two chromosomes, has two). The function is unknown. 366 matched cddid_all.tbl CDD TIGR02422 TIGR02422 131475 protocat_beta protocatechuate 3,4-dioxygenase, beta subunit. This model represents the beta chain of protocatechuate 3,4-dioxygenase. The most closely related family outside this family is that of the alpha chain (TIGR02423), typically encoded in an adjacent locus. This enzyme acts in the degradation of aromatic compounds by way of p-hydroxybenzoate to succinate and acetyl-CoA. [Energy metabolism, Other] 220 matched cddid_all.tbl CDD TIGR02423 TIGR02423 274126 protocat_alph protocatechuate 3,4-dioxygenase, alpha subunit. This model represents the alpha chain of protocatechuate 3,4-dioxygenase. The most closely related family outside this family is that of the beta chain (TIGR02422), typically encoded in an adjacent locus. This enzyme acts in the degradation of aromatic compounds by way of p-hydroxybenzoate to succinate and acetyl-CoA. [Energy metabolism, Other] 193 matched cddid_all.tbl CDD TIGR02424 TIGR02424 274127 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria. [Energy metabolism, Other, Regulatory functions, DNA interactions] 300 matched cddid_all.tbl CDD TIGR02425 TIGR02425 131478 decarb_PcaC 4-carboxymuconolactone decarboxylase. Members of this family are 4-carboxymuconolactone decarboxylase, which catalyzes the third step in the catabolism of protocatechuate (and therefore the fourth step in the catabolism of para-hydroxybenzoate, of 3-hydroxybenzoate, of vanillate, etc.). Most members of this family are encoded within protocatechuate catabolism operons. This protein is sometimes found as a fusion protein with other enzymes of the pathway, as in Rhodococcus opacus, Streptomyces avermitilis, and Caulobacter crescentus. [Energy metabolism, Other] 123 matched cddid_all.tbl CDD TIGR02426 TIGR02426 274128 protocat_pcaB 3-carboxy-cis,cis-muconate cycloisomerase. Members of this family are 3-carboxy-cis,cis-muconate cycloisomerase, the enzyme the catalyzes the second step in the protocatechuate degradation to beta-ketoadipate and then to succinyl-CoA and acetyl-CoA. 4-hydroxybenzoate, 3-hydroxybenzoate, and vanillate all can be converted in one step to protocatechuate. All members of the seed alignment for this model were chosen from within protocatechuate degradation operons of at least three genes of the pathway, from genomes with the complete pathway through beta-ketoadipate. [Energy metabolism, Other] 338 matched cddid_all.tbl CDD TIGR02427 TIGR02427 131480 protocat_pcaD 3-oxoadipate enol-lactonase. Members of this family are 3-oxoadipate enol-lactonase. Note that the substrate is known as 3-oxoadipate enol-lactone, 2-oxo-2,3-dihydrofuran-5-acetate, 4,5-Dihydro-5-oxofuran-2-acetate, and 5-oxo-4,5-dihydrofuran-2-acetate. The enzyme the catalyzes the fourth step in the protocatechuate degradation to beta-ketoadipate and then to succinyl-CoA and acetyl-CoA. 4-hydroxybenzoate, 3-hydroxybenzoate, and vanillate all can be converted in one step to protocatechuate. This enzyme also acts in catechol degradation. In genomes that catabolize both catechol and protocatechuate, two forms of this enzyme may be found. All members of the seed alignment for this model were chosen from within protocatechuate degradation operons of at least three genes of the pathway, from genomes with the complete pathway through beta-ketoadipate. [Energy metabolism, Other] 251 matched cddid_all.tbl CDD TIGR02428 TIGR02428 188219 pcaJ_scoB_fam 3-oxoacid CoA-transferase, B subunit. Various members of this family are characterized as the B subunits of succinyl-CoA:3-ketoacid-CoA transferase (EC 2.8.3.5), beta-ketoadipate:succinyl-CoA transferase (EC 2.8.3.6), acetyl-CoA:acetoacetate CoA transferase (EC 2.8.3.8), and butyrate-acetoacetate CoA-transferase (EC 2.8.3.9). This represents a very distinct clade with strong sequence conservation within the larger family defined by pfam01144. The A subunit represents a different clade in pfam01144. 207 matched cddid_all.tbl CDD TIGR02429 TIGR02429 131482 pcaI_scoA_fam 3-oxoacid CoA-transferase, A subunit. Various members of this family are characterized as the A subunits of succinyl-CoA:3-ketoacid-CoA transferase (EC 2.8.3.5), beta-ketoadipate:succinyl-CoA transferase (EC 2.8.3.6), acetyl-CoA:acetoacetate CoA transferase (EC 2.8.3.8), and butyrate-acetoacetate CoA-transferase (EC 2.8.3.9). This represents a very distinct clade with strong sequence conservation within the larger family defined by pfam01144. The B subunit represents a different clade in pfam01144, described by TIGR02428. The two are found in general as tandem genes and occasionally as a fusion. 222 matched cddid_all.tbl CDD TIGR02430 TIGR02430 131483 pcaF 3-oxoadipyl-CoA thiolase. Members of this family are designated beta-ketoadipyl CoA thiolase, an enzyme that acts at the end of pathways for the degradation of protocatechuate (from benzoate and related compounds) and of phenylacetic acid. 400 matched cddid_all.tbl CDD TIGR02431 TIGR02431 131484 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU. [Regulatory functions, DNA interactions] 248 matched cddid_all.tbl CDD TIGR02432 TIGR02432 274129 lysidine_TilS_N tRNA(Ile)-lysidine synthetase, N-terminal domain. The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop) vs. UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This family describes a protein domain found, apparently, in all bacteria in a single copy. Eukaryotic sequences appear to be organellar. The domain archictecture of this protein family is variable; some, including characterized proteins of E. coli and B. subtilis known to be tRNA(Ile)-lysidine synthetase, include a conserved 50-residue domain that many other members lack. This protein belongs to the ATP-binding PP-loop family ( pfam01171). It appears in the literature and protein databases as TilS, YacA, and putative cell cycle protein MesJ (a misnomer). [Protein synthesis, tRNA and rRNA base modification] 189 matched cddid_all.tbl CDD TIGR02433 TIGR02433 274130 lysidine_TilS_C tRNA(Ile)-lysidine synthetase, C-terminal domain. TIGRFAMs model TIGR02432 describes the family of the N-terminal domain of tRNA(Ile)-lysidine synthetase. This family (TIGR02433) describes a small C-terminal domain of about 50 residues present in about half the members of family TIGR02432,and in no other protein. Characterized examples of tRNA(Ile)-lysidine synthetase from E. coli and Bacillus subtilis both contain this domain. [Protein synthesis, tRNA and rRNA base modification] 47 matched cddid_all.tbl CDD TIGR02434 TIGR02434 131487 CobF precorrin-6A synthase (deacetylating). In the aerobic cobalamin biosythesis pathway, four enzymes are involved in the conversion of precorrin-3A to precorrin-6A. The first of the four steps is carried out by EC 1.14.13.83, precorrin-3B synthase (CobG), yielding precorrin-3B as the product. This is followed by three methylation reactions, which introduce a methyl group at C-17 (CobJ; EC 2.1.1.131), C-11 (CobM; EC 2.1.1.133) and C-1 (CobF; EC 2.1.1.152) of the macrocycle, giving rise to precorrin-4, precorrin-5 and precorrin-6A, respectively. This model identifies CobF in High GC gram positive, alphaproteobacteria and pseudomonas-related species. 249 matched cddid_all.tbl CDD TIGR02435 TIGR02435 274131 CobG precorrin-3B synthase. An iron-sulfur protein. An oxygen atom from dioxygen is incorporated into the macrocycle at C-20. In the aerobic cobalamin biosythesis pathway, four enzymes are involved in the conversion of precorrin-3A to precorrin-6A. The first of the four steps is carried out by EC 1.14.13.83, precorrin-3B synthase (CobG), yielding precorrin-3B as the product. This is followed by three methylation reactions, which introduce a methyl group at C-17 (CobJ; EC 2.1.1.131), C-11 (CobM; EC 2.1.1.133) and C-1 (CobF; EC 2.1.1.152) of the macrocycle, giving rise to precorrin-4, precorrin-5 and precorrin-6A, respectively. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 390 matched cddid_all.tbl CDD TIGR02436 TIGR02436 274132 TIGR02436 four helix bundle protein. This family describes a protein of unknown function whose structure is a bundle of four long alpha helices. Some of the first members of this family were found encoded in the (atypically large) intervening sequence (IVS) of Leptospira 23S RNA, a region often present in the rRNA gene and removed during rRNA processing without re-ligation. However, this location is not conserved, and naming this protein as a 23S RNA protein is both confusing and inaccurate. 108 matched cddid_all.tbl CDD TIGR02437 TIGR02437 131490 FadB fatty oxidation complex, alpha subunit FadB. Members represent alpha subunit of multifunctional enzyme complex of the fatty acid degradation cycle. Activities include: enoyl-CoA hydratase (EC 4.2.1.17), dodecenoyl-CoA delta-isomerase activity (EC 5.3.3.8), 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35), 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A representative is E. coli FadB (SP:P21177). This model excludes the FadJ family represented by SP:P77399. [Fatty acid and phospholipid metabolism, Degradation] 714 matched cddid_all.tbl CDD TIGR02438 TIGR02438 274133 catachol_actin catechol 1,2-dioxygenase, Actinobacterial. Members of this family are catechol 1,2-dioxygenases of the Actinobacteria. They are more closely related to actinobacterial chlorocatechol 1,2-dioxygenases than to proteobacterial catechol 1,2-dioxygenases, and so are built in this separate model. The member from Rhodococcus rhodochrous NCIMB 13259 (GB|AAC33003.1) is described as a homodimer with bound Fe, similarly active on catechol, 3-methylcatechol and 4-methylcatechol. 281 matched cddid_all.tbl CDD TIGR02439 TIGR02439 274134 catechol_proteo catechol 1,2-dioxygenase, proteobacterial. Members of this family known so far are catechol 1,2-dioxygenases of the Proteobacteria. They are distinct from catechol 1,2-dioxygenases and chlorocatechol 1,2-dioxygenases of the Actinobacteria, which are quite similar to each other and resolved by separate models. This enzyme catalyzes intradiol cleavage in which catechol + O2 becomes cis,cis-muconate. Catechol is an intermediate in the catabolism of many different aromatic compounds, as is the alternative intermediate protocatechuate. In Acinetobacter lwoffii, two isozymes are present with abilities, differing somewhat, to act on catechol analogs 3-methylcatechol, 4-methylcatechol, 4-methoxycatechol, and 4-chlorocatechol. [Energy metabolism, Other] 285 matched cddid_all.tbl CDD TIGR02440 TIGR02440 131493 FadJ fatty oxidation complex, alpha subunit FadJ. Members represent alpha subunit of multifunctional enzyme complex of the fatty acid degradation cycle. Plays a minor role in aerobic beta-oxidation of fatty acids. FadJI complex is necessary for anaerobic growth on short-chain acids with nitrate as an electron acceptor. Activities include: enoyl-CoA hydratase (EC 4.2.1.17),3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35), 3-hydroxybutyryl-CoA epimerase (EC 5.1.2.3). A representative is E. coli FadJ (aka YfcX) (SP:P77399). This model excludes the FadB of TIGR02437 equivalog model. [Fatty acid and phospholipid metabolism, Degradation] 699 matched cddid_all.tbl CDD TIGR02441 TIGR02441 131494 fa_ox_alpha_mit fatty acid oxidation complex, alpha subunit, mitochondrial. Members represent alpha subunit of mitochondrial multifunctional fatty acid degradation enzyme complex. Subunit activities include: enoyl-CoA hydratase (EC 4.2.1.17) & 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35). Some characterization in human (SP:P40939), pig (SP:Q29554), and rat (SP:Q64428). The beta subunit has activity: acetyl-CoA C-acyltransferase (EC 2.3.1.16). 737 matched cddid_all.tbl CDD TIGR02442 TIGR02442 274135 Cob-chelat-sub cobaltochelatase subunit. Cobaltochelatase is responsible for the insertion of cobalt into the corrin ring of coenzyme B12 during its biosynthesis. Two versions have been well described. CbiK/CbiX is a monomeric, anaerobic version which acts early in the biosynthesis (pfam06180). CobNST is a trimeric, ATP-dependent, aerobic version which acts late in the biosynthesis (TIGR02257/TIGR01650/TIGR01651). A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis. 633 matched cddid_all.tbl CDD TIGR02443 TIGR02443 131496 TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria. 59 matched cddid_all.tbl CDD TIGR02444 TIGR02444 274136 TIGR02444 TIGR02444 family protein. Members of this family are bacterial hypothetical proteins, about 160 amino acids in length, found in various Proteobacteria, including members of the genera Pseudomonas and Vibrio. The C-terminal region is poorly conserved and is not included in the model. [Hypothetical proteins, Conserved] 116 matched cddid_all.tbl CDD TIGR02445 TIGR02445 131498 fadA fatty oxidation complex, beta subunit FadA. This subunit of the FadBA complex has acetyl-CoA C-acyltransferase (EC 2.3.1.16) activity, and is also known as beta-ketothiolase and fatty oxidation complex, beta subunit. This protein is almost always located adjacent to FadB (TIGR02437). The FadBA complex is the major complex active for beta-oxidation of fatty acids in E. coli. [Fatty acid and phospholipid metabolism, Degradation] 385 matched cddid_all.tbl CDD TIGR02446 TIGR02446 131499 FadI fatty oxidation complex, beta subunit FadI. This subunit of the FadJI complex has acetyl-CoA C-acyltransferase (EC 2.3.1.16) activity, and is also known as beta-ketothiolase and fatty oxidation complex, beta subunit, and YfcY. This protein is almost always located adjacent to FadJ (TIGR02440). The FadJI complex is needed for anaerobic beta-oxidation of short-chain fatty acids in E. coli. [Fatty acid and phospholipid metabolism, Degradation] 430 matched cddid_all.tbl CDD TIGR02447 TIGR02447 131500 yiiD_Cterm thioesterase domain, putative. This family consists of a broadly distributed uncharacterized domain found often as a standalone protein. The member from Shewanella oneidensis, PDB|1T82_A (Forouhar, et al., unpublished) is described from crystallography work as a putative thioesterase. About half of the members of this family are fused to an Acetyltransf_1 domain (pfam00583). The function of this protein is unknown. 138 matched cddid_all.tbl CDD TIGR02448 TIGR02448 274137 TIGR02448 conserverd hypothetical protein. This family consists of small hypothetical proteins, about 100 amino acids in length. The family includes five members (three in tandem) in Pseudomonas aeruginosa PAO1, and also in Pseudomonas putida KT2440, four in Pseudomonas syringae DC3000, and single members in several other Proteobacteria. The function is unknown. 101 matched cddid_all.tbl CDD TIGR02449 TIGR02449 131502 TIGR02449 TIGR02449 family protein. Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown. 65 matched cddid_all.tbl CDD TIGR02450 TIGR02450 131503 TIGR02450 tryptophan-rich conserved hypothetical protein. Members of this family are small hypothetical proteins of 60 to 100 residues from Cyanobacteria and some Proteobacteria. Prochlorococcus marinus strains have two members, other species one only. Interestingly, of the eight most conserved residues, four are aromatic and three are invariant tryptophans. It appears all species that encode this protein can synthesize tryptophan de novo. 61 matched cddid_all.tbl CDD TIGR02451 TIGR02451 131504 anti_sig_ChrR anti-sigma factor, putative, ChrR family. The member of this family from Rhodobacter sphaeroides has been shown both to form a complex with sigma(E) and to negatively regulate tetrapyrrole biosynthesis. This protein likely contains (at least) two distinct functional domains; several smaller homologs (excluded by the model) show homology only to the C-terminal, including a motif PxHxHxGxE. [Regulatory functions, Other] 215 matched cddid_all.tbl CDD TIGR02452 TIGR02452 131505 TIGR02452 TIGR02452 family protein. Members of this uncharacterized protein family are found in Streptomyces, Nostoc sp. PCC 7120, Clostridium acetobutylicum, Lactobacillus johnsonii NCC 533, Deinococcus radiodurans, and Pirellula sp. for a broad but sparse phylogenetic distibution that at least suggests lateral gene transfer. 266 matched cddid_all.tbl CDD TIGR02453 TIGR02453 274138 TIGR02453 TIGR02453 family protein. Members of this family are widely (though sparsely) distributed bacterial proteins about 230 residues in length. All members have a motif RxxRDxRFxxx[DN]KxxY. The function of this protein family is unknown. In several fungi, this model identifies a conserved region of a longer protein. Therefore, it may be incorrect to speculate that all members share a common function. 217 matched cddid_all.tbl CDD TIGR02454 TIGR02454 274139 ECF_T_CbiQ cobalt ECF transporter T component CbiQ. This model represents the CbiQ component of the cobalt-specific ECF-type. CbiQ is now recognized as the T component of energy-coupling factor (ECF)-type transporters. The S component confers specificity (CbiM-N for cobalt systems), which CbiO is the ABC-family ATPase. In general, proteins found by this model reside next to the other putative subunits of the complex, identified as CbiN, CbiO, or CbiM. Note that the designation of cobalt transporter has been spread excessively among ECF system transporters with many other specificities. [Transport and binding proteins, Cations and iron carrying compounds] 198 matched cddid_all.tbl CDD TIGR02455 TIGR02455 131508 TreS_stutzeri trehalose synthase, Pseudomonas stutzeri type. Trehalose synthase catalyzes a one-step conversion of maltose to trehalose. This is an alternative to the OtsAB and TreYZ pathways. This family includes a characterized example from Pseudomonas stutzeri plus very closely related sequences from other Pseudomonads. Cutoff scores are set to find a more distantly related sequence from Desulfovibrio vulgaris, likely to be functionally equivalent, between trusted and noise limits. [Energy metabolism, Biosynthesis and degradation of polysaccharides, Cellular processes, Adaptations to atypical conditions] 688 matched cddid_all.tbl CDD TIGR02456 TIGR02456 274140 treS_nterm trehalose synthase. Trehalose synthase interconverts maltose and alpha, alpha-trehalose by transglucosylation. This is one of at least three mechanisms for biosynthesis of trehalose, an important and widespread compatible solute. However, it is not driven by phosphate activation of sugars and its physiological role may tend toward trehalose degradation. This view is accentuated by numerous examples of fusion to a probable maltokinase domain. The sequence region described by this model is found both as the whole of a trehalose synthase and as the N-terminal region of a larger fusion protein that includes trehalose synthase activity. Several of these fused trehalose synthases have a domain homologous to proteins with maltokinase activity from Actinoplanes missouriensis and Streptomyces coelicolor (). [Energy metabolism, Biosynthesis and degradation of polysaccharides] 539 matched cddid_all.tbl CDD TIGR02457 TIGR02457 274141 TreS_Cterm trehalose synthase-fused probable maltokinase. Three pathways for the biosynthesis of trehalose, an osmoprotectant that in some species is also a precursor of certain cell wall glycolipids. Trehalose synthase, TreS, can interconvert maltose and trehalose, but while the equilibrium may favor trehalose, physiological concentrations of trehalose may be much greater than that of maltose and TreS may act largely in its degradation. This model describes a domain found only as a C-terminal fusion to TreS proteins. The most closely related proteins outside this family, Pep2 of Streptomyces coelicolor and Mak1 of Actinoplanes missouriensis, have known maltokinase activity. We suggest this domain acts as a maltokinase and helps drive conversion of trehalose to maltose. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 528 matched cddid_all.tbl CDD TIGR02458 TIGR02458 274142 CbtA cobalt transporter subunit CbtA (proposed). This model represents a family of proteins which have been proposed to act as cobalt transporters acting in concert with vitamin B12 biosynthesis systems. Evidence for this assignment includes 1) prediction of five trans-membrane segments, 2) positional gene linkage with known B12 biosynthesis genes, 3) upstream proximity of B12 transcriptional regulatory sites, 4) the absence of other known cobalt import systems and 5) the obligate co-localization with a small protein (CbtB) having a single additional trans-membrane segment and a C-terminal histidine-rich motif likely to be a metal-binding site. 225 matched cddid_all.tbl CDD TIGR02459 TIGR02459 131512 CbtB cobalt transporter subunit CbtB (proposed). This model represents a family of proteins which have been proposed to act as cobalt transporters acting in concert with vitamin B12 biosynthesis systems. Evidence for this assignment includes 1) prediction of a single trans-membrane segment and a C-terminal histidine-rich motif likely to be a metal-binding site, 2) positional gene linkage with known B12 biosynthesis genes, 3) upstream proximity of B12 transcriptional regulatory sites, 4) the absence of other known cobalt import systems and 5) the obligate co-localization with a protein (CbtA) predicted to have five additional trans-membrane segments. 60 matched cddid_all.tbl CDD TIGR02460 TIGR02460 162866 osmo_MPGsynth mannosyl-3-phosphoglycerate synthase. This family consists of examples of mannosyl-3-phosphoglycerate synthase (MPGS), which together mannosyl-3-phosphoglycerate phosphatase (MPGP) comprises a two-step pathway for mannosylglycerate biosynthesis. Mannosylglycerate is a compatible solute that tends to be restricted to extreme thermophiles of archaea and bacteria. Note that in Rhodothermus marinus, this pathway is one of two; the other is condensation of GDP-mannose with D-glycerate by mannosylglycerate synthase. 381 matched cddid_all.tbl CDD TIGR02461 TIGR02461 131514 osmo_MPG_phos mannosyl-3-phosphoglycerate phosphatase. Members of this family are mannosyl-3-phosphoglycerate phosphatase (EC 3.1.3.70). It acts sequentially after mannosyl-3-phosphoglycerate synthase (EC 2.4.1.217) in a two-step pathway of biosynthesis of the compatible solute mannosylglycerate, a typical osmolyte of thermophiles. 225 matched cddid_all.tbl CDD TIGR02462 TIGR02462 274143 pyranose_ox pyranose oxidase. Pyranose oxidase (also called glucose 2-oxidase) converts D-glucose and molecular oxygen to 2-dehydro-D-glucose and hydrogen peroxide. Peroxide production is believed to be important to the wood rot fungi in which this enzyme is found for lignin degradation. 547 matched cddid_all.tbl CDD TIGR02463 TIGR02463 131516 MPGP_rel mannosyl-3-phosphoglycerate phosphatase-related protein. This family consists of members of the HAD superfamily, subfamily IIB. All members are closely related to mannosyl-3-phosphoglycerate phosphatase, the second enzyme in a two-step pathway for biosynthesis of mannosylglycerate, a compatible solute present in some thermophiles and in Dehalococcoides ethenogenes. However, members of this family are separable in a neighbor-joining tree constructed from a multiple sequence alignment and are found only in mesophiles that lack the companion mannosyl-3-phosphoglycerate synthase (TIGR02460). Members of this family are like to act on a compound related to yet distinct from mannosyl-3-phosphoglycerate. [Unknown function, General] 221 matched cddid_all.tbl CDD TIGR02464 TIGR02464 274144 ribofla_fusion conserved hypothetical protein, ribA/ribD-fused. This model describes a sequence region that occurs in at least three different polypeptide contexts. It is found fused to GTP cyclohydrolase II, the RibA of riboflavin biosynthesis (TIGR00505), as in Vibrio vulnificus. It is found fused to riboflavin biosynthesis protein RibD (TIGR00326) in rice and Arabidopsis. It occurs as a standalone protein in a number of bacterial species in varied contexts, including single gene operons and bacteriophage genomes. The member from E. coli currently is named YbiA. The function(s) of members of this family is unknown. 153 matched cddid_all.tbl CDD TIGR02465 TIGR02465 131518 chlorocat_1_2 chlorocatechol 1,2-dioxygenase. Members of this protein family are chlorocatechol 1,2-dioxygenase. This protein is closely related to catechol 1,2-dioxygenase, TIGR02439, EC 1.13.11.1. Note that annotated database entries have appeared for the present protein family with the EC number that refers to that of family TIGR02439. This protein acts in pathways of the biodegradation of chlorinated aromatic compounds. 246 matched cddid_all.tbl CDD TIGR02466 TIGR02466 274145 TIGR02466 conserved hypothetical protein. This family consists of uncharacterized proteins in Caulobacter crescentus CB15, Bdellovibrio bacteriovorus HD100, Synechococcus sp. WH 8102, Silicibacter pomeroyi DSS-3, and Hyphomonas neptunium ATCC 15444. The context of nearby genes differs substantially between members and does point to any specific biological role. [Hypothetical proteins, Conserved] 201 matched cddid_all.tbl CDD TIGR02467 TIGR02467 274146 CbiE precorrin-6y C5,15-methyltransferase (decarboxylating), CbiE subunit. This model recognizes the CbiE methylase which is responsible, in part (along with CbiT), for methylating precorrin-6y (or cobalt-precorrin-6y) at both the 5 and 15 positions as well as the concomitant decarbozylation at C-12. In many organisms, this protein is fused to the CbiT subunit. The fused protein, when found in organisms catalyzing the oxidative version of the cobalamin biosynthesis pathway, is called CobL. 204 matched cddid_all.tbl CDD TIGR02468 TIGR02468 274147 sucrsPsyn_pln sucrose phosphate synthase/possible sucrose phosphate phosphatase, plant. Members of this family are sucrose-phosphate synthases of plants. This enzyme is known to exist in multigene families in several species of both monocots and dicots. The N-terminal domain is the glucosyltransferase domain. Members of this family also have a variable linker region and a C-terminal domain that resembles sucrose phosphate phosphatase (SPP) (EC 3.1.3.24) (see TIGR01485), the next and final enzyme of sucrose biosynthesis. The SPP-like domain likely serves a binding and not a catalytic function, as the reported SPP is always encoded by a distinct protein. 1050 matched cddid_all.tbl CDD TIGR02469 TIGR02469 274148 CbiT precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit. This model recognizes the CbiT methylase which is responsible, in part (along with CbiE), for methylating precorrin-6y (or cobalt-precorrin-6y) at both the 5 and 15 positions as well as the concomitant decarbozylation at C-12. In many organisms, this protein is fused to the CbiE subunit. The fused protein, when found in organisms catalyzing the oxidative version of the cobalamin biosynthesis pathway, is called CobL. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 124 matched cddid_all.tbl CDD TIGR02470 TIGR02470 274149 sucr_synth sucrose synthase. This model represents sucrose synthase, an enzyme that, despite its name, generally uses rather produces sucrose. Sucrose plus UDP (or ADP) becomes D-fructose plus UDP-glucose (or ADP-glucose), which is then available for cell wall (or starch) biosynthesis. The enzyme is homologous to sucrose phosphate synthase, which catalyzes the penultimate step in sucrose synthesis. Sucrose synthase is found, so far, exclusively in plants and cyanobacteria. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 784 matched cddid_all.tbl CDD TIGR02471 TIGR02471 131524 sucr_syn_bact_C sucrose-phosphate synthase, sucrose phosphatase-like domain, bacterial. Sucrose phosphate synthase (SPS) and sucrose phosphate phosphatase (SPP) are the last two enzymes of sucrose biosynthesis. In cyanobacteria and plants, the C-terminal region of most or all versions of SPS has a domain homologous to the known SPP. This domain may serve a binding or regulatory rather than catalytic function. Sequences in this family are bacterial C-terminal regions found in all but two of the putative bacterial sucrose phosphate synthases described by TIGR02472. 236 matched cddid_all.tbl CDD TIGR02472 TIGR02472 131525 sucr_P_syn_N sucrose-phosphate synthase, putative, glycosyltransferase domain. This family consists of the N-terminal regions, or in some cases the entirety, of bacterial proteins closely related to plant sucrose-phosphate synthases (SPS). The C-terminal domain (TIGR02471), found with most members of this family, resembles both bona fide plant sucrose-phosphate phosphatases (SPP) and the SPP-like domain of plant SPS. At least two members of this family lack the SPP-like domain, which may have binding or regulatory rather than enzymatic activity by analogy to plant SPS. This enzyme produces sucrose 6-phosphate and UDP from UDP-glucose and D-fructose 6-phosphate, and may be encoded near the gene for fructokinase. 439 matched cddid_all.tbl CDD TIGR02473 TIGR02473 131526 flagell_FliJ flagellar export protein FliJ. Members of this family are the FliJ protein found, in nearly every case, in the midst of other flagellar biosynthesis genes in bacgterial genomes. Typically the fliJ gene is found adjacent to the gene for the flagellum-specific ATPase FliI. Sequence scoring in the gray zone between trusted and noise cutoffs include both probable FliJ proteins and components of bacterial type III secretion systems. 141 matched cddid_all.tbl CDD TIGR02474 TIGR02474 274150 pec_lyase pectate lyase, PelA/Pel-15E family. Members of this family are isozymes of pectate lyase (EC 4.2.2.2), also called polygalacturonic transeliminase and alpha-1,4-D-endopolygalacturonic acid lyase. [Energy metabolism, Biosynthesis and degradation of polysaccharides] 290 matched cddid_all.tbl CDD TIGR02475 TIGR02475 274151 CobW cobalamin biosynthesis protein CobW. The family of proteins identified by this model is generally found proximal to the trimeric cobaltochelatase subunit CobN which is essential for vitamin B12 (cobalamin) biosynthesis. The protein contains an P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. A broader CobW family is delineated by two Pfam models which identify the N- and C-terminal domains (pfam02492 and pfam07683). [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 341 matched cddid_all.tbl CDD TIGR02476 TIGR02476 162875 BluB 5,6-dimethylbenzimidazole synthase. A previously published hypothesis that BluB, involved in cobalamin biosynthesis, is EC 1.16.8.1 (cob(II)yrinic acid a,c-diamide reductase) is now contradicted by newer work ascribing a role in 5,6-dimethylbenzimidazole (DMB) biosynthesis. The BluB protein is related to the nitroreductase family (pfam0881). [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 205 matched cddid_all.tbl CDD TIGR02477 TIGR02477 131530 PFKA_PPi diphosphate--fructose-6-phosphate 1-phosphotransferase. Diphosphate--fructose-6-phosphate 1-phosphotransferase catalyzes the addition of phosphate from diphosphate (PPi) to fructose 6-phosphate to give fructose 1,6-bisphosphate (EC 2.7.1.90). The enzyme is also known as pyrophosphate-dependent phosphofructokinase. The usage of PPi-dependent enzymes in glycolysis presumably frees up ATP for other processes. TIGR02482 represents the ATP-dependent 6-phosphofructokinase enzyme contained within pfam00365: Phosphofructokinase. This model hits primarily bacterial, plant alpha, and plant beta sequences. [Energy metabolism, Glycolysis/gluconeogenesis] 539 matched cddid_all.tbl CDD TIGR02478 TIGR02478 274152 6PF1K_euk 6-phosphofructokinase, eukaryotic type. Members of this family are eukaryotic (with one exception) ATP-dependent 6-phosphofructokinases (EC 2.7.1.11) in which two tandem copies of the phosphofructokinase are found. Members are found, often including several isozymes, in animals and fungi and in the bacterium Propionibacterium acnes KPA171202 (a human skin commensal). 746 matched cddid_all.tbl CDD TIGR02479 TIGR02479 274153 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium. 224 matched cddid_all.tbl CDD TIGR02480 TIGR02480 131533 fliN flagellar motor switch protein FliN. Proteins that consist largely of the domain described by this model for this protein family can be designated flagellar motor switch protein FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside the scope of this family, are associated with type III secretion and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica. [Cellular processes, Chemotaxis and motility] 77 matched cddid_all.tbl CDD TIGR02481 TIGR02481 274154 hemeryth_dom hemerythrin-like metal-binding domain. This model describes both members of the hemerythrin (TIGR00058) family of marine invertebrates and a broader collection of bacterial and archaeal homologs. Many of the latter group are multidomain proteins with signal-transducing domains such as the GGDEF diguanylate cyclase domain (TIGR00254, pfam00990) and methyl-accepting chemotaxis protein signaling domain (pfam00015). Most hemerythrins are oxygen-carriers with a bound non-heme iron, but at least one example is a cadmium-binding protein, apparently with a role in sequestering toxic metals rather than in binding oxygen. Patterns of conserved residues suggest that all prokaryotic instances of this domain bind iron or another heavy metal, but the exact function is unknown. Not surprisingly, the prokaryote with the most instances of this domain is Magnetococcus sp. MC-1, a magnetotactic bacterium. 126 matched cddid_all.tbl CDD TIGR02482 TIGR02482 213713 PFKA_ATP 6-phosphofructokinase. 6-phosphofructokinase (EC 2.7.1.11) catalyzes the addition of phosphate from ATP to fructose 6-phosphate to give fructose 1,6-bisphosphate. This represents a key control step in glycolysis. This model hits bacterial ATP-dependent 6-phosphofructokinases which lack a beta-hairpin loop present in TIGR02483 family members. TIGR02483 contains members that are ATP-dependent as well as members that are pyrophosphate-dependent. TIGR02477 represents the pyrophosphate-dependent phosphofructokinase, diphosphate--fructose-6-phosphate 1-phosphotransferase (EC 2.7.1.90). [Energy metabolism, Glycolysis/gluconeogenesis] 301 matched cddid_all.tbl CDD TIGR02483 TIGR02483 274155 PFK_mixed phosphofructokinase. Members of this family that are characterized, save one, are phosphofructokinases dependent on pyrophosphate (EC 2.7.1.90) rather than ATP (EC 2.7.1.11). The exception is one of three phosphofructokinases from Streptomyces coelicolor. Family members are both bacterial and archaeal. [Energy metabolism, Glycolysis/gluconeogenesis] 324 matched cddid_all.tbl CDD TIGR02484 TIGR02484 274156 CitB CitB domain protein. This model identifies proteins of two distinct names which may or may not have two distinct functions. CitB has been identified in salmonella and E. coli as the signal transduction component of a two-component system for citrate in which CitA acts as a citrate transporter. CobZ is essential for cobalamin biosynthesis (by knockout of the R. capsulatus gene) and is complemented by the characterized precorrin 3B synthase CobG. The enzyme has been shown to contain flavin, heme and Fe-S cluster cofactors and is believed to require dioxygen as a substrate. This model identifies the C-terminal domain of the R. capsulatus CobZ, which, in most other species exists as a separate gene adjacent to CobZ. 372 matched cddid_all.tbl CDD TIGR02485 TIGR02485 274157 CobZ_N-term precorrin 3B synthase CobZ. CobZ is essential for cobalamin biosynthesis (by knockout of the R. capsulatus gene) and is complemented by the characterized precorrin 3B synthase CobG. The enzyme has been shown to contain flavin, heme and Fe-S cluster cofactors and is believed to require dioxygen as a substrate. This model identifies the N-terminal portion of the R. capsulatus gene which, in other species exists as a separate protein. The C-terminal portion is homologous to the 2-component signal transduction system protein CitB (TIGR02484). [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 432 matched cddid_all.tbl CDD TIGR02486 TIGR02486 274158 RDH reductive dehalogenase. This model represents a family of corrin and 8-iron Fe-S cluster-containing reductive dehalogenases found primarily in halorespiring microorganisms such as dehalococcoides ethenogenes which contains as many as 17 enzymes of this type with varying substrate ranges. One example of a characterized species is the tetrachloroethene reductive dehalogenase (1.97.1.8) which also acts on trichloroethene converting it to dichloroethene. 314 matched cddid_all.tbl CDD TIGR02487 TIGR02487 274159 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism] 579 matched cddid_all.tbl CDD TIGR02488 TIGR02488 131541 flgG_G_neg flagellar basal-body rod protein FlgG, Gram-negative bacteria. This family consists of the FlgG protein of the flagellar apparatus in the Proteobacteria and spirochetes. [Cellular processes, Chemotaxis and motility] 259 matched cddid_all.tbl CDD TIGR02489 TIGR02489 131542 flgE_epsilon flagellar hook protein FlgE, epsilon proteobacterial. Members of this family are flagellar hook proteins, designated FlgE, as found in the epsilon subdivision of the Proteobacteria (Helicobacter, Wolinella, and Campylobacter). These proteins differ significantly in architecture from proteins designated FlgE in other lineages; the N-terminal and C-terminal domains are homologous, but members of this family only contain a large central domain that is surface-exposed and variable between strains. 719 matched cddid_all.tbl CDD TIGR02490 TIGR02490 274160 flgF flagellar basal-body rod protein FlgF. Members of this protein are FlgF, one of several homologous flagellar basal-body rod proteins in bacteria. [Cellular processes, Chemotaxis and motility] 89 matched cddid_all.tbl CDD TIGR02491 TIGR02491 274161 NrdG anaerobic ribonucleoside-triphosphate reductase activating protein. This enzyme is a member of the radical-SAM family (pfam04055) and utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487). The two components form an alpha-2/beta-2 heterodimer. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism, Protein fate, Protein modification and repair] 154 matched cddid_all.tbl CDD TIGR02492 TIGR02492 274162 flgK_ends flagellar hook-associated protein FlgK. The flagellar hook-associated protein FlgK of bacterial flagella has conserved N- and C-terminal domains. The central region is highly variable in length and sequence, and often contains substantial runs of low-complexity sequence. This model is built from an alignment of FlgK sequences with the central region excised. Note that several other proteins of the flagellar apparatus also are homologous in the N- and C-terminal regions to FlgK, but are excluded from this model. [Cellular processes, Chemotaxis and motility] 323 matched cddid_all.tbl CDD TIGR02493 TIGR02493 131546 PFLA pyruvate formate-lyase 1-activating enzyme. An iron-sulfur protein with a radical-SAM domain (pfam04055). A single glycine residue in EC 2.3.1.54, formate C-acetyltransferase (formate-pyruvate lyase), is oxidized to the corresponding radical by transfer of H from its CH2 to AdoMet with concomitant cleavage of the latter. The reaction requires Fe2+. The first stage is reduction of the AdoMet to give methionine and the 5'-deoxyadenosin-5-yl radical, which then abstracts a hydrogen radical from the glycine residue. [Energy metabolism, Anaerobic, Protein fate, Protein modification and repair] 235 matched cddid_all.tbl CDD TIGR02494 TIGR02494 274163 PFLE_PFLC glycyl-radical enzyme activating protein. This subset of the radical-SAM family (pfam04055) includes a number of probable activating proteins acting on different enzymes all requiring an amino-acid-centered radical. The closest relatives to this family are the pyruvate-formate lyase activating enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic ribonucleotide reductase activating enzyme (TIGR02491). Included within this subfamily are activators of hydroxyphenyl acetate decarboxylase (HdpA), benzylsuccinate synthase (BssD), gycerol dehydratase (DhaB2) as well as enzymes annotated in E. coli as activators of different isozymes of pyruvate-formate lyase (PFLC and PFLE) however, these appear to lack characterization and may activate enzymes with distinctive functions. Most of the sequence-level variability between these forms is concentrated within an N-terminal domain which follows a conserved group of three cysteines and contains a variable pattern of 0 to 8 additional cysteines. 295 matched cddid_all.tbl CDD TIGR02495 TIGR02495 274164 NrdG2 anaerobic ribonucleoside-triphosphate reductase activating protein. This enzyme is a member of the radical-SAM family (pfam04055). It is often gene clustered with the class III (anaerobic) ribonucleotide triphosphate reductase (NrdD, TIGR02487) and presumably fulfills the identical function as NrdG, which utilizes S-adenosyl methionine, an iron-sulfur cluster and a reductant (dihydroflavodoxin) to produce a glycine-centered radical in NrdD. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism, Protein fate, Protein modification and repair] 192 matched cddid_all.tbl CDD TIGR02497 TIGR02497 131549 yscI_hrpB_dom type III secretion apparatus protein, YscI/HrpB, C-terminal domain. This model represents the conserved C-terminal domain of a protein conserved in across species in the bacterial type III secretion apparatus. This protein is designated YscI (Yop proteins translocation protein I) in Yersinia and HrpB (hypersensitivity response and pathogenicity protein B) in plant pathogens such as Pseudomonas syringae. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 39 matched cddid_all.tbl CDD TIGR02498 TIGR02498 131550 type_III_ssaH type III secretion system protein, SsaH family. This family describes a small protein, always smaller than 100 amino acids, encoded in pathogenicity islands for bacterial type III secretion systems in various strains of Yersinia, Salmonella, and enteropathogenic E. coli, as well as Chromobacterium violaceum and Citrobacter rodentium. Although strictly associated with type III secretion systems, this protein seems not yet to have been characterized as part of the apparatus or as an effector protein. [Cellular processes, Pathogenesis] 79 matched cddid_all.tbl CDD TIGR02499 TIGR02499 274165 HrpE_YscL_not type III secretion apparatus protein, HrpE/YscL family. This model is related to pfam06188, but is broader. pfam06188 describes HrpE-like proteins, components of bacterial type III secretion systems primarily in bacteria that infect plants. This model includes also the homologous proteins of animal pathogens, such as YscL of Yersinia pestis. This model excludes the related protein FliH of the bacterial flagellar apparatus (see pfam02108) [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 166 matched cddid_all.tbl CDD TIGR02500 TIGR02500 274166 type_III_yscD type III secretion apparatus protein, YscD/HrpQ family. This family represents a conserved protein of bacterial type III secretion systems. Gene symbols are variable from species to species. Members are designated YscD in Yersinia, HrpQ in Pseudomonas syringae, and EscD in enteropathogenic Escherichia coli. In the Chlamydiae, this model describes the C-terminal 400 residues of a longer protein. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 410 matched cddid_all.tbl CDD TIGR02501 TIGR02501 274167 type_III_yscE type III secretion system protein, YseE family. Members of this family are found exclusively in type III secretion appparatus gene clusters in bacteria. Those bacteria with a protein from this family tend to target animal cells, as does Yersinia pestis. This protein is small (about 70 amino acids) and not well characterized. [Cellular processes, Pathogenesis] 67 matched cddid_all.tbl CDD TIGR02502 TIGR02502 131554 type_III_YscX type III secretion protein, YscX family. Members of this family are encoded within bacterial type III secretion gene clusters. Among all species with type III secretion, those with this protein are found among those that target animal rather than plant cells. The member of this family in Yersinia was shown by mutation to be required for type III secretion of Yops effector proteins and therefore is believe to be part of the secretion machinery. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 121 matched cddid_all.tbl CDD TIGR02503 TIGR02503 131555 type_III_SycN type III secretion chaperone SycN. Members of this protein family are part of the machinery of bacterial type III secretion in a number of bacteria that target animal cells. In the well-studied system from Yersinia, a complex of this protein (SycN) and YscB (pfam07329) acts as a chaperone for the export of YopN (). YopN then acts to control effector protein secretion, in response to calcium levels, so that secretion occurs only after contact with the targeted eukaryotic cell. [Protein fate, Protein folding and stabilization, Cellular processes, Pathogenesis] 119 matched cddid_all.tbl CDD TIGR02504 TIGR02504 274168 NrdJ_Z ribonucleoside-diphosphate reductase, adenosylcobalamin-dependent. This model represents a group of adenosylcobalamin(B12)-dependent ribonucleotide reductases (Class II RNRs) related to the characterized species from Pyrococcus, Thermoplasma, Corynebacterium, and Deinococcus. RNR's are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA. This is the rate-limiting step of DNA biosynthesis. This model identifies genes in a wide range of deeply branching bacteria. All are structurally related to the class I (non-heme iron dependent) RNRs. In most species this gene is known as NrdJ, while in mycobacteria it is called NrdZ. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism] 575 matched cddid_all.tbl CDD TIGR02505 TIGR02505 274169 RTPR ribonucleoside-triphosphate reductase, adenosylcobalamin-dependent. This model represents a group of adenosylcobalamin(B12)-dependent ribonucleotide reductases (RNR) related to the characterized species from Lactococcus leichmannii. RNR's are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA. This is the rate-limiting step of DNA biosynthesis. Thus model identifies NrdJ enzymes only in cyanobacteria, lactococcus and certain bacteriophage. A separate model (TIGR02504) identifies a larger group of divergent B12-dependent RNR's. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism] 713 matched cddid_all.tbl CDD TIGR02506 TIGR02506 274170 NrdE_NrdA "ribonucleoside-diphosphate reductase, alpha subunit. This model represents the alpha (large) chain of the class I ribonucleotide reductase (RNR). RNR's are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA. This is the rate-limiting step of DNA biosynthesis. Class I RNR's generate the required radical (on tyrosine) via a ""non-heme"" iron cofactor which resides in the beta (small) subunit. The alpha subunit contains the catalytic and allosteric regulatory sites. The mechanism of this enzyme requires molecular oxygen. E. Coli contains two versions of this enzyme which are regulated independently (NrdAB and NrdEF, where NrdA and NrdE are the large chains). Most organisms contain only one, but the application of the gene symbols NrdA and NrdE are somewhat arbitrary. This model identifies RNR's in diverse clades of bacteria, eukaryotes as well as numerous DNA viruses and phage. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism]" 617 matched cddid_all.tbl CDD TIGR02507 TIGR02507 131559 MtrF tetrahydromethanopterin S-methyltransferase, F subunit. This small protein (MtrF) is one of eight subunits of the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase in methanogenic archaea. This methyltranferase is membrane-associated enzyme complex that uses methy-transfer reaction to drive sodium-ion pump. Archaea domain, have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase. 65 matched cddid_all.tbl CDD TIGR02508 TIGR02508 131560 type_III_yscG type III secretion protein, YscG family. YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designate Yops (Yersinia outer proteins) in Yersinia. This family consists of YscG of Yersinia, and functionally equivalent type III secretion machinery protein in other species: AscG in Aeromonas, LscG in Photorhabdus luminescens, etc. [Protein fate, Protein folding and stabilization, Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 115 matched cddid_all.tbl CDD TIGR02509 TIGR02509 131561 type_III_yopR type III secretion effector, YopR family. Members of this family are type III secretion system effectors, named differently in different species and designated YopR (Yersinia outer protein R), encoded by the YscH (Yersinia secretion H) gene. This Yops protein is unusual in that it is released to extracellularly rather than injected directly into the target cell as are most Yops. [Cellular processes, Pathogenesis] 131 matched cddid_all.tbl CDD TIGR02510 TIGR02510 188230 NrdE-prime ribonucleoside-diphosphate reductase, alpha chain. This model represents a small clade of ribonucleoside-diphosphate reductase, alpha chains which are sufficiently divergent from the usual Class I RNR alpha chains (NrdE or NrdA, TIGR02506) as to warrant their own model. The genes from Thermus thermophilus, Dichelobacter and Salinibacter are adjacent to the usual RNR beta chain. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism] 548 matched cddid_all.tbl CDD TIGR02511 TIGR02511 131563 type_III_tyeA type III secretion effector delivery regulator, TyeA family. Members of this family include both small proteins, about 90 amino acids, in which this model covers the whole, and longer proteins of about 360 residues which match in the C-terminal region. The longer proteins (HrpJ) have N-terminal regions that match pfam07201. Members of this family belong to bacterial type III secretion systems, and include TyeA from the well-studied Yersinia systems. TyeA appears involved in calcium-responsive regulation of the delivery of type III effectors. 79 matched cddid_all.tbl CDD TIGR02512 TIGR02512 274171 FeFe_hydrog_A [FeFe] hydrogenase, group A. This model describes iron-only hydrogenases of anaerobic and microaerophilic bacteria and protozoa. This model is narrower, and covers a longer stretch of sequence, than pfam02906. This family represents a division among families that belong to pfam02906, which also includes proteins such as nuclear prelamin A recognition factor in animals. Note that this family shows some heterogeneity in terms of periplasmic, cytosolic, or hydrogenosome location, NAD or NADP dependence, and overal protein protein length. 374 matched cddid_all.tbl CDD TIGR02513 TIGR02513 131565 type_III_yscB type III secretion system chaperone, YscB family. Members of this family include YscB of Yersinia and functionally equivalent (but differently named) proteins from type III secretion systems of other pathogens that affect animal cells. YscB acts, along with SycN (TIGR02503), as a chaperone for YopN, a key part of a complex that regulates type III secretion so it responds to contact with the eukaryotic target cell. 139 matched cddid_all.tbl CDD TIGR02514 TIGR02514 274172 type_III_yscP type III secretion system needle length determinant. Members of this family include YscP of the Yersinia type III secretion system and equivalent proteins in other animal pathogen bacterial type III secretion systems. The model describes the conserved C-terminal region. N-terminal regions are poorly conserved and variable in length with some low-complexity sequence. 129 matched cddid_all.tbl CDD TIGR02515 TIGR02515 274173 IV_pilus_PilQ type IV pilus secretin (or competence protein) PilQ. A number of proteins homologous to PilQ are involved in type IV pilus formation, competence for transformation, type III secretion, and type II secretion (also called the main terminal branch of the general secretion pathway). Members of this family include PilQ itself, which is a component of the type IV pilus structure, from a number of species. In Haemophilus influenzae, the member of this family is associated with competence for transformation with exogenous DNA rather than with formation of a type IV pilus; the surface structure required for competence may be considered an unusual, incomplete type IV pilus structure. [Cell envelope, Surface structures] 418 matched cddid_all.tbl CDD TIGR02516 TIGR02516 274174 type_III_yscC type III secretion outer membrane pore, YscC/HrcC family. A number of proteins homologous to the type IV pilus secretin PilQ (TIGR02515) are involved in type IV pilus formation, competence for transformation, type III secretion, and type II secretion (also called the main terminal branch of the general secretion pathway). The clade described by this model contains the outer membrane pore proteins of bacterial type III secretion systems, typified by YscC for animal pathogens and HrcC for plant pathogens. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 462 matched cddid_all.tbl CDD TIGR02517 TIGR02517 274175 type_II_gspD type II secretion system protein D. In Gram-negative bacteria, proteins that have first crossed the inner member by Sec-dependent protein transport can be exported across the outer membrane by type II secretion, also called the main terminal branch of the general secretion pathway. Members of this family are general secretion pathway protein D. In Yersinia enterocolitica, a second member of this family is part of a novel second type II secretion system specifically associated with virulence (See ). This family is closely homologous to the type IV pilus outer membrane secretin PilQ (TIGR02515) and to the type III secretion system pore YscC/HrcC (TIGR02516). [Protein fate, Protein and peptide secretion and trafficking] 594 matched cddid_all.tbl CDD TIGR02518 TIGR02518 131570 EutH_ACDH acetaldehyde dehydrogenase (acetylating). 488 matched cddid_all.tbl CDD TIGR02519 TIGR02519 274176 pilus_MshL pilus (MSHA type) biogenesis protein MshL. Members of this family are predicted secretins, that is, outer membrane pore proteins associated with delivery of proteins from periplasm to the outside of the cell. Related families include GspD of type II secretion (TIGR02517), the YscC/HrcC family from type III secretion (TIGR02516), and the PilQ secretin of type IV pilus formation (TIGR02515). Members of this family are found in gene clusters associated with MSHA (mannose-sensitive hemagglutinin) and related pili, and appear to be the secretin of this pilus system. [Cell envelope, Surface structures] 290 matched cddid_all.tbl CDD TIGR02520 TIGR02520 274177 pilus_B_mal_scr type IVB pilus formation outer membrane protein, R64 PilN family. Several related protein families encode outer membrane pore proteins for type II secretion, type III secretion, and type IV pilus formation. This protein family appears to encode a secretin for pilus formation, although it is quite different from PilQ. Members include the PilN lipoprotein of the plasmid R64 thin pilus, a type IV pilus. Scoring between the trusted and noise cutoffs are examples of bundle-forming pilus B (bfpB). [Cell envelope, Surface structures, Protein fate, Protein and peptide secretion and trafficking] 497 matched cddid_all.tbl CDD TIGR02521 TIGR02521 131573 type_IV_pilW type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF and PilW. This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain. 234 matched cddid_all.tbl CDD TIGR02522 TIGR02522 274178 pilus_cpaD pilus (Caulobacter type) biogenesis lipoprotein CpaD. This family consists of a pilus biogenesis protein, CpaD, from Caulobacter, and homologs in other bacteria, including three in the root nodule bacterium Bradyrhizobium japonicum. The molecular function is not known. [Cell envelope, Surface structures] 198 matched cddid_all.tbl CDD TIGR02523 TIGR02523 131575 type_IV_pilV type IV pilus modification protein PilV. Pilus systems categorized as type IV pilins differ greatly from one another, with some showing greater similarty to type II or type III secretion systems than to each other. Members of this protein family represent the PilV protein of type IV pilus systems as found in Pseudomonas aeruginosa PAO1, Pseudomonas syringae DC3000, Neisseria meningitidis MC58, Xylella fastidiosa 9a5c, etc. [Cell envelope, Surface structures, Protein fate, Protein modification and repair] 139 matched cddid_all.tbl CDD TIGR02524 TIGR02524 131576 dot_icm_DotB Dot/Icm secretion system ATPase DotB. Members of this protein family are the DotB component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the liturature now seems to favor calling this the Dot/Icm system. This family is most closely related to TraJ proteins of plasmid transfer, rather than to proteins of other type IV secretion systems. 358 matched cddid_all.tbl CDD TIGR02525 TIGR02525 131577 plasmid_TraJ plasmid transfer ATPase TraJ. Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524). [Mobile and extrachromosomal element functions, Plasmid functions] 372 matched cddid_all.tbl CDD TIGR02526 TIGR02526 131578 eut_PduT PduT-like ethanolamine utilization protein. This gene shows up in ethanolamine utilization operons in which a proteinaceous coat organelle is also encoded. It is closely related to the PduT protein in propane-diol operons with the same structure. 182 matched cddid_all.tbl CDD TIGR02527 TIGR02527 274179 dot_icm_IcmQ Dot/Icm secretion system protein IcmQ. Members of this protein family are the IcmQ component of Dot/Icm secretion systems, as found in obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the literature now seems to favor calling this the Dot/Icm system. This protein was shown to be essential for translocation (). 179 matched cddid_all.tbl CDD TIGR02528 TIGR02528 131580 EutP ethanolamine utilization protein, EutP. This protein is found within operons which code for polyhedral organelles containing the enzyme ethanolamine ammonia lyase. The function of this gene is unknown, although the presence of an N-terminal GxxGxGK motif implies a GTP-binding site. [Energy metabolism, Amino acids and amines] 142 matched cddid_all.tbl CDD TIGR02529 TIGR02529 274180 EutJ ethanolamine utilization protein EutJ family protein. 239 matched cddid_all.tbl CDD TIGR02530 TIGR02530 274181 flg_new flagellar operon protein. Members of this family are found in a subset of bacterial flagellar operons, generally between genes designated flgD and flgE, in species as diverse as Bacillus halodurans and various other Firmicutes, Geobacter sulfurreducens, and Bdellovibrio bacteriovorus. The specific molecular function is unknown. [Cellular processes, Chemotaxis and motility] 96 matched cddid_all.tbl CDD TIGR02531 TIGR02531 188231 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence. [Unknown function, General] 87 matched cddid_all.tbl CDD TIGR02532 TIGR02532 274182 IV_pilin_GFxxxE prepilin-type N-terminal cleavage/methylation domain. This model describes many but not all examples of the N-terminal region of bacterial proteins that resemble type IV pilins at their N-terminus, with a cleavage site G^FxxxE followed by a hydrophobic stretch. The new N-terminal residue, usually Phe, is methylated. Separate domains of the prepilin peptidase appear responsible for cleavage and methylation. Proteins with this N-terminal region include type IV pilins and other components of pilus biogenesis, competence proteins, and type II secretion proteins. Typically several proteins in a single operon have this N-terminal domain. The N-terminal cleavage and methylation site is described by PROSITE motif PS00409 as [KRHEQSTAG]-G-[FYLIVM]-[ST]-[LT]-[LIVP]-E-[LIVMFWSTAG](14). [Cell envelope, Surface structures, Protein fate, Protein and peptide secretion and trafficking] 24 matched cddid_all.tbl CDD TIGR02533 TIGR02533 131585 type_II_gspE type II secretion system protein E. This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 486 matched cddid_all.tbl CDD TIGR02534 TIGR02534 162905 mucon_cyclo muconate and chloromuconate cycloisomerases. This model encompasses muconate cycloisomerase (EC 5.5.1.1) and chloromuconate cycloisomerase (EC 5.5.1.7), enzymes that often overlap in specificity. It excludes more distantly related proteins such as mandelate racemase (5.1.2.2). 368 matched cddid_all.tbl CDD TIGR02535 TIGR02535 274183 hyp_Hser_kinase proposed homoserine kinase. The genes in this family are largely adjacent to genes involved in the biosynthesis of threonine (aspartate kinase, homoserine dehydrogenase and threonine synthase) in genomes which are lacking any other known homoserine kinase, and in which the presence of a homoserine kinase would indicate a complete pathway for the biosynthesis of threonine. These genes are a member of the (now subfamily, formerly equivalog) TIGR00306 model describing the archaeal form of 2,3-bisphosphoglycerate-independent phosphoglycerate mutase. All of these are members of a superfamily (pfam01676) of metalloenzyme also including phosphopentomutase alkaline phosphatases and sulfatases. The proposal that this family encodes a kinase is based on analogy to phosphomutases which are intramolecular phosphotransferases. A mutase active site could evolve to bring together homoserine and a phosphate donor such as phosphoenolpyruvate resulting in a kinase activity. 396 matched cddid_all.tbl CDD TIGR02536 TIGR02536 274184 eut_hyp ethanolamine utilization protein. This family of proteins is found in operons for the polyhedral organelle-based degradation of ethanolamine. This family is not found in proteobacterial species which otherwise have the same suite of genes in the eut operon. Proteobacteria have two genes that are not found in non-proteobacteria which may complement this genes function, a phosphotransacetylase (pfam01515) and the EutJ protein (TIGR02529) of unknown function. 207 matched cddid_all.tbl CDD TIGR02537 TIGR02537 274185 arch_flag_Nterm archaeal flagellin N-terminal-like domain. This model describes a hydrophobic N-terminal sequence of archaeal flagellins and other archaeal proteins. The sequence is directly analogous to bacterial sequences recognized by TIGR02532, which has cleavage motif resembling G^FxxxE followed by strongly hydrophobic sequence. Such sequences are the recognized for cleavage and methylation, and include pilins and other pilus components and competence and type II secretion secretion proteins. In the present family, the E is not conversed and sequence differs enough that there is no overlap between this family and TIGR02532. 24 matched cddid_all.tbl CDD TIGR02538 TIGR02538 274186 type_IV_pilB type IV-A pilus assembly ATPase PilB. This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems. [Cell envelope, Surface structures, Protein fate, Protein and peptide secretion and trafficking] 564 matched cddid_all.tbl CDD TIGR02539 TIGR02539 274187 SepCysS O-phospho-L-seryl-tRNA:Cys-tRNA synthase. Aminoacylation of tRNA(Cys) with Cys, and cysteine biosynthesis in the process, happens in Methanocaldococcus jannaschii and several other archaea by misacylation of tRNA(Cys) with O-phosphoserine (Sep), followed by modification of the phosphoserine to cysteine. In some species, direct tRNA-cys aminoacylation also occurs but this pathway is required for Cys biosynthesis. Members of this protein catalyze the second step in this two step pathway, using pyridoxal phosphate and a sulfur donor to synthesize Cys from Sep while attached to the tRNA. 369 matched cddid_all.tbl CDD TIGR02540 TIGR02540 131592 gpx7 putative glutathione peroxidase Gpx7. This model represents one of several families of known and probable glutathione peroxidases. This family is restricted to animals and designated GPX7. 153 matched cddid_all.tbl CDD TIGR02541 TIGR02541 274188 flagell_FlgJ flagellar rod assembly protein/muramidase FlgJ. The N-terminal region of this protein acts directly in flagellar rod assembly. The C-terminal region is a flagellum-specific muramidase (peptidoglycan hydrolase) required for formation of the outer membrane L ring. 294 matched cddid_all.tbl CDD TIGR02542 TIGR02542 211749 T_forsyth_147 TANFOR domain. The longest predicted protein in Tannerella forsythia (Bacteroides forsythus) ATCC 43037 is over 3000 residues long and lacks homology to other known proteins. Immediately after the signal sequence are four tandem repeats, approximately 147 residues long. This model describes that repeat, plus homologous single copy N-terminal domains in other large bacterial proteins. We designate this region the TANFOR domain. Many proteins with this domain also have fibronectin type III domains. 145 matched cddid_all.tbl CDD TIGR02543 TIGR02543 274189 List_Bact_rpt Listeria/Bacterioides repeat. This model describes a conserved core region, about 43 residues in length, of at least two families of tandem repeats. These include 78-residue repeats from 2 to 15 in number, in some proteins of Bacteroides forsythus ATCC 43037, and 70-residue repeats in families of internalins of Listeria species. Single copies are found in proteins of Fibrobacter succinogenes, Geobacter sulfurreducens, and a few bacteria. [Unknown function, General] 43 matched cddid_all.tbl CDD TIGR02544 TIGR02544 274190 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family. All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related proteins outside this family are examples of the flagellar M-ring protein FliF. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 193 matched cddid_all.tbl CDD TIGR02546 TIGR02546 274191 III_secr_ATP type III secretion apparatus H+-transporting two-sector ATPase. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 422 matched cddid_all.tbl CDD TIGR02547 TIGR02547 274192 casA_cse1 CRISPR type I-E/ECOLI-associated protein CasA/Cse1. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model family, represented by CT1972 from Chlorobium tepidum, is found in Ecoli subtype CRISPR/Cas regions of many bacteria, most of which are mesophiles, and not in Archaea. It is designated Cse1. 502 matched cddid_all.tbl CDD TIGR02548 TIGR02548 274193 casB_cse2 CRISPR type I-E/ECOLI-associated protein CasB/Cse2. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This model family is found in Ecoli subtype CRISPR/Cas regions of many bacteria, most of which are mesophiles, and not in Archaea. It was designated Cse2 originally, and renamed CasB based on its characterization in the CASCADE complex. 160 matched cddid_all.tbl CDD TIGR02549 TIGR02549 274194 CRISPR_DxTHG CRISPR-associated DxTHG motif protein. This model describes a short region highly conserved between two otherwise substantially different CRISPR-associated (cas) proteins, TIGR02221 and TIGR01987. This region includes the motif [VIL]-D-x-[ST]-H-[GS]. 21 matched cddid_all.tbl CDD TIGR02550 TIGR02550 274195 flagell_flgL flagellar hook-associated protein 3. This protein family consists of flagellar hook-associated proteins designated FlgL (or HAP3) encoded in bacterial flagellar operons. A N-terminal region of about 150 residues and a C-terminal region of about 85 residues are conserved. Members show considerable length heterogeneity between these two well-conserved terminal regions; the seed alignment 486 columns, 393 of which are represented in the model, while members of this family are from 287 to over 500 residues in length. This model distinguishes FlgL from the flagellin gene product FliC. [Cellular processes, Chemotaxis and motility] 306 matched cddid_all.tbl CDD TIGR02551 TIGR02551 274196 SpaO_YscQ type III secretion system apparatus protein YscQ/HrcQ. Genes in this family are found in type III secretion operons. The gene (YscQ) in Yersinia is essential for YOPs secretion, while SpaO in Shigella is involved in the Surface Presentation of Antigens apparatus found on the virulence plasmid, and HrcQ is involved in the Harpin secretory system in organisms like Pseudomonas syringae. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 298 matched cddid_all.tbl CDD TIGR02552 TIGR02552 274197 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD. Genes in this family are found in type III secretion operons. LcrH, from Yersinia is believed to have a regulatory function in the low-calcium response of the secretion system. The same protein is also known as SycD (SYC = Specific Yop Chaperone) for its chaperone role. In Pseudomonas, where the homolog is known as PcrH, the chaperone role has been demonstrated and the regulatory role appears to be absent. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array. 135 matched cddid_all.tbl CDD TIGR02553 TIGR02553 274198 SipD_IpaD_SspD type III effector protein IpaD/SipD/SspD. These proteins are found within type III secretion operons and have been shown to be secreted by that system. 313 matched cddid_all.tbl CDD TIGR02554 TIGR02554 131605 PrgH type III secretion system protein PrgH/EprH. In Samonella, this gene is part of a four-gene operon PrgHIJK and in general is found in type III secretion operons. PrgH has been shown to be required for secretion, as well as being a structural component of the needle complex. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 389 matched cddid_all.tbl CDD TIGR02555 TIGR02555 131606 OrgA_MxiK type III secretion apparatus protein OrgA/MxiK. This gene is found in type III secretion operons and has been shown to be essential for the invasion phenotype in Salmonella and a component of the secretion apparatus. The protein is known as OrgA in Salmonella due to its oxygen-dependent expression pattern in which low-oxygen levels up-regulate the gene. In Shigella the ghene is called MxiK and has been shown to be sessential for the proper assembly of the secretion needle complex. 185 matched cddid_all.tbl CDD TIGR02556 TIGR02556 274199 cas_TM1802 CRISPR-associated protein, TM1802 family. This minor cas protein is found in CRISPR/cas regions of at least five prokaryotic genomes: Methanosarcina mazei, Sulfurihydrogenibium azorense, Thermotoga maritima, Carboxydothermus hydrogenoformans, and Dictyoglomus thermophilum, the first of which is archaeal while the rest are bacterial. 555 matched cddid_all.tbl CDD TIGR02557 TIGR02557 274200 HpaP type III secretion protein HpaP. This family of genes is always found in type III secretion operons, althought its function in the processes of secretion and virulence is unclear. Hpa stands for Hrp-associated gene, where Hrp stands for hypersensitivity response and virulence. 201 matched cddid_all.tbl CDD TIGR02558 TIGR02558 131609 HrpB2 type III secretion protein HrpB2. This family of genes is found in type III secretion operons in a narrow group of species including Xanthomonas, Burkholderia and Ralstonia. 124 matched cddid_all.tbl CDD TIGR02559 TIGR02559 131610 HrpB7 type III secretion protein HrpB7. This family of genes is found in type III secretion operons in a narrow range of species including Xanthomonas, Burkholderia and Ralstonia. 158 matched cddid_all.tbl CDD TIGR02560 TIGR02560 131611 HrpB4 type III secretion protein HrpB4. This family of genes are always found in type III secretion operons in a limited number of species including Burkholderia, Xanthomonas and Ralstonia. 210 matched cddid_all.tbl CDD TIGR02561 TIGR02561 131612 HrpB1_HrpK type III secretion protein HrpB1/HrpK. This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia. 153 matched cddid_all.tbl CDD TIGR02562 TIGR02562 274201 cas3_yersinia CRISPR-associated helicase Cas3, subtype I-F/YPEST. The helicase in many CRISPR-associated (cas) gene clusters is designated Cas3, and most Cas3 proteins are described by model TIGR01587. Members of this family are considerably larger, show a number of motifs in common with TIGR01587 sequences, and replace Cas3 in some CRISPR/cas loci in a number of Proteobacteria, including Yersinia pestis, Chromobacterium violaceum, Erwinia carotovora subsp. atroseptica SCRI1043, Photorhabdus luminescens subsp. laumondii TTO1, Legionella pneumophila, etc. 1110 matched cddid_all.tbl CDD TIGR02563 TIGR02563 274202 cas_Csy4 CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family, typified by YPO2462 of Yersinia pestis, is a CRISPR-associated (Cas) family strictly associated with the Ypest subtype of CRISPR/Cas locus. This family is designated Csy4, for CRISPR/Cas Subtype Ypest protein 4. 185 matched cddid_all.tbl CDD TIGR02564 TIGR02564 274203 cas_Csy1 CRISPR type I-F/YPEST-associated protein Csy1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family, typified by YPO2465 of Yersinia pestis, is a CRISPR-associated (Cas) family strictly associated with the Ypest subtype of CRISPR/Cas locus. This family is designated Csy1, for CRISPR/Cas Subtype Ypest protein 1. 384 matched cddid_all.tbl CDD TIGR02565 TIGR02565 274204 cas_Csy2 CRISPR type I-F/YPEST-associated protein Csy2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family, typified by YPO2464 of Yersinia pestis, is a CRISPR-associated (Cas) family strictly associated with the Ypest subtype of CRISPR/Cas locus. This family is designated Csy2, for CRISPR/Cas Subtype Ypest protein 2. 296 matched cddid_all.tbl CDD TIGR02566 TIGR02566 274205 cas_Csy3 CRISPR type I-F/YPEST-associated protein Csy3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family, typified by YPO2463 of Yersinia pestis, is a CRISPR-associated (Cas) family strictly associated with the Ypest subtype of CRISPR/Cas locus. This family is designated Csy3, for CRISPR/Cas Subtype Ypest protein 3. 341 matched cddid_all.tbl CDD TIGR02567 TIGR02567 131618 YscW type III secretion system chaperone YscW. This family of proteins is found within type III secretion operons. The protein has been characterized as a chaperone for the outer membrane pore component YscC (TIGR02516). YscW is a lipoprotein which is itself localized to the outer membrane and, it is believed, facilitates the oligomerization and localization of YscC. 124 matched cddid_all.tbl CDD TIGR02568 TIGR02568 274206 LcrE type III secretion regulator YopN/LcrE/InvE/MxiC. This protein is found in type III secretion operons and, in Yersinia is localized to the cell surface and is involved in the Low-Calicium Response (LCR), possibly by sensing the calcium concentration. In Salmonella, the gene is known as InvE and is believed to perform an essential role in the secretion process and interacts with the proteins SipBCD and SicA.//Altered name to reflect regulatory role. Added GO and role IDs . Negative regulation of type III secretion in Y pestis is mediated in part by a multiprotein complex that has been proposed to act as a physical impediment to type III secretion by blocking the entrance to the secretion apparatus prior to contact with mammalian cells. This complex is composed of YopN, its heterodimeric secretion chaperone SycN-YscB, and TyeA. 3[SS 6/3/05] [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 240 matched cddid_all.tbl CDD TIGR02569 TIGR02569 131620 TIGR02569_actnb TIGR02569 family protein. This protein family is found, so far, only in Actinobacteria, including as least five species of Mycobacterium, three of Corynebacterium, and Nocardia farcinica, always in a single copy per genome. The function is unknown. [Hypothetical proteins, Conserved] 272 matched cddid_all.tbl CDD TIGR02570 TIGR02570 274207 cas7_GSU0053 CRISPR-associated protein GSU0053/csb1, Dpsyc system. Members of this family are found in association with CRISPR repeats and other CRISPR-associated (cas) genes in the genomes of Geobacter sulfurreducens PCA and Desulfotalea psychrophila LSv54 (both Desulfobacterales from the Deltaproteobacteria), Gemmata obscuriglobus (Planctomycete), and Actinomyces naeslundii MG1 (Actinobacteria). This CRISPR/Cas type is designated Dpsych. 172 matched cddid_all.tbl CDD TIGR02571 TIGR02571 131622 ComEB "ComE operon protein 2. This protein is found in the ComE operon for ""late competence"" as characterized in B. subtilis. Proteins in this family contain homology to a cytidine/deoxycytidine deaminase domain family (pfam00383), and may carry out this activity." 151 matched cddid_all.tbl CDD TIGR02572 TIGR02572 131623 LcrR type III secretion system regulator LcrR. This protein is found in type III secretion operons and has been characterized in Yersinia as a regulator of the Low-Calcium Respone (LCR). [Protein fate, Protein and peptide secretion and trafficking] 139 matched cddid_all.tbl CDD TIGR02573 TIGR02573 131624 LcrG_PcrG type III secretion protein LcrG. This protein is found in type III secretion operons, along with LcrR, H and V. Also known as PcrG in Pseudomonas, the protein is believed to make a 1:1 complex with PcrV (LcrV). Mutants of LcrG cause premature secretion of effector proteins into the medium . 90 matched cddid_all.tbl CDD TIGR02574 TIGR02574 131625 stabl_TIGR02574 putative addiction module component, TIGR02574 family. Members of this family are bacterial proteins, typically are about 75 amino acids long, always found as part of a pair (at least) of two small genes. The other in the pair always belongs to a subfamily of the larger family pfam05016 (although not necessarily scoring above the designated cutoff), which contains plasmid stabilization proteins. It is likely that this protein and its pfam05016 member partner comprise some form of addiction module, although these gene pairs usually are found on the bacterial main chromosome. [Mobile and extrachromosomal element functions, Other] 63 matched cddid_all.tbl CDD TIGR02577 TIGR02577 274208 cas_TM1794_Cmr2 CRISPR-associated protein Cas10/Cmr2, subtype III-B. This model represent a Crm2 family of the CRISPR-associated RAMP module, a set of six genes recurring found together in prokaryotic genomes. This gene cluster is found only in species with CRISPR repeats, usually near the repeats themselves. Because most of the six (but not this family) contain RAMP domains, and because its appearance in a genome appears to depend on other CRISPR-associated Cas genes, the set is designated the CRISPR RAMP module. This protein, typified by TM1794 from Thermotoga maritima, is designated Crm2, for CRISPR RAMP Module protein 2. 483 matched cddid_all.tbl CDD TIGR02578 TIGR02578 274209 cas_TM1811_Csm1 CRISPR-associated protein Cas10/Csm1, subtype III-A/MTUBE. The family is designated Csm2, for CRISPR/Cas Subtype Mtube Protein 2. A typical example is TM1811 from Thermotoga maritima. CRISPR are Clustered Regularly Interspaced Short Palindromic Repeats. This protein family belongs to a conserved gene cluster regularly found near CRISPR repeats. 648 matched cddid_all.tbl CDD TIGR02579 TIGR02579 131628 cas_csx3 CRISPR-associated protein, Csx3 family. Members of this family are found encoded in CRISPR-associated (cas) gene clusters, near CRISPR repeats, in the genomes of several different thermophiles: Archaeoglobus fulgidus (archaeal), Aquifex aeolicus (Aquificae), Dictyoglomus thermophilum (Dictyoglomi), and a thermophilic Synechococcus (Cyanobacteria). It is not yet assigned to a specific CRISPR/cas subtype (hence the x designation csx3). 83 matched cddid_all.tbl CDD TIGR02580 TIGR02580 274210 cas_RAMP_Cmr4 CRISPR type III-B/RAMP module RAMP protein Cmr4. This model represents a CRISPR-associated protein from the family that includes TM1792 of Thermotoga maritima. This family is part of the broad RAMP superfamily (pfam03787) collection of CRISPR-associated proteins. It is the fourth of a recurring set of six proteins, four of are in the RAMP superfamily, that we designate the CRISPR RAMP module. 280 matched cddid_all.tbl CDD TIGR02581 TIGR02581 274211 cas_cyan_RAMP CRISPR-associated RAMP protein, SSO1426 family. Members of this CRISPR-associated (cas) gene family are found in the RAMP-2 subtype of CRISPR/cas locus and designated TM1809 family. 217 matched cddid_all.tbl CDD TIGR02582 TIGR02582 274212 cas7_TM1809 CRISPR type III-A/MTUBE-associated RAMP protein Csm3. Members of this CRISPR-associated (cas) gene family are found in the mtube subtype of CRISPR/cas locus and designated Csm3, for CRISPR/cas Subtype Mtube, protein 3. 204 matched cddid_all.tbl CDD TIGR02583 TIGR02583 274213 DevR_archaea CRISPR-associated protein Cas7/Csa2, subtype I-A/APERN. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This model represents one such family, typified by MJ0381 of Methanococcus jannaschii. This archaeal clade is a member of the DevR family (TIGR01875) which includes the DevR protein of Myxococcus xanthus, a protein whose expression appears to regulated through a number of means, including both location and autorepression; DevR mutants are incapable of fruiting body development. This subfamily is found in a CRISPR/Cas locus we designate APERN, so the family is designated Csa2, for CRISPR/Cas Subtype Protein 2. 285 matched cddid_all.tbl CDD TIGR02584 TIGR02584 274214 cas_NE0113 CRISPR-associated protein, NE0113 family. Members of this minor CRISPR-associated (Cas) protein family are found in cas gene clusters in Vibrio vulnificus YJ016, Nitrosomonas europaea ATCC 19718, Mannheimia succiniciproducens MBEL55E, and Verrucomicrobium spinosum. 209 matched cddid_all.tbl CDD TIGR02585 TIGR02585 274215 cas_Cst2_DevR CRISPR-associated protein Cas7/Cst2/DevR, subtype I-B/TNEAP. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This clade is a member of the DevR family (TIGR01875) and includes the DevR protein of Myxococcus xanthus, a protein whose expression appears to be regulated through a number of means, including both location and autorepression; DevR mutants are incapable of fruiting body development. 310 matched cddid_all.tbl CDD TIGR02586 TIGR02586 131635 cas5_cmx5_devS CRISPR-associated protein Cas5/DevS, subtype MYXAN. This model represents DevS of Myxococcus xanthus and related proteins of Leptospira interrogans and Gemmata obscuriglobus. This protein is encoded in a cluster of CRISPR-associated (cas) genes, and in the special case of Myxococcus xanthus has taken on a role in the control of fruiting body development. CRISPRs are clustered, regularly interspaced short palidromic repeats. This protein family is related to models TIGR01868, TIGR01895, and TIGR01876. 188 matched cddid_all.tbl CDD TIGR02587 TIGR02587 131636 TIGR02587 putative integral membrane protein TIGR02587. Members of this family are found in Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Sinorhizobium meliloti, and Gloeobacter violaceus in a conserved two-gene neighborhood. This family, as defined, includes some members of COG4711 but is narrower and strictly bacterial. Members appear to span the membrane seven times. [Cell envelope, Other] 271 matched cddid_all.tbl CDD TIGR02588 TIGR02588 131637 TIGR02588 TIGR02588 family protein. The function of this protein is unknown. It is always found as part of a two-gene operon with TIGR02587, a protein that appears to span the membrane seven times. It is found in Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Sinorhizobium meliloti, and Gloeobacter violaceus, so far, all of which are bacterial. [Hypothetical proteins, Conserved] 122 matched cddid_all.tbl CDD TIGR02589 TIGR02589 274216 cas_Csd2 CRISPR-associated protein Cas7/Csd2, subtype I-C/DVULG. This model represents one of two closely related CRISPR-associated proteins that belong to the larger family of TIGR01595. Members are the Csd2 protein of the Dvulg subtype of CRISPR/cas system. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. The related model is TIGR02590, the Csh2 protein of the Hmari CRISPR subtype. 284 matched cddid_all.tbl CDD TIGR02590 TIGR02590 274217 cas_Csh2 CRISPR-associated protein Cas7/Csh2, subtype I-B/HMARI. This model represents one of two closely related CRISPR-associated proteins that belong to the larger family of TIGR01595. Members are the Csh2 protein of the Hmari subtype of CRISPR/cas system. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. The related model is TIGR02589, the Csd3 protein of the Dvulg CRISPR subtype. 286 matched cddid_all.tbl CDD TIGR02591 TIGR02591 188234 cas_Csh1 CRISPR-associated protein Cas8b/Csh1, subtype I-B/HMARI. This domain is found in the C-terminal 2/3 of a family of CRISPR associated proteins of the Hmari subtype. Except for the two sequences from halophilic archaea this domain contains a pair of CXXC motifs. 393 matched cddid_all.tbl CDD TIGR02592 TIGR02592 131641 cas_Cas5h CRISPR-associated protein Cas5, subtype I-B/HMARI. This is a CRISPR-associated protein unique to the hmari subtype of cas genes and CRISPR repeat, which is the only subtype present in Haloarcula marismortui ATCC 43049. The hmari type, though uncommon, is also found in the Aquificae, Thermotogae, Firmicutes, and Dictyoglomi. 241 matched cddid_all.tbl CDD TIGR02593 TIGR02593 274218 CRISPR_cas5 CRISPR-associated protein Cas5, N-terminal domain. This model represents a shared N-terminal domain, about 43 amino acids in length, common to a number of related protein families each of which is associated with a distinct subtype of CRISPR/cas system, where CRISPR is an acronym for Clustered Regularly Interspaced Short Palindromic Repeat and Cas is an abbreviation for CRISPR-associated. Members of this family are widely distributed enough that we designated the family Cas5. Homology appears remote, or absent, between the more C-terminal regions different subfamilies of these proteins, which typically are 210 to 265 amino acids in total length. Cas5 proteins of six different CRISPR/cas subtypes so far defined are described by respective full-length models TIGR01868, TIGR01876, TIGR01895, TIGR01874, TIGR02586, and TIGR02592. The best characterized protein in this family is DevS or Myxococcus xanthus, a Cas protein that appears to participate in a species-specific developmental pathway. 42 matched cddid_all.tbl CDD TIGR02594 TIGR02594 131643 TIGR02594 TIGR02594 family protein. Members of this protein family known so far are restricted to the bacteria, and for the most to the proteobacteria. The function is unknown. 129 matched cddid_all.tbl CDD TIGR02595 TIGR02595 131644 PEP_exosort PEP-CTERM protein-sorting domain. This model describes a 25-residue domain that includes a near-invariant Pro-Glu-Pro (PEP) motif, a thirteen residue strongly hydrophobic sequence likely to span the membrane, and a five-residue strongly basic motif that often contains four Arg residues. In nearly every case, this motif is found within nine residues, and usually within five residues, of the extreme C-terminus of the protein. Proteins with this motif typically have signal sequences at the N-terminus. This region appears many times per genome or not at all, and co-occurs in genomes with a proposed protein-sorting integral membrane protein we designate exosortase (see TIGR02602). PEP-CTERM proteins frequently are poorly conserved, Ser/Thr-rich proteins and may become extensively modified proteinaceous constituents of extracellular material in bacterial biofilms. [Cell envelope, Surface structures] 24 matched cddid_all.tbl CDD TIGR02596 TIGR02596 274219 TIGR02596 Verru_Chthon cassette protein D. This model describes a nearly twenty member protein family in Verrucomicrobium spinosum and a somewhat smaller paralogous family in Chthoniobacter flavus. All members share a type IV pilin-like N-terminal leader sequence (TIGR02532). These proteins occur in the four-gene Verru_Chthon cassette, in which two other genes likewise encode a cleavage/methylation domain. Most of these cassettes occur next to an unusually large PEP-CTERM protein with an autotransporter domain. [Cell envelope, Surface structures] 195 matched cddid_all.tbl CDD TIGR02597 TIGR02597 274220 TIGR02597 TIGR02597 family protein. This model describes a paralogous family with at least ten members in Verrucomicrobium spinosum. Two additional predicted proteins match more weakly and score between the trusted and noise cutoffs, while a third contains a point mutation. Eleven of the thirteen genes are found in a single tandem array. 361 matched cddid_all.tbl CDD TIGR02598 TIGR02598 131647 TIGR02598 Verru_Chthon cassette protein B. This family consists sets of paralogous family of proteins in the Verrucomicrobium spinosum and Chthoniobacter flavus. All members contain the prepilin-type N-terminal cleavage/methylation domain (TIGR02532) at the N-terminus. The mature protein would be about 150 amino acids long. These proteins occur in the four-gene Verru_Chthon cassette, in which two other genes likewise encode a cleavage/methylation domain. Most of these cassettes occur next to an unusually large PEP-CTERM protein with an autotransporter domain. [Cell envelope, Surface structures] 151 matched cddid_all.tbl CDD TIGR02599 TIGR02599 274221 TIGR02599 Verru_Chthon cassette protein C. This family consists sets of paralogous family of proteins in the Verrucomicrobium spinosum and Chthoniobacter flavus. All members contain the prepilin-type N-terminal cleavage/methylation domain (TIGR02532) at the N-terminus. The mature protein would be about 350 amino acids long. These proteins occur in the four-gene Verru_Chthon cassette, in which two other genes likewise encode a cleavage/methylation domain. Most of these cassettes occur next to an unusually large PEP-CTERM protein with an autotransporter domain. [Cell envelope, Surface structures] 339 matched cddid_all.tbl CDD TIGR02600 TIGR02600 274222 Verru_Chthon_A Verru_Chthon cassette protein A. In Verrucomicrobium spinosum and Chthoniobacter flavus, a four-gene operon that includes proteins with an N-terminal signal sequence for cleavage and methylation recurs many times. Each operon is likely to encode a membrane complex, the function of which is unknown. This model represents a long protein from this putative membrame complex, with members averaging about 1300 amino acids. The N-terminal region includes an apparent signal sequence. The function is unknown. Most cassettes are adjacent to an unusually large protein with both an outer membrane autotransporter region and PEP-CTERM putative protein-sorting motif. [Cell envelope, Surface structures] 1265 matched cddid_all.tbl CDD TIGR02601 TIGR02601 274223 autotrns_rpt autotransporter-associated beta strand repeat. This model represent a core 32-residue region of a class of bacterial protein repeat found in one to 30 copies per protein. Most proteins with a copy of this repeat have domains associated with membrane autotransporters (pfam03797, TIGR01414). The repeats occur with a periodicity of 60 to 100 residues. A pattern of sequence conservation is that every second residue is well-conserved across most of the domain. pfam05594 is based on a longer, much more poorly conserved multiple sequence alignment and hits some of the same proteins as this model with some overlap between the hit regions of the two models. It describes these repeats as likely to have a beta-helical structure. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 32 matched cddid_all.tbl CDD TIGR02602 TIGR02602 131651 8TM_EpsH exosortase. This family is designated exosortase, and it is the predicted protein-sorting transpeptidase for the PEP-CTERM protein-sorting signal of many biofilm-producing Gram-negative bacteria. This system is analogous to the sortase/LPXTG system found mostly in Gram-positive bacteria. Members of this family are integral membrane proteins with eight predicted transmembrane helices in common, and with a triad of invariant residues that matches the catalytic triad of sortases. Some members of this family have long trailing sequences past the region described by this model, which in other species is a separate protein EpsI. This model does not include the region of the first predicted transmembrane region. The only partially characterized member is EpsH of Methylobacillus sp. 12S, part of a locus associated with biosynthesis of the exopolysaccharide methanolan but itself not involved in polysaccharide biosynthesis. [Protein fate, Protein and peptide secretion and trafficking] 241 matched cddid_all.tbl CDD TIGR02603 TIGR02603 274224 CxxCH_TIGR02603 putative heme-binding domain, Pirellula/Verrucomicrobium type. This model represents a domain limited to very few species but expanded into large paralogous families in some species that conain it. We find it in over 20 copies each in Pirellula sp. strain 1 (phylum Planctomycetes) and Verrucomicrobium spinosum DSM 4136 (phylum Verrucomicrobia), and no matches above trusted cutoff an any other species so far. This domain, about 140 amino acids long, contains an absolutely conserved motif CxxCH, the cytochrome c family heme-binding site signature (PS00190). 133 matched cddid_all.tbl CDD TIGR02604 TIGR02604 274225 Piru_Ver_Nterm putative membrane-bound dehydrogenase domain. All proteins that score above the trusted cutoff score of 45 to this model are large proteins of either Pirellula sp. 1 or Verrucomicrobium spinosum. These proteins all contain, in addition to this domain, several hundred residues of highly variable sequence, and then a well-conserved C-terminal domain (TIGR02603) that features a putative cytochrome c-type heme binding motif CXXCH. The membrane-bound L-sorbosone dehydrogenase from Acetobacter liquefaciens (Gluconacetobacter liquefaciens) (SP|Q44091) is homologous to this domain but lacks additional sequence regions shared by members of this family and belongs to a different clade of the larger family of homologs. It and its closely related homologs are excluded from the this model by scoring between the trusted (45) and noise (18) cutoffs. 367 matched cddid_all.tbl CDD TIGR02605 TIGR02605 274226 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (SP:Q50229, ). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors. [Regulatory functions, DNA interactions] 52 matched cddid_all.tbl CDD TIGR02606 TIGR02606 274227 antidote_CC2985 putative addiction module antidote protein, CC2985 family. This bacterial protein family has a very similar seed alignment to that of pfam03693 but is a more stringent model with higher cutoff scores. Proteins that score above the trusted cutoff to this model almost invariably are found adjacent to a ParE family protein (pfam05016), where ParE is the killing partner of an addiction module for plasmid stabilization. Members of this family, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear chromosomal. A genome may contain several identical copies, such as the four in Magnetococcus sp. MC-1. This family is named for one member, CC2985 of Caulobacter crescentus CB15. [Cellular processes, Other, Mobile and extrachromosomal element functions, Plasmid functions] 69 matched cddid_all.tbl CDD TIGR02607 TIGR02607 274228 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other] 78 matched cddid_all.tbl CDD TIGR02608 TIGR02608 274229 delta_60_rpt delta-60 repeat domain. This domain occurs in tandem repeats, as many as 13, in proteins from Bdellovibrio bacteriovorus, Azotobacter vinelandii, Geobacter sulfurreducens, Pirellula sp. 1, Myxococcus xanthus, and others, many of which are Deltaproteobacteria. The periodicity of the repeat ranges from about 57 to 61 amino acids, and a core region of about 54 is represented by this model and seed alignment. 54 matched cddid_all.tbl CDD TIGR02609 TIGR02609 274230 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids. [Mobile and extrachromosomal element functions, Other] 74 matched cddid_all.tbl CDD TIGR02610 TIGR02610 131659 PHA_gran_rgn putative polyhydroxyalkanoic acid system protein. All members of this family are encoded by genes polyhydroxyalkanoic acid (PHA) biosynthesis and utilization genes, including proteins at found at the surface of PHA granules. Examples so far are found in the Pseudomonales, Xanthomonadales, and Vibrionales, all of which belong to the Gammaproteobacteria. 91 matched cddid_all.tbl CDD TIGR02611 TIGR02611 131660 TIGR02611 TIGR02611 family protein. Members of this family are Actinobacterial putative proteins of about 150 amino acids in length with three apparent transmembrane helix and an unusual motif with consensus sequence PGPGW. [Hypothetical proteins, Conserved] 121 matched cddid_all.tbl CDD TIGR02612 TIGR02612 274231 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381). [Unknown function, General] 150 matched cddid_all.tbl CDD TIGR02613 TIGR02613 131662 mob_myst_B mobile mystery protein B. Members of this protein family, which we designate mobile mystery protein B, are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein A (TIGR02612), a member of the family of helix-turn-helix DNA binding proteins (pfam01381). This protein is encoded by the downstream member of the gene pair and belongs to the Fic protein family (pfam02661), where Fic (filamentation induced by cAMP) is a regulator of cell division. The characteristics of having a two-gene operon in a varied context and often on plasmids, with one member affecting cell division and the other able to bind DNA, suggests similarity to addiction modules. 186 matched cddid_all.tbl CDD TIGR02614 TIGR02614 274232 ftsW cell division protein FtsW. This family consists of FtsW, an integral membrane protein with ten transmembrane segments. In general, it is one of two paralogs involved in peptidoglycan biosynthesis, the other being RodA, and is essential for cell division. All members of the seed alignment for this model are encoded in operons for the biosynthesis of UDP-N-acetylmuramoyl-pentapeptide, a precursor of murein (peptidoglycan). The FtsW designation is not used in endospore-forming bacterial (e.g. Bacillus subtilis), where the member of this family is designated SpoVE and three or more RodA/FtsW/SpoVE family paralogs are present. SpoVE acts in spore cortex formation and is dispensible for growth. Biological rolls for FtsW in cell division include recruitment of penicillin-binding protein 3 to the division site. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan, Cellular processes, Cell division] 356 matched cddid_all.tbl CDD TIGR02615 TIGR02615 131664 spoVE stage V sporulation protein E. This model represents an exception within the members of the FtsW model TIGR02614. This exception occurs only in endospore-forming genera such as Bacillus, Geobacillus, and Oceanobacillus. Like FtsW, members are found in a peptidoglycan operon context, but in these genera they part of a larger set of paralogs (not just the pair FtsW and RodA) and are required specifically for sporulation, not for viability. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan, Cellular processes, Sporulation and germination] 354 matched cddid_all.tbl CDD TIGR02616 TIGR02616 274233 tnaC_leader tryptophanase leader peptide. Members of this family are the apparent leader peptides of tryptophanase operons in Esherichia coli, Vibrio cholerae, Photobacterium profundum, Haemophilus influenzae type b, and related species. All members of the seed alignment are examples ORFs upstream of tryptophanase, with a start codon, a conserved single Trp residue, and several other conserved residues. It is suggested (Konan KV and Yanofsky C) that the nascent peptide interacts with the ribosome once (if) the ribosome reaches the stop codon. Note that this model describes a much broader set (and shorter protein region) than pfam08053. [Energy metabolism, Amino acids and amines, Transcription, Other] 22 matched cddid_all.tbl CDD TIGR02617 TIGR02617 131666 tnaA_trp_ase tryptophanase, leader peptide-associated. Members of this family belong to the beta-eliminating lyase family (pfam01212) and act as tryptophanase (L-tryptophan indole-lyase). The tryptophanases of this family, as a rule, are found with a tryptophanase leader peptide (TnaC) encoded upstream. Both tryptophanases (4.1.99.1) and tyrosine phenol-lyases (EC 4.1.99.2) are found between trusted and noise cutoffs, but this model captures nearly all tryptophanases for which the leader peptide gene tnaC can be found upstream. [Energy metabolism, Amino acids and amines] 467 matched cddid_all.tbl CDD TIGR02618 TIGR02618 131667 tyr_phenol_ly tyrosine phenol-lyase. This model describes a group of tyrosine phenol-lyase (4.1.99.2) (beta-tyrosinase), a pyridoxal-phosphate enzyme closely related to tryptophanase (4.1.99.1) (see model TIGR02617). Both belong to the beta-eliminating lyase family (pfam01212) [Energy metabolism, Amino acids and amines] 450 matched cddid_all.tbl CDD TIGR02619 TIGR02619 274234 TIGR02619 putative CRISPR-associated protein, APE2256 family. This model represents a conserved domain of about 150 amino acids found in at least five archaeal species and three bacterial species, exclusively in species with CRISPR (Clustered Regularly Interspaced Short Palidromic Repeats). In six of eight species, the member of this family is in the vicinity of a CRISPR/Cas locus. 149 matched cddid_all.tbl CDD TIGR02620 TIGR02620 200203 cas_VVA1548 putative CRISPR-associated protein, VVA1548 family. This model represents a conserved domain of about 95 amino acids exclusively in species with CRISPR (Clustered Regularly Interspaced Short Palidromic Repeats). In all bacterial species with members so far (Vibrio vulnificus YJ016, Mannheimia succiniciproducens MBEL55E, and Nitrosomonas europaea ATCC 19718) and but not in the archaeon Methanothermobacter thermautotrophicus str. Delta H, the gene for this protein is in the midst of a cluster of Cas protein gene near CRISPR repeats. 93 matched cddid_all.tbl CDD TIGR02621 TIGR02621 274235 cas3_GSU0051 CRISPR-associated helicase Cas3, subtype Dpsyc. This model describes a CRISPR-associated putative DEAH-box helicase, or Cas3, of a subtype found in Actinomyces naeslundii MG1, Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, and Desulfotalea psychrophila. This protein includes both DEAH and HD motifs. 862 matched cddid_all.tbl CDD TIGR02622 TIGR02622 274236 CDP_4_6_dhtase CDP-glucose 4,6-dehydratase. Members of this protein family are CDP-glucose 4,6-dehydratase from a variety of Gram-negative and Gram-positive bacteria. Members typically are encoded next to a gene that encodes a glucose-1-phosphate cytidylyltransferase, which produces the substrate, CDP-D-glucose, used by this enzyme to produce CDP-4-keto-6-deoxyglucose. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 349 matched cddid_all.tbl CDD TIGR02623 TIGR02623 131672 G1P_cyt_trans glucose-1-phosphate cytidylyltransferase. Members of this family are the enzyme glucose-1-phosphate cytidylyltransferase, also called CDP-glucose pyrophosphorylase, the product of the rfbF gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 254 matched cddid_all.tbl CDD TIGR02624 TIGR02624 131673 rhamnu_1P_ald rhamnulose-1-phosphate aldolase. Members of this family are the enzyme RhaD, rhamnulose-1-phosphate aldolase. 270 matched cddid_all.tbl CDD TIGR02625 TIGR02625 131674 YiiL_rotase L-rhamnose mutarotase. Members of this protein family are rhamnose mutarotase from Escherichia coli, previously designated YiiL as an uncharacterized protein, and close homologs also associated with rhamnose dissimilation operons in other bacterial genomes. Mutarotase is a term for an epimerase that changes optical activity. This enzyme was shown experimentally to interconvert alpha and beta stereoisomers of the pyranose form of L-rhamnose. The crystal structure of this small (104 amino acid) protein shows a locally asymmetric dimer with active site residues of His, Tyr, and Trp. [Energy metabolism, Sugars] 102 matched cddid_all.tbl CDD TIGR02627 TIGR02627 274237 rhamnulo_kin rhamnulokinase. This model describes rhamnulokinase, an enzyme that catalyzes the second step in rhamnose catabolism. 454 matched cddid_all.tbl CDD TIGR02628 TIGR02628 131676 fuculo_kin_coli L-fuculokinase. Members of this family are L-fuculokinase, from the clade that includes the L-fuculokinase of Escherichia coli. This enzyme catalyzes the second step in fucose catabolism. This family belongs to FGGY family of carbohydrate kinases (pfam02782, pfam00370). It is encoded by the kinase (K) gene of the fucose (fuc) operon. [Energy metabolism, Sugars] 465 matched cddid_all.tbl CDD TIGR02629 TIGR02629 131677 L_rham_iso_rhiz L-rhamnose catabolism isomerase, Pseudomonas stutzeri subtype. Members of this family are isomerases in the pathway of L-rhamnose catabolism as found in Pseudomonas stutzeri and in a number of the Rhizobiales. This family differs from the L-rhamnose isomerases of Escherichia coli (see TIGR01748). This enzyme catalyzes the isomerization step in rhamnose catabolism. Genetic evidence in Rhizobium leguminosarum bv. trifolii suggests phosphorylation occurs first, then isomerization of the the phosphorylated sugar, but characterization of the recombinant enzyme from Pseudomonas 412 matched cddid_all.tbl CDD TIGR02630 TIGR02630 274238 xylose_isom_A xylose isomerase. Members of this family are the enzyme xylose isomerase (5.3.1.5), which interconverts D-xylose and D-xylulose. [Energy metabolism, Sugars] 434 matched cddid_all.tbl CDD TIGR02631 TIGR02631 131679 xylA_Arthro xylose isomerase, Arthrobacter type. This model describes a D-xylose isomerase that is also active as a D-glucose isomerase. It is tetrameric and dependent on a divalent cation Mg2+, Co2+ or Mn2+ as characterized in Arthrobacter. Members of this family differ substantially from the D-xylose isomerases of family TIGR02630. 382 matched cddid_all.tbl CDD TIGR02632 TIGR02632 131680 RhaD_aldol-ADH rhamnulose-1-phosphate aldolase/alcohol dehydrogenase. 676 matched cddid_all.tbl CDD TIGR02633 TIGR02633 131681 xylG D-xylose ABC transporter, ATP-binding protein. Several bacterial species have enzymes xylose isomerase and xylulokinase enzymes for xylose utilization. Members of this protein family are the ATP-binding cassette (ABC) subunit of the known or predicted high-affinity xylose ABC transporter for xylose import. These genes, which closely resemble other sugar transport ABC transporter genes, typically are encoded near xylose utilization enzymes and regulatory proteins. Note that this form of the transporter contains two copies of the ABC transporter domain (pfam00005). [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 500 matched cddid_all.tbl CDD TIGR02634 TIGR02634 188237 xylF D-xylose ABC transporter, substrate-binding protein. Members of this family are periplasmic (when in Gram-negative bacteria) binding proteins for D-xylose import by a high-affinity ATP-binding cassette (ABC) transporter. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 302 matched cddid_all.tbl CDD TIGR02635 TIGR02635 274239 RhaI_grampos L-rhamnose isomerase, Streptomyces subtype. This clade of sequences is closely related to the L-rhamnose isomerases found in Pseudomonas stutzeri and in a number of the Rhizobiales (TIGR02629). The genes of the family represented here are found in similar genomic contexts which contain genes apparently involved in rhamnose catabolism such as rhamnulose-1-phosphate aldolase (TIGR02632), sugar kinases, and sugar transporters. [Energy metabolism, Sugars] 378 matched cddid_all.tbl CDD TIGR02636 TIGR02636 274240 galM_Leloir galactose mutarotase. Members of this protein family act as galactose mutarotase (D-galactose 1-epimerase) and participate in the Leloir pathway for galactose/glucose interconversion. All members of the seed alignment for this model are found in gene clusters with other enzymes of the Leloir pathway. This enzyme family belongs to the aldose 1-epimerase family, described by pfam01263. However, the enzyme described as aldose 1-epimerase itself (EC 5.1.3.3) is called broadly specific for D-glucose, L-arabinose, D-xylose, D-galactose, maltose and lactose. The restricted genome context for genes in this family suggests members should act primarily on D-galactose. 336 matched cddid_all.tbl CDD TIGR02637 TIGR02637 131685 RhaS rhamnose ABC transporter, rhamnose-binding protein. This sugar-binding component of ABC transporter complexes is found in rhamnose catabolism operon contexts. Mutation of this gene in Rhizobium leguminosarum abolishes rhamnose transport and prevents growth on rhamnose as a carbon source. 302 matched cddid_all.tbl CDD TIGR02638 TIGR02638 131686 lactal_redase lactaldehyde reductase. This clade of genes encoding iron-containing alcohol dehydrogenase (pfam00465) proteins is generally found in apparent operons for the catabolism of rhamnose or fucose. Catabolism of both of these monosaccharides results in lactaldehyde which is reduced by this enzyme to 1,2 propanediol. This protein is alternatively known by the name 1,2 propanediol oxidoreductase. This enzyme is active under anaerobic conditions in E. coli while being inactivated by reactive oxygen species under aerobic conditions. Under aerobic conditions the lactaldehyde product of rhamnose and fucose catabolism is believed to be oxidized to lactate by a separate enzyme, lactaldehyde dehydrogenase. [Energy metabolism, Sugars] 379 matched cddid_all.tbl CDD TIGR02639 TIGR02639 274241 ClpA ATP-dependent Clp protease ATP-binding subunit clpA. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 730 matched cddid_all.tbl CDD TIGR02640 TIGR02640 131688 gas_vesic_GvpN gas vesicle protein GvpN. Members of this family are the GvpN protein associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy. This family belongs to a larger family of ATPases (pfam07728). [Cellular processes, Other] 262 matched cddid_all.tbl CDD TIGR02641 TIGR02641 274242 gvpC_cyan_rpt gas vesicle protein GvpC repeat. This model describes a 33-amino acid repeated domain in bacterial versions of the gas vesicle protein GvpC, a structural protein less abundant than GvpA. [Cellular processes, Other] 33 matched cddid_all.tbl CDD TIGR02642 TIGR02642 274243 phage_xxxx uncharacterized phage protein. This uncharacterized protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus YJ016, Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to phage lambda antitermination protein Q. [Mobile and extrachromosomal element functions, Prophage functions] 186 matched cddid_all.tbl CDD TIGR02643 TIGR02643 131691 T_phosphoryl thymidine phosphorylase. Thymidine phosphorylase (alternate name: pyrimidine phosphorylase), EC 2.4.2.4, is the designation for the enzyme of E. coli and other Proteobacteria involved in (deoxy)nucleotide degradation. It often occurs in an operon with a deoxyribose-phosphate aldolase, phosphopentomutase and a purine nucleoside phosphorylase. In many other lineages, the corresponding enzyme is designated pyrimidine-nucleoside phosphorylase (EC 2.4.2.2); the naming convention imposed by this model represents standard literature practice. [Purines, pyrimidines, nucleosides, and nucleotides, Other] 437 matched cddid_all.tbl CDD TIGR02644 TIGR02644 274244 Y_phosphoryl pyrimidine-nucleoside phosphorylase. In general, members of this protein family are designated pyrimidine-nucleoside phosphorylase, enzyme family EC 2.4.2.2, as in Bacillus subtilis, and more narrowly as the enzyme family EC 2.4.2.4, thymidine phosphorylase (alternate name: pyrimidine phosphorylase), as in Escherichia coli. The set of proteins encompassed by this model is designated subfamily rather than equivalog for this reason; the protein name from this model should be used when TIGR02643 does not score above trusted cutoff. [Purines, pyrimidines, nucleosides, and nucleotides, Other] 405 matched cddid_all.tbl CDD TIGR02645 TIGR02645 274245 ARCH_P_rylase putative thymidine phosphorylase. Members of this family are closely related to characterized examples of thymidine phosphorylase (EC 2.4.2.4) and pyrimidine nucleoside phosphorylase (RC 2.4.2.2). Most examples are found in the archaea, but other examples in Legionella pneumophila str. Paris and Rhodopseudomonas palustris CGA009. 493 matched cddid_all.tbl CDD TIGR02646 TIGR02646 131694 TIGR02646 TIGR02646 family protein. Members of this uncharacterized protein family are found exclusively in bacteria. Neighboring genes in various genomes are also uncharacterized or may annotated as similar to restriction system proteins. [Hypothetical proteins, Conserved] 144 matched cddid_all.tbl CDD TIGR02647 TIGR02647 131695 DNA TIGR02647 family protein. Members of this family are found, so far, only in the Gammaproteobacteria. The function is unknown. The location on the chromosome usually is not far from housekeeping genes rather than in what is clearly, say, a prophage region. Some members have been annotated in public databases as DNA-binding protein inhibitor Id-2-related protein, putative transcriptional regulator, or hypothetical DNA binding protein. [Hypothetical proteins, Conserved] 77 matched cddid_all.tbl CDD TIGR02648 TIGR02648 131696 rep_term_tus DNA replication terminus site-binding protein. Members of this protein family are found on the main chromosomes of a number of the Gammaproteobacteria; this model excludes related plasmid proteins, which score between trusted and noise cutoffs. This protein, DNA replication terminus site-binding protein, binds specific DNA sites near the replication terminus to arrest the DNA replication fork. [DNA metabolism, DNA replication, recombination, and repair] 300 matched cddid_all.tbl CDD TIGR02649 TIGR02649 131697 true_RNase_BN ribonuclease BN. Members of this protein family are ribonuclease BN of Escherichia coli K-12 and closely related proteins believed to be equivalent in function. Note that E. coli appears to lack RNase Z per se, and this protein of E. coli appears orthologous to (but not functionally equivalent to) RNase Z of Bacillus subtilis and various other species. Meanwhile, the yihY gene product of E. coli previously was incorrectly identified as RNase BN. [Transcription, RNA processing] 303 matched cddid_all.tbl CDD TIGR02650 TIGR02650 188239 RNase_Z_T_toga ribonuclease Z, Thermotoga type. Members of this protein family are ribonuclease Z as found in the genus Thermotoga, where the enzyme cleaves after the CCA, in contrast to the activities characterized for other enzymes also designated ribonuclease Z. In other systems, cleavage occurs 5-prime to the location of the CCA sequence, and CCA is added subsequently. A species may lack ribonuclease Z if all tRNA genes encode the CCA sequence, or if the CCA is exposed by exonuclease activity rather than endonuclease activity. Note that members of this sequence family differ considerably from the majority of RNase Z sequences. [Transcription, RNA processing] 277 matched cddid_all.tbl CDD TIGR02651 TIGR02651 274246 RNase_Z ribonuclease Z. Processing of the 3-prime end of tRNA precursors may be the result of endonuclease or exonuclease activity, and differs in different species. Member of this family are ribonuclease Z, a tRNA 3-prime endonuclease that processes tRNAs to prepare for addition of CCA. In species where all tRNA sequences already have the CCA tail, such as E. coli, the need for such an enzyme is unclear. Protein similar to the E. coli enzyme, matched by TIGRFAMs model TIGR02649, are designated ribonuclease BN. [Transcription, RNA processing] 299 matched cddid_all.tbl CDD TIGR02652 TIGR02652 131700 TIGR02652 TIGR02652 family protein. Members of this family of conserved hypothetical proteins are found, so far, only in the Cyanobacteria. Members are about 170 amino acids long and share a motif CxxCx(14)CxxH near the amino end. [Hypothetical proteins, Conserved] 163 matched cddid_all.tbl CDD TIGR02653 TIGR02653 131701 Lon_rel_chp conserved hypothetical protein. This model describes a protein family of unknown function, about 690 residues in length, in which some members show C-terminal sequence similarity to pfam05362, which is the Lon protease C-terminal proteolytic domain, from MEROPS family S16. However, the annotated catalytic sites of E. coli Lon protease are not conserved in members of this family. Members have a motif GP[RK][GS]TGKS, similar to the ATP-binding P-loop motif GxxGxGK[ST]. [Hypothetical proteins, Conserved] 675 matched cddid_all.tbl CDD TIGR02654 TIGR02654 211759 circ_KaiB circadian clock protein KaiB. Members of this protein family are the circadian clock protein KaiB of Cyanobacteria, encoded in the circadian clock gene cluster kaiABC. KaiB has homologs of unknown function in some Archaea and Proteobacteria, and has paralogs of unknown function in some Cyanobacteria. KaiB forms homodimers, homotetramers, and multimeric complexes with KaiA and/or KaiC. [Cellular processes, Other] 87 matched cddid_all.tbl CDD TIGR02655 TIGR02655 131703 circ_KaiC circadian clock protein KaiC. Members of this family are the circadian clock protein KaiC, part of the kaiABC operon that controls circadian rhythm. It may be universal in Cyanobacteria. Each member has two copies of the KaiC domain (pfam06745), which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. [Cellular processes, Other] 484 matched cddid_all.tbl CDD TIGR02656 TIGR02656 274247 cyanin_plasto plastocyanin. Members of this family are plastocyanin, a blue copper protein related to pseudoazurin, halocyanin, amicyanin, etc. This protein, located in the thylakoid luman, performs electron transport to photosystem I in Cyanobacteria and chloroplasts. [Energy metabolism, Electron transport, Energy metabolism, Photosynthesis] 99 matched cddid_all.tbl CDD TIGR02657 TIGR02657 131705 amicyanin amicyanin. Members of this family are amicyanin, a type I blue copper protein that accepts electrons from the tryptophan tryptophylquinone (TTQ) cofactor of the methylamine dehydrogenase light chain and then transfers them to the heme group of cytochrome c-551i. Amicyanin, methylamine dehydrogenase, and cytochrome c-551i are periplasmic and form a complex. This system has been studied primarily in Paracoccus denitrificans and Methylobacterium extorquens. Related type I blue copper proteins include plastocyanin, pseudoazurin, halocyanin, etc. [Energy metabolism, Electron transport] 83 matched cddid_all.tbl CDD TIGR02658 TIGR02658 131706 TTQ_MADH_Hv methylamine dehydrogenase (amicyanin) heavy chain. This family consists of the heavy chain of methylamine dehydrogenase light chain, a periplasmic enzyme. The enzyme contains a tryptophan tryptophylquinone (TTQ) prothetic group derived from two Trp residues in the light subunity. The enzyme forms a complex with the type I blue copper protein amicyanin and a cytochrome. Electron transfer procedes from TQQ to the copper and then to the heme group of the cytochrome. [Energy metabolism, Amino acids and amines] 352 matched cddid_all.tbl CDD TIGR02659 TIGR02659 131707 TTQ_MADH_Lt methylamine dehydrogenase (amicyanin) light chain. This family consists of the light chain of methylamine dehydrogenase light chain, a periplasmic enzyme. This subunit contains a tryptophan tryptophylquinone (TTQ) prothetic group derived from Trp-114 and Trp-165 of the precursor, numbered according to the sequence from Paracoccus denitrificans. The enzyme forms a complex with the type I blue copper protein amicyanin and cytochrome. Electron transfer procedes from TQQ to the copper and then to the heme group of the cytochrome. [Energy metabolism, Amino acids and amines] 186 matched cddid_all.tbl CDD TIGR02660 TIGR02660 274248 nifV_homocitr homocitrate synthase NifV. This family consists of the NifV clade of homocitrate synthases, most of which are found in operons for nitrogen fixation. Members are closely homologous to enzymes that include 2-isopropylmalate synthase, (R)-citramalate synthase, and homocitrate synthases associated with other processes. The homocitrate made by this enzyme becomes a part of the iron-molybdenum cofactor of nitrogenase. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Central intermediary metabolism, Nitrogen fixation] 365 matched cddid_all.tbl CDD TIGR02661 TIGR02661 131709 MauD methylamine dehydrogenase accessory protein MauD. This protein, MauD, appears critical to proper formation of the small subunit of methylamine dehydrogenase, which has both an unusual tryptophan tryptophylquinone cofactor and multiple disulfide bonds. MauD shares sequence similarity, including a CPxC motif, with a number of thiol:disulfide interchange proteins. In MauD mutants, the small subunit apparently does not form properly and is rapidly degraded. [Protein fate, Protein folding and stabilization, Energy metabolism, Amino acids and amines] 189 matched cddid_all.tbl CDD TIGR02662 TIGR02662 131710 dinitro_DRAG ADP-ribosyl-[dinitrogen reductase] hydrolase. Members of this family are the enzyme ADP-ribosyl-[dinitrogen reductase] hydrolase (EC 3.2.2.24), better known as Dinitrogenase Reductase Activating Glycohydrolase, DRAG. This enzyme reverses a regulatory inactivation of dinitrogen reductase caused by the action of NAD(+)--dinitrogen-reductase ADP-D-ribosyltransferase (EC 2.4.2.37) (DRAT). This enzyme is restricted to nitrogen-fixing bacteria and belongs to the larger family of ADP-ribosylglycohydrolases described by pfam03747. [Central intermediary metabolism, Nitrogen fixation] 287 matched cddid_all.tbl CDD TIGR02663 TIGR02663 131711 nifX nitrogen fixation protein NifX. Members of this family are NifX proteins encoded within operons for nitrogen fixation in a number of bacteria. NifX, NafY, and the C-terminal region of NifB all belong to the pfam02579 and are involved in MoFe cofactor biosynthesis. NifX is a nitrogenase accessory protein with a role in expression of the MoFe cofactor. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Central intermediary metabolism, Nitrogen fixation] 119 matched cddid_all.tbl CDD TIGR02664 TIGR02664 131712 nitr_red_assoc conserved hypothetical protein. Most members of this protein family are found in the Cyanobacteria, and these mostly near nitrate reductase genes and molybdopterin biosynthesis genes. We note that molybdopterin guanine dinucleotide is a cofactor for nitrate reductase. This protein is sometimes annotated as nitrate reductase-associated protein. Its function is unknown. 145 matched cddid_all.tbl CDD TIGR02665 TIGR02665 274249 molyb_mobA molybdenum cofactor guanylyltransferase, proteobacterial. In many molybdopterin-containing enzymes, including nitrate reductase and dimethylsulfoxide reductase, the cofactor is molybdopterin-guanine dinucleotide. The family described here contains MobA, molybdenum cofactor guanylyltransferase, from the Proteobacteria only. MobA can reconstitute molybdopterin-guanine dinucleotide biosynthesis without the product of the neighboring gene MobB. The probable MobA proteins of other lineages differ sufficiently that they are not included in scope of this family. [Biosynthesis of cofactors, prosthetic groups, and carriers, Molybdopterin] 186 matched cddid_all.tbl CDD TIGR02666 TIGR02666 274250 moaA molybdenum cofactor biosynthesis protein A, bacterial. The model for this family describes molybdenum cofactor biosynthesis protein A, or MoaA, as found in bacteria. It does not include the family of probable functional equivalent proteins from the archaea. MoaA works together with MoaC to synthesize precursor Z from guanine. [Biosynthesis of cofactors, prosthetic groups, and carriers, Molybdopterin] 334 matched cddid_all.tbl CDD TIGR02667 TIGR02667 131715 moaB_proteo molybdenum cofactor biosynthesis protein B, proteobacterial. This model represents the MoaB protein molybdopterin biosynthesis regions in Proteobacteria. This crystallized but incompletely characterized protein is thought to be involved in, though not required for, early steps in molybdopterin biosynthesis. It may bind a molybdopterin precursor. A distinctive conserved motif PCN near the C-terminus helps distinguish this clade from other homologs, including sets of proteins designated MogA. [Biosynthesis of cofactors, prosthetic groups, and carriers, Molybdopterin] 163 matched cddid_all.tbl CDD TIGR02668 TIGR02668 274251 moaA_archaeal probable molybdenum cofactor biosynthesis protein A, archaeal. This model describes an archaeal family related, and predicted to be functionally equivalent, to molybdenum cofactor biosynthesis protein A (MoaA) of bacteria (see TIGR02666). [Biosynthesis of cofactors, prosthetic groups, and carriers, Molybdopterin] 302 matched cddid_all.tbl CDD TIGR02669 TIGR02669 274252 SpoIID_LytB SpoIID/LytB domain. This model describes a domain found typically in two or three proteins per genome in Cyanobacteria and Firmicutes, and sporadically in other genomes. One member is SpoIID of Bacillus subtilis. Another in B. subtilis is the C-terminal half of LytB, encoded immediately upstream of an amidase, the autolysin LytC, to which its N-terminus is homologous. Gene neighborhoods are not well conserved for members of this family, as many, such as SpoIID, are monocistronic. One early modelling-based study suggests a DNA-binding role for SpoIID, but the function of this domain is unknown. [Unknown function, General] 267 matched cddid_all.tbl CDD TIGR02670 TIGR02670 274253 cas_csx8 CRISPR-associated protein Cas8a1/Csx8, subtype I. In three genomes so far, a member of this protein appears in the midst of a CRISPR-associated (cas) gene operon, immediately upstream of a member of family TIGR01875 (CRISPR-associated autoregulator, DevR family). The genomes so far are Nocardia farcinica IFM10152, Clostridium perfringens SM101, and Clostridium tetani E88. 441 matched cddid_all.tbl CDD TIGR02671 TIGR02671 131719 cas_csx9 CRISPR-associated protein Cas8a2/Csx9, subtype I-A/APERN. Members of this family, so far, are archaeal proteins found in CRISPR-associated (cas) gene regions. So far, this rare cas protein is found in only three genomes: Pyrococcus horikoshii shinkaj OT3, Pyrococcus abyssi GE5, and Thermococcus kodakarensis KOD1. In each case it is found immediately upstream of cas3 in loci that resemble the Apern type but lack Csa1 and Csa4 genes. 377 matched cddid_all.tbl CDD TIGR02672 TIGR02672 131720 cas_csm6 CRISPR type III-A/MTUBE-associated protein Csm6. Members of this family as found in CRISPR-associated (cas) gene regions in Streptococcus thermophilus CNRZ1066, Staphylococcus epidermidis RP62A, and Mycobacterium tuberculosis (strains CDC1551 and H37Rv), as part of Mtube-type CRISPR/Cas systems. CRISPR is a widespread form of direct repeat found in archaea and bacteria, with distinctive subtypes each of which has a characteristic sporadic distribution. 362 matched cddid_all.tbl CDD TIGR02673 TIGR02673 131721 FtsE cell division ATP-binding protein FtsE. This model describes FtsE, a member of the ABC transporter ATP-binding protein family. This protein, and its permease partner FtsX, localize to the division site. In a number of species, the ftsEX gene pair is located next to FtsY, the signal recognition particle-docking protein. [Cellular processes, Cell division] 214 matched cddid_all.tbl CDD TIGR02674 TIGR02674 131722 cas_cyan_RAMP_2 CRISPR-associated RAMP protein, Csx10 family. CRISPR is a widespread repeat family in prokaryotes. At least 45 different protein families occur in prokaryotes only when these repeats are present. This family, a minor CRISPR-associated protein family, seems largely restricted to the Cyanobacteria. It belongs to the RAMP superfamily (pfam03787). 393 matched cddid_all.tbl CDD TIGR02675 TIGR02675 131723 tape_meas_nterm tape measure domain. Proteins containing this domain are strictly bacterial, including bacteriophage and prophage regions of bacterial genomes. Most members are 800 to 1800 amino acids long, making them among the longest predicted proteins of their respective phage genomes, where they are encoded in tail protein regions. This roughly 80-residue domain described here usually begins between residue 100 and 250. Many members are known or predicted to act as phage tail tape measure proteins, a minor tail component that regulates tail length. 75 matched cddid_all.tbl CDD TIGR02677 TIGR02677 131724 TIGR02677 TIGR02677 family protein. Members of this protein belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). [Hypothetical proteins, Conserved] 494 matched cddid_all.tbl CDD TIGR02678 TIGR02678 274254 TIGR02678 TIGR02678 family protein. Members of this protein belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). [Hypothetical proteins, Conserved] 375 matched cddid_all.tbl CDD TIGR02679 TIGR02679 274255 TIGR02679 TIGR02679 family protein. Members of this protein belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). [Hypothetical proteins, Conserved] 385 matched cddid_all.tbl CDD TIGR02680 TIGR02680 274256 TIGR02680 TIGR02680 family protein. Members of this protein family belong to a conserved gene four-gene neighborhood found sporadically in a phylogenetically broad range of bacteria: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). Proteins in this family average over 1400 amino acids in length. [Hypothetical proteins, Conserved] 1353 matched cddid_all.tbl CDD TIGR02681 TIGR02681 131728 phage_pRha phage regulatory protein, rha family. Members of this protein family are found in temperate phage and bacterial prophage regions. Members include the product of the rha gene of the lambdoid phage phi-80, a late operon gene. The presence of this gene interferes with infection of bacterial strains that lack integration host factor (IHF), which regulates the rha gene. It is suggested that pRha is a phage regulatory protein. [Mobile and extrachromosomal element functions, Prophage functions] 108 matched cddid_all.tbl CDD TIGR02682 TIGR02682 274257 cas_csx11 CRISPR-associated protein, Csx11 family. Members of this uncommon, sporadically distributed protein family are large (>900 amino acids) and strictly associated, so far, with CRISPR-associated (Cas) gene clusters. Nearby Cas genes always include members of the RAMP superfamily and the six-gene CRISPR-associated RAMP module. Species in which it is found, so far, include three archaea (Methanosarcina mazei, M. barkeri and Methanobacterium thermoautotrophicum) and two bacteria (Thermodesulfovibrio yellowstonii DSM 11347 and Sulfurihydrogenibium azorense). 918 matched cddid_all.tbl CDD TIGR02683 TIGR02683 162974 upstrm_HI1419 putative addiction module killer protein. Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the upstream member of a gene pair, where the downstream member is a predicted DNA-binding protein from a clade within Pfam helix-turn-helix family pfam01381. These gene pairs, when found on the bacterial chromosome, often are located with prophage regions, but also in both integrated plasmid regions and near housekeeping genes. Analysis suggests that the gene pair may serve as an addiction module. 95 matched cddid_all.tbl CDD TIGR02684 TIGR02684 188241 dnstrm_HI1420 probable addiction module antidote protein. Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the downstream member of a gene pair. It is a predicted DNA-binding protein from a clade within Pfam helix-turn-helix family pfam01381. These gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module. [Mobile and extrachromosomal element functions, Other] 89 matched cddid_all.tbl CDD TIGR02685 TIGR02685 131732 pter_reduc_Leis pteridine reductase. Pteridine reductase is an enzyme used by trypanosomatids (including Trypanosoma cruzi and Leishmania major) to obtain reduced pteridines by salvage rather than biosynthetic pathways. Enzymes in T. cruzi described as pteridine reductase 1 (PTR1) and pteridine reductase 2 (PTR2) have different activity profiles. PTR1 is more active with with fully oxidized biopterin and folate than with reduced forms, while PTR2 reduces dihydrobiopterin and dihydrofolate but not oxidized pteridines. T. cruzi PTR1 and PTR2 are more similar to each other in sequence than either is to the pteridine reductase of Leishmania major, and all are included in this family. 267 matched cddid_all.tbl CDD TIGR02686 TIGR02686 274258 relax_trwC conjugative relaxase domain, TrwC/TraI family. This domain is in the N-terminal (relaxase) region of TrwC, a relaxase-helicase that acts in plasmid R388 conjugation. The relaxase domain has DNA cleavage and strand transfer activities. Plasmid transfer protein TraI is also a member of this domain family. Members of this family on bacterial chromosomes typically are found near other genes typical of conjugative plasmids and appear to mark integrated plasmids. [Mobile and extrachromosomal element functions, Plasmid functions] 283 matched cddid_all.tbl CDD TIGR02687 TIGR02687 274259 TIGR02687 TIGR02687 family protein. Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 880 amino acids in length. This protein is repeatedly found upstream of another uncharacterized protein of about 470 amino acids in length, modeled by TIGR02688. 844 matched cddid_all.tbl CDD TIGR02688 TIGR02688 131735 TIGR02688 TIGR02688 family protein. Members of this family are uncharacterized proteins sporadically distributed in bacteria and archaea, about 470 amino acids in length. Several members of this family appear in public databases with annotation as ATP-dependent protease La, despite the lack of similarity to families TIGR00763 (ATP-dependent protease La) or pfam02190 (ATP-dependent protease La (LON) domain). This protein is repeatedly found downstream of another uncharacterized protein of about 880 amino acids in length, described by model TIGR02687. [Hypothetical proteins, Conserved] 449 matched cddid_all.tbl CDD TIGR02689 TIGR02689 131736 ars_reduc_gluta arsenate reductase, glutathione/glutaredoxin type. Members of this protein family represent a novel form of arsenate reductase, using glutathione and glutaredoxin rather than thioredoxin for reducing equivalents as do some homologous arsenate reductases. An example of this type is Synechocystis sp. strain PCC 6803 slr0946, and of latter type (excluded from this model) is Staphylococcus aureus plasmid pI258 ArsC. Both are among the subset of arsenate reductases that belong the the low-molecular-weight protein-tyrosine phosphatase superfamily. [Cellular processes, Detoxification] 126 matched cddid_all.tbl CDD TIGR02690 TIGR02690 274260 resist_ArsH arsenical resistance protein ArsH. Members of this protein family occur in arsenate resistance operons that include at least two different types of arsenate reductase. ArsH is not required for arsenate resistance in some systems. This family belongs to the larger family of NADPH-dependent FMN reductases (pfam03358). The function of ArsH is not known. [Cellular processes, Detoxification] 219 matched cddid_all.tbl CDD TIGR02691 TIGR02691 131738 arsC_pI258_fam arsenate reductase (thioredoxin). This family describes the well-studied thioredoxin-dependent arsenate reductase of Staphylococcus aureaus plasmid pI258 and other mechanistically similar arsenate reductases. The mechanism involves an intramolecular disulfide bond cascade, and aligned members of this family have four absolutely conserved Cys residues. This group of arsenate reductases belongs to the low-molecular weight protein-tyrosine phosphatase family (pfam01451), as does a group of glutathione/glutaredoxin type arsenate reductases (TIGR02689). At least two other, non-homologous groups of arsenate reductases involved in arsenical resistance are also known. This enzyme reduces arsenate to arsenite, which may be more toxic but which is more easily exported. [Cellular processes, Detoxification] 129 matched cddid_all.tbl CDD TIGR02692 TIGR02692 131739 tRNA_CCA_actino tRNA adenylyltransferase. The enzyme tRNA adenylyltransferase, also called tRNA-nucleotidyltransferase and CCA-adding enzyme, can add or repair the required CCA triplet at the 3'-end of tRNA molecules. Genes encoding tRNA include the CCA tail in some but not all bacteria, and this enzyme may be required for viability. Members of this family represent a distinct clade within the larger family pfam01743 (tRNA nucleotidyltransferase/poly(A) polymerase family protein). The example from Streptomyces coelicolor was shown to act as a CCA-adding enzyme and not as a poly(A) polymerase. [Protein synthesis, tRNA and rRNA base modification] 466 matched cddid_all.tbl CDD TIGR02693 TIGR02693 274261 arsenite_ox_L arsenite oxidase, large subunit. This model represents the large subunit of an arsenite oxidase complex. The small subunit is a Rieske protein. Homologs to both large and small subunits that score in the gray zone between the set trusted and noise bit score cutoffs for the respective models are found in Aeropyrum pernix K1 and in Sulfolobus tokodaii str. 7. This enzyme acts in energy metabolim by arsenite oxidation, rather than detoxification by reduction of arsenate to arsenite prior to export. [Energy metabolism, Electron transport] 806 matched cddid_all.tbl CDD TIGR02694 TIGR02694 131741 arsenite_ox_S arsenite oxidase, small subunit. This model represents the small subunit of an arsenite oxidase complex. It is a Rieske protein and appears to rely on the Tat (twin-arginine translocation) system to cross the membrane. Although this enzyme could run in the direction of arsenate reduction to arsenite in principle, the relevant biological function is arsenite oxidation for energy metabolism, not arsenic resistance. Homologs to both large (TIGR02693) and small subunits that score in the gray zone between the set trusted and noise bit score cutoffs for the respective models are found in Aeropyrum pernix K1 and in Sulfolobus tokodaii str. 7. [Energy metabolism, Electron transport] 129 matched cddid_all.tbl CDD TIGR02695 TIGR02695 131742 azurin azurin. Azurin is a blue copper-binding protein in the plastocyanin/azurin family (see pfam00127). It serves as a redox partner to enzymes such as nitrite reductase or arsenite oxidase. The most closely related copper-binding proteins to this family are auracyanins, as in Chloroflexus aurantiacus, which have similar redox activities. [Energy metabolism, Electron transport] 125 matched cddid_all.tbl CDD TIGR02696 TIGR02696 131743 pppGpp_PNP guanosine pentaphosphate synthetase I/polynucleotide phosphorylase. Sohlberg, et al. present characterization of two proteins from Streptomyces coelicolor. The protein in this family was shown to have poly(A) polymerase activity and may be responsible for polyadenylating RNA in this species. Reference 2 showed that a nearly identical plasmid-encoded protein from Streptomyces antibioticus is a bifunctional enzyme that acts also as a guanosine pentaphosphate synthetase. 719 matched cddid_all.tbl CDD TIGR02697 TIGR02697 131744 WPE_wolbac Wolbachia palindromic element (WPE) domain. This domain conceptually resembles TIGR01045, the Rickettsial palindromic element (RPE) domain. In both cases, a protein-coding palindromic element spreads through a genome, inserting usually in protein-coding regions. The additional protein coding sequence is thought to allow function of the host protein because of location in surface-exposed regions of the protein structure. Note that this model appears to work better in fragment mode. [Mobile and extrachromosomal element functions, Other] 36 matched cddid_all.tbl CDD TIGR02698 TIGR02698 131745 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI. [Transport and binding proteins, Cations and iron carrying compounds, Regulatory functions, DNA interactions] 130 matched cddid_all.tbl CDD TIGR02699 TIGR02699 131746 archaeo_AfpA archaeoflavoprotein AfpA. The prototypical member of this archaeal protein family is AF1518 from Archaeoglobus fulgidus. This homodimer with two non-covalently bound FMN cofactors can receive electrons from ferredoxin, but not from a number of other electron donors such as NADH or rubredoxin. It can then donate electrons to various reductases. [Energy metabolism, Electron transport] 174 matched cddid_all.tbl CDD TIGR02700 TIGR02700 131747 flavo_MJ0208 archaeoflavoprotein, MJ0208 family. This model describes one of two paralogous families of archaealflavoprotein. The other, described by TIGR02699 and typified by the partially characterized AF1518 of Archaeoglobus fulgidus, is a homodimeric FMN-containing flavoprotein that accepts electrons from ferredoxin and can transfer them to various oxidoreductases. The function of this protein family is unknown. [Unknown function, General] 234 matched cddid_all.tbl CDD TIGR02701 TIGR02701 274262 shell_carb_anhy carboxysome shell carbonic anhydrase. This model describes a carboxysome shell protein that proves to be a novel class, designated epsilon, of carbonic anhydrase. It tends to be encoded near genes for RuBisCo and for other carboxysome shell proteins. [Central intermediary metabolism, One-carbon metabolism] 450 matched cddid_all.tbl CDD TIGR02702 TIGR02702 131749 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Regulatory functions, DNA interactions] 203 matched cddid_all.tbl CDD TIGR02703 TIGR02703 131750 carboxysome_A carboxysome peptide A. This model distinguishes one of two closely related paralogs encoded by nearby genes in the carboxysome operons of a number of cyanobacteria and chemoautotrophic bacteria. More distantly related proteins, also belonging to pfam03319, participate in other types of shell such as the ethanolamine degradation organelle. [Central intermediary metabolism, One-carbon metabolism] 81 matched cddid_all.tbl CDD TIGR02704 TIGR02704 131751 carboxysome_B carboxysome peptide B. This model distinguishes one of two closely related paralogs encoded by nearby genes in the carboxysome operons of a number of cyanobacteria and chemoautotrophic bacteria. More distantly related proteins, also belonging to pfam03319, participate in other types of shell such as the ethanolamine degradation organelle. [Central intermediary metabolism, One-carbon metabolism] 80 matched cddid_all.tbl CDD TIGR02705 TIGR02705 131752 nudix_YtkD nucleoside triphosphatase YtkD. The functional assignment to the proteins of this family is contentious, with papers disagreeing in both interpretation and enzyme assay results. This protein belongs to the nudix family and shares some sequence identity with E. coli MutT but appears not to be functionally interchangeable with it. [DNA metabolism, DNA replication, recombination, and repair] 156 matched cddid_all.tbl CDD TIGR02706 TIGR02706 162980 P_butyryltrans phosphate butyryltransferase. Members of this family are phosphate butyryltransferase, also called phosphotransbutyrylase. In general, this enzyme is found in butyrate-producing anaerobic bacteria, encoded next to the gene for butyrate kinase. Together, these two enzymes represent what may be the less common of two pathways for butyrate production from butyryl-CoA. The alternative is transfer of the CoA group to acetate by butyryl-CoA:acetate CoA transferase. Cutoffs for this model are set such that the homolog from Thermotoga maritima, whose activity on butyryl-CoA is only 30 % of its activity with acetyl-CoA, scores in the zone between trusted and noice cutoffs. [Energy metabolism, Fermentation] 294 matched cddid_all.tbl CDD TIGR02707 TIGR02707 162981 butyr_kinase butyrate kinase. This model represents an enzyme family in which members are designated either butryate kinase or branched-chain carboxylic acid kinase. The EC designation 2.7.2.7 describes an enzyme with relatively broad specificity; gene products whose context suggests a role in metabolism of aliphatic amino acids are likely to act as branched-chain carboxylic acid kinase. The gene typically found adjacent, ptb (phosphate butyryltransferase), likewise encodes an enzyme that may have a broad specificity that includes a role in aliphatic amino acid cabolism. [Energy metabolism, Fermentation] 351 matched cddid_all.tbl CDD TIGR02708 TIGR02708 131755 L_lactate_ox L-lactate oxidase. Members of this protein oxidize L-lactate to pyruvate, reducing molecular oxygen to hydrogen peroxide. The enzyme is known in Aerococcus viridans, Streptococcus iniae, and some strains of Streptococcus pyogenes where it appears to contribute to virulence. [Energy metabolism, Other] 367 matched cddid_all.tbl CDD TIGR02709 TIGR02709 131756 branched_ptb branched-chain phosphotransacylase. This model distinguishes branched-chain phosphotransacylases like that of Enterococcus faecalis from closely related subfamilies of phosphate butyryltransferase (EC 2.3.1.19) (TIGR02706) and phosphate acetyltransferase (EC 2.3.1.8) (TIGR00651). Members of this family and of TIGR02706 show considerable crossreactivity, and the occurrence of a member of either family near an apparent leucine dehydrogenase will suggest activity on branched chain-acyl-CoA compounds. [Energy metabolism, Amino acids and amines] 271 matched cddid_all.tbl CDD TIGR02710 TIGR02710 274263 TIGR02710 CRISPR-associated protein, TIGR02710 family. Members of this family are found, exclusively in the vicinity of CRISPR repeats and other CRISPR-associated (cas) genes, in Methanothermobacter thermautotrophicus (Archaea), Thermus thermophilus (Deinococcus-Thermus), Chloroflexus aurantiacus (Chloroflexi), and Thermomicrobium roseum (Thermomicrobia). 380 matched cddid_all.tbl CDD TIGR02711 TIGR02711 131758 symport_actP cation/acetate symporter ActP. Members of this family belong to the Sodium:solute symporter family. Both members of this family and other close homologs tend to be encoded next to a member of pfam04341, a set of uncharacterized membrane proteins. The characterized member from E. coli is encoded near and cotranscribed with the acetyl coenzyme A synthetase (acs) gene. Proximity to an acs gene was used as one criterion for determining the trusted cutoff for this model. Closely related proteins may differ in function and are excluded by the high cutoffs of this model; members of the family of phenylacetic acid transporter PhaJ can score as high as 1011 bits. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 549 matched cddid_all.tbl CDD TIGR02712 TIGR02712 274264 urea_carbox urea carboxylase. Members of this family are ATP-dependent urea carboxylase, including characterized members from Oleomonas sagaranensis (alpha class Proteobacterium) and yeasts such as Saccharomyces cerevisiae. The allophanate hydrolase domain of the yeast enzyme is not included in this model and is represented by an adjacent gene in Oleomonas sagaranensis. The fusion of urea carboxylase and allophanate hydrolase is designated urea amidolyase. The enzyme from Oleomonas sagaranensis was shown to be highly active on acetamide and formamide as well as urea. [Central intermediary metabolism, Nitrogen metabolism] 1201 matched cddid_all.tbl CDD TIGR02713 TIGR02713 274265 allophanate_hyd allophanate hydrolase. Allophanate hydrolase catalyzes the second reaction in an ATP-dependent two-step degradation of urea to ammonia and C02, following the action of the biotin-containing urea carboxylase. The yeast enzyme, a fusion of allophanate hydrolase to urea carboxylase, is designated urea amidolyase. [Central intermediary metabolism, Nitrogen metabolism] 561 matched cddid_all.tbl CDD TIGR02714 TIGR02714 274266 amido_AtzD_TrzD ring-opening amidohydrolases. Members of this family are are ring-opening amidohydrolases, including cyanuric acid amidohydrolase (EC 3.5.2.15) (AtzD and TrzD) and barbiturase. Note that barbiturase does not act as defined for EC 3.5.2.1 (barbiturate + water = malonate + urea) but rather catalyzes the ring-opening of barbituric acid to ureidomalonic acid (see Soong, et al., ). 366 matched cddid_all.tbl CDD TIGR02715 TIGR02715 274267 amido_AtzE amidohydrolase, AtzE family. Members of this protein family are aminohydrolases related to, but distinct from, glutamyl-tRNA(Gln) amidotransferase subunit A. The best characterized member is the biuret hydrolase of Pseudomonas sp. ADP, which hydrolyzes ammonia from the three-nitrogen compound biuret to yield allophanate. Allophanate is also an intermediate in urea degradation by the urea carboxylase/allophanate hydrolase pathway, an alternative to urease. [Unknown function, Enzymes of unknown specificity] 452 matched cddid_all.tbl CDD TIGR02716 TIGR02716 131763 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d. [Biosynthesis of cofactors, prosthetic groups, and carriers, Chlorophyll and bacteriochlorphyll] 306 matched cddid_all.tbl CDD TIGR02717 TIGR02717 131764 AcCoA-syn-alpha acetyl coenzyme A synthetase (ADP forming), alpha domain. Although technically reversible, it is believed that this group of ADP-dependent acetyl-CoA synthetases (ACS) act in the direction of acetate and ATP production in the organisms in which it has been characterized. In most species this protein exists as a fused alpha-beta domain polypeptide. In Pyrococcus and related species, however the domains exist as separate polypeptides. This model represents the alpha (N-terminal) domain. In Pyrococcus and related species there appears to have been the development of a paralogous family such that four other proteins are close relatives. In reference, one of these (along with its beta-domain partner) was characterized as ACS-II showing specificity for phenylacetyl-CoA. This model has been constructed to exclude these non-ACS-I paralogs. This may result in new, authentic ACS-I sequences falling below the trusted cutoff. 447 matched cddid_all.tbl CDD TIGR02718 TIGR02718 131765 sider_RhtX_FptX siderophore transporter, RhtX/FptX family. RhtX from Sinorhizobium meliloti 2011 and FptX from Pseudomonas aeruginosa appear to be single polypeptide transporters, from the major facilitator family (see pfam07690) for import of siderophores as a means to import iron. This function was suggested by proximity to siderophore biosynthesis genes and then confirmed by study of knockout and heterologous expression phenotypes. [Transport and binding proteins, Cations and iron carrying compounds] 390 matched cddid_all.tbl CDD TIGR02719 TIGR02719 131766 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551). [Regulatory functions, DNA interactions] 138 matched cddid_all.tbl CDD TIGR02720 TIGR02720 213733 pyruv_oxi_spxB pyruvate oxidase. Members of this family are examples of pyruvate oxidase (EC 1.2.3.3), an enzyme with FAD and TPP as cofactors that catalyzes the reaction pyruvate + phosphate + O2 + H2O = acetyl phosphate + CO2 + H2O2. It should not be confused with pyruvate dehydrogenase [cytochrome] (EC 1.2.2.2) as in E. coli PoxB, although the E. coli enzyme is closely homologous and has pyruvate oxidase as an alternate name. [Energy metabolism, Aerobic] 575 matched cddid_all.tbl CDD TIGR02721 TIGR02721 274268 ycfN_thiK thiamine kinase. Members of this family are the ycfN gene product of Escherichia coli, now identified as the salvage enzyme thiamine kinase (thiK), and additional proteobacterial homologs taken to be orthologs with equivalent function. [Biosynthesis of cofactors, prosthetic groups, and carriers, Thiamine] 256 matched cddid_all.tbl CDD TIGR02722 TIGR02722 274269 lp_ uncharacterized proteobacterial lipoprotein. Members of this protein family are restricted to the Proteobacteria, and all are predicted lipoproteins. In genomes that contain the thiK gene for the salvage enzyme thiamin kinase, the member of this family is encoded nearby. [Cell envelope, Other] 189 matched cddid_all.tbl CDD TIGR02723 TIGR02723 131770 phenyl_P_alpha phenylphosphate carboxylase, alpha subunit. Members of this protein family are the alpha subunit of phenylphosphate carboxylase. Phenol (methyl-benzene) is converted to phenylphosphate, then para-carboxylated by this four-subunit enzyme, with the release of phosphate, to 4-hydroxybenzoate. The enzyme contains neither biotin nor thiamin pyrophosphate. This alpha subunit is homologous to the beta subunit and, more broadly, to UbiD family decarboxylases. [Energy metabolism, Anaerobic] 485 matched cddid_all.tbl CDD TIGR02724 TIGR02724 131771 phenyl_P_beta phenylphosphate carboxylase, beta subunit. Members of this protein family are the beta subunit of phenylphosphate carboxylase. Phenol (methyl-benzene) is converted to phenylphosphate, then para-carboxylated by this four-subunit enzyme, with the release of phosphate, to 4-hydroxybenzoate. The enzyme contains neither biotin nor thiamin pyrophosphate. This beta subunit is homologous to the alpha subunit and, more broadly, to UbiD family decarboxylases. 472 matched cddid_all.tbl CDD TIGR02725 TIGR02725 131772 phenyl_P_gamma phenylphosphate carboxylase, gamma subunit. Members of this protein family are the gamma subunit of phenylphosphate carboxylase. Phenol (methyl-benzene) is converted to phenylphosphate, then para-carboxylated by this four-subunit enzyme, with the release of phosphate, to 4-hydroxybenzoate. The enzyme contains neither biotin nor thiamin pyrophosphate. The gamma subunit has no known homologs. 84 matched cddid_all.tbl CDD TIGR02726 TIGR02726 131773 phenyl_P_delta phenylphosphate carboxylase, delta subunit. Members of this protein family are the alpha subunit of phenylphosphate carboxylase. Phenol (methyl-benzene) is converted to phenylphosphate, then para-carboxylated by this four-subunit enzyme, with the release of phosphate, to 4-hydroxybenzoate. The enzyme contains neither biotin nor thiamin pyrophosphate. This delta subunit belongs to HAD family hydrolases. [Energy metabolism, Anaerobic] 169 matched cddid_all.tbl CDD TIGR02727 TIGR02727 274270 MTHFS_bact 5,10-methenyltetrahydrofolate synthetase. This enzyme, 5,10-methenyltetrahydrofolate synthetase, is also called 5-formyltetrahydrofolate cycloligase. Function of bacterial proteins in this family was inferred originally from the known activity of eukaryotic homologs. Recently, activity was shown explicitly for the member from Mycoplasma pneumonia. Members of this family from alpha- and gamma-proteobacteria, designated ygfA, are often found in an operon with 6S structural RNA, and show a similar pattern of high expression during stationary phase. The function may be to deplete folate to slow 1-carbon biosynthetic metabolism. [Central intermediary metabolism, One-carbon metabolism] 179 matched cddid_all.tbl CDD TIGR02728 TIGR02728 131775 spore_gerQ spore coat protein GerQ. Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria). This protein is cross-linked by a spore coat-associated transglutaminase. [Cellular processes, Sporulation and germination] 82 matched cddid_all.tbl CDD TIGR02729 TIGR02729 274271 Obg_CgtA Obg family GTPase CgtA. This model describes a univeral, mostly one-gene-per-genome GTP-binding protein that associates with ribosomal subunits and appears to play a role in ribosomal RNA maturation. This GTPase, related to the nucleolar protein Obg, is designated CgtA in bacteria. Mutations in this gene are pleiotropic, but it appears that effects on cellular functions such as chromosome partition may be secondary to the effect on ribosome structure. Recent work done in Vibrio cholerae shows an essential role in the stringent response, in which RelA-dependent ability to synthesize the alarmone ppGpp is required for deletion of this GTPase to be lethal. [Protein synthesis, Other] 328 matched cddid_all.tbl CDD TIGR02730 TIGR02730 131777 carot_isom carotene isomerase. Members of this family, including sll0033 (crtH) of Synechocystis sp. PCC 6803, catalyze a cis-trans isomerization of carotenes to the all-trans lycopene, a reaction that can also occur non-enzymatically in light through photoisomerization. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 493 matched cddid_all.tbl CDD TIGR02731 TIGR02731 131778 phytoene_desat phytoene desaturase. Plants and cyanobacteria (and, supposedly, Chlorobium tepidum) have a conserved pathway from two molecules geranylgeranyl-PP to one of all-trans-lycopene. Members of this family are the enzyme pytoene desaturase (also called phytoene dehydrogenase). This model does not include the region of the chloroplast transit peptide in plants. A closely related family, excluded by this model, is zeta-carotene desaturase, another enzyme in the same pathway. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 453 matched cddid_all.tbl CDD TIGR02732 TIGR02732 131779 zeta_caro_desat 9,9'-di-cis-zeta-carotene desaturase. Carotene 7,8-desaturase, also called zeta-carotene desaturase, catalyzes multiple steps in the pathway from geranylgeranyl-PP to all-trans-lycopene in plants and cyanobacteria. A similar enzyme and pathway is found in the green sulfur bacterium Chlorobium tepidum. 474 matched cddid_all.tbl CDD TIGR02733 TIGR02733 274272 desat_CrtD C-3',4' desaturase CrtD. Members of this family are slr1293, a carotenoid biosynthesis protein which was shown to be the C-3',4' desaturase (CrtD) of myxoxanthophyll biosynthesis in Synechocystis sp. strain PCC 6803, and close homologs (presumed to be functionally equivalent) from other cyanobacteria, where myxoxanthophyll biosynthesis is either known or expected. This enzyme can act on neurosporene and so presumably catalyzes the first step that is committed to myxoxanthophyll. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 492 matched cddid_all.tbl CDD TIGR02734 TIGR02734 274273 crtI_fam phytoene desaturase. Phytoene is converted to lycopene by desaturation at four (two symmetrical pairs of) sites. This is achieved by two enzymes (crtP and crtQ) in cyanobacteria (Gloeobacter being an exception) and plants, but by a single enzyme in most other bacteria and in fungi. This single enzyme is called the bacterial-type phytoene desaturase, or CrtI. Most members of this family, part of the larger pfam01593, which also contains amino oxidases, are CrtI itself; it is likely that all members act on either phytoene or on related compounds such as dehydrosqualene, for carotenoid biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 495 matched cddid_all.tbl CDD TIGR02735 TIGR02735 131782 purC_vibrio phosphoribosylaminoimidazole-succinocarboxamide synthase, Vibrio type. Members of this protein family appear to represent a novel form of phosphoribosylaminoimidazole-succinocarboxamide synthase (SAICAR synthetase), significantly different in sequence and gap pattern from a form (see TIGR00081) shared by a broad range of bacteria and eukaryotes. Members of this family are found within the gammaproteobacteria in the genera Vibrio, Shewanella, and Colwellia, and also (reported as a fragment) in the primitive eukarote Guillardia theta. [Purines, pyrimidines, nucleosides, and nucleotides, Purine ribonucleotide biosynthesis] 365 matched cddid_all.tbl CDD TIGR02736 TIGR02736 131783 cbb3_Q_epsi cytochrome c oxidase, cbb3-type, CcoQ subunit, epsilon-Proteobacterial. Members of this protein family are restricted to the epsilon branch of the Proteobacteria. All members are found in operons containing the other three structural subunits of the cbb3 type of cytochrome c oxidase. These small proteins show remote sequence similarity to the CcoQ subunit in other cytochrome c oxidase systems, so this family is assumed to represent the epsilonproteobacterial variant of CcoQ. [Energy metabolism, Electron transport] 56 matched cddid_all.tbl CDD TIGR02737 TIGR02737 131784 caa3_CtaG cytochrome c oxidase assembly factor CtaG. Members of this family are the CtaG protein required for assembly of active cytochrome c oxidase of the caa3 type, as in Bacillus subtilis. 281 matched cddid_all.tbl CDD TIGR02738 TIGR02738 131785 TrbB type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB. This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold, contains a conserved pair of cysteines and has been shown to function as a thiol disulfide isomerase by complementation of an Ecoli DsbA defect. The protein is believed to be involved in pilin assembly. The protein is closely related to TraF (TIGR02739) which is somewhat longer, lacks the cysteine motif and is apparently not functional as a disulfide bond isomerase. 153 matched cddid_all.tbl CDD TIGR02739 TIGR02739 274274 TraF type-F conjugative transfer system pilin assembly protein TraF. This protein is part of a large group of proteins involved in conjugative transfer of plasmid DNA, specifically the F-type system. This protein has been predicted to contain a thioredoxin fold and has been shown to be localized to the periplasm. Unlike the related protein TrbB (TIGR02738), TraF does not contain a conserved pair of cysteines and has been shown not to function as a thiol disulfide isomerase by complementation of an Ecoli DsbA defect. The protein is believed to be involved in pilin assembly. Even more closely related than TrbB is a clade of genes (TIGR02740) which do contain the CXXC motif, but it is unclear whether these genes are involved in type-F conjugation systems per se. 256 matched cddid_all.tbl CDD TIGR02740 TIGR02740 274275 TraF-like TraF-like protein. This protein is related to the F-type conjugation system pilus assembly proteins TraF (TIGR02739)and TrbB (TIGR02738) both of which exhibit a thioredoxin fold. The protein represented by this model has the same length and architecture as TraF, but lacks the CXXC-motif found in TrbB and believed to be responsible for the disulfide isomerase activity of that protein. 271 matched cddid_all.tbl CDD TIGR02741 TIGR02741 131788 TraQ type-F conjugative transfer system pilin chaperone TraQ. This protein makes a specific interaction with the pilin (TraA) protein to aid its transfer through the inner membrane during the process of F-type conjugative pilus assembly. 80 matched cddid_all.tbl CDD TIGR02742 TIGR02742 131789 TrbC_Ftype type-F conjugative transfer system pilin assembly protein TrbC. This protein is an essential component of the F-type conjugative pilus assembly system for the transfer of plasmid DNA. The N-terminal portion of these proteins are heterogeneous and are not covered by this model. 130 matched cddid_all.tbl CDD TIGR02743 TIGR02743 274276 TraW type-F conjugative transfer system protein TraW. This protein is an essential component of the F-type conjugative transfer sytem for plasmid DNA transfer and has been shown to be localized to the periplasm. 202 matched cddid_all.tbl CDD TIGR02744 TIGR02744 274277 TrbI_Ftype type-F conjugative transfer system protein TrbI. This protein is an essential component of the F-type conjugative transfer sytem for plasmid DNA transfer and has been shown to be localized to the periplasm. 112 matched cddid_all.tbl CDD TIGR02745 TIGR02745 274278 ccoG_rdxA_fixG cytochrome c oxidase accessory protein FixG. Member of this ferredoxin-like protein family are found exclusively in species with an operon encoding the cbb3 type of cytochrome c oxidase (cco-cbb3), and near the cco-cbb3 operon in about half the cases. The cco-cbb3 is found in a variety of proteobacteria and almost nowhere else, and is associated with oxygen use under microaerobic conditions. Some (but not all) of these proteobacteria are also nitrogen-fixing, hence the gene symbol fixG. FixG was shown essential for functional cco-cbb3 expression in Bradyrhizobium japonicum. 434 matched cddid_all.tbl CDD TIGR02746 TIGR02746 274279 TraC-F-type type-IV secretion system protein TraC. The protein family described here is common among the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The protein conyains the Walker A and B motifs and so is a putative nucleotide triphosphatase. 797 matched cddid_all.tbl CDD TIGR02747 TIGR02747 274280 TraV type IV conjugative transfer system lipoprotein TraV. The TraV protein is a component of conjugative type IV secretion systems. TraV is an outer membrane lipoprotein and is believed to interact with the secretin TraK. The alignment contains three conserved cysteines in the N-terminal half. 144 matched cddid_all.tbl CDD TIGR02748 TIGR02748 131795 GerC3_HepT heptaprenyl diphosphate synthase component II. Members of this family are component II of the heterodimeric heptaprenyl diphosphate synthase. The trusted cutoff was set such that all members identified are encoded near to a recognizable gene for component I (in pfam07307). This enzyme acts in menaquinone-7 isoprenoid side chain biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 319 matched cddid_all.tbl CDD TIGR02749 TIGR02749 131796 prenyl_cyano solanesyl diphosphate synthase. Members of this family all are from cyanobacteria or plastid-containing eukaryotes. A member from Arabidopsis (where both plastoquinone and ubiquinone contain the C(45) prenyl moiety) was characterized by heterologous expression as a solanesyl diphosphate synthase. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 322 matched cddid_all.tbl CDD TIGR02750 TIGR02750 274281 TraN_Ftype type-F conjugative transfer system mating-pair stabilization protein TraN. TraN is a large cysteine-rich outer membrane protein involved in the mating-pair stabilization (adhesin) component of the F-type conjugative plamid transfer system. TraN is believed to interact with the core type IV secretion system apparatus through the TraV protein. 572 matched cddid_all.tbl CDD TIGR02751 TIGR02751 131798 PEPCase_arch phosphoenolpyruvate carboxylase, archaeal type. This family is the archaeal-type phosphoenolpyruvate carboxylase, although not every host species is archaeal. These sequences bear little resemblance to the bacterial/eukaryotic type. The members from Sulfolobus solfataricus and Methanothermobacter thermautotrophicus were verified experimentally, while the activity is known to be present in a number of other archaea. [Energy metabolism, Other] 506 matched cddid_all.tbl CDD TIGR02752 TIGR02752 131799 MenG_heptapren demethylmenaquinone methyltransferase. MenG is a generic term for a methyltransferase that catalyzes the last step in menaquinone biosynthesis; the exact enzymatic activity differs for different MenG because the menaquinone differ in their prenoid side chains in different species. Members of this MenG protein family are 2-heptaprenyl-1,4-naphthoquinone methyltransferase, and are found together in operons with the two subunits of the heptaprenyl diphosphate synthase in Bacillus subtilis and related species. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 231 matched cddid_all.tbl CDD TIGR02753 TIGR02753 131800 sodN superoxide dismutase, Ni. This superoxide dismutase uses nickel, rather than iron, manganese, copper, or zinc. Its gene is always accompanied by a gene for a required protease. 145 matched cddid_all.tbl CDD TIGR02754 TIGR02754 274282 sod_Ni_protease nickel-type superoxide dismutase maturation protease. Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad. [Cellular processes, Detoxification, Protein fate, Protein modification and repair] 90 matched cddid_all.tbl CDD TIGR02755 TIGR02755 131802 TraX_Ftype type-F conjugative transfer system pilin acetylase TraX. TraX is responsible for the acetylation of the F-pilin TraA during conjugative plasmid transfer. The purpose of this acetylation is unclear, but the reported transcriptional regulation of TraX may indicate that it is involved in the process of pilu extension/retraction. 224 matched cddid_all.tbl CDD TIGR02756 TIGR02756 274283 TraK_Ftype type-F conjugative transfer system secretin TraK. The TraK protein is predicted to interact with the TraV and TraB proteins as part of the scaffold which extends from the inner membrane, through the periplasm to the cell envelope and through which the F-type conjugative pilus passes. TraK is homologous to the P-type IV secretion system protein TrbG, the Ti-type protein VirB9 and the I-type TraN protein. The protein is related to the secretin family especially the HrcC subgroup of the type III secretion system. The protein is hypothesized to oligomerize to form a ring structure akin to other secretins. 232 matched cddid_all.tbl CDD TIGR02757 TIGR02757 274284 TIGR02757 TIGR02757 family protein. Members of this uncharacterized protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighborhoods show little conservation. [Hypothetical proteins, Conserved] 229 matched cddid_all.tbl CDD TIGR02758 TIGR02758 131805 TraA_TIGR type IV conjugative transfer system pilin TraA. TraA is the single structural subunit of the pilus found in type IV conjugative transfer systems. This family is generally found in gammaproteobacteria. The pilins show considerable heterogeneity among the different conjugative plasmit types. All of them however contain an N-terminal part which is cleaved off by a leader peptidase (LepB, or similar) to result in a 68-78 amino acid product. Pilins may be further processed by acetylation (in F-like systems by the TraX protein) or by cyclization (in P-like systems by the TraF protein). 93 matched cddid_all.tbl CDD TIGR02759 TIGR02759 131806 TraD_Ftype type IV conjugative transfer system coupling protein TraD. The TraD protein performs an essential coupling function in conjugative type IV secretion systems. This protein sits at the inner membrane in contact with the assembled pilus and its scaffold as well as the relaxosome-plasmid DNA complex (through TraM). 566 matched cddid_all.tbl CDD TIGR02760 TIGR02760 274285 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein. 1960 matched cddid_all.tbl CDD TIGR02761 TIGR02761 163004 TraE_TIGR type IV conjugative transfer system protein TraE. TraE is a component of type IV secretion systems involved in conjugative transfer of plasmid DNA. The function of the TraE protein is unknown. 181 matched cddid_all.tbl CDD TIGR02762 TIGR02762 274286 TraL_TIGR type IV conjugative transfer system protein TraL. This protein is part of the type IV secretion system for conjugative plasmid transfer. The function of the TraL protein is unknown. [Cellular processes, Conjugation] 94 matched cddid_all.tbl CDD TIGR02763 TIGR02763 131810 chlamy_scaf chlamydiaphage internal scaffolding protein. Members of this protein family are encoded by genes in chlamydiaphage such as Chp2, viruses with around eight genes that infect obligately intracellular bacterial pathogens of the genus Chlamydia. This protein, initially designated VP3 (as if a structural protein of mature viral particles), is displaced from procapsids as DNA is packaged, and therefore is described as a scafolding protein. [Mobile and extrachromosomal element functions, Prophage functions] 114 matched cddid_all.tbl CDD TIGR02764 TIGR02764 274287 spore_ybaN_pdaB polysaccharide deacetylase family sporulation protein PdaB. This model describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reducted sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in sporulation had been masked by functional redundancy. Members of this family are homologous to a characterized polysaccharide deacetylase; the exact function this protein family is unknown. [Cellular processes, Sporulation and germination] 191 matched cddid_all.tbl CDD TIGR02765 TIGR02765 274288 crypto_DASH cryptochrome, DASH family. Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes. [Cellular processes, Adaptations to atypical conditions] 429 matched cddid_all.tbl CDD TIGR02766 TIGR02766 131813 crypt_chrom_pln cryptochrome, plant family. At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light. 475 matched cddid_all.tbl CDD TIGR02767 TIGR02767 131814 TraG-Ti Ti-type conjugative transfer system protein TraG. This protein is found in the Agrobacterium tumefaciens Ti plasmid tra region responsible for conjugative transfer of the entire plasmid among Agrobacterium strains. The protein is distantly related to the F-type conjugation system TraG protein. Both of these systems are examples of type IV secretion systems. 623 matched cddid_all.tbl CDD TIGR02768 TIGR02768 274289 TraA_Ti Ti-type conjugative transfer relaxase TraA. This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer. 744 matched cddid_all.tbl CDD TIGR02769 TIGR02769 131816 nickel_nikE nickel import ATP-binding protein NikE. This family represents the NikE subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase. [Transport and binding proteins, Cations and iron carrying compounds] 265 matched cddid_all.tbl CDD TIGR02770 TIGR02770 131817 nickel_nikD nickel import ATP-binding protein NikD. This family represents the NikD subunit of a multisubunit nickel import ABC transporter complex. Nickel, once imported, may be used in urease and in certain classes of hydrogenase and superoxide dismutase. NikD and NikE are homologous. [Transport and binding proteins, Cations and iron carrying compounds] 230 matched cddid_all.tbl CDD TIGR02771 TIGR02771 131818 TraF_Ti conjugative transfer signal peptidase TraF. This protein is found in apparent operons encoding elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as lepB. This family is present in both Ti-type and I-type conjugative systems. 171 matched cddid_all.tbl CDD TIGR02772 TIGR02772 274290 Ku_bact Ku protein, prokaryotic. Members of this protein family are Ku proteins of non-homologous end joining (NHEJ) DNA repair in bacteria and in at least one member of the archaea (Archaeoglobus fulgidus). Most members are encoded by a gene adjacent to the gene for the DNA ligase that completes the repair. The NHEJ system is broadly but rather sparsely distributed, being present in about one fifth of the first 250 completed prokarytotic genomes. A few species (e.g. Archaeoglobus fulgidus and Bradyrhizobium japonicum) have multiple copies that appear to represent recent paralogous family expansion. [DNA metabolism, DNA replication, recombination, and repair] 258 matched cddid_all.tbl CDD TIGR02773 TIGR02773 213736 addB_Gpos helicase-exonuclease AddAB, AddB subunit. DNA repair is accomplished by several different systems in prokaryotes. Recombinational repair of double-stranded DNA breaks involves the RecBCD pathway in some lineages, and AddAB (also called RexAB) in other. The AddA protein is conserved between the firmicutes and the alphaproteobacteria, while the partner protein is not. Nevertheless, the partner is designated AddB in both systems. This model describes the AddB protein as found Bacillus subtilis and related species. Although the RexB protein of Streptococcus and Lactococcus is considered to be orthologous, functionally equivalent, and merely named differently, all members of this protein family have a P-loop nucleotide binding motif GxxGxGK[ST] at the N-terminus, unlike RexB proteins, and a CxxCxxxxxC motif at the C-terminus, both of which may be relevant to function. [DNA metabolism, DNA replication, recombination, and repair] 1160 matched cddid_all.tbl CDD TIGR02774 TIGR02774 274291 rexB_recomb ATP-dependent nuclease subunit B. DNA repair is accomplished by several different systems in prokaryotes. Recombinational repair of double-stranded DNA breaks involves the RecBCD pathway in some lineages, and AddAB (also called RecAB) in other. The AddA protein is conserved between the firmicutes and the alphaproteobacteria, while the partner protein is not. The partner may be designated AddB, as in Bacillus and in alphaproteobacteria, or RexB as in Streptococcus and Lactococcus. Note, however, that RexB proteins lack an N-terminal GxxGxGK[ST] ATP-binding motif found in Bacillus subtilis and related species, and this difference may be important; this model represents specifically RexB proteins as found in Streptococcus and Lactococcus. [DNA metabolism, DNA replication, recombination, and repair] 1076 matched cddid_all.tbl CDD TIGR02775 TIGR02775 274292 TrbG_Ti P-type conjugative transfer protein TrbG. The TrbG protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbG is a homolog of the F-type TraK protein (which is believed to be an outer membrane pore-forming secretin, TIGR02756) as well as the vir system VirB9 protein. [Cellular processes, Conjugation] 206 matched cddid_all.tbl CDD TIGR02776 TIGR02776 274293 NHEJ_ligase_prk DNA ligase D. Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this model. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; it only represents the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku. [DNA metabolism, DNA replication, recombination, and repair] 552 matched cddid_all.tbl CDD TIGR02777 TIGR02777 131824 LigD_PE_dom DNA ligase D, 3'-phosphoesterase domain. Most sequences in this family are the 3'-phosphoesterase domain of a multidomain, multifunctional DNA ligase, LigD, involved, along with bacterial Ku protein, in non-homologous end joining, the less common of two general mechanisms of repairing double-stranded breaks in DNA sequences. LigD is variable in architecture, as it lacks this domain in Bacillus subtilis, is permuted in Mycobacterium tuberculosis, and occasionally is encoded by tandem ORFs rather than as a multifuntional protein. In a few species (Dehalococcoides ethenogenes and the archaeal genus Methanosarcina), sequences corresponding to the ligase and polymerase domains of LigD are not found, and the role of this protein is unclear. [DNA metabolism, DNA replication, recombination, and repair] 156 matched cddid_all.tbl CDD TIGR02778 TIGR02778 274294 ligD_pol DNA ligase D, polymerase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain. 245 matched cddid_all.tbl CDD TIGR02779 TIGR02779 274295 NHEJ_ligase_lig DNA ligase D, ligase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the ligase domain. 298 matched cddid_all.tbl CDD TIGR02780 TIGR02780 131827 TrbJ_Ti P-type conjugative transfer protein TrbJ. The TrbJ protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbJ is a homolog of the F-type TraE protein (which is believed to be an inner membrane pore-forming protein, TIGR02761) as well as the vir system VirB5 protein. 246 matched cddid_all.tbl CDD TIGR02781 TIGR02781 274296 VirB9 P-type conjugative transfer protein VirB9. The VirB9 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in a type IV secretion system . VirB9 is a homolog of the F-type conjugative transfer system TraK protein (which is believed to be an outer membrane pore-forming secretin, TIGR02756) as well as the Ti system TrbG protein. [Cellular processes, Conjugation] 243 matched cddid_all.tbl CDD TIGR02782 TIGR02782 274297 TrbB_P P-type conjugative transfer ATPase TrbB. The TrbB protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbB is a homolog of the vir system VirB11 ATPase, and the Flp pilus sytem ATPase TadA. [Cellular processes, Conjugation] 299 matched cddid_all.tbl CDD TIGR02783 TIGR02783 131830 TrbL_P P-type conjugative transfer protein TrbL. The TrbL protein is found in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer. TrbL is a homolog of the F-type TraG protein (which is believed to be a mating pair stabilization pore-forming protein, pfam07916) as well as the vir system VirB6 protein. [Cellular processes, Conjugation] 298 matched cddid_all.tbl CDD TIGR02784 TIGR02784 274298 addA_alphas double-strand break repair helicase AddA, alphaproteobacterial type. AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the alphaproteobacteria (as modeled here) and the Firmicutes, while the partner AddB proteins show no strong homology across the two groups of species. [DNA metabolism, DNA replication, recombination, and repair] 1135 matched cddid_all.tbl CDD TIGR02785 TIGR02785 274299 addA_Gpos helicase-exonuclease AddAB, AddA subunit, Firmicutes type. AddAB, also called RexAB, substitutes for RecBCD in several bacterial lineages. These DNA recombination proteins act before synapse and are particularly important for DNA repair of double-stranded breaks by homologous recombination. The term AddAB is used broadly, with AddA homologous between the Firmicutes (as modeled here) and the alphaproteobacteria, while the partner AddB proteins show no strong homology across the two groups of species. [DNA metabolism, DNA replication, recombination, and repair] 1230 matched cddid_all.tbl CDD TIGR02786 TIGR02786 274300 addB_alphas double-strand break repair protein AddB, alphaproteobacterial type. AddAB is a system well described in the Firmicutes as a replacement for RecBCD in many prokaryotes for the repair of double stranded break DNA damage. More recently, a distantly related gene pair conserved in many alphaproteobacteria was shown also to function in double-stranded break repair in Rhizobium etli. This family consists of AddB proteins of the alphaproteobacteial type. [DNA metabolism, DNA replication, recombination, and repair] 1021 matched cddid_all.tbl CDD TIGR02787 TIGR02787 131834 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam. [Regulatory functions, DNA interactions] 251 matched cddid_all.tbl CDD TIGR02788 TIGR02788 274301 VirB11 P-type DNA transfer ATPase VirB11. The VirB11 protein is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer. VirB11 is believed to be an ATPase. VirB11 is a homolog of the P-like conjugation system TrbB protein and the Flp pilus sytem protein TadA. 308 matched cddid_all.tbl CDD TIGR02789 TIGR02789 131836 nickel_nikB nickel ABC transporter, permease subunit NikB. This family consists of the NikB family of nickel ABC transporter permeases. Operons that contain this protein also contain a homologous permease subunit NikC. Nickel is used in cells as part of urease or certain hydrogenases or superoxide dismutases. [Transport and binding proteins, Cations and iron carrying compounds] 314 matched cddid_all.tbl CDD TIGR02790 TIGR02790 131837 nickel_nikC nickel ABC transporter, permease subunit NikC. This family consists of the NikC family of nickel ABC transporter permeases. Operons that contain this protein also contain a homologous permease subunit NikB. Nickel is used in cells as part of urease or certain hydrogenases or superoxide dismutases. [Transport and binding proteins, Cations and iron carrying compounds] 258 matched cddid_all.tbl CDD TIGR02791 TIGR02791 274302 VirB5 P-type DNA transfer protein VirB5. The VirB5 protein is involved in the type IV DNA secretion systems typified by the Agrobacterium Ti plasmid vir system where it interacts with several other proteins essential for proper pilus formation. VirB5 is homologous to the IncN (N-type) conjugation system protein TraC as well as the P-type protein TrbJ and the F-type protein TraE. 220 matched cddid_all.tbl CDD TIGR02792 TIGR02792 131839 PCA_ligA protocatechuate 4,5-dioxygenase, alpha subunit. Protocatechuate (PCA) 4,5-dioxygenase is the first enzyme in the PCA 4,5-cleavage pathway that is an alternative to PCA 3,4-cleavage and PCA 2,3 cleavage pathways. PCA is an intermediate in the breakdown of lignin (hence the gene symbol ligA) and other compounds. Members of this family are the alpha chain of PCA 4,5-dioxygenase, or the equivalent domain of a fusion protein. [Energy metabolism, Aerobic] 117 matched cddid_all.tbl CDD TIGR02793 TIGR02793 131840 nikR nickel-responsive transcriptional regulator NikR. Three members of the seed for this model, from Escherichia coli, Pseudomonas putida, and Brucella melitensis, are found associated with a nickel ABC transporter operon that acts to import nickel for use as a cofactor in urease or hydrogenase. These proteins, with characterized nickel-binding and DNA-binding domains, act as nickel-responsive transcriptional regulators. In the larger family of full-length homologs, most others both lack proximity to the nickel ABC transporter operon and form a separate clade. Several of the homologs not within the scope of this model, but rather scoring between the trusted and noise cutoffs, have been shown to bind nickel, copper, or both, and to regulate genes in response to nickel. [Regulatory functions, DNA interactions] 129 matched cddid_all.tbl CDD TIGR02794 TIGR02794 274303 tolA_full TolA protein. TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] 346 matched cddid_all.tbl CDD TIGR02795 TIGR02795 188247 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction. 117 matched cddid_all.tbl CDD TIGR02796 TIGR02796 131843 tolQ TolQ protein. TolQ is one of the essential components of the Tol-Pal system. Together with TolR, it harnesses protonmotive force to energize TolA, which spans the periplasm to reach the complex of TolB and Pal at the outer member. The tol-pal system proves to be important for maintaining outer membrane integrity. Gene pairs similar to the TolQ and TolR gene pair often number several per genome, but this model describes specificially TolQ per se, as found in tol-pal operons. A close homolog, excluded from this model, is ExbB of the ExbB/ExbD/TonB protein complex, which powers transport of siderophores and vitamin B12 across the bacterial outer membrane. The Tol-Pal system is exploited by colicin and filamentous phage DNA to enter the cell. It is also implicated in pathogenesis in several bacterial species [Transport and binding proteins, Other, Cellular processes, Pathogenesis] 215 matched cddid_all.tbl CDD TIGR02797 TIGR02797 131844 exbB tonB-system energizer ExbB. This model describes ExbB proteins, part of the MotA/TolQ/ExbB protein family. The paired proteins MotA and MotB, TolQ and TolR, and ExbB and ExbD harness the proton-motive force to drive the flagellar motor, energize the Tol-Pal system, or energize TonB, respectively. Tol-Pal and TonB are both active at the outer membrane. Genomes may have many different TonB-dependent receptors, of which many of those characterized are involved in siderophore transport across the outer membrane. [Transport and binding proteins, Cations and iron carrying compounds] 211 matched cddid_all.tbl CDD TIGR02798 TIGR02798 131845 ligK_PcmE 4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase. Members of this protein family 4-carboxy-4-hydroxy-2-oxoadipate aldolase, also called 4-oxalocitramalate aldolase. This enzyme of the protocatechuate 4,5-cleavage pathway converts its substrate to pyruvate plus oxaloacetate. Protocatechuate is an intermediate in many pathways for degrading aromatic compounds, including lignin, fluorene, etc. Hara, et al. showed the LigK gene was not only a 4-carboxy-4-hydroxy-2-oxoadipate aldolase but also the enzyme of the following step, oxaloacetate decarboxylase. 222 matched cddid_all.tbl CDD TIGR02799 TIGR02799 274304 thio_ybgC tol-pal system-associated acyl-CoA thioesterase. The tol-pal system consists of five critical genes. Inner membrane proteins TolQ and TolR convert protomotive force to energy that is transduced through TolA to an outer membrane complex of TolB and Pal. The system is known to be required to maintain outer membrane integrity. In a system with several homologous parts, ExbB and ExbD transduces energy through TonB to a variety of outer membrane proteins, many of which are siderophore receptors. The tol-pal system therefore may also be involved in transport. This family consists of a protein nearly always found in operons with the genes of the tol-pal system. The significance of this thioesterase to the tol-pal system is unclear, but either of two observations may be relevant. First, Pal, or peptidoglycan-associated lipoprotein, has a conserved N-terminal cleavage and acylation that makes it a lipoprotein. Second, the tol-pal system is implicated not only in the import of certain organics but also in the maintenance of outer membrane integrity (by an unknown mechanism). 126 matched cddid_all.tbl CDD TIGR02800 TIGR02800 274305 propeller_TolB tol-pal system beta propeller repeat protein TolB. Members of this protein family are the TolB periplasmic protein of Gram-negative bacteria. TolB is part of the Tol-Pal (peptidoglycan-associated lipoprotein) multiprotein complex, comprising five envelope proteins, TolQ, TolR, TolA, TolB and Pal, which form two complexes. The TolQ, TolR and TolA inner-membrane proteins interact via their transmembrane domains. The {beta}-propeller domain of the periplasmic protein TolB is responsible for its interaction with Pal. TolB also interacts with the outer-membrane peptidoglycan-associated proteins Lpp and OmpA. TolA undergoes a conformational change in response to changes in the proton-motive force, and interacts with Pal in an energy-dependent manner. The C-terminal periplasmic domain of TolA also interacts with the N-terminal domain of TolB. The Tol-PAL system is required for bacterial outer membrane integrity. E. coli TolB is involved in the tonB-independent uptake of group A colicins (colicins A, E1, E2, E3 and K), and is necessary for the colicins to reach their respective targets after initial binding to the bacteria. It is also involved in uptake of filamentous DNA. Study of its structure suggest that the TolB protein might be involved in the recycling of peptidoglycan or in its covalent linking with lipoproteins. The Tol-Pal system is also implicated in pathogenesis of E. coli, Haemophilus ducreyi , Salmonella enterica and Vibrio cholerae, but the mechanism(s) is unclear. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] 417 matched cddid_all.tbl CDD TIGR02801 TIGR02801 274306 tolR TolR protein. The model describes the inner membrane protein TolR, part of the TolR/TolQ complex that transduces energy from the proton-motive force, through TolA, to an outer membrane complex made up of TolB and Pal (peptidoglycan-associated lipoprotein). The complex is required to maintain outer membrane integrity, and defects may cause a defect in the import of some organic compounds in addition to the resulting morphologic. While several gene pairs homologous to talR and tolQ may be found in a single genome, but the scope of this model is set to favor finding only bone fide TolR, supported by operon structure as well as by score. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] 129 matched cddid_all.tbl CDD TIGR02802 TIGR02802 274307 Pal_lipo peptidoglycan-associated lipoprotein. Members of this protein are Pal (also called OprL), the Peptidoglycan-Associated Lipoprotein of the Tol-Pal system. The system appears to be involved both in the maintenance of outer membrane integrity and in the import of certain organic molecules as nutrients. Members of this family contain a hydrodrophobic lipoprotein signal sequence, a conserved N-terminal cleavage and modification site, a poorly conserved low-complexity region, together comprising about 65 amino acids, and a well-conserved C-terminal domain. The seed alignment for this model includes only the conserved C-terminal domain. 104 matched cddid_all.tbl CDD TIGR02803 TIGR02803 131850 ExbD_1 TonB system transport protein ExbD, group 1. Members of this family are Gram-negative bacterial inner membrane proteins, generally designated ExbD, related to the TolR family modeled by TIGRFAMs TIGR02801. Members always are encoded next to a protein designated ExbB (TIGR02797), related to the TolQ family modeled by TIGRFAMs TIGR02796. ExbD and ExbB together form a proton channel through which they can harness the proton-motive force to energize TonB, which in turn energizes TonB-dependent receptors in the outer membrane. TonB-dependent receptors with known specificity tend to import siderophores or vitamin B12. A TonB system and Tol-Pal system often will co-exist in a single bacterial genome. 122 matched cddid_all.tbl CDD TIGR02804 TIGR02804 131851 ExbD_2 TonB system transport protein ExbD, group 2. Members of this family are Gram-negative bacterial inner membrane proteins, generally designated ExbD, related to the TolR family modeled by TIGRFAMs TIGR02801. Members always are encoded next to a protein designated ExbB (TIGR02797), related to the TolQ family modeled by TIGRFAMs TIGR02796. ExbD and ExbB together form a proton channel through which they can harness the proton-motive force to energize TonB, which in turn energizes TonB-dependent receptors in the outer membrane. TonB-dependent receptors with known specificity tend to import siderophores or vitamin B12. A TonB system and Tol-Pal system often will co-exist in a single bacterial genome. 121 matched cddid_all.tbl CDD TIGR02805 TIGR02805 131852 exbB2 tonB-system energizer ExbB, group 2. Members of this protein family appear to be the ExbB protein of an ExbBD proton-transporting membrane complex that, by means of TonB, energizes transport by TonB-dependent receptors. Note that this family represents one of at least two distinct groups TolQ homologs designated ExbB - see also TIGR02797. Each group associates with a distinct group of ExbD proteins, and a single species may have two ExbB/ExbD/TonB systems. [Transport and binding proteins, Cations and iron carrying compounds] 138 matched cddid_all.tbl CDD TIGR02806 TIGR02806 131853 clostrip clostripain. Clostripain is a cysteine protease characterized from Clostridium histolyticum, and also known from Clostridium perfringens. It is a heterodimer processed from a single precursor polypeptide, specific for Arg-|-Xaa peptide bonds. The older term alpha-clostripain refers to the most active, most reduced form, rather than to the product of one of several different genes. Clostripain belongs to the peptidase family C11, or clostripain family (see pfam03415). [Protein fate, Degradation of proteins, peptides, and glycopeptides, Cellular processes, Pathogenesis] 476 matched cddid_all.tbl CDD TIGR02807 TIGR02807 274308 cas6_cmx6 CRISPR-associated protein Cas6, subtype MYXAN. Members of this protein family resemble the Cas6 proteins described by TIGR01877 in having a C-terminal motif GXGXXXXXGXG, where the single X of each GXG is hydrophobic and the spacer XXXXX has at least one Lys or Arg. Examples are found in cas gene operons of CRISPR regions in Anabaena variabilis ATCC 29413, Leptospira interrogans, Gemmata obscuriglobus UQM 2246, and twice in Myxococcus xanthus DK 1622. Oddly, an orphan member is found in Thiobacillus denitrificans ATCC 25259, whose genome does not seem to contain other evidence of CRISPR repeats or cas genes. 190 matched cddid_all.tbl CDD TIGR02808 TIGR02808 131855 short_TIGR02808 TIGR02808 family protein. This very small protein (about 46 amino acids) consists largely of a single predicted membrane-spanning region. It is found in Photobacterium profundum SS9 and in three species of Vibrio, always near periplasmic nitrate reductase genes, but far from the periplasmic nitrate reductase genes in Aeromonas hydrophila ATCC7966. [Hypothetical proteins, Conserved] 42 matched cddid_all.tbl CDD TIGR02809 TIGR02809 131856 phasin_3 phasin family protein. Members of this protein family are encoded in polyhydroxyalkanoic acid storage system regions in Vibrio, Photobacterium profundum SS9, Acinetobacter sp., Aeromonas hydrophila, and several species of Vibrio. Members appear distantly related to the phasin family proteins modeled by TIGR01841 and TIGR01985. 110 matched cddid_all.tbl CDD TIGR02810 TIGR02810 274309 agaZ_gatZ D-tagatose-bisphosphate aldolase, class II, non-catalytic subunit. Aldolases specific for D-tagatose-bisphosphate occur in distinct pathways in Escherichia coli and other bacteria, one for the degradation of galactitol (formerly dulcitol) and one for degradation of N-acetyl-galactosamine and D-galactosamine. This family represents a protein of both systems that behaves as a non-catalytic subunit of D-tagatose-bisphosphate aldolase, required both for full activity and for good stability of the aldolase. Note that members of this protein family appear in public databases annotated as putative tagatose 6-phosphate kinases, possibly in error. [Energy metabolism, Sugars] 420 matched cddid_all.tbl CDD TIGR02811 TIGR02811 274310 formate_TAT formate dehydrogenase region TAT target. Members of this uncharacterized protein family are all small, extending 70 or fewer residues from their respective likely start codons. All have the twin-arginine-dependent tranport (TAT) signal sequence at the N-terminus and a conserved 20-residue C-terminal region that includes the motif Y-[HRK]-X-[TS]-X-H-[IV]-X-X-[YF]-Y. The TAT signal sequence suggests a bound cofactor. All members are encoded near genes for subunits of formate dehydrogenase, and may themselves be a subunit or accessory protein. [Unknown function, General] 66 matched cddid_all.tbl CDD TIGR02812 TIGR02812 163028 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function. [Fatty acid and phospholipid metabolism, Biosynthesis, Fatty acid and phospholipid metabolism, Degradation, Regulatory functions, DNA interactions] 235 matched cddid_all.tbl CDD TIGR02813 TIGR02813 274311 omega_3_PfaA polyketide-type polyunsaturated fatty acid synthase PfaA. Members of the seed for this alignment are involved in omega-3 polyunsaturated fatty acid biosynthesis, such as the protein PfaA from the eicosapentaenoic acid biosynthesis operon in Photobacterium profundum strain SS9. PfaA is encoded together with PfaB, PfaC, and PfaD, and the functions of the individual polypeptides have not yet been described. More distant homologs of PfaA, also included with the reach of this model, appear to be involved in polyketide-like biosynthetic mechanisms of polyunsaturated fatty acid biosynthesis, an alternative to the more familiar iterated mechanism of chain extension and desaturation, and in most cases are encoded near genes for homologs of PfaB, PfaC, and/or PfaD. 2582 matched cddid_all.tbl CDD TIGR02814 TIGR02814 274312 pfaD_fam PfaD family protein. The protein PfaD is part of four gene locus, similar to polyketide biosynthesis systems, responsible for omega-3 polyunsaturated fatty acid biosynthesis in several high pressure and/or cold-adapted bacteria. Several other members of the seed alignment for this model are found in loci presumed to act in polyketide biosyntheses per se. 444 matched cddid_all.tbl CDD TIGR02815 TIGR02815 131862 agaS_fam putative sugar isomerase, AgaS family. Some members of this protein family are found in regions associated with N-acetyl-galactosamine and galactosamine untilization and are suggested to be isomerases. 372 matched cddid_all.tbl CDD TIGR02816 TIGR02816 131863 pfaB_fam PfaB family protein. The protein PfaB is part of four gene locus, similar to polyketide biosynthesis systems, responsible for omega-3 polyunsaturated fatty acid biosynthesis in several high pressure and/or cold-adapted bacteria. The fairly permissive trusted cutoff set for this model allows detection of homologs encoded near homologs to other proteins of the locus: PfaA, PfaC, and/or PfaD. The likely role in every case is either polyunsaturated fatty acid or polyketide biosynthesis. 538 matched cddid_all.tbl CDD TIGR02817 TIGR02817 274313 adh_fam_1 zinc-binding alcohol dehydrogenase family protein. Members of this model form a distinct subset of the larger family of oxidoreductases that includes zinc-binding alcohol dehydrogenases and NADPH:quinone reductases (pfam00107). While some current members of this family carry designations as putative alginate lyase, it seems no sequence with a direct characterization as such is detected by this model. [Energy metabolism, Fermentation] 336 matched cddid_all.tbl CDD TIGR02818 TIGR02818 131865 adh_III_F_hyde S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase. The members of this protein family show dual function. First, they remove formaldehyde, a toxic metabolite, by acting as S-(hydroxymethyl)glutathione dehydrogenase (1.1.1.284). S-(hydroxymethyl)glutathione can form spontaneously from formaldehyde and glutathione, and so this enzyme previously was designated glutathione-dependent formaldehyde dehydrogenase. These same proteins are also designated alcohol dehydrogenase (EC 1.1.1.1) of class III, for activities that do not require glutathione; they tend to show poor activity for ethanol among their various substrate alcohols. [Cellular processes, Detoxification, Energy metabolism, Fermentation] 368 matched cddid_all.tbl CDD TIGR02819 TIGR02819 274314 fdhA_non_GSH formaldehyde dehydrogenase, glutathione-independent. Members of this family represent a distinct clade within the larger family of zinc-dependent dehydrogenases of medium chain alcohols, a family that also includes the so-called glutathione-dependent formaldehyde dehydrogenase. Members of this protein family have a tightly bound NAD that can act as a true cofactor, rather than a cosubstrate in dehydrogenase reactions, in dismutase reactions for some aldehydes. The name given to this family, however, is formaldehyde dehydrogenase, glutathione-independent. [Central intermediary metabolism, One-carbon metabolism] 393 matched cddid_all.tbl CDD TIGR02820 TIGR02820 131867 formald_GSH S-(hydroxymethyl)glutathione synthase. The formation of S-(hydroxymethyl)glutathione synthase from glutathione and formaldehyde occurs naturally, but this enzyme speeds its formation in some species as part of a pathway of formaldehyde detoxification. [Cellular processes, Detoxification, Central intermediary metabolism, One-carbon metabolism] 182 matched cddid_all.tbl CDD TIGR02821 TIGR02821 131868 fghA_ester_D S-formylglutathione hydrolase. This model describes a protein family from bacteria, yeast, and human, with a conserved critical role in formaldehyde detoxification as S-formylglutathione hydrolase (EC 3.1.2.12). Members in eukaryotes such as the human protein are better known as esterase D (EC 3.1.1.1), an enzyme with broad specificity, although S-formylglutathione hydrolase has now been demonstrated as well. [Cellular processes, Detoxification] 275 matched cddid_all.tbl CDD TIGR02822 TIGR02822 131869 adh_fam_2 zinc-binding alcohol dehydrogenase family protein. Members of this model form a distinct subset of the larger family of oxidoreductases that includes zinc-binding alcohol dehydrogenases and NADPH:quinone reductases (pfam00107). The gene neighborhood of members of this family is not conserved and it appears that no members are characterized. The sequence of the family includes 6 invariant cysteine residues and one invariant histidine. It appears that no member is characterized. [Energy metabolism, Fermentation] 329 matched cddid_all.tbl CDD TIGR02823 TIGR02823 274315 oxido_YhdH putative quinone oxidoreductase, YhdH/YhfP family. This model represents a subfamily of pfam00107 as defined by Pfam, a superfamily in which some members are zinc-binding medium-chain alcohol dehydrogenases while others are quinone oxidoreductases with no bound zinc. This subfamily includes proteins studied crystallographically for insight into function: YhdH from Escherichia coli and YhfP from Bacillus subtilis. Members bind NADPH or NAD, but not zinc. [Unknown function, Enzymes of unknown specificity] 323 matched cddid_all.tbl CDD TIGR02824 TIGR02824 274316 quinone_pig3 putative NAD(P)H quinone oxidoreductase, PIG3 family. Members of this family are putative quinone oxidoreductases that belong to the broader superfamily (modeled by Pfam pfam00107) of zinc-dependent alcohol (of medium chain length) dehydrogenases and quinone oxiooreductases. The alignment shows no motif of conserved Cys residues as are found in zinc-binding members of the superfamily, and members are likely to be quinone oxidoreductases instead. A member of this family in Homo sapiens, PIG3, is induced by p53 but is otherwise uncharacterized. [Unknown function, Enzymes of unknown specificity] 325 matched cddid_all.tbl CDD TIGR02825 TIGR02825 131872 B4_12hDH leukotriene B4 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase. Leukotriene B4 12-hydroxydehydrogenase is an NADP-dependent enzyme of arachidonic acid metabolism, responsible for converting leukotriene B4 to the much less active metabolite 12-oxo-leukotriene B4. The BRENDA database lists leukotriene B4 12-hydroxydehydrogenase as one of the synonyms of 2-alkenal reductase (EC 1.3.1.74), while 1.3.1.48 is 15-oxoprostaglandin 13-reductase. 325 matched cddid_all.tbl CDD TIGR02826 TIGR02826 274317 RNR_activ_nrdG3 anaerobic ribonucleoside-triphosphate reductase activating protein. Members of this family represent a set of radical SAM enzymes related to, yet architecturally different from, the activating protein for the glycine radical-containing, oxygen-sensitive ribonucleoside-triphosphate reductase (RNR) as described in model TIGR02491. Members of this family are found paired with members of a similarly divergent set of anaerobic ribonucleoside-triphosphate reductases. Identification of this protein as an RNR activitating protein is partly from pairing with a candidate RNR. It is further supported by our finding that upstream of these operons are examples of a conserved regulatory element (described Rodionov and Gelfand) that is found in nearly all bacteria and that occurs specifically upstream of operons for all three classes of RNR genes. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism] 147 matched cddid_all.tbl CDD TIGR02827 TIGR02827 274318 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism] 595 matched cddid_all.tbl CDD TIGR02828 TIGR02828 131875 TIGR02828 putative membrane fusion protein. Members of this family show similarity to the members of TIGR00999, the membrane fusion protein (MFP) cluster 2 family, which is linked to RND transport systems. [Transport and binding proteins, Unknown substrate] 188 matched cddid_all.tbl CDD TIGR02829 TIGR02829 213743 spore_III_AE stage III sporulation protein AE. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AE. [Cellular processes, Sporulation and germination] 381 matched cddid_all.tbl CDD TIGR02830 TIGR02830 274319 spore_III_AG stage III sporulation protein AG. CC A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AG. [Cellular processes, Sporulation and germination] 186 matched cddid_all.tbl CDD TIGR02831 TIGR02831 131878 spo_II_M stage II sporulation protein M. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This predicted integral membrane protein is designated stage II sporulation protein M. [Cellular processes, Sporulation and germination] 200 matched cddid_all.tbl CDD TIGR02832 TIGR02832 131879 spo_yunB sporulation protein YunB. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. Mutation of this sigma E-regulated gene, designated yunB, has been shown to cause a sporulation defect. [Cellular processes, Sporulation and germination] 204 matched cddid_all.tbl CDD TIGR02833 TIGR02833 131880 spore_III_AB stage III sporulation protein AB. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage III sporulation protein AB. [Cellular processes, Sporulation and germination] 170 matched cddid_all.tbl CDD TIGR02834 TIGR02834 274320 spo_ytxC putative sporulation protein YtxC. This uncharacterized protein is part of a panel of proteins conserved in all known endospore-forming Firmicutes (low-GC Gram-positive bacteria), including Carboxydothermus hydrogenoformans, and nowhere else. [Cellular processes, Sporulation and germination] 276 matched cddid_all.tbl CDD TIGR02835 TIGR02835 131882 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active. [Transcription, Transcription factors, Cellular processes, Sporulation and germination] 234 matched cddid_all.tbl CDD TIGR02836 TIGR02836 131883 spore_IV_A stage IV sporulation protein A. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis. [Cellular processes, Sporulation and germination] 492 matched cddid_all.tbl CDD TIGR02837 TIGR02837 131884 spore_II_R stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage II sporulation protein R. [Cellular processes, Sporulation and germination] 168 matched cddid_all.tbl CDD TIGR02838 TIGR02838 131885 spore_V_AC stage V sporulation protein AC. This model describes stage V sporulation protein AC, a paralog of stage V sporulation protein AE. Both are proteins found to present in a species if and only if that species is one of the Firmicutes capable of endospore formation, as of the time of the publication of the genome of Carboxydothermus hydrogenoformans. Mutants in spoVAC have a stage V sproulation defect. [Cellular processes, Sporulation and germination] 141 matched cddid_all.tbl CDD TIGR02839 TIGR02839 131886 spore_V_AE stage V sporulation protein AE. This model describes stage V sporulation protein AE, a paralog of stage V sporulation protein AC. Both are proteins found to present in a species if and only if that species is one of the Firmicutes capable of endospore formation, as of the time of the publication of the genome of Carboxydothermus hydrogenoformans. Mutants in spoVAE have a stage V sproulation defect. [Cellular processes, Sporulation and germination] 114 matched cddid_all.tbl CDD TIGR02840 TIGR02840 274321 spore_YtaF putative sporulation protein YtaF. This protein family was identified, at the time of the publication of the Carboxydothermus hydrogenoformans genome, as having a phylogenetic profile that exactly matches the subset of the Firmicutes capable of forming endospores. The species include Bacillus anthracis, Clostridium tetani, Thermoanaerobacter tengcongensis, Geobacillus kaustophilus, etc. This protein, previously named YtaF, is therefore a putative sporulation protein. [Cellular processes, Sporulation and germination] 206 matched cddid_all.tbl CDD TIGR02841 TIGR02841 131888 spore_YyaC putative sporulation protein YyaC. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, also called YyaC, is a member of that panel and is otherwise uncharacterized. The second round of PSI-BLAST shows many similarities to the germination protease GPR, which is found in exactly the same set of organisms and has a known role in the sporulation/germination process. [Cellular processes, Sporulation and germination] 140 matched cddid_all.tbl CDD TIGR02842 TIGR02842 131889 CyoC cytochrome o ubiquinol oxidase, subunit III. Cytochrome o terminal oxidase complex is the component of the aerobic respiratory chain which reacts with oxygen, reducing it to water with the concomitant transport of 4 protons across the membrane. Also known as the cytochrome bo complex, cytochrome o ubiquinol oxidase contains four subunits, two heme b cofactors and a copper atom which is believed to be the oxygen active site. This complex is structurally related to the cytochrome caa3 oxidases which utilize cytochrome c as the reductant and contain heme a cofactors, as well as the intermediate form aa3 oxidases which also react directly with quinones as the reductant. [Energy metabolism, Electron transport] 180 matched cddid_all.tbl CDD TIGR02843 TIGR02843 131890 CyoB cytochrome o ubiquinol oxidase, subunit I. Cytochrome o terminal oxidase complex is the component of the aerobic respiratory chain which reacts with oxygen, reducing it to water with the concomitant transport of 4 protons across the membrane. Also known as the cytochrome bo complex, cytochrome o ubiquinol oxidase contains four subunits, two heme b cofactors and a copper atom which is believed to be the oxygen active site. This complex is structurally related to the cytochrome caa3 oxidases which utilize cytochrome c as the reductant and contain heme a cofactors, as well as the intermediate form aa3 oxidases which also react directly with quinones as the reductant. [Energy metabolism, Electron transport] 646 matched cddid_all.tbl CDD TIGR02844 TIGR02844 131891 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes. [Regulatory functions, DNA interactions, Cellular processes, Sporulation and germination] 80 matched cddid_all.tbl CDD TIGR02845 TIGR02845 188254 spore_V_AD stage V sporulation protein AD. Bacillus and Clostridium species contain about 10 % dipicolinic acid (pyridine-2,6-dicarboxylic acid) by weight. This protein family, SpoVAD, belongs to the spoVA operon that is suggested to act in the transport of dipicolinic acid (DPA) from the mother cell, where DPA is synthesized, to the forespore, a process essential to sporulation. Members of this protein family are found, so far, in exactly those species believed capable of endospore formation. [Cellular processes, Sporulation and germination] 327 matched cddid_all.tbl CDD TIGR02846 TIGR02846 131893 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K. [Transcription, Transcription factors, Cellular processes, Sporulation and germination] 227 matched cddid_all.tbl CDD TIGR02847 TIGR02847 131894 CyoD cytochrome o ubiquinol oxidase subunit IV. Cytochrome o terminal oxidase complex is the component of the aerobic respiratory chain which reacts with oxygen, reducing it to water with the concomitant transport of 4 protons across the membrane. Also known as the cytochrome bo complex, cytochrome o ubiquinol oxidase contains four subunits, two heme b cofactors and a copper atom which is believed to be the oxygen active site. This complex is structurally related to the cytochrome caa3 oxidases which utilize cytochrome c as the reductant and contain heme a cofactors, as well as the intermediate form aa3 oxidases which also react directly with quinones as the reductant. [Energy metabolism, Electron transport] 96 matched cddid_all.tbl CDD TIGR02848 TIGR02848 131895 spore_III_AC stage III sporulation protein AC. Members of this protein family are designated SpoIIIAC, part of the spoIIIA operon of sporulation genes whose mutant phenotype is linked to sporulation stage III. Members of this family are encoded by the genome of a species if and only if that species is capable of endospore formation, as in Bacillus subtilis. The molecular function of this small, probable integral membrane protein is unknown. [Cellular processes, Sporulation and germination] 64 matched cddid_all.tbl CDD TIGR02849 TIGR02849 131896 spore_III_AD stage III sporulation protein AD. Members of this family are the uncharacterized protein SpoIIIAD, part of the spoIIIA operon that acts at sporulation stage III as part of a cascade of events leading to endospore formation. Note that the start sites of members of this family as annotated tend to be variable; quite a few members have apparent homologous protein-coding regions continuing upstream of the first available start codon. The length of the alignment and the scoring cutoff thresholds for the model have been set to try to detect all valid members of the family, even if annotation of the start site begins too far downstream. [Cellular processes, Sporulation and germination] 101 matched cddid_all.tbl CDD TIGR02850 TIGR02850 131897 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor. [Transcription, Transcription factors, Cellular processes, Sporulation and germination] 254 matched cddid_all.tbl CDD TIGR02851 TIGR02851 131898 spore_V_T stage V sporulation protein T. Members of this protein family are the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB (See pfam04014). [Regulatory functions, DNA interactions, Cellular processes, Sporulation and germination] 180 matched cddid_all.tbl CDD TIGR02852 TIGR02852 188255 spore_dpaB dipicolinic acid synthetase, B subunit. Members of this family represent the B subunit of dipicolinic acid synthetase, an enzyme that synthesizes a small molecule that appears to confer heat stability to bacterial endospores such as those of Bacillus subtilis. The A and B subunits are together in what was originally designated the spoVF locus for stage V of endospore formation. [Cellular processes, Sporulation and germination] 187 matched cddid_all.tbl CDD TIGR02853 TIGR02853 131900 spore_dpaA dipicolinic acid synthetase, A subunit. This predicted Rossman fold-containing protein is the A subunit of dipicolinic acid synthetase as found in most, though not all, endospore-forming low-GC Gram-positive bacteria; it is absent in Clostridium. The B subunit is represented by TIGR02852. This protein is also known as SpoVFA. [Cellular processes, Sporulation and germination] 287 matched cddid_all.tbl CDD TIGR02854 TIGR02854 131901 spore_II_GA sigma-E processing peptidase SpoIIGA. Members of this protein family are the stage II sporulation protein SpoIIGA. This protein acts as an activating protease for Sigma-E, one of several specialized sigma factors of the sporulation process in Bacillus subtilis and related endospore-forming bacteria. [Cellular processes, Sporulation and germination] 288 matched cddid_all.tbl CDD TIGR02855 TIGR02855 274322 spore_yabG sporulation peptidase YabG. Members of this family are the protein YabG, demonstrated for Bacillus subtilis to be an endopeptidase able to release N-terminal peptides from a number of sporulation proteins, including CotT, CotF, and SpoIVA. It appears to be expressed under control of sigma-K. [Cellular processes, Sporulation and germination] 283 matched cddid_all.tbl CDD TIGR02856 TIGR02856 131903 spore_yqfC sporulation protein YqfC. This small protein, designated YqfC in Bacillus subtilis, is both restricted to and universal in sporulating species of the Firmcutes, such as Bacillus subtilis and Clostridium perfringens. It is part of the sigma(E)-controlled regulon, and its mutation leads to a sporulation defect. [Cellular processes, Sporulation and germination] 85 matched cddid_all.tbl CDD TIGR02857 TIGR02857 274323 CydD thiol reductant ABC exporter, CydD subunit. The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex. Unfortunately, the gene symbol nomenclature adopted based on this operon in B. subtilis assigns cydC to the third gene in the operon where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologs in this family in accordance with the precedence of publication of the E. coli name, CydD 529 matched cddid_all.tbl CDD TIGR02858 TIGR02858 274324 spore_III_AA stage III sporulation protein AA. Members of this protein are the stage III sporulation protein AA, encoded by one of several genes in the spoIIIA locus. It seems that this protein is found in a species if and only if that species is capable of endospore formation. [Cellular processes, Sporulation and germination] 270 matched cddid_all.tbl CDD TIGR02859 TIGR02859 131906 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs in Listeria score well against this model, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt. [Transcription, Transcription factors, Cellular processes, Sporulation and germination] 198 matched cddid_all.tbl CDD TIGR02860 TIGR02860 274325 spore_IV_B stage IV sporulation protein B. SpoIVB, the stage IV sporulation protein B of endospore-forming bacteria such as Bacillus subtilis, is a serine proteinase, expressed in the spore (rather than mother cell) compartment, that participates in a proteolytic activation cascade for Sigma-K. It appears to be universal among endospore-forming bacteria and occurs nowhere else. [Cellular processes, Sporulation and germination] 402 matched cddid_all.tbl CDD TIGR02861 TIGR02861 274326 SASP_H small acid-soluble spore protein, H-type. This model is derived from pfam08141 but has been expanded to include in the seed corresponding proteins from three species of Clostridium. Members of this family should occur only in endospore-forming bacteria, typically with two members per genome, but may be absent from the genomes of some endospore-forming bacteria. SspH (previously designated YfjU) was shown to be expressed specifically in spores of Bacillus subtilis. [Cellular processes, Sporulation and germination] 58 matched cddid_all.tbl CDD TIGR02862 TIGR02862 163046 spore_BofA pro-sigmaK processing inhibitor BofA. Members of this protein family are found only in endospore-forming bacteria, such as Bacillus subtilis and Clostridium tetani. Among such bacteria, it appears only Symbiobacterium thermophilum lacks a member of this family. The protein, designated BofA, is an integral membrane protein that regulates the proteolytic activation of the RNA polymerase sigma factor K. [Cellular processes, Sporulation and germination] 83 matched cddid_all.tbl CDD TIGR02863 TIGR02863 131910 spore_sspJ small, acid-soluble spore protein, SspJ. New small, acid-soluble proteins unique to spores of Bacillus subtilis [Cellular processes, Sporulation and germination] 47 matched cddid_all.tbl CDD TIGR02864 TIGR02864 274327 spore_sspO small, acid-soluble spore protein O. This model represents a minor (low-abundance) spore protein, designated SspO. It is found in a very limited subset of the already small group of endospore-forming bacteria, but these species include Oceanobacillus iheyensis, Geobacillus kaustophilus, Bacillus subtilis, B. halodurans, and B. cereus. This protein was previously called CotK. [Cellular processes, Sporulation and germination] 50 matched cddid_all.tbl CDD TIGR02865 TIGR02865 274328 spore_II_E stage II sporulation protein E. Stage II sporulation protein E (SpoIIE) is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation. By means of it protein phosphatase activity, located in the C-terminal region, it activates sigma-F. All proteins that score above the trusted cutoff to this model are found in endospore-forming Gram-positive bacteria. Surprisingly, a sequence from the Cyanobacterium-like (and presumably non-spore-forming) photosynthesizer Heliobacillus mobilis is homologous, and scores between the trusted and noise cutoffs. [Cellular processes, Sporulation and germination] 764 matched cddid_all.tbl CDD TIGR02866 TIGR02866 274329 CoxB cytochrome c oxidase, subunit II. Cytochrome c oxidase is the terminal electron acceptor of mitochondria (and one of several possible acceptors in prokaryotes) in the electron transport chain of aerobic respiration. The enzyme couples the oxidation of reduced cytochrome c with the reduction of molecular oxygen to water. This process results in the pumping of four protons across the membrane which are used in the proton gradient powered synthesis of ATP. The oxidase contains two heme a cofactors and three copper atoms as well as other bound ions. [Energy metabolism, Electron transport] 199 matched cddid_all.tbl CDD TIGR02867 TIGR02867 274330 spore_II_P stage II sporulation protein P. Stage II sporulation protein P is a protein of the endospore formation program in a number of lineages in the Firmicutes (low-GC Gram-positive bacteria). It is expressed in the mother cell compartment, under control of Sigma-E. SpoIIP, along with SpoIIM and SpoIID, is one of three major proteins involved in engulfment of the forespore by the mother cell. This protein family is named for the single member in Bacillus subtilis, although most sporulating bacteria have two members. [Cellular processes, Sporulation and germination] 196 matched cddid_all.tbl CDD TIGR02868 TIGR02868 274331 CydC thiol reductant ABC exporter, CydC subunit. The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain (pfam00664) and a C-terminal ATP-binding domain (pfam00005). In E. coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in export of redox-active thiol compounds such as cysteine and glutathione. The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components. The genes used as the seed members for this model are all either found in the gammproteobacterial context or the CydABCD context. All members of this family scoring above trusted at the time of its creation were from genomes which encode a cytochrome bd complex. 530 matched cddid_all.tbl CDD TIGR02869 TIGR02869 213747 spore_SleB spore cortex-lytic enzyme. Members of this protein family are the spore cortex-lytic enzyme SleB from Bacillus subtilis and other Gram-positive, endospore-forming bacterial species. This protein is stored in an inactive form in the spore and activated during germination. [Cellular processes, Sporulation and germination] 200 matched cddid_all.tbl CDD TIGR02870 TIGR02870 274332 spore_II_D stage II sporulation protein D. Stage II sporulation protein D (SpoIID) is a protein of the endospore formation program in a number of lineages in the Firmicutes (low-GC Gram-positive bacteria). It is expressed in the mother cell compartment, under control of Sigma-E. SpoIID, along with SpoIIM and SpoIIP, is one of three major proteins involved in engulfment of the forespore by the mother cell. [Cellular processes, Sporulation and germination] 338 matched cddid_all.tbl CDD TIGR02871 TIGR02871 274333 spore_ylbJ sporulation integral membrane protein YlbJ. Members of this protein family are found exclusively in Firmicutes (low-GC Gram-positive bacterial) and are known from studies in Bacillus subtilis to be part of the sigma-E regulon. Mutation leads to a sporulation defect, confirming that members of this protein family, YlbJ, are sporulation proteins. This protein appears to be universal among endospore-forming bacteria, but is encoded by a pair ORFs distant from eash other in Symbiobacterium thermophilum IAM14863. [Cellular processes, Sporulation and germination] 362 matched cddid_all.tbl CDD TIGR02872 TIGR02872 274334 spore_ytvI sporulation integral membrane protein YtvI. Three lines of evidence show this protein to be involved in sporulation. First, it is under control of a sporulation-specific sigma factor, sigma-E. Second, mutation leads to a sporulation defect. Third, it if found in exactly those genomes whose bacteria are capable of sporulation, except for being absent in Clostridium acetobutylicum ATCC824. This protein has extensive hydrophobic regions and is likely an integral membrane protein. [Cellular processes, Sporulation and germination] 341 matched cddid_all.tbl CDD TIGR02873 TIGR02873 131920 spore_ylxY probable sporulation protein, polysaccharide deacetylase family. Members of this protein family are most closely related to TIGR02764, a subset of polysaccharide deacetylase family proteins found in a species if and only if the species forms endospores like those of Bacillus subtilis or Clostridium tetani. This family is likewise restricted to spore-formers, but is not universal among them in having sequences with full-length matches to the model. [Energy metabolism, Biosynthesis and degradation of polysaccharides, Cellular processes, Sporulation and germination] 268 matched cddid_all.tbl CDD TIGR02874 TIGR02874 131921 spore_ytfJ sporulation protein YtfJ. Members of this protein family, exemplified by YtfJ of Bacillus subtilis, are encoded by bacterial genomes if and only if the species is capable of endospore formation. YtfJ was confirmed in spores of Bacillus subtilis; it appears to be expressed in the forespore under control of SigF (see ). [Cellular processes, Sporulation and germination] 125 matched cddid_all.tbl CDD TIGR02875 TIGR02875 131922 spore_0_A sporulation transcription factor Spo0A. Spo0A, the stage 0 sporulation protein A, is a transcription factor critical for the initiation of sporulation. It contains a response regulator receiver domain (pfam00072). In Bacillus subtilis, it works together with response regulator Spo0F and the phosphotransferase Spo0B, both of which are missing from at least some sporulating species and thus not part of the endospore forming bacteria minimal gene set. Spo0A, however, is universal among endospore-forming species. [Cellular processes, Sporulation and germination] 262 matched cddid_all.tbl CDD TIGR02876 TIGR02876 274335 spore_yqfD sporulation protein YqfD. YqfD is part of the sigma-E regulon in the sporulation program of endospore-forming Gram-positive bacteria. Mutation results in a sporulation defect in Bacillus subtilis. Members are found in all currently known endospore-forming bacteria, including the genera Bacillus, Symbiobacterium, Carboxydothermus, Clostridium, and Thermoanaerobacter. [Cellular processes, Sporulation and germination] 382 matched cddid_all.tbl CDD TIGR02877 TIGR02877 274336 spore_yhbH sporulation protein YhbH. This protein family, typified by YhbH in Bacillus subtilis, is found in nearly every endospore-forming bacterium and in no other genome (but note that the trusted cutoff score is set high to exclude a single high-scoring sequence from Nitrosococcus oceani ATCC 19707, which is classified in the Gammaproteobacteria). The gene in Bacillus subtilis was shown to be in the regulon of the sporulation sigma factor, sigma-E, and its mutation was shown to create a sporulation defect. [Cellular processes, Sporulation and germination] 371 matched cddid_all.tbl CDD TIGR02878 TIGR02878 131925 spore_ypjB sporulation protein YpjB. Members of this protein, YpjB, family are restricted to a subset of endospore-forming bacteria, including Bacillus species but not CLostridium or some others. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon, where sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect. This protein family is not, however, a part of the endospore formation minimal gene set. [Cellular processes, Sporulation and germination] 233 matched cddid_all.tbl CDD TIGR02880 TIGR02880 200217 cbbX_cfxQ probable Rubsico expression protein CbbX. Proteins in this family are now designated CbbX. Some previously were CfxQ (carbon fixation Q). Its gene is often found immmediately downstream of the Rubisco large and small chain genes, and it is suggested to be necessary for Rubisco expression. CbbX has been shown to be necessary for photoautotrophic growth. This protein belongs to the larger family of pfam00004, ATPase family Associated with various cellular Activities. Within that larger family, members of this family are most closely related to the stage V sporulation protein K, or SpoVK, in endospore-forming bacteria such as Bacillus subtilis. 284 matched cddid_all.tbl CDD TIGR02881 TIGR02881 163057 spore_V_K stage V sporulation protein K. Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group. [Cellular processes, Sporulation and germination] 261 matched cddid_all.tbl CDD TIGR02882 TIGR02882 131928 QoxB cytochrome aa3 quinol oxidase, subunit I. This family (QoxB) encodes subunit I of the aa3-type quinone oxidase, one of several bacterial terminal oxidases. This complex couples oxidation of reduced quinones with the reduction of molecular oxygen to water and the pumping of protons to form a proton gradient utilized for ATP production. aa3-type oxidases contain two heme a cofactors as well as copper atoms in the active site. [Energy metabolism, Electron transport] 643 matched cddid_all.tbl CDD TIGR02883 TIGR02883 274337 spore_cwlD N-acetylmuramoyl-L-alanine amidase CwlD. Members of this protein family are the CwlD family of N-acetylmuramoyl-L-alanine amidase. This family has been called the germination-specific N-acetylmuramoyl-L-alanine amidase. CwlD is required, along with the putative deactylase PdaA, to make muramic delta-lactam, a novel peptidoglycan constituent found only in spores. CwlD mutants show a germination defect. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan, Cellular processes, Sporulation and germination] 189 matched cddid_all.tbl CDD TIGR02884 TIGR02884 131930 spore_pdaA delta-lactam-biosynthetic de-N-acetylase. Muramic delta-lactam is an unusual constituent of peptidoglycan, found only in bacterial spores in the peptidoglycan wall, or spore cortex. The proteins in this family are PdaA (yfjS), a member of a larger family of polysaccharide deacetylases, and are specificially involved in delta-lactam biosynthesis. PdaA acts immediately after CwlD, an N-acetylmuramoyl-L-alanine amidase and performs a de-N-acetylation. PdaA may also perform the following transpeptidation for lactam ring formation, as heterologous expression in E. coli of CwlD and PdaA together is sufficient for delta-lactam production. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan, Cellular processes, Sporulation and germination] 224 matched cddid_all.tbl CDD TIGR02885 TIGR02885 131931 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore. [Transcription, Transcription factors, Cellular processes, Sporulation and germination] 231 matched cddid_all.tbl CDD TIGR02886 TIGR02886 131932 spore_II_AA anti-sigma F factor antagonist. The anti-sigma F factor antagonist, also called stage II sporulation protein AA, is a protein universal among endospore-forming bacteria, all of which belong to the Firmcutes [Regulatory functions, Protein interactions, Cellular processes, Sporulation and germination] 106 matched cddid_all.tbl CDD TIGR02887 TIGR02887 274338 spore_ger_x_C germination protein, Ger(x)C family. Members of this protein family are restricted to endospore-forming members of the Firmicutes lineage of bacteria, including the genera Bacillus, Clostridium, Thermoanaerobacter, Carboxydothermus, etc. Members are nearly all predicted lipoproteins and belong to probable transport operons, some of which have been characterized as crucial to germination in response to alanine. Members typically have been gene symbols gerKC, gerAC, gerYC, etc. [Transport and binding proteins, Amino acids, peptides and amines, Cellular processes, Sporulation and germination] 371 matched cddid_all.tbl CDD TIGR02888 TIGR02888 274339 spore_YlmC_YmxH sporulation protein, YlmC/YmxH family. Members of this family belong to the broader family of PRC-barrel domain proteins (see pfam05239), but are found only in endospore-forming bacteria of the Firmicutes lineage. Most such species have exactly two members of this family and all have at least one; the function is unknown. One of two members from Bacillus subtilis, YmxH, is strongly induced by the mother cell-specific sigma-E factor. [Cellular processes, Sporulation and germination] 76 matched cddid_all.tbl CDD TIGR02889 TIGR02889 131935 spore_YpeB germination protein YpeB. Members of this family are YpeB, a protein usually encoded with the putative spore-cortex-lytic enzyme SleB and required, together with SleB, for normal germination. This family is retricted to endospore-forming species in the Firmicutes lineage of bacteria, and found in all such species to date except Clostridium perfringens. The matching phenotypes of mutants in SleB (called a lytic transglycosylase) and YpeB suggests that YpeB is necessary to allow SleB to function. [Cellular processes, Sporulation and germination] 435 matched cddid_all.tbl CDD TIGR02890 TIGR02890 274340 bacill_yteA regulatory protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to Pfam family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. Smaller proteins from the proteobacteria with just the N-terminal domain, including DksA and DksA2 are RNA polymerase-binding regulatory proteins even if the Zn-binding site is not conserved. [Unknown function, General] 159 matched cddid_all.tbl CDD TIGR02891 TIGR02891 213748 CtaD_CoxA cytochrome c oxidase, subunit I. This large family represents subunit I's (CtaD, CoxA, CaaA) of cytochrome c oxidases of bacterial origin. Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Subunits I-III form the functional core of the enzyme complex. Subunit I is the catalytic subunit of the enzyme. Electrons originating in cytochrome c are transferred via the copper A center of subunit II and heme a of subunit I to the bimetallic center formed by heme a3 and copper B. This cytochrome c oxidase shows proton pump activity across the membrane in addition to the electron transfer. In the bacilli an apparent split (paralogism) has created a sister clade (TIGR02882) encoding subunits (QoxA) of the aa3-type quinone oxidase complex which reacts directly with quinones, bypassing the interaction with soluble cytochrome c. This model attempts to exclude these sequences, placing them between the trusted and noise cutoffs. These families, as well as archaeal and eukaryotic cytochrome c subunit I's are included within the superfamily model, pfam00115. [Energy metabolism, Electron transport] 499 matched cddid_all.tbl CDD TIGR02892 TIGR02892 274341 spore_yabP sporulation protein YabP. Members of this protein family are the YabP protein of the bacterial sporulation program, as found in Bacillus subtilis, Clostridium tetani, and other spore-forming members of the Firmicutes. In Bacillus subtilis, a yabP single mutant appears to sporulate and germinate normally (), but is in an operon with yabQ (essential for formation of the spore cortex), it near-universal among endospore-forming bacteria, and is found nowhere else. It is likely, therefore, that YabP does have a function in sporulation or germination, one that is either unappreciated or partially redundant with that of another protein. [Cellular processes, Sporulation and germination] 85 matched cddid_all.tbl CDD TIGR02893 TIGR02893 131939 spore_yabQ spore cortex biosynthesis protein YabQ. YabQ, a protein predicted to span the membrane several times, is found in exactly those genomes whose species perform sporulation in the style of Bacillus subtilis, Clostridium tetani, and others of the Firmicutes. Mutation of this sigma(E)-dependent gene blocks development of the spore cortex. The length of the C-terminal region, including some hydrophobic regions, is rather variable between members. [Cellular processes, Sporulation and germination] 130 matched cddid_all.tbl CDD TIGR02894 TIGR02894 274342 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO. [Regulatory functions, DNA interactions, Cellular processes, Sporulation and germination] 161 matched cddid_all.tbl CDD TIGR02895 TIGR02895 131941 spore_sigI RNA polymerase sigma-I factor. Members of this sigma factor protein family are strictly limited to endospore-forming species in the Firmicutes lineage of bacteria, but are not universally present among such species. Sigma-I was shown to be induced by heat shock () in Bacillus subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation (). [Transcription, Transcription factors, Cellular processes, Sporulation and germination] 218 matched cddid_all.tbl CDD TIGR02896 TIGR02896 131942 spore_III_AF stage III sporulation protein AF. This family represents the stage III sporulation protein AF of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of this protein is poorly conserved, so only the N-terminal region, which includes two predicted transmembrane domains, is included in the seed alignment. [Cellular processes, Sporulation and germination] 106 matched cddid_all.tbl CDD TIGR02897 TIGR02897 131943 QoxC cytochrome aa3 quinol oxidase, subunit III. This family (QoxC) encodes subunit III of the aa3-type quinone oxidase, one of several bacterial terminal oxidases. This complex couples oxidation of reduced quinones with the reduction of molecular oxygen to water and the pumping of protons to form a proton gradient utilized for ATP production. aa3-type oxidases contain two heme a cofactors as well as copper atoms in the active site. [Energy metabolism, Electron transport] 190 matched cddid_all.tbl CDD TIGR02898 TIGR02898 131944 spore_YhcN_YlaJ sporulation lipoprotein, YhcN/YlaJ family. YhcN and YlaJ are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic 40-residue C-terminal domain that is not included in the seed alignment for this model. A portion of the low-complexity region between the lipoprotein signal sequence and the main conserved region of the protein family was also excised from the seed alignment. [Cellular processes, Sporulation and germination] 158 matched cddid_all.tbl CDD TIGR02899 TIGR02899 131945 spore_safA spore coat assembly protein SafA. SafA (YrbB) (SafA) of Bacillus subtilis is a protein found at the interface of the spore cortex and spore coat, and is dependent on SpoVID for its localization. This model is based on the N-terminal LysM (lysin motif) domain (see pfamAM model pfam01476) of SafA and, from several other spore-forming species, the protein with the most similar N-terminal region. However, this set of proteins differs greatly in C-terminal of the LysM domaim; blocks of 12-residue and 13-residue repeats are found in the Bacillus cereus group, tandem LysM domains in Thermoanaerobacter tengcongensis MB4, etc. in which one of which is found in most examples of endospore-forming bacteria. [Cellular processes, Sporulation and germination] 44 matched cddid_all.tbl CDD TIGR02900 TIGR02900 274343 spore_V_B stage V sporulation protein B. SpoVB is the stage V sporulation protein B of the bacterial endopore formation program in Bacillus subtilis and various other Firmcutes. It is nearly universal among endospore-formers. Paralogs with rather high sequence similarity to SpoVB exist, including YkvU in B. subtilis and a number of proteins in the genus Clostridium. [Cellular processes, Sporulation and germination] 488 matched cddid_all.tbl CDD TIGR02901 TIGR02901 200218 QoxD cytochrome aa3 quinol oxidase, subunit IV. This family (QoxD) encodes subunit IV of the aa3-type quinone oxidase, one of several bacterial terminal oxidases. This complex couples oxidation of reduced quinones with the reduction of molecular oxygen to water and the pumping of protons to form a proton gradient utilized for ATP production. aa3-type oxidases contain two heme a cofactors as well as copper atoms in the active site. [Energy metabolism, Electron transport] 94 matched cddid_all.tbl CDD TIGR02902 TIGR02902 131948 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis. [Protein fate, Degradation of proteins, peptides, and glycopeptides, Cellular processes, Sporulation and germination] 531 matched cddid_all.tbl CDD TIGR02903 TIGR02903 274344 spore_lon_C ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC. [Protein fate, Degradation of proteins, peptides, and glycopeptides, Cellular processes, Sporulation and germination] 615 matched cddid_all.tbl CDD TIGR02904 TIGR02904 274345 spore_ysxE spore coat protein YsxE. Members of this family are homologs of the Bacillus subtilis spore coat protein CotS. Members of this family, designated YsxE, are found only in the family Bacillaceae, from among the endospore-forming members of the Firmicutes branch of the Bacteria. As a rule, the ysxE gene is found immediately downstream of spoVID, a gene necessary for spore coat assembly. The protein has been shown to be part of the spore coat. [Cellular processes, Sporulation and germination] 309 matched cddid_all.tbl CDD TIGR02905 TIGR02905 131951 spore_yutH spore coat protein YutH. Members of this family are homologs of the Bacillus subtilis spore coat protein CotS. Members of this family, designated YutH, are found only in the family Bacillaceae from among the endospore-forming members of the Firmicutes branch of the Bacteria. [Cellular processes, Sporulation and germination] 313 matched cddid_all.tbl CDD TIGR02906 TIGR02906 131952 spore_CotS spore coat protein, CotS family. Members of this family include the spore coat proteins CotS and YtaA from Bacillus subtilis and, from other endospore-forming bacteria, homologs that are more closely related to these two than to the spore coat proteins YutH and YsxE. The CotS family is more broadly distributed than YutH or YsxE, but still is not universal among spore-formers. [Cellular processes, Sporulation and germination] 313 matched cddid_all.tbl CDD TIGR02907 TIGR02907 274346 spore_VI_D stage VI sporulation protein D. SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation. [Cellular processes, Sporulation and germination] 338 matched cddid_all.tbl CDD TIGR02908 TIGR02908 131954 CoxD_Bacillus cytochrome c oxidase, subunit IVB. This model represents a small clade of cytochrome oxidase subunit IV's found in the Bacilli. [Energy metabolism, Electron transport] 110 matched cddid_all.tbl CDD TIGR02909 TIGR02909 131955 spore_YkwD uncharacterized protein, YkwD family. Members of this protein family represent a subset of those belonging to pfam00188 (SCP-like extracellular protein). Based on currently cuttoffs for this model, all member proteins are found in Bacteria capable of endospore formation. Members include a named but uncharacterized protein, YkwD of Bacillus subtilis. Only the C-terminal region is well-conserved and is included in the seed alignment for this model. Three members of this family have an N-terminal domain homologous to the spore coat assembly protein SafA. 127 matched cddid_all.tbl CDD TIGR02910 TIGR02910 131956 sulfite_red_A sulfite reductase, subunit A. Members of this protein family include the A subunit, one of three subunits, of the anaerobic sulfite reductase of Salmonella, and close homologs from various Clostridum species, where the three-gene neighborhood is preserved. Two such gene clusters are found in Clostridium perfringens, but it may be that these sets of genes correspond to the distinct assimilatory and dissimilatory forms as seen in Clostridium pasteurianum. Note that any one of these enzymes may have secondary substates such as NH2OH, SeO3(2-), and SO3(2-). Heterologous expression of the anaerobic sulfite reductase of Salmonella confers on Escherichia coli the ability to produce hydrogen sulfide gas from sulfite. [Central intermediary metabolism, Sulfur metabolism] 334 matched cddid_all.tbl CDD TIGR02911 TIGR02911 131957 sulfite_red_B sulfite reductase, subunit B. Members of this protein family include the B subunit, one of three subunits, of the anaerobic sulfite reductase of Salmonella, and close homologs from various Clostridum species, where the three-gene neighborhood is preserved. Two such gene clusters are found in Clostridium perfringens, but it may be that these sets of genes correspond to the distinct assimilatory and dissimilatory forms as seen in Clostridium pasteurianum. [Central intermediary metabolism, Sulfur metabolism] 261 matched cddid_all.tbl CDD TIGR02912 TIGR02912 131958 sulfite_red_C sulfite reductase, subunit C. Members of this protein family include the C subunit, one of three subunits, of the anaerobic sulfite reductase of Salmonella, and close homologs from various Clostridum species, where the three-gene neighborhood is preserved. Two such gene clusters are found in Clostridium perfringens, but it may be that these sets of genes correspond to the distinct assimilatory and dissimilatory forms as seen in Clostridium pasteurianum. Note that any one of these enzymes may have secondary substates such as NH2OH, SeO3(2-), and SO3(2-). Heterologous expression of the anaerobic sulfite reductase of Salmonella confers on Escherichia coli the ability to produce hydrogen sulfide gas from sulfite. [Central intermediary metabolism, Sulfur metabolism] 314 matched cddid_all.tbl CDD TIGR02913 TIGR02913 131959 HAF_rpt probable extracellular repeat, HAF family. The model for this family detects a homology domain of about 40 amino acids. Member proteins always have a least two tandem copies and as many as seven. The spacing between repeats as defined here usually is four residues exactly. This repeat is named for a tripeptide motif HAF found in most members. Some members proteins are found in species with no outer membrane (archaea and Gram-positive bacteria) while others have C-terminal autotransporter domains that suggest that the repeat region is transported across the outer membrane. This domain seems likely to be an extracellular protein repeat. 39 matched cddid_all.tbl CDD TIGR02914 TIGR02914 274347 EpsI_fam EpsI family protein. In Methylobacillus sp strain 12S, EpsI is encoded immediately downstream of the multiple-membrane-spanning putative transporter EpsH, and is predicted to be a periplasmic protein involved in, but not required for, expression of the exopolysaccharide methanolan. In a number of other species, protein homologous to EpsI is encoded either next to EpsH or, more often, combined in a fused gene. We have proposed renaming EpsH, or the EpsHI fusion protein, to exosortase, based on its phylogenetic association with the PEP-CTERM proposed protein targeting signal. [Transport and binding proteins, Unknown substrate] 174 matched cddid_all.tbl CDD TIGR02915 TIGR02915 274348 PEP_resp_reg PEP-CTERM-box response regulator transcription factor. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC (see SP|Q06065). These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158). [Regulatory functions, DNA interactions] 445 matched cddid_all.tbl CDD TIGR02916 TIGR02916 274349 PEP_his_kin putative PEP-CTERM system histidine kinase. Members of this protein family have a novel N-terminal domain, a single predicted membrane-spanning helix, and a predicted cystosolic histidine kinase domain. We designate this protein PrsK, and its companion DNA-binding response regulator protein (TIGR02915) PrsR. These predicted signal-transducing proteins appear to enable enhancer-dependent transcriptional activation. The prsK gene is often associated with exopolysaccharide biosynthesis genes. [Protein fate, Protein and peptide secretion and trafficking, Signal transduction, Two-component systems] 679 matched cddid_all.tbl CDD TIGR02917 TIGR02917 274350 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator. 899 matched cddid_all.tbl CDD TIGR02918 TIGR02918 131964 TIGR02918 accessory Sec system glycosylation protein GtfA. Members of this protein family are found only in Gram-positive bacteria of the Firmicutes lineage, including several species of Staphylococcus, Streptococcus, and Lactobacillus. Members are associated with glycosylation of serine-rich glycoproteins exported by the accessory Sec system. [Protein fate, Protein modification and repair] 500 matched cddid_all.tbl CDD TIGR02919 TIGR02919 274351 TIGR02919 accessory Sec system glycosyltransferase GtfB. Members of this protein family are found only in Gram-positive bacteria of the Firmicutes lineage, including several species of Staphylococcus, Streptococcus, and Lactobacillus. [Protein fate, Protein modification and repair] 438 matched cddid_all.tbl CDD TIGR02920 TIGR02920 131966 acc_sec_Y2 accessory Sec system translocase SecY2. Members of this family are restricted to the Firmicutes lineage (low-GC Gram-positive bacteria) and appear to be paralogous to, and much more divergent than, the preprotein translocase SecY. Members include the SecY2 protein of the accessory Sec system in Streptococcus gordonii, involved in export of the highly glycosylated platelet-binding protein GspB. [Protein fate, Protein and peptide secretion and trafficking] 395 matched cddid_all.tbl CDD TIGR02921 TIGR02921 131967 PEP_integral PEP-CTERM family integral membrane protein. Members of this protein family, found in eighteen genera so far, have a PEP-CTERM sequence at the carboxyl-terminus (see model TIGR02595), but are unusual among PEP-CTERM proteins in having multiple predicted transmembrane segments. The function is unknown. It is proposed that an exosortase (see TIGR02602), recognizes and cleaves PEP-CTERM proteins in a manner analogous to the cleavage of LPXTG proteins by sortase (see Haft, et al., 2006). In at least six species, a gene encoding what appears to be a dedicated (single target) exosortase is adjacent. In that subset, the PEP-CTERM motif takes the form VPEPxxWxL. 952 matched cddid_all.tbl CDD TIGR02922 TIGR02922 131968 TIGR02922 TIGR02922 family protein. Two members of this family are found in Colwellia psychrerythraea 34H and one each in various other species of Colwellia and Shewanella. One member from C. psychrerythraea is of special interest because it is preceded by the same cis-regulatory site as a number of genes that have the PEP-CTERM domain described by TIGR02595. [Hypothetical proteins, Conserved] 67 matched cddid_all.tbl CDD TIGR02923 TIGR02923 274352 AhaC "ATP synthase A1, C subunit. The A1/A0 ATP synthase is homologous to the V-type (V1/V0, vacuolar) ATPase, but functions in the ATP synthetic direction as does the F1/F0 ATPase of bacteria. The C subunit is part of the hydrophilic A1 ""stalk"" complex (AhaABCDEFG), which is the site of ATP generation and is coupled to the membrane-embedded proton translocating A0 complex." 343 matched cddid_all.tbl CDD TIGR02924 TIGR02924 274353 ICDH_alpha isocitrate dehydrogenase. This family of mainly alphaproteobacterial enzymes is a member of the isocitrate/isopropylmalate dehydrogenase superfamily described by pfam00180. Every member of the seed of this model appears to have a TCA cycle lacking only a determined isocitrate dehydrogenase. The precise identity of the cofactor (NADH -- 1.1.1.41 vs. NADPH -- 1.1.1.42) is unclear. [Energy metabolism, TCA cycle] 473 matched cddid_all.tbl CDD TIGR02925 TIGR02925 131971 cis_trans_EpsD peptidyl-prolyl cis-trans isomerase, EpsD family. Members of this family belong to the peptidyl-prolyl cis-trans isomerase family and are found in loci associated with exopolysaccharide biosynthesis. All members are encoded near a homolog of EpsH, as detected by TIGR02602. 232 matched cddid_all.tbl CDD TIGR02926 TIGR02926 131972 AhaH "ATP synthase archaeal, H subunit. he A1/A0 ATP synthase is homologous to the V-type (V1/V0, vacuolar) ATPase, but functions in the ATP synthetic direction as does the F1/F0 ATPase of bacteria. The hydrophilic A1 ""stalk"" complex (AhaABCDEFG) is the site of ATP generation and is coupled to the membrane-embedded proton translocating A0 complex. It is unclear precisely where AhaH fits into these complexes." 85 matched cddid_all.tbl CDD TIGR02927 TIGR02927 200219 SucB_Actino 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase. This model represents an Actinobacterial clade of E2 enzyme, a component of the 2-oxoglutarate dehydrogenase complex involved in the TCA cycle. These proteins have multiple domains including the catalytic domain (pfam00198), one or two biotin domains (pfam00364) and an E3-component binding domain (pfam02817). 579 matched cddid_all.tbl CDD TIGR02928 TIGR02928 274354 TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other. [DNA metabolism, DNA replication, recombination, and repair] 365 matched cddid_all.tbl CDD TIGR02929 TIGR02929 131975 anfG_nitrog Fe-only nitrogenase, delta subunit. Nitrogenase, also called dinitrogenase, is the enzyme of biological nitrogen fixation. The most wide-spread and most efficient nitrogenase contains a molybdenum cofactor. This protein family, AnfG, represents the delta subunit of the Fe-only alternative nitrogenase. It is homologous to VnfG, the delta subunit of the V-containing (vanadium) nitrogenase. [Central intermediary metabolism, Nitrogen fixation] 109 matched cddid_all.tbl CDD TIGR02930 TIGR02930 131976 vnfG_nitrog V-containing nitrogenase, delta subunit. Nitrogenase is the enzyme of biological nitrogen fixation. The most wide-spread and most efficient nitrogenase contains a molybdenum cofactor. This protein family, VnfG, represents the delta subunit of the V-containing (vanadium) alternative nitrogenase. It is homologous to AnfG, the delta subunit of the Fe-only nitrogenase. [Central intermediary metabolism, Nitrogen fixation] 109 matched cddid_all.tbl CDD TIGR02931 TIGR02931 131977 anfK_nitrog Fe-only nitrogenase, beta subunit. Nitrogenase is the enzyme of biological nitrogen fixation. The most wide-spread and most efficient nitrogenase contains a molybdenum cofactor. This protein family, AnfK, represents the beta subunit of the iron-only alternative nitrogenase. It is homologous to NifK and VnfK, of the molybdenum-containing and the vanadium (V)-containing types, respectively. [Central intermediary metabolism, Nitrogen fixation] 461 matched cddid_all.tbl CDD TIGR02932 TIGR02932 131978 vnfK_nitrog V-containing nitrogenase, beta subunit. Nitrogenase is the enzyme of biological nitrogen fixation. The most wide-spread and most efficient nitrogenase contains a molybdenum cofactor. This protein family, VnfK, represents the beta subunit of the vanadium (V)-containing alternative nitrogenase. It is homologous to NifK and AnfK, of the molybdenum-containing and the iron (Fe)-only types, respectively. [Central intermediary metabolism, Nitrogen fixation] 457 matched cddid_all.tbl CDD TIGR02933 TIGR02933 131979 nifM_nitrog nitrogen fixation protein NifM. Members of this protein family, found in a subset of nitrogen-fixing bacteria, are the nitrogen fixation protein NifM. NifM, homologous to peptidyl-prolyl cis-trans isomerases, appears to be an accessory protein for NifH, the Fe protein, also called component II or dinitrogenase reductase, of nitrogenase. [Central intermediary metabolism, Nitrogen fixation] 256 matched cddid_all.tbl CDD TIGR02934 TIGR02934 274355 nifT_nitrog probable nitrogen fixation protein FixT. This largely uncharacterized protein family is assigned a role in nitrogen fixation by two criteria. First, its gene occurs, generally, among genes essential for expression of active nitrogenase. Second, its phylogenetic profile closely matches that of nitrogen-fixing bacteria. However, mutational studies in Klebsiella pneumoniae failed to demonstrate any phenotype for deletion or overexpression of the protein. 68 matched cddid_all.tbl CDD TIGR02935 TIGR02935 131981 TIGR02935 probable nitrogen fixation protein. Members of this protein family, called DUF269 by pfam03270, are strictly limited to nitrogen-fixing species, although not universal among them. The gene typically is found next to the nifX gene (see TIGRFAMs model TIGR02663). [Central intermediary metabolism, Nitrogen fixation] 140 matched cddid_all.tbl CDD TIGR02936 TIGR02936 274356 fdxN_nitrog ferredoxin III, nif-specific. Members of this family are homodimeric ferredoxins from nitrogen fixation regions of many nitrogen-fixing bacteria. As characterized in Rhodobacter capsulatus, these proteins are homodimeric, with two 4Fe-4S clusters bound per monomer. Although nif-specific, this protein family is not usiveral, as other nitrogenase systems may substitute flavodoxins, or different types of ferredoxin. [Central intermediary metabolism, Nitrogen fixation] 91 matched cddid_all.tbl CDD TIGR02937 TIGR02937 274357 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs. 158 matched cddid_all.tbl CDD TIGR02938 TIGR02938 131984 nifL_nitrog nitrogen fixation negative regulator NifL. NifL is a modulator of the nitrogen fixation positive regulator protein NifA, and is therefore a negative regulator. It binds NifA. NifA and NifL are encoded by adjacent genes. [Central intermediary metabolism, Nitrogen fixation, Regulatory functions, Protein interactions] 494 matched cddid_all.tbl CDD TIGR02939 TIGR02939 131985 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU. 190 matched cddid_all.tbl CDD TIGR02940 TIGR02940 274358 anfO_nitrog Fe-only nitrogenase accessory protein AnfO. Members of this protein family, called Anf1 in Rhodobacter capsulatus and AnfO in Azotobacter vinelandii, are found only in species with the Fe-only nitrogenase and are encoded immediately downstream of the structural genes in the above named species. 214 matched cddid_all.tbl CDD TIGR02941 TIGR02941 131987 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria, and Bacillus. 255 matched cddid_all.tbl CDD TIGR02943 TIGR02943 274359 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. 188 matched cddid_all.tbl CDD TIGR02944 TIGR02944 131989 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Regulatory functions, DNA interactions] 130 matched cddid_all.tbl CDD TIGR02945 TIGR02945 131990 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 99 matched cddid_all.tbl CDD TIGR02946 TIGR02946 274360 acyl_WS_DGAT acyltransferase, WS/DGAT/MGAT. This bacteria-specific protein family includes a characterized, homodimeric, broad specificity acyltransferase from Acinetobacter sp. strain ADP1, active as wax ester synthase, as acyl coenzyme A:diacylglycerol acyltransferase, and as acyl-CoA:monoacylglycerol acyltransferase. [Unknown function, Enzymes of unknown specificity] 446 matched cddid_all.tbl CDD TIGR02947 TIGR02947 131992 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon. 193 matched cddid_all.tbl CDD TIGR02948 TIGR02948 131993 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales. 187 matched cddid_all.tbl CDD TIGR02949 TIGR02949 188261 anti_SigH_actin anti-sigma factor, TIGR02949 family. This group of anti-sigma factors are associated in an apparent operon with a family of sigma-70 family sigma factors (TIGR02947). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria. [Transcription, Transcription factors] 84 matched cddid_all.tbl CDD TIGR02950 TIGR02950 274361 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: 154 matched cddid_all.tbl CDD TIGR02951 TIGR02951 131996 DMSO_dmsB DMSO reductase, iron-sulfur subunit. This family consists of the iron-sulfur subunit, or chain B, of an enzyme called the anaerobic dimethyl sulfoxide reductase. Chains A and B are catalytic, while chain C is a membrane anchor. 161 matched cddid_all.tbl CDD TIGR02952 TIGR02952 131997 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages. 170 matched cddid_all.tbl CDD TIGR02953 TIGR02953 131998 penta_MxKDx pentapeptide MXKDX repeat protein. Members of this protein family are small bacterial proteins, each with an N-terminal signal sequence followed by up to 11 imperfect repeats of a pentapeptide. The pentapeptide repeat usually follows the form Met-Xaa-Lys-Asp-Xaa. 75 matched cddid_all.tbl CDD TIGR02954 TIGR02954 213752 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species. 169 matched cddid_all.tbl CDD TIGR02955 TIGR02955 132000 TMAO_TorT TMAO reductase system periplasmic protein TorT. Members of this family are the periplasmic protein TorT which, together with the the TorS/TorR histidine kinase/response regulator system, regulates expression of the torCAD operon for trimethylamine N-oxide reductase (TMAO reductase). It appears to bind an inducer for TMAO reductase, and shows homology to a periplasmic D-ribose binding protein. 295 matched cddid_all.tbl CDD TIGR02956 TIGR02956 274362 TMAO_torS TMAO reductase sytem sensor TorS. This protein, TorS, is part of a regulatory system for the torCAD operon that encodes the pterin molybdenum cofactor-containing enzyme trimethylamine-N-oxide (TMAO) reductase (TorA), a cognate chaperone (TorD), and a penta-haem cytochrome (TorC). TorS works together with the inducer-binding protein TorT and the response regulator TorR. TorS contains histidine kinase ATPase (pfam02518), HAMP (pfam00672), phosphoacceptor (pfam00512), and phosphotransfer (pfam01627) domains and a response regulator receiver domain (pfam00072). [Signal transduction, Two-component systems] 968 matched cddid_all.tbl CDD TIGR02957 TIGR02957 132002 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152. 281 matched cddid_all.tbl CDD TIGR02959 TIGR02959 132004 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded). 170 matched cddid_all.tbl CDD TIGR02960 TIGR02960 132005 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. 324 matched cddid_all.tbl CDD TIGR02961 TIGR02961 274363 allantoicase allantoicase. Members of this family are the enzyme allantoicase (EC 3.5.3.4), also called allantoate amidinohydrolase. This enzyme hydrolyzes allantoate to (S)-ureidoglycolate and urea; it can also degrade (R)-ureidoglycolate to glyoxylate and urea. Allantoinase (EC 3.5.2.5) hydrolyzes (S)-allantoin (a xanthine metabolite, via urate) to allantoate. Allantoate can then be degraded either by this enzyme, allantoicase, or by allantoate deiminase (EC 3.5.3.9). Members of the seed alignment for this model were taken from BRENDA. Proteins in this family contain two copies of the allantoicase repeat (pfam03561). A different but similarly named enzyme, allantoate amidohydrolase (EC 3.5.3.9), simultaneously breaks down the urea to ammonia and carbon dioxide. [Purines, pyrimidines, nucleosides, and nucleotides, Other, Energy metabolism, Other] 322 matched cddid_all.tbl CDD TIGR02962 TIGR02962 274364 hdxy_isourate hydroxyisourate hydrolase. Members of this family, hydroxyisourate hydrolase, represent a distinct clade of transthyretin-related proteins. Bacterial members typically are encoded next to ureidoglycolate hydrolase and often near either xanthine dehydrogenase or xanthine/uracil permease genes and have been demonstrated to have hydroxyisourate hydrolase activity. In eukaryotes, a clade separate from the transthyretins (a family of thyroid-hormone binding proteins) has also been shown to have HIU hydrolase activity in urate catabolizing organisms. Transthyretin, then, would appear to be the recently diverged paralog of the more ancient HIUH family. [Purines, pyrimidines, nucleosides, and nucleotides, Other] 112 matched cddid_all.tbl CDD TIGR02963 TIGR02963 274365 xanthine_xdhA xanthine dehydrogenase, small subunit. Members of this protein family are the small subunit (or, in eukaryotes, the N-terminal domain) of xanthine dehydrogenase, an enzyme of purine catabolism via urate. The small subunit contains both an FAD and a 2Fe-2S cofactor. Aldehyde oxidase (retinal oxidase) appears to have arisen as a neofunctionalization among xanthine dehydrogenases in eukaryotes and [Purines, pyrimidines, nucleosides, and nucleotides, Other] 467 matched cddid_all.tbl CDD TIGR02964 TIGR02964 274366 xanthine_xdhC xanthine dehydrogenase accessory protein XdhC. Members of this protein family are the accessory protein XdhC for insertion of the molybdenum cofactor into the xanthine dehydrogenase large chain, XdhB, in bacteria. This protein is not part of the mature xanthine dehydrogenase. Xanthine dehydrogenase is an enzyme for purine catabolism, from other purines to xanthine to urate to further breakdown products. [Protein fate, Protein folding and stabilization, Purines, pyrimidines, nucleosides, and nucleotides, Other] 246 matched cddid_all.tbl CDD TIGR02965 TIGR02965 274367 xanthine_xdhB xanthine dehydrogenase, molybdopterin binding subunit. Members of the protein family are the molybdopterin-containing large subunit (or, in, eukaryotes, the molybdopterin-binding domain) of xanthine dehydrogenase, and enzyme that reduces the purine pool by catabolizing xanthine to urate. This model is based primarily on bacterial sequences; it does not manage to include all eukaryotic xanthine dehydrogenases and thereby discriminate them from the closely related enzyme aldehyde dehydrogenase. [Purines, pyrimidines, nucleosides, and nucleotides, Other] 758 matched cddid_all.tbl CDD TIGR02966 TIGR02966 274368 phoR_proteo phosphate regulon sensor kinase PhoR. Members of this protein family are the regulatory histidine kinase PhoR associated with the phosphate ABC transporter in most Proteobacteria. Related proteins from Gram-positive organisms are not included in this model. The phoR gene usually is adjacent to the response regulator phoB gene (TIGR02154). [Signal transduction, Two-component systems] 333 matched cddid_all.tbl CDD TIGR02967 TIGR02967 132012 guan_deamin guanine deaminase. This model describes guanine deaminase, which hydrolyzes guanine to xanthine and ammonia. Xanthine can then be converted to urate by xanthine dehydrogenase, and urate subsequently degraded. In some bacteria, the guanine deaminase gene is found near the xdhABC genes for xanthine dehydrogenase. Non-homologous forms of guanine deaminase also exist, as well as distantly related forms outside the scope of this model. [Purines, pyrimidines, nucleosides, and nucleotides, Other] 401 matched cddid_all.tbl CDD TIGR02968 TIGR02968 274369 succ_dehyd_anc succinate dehydrogenase, hydrophobic membrane anchor protein. In E. coli and many other bacteria, two small, hydrophobic, mutually homologous subunits of succinate dehydrogenase, a TCA cycle enzyme, are SdhC and SdhD. This family is the SdhD, the hydrophobic membrane anchor protein. SdhC is apocytochrome b558, which also plays a role in anchoring the complex. [Energy metabolism, TCA cycle] 105 matched cddid_all.tbl CDD TIGR02969 TIGR02969 132014 mam_aldehyde_ox aldehyde oxidase. Members of this family are mammalian aldehyde oxidase (EC 1.2.3.1) isozymes, closely related to xanthine dehydrogenase/oxidase. 1330 matched cddid_all.tbl CDD TIGR02970 TIGR02970 274370 succ_dehyd_cytB succinate dehydrogenase, cytochrome b556 subunit. In E. coli and many other bacteria, two small, hydrophobic, mutually homologous subunits of succinate dehydrogenase, a TCA cycle enzyme, are SdhC and SdhD. This family is the SdhC, the cytochrome b subunit, called b556 in bacteria and b560 in mitochondria. SdhD (see TIGR02968) is called the hydrophobic membrane anchor subunit, although both SdhC and SdhD participate in anchoring the complex. In some bacteria, this cytochrome b subunit is replaced my a member of the cytochrome b558 family (see TIGR02046). [Energy metabolism, TCA cycle] 120 matched cddid_all.tbl CDD TIGR02971 TIGR02971 213754 heterocyst_DevB ABC exporter membrane fusion protein, DevB family. Members of this protein family are found mostly in the Cyanobacteria, but also in the Planctomycetes. DevB from Anabaena sp. strain PCC 7120 is partially characterized as a membrane fusion protein of the DevBCA ABC exporter, probably a glycolipid exporter, required for heterocyst formation. Most Cyanobacteria have one member only, but Nostoc sp. PCC 7120 has seven members. 327 matched cddid_all.tbl CDD TIGR02972 TIGR02972 132017 TMAO_torE trimethylamine N-oxide reductase system, TorE protein. Members of this small, apparent transmembrane protein are designated TorE and occur in operons for the trimethylamine N-oxide (TMAO) reductase system. Members are closely related to the NapE protein of the related periplasmic nitrate reductase system. It may be that TorE is an integral membrane subunit of a complex with the reductase TorA. [Energy metabolism, Anaerobic] 47 matched cddid_all.tbl CDD TIGR02973 TIGR02973 132018 nitrate_rd_NapE periplasmic nitrate reductase, NapE protein. NapE, homologous to TorE (TIGR02972), is a membrane protein of unknown function that is part of the periplasmic nitrate reductase system; it may be part of the enzyme complex. The periplasmic nitrate reductase allows for nitrate respiration in anaerobic conditions. [Energy metabolism, Anaerobic, Energy metabolism, Electron transport] 42 matched cddid_all.tbl CDD TIGR02974 TIGR02974 274371 phageshock_pspF psp operon transcriptional activator PspF. Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH [Regulatory functions, DNA interactions] 329 matched cddid_all.tbl CDD TIGR02975 TIGR02975 132020 phageshock_pspG phage shock protein G. This protein previously was designated yjbO in E. coli. It is found only in genomes that have the phage shock operon (psp), but only rarely is encoded near other psp genes. The psp regulon is upregulated in response to a number of stress conditions, including ethanol, expression of the filamentous phage secretin protein IV and other secretins, and heat shock. [Cellular processes, Adaptations to atypical conditions] 64 matched cddid_all.tbl CDD TIGR02976 TIGR02976 132021 phageshock_pspB phage shock protein B. This model describes the PspB protein of the psp (phage shock protein) operon, as found in Escherichia coli and many related species. Expression of a phage protein called secretin protein IV, and a number of other stresses including ethanol, heat shock, and defects in protein secretion trigger sigma-54-dependent expression of the phage shock regulon. PspB is both a regulator and an effector protein of the phage shock response. [Cellular processes, Adaptations to atypical conditions] 75 matched cddid_all.tbl CDD TIGR02977 TIGR02977 274372 phageshock_pspA phage shock protein A. Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects. [Cellular processes, Adaptations to atypical conditions] 219 matched cddid_all.tbl CDD TIGR02978 TIGR02978 132023 phageshock_pspC phage shock protein C. All members of this protein family are the phage shock protein PspC. These proteins contain a PspC domain, as do other members of the larger family of proteins described by pfam04024. The phage shock regulon is restricted to the Proteobacteria and somewhat sparsely distributed there. It is expressed, under positive control of a sigma-54-dependent transcription factor, PspF, which binds and is modulated by PspA. Stresses that induce the psp regulon include phage secretin overexpression, ethanol, heat shock, and protein export defects. [Cellular processes, Adaptations to atypical conditions] 121 matched cddid_all.tbl CDD TIGR02979 TIGR02979 132024 phageshock_pspD phage shock protein PspD. Members of this family are phage shock protein PspD, found in a minority of bacteria that carry the defining genes of the phage shock regulon (pspA, pspB, pspC, and pspF). It is found in Escherichia coli, Yersinia pestis, and closely related species, where it is part of the phage shock operon. It is known to be expressed but its function is unknown. [Cellular processes, Adaptations to atypical conditions] 59 matched cddid_all.tbl CDD TIGR02980 TIGR02980 274373 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage. 227 matched cddid_all.tbl CDD TIGR02981 TIGR02981 132026 phageshock_pspE phage shock operon rhodanese PspE. Members of this very narrowly defined protein family are proteins active as rhodanese (EC 2.8.1.1) and found in the extended variants of the phage shock protein (psp operon) in Escherichia coli and a few closely related species. Note that the designation phage shock protein PspE has been applied, incorrectly, in many instances where the genome lacks the phage shock regulon entirely. 101 matched cddid_all.tbl CDD TIGR02982 TIGR02982 274374 heterocyst_DevA ABC exporter ATP-binding subunit, DevA family. Members of this protein family are found mostly in the Cyanobacteria, but also in the Planctomycetes. Cyanobacterial examples are involved in heterocyst formation, by which some fraction of members of the colony undergo a developmental change and become capable of nitrogen fixation. The DevBCA proteins are thought export of either heterocyst-specific glycolipids or an enzyme essential for formation of the laminated layer found in heterocysts. 220 matched cddid_all.tbl CDD TIGR02983 TIGR02983 132028 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives. 162 matched cddid_all.tbl CDD TIGR02984 TIGR02984 274375 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found). 189 matched cddid_all.tbl CDD TIGR02985 TIGR02985 274376 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium. 161 matched cddid_all.tbl CDD TIGR02986 TIGR02986 132031 restrict_Alw26I type II restriction endonuclease, Alw26I/Eco31I/Esp3I family. Members of this family are type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family. Characterized specificities of three members are GGTCTC, CGTCTC, and the shared subsequence GTCTC. [DNA metabolism, Restriction/modification] 424 matched cddid_all.tbl CDD TIGR02987 TIGR02987 274377 met_A_Alw26 type II restriction m6 adenine DNA methyltransferase, Alw26I/Eco31I/Esp3I family. Members of this family are the m6-adenine DNA methyltransferase protein, or domain of a fusion protein that also carries m5 cytosine methyltransferase activity, of type II restriction systems of the Alw26I/Eco31I/Esp3I family. A methyltransferase of this family is alway accompanied by a type II restriction endonuclease from the Alw26I/Eco31I/Esp3I family (TIGR02986) and by an adenine-specific modification methyltransferase. Members of this family are unusual in that regions of similarity to homologs outside this family are circularly permuted. [DNA metabolism, Restriction/modification] 524 matched cddid_all.tbl CDD TIGR02988 TIGR02988 274378 YaaA_near_RecF S4 domain protein YaaA. This small protein has a single S4 domain (pfam01479), as do bacterial ribosomal protein S4, some pseudouridine synthases, tyrosyl-tRNA synthetases. The S4 domain may bind RNA. Members of this protein family are found almost exclusively in the Firmicutes, and almost invariably just a few nucleotides upstream of the gene for the DNA replication and repair protein RecF. The few members of this family that are not near recF are found instead near dnaA and/or dnaN, the usual neighbors of recF, near the origin of replication. The conserved location suggests a possible role in replication in the Firmicutes lineage. [DNA metabolism, DNA replication, recombination, and repair] 59 matched cddid_all.tbl CDD TIGR02989 TIGR02989 274379 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2). 159 matched cddid_all.tbl CDD TIGR02990 TIGR02990 132035 ectoine_eutA ectoine utilization protein EutA. Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti and Silicibacter pomeroyi. It is missing from two other species with the other ectoine transport and utilization genes: Pseudomonas putida and Agrobacterium tumefaciens. 239 matched cddid_all.tbl CDD TIGR02991 TIGR02991 132036 ectoine_eutB ectoine utilization protein EutB. Members of this protein family are EutB, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti, Silicibacter pomeroyi, Agrobacterium tumefaciens, and Pseudomonas putida. Members of this family resemble threonine dehydratases. 317 matched cddid_all.tbl CDD TIGR02992 TIGR02992 132037 ectoine_eutC ectoine utilization protein EutC. Members of this protein family are EutA, a predicted arylmalonate decarboxylase found in a conserved ectoine utilization operon of species that include Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti, Silicibacter pomeroyi, Agrobacterium tumefaciens, and Pseudomonas putida. This family belongs to the ornithine cyclodeaminase/mu-crystallin family (pfam02423). 326 matched cddid_all.tbl CDD TIGR02993 TIGR02993 274380 ectoine_eutD ectoine utilization protein EutD. Members of this family are putative peptidases or hydrolases similar to Xaa-Pro aminopeptidase (pfam00557). They belong to ectoine utilization operons, as found in Sinorhizobium meliloti 1021 (where it is known to be induced by ectoine), Mesorhizobium loti, Silicibacter pomeroyi, Agrobacterium tumefaciens, and Pseudomonas putida. The exact function is unknown. 391 matched cddid_all.tbl CDD TIGR02994 TIGR02994 132039 ectoine_eutE ectoine utilization protein EutE. Members of this family, part of the succinylglutamate desuccinylase / aspartoacylase family (pfam04952), belong to ectoine utilization operons, as found in Sinorhizobium meliloti 1021 (where it the operon is known to be induced by ectoine), Mesorhizobium loti, Silicibacter pomeroyi, Agrobacterium tumefaciens, and Pseudomonas putida. 325 matched cddid_all.tbl CDD TIGR02995 TIGR02995 132040 ectoine_ehuB ectoine/hydroxyectoine ABC transporter solute-binding protein. Members of this family are the extracellular solute-binding proteins of ABC transporters that closely resemble amino acid transporters. The member from Sinorhizobium meliloti is involved in ectoine uptake, both for osmoprotection and for catabolism. All other members of the seed alignment are found associated with ectoine catabolic genes. [Transport and binding proteins, Amino acids, peptides and amines] 275 matched cddid_all.tbl CDD TIGR02996 TIGR02996 274381 rpt_mate_G_obs repeat-companion domain TIGR02996. This model describes an abundant paralogous domain of Gemmata obscuriglobus UQM 2246, a member of the Planctomycetes. The domain also occurs, although rarely, in Myxococcus xanthus DK 1622 and related species. Most member proteins have extensive repeats similar to the leucine-rich repeat, or another repeat class or region of low-complexity sequence. This domain is not repeated, and in Gemmata is usually found at the protein N-terminus. 42 matched cddid_all.tbl CDD TIGR02997 TIGR02997 274382 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393). 298 matched cddid_all.tbl CDD TIGR02998 TIGR02998 132043 RraA_entero "regulator of ribonuclease activity A. This family includes a number of closely related sequences from certain enterobacteria. The E. coli member of this family has been characterized as a regulator of RNase E and its crystal structure has been analyzed. The broader subfamily which includes this equivalog, TIGR01935, was initially classified as a ""hypothetical equivalog"" with the name ""regulator of ribonuclease activity A"" based on the same evidence for this model. It now appears that, considering the second group of enterobacterial sequences within TIGR01935, the functional assignment is unsupported. THIS PROTEIN IS _NOT_ MenG, AKA S-adenosylmethionine: 2-demethylmenaquinone methyltransferase (EC 2.1.-.-). See the references characterizing this as a case of transitive annotation error. [Transcription, Degradation of RNA, Regulatory functions, Protein interactions]" 161 matched cddid_all.tbl CDD TIGR02999 TIGR02999 132044 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five. 183 matched cddid_all.tbl CDD TIGR03000 TIGR03000 274383 plancto_dom_1 Planctomycetes uncharacterized domain TIGR03000. Domains described by this model are found, so far, only in the Planctomycetes (Pirellula sp. strain 1 and Gemmata obscuriglobus), in up to six proteins per genome, and may be duplicated within a protein. The function is unknown. 75 matched cddid_all.tbl CDD TIGR03001 TIGR03001 188267 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired. 244 matched cddid_all.tbl CDD TIGR03002 TIGR03002 274384 outer_YhbN_LptA lipopolysaccharide transport periplasmic protein LptA. Members of this protein family include LptA (previously called YhbN). It was shown to be an essential protein in E. coli, implicated in cell envelope integrity, and to play a role in the delivery of LPS to the outer leaflet of the outer membrane. It works with LptB (formerly yhbG), a homolog of ABC transporter ATP-binding proteins, encoded by an adjacent gene. Numerous homologs in other Proteobacteria are found in a conserved location near lipopolysaccharide inner core biosynthesis genes. This family is related to organic solvent tolerance protein (OstA), though distantly. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides, Transport and binding proteins, Other] 142 matched cddid_all.tbl CDD TIGR03003 TIGR03003 132048 ectoine_ehuD ectoine/hydroxyectoine ABC transporter, permease protein EhuD. Members of this family are presumed to act as permease subunits of ectoine ABC transporters. Operons containing this gene also contain the other genes of the ABC transporter and typically are found next to either ectoine utilization or ectoine biosynthesis operons. 212 matched cddid_all.tbl CDD TIGR03004 TIGR03004 132049 ectoine_ehuC ectoine/hydroxyectoine ABC transporter, permease protein EhuC. Members of this family are presumed to act as permease subunits of ectoine ABC transporters. Operons containing this gene also contain the other genes of the ABC transporter and typically are found next to either ectoine utilization or ectoine biosynthesis operons. Permease subunits EhuC and EhuD are homologous. 214 matched cddid_all.tbl CDD TIGR03005 TIGR03005 132050 ectoine_ehuA ectoine/hydroxyectoine ABC transporter, ATP-binding protein. Members of this family are the ATP-binding protein of a conserved four gene ABC transporter operon found next to ectoine unilization operons and ectoine biosynthesis operons. Ectoine is a compatible solute that protects enzymes from high osmolarity. It is released by some species in response to hypoosmotic shock, and it is taken up by a number of bacteria as a compatible solute or for consumption. This family shows strong sequence similiarity to a number of amino acid ABC transporter ATP-binding proteins. 252 matched cddid_all.tbl CDD TIGR03006 TIGR03006 274385 pepcterm_polyde polysaccharide deacetylase family protein, PEP-CTERM locus subfamily. Members of this protein family belong to the family of polysaccharide deacetylases (pfam01522). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. The highest scoring homologs below the trusted cutoff for this model are found in several species of Methanosarcina, an archaeal genus. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 271 matched cddid_all.tbl CDD TIGR03007 TIGR03007 274386 pepcterm_ChnLen polysaccharide chain length determinant protein, PEP-CTERM locus subfamily. Members of this protein family belong to the family of polysaccharide chain length determinant proteins (pfam02706). All are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria, and are found near the epsH homolog that is the putative exosortase gene. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 498 matched cddid_all.tbl CDD TIGR03008 TIGR03008 163100 pepcterm_CAAX CAAX prenyl protease-related protein. The CAAX prenyl protease, in eukaryotes, catalyzes three covalent modifications, including cleavage and acylation, at the C-terminus of certain proteins in a process connected to protein sorting. This family describes a bacterial protein family homologous to one domain of the CAAX-processing enzyme. Members of this protein family are found in genomes that carry a predicted protein sorting system, PEP-CTERM/exosortase, usually in the vicinity of the EpsH homolog that is the hallmark of the system. The function of this protein is unknown, but it may relate to protein motification. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 222 matched cddid_all.tbl CDD TIGR03009 TIGR03009 274387 plancto_dom_2 Planctomycetes uncharacterized domain TIGR03009. Domains described by this model are found, so far, only in the Planctomycetes (Pirellula sp. strain 1 and Gemmata obscuriglobus), in up to four proteins per genome. The function is unknown. [Hypothetical proteins, Conserved] 210 matched cddid_all.tbl CDD TIGR03010 TIGR03010 200229 sulf_tusC_dsrF sulfur relay protein TusC/DsrF. The three proteins TusB, TusC, and TusD form a heterohexamer responsible for a sulfur relay reaction. In large numbers of proteobacterial species, this complex acts on a Cys-derived persulfide moiety, delivered by the cysteine desulfurase IscS to TusA, then to TusBCD. The activated sulfur group is then transferred to TusE (DsrC), then by MnmA (TrmU) for modification of an anticodon nucleotide in tRNAs for Glu, Lys, and Gln. The sulfur relay complex TusBCD is also found, under the designation DsrEFH, in phototrophic and chemotrophic sulfur bacteria, such as Chromatium vinosum. In these organisms, it seems the primary purpose is related to sulfur flux, such as oxidation from sulfide to molecular sulfur to sulfate. [Protein synthesis, tRNA and rRNA base modification] 116 matched cddid_all.tbl CDD TIGR03011 TIGR03011 274388 sulf_tusB_dsrH sulfur relay protein TusB/DsrH. The three proteins TusB, TusC, and TusD form a heterohexamer responsible for a sulfur relay reaction. In large numbers of proteobacterial species, this complex acts on a Cys-derived persulfide moiety, delivered by the cysteine desulfurase IscS to TusA, then to TusBCD. The activated sulfur group is then transferred to TusE (DsrC), then by MnmA (TrmU) for modification of an anticodon nucleotide in tRNAs for Glu, Lys, and Gln. The sulfur relay complex TusBCD is also found, under the designation DsrEFH, in phototrophic and chemotrophic sulfur bacteria, such as Chromatium vinosum. In these organisms, it seems the primary purpose is related to sulfur flux, such as oxidation from sulfide to molecular sulfur to sulfate. [Protein synthesis, tRNA and rRNA base modification] 94 matched cddid_all.tbl CDD TIGR03012 TIGR03012 274389 sulf_tusD_dsrE sulfur relay protein TusD/DsrE. The three proteins TusB, TusC, and TusD form a heterohexamer responsible for a sulfur relay reaction. In large numbers of proteobacterial species, this complex acts on a Cys-derived persulfide moiety, delivered by the cysteine desulfurase IscS to TusA, then to TusBCD. The activated sulfur group is then transferred to TusE (DsrC), then by MnmA (TrmU) for modification of an anticodon nucleotide in tRNAs for Glu, Lys, and Gln. The sulfur relay complex TusBCD is also found, under the designation DsrEFH, in phototrophic and chemotrophic sulfur bacteria, such as Chromatium vinosum. In these organisms, it seems the primary purpose is related to sulfur flux, such as oxidation from sulfide to molecular sulfur to sulfate. [Protein synthesis, tRNA and rRNA base modification] 127 matched cddid_all.tbl CDD TIGR03013 TIGR03013 274390 EpsB_2 "sugar transferase, PEP-CTERM system associated. Members of this protein family belong to the family of bacterial sugar transferases (pfam02397). Nearly all are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria (notable exceptions appear to include Magnetococcus sp. MC-1 and Myxococcus xanthus DK 1622 ). These genes are generally found near one or more of the PrsK, PrsR or PrsT genes that have been related to the PEP-CTERM system by phylogenetic profiling methods. The nature of the sugar transferase reaction catalyzed by members of this clade is unknown and may conceivably be variable with respect to substrate by species. These proteins are homologs of the EpsB protein found in Methylobacillus sp. strain 12S, which is also associated with a PEP-CTERM system, but of a distinct type. A name which appears attached to a number of genes (by transitive annotation) in this family is ""undecaprenyl-phosphate galactose phosphotransferase"", which comes from relatively distant characterized enterobacterial homologs, and is considerably more specific than warranted from the currently available evidence." 442 matched cddid_all.tbl CDD TIGR03014 TIGR03014 132059 EpsL "exopolysaccharide biosynthesis operon protein EpsL. The epsL gene is described as a component of the methanolan exopolysaccharide biosynthesis operon in Methylobacillus sp strain 12S, although no other information regarding its possible function is suggested. Homologs of this gene are found in several other exopolysaccharide operons in a small number of species. These operons contain a subset of the methanolan operon genes by homology and synteny, including the epsH gene which is proposed to act as an ""exosortase"" directing proteins with a C-terminal tag (PEP-CTERM) to the exopolysaccharide layer. Each of the genomes in which these genes and epsL are found also encode genes with these C-terminal tags." 381 matched cddid_all.tbl CDD TIGR03015 TIGR03015 132060 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems. [Protein fate, Protein and peptide secretion and trafficking] 269 matched cddid_all.tbl CDD TIGR03016 TIGR03016 274391 pepcterm_hypo_1 uncharacterized protein, PEP-CTERM system associated. Members of this protein family are found predominantly in exopolysaccharide biosynthesis operons marked by the presence of the EpsH-family putative exosortase and presence in the genome of the PEP-CTERM protein sorting signal. Members of this family may be distantly related to the EpsL family modeled in TIGR03014. 431 matched cddid_all.tbl CDD TIGR03017 TIGR03017 132062 EpsF chain length determinant protein EpsF. Sequences in this family of proteins are members of the chain length determinant family (pfam02706) which includes the wzc protein from E.coli. This family of proteins are homologous to the EpsF protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer. 444 matched cddid_all.tbl CDD TIGR03018 TIGR03018 274392 pepcterm_TyrKin exopolysaccharide/PEP-CTERM locus tyrosine autokinase. Members of this protein family are related to a known protein-tyrosine autokinase and to numerous homologs from exopolysaccharide biosynthesis region proteins, many of which are designated as chain length determinants. Most members of this family contain a short region, immediately C-terminal to the region modeled here, with an abundance of Tyr residues. These C-terminal tyrosine residues are likely to be autophosphorylation sites. Some members of this family are fusion proteins. 207 matched cddid_all.tbl CDD TIGR03019 TIGR03019 132064 pepcterm_femAB FemAB-related protein, PEP-CTERM system-associated. Members of this protein family are found always as part of extended exopolysaccharide biosynthesis loci in bacteria. In nearly every case, these loci contain determinants for the processing of the PEP-CTERM proposed C-terminal protein sorting signal. This family shows remote, local sequence similarity to the FemAB protein family (see pfam02388), whose members [Unknown function, General] 330 matched cddid_all.tbl CDD TIGR03020 TIGR03020 274393 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes. 247 matched cddid_all.tbl CDD TIGR03021 TIGR03021 274394 pilP_fam type IV pilus biogenesis protein PilP. Members of this protein family are found in type IV pilus biogenesis loci and include proteins designated PilP. [Cell envelope, Surface structures] 118 matched cddid_all.tbl CDD TIGR03022 TIGR03022 274395 WbaP_sugtrans "Undecaprenyl-phosphate galactose phosphotransferase, WbaP. The WbaP (formerly RfbP) protein has been characterized as the first enzyme in O-antigen biosynthesis in Salmonella typhimurium. The enzyme transfers galactose from UDP-galactose to a polyprenyl carrier (utilizing the highly conserved C-terminal sugar transferase domain, pfam02397) a reaction which takes place at the cytoplasmic face of the inner membrane. The N-terminal hydrophobic domain is then believed to facilitate the ""flippase"" function of transferring the liposaccharide unit from the cytoplasmic face to the periplasmic face of the inner membrane. This model includes the enterobacterial enzymes, where the function is presumed to be identical to the S. typhimurium enzyme as well as a somewhat broader group which are likely to catalyze the same or highly similar reactions based on a phylogenetic tree-building analysis of the broader sugar transferase family. Most of these genes are found within large operons dedicated to the production of complex exopolysaccharides such as the enterobacterial O-antigen. The most likely heterogeneity would be in the precise nature of the sugar molecule transferred." 456 matched cddid_all.tbl CDD TIGR03023 TIGR03023 274396 WcaJ_sugtrans "Undecaprenyl-phosphate glucose phosphotransferase. This family of proteins encompasses the E. coli WcaJ protein involved in colanic acid biosynthesis, the Methylobacillus EpsB protein involved in methanolan biosynthesis, as well as the GumD protein involved in the biosynthesis of xanthan. All of these are closely related to the well-characterized WbaP (formerly RfbP) protein, which is the first enzyme in O-antigen biosynthesis in Salmonella typhimurium. The enzyme transfers galactose from UDP-galactose (NOTE: not glucose) to a polyprenyl carrier (utilizing the highly conserved C-terminal sugar transferase domain, pfam02397) a reaction which takes place at the cytoplasmic face of the inner membrane. The N-terminal hydrophobic domain is then believed to facilitate the ""flippase"" function of transferring the liposaccharide unit from the cytoplasmic face to the periplasmic face of the inner membrane. Most of these genes are found within large operons dedicated to the production of complex exopolysaccharides such as the enterobacterial O-antigen. Colanic acid biosynthesis utilizes a glucose-undecaprenyl carrier, knockout of EpsB abolishes incorporation of UDP-glucose into the lipid phase, and the C-terminal portion of GumD has been shown to be responsible for the glucosyl-1-transferase activity." 450 matched cddid_all.tbl CDD TIGR03024 TIGR03024 274397 arch_PEF_CTERM PEF-CTERM protein sorting domain. This domain, distantly related to the PEP-Cterm domain described in model TIGR02595, is found in Methanosarcina mazei in four different proteins, as well as in other archaea such as Methanococcoides burtonii. Several proteins with this domain have their genes only a short distance from archaeosortase C, a proposed integral membrane transpeptidase. This family should exclude members of the PEFG-CTERM domain family (TIGR04296), specific to the Thaumarchaeota. 25 matched cddid_all.tbl CDD TIGR03025 TIGR03025 274398 EPS_sugtrans "exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase. Members of this family are generally found near other genes involved in the biosynthesis of a variety of exopolysaccharides. These proteins consist of two fused domains, an N-terminal hydrophobic domain of generally low conservation and a highly conserved C-terminal sugar transferase domain (pfam02397). Characterized and partially characterized members of this subfamily include Salmonella WbaP (originally RfbP), E. coli WcaJ, Methylobacillus EpsB, Xanthomonas GumD, Vibrio CpsA, Erwinia AmsG, Group B Streptococcus CpsE (originally CpsD), and Streptococcus suis Cps2E. Each of these is believed to act in transferring the sugar from, for instance, UDP-glucose or UDP-galactose, to a lipid carrier such as undecaprenyl phosphate as the first (priming) step in the synthesis of an oligosaccharide ""block"". This function is encoded in the C-terminal domain. The liposaccharide is believed to be subsequently transferred through a ""flippase"" function from the cytoplasmic to the periplasmic face of the inner membrane by the N-terminal domain. Certain closely related transferase enzymes, such as Sinorhizobium ExoY and Lactococcus EpsD, lack the N-terminal domain and are not found by this model." 445 matched cddid_all.tbl CDD TIGR03026 TIGR03026 274399 NDP-sugDHase nucleotide sugar dehydrogenase. Enzymes in this family catalyze the NAD-dependent alcohol-to-acid oxidation of nucleotide-linked sugars. Examples include UDP-glucose 6-dehydrogenase (1.1.1.22), GDP-mannose 6-dehydrogenase (1.1.1.132), UDP-N-acetylglucosamine 6-dehydrogenase (1.1.1.136), UDP-N-acetyl-D-galactosaminuronic acid dehydrogenase, and UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase. These enzymes are most often involved in the biosynthesis of polysaccharides and are often found in operons devoted to that purpose. All of these enzymes contain three Pfam domains, pfam03721, pfam00984, and pfam03720 for the N-terminal, central, and C-terminal regions respectively. 409 matched cddid_all.tbl CDD TIGR03027 TIGR03027 132072 pepcterm_export putative polysaccharide export protein, PEP-CTERM sytem-associated. This protein family belongs to the larger set of polysaccharide biosynthesis/export proteins described by pfam02563. Members of this family are variable in either containing of lacking a 78-residue insert, but appear to fall within a single clade, nevertheless, where the regions in which the gene is found encode components of the PEP-CTERM/EpsH proposed exosortase protein sorting system. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 165 matched cddid_all.tbl CDD TIGR03028 TIGR03028 132073 EpsE polysaccharide export protein EpsE. Sequences in this family of proteins are members of a polysaccharide export protein family (pfam02563) which includes the wza protein from E.coli. This family of proteins are homologous to the EpsE protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer. 239 matched cddid_all.tbl CDD TIGR03029 TIGR03029 132074 EpsG chain length determinant protein tyrosine kinase EpsG. The proteins in this family are homologs of the EpsG protein found in Methylobacillus strain 12S and are generally found in operons with other Eps homologs. The protein is believed to function as the protein tyrosine kinase component of the chain length regulator (along with the transmembrane component EpsF). 274 matched cddid_all.tbl CDD TIGR03030 TIGR03030 274400 CelA cellulose synthase catalytic subunit (UDP-forming). Cellulose synthase catalyzes the beta-1,4 polymerization of glucose residues in the formation of cellulose. In bacteria, the substrate is UDP-glucose. The synthase consists of two subunits (or domains in the frequent cases where it is encoded as a single polypeptide), the catalytic domain modelled here and the regulatory domain (pfam03170). The regulatory domain binds the allosteric activator cyclic di-GMP. The protein is membrane-associated and probably assembles into multimers such that the individual cellulose strands can self-assemble into multi-strand fibrils. 713 matched cddid_all.tbl CDD TIGR03031 TIGR03031 274401 cas_csx12 CRISPR system subtype II-B RNA-guided endonuclease Cas9/Csx12. Members of this family of CRISPR-associated (cas) protein are found, so far, in CRISPR/cas loci in Wolinella succinogenes DSM 1740, Legionella pneumophila str. Paris, and Francisella tularensis, where the last probably is an example of a degenerate CRISPR locus, having neither repeats nor a functional Cas1. The characteristic repeat length is 37 base pairs and period is about 72. One region of this large protein shows sequence similarity to pfam01844, HNH endonuclease. 802 matched cddid_all.tbl CDD TIGR03032 TIGR03032 274402 TIGR03032 TIGR03032 family protein. This protein family is uncharacterized. A number of motifs are conserved perfectly among all member sequences. The function of this protein is unknown. [Hypothetical proteins, Conserved] 335 matched cddid_all.tbl CDD TIGR03033 TIGR03033 200235 phage_rel_nuc putative phage-type endonuclease. Members of this protein family are found often in phage genomes and in prokaryotic genomes in uncharacterized regions that resemble integrated prophage regions. 153 matched cddid_all.tbl CDD TIGR03034 TIGR03034 132079 TIGR03034 conserved hypothetical protein. Members of this protein family have been found in several species of gammaproteobacteria, including Yersinia pestis and Y. pseudotuberculosis, Xylella fastidiosa, and Escherichia coli UTI89. As many as five members can be found in a single genome. The function is unknown. [Hypothetical proteins, Conserved] 274 matched cddid_all.tbl CDD TIGR03035 TIGR03035 132080 trp_arylform arylformamidase. One of several pathways of tryptophan degradation is as follows: tryptophan 2,3-dioxygenase (1.13.11.11) uses 02 to convert Trp to L-formylkynurenine. Arylformamidase (3.5.1.9) hydrolyzes the product to L-kynurenine and formate. Kynureninase (3.7.1.3) hydrolyzes L-kynurenine to anthranilate plus alanine. Members of the seed alignment for this model are bacterial predicted metal-dependent hydrolases. All are supported as arylformamidase (3.5.1.9) by an operon structure in which kynureninase and/or tryptophan 2,3-dioxygenase genes are adjacent. The members from Bacillus cereus, Pseudomonas aeruginosa and Ralstonia metallidurans were characterized. An example from Pseudomonas fluorescens is given the gene symbol qbsH instead of kynB because of its role in quinolobactin biosynthesis, which begins with tryptophan. All members of this family should be arylformamidase (3.5.1.9). [Energy metabolism, Amino acids and amines] 206 matched cddid_all.tbl CDD TIGR03036 TIGR03036 188272 trp_2_3_diox tryptophan 2,3-dioxygenase. Members of this family are tryptophan 2,3-dioxygenase, as confirmed by several experimental characterizations, and by conserved operon structure for many of the other members. This enzyme represents the first of a two-step degradation to L-kynurenine, and a three-step pathway (via kynurenine) to anthranilate plus alanine. [Energy metabolism, Amino acids and amines] 264 matched cddid_all.tbl CDD TIGR03037 TIGR03037 132082 anthran_nbaC 3-hydroxyanthranilate 3,4-dioxygenase. Members of this protein family, from both bacteria and eukaryotes, are the enzyme 3-hydroxyanthranilate 3,4-dioxygenase. This enzyme acts on the tryptophan metabolite 3-hydroxyanthranilate and produces 2-amino-3-carboxymuconate semialdehyde, which can rearrange spontaneously to quinolinic acid and feed into nicotinamide biosynthesis, or undergo further enzymatic degradation. 159 matched cddid_all.tbl CDD TIGR03038 TIGR03038 274403 PS_II_psbM photosystem II reaction center protein PsbM. Members of this protein family are the photosystem II reaction center M protein, product of the psbM gene, in Cyanobacteria and their derived organelles in plants. This model resembles pfam05151 but has cutoffs set to avoid false-positive matches to similar (not necessarily homologous) sequences in species that are not photosynthetic. [Energy metabolism, Photosynthesis] 33 matched cddid_all.tbl CDD TIGR03039 TIGR03039 163117 PS_II_CP47 photosystem II chlorophyll-binding protein CP47. [Energy metabolism, Photosynthesis] 504 matched cddid_all.tbl CDD TIGR03041 TIGR03041 213761 PS_antenn_a_b chlorophyll a/b binding light-harvesting protein. This model represents a family of proteins from the Cyanobacteria, closely homologous to and yet distinct from PbsC, a chlorophyll a antenna protein of photosystem II. Members are not univerally present in Cyanobacteria, while the family has several members per genome in Prochlorococcus marinus, with seven members in a strain adapted to low light conditions. These antenna proteins may deliver light energy to photosystem I and/or photosystem II. [Energy metabolism, Photosynthesis] 321 matched cddid_all.tbl CDD TIGR03042 TIGR03042 274404 PS_II_psbQ_bact photosystem II protein PsbQ. This protein through the member sll1638 from Synechocystis sp. PCC 6803, was shown to be part of the cyanobacteria photosystem II. It is homologous to (but quite diverged from) the chloroplast PsbQ protein, called oxygen-evolving enhancer protein 3 (OEE3). We designate this cyanobacteria protein PsbQ by homology. [Energy metabolism, Photosynthesis] 142 matched cddid_all.tbl CDD TIGR03043 TIGR03043 274405 PS_II_psbZ photosystem II core protein PsbZ. PsbZ is a core protein of photosystem II in thylakoid-containing Cyanobacteria and plant chloroplasts. The original Chlamydomonas gene symbol, ycf9, is a synonym. PsbZ controls the interaction of the reaction center core with the light-harvesting antenna. [Energy metabolism, Photosynthesis] 58 matched cddid_all.tbl CDD TIGR03044 TIGR03044 274406 PS_II_psb27 photosystem II protein Psb27. Members of this family are the Psb27 protein of the cyanobacterial photosynthetic supracomplex, photosystem II. Although most protein components of both cyanobacterial and chloroplast versions of photosystem II are closely related and described together by single models, this family is strictly bacterial. Some uncharacterized proteins with highly divergent sequences, from Arabidopsis, score between trusted and noise cutoffs for this model but are not at this time assigned as functionally equivalent photosystem II proteins. [Energy metabolism, Photosynthesis] 135 matched cddid_all.tbl CDD TIGR03045 TIGR03045 274407 PS_II_C550 cytochrome c-550. Members of this protein family are cytochrome c-550, the PsbV extrinsic protein of photosystem II, from both Cyanobacteria and chloroplasts. A paralog to this protein, PsbV2, is found in some species in addition to PsbV itself. [Energy metabolism, Photosynthesis] 159 matched cddid_all.tbl CDD TIGR03046 TIGR03046 274408 PS_II_psbV2 photosystem II cytochrome PsbV2. Members of this protein family are PsbV2, a protein closely related cytochrome c-550 (PsbV), a protein important to the water-splitting and oxygen-evolving activity of photosystem II. Mutant studies in Thermosynechococcus elongatus showed PsbV2 can partially replace PsbV, from which it appears to have arisen first by duplication, then by intergenic recombination with a different gene. [Energy metabolism, Photosynthesis] 155 matched cddid_all.tbl CDD TIGR03047 TIGR03047 274409 PS_II_psb28 photosystem II reaction center protein Psb28. Members of this protein family are the Psb28 protein of photosystem II. Two different protein families, apparently without homology between them, have been designated PsbW. Cyanobacterial proteins previously designated PsbW are members of the family described here. However, while members of the plant PsbW family are not found (so far) in Cyanobacteria, members of the present family do occur in plants. We therefore support the alternative designation that has emerged for this protein family, Psp28, rather than PsbW. [Energy metabolism, Photosynthesis] 108 matched cddid_all.tbl CDD TIGR03048 TIGR03048 132092 PS_I_psaC photosystem I iron-sulfur protein PsaC. Members of this family are PsaC, an essential component of photosystem I (PS-I) reaction center in Cyanobacteria and chloroplasts. This small protein, about 80 amino acids in length, contains two copies of the ferredoxin-like 4Fe-4S binding site (pfam00037) and therefore eight conserved Cys residues. This protein is also called photosystem I subunit VII. [Energy metabolism, Photosynthesis] 80 matched cddid_all.tbl CDD TIGR03049 TIGR03049 274410 PS_I_psaK photosystem I reaction center subunit PsaK. Members of this protein family are the PsaK of the photosystem I reaction center. Photosystems I and II occur together in the same sets of organisms. Photosystem I uses light energy to transfer electrons from plastocyanin to ferredoxin, while photosystem II uses light energy to split water and releases molecular oxygen. [Energy metabolism, Photosynthesis] 81 matched cddid_all.tbl CDD TIGR03050 TIGR03050 188274 PS_I_psaK_plant photosystem I reaction center PsaK, plant form. This protein family is based on a model that separates the photosystem I PsaK subunit of chloroplasts from chloroplast PsaG protein and from Cyanobacterial PsaK, both of which show sequence similarity. 83 matched cddid_all.tbl CDD TIGR03051 TIGR03051 132095 PS_I_psaG_plant photosystem I reaction center subunit V, chloroplast. 88 matched cddid_all.tbl CDD TIGR03052 TIGR03052 132096 PS_I_psaI photosystem I reaction center subunit VIII. Members of this protein family are PsaI, subunit VIII of the photosystem I reaction center. This protein is found in both the Cyanobacteria and the chloroplasts of plants, but is absent from non-oxygenic photosynthetic bacteria such as Rhodobacter sphaeroides. Species that contain photosystem I also contain photosystem II, which splits water and releases molecular oxygen. [Energy metabolism, Photosynthesis] 31 matched cddid_all.tbl CDD TIGR03053 TIGR03053 274411 PS_I_psaM photosystem I reaction center subunit XII. Members of this protein family are PsaM, which is subunit XII of the photosystem I reaction center. This protein is found in both the Cyanobacteria and the chloroplasts of plants, but is absent from non-oxygenic photosynthetic bacteria such as Rhodobacter sphaeroides. Species that contain photosystem I also contain photosystem II, which splits water and releases molecular oxygen. The seed alignment for this model includes sequences from pfam07465 and additional sequences, as from Prochlorococcus. [Energy metabolism, Photosynthesis] 29 matched cddid_all.tbl CDD TIGR03054 TIGR03054 213764 photo_alph_chp1 putative photosynthetic complex assembly protein. In twenty or so anoxygenic photosynthetic alpha-Proteobacteria known so far, a gene for a member of this protein family is present and is found in the vicinity of puhA, which encodes a component of the photosynthetic reaction center, and other genes associated with photosynthesis. This protein family is suggested, consequently, as a probable assembly factor for the photosynthetic reaction center, but its seems its actual function has not yet been demonstrated. [Energy metabolism, Photosynthesis] 135 matched cddid_all.tbl CDD TIGR03055 TIGR03055 188275 photo_alph_chp2 putative photosynthetic complex assembly protein 2. This uncharacterized protein family was identified, by the method of partial phylogenetic profiling, as having a matching phylogenetic distribution to that of the photosynthetic reaction center of the alpha-proteobacterial type. It is nearly always encoded near other photosynthesis-related genes, including puhA. [Energy metabolism, Photosynthesis] 245 matched cddid_all.tbl CDD TIGR03056 TIGR03056 132100 bchO_mg_che_rel putative magnesium chelatase accessory protein. Members of this family belong to the alpha/beta fold family hydrolases (pfam00561). Members are found in bacterial genomes if and only if they encoded for anoxygenic photosynthetic systems similar to that of Rhodobacter capsulatus and other alpha-Proteobacteria. Members often are encoded in the same operon as subunits of the protoporphyrin IX magnesium chelatase, and were once designated BchO. No literature supports a role as an actual subunit of magnesium chelatase, but an accessory role is possible, as suggested by placement by its probable hydrolase activity. [Energy metabolism, Photosynthesis] 278 matched cddid_all.tbl CDD TIGR03057 TIGR03057 274412 xxxLxxG_by_4 X-X-X-Leu-X-X-Gly heptad repeats. This model represents a 28-column alignment, comprising four tandem sets of seven residues each, in which the fourth residue tends to be Leu and the seventh tends to be Gly in each set. This heptad periodicity, corresponding to two turns of an alpha helix, suggests alpha-helical structure; in many proteins this 28-region model hits many times in tandem. Arrangement of these sequences on a helical wheel would show a strict alternation of Leu and Gly residues on one side of the helix, that is, an extremely bulky side chain alternating with the virtual absence of one. This suggests an extended zippering of one alpha helix to another, analogous to the shorter leucine zippers found in many dimerizing transcription factors. Proteins in which these heptad repeats occur often have higher order repeats of a unit comprised of several heptads. 28 matched cddid_all.tbl CDD TIGR03058 TIGR03058 132102 rpt_csmH chlorosome envelope protein H repeat. CsmH, as studied in Chlorobium tepidum, is one of at least ten surface-exposed proteins of the chloroplast, a bacteriochlorophyll-rich structure with a lipid-protein envelope. CsmH contain typically three copies of a repeated sequence, represented by this model. [Energy metabolism, Photosynthesis] 27 matched cddid_all.tbl CDD TIGR03059 TIGR03059 132103 psaOeuk photosystem I protein PsaO. Members of this family are the PsaO protein of photosystem I. This protein is found in chloroplasts but not in Cyanobacteria. 82 matched cddid_all.tbl CDD TIGR03060 TIGR03060 213765 PS_II_psb29 photosystem II biogenesis protein Psp29. Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function. [Energy metabolism, Photosynthesis] 214 matched cddid_all.tbl CDD TIGR03061 TIGR03061 274413 pip_yhgE_Nterm "YhgE/Pip N-terminal domain. This family contains the N-terminal domain of a family of multiple membrane-spanning proteins of Gram-positive bacteria. One member was shown to be a host protein essential for phage infection, so many members of this family are called ""phage infection protein"". A separate model, TIGR03062, represents the conserved C-terminal domain. The domains are separated by regions highly variable in both length and sequence, often containing extended heptad repeats as described in model TIGR03057." 164 matched cddid_all.tbl CDD TIGR03062 TIGR03062 274414 pip_yhgE_Cterm "YhgE/Pip C-terminal domain. This family contains the C-terminal domain of a family of multiple membrane-spanning proteins of Gram-positive bacteria. One member was shown to be a host protein essential for phage infection, so many members of this family are called ""phage infection protein"". A separate model, TIGR03061, represents the conserved N-terminal domain. The domains are separated by regions highly variable in both length and sequence, often containing extended heptad repeats as described in model TIGR03057." 208 matched cddid_all.tbl CDD TIGR03063 TIGR03063 213766 srtB_target sortase B cell surface sorting signal. Two different classes of sorting signal, both analogous to the sortase A signal LPXTG, may be recognized by the sortase SrtB. These are given as NXZTN and NPKXZ. Proteins sorted by this class of sortase are less common than the sortase A and LPXTG system. This model describes a number of cell surface protein C-terminal regions from Gram-positive bacteria that appear to be sortase B (SrtB) sorting signals. 29 matched cddid_all.tbl CDD TIGR03064 TIGR03064 211782 sortase_srtB sortase, SrtB family. Members of this transpeptidase family are, in most cases, designated sortase B, product of the srtB gene. This protein shows only distant similarity to the sortase A family, for which there may be several members in a single bacterial genome. Typical SrtB substrate motifs include NAKTN, NPKSS, etc, and otherwise resemble the LPXTG sorting signals recognized by sortase A proteins. [Cell envelope, Other, Protein fate, Protein and peptide secretion and trafficking] 232 matched cddid_all.tbl CDD TIGR03065 TIGR03065 132109 srtB_sig_QVPTGV sortase B signal domain, QVPTGV class. This model represents a boutique (unusual) sorting signal, recognized by a member of the sortase SrtB family rather than by the housekeeping sortase, SrtA. 32 matched cddid_all.tbl CDD TIGR03066 TIGR03066 132110 Gem_osc_para_1 Gemmata obscuriglobus paralogous family TIGR03066. This model represents an uncharacterized paralogous family in Gemmata obscuriglobus UQM 2246, a member of the Planctomycetes. This family shows sequence similarity to TIGR03067, which is also found in Gemmata obscuriglobus as well as in a few other species. [Hypothetical proteins, Conserved] 111 matched cddid_all.tbl CDD TIGR03067 TIGR03067 274415 Planc_TIGR03067 Planctomycetes uncharacterized domain TIGR03067. This domain occurs in several species, mostly from the Planctomycetes division of the bacteria. It is expanded into a paralogous family of at least twenty-five members in Gemmata obscuriglobus UQM 2246. This family appears related to TIGR03066, which also is expanded into a large paralogous family in Gemmata obscuriglobus. [Unknown function, General] 107 matched cddid_all.tbl CDD TIGR03068 TIGR03068 132112 srtB_sig_NPQTN sortase B signal domain, NPQTN class. This model represents one of the boutique (rare) sortase signals, recognized by sortase B (SrtB) rather than by the housekeeping-type SrtA class sortase. This sequence, beginning NPQTN, shows little similarity to several other SrtB substrates. 33 matched cddid_all.tbl CDD TIGR03069 TIGR03069 132113 PS_II_S4 photosystem II S4 domain protein. Members of this protein family are about 265 residues long and each contains an S4 RNA-binding domain of about 48 residues. The member from the Cyanobacterium, Synechocystis sp. PCC 6803, was detected as a novel polypeptide in a highly purified preparation of active photosystem II (Kashino, et al., 2002). The phylogenetic distribution, including Cyanobacteria and Arabidopsis, supports a role in photosystem II, although the high bit score cutoffs for this model reflect similar sequences in non-photosynthetic organisms such as Carboxydothermus hydrogenoformans, a Gram-positive bacterium. [Energy metabolism, Photosynthesis] 257 matched cddid_all.tbl CDD TIGR03070 TIGR03070 213767 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions] 58 matched cddid_all.tbl CDD TIGR03071 TIGR03071 274416 couple_hipA HipA N-terminal domain. Although Pfam models pfam07805 and pfam07804 currently are called HipA-like N-terminal domain and HipA-like C-terminal domain, respectively, those models hit the central and C-terminal regions of E. coli HipA but not the N-terminal region. This model hits the N-terminal region of HipA and its homologs, and also identifies proteins that lack match regions for pfam07804 and pfam07805. 101 matched cddid_all.tbl CDD TIGR03072 TIGR03072 213768 release_prfH putative peptide chain release factor H. Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). The member from Escherichia coli K-12, designated prfH, appears to be a pseudogene. This class I release factor is always found as the downstream gene of a two-gene operon. [Protein synthesis, Translation factors] 200 matched cddid_all.tbl CDD TIGR03073 TIGR03073 274417 release_rtcB release factor H-coupled RctB family protein. Members of this family are related to RctB. RctB a protein of known structure but unknown function that often is encoded near RNA cyclase and therefore is suggested to be a tRNA or mRNA processing enzyme. This family of RctB-like proteins in encoded upstream of, and apparently is translationally coupled to, the putative peptide chain release factor RF-H (TIGR03072), product of the prfH gene. Note that a large deletion at the junction between this gene and the prfH gene in Escherichia coli K-12 marks both as probable pseudogenes. [Protein synthesis, Other] 356 matched cddid_all.tbl CDD TIGR03074 TIGR03074 274418 PQQ_membr_DH membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family. This protein family has a phylogenetic distribution very similar to that coenzyme PQQ biosynthesis enzymes, as shown by partial phylogenetic profiling. Members of this family have several predicted transmembrane helices in the N-terminal region, and include the quinoprotein glucose dehydrogenase (EC 1.1.5.2) of Escherichia coli and the quinate/shikimate dehydrogenase of Acinetobacter sp. ADP1 (EC 1.1.99.25). Sequences closely related except for the absense of the N-terminal hydrophobic region, scoring in the gray zone between the trusted and noise cutoffs, include PQQ-dependent glycerol (EC 1.1.99.22) and and other polyol (sugar alcohol) dehydrogenases. 764 matched cddid_all.tbl CDD TIGR03075 TIGR03075 274419 PQQ_enz_alc_DH PQQ-dependent dehydrogenase, methanol/ethanol family. This protein family has a phylogenetic distribution very similar to that coenzyme PQQ biosynthesis enzymes, as shown by partial phylogenetic profiling. Genes in this family often are found adjacent to the PQQ biosynthesis genes themselves. An unusual, strained disulfide bond between adjacent Cys residues contributes to PQQ-binding, as does a Trp residue that is part of a PQQ enzyme repeat (see pfam01011). Characterized members include the dehydrogenase subunit of a membrane-anchored, three subunit alcohol (ethanol) dehydrogenase of Gluconobacter suboxydans, a homodimeric ethanol dehydrogenase in Pseudomonas aeruginosa, and the large subunit of an alpha2/beta2 heterotetrameric methanol dehydrogenase in Methylobacterium extorquens. 527 matched cddid_all.tbl CDD TIGR03076 TIGR03076 213771 near_not_gcvH Chlamydial GcvH-like protein upstream region protein. The H protein (GcvH) of the glycine cleavage system shuttles the methylamine group of glycine from the P protein to the T protein. Most Chlamydia but lack the P and T proteins, and have a single homolog of GcvH that appears deeply split from canonical GcvH in molecular phylogenetic trees. The protein family modeled here is observed so far only in the Chlamydiae, always as part of a two-gene operon, upstream of the homolog of GcvH. Its function is unknown. [Unknown function, General] 686 matched cddid_all.tbl CDD TIGR03077 TIGR03077 132121 not_gcvH glycine cleavage protein H-like protein, Chlamydial. The H protein (GcvH) of the glycine cleavage system shuttles the methylamine group of glycine from the P protein to the T protein. Most Chlamydia but lack the P and T proteins, and have a single homolog of GcvH that appears deeply split from canonical GcvH in molecular phylogenetic trees. The protein family modeled here is observed the Chlamydial GcvH homolog, so far always seen as part of a two-gene operon, downstream of a member of the uncharacterized protein family TIGR03076. The function of this protein is unknown. 110 matched cddid_all.tbl CDD TIGR03078 TIGR03078 274420 CH4_NH3mon_ox_C methane monooxygenase/ammonia monooxygenase, subunit C. Both ammonia oxidizers such as Nitrosomonas europaea and methanotrophs (obligate methane oxidizers) such as Methylococcus capsulatus each can grow only on their own characteristic substrate. However, both groups have the ability to oxidize both substrates, and so the relevant enzymes must be named here according to their ability to oxidze both. The protein family represented here reflects subunit C of both the particulate methane monooxygenase of methylotrophs and the ammonia monooxygenase of nitrifying bacteria. 231 matched cddid_all.tbl CDD TIGR03079 TIGR03079 132123 CH4_NH3mon_ox_B methane monooxygenase/ammonia monooxygenase, subunit B. Both ammonia oxidizers such as Nitrosomonas europaea and methanotrophs (obligate methane oxidizers) such as Methylococcus capsulatus each can grow only on their own characteristic substrate. However, both groups have the ability to oxidize both substrates, and so the relevant enzymes must be named here according to their ability to oxidze both. The protein family represented here reflects subunit B of both the particulate methane monooxygenase of methylotrophs and the ammonia monooxygenase of nitrifying bacteria. 399 matched cddid_all.tbl CDD TIGR03080 TIGR03080 132124 CH4_NH3mon_ox_A methane monooxygenase/ammonia monooxygenase, subunit A. Both ammonia oxidizers such as Nitrosomonas europaea and methanotrophs (obligate methane oxidizers) such as Methylococcus capsulatus each can grow only on their own characteristic substrate. However, both groups have the ability to oxidize both substrates, and so the relevant enzymes must be named here according to their ability to oxidze both. The protein family represented here reflects subunit A of both the particulate methane monooxygenase of methylotrophs and the ammonia monooxygenase of nitrifying bacteria. 243 matched cddid_all.tbl CDD TIGR03081 TIGR03081 213772 metmalonyl_epim methylmalonyl-CoA epimerase. Members of this protein family are the enzyme methylmalonyl-CoA epimerase (EC 5.1.99.1), also called methylmalonyl-CoA racemase. This enzyme converts (2R)-methylmalonyl-CoA to (2S)-methylmalonyl-CoA, which is then a substrate for methylmalonyl-CoA mutase (TIGR00642). It is known in bacteria, archaea, and as a mitochondrial protein in animals. It is closely related to lactoylglutathione lyase (TIGR00068), which is also called glyoxylase I, and is also a homodimer. 128 matched cddid_all.tbl CDD TIGR03082 TIGR03082 274421 Gneg_AbrB_dup membrane protein AbrB duplication. The model describes a hydrophobic sequence region that is duplicated to form the AbrB protein of Escherichia coli (not to be confused with a Bacillus subtilis protein with the same gene symbol). In some species, notably the Cyanobacteria and Thermus thermophilus, proteins consist of a single copy rather than two copies. The member from Pseudomonas putida, PP_1415, was suggested to be an ammonia monooxygenase characteristic of heterotrophic nitrifiers, based on an experimental indication of such activity in the organism and a glimmer of local sequence similarity between parts of P. putida protein and an instance of the AmoA protein from Nitrosomonas europaea (; we do not believe the sequence similarity to be meaningful. The member from E. coli (b0715, ybgN) appears to be the largely uncharacterized AbrB (aidB regulator) protein of E. coli cited in Volkert, et al. (PMID 8002588), although we did not manage to trace the origin of association of the article to the sequence. 156 matched cddid_all.tbl CDD TIGR03083 TIGR03083 274422 TIGR03083 uncharacterized Actinobacterial protein TIGR03083. This protein family pulls together several groups of proteins, each very different from the others. They share in common three conserved regions. The first is a region of about 38 amino acids, nearly always at the N-terminus of a protein. This region has a bulky hydrophobic residue, usually Trp, at position 29, and a His residue at position 37 that is invariant, so far, in over 150 instances. The second conserved region has a motif [DE]xxxHxxD. The third conserved region contains a hydrophobic patch and a well-conserved Arg residue. Most examples are found in the Actinobacteria, including the genera Mycobacterium, Corynebacterium, Streptomyces, Nocardia, Frankia, etc. The pattern of near-invariant residues against a backdrop of extreme sequence divergence suggests enzymatic activity and conservation of active site residues. 202 matched cddid_all.tbl CDD TIGR03084 TIGR03084 274423 TIGR03084 TIGR03084 family protein. This family, like pfam07398, belongs to the larger set of probable enzymes modeled by TIGRFAMs family TIGR03083. Members are found primarily in the Actinobacteria (Mycobacterium, Streptomyces, etc.). The family is uncharacterized. [Hypothetical proteins, Conserved] 253 matched cddid_all.tbl CDD TIGR03085 TIGR03085 132129 TIGR03085 TIGR03085 family protein. This family, like pfam07398 and TIGRFAMs family TIGR03084, belongs to the larger set of probable enzymes defined in family TIGR03083. Members are found primarily in the Actinobacteria (Mycobacterium, Streptomyces, etc.). The family is uncharacterized. [Hypothetical proteins, Conserved] 199 matched cddid_all.tbl CDD TIGR03086 TIGR03086 274424 TIGR03086 TIGR03086 family protein. This family, like pfam07398 and TIGRFAMs family TIGR030834, belongs to the larger set of probable enzymes defined in family TIGR03083. Members are found primarily in the Actinobacteria (Mycobacterium, Streptomyces, etc.). The family is uncharacterized. 180 matched cddid_all.tbl CDD TIGR03087 TIGR03087 274425 stp1 sugar transferase, PEP-CTERM/EpsH1 system associated. Members of this family include a match to the pfam00534 Glycosyl transferases group 1 domain. Nearly all are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria. In particular, these transferases are found proximal to a particular variant of exosortase, EpsH1, which appears to travel with a conserved group of genes summarized by Genome Property GenProp0652. The nature of the sugar transferase reaction catalyzed by members of this clade is unknown and may conceivably be variable with respect to substrate by species, but we hypothesize a conserved substrate. 397 matched cddid_all.tbl CDD TIGR03088 TIGR03088 132132 stp2 sugar transferase, PEP-CTERM/EpsH1 system associated. Members of this family include a match to the pfam00534 Glycosyl transferases group 1 domain. Nearly all are found in species that encode the PEP-CTERM/exosortase system predicted to act in protein sorting in a number of Gram-negative bacteria. In particular, these transferases are found proximal to a particular variant of exosortase, EpsH1, which appears to travel with a conserved group of genes summarized by Genome Property GenProp0652. The nature of the sugar transferase reaction catalyzed by members of this clade is unknown and may conceivably be variable with respect to substrate by species, but we hypothesize a conserved substrate. 374 matched cddid_all.tbl CDD TIGR03089 TIGR03089 274426 TIGR03089 TIGR03089 family protein. This protein family is found, so far, only in the Actinobacteria (Streptomyces, Mycobacterium, Corynebacterium, Nocardia, Propionibacterium, etc.) and never more than one to a genome. Members show twilight-level sequence similarity to family of AMP-binding enzymes described by pfam00501. 228 matched cddid_all.tbl CDD TIGR03090 TIGR03090 163133 SASP_tlp small, acid-soluble spore protein tlp. This protein family is restricted to a subset of endospore-forming bacteria such as Bacillus subtilis, all of which are in the Firmicutes (low-GC Gram-positive) lineage. Although previously designated tlp (thioredoxin-like protein), the B. subtilis protein was shown to be a minor small acid-soluble spore protein SASP, unique to spores. The motif E[VIL]XDE near the C-terminus probably represents at a germination protease cleavage site. [Cellular processes, Sporulation and germination] 70 matched cddid_all.tbl CDD TIGR03091 TIGR03091 274427 SASP_sspK small, acid-soluble spore protein K. This protein family is restricted to a subset of endospore-forming bacteria such as Bacillus subtilis, all of which are in the Firmicutes (low-GC Gram-positive) lineage. It is a minor SASP (small, acid-soluble spore protein) designated SspK. [Cellular processes, Sporulation and germination] 32 matched cddid_all.tbl CDD TIGR03092 TIGR03092 132136 SASP_sspI small, acid-soluble spore protein I. This protein family is restricted to a subset of endospore-forming bacteria such as Bacillus subtilis, all of which are in the Firmicutes (low-GC Gram-positive) lineage. It is a minor SASP (small, acid-soluble spore protein) designated SspI. The gene in Bacillus subtilis previously was designated ysfA. [Cellular processes, Sporulation and germination] 65 matched cddid_all.tbl CDD TIGR03093 TIGR03093 132137 SASP_sspL small, acid-soluble spore protein L. This protein family is restricted to a subset of endospore-forming bacteria such as Bacillus subtilis, all of which are in the Firmicutes (low-GC Gram-positive) lineage. It is a minor SASP (small, acid-soluble spore protein) designated SspL. [Cellular processes, Sporulation and germination] 36 matched cddid_all.tbl CDD TIGR03094 TIGR03094 132138 sulfo_cyanin sulfocyanin. Members of this family are blue-copper redox proteins designated sulfocyanin, from the archaeal genera Sulfolobus, Ferroplasma, and Picrophilus. The most closely related proteins characterized as functionally different are the rustacyanins. [Energy metabolism, Electron transport] 195 matched cddid_all.tbl CDD TIGR03095 TIGR03095 132139 rusti_cyanin rusticyanin. Rusticyanin is a blue copper protein, described in an obligate acidophilic chemolithoautroph, Acidithiobacillus ferrooxidans, as an electron transfer protein. It can constitute up to 5 percent of protein in cells grown on Fe(II) and is thought to be part of an electron chain for Fe(II) oxidation, with two c-type cytochromes, an aa3-type cytochrome oxidase, and 02 as terminal electron acceptor. It is rather closely related to sulfocyanin (TIGR03094). [Energy metabolism, Electron transport] 148 matched cddid_all.tbl CDD TIGR03096 TIGR03096 132140 nitroso_cyanin nitrosocyanin. Nitrosocyanin, as described from the obligate chemolithoautotroph Nitrosomonas europaea, is a red copper protein of unknown function with sequence similarity to a number of blue copper redox proteins. [Energy metabolism, Electron transport] 135 matched cddid_all.tbl CDD TIGR03097 TIGR03097 132141 PEP_O_lig_1 probable O-glycosylation ligase, exosortase A-associated. These proteins are members of the O-antigen polymerase (wzy) family described by pfam04932. This group is associated with genomes and ususally genomic contexts containing elements of the exosortase/PEP-CTERM protein export system, specificially the type 1 variety of this system described by the Genome Property, GenProp0652. 402 matched cddid_all.tbl CDD TIGR03098 TIGR03098 211788 ligase_PEP_1 acyl-CoA ligase (AMP-forming), exosortase A-associated. This group of proteins contains an AMP-binding domain (pfam00501) associated with acyl CoA-ligases. These proteins are generally found in genomes containing the exosortase/PEP-CTERM protein expoert system, specifically the type 1 variant of this system described by the Genome Property GenProp0652. When found in this context they are invariably present next to a decarboxylase enzyme. A number of sequences from Burkholderia species also hit this model, but the genomic context is obviously different. The hypothesis of a constant substrate for this family is only strong where the exosortase context is present. 517 matched cddid_all.tbl CDD TIGR03099 TIGR03099 132143 dCO2ase_PEP1 pyridoxal-dependent decarboxylase, exosortase A system-associated. The sequences in this family contain the pyridoxal binding domain (pfam02784) and C-terminal sheet domain (pfam00278) of a family of Pyridoxal-dependent decarboxylases. Characterized enzymes in this family decarboxylate substrates such as ornithine, diaminopimelate and arginine. The genes of the family modeled here, with the exception of those observed in certain Burkholderia species, are all found in the context of exopolysaccharide biosynthesis loci containing the exosortase/PEP-CTERM protein sorting system. More specifically, these are characteristic of the type 1 exosortase system represented by the Genome Property GenProp0652. The substrate of these enzymes may be a precursor of the carrier or linker which is hypothesized to release the PEP-CTERM protein from the exosortase enzyme. These enzymes are apparently most closely related to the diaminopimelate decarboxylase modeled by TIGR01048 which may suggest a similarity (or identity) of substrate. 398 matched cddid_all.tbl CDD TIGR03100 TIGR03100 132144 hydr1_PEP exosortase A system-associated hydrolase 1. This group of proteins are members of the alpha/beta hydrolase superfamily. These proteins are generally found in genomes containing the exosortase/PEP-CTERM protein expoert system, specifically the type 1 variant of this system described by the Genome Property GenProp0652. When found in this context they are invariably present in the vicinity of a second, relatively unrelated enzyme (ortholog 2, TIGR03101) of the same superfamily. 274 matched cddid_all.tbl CDD TIGR03101 TIGR03101 274428 hydr2_PEP exosortase A system-associated hydrolase 2. This group of proteins are members of the alpha/beta hydrolase superfamily. These proteins are generally found in genomes containing the exosortase/PEP-CTERM protein expoert system, specifically the type 1 variant of this system described by the Genome Property GenProp0652. When found in this context they are invariably present in the vicinity of a second, relatively unrelated enzyme (ortholog 1, TIGR03100) of the same superfamily. 266 matched cddid_all.tbl CDD TIGR03102 TIGR03102 274429 halo_cynanin halocyanin domain. Halocyanins are blue (type I) copper redox proteins found in halophilic archaea such as Natronobacterium pharaonis. This model represents a domain duplicated in some halocyanins, while appearing once in others. This domain includes the characteristic copper ligand residues. This family does not include plastocyanins, and does not include certain divergent paralogs of halocyanin. 115 matched cddid_all.tbl CDD TIGR03103 TIGR03103 132147 trio_acet_GNAT GNAT-family acetyltransferase TIGR03103. Members of this protein family belong to the GNAT family of acetyltransferases. Each is part of a conserved three-gene cassette sparsely distributed across at least twenty different species known so far, including alpha, beta, and gamma Proteobacteria, Mycobacterium, and Prosthecochloris, which is a member of the Chlorobi. The other two members of the cassette are a probable protease and an asparagine synthetase family protein. 547 matched cddid_all.tbl CDD TIGR03104 TIGR03104 274430 trio_amidotrans asparagine synthase family amidotransferase. Members of this protein family are closely related to several isoforms of asparagine synthetase (glutamine amidotransferase) and typically have been given this name in genome annotation to date. Each is part of a conserved three-gene cassette sparsely distributed across at least twenty different species known so far, including alpha, beta, and gamma Proteobacteria, Mycobacterium, and Prosthecochloris, which is a member of the Chlorobi. The other two members of the cassette are a probable protease and a member of the GNAT family of acetyltransferases. 589 matched cddid_all.tbl CDD TIGR03105 TIGR03105 274431 gln_synth_III glutamine synthetase, type III. This family consists of the type III isozyme of glutamine synthetase, originally described in Rhizobium meliloti, where types I and II also occur. 435 matched cddid_all.tbl CDD TIGR03106 TIGR03106 132150 trio_M42_hydro hydrolase, peptidase M42 family. This model describes a subfamily of MEROPS peptidase family M42, a glutamyl aminopeptidase family that also includes the cellulase CelM from Clostridium thermocellum and deblocking aminopeptidases that can remove acylated amino acids. Members of this family occur in a three gene cassette with an amidotransferase (TIGR03104)in the asparagine synthase (glutamine-hydrolyzing) family, and a probable acetyltransferase (TIGR03103) in the GNAT family. 343 matched cddid_all.tbl CDD TIGR03107 TIGR03107 132151 glu_aminopep glutamyl aminopeptidase. This model represents the M42.001 clade within MEROPS family M42. M42 includes glutamyl aminopeptidase as in the present model, deblocking aminopeptidases as from Pyrococcus horikoshii and related species, and endo-1,4-beta-glucanase (cellulase M) as from Clostridium thermocellum. The current family includes [Protein fate, Degradation of proteins, peptides, and glycopeptides] 350 matched cddid_all.tbl CDD TIGR03108 TIGR03108 132152 eps_aminotran_1 exosortase A system-associated amidotransferase 1. The predicted protein-sorting transpeptidase that we call exosortase (see TIGR02602) has distinct subclasses that associated with different types of exopolysaccharide production loci. This model represents a distinct clade among a set of amidotransferases largely annotated (not necessarily accurately) as glutatime-hydrolyzing asparagine synthases. Members of this clade are essentially restricted to the characteristic exopolysaccharide (EPS) regions that contain the exosortase 1 genome (xrtA), in genomes that also have numbers of PEP-CTERM domain (TIGR02595) proteins. 628 matched cddid_all.tbl CDD TIGR03109 TIGR03109 274432 exosortase_1 exosortase A. The predicted protein-sorting transpeptidase that we call exosortase (see TIGR02602) has distinct subclasses that associated with different types of exopolysaccharide production loci. We designate this, the most common type so far, exosortase 1. We propose the gene symbol xrtA, analogous to srtA for the most common type of sortase in Gram-positive bacteria. 267 matched cddid_all.tbl CDD TIGR03110 TIGR03110 188282 exosort_Gpos exosortase family protein XrtG. Members of this protein family are found in a modest number of non-pathogenic Gram-positive bacteria, including three species of Lactococcus and three paralogs in Clostridium acetobutylicum. This protein appears related to the conserved core region of a family of proposed transpeptidases, exosortase (previously EpsH), thought to act on PEP-CTERM proteins. Members of the seed alignment include all exosortase proposed active site residues. However, in contrast to canonical exosortase (TIGR02602) and archaeal (TIGR03762), and cyanobacterial (TIGR03763) variants, this family has not yet been matched to a cognate PEP-CTERM-like sorting signal. This protein is assigned the gene symbol XrtG (eXosoRTase family protein of Gram-positives). 187 matched cddid_all.tbl CDD TIGR03111 TIGR03111 132155 glyc2_xrt_Gpos1 putative glycosyltransferase, exosortase G-associated. Members of this protein family are probable glycosyltransferases of family 2, whose genes are near those for the exosortase homolog XrtG (TIGR03110), which is restricted to Gram-positive bacteria. Other genes in the conserved gene neighborhood include a 6-pyruvoyl tetrahydropterin synthase homolog (TIGR03112) and an uncharacterized intergral membrane protein (TIGR03766). 439 matched cddid_all.tbl CDD TIGR03112 TIGR03112 132156 6_pyr_pter_rel 6-pyruvoyl tetrahydropterin synthase-related domain. Members of this family are small proteins, or small domains of larger proteins, that occur in certain Firmicutes in the same regions as members of families TIGR03110 and TIGR03111. Members of TIGR03110 resemble exosortase, a proposed protein sorting transpeptidase (see TIGR02602). TIGR03111 represents a small clade among the group 2 glycosyltransferases. Members of the current protein family resemble eukaryotic known and prokaryotic predicted 6-pyruvoyl tetrahydropterin synthases. 113 matched cddid_all.tbl CDD TIGR03113 TIGR03113 274433 exosortase_2 exosortase B. The predicted protein-sorting transpeptidase that we call exosortase (see TIGR02602) has distinct subclasses that associated with different types of exopolysaccharide production loci. We designate this relatively uncommon proteobacterial type to be type 2. We propose the gene symbol xrtB. Most species encountered so far with xrtB also contain xrtA (TIGR03109). 268 matched cddid_all.tbl CDD TIGR03114 TIGR03114 274434 cas8u_csf1 CRISPR type AFERR-associated protein Csf1. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf1 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies closest to the repeats. 202 matched cddid_all.tbl CDD TIGR03115 TIGR03115 274435 cas7_csf2 CRISPR type IV/AFERR-associated protein Csf2. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf2 (CRISPR/cas Subtype as in A. ferrooxidans protein 2), as it lies second closest to the repeats. 344 matched cddid_all.tbl CDD TIGR03116 TIGR03116 132160 cas5_csf3 CRISPR type IV/AFERR-associated protein Csf3. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf3 (CRISPR/cas Subtype as in A. ferrooxidans protein 3), as it lies third closest to the repeats. 214 matched cddid_all.tbl CDD TIGR03117 TIGR03117 274436 cas_csf4 CRISPR type AFERR-associated DEAD/DEAH-box helicase Csf4. Members of this family show up near CRISPR repeats in Acidithiobacillus ferrooxidans ATCC 23270, Azoarcus sp. EbN1, and Rhodoferax ferrireducens DSM 15236. In the latter two species, the CRISPR/cas locus is found on a plasmid. This family is one of several characteristic of a type of CRISPR-associated (cas) gene cluster we designate Aferr after A. ferrooxidans, where it is both chromosomal and the only type of cas gene cluster found. The gene is designated csf4 (CRISPR/cas Subtype as in A. ferrooxidans protein 1), as it lies farthest (fourth closest) from the repeats in the A. ferrooxidans genome. 636 matched cddid_all.tbl CDD TIGR03118 TIGR03118 132162 PEPCTERM_chp_1 TIGR03118 family protein. This model describes and uncharacterized conserved hypothetical protein. Members are found with the C-terminal putative exosortase interaction domain, PEP-CTERM, in Nitrosospira multiformis, Rhodoferax ferrireducens, Solibacter usitatus Ellin6076, and Acidobacteria bacterium Ellin345. It is found without the PEP-CTERM domain in several other species, including Burkholderia ambifaria, Gloeobacter violaceus PCC 7421, and three copies in the Acanthamoeba polyphaga mimivirus. [Hypothetical proteins, Conserved] 336 matched cddid_all.tbl CDD TIGR03119 TIGR03119 132163 one_C_fhcD formylmethanofuran--tetrahydromethanopterin N-formyltransferase. Members of this protein family are the FhcD protein of tetrahydromethanopterin (H4MPT)-dependent C-1 carrier metabolism. In the archaea, FhcD is designated formylmethanofuran--tetrahydromethanopterin N-formyltransferase, while in bacteria it is commonly designated as formyltransferase/hydrolase complex subunit D. FhcD is essential for one-carbon metabolism in at least three groups of prokaryotes: methanogenic archaea, sulfate-reducing archaea, and methylotrophic bacteria. [Central intermediary metabolism, One-carbon metabolism] 287 matched cddid_all.tbl CDD TIGR03120 TIGR03120 274437 one_C_mch methenyltetrahydromethanopterin cyclohydrolase. Members of this protein family are the enzyme methenyltetrahydromethanopterin cyclohydrolase, a key enzyme for tetrahydromethanopterin (H4MPT)-linked C1 transfer metabolism. [Central intermediary metabolism, One-carbon metabolism] 313 matched cddid_all.tbl CDD TIGR03121 TIGR03121 274438 one_C_dehyd_A formylmethanofuran dehydrogenase subunit A. Members of this largely archaeal protein family are subunit A of the formylmethanofuran dehydrogenase. Nomenclature in some bacteria may reflect inclusion of the formyltransferase described by TIGR03119 as part of the complex, and therefore call this protein formyltransferase/hydrolase complex Fhc subunit A. Note that this model does not distinguish tungsten (FwdA) from molybdenum-containing (FmdA) forms of this enzyme; a single gene from this family is expressed constitutively in Methanobacterium thermoautotrophicum, which has both tungsten and molybdenum forms and may work interchangeably. 556 matched cddid_all.tbl CDD TIGR03122 TIGR03122 274439 one_C_dehyd_C formylmethanofuran dehydrogenase subunit C. Members of this largely archaeal protein family are subunit C of the formylmethanofuran dehydrogenase. Nomenclature in some bacteria may reflect inclusion of the formyltransferase described by TIGR03119 as part of the complex, and therefore call this protein formyltransferase/hydrolase complex Fhc subunit C. Note that this model does not distinguish tungsten (FwdC) from molybdenum-containing (FmdC) forms of this enzyme. 257 matched cddid_all.tbl CDD TIGR03123 TIGR03123 163144 one_C_unchar_1 probable H4MPT-linked C1 transfer pathway protein. This protein family was identified, by the method of partial phylogenetic profiling, as related to the use of tetrahydromethanopterin (H4MPT) as a C-1 carrier. Characteristic markers of the H4MPT-linked C1 transfer pathway include formylmethanofuran dehydrogenase subunits, methenyltetrahydromethanopterin cyclohydrolase, etc. Tetrahydromethanopterin, a tetrahydrofolate analog, occurs in methanogenic archaea, bacterial methanotrophs, planctomycetes, and a few other lineages. [Central intermediary metabolism, One-carbon metabolism] 318 matched cddid_all.tbl CDD TIGR03124 TIGR03124 163145 citrate_citX holo-ACP synthase CitX. Members of this protein family are the CitX protein, or CitX domain of the CitXG bifunctional protein, of the citrate lyase system. CitX transfers the prosthetic group 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA to the citrate lyase gamma chain, an acyl carrier protein. This enzyme may be designated holo-ACP synthase, holo-citrate lyase synthase, or apo-citrate lyase phosphoribosyl-dephospho-CoA transferase. In a few genera, including Haemophilus, this protein occurs as a fusion protein with CitG (2.7.8.25), an enzyme involved in prosthetic group biosynthesis. This CitX family is easily separated from the holo-ACP synthases of other enzyme systems. [Energy metabolism, Fermentation, Protein fate, Protein modification and repair] 165 matched cddid_all.tbl CDD TIGR03125 TIGR03125 132169 citrate_citG triphosphoribosyl-dephospho-CoA synthase CitG. Triphosphoribosyl-dephospho-CoA is transferred to, and becomes the prosthetic group of, the respective acyl carrier protein subunits of both citrate lyase and malonate decarboxylase. Members of this protein family are triphosphoribosyl-dephospho-CoA synthases specifically from citrate lyase systems. This protein sometimes occurs as a fusion protein with CitX, the phosphoribosyl-dephospho-CoA transferase. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Energy metabolism, Fermentation] 275 matched cddid_all.tbl CDD TIGR03126 TIGR03126 132170 one_C_fae formaldehyde-activating enzyme. This family consists of formaldehyde-activating enzyme, or the corresponding domain of longer, bifunctional proteins. It links formaldehyde to the C1 carrier tetrahydromethanopterin (H4MPT), an analog of tetrahydrofolate, and is common among species with H4MPT. The ribulose monophosphate (RuMP) pathway, which removes the toxic metabolite formaldehyde by assimilation, runs in the opposite direction in some species to produce ribulose 5-phosphate for nucleotide biosynthesis, leaving formaldehyde as an additional metabolite. In these species, formaldehyde activating enzyme may occur as a fusion protein with D-arabino 3-hexulose 6-phosphate formaldehyde lyase from the RuMP pathway. 160 matched cddid_all.tbl CDD TIGR03127 TIGR03127 132171 RuMP_HxlB 6-phospho 3-hexuloisomerase. Members of this protein family are 6-phospho 3-hexuloisomerase (PHI), or the PHI domain of a fusion protein. This enzyme is part of the ribulose monophosphate (RuMP) pathway, which in one direction removes the toxic metabolite formaldehyde by assimilation into fructose-6-phosphate. In the other direction, in species lacking a complete pentose phosphate pathway, the RuMP pathway yields ribulose-5-phosphate, necessary for nucleotide biosynthesis, at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin. 179 matched cddid_all.tbl CDD TIGR03128 TIGR03128 132172 RuMP_HxlA 3-hexulose-6-phosphate synthase. Members of this protein family are 3-hexulose-6-phosphate synthase (HPS), or the HPS domain of a fusion protein. This enzyme is part of the ribulose monophosphate (RuMP) pathway, which in one direction removes the toxic metabolite formaldehyde by assimilation into fructose-6-phosphate. In the other direction, in species lacking a complete pentose phosphate pathway, the RuMP pathway yields ribulose-5-phosphate, necessary for nucleotide biosynthesis, at the cost of also yielding formaldehyde. These latter species tend usually have a formaldehyde-activating enzyme to attach formaldehyde to the C1 carrier tetrahydromethanopterin. In these species, the enzyme is viewed as a lyase rather than a synthase and is called D-arabino 3-hexulose 6-phosphate formaldehyde lyase. Note that there is some overlap in specificity with the Escherichia coli enzyme 3-keto-L-gulonate 6-phosphate decarboxylase. 206 matched cddid_all.tbl CDD TIGR03129 TIGR03129 132173 one_C_dehyd_B formylmethanofuran dehydrogenase subunit B. Members of this largely archaeal protein family are subunit B of the formylmethanofuran dehydrogenase. Nomenclature in some bacteria may reflect inclusion of the formyltransferase described by TIGR03119 as part of the complex, and therefore call this protein formyltransferase/hydrolase complex Fhc subunit C. Note that this model does not distinguish tungsten (FwdB) from molybdenum-containing (FmdB) forms of this enzyme. 421 matched cddid_all.tbl CDD TIGR03130 TIGR03130 188283 malonate_delta malonate decarboxylase acyl carrier protein. Members of this protein family are the acyl carrier protein, also called the delta subunit, of malonate decarboxylase. This subunit has the same covalently bound prosthetic group, derived from and similar to coenzyme A, as does citrate lyase, although this protein and the acyl carrier protein of citrate lyase do not show significant sequence similarity. Both malonyl and acetyl groups are transferred to the prosthetic group for catalysis. 98 matched cddid_all.tbl CDD TIGR03131 TIGR03131 132175 malonate_mdcH malonate decarboxylase, epsilon subunit. Members of this protein family are the epsilon subunit of malonate decarboxylase. This subunit has malonyl-CoA/dephospho-CoA acyltransferase activity. Malonate decarboxylase may be a soluble enzyme, or linked to membrane subunits and active as a sodium pump. The epsilon subunit is closely related to the malonyl CoA-acyl carrier protein (ACP) transacylase family described by TIGR00128, but acts on an ACP subunit of malonate decarboxylase that has an unusual coenzyme A derivative as its prothetic group. 295 matched cddid_all.tbl CDD TIGR03132 TIGR03132 274440 malonate_mdcB triphosphoribosyl-dephospho-CoA synthase MdcB. This protein acts in cofactor biosynthesis, preparing the coenzyme A derivative that becomes attached to the malonate decarboxylase acyl carrier protein (or delta subunit). The closely related protein CitG of citrate lyase produces the same molecule, but the two families are nonetheless readily separated. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 272 matched cddid_all.tbl CDD TIGR03133 TIGR03133 188285 malonate_beta biotin-independent malonate decarboxylase, beta subunit. Members of this protein family are the beta subunit of malonate decarboxylase. Malonate decarboxylase may be a soluble enzyme, or linked to membrane subunits and active as a sodium pump. In the malonate decarboxylase complex, the beta subunit appears to act as a malonyl-CoA decarboxylase. 274 matched cddid_all.tbl CDD TIGR03134 TIGR03134 274441 malonate_gamma biotin-independent malonate decarboxylase, gamma subunit. Members of this protein family are the gamma subunit of malonate decarboxylase. Malonate decarboxylase may be a soluble enzyme, or linked to membrane subunits and active as a sodium pump. In the malonate decarboxylase complex, the beta subunit appears to act as a malonyl-CoA decarboxylase, while the gamma subunit appears either to mediate subunit interaction or to act as a co-decarboxylase with the beta subunit. The beta and gamma subunits exhibit some local sequence similarity. 238 matched cddid_all.tbl CDD TIGR03135 TIGR03135 274442 malonate_mdcG malonate decarboxylase holo-[acyl-carrier-protein] synthase. Malonate decarboxylase, like citrate lyase, has a unique acyl carrier protein subunit with a prosthetic group derived from, and distinct from, coenzyme A. Members of this protein family are the phosphoribosyl-dephospho-CoA transferase specific to the malonate decarboxylase system. This enzyme can also be designated holo-ACP synthase (2.7.7.61). The corresponding component of the citrate lyase system, CitX, shows little or no sequence similarity to this family. [Energy metabolism, Other] 202 matched cddid_all.tbl CDD TIGR03136 TIGR03136 188287 malonate_biotin Na+-transporting malonate decarboxylase, carboxybiotin decarboxylase subunit. Malonate decarboxylase can be a soluble enzyme, or a sodium ion-translocating with additional membrane-bound components. Members of this protein family are integral membrane proteins required to couple decarboxylation to sodium ion export. This family belongs to a broader family, TIGR01109 of sodium ion-translocating decarboxylase beta subunits. [Transport and binding proteins, Cations and iron carrying compounds] 399 matched cddid_all.tbl CDD TIGR03137 TIGR03137 211789 AhpC peroxiredoxin. This peroxiredoxin (AhpC, alkylhydroperoxide reductase subunit C) is one subunit of a two-subunit complex with subunit F(TIGR03140). Usually these are found as an apparent operon. The gene has been characterized in Bacteroides fragilis, where it is important in oxidative stress defense. This gene contains two invariant cysteine residues, one near the N-terminus and one near the C-terminus, each followed immediately by a proline residue. [Cellular processes, Detoxification, Cellular processes, Adaptations to atypical conditions] 187 matched cddid_all.tbl CDD TIGR03138 TIGR03138 274443 QueF 7-cyano-7-deazaguanine reductase. This enzyme catalyzes the 4-electron reduction of the cyano group of 7-cyano-7-deazaguanine (preQ0) to an amine. Although related to a large family of GTP cyclohydrolases (pfam01227), the relationship is structural and not germane to the catalytic mechanism. This mode represents the longer, gram-negative version of the enzyme as found in E. coli. The enzymatic step represents the first point at which the biosynthesis of queuosine in bacteria and eukaryotes is distinguished from the biosynthesis of archaeosine in archaea. [Transcription, RNA processing] 275 matched cddid_all.tbl CDD TIGR03139 TIGR03139 213775 QueF-II 7-cyano-7-deazaguanine reductase. This enzyme catalyzes the 4-electron reduction of the cyano group of 7-cyano-7-deazaguanine (proQ1) to an amine. Although related to a large family of GTP cyclohydrolases (pfam01227), the relationship is structural and not germane to the catalytic mechanism. This mode represents the shorter, gram-positive version of the enzyme as found in B. subtilis. The enzymatic step represents the first point at which the biosynthesis of queuosine in bacteria and eukaryotes is distinguished from the biosynthesis of archaeosine in archaea. 115 matched cddid_all.tbl CDD TIGR03140 TIGR03140 274444 AhpF alkyl hydroperoxide reductase subunit F. This enzyme is the partner of the peroxiredoxin (alkyl hydroperoxide reductase) AhpC which contains the peroxide-reactive cysteine. AhpF contains the reductant (NAD(P)H) binding domain (pfam00070) and presumably acts to resolve the disulfide which forms after oxidation of the active site cysteine in AphC. This proteins contains two paired conserved cysteine motifs, CxxCP and CxHCDGP. [Cellular processes, Detoxification, Cellular processes, Adaptations to atypical conditions] 515 matched cddid_all.tbl CDD TIGR03141 TIGR03141 274445 cytochro_ccmD heme exporter protein CcmD. The model for this protein family describes a small, hydrophobic, and only moderately well-conserved protein, tricky to identify accurately for all of these reasons. However, members are found as part of large operons involved in heme export across the inner membrane for assembly of c-type cytochromes in a large number of bacteria. The gray zone between the trusted cutoff (13.0) and noise cutoff (4.75) includes both low-scoring examples and false-positive matches to hydrophobic domains of longer proteins. 45 matched cddid_all.tbl CDD TIGR03142 TIGR03142 274446 cytochro_ccmI cytochrome c-type biogenesis protein CcmI. This TPR repeat-containing protein is the CcmI protein (also called CycH) of c-type cytochrome biogenesis. CcmI is thought to act as an apo-cytochrome c chaperone. This model describes the N-terminal region of the protein, Members of this protein family [Protein fate, Protein folding and stabilization, Energy metabolism, Electron transport] 117 matched cddid_all.tbl CDD TIGR03143 TIGR03143 132187 AhpF_homolog putative alkyl hydroperoxide reductase F subunit. This family of thioredoxin reductase homologs is found adjacent to alkylhydroperoxide reductase C subunit predominantly in cases where there is only one C subunit in the genome and that genome is lacking the F subunit partner (also a thioredcxin reductase homolog) that is usually found (TIGR03140). 555 matched cddid_all.tbl CDD TIGR03144 TIGR03144 274447 cytochr_II_ccsB cytochrome c-type biogenesis protein CcsB. Members of this protein family represent one of two essential proteins of system II for c-type cytochrome biogenesis. Additional proteins tend to be part of the system but can be replaced by chemical reductants such as dithiothreitol. This protein is designated CcsB in Bordetella pertussis and some other bacteria, resC in Bacillus (where there is additional N-terminal sequence), and CcsA in chloroplast. We use the CcsB designation here. Member sequences show regions of strong sequence conservation and variable-length, poorly conserved regions in between; sparsely filled columns were removed from the seed alignment prior to model construction. [Energy metabolism, Electron transport, Protein fate, Protein modification and repair] 245 matched cddid_all.tbl CDD TIGR03145 TIGR03145 274448 cyt_nit_nrfE cytochrome c nitrate reductase biogenesis protein NrfE. Members of this protein family closely resemble the CcmF protein of the CcmABCDEFGH system, or system I, for c-type cytochrome biogenesis (GenProp0678). Members are found, as a rule, next to closely related paralogs of CcmG and CcmH and always located near other genes associated with the cytochrome c nitrite reductase enzyme complex. As a rule, members are found in species that also encode bona fide members of the CcmF, CcmG, and CcmH families. 614 matched cddid_all.tbl CDD TIGR03146 TIGR03146 132190 cyt_nit_nrfB cytochrome c nitrite reductase, pentaheme subunit. Members of this protein family contain five copies of the CXXCH heme-binding motif, and are the NrfB component of the multisubunit enzyme, cytochrome c nitrite reductase. [Energy metabolism, Electron transport] 145 matched cddid_all.tbl CDD TIGR03147 TIGR03147 274449 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF. [Energy metabolism, Electron transport] 126 matched cddid_all.tbl CDD TIGR03148 TIGR03148 274450 cyt_nit_nrfD cytochrome c nitrite reductase, NrfD subunit. Members of this protein family are NrfD, a highly hydrophobic protein encoded in the nrf operon, which encodes cytochrome c nitrite reductase. This multiple heme-containing enzyme can reduce nitrite to ammonia. Members belong to a broader Pfam protein family, pfam03916, which also contains an NrfD-related subunit of polysulphide reductase. [Energy metabolism, Electron transport] 316 matched cddid_all.tbl CDD TIGR03149 TIGR03149 274451 cyt_nit_nrfC cytochrome c nitrite reductase, Fe-S protein. Members of this protein family are the Fe-S protein, NrfC, of a cytochrome c nitrite reductase system for which the pentaheme cytochrome c protein, NrfB (family TIGR03146) is an unambiguous marker. Members of this protein family show similarity to other ferredoxin-like proteins, including a subunit of a polysulfide reductase. [Energy metabolism, Electron transport] 225 matched cddid_all.tbl CDD TIGR03150 TIGR03150 274452 fabF beta-ketoacyl-acyl-carrier-protein synthase II. 3-oxoacyl-[acyl-carrier-protein] synthase 2 (KAS-II, FabF) is involved in the condensation step of fatty acid biosynthesis in which the malonyl donor group is decarboxylated and the resulting carbanion used to attack and extend the acyl group attached to the acyl carrier protein. Most genomes encoding fatty acid biosynthesis contain a number of condensing enzymes, often of all three types: 1, 2 and 3. Synthase 2 is mechanistically related to synthase 1 (KAS-I, FabB) containing a number of absolutely conserved catalytic residues in common. This model is based primarily on genes which are found in apparent operons with other essential genes of fatty acid biosynthesis (GenProp0681). The large gap between the trusted cutoff and the noise cutoff contains many genes which are not found adjacent to genes of the fatty acid pathway in genomes that often also contain a better hit to this model. These genes may be involved in other processes such as polyketide biosyntheses. Some genomes contain more than one above-trusted hit to this model which may result from recent paralogous expansions. Second hits to this model which are not next to other fatty acid biosynthesis genes may be involved in other processes. FabB sequences should fall well below the noise cutoff of this model. [Fatty acid and phospholipid metabolism, Biosynthesis] 407 matched cddid_all.tbl CDD TIGR03151 TIGR03151 132195 enACPred_II putative enoyl-[acyl-carrier-protein] reductase II. This oxidoreductase of the 2-nitropropane dioxygenase family (pfam03060) is commonly found in apparent operons with genes involved in fatty acid biosynthesis. Furthermore, this genomic context generally includes the fabG 3-oxoacyl-[ACP] reductase and lacks the fabI enoyl-[ACP] reductase. 307 matched cddid_all.tbl CDD TIGR03152 TIGR03152 200248 cyto_c552_HCOOH formate-dependent cytochrome c nitrite reductase, c552 subunit. Members of this protein family are cytochrome c552, a component of cytochrome c nitrite reductase, which is known more formally as nitrite reductase (cytochrome; ammonia-forming) (EC 1.7.2.2). Nitrate can be reduced by several enzymes. EC 1.7.2.2 reduces nitrite all the way to ammonia, rather than to ammonium hydroxide (nitrite reductase (NAD(P)H), EC 1.7.1.4) or nitric oxide (nitrite reductase (NO-forming), EC 1.7.2.1). Some examples of EC 1.7.2.2 occur in a seven gene system that enables formate-dependent nitrite reduction, but is also found in simpler contexts. Members of this protein family, however, belong to the formate-dependent system. [Energy metabolism, Electron transport] 439 matched cddid_all.tbl CDD TIGR03153 TIGR03153 274453 cytochr_NrfH cytochrome c nitrite reductase, small subunit. Members of this protein family are NrfH, a tetraheme cytochrome c. NrfH is the cytochrome c nitrite reductase small subunit, and forms a heterodimer with NrfA, the catalytic subunit. While NrfA can act as a monomer, NrfH can bind to and anchor NrfA in the membrane and enables electron transfer to NrfA from quinones. [Energy metabolism, Electron transport] 135 matched cddid_all.tbl CDD TIGR03154 TIGR03154 132198 sulfolob_CbsA cytochrome b558/566, subunit A. Members of this protein family are CbsA, one subunit of a highly glycosylated, heterodimeric, mono-heme cytochrome b558/566, found in Sulfolobus acidocaldarius and several other members of the Sulfolobales, a branch of the Crenarchaeota. 465 matched cddid_all.tbl CDD TIGR03155 TIGR03155 274454 sulfolob_CbsB cytochrome b558/566, subunit B. Members of this protein family are CbsB, one subunit of a highly glycosylated, heterodimeric, mono-heme cytochrome b558/566, found in Sulfolobus acidocaldarius and several other members of the Sulfolobales, a branch of the Crenarchaeota. 302 matched cddid_all.tbl CDD TIGR03156 TIGR03156 274455 GTP_HflX GTP-binding protein HflX. This protein family is one of a number of homologous small, well-conserved GTP-binding proteins with pleiotropic effects. Bacterial members are designated HflX, following the naming convention in Escherichia coli where HflX is encoded immediately downstream of the RNA chaperone Hfq, and immediately upstream of HflKC, a membrane-associated protease pair with an important housekeeping function. Over large numbers of other bacterial genomes, the pairing with hfq is more significant than with hflK and hlfC. The gene from Homo sapiens in this family has been named PGPL (pseudoautosomal GTP-binding protein-like). [Unknown function, General] 351 matched cddid_all.tbl CDD TIGR03157 TIGR03157 274456 cas_Csc2 CRISPR type I-D/CYANO-associated protein Csc2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family is a CRISPR-associated (Cas) family strictly associated with the Cyano subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. This family is designated Csc2 for CRISPR/Cas Subtype Cyano protein 2, as it is often the second gene upstream of the core cas genes, cas3-cas4-cas1-cas2. 282 matched cddid_all.tbl CDD TIGR03158 TIGR03158 274457 cas3_cyano CRISPR-associated helicase Cas3, subtype CYANO. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family is a CRISPR-associated (Cas) family strictly associated with the Cyano subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. It contains helicase motifs and appears to represent the Cas3 protein of the Cyano subtype of CRISPR/Cas system. 357 matched cddid_all.tbl CDD TIGR03159 TIGR03159 274458 cas_Csc1 CRISPR type I-D/CYANO-associated protein Csc1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family is a CRISPR-associated (Cas) family strictly associated with the Cyano subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. This family is designated Csc1 for CRISPR/Cas Subtype Cyano protein 1, as it is often the first gene upstream of the core cas genes, cas3-cas4-cas1-cas2. 225 matched cddid_all.tbl CDD TIGR03160 TIGR03160 274459 cobT_DBIPRT nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase. Members of this family are nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase, an enzyme of cobalamin biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 333 matched cddid_all.tbl CDD TIGR03161 TIGR03161 274460 ribazole_CobZ alpha-ribazole phosphatase CobZ. Sequences in the seed alignment were the experimentally characterized CobZ of the methanogenic archaeon Methanosarcina mazei, and other archaeal proteins found similarly next to or very near to other cobalamin biosynthesis genes. CobZ replaces the alpha-ribazole-phosphate phosphatase (EC 3.1.3.73) called CobC in analogous bacterial pathways for cobalamin biosynthesis under anaerobic conditions. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 139 matched cddid_all.tbl CDD TIGR03162 TIGR03162 274461 ribazole_cobC alpha-ribazole phosphatase. Members of this protein family include the known CobC protein of Salmonella and Eschichia coli species, and homologous proteins found in cobalamin biosynthesis regions in other bacteria. This protein is alpha-ribazole phosphatase (EC 3.1.3.73) and, like many phosphatases, can be closely related in sequence to other phosphatases with different functions. Close homologs excluded from this model include proteins with duplications, so this model is built in -g mode to suppress hits to those proteins. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 177 matched cddid_all.tbl CDD TIGR03164 TIGR03164 132208 UHCUDC OHCU decarboxylase. Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) has been recently been shown to be catalyzed by this enzyme in Mus musculus. Homologs of this enzyme are found adjacent to and fused with uricase in a number of prokaryotes and are represented by this model. 157 matched cddid_all.tbl CDD TIGR03165 TIGR03165 274462 F1F0_chp_2 F1/F0 ATPase, Methanosarcina type, subunit 2. Members of this protein family are uncharacterized, highly hydrophobic proteins encoded in the middle of apparent F1/F0 ATPase operons. We note, however, that this protein is both broadly and sparsely distributed. It is found in about only about two percent of microbial genomes sequenced, with the first ten examples found coming from the Euryarchaeota, Chlorobia, Betaproteobacteria, Deltaproteobacteria, and Planctomycetes. In most of these species, surrounding operon appears to represent a second F1/F0 ATPase system, and the member proteins belong to subfamilies with the same phylogenetic distribution as the current protein family. 83 matched cddid_all.tbl CDD TIGR03166 TIGR03166 132210 alt_F1F0_F1_eps alternate F1F0 ATPase, F1 subunit epsilon. A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 epsilon subunit of this apparent second ATP synthase. 122 matched cddid_all.tbl CDD TIGR03167 TIGR03167 274463 tRNA_sel_U_synt tRNA 2-selenouridine synthase. The Escherichia coli YbbB protein was shown to encode a selenophosphate-dependent tRNA 2-selenouridine synthase, essential for modification of some tRNAs to replace a sulfur atom with selenium. This enzyme works with SelD, the selenium donor protein, which also acts in selenocysteine incorporation. Although the members of this protein family show a fairly deep split, sequences from both sides of the split are supported by co-occurence with, and often proximity to, the selD gene. [Protein synthesis, tRNA and rRNA base modification] 311 matched cddid_all.tbl CDD TIGR03168 TIGR03168 274464 1-PFK hexose kinase, 1-phosphofructokinase family. This family consists largely of 1-phosphofructokinases, but also includes tagatose-6-kinases and 6-phosphofructokinases. 303 matched cddid_all.tbl CDD TIGR03169 TIGR03169 274465 Nterm_to_SelD pyridine nucleotide-disulfide oxidoreductase family protein. Members of this protein family include N-terminal sequence regions of (probable) bifunctional proteins whose C-terminal sequences are SelD, or selenide,water dikinase, the selenium donor protein necessary for selenium incorporation into protein (as selenocysteine), tRNA (as 2-selenouridine), or both. However, some members of this family occur in species that do not show selenium incorporation, and the function of this protein family is unknown. 364 matched cddid_all.tbl CDD TIGR03170 TIGR03170 274466 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by pfam08666. [Cellular processes, Chemotaxis and motility] 122 matched cddid_all.tbl CDD TIGR03171 TIGR03171 132215 soxL2 Rieske iron-sulfur protein SoxL2. This iron-sulfur protein is found in a contiguous genomic region with subunits of cytochrome b558/566 in several archaeal species, and appears to be part of a cytochrome bc1-analogous system. 321 matched cddid_all.tbl CDD TIGR03172 TIGR03172 274467 TIGR03172 probable selenium-dependent hydroxylase accessory protein YqeC. This uncharacterized protein family includes YqeC from Escherichia coli. A phylogenetic profiling analysis shows correlation with SelD, the selenium donor protein, even in species where SelD contributes to neither selenocysteine nor selenouridine biosynthesis. Instead, this family, and families TIGR03309 and TIGR03310 appear to mark selenium-dependent molybdenum hydroxylase maturation systems. [Unknown function, General] 210 matched cddid_all.tbl CDD TIGR03173 TIGR03173 274468 pbuX xanthine permease. All the seed members of this model are observed adjacent to genes for either xanthine phosphoribosyltransferase (for the conversion of xanthine to guanine, GenProp0696) or genes for the conversion of xanthine to urate and its concomitant catabolism (GenProp0640, GenProp0688, GenProp0686 and GenProp0687). A number of sequences scoring higher than trusted to this model are found in different genomic contexts, and the possibility exist that these transport related compounds in addition to or instead of xanthine itself. The outgroup to this family are sequences which are characterized as uracil permeases or are adjacent to established uracil phosphoribosyltransferases. 406 matched cddid_all.tbl CDD TIGR03174 TIGR03174 274469 cas_Csc3 CRISPR type I-D/CYANO-associated protein Csc3/Cas10d. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family is a CRISPR-associated (Cas) family strictly associated with the Cyano subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. This family is designated Csc3 for CRISPR/Cas Subtype Cyano protein 3, as it is often the third gene upstream of the core cas genes, cas3-cas4-cas1-cas2. 953 matched cddid_all.tbl CDD TIGR03175 TIGR03175 274470 AllD ureidoglycolate dehydrogenase. This enzyme converts ureidoglycolate to oxalureate in the non-urea-forming catabolism of allantoin (GenProp0687). The pathway has been characterized in E. coli and is observed in the genomes of Entercoccus faecalis and Bacillus licheniformis. 349 matched cddid_all.tbl CDD TIGR03176 TIGR03176 274471 AllC allantoate amidohydrolase. This enzyme catalyzes the breakdown of allantoate, first to ureidoglycine by hydrolysis and then decarboxylation of one of the two equivalent ureido groups. Ureidoglycine then spontaneously exchanges ammonia for water resulting in ureidoglycolate. This enzyme is an alternative to allantoicase (3.5.3.4) which releases urea. [Central intermediary metabolism, Nitrogen metabolism] 406 matched cddid_all.tbl CDD TIGR03177 TIGR03177 274472 pilus_cpaB Flp pilus assembly protein CpaB. Members of this protein family are the CpaB protein of Flp-type pilus assembly. Similar proteins include the FlgA protein of bacterial flagellum biosynthesis. 261 matched cddid_all.tbl CDD TIGR03178 TIGR03178 163175 allantoinase allantoinase. This enzyme carries out the first step in the degradation of allantoin, a ring-opening hydrolysis. The seed members of this model are all in the vicinity of other genes involved in the processes of xanthine/urate/allantoin catabolism. Although not included in the seed, many eukaryotic homologs of this family are included above the trusted cutoff. Below the noise cutoff are related hydantoinases. 443 matched cddid_all.tbl CDD TIGR03180 TIGR03180 188295 UraD_2 OHCU decarboxylase. Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) has been recently been shown to be catalyzed by this enzyme in Mus musculus. Homologs of this enzyme are found adjacent to and fused with uricase in a number of prokaryotes and are represented by this model. This model is a separate (but related) clade from that represented by TIGR3164. This model places a second homolog in streptomyces species which (are not in the vicinity of other urate catabolism associated genes) below the trusted cutoff. 158 matched cddid_all.tbl CDD TIGR03181 TIGR03181 213783 PDH_E1_alph_x pyruvate dehydrogenase E1 component, alpha subunit. Members of this protein family are the alpha subunit of the E1 component of pyruvate dehydrogenase (PDH). This model represents one branch of a larger family that E1-alpha proteins from 2-oxoisovalerate dehydrogenase, acetoin dehydrogenase, another PDH clade, etc. [Energy metabolism, Pyruvate dehydrogenase] 341 matched cddid_all.tbl CDD TIGR03182 TIGR03182 274473 PDH_E1_alph_y pyruvate dehydrogenase E1 component, alpha subunit. Members of this protein family are the alpha subunit of the E1 component of pyruvate dehydrogenase (PDH). This model represents one branch of a larger family that E1-alpha proteins from 2-oxoisovalerate dehydrogenase, acetoin dehydrogenase, another PDH clade, etc. [Energy metabolism, Pyruvate dehydrogenase] 315 matched cddid_all.tbl CDD TIGR03183 TIGR03183 163177 DNA_S_dndC putative sulfurtransferase DndC. Members of this protein family are the DndC protein from the dnd (degradation during electrophoresis) operon. The dnd phenotype reflects a sulfur-containing modification to DNA. This operon is sparsely and sporadically distributed among bactera; among the first eight examples are members from the Actinobacteria, Firmicutes, Gammaproteobacteria, Cyanobacteria. DndC is suggested to be a sulfurtransferase. [DNA metabolism, Restriction/modification] 447 matched cddid_all.tbl CDD TIGR03184 TIGR03184 274474 DNA_S_dndE DNA sulfur modification protein DndE. This model describes the DndE protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndE is a putative carboxylase homologous to NCAIR synthetases. [DNA metabolism, Restriction/modification] 105 matched cddid_all.tbl CDD TIGR03185 TIGR03185 274475 DNA_S_dndD DNA sulfur modification protein DndD. This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria. [DNA metabolism, Restriction/modification] 650 matched cddid_all.tbl CDD TIGR03186 TIGR03186 132230 AKGDH_not_PDH alpha-ketoglutarate dehydrogenase. Several bacterial species have a paralog to homodimeric form of the pyruvate dehydrogenase E1 component (see model TIGR00759), often encoded next to L-methionine gamma-lyase gene (mdeA). The member from a strain of Pseudomonas putida was shown to act on alpha-ketobutyrate, which is produced by MdeA.This model serves as an exception model to TIGR00759, as other proteins hitting TIGR00759 should be identified as the pyruvate dehydrogenase E1 component. 889 matched cddid_all.tbl CDD TIGR03187 TIGR03187 274476 DGQHR DGQHR domain. This highly divergent, uncharacterized domain has several absolutely conserved residues, including a QR pair and FxxxN motif. Its most striking feature, however, is a near invariant pentapeptide motif DGQHR. Several different subfamilies occur specifically as a part of DNA phosphorothioation systems, previously called DND (DNA instability during electrophoresis), while others (e.g. CPS_2936) occur in other contexts suggestive of lateral gene transfer (sporadic distribution of helicase-containing cassettes). The region described by this model is about 280 amino acids in length; additional sequences show local sequence similarity. 272 matched cddid_all.tbl CDD TIGR03188 TIGR03188 274477 histidine_hisI phosphoribosyl-ATP pyrophosphohydrolase. This enzyme, phosphoribosyl-ATP pyrophosphohydrolase, catalyses the second step in the histidine biosynthesis pathway. It often occurs as a fusion protein. This model a somewhat narrower scope than pfam01503, as some paralogs that appear to be functionally distinct are excluded from this model. [Amino acid biosynthesis, Histidine family] 84 matched cddid_all.tbl CDD TIGR03189 TIGR03189 132233 dienoyl_CoA_hyt cyclohexa-1,5-dienecarbonyl-CoA hydratase. This enzyme, cyclohexa-1,5-dienecarbonyl-CoA hydratase, also called dienoyl-CoA hydratase, acts on the product of benzoyl-CoA reductase (EC 1.3.99.15). Benzoyl-CoA is a common intermediate in the degradation of many aromatic compounds, and this enzyme is part of an anaerobic pathway for dearomatization and degradation. 251 matched cddid_all.tbl CDD TIGR03190 TIGR03190 132234 benz_CoA_bzdN benzoyl-CoA reductase, bzd-type, N subunit. Members of this family are the N subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene. 377 matched cddid_all.tbl CDD TIGR03191 TIGR03191 132235 benz_CoA_bzdO benzoyl-CoA reductase, bzd-type, O subunit. Members of this family are the O subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene. 430 matched cddid_all.tbl CDD TIGR03192 TIGR03192 132236 benz_CoA_bzdQ benzoyl-CoA reductase, bzd-type, Q subunit. Members of this family are the Q subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene. 293 matched cddid_all.tbl CDD TIGR03193 TIGR03193 132237 4hydroxCoAred 4-hydroxybenzoyl-CoA reductase, gamma subunit. 4-hydroxybenzoyl-CoA reductase converts 4-hydroxybenzoyl-CoA to benzoyl-CoA, a common intermediate in the degradation of aromatic compounds. This protein family represents the gamma chain of this three-subunit enzyme. 148 matched cddid_all.tbl CDD TIGR03194 TIGR03194 132238 4hydrxCoA_A 4-hydroxybenzoyl-CoA reductase, alpha subunit. This model represents the largest chain, alpha, of the enzyme 4-hydroxybenzoyl-CoA reductase. In species capable of degrading various aromatic compounds by way of benzoyl-CoA, this enzyme can convert 4-hydroxybenzoyl-CoA to benzoyl-CoA. 746 matched cddid_all.tbl CDD TIGR03195 TIGR03195 132239 4hydrxCoA_B 4-hydroxybenzoyl-CoA reductase, beta subunit. This model represents the second largest chain, beta, of the enzyme 4-hydroxybenzoyl-CoA reductase. In species capable of degrading various aromatic compounds by way of benzoyl-CoA, this enzyme can convert 4-hydroxybenzoyl-CoA to benzoyl-CoA. 321 matched cddid_all.tbl CDD TIGR03196 TIGR03196 132240 pucD xanthine dehydrogenase D subunit. This gene has been characterized in B. subtilis as the molybdopterin binding-subunit of xanthine dehydrogenase (pucD), acting in conjunction with pucC, the FAD-binding subunit and pucE, the FeS-binding subunit. The more common XDH complex (GenProp0640) includes the xdhB gene which is related to pucD. It appears that most of the relatives of pucD outside of this narrow clade are involved in other processes as they are found in unrelated genomic contexts, contain the more common XDH complex and/or do not appear to process purines to allantoin. 768 matched cddid_all.tbl CDD TIGR03197 TIGR03197 274478 MnmC_Cterm tRNA U-34 5-methylaminomethyl-2-thiouridine biosynthesis protein MnmC, C-terminal domain. In Escherichia coli, the protein previously designated YfcK is now identified as the bifunctional enzyme MnmC. It acts, following the action of the heterotetramer of GidA and MnmE, in the modification of U-34 of certain tRNA to 5-methylaminomethyl-2-thiouridine (mnm5s2U). In other bacterial, the corresponding proteins are usually but always found as a single polypeptide chain, but occasionally as the product of tandem genes. This model represents the C-terminal region of the multifunctional protein. [Protein synthesis, tRNA and rRNA base modification] 381 matched cddid_all.tbl CDD TIGR03198 TIGR03198 132242 pucE xanthine dehydrogenase E subunit. This gene has been characterized in B. subtilis as the Iron-sulfur cluster binding-subunit of xanthine dehydrogenase (pucE), acting in conjunction with pucC, the FAD-binding subunit and pucD, the molybdopterin binding subunit. The more common XDH complex (GenProp0640) includes the xdhA gene as the Fe-S cluster binding component. 151 matched cddid_all.tbl CDD TIGR03199 TIGR03199 274479 pucC xanthine dehydrogenase C subunit. This gene has been characterized in B. subtilis as the FAD binding-subunit of xanthine dehydrogenase (pucC), acting in conjunction with pucD, the molybdopterin-binding subunit and pucE, the FeS-binding subunit. 264 matched cddid_all.tbl CDD TIGR03200 TIGR03200 132244 dearomat_oah 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase. Members of this protein family are 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase, a ring-hydrolyzing enzyme in the anaerobic metabolism of aromatic enzymes by way of benzoyl-CoA, as seen in Thauera aromatica, Geobacter metallireducens, and Azoarcus sp. Note that Rhodopseudomonas palustris uses a different pathway to perform a similar degradation of benzoyl-CoA to 3-hydroxpimelyl-CoA. 360 matched cddid_all.tbl CDD TIGR03201 TIGR03201 132245 dearomat_had 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase. Members of this protein family are 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase, an enzyme in the anaerobic metabolism of aromatic enzymes by way of benzoyl-CoA, as seen in Thauera aromatica, Geobacter metallireducens, and Azoarcus sp. The experimentally characterized form from T. aromatica uses only NAD+, not NADP+. Note that Rhodopseudomonas palustris uses a different pathway to perform a similar degradation of benzoyl-CoA to 3-hydroxpimelyl-CoA. 349 matched cddid_all.tbl CDD TIGR03202 TIGR03202 132246 pucB xanthine dehydrogenase accessory protein pucB. In Bacillus subtilis the expression of this protein, located in an operon with the structural subunits of xanthine dehydrogenase, has been found to be essential for XDH activity. Some members of this family appear to have a distant relationship to the MobA protein involved in molybdopterin biosynthesis, although this may be coincidental. 190 matched cddid_all.tbl CDD TIGR03203 TIGR03203 132247 pimD_small pimeloyl-CoA dehydrogenase, small subunit. Members of this protein family are the PimD proteins of species such as Rhodopseudomonas palustris, Bradyrhizobium japonicum. The pimFABCDE operon encodes proteins for the metabolism of straight chain dicarboxylates of seven to fourteen carbons. Especially relevant is pimeloyl-CoA, basis of the gene symbol, as it is a catabolite of benzoyl-CoA degradation, which occurs in Rhodopseudomonas palustris. 378 matched cddid_all.tbl CDD TIGR03204 TIGR03204 132248 pimC_large pimeloyl-CoA dehydrogenase, large subunit. Members of this protein family are the PimC proteins of species such as Rhodopseudomonas palustris and Bradyrhizobium japonicum. The pimFABCDE operon encodes proteins for the metabolism of straight chain dicarboxylates of seven to fourteen carbons. Especially relevant is pimeloyl-CoA, basis of the gene symbol, as it is a catabolite of benzoyl-CoA degradation, which occurs in Rhodopseudomonas palustris. 395 matched cddid_all.tbl CDD TIGR03205 TIGR03205 132249 pimA dicarboxylate--CoA ligase PimA. PimA, a member of a large family of acyl-CoA ligases, is found in a characteristic operon pimFABCDE for the metabolism of pimelate and related compounds. It is found, so far, in Bradyrhizobium japonicum and several strains of Rhodopseudomonas palustris. PimA from R. palustris was shown to be active as a CoA ligase for C(7) to C(14) dicarboxylates and fatty acids. 541 matched cddid_all.tbl CDD TIGR03206 TIGR03206 132250 benzo_BadH 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase. Members of this protein family are the enzyme 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase. The enzymatic properties were confirmed experimentally in Rhodopseudomonas palustris; the enzyme is homotetrameric, and not sensitive to oxygen. This enzyme is part of proposed pathway for degradation of benzoyl-CoA to 3-hydroxypimeloyl-CoA that differs from the analogous in Thauera aromatica. It also may occur in degradation of the non-aromatic compound cyclohexane-1-carboxylate. 250 matched cddid_all.tbl CDD TIGR03207 TIGR03207 132251 cyc_hxne_CoA_dh cyclohexanecarboxyl-CoA dehydrogenase. Cyclohex-1-ene-1carboxyl-CoA is an intermediate in the anaerobic degradation of benzoyl-CoA derived from varioius aromatic compounds, in Rhodopseudomonas palustris but not Thauera aromatica. The aliphatic compound cyclohexanecarboxylate, can be converted to the same intermediate in two steps. The first step is its ligation to coenzyme A. The second is the action of this enzyme, cyclohexanecarboxyl-CoA dehydrogenase. 372 matched cddid_all.tbl CDD TIGR03208 TIGR03208 132252 cyc_hxne_CoA_lg cyclohexanecarboxylate-CoA ligase. Members of this protein family are cyclohexanecarboxylate-CoA ligase. This enzyme prepares the aliphatic ring compound, cyclohexanecarboxylate, for dehydrogenation and then degradation by a pathway also used in benzoyl-CoA degradation in Rhodopseudomonas palustris. 538 matched cddid_all.tbl CDD TIGR03209 TIGR03209 132253 P21_Cbot clostridium toxin-associated regulator BotR. Clostridium botulinum neurotoxin production is regulated by a regulatory sigma-70 protein, BotR transcription regulator. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo. 142 matched cddid_all.tbl CDD TIGR03210 TIGR03210 132254 badI 2-ketocyclohexanecarboxyl-CoA hydrolase. Members of this protein family are 2-ketocyclohexanecarboxyl-CoA hydrolase, a ring-opening enzyme that acts in catabolism of molecules such as benzoyl-CoA and cyclohexane carboxylate. It converts -ketocyclohexanecarboxyl-CoA to pimelyl-CoA. It is not sensitive to oxygen. 256 matched cddid_all.tbl CDD TIGR03211 TIGR03211 274480 catechol_2_3 catechol 2,3 dioxygenase. Members of this family all are enzymes active as catechol 2,3 dioxygenase (1.13.11.2), although some members have highly significant activity on catechol derivatives such as 3-methylcatechol, 3-chlorocatechol, and 4-chlorocatechol (see Mars, et al.). This enzyme is also called metapyrocatechase, as it performs a meta-cleavage (an extradiol ring cleavage), in contrast to the ortho-cleavage (intradiol ring cleavage)performed by catechol 1,2-dioxygenase (EC 1.13.11.1), also called pyrocatechase. [Energy metabolism, Other] 303 matched cddid_all.tbl CDD TIGR03212 TIGR03212 211797 uraD_N-term-dom putative urate catabolism protein. This model represents a protein that is predominantly found just upstream of the UraD protein (OHCU decarboxylase) and in a number of instances as a N-terminal fusion with it. UraD itself catalyzes the last step in the catabolism of urate to allantoate. The function of this protein is presently unknown. It shows homology with the pfam01522 polysaccharide deacetylase domain family. 297 matched cddid_all.tbl CDD TIGR03213 TIGR03213 132257 23dbph12diox 2,3-dihydroxybiphenyl 1,2-dioxygenase. Members of this protein family all have activity as 2,3-dihydroxybiphenyl 1,2-dioxygenase, the third enzyme of a pathway for biphenyl degradation. Many of the extradiol ring-cleaving dioxygenases, to which these proteins belong, act on a range of related substrates. Note that some members of this family may be found operons for toluene or naphthalene degradation, where other activities of the same enzyme may be more significant; the trusted cutoff for this model is set relatively high to exclude most such instances. [Energy metabolism, Other] 286 matched cddid_all.tbl CDD TIGR03214 TIGR03214 200251 ura-cupin putative allantoin catabolism protein. This model represents a protein containing a tandem arrangement of cupin domains (N-terminal part of pfam07883 and C-terminal more distantly related to pfam00190). This protein is found in the vicinity of genes involved in the catabolism of allantoin, a breakdown product of urate and sometimes of urate iteslf. The distribution of pathway components in the genomes in which this family is observed suggests that the function is linked to the allantoate catabolism to glyoxylate pathway (GenProp0686) since it is sometimes found in genomes lacking any elements of the xanthine-to-allantoin pathways (e.g. in Enterococcus faecalis). 252 matched cddid_all.tbl CDD TIGR03215 TIGR03215 132259 ac_ald_DH_ac acetaldehyde dehydrogenase (acetylating). Members of this protein family are acetaldehyde dehydrogenase (acetylating), EC 1.2.1.10. This enzyme oxidizes acetaldehyde, using NAD(+), and attaches coenzyme A (CoA), yielding acetyl-CoA. It occurs as a late step in the meta-cleavage pathways of a variety of compounds, including catechol, biphenyl, toluene, salicylate, etc. 285 matched cddid_all.tbl CDD TIGR03216 TIGR03216 132260 OH_muco_semi_DH 2-hydroxymuconic semialdehyde dehydrogenase. Members of this protein family are 2-hydroxymuconic semialdehyde dehydrogenase. Many aromatic compounds are catabolized by way of the catechol, via the meta-cleavage pathway, to pyruvate and acetyl-CoA. This enzyme performs the second of seven steps in that pathway for catechol degradation. [Energy metabolism, Other] 481 matched cddid_all.tbl CDD TIGR03217 TIGR03217 274481 4OH_2_O_val_ald 4-hydroxy-2-oxovalerate aldolase. Members of this protein family are 4-hydroxy-2-oxovalerate aldolase, also called 4-hydroxy-2-ketovalerate aldolase and 2-oxo-4-hydroxypentanoate aldolase. This enzyme, part of the pathway for the meta-cleavage of catechol, produces pyruvate and acetaldehyde. Acetaldehyde is then converted by acetaldehyde dehydrogenase (acylating) (DmpF; EC 1.2.1.10) to acetyl-CoA. The two enzymes are tightly associated. [Energy metabolism, Other] 333 matched cddid_all.tbl CDD TIGR03218 TIGR03218 132262 catechol_dmpH 4-oxalocrotonate decarboxylase. Members of this protein family are 4-oxalocrotonate decarboxylase. Note that this protein, as characterized (indirectly) in Pseudomonas sp. strain CF600, was inactive except when coexpressed with DmpE, 2-oxopent-4-enoate hydratase, a homologous protein from the same operon. Both of these enzymes are active in the degradation of catechol, a common intermediate in the degradation of aromatic compounds such as benzoate, toluene, phenol, dimethylphenol (dmp), salicylate, etc. [Energy metabolism, Other] 263 matched cddid_all.tbl CDD TIGR03219 TIGR03219 274482 salicylate_mono salicylate 1-monooxygenase. Members of this protein family are salicylate 1-monooxygenase, also called salicylate hydroxylase. This enzyme converts salicylate to catechol, which is a common intermediate in the degradation of a number of aromatic compounds (phenol, toluene, benzoate, etc.). The gene for this protein may occur in catechol degradation genes, such as those of the meta-cleavage pathway. 414 matched cddid_all.tbl CDD TIGR03220 TIGR03220 132264 catechol_dmpE 2-oxopent-4-enoate hydratase. Members of this protein family are 2-oxopent-4-enoate hydratase, which is also called 2-hydroxypent-2,4-dienoate hydratase. It is closely related to another gene found in the same operon, 4-oxalocrotonate decarboxylase, with which it interacts closely. 255 matched cddid_all.tbl CDD TIGR03221 TIGR03221 213786 muco_delta muconolactone delta-isomerase. Members of this protein family are muconolactone delta-isomerase (EC 5.3.3.4), the CatC protein of the ortho cleavage pathway for metabolizing aromatic compounds by way of catechol. [Energy metabolism, Other] 90 matched cddid_all.tbl CDD TIGR03222 TIGR03222 213787 benzo_boxC benzoyl-CoA-dihydrodiol lyase. In the presence of O2, the benzoyl-CoA oxygenase/reductase BoxBA BoxAB converts benzoyl-CoA to 2,3-dihydro-2,3-dihydroxybenzoyl-CoA. Members of this family, BoxC, homologous to enoyl-CoA hydratases/isomerases, hydrolyze this compound to 3,4-dehydroadipyl-CoA semialdehyde + HCOOH. 546 matched cddid_all.tbl CDD TIGR03223 TIGR03223 274483 Phn_opern_protn "putative phosphonate metabolism protein. This family of proteins is observed in the vicinity of other caharacterized genes involved in the catabolism of phosphonates via the3 C-P lyase system (GenProp0232), its function is unknown. These proteins are members of the somewhat broader pfam06299 model ""Protein of unknown function (DUF1045)"" which contains proteins found in a different genomic context as well." 228 matched cddid_all.tbl CDD TIGR03224 TIGR03224 132268 benzo_boxA benzoyl-CoA oxygenase/reductase, BoxA protein. Members of this protein family are BoxA, the A component of the BoxAB benzoyl-CoA oxygenase/reductase. This oxygen-requiring enzyme acts in an aerobic pathway of benzoate catabolism via coenzyme A ligation. BoxA is a homodimeric iron-sulphur-flavoprotein and acts as an NADPH-dependent reductase for BoxB. [Energy metabolism, Other] 411 matched cddid_all.tbl CDD TIGR03225 TIGR03225 200253 benzo_boxB benzoyl-CoA oxygenase, B subunit. Members of this protein family are BoxB, the B subunit of benzoyl-CoA oxygenase. This oxygen-requiring enzyme acts in an aerobic pathway of benzoate catabolism via coenzyme A ligation. [Energy metabolism, Other] 471 matched cddid_all.tbl CDD TIGR03226 TIGR03226 274484 PhnU 2-aminoethylphosphonate ABC transporter, permease protein. This ABC transporter permease (membrane-spanning) component is found in a region of the salmonella typhimurium LT2 genome responsible for the catabolism of 2-aminoethylphosphonate via the phnWX pathway (GenProp0238). 288 matched cddid_all.tbl CDD TIGR03227 TIGR03227 132271 PhnS "2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate binding protein. This ABC transporter periplasmic substrate binding protein component is found in a region of the salmonella typhimurium LT2 genome responsible for the catabolism of 2-aminoethylphosphonate via the phnWX pathway (GenProp0238). The protein contains a match to pfam01547 for the ""Bacterial extracellular solute-binding protein"" domain." 367 matched cddid_all.tbl CDD TIGR03228 TIGR03228 132272 anthran_1_2_A anthranilate 1,2-dioxygenase, large subunit. Anthranilate (2-aminobenzoate) is an intermediate of tryptophan (Trp) biosynthesis and degradation. Members of this family are the large subunit of anthranilate 1,2-dioxygenase, which acts in Trp degradation by converting anthranilate to catechol. Closely related paralogs typically are the benzoate 1,2-dioxygenase large subunit, among the larger set of ring-hydroxylating dioxygenases. [Energy metabolism, Amino acids and amines] 438 matched cddid_all.tbl CDD TIGR03229 TIGR03229 132273 benzo_1_2_benA benzoate 1,2-dioxygenase, large subunit. Benzoate 1,2-dioxygenase (EC 1.14.12.10) belongs to the larger family of aromatic ring-hydroxylating dioxygenases. Members of this family all act on benzoate, but may have additional activities on various benozate analogs. This model describes the large subunit. Between the trusted and noise cutoffs are similar enzymes, likely to act on benzoate but perhaps best identified according to some other activity, such as 2-chlorobenzoate 1,2-dioxygenase (1.14.12.13). [Energy metabolism, Other] 433 matched cddid_all.tbl CDD TIGR03230 TIGR03230 132274 lipo_lipase lipoprotein lipase. Members of this protein family are lipoprotein lipase (EC 3.1.1.34), a eukaryotic triacylglycerol lipase active in plasma and similar to pancreatic and hepatic triacylglycerol lipases (EC 3.1.1.3). It is also called clearing factor. It cleaves chylomicron and VLDL triacylglycerols; it also has phospholipase A-1 activity. 442 matched cddid_all.tbl CDD TIGR03231 TIGR03231 132275 anthran_1_2_B anthranilate 1,2-dioxygenase, small subunit. Anthranilate (2-aminobenzoate) is an intermediate of tryptophan (Trp) biosynthesis and degradation. Members of this family are the small subunit of anthranilate 1,2-dioxygenase, which acts in Trp degradation by converting anthranilate to catechol. Closely related paralogs typically are the benzoate 1,2-dioxygenase small subunit, among the larger set of ring-hydroxylating dioxygenases. [Energy metabolism, Amino acids and amines] 155 matched cddid_all.tbl CDD TIGR03232 TIGR03232 132276 benzo_1_2_benB benzoate 1,2-dioxygenase, small subunit. Benzoate 1,2-dioxygenase (EC 1.14.12.10) belongs to the larger family of aromatic ring-hydroxylating dioxygenases. Members of this family should all act on benzoate, but several have additional known activities on various benozate analogs. Some members actually may be named more suitably according to such alternate an activity, such as 2-chlorobenzoate 1,2-dioxygenase (1.14.12.13). 155 matched cddid_all.tbl CDD TIGR03233 TIGR03233 163189 DNA_S_dndB DNA sulfur modification protein DndB. This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndB is described as a putative ATPase. [DNA metabolism, Restriction/modification] 355 matched cddid_all.tbl CDD TIGR03234 TIGR03234 163190 OH-pyruv-isom hydroxypyruvate isomerase. This enzyme interconverts tartronate semi-aldehyde (TSA, aka 2-hydroxy 3-oxopropionate) and hydroxypyruvate. The E. coli enzyme has been characterized and found to be specific for TSA, contain no cofactors, and have a rather high Km for hydroxypyruvate of 12.5 mM. The gene is ofter found in association with glyoxalate carboligase (which produces TSA), but has been shown to have no effect on growth on glyoxalate when knocked out. This is consistent with the fact that the gene for tartronate semialdehyde reductase (glxR) is also associated and may have primary responsibility for the catabolism of TSA. 254 matched cddid_all.tbl CDD TIGR03235 TIGR03235 163191 DNA_S_dndA cysteine desulfurase DndA. This model describes DndA, a protein related to IscS and part of a larger family of cysteine desulfurases. It is encoded, typically, divergently from a conserved, sparsely distributed operon for sulfur modification of DNA. This modification system is designated dnd, after the phenotype of DNA degradation during electrophoresis. The system is sporadically distributed in bacteria, much like some restriction enzyme operons. DndB is described as a putative ATPase. [DNA metabolism, Restriction/modification] 353 matched cddid_all.tbl CDD TIGR03236 TIGR03236 274485 dnd_assoc_1 DNA phosphorothioation-dependent restriction protein DptG. A DNA sulfur modification (phosphorothioation) system, dnd (degradation during electrophoresis), is sparsely and sporadically distributed among the bacteria. This protein is one member of a three-gene restriction enzyme cassette that depends on DNA phosphorothioation. [DNA metabolism, Restriction/modification] 363 matched cddid_all.tbl CDD TIGR03237 TIGR03237 132281 dnd_assoc_2 DNA phosphorothioation-dependent restriction protein DptH. A DNA sulfur modification (phosphorothioation) system, dnd (degradation during electrophoresis), is sparsely and sporadically distributed among the bacteria. This protein is one member of a three-gene restriction enzyme cassette that depends on DNA phosphorothioation. [DNA metabolism, Restriction/modification] 1256 matched cddid_all.tbl CDD TIGR03238 TIGR03238 132282 dnd_assoc_3 DNA phosphorothioation-dependent restriction protein DptF. A DNA sulfur modification (phosphorothioation) system, dnd (degradation during electrophoresis), is sparsely and sporadically distributed among the bacteria. This protein is one member of a three-gene restriction enzyme cassette that depends on DNA phosphorothioation. [DNA metabolism, Restriction/modification] 504 matched cddid_all.tbl CDD TIGR03239 TIGR03239 132283 GarL 2-dehydro-3-deoxyglucarate aldolase. In E. coli this enzyme (GarL) 2-dehydro-3-deoxyglucarate aldolase acts in the catabolism of several sugars including D-galactarate, D-glucarate and L-idarate. In fact, 5-dehydro-4-deoxy-D-glucarate aldolase is a synonym for this enzyme as it is unclear in the literature whether the enzyme acts on only one of these or, as seems likely, has no preference. (Despite the apparent large difference in substrate stucture indicated by their names, 2-DH-3DO- and 5-DH-4DO-glucarate differ only by the chirality of most central hydroxyl-bearing carbon and is alternately named 2-DH-3DO-galactarate.) The reported product of D-galactarate dehydratase (4.2.1.42) is the 5DH-4DO-glucarate isomer and this enzyme is found proximal to the aldolase in many genomes (GenProp0714) where no epimerase is known. Similarly, the product of D-glucarate dehydratase (4.2.1.40) is again the 5-DH-4DO isomer, so the provenance of the 2-DH-3DO-glucarate isomer for which this enzyme is named is unclear. 249 matched cddid_all.tbl CDD TIGR03240 TIGR03240 274486 arg_catab_astD succinylglutamate-semialdehyde dehydrogenase. Members of this protein family are succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71), the fourth enzyme in the arginine succinyltransferase (AST) pathway for arginine catabolism. [Energy metabolism, Amino acids and amines] 484 matched cddid_all.tbl CDD TIGR03241 TIGR03241 132285 arg_catab_astB succinylarginine dihydrolase. Members of this family are succinylarginine dihydrolase (EC 3.5.3.23), the second of five enzymes in the arginine succinyltransferase (AST) pathway. [Energy metabolism, Amino acids and amines] 443 matched cddid_all.tbl CDD TIGR03242 TIGR03242 132286 arg_catab_astE succinylglutamate desuccinylase. Members of this protein family are succinylglutamate desuccinylase, the fifth and final enzyme of the arginine succinyltransferase (AST) pathway for arginine catabolism. This model excludes the related protein aspartoacylase. [Energy metabolism, Amino acids and amines] 319 matched cddid_all.tbl CDD TIGR03243 TIGR03243 274487 arg_catab_AOST arginine and ornithine succinyltransferase subunits. In many bacteria, the sole member of this protein family is arginine N-succinyltransferase (EC 2.3.1.109), the AstA protein of the arginine succinyltransferase (ast) pathway. However, in Pseudomonas aeruginosa and several other species, a tandem gene pair encodes alpha and beta subunits of a heterodimer that is designated arginine and ornithine succinyltransferase (AOST). 335 matched cddid_all.tbl CDD TIGR03244 TIGR03244 274488 arg_catab_AstA arginine N-succinyltransferase. In many bacteria, the arginine succinyltransferase (ast) pathway operon consists of five genes, including this protein, arginine N-succinyltransferase (EC 2.3.1.109). In a few species, such as Pseudomonas aeruginosa, the member of this family is encoded adjacent to a paralog, and the two polypeptides form a heterodimeric enzyme, active on both arginine and ornithine. In such species, this polypeptide may be treated as the beta subunit of an enzyme that may be named either arginine N-succinyltransferase (AST) or arginine and orthithine N-succinyltransferase (AOST). [Energy metabolism, Amino acids and amines] 336 matched cddid_all.tbl CDD TIGR03245 TIGR03245 274489 arg_AOST_alph arginine/ornithine succinyltransferase, alpha subunit. In some bacteria, including Pseudomonas aeruginosa, the astB gene (arginine N-succinyltransferase) is replaced by tandem paralogs that form a heterodimer. This heterodimer from P. aeruginosa is characterized as arginine and ornithine N-2 succinyltransferase (AOST). Members of this protein family represent the less widespread paralog, designated AruI, or arginine/ornithine succinyltransferase, alpha subunit. 336 matched cddid_all.tbl CDD TIGR03246 TIGR03246 274490 arg_catab_astC succinylornithine transaminase family. Members of the seed alignment for this protein family are the enzyme succinylornithine transaminase (EC 2.6.1.81), which catalyzes the third of five steps in arginine succinyltransferase (AST) pathway, an ammonia-releasing pathway of arginine degradation. All seed alignment sequences are found within arginine succinyltransferase operons, and all proteins that score above 820.0 bits should function as succinylornithine transaminase. However, a number of sequences extremely closely related in sequence, found in different genomic contexts, are likely to act in different biological processes and may act on different substrates. This model is desigated subfamily rather than equivalog, pending further consideration, for this reason. [Energy metabolism, Amino acids and amines] 397 matched cddid_all.tbl CDD TIGR03247 TIGR03247 211799 glucar-dehydr glucarate dehydratase. Glucarate dehydratase converts D-glucarate (and L-idarate, a stereoisomer) to 5-dehydro-4-deoxyglucarate which is subsequently acted on by GarL, tartronate semialdehyde reductase and glycerate kinase (GenProp0716). The E. coli enzyme has been well-characterized. 441 matched cddid_all.tbl CDD TIGR03248 TIGR03248 274491 galactar-dH20 galactarate dehydratase. Galactarate dehydratase converts D-galactarate to 5-dehydro-4-deoxyglucarate which is subsequently acted on by GarL, tartronate semialdehyde reductase and glycerate kinase (GenProp0714). 506 matched cddid_all.tbl CDD TIGR03249 TIGR03249 132293 KdgD 5-dehydro-4-deoxyglucarate dehydratase. 5-dehydro-4-deoxyglucarate dehydratase not only catalyzes the dehydration of the substrate (diol to ketone + water), but causes the decarboxylation of the intermediate product to yield 2-oxoglutarate semialdehyde (2,5-dioxopentanoate). The gene for the enzyme is usually observed in the vicinity of transporters and dehydratases handling D-galactarate and D-gluconate as well as aldehyde dehydrogenases which convert the product to alpha-ketoglutarate. 296 matched cddid_all.tbl CDD TIGR03250 TIGR03250 132294 PhnAcAld_DH putative phosphonoacetaldehyde dehydrogenase. This family of genes are members of the pfam00171 NAD-dependent aldehyde dehydrogenase family. These genes are observed in Ralstonia eutropha JMP134, Sinorhizobium meliloti 1021, Burkholderia mallei ATCC 23344, Burkholderia thailandensis E264, Burkholderia cenocepacia AU 1054, Burkholderia pseudomallei K96243 and 1710b, Burkholderia xenovorans LB400, Burkholderia sp. 383 and Polaromonas sp. JS666 in close proximity to the PhnW gene (TIGR02326) encoding 2-aminoethyl phosphonate aminotransferase (which generates phosphonoacetaldehyde) and PhnA (TIGR02335) encoding phosphonoacetate hydrolase (not to be confused with the alkylphosphonate utilization operon protein PhnA modeled by TIGR00686). Additionally, transporters believed to be specific for 2-aminoethyl phosphonate are often present. PhnW is, in other organisms, coupled with PhnX (TIGR01422) for the degradation of phosphonoacetaldehyde (GenProp0238), but PhnX is apparently absent in each of the organisms containing this aldehyde reductase. PhnA, characterized in a strain of Pseudomonas fluorescens that has not het been genome sequenced, is only rarely found outside of the PhnW and aldehyde dehydrogenase context. For instance in Rhodopseudomonas and Bordetella bronchiseptica, where it is adjacent to transporters presumably specific for the import of phosphonoacetate. It seems reasonably certain then, that this enzyme catalyzes the NAD-dependent oxidation of phosphonoacetaldehyde to phosphonoacetate, bridging the metabolic gap between PhnW and PhnA. We propose the name phosphonoacetaldehyde dehydrogenase and the gene symbol PhnY for this enzyme. 472 matched cddid_all.tbl CDD TIGR03251 TIGR03251 274492 LAT_fam L-lysine 6-transaminase. Characterized members of this protein family are L-lysine 6-transaminase, also called lysine epsilon-aminotransferase (LAT). The immediate product of the reaction of this enzyme on lysine, 2-aminoadipate 6-semialdehyde, becomes 1-piperideine 6-carboxylate, or P6C. This product may be converted subsequently to pipecolate or alpha-aminoadipate, lysine catabolites that may be precursors of certain seconary metabolites. 431 matched cddid_all.tbl CDD TIGR03252 TIGR03252 132296 TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730). [DNA metabolism, DNA replication, recombination, and repair] 177 matched cddid_all.tbl CDD TIGR03253 TIGR03253 211800 oxalate_frc formyl-CoA transferase. This enzyme, formyl-CoA transferase, transfers coenzyme A from formyl-CoA to oxalate. It forms a pathway, together with oxalyl-CoA decarboxylase, for oxalate degradation; decarboxylation by the latter gene regenerates formyl-CoA. The two enzymes typically are encoded by a two-gene operon. [Cellular processes, Detoxification] 415 matched cddid_all.tbl CDD TIGR03254 TIGR03254 132298 oxalate_oxc oxalyl-CoA decarboxylase. In a number of bacteria, including Oxalobacter formigenes from the human gut, a two-gene operon of oxc (oxalyl-CoA decarboxylase) and frc (formyl-CoA transferase) encodes a system for degrading and therefore detoxifying oxalate. Members of this family are the thiamine pyrophosphate (TPP)-containing enzyme oxalyl-CoA decarboxylase. [Cellular processes, Detoxification] 554 matched cddid_all.tbl CDD TIGR03255 TIGR03255 132299 PhnV 2-aminoethylphosphonate ABC transport system, membrane component PhnV. This membrane component of an ABC transport system is found in Salmonella and Burkholderia lineages in the vicinity of enzymes for the breakdown of 2-aminoethylphosphonate. 272 matched cddid_all.tbl CDD TIGR03256 TIGR03256 132300 met_CoM_red_alp methyl-coenzyme M reductase, alpha subunit. Members of this protein family are the alpha subunit of methyl coenzyme M reductase, also called coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). This enzyme, with alpha, beta, and gamma subunits, catalyzes the last step in methanogenesis. Several methanogens have encode two such enzymes, designated I and II; this model does not separate the isozymes. [Energy metabolism, Methanogenesis] 548 matched cddid_all.tbl CDD TIGR03257 TIGR03257 132301 met_CoM_red_bet methyl-coenzyme M reductase, beta subunit. Members of this protein family are the beta subunit of methyl coenzyme M reductase, also called coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). This enzyme, with alpha, beta, and gamma subunits, catalyzes the last step in methanogenesis. Several methanogens have encode two such enzymes, designated I and II; this model does not separate the isozymes. [Energy metabolism, Methanogenesis] 433 matched cddid_all.tbl CDD TIGR03258 TIGR03258 132302 PhnT 2-aminoethylphosphonate ABC transport system, ATP-binding component PhnT. This ATP-binding component of an ABC transport system is found in Salmonella and Burkholderia lineages in the vicinity of enzymes for the breakdown of 2-aminoethylphosphonate. 362 matched cddid_all.tbl CDD TIGR03259 TIGR03259 132303 met_CoM_red_gam methyl-coenzyme M reductase, gamma subunit. Members of this protein family are the gamma subunit of methyl coenzyme M reductase, also called coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). This enzyme, with alpha, beta, and gamma subunits, catalyzes the last step in methanogenesis. Several methanogens have encode two such enzymes, designated I and II; this model does not separate the isozymes. [Energy metabolism, Methanogenesis] 244 matched cddid_all.tbl CDD TIGR03260 TIGR03260 274493 met_CoM_red_D methyl-coenzyme M reductase operon protein D. Members of this protein family are protein D, a non-structural protein, of the operon for methyl coenzyme M reductase, also called coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). That enzyme, with alpha, beta, and gamma subunits, catalyzes the last step in methanogenesis; it has several modified sites, so accessory proteins are expected. Several methanogens have encode two such enzymes, designated I and II; this model does not separate the isozymes. Proteins in this family are expressed at much lower levels than the methyl-coenzyme M reductase itself and associate and have been shown to form at least transient associations. The precise function is unknown. [Energy metabolism, Methanogenesis] 150 matched cddid_all.tbl CDD TIGR03261 TIGR03261 274494 phnS2 putative 2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate-binding protein. This ABC transporter extracellular solute-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely. [Transport and binding proteins, Amino acids, peptides and amines] 334 matched cddid_all.tbl CDD TIGR03262 TIGR03262 274495 PhnU2 putative 2-aminoethylphosphonate ABC transporter, permease protein. [Transport and binding proteins, Amino acids, peptides and amines] 546 matched cddid_all.tbl CDD TIGR03263 TIGR03263 213788 guanyl_kin guanylate kinase. Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP. [Purines, pyrimidines, nucleosides, and nucleotides, Nucleotide and nucleoside interconversions] 179 matched cddid_all.tbl CDD TIGR03264 TIGR03264 132308 met_CoM_red_C methyl-coenzyme M reductase I operon protein C. Members of this protein family are protein C, a non-structural protein, of the operon for methyl coenzyme M reductase, also called coenzyme-B sulfoethylthiotransferase (EC 2.8.4.1). That enzyme, with alpha, beta, and gamma subunits, catalyzes the last step in methanogenesis; it has several modified sites, so accessory proteins are expected. Several methanogens have encode two such enzymes, designated I and II; this protein occurs only operons of type I. The precise function is unknown. [Energy metabolism, Methanogenesis] 194 matched cddid_all.tbl CDD TIGR03265 TIGR03265 274496 PhnT2 putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein. This ABC transporter ATP-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely. [Transport and binding proteins, Amino acids, peptides and amines] 353 matched cddid_all.tbl CDD TIGR03266 TIGR03266 132310 methan_mark_1 putative methanogenesis marker protein 1. Members of this protein family represent a distinct clade among the larger set of proteins that belong to families TIGR00702 and pfam02624. Proteins from this clade are found in genome sequence if and only if the species sequenced is one of the methanogens. All methanogens belong to the archaea; some but not all of those sequenced are hyperthermophiles. This protein family was detected by the method of partial phylogenetic profiling (see Haft, et al., 2006). 376 matched cddid_all.tbl CDD TIGR03267 TIGR03267 132311 methan_mark_2 putative methanogenesis marker protein 2. A single member of this protein family is found in each of the first ten complete genome sequences of archaeal methanogens, and nowhere else. Sequence similarity to various bacterial proteins is reflected in Pfam models pfam00586 and pfam02769, AIR synthase related protein N-terminal and C-terminal domains, respectively. The functions of proteins in this family are unknown, but their role is likely one essential to methanogenesis. [Energy metabolism, Methanogenesis] 323 matched cddid_all.tbl CDD TIGR03268 TIGR03268 132312 methan_mark_3 putative methanogenesis marker protein 3. A single member of this protein family is found in each of the first ten complete genome sequences of archaeal methanogens, and nowhere else. This protein family was detected by the method of partial phylogenetic profiling (see Haft, et al., 2006). The functions of proteins in this family are unknown, but their role is likely one essential to methanogenesis. [Energy metabolism, Methanogenesis] 503 matched cddid_all.tbl CDD TIGR03269 TIGR03269 132313 met_CoM_red_A2 methyl coenzyme M reductase system, component A2. The enzyme that catalyzes the final step in methanogenesis, methyl coenzyme M reductase, contains alpha, beta, and gamma chains. In older literature, the complex of alpha, beta, and gamma chains was termed component C, while this single chain protein was termed methyl coenzyme M reductase system component A2. [Energy metabolism, Methanogenesis] 520 matched cddid_all.tbl CDD TIGR03270 TIGR03270 274497 methan_mark_4 putative methanogen marker protein 4. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely linked to it. Some members have been suggested to be a methyltransferase, based on the proximity of its gene to genes of the multi-subunit complex, N5-methyl-tetrahydromethanopterin--coenzyme M methyltransferase. That context is not conserved, however. The family shows similarity to various phosphate acyltranferases. [Energy metabolism, Methanogenesis] 202 matched cddid_all.tbl CDD TIGR03271 TIGR03271 132315 methan_mark_5 putative methanogenesis marker protein 5. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. [Energy metabolism, Methanogenesis] 142 matched cddid_all.tbl CDD TIGR03272 TIGR03272 274498 methan_mark_6 putative methanogenesis marker protein 6. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. [Energy metabolism, Methanogenesis] 132 matched cddid_all.tbl CDD TIGR03274 TIGR03274 132317 methan_mark_7 putative methanogenesis marker protein 7. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. 302 matched cddid_all.tbl CDD TIGR03275 TIGR03275 132318 methan_mark_8 putative methanogenesis marker protein 8. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. 259 matched cddid_all.tbl CDD TIGR03276 TIGR03276 132319 Phn-HD phosphonate degradation operons associated HDIG domain protein. This small clade of proteins are found adjacent to other genes implicated in the catabolism of phosphonates. They are members of the TIGR00277 domain family and contain a series of five invariant histidines (the domain in general has only four). 179 matched cddid_all.tbl CDD TIGR03277 TIGR03277 132320 methan_mark_9 putative methanogenesis marker domain 9. A gene for a protein that contains a copy of this domain, to date, is found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. A 69-amino acid core region of this 110-amino acid domain contains eight invariant Cys residues, including two copies of a motif [WFY]CCxxKPC. These motifs could be consistent with predicted metal-binding transcription factor as was suggested for the COG4008 family. Some members of this family have an additional N-terminal domain of about 250 amino acids from the nifR3 family of predicted TIM-barrel proteins. 109 matched cddid_all.tbl CDD TIGR03278 TIGR03278 132321 methan_mark_10 methanogenesis marker radical SAM protein. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. It is a radical SAM enzyme by homology. The exact function is unknown, but likely is linked to methanogenesis. In most genomes, the member of this family is encoded by a gene next to, and divergently transcribed from, the methyl coenzyme M reductase operon. 404 matched cddid_all.tbl CDD TIGR03279 TIGR03279 132322 cyano_FeS_chp putative radical SAM enzyme, TIGR03279 family. Members of this protein family are predicted radical SAM enzymes of unknown function, apparently restricted to and universal across the Cyanobacteria. The high trusted cutoff score for this model, 700 bits, excludes homologs from other lineages. This exclusion seems justified because a significant number of sequence positions are simultaneously unique to and invariant across the Cyanobacteria, suggesting a specialized, conserved function, perhaps related to photosynthesis. A distantly related protein family, TIGR03278, in universal in and restricted to archaeal methanogens, and may be linked to methanogenesis. 433 matched cddid_all.tbl CDD TIGR03280 TIGR03280 213789 methan_mark_11 methanogenesis imperfect marker protein 11. The first twenty-nine completed genomes with a member of this protein family include twenty-eight archaeal methanogens and one other related archaeon, Ferroglobus placidus DSM 10642. The exact function is unknown, but the protein likely belongs to a system usually tightly linked to methanogenesis. 292 matched cddid_all.tbl CDD TIGR03281 TIGR03281 132324 methan_mark_12 putative methanogenesis marker protein 12. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. [Energy metabolism, Methanogenesis] 326 matched cddid_all.tbl CDD TIGR03282 TIGR03282 274499 methan_mark_13 putative methanogenesis marker 13 metalloprotein. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. This metal cluster-binding family is related to nitrogenase structural protein NifD and accessory protein NifE, among others. [Energy metabolism, Methanogenesis] 352 matched cddid_all.tbl CDD TIGR03283 TIGR03283 132326 thy_syn_methano thymidylate synthase, methanogen type. Thymidylate synthase makes dTMP for DNA synthesis, and is among the most widely distributed of all enzymes. Members of this protein family are encoded within a completed genome sequence if and only if that species is one of the methanogenenic archaea. In these species, tetrahydromethanopterin replaces tetrahydrofolate, The member from Methanobacterium thermoautotrophicum was shown to behave as a thymidylate synthase based on similar side reactions (the exchange of a characteristic proton with water), although the full reaction was not reconstituted. Partial sequence data showed no similarity to known thymidylate synthases simply because the region sequenced was from a distinctive N-terminal region not found in other thymidylate synthases. Members of this protein family appear, therefore, to a novel, tetrahydromethanopterin-dependent thymidylate synthase. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism] 199 matched cddid_all.tbl CDD TIGR03284 TIGR03284 213790 thym_sym thymidylate synthase. Members of this protein family are thymidylate synthase, an enzyme that produces dTMP from dUMP. In prokaryotes, its gene usually is found close to that for dihydrofolate reductase, and in some systems the two enzymes are found as a fusion protein. This model excludes a set of related proteins (TIGR03283) that appears to replace this family in archaeal methanogens, where tetrahydrofolate is replaced by tetrahydromethanopterin. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism] 295 matched cddid_all.tbl CDD TIGR03285 TIGR03285 274500 methan_mark_14 putative methanogenesis marker protein 14. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. [Energy metabolism, Methanogenesis] 445 matched cddid_all.tbl CDD TIGR03286 TIGR03286 132329 methan_mark_15 putative methanogenesis marker protein 15. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. Related proteins include the BadF/BadG/BcrA/BcrD ATPase family (pfam01869), which includes an activator for (R)-2-hydroxyglutaryl-CoA dehydratase. [Energy metabolism, Methanogenesis] 404 matched cddid_all.tbl CDD TIGR03287 TIGR03287 274501 methan_mark_16 putative methanogenesis marker 16 metalloprotein. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. This protein is a predicted to bind FeS clusters, based on the presence of two copies of the Fer4 domain (pfam00037), with each copy having four Cys residues invariant across all members. [Energy metabolism, Methanogenesis] 391 matched cddid_all.tbl CDD TIGR03288 TIGR03288 132331 CoB_CoM_SS_B CoB--CoM heterodisulfide reductase, subunit B. Members of this protein family are subunit B of the CoB--CoM heterodisulfide reductase, or simply heterodisulfide reductase, found in methanogenic archaea. Some archaea species have two copies, HdrB1 and HdrB2. 290 matched cddid_all.tbl CDD TIGR03289 TIGR03289 274502 frhB coenzyme F420 hydrogenase, subunit beta. This model represents that clade of F420-dependent hydrogenases (FRH) beta subunits found exclusively and universally in methanogenic archaea. The N- and C-terminal domains of this protein are modelled by pfam04422 and pfam04423 respectively. 275 matched cddid_all.tbl CDD TIGR03290 TIGR03290 132333 CoB_CoM_SS_C CoB--CoM heterodisulfide reductase, subunit C. The last step in methanogenesis leaves two coenzymes of methanogenesis, CoM and CoB, linked by a disulfide bond. Members of this protein family are the C subunit of the enzyme that reduces the heterodisulfide to CoB-SH and CoM-SH. Similar enzyme complex subunits are found in various other species, but likely act on a different substrate. 144 matched cddid_all.tbl CDD TIGR03291 TIGR03291 274503 methan_mark_17 putative methanogenesis marker protein 17. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. [Energy metabolism, Methanogenesis] 185 matched cddid_all.tbl CDD TIGR03292 TIGR03292 274504 PhnH_redo phosphonate C-P lyase system protein PhnH. PhnH is a component of the C-P lyase system (GenProp0232) for the catabolism of phosphonate compounds. The specific function of this component is unknown. This model is based on pfam05845.2, and has been broadened to include sequences missed by that model which are clearly true positive hits based on genome context. 174 matched cddid_all.tbl CDD TIGR03293 TIGR03293 274505 PhnG_redo phosphonate C-P lyase system protein PhnG. PhnH is a component of the C-P lyase system (GenProp0232) for the catabolism of phosphonate compounds. The specific function of this component is unknown. This model is based on pfam06754.2, and has been broadened to include sequences missed by that model which are clearly true positive hits based on genome context. 144 matched cddid_all.tbl CDD TIGR03294 TIGR03294 132337 FrhG "coenzyme F420 hydrogenase, subunit gamma. This model represents that clade of F420-dependent hydrogenases (FRH) beta subunits found exclusively and universally in methanogenic archaea. This protein contains two 4Fe-4S cluster binding domains (pfam00037) and scores above the trusted cutoff to model pfam01058 for the ""NADH ubiquinone oxidoreductase, 20 Kd subunit"" family." 228 matched cddid_all.tbl CDD TIGR03295 TIGR03295 274506 frhA coenzyme F420 hydrogenase, subunit alpha. This model represents that clade of F420-dependent hydrogenases (FRH) beta subunits found exclusively and universally in methanogenic archaea. This protein is a member of the Nickel-dependent hydrogenase superfamily represented by Pfam model, pfam00374. 408 matched cddid_all.tbl CDD TIGR03296 TIGR03296 274507 M6dom_TIGR03296 M6 family metalloprotease domain. This model describes a metalloproteinase domain, with a characteristic HExxH motif. Examples of this domain are found in proteins in the family of immune inhibitor A, which cleaves antibacterial peptides, and in other, only distantly related proteases. This model is built to be broader and more inclusive than pfam05547. 285 matched cddid_all.tbl CDD TIGR03297 TIGR03297 274508 Ppyr-DeCO2ase phosphonopyruvate decarboxylase. This family consists of examples of phosphonopyruvate an decarboxylase enzyme that produces phosphonoacetaldehyde (Pald), the second step in the biosynthesis phosphonate-containing compounds. Since the preceding enzymate step, PEP phosphomutase (AepX, TIGR02320) favors the substrate PEP energetically, the decarboxylase is required to drive the reaction in the direction of phosphonate production. Pald is a precursor of natural products including antibiotics like bialaphos and phosphonothricin in Streptomyces species, phosphonate-modified molecules such as the polysaccharide B of Bacteroides fragilis, the phosphonolipids of Tetrahymena pyroformis, the glycosylinositolphospholipids of Trypanosoma cruzi. This gene generally occurs in prokaryotic organisms adjacent to the gene for AepX. Most often an aminotansferase (aepZ) is also present which leads to the production of the most common phosphonate compound, 2-aminoethylphosphonate (AEP). 361 matched cddid_all.tbl CDD TIGR03298 TIGR03298 274509 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity. [Cellular processes, Toxin production and resistance, DNA metabolism, DNA replication, recombination, and repair, Regulatory functions, DNA interactions] 292 matched cddid_all.tbl CDD TIGR03299 TIGR03299 274510 LGT_TIGR03299 phage/plasmid-like protein TIGR03299. Members of this uncharacterized protein family are found in various Mycobacterium phage genomes, in Streptomyces coelicolor plasmid SCP1, and in bacterial genomes near various markers that suggest lateral gene transfer. The function is unknown. [Mobile and extrachromosomal element functions, Other] 309 matched cddid_all.tbl CDD TIGR03300 TIGR03300 274511 assembly_YfgL outer membrane assembly lipoprotein YfgL. Members of this protein family are YfgL, a lipoprotein component of a complex that acts protein insertion into the bacterial outer membrane. Other members of this complex are NlpB, YfiO, and YaeT. This protein contains multiple copies of a repeat that, in other contexts, are associated with binding of the coenzyme PQQ. [Protein fate, Protein and peptide secretion and trafficking] 377 matched cddid_all.tbl CDD TIGR03301 TIGR03301 274512 PhnW-AepZ 2-aminoethylphosphonate aminotransferase. This family includes a number of 2-aminoethylphosphonate aminotransferases, some of which are indicated to operate in the catabolism of 2-aminoethylphosphonate (AEP) and others which are involved in the biosynthesis of the same compound. The catabolic enzyme (PhnW) is known to use pyruvate:alanine as the transfer partner and is modeled by the equivalog-level model (TIGR02326). The PhnW family is apparently a branch of a larger tree including genes (AepZ) adjacent to others responsible for the biosynthesis of phosphonoacetaldehyde. The identity of the transfer partner is unknown for these enzymes and considering the reversed flux compared to PhnW, it may very well be different. 355 matched cddid_all.tbl CDD TIGR03302 TIGR03302 274513 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795). [Protein fate, Protein and peptide secretion and trafficking] 235 matched cddid_all.tbl CDD TIGR03303 TIGR03303 274514 OM_YaeT outer membrane protein assembly complex, YaeT protein. Members of this protein family are the YaeT protein of the YaeT/YfiO complex for assembling proteins into the outer membrane of Gram-negative bacteria. This protein is similar in sequence and function to a non-essential paralog, YtfM, that is also in the Omp85 family. Members of this family typically have five tandem copies of the surface antigen variable number repeat (pfam07244), followed by an outer membrane beta-barrel domain (pfam01103), while the YtfM family typically has a single pfam07244 repeat. [Protein fate, Protein and peptide secretion and trafficking] 741 matched cddid_all.tbl CDD TIGR03304 TIGR03304 274515 OMP85_target outer membrane insertion C-terminal signal. This hidden Markov model detects a 10-residue targeting sequence common to beta-barrel outer membrane proteins (OMP) that rely on Omp85-like proteins for insertion into the outer membrane. Hits should be trusted if they include the last amino acid of a protein sequence that occurs in Gram-negative bacteria. It has been noted that Omp85 target sequences differ somewhat by species, while this model works generally for most Proteobacteria. 10 matched cddid_all.tbl CDD TIGR03305 TIGR03305 132348 alt_F1F0_F1_bet alternate F1F0 ATPase, F1 subunit beta. A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 beta subunit of this apparent second ATP synthase. 449 matched cddid_all.tbl CDD TIGR03306 TIGR03306 132349 altF1_A alternate F1F0 ATPase, F0 subunit A. A small number of taxonomically diverse prokaryotic species have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F0 subunit A of this apparent second ATP synthase. 217 matched cddid_all.tbl CDD TIGR03307 TIGR03307 163212 PhnP phosphonate metabolism protein PhnP. This family of proteins found in operons encoding phosphonate C-P lyase systems as is observed in E. coli and is a member of the metallo-beta-lactamase superfamily (pfam00753). As defined by this model, all instances of this protein are associated with the C-P lyase, but not all genomes containing the C-P lyase system contain phnP. 238 matched cddid_all.tbl CDD TIGR03308 TIGR03308 132351 phn_thr-fam phosphonate metabolism protein, transferase hexapeptide repeat family. This family of proteins contains copies of the Bacterial transferase hexapeptide repeat family (pfam00132) and is only found in operons encoding the phosphonate C-P lyase system (GenProp0232). Many C-P lyase operons, however, lack a homolog of this protein. 204 matched cddid_all.tbl CDD TIGR03309 TIGR03309 132352 matur_yqeB selenium-dependent molybdenum hydroxylase system protein, YqeB family. Members of this protein family are probable accessory proteins for the biosynthesis of enzymes with labile selenium-containing centers, different from selenocysteine-containing proteins. 256 matched cddid_all.tbl CDD TIGR03310 TIGR03310 274516 matur_MocA_YgfJ molybdenum cofactor cytidylyltransferase. Members of this protein include MocA, which transfers cytosine from CTP to molybdopterin during molybdopterin cytosine dinucleotide (MCD) cofactor biosynthesis. It is distantly related to MobA, the GTP:molybdopterin guanylyltransferase. The MocA family is particularly closely related in phylogenetic distribution to other markers of selenium-dependent molybdenum hydroxylases (SDMH), suggesting most SDMH must use MCD rather than molybdopterin guanine dinucleotide. 188 matched cddid_all.tbl CDD TIGR03311 TIGR03311 132354 Se_dep_XDH selenium-dependent xanthine dehydrogenase. Members of this protein resemble conventional xanthine dehydrogenase enzymes, which depend on molybdenum cofactor - molybdopterin bound to molybdate with two sulfur atoms as ligands. But all members of this family occur in species that contain markers for the biosynthesis of enzymes with a selenium-containing form of molybdenum cofactor. The member of this family from Enterococcus faecalis has been shown to act as a xanthine dehydrogenenase, and its activity if dependent on SelD (selenophosphate synthase), selenium, and molybdenum. [Purines, pyrimidines, nucleosides, and nucleotides, Other] 848 matched cddid_all.tbl CDD TIGR03312 TIGR03312 132355 Se_sel_red_FAD probable selenate reductase, FAD-binding subunit. This protein is suggested by Bebien, et al., to be the FAD-binding subunit of a molydbopterin-containing selenate reductase. Our comparative genomics suggests it to be a subunit of a selenium-dependent molybdenum hydroxylase for an unknown substrate. 257 matched cddid_all.tbl CDD TIGR03313 TIGR03313 132356 Se_sel_red_Mo probable selenate reductase, molybdenum-binding subunit. Our comparative genomics suggests this protein family to be a subunit of a selenium-dependent molybdenum hydroxylase, although the substrate is not specified. This protein is suggested by Bebien, et al., to be the molybdenum-binding subunit of a molydbopterin-containing selenate reductase. Xi, et al, however, show that mutation of this gene in E. coli conferred sensitivity to adenine, suggesting a defect in purine interconversion. This finding, plus homology of nearby genes in a 23-gene purine catabolism region in E. coli to xanthine dehydrogase subunits suggests xanthine dehydrogenase activity. 951 matched cddid_all.tbl CDD TIGR03314 TIGR03314 132357 Se_ssnA putative selenium metabolism protein SsnA. Members of this protein family are found exclusively in genomes that contain putative set of labile selenium-dependent enzyme accessory proteins as well as homologs of a labile selenium-dependent purine hydroxylase. A mutant in this gene in Escherichia coli had improved stationary phase viability. The function is unknown. 441 matched cddid_all.tbl CDD TIGR03315 TIGR03315 132358 Se_ygfK putative selenate reductase, YgfK subunit. Members of this protein family are YgfK, predicted to be one subunit of a three-subunit, molybdopterin-containing selenate reductase. This enzyme is found, typically, in genomic regions associated with xanthine dehydrogenase homologs predicted to belong to the selenium-dependent molybdenum hydroxylases (SDMH). Therefore, the selenate reductase is suggested to play a role in furnishing selenide for SelD, the selenophosphate synthase. 1012 matched cddid_all.tbl CDD TIGR03316 TIGR03316 274517 ygeW knotted carbamoyltransferase YgeW. Members of this protein family include the ygeW gene product of Escherichia coli. The function is unknown. Members show homology to ornithine carbamoyltransferase (TIGR00658) and aspartate carbamoyltransferase (carbamoyltransferase), and therefore may belong to the carbamoyltransferases in function. Members often are found in a large, conserved genomic region associated with selenium-dependent molybdenum hydroxylases. 391 matched cddid_all.tbl CDD TIGR03317 TIGR03317 274518 ygfZ_signature folate-binding protein YgfZ. YgfZ is a protein from Escherichia coli, homologous to the glycine cleavage system T protein, or aminomethyltransferase, GcvT (TIGR00528). Homologs of YgfZ other than members of the GcvT family share a well-conserved signature region that includes the motif, KGCYxGQE. Elsewhere, sequence diverge and length variation are substantial. Members of this family are mostly bacterial, largely absent from the Firmicutes and otherwise usually present. A few eukaryotic examples are found among the Apicomplexa, and a few archaeal sequences are found. Two functions implicated for this folate-binding protein are RNA modification (a function likely to be conserved) and replication initiation (a function likely to be highly variable). Many members of this family are, at the time of construction of this model, misnamed as the glycine cleavage system T protein. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 67 matched cddid_all.tbl CDD TIGR03318 TIGR03318 132361 YdfZ_fam putative selenium-binding protein YdfZ. This small protein has a very limited distribution, being found so far only among some gamma-Proteobacteria. The member from Escherichia coli was shown to bind selenium in the absence of a working SelD-dependent selenium incorporation system. Note that while the E. coli member contains a single Cys residue, a likely selenium binding site, some other members of this protein family contain two Cys residues or none. [Unknown function, General] 65 matched cddid_all.tbl CDD TIGR03319 TIGR03319 188306 RNase_Y ribonuclease Y. Members of this family are RNase Y, an endoribonuclease. The member from Bacillus subtilis, YmdA, has been shown to be involved in turnover of yitJ riboswitch. [Transcription, Degradation of RNA] 514 matched cddid_all.tbl CDD TIGR03321 TIGR03321 132364 alt_F1F0_F0_B alternate F1F0 ATPase, F0 subunit B. A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, CC and in principle may run in either direction. This model represents the F0 subunit B of this apparent second ATP synthase. 246 matched cddid_all.tbl CDD TIGR03322 TIGR03322 132365 alt_F1F0_F0_C alternate F1F0 ATPase, F0 subunit C. A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F0 subunit C of this apparent second ATP synthase. 86 matched cddid_all.tbl CDD TIGR03323 TIGR03323 274519 alt_F1F0_F1_gam alternate F1F0 ATPase, F1 subunit gamma. A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 gamma subunit of this apparent second ATP synthase. 285 matched cddid_all.tbl CDD TIGR03324 TIGR03324 132367 alt_F1F0_F1_al alternate F1F0 ATPase, F1 subunit alpha. A small number of taxonomically diverse prokaryotic species, including Methanosarcina barkeri, have what appears to be a second ATP synthase, in addition to the normal F1F0 ATPase in bacteria and A1A0 ATPase in archaea. These enzymes use ion gradients to synthesize ATP, and in principle may run in either direction. This model represents the F1 alpha subunit of this apparent second ATP synthase. 497 matched cddid_all.tbl CDD TIGR03325 TIGR03325 132368 BphB_TodD cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase. Members of this family occur as the BphD protein of biphenyl catabolism and as the TodD protein of toluene catabolism. Members catalyze the second step in each pathway and proved interchangeable when tested; the first and fourth enzymes in each pathway confer metabolic specificity. In the context of biphenyl degradation, the enzyme acts as cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (EC 1.3.1.56), while in toluene degradation it acts as cis-toluene dihydrodiol dehydrogenase. 262 matched cddid_all.tbl CDD TIGR03326 TIGR03326 188307 rubisco_III ribulose bisphosphate carboxylase, type III. Members of this protein family are the archaeal, single chain, type III form of ribulose bisphosphate carboxylase, or RuBisCO. Members act is a three-step pathway for conversion of the sugar moiety of AMP to two molecules of 3-phosphoglycerate. Many of these species use ADP-dependent sugar kinases, which form AMP, for glycolysis. [Energy metabolism, Sugars] 411 matched cddid_all.tbl CDD TIGR03327 TIGR03327 274520 AMP_phos AMP phosphorylase. This enzyme family is found, so far, strictly in the Archaea, and only in those with a type III Rubisco enzyme. Most of the members previously were annotated as thymidine phosphorylase, or DeoA. The AMP metabolized by this enzyme may be produced by ADP-dependent sugar kinases. 494 matched cddid_all.tbl CDD TIGR03328 TIGR03328 274521 salvage_mtnB methylthioribulose-1-phosphate dehydratase. Members of this family are the methylthioribulose-1-phosphate dehydratase of the methionine salvage pathway. This pathway allows methylthioadenosine, left over from polyamine biosynthesis, to be recycled to methionine. [Amino acid biosynthesis, Aspartate family] 192 matched cddid_all.tbl CDD TIGR03329 TIGR03329 274522 Phn_aa_oxid putative aminophosphonate oxidoreductase. This clade of sequences are members of the pfam01266 family of FAD-dependent oxidoreductases. Characterized proteins within this family include glycerol-3-phosphate dehydrogenase (1.1.99.5), sarcosine oxidase beta subunit (1.5.3.1) and a number of deaminating amino acid oxidases (1.4.-.-). These genes have been consistently observed in a genomic context including genes for the import and catabolism of 2-aminoethylphosphonate (AEP). If the substrate of this oxidoreductase is AEP itself, then it is probably acting in the manner of a deaminating oxidase, resulting in the same product (phosphonoacetaldehyde) as the transaminase PhnW (TIGR02326), but releasing ammonia instead of coupling to pyruvate:alanine. Alternatively, it is reasonable to suppose that the various ABC cassette transporters which are also associated with these loci allow the import of phosphonates closely related to AEP which may not be substrates for PhnW. 460 matched cddid_all.tbl CDD TIGR03330 TIGR03330 274523 SAM_DCase_Bsu S-adenosylmethionine decarboxylase proenzyme, Bacillus form. Members of this protein family are the single chain precursor of the two chains of the mature S-adenosylmethionine decarboxylase as found in Methanocaldococcus jannaschii, Bacillus subtilis, and a wide range of other species. It differs substantially in architecture from the form as found in Escherichia coli, and lacks any extended homology to the eukaryotic form (TIGR00535). [Central intermediary metabolism, Polyamine biosynthesis] 112 matched cddid_all.tbl CDD TIGR03331 TIGR03331 274524 SAM_DCase_Eco S-adenosylmethionine decarboxylase proenzyme, Escherichia coli form. Members of this protein family are the single chain precursor of the S-adenosylmethionine decarboxylase as found in Escherichia coli. This form shows a substantially different architecture from the form shared by the Archaea, Bacillus, and many other species (TIGR03330). It shows little or no similarity to the form found in eukaryotes (TIGR00535). [Central intermediary metabolism, Polyamine biosynthesis] 259 matched cddid_all.tbl CDD TIGR03332 TIGR03332 132375 salvage_mtnW 2,3-diketo-5-methylthiopentyl-1-phosphate enolase. Members of this family are the methionine salvage pathway enzyme 2,3-diketo-5-methylthiopentyl-1-phosphate enolase, a homolog of RuBisCO. This protein family seems restricted to Bacillus subtilis and close relatives, where two separate proteins carry the enolase and phosphatase activities that in other species occur in a single protein, MtnC (TIGR01691). [Amino acid biosynthesis, Aspartate family, Central intermediary metabolism, Sulfur metabolism] 407 matched cddid_all.tbl CDD TIGR03333 TIGR03333 213797 salvage_mtnX 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate phosphatase. Members of this family are the methionine salvage enzyme MnxX, a member of the HAD-superfamily hydrolases, subfamily IB (see TIGR01488). Members are found in Bacillus subtilis and related species, paired with MtnW (TIGR03332). In most species that recycle methionine from methylthioadenosine, the single protein MtnC replaces the MtnW/MtnX pair. In B. subtilis, mtnX was first known as ykrX. [Amino acid biosynthesis, Aspartate family, Central intermediary metabolism, Sulfur metabolism] 214 matched cddid_all.tbl CDD TIGR03334 TIGR03334 274525 IOR_beta indolepyruvate ferredoxin oxidoreductase, beta subunit. This model represents the beta subunit of indolepyruvate ferredoxin oxidoreductase, an alpha(2)/beta(2) tetramer, as found in Pyrococcus furiosus and Methanobacterium thermoautotrophicum. Cofactors for the tetramer include TPP, 4Fe4S, and 3Fe-4S. It shows considerable sequence similarity to subunits of several other ketoacid oxidoreductases. 189 matched cddid_all.tbl CDD TIGR03335 TIGR03335 132378 F390_ftsA coenzyme F390 synthetase. This enzyme, characterized in Methanobacterium thermoautotrophicum and found in several other methanogens, modifies coenzyme F420 by ligation of AMP (or GMP) from ATP (or GTP). On F420, it activates an aromatic hydroxyl group, which is unusual chemistry for an adenylyltransferase. This enzyme name has been attached to numbers of uncharacterized genes likely to instead act as phenylacetate CoA ligase, based on proximity to predicted indolepyruvate ferredoxin oxidoreductase (1.2.7.8) genes. The enzyme acts during transient exposure of the organism to oxygen. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Energy metabolism, Methanogenesis] 445 matched cddid_all.tbl CDD TIGR03336 TIGR03336 274526 IOR_alpha indolepyruvate ferredoxin oxidoreductase, alpha subunit. Indolepyruvate ferredoxin oxidoreductase (IOR) is an alpha 2/beta 2 tetramer related to ketoacid oxidoreductases for pyruvate (1.2.7.1, POR), 2-ketoglutarate (1.2.7.3, KOR), and 2-oxoisovalerate (1.2.7.7, VOR). These multi-subunit enzymes typically are found in anaerobes and are inactiviated by oxygen. IOR in Pyrococcus acts in fermentation of all three aromatic amino acids, following removal of the amino group by transamination. In Methanococcus maripaludis, by contrast, IOR acts in the opposite direction, in pathways of amino acid biosynthesis from phenylacetate, indoleacetate, and p-hydroxyphenylacetate. In M. maripaludis and many other species, iorA and iorB are found next to an apparent phenylacetate-CoA ligase. 595 matched cddid_all.tbl CDD TIGR03337 TIGR03337 132380 phnR phosphonate utilization transcriptional regulator PhnR. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii. [Regulatory functions, DNA interactions] 231 matched cddid_all.tbl CDD TIGR03338 TIGR03338 132381 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter. 212 matched cddid_all.tbl CDD TIGR03339 TIGR03339 132382 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466). [Regulatory functions, DNA interactions] 279 matched cddid_all.tbl CDD TIGR03340 TIGR03340 274527 phn_DUF6 phosphonate utilization associated putative membrane protein. This family of hydrophobic proteins has some homology to families of integral membrane proteins such as (pfam00892) and may be a permease. It occurs in the vicinity of various types of operons for the catabolism of phosphonates in Vibrio, Pseudomonas, Polaromonas and Thiomicrospira. 281 matched cddid_all.tbl CDD TIGR03341 TIGR03341 132384 YhgI_GntY IscR-regulated protein YhgI. IscR (TIGR02010) is an iron-sulfur cluster-binding transcriptional regulator (see Genome Property GenProp0138). Members of this protein family include YhgI, whose expression is under control of IscR, and show sequence similarity to IscA, a known protein of iron-sulfur cluster biosynthesis. These two lines of evidence strongly suggest a role as an iron-sulfur cluster biosynthesis protein. An older study designated this protein GntY and suggested a role for it and for the product of an adjacent gene, based on complementation studies, in gluconate utilization. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 190 matched cddid_all.tbl CDD TIGR03342 TIGR03342 213798 dsrC_tusE_dsvC sulfur relay protein, TusE/DsrC/DsvC family. Members of this protein family may be described as TusE, a partner to TusBCD in a sulfur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Other members are DsrC, a functionally similar protein in species where the sulfur relay system exists primarily for sulfur metabolism rather than tRNA base modification. Some members of this family are known explicitly as the gamma subunit of sulfite reductases. 108 matched cddid_all.tbl CDD TIGR03343 TIGR03343 132386 biphenyl_bphD 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase. Members of this family are 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase, or HOPD hydrolase, the BphD protein of biphenyl degradation. BphD acts on the product of ring meta-cleavage by BphC. Many species carrying bphC and bphD are capable of degrading polychlorinated biphenyls as well as biphenyl itself. 282 matched cddid_all.tbl CDD TIGR03344 TIGR03344 213799 VI_effect_Hcp1 type VI secretion system effector, Hcp1 family. This family includes Hcp1 (hemolysin coregulated protein 1), an exported, homohexameric ring-forming virulence protein from Pseudomonas aeruginosa. Hcp1 lacks a conventional signal sequence and is instead exported by means of the type VI secretion system, encoded by a pathogenicity cluster of a class previously designated IAHP (IcmF-associated homologous protein). Homologs of Hcp1, in this protein family, are found in various bacteria of which most but not all are known pathogens. Pathogens may have many multiple members of this family, with three to ten in Erwinia carotovora, Yersinia pestis, uropathogenic Escherichia coli, and the insect pathogen Photorhabdus luminescens. [Cellular processes, Pathogenesis] 166 matched cddid_all.tbl CDD TIGR03345 TIGR03345 274528 VI_ClpV1 type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 852 matched cddid_all.tbl CDD TIGR03346 TIGR03346 274529 chaperone_ClpB ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins. [Protein fate, Protein folding and stabilization] 850 matched cddid_all.tbl CDD TIGR03347 TIGR03347 274530 VI_chp_1 type VI secretion protein, VC_A0111 family. Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 300 matched cddid_all.tbl CDD TIGR03348 TIGR03348 274531 VI_IcmF type VI secretion protein IcmF. Members of this protein family are IcmF homologs and tend to be associated with type VI secretion systems. [Cellular processes, Pathogenesis] 1169 matched cddid_all.tbl CDD TIGR03349 TIGR03349 274532 IV_VI_DotU type IV / VI secretion system protein, DotU family. At least two families of proteins, often encoded by adjacent genes, show sequence similarity due to homology between type IV secretion systems and type VI secretion systems. One is the IcmF family (TIGR03348). The other is the family described by this model. Members include DotU from the Legionella pneumophila type IV secretion system. Many of the members of this protein family from type VI secretion systems have an additional C-terminal domain with OmpA/MotB homology. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 183 matched cddid_all.tbl CDD TIGR03350 TIGR03350 274533 type_VI_ompA type VI secretion system peptidoglycan-associated domain. The flagellar motor protein MotB, the Gram-negative bacterial outer membrane protein OmpA (with an N-terminal outer membrane beta barrel domain) share a C-terminal peptidoglycan-associating homology region. This model describes a domain found fused to type VI secretion system homologs of the type IV system protein DotU (see model TIGR03349), with OmpA/MotB homology. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 137 matched cddid_all.tbl CDD TIGR03351 TIGR03351 274534 PhnX-like "phosphonatase-like hydrolase. This clade of sequences are the closest homologs to the PhnX enzyme, phosphonoacetaldehyde (Pald) hydrolase (phosphonatase, TIGR01422). This phosphonatase-like enzyme and PhnX itself are members of the haloacid dehalogenase (HAD) superfamily (pfam00702) having a a number of distinctive features that set them apart from typical HAD enzymes. The typical HAD N-terminal motif DxDx(T/V) here is DxAGT and the usual conserved lysine prior to the C-terminal motif is instead an arginine. Also distinctive of phosphonatase, and particular to its bi-catalytic mechanism is a conserved lysine in the variable ""cap"" domain. This lysine forms a Schiff base with the aldehyde of phosphonoacetaldehyde, providing, through the resulting positive charge, a polarization of the C-P bond necesary for cleavage as well as a route to the initial product of cleavage, an ene-amine. The conservation of these elements in this phosphonatase-like enzyme suggests that the substrate is also, like Pald, a 2-oxo-ethylphosphonate. Despite this, the genomic context of members of this family are quite distinct from PhnX, which is almost invariably associated with the 2-aminoethylphosphonate transaminase PhnW (TIGR02326), the source of the substrate Pald. Members of this clade are never associated with PhnW, but rather associate with families of FAD-dependent oxidoreductases related to deaminating amino acid oxidases (pfam01266) as well as zinc-dependent dehydrogenases (pfam00107). Notably, family members from Arthrobacter aurescens TC1 and Nocardia farcinica IFM 10152 are adjacent to the PhnCDE ABC cassette phosphonates transporter (GenProp0236) typically found in association with the phosphonates C-P lyase system (GenProp0232). These observations suggest two possibilities. First, the substrate for this enzyme family is also Pald, the non-association with PhnW not withstanding. Alternatively, the substrate is something very closely related such as hydroxyphosphonoacetaldehyde (Hpald). Hpald could come from oxidative deamination of 1-hydroxy-2-aminoethylphosphonate (HAEP) by the associated oxidase. HAEP would not be a substrate for PhnW due to its high specificity for AEP. HAEP has been shown to be a constituent of the sphingophosphonolipid of Bacteriovorax stolpii, and presumably has other natural sources. If Hpald is the substrate, the product would be glycoaldehyde (hydroxyacetaldehyde), and the associated alcohol dehydrogenase may serve to convert this to glycol." 220 matched cddid_all.tbl CDD TIGR03352 TIGR03352 274535 VI_chp_3 type VI secretion lipoprotein, VC_A0113 family. Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 130 matched cddid_all.tbl CDD TIGR03353 TIGR03353 274536 VI_chp_4 type VI secretion protein, VC_A0114 family. Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 439 matched cddid_all.tbl CDD TIGR03354 TIGR03354 274537 VI_FHA type VI secretion system FHA domain protein. Members of this protein family are FHA (forkhead-associated) domain-containing proteins that are part of type VI secretion loci in a considerable number of bacteria, most of which are known pathogens. Species include Pseudomonas aeruginosa PAO1, Aeromonas hydrophila, Yersinia pestis, Burkholderia mallei, etc. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 396 matched cddid_all.tbl CDD TIGR03355 TIGR03355 274538 VI_chp_2 type VI secretion protein, EvpB/VC_A0108 family. Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 473 matched cddid_all.tbl CDD TIGR03356 TIGR03356 274539 BGL beta-galactosidase. 426 matched cddid_all.tbl CDD TIGR03357 TIGR03357 274540 VI_zyme type VI secretion system lysozyme-like protein. The description for Pfam family pfam04965 cites acidic lysozyme activity for some phage-encoded members. This family represents a different subgroup of the proteins from pfam04965, where all members are associated with bacterial type VI secretion system genomic contexts. 133 matched cddid_all.tbl CDD TIGR03358 TIGR03358 132401 VI_chp_5 type VI secretion protein, VC_A0107 family. Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 159 matched cddid_all.tbl CDD TIGR03359 TIGR03359 274541 VI_chp_6 type VI secretion protein, VC_A0110 family. This protein family is associated with type VI secretion in a number of pathogenic bacteria. Mutation is associated with impaired virulence, such as impaired infection of plants by Rhizobium leguminosarum. 598 matched cddid_all.tbl CDD TIGR03360 TIGR03360 132403 VI_minor_1 type VI secretion-associated protein, VC_A0118 family. Members of this protein family, including VC_A0118 from Vibrio cholerae El Tor N16961, are restricted to a subset of bacteria with the type VI secretion system, and are encoded among the type VI-associated pathogenicity islands. However, many species with type VI secretion lack a member of this family. This lack suggests that members of this family may be targets rather than components of the type VI secretion system. 185 matched cddid_all.tbl CDD TIGR03361 TIGR03361 274542 VI_Rhs_Vgr type VI secretion system Vgr family protein. Members of this protein family belong to the Rhs element Vgr protein family (see TIGR01646), but furthermore all are found in genomes with type VI secretion loci. However, members of this protein family, although recognizably correlated to type VI secretion according the partial phylogenetic profiling algorithm, are often found far the type VI secretion locus. 513 matched cddid_all.tbl CDD TIGR03362 TIGR03362 274543 VI_chp_7 type VI secretion-associated protein, VC_A0119 family. This protein family is one of two related families in type VI secretion systems that contain an ImpA-related N-terminal domain (pfam06812). [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 301 matched cddid_all.tbl CDD TIGR03363 TIGR03363 274544 VI_chp_8 type VI secretion-associated protein, ImpA family. This protein family is one of two related families in type VI secretion systems that contain an ImpA-related N-terminal domain (pfam06812). 353 matched cddid_all.tbl CDD TIGR03364 TIGR03364 132407 HpnW_proposed FAD dependent oxidoreductase TIGR03364. This clade of FAD dependent oxidoreductases (members of the pfam01266 family) is syntenically associated with a family of proposed phosphonatase-like enzymes (TIGR03351) and is also found (less frequently) in association with phosphonate transporter components. A likely role for this enzyme involves the oxidative deamination of an aminophosphonate differring slightly from 2-aminoethylphosphonate, possibly 1-hydroxy-2-aminoethylphosphonate (see the comments for TIGR03351). Many members of the larger FAD dependent oxidoreductase family act as amino acid oxidative deaminases. 365 matched cddid_all.tbl CDD TIGR03365 TIGR03365 274545 Bsubt_queE 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE. This uncharacterized enzyme, designated QueE, participates in the biosynthesis, from GTP, of 7-cyano-7-deazaguanosine, also called preQ0 because in many species it is a precursor of queuosine. In most Archaea, it is instead the precursor of a different tRNA modified base, archaeosine. [Protein synthesis, tRNA and rRNA base modification] 238 matched cddid_all.tbl CDD TIGR03366 TIGR03366 274546 HpnZ_proposed putative phosphonate catabolism associated alcohol dehydrogenase. This clade of zinc-binding alcohol dehydrogenases (members of pfam00107) are repeatedly associated with genes proposed to be involved with the catabolism of phosphonate compounds. 280 matched cddid_all.tbl CDD TIGR03367 TIGR03367 274547 queuosine_QueD queuosine biosynthesis protein QueD. Members of this protein family, closely related to eukaryotic 6-pyruvoyl tetrahydrobiopterin synthase enzymes, are the QueD protein of queuosine biosynthesis. Queuosine is a hypermodified base in the wobble position of tRNAs for Tyr, His, Asp, and Asn in many species. This modification, although widespread, appears not to be important for viability. The queuosine precursor made by this enzyme may be converted instead to archeaosine as in some Archaea. [Protein synthesis, tRNA and rRNA base modification] 89 matched cddid_all.tbl CDD TIGR03368 TIGR03368 132411 cellulose_yhjU cellulose synthase operon protein YhjU. This protein was identified by the partial phylogenetic profiling algorithm () as part of the system for cellulose biosynthesis in bacteria, and in fact is found in cellulose biosynthesis gene regions. The protein was designated YhjU in Salmonella enteritidis, where disruption of its gene disrupts cellulose biosynthesis and biofilm formation (). [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 518 matched cddid_all.tbl CDD TIGR03369 TIGR03369 274548 cellulose_bcsE cellulose biosynthesis protein BcsE. This protein, called BcsE (bacterial cellulose synthase E) or YhjS, is required for cellulose biosynthesis in Salmonella enteritidis. Its role is this process across multiple bacterial species is implied by the partial phylogenetic profiling algorithm. Members are found in the vicinity of other cellulose biosynthesis genes. The model does not include a much less well-conserved N-terminal region about 150 amino acids in length for most members. Solano, et al. suggest this protein acts as a protease. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 322 matched cddid_all.tbl CDD TIGR03370 TIGR03370 132413 VPLPA-CTERM VPLPA-CTERM protein sorting domain. A probable protein export sorting signal, PEP-CTERM, was described by Haft, et al. (). It is predicted to interact with a putative transpeptidase we designate exosortase. This model describes a variant with conserved motif VPLPA, rather than VPEP. It appears to be the recognition sequences for exosortase D (TIGR04152). This variant is found prominently in two members of the Rhodobacterales, namely Jannaschia sp. CCS1 and Roseobacter denitrificans OCh 114. One interesting member protein has a full-length duplication and therefore two copies of this putative sorting domain. 25 matched cddid_all.tbl CDD TIGR03371 TIGR03371 274549 cellulose_yhjQ cellulose synthase operon protein YhjQ. Members of this family are the YhjQ protein, found immediately upsteam of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae. In several species it is seen clearly as part of the bcs operon. It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm (), based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 246 matched cddid_all.tbl CDD TIGR03372 TIGR03372 132415 putres_am_tran putrescine aminotransferase. Members of this family are putrescine aminotransferase, as found in Escherichia coli, Erwinia carotovora subsp. atroseptica, and closely related species. This pyridoxal phosphate enzyme, as characterized in E. coli, can act also on cadaverine and, more weakly, spermidine. [Central intermediary metabolism, Polyamine biosynthesis] 442 matched cddid_all.tbl CDD TIGR03373 TIGR03373 132416 VI_minor_4 type VI secretion-associated protein, BMA_A0400 family. Members of this protein family are found exclusively, although not universally, in bacterial species that possess a type VI secretion system. Genes are found in type VI secretion-associated gene clusters. The specific function is unknown. This model represents the rather well-conserved amino-terminal domain of a protein family in which carboxy-terminal regions, when present, show little conservation. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 136 matched cddid_all.tbl CDD TIGR03374 TIGR03374 132417 ABALDH 1-pyrroline dehydrogenase. Members of this protein family are 1-pyrroline dehydrogenase (1.5.1.35), also called gamma-aminobutyraldehyde dehydrogenase. This enzyme can follow putrescine transaminase (EC 2.6.1.82) for a two-step conversion of putrescine to gamma-aminobutyric acid (GABA). The member from Escherichia coli is characterized as a homotetramer that binds one NADH per momomer. This enzyme belongs to the medium-chain aldehyde dehydrogenases, and is quite similar in sequence to the betaine aldehyde dehydrogenase (EC 1.2.1.8) family. 472 matched cddid_all.tbl CDD TIGR03375 TIGR03375 274550 type_I_sec_LssB type I secretion system ATPase, LssB family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 694 matched cddid_all.tbl CDD TIGR03376 TIGR03376 274551 glycerol3P_DH glycerol-3-phosphate dehydrogenase (NAD(+)). Members of this protein family are the eukaryotic enzyme, glycerol-3-phosphate dehydrogenase (NAD(+)) (EC 1.1.1.8). Enzymatic activity for 1.1.1.8 is defined as sn-glycerol 3-phosphate + NAD(+) = glycerone phosphate + NADH. Note the very similar reactions of enzymes defined as EC 1.1.1.94 and 1.1.99.5, assigned to families of proteins in the bacteria. 342 matched cddid_all.tbl CDD TIGR03377 TIGR03377 274552 glycerol3P_GlpA glycerol-3-phosphate dehydrogenase, anaerobic, A subunit. Members of this protein family are the A subunit, product of the glpA gene, of a three-subunit, membrane-anchored, FAD-dependent anaerobic glycerol-3-phosphate dehydrogenase. [Energy metabolism, Anaerobic] 516 matched cddid_all.tbl CDD TIGR03378 TIGR03378 213807 glycerol3P_GlpB glycerol-3-phosphate dehydrogenase, anaerobic, B subunit. Members of this protein family are the B subunit, product of the glpB gene, of a three-subunit, membrane-anchored, FAD-dependent anaerobic glycerol-3-phosphate dehydrogenase. [Energy metabolism, Anaerobic] 419 matched cddid_all.tbl CDD TIGR03379 TIGR03379 132422 glycerol3P_GlpC glycerol-3-phosphate dehydrogenase, anaerobic, C subunit. Members of this protein family are the membrane-anchoring, non-catalytic C subunit, product of the glpC gene, of a three-subunit, FAD-dependent, anaerobic glycerol-3-phosphate dehydrogenase. GlpC lasks classical hydrophobic transmembrane helices; Cole, et al suggest interaction with the membrane may involve amphipathic helices. GlcC has conserved Cys-containing motifs suggestive of iron-sulfur binding. This complex is found mostly in Escherichia coli and closely related species. [Energy metabolism, Anaerobic] 397 matched cddid_all.tbl CDD TIGR03380 TIGR03380 132423 agmatine_aguA agmatine deiminase. Members of this family are agmatine deiminase (3.5.3.12), as characterized in Pseudomonas aeruginosa and plants. Related deiminases include the peptidyl-arginine deiminase (3.5.3.15) as found in Porphyromonas gingivalis. [Central intermediary metabolism, Polyamine biosynthesis] 357 matched cddid_all.tbl CDD TIGR03381 TIGR03381 274553 agmatine_aguB N-carbamoylputrescine amidase. Members of this family are N-carbamoylputrescine amidase (3.5.1.53). Bacterial genes are designated AguB. The AguAB pathway replaces SpeB for conversion of agmatine to putrescine in two steps rather than one. [Central intermediary metabolism, Polyamine biosynthesis] 279 matched cddid_all.tbl CDD TIGR03382 TIGR03382 213808 GC_trans_RRR Myxococcales GC_trans_RRR domain. The domain described here is small (about 30 amino acids), hydrophobic, only moderately conserved, and similar to numerous other transmembrane helix-containing sequence regions from convergent evolution. This domain is found, once per protein but in many proteins per genome in several bacteria of the order Myxococcales. It begins with a signature Gly-Cys motif. Its other features, including a hydrophobic transmembrane helix, Arg-rich cluster, and location at the protein C-terminus, resemble the PEP-CTERM proposed protein targeting domain. 27 matched cddid_all.tbl CDD TIGR03383 TIGR03383 274554 urate_oxi urate oxidase. Members of this protein family are urate oxidase, also called uricase. This protein contains two copies of the domain described by the uricase model pfam01014. In animals, this enzyme has been lost from primates and birds. [Central intermediary metabolism, Other] 282 matched cddid_all.tbl CDD TIGR03384 TIGR03384 132427 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme. [Regulatory functions, DNA interactions] 189 matched cddid_all.tbl CDD TIGR03385 TIGR03385 163244 CoA_CoA_reduc CoA-disulfide reductase. Members of this protein family are CoA-disulfide reductase (EC 1.8.1.14), as characterized in Staphylococcus aureus, Pyrococcus horikoshii, and Borrelia burgdorferi, and inferred in several other species on the basis of high levels of CoA and an absence of glutathione as a protective thiol. [Cellular processes, Detoxification] 427 matched cddid_all.tbl CDD TIGR03388 TIGR03388 274555 ascorbase L-ascorbate oxidase, plant type. Members of this protein family are the copper-containing enzyme L-ascorbate oxidase (EC 1.10.3.3), also called ascorbase. This family is found in flowering plants, and shows greater sequence similarity to a family of laccases (EC 1.10.3.2) from plants than to other known ascorbate oxidases. 541 matched cddid_all.tbl CDD TIGR03389 TIGR03389 274556 laccase laccase, plant. Members of this protein family include the copper-containing enzyme laccase (EC 1.10.3.2), often several from a single plant species, and additional, uncharacterized, closely related plant proteins termed laccase-like multicopper oxidases. This protein family shows considerable sequence similarity to the L-ascorbate oxidase (EC 1.10.3.3) family. Laccases are enzymes of rather broad specificity, and classification of all proteins scoring about the trusted cutoff of this model as laccases may be appropriate. 539 matched cddid_all.tbl CDD TIGR03390 TIGR03390 132431 ascorbOXfungal L-ascorbate oxidase, fungal type. This model describes a family of fungal ascorbate oxidases, within a larger family of multicopper oxidases that also includes plant ascorbate oxidases (TIGR03388), plant laccases and laccase-like proteins (TIGR03389), and related proteins. The member from Acremonium sp. HI-25 is characterized. 538 matched cddid_all.tbl CDD TIGR03391 TIGR03391 274557 FeS_syn_CsdE cysteine desulfurase, sulfur acceptor subunit CsdE. Members of this protein family are CsdE, formerly called YgdK. This protein, found as a paralog to SufE in Escherichia coli, Yersinia pestis, Photorhabdus luminescens, and related species, works together and physically interacts with CsdA (a paralog of SufS). CsdA has cysteine desulfurase activity that is enhanced by this protein (CsdE), in which Cys-61 (numbered as in E. coli) is a sulfur acceptor site. This gene pair, although involved in FeS cluster biosynthesis, is not found next to other such genes as are its paralogs from the Suf or Isc systems. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 139 matched cddid_all.tbl CDD TIGR03392 TIGR03392 274558 FeS_syn_CsdA cysteine desulfurase, catalytic subunit CsdA. Members of this protein family are CsdS. This protein, found Escherichia coli, Yersinia pestis, Photorhabdus luminescens, and related species, and related to SufS, works together with and physically interacts with CsdE (a paralog of SufE). CsdA has cysteine desulfurase activity that is enhanced by CsdE, a sulfur acceptor protein. This gene pair, although involved in FeS cluster biosynthesis, is not found next to other such genes as are its paralogs from the Suf or Isc systems. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 398 matched cddid_all.tbl CDD TIGR03393 TIGR03393 274559 indolpyr_decarb indolepyruvate decarboxylase, Erwinia family. A family of closely related, thiamine pyrophosphate-dependent enzymes includes indolepyruvate decarboxylase (EC 4.1.1.74), phenylpyruvate decarboxylase (EC 4.1.1.43), pyruvate decarboxylase (EC 4.1.1.1), branched-chain alpha-ketoacid decarboxylase, etc.. Members of this group of homologs may overlap in specificity. Within the larger family, this model represents a clade of bacterial indolepyruvate decarboxylases, part of a pathway for biosynthesis of the plant hormone indole-3-acetic acid. Typically, these species interact with plants, as pathogens or as beneficial, root-associated bacteria. [Central intermediary metabolism, Other] 539 matched cddid_all.tbl CDD TIGR03394 TIGR03394 274560 indol_phenyl_DC indolepyruvate/phenylpyruvate decarboxylase, Azospirillum family. A family of closely related, thiamine pyrophosphate-dependent enzymes includes indolepyruvate decarboxylase (EC 4.1.1.74), phenylpyruvate decarboxylase (EC 4.1.1.43), pyruvate decarboxylase (EC 4.1.1.1), branched-chain alpha-ketoacid decarboxylase, etc.. Members of this group of homologs may overlap in specificity. This model represents a clade that includes a Azospirillum brasilense member active as both phenylpyruvate decarboxylase and indolepyruvate decarboxylase. 535 matched cddid_all.tbl CDD TIGR03395 TIGR03395 132436 sphingomy sphingomyelin phosphodiesterase. Members of this family are bacterial proteins that act as sphingomyelin phosphodiesterase (EC 3.1.4.12), also called sphingomyelinase. Some members of this family have been shown to act as hemolysins. [Cellular processes, Pathogenesis] 283 matched cddid_all.tbl CDD TIGR03396 TIGR03396 274561 PC_PLC phospholipase C, phosphocholine-specific, Pseudomonas-type. Members of this protein family are bacterial, phosphatidylcholine-hydrolyzing phospholipase C enzymes, with a characteristic domain architecture as found in hemolytyic (PlcH) and nonhemolytic (PlcN) secreted enzymes of Pseudomonas aeruginosa. PlcH hydrolyzes phosphatidylcholine to diacylglycerol and phosphocholine, but unlike PlcN can also hydrolyze sphingomyelin to ceramide ((N-acylsphingosine)) and phosphocholine. Members of this family share the twin-arginine signal sequence for Sec-independent transport across the plasma membrane. PlcH is secreted as a heterodimer with a small chaperone, PlcR, encoded immediately downstream. [Cellular processes, Pathogenesis] 689 matched cddid_all.tbl CDD TIGR03397 TIGR03397 274562 acid_phos_Burk acid phosphatase, Burkholderia-type. A member of this family, AcpA from Burkholderia mallei, has been charactized as a surface-bound glycoprotein with acid phosphatase activity, as can be shown with the colorigenic substrate 5-bromo-4-chloro-3-indolyl phosphate. This family shares regions of sequence similarity with phosphocholine-preferring phospholipase C enzymes (TIGR03396) from many of the same species. 483 matched cddid_all.tbl CDD TIGR03398 TIGR03398 132439 plc_access_R phospholipase C accessory protein PlcR. The class of microbial phosphocholine-preferring phospholipase C enzymes described by model TIGR03396 has two members in Pseudomonas aeruginosa, one of which (PlcH) is hemolytic and can hydrolyzes sphingomyelin as well as phosphatidylcholine. This model describes PlcR, an accessory protein for PlcH with which it forms a heterodimer. The member of the family from P. aeruginosa, although not the members from various Burkholderia species, is encoded immediately downstream of phospholipase C. 141 matched cddid_all.tbl CDD TIGR03399 TIGR03399 274563 RNA_3prim_cycl RNA 3'-phosphate cyclase. Members of this protein family are RNA 3'-phosphate cyclase (6.5.1.4), an enzyme whose function is conserved from E. coli to human. The modification this enzyme performs enables certain RNA ligations to occur, although the full biological roll for this enzyme is not fully described. This model separates this enzyme from a related protein, present only in eukaryotes, localized to the nucleolus, and involved in ribosomal modification. [Transcription, RNA processing] 326 matched cddid_all.tbl CDD TIGR03400 TIGR03400 274564 18S_RNA_Rcl1p 18S rRNA biogenesis protein RCL1. Members of this strictly eukaryotic protein family are not RNA 3'-phosphate cyclase (6.5.1.4), but rather a homolog with a distinct function, found in the nucleolus and required for ribosomal RNA processing. Homo sapiens has both a member of this RCL (RNA terminal phosphate cyclase like) family and EC 6.5.1.4, while Saccharomyces has a member of this family only. 360 matched cddid_all.tbl CDD TIGR03401 TIGR03401 188314 cyanamide_fam HD domain protein, cyanamide hydratase family. Members of this protein family are known, so far, in the Ascomycota, a branch of the Fungi, and contain an HD domain (pfam01966), found typically in various metal-dependent phosphohydrolases. The only characterized member of this family, from the soil fungus Myrothecium verrucaria, is cyanamide hydratase (EC 4.2.1.69), a zinc-containing homohexamer that adds water to the fertilizer cyanamide (NCNH2), a nitrile compound, to produce urea (NH2-CO-NH2). Homologs are likely to be nitrile hydratases. 228 matched cddid_all.tbl CDD TIGR03402 TIGR03402 132443 FeS_nifS cysteine desulfurase NifS. Members of this protein family are NifS, one of several related families of cysteine desulfurase involved in iron-sulfur (FeS) cluster biosynthesis. NifS is part of the NIF system, usually associated with other nif genes involved in nitrogenase expression and nitrogen fixation. The protein family is given a fairly broad interpretation here. It includes a clade nearly always found in extended nitrogen fixation genomic regions, plus a second clade more closely related to the first than to IscS and also part of NifS-like/NifU-like systems. This model does not extend to a more distantly clade found in the epsilon proteobacteria such as Helicobacter pylori, also named NifS in the literature, built instead in TIGR03403. 379 matched cddid_all.tbl CDD TIGR03403 TIGR03403 132444 nifS_epsilon cysteine desulfurase, NifS family, epsilon proteobacteria type. Members of this family are the NifS-like cysteine desulfurase of the epsilon division of the Proteobacteria, similar to the NifS protein of nitrogen-fixing bacteria. Like NifS, and unlike IscS, this protein is found as part of a system of just two proteins, a cysteine desulfurase and a scaffold, for iron-sulfur cluster biosynthesis. This protein is called NifS by Olsen, et al. (), so we use this designation. 382 matched cddid_all.tbl CDD TIGR03404 TIGR03404 274565 bicupin_oxalic bicupin, oxalate decarboxylase family. Members of this protein family are defined as bicupins as they have two copies of the cupin domain (pfam00190). Two different known activities for members of this family are oxalate decarboxylase (EC 4.1.1.2) and oxalate oxidase (EC 1.2.3.4), although the latter activity has more often been found in distantly related monocupin (germin) proteins. 367 matched cddid_all.tbl CDD TIGR03405 TIGR03405 274566 Phn_Fe-ADH phosphonate metabolism-associated iron-containing alcohol dehydrogenase. This small clade of iron-containing alcohol dehydrogenases of the pfam00465 family is found in genomic contexts indicating a role in the metabolism of phosphonates. In Delftia acidovorans SPH-1, the gene ZP_01580650.1 is adjacent to and running in the same direction as ZP_01580649.1 encoding the enzyme phosphonatase (PhnX, TIGR01422). Upstream are also found genes encoding components of a phosphonate ABC transport complex. In Ralstonia eutropha H16 and Verminephrobacter eiseniae EF01-2 the dehydrogenase is followed by a homolog of the PhnB gene, a putative phosphonate-specific MFS-type transporter. In Azoarcus BH72 the gene is preceded by Phosphoenolpyruvate phosphomutase (aepX) and a putative phosphonopyruvate decarboxylase (aepY), two genes involved in the biosynthesis of phosphonoacetaldehyde (Pald). Ususally these two are accompanied by a specific transaminase, AepZ, which converts Pald to 2-aminoethylphosphonate (2-AEP). 2-hydroxyethylphosphonate (2-HEP), the presumed product of the reaction of Pald with an alcohol dehydrogenase, is a biologically novel but reasonable analog of 2-AEP and may be a constituent of as-yet undescribed natural products. In the case of Azoarcus, downstream of the dehydrogenase is a CDP-glycerol:glycerophosphate transferase homolog that may indicate the existence of a pathway for 2-HEP-derived phosphonolipid biosynthesis. 355 matched cddid_all.tbl CDD TIGR03406 TIGR03406 213809 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 174 matched cddid_all.tbl CDD TIGR03407 TIGR03407 132448 urea_ABC_UrtA urea ABC transporter, urea binding protein. Members of this protein family are ABC transporter substrate-binding proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity. Members of this protein family tend to have the twin-arginine signal for Sec-independent transport across the plasma membrane. [Transport and binding proteins, Amino acids, peptides and amines] 359 matched cddid_all.tbl CDD TIGR03408 TIGR03408 132449 urea_trans_UrtC urea ABC transporter, permease protein UrtC. Members of this protein family are ABC transporter permease proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity. [Transport and binding proteins, Amino acids, peptides and amines] 313 matched cddid_all.tbl CDD TIGR03409 TIGR03409 200272 urea_trans_UrtB urea ABC transporter, permease protein UrtB. Members of this protein family are ABC transporter permease proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity. [Transport and binding proteins, Amino acids, peptides and amines] 291 matched cddid_all.tbl CDD TIGR03410 TIGR03410 274567 urea_trans_UrtE urea ABC transporter, ATP-binding protein UrtE. Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity. [Transport and binding proteins, Amino acids, peptides and amines] 230 matched cddid_all.tbl CDD TIGR03411 TIGR03411 274568 urea_trans_UrtD urea ABC transporter, ATP-binding protein UrtD. Members of this protein family are ABC transporter ATP-binding subunits associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity. [Transport and binding proteins, Amino acids, peptides and amines] 242 matched cddid_all.tbl CDD TIGR03412 TIGR03412 132453 iscX_yfhJ FeS assembly protein IscX. Members of this protein family are YfhJ, a protein of the ISC system for iron-sulfur cluster assembly. Other genes in the system include iscSUA, hscBA, and fdx. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 63 matched cddid_all.tbl CDD TIGR03413 TIGR03413 274569 GSH_gloB hydroxyacylglutathione hydrolase. Members of this protein family are hydroxyacylglutathione hydrolase, a detoxification enzyme known as glyoxalase II. It follows lactoylglutathione lyase, or glyoxalase I, and acts to remove the toxic metabolite methylglyoxal and related compounds. This protein belongs to the broader metallo-beta-lactamase family (pfam00753). [Cellular processes, Detoxification] 248 matched cddid_all.tbl CDD TIGR03414 TIGR03414 188316 ABC_choline_bnd choline ABC transporter, periplasmic binding protein. Partial phylogenetic profiling () vs. the genome property of glycine betaine biosynthesis from choline consistently reveals a member of this ABC transporter periplasmic binding protein as the best match, save for the betaine biosynthesis enzymes themselves. Genomes often carry several paralogs, one encoded together with the permease and ATP-binding components and another encoded next to a choline-sulfatase gene, suggesting that different members of this protein family interact with shared components and give some flexibility in substrate. Of two members from Sinorhizobium meliloti 1021, one designated ChoX has been shown experimentally to bind choline (though not various related compounds such as betaine) and to be required for about 60 % of choline uptake. Members of this protein have an invariant Cys residue near the N-terminus and likely are lipoproteins. [Transport and binding proteins, Amino acids, peptides and amines] 290 matched cddid_all.tbl CDD TIGR03415 TIGR03415 188317 ABC_choXWV_ATP choline ABC transporter, ATP-binding protein. Members of this protein family are the ATP-binding subunit of a three-protein transporter. This family belongs, more broadly, to the family of proline and glycine-betaine transporters, but members have been identified by direct characterization and by bioinformatic means as choline transporters. Many species have several closely-related members of this family, probably with variable abilities to act additionally on related quaternary amines. [Transport and binding proteins, Amino acids, peptides and amines] 382 matched cddid_all.tbl CDD TIGR03416 TIGR03416 188318 ABC_choXWV_perm choline ABC transporter, permease protein. 267 matched cddid_all.tbl CDD TIGR03417 TIGR03417 274570 chol_sulfatase choline-sulfatase. 500 matched cddid_all.tbl CDD TIGR03418 TIGR03418 188320 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate. 291 matched cddid_all.tbl CDD TIGR03419 TIGR03419 132460 NifU_clost FeS cluster assembly scaffold protein NifU, Clostridium type. NifU and NifS form a pair of iron-sulfur (FeS) cluster biosynthesis proteins much simpler than the ISC and SUF systems. Members of this protein family are a distinct group of NifU-like proteins, found always to a NifS-like protein and restricted to species that lack a SUF system. Typically, NIF systems service a smaller number of FeS-containing proteins than do ISC or SUF. Members of this particular branch typically are found, almost half the time, near the mnmA gene, involved in the carboxymethylaminomethyl modification of U34 in some tRNAs (see GenProp0704). While other NifU proteins are associated with nitrogen fixation, this family is not. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 121 matched cddid_all.tbl CDD TIGR03420 TIGR03420 274571 DnaA_homol_Hda DnaA regulatory inactivator Hda. Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP. [DNA metabolism, DNA replication, recombination, and repair] 226 matched cddid_all.tbl CDD TIGR03421 TIGR03421 274572 FeS_CyaY iron donor protein CyaY. Members of this protein family are the iron-sulfur cluster (FeS) metabolism protein CyaY, a homolog of eukaryotic frataxin. ISC is one of several bacterial systems for FeS assembly; we find by Partial Phylogenetic Profiling vs. the ISC system that CyaY most like work with the ISC system for FeS cluster biosynthesis. A study of of cyaY mutants in Salmonella enterica bears this out. Although the trusted cutoff is set low enough to include eukaryotic frataxin sequences, a narrower, exception-type model (TIGR03421) identifies identifies members of that specific set. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 102 matched cddid_all.tbl CDD TIGR03422 TIGR03422 132463 mito_frataxin frataxin. Frataxin is a mitochondrial protein, mutation of which leads to the disease Friedreich's ataxia. Its orthologs are widely distributed in the bacteria, associated with the ISC system for iron-sulfur cluster assembly, and designated CyaY. This exception-type model allows those examples of frataxin per se that score above the trusted cutoff to the CyaY equivalog-type model (TIGR03421) to be named appropriately. 97 matched cddid_all.tbl CDD TIGR03423 TIGR03423 274573 pbp2_mrdA penicillin-binding protein 2. Members of this protein family are penicillin-binding protein 2 (PBP-2), a protein whose gene (designated pbpA or mrdA) generally is found next to the gene for RodA, a protein required for rod (bacillus) shape in many bacteria. PBP-2 acts as a transpeptidase for cell elongation (hence, rod-shape). [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 592 matched cddid_all.tbl CDD TIGR03424 TIGR03424 132465 urea_degr_1 urea carboxylase-associated protein 1. A number of bacteria degrade urea as a nitrogen source by the urea carboxylase/allophanate hydrolase pathway, which uses biotin and consumes ATP, rather than my means of the nickel-dependent enzyme urease. This model represents one of a pair of homologous, tandem uncharacterized genes found together with the urea carboxylase and allophanate hydrolase genes. 198 matched cddid_all.tbl CDD TIGR03425 TIGR03425 163257 urea_degr_2 urea carboxylase-associated protein 2. A number of bacteria degrade urea as a nitrogen source by the urea carboxylase/allophanate hydrolase pathway, which uses biotin and consumes ATP, rather than my means of the nickel-dependent enzyme urease. This model represents one of a pair of homologous, tandem uncharacterized genes found together with the urea carboxylase and allophanate hydrolase genes. 233 matched cddid_all.tbl CDD TIGR03426 TIGR03426 274574 shape_MreD rod shape-determining protein MreD. Members of this protein family are the MreD protein of bacterial cell shape determination. Most rod-shaped bacteria depend on MreB and RodA to achieve either a rod shape or some other non-spherical morphology such as coil or stalk formation. MreD is encoded in an operon with MreB, and often with RodA and PBP-2 as well. It is highly hydrophobic (therefore somewhat low-complexity) and highly divergent, and therefore sometimes tricky to discover by homology, but this model finds most examples. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 152 matched cddid_all.tbl CDD TIGR03427 TIGR03427 213811 ABC_peri_uca ABC transporter periplasmic binding protein, urea carboxylase region. Members of this family are ABC transporter periplasmic binding proteins associated with the urea carboxylase/allophanate hydrolase pathway, an alternative to urease for urea degradation. The protein is restricted to bacteria with the pathway, with its gene close to the urea carboxylase and allophanate hydrolase genes. The substrate for this transporter therefore is likely to be urea or a compound from which urea is easily derived. [Transport and binding proteins, Unknown substrate] 328 matched cddid_all.tbl CDD TIGR03428 TIGR03428 132469 ureacarb_perm permease, urea carboxylase system. A number of bacteria obtain nitrogen by biotin- and ATP-dependent urea degradation system distinct from urease. The two characterized proteins of this system are the enzymes urea carboxylase and allophanate hydrolase, but other, uncharacterized proteins co-occur as genes encoded nearby in multiple organisms. This family includes predicted permeases of the amino acid permease family, likely to transport either urea or a compound from which urea is derived. It is found so far only Actinobacteria, whereas a number of other species with the urea carboxylase have an adjacent ABC transporter operon. 475 matched cddid_all.tbl CDD TIGR03429 TIGR03429 274575 arom_pren_DMATS aromatic prenyltransferase, DMATS type. Members of this protein family are mostly fungal enzymes of secondary metabolite production. Characterized or partially characterized members include several examples of dimethylallyltryptophan synthase, a brevianamide F prenyltransferase, LtxC from lyngbyatoxin biosynthesis, and a probable dimethylallyl tyrosine synthase. 405 matched cddid_all.tbl CDD TIGR03430 TIGR03430 132471 trp_dimet_allyl tryptophan dimethylallyltransferase. Members of this family are the enzyme tryptophan dimethylallyltransferase (EC 2.5.1.34), a distinct clade within a larger group of aromatic prenyltransferases that may act on on trp-containing cyclic dipeptides, or on tyrosine or other related substrates. Tryptophan dimethylallyltransferase and related enzymes typically are of fungal origin are involved in the biosynthesis of secondary metabolites such as ergot alkaloids. 419 matched cddid_all.tbl CDD TIGR03431 TIGR03431 132472 PhnD phosphonate ABC transporter, periplasmic phosphonate binding protein. This model is a subset of the broader subfamily of phosphate/phosphonate binding protein ABC transporter components, TIGR01098. In this model all members of the seed have support from genomic context for association with pathways for the metabolims of phosphonates, particularly the C-P lyase system, GenProp0232. This model includes the characterized phnD gene from E. coli. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function. 288 matched cddid_all.tbl CDD TIGR03432 TIGR03432 163260 yjhG_yagF putative dehydratase, YjhG/YagF family. This homolog of dihydroxy-acid dehydratases has an odd, sparse distribution. Members are found in two Acidobacteria, two Planctomycetes, Bacillus clausii KSM-K16, and (in two copies each) in strains K12-MG1655 and W3110 of Escherichia coli. The local context is not well conserved, but a few members are adjacent to homologs of the gluconate:H+ symporter (see TIGR00791). [Unknown function, Enzymes of unknown specificity] 640 matched cddid_all.tbl CDD TIGR03433 TIGR03433 163261 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein [Regulatory functions, DNA interactions] 100 matched cddid_all.tbl CDD TIGR03434 TIGR03434 274576 ADOP Acidobacterial duplicated orphan permease. Members of this protein family are found, so far, only in three species of Acidobacteria, namely Acidobacteria bacterium Ellin345, Acidobacterium capsulatum ATCC 51196, and Solibacter usitatus Ellin6076, where they form large paralogous families. Each protein contains two copies of a domain called the efflux ABC transporter permease protein (pfam02687). However, unlike other members of that family (including LolC, FtsX, and MacB), genes for these proteins are essentially never found fused or adjacent to ABC transporter ATP-binding protein (pfam00005) genes. We name this family ADOP, for Acidobacterial Duplicated Orphan Permease, to reflect the restricted lineage, internal duplication, lack of associated ATP-binding cassette proteins, and permease homology. The function is unknown. 803 matched cddid_all.tbl CDD TIGR03435 TIGR03435 132476 Soli_TIGR03435 soil-associated protein, TIGR03435 family. Bacterial reference strains encoding members of this protein family are all isolated from soil. These include 39 members from Solibacter usitatus Ellin6076, 27 from Acidobacterium sp. MP5ACTX8 (both Acidobacteria), and four from Pedosphaera parvula Ellin514 (Verrucomicrobia). The family is well-diversified, with few pairs showing greater than 50 % pairwise identity. A few members are fused to Peptidase_M56 domains (see pfam05569), to Sigma70_r2 domains (see pfam04542), or have a duplication of this domain. 237 matched cddid_all.tbl CDD TIGR03436 TIGR03436 274577 acidobact_VWFA VWFA-related Acidobacterial domain. Members of this family are bacterial domains that include a region related to the von Willebrand factor type A (VWFA) domain (pfam00092). These domains are restricted to, and have undergone a large paralogous family expansion in, the Acidobacteria, including Solibacter usitatus and Acidobacterium capsulatum ATCC 51196. 296 matched cddid_all.tbl CDD TIGR03437 TIGR03437 274578 Soli_cterm Solibacter uncharacterized C-terminal domain. This model describes a protein domain found in 90 proteins of Solibacter usitatus Ellin6076, nearly always as the C-terminal domain of a much larger protein. No homologs to this domain are detected outside of S. usitatus, a member of the Acidobacteria. 215 matched cddid_all.tbl CDD TIGR03438 TIGR03438 274579 egtD_ergothio dimethylhistidine N-methyltransferase. This model represents a distinct set of uncharacterized proteins found in the bacteria. Analysis by PSI-BLAST shows remote sequence homology to methyltransferases [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 301 matched cddid_all.tbl CDD TIGR03439 TIGR03439 274580 methyl_EasF probable methyltransferase domain, EasF family. This model represents an uncharacterized domain of about 300 amino acids with homology to S-adenosylmethionine-dependent methyltransferases. Proteins with this domain are exclusively fungal. A few, such as EasF from Neotyphodium lolii, are associated with the biosynthesis of ergot alkaloids, a class of fungal secondary metabolites. EasF may, in fact, be the AdoMet:dimethylallyltryptophan N-methyltransferase, the enzyme that follows tryptophan dimethylallyltransferase (DMATS) in ergot alkaloid biosynthesis. Several other members of this family, including mug158 (meiotically up-regulated gene 158 protein) from Schizosaccharomyces pombe, contain an additional uncharacterized domain DUF323 (pfam03781). 319 matched cddid_all.tbl CDD TIGR03440 TIGR03440 274581 egtB_TIGR03440 ergothioneine biosynthesis protein EgtB. Members of this family include EgtB, and enzyme of the ergothioneine biosynthesis, as found in numerous Actinobacteria. Characterized homologs to this family include a formylglycine-generating enzyme that serves as a maturase for an aerobic sulfatase (cf. the radical SAM enzymes that serve as anaerobic sulfatase maturases). [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 406 matched cddid_all.tbl CDD TIGR03441 TIGR03441 163267 urea_trans_yut urea transporter, Yersinia type. Members of this protein family are bacterial urea transporters, found not only is species that contain urease, but adjacent to the urease operon. It was characterized in Yersinia pseudotuberculosis. Members are homologous to eukaryotic members of solute carrier family 14, a family that includes urea transporters, and to bacterial proteins in species with no detectable urea degradation system. [Transport and binding proteins, Other] 292 matched cddid_all.tbl CDD TIGR03442 TIGR03442 132483 TIGR03442 ergothioneine biosynthesis protein EgtC. Members of this strictly bacterial protein family show similarity to class II glutamine amidotransferases (see pfam00310). They are distinguished by appearing in a genome context with, and usually adjacent to or between, members of families TIGR03438 (an uncharacterized methyltransferase) and TIGR03440 (an uncharacterized protein). [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 251 matched cddid_all.tbl CDD TIGR03443 TIGR03443 274582 alpha_am_amid L-aminoadipate-semialdehyde dehydrogenase. Members of this protein family are L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31), product of the LYS2 gene. It is also called alpha-aminoadipate reductase. In fungi, lysine is synthesized via aminoadipate. Currently, all members of this family are fungal. 1389 matched cddid_all.tbl CDD TIGR03444 TIGR03444 274583 EgtA_Cys_ligase ergothioneine biosynthesis glutamate--cysteine ligase EgtA. Members of this bacterial protein family, EgtA, resemble the glutamate--cysteine ligase of the two-step pathway for glutathione (GSH) biosynthesis, but instead are involved in the biosynthesis of the histidine-derived thiol, ergothioneine (EGT). Successful in vitro reconstitution of EGT biosynthesis using EgtBCDE and gamma-L-glutamyl-L-cysteine suggests that this enzyme is a bone fide glutamate--cysteine ligase. [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 390 matched cddid_all.tbl CDD TIGR03445 TIGR03445 274584 mycothiol_MshB N-acetyl-1-D-myo-inositol-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase. Members of this protein family are N-acetyl-1-D-myo-inositol-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase, also called 1D-myo-inosityl-2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase, the MshB protein of mycothiol biosynthesis in Mycobacterium tuberculosis and related species. [Cellular processes, Detoxification] 284 matched cddid_all.tbl CDD TIGR03446 TIGR03446 132487 mycothiol_Mca mycothiol conjugate amidase Mca. Mycobacterium tuberculosis, Corynebacterium glutamicum, and related species use the thiol mycothiol in place of glutathione. This enzyme, homologous to the (dispensible) MshB enzyme of mycothiol biosynthesis, is described as an amidase that acts on conjugates to mycothiol. It is a detoxification enzyme. [Cellular processes, Detoxification] 283 matched cddid_all.tbl CDD TIGR03447 TIGR03447 132488 mycothiol_MshC cysteine--1-D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase. Members of this protein family are MshC, l-cysteine:1-D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase, an enzyme that uses ATP to ligate a Cys residue to a mycothiol precursor molecule, in the second to last step in mycothiol biosynthesis. This enzyme shows considerable homology to Cys--tRNA ligases, and many instances are misannotated as such. Mycothiol is found in Mycobacterium tuberculosis, Corynebacterium glutamicum, Streptomyces coelicolor, and various other members of the Actinobacteria. Mycothiol is an analog to glutathione. [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 411 matched cddid_all.tbl CDD TIGR03448 TIGR03448 132489 mycothiol_MshD mycothiol synthase. Members of this family are MshD, the acetyltransferase that catalyzes the final step of mycothiol biosynthesis in various members of the Actinomyctes, Mycothiol replaces glutathione in these species. [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 292 matched cddid_all.tbl CDD TIGR03449 TIGR03449 132490 mycothiol_MshA D-inositol-3-phosphate glycosyltransferase. Members of this protein family, found exclusively in the Actinobacteria, are MshA, the glycosyltransferase of mycothiol biosynthesis. Mycothiol replaces glutathione in these species. 405 matched cddid_all.tbl CDD TIGR03450 TIGR03450 132491 mycothiol_INO1 inositol 1-phosphate synthase, Actinobacterial type. This enzyme, inositol 1-phosphate synthase as found in Actinobacteria, produces an essential precursor for several different products, including mycothiol, which is a glutathione analog, and phosphatidylinositol, which is a phospholipid. 351 matched cddid_all.tbl CDD TIGR03451 TIGR03451 132492 mycoS_dep_FDH S-(hydroxymethyl)mycothiol dehydrogenase. Members of this protein family are mycothiol-dependent formaldehyde dehydrogenase (EC 1.2.1.66). This protein is found, so far, only in the Actinobacteria (Mycobacterium sp., Streptomyces sp., Corynebacterium sp., and related species), where mycothione replaces glutathione. [Cellular processes, Detoxification] 358 matched cddid_all.tbl CDD TIGR03452 TIGR03452 132493 mycothione_red mycothione reductase. Mycothiol, a glutathione analog in Mycobacterium tuberculosis and related species, can form a disulfide-linked dimer called mycothione. This enzyme can reduce mycothione to regenerate two mycothiol molecules. The enzyme shows some sequence similarity to glutathione-disulfide reductase, trypanothione-disulfide reductase, and dihydrolipoamide dehydrogenase. The characterized protein from M. tuberculosis, a homodimer, has FAD as a cofactor, one per monomer, and uses NADPH as a substrate. 452 matched cddid_all.tbl CDD TIGR03453 TIGR03453 274585 partition_RepA plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error. [Mobile and extrachromosomal element functions, Plasmid functions] 387 matched cddid_all.tbl CDD TIGR03454 TIGR03454 274586 partition_RepB plasmid partitioning protein RepB. Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently. [Mobile and extrachromosomal element functions, Plasmid functions] 325 matched cddid_all.tbl CDD TIGR03455 TIGR03455 274587 HisG_C-term ATP phosphoribosyltransferase, C-terminal domain. This domain corresponds to the C-terminal third of the HisG protein. It is absent in many lineages. 92 matched cddid_all.tbl CDD TIGR03457 TIGR03457 132497 sulphoacet_xsc sulfoacetaldehyde acetyltransferase. Members of this protein family are sulfoacetaldehyde acetyltransferase, an enzyme of taurine utilization. Taurine, or 2-aminoethanesulfonate, can be used by bacteria as a source of carbon, nitrogen, and sulfur. [Central intermediary metabolism, Other] 579 matched cddid_all.tbl CDD TIGR03458 TIGR03458 274588 YgfH_subfam succinate CoA transferase. This family of CoA transferases includes enzymes catalyzing at least two related but distinct activities. The E. coli YgfH protein has been characterized as a propionyl-CoA:succinate CoA transferase where it appears to be involved in a pathway for the decarboxylation of succinate to propionate. The Clostridium kluyveri CAT1 protein has been characterized as a acetyl-CoA:succinate CoA transferase and is believed to be involved in anaerobic succinate degradation. The propionate:succinate transferase activity has been reported in the propionic acid fermentation of propionibacterium species, where it is distinct from the coupled activities of distinct nucleotide-triphosphate dependent succinate and propionate/acetate CoA transferases (as inferred from activity in the absence of NTPs). The family represented by this model includes a member from Propionibacterium acnes KPA171202 which is likely to be responsible for this activity. A closely related clade not included in this family are the Ach1p proteins of fungi which are acetyl-CoA hydrolases. This name has been applied to many of the proteins represented by this model, possibly erroneously. 485 matched cddid_all.tbl CDD TIGR03459 TIGR03459 274589 crt_membr carotene biosynthesis associated membrane protein. This model represents a family of hydrophobic and presumed membrane proteins found in the Actinobacteria. The genes encoding these proteins are syntenically associated with (found proximal to) genes of carotene biosynthesis ususally including phytoene synthase (crtB), phytoene dehydrogenase (crtI) and geranylgeranyl pyrophosphate synthase (ispA). 456 matched cddid_all.tbl CDD TIGR03460 TIGR03460 132500 crt_membr_arch carotene biosynthesis associated membrane protein. 232 matched cddid_all.tbl CDD TIGR03461 TIGR03461 132501 pabC_Proteo aminodeoxychorismate lyase. Members of this protein family are aminodeoxychorismate lyase (ADC lyase), EC 4.1.3.38, the PabC protein of PABA biosynthesis. PABA (para-aminobenzoate) is a precursor of folate, needed for de novo purine biosynthesis. This enzyme is a pyridoxal-phosphate-binding protein in the class IV aminotransferase family (pfam01063). [Biosynthesis of cofactors, prosthetic groups, and carriers, Folic acid] 261 matched cddid_all.tbl CDD TIGR03462 TIGR03462 274590 CarR_dom_SF lycopene cyclase domain. This domain is often repeated twice within the same polypeptide, as is observed in Archaea, Thermus, Sphingobacteria and Fungi. In the fungal sequences, this tandem domain pair is observed as the N-terminal half of a bifunctional protein, where it has been characterized as a lycopene beta-cyclase and the C-terminal half is a phytoene synthetase. In Myxococcus and Actinobacterial genomes this domain appears as a single polypeptide, tandemly repeated and usually in a genomic context consistent with a role in carotenoid biosynthesis. It is unclear whether any of the sequences in this family truly encode lycopene epsilon cyclases. However a number are annotated as such. The domain is generally hydrophobic with a number of predicted membrane spanning segments and contains a distinctive motif (hPhEEhhhhhh). In certain sequences one of either the proline or glutamates may vary, but always one of the tandem pair appear to match this canonical sequence exactly. 89 matched cddid_all.tbl CDD TIGR03463 TIGR03463 274591 osq_cycl 2,3-oxidosqualene cyclase. This model identifies 2,3-oxidosqualene cyclases from Stigmatella aurantiaca which produces cycloartenol, and Gemmata obscuriglobus and Methylococcus capsulatus, which each produce the closely related sterol, lanosterol. 634 matched cddid_all.tbl CDD TIGR03464 TIGR03464 274592 HpnC squalene synthase HpnC. This family of genes are members of a superfamily (pfam00494) of phytoene and squalene synthases which catalyze the head-t0-head condensation of polyisoprene pyrophosphates. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnD gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated. 266 matched cddid_all.tbl CDD TIGR03465 TIGR03465 163278 HpnD squalene synthase HpnD. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. In the organisms Zymomonas mobilis and Bradyrhizobium japonicum these genes have been characterized as squalene synthases (farnesyl-pyrophosphate ligases). Often, these genes appear in tandem with the HpnC gene which appears to have resulted from an ancient gene duplication event. Presumably these proteins form a heteromeric complex, but this has not yet been experimentally demonstrated. 266 matched cddid_all.tbl CDD TIGR03466 TIGR03466 163279 HpnA hopanoid-associated sugar epimerase. The sequences in this family are members of the pfam01370 superfamily of NAD-dependent epimerases and dehydratases typically acting on nucleotide-sugar substrates. The genes of the family modeled here are generally in the same locus with genes involved in the biosynthesis and elaboration of hopene, the cyclization product of the polyisoprenoid squalene. This gene and its association with hopene biosynthesis in Zymomonas mobilis has been noted in the literature where the gene symbol hpnA was assigned. Hopanoids are known to be components of the plasma membrane and to have polar sugar head groups in Z. mobilis and other species. 328 matched cddid_all.tbl CDD TIGR03467 TIGR03467 274593 HpnE squalene-associated FAD-dependent desaturase. The sequences in this family are members of the pfam01593 superfamily of flavin-containing amine oxidases which include the phytoene desaturases. These sequences also include a FAD-dependent oxidoreductase domain, pfam01266. The genes of the family modeled here are generally in the same locus with genes involved in the biosynthesis and elaboration of squalene, the condensation product of the polyisoprenoid farnesyl pyrophosphate. This gene and its association with hopene biosynthesis in Zymomonas mobilis has been noted in the literature where the gene symbol hpnE was assigned. This gene is also found in contexts where the downstream conversion of squalene to hopenes is not evidence. The precise nature of the reaction catalyzed by this enzyme is unknown at this time. 419 matched cddid_all.tbl CDD TIGR03468 TIGR03468 274594 HpnG hopanoid-associated phosphorylase. The sequences in this family are members of the pfam01048 family of phosphorylases typically acting on nucleotide-sugar substrates. The genes of the family modeled here are generally in the same locus with genes involved in the biosynthesis and elaboration of hopene, the cyclization product of the polyisoprenoid squalene. This gene is adjacent to the genes PhnA-E and squalene-hopene cyclase (which would be HpnF) in Zymomonas mobilis and their association with hopene biosynthesis has been noted in the literature. Extending the gene symbol sequence, we suggest the symbol HpnG for the product of this gene. Hopanoids are known to be components of the plasma membrane and to have polar sugar head groups in Z. mobilis and other species. 212 matched cddid_all.tbl CDD TIGR03469 TIGR03469 213815 HpnB hopene-associated glycosyltransferase HpnB. This family of genes include a glycosyl transferase, group 2 domain (pfam00535) which are responsible, generally for the transfer of nucleotide-diphosphate sugars to substrates such as polysaccharides and lipids. The genes of this family are often found in the same genetic locus with squalene-hopene cyclase genes, and are never associated with genes for the metabolism of phytoene. Indeed, the members of this family appear to never be found in a genome lacking squalene-hopene cyclase (SHC), although not all genomes encoding SHC have this glycosyl transferase. In the organism Zymomonas mobilis the linkage of this gene to hopanoid biosynthesis has been noted and the gene named HpnB. Hopanoids are known to feature polar glycosyl head groups in many organisms. 384 matched cddid_all.tbl CDD TIGR03470 TIGR03470 274595 HpnH hopanoid biosynthesis associated radical SAM protein HpnH. The sequences represented by this model are members of the radical SAM superfamily of enzymes (pfam04055). These enzymes utilize an iron-sulfur redox cluster and S-adenosylmethionine to carry out diverse radical mediated reactions. The members of this clade are frequently found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. The linkage between SHC and this radical SAM enzyme is strong; one is nearly always observed in the same genome where the other is found. A hopanoid biosynthesis locus was described in Zymomonas mobilis consisting of the genes HpnA-E and SHC (HpnF). Continuing past SHC are found a phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and this radical SAM enzyme (ZMO0874) which we name here HpnH. Granted, in Z. mobilis, HpnH is in a convergent orientation with respect to HpnA-G, but one gene beyond HpnH and running in the same convergent direction is IspH (ZM0875, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase), an essential enzyme of IPP biosynthesis and therefore essential for the biosynthesis of hopanoids. One of the well-described hopanoid intermediates is bacteriohopanetetrol. In the conversion from hopene several reactions must occur in the side chain for which a radical mechanism might be reasonable. These include the four (presumably anaerobic) hydroxylations and a methyl shift. 318 matched cddid_all.tbl CDD TIGR03471 TIGR03471 132511 HpnJ hopanoid biosynthesis associated radical SAM protein HpnJ. The sequences represented by this model are members of the radical SAM superfamily of enzymes (pfam04055). These enzymes utilize an iron-sulfur redox cluster and S-adenosylmethionine to carry out diverse radical mediated reactions. The member of this clade from Acidithiobacillus ferrooxidans ATCC 23270 (AFE_0975) is found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. Similarly, in Ralstonia eutropha JMP134 (Reut_B4901) this gene is adjacent to HpnAB, IspH and HpnH (TIGR03470), although SHC itself is elsewhere in the genome. Notably, this gene (here named HpnJ) and three others form a conserved set (HpnIJKL) which occur in a subset of all genomes containing the SHC enzyme. This relationship was discerned using the method of partial phylogenetic profiling. This group includes Zymomonas mobilis, the organism where the initial hopanoid biosynthesis locus was described consisting of the genes HpnA-E and SHC (HpnF). Continuing past SHC are found a phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and another radical SAM enzyme (ZMO0874), HpnH. Although discontinuous in Z. mobilis, we continue the gene symbol sequence with HpnIJKL. One of the well-described hopanoid intermediates is bacteriohopanetetrol. In the conversion from hopene several reactions must occur in the side chain for which a radical mechanism might be reasonable. These include the four (presumably anaerobic) hydroxylations and a methyl shift. 472 matched cddid_all.tbl CDD TIGR03472 TIGR03472 132512 HpnI hopanoid biosynthesis associated glycosyl transferase protein HpnI. This family of genes include a glycosyl transferase, group 2 domain (pfam00535) which are responsible, generally for the transfer of nucleotide-diphosphate sugars to substrates such as polysaccharides and lipids. The member of this clade from Acidithiobacillus ferrooxidans ATCC 23270 (AFE_0974) is found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. Similarly, in Ralstonia eutropha JMP134 (Reut_B4902) this gene is adjacent to HpnAB, IspH and HpnH (TIGR03470), although SHC itself is elsewhere in the genome. Notably, this gene (here named HpnI) and three others form a conserved set (HpnIJKL) which occur in a subset of all genomes containing the SHC enzyme. This relationship was discerned using the method of partial phylogenetic profiling. This group includes Zymomonas mobilis, the organism where the initial hopanoid biosynthesis locus was described consisting of the genes HpnA-E and SHC (HpnF). Continuing past SHC are found a phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and another radical SAM enzyme (ZMO0874), HpnH. Although discontinuous in Z. mobilis, we continue the gene symbol sequence with HpnIJKL. Hopanoids are known to feature polar glycosyl head groups in many organisms. 373 matched cddid_all.tbl CDD TIGR03473 TIGR03473 132513 HpnK "hopanoid biosynthesis associated protein HpnK. The sequences represented by this model are members of the pfam04794 ""YdjC-like"" family of uncharacterized proteins. The member of this clade from Acidithiobacillus ferrooxidans ATCC 23270 (AFE_0976) is found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. Similarly, in Ralstonia eutropha JMP134 (Reut_B4902) this gene is adjacent to HpnAB, IspH and HpnH (TIGR03470), although SHC itself is elsewhere in the genome. Notably, this gene (here named HpnK) and three others form a conserved set (HpnIJKL) which occur in a subset of all genomes containing the SHC enzyme. This relationship was discerned using the method of partial phylogenetic profiling. This group includes Zymomonas mobilis, the organism where the initial hopanoid biosynthesis locus was described consisting of the genes HpnA-E and SHC (HpnF). Continuing past SHC are found a phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and a radical SAM enzyme (ZMO0874), HpnH. Although discontinuous in Z. mobilis, we continue the gene symbol sequence with HpnIJKL." 283 matched cddid_all.tbl CDD TIGR03474 TIGR03474 132514 incFII_RepA incFII family plasmid replication initiator RepA. Members of this protein are the plasmid replication initiator RepA of incFII (plasmid incompatibility group F-II) plasmids. R1 and R100 are plasmids in this group. Immediately upstream of repA is found tap, a leader peptide of about 24 amino acids, often not assigned as a gene in annotated plasmid sequences. Note that other, non-homologous plasmid replication proteins share the gene symbol (repA) and similar names (plasmid replication protein RepA). 275 matched cddid_all.tbl CDD TIGR03475 TIGR03475 132515 tap_IncFII_lead RepA leader peptide Tap. This protein is a translated leader peptide that actis in the regulation of the expression of the plasmid replication protein RepA in incF2 group plasmids. [Mobile and extrachromosomal element functions, Plasmid functions] 25 matched cddid_all.tbl CDD TIGR03476 TIGR03476 274596 HpnL putative membrane protein. This family of hydrophobic proteins is observed in two distinct contexts. It is primarily found in the presence of genes for the biosynthesis and elaboration of hopene where we assign the gene symbol HpnL. In a subset of the genomes containing HpnL a second, often plasmid-encoded, homolog is observed in a context implying the biosynthesis of 2-aminoethylphosphonate head-group containing lipids. 318 matched cddid_all.tbl CDD TIGR03477 TIGR03477 274597 DMSO_red_II_gam DMSO reductase family type II enzyme, heme b subunit. This model represents a heme b-binding subunit, typically called the gamma subunit, of various proteins that also contain a molybdopterin subunit and an iron-sulfur protein. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase and ethylbenzene dehydrogenase. [Energy metabolism, Electron transport] 206 matched cddid_all.tbl CDD TIGR03478 TIGR03478 132518 DMSO_red_II_bet DMSO reductase family type II enzyme, iron-sulfur subunit. This model represents the iron-sulfur subunit, typically called the beta subunit, of various proteins that also contain a molybdopterin subunit and a heme b subunit. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase and ethylbenzene dehydrogenase. [Energy metabolism, Anaerobic, Energy metabolism, Electron transport] 321 matched cddid_all.tbl CDD TIGR03479 TIGR03479 132519 DMSO_red_II_alp DMSO reductase family type II enzyme, molybdopterin subunit. This model represents the molybdopterin subunit, typically called the alpha subunit, of various proteins that also contain an iron-sulfur subunit and a heme b subunit. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase, ethylbenzene dehydrogenase, and an archaeal respiratory nitrate reductase. This alpha subunit has a twin-arginine translocation (TAT) signal for Sec-independent translocation across the plasma membrane. 912 matched cddid_all.tbl CDD TIGR03480 TIGR03480 274598 HpnN hopanoid biosynthesis associated RND transporter like protein HpnN. The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins appear to be related to the RND family of export proteins, particularly the hydrophobe/amphiphile efflux-3 (HAE3) family represented by TIGR00921. 862 matched cddid_all.tbl CDD TIGR03481 TIGR03481 274599 HpnM "hopanoid biosynthesis associated membrane protein HpnM. The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins are members of the pfam05494 family of putative transporters known as ""toluene tolerance protein Ttg2D"", although it is unlikely that the members included here have anything to do with toluene per-se." 198 matched cddid_all.tbl CDD TIGR03482 TIGR03482 274600 DMSO_red_II_cha DMSO reductase family type II enzyme chaperone. Type II members of the DMSO reductase family are heterotrimeric proteins with bis(molybdopterin guanine dinucleotide)Mo, iron-sulfur, and heme b prosthetic groups bound by the alpha, beta, and gamma subunits respectively. Members of this protein family are not part of the mature protein, although they are the product of a fourth clustered gene. Proteins in this family are interpreted as a chaperone, analogous to NarJ of nitrate reductases. 197 matched cddid_all.tbl CDD TIGR03483 TIGR03483 274601 FtsZ_alphas_C cell division protein FtsZ, alphaProteobacterial C-terminal extension. This model describes a domain found as a C-terminal extension to the cell division protein FtsZ in many but not all members of the alphaProteobacteria. [Cellular processes, Cell division] 121 matched cddid_all.tbl CDD TIGR03485 TIGR03485 132524 cas_csx13_N CRISPR-associated protein Cas8a1/Csx13, MYXAN subtype. Members of this family are found among cas (CRISPR-Associated) genes close to CRISPR repeats in Leptospira interrogans (a spirochete), Myxococcus xanthus (a delta-proteobacterium), and Lyngbya sp. PCC 8106 (a cyanobacterium). It is found with other cas genes in Anabaena variabilis ATCC 29413. In Lyngbya sp., the protein is split into two tandem genes. This model corresponds to the N-terminal region or upstream gene; the C-terminal region is described by TIGR03486. CRISPR/cas systems are associated with prokaryotic acquired resistance to phage and other exogenous DNA. 316 matched cddid_all.tbl CDD TIGR03486 TIGR03486 132525 cas_csx13_C CRISPR-associated protein Cas8a1/Csx13, MYXAN subtype, C-terminal region. Members of this family are found among cas (CRISPR-Associated) genes close to CRISPR repeats in Leptospira interrogans (a spirochete), Myxococcus xanthus (a delta-proteobacterium), and Lyngbya sp. PCC 8106 (a cyanobacterium). It is found with other cas genes in Anabaena variabilis ATCC 29413. In Lyngbya sp., the protein is split into two tandem genes. This model corresponds to the C-terminal region or downstream gene; the N-terminal region is modeled by TIGR03485. CRISPR/cas systems are associated with prokaryotic acquired resistance to phage and other exogenous DNA. 152 matched cddid_all.tbl CDD TIGR03487 TIGR03487 132526 cas_csp2 CRISPR-associated protein Cas8c/Csp2, subtype PGING. Members of this protein family are cas, or CRISPR-associated, proteins. The two sequences in the alignment seed are found within cas gene clusters that are adjacent to CRISPR DNA repeats in two members of the order Bacteroidales, Porphyromonas gingivalis W83 and Bacteroides forsythus ATCC 43037. This cas protein family is unique to the Pging (Porphyromonas gingivalis) subtype. 489 matched cddid_all.tbl CDD TIGR03488 TIGR03488 132527 cas_Cas5p CRISPR-associated protein Cas5, subtype PGING. CC Members of this protein family are cas, or CRISPR-associated, proteins. The two sequences in the alignment seed are found within cas gene clusters that are adjacent to CRISPR DNA repeats in two members of the order Bacteroidales, Porphyromonas gingivalis W83 and Bacteroides forsythus ATCC 43037. This cas protein family is unique to the Pgingi (Porphyromonas gingivalis) subtype, but shows some sequence similarity to genes of the Cas5 type (see TIGR02593). 237 matched cddid_all.tbl CDD TIGR03489 TIGR03489 132528 cas_csp1 CRISPR-associated protein Cas7/Csp1, subtype PGING. Members of this protein family are Csp1, a CRISPR-associated (cas) gene marker for the Pging subtype of CRISPR/cas system, as found in Porphyromonas gingivalis W83 and Bacteroides forsythus ATCC 43037. This protein belongs to the family of DevR (TIGR01875), a regulator of development in Myxococcus xanthus located in a cas gene region. A different branch of the DevR family, Cst2 (TIGR02585), is a marker for the Tneap subtype of CRISPR/cas system. 292 matched cddid_all.tbl CDD TIGR03490 TIGR03490 274602 Mycoplas_LppA mycoides cluster lipoprotein, LppA/P72 family. Members of this protein family occur in Mycoplasma mycoides, Mycoplasma hyopneumoniae, and related Mycoplasmas in small paralogous families that may also include truncated forms and/or pseudogenes. Members are predicted lipoproteins with a conserved signal peptidase II processing and lipid attachment site. Note that the name for certain characterized members, p72, reflects an anomalous apparent molecular weight, given a theoretical MW of about 61 kDa. 541 matched cddid_all.tbl CDD TIGR03491 TIGR03491 274603 TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats. 457 matched cddid_all.tbl CDD TIGR03492 TIGR03492 274604 TIGR03492 conserved hypothetical protein. This protein family is restricted to the Cyanobacteria, in one or two copies, save for instances in the genus Deinococcus. This protein shows some sequence similarity, especially toward the C-terminus, to lipid-A-disaccharide synthase (TIGR00215 or pfam02684). The function is unknown. 396 matched cddid_all.tbl CDD TIGR03493 TIGR03493 274605 cellullose_BcsF celllulose biosynthesis operon protein BcsF/YhjT. Members of this protein family are found invariably together with genes of bacterial cellulose biosynthesis, and are presumed to be involved in the process. Members average about 63 amino acids in length and are not uncharacterized. The gene has been designated both YhjT and BcsF (bacterial cellulose synthesis F). [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 62 matched cddid_all.tbl CDD TIGR03494 TIGR03494 132533 salicyl_syn salicylate synthase. Members of this protein family are salicylate synthases, bifunctional enzymes that make salicylate, in two steps, from chorismate. Members are homologous to anthranilate synthase component I from Trp biosynthesis. Members typically are found in gene regions associated with siderophore or other secondary metabolite biosynthesis. 425 matched cddid_all.tbl CDD TIGR03495 TIGR03495 274606 phage_LysB phage lysis regulatory protein, LysB family. Members of this protein family are phage lysis regulatory protein, including the well-studied protein LysB (lysis protein B) of Enterobacteria phage P2. For members of this family, genes are found in phage or in prophage regions of bacterial genomes, typically near a phage lysozyme or phage holin. 135 matched cddid_all.tbl CDD TIGR03496 TIGR03496 274607 FliI_clade1 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively. [Cellular processes, Chemotaxis and motility] 411 matched cddid_all.tbl CDD TIGR03497 TIGR03497 274608 FliI_clade2 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively. [Cellular processes, Chemotaxis and motility] 413 matched cddid_all.tbl CDD TIGR03498 TIGR03498 163293 FliI_clade3 flagellar protein export ATPase FliI. Members of this protein family are the FliI protein of bacterial flagellum systems. This protein acts to drive protein export for flagellar biosynthesis. The most closely related family is the YscN family of bacterial type III secretion systems. This model represents one (of three) segment of the FliI family tree. These have been modeled separately in order to exclude the type III secretion ATPases more effectively. 418 matched cddid_all.tbl CDD TIGR03499 TIGR03499 274609 FlhF flagellar biosynthetic protein FlhF. [Cellular processes, Chemotaxis and motility] 282 matched cddid_all.tbl CDD TIGR03500 TIGR03500 274610 FliO_TIGR "flagellar biosynthetic protein FliO. This short protein found in flagellar biosynthesis operons contains a highly hydrophobic N-terminal sequence followed generally by two basic amino acids. This region is reminiscent of but distinct from the twin-arginine translocation signal sequence. Some instances of this gene have been names ""FliZ"" but phylogenetic tree building supports a single FliO family." 69 matched cddid_all.tbl CDD TIGR03501 TIGR03501 274611 GlyGly_CTERM GlyGly-CTERM domain. This homology domain, GlyGly-CTERM, shares a species distribution with rhombosortase (TIGR03902), a subfamily of rhomboid-like intramembrane serine proteases. It is probably a recognition sequence for protein sorting and then cleavage by rhombosortase. Shewanella species have the largest number of target proteins per genome, up to thirteen. The domain occurs at the extreme carboxyl-terminus of a diverse set of proteins, most of which are enzymes with conventional signal sequences and with hydrolytic activities: nucleases, proteases, agarases, etc. The agarase AgaA from Vibro sp. strain JT0107 is secreted into the medium, while the same protein heterologously expressed in E. coli is retained in the cell fraction. This suggests cleavage and release in species with this domain. Both this suggestion, and the chemical structure of the domain (motif, hydrophobic predicted transmembrane helix, cluster of basic residues) closely parallels that of the LPXTG/sortase system and the PEP-CTERM/exosortase(EpsH) system. For this reason, the putative processing enzyme is designated rhombosortase. 22 matched cddid_all.tbl CDD TIGR03502 TIGR03502 274612 lipase_Pla1_cef extracellular lipase, Pla-1/cef family. Members of this protein family are bacterial lipoproteins largely from the Gammaproteobacteria. Characterized members are expressed extracellularly and have esterase activity. Members include the lipase Pla-1 from Aeromonas hydrophila (AF092033) and CHO cell elongation factor (cef) from Vibrio hollisae 792 matched cddid_all.tbl CDD TIGR03503 TIGR03503 274613 TIGR03503 TIGR03503 family protein. This set of conserved hypothetical protein has a phylogenetic range that closely matches that of TIGR03501, a putative C-terminal protein targeting signal. 374 matched cddid_all.tbl CDD TIGR03504 TIGR03504 274614 FimV_Cterm FimV C-terminal domain. This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems. 44 matched cddid_all.tbl CDD TIGR03505 TIGR03505 274615 FimV_core FimV N-terminal domain. This region is found at, or about 200 amino acids from, the N-terminus of FimV from Pseudomonas aeruginosa, TspA of Neisseria meningitidis, and related proteins. Disruption of FimV blocks twitching motility from type IV pili; Semmler, et al. suggest a role for this family in peptidoglycan layer remodelling required by type IV fimbrial systems. Most but not all members of this protein family have a C-terminal region recognized by TIGR03504. In between is a highly variable, often repeat-filled region rich in the negatively charged amino acids Asp and Glu. 74 matched cddid_all.tbl CDD TIGR03506 TIGR03506 274616 FlgEFG_subfam flagellar hook-basal body protein. This model encompasses three closely related flagellar proteins usually denoted FlgE, FlgF and FlgG. The names have often been mis-assigned, however. Three equivalog models, TIGR02489, TIGR02490 and TIGR02488, respectively, separate the individual forms into three genome-context consistent groups. The major differences between these genes are architectural, with variable central sections between relatively conserved N- and C-terminal domains. More distantly related are two other flagellar apparatus familis, FlgC (TIGR01395) which consists of little else but the N-and C-terminal domains and FlgK (TIGR02492) with a substantial but different central domain. 231 matched cddid_all.tbl CDD TIGR03507 TIGR03507 274617 decahem_SO1788 decaheme c-type cytochrome, OmcA/MtrC family. The protein SO_1778 (MtrC) of Shewanella oneidensis MR-1, and its paralog SO_1779 (OmcA), with which it intteracts, are large decaheme proteins, about 900 amino acids in length, involved in the use of manganese [Mn(III/IV)] and iron [Fe(III)] as terminal electron acceptors. This model represents these and similar decaheme proteins, found also in Rhodoferax ferrireducens DSM 15236, Aeromonas hydrophila ATCC7966, and a few other bacterial species. [Energy metabolism, Electron transport] 659 matched cddid_all.tbl CDD TIGR03508 TIGR03508 274618 decahem_SO decaheme c-type cytochrome, DmsE family. Members of this family are small, decaheme c-type cytochromes, related DmsE of Shewanella oneidensis MR-1, which has been shown to be part of an anaerobic dimethyl sulfoxide reductase. 258 matched cddid_all.tbl CDD TIGR03509 TIGR03509 274619 OMP_MtrB_PioB decaheme-associated outer membrane protein, MtrB/PioB family. Members of this protein family are integral proteins of the bacterial outer membrane, associated with multiheme c-type cytochromes involved in electron transfer. The MtrB protein of Shewanella oneidensis MR-1 (SO1776) has been shown to form a complex with 1:1:1 stochiometry with the small, periplasmic decaheme cytochrome MtrA and large, surface-exposed decaheme cytochrome MtrC. [Energy metabolism, Electron transport] 649 matched cddid_all.tbl CDD TIGR03510 TIGR03510 274620 XapX XapX domain. This model describes an uncharacterized small, hydrophobic protein of about 50 amino acids, found between the xapB and xapR genes of the E. coli xanthosine utilization system, and homologous regions in other small proteins, such as the N-terminal region of DUF1427 (pfam07235). We name this domain XapX, as it comprises the full length of the protein encoded between the genes for the well-studied XapB and XapR proteins. [Unknown function, General] 49 matched cddid_all.tbl CDD TIGR03511 TIGR03511 274621 GldH_lipo gliding motility-associated lipoprotein GldH. Members of this protein family are predicted lipoproteins, exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). Members include GldH, a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Not all Bacteroidetes with members of this protein family may have gliding motility. [Cellular processes, Chemotaxis and motility] 156 matched cddid_all.tbl CDD TIGR03512 TIGR03512 132551 GldD_lipo gliding motility-associated lipoprotein GldD. Members of this protein family are found a number of Bacteriodetes lineage bacteria, including both species such as Flavobacterium johnsoniae, which possess a poorly understood form of rapid gliding motility, and other species which apparently do not. Mutation of GldD blocks both this motility and chitin utilization in the model species, Flavobacterium johnsoniae. [Cellular processes, Chemotaxis and motility] 186 matched cddid_all.tbl CDD TIGR03513 TIGR03513 274622 GldL_gliding gliding motility-associated protein GldL. This protein family, GldL, is named for the member from Flavobacterium johnsoniae, which is required for a type of rapid gliding motility found in certain members of the Bacteriodetes. However, members are found also in several members of the Bacteriodetes that appear not to be motile [Cellular processes, Chemotaxis and motility] 202 matched cddid_all.tbl CDD TIGR03514 TIGR03514 274623 GldB_lipo gliding motility-associated lipoprotein GldB. 319 matched cddid_all.tbl CDD TIGR03515 TIGR03515 132554 GldC gliding motility-associated protein GldC. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldC is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldC do not abolish the gliding phenotype but do impair it. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility. 108 matched cddid_all.tbl CDD TIGR03516 TIGR03516 132555 ppisom_GldI peptidyl-prolyl isomerase, gliding motility-associated. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldI is a FKBP-type peptidyl-prolyl cis-trans isomerase (pfam00254) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockout of this gene abolishes the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. This family is only found in Bacteroidetes containing the suite of genes proposed to confer the gliding motility phenotype. 177 matched cddid_all.tbl CDD TIGR03517 TIGR03517 274624 GldM_gliding gliding motility-associated protein GldM. This protein family, GldM, is named for the member from Flavobacterium johnsoniae, which is required for a type of rapid gliding motility found in certain members of the Bacteriodetes. However, members are found also in several members of the Bacteriodetes that appear not to be motile. The best conserved region, toward the N-terminus, is centered on a highly hydrobobic probable transmembrane helix. Two paralogs are found in Cytophaga hutchinsonii. 523 matched cddid_all.tbl CDD TIGR03518 TIGR03518 132557 ABC_perm_GldF gliding motility-associated ABC transporter permease protein GldF. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldF is believed to be a ABC transporter permease protein (along with ATP-binding subunit, GldA and a sunstrate-binding subunit, GldG) and is linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldF abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility. 240 matched cddid_all.tbl CDD TIGR03519 TIGR03519 274625 T9SS_PorP_fam type IX secretion system membrane protein, PorP/SprF family. This model describes a protein family unique to, and greatly expanded in, the Bacteriodetes. Species in this lineage include several, such as Cytophaga hutchinsonii and Flavobacterium johnsoniae, that have type IX secretion systems (T9SS) and exhibit a poorly understood rapid gliding phenotype. Several members of this protein family are found in operons with other genes whose loss leads to a loss a this motility. 291 matched cddid_all.tbl CDD TIGR03520 TIGR03520 274626 GldE gliding motility-associated protein GldE. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldC is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. GldE was discovered because of its adjacency to GldD in F. johnsonii. Overexpression of GldE partially supresses the effects of a GldB point mutant suggesting that GldB and GldE interact. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Not all Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility and in fact some do not appear to express the gliding phenotype. 407 matched cddid_all.tbl CDD TIGR03521 TIGR03521 274627 GldG gliding-associated putative ABC transporter substrate-binding component GldG. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldG is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldG abolish the gliding phenotype. GldG, along with GldA and GldF are believed to compose an ABC transporter and are observed as an operon. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility. 552 matched cddid_all.tbl CDD TIGR03522 TIGR03522 132561 GldA_ABC_ATP gliding motility-associated ABC transporter ATP-binding subunit GldA. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldA is an ABC transporter ATP-binding protein (pfam00005) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldA abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility. 301 matched cddid_all.tbl CDD TIGR03523 TIGR03523 274628 GldN gliding motility associated protien GldN. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldN is a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldN abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein also include those which are not believed to express the gliding phenotype, such as Prevotella intermedia and Porphyromonas gingivales. 280 matched cddid_all.tbl CDD TIGR03524 TIGR03524 132563 GldJ gliding motility-associated lipoprotein GldJ. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldJ is a lipoprotein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae. Knockouts of GldJ abolish the gliding phenotype. GldJ is homologous to GldK. There is a GldJ homolog in Cytophaga hutchinsonii and several other species that has a different, shorter architecture and is represented by a separate model. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility. 559 matched cddid_all.tbl CDD TIGR03525 TIGR03525 274629 GldK gliding motility-associated lipoprotein GldK. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldK is a lipoprotein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae. Knockouts of GldK abolish the gliding phenotype. GldK is homologous to GldJ. There is a GldK homolog in Cytophaga hutchinsonii and several other species that has a different, shorter architecture and is represented by a separate model. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility. 450 matched cddid_all.tbl CDD TIGR03526 TIGR03526 132565 selenium_YgeY putative selenium metabolism hydrolase. SelD, selenophosphate synthase, is the selenium donor protein for both selenocysteine and selenouridine biosynthesis systems, but it occurs also in a few prokaryotes that have neither of those pathways. The method of partial phylogenetic profiling, starting from such orphan-selD genomes, identifies this protein as one of those most strongly correlated to SelD occurrence. Its distribution is also well correlated with that of family TIGR03309, a putative accessory protein of labile selenium (non-selenocysteine) enzyme maturation. This family includes the uncharacterized YgeY of Escherichia coli, and belongs to a larger family of metalloenzymes in which some are known peptidases, others enzymes of different types. 395 matched cddid_all.tbl CDD TIGR03527 TIGR03527 274630 selenium_YedF selenium metabolism protein YedF. Members of this protein family are about 200 amino acids in size, and include the uncharacterized YedF protein of Escherichia coli. This family shares an N-terminal domain, modeled by pfam01206, with the sulfurtransferase TusA (also called SirA). The C-terminal domain includes a typical redox-active disulfide motif, CGXC. This protein family found only among those genomes that also carry the selenium donor protein SelD, and its connection to selenium metabolism is indicated by the method of partial phylogenetic profiling vs. SelD. Its gene typically is found next to selD. Members of this family are found even when selenocysteine and selenouridine biosynthesis pathways are, except for SelD, completely absent, as in Enterococcus faecalis. Its role in selenium metabolism is unclear, but may include either detoxification or a role in labile selenoprotein biosynthesis. 194 matched cddid_all.tbl CDD TIGR03528 TIGR03528 274631 2_3_DAP_am_ly diaminopropionate ammonia-lyase. Members of this protein family are the homodimeric, pyridoxal phosphate enzyme diaminopropionate ammonia-lyase, which adds water to remove two amino groups, leaving pyruvate. 396 matched cddid_all.tbl CDD TIGR03529 TIGR03529 274632 GldK_short gliding motility-associated lipoprotein GldK. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldK is a lipoprotein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae. Knockouts of GldK abolish the gliding phenotype. GldK is homologous to GldJ. This model represents a GldK homolog in Cytophaga hutchinsonii and several other species that has a different, shorter architecture than that found in Flavobacterium johnsoniae and related species (represented by (TIGR03525). Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility. 344 matched cddid_all.tbl CDD TIGR03530 TIGR03530 132569 GldJ_short gliding motility-associated lipoprotein GldJ. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldJ is a lipoprotein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae. Knockouts of GldJ abolish the gliding phenotype. GldJ is homologous to GldK. This model represents the GldJ homolog in Cytophaga hutchinsonii and several other species which is of shorter architecture than that found in Flavobacterium johnsoniae and is represented by a separate model (TIGR03524). Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility. 402 matched cddid_all.tbl CDD TIGR03531 TIGR03531 211833 selenium_SpcS O-phosphoseryl-tRNA(Sec) selenium transferase. In the archaea and eukaryotes, the conversion of the mischarged serine to selenocysteine (Sec) on its tRNA is accomplished in two steps. This enzyme, O-phosphoseryl-tRNA(Sec) selenium transferase, acts second, after a phosphophorylation step catalyzed by a homolog of the bacterial SelA protein. [Protein synthesis, tRNA aminoacylation] 444 matched cddid_all.tbl CDD TIGR03532 TIGR03532 132571 DapD_Ac 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase. This enzyme is part of the diaminopimelate pathway of lysine biosynthesis. Alternate name: tetrahydrodipicolinate N-acetyltransferase. Note that IUBMB lists this alternate name as the accepted name. Unfortunately, the related succinyl transferase acting on the same substrate (EC:2.3.1.117, TIGR00695) uses the opposite standard. We have decided to give these two enzymes names which more clearly indicated that they act on the same substrate. 231 matched cddid_all.tbl CDD TIGR03533 TIGR03533 274633 L3_gln_methyl protein-(glutamine-N5) methyltransferase, ribosomal protein L3-specific. Members of this protein family methylate ribosomal protein L3 on a glutamine side chain. This family is related to HemK, a protein-glutamine methyltranferase for peptide chain release factors. [Protein synthesis, Ribosomal proteins: synthesis and modification] 284 matched cddid_all.tbl CDD TIGR03534 TIGR03534 274634 RF_mod_PrmC protein-(glutamine-N5) methyltransferase, release factor-specific. Members of this protein family are HemK (PrmC), a protein once thought to be involved in heme biosynthesis but now recognized to be a protein-glutamine methyltransferase that modifies the peptide chain release factors. All members of the seed alignment are encoded next to the release factor 1 gene (prfA) and confirmed by phylogenetic analysis. SIMBAL analysis (manuscript in prep.) shows the motif [LIV]PRx[DE]TE (in Escherichia coli, IPRPDTE) confers specificity for the release factors rather than for ribosomal protein L3. [Protein fate, Protein modification and repair] 250 matched cddid_all.tbl CDD TIGR03535 TIGR03535 274635 DapD_actino 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase. This enzyme is part of the diaminopimelate pathway of lysine biosynthesis. This model represents a clade of the enzyme specific to Actinobacteria. Alternate name: tetrahydrodipicolinate N-succinyltransferase. 319 matched cddid_all.tbl CDD TIGR03536 TIGR03536 211834 DapD_gpp "2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase. 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase (DapD) is involved in the succinylated branch of the ""lysine biosynthesis via diaminopimelate (DAP)"" pathway (GenProp0125). This model represents a clade of DapD sequences most closely related to the actinobacterial DapD family represented by the TIGR03535 model. All of the genes evaluated for the seed of this model are found in genomes where the downstream desuccinylase is present, but known DapD genes are absent. Additionally, many of the genes identified by this model are found proximal to genes involved in this lysine biosynthesis pathway." 341 matched cddid_all.tbl CDD TIGR03537 TIGR03537 274636 DapC succinyldiaminopimelate transaminase. The four sequences which make up the seed for this model are not closely related, although they are all members of the pfam00155 family of aminotransferases and are more closely related to each other than to anything else. Additionally, all of them are found in the vicinity of genes involved in the biosynthesis of lysine via the diaminopimelate pathway (GenProp0125), although this amount to a separation of 12 genes in the case of Sulfurihydrogenibium azorense Az-Fu1. None of these genomes contain another strong candidate for this role in the pathway. Note: the detailed information included in the EC:2.6.1.17 record includes the assertions that the enzyme uses the pyridoxal pyrophosphate cofactor, which is consistent with the pfam00155 family, and the assertion that the amino group donor is L-glutamate, which is undetermined for the sequences in this clade. 350 matched cddid_all.tbl CDD TIGR03538 TIGR03538 274637 DapC_gpp succinyldiaminopimelate transaminase. This family of succinyldiaminopimelate transaminases (DapC) includes the experimentally characterized enzyme from Bordatella pertussis. The majority of genes in this family are proximal to genes encoding components of the lysine biosynthesis via diaminopimelate pathway (GenProp0125). 393 matched cddid_all.tbl CDD TIGR03539 TIGR03539 132578 DapC_actino succinyldiaminopimelate transaminase. This family of actinobacterial succinyldiaminopimelate transaminase enzymes (DapC) are members of the pfam00155 superfamily. Many of these genes appear adjacent to other genes encoding enzymes of the lysine biosynthesis via diaminopimelate pathway (GenProp0125). 357 matched cddid_all.tbl CDD TIGR03540 TIGR03540 274638 DapC_direct LL-diaminopimelate aminotransferase. This clade of the pfam00155 superfamily of aminotransferases includes several which are adjacent to elements of the lysine biosynthesis via diaminopimelate pathway (GenProp0125). Every member of this clade is from a genome which possesses most of the lysine biosynthesis pathway but lacks any of the known aminotransferases, succinylases, desuccinylases, acetylases or deacetylases typical of the acylated versions of this pathway nor do they have the direct, NADPH-dependent enzyme (ddh). Although there is no experimental characterization of any of the sequences in this clade, a direct pathway is known in plants and Chlamydia and the clade containing the Chlamydia gene is a neighboring one in the same pfam00155 superfamily so it seems quite reasonable that these enzymes catalyze the same transformation. 383 matched cddid_all.tbl CDD TIGR03541 TIGR03541 132580 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene. 232 matched cddid_all.tbl CDD TIGR03542 TIGR03542 163316 DAPAT_plant LL-diaminopimelate aminotransferase. This clade of the pfam00155 superfamily of aminotransferases includes several which are adjacent to elements of the lysine biosynthesis via diaminopimelate pathway (GenProp0125). This clade includes characterized species in plants and Chlamydia. Every member of this clade is from a genome which possesses most of the lysine biosynthesis pathway but lacks any of the known succinylases, desuccinylases, acetylases or deacetylases typical of the acylated versions of this pathway nor do they have the direct, NADPH-dependent enzyme (ddh). 402 matched cddid_all.tbl CDD TIGR03543 TIGR03543 188337 divI1A_rptt_fam DivIVA domain repeat protein. Members of this protein family contain two full and two partial repeats of a domain found at the N-terminus of Bacillus subtilis cell-division initiation protein DivIVA. The portion repeated four times in these proteins includes the motif GYxxxxVD. 178 matched cddid_all.tbl CDD TIGR03544 TIGR03544 274639 DivI1A_domain DivIVA domain. This model describes a domain found in Bacillus subtilis cell division initiation protein DivIVA, and homologs, toward the N-terminus. It is also found as a repeated domain in certain other proteins, including family TIGR03543. 34 matched cddid_all.tbl CDD TIGR03545 TIGR03545 274640 TIGR03545 TIGR03545 family protein. This model represents a relatively rare but broadly distributed uncharacterized protein family, distributed in 1-2 percent of bacterial genomes, all of which have outer membranes. In many of these genomes, it is part of a two-gene pair. 555 matched cddid_all.tbl CDD TIGR03546 TIGR03546 200289 TIGR03546 TIGR03546 family protein. Members of this family are uncharacterized proteins, usually encoded by a gene adjacent to a member of family TIGR03545, which is also uncharacterized. 154 matched cddid_all.tbl CDD TIGR03547 TIGR03547 274641 muta_rot_YjhT mutatrotase, YjhT family. Members of this protein family contain multiple copies of the beta-propeller-forming Kelch repeat. All are full-length homologs to YjhT of Escherichia coli, which has been identified as a mutarotase for sialic acid. This protein improves bacterial ability to obtain host sialic acid, and thus serves as a virulence factor. Some bacteria carry what appears to be a cyclically permuted homolog of this protein. 346 matched cddid_all.tbl CDD TIGR03548 TIGR03548 274642 mutarot_permut cyclically-permuted mutarotase family protein. Members of this protein family show essentially full-length homology, cyclically permuted, to YjhT from Escherichia coli. YjhT was shown to act as a mutarotase for sialic acid, and by this ability to be able to act as a virulence factor. Members of the YjhT family (TIGR03547) and this cyclically-permuted family have multiple repeats of the beta-propeller-forming Kelch repeat. 331 matched cddid_all.tbl CDD TIGR03549 TIGR03549 132588 TIGR03549 YcaO domain protein. This family consists of remarkably well-conserved proteins from gamma and beta Proteobacteria, heavily skewed towards organisms of marine environments. Its gene neighborhood is not conserved. This family has an OsmC-like N-terminal domain. It shares a YcaO domain, frequently associated with ATP-dependent cyclodehydration for peptide modification. The function is unknown. Fifteen of the first sixteen members of this family are from selenouridine-positive genomes, but this correlation may not be meaningful. 718 matched cddid_all.tbl CDD TIGR03550 TIGR03550 132589 F420_cofG 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofG subunit. This model represents either a subunit or a domain, depending on whether or not the genes are fused, of a bifunctional protein that completes the synthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin, or FO. FO is the chromophore of coenzyme F(420), involved in methanogenesis in methanogenic archaea but found in certain other lineages as well. The chromophore also occurs as a cofactor in DNA photolyases in Cyanobacteria. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 322 matched cddid_all.tbl CDD TIGR03551 TIGR03551 132590 F420_cofH 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, CofH subunit. This enzyme, together with CofG, complete the biosynthesis of 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase, the chromophore of coenzyme F420. The chromophore is also used in cyanobacteria DNA photolyases. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 343 matched cddid_all.tbl CDD TIGR03552 TIGR03552 274643 F420_cofC 2-phospho-L-lactate guanylyltransferase. Members of this protein family are the CofC enzyme of coenzyme F420 biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 195 matched cddid_all.tbl CDD TIGR03553 TIGR03553 132592 F420_FbiB_CTERM F420 biosynthesis protein FbiB, C-terminal domain. Coenzyme F420 differs between the Archaea and the Actinobacteria, where the numbers of glutamate residues attached are 2 (Archaea) or 5-6 (Mycobacterium). The enzyme in the Archaea is homologous to the N-terminal domain of FbiB from Mycobacterium bovis, and is responsible for glutamate ligation. Therefore it seems likely that the C-terminal domain of FbiB modeled here, is involved in additional glutamate ligation. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 194 matched cddid_all.tbl CDD TIGR03554 TIGR03554 213827 F420_G6P_DH glucose-6-phosphate dehydrogenase (coenzyme-F420). This family consists of the F420-dependent glucose-6-phosphate dehydrogenase of Mycobacterium and Nocardia. It shows homology to several other F420-dependent enzymes rather than to the NAD or NADP-dependent glucose-6-phosphate dehydrogenases. [Energy metabolism, Pentose phosphate pathway] 331 matched cddid_all.tbl CDD TIGR03555 TIGR03555 132594 F420_mer 5,10-methylenetetrahydromethanopterin reductase. Members of this protein family are 5,10-methylenetetrahydromethanopterin reductase, an F420-dependent enzyme of methanogenesis. It is restricted to the Archaea. [Energy metabolism, Methanogenesis] 325 matched cddid_all.tbl CDD TIGR03556 TIGR03556 274644 photolyase_8HDF deoxyribodipyrimidine photo-lyase, 8-HDF type. This model describes a narrow clade of cyanobacterial deoxyribodipyrimidine photo-lyase. This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA photolyase and FO in most literature on coenzyme F420. [DNA metabolism, DNA replication, recombination, and repair] 471 matched cddid_all.tbl CDD TIGR03557 TIGR03557 274645 F420_G6P_family F420-dependent oxidoreductase, G6PDH family. Members of this protein family include F420-dependent glucose-6-phosphate dehydrogenases (TIGR03554) and related proteins. All members of this family come from species that synthesize coenzyme F420, with the exception of those that belong to TIGR03885, a clade within this family in which cofactor binding may instead be directed to FMN. [Unknown function, Enzymes of unknown specificity] 316 matched cddid_all.tbl CDD TIGR03558 TIGR03558 274646 oxido_grp_1 luciferase family oxidoreductase, group 1. The Pfam domain family pfam00296 is named for luciferase-like monooxygenases, but the family also contains several coenzyme F420-dependent enzymes. This protein family represents a well-resolved clade within family pfam00296 and shows no restriction to coenzyme F420-positive species, unlike some other clades within pfam00296. [Unknown function, Enzymes of unknown specificity] 323 matched cddid_all.tbl CDD TIGR03559 TIGR03559 274647 F420_Rv3520c probable F420-dependent oxidoreductase, Rv3520c family. Members of this protein family are predicted to be oxidoreductases dependent on coenzyme F420. The family includes a single member in Mycobacterium tuberculosis (Rv3520c/MT3621) but four in Mycobacterium smegmatis. Prediction that this family is F420-dependent is based primarily on Partial Phylogenetic Profiling vs. F420 biosynthesis. [Unknown function, Enzymes of unknown specificity] 325 matched cddid_all.tbl CDD TIGR03560 TIGR03560 274648 F420_Rv1855c probable F420-dependent oxidoreductase, Rv1855c family. Coenzyme F420 has a limited phylogenetic distribution, including methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea 34H, Rhodopseudomonas palustris HaA2, and others. Partial phylogenetic profiling identifies protein subfamilies, within the larger family called luciferase-like monooxygenanases (pfam00296), that appear only in F420-positive genomes and are likely to be F420-dependent. This model describes one such subfamily, exemplified by Rv1855c from Mycobacterium tuberculosis. [Unknown function, Enzymes of unknown specificity] 227 matched cddid_all.tbl CDD TIGR03561 TIGR03561 274649 organ_hyd_perox peroxiredoxin, Ohr subfamily. pfam02566, OsmC-like protein, contains several deeply split clades of homologous proteins. The clade modeled here includes the protein Ohr, or organic hydroperoxide resistance protein. [Cellular processes, Detoxification] 134 matched cddid_all.tbl CDD TIGR03562 TIGR03562 274650 osmo_induc_OsmC peroxiredoxin, OsmC subfamily. pfam02566, OsmC-like protein, contains several deeply split clades of homologous proteins. The clade modeled here includes the protein OsmC, or osmotically induced protein C. The member from Thermus thermophilus was shown to have hydroperoxide peroxidase activity. In many species, this protein is induced by stress and helps resist oxidative stress. [Cellular processes, Detoxification] 135 matched cddid_all.tbl CDD TIGR03563 TIGR03563 132602 perox_SACOL1771 peroxiredoxin, SACOL1771 subfamily. This protein family belongs to the OsmC/Ohr family (pfam02566, OsmC-like protein) of peroxiredoxins. 138 matched cddid_all.tbl CDD TIGR03564 TIGR03564 274651 F420_MSMEG_4879 F420-dependent oxidoreductase, MSMEG_4879 family. Coenzyme F420 is produced by methanogenic archaea, a number of the Actinomycetes (including Mycobacterium tuberculosis), and rare members of other lineages. The resulting information-rich phylogenetic profile identifies candidate F420-dependent oxidoreductases within the family of luciferase-like enzymes (pfam00296), where the species range for the subfamily encompasses many F420-positive genomes without straying beyond. This family is uncharacterized, and named for member MSMEG_4879 from Mycobacterium smegmatis. [Unknown function, Enzymes of unknown specificity] 265 matched cddid_all.tbl CDD TIGR03565 TIGR03565 274652 alk_sulf_monoox alkanesulfonate monooxygenase, FMNH(2)-dependent. Members of this protein family are monooxygenases that catalyze desulfonation of aliphatic sulfonates such as methane sulfonate. This enzyme uses reduced FMN, although various others members of the same luciferase-like monooxygenase family (pfam00296) are F420-dependent enzymes. [Central intermediary metabolism, Sulfur metabolism] 346 matched cddid_all.tbl CDD TIGR03566 TIGR03566 211840 FMN_reduc_MsuE FMN reductase, MsuE subfamily. Members of this protein family use NAD(P)H to reduce FMN and regenerate FMNH2. Members include the NADH-dependent enzyme MsuE from Pseudomonas aeruginosa, which serves as a partner to an FMNH2-dependent alkanesulfonate monooxygenase. The NADP-dependent enzyme from E. coli is outside the scope of this model. 174 matched cddid_all.tbl CDD TIGR03567 TIGR03567 274653 FMN_reduc_SsuE FMN reductase, SsuE family. Members of this protein family use NAD(P)H to reduce FMN and regenerate FMNH2. Members include the homodimeric, NAD(P)H-dependent enzyme SsuE from Escherichia coli, which serves as a partner to an FMNH2-dependent alkanesulfonate monooxygenase. It is induced by sulfate starvation. The NADH-dependent enzyme MsuE from Pseudomonas aeruginosa is outside the scope of this model (see model TIGR03566). [Central intermediary metabolism, Sulfur metabolism] 171 matched cddid_all.tbl CDD TIGR03568 TIGR03568 274654 NeuC_NnaA UDP-N-acetyl-D-glucosamine 2-epimerase, UDP-hydrolysing. This family of enzymes catalyzes the combined epimerization and UDP-hydrolysis of UDP-N-acetylglucosamine to N-acetylmannosamine. This is in contrast to the related enzyme WecB (TIGR00236) which retains the UDP moiety. NeuC acts in concert with NeuA and NeuB to synthesize CMP-N5-acetyl-neuraminate. 364 matched cddid_all.tbl CDD TIGR03569 TIGR03569 274655 NeuB_NnaB N-acetylneuraminate synthase. This family is a subset of the pfam03102 and is believed to include only authentic NeuB N-acetylneuraminate (sialic acid) synthase enzymes. The majority of the genes identified by this model are observed adjacent to both the NeuA and NeuC genes which together effect the biosynthesis of CMP-N-acetylneuraminate from UDP-N-acetylglucosamine. 329 matched cddid_all.tbl CDD TIGR03570 TIGR03570 274656 NeuD_NnaD sugar O-acyltransferase, sialic acid O-acetyltransferase NeuD family. This family of proteins includes the characterized NeuD sialic acid O-acetyltransferase enzymes from E. coli and Streptococcus agalactiae (group B strep). These two are quite closely related to one another, so extension of this annotation to other members of the family in unsupported without additional independent evidence. The neuD gene is often observed in close proximity to the neuABC genes for the biosynthesis of CMP-N-acetylneuraminic acid (CMP-sialic acid), and NeuD sequences from these organisms were used to construct the seed for this model. Nevertheless, there are numerous instances of sequences identified by this model which are observed in a different genomic context (although almost universally in exopolysaccharide biosynthesis-related loci), as well as in genomes for which the biosynthesis of sialic acid (SA) is undemonstrated. Even in the cases where the association with SA biosynthesis is strong, it is unclear in the literature whether the biological substrate is SA iteself, CMP-SA, or a polymer containing SA. Similarly, it is unclear to what extent the enzyme has a preference for acetylation at the 7, 8 or 9 positions. In the absence of evidence of association with SA, members of this family may be involved with the acetylation of differring sugar substrates, or possibly the delivery of alternative acyl groups. The closest related sequences to this family (and those used to root the phylogenetic tree constructed to create this model) are believed to be succinyltransferases involved in lysine biosynthesis. These proteins contain repeats of the bacterial transferase hexapeptide (pfam00132), although often these do not register above the trusted cutoff. 201 matched cddid_all.tbl CDD TIGR03571 TIGR03571 274657 lucif_BA3436 luciferase-type oxidoreductase, BA3436 family. This family is a distinct subgroup among members of the luciferase monooxygenase domain family. The larger family contains both FMN-binding enzymes (luciferase, alkane monooxygenase) and F420-binding enzymes (methylenetetrahydromethanopterin reductase, secondary alcohol dehydrogenase, glucose-6-phosphate dehydrogenase). Although some members of the domain family bind coenzyme F420 rather than FMN, members of this family are from species that lack the genes for F420 biosynthesis. A crystal structure, but not function, is known (but unpublished) for the member from Bacillus cereus, PDB|2B81. [Unknown function, Enzymes of unknown specificity] 298 matched cddid_all.tbl CDD TIGR03572 TIGR03572 132611 WbuZ glycosyl amidation-associated protein WbuZ. This clade of sequences is highly similar to the HisF protein, but generally represents the second HisF homolog in the genome where the other is an authentic HisF observed in the context of a complete histidine biosynthesis operon. The similarity between these WbuZ sequences and true HisFs is such that often the closest match by BLAST of a WbuZ is a HisF. Only by making a multiple sequence alignment is the homology relationship among the WbuZ sequences made apparent. WbuZ genes are invariably observed in the presence of a homolog of the HisH protein (designated WbuY) and a proposed N-acetyl sugar amidotransferase designated in WbuX in E. coli, IfnA in P. aeriginosa and PseA in C. jejuni. Similarly, this trio of genes is invariably found in the context of saccharide biosynthesis loci. It has been shown that the WbuYZ homologs are not essential components of the activity expressed by WbuX, leading to the proposal that these to proteins provide ammonium ions to the amidotransferase when these are in low concentration. WbuY (like HisH) is proposed to act as a glutaminase to release ammonium. In histidine biosynthesis this is also dispensible in the presence of exogenous ammonium ion. HisH and HisF form a complex such that the ammonium ion is passed directly to HisF where it is used in an amidation reaction causing a subsequent cleavage and cyclization. In the case of WbuYZ, the ammonium ion would be passed from WbuY to WbuZ. WbuZ, being non-essential and so similar to HisF that a sugar substrate is unlikely, would function instead as a amoonium channel to the WbuX protein which does the enzymatic work. 232 matched cddid_all.tbl CDD TIGR03573 TIGR03573 274658 WbuX N-acetyl sugar amidotransferase. This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an invariable contextual association with homologs of the HisH and HisF proteins known as WbuY and WbuZ, respectively. These two proteins are believed to supply the enzyme with ammonium by hydrolysis of glutamine and delivery through an ammonium conduit. 343 matched cddid_all.tbl CDD TIGR03574 TIGR03574 132613 selen_PSTK L-seryl-tRNA(Sec) kinase, archaeal. Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents archaeal proteins with this activity. [Protein synthesis, tRNA aminoacylation] 249 matched cddid_all.tbl CDD TIGR03575 TIGR03575 188340 selen_PSTK_euk L-seryl-tRNA(Sec) kinase, eukaryotic. Members of this protein are L-seryl-tRNA(Sec) kinase. This enzyme is part of a two-step pathway in Eukaryota and Archaea for performing selenocysteine biosynthesis by changing serine misacylated on selenocysteine-tRNA to selenocysteine. This enzyme performs the first step, phosphorylation of the OH group of the serine side chain. This family represents eukaryotic proteins with this activity. 340 matched cddid_all.tbl CDD TIGR03576 TIGR03576 213830 pyridox_MJ0158 pyridoxal phosphate enzyme, MJ0158 family. Members of this archaeal protein family are pyridoxal phosphate enzymes of unknown function. Sequence similarity to SelA, a bacterial enzyme of selenocysteine biosynthesis, has led to some members being misannotated as functionally equivalent, but selenocysteine is made on tRNA in Archaea by a two-step process that does not involve a SelA homolog. [Unknown function, Enzymes of unknown specificity] 346 matched cddid_all.tbl CDD TIGR03577 TIGR03577 132616 EF_0830 conserved hypothetical protein EF_0830/AHA_3911. Members of this family of small (about 120 amino acid), relatively rare proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. The function is unknown. [Hypothetical proteins, Conserved] 115 matched cddid_all.tbl CDD TIGR03578 TIGR03578 213831 EF_0831 conserved hypothetical protein EF_0831/AHA_3912. Members of this family of small (about 100 amino acid), relatively rare proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. The function is unknown. [Hypothetical proteins, Conserved] 96 matched cddid_all.tbl CDD TIGR03579 TIGR03579 132618 EF_0833 conserved hypothetical protein EF_0833/AHA_3914. Members of this family of relatively rare proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. The function is unknown. 209 matched cddid_all.tbl CDD TIGR03580 TIGR03580 274659 EF_0832 conserved hypothetical protein EF_0832/AHA_3913. Members of this family of relatively rare proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. The function is unknown. [Unknown function, General] 246 matched cddid_all.tbl CDD TIGR03581 TIGR03581 188342 EF_0839 conserved hypothetical protein EF_0839/AHA_3917. Members of this family of relatively uncommon proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. The function is unknown. [Hypothetical proteins, Conserved] 227 matched cddid_all.tbl CDD TIGR03582 TIGR03582 132621 EF_0829 PRD domain protein EF_0829/AHA_3910. Members of this family of relatively uncommon proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. This protein contains a PRD domain (see pfam00874). The function is unknown. [Unknown function, General] 107 matched cddid_all.tbl CDD TIGR03583 TIGR03583 132622 EF_0837 probable amidohydrolase EF_0837/AHA_3915. Members of this family of relatively uncommon proteins are found in both Gram-positive (e.g. Enterococcus faecalis) and Gram-negative (e.g. Aeromonas hydrophila) bacteria, as part of a cluster of conserved proteins. These proteins resemble aminohydrolases (see pfam01979), including dihydroorotases. The function is unknown. [Hypothetical proteins, Conserved] 365 matched cddid_all.tbl CDD TIGR03584 TIGR03584 274660 PseF pseudaminic acid cytidylyltransferase. The sequences in this family include the pfam02348 (cytidyltransferase) domain and are homologous to the NeuA protein responsible for the transfer of CMP to neuraminic acid. According to, this gene is responsible for the transfer of CMP to the structurally related sugar, pseudaminic acid which is observed as a component of sugar modifications of flagellin in Campylobacter species. This gene is commonly observed in apparent operons with other genes responsible for the biosynthesis of pseudaminic acid and as a component of flagellar and exopolysaccharide biosynthesis loci. 222 matched cddid_all.tbl CDD TIGR03585 TIGR03585 274661 PseH UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine N-acetyltransferase. Sequences in this family are members of the pfam00583 (GNAT) superfamily of acetyltransferases and are proposed to perform a N-acetylation step in the process of pseudaminic acid biosynthesis in Campylobacter species. This gene is commonly observed in apparent operons with other genes responsible for the biosynthesis of pseudaminic acid and as a component of flagellar and exopolysaccharide biosynthesis loci. Significantly, many genomes containing other components of this pathway lack this gene, indicating that some other N-acetyl transferases may be incolved and/or the step is optional, resulting in a non-acetylated pseudaminic acid variant sugar. 152 matched cddid_all.tbl CDD TIGR03586 TIGR03586 163337 PseI pseudaminic acid synthase. Members of this family are included within the larger pfam03102 (NeuB) family. NeuB itself (TIGR03569) is involved in the biosynthesis of neuraminic acid by the condensation of phosphoenolpyruvate (PEP) with N-Acetyl-D-Mannosamine. In an analagous reaction, this enzyme, PseI, condenses PEP with 6-deoxy-beta-L-AltNAc4NAc to generate pseudaminic acid. 327 matched cddid_all.tbl CDD TIGR03587 TIGR03587 132626 Pse_Me-ase pseudaminic acid biosynthesis-associated methylase. Members of this small clade are methyltransferases of the pfam08241 family and are observed within operons for the biosynthesis of pseudaminic acid, a component of exopolysaccharide and flagellin glycosyl modifications. Notable among these genomes is Pseudomonas fluorescens PfO-1. Possibly one of the two hydroxyl groups of pseudaminic acid, at positions 4 and 8 is converted to a methoxy group by this enzyme 204 matched cddid_all.tbl CDD TIGR03588 TIGR03588 274662 PseC UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine transaminase. This family of enzymes are aminotransferases of the pfam01041 family involved in the biosynthesis of pseudaminic acid. They convert UDP-4-keto-6-deoxy-N-acetylglucosamine into UDP-4-amino-4,6-dideoxy-N-acetylgalactose. Pseudaminic acid has a role in surface polysaccharide in Pseudomonas as well as in the modification of flagellin in Campylobacter and Helicobacter species. 380 matched cddid_all.tbl CDD TIGR03589 TIGR03589 132628 PseB UDP-N-acetylglucosamine 4,6-dehydratase (inverting). This enzyme catalyzes the first step in the biosynthesis of pseudaminic acid, the conversion of UDP-N-acetylglucosamine to UDP-4-keto-6-deoxy-N-acetylglucosamine. These sequences are members of the broader pfam01073 (3-beta hydroxysteroid dehydrogenase/isomerase family) family. 324 matched cddid_all.tbl CDD TIGR03590 TIGR03590 274663 PseG UDP-2,4-diacetamido-2,4,6-trideoxy-beta-L-altropyranose hydrolase. This protein is found in association with enzymes involved in the biosynthesis of pseudaminic acid, a component of polysaccharide in certain Pseudomonas strains as well as a modification of flagellin in Campylobacter and Hellicobacter. The role of this protein is unclear, although it may participate in N-acetylation in conjunction with, or in the absence of PseH (TIGR03585) as it often scores above the trusted cutoff to pfam00583 representing a family of acetyltransferases. 279 matched cddid_all.tbl CDD TIGR03591 TIGR03591 274664 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family). [Transcription, Degradation of RNA] 688 matched cddid_all.tbl CDD TIGR03592 TIGR03592 274665 yidC_oxa1_cterm membrane protein insertase, YidC/Oxa1 family, C-terminal domain. This model describes full-length from some species, and the C-terminal region only from other species, of the YidC/Oxa1 family of proteins. This domain appears to be univeral among bacteria (although absent from Archaea). The well-characterized YidC protein from Escherichia coli and its close homologs contain a large N-terminal periplasmic domain in addition to the region modeled here. [Protein fate, Protein and peptide secretion and trafficking] 179 matched cddid_all.tbl CDD TIGR03593 TIGR03593 274666 yidC_nterm membrane protein insertase, YidC/Oxa1 family, N-terminal domain. Essentially all bacteria have a member of the YidC family, whose C-terminal domain is modeled by TIGR03592. The two copies are found in endospore-forming bacteria such as Bacillus subtilis appear redundant during vegetative growth, although the member designated spoIIIJ (stage III sporulation protein J) has a distinct role in spore formation. YidC, its mitochondrial homolog Oxa1, and its chloroplast homolog direct insertion into the bacterial/organellar inner (or only) membrane. This model describes an N-terminal sequence region, including a large periplasmic domain lacking in YidC members from Gram-positive species. The multifunctional YidC protein acts both with and independently of the Sec system. [Protein fate, Protein and peptide secretion and trafficking] 366 matched cddid_all.tbl CDD TIGR03594 TIGR03594 274667 GTPase_EngA ribosome-associated GTPase EngA. EngA (YfgK, Der) is a ribosome-associated essential GTPase with a duplication of its GTP-binding domain. It is broadly to universally distributed among bacteria. It appears to function in ribosome biogenesis or stability. [Protein synthesis, Other] 428 matched cddid_all.tbl CDD TIGR03595 TIGR03595 274668 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence. 69 matched cddid_all.tbl CDD TIGR03596 TIGR03596 274669 GTPase_YlqF ribosome biogenesis GTP-binding protein YlqF. Members of this protein family are GTP-binding proteins involved in ribosome biogenesis, including the essential YlqF protein of Bacillus subtilis, which is an essential protein. They are related to Era, EngA, and other GTPases of ribosome biogenesis, but are circularly permuted. This family is not universal, and is not present in Escherichia coli, and so is not as well studied as some other GTPases. This model is built for bacterial members. [Protein synthesis, Other] 276 matched cddid_all.tbl CDD TIGR03597 TIGR03597 213834 GTPase_YqeH ribosome biogenesis GTPase YqeH. This family describes YqeH, a member of a larger family of GTPases involved in ribosome biogenesis. Like YqlF, it shows a cyclical permutation relative to GTPases EngA (in which the GTPase domain is duplicated), Era, and others. Members of this protein family are found in a relatively small number of bacterial species, including Bacillus subtilis but not Escherichia coli. [Protein synthesis, Other] 360 matched cddid_all.tbl CDD TIGR03598 TIGR03598 274670 GTPase_YsxC ribosome biogenesis GTP-binding protein YsxC/EngB. Members of this protein family are a GTPase associated with ribosome biogenesis, typified by YsxC from Bacillus subutilis. The family is widely but not universally distributed among bacteria. Members commonly are called EngB based on homology to EngA, one of several other GTPases of ribosome biogenesis. Cutoffs as set find essentially all bacterial members, but also identify large numbers of eukaryotic (probably organellar) sequences. This protein is found in about 80 percent of bacterial genomes. [Protein synthesis, Other] 179 matched cddid_all.tbl CDD TIGR03599 TIGR03599 274671 YloV DAK2 domain fusion protein YloV. This model describes a protein family that contains an N-terminal DAK2 domain (pfam02734), so named because of similarity to the dihydroxyacetone kinase family family. The GTP-binding protein CgtA (a member of the obg family) is a bacterial GTPase associated with ribosome biogenesis, and it has a characteristic extension (TIGR03595) in certain lineages. This protein family described here was found, by the method of partial phylognetic profiling, to have a phylogenetic distribution strongly correlated to that of TIGR03595. This correlation implies some form of functional coupling. 530 matched cddid_all.tbl CDD TIGR03600 TIGR03600 274672 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model. [Mobile and extrachromosomal element functions, Prophage functions] 420 matched cddid_all.tbl CDD TIGR03601 TIGR03601 274673 B_an_ocin bacteriocin, heterocycloanthracin/sonorensin family. Numerous bacteria encode systems for producing bacteriocins by extensive modification of ribosomally produced precursors. Members of the TOMM class (thiazole/oxazole-modified microcins) are recognizable by association with cyclodehydratase (and often dehydrogenase) maturation proteins. This family consists of a special subclass, the heterocycloanthracin family, that share a homologous leader peptide region and then a repeat region with Cys as every third residue. In Bacillus anthracis and Bacillus cereus, the RiPP (ribosomally translated and post-translationally modified natural product) precursor is encoded far from its maturase genes, and every strain has the system. In other species (e.g. B. licheniformis, B. sorenensis), precursor and maturase genes are close together. Sonorensin, from B. sonorensis MT93, was shown to have broad spectrum antimicrobial activity, affecting Gram-positive and Gram-negative bacteria. [Cellular processes, Toxin production and resistance] 88 matched cddid_all.tbl CDD TIGR03602 TIGR03602 132641 streptolysinS bacteriocin protoxin, streptolysin S family. Members of this family are bacteriocin precursors. These small, ribosomally produced polypeptide precursors are extensively processed post-translationally. This family belongs to a class of heterocycle-containing bacteriocins, including streptolysin S from Streptococcus pyogenes, and related bacteriocins from Streptococcus iniae and Clostridium botulinum. Streptolysin S is hemolytic. Bacteriocin genes in general are small and highly diverse, with odd sequence composition, and are easily missed by many gene-finding programs. [Cellular processes, Toxin production and resistance] 56 matched cddid_all.tbl CDD TIGR03603 TIGR03603 200298 cyclo_dehy_ocin thiazole/oxazole-forming peptide maturase, SagC family component. Members of this protein family include enzymes related to SagC, a protein involved in thiazole/oxazole cyclodehydration modifications during biosynthesis of streptolysin S in Streptococcus pyogenes from the protoxin polypeptide (product of the sagA gene). Recent evidence suggests that the YcaO/SagD-like component, not this component, performs an ATP-dependent cyclodehydration. This protein family serves as a marker for widely distributed prokaryotic systems for making a general class of heterocycle-containing bacteriocins. Note that this model does not find all possible examples of bacteriocin biosynthesis cyclodehydratases, an in particular misses the E. coli plasmid protein McbB of microcin B17 biosynthesis. [Cellular processes, Pathogenesis] 319 matched cddid_all.tbl CDD TIGR03604 TIGR03604 274674 TOMM_cyclo_SagD thiazole/oxazole-forming peptide maturase, SagD family component. Members of this protein family include enzymes related to SagD, previously referred to as a scaffold or docking protein involved in the biosynthesis of streptolysin S in Streptococcus pyogenes from the protoxin polypeptide (product of the sagA gene). Newer evidence describes an enzymatic activity, an ATP-dependent cyclodehydration reaction, previously ascribed to the SagC component. This protein family serves as a marker for widely distributed prokaryotic systems for making a general class of heterocycle-containing bacteriocins. 377 matched cddid_all.tbl CDD TIGR03605 TIGR03605 188352 antibiot_sagB "SagB-type dehydrogenase domain. SagB of Sterptococcus pyogenes participates in the maturation of streptolysin S from a ribosomally produced precursor polypeptide. Chemically similar systems operate on highly diverse sets of bacteriocin precursors in numerous other bacteria. This model describes a domain within SgaB and homologous regions from other proteins, many of which appear to be involved in biosynthesis of secondary metabolites. While some substrates may be intermediates in non-ribosomal peptide syntheses, others are involved in heterocycle-containing bacteriocin biosynthesis, and can be found near SgaC-like (see TIGR03603, cyclodehydratase) and SgaD-like (see TIGR03604, ""docking"") proteins. Members of this domain family are heterogeneous in length, as many have a partial second copy of the domain represented here. The incomplete second domain scores below the cutoffs to this model in most cases." 173 matched cddid_all.tbl CDD TIGR03606 TIGR03606 274675 non_repeat_PQQ dehydrogenase, PQQ-dependent, s-GDH family. PQQ, or pyrroloquinoline-quinone, serves as a cofactor for a number of sugar and alcohol dehydrogenases in a limited number of bacterial species. Most characterized PQQ-dependent enzymes have multiple repeats of a sequence region described by pfam01011 (PQQ enzyme repeat), but this protein family in unusual in lacking that repeat. Below the noise cutoff are related proteins mostly from species that lack PQQ biosynthesis. 454 matched cddid_all.tbl CDD TIGR03607 TIGR03607 274676 TIGR03607 patatin-related protein. This bacterial protein family contains an N-terminal patatin domain, where patatins are plant storage proteins capable of phospholipase activity (see pfam01734). Regions of strong sequence conservation are separated by regions of significant sequence and length variability. Members of the family are distributed sporadically among bacteria. The function is unknown. [Unknown function, General] 738 matched cddid_all.tbl CDD TIGR03608 TIGR03608 188353 L_ocin_972_ABC putative bacteriocin export ABC transporter, lactococcin 972 group. A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins. [Cellular processes, Toxin production and resistance, Transport and binding proteins, Unknown substrate] 206 matched cddid_all.tbl CDD TIGR03609 TIGR03609 132648 S_layer_CsaB polysaccharide pyruvyl transferase CsaB. The CsaB protein (cell surface anchoring B) of Bacillus anthracis adds a pyruvoyl group to peptidoglycan-associated polysaccharide. This addition is required for proteins with an S-layer homology domain (pfam00395) to bind. Within the larger group of proteins described by pfam04230, this model represents a distinct clade that nearly exactly follows the phylogenetic distribution of the S-layer homology domain (pfam00395). [Cell envelope, Surface structures, Protein fate, Protein and peptide secretion and trafficking] 298 matched cddid_all.tbl CDD TIGR03610 TIGR03610 274677 RutC pyrimidine utilization protein C. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the endoribonuclease L-PSP family defined by pfam01042. 127 matched cddid_all.tbl CDD TIGR03611 TIGR03611 211851 RutD pyrimidine utilization protein D. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the hydrolase, alpha/beta fold family defined by pfam00067. 248 matched cddid_all.tbl CDD TIGR03612 TIGR03612 163355 RutA pyrimidine utilization protein A. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the luciferase family defined by pfam00296 and is likely a FMN-dependent monoxygenase. [Unknown function, Enzymes of unknown specificity] 355 matched cddid_all.tbl CDD TIGR03613 TIGR03613 274678 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region). 202 matched cddid_all.tbl CDD TIGR03614 TIGR03614 163356 RutB pyrimidine utilization protein B. 226 matched cddid_all.tbl CDD TIGR03615 TIGR03615 132654 RutF pyrimidine utilization flavin reductase protein F. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the flavin reductase family defined by pfam01613. Presumably, this protein recycles the flavin of the RutA luciferase-like oxidoreductase. 156 matched cddid_all.tbl CDD TIGR03616 TIGR03616 132655 RutG pyrimidine utilization transport protein G. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the uracil-xanthine permease family defined by TIGR00801. As well as the The Nucleobase:Cation Symporter-2 (NCS2) Family (TC 2.A.40). 429 matched cddid_all.tbl CDD TIGR03617 TIGR03617 132656 F420_MSMEG_2256 probable F420-dependent oxidoreductase, MSMEG_2256 family. Coenzyme F420 has a limited phylogenetic distribution, including methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea 34H, Rhodopseudomonas palustris HaA2, and others. Partial phylogenetic profiling identifies protein subfamilies, within the larger family called luciferase-like monooxygenanases (pfam00296), that appear only in F420-positive genomes and are likely to be F420-dependent. This model describes one such subfamily, exemplified by MSMEG_2256 from Mycobacterium smegmatis. [Unknown function, Enzymes of unknown specificity] 318 matched cddid_all.tbl CDD TIGR03618 TIGR03618 274679 Rv1155_F420 PPOX class probable F420-dependent enzyme. A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomyces, make F420. The Partial Phylogenetic Profiling algorithm identifies this members of this protein family as high-scoring proteins to the F420 biosynthesis profile. A member of this family, Rv1155, was crytallized after expression in Escherichia coli, which does not synthesize F420; the crystal structure shown to resemble FMN-binding proteins, but with a recognizable empty cleft corresponding to, yet differing profounding from, the FMN site of pyridoxine 5'-phosphate oxidase. We propose that this protein family consists of F420-binding enzymes. [Unknown function, Enzymes of unknown specificity] 126 matched cddid_all.tbl CDD TIGR03619 TIGR03619 274680 F420_Rv2161c probable F420-dependent oxidoreductase, Rv2161c family. Coenzyme F420 has a limited phylogenetic distribution, including methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea 34H, Rhodopseudomonas palustris HaA2, and others. Partial phylogenetic profiling identifies protein subfamilies, within the larger family called luciferase-like monooxygenanases (pfam00296), that appear only in F420-positive genomes and are likely to be F420-dependent. This model describes a domain found in a distinctive subset of bacterial luciferase homologs, found only in F420-biosynthesizing members of the Actinobacteria. [Unknown function, Enzymes of unknown specificity] 246 matched cddid_all.tbl CDD TIGR03620 TIGR03620 274681 F420_MSMEG_4141 probable F420-dependent oxidoreductase, MSMEG_4141 family. Members of this protein family, related to F420-dependent oxidoreductases within the larger family of a bacterial luciferase (an FMN-dependent enzyme), occurs only within the small subset of species that synthesize F420. Most such proteins are from members of the Actinobacteria, but at least one species, Sphingomonas wittichii, belongs to the Alphaproteobacteria. [Unknown function, Enzymes of unknown specificity] 278 matched cddid_all.tbl CDD TIGR03621 TIGR03621 200301 F420_MSMEG_2516 probable F420-dependent oxidoreductase, MSMEG_2516 family. Coenzyme F420 is produced by methanogenic archaea, a number of the Actinomycetes (including Mycobacterium tuberculosis), and rare members of other lineages. The resulting information-rich phylogenetic profile identifies candidate F420-dependent oxidoreductases within the family of luciferase-like enzymes (pfam00296), where the species range for the subfamily encompasses many F420-positive genomes without straying beyond. This family is uncharacterized, and named for member MSMEG_2516 from Mycobacterium smegmatis. [Unknown function, Enzymes of unknown specificity] 295 matched cddid_all.tbl CDD TIGR03622 TIGR03622 132661 urea_t_UrtB_arc urea ABC transporter, permease protein UrtB. Members of this protein family are ABC transporter permease subunits restricted to the Archaea. Several lines of evidence suggest this protein is functionally analogous, as well as homologous, to the UrtB subunit of the Corynebacterium glutamicum urea transporter. All members of the operon show sequence similarity to urea transport subunits, the gene is located near the urease structural subunits in two of three species, and partial phylogenetic profiling identifies this permease subunit as closely matching the profile of urea utilization. 283 matched cddid_all.tbl CDD TIGR03623 TIGR03623 274682 TIGR03623 probable DNA repair protein. Members of this protein family are bacterial proteins of about 900 amino acids in length. Members show extended homology to proteins in TIGR02786, the AddB protein of double-strand break repair via homologous recombination. Members of this family, therefore, may be DNA repair proteins. 874 matched cddid_all.tbl CDD TIGR03624 TIGR03624 274683 TIGR03624 putative hydrolase. Members of this protein family have a phylogenetic distribution skewed toward the Actinobacteria (high GC Gram-positive bacteria), but with a few members occuring in the Archaea and Chloroflexi. The function is unknown. [Unknown function, General] 346 matched cddid_all.tbl CDD TIGR03625 TIGR03625 274684 L3_bact 50S ribosomal protein uL3, bacterial form. This model describes bacterial (and mitochondrial and chloroplast) class of ribosomal protein L3. A separate model describes the archaeal form, where both belong to pfam00297. The name is phrased to meet the needs of bacterial genome annotation. Organellar forms typically will have transit peptides, N-terminal to the region modeled here. 202 matched cddid_all.tbl CDD TIGR03626 TIGR03626 274685 L3_arch ribosomal protein uL3, archaeal form. This model describes exclusively the archaeal class of ribosomal protein L3. A separate model (TIGR03625) describes the bacterial/organelle form, and both belong to pfam00297. Eukaryotic proteins are excluded from this model. [Protein synthesis, Ribosomal proteins: synthesis and modification] 330 matched cddid_all.tbl CDD TIGR03627 TIGR03627 132666 uS9_arch ribosomal protein uS9, archaeal form. This model describes exclusively the archaeal ribosomal protein S9P. Homologous eukaryotic and bacterial ribosomal proteins are excluded from this model. [Protein synthesis, Ribosomal proteins: synthesis and modification] 130 matched cddid_all.tbl CDD TIGR03628 TIGR03628 274686 arch_S11P ribosomal protein uS11P, archaeal form. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria. [Protein synthesis, Ribosomal proteins: synthesis and modification] 117 matched cddid_all.tbl CDD TIGR03629 TIGR03629 213839 uS13_arch ribosomal protein uS13, archaeal form. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13. [Protein synthesis, Ribosomal proteins: synthesis and modification] 144 matched cddid_all.tbl CDD TIGR03630 TIGR03630 274687 uS17_arch ribosomal protein uS17, archaeal form. This model describes exclusively the archaeal ribosomal protein S17P. It excludes the homologous ribosomal protein S17 from bacteria, and is not intended for use on eukaryotic sequences, where some instances of ribosomal proteins S11 score above the trusted cutoff. [Protein synthesis, Ribosomal proteins: synthesis and modification] 102 matched cddid_all.tbl CDD TIGR03631 TIGR03631 274688 uS13_bact ribosomal protein uS13, bacterial form. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type. [Protein synthesis, Ribosomal proteins: synthesis and modification] 113 matched cddid_all.tbl CDD TIGR03632 TIGR03632 274689 uS11_bact ribosomal protein uS11, bacterial form. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected. [Protein synthesis, Ribosomal proteins: synthesis and modification] 108 matched cddid_all.tbl CDD TIGR03633 TIGR03633 163366 arc_protsome_A proteasome endopeptidase complex, archaeal, alpha subunit. This protein family describes the archaeal proteasome alpha subunit, homologous to both the beta subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 224 matched cddid_all.tbl CDD TIGR03634 TIGR03634 274690 arc_protsome_B proteasome endopeptidase complex, archaeal, beta subunit. This protein family describes the archaeal proteasome beta subunit, homologous to both the alpha subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 185 matched cddid_all.tbl CDD TIGR03635 TIGR03635 274691 uS17_bact ribosomal protein uS17, bacterial form. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17. [Protein synthesis, Ribosomal proteins: synthesis and modification] 72 matched cddid_all.tbl CDD TIGR03636 TIGR03636 274692 uL23_arch ribosomal protein uL23, archaeal form. This model describes the archaeal ribosomal protein L23P and rigorously excludes the bacterial counterpart L23. In order to capture every known instance of archaeal L23P, the trusted cutoff is set lower than a few of the highest scoring eukaryotic cytosolic ribosomal counterparts. [Protein synthesis, Ribosomal proteins: synthesis and modification] 77 matched cddid_all.tbl CDD TIGR03637 TIGR03637 132676 cas1_YPEST CRISPR-associated endonuclease Cas1, subtype I-F/YPEST. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes the Cas1 protein particular to the YPEST subtype of CRISPR/Cas system. 307 matched cddid_all.tbl CDD TIGR03638 TIGR03638 274693 cas1_ECOLI CRISPR-associated endonuclease Cas1, subtype I-E/ECOLI. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes the Cas1 protein particular to the ECOLI subtype of CRISPR/Cas system. 268 matched cddid_all.tbl CDD TIGR03639 TIGR03639 274694 cas1_NMENI CRISPR-associated endonuclease Cas1, subtype II/NMENI. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is a prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes the Cas1 variant of the NMENI subtype of CRISPR/Cas system. 278 matched cddid_all.tbl CDD TIGR03640 TIGR03640 188360 cas1_DVULG CRISPR-associated endonuclease Cas1, subtype I-C/DVULG. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes the Cas1 protein particular to the DVULG subtype of CRISPR/Cas system. 340 matched cddid_all.tbl CDD TIGR03641 TIGR03641 274695 cas1_HMARI CRISPR-associated endonuclease Cas1, subtype I-B/HMARI/TNEAP. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes Cas1 subgroup that includes Cas1 proteins of the related HMARI and TNEAP subtypes of CRISPR/Cas system. 320 matched cddid_all.tbl CDD TIGR03642 TIGR03642 274696 cas_csx14 CRISPR-associated protein, Csx14 family. This model describes a protein N-terminal protein sequence domain strictly associated with CRISPR and CRISPR-associated protein systems. This model and TIGR02584 identify two separate clades from a larger homology domain family, both CRISPR-associated, while other homologs are found that may not be. Members are found in bacteria that include Pelotomaculum thermopropionicum SI, Thermoanaerobacter tengcongensis MB4, and Roseiflexus sp. RS-1, and in archaea that include Thermoplasma volcanium, Picrophilus torridus, and Methanospirillum hungatei. The molecular function is unknown. 124 matched cddid_all.tbl CDD TIGR03643 TIGR03643 132682 TIGR03643 TIGR03643 family protein. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies. [Hypothetical proteins, Conserved] 72 matched cddid_all.tbl CDD TIGR03644 TIGR03644 274697 marine_trans_1 probable ammonium transporter, marine subtype. Members of this protein family are well conserved subclass of putative ammonimum transporters, belonging to the much broader set of ammonium/methylammonium transporter described by TIGR00836. Species with this transporter tend to be marine bacteria. Partial phylogenetic profiling (PPP) picks a member of this protein family as the single best-scoring protein vs. a reference profile for the marine environment Genome Property for a large number of different query genomes. This finding by PPP suggests that this transporter family represents an important adaptation to the marine environment. 404 matched cddid_all.tbl CDD TIGR03645 TIGR03645 132684 glyox_marine lactoylglutathione lyase family protein. Members of this protein family share homology with lactoylglutathione lyase (glyoxalase I) and are found mainly in marine members of the gammaproteobacteria, including CPS_0532 from Colwellia psychrerythraea 34H. This family excludes a well-separated, more narrowly distributed paralogous family, exemplified by CPS_3492 from C. psychrerythraea. The function is of this protein family is unknown. 162 matched cddid_all.tbl CDD TIGR03646 TIGR03646 132685 YtoQ_fam YtoQ family protein. Members of this family are uncharacterized proteins, including YtoQ from Bacillus subtilis. This family shows some sequence similarity to a family of nucleoside 2-deoxyribosyltransferases (COG3613 as iterated through CDD), but sufficiently remote that PSI-BLAST starting from YtoQ and exploring outwards does not discover the relationship. 144 matched cddid_all.tbl CDD TIGR03647 TIGR03647 132686 Na_symport_sm putative solute:sodium symporter small subunit. Members of this family are highly hydrophobic bacterial proteins of about 90 amino acids in length. Members usually are found immediately upstream (sometimes fused to) a member of the solute:sodium symporter family, and therefore are a putative sodium:solute symporter small subunit. Members tend to be found in aquatic species, especially those from marine or other high salt environments. [Transport and binding proteins, Unknown substrate] 77 matched cddid_all.tbl CDD TIGR03648 TIGR03648 274698 Na_symport_lg probable sodium:solute symporter, VC_2705 subfamily. This family belongs to a larger family of transporters of the sodium:solute symporter superfamily, TC 2.A.21. Members of this strictly bacterial protein subfamily are found almost invariably immediately downstream from a member of family TIGR03647. Occasionally, the two genes are fused. 552 matched cddid_all.tbl CDD TIGR03649 TIGR03649 274699 ergot_EASG ergot alkaloid biosynthesis protein, AFUA_2G17970 family. This family consists of fungal proteins of unknown function associated with secondary metabolite biosynthesis, such as of the ergot alkaloids such as ergovaline. Nomenclature differs because gene order differs - this is EasG in Neotyphodium lolii but is designated ergot alkaloid biosynthetic protein A in several other fungi. 285 matched cddid_all.tbl CDD TIGR03650 TIGR03650 132689 violacein_E violacein biosynthesis enzyme VioE. This enzyme catalyzes the third step in violacein biosynthesis from a pair of Trp residues, as in Chromobacterium violaceum, but the first step that distinguishes that pathway from staurosporine (an indolocarbazole antibiotic) biosynthesis. [Cellular processes, Toxin production and resistance] 184 matched cddid_all.tbl CDD TIGR03651 TIGR03651 274700 circ_ocin_uber circular bacteriocin, circularin A/uberolysin family. Circular bacteriocins are antibiotic proteins made by ribosomal translation of a precursor molecular, followed by cleavage and circularization. Members of this subclass of the circular bacteriocins include circularin A from Clostridium beijerinckii, bacteriocin AS-48 from Enterococcus faecalis, uberolysin from Streptococcus uberis, and carnocyclin A from Carnobacterium maltaromaticum. The mature circularized peptides average about 70 amino acids in size. [Cellular processes, Toxin production and resistance] 73 matched cddid_all.tbl CDD TIGR03652 TIGR03652 274701 FeS_repair_RIC iron-sulfur cluster repair di-iron protein. Members of this protein family, designated variously as YftE, NorA, DrnN, and NipC, are di-iron proteins involved in the repair of iron-sulfur clusters. Previously assigned names reflect pleiotropic effects of damage from NO or other oxidative stress when this protein is mutated. The suggested name now is RIC, for Repair of Iron Centers. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 216 matched cddid_all.tbl CDD TIGR03653 TIGR03653 274702 uL6_arch ribosomal protein uL6, archaeal form. Members of this protein family are the archaeal form ofribosomal protein uL6 (previously L9 in yeast and human). The top-scoring proteins not selected by this model are eukaryotic cytosolic uL6. Bacterial ribosomal protein L6 scores lower and is described by a distinct model. [Protein synthesis, Ribosomal proteins: synthesis and modification] 170 matched cddid_all.tbl CDD TIGR03654 TIGR03654 274703 L6_bact ribosomal protein L6, bacterial type. [Protein synthesis, Ribosomal proteins: synthesis and modification] 175 matched cddid_all.tbl CDD TIGR03655 TIGR03655 274704 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes. [Mobile and extrachromosomal element functions, Prophage functions, DNA metabolism, Restriction/modification] 53 matched cddid_all.tbl CDD TIGR03656 TIGR03656 274705 IsdC heme uptake protein IsdC. Isd proteins are iron-regulated surface proteins found in Bacillus, Staphylococcus and Listeria species and are responsible for heme scavenging from hemoproteins. The IsdC protein consists of an N-terminal hydrophobic signal sequence, a central NEAT (NEAr Transporter, pfam05031) domain, which confers the ability to bind heme, and a C-terminal SrtB processing signal which targets the protein to the cell wall. IsdC is believed to make a direct contact with, and transfer heme to, the heme-binding component (IsdE) of an ABC transporter in the cytoplasmic membrane, and to receive heme from other NEAT-containing heme-binding proteins also localized in the cell wall. 217 matched cddid_all.tbl CDD TIGR03657 TIGR03657 213844 IsdB heme uptake protein IsdB. Isd proteins are iron-regulated surface proteins found in Bacillus, Staphylococcus and Listeria species and are responsible for heme scavenging from hemoproteins. The IsdB protein is only observed in Staphylococcus and consists of an N-terminal hydrophobic signal sequence, a pair of tandem NEAT (NEAr Transporter, pfam05031) domains, which confers the ability to bind heme, and a C-terminal sortase processing signal which targets the protein to the cell wall. IsdB is believed to make a direct contact with methemoglobin facilitating transfer of heme to IsdB. The heme is then transferred to other cell wall-bound NEAT domain proteins such as IsdA and IsdC. 644 matched cddid_all.tbl CDD TIGR03658 TIGR03658 132697 IsdH_HarA haptoglobin-binding heme uptake protein HarA. HarA is a heme-binding NEAT-domain (NEAr Transporter, pfam05031) protein which has been shown to bind to the haptoglobin-hemoglobin complex in order to extract heme from it. HarA has also been reported to bind hemoglobin directly. HarA (also known as IsdH) contains three NEAT domains as well as a sortase A C-terminal signal for localization to the cell wall. The heme bound at the third of these NEAT domains has been shown to be transferred to the IsdA protein also localized at the cell wall, presumably through an additional specific protein-protein interaction. Haptoglobin is a hemoglobin carrier protein involved in scavenging hemoglobin in the blood following red blood cell lysis and targetting it to the liver. 895 matched cddid_all.tbl CDD TIGR03659 TIGR03659 274706 IsdE heme ABC transporter, heme-binding protein isdE. This family of ABC substrate-binding proteins is observed primarily in close proximity with proteins localized to the cell wall and bearing the NEAT (NEAr Transporter, pfam05031) heme-binding domain. IsdE has been shown to bind heme and is involved in the process of scavenging heme for the purpose of obtaining iron. 289 matched cddid_all.tbl CDD TIGR03660 TIGR03660 132699 T1SS_rpt_143 T1SS-143 repeat domain. This model represents a domain of about 143 amino acids that may occur singly or in up to 23 tandem repeats in very large proteins in the genus Vibrio, and in related species such as Legionella pneumophila, Photobacterium profundum, Rhodopseudomonas palustris, Shewanella pealeana, and Aeromonas hydrophila. Proteins with these domains represent a subset of a broader set of proteins with a particular signal for type 1 secretion, consisting of several glycine-rich repeats modeled by pfam00353, followed by a C-terminal domain modeled by TIGR03661. Proteins with this domain tend to share several properties with the RtxA (Repeats in Toxin) protein of Vibrio cholerae, including a large size often containing tandemly repeated domains and a C-terminal signal for type 1 secretion. [Cellular processes, Pathogenesis] 137 matched cddid_all.tbl CDD TIGR03661 TIGR03661 274707 T1SS_VCA0849 type I secretion C-terminal target domain (VC_A0849 subclass). This model represents a C-terminal domain associated with secretion by type 1 secretion systems (T1SS). Members of this subclass do not include the RtxA toxin of Vibrio cholerae and its homologs, although the two classes of proteins share large size, occurrence in genomes with T1SS, regions with long tandem repeats, and regions with the glycine-rich repeat modeled by pfam00353. [Cellular processes, Pathogenesis] 88 matched cddid_all.tbl CDD TIGR03662 TIGR03662 274708 Chlor_Arch_YYY Chlor_Arch_YYY domain. Members of this highly hydrophobic probable integral membrane family belong to two classes. In one, a single copy of the region covered by this model represents essentially the full length of a strongly hydrophobic protein of about 700 to 900 residues (variable because of long inserts in some). The domain architecture of the other class consists of an additional N-terminal region, two copies of the region represented by this model, and three to four repeats of TPR, or tetratricopeptide repeat. The unusual species range includes several Archaea, several Chloroflexi, and Clostridium phytofermentans. An unusual motif YYYxG is present, and we suggest the name Chlor_Arch_YYY protein. The function is unknown. 723 matched cddid_all.tbl CDD TIGR03663 TIGR03663 274709 TIGR03663 TIGR03663 family protein. Members of this protein family, uncommon and rather sporadically distributed, are found almost always in the same genomes as members of family TIGR03662, and frequently as a nearby gene. Members show some N-terminal sequence similarity with pfam02366, dolichyl-phosphate-mannose-protein mannosyltransferase. The few invariant residues in this family, found toward the N-terminus, include a dipeptide DE, a tripeptide HGP, and two different Arg residues. Up to three members may be found in a genome. The function is unknown. 439 matched cddid_all.tbl CDD TIGR03664 TIGR03664 274710 fut_nucase futalosine hydrolase. This enzyme catalyzes the conversion of futalosine to de-hypoxanthine futalosine in a pathway for the biosynthesis of menaquinone distinct from the pathway observed in E. coli. 222 matched cddid_all.tbl CDD TIGR03665 TIGR03665 274711 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed, and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA. 172 matched cddid_all.tbl CDD TIGR03666 TIGR03666 274712 Rv2061_F420 PPOX class probable F420-dependent enzyme, Rv2061 family. A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. A variant of the Partial Phylogenetic Profiling algorithm, SIMBAL, shows that this protein likely binds F420 in a cleft similar to that in which the homologous enzyme pyridoxamine phosphate oxidase (PPOX) binds FMN. [Unknown function, Enzymes of unknown specificity] 132 matched cddid_all.tbl CDD TIGR03667 TIGR03667 132706 Rv3369 PPOX class probable F420-dependent enzyme, Rv3369 family. A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. A variant of the Partial Phylogenetic Profiling algorithm, SIMBAL, shows that this protein likely binds F420 in a cleft similar to that in which the homologous enzyme pyridoxamine phosphate oxidase (PPOX) binds FMN. [Unknown function, Enzymes of unknown specificity] 130 matched cddid_all.tbl CDD TIGR03668 TIGR03668 132707 Rv0121_F420 PPOX class probable F420-dependent enzyme, Rv0121 family. A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. A variant of the Partial Phylogenetic Profiling algorithm, SIMBAL, shows that this protein likely binds F420 in a cleft similar to that in which the homologous enzyme pyridoxamine phosphate oxidase (PPOX) binds FMN. [Unknown function, Enzymes of unknown specificity] 141 matched cddid_all.tbl CDD TIGR03669 TIGR03669 132708 urea_ABC_arch urea ABC transporter, substrate-binding protein, archaeal type. Members of this protein family are identified as the substrate-binding protein of a urea ABC transport system by similarity to a known urea transporter from Corynebacterium glutamicum, operon structure, proximity of its operons to urease (urea-utilization protein) operons, and by Partial Phylogenetic Profiling vs. urea utilization. [Transport and binding proteins, Amino acids, peptides and amines] 374 matched cddid_all.tbl CDD TIGR03670 TIGR03670 274713 rpoB_arch DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes. 599 matched cddid_all.tbl CDD TIGR03671 TIGR03671 274714 cca_archaeal CCA-adding enzyme. 408 matched cddid_all.tbl CDD TIGR03672 TIGR03672 274715 rpl4p_arch 50S ribosomal protein uL4, archaeal form. One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome. 251 matched cddid_all.tbl CDD TIGR03673 TIGR03673 274716 uL14_arch 50S ribosomal protein uL14, archaeal form. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in 2 intersubunit bridges. 131 matched cddid_all.tbl CDD TIGR03674 TIGR03674 274717 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA 338 matched cddid_all.tbl CDD TIGR03675 TIGR03675 274718 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined as arCOG01782. 630 matched cddid_all.tbl CDD TIGR03676 TIGR03676 274719 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1. [Protein synthesis, Translation factors] 403 matched cddid_all.tbl CDD TIGR03677 TIGR03677 188367 eL8_ribo ribosomal protein eL8, archaeal form. This model specifically identifies the archaeal version of the large ribosomal complex protein eL8, previously designated L8 in yeast and L7Ae in the archaea. The family is a narrower version of the pfam01248 model which also recognizes the L30 protein. 117 matched cddid_all.tbl CDD TIGR03678 TIGR03678 163391 het_cyc_patell bacteriocin leader peptide, microcyclamide/patellamide family. This model represents a conserved N-terminal region shared by microcyclamide and patellamide bacteriocins precursors. These bacteriocin precursors are associated with heterocyclization. Related precursors are found in family TIGR04446. 34 matched cddid_all.tbl CDD TIGR03679 TIGR03679 188368 arCOG00187 arCOG00187 universal archaeal metal-binding-domain/4Fe-4S-binding-domain containing ABC transporter, ATP-binding protein. This protein consists of an N-terminal possible metal-binding domain (pfam04068) followed by a 4Fe-4S cluster binding domain (pfam00037) followed by a C-terminal ABC transporter, ATP-binding domain (pfam00005). This combination of N-terminal domains is observed in the RNase L inhibitor, RLI. This model has the same scope as an archaeal COG (arCOG00187) and is found in all completely sequenced archaea and does not recognize any known non-archaeal genes. 218 matched cddid_all.tbl CDD TIGR03680 TIGR03680 274720 eif2g_arch translation initiation factor 2 subunit gamma. This model represents the archaeal translation initiation factor 2 subunit gamma and is found in all known archaea. eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. 406 matched cddid_all.tbl CDD TIGR03682 TIGR03682 274721 arCOG04112 diphthamide biosynthesis enzyme Dph2. Members of this family are the archaeal protein Dph2, members of the universal archaeal protein family designated arCOG04112. The chemical function of this protein is analogous to the radical SAM family (pfam04055), although the sequence is not homologous. The chemistry involves [4Fe-4S]-aided formation of a 3-amino-3-carboxypropyl radical rather than the canonical 5'-deoxyadenosyl radical of the radical SAM family. 308 matched cddid_all.tbl CDD TIGR03683 TIGR03683 274722 A-tRNA_syn_arch alanyl-tRNA synthetase. This family of alanyl-tRNA synthetases is limited to the archaea, and is a subset of those sequences identified by the model pfam07973 covering the second additional domain (SAD) of alanyl and threonyl tRNA synthetases . 902 matched cddid_all.tbl CDD TIGR03684 TIGR03684 274723 arCOG00985 arCOG04150 universal archaeal PUA-domain protein. This universal archaeal protein contains a domain possibly associated with RNA binding (pfam01472, TIGR00451). 150 matched cddid_all.tbl CDD TIGR03685 TIGR03685 274724 ribo_P1_arch 50S ribosomal protein P1. This model represents P1 the L12P protein of the large (50S) subunit of the archaeal ribosome. 105 matched cddid_all.tbl CDD TIGR03686 TIGR03686 274725 pupylate_PafA Pup--protein ligase. Members of this family are the Pup--protein ligase PafA (proteasome accessory factor A), a protein shown to regulate steady-state levels of certain proteasome targets in Mycobacterium tuberculosis. Iyer, et al (2008) first suggested that PafA is the ligase for Pup, a ubiquitin analog attached to an epsilon-amino group of a Lys side-chain to direct the target to the proteasome. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 453 matched cddid_all.tbl CDD TIGR03687 TIGR03687 200311 pupylate_cterm ubiquitin-like protein Pup. Members of this protein family are Pup, a small protein whose ligation to target proteins steers them toward degradation. This protein family occurs in a number of bacteria, especially Actinobacteria such as Mycobacterium tuberculosis, that possess an archeal-type proteasome. All members of this protein family known during model construction end with the C-terminal motif [FY][VI]QKGG[QE]. Ligation is thought to occur between the C-terminal COOH of Pup and an epsilon-amino group of a Lys on the target protein. The N-terminal half of this protein is poorly conserved and not represented in the seed alignment. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 33 matched cddid_all.tbl CDD TIGR03688 TIGR03688 274726 pupylate_PafA2 proteasome accessory factor PafA2. This protein family is paralogous to (and distinct from) the PafA (proteasome accessory factor) first described in Mycobacterium tuberculosis (see TIGR03686). Members of both this family and TIGR03686 itself tend to cluster with each other, with the ubiquitin analog Pup (TIGR03687) associated with targeting to the proteasome, and with proteasome subunits themselves. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 485 matched cddid_all.tbl CDD TIGR03689 TIGR03689 200312 pup_AAA proteasome ATPase. In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 512 matched cddid_all.tbl CDD TIGR03690 TIGR03690 163402 20S_bact_beta proteasome, beta subunit, bacterial type. Members of this family are the beta subunit of the 20S proteasome as found in Actinobacteria such as Mycobacterium, Rhodococcus, and Streptomyces. In Streptomyces, maturation during proteasome assembly was shown to remove a 53-amino acid propeptide. Most of the length of the propeptide is not included in this model. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 219 matched cddid_all.tbl CDD TIGR03691 TIGR03691 163403 20S_bact_alpha proteasome, alpha subunit, bacterial type. Members of this family are the alpha subunit of the 20S proteasome as found in Actinobacteria such as Mycobacterium, Rhodococcus, and Streptomyces. In most Actinobacteria (an exception is Propionibacterium acnes), the proteasome is accompanied by a system of tagging proteins for degradation with Pup. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 228 matched cddid_all.tbl CDD TIGR03692 TIGR03692 274727 ATP_dep_HslV ATP-dependent protease HslVU, peptidase subunit. The ATP-dependent protease HslVU, a complex of hexameric HslU active as a protein-unfolding ATPase and dodecameric HslV, the catalytic threonine protease. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 171 matched cddid_all.tbl CDD TIGR03693 TIGR03693 163405 ocin_ThiF_like putative thiazole-containing bacteriocin maturation protein. Members of this protein family are found in a three-gene operon in Bacillus anthracis and related Bacillus species, where the other two genes are clearly identified with maturation of a putative thiazole-containing bacteriocin precursor. While there is no detectable pairwise sequence similarity between members of this family and the proposed cyclodehydratases such as SagC of Streptococcus pyogenes (see family TIGR03603), both families show similarity through PSI-BLAST to ThiF, a protein involved in biosynthesis of the thiazole moiety for thiamine biosynthesis. This family, therefore, may contribute to cyclodehydratase function in heterocycle-containing bacteriocin biosyntheses. In Bacillus licheniformis ATCC 14580, the bacteriocin precursor gene is adjacent to the gene for this protein. [Cellular processes, Toxin production and resistance] 637 matched cddid_all.tbl CDD TIGR03694 TIGR03694 274728 exosort_acyl N-acyl amino acid synthase, PEP-CTERM/exosortase system-associated. Members of this protein family are restricted to bacterial species with the PEP-CTERM/exosortase system predicted to act in exopolysaccharide-associated protein targeting. PSI-BLAST and CDD reveal relationships to the acyltransferase family that includes N-acyl-L-homoserine lactone synthetase, and recent work shows long-chain N-acyl amino acid biosynthesis activity. Several members of this family may be found in a single genome. These acyltransferases may produce a quorum signalling molecule or may contribute to chemical modifications in exopolysaccharide and biofilm structural material production. 241 matched cddid_all.tbl CDD TIGR03695 TIGR03695 274729 menH_SHCHC 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase. This protein catalyzes the formation of SHCHC, or (1 R,6 R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate, by elmination of pyruvate from 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC). Note that SHCHC synthase activity previously was attributed to MenD, which in fact is SEPHCHC synthase. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 252 matched cddid_all.tbl CDD TIGR03696 TIGR03696 274730 Rhs_assc_core RHS repeat-associated core domain. This model represents a conserved unique core sequence shared by large numbers of proteins. It is occasional in the Archaea Methanosarcina barkeri) but common in bacteria and eukaryotes. Most fall into two large classes. One class consists of long proteins in which two classes of repeats are abundant: an FG-GAP repeat (pfam01839) class, and an RHS repeat (pfam05593) or YD repeat (TIGR01643). This class includes secreted bacterial insecticidal toxins and intercellular signalling proteins such as the teneurins in animals. The other class consists of uncharacterized proteins shorter than 400 amino acids, where this core domain of about 75 amino acids tends to occur in the N-terminal half. Over twenty such proteins are found in Pseudomonas putida alone; little sequence similarity or repeat structure is found among these proteins outside the region modeled by this domain. 77 matched cddid_all.tbl CDD TIGR03697 TIGR03697 163409 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C. [Regulatory functions, DNA interactions] 193 matched cddid_all.tbl CDD TIGR03698 TIGR03698 163410 clan_AA_DTGF clan AA aspartic protease, AF_0612 family. Members of this protein family are clan AA aspartic proteases, related to family TIGR02281. These proteins resemble retropepsins, pepsin-like proteases of retroviruses such as HIV. Members of this family are found in archaea and bacteria. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 107 matched cddid_all.tbl CDD TIGR03699 TIGR03699 274731 menaquin_MqnC dehypoxanthine futalosine cyclase. members of this protein family are involved in menaquinone biosynthesis by an alternate pathway via futalosine. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 340 matched cddid_all.tbl CDD TIGR03700 TIGR03700 213851 mena_SCO4494 putative menaquinone biosynthesis radical SAM enzyme, SCO4494 family. Members of this protein family appear to be involved in menaquinone biosynthesis by an alternate pathway via futalosine, based on close phylogenetic correlation with known markers of the futalosine pathway, gene clustering in many organisms, and paralogy with the SCO4550 protein. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 351 matched cddid_all.tbl CDD TIGR03701 TIGR03701 163413 mena_SCO4490 menaquinone biosynthesis decarboxylase, SCO4490 family. Members of this protein family are putative decarboxylases involved in a late stage of the alternative pathway for menaquinone, via futalosine, as in Streptomyces coelicolor and Helicobacter pylori. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone] 433 matched cddid_all.tbl CDD TIGR03702 TIGR03702 163414 lip_kinase_YegS lipid kinase YegS. Members of this protein family are designated YegS, an apparent lipid kinase family in the Proteobacteria. Bakali, et al. report phosphatidylglycerol kinase activity for the member from Escherichia coli, but refrain from calling that activity synonymous with its biological role. Note that a broader, subfamily-type model (TIGR00147), includes this family but also multiple paralogs in some species and varied functions. [Unknown function, Enzymes of unknown specificity] 293 matched cddid_all.tbl CDD TIGR03703 TIGR03703 274732 plsB glycerol-3-phosphate O-acyltransferase. Members of this protein family are PlsB, glycerol-3-phosphate O-acyltransferase, present in E. coli and numerous related species. In many bacteria, PlsB is not found, and appears to be replaced by a two enzyme system for 1-acyl-glycerol-3-phosphate biosynthesis, the PlsX/Y system. [Fatty acid and phospholipid metabolism, Biosynthesis] 799 matched cddid_all.tbl CDD TIGR03704 TIGR03704 274733 PrmC_rel_meth putative protein-(glutamine-N5) methyltransferase, unknown substrate-specific. This protein family is closely related to two different families of protein-(glutamine-N5) methyltransferase. The first is PrmB, which modifies ribosomal protein L3 in some bacteria. The second is PrmC (HemK), which modifies peptide chain release factors 1 and 2 in most bacteria and also in eukaryotes. The glutamine side chain-binding motif NPPY shared by PrmB and PrmC is N[VAT]PY in this family. The protein substrate is unknown. [Protein synthesis, Ribosomal proteins: synthesis and modification] 251 matched cddid_all.tbl CDD TIGR03705 TIGR03705 274734 poly_P_kin polyphosphate kinase 1. Members of this protein family are the enzyme polyphosphate kinase 1 (PPK1). This family is found in many prokaryotes and also in Dictyostelium. Sequences in the seed alignment were taken from prokaryotic consecutive two-gene pairs in which the other gene encodes an exopolyphosphatase. It synthesizes polyphosphate from the terminal phosphate of ATP but not GTP, in contrast to PPK2. [Central intermediary metabolism, Phosphorus compounds] 672 matched cddid_all.tbl CDD TIGR03706 TIGR03706 274735 exo_poly_only exopolyphosphatase. It appears that a single enzyme may act as both exopolyphosphatase (Ppx) and guanosine pentaphosphate phosphohydrolase (GppA) in a number of species. Members of the seed alignment use to define this exception-level model are encoded adjacent to a polyphosphate kinase 1 gene, and the trusted cutoff is set high enough (425) that no genome has a second hit. Therefore all members may be presumed to at least share exopolyphospatase activity, and may lack GppA activity. GppA acts in the stringent response. [Central intermediary metabolism, Phosphorus compounds] 300 matched cddid_all.tbl CDD TIGR03707 TIGR03707 213852 PPK2_P_aer polyphosphate kinase 2, PA0141 family. Members of this protein family are designated polyphosphate kinase 2 (PPK2) after the characterized protein in Pseudomonas aeruginosa. This family comprises one of three well-separated clades in the larger family described by pfam03976. PA0141 from this family has been shown capable of operating in reverse, with GDP preferred (over ADP) as a substrate, producing GTP (or ATP) by transfer of a phosphate residue from polyphosphate. Most species with a member of this family also encode a polyphosphate kinase 1 (PPK1). [Central intermediary metabolism, Phosphorus compounds] 230 matched cddid_all.tbl CDD TIGR03708 TIGR03708 274736 poly_P_AMP_trns polyphosphate:AMP phosphotransferase. Members of this protein family contain a domain duplication. The characterized member from Acinetobacter johnsonii is polyphosphate:AMP phosphotransferase (PAP), which can transfer the terminal phosphate from poly(P) to AMP, yielding ADP. In the opposite direction, this enzyme can synthesize poly(P). Each domain of this protein family is homologous to polyphosphate kinase, an enzyme that can run in the forward direction to extend a polyphosphate chain with a new terminal phosphate from ATP, or in reverse to make ATP (or GTP) from ADP (or GDP). [Central intermediary metabolism, Phosphorus compounds] 493 matched cddid_all.tbl CDD TIGR03709 TIGR03709 274737 PPK2_rel_1 polyphosphate:nucleotide phosphotransferase, PPK2 family. Members of this protein family belong to the polyphosphate kinase 2 (PPK2) family, which is not related in sequence to PPK1. While PPK1 tends to act in the biosynthesis of polyphosphate, or poly(P), members of the PPK2 family tend to use the terminal phosphate of poly(P) to regenerate ATP or GTP from the corresponding nucleoside diphosphate, or ADP from AMP as is the case with polyphosphate:AMP phosphotransferase (PAP). Members of this protein family most likely transfer the terminal phosphate between poly(P) and some nucleotide, but it is not clear which. [Central intermediary metabolism, Phosphorus compounds] 264 matched cddid_all.tbl CDD TIGR03710 TIGR03710 274738 OAFO_sf 2-oxoacid:acceptor oxidoreductase, alpha subunit. This family of proteins contains a C-terminal thiamine diphosphate (TPP) binding domain typical of flavodoxin/ferredoxin oxidoreductases (pfam01855) as well as an N-terminal domain similar to the gamma subunit of the same group of oxidoreductases (pfam01558). The genes represented by this model are always found in association with a neighboring gene for a beta subunit (TIGR02177) which also occurs in a 4-subunit (alpha/beta/gamma/ferredoxin) version of the system. This alpha/gamma plus beta structure was used to define the set of sequences to include in this model. This pair of genes is not consistantly observed in proximity to any electron acceptor genes, but is found next to putative ferredoxins or ferredoxin-domain proteins in Azoarcus sp. EbN1, Bradyrhizobium japonicum USDA 110, Frankia sp. CcI3, Rhodoferax ferrireducens DSM 15236, Rhodopseudomonas palustris BisB5, Os, Sphingomonas wittichii RW1 and Streptomyces clavuligerus. Other potential acceptors are also sporadically observed in close proximity including ferritin-like proteins, reberythrin, peroxiredoxin and a variety of other flavin and iron-sulfur cluster-containing proteins. The phylogenetic distribution of this family encompasses archaea, a number of deeply-branching bacterial clades and only a small number of firmicutes and proteobacteria. The enzyme from Sulfolobus has been characterized with respect to its substrate specificity, which is described as wide, encompassing various 2-oxoacids such as 2-oxoglutarate, 2-oxobutyrate and pyruvate. The enzyme from Hydrogenobacter thermophilus has been shown to have a high specificity towards 2-oxoglutarate and is one of the key enzymes in the reverse TCA cycle in this organism. Furthermore, considering its binding of coenzyme A, it can be reasonably inferred that the product of the reaction is succinyl-CoA. The genes for this enzyme in Prevotella intermedia 17, Persephonella marina EX-H1 and Picrophilus torridus DSM 9790 are in close proximity to a variety of TCA cycle genes. Persephonella marina and P. torridus are believed to encode complete TCA cycles, and none of these contains the lipoate-based 2-oxoglutarate dehydrogenase (E1/E2/E3) system. That system is presumed to be replaced by this one. In fact, the lipoate system is absent in most organisms possessing a member of this family, providing additional circumstantial evidence that many of these enzymes are capable of acting as 2-oxoglutarate dehydrogenases and 562 matched cddid_all.tbl CDD TIGR03711 TIGR03711 163423 acc_sec_asp3 accessory Sec system protein Asp3. This protein is designated Asp3 because, along with SecY2, SecA2, and other proteins it is part of the accessory Sec system. The system is involved in the export of serine-rich glycoproteins important for virulence in a number of Gram-positive species, including Streptococcus gordonii and Staphylococcus aureus. This protein family is assigned to transport rather than glycosylation function, but the specific molecular role is unknown. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 135 matched cddid_all.tbl CDD TIGR03712 TIGR03712 274739 acc_sec_asp2 accessory Sec system protein Asp2. This protein is designated Asp2 because, along with SecY2, SecA2, and other proteins it is part of the accessory secretory protein system. The system is involved in the export of serine-rich glycoproteins important for virulence in a number of Gram-positive species, including Streptococcus gordonii and Staphylococcus aureus. This protein family is assigned to transport rather than glycosylation function, but the specific molecular role is unknown. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 511 matched cddid_all.tbl CDD TIGR03713 TIGR03713 274740 acc_sec_asp1 accessory Sec system protein Asp1. This protein is designated Asp1 because, along with SecY2, SecA2, and other proteins it is part of the accessory secretory protein system. The system is involved in the export of serine-rich glycoproteins important for virulence in a number of Gram-positive species, including Streptococcus gordonii and Staphylococcus aureus. This protein family is assigned to transport rather than glycosylation function, but the specific molecular role is unknown. [Protein fate, Protein and peptide secretion and trafficking, Cellular processes, Pathogenesis] 519 matched cddid_all.tbl CDD TIGR03714 TIGR03714 163426 secA2 accessory Sec system translocase SecA2. Members of this protein family are homologous to SecA and part of the accessory Sec system. This system, including both five core proteins for export and a variable number of proteins for glycosylation, operates in certain Gram-positive pathogens for the maturation and delivery of serine-rich glycoproteins such as the cell surface glycoprotein GspB in Streptococcus gordonii. [Protein fate, Protein and peptide secretion and trafficking] 762 matched cddid_all.tbl CDD TIGR03715 TIGR03715 274741 KxYKxGKxW KxYKxGKxW signal peptide. This model describes a novel form of signal peptide that occurs as an N-terminal domain with a recognizable motif, reminiscent of the YSIRK and PEP-CTERM forms of signal peptide. This domain tends to occur on long, low-complexity (usually Serine-rich and heavily glycosylated) proteins of the Firmicutes, and (as with YSIRK) the majority of these proteins have the LPXTG cell wall-anchoring motif at the C-terminus. 23 matched cddid_all.tbl CDD TIGR03716 TIGR03716 274742 R_switched_YkoY integral membrane protein, YkoY family. Rfam model RF00080 describes a structured RNA element called the yybP-ykoY leader, or SraF, which may precede one or several genes in a genome. Members of this highly hydrophobic protein family often are preceded by a yybP-ykoY leader, which may serve as a riboswitch. From the larger group of TerC homologs (pfam03741), this subfamily contains proteins YceF and YkoY from Bacillus subtilis. A transport function is proposed. 215 matched cddid_all.tbl CDD TIGR03717 TIGR03717 163429 R_switched_YjbE integral membrane protein, YjbE family. Rfam model RF00080 describes a structured RNA element called the yybP-ykoY leader, or SraF, which may precede one or several genes in a genome. Members of this highly hydrophobic protein family commonly are preceded by a yybP-ykoY leader, which may serve as a riboswitch. From the larger group of TerC homologs (pfam03741), this subfamily contains protein YjbE from Bacillus subtilis. A transport function is proposed. 176 matched cddid_all.tbl CDD TIGR03718 TIGR03718 274743 R_switched_Alx integral membrane protein, TerC family. Rfam model RF00080 describes a structured RNA element called the yybP-ykoY leader, or SraF, which may precede one or several genes in a genome. Members of this highly hydrophobic protein family often are preceded by a yybP-ykoY leader, which may serve as a riboswitch. From the larger group of TerC homologs (pfam03741), this subfamily contains TerC itself from Alcaligenes sp. plasmid IncHI2 pMER610 and from Proteus mirabilis. It also contains the alkaline-inducible E. coli protein Alx, which unlike the two TerC examples is preceded by a yybP-ykoY leader. 302 matched cddid_all.tbl CDD TIGR03719 TIGR03719 274744 ABC_ABC_ChvD ATP-binding cassette protein, ChvD family. Members of this protein family have two copies of the ABC transporter ATP-binding cassette, but are found outside the common ABC transporter operon structure that features integral membrane permease proteins and substrate-binding proteins encoded next to the ATP-binding cassette (ABC domain) protein. The member protein ChvD from Agrobacterium tumefaciens was identified as both a candidate to interact with VirB8, based on yeast two-hybrid analysis, and as an apparent regulator of VirG. The general function of this protein family is unknown. 552 matched cddid_all.tbl CDD TIGR03720 TIGR03720 274745 exospor_lead exosporium leader peptide. This domain is found as a leader peptide in at least two proteins targeted to the exosporium, a structure that occurs as the outermost layer of Bacillus anthracis, B. cereus, and B. thuringiensis spores. The exosporium consists of a basal layer and a nap of hair-like filaments. BclA, the major protein of the nap filaments, is targeted there by this leader peptide. [Cellular processes, Sporulation and germination] 19 matched cddid_all.tbl CDD TIGR03721 TIGR03721 274746 exospore_TM BclB C-terminal domain. This domain occurs as the C-terminal region in a number of proteins that have extensive collagen-like triple helix repeat regions. Member domains are predicted by TmHMM to have four or five transmembrane helices. Members are found mostly in the Firmicutes, but also in Acanthamoeba polyphaga mimivirus. Members include spore surface glycoprotein BclB from Bacillus anthracis, a protein of the exosporium. The exosporium is an additional outermost spore layer, lacking in B. subtilis and most other spore formers, consisting of a basal layer and, above it, a nap of fine filaments. 165 matched cddid_all.tbl CDD TIGR03722 TIGR03722 274747 arch_KAE1 universal archaeal protein Kae1. This family represents the archaeal protein Kae1. Its partner Bud32 is fused with it in about half of the known archaeal genomes. The pair, which appears universal in the archaea, corresponds to EKC/KEOPS complex in eukaryotes. A recent characterization of the member from Pyrococcus abyssi, as an iron-binding, atypical DNA-binding protein with an apurinic lyase activity, challenges the common annotation of close homologs as O-sialoglycoprotein endopeptidase. The latter annotation is based on a characterized protein from the bacterium Pasteurella haemolytica. [DNA metabolism, DNA replication, recombination, and repair] 322 matched cddid_all.tbl CDD TIGR03723 TIGR03723 274748 T6A_TsaD_YgjD tRNA threonylcarbamoyl adenosine modification protein TsaD. This model represents bacterial members of a protein family that is widely distributed. In a few pathogenic species, the protein is exported in a way that may represent an exceptional secondary function. This model plus companion (archaeal) model TIGR03722 together span the prokaryotic member sequences of TIGR00329, a protein family that appears universal in life, and whose broad function is unknown. A member of TIGR03722 has been characterized as a DNA-binding protein with apurinic endopeptidase activity. In contrast, the rare characterized members of the present family show O-sialoglycoprotein endopeptidase (EC. 3.4.24.57) activity after export. These include glycoprotease (gcp) from Pasteurella haemolytica A1 and a cohemolysin from Riemerella anatipestifer (GB|AAG39646.1). The member from Staphylococcus aureus is essential and is related to cell wall dynamics and the modulation of autolysis, but members are also found in the Mycoplasmas (which lack a cell wall). A reasonable hypothesis is that virulence-related activities after export are secondary to a bacterial domain-wide unknown function. [Protein synthesis, tRNA and rRNA base modification] 313 matched cddid_all.tbl CDD TIGR03724 TIGR03724 274749 arch_bud32 Kae1-associated kinase Bud32. Members of this protein family are the Bud32 protein associated with Kae1 (kinase-associated endopeptidase 1) in the Archaea. In many Archaeal genomes, Kae1 and Bud32 are fused. The complex is homologous to the Kae1 and Bud32 subunits of the eukaryotic KEOPS complex, an apparently ancient protein kinase-containing molecular machine. [Unknown function, General] 199 matched cddid_all.tbl CDD TIGR03725 TIGR03725 274750 T6A_YeaZ tRNA threonylcarbamoyl adenosine modification protein YeaZ. This family describes a protein family, YeaZ, now associated with the threonylcarbamoyl adenosine (t6A) tRNA modification. Members of this family may occur as fusions with ygjD (previously gcp) or the ribosomal protein N-acetyltransferase rimI, and is frequently encoded next to rimI. [Protein synthesis, tRNA and rRNA base modification] 204 matched cddid_all.tbl CDD TIGR03726 TIGR03726 274751 strep_RK_lipo putative cross-wall-targeting lipoprotein signal. The YSIRK signal domain targets proteins to the cross-wall, or septum, of dividing Gram-positive bacterial. Lipoprotein signal motifs direct a characteristic N-terminal cleavage and lipid modification for membrane anchoring. This Streptococcal-only signal peptide variant appears to be a hybrid between the two, likely directing protein targeting of nascent surface lipoproteins to the cross-wall. Nearly all members of this family have the characteristic LPXTG cell wall anchor signal at the C-terminus. 34 matched cddid_all.tbl CDD TIGR03727 TIGR03727 274752 urea_t_UrtC_arc urea ABC transporter, permease protein UrtC, archaeal type. Members of this protein family are ABC transporter permease subunits restricted to the Archaea. Several lines of evidence suggest this protein is functionally analogous, as well as homologous, to the UrtC subunit of the Corynebacterium glutamicum urea transporter. All members of the operon show sequence similarity to urea transport subunits, the gene is located near the urease structural subunits in two of three species, and partial phylogenetic profiling identifies this permease subunit as closely matching the profile of urea utilization. 369 matched cddid_all.tbl CDD TIGR03728 TIGR03728 163440 glyco_access_1 glycosyltransferase, SP_1767 family. Members of this protein family are putative glycosyltransferases. Some members are found close to genes for the accessory secretory (SecA2) system, and are suggested by Partial Phylogenetic Profiling to correlate with SecA2 systems. Glycosylation, therefore, may occur in the cytosol prior to secretion. 265 matched cddid_all.tbl CDD TIGR03729 TIGR03729 163441 acc_ester putative phosphoesterase. Members of this protein family belong to the larger family pfam00149 (calcineurin-like phosphoesterase), a family largely defined by small motifs of metal-chelating residues. The subfamily in this model shows a good but imperfect co-occurrence in species with domain TIGR03715 that defines a novel class of signal peptide typical of the accessory secretory system. 239 matched cddid_all.tbl CDD TIGR03730 TIGR03730 163442 tungstate_WtpA tungstate ABC transporter binding protein WtpA. Members of this protein family are tungstate (and, more weakly, molybdate) binding proteins of tungstate(/molybdate) ABC transporters, as first characterized in Pyrococcus furiosus. Model seed members and cutoffs, pending experimental evidence for more distant homologs, were chosen such that this model identifies select archaeal proteins, excluding weaker archaeal and all bacterial homologs. Note that this family is homologous to molybdate transporters, and that at least one other family of tungstate transporter binding protein, TupA, also exists. 273 matched cddid_all.tbl CDD TIGR03731 TIGR03731 274753 lantibio_gallid lantibiotic, gallidermin/nisin family. Members of this family are lantibiotic precursors in the family that includes gallidermin, nisin, mutacin, epidermin, and streptin. [Cellular processes, Toxin production and resistance] 48 matched cddid_all.tbl CDD TIGR03732 TIGR03732 274754 lanti_perm_MutE lantibiotic protection ABC transporter permease subunit, MutE/EpiE family. Model TIGR03731 represents the family of all lantibiotics related to gallidermin, including epidermin, mutatin, and nisin. This protein family is largely restricted to gallidermin-family lantibiotic cassettes, but also include orphan transporter cassettes in species that lack candidate lantibiotic precursor and synthetase genes. In most species, this subunit is paralogous to an adjacent gene, modeled separately. 241 matched cddid_all.tbl CDD TIGR03733 TIGR03733 163445 lanti_perm_MutG lantibiotic protection ABC transporter permease subunit, MutG family. Model TIGR03731 represents the family of all lantibiotics related to gallidermin, including epidermin, mutatin, and nisin. This protein family is largely restricted to gallidermin-family lantibiotic cassettes, but also include orphan transporter cassettes in species that lack candidate lantibiotic precursor and synthetase genes. In most species, this subunit is paralogous to an adjacent gene modeled separate by TIGR03732, while in some species only one subunit is found. 248 matched cddid_all.tbl CDD TIGR03734 TIGR03734 274755 PRTRC_parB PRTRC system ParB family protein. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family the member related to ParB, and is designated PRTRC system ParB family protein. 554 matched cddid_all.tbl CDD TIGR03735 TIGR03735 163447 PRTRC_A PRTRC system protein A. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated protein A. 192 matched cddid_all.tbl CDD TIGR03736 TIGR03736 163448 PRTRC_ThiF PRTRC system ThiF family protein. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. This family is the PRTRC system ThiF family protein. 244 matched cddid_all.tbl CDD TIGR03737 TIGR03737 274756 PRTRC_B PRTRC system protein B. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. This protein family is designated protein B. 228 matched cddid_all.tbl CDD TIGR03738 TIGR03738 163450 PRTRC_C PRTRC system protein C. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated PRTRC system protein C. 66 matched cddid_all.tbl CDD TIGR03739 TIGR03739 274757 PRTRC_D PRTRC system protein D. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated PRTRC system protein D. The gray zone, between trusted and noise, includes proteins found in the same genomes as other proteins of the PRTRC systems, but not in the same contiguous gene region. 320 matched cddid_all.tbl CDD TIGR03740 TIGR03740 163452 galliderm_ABC gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit. Model TIGR03731 represents the family of all lantibiotics related to gallidermin, including epidermin, mutatin, and nisin. This protein family describes the ATP-binding subunit of a gallidermin/epidermin class lantibiotic protection transporter. It is largely restricted to gallidermin-family lantibiotic biosynthesis and export cassettes, but also occurs in orphan transporter cassettes in species that lack candidate lantibiotic precursor and synthetase genes. 223 matched cddid_all.tbl CDD TIGR03741 TIGR03741 274758 PRTRC_E PRTRC system protein E. A novel genetic system characterized by six or seven major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family averages about 150 amino acids in length, but the last third contains low-complexity sequence that complicates sequence comparisons. This model does not include the low-complexity region. 104 matched cddid_all.tbl CDD TIGR03742 TIGR03742 274759 PRTRC_F PRTRC system protein F. A novel genetic system characterized by seven (usually) major proteins, including a ParB homolog and a ThiF homolog, is commonly found on plasmids or in bacterial chromosomal regions near phage, plasmid, or transposon markers. It is most common among the beta Proteobacteria. We designate the system PRTRC, or ParB-Related,ThiF-Related Cassette. This protein family is designated protein F. It is the most divergent of the families. 342 matched cddid_all.tbl CDD TIGR03743 TIGR03743 274760 SXT_TraD conjugative coupling factor TraD, SXT/TOL subfamily. Members of this protein family are the putative conjugative coupling factor, TraD (or TraG), rather distantly related to the well-characterized TraD of the F plasmid. Members are associated with conjugative-transposon-like mobile genetic elements of the class that includes SXT, an antibiotic resistance transfer element in some Vibrio cholerae strains. [Mobile and extrachromosomal element functions, Other] 634 matched cddid_all.tbl CDD TIGR03744 TIGR03744 274761 traC_PFL_4706 conjugative transfer ATPase, PFL_4706 family. Members of this protein family are predicted ATP-binding proteins apparently associated with DNA conjugal transfer. Members are found both in plasmids and in bacterial chromosomal regions that appear to derive from integrative elements such as conjugative transposons. More distant homologs, outside the scope of this family, include type IV secretion/conjugal transfer proteins such as TraC, VirB4 and TrsE. The granularity of this protein family definition is chosen so as to represent one distinctive clade and act as a marker through which to define and recognize the class of mobile element it serves. [Mobile and extrachromosomal element functions, Plasmid functions] 893 matched cddid_all.tbl CDD TIGR03745 TIGR03745 274762 conj_TIGR03745 integrating conjugative element membrane protein, PFL_4702 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in a region flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions] 105 matched cddid_all.tbl CDD TIGR03746 TIGR03746 163458 conj_TIGR03746 integrating conjugative element protein, PFL_4703 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. The function is unknown. [Mobile and extrachromosomal element functions, Plasmid functions] 202 matched cddid_all.tbl CDD TIGR03747 TIGR03747 163459 conj_TIGR03747 integrating conjugative element membrane protein, PFL_4697 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions] 233 matched cddid_all.tbl CDD TIGR03748 TIGR03748 163460 conj_PilL conjugative transfer region protein, TIGR03748 family. This model describes the conserved N-terminal region of a variable length protein family associated with laterally transfered regions flanked by markers of conjugative plasmid integration and/or transposition. Most members of the family have the lipoprotein signal peptide motif. A member of the family from a pathogenicity island in Salmonella enterica serovar Dublin strain was designated PilL for nomenclature consistency with a neighboring gene for the pilin structural protein PilS. However, the species distribution of this protein family tracks much better with markers of conjugal transfer than with markers of PilS-like pilin structure. [Mobile and extrachromosomal element functions, Plasmid functions] 105 matched cddid_all.tbl CDD TIGR03749 TIGR03749 163461 conj_TIGR03749 integrating conjugative element protein, PFL_4704 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in a region flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions] 257 matched cddid_all.tbl CDD TIGR03750 TIGR03750 274763 conj_TIGR03750 conjugative transfer region protein, TIGR03750 family. Members of this protein family are found occasionally on plasmids. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions] 111 matched cddid_all.tbl CDD TIGR03751 TIGR03751 274764 conj_TIGR03751 conjugative transfer region lipoprotein, TIGR03751 family. Members of this protein family are found occasionally on plasmids. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions] 124 matched cddid_all.tbl CDD TIGR03752 TIGR03752 274765 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions] 472 matched cddid_all.tbl CDD TIGR03753 TIGR03753 274766 blh_monoox beta-carotene 15,15'-monooxygenase, Brp/Blh family. This integral membrane protein family includes Brp (bacterio-opsin related protein) and Blh (Brp-like protein). Bacteriorhodopsin is a light-driven proton pump with a covalently bound retinal cofactor that appears to be derived beta-carotene. Blh has been shown to cleave beta-carotene to product two all-trans retinal molecules. Mammalian enzymes with similar enzymatic function are not multiple membrane spanning proteins and are not homologous. 259 matched cddid_all.tbl CDD TIGR03754 TIGR03754 274767 conj_TOL_TraD conjugative coupling factor TraD, TOL family. Members of this protein are assigned by homology to the TraD family of conjugative coupling factor. This particular clade serves as a marker for an extended gene region that occurs occasionally on plasmids, including the toluene catabolism TOL plasmid. More commonly, the gene region is chromosomal, flanked by various markers of conjugative transfer and insertion. 643 matched cddid_all.tbl CDD TIGR03755 TIGR03755 274768 conj_TIGR03755 integrating conjugative element protein, PFL_4711 family. Members of this protein family are found in genomic regions associated with conjugative transfer and integrated TOL-like plasmids. The specific function is unknown. [Mobile and extrachromosomal element functions, Plasmid functions] 418 matched cddid_all.tbl CDD TIGR03756 TIGR03756 274769 conj_TIGR03756 integrating conjugative element protein, PFL_4710 family. Members of this protein family are found in genomic regions associated with conjugative transfer and integrated TOL-like plasmids. The specific function is unknown. [Mobile and extrachromosomal element functions, Plasmid functions] 297 matched cddid_all.tbl CDD TIGR03757 TIGR03757 163469 conj_TIGR03757 integrating conjugative element protein, PFL_4709 family. Members of this protein belong to extended genomic regions that appear to be spread by conjugative transfer. [Mobile and extrachromosomal element functions, Plasmid functions] 113 matched cddid_all.tbl CDD TIGR03758 TIGR03758 163470 conj_TIGR03758 integrating conjugative element protein, PFL_4701 family. Members of this family of small, hydrophobic proteins are found occasionally on plasmids such as the Pseudomonas putida TOL (toluene catabolic) plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition. [Mobile and extrachromosomal element functions, Plasmid functions] 65 matched cddid_all.tbl CDD TIGR03759 TIGR03759 274770 conj_TIGR03759 integrating conjugative element protein, PFL_4693 family. Members of this protein family, such as model protein PFL_4693 from Pseudomonas fluorescens Pf-5, belong to extended genomic regions that appear to be spread by conjugative transfer. Most members have a predicted N-terminal signal sequence. The function is unknown. [Mobile and extrachromosomal element functions, Plasmid functions] 200 matched cddid_all.tbl CDD TIGR03760 TIGR03760 163472 ICE_TraI_Pfluor integrating conjugative element relaxase, PFL_4751 family. Members of this protein family are the TraI putative relaxases required for transfer by a subclass of integrating conjugative elements (ICE) as found in Pseudomonas fluorescens Pf-5, and understood from study of two related ICE, SXT and R391. This model represents the N-terminal domain. Note that no homology is detected to the similarly named TraI relaxase of the F plasmid. 218 matched cddid_all.tbl CDD TIGR03761 TIGR03761 274771 ICE_PFL4669 integrating conjugative element protein, PFL_4669 family. Members of this protein family, such as PFL4669, are found in integrating conjugative elements (ICE) of the PFGI-1 class as in Pseudomonas fluorescens. 216 matched cddid_all.tbl CDD TIGR03762 TIGR03762 274772 archaeo_artC archaeosortase C, PEF-CTERM variant. Members of this family are archaeal homologs to bacterial PEP-CTERM-sorting protein exosortase (TIGR02602). Members of this family are found in species with an archaeal variant sorting motif, PEF-CTERM (TIGR03024). Members are found in the thermoacidophilic Aciduliprofundum boonei, the mesophilic psychromethanogens Methanosarcina mazei and Methanococcoides burtonii, and in Ferroglobus placidus DSM 10642. [Protein fate, Protein and peptide secretion and trafficking] 274 matched cddid_all.tbl CDD TIGR03763 TIGR03763 163475 cyanoexo_CrtA cyanoexosortase A. The predicted protein-sorting transpeptidase that we call exosortase (see TIGR02602) has distinct subclasses that associated with different types of exopolysaccharide production loci and/or different taxonomic lineages. We designate this relatively divergent cyanobacterial type to be type 3. We propose the gene symbol xrtC. This type coexists with a TIGR02602-recognized form in Nostoc sp. PCC 7120. [Protein fate, Protein and peptide secretion and trafficking] 260 matched cddid_all.tbl CDD TIGR03764 TIGR03764 213858 ICE_PFGI_1_parB integrating conjugative element, PFGI_1 class, ParB family protein. Members of this protein family carry the ParB-type nuclease domain and are found in integrating conjugative elements (ICE) in the same class as PFGI-1 of Pseudomonas fluorescens Pf-5. 258 matched cddid_all.tbl CDD TIGR03765 TIGR03765 274773 ICE_PFL_4695 integrating conjugative element protein, PFL_4695 family. This model describes a protein family exemplified by PFL_4695 of Pseudomonas fluorescens Pf-5. Full-length proteins in this family show some architectural variety, but this model represents a conserved domain. Most or all member proteins belong to laterally transferred chromosomal islands called integrative conjugative elements, or ICE. 105 matched cddid_all.tbl CDD TIGR03766 TIGR03766 274774 TIGR03766 conserved hypothetical integral membrane protein. Models TIGR03110, TIGR03111, and TIGR03112 describe a three-gene system found in several Gram-positive bacteria, where TIGR03110 (XrtG) is distantly related to a putative transpeptidase, exosortase (TIGR02602). This model describes a small clade that correlates by both gene clustering and phyletic pattern, although imperfectly, to the three gene system. Both this narrow clade, and the larger set of full-length homologous integral membrane proteins, have an especially well-conserved region near the C-terminus with an invariant tyrosine. The function is unknown. 483 matched cddid_all.tbl CDD TIGR03767 TIGR03767 213859 P_acnes_RR metallophosphoesterase, PPA1498 family. This model describes a small collection of probable metallophosphoresterases, related to pfam00149 but with long inserts separating some of the shared motifs such that the homology is apparent only through multiple sequence alignment. Members of this protein family, in general, have a Sec-independent TAT (twin-arginine translocation) signal sequence, N-terminal to the region represented by this model. Members include YP_056203.1 from Propionibacterium acnes KPA171202. 496 matched cddid_all.tbl CDD TIGR03768 TIGR03768 163480 RPA4764 metallophosphoesterase, RPA4764 family. This model describes a small collection of probable metallophosphoresterases, related to pfam00149. Members of this protein family usually have a Sec-independent TAT (twin-arginine translocation) signal sequence, N-terminal to the region represented by this model. This model and TIGR03767 divide a narrow clade of pfam00149-related enzymes. 492 matched cddid_all.tbl CDD TIGR03769 TIGR03769 274775 P_ac_wall_RPT actinobacterial surface-anchored protein domain. This model describes a repeat domain that one to three times in Actinobacterial proteins, some of which have LPXTG-type sortase recognition motifs for covalent attachment to the Gram-positive cell wall. Where it occurs with duplication in an LPXTG-anchored protein, it tends to be adjacent to the substrate-binding protein of the gene trio of an ABC transporter system, where that substrate-binding protein has a single copy of this same domain. This arrangement suggests a substrate-binding relay system, with the LPXTG protein acting as a substrate receptor. 41 matched cddid_all.tbl CDD TIGR03770 TIGR03770 163482 anch_rpt_perm anchored repeat-type ABC transporter, permease subunit. This protein family is the permease subunit of binding protein-dependent ABC transporter complex that strictly co-occurs with TIGR03769. TIGRFAMs model TIGR03769 describes a protein domain that occurs singly or as one of up to three repeats in proteins of a number of Actinobacteria, including Propionibacterium acnes KPA171202. The TIGR03769 domain occurs both in the adjacent gene for the substrate-binding protein and in additional (often nearby) proteins, often with LPXTG-like sortase recognition signals. Homologous permease subunits outside the scope of this family include manganese transporter MntB in Synechocystis sp. PCC 6803 and chelated iron transporter subunits. The function of this transporter complex is unknown. [Transport and binding proteins, Unknown substrate] 270 matched cddid_all.tbl CDD TIGR03771 TIGR03771 163483 anch_rpt_ABC anchored repeat-type ABC transporter, ATP-binding subunit. This protein family is the ATP-binding cassette subunit of binding protein-dependent ABC transporter complex that strictly co-occurs with TIGR03769. TIGRFAMs model TIGR03769 describes a protein domain that occurs singly or as one of up to three repeats in proteins of a number of Actinobacteria, including Propionibacterium acnes KPA171202. The TIGR03769 domain occurs both in an adjacent gene for the substrate-binding protein and in additional (often nearby) proteins, often with LPXTG-like sortase recognition signals. Homologous ATP-binding subunits outside the scope of this family include manganese transporter MntA in Synechocystis sp. PCC 6803 and chelated iron transporter subunits. The function of this transporter complex is unknown. [Transport and binding proteins, Unknown substrate] 223 matched cddid_all.tbl CDD TIGR03772 TIGR03772 163484 anch_rpt_subst anchored repeat ABC transporter, substrate-binding protein. Members of this protein family are ABC transporter permease subunits as identified by pfam00950, but additionally contain the Actinobacterial insert domain described by TIGR03769. Some homologs (lacking the insert) have been described as transporters of manganese or of chelated iron. Members of this family typically are found along with an ATP-binding cassette protein, a permease, and an LPXTG-anchored protein with two or three copies of the TIGR03769 insert that occurs just once in this protein family. [Transport and binding proteins, Unknown substrate] 479 matched cddid_all.tbl CDD TIGR03773 TIGR03773 274776 anch_rpt_wall putative ABC transporter-associated repeat protein. Members of this protein family occur in genomes that contain a three-gene ABC transporter operon associated with the presence of domain TIGR03769. That domain occurs as a single-copy insert in the substrate-binding protein, and occurs in two or more copies in members of this protein family. Members of this family typically are encoded adjacent to the said transporter operon and may serve as a substrate receptor. 513 matched cddid_all.tbl CDD TIGR03774 TIGR03774 163486 RPE2 Rickettsial palindromic element RPE2 domain. This model describes protein translations of a second family, RPE2, of Rickettsia palindromic elements (RPE). The elements spread within a genome as selfish genetic elements, inserting into genes additional coding regions that does not disrupt the reading frame. This model finds RPE-encoded regions in several Rickettsial species and, so far, no where else. 35 matched cddid_all.tbl CDD TIGR03775 TIGR03775 163487 RPE3 Rickettsial palindromic element RPE3 domain. This model describes protein translations of a second family, RPE3, of Rickettsia palindromic elements (RPE). The elements spread within a genome as selfish genetic elements, inserting into genes additional coding regions that does not disrupt the reading frame. This model finds RPE-encoded regions in several Rickettsial species and, so far, no where else. 43 matched cddid_all.tbl CDD TIGR03776 TIGR03776 163488 RPE5 Rickettsial palindromic element RPE5 domain. This model describes protein translations of a family, RPE5, of Rickettsia palindromic elements (RPE). The elements spread within a genome as selfish genetic elements, inserting into genes additional coding region that does not disrupt the reading frame. This model finds RPE-encoded regions in several Rickettsial species and, so far, no where else. 43 matched cddid_all.tbl CDD TIGR03777 TIGR03777 274777 RPE4 Rickettsial palindromic element RPE4 domain. This model describes protein translations of a family, RPE4, of Rickettsia palindromic elements (RPE). The elements spread within a genome as selfish genetic elements, inserting into genes additional coding region that does not disrupt the reading frame. This model finds RPE-encoded regions in several Rickettsial species and, so far, no where else. 32 matched cddid_all.tbl CDD TIGR03778 TIGR03778 274778 VPDSG_CTERM VPDSG-CTERM protein sorting domain. Through in silico analysis, we previously described the PEP-CTERM/exosortase system (). This model describes a PEP-CTERM-like variant C-terminal protein sorting signal, as found at the C-terminus of twenty otherwise unrelated proteins in Verrucomicrobiae bacterium DG1235. The variant motif, VPDSG, seems an intermediate between the VPEP motif (TIGR02595) of typical exosortase systems and the classical LPXTG of sortase in Gram-positive bacteria. 24 matched cddid_all.tbl CDD TIGR03779 TIGR03779 274779 Bac_Flav_CT_M Bacteroides conjugative transposon TraM protein. Members of this protein family are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage. [Cellular processes, DNA transformation] 410 matched cddid_all.tbl CDD TIGR03780 TIGR03780 163492 Bac_Flav_CT_N Bacteroides conjugative transposon TraN protein. Members of this family are the TraN protein encoded by transfer region genes of conjugative transposons of Bacteroides. The family is related to conjugative transfer proteins VirB9 and TrbG of Agrobacterium Ti plasmids. [Cellular processes, DNA transformation] 285 matched cddid_all.tbl CDD TIGR03781 TIGR03781 200324 Bac_Flav_CT_K Bacteroides conjugative transposon TraK protein. Members of this protein family are designated TraK and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage. PSI-BLAST reveals a distant relationship to proteins TrbF and VirB8 in Proteobacterial conjugal transfer systems. [Cellular processes, DNA transformation] 202 matched cddid_all.tbl CDD TIGR03782 TIGR03782 274780 Bac_Flav_CT_J Bacteroides conjugative transposon TraJ protein. Members of this protein family are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage. This family is related conjugation system proteins in the Proteobacteria, including TrbL of Agrobacterium Ti plasmids and VirB6. [Cellular processes, DNA transformation] 323 matched cddid_all.tbl CDD TIGR03783 TIGR03783 163495 Bac_Flav_CT_G Bacteroides conjugation system ATPase, TraG family. Members of this family include the predicted ATPase, TraG, encoded by transfer region genes of conjugative transposons of Bacteroides, such as CTnDOT, found on the main chromosome. Members also include TraG homologs borne on plasmids in Bacteroides. The protein family is related to the conjugative transfer system ATPase VirB4. [Cellular processes, DNA transformation] 829 matched cddid_all.tbl CDD TIGR03784 TIGR03784 163496 marine_sortase sortase, marine proteobacterial type. Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with a Vault protein inter-alpha-trypsin domain (pfam08487) and a von Willebrand factor type A domain (pfam00092), encoded by an adjacent gene. These sortases are designated subfamily 6 according to Comfort and Clubb (2004). 174 matched cddid_all.tbl CDD TIGR03785 TIGR03785 163497 marine_sort_HK proteobacterial dedicated sortase system histidine kinase. This histidine kinase protein is paired with an adjacent response regulator (TIGR03787) gene. It co-occurs with a variant sortase enzyme (TIGR03784), usually in the same gene neighborhood, in proteobacterial species most of which are marine, and with an LPXTG motif-containing sortase target conserved protein (TIGR03788). Sortases and LPXTG proteins are far more common in Gram-positive bacteria, where sortase systems mediate attachment to the cell wall or cross-linking of pilin structures. We give this predicted sensor histidine kinase the gene symbol psdS, for Proteobacterial Dedicated Sortase system Sensor histidine kinase. 703 matched cddid_all.tbl CDD TIGR03786 TIGR03786 274781 strep_pil_rpt streptococcal pilin isopeptide linkage domain. This model describes a domain that occurs once in the major pilin of Streptococcus pyogenes, Spy0128, but in higher copy numbers in other streptococcal proteins. The domain occurs nine times in a surface-anchored protein of Bifidobacterium longum. All members of this family have LPXTG-type sortase target sequences. The S. pyogenes major pilin has been shown to undergo isopeptide bond cross-linking, mediated by sortases, that are critical to maintaining pilus structural integrity. One such Lys-to-Asn isopeptide bond is to a near-invariant Asn near the C-terminal end of this domain (column 81 of the seed alignment). A Glu in the S. pyogenes major pilin (column 25 of the seed alignment), invariant as Glu or Gln, is described as catalytic for isopeptide bond formation. 63 matched cddid_all.tbl CDD TIGR03787 TIGR03787 163499 marine_sort_RR proteobacterial dedicated sortase system response regulator. This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator. 227 matched cddid_all.tbl CDD TIGR03788 TIGR03788 274782 marine_srt_targ marine proteobacterial sortase target protein. Members of this protein family are restricted to the Proteobacteria. Each contains a C-terminal sortase-recognition motif, transmembrane domain, and basic residues cluster at the the C-terminus, and is encoded adjacent to a sortase gene. This protein is frequently the only sortase target in its genome, which is as unusual its occurrence in Gram-negative rather than Gram-positive genomes. Many bacteria with this system are marine. In addition to the LPXTG signal, members carry a vault protein inter-alpha-trypsin inhibitor domain (pfam08487) and a von Willebrand factor type A domain (pfam00092). 596 matched cddid_all.tbl CDD TIGR03789 TIGR03789 274783 pdsO proteobacterial sortase system peptidoglycan-associated protein. A newly defined histidine kinase (TIGR03785) and response regulator (TIGR03787) gene pair occurs exclusively in Proteobacteria, mostly of marine origin, nearly all of which contain a subfamily 6 sortase (TIGR03784) and its single dedicated target protein (TIGR03788) adjacent to to the sortase. This protein family shows up in only in those species with the histidine kinase/response regulator gene pair, and often adjacent to that pair. It belongs to the pfam00691 domain family, which is the peptidoglycan-associated region of flagellar motor protein MotB, OmpA (whose N-terminal region forms an outer membrane beta barrel), and peptidoglycan-associated lipoprotein Pal. Its function is unknown. We assign the gene symbol pdsO, for Proteobacterial Dedicated Sortase system OmpA family protein. [Protein fate, Protein and peptide secretion and trafficking] 243 matched cddid_all.tbl CDD TIGR03790 TIGR03790 274784 TIGR03790 TIGR03790 family protein. Despite a broad and sporadic distribution (Cyanobacteria, Verrucomicrobia, Acidobacteria, beta and delta Proteobacteria, and Planctomycetes), this uncharacterized protein family occurs only among the roughly 8 percent of prokarotyic species that carry homologs of the integral membrane protein exosortase (see TIGR02602), a proposed protein-sorting system transpeptidase. 322 matched cddid_all.tbl CDD TIGR03791 TIGR03791 163503 TTQ_mauG tryptophan tryptophylquinone biosynthesis enzyme MauG. Members of this protein family are the tryptophan tryptophylquinone biosynthesis (TTQ) enzyme MauG, as found in Methylobacterium extorquens and related species. This protein is required to complete the maturation of the TTQ cofactor in the methylamine dehydrogenase light (beta) chain. 291 matched cddid_all.tbl CDD TIGR03792 TIGR03792 274785 TIGR03792 uncharacterized cyanobacterial protein, TIGR03792 family. Members of this family are found, no more than one to a genome, exclusively in (but not universal to) the Cyanobacteria. These proteins are small, 100-150 amino acids. The function is unknown. [Unknown function, General] 90 matched cddid_all.tbl CDD TIGR03793 TIGR03793 274786 TOMM_pelo NHLP leader peptide domain. This model represents a domain that is conserved among a large number of putative ribosomal natural products (RNP) precursor, including the thiazole/oxazole-modified microcins (TOMMs). As a leader peptide domain, likely to be removed from the mature product, this domain is unusual in several ways. First, it is longer than most previously described RNP leader peptides. Second, most of the domain is homologous to nitrile hydratase alpha subunits. Finally, it appears that this domain correlates with a specific family of cleavage/export proteins while members undergo modifications by different classes of peptide maturase, including cyclodehydratases, lantibiotic synthases, radical SAM peptide maturases. This family is expanded especially in Pelotomaculum thermopropionicum SI. [Cellular processes, Biosynthesis of natural products] 77 matched cddid_all.tbl CDD TIGR03794 TIGR03794 274787 NHLM_micro_HlyD NHLM bacteriocin system secretion protein. Members of this protein family are homologs of the HlyD membrane fusion protein of type I secretion systems. Their occurrence in prokaryotic genomes is associated with the occurrence of a novel class of microcin (small bacteriocins) with a leader peptide region related to nitrile hydratase. We designate the class of bacteriocin as Nitrile Hydratase Leader Microcin, or NHLM. This family, therefore, is designated as NHLM bacteriocin system secretion protein. Some but not all NHLM-class putative microcins belong to the TOMM (thiazole/oxazole modified microcin) class as assessed by the presence of the scaffolding protein and/or cyclodehydratase in the same gene clusters. [Transport and binding proteins, Amino acids, peptides and amines, Cellular processes, Biosynthesis of natural products] 421 matched cddid_all.tbl CDD TIGR03795 TIGR03795 163507 RNP_Burkhold ribosomal natural product, two-chain TOMM family. Members of this protein family are found sparsely, mostly in members of the genus Burkholderia. Members often occur as tandem homologous genes, such as BMA_0021 and BMA_0022 in Burkholderia mallei ATCC 23344, or else have a duplication. The genes regularly are encoded near a cyclodehydrogenase/docking protein fusion protein of TOMM (thiazole/oxazole-modified microcins) biosynthetic clusters, suggesting a role in bacteriocin biosynthesis. The role of the putative natural product is unknown, but function as a two-chain bacteriocin is suggested. [Cellular processes, Biosynthesis of natural products] 114 matched cddid_all.tbl CDD TIGR03796 TIGR03796 274788 NHLM_micro_ABC1 NHLM bacteriocin system ABC transporter, peptidase/ATP-binding protein. This protein describes a multidomain ABC transporter subunit that is one of three protein families associated with some regularity with a distinctive family of putative bacteriocins. It includes a bacteriocin-processing peptidase domain at the N-terminus. Model TIGR03793 describes a conserved propeptide region for this bacteriocin family, unusual because it shows obvious homology a region of the enzyme nitrile hydratase up to the classic Gly-Gly cleavage motif. This family is therefore predicted to be a subunit of a bacteriocin processing and export system characteristic to this system that we designate NHLM, Nitrile Hydratase Leader Microcin. [Transport and binding proteins, Amino acids, peptides and amines, Cellular processes, Biosynthesis of natural products] 710 matched cddid_all.tbl CDD TIGR03797 TIGR03797 274789 NHLM_micro_ABC2 NHLM bacteriocin system ABC transporter, ATP-binding protein. Members of this protein family are ABC transporter ATP-binding subunits, part of a three-gene putative bacteriocin transport operon. The other subunits include another ATP-binding subunit (TIGR03796), which has an N-terminal leader sequence cleavage domain, and an HlyD homolog (TIGR03794). In a number of genomes, members of protein families related to nitrile hydratase alpha subunit or to nif11 have undergone paralogous family expansions, with members possessing a putative bacteriocin cleavage region ending with a classic Gly-Gly motif. Those sets of putative bacteriocins, members of this protein family and its partners TIGR03794 and TIGR03796, and cyclodehydratase/docking scaffold fusion proteins of thiazole/oxazole biosynthesis frequently show correlated species distribution and co-clustering within many of those genomes. [Transport and binding proteins, Amino acids, peptides and amines, Cellular processes, Biosynthesis of natural products] 686 matched cddid_all.tbl CDD TIGR03798 TIGR03798 274790 ocin_TIGR03798 nif11-like leader peptide domain. This model describes a conserved, fairly long (about 65 residue) leader peptide region for a family of putative ribosomal natural products (RNP) of small size. Members of the seed alignment tend to have the Gly-Gly motif as the last two residues of the matched region. This is a cleavage site for a combination processing/export ABC transporter with a peptidase domain. Members include the prochlorosins, lantipeptides from Prochlorococcus. [Cellular processes, Biosynthesis of natural products] 64 matched cddid_all.tbl CDD TIGR03799 TIGR03799 274791 NOD_PanD_pyr putative pyridoxal-dependent aspartate 1-decarboxylase. This enzyme is proposed here to be a form of aspartate 1-decarboxylase, pyridoxal-dependent, that represents a non-orthologous displacement to the more widely distributed pyruvoyl-dependent form (TIGR00223). Aspartate 1-decarboxylase makes beta-alanine, used usually in pathothenate biosynthesis, by decarboxylation from asparatate. A number of species with the PanB and PanC enzymes, however, lack PanD. This protein family occurs in a number of Proteobacteria that lack PanD. This enzyme family appears to be a pyridoxal-dependent enzyme (see pfam00282). The family was identified by Partial Phylogenetic Profiling; members in Geobacter sulfurreducens, G. metallireducens, and Pseudoalteromonas atlantica are clustered with the genes for PanB and PanC. We suggest the gene symbol panP (panthothenate biosynthesis enzyme, Pyridoxal-dependent). [Biosynthesis of cofactors, prosthetic groups, and carriers, Pantothenate and coenzyme A] 522 matched cddid_all.tbl CDD TIGR03800 TIGR03800 274792 PLP_synth_Pdx2 pyridoxal 5'-phosphate synthase, glutaminase subunit Pdx2. Pyridoxal 5'-phosphate (PLP) is synthesized by the PdxA/PdxJ pathway in some species (mostly within the gamma subdivision of the proteobacteria) and by the Pdx1/Pdx2 pathway in most other organisms. This family describes Pdx2, the glutaminase subunit of the PLP synthase. [Biosynthesis of cofactors, prosthetic groups, and carriers, Pyridoxine] 184 matched cddid_all.tbl CDD TIGR03801 TIGR03801 163513 asp_4_decarbox aspartate 4-decarboxylase. This enzyme, aspartate 4-decarboxylase (EC 4.1.1.12), removes the side-chain carboxylate from L-aspartate, converting it to L-alanine plus carbon dioxide. It is a PLP-dependent enzyme, homologous to aspartate aminotransferase (EC 2.6.1.1). [Energy metabolism, Amino acids and amines] 521 matched cddid_all.tbl CDD TIGR03802 TIGR03802 274793 Asp_Ala_antiprt aspartate-alanine antiporter. All members of the seed alignment for this model are asparate-alanine anti-transporters (AspT) encoded next to the gene for aspartate 4-decarboxylase (AspD), which converts asparate to alanine, releasing CO2. The exchange of Asp for Ala is electrogenic, so the AspD/AspT system confers a proton-motive force. This transporter contains two copies of the AspT/YidE/YbjL antiporter duplication domain (TIGR01625). 562 matched cddid_all.tbl CDD TIGR03803 TIGR03803 274794 Gloeo_Verruco Gloeo_Verruco repeat. This model describes a rare protein repeat, found so far in two species of Verrucomicrobia (Chthoniobacter flavus and Verrucomicrobium spinosum) and in four different proteins of Gloeobacter violaceus PCC7421. In the Verrucomicrobial species, the repeat region is followed by a PEP-CTERM protein-sorting signal, suggesting an extracellular location. 34 matched cddid_all.tbl CDD TIGR03804 TIGR03804 274795 para_beta_helix parallel beta-helix repeat (two copies). This model represents a tandem pair of an approximately 22-amino acid (each) repeat homologous to the beta-strand repeats that stack in a right-handed parallel beta-helix in the periplasmic C-5 mannuronan epimerase, AlgA, of Pseudomonas aeruginosa. A homology domain consisting of a longer tandem array of these repeats is described in the SMART database as CASH (SM00722), and is found in many carbohydrate-binding proteins and sugar hydrolases. A single repeat is represented by SM00710. This TIGRFAMs model represents a flavor of the parallel beta-helix-forming repeat based on prokaryotic sequences only in its seed alignment, although it also finds many eukaryotic sequences. 44 matched cddid_all.tbl CDD TIGR03805 TIGR03805 163517 beta_helix_1 parallel beta-helix repeat-containing protein. Members of this protein family contain a tandem pair of beta-helix repeats (see TIGR03804). Each repeat is expected to consist of three beta strands that form a single turn as they form a right-handed helix of stacked beta-structure. Member proteinsa occur regularly in two-gene pairs along with another uncharacterized protein family; both protein families exhibit either lipoprotein or regular signal peptides, suggesting transit through the plasma membrane, and the two may be fused. The function of the pair is unknown. [Unknown function, General] 314 matched cddid_all.tbl CDD TIGR03806 TIGR03806 163518 chp_HNE_0200 conserved hypothetical protein, HNE_0200 family. The model TIGR03805 describes an uncharacterized protein family that contains repeats associated with the formation of a right-handed helical stack of parallel beta strands, homologous to those found in a number of carbohydrate-binding proteins and sugar hydrolases. This model describes another uncharacterized protein family, found in the same species as TIGR03805 member proteins, usually as the adjacent gene or in a fusion protein. An example is HNE_0200 from Hyphomonas neptunium ATCC 15444. Sometimes two members of this family are with a single member of TIGR03805. The function is unknown. [Hypothetical proteins, Conserved] 317 matched cddid_all.tbl CDD TIGR03807 TIGR03807 213864 RR_fam_repeat putative cofactor-binding repeat. This model describes a small repeat found in a family of proteins that crosses the plasma membrane by twin-arginine translation, which usually signifies the presence of a bound cofactor. This repeat shows similarity to the beta-helical repeat, in which three beta-strands per repeat wind once per repeat around in a right-handed helical stack of parallel beta structure. 27 matched cddid_all.tbl CDD TIGR03808 TIGR03808 163520 RR_plus_rpt_1 twin-arg-translocated uncharacterized repeat protein. Members of this protein family have a Sec-independent twin-arginine tranlocation (TAT) signal sequence, which enables tranfer of proteins folded around prosthetic groups to cross the plasma membrane. These proteins have four copies of a repeat of about 23 amino acids that resembles the beta-helix repeat. Beta-helix refers to a structural motif in which successive beta strands wind around to stack parallel in a right-handed helix, as in AlgG and related enzymes of carbohydrate metabolism. The twin-arginine motif suggests that members of this protein family bind some unknown cofactor. 455 matched cddid_all.tbl CDD TIGR03809 TIGR03809 163521 TIGR03809 TIGR03809 family protein. This protein family contains proteins with a median length of about 175, including a strongly conserved N-terminal region of about 55 amino acids, a conserved extreme C-terminal region of about 15 amino acids, and highly variable sequence in between the two. Members are found invariably with a member of family TIGR03808. 168 matched cddid_all.tbl CDD TIGR03810 TIGR03810 163522 arg_ornith_anti arginine-ornithine antiporter. Members of this protein family are the arginine/ornithine antiporter, ArcD. This exchanger of ornithine for arginine occurs in a system with arginine deiminase, ornithine carbamoyltransferase, and carbamate kinase, with together turn arginine to ornithine with the generation of ATP and release of CO2. [Transport and binding proteins, Amino acids, peptides and amines] 468 matched cddid_all.tbl CDD TIGR03811 TIGR03811 163523 tyr_de_CO2_Ent tyrosine decarboxylase, Enterococcus type. This model represents tyrosine decarboxylases in the family of the Enterococcus faecalis enzyme Tdc. These enzymes often are encoded next to tyrosine/tyramine antiporter, together comprising a system in which tyrosine decarboxylation can protect against exposure to acid conditions. This clade differs from the archaeal tyrosine decarboxylases associated with methanofuran biosynthesis. [Cellular processes, Adaptations to atypical conditions] 608 matched cddid_all.tbl CDD TIGR03812 TIGR03812 274796 tyr_de_CO2_Arch tyrosine decarboxylase MnfA. Members of this protein family are the archaeal form, MnfA, of tyrosine decarboxylase, and are involved in methanofuran biosynthesis. Members show clear homology to the Enterococcus form, Tdc, that is involved in tyrosine decarboxylation for resistance to acidic conditions. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 373 matched cddid_all.tbl CDD TIGR03813 TIGR03813 163525 put_Glu_GABA_T putative glutamate/gamma-aminobutyrate antiporter. Members of this protein family are putative putative glutamate/gamma-aminobutyrate antiporters. Each member of the seed alignment is found adjacent to a glutamate decarboxylase, which converts glutamate (Glu) to gamma-aminobutyrate (GABA). However, the majority belong to genome contexts with a glutaminase (converts Gln to Glu) as well as the decarboxylase that converts Glu to GABA. The specificity of the transporter remains uncertain. 474 matched cddid_all.tbl CDD TIGR03814 TIGR03814 274797 Gln_ase glutaminase A. This family describes the enzyme glutaminase, from a larger family that includes serine-dependent beta-lactamases and penicillin-binding proteins. Many bacteria have two isozymes. This model is based on selected known glutaminases and their homologs within prokaryotes, with the exclusion of highly-derived (long branch) and architecturally varied homologs, so as to achieve conservative assignments. A sharp drop in scores occurs below 250, and cutoffs are set accordingly. The enzyme converts glutamine to glutamate, with the release of ammonia. Members tend to be described as glutaminase A (glsA), where B (glsB) is unknown and may not be homologous (as in Rhizobium etli). Some species have two isozymes that may both be designated A (GlsA1 and GlsA2). [Energy metabolism, Amino acids and amines] 300 matched cddid_all.tbl CDD TIGR03815 TIGR03815 274798 CpaE_hom_Actino helicase/secretion neighborhood CpaE-like protein. Members of this protein family belong to the MinD/ParA family of P-loop NTPases, and in particular show homology to the CpaE family of pilus assembly proteins (see ). Nearly all members are found, not only in a gene context consistent with pilus biogenesis or a pilus-like secretion apparatus, but also near a DEAD/DEAH-box helicase, suggesting an involvement in DNA transfer activity. The model describes a clade restricted to the Actinobacteria. 322 matched cddid_all.tbl CDD TIGR03816 TIGR03816 274799 tadE_like_DECH helicase/secretion neighborhood TadE-like protein. Members of this small, highly hydrophobic protein family occur in a pilus/secretion-like region that usually is next to an uncharacterized DEAH-box helicase, in Actinobacteria. Members show sequence similarity to the TadE-like family described by pfam07811. The function is unknown. [Unknown function, General] 109 matched cddid_all.tbl CDD TIGR03817 TIGR03817 274800 DECH_helic helicase/secretion neighborhood putative DEAH-box helicase. A conserved gene neighborhood widely spread in the Actinobacteria contains this uncharacterized DEAH-box family helicase encoded convergently towards an operon of genes for protein homologous to type II secretion and pilus formation proteins. The context suggests that this helicase may play a role in conjugal transfer of DNA. 742 matched cddid_all.tbl CDD TIGR03818 TIGR03818 274801 MotA1 "flagellar motor stator protein MotA. The MotA protein, along with its partner MotB, comprise the stator complex of the bacterial flagellar motor. MotAB span the cytoplasmic membrane and undergo conformational changes powered by the translocation of protons. These conformational changes in turn are communicated to the rotor assembly, producing torque. This model represents one family of MotA proteins which are often not identified by the ""transporter, MotA/TolQ/ExbB proton channel family"" model, pfam01618." 282 matched cddid_all.tbl CDD TIGR03819 TIGR03819 200328 heli_sec_ATPase helicase/secretion neighborhood ATPase. Members of this protein family comprise a distinct clade of putative ATPase associated with an integral membrane complex likely to act in pilus formation, secretion, or conjugal transfer. The association of most members with a nearby gene for a DEAH-box helicase suggests a role in conjugal transfer. 340 matched cddid_all.tbl CDD TIGR03820 TIGR03820 163532 lys_2_3_AblA lysine-2,3-aminomutase. This model describes lysine-2,3-aminomutase as found along with beta-lysine acetyltransferase in a two-enzyme pathway for making the compatible solute N-epsilon-acetyl-beta-lysine. This compatible solute, or osmolyte, is known to protect a number of methanogenic archaea against salt stress. The trusted cutoff distinguishes a tight clade with essentially full-length homology from additional homologs that are shorter or highly diverged in the C-terminal region. All members of this family have the radical SAM motif CXXXCXXC, while some but not all have a second copy of the motif in the C-terminal region. 417 matched cddid_all.tbl CDD TIGR03821 TIGR03821 163533 EFP_modif_epmB EF-P beta-lysylation protein EpmB. Members of this radical SAM protein subfamily, including yjeK in E. coli, form a distinctive clade, homologous to lysine-2,3-aminomutase of Bacillus, Clostridium, and methanogenic archaea. Members of this family are found in E. coli, Buchnera, Yersinia, etc. The gene symbol is now reassigned as EpmB (Elongation factor P Modification B). [Protein fate, Protein modification and repair] 321 matched cddid_all.tbl CDD TIGR03822 TIGR03822 163534 AblA_like_2 lysine-2,3-aminomutase-related protein. Members of this protein form a distinctive clade, homologous to lysine-2,3-aminomutase (of Bacillus, Clostridium, and methanogenic archaea) and likely similar in function. Members of this family are found in Rhodopseudomonas, Caulobacter crescentus, Bradyrhizobium, etc. 321 matched cddid_all.tbl CDD TIGR03823 TIGR03823 163535 FliZ flagellar regulatory protein FliZ. FliZ is involved in the regulation of flagellar assembly and possibly also the down-regulation of the motile phenotype. FliZ interacts with the flagellar translational activator FlhCD complex. 168 matched cddid_all.tbl CDD TIGR03824 TIGR03824 274802 FlgM_jcvi flagellar biosynthesis anti-sigma factor FlgM. FlgM interacts with and inhibits the alternative sigma factor sigma(28) FliA. The C-terminus of FlgM contains the sigma(28)-binding domain. 95 matched cddid_all.tbl CDD TIGR03825 TIGR03825 274803 FliH_bacil flagellar assembly protein FliH. This bacillus clade of FliH proteins is not found by the Pfam FliH model pfam02108, but is closely related to the sequences identified by that model. Sequences identified by this model are observed in flagellar operons in an analogous position relative to other flagellar operon genes. 255 matched cddid_all.tbl CDD TIGR03826 TIGR03826 163538 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597. 137 matched cddid_all.tbl CDD TIGR03827 TIGR03827 163539 GNAT_ablB putative beta-lysine N-acetyltransferase. Members of this protein family are GNAT family acetyltransferases, based on a seed alignment in which every member is associated with a lysine 2,3-aminomutase family protein, usually as the adjacent gene. This family includes AblB, the enzyme beta-lysine acetyltransferase that completes the two-step synthesis of the osmolyte (compatible solute) N-epsilon-acetyl-beta-lysine; all members of the family may have this function. Note that N-epsilon-acetyl-beta-lysine has been observed only in methanogenic archaea (e.g. Methanosarcina) but that this model, paired with TIGR03820, suggests a much broader distribution. 266 matched cddid_all.tbl CDD TIGR03828 TIGR03828 274804 pfkB 1-phosphofructokinase. This enzyme acts in concert with the fructose-specific phosphotransferase system (PTS) which imports fructose as fructose-1-phosphate. The action of 1-phosphofructokinase results in beta-D-fructose-1,6-bisphosphate and is an entry point into glycolysis (GenProp0688). 304 matched cddid_all.tbl CDD TIGR03829 TIGR03829 163541 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context. [Unknown function, General] 89 matched cddid_all.tbl CDD TIGR03830 TIGR03830 274805 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation. 127 matched cddid_all.tbl CDD TIGR03831 TIGR03831 274806 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381. 46 matched cddid_all.tbl CDD TIGR03832 TIGR03832 163544 Tyr_2_3_mutase tyrosine 2,3-aminomutase. Members of this protein family are tyrosine 2,3-aminomutase. It is variable from member to member as to whether the (R)-beta-Tyr or (S)-beta-Tyr is the preferred product from L-Tyr. This enzyme tends to occur in secondary metabolite biosynthesis systems, as in the production of chondramides in Chondromyces crocatus. This class of enzyme has a prosthetic group, MIO (4-methylideneimidazol-5-one), that forms posttranslationally from an Ala-Ser-Gly motif. 507 matched cddid_all.tbl CDD TIGR03833 TIGR03833 274807 TIGR03833 conserved hypothetical protein. A pair of adjacent genes, ablAB (acetyl-beta-lysine biosynthesis) encodes lysine 2,3-aminomutase and beta-lysine acetyltransferase in methanogenic archaea. Homologous pairs, possibly with identical function, occur in a wide range of species, including Bacillus subtilis. This model describes a conserved hypothetical protein, small in size, with a phylogenetic distribution moderately well correlated to that of the acetyltransferase family. This protein family is also described as DUF2196 and COG4895. The function is unknown. [Hypothetical proteins, Conserved] 62 matched cddid_all.tbl CDD TIGR03834 TIGR03834 213869 EAGR_box EAGR box. The EAGR box (Enriched in Aromatic and Glycine Residues) is found in three different proteins of the Mycoplasma genitalium terminal organelle, which acts in both cytadherence and gliding motility. The presence of this domain in a genome predicts the Mycoplasma-type terminal organelle structure, gliding motility, and cytadherence. The EAGR box may occur from one to nine times in a protein. 28 matched cddid_all.tbl CDD TIGR03835 TIGR03835 274808 termin_org_DnaJ terminal organelle assembly protein TopJ. This model describes TopJ (MG_200, CbpA), a DnaJ homolog and probable assembly protein of the Mycoplasma terminal organelle. The terminal organelle is involved in both cytadherence and gliding motility. [Cellular processes, Chemotaxis and motility] 871 matched cddid_all.tbl CDD TIGR03836 TIGR03836 163548 termin_org_HMW1 cytadherence high molecular weight protein 1 N-terminal region. This model describes the N-terminal region of the Mycoplasma cytadherence protein HMW1, up to but not including the first EAGR box domain. The apparent orthologs in different Mycoplasma species differ profoundly in archictecture C-terminally to the region described here. 82 matched cddid_all.tbl CDD TIGR03837 TIGR03837 274809 EarP Elongation-Factor P (EF-P) rhamnosyltransferase EarP. This model describes a conserved protein that typically is encoded next to the gene efp for translation elongation factor P. 371 matched cddid_all.tbl CDD TIGR03838 TIGR03838 274810 queuosine_YadB glutamyl-queuosine tRNA(Asp) synthetase. This protein resembles a shortened glutamyl-tRNA ligase, but its purpose is to modify tRNA(Asp) at a queuosine position in the anticodon rather than to charge a tRNA with its cognate amino acid. [Protein synthesis, tRNA and rRNA base modification] 271 matched cddid_all.tbl CDD TIGR03839 TIGR03839 274811 termin_org_P1 adhesin P1. Members of this protein family are the major adhesin of the Mycoplasma terminal organelle. The protein is called adhesin P1, cytadhesin P1, P140, attachment protein, and MgPa, with locus names MG191 in Mycoplasma genitalium and MPN141 in M. pneumoniae. A conserved C-terminal region is shared by additional paralogs in M. pneumoniae and M. gallisepticum, as well as by the member of this family. [Cell envelope, Surface structures, Cellular processes, Pathogenesis] 1425 matched cddid_all.tbl CDD TIGR03840 TIGR03840 213871 TMPT_Se_Te thiopurine S-methyltransferase, Se/Te detoxification family. Members of this family are thiopurine S-methyltransferase from a branch in which at least some member proteins can perform selenium methylation as a means to detoxify selenium, or perform a related detoxification of tellurium. Note that the EC number definition does not specify a particular thiopurine, but rather represents a class of activity. 213 matched cddid_all.tbl CDD TIGR03841 TIGR03841 274812 F420_Rv3093c probable F420-dependent oxidoreductase, Rv3093c family. This model describes a small family of enzymes in the bacterial luciferase-like monooxygenase family, which includes F420-dependent enzymes such as N5,N10-methylenetetrahydromethanopterin reductase as well as FMN-dependent enzymes. All members of this family are from species that produce coenzyme F420; SIMBAL analysis suggests that members of this family bind F420 rather than FMN. [Unknown function, Enzymes of unknown specificity] 301 matched cddid_all.tbl CDD TIGR03842 TIGR03842 163554 F420_CPS_4043 F420-dependent oxidoreductase, CPS_4043 family. This model represents a family of putative F420-dependent oxidoreductases, fairly closely related to 5,10-methylenetetrahydromethanopterin reductase (mer, TIGR03555), both within the bacterial luciferase-like monoxygenase (LLM) family. A fairly deep split (to about 40 % sequence identity) in the present family separates a strictly Actinobacterial clade from an alpha/beta/gamma-proteobacterial clade, in which the member is often the only apparent F420-dependent LLM family member. The specific function, and whether Actinobacterial and Proteobacterial clades differ in function, are unknown. [Unknown function, Enzymes of unknown specificity] 330 matched cddid_all.tbl CDD TIGR03843 TIGR03843 274813 TIGR03843 conserved hypothetical protein. This model represents a protein family largely restricted to the Actinobacteria (high-GC Gram-positives), although it is also found in the Chloroflexi. Distant similarity to the phosphatidylinositol 3- and 4-kinase is suggested by the matching of some members to pfam00454. 226 matched cddid_all.tbl CDD TIGR03844 TIGR03844 163556 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Energy metabolism, Methanogenesis] 398 matched cddid_all.tbl CDD TIGR03845 TIGR03845 163557 sulfopyru_alph sulfopyruvate decarboxylase, alpha subunit. This model represents the alpha subunit, or the N-terminal region, of sulfopyruvate decarboxylase, an enzyme of coenzyme M biosynthesis. Coenzyme M is found almost exclusively in the methanogenic archaea. However, the enzyme also occurs in Roseovarius nubinhibens ISM in a degradative pathway, where the resulting sulfoacetaldehyde is desulfonated to acetyl phosphate, then converted to acetyl-CoA (see ). [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Energy metabolism, Methanogenesis] 157 matched cddid_all.tbl CDD TIGR03846 TIGR03846 274814 sulfopy_beta sulfopyruvate decarboxylase, beta subunit. Nearly every member of this protein family is the beta subunit, or else the C-terminal region, of sulfopyruvate decarboxylase, in an archaeal species capable of coenzyme M biosynthesis. However, the enzyme also occurs in Roseovarius nubinhibens ISM in a degradative pathway, where the resulting sulfoacetaldehyde is desulfonated to acetyl phosphate, then converted to acetyl-CoA (see ). 181 matched cddid_all.tbl CDD TIGR03847 TIGR03847 213872 TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria. 177 matched cddid_all.tbl CDD TIGR03848 TIGR03848 163560 MSMEG_4193 probable phosphomutase, MSMEG_4193 family. A three-gene system broadly conserved among the Actinobacteria includes MSMEG_4193 and homologs, a subgroup among the larger phosphoglycerate mutase family protein (pfam00300). Another member of the trio is a probable kinase, related to phosphatidylinositol kinases; that context supports the hypothesis that this protein acts as a phosphomutase. 204 matched cddid_all.tbl CDD TIGR03849 TIGR03849 163561 arch_ComA phosphosulfolactate synthase. This model finds the ComA (Coenzyme M biosynthesis A) protein, phosphosulfolactate synthase, in methanogenic archaea. The ComABC pathway is one of at least two pathways to the intermediate sulfopyruvate. Coenzyme M occurs rarely and sporadically outside of the archaea, as for expoxide metabolism in Xanthobacter autotrophicus Py2, but candidate phosphosulfolactate synthases from that and other species occur fall below the cutoff and outside the scope of this model. This model deliberately is narrower in scope than pfam02679. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Energy metabolism, Methanogenesis] 237 matched cddid_all.tbl CDD TIGR03850 TIGR03850 274815 bind_CPR_0540 carbohydrate ABC transporter substrate-binding protein, CPR_0540 family. Members of this protein are the substrate-binding protein of a predicted carbohydrate transporter operon, together with permease subunits of ABC transporter homology families. This substrate-binding protein frequently co-occurs in genomes with a family of disaccharide phosphorylases, TIGR02336, suggesting that the molecule transported will include beta-D-galactopyranosyl-(1->3)-N-acetyl-D-glucosamine and related carbohydrates. Members of this family are sporadically strain by strain, often in species with a human host association, including Propionibacterium acnes and Clostridium perfringens, and Bacillus cereus. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 437 matched cddid_all.tbl CDD TIGR03851 TIGR03851 274816 chitin_NgcE carbohydrate ABC transporter, N-acetylglucosamine/diacetylchitobiose-binding protein. Members of this protein family are the substrate-binding protein, a lipid-anchored protein of Gram-positive bacteria in all examples found so far, that include NgcE of the chitin-degrader, Streptomyces olivaceoviridis, and close homologs from other species likely to share the same function. NgcE binds both N-acetylglucosamine and the chitin dimer, N,N'-diacetylchitobiose. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 450 matched cddid_all.tbl CDD TIGR03852 TIGR03852 163564 sucrose_gtfA sucrose phosphorylase. In the forward direction, this enzyme uses phosphate to cleave sucrose into D-fructose + alpha-D-glucose 1-phosphate. Characterized representatives from Streptococcus mutans and Bifidobacterium adolescentis represent well-separated branches of a molecular phylogenetic tree. In S. mutans, the region including this gene has been associated with neighboring transporter genes and multiple sugar metabolism. 470 matched cddid_all.tbl CDD TIGR03853 TIGR03853 163565 matur_matur probable metal-binding protein. This model describes a family of small cytosolic proteins, about 80 amino acids in length, in which the eight invariant residues include three His residues and two Cys residues. Two pairs of these invariant residues occur in motifs HxH (where x is A or G) and CxH, both of which suggest metal-binding activity. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulfatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulfur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulfatase/maturase systems. 77 matched cddid_all.tbl CDD TIGR03854 TIGR03854 163566 F420_MSMEG_3544 probable F420-dependent oxidoreductase, MSMEG_3544 family. Coenzyme F420 has a limited phylogenetic distribution, including methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea 34H, Rhodopseudomonas palustris HaA2, and others. Partial phylogenetic profiling identifies protein subfamilies, within the larger family called luciferase-like monooxygenanases (pfam00296), that appear only in F420-positive genomes and are likely to be F420-dependent. This model describes a small family, closely related to other such families in the putative F420-binding region, exemplified by MSMEG_3544 in Mycobacterium smegmatis. [Unknown function, Enzymes of unknown specificity] 290 matched cddid_all.tbl CDD TIGR03855 TIGR03855 163567 NAD_NadX aspartate dehydrogenase. Members of this protein family are L-aspartate dehydrogenase, as shown for the NADP-dependent enzyme TM_1643 of Thermotoga maritima. Members lack homology to NadB, the aspartate oxidase (EC 1.4.3.16) of most mesophilic bacteria (described by TIGR00551), which this enzyme replaces in the generation of oxaloacetate from aspartate for the NAD biosynthetic pathway. All members of the seed alignment are found adjacent to other genes of NAD biosynthesis, although other uses of L-aspartate dehydrogenase may occur. 229 matched cddid_all.tbl CDD TIGR03856 TIGR03856 213873 F420_MSMEG_2906 probable F420-dependent oxidoreductase, MSMEG_2906 family. This model describes a small family of enzymes in the bacterial luciferase-like monooxygenase family, which includes F420-dependent enzymes such as N5,N10-methylenetetrahydromethanopterin reductase as well as FMN-dependent enzymes. All members of this family are from species that produce coenzyme F420; SIMBAL analysis suggests that members of this family bind F420 rather than FMN. [Unknown function, Enzymes of unknown specificity] 249 matched cddid_all.tbl CDD TIGR03857 TIGR03857 213874 F420_MSMEG_2249 probable F420-dependent oxidoreductase, MSMEG_2249 family. Coenzyme F420 has a limited phylogenetic distribution, including methanogenic archaea, Mycobacterium tuberculosis and related species, Colwellia psychrerythraea 34H, Rhodopseudomonas palustris HaA2, and others. Partial phylogenetic profiling identifies protein subfamilies, within the larger family called luciferase-like monooxygenanases (pfam00296), that appear only in F420-positive genomes and are likely to be F420-dependent. This model describes a distinctive subfamily, found only in F420-biosynthesizing members of the Actinobacteria of the bacterial luciferase-like monooxygenase (LLM) superfamily. [Unknown function, Enzymes of unknown specificity] 329 matched cddid_all.tbl CDD TIGR03858 TIGR03858 274817 LLM_2I7G probable oxidoreductase, LLM family. This model describes a highly conserved, somewhat broadly distributed family withing the luciferase-like monooxygenase (LLM) superfamily. Most members are from species incapable of synthesizing coenzyme F420, bound by some members of the LLM superfamily. Members, therefore, are more likely to use FMN as a cofactor. 337 matched cddid_all.tbl CDD TIGR03859 TIGR03859 274818 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 81 matched cddid_all.tbl CDD TIGR03860 TIGR03860 274819 FMN_nitrolo FMN-dependent oxidoreductase, nitrilotriacetate monooxygenase family. This model represents a distinctive clade, in which all characterized members are FMN-binding, within the larger family of luciferase-like monooxygenases (LLM), among which there are both FMN- and F420-binding enzymes. A well-characterized member is nitrilotriacetate monooxygenase from Aminobacter aminovorans (Chelatobacter heintzii), where nitrilotriacetate is a chelating agent used in detergents. [Unknown function, Enzymes of unknown specificity] 422 matched cddid_all.tbl CDD TIGR03861 TIGR03861 163573 phenyl_ABC_PedC alcohol ABC transporter, permease protein. Members of this protein family, part of a larger class of efflux-type ABC transport permease proteins, are found exclusively in genomic contexts with pyrroloquinoline-quinone (PQQ) biosynthesis enzymes and/or PQQ-dependent alcohol dehydrogenases, such as the phenylethanol dehydrogenase PedE of Pseudomonas putida U. Members include PedC, an apparent phenylethanol transport protein whose suggested role is efflux to limit intracellular concentrations of toxic metabolites during phenylethanol catalysis. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 253 matched cddid_all.tbl CDD TIGR03862 TIGR03862 274820 flavo_PP4765 uncharacterized flavoprotein, PP_4765 family. This model describes a sharply distinctive clade of proteins within the larger family of flavoproteins described by pfam03486 and TIGRFAMs model TIGR00275. The function is unknown. 376 matched cddid_all.tbl CDD TIGR03863 TIGR03863 274821 PQQ_ABC_bind ABC transporter, substrate binding protein, PQQ-dependent alcohol dehydrogenase system. Members of this protein family are putative substrate-binding proteins of an ABC transporter family that associates, in gene neighborhood and phylogenomic profile, with pyrroloquinoline-quinone (PQQ)-dependent degradation of certain alcohols, such as 2-phenylethanol in Pseudomonas putida U. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 347 matched cddid_all.tbl CDD TIGR03864 TIGR03864 274822 PQQ_ABC_ATP ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system. Members of this protein family are the ATP-binding subunit of an ABC transporter system that is associated with PQQ biosynthesis and PQQ-dependent alcohol dehydrogenases. While this family shows homology to several efflux ABC transporter subunits, the presence of a periplasmic substrate-binding protein and association with systems for catabolism of alcohols suggests a role in import rather than detoxification. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 236 matched cddid_all.tbl CDD TIGR03865 TIGR03865 274823 PQQ_CXXCW PQQ-dependent catabolism-associated CXXCW motif protein. Members of this protein family have a CXXXCW motif, consistent with a possible role in redox cofactor binding. This protein family shows strong relationships by phylogenetic profiling and conserved gene neighborhoods with a transport system for alcohols metabolized by PQQ-dependent enzymes. 162 matched cddid_all.tbl CDD TIGR03866 TIGR03866 274824 PQQ_ABC_repeats PQQ-dependent catabolism-associated beta-propeller protein. Members of this protein family consist of seven repeats each of the YVTN family beta-propeller repeat (see TIGR02276). Members occur invariably as part of a transport operon that is associated with PQQ-dependent catabolism of alcohols such as phenylethanol. 310 matched cddid_all.tbl CDD TIGR03867 TIGR03867 274825 MprA_tail MprA protease C-terminal rhombosortase-interaction domain. This model describes the Ralstonia lineage variant of the GlyGly-CTERM domain (TIGR03501), a predicted target for protein sorting and cleavage by rhombosortase, a member of the family of rhomboid proteases. Note that some MprA family proteases are full-length homologs except for the lack of this domain. All members of the present family are predicted serine proteases. 27 matched cddid_all.tbl CDD TIGR03868 TIGR03868 274826 F420-O_ABCperi proposed F420-0 ABC transporter, periplasmic F420-0 binding protein. This small clade of ABC-type transporter periplasmic binding protein components is found as a three gene cassette along with a permease (TIGR03869) and an ATPase (TIGR03873). The organisms containing this cassette are all Actinobacteria and all contain numerous genes requiring the coenzyme F420. This model was defined based on five such organisms, four of which are lacking all F420 biosynthetic capability save the final side-chain polyglutamate attachment step (via the gene cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and marine actinobacterium PHSC20C1 this cassette is in an apparent operon with the cofE gene and, in PHSC20C1, also with a F420-dependent glucose-6-phosphate dehydrogenase (TIGR03554). Based on these observations we propose that this periplasmic binding protein is a component of an F420-0 (that is, F420 lacking only the polyglutamate tail) transporter. 287 matched cddid_all.tbl CDD TIGR03869 TIGR03869 163581 F420-0_ABCperm proposed F420-0 ABC transporter, permease protein. his small clade of ABC-type transporter permease protein components is found as a three gene cassette along with a periplasmic substrate-binding protein (TIGR03868) and an ATPase (TIGR03873). The organisms containing this cassette are all Actinobacteria and all contain numerous genes requiring the coenzyme F420. This model was defined based on five such organisms, four of which are lacking all F420 biosynthetic capability save the final side-chain polyglutamate attachment step (via the gene cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and marine actinobacterium PHSC20C1 this cassette is in an apparent operon with the cofE gene and, in PHSC20C1, also with an F420-dependent glucose-6-phosphate dehydrogenase (TIGR03554). Based on these observations we propose that this permease protein is a component of a F420-0 (that is, F420 lacking only the polyglutamate tail) transporter. 325 matched cddid_all.tbl CDD TIGR03870 TIGR03870 274827 ABC_MoxJ methanol oxidation system protein MoxJ. This predicted periplasmic protein, called MoxJ or MxaJ, is required for methanol oxidation in Methylobacterium extorquens. Two differing lines of evidence suggest two different roles. Forming one view, homology suggests it is the substrate-binding protein of an ABC transporter associated with methanol oxidation. The gene, furthermore, is found regular in genomes with, and only two or three genes away from, a corresponding permease and ATP-binding cassette gene pair. The other view is that this protein is an accessory factor or additional subunit of methanol dehydrogenase itself. Mutational studies show a dependence on this protein for expression of the PQQ-dependent, two-subunit methanol dehydrogenase (MxaF and MxaI) in Methylobacterium extorquens, as if it is a chaperone for enzyme assembly or a third subunit. A homologous N-terminal sequence was found in Paracoccus denitrificans as a 32Kd third subunit. This protein may, in fact, be both, a component of a periplasmic enzyme that converts methanol to formaldehyde and a component of an ABC transporter that delivers the resulting formaldehyde to the cell's interior. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids, Energy metabolism, Other] 246 matched cddid_all.tbl CDD TIGR03871 TIGR03871 274828 ABC_peri_MoxJ_2 quinoprotein dehydrogenase-associated probable ABC transporter substrate-binding protein. This protein family, a sister family to TIGR03870, is found more broadly. It occurs a range of PQQ-biosynthesizing species, not just in known methanotrophs. Interpretation of evidence by homology and by direct experimental work suggest two different roles. By homology, this family appears to be the periplasmic substrate-binding protein of an ABC transport family. However, mutational studies and direct characterization for some sequences related to this family suggests this family may act as a maturation chaperone or additional subunit of a methanol dehydrogenase-like enzyme. 232 matched cddid_all.tbl CDD TIGR03872 TIGR03872 274829 cytochrome_MoxG cytochrome c(L), periplasmic. This model describes a periplasmic c-type cytochrome that serves as the primary electron acceptor for the quinoprotein methanol dehydrogenase, a PQQ enzyme. The member from Paracoccus denitrificans is also characterized as an electron acceptor for methylamine dehydrogenase, a tryptophan tryptophylquinone enzyme. This protein is called cytochrome c(L) in methylotrophic bacteria such Methylobacterium extorquens, but c551i in Paracoccus denitrificans. [Energy metabolism, Electron transport] 133 matched cddid_all.tbl CDD TIGR03873 TIGR03873 163585 F420-0_ABC_ATP proposed F420-0 ABC transporter, ATP-binding protein. This small clade of ABC-type transporter ATP-binding protein components is found as a three gene cassette along with a periplasmic substrate-binding protein (TIGR03868) and a permease (TIGR03869). The organisms containing this cassette are all Actinobacteria and all contain numerous genes requiring the coenzyme F420. This model was defined based on five such organisms, four of which are lacking all F420 biosynthetic capability save the final side-chain polyglutamate attachment step (via the gene cofE: TIGR01916). In Jonesia denitrificans DSM 20603 and marine actinobacterium PHSC20C1 this cassette is in an apparent operon with the cofE gene and, in PHSC20C1, also with a F420-dependent glucose-6-phosphate dehydrogenase (TIGR03554). Based on these observations we propose that this ATP-binding protein is a component of an F420-0 (that is, F420 lacking only the polyglutamate tail) transporter. 256 matched cddid_all.tbl CDD TIGR03874 TIGR03874 163586 4cys_cytochr c-type cytochrome, methanol metabolism-related. This family represents a c-type cytochrome related to (but excluding) cytochrome c-555 of Methylococcus capsulatus. Members contain four invariant Cys residues, including two from a heme-binding motif shared with c-555, and two others. 143 matched cddid_all.tbl CDD TIGR03875 TIGR03875 163587 RNA_lig_partner RNA ligase partner, MJ_0950 family. This uncharacterized protein family is found almost perfectly in the same set of genomes as the Pab1020 family described by model TIGR01209. These pairs are found mostly in Archaea, but also in a few bacteria (e.g. Alkalilimnicola ehrlichei MLHE-1, Aquifex aeolicus). While the partner protein has been described as homodimeric ligase that has RNA circularization activity, the function of this protein (also called UPF0278) is unknown. 206 matched cddid_all.tbl CDD TIGR03876 TIGR03876 274830 cas_csaX CRISPR type I-A/APERN-associated protein CsaX. This family comprises a minor CRISPR-associated protein family. It occurs only in the context of the (strictly archaeal) Apern subtype of CRISPR/Cas system, and is further restricted to the Sulfolobales, including Metallosphaera sedula DSM 5348 and multiple species of the genus Sulfolobus. 281 matched cddid_all.tbl CDD TIGR03877 TIGR03877 163589 thermo_KaiC_1 KaiC domain protein, Ph0284 family. Members of this family contain a single copy of the KaiC domain (pfam06745) that occurs in two copies of the circadian clock protein kinase KaiC itself. Members occur primarily in thermophilic archaea and in Thermotoga. 237 matched cddid_all.tbl CDD TIGR03878 TIGR03878 274831 thermo_KaiC_2 KaiC domain protein, AF_0795 family. This KaiC domain-containing protein family occurs sporadically across a broad taxonomic range (Euryarchaeota, Aquificae, Dictyoglomi, Epsilonproteobacteria, and Firmicutes), but exclusively in thermophiles. 259 matched cddid_all.tbl CDD TIGR03879 TIGR03879 163591 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation. 73 matched cddid_all.tbl CDD TIGR03880 TIGR03880 163592 KaiC_arch_3 KaiC domain protein, AF_0351 family. This model represents a rather narrowly distributed archaeal protein family in which members have a single copy of the KaiC domain. This stands in contrast to the circadian clock protein KaiC itself, with two copies of the domain. Members are expected to have weak ATPase activity, by homology to the autokinase/autophosphorylase KaiC itself. 224 matched cddid_all.tbl CDD TIGR03881 TIGR03881 163593 KaiC_arch_4 KaiC domain protein, PAE1156 family. Members of this protein family are archaeal single-domain KaiC_related proteins, homologous to the Cyanobacterial circadian clock cycle protein KaiC, an autokinase/autophosphorylase that has two copies of the domain. 229 matched cddid_all.tbl CDD TIGR03882 TIGR03882 274832 cyclo_dehyd_2 bacteriocin biosynthesis cyclodehydratase domain. This model describes a ThiF-like domain of a fusion protein found in clusters associated with the production of TOMMs (thiazole/oxazole-modified microcins), small bacteriocins with characteristic heterocycle modifications. This domain is presumed to act as a cyclodehydratase, as do members of the SagC family modeled by TIGR03603. 164 matched cddid_all.tbl CDD TIGR03883 TIGR03883 274833 DUF2342_F420 uncharacterized protein, coenzyme F420 biosynthesis associated. A phylogenetic tree of the DUF2342 family (TIGR03624) consists of two major branches. One of these branches, modeled here, is observed almost entirely to be found in coenzyme F420 biosynthesizing species of the Actinobacterial, Chloroflexi and Archaeal lineages. The few organisms having genes within this family and lacking F420 biosynthesis may either have an undiscovered F420 transporter, or may represent F420-to-FMN revertants. This family includes a Chloroflexus Aurantiacus protein whose crystal structure has been determined (PDB:3CMN_A). This has been annotated as a putative hydrolase, but the support for that assertion is untraceable. There is no cofactor present in the structure. 346 matched cddid_all.tbl CDD TIGR03884 TIGR03884 163596 sel_bind_Methan selenium-binding protein. This model describes a homopentameric selenium-binding protein with a suggested role in selenium transport and delivery to selenophosphate synthase, the SelD protein. This protein family is closely related to pfam01906, but is shorter because of several deleted regions. It is restricted to the archaeal genus Methanococcus. 74 matched cddid_all.tbl CDD TIGR03885 TIGR03885 274834 flavin_revert probable non-F420 flavinoid oxidoreductase. This model represents a clade of proteins within the larger subfamily TIGR03557. The parent model includes the F420-dependent glucose-6-phosphate dehydrogenase (TIGR03554) and many other proteins. Excepting the members of this family, all members of TIGR03557 occur in species capable of synthesizing coenzyme F420. All members of the seed alignment for this model are from species that lack F420 biosynthesis. It is suggested that members of this family bind FMN, or FO, or a novel flavinoid cofactor, but not F420 per se. [Unknown function, Enzymes of unknown specificity] 315 matched cddid_all.tbl CDD TIGR03886 TIGR03886 188401 lyase_spl_fam spore photoproduct lyase family protein. This uncharacterized radical SAM domain protein occurs rarely and sporadically in species that include select Alphaproteobacteria and Actinobacteria, and in Deinococcus deserti VCD115. It is a distant but full-length homolog to the Bacillus subtilis spore photoproduct lyase (spl), which monomerizes thymine dimers created as DNA damage by uv radiation. 346 matched cddid_all.tbl CDD TIGR03887 TIGR03887 188402 thiocyan_alph thiocyanate hydrolase, gamma subunit. Members of this family are the gamma subunit of thiocyanate hydrolase. This family is closely related to the nitrile hydratase, alpha subunit (TIGR01323). 200 matched cddid_all.tbl CDD TIGR03888 TIGR03888 274835 nitrile_beta nitrile hydratase, beta subunit. Members of this protein family are the beta subunit of nitrile hydratase. The alpha subunit is represented by model TIGR01323. While nitrile hydratase is given the specific EC number 4.2.1.84, nitriles are a class of compounds, and one genome may carry more than one nitrile hydratase. The enzyme occurs in both non-heme iron and non-corrin cobalt forms. [Energy metabolism, Amino acids and amines] 223 matched cddid_all.tbl CDD TIGR03889 TIGR03889 188404 nitrile_acc nitrile hydratase accessory protein. Members of this protein family are found in operons with the alpha and beta subunits of nitrile hydratase, an enzyme with Fe(III) or Co(III) at the active site, and appear to be accessory proteins for maturation or activation of the enzyme. This protein is homologous to the beta subunit (see TIGR03888). 74 matched cddid_all.tbl CDD TIGR03890 TIGR03890 188405 nif11_cupin nif11 domain/cupin domain protein. Members of this protein family occur exclusively in the Cyanobacteria and contain both a nif11 and a cupin domain. The function is unknown. 171 matched cddid_all.tbl CDD TIGR03891 TIGR03891 274836 thiopep_ocin thiopeptide-type bacteriocin biosynthesis domain. This domain occurs within longer proteins that contain lantibiotic dehydratase domains (see pfam04737 and pfam04738), and as single-domain proteins in bacteriocin biosynthesis genomic contexts. Three named genes in this family, SioK in Streptomyces sioyaensis, TsrD in Streptomyces laurentii, and NosD in Streptomyces actuosus, all occur in regions associated with thiopeptide biosynthesis. [Cellular processes, Toxin production and resistance] 263 matched cddid_all.tbl CDD TIGR03892 TIGR03892 200334 thiopep_precurs thiazolylpeptide-type bacteriocin precursor. Members of this protein family are the precursors of a family of small bacteriocins (i.e. microcins) with thiopeptide type modifications, a highly modified subclass of heterocycle-containing peptide antibiotics. Members tend to be found clustered in genomes with proteins recognized by TIGR03891 and proteins/domains annotated as lantibiotic dehydratase (pfam04737, pfam04738), and with a cyclodehydratase/docking protein fusion protein characteristic of heterocycle formation. The seed alignment includes both an N-terminal leader peptide region and a C-terminal low-complexity region consisting mostly of Cys and Ser residues. Members with known function block translation by inhibiting translation factor activity. [Cellular processes, Toxin production and resistance] 43 matched cddid_all.tbl CDD TIGR03893 TIGR03893 274837 lant_SP_1948 type 2 lantibiotic, SP_1948 family. This model recognizes a number of type 2 lantibiotic-type bacteriocins, related to but distinct from the family that includes lichenicidin and mersacidin. Sequence similarity among members consists largely of a 20-residue block of conserved sequence that covers most of the leader peptide region, absent from the mature lantibiotic. This is followed by a region with characteristic composition for lantibiotic precursor regions, rich in Ser and Thr and including a near-invariant Cys near or at the C-terminus, involved in cyclization. Members of this family typically are shorter than 70 amino acids. [Cellular processes, Toxin production and resistance] 61 matched cddid_all.tbl CDD TIGR03894 TIGR03894 188409 chp_P_marinus_1 conserved hypothetical protein, TIGR03894 family. This protein family is restricted to the Prochlorococcus and Synechococcus lineages of the Cyanobacteria, and is sporadic in those lineages. Members average 100 amino acids in length, including a 30-residue, highly polar, low complexity region sandwiched between an N-terminal region of about 60 residues and a C-terminal [KR]VVR[KR]RS motif, both well-conserved. The function is unknown. [Hypothetical proteins, Conserved] 95 matched cddid_all.tbl CDD TIGR03895 TIGR03895 274838 protease_PatA cyanobactin maturation protease, PatA/PatG family. This model describes a protease domain associated with the maturation of various members of the cyanobactin family of ribosomally produced, heavily modified bioactive metabolites. Members include the PatA protein and C-terminal domain of the PatG protein of Prochloron didemni, TenA and a region of TenG from Nostoc spongiaeforme var. tenue, etc. 602 matched cddid_all.tbl CDD TIGR03896 TIGR03896 274839 cyc_nuc_ocin bacteriocin-type transport-associated protein. Members of this protein family are uncharacterized and contain two copies of the cyclic nucleotide-binding domain pfam00027. Members are restricted to select cyanobacteria but are found regularly in association with a transport operon that, in turn, is associated with the production of putative bacteriocins. The models describing the transport operon are TIGR03794, TIGR03796, and TIGR03797. 317 matched cddid_all.tbl CDD TIGR03897 TIGR03897 274840 lanti_2_LanM type 2 lantibiotic biosynthesis protein LanM. Members of this family are known generally as LanM, a multifunctional enzyme of lantibiotic biosynthesis. This catalysis by LanM distinguishes the type 2 lantibiotics, such as mersacidin, cinnamycin, and lichenicidin, from LanBC-produced type 1 lantibiotics such as nisin and subtilin. The N-terminal domain contains regions associated with Ser and Thr dehydration. The C-terminal region contains a pfam05147 domain, which catalyzes the formation of the lanthionine bridge. [Cellular processes, Toxin production and resistance] 931 matched cddid_all.tbl CDD TIGR03898 TIGR03898 274841 lanti_MRSA_kill type 2 lantibiotic, mersacidin/lichenicidin family. This model recognizes a number of type 2 lantibiotic-type bacteriocins, including mersacidin and lichenicidin. Members often are found as gene pairs encoding two-chain bacteriocins. Maturation is accomplished, at least in part, by a LanM-type enzyme (TIGR03897). This model describes only the leader peptide region. [Cellular processes, Toxin production and resistance] 44 matched cddid_all.tbl CDD TIGR03899 TIGR03899 274842 TIGR03899 TIGR03899 family protein. Members of this protein family are conserved hypothetical proteins with a limited species distribution within the Gammaproteobacteria. It is common in the genera Vibrio and Shewanella, and in this resembles the C-terminal domain and putative protein sorting motif TIGR03501. This model, but design, does not extend to all homologs,but rather represents a particular clade. 250 matched cddid_all.tbl CDD TIGR03900 TIGR03900 274843 prc_long_Delta putative carboxyl-terminal-processing protease, deltaproteobacterial. This model describes a multidomain protein of about 1070 residues, restricted to the order Myxococcales in the Deltaproteobacteria. Members contain a PDZ domain (pfam00595), an S41 family peptidase domain (pfam03572), and an SH3 domain (pfam06347). A core region of this family, including PDZ and S41 regions, is described by TIGR00225, C-terminal processing peptidase, which recognizes the Prc protease. The species distribution of this family approximates that of largely Deltaproteobacterial C-terminal putative protein-sorting domain, TIGR03901, analogous to LPXTG and PEP-CTERM, but the co-occurrence may reflect shared restriction to the Myxococcales rather than a substrate/target relationship. 973 matched cddid_all.tbl CDD TIGR03901 TIGR03901 274844 MYXO-CTERM MYXO-CTERM domain. This model describes MYXO-CTERM, a C-terminal putative protein sorting domain, analogous to LPXTG (TIGR01167) and PEP-CTERM (TIGR02595). It is restricted to the Myxococcales, a division of the Deltaproteobacteria, with over 60 members occurring in Plesiocystis pacifica SIR-1. An example protein is TraA, involved in outer membrane exchange (lipids and proteins) through which one strain of Myxococcus can repair a mobility defect in another. The trusted cutoff for this model is set artificially high to avoid false positives, and consequently only about half of all members are recognized. 31 matched cddid_all.tbl CDD TIGR03902 TIGR03902 274845 rhom_GG_sort rhomboid family GlyGly-CTERM serine protease. This model describes a rhomboid-like intramembrane serine protease. Its species distribution closely matches model TIGR03501, GlyGly-CTERM, which describes a protein targeting domain analogous to LPXTG and PEP-CTERM. In a number of species (Ralstonia eutropha ,R. metallidurans, R. solanacearum, Marinobacter aquaeolei, etc) with just one GlyGly-CTERM protein (i.e., a dedicated system), the rhombosortase and GlyGly-CTERM genes are adjacent. 154 matched cddid_all.tbl CDD TIGR03903 TIGR03903 274846 TOMM_kin_cyc TOMM system kinase/cyclase fusion protein. This model represents proteins of 1350 in length, in multiple species of Burkholderia, in Acidovorax avenae subsp. citrulli AAC00-1 and Delftia acidovorans SPH-1, and in multiple copies in Sorangium cellulosum, in genomic neighborhoods that include a cyclodehydratase/docking scaffold fusion protein (TIGR03882) and a member of the thiazole/oxazole modified metabolite (TOMM) precursor family TIGR03795. It has a kinase domain in the N-terminal 300 amino acids, followed by a cyclase homology domain, followed by regions without named domain definitions. It is a probable bacteriocin-like metabolite biosynthesis protein. [Cellular processes, Toxin production and resistance] 1266 matched cddid_all.tbl CDD TIGR03904 TIGR03904 274847 SAM_YgiQ uncharacterized radical SAM protein YgiQ. Members of this family are fairly widespread uncharacterized radical SAM family proteins, many of which are designated YgiQ. [Unknown function, Enzymes of unknown specificity] 559 matched cddid_all.tbl CDD TIGR03905 TIGR03905 188420 TIGR03905_4_Cys uncharacterized protein TIGR03905. This model describes a family of conserved hypothetical proteins of small size, typically ~85 residues, with four invariant Cys residues. This small protein is distantly homologous to a C-terminal domain found in proteins identified by N-terminal homology as ribonucleotide reductases. The rare and sporadic distribution of this protein family falls mostly within the subset of bacterial genomes containing the uncharacterized radical SAM protein modeled by TIGR03904. [Unknown function, General] 78 matched cddid_all.tbl CDD TIGR03906 TIGR03906 274848 quino_hemo_SAM quinohemoprotein amine dehydrogenase maturation protein. Members of this protein family are radical SAM enzymes responsible for post-translational modifications to the gamma subunit of quinohemoprotein amine dehydrogenases. Ono, et al. () suggest that this protein is responsible for intrapeptidyl thioether cross-linking rather than cysteine tryptophylquinone biogenesis in the gamma subunit. [Protein fate, Protein modification and repair] 467 matched cddid_all.tbl CDD TIGR03907 TIGR03907 211887 QH_beta quinohemoprotein amine dehydrogenase, beta subunit. Quinohemoprotein amine dehydrogenase is a three subunit enzyme with both a heme group and a cysteine tryptophylquinone group derived by post-translational modification of the gamma subunit. This model describes the beta subunit. This enzyme catalyzes oxidative deamination of primary aliphatic and aromatic amines (). [Energy metabolism, Amino acids and amines] 338 matched cddid_all.tbl CDD TIGR03908 TIGR03908 274849 QH_alpha quinohemoprotein amine dehydrogenase, alpha subunit. Quinohemoprotein amine dehydrogenase is a three subunit enzyme with both a heme group and a cysteine tryptophylquinone group derived by post-translational modification of the gamma subunit. This model describes the beta subunit. This enzyme catalyzes oxidative deamination of primary aliphatic and aromatic amines (). [Energy metabolism, Amino acids and amines] 510 matched cddid_all.tbl CDD TIGR03909 TIGR03909 188424 pyrrolys_PylC pyrrolysine biosynthesis protein PylC. This protein is PylC, part of a three-gene cassette that is sufficient to direct the biosynthesis of pyrrolysine, the twenty-second amino acid, incorporated in some species at a UAG canonical stop codon. [Amino acid biosynthesis, Other] 374 matched cddid_all.tbl CDD TIGR03910 TIGR03910 188425 pyrrolys_PylB pyrrolysine biosynthesis radical SAM protein. This model describes a radical SAM protein, PylB, that is part of the three-gene cassette sufficient for the biosynthesis of pyrrolysine (the twenty-second amino acid) when expressed heterologously in E. coli. The pyrrolysine next is ligated to its own tRNA and incorporated at special UAG codons. [Amino acid biosynthesis, Other] 347 matched cddid_all.tbl CDD TIGR03911 TIGR03911 188426 pyrrolys_PylD pyrrolysine biosynthesis protein PylD. This protein is PylD, part of a three-gene cassette that is sufficient to direct the biosynthesis of pyrrolysine, the twenty-second amino acid, incorporated in some species at a UAG canonical stop codon. [Amino acid biosynthesis, Other] 266 matched cddid_all.tbl CDD TIGR03912 TIGR03912 188427 PylS_Nterm pyrrolysyl-tRNA synthetase, N-terminal region. PylS is the enzyme responsible for charging the pyrrolysine tRNA, PylT, by ligating a free molecule of pyrrolysine. Pyrrolysine is encoded at an in-frame UAG (amber) at least in several corrinoid-dependent methyltransferases of the archaeal genera Methanosarcina and Methanococcoides, such as trimethylamine methyltransferase. This protein occurs as a fusion protein in Methanosarcina but as split genes in Desulfitobacterium hafniense and other bacteria. This model describes the small, N-terminal region. [Protein synthesis, tRNA aminoacylation] 89 matched cddid_all.tbl CDD TIGR03913 TIGR03913 188428 rad_SAM_trio Y_X(10)_GDL-associated radical SAM protein. This narrowly distributed protein family contains an N-terminal radical SAM domain. It occurs in Pseudomonas fluorescens Pf0-1, Ralstonia solanacearum, and numerous species and strains of Burkholderia. Members always occur next to a trio of three mutually homologous genes, all of which contain the domain pfam08898 as the whole of the protein (about 60 amino acids) or as the C-terminal domain. The function is unknown, but the fact that all phylogenetically correlated proteins are mutually homologous with prominent invariant motifs (an invariant tyrosine and a GDL motif) and as small as 60 amino acids suggests that post-translational modification of pfam08898 domain-containing proteins may be its function. This view is supported by closer homology to the PqqE radical SAM protein involved in PQQ biosynthesis from the PqqA precursor peptide than to other characterized radical SAM proteins. [Unknown function, Enzymes of unknown specificity] 477 matched cddid_all.tbl CDD TIGR03914 TIGR03914 274850 UDG_fam_dom uracil-DNA glycosylase family domain. This model represents a clade within the uracil-DNA glycosylase superfamily. Among characterized proteins, it most closely resembles the Thermus thermophilus uracil-DNA glycosylase TTUDGA, which acts uracil (deamidated cytosine) in both single-stranded DNA and U/G pairs of double-stranded DNA. This domain may occur either as a stand-alone protein or as the C-terminal domain of a fusion with another domain that always pairs with a particular radical-SAM family protein. 230 matched cddid_all.tbl CDD TIGR03915 TIGR03915 274851 SAM_7_link_chp probable DNA metabolism protein. This model represents a conserved hypothetical protein that almost invariably pairs with an uncharacterized radical SAM protein. The pair occurs in about twenty percent of completed prokaryotic genomes. About forty percent of the members of this family occur as fusion proteins, where the C-terminal domain belongs to the uracil-DNA glycosylase family, a DNA repair family (because uracil in DNA is deamidated cytosine). The linkage by gene clustering and correlated species distribution to a radical SAM protein, and by gene fusion to a DNA repair protein family, suggests a role in DNA modification and/or repair. 241 matched cddid_all.tbl CDD TIGR03916 TIGR03916 188431 rSAM_link_UDG putative DNA modification/repair radical SAM protein. This uncharacterized protein of about 400 amino acids in length contains a radical SAM protein in the N-terminal half. Members are present in about twenty percent of prokaryotic genomes, always paired with a member of the conserved hypothetical protein TIGR03915. Roughly forty percent of the members of that family exist as fusions with a uracil-DNA glycosylase-like region, TIGR03914. In DNA, uracil results from deamidation of cytosine, forming U/G mismatches that lead to mutation, and so uracil-DNA glycosylase is a DNA repair enzyme. This indirect connection, and the recurring role or radical SAM protein in modification chemistries, suggest that this protein may act in DNA modification, repair, or both. [Unknown function, Enzymes of unknown specificity] 415 matched cddid_all.tbl CDD TIGR03917 TIGR03917 274852 Frankia_40_dom Frankia-40 domain. This model describes a paralogous domain of length 40, restricted to smaller proteins of the genus Frankia, a member of the Actinobacteria. The function is unknown. 40 matched cddid_all.tbl CDD TIGR03918 TIGR03918 274853 GTP_HydF [FeFe] hydrogenase H-cluster maturation GTPase HydF. This model describes the family of the [Fe] hydrogenase maturation protein HypF as characterized in Chlamydomonas reinhardtii and found, in an operon with radical SAM proteins HydE and HydG, in numerous bacteria. It has GTPase activity, can bind an 4Fe-4S cluster, and is essential for hydrogenase activity. [Protein fate, Protein modification and repair] 391 matched cddid_all.tbl CDD TIGR03919 TIGR03919 274854 T7SS_EccB type VII secretion protein EccB, Actinobacterial. This model represents the transmembrane protein EccB of the actinobacterial flavor of type VII secretion systems. Species such as Mycobacterium tuberculosis have several instances of this system per genome, designated EccB1, EccB2, etc. This model does not identify functionally related proteins in the Firmicutes such as Staphylococcus aureus and Bacillus anthracis. [Protein fate, Protein and peptide secretion and trafficking] 456 matched cddid_all.tbl CDD TIGR03920 TIGR03920 274855 T7SS_EccD type VII secretion integral membrane protein EccD. Members of this family are EccD, a component of actinobacterial type VII secretion systems (T7SS) with ten to eleven predicted transmembrane helix regions. [Protein fate, Protein and peptide secretion and trafficking] 453 matched cddid_all.tbl CDD TIGR03921 TIGR03921 274856 T7SS_mycosin type VII secretion-associated serine protease mycosin. Members of this family are subtilisin-related serine proteases, found strictly in the Actinobacteria and associated with type VII secretion operons. The designation mycosin is used for members from Mycobacterium. [Protein fate, Protein and peptide secretion and trafficking, Protein fate, Protein modification and repair] 350 matched cddid_all.tbl CDD TIGR03922 TIGR03922 188437 T7SS_EccA type VII secretion AAA-ATPase EccA. This model represents the AAA family ATPase, EccA, of the actinobacterial flavor of type VII secretion systems. Species such as Mycobacterium tuberculosis have several instances of this system per genome, designated EccA1, EccA2, etc. [Protein fate, Protein and peptide secretion and trafficking] 557 matched cddid_all.tbl CDD TIGR03923 TIGR03923 274857 T7SS_EccE type VII secretion protein EccE. This model represents the transmembrane protein EccB of the actinobacterial flavor of type VII secretion systems. Species such as Mycobacterium tuberculosis have several instances of this system per genome, designated EccE1, EccE2, etc. This model represents a conserved core region, and many members have 200 or more additional C-terminal residues. [Protein fate, Protein and peptide secretion and trafficking] 341 matched cddid_all.tbl CDD TIGR03924 TIGR03924 274858 T7SS_EccC_a type VII secretion protein EccCa. This model represents the N-terminal domain or EccCa subunit of the type VII secretion protein EccC as found in the Actinobacteria. Type VII secretion is defined more broadly as including secretion systems for ESAT-6-like proteins in the Firmicutes as well as in the Actinobacteria, but this family does not show close homologs in the Firmicutes. [Protein fate, Protein and peptide secretion and trafficking] 658 matched cddid_all.tbl CDD TIGR03925 TIGR03925 274859 T7SS_EccC_b type VII secretion protein EccCb. This model represents the C-terminal domain or EccCb subunit of the type VII secretion protein EccC as found in the Actinobacteria. Type VII secretion is defined more broadly as including secretion systems for ESAT-6-like proteins in the Firmicutes as well as in the Actinobacteria, but this family does not show close homologs in the Firmicutes. [Protein fate, Protein and peptide secretion and trafficking] 566 matched cddid_all.tbl CDD TIGR03926 TIGR03926 188441 T7_EssB type VII secretion protein EssB. Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This protein is designated YukC in Bacillus subtilis and EssB is Staphylococcus aureus. [Protein fate, Protein and peptide secretion and trafficking] 377 matched cddid_all.tbl CDD TIGR03927 TIGR03927 200340 T7SS_EssA_Firm type VII secretion protein EssA. Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions. [Protein fate, Protein and peptide secretion and trafficking] 150 matched cddid_all.tbl CDD TIGR03928 TIGR03928 274860 T7_EssCb_Firm type VII secretion protein EssC, C-terminal domain. This model describes the C-terminal domain, or longer subunit, of the Firmicutes type VII secretion protein EssC. This protein (homologous to EccC in Actinobacteria) and the WXG100 target proteins are the only homologous parts of type VII secretion between Firmicutes and Actinobacteria. [Protein fate, Protein and peptide secretion and trafficking] 1296 matched cddid_all.tbl CDD TIGR03929 TIGR03929 274861 T7_esaA_Nterm type VII secretion protein EsaA, N-terminal domain. Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This model represents the conserved N-terminal domain. 193 matched cddid_all.tbl CDD TIGR03930 TIGR03930 274862 WXG100_ESAT6 WXG100 family type VII secretion target. Members of this protein family include secretion targets for the two main variants of type VII secretion systems (T7SS), one found in the Actinobacteria, one found in the Firmicutes. This model was derived through iteration from pfam06013. The best characterized member of this family is ESAT-6 from Mycobacterium tuberculosis. Members of this family usually are ~100 amino acids in length but occasionally have a long C-terminal extension. 90 matched cddid_all.tbl CDD TIGR03931 TIGR03931 274863 T7SS_Rv3446c type VII secretion-associated protein, Rv3446c family, C-terminal domain. Members of this protein family occur as part of the ESX-4 cluster of type VII secretion system (T7SS) proteins in Mycobacterium tuberculosis and in similar T7SS clusters in other Actinobacteria genera, including Corynebacterium, Nocardia, Rhodococcus, and Saccharopolyspora. This model describes the better-conserved C-terminal region. [Protein fate, Protein and peptide secretion and trafficking] 172 matched cddid_all.tbl CDD TIGR03932 TIGR03932 188447 PIA_icaD intracellular adhesion protein D. Members of this protein family are IcaD (intracellular adhesion protein D), which with catalytic subunit IcaA forms an N-acetylglucosaminyltransferase. In the absence of IcaC, this enzyme forms N-acetylglucosamine oligomers up to 20 in length. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 88 matched cddid_all.tbl CDD TIGR03933 TIGR03933 188448 PIA_icaB intercellular adhesin biosynthesis polysaccharide N-deacetylase. A common motif in bacterial biosynthesis of polysaccharide for export is modification that follows polymerization. This model describes a subfamily of polysaccharide N-deacetylases that acts on poly-beta-1,6-N-acetyl-D-glyscosamine as produced by Staphylococcus epidermidis and S. aureus. The end product in these species is designated polysaccharide intercellular adhesin (PIA), and this gene designated icaB (intercellular adhesion protein B). [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides, Cellular processes, Pathogenesis] 245 matched cddid_all.tbl CDD TIGR03934 TIGR03934 274864 TQXA_dom TQXA domain. This model describes a domain of about 40 residues with an invariant TQ dipeptide in an almost invariant TQxA[VI]W motif. This domain occurs in surface-expressed proteins of Gram-positive bacteria, many of which are anchored by LPXTG-containing sortase target domains. Numerous members of this family have domains pfam05738 (Cna protein B-type domain) and pfam08341 (fibronectin-binding protein signal sequence). 42 matched cddid_all.tbl CDD TIGR03935 TIGR03935 188450 fragilysin fragilysin. Members of this family are fragilysin, the Bacteroides fragilis enterotoxin. This enzyme is a Zn metalloprotease. Three distinct subtypes included in this family all are produced by enterotoxigenic (by definition) strains of Bacteroides fragilis. [Cellular processes, Pathogenesis] 386 matched cddid_all.tbl CDD TIGR03936 TIGR03936 274865 sam_1_link_chp radical SAM-linked protein. This model describes an uncharacterized protein encoded adjacent to, or as a fusion protein with, an uncharacterized radical SAM protein. 208 matched cddid_all.tbl CDD TIGR03937 TIGR03937 274866 PgaC_IcaA poly-beta-1,6 N-acetyl-D-glucosamine synthase. Members of this protein family are biofilm-forming enzymes that polymerize N-acetyl-D-glucosamine residues in beta(1,6) linkage. One named members is IcaA (intercellular adhesin protein A), an enzyme that acts (with aid of subunit IcaD) in Polysaccharide Intercellular Adhesin (PIA) biosynthesis in Staphylococcus epidermis). The homologous member in E. coli is designated PgaC. Members are often encoded next to a polysaccharide deacetylase and involved in biofilm formation. Note that chitin, although also made from N-acetylglucosamine, is formed with beta-1,4 linkages. 407 matched cddid_all.tbl CDD TIGR03938 TIGR03938 274867 deacetyl_PgaB poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB. Two well-characterized systems produce polysaccharide based on N-acetyl-D-glucosamine in straight chains with beta-1,6 linkages. These are encoded by the icaADBC operon in Staphylococcus species, where the system is designated polysaccharide intercellular adhesin (PIA), and the pgaABCD operon in Gram-negative bacteria such as E. coli. Both systems include a putative polysaccharide deacetylase. The PgaB protein, described here, contains an additional domain lacking from its Gram-positive counterpart IcaB (TIGR03933). Deacetylation by this protein appears necessary to allow export through the porin PgaA [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 619 matched cddid_all.tbl CDD TIGR03939 TIGR03939 274868 PGA_TPR_OMP poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA. Members of this protein family are the poly-beta-1,6 N-acetyl-D-glucosamine (PGA) export porin PgaA of Gram-negative bacteria. There is no counterpart in the poly-beta-1,6 N-acetyl-D-glucosamine biosynthesis systems of Gram-positive bacteria such as Staphylococcus epidermidis. The PGA polysaccharide adhesin is a critical determinant of biofilm formation. The conserved C-terminal domain of this outer membrane protein is preceded by a variable number of TPR repeats. 800 matched cddid_all.tbl CDD TIGR03940 TIGR03940 188455 PGA_PgaD poly-beta-1,6-N-acetyl-D-glucosamine biosynthesis protein PgaD. Members of this protein family are PgaD, essential to the production of poly-beta-1,6-N-acetyl-D-glucosamine (PGA). This cytoplasmic membrane protein appears to be an auxiliary subunit to the PGA synthase, PgaC (TIGR03937). [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 141 matched cddid_all.tbl CDD TIGR03941 TIGR03941 274869 tRNA_deam_assoc putative tRNA adenosine deaminase-associated protein. This model describes a protein family about 200 amino acids in length with only five invariant residues, including an Arg, a Ser-Asp pair, and two Gly residues. Members always are found exclusively in Actinobacteria, and always adjacent to homologs of TadA, a tRNA-specific adenosine deaminase from Escherichia coli. Homology, phyletic pattern, and gene neighborhood together suggest a housekeeping function in tRNA metabolism. [Unknown function, General] 154 matched cddid_all.tbl CDD TIGR03942 TIGR03942 188457 sulfatase_rSAM anaerobic sulfatase-maturating enzyme. Members of this protein family are radical SAM family enzymes, maturases that prepare the oxygen-sensitive radical required in the active site of anaerobic sulfatases. This maturase role has led to many misleading legacy annotations suggesting that this enzyme maturase is instead a sulfatase regulatory protein. All members of the seed alignment are radical SAM enzymes encoded next to or near an anaerobic sulfatase. Note that a single genome may encode more than one sulfatase/maturase pair. [Protein fate, Protein modification and repair] 363 matched cddid_all.tbl CDD TIGR03943 TIGR03943 274870 TIGR03943 TIGR03943 family protein. Members of this occur in gene pairs with members of pfam03773. The N-terminal region contains several predicted transmembrane helix regions while the few invariant residues (G, CxxD, and W) occur in the C-terminal region. 219 matched cddid_all.tbl CDD TIGR03944 TIGR03944 274871 dehyd_SbnB_fam 2,3-diaminopropionate biosynthesis protein SbnB. Members of this protein family are probable NAD-dependent dehydrogenases related to the alanine dehydrogenase of Archaeoglobus fulgidus (see TIGR02371, PDB structure 1OMO and ) and more distantly to ornithine cyclodeaminase. Members include the staphylobactin biosynthesis protein SbnB and tend to occur in contexts suggesting non-ribosomal peptide synthesis, always adjacent to (occasionally fused with) a pyridoxal phosphate-dependent enzyme, SbnA. The pair appears to provide 2,3-diaminopropionate for biosynthesis of siderophores or other secondary metabolites. [Cellular processes, Biosynthesis of natural products] 327 matched cddid_all.tbl CDD TIGR03945 TIGR03945 274872 PLP_SbnA_fam 2,3-diaminopropionate biosynthesis protein SbnA. Members of this family include SbnA, a protein of the staphyloferrin B biosynthesis operon of Staphylococcus aureus. SbnA and SbnB together appear to synthesize 2,3-diaminopropionate, a precursor of certain siderophores and other secondary metabolites. SbnA is a pyridoxal phosphate-dependent enzyme. [Cellular processes, Biosynthesis of natural products] 304 matched cddid_all.tbl CDD TIGR03946 TIGR03946 188461 viomycin_VioC arginine beta-hydroxylase, Fe(II)/alpha-ketoglutarate-dependent. Members of this protein family are L-arginine beta-hydroxylase, members of a broader family of enzymes dependent on Fe(II), alpha-ketoglutarate, and molecular oxygen. Enzymes in the broader family but excluded by this model include clavaminate synthase, taurine dioxygenase, and prolyl-4-hydroxylase. [Cellular processes, Biosynthesis of natural products] 333 matched cddid_all.tbl CDD TIGR03947 TIGR03947 188462 viomycin_VioD capreomycidine synthase. Members of this family are the enzyme capreomycidine synthase, which performs the second of two steps in the biosynthesis of 2S,3R-capreomycidine from arginine. Capreomycidine is an unusual amino acid used by non-ribosomal peptide synthases (NRPS) to make the tuberactinomycin class of peptide antibiotic. The best characterized member is VioD from the biosynthetic pathway for viomycin. [Cellular processes, Biosynthesis of natural products] 359 matched cddid_all.tbl CDD TIGR03948 TIGR03948 188463 butyr_acet_CoA butyryl-CoA:acetate CoA-transferase. This enzyme represents one of at least two mechanisms for reclaiming CoA from butyryl-CoA at the end of butyrate biosynthesis (an important process performed by some colonic bacteria), namely transfer of CoA to acetate. An alternate mechanism transfers the butyrate onto inorganic phosphate, after which butyrate kinase transfers the phosphate onto ADP, creating ATP. [Energy metabolism, Fermentation] 445 matched cddid_all.tbl CDD TIGR03949 TIGR03949 274873 bact_IIb_cerein class IIb bacteriocin, lactobin A/cerein 7B family. Members of this protein family are described variably as bacteriocins per se, one chain of a two-chain bacteriocin, or bacteriocin enhancer proteins. All members of the seed alignment occur in paired gene contexts with another member of the same protein family. This family includes bacteriocins that appear not to undergo post-translational modification, other than cleavage at a Gly-Gly motif coupled to sec-independent export. For many members, the N-terminal bacteriocin cleavage motif region is recognized by TIGR01847. C-terminal to the cleavage motif, these proteins are hydrophobic and low in complexity, consistent with pore-forming activity as a mechanism of bacteriocin action. 45 matched cddid_all.tbl CDD TIGR03950 TIGR03950 274874 sidero_Fe_reduc siderophore ferric iron reductase, AHA_1954 family. Members of this protein family are 2Fe-2S cluster binding proteins, found regularly in the context of siderophore transporters. Members are distantly related to FhuF from E. coli, a ferric iron reductase linked to removal of iron from hydroxamate-type siderophores (). [Energy metabolism, Electron transport, Transport and binding proteins, Cations and iron carrying compounds] 223 matched cddid_all.tbl CDD TIGR03951 TIGR03951 274875 Fe_III_red_FhuF siderophore-iron reductase FhuF. Members of this protein family, including FhuF of E. coli, are siderophore ferric iron reductases that appear to play a role in iron removal from certain hydroxamate-type siderophores, including coprogen, ferrichrome, ferrioxamine B, and aerobactin. Genes occur in regularly in siderophore transport and/or biosynthesis clusters. The C-terminus includes four Cys residues in a C-C-10(X)-C-X-X-C motif that binds a 2Fe-2S cluster. Family TIGR03950 is similar, but especially in the C-terminal region, but likely acts on a different panel of siderophores. [Energy metabolism, Electron transport, Transport and binding proteins, Cations and iron carrying compounds] 182 matched cddid_all.tbl CDD TIGR03952 TIGR03952 274876 metzin_BF0631 zinc-dependent metalloproteinase lipoprotein, BF0631 family. Members of this protein family are zinc-dependent metalloproteinases, related to ulilysin and other members of the pappalysin family. Members occur as predicted lipoproteins and occur mostly in the genera Bacteriodes and Prevotella. [Protein fate, Degradation of proteins, peptides, and glycopeptides] 351 matched cddid_all.tbl CDD TIGR03953 TIGR03953 274877 rplD_bact 50S ribosomal protein L4, bacterial/organelle. Members of this protein family are ribosomal protein L4. This model recognizes bacterial and most organellar forms, but excludes homologs from the eukaryotic cytoplasm and from archaea. [Protein synthesis, Ribosomal proteins: synthesis and modification] 188 matched cddid_all.tbl CDD TIGR03954 TIGR03954 274878 integ_memb_HG integral membrane protein. This model describes a strictly bacterial integral membrane domain of about 85 residues in length. It occurs in proteins that on rare occasions are fused to transporter domains such as the major facilitator superfamily domain. Of three invariant residues, two occur as a His-Gly dipeptide in the middle of three predicted transmembrane helices. [Unknown function, General] 85 matched cddid_all.tbl CDD TIGR03955 TIGR03955 274879 rSAM_HydG [FeFe] hydrogenase H-cluster radical SAM maturase HydG. This model describes the radical SAM protein HydG. It is part of an enzyme metallocenter maturation system, working together with GTP-binding protein HydF and another radical SAM enzyme, HydE, in H-cluster maturation in [FeFe] hydrogenases. [Protein fate, Protein modification and repair] 471 matched cddid_all.tbl CDD TIGR03956 TIGR03956 274880 rSAM_HydE [FeFe] hydrogenase H-cluster radical SAM maturase HydE. This model describes the radical SAM protein HydE, one of a pair of radical SAM proteins, along with GTP-binding protein HydF, for maturation of [Fe] hydrogenase in Chlamydomonas reinhardtii and numerous bacteria. [Protein fate, Protein modification and repair] 340 matched cddid_all.tbl CDD TIGR03957 TIGR03957 188472 rSAM_HmdB 5,10-methenyltetrahydromethanopterin hydrogenase cofactor biosynthesis protein HmdB. Members of this archaeal protein family are HmdB, a partially characterized radical SAM protein with an unusual CX5CX2C motif. Its gene flanks the H2-forming methylene-H4-methanopterin dehydrogenase gene hmdA, found in hydrogenotrophic methanogens. HmdB appears to act in in biosynthesis of the novel cofactor of HmdA. [Protein fate, Protein modification and repair, Energy metabolism, Methanogenesis] 317 matched cddid_all.tbl CDD TIGR03958 TIGR03958 274881 monoFe_hyd_HmdC 5,10-methenyltetrahydromethanopterin hydrogenase cofactor biosynthesis protein HmdC. Members of this protein family are HmdC, whose gene regularly occurs in the context of genes for HmdA (5,10-methenyltetrahydromethanopterin hydrogenase) and the radical SAM protein HmdB involved in biosynthesis of the HmdA cofactor. Bioinformatics suggests this protein, a homolog of eukaryotic fibrillarin, may be involved in biosynthesis of the guanylyl pyridinol cofactor in HmdA. [Protein fate, Protein modification and repair, Energy metabolism, Methanogenesis] 505 matched cddid_all.tbl CDD TIGR03959 TIGR03959 274882 hyd_TM1266 putative iron-only hydrogenase system regulator. Members of this protein family occur as part of a system for producing iron-only hydrogenases, dependent on radical SAM proteins HydE and HydG and GTPase HydF. One member of this family, TM_1266 from Thermotoga maritima, has a known crystal structure. The small size, about 80 residues, and a distant relationship to the nickel regulator NikR of the CopG transcriptional regulator family suggest a role as a transcription factor. [Regulatory functions, DNA interactions] 76 matched cddid_all.tbl CDD TIGR03960 TIGR03960 188475 rSAM_fuse_unch radical SAM family uncharacterized protein. This model describes a radical SAM protein, or protein region, regularly found paired with or fused to a region described by TIGR03936. PSI-BLAST analysis of TIGR03936 suggests a relationship to the tRNA pseudouridine synthase TruA, suggesting that this system may act in RNA modification. [Unknown function, Enzymes of unknown specificity] 605 matched cddid_all.tbl CDD TIGR03961 TIGR03961 188476 rSAM_PTO1314 archaeal radical SAM protein, PTO1314 family. Members of this protein family average about 340 residues in length, with a radical SAM domain in the N-terminal 200 residues. The taxonomic distribution is restricted to non-methanogenic archaea, including Picrophilus torridus (locus PTO1314), Sulfolobus sp., Thermoplasma sp., Picrophilus torridus, and Metallosphaera sedula. The gene neighborhood is not conserved, and the function of this family is unknown. [Unknown function, Enzymes of unknown specificity] 332 matched cddid_all.tbl CDD TIGR03962 TIGR03962 188477 mycofact_rSAM mycofactocin radical SAM maturase. Members of this family are uncharacterized radical SAM proteins from the Mycobacterium tuberculosis and many other Actinobacteria, as well as some deltaproteobacteria (e.g. Geobacter uraniireducens), firmicutes (Pelotomaculum thermopropionicum and Desulfotomaculum acetoxidans), and Chloroflexi (Thermomicrobium roseum DSM 5159 and Sphaerobacter thermophilus DSM 20745). They resemble several characterized radical SAM enzymes of peptide modification (PqqE, AlbA), and are always found next to the proposed target, TIGR03969, the putative mycofactocin precursor. [Unknown function, Enzymes of unknown specificity] 339 matched cddid_all.tbl CDD TIGR03963 TIGR03963 188478 rSAM_QueE_Clost putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, clostridial. Members of this radical SAM domain protein family appear to be the Clostridial form of the queuosine biosynthesis protein QueE. QueE is involved in making preQ0 (7-cyano-7-deazaquanine), a precursor of both the bacterial/eukaryotic modified tRNA base queuosine and the archaeal modified base archaeosine. Members occur in preQ0 operons species that lack members of related protein family TIGR03365. [Protein synthesis, tRNA and rRNA base modification] 219 matched cddid_all.tbl CDD TIGR03964 TIGR03964 274883 mycofact_creat mycofactocin system creatininase family protein. Members of this protein family are uncharacterized Actinobacterial proteins, with homology to creatinine amidohydrolase from Pseudomonas. Members occur only in the context of the mycofactocin system. [Unknown function, Enzymes of unknown specificity] 228 matched cddid_all.tbl CDD TIGR03965 TIGR03965 274884 mycofact_glyco mycofactocin system glycosyltransferase. Members of this protein family are putative glycosyltransferases, members of pfam00535 (glycosyl transferase family 2). Members appear mostly in the Actinobacteria, where they appear to be part of a system for converting a precursor peptide (TIGR03969) into a novel redox carrier designated mycofactocin. A radical SAM enzyme, TIGR03962, is a proposed to be a key maturase for mycofactocin. 466 matched cddid_all.tbl CDD TIGR03966 TIGR03966 274885 actino_HemFlav heme/flavin dehydrogenase, mycofactocin system. Members of this protein family possess an N-terminal heme-binding domain and C-terminal flavodehydrogenase domain, and share homology to yeast flavocytochrome b2, to E. coli L-lactate dehydrogenase [cytochrome], to (S)-mandelate dehydrogenase, etc. This enzyme appears only in the context of the mycofactocin system. Interestingly, it is absent from the four species detected so far with mycofactocin but without an F420 biosynthesis system. 385 matched cddid_all.tbl CDD TIGR03967 TIGR03967 274886 mycofact_MftB putative mycofactocin binding protein MftB. Families TIGR03969 and TIGR03962 describe, respectively, the putative mycofactocin precursor and its cognate radical SAM peptide maturase. This small protein family appears in the same sporadically distributed cassette and may serve as a scaffolding protein during mycofactocin maturation or as a carrier protein for the mature product, a putative novel redox carrier. A feature of mycofactocin-encoding genomes is co-clustering with sets of NAD-binding oxidoreductases in which the NAD is not exchangeable. Therefore it is proposed that mature mycofactocin, bound by a member of this family as a carrier protein, docks with the nicotinoprotein to allow electron transfer. Mediation of electron transfer through this system would define a segregated redox pool. [Unknown function, General] 81 matched cddid_all.tbl CDD TIGR03968 TIGR03968 188483 mycofact_TetR mycofactocin system transcriptional regulator. Members of this family are TetR family putative transcriptional regulators that occur in genome contexts near proteins of the mycofactocin system. These include the precursor peptide (TIGR03969), a radical SAM peptide maturase (TIGR03962), and a putative carrier protein (TIGR03967). [Regulatory functions, DNA interactions] 190 matched cddid_all.tbl CDD TIGR03969 TIGR03969 274887 mycofactocin mycofactocin precursor. Members of this protein family occur in Mycobacterium tuberculosis and many other Actinobacteria, as well as some delta-Proteobacteria (e.g. Geobacter uraniireducens), Firmicutes (Pelotomaculum thermopropionicum and Desulfotomaculum acetoxidans), and Chloroflexi (Thermomicrobium roseum DSM 5159 and Sphaerobacter thermophilus DSM 20745). Members sometimes are missed during gene model identification but always occur in the vicinity of radical SAM (rSAM) enzyme TIGR03962, which resembles several rSAM enzymes of peptide maturation (PqqE, AlbA). Species with this protein always carry members of unusual clades of nicotinoproteins that are restricted to mycofactocin-containing species and in which the NAD, when studied, has appeared non-exchangeable. It is proposed that the mature form of mycofactocin is a novel redox carrier for a segregated redox pool. 23 matched cddid_all.tbl CDD TIGR03970 TIGR03970 274888 Rv0697 dehydrogenase, Rv0697 family. This model describes a set of dehydrogenases belonging to the glucose-methanol-choline oxidoreductase (GMC oxidoreductase) family. Members of the present family are restricted to Actinobacterial genome contexts containing also members of families TIGR03962 and TIGR03969 (the mycofactocin system), and are proposed to be uniform in function. 487 matched cddid_all.tbl CDD TIGR03971 TIGR03971 274889 SDR_subfam_1 SDR family mycofactocin-dependent oxidoreductase. Members of this protein subfamily are putative oxidoreductases belonging to the larger SDR family. All members occur in genomes that encode a cassette for the biosynthesis of mycofactocin, a proposed electron carrier of a novel redox pool. Characterized members of this family are described as NDMA-dependent, meaning that a blue aniline dye serving as an artificial electron acceptor is required for members of this family to cycle in vitro, since the bound NAD residue is not exchangeable. See EC 1.1.99.36. [Unknown function, Enzymes of unknown specificity] 270 matched cddid_all.tbl CDD TIGR03972 TIGR03972 274890 rSAM_TYW1 wyosine biosynthesis protein TYW1. Members of this protein family are the archaeal protein TWY1, a radical SAM protein that catalyzes the second step in creating the wye-bases, wyosine and derivatives such as wybutosine, for tRNA base modification. [Protein synthesis, tRNA and rRNA base modification] 297 matched cddid_all.tbl CDD TIGR03973 TIGR03973 274891 six_Cys_in_45 six-cysteine peptide SCIFF. Members of this protein family are essentially universal in the class Clostidia and therefore highly abundant in the human gut microbiome. This short peptide is designated SCIFF, for Six Cysteines in Forty-Five residues. It is a presumed ribosomal natural product precursor, always found associated with a yet-uncharacterized radical SAM protein, family TIGR03974, that resembles other peptide modification radical SAM enzymes and is designated SCIFF radical SAM maturase. 43 matched cddid_all.tbl CDD TIGR03974 TIGR03974 274892 rSAM_six_Cys SCIFF radical SAM maturase. Members of this protein family are predicted radical SAM enzymes universally associated with Six Cysteines in Forty-Five protein, or SCIFF (family TIGR03973), a predicted ribosomal natural product precursor that is nearly universal in the class Clostridia. Similarity of this family to radical SAM maturases (PqqE and subtilosin A maturase) found in the vicinity of other peptide precursors suggests this protein is the SCIFF radical SAM maturase. [Cellular processes, Biosynthesis of natural products] 451 matched cddid_all.tbl CDD TIGR03975 TIGR03975 274893 rSAM_ocin_1 ribosomal peptide maturation radical SAM protein 1. Models TIGR03793 and TIGR03798 describe bacteriocin precursor families to occur often in large paralogous families and are subject to various modifications, including by LanM family lantibiotic synthases and by cyclodehydratases. This model represents a radical SAM protein family that regularly occurs in the context of these bacteriocins, and may occur where other familiar peptide modification enzymes are absent. [Cellular processes, Toxin production and resistance] 606 matched cddid_all.tbl CDD TIGR03976 TIGR03976 274894 chp_LLNDYxLRE His-Xaa-Ser system protein HxsD. This rare conserved hypothetical protein of small size occurs exclusively, and perhaps universally, in the context of a pair of (uncharacterized) radical SAM proteins, TIGR03977 and TIGR03978. Many members of this family have invariant motifs LYW and LLNDYxLRE, but PSI-BLAST starting from family members well below 20 % pairwise sequence identity to this group eventually brings in the entire family as modeled here. The family TIGR03979 represents the fourth regularly conserved member of this system. 90 matched cddid_all.tbl CDD TIGR03977 TIGR03977 274895 rSAM_pair_HxsC His-Xaa-Ser system radical SAM maturase HxsC. This model describes the downstream member, HxsC, of a pair of uncharacterized radical SAM proteins, regularly found in the context of a small protein with four or more repeats of the tripeptide His-Xaa-Ser (HXS). This enzyme appears to be part of a peptide modification system. 292 matched cddid_all.tbl CDD TIGR03978 TIGR03978 274896 rSAM_paired_1 His-Xaa-Ser system radical SAM maturase HxsB. This model describes the upstream member, HxsB, of a pair of uncharacterized radical SAM proteins, regularly found in the context of a small protein with four or more repeats of the tripeptide His-Xaa-Ser (HXS). This enzyme appears to be part of a peptide modification system. 466 matched cddid_all.tbl CDD TIGR03979 TIGR03979 274897 His_Ser_Rich His-Xaa-Ser repeat protein HxsA. Members of this protein share two defining regions. One is a histidine/serine-rich cluster, typically H-R-S-H-S-S-H-R-S-H-S-S-H. Members are found always in the context of a pair of radical SAM proteins, HxsB and HxsC, and a fourth protein HxsD. The system is predicted to perform peptide modifications, likely in the His-Xaa-Ser region, to produce some uncharacterized natural product. 186 matched cddid_all.tbl CDD TIGR03980 TIGR03980 274898 prismane_assoc hybrid cluster protein-associated redox disulfide domain. Members of this protein family resemble the domain of unknown function DUF1858 described by pfam08984, but all members contain an apparent redox-active disulfide. In at least one member protein, a cysteine in the CXXC motif is substituted by a selenocysteine. Most member proteins consist of this domain only, but a few members are fused to or adjacent to members of the hybrid-cluster (prismane) family or the nitrite/sulfite reductase family. [Energy metabolism, Electron transport] 58 matched cddid_all.tbl CDD TIGR03981 TIGR03981 188496 SAM_quin_mod His-Xaa-Ser system putative quinone modification maturase. One clue for the interpretation of this protein family is homology to the MauG protein (see TIGR03791) involved in the tryptophan tryptophylquinone post-translational modification of methylamine dehydrogenase light (beta) chain. The other is occurrence only in a five gene context in which two members are radical SAM proteins (TIGR03977 and TIGR03978) also likely involved in post-translational modification. 411 matched cddid_all.tbl CDD TIGR03982 TIGR03982 188497 TIGR03982 His-Xaa-Ser system protein, TIGR03982 family. Members of this rare protein family occur in the presence of TIGR03981 and TIGR03979, which in turn occur only in the context of radical SAM protein families TIGR03977 and TIGR03978. The function is unknown. 117 matched cddid_all.tbl CDD TIGR03983 TIGR03983 274899 cas1_MYXAN CRISPR-associated endonuclease Cas1, subtype MYXAN. Members of this protein are the Cas1 endonuclease, or Cas1 domain in Cas4/Cas1 fusion proteins, of the MYXAN subtype of CRISPR/Cas systems. These systems typically feature repeats and spacers each about 36 base pairs in length. Species with this type of CRISPR system include Myxococcus xanthus, Cyanothece sp., Leptospira interrogans, Sorangium cellulosum, Anabaena variabilis ATCC 29413, etc. 347 matched cddid_all.tbl CDD TIGR03984 TIGR03984 274900 TIGR03984 CRISPR-associated protein, TIGR03984 family. Members of this protein family are found exclusively in CRISPR-containing organisms, in operon contexts with RAMP (repeat-associated mystery protein) proteins also linked to CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats). 147 matched cddid_all.tbl CDD TIGR03985 TIGR03985 274901 TIGR03985 CRISPR-associated protein, TIGR03985 family. Members of this protein family belong to CRISPR-associated (Cas) gene clusters. The majority of members are Cyanobacterial. 248 matched cddid_all.tbl CDD TIGR03986 TIGR03986 274902 TIGR03986 CRISPR-associated protein. Members of this protein family, part of the larger RAMP family, are found exclusively in species with CRISPR systems, in local contexts containing other RAMP (Repeat-Associated Mystery Proteins). 562 matched cddid_all.tbl CDD TIGR03987 TIGR03987 274903 TIGR03987 TIGR03987 family protein. Conserved hypothetical protein 120 matched cddid_all.tbl CDD TIGR03988 TIGR03988 274904 antisig_RsrA mycothiol system anti-sigma-R factor. Members of this family are the anti-sigma-R factor RsrA, which contains a CXXC motif as a thiol-disulphide redox switch. It interacts with sigma-R. It regulates and is regulated by the mycothiol system, which occurs in many actinomycetes. [Transcription, Transcription factors] 77 matched cddid_all.tbl CDD TIGR03989 TIGR03989 274905 Rxyl_3153 NDMA-dependent alcohol dehydrogenase, Rxyl_3153 family. This model describes a clade within the family pfam00107 of zinc-binding dehydrogenases. The family pfam00107 contains class III alcohol dehydrogenases, including enzymes designated S-(hydroxymethyl)glutathione dehydrogenase and NAD/mycothiol-dependent formaldehyde dehydrogenase. Members of the current family occur only in species that contain the very small protein mycofactocin (TIGR03969), a possible cofactor precursor, and radical SAM protein TIGR03962. We name this family for Rxyl_3153, where the lone member of the family co-clusters with these markers in Rubrobacter xylanophilus. [Unknown function, Enzymes of unknown specificity] 369 matched cddid_all.tbl CDD TIGR03990 TIGR03990 274906 Arch_GlmM phosphoglucosamine mutase. The MMP1680 protein from Methanococcus maripaludis has been characterized as the archaeal protein responsible for the second step of UDP-GlcNAc biosynthesis. This GlmM protein catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate. The first-characterized bacterial GlmM protein is modeled by TIGR01455. These two families are members of the larger phosphoglucomutase/phosphomannomutase family (characterized by three domains: pfam02878, pfam02879 and pfam02880), but are not nearest neighbors to each other. This model also includes a number of sequences from non-archaea in the Bacteroides, Chlorobi, Chloroflexi, Planctomycetes and Spirochaetes lineages. Evidence supporting their inclusion in this equivalog as having the same activity comes from genomic context and phylogenetic profiling. A large number of these organisms are known to produce exo-polysaccharide and yet only appeared to contain the GlmS enzyme of the GlmSMU pathway for UDP-GlcNAc biosynthesis (GenProp0750). In some organisms including Leptospira, this archaeal GlmM is found adjacent to the GlmS as well as a putative GlmU non-orthologous homolog. Phylogenetic profiling of the GlmS-only pattern using PPP identifies members of this archaeal GlmM family as the highest-scoring result. [Central intermediary metabolism, Amino sugars] 443 matched cddid_all.tbl CDD TIGR03991 TIGR03991 274907 alt_bact_glmU UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase. The MJ_1101 protein from Methanococcus jannaschii has been characterized as the GlmU enzyme catalyzing the final two steps of UDP-GlcNAc biosynthesis. Homologs of this enzyme are identified in a number of bacterial organisms and modeled here. A number of these are observed in proximity to the GlmS and GlmM genes, and phylogenetic profiling by PPP identifies the LEPBI_I0518 gene in Leptospira biflexa as a likely Glm-system candidate. Multiple sequence alignments of these bacterial homologs with their archaeal counterparts reveals significant structural differences, necessitating the construction of separate models. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan, Central intermediary metabolism, Amino sugars] 337 matched cddid_all.tbl CDD TIGR03992 TIGR03992 274908 Arch_glmU UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase. The MJ_1101 protein from Methanococcus jannaschii has been characterized as the GlmU enzyme catalyzing the final two steps of UDP-GlcNAc biosynthesis. Many of the genes identified by this model are in proximity to the GlmS and GlmM genes and are also presumed to be GlmU. However, some archaeal genomes contain multiple closely-related homologs from this family and it is not clear what the substrate specificity is for each of them. 393 matched cddid_all.tbl CDD TIGR03993 TIGR03993 274909 hydrog_HybE [NiFe] hydrogenase assembly chaperone, HybE family. Members of this family are chaperones for the assembly of [NiFe] hydrogenases, in the family of HybE, which is specific for hydrogenase-2 of Escherichia coli. Members often have an additional N-terminal rubredoxin domain. 143 matched cddid_all.tbl CDD TIGR03994 TIGR03994 274910 rSAM_HemZ coproporphyrinogen dehydrogenase HemZ. Members of this radical SAM protein family are HemZ, a protein involved in coproporphyrinogen III decarboxylation. Alternative names for this enzyme (EC 1.3.99.22) include coproporphyrinogen dehydrogenase and oxygen-independent coproporphyrinogen III oxidase. The family is related to, but distinct from HemN, and in Bacillus subtilis was shown to be connected to peroxide stress and catalase formation. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 401 matched cddid_all.tbl CDD TIGR03995 TIGR03995 274911 target_X_rSAM putative rSAM target protein, CGCGG family. Members of this family of small proteins, approx. 100 amino acids in length, co-occur with a subfamily of radical SAM protein in several species in the Halobacteria and in Bacillus. The radical SAM protein belongs to a branch in which most characterized members act on peptide substrates. The lack of homology of this family to any known enzyme and the distinctive C-terminal region motif, with the common modification target residue Cys flanked by sterically permissive Gly residues. 84 matched cddid_all.tbl CDD TIGR03996 TIGR03996 188511 mycofact_OYE_1 mycofactocin system FadH/OYE family oxidoreductase 1. The yeast protein called old yellow enzyme and FadH from Escherichia coli (2,4-dienoyl CoA reductase) are enzymes with 4Fe-4S, FMN, and FAD prosthetic groups, and interact with NADPH as well as substrate. Members of this related protein family occur in the vicinity of the putative mycofactocin biosynthesis operon in a number of Actinobacteria such as Frankia sp. and Rhodococcus sp. The function of this oxidoreductase is unknown. 633 matched cddid_all.tbl CDD TIGR03997 TIGR03997 274912 mycofact_OYE_2 mycofactocin system FadH/OYE family oxidoreductase 2. The yeast protein called old yellow enzyme and FadH from Escherichia coli (2,4-dienoyl CoA reductase) are enzymes with 4Fe-4S, FMN, and FAD prosthetic groups, and interact with NADPH as well as substrate. Members of this related protein family occur in the vicinity of the putative mycofactocin biosynthesis operon in a number of Actinobacteria such as Frankia sp. and Rhodococcus sp., in Pelotomaculum thermopropionicum SI (Firmicutes), and in Geobacter uraniireducens Rf4 (Deltaproteobacteria). The function of this oxidoreductase is unknown. 644 matched cddid_all.tbl CDD TIGR03998 TIGR03998 274913 thiol_BshC bacillithiol biosynthesis cysteine-adding enzyme BshC. Members of this protein family are BshC, an enzyme required for bacillithiol biosynthesis and described as a cysteine-adding enzyme. Bacillithiol is a low-molecular-weight thiol, an analog of glutathione and mycothiol, and is found largely in the Firmicutes. [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 528 matched cddid_all.tbl CDD TIGR03999 TIGR03999 274914 thiol_BshA N-acetyl-alpha-D-glucosaminyl L-malate synthase BshA. Members of this protein family are BshA, a glycosyltransferase required for bacillithiol biosynthesis. This enzyme combines UDP-GlcNAc and L-malate to form N-acetyl-alpha-D-glucosaminyl L-malate synthase. Bacillithiol is a low-molecular-weight thiol, an analog of glutathione and mycothiol, and is found largely in the Firmicutes. [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 374 matched cddid_all.tbl CDD TIGR04000 TIGR04000 188515 thiol_BshB2 bacillithiol biosynthesis deacetylase BshB2. Members of this protein family are BshB2 (YojG), an enzyme of bacillithiol biosynthesis; either BshB1 (YpjG) or BshB2 must be present, and often both are present. Bacillithiol is a low-molecular-weight thiol, an analog of glutathione and mycothiol, and is found largely in the Firmicutes. [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 217 matched cddid_all.tbl CDD TIGR04001 TIGR04001 274915 thiol_BshB1 bacillithiol biosynthesis deacetylase BshB1. Members of this protein family are BshB1 (YpjG), an enzyme of bacillithiol biosynthesis; either BshB1 or BshB2 (YojG) must be present, and often both are present. Bacillithiol is a low-molecular-weight thiol, an analog of glutathione and mycothiol, and is found largely in the Firmicutes. [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 226 matched cddid_all.tbl CDD TIGR04002 TIGR04002 188517 TIGR04002 TIGR04002 family protein. TIGR04002 family proteins, a division within DUF1393 ( pfam07155), occur strictly as part of a tandem gene pair with an uncharacterized radical SAM protein. [Unknown function, General] 151 matched cddid_all.tbl CDD TIGR04003 TIGR04003 188518 rSAM_BssD [benzylsuccinate synthase]-activating enzyme. Members of this radical SAM protein family are [benzylsuccinate synthase]-activating enzyme, a glycyl radical active site-creating enzyme related to [pyruvate formate-lyase]-activating enzyme and additional uncharacterized homologs activating additional glycyl radical-containing enzymes. [Protein fate, Protein modification and repair] 314 matched cddid_all.tbl CDD TIGR04004 TIGR04004 188519 WcaM colanic acid biosynthesis protein WcaM. This protein of uncharacterized function is the final gene in the conserved colanic acid biosynthesis cluster observed in Enterobacteraceae. 464 matched cddid_all.tbl CDD TIGR04005 TIGR04005 188520 wcaL colanic acid biosynthesis glycosyltransferase WcaL. This gene is one of the glycosyl transferases involved in the biosynthesis of colanic acid, an exopolysaccharide expressed in Enterobacteraceae species. 406 matched cddid_all.tbl CDD TIGR04006 TIGR04006 188521 wcaK colanic acid biosynthesis pyruvyl transferase WcaK. This gene is the pyruvyl transferase involved in the biosynthesis of colanic acid, an exopolysaccharide expressed in Enterobacteraceae species. 426 matched cddid_all.tbl CDD TIGR04007 TIGR04007 188522 wcaI colanic acid biosynthesis glycosyl transferase WcaI. This gene is one of the glycosyl transferases involved in the biosynthesis of colanic acid, an exopolysaccharide expressed in Enterobacteraceae species. 407 matched cddid_all.tbl CDD TIGR04008 TIGR04008 188523 WcaF colanic acid biosynthesis acetyltransferase WcaF. This gene is one of the glycosyl transferases involved in the biosynthesis of colanic acid, an exopolysaccharide expressed in Enterobacteraceae species. This acetyltransferase is believed to catalyze the addition of the acetyl group that is attached through an O linkage to the first fucosyl residue of the colanic acid repetitive unit (E unit) 180 matched cddid_all.tbl CDD TIGR04009 TIGR04009 188524 wcaE colanic acid biosynthesis glycosyl transferase WcaE. This gene is one of the glycosyl transferases involved in the biosynthesis of colanic acid, an exopolysaccharide expressed in Enterobacteraceae species. 248 matched cddid_all.tbl CDD TIGR04010 TIGR04010 188525 WcaD putative colanic acid polymerase WcaD. This membrane protein is believed to function as the colanic acid repeating unit polymerase (in an analagous fashion to wzy proteins in O-antigen polymerization). 404 matched cddid_all.tbl CDD TIGR04011 TIGR04011 274916 poly_gGlu_PgsC poly-gamma-glutamate biosynthesis protein PgsC/CapC. Of four genes commonly found to be involved in biosynthesis and export of poly-gamma-glutamate, pgsB(capB) and pgsC(capC) are found to be involved in the synthesis per se. Members of this family are designated PgsC, covering both cases in which the poly-gamma-glutamate is secreted and those in which it is retained to form capsular material. PgsC binds tightly to PgsB, which has been shown to have poly-gamma-glutamate activity. [Cell envelope, Other] 132 matched cddid_all.tbl CDD TIGR04012 TIGR04012 188527 poly_gGlu_PgsB poly-gamma-glutamate synthase PgsB/CapB. Of four genes commonly found to be involved in biosynthesis and export of poly-gamma-glutamate, pgsB(capB) and pgsC(capC) are found to be involved in the synthesis per se. Members of this family are designated PgsB, a nomeclature that covers both cases in which the poly-gamma-glutamate is secreted and those in which it is retained to form capsular material.PgsB has been shown to have poly-gamma-glutamate activity by itself but is bound tightly by PgsC (TIGR04011). [Cell envelope, Other] 366 matched cddid_all.tbl CDD TIGR04013 TIGR04013 274917 B12_SAM_MJ_1487 B12-binding domain/radical SAM domain protein, MJ_1487 family. Members of this family have both a B12 binding homology domain (pfam02310) and a radical SAM domain (pfam04055), and occur only once per genome. Some species with members of this family have a related protein with similar domain architecture. This protein is occurs largely in archaeal methanogens but also in a few bacteria, including Thermotoga maritima and Myxococcus xanthus. [Unknown function, Enzymes of unknown specificity] 383 matched cddid_all.tbl CDD TIGR04014 TIGR04014 274918 B12_SAM_MJ_0865 B12-binding domain/radical SAM domain protein, MJ_0865 family. Members of this family have both a B12 binding homology domain (pfam02310) and a radical SAM domain (pfam04055), and occur only once per genome. This protein occurs so far only in methanogenic archaea. Some species with members of this family have a related protein with similar domain architecture (see TIGR04013). [Unknown function, Enzymes of unknown specificity] 434 matched cddid_all.tbl CDD TIGR04015 TIGR04015 274919 WcaC colanic acid biosynthesis glycosyl transferase WcaC. This gene is one of the glycosyl transferases involved in the biosynthesis of colanic acid, an exopolysaccharide expressed in Enterobacteraceae species. 405 matched cddid_all.tbl CDD TIGR04016 TIGR04016 188531 WcaB colanic acid biosynthesis acetyltransferase WcaB. This gene is one of the acetyl transferases involved in the biosynthesis of colanic acid, an exopolysaccharide expressed in Enterobacteraceae species. 146 matched cddid_all.tbl CDD TIGR04017 TIGR04017 274920 WcaA colanic acid biosynthesis glycosyl transferase WcaA. This gene is one of the glycosyl transferases involved in the biosynthesis of colanic acid, an exopolysaccharide expressed in Enterobacteraceae species. 279 matched cddid_all.tbl CDD TIGR04018 TIGR04018 188533 Bthiol_YpdA putative bacillithiol system oxidoreductase, YpdA family. Members of this protein family, including YpdA from Bacillus subtilis, are apparent oxidoreductases present only in species with an active bacillithiol system. They have been suggested actually to be thiol disulfide oxidoreductases (TDOR), although the evidence is incomplete. [Unknown function, Enzymes of unknown specificity] 316 matched cddid_all.tbl CDD TIGR04019 TIGR04019 274921 B_thiol_YtxJ bacillithiol system protein YtxJ. Members of this protein family, including YtxJ from Bacillus subtilis, occur in species that encode proteins for synthesizing bacillithiol. The protein is described as thioredoxin-like, while another bacillithiol-associated protein, YpdA (TIGR04018), is described as thioredoxin reductase-like. [Unknown function, Enzymes of unknown specificity] 105 matched cddid_all.tbl CDD TIGR04020 TIGR04020 274922 seco_metab_LLM natural product biosynthesis luciferase-like monooxygenase domain. This model describes a subfamily within the bacterial luciferase-like monooxygenase (LLM) family that regularly occurs within large non-ribosomal protein synthases/polyketide synthases, but also as small proteins. The LLM family includes members that bind either FMN or F420, and FMN is more likely in this case because many members are from species that lack F420 biosynthesis capability. An example member is the MupA protein of mupirocin biosynthesis in Pseudomonas fluorescens NCIMB 10586. 341 matched cddid_all.tbl CDD TIGR04021 TIGR04021 274923 LLM_DMSO2_sfnG dimethyl sulfone monooxygenase SfnG. This family of FMNH2-dependent members of the luciferase-like monooxygenase (LLM) family includes SfnG, a monooxygenase that converts dimethylsulphone (DMSO2) to methanesulphonate. This step can be followed immediately by methanesulfonate sulfonatase (an alkanesulfonate monooxygenase - see TIGR03565) for the FMNH2-dependent conversion an inorganic form. [Central intermediary metabolism, Sulfur metabolism] 350 matched cddid_all.tbl CDD TIGR04022 TIGR04022 274924 sulfur_SfnB sulfur acquisition oxidoreductase, SfnB family. Members of this protein family belong to the greater family of acyl-CoA dehydrogenases. This family includes the sulfate starvation induced protein SfnB of Pseudomonas putida strain DS1, which is both encoded nearby to and phylogenetically closely correlated with the dimethyl sulphone monooxygenase SfnG. This family shows considerable sequence similarity to the Rhodococcus dibenzothiophene desulfurization enzyme DszC, although that enzyme falls outside of the scope of this family. [Central intermediary metabolism, Sulfur metabolism] 391 matched cddid_all.tbl CDD TIGR04023 TIGR04023 274925 PPOX_MSMEG_5819 PPOX class F420-dependent enzyme, MSMEG_5819/OxyR family. A Genome Properties metabolic reconstruction for F420 biosynthesis shows that slightly over 10 percent of all prokaryotes with fully sequenced genomes, including about two thirds of the Actinomycetales, make F420. This subfamily within the PPOX family occurs in at least 19 distinct species of F420 producers and is likely to bind F420 rather than FMN. The member OxyR was shown to use F420 to catalyze a C5a-C11a reduction in oxytetracycline biosynthesis. [Unknown function, Enzymes of unknown specificity] 115 matched cddid_all.tbl CDD TIGR04024 TIGR04024 188539 F420_NP1902A coenzyme F420-dependent oxidoreductase, NP1902A family. This subfamily of the luciferase-like monooxygenases is restricted to the order Halobacteriales. SIMBAL analysis strongly suggests this oxidoreductase binds coenzyme F420 rather than FMN. Occasional annotations of members of this family as N5,N10-methylenetetrahydromethanopterin reductase appear to represent overly aggressive transfer of annotation. [Unknown function, Enzymes of unknown specificity] 330 matched cddid_all.tbl CDD TIGR04025 TIGR04025 274926 PPOX_FMN_DR2398 PPOX class probable FMN-dependent enzyme, DR_2398 family. Members of the PPOX family (see pfam01243) may contain either FMN or F420 as cofactor. This subfamily consists of proteins mostly from species that lack the capability to synthesize F420, and therefore most likely all bind FMN. 197 matched cddid_all.tbl CDD TIGR04026 TIGR04026 274927 PPOX_FMN_cyano PPOX class probable FMN-dependent enzyme, alr4036 family. Members of the PPOX family (see pfam01243) may contain either FMN or F420 as cofactor. This subfamily described here is widespread in Cyanobacteria and plants, and is named for alr4036 from Nostoc sp. PCC 7120. The family consists mostly of proteins from species that lack the capability to synthesize F420, so it is probable that all members bind FMN rather than F420. [Unknown function, Enzymes of unknown specificity] 185 matched cddid_all.tbl CDD TIGR04027 TIGR04027 274928 LLM_KPN_01858 putative FMN-dependent luciferase-like monooxygenase, KPN_01858 family. This protein family consists of luciferase-like monooxygenases (LLM), and include KPN_01858 from Klebsiella pneumoniae as a representative member. Most are from species that lack F420 biosynthesis, so the family is likely to bind FMN as its cofactor. This family is closely associated with a binding protein-dependent ABC transporter, suggesting a role in catabolism. [Unknown function, Enzymes of unknown specificity] 326 matched cddid_all.tbl CDD TIGR04028 TIGR04028 274929 SBP_KPN_01854 ABC transporter substrate binding protein, KPN_01854 family. Members of this protein family are ABC transporter substrate-binding proteins related to KPN_01854 from Klebsiella pneumoniae, and occur in both Gram-positive and Gram-negative species. This transport protein family is closely associated with a putative FMN-dependent luciferase-like monooxygenase of unknown function (TIGR04027), as well as with the other proteins of its transporter complex. [Transport and binding proteins, Unknown substrate] 509 matched cddid_all.tbl CDD TIGR04029 TIGR04029 213885 CMD_Avi_7170 CMD domain protein, Avi_7170 family. Sequences in this family occur as the N-terminal domain of a fusion protein with a C-terminal peroxidase-like protein, or as discrete protein encoded next to a peroxidase-like protein. The two partners regularly are encoded near to, and in the same genomes as, a putative FMN-dependent luciferase-like monooxygenase (LLM) (TIGR04027), and an ABC transporter in which TIGR04028 models the substrate-binding protein. CDD identifies this family as falling within the CMD superfamily that includes carboxymuconolactone decarboxylase. 174 matched cddid_all.tbl CDD TIGR04030 TIGR04030 188545 perox_Avi_7169 alkylhydroperoxidase domain protein, Avi_7169 family. Members of this family represent a narrow clade that falls within a family of alkylhydroperoxidase-related proteins, fused to or adjacent to a sequence described by TIGR04029. These two partners occur almost always in the context of a putative FMN-dependent luciferase-like monooxygenase (LLM) (TIGR04027), and an ABC transporter in which TIGR04028 models the substrate-binding protein. 185 matched cddid_all.tbl CDD TIGR04031 TIGR04031 188546 Htur_1727_fam rSAM-partnered protein, Htur_1727 family. Members of this protein family show homology to the putative PaaH (or PaaB) subunit of the phenylacetate-CoA oxygenase complex. However, all members are found in the Halobacteriales in the vicinity of a radical SAM protein homologous to the PqqE protein of pyroquinoline quinone (PQQ) biosynthesis. Members are well-conserved to about residue 75, but then become low-complexity and hypervariable. 71 matched cddid_all.tbl CDD TIGR04032 TIGR04032 274930 toxin_SdpC antimicrobial peptide, SdpC family. This protein family contains the antimicrobial peptide SdpC, used in cannibalistic killing by Bacillus subtilis, and related sequences in species as distant as Myxococcus xanthus from the Deltaproteobacteria. A conserved gene neighborhood includes proteins associated with immunity. 172 matched cddid_all.tbl CDD TIGR04033 TIGR04033 274931 export_SdpB antimicrobial peptide system protein, SdpB family. Members of this protein family resemble SdpB (Sporulation Delaying Protein B), an integral membrane protein associated with production of the cannibalism peptide SdpC in Bacillus subtilis. Similar proteins are found in Myxococcus xanthus. 276 matched cddid_all.tbl CDD TIGR04034 TIGR04034 274932 export_SdpA antimicrobial peptide system protein, SdpA family. Members of this protein family resemble SdpA (Sporulation Delaying Protein A), a protein associated with production and export of the cannibalism peptide SdpC in Bacillus subtilis. Similar proteins are found in Myxococcus xanthus, Stigmatella aurantiaca DW4/3-1, Streptomyces sp. ACTE, etc. 156 matched cddid_all.tbl CDD TIGR04035 TIGR04035 274933 glucan_65_rpt glucan-binding repeat. This model describes a region of about 63 amino acids that is composed of three repeats of a more broadly distributed family of shorter repeats modeled by pfam01473. While the shorter repeats are often associated with choline binding (and therefore with cell wall binding), the longer repeat described here represents a subgroup of repeat sequences associated with glucan binding, as found in a number glycosylhydrolases. Shah, et al. describe a repeat consensus, WYYFDANGKAVTGAQTINGQTLYFDQDGKQVKG, that corresponds to half of the repeat as modeled here and one and a half copies of the repeat as modeled by pfam01473. 62 matched cddid_all.tbl CDD TIGR04036 TIGR04036 274934 LLM_CE1758_fam putative luciferase-like monooxygenase, FMN-dependent, CE1758 family. This tightly conserved subfamily of the bacterial luciferase-like monooxygenase (LLM) family, with members showing > 60 % pairwise sequence identity, includes proteins from both species with and species without the ability to make coenzyme F420. Therefore, the like cofactor is FMN rather than F420. The presence of three members in Kineococcus radiotolerans SRS30216 and two in Saccharopolyspora erythraea NRRL 2338 suggest closely related (subfamily) rather than exactly conserved (equivalog) function. Gene neighborhoods around members are not conserved. [Unknown function, Enzymes of unknown specificity] 355 matched cddid_all.tbl CDD TIGR04037 TIGR04037 274935 LLM_duo_CE1759 LLM-partnered FMN reductase, CE1759 family. This family represents a distinct clade within pfam03358. That family includes enzymes such as the NADH-dependent FMN reductase MsuE. Members of the present family regularly co-occur in genomes, typically as gene pairs, with members of TIGR04036, a probable FMN-dependent member of the bacterial luciferase-like monooxygenase (LLM) family. At least one member, RF|YP_001509627.1 from Frankia sp. EAN1pec, is fused to the LLM protein. The function of these gene pairs is unknown. 198 matched cddid_all.tbl CDD TIGR04038 TIGR04038 274936 tatD_link_rSAM radical SAM protein, TatD family-associated. Members of this family are radical SAM proteins found in about 5 percent of microbial genomes. A portion occur as gene fusions with, or adjacent to, members of the TatD family of hydrolases (pfam01026). The TatD family may have several paralogs per genome, including TatD itself from E. coli (a soluble protein not actually part of the twin-arginine translocation complex), which appears to act in quality control for TAT, directing turnover of misfolded TAT substrates. The functions of TatD family hydrolases in general (other than TatD itself, which may be exceptional within its larger family), and of this radical SAM domain protein modeled here, are unknown. 191 matched cddid_all.tbl CDD TIGR04039 TIGR04039 188554 MXAN_0977_Heme2 di-heme enzyme, MXAN_0977 family. This model describes a subfamily of di-heme proteins related to the di-heme cytochrome c peroxidase and to MauG (methylamine utilization G), an enzyme that performs a tryptophan tryptophylquinone modification to the methylamine dehydrogenase light chain. 336 matched cddid_all.tbl CDD TIGR04040 TIGR04040 274937 glycyl_YjjI glycine radical enzyme, YjjI family. Members of this family are homologs to enzymes known to undergo activation by a radical SAM protein to create an active site glycyl radical. This family appears to be activated by the YjjW radical SAM protein, usually encoded by an adjacent gene. [Unknown function, Enzymes of unknown specificity] 497 matched cddid_all.tbl CDD TIGR04041 TIGR04041 274938 activase_YjjW glycine radical enzyme activase, YjjW family. Members of this family are radical SAM enzymes, designated YjjW in E. coli, that are paired with and appear to activate a glycyl radical enzyme of unknown function, designated YjjI. This activase and its target are found in Clostridial species as well as E. coli and cousins. Members of this family may be misannotated as pyruvate formate lyase activating enzyme. [Protein fate, Protein modification and repair] 276 matched cddid_all.tbl CDD TIGR04042 TIGR04042 274939 MSMEG_0570_fam MSMEG_0570 family protein. This small protein, about 90 residues long, has no detectable homologs outside the set used to characterize this model. Member proteins serve as markers for an eight-gene region whose overall function is unknown. One member of the cluster is a radical SAM protein with some similarity to enzymes of cofactor biosynthesis, another a glycosyltransferase, several hydrolases or oxidoreductases, and several unknown. 90 matched cddid_all.tbl CDD TIGR04043 TIGR04043 274940 rSAM_MSMEG_0568 radical SAM protein, MSMEG_0568 family. Members of this protein family are radical SAM proteins related to MSMEG_0568 from Mycobacterium smegmatis. Members occur within 8-gene operons in species as diverse as M. smegmatis, Rhizobium leguminosarum, Synechococcus elongatus, and Sorangium cellulosum. The function of the operon is unknown, but similarity of MSMEG_0568 to some cofactor biosynthesis radical SAM proteins suggests a similar biosynthetic function. [Unknown function, Enzymes of unknown specificity] 354 matched cddid_all.tbl CDD TIGR04044 TIGR04044 188559 MSMEG_0572_fam MSMEG_0572 family protein. This model describes a family of proteins with remote similarity to the DsrE/DsrF-like family (see pfam02635). All members are found in a context of at least seven genes that includes a radical SAM protein, suggesting biosynthesis. The system is sparsely but broadly distributed in bacteria, including Actinobacteria, Proteobacteria, and Cyanobacteria. 159 matched cddid_all.tbl CDD TIGR04045 TIGR04045 274941 MSMEG_0567_GNAT putative N-acetyltransferase, MSMEG_0567 N-terminal domain family. Members of this family belong to the GNAT family (pfam00583), in which numerous characterized examples, though not all, are are shown to be N-acetyltransferases or to interact with acetyl-CoA. This family occurs in a sparsely distributed biosynthetic cluster that occurs in Actinobacteria, Cyanobacteria, and Proteobacteria. 153 matched cddid_all.tbl CDD TIGR04046 TIGR04046 274942 MSMEG_0569_nitr flavin-dependent oxidoreductase, MSMEG_0569 family. Members of this protein family belong to a conserved seven-gene biosynthetic cluster found sparsely in Cyanobacteria, Proteobacteria, and Actinobacteria. Distant homologies to characterized proteins suggest that members are enzymes dependent on a flavinoid cofactor. 400 matched cddid_all.tbl CDD TIGR04047 TIGR04047 274943 MSMEG_0565_glyc glycosyltransferase, MSMEG_0565 family. A conserved gene cluster found sporadically from Actinobacteria to Proteobacteria to Cyanobacteria features a radical SAM protein, an N-acetyltransferase, an oxidoreductase, and two additional proteins whose functional classes are unclear. The metabolic role of the cluster is probably biosynthetic. This glycosyltransferase, named from member MSMEG_0565 from Mycobacterium smegmatis, occurs in most but not all instances of the cluster. [Unknown function, Enzymes of unknown specificity] 373 matched cddid_all.tbl CDD TIGR04048 TIGR04048 188563 nitrile_sll0784 putative nitrilase, sll0784 family. This family represents a subfamily of a C-N bond-cleaving hydrolases (see pfam00795). Members occur as part of a cluster of genes in a probable biosynthetic cluster that contains a radical SAM protein, an N-acetyltransferase, a flavoprotein, several proteins of unknown function, and usually a glycosyltransferase. Members are closely related to a characterized aliphatic nitrilase from Rhodopseudomonas rhodochrous J1, for which an active site Cys was found at position 165. [Unknown function, Enzymes of unknown specificity] 301 matched cddid_all.tbl CDD TIGR04049 TIGR04049 188564 AIR_rel_sll0787 AIR synthase-related protein, sll0787 family. Members of this family include sll0787 from Synechocystis sp. PCC 6803 and resemble the C-terminal region of MSMEG_0567 from Mycobacterium smegmatis, where the N-terminal is a GNAT family N-acetyltransferase. The conserved cluster is found broadly (Cyanobacteria, Proteobacteria, Actinobacteria) in about 8 percent of genomes and appears to be biosynthetic. The product is unkown. [Unknown function, Enzymes of unknown specificity] 316 matched cddid_all.tbl CDD TIGR04050 TIGR04050 274944 MSMEG_0567_Cter AIR synthase-related protein, MSMEG_0567 C-terminal family. Members of this family include the C-terminal region of MSMEG_0567 from Mycobacterium smegmatis, where the N-terminal is a GNAT family N-acetyltransferase, and resemble the full length of sll0787 from Synechocystis sp. PCC 6803. The conserved cluster that contains these is found broadly (Cyanobacteria, Proteobacteria, Actinobacteria) in about 8 percent of genomes and appears to be biosynthetic. The product is unkown. [Unknown function, Enzymes of unknown specificity] 296 matched cddid_all.tbl CDD TIGR04051 TIGR04051 188566 rSAM_NirJ heme d1 biosynthesis radical SAM protein NirJ. Heme d1 occurs in the cytochrome cd1 subunit of nitrite reductase in species such as Pseudomonas stutzeri. NirJ is a radical SAM protein involved in its bioynthesis. In a number of species, distinct genes NirJ1 and NirJ2 are found in similar genomic regions; this model describe authentic NirJ from genomes with NirJ only. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 354 matched cddid_all.tbl CDD TIGR04052 TIGR04052 188567 AZL_007920_fam AZL_007920/MXAN_0976 family protein. Members of this rare protein family regularly occur next to a member of the MXAN_0977 subfamily (TIGR04039) of the di-heme cytochrome c peroxidase/MauG family (pfam03150). MauG itself (TIGR03791) is a protein modification enzyme responsible for the tryptophan tryptophylquinone (TTQ) modification involved in methylamine dehydrogenase activation. All members of this family have a motif of four spaced invariant Cys residues, while additional homologs outside the scope of this family lack the four Cys residues. 206 matched cddid_all.tbl CDD TIGR04053 TIGR04053 274945 sam_11 radical SAM protein, BA_1875 family. Members of this subfamily of the radical SAM domain superfamily show closer sequence relationships to peptide-modifying proteins of bacteriocin and PQQ biosynthesis than to other characterized radical SAM proteins. Within this subfamily, targets are likely to be diverse. [Unknown function, Enzymes of unknown specificity] 365 matched cddid_all.tbl CDD TIGR04054 TIGR04054 274946 rSAM_NirJ1 putative heme d1 biosynthesis radical SAM protein NirJ1. Members of this radical SAM protein subfamily, designated NirJ1, occur in genomic contexts with a paralog NirJ2 and with other nitrite reductase operon genes associated with heme d1 biosynthesis, as in Heliobacillus mobilis and Heliophilum fasciatum. NirJ1 is presumed by bioinformatics analysis (Xiong, et al.) to be a heme d1 biosynthesis protein by context, perhaps involved in conversions of acetate groups to methyl groups in conversion from uroporphyrinogen III. A very closely related protein, involved in alternative heme b biosynthesis, occurs in Desulfovibrio and in methanogens. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 387 matched cddid_all.tbl CDD TIGR04055 TIGR04055 274947 rSAM_NirJ2 putative heme d1 biosynthesis radical SAM protein NirJ2. Members of this radical SAM protein subfamily, designated NirJ2, occur in genomic contexts with a paralog NirJ1 and with other nitrite reductase operon genes associated with heme d1 biosynthesis, as in Heliobacillus mobilis and Heliophilum fasciatum. NirJ2 is presumed by bioinformatics analysis (Xiong, et al.) to be a heme d1 biosynthesis protein by context. This model has been redone (2014) to remove the branch (TIGR04545) that included DVU_0855, from a similar pathway for heme b biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 326 matched cddid_all.tbl CDD TIGR04056 TIGR04056 274948 OMP_RagA_SusC TonB-linked outer membrane protein, SusC/RagA family. This model describes a distinctive clade among the TonB-linked outer membrane proteins (OMP). Members of this family are restricted to the Bacteriodetes lineage (except for Gemmatimonas aurantiaca T-27 from the novel phylum Gemmatimonadetes) and occur in high copy numbers, with over 100 members from Bacteroides thetaiotaomicron VPI-5482 alone. Published descriptions of members of this family are available for RagA from Porphyromonas gingivalis, SusC from Bacteroides thetaiotaomicron, and OmpW from Bacteroides caccae. Members form pairs with members of the SusD/RagB family (pfam07980). Transporter complexes including these outer membrane proteins are likely to import large degradation products of proteins (e.g. RagA) or carbohydrates (e.g. SusC) as nutrients, rather than siderophores. [Transport and binding proteins, Unknown substrate] 981 matched cddid_all.tbl CDD TIGR04057 TIGR04057 274949 SusC_RagA_signa TonB-dependent outer membrane receptor, SusC/RagA subfamily, signature region. This model describes a 31-residue signature region of the SusC/RagA family of outer membrane proteins from the Bacteriodetes. While many TonB-dependent outer membrane receptors are associated with siderophore import, this family seems to include generalized nutrient receptors that may convey fairly large oligomers of protein or carbohydrate. This family occurs in high copy numbers in the most abundant species of the human gut microbiome. 31 matched cddid_all.tbl CDD TIGR04058 TIGR04058 188573 AcACP_reductase long-chain fatty acyl-ACP reductase (aldehyde-forming). This enzyme, found in cyanobacteria, reduces a long-chain (mainly C16 or C18) fatty acyl ACP ester to its corresponding fatty aldehyde, releasing the acyl carrier protein (ACP). NADPH or NADH is the reductant for this reaction. This enzyme may be distantly related to the short-chain dehydrogenase or reductase (SDR) family (pfam00106). The purpose of this reaction is in the first step of alkane biosynthesis (GenProp0942). [Central intermediary metabolism, Other] 339 matched cddid_all.tbl CDD TIGR04059 TIGR04059 274950 Ald_deCOase long-chain fatty aldehyde decarbonylase. This cyanobacterial family of fatty aldehyde decarbonylases acts on mainly C16 and C18 substrates to form hydrocarbons and carbon monoxide. Note that the corresponding EC number (4.1.99.5) dating from 1989 refers to a nonorthologous Pisum sativum enzyme that acts on C18 and longer chains and attaches the overly narrow narrow name octadecanal decarbonylase. [Central intermediary metabolism, Other] 220 matched cddid_all.tbl CDD TIGR04060 TIGR04060 274951 formate_focA formate transporter FocA. FocA (formate channel A) forms a pentameric formate-selective channel through the plasma membrane. The focA gene is largely restricted to Proteobacteria and occurs adjacent to genes for pyruvate formate lyase (PFL) and the PFL activase, a radical SAM protein. FocA is homologous to a nitrite transport protein, NirC. [Transport and binding proteins, Carbohydrates, organic alcohols, and acids] 267 matched cddid_all.tbl CDD TIGR04061 TIGR04061 274952 AZL_007950_fam AZL_007950 family protein. This set of proteins includes PP_3335 from Pseudomonas putida, a protein of unknown function, and AZL_007950, a member of a putative biosynthetic cluster from Azospirillum sp. B510. 164 matched cddid_all.tbl CDD TIGR04062 TIGR04062 274953 dnd_assoc_4 dnd system-associated protein 4. A DNA sulfur modification system, dnd (degradation during electrophoresis), is sparsely and sporadically distributed among the bacteria. Members of this protein fam ily are strictly limited to species with the dnd operon, and are found close to the dnd operon on the chromosomes of species such as Nostoc sp. PCC 7120, Geobacter uraniireducens Rf4, and Roseobacter denitrificans OCh 114. [DNA metabolism, Restriction/modification] 151 matched cddid_all.tbl CDD TIGR04063 TIGR04063 274954 stp3 PEP-CTERM/exosortase A-associated glycosyltransferase, Daro_2409 family. PEP-CTERM/exosortase is a protein-sorting system associated with exopolysaccharide production. Members of this protein family are group 1 glycosyltransferases (see pfam00534) in which the overwhelming majority occur in species with the EpsH1 form of exosortase (see TIGR03109), and usually co-clustered with the exosortase. A typical member is Daro_2409 from Dechloromonas aromatica RCB. 397 matched cddid_all.tbl CDD TIGR04064 TIGR04064 274955 rSAM_nif11 nif11-like peptide radical SAM maturase. Members of this family are radical SAM enzymes that occur co-clustered with nif11-related ribosomal natural product (RNP) precursors described by TIGRFAMs model TIGR03798. Homology within the bacteriocin family reflects largely constraints on the leader peptide, tied to processes such as cleavage and export, and members associate with various families of maturation enzyme. The gene symbol assigned is nlpM, for Nif11-class Leader Peptide family Radical SAM Maturase. [Cellular processes, Toxin production and resistance] 458 matched cddid_all.tbl CDD TIGR04065 TIGR04065 274956 ocin_CLI_3235 putative bacteriocin precursor, CLI_3235 family. Members of this protein family are Cys-rich putative bacteriocin precursor peptides restricted to the Clostridia but found in multiple species with up to three per genome. They are found next to a CLI_3234 family radical SAM protein that may perform post-translational modification. This model describes approximately 35 residues starting from the N-terminus. Precursor peptides average about 50 amino acids in length. [Cellular processes, Toxin production and resistance] 34 matched cddid_all.tbl CDD TIGR04066 TIGR04066 274957 nat_prod_clost peptide maturation system protein, TIGR04066 family. Members of this protein family occur in various Clostridial genomes, always in the context of a short peptide and a radical SAM protein predicted to modify the short peptide. PSI-BLAST analysis suggests a sequence relationship to archaeal proteins designated as subunits of an H+-transporting two-sector ATPase. The modified peptide is likely to be a bacteriocin, and this protein is a candidate to act in either maturation or immunity. 361 matched cddid_all.tbl CDD TIGR04067 TIGR04067 188582 oc_CLOSPO_01332 putative bacteriocin precursor, CLOSPO_01332 family. Members of this protein family are Cys-rich putative bacteriocin precursor peptides found in a few strains of Clostridium and Anaerococcus. This family is related to the family of CLI_3235 (TIGR04065). Members of both families are found next to a CLI_3234 family radical SAM protein that appears to perform post-translational modification. 59 matched cddid_all.tbl CDD TIGR04068 TIGR04068 274958 rSAM_ocin_clost Cys-rich peptide radical SAM maturase CcpM. Members of this family are radical SAM enzymes that occur next to clostridial Cys-rich predicted bacteriocin (or other class of ribosomal natural product) precursors (see families TIGR04065 and TIGR04067). They include a TIGR04085 C-terminal additional 4Fe4S cluster-binding domain that is associated with peptide modification by radical SAM enzymes, and they are proposed to be ribosomal natural product maturases. The gene symbol ccpM is assigned, for Clostridial Cys-rich Peptide Maturase. [Cellular processes, Toxin production and resistance] 459 matched cddid_all.tbl CDD TIGR04069 TIGR04069 274959 ocin_ACP_rel peptide maturation system acyl carrier-related protein. Both PSI-BLAST and large numbers of noise-level HMM hits show a relationship between this family and the phosphopantetheine attachment site domain modeled by pfam00550. That domain includes acyl carrier proteins (ACP) and features an essentially invariant serine residue that is the attachment site for the phosphopantetheine prosthetic group. In this family, the corresponding residue is not Ser and is not conserved. Members are found in genomic contexts associated with a small Cys-rich peptide and a radical SAM protein we predict modifies the peptide. [Cellular processes, Toxin production and resistance] 77 matched cddid_all.tbl CDD TIGR04070 TIGR04070 213890 photo_TT_lyase spore photoproduct lyase. DNA damage to bacterial spores from ultraviolet light accumulates in the form of 5-thyminyl-5,6-dihydrothymine, spore photoproduct. The damage is repaired by spore photoproduct lyase, a member of the radical SAM family of enzymes. The score of this model is set to restrict itself to spore-forming members of the Firmicutes, but additional homologs scoring below the trusted cutoff tend to occur in radioresistant organisms (e.g. Kineococcus radiotolerans) and may be functionally equivalent. A related family in the Mycobacterium lineage is described by family TIGR03886, and may or may not be equivalent in function. [DNA metabolism, DNA replication, recombination, and repair, Cellular processes, Sporulation and germination] 338 matched cddid_all.tbl CDD TIGR04071 TIGR04071 274960 methanobac_OB3b methanobactin precursor, Mb-OB3b family. Methanobactins are siderophore-like copper-chelating natural products with considerable variety from species to species. The 11-residue methanobactin of Methylosinus trichosporium OB3b is derived from a 30-residue precursor. A very similar 31-residue precursor is found in the rice endophyte Azospirillum sp. B510, which has not yet been shown to produce a methanobactin. This model models the shared region of the first 25 amino acids, including a Cys-Gly-Ser motif. 30 matched cddid_all.tbl CDD TIGR04072 TIGR04072 188587 rSAM_ladder_B12 lipid biosynthesis B12-binding/radical SAM protein. Members of this protein family occur in conserved genomic contexts highly suggestive of lipid biosynthesis, including an island shared between Kuenenia stuttgartiensis, which produces ladderanes, and Desulfotalea psychrophila, which produces a different kind of unusual polyunsaturated hydrocarbon. 151 matched cddid_all.tbl CDD TIGR04073 TIGR04073 274961 exo_TIGR04073 putative exosortase-associated protein, TIGR04073 family. Members of this protein family are found in beta, gamma, and delta proteobacteria, and in the verrucomicrobia. Twenty-two of twenty-four species encountered contain the PEP-CTERM/exosortase system for modulating extracellular polysaccharide biosynthesis production, suggesting a role in protein sorting. The N-terminal signal sequence is divergent and not included in the model. PSI-BLAST and HMM searches suggest a distant sequence relationship between a region of this protein of about 100 amino acids and a corresponding region of the very large eukaryotic protein vps13, associated with vacuolar protein sorting in yeast. 75 matched cddid_all.tbl CDD TIGR04074 TIGR04074 274962 bacter_Hen1 3' terminal RNA ribose 2'-O-methyltransferase Hen1. Members of this protein family are bacterial Hen1, a 3' terminal RNA ribose 2'-O-methyltransferase that acts in bacterial RNA repair. All members of the seed alignment belong to a cassette with the RNA repair enzyme polynucleotide kinase-phosphatase (Pnkp). Chemically similar Hen1 in eukaryotes acts instead on small regulatory RNAs. [Transcription, RNA processing, Protein synthesis, tRNA and rRNA base modification] 462 matched cddid_all.tbl CDD TIGR04075 TIGR04075 274963 bacter_Pnkp polynucleotide kinase-phosphatase. Members of this protein family are the bacterial polynucleotide kinase-phosphatase (Pnkp) whose genes occur paired with genes for the 3' terminal RNA ribose 2'-O-methyltransferase Hen1. All members of the seed alignment belong to a cassette with the Hen1. The pair acts in bacterial RNA repair. This enzyme performs end-healing reactions on broken RNA, preparing from the RNA ligase to close the break. The working hypothesis is that the combination of Pnkp (RNA repair) and Hen1 (RNA modification) serves to first repair RNA damage from ribotoxins and then perform a modification that prevents the damage from recurring. [Transcription, RNA processing] 851 matched cddid_all.tbl CDD TIGR04076 TIGR04076 274964 TIGR04076 TIGR04076 family protein. Members of this protein family are uncharacterized. The only invariant residue, and one of three other residues better than 90 percent conserved are both Cys. Phylogenetic profiling results and occasional fusion genes suggest a role for members of this family in redox reactions or iron cluster metabolism. Species occasionally have two or three copies. 89 matched cddid_all.tbl CDD TIGR04077 TIGR04077 188592 expor_sig_YdyF exported signaling peptide, YydF/SAG_2028 family. This family describes a rare family of small proteins, about 50 residues in length, that includes YydF from Bacillus subtilis and SAG_2028 from Streptococcus agalactiae 2603V/R. Mutational analysis and genomic context show that members of this family likely are modified by a (variably present) radical SAM enzyme, are exported by an ABC transporter, and serve as signaling peptide. The member from Bacillus subtilis induces the LiaRS two-component system. [Regulatory functions, Protein interactions] 49 matched cddid_all.tbl CDD TIGR04078 TIGR04078 188593 rSAM_yydG peptide modification radical SAM enzyme, YydG family. Members of this radical SAM protein family for peptide modification occur only in the context of members of family TIGR04077, which average about 50 amino acids in length. In Bacillus subtilis, this protein (YydG) appears to act on its cognate target peptide (YydF) prior to its export, and result in the creation of a signaling molecule that induces the LiaRS two-component system. [Regulatory functions, Protein interactions] 309 matched cddid_all.tbl CDD TIGR04079 TIGR04079 188594 phero_cyc_pep KxxxW-cyclized secreted peptide. Members of this family are short precursor peptides in which the mature form undergoes a cyclization between a Lys and a Trp four residues away. The modification enzyme appears to be an adjacent encoded radical SAM protein. Genomes encoding this system include Streptococcus thermophilus LMD-9 and Lactococcus lactis subsp. cremoris MG1363, among others. [Cellular processes, Biosynthesis of natural products] 23 matched cddid_all.tbl CDD TIGR04080 TIGR04080 188595 rSAM_pep_cyc KxxxW cyclic peptide radical SAM maturase. Members of this family are radical SAM enzymes that appear to perform a cyclization on an adjacent cognate peptide from family TIGR04079. Genomes with the complete system include Streptococcus thermophilus LMD-9 and Lactococcus lactis subsp. cremoris MG1363, among others. The gene symbol assigned is kwcM, for KxxxW Cyclic peptide Maturase. [Protein fate, Protein modification and repair] 440 matched cddid_all.tbl CDD TIGR04081 TIGR04081 188596 selen_ocin radical SAM modification target peptide, selenobiotic family. Members of this protein family are small peptides found in the vicinity of a peptide modification-type radical SAM protein family. Multiple members of this protein family occur in species with a selenocysteine incorporation systems and have a TGA stop codon at position that aligns with cysteine residues from other homologs. This finding strongly suggests that GSU_1558 and similar members of the family are selenopeptides. The selenocysteine insertion sequence (SECIS) finder bSECISearch finds two homologous SECIS elements for two TGA codons in the extension of GSU_1558. Meanwhile, the pairing with the radical SAM enzyme suggests additional modification. 37 matched cddid_all.tbl CDD TIGR04082 TIGR04082 274965 rSAM_for_selen selenobiotic family peptide radical SAM maturase. Members of this protein family are radical SAM (rSAM) enzymes similar in sequence to others with known or postulated roles in peptide modification, and regularly found adjacent to members of the GSU_1558 peptide family described by model TIGR04081. GSU_1558 and several other members of that family appear to be selenoproteins, hence the term selenobiotic. 516 matched cddid_all.tbl CDD TIGR04083 TIGR04083 274966 rSAM_pep_methan putative peptide-modifying radical SAM enzyme, Mhun_1560 family. Members of this family are radical SAM enzymes, homologous to a variety of other peptide-modifying radical SAM, and found primarily in methanogenic archaea. 376 matched cddid_all.tbl CDD TIGR04084 TIGR04084 274967 rSAM_AF0577 putative peptide-modifying radical SAM enzyme, AF0577 family. This radical SAM family contains a C-terminal region motif CXXCX5CX3C that is found in PqqE and other radical SAM enzymes that act on peptide substrates. Members of this family are found primarily in the Archaea, but also several eukaryotes (Trichomonas vaginalis G3, Entamoeba dispar SAW760, Giardia intestinalis ATCC 50581, etc.). The function is unknown. 347 matched cddid_all.tbl CDD TIGR04085 TIGR04085 274968 rSAM_more_4Fe4S radical SAM additional 4Fe4S-binding SPASM domain. This domain contains regions binding additional 4Fe4S clusters found in various radical SAM proteins C-terminal to the domain described by model pfam04055. Radical SAM enzymes with this domain tend to be involved in protein modification, including anaerobic sulfatase maturation proteins, a quinohemoprotein amine dehydrogenase biogenesis protein, the Pep1357-cyclizing radical SAM enzyme, and various bacteriocin biosynthesis proteins. The motif CxxCxxxxxCxxxC is nearly invariant for members of this family, although PqqE has a variant form. We name this domain SPASM for Subtilosin, PQQ, Anaerobic Sulfatase, and Mycofactocin. 93 matched cddid_all.tbl CDD TIGR04086 TIGR04086 274969 TIGR04086_membr putative membrane protein, TIGR04086 family. Members of this family of strongly hydrophobic putative transmembrane protein average about 125 amino acids in length and occur mostly, but not exclusively, in the Firmicutes. Members are quite diverse in sequence. The function is unknown. 115 matched cddid_all.tbl CDD TIGR04087 TIGR04087 274970 YqxM_for_SipW YqxM protein. Members of this protein, including the partially characterized YqxM of Bacillus subtilis, are always found adjacent to a variant form, SipW, of signal peptidase, and are targets for this signal peptide, as is the biofilm protein constituent TasA. The function may always be associated with biofilm formation. In one instance, this protein is fused with the SipW signal peptidase. 186 matched cddid_all.tbl CDD TIGR04088 TIGR04088 274971 cognate_SipW SipW-cognate class signal peptide. This model describes a protein N-terminal domain found regularly in proteins encoded near a variant form of signal peptidase I such as the SipW protein of Bacillus subtilis. Many though not all members are homologs of camelysin (a casein-cleaving metalloprotease) and TasA (CotN), a metalloprotease that is secreted, along with extracellular polysaccharide (EPS), to be the major protein constituent of the Bacillus subtilis biofilm matrix. Sequencing from several known TasA/CotN proteins shows the cleavage location to be near the center of the alignment and typical of type I signal peptidases, with small residues at -3 and -1. This domain, therefore, appears to be a special subclass of signal peptide. 34 matched cddid_all.tbl CDD TIGR04089 TIGR04089 274972 exp_by_SipW_III alternate signal-mediated exported protein, RER_14450 family. Members of this Actinobacterial protein family contain the cognate signal peptide domain, modeled by TIGR04088, for the variant SipW form of the signal peptidase I family. The remainder of this protein, however, differs from families such as Peptidase_M73 (pfam12389) and YqxM (TIGR04087) that share the same signal peptide domain. Some additional homologs to this family lack full-length homology and are excluded by the trusted cutoff as set. The two known targets for export by the SipW signal peptidase in Bacillus subtilis act in producing biofilm matrix material. 179 matched cddid_all.tbl CDD TIGR04090 TIGR04090 274973 exp_by_SipW_IV alternate signal-mediated exported protein, CPF_0494 family. Members of this largely Clostridial protein family contain the cognate signal peptide domain, modeled by TIGR04088, for the variant SipW form of the signal peptidase I family. The remainder of this protein, however, differs from families such as Peptidase_M73 (pfam12389) and YqxM (TIGR04087) that share the same signal peptide domain. Some additional homologs to this family lack full-length homology and are excluded by the trusted cutoff as set. The two known targets for export by the SipW signal peptidase in Bacillus subtilis act in producing biofilm matrix material. Members include CPF_0494, adjacent to SipW homolog CPF_0493. 244 matched cddid_all.tbl CDD TIGR04091 TIGR04091 274974 LTA_dltB D-alanyl-lipoteichoic acid biosynthesis protein DltB. Members of this protein family are DltB, part of a four-gene operon for D-alanyl-lipoteichoic acid biosynthesis that is present in the vast majority of low-GC Gram-positive organisms. This protein may be involved in transport of D-alanine across the plasma membrane. [Cell envelope, Biosynthesis and degradation of murein sacculus and peptidoglycan] 380 matched cddid_all.tbl CDD TIGR04092 TIGR04092 274975 LTA_DltD D-alanyl-lipoteichoic acid biosynthesis protein DltD. Members of this protein family are DltD, part of the DltABCD system widely distributed in the Firmicutes for D-alanylation of lipoteichoic acids. The most common form of LTA, as in Staphylococcus aureus, has a backbone of polyglycerolphosphate. 384 matched cddid_all.tbl CDD TIGR04093 TIGR04093 274976 cas1_CYANO CRISPR-associated endonuclease Cas1, subtype CYANO. The CRISPR-associated protein Cas1 is virtually universal to CRISPR systems. CRISPR, an acronym for Clustered Regularly Interspaced Short Palindromic Repeats, is prokaryotic immunity system for foreign DNA, mostly from phage. CRISPR systems belong to different subtypes, distinguished by both nature of the repeats, the makeup of the cohort of associated Cas proteins, and by molecular phylogeny within the more universal Cas proteins such as this one. This model is of type EXCEPTION and provides more specific information than the EQUIVALOG model TIGR00287. It describes a clade of Cas1 limited to the CYANO subtype of CRISPR/Cas system and most often the type found there. 323 matched cddid_all.tbl CDD TIGR04094 TIGR04094 274977 adjacent_YSIRK YSIRK-targeted surface antigen transcriptional regulator. Bacteria whose genomes encode only one protein with the YSIRK variant form of signal peptide (TIGR01168) were examined for conserved genes near that one tagged protein. This protein is found adjacent to at various classes of repetitive or low-complexity YSIRK proteins (whether unique in genome or not), in a range of species (Enterococcus faecalis X98, Ruminococcus torques, Coprobacillus sp. D7, Lysinibacillus fusiformis ZC1, Streptococcus equi subsp. equi 4047, etc). The affliated YSIRK proteins include Streptococcal protective antigen (see ) and proteins with the Rib/alpha/Esp surface antigen repeat (see TIGR02331). The last quarter of this protein has an AraC family helix-turn-helix (HTH)transcriptional regulator domain. 383 matched cddid_all.tbl CDD TIGR04095 TIGR04095 274978 dnd_restrict_1 DNA phosphorothioation system restriction enzyme. The DNA phosphorothioate modification system dnd (DNA instability during electrophoresis) recently has been shown to provide a modification essential to a restriction system. This protein family was detected by Partial Phylogenetic Profiling as linked to dnd, and its members usually are clustered with the dndABCDE genes. 451 matched cddid_all.tbl CDD TIGR04096 TIGR04096 274979 dnd_rel_methyl DNA phosphorothioation-associated putative methyltransferase. Members of this protein family show distant local sequence similarity to a number of S-adenosyl-methionine-dependent methyltransferases. The family is identified by Partial Phylogenetic Profiling as closely tied to the DNA phosphorothioation system (dnd), and members are found adjacent to dnd genes in at least 13 species (Streptomyces lividans TK24, Shewanella frigidimarina NCIMB 400, Mycobacterium abscessus ATCC 19977, Nostoc punctiforme PCC 73102, Vibrio fischeri MJ11, etc.). The DNA phosphorothioation enables a novel form of restriction enzyme activity. Most members of this family appear in species with the DNA phosphorothioation system. [DNA metabolism, Restriction/modification] 478 matched cddid_all.tbl CDD TIGR04098 TIGR04098 274980 biosyn_clust_1 biosynthesis cluster domain. Radical SAM family TIGR04043 is a marker for a widespread eight-gene probable biosynthetic cluster of unknown function. This protein family describes a domain that occurs as an additional protein for some of those clusters, but also as the N-terminal domain of large, multidomain polyketide synthases and in other contexts. 270 matched cddid_all.tbl CDD TIGR04099 TIGR04099 274981 biosn_Pnap_2097 probable biosynthetic protein, Pnap_2097 family. Radical SAM family TIGR04043 is a marker for a widespread eight-gene probable biosynthetic cluster of unknown function. This protein family occurs only in the context of TIGR04043 member-containing biosynthetic clusters, although in a minority of such clusters. This protein family belongs to the TIGR04098 domain family, which also includes N-terminal domains of several probable polyketide synthases. A role in biosynthetic processes is suspected. 258 matched cddid_all.tbl CDD TIGR04100 TIGR04100 188615 rSAM_pair_X radical SAM enzyme, TIGR04100 family. Members of this protein family are radical SAM enzymes that appear paired with members of TIGR04002, a family of small (~170 residue), mostly hydrophobic protein. This family of radical SAM enzymes belongs to a larger family TIGR04038, in which some members show regularly in contexts with TatD. 197 matched cddid_all.tbl CDD TIGR04101 TIGR04101 200352 CCGSCS CCGSCS motif protein. This protein family, with average protein length about 58 residues, occurs in several marine bacteria, such as Shewanella benthica KT99, Marinobacter sp. ELB17, and Photobacterium profundum 3TCK. The striking feature is a C-terminal motif CCGSCS, which (perhaps coincidentally) resembles conserved core motif [LC]CGSC shared by two methanobactin precursors (see TIGR04071). There is no detectable conserved gene region for these proteins. 59 matched cddid_all.tbl CDD TIGR04102 TIGR04102 200353 SWIM_PBPRA1643 SWIM/SEC-C metal-binding motif protein, PBPRA1643 family. Members of this protein family have a SWIM, or SEC-C, domain (see pfam02810), a 21-amino acid putative Zn-binding domain that is shared with SecA, plant MuDR transposases, etc. This small protein family of unknown function occurs primarily in marine bacteria. 108 matched cddid_all.tbl CDD TIGR04103 TIGR04103 200354 rSAM_nif11_3 nif11-class peptide radical SAM maturase 3. Members of this protein family are peptide-modifying radical SAM enzymes, with a C-terminal additional 4Fe-4S cluster binding domain like many other peptide-modifying radical SAM enzymes. This form occurs primarily in the genera Cyanothece and Nostoc. 412 matched cddid_all.tbl CDD TIGR04104 TIGR04104 274982 cxxc_20_cxxc cxxc_20_cxxc protein. This small, uncommon, poorly conserved protein is found primarily in the Firmicutes. It features are pair of CxxC motifs separated by about 20 amino acids, followed by a highly hydrophobic region of about 45 amino acids. It has no conserved gene neighborhood, and its function is unknown. 94 matched cddid_all.tbl CDD TIGR04105 TIGR04105 274983 FeFe_hydrog_B1 [FeFe] hydrogenase, group B1/B3. See for descriptions of different groups. 462 matched cddid_all.tbl CDD TIGR04106 TIGR04106 274984 cas8c_GSU0052 CRISPR-associated protein GSU0052/csb3, Dpsyc system. This model describes a CRISPR-associated (cas) protein unique to the Dpsyc subtype (named for Desulfotalea psychrophila), a variant type I-C subtype, although not universal to the that subtype. Members of this family occur in CRISPR loci of Geobacter sulfurreducens PCA, Gemmata obscuriglobus UQM 2246, Rhodospirillum centenum SW, Planctomyces limnophilus DSM 3776, and Methylosinus trichosporium OB3b. 282 matched cddid_all.tbl CDD TIGR04107 TIGR04107 274985 rSAM_HutW putative heme utilization radical SAM enzyme HutW. HutW is a radical SAM enzyme closely related to HemN, the heme biosynthetic oxygen-independent coproporphyrinogen oxidase. It belongs to operons associated with heme uptake and utilization in Vibrio cholerae and related species, but neither it not HutX has been shown to be needed, as is HutZ, for heme utilization. HutW failed to complement a Salmonella enterica hemN mutant (), suggesting a related but distinct activity. Some members of this family are fused to hutX. 420 matched cddid_all.tbl CDD TIGR04108 TIGR04108 274986 HutX putative heme utilization carrier protein HutX. Members of this protein family are HutX, found paired with HutW in some heme utilization loci although not shown directly to be necessary for heme utilization. This protein is homologous to the heme carrier protein HemS, while its partner HutW is homologous to (but does not complement) HemN, the radical SAM enzyme oxygen-independent coproporphyrinogen III oxidase involved in heme biosynthesis. 154 matched cddid_all.tbl CDD TIGR04109 TIGR04109 200360 heme_ox_HugZ heme oxygenase, HugZ family. Members of this protein family are HugZ, a class of heme oxygenase that belongs to the PPOX family (pfam01243) and lacks homology to the HmuO family (pfam01126). Characterized members of this family include HP0318 from Helicobacter pylori and CJ1613c from Campylobacter jejuni. This enzyme releases iron during the conversion of heme to biliverdin. 243 matched cddid_all.tbl CDD TIGR04110 TIGR04110 200361 heme_HutZ heme utilization protein HutZ. Members of this family are heme utilization proteins, typically designated HutZ. They are members of the PPOX family (pfam01243) and, except for the lack of an N-terminal extension, are closely related to one form of heme oxidase (1.14.99.3), HugZ (TIGR04109). Members typically are found in a three-gene operon with radical SAM enzyme HutW and a protein of unknown function, HutX. 168 matched cddid_all.tbl CDD TIGR04111 TIGR04111 274987 BcepMu_gp16 phage-associated protein, BcepMu gp16 family. Members of this protein family occur in Burkholderia phage BcepMu, Pseudomonas phage B3, and Burkholderia phage KS10, and many bacterial putative prophage regions. The member from Burkholderia phage BcepMu is named gp16. Homology suggests DNA-binding activity. [Mobile and extrachromosomal element functions, Prophage functions] 55 matched cddid_all.tbl CDD TIGR04112 TIGR04112 274988 seleno_YedE putative selenium metabolism protein, YedE family. For 79 of the first 80 reference genomes in which a member of this protein family, YedE, is found, a selenium utilization system is found, spread over a broad taxonomic range (Firmicutes, spirochetes, delta-proteobacteria, Fusobacteria, Bacteriodes, etc. This family is less widespread than YedF, also involved in selenium metabolism. 337 matched cddid_all.tbl CDD TIGR04113 TIGR04113 274989 cas_csx17 CRISPR-associated protein Csx17, subtype Dpsyc. Members of this protein family are found exclusively in CRISPR-associated (cas) type I system gene clusters of the Dpsyc subtype. Markers for that type include a variant form of cas3 (model TIGR02621) and the GSU0054-like protein family (model TIGR02165). This family occurs in less than half of known Dpsyc clusters. 703 matched cddid_all.tbl CDD TIGR04114 TIGR04114 274990 tSAM_targ_Cxxx modification target Cys-rich repeat. This model describes a cysteine-rich repeat found in a number of bacterial putative radical-SAM modified natural product precursors. A substantial fraction of members of this family have been missed during gene-finding. A true hit to the model must exceed both TC on the whole and trusted cutoff 2 for at least one domain, to avoid false-positives from African swine fever virus proteins. 18 matched cddid_all.tbl CDD TIGR04115 TIGR04115 200366 rSAM_Cxxx_rpt radical SAM peptide maturase, CXXX-repeat target family. Members of this radical SAM domain protein are predicted peptide maturases, similar to PqqE, AlbA, the mycofactocin radical SAM maturase, and many others that share the peptide modification radical SAM protein C-terminal additional 4Fe4S-binding domain (TIGR04085). Members co-occur with a protein of unknown function that may be a chaperone or immunity protein and with a peptide that may have twelve or more cysteines occurring regularly spaced every fourth residue. These Cys residues tend to be flanked by residues with small side chains that provide minimal steric hindrance to crosslink formation by the radical SAM enzyme as in the subtilosin A system. 359 matched cddid_all.tbl CDD TIGR04116 TIGR04116 274991 CXXX_rpt_assoc CXXX repeat peptide modification system protein. Members of this protein family occur strictly in the presence of a peptide modification radical SAM enzyme described by model TIGR04115 and some small peptide in which, for a stretch, every fourth amino acid is Cys. Cysteine residues usually are flanked by residues with sterically small side chains, as with many radical SAM-modified peptides. Many of the latter are recognized by model TIGR04114. 90 matched cddid_all.tbl CDD TIGR04117 TIGR04117 274992 Syntroph_Cxxx Syntrophus aciditrophicus Cys-Xaa-Xaa-Xaa repeat radical SAM target protein. This model represents a paralogous family, in Syntrophus aciditrophicus SB, of peptides a conserved N-terminal region followed by ten to seventeen direct repeats of the sequence CXXX (see repeats model TIGR04114). The N-terminal region includes a hydrophobic patch that is not shared by most members of family TIGR04114. 95 matched cddid_all.tbl CDD TIGR04118 TIGR04118 200369 Cxxx_AC3_0185 modification target Cys-rich peptide, AC3_0185 family. Radical SAM enzyme family TIGR04115 is paired with a number of short peptides with multiple tandem repeats of Cys-Xaa-Xaa-Xaa (see TIGR04114). This family represent a peptide family with a TIGR04114-like region, although the repeat region is relatively short in this group. 46 matched cddid_all.tbl CDD TIGR04119 TIGR04119 200370 CXXX_matur CXXX repeat peptide maturase. This model describes a peptide maturase that works with, usually fused to, a radical SAM enzyme in a system that modifies peptides with multiple tandem repeats of CXXX sequences. This protein includes an iron-sulfur cluster binding region associated with peptide modification as described in domain model TIGR04085. 210 matched cddid_all.tbl CDD TIGR04120 TIGR04120 274993 DNA_lig_bact DNA ligase, ATP-dependent, PP_1105 family. This model describes a family of ATP-dependent DNA ligases present in about 12 % of prokaryotic genomes. It occurs as part of a four-gene system with an exonuclease, a helicase and a phosphoesterase, with all four genes clustered or at least the first two and last two paired. This family resembles DNA ligase I (see TIGR00574 and pfam01068), and its presumed function may be in DNA repair, replication, or recombination. 526 matched cddid_all.tbl CDD TIGR04121 TIGR04121 274994 DEXH_lig_assoc DEXH box helicase, DNA ligase-associated. Members of this protein family are DEAD/DEAH box helicases found associated with a bacterial ATP-dependent DNA ligase, part of a four-gene system that occurs in about 12 % of prokaryotic reference genomes. The actual motif in this family is DE[VILW]H. 804 matched cddid_all.tbl CDD TIGR04122 TIGR04122 274995 Xnuc_lig_assoc putative exonuclease, DNA ligase-associated. Members of this protein family frequently are found annotated as a putative exonuclease involved in mRNA processing. This protein is found, exclusively in bacteria, associated with three other proteins: an ATP-dependent DNA ligase, a helicase, and putative phosphoesterase. 326 matched cddid_all.tbl CDD TIGR04123 TIGR04123 274996 P_estr_lig_assc metallophosphoesterase, DNA ligase-associated. Members of this protein family are an uncharacterized putative metallophosphoesterase associated with a DNA ligase, a helicase, and a putative exonuclease. It may play a role in DNA repair. Its system is present in about 12 % of prokaryotic reference genomes. 208 matched cddid_all.tbl CDD TIGR04124 TIGR04124 274997 archaeo_artE archaeosortase family protein ArtE. This protein family is related to the predicted protein-sorting transpeptidase Exosortase (EpsH), with the Cys, Arg, and His putative active site residues preserved, but it is strictly archaeal and is not associated with any known PEP-CTERM-like target sequence. The immediate gene neighborhood in most genomes suggests RNA (methylase, cyclase) and cofactor (thiamine pyrophosphate) metabolism. The function is unknown. It is designated archaeosortase family protein ArtE. 153 matched cddid_all.tbl CDD TIGR04125 TIGR04125 274998 exosort_PGF_TRM archaeosortase A, PGF-CTERM-specific. This family is an archaeal variant of the (normally bacterial) putative protein-sorting integral membrane protein exosortase, hence archaeosortase. In species a member of this family, its PGF-CTERM cognate sequence (TIGR04126) occurs at the C-termini of from two to over fifty proteins per genome. Those target proteins may not share homology to each other in regions N-terminal to the PGF-CTERM region. 262 matched cddid_all.tbl CDD TIGR04126 TIGR04126 274999 PGF_CTERM PGF-CTERM archaeal protein-sorting signal. This model describes a strictly archaeal putative protein-sorting motif, PGF-CTERM. It is the (predicted) recognition sequence for an exosortase homolog, archaeosortase (TIGR04125). In some archaea, up to fifty proteins have this domain as their C-terminal region, usually preceded by a Thr-rich region likely to be heavily glycosylated. The removal of this sorting signal may be associated with a C-terminal prenyl group modification in the halobacterial major cell surface glycoprotein, an S-layer protein. 28 matched cddid_all.tbl CDD TIGR04127 TIGR04127 275000 flavo_near_exo exosortase F-associated protein. Members of this protein family are always found next to an exosortase/archaeosortase-like protein, and occur so far only in the flavobacteria, within the Bacteroidetes. Members do not have an obvious PEP-CTERM-like C-terminal protein sorting domain. 136 matched cddid_all.tbl CDD TIGR04128 TIGR04128 275001 exoso_Fjoh_1448 exosortase family protein XrtF. Members of this protein family are exosortase-related proteins found always in association with a member of family TIGR04127, a small, hydrophobic, uncharacterized protein limited to the Bacteriodetes. Exosortases are proposed transpeptidases with a cysteine active site (3.4.22.-), but usually are associated with specific C-terminal target motifs (PEP-CTERM, PEF-CTERM, PGF-CTERM, etc). 174 matched cddid_all.tbl CDD TIGR04129 TIGR04129 275002 CxxH_BA5709 CxxH/CxxC protein, BA_5709 family. Members of this protein family occur exclusively in the Firmicutes, in at least 50 different species. Members average about 55 residues in length, and four of the five invariant or nearly invariant residues occur in motifs CxxH and CxxC. The function is unknown. 49 matched cddid_all.tbl CDD TIGR04130 TIGR04130 275003 FnlA UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase. The FnlA enzyme is the first step in the biosynthesis of UDP-FucNAc from UDP-GlcNAc in E. coli (along with FnlB and FnlC). The proteins identified by this model include FnlA homologs in the O-antigen clusters of O4, O25, O26, O29 (Shigella D11), O118, O145 and O172 serotype strains, all of which produce O-antigens containing FucNAc (or the further modified FucNAm). A homolog from Pseudomonas aerugiosa serotype O11, WbjB, also involved in the biosynthesis of UDP-FucNAc has been characterized and is now believed to carry out both the initial 4,6-dehydratase reaction and the subsequent epimerization of the resulting methyl group at C-5. A phylogenetic tree of related sequences shows a distinct clade of enzymes involved in the biosynthesis of UDP-QuiNAc (Qui=qinovosamine). This clade appears to be descendant from the common ancestor of the Pseudomonas and E. coli fucose-biosynthesis enzymes. It has been hypothesized that the first step in the biosynthesis of these two compounds may be the same, and thus that these enzymes all have the same function. At present, lacking sufficient confirmation of this, the current model trusted cutoff only covers the tree segment surrounding the E. coli genes. The clades containing the Pseudomonas and QuiNAc biosynthesis enzymes score above the noise cutoff. Immediately below the noise cutoff are enzymes involved in the biosynthesis of UDP-RhaNAc (Rha=rhamnose), which again may or may not produce the same product. 337 matched cddid_all.tbl CDD TIGR04131 TIGR04131 275004 Bac_Flav_CTERM gliding motility-associated C-terminal domain. This model describes a protein homology domain unique to, and greatly expanded in, the Bacteriodetes. Species in this lineage include several, such as Cytophaga hutchinsonii and Flavobacterium johnsoniae, that exhibit a poorly understood rapid gliding phenotype. Several members of this protein family are found in operons with other genes whose loss leads to a loss a this motility. Proteins with this domain frequently pair with members of family TIGR03519, whether one such pair or many occur in a genome. More than 30 members may occur in one genome. 85 matched cddid_all.tbl CDD TIGR04132 TIGR04132 275005 intra_fol_E_lig putative folate metabolism gamma-glutamate ligase. This protein family is related to CofE, a gamma-glutamyl ligase of coenzyme F420 biosynthesis. However, it occurs in a different gamma-glutamyl ligase context, polyglutamylated tetrahydrofolate biosynthesis-like regions in two widely separated lineages that both occur as intracellular bacteria - Chlamydia and Wolbachia. 241 matched cddid_all.tbl CDD TIGR04133 TIGR04133 200384 rSAM_w_lipo radical SAM enzyme, rSAM/lipoprotein system. Members of this protein family are radical SAM enzymes with an additional 4Fe4S cluster-binding C-terminal domain (TIGR04085) shared with PqqE and many other peptide and protein-modifying radical SAM enzymes. All members occur in the context of a predicted lipoprotein that usually is encoded by an adjacent gene. 350 matched cddid_all.tbl CDD TIGR04134 TIGR04134 200385 lipo_with_rSAM putative lipoprotein, rSAM/lipoprotein system. Members of this family are Bacteroidetes lineage putative lipoproteins that always occur in pairs with a radical SAM enzyme, TIGR04133, from a branch of the radical SAM superfamily in which many members perform peptide or protein modifications. In some members, the region distal to the Cys of the putative lipoprotein cleavage motif is duplicated. 150 matched cddid_all.tbl CDD TIGR04135 TIGR04135 200386 FibroRuminTarg Cys-rich radical SAM target, FibroRumin family. Members of this protein family are cysteine-rich small peptides, about 52 amino acids long, that are proposed targets for modification by a radical SAM enzyme. Known occurrences are as tandem gene pairs Fibrobacter succinogenes subsp. succinogenes S85 (missed gene calls) and in Ruminococcus albus 8. 52 matched cddid_all.tbl CDD TIGR04136 TIGR04136 200387 rSAM_FibroRumin radical SAM peptide maturase, FibroRumin system. Members of this protein family are radical SAM enzymes proposed to act on small, Cys-rich peptides encoded by tandem gene pairs. Members occur in enzymes Fibrobacter succinogenes subsp. succinogenes S85 (genes for their target peptides missed) and in Ruminococcus albus 8. This enzyme family is similar in sequence to the SCIFF (Six Cysteines in Forty-Five) system maturase (TIGR03974). 458 matched cddid_all.tbl CDD TIGR04137 TIGR04137 275006 Chlam_Ver_rRNA Chlam_Verruc_Plancto small basic protein. Members of this protein family are commonly found next to markers of rRNA processing such as YbeY. They are extremely lineage-restricted, in the Planctomycetes and Chlamydiae/Verrucomicrobia group. Since classification is based on rRNA molecular phylogeny, this provides additional support for a role in rRNA metabolism. This small protein, about 50 amino acids in length, is rich in basic residues, a third line of support for rRNA interaction. 50 matched cddid_all.tbl CDD TIGR04138 TIGR04138 275007 Plancto_Ver_chp Verruc_Plancto-restricted protein. Members of this protein family are extremely lineage-restricted, occurring exclusively in the Planctomycetes and Chlamydiae/Verrucomicrobia group, although not in Chlamydia itself. The function is unknown; the lack of invariant residues other than a single Phe suggests an ancient, conserved, non-enzymatic role. 122 matched cddid_all.tbl CDD TIGR04139 TIGR04139 200390 CxxCx5CxxC_targ putative peptide modification target, TIGR04139 family. This model describes a rare family of small putative polypeptides, including three encoded in tandem in Sphingobacterium spiritivorum ATCC 33300, in the vicinity of a TIGR04085 protein. This pairing is conserved in Chryseobacterium gleum ATCC 35910, Kordia algicida OT-1, and other species. TIGR04085 describes a C-terminal additional 4Fe4S-binding domain in PqqE and other radical SAM enzymes that seems to be a marker for peptide modification, and the family modeled here is a candidate modified peptide precursor. 66 matched cddid_all.tbl CDD TIGR04140 TIGR04140 275008 chp_AF_0576 TIGR04140 family protein. This model represents an uncharacterized small archaeal protein. 66 matched cddid_all.tbl CDD TIGR04141 TIGR04141 275009 TIGR04141 sporadically distributed protein, TIGR04141 family. This model describes a sporadically distributed conserved hypothetical protein in which complete members average over 500 amino acids in length, although matching sequences frequently are truncated or broken into tandem ORFs. Regular co-clustering with known markers of mobility (integrases, transposases, phage proteins, restriction enzymes, etc.) suggests this family also is part of the mobilome. The function is unknown. 516 matched cddid_all.tbl CDD TIGR04142 TIGR04142 200393 PCisTranLspir putative peptidyl-prolyl cis-trans isomerase, LIC12922 family. Members of this protein family have a known crystal structure (3NRK) showing similarity to the peptidyl-prolyl cis-trans isomerase SurA. Members are found in Leptospira species next to an uncharacterized radical SAM enzyme and a cytidylyltransferase family protein. 315 matched cddid_all.tbl CDD TIGR04143 TIGR04143 200394 VPxxxP_CTERM VPXXXP-CTERM protein sorting domain. This C-terminal protein sorting domain is detected, so far, in Methanohalophilus mahii DSM 5219 (five members) and Methanohalobium evestigatum Z-7303 (nine members). This domain resembles the PEP-CTERM, PEF-CTERM, and PGF-CTERM domains of other exosortase/archaeosortase systems. Member proteins co-cluster with a variant member of the exosortase/archaeosortase protein family, and represent a boutique second sorting system in these species. 25 matched cddid_all.tbl CDD TIGR04144 TIGR04144 200395 archaeo_VPXXXP archaeosortase B, VPXXXP-CTERM-specific. Members of this protein family are found so far in Methanohalophilus mahii DSM 5219 and Methanohalobium evestigatum Z-7303, along with five and nine proteins, respectively, with the VPXXXP-CTERM protein sorting signal (TIGR04143). In these species, this boutique system represents a second exosortase/archaeosortase-type system. 156 matched cddid_all.tbl CDD TIGR04145 TIGR04145 200396 Firmicu_CTERM Firmicu-CTERM domain. This C-terminal domain is found only in the Firmicutes, where its presence is sporadically distributed. Proteins with this domain are most conserved in the C-terminal region, where the pattern of ending with a transmembrane domain resembles both the LPXTG (sortase target) and PEP-CTERM (exosortase target) domain structures. However, members occur exclusively in the presence of an exosortase-like protein XrtG (TIGR03110), a putative glycosyltransferase (TIGR03111), and a 6-pyruvoyl tetrahydropterin synthase-related protein (TIGR03112). 45 matched cddid_all.tbl CDD TIGR04146 TIGR04146 275010 GGGPS_Afulg phosphoglycerol geranylgeranyltransferase. This enzyme, known also as GGGP synthase and GGGPS, catalyzes the stereospecific first step in the biosynthesis of the characteristic membrane diether lipids of archaea. Interestingly, the closest homologs outside this family are not the functionally equivalent enzymes of other archaea, but rather functionally distinct bacterial enzymes. 221 matched cddid_all.tbl CDD TIGR04147 TIGR04147 275011 GGGPS_Halobact phosphoglycerol geranylgeranyltransferase, putative. In most archaea, phosphoglycerol geranylgeranyltransferase (EC 2.5.1.41), also known as GGGP synthase and GGGPS, catalyzes the stereospecific first step in the biosynthesis of their characteristic membrane diether lipids. However, some groups of archaeal GGGPS homologs are more closely related to certain bacterial proteins than to each other. This family represents the putative GGGPS family as found in the Halobacteria. 229 matched cddid_all.tbl CDD TIGR04148 TIGR04148 200399 GG_samocin_CFB radical SAM peptide maturase, GG-Bacteroidales family. Members of this protein family are radical SAM enzymes (pfam04055) with the additional C-terminal region (TIGR04085) that is frequently a marker of peptide modification. Many members of this family are found in the vicinity of one or several ORFs encoding short polypeptides with a Gly-Gly motif (common for bacteriocin leader peptide cleavage), followed by a Cys-rich patch and then poorly conserved sequences. 411 matched cddid_all.tbl CDD TIGR04149 TIGR04149 275012 GG_sam_targ_CFB natural product precursor, GG-Bacteroidales family. Sequences in this protein domain family include a leader peptide region, up to and including a Gly-Gly cleavage motif, and about 15 additional residues, usually Cys-rich, from a family of predicted ribosomal natural product precursors. Many of these are associated with peptide-modifying radical SAM enzymes. The core region, up through the diglycine motif, resembles and contains some overlapping hits with the bacteriocin precuror leader peptide region modeled by TIGR01847, but is longer with an extreme N-terminal region with consensus sequence MKKLKKLKL. [Cellular processes, Biosynthesis of natural products] 43 matched cddid_all.tbl CDD TIGR04150 TIGR04150 275013 pseudo_rSAM_GG pseudo-rSAM protein, GG-Bacteroidales system. Many peptide-modifying radical SAM enzymes have two 4Fe4S-binding regions, an N-terminal one recognized by Pfam radical SAM domain-defining model pfam04055 and a C-terminal one recognized by TIGR04085. Members of this protein family occur in cassettes with such a radical SAM family (TIGR04148) and with a peptide modification target (TIGR04149). Surprisingly, members of this family show full-length homology to each other, with several scoring at least borderline hits to both pfam04055 and TIGR04085, and yet differ in the presence/absence of a signature CX(3)CX(2)CX(9)C motif. Instead, members are best-conserved in the TIGR04085-like C-terminal region. Therefore, this protein family is designated a pseudo-radical-SAM protein, which likely works in partnership with a TIGR04148 family protein. 407 matched cddid_all.tbl CDD TIGR04151 TIGR04151 200402 exosort_VPDSG exosortase C, VPDSG-CTERM-specific. Through in silico analysis, we previously described the PEP-CTERM/exosortase system (). This model describes the exosortase subtype specific for the VPDSG-CTERM variant (TIGR03778) of PEP-CTERM. Systems are found, so far, in Verrucomicrobiae bacterium DG1235 (twenty) and bacterium Ellin514 (two). This system may coexist with other system variants. [Protein fate, Protein and peptide secretion and trafficking] 309 matched cddid_all.tbl CDD TIGR04152 TIGR04152 275014 exosort_VPLPA exosortase D, VPLPA-CTERM-specific. This model describes a variant sub class, exosortase D, of protein sorting enzyme (see parent exosortase model TIGR02602), specific for the VPLPA-CTERM variant (TIGR03370) of the PEP-CTERM protein sorting signal. [Protein fate, Protein and peptide secretion and trafficking] 486 matched cddid_all.tbl CDD TIGR04153 TIGR04153 275015 cyanosortA_assc cyanosortase A-associated protein. Members of this protein family are found exclusively in the Cyanobacteria, usually usually encoded next to and in at least one case fused to a gene encoding cyanoexosortase A. Note that family TIGR04533 shows a similar relationship to cyanoexosortase B (TIGR04156), and no EpsI is found. 186 matched cddid_all.tbl CDD TIGR04154 TIGR04154 275016 archaeo_STT3 oligosaccharyl transferase, archaeosortase A system-associated. Members of this protein family occur, one to three members per genome, in the same species of Euryarchaeota as contain the predicted protein-sorting enzyme archaeosortase (TIGR04125) and its cognate protein-sorting signal PGF-CTERM (TIGR04126). 817 matched cddid_all.tbl CDD TIGR04155 TIGR04155 275017 cyano_PEP PEP-CTERM protein sorting domain, cyanobacterial subclass. This domain model describes a subclass with family TIGR02595 of PEP-CTERM protein sorting signals associated with bacterial exosortases. This subclass is restricted to Cyanobacteria, including the genera Cyanothece, Nostoc, Trichodesmium, Lyngbya, Arthospira, etc. This PEP-CTERM subclass features strongly conserved residues within the transmembrane region, including a Gx4GxG motif. Model TIGR03763 describes a corresponding cyanobacterial form of exosortase found in most species with this domain. 25 matched cddid_all.tbl CDD TIGR04156 TIGR04156 275018 cyanoexo_CrtB cyanoexosortase B. This model describes a cyanobacterial-restricted form of exosortase, associated with a PEP-CTERM domain subclass described in model TIGR04155. This is one of two such cyanoexosortases, either of which is sufficient to accompany TIGR04155 family members. The cyanoexosortase is TIGR03763. [Protein fate, Protein and peptide secretion and trafficking] 280 matched cddid_all.tbl CDD TIGR04157 TIGR04157 275019 glyco_rSAM_CFB glycosyltransferase, GG-Bacteroidales peptide system. Members of this protein family are predicted glycosyltransferases that occur in conserved gene neighborhoods in various members of the Bacteroidales. These neighborhoods feature a radical SAM enzyme predicted to act in peptide modification (family TIGR04148), peptides from family TIGR04149 with a characteristic GG cleavage motif, and several other proteins. 405 matched cddid_all.tbl CDD TIGR04158 TIGR04158 275020 rSAM_MIA_synth 3-methyl-2-indolic acid synthase. Members are a radical SAM enzyme that converts L-Trp to 3-methyl-2-indolic acid synthase through a complex rearrangement. This enzyme is closest to ThiH, which also does a complex rearrangement, among other characterized radical SAM enzymes. 368 matched cddid_all.tbl CDD TIGR04159 TIGR04159 200410 methbact_MbnB methanobactin biosynthesis cassette protein MbnB. The first characterized methanobactin is made from a ribosomal precursor in Methylosinus trichosporium OB3b. Two additional species with homologous precursor peptides (family TIGR04071) are Azospirillum sp. B510 and Gluconacetobacter sp. SXCC-1. This model describes a clique of related sequences, domain or full-length, that occurs always and only next to a methanobactin precursor. The model excludes some close homologs from species where no similar precursor can be found. 91 matched cddid_all.tbl CDD TIGR04160 TIGR04160 275021 methbact_MbnC methanobactin biosynthesis cassette protein MbnC. The first characterized methanobactin is made from a ribosomal precursor in Methylosinus trichosporium OB3b. Two additional species with homologous precursor peptides (family TIGR04071) are Azospirillum sp. B510 and Gluconacetobacter sp. SXCC-1. This model describes a clique of related sequences, domain or full-length, that occurs always and only next to a methanobactin precursor of the Mb-OB3b type. The model excludes several Pseudomonas proteins whose function is unknown, which likewise are in model TIGR04061, but which diverge toward the C-terminus. 89 matched cddid_all.tbl CDD TIGR04161 TIGR04161 275022 VPEID-CTERM VPEID-CTERM protein sorting domain. Proteins belonging to this family are small, 80 to 120 residues, including a signal peptide, a central low-complexity region, and this roughly 31-amino acid extreme C-terminal region. Members occur paired with a variant form of exosortase. Species include Ruegeria sp., Phaeobacter gallaeciensis, Roseovarius nubinhibens ISM, and two in Methylobacter tundripaludum. 31 matched cddid_all.tbl CDD TIGR04162 TIGR04162 200413 exo_VPEID exosortase E/protease, VPEID-CTERM system. Members of this protein family are fusion proteins of exosortase (N-terminal) and a CAAX prenyl protease domain (C-terminal). Members are restricted to the alpha Proteobacteria. The variant C-terminal protein sequence VPEID-CTERM occurs only in these species, often adjacent. 519 matched cddid_all.tbl CDD TIGR04163 TIGR04163 200414 rSAM_cobopep peptide-modifying radical SAM enzyme CbpB. Members of this family are radical SAM enzymes that modify a short peptide encoded by an upstream gene. A role in metal chelation is suggested. 428 matched cddid_all.tbl CDD TIGR04164 TIGR04164 200415 cobo_pep modified peptide precursor CbpA. Members of this family are short peptides predicted to reach mature form after modification by a radical SAM enzyme (TIGR04163). 25 matched cddid_all.tbl CDD TIGR04165 TIGR04165 275023 methano_modCys Cys-rich peptide, TIGR04165 family. Members of this small peptide family occur strictly in a subset of archaeal methanogens. Members have four invariant Cys residues in two Cys-Xaa-Xaa-Cys-Gly motifs and may have other Cys residues as well. At least two members occur next to family TIGR04083 radical SAM enzymes predicted to act in peptide or protein modification. 50 matched cddid_all.tbl CDD TIGR04166 TIGR04166 275024 methano_MtrB tetrahydromethanopterin S-methyltransferase, subunit B. Members of this protein family are the MtrB protein of the tetrahydromethanopterin S-methyltransferase complex. This system is universal in archaeal methanogens. [Energy metabolism, Methanogenesis] 95 matched cddid_all.tbl CDD TIGR04167 TIGR04167 275025 rSAM_SeCys radical SAM/Cys-rich domain protein. Members of this protein family have an N-terminal radical SAM domain (pfam04055) and a C-terminal pfam12345 domain. The C-terminal region has several conserved Cys residues, one of which is replaced by selenocysteine in at least five bacterial reference genomes. 303 matched cddid_all.tbl CDD TIGR04168 TIGR04168 275026 TIGR04168 TIGR04168 family protein. Members of this uncharacterized protein family are restricted, in 49 of 50 genomes, to organisms with a family TIGR04167 radical SAM protein, which occasionally is a selenoprotein. 269 matched cddid_all.tbl CDD TIGR04169 TIGR04169 200420 perox_w_seleSAM alkylhydroperoxidase/carboxymuconolactone decarboxylase family protein. Members of this family are usually annotated as putative carboxymuconolactone decarboxylases, are related also to alkylhydroperoxidase AhpD, and contain a peroxidase-like Cys-X-X-Cys putative redox-active disulfide. All members occur in genomes with a radical SAM protein of family TIGR04167, which occasionally are selenoproteins. 109 matched cddid_all.tbl CDD TIGR04170 TIGR04170 211905 RNR_1b_NrdE ribonucleoside-diphosphate reductase, class 1b, alpha subunit. Members of this family are NrdE, the alpha subunit of class 1b ribonucleotide reductase. This form uses a dimanganese moiety associated with a tyrosine radical to reduce the cellular requirement for iron. 698 matched cddid_all.tbl CDD TIGR04171 TIGR04171 275027 RNR_1b_NrdF ribonucleoside-diphosphate reductase, class 1b, beta subunit. Members of this family are NrdF, the beta subunit of class 1b ribonucleotide reductase. This form uses a dimanganese moiety associated with a tyrosine radical to reduce the cellular requirement for iron. [Purines, pyrimidines, nucleosides, and nucleotides, 2'-Deoxyribonucleotide metabolism] 313 matched cddid_all.tbl CDD TIGR04172 TIGR04172 275028 DGQHR_dnd_1 DNA phosphorothioation-associated DGQHR protein 1. The DND system produces an phosphorothioation modification to DNA, replacing a non-bridging oxygen of a phosphate group with sulfur. The modification causes DNA degradation during electrophoresis in Tris buffer. This protein, like DndB (TIGR03233), contains a DGQHR domain (TIGR03187), which also occurs in several contexts that suggest lateral transfer rather than DNA phosphorothioation-dependent restriction. 378 matched cddid_all.tbl CDD TIGR04173 TIGR04173 200424 PIP_CTERM PIP-CTERM protein sorting domain. Proteins closely related to MJ_1469.1 from Methanocaldococcus jannaschii DSM 2661 are designated archaeosortase D (ArtD). ArtD appears to be a dedicated protein-sorting enzyme with a single target, a PKD domain (pfam00801) repeat protein encoded by adjacent gene. This model describes the C-terminal putative protein-sorting region structurally similar to PEP-CTERM (TIGR02602) and found only on these methanogen PKD domain proteins. 27 matched cddid_all.tbl CDD TIGR04174 TIGR04174 275029 IPTL_CTERM IPTL-CTERM protein sorting domain. This model describes a variant form of the PEP-CTERM C-terminal protein-sorting domain, with a consensus motif IPTL replacing the more typical VPEP. A majority of these sequences have a WG (Trp-Gly) motif at positions 7-8 of the domain. Species with multiple (up to 15) copies of this domain include Acidovorax citrulli, Acidovorax delafieldii 2AN, Delftia acidovorans SPH-1, and gamma proteobacterium NOR5-3. 27 matched cddid_all.tbl CDD TIGR04175 TIGR04175 200426 archaeo_artD archaeosortase D. This model describes archaeosortase D, one of several strictly archaeal subfamilies related to exosortase, the bacterial protein-sorting putative transpeptidase (see TIGR02602). ArtD is found in the genus Methanocaldococcus. Its predicted target, encoded by an adjacent gene, has a C-terminal VPIP motif-containing region (TIGR04173) likely to be its recognition site. 150 matched cddid_all.tbl CDD TIGR04176 TIGR04176 275030 MarR_EPS EPS-associated transcriptional regulator, MarR family. Members of this family of MarR-family transcriptional regulators are associated with long genomic loci consisting of genes encoding enzymes for the biosynthesis of exopolysaccharides. These genes include glycosyl transferases, sugar modifying enzymes (epimerases, isomerases, methyltransferases, aminotransferases, etc.), and exopolysaccharide polymerases (wzx, wzy). In Leptospira interrogans, borgpeterenii and biflexa, this gene is observed first in unidirectional EPS biosynthesis loci as long as 90 genes. MarR genes (pfam01407) are known to bind to DNA regions with palindromic or pseudopalindromic sequences as homodimers, and to bind small molecules as triggers for conformational changes controlling on/off states. 105 matched cddid_all.tbl CDD TIGR04177 TIGR04177 200428 exosort_XrtH exosortase H, IPTLxxWG-CTERM-specific. This model describes exosortase subfamily H, for which most cognate recognition sequences are found by the IPTLxxWG-CTERM model TIGR04174. Species with this exosortase and multiple (up to 15) copies of the target domain include Acidovorax citrulli, Acidovorax delafieldii 2AN, Delftia acidovorans SPH-1, and gamma proteobacterium NOR5-3. [Protein fate, Protein and peptide secretion and trafficking] 158 matched cddid_all.tbl CDD TIGR04178 TIGR04178 275031 exo_archaeo exosortase/archaeosortase family protein. This model represents the most conserved region of the multitransmembrane protein family of exosortases and archaeosortases. The region includes nearly invariant motifs at the ends of three predicted transmembrane helices on the extracytoplasmic face: a Cys (often Cys-Xaa-Gly), Asn-Xaa-Xaa-Arg, and His. This model is much broader than the bacterial exosortase model (TIGR02602), and has in intended scope similar to (or broader than) pfam09721. 97 matched cddid_all.tbl CDD TIGR04179 TIGR04179 275032 rhombo_lipo rhombotail lipoprotein. Members of this protein family are probable lipoproteins. Nearly every member ends with a C-terminal region consisting of a glycine-rich probable cleavage site, a hydrophobic probable transmembrane helix, and a cluster of basic residues, as described in putative protein sorting region model TIGR03501. Furthermore, members tend to be encoded next to a rhomboid family protease, called rhombosortase (TIGR03902) predicted to perform a C-terminal cleavage. 258 matched cddid_all.tbl CDD TIGR04180 TIGR04180 275033 EDH_00030 NAD dependent epimerase/dehydratase, LLPSF_EDH_00030 family. This clade within the NAD dependent epimerase/dehydratase superfamily (pfam01370) is characterized by inclusion of its members within a cassette of seven distinctive enzymes. These include four genes homologous to the elements of the neuraminic (sialic) acid biosynthesis cluster (NeuABCD), an aminotransferase and a nucleotidyltransferase in addition to the epimerase/dehydratase. Together it is very likely that these enzymes direct the biosynthesis of a nine-carbon sugar analagous to CMP-neuraminic acid. These seven genes form the core of the cassette, although they are often accompanied by additional genes that may further modify the product sugar. Although this cassette is widely distributed in bacteria, the family nomenclature arises from the instance in Leptospira interrogans serovar Lai, str. 56601, where it appears as the 30th gene in the 91-gene lipopolysaccharide biosynthesis cluster. 297 matched cddid_all.tbl CDD TIGR04181 TIGR04181 275034 NHT_00031 aminotransferase, LLPSF_NHT_00031 family. This clade of aminotransferases is a member of the pfam01041 (DegT/DnrJ/EryC1/StrS) superfamily. The family is named after the instance in Leptospira interrogans serovar Lai, str. 56601, where it is the 31st gene in the 91-gene lipopolysaccharide biosynthesis locus. Members of this family are generally found within a subcluster of seven or more genes including an epimerase/dehydratase, four genes homologous to the elements of the neuraminic (sialic) acid biosynthesis cluster (NeuABCD) and a nucleotidyl transferase. Together it is very likely that these enzymes direct the biosynthesis of a nine-carbon sugar analogous to CMP-neuraminic acid. These seven genes form the core of the cassette, although they are often accompanied by additional genes that may further modify the product sugar. 359 matched cddid_all.tbl CDD TIGR04182 TIGR04182 275035 glyco_TIGR04182 glycosyltransferase, TIGR04182 family. Members of this family are glycosyltransferases restricted to the archaea. All but two members are from species with the PGF-CTERM/archaeosortase A system, a proposed maturation system for exported, glycosylated proteins as are found often in S-layers. 293 matched cddid_all.tbl CDD TIGR04183 TIGR04183 275036 Por_Secre_tail Por secretion system C-terminal sorting domain. Species that include Porphyromonas gingivalis, Fibrobacter succinogenes, Flavobacterium johnsoniae, Cytophaga hutchinsonii, Gramella forsetii, Prevotella intermedia, and Salinibacter ruber average twenty or more copies of a C-terminal domain, represented by this model, associated with sorting to the outer membrane and covalent modification. 72 matched cddid_all.tbl CDD TIGR04184 TIGR04184 275037 ATPgraspMvdD ATP-grasp ribosomal peptide maturase, MvdD family. The pair of ATP-grasp proteins MvdD and MvdC (microviridin D and C), as well as an acetyltransferase, produce microviridin K, an example of a RiPP (ribosomally synthesized and posttranslationally modified peptide). Microviridins are peptidase inhibitors. 321 matched cddid_all.tbl CDD TIGR04185 TIGR04185 275038 ATPgraspMvdC ATP-grasp ribosomal peptide maturase, MvdC family. The pair of ATP-grasp proteins MvdD and MvdC (microviridin D and C), as well as an acetyltransferase, produce microviridin K, an example of a RiPP (ribosomally synthesized and posttranslationally modified peptide). Microviridins are peptidase inhibitors. This family includes MvdC and corresponding members of similar cassettes. 318 matched cddid_all.tbl CDD TIGR04186 TIGR04186 275039 GRASP_targ putative ATP-grasp target RiPP. A RiPP is a ribosomally produced, post-translationally modified peptide. This family regularly occurs next to ATP-grasp enzymes related to those of microviridin maturation and next to a methyltransferase. 72 matched cddid_all.tbl CDD TIGR04187 TIGR04187 275040 GRASP_SAV_5884 ATP-grasp ribosomal peptide maturase, SAV_5884 family. Members of this protein family are ATP-grasp ligase family enzymes that regularly occur in a contexts with a methyltransferase and a putative ribosomally translated post-translationally modified peptide precursor. Because of this conserved gene neighborhood and close sequence similarity to ATP-grasp enzymes from microviridin/marinostatin biosynthesis cassettes, this enzyme is suggested also to serve as a peptide maturase. 312 matched cddid_all.tbl CDD TIGR04188 TIGR04188 275041 methyltr_grsp methyltransferase, ATP-grasp peptide maturase system. Members of this protein family are predicted SAM-dependent methyltransferases that regularly occur in the context of a putative peptide modification ATP-grasp enzyme (TIGR04187, related to enzymes of microviridin maturation) and a putative ribosomal peptide modification target (TIGR04186). 363 matched cddid_all.tbl CDD TIGR04189 TIGR04189 275042 surface_SprA cell surface protein SprA. SprA is a cell surface protein widely distributed in the Bacteroidetes lineage. In Flavobacterium johnsoniae, a species that shows gliding motility, mutation disrupts gliding. 2315 matched cddid_all.tbl CDD TIGR04190 TIGR04190 211913 B12_SAM_Ta0216 B12-binding domain/radical SAM domain protein, Ta0216 family. Members of this family are enzymes with an N-terminal B12-binding domain and central radical SAM domain. Families TIGR03975, TIGR04013 and TIGR04014 exhibit a similar architecture, which may be associated with lipid metabolism. 553 matched cddid_all.tbl CDD TIGR04191 TIGR04191 275043 YphP_YqiW putative bacilliredoxin, YphP/YqiW family. This protein family is one of several observed in species that express bacillithiol, an analog of glutathione and mycothiol. Rather than being involved in bacillithiol biosynthesis, members are likely to act in bacillithiol-dependent processes. A suggested term is bacilliredoxin (a glutaredoxin-like thiol-dependent oxidoreductase), and a suggested role of YphP is de-bacillithiolation - removing bacillithiol that became linked to protein thiols under oxidative stress. An older description of YphP as a disulphide isomerase therefore may be wrong. 136 matched cddid_all.tbl CDD TIGR04192 TIGR04192 275044 GRASP_w_spasm ATP-GRASP peptide maturase, grasp-with-spasm system. Members of this protein family are ATP-GRASP proteins that occur in a peptide maturation cassette with a SPASM domain protein. SPASM (TIGR04085) usually occurs as a C-terminal extension to radical SAM enzymes that act as peptide maturases, although it can occur independently. 318 matched cddid_all.tbl CDD TIGR04193 TIGR04193 211916 SPASM_w_grasp SPASM domain peptide maturase, grasp-with-spasm system. A 4Fe-4S-binding C-terminal domain is shared by radical SAM maturases for Subtilosin A (S), PQQ (P), Anaerobic sulfatases (AS), and mycofactocin (M), hence SPASM. Radical SAM proteins with SPASM tend to be peptide maturases. All members of this family, like some members of the quasi-rSAM family TIGR04105, lack the 4Fe-4S cluster of the radical SAM domain (pfam04055) in the N-terminal region. Members of this family occur with an ATP-GRASP family protein, known as a possible maturase from microviridin biosynthetic clusters. Systems occur in Microscilla marina ATCC 23134, Kordia algicida OT-1, Sphingobacterium spiritivorum ATCC 33300, etc. 342 matched cddid_all.tbl CDD TIGR04194 TIGR04194 211917 grasp_w_spasm_A grasp-with-spasm leader A domain. This model describes the leader peptide domain, ending in a Gly-Gly cleavage motif, for a post-ribosomal natural product (PRNP) precursor. The corresponding modification enzymes include an ATP-GRASP enzyme and a SPASM-domain protein, related to the C-terminal region of numerous peptide-modification radical SAM enzymes. 28 matched cddid_all.tbl CDD TIGR04195 TIGR04195 211918 S_glycosyl_SunS peptide S-glycosyltransferase, SunS family. Members of this family include SunS, the S-glycosyltransferase that transfers a sugar (substrate is variable in reconstitution assays) onto the precursor of the glycopeptide sublancin, which once was thought to be a lantibiotic. 422 matched cddid_all.tbl CDD TIGR04196 TIGR04196 211919 glycopep_SunS glycopeptide, sublancin family. Members of this family, including sublancin, are post-ribosomal natural products (PRNP) with an S-linked glycosylation. Sublancin itself also has two disulfide bonds. A related gene cluster in Bacillus cereus E33L includes the four Cys involved in the disulfide cluster but lacks the region with the glycosylated Cys, and have been excluded. 80 matched cddid_all.tbl CDD TIGR04197 TIGR04197 275045 T7SS_SACOL2603 type VII secretion effector, SACOL2603 family. Members of this protein family are similar in length and sequence (although remotely) to the WXG100 family of type VII secretion system (T7SS) targets, described by family TIGR03930. Phylogenetic profiling shows that members of this family are similarly restricted to species with T7SS, marking this family as a related set of T7SS effectors. Members include SACOL2603 from Staphylococcus aureus subsp. aureus COL. Oddly, members of family pfam10824 (DUF2580), which appears also to be related, seem not to be tied to T7SS. 85 matched cddid_all.tbl CDD TIGR04198 TIGR04198 275046 paramyx_RNAcap mRNA capping enzyme, paramyxovirus family. This model represents a common C-terminal region shared by paramyxovirus-like RNA-dependent RNA polymerases (see pfam00946). Polymerase proteins described by these two models are often called L protein (large polymerase protein). Capping of mRNA requires RNA triphosphatase and guanylyl transferase activities, demonstrated for the rinderpest virus L protein and at least partially localized to the region of this model. 893 matched cddid_all.tbl CDD TIGR04199 TIGR04199 275047 exosort_xrtJ exosortase J. Exosortase J occurs as a three-member paralogous family in Acidobacterium sp. MP5ACTX8. It contains an N-terminal exosortase/archaeosortase domain and a novel C-terminal domain comprising about half of total protein length. The presumptive target, found as an adjacent gene for two of the three paralogs, consists of a possible lipoprotein signal peptide followed almost immediately by a C-terminal region with some PEP-CTERM-like characteristics. 522 matched cddid_all.tbl CDD TIGR04200 TIGR04200 211923 targ_of_XrtJ XrtJ-associated TM-motif-TM protein. This model represents essentially the full length, ~60 residues, of a two-gene paralogous family from Acidobacterium sp. MP5ACTX8. Sequences consist of an N-terminal signal sequence ending in a GC motif, suggestive of the lipoprotein signal sequence, followed immediately by a C-terminal domain sequence with characteristics PEP-CTERM-like sequences, including a PExP motif and a transmembrane helix. Both members occur next to the novel exosortase variant, XrtJ, which contains a novel C-terminal domain. 62 matched cddid_all.tbl CDD TIGR04201 TIGR04201 275048 Myxo_Cys_RPT Cys-rich repeat, Myxococcales-type. This repeat is restricted to the Myxococcales, a division of the deltaproteobacteria. It occurs in several surface proteins, and may form a stalk region. The repeat averages about 21 amino acids in length with four or five Cys, three of which are nearly invariant. 22 matched cddid_all.tbl CDD TIGR04202 TIGR04202 275049 capSnatchArena RNA endonuclease, cap-snatching, arenavirus family. This model describes a shared signature region from an RNA endonuclease region associated with cap-snatching for mRNA production by RNA viruses. This domain usually is part of a multifunctional protein, the L protein responsible for RNA-dependent RNA polymerase activity. Cap-snatching is a viral alternative to synthesizing a eukaryotic-like mRNA cap itself. 61 matched cddid_all.tbl CDD TIGR04203 TIGR04203 275050 RPT_S_cricet Streptococcal surface-anchored protein repeat, S. criceti family. This model describes a repeat sequence that occurs primarily LPXTG-anchored Streptococcus surface proteins, although it does occur elsewhere. It can comprise a major fraction of the length of repeat proteins taht exceed 2000 in length. 38 matched cddid_all.tbl CDD TIGR04204 TIGR04204 275051 MAST_ArtA_sort MAST domain. This model describes a domain (or in most cases the full length) of archaeal surface proteins that are putative targets for C-terminal processing by archaeosortase A (TIGR04125). Most members of this family belong to proteins encoded by tandem genes in the genus Methanosarcina. The putative processing signal, PGF-CTERM (TIGR04126), included within the domain definition, takes a variant form, with consensus motif PAF instead of PGF. We suggest the name MAST domain: Methanosarcina Archaeosortase-Sorted Tandem gene family domain. 182 matched cddid_all.tbl CDD TIGR04205 TIGR04205 275052 classIII_w_PIP class III signal peptide protein, archaeosortase D/PIP-CTERM system. Members of this protein family are short proteins that consist largely of the archaeal class III signal peptide (see pfam04021). Members are encoded in a gene cassette between archaeosortase D (TIGR04175) and its PIP-CTERM target protein (TIGR04173). 67 matched cddid_all.tbl CDD TIGR04206 TIGR04206 275053 near_ArtA TIGR04206 family protein. Members of this integral membrane protein family are found exclusively in halophilic archaea. In at least three species (Haloarcula marismortui, Haloquadratum walsbyi, and Haloferax volcanii), members are found in the gene neighborhood of archaeosortase A, suggesting a role in protein sorting. 139 matched cddid_all.tbl CDD TIGR04207 TIGR04207 275054 halo_sig_pep surface glycoprotein signal peptide. This N-terminal homology domain appears to be a specialized class of signal peptide. It occurs mostly in the halophilic archaea, primarily on proteins with the C-terminal PGF-CTERM domain, including the S-layer-forming major surface glycoprotein of several species. The PGF-CTERM domain is the putative archaeosortase A recognition sequence. However, this N-terminal domain occurs also in several archaeal proteins that lack PGF-CTERM, and occurs in bacteria on a protein from Clostridium leptum DSM 753. 30 matched cddid_all.tbl CDD TIGR04209 TIGR04209 275055 sarcinarray sarcinarray family protein. Members of this protein family are exclusive to archaea, probably all of which have S-layer surface protein arrays. All member proteins have an N-terminal signal sequence. The majority of known members belong to codirectional tandem arrays in the genus Methanosarcina (nine in M. barkeri str. Fusaro). Nearly all members have an additional 50 residues, (trimmed from the seed alignment for this model), consisting of low-complexity sequence rich in E,N,Q,T,S, and P, followed by a variant (PAF) form of the PGF-CTERM putative archaeal surface glycoprotein sorting signal. The coined name, sarcinarray family protein, evokes the predicted archaeal surface layer localization, the taxonomic bias of known members, and the tandem organization of most members. 144 matched cddid_all.tbl CDD TIGR04210 TIGR04210 211933 bunya_NSm bunyavirus nonstructural protein NSm. This model describes a protein region that is cleaved from a bunyavirus polyprotein to become the nonstructural protein NSm (encoded by the M segment). It is flanked by glycoprotein GP2 and glycoprotein GP1. 173 matched cddid_all.tbl CDD TIGR04211 TIGR04211 275056 SH3_and_anchor SH3 domain protein. Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region. 198 matched cddid_all.tbl CDD TIGR04212 TIGR04212 275057 GlyGly_RbtA Acinetobacter rhombotarget A. Members of this protein family are found, so far, exclusively in the genus Acinetobacter. Members average just over 600 amino acids in length, including a 22-amino acid C-terminal putative protein sorting recognition sequence, GlyGly-CTERM (TIGR03501). The GlyGly-CTERM signal always co-occurs with a subfamily of the rhomboid family intramembrane serine proteases called rhombosortase (TIGR03902). Members occur paired with a second rhombosortase target, with which it also shares an N-terminal motif CSLREA. This protein is designated Acinetobacter rhombotarget A (rbtA). 605 matched cddid_all.tbl CDD TIGR04213 TIGR04213 275058 PGF_pre_PGF PGF-pre-PGF domain. This domain occurs in archaeal species. Most domains in this family end with a motif PGF, after which the member sequences change in character to low-complexity sequence (usually Thr-rich) for about 40 residues. The low complexity region usually is followed by a PGF-CTERM domain (TIGR04126), which we suggest is the recognition sequence for archaeosortase A (TIGR04125), a putative protein-sorting transpeptidase. The similarity between the PGF motif in this domain and in the PGF-CTERM domain is highly suggestive. 153 matched cddid_all.tbl CDD TIGR04214 TIGR04214 211937 CSLREA_Nterm CSLREA domain. This model describes an N-terminal region, with a motif CSLREA, shared by tandem genes in Acinetobacter that both have the GlyGly-CTERM putative protein-sorting domain. Many proteins with this domain are putative outer membrane proteins (OMPs) with predicted beta strand-forming repeats. 27 matched cddid_all.tbl CDD TIGR04215 TIGR04215 275059 choice_anch_A choice-of-anchor A domain. This domain may occur as essentially the full length of a protein, except for an N-terminal sequence and a C-terminal protein-sorting signal such as PEP-CTERM or LPXTG. Most often, the putative surface protein is longer and contains repetitive sequence regions. This is one of very few domains for which both anchoring domains occur, and designated choice-of-anchor A domain. The best characterized member is Bacillus anthracis protein BA0871, a collagen-binding protein with five CNA-family protein B-type repeats toward the C-terminus and an LPXTG cell wall attachment motif. 249 matched cddid_all.tbl CDD TIGR04216 TIGR04216 275060 halo_surf_glyco major cell surface glycoprotein. Members of this family are the S-layer-forming halobacterial major cell surface glycoprotein. The highest scores below model cutoffs are fragmentary paralogs to actual members of the family. Modifications include at N-linked and O-linked glycosylation, a C-terminal diphytanylglyceryl modification, and probable cleavage of the PGF-CTERM tail. 763 matched cddid_all.tbl CDD TIGR04217 TIGR04217 211940 archae_ser_T archaetidylserine synthase. The activity CDP-2,3-di-O-geranylgeranyl-sn-glycerol:L-serine O-archaetidyltransferase (archaetidylserine synthase) was demonstrated experimentally in Methanothermobacter thermautotrophicus. Members represent an exception within the broader family (TIGR00473) of CDP-diacylglycerol-serine O-phosphatidyltransferases. 221 matched cddid_all.tbl CDD TIGR04218 TIGR04218 211941 TOMM_plantaz ribosomal natural product, plantazolicin-class. Members of this protein family are precursors of TOMMs, that is, thizazole/oxazole-modified microcins. Members are about 42 residues in length, have a C-terminal region of extremely low complexity rich in Ser, and are often missed by ab initio gene callers. The plantazolicin from Bacillus amyloliquefaciens FZB42 is a peptide antibiotic effective against Bacillus anthracis. 41 matched cddid_all.tbl CDD TIGR04219 TIGR04219 275061 OMP_w_GlyGly outer membrane protein. Members of this protein family are outer membrane proteins (OMP), as can be seen by their homology to YfaZ protein (see ) and by the OMP targeting region at the C-terminus, including a C-terminal Phe residue. Members of this protein family are found in the great majority of genomes with the GlyGly-CTERM protein sorting signal and the rhombosortase putative sorting enzyme, although the relationship may be fortuitous. 233 matched cddid_all.tbl CDD TIGR04220 TIGR04220 211943 patB_acyB_mcaB cyanobactin biosynthesis protein, PatB/AcyB/McaB family. Members of this protein family are small (~ 80 amino acids) and occur in biosynthesis clusters for cyanobactins, a type of ribosomal natural product, thiazole/oxazole-modified microcin (TOMM). The function of this protein family is unknown, and the recognized cyanobactin precursors (e.g. microcyclamides and patellamides) are encoded by a different protein (see TIGR03678). In this protein family, however, a core region of about 62 amino acids (modeled) is followed by a hypervariable region of 5 to 23 amino acids, with hallmarks of possible cyclodehydratase modification sites. The hallmarks include Cys residues flanked by Gly, and variable length Ser-rich tripeptide repeats. Further, members of this family were shown dispensible for patellamide biosynthesis, and two may occur in a cluster. Therefore, this family may represent a precursor of another type of ribosomal natural product. 61 matched cddid_all.tbl CDD TIGR04221 TIGR04221 275062 SecA2_Mycobac accessory Sec system translocase SecA2, Actinobacterial type. Members of this family are the SecA2 subunit of the Mycobacterial type of accessory secretory system. This family is quite different SecA2 of the Staph/Strep type (TIGR03714). 762 matched cddid_all.tbl CDD TIGR04222 TIGR04222 275063 near_uncomplex TIGR04222 domain. The majority of the proteins with a domain as described by this model have an extreme C-terminal sequence that is consists of extremely low-complexity sequence, rich in Ser or in Gly interspersed with Cys. That C-terminal region resembles ribosomal natural product precursors, although there is no evidence that C-terminal regions of these proteins undergo any modification or have any such function. 227 matched cddid_all.tbl CDD TIGR04223 TIGR04223 275064 quorum_AgrD cyclic lactone autoinducer peptide. Members of this family of short peptides are precursors to thiolactone (unless Cys is replaced by Ser) cyclic autoinducer peptides, used in quorum-sensing systems in Gram-positive bacteria. The best characterized is the AgrD precursor, processed by the AgrB protein. Nearby proteins regularly encountered include a histidine kinase and a response regulator. This model is related to pfam05931 but is newer and currently broader in scope. 37 matched cddid_all.tbl CDD TIGR04224 TIGR04224 275065 ser_adhes_Nterm serine-rich repeat adhesion glycoprotein AST domain. This model describes a definitive conserved N-terminal domain shared by Streptococcal serine-rich adhesion glycoproteins. These highly repetitive proteins may exceed 4000 amino acids in length, consisting largely of long regions in which every second amino acid is Ser. Members of this family, if sequenced completely and assigned the correct start site, begin with a KxYKxGKxW motif region (see TIGR03715) and end with an LPXTG motif region (see TIGR01167). Members are exported by the accessory secretory system (SecA2 and SecY2). They are highly variable among the Streptococci and may help determine host ranges for pathogenesis. 50 matched cddid_all.tbl CDD TIGR04225 TIGR04225 275066 CshA_fibril_rpt CshA-type fibril repeat. Many proteins with this repeat are LPXTG-anchored surface proteins of Firmicutes species, but the repeat occurs more broadly. Members include CshA from Streptococcus gordonii. 103 matched cddid_all.tbl CDD TIGR04226 TIGR04226 275067 RrgB_K2N_iso_D2 fimbrial isopeptide formation D2 domain. The Streptococcus Pneumoniae pilus backbone protein, RrgB, has three tandem domains with Lys-to-Asn isopeptide bonds, but these three regions are extremely divergent in sequence. This model represents the homology domain family of the D2 domain. It occurs just once in many surface proteins but up to twenty times in some pilin subunit proteins. Three of every four members have the typical Gram-positive C-terminal motif, LPXTG, although in many cases this motif may be involved in pilin subunit cross-linking rather than cell wall attachment. Proteins with this domain include fimbrial proteins with lectin-like adhesion functions, and the majority of characterized members are involved in surface adhesion to host structures. 124 matched cddid_all.tbl CDD TIGR04227 TIGR04227 211950 zmp_18_rpt zinc metalloproteinase 18-residue repeat. This model describes a short (18-amino acid) tandem repeat that occurs variable numbers of times in zinc metalloproteinase C (zmpC) homologs in various species of Streptococcus. This repeat occurs, oddly, as an interruption in a region of tandem repeats of another type. 18 matched cddid_all.tbl CDD TIGR04228 TIGR04228 275068 isopep_sspB_C2 adhesin isopeptide-forming domain, sspB-C2 type. This domain has a conserved Lys (position 3 in seed alignment) and Asn at 177 that form an intramolecular isopeptide bond. The Asp (or Glu) at position 59 173 matched cddid_all.tbl CDD TIGR04229 TIGR04229 275069 geopeptide putative radical SAM-modified peptide. This family of short peptides occurs near radical SAM/SPASM domain proteins and is proposed to be modified by that enzyme. 23 matched cddid_all.tbl CDD TIGR04230 TIGR04230 275070 seadorna_VP11 seadornavirus VP11 protein. This protein family occurs in the seadornavirus virus group, with designations VP11 in Banna virus, and VP12 in Kadipiro virus and Liao ning virus. The function has not been assigned. 175 matched cddid_all.tbl CDD TIGR04231 TIGR04231 275071 seadorna_VP5 seadornavirus VP5 protein. This protein family occurs in the seadornavirus virus group, with designations VP5 in Banna virus, and VP6 in Kadipiro virus and Liao ning virus. The function is unassigned. 505 matched cddid_all.tbl CDD TIGR04232 TIGR04232 211955 seadorna_VP3 seadornavirus VP3 protein. Members of this protein family are VP3 proteins in the seadornavirus group. Sequences show sequence similarity to methyltransferases. 731 matched cddid_all.tbl CDD TIGR04233 TIGR04233 211956 seadorna_VP8 seadornavirus VP8 protein. This protein family occurs in the seadornavirus virus group, with designations VP8 in Banna virus, and VP9 in Kadipiro virus and Liao ning virus. The function has not been assigned. 291 matched cddid_all.tbl CDD TIGR04234 TIGR04234 275072 seadorna_RNAP seadornavirus RNA-directed RNA polymerase. Members of this protein family are the seadornavirus VP1 protein, the RNA-directed RNA polymerase. 1144 matched cddid_all.tbl CDD TIGR04235 TIGR04235 211958 seadorna_VP4 seadornavirus VP4 protein. This protein family occurs in the seadornavirus virus group, with designation VP4 in Banna virus, Kadipiro virus, and Liao ning virus. Although this family has been suggested to resemble methyltransferases, members show apparent N-terminal sequence similarity to the outer capsid protein VP5 of the orbivirus group, such as bluetongue virus, which also belong to the Reoviridae. 618 matched cddid_all.tbl CDD TIGR04236 TIGR04236 275073 seadorna_VP2 seadornavirus VP2 protein. This protein family occurs in the seadornavirus virus group, with the designation VP2 in Banna virus, Kadipiro virus, and Liao ning virus. 953 matched cddid_all.tbl CDD TIGR04237 TIGR04237 211960 seadorna_VP9 seadornavirus/coltivirus VP9 protein. This model, broader than related pfam08978, describes proteins VP9 in Coltivirus, and proteins with various designations in the seadornavirus group: VP9 in Banna virus, VP10 in Liao ning virus, and VP11 in Kadipiro virus. 280 matched cddid_all.tbl CDD TIGR04238 TIGR04238 275074 seadorna_dsRNA seadornavirus double-stranded RNA-binding protein. This protein family occurs in the seadornavirus virus group, with an N-terminal domain for binding double-stranded RNA, is designated VP12 in Banna virus, VP8 in Kadipiro virus, and VP11 in Liao ning virus. 201 matched cddid_all.tbl CDD TIGR04239 TIGR04239 275075 rhombo_GlpG rhomboid family protease GlpG. GlpG in E. coli is a rhomboid family intramembrane serine protease that has been extensively characterized as a proxy for rhomboid family proteases in animals. It efficiently cleaves eukaryote-derived model substrates. This multiple membrane-spanning protein excludes inappropriate substrates from access to its cleavage site, and shows activity against truncated versions, but not full-length versions, of the E. coli multidrug transporter MdfA. This finding suggests a housekeeping function in removing faulty proteins. In contrast, several eukaryotic rhomboid family proteases release peptide hormones for signaling functions, and the Shewanella and Vibrio protein rhombosortase appears to be part of a protein-sorting system, cleaving a C-terminal anchoring helix domain. 270 matched cddid_all.tbl CDD TIGR04240 TIGR04240 213897 flavi_E_stem flavivirus envelope glycoprotein E, stem/anchor domain. This model describes the C-terminal domain, containing a stem region followed by two transmembrane anchor domains, of the envelope protein E. This protein is cleaved from the large flavivirus polyprotein, which yields three structural and seven nonstructural proteins. 97 matched cddid_all.tbl CDD TIGR04241 TIGR04241 211964 adenoE3CR1rpt mastadenovirus E3 CR1-alpha-1. This domain occurs only in the adenovirus E3 region CR1-alpha-1 protein. It may occur once, twice, or three times. 81 matched cddid_all.tbl CDD TIGR04242 TIGR04242 275076 nodulat_NodC chitooligosaccharide synthase NodC. Members of this family are NodC, an N-acetylglucosaminyltransferase involved in the production of nodulation factors through which rhizobia establish symbioses with leguminous plants. 395 matched cddid_all.tbl CDD TIGR04243 TIGR04243 211966 nodulat_NodB chitooligosaccharide deacetylase NodB. Nodulation factors are lipooligosaccharide signalling molecules produced by rhizobia, the symbiotic nitrogen-fixing bacteria that form nodules in plants. These Nod factor sustems have the NodABC genes in common but differ subtly in what they produce, which affects host range. NodB is a chitooligosaccharide deacetylase. 197 matched cddid_all.tbl CDD TIGR04244 TIGR04244 275077 nitrous_NosZ_RR nitrous-oxide reductase, TAT-dependent. Members of this family are the nitrous-oxide reductase structural protein, NosZ, with an N-terminal twin-arginine translocation (TAT) signal sequence (see TIGR01409). The TAT system replaces the Sec system for export of proteins with bound cofactor. 627 matched cddid_all.tbl CDD TIGR04245 TIGR04245 211968 nodulat_NodA N-acyltransferase NodA. Nodulation factors are lipo-chitooligosaccharides made by bacterial nitrogen-fixing bacteria as a signal to plant hosts. Nod factors differ slightly from system to system are serve as host range determinants. Because the N-acyl group varies from one NodA to another, the family treated as a subfamily, but all members of this family belong to NodABC systems. 193 matched cddid_all.tbl CDD TIGR04246 TIGR04246 275078 nitrous_NosZ_Gp nitrous-oxide reductase, Sec-dependent. This model represents the nitrous-oxide reductase protein NosZ as characterized in Geobacillus thermodenitrificans. In contrast to the related form in Pseudomonas stutzeri, this version lacks a recognizable twin-arginine translocation (TAT) signal at the N-terminus. Consequently, its accessory protein may differ. Some members of this family have an additional cytochrome c-like domain at the C-terminus. 578 matched cddid_all.tbl CDD TIGR04247 TIGR04247 275079 NosD_copper_fam nitrous oxide reductase family maturation protein NosD. Members of this family include NosD, a repetitive periplasmic protein required for the maturation of the copper-containing enzyme nitrous-oxide reductase. NosD appears to be part of a complex with NosF (an ABC transporter family ATP-binding protein) and NosY (a six-helix transmembrane protein in the ABC-2 permease family). However, NosDFY-like complexes appear to occur also in species whose copper requiring enzymes are something other than nitrous-oxide reductase. 377 matched cddid_all.tbl CDD TIGR04248 TIGR04248 211971 SCM_PqqD_rel SynChlorMet cassette protein ScmD. A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homolog, and a conserved hypothetical protein. These components suggest modification of a ribosomally produced peptide precursor, but the precursor has not been identified. Members of this family are the PqqD-like protein. 84 matched cddid_all.tbl CDD TIGR04249 TIGR04249 275080 SCM_chp_ScmC SynChlorMet cassette protein ScmC. A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homolog, and a conserved hypothetical protein. These components suggest modification of a ribosomally produced peptide precursor, but the precursor has not been identified. Members of this family are designated ScmC. 292 matched cddid_all.tbl CDD TIGR04250 TIGR04250 211973 SCM_rSAM_ScmE SynChlorMet cassette radical SAM/SPASM protein ScmE. A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homolog, and a conserved hypothetical protein. These components suggest modification of a ribosomally produced peptide precursor, but the precursor has not been identified. Of the two PqqE homologs of the cassette, this family is the closer in sequence. 358 matched cddid_all.tbl CDD TIGR04251 TIGR04251 211974 SCM_rSAM_ScmF SynChlorMet cassette radical SAM/SPASM protein ScmF. A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homolog, and a conserved hypothetical protein. These components suggest modification of a ribosomally produced peptide precursor, but the precursor has not been identified. Of the two PqqE homologs of the cassette, this family is the more distant in sequence. 353 matched cddid_all.tbl CDD TIGR04252 TIGR04252 211975 SCM_precur_ScmA SynChlorMet cassette protein ScmA. A biosynthesis cassette found in Syntrophobacter fumaroxidans MPOB, Chlorobium limicola DSM 245, Methanocella paludicola SANAE, and delta proteobacterium NaphS2 contains two PqqE-like radical SAM/SPASM domain proteins, a PqqD homolog, and a conserved hypothetical protein. This model identifies a conserved open reading frame that was identified as a predicted gene in only one of those species (Chlorobium), but that may represent the ribosomally produced peptide precursor of the system. As with most other radical SAM enzyme-modified ribosomal natural products, these polypeptides are Cys-rich in the C-terminal half. 49 matched cddid_all.tbl CDD TIGR04253 TIGR04253 211976 mesacon_CoA_iso mesaconyl-CoA isomerase. Members of this protein family belong by homology to the family of CoA transferases. However, the characterized member from Chloroflexus aurantiacus appears to perform an intramolecular transfer, making it an isomerase. The enzyme converts mesaconyl-C1-CoA to mesaconyl-C4-CoA as part of the bicyclic 3-hydroxyproprionate pathway for carbon fixation. 403 matched cddid_all.tbl CDD TIGR04254 TIGR04254 275081 OpituPEPCTERM_1 putative globular PEP-CTERM protein. Representatives of this family include a 13-member paralogous family of proteins about 215 amino acids in length from the termite gut bacterium Opitutaceae bacterium TAV2, a member of the Verrucomicrobia. The signal peptide (N-terminal) and PEP-CTERM putative protein sorting signal (C-terminal) are not included in the seed alignment. Conserved residues such as an invariant Arg and a lack of conspicuous low-complexity sequence suggest a globular structure and possible enzymatic activity. Members average about thirty percent sequence identify overall, but over seventy percent in the PEP-CTERM region. The function of this family is unknown. 136 matched cddid_all.tbl CDD TIGR04255 TIGR04255 275082 sporadTIGR04255 TIGR04255 family protein. Members of this uncharacterized protein family are found broadly but sporadically among bacteria and archaea, including members of the genera Mycobacterium, Nostoc, Acinetobacter, Planctomyces, Geobacter, Streptomyces, Methanospirillum, etc. The function is unknown. 249 matched cddid_all.tbl CDD TIGR04256 TIGR04256 275083 GxxExxY GxxExxY protein. Members of this protein family average about 130 residues in length and include an almost perfectly conserved motif GxxExxY. Members occur in a wide range of prokaryotes, including Proteobacteria, Perrucomicrobia, Cyanobacteria, Bacteriodetes, Archaea, etc. 116 matched cddid_all.tbl CDD TIGR04257 TIGR04257 275084 nanowire_3heme c(7)-type cytochrome triheme domain. This domain binds three hemes, and itself occurs as a repeating unit. It occurs, for instance, four times in the dodecaheme c-type cytochrome protein GSU_1996, whose crystal structure shows elongation and a nanowire-like arrangement of twelve hemes that could function in extracellular electron transport processes. 75 matched cddid_all.tbl CDD TIGR04258 TIGR04258 275085 4helix_suffix four helix bundle suffix domain. This domain occurs as a suffix domain to some members of the much broader protein family TIGR02436, a few of whose other members are encoded within intervening sequences of bacterial 23S ribosomal RNA. Some proteins with this domain, in turn, are followed by a predicted DNA topoisomerase type C4 zinc finger. 49 matched cddid_all.tbl CDD TIGR04259 TIGR04259 275086 oxa_formateAnti oxalate/formate antiporter. This model represents a subgroup of the more broadly defined model TIGR00890, which in turn belongs to the Major Facilitator transporter family. Seed members for this family include the known oxalate/formate antiporter of Oxalobacter formigenes, as well as transporter subunits co-clustered with the two genes of a system that decarboxylates oxalate into formate. In many of these cassettes, two subunits are found rather than one, suggesting the antiporter is sometimes homodimeric, sometimes heterodimeric. 405 matched cddid_all.tbl CDD TIGR04260 TIGR04260 275087 Cyano_gly_rpt rSAM-associated Gly-rich repeat protein. Members of this protein family average 125 in length, roughly half of which is the repetitive and extremely Gly-rich C-terminal region. Virtually all members occur in the Cyanobacteria, in a neighborhood that includes a radical SAM/SPASM domain, often a marker of peptide modification systems. 119 matched cddid_all.tbl CDD TIGR04261 TIGR04261 211984 rSAM_GlyRichRpt radical SAM/SPASM domain protein, GRRM system. Members of this protein family are radical SAM/SPASM domain proteins (see pfam04055 and TIGR04085) related to anaeroboic sulfatase maturating enzymes and the peptide modification enzyme PqqE. Members are found primarily in Cyanobacteria adjacent to a short protein, ~150 residues, in which the last ~60 residues tends to be repetitive and highly glycine-rich (see TIGR04260). The arrangement suggests modifications to the repetitive C-terminal region by this radical SAM domain enzyme, but the purpose of this system on the whole is unknown. 363 matched cddid_all.tbl CDD TIGR04262 TIGR04262 275088 orph_peri_GRRM extracellular substrate-binding orphan protein, GRRM family. This subfamily belongs to bacterial extracellular solute-binding protein family 3 (pfam00497). In that family, most members are ABC transporter periplasmic substrate-binding proteins. However, members of the present subfamily are orphans in the sense of being adjacent to neither ABC transporter ATP-binding proteins or permease subunits. Instead, most members are encoded next to the two signature proteins of the proposed Glycine-Rich Repeat Modification (GRRM) system, a radical SAM/SPASM protein GrrM (TIGR04261) and the Gly-rich repeat protein itself GrrA (TIGR04260). 257 matched cddid_all.tbl CDD TIGR04263 TIGR04263 275089 SasC_Mrp_aggreg SasC/Mrp/FmtB intercellular aggregation domain. This domain, about 375 amino acids long on average, occurs only in Staphylococcus and Streptococcus. It occurs as a non-repetitive N-terminal domain of LPXTG-anchored surface proteins, including SasC, Mrp, and FmtB. This region in SasC was shown to be involved in cell aggregation and biofilm formation, which may explain the methicillin resistance seen for Mrp and FmtB. 366 matched cddid_all.tbl CDD TIGR04264 TIGR04264 275090 hyperosmo_Ebh hyperosmolarity resistance protein Ebh, N-terminal domain. Staphylococcal protein Ebh (extracellular matrix-binding protein homolog) is a giant protein, sometimes over 10,000 amino acids long as reported. This model describes a non-repetitive amino-terminal domain of about 2400 amino acids. 2354 matched cddid_all.tbl CDD TIGR04265 TIGR04265 211988 bac_cardiolipin cardiolipin synthase. This model is based on experimentally characterized bacterial cardiolipin synthases (cls) from E. coli, Staphylococcus aureus (two), and Bacillus pseudofirmus OF4. This model describes just one of several homologous but non-orthologous forms of cls. The cutoff score is set arbitrarily high to avoid false-positives. Note that there are two enzymatic activites called cardiolipin synthase. This model represents type 1, which does not rely on a CDP-linked donor, but instead does a reversible transfer of a phosphatidyl group from one phosphatidylglycerol molecule to another. 483 matched cddid_all.tbl CDD TIGR04266 TIGR04266 211989 NDMA_methanol NDMA-dependent methanol dehydrogenase. Members of this family belong to the iron-dependent alcohol dehydrogenase family (see pfam00465). The NADP(H) cofactor is bound too tightly for exchange (although non-convalently), so enzymatic activity depends on a second substrate or electron carrier. The radical SAM-modified natural product mycofactocin is proposed to fill this role. In Rhodococcus erythropolis N9T-4, a role was shown for this protein in CO2 fixation during extreme oligotrophic (or possibly chemoautotrophic) growth. 420 matched cddid_all.tbl CDD TIGR04267 TIGR04267 275091 mod_HExxH HEXXH motif domain. Some proteins with this domain toward the C-terminus have an N-terminal region with a radical SAM domain (pfam04055) and a SPASM domain (TIGR04085), a combination frequently associated with peptide modification. All seed alignment members, and all family members that are not fused to a radical SAM domain, have a motif HEXXH that suggests metalloprotease activity. A role in peptide or protein maturation is suggested. 399 matched cddid_all.tbl CDD TIGR04268 TIGR04268 275092 FxSxx-COOH FXSXX-COOH protein. Members of this family are very short (~60 residue) polypeptides, among which the fifth and third to last residues are nearly always Phe and Ser, respectively. Because members occur in a conserved context with a putative peptide-modifying radical SAM/SPASM domain protein, we suggest that members of this family may be the modification target. The gene symbol fxsA reflects both the FXA motif and the proposed role as a ribosomal natural product. 44 matched cddid_all.tbl CDD TIGR04269 TIGR04269 275093 SAM_SPASM_FxsB radical SAM/SPASM domain protein, FxsB family. This model describes a radical SAM (pfam04055)/SPASM domain (TIGR04085) fusion subfamily distinct from PqqE, MftC, anaerobic sulfatase maturases, and other peptide maturases. The combined region described in this model can itself be fused to another domain, such as TIGR04267, or stand alone. Members occurring in the same cassette as a member of family TIGR04268 should be designated FxsB. 363 matched cddid_all.tbl CDD TIGR04270 TIGR04270 211993 Rama_corrin_act methylamine methyltransferase corrinoid protein reductive activase. Members of this family occur as paralogs in species capable of generating methane from mono-, di-, and tri-methylamine. Members include RamA (Reductive Activation of Methyltransfer, Amines) from Methanosarcina barkeri MS (DSM 800). Member proteins have two C-terminal motifs with four Cys each, likely to bind one 4Fe-4S cluster per motif. 535 matched cddid_all.tbl CDD TIGR04271 TIGR04271 275094 ThiI_C_thiazole thiazole biosynthesis domain. The ThiI protein of Escherichia coli is a bifunctional protein in which most of the length of the protein is responsible for sulfurtransferase activity in 4-thiouridine modification to tRNA (EC 2.8.1.4 - see model TIGR00342). This rhodanese-like C-terminal domain, by itself, is able to synthesize the thiazole moiety during thiamin biosynthesis. Note that the invariant Cys residue in this domain is unusual in being required for both activities of the bifunctional ThiI protein. 101 matched cddid_all.tbl CDD TIGR04272 TIGR04272 275095 cxxc_cxxc_Mbark CxxC-x17-CxxC domain. This domain, with a pair of CXXC motifs separated by 17 amino acids, is a candidate zinc finger domain based on these motifs. Some proteins have two copies of the domain, while others are fused to another probable zinc-binding domain, described by pfam13451. 37 matched cddid_all.tbl CDD TIGR04273 TIGR04273 275096 Y_sulf_Ax21 sulfation-dependent quorum factor, Ax21 family. This family consists of proteins closely related to Ax21 (Activator of XA21-mediated immunity), a protein that is secreted by a type I secretion system (RaxABC), and that appears to be sulfated on an N-terminal region tryosine in a motif LSYN. Ax21 acts in a quorum-sensing system. Homologous peptide-mediated quorum-sensing systems appear to exist in other species, such as the emerging opportunistic pathogen Stenotrophomonas maltophilia. Intriguingly, the rice genome encodes a receptor (XA21) for this protein that triggers innate immunity. [Cellular processes, Pathogenesis] 186 matched cddid_all.tbl CDD TIGR04274 TIGR04274 211997 hypoxanDNAglyco hypoxanthine-DNA glycosylase. Members of this protein family represent family 6 of the uracil-DNA glycosylase superfamily, where the five previously described families all act as uracil-DNA glycosylase (EC 3.2.2.27) per se. This family, instead, acts as a hypoxanthine-DNA glycosylase, where hypoxanthine results from deamination of adenine. Activity was shown directly for members from Methanosarcina barkeri and Methanosarcina acetivorans. 150 matched cddid_all.tbl CDD TIGR04275 TIGR04275 275097 beta_prop_Msarc beta propeller repeat, Methanosarcina surface protein type. This model describes a repeat region found mostly in cell surface proteins of various methanogens. Methanosarcina barkeri, for example, has twenty such proteins, often with either seven or fourteen repeats. These repeats resemble the beta propeller repeats of the TolB periplasmic protein of Gram-negative bacteria, part of a complex associated with various functions including biopolymer transport (see TIGR02800). 40 matched cddid_all.tbl CDD TIGR04276 TIGR04276 275098 FxsC_Cterm FxsC C-terminal domain. This model describes a sequence region found regularly as the C-terminal domain of a protein (where the N-terminal domain resembles a TIR domain - see pfam13676) in the vicinity of a proposed peptide-modifying radical SAM/SPASM domain protein, FxsB (TIGR04269). 196 matched cddid_all.tbl CDD TIGR04277 TIGR04277 212000 squa_tetra_cyc squalene--tetrahymanol cyclase. This enzyme, also called squalene--tetrahymanol cyclase, occurs a small number of eukaryotes, some of them anaerobic. The pathway can occur under anaerobic conditions, and the product is thought to replace sterols, letting organisms with this compound build membrane suitable for performing phagocytosis. 624 matched cddid_all.tbl CDD TIGR04278 TIGR04278 212001 viperin antiviral radical SAM protein viperin. Viperin (Virus Inhibitory Protein, ER-associated, Iterferon-inducible) is a radical SAM enzyme found in human and other vertebrates. It is both induced by interferon and demonstrably active in blocking replication by several types of virus, apparently by modifying lipid chemistries in lipid droplets and membrane rafts. 347 matched cddid_all.tbl CDD TIGR04279 TIGR04279 275099 TIGR04279 TIGR04279 methanogen extracellular domain. This domain, with length just over 300 amino acids, occurs in predicted extracellular proteins in a number of methanogens, in one to three proteins per genome. The aromatic residue tyrosine, comprising about five percent of the amino acid composition, is overrepresented among the most highly conserved columns of the multiple sequence alignment. The three members of this family in Methanosarcina barkeri occur all within a six-gene region. 316 matched cddid_all.tbl CDD TIGR04280 TIGR04280 275100 geopep_mat_rSAM putative geopeptide radical SAM maturase. This family is the radical SAM/SPASM domain putative peptide maturase for geopeptide, described by model TIGR04229. The SPASM domain (see model TIGR04085) frequently marks peptide-modifying radical SAM enzymes. 428 matched cddid_all.tbl CDD TIGR04281 TIGR04281 275101 peripla_PGF_1 putative ABC transporter PGF-CTERM-modified substrate-binding protein. Members of this archaeal protein family resemble periplasmic substrate-binding proteins of ABC transporters and appear in gene neighborhoods with permease and ATP-binding cassette proteins. Notably, essentially all members also have the PGF-CTERM putative protein-sorting domain at the C-terminus, while more distant homologs (excluded by the trusted cutoff) instead have what appear to be lipoprotein signal peptides at the N-terminus. 330 matched cddid_all.tbl CDD TIGR04282 TIGR04282 275102 glyco_like_cofC transferase 1, rSAM/selenodomain-associated. Members of this protein family show strongly correlated phylogenetic distribution, and in most cases co-clustering, with an unusual radical SAM enzyme (TIGR04167) whose C-terminal pfam12345 domain often contains a selenocysteine residue. Other members of the conserved gene neighborhood include another putative glycosyltransferase, an alkylhydroperoxidase family protein (TIGR04169), and a phosphoesterase family protein (TIGR04168). The cassette is likely to be biosynthetic but its exact function is unknown. [Unknown function, Enzymes of unknown specificity] 189 matched cddid_all.tbl CDD TIGR04283 TIGR04283 275103 glyco_like_mftF transferase 2, rSAM/selenodomain-associated. This enzyme may transfer a nucleotide, or it sugar moiety, as part of a biosynthetic pathway. Other proposed members of the pathway include another transferase (TIGR04282), a phosphoesterase, and a radical SAM enzyme (TIGR04167) whose C-terminal domain (pfam12345) frequently contains a selenocysteine. [Unknown function, Enzymes of unknown specificity] 220 matched cddid_all.tbl CDD TIGR04284 TIGR04284 275104 aldehy_Rv0768 aldehyde dehydrogenase, Rv0768 family. This family describes a branch of the aldehyde dehydrogenase (NAD) family (see pfam00171) that includes Rv0768 from Mycobacterium tuberculosis. All members of this family belong to species predicted to synthesize mycofactocin, suggesting that this enzyme or another upstream or downstream in the same pathway might be mycofactocin-dependent. However, the taxonomic range of this family is not nearly broad enough to make that relationship conclusive. [Unknown function, Enzymes of unknown specificity] 480 matched cddid_all.tbl CDD TIGR04285 TIGR04285 275105 nucleoid_noc nucleoid occlusion protein. This model describes nucleoid occlusion protein, a close homolog to ParB chromosome partitioning proteins including Spo0J in Bacillus subtilis. Its gene often is located near the gene for the Spo0J ortholog. This protein bind a specific DNA sequence and blocks cytokinesis from happening until chromosome segregation is complete. 255 matched cddid_all.tbl CDD TIGR04286 TIGR04286 275106 MSEP-CTERM MSEP-CTERM protein. Members of this protein family average over 900 residues in length and appear to have multiple membrane-spanning helices in the N-terminal half. The extreme C-terminal region consists of a motif with consensus sequence MSEP, then a transmembrane alpha helix, then a short region with several basic residues. This region, hereby dubbed MSEP-CTERM, resembles other putative sorting signals associated with the archaeosortase/exosortase protein family (see TIGR04178). Genes for all members of this family are found next to a gene for exosortase K. 920 matched cddid_all.tbl CDD TIGR04287 TIGR04287 213900 exosort_XrtK exosortase K. Members of this protein family are exosortase K, a bacterial branch of the archaeosortase/exosortase family of protein-processing enzymes (see TIGR04178). All members of the seed alignment are encoded next to a member of family TIGR04286, which has the putative processing signal MSEP-CTERM (see family TIGR04286) at the extreme C-terminus. 163 matched cddid_all.tbl CDD TIGR04288 TIGR04288 213901 CGP_CTERM CGP-CTERM domain. This domain has an essentially invariant motif, Cys-Gly-Pro, followed by a highly hydrophobic transmembrane domain, always at the protein C-terminus. It occurs, so far, strictly in the family Thermococcaceae (includes Thermococcus and Pyrococcus) within the Euryarchaeota. It occurs in ten proteins per genome on average, and proteins with the domain may lack similarity elsewhere. The presumed sorting/processing protein, for which this domain contains the recognition sequence, is unknown, but it is unlikely to be a member of the exosortase/archaeosortase family. The Cys residue suggests a lipid modification. Upstream, from this domain, most member proteins have an extremely Thr-rich sequence, suggesting archaeal surface protein O-linked glycosylation. 20 matched cddid_all.tbl CDD TIGR04289 TIGR04289 275107 heavy_Cys eight-cysteine-cluster domain. In this domain of about 50 residues, eight of twelve invariant residues are Cys. Proteins with this domain tend to have N-terminal signal sequences, suggesting an extracytoplasmic location for this domain. 52 matched cddid_all.tbl CDD TIGR04290 TIGR04290 275108 meth_Rta_06860 methyltransferase, Rta_06860 family. Members of this family are methyltransferases that mark a widely distributed large conserved gene neighborhood of unknown function. It appears most common in soil and rhizosphere bacteria. 226 matched cddid_all.tbl CDD TIGR04291 TIGR04291 275109 arsen_driv_ArsA arsenical pump-driving ATPase. The broader family (TIGR00345) to which the current family belongs consists of transport-energizing ATPases, including to TRC40/GET3 family involved in post-translational insertion of protein C-terminal transmembrane anchors into membranes from the cyotosolic face. This family, however, is restricted to ATPases that energize pumps that export arsenite (or antimonite). 566 matched cddid_all.tbl CDD TIGR04292 TIGR04292 275110 heavy_Cys_CGP heavy-Cys/CGP-CTERM domain protein. Members of this protein family are restricted to the Pyrococcus and Thermococcus genera of the archaea. Member proteins have a C-terminal, Cys-containing predicted surface anchor domain, where the Cys may be the site of cleavage and lipid attachment (see domain TIGR04288). Members also contain a region crowded with 10 invariant Cys in 60 residues (see domain TIGR04289), possible ligands to some redox cofactor. Note that a sorting motif is CGP. Previously, the motif was named incorrectly as GCP-CTERM in this model due to a typographical error. 373 matched cddid_all.tbl CDD TIGR04293 TIGR04293 213906 archaeo_artF archaeosortase family protein ArtF. Members of this protein family, ArtF, belong to the archaeosortase/exosortase family, in which many members associate with specific protein C-terminal putative protein sorting domains (exosortase A with PEP-CTERM, archaeosortase A with PGF-CTERM, etc.). This subgroup is observed in Thermococcus gammatolerans EJ3 and Thermococcus sp. AM4, but the gene neighborhood is not conserved. The cognate sequence to ArtF is unknown, but should not be ICGP-CTERM (model TIGR04288), found also in many Pyrococcus species that lack any archaeosortase family member. 166 matched cddid_all.tbl CDD TIGR04294 TIGR04294 213907 pre_pil_HX9DG prepilin-type processing-associated H-X9-DG domain. This model describes a region of ~16 residues found typically about 30 residues away from the C-terminus of large numbers of proteins in the Planctomycetes, Lentisphaerae, and Verrucomicrobia, on proteins with a prepilin-type N-terminal cleavage/methylation domain (see TIGR02532). The motif H-X(9)-D-G is nearly invariant. Single genomes may encode over 200 such proteins. 16 matched cddid_all.tbl CDD TIGR04295 TIGR04295 275111 B12_rSAM_oligo B12-binding domain/radical SAM domain protein, rhizo-twelve system. A variety of bacteria, including multiple species of Bradyrhizobium, Mesorhizobium, and Methylobacterium, have a typically twelve-gene cassette (hence the designation rhizo-twelve) for the biosynthesis of some unknown oligosaccaride. This family is a B12-binding domain/radical SAM domain protein found in roughly have of these cassettes, but nowhere else. 422 matched cddid_all.tbl CDD TIGR04296 TIGR04296 275112 PEFG-CTERM PEFG-CTERM domain. This putative protein sorting/processing domain occurs about ten times per genome in members of the Thaumarchaeota. Its putative handling protein, a member of the archaeosortase/exosortase protein family, is exceptional in having a Ser rather than Cys at the putative active site. The highly conserved motif resembles the PEF-CTERM protein sorting domain of family TIGR03024, but membership does not overlap. 30 matched cddid_all.tbl CDD TIGR04297 TIGR04297 213910 thauma_sortase thaumarchaeosortase. This member of the archaeosortase/exosortase family occurs exclusively in the Thaumarchaeota, where the corresponding proposed sorting signal is PEFG-CTERM (see model TIGR04296). This family is unusual in that the suspected active site residue, Cys in every other defined subfamily of archaeosortases and exosortases is replaced by Ser. 307 matched cddid_all.tbl CDD TIGR04298 TIGR04298 213911 his_histam_anti histidine-histamine antiporter. Members of this protein family are antiporters that exchange histidine with histamine, product of histidine decarboxylation. A system consisting of this protein, and a histidine decarboxylase encoded by an adjacent gene, creates decarboxylation/antiport proton-motive cycle that provides a transient resistance to acidic conditions. 429 matched cddid_all.tbl CDD TIGR04299 TIGR04299 213912 antiport_PotE putrescine-ornithine antiporter. Members of this protein family are putrescine-ornithine antiporter. They work together with an enzyme that decarboxylates ornithine to putrescine. This two-gene system has the net effect of removing a protein from the cytosol, providing transient resistance to acid conditions. 430 matched cddid_all.tbl CDD TIGR04300 TIGR04300 213913 exosort_XrtM exosortase family protein XrtM. Members of this family, part of the larger exosortase/archaeosortase family, are known from five related cassettes of genes in Methylomonas methanica MC09, a gammaproteobacterial methanotroph. Each xrtM gene occurs near a large YD repeat (see TIGR01643) protein of 1500-2500 residues and a small, uncharacterized protein of about 200 residues. No PEP-CTERM-like recognition sequence has been identified, so this protein is designated as exosortase family, but not necessarily a functional exosortase. 150 matched cddid_all.tbl CDD TIGR04301 TIGR04301 275113 ODC_inducible ornithine decarboxylase SpeF. Members of this family are known or trusted examples of ornithine decarboxylase, all encoded in the immediate vicinity of an ornithine-putrescine antiporter. Decarboxylation of ornithine to putrescine, followed by exchange of a putrescine for a new ornithine, is a proton-motive cycle that can be induced by low pH and protect a bacterium against transient exposure to acidic conditions. 719 matched cddid_all.tbl CDD TIGR04302 TIGR04302 213915 geo_PqqD_fam GeoRSP system PqqD family protein. Members of this PqqD-related family so far occur only in the genus Geobacter, always together with a PqqE-like radical SAM domain/SPASM domain protein and a second SPASM domain protein with traces of a degenerate radical SAM domain. The extended gene region includes a high-molecular-weight cytochrome c family protein. Besides authentic PqqD (TIGR03859), another example of a PqqD family protein occurs in the SynChlorMet cassette, again with two PqqE-like proteins. The system is named GeoRSP for its prevalence in Geobacter, its Radical SAM protein, is SPASM domain protein, and its PqqD family protein. 102 matched cddid_all.tbl CDD TIGR04303 TIGR04303 213916 GeoRSP_rSAM GeoRSP system radical SAM/SPASM protein. Members of this family are radical SAM/SPASM domain proteins from a cassette restricted to the genus Geobacter. Genes always found adjacent include a non-radical SAM protein with a closely related SPASM domain and a short stretch of N-terminal homology as well to this family, and also a PqqD-like protein. The three-gene cassette is designated GeoRSP for the genus Geobacter, this radical SAM protein, the SPASM domain protein, and the PqqD family protein. 325 matched cddid_all.tbl CDD TIGR04304 TIGR04304 213917 GeoRSP_SPASM "GeoRSP system SPASM domain protein. Members of this protein family are encoded by one of two consecutive genes for SPASM domain proteins. The two are closely homologous in the SPASM domain regions, and also in a small N-terminal region, but the other family (TIGR04303) has an intact radical SAM domain (pfam04055) that this ""quasi-rSAM"" protein lacks. A PqqD-family protein, TIGR04302, is always adjacent." 293 matched cddid_all.tbl CDD TIGR04305 TIGR04305 275114 fol_rel_CADD putative folate metabolism protein, CADD family. This protein family, related to but outside the family of PqqC proteins involved in PQQ biosynthesis, includes the well-studied Chlamydia protein CADD (Chlamydia protein Associating with Death Domains), which can induce apoptosis in a host cell. Other members of this family occur in Rickettsia and Wolbachia, unrelated in terms of phylogeny (both are alphaproteobacteria) but similar in living intracellularly. Local gene context in these species, although not in Trichodesmium or Nitrosomonas eutropha, suggests a role in folate metabolism, and some species with this protein lack FolE but have other folate synthesis proteins. 212 matched cddid_all.tbl CDD TIGR04306 TIGR04306 213919 salvage_TenA thiaminase II. The TenA protein of Bacillus subtilis and Staphylococcus aurues, and the C-terminal region of trifunctional protein Thi20p from Saccharomyces cerevisiae, perform cleavages on thiamine and related compounds to produce 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP), a substrate a salvage pathway for thiamine biosynthesis. The gene symbol tenA, for Transcription ENhancement A, reflects a misleading early characterization as a regulatory protein. This family is related to PqqC from the PQQ biosynthesis system (see TIGR02111), heme oxygenase (pfam01126), and CADD (Chlamydia protein Associating with Death Domains), a putative folate metabolism enzyme (see TIGR04305). 208 matched cddid_all.tbl CDD TIGR04307 TIGR04307 213920 ProTailRpt proline-rich tail region repeat. This model describes a proline-rich tandem repeat of about 24 residues found in C-terminal regions of Gram-positive surface proteins with LPXTG sequences for processing and cell surface attachment by sortase. 23 matched cddid_all.tbl CDD TIGR04308 TIGR04308 275115 repeat_SSSPR51 surface protein repeat SSSPR-51. This repeat domain is designated SSRS51, Streptococcal and Staphylococcal Surface Protein Repeat of size 51. These repeats are homologous to the listerial repeats of pfam13461, but shorter on average by about 8 amino acids. Up to twelve tandem repeats can occur, on some of the longest proteins of their respective species. Nearly all member proteins carry the C-terminal sortase target sequence, LPXTG, recognizable by model TIGR01167. The repeat structure and probable surface location suggest a possible adhesion function. A protein with this class of repeats may have other classes as well. 48 matched cddid_all.tbl CDD TIGR04309 TIGR04309 213922 amanitin amanitin/phalloidin family toxin. Members of this family are ribosomally produced precursors of toxins produced by several mushrooms. These precursors undergo extensive post-translational modification to become amatoxins (e.g. alpha-amanitin) and phallotoxins (e.g. phalloidin). 33 matched cddid_all.tbl CDD TIGR04310 TIGR04310 213923 pantocin_A_pre pantocin A family RiPP. Members of this family are ribosomally-synthesized and posttranslationally-modified peptide (RiPP) precursors about 30 amino acids in length encoded in the vicinity of PaaA and PaaB homologs. Members include PaaP from Pantoea agglomerans, whose central tripeptide EEN appears to be the source of the mature product, pantocin A. Note, however, that the corresponding residues in Photobacterium sp. SKA34 and Photobacterium asymbiotica are EEK rather than EEN. This family, therefore, resembles the PQQ precursor PqqA as a peptide precursor of an extremely small mature product. 29 matched cddid_all.tbl CDD TIGR04311 TIGR04311 275116 rSAM_Geo_metal putative metalloenzyme radical SAM/SPASM domain maturase. This model describes a family of radical SAM/SPASM enzymes largely from the deltaproteobacteria. The family is most closely related to radical SAM enzyme family regularly in archaea in the vicinity of tungsten-containing oxidoreductases. A single member of the family in archaea may correspond to multiple tungsten enzymes, e.g. five in Pyrococcus furiosus. Therefore, the lack of a conserved gene neighborhood for members of this family in deltaprotebacteria suggests members may be involved in the maturation of multiple metalloenzymes. 423 matched cddid_all.tbl CDD TIGR04312 TIGR04312 275117 choice_anch_B choice-of-anchor B domain. This domain, about 385 amino acids long, can have either of at least two types of C-terminal sorting signal. Members from Shewanella and allies have the rhombosortase target domain GlyGly-CTERM (TIGR03501), while members of the Bacteroidetes have the Por secretion system C-terminal domain (TIGR04183). Most other members lack any C-terminal extension, but in most of those, the normal signal sequence is replaced by a lipoprotein signal sequence. Member sequences show a region of local similarity to the LVIVD repeat sequence (pfam08309). 364 matched cddid_all.tbl CDD TIGR04313 TIGR04313 275118 aro_clust_Mycop aromatic cluster surface protein. Members of this family are absolutely restricted to the Mollicutes (Mycoplasma and Ureaplasma). All have a signal peptide, usually of the lipoprotein type, suggesting surface expression. Most members have lengths of about 280 residues but some members have a nearly full-length duplication. The mostly nearly invariant residue, a Trp,is part of a strongly conserved 9-residue motif, [ND]-W-[LY]-[WF]-X-[LF]-X-N-[LI], where X usually is hydrophobic. Because the hydrophobic six-residue core of this motif almost always contains three to four aromatic residues, we name this family aromatic cluster surface protein. Multiple paralogs may occur in a given Mycoplasma, usually clustered on the genome. 293 matched cddid_all.tbl CDD TIGR04314 TIGR04314 213927 methano7heme methanogenesis multiheme c-type cytochrome. Members of this protein family are multiheme cytochrome c proteins of Methanosarcina acetivorans C2A and several other archaeal methanogens. All members have N-terminal signal peptides and are presumed to act in electron transfer reactions associated with methanogenesis. Putative heme-binding motifs include five (or six) CXXCH motifs, a CXXXCH motif, and a CXXXXCH motif. These proteins show multiple regions of local homology, in the same order, with multiheme cytochrome c proteins such as octaheme tetrathionate reductase from Shewanella. 494 matched cddid_all.tbl CDD TIGR04315 TIGR04315 275119 octaheme_Shew octaheme c-type cytochrome, tetrathionate reductase family. Members of this protein family bind heme covalently and contain eight (at least) CXXCH heme-binding motifs. A characterized member is the respiratory enzyme octaheme tetrathionate reductase from Shewanella. 430 matched cddid_all.tbl CDD TIGR04316 TIGR04316 275120 dhbA_paeA 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase. Members of this family are 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase (EC 1.3.1.28), the third enzyme in the biosynthesis of 2,3-dihydroxybenzoic acid (DHB) from chorismate. The first two enzymes are isochorismate synthase (EC 5.4.4.2) and isochorismatase (EC 3.3.2.1). Synthesis is often followed by adenylation by the enzyme DHBA-AMP ligase (EC 2.7.7.58) to activate (DHB) for a non-ribosomal peptide synthetase. 250 matched cddid_all.tbl CDD TIGR04317 TIGR04317 275121 W_rSAM_matur tungsten cofactor oxidoreducase radical SAM maturase. Members of this family are radical SAM enzymes involved in the maturation of tungsten (W)-containing cofactors in the enzymes aldehyde ferredoxin oxidoreductase, formaldehyde ferredoxin oxidoreductase, and others, and tend to be encoded by an adjacent gene. 349 matched cddid_all.tbl CDD TIGR04318 TIGR04318 275122 lacto_ODC_hypo putative ornithine decarboxylase. In at least ten species of Lactobacillus, this close homolog to known ornithine decarboxylase occurs in a three-gene neighborhood, along with an amino acid permease family transporter and pyridoxal phosphate-dependent enyzme from the cystathionine gamma-lyase family. Species include L. acidophilus, L. amylovorus, L. crispatus, L. delbrueckii, L. farciminis, L. helveticus, L. johnsonii, etc. The combination of a decarboxylase with an antiporter in a two-gene system suggests a decarboxylation/antiport proton-motive cycle for transient resistance to acidic conditions. The substrate for this decarboxylase might be ornithine but is unknown. 695 matched cddid_all.tbl CDD TIGR04319 TIGR04319 275123 SerAla_Lrha_rpt surface protein repeat Ser-Ala-175. This serine and alanine-rich surface protein repeat, about 175 amino acids long, occurs up to nine times in surface proteins of some Lactobacillus strains, particularly in Lactobacillus rhamnosus. Members proteins have the N-terminal variant signal sequence described by TIGR03715 and C-terminal LPXTG signals for surface attachment by sortase. 175 matched cddid_all.tbl CDD TIGR04320 TIGR04320 275124 Surf_Exclu_PgrA SEC10/PgrA surface exclusion domain. This model describes a conserved domain found in surface proteins of a number of Firmutes. Many members have LPXTG C-terminal anchoring motifs and a substantial number have the KxYKxGKxW putative sorting signal at the N-terminus. The tetracycline resistance plasmid pCF10 in Enterococcus faecalis promotes conjugal plasmid transfer in response to sex pheromones, but PgrA/Sec10 encoded by that plasmid, a member of this family, specifically inhibits the ability of cells to receive homologous plasmids. The phenomenon is called surface exclusion. 356 matched cddid_all.tbl CDD TIGR04321 TIGR04321 275125 spiroSPASM spiro-SPASM protein. This three-domain protein is restricted to the spirochetes and widely distributed (excepting Borrelia). It has a conserved C-terminal SPASM domain, a 4Fe-4S binding domain shared by a number of peptide-modifying and heme-modifying radical SAM proteins. It has a central radical SAM domain, although half the members have lost the signature 4Fe-4S-binding Cys residues, fail to register with the radical SAM domain definition of pfam04055, and must be considered pseudo-SAM proteins. PSI-BLAST shows a relationship between the N-terminal domain and various predicted glycosyltransferases (e.g. Bacillus subtilis SpsF) and cytidyltransferases. In some Treponema species, this protein appears to split into two tandem genes. 508 matched cddid_all.tbl CDD TIGR04322 TIGR04322 275126 rSAM_QueE_Ecoli putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE. Members of this radical SAM domain protein family appear to be the E. coli form of the queuosine biosynthesis protein QueE. QueE is involved in making preQ0 (7-cyano-7-deazaquanine), a precursor of both the bacterial/eukaryotic modified tRNA base queuosine and the archaeal modified base archaeosine. Members occur in species that lack known forms of QueE but usually are not found in queuosine biosynthesis operons. Members of this family tend to form bi-directional best hit matches to members of known (TIGR03365) and putative (TIGR03963) QueE families from other lineages. 215 matched cddid_all.tbl CDD TIGR04323 TIGR04323 213936 SpoChoClust_1 sporadic carbohydrate cluster protein, LIC12192 family. Members of this uncharacterized protein family mark a rare but widely distributed carbohydrate biosynthesis cluster found sporadically in genera Bradyrhizobium, Leptospira, Magnetospirillum, Oscillatoria, Prochlorococcus, etc. 122 matched cddid_all.tbl CDD TIGR04324 TIGR04324 275127 SpoChoClust_2 sporadic carbohydrate cluster 2OG-Fe(II) oxygenase. This family, related to streptomycin biosynthesis protein StrG and to phytanoyl-CoA dioxygenase, belongs to the 2-oxoglutarate and Fe(II)-dependent oxygenase superfamily, which includes not just dioxygenases, but also some chlorinating enzymes involved in natural product biosynthesis. Most members of this family are adjacent to a member of TIGR04323, and occur in a larger carbohydrate biosynthesis cluster found sporadically in genera Bradyrhizobium, Leptospira, Magnetospirillum, Oscillatoria, Prochlorococcus, etc. 248 matched cddid_all.tbl CDD TIGR04325 TIGR04325 275128 MTase_LIC12133 putative methyltransferase, LIC12133 family. Members of this family tend to occur next to glycosyltransferases and other characteristic enzymes of O-antigen biosynthetic regions. The founding member is LIC12133 from Leptospira interrogans serovar Copenhageni. PSI-BLAST reveals distant homology to known SAM-dependent methyltransferases, as in pfam13489. 235 matched cddid_all.tbl CDD TIGR04326 TIGR04326 275129 O_ant_LIC13510 surface carbohydrate biosynthesis protein, LIC13510 family. This uncharacterized, rare protein occurs in the highly variable O-antigen region of some strains of Leptospira, as well as strains of and serves as a phylogenetic marker for the likely presence of six additional proteins, including an activated sugar-nucleotidyltransferase, an activated sugar epimerase and a dehydratase, an aldolase, and a DegT family aminotransferase. The patterns suggests a role in preparing a novel sugar for O-antigen incorporation. 602 matched cddid_all.tbl CDD TIGR04327 TIGR04327 275130 OMP_LA_2444 outer membrane protein, LA_2444/LA_4059 family. Members of this family are predicted outer membrane proteins, apparently restricted to the Leptospiraceae (Leptospira and Leptonema). 291 matched cddid_all.tbl CDD TIGR04328 TIGR04328 213941 cas4_PREFRAN CRISPR-associated protein Cas4, subtype PREFRAN. Members of this family are the Cas4 protein of a novel CRISPR subtype, PREFRAN, found in Prevotella bryantii B14, Prevotella disiens FB035-09AN, Francisella tularensis subsp. novicida, Francisella philomiragia, Butyrivibrio proteoclasticus B316, Helcococcus kunzii ATCC 51366, etc. 178 matched cddid_all.tbl CDD TIGR04329 TIGR04329 213942 cas1_PREFRAN CRISPR-associated endonuclease Cas1, subtype PREFRAN. Members of this family are the Cas1 endonuclease of a novel CRISPR subtype, PREFRAN, found in Prevotella bryantii B14, Prevotella disiens FB035-09AN, Francisella tularensis subsp. novicida, Francisella philomiragia, Butyrivibrio proteoclasticus B316, Helcococcus kunzii ATCC 51366, etc. 317 matched cddid_all.tbl CDD TIGR04330 TIGR04330 275131 cas_Cpf1 CRISPR-associated protein Cpf1, subtype PREFRAN. This family is the long protein of a novel CRISPR subtype, PREFRAN, which is most common in Prevotella and Francisella, although widely distributed. The PREFRAN type has Cas1, Cas2, and Cas4, but lacks the helicase Cas3 and endonuclease Cas3-HD. 1286 matched cddid_all.tbl CDD TIGR04331 TIGR04331 275132 o_ant_LIC12162 putative transferase, LIC12162 family. This protein family shows C-terminal sequence similarity to various surface carbohydrate biosynthesis enzymes: spore coat polysaccharide biosynthesis protein SpsB, UDP-N-acetyl-D-glucosamine 2-epimerase, lipid A disaccharide synthetase LpxB, etc. It may occur in O-antigen biosythesis regions. 585 matched cddid_all.tbl CDD TIGR04332 TIGR04332 275133 gamma_Glu_sys poly-gamma-glutamate system protein. Poly(gamma-glutamic acid), or PGA, is an extracellular structural polymer found in Bacillus subtilis and a number of other species. PGA is sometimes capsule-forming, sometimes secretory, and may be produced by Gram-positive (single plasma membrane) and Gram-negative (inner and outer membranes), so export and/or attachment machinery may differ from system to system. Members of this family occur in a subset of PGA operons, in lineages that include Francisella, Leptospira, Treponema, Thermotoga, Fusobacterium, and Clostridium, among others. Because gene symbols pgsWXYZ are not yet in use, we suggest pgsW, as one of a series of poly-gamma-glutamate synthesis auxiliary proteins. 307 matched cddid_all.tbl CDD TIGR04333 TIGR04333 213946 Clo7Bot_mod_Cys Cys-rich peptide, Clo7bot family. Members of this protein family range in size from 34 to 53 residues, including from four to seven Cys residues. Multiple strains of Clostridium botulinum show seven tandem members upstream of a radical SAM/SPASM domain protein likely to act as a ribosomal natural product maturase. By analogy to subtilosin A, the Cys residues are likely targets for modifications that may introduce new crosslinks. Across multiple strains of Clostridium botulinum and C. sporogenes, the adjacent radical SAM enzyme is nearly invariant. 34 matched cddid_all.tbl CDD TIGR04334 TIGR04334 213947 rSAM_Clo7bot radical SAM/SPASM domain Clo7bot peptide maturase. In multiple strains of Clostridium botulinum, this single radical SAM domain protein occurs next to a tandem array of seven homologous Cys-rich small peptides (see TIGR04333). Because this radical SAM enzyme contains the SPASM domain, associated with peptide modification, it is proposed to modify all seven C. botulinum targets, hence the name Clo7bot for this system. Suggested gene symbol is ctpM (Clostridial Tandem Peptide Maturase). [Protein fate, Protein modification and repair] 440 matched cddid_all.tbl CDD TIGR04335 TIGR04335 275134 AmmeMemoSam_A AmmeMemoRadiSam system protein A. Members of this protein family belong to the same domain family as AMMECR1, a mammalian protein named for AMME - Alport syndrome, Mental Retardation, Midface hypoplasia, and Elliptocytosis. Members of the present family occur as part of a three gene system with a homolog of the mammalian protein Memo (Mediator of ErbB2-driven cell MOtility), and an uncharacterized radical SAM enzyme. 174 matched cddid_all.tbl CDD TIGR04336 TIGR04336 275135 AmmeMemoSam_B AmmeMemoRadiSam system protein B. Members of this protein family belong to the same domain family as the mammalian protein Memo (Mediator of ErbB2-driven cell MOtility). Members of the present family occur as part of a three gene system with an uncharacterized radical SAM enzyme and a homolog of the mammalian protein AMMECR1, a mammalian protein named for AMME - Alport syndrome, Mental Retardation, Midface hypoplasia, and Elliptocytosis. Memo in humans has protein-protein interaction activity with binding of phosphorylated Try, but members of this family may be active as enzymes, as suggested by homology to a class of nonheme iron dioxygenases. 269 matched cddid_all.tbl CDD TIGR04337 TIGR04337 275136 AmmeMemoSam_rS AmmeMemoRadiSam system radical SAM enzyme. Members of this protein family are uncharacterized radical SAM enzymes that occur in a prokaryotic three-gene system along with homologs of mammalian proteins Memo (Mediator of ErbB2-driven cell MOtility) and AMMERCR1 (Alport syndrome, Mental Retardation, Midface hypoplasia, and Elliptocytosis). Among radical SAM enzymes that have been experimentally characterized, the most closely related in sequence include activases of pyruvate formate-lyase and of benzylsuccinate synthase. 349 matched cddid_all.tbl CDD TIGR04338 TIGR04338 275137 HEXXH_Rv0185 putative metallohydrolase, TIGR04338 family. This protein family is restricted to the Actinomycetales, including Mycobacterium, Rhodococcus, Nocardia, Gordonii, and others. The invariant motif HEXXH, at the core of the best conserved region in the protein, suggests metallohydrolase activity, as does local sequence similarity in this region to other metallohydrolases. 159 matched cddid_all.tbl CDD TIGR04339 TIGR04339 213952 PQQ_MSMEG_3727 Actinobacterial PQQ system protein. Members of this protein family are restricted to members of the Actinobacteria (Mycobacterium smegmatis, Streptomyces hygroscopicus, Geodermatophilus obscurus, Pseudonocardia dioxanivorans, Saccharomonospora marina, etc) that synthesize PQQ. This small protein, 155 amino acids long on average, is found regularly next to a much larger protein, a PQQ-dependent oxidoreductase, and might be a companion subunit or an accessory protein such as chaperone involved in cofactor insertion. 151 matched cddid_all.tbl CDD TIGR04340 TIGR04340 213953 rSAM_ACGX radical SAM/SPASM domain protein, ACGX system. Members of this protein family are radical SAM/SPASM domain proteins likely to be involved in the modification of small, Cys-rich peptides. Members of the family of proposed target sequences, TIGR04341, average 75 amino acids in length and average six instances of the motif ACGX, where X is A, S, or T. 341 matched cddid_all.tbl CDD TIGR04341 TIGR04341 213954 target_ACGX ACGX-repeat peptide. Members of this family average 75 amino acids in length and average six instances of the motif ACGX, where X is A, S, or T. Members are proposed target sequences for modification by adjacent radical SAM/SPASM domain proteins (family TIGR04340). Cys residues adjacent to Gly residues are common as proposed sites for modification by radical SAM enzymes. 57 matched cddid_all.tbl CDD TIGR04342 TIGR04342 275138 EXLDI EXLDI protein. The most conserved region in this protein family is the C-terminal pentapeptide, with motif ExLDI. Members from the Firmicutes average about 120 amino acids in length, while members from the Actinobacteria have an additional 45-residue amino-terminal segment not included in the model. In it is suggested that the member from Streptococcus mutans UA159, and its homologs, participate in bacteriocin production, export, or immunity. 124 matched cddid_all.tbl CDD TIGR04343 TIGR04343 275139 egtE_PLP_lyase ergothioneine biosynthesis PLP-dependent enzyme EgtE. Members of this protein family are the pyridoxal phosphate-dependent enzyme EgtE, which catalyzes the final step in the biosynthesis of ergothioneine. [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 370 matched cddid_all.tbl CDD TIGR04344 TIGR04344 275140 ovoA_Nterm 5-histidylcysteine sulfoxide synthase. Ovothiol A is N1-methyl-4-mercaptohistidine. In the absence of S-adenosylmethione, a methyl donor, the intermediate produced is 4-mercaptohistidine. In both Erwinia tasmaniensis and Trypanosoma cruzi, a protein occurs with 5-histidylcysteine sulfoxide synthase activity, but these two enzymes and most homologs share an additional C-terminal methyltransferase domain. Thus OvoA may be a bifunctional enzyme with 5-histidylcysteine sulfoxide synthase and 4-mercaptohistidine N1-methyltranferase activity. This model describes the 5-histidylcysteine sulfoxide synthase domain, a homolog of the ergothioneine biosynthesis protein EgtB. [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 442 matched cddid_all.tbl CDD TIGR04345 TIGR04345 275141 ovoA_Cterm putative 4-mercaptohistidine N1-methyltranferase. Ovothiol A is N1-methyl-4-mercaptohistidine. In the absence of S-adenosylmethione, a methyl donor, the intermediate produced is 4-mercaptohistidine. In both Erwinia tasmaniensis and Trypanosoma cruzi, a protein occurs with 5-histidylcysteine sulfoxide synthase activity, but these two enzymes and most homologs share an additional C-terminal methyltransferase domain. Thus OvoA may be a bifunctional enzyme with 5-histidylcysteine sulfoxide synthase and 4-mercaptohistidine N1-methyltranferase activity. This model describes C-terminal putative 4-mercaptohistidine N1-methyltranferase domain. [Biosynthesis of cofactors, prosthetic groups, and carriers, Glutathione and analogs] 242 matched cddid_all.tbl CDD TIGR04346 TIGR04346 275142 DotA_TraY conjugal transfer/type IV secretion protein DotA/TraY. Members of this protein family include transfer protein TraY of IncI1 plasmid R64 and DotA (defect in organelle trafficking A) of Legionella pneumophila. 652 matched cddid_all.tbl CDD TIGR04347 TIGR04347 275143 pseudo_SAM_Halo pseudo-rSAM protein/SPASM domain protein. Members of this family all have a C-terminal SPASM domain (see model TIGR04085), a region usually found as a C-terminal second 4Fe-4S domain of radical SAM domain (see pfam04055) proteins. A majority of rSAM/SPASM proteins modify ribosomally produced peptides. In a few members of this family, the key Cys residues of the radical SAM domain have been lost, making this a pseudo-rSAM family. Members of this family are restricted so far to Haloarchaea, always occur next a member of family TIGR04031, and are often accompanied by another rSAM/SPASM domain protein. The function of this two or three gene cassette is unknown. 390 matched cddid_all.tbl CDD TIGR04348 TIGR04348 275144 TIGR04348 putative glycosyltransferase, TIGR04348 family. This putative glycosyltransferase is found in marine bacteria such as Marinobacter and soil bacteria such as Anaeromyxobacter, but does not seem to occur in known pathogenic bacteria. 310 matched cddid_all.tbl CDD TIGR04349 TIGR04349 275145 rSAM_QueE_gams putative 7-cyano-7-deazaguanosine (preQ0) biosynthesis protein QueE, gammaproteobacterial type. Members of this radical SAM domain protein family appear to be a form of the queuosine biosynthesis protein QueE. QueE is involved in making preQ0 (7-cyano-7-deazaquanine), a precursor of both the bacterial/eukaryotic modified tRNA base queuosine and the archaeal modified base archaeosine. Members occur in preQ0 operons species that lack members of related protein family TIGR03365. 210 matched cddid_all.tbl CDD TIGR04350 TIGR04350 275146 C_S_lyase_PatB putative C-S lyase. Members of this subfamily are probable C-S lyases from a family of pyridoxal phosphate-dependent enzymes that tend to be (mis)annotated as probable aminotransferases. One member is PatB of Bacillus subtilis, a proven C-S-lyase. Another is the virulence factor cystalysin from Treponema denticola, whose hemolysin activity may stem from H2S production. Members of the seed alignment occur next to examples of the enzyme 5-histidylcysteine sulfoxide synthase, from ovothiol A biosynthesis, and would be expected to perform a C-S cleavage of 5-histidylcysteine sulfoxide to leave 1-methyl-4-mercaptohistidine (ovothiol A). 384 matched cddid_all.tbl CDD TIGR04351 TIGR04351 213964 TOMM_nitrile_2 putative TOMM peptide. Members of this family of short peptides average about 110 amino acids in length, with greatest variability in the last thirty. The conserved region resembles the alpha subunit of nitrile hydratase, as with the NHLP leader peptide domain (TIGR03793), and members usually are found near a cyclodehydratase (maturase) enzyme, marking these as like thiazole/oxazole-modified microcins (TOMM), but these precursor forms lack the GlyGly cleavage motif that marks the clear end of a leader peptide region. Genomes with this system include Streptomyces clavuligerus ATCC 27064, Verrucosispora maris AB-18-032, and Kitasatospora setae KM-6054. 48 matched cddid_all.tbl CDD TIGR04352 TIGR04352 275147 HprK_rel_A HprK-related kinase A. A number of protein families resemble HPr kinase (see TIGR00679) but do not belong to that system. They include this family, which appears instead to be the marker for a different type of gene neighborhood, in which one of the conserved neighboring proteins resembles (but is distinct from) PqqD. 280 matched cddid_all.tbl CDD TIGR04353 TIGR04353 275148 PqqD_rel_X PqqD family protein, HPr-rel-A system. Members of this protein show distant homology to PqqD, and belong to a three-gene cassette that included the HPr kinase related protein family of TIGR04352. The role of the cassette, and of this protein, are unknown. 73 matched cddid_all.tbl CDD TIGR04354 TIGR04354 275149 amphi-Trp amphi-Trp domain. This domain usually comprises most of the span of bacterial or archaeal proteins with a length of about 90 amino acids. Some members, however, are extended by one or two copies of domain pfam07411 in the C-terminal region. No residue in this domain is invariant. A striking feature of this domain is a C-terminal region that alternates strongly charged with strongly hydrophobic residues and usually ends with a Trp residue, e.g. LEIEIEW or FEIKVRW, suggesting an amphipathic beta strand structure. We suggest the name amphi-Trp for this domain. Some members of this function occur regularly in genomic contexts that include putative kinases of unknown specificity related to (but distinct from) HPr kinase, a Ser-specific protein kinase. The function is unknown. 67 matched cddid_all.tbl CDD TIGR04355 TIGR04355 275150 HprK_rel_B HprK-related kinase B. Members of this protein family resemble (and often are misannotated as) HprK, the serine kinase/phosphatase of the phosphocarrier protein HPr. However, members do not occur with an HPr homolog, but instead as part of a distinctive gene cassette of unknown function. 351 matched cddid_all.tbl CDD TIGR04356 TIGR04356 213969 grasp_GAK ATP-grasp enzyme, GAK system. Members of this family are ATP-grasp family enzymes related to a number of characterized glutamate ligases, including the ribosomal protein S6 modification enzyme RimK. This group belongs to a conserved gene neighborhood that also features an HPr kinase-related protein (see TIGR04355). We assign this system the initial designation GAK, for Grasp (this ATP-grasp family enzyme), Amphipathic (for the member of family TIGR04354, designated Amphi-Trp), and Kinase, for the HPr-kinase homolog TIGR04355. 287 matched cddid_all.tbl CDD TIGR04357 TIGR04357 275151 CofD_rel_GAK CofD-related protein, GAK system. Members of this family are distantly related to CofD, the enzyme LPPG:FO 2-phospho-L-lactate transferase, involved in coenzyme F420 biosynthesis. This family appears to belong to a biosynthesis cassette of unknown function. 368 matched cddid_all.tbl CDD TIGR04358 TIGR04358 275152 XXXCH_domain XXXCH domain. Members of this family show C-terminal sequence similarity, perhaps indicating distant homology, to cytochrome c-prime (see pfam01322). However, the motif CxxCH is replaced by xxxCH. Genes for this protein occur in a sporadically distributed genome context, largely in deltaProteobacteria, in which an ATP-grasp family glutamate ligase homolog and a CofD (LPPG:FO 2-phospho-L-lactate transferase) homolog suggest a novel biosynthesis. 90 matched cddid_all.tbl CDD TIGR04359 TIGR04359 275153 TrbK_RP4 entry exclusion lipoprotein TrbK. The characterized model example of TrbK, from incompatibility group P (IncP) plasmid RP4, is an N-terminally processed lipoprotein, localized to the periplasmic face of the plasma membrane. TrbK prevents entry through conjugation by other IncP plasmids. Unrelated, uncharacterized proteins encoded in equivalent positions in other plasmid P-type conjugative transfer regions (e.g. TIGR04360) may have analogous functions. [Mobile and extrachromosomal element functions, Plasmid functions] 66 matched cddid_all.tbl CDD TIGR04360 TIGR04360 275154 other_trbK conjugative transfer region protein TrbK. Members of this family regularly are encoded between the TrbJ and TrbL proteins essential for P-type conjugal transfer, and therefore are designated TrbK. Positional analogy to family TIGR04359 (the entry exclusion lipoprotein TrbK of IncP plasmid RP4), which is a lipoprotein and not homologous, suggests this protein may also be involved in entry exclusion. Members of this family are small, with a non-lipoprotein signal peptide and a conserved disulfide bond. [Mobile and extrachromosomal element functions, Plasmid functions] 74 matched cddid_all.tbl CDD TIGR04361 TIGR04361 275155 TrbK_Ti entry exclusion protein TrbK, Ti-type. Members of this family are encoded between the genes for TrbJ and TrbL of P-type plasmid conjugal transfer systems, and therefore are TrbK, a member of a guild of unrelated TrbK protein families. The similarly located TrbK of plasmid RP4 (family TIGR04359) functions in entry exclusion, and the current family may as well, despite lacking any detectable homology. Members of this family include TrbK of the Ti plasmid from Agrobacterium, shown not to be required for transfer, which would be consistent with a role in entry exclusion rather than transfer itself. Li et al. cite unpublished results that showed an entry exclusion function for TrbK of the Ti plasmid. This small protein shares close C-terminal sequence homology to the much longer protein encoded by the neighboring gene TrbJ. [Mobile and extrachromosomal element functions, Plasmid functions] 62 matched cddid_all.tbl CDD TIGR04362 TIGR04362 275156 choice_anch_C choice-of-anchor C domain. This family describes an extracellular bacterial domain that occurs on a number of proteins with PEP-CTERM (exosortase recognition site) sequences at the C-terminus, as well some with an apparent alternate anchor sequence. Note that related pfam04862 (DUF642), as of release 26, is double the length of this model because it has two tandem regions homologous to this domain. pfam04862, in turn, belongs to a Pfam clan called the galactose-binding domain-like superfamily. 157 matched cddid_all.tbl CDD TIGR04363 TIGR04363 275157 LD_lanti_pre FxLD family lantipeptide. Members of this protein family occur with a cassette of lanthionine-type peptide modification enzymes. Members are small (about 60 amino acids long), rich in Cys, and variable in copy number per genome (from one to three). These features suggest that members of this family are modified to become lantipeptides, although not necessarily a lantibiotic. There is no GlyGly cleavage motif to separate a leader peptide from core region.The considerable abundance in Streptomyces and relatively strong consideration hints at a non-antibiotic function. The motif FxLD in the N-terminal region is nearly invariant. 37 matched cddid_all.tbl CDD TIGR04364 TIGR04364 275158 methyltran_FxLD methyltransferase, FxLD system. Members of this family resemble occur regularly in the vicinity of lantibiotic biosynthesis enzymes and their probable target, the FxLD family of putative ribosomal natural product precursor (TIGR04363). Members resemble protein-L-isoaspartate O-methyltransferase (TIGR00080) and a predicted methyltranserase, TIGR04188, of another putative peptide modification system. 394 matched cddid_all.tbl CDD TIGR04365 TIGR04365 213978 spare_glycyl autonomous glycyl radical cofactor GrcA. This small protein, previously designated YfiD in E. coli, is closely homologous to pyruvate formate_lyase (PFL) in a region surrounding the stable glycyl radical that is prepared by the action of pyruvate formate-lyase activase, a radical SAM enzyme. When damage at the site of this radical breaks the main chain of PFL, this protein acts as a spare part that reintroduces the needed stable glycyl radical. Cutoffs for this model are set to exclude a set of closely related phage proteins that appear to have a corresponding function. 124 matched cddid_all.tbl CDD TIGR04366 TIGR04366 275159 cupin_WbuC cupin fold metalloprotein, WbuC family. Members of this family show sequence similarity to cupin fold proteins (see pfam07883), including conserved His residues likely to serve as metal-binding ligands. Many members occur in bacterial O-antigen biosynthesis regions. Some members have acquired the gene symbol wbuC (e.g. Jarvis, et al, 2011), but publications using this term do not ascribe a function. 132 matched cddid_all.tbl CDD TIGR04367 TIGR04367 275160 HpnR_B12_rSAM hopanoid C-3 methylase HpnR. Members of this are family are a B12-binding domain/radical SAM domain protein required for 3-methylhopanoid production. Activity was confirmed by mutant phenotype by disrupting this gene in Methylococcus capsulatus strain Bath. This protein family should only occur in genomes that encode a squalene-hopene cyclase (see TIGR01507). [Fatty acid and phospholipid metabolism, Biosynthesis] 490 matched cddid_all.tbl CDD TIGR04368 TIGR04368 275161 Glu_2_3_NH3_mut glutamate 2,3-aminomutase. Members of this family are glutamate 2,3-aminomutase, a radical SAM enzyme with a pyridoxal phosphate group. It is closely related to lysine 2,3-aminomutase, but distinguished by architecture (longer N-terminal region, shorter C-terminal region) and replacement of key lysine-binding residues Asp293 and Asp330 (inferred from the crystal structure) by glutamate-binding residues Lys and Asn. Activity was demonstrated for sequences from Clostridium difficile, Thermoanaerobacter tengcongensis MB4, and Syntrophomonas wolfei str. Goettingen. The action of this enzyme creates beta-glutamate, an osmolyte. [Cellular processes, Adaptations to atypical conditions] 404 matched cddid_all.tbl CDD TIGR04369 TIGR04369 275162 fusion_not_SelD oxidoreductase/SelD-related fusion protein. Some selenium donor proteins (selenide,water dikase, product of the selD gene, model TIGR00476) are fusion proteins with an N-terminal extension described by model TIGR03169. Members of this family have a C-terminal region similar to yet outside the scope of the SelD model, fused to an N-terminal region similar to but outside the scope of TIGR03169. 702 matched cddid_all.tbl CDD TIGR04370 TIGR04370 275163 glyco_rpt_poly oligosaccharide repeat unit polymerase. Members of this subfamily of highly hydrophobic proteins, with few highly conserved residues, all may act to polymerize the oligosaccharide repeat units of surface polysaccharides, including O-antigen in Gram-negative bacteria such as Leptospira (assign gene symbol wzy) and capsular polysaccharide in Gram-positive bacteria such as Streptococcus. O-antigen biosynthesis enzymes produce a repeat unit, usually an oligosaccharide, which itself is polymerized. O-antigen polymerase, usually designated Wzy. This family bears homology to the O-antigen ligase WaaL, but known examples of WaaL fall outside the bounds defined here. This model is much broader than pfam14296. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 392 matched cddid_all.tbl CDD TIGR04371 TIGR04371 275164 methyltran_NanM putative sugar O-methyltransferase. Members of this family appear to be SAM-dependent O-methyltransferases acting on sugars, based on iterated sequence searches and gene context. Members occur in Leptospira O-antigen regions, as well NanM from the biosynthesis cluster for nanchangmycin, which produces 4-O-methyl-L-rhodinose as an intermediate. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 273 matched cddid_all.tbl CDD TIGR04372 TIGR04372 275165 glycosyl_04372 putative glycosyltransferase, TIGR04372 family. This domain occurs in proteins of various lengths, in contexts that include O-antigen biosynthesis regions of various Leptospira species. Hits to this model and PSI-BLAST analysis suggest distant sequence similarity to family 9 glycosyltransferases (pfam01075), including ADP-heptose:LPS heptosyltransferase (RfaF), an enzyme involved in LPS inner core region biosynthesis. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 205 matched cddid_all.tbl CDD TIGR04373 TIGR04373 275166 egtB_X_signatur EgtB-related enzyme signature domain. This model represents a signature C-terminal region of a distinct clade in the EgtB subfamily, other members of which participate in ergothioneine biosynthesis 50 matched cddid_all.tbl CDD TIGR04374 TIGR04374 275167 small_w_EgtBD hercynine metabolism small protein. Hercynine is the betaine (trimethylated amino group) form of histidine. This small protein occurs in a conserved four-gene cyanobacterial cassette along with a EgtD, the methyltransferase that converts histidine to hercynine, and an EgtB homolog as in ergothioneine biosynthesis, likely to attach some thiol through its sulfur to the imidazole ring. 73 matched cddid_all.tbl CDD TIGR04375 TIGR04375 275168 cyano_w_EgtBD hercynine metabolism protein. Hercynine is the betaine (trimethylated amino group) form of histidine. This protein occurs in a conserved four-gene cyanobacterial cassette along with a EgtD, the methyltransferase that converts histidine to hercynine as in ergothioneine biosynthesis, an EgtB homolog that is likely to attach some thiol (e.g. gamma-glutamyl-cysteine) through its sulfur to the hercynine imidazole ring, and a small protein of unknown function (TIGR04374). Members are distantly related to phage shock protein A (PspA). 154 matched cddid_all.tbl CDD TIGR04376 TIGR04376 275169 TIGR04376 TIGR04376 family protein. Members of this protein family resemble TIGR04375 and, more distantly, to phage shock protein A (PspA). Members are restricted to the Cyanobacteria. 189 matched cddid_all.tbl CDD TIGR04377 TIGR04377 275170 myo_inos_iolD 3,5/4-trihydroxycyclohexa-1,2-dione hydrolase. Members of this protein family, 3,5/4-trihydroxycyclohexa-1,2-dione hydrolase (iolD), represent one of eight enzymes in a pathway converting myo-inositol to acetyl-CoA. IolD hydrolyzes the cyclic molecule 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione to yield 5-deoxy-D-glucuronic acid. TPP is a cofactor. [Energy metabolism, Sugars] 615 matched cddid_all.tbl CDD TIGR04378 TIGR04378 275171 myo_inos_iolB 5-deoxy-glucuronate isomerase. Members of this protein family, 5-deoxy-glucuronate isomerase (iolB), represent one of eight enzymes in a pathway converting myo-inositol to acetyl-CoA. [Energy metabolism, Sugars] 247 matched cddid_all.tbl CDD TIGR04379 TIGR04379 275172 myo_inos_iolE myo-inosose-2 dehydratase. Members of this family include the enzyme myo-inosose-2 dehydratase, product of the gene iolE, as found in inositol utilization cassettes in many species. [Energy metabolism, Sugars] 290 matched cddid_all.tbl CDD TIGR04380 TIGR04380 275173 myo_inos_iolG inositol 2-dehydrogenase. All members of the seed alignment for this model are known or predicted inositol 2-dehydrogenase sequences co-clustered with other enzymes for catabolism of myo-inositol or closely related compounds. Inositol 2-dehydrogenase catalyzes the first step in inositol catabolism. Members of this family may vary somewhat in their ranges of acceptable substrates and some may act on analogs to myo-inositol rather than myo-inositol per se. [Energy metabolism, Sugars] 330 matched cddid_all.tbl CDD TIGR04381 TIGR04381 275174 HTH_TypR TyrR family helix-turn-helix domain. This model describes the C-terminal DNA-binding helix-turn-helix domain of several regulators of aromatic amino acid metabolism. Examples include TyrR in Escherichia coli and PhhR in Pseudomonas putida. Most members of this family have a sigma-54 interaction domain. [Regulatory functions, DNA interactions] 49 matched cddid_all.tbl CDD TIGR04382 TIGR04382 275175 myo_inos_iolC_N 5-dehydro-2-deoxygluconokinase. All members of the seed alignment for this model are translated from the iolC gene of known or putative inositol catabolism operons. Members with characterized function are 5-dehydro-2-deoxygluconokinase, the enzyme catalyzing the fifth step in degradation from myo-inositol or closely related compounds. Note that many members of this family are fusion proteins with an additional C-terminal domain, of unknown function, described by pfam09863. [Energy metabolism, Sugars] 309 matched cddid_all.tbl CDD TIGR04383 TIGR04383 275176 acidic_w_LPXTA processed acidic surface protein. Members of this family are acidic surface proteins with an N-terminal signal peptide and a variant C-terminal sortase recognition sequence, LPXTA rather than LPXTG. The N-terminal region past the signal peptide is repeated a second or third time in many members of this family. Members occur in Firmicutes, encoded next to a dedicated sortase related to SrtC that assembles pilins, suggesting that this protein serves a structural rather than enzymatic role. Processing by the neighboring sortase may result in polymerization as well as surface attachment. [Cell envelope, Surface structures] 316 matched cddid_all.tbl CDD TIGR04384 TIGR04384 275177 putr_carbamoyl putrescine carbamoyltransferase. Members of this family are putrescine carbamoyltransferase (EC 2.1.3.6). There is some overlapping specificity with ornithine carbamoyltransferase (EC 2.1.3.3). The gene regularly is found next to agmatine deiminase and a carbamate kinase, suggesting a conserved catabolic agmatine deiminase pathway. [Energy metabolism, Amino acids and amines] 330 matched cddid_all.tbl CDD TIGR04385 TIGR04385 275178 B12_rSAM_cofa1 putative variant cofactor biosynthesis B12-binding domain/radical SAM domain protein 1. Members of this protein family are one of two tandem B12-binding domain/radical SAM domain proteins that occur in a genome context with a pair of homologs to ThiC (phosphomethylpyrimidine synthase, EC 4.1.99.17), an enzyme that performs a complex rearrangement involved in thiamin biosynthesis, and a putative CobT (nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase), an enzyme of cobalamin biosynthesis. 438 matched cddid_all.tbl CDD TIGR04386 TIGR04386 275179 ThiC_like_1 ThiC-like protein 1. Members of this protein family closely resemble ThiC, an enzyme that performs a complex rearrangement during thiamin biosynthesis, but instead occur as one of two adjacent additional paralogs to bona fide ThiC, in a conserved gene neighborhood with a pair of B12 binding domain/radical SAM domain proteins. Members of the ThiC family are non-canonical radical SAM enzymes, using a C-terminal Cys-rich motif to ligand a 4Fe-4S cluster that cleaves S-adenosylmethionine (SAM), but that sequence region does not belong to pfam04055. 426 matched cddid_all.tbl CDD TIGR04387 TIGR04387 275180 capsid_maj_N4 major capsid protein, N4-gp56 family. Members of this family are phage major capsid proteins as found in phage N4 (a double-stranded DNA virus) plus many additional lytic phage and integrated prophage regions. [Mobile and extrachromosomal element functions, Prophage functions] 315 matched cddid_all.tbl CDD TIGR04388 TIGR04388 275181 Lepto_longest putative large structural protein. Members of this family are restricted so far to the lineage Leptospira, where they may be the longest protein encoded by the genome. Two or three paralogs are often found. The seed alignment for this model includes sequences with significant length variability, and stops adjacent to an intein feature most full-length members of this family share. Oddly, members closely related in sequence up to the start of the intein (see TIGR01445) usually show very little sequence similarity C-terminal to the end of the intein (see TIGR01443). [Unknown function, General] 1134 matched cddid_all.tbl CDD TIGR04389 TIGR04389 275182 Lepto_lipo_1 lipoprotein, Leptospiral tandem type. Members of this family are lipoproteins restricted (so far) to the genus Leptospira, sometimes with several paralogs clustered with each other, such as four in a row (out of six) in Leptospira interrogans str. UI 13372. The tandem set may be co-clustered with a putative structural protein that is usually the longest encoded by the leptospiral genome (and that often is an intein-containing protein). [Cell envelope, Other] 201 matched cddid_all.tbl CDD TIGR04390 TIGR04390 275183 OMP_YaiO_dom outer membrane protein, YaiO family. Members of this family share a domain of bacterial outer membrane beta barrel, up to the protein C-terminal residue (usually Phe or Trp). The member YaiO was shown experimentally to be localized to the outer membrane. [Unknown function, General] 230 matched cddid_all.tbl CDD TIGR04391 TIGR04391 275184 CcmD_alt_fam CcmD family protein. Members of this protein family are small (typically less than 50 amino acids in length), with the first half highly hydrophobic like transmembrane alpha helices and containing a nearly invariant tyrosine residue. Members from the Desulfovibrionales appear in the position of ccmD of system I c-type cytochrome biogenesis operons (see pfam04995). This family and pfam04995 appear very similar in sequence properties, but the very low level of actual sequence identify makes it unclear that the similarity reflects homology per se. 36 matched cddid_all.tbl CDD TIGR04392 TIGR04392 275185 haoB_nitrify hydroxylamine oxidation protein HaoB. Members of this family occur as the HaoB (hydroxylamine oxidation B) protein encoded next to the homotrimeric HaoA, hydroxylamine oxidoreductase, a protein with eight heme groups. It appears all species with this enzyme are nitrifying bacteria. 312 matched cddid_all.tbl CDD TIGR04393 TIGR04393 275186 rpt_T5SS_PEPC T5SS/PEP-CTERM-associated repeat. This model describes a repeat about 50 amino acids in length, appearing sometimes more than ten times in tandem in a single protein. Most proteins with this repeat have a C-terminal autotransporter domain (TIGR01414, pfam03797) and/or an N-terminal type V secretion system signal peptide (pfam13018), while others instead have a C-terminal PEP-CTERM domain (TIGR02595). 49 matched cddid_all.tbl CDD TIGR04394 TIGR04394 275187 choline_CutC choline trimethylamine-lyase. Members of this family, homologs to pyruvate formate-lyases and benzylsuccinate synthases, are glycine radical enzymes that appear to act as choline TMA-lyase, that is, to perform a C-N bond cleavage turning choline into trimethylamine (TMA) plus acetaldehyde. The gene symbol is cutC, for choline utilization. The activase, CutD, is a radical SAM enzyme. [Energy metabolism, Amino acids and amines] 789 matched cddid_all.tbl CDD TIGR04395 TIGR04395 275188 cutC_activ_rSAM choline TMA-lyase-activating enzyme. Members of this family are CutD, a radical enzyme that serves as an activase for choline TMA-lyase, CutC. CutC is a glycyl radical enzyme related to pyruvate formate-lyase, and this enzyme, CutD, is related to pyruvate formate-lyase activase. [Energy metabolism, Amino acids and amines] 309 matched cddid_all.tbl CDD TIGR04396 TIGR04396 275189 surf_polysacc surface carbohydrate biosynthesis protein. This model describes an uncharacterized homology region found broadly in proteins of surface carbohydrate biosynthesis regions. This family shows distant homology to regions of family TIGR04326, of spore coat polysaccharide biosynthesis protein SpsB from Bacillus subtilis, etc. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 321 matched cddid_all.tbl CDD TIGR04397 TIGR04397 275190 SecA2_Bac_anthr accessory Sec system translocase SecA2, Bacillus type. Members of this family always occur in genomes with the preprotein translocase SecA (TIGR00963) and closely resemble it, hence the designation SecA2. However, this appears to mark a different type of accessory Sec system SecA2 (TIGR03714) from the serine-rich glycoprotein type found in Staphylococcus and Streptococcus, and the actinobacterial SecA2 (TIGR04221). This type occurs in species including Bacillus anthracis, Geobacillus thermoglucosidasius, Solibacillus silvestris, etc. [Protein fate, Protein and peptide secretion and trafficking] 774 matched cddid_all.tbl CDD TIGR04398 TIGR04398 275191 SLAP_DUP SLAP domain. This domain is duplicated in SlaP (S-layer assembly protein), a partner of SecA2 in the Bacillus anthracis type of accessory Sec system (see TIGR04397). The domain is found, either once or twice, in additional Firmicutes species. 125 matched cddid_all.tbl CDD TIGR04399 TIGR04399 275192 acc_Sec_SLAP accessory Sec system S-layer assembly protein. Members of this family, designated S-layer assembly protein (SlaP), occur next to a Bacillus anthracis-type accessory Sec system SecA2. . Members have two tandem copies of a duplicated domain (TIGR04398) that may also occur in other contexts. SlaP is found both free in the cytoplasm and membrane-associated. SecA2 and SlaP appear to work together to modify Sec for efficient S-layer secretion. [Protein fate, Protein and peptide secretion and trafficking] 288 matched cddid_all.tbl CDD TIGR04400 TIGR04400 275193 RK_trnsloc_Pase Arg-Lys translocation region protein phosphatase. The Sec-independent protein export system TAT, or twin-arginine translocation, is unusual in Leptospira, with Lys replacing Arg in the second position of the twin-Arg motif. This protein, restricted to Leptospira and showing distant homology to the phosphoserine phosphatases RsbU and SpoIIE, is always encoded immediately downstream of the tatC gene and appears to be part of the variant TAT system. It lacks a TAT signal itself, and so is more likely to be part of the Sec-independent translocation machinery than to be a substrate. The suggested symbol is rktP, for RK-Translocation Phosphatase. [Protein fate, Protein and peptide secretion and trafficking] 358 matched cddid_all.tbl CDD TIGR04401 TIGR04401 275194 TAT_Cys_rich twin-arginine translocation signal/Cys-rich four helix bundle protein. Members of this family average about 150 amino acids in length, beginning with a twin-arginine translocation signal sequence, then a His-rich spacer region, followed by a ~105-residue region in which thirteen positions are nearly invariant Cys residues. CDD (Conserved Domain Database) assigns members of this family to clan cl13994, the DUF326 superfamily, based on homology to PA2107 from Pseudomonas aeruginosa. PA2107 is a cysteine-rich four helical bundle protein, with solved structure PDB:3KAW. 150 matched cddid_all.tbl CDD TIGR04402 TIGR04402 275195 mob_CxxC_CxxC mobilome CxxCx(11)CxxC protein. Members of this family share twin CxxC motifs near the C-terminus, suggesting a DNA- or RNA-binding activity. The spacing between CxxC motifs is variable, from 11 to 16 amino acids. Members in general occur on plasmids or near other markers of lateral gene transfer (transposases, integrases, endonucleases, etc). 186 matched cddid_all.tbl CDD TIGR04403 TIGR04403 275196 rSAM_skfB sporulation killing factor system radical SAM maturase. Members of this family are a radical SAM enzyme of post-translational modification of ribosomally translated peptides. In Bacillus subtilis, the enzyme SkfB creates a sactipeptide (sulfur-to-alpha-carbon) crosslink of Cys-4 to Met-12 of the mature form of sporulation killing factor (SkfA). In Paenibacillus larvae subsp. larvae B-3650, the Met is replaced by Leu, so the modification must be different. SkfB has 2 4Fe-4S clusters, one in its radical SAM domain (pfam04055) and one in a region that somewhat resembles the SPASM domain (TIGR04085). 402 matched cddid_all.tbl CDD TIGR04404 TIGR04404 275197 RiPP_SkfA sporulation killing factor. Members of this family are ribosomally synthesized and post-translationally modified peptide natural products, modified by sulfur-to-alpha-carbon cross-link introduced by a radical SAM enzyme, SkfB (TIGR04403). 53 matched cddid_all.tbl CDD TIGR04405 TIGR04405 275198 SkfF sporulation killing factor system integral membrane protein. Members of this family, SkfF, occur only in cassettes of the sporulation killing factor system. This protein has multiple membrane-spanning domains and is encoded next to a protein with ATP-binding cassette (ABC) homology (SkfE), suggesting ABC transporter permease activity for this protein. 472 matched cddid_all.tbl CDD TIGR04406 TIGR04406 275199 LPS_export_lptB LPS export ABC transporter ATP-binding protein. Members of this fmaily are LptB, the ATP-binding cassette protein of an ABC transporter involved in lipopolysaccharide export. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides, Transport and binding proteins, Other] 239 matched cddid_all.tbl CDD TIGR04407 TIGR04407 275200 LptF_YjgP LPS export ABC transporter permease LptF. Members of this family are LptF, one of homologous, two tandem-encoded permease genes of an export ATP transporter for lipopolysaccharide (LPS) assembly in most Gram-negative bacteria. The other permease subunit is LptG (TIGR04408). [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides, Transport and binding proteins, Other] 346 matched cddid_all.tbl CDD TIGR04408 TIGR04408 275201 LptG_lptG LPS export ABC transporter permease LptG. Members of this family are LptG, one of homologous, two tandem-encoded permease genes of an export ATP transporter for lipopolysaccharide (LPS) assembly in most Gram-negative bacteria. The other permease subunit is LptF (TIGR04407). [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides, Transport and binding proteins, Other] 351 matched cddid_all.tbl CDD TIGR04409 TIGR04409 275202 LptC_YrbK LPS export ABC transporter periplasmic protein LptC. Members of this family are LptC, a periplasmic protein tethered to the inner membrane in the lipopolysaccharide (LPS)exporter transenvelope complex (Lpt), which is responsible for conducting LPS to the outer leaflet of the outer membrane in most Gram-negative bacteria. LptC is homologous to LptA, another member of the transenvelope complex. Genes lptC and lptA are often adjacent. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides, Transport and binding proteins, Other] 180 matched cddid_all.tbl CDD TIGR04410 TIGR04410 275203 Spiro_T2SS_lipo type II secretion system-associated lipoprotein. Members of this family occur only in spirochetes (Leptospira, Leptonema, Turneriella), as part of a type II secretion system (T2SS) cassette. Properly extended gene models always include an N-terminal signal sequence ending with a Cys residue, suggesting this small protein (about 100 amino acids) is a lipoprotein. 117 matched cddid_all.tbl CDD TIGR04411 TIGR04411 275204 T2SS_GspN_Lepto type II secretion system protein N, Leptospira/Geobacter-type. Members of this family are the N (or GspN) protein of type II secretion systems (T2SS) as found in Leptospira, Geobacter, Myxococcus, and several other genera. Sequence similarity to GspN as found in, say, Gammaproteobacteria (see pfam01203) is extremely remote. [Protein fate, Protein and peptide secretion and trafficking] 279 matched cddid_all.tbl CDD TIGR04412 TIGR04412 275205 T2SS_GspM_XcpZ type II secretion system protein M, XcpZ-type. Members of this family are a variant form of the type II secretion system (T2SS) protein M, GspM, as found in several species of Pseudomonas. Members, including XcpZ, are short relatives to most members of pfam04612 (as of release 26.0). 126 matched cddid_all.tbl CDD TIGR04413 TIGR04413 275206 MYXAN_cmx8 CRISPR type MYXAN-associated protein Cmx8. Members of this family occur only in CRISPR/cas loci of the MYXAN type, but are present in a minority of such systems. This protein appears to replace the MYXAN system Cas8a1/Csx13 protein (TIGR03485/TIGR03486), compared to which it shows similar length and composition but only about 12 percent sequence identity. 528 matched cddid_all.tbl CDD TIGR04414 TIGR04414 275207 hepto_Aah_TibC autotransporter strand-loop-strand O-heptosyltransferase. Both Aah (autotransporter adhesin heptosyltransferase) and TibC (tib is enterotoxigenic invasion locus B) are protein O-heptosyltransferases that act on multiple sites from repeat regions of proteins exported by autotransporters. Aah glycosylates AIDA, or autotransporter adhesin involved in diffuse adherence, TibC acts on TibA, but TibC can replace Aah. [Protein fate, Protein modification and repair] 374 matched cddid_all.tbl CDD TIGR04415 TIGR04415 275208 O_hepto_targRPT autotransporter passenger strand-loop-strand repeat. This model describes two tandem copies of a strand-loop-strand repeat that occurs often in type V secretion system (T5SS). These repeats usually occur in the passenger domain of the classical monomeric autotransporter. Proteins with this repeat often are encoded next to a member of family TIGR04414, the Aah/TibC family O-heptosyltransferase, and may be glycosylated in regions with this repeat. 38 matched cddid_all.tbl CDD TIGR04416 TIGR04416 275209 group_II_RT_mat group II intron reverse transcriptase/maturase. Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other] 354 matched cddid_all.tbl CDD TIGR04417 TIGR04417 275210 PFTS_polysacc polysaccharide biosynthesis PFTS motif protein. Members of this protein family are found in O-antigen biosynthesis loci in Leptospira, two tandem homologs in a polysaccharide biosynthesis region in the archaeon Methanoregula formicicum, in Rhizobium leguminosarum bv. trifolii WSM2297, etc. Members are more strongly conserved in the C-terminal region, where an invariant sequence PFTS is found. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 519 matched cddid_all.tbl CDD TIGR04418 TIGR04418 275211 PriB_gamma primosomal replication protein PriB. Members of this protein family are primosomal replication protein N (PriB), virtually always encoded between rpsF (ribosomal protein S6) and rpsR (ribosomal protein S18). Note that only this short form, as found primarily in the gamma-Proteobacteria, of the single-stranded DNA binding protein family (see model TIGR00621) may partner with PriA and be involved in priming for re-initiation of replication. [DNA metabolism, DNA replication, recombination, and repair] 96 matched cddid_all.tbl CDD TIGR04419 TIGR04419 275212 no_iron_rSAM HemN-related non-iron pseudo-SAM protein PsgB. Members of this protein family are related to radical SAM enzymes HemN (oxygen-independent coproporphyrinogen III oxidase) and HutW (a putative heme utilization enzyme) but lack the signature CxxxCxxC motif for 4Fe-4S binding. Members occur exclusively in Borrelia, which appears to live without iron, as the only radical SAM enzyme homolog in any Borrelia genome. We designate this enzyme PsgB (Pseudo-SAM, Genus Borrelia). 378 matched cddid_all.tbl CDD TIGR04420 TIGR04420 275213 Sec_Non_Glob Sec region non-globular protein. Members of this family occur only in the genus Leptospira, always encoded between genes for the YajC and SecD components of the Sec preprotein translocase. Sequences have an N-terminal signal peptide and a C-terminal transmembrane segment. Between these are regions of non-globular, low-complexity sequence including Lys-rich and Ser/Thr/Asn/Glu-rich regions. 241 matched cddid_all.tbl CDD TIGR04421 TIGR04421 275214 FemAB_IMCC1989 FemAB family protein. Members of this family are FemA/FemB family proteins from a cassette that some Leptospira have in their O-antigen biosynthesis regions and share with a cassette from gamma proteobacterium IMCC1989. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 345 matched cddid_all.tbl CDD TIGR04422 TIGR04422 275215 PLP_IMCC1989 putative PLP-dependent aminotransferase. Members of this family are PLP-dependent enzymes, probable aminotransferases of the DegT/DnrJ/EryC1/StrS. Members occur in some Leptospira have in their O-antigen biosynthesis regions and in a related cassette in gamma proteobacterium IMCC1989. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 315 matched cddid_all.tbl CDD TIGR04423 TIGR04423 275216 casT3_TIGR04423 CRISPR type III-associated protein, TIGR04423 family. Members of this protein family occur only in species with CRISPR systems, in the context of type III systems that resemble type III-A (MTUBE) and III-B (the RAMP module). It occurs in several species of Prevotella, Helicobacter, Campylobacter, and Bacteroides. 124 matched cddid_all.tbl CDD TIGR04424 TIGR04424 275217 metallo_McbB McbB family protein. This family includes the partially characterized zinc metalloprotein McbB, part of the maturase system for microcin B17, a thiazole/oxazole-modified microcin (TOMM). Other members of this family belong to very different gene neighborhoods. The Cys residues that act as zinc ligands are conserved in most members, but for rare members are jointly absent. 286 matched cddid_all.tbl CDD TIGR04425 TIGR04425 275218 P_lya_rel_AroB putative sugar phosphate phospholyase (cyclizing). Members of this family tend to be found in O-antigen biosynthesis regions. Members frequently are misidentified as the closely related 3-dehydroquinate synthase, AroB (see family TIGR01357), the phospholyase that converts 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate to 3-dehydroquinate during chorismate biosynthesis. Most bacteria with this enzyme have a true AroB in a chorismate biosynthesis gene cluster. [Biosynthesis of cofactors, prosthetic groups, and carriers, Lipoate] 348 matched cddid_all.tbl CDD TIGR04426 TIGR04426 275219 rSAM_desII TDP-4-amino-4,6-dideoxy-D-glucose deaminase. Members of this protein family, including DesII, are radical SAM enzymes that deaminate TDP-4-amino-4,6-dideoxy-D-glucose to TDP-3-keto-4,6-dideoxy-D-glucose. This is the fourth step of the six step pathway in Streptomyces venezuelae for synthesizing D-desosamine, or 3-(dimethylamino)-3,4,6-trideoxyglucose, a precursor for many macrolide antibiotics. 468 matched cddid_all.tbl CDD TIGR04427 TIGR04427 275220 PLP_DesI dTDP-4-dehydro-6-deoxyglucose aminotransferase. Members of this family are pyridoxal phosphate-dependent aminotransferases that convert TDP-4-keto-6-deoxy-D-glucose to the 4-amino sugar form, TDP-4-amino-4,6-dideoxy-D-glucose. In Streptomyces venezuelae, this enzyme is designated DesI, catalyzing the third of six steps in the biosynthesis of TDP-D-desosamine, a component of a number of different macrolide antibiotics made by that organism. Related proteins, scoring below the trusted cutoff, include sugar aminotranferases in O-antigen biosynthesis regions. 390 matched cddid_all.tbl CDD TIGR04428 TIGR04428 275221 B12_rSAM_trp_MT tryptophan 2-C-methyltransferase. Members of this family are the B12-binding domain/radical SAM domain enzyme tryptophan methyltransferase, named TsrT in the cassette for thiostrepton biosynthesis. Thiostrepton and related thiopeptides are synthesized by extensive modification of a ribosomally translated product, but this enzyme is involved in a pathway that converts a free Trp residue to a quinaldic acid moiety before it is appended. [Cellular processes, Toxin production and resistance] 545 matched cddid_all.tbl CDD TIGR04429 TIGR04429 275222 Phr_nterm Phr family secreted Rap phosphatase inhibitor. Phr peptides are short peptides, best conserved in their amino-terminal regions, that are almost always encoded immediately downstream of a Rap phosphatase. A portion of the Phr peptide is secreted, enters another cell, and forms a quorum-sensing system by inhibiting its Rap phosphatase partner. The set of Phr peptides recognized by this N-terminal region model is disjoint from the PhrC/PhrF set recognized by pfam11131. [Regulatory functions, Protein interactions] 28 matched cddid_all.tbl CDD TIGR04430 TIGR04430 275223 OM_asym_MlaD outer membrane lipid asymmetry maintenance protein MlaD. Members of this protein family are the MlaD (maintenance of Lipid Asymmetry D) protein of an ABC transport system that seems to remove phospholipid from the outer leaflet of the Gram-negative bacterial outer membrane (OM), leaving only lipopolysaccharide in the outer leaflet. The Mla locus has long been associated with toluene tolerance, consistent with the proposed role in retrograde transport of phospholipid and therefore with maintaining the integrity of the OM as a protective barrier. 146 matched cddid_all.tbl CDD TIGR04431 TIGR04431 275224 N6_acetyl_AAC6 aminoglycoside N(6')-acetyltransferase, AacA4 family. Members of this family are the aacA4 type of aminoglycoside N(6')-acetyltransferase (EC 2.3.1.82), an enzyme that modifies and inactivates aminoglycoside antibiotics such as kanamycin, neomycin, tobramycin, and amikacin. Members are regularly spread among pathogens into integron, transposon, and plasmid loci, with recombination often happening within the protein-coding region. Most of the region amino-terminal to the recombination site or sites was removed from this model. [Cellular processes, Toxin production and resistance] 184 matched cddid_all.tbl CDD TIGR04432 TIGR04432 275225 rSAM_Cfr 23S rRNA (adenine(2503)-C(8))-methyltransferase Cfr. This model identifies Cfr, a 23S rRNA methyltransferase, EC 2.1.1.224, responsible for a transmissible form of chloramphenicol/florfenicol resistance. It is closely related to RlmN (see TIGR00048), an adenine C2-methyltransferase that acts at the same site where Cfr acts as a C8-methyltransferase [Protein synthesis, tRNA and rRNA base modification] 341 matched cddid_all.tbl CDD TIGR04433 TIGR04433 275226 UrcA_uranyl UrcA family protein. Members of this family feature an N-terminal signal sequence, small size, and two invariant Cys residues, 10-20 residues apart. One member of this family, UrcA from the aerobic bacterium Caulobacter crescentus, is expressed so highly in response to uranium, but not other heavy metals, that a genetically engineered strain expressing green fluorescent protein in place of UrcA serves as a biodetector for micromolar uranyl ion. Caulobacter crescentus tolerates high levels of U(VI) exposure by mineralizing the uranium. UrcA and its homologs may participate in such a process. 91 matched cddid_all.tbl CDD TIGR04434 TIGR04434 275227 rSAM_Pput_1520 B12-binding domain/radical SAM domain protein, Pput_1520 family. Members of this family are radical SAM domain (pfam04055) enzymes with an N-terminal B12-binding domain (pfam02310), as is fairly common for radical SAM enzymes with lipid substrates. However, both domains as found in this family seem to be long-branch. The function is unknown, but all cases a PLP-dependent enzyme (a cysteine desulfurase homolog) is found nearby. 515 matched cddid_all.tbl CDD TIGR04435 TIGR04435 275228 restrict_AAA_1 restriction system-associated AAA family ATPase. Members of this family are AAA family ATPases by homology. They occur regularly in a conserved gene neighborhood with the restriction (R), modification (M), and specificity (S) proteins of an apparent type I restriction enzyme system, plus one additional uncharacterized protein. It is not clear whether members of this family contribute to restriction per se, or to another process such as transfer of mobile elements. 555 matched cddid_all.tbl CDD TIGR04436 TIGR04436 275229 SpoChoClust_3 putative 2OG-Fe(II) oxygenase. This family, related to streptomycin biosynthesis protein StrG and to phytanoyl-CoA dioxygenase, belongs to the 2-oxoglutarate and Fe(II)-dependent oxygenase clan, which includes not just dioxygenases such as phytanoyl-CoA dioxygenase PhyH, but also some chlorinating enzymes involved in natural product biosynthesis. Members of this family occur so far only in O-antigen biosynthesis regions of select Leptospira, and include an ~80 residue additional C-terminal region shared by no other proteins. 300 matched cddid_all.tbl CDD TIGR04437 TIGR04437 275230 WaaZ_KDO_III Kdo-III transferase WaaZ. Members of this family are WaaZ, or Kdo-III transferase. This enzyme, present in some strains of E. coli and its allies but not others, performs a non-stoichiometric addition of a third 3-deoxy-D-manno-oct-2-ulosonic acid (KDO-III) onto some fraction of KDO-II in the lipopolysaccharide (LPS) inner core. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 252 matched cddid_all.tbl CDD TIGR04438 TIGR04438 275231 small_Trp_rich small Trp-rich protein. Members of this bacterial protein family average 80 residues in length, and average nearly 6 Trp residues (two of which are invariant) in the first 45, which are strongly hydrophobic. Past this region, the protein is highly charged, with large numbers of Lys, Arg, Asp, and Glu residues. Members usually are divergently transcribed from a gene encoding a c-type cytochrome. 76 matched cddid_all.tbl CDD TIGR04439 TIGR04439 275232 histamin_N_OH putative histamine N-monooxygenase. Members of this family are involved in synthesizing N-hydroxyhistamine as a precursor to acinetobactin, a siderophore found in Acinetobacter baumannii. Assuming histidine is first decarboxylated to histamine, then hydroxylated, members of this family are histamine N-monooxygenase. The putative histidine decarboxylase is found in the same biosynthetic cluster. 431 matched cddid_all.tbl CDD TIGR04440 TIGR04440 275233 glyco_TIGR04440 glycosyltransferase domain. This model describes a putative glycotransferase domain, related to the group 2 family glycosyltransferases of pfam00535. 215 matched cddid_all.tbl CDD TIGR04441 TIGR04441 275234 lept_O_ant_chp1 surface carbohydrate biosynthesis protein. Members of this protein family occur only in a subset of Leptospira species, and in those species occur only in O-antigen biosynthesis regions. Members average about 375 amino acids in length. The function is unknown. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 373 matched cddid_all.tbl CDD TIGR04442 TIGR04442 275235 TIGR04442 TIGR04442 family protein. Members of this family occur exclusively in certain Deltaproteobacteria, including Geobacter and Pelobacter. The function is unknown. 608 matched cddid_all.tbl CDD TIGR04443 TIGR04443 275236 F420_CofF coenzyme gamma-F420-2:alpha-L-glutamate ligase. Members of this family are the CofF, a RimK-related glutamate ligase that caps the gamma-glutamyl tail of the archaeal form of coenzyme F420, a hydride carrier. This enzyme does not appear in bacterial species, such as Mycobacterium tuberculosis, that make F420 with a different type of tail. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other] 283 matched cddid_all.tbl CDD TIGR04444 TIGR04444 275237 chori_FkbO_Hyg5 chorismatase, FkbO/Hyg5 family. Members of this include two chemically distinct enzymes that cleave pyruvate from chorismate. FkbO and RapK convert chorismate to pyruvate plus (4R,5R)-4,5-dihydroxycyclohexa-1,5-dienecarboxylic acid (DCDC). HygB and Bra8 convert chorismate to pyruvate, water, and 3-hydroxybenzoate. These two enzymes are closely related, and lack homology to chorismate lyase, EC 4.1.3.40, which converts chorismate to pyruvate plus 4-hydroxybenzoate. 311 matched cddid_all.tbl CDD TIGR04445 TIGR04445 275238 preny_LynF_TruF peptide O-prenyltransferase, LynF/TruF/PatF family. Members of this family are prenytransferases that modify mostly, perhaps exclusively, ribosomally derived cyclic peptides. Note that in some cases, the natural product becomes C-prenylated through a non-enzymatic rearrangement after initial O-prenylation. Prenylated products carry names such as prenylagaramide, anacyclamide, and piricyclamide. 282 matched cddid_all.tbl CDD TIGR04446 TIGR04446 275239 pren_cyc_PirE prenylated cyclic peptide, anacyclamide/piricyclamide family. Members of this protein family occur primarily in Cyanobacteria. They average about 50 residues in length and are the ribosomally translated precursors of peptide natural products whose modifications include cleavage, cyclization, and prenylation. Sequences are well-conserved in the N-terminal region. They are nearly invariant over the last eight residues, but hypervariable just before that stretch. A related family, often in a similar genome context, is TIGR03678. 48 matched cddid_all.tbl CDD TIGR04447 TIGR04447 275240 PatC_TenC_TruC cyanobactin cluster PatC/TenC/TruC protein. Members of this family usually are small proteins (PatC, TenC, TruC) of unknown function in cyanobactin (prenylated cyclic peptide) biosynthesis clusters, where a different small protein is a known cyanobactin precursor (patellamide, anacyclamide, piricyclamide, etc). They may instead be the C-terminal domain of a longer protein that otherwise consists mostly of lectin-like or VWF type A domains, in similar context. Similar to the cyanobactin precursors, members of this family have two very strongly conserved regions separated by a hypervariable region, suggesting these proteins may undergo a similar maturation. 34 matched cddid_all.tbl CDD TIGR04448 TIGR04448 275241 creatininase creatininase. Members of this family are creatininase (EC 3.5.2.10), an amidohydrolase that interconverts creatinine + H(2)O with creatine. It should not be confused with creatinase (EC 3.5.3.3), which hydrolyzes creatine to sarcosine plus urea. [Central intermediary metabolism, Nitrogen metabolism] 246 matched cddid_all.tbl CDD TIGR04449 TIGR04449 275242 halocin_C8_dom halocin C8-like bacteriocin domain. This model describes the 76-amino C-terminal domain of the halocin C8 precursor that actually becomes the mature bacteriocin halocin C8 after export and cleavage, as well as homologous C-terminal regions from many other archaea. Surprisingly, this Cys-rich region occurs also in many strains of Staphylococcus epidermidis. Gene regions do not provide evidence for post-translational modification other than cleavage. Halocin C8 is active against a broad range of archaea; the region N-terminal to the bacteriocin domain modeled here serves as the immunity protein for the cell secreting the bacteriocin. [Cellular processes, Toxin production and resistance] 69 matched cddid_all.tbl CDD TIGR04450 TIGR04450 275243 Gpos_C8_like putative immunity protein/bacteriocin. This model describes full-length proteins of Gram-positive bacteria that consist of an N-terminal signal peptide, a central region of unknown function, and a Cys-rich C-terminal region. In both the overall architecture and the apparent weak homology of the C-terminal region itself, these proteins resemble archaeal proteins such as the halocin C8 precursor. In that precursor, the C-terminal region is a bacteriocin but the N-terminal region functions as the immunity protein. The related family of halocin C8-like bacteriocins and their bacterial homologs are recognized by model TIGR04449. 234 matched cddid_all.tbl CDD TIGR04451 TIGR04451 275244 lanti_SCO0268 lantipeptide, SCO0268 family. Members of this family are putative lantipeptide (most likely lantibiotic) precursors, about 53 amino acids long, found in a lantibiotic-type biosynthetic cluster in several species of Streptomyces (S. coelicolor, S. griseoflavus, S. ambofaciens, etc.). This family is described in AntiSMASH as Streptomyces PEQAXS motif lantipeptide precursor. 53 matched cddid_all.tbl CDD TIGR04452 TIGR04452 275245 Lepto_Lipo_YY_C small lipoprotein, LA_3946 family. Members of this family of small lipoproteins that occur in at least nineteen species of Leptospira, but not so far anywhere outside that genus. Notable features include the putative lipoprotein modification Cys and an additional Cys near the C-terminus, both invariant, plus a well-conserved (although not invariant) Tyr-Tyr pair. From one to four paralogs occur in most Leptospira species. Members include LA_3946. 115 matched cddid_all.tbl CDD TIGR04453 TIGR04453 275246 Lepto_8Cys Cys-rich protein, LA_1312 family. Members of this protein family occur, so far, exclusively in the genus Leptospira. Members, although small (about 90 amino acids), have a predicted signal peptide followed by a region with eight invariant Cys residues. Some members have an additional Cys in the signal peptide region that suggests handling as a lipoprotein, but this Cys is not well conserved. 85 matched cddid_all.tbl CDD TIGR04454 TIGR04454 275247 Lepto_4Cys small lipoprotein, LB_250 family. Members of this family average about 92 amino acids in length, including an apparent lipoprotein signal peptide and a mature portion with four additional invariant Cys residues. This family is universal, so far, across at least twenty species of Leptospira but unknown outside the genus. 92 matched cddid_all.tbl CDD TIGR04455 TIGR04455 275248 lipo_MXAN_6521 probable lipoprotein, LA_1396/MXAN_6521 family. Members of this family are predicted lipoproteins, near 200 residues in length, found in multiple species of Leptospira (a spirochete) but also in the Myxococcales branch of the Deltaproteobacteria (Myxococcus xanthus, Chondromyces apiculatus, Cystobacter fuscus, Corallococcus coralloides), an uncommon mix of species. In both lineages, the N-terminal region appears to be a lipoprotein signal peptide. 191 matched cddid_all.tbl CDD TIGR04456 TIGR04456 275249 LruC_dom LruC domain. This domain is abundant in the Leptospira, in Bacteroides, and in Vibrio (three widely separated lineages). Most members have plausible lipoprotein signal peptides, including lipoprotein LruC from Leptospira interrogans and BACOVA_00967, from Bacteroides ovatus, with a solved crystal structure. Note that the C-terminal region of pfam13448 (length 83) matches the N-terminal region of some members of this domain (length 243). 242 matched cddid_all.tbl CDD TIGR04457 TIGR04457 275250 lipo_LenA_lepto lipoprotein LenA. Members of this family are LenA (Leptospira Endostatin-like protein A), found in pathogenic and intermediate species of Leptospira but not in saprophytes. LenA binds plasminogen, laminin, and complement regulator factor H. Behavior during outer membrane solubilization by low concentrations of Triton X-114 and conservation in all family members of an apparent lipoprotein signal sequence, with invariant Cys residue, strongly suggest that LenA is a lipoprotein. Just outside this family is a full-length homolog found in another spirochete, Turneriella parva DSM 21527. 224 matched cddid_all.tbl CDD TIGR04458 TIGR04458 275251 CYP450_TxtE 4-nitrotryptophan synthase. Members of this family are cytochrome P450 enzymes that convert L-tryptophan into L-4-nitrotryptophan. In thaxtomin gene clusters, this enzyme (TxtE) uses nitric acid (NO) derived from arginine by the nitric oxide synthase TxtD, and O2, to perform the tryptophan nitration. L-4-nitrotryptophan is then used as a non-proteinogenic amino acid by non-ribosomal peptide synthases (NRPS). 403 matched cddid_all.tbl CDD TIGR04459 TIGR04459 275252 TisB_tox type I toxin-antitoxin system toxin TisB. Members of this family are the TisB toxin protein of a type I toxin-antitoxin system, meaning that the antitoxin is a non-coding RNA. TisB is induced by some types of stress (SOS, ciprofloxacin) and appears to induce a persister state by dissipating transmembrane potential, thus depleting ATP. Persister cells, unable to grow until the persister state changes, survive a number of challenges, including exposure to most antibiotics. [Cellular processes, Adaptations to atypical conditions] 29 matched cddid_all.tbl CDD TIGR04460 TIGR04460 275253 endura_MppR enduracididine biosynthesis enzyme MppR. Members of this family are MppR, one of three enzymes involved in synthesizing enduracididine, a non-proteinogenic amino acid used in non-ribosomal peptide synthases to make natural products such as enduracidin from Streptomyces fungicidicus ATCC 21013. MppR is belongs to the acetoacetate decarboxylase-like superfamily. MppR catalyzes an aldol condensation and a dehydration, not a decarboxylation. 257 matched cddid_all.tbl CDD TIGR04461 TIGR04461 275254 endura_MppQ enduracididine biosynthesis enzyme MppQ. Members of this family are MppQ, one of three enzymes involved in synthesizing enduracididine, a non-proteinogenic amino acid used in non-ribosomal peptide synthases to make natural products such as enduracidin from Streptomyces fungicidicus ATCC 21013. MppQ is a PLP-dependent enzyme, predicted by homology to be an aminotransferase. 392 matched cddid_all.tbl CDD TIGR04462 TIGR04462 275255 endura_MppP enduracididine biosynthesis enzyme MppP. Members of this family are MppP, one of three enzymes involved in synthesizing enduracididine, a non-proteinogenic amino acid used in non-ribosomal peptide synthases to make natural products such as enduracidin from Streptomyces fungicidicus ATCC 21013. MppP is a PLP-dependent enzyme, predicted by homology to be an aminotransferase. 289 matched cddid_all.tbl CDD TIGR04463 TIGR04463 275256 rSAM_vs_C_rich radical SAM/SPASM domain protein maturase. Members of this family are probable protein/peptide-modifying radical SAM/SPASM domain proteins. The majority of members of this family seem to target Cys-rich repetitive regions of large proteins rather than of bacteriocin-sized small precursors. This arrangement suggests the modification target may be multifunctional, with the C-terminal domain behaving like a bacteriocin but other parts of the same precursor serving an immunity function, as occurs for the halocin C8 precursor. 439 matched cddid_all.tbl CDD TIGR04464 TIGR04464 275257 chaper_lep LipL41-expression chaperone Lep. Members of this protein family are Lep, an outer membrane lipoprotein LipL41-binding protein that appears to function as a chaperone important to its expression. LipL41 is the third most abundant lipoprotein in the pathogen Leptospira interrogans, but is found in saprophytic Leptospira species as well and is not essential for virulence. 114 matched cddid_all.tbl CDD TIGR04465 TIGR04465 275258 ArgArg_F420 TAT-translocated F420-dependent dehydrogenase, FGD2 family. Members of this family are F420-binding enzymes with a proven functional N-terminal twin-arginine translocation (TAT) signal. Members are homologous to the cytosolic F420-dependent glucose-6-phosphate dehydrogenase but do not share the same function. 364 matched cddid_all.tbl CDD TIGR04466 TIGR04466 275259 rSAM_BlsE cytosylglucuronate decarboxylase. BlsE, part of the blasticidin S biosynthetic pathway, is a radical SAM enzyme that performs a decarboxylation at C5 of the glucoside residue. MilG in mildiomycin biosynthesis is equivalent. This enzyme follows CGA synthase and makes the pyranoside core moiety of a class of peptidyl nucleoside antibiotics. [Cellular processes, Toxin production and resistance] 327 matched cddid_all.tbl CDD TIGR04467 TIGR04467 275260 CGA_synthase hydroxymethylcytosylglucuronate/cytosylglucuronate synthase. Members of this family synthesize cytosylglucuronate (or hydroxymethylcytosylglucuronate) from UDP-glucuronate and free cytosine (or hydroxymethylcytosine). This reaction is followed by a decarboxylation at C5 of the glucoside residue. The net reaction makes the pyranoside core moiety of a class of peptidyl nucleoside antibiotics. 386 matched cddid_all.tbl CDD TIGR04468 TIGR04468 275261 arg_2_3_am_muta arginine 2,3-aminomutase. Members of this family are arginine 2,3-aminomutase, a radical SAM enzyme more closely related to lysine 2,3-aminomutase than to glutamate 2,3-aminomutase. The enzyme makes L-beta-arginine, sometimes in the context of antibiotic biosynthesis (blasticidin S, mildiomycin, etc). Activity is proven in Streptomyces griseochromogenes, which makes blasticidin S. 351 matched cddid_all.tbl CDD TIGR04469 TIGR04469 275262 CGA_synth_rel CGA synthase-related protein. Members of this family are related to cytosylglucuronate (CGA) synthase (TIGR04466), and found in the same clusters as CGA synthase and CGA decarboxylase. These clusters produce peptidyl nucleoside antibiotics with a pyranoside core moiety, found in a number of Streptomyces species. Removal of the S. griseochromogenes member of this family, BlsF, from a heterologous expression system caused an increase, not blockage, of blasticidin S. [Cellular processes, Toxin production and resistance] 297 matched cddid_all.tbl CDD TIGR04470 TIGR04470 275263 rSAM_mob_pairB radical SAM mobile pair protein B. Members of this family are the downstream member (B) of a pair of tandem-encoded radical SAM enzymes. Most of these radical SAM gene pairs have an additional upstream regulatory gene in the MarR family. Examples of high sequence identity (over 96 percent) from cassettes in several Treponema species of the oral cavity to those in multiple Firmicutes in the gut microbiome suggest recent lateral gene transfer, as might be expected for antibiotic resistance genes. The function is unknown. 285 matched cddid_all.tbl CDD TIGR04471 TIGR04471 275264 rSAM_mob_pairA radical SAM mobile pair protein A. Members of this family are the upstream member (A) of a pair of tandem-encoded radical SAM enzymes. Most of these radical SAM gene pairs have an additional upstream regulatory gene in the MarR family. Examples of high sequence identity (over 96 percent) from cassettes in several Treponema species of the oral cavity to those in multiple Firmicutes in the gut microbiome suggest recent lateral gene transfer, as might be expected for antibiotic resistance genes. The function is unknown. 220 matched cddid_all.tbl CDD TIGR04472 TIGR04472 275265 reg_rSAM_mob mobile rSAM pair MarR family regulator. A number of human microbiome species from both the Firmicutes and the spirochete genus Treponema share a gene cassette encoding a pair of radical SAM enzymes and, in most cases, this MarR family transcriptional regulator as well. Sequence identity can exceed 96 percent, suggesting recent lateral transfer. These observations suggest the cassette confers resistance to a toxic compound such as an antibiotic. 141 matched cddid_all.tbl CDD TIGR04473 TIGR04473 275266 taxol_Phe_23mut phenylalanine aminomutase (L-beta-phenylalanine forming). Members of this family are the phenylalanine aminomutase known from taxol biosynthesis. This enzyme has the MIO prosthetic group (4-methylideneimidazole-5-one), derived from an Ala-Ser-Gly motif. Other MIO enzymes include Phe, Tyr, and His ammonia-lyases. This model serves as an exception to overrule assignments by equivalog model TIGR01226 for phenylalanine ammonia-lyase. 687 matched cddid_all.tbl CDD TIGR04474 TIGR04474 275267 tcm_partner three-Cys-motif partner protein. Members of this family occur regularly as a partner to as a member of family pfam07505, which has been called a phage protein but which seems to occur also in other contexts. Members average about 400 residues in length, but the conserved region covered by the model averages 260 residues and excludes the C-terminus. Conserved motifs suggest enzymatic activity. Note that its frequent partner protein (see pfam07505) has a three-cysteine motif that resembles the Cx3CxxC motif of radical SAM proteins, and that in one branch (see TIGR04471) actually becomes Cx3CxxC. We suggest the name three-Cys-motif partner protein (tcmP), and renaming pfam07505 to three-Cys-motif family protein 262 matched cddid_all.tbl CDD TIGR04475 TIGR04475 275268 Phe_D_beta_mut phenylalanine aminomutase (D-beta-phenylalanine forming). Members of this family have the MIO prosthetic group (4-methylideneimidazole-5-one), derived from an Ala-Ser-Gly motif. Other MIO enzymes include Phe, Tyr, and His ammonia-lyases. The member from Pantoea agglomerans, and probably all members, convert Phe to D-beta-phenylalanine (EC 5.4.3.11). By contrast, members of family TIGR04473 convert Phe to L-beta-phenylalanine (5.4.3.10), as in taxol biosynthesis. 510 matched cddid_all.tbl CDD TIGR04476 TIGR04476 275269 exosort_XrtN exosortase N. Members of this family are exosortase N (xrtN), a bacterial exosortase variant whose single target, encoded always by an adjacent gene, belongs to the vault protein inter-alpha-trypsin family. This system occurs in a number of spirochete (Leptospira) and Bacteriodetes species. 403 matched cddid_all.tbl CDD TIGR04477 TIGR04477 275270 sorted_by_XrtN XrtN system VIT domain protein. Members of this subfamily average about 850 amino acids in length, ending with a variant form of PEP-CTERM sorting signal. Members have a VIT (vault protein inter-alpha-trypsin inhibitor heavy chain) domain (pfam08487). Other bacterial subfamilies of VIT domain proteins have members with either GlyGly-CTERM or LPXTG C-terminal sorting signals. Members of this subfamily occur only in context next to a protein sorting/processing enzyme, exosortase N (XrtN). These subsystems occur both among the Bacteriodetes and in the spirochete genus Leptospira. 822 matched cddid_all.tbl CDD TIGR04478 TIGR04478 275271 rSAM_YfkAB radical SAM/CxCxxxxC motif protein YfkAB. Members of this highly conserved family in some Firmicutes have an N-terminal radical SAM domain (pfam04055) and a C-terminal pfam08756 domain with a CxCxxxxC motif that suggests binding to an additional metallocluster. It appears all correct sequences in this family are about 370 amino acids in length, containing the YfkA and YfkB regions originally reported as separate ORFs in Bacillus subtilis. Partial Phylogenetic Profiling shows occurrences almost exclusively in the Bacilli, with very few examples of either lateral transfer or gene loss. The essentially monophyletic distribution suggests a housekeeping function. Members have no well-conserved gene neighborhood. The function is unknown. [Unknown function, Enzymes of unknown specificity] 363 matched cddid_all.tbl CDD TIGR04479 TIGR04479 275272 bcpD_PhpK_rSAM radical SAM P-methyltransferase, PhpK family. Characterized members of this family are B12-binding domain/radical SAM domain enzymes that use methylcobalamin as a methyl donor to methylate a phosphorous atom during the biosynthesis of natural products such as bialaphos and phosalacine. These syntheses create an extremely rare C-P-C bond. All members of the seed alignment derive from genomic regions that include a non-ribosomal peptide synthase. Note that a single organism, Pelosinus fermentans JBW45 from Cr(VI)-contaminated groundwater, has eight additional homologs of unknown function that score between trusted and noise cutoffs of this model. [Cellular processes, Toxin production and resistance] 504 matched cddid_all.tbl CDD TIGR04480 TIGR04480 275273 D_pro_red_PrdA D-proline reductase (dithiol), PrdA proprotein. Members of this family are the PrdA proprotein. The polypeptide undergoes an autocatalytic cleavage that creates two subunits, one with a Cys-derived pyruvoyl motiety critical for activity. The D-proline reductase complex also contains a subunit derived from the prdB gene. The complex acts on D-proline, which may be supplied from L-proline by an active proline racemase encoded nearby. 587 matched cddid_all.tbl CDD TIGR04481 TIGR04481 275274 PR_assoc_PrdC proline reductase-associated electron transfer protein PrdC. Members of this family are encoded near the prdA and prdB genes for proteins of the proline reductase complex, are induced by proline, and are designated PrdC by Bouillaut, et al. Some members are selenoproteins (at two different positions), as is PrdB. Members are homologous to, but distinct from, electron transport protein RnfC. 425 matched cddid_all.tbl CDD TIGR04482 TIGR04482 275275 D_pro_red_PrdD proline reductase cluster protein PrdD. Members of this family are PrdD, encoded in the proline reductase gene cluster. Members are closely homologous to PrdA, which cleaves during maturation to create two subunits of the subunits of the proline reductase complex, one of which has a Cys-derived pyruvoyl active site. 246 matched cddid_all.tbl CDD TIGR04483 TIGR04483 275276 D_pro_red_PrdB D-proline reductase (dithiol), PrdB protein. Members of this family form the PrdB subunit, usually a selenoprotein, in the D-proline reductase complex. The usual pathway is conversion of L-protein to D-proline by a racemase, then use of D-proline as an electron acceptor coupled to ATP generation under anaerobic conditions. 238 matched cddid_all.tbl CDD TIGR04484 TIGR04484 275277 thiosulf_SoxA sulfur oxidation c-type cytochrome SoxA. Members of this family are SoxA, a c-type cytochrome with a CxxCH motif, part of a heterodimer with SoxX. SoxXA, SoxYZ, and SoxB contribute to thiosulfate oxidation to sulfate. 211 matched cddid_all.tbl CDD TIGR04485 TIGR04485 275278 thiosulf_SoxX sulfur oxidation c-type cytochrome SoxX. Members of this family are SoxX, a c-type cytochrome with a CxxCH motif, part of a heterodimer with SoxA. SoxXA, SoxYZ, and SoxB contribute to thiosulfate oxidation to sulfate. 78 matched cddid_all.tbl CDD TIGR04486 TIGR04486 275279 thiosulf_SoxB thiosulfohydrolase SoxB. SoxB, a di-manganese(II) enzyme, works with SoxYZ and the c-type cytochrome SoxXA in oxidation of thiosulfate to sulfate. 556 matched cddid_all.tbl CDD TIGR04487 TIGR04487 275280 SoxY_para_1 SoxY-related AACIE arm protein. Members of this family are paralogs to the authentic thiosulfate oxidation system protein SoxY. True SoxY end with the sequence GGCG(G), the swinging arm in which the Cys residue covalently binds the inorganic sulfur moiety. In this family, members end with a different swinging arm sequence, [AS]AC[IVT]E. The few species with a member of this family always have authentic SoxY. 145 matched cddid_all.tbl CDD TIGR04488 TIGR04488 275281 SoxY_true_GGCGG thiosulfate oxidation carrier protein SoxY. Members of this family are bona fide SoxY, the sulfate carrier protein with the GGCGG ir GGCG swinging arm C-terminal sequence. The Cys in the swinging arm is the residue to which the inorganic sulfate moiety becomes covalently attached. In some species, a closely related paralog occurs as well (TIGR04487), with a swinging arm sequence AACIE. More distantly related forms have an additional C-terminal SoxZ-related domain. All members are periplasmic and have an N-terminal twin-arginine translocation (TAT) signal sequence. 148 matched cddid_all.tbl CDD TIGR04489 TIGR04489 275282 exosort_XrtO exosortase O. Members of this protein are a variant form of exosortase, XrtO, with a dedicated target typically encoded by the adjacent gene. Members have a unique C-terminal extension very different from EpsI (TIGR02914), the extension that many exosortases have. The targets of XrtO all are members of family TIGR02921, which describes a PEP-CTERM protein about 950 residues long, found in more than 15 genera so far. These PEP-CTERM proteins are unusually hydrophobic in stretches, suggesting an integral membrane location, which is unusual. About one third of the members of TIGR02921 are in genomes with this protein, exosortase O, always encoded by an adjacent gene. Genomes include Synechocystis sp. PCC 7509, Xenococcus sp. PCC 7305,Pleurocapsa sp. PCC 7327, Microcoleus vaginatus, Hahella chejuensis, Vibrio azureus NBRC 104587, etc. 450 matched cddid_all.tbl CDD TIGR04490 TIGR04490 275283 SoxZ_true thiosulfate oxidation carrier complex protein SoxZ. SoxZ forms a heterodimer with SoxY, the subunit that forms a covalent bond with a sulfur moiety during thiosulfate oxidation to sulfate. Note that virtually all proteins that have a SoxY domain fused to a SoxZ domain are functionally distinct and not involved in thiosulfate oxidation. 95 matched cddid_all.tbl CDD TIGR04491 TIGR04491 275284 reactive_PduG diol dehydratase reactivase alpha subunit. Members of this family are the alpha (large) subunit of the alpha-2/beta-2 tetrameric enzyme that reactivates B12-dependent trimeric diol dehydratases (1,2-propanediol dehydratase, glycerol dehydratase). Note that the beta subunit of the reactivase is homologous to the beta (medium) subunit of the diol dehydratase. The reactivase catalyzes the exchange of chemically inactivated B-12 for active B12. This model excludes homologs from Mycobacterium (e.g. M. smegmatis), where the several paralogous forms of the dehydratase occur and are exceptional also by not being found in a carboxysome-like microcompartment. 598 matched cddid_all.tbl CDD TIGR04492 TIGR04492 275285 VioB iminophenyl-pyruvate dimer synthase VioB. Following the action of a flavin-dependent L-amino acid oxidase that converts L-tryptophan to indole-3-pyruvate imine, the enzymes VioB (this family), RebD, and StaD can ligate two molecules, forming a coupled iminophenyl-pyruvate dimer. In the violacein biosynthesis pathway, this compound is acted on by VioE before it cyclizes spontaneously to chromopyrrolic acid. In the pathways of homolog StaD (staurosporine), chromopyrrolate is formed, and the enzyme is referred to as chromopyrrolate synthase. RebD is very similar to StaD, but acts on chlorinated Trp-derived molecules. [Cellular processes, Biosynthesis of natural products] 1003 matched cddid_all.tbl CDD TIGR04493 TIGR04493 275286 microcomp_PduM microcompartment protein PduM. Members of this family are PduM, a protein essential for forming functional microcompartments in which a trimeric B12-dependent enzyme acts as a dehydratase for 1,2-propanediol (Salmonella enterica) or glycerol (Lactobacillus reuteri). 153 matched cddid_all.tbl CDD TIGR04494 TIGR04494 275287 c550_PedF cytochrome c-550 PedF. Members of this family are c-type cytochromes with some remote similarity to the sulfur oxidation cytochrome SoxX. 133 matched cddid_all.tbl CDD TIGR04495 TIGR04495 275288 RiPP_XyeA putative rSAM-modified RiPP, XyeA family. Members of this family are short polypeptides with a conserved GG motif as found in bacteriocins that are cleaved upon export. Each gene occurs immediately upstream of a gene for a peptide-modifying radical SAM/SPASM domain protein. The system is designated Xye for genera Xenorhabdus, Yersinia, and Erwinia, hence XyeA for the precursor peptide. The vicinity will also contain a transport protein with a C39 family peptidase domain (see pfam03412), characteristic of GG motif cleave-on-export systems. The function of this RiPP family is unknown. 52 matched cddid_all.tbl CDD TIGR04496 TIGR04496 275289 rSAM_XyeB radical SAM/SPASM domain peptide maturase, XyeB family. Members of this family are radical SAM/SPASM domain enzymes associated with maturation of the XyeA family of GG-motif containing RiPP (Ribosomally synthesized, Post-translationally modified Peptide) natural products. 385 matched cddid_all.tbl CDD TIGR04497 TIGR04497 275290 GRASP_targ_2 putative ATP-grasp target RiPP. Members of this small family are putative RiPP (Ribosomally translated, Post-translationally modified Peptides) precursors, modified by RimK-like ATP-grasp proteins. Members are encoded near both an ATP-grasp protein and C39 peptidase domain-containing transporter. Members are short polypeptides that contain the GG motif expected for cleavage on export. 46 matched cddid_all.tbl CDD TIGR04498 TIGR04498 275291 AbiV_defense abortive infection protein, AbiV family. This family includes AbiV (abortive infection system V) from Lactococcus lactis, a phage resistance protein that causes certain phage infections to fail to lead to successful phage replication. Abortive infection mechanisms differ greatly. AbiV interacts directly with the protein SaV in phage p2 and blocks translation of phage proteins. 141 matched cddid_all.tbl CDD TIGR04499 TIGR04499 275292 abortive_AbiA abortive infection protein, AbiA family. Members of this protein family average about 650 amino acids in length, with an N-terminal region related to reverse transcriptases. The only characterized member is AbiA, with reported activity as an abortive infection protein for phage defense in Lactococcus lactis and (heterologously) in Streptococcus thermophilus. 615 matched cddid_all.tbl CDD TIGR04500 TIGR04500 275293 PpiC_rel_mature putative peptide maturation system protein. Members of this protein family have a novel N-terminal sequence region. Close homologs to the C-terminal region of this protein score well to PpiC-type peptidyl-prolyl cis-trans isomerase models (see pfam00639), yet no sequence within the family scores well to such models, suggesting origin within a branch of the PpiC family but subsequent neofunctionalization with a rapid change of sequence. The genome context for members always includes an ATP-grasp enzyme associated with peptide modification and a short polypeptide likely to be the modification target. 337 matched cddid_all.tbl CDD TIGR04501 TIGR04501 275294 microcomp_PduB microcompartment protein PduB. Members of this family are PduB, a protein of bacterial microcompartments for coenzyme B(12)-dependent utilization of 1,2-propanediol (hence pdu) or glycerol. The most closely related protein in ethanolamine utilization microcompartments is EutL (TIGR04502). 225 matched cddid_all.tbl CDD TIGR04502 TIGR04502 275295 microcomp_EutL microcompartment protein EutL. Members of this family are EutL, a protein of bacterial microcompartments for ethanolamine utilization (eut). The most closely related protein in microcompartments for utilization of 1,2-propanediol (hence pdu) or glycerol is PduB (TIGR04501). 214 matched cddid_all.tbl CDD TIGR04503 TIGR04503 275296 mft_etfB electron transfer flavoprotein, mycofactocin-associated. Members of this small protein family are putative electron transfer flavoproteins, related to FixA from E. coli and EtfB from Methylophilus methylotrophus but clearly forming a distinctive clade. All members occur in species with a mycofactocin system. We have proposed that mycofactocin is a redox carrier synthesized from a ribosomally translated peptide with aid from a radical SAM enzyme, analogous to PQQ. 290 matched cddid_all.tbl CDD TIGR04504 TIGR04504 275297 SDR_subfam_2 SDR family mycofactocin-dependent oxidoreductase. Members of this protein subfamily are putative oxidoreductases belonging to the larger SDR family. All members occur in genomes that encode a cassette for the biosynthesis of mycofactocin, a proposed electron carrier of a novel redox pool. Characterized members of this family are described as NDMA-dependent, meaning that a blue aniline dye serving as an artificial electron acceptor is required for members of this family to cycle in vitro, since the bound NAD residue is not exchangeable. This family resembles TIGR03971 most closely in the N-terminal region, consistent with the published hypothesis of NAD interaction with mycofactocin. See EC 1.1.99.36. [Unknown function, Enzymes of unknown specificity] 259 matched cddid_all.tbl CDD TIGR04505 TIGR04505 275298 PtsS_plasma phosphate ABC transporter substrate-binding protein. Members of this family are the substrate-binding protein of the phosphate ABC transporter as found in Mollicutes genera such as Mycoplasma, Mesoplasma, and Spiroplasma. The most similar sequences outside this family are PtsS in family TIGR02136, but sequence architecture differs considerably. Members of this family are never lipoproteins. 328 matched cddid_all.tbl CDD TIGR04506 TIGR04506 275299 F_threo_transal fluorothreonine transaldolase. Members of this family are fluorothreonine transaldolase, and enzyme involved in biosynthesis of 4-fluorothreonine, one of the few known known naturally occurring organofluorine compounds. [Cellular processes, Biosynthesis of natural products] 609 matched cddid_all.tbl CDD TIGR04507 TIGR04507 275300 fluorinase adenosyl-fluoride synthase. Members of this family are fluorinase (adenosyl-fluoride synthase, EC 2.5.1.63), an enzyme involved in the first committed step in the biosynthesis of at least two different organofluorine compounds. Few organofluorine natural products are known. Related enzymes include chlorinases (EC 2.5.1.94) that lack fluorinase activity, although a fluorinase may show chlorinase activity. [Cellular processes, Biosynthesis of natural products] 285 matched cddid_all.tbl CDD TIGR04508 TIGR04508 275301 queE_Cx14CxxC 7-carboxy-7-deazaguanine synthase, Cx14CxxC type. In the pathway of 7-cyano-7-deazaquanine (preQ0) biosynthesis, the radical SAM enzyme QueE is quite variable. This model describes a variant form in which the three-Cys motif that binds the signature 4Fe-4S cluster takes the form Cx14CxxC, as in Burkholderia multivorans ATCC 17616. The crystal structure is known. 208 matched cddid_all.tbl CDD TIGR04509 TIGR04509 275302 mod_pep_NH_fam putative modified peptide. Members of this family average 110 residues in length, with strong N-terminal homology to both the nitrile hydratase (NH) alpha subunit and family TIGR03793 of NH-related ribosomally translated natural product precursors. A neighboring gene resembles SagB, the dehydrogenase of many thiazole and oxazole modified peptide systems, supporting the hypothesis that members of this family are post-translationally modified. 85 matched cddid_all.tbl CDD TIGR04510 TIGR04510 275303 mod_pep_cyc putative peptide modification system cyclase. Members of this family show homology to mononucleotidyl cyclases and to tetratricopeptide repeat (TPR) proteins. Members occur in next to two other markers of ribosomal peptide modification systems. One is a dehydrogenase related to SagB proteins from thiazole/oxazole modification systems. The other is the putative precursor, related to the nitrile hydratase-related leader peptide (NHLP) and nitrile hydratase alpha subunit families. These systems occur in many species of Xanthomonas and Stenotrophomonas, among others. 814 matched cddid_all.tbl CDD TIGR04511 TIGR04511 275304 SagB_rel_DH_2 putative peptide maturation dehydrogenase. Members resemble the peptide maturation dehydrogenase SagB of thiazole and oxazole modification systems, and occur in a what appears to be a new type of peptide modification system. One adjacent marker is a new type of nitrile hydratase alpha subunit-related putative precursor, TIGR04509, distantly related the NHLP leader peptide family TIGR03793. Another is a large protein, TIGR04510, with regions similar to adenylate cyclases and TPR proteins. 380 matched cddid_all.tbl CDD TIGR04512 TIGR04512 275305 Mycopla_NOT_gsn STREFT protein. Members of this family occur strictly in the genus Mycoplasma, average 1050 in length with little length variability, have an N-terminal signal sequence, and exhibit no detectable sequence similarity to any characterized protein. Up to four tandem copies occur in some Mycoplasma (e.g. M. putrefaciens KS1). Incorrect inclusion of a 57-amino acid stretch of one family member in pfam08178, for a helix-turn-helix transcriptional regulator in several E. coli phage, has caused many members of this family to be annotated, in error, as GnsA/GnsB family proteins. We suggest the name STREFT (Secreted Thousand Residue Frequently Tandem) protein as a distinctive name to spread and replace the incorrect GnsA/GnsB designation. [Unknown function, General] 1041 matched cddid_all.tbl CDD TIGR04513 TIGR04513 275306 VPAMP_CTERM VPAMP-CTERM protein sorting domain. This domain is found as the extreme C-terminal region of four extracellular protein (mostly protease) precursor sequences in Chthoniobacter flavus Ellin428, first representative sequenced from the Spartobacteria class of phylum Verrucomicrobia. This domain contains the cognate signal for one four exosortase family enzymes in the C. flavus genome, and coexists with the more common PEP-CTERM domain, found on more than 50 proteins. 28 matched cddid_all.tbl CDD TIGR04514 TIGR04514 275307 GWxTD_dom GWxTD domain. This domain, about 100 amino acids long, occurs in Actinobacteria and other little-studied Gram-negative bacteria, Sec-dependent proteins 300-800 in length. The domain is rich in aromatic residues, with Trp, Tyr, or Phe as the majority amino acid in ten of the twenty-four most-conserved residue positions. 105 matched cddid_all.tbl CDD TIGR04515 TIGR04515 275308 P450_rel_GT_act P450-derived glycosyltranferase activator. Members of this family resemble cytochrome P450 by homolog, but lack a critical heme-binding Cys residue. Members in general are encoded next to a glycosyltransferase gene in a natural products biosynthesis cluster, physically interact with it, and help the glycosyltransferase achieve high specificity while retaining high activity. Many members of this family assist in the attachment of a sugar moiety to a natural product such as a polyketide. 384 matched cddid_all.tbl CDD TIGR04516 TIGR04516 275309 glycosyl_450act glycosyltransferase, activator-dependent family. Many biosynthesis clusters for secondary metabolites feature a glycosyltransferase gene next to a P450 homolog, often with the P450 lacking a critical heme-binding Cys. These P540-derived sequences seem to be allosteric activators of glycosyltransferases such as the member of this family. This model describes a set of related glycosyltransferases, many of which can be recognized as activator-dependent from genomic context. 418 matched cddid_all.tbl CDD TIGR04517 TIGR04517 275310 rSAM_PoyD radical SAM family RiPP maturation amino acid epimerase. This model describes PoyD and its homologs. These are divergent putative radical SAM enzymes, with the classical CxxxCxxC motif but with few members approaching the cutoff score of pfam04055. PoyD appears responsible for catalyzing a unidirectional L-to-D epimerization of 18 the 48 residues in the core peptide of the first characterized polytheonamide. The RiPP (ribosomally translated natural product) precursor, and peptides encoded near many other members of this family, belong to the nitrile hydratase leader peptide (NHLP) family. 445 matched cddid_all.tbl CDD TIGR04518 TIGR04518 275311 ECF_S_folT_fam ECF transporter S component, folate family. Members of this model are the multiple membrane-spanning S (specificity) component of ECF (energy coupling factor) type uptake transporters. All seed members were found in the vicinity of the bifunctional enzyme folC, involved in making active cofactor from imported folate. However, some species have multiple members of this family, suggesting some diversity of function. [Transport and binding proteins, Unknown substrate] 162 matched cddid_all.tbl CDD TIGR04519 TIGR04519 275312 MoCo_extend_TAT MoCo/4Fe-4S cofactor protein extended Tat translocation domain. This model describes a forty-five residue domain in which the last six residues represent the start of a TAT (Twin-Arginine Translocation) sorting signal. TAT allows proteins already folded, with cofactor already bound, to transit the membrane and reach the periplasm with the ability to perform redox or other cofactor-dependent activities. TAT signals are not normally seen so far from a well-supported start site. Member proteins may all be mutually homologous, with both a molybdenum cofactor-binding domain and a 4Fe-4S dicluster-binding domain. 43 matched cddid_all.tbl CDD TIGR04520 TIGR04520 275313 ECF_ATPase_1 energy-coupling factor transporter ATPase. Members of this family are ATP-binding cassette (ABC) proteins by homology, but belong to energy coupling factor (ECF) transport systems. The architecture in general is two ATPase subunits (or a double-length fusion protein), a T component, and a substrate capture (S) component that is highly variable, and may be interchangeable in genomes with only one T component. This model identifies many but not examples of the upstream member of the pair of ECF ATPases in Firmicutes and Mollicutes. [Transport and binding proteins, Unknown substrate] 268 matched cddid_all.tbl CDD TIGR04521 TIGR04521 275314 ECF_ATPase_2 energy-coupling factor transporter ATPase. Members of this family are ATP-binding cassette (ABC) proteins by homology, but belong to energy coupling factor (ECF) transport systems. The architecture in general is two ATPase subunits (or a double-length fusion protein), a T component, and a substrate capture (S) component that is highly variable, and may be interchangeable in genomes with only one T component. This model identifies many but not examples of the downstream member of the pair of ECF ATPases in Firmicutes and Mollicutes. [Transport and binding proteins, Unknown substrate] 277 matched cddid_all.tbl CDD TIGR04522 TIGR04522 275315 EcfS_MSC_0063 putative energy coupling factor transporter S component, MSC_0063 family. This family of proteins is restricted to the Mollicutes (including Mycoplasma, Spiroplasma, and Ureaplasma). Members belong to a superfamily of multiple membrane-spanning proteins, among which those with assigned activities function as the S component (the specificity component) of ECF transporters. However, members fail to score better than the trusted cutoffs to previously built models for S component proteins (see pfam07155). [Transport and binding proteins, Unknown substrate] 151 matched cddid_all.tbl CDD TIGR04523 TIGR04523 275316 Mplasa_alph_rch helix-rich Mycoplasma protein. Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown. 745 matched cddid_all.tbl CDD TIGR04524 TIGR04524 275317 mycoplas_M_dom IgG-blocking virulence domain. This model defines a domain restricted to Mycoplasma and Ureaplasma proteins. Members include protein M of Mycoplasma genitalium, MG_281, a virulence protein that binds the IgG light chain to block the binding of antibody to antigen. The crystal structure of the protein M antibody-binding region is solved (PDB|4NZR), and includes this homology domain. Full-length homologs to MG_281 are known in a few other Mycoplasma species, but this model's seed alignment demonstrates distant homology to many additional proteins with a much wider distribution across the Mollicutes. Member proteins include paralogous families in some species, such as MCAP_0345, MCAP_0347, MCAP_0349, and MCAP_0351 in Mycoplasma capricolum. [Cellular processes, Pathogenesis] 251 matched cddid_all.tbl CDD TIGR04525 TIGR04525 275318 prot_M_MG281 IgG-blocking protein M. Members of this family, including MG_281 of Mycoplasma genitalium, bind conserved regions of the IgG light chain sequences, blocking IgG's normal function of antigen-specific binding. It is therefore an important virulence protein. Members of this family are found also in Mycoplasma pneumoniae, M. penetrans, M. gallisepticum, and M. iowae. Model TIGR04524 describes a region within this protein that is shared by many additional Mycoplasma and Ureaplasma proteins. [Cellular processes, Pathogenesis] 526 matched cddid_all.tbl CDD TIGR04526 TIGR04526 275319 predic_Ig_block putative immunoglobulin-blocking virulence protein. Members of this family are putative virulence proteins of Mycoplasma and Ureaplasma species. Members share a region of sequence similarity (see TIGR04524) with protein M, a Mycoplasma genitalium protein that binds a conserved light chain region of IgG and blocks its protective function of antigen-specific binding. The seed alignment for this model includes an N-terminal signal-anchor domain and a proline-rich linker domain, and a C-terminal extension, in addition to the protein M-like domain recognized by TIGR04524. [Cellular processes, Pathogenesis] 692 matched cddid_all.tbl CDD TIGR04527 TIGR04527 275320 mycoplas_twoTM two transmembrane protein. Members of this family are uncharacterized proteins from the genus Mycoplasma, typically about 260 amino acids long, with a hydrophobic predicted transmembrane alpha helix toward each end. Often two family members are encoded in tandem, e.g. MG_279 and MG_280 from Mycoplasma genitalium. 245 matched cddid_all.tbl CDD TIGR04528 TIGR04528 275321 acido_non_PQQ acido-empty-quinoprotein group A. Members of this family closely resemble quinoproteins and quinohemoproteins such as PQQ-dependent methanol, glucose, and shikimate dehydrogenases, but restricted to species of Acidobacteria unable to synthesize PQQ. Seven members occur in candidatus Solibacter usitatus Ellin6076, eleven in Acidobacteriaceae bacterium KBS 96, etc. Members have N-terminal signal sequences. They lack the pair of adjacent Cys residues, involved in electron transfer, typical for family TIGR03075, and they lack CxxCH motifs for cytochrome c-like heme-binding. What cofactor these paralogous families of enzymes might use is unclear. 491 matched cddid_all.tbl CDD TIGR04529 TIGR04529 275322 MTB_hemophore hemophore-related protein, Rv0203/Rv1174c family. Members of this family occur as paralogs in most Mycobacterium strains, including 2 in M. tuberculosis, 6 in M. avium, and 9 in M. smegmatis. Members have a cleaved N-terminal signal peptide and exactly two Cys residues in the mature protein, both at invariant positions. The best characterized member, Rv0203, is a hemophore, that is, a secreted polypeptide that binds heme and delivers it to a transport system for import. Hemophores are protein analogs of siderophores, natural products that chelate non-heme iron and deliver it to receptors for transport. The unrelated HasA family of hemophores has been described in Gram-negative bacteria such as Yersinia pestis and Pseudomonas aeruginosa. [Transport and binding proteins, Other] 77 matched cddid_all.tbl CDD TIGR04530 TIGR04530 275323 hemophoreRv0203 hemophore, mycobacterial-type. Members of this family, including Rv0203 from Mycobacterium tuberculosis, are secreted heme-binding proteins used in heme acquisition. Such proteins are called hemophores. Members have a cleavable N-terminal signal peptide, and a mature region just over 100 amino acids long with a pair of invariant Cys residues. An unrelated hemophore, HasA, occurs in Gram-negative pathogens such as Yersinia pestis. [Transport and binding proteins, Other] 113 matched cddid_all.tbl CDD TIGR04531 TIGR04531 275324 nonproteo_OH putative nonproteinogenic amino acid hydroxylase. This extremely rare protein family, a branch of the 2-oxoglutarate dependent oxygenase family related to proline 3-hydroxylase, appears only in natural product biosynthetic clusters that include nonribosomal peptide synthases. One members is PlyP from the polyoxypeptin A cluster, suggested to hydroxylate 3-methylproline. Another, GetF from the GE81112 biosynthetic gene cluster, is a proposed to hydroxylate pipecolic acid. 277 matched cddid_all.tbl CDD TIGR04532 TIGR04532 275325 PT_fungal_PKS iterative type I PKS product template domain. Sequences found by this model are the so-called product template (PT) domain of various fungal iterative type I polyketide synthases. This domain resembles pfam14765, designated polyketide synthase dehydratase by Pfam, but members of that family are primarily bacterial, where type I PKS are predominantly modular, not iterative. The dehydratase active site residues well-conserved in pfam14765 (His in the first hot dog domain, Asp in the second hot dog domain) seem well conserved in this family also. 324 matched cddid_all.tbl CDD TIGR04533 TIGR04533 275326 cyanosortB_assc cyanoexosortase B-associated protein. Members of this protein family are found exclusively in the Cyanobacteria, usually encoded next to a gene encoding cyanoexosortase B (TIGR04156). This relationship resembles the association of the unrelated protein family TIGR04153 with cyanoexosortase A (TIGR03763), and of most exosortases with EpsI. 221 matched cddid_all.tbl CDD TIGR04534 TIGR04534 275327 ELWxxDGT_rpt ELWxxDGT repeat. This model describes protein repeat with a well-conserved motif ELWxxDGT, and a periodicity of about 48. A single protein may have as many as 18 repeats. It may consist nearly entirely of this repeat, or may have other repeats as well (e.g. hyalin repeat). It is most common in the Deltaproteobacteria. 47 matched cddid_all.tbl CDD TIGR04535 TIGR04535 275328 ferrit_encaps ferritin-like protein. Two families of proteins are known to be encoded, with some regularity, next to the gene for encapsulin (pfam04454), with surrounds the target protein to form a prokaryotic proteinaceous organelle. One is the family of enzymes that includes Dyp-type peroxidases. The other is this family, with a resemblance to bacterioferritins. Encapsulin-associated forms of the proteins in these two families have a necessary C-terminal motif that resembles DGSL[SGN]IGSL[KR]. Members of this family that include the last columns of the model in the hit region (and are encoded next to the encapsulin gene) should be designated encapsulin-associated ferritin-like protein. 113 matched cddid_all.tbl CDD TIGR04536 TIGR04536 275329 geobac_encap encapsulated protein. Members of this family are lineage-restricted uncharacterized proteins found mostly in Brevibacillus and Geobacillus. Members are encoded next to the gene for encapsulin (which once was called a bacteriocin), and have the C-terminal motif for associating with encapsulin. [Unknown function, Enzymes of unknown specificity] 194 matched cddid_all.tbl CDD TIGR04537 TIGR04537 275330 encap_target encapsulation C-terminal sorting signal. This model describes a diverse region of extremely small size (11 residues), so unavoidably there are both false-positives and false-negatives. All true hits should occur in proteins encoded next to an encapsulating protein (see pfam04454), and should occur near the extreme C-terminus. Families previously known to have this domain on some members to mediate encapsulation include dye-decolorizing peroxidases and a ferritin-like protein, but (as this model helps show) there are others, including some hemerythrin family proteins and novel family TIGR04536. 11 matched cddid_all.tbl CDD TIGR04538 TIGR04538 275331 P450_cycloAA_1 cytochrome P450, cyclodipeptide synthase-associated. Members of this subfamily are cytochrome P450 enzymes that occur next to tRNA-dependent cyclodipeptide synthases. This group does NOT include CYP121 (Rv2275) from Mycobacterium tuberculosis, adjacent to the cyclodityrosine synthetase Rv2276. 395 matched cddid_all.tbl CDD TIGR04539 TIGR04539 275332 tRNA_cyclodipep tRNA-dependent cyclodipeptide synthase. Members of this family take two aminoacylated tRNA molecules and produce a cyclic dipeptide with two peptide bonds. This enzyme therefore produces a type of nonribosomal peptide, but by a mechanism entirely different from the typical non-ribosomal peptide synthase (NRPS) that relies on adenylation to activate amino acids. Three characterized members of this family are the cyclodityrosine synthase of Mycobacterium tuberculosis (an essential gene), a cyclo(L-Phe-L-Leu) synthase from Streptomyces noursei involved in natural product biosynthesis, and cyclodileucine synthase YvmC from Bacillus licheniformis. Many cyclodipeptide synthases are found next to a cytochrome P450 that further modifies the product. 220 matched cddid_all.tbl CDD TIGR04540 TIGR04540 275333 CLB_0814_fam conserved hypothetical protein. Members of this family are conserved hypothetical proteins in a narrow range of species. In Clostridium botulinum A ATCC 19397, the gene occurs immediately after a five gene operon for biosynthesis of the natural product bacimethrin, a thiamin antivitamin antibiotic. 73 matched cddid_all.tbl CDD TIGR04541 TIGR04541 275334 thiaminase_BcmE thiamine pyridinylase. Members of this family are thiamine pyridinylase (EC 2.5.1.2), also called thiaminase I. Most examples of this secreted, thiamine-degrading enzyme are encoded with a cluster for biosynthesis of the thiamine antivitamin bacimethrin. [Cellular processes, Biosynthesis of natural products] 381 matched cddid_all.tbl CDD TIGR04542 TIGR04542 275335 GMC_mycofac_2 GMC family mycofactocin-associated oxidreductase. This model describes a set of dehydrogenases belonging to the glucose-methanol-choline oxidoreductase (GMC oxidoreductase) family. Members of the present family are restricted to the bacterial genus Gordonia, and seem to replace the related family TIGR03970, which occurs in Actinobacteria generally but not in the genus Gordonia. Members of both this family and TIGR03970 are associated with the mycofactocin biosynthesis operon in Actinobacteria. [Unknown function, Enzymes of unknown specificity] 425 matched cddid_all.tbl CDD TIGR04543 TIGR04543 275336 ketoArg_3Met 2-ketoarginine methyltransferase. This SAM-dependent C-methyltransferase performs the middle step of a three step conversion from arginine to beta-methylarginine. It performs a C-methylation at position 3 of 5-guanidino-2-oxopentanoic acid (keto-arginine). An aminotransferase converts arginine to 5-guanidino-2-oxopentanoic acid, and later converts 5-guanidino-3-methyl-2-oxopentanoic acid to beta-methylarginine. 331 matched cddid_all.tbl CDD TIGR04544 TIGR04544 275337 3metArgNH2trans beta-methylarginine biosynthesis bifunctional aminotransferase. Members of this family are the bifunctional aminotransferase that catalyzes the first and third steps in the three-step conversion of arginine to beta-methylarginine. It first converts arginine to 2-ketoarginine, then converts 3-methyl-2-ketoarginine to 3-methylarginine. All members of the seed alignment are encoded next to a 2-ketoarginine methyltransferase (EC 2.1.1.243). 366 matched cddid_all.tbl CDD TIGR04545 TIGR04545 275338 rSAM_ahbD_hemeb heme b synthase. Members of this family are AhbD (alternative heme biosynthetic protein D), a radical SAM enzyme in sulfate-reducing bacteria and methanogens that performs the last decarboxylations to synthesize heme b from Fe-coproporphyrin III. Members include DVU_0855, previously included in error in TIGR04055, the NirJ2 family thought to be involved in heme d1 biosynthesis. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 339 matched cddid_all.tbl CDD TIGR04546 TIGR04546 275339 rSAM_ahbC_deAc 12,18-didecarboxysiroheme deacetylase. This model describes one of a pair of radical SAM enzymes involved in the alternative heme biosynthesis (ahb) pathway for heme b biosynthesis from siroheme. This anaerobic pathway occurs in sulfate-reducing bacteria and methanogens. A very similar pair of radical SAM enzymes (TIGR04054, TIGR04055) is involved in heme d1 biosynthesis in species such as Heliobacillus mobilis and Heliophilum fasciatum. [Biosynthesis of cofactors, prosthetic groups, and carriers, Heme, porphyrin, and cobalamin] 390 matched cddid_all.tbl CDD TIGR04547 TIGR04547 275340 Mollicu_LP MOLPALP family lipoprotein. Members of this family are surface lipoproteins, about 900 amino acids long on average, found only in the Mollicutes (Mycoplasma, Entomoplasma, Acholeplasma, Mesoplasma, Spiroplasma). Paralogs occur, such as MCAP_0360, MCAP_0361, and MCAP_0362 in Mycoplasma capricolum. This family shares significant N-terminal sequence similarity with STREFT (Secreted Thousand Residue Frequently Tandem), described by model TIGR04512; several members of the STREFT family have been misannotated as GnsA/GnsB family proteins. For proteins in this family, we suggest the name MOLPALP (Mollicutes Paralogous Lipoprotein) family lipoprotein [Cell envelope, Surface structures] 805 matched cddid_all.tbl CDD TIGR04548 TIGR04548 275341 DnaD_Mollicutes DnaD family protein, Mollicutes type. This model describes the full length of a family of proteins in the Mollicutes (Mycoplasma, Spiroplasma, Mesoplasma, etc.) homologous to the N-terminal region of DnaD from Bacillus subtilis. [DNA metabolism, DNA replication, recombination, and repair] 178 matched cddid_all.tbl CDD TIGR04549 TIGR04549 275342 LP_HExxH_w_tonB substrate import-associated zinc metallohydrolase lipoprotein. Members of this family are lipoproteins with the typical zinc metallohydrolase HExxH motif and additional similarities to a better-documented zinc peptidase family, pfam06167. The seed alignment begins immediately after the lipoprotein motif Cys residue. Up to five members of this protein family occur per genome, in the context of certain gene pairs related to RagA and RagB, or to SusC and SusD. Those gene pairs, like the present family, are restricted to the Bacteriodetes, may number up to 100 pairs per genome, and are linked to TonB-dependent uptake of biopolymer-derived nutrients such as glycans. A possible function for this lipoprotein is to hydrolyse larger molecules to prepare substrates for import and utilization. [Unknown function, Enzymes of unknown specificity] 261 matched cddid_all.tbl CDD TIGR04550 TIGR04550 275343 sMetMonox_MmoD soluble methane monooxygenase-binding protein MmoD. Members of this family are MmoD, a protein that binds the soluble (as opposed to the membrane-bound, copper-rich, particulate) methane monooxygenase and may regulate its activity. Recent work suggests that MmoD, together with methanobactin, acts a copper switch to regulate which enzyme form is produced. 64 matched cddid_all.tbl CDD TIGR04551 TIGR04551 275344 TIGR04551 TIGR04551 family protein. Members of this family are proteins of unknown function, about 620 amino acids in length, and universal in but restricted to the Myxococcales, an order within the Deltaproteobacteria with at least 15 sequenced genomes as of 8/2014. The most closely related homologs outside the Myxococcales show localized homology only and display sharply lower scores. Relatively few protein families (roughly 20) could be built to have a comparable restriction to the Myxococcales. The putative protein sorting signal MYXO-CTERM (TIGR03901) appears so far universal in but restricted to the Myxococcales, making the present family a candidate to be involved in recognizing and processing proteins with that signal. 523 matched cddid_all.tbl CDD TIGR04552 TIGR04552 275345 TIGR04552 TIGR04552 family protein. Members of this family are bacterial proteins, roughly 400 amino acids in length. Most members belong to the Deltaproteobacteria. All members of the Myxococcales, and order withing the Deltaproteobacteria, have a member. The arrangement of conserved residues into invariant motifs suggests enzymatic activity. The function is unknown. 353 matched cddid_all.tbl CDD TIGR04553 TIGR04553 275346 ABC_peri_selen putative selenate ABC transporter periplasmic binding protein. Members of this family ABC transporter periplasmic binding proteins and represent one clade within a larger family that includes phosphate, phosphite, and phosphonate transporters. All members of the seed alignment occur near a gene for SelD, the selenium-activating protein needed to make selenocysteine or selenouridine. Context therefore suggests members should be able to transport selenate, although transporting other substrates as well (e.g. phosphonates) is possible. This model has no overlap with TIGR03431, whose members are found regularly with phosphonate catabolism operons. 266 matched cddid_all.tbl CDD TIGR04554 TIGR04554 275347 3TM_mycoplas three transmembrane helix protein. Members of this rare family are small, highly hydrophobic, and restricted so far to the genus Mycoplasma, where it appears not be be essential. All members have three hydrophobic transmembrane helical segments. 105 matched cddid_all.tbl CDD TIGR04555 TIGR04555 275348 sulfite_DH_soxC sulfite dehydrogenase. Members of this family are the sulfite dehydrogenase SoxC. All members have a twin-arginine translocation (TAT) signal for secretion of proteins with bound cofactor across the plasma membrane. 408 matched cddid_all.tbl CDD TIGR04556 TIGR04556 275349 PKS_assoc polyketide synthase-associated domain. This model describes a rare domain found as the N-terminal region of a number of dinoflagellate-specific proteins that resemble type I polyketide synthases. 228 matched cddid_all.tbl CDD TIGR04557 TIGR04557 275350 fuse_rel_SoxYZ quinoprotein dehydrogenase-associated SoxYZ-like carrier. Members of this family are fusion proteins, with the N-terminal region similar to the sulfur oxidation protein SoxY (TIGR04488) and the C-terminal region similar to sulfur oxidation protein SoxZ (TIGR04490). Members occur exclusively in species with PQQ-dependent enzymes that have a Cys-Cys motif (TIGR03075) for electron transfer to c550 family cytochrome. By homology to the sulfur moiety-binding subunit SoxY, we predict the conserved Cys in the Gly-Gly-Cys motif binds some unknown adduct. 225 matched cddid_all.tbl CDD TIGR04558 TIGR04558 275351 SoxH_rel_PQQ_1 quinoprotein relay system zinc metallohydrolase 1. By homology, members are Zn metallohydrolases in the same family as the SoxH protein associated with sulfate metabolism, Bacillus cereus beta-lactamase II (see PDB:1bc2), and, more distantly, hydroxyacylglutathione hydrolase (glyoxalase II). All members occur in genomes with both PQQ biosynthesis and a PQQ-dependent (quinoprotein) dehydrogenase that has a motif of two consecutive Cys residues (see TIGR03075). The Cys-Cys motif is associated with electron transfer by specialized cytochromes such as c551. All these genomes also include a fusion protein (TIGR04557) whose domains resemble SoxY and SoxZ from thiosulfate oxidation. A conserved Cys in this fusion protein aligns to the Cys residue in SoxY that carries sulfur cycle intermediates. In many genomes, the genes for PQQ biosynthesis enzymes, PQQ-dependent enzymes, their associated cytochromes, and members of this family are clustered. Note that one to three closely related Zn metallohydrolases may occur; this family represents a specific clade among them. [Unknown function, Enzymes of unknown specificity] 285 matched cddid_all.tbl CDD TIGR04559 TIGR04559 275352 SoxH_rel_PQQ_2 quinoprotein relay system zinc metallohydrolase 2. By homology, members are Zn metallohydrolases in the same family as the SoxH protein associated with sulfate metabolism, Bacillus cereus beta-lactamase II (see PDB:1bc2), and, more distantly, hydroxyacylglutathione hydrolase (glyoxalase II). All members occur in genomes with both PQQ biosynthesis and a PQQ-dependent (quinoprotein) dehydrogenase that has a motif of two consecutive Cys residues (see TIGR03075). The Cys-Cys motif is associated with electron transfer by specialized cytochromes such as c551. All these genomes also include a fusion protein (TIGR04557) whose domains resemble SoxY and SoxZ from thiosulfate oxidation. A conserved Cys in this fusion protein aligns to the Cys residue in SoxY that carries sulfur cycle intermediates. In many genomes, the genes for PQQ biosynthesis enzymes, PQQ-dependent enzymes, their associated cytochromes, and members of this family are clustered. Note that one to three closely related Zn metallohydrolases may occur; this family represents a specific clade among them. Some members of this family have a short additional N-terminal domain with four conserved Cys residues. [Unknown function, Enzymes of unknown specificity] 283 matched cddid_all.tbl CDD TIGR04560 TIGR04560 275353 ribo_THX ribosomal small subunit protein bTHX. Members of this protein are the lineage-specific bacterial ribosomal small subunit proteint bTHX (previously THX), originally shown to exist in the genus Thermus. The protein is conserved for the first 26 amino acids, past which some members continue with additional sequence, often repetitive or low-complexity. This model also finds eukaryotic organelle forms, which have additional N-terminal transit peptides. [Protein synthesis, Ribosomal proteins: synthesis and modification] 26 matched cddid_all.tbl CDD TIGR04561 TIGR04561 275354 membra_charge integral membrane protein. Members of this protein are short (about 85-residue), low-complexity sequences of unknown function, with a highly hydrophobic N-terminal region of about 40 amino acids followed by a charged (Asp, Glu, Lys, and Arg-rich), sometimes repetitive C-terminal region. Members occur exclusively among the Mollicutes (Mycoplasma, Mesoplasma, Acholeplasma, Spiroplasma, Entomoplasma). The gene neighborhood of this protein is not conserved. 82 matched cddid_all.tbl CDD TIGR04562 TIGR04562 275355 TIGR04562 TIGR04562 family protein. Members of this family are proteins of unknown function, about 400 amino acids in length. Members are universal among the Myxococcales (a branch of the Deltaproteobacteria) and occur sporadically elsewhere. [Unknown function, General] 355 matched cddid_all.tbl CDD TIGR04563 TIGR04563 275356 TIGR04563 MXAN_4361/MXAN_4362 family small protein. Members of this family are small proteins that appears to be restricted to and yet universal in the Myxococcales. The function is unknown. Members include two tandem loci in Myxococcus xanthus DK 1622, MXAN_4361 and MXAN_4362, although members are not tandem in other Myxococcales. 53 matched cddid_all.tbl CDD TIGR04564 TIGR04564 275357 Synergist_CTERM Synergist-CTERM protein sorting domain. This model identifies a C-terminal domain of about 27 residues whose features are 1) a short Gly/Ser-rich region that ends in an invariant Gly-Cys motif, 2) a highly hydrophobic probable transmembrane alpha helix with a nearly invariant Pro near the end, and 3) a cluster of basic residues (Arg, Lys), and then the end of the protein. This domain occurs, so far, only in species of Synergistetes (Dethiosulfovibrio peptidovorans, Aminiphilus circumscriptus, Aminomonas paucivorans, Fretibacterium fastidiosum, Cloacibacillus evryensis, Synergistes jonesii, etc). This region closely resembles the MXYO-CTERM region of the Myxococcales, a division of the Deltaproteobacteria (see TIGR03901), but that domain lacks the the conserved Pro, frequently has two Cys residues instead of one, and most importantly, has a spacer region separating the Gly-Cys motif from the transmembrane segment. As with MYXO-CTERM, the enzyme presumed to recognize and cleave the sorting signal is not known. The lack of a spacer region between motif and TM segment suggests the presumed protease is located largely within the membrane, like rhombosortase and archaeosortase, rather than merely tethered to it like sortase. 26 matched cddid_all.tbl CDD TIGR04565 TIGR04565 275358 OMP_myx_plus outer membrane beta-barrel protein. Members of this family are outer membrane beta-barrel proteins, as inferred by distant homologies to other families (e.g. pfam13505) and by the concentration of aromatic residues, especially Phe, in the OMP signal region, which is flush with the C-terminus in some members, but followed by a few residues in others. Members have variable insertions and deletions, affecting scores, so this model does not cleanly separate all members from all non-members. Members are common in the Myxococcales, with five occurring in Myxococcus xanthus DK 1622. 157 matched cddid_all.tbl CDD TIGR04566 TIGR04566 275359 myxo_TraA_Nterm outer membrane exchange protein TraA, N-terminal region. In Myxococcus xanthus, the protein pair TraA (MXAN_6895) and TraB (MXAN_6898) are required for contact-dependent exchange of outer membrane proteins. The C-terminal half of TrA consists largely of Cys-rich tandem repeats. This model describes the N-terminal region of TraA, and related protein MXAN_4924. This region is suggested to be similar to the lectin PA14. Members of this family are restricted to a subset of the Myxococcales, and so have a narrower species distribution than the MYXO-CTERM putative protein sorting signal (TIGR03901), which is universal in the Myxococcales. Note that TIGR04201 matches at least seven repeats in the C-terminal region of TraA. T [Protein fate, Protein and peptide secretion and trafficking] 240 matched cddid_all.tbl CDD TIGR04567 TIGR04567 275360 RNAP_delt_lowGC DNA-directed RNA polymerase delta subunit. Members of this family are the RNA polymerase delta subunit, as found in the Firmicutes and the Mollicutes. All members of the seed alignment have an extended C-terminal low-complexity region, consisting largely of Asp and Glu, that is not included in the model. Proteins giving borderline scores should be checked to confirm a similar acidic C-terminal domain. [Transcription, DNA-dependent RNA polymerase] 83 matched cddid_all.tbl CDD TIGR04568 TIGR04568 275361 arch_SelU_Nterm selenouridine synthase, SelU N-terminal-like subunit. This protein is involved in biosynthesis of a selenonucleotide, probably 2-selenouridine, in tRNA of some archaea, such as Methanococcus maripaludis. This protein resembles the N-terminal region of bacterial SelU, and its partner protein resembles the C-terminal region. [Protein synthesis, tRNA and rRNA base modification] 215 matched cddid_all.tbl CDD TIGR04569 TIGR04569 275362 arch_SelU_Cterm selenouridine synthase, SelU C-terminal-like subunit. This protein is involved in biosynthesis of a selenonucleotide, probably 2-selenouridine, in tRNA of some archaea, such as Methanococcus maripaludis. This protein resembles the C-terminal region of bacterial SelU, and its partner protein resembles the N-terminal region. [Protein synthesis, tRNA and rRNA base modification] 217 matched cddid_all.tbl CDD TIGR04570 TIGR04570 275363 mollicut_2TM small integral membrane protein. Members of this extremely rare protein family occur in Mycoplasma mycoides and two species of Spiroplasma. The protein is small and hydrophobic with two predicted transmembrane (TM) regions. [Unknown function, General] 87 matched cddid_all.tbl CDD TIGR04571 TIGR04571 275364 LmtA_Leptospira lipid A Kdo2 1-phosphate O-methyltransferase. This family describes LmtA, which methylates a phosphate on the Kdo2 sugar of lipid A. The model is classified as exception (more specific than equivalog) to reflect that its scope is limited to the genus Leptospira, whereas homologs with matching activity might exist more broadly. Members of this family belong to the broader family of pfam04191, phospholipid methyltransferase, which includes a characterized yeast enzyme that acts on a range of unsaturated phospholipids. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides] 252 matched cddid_all.tbl CDD cd00001 cd00001 237975 PTS_IIB_man PTS_IIB, PTS system, Mannose/sorbose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. The active site histidine receives a phosphate group from the IIA subunit and transfers it to the substrate. 151 matched cddid_all.tbl CDD cd00002 cd00002 237976 YbaK_deacylase This CD includes cysteinyl-tRNA(Pro) deacylases from Haemophilus influenzae and Escherichia coli and other related bacterial proteins. These trans-acting, single-domain proteins are homologs of ProX and also the cis-acting prolyl-tRNA synthetase (ProRS) inserted (INS) editing domain. The bacterial amino acid trans-editing enzyme YbaK is a deacylase that hydrolyzes cysteinyl-tRNA(Pro)'s mischarged by prolyl-tRNA synthetase. YbaK also hydrolyzes glycyl-tRNA's, alanyl-tRNA's, seryl-tRNA's, and prolyl-tRNA's. YbaK is homologous to the INS domain of prolyl-tRNA synthetase (ProRS) as well as the trans-editing enzyme ProX of Aeropyrum pernix which hydrolyzes alanyl-tRNA's and glycyl-tRNA's. 152 matched cddid_all.tbl CDD cd00003 cd00003 237977 PNPsynthase Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in the biosynthesis of vitamin B6. PNP synthase, a homooctameric enzyme, catalyzes the final step in PNP biosynthesis, the condensation of 1-amino-acetone 3-phosphate and 1-deoxy-D-xylulose 5-phosphate. PNP synthase adopts a TIM barrel topology, intersubunit contacts are mediated by three ''extra'' helices, generating a tetramer of symmetric dimers with shared active sites; the open state has been proposed to accept substrates and to release products, while most of the catalytic events are likely to occur in the closed state; a hydrophilic channel running through the center of the barrel was identified as the essential structural feature that enables PNP synthase to release water molecules produced during the reaction from the closed, solvent-shielded active site. 234 matched cddid_all.tbl CDD cd00004 cd00004 320674 Sortase Sortase domain. Sortases are cysteine transpeptidases, mainly found in Gram-positive bacteria, which either anchor surface proteins to peptidoglycans of the bacterial cell wall envelope or link proteins together to form pili by working alone, or in concert with other enzymes. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. Sortases are grouped into different classes based on sequence, membrane topology, genomic positioning, and cleavage site preference. The different classes are called class A to F sortases. Most Gram-positive bacteria contain more than one sortase and it is thought that the different sortases attach different surface protein classes. The typical eight-stranded beta-barrel fold is observed in all known sortases, along with the conserved catalytic triad consisting of cysteine, histidine and arginine residues. Some sortases contain an N-terminal signal peptide only and the C-terminus serves as a membrane anchor, which represents a type I membrane topology, with the N-terminal enzymatic portion projecting towards the bacterial surface and the C-terminal end residing in the cytoplasm. Other sortases adopt a type II membrane topology, with the N-terminal hydrophobic segment inside the cytoplasm and the C-terminal enzymatic portion located across the plasma membrane. The N-terminus either functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring. Sortases are also present in some Gram-negative and Archaebacterial species, but the functions of these enzymes are unknown. 125 matched cddid_all.tbl CDD cd00005 cd00005 187674 CBM9_like_1 DOMON-like type 9 carbohydrate binding module of xylanases. Family 9 carbohydrate-binding modules (CBM9) play a role in the microbial degradation of cellulose and hemicellulose (materials found in plants). The domain has previously been called cellulose-binding domain. The polysaccharide binding sites of CBMs with available 3D structure have been found to be either flat surfaces with interactions formed by predominantly aromatic residues (tryptophan and tyrosine), or extended shallow grooves. The CBM9 domain frequently occurs in tandem repeats; members found in this subfamily typically co-occur with glycosyl hydrolase family 10 domains and are annotated as endo-1,4-beta-xylanases. CBM9 from Thermotoga maritima xylanase 10A is reported to have specificity for polysaccharide reducing ends. 185 matched cddid_all.tbl CDD cd00006 cd00006 237978 PTS_IIA_man PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. IIA subunits receive phosphoryl groups from HPr and transfer them to IIB subunits, which in turn phosphorylate the substrate. 122 matched cddid_all.tbl CDD cd00008 cd00008 350199 PIN_53EXO-like FEN-like PIN domains of the 5'-3' exonucleases of DNA polymerase I, bacteriophage T4 RNase H and T5-5' nucleases, and homologs. PIN (PilT N terminus) domains of the 5'-3' exonucleases (53EXO) of multi-domain DNA polymerase I and single domain protein homologs, as well as, the PIN domains of bacteriophage T5-5'nuclease (T5FEN or 5'-3'exonuclease), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar nucleases are included in this family. The 53EXO of DNA polymerase I recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3'exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. These nucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 158 matched cddid_all.tbl CDD cd00009 cd00009 99707 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases. 151 matched cddid_all.tbl CDD cd00010 cd00010 237980 AAI_LTSS AAI_LTSS: Alpha-Amylase Inhibitors (AAI), Lipid Transfer (LT) and Seed Storage (SS) Protein family; a protein family unique to higher plants that includes cereal-type alpha-amylase inhibitors, lipid transfer proteins, seed storage proteins, and similar proteins. Proteins in this family are known to play important roles, in defending plants from insects and pathogens, lipid transport between intracellular membranes, and nutrient storage. Many proteins of this family have been identified as allergens in humans. These proteins contain a common pattern of eight cysteines that form four disulfide bridges. 63 matched cddid_all.tbl CDD cd00011 cd00011 153270 BAR_Arfaptin_like The Bin/Amphiphysin/Rvs (BAR) domain of Arfaptin-like proteins, a dimerization module that binds and bends membranes. The BAR domain of Arfaptin-like proteins, also called the Arfaptin domain, is a dimerization, lipid binding and curvature sensing module present in Arfaptins, PICK1, ICA69, and similar proteins. Arfaptins are ubiquitously expressed proteins implicated in mediating cross-talk between Rac, a member of the Rho family GTPases, and Arf (ADP-ribosylation factor) small GTPases. Arfaptins bind to GTP-bound Arf1, Arf5, and Arf6, with strongest binding to GTP-Arf1. Arfaptins also binds to Rac-GTP and Rac-GDP with similar affinities. The Arfs are thought to bind to the same surface as Rac, and their binding is mutually exclusive. Protein Interacting with C Kinase 1 (PICK1) plays a key role in the trafficking of AMPA receptors, which are critical for regulating synaptic strength and may be important in cellular processes involved in learning and memory. Islet cell autoantigen 69-kDa (ICA69) is a diabetes-associated autoantigen that is involved in membrane trafficking at the Golgi complex in neurosecretory cells. ICA69 associates with PICK1 through their BAR domains to form a heterodimer which is involved in regulating the synaptic targeting and surface expression of AMPA receptors. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 203 matched cddid_all.tbl CDD cd00012 cd00012 466786 ASKHA_ATPase-like ATPase-like domain of the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily. The ASKHA superfamily, also known as actin-like ATPase domain superfamily, includes acetate and sugar kinases, heat-shock cognate 70 (Hsp70) and actin family proteins. They either function as conformational hydrolases (e.g. Hsp70, actin) that perform simple ATP hydrolysis, or as metabolite kinases (e.g. glycerol kinase) that catalyze the transfer of a phosphoryl group from ATP to their cognate substrates. Both activities depend on the presence of specific metal cations. ASKHA superfamily members share a common core fold that includes an actin-like ATPase domain consisting of two subdomains (denoted I & II) with highly similar ribonuclease (RNase) H-like folds. The fold of each subdomain is characterized by a central five strand beta-sheet and flanking alpha-helices. The two subdomains form an active site cleft in which ATP binds at the bottom. Another common feature of ASKHA superfamily members is the coupling of phosphoryl-group transfer to conformational rearrangement, leading to domain closure. Substrate binding triggers protein motion. 135 matched cddid_all.tbl CDD cd00013 cd00013 200435 ADF_gelsolin Actin depolymerization factor/cofilin- and gelsolin-like domains. Actin depolymerization factor/cofilin-like domains are present in a family of essential eukaryotic actin regulatory proteins; these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments. 97 matched cddid_all.tbl CDD cd00014 cd00014 409031 CH_SF calponin homology (CH) domain superfamily. CH domains are actin filament (F-actin) binding motifs, which may be present as a single copy or in tandem repeats (which increase binding affinity). They either function as autonomous actin binding motifs or serve a regulatory function. CH domains are found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, as well as proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav). 103 matched cddid_all.tbl CDD cd00015 cd00015 237982 ALBUMIN Albumin domain, contains five or six internal disulphide bonds; albuminoid superfamily includes alpha-fetoprotein which binds various cations, fatty acids and bilirubin; vitamin D-binding protein which binds to vitamin D, its metabolites, and fatty acids; alpha-albumin which binds water, cations (such as Ca2+, Na+ and K+), fatty acids, hormones, bilirubin and drugs; and afamin of which little is known; these belong to a multigene family with highly conserved intron/exon organization and encoded protein structures; evolutionary comparisons strongly support vitamin D-binding protein as the original gene in this group with subsequent local duplications generating the remaining genes in the cluster 185 matched cddid_all.tbl CDD cd00016 cd00016 293732 ALP_like alkaline phosphatases and sulfatases. This family includes alkaline phosphatases and sulfatases. Alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH. Alkaline phosphatase exists as a dimer, each monomer binding 2 zinc atoms and one magnesium atom, which are essential for enzymatic activity. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. Both alkaline phosphatase and sulfatase are essential for human metabolism. Deficiency of individual enzyme cause genetic diseases. 237 matched cddid_all.tbl CDD cd00017 cd00017 237984 ANATO Anaphylatoxin homologous domain; C3a, C4a and C5a anaphylatoxins are protein fragments generated enzymatically in serum during activation of complement molecules C3, C4, and C5. They induce smooth muscle contraction. These fragments are homologous to repeats in fibulins. 70 matched cddid_all.tbl CDD cd00018 cd00018 237985 AP2 DNA-binding domain found in transcription regulators in plants such as APETALA2 and EREBP (ethylene responsive element binding protein). In EREBPs the domain specifically binds to the 11bp GCC box of the ethylene response element (ERE), a promotor element essential for ethylene responsiveness. EREBPs and the C-repeat binding factor CBF1, which is involved in stress response, contain a single copy of the AP2 domain. APETALA2-like proteins, which play a role in plant development contain two copies. 61 matched cddid_all.tbl CDD cd00019 cd00019 237986 AP2Ec AP endonuclease family 2; These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites; the alignment also contains hexulose-6-phosphate isomerases, enzymes that catalyze the epimerization of D-arabino-6-hexulose 3-phosphate to D-fructose 6-phosphate, via cleaving the phosphoesterbond with the sugar. 279 matched cddid_all.tbl CDD cd00021 cd00021 380813 Bbox_SF B-box-type zinc finger superfamily. The B-box-type zinc finger is a short zinc binding domain of around 40 amino acid residues in length. It has been found in transcription factors, ribonucleoproteins and proto-oncoproteins, such as in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). The B-box-type zinc finger often presents in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interactions. Based on different consensus sequences and the spacing of the 7-8 zinc-binding residues, B-box-type zinc fingers can be divided into two groups, type 1 (Bbox1: C6H2) and type 2 (Bbox2: CHC3H2). 39 matched cddid_all.tbl CDD cd00022 cd00022 237989 BIR Baculoviral inhibition of apoptosis protein repeat domain; Found in inhibitors of apoptosis proteins (IAPs) and other proteins. In higher eukaryotes, BIR domains inhibit apoptosis by acting as direct inhibitors of the caspase family of protease enzymes. In yeast, BIR domains are involved in regulating cytokinesis. This novel fold is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues and resembles a classical zinc finger. 69 matched cddid_all.tbl CDD cd00023 cd00023 237990 BBI Bowman-Birk type proteinase inhibitor (BBI); family of plant serine protease inhibitors that block trypsin or chymotrypsin.They are either single-headed (one reactive site, one inactive site, present mainly in monocotyledonous seeds) or double-headed (two reactive sites, present mainly in dicotyledonous seeds). 55 matched cddid_all.tbl CDD cd00024 cd00024 349274 CD_CSD CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains. Members of this group are chromodomains or chromo shadow domains; these are SH3-fold-beta-barrel domains of the chromo-like superfamily. Chromodomains lack the first strand of the SH3-fold-beta-barrel, this first strand is altered by insertion in the chromo shadow domains. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. Chromodomain-containing proteins include: i) those having an N-terminal chromodomain followed by a related chromo shadow domain, such as Drosophila and human heterochromatin protein Su(var)205 (HP1), and mammalian modifier 1 and 2; ii) those having a single chromodomain, such as Drosophila protein Polycomb (Pc), mammalian modifier 3, human Mi-2 autoantigen, and several yeast and Caenorhabditis elegans proteins of unknown function; iii) those having paired tandem chromodomains, such as mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1; (iv) and elongation factor eEF3, a member of the ATP-binding cassette (ABC) family of proteins, that serves an essential function in the translation cycle of fungi. eEF3 is a soluble factor lacking a transmembrane domain and having two ABC domains arranged in tandem, with a unique chromodomain inserted within the ABC2 domain. 50 matched cddid_all.tbl CDD cd00025 cd00025 237992 BPI1 BPI/LBP/CETP N-terminal domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) N-terminal domain; binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria.; Apolar pockets on the concave surface bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of lipopolysaccharide. 223 matched cddid_all.tbl CDD cd00026 cd00026 237993 BPI2 BPI/LBP/CETP C-terminal domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) C-terminal domain; binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria.; Apolar pockets on the concave surface bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of lipopolysaccharide. 200 matched cddid_all.tbl CDD cd00027 cd00027 349339 BRCT C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains. The BRCT (BRCA1 C-terminus) domain is found within many DNA damage repair and cell cycle checkpoint proteins. BRCT domains interact with each other forming homo/hetero BRCT multimers, but are also involved in BRCT-non-BRCT interactions and interactions within DNA strand breaks. BRCT tandem repeats bind to phosphopeptides; it has been shown that the repeats in human BRCA1 bind specifically to pS-X-X-F motifs, mediating the interaction between BRCA1 and the DNA helicase BACH1, or BRCA1 and CtIP, a transcriptional corepressor. It is assumed that BRCT repeats play similar roles in many signaling pathways associated with the response to DNA damage. 68 matched cddid_all.tbl CDD cd00028 cd00028 237995 B_lectin Bulb-type mannose-specific lectin. The domain contains a three-fold internal repeat (beta-prism architecture). The consensus sequence motif QXDXNXVXY is involved in alpha-D-mannose recognition. Lectins are carbohydrate-binding proteins which specifically recognize diverse carbohydrates and mediate a wide variety of biological processes, such as cell-cell and host-pathogen interactions, serum glycoprotein turnover, and innate immune responses. 116 matched cddid_all.tbl CDD cd00029 cd00029 410341 C1 protein kinase C conserved region 1 (C1 domain) superfamily. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains. It contains the motif HX12CX2CXnCX2CX4HX2CX7C, where C and H are cysteine and histidine, respectively; X represents other residues; and n is either 13 or 14. C1 has a globular fold with two separate Zn(2+)-binding sites. It was originally discovered as lipid-binding modules in protein kinase C (PKC) isoforms. C1 domains that bind and respond to phorbol esters (PE) and diacylglycerol (DAG) are referred to as typical, and those that do not respond to PE and DAG are deemed atypical. A C1 domain may also be referred to as PKC or non-PKC C1, based on the parent protein's activity. Most C1 domain-containing non-PKC proteins act as lipid kinases and scaffolds, except PKD which acts as a protein kinase. PKC C1 domains play roles in membrane translocation and activation of the enzyme. 50 matched cddid_all.tbl CDD cd00030 cd00030 175973 C2 C2 domain. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 102 matched cddid_all.tbl CDD cd00031 cd00031 206635 CA_like Cadherin repeat-like domain. Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. This family also includes the cadherin-like repeats of extracellular alpha-dystroglycan. 98 matched cddid_all.tbl CDD cd00032 cd00032 237997 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs. 243 matched cddid_all.tbl CDD cd00033 cd00033 153056 CCP Complement control protein (CCP) modules (aka short consensus repeats SCRs or SUSHI repeats) have been identified in several proteins of the complement system. SUSHI repeats (short complement-like repeat, SCR) are abundant in complement control proteins. The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. Typically, 2 to 4 modules contribute to a binding site, implying that the orientation of the modules to each other is critical for function. 57 matched cddid_all.tbl CDD cd00034 cd00034 349275 CSD chromo shadow domain. The chromo shadow domain (CSD) is always found in association with a related N-terminal chromo (CHRromatin Organization MOdifier) domain. CSD domains have only been found in proteins that also possess a chromodomain, while chromodomains can exist in isolation. CSDs are found for example in Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3. 52 matched cddid_all.tbl CDD cd00035 cd00035 211311 ChtBD1 Hevein or type 1 chitin binding domain. Hevein or type 1 chitin binding domain (ChtBD1), a lectin domain found in proteins from plants and fungi that bind N-acetylglucosamine, plant endochitinases, wound-induced proteins such as hevein, a major IgE-binding allergen in natural rubber latex, and the alpha subunit of Kluyveromyces lactis killer toxin. This domain is involved in the recognition and/or binding of chitin subunits; it typically occurs N-terminal to glycosyl hydrolase domains in chitinases, together with other carbohydrate-binding domains, or by itself in tandem-repeat arrangements. 39 matched cddid_all.tbl CDD cd00036 cd00036 213175 ChtBD3 Chitin/cellulose binding domains of chitinase and related enzymes. This group contains proteins related to the cellulose-binding domain of Erwinia chrysanthemi endoglucanase Z (EGZ) and Serratia marcescens chitinase B (ChiB). Gram negative plant parasite Erwinia chrysanthemi produces a variety of depolymerizing enzymes to metabolize pectin and cellulose on the host plant. Cellulase EGZ has a modular structure, with an N-terminal catalytic domain linked to a C-terminal cellulose-binding domain (CBD). CBD mediates the secretion activity of EGZ. Chitinases allow certain bacteria to utilize chitin as a energy source. Typically, non-plant chitinases are of the glycosidase family 18. Bacillus circulans Glycosidase ChiA1 hydrolyzes chitin and is comprised of several domains: the C-terminal chitin binding domain, an N-terminal catalytic domain, and 2 fibronectin type III-like domains. Bacillus circulans WL-12 ChiA1 facilitates invasion of fungal cell walls. The ChiA1 chitin binding domain is required for the specific recognition of insoluble chitin. although topologically and structurally related, ChiA1 lacks the characteristic aromatic residues of Erwinia chrysanthemi endoglucanase Z (CBD(EGZ)). Streptomyces griseus Chitinase C is a family 19 chitinase, and consists of a N-terminal chitin binding domain and a C-terminal chitin-catalytic domain that effects degradation. ChiC contains the characteristic chitin-binding aromatic residues. Chitinases function in invertebrates in the degradation of old exoskeletons, in fungi to utilize chitin in cell walls, and in bacteria which use chitin as an energy source. 40 matched cddid_all.tbl CDD cd00037 cd00037 153057 CLECT C-type lectin (CTL)/C-type lectin-like (CTLD) domain. CLECT: C-type lectin (CTL)/C-type lectin-like (CTLD) domain; protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. This group is chiefly comprised of eukaryotic CTLDs, but contains some, as yet functionally uncharacterized, bacterial CTLDs. Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces, including CaCO3 and ice. Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. For example: mannose-binding lectin and lung surfactant proteins A and D bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, and apoptotic cells) and mediate functions associated with killing and phagocytosis; P (platlet)-, E (endothelial)-, and L (leukocyte)- selectins (sels) mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration. CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose. Several CTLDs bind to protein ligands, and only some of these binding interactions are Ca2+-dependent; including the CTLDs of Coagulation Factors IX/X (IX/X) and Von Willebrand Factor (VWF) binding proteins, and natural killer cell receptors. C-type lectins, such as lithostathine, and some type II antifreeze glycoproteins function in a Ca2+-independent manner to bind inorganic surfaces. Many proteins in this group contain a single CTLD; these CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers, from which ligand-binding sites project in different orientations. Various vertebrate type 1 transmembrane proteins including macrophage mannose receptor, endo180, phospholipase A2 receptor, and dendritic and epithelial cell receptor (DEC205) have extracellular domains containing 8 or more CTLDs; these CTLDs remain in the parent model. In some members (IX/X and VWF binding proteins), a loop extends to the adjoining domain to form a loop-swapped dimer. A similar conformation is seen in the macrophage mannose receptor CRD4's putative non-sugar bound form of the domain in the acid environment of the endosome. Lineage specific expansions of CTLDs have occurred in several animal lineages including Drosophila melanogaster and Caenorhabditis elegans; these CTLDs also remain in the parent model. 116 matched cddid_all.tbl CDD cd00038 cd00038 237999 CAP_ED effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels 115 matched cddid_all.tbl CDD cd00039 cd00039 119409 COLIPASE Colipase; a stoichiometric cofactor for pancreatic lipase, allowing the enzyme to anchor itself to the water-lipid interface and stabilizing the active enzyme conformation 90 matched cddid_all.tbl CDD cd00040 cd00040 238000 CSF2 Granulocyte Macrophage Colony Stimulating Factor (GM-CSF) is a member of the large family of polypeptide growth factors called cytokines. It stimulates a wide variety of hematopoietic and nonhematopoietic cell types via binding to members of the cytokine receptor family, mainly the GM-CSF receptor. 121 matched cddid_all.tbl CDD cd00041 cd00041 238001 CUB CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast. 113 matched cddid_all.tbl CDD cd00042 cd00042 238002 CY Substituted updates: Jan 30, 2002 105 matched cddid_all.tbl CDD cd00043 cd00043 410207 CYCLIN_SF Cyclin box fold superfamily. The cyclin box is a protein binding domain that functions in cell-cycle and transcriptional control. It is about 100 amino acids in length, composed of five helices, and is present in cyclins, transcription initiation factor IIB (TFIIB), and retinoblastoma tumour suppressor protein (Rb). Cyclins consist of 8 classes of cell cycle regulators that function as regulatory subunits of cyclin-dependent kinases (CDKs), which are serine/threonine kinases. The catalytic activities of CDKs are modulated not only by their interactions with cyclins but also by CDK inhibitors (CKIs). CDKs, cyclins and CKIs play key roles in transcription, epigenetic regulation, metabolism, stem cell self-renewal, neuronal functions, and spermatogenesis. TFIIB is a transcription factor that binds the TATA box. Members in this superfamily contain one or two copies of the cyclin box. 82 matched cddid_all.tbl CDD cd00044 cd00044 238004 CysPc Calpains, domains IIa, IIb; calcium-dependent cytoplasmic cysteine proteinases, papain-like. Functions in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. 315 matched cddid_all.tbl CDD cd00045 cd00045 260016 DED Death Effector Domain: a protein-protein interaction domain. Death Effector Domains comprise a subfamily of the Death Domain (DD) superfamily. DED-containing proteins include Fas-Associated via Death Domain (FADD), Astrocyte phosphoprotein PEA-15, the initiator caspases (caspase-8 and -10), and FLICE-inhibitory protein (FLIP), among others. These proteins are prominent components of the programmed cell death (apoptosis) pathway. Some members also have non-apoptotic functions such as regulation of insulin signaling (DEDD and PEA15) and cell cycle progression (DEDD). DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. 77 matched cddid_all.tbl CDD cd00046 cd00046 350668 SF2-N N-terminal DEAD/H-box helicase domain of superfamily 2 helicases. The DEAD/H-like superfamily 2 helicases comprise a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This N-terminal domain contains the ATP-binding region. 146 matched cddid_all.tbl CDD cd00047 cd00047 350343 PTPc catalytic domain of protein tyrosine phosphatases. Protein tyrosine phosphatases (PTP, EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr (pTyr) residues, instead of pSer or pThr. This family has a distinctive active site signature motif, HCSAGxGRxG, and are characterized as either transmembrane, receptor-like or non-transmembrane (soluble) PTPs. Receptor-like PTP domains tend to occur in two copies in the cytoplasmic region of the transmembrane proteins, only one copy may be active. 200 matched cddid_all.tbl CDD cd00048 cd00048 380679 DSRM_SF double-stranded RNA binding motif (DSRM) superfamily. DSRM (also known as dsRBM) is a 65-70 amino acid domain that adopts an alpha-beta-beta-beta-alpha fold. It is not sequence specific, but highly specific for double-stranded RNAs (dsRNAs) of various origin and structure. The DSRM domains are found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila Staufen protein, E. coli RNase III, RNase H1, and dsRNA dependent adenosine deaminases. They are involved in numerous cellular mechanisms ranging from localization and transport of messenger RNAs, through maturation and degradation of RNAs, to viral response and signal transduction. Some members harbor tandem DSRMs that act in small RNA biogenesis. 57 matched cddid_all.tbl CDD cd00049 cd00049 199811 MH1 N-terminal Mad Homology 1 (MH1) domain. The MH1 is a small DNA-binding domain present in SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. MH1 binds to the DNA major groove in an unusual manner via a beta hairpin structure. It negatively regulates the functions of the MH2 domain, the C-terminal domain of SMAD. Receptor-regulated SMAD proteins (R-SMADs, including SMAD1, SMAD2, SMAD3, SMAD5, and SMAD9) are activated by phosphorylation by transforming growth factor (TGF)-beta type I receptors. The active R-SMAD associates with a common mediator SMAD (Co-SMAD or SMAD4) and other cofactors, which together translocate to the nucleus to regulate gene expression. The inhibitory or antagonistic SMADs (I-SMADs, including SMAD6 and SMAD7) negatively regulate TGF-beta signaling by competing with R-SMADs for type I receptor or Co-SMADs. MH1 domains of R-SMAD and SMAD4 contain a nuclear localization signal as well as DNA-binding activity. The activated R-SMAD/SMAD4 complex then binds with very low affinity to a DNA sequence CAGAC called SMAD-binding element (SBE) via the MH1 domain. 121 matched cddid_all.tbl CDD cd00050 cd00050 199819 MH2 C-terminal Mad Homology 2 (MH2) domain. The MH2 domain is found in the SMAD (small mothers against decapentaplegic) family of proteins and is responsible for type I receptor interactions, phosphorylation-triggered homo- and hetero-oligomerization, and transactivation. It is negatively regulated by the N-terminal MH1 domain which prevents it from forming a complex with SMAD4. The MH2 domain is multifunctional and provides SMADs with their specificity and selectivity, as well as transcriptional activity. Several transcriptional co-activators and repressors have also been reported to regulate SMAD signaling by interacting with the MH2 domain. Mutations in the MH2 domains of SMAD2 and especially SMAD4 have been detected in colorectal and other human cancers. 170 matched cddid_all.tbl CDD cd00051 cd00051 238008 EFh EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers. 63 matched cddid_all.tbl CDD cd00052 cd00052 238009 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs. 67 matched cddid_all.tbl CDD cd00053 cd00053 238010 EGF Epidermal growth factor domain, found in epidermal growth factor (EGF) presents in a large number of proteins, mostly animal; the list of proteins currently known to contain one or more copies of an EGF-like pattern is large and varied; the functional significance of EGF-like domains in what appear to be unrelated proteins is not yet clear; a common feature is that these repeats are found in the extracellular domain of membrane-bound proteins or in proteins known to be secreted (exception: prostaglandin G/H synthase); the domain includes six cysteine residues which have been shown to be involved in disulfide bonds; the main structure is a two-stranded beta-sheet followed by a loop to a C-terminal short two-stranded sheet; Subdomains between the conserved cysteines vary in length; the region between the 5th and 6th cysteine contains two conserved glycines of which at least one is present in most EGF-like domains; a subset of these bind calcium. 36 matched cddid_all.tbl CDD cd00054 cd00054 238011 EGF_CA Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the N-terminus of particular EGF-like domains; calcium-binding may be crucial for numerous protein-protein interactions. Six conserved core cysteines form three disulfide bridges as in non calcium-binding EGF domains, whose structures are very similar. EGF_CA can be found in tandem repeat arrangements. 38 matched cddid_all.tbl CDD cd00055 cd00055 238012 EGF_Lam Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in tandem arrays; the domain contains 4 disulfide bonds (loops a-d) the first three resemble epidermal growth factor (EGF); the number of copies of this domain in the different forms of laminins is highly variable ranging from 3 up to 22 copies 50 matched cddid_all.tbl CDD cd00056 cd00056 238013 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases 158 matched cddid_all.tbl CDD cd00057 cd00057 238014 FA58C Substituted updates: Jan 31, 2002 143 matched cddid_all.tbl CDD cd00058 cd00058 466989 beta-trefoil_FGF FGF domain, beta-trefoil fold, found in acidic and basic fibroblast growth factor (FGF) superfamily. The FGF superfamily includes FGF1-23 and similar proteins. FGFs are mitogens, which stimulate growth or differentiation of cells of mesodermal or neuroectodermal origin. They play essential roles in patterning and differentiation during vertebrate embryogenesis and have neurotrophic activities. FGFs have a high affinity for heparan sulfate proteoglycans and require heparan sulfate to activate one of four cell surface FGF receptors. Upon binding to FGF, the receptors dimerize, and their intracellular tyrosine kinase domains become active. The structure of FGFs is typical of the beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 127 matched cddid_all.tbl CDD cd00059 cd00059 410788 FH_FOX "Forkhead (FH) domain found in Forkhead box (FOX) family of transcription factors and similar proteins. The FOX family comprises diverse tissue- and cell type-specific transcription factors with an evolutionary conserved ""Forkhead (FH)"" or ""winged helix"" DNA-binding domain. FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. The structure of the FH domain contains 2 flexible loops or ""wings"" in the C-terminal region, hence the term winged helix. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. They participate in a variety of cellular processes, such as cell cycle progression, proliferation, differentiation, migration, metabolism, and DNA damage response. Their expression can be regulated by multiple factors, and they can act as co-activators and/or transcriptional repressors. Fifty FOX-encoding genes in humans have been categorized into 19 subfamilies based on protein sequence homology (FOXA to FOXS)." 75 matched cddid_all.tbl CDD cd00060 cd00060 438714 FHA forkhead associated (FHA) domain superfamily. Forkhead-associated (FHA) domains are small phosphopeptide recognition modules mostly found in eubacteria and eukaryotes. It is about 95-120 residues long that fold into an 11-stranded beta-sandwich. FHA domains can mediate the recognition of phosphorylated and non-phosphorylated substrates, as well as protein oligomerization. They specifically recognize threonine phosphorylation (pThr) accompanying activation of protein serine/threonine kinases. FHA domains show diverse ligand specificity. They may recognize the pTXXD motif, the pTXXI/L motif, and TQ clusters (singly and multiply phosphorylated). In eukaryotes, FHA superfamily members include forkhead-type transcription factors, as well as other signaling proteins, such as many regulatory proteins, kinases, phosphatases, motor proteins called kinesins, and metabolic enzymes. Many of them localize to the nucleus, where they participate in establishing or maintaining cell cycle checkpoints, DNA repair, or transcriptional regulation. FHA domains play important roles in human diseases, particularly in relation to DNA damage responses and cancers. In bacteria, FHA domain-containing proteins may participate in injection of viral proteins into host cells, transmembrane transporters, and cell division. FHA domain-containing proteins rarely include more than one copy of the domain. The only exception in eukaryotes is the checkpoint kinase Rad53 from Saccharomyces cerevisiae, which harbors two FHA domains (FHA1 and FHA2) flanking a central kinase domain. The two FHA domains recognize different phosphorylated targets and function independently from one another. In contrast, Mycobacterium tuberculosis ABC transporter Rv1747 contains two FHA domains but only one of them is essential for protein function. 92 matched cddid_all.tbl CDD cd00061 cd00061 238018 FN1 Fibronectin type 1 domain, approximately 40 residue long with two conserved disulfide bridges. FN1 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices. Dimers of nearly identical subunits are linked by a disulfide bond close to their C-terminus. FN1 domains also found in coagulation factor XII, HGF activator, and tissue-type plasminogen activator. In tissue plasminogen activator, FN1 domains may form functional fibrin-binding units with EGF-like domains C-terminal to FN1. 43 matched cddid_all.tbl CDD cd00062 cd00062 238019 FN2 Fibronectin Type II domain: FN2 is one of three types of internal repeats which combine to form larger domains within fibronectin. Fibronectin, a plasma protein that binds cell surfaces and various compounds including collagen, fibrin, heparin, DNA, and actin, usually exists as a dimer in plasma and as an insoluble multimer in extracellular matrices. Dimers of nearly identical subunits are linked by a disulfide bond close to their C-terminus. Fibronectin is composed of 3 types of modules, FN1,FN2 and FN3. The collagen binding domain contains four FN1 and two FN2 repeats. 48 matched cddid_all.tbl CDD cd00063 cd00063 238020 FN3 Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all animal proteins contain the FN3 repeat; including extracellular and intracellular proteins, membrane spanning cytokine receptors, growth hormone receptors, tyrosine phosphatase receptors, and adhesion molecules. FN3-like domains are also found in bacterial glycosyl hydrolases. 93 matched cddid_all.tbl CDD cd00064 cd00064 238021 FU Furin-like repeats. Cysteine rich region. Exact function of the domain is not known. Furin is a serine-kinase dependent proprotein processor. Other members of this family include endoproteases and cell surface receptors. 49 matched cddid_all.tbl CDD cd00065 cd00065 277249 FYVE_like_SF FYVE domain like superfamily. FYVE domain is a 60-80 residue double zinc finger motif-containing module named after the four proteins, Fab1, YOTB, Vac1, and EEA1. The canonical FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif, which form a compact phosphatidylinositol 3-phosphate (PtdIns3P, also termed PI3P)-binding site. They are found in many membrane trafficking regulators, including EEA1, Hrs, Vac1p, Vps27p, and FENS-1, which locate to early endosomes, specifically bind PtdIns3P, and play important roles in vesicular traffic and in signal transduction. Some proteins, such as rabphilin-3A and alpha-Rab3-interacting molecules (RIMs), are also involved in membrane trafficking and bind to members of the Rab subfamily of GTP hydrolases. However, they contain FYVE-related domains that are structurally similar to the canonical FYVE domains but lack the three signature sequences. At this point, they may not bind to phosphoinositides. In addition, this superfamily also contains the third group of proteins, caspase-associated ring proteins CARP1 and CARP2. They do not localize to membranes in the cell and are involved in the negative regulation of apoptosis, specifically targeting two initiator caspases, caspase 8 and caspase 10, which are distinguished from other FYVE-type proteins. Moreover, these proteins have an altered sequence in the basic ligand binding patch and lack the WxxD motif that is conserved only in phosphoinositide binding FYVE domains. Thus they constitute a family of unique FYVE-type domains called FYVE-like domains. The FYVE domain is structurally similar to the RING domain and the PHD finger. This superfamily also includes ADDz zinc finger domain, which is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. 52 matched cddid_all.tbl CDD cd00066 cd00066 206639 G-alpha Alpha subunit of G proteins (guanine nucleotide binding). The alpha subunit of G proteins contains the guanine nucleotide binding site. The heterotrimeric GNP-binding proteins are signal transducers that communicate signals from many hormones, neurotransmitters, chemokines, and autocrine and paracrine factors. Extracellular signals are received by receptors, which activate the G proteins, which in turn route the signals to several distinct intracellular signaling pathways. The alpha subunit of G proteins is a weak GTPase. In the resting state, heterotrimeric G proteins are associated at the cytosolic face of the plasma membrane and the alpha subunit binds to GDP. Upon activation by a receptor GDP is replaced with GTP, and the G-alpha/GTP complex dissociates from the beta and gamma subunits. This results in activation of downstream signaling pathways, such as cAMP synthesis by adenylyl cyclase, which is terminated when GTP is hydrolized and the heterotrimers reconstitute. 315 matched cddid_all.tbl CDD cd00067 cd00067 238023 GAL4 GAL4-like Zn2Cys6 binuclear cluster DNA-binding domain; found in transcription regulators like GAL4. Domain consists of two helices organized around a Zn(2)Cys(6 )motif; Binds to sequences containing 2 DNA half sites comprised of 3-5 C/G combinations 36 matched cddid_all.tbl CDD cd00068 cd00068 238024 GGL G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors 57 matched cddid_all.tbl CDD cd00069 cd00069 200450 GHB_like Glycoprotein hormone beta chain homologues. This family of cystine-knot hormones includes the beta chains of gonadotropins, thyrotropins, follitropins, choriogonadotropins and more. The members are reproductive hormones that consist of two glycosylated chains (alpha and beta), which form a tightly bound dimer. 96 matched cddid_all.tbl CDD cd00070 cd00070 238025 GLECT Galectin/galactose-binding lectin. This domain exclusively binds beta-galactosides, such as lactose, and does not require metal ions for activity. GLECT domains occur as homodimers or tandemly repeated domains. They are developmentally regulated and may be involved in differentiation, cell-cell interaction and cellular regulation. 127 matched cddid_all.tbl CDD cd00071 cd00071 238026 GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines. 137 matched cddid_all.tbl CDD cd00072 cd00072 238027 GYF GYF domain: contains conserved Gly-Tyr-Phe residues; Proline-binding domain in CD2-binding and other proteins. Involved in signaling lymphocyte activity. Also present in other unrelated proteins (mainly unknown) derived from diverse eukaryotic species. 57 matched cddid_all.tbl CDD cd00073 cd00073 238028 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber 88 matched cddid_all.tbl CDD cd00074 cd00074 467020 HFD_H2A histone-fold domain found in histone H2A and similar proteins. Histone H2A is the core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. 89 matched cddid_all.tbl CDD cd00075 cd00075 340391 HATPase Histidine kinase-like ATPase domain. This superfamily includes the histidine kinase-like ATPase (HATPase) domains of several ATP-binding proteins such as histidine kinase, DNA gyrase B, topoisomerases, heat shock protein 90 (HSP90), phytochrome-like ATPases and DNA mismatch repair proteins. Domains belonging to this superfamily are also referred to as GHKL (gyrase, heat-shock protein 90, histidine kinase, MutL) ATPase domains. 102 matched cddid_all.tbl CDD cd00076 cd00076 467021 HFD_SF histone fold domain (HFD) superfamily. The histone fold domain (HFD) is a structurally conserved interaction motif involved in heterodimerization of the core histones and their assembly into the nucleosome octamer. Histone fold heterodimers play crucial roles in gene regulation. The minimal HFD consists of three alpha helices connected by two short, unstructured loops. The HFD is found in core histones, TATA box-binding protein-associated factors (TAFs), and many other transcription factors. HFD plays a role in the nucleosomal core particle by conserving histone interactions; these contain more than one HFD. The structure of the nucleosome core particle has two modes that have the largest interaction surfaces, and these are the H3-H4 and H2A-H2B heterodimer interactions. Several TAFs interact via histone-fold (HF) motifs. Five HF-containing TAF pairs have been described in transcription factor II D (TFIID): TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10. 63 matched cddid_all.tbl CDD cd00077 cd00077 238032 HDc Metal dependent phosphohydrolases with conserved 'HD' motif 145 matched cddid_all.tbl CDD cd00078 cd00078 238033 HECTc HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains. 352 matched cddid_all.tbl CDD cd00080 cd00080 188616 H3TH_StructSpec-5'-nucleases H3TH domains of structure-specific 5' nucleases (or flap endonuclease-1-like) involved in DNA replication, repair, and recombination. The 5' nucleases of this superfamily are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. The superfamily includes the H3TH (helix-3-turn-helix) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the H3TH domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4 RNase H, T5-5'nuclease, and other homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the C-terminal region of the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. Typically, the nucleases within this superfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one or two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. 71 matched cddid_all.tbl CDD cd00081 cd00081 238035 Hint Hedgehog/Intein domain, found in Hedgehog proteins as well as proteins which contain inteins and undergo protein splicing (e.g. DnaB, RIR1-2, GyrA and Pol). In protein splicing an intervening polypeptide sequence - the intein - is excised from a protein, and the flanking polypeptide sequences - the exteins - are joined by a peptide bond. In addition to the autocatalytic splicing domain, many inteins contain an inserted endonuclease domain, which plays a role in spreading inteins. Hedgehog proteins are a major class of intercellular signaling molecules, which control inductive interactions during animal development. The mature signaling forms of hedgehog proteins are the N-terminal fragments, which are covalently linked to cholesterol at their C-termini. This modification is the result of an autoprocessing step catalyzed by the C-terminal fragments, which are aligned here. 136 matched cddid_all.tbl CDD cd00082 cd00082 119399 HisKA Histidine Kinase A (dimerization/phosphoacceptor) domain; Histidine Kinase A dimers are formed through parallel association of 2 domains creating 4-helix bundles; usually these domains contain a conserved His residue and are activated via trans-autophosphorylation by the catalytic domain of the histidine kinase. They subsequently transfer the phosphoryl group to the Asp acceptor residue of a response regulator protein. Two-component signalling systems, consisting of a histidine protein kinase that senses a signal input and a response regulator that mediates the output, are ancient and evolutionarily conserved signaling mechanisms in prokaryotes and eukaryotes. 65 matched cddid_all.tbl CDD cd00083 cd00083 381392 bHLH_SF basic Helix Loop Helix (bHLH) domain superfamily. bHLH proteins are transcriptional regulators that are found in organisms from yeast to humans. Members of the bHLH superfamily have two highly conserved and functionally distinct regions. The basic part is at the amino end of the bHLH that may bind DNA to a consensus hexanucleotide sequence known as the E box (CANNTG). Different families of bHLH proteins recognize different E-box consensus sequences. At the carboxyl-terminal end of the region is the HLH region that interacts with other proteins to form homo- and heterodimers. bHLH proteins function as a diverse set of regulatory factors because they recognize different DNA sequences and dimerize with different proteins. The bHLH proteins can be divided to cell-type specific and widely expressed proteins. The cell-type specific members of bHLH superfamily are involved in cell-fate determination and act in neurogenesis, cardiogenesis, myogenesis, and hematopoiesis. 46 matched cddid_all.tbl CDD cd00084 cd00084 438789 HMG-box_SF high mobility group (HMG)-box domain superfamily. The High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenetically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4, and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions. 59 matched cddid_all.tbl CDD cd00085 cd00085 238038 HNHc HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins. 57 matched cddid_all.tbl CDD cd00086 cd00086 238039 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner. 59 matched cddid_all.tbl CDD cd00087 cd00087 238040 FReD Fibrinogen-related domains (FReDs); C terminal globular domain of fibrinogen. Fibrinogen is involved in blood clotting, being activated by thrombin to assemble into fibrin clots. The N-termini of 2 times 3 chains come together to form a globular arrangement called the disulfide knot. The C termini of fibrinogen chains end in globular domains, which are not completely equivalent. C terminal globular domains of the gamma chains (C-gamma) dimerize and bind to the GPR motif of the N-terminal domain of the alpha chain, while the GHR motif of N-terminal domain of the beta chain binds to the C terminal globular domains of another beta chain (C-beta), which leads to lattice formation. 215 matched cddid_all.tbl CDD cd00088 cd00088 238041 HPT Histidine Phosphotransfer domain, involved in signalling through a two part component systems in which an autophosphorylating histidine protein kinase serves as a phosphoryl donor to a response regulator protein; the response regulator protein is modulated by phosphorylation and dephosphorylation of a conserved aspartic acid residue; two-component proteins are abundant in most eubacteria; In E. coli there are 62 two-component proteins involved in a variety of processes such as chemotaxis, osmoregulation, metabolism and transport 1; also present in both Gram positive and Gram negative pathogenic bacteria where they regulate basic housekeeping functions and control expression of toxins and other proteins important for pathogenesis; in archaea and eukaryotes, two-component pathways constitute a very small number of all signaling systems; in fungi they mediate environmental stress responses and, in pathogenic yeast, hyphal development. In Dictyostelium and in plants, they are involved in important processes such as osmoregulation, cell growth, and differentiation; to date two-component proteins have not been identified in animals; in most prokaryotic systems, the output response is effected directly by the RR, which functions as a transcription factor while in eukaryotic systems, two-component proteins are found at the beginning of signaling pathways where they interface with more conventional eukaryotic signaling strategies such as MAP kinase and cyclic nucleotide cascades 94 matched cddid_all.tbl CDD cd00089 cd00089 212008 HR1 Protein kinase C-related kinase homology region 1 (HR1) domain that binds Rho family small GTPases. The HR1 domain, also called the ACC (anti-parallel coiled-coil) finger domain or Rho-binding domain binds small GTPases from the Rho family. It is found in Rho effector proteins including PKC-related kinases such as vertebrate PRK1 (or PKN) and yeast PKC1 protein kinases C, as well as in rhophilins and Rho-associated kinase (ROCK). Rho family members function as molecular switches, cycling between inactive and active forms, controlling a variety of cellular processes. HR1 domains may occur in repeat arrangements (PKN contains three HR1 domains), separated by a short linker region. 68 matched cddid_all.tbl CDD cd00090 cd00090 238042 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions. 78 matched cddid_all.tbl CDD cd00091 cd00091 238043 NUC DNA/RNA non-specific endonuclease; prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases. They exists as monomers and homodimers. 241 matched cddid_all.tbl CDD cd00092 cd00092 238044 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family. 67 matched cddid_all.tbl CDD cd00093 cd00093 238045 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators. 58 matched cddid_all.tbl CDD cd00094 cd00094 238046 HX Hemopexin-like repeats.; Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metalloproteinases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of metalloproteinases (TIMPs). This CD contains 4 instances of the repeat. 194 matched cddid_all.tbl CDD cd00095 cd00095 238047 IFab Interferon alpha, beta. Includes also interferon omega and tau. Different from interferon gamma family. Type I interferons(alpha, beta) belong to the larger helical cytokine superfamily, which includes growth hormones, interleukins, several colony-stimulating factors and several other regulatory molecules. All function as regulators of cellular activty by interacting with cell-surface receptors and activating various signalling pathways. Interferons produce antiviral and antiproliferative responses in cells. Receptor specificity determines function of the various members of the family. 152 matched cddid_all.tbl CDD cd00096 cd00096 409353 Ig "Immunoglobulin domain. The members here are composed of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, including T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, including butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. Ig superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Typically, the V-set domains have A, B, E, and D strands in one sheet and A', G, F, C, C' and C"" in the other. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other by strands G, F, C, and C'. Moreover, a C1-set Ig domain contains a short C' strand (three residues) and lacks A' and C"" strand. Unlike other Ig domain sets, C2-set structures do not have a D strand. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 70 matched cddid_all.tbl CDD cd00098 cd00098 409354 IgC1 Immunoglobulin Constant-1 (C1)-set domain. The members here are composed of C1-set domains, classical Ig-like domains resembling the antibody constant domain. Members of the IgC1 family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, while the IgC domain is involved in oligomerization and molecular interactions. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other strands by G, F, C, and C'. 95 matched cddid_all.tbl CDD cd00099 cd00099 409355 IgV "Immunoglobulin variable domain (IgV). The members here are composed of the immunoglobulin variable domain (IgV). The IgV family contains the standard Ig superfamily V-set AGFCC'C""/DEB domain topology, and are components of immunoglobulin (Ig) and T cell receptors. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. Within the variable domain, there are regions of even more variability called the hypervariable or complementarity-determining regions (CDRs) which are responsible for antigen binding. A predominant feature of most Ig domains is the disulfide bridge connecting 2 beta-sheets with a tryptophan residue packed against the disulfide bond. Ig superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Typically, the V-set domains have A, B, E and, D strands in one sheet and A', G, F, C, C', and C"" strands in the other." 111 matched cddid_all.tbl CDD cd00100 cd00100 466776 beta-trefoil_IL1 beta-trefoil domain found in the interleukin-1 (IL-1) family of cytokines. The IL-1 family of cytokines comprises 11 members, including 7 pro-inflammatory agonists (IL-1alpha, IL-1beta, IL-18, IL-33, IL-36alpha, IL-36beta, IL-36gamma) and 4 defined or putative antagonists (IL-1R antagonist (IL-1Ra), IL-36Ra, IL-37, and IL-38) exerting anti-inflammatory activities. These members can have complimentary or distinct biological functions. All family members share a common structure at the C-terminus, which is comprised by of a typical beta-trefoil fold consisting of 12-beta-strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 145 matched cddid_all.tbl CDD cd00101 cd00101 238049 IlGF_like "Insulin/insulin-like growth factor/relaxin family; insulin family of proteins. Members include a number of active peptides which are evolutionary related including insulin, relaxin, prorelaxin, insulin-like growth factors I and II, mammalian Leydig cell-specific insulin-like peptide (gene INSL3), early placenta insulin-like peptide (ELIP; gene INSL4), insect prothoracicotropic hormone (bombyxin), locust insulin-related peptide (LIRP), molluscan insulin-related peptides 1 to 5 (MIP), and C. elegans insulin-like peptides. Typically, the active forms of these peptide hormones are composed of two chains (A and B) linked by two disulfide bonds; the arrangement of four cysteines is conserved in the ""A"" chain: Cys1 is linked by a disulfide bond to Cys3, Cys2 and Cys4 are linked by interchain disulfide bonds to cysteines in the ""B"" chain. This alignment contains both chains, plus the intervening linker region, arranged as found in the propeptide form. Propeptides are cleaved to yield two separate chains linked covalently by the two disulfide bonds." 41 matched cddid_all.tbl CDD cd00102 cd00102 238050 IPT Immunoglobulin-like fold, Plexins, Transcription factors (IPT). IPTs are also known as Transcription factor ImmunoGlobin (TIG) domains. They are present in intracellular transcription factors, cell surface receptors (such as plexins and scatter factor receptors), as well as, cyclodextrin glycosyltransferase and similar enzymes. Although they are involved in DNA binding in transcription factors, their function in other proteins is unknown. In these transcription factors, IPTs form homo- or heterodimers with the exception of the nuclear factor of activated Tcells (NFAT) transcription factors which are mainly monomers. 89 matched cddid_all.tbl CDD cd00103 cd00103 238051 IRF Interferon Regulatory Factor (IRF); also known as tryptophan pentad repeat. The family of IRF transcription factors is important in the regulation of interferons in response to infection by virus and in the regulation of interferon-inducible genes. The IRF family is characterized by a unique 'tryptophan cluster' DNA-binding region. Viral IRFs bind to cellular IRFs; block type I and II interferons and host IRF-mediated transcriptional activation. 107 matched cddid_all.tbl CDD cd00104 cd00104 238052 KAZAL_FS Kazal type serine protease inhibitors and follistatin-like domains. Kazal inhibitors inhibit serine proteases, such as, trypsin, chyomotrypsin, avian ovomucoids, and elastases. The inhibitory domain has one reactive site peptide bond, which serves the cognate enzyme as substrate. The reactive site peptide bond is a combining loop which has an identical conformation in all Kazal inhibitors and in all enzyme/inhibitor complexes. These Kazal domains (small hydrophobic core of alpha/beta structure with 3 to 4 disulfide bonds) often occur in tandem arrays. Similar domains are also present in follistatin (FS) and follistatin-like family members, which play an important role in tissue specific regulation. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a Kazal-like domain and has five disulfide bonds. Although the Kazal-like FS substructure is similar to Kazal proteinase inhibitors, no FS domain has yet been shown to be a proteinase inhibitor. Follistatin-like family members include SPARC, also known as, BM-40 or osteonectin, the Gallus gallus Flik protein, as well as, agrin which has a long array of FS domains. The kazal-type inhibitor domain has also been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The distant homolog, Ascidian trypsin inhibitor, is included in this CD. 41 matched cddid_all.tbl CDD cd00105 cd00105 411802 KH-I K homology (KH) RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability. 63 matched cddid_all.tbl CDD cd00106 cd00106 276812 KISc Kinesin motor domain. Kinesin motor domain. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type), in some its is found in the middle (M-type), or C-terminal (C-type). N-type and M-type kinesins are (+) end-directed motors, while C-type kinesins are (-) end-directed motors, i.e. they transport cargo towards the (-) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. 326 matched cddid_all.tbl CDD cd00107 cd00107 238055 Knot1 "The ""knottin"" fold is stable cysteine-rich scaffold, in which one disulfide bridge crosses the macrocycle made by two other disulfide bridges and the connecting backbone segments. Members include plant lectins/antimicrobial peptides, plant proteinase/amylase inhibitors, plant gamma-thionins, and arthropod defensins." 33 matched cddid_all.tbl CDD cd00108 cd00108 238056 KR Kringle domain; Kringle domains are believed to play a role in binding mediators, such as peptides, other proteins, membranes, or phospholipids. They are autonomous structural domains, found in a varying number of copies, in blood clotting and fibrinolytic proteins, some serine proteases and plasma proteins. Plasminogen-like kringles possess affinity for free lysine and lysine-containing peptides. 83 matched cddid_all.tbl CDD cd00109 cd00109 438633 Kunitz-type Kunitz/Bovine pancreatic trypsin inhibitor (BPTI) domain. This family contains the Kunitz domain which is a common structural fold found in a family of reversible serine protease inhibitors. This domain is thought to have evolved over 500 million years and is ubiquitous in all kingdoms of life and has been incorporated into many different genes. In general, each domain is encoded by a single exon. Some genes encode proteins with a single Kunitz domain, e.g. bovine pancreatic trypsin inhibitor (BPTI), trophoblast Kunitz domain protein (TKDP), amyloid beta-protein precursor (ABPP), as well as Kunitz-type venom peptides such as dendrotoxin. Genes that encode multiple Kunitz domains include hepatocyte growth factor activator inhibitors HAI1 and HAI2 (two domains), tissue factor pathway inhibitor TFPI1 and TFPI2 (three domains) and Caenorhabditis elegans papilin (eleven domains). In addition, the Kunitz domain has been integrated into multi-domain proteins, e.g. the collagen alpha3(VI), alpha1(VII) and alpha1(XXVIII) chains, WFIKKN1 (containing WAP, Follistatin/Kazal, Immunoglobulin, two Kunitz and NTR domains) and papilin. Furthermore, each domain within a multi-Kunitz domain protein may exhibit different protease activity, such as for the three tandemly repeated domains within both tissue factor pathway inhibitors 1 and 2. The Kunitz domain is a representative of alpha/beta proteins with irregular secondary structure stabilized by three disulfide bonds and presenting three peptide loops that can be varied without introducing much destabilization to the scaffold. Protease inhibitors meet the scaffold criteria in that they are small, stable and capable of evolving the binding activity of exposed peptide loops through targeted randomization to construct combinatorial libraries. Kunitz domain-based scaffolds have been successfully utilized to construct and select a library of protease inhibitors with the potential for therapeutic application. 51 matched cddid_all.tbl CDD cd00110 cd00110 238058 LamG Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of purposes including signal transduction via cell-surface steroid receptors, adhesion, migration and differentiation through mediation of cell adhesion molecules. 151 matched cddid_all.tbl CDD cd00111 cd00111 238059 Trefoil P or trefoil or TFF domain; Trefoil factor family domain peptides are mucin-associated molecules, largely found in epithelia of gastrointestinal tissues. Function is not known but it was originally identified from mucosal tissues, where it may have a regulatory or structural role and has also been implicated as a growth fractor in other tissues.The domain is found in 1 to 6 copies where it occurs. 44 matched cddid_all.tbl CDD cd00112 cd00112 238060 LDLa Low Density Lipoprotein Receptor Class A domain, a cysteine-rich repeat that plays a central role in mammalian cholesterol metabolism; the receptor protein binds LDL and transports it into cells by endocytosis; 7 successive cysteine-rich repeats of about 40 amino acids are present in the N-terminal of this multidomain membrane protein; other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement; the binding of calcium is required for in vitro formation of the native disulfide isomer and is necessary in establishing and maintaining the modular structure 35 matched cddid_all.tbl CDD cd00113 cd00113 238061 PLAT PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates. 116 matched cddid_all.tbl CDD cd00114 cd00114 238062 LIGANc NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only. 307 matched cddid_all.tbl CDD cd00115 cd00115 319970 LMWP Low molecular weight phosphatase family. Substituted updates: Aug 22, 2001 137 matched cddid_all.tbl CDD cd00116 cd00116 238064 LRR_RI Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond to structural units consisting of a beta strand (LxxLxLxxN/CxL conserved pattern) and an alpha helix. This alignment contains 12 strands corresponding to 11 full repeats, consistent with the extent observed in the subfamily acting as Ran GTPase Activating Proteins (RanGAP1). 319 matched cddid_all.tbl CDD cd00117 cd00117 467060 TFP three-fingered protein (TFP) fold found in Ly6/uPAR (LU) and snake toxin superfamily. The LU (also known as Ly-6 antigen/uPA receptor)-like extracellular domain (ECD) occurs singly in GPI-linked cell-surface glycoproteins (Ly-6 family, CD59, thymocyte B cell antigen, Sgp-2) or as three-fold repeated domain in urokinase-type plasminogen activator receptor. It is a structural domain involved in protein-protein interactions, tolerating an unusual degree of variation and binding with high specificity to a broad spectrum of targets. The snake toxin domain is present in short and long neurotoxins, cytotoxins, and short toxins, and in other miscellaneous venom peptides. The toxin acts by binding to the nicotinic acetylcholine receptors in the postsynaptic membrane of skeletal muscles and preventing the binding of acetylcholine, thereby blocking the excitation of muscles. Both the LU-like ECD and the snake toxin domain belong to three-fingered protein (TFP) fold, which is characterized by containing 70 to 100 amino acids including eight to ten cysteine residues spaced at conserved distances. 81 matched cddid_all.tbl CDD cd00118 cd00118 212030 LysM Lysin Motif is a small domain involved in binding peptidoglycan. LysM, a small globular domain with approximately 40 amino acids, is a widespread protein module involved in binding peptidoglycan in bacteria and chitin in eukaryotes. The domain was originally identified in enzymes that degrade bacterial cell walls, but proteins involved in many other biological functions also contain this domain. It has been reported that the LysM domain functions as a signal for specific plant-bacteria recognition in bacterial pathogenesis. Many of these enzymes are modular and are composed of catalytic units linked to one or several repeats of LysM domains. LysM domains are found in bacteria and eukaryotes. 45 matched cddid_all.tbl CDD cd00119 cd00119 340357 LYZ C-type lysozyme and alpha-lactalbumin. C-type lysozyme (chicken or conventional type, 1,4-beta-N-acetylmuramidase) and alpha-lactalbumin (lactose synthase B protein, LA). They have a close evolutionary relationship and similar tertiary structure, however, functionally they are quite different. Lysozymes have primarily bacteriolytic function; hydrolysis of peptidoglycans of prokaryotic cell walls and transglycosylation. LA is a calcium-binding metalloprotein that is expressed exclusively in the mammary gland during lactation. LA is the regulatory subunit of the enzyme lactose synthase. The association of LA with the catalytic component of lactose synthase, galactosyltransferase, alters the acceptor substrate specificity of this glycosyltransferase, facilitating biosynthesis of lactose. Some lysozymes have evolved into digestive enzymes, both in mammals and invertebrates. 122 matched cddid_all.tbl CDD cd00120 cd00120 238067 MADS MADS: MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptonal regulators. Binds DNA and exists as hetero and homo-dimers. Composed of 2 main subgroups: SRF-like/Type I and MEF2-like (myocyte enhancer factor 2)/ Type II. These subgroups differ mainly in position of the alpha 2 helix responsible for the dimerization interface; Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi. 59 matched cddid_all.tbl CDD cd00121 cd00121 238068 MATH MATH (meprin and TRAF-C homology) domain; an independent folding unit with an eight-stranded beta-sandwich structure found in meprins, TRAFs and other proteins. Meprins comprise a class of extracellular metalloproteases which are anchored to the membrane and are capable of cleaving growth factors, extracellular matrix proteins, and biologically active peptides. TRAF molecules serve as adapter proteins that link cell surface receptors of the Tumor Necrosis Factor and 1nterleukin-1/Toll-like families to downstream kinase cascades, which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. Other members include the ubiquitin ligases, TRIM37 and SPOP, and the ubiquitin-specific proteases, HAUSP and Ubp21p. A large number of uncharacterized members mostly from lineage-specific expansions in C. elegans and rice contain MATH and BTB domains, similar to SPOP. The MATH domain has been shown to bind peptide/protein substrates in TRAFs and HAUSP. It is possible that the MATH domain in other members of this superfamily also interacts with various protein substrates. The TRAF domain may also be involved in the trimerization of TRAFs. Based on homology, it is postulated that the MATH domain in meprins may be involved in its tetramer assembly and that the MATH domain, in general, may take part in diverse modular arrangements defined by adjacent multimerization domains. 126 matched cddid_all.tbl CDD cd00122 cd00122 238069 MBD MeCP2, MBD1, MBD2, MBD3, MBD4, CLLD8-like, and BAZ2A-like proteins constitute a family of proteins that share the methyl-CpG-binding domain (MBD). The MBD consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. The MBDs present in putative chromatin remodelling subunit, BAZ2A, and putative histone methyltransferase, CLLD8, represent two phylogenetically distinct groups within the MBD protein family. 62 matched cddid_all.tbl CDD cd00123 cd00123 238070 DmpA_OAT DmpA/OAT superfamily; composed of L-aminopeptidase D-amidase/D-esterase (DmpA), ornithine acetyltransferase (OAT) and similar proteins. DmpA is an aminopeptidase that releases N-terminal D and L amino acids from peptide substrates. This group represents one of the rare aminopeptidases that are not metalloenzymes. DmpA shows similarity in catalytic mechanism to N-terminal nucleophile (Ntn) hydrolases, which are enzymes that catalyze the cleavage of amide bonds through the nucleophilic attack of the side chain of an N-terminal serine, threonine, or cysteine. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in the arginine biosynthetic pathway. The superfamily also contains an enzyme, endo-type 6-aminohexanoate-oligomer hydrolase, that have been shown to be involved in nylon degradation. Proteins in this superfamily undergo autocatalytic cleavage of an inactive precursor at the site immediately upstream to the catalytic nucleophile. 286 matched cddid_all.tbl CDD cd00124 cd00124 276950 MYSc Myosin motor domain superfamily. Myosin motor domain. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 633 matched cddid_all.tbl CDD cd00125 cd00125 153091 PLA2c PLA2c: Phospholipase A2, a family of secretory and cytosolic enzymes; the latter are either Ca dependent or Ca independent. PLA2 cleaves the sn-2 position of the glycerol backbone of phospholipids (PC or phosphatidylethanolamine), usually in a metal-dependent reaction, to generate lysophospholipid (LysoPL) and a free fatty acid (FA). The resulting products are either dietary or used in synthetic pathways for leukotrienes and prostaglandins. Often, arachidonic acid is released as a free fatty acid and acts as second messenger in signaling networks. Secreted PLA2s have also been found to specifically bind to a variety of soluble and membrane proteins in mammals, including receptors. As a toxin, PLA2 is a potent presynaptic neurotoxin which blocks nerve terminals by binding to the nerve membrane and hydrolyzing stable membrane lipids. The products of the hydrolysis (LysoPL and FA) cannot form bilayers leading to a change in membrane conformation and ultimately to a block in the release of neurotransmitters. PLA2 may form dimers or oligomers. 115 matched cddid_all.tbl CDD cd00126 cd00126 238072 PAH Pancreatic Hormone domain, a regulator of pancreatic and gastrointestinal functions; neuropeptide Y (NPY)b, peptide YY (PYY), and pancreatic polypetide (PP) are closely related; propeptide is enzymatically cleaved to yield the mature active peptide with amidated C-terminal ends; receptor binding and activation functions may reside in the N- and C-termini respectively; occurs in neurons, intestinal endocrine cells, and pancreas; exist as monomers and dimers 36 matched cddid_all.tbl CDD cd00128 cd00128 350200 PIN_FEN1_EXO1-like FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like and exonuclease-1 (EXO1)-like nucleases, structure-specific, divalent-metal-ion dependent, 5' nucleases. PIN (PilT N terminus) domain of Flap endonuclease-1 (FEN1) and exonuclease-1 (EXO1)-like nucleases: FEN1, EXO1, Mkt1, Gap endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. These nucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 162 matched cddid_all.tbl CDD cd00129 cd00129 238074 PAN_APPLE PAN/APPLE-like domain; present in N-terminal (N) domains of plasminogen/ hepatocyte growth factor proteins, plasma prekallikrein/coagulation factor XI and microneme antigen proteins, plant receptor-like protein kinases, and various nematode and leech anti-platelet proteins. Common structural features include two disulfide bonds that link the alpha-helix to the central region of the protein. PAN domains have significant functional versatility, fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions. 80 matched cddid_all.tbl CDD cd00130 cd00130 238075 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction. 103 matched cddid_all.tbl CDD cd00131 cd00131 238076 PAX Paired Box domain 128 matched cddid_all.tbl CDD cd00132 cd00132 238077 CRIB PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. CRIB-containing effector proteins are functionally diverse and include serine/threonine kinases, tyrosine kinases, actin-binding proteins, and adapter molecules. 42 matched cddid_all.tbl CDD cd00133 cd00133 99904 PTS_IIB PTS_IIB: subunit IIB of enzyme II (EII) is the central energy-coupling domain of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In the multienzyme PTS complex, EII is a carbohydrate-specific permease consisting of two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include chitobiose/lichenan, ascorbate, lactose, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system. The PTS is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, polyols, amino sugars, and other sugar derivatives. The four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB), can phosphorylate or interact with numerous non-PTS proteins thereby regulating their activity. 84 matched cddid_all.tbl CDD cd00135 cd00135 238079 PDGF Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family domain; PDGF is a potent activator for cells of mesenchymal origin; PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer; VEGF is a potent mitogen in embryonic and somatic angiogenesis with a unique specificity for vascular endothelial cells; VEGF forms homodimers and exists in 4 different isoforms; overall, the VEGF monomer resembles that of PDGF, but its N-terminal segment is helical rather than extended; the cysteine knot motif is a common feature of this domain 86 matched cddid_all.tbl CDD cd00136 cd00136 467153 PDZ_canonical canonical PDZ domain. Canonical PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain. PDZ domains usually bind to short specific peptide sequences located at the C-terminal end of their partner proteins known as PDZ binding motifs. These domains can also interact with internal peptide motifs and certain lipids, and can take part in a head-to-tail oligomerization with other PDZ domains. The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 81 matched cddid_all.tbl CDD cd00137 cd00137 176497 PI-PLCc Catalytic domain of prokaryotic and eukaryotic phosphoinositide-specific phospholipase C. This subfamily corresponds to the catalytic domain present in prokaryotic and eukaryotic phosphoinositide-specific phospholipase C (PI-PLC), which is a ubiquitous enzyme catalyzing the cleavage of the sn3-phosphodiester bond in the membrane phosphoinositides (phosphatidylinositol, PI; Phosphatidylinositol-4-phosphate, PIP; phosphatidylinositol 4,5-bisphosphate, PIP2) to yield inositol phosphates (inositol monosphosphate, InsP; inositol diphosphate, InsP2; inositol trisphosphate, InsP3) and diacylglycerol (DAG). The higher eukaryotic PI-PLCs (EC 3.1.4.11) have a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. They play a critical role in most signal transduction pathways, controlling numerous cellular events, such as cell growth, proliferation, excitation and secretion. These PI-PLCs strictly require Ca2+ for their catalytic activity. They display a clear preference towards the hydrolysis of the more highly phosphorylated PI-analogues, PIP2 and PIP, to generate two important second messengers, InsP3 and DAG. InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. In contrast, bacterial PI-PLCs contain a single catalytic domain. Although their precise physiological function remains unclear, bacterial PI-PLCs may function as virulence factors in some pathogenic bacteria. They participate in Ca2+-independent PI metabolism. They are characterized as phosphatidylinositol-specific phospholipase C (EC 4.6.1.13) that selectively hydrolyze PI, not PIP or PIP2. The TIM-barrel type catalytic domain in bacterial PI-PLCs is very similar to the one in eukaryotic PI-PLCs, in which the catalytic domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. The catalytic mechanism of both prokaryotic and eukaryotic PI-PLCs is based on general base and acid catalysis utilizing two well conserved histidines, and consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes a distinctly different type of eukaryotic PLC, glycosylphosphatidylinositol-specific phospholipase C (GPI-PLC), an integral membrane protein characterized in the protozoan parasite Trypanosoma brucei. T. brucei GPI-PLC hydrolyzes the GPI-anchor on the variant specific glycoprotein (VSG), releasing dimyristyl glycerol (DMG), which may facilitate the evasion of the protozoan to the host#s immune system. It does not require Ca2+ for its activity and is more closely related to bacterial PI-PLCs, but not mammalian PI-PLCs. 274 matched cddid_all.tbl CDD cd00138 cd00138 197200 PLDc_SF Catalytic domain of phospholipase D superfamily proteins. Catalytic domain of phospholipase D (PLD) superfamily proteins. The PLD superfamily is composed of a large and diverse group of proteins including plant, mammalian and bacterial PLDs, bacterial cardiolipin (CL) synthases, bacterial phosphatidylserine synthases (PSS), eukaryotic phosphatidylglycerophosphate (PGP) synthase, eukaryotic tyrosyl-DNA phosphodiesterase 1 (Tdp1), and some bacterial endonucleases (Nuc and BfiI), among others. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze the transphosphatidylation of phospholipids to acceptor alcohols. The majority of members in this superfamily contain a short conserved sequence motif (H-x-K-x(4)-D, where x represents any amino acid residue), called the HKD signature motif. There are varying expanded forms of this motif in different family members. Some members contain variant HKD motifs. Most PLD enzymes are monomeric proteins with two HKD motif-containing domains. Two HKD motifs from two domains form a single active site. Some PLD enzymes have only one copy of the HKD motif per subunit but form a functionally active dimer, which has a single active site at the dimer interface containing the two HKD motifs from both subunits. Different PLD enzymes may have evolved through domain fusion of a common catalytic core with separate substrate recognition domains. Despite their various catalytic functions and a very broad range of substrate specificities, the diverse group of PLD enzymes can bind to a phosphodiester moiety. Most of them are active as bi-lobed monomers or dimers, and may possess similar core structures for catalytic activity. They are generally thought to utilize a common two-step ping-pong catalytic mechanism, involving an enzyme-substrate intermediate, to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. 119 matched cddid_all.tbl CDD cd00139 cd00139 340436 PIPKc Phosphatidylinositol phosphate kinase (PIPK) catalytic domain family. The Phosphatidylinositol phosphate kinase (PIPK) catalytic domain family includes phosphatidylinositol 5-phosphate 4-kinases (PIP5Ks) and similar proteins. PIP5Ks catalyze the phosphorylation of phosphatidylinositol phosphate on the fourth or fifth hydroxyl of the inositol ring, to form phosphatidylinositol bisphosphate. The family includes type I and II PIP5Ks (-alpha, -beta, and -gamma) kinases. Signalling by phosphorylated species of phosphatidylinositol regulates secretion, vesicular trafficking, membrane translocation, cell adhesion, chemotaxis, DNA synthesis, and cell cycling. 253 matched cddid_all.tbl CDD cd00140 cd00140 238082 beta_clamp Beta clamp domain. The beta subunit (processivity factor) of DNA polymerase III holoenzyme, refered to as the beta clamp, forms a ring shaped dimer that encircles dsDNA (sliding clamp) in bacteria. The beta-clamp is structurally similar to the trimeric ring formed by PCNA (found in eukaryotes and archaea) and the processivity factor (found in bacteriophages T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds. 365 matched cddid_all.tbl CDD cd00141 cd00141 143386 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family. 307 matched cddid_all.tbl CDD cd00142 cd00142 270621 PI3Kc_like Catalytic domain of Phosphoinositide 3-kinase and similar proteins. Members of the family include PI3K, phosphoinositide 4-kinase (PI4K), PI3K-related protein kinases (PIKKs), and TRansformation/tRanscription domain-Associated Protein (TRAPP). PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives, while PI4K catalyze the phosphorylation of the 4-hydroxyl of PtdIns. PIKKs are protein kinases that catalyze the phosphorylation of serine/threonine residues, especially those that are followed by a glutamine. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI4Ks produce PtdIns(4)P, the major precursor to important signaling phosphoinositides. PIKKs have diverse functions including cell-cycle checkpoints, genome surveillance, mRNA surveillance, and translation control. The PI3K-like catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 216 matched cddid_all.tbl CDD cd00143 cd00143 238083 PP2Cc Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity. 254 matched cddid_all.tbl CDD cd00144 cd00144 277316 MPP_PPP_family phosphoprotein phosphatases of the metallophosphatase superfamily, metallophosphatase domain. The PPP (phosphoprotein phosphatase) family is one of two known protein phosphatase families specific for serine and threonine. This family includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all eukaryotes, and in most bacterial and archeal genomes. Dephosphorylation of phosphoserines and phosphothreonines on target proteins plays a central role in the regulation of many cellular processes. PPPs belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 229 matched cddid_all.tbl CDD cd00145 cd00145 99912 POLBc DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is made up of distinct domains and sub-domains. The polymerase domain of DNA polymerase type B (Pol domain) is responsible for the template-directed polymerization of dNTPs onto the growing primer strand of duplex DNA that is usually magnesium dependent. In general, the architecture of the Pol domain has been likened to a right hand with fingers, thumb, and palm sub-domains with a deep groove to accommodate the nucleic acid substrate. There are a few conserved motifs in the Pol domain of family B DNA polymerases. The conserved aspartic acid residues in the DTDS motifs of the palm sub-domain is crucial for binding to divalent metal ion and is suggested to be important for polymerase catalysis. 323 matched cddid_all.tbl CDD cd00146 cd00146 238084 PKD polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases. 81 matched cddid_all.tbl CDD cd00147 cd00147 132835 cPLA2_like "Cytosolic phospholipase A2, catalytic domain; hydrolyses arachidonyl phospholipids. Catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both ""closed lid"" and ""open lid"" forms. Movement of the cPLA2 lid possibly exposes a greater hydrophobic surface and the active site. cPLA2 belongs to the alpha-beta hydrolase family which is identified by a characteristic nucleophile elbow with a consensus sequence of Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu = nucleophile). Calcium is required for cPLA2 to bind with membranes or phospholipids. Group IV cPLA2 includes six intercellular enzymes: cPLA2alpha, cPLA2beta, cPLA2gamma, cPLA2delta, cPLA2epsilon, and cPLA2zeta." 438 matched cddid_all.tbl CDD cd00148 cd00148 238085 PROF Profilin binds actin monomers, membrane polyphosphoinositides such as PI(4,5)P2, and poly-L-proline. Profilin can inhibit actin polymerization into F-actin by binding to monomeric actin (G-actin) and terminal F-actin subunits, but - as a regulator of the cytoskeleton - it may also promote actin polymerization. It plays a role in the assembly of branched actin filament networks, by activating WASP via binding to WASP's proline rich domain. Profilin may link the cytoskeleton with major signalling pathways by interacting with components of the phosphatidylinositol cycle and Ras pathway. 127 matched cddid_all.tbl CDD cd00150 cd00150 119410 PlantTI Plant trypsin inhibitors such as squash trypsin inhibitor. Plant proteinase inhibitors play important roles in natural plant defense. Proteinase inhibitors from squash seeds form an uniform family of small proteins cross-linked with three disulfide bridges. 27 matched cddid_all.tbl CDD cd00152 cd00152 238086 PTX "Pentraxins are plasma proteins characterized by their pentameric discoid assembly and their Ca2+ dependent ligand binding, such as Serum amyloid P component (SAP) and C-reactive Protein (CRP), which are cytokine-inducible acute-phase proteins implicated in innate immunity. CRP binds to ligands containing phosphocholine, SAP binds to amyloid fibrils, DNA, chromatin, fibronectin, C4-binding proteins and glycosaminoglycans. ""Long"" pentraxins have N-terminal extensions to the common pentraxin domain; one group, the neuronal pentraxins, may be involved in synapse formation and remodeling, and they may also be able to form heteromultimers." 201 matched cddid_all.tbl CDD cd00153 cd00153 340449 RA_RalGDS_like Ras-associating (RA) domain of RalGDS family. The RalGDS family RA domains can interact with activated Ras and may function as effectors for other Ras family. Ras proteins are small GTPases that are involved in cellular signal transduction. The RA domain has the beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin (Ub); Ub is a protein modifier in eukaryotes and is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. The RalGDS family includes RalGDS, RGL, RGL2/Rlf and RGL3. All family members have similar domain structure: a central CDC25 homology domain with an upstream Ras Exchange motif (REM), and a C-terminal RA domain. The RA domain mediates the GTP-dependent interaction with Ras and Ras-related proteins. 88 matched cddid_all.tbl CDD cd00154 cd00154 206640 Rab Ras-related in brain (Rab) family of small guanosine triphosphatases (GTPases). Rab GTPases form the largest family within the Ras superfamily. There are at least 60 Rab genes in the human genome, and a number of Rab GTPases are conserved from yeast to humans. Rab GTPases are small, monomeric proteins that function as molecular switches to regulate vesicle trafficking pathways. The different Rab GTPases are localized to the cytosolic face of specific intracellular membranes, where they regulate distinct steps in membrane traffic pathways. In the GTP-bound form, Rab GTPases recruit specific sets of effector proteins onto membranes. Through their effectors, Rab GTPases regulate vesicle formation, actin- and tubulin-dependent vesicle movement, and membrane fusion. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which mask C-terminal lipid binding and promote cytosolic localization. While most unicellular organisms possess 5-20 Rab members, several have been found to possess 60 or more Rabs; for many of these Rab isoforms, homologous proteins are not found in other organisms. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Since crystal structures often lack C-terminal residues, the lipid modification site is not available for annotation in many of the CDs in the hierarchy, but is included where possible. 159 matched cddid_all.tbl CDD cd00155 cd00155 238087 RasGEF Guanine nucleotide exchange factor for Ras-like small GTPases. Small GTP-binding proteins of the Ras superfamily function as molecular switches in fundamental events such as signal transduction, cytoskeleton dynamics and intracellular trafficking. Guanine-nucleotide-exchange factors (GEFs) positively regulate these GTP-binding proteins in response to a variety of signals. GEFs catalyze the dissociation of GDP from the inactive GTP-binding proteins. GTP can then bind and induce structural changes that allow interaction with effectors. 237 matched cddid_all.tbl CDD cd00156 cd00156 381085 REC phosphoacceptor receiver (REC) domain of response regulators (RRs) and pseudo response regulators (PRRs). Two-component systems (TCSs) involving a sensor and a response regulator are used by bacteria to adapt to changing environments. Processes regulated by two-component systems in bacteria include sporulation, pathogenicity, virulence, chemotaxis, and membrane transport. Response regulators (RRs) share the common phosphoacceptor REC domain and different effector/output domains such as DNA, RNA, ligand-binding, protein-binding, or enzymatic domains. Response regulators regulate transcription, post-transcription or post-translation, or have functions such as methylesterases, adenylate or diguanylate cyclase, c-di-GMP-specific phosphodiesterases, histidine kinases, serine/threonine protein kinases, and protein phosphatases, depending on their output domains. The function of some output domains are still unknown. TCSs are found in all three domains of life - bacteria, archaea, and eukaryotes, however, the presence and abundance of particular RRs vary between the lineages. Archaea encode very few RRs with DNA-binding output domains; most are stand-alone REC domains. Among eukaryotes, TCSs are found primarily in protozoa, fungi, algae, and green plants. REC domains function as phosphorylation-mediated switches within RRs, but some also transfer phosphoryl groups in multistep phosphorelays. 99 matched cddid_all.tbl CDD cd00157 cd00157 206641 Rho Ras homology family (Rho) of small guanosine triphosphatases (GTPases). Members of the Rho (Ras homology) family include RhoA, Cdc42, Rac, Rnd, Wrch1, RhoBTB, and Rop. There are 22 human Rho family members identified currently. These proteins are all involved in the reorganization of the actin cytoskeleton in response to external stimuli. They also have roles in cell transformation by Ras in cytokinesis, in focal adhesion formation and in the stimulation of stress-activated kinase. These various functions are controlled through distinct effector proteins and mediated through a GTP-binding/GTPase cycle involving three classes of regulating proteins: GAPs (GTPase-activating proteins), GEFs (guanine nucleotide exchange factors), and GDIs (guanine nucleotide dissociation inhibitors). Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Since crystal structures often lack C-terminal residues, this feature is not available for annotation in many of the CDs in the hierarchy. 171 matched cddid_all.tbl CDD cd00158 cd00158 238089 RHOD Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins. 89 matched cddid_all.tbl CDD cd00159 cd00159 238090 RhoGAP RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins. 169 matched cddid_all.tbl CDD cd00160 cd00160 238091 RhoGEF Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains. 181 matched cddid_all.tbl CDD cd00161 cd00161 467293 beta-trefoil_Ricin-like ricin B-type lectin domain, beta-trefoil fold. The ricin B-type lectin domain is a carbohydrate-binding domain formed from presumed gene triplication. It shows a beta-trefoil fold characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain was originally found in Ricin, which is a legume lectin from the seeds of the castor bean plant, Ricinus communis. It is also found in many carbohydrate-recognition proteins like plant and bacterial AB-toxins, glycosidases, or proteases, which serve diverse functions such as inhibitory toxicity, enzymatic activity, and signal transduction. The ricin B-type lectin domain can be present in one or more copies and has been shown in some instances to bind simple sugars, such as galactose or lactose. The most characteristic, though not completely conserved, sequence feature is the presence of a Q-W pattern. Consequently, the ricin B-type lectin domain has also been referred as the (QxW)3 domain and the three homologous regions as the QxW repeats. A disulfide bond is also conserved in some QxW repeats. 134 matched cddid_all.tbl CDD cd00162 cd00162 438111 RING_Ubox "RING finger (Really Interesting New Gene) domain and U-box domain superfamily. The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the ""cross-brace"" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers: some have different Cys/His patterns while some lack a single Cys or His residue at typical Zn ligand positions (the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can indeed chelate Zn in a RING finger as well). C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type RING fingers are closely related to RING-HC fingers. In contrast, C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type RING fingers are more closely related to RING-H2 fingers. However, not all RING finger-containing proteins display regular RING finger features, and the RING finger family has turned out to be multifarious. The degenerate RING fingers of the Siz/PIAS RING (SP-RING) family proteins and sporulation protein RMD5, are characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues. They bind only one Zn2+ ion. On the other hand, the RING fingers of the human APC11 and RBX1 proteins can bind a third Zn atom since they harbor four additional Zn ligands. U-box is a modified form of the RING finger domain that lacks metal chelating Cys and His residues. It resembles the cross-brace RING structure consisting of three beta-sheets and a single alpha-helix, which would be stabilized by salt bridges instead of chelated metal ions. U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms. RING finger/U-box-containing proteins are a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enable efficient transfer of ubiquitin from E2 to the substrates." 42 matched cddid_all.tbl CDD cd00163 cd00163 119386 RNase_A "RNase A family, or Pancreatic RNases family; includes vertebrate RNase homologs to the bovine pancreatic ribonuclease A (RNase A). Many of these enzymes have special biological activities; for example, some stimulate the development of vascular endothelial cells, dendritic cells, and neurons, are cytotoxic/anti-tumoral and/or anti-pathogenic. RNase A is involved in endonucleolytic cleavage of 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates. The catalytic mechanism is a transphosphorylation of P-O 5' bonds on the 3' side of pyrimidines and subsequent hydrolysis to generate 3' phosphate groups. The RNase A family proteins have a conserved catalytic triad (two histidines and one lysine); recently some family members lacking the catalytic residues have been identified. They also share three or four disulfide bonds. The most conserved disulfide bonds are close to the N and C termini and contribute most significantly to the conformational stability. 8 RNase A homologs had initially been identified in the human genome, pancreatic RNase (RNase 1), Eosinophil Derived Neurotoxin (EDN/RNASE 2), Eosinophil Cationic Protein (ECP/RNase 3), RNase 4, Angiogenin (RNase 5), RNase 6 or k6, the skin derived RNase (RNase 7) and RNase 8. These eight human genes are all located in a cluster on chromosome 14. Recent genomic analysis has extended the family to 13 sequences. However only the first eight identified human RNases, which are refered to as ""canonical"" RNases, contain the catalytic residues required for RNase A activity. The new genes corresponding to RNases 9-13 are also located in the same chromosome cluster and seem to be related to male-reproductive functions. RNases 9-13 have the characteristic disulfide bridge pattern but are unlikely to share RNase activity. The RNase A family most likely started off in vertebrates as a host-defense protein, and comparative analysis in mammals and birds indicates that the family may have originated from a RNase 5-like gene. This hypothesis is supported by the fact that only RNase 5-like RNases have been reported outside the mammalian class. The RNase 5 group would therefore be the most ancient form of this family, and all other members would have arisen during mammalian evolution." 119 matched cddid_all.tbl CDD cd00164 cd00164 238094 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold. 65 matched cddid_all.tbl CDD cd00165 cd00165 238095 S4 S4/Hsp/ tRNA synthetase RNA-binding domain; The domain surface is populated by conserved, charged residues that define a likely RNA-binding site; Found in stress proteins, ribosomal proteins and tRNA synthetases; This may imply a hitherto unrecognized functional similarity between these three protein classes. 70 matched cddid_all.tbl CDD cd00167 cd00167 238096 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA. 45 matched cddid_all.tbl CDD cd00168 cd00168 349397 CAP CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain family. The CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain, also called SCP (sperm-coating glycoprotein), is found in eukaryotes and prokaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), which accumulates after infections with pathogens, and may act as an anti-fungal agent or be involved in cell wall loosening. This family also includes CRISPs (cysteine-rich secretory proteins), which combine the CAP/SCP domain with a C-terminal cysteine rich domain, and allergen 5 from vespid venom. Roles for CRISP, in response to pathogens, fertilization, and sperm maturation have been proposed. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. The human GAPR-1 protein has been reported to dimerize, and such a dimer may form an active site containing a catalytic triad. CAP/SCP has also been proposed to be a Ca++ chelating serine protease. The Ca++-chelating function would fit with various signaling processes that members of this family, such as the CRISPs, are involved in, and is supported by sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how helothermine, a toxic peptide secreted by the beaded lizard, blocks Ca++ transporting ryanodine receptors. Little is known about the biological roles of the bacterial and archaeal CAP/SCP domains. 128 matched cddid_all.tbl CDD cd00169 cd00169 238098 Chemokine Chemokine: small cytokines, including a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; distinguished from other cytokines by their receptors, which are G-protein coupled receptors; divided into 4 subfamilies based on the arrangement of the two N-terminal cysteines; some members can bind multiple receptors and many chemokine receptors can bind more than one chemokine; this redundancy allows precise control in stimulating the immune system and in contributing to the homeostasis of a cell; when expressed inappropriately, chemokines play a role in autoimmune diseases, vascular irregularities, graft rejection, neoplasia, and allergies; exist as monomers, dimers and multimers, but are believed to function as monomers; found only in vertebrates and a few viruses. See CDs: Chemokine_CXC (cd00273), Chemokine_CC (cd00272), Chemokine_C (cd00271), and Chemokine_CX3C (cd00274) for chemokine subgroups. 59 matched cddid_all.tbl CDD cd00170 cd00170 469559 SEC14 Sec14p-like lipid-binding domain. Sec14p-like lipid-binding domains are found in secretory proteins, such as S. cerevisiae phosphatidylinositol transfer protein (Sec14p), and in lipid regulated proteins such as RhoGAPs, RhoGEFs and neurofibromin (NF1). SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits. 156 matched cddid_all.tbl CDD cd00171 cd00171 238100 Sec7 Sec7 domain; Domain named after the S. cerevisiae SEC7 gene product. The Sec7 domain is the central domain of the guanine-nucleotide-exchange factors (GEFs) of the ADP-ribosylation factor family of small GTPases (ARFs) . It carries the exchange factor activity. 185 matched cddid_all.tbl CDD cd00172 cd00172 381000 serpin SERine Proteinase INhibitors (serpin) family. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 365 matched cddid_all.tbl CDD cd00173 cd00173 198173 SH2 Src homology 2 (SH2) domain. In general, SH2 domains are involved in signal transduction; they bind pTyr-containing polypeptide ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. They are present in a wide array of proteins including: adaptor proteins (Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1), kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1, Shp-2), transcription factors (STAT1), Ras signaling molecules (Ras-Gap), ubiquitination factors (c-Cbl), cytoskeleton regulators (Tensin), signal regulators (SAP), and phospholipid second messengers (PLCgamma), amongst others. 79 matched cddid_all.tbl CDD cd00174 cd00174 212690 SH3 Src Homology 3 domain superfamily. Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction. 51 matched cddid_all.tbl CDD cd00175 cd00175 238102 SNc Staphylococcal nuclease homologues. SNase homologues are found in bacteria, archaea, and eukaryotes. They contain no disufide bonds. 129 matched cddid_all.tbl CDD cd00176 cd00176 238103 SPEC Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; the repeats are independent folding units; tandem repeats are found in differing numbers and arrange in an antiparallel manner to form dimers; the repeats are defined by a characteristic tryptophan (W) residue in helix A and a leucine (L) at the carboxyl end of helix C and separated by a linker of 5 residues; two copies of the repeat are present here 213 matched cddid_all.tbl CDD cd00177 cd00177 176851 START Lipid-binding START domain of mammalian STARD1-STARD15 and related proteins. This family includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and related domains, such as the START domain of the Arabidopsis homeobox protein GLABRA 2. The mammalian STARDs are grouped into 8 subfamilies. This family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. For some members of this family, specific lipids that bind in this pocket are known; these include cholesterol (STARD1/STARD3/ STARD4/STARD5), 25-hydroxycholesterol (STARD5), phosphatidylcholine (STARD2/ STARD7/STARD10), phosphatidylethanolamine (STARD10) and ceramides (STARD11). The START domain is found either alone or in association with other domains. Mammalian STARDs participate in the control of various cellular processes including lipid trafficking between intracellular compartments, lipid metabolism, and modulation of signaling events. Mutation or altered expression of STARDs is linked to diseases such as cancer, genetic disorders, and autoimmune disease. The Arabidopsis homeobox protein GLABRA 2 suppresses root hair formation in hairless epidermal root cells. 193 matched cddid_all.tbl CDD cd00178 cd00178 467384 beta-trefoil_STI soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold. The STI-like domain is found in the soybean trypsin inhibitor (Kunitz) family of protease inhibitors. They inhibit proteases by binding with high affinity to their active sites. Plant Kunitz-type inhibitors are thought to be important in defense, especially against insect pests. The STI-like domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 161 matched cddid_all.tbl CDD cd00179 cd00179 238105 SynN Syntaxin N-terminus domain; syntaxins are nervous system-specific proteins implicated in the docking of synaptic vesicles with the presynaptic plasma membrane; they are a family of receptors for intracellular transport vesicles; each target membrane may be identified by a specific member of the syntaxin family; syntaxins contain a moderately well conserved amino-terminal domain, called Habc, whose structure is an antiparallel three-helix bundle; a linker of about 30 amino acids connects this to the carboxy-terminal region, designated H3 (t_SNARE), of the syntaxin cytoplasmic domain; the highly conserved H3 region forms a single, long alpha-helix when it is part of the core SNARE complex and anchors the protein on the cytoplasmic surface of cellular membranes; H3 is not included in defining this domain 151 matched cddid_all.tbl CDD cd00180 cd00180 270622 PKc Catalytic domain of Protein Kinases. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine or tyrosine residues on protein substrates. PKs make up a large family of serine/threonine kinases (STKs), protein tyrosine kinases (PTKs), and dual-specificity PKs that phosphorylate both serine/threonine and tyrosine residues of target proteins. Majority of protein phosphorylation occurs on serine residues while only 1% occurs on tyrosine residues. Protein phosphorylation is a mechanism by which a wide variety of cellular proteins, such as enzymes and membrane channels, are reversibly regulated in response to certain stimuli. PKs often function as components of signal transduction pathways in which one kinase activates a second kinase, which in turn, may act on other kinases; this sequential action transmits a signal from the cell surface to target proteins, which results in cellular responses. The PK family is one of the largest known protein families with more than 100 homologous yeast enzymes and more than 500 human proteins. A fraction of PK family members are pseudokinases that lack crucial residues for catalytic activity. The mutiplicity of kinases allows for specific regulation according to substrate, tissue distribution, and cellular localization. PKs regulate many cellular processes including proliferation, division, differentiation, motility, survival, metabolism, cell-cycle progression, cytoskeletal rearrangement, immunity, and neuronal functions. Many kinases are implicated in the development of various human diseases including different types of cancer. The PK family is part of a larger superfamily that includes the catalytic domains of RIO kinases, aminoglycoside phosphotransferase, choline kinase, phosphoinositide 3-kinase (PI3K), and actin-fragmin kinase. 215 matched cddid_all.tbl CDD cd00181 cd00181 438624 chemoreceptor_sensor 4-helix bundle ligand binding sensor domain of chemoreceptors such as Tar or Tsr. The ligand binding sensor domain of chemoreceptors and related sensor histidine kinases forms homodimers and binds to ligands via the dimerization interface, a feature that appears to be conserved in this domain superfamily. This family includes ligand binding sensor domain of several chemoreceptors, such as Escherichia coli Tar, Tsr, NarQ, NarX, Pseudomonas aeruginosa KinB, Rhodopseudomonas palustris histidine kinase HK9 chemoreceptors, Comamonas testosteroni CNB-2 MCP2201 and Anaeromyxobacter dehalogenans histidine kinase Adeh_2942, among others. 119 matched cddid_all.tbl CDD cd00182 cd00182 410312 T-box DNA-binding domain of the T-box transcription factor family. The T-box family is an ancient family of transcription factors which plays a multitude of diverse functions throughout development. The founding member of the family is Brachyury (also known as TBXT, or T). Members share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. The T-box factors in Caenorhabditis elegans have evolved very differently than those in other organisms; its genome contains 22 T-box genes which encode factors which are diverse in DNA-binding specificity, function and sequence, and only 3 of these factors fall into the conserved T-box subfamilies. 176 matched cddid_all.tbl CDD cd00183 cd00183 238107 TFIIS_I N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme 76 matched cddid_all.tbl CDD cd00184 cd00184 238108 TNF Tumor Necrosis Factor; TNF superfamily members include the cytokines: TNF (TNF-alpha), LT (lymphotoxin-alpha, TNF-beta), CD40 ligand, Apo2L (TRAIL), Fas ligand, and osteoprotegerin (OPG) ligand. These proteins generally have an intracellular N-terminal domain, a short transmembrane segment, an extracellular stalk, and a globular TNF-like extracellular domain of about 150 residues. They initiate apoptosis by binding to related receptors, some of which have intracellular death domains. They generally form homo- or hetero- trimeric complexes.TNF cytokines bind one elongated receptor molecule along each of three clefts formed by neighboring monomers of the trimer with ligand trimerization a requiste for receptor binding. 137 matched cddid_all.tbl CDD cd00185 cd00185 276900 TNFRSF Tumor necrosis factor receptor superfamily (TNFRSF). Members of TNFR superfamily (TNFRSF) interactions with TNF superfamily (TNFSF) ligands (TNFL) control key cellular processes such as differentiation, proliferation, apoptosis, and cell growth. Dysregulation of these pathways has been shown to result in a wide range of pathological conditions, including autoimmune diseases, inflammation, cancer, and viral infection. There are 29 very diverse family members of TNFRSF reported in humans: 22 are type I transmembrane receptors (single pass with the N terminus on extracellular side of the cell membrane) and have a clear signal peptide; the remaining 7 members are either type III transmembrane receptors (single pass with the N terminus on extracellular side of the membrane but no signal sequence; TNFR13B, TNFR13C, TNFR17, and XEDAR), or attached to the membrane via a glycosylphosphatidylinositol (GPI) linker (TNFR10C), or secreted as soluble receptors (TNFR11B and TNFR6B). All TNFRs contain relatively short cysteine-rich domains (CRDs) in the ectodomain, and are involved in interaction with the TNF homology domain (THD) of their ligands. TNFRs often have multiple CRDs (between one and six), with the most frequent configurations of three or four copies; most CRDs possess three disulfide bridges, but could have between one and four. Localized or genome-wide duplication and evolution of the TNFRSF members appear to have paralleled the emergence of the adaptive immune system; teleosts (i.e. ray-finned, bony fish), which possess an immune system with B and T cells, possess primary and secondary lymphoid organs, and are capable of adaptive responses to pathogens also display several characteristics that are different from the mammalian immune system, making teleost TNFSF orthologs and paralogs of interest to better understand immune system evolution and the immunological pathways elicited to pathogens. 87 matched cddid_all.tbl CDD cd00186 cd00186 238110 TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand. 381 matched cddid_all.tbl CDD cd00187 cd00187 238111 TOP4c DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth. 445 matched cddid_all.tbl CDD cd00188 cd00188 173773 TOPRIM Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. 83 matched cddid_all.tbl CDD cd00190 cd00190 238113 Tryp_SPc Trypsin-like serine protease; Many of these are synthesized as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. Alignment contains also inactive enzymes that have substitutions of the catalytic triad residues. 232 matched cddid_all.tbl CDD cd00191 cd00191 238114 TY Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases 66 matched cddid_all.tbl CDD cd00192 cd00192 270623 PTKc Catalytic domain of Protein Tyrosine Kinases. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. They can be classified into receptor and non-receptor tyr kinases. PTKs play important roles in many cellular processes including, lymphocyte activation, epithelium growth and maintenance, metabolism control, organogenesis regulation, survival, proliferation, differentiation, migration, adhesion, motility, and morphogenesis. Receptor tyr kinases (RTKs) are integral membrane proteins which contain an extracellular ligand-binding region, a transmembrane segment, and an intracellular tyr kinase domain. RTKs are usually activated through ligand binding, which causes dimerization and autophosphorylation of the intracellular tyr kinase catalytic domain, leading to intracellular signaling. Some RTKs are orphan receptors with no known ligands. Non-receptor (or cytoplasmic) tyr kinases are distributed in different intracellular compartments and are usually multi-domain proteins containing a catalytic tyr kinase domain as well as various regulatory domains such as SH3 and SH2. PTKs are usually autoinhibited and require a mechanism for activation. In many PTKs, the phosphorylation of tyr residues in the activation loop is essential for optimal activity. Aberrant expression of PTKs is associated with many development abnormalities and cancers.The PTK family is part of a larger superfamily that includes the catalytic domains of serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 262 matched cddid_all.tbl CDD cd00193 cd00193 277192 SNARE SNARE motif. SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, Qb- and Qc-SNAREs are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. 54 matched cddid_all.tbl CDD cd00194 cd00194 270455 UBA_like_SF UBA domain-like superfamily. The ubiquitin-associated (UBA) domain-like superfamily contains alpha-helical structural homology ubiquitin-binding domains, including UBA domains and coupling of ubiquitin conjugation to endoplasmic reticulum degradation (CUE) domains which share a common three-helical bundle architecture. UBA domains are commonly occurring sequence motifs found in proteins involved in ubiquitin-mediated proteolysis. They contribute to ubiquitin (Ub) binding or ubiquitin-like (UbL) domain binding. However, some kinds of UBA domains can only bind the UbL domain, but not the Ub domain. UBA domains are normally comprised of compact three-helix bundles which contain a conserved GF/Y-loop. They can bind polyubiquitin with high affinity. They also bind monoubiquitin and other proteins. Most UBA domain-containing proteins have one UBA domain, but some harbor two or three UBA domains. CUE domain containing proteins are characterized by an FP and a di-leucine-like sequence and bind to monoubiquitin with varying affinities. Some higher eukaryotic CUE domain proteins do not bind monoubiquitin efficiently, since they carry LP, rather than FP among CUE domains. This superfamily also includes many UBA-like domains found in AMP-activated protein kinase (AMPK) related kinases, the NXF family of mRNA nuclear export factors, elongation factor Ts (EF-Ts), nascent polypeptide-associated complex subunit alpha (NACA) and similar proteins. Although many UBA-like domains may have a conserved TG but not GF/Y-loop, they still show a high level of structural and sequence similarity with three-helical ubiquitin binding domains. 28 matched cddid_all.tbl CDD cd00195 cd00195 467407 UBCc_UEV Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain/ubiquitin E2 variant (UEV) domain. The family includes ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain and ubiquitin (Ub) E2 variant (UEV) domain. They belong to the ubiquitin-conjugating (UBC) superfamily that represents a structural domain with an alpha-beta(4)-alpha(3) core fold. E2 is part of the ubiquitin-mediated protein degradation pathway in which a thioester linkage forms between a conserved cysteine and the C-terminus of ubiquitin, and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thioester linkages without the use of E3s. Several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) contains the UEV domain, which lacks the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways. 112 matched cddid_all.tbl CDD cd00196 cd00196 340450 Ubiquitin_like_fold Beta-grasp ubiquitin-like fold. Ubiquitin is a protein modifier that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. The ubiquitination process comprises a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. Ubiquitin-like proteins have similar ubiquitin beta-grasp fold and attach to other proteins in a ubiquitin-like manner but with biochemically distinct roles. Ubiquitin and ubiquitin-like proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some other ubiquitin-like domains have adaptor roles in ubiquitin-signaling by mediating protein-protein interaction. In addition to Ubiquitin-like (Ubl) domain, Ras-associating (RA) domain, F0/F1 sub-domain of FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, TGS (ThrRS, GTPase and SpoT) domain, Ras-binding domain (RBD), Ubiquitin regulatory domain X (UBX), Dublecortin-like domain, and RING finger- and WD40-associated ubiquitin-like (RAWUL) domain have beta-grasp ubiquitin-like folds, and are included in this superfamily. 68 matched cddid_all.tbl CDD cd00197 cd00197 340764 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily. This superfamily is composed of proteins containing a VHS, CID, ENTH, or ANTH domain. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It is located at the N-termini of proteins involved in intracellular membrane trafficking. The CTD-Interacting Domain (CID) is present in several RNA-processing factors and binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase II (RNAP II or Pol II). The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-Terminal Homology (ANTH) domain. VHS, ENTH, and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH and ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH domain-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the Trans-Golgi Network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding. 115 matched cddid_all.tbl CDD cd00198 cd00198 238119 vWFA Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains. 161 matched cddid_all.tbl CDD cd00199 cd00199 238120 WAP whey acidic protein-type four-disulfide core domains. Members of the family include whey acidic protein, elafin (elastase-specific inhibitor), caltrin-like protein (a calcium transport inhibitor) and other extracellular proteinase inhibitors. A group of proteins containing 8 characteristically-spaced cysteine residuesforming disulphide bonds, have been termed '4-disulphide core' proteins. Protease inhibition occurs by insertion of the inhibitory loop into the active site pocket and interference with the catalytic residues of the protease. 60 matched cddid_all.tbl CDD cd00200 cd00200 238121 WD40 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands; 7 copies of the repeat are present in this alignment. 289 matched cddid_all.tbl CDD cd00201 cd00201 238122 WW Two conserved tryptophans domain; also known as the WWP or rsp5 domain; around 40 amino acids; functions as an interaction module in a diverse set of signalling proteins; binds specific proline-rich sequences but at low affinities compared to other peptide recognition proteins such as antibodies and receptors; WW domains have a single groove formed by a conserved Trp and Tyr which recognizes a pair of residues of the sequence X-Pro; variable loops and neighboring domains confer specificity in this domain; there are five distinct groups based on binding: 1) PPXY motifs 2) the PPLP motif; 3) PGM motifs; 4) PSP or PTP motifs; 5) PR motifs. 31 matched cddid_all.tbl CDD cd00202 cd00202 238123 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C 54 matched cddid_all.tbl CDD cd00203 cd00203 238124 ZnMc Zinc-dependent metalloprotease. This super-family of metalloproteases contains two major branches, the astacin-like proteases and the adamalysin/reprolysin-like proteases. Both branches have wide phylogenetic distribution, and contain sub-families, which are involved in vertebrate development and disease. 167 matched cddid_all.tbl CDD cd00205 cd00205 119412 rhv_like Picornavirus capsid protein domain_like. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids composed of 60 copies each of 4 virus encoded proteins; alignment includes picornaviridae, like poliovirus, hepatitis A virus, rhinovirus, foot-and-mouth disease virus and encephalomyocarditis virus; common structure is an 8-stranded beta sandwich 178 matched cddid_all.tbl CDD cd00206 cd00206 467061 TFP_snake_toxin Snake toxin domain. The snake toxin domain is present in short and long neurotoxins, cytotoxins and short toxins, and in other miscellaneous venom peptides. The toxin acts by binding to the nicotinic acetylcholine receptors in the postsynaptic membrane of skeletal muscles and preventing the binding of acetylcholine, thereby blocking the excitation of muscles. This domain contains 60-75 amino acids that are fixed by 4-5 disulfide bridges and is nearly all beta sheets; it exists as either a monomer or a dimer. The snake toxin domain exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold), which also includes extracellular domain (ECD) found in Ly-6 antigen/uPA receptor-like (LU) superfamily. 64 matched cddid_all.tbl CDD cd00207 cd00207 238126 fer2 2Fe-2S iron-sulfur cluster binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins, which act as electron carriers in photosynthesis and ferredoxins, which participate in redox chains (from bacteria to mammals). Fold is ismilar to thioredoxin. 84 matched cddid_all.tbl CDD cd00208 cd00208 100038 LbetaH Left-handed parallel beta-Helix (LbetaH or LbH) domain: The alignment contains 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity, however, some subfamilies in this hierarchy also show activities related to ion transport or translation initiation. Many are trimeric in their active forms. 78 matched cddid_all.tbl CDD cd00209 cd00209 238127 DHFR Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5,10-methylenetetrahydrofolate which is then utilized by thymidylate synthase. Inhibition of DHFR interrupts thymidilate synthesis and DNA replication, inhibitors of DHFR (such as Methotrexate) are used in cancer chemotherapy. 5,6,7,8-tetrahydrofolate also is involved in glycine, serine, and threonine metabolism and aminoacyl-tRNA biosynthesis. 158 matched cddid_all.tbl CDD cd00210 cd00210 238128 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. 124 matched cddid_all.tbl CDD cd00211 cd00211 238129 PTS_IIA_fru PTS_IIA, PTS system, fructose/mannitol specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. 136 matched cddid_all.tbl CDD cd00212 cd00212 238130 PTS_IIB_glc PTS_IIB, PTS system, glucose/sucrose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation 78 matched cddid_all.tbl CDD cd00213 cd00213 238131 S-100 "S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. Intracellularly, S100 proteins act as Ca-signaling or Ca-buffering proteins. The most unusual characteristic of certain S100 proteins is their occurrence in extracellular space, where they act in a cytokine-like manner through RAGE, the receptor for advanced glycation products. Structural data suggest that many S100 members exist within cells as homo- or heterodimers and even oligomers; oligomerization contributes to their functional diversification. Upon binding calcium, most S100 proteins change conformation to a more open structure exposing a hydrophobic cleft. This hydrophobic surface represents the interaction site of S100 proteins with their target proteins. There is experimental evidence showing that many S100 proteins have multiple binding partners with diverse mode of interaction with different targets. In addition to S100 proteins (such as S100A1,-3,-4,-6,-7,-10,-11,and -13), this group includes the ''fused'' gene family, a group of calcium binding S100-related proteins. The ''fused'' gene family includes multifunctional epidermal differentiation proteins - profilaggrin, trichohyalin, repetin, hornerin, and cornulin; functionally these proteins are associated with keratin intermediate filaments and partially crosslinked to the cell envelope. These ''fused'' gene proteins contain N-terminal sequence with two Ca-binding EF-hands motif, which may be associated with calcium signaling in epidermal cells and autoprocessing in a calcium-dependent manner. In contrast to S100 proteins, ""fused"" gene family proteins contain an extraordinary high number of almost perfect peptide repeats with regular array of polar and charged residues similar to many known cell envelope proteins." 88 matched cddid_all.tbl CDD cd00214 cd00214 238132 Calpain_III Calpain, subdomain III. Calpains are calcium-activated cytoplasmic cysteine proteinases, participate in cytoskeletal remodeling processes, cell differentiation, apoptosis and signal transduction. Catalytic domain and the two calmodulin-like domains are separated by C2-like domain III. Domain III plays an important role in calcium-induced activation of calpain involving electrostatic interactions with subdomain II. Proposed to mediate calpain's interaction with phospholipids and translocation to cytoplasmic/nuclear membranes. CD includes subdomain III of typical and atypical calpains. 150 matched cddid_all.tbl CDD cd00215 cd00215 238133 PTS_IIA_lac PTS_IIA, PTS system, lactose/cellobiose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. This family of proteins normally function as a homotrimer, stabilized by a centrally located metal ion. Separation into subunits is thought to occur after phosphorylation. 97 matched cddid_all.tbl CDD cd00216 cd00216 199833 PQQ_DH_like PQQ-dependent dehydrogenases and related proteins. This family is composed of dehydrogenases with pyrroloquinoline quinone (PQQ) as a cofactor, such as ethanol, methanol, and membrane-bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller, and the family also includes distantly related proteins which are not enzymatically active and do not bind PQQ. 434 matched cddid_all.tbl CDD cd00217 cd00217 271174 INT_Flp_C Flp Tyrosine-based site-specific recombinases (also called integrases), C-terminal catalytic domain. Yeast Flp-like recombinases mediate the amplification of the 2 micron circular plasmid copy number by catalyzing the intra-molecular recombination between two inverted repeats during replication. They belong to the DNA breaking-rejoining enzyme superfamily, which also includes prokaryotic tyrosine recombinases and type IB topoisomerases. These enzymes share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism. Flp-like recombinases are almost exclusively found in yeast and are highly diverged in sequence from the prokaryotic tyrosine recombinases. They cleave their target DNA in trans with a composite active site in which the catalytic tyrosine is provided by a promoter bound to a site other than the one being cleaved. Thus each active site within Flp complexes is assembled by domain swapping and contains catalytic residues from two different monomers. Two DNA segments are synapsed by the tetrameric enzyme, carrying the nucleophilic tyrosine in each active site with only two of the four monomers active at a given time. The catalytic domain is linked through a flexible loop to the N-terminal domain, which is largely responsible for non-specific DNA binding and isomerization. Its overall fold is similar to the SAM domain fold also found in the N-terminal domains of lambda integrase and XerD recombinase. 410 matched cddid_all.tbl CDD cd00218 cd00218 132995 GlcAT-I Beta1,3-glucuronyltransferase I (GlcAT-I) is involved in the initial steps of proteoglycan synthesis. Beta1,3-glucuronyltransferase I (GlcAT-I) domain; GlcAT-I is a Key enzyme involved in the initial steps of proteoglycan synthesis. GlcAT-I catalyzes the transfer of a glucuronic acid moiety from the uridine diphosphate-glucuronic acid (UDP-GlcUA) to the common linkage region of trisaccharide Gal-beta-(1-3)-Gal-beta-(1-4)-Xyl of proteoglycans. The enzyme has two subdomains that bind the donor and acceptor substrate separately. The active site is located at the cleft between both subdomains in which the trisaccharide molecule is oriented perpendicular to the UDP. This family has been classified as Glycosyltransferase family 43 (GT-43). 223 matched cddid_all.tbl CDD cd00219 cd00219 119405 ToxGAP GTPase-activating protein (GAP) domain found in bacterial cytotoxins, ExoS, SptP, and YopE. Part of protein secretion system; stimulates Rac1- dependent cytoskeletal changes that promote bacterial internalization. 120 matched cddid_all.tbl CDD cd00220 cd00220 238135 VMO-I Vitelline membrane outer layer protein I (VMO-I) domain, VMO-I is one of the proteins found in the outer layer of the vitelline membrane of poultry eggs; VMO-I, lysozyme, and VMO-II are tightly bound to ovomucin; this complex forms the backbone of the outer layer; VMO-I has three distinct internal repeats; all three repeats are used to define the domain here; VMO-I has recently been shown to synthesize N-acetylchito-oligosaccharides from N-acetylglucosamine; may be a carbohydrate-binding protein; member of the beta-prism-fold family 177 matched cddid_all.tbl CDD cd00221 cd00221 411702 Vsr Very short patch repair endonuclease. Very short patch repair (Vsr) is an endonuclease functioning in DNA repair that recognizes damaged DNA and cleaves the phosphodiester backbone. Vsr endonucleases have a common endonuclease topology that has been tailored for recognition of TG mismatches. It belongs to a superfamily of nucleases including archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 133 matched cddid_all.tbl CDD cd00222 cd00222 212461 CollagenBindB Repeat unit of collagen-binding protein domain B. The collagen-binding protein mediates bacterial adherence to collagen; the primary sequence has a non-repetitive, collagen-binding A region, followed by instances of this B region repetitive unit. The B region has one to four 23 kDa repeat units (B1-B4), which have been suggested to serve as 'stalks' that project the A region from the bacterial surface and thus facilitate bacterial adherence to collagen. Each B repeat unit has two highly similar domains (D1 and D2) placed side-by-side; both D1 and D2 are included in this model. They exhibit a unique inverse IgG-like domain fold. 92 matched cddid_all.tbl CDD cd00223 cd00223 173774 TOPRIM_TopoIIB_SPO TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. TopoVI enzymes are heterotetramers found in archaea and plants. Spo11 plays a role in generating the double strand breaks that initiate homologous recombination during meiosis. S. shibatae TopoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD. For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. 160 matched cddid_all.tbl CDD cd00224 cd00224 238137 Mog1 homolog to Ran-Binding Protein Mog1p; binds to the small GTPase Ran, which plays an important role in nuclear import. Binding is independent of Ran's nucleotide state (RanGTP/RanGDP) 173 matched cddid_all.tbl CDD cd00225 cd00225 119406 API3 Ascaris pepsin inhibitor-3 (API3); protein inhibitor that reversibly inhibits aspartic proteinase cathepsin E, and gastric enzymes pepsin and gastricsin. 159 matched cddid_all.tbl CDD cd00226 cd00226 238138 PRCH Photosynthetic reaction center (RC) complex, subunit H; RC is an integral membrane protein-pigment complex which catalyzes light-induced reduction of ubiquinone to ubiquinol, generating a transmembrane electrochemical gradient of protons used to produce ATP by ATP synthase. Subunit H is positioned mainly in the cytoplasm with one transmembrane alpha helix. Provides proton transfer pathway (water channels) connecting the terminal quinone electron acceptor of RC, to the aqueous phase. Found in photosynthetic bacteria: alpha, beta, and gamma proteobacteria. 246 matched cddid_all.tbl CDD cd00227 cd00227 238139 CPT Chloramphenicol (Cm) phosphotransferase (CPT). Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II. 175 matched cddid_all.tbl CDD cd00228 cd00228 238140 eu-GS Eukaryotic Glutathione Synthetase (eu-GS); catalyses the production of glutathione from gamma-glutamylcysteine and glycine in an ATP-dependent manner. Belongs to the ATP-grasp superfamily. 471 matched cddid_all.tbl CDD cd00229 cd00229 238141 SGNH_hydrolase SGNH_hydrolase, or GDSL_hydrolase, is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid. 187 matched cddid_all.tbl CDD cd00231 cd00231 238142 ZipA ZipA C-terminal domain. ZipA, a membrane-anchored protein, is one of at least nine essential gene products necessary for assembly of the septal ring which mediates cell division in E.coli. ZipA and FtsA directly bind FtsZ, a homolog of eukaryotic tubulins, at the prospective division site, followed by the sequential addition of FtsK, FtsQ, FtsL, FtsW, FtsI, and FtsN. ZipA contains three domains: a short N-terminal membrane-anchored domain, a central P/Q domain that is rich in proline and glutamine and a C-terminal domain, which comprises almost half the protein. 130 matched cddid_all.tbl CDD cd00232 cd00232 350855 HemeO-like heme oxygenase. Heme oxygenase (HO, EC 1.14.14.18) catalyzes the rate limiting step in the degradation of heme to biliverdin in a multi-step reaction. HO is essential for recycling iron from heme which is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This family serves a variety of specific needs in different branches of life: in vertebrates, HO plays a role in heme homeostasis and oxidative stress response, and cellular signaling in mammals that include isoforms HO-1 and HO-2; in photosynthetic organisms including cyanobacteria, algae, and higher plants, biliverdin is used for photosynthetic pigment formation or light-sensing; and, in pathogenic bacteria, HO is part of a pathway for iron acquisition from host heme and heme products. HO shares tertiary structure similarity to methane monooxygenase (EC 1.14.13.25), ribonucleotide reductase (EC 1.17.4.1) and thiaminase II (EC 3.5.99.2), but shares little sequence homology. 201 matched cddid_all.tbl CDD cd00233 cd00233 238144 VIP2 VIP2; A family of actin-ADP-ribosylating toxin. A member of the Bacillus-prodiced vegetative insecticidal proteins (VIPs) possesses high specificity against the major insect pest, corn rootworms, and belongs to a classs of binary toxins and regulators of biological pathways distinct from classical A-B toxins. A novel family of insecticidal ADP-ribosyltransferses were isolated from Bacillus cereus during vegetative growth, where VIP1 likely targets insect cells and VIP2 ribosylates actin. VIP2 shares significant sequence similarity with enzymatic components of other binary toxins, Clostridium botulinum C2 toxin, C. perfringens iota toxin, C. piroforme toxin, C. piroforme toxin and C. difficile toxin. 201 matched cddid_all.tbl CDD cd00235 cd00235 119413 TLP-20 Telokin-like protein-20 (TLP-20) domain; a baculovirus protein that shares some antigenic similarities to the smooth muscle protein telokin, a kinase-related protein 108 matched cddid_all.tbl CDD cd00236 cd00236 238145 FinO_conjug_rep FinO bacterial conjugation repressor domain; the basic protein FinO is part of the the two component FinOP system which is responsible for repressing bacterial conjugation; the FinOP system represses the transfer (tra) operon of the F-plasmid which encodes the proteins responsible for conjugative transfer of this plasmid from host to recipient Escherichia coli cells; antisense RNA, FinP is thought to interact with traJ mRNA to occlude its ribosome binding site, blocking traJ translation and thereby inhibiting transcription of the tra operon; FinO protects FinP against degradation by binding to FinP and sterically blocking the cellular endonuclease RNase E; FinO also also binds to the complementary stem-loop structures in traJ mRNA and promotes duplex formation between FinP and traJ RNA in vitro; this domain contains two independent RNA binding regions 146 matched cddid_all.tbl CDD cd00237 cd00237 107218 p23 p23 binds heat shock protein (Hsp)90 and participates in the folding of a number of Hsp90 clients, including the progesterone receptor. p23 also has a passive chaperoning activity and in addition may participate in prostaglandin synthesis. 106 matched cddid_all.tbl CDD cd00238 cd00238 238146 ERp29c ERp29 and ERp38, C-terminal domain; composed of the protein disulfide isomerase (PDI)-like proteins ERp29 and ERp38. ERp29 (also called ERp28) is a ubiquitous endoplasmic reticulum (ER)-resident protein expressed in high levels in secretory cells. It contains a redox inactive TRX-like domain at the N-terminus. The expression profile of ERp29 suggests a role in secretory protein production, distinct from that of PDI. It has also been identified as a member of the thyroglobulin folding complex and is essential in regulating the secretion of thyroglobulin. The Drosophila homolog, Wind, is the product of windbeutel, an essential gene in the development of dorsal-ventral patterning. Wind is required for correct targeting of Pipe, a Golgi-resident type II transmembrane protein with homology to 2-O-sulfotransferase. ERp38 is a P5-like protein, first isolated from alfalfa (the cDNA clone was named G1), which contains two redox active TRX domains at the N-terminus, like human P5. However, unlike human P5, ERp38 also contains a C-terminal domain with homology to the C-terminal domain of ERp29. It may be a glucose-regulated protein. The function of the all-helical C-terminal domain of ERp29 and ERp38 remains unclear. The C-terminal domain of Wind is thought to provide a distinct site required for interaction with its substrate, Pipe. 93 matched cddid_all.tbl CDD cd00239 cd00239 119414 PapG_CBD PapG carbohydrate / receptor binding domain (CBD); PapG, the adhesin of the P-pili, is situated at the tip, mediating the attachment of uropathogenic Escherichia coli to the uroepithelium of the human kidney; PapG has a two-domain architecture: a carbohydrate binding N-terminus (this domain) and chaperone binding C-terminus (C-terminal pilin region). The carbohydrate-binding domain interacts with the receptor glycan. There are 3 PapG alleles, class I-III, which bind to different receptor isotypes, GbO3, GbO4, and GbO5, respectively. 194 matched cddid_all.tbl CDD cd00240 cd00240 238147 TFIIFa Transcription initiation factor IIF, alpha subunit, N-terminal region of RAP74. Subunit of transcription initiation complex involved in initiation, elongation and promoter escape.Tetramer of 2 alpha and 2 beta TFIIF subunits interacts directly with RNA polymerase II. TFIIF inhibits non-specific transcription initiation by PolII and recruits the polymerase to the preinitiation complex on promoter DNA for site-specific transcription initiation. The PolII/TFIIF-complex attaches through direct interactions of TFIIF with promoter DNA, TFIIB and the TAF250 subunit of TFIID, and provides scaffolding for addition of TFIIE and TFIIH. Together with TFIIE, TFIIF participates in DNA strand separation (open complex formation). N-terminal domains of RAP30 and RAP74 co-fold to form a single core structure, a triple barrel heterodimer, and has pseudo-2-fold symmetry. 162 matched cddid_all.tbl CDD cd00241 cd00241 187675 DOMON_like Domon-like ligand-binding domains. DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases. 158 matched cddid_all.tbl CDD cd00242 cd00242 153074 Ecotin Protease Inhibitor Ecotin; homodimeric protease inhibitor. Protease Inhibitor Ecotin; homodimeric protease inhibitor which binds two chymotrypsin-like serine proteases to form a heterotetramer. Found in bacterial periplasm. Inhibits a broad range of serine proteases including collagenase, trypsin, chymotrypsin, elastase, and factor Xa but not thrombin. Inhibition mechanism involves binding at two different protease contact sites: the primary and secondary binding sites. Primary site loops of ecotin bind to the active site of target proteases in a substrate-like manner with the P1 residue in ecotin mimicking the interactions of a canonical P1 substrate residue. 136 matched cddid_all.tbl CDD cd00243 cd00243 119415 Lysin-Sp18 Sp18 and Lysin from Archaegastropoda (marine mollusks of the families Halotidae and Trochidae) sperm. Both proteins play an important role in fertilization: sp18 mediates fusion between sperm and egg cell membrane, lysin dissolves the vitelline envelope surrounding the egg; they are believed to be a product of gene duplication and subsequent divergence. 122 matched cddid_all.tbl CDD cd00244 cd00244 238148 AlgLyase Alginate Lyase A1-III; enzymatically depolymerizes alginate, a complex copolymer of beta-D-mannuronate and alpha-L-guluronate, by cleaving the beta-(1,4) glycosidic bond. 339 matched cddid_all.tbl CDD cd00245 cd00245 238149 Glm_e Coenzyme B12-dependent glutamate mutase epsilon subunit-like family; contains proteins similar to Clostridium cochlearium glutamate mutase (Glm) and Streptomyces tendae Tu901 NikV. Glm catalyzes a carbon-skeleton rearrangement of L-glutamate to L-threo-3-methylaspartate. The first step in the catalysis is a homolytic cleavage of the Co-C bond of the coenzyme B12 cofactor to generate a 5'-deoxyadenosyl radical. This radical then initiates the rearrangement reaction. C. cochlearium Glm is a sigma2epsilon2 heterotetramer. Glm plays a role in glutamate fermentation in Clostridium sp. and in members of the family Enterobacteriaceae, and in the synthesis of the lipopeptide antibiotic friulimicin in Actinoplanes friuliensis. S. tendae Tu901 glutamate mutase-like proteins NikU and NIkV participate in the synthesis of the peptidyl nucleoside antibiotic nikkomycin. NikU and NikV proteins have sequence similarity to Clostridium Glm sigma and epsilon components respectively, and may catalyze the rearrangement of 2-oxoglutaric acid to 2-keto-3-methylsuccinic acid during nikkomycin synthesis. 428 matched cddid_all.tbl CDD cd00246 cd00246 238150 RabGEF Nucleotide exchange factor for Rab-like small GTPases (RabGEF), Mss4 type; RabGEF positely regulates the function of Rab GTPase by promoting exchange of GDP for GTP; members of the Rab subfamily of Ras GTPases are important in vesicular transport; 103 matched cddid_all.tbl CDD cd00247 cd00247 238151 Endostatin-like Endostatin-like domain; the angiogenesis inhibitor endostatin is a C-terminal fragment of collagen XV/XVIII, a proteoglycan/collagen found in vessel walls and basement membranes; this domain has a compact globular fold similar to that of C-type lectins; endostatin XVIII is monomeric and contains a heparin-binding epitope and zinc binding sites while endostatin XV is trimeric and contains neither of these sites; the generation of endostatin or endostatin-like collagen XV/XVIII fragments is catalyzed by proteolytic enzymes within the protease-sensitive hinge region of the C-terminal domain; endostatin inhibits endothelial cell migration in vitro and appears to be highly effective in murine in vivo studies 171 matched cddid_all.tbl CDD cd00248 cd00248 238152 Mth938-like Mth938-like domain. The members of this family include: Mth938, 2P1, Xcr35, Rpa2829, and several uncharacterized sequences. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. 2P1 is a partially characterized nuclear protein which is homologous to E3-3 from rat and known to be alternately spliced. Xcr35 and Rpa2829 are hypothetical proteins of unknown function from the Xanthomonas campestris and Rhodopseudomonas palustris genomes, respectively, for which the crystal structures have been determined. 109 matched cddid_all.tbl CDD cd00249 cd00249 238153 AGE AGE domain; N-acyl-D-glucosamine 2-epimerase domain; Responsible for intermediate epimerization during biosynthesis of N-acetylneuraminic acid. Catalytic mechanism is believed to be via nucleotide elimination and readdition and is ATP modulated. AGE is structurally and mechanistically distinct from the other four types of epimerases. The AGE domain monomer is composed of an alpha(6)/alpha(6)-barrel, the structure of which is also found in glucoamylase and cellulase. The active form is a homodimer. The alignment also contains subtype III mannose 6-phosphate isomerases. 384 matched cddid_all.tbl CDD cd00250 cd00250 238154 CAS_like Clavaminic acid synthetase (CAS) -like; CAS is a trifunctional Fe(II)/ 2-oxoglutarate (2OG) oxygenase carrying out three reactions in the biosynthesis of clavulanic acid, an inhibitor of class A serine beta-lactamases. In general, Fe(II)-2OG oxygenases catalyze a hydroxylation reaction, which leads to the incorporation of an oxygen atom from dioxygen into a hydroxyl group and conversion of 2OG to succinate and CO2 262 matched cddid_all.tbl CDD cd00251 cd00251 119403 Mth_Ecto The ectodomain of Methuselah (Mth); Mth mutants have a 35% increase in average lifespan and increased resistance to several forms of stress, including heat, starvation, and oxidative damage; The protein affected by this mutation is related to G protein-coupled receptors of the secretin receptor family; Mth, like secretin receptor family members, has a large N-terminal ectodomain, which may constitute the ligand binding site. 176 matched cddid_all.tbl CDD cd00252 cd00252 320009 EFh_SPARC_EC EF-hand, extracellular calcium-binding (EC) motif, found in secreted protein acidic and rich in cysteine (SPARC)-like proteins. The SPARC protein family represents a diverse group of proteins that share a follistatin-like (FS) domain and an extracellular calcium-binding (EC) domain with two EF-hand motifs. It includes SPARC (for secreted protein acidic and rich in cysteine, also termed osteonectin/ON, or basement-membrane protein 40/BM-40), SPARC-like protein 1 (for secreted protein, acidic and rich in cysteines-like 1/ SPARCL1, also termed high endothelial venule protein/Hevi, or MAST 9, or SC-1, or RAGS-1, or QR1, or ECM 2), testicans 1, 2, and 3 (also termed SPARC/osteonectin, CWCV, and Kazal-like domains proteoglycans, or SPOCK), secreted modular calcium-binding protein SMOC-1 (also termed SPARC-related modular calcium-binding protein 1) and SMOC-2 (also termed SPARC-related modular calcium-binding protein 2, or smooth muscle-associated protein 2/SMAP-2), follistatin-related protein 1 (FRP-1, also termed follistatin-like protein 1/fstl-1, TSC-36/Flik, TGF-beta inducible protein). The SPARC proteins have been implicated in modulating cell interaction with the extracellular milieu, including regulation of extracellular matrix assembly and deposition, counter-adhesion, effects on extracellular protease activity, and modulation of growth factor/cytokine signaling pathways, as well as in development and disease. 107 matched cddid_all.tbl CDD cd00253 cd00253 238156 PL_Passenger_AT Pertactin-like passenger domains (virulence factors) of autotransporter proteins of the type V secretion system. Autotransporters are proteins used by Gram-negative bacteria to transport proteins across their outer membranes. The C-terminal (beta) domain of autotransporters forms a pore in the outer membrane through which the N-terminal passenger domain is transported. Following transport, the passenger domain is generally cleaved by an outer membrane protease with the passenger domain either remaining in contact with the surface via a noncovalent interaction with the beta domain or cleaved to release a soluble protein. These proteins are highly diverse and perform a variety of functions that promote virulence, including catalyzing proteolysis, serving as an adhesin, mediating actin-promoted motility, or serving as a cytotoxin. Proteins in this family share similarity in the C-terminal region of the passenger domain as seen in the pertactin structure P.69, a Bordetella pertussis agglutinogen responsible for human pertussis. The P.69 protein consists of a 16-stranded parallel beta-helix with a V-shaped cross-section, and is one of the largest beta-helix known to date. 186 matched cddid_all.tbl CDD cd00254 cd00254 381594 LT-like "lytic transglycosylase(LT)-like domain. Members include the soluble and insoluble membrane-bound LTs in bacteria and LTs in bacteriophage lambda. LTs catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), as do ""goose-type"" lysozymes. However, in addition to this, they also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue." 111 matched cddid_all.tbl CDD cd00255 cd00255 238158 nidG2 Nidogen, G2 domain; Nidogen is an important component of the basement membrane, an extracellular sheet-like matrix. Nidogen is a multifunctional protein that interacts with many other basement membrane proteins, like collagen, perlecan, lamin, and has a potential role in the assembly and connection of networks. Nidogen consists of 3 globular domains (G1-G3), G3 is the lamin-binding domain, while G2 binds collagen IV and perlecan. Also found in hemicentin, a protein which functions at various cell-cell and cell-matrix junctions and might assist in refining broad regions of cell contact into oriented, line-shaped junctions. Nidogen G2 consists of an N-terminal EGF-like domain (excluded from this alignment model) and an 11-stranded beta-barrel with a central helix, a topology that exhibits high structural similarity to the green flourescent proteins of Cnidaria. 224 matched cddid_all.tbl CDD cd00256 cd00256 238159 VATPase_H VATPase_H, regulatory vacuolar ATP synthase subunit H (Vma13p); activation component of the peripheral V1 complex of V-ATPase, a heteromultimeric enzyme which uses ATP to actively transport protons into organelles and extracellular compartments. The topology is that of a superhelical spiral, in part the geometry is similar to superhelices composed of armadillo repeat motifs, as found in importins for example. 429 matched cddid_all.tbl CDD cd00257 cd00257 467441 beta-trefoil_FSCN-like fascin-like domain, beta-trefoil fold, found in the fascin-like family. The fascin-like family includes actin-bundling/crosslinking proteins facsin1-4, singed, hisactophilin, and FSHD region gene 1 protein (FRG1). Fascin, also called fascin-1, is an actin-binding protein that contains 2 major actin binding sites. It is involved in the organization of actin filament bundles and the formation of microspikes, membrane ruffles, and stress fibers. It plays an important role for the formation of a diverse set of cell protrusions, such as filopodia, and for cell motility and migration. It mediates reorganization of the actin cytoskeleton and axon growth cone collapse in response to nerve growth factor (NGF). Fascin-2, also called retinal fascin, is a photoreceptor-specific paralog of the actin-bundling protein fascin. It may play a pivotal role in photoreceptor cell-specific events, such as disk morphogenesis. Fascin-3, also called testis fascin, is a novel paralog of the actin-bundling protein fascin expressed specifically in the elongate spermatid head. Protein singed acts as an actin-bundling protein that may have a role in the asymmetric organization and/or movement of cytoplasmic components. It has a role in somatic cells during the formation of adult bristles and hairs, and in the female germline during oogenesis. Hisactophilin is a histidine-rich actin-binding protein from Dictyostelium discoideum. It exists in two isoforms, hisactophilin-1 (HatA, also called HS I) and hisactophilin-2 (HatB, also called HS II), which are both myristoylated and distributed between plasma membrane and cytoplasm. Hisactophilin may act as an intracellular pH sensor that links chemotactic signals to responses in the microfilament system of the cells by nucleating actin polymerization or stabilizing the filaments. Protein FRG1 binds to mRNA in a sequence-independent manner. It may play a role in regulation of pre-mRNA splicing or in the assembly of rRNA into ribosomal subunits. It may be involved in mRNA transport, as well as in epigenetic regulation of muscle differentiation through regulation of activity of the histone-lysine N-methyltransferase KMT5B. This family also contains many homologs from bacteria, such as Zobellia galactanivorans beta-porphyranase A (PorA). PorA (EC 3.2.1.178) cleaves the sulfated polysaccharide porphyran at the (1->4) linkages between beta-D-galactopyranose and alpha-L-galactopyranose-6-sulfate, forming mostly the disaccharide alpha-L-galactopyranose-6-sulfate-(1->3)-beta-D-galactose. It is inactive on the non-sulfated agarose portion of the porphyran backbone and displays a strict requirement for C6-sulfate in the -2 and +1-binding subsites. Members of this family contain a fascin-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The fascin subfamily contains four copies of the fascin-like domain. 124 matched cddid_all.tbl CDD cd00258 cd00258 238161 GM2-AP GM2 activator protein (GM2-AP) is a non-enzymatic lysosomal protein that acts as cofactor in the sequential degradation of gangliosides. GM2A is an essential cofactor for beta-hexosaminidase A (Hex A) in the enzymatic hydrolysis of GM2 ganglioside to GM3. Mutation of the gene results in the AB variant of Tay-Sachs disease. GM2-AP and similar proteins belong to the ML domain family. 162 matched cddid_all.tbl CDD cd00259 cd00259 119404 STNV "STNV domain; satellite tobacco necrosis virus (STNV) are small plant viruses which are completely dependent on the presence of a specific helper virus, TNV, for their replication; 60 identical subunits, this domain is one of them; form an icosahedral shell around a single RNA molecule. Half of the RNA codes for the coat protein with the other half being non-coding. The STNV domain has a ""Swiss roll"" Greek key topology with its two 4-stranded antiparallel beta sheets" 195 matched cddid_all.tbl CDD cd00260 cd00260 271229 Sialidase sialidases/neuraminidases. Sialidases or neuraminidases function to bind and hydrolyze terminal sialic acid residues from various glycoconjugates as well as playing roles in pathogenesis, bacterial nutrition and cellular interactions. They have a six-bladed beta-propeller fold. This hierarchy includes eubacterial, eukaryotic, and viral sialidases. 361 matched cddid_all.tbl CDD cd00261 cd00261 238163 AAI_SS AAI_SS: Alpha-Amylase Inhibitors (AAIs) and Seed Storage (SS) Protein subfamily; composed of cereal-type AAIs and SS proteins. They are mainly present in the seeds of a variety of plants. AAIs play an important role in the natural defenses of plants against insects and pathogens such as fungi, bacteria and viruses. AAIs impede the digestion of plant starch and proteins by inhibiting digestive alpha-amylases and proteinases. Also included in this subfamily are SS proteins such as 2S albumin, gamma-gliadin, napin, and prolamin. These AAIs and SS proteins are also known allergens in humans. 110 matched cddid_all.tbl CDD cd00264 cd00264 238164 BPI BPI/LBP/CETP domain; Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) domain; binds to and neutralizes lipopolysaccharides from the outer membrane of Gram-negative bacteria.; Apolar pockets on the concave surface bind a molecule of phosphatidylcholine, primarily by interacting with their acyl chains; this suggests that the pockets may also bind the acyl chains of lipopolysaccharide. 208 matched cddid_all.tbl CDD cd00265 cd00265 238165 MADS_MEF2_like MEF2 (myocyte enhancer factor 2)-like/Type II subfamily of MADS ( MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero and homo-dimers. Differs from SRF-like/Type I subgroup mainly in position of the alpha helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi. 77 matched cddid_all.tbl CDD cd00266 cd00266 238166 MADS_SRF_like SRF-like/Type I subfamily of MADS (MCM1, Agamous, Deficiens, and SRF (serum response factor) box family of eukaryotic transcriptional regulators. Binds DNA and exists as hetero- and homo-dimers. Differs from the MEF-like/Type II subgroup mainly in position of the alpha 2 helix responsible for the dimerization interface. Important in homeotic regulation in plants and in immediate-early development in animals. Also found in fungi. 83 matched cddid_all.tbl CDD cd00267 cd00267 213179 ABC_ATPase ATP-binding cassette transporter nucleotide-binding domain. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 157 matched cddid_all.tbl CDD cd00268 cd00268 350669 DEADc DEAD-box helicase domain of DEAD box helicases. DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 196 matched cddid_all.tbl CDD cd00270 cd00270 238168 MATH_TRAF_C Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF domain, C-terminal MATH subdomain; TRAF molecules serve as adapter proteins that link cell surface TNFRs and receptors of the interleukin-1/Toll-like family to downstream kinase signaling cascades which results in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses in the immune and inflammatory systems. There are at least six mammalian and three Drosophila proteins containing TRAF domains. The mammalian TRAFs display varying expression profiles, indicating independent and cell type-specific regulation. They display distinct, as well as overlapping functions and interactions with receptors. Most TRAFs, except TRAF1, share N-terminal homology and contain a RING domain, multiple zinc finger domains, and a TRAF domain. TRAFs form homo- and heterotrimers through its TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors. 149 matched cddid_all.tbl CDD cd00271 cd00271 238169 Chemokine_C Chemokine_C, C or lymphotactin subgroup, 1 of 4 subgroup designations of chemokines based on the arrangement of two N-terminal, conserved cysteine residues. Most of the known chemokines (cd00169) belong to either the CC (cd00272) or CXC (cd00273) subclass. The two other subclasses each have a single known member: fractalkine for the CX3C (cd00274) class and lymphotactin for the C (cd00271) class. Chemokine_Cs differ structurally since they contain only one of the two disulfide bridges that are conserved in all other chemokines and they possess a unique C-terminal extension, which is required for biological activity and thought to play a role in receptor binding. Lymphotactin, a mediator of mucosal immunity, has been found to chemoattract neutrophils and B cells through the XCR1 receptor and thought to be a factor in acute allograft rejection and inflammatory bowel disease. 72 matched cddid_all.tbl CDD cd00272 cd00272 238170 Chemokine_CC Chemokine_CC: 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; some members (e.g. 2HCC) contain an additional disulfide bond which is thought to compensate for the highly conserved Trp missing in these; chemotatic for monocytes, macrophages, eosinophils, basophils, and T cells, but not neutrophils; exist as monomers and dimers, but are believed to be functional as monomers; found only in vertebrates and a few viruses; a subgroup of CC, identified by an N-terminal DCCL motif (Exodus-1, Exodus-2, and Exodus-3), has been shown to inhibit specific types of human cancer cell growth in a mouse model. See CDs: Chemokine (cd00169) for the general alignment of chemokines, or Chemokine_CXC (cd00273), Chemokine_C (cd00271), and Chemokine_CX3C (cd00274) for the additional chemokine subgroups, and Chemokine_CC_DCCL for the DCCL subgroup of this CD. 57 matched cddid_all.tbl CDD cd00273 cd00273 238171 Chemokine_CXC Chemokine_CXC: 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; many members contain an RCxC motif which may be a general requirement for binding to CXC chemokine receptors; those with the ELR motif are chemotatic for neutrophils and have been shown to be angiogenic, while those without the motif act on T and B cells, and are typically angiostatic; exist as monomers and dimers, but are believed to be functional as monomers; found only in vertebrates and a few viruses. See CDs: Chemokine (cd00169) for the general alignment of chemokines, or Chemokine_CC (cd00272), Chemokine_C (cd00271), and Chemokine_CX3C (cd00274) for the additional chemokine subgroups. 64 matched cddid_all.tbl CDD cd00274 cd00274 238172 Chemokine_CX3C Chemokine_CX3C: 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteines; differ structurally from the other subgroups in that they are attached to a membrane-spanning domain via a mucin-like stalk and can be proteolytically cleaved to a freely diffusible form; chemotatic for T cells, monocytes, and natural killer cells; function as monomers and are found only in vertebrates and a few viruses; currently only fractalkine (sometimes called neurotactin) has been identified as a member of this subfamily; the primary source of fractalkine is neurons, and they exhibit cell adhesion and chemoattractive properties in the central nervous system. See CDs: Chemokine (cd00169) for the general alignment of chemokines, or Chemokine_CXC (cd00273), Chemokine_CC (cd00272), and Chemokine_C (cd00271) for the additional chemokine subgroups. 76 matched cddid_all.tbl CDD cd00275 cd00275 175974 C2_PLC_like C2 domain present in Phosphoinositide-specific phospholipases C (PLC). PLCs are involved in the hydrolysis of phosphatidylinositol-4,5-bisphosphate (PIP2) to d-myo-inositol-1,4,5-trisphosphate (1,4,5-IP3) and sn-1,2-diacylglycerol (DAG). 1,4,5-IP3 and DAG are second messengers in eukaryotic signal transduction cascades. PLC is composed of a N-terminal PH domain followed by a series of EF hands, a catalytic TIM barrel and a C-terminal C2 domain. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. Members here have a type-II topology. 128 matched cddid_all.tbl CDD cd00276 cd00276 175975 C2B_Synaptotagmin C2 domain second repeat present in Synaptotagmin. Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. There are several classes of Synaptotagmins. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-I topology. 134 matched cddid_all.tbl CDD cd00279 cd00279 238173 YlxR Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation 79 matched cddid_all.tbl CDD cd00280 cd00280 238174 TRFH Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain Homology; TRFH. Telomeres are protein/DNA complexes that make up the physical ends of eukaryotic linear chromosomes and are essential for chromosome stability, protecting the chromosome ends from degradation and end-to-end fusion. Proteins TRF1, TRF2 and Taz1 bind telomeric DNA and are also involved in recruiting interacting proteins, TIN2, and Rap1, to the telomeres. It has also been demonstrated that PARP1 associates with TRF2 and is capable of poly(ADP-ribosyl)ation of TRF2, which affects binding of TRF2 to telomeric DNA. TRF1, TRF2 and Taz1 proteins contain three functional domains: an N-terminal acidic domain, a central TRF-specific/dimerization domain, and a C-terminal DNA binding domain with a single Myb-like repeat. Homodimerization, a prerequisite to DNA binding, results in the juxtaposition of two Myb DNA binding domains. 200 matched cddid_all.tbl CDD cd00281 cd00281 176449 DAP_dppA Peptidase M55, D-aminopeptidase dipeptide-binding protein family. M55 Peptidase, D-Aminopeptidase dipeptide-binding protein (dppA; DAP dppA; EC 3.4.11.-) domain: Peptide transport systems are found in many bacterial species and generally function to accumulate intact peptides in the cell, where they are hydrolyzed. The dipeptide-binding protein (dppA) of Bacillus subtilis belongs to the dipeptide ABC transport (dpp) operon expressed early during sporulation. It is a binuclear zinc-dependent, D-specific aminopeptidase. The biologically active enzyme is a homodecamer with active sites buried in its channel. These self-compartmentalizing proteases are characterized by a SXDXEG motif. D-Ala-D-Ala and D-Ala-Gly-Gly are the preferred substrates. Bacillus subtilis dppA is thought to function as an adaptation to nutrient deficiency; hydrolysis of its substrate releases D-Ala which can be used subsequently as metabolic fuel. This family also contains a number of uncharacterized putative peptidases. 265 matched cddid_all.tbl CDD cd00283 cd00283 238175 GIY-YIG_Cterm GIYX(10-11)YIG family of class I homing endonucleases C-terminus (GIY-YIG_Cterm). Homing endonucleases promote the mobility of intron or intein by recognizing and cleaving a homologous allele that lacks the sequence. They catalyze a double-strand break in the DNA near the insertion site of that element to facilitate homing at that site. Class I homing endonucleases are sorted into four families based on the presence of these motifs in their respective N-termini: LAGLIDADG, His-Cys box, HNH, and GIY-YIG. This CD contains several but not all members of the GIY-YIG family. The C-terminus of GIY-YIG is a DNA-binding domain which is separated from the N-terminus by a long, flexible linker. The DNA-binding domain consists of a minor-groove binding alpha-helix, and a helix-turn-helix. Some also contain a zinc finger (i.e. I-TevI) which is not required for DNA binding or catalysis, but is a component of the linker and directs the catalytic domain to cleave the homing site at a fixed distance from the intron insertion site. 113 matched cddid_all.tbl CDD cd00284 cd00284 238176 Cytochrome_b_N Cytochrome b (N-terminus)/b6/petB: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria, cytochrome b6 is analogous to eukaryote cytochrome b, containing two chains: helices A-D are encoded by the petB gene and helices E-H are encoded by the petD gene in these organisms. Cytochrome b/b6 contains two bound hemes and two ubiquinol/ubiquinone binding sites. The C-terminal portion of cytochrome b is described in a separate CD. 200 matched cddid_all.tbl CDD cd00286 cd00286 276954 Tubulin_FtsZ_Cetz-like Tubulin protein family of FtsZ and CetZ-like. This family includes tubulin alpha-, beta-, gamma-, delta-, epsilon, and zeta-tubulins as well as FtsZ and CetZ, all of which are involved in polymer formation. Tubulin is the major component of microtubules, but also exists as a heterodimer and as a curved oligomer. Microtubules exist in all eukaryotic cells and are responsible for many functions, including cellular transport, cell motility, and mitosis. FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria, archaea, and chloroplasts. A recent study found that CetZ proteins, formerly annotated FtsZ type 2, are not required for cell division, whereas FtsZ proteins play an important role. Instead, CetZ proteins are shown to be involved in controlling archaeal cell shape dynamics. The results from inactivation studies of CetZ proteins in Haloferax volcanii suggest that CetZ1 is essential for normal swimming motility and rod-cell development. 332 matched cddid_all.tbl CDD cd00287 cd00287 238177 ribokinase_pfkB_like ribokinase/pfkB superfamily: Kinases that accept a wide variety of substrates, including carbohydrates and aromatic small molecules, all are phosphorylated at a hydroxyl group. The superfamily includes ribokinase, fructokinase, ketohexokinase, 2-dehydro-3-deoxygluconokinase, 1-phosphofructokinase, the minor 6-phosphofructokinase (PfkB), inosine-guanosine kinase, and adenosine kinase. Even though there is a high degree of structural conservation within this superfamily, their multimerization level varies widely, monomeric (e.g. adenosine kinase), dimeric (e.g. ribokinase), and trimeric (e.g THZ kinase). 196 matched cddid_all.tbl CDD cd00288 cd00288 238178 Pyruvate_Kinase Pyruvate kinase (PK): Large allosteric enzyme that regulates glycolysis through binding of the substrate, phosphoenolpyruvate, and one or more allosteric effectors. Like other allosteric enzymes, PK has a high substrate affinity R state and a low affinity T state. PK exists as several different isozymes, depending on organism and tissue type. In mammals, there are four PK isozymes: R, found in red blood cells, L, found in liver, M1, found in skeletal muscle, and M2, found in kidney, adipose tissue, and lung. PK forms a homotetramer, with each subunit containing three domains. The T state to R state transition of PK is more complex than in most allosteric enzymes, involving a concerted rotation of all 3 domains of each monomer in the homotetramer. 480 matched cddid_all.tbl CDD cd00290 cd00290 238179 cytochrome_b_C Cytochrome b(C-terminus)/b6/petD: Cytochrome b is a subunit of cytochrome bc1, an 11-subunit mitochondrial respiratory enzyme. Cytochrome b spans the mitochondrial membrane with 8 transmembrane helices (A-H) in eukaryotes. In plants and cyanobacteria, cytochrome b6 is analogous to eukaryote cytochrome b, containing two chains: helices A-D are encoded by the petB gene and helices E-H are encoded by the petD gene in these organisms. Cytochrome b/b6 contains two bound hemes and two ubiquinol/ubiquinone binding sites. The C-terminal domain is involved in forming the ubiquinol/ubiquinone binding sites, but not the heme binding sites. The N-terminal portion of cytochrome b, which contains both heme binding sites, is described in a separate CD. 147 matched cddid_all.tbl CDD cd00291 cd00291 238180 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding. 69 matched cddid_all.tbl CDD cd00292 cd00292 238181 EF1B Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this exchange reaction. 88 matched cddid_all.tbl CDD cd00293 cd00293 467483 USP-like "universal stress protein (USP) and similar proteins. The universal stress protein (USP) is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. USP enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general ""stress endurance"" activity. The crystal structure of Haemophilus influenzae Usp reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP, although USP lacks ATP-binding activity." 135 matched cddid_all.tbl CDD cd00295 cd00295 238183 RNA_Cyclase RNA 3' phosphate cyclase domain - RNA phosphate cyclases are enzymes that catalyze the ATP-dependent conversion of 3'-phosphate at the end of RNA into 2', 3'-cyclic phosphodiester bond. The enzymes are conserved in eucaryotes, bacteria and archaea. The exact biological role of this enzyme is unknown, but it has been proposed that it is likely to function in cellular RNA metabolism and processing. RNA phosphate cyclase has been characterized in human (with at least three isozymes), and E. coli, and it seems to be taxonomically widespread. The crystal structure of RNA phospate cyclase shows that it consists of two domains. The larger domain contains three repeats of a fold originally identified in the bacterial translation initiation factor IF3. 338 matched cddid_all.tbl CDD cd00296 cd00296 238184 SIR2 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines. 222 matched cddid_all.tbl CDD cd00298 cd00298 107219 ACD_sHsps_p23-like This domain family includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is this ACD. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. p23 is a cochaperone of the Hsp90 chaperoning pathway. It binds Hsp90 and participates in the folding of a number of Hsp90 clients including the progesterone receptor. p23 also has a passive chaperoning activity. p23 in addition may act as the cytosolic prostaglandin E2 synthase. Included in this family is the p23-like C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1) and the p23-like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR). 80 matched cddid_all.tbl CDD cd00299 cd00299 198286 GST_C_family C-terminal, alpha helical domain of the Glutathione S-transferase family. Glutathione S-transferase (GST) family, C-terminal alpha helical domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction and isomerization of certain compounds. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxins, stringent starvation protein A, and aminoacyl-tRNA synthetases. 100 matched cddid_all.tbl CDD cd00300 cd00300 133418 LDH_like L-lactate dehydrogenase-like enzymes. Members of this subfamily are tetrameric NAD-dependent 2-hydroxycarboxylate dehydrogenases including LDHs, L-2-hydroxyisocaproate dehydrogenases (L-HicDH), and LDH-like malate dehydrogenases (MDH). Dehydrogenases catalyze the conversion of carbonyl compounds to alcohols or amino acids. LDHs catalyze the last step of glycolysis in which pyruvate is converted to L-lactate. Vertebrate LDHs are non-allosteric, but some bacterial LDHs are activated by an allosteric effector such as fructose-1,6-bisphosphate. L-HicDH catalyzes the conversion of a variety of 2-oxo carboxylic acids with medium-sized aliphatic or aromatic side chains. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH-like subfamily is part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. 300 matched cddid_all.tbl CDD cd00301 cd00301 381182 lipocalin_FABP lipocalin/cytosolic fatty acid-binding protein family. Lipocalins are diverse, mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules as well as membrane bound-receptors. They have a large beta-barrel ligand-binding cavity. Members include retinol-binding protein, retinoic acid-binding protein, complement protein C8 gamma, Can f 2, apolipoprotein D, extracellular fatty acid-binding protein, beta-lactoglobulin, oderant-binding protein, and bacterial lipocalin Blc. Lipocalins are involved in many important processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty acid-binding proteins also bind hydrophobic ligands in a non-covalent, reversible manner, and are involved in protection and shuttling of fatty acids within the cell, and in acquisition and removal of fatty acids from intracellular sites. 109 matched cddid_all.tbl CDD cd00302 cd00302 410651 cytochrome_P450 cytochrome P450 (CYP) superfamily. Cytochrome P450 (P450, CYP) is a large superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs with > 40% sequence identity are members of the same family. There are approximately 2250 CYP families: mammals, insects, plants, fungi, bacteria, and archaea have around 18, 208, 277, 805, 591, and 14 families, respectively. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. Their monooxygenase activity relies on the reductive scission of molecular oxygen bound to the P450 heme iron, and the delivery of two electrons to the heme iron during the catalytic cycle. CYPs use a variety of redox partners, such as the eukaryotic diflavin enzyme NADPH-cytochrome P450 oxidoreductase and the bacterial/mitochondrial NAD(P)H-ferredoxin reductase and ferredoxin partners. Some CYPs are naturally linked to their redox partners and others have evolved to bypass requirements for redox partners, and instead react directly with hydrogen peroxide or NAD(P)H to facilitate oxidative or reductive catalysis. 391 matched cddid_all.tbl CDD cd00303 cd00303 133136 retropepsin_like Retropepsins; pepsin-like aspartate proteases. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements, as well as eukaryotic dna-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A. 92 matched cddid_all.tbl CDD cd00304 cd00304 238185 RT_like RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. 98 matched cddid_all.tbl CDD cd00305 cd00305 238186 Cu-Zn_Superoxide_Dismutase Copper/zinc superoxide dismutase (SOD). superoxide dismutases catalyse the conversion of superoxide radicals to molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene causes familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Cytoplasmic and periplasmic SODs exist as dimers, whereas chloroplastic and extracellular enzymes exist as tetramers. Structure supports independent functional evolution in prokaryotes (P-class) and eukaryotes (E-class) [PMID:8176730]. 144 matched cddid_all.tbl CDD cd00306 cd00306 173787 Peptidases_S8_S53 Peptidase domain in the S8 and S53 families. Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) family include endopeptidases and exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin. The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base. However, the aspartic acid residue that acts as an electrophile is quite different. In S53, it follows glutamic acid, while in S8 it precedes histidine. The stability of these enzymes may be enhanced by calcium; some members have been shown to bind up to 4 ions via binding sites with different affinity. There is a great diversity in the characteristics of their members: some contain disulfide bonds, some are intracellular while others are extracellular, some function at extreme temperatures, and others at high or low pH values. 241 matched cddid_all.tbl CDD cd00307 cd00307 238187 RuBisCO_small_like Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit and related proteins. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits. This superfamily also contains specific proteins from cyanobacteria. CcmM plays a role in a CO2 concentrating mechanism, which cyanobacteria need to to overcome the low specificity of their Rubisco and fusions to Rubisco activase, a type of chaperone, which promotes and maintains the catalytic activity of Rubisco. CcmM contains an N-terminal carbonic anhydrase fused to four copies of the Rubisco-small subunit domain 84 matched cddid_all.tbl CDD cd00308 cd00308 238188 enolase_like Enolase-superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. Enolase superfamily contains different enzymes, like enolases, glutarate-, fucanate- and galactonate dehydratases, o-succinylbenzoate synthase, N-acylamino acid racemase, L-alanine-DL-glutamate epimerase, mandelate racemase, muconate lactonizing enzyme and 3-methylaspartase. 229 matched cddid_all.tbl CDD cd00309 cd00309 238189 chaperonin_type_I_II chaperonin families, type I and type II. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. 464 matched cddid_all.tbl CDD cd00310 cd00310 349411 ATP-synt_Fo_a_6 ATP synthase Fo complex, subunit 6 (eukaryotes) and subunit a (prokaryotes). Bacterial forms are designated as ATP synthase, Fo complex, subunit a; eukaryotic (chloroplast and mitochondrial) forms are designated as ATP synthase, Fo complex, subunit 6. The F-ATP synthases (also called FoF1-ATPases) consist of two structural domains: F1 (factor one) complex containing the soluble catalytic core, and Fo (oligomycin sensitive factor) complex containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. F-ATP synthases are primarily found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts or in the plasma membranes of bacteria. F-ATP synthase has also been found in the archaea Methanosarcina acetivorans. F-ATP synthases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. 156 matched cddid_all.tbl CDD cd00311 cd00311 238190 TIM Triosephosphate isomerase (TIM) is a glycolytic enzyme that catalyzes the interconversion of dihydroxyacetone phosphate and D-glyceraldehyde-3-phosphate. The reaction is very efficient and requires neither cofactors nor metal ions. TIM, usually homodimeric, but in some organisms tetrameric, is ubiqitous and conserved in function across eukaryotes, bacteria and archaea. 242 matched cddid_all.tbl CDD cd00312 cd00312 238191 Esterase_lipase Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate. 493 matched cddid_all.tbl CDD cd00313 cd00313 349412 ATP-synt_Fo_Vo_Ao_c ATP synthase, membrane-bound Fo/Vo/Ao complexes, subunit c. Subunit c of the Fo/Vo/Ao complex is the main transmembrane subunit of F-, V- or A-type family of ATP synthases with rotary motors. These ion-transporting rotary ATP synthases are composed of two linked multi-subunit complexes: the F1, V1, and A1 complexes contains three copies each of the alpha and beta subunits that form the soluble catalytic core, which is involved in ATP synthesis/hydrolysis, and the Fo, Vo, or Ao (oligomycin sensitive) complex that forms the membrane-embedded proton pore. The F-ATP synthases (also called FoF1-ATPases) are found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts, or in the plasma membranes of bacteria. F-ATPases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. The A-ATP synthase (AoA1-ATPases) is exclusively found in archaea and function like F-ATP synthase. Structurally, however, the A-ATP synthase is more closely related to the V-ATP synthase (vacuolar VoV1-ATPase), which is a proton-translocating ATPase responsible for acidification of eukaryotic intracellular compartments and for ATP synthesis in archaea and some eubacteria. Collectively, F-, V-, and A-type synthases can function in both ATP synthesis and hydrolysis modes. 65 matched cddid_all.tbl CDD cd00314 cd00314 173823 plant_peroxidase_like Heme-dependent peroxidases similar to plant peroxidases. Along with animal peroxidases, these enzymes belong to a group of peroxidases containing a heme prosthetic group (ferriprotoporphyrin IX), which catalyzes a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. The plant peroxidase-like superfamily is found in all three kingdoms of life and carries out a variety of biosynthetic and degradative functions. Several sub-families can be identified. Class I includes intracellular peroxidases present in fungi, plants, archaea and bacteria, called catalase-peroxidases, that can exhibit both catalase and broad-spectrum peroxidase activities depending on the steady-state concentration of hydrogen peroxide. Catalase-peroxidases are typically comprised of two homologous domains that probably arose via a single gene duplication event. Class II includes ligninase and other extracellular fungal peroxidases, while class III is comprised of classic extracellular plant peroxidases, like horseradish peroxidase. 255 matched cddid_all.tbl CDD cd00315 cd00315 238192 Cyt_C5_DNA_methylase Cytosine-C5 specific DNA methylases; Methyl transfer reactions play an important role in many aspects of biology. Cytosine-specific DNA methylases are found both in prokaryotes and eukaryotes. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the mammalian genome. These effects include transcriptional repression via inhibition of transcription factor binding or the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. 275 matched cddid_all.tbl CDD cd00316 cd00316 238193 Oxidoreductase_nitrogenase The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. This group contains both alpha and beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent nitrogenase (Mo-nitrogenase), a vanadium-dependent nitrogenase (V-nitrogenase), and an iron-only nitrogenase (Fe-nitrogenase) and, both subunits of Protochlorophyllide (Pchlide) reductase and chlorophyllide (chlide) reductase. The nitrogenase systems consist of component 1 (MoFe protein, VFe protein or, FeFe protein respectively) and, component 2 (Fe protein). The most widespread and best characterized nitrogenase is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer, the alternative nitrogenases are alpha2beta2delta2 hexamers whose alpha and beta subunits are similar to the alpha and beta subunits of MoFe. For MoFe, each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (FeMoco) contained within the alpha subunit. The Fe protein contains a single [4Fe-4S] cluster from which, electrons are transferred to the P-cluster of the MoFe and in turn, to FeMoCo at the site of substrate reduction. The V-nitrogenase requires an iron-vanadium cofactor (FeVco), the iron only-nitrogenase an iron only cofactor (FeFeco). These cofactors are analogous to the FeMoco. The V-nitrogenase has P clusters identical to those of MoFe. Pchlide reductase and chlide reductase participate in the Mg-branch of the tetrapyrrole biosynthetic pathway. Pchlide reductase catalyzes the reduction of the D-ring of Pchlide during the synthesis of chlorophylls (Chl) and bacteriochlorophylls (BChl). Chlide-a reductase catalyzes the reduction of the B-ring of Chlide-a during the synthesis of BChl-a. The Pchlide reductase NB complex is a an N2B2 heterotetramer resembling nitrogenase FeMo, N and B proteins are homologous to the FeMo alpha and beta subunits respectively. The NB complex may serve as a catalytic site for Pchlide reduction and, the ZY complex as a site of chlide reduction, similar to MoFe for nitrogen reduction. 399 matched cddid_all.tbl CDD cd00317 cd00317 238194 cyclophilin cyclophilin: cyclophilin-type peptidylprolyl cis- trans isomerases. This family contains eukaryotic, bacterial and archeal proteins which exhibit a peptidylprolyl cis- trans isomerases activity (PPIase, Rotamase) and in addition bind the immunosuppressive drug cyclosporin (CsA). Immunosuppression in vertebrates is believed to be the result of the cyclophilin A-cyclosporin protein drug complex binding to and inhibiting the protein-phosphatase calcineurin. PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. Cyclophilins are a diverse family in terms of function and have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. This group contains human cyclophilin 40, a co-chaperone of the hsp90 chaperone system; human cyclophilin A, a chaperone in the HIV-1 infectious process and; human cyclophilin H, a component of the U4/U6 snRNP, whose isomerization or chaperoning activities may play a role in RNA splicing. 146 matched cddid_all.tbl CDD cd00318 cd00318 238195 Phosphoglycerate_kinase Phosphoglycerate kinase (PGK) is a monomeric enzyme which catalyzes the transfer of the high-energy phosphate group of 1,3-bisphosphoglycerate to ADP, forming ATP and 3-phosphoglycerate. This reaction represents the first of the two substrate-level phosphorylation events in the glycolytic pathway. Substrate-level phosphorylation is defined as production of ATP by a process, which is catalyzed by water-soluble enzymes in the cytosol; not involving membranes and ion gradients. 397 matched cddid_all.tbl CDD cd00319 cd00319 238196 Ribosomal_S12_like Ribosomal protein S12-like family; composed of prokaryotic 30S ribosomal protein S12, eukaryotic 40S ribosomal protein S23 and similar proteins. S12 and S23 are located at the interface of the large and small ribosomal subunits, adjacent to the decoding center. They play an important role in translocation during the peptide elongation step of protein synthesis. They are also involved in important RNA and protein interactions. Ribosomal protein S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. S23 interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes translocation. Mutations in S12 and S23 have been found to affect translational accuracy. Antibiotics such as streptomycin may also bind S12/S23 and cause the ribosome to misread the genetic code. 95 matched cddid_all.tbl CDD cd00320 cd00320 238197 cpn10 Chaperonin 10 Kd subunit (cpn10 or GroES); Cpn10 cooperates with chaperonin 60 (cpn60 or GroEL), an ATPase, to assist the folding and assembly of proteins and is found in eubacterial cytosol, as well as in the matrix of mitochondria and chloroplasts. It forms heptameric rings with a dome-like structure, forming a lid to the large cavity of the tetradecameric cpn60 cylinder and thereby tightly regulating release and binding of proteins to the cpn60 surface. 93 matched cddid_all.tbl CDD cd00321 cd00321 238198 SO_family_Moco Sulfite oxidase (SO) family, molybdopterin binding domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). SO catalyzes the terminal reaction in the oxidative degradation of the sulfur-containing amino acids cysteine and methionine. Assimilatory NRs catalyze the reduction of nitrate to nitrite which is subsequently converted to NH4+ by nitrite reductase. Common features of all known members of this family are that they contain one single pterin cofactor and part of the coordination of the metal (Mo) is a cysteine ligand of the protein and that they catalyze the transfer of an oxygen to or from a lone pair of electrons on the substrate. 156 matched cddid_all.tbl CDD cd00322 cd00322 99778 FNR_like Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in many organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H). 223 matched cddid_all.tbl CDD cd00323 cd00323 271245 uS7 Ribosomal protein S7. uS7, also known as Ribosomal protein (RP)S7, is an important part of the translation process which is universally present in the small subunit of prokaryotic and eukaryotic ribosomes. The ribosome small subunit is one of the two subunits of ribosome organelles that use mRNA as a template for protein synthesis in a process called translation. The small subunits of bacteria and eukaryotes have the same shape of head, body, platform, beak, and shoulder. RPS7 is located at the head of the small subunit. RPS7 is a primary ribosomal RNA (rRNA) binding protein that assists in rRNA folding and the binding of other proteins during small subunit assembly in all species. RPS7 is also involved in the formation of the mRNA exit channel at the interface of the large and small subunits. Some ribosomal proteins have extra ribosomal functions in cell differentiation and apoptosis. 130 matched cddid_all.tbl CDD cd00325 cd00325 381595 chitinase_GH19 Glycoside hydrolase family 19, chitinase domain. Chitinases are enzymes that catalyze the hydrolysis of the beta-1,4-N-acetyl-D-glucosamine linkages in chitin polymers. Glycoside hydrolase family 19 chitinases are found primarily in plants (classes I, III, and IV), but some are found in bacteria. Class I and II chitinases are similar in their catalytic domains. Class I chitinases have an N-terminal cysteine-rich, chitin-binding domain which is separated from the catalytic domain by a proline and glycine-rich hinge region. Class II chitinases lack both the chitin-binding domain and the hinge region. Class IV chitinases are similar to class I chitinases, but they are smaller in size due to certain deletions. Despite lacking any significant sequence homology with lysozymes, structural analysis reveals that family 19 chitinases, together with family 46 chitosanases, are similar to several lysozymes including those from T4-phage and from goose. The structures reveal that the different enzyme groups arose from a common ancestor glycohydrolase antecedent to the prokaryotic/eukaryotic divergence. 224 matched cddid_all.tbl CDD cd00326 cd00326 238200 alpha_CA Carbonic anhydrase alpha (vertebrate-like) group. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues and a fourth conserved histidine plays a potential role in proton transfer. 227 matched cddid_all.tbl CDD cd00327 cd00327 238201 cond_enzymes Condensing enzymes; Family of enzymes that catalyze a (decarboxylating or non-decarboxylating) Claisen-like condensation reaction. Members are share strong structural similarity, and are involved in the synthesis and degradation of fatty acids, and the production of polyketides, a diverse group of natural products. 254 matched cddid_all.tbl CDD cd00328 cd00328 163705 catalase Catalase heme-binding enzyme. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes, which is involved in the protection of cells from the toxic effects of peroxides. It catalyzes the conversion of hydrogen peroxide to water and molecular oxygen. Catalases also utilize hydrogen peroxide to oxidize various substrates such as alcohol or phenols. Most catalases exist as tetramers of 65KD subunits containing a protoheme IX group buried deep inside the structure. In eukaryotic cells, catalases are located in peroxisomes. 433 matched cddid_all.tbl CDD cd00329 cd00329 238202 TopoII_MutL_Trans MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2. MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch repair (MMR). Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families. 107 matched cddid_all.tbl CDD cd00330 cd00330 153075 phosphagen_kinases Phosphagen (guanidino) kinases. Phosphagen (guanidino) kinases are enzymes that transphosphorylate a high energy phosphoguanidino compound, like phosphocreatine (PCr) in the case of creatine kinase (CK) or phosphoarginine in the case of arginine kinase, which is used as an energy-storage and -transport metabolite, to ADP, thereby creating ATP. The substrate binding site is located in the cleft between the N and C-terminal domains, but most of the catalytic residues are found in the larger C-terminal domain. In higher eukaryotes, CK exists in tissue-specific (muscle, brain), as well as compartment-specific (mitochondrial and cytosolic) isoforms. They are either coupled to glycolysis (cytosolic form) or oxidative phosphorylation (mitochondrial form). Besides CK and AK, the most studied members of this family are also other phosphagen kinases with different substrate specificities, like glycocyamine kinase (GK), lombricine kinase (LK), taurocyamine kinase (TK) and hypotaurocyamine kinase (HTK). The majority of bacterial phosphagen kinases appear to lack the N-terminal domain and have not been functionally characterized. 236 matched cddid_all.tbl CDD cd00331 cd00331 238203 IGPS Indole-3-glycerol phosphate synthase (IGPS); an enzyme in the tryptophan biosynthetic pathway, catalyzing the ring closure reaction of 1-(o-carboxyphenylamino)-1-deoxyribulose-5-phosphate (CdRP) to indole-3-glycerol phosphate (IGP), accompanied by the release of carbon dioxide and water. IGPS is active as a separate monomer in most organisms, but is also found fused to other enzymes as part of a bifunctional or multifunctional enzyme involved in tryptophan biosynthesis. 217 matched cddid_all.tbl CDD cd00332 cd00332 176460 PAL-HAL Phenylalanine ammonia-lyase (PAL) and histidine ammonia-lyase (HAL). PAL and HAL are members of the Lyase class I_like superfamily of enzymes that, catalyze similar beta-elimination reactions and are active as homotetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. PAL, present in plants and fungi, catalyzes the conversion of L-phenylalanine to E-cinnamic acid. HAL, found in several bacteria and animals, catalyzes the conversion of L-histidine to E-urocanic acid. Both PAL and HAL contain the cofactor 3, 5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) which is formed by autocatalytic excision/cyclization of the internal tripeptide, Ala-Ser-Gly. PAL is being explored as enzyme substitution therapy for Phenylketonuria (PKU), a disorder which involves an inability to metabolize phenylalanine. HAL failure in humans results in the disease histidinemia. 444 matched cddid_all.tbl CDD cd00333 cd00333 238204 MIP Major intrinsic protein (MIP) superfamily. Members of the MIP superfamily function as membrane channels that selectively transport water, small neutral molecules, and ions out of and between cells. The channel proteins share a common fold: the N-terminal cytosolic portion followed by six transmembrane helices, which might have arisen through gene duplication. On the basis of sequence similarity and functional characteristics, the superfamily can be subdivided into two major groups: water-selective channels called aquaporins (AQPs) and glycerol uptake facilitators (GlpFs). AQPs are found in all three kingdoms of life, while GlpFs have been characterized only within microorganisms. 228 matched cddid_all.tbl CDD cd00336 cd00336 238205 Ribosomal_L22 Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper folding and stabilizing the conformation of 23S rRNA. L22 is the largest protein contributor to the surface of the polypeptide exit channel, the tunnel through which the polypeptide product passes. L22 is also one of six proteins located at the putative translocon binding site on the exterior surface of the ribosome. 105 matched cddid_all.tbl CDD cd00337 cd00337 466774 Ribosomal_uL14 "Ribosomal protein uL14. Ribosomal protein uL14 (L14 in bacteria and mitochondria, L23 in eukaryotes, L38 in fungal mitochondria) is part of the large ribosomal subunit, located between the centers of activity for peptidyl transferase and GTPase. uL14 has an ""all beta"" fold that binds 23S rRNA. Ribosomal proteins, which are components of ribosomal subunits, are RNA-binding proteins that might have multiple extra ribosomal functions and may be involved in tumorigenesis in mammals." 114 matched cddid_all.tbl CDD cd00338 cd00338 238206 Ser_Recombinase Serine Recombinase family, catalytic domain; a DNA binding domain may be present either N- or C-terminal to the catalytic domain. These enzymes perform site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and serine recombinase. Serine recombinases demonstrate functional versatility and include resolvases, invertases, integrases, and transposases. Resolvases and invertases (i.e. Tn3, gamma-delta, Tn5044 resolvases, Gin and Hin invertases) in this family contain a C-terminal DNA binding domain and comprise a major phylogenic group. Also included are phage- and bacterial-encoded recombinases such as phiC31 integrase, SpoIVCA excisionase, and Tn4451 TnpX transposase. These integrases and transposases have larger C-terminal domains compared to resolvases/invertases and are referred to as large serine recombinases. Also belonging to this family are proteins with N-terminal DNA binding domains similar to IS607- and IS1535-transposases from Helicobacter and Mycobacterium. 137 matched cddid_all.tbl CDD cd00340 cd00340 238207 GSH_Peroxidase Glutathione (GSH) peroxidase family; tetrameric selenoenzymes that catalyze the reduction of a variety of hydroperoxides including lipid peroxidases, using GSH as a specific electron donor substrate. GSH peroxidase contains one selenocysteine residue per subunit, which is involved in catalysis. Different isoenzymes are known in mammals,which are involved in protection against reactive oxygen species, redox regulation of many metabolic processes, peroxinitrite scavenging, and modulation of inflammatory processes. 152 matched cddid_all.tbl CDD cd00342 cd00342 238208 gram_neg_porins Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane. Individual 16-strand anti-parallel beta-barrels form a central pore, and trimerizes thru mainly hydrophobic interactions at the interface. Trimers are stabilized by hytrophillic clamping of Loop L2. Loop 3 bends into the pore, creating an elliptical constriction of about 7 x 11A, large enough to allow passage of a glucose molecule without steric hindrance. Removal of the C-terminal residue (usuallly F) destabilizes the trimer and removal of the 16th beta-sheet abolishes trimerization. Unlike typical membrane proteins, porins lack long hydrophobic stretches. Short turns are found at the smooth, periplasmic end, longer irregular loops are found at the rough, extracellular end. C-terminal residue forms salt bridge with N-terminus. 329 matched cddid_all.tbl CDD cd00344 cd00344 188629 FBP_aldolase_I Fructose-bisphosphate aldolase class I. Fructose-bisphosphate aldolase class I. Fructose-1,6-bisphosphate aldolase is an enzyme of the glycolytic and gluconeogenic pathways found in vertebrates, plants, and bacteria. The enzyme catalyzes the cleavage of fructose 1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). Mutations in the aldolase genes in humans cause hemolytic anemia and hereditary fructose intolerance. The enzyme is a member of the class I aldolase family, which utilizes covalent catalysis through a Schiff base formed between a lysine residue of the enzyme and ketose substrates. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin. 328 matched cddid_all.tbl CDD cd00347 cd00347 238209 Flavin_utilizing_monoxygenases Flavin-utilizing monoxygenases 90 matched cddid_all.tbl CDD cd00349 cd00349 100101 Ribosomal_L11 "Ribosomal protein L11. Ribosomal protein L11, together with proteins L10 and L7/L12, and 23S rRNA, form the L7/L12 stalk on the surface of the large subunit of the ribosome. The homologous eukaryotic cytoplasmic protein is also called 60S ribosomal protein L12, which is distinct from the L12 involved in the formation of the L7/L12 stalk. The C-terminal domain (CTD) of L11 is essential for binding 23S rRNA, while the N-terminal domain (NTD) contains the binding site for the antibiotics thiostrepton and micrococcin. L11 and 23S rRNA form an essential part of the GTPase-associated region (GAR). Based on differences in the relative positions of the L11 NTD and CTD during the translational cycle, L11 is proposed to play a significant role in the binding of initiation factors, elongation factors, and release factors to the ribosome. Several factors, including the class I release factors RF1 and RF2, are known to interact directly with L11. In eukaryotes, L11 has been implicated in regulating the levels of ubiquinated p53 and MDM2 in the MDM2-p53 feedback loop, which is responsible for apoptosis in response to DNA damage. In bacteria, the ""stringent response"" to harsh conditions allows bacteria to survive, and ribosomes that lack L11 are deficient in stringent factor stimulation." 131 matched cddid_all.tbl CDD cd00350 cd00350 238210 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity. 33 matched cddid_all.tbl CDD cd00351 cd00351 238211 TS_Pyrimidine_HMase Thymidylate synthase and pyrimidine hydroxymethylase: Thymidylate synthase (TS) and deoxycytidylate hydroxymethylase (dCMP-HMase) are homologs that catalyze analogous alkylation of C5 of pyrimidine nucleotides. Both enzymes are involved in the biosynthesis of DNA precursors and are active as homodimers. However, they exhibit distinct pyrimidine base specificities and differ in the details of their catalyzed reactions. TS is biologically ubiquitous and catalyzes the conversion of dUMP and methylene-tetrahydrofolate (CH2THF) to dTMP and dihydrofolate (DHF). It also acts as a regulator of its own expression by binding and inactivating its own RNA. Due to its key role in the de novo pathway for thymidylate synthesis and, hence, DNA synthesis, it is one of the most conserved enzymes across species and phyla. TS is a well-recognized target for anticancer chemotherapy, as well as a valuable new target against infectious diseases. Interestingly, in several protozoa, a single polypeptide chain codes for both, dihydrofolate reductase (DHFR) and thymidylate synthase (TS), forming a bifunctional enzyme (DHFR-TS), possibly through gene fusion at a single evolutionary point. DHFR-TS is also active as a dimer. Virus encoded dCMP-HMase catalyzes the reversible conversion of dCMP and CH2THF to hydroxymethyl-dCMP and THF. This family also includes dUMP hydroxymethylase, which is encoded by several bacteriophages that infect Bacillus subtilis, for their own protection against the host restriction system, and contain hydroxymethyl-dUMP instead of dTMP in their DNA. 215 matched cddid_all.tbl CDD cd00352 cd00352 238212 Gn_AT_II Glutamine amidotransferases class-II (GATase). The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to members of the Ntn (N-terminal nucleophile) hydrolase superfamily and is found at the N-terminus of enzymes such as glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), beta lactam synthetase (beta-LS) and glutamate synthase (GltS). GLMS catalyzes the formation of glucosamine 6-phosphate from fructose 6-phosphate and glutamine in amino sugar synthesis. GPATase catalyzes the first step in purine biosynthesis, an amide transfer from glutamine to PRPP, resulting in phosphoribosylamine, pyrophosphate and glutamate. Asparagine synthetase B synthesizes asparagine from aspartate and glutamine. Beta-LS catalyzes the formation of the beta-lactam ring in the beta-lactamase inhibitor clavulanic acid. GltS synthesizes L-glutamate from 2-oxoglutarate and L-glutamine. These enzymes are generally dimers, but GPATase also exists as a homotetramer. 220 matched cddid_all.tbl CDD cd00353 cd00353 238213 Ribosomal_S15p_S13e Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome. S15 also plays an important autoregulatory role by binding and preventing its own mRNA from being translated. S15 has a predominantly alpha-helical fold that is highly structured except for the N-terminal alpha helix. 80 matched cddid_all.tbl CDD cd00354 cd00354 238214 FBPase Fructose-1,6-bisphosphatase, an enzyme that catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. The alignment model also includes chloroplastic FBPases and sedoheptulose-1,7-biphosphatases that play a role in pentose phosphate pathway (Calvin cycle). 315 matched cddid_all.tbl CDD cd00355 cd00355 100098 Ribosomal_L30_like Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome. The eukaryotic L30 members have N- and/or C-terminal extensions not found in their prokaryotic orthologs. L30 is closely related to the ribosomal L7 protein found in eukaryotes and archaea. 53 matched cddid_all.tbl CDD cd00361 cd00361 238215 arom_aa_hydroxylase Biopterin-dependent aromatic amino acid hydroxylase; a family of non-heme, iron(II)-dependent enzymes that includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH), eukaryotic tyrosine hydroxylase (TyrOH) and eukaryotic tryptophan hydroxylase (TrpOH). PheOH converts L-phenylalanine to L-tyrosine, an important step in phenylalanine catabolism and neurotransmitter biosynthesis, and is linked to a severe variant of phenylketonuria in humans. TyrOH and TrpOH are involved in the biosynthesis of catecholamine and serotonin, respectively. The eukaryotic enzymes are all homotetramers. 221 matched cddid_all.tbl CDD cd00363 cd00363 238216 PFK Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to PFK family that includes ATP- and pyrophosphate (PPi)- dependent phosphofructokinases. Some members evolved by gene duplication and thus have a large C-terminal/N-terminal extension comprising a second PFK domain. Generally, ATP-PFKs are allosteric homotetramers, and PPi-PFKs are dimeric and nonallosteric except for plant PPi-PFKs which are allosteric heterotetramers. 338 matched cddid_all.tbl CDD cd00364 cd00364 466775 Ribosomal_uS17 Ribosomal protein uS17. Ribosomal protein uS17 is one of the three primary assembly proteins (S4, S17 and S20) that stabilize the entire 5' rRNA domain and increase the global stability of the rRNA structure. uS17 is highly conserved in all three major phylogenetic divisions. In eukaryotes, the S17 ortholog of the cytoplasmic ribosome is called S11 as are those of the mitochondrial and chloroplast ribosomes. uS17 plays a critical role in both subunit assembly and translational fidelity. 73 matched cddid_all.tbl CDD cd00365 cd00365 153080 HMG-CoA_reductase Hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR). Hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR) is a tightly regulated enzyme, which catalyzes the synthesis of coenzyme A and mevalonate in isoprenoid synthesis. In mammals, this is the rate limiting committed step in cholesterol biosynthesis. Bacteria, such as Pseudomonas mevalonii, which rely solely on mevalonate for their carbon source, catalyze the reverse reaction, using an NAD-dependent HMGR to deacetylate mevalonate into 3-hydroxy-3-methylglutaryl-CoA. There are two classes of HMGR: class I enzymes which are found predominantly in eukaryotes and contain N-terminal membrane regions and class II enzymes which are found primarily in prokaryotes and are soluble as they lack the membrane region. With the exception of Archaeoglobus fulgidus, most archeae are assigned to class I, based on sequence similarity of the active site, even though they lack membrane regions. Yeast and human HMGR are divergent in their N-terminal regions, but are conserved in their active site. In contrast, human and bacterial HMGR differ in their active site architecture. While the prokaryotic enzyme is a homodimer, the eukaryotic enzyme is a homotetramer. 376 matched cddid_all.tbl CDD cd00366 cd00366 466787 ASKHA_NBD_FGGY nucleotide-binding domain (NBD) of the FGGY family of carbohydrate kinases. This family is predominantly composed of glycerol kinase (GK) and similar carbohydrate kinases including rhamnulokinase (RhuK), xylulokinase (XK), gluconokinase (GntK), ribulokinase (RBK), and fuculokinase (FK). These enzymes catalyze the transfer of a phosphate group, usually from ATP, to their carbohydrate substrates. The monomer of FGGY proteins contains two large domains, which are separated by a deep cleft that forms the active site. One domain is primarily involved in sugar substrate binding, and the other is mainly responsible for ATP binding. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. Substrate-induced conformational changes and a divalent cation may be required for the catalytic activity. The FGGY family belongs to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 392 matched cddid_all.tbl CDD cd00367 cd00367 238217 PTS-HPr_like Histidine-containing phosphocarrier protein (HPr)-like proteins. HPr is a central component of the bacterial phosphoenolpyruvate sugar phosphotransferase system (PTS). The PTS catalyses the phosphorylation of sugar substrates during their translocation across the cell membrane. The phosphoryl group from phosphoenolpyruvate is transferred to HPr by enzyme I (EI). Phospho-HPr then transfers the phosphoryl group to one of several sugar-specific phosphoprotein intermediates. The conserved histidine in the N-terminus of HPr serves as an acceptor for the phosphoryl group of EI. In addition to the phosphotransferase proteins HPr and E1, this family also includes the closely related Carbon Catabolite Repressor (CCR) proteins which use the same phosphorylation mechanism and interact with transcriptional regulators to control expression of genes coding for utilization of less favored carbon sources. 77 matched cddid_all.tbl CDD cd00368 cd00368 238218 Molybdopterin-Binding Molybdopterin-Binding (MopB) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is the eukaryotic/eubacterial protein domain family of the 75-kDa subunit/Nad11/NuoG (second domain) of respiratory complex 1/NADH-quinone oxidoreductase which is postulated to have lost an ancestral formate dehydrogenase activity and only vestigial sequence evidence remains of a molybdopterin binding site. 374 matched cddid_all.tbl CDD cd00371 cd00371 238219 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions. 63 matched cddid_all.tbl CDD cd00374 cd00374 238220 RNase_T2 "Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases). Plant T2 RNases are expressed during leaf senescence in order to scavenge phosphate from ribonucleotides. They are also expressed in response to wounding or pathogen invasion. S-RNases are thought to prevent self-fertilization by acting as selective cytotoxins of ""self"" pollen." 195 matched cddid_all.tbl CDD cd00375 cd00375 238221 Urease_alpha Urease alpha-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, fungi and plants. Their primary role is to allow the use of external and internally generated urea as a nitrogen source. The enzyme consists of 3 subunits, alpha, beta and gamma, which can be fused and present on a single protein chain and which in turn forms multimers, mainly trimers. The large alpha subunit is the catalytic domain containing an active site with a bi-nickel center complexed by a carbamylated lysine. The beta and gamma subunits play a role in subunit association to form the higher order trimers. 567 matched cddid_all.tbl CDD cd00377 cd00377 119340 ICL_PEPM Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate lyase (ICL), and 2-methylisocitrate lyase (MICL). Isocitrate lyase (ICL) catalyzes the conversion of isocitrate to succinate and glyoxylate, the first committed step in the glyoxylate pathway. This carbon-conserving pathway is present in most prokaryotes, lower eukaryotes and plants, but has not been observed in vertebrates. PEP mutase (PEPM) turns phosphoenolpyruvate (PEP) into phosphonopyruvate (P-pyr), an important intermediate in the formation of organophosphonates, which function as antibiotics or play a role in pathogenesis or signaling. P-pyr can be hydrolyzed by phosphonopyruvate hydrolase (PPH) to from pyruvate and phosphate. Oxaloacetate acetylhydrolase (OAH) catalyzes the hydrolytic cleavage of oxaloacetate to form acetate and oxalate, an important pathway to produce oxalate in filamentous fungi. 2-methylisocitrate lyase (MICL) cleaves 2-methylisocitrate to pyruvate and succinate, part of the methylcitrate cycle for the alpha-oxidation of propionate. 243 matched cddid_all.tbl CDD cd00378 cd00378 99733 SHMT Serine-glycine hydroxymethyltransferase (SHMT). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). SHMT carries out interconversion of serine and glycine; it catalyzes the transfer of hydroxymethyl group of N5, N10-methylene tetrahydrofolate to glycine resulting in the formation of serine and tetrahydrofolate. Both eukaryotic and prokaryotic SHMT enzymes form tight obligate homodimers; the mammalian enzyme forms a homotetramer comprising four pyridoxal phosphate-bound active sites. 402 matched cddid_all.tbl CDD cd00379 cd00379 238222 Ribosomal_L10_P0 Ribosomal protein L10 family; composed of the large subunit ribosomal protein called L10 in bacteria, P0 in eukaryotes, and L10e in archaea, as well as uncharacterized P0-like eukaryotic proteins. In all three kingdoms, L10 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein and forms the base of the L7/L12 stalk, while the extended C-terminal helix binds to two or three dimers of the NTD of L7/L12 (L7 and L12 are identical except for an acetylated N-terminus). The L7/L12 stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). Some eukaryotic P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2. 155 matched cddid_all.tbl CDD cd00380 cd00380 240504 KOW KOW: an acronym for the authors' surnames (Kyrpides, Ouzounis and Woese). KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The KOW motif contains an invariants glycine residue and comprises alternating blocks of hydrophilic and hydrophobic residues. 49 matched cddid_all.tbl CDD cd00381 cd00381 238223 IMPDH IMPDH: The catalytic domain of the inosine monophosphate dehydrogenase. IMPDH catalyzes the NAD-dependent oxidation of inosine 5'-monophosphate (IMP) to xanthosine 5' monophosphate (XMP). It is a rate-limiting step in the de novo synthesis of the guanine nucleotides. There is often a CBS domain inserted in the middle of this domain, which is proposed to play a regulatory role. IMPDH is a key enzyme in the regulation of cell proliferation and differentiation. It has been identified as an attractive target for developing chemotherapeutic agents. 325 matched cddid_all.tbl CDD cd00382 cd00382 238224 beta_CA Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. CAs are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionarily distinct families of CAs (the alpha-, beta-, and gamma-CAs) which show no significant sequence identity or structural similarity. Within the beta-CA family there are four evolutionarily distinct clades (A through D). The beta-CAs are multimeric enzymes (forming dimers,tetramers,hexamers and octamers) which are present in higher plants, algae, fungi, archaea and prokaryotes. 119 matched cddid_all.tbl CDD cd00383 cd00383 294013 trans_reg_C DNA-binding effector domain of two-component system response regulators. Bacteria and some eukaryotes use two-component signal transduction systems to detect and respond to changes in the environment. The systems consists of a sensor histidine kinase and a response regulator. The former autophosphorylates a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. This C-terminal effector domain belongs to the winged helix-turn-helix family of transcriptional regulators and contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunit of RNA polymerase. 89 matched cddid_all.tbl CDD cd00384 cd00384 238226 ALAD_PBGS Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between the substrate and the enzyme. PBGSs are metalloenzymes, some of which have a second, allosteric metal binding site, beside the metal ion binding site in their active site. Although PBGS is a family of homologous enzymes, its metal ion utilization at catalytic site varies between zinc and magnesium and/or potassium. PBGS can be classified into two groups based on differences in their active site metal binding site. They either contain a cysteine-rich zinc binding site (consensus DXCXCX(Y/F)X3G(H/Q)CG) or an aspartate-rich magnesium binding site (consensus DXALDX(Y/F)X3G(H/Q)DG). The cysteine-rich zinc binding site appears more common. Most members represented by this model also have a second allosteric magnesium binding site (consensus RX~164DX~65EXXXD, missing in a eukaryotic subfamily with cysteine-rich zinc binding site). 314 matched cddid_all.tbl CDD cd00385 cd00385 173830 Isoprenoid_Biosyn_C1 Isoprenoid Biosynthesis enzymes, Class 1. Superfamily of trans-isoprenyl diphosphate synthases (IPPS) and class I terpene cyclases which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, and diterpenes; and are widely distributed among archaea, bacteria, and eukaryota.The enzymes in this superfamily share the same 'isoprenoid synthase fold' and include several subgroups. The head-to-tail (HT) IPPS catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. Cyclic monoterpenes, diterpenes, and sesquiterpenes, are formed from their respective linear isoprenoid diphosphates by class I terpene cyclases. The head-to-head (HH) IPPS catalyze the successive 1'-1 condensation of 2 farnesyl or 2 geranylgeranyl isoprenoid diphosphates. Cyclization of these 30- and 40-carbon linear forms are catalyzed by class II cyclases. Both the isoprenoid chain elongation reactions and the class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, stabilizing reactive carbocation intermediates. Generally, the enzymes in this family exhibit an all-trans reaction pathway, an exception, is the cis-trans terpene cyclase, trichodiene synthase. Mechanistically and structurally distinct, class II terpene cyclases and cis-IPPS are not included in this CD. 243 matched cddid_all.tbl CDD cd00386 cd00386 238227 Heme_Cu_Oxidase_III_like Heme-copper oxidase subunit III. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The heme-copper oxidase superfamily is diverse in terms of electron donors, subunit composition, and heme types. This superfamily includes cytochrome c and ubiquinol oxidases. Bacterial oxidases typically contain 3 or 4 subunits in contrast to the 13 subunit bovine cytochrome c oxidase (CcO). Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Subunits I, II and III of ubiquinol oxidase are homologous to the corresponding subunits in CcO. This group additionally contains proteins which are fusions between subunits I and III, such as Sulfolobus acidocaldarius SoxM, a subunit of the SoxM terminal oxidase complex. It also includes NorE which has been speculated to be a subunit of nitric oxide reductase. Some archaebacterial cytochrome oxidases lack subunit III. Although not required for catalytic activity, subunit III is believed to play a role in assembly of the multimer complex. Rhodobacter CcO subunit III stabilizes the integrity of the binuclear center in subunit I. It has been proposed that archaea acquired heme-copper oxidases through gene transfer from gram-positive bacteria. 183 matched cddid_all.tbl CDD cd00387 cd00387 100102 Ribosomal_L7_L12 Ribosomal protein L7/L12. Ribosomal protein L7/L12 refers to the large ribosomal subunit proteins L7 and L12, which are identical except that L7 is acetylated at the N terminus. It is a component of the L7/L12 stalk, which is located at the surface of the ribosome. The stalk base consists of a portion of the 23S rRNA and ribosomal proteins L11 and L10. An extended C-terminal helix of L10 provides the binding site for L7/L12. L7/L12 consists of two domains joined by a flexible hinge, with the helical N-terminal domain (NTD) forming pairs of homodimers that bind to the extended helix of L10. It is the only multimeric ribosomal component, with either four or six copies per ribosome that occur as two or three dimers bound to the L10 helix. L7/L12 is the only ribosomal protein that does not interact directly with rRNA, but instead has indirect interactions through L10. The globular C-terminal domains of L7/L12 are highly mobile. They are exposed to the cytoplasm and contain binding sites for other molecules. Initiation factors, elongation factors, and release factors are known to interact with the L7/L12 stalk during their GTP-dependent cycles. The binding site for the factors EF-Tu and EF-G comprises L7/L12, L10, L11, the L11-binding region of 23S rRNA, and the sarcin-ricin loop of 23S rRNA. Removal of L7/L12 has minimal effect on factor binding and it has been proposed that L7/L12 induces the catalytically active conformation of EF-Tu and EF-G, thereby stimulating the GTPase activity of both factors. In eukaryotes, the proteins that perform the equivalent function to L7/L12 are called P1 and P2, which do not share sequence similarity with L7/L12. However, a bacterial L7/L12 homolog is found in some eukaryotes, in mitochondria and chloroplasts. In archaea, the protein equivalent to L7/L12 is called aL12 or L12p, but it is closer in sequence to P1 and P2 than to L7/L12. 127 matched cddid_all.tbl CDD cd00389 cd00389 238228 microbial_RNases microbial_RNases. Ribonucleases (RNAses) cleave phosphodiester bonds in RNA and are essential for both non-specific RNA degradation and for numerous forms of RNA processing. The alignment contains fungal RNases (U2, T1, F1, Th, Pb, N1, and Ms) and bacterial RNases (barnase, binase, RNase Sa) , the majority of which are guanyl specific and fungal ribotoxins. 71 matched cddid_all.tbl CDD cd00390 cd00390 238229 Urease_gamma Urease gamma-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of external and internally-generated urea as a nitrogen source. The enzyme consists of three subunits, alpha, beta and gamma, which can exist as separate proteins or can be fused on a single protein chain. The alpha-beta-gamma heterotrimer forms multimers, mainly trimers. The large alpha subunit is the catalytic domain containing an active site with a bi-nickel center complexed by a carbamylated lysine. The beta and gamma subunits play a role in subunit association to form the higher order trimers. 96 matched cddid_all.tbl CDD cd00392 cd00392 238230 Ribosomal_L13 Ribosomal protein L13. Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site. It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 has been identified as a homolog of the human breast basic conserved protein 1 (BBC1), a protein identified through its increased expression in breast cancer. L13 expression is also upregulated in a variety of human gastrointestinal cancers, suggesting it may play a role in the etiology of a variety of human malignancies. 114 matched cddid_all.tbl CDD cd00394 cd00394 132923 Clp_protease_like Caseinolytic protease (ClpP) is an ATP-dependent protease. Clp protease (caseinolytic protease; ClpP; endopeptidase Clp; Peptidase S14; ATP-dependent protease, ClpAP)-like enzymes are highly conserved serine proteases and belong to the ClpP/Crotonase superfamily. Included in this family are Clp proteases that are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. The functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP. Active site consists of the triad Ser, His and Asp, preferring hydrophobic or non-polar residues at P1 or P1' positions. The protease exists as a tetradecamer made up of two heptameric rings stacked back-to-back such that the catalytic triad of each subunit is located at the interface between three monomers, thus making oligomerization essential for function. Another family included in this class of enzymes is the signal peptide peptidase A (SppA; S49) which is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Mutagenesis studies suggest that the catalytic center of SppA comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. In addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members, the E. coli SppA contains an amino-terminal domain. Others, including sohB peptidase, protein C, protein 1510-N and archaeal signal peptide peptidase, do not contain the amino-terminal domain. The third family included in this hierarchy is nodulation formation efficiency D (NfeD) which is a membrane-bound Clp-class protease and only found in bacteria and archaea. Majority of the NfeD genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named stomatin operon partner protein (STOPP). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 from Pyrococcus horikoshii has been shown to possess serine protease activity having a Ser-Lys catalytic dyad. 161 matched cddid_all.tbl CDD cd00395 cd00395 173893 Tyr_Trp_RS_core catalytic core domain of tyrosinyl-tRNA and tryptophanyl-tRNA synthetase. Tyrosinyl-tRNA synthetase (TyrRS)/Tryptophanyl-tRNA synthetase (TrpRS) catalytic core domain. These enzymes attach Tyr or Trp, respectively, to the appropriate tRNA. These class I enzymes are homodimers, which aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding. 273 matched cddid_all.tbl CDD cd00396 cd00396 100027 PurM-like AIR (aminoimidazole ribonucleotide) synthase related protein. This family includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM (formylglycinamidine ribonucleotide) synthase and Selenophosphate synthetase (SelD). The N-terminal domain of AIR synthase forms the dimer interface of the protein, and is suggested as a putative ATP binding domain. 222 matched cddid_all.tbl CDD cd00397 cd00397 271175 DNA_BRE_C DNA breaking-rejoining enzymes, C-terminal catalytic domain. The DNA breaking-rejoining enzyme superfamily includes type IB topoisomerases and tyrosine based site-specific recombinases (integrases) that share the same fold in their catalytic domain containing conserved active site residues. The best-studied members of this diverse superfamily include Human topoisomerase I, the bacteriophage lambda integrase, the bacteriophage P1 Cre recombinase, the yeast Flp recombinase, and the bacterial XerD/C recombinases. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. The enzymes differ in that topoisomerases cleave and then rejoin the same 5' and 3' termini, whereas a site-specific recombinase transfers a 5' hydroxyl generated by recombinase cleavage to a new 3' phosphate partner located in a different duplex region. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity. 167 matched cddid_all.tbl CDD cd00398 cd00398 238232 Aldolase_II Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II). Class II enzymes are further divided into two sub-classes A and B. This family includes class II A aldolases and adducins which has not been ascribed any enzymatic function. Members of this class are primarily bacterial and eukaryotic in origin and include L-fuculose-1-phosphate, L-rhamnulose-1-phosphate aldolases and L-ribulose-5-phosphate 4-epimerases. They all share the ability to promote carbon-carbon bond cleavage and stabilize enolate intermediates using divalent cations. 209 matched cddid_all.tbl CDD cd00399 cd00399 259843 RNAP_largest_subunit_N Largest subunit of RNA polymerase (RNAP), N-terminal domain. This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit. 528 matched cddid_all.tbl CDD cd00400 cd00400 238233 Voltage_gated_ClC CLC voltage-gated chloride channel. The ClC chloride channels catalyse the selective flow of Cl- ions across cell membranes, thereby regulating electrical excitation in skeletal muscle and the flow of salt and water across epithelial barriers. This domain is found in the halogen ions (Cl-, Br- and I-) transport proteins of the ClC family. The ClC channels are found in all three kingdoms of life and perform a variety of functions including cellular excitability regulation, cell volume regulation, membrane potential stabilization, acidification of intracellular organelles, signal transduction, transepithelial transport in animals, and the extreme acid resistance response in eubacteria. They lack any structural or sequence similarity to other known ion channels and exhibit unique properties of ion permeation and gating. Unlike cation-selective ion channels, which form oligomers containing a single pore along the axis of symmetry, the ClC channels form two-pore homodimers with one pore per subunit without axial symmetry. Although lacking the typical voltage-sensor found in cation channels, all studied ClC channels are gated (opened and closed) by transmembrane voltage. The gating is conferred by the permeating ion itself, acting as the gating charge. In addition, eukaryotic and some prokaryotic ClC channels have two additional C-terminal CBS (cystathionine beta synthase) domains of putative regulatory function. 383 matched cddid_all.tbl CDD cd00401 cd00401 240619 SAHH S-Adenosylhomocysteine Hydrolase, NAD-binding and catalytic domains. S-adenosyl-L-homocysteine hydrolase (SAHH, AdoHycase) catalyzes the hydrolysis of S-adenosyl-L-homocysteine (AdoHyc) to form adenosine (Ado) and homocysteine (Hcy). The equilibrium lies far on the side of AdoHyc synthesis, but in nature the removal of Ado and Hyc is sufficiently fast, so that the net reaction is in the direction of hydrolysis. Since AdoHyc is a potent inhibitor of S-adenosyl-L-methionine dependent methyltransferases, AdoHycase plays a critical role in the modulation of the activity of various methyltransferases. The enzyme forms homotetramers, with each monomer binding one molecule of NAD+. 402 matched cddid_all.tbl CDD cd00402 cd00402 293928 Riboflavin_synthase_like Riboflavin synthase and similar proteins. Riboflavin synthase catalyzes the dismutation of two molecules of 6,7-dimethyl-8-(1'-D-ribityl)-lumazine (DMRL) to yield riboflavin (vitamin B12) and 4-ribitylamino-5-amino-2,6-dihydroxypyrimidine (RAADP). Riboflavin synthase is a homotrimer and the catalysis does not require any cofactors. Active sites are located between pairs of monomers, but only one active site catalyzes a reaction, the other two sites are inactive. Humans do not produce riboflavin synthase, and thus it is a good target for antimicrobial agents. This family also include lumazine protein (LumP) from bioluminescent bacteria. LumP serves as an optical transponder in bioluminescence emission. 185 matched cddid_all.tbl CDD cd00403 cd00403 238235 Ribosomal_L1 Ribosomal protein L1. The L1 protein, located near the E-site of the ribosome, forms part of the L1 stalk along with 23S rRNA. In bacteria and archaea, L1 functions both as a ribosomal protein that binds rRNA, and as a translation repressor that binds its own mRNA. Like several other large ribosomal subunit proteins, L1 displays RNA chaperone activity. L1 is one of the largest ribosomal proteins. It is composed of two domains that cycle between open and closed conformations via a hinge motion. The RNA-binding site of L1 is highly conserved, with both mRNA and rRNA binding the same binding site. 208 matched cddid_all.tbl CDD cd00404 cd00404 238236 Aconitase_swivel Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme mechanism. The aconitase family contains the following proteins: - Iron-responsive element binding protein (IRE-BP). IRE-BP is a cytosolic protein that binds to iron-responsive elements (IREs). IREs are stem-loop structures found in the 5'UTR of ferritin, and delta aminolevulinic acid synthase mRNAs, and in the 3'UTR of transferrin receptor mRNA. IRE-BP also express aconitase activity. - 3-isopropylmalate dehydratase (isopropylmalate isomerase), the enzyme that catalyzes the second step in the biosynthesis of leucine. - Homoaconitase (homoaconitate hydratase), an enzyme that participates in the alpha-aminoadipate pathway of lysine biosynthesis and that converts cis-homoaconitate into homoisocitric acid. 88 matched cddid_all.tbl CDD cd00405 cd00405 238237 PRAI Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are monomeric, monofunctional and thermolabile, but in some thermophile organisms PRAI is dimeric for reasons of stability and in others it is fused to other components of the tryptophan biosynthesis pathway to form multifunctional enzymes. 203 matched cddid_all.tbl CDD cd00407 cd00407 238238 Urease_beta Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of external and internally-generated urea as a nitrogen source. The enzyme consists of three subunits, alpha, beta and gamma, which can exist as separate proteins or can be fused on a single protein chain. The alpha-beta-gamma heterotrimer forms multimers, mainly trimers. The large alpha subunit is the catalytic domain containing an active site with a bi-nickel center complexed by a carbamylated lysine. The beta and gamma subunits play a role in subunit association to form the higher order trimers. 101 matched cddid_all.tbl CDD cd00408 cd00408 188630 DHDPS-like Dihydrodipicolinate synthase family. Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stabilizes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways and includes such proteins as N-acetylneuraminate lyase, MosA protein, 5-keto-4-deoxy-glucarate dehydratase, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase, trans-2'-carboxybenzalpyruvate hydratase-aldolase, and 2-keto-3-deoxy- gluconate aldolase. The family is also referred to as the N-acetylneuraminate lyase (NAL) family. 281 matched cddid_all.tbl CDD cd00411 cd00411 199205 L-asparaginase_like Bacterial L-asparaginases and related enzymes. Asparaginases (amidohydrolases, E.C. 3.5.1.1) are dimeric or tetrameric enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases, one highly specific for asparagine and localized to the periplasm (type II L-asparaginase), and a second (asparaginase- glutaminase) present in the cytosol (type I L-asparaginase) that hydrolyzes both asparagine and glutamine with similar specificities and has a lower affinity for its substrate. Bacterial L-asparaginases (type II) are potent antileukemic agents and have been used in the treatment of acute lymphoblastic leukemia (ALL). A conserved threonine residue is thought to supply the nucleophile hydroxy-group that attacks the amide bond. Many bacterial L-asparaginases have both L-asparagine and L-glutamine hydrolysis activities, to a different degree, and some of them are annotated as asparaginase/glutaminase. This wider family also includes a subunit of an archaeal Glu-tRNA amidotransferase. 320 matched cddid_all.tbl CDD cd00412 cd00412 238239 pyrophosphatase Inorganic pyrophosphatase. These enzymes hydrolyze inorganic pyrophosphate (PPi) to two molecules of orthophosphates (Pi). The reaction requires bivalent cations. The enzymes in general exist as homooligomers. 155 matched cddid_all.tbl CDD cd00413 cd00413 185683 Glyco_hydrolase_16 glycosyl hydrolase family 16. The O-Glycosyl hydrolases are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A glycosyl hydrolase classification system based on sequence similarity has led to the definition of more than 95 different families inlcuding glycosyl hydrolase family 16. Family 16 includes lichenase, xyloglucan endotransglycosylase (XET), beta-agarase, kappa-carrageenase, endo-beta-1,3-glucanase, endo-beta-1,3-1,4-glucanase, and endo-beta-galactosidase, all of which have a conserved jelly roll fold with a deep active site channel harboring the catalytic residues. 210 matched cddid_all.tbl CDD cd00418 cd00418 185672 GlxRS_core "catalytic core domain of glutamyl-tRNA and glutaminyl-tRNA synthetase. Glutamyl-tRNA synthetase(GluRS)/Glutaminyl-tRNA synthetase (GlnRS) cataytic core domain. These enzymes attach Glu or Gln, respectively, to the appropriate tRNA. Like other class I tRNA synthetases, they aminoacylate the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. These enzymes function as monomers. Archaea, cellular organelles, and some bacteria lack GlnRS. In these cases, the ""non-discriminating"" form of GluRS aminoacylates both tRNA(Glu) and tRNA(Gln) with Glu, which is converted to Gln when appropriate by a transamidation enzyme. The discriminating form of GluRS differs from GlnRS and the non-discriminating form of GluRS in their C-terminal anti-codon binding domains." 230 matched cddid_all.tbl CDD cd00419 cd00419 238240 Ferrochelatase_C Ferrochelatase, C-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is ubiquitous in nature and widely distributed in bacteria and eukaryotes. Recently, some archaeal members have been identified. The oligomeric state of these enzymes varies depending on the presence of a dimerization motif at the C-terminus. 135 matched cddid_all.tbl CDD cd00421 cd00421 238241 intradiol_dioxygenase Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. This family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases which are mononuclear non-heme iron enzymes that catalyze the oxygenation of catecholates to aliphatic acids via the cleavage of aromatic rings. The members are intradiol-cleaving enzymes which break the catechol C1-C2 bond and utilize Fe3+, as opposed to the extradiol-cleaving enzymes which break the C2-C3 or C1-C6 bond and utilize Fe2+ and Mn+. Catechol 1,2-dioxygenases are mostly homodimers with one catalytic ferric ion per monomer. Protocatechuate 3,4-dioxygenases form more diverse oligomers. 146 matched cddid_all.tbl CDD cd00423 cd00423 238242 Pterin_binding Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and protein biosynthesis. Prokaryotes (and some lower eukaryotes) must synthesize folate de novo, while higher eukaryotes are able to utilize dietary folate and therefore lack DHPS. Sulfonamide drugs, which are substrate analogs of pABA, target DHPS. Cobalamin-dependent methyltransferases catalyze the transfer of a methyl group via a methyl- cob(III)amide intermediate. These include MeTr, a functional heterodimer, and the folate binding domain of MetH. 258 matched cddid_all.tbl CDD cd00424 cd00424 176453 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion. Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention. 343 matched cddid_all.tbl CDD cd00427 cd00427 238243 Ribosomal_L29_HIP Ribosomal L29 protein/HIP. L29 is a protein of the large ribosomal Subunit. A homolog, called heparin/heparan sulfate interacting protein (HIP), has also been identified in mammals. L29 is located on the surface of the large ribosomal subunit, where it participates in forming a protein ring that surrounds the polypeptide exit channel, providing structural support for the ribosome. L29 is involved in forming the translocon binding site, along with L19, L22, L23, L24, and L31e. In addition, L29 and L23 form the interaction site for trigger factor (TF) on the ribosomal surface, adjacent to the exit tunnel. L29 forms numerous interactions with L23 and with the 23S rRNA. In some eukaryotes, L29 is referred to as L35, which is distinct from L35 found in bacteria and some eukaryotes (primarily plastids and mitochondria). The mammalian homolog, HIP, is found on the surface of many tissues and cell lines. It is believed to play a role in cell adhesion and modulation of blood coagulation. It has also been shown to inhibit apoptosis in cancer cells. 57 matched cddid_all.tbl CDD cd00429 cd00429 238244 RPE Ribulose-5-phosphate 3-epimerase (RPE). This enzyme catalyses the interconversion of D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate, as part of the Calvin cycle (reductive pentose phosphate pathway) in chloroplasts and in the oxidative pentose phosphate pathway. In the Calvin cycle Ru5P is phosphorylated by phosphoribulose kinase to ribulose-1,5-bisphosphate, which in turn is used by RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) to incorporate CO2 as the central step in carbohydrate synthesis. 211 matched cddid_all.tbl CDD cd00430 cd00430 143481 PLPDE_III_AR Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase. This family includes predominantly bacterial alanine racemases (AR), some serine racemases (SerRac), and putative bifunctional enzymes containing N-terminal UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase (murF) and C-terminal AR domains. These proteins are fold type III PLP-dependent enzymes that play essential roles in peptidoglycan biosynthesis. AR catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. SerRac converts L-serine into its D-enantiomer (D-serine) for peptidoglycan synthesis. murF catalyzes the addition of D-Ala-D-Ala to UDPMurNAc-tripeptide, the final step in the synthesis of the cytoplasmic precursor of bacterial cell wall peptidoglycan. Members of this family contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. AR and other members of this family require dimer formation and the presence of the PLP cofactor for catalytic activity. Fungal ARs and eukaryotic serine racemases, which are fold types I and II PLP-dependent enzymes respectively, are excluded from this family. 367 matched cddid_all.tbl CDD cd00431 cd00431 238245 cysteine_hydrolases Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It also contains isochorismatase, an enzyme that catalyzes the conversion of isochorismate to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of the vinyl ether bond, and other related enzymes with unknown function. 161 matched cddid_all.tbl CDD cd00432 cd00432 238246 Ribosomal_L18_L5e Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified. 103 matched cddid_all.tbl CDD cd00433 cd00433 238247 Peptidase_M17 Cytosol aminopeptidase family, N-terminal and catalytic domains. Family M17 contains zinc- and manganese-dependent exopeptidases ( EC 3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and play a key role in protein degradation and in the metabolism of biologically active peptides. They do not contain HEXXH motif (which is used as one of the signature patterns to group the peptidase families) in the metal-binding site. The two associated zinc ions and the active site are entirely enclosed within the C-terminal catalytic domain in leucine aminopeptidase. The enzyme is a hexamer, with the catalytic domains clustered around the three-fold axis, and the two trimers related to one another by a two-fold rotation. The N-terminal domain is structurally similar to the ADP-ribose binding Macro domain. This family includes proteins from bacteria, archaea, animals and plants. 468 matched cddid_all.tbl CDD cd00435 cd00435 238248 ACBP Acyl CoA binding protein (ACBP) binds thiol esters of long fatty acids and coenzyme A in a one-to-one binding mode with high specificity and affinity. Acyl-CoAs are important intermediates in fatty lipid synthesis and fatty acid degradation and play a role in regulation of intermediary metabolism and gene regulation. The suggested role of ACBP is to act as a intracellular acyl-CoA transporter and pool former. ACBPs are present in a large group of eukaryotic species and several tissue-specific isoforms have been detected. 85 matched cddid_all.tbl CDD cd00436 cd00436 350155 UP_TbUP-like uridine phosphorylases similar to Trypanosoma brucei UP. Uridine phosphorylase (UP) catalyzes the reversible phosphorolysis of uracil ribosides and analogous compounds to their respective nucleobases and ribose 1-phosphate. Trypanosoma brucei UP has a high specificity for uracil-containing (deoxy)nucleosides, and may function as a dimer. This subfamily belongs to the nucleoside phosphorylase-I (NP-I) family, whose members accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. The NP-1 family includes phosphorolytic nucleosidases, such as purine nucleoside phosphorylase (PNPs, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases, such as AMP nucleosidase (AMN, EC 3.2.2.4), and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). The NP-I family is distinct from nucleoside phosphorylase-II, which belongs to a different structural family. 282 matched cddid_all.tbl CDD cd00438 cd00438 380337 cupin_RmlC "RmlC carbohydrate epimerase, involved in dTDP-L-rhamnose production. RmlC (deoxythymidine diphosphate (dTDP)-4-keto-6-deoxy-D-hexulose 3, 5-epimerase or dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase; also known as RfbC) is a carbohydrate epimerase involved in the production of dTDP-L-rhamnose, a precursor of the bacterial cell wall constituent, L-rhamnose. L-Rhamnose (6-deoxy-l-mannose) plays an important role in the cell-wall structure of many bacterial species. It has been found to contribute to the virulence of several species, including the Gram-negative Salmonella enterica and Vibrio cholerae, where it is present as a part of the O-antigen, and is essential for the growth of Gram-positive bacteria such as Streptococcus pyogenes. RmlC converts dTDP-6-deoxy-D-xylo-4-hexulose to dTDP-6-deoxy-L-xylo-hexulose by catalyzing the epimerization of the 5-methyl and 3-hydroxyl groups of hexulose, the third of four steps in the dTDP-L-rhamnose biosynthetic pathway. RmlC belongs to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 168 matched cddid_all.tbl CDD cd00439 cd00439 188631 Transaldolase Transaldolase. Transaldolase. Enzymes found in the non-oxidative branch of the pentose phosphate pathway, that catalyze the reversible transfer of a dihydroxyacetone group from fructose-6-phosphate to erythrose-4-phosphate yielding sedoheptulose-7-phosphate and glyceraldehyde-3-phosphate. They are members of the class I aldolases, who are characterized by using a Schiff-base mechanism for stabilization of the reaction intermediates. 252 matched cddid_all.tbl CDD cd00442 cd00442 381596 Lyz-like lysozyme-like domains. This family contains several members, including soluble lytic transglycosylases (SLT), goose egg-white lysozymes (GEWL), hen egg-white lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, chitosanases, and pesticin. Typical members are involved in the hydrolysis of beta-1,4- linked polysaccharides. 59 matched cddid_all.tbl CDD cd00443 cd00443 238250 ADA_AMPD Adenosine/AMP deaminase. Adenosine deaminases (ADAs) are present in pro- and eukaryotic organisms and catalyze the zinc dependent irreversible deamination of adenosine nucleosides to inosine nucleosides and ammonia. The eukaryotic AMP deaminase catalyzes a similar reaction leading to the hydrolytic removal of an amino group at the 6 position of the adenine nucleotide ring, a branch point in the adenylate catabolic pathway. 305 matched cddid_all.tbl CDD cd00445 cd00445 238251 Uricase Urate oxidase (UO, uricase) is a peroxisomal enzyme that catalyzes the oxidation of uric acid to allantoin in most fish, amphibian, and mammalian species. The enzymatic process involves catalyzing the oxidative opening of the purine ring during the purine degradation pathway. In humans and certain other primates, however, the enzyme has been lost by some unknown mechanism. Each monomer contains two instances of this domain. Its functional form is a homotetramer for most species, though there are reports that some may form heterotetramers based on a few biochemical studies. 286 matched cddid_all.tbl CDD cd00446 cd00446 271355 GrpE nucleotide exchange factor GrpE. GrpE is the adenine nucleotide exchange factor of DnaK (Hsp70)-type ATPases. In bacteria, the DnaK-DnaJ-GrpE (KJE) chaperone system functions at the fulcrum of protein homeostasis. GrpE participates actively in response to heat shock by preventing aggregation of stress-denatured proteins; unfolded proteins initially bind to DnaJ, the J-domain ATPase-activating protein (Hsp40 family), whereupon DnaK hydrolyzes its bound ATP, resulting in a stable complex. The GrpE dimer binds to the ATPase domain of Hsp70 catalyzing the dissociation of ADP, which enables rebinding of ATP, one step in the Hsp70 reaction cycle in protein folding. In eukaryotes, only the mitochondrial Hsp70, not the cytosolic form, is GrpE dependent. Over-expression of Hsp70 molecular chaperones is important in suppressing toxicity of aberrantly folded proteins that occur in Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis, as well as several polyQ-diseases such as Huntington's disease and ataxias. 136 matched cddid_all.tbl CDD cd00447 cd00447 238253 NusB_Sun RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-specific 5-methylcytidine transferase (m5C-methyltransferase) Sun. The NusB protein plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation. The m5C-methyltransferase Sun shares the N-terminal non-catalytic RNA-binding domain with NusB. 129 matched cddid_all.tbl CDD cd00448 cd00448 100004 YjgF_YER057c_UK114_family YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site. 107 matched cddid_all.tbl CDD cd00449 cd00449 238254 PLPDE_IV PyridoxaL 5'-Phosphate Dependent Enzymes class IV (PLPDE_IV). This D-amino acid superfamily, one of five classes of PLPDE, consists of branched-chain amino acid aminotransferases (BCAT), D-amino acid transferases (DAAT), and 4-amino-4-deoxychorismate lyases (ADCL). BCAT catalyzes the reversible transamination reaction between the L-branched-chain amino and alpha-keto acids. DAAT catalyzes the synthesis of D-glutamic acid and D-alanine, and ADCL converts 4-amino-4-deoxychorismate to p-aminobenzoate and pyruvate. Except for a few enzymes, i. e., Escherichia coli and Salmonella BCATs, which are homohexamers arranged as a double trimer, the class IV PLPDEs are homodimers. Homodimer formation is required for catalytic activity. 256 matched cddid_all.tbl CDD cd00451 cd00451 212095 GH38N_AMII_euk N-terminal catalytic domain of eukaryotic class II alpha-mannosidases; glycoside hydrolase family 38 (GH38). The family corresponds to a group of eukaryotic class II alpha-mannosidases (AlphaMII), which contain Golgi alpha-mannosidases II (GMII), the major broad specificity lysosomal alpha-mannosidases (LAM, MAN2B1), the noval core-specific lysosomal alpha 1,6-mannosidases (Epman, MAN2B2), and similar proteins. GMII catalyzes the hydrolysis of the terminal both alpha-1,3-linked and alpha-1,6-linked mannoses from the high-mannose oligosaccharide GlcNAc(Man)5(GlcNAc)2 to yield GlcNAc(Man)3(GlcNAc)2 (GlcNAc, N-acetylglucosmine), which is the committed step of complex N-glycan synthesis. LAM is a broad specificity exoglycosidase hydrolyzing all known alpha 1,2-, alpha 1,3-, and alpha 1,6-mannosidic linkages from numerous high mannose type oligosaccharides. Different from LAM, Epman can efficiently cleave only the alpha 1,6-linked mannose residue from (Man)3GlcNAc, but not (Man)3(GlcNAc)2 or other larger high mannose oligosaccharides, in the core of N-linked glycans. Members in this family are retaining glycosyl hydrolases of family GH38 that employs a two-step mechanism involving the formation of a covalent glycosyl enzyme complex. Two carboxylic acids positioned within the active site act in concert: one as a catalytic nucleophile and the other as a general acid/base catalyst. 258 matched cddid_all.tbl CDD cd00452 cd00452 188632 KDPG_aldolase KDPG and KHG aldolase. KDPG and KHG aldolase. This family belongs to the class I adolases whose reaction mechanism involves Schiff base formation between a substrate carbonyl and lysine residue in the active site. 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase, is best known for its role in the Entner-Doudoroff pathway of bacteria, where it catalyzes the reversible cleavage of KDPG to pyruvate and glyceraldehyde-3-phosphate. 2-keto-4-hydroxyglutarate (KHG) aldolase, which has enzymatic specificity toward glyoxylate, forming KHG in the presence of pyruvate, and is capable of regulating glyoxylate levels in the glyoxylate bypass, an alternate pathway when bacteria are grown on acetate carbon sources. 190 matched cddid_all.tbl CDD cd00453 cd00453 238255 FTBP_aldolase_II Fructose/tagarose-bisphosphate aldolase class II. This family includes fructose-1,6-bisphosphate (FBP) and tagarose 1,6-bisphosphate (TBP) aldolases. FBP-aldolase is homodimeric and used in gluconeogenesis and glycolysis; the enzyme controls the condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to yield fructose-1,6-bisphosphate. TBP-aldolase is tetrameric and produces tagarose-1,6-bisphosphate. There is an absolute requirement for a divalent metal ion, usually zinc, and in addition the enzymes are activated by monovalent cations such as Na+. Although structurally similar, the class I aldolases use a different mechanism and are believed to have an independent evolutionary origin. 340 matched cddid_all.tbl CDD cd00454 cd00454 381253 TrHb1_N truncated hemoglobins (TrHbs, 2/2Hb, 2/2 globins); group 1 (N). The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. They are classified into three main groups based on their structural properties and named after Mycobacterium sp. genes glbN, glbO, and glbP: TrHb1s (N), TrHb2s (O) and TrHb3s (P). Typical of the TrHb1s (N) group is a protein matrix tunnel. It includes a Mycobacterium tuberculosis TrHb1, Mt-trHbN, which is encoded by the glbN gene. Mt-trHbN is expressed during the Mycobacterium stationary phase, and plays a specific defense role against nitrosative stress. The cyanobacterium Synechococcus sp. PCC 7002 TrHb1 GlbN, is constitutively expressed, and likely also protects cells from reactive nitrogen species. 111 matched cddid_all.tbl CDD cd00455 cd00455 238257 nuc_hydro nuc_hydro: Nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity. This group contains eukaryotic, bacterial and archeal proteins similar to the inosine-uridine preferring nucleoside hydrolase from Crithidia fasciculata, the xanthosine-inosine-uridine-adenosine-preferring nucleoside hydrolase RihC from Salmonella enterica serovar Typhimurium, the purine-specific inosine-adenosine-guanosine-preferring nucleoside hydrolase from Trypanosoma vivax and, pyrimidine-specific uridine-cytidine preferring nucleoside hydrolases such as URH1 from Saccharomyces cerevisiae, RihA and RihB from Escherichia coli. Nucleoside hydrolases are of interest as a target for antiprotozoan drugs as, no nucleoside hydrolase activity or genes encoding these enzymes have been detected in humans and, parasitic protozoans lack de novo purine synthesis relying on nucleoside hydrolase to scavenge purine and/or pyrimidines from the environment. 295 matched cddid_all.tbl CDD cd00457 cd00457 176642 PEBP PhosphatidylEthanolamine-Binding Protein (PEBP) domain. PhosphatidylEthanolamine-Binding Proteins (PEBPs) are represented in all three major phylogenetic divisions (eukaryotes, bacteria, archaea). A number of biological roles for members of the PEBP family include serine protease inhibition, membrane biogenesis, regulation of flowering plant stem architecture, and Raf-1 kinase inhibition. Although their overall structures are similar, the members of the PEBP family bind very different substrates including phospholipids, opioids, and hydrophobic odorant molecules as well as having different oligomerization states (monomer/dimer/tetramer). 159 matched cddid_all.tbl CDD cd00458 cd00458 238258 SugarP_isomerase SugarP_isomerase: Sugar Phosphate Isomerase family; includes type A ribose 5-phosphate isomerase (RPI_A), glucosamine-6-phosphate (GlcN6P) deaminase, and 6-phosphogluconolactonase (6PGL). RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium, the last step of the metabolic pathway of N-acetyl-D-glucosamine-6-phosphate. 6PGL converts 6-phosphoglucono-1,5-lactone to 6-phosphogluconate, the second step of the oxidative phase of the pentose phosphate pathway. 169 matched cddid_all.tbl CDD cd00460 cd00460 132901 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts. 86 matched cddid_all.tbl CDD cd00462 cd00462 238259 PTH Peptidyl-tRNA hydrolase (PTH) is a monomeric protein that cleaves the ester bond linking the nascent peptide and tRNA when peptidyl-tRNA is released prematurely from the ribosome. This ensures the recycling of peptidyl-tRNAs into tRNAs produced through abortion of translation and is essential for cell viability.This group also contains chloroplast RNA splicing 2 (CRS2), which is closely related nuclear-encoded protein required for the splicing of nine group II introns in chloroplasts. 171 matched cddid_all.tbl CDD cd00463 cd00463 199209 Ribosomal_L31e Eukaryotic/archaeal ribosomal protein L31. Ribosomal protein L31e, which is present in archaea and eukaryotes, binds the 23S rRNA and is one of six protein components encircling the polypeptide exit tunnel. It is a component of the eukaryotic 60S (large) ribosomal subunit, and the archaeal 50S (large) ribosomal subunit. 83 matched cddid_all.tbl CDD cd00464 cd00464 238260 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP. 154 matched cddid_all.tbl CDD cd00465 cd00465 238261 URO-D_CIMS_like The URO-D_CIMS_like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases, as well as cobalamine (B12) independent methionine synthases. Despite their sequence similarities, members of this family have clearly different functions. Uroporphyrinogen decarboxylase (URO-D) decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, an important branching point of the tetrapyrrole biosynthetic pathway. The methyltransferases represented here are important for ability of methanogenic organisms to use other compounds than carbon dioxide for reduction to methane, and methionine synthases transfer a methyl group from a folate cofactor to L-homocysteine in a reaction requiring zinc. 306 matched cddid_all.tbl CDD cd00466 cd00466 238262 DHQase_II Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway and the catabolic quinate pathway. There are two types of DHQases, which are distinct from each other in amino acid sequence and three-dimensional structure. Type I enzymes usually catalyze the biosynthetic reaction using a syn elimination mechanism. In contrast, type II enzymes, found in the quinate pathway of fungi and in the shikimate pathway of many bacteria, are dodecameric enzymes that employ an anti elimination reaction mechanism. 140 matched cddid_all.tbl CDD cd00468 cd00468 238263 HIT_like HIT family: HIT (Histidine triad) proteins, named for a motif related to the sequence HxHxH/Qxx (x, a hydrophobic amino acid), are a superfamily of nucleotide hydrolases and transferases, which act on the alpha-phosphate of ribonucleotides. On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified in the literacture into three major branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Further sequence analysis reveals several new closely related, yet uncharacterized subgroups. 86 matched cddid_all.tbl CDD cd00470 cd00470 238264 PTPS 6-pyruvoyl tetrahydropterin synthase (PTPS). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids, as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after uptake by a carrier-mediated active transport system. Most microbes and plants lack this system and must synthesize folates de novo from guanosine triphosphate. One enzyme from this pathway is PTPS which catalyzes the conversion of dihydroneopterin triphosphate to 6-pyruvoyl tetrahydropterin. The functional enzyme is a hexamer of identical subunits. 135 matched cddid_all.tbl CDD cd00472 cd00472 100103 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identified in bacteria, but a functionally equivalent protein may exist. Bacterial L19 forms an interprotein beta sheet with L14 that is similar to the L24e/L14 interprotein beta sheet observed in the archaeal L24e structures. Some eukaryotic L24 proteins were initially identified as L30, and this alignment model contains several sequences called L30. 54 matched cddid_all.tbl CDD cd00473 cd00473 275385 bS6 Bacterial ribosomal protein S6. bS6 is one of the components of the small subunit of the prokaryotic ribosome, a ribonucleoprotein organelle that decodes the genetic information in messenger RNA and forms peptide bonds to synthesize the corresponding polypeptides. Ribosomes consist of a large and a small subunit, which assemble during the initiation stage of protein synthesis. Prokaryotic ribosomes consist of three molecules of RNA and more than 50 proteins. The small subunits of bacterial and eukaryotic ribosomes have the same overall shapes (with structural elements described as head, body, platform, beak and shoulder). The bacterial ribosomal protein S6 is important for the assembly of the central domain of the small subunit via heterodimerization with ribosomal protein S18. 91 matched cddid_all.tbl CDD cd00474 cd00474 211317 eIF1_SUI1_like Eukaryotic initiation factor 1 and related proteins. Members of the eIF1/SUI1 (eukaryotic initiation factor 1) family are found in eukaryotes, archaea, and some bacteria; eukaryotic members are understood to play an important role in accurate initiator codon recognition during translation initiation. eIF1 interacts with 18S rRNA in the 40S ribosomal subunit during eukaryotic translation initiation. Point mutations in the yeast eIF1 implicate the protein in maintaining accurate start-site selection but its mechanism of action is unknown. The function of non-eukaryotic family members is also unclear. 78 matched cddid_all.tbl CDD cd00475 cd00475 259850 Cis_IPPS Cis (Z)-Isoprenyl Diphosphate Synthases. Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS) catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates. A few can also catalyze the condensation of IPP to trans-geranyl diphosphate to form the short-chain cis,trans- FPP. In prokaryotes, the cis-IPPS, undecaprenyl diphosphate synthase (UPP synthase), catalyzes the formation of the carrier lipid UPP in bacterial cell wall peptidoglycan biosynthesis. Similarly, in eukaryotes, the cis-IPPS, dehydrodolichyl diphosphate (dedol-PP) synthase catalyzes the formation of the polyisoprenoid glycosyl carrier lipid dolichyl monophosphate. cis-IPPS form homodimers and are mechanistically and structurally distinct from trans-IPPS, which lack the DDXXD motifs, yet require Mg2+ for activity. 219 matched cddid_all.tbl CDD cd00476 cd00476 133468 SAICAR_synt 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase. SAICAR synthetase (the PurC gene product) catalyzes the seventh step of the de novo biosynthesis of purine nucleotides (also reported as eighth step). It converts 5-aminoimidazole-4-carboxyribonucleotide (CAIR), ATP, and L-aspartate into 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR), ADP, and phosphate. 230 matched cddid_all.tbl CDD cd00477 cd00477 349750 FTHFS formyltetrahydrofolate synthetase. Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2 fixation (acetogenesis) and the glycine synthase/reductase pathways of purinolysis. The key physiological role of this enzyme in acetogens is to catalyze the formylation of tetrahydrofolate, an initial step in the reduction of carbon dioxide and other one-carbon precursors to acetate. In purinolytic organisms, the enzymatic reaction is reversed, liberating formate from 10-formyltetrahydrofolate with concurrent production of ATP. 540 matched cddid_all.tbl CDD cd00480 cd00480 238267 malate_synt Malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their carbon requirements from two-carbon compounds, by bypassing the two carboxylation steps of the citric acid cycle. 511 matched cddid_all.tbl CDD cd00481 cd00481 238268 Ribosomal_L19e Ribosomal protein L19e. L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small subunit. The other exposed end is involved in forming the translocon binding site, along with L22, L23, L24, L29, and L31e subunits. 145 matched cddid_all.tbl CDD cd00483 cd00483 238269 HPPK 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after uptake by a carrier-mediated active transport system. Most microbes and plants lack this system and must synthesize folates de novo from guanosine triphosphate. One enzyme from this pathway is HPPK which catalyzes pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin (HP). The functional enzyme is a monomer. Mammals lack many of the enzymes in the folate pathway including, HPPK. 128 matched cddid_all.tbl CDD cd00484 cd00484 238270 PEPCK_ATP Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity, this model describes the ATP-dependent groups. 508 matched cddid_all.tbl CDD cd00487 cd00487 238271 Pep_deformylase Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II) as the catalytic metal ion, which can be replaced with a nickel or cobalt ion with no loss of activity. There are two types of peptide deformylases, types I and II, which differ in structure only in the outer surface of the domain. Because these enzymes are essential only in prokaryotes (although eukaryotic gene sequences have been found), they are a target for a new class of antibacterial agents. 141 matched cddid_all.tbl CDD cd00488 cd00488 238272 PCD_DCoH PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein). Two DCoH proteins have been identifed in humans: DCoH1 and DCoH2. Mutations in human DCoH1 cause hyperphenylalaninemia. Loss of enzymic activity of DCoH in humans is associated with the depigmentation disorder vitiligo. DCoH1 has been reported to be overexpessed in colon cancer carcinomas and in malignant melanomas. 75 matched cddid_all.tbl CDD cd00489 cd00489 238273 Barstar_like Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it, thus inhibiting its potentially lethal RNase activity inside the cell. Barstar also binds and inhibits a ribonuclease called RNase Sa (produced by Streptomyces aureofaciens) which belongs to the same enzyme family as does barnase. 85 matched cddid_all.tbl CDD cd00490 cd00490 119402 Met_repressor_MetJ Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer. 103 matched cddid_all.tbl CDD cd00491 cd00491 238274 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers. 58 matched cddid_all.tbl CDD cd00493 cd00493 238275 FabA_FabZ FabA/Z, beta-hydroxyacyl-acyl carrier protein (ACP)-dehydratases: One of several distinct enzyme types of the dissociative, type II, fatty acid synthase system (found in bacteria and plants) required to complete successive cycles of fatty acid elongation. The third step of the elongation cycle, the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, is catalyzed by FabA or FabZ. FabA is bifunctional and catalyzes an additional isomerization reaction of trans-2-acyl-ACP to cis-3-acyl-ACP, an essential reaction to unsaturated fatty acid synthesis. FabZ is the primary dehydratase that participates in the elongation cycles of saturated as well as unsaturated fatty acid biosynthesis, whereas FabA is more active in the dehydration of beta-hydroxydecanoyl-ACP. The FabA structure is homodimeric with two independent active sites located at the dimer interface. 131 matched cddid_all.tbl CDD cd00494 cd00494 270213 PBP2_HMBS Hydroxymethylbilane synthase possesses the type 2 periplasmic binding protein fold. Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, vitamin B12 and related macrocycles. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This family includes the three domains of HMBS. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. 274 matched cddid_all.tbl CDD cd00495 cd00495 198379 Ribosomal_L25_TL5_CTC Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain. L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC. CTC is a known stress protein, and proteins of this family are believed to have two functions, acting as both ribosomal and stress proteins. In Escherichia coli, cells deleted for L25 were found to be viable; however, these cells grew slowly and had impaired protein synthesis capability. In Bacillus subtilis, CTC is induced under stress conditions and located in the ribosome; it has been proposed that CTC may be necessary for accurate translation under stress conditions. Ribosomal_L25_TL5_CTC is mostly found in bacteria, with a few exceptions such as plants or stramenopiles. Due to its limited taxonomic diversity and the viability of cells deleted for L25, this protein is not believed to be necessary for ribosomal assembly. Eukaryotes contain a protein called L25, which is not homologous to bacterial L25, but rather to bacterial L23. 90 matched cddid_all.tbl CDD cd00496 cd00496 238277 PheRS_alpha_core Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer. 218 matched cddid_all.tbl CDD cd00497 cd00497 211322 PseudoU_synth_TruA_like Pseudouridine synthase, TruA family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruA, Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus3p Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae PUS1 catalyzes the formation of psi34 and psi36 in the intron containing tRNAIle, psi35 in the intron containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes psi 26, 65 and 67. C. elegans Pus1p does not modify psi44 in U2 snRNA. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Psi44 in U2 snRNA and, psi38 and psi39 in tRNAs are highly phylogenetically conserved. Psi 26,27,28,34,35,36,65 and 67 in tRNAs are less highly conserved. Mouse Pus1p regulates nuclear receptor activity through pseudouridylation of Steroid Receptor RNA Activator. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA). 215 matched cddid_all.tbl CDD cd00498 cd00498 238278 Hsp33 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat shock), the Cys are reversibly oxidized to disulfide bonds, which causes the chaperone activity to be turned on. Hsp33 is homodimeric in its functional form. 275 matched cddid_all.tbl CDD cd00501 cd00501 238279 Peptidase_C15 Pyroglutamyl peptidase (PGP) type I, also known as pyrrolidone carboxyl peptidase (pcp) type I: Enzymes responsible for cleaving pyroglutamate (pGlu) from the N-terminal end of specialized proteins. The N-terminal pGlu protects these proteins from proteolysis by other proteases until the pGlu is removed by a PGP. PGPs are cysteine proteases with a Cys-His-Glu/Asp catalytic triad. Type I PGPs are found in a wide variety of prokaryotes and eukaryotes. It is not clear whether the functional form is a monomer, a homodimer, or a homotetramer. 194 matched cddid_all.tbl CDD cd00502 cd00502 188633 DHQase_I Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase). Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase). Catalyzes the cis-dehydration of 3-dehydroquinate via a covalent imine intermediate to produce dehydroshikimate. Dehydroquinase is the third enzyme in the shikimate pathway, which is involved in the biosynthesis of aromatic amino acids. Type I DHQase exists as a homodimer. Type II 3-dehydroquinase also catalyzes the same overall reaction, but is unrelated in terms of sequence and structure, and utilizes a completely different reaction mechanism. 225 matched cddid_all.tbl CDD cd00503 cd00503 238280 Frataxin Frataxin is a nuclear-encoded mitochondrial protein implicated in Friedreich's ataxia (FRDA), an human autosomal recessive neurodegenerative disease; Frataxin is found in eukaryotes and in purple bacteria; lack of frataxin causes iron to accumulate in the mitochondrial matrix suggesting that frataxin is involved in mitochondrial iron homeostasis and possibly in iron transport; the domain has an alpha-beta fold consisting of two helices flanking an antiparallel beta sheet. 105 matched cddid_all.tbl CDD cd00504 cd00504 238281 GXGXG GXGXG domain. This domain of unknown function is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS), in subunit C of tungsten formylmethanofuran dehydrogenase (FwdC) and in subunit C of molybdenum formylmethanofuran dehydrogenase (FmdC). It is also found in a primarily archeal group of proteins predicted to encode part of the large subunit of GltS. It is characterized by a repeated GXXGXXXG motif. GltS is a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the transfer of ammonia and electrons among three distinct active centers that carry out L-Gln hydrolysis, conversion of 2-oxoglutarate into L-Glu, and electron uptake from a donor. These catalytic sites occur in other domains within the protein or or encoded by separate genes, and are not present in the domain in this CD. FwdC and FmdC are reversible ion pumps that catalyze the formylation and deformylation of methanofuran in hyperthermophiles and bacteria. They require the presence of either tungstun (FwdC) or molybdenum (FmdC). The specific function of this domain also remains unidentified in the formylmethanofuran dehydrogenases. 149 matched cddid_all.tbl CDD cd00505 cd00505 132996 Glyco_transf_8 Members of glycosyltransferase family 8 (GT-8) are involved in lipopolysaccharide biosynthesis and glycogen synthesis. Members of this family are involved in lipopolysaccharide biosynthesis and glycogen synthesis. GT-8 comprises enzymes with a number of known activities: lipopolysaccharide galactosyltransferase, lipopolysaccharide glucosyltransferase 1, glycogenin glucosyltransferase, and N-acetylglucosaminyltransferase. GT-8 enzymes contains a conserved DXD motif which is essential in the coordination of a catalytic divalent cation, most commonly Mn2+. 246 matched cddid_all.tbl CDD cd00506 cd00506 211323 PseudoU_synth_TruB_like Pseudouridine synthase, TruB family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruB, Saccharomyces cerevisiae Pus4, M. tuberculosis TruB, S. cerevisiae Cbf5 and human dyskerin. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruB, M. tuberculosis TruB and S. cerevisiae Pus4, make psi55 in the T loop of tRNAs. Pus4 catalyses the formation of psi55 in both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. Mutations in human dyskerin cause X-linked dyskeratosis congenitas. 210 matched cddid_all.tbl CDD cd00508 cd00508 238282 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. 120 matched cddid_all.tbl CDD cd00512 cd00512 238283 MM_CoA_mutase Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM)-like family; contains proteins similar to MCM, and the large subunit of Streptomyces coenzyme B12-dependent isobutyryl-CoA mutase (ICM). MCM catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA. The reaction proceeds via radical intermediates beginning with a substrate-induced homolytic cleavage of the Co-C bond of coenzyme B12 to produce cob(II)alamin and the deoxyadenosyl radical. MCM plays an important role in the conversion of propionyl-CoA to succinyl-CoA during the degradation of propionate for the Krebs cycle. In higher animals, MCM is involved in the breakdown of odd-chain fatty acids, several amino acids, and cholesterol. Methylobacterium extorquens MCM participates in the glyoxylate regeneration pathway. In M. extorquens, MCM forms a complex with MeaB; MeaB may protect MCM from irreversible inactivation. In some bacteria, MCM is involved in the reverse metabolic reaction, the rearrangement of succinyl-CoA to methylmalonyl-CoA. Examples include Propionbacterium shermanni MCM during propionic acid fermentation, E.coli MCM in a pathway for the conversion of succinate to propionate and Streptomyces MCM in polyketide biosynthesis. P. shermanni and Streptomyces cinnamonensis MCMs are alpha/beta heterodimers, with both subunits being homologous members of this family. It has been shown for P. shermanni MCM that only the alpha subunit binds coenzyme B12 and substrates. Human MCM is a homodimer with two active sites. Mouse and E.coli MCMs are also homodimers. ICM from S. cinnamonensis is comprised of a large and a small subunit. The holoenzyme appears to be an alpha2beta2 heterotetramer with up to 2 molecules of coenzyme B12 bound. The small subunit binds coenzyme B12. ICM catalyzes the reversible rearrangement of n-butyryl-CoA to isobutyryl-CoA (intermediates in fatty acid and valine catabolism, which in S. cinnamonensis can be converted to methylmalonyl-CoA and used in polyketide synthesis). In humans, impaired activity of MCM results in methylmalonic aciduria, a disorder of propionic acid metabolism. 399 matched cddid_all.tbl CDD cd00513 cd00513 238284 Ribosomal_L32_L32e "Ribosomal_L32_L32e: L32 is a protein from the large subunit that contains a surface-exposed globular domain and a finger-like projection that extends into the RNA core to stabilize the tertiary structure. L32 does not appear to play a role in forming the A (aminacyl), P (peptidyl) or E (exit) sites of the ribosome, but does interact with 23S rRNA, which has a ""kink-turn"" secondary structure motif. L32 is overexpressed in human prostate cancer and has been identified as a stably expressed housekeeping gene in macrophages of human chronic obstructive pulmonary disease (COPD) patients. In Schizosaccharomyces pombe, L32 has also been suggested to play a role as a transcriptional regulator in the nucleus. Found in archaea and eukaryotes, this protein is known as L32 in eukaryotes and L32e in archaea." 107 matched cddid_all.tbl CDD cd00515 cd00515 238285 HAM1 NTPase/HAM1. This family consists of the HAM1 protein and pyrophosphate-releasing xanthosine/ inosine triphosphatase. HAM1 protects the cell against mutagenesis by the base analog 6-N-hydroxylaminopurine (HAP) in E. Coli and S. cerevisiae. A Ham1-related protein from Methanococcus jannaschii is a novel NTPase that has been shown to hydrolyze nonstandard nucleotides such as XTP to XMP and ITP to IMP, but not the standard nucleotides, in the presence of Mg or Mn ions. The enzyme exists as a homodimer. The HAM1 protein may be acting as an NTPase by hydrolyzing the HAP triphosphate. 183 matched cddid_all.tbl CDD cd00516 cd00516 238286 PRTase_typeII Phosphoribosyltransferase (PRTase) type II; This family contains two enzymes that play an important role in NAD production by either allowing quinolinic acid (QA) , quinolinate phosphoribosyl transferase (QAPRTase), or nicotinic acid (NA), nicotinate phosphoribosyltransferase (NAPRTase), to be used in the synthesis of NAD. QAPRTase catalyses the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide, an important step in the de novo synthesis of NAD. NAPRTase catalyses a similar reaction leading to NAMN and pyrophosphate, using nicotinic acid an PPRP as substrates, used in the NAD salvage pathway. 281 matched cddid_all.tbl CDD cd00517 cd00517 173895 ATPS ATP-sulfurylase. ATP-sulfurylase (ATPS), also known as sulfate adenylate transferase, catalyzes the transfer of an adenylyl group from ATP to sulfate, forming adenosine 5'-phosphosulfate (APS). This reaction is generally accompanied by a further reaction, catalyzed by APS kinase, in which APS is phosphorylated to yield 3'-phospho-APS (PAPS). In some organisms the APS kinase is a separate protein, while in others it is incorporated with ATP sulfurylase in a bifunctional enzyme that catalyzes both reactions. In bifunctional proteins, the domain that performs the kinase activity can be attached at the N-terminal end of the sulfurylase unit or at the C-terminal end, depending on the organism. While the reaction is ubiquitous among organisms, the physiological role of the reaction varies. In some organisms it is used to generate APS from sulfate and ATP, while in others it proceeds in the opposite direction to generate ATP from APS and pyrophosphate. ATP sulfurylase can be a monomer, a homodimer, or a homo-oligomer, depending on the organism. ATPS belongs to a large superfamily of nucleotidyltransferases that includes pantothenate synthetase (PanC), phosphopantetheine adenylyltransferase (PPAT), and the amino-acyl tRNA synthetases. The enzymes of this family are structurally similar and share a dinucleotide-binding domain. 353 matched cddid_all.tbl CDD cd00518 cd00518 99872 H2MP Hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). These enzymes belong to the peptidase family M52. Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE, the large subunit of hydrogenase 3. This cleavage is nickel dependent. This CD also includes such hydrogenase-processing proteins as HydD, HupW, and HoxW, as well as, proteins of the F420-reducing hydrogenase of methanogens (e.g., FrcD). Also included, is the Pyrococcus furiosus FrxA protein, a bifunctional endopeptidase/ sulfhydrogenase found in NADP-reducing hyperthermophiles.The Pyrococcus FrxA is not related to those found in Helicobacter pylori. 139 matched cddid_all.tbl CDD cd00519 cd00519 238287 Lipase_3 "Lipase (class 3). Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is ""interfacial activation,"" the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure. A ""lid"" or ""flap"" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site. " 229 matched cddid_all.tbl CDD cd00520 cd00520 238288 RRF "Ribosome recycling factor (RRF). Ribosome recycling factor dissociates the posttermination complex, composed of the ribosome, deacylated tRNA, and mRNA, after termination of translation. Thus ribosomes are ""recycled"" and ready for another round of protein synthesis. RRF is believed to bind the ribosome at the A-site in a manner that mimics tRNA, but the specific mechanisms remain unclear. RRF is essential for bacterial growth. It is not necessary for cell growth in archaea or eukaryotes, but is found in mitochondria or chloroplasts of some eukaryotic species." 179 matched cddid_all.tbl CDD cd00522 cd00522 213981 Hemerythrin-like "Hemerythrin family. Hemerythrin (Hr) and related proteins are found in bacteria, archaea and eukaryotes. They are non-heme diiron oxygen transport proteins. In addition to oxygen transport, members are involved in cadmium fixation and host anti-bacterial defense. They have the same ""four alpha helix bundle"" motif and similar active site structures. Some members, like Hr, form oligomers, the octameric form being most prevalent, while others are monomeric." 103 matched cddid_all.tbl CDD cd00523 cd00523 411703 Holliday_junction_resolvase Holliday junction resolvase. Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJRs occur in archaea, bacteria, and in the mitochondria of certain eukaryotes; however, this CD includes only the archeal HJRs. The bacterial and archeal HJRs perform a similar function but differ in both sequence and structure. Structural similarity does however, exist between the archeal HJRs and type II restriction endonucleases, such as EcoRV, BglII, and Fok, and this similarity includes their active site configurations. 126 matched cddid_all.tbl CDD cd00524 cd00524 238290 SORL Superoxide reductase-like (SORL) domain; present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals as a defense mechanism against reactive oxygen species and are found in anaerobic bacteria and archeae, and microaerophilic Treponema pallidum. The SORL domain contains an active iron site, Fe[His4Cys(Glu)], which in the reduced state loses the glutamate ligand. Superoxide reductase (class II) forms a homotetramer with four Fe[His4Cys(Glu)] centers. Desulfoferrodoxin (class I) is a homodimeric protein, with each protomer comprised of two domains, the N-terminal desulforedoxin (DSRD) domain and C-terminal SORL domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)]. 86 matched cddid_all.tbl CDD cd00525 cd00525 238291 AE_Prim_S_like AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. In addition to its catalytic role in replication, eukaryotic DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. Pfu41 and Pfu46 comprise the primase complex of the archaea Pyrococcus furiosus; these proteins have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the primase activity of Pfu41. Also found in this group is the primase-polymerase (primpol) domain of replicases from archaeal plasmids including the ORF904 protein of pRN1 from Sulfolobus islandicus (pRN1 primpol). The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. The pRN1 primpol primase activity prefers dNTPs to rNTPs; however incorporation of dNTPs requires rNTP as cofactor. This group also includes the Pol domain of bacterial LigD proteins such Mycobacterium tuberculosis (Mt)LigD. MtLigD contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. LigD Pol plays a role in non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB) in vivo, perhaps by filling in short 5'-overhangs with ribonucleotides; the filled in termini would be sealed by the associated LigD ligase domain. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. 136 matched cddid_all.tbl CDD cd00527 cd00527 238292 IF6 Ribosome anti-association factor IF6 binds the large ribosomal subunit and prevents the two subunits from associating during translation initiation. IF6 comprises a family of translation factors that includes both eukaryotic (eIF6) and archeal (aIF6) members. All members of this family have a conserved pentameric fold referred to as a beta/alpha propeller. The eukaryotic IF6 members have a moderately conserved C-terminal extension which is not required for ribosomal binding, and may have an alternative function. 220 matched cddid_all.tbl CDD cd00528 cd00528 238293 MoaC MoaC family. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor Z by inserting the carbon-8 of the purine between the 2' and 3' ribose carbon atoms, which is the first of three phases of Moco biosynthesis. 136 matched cddid_all.tbl CDD cd00529 cd00529 438561 RuvC-like Crossover junction endodeoxyribonuclease RuvC and similar proteins. The RuvC-like family consists of bacterial RuvC, fungal Cruciform cutting endonuclease 1 (CCE1), bacterial YqgF and monokaryotic chloroplast 1 protein (MOC1). RuvC, CCE1 and MOC1 are Holliday junction resolvases (HJRs), endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. RuvC is part of the RuvABC pathway in Escherichia coli and other Gram-negative bacteria that is involved in processing Holliday junctions, which are formed by the reciprocal exchange of strands between two DNA duplexes. CCE1 is a HJR specific for 4-way junctions; it is involved in the maintenance of mitochondrial DNA. Escherichia coli YqgF has been shown to act as a pre-16S rRNA nuclease, presumably as a monomer. It is involved in the processing of pre-16S rRNA during ribosome maturation. HJRs occur in archaea, bacteria, and in the mitochondria of certain fungi. RuvC and its orthologs are homodimers and display structural similarity to RNase H and Hsp70. 110 matched cddid_all.tbl CDD cd00530 cd00530 238295 PTE Phosphotriesterase (PTE) catalyzes the hydrolysis of organophosphate nerve agents, including the chemical warfare agents VX, soman, and sarin as well as the insecticide paraoxon. PTE exists as a homodimer with one active site per monomer. The active site is located next to a binuclear metal center, at the C-terminal end of a TIM alpha- beta barrel motif. The native enzyme contains two zinc ions at the active site however these can be replaced with other metals such as cobalt, cadmium, nickel or manganese and the enzyme remains active. 293 matched cddid_all.tbl CDD cd00531 cd00531 238296 NTF2_like Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of divergent evolution wherein the proteins have many common structural details but diverge greatly in their function. For example, nuclear transport factor 2 (NTF2) mediates the nuclear import of RanGDP and binds to both RanGDP and FxFG repeat-containing nucleoporins while Ketosteroid isomerases catalyze the isomerization of delta-5-3-ketosteroid to delta-4-3-ketosteroid, by intramolecular transfer of the C4-beta proton to the C6-beta position. While the function of the beta sub-unit of the Ring hydroxylating dioxygenases is not known, Scytalone Dehydratases catalyzes two reactions in the biosynthetic pathway that produces fungal melanin. Members of the NTF2-like superfamily are widely distributed among bacteria, archaea and eukaryotes. 124 matched cddid_all.tbl CDD cd00532 cd00532 238297 MGS-like MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate synthetase (CPS) where it catalyzes the last phosphorylation of a coaboxyphosphate intermediate to form the product carbamoyl phosphate and may also play a regulatory role. This family also includes inosine monophosphate cyclohydrolase. The known structures in this family show a common phosphate binding site. 112 matched cddid_all.tbl CDD cd00534 cd00534 238298 DHNA_DHNTPE Dihydroneopterin aldolase (DHNA) and 7,8-dihydroneopterin triphosphate epimerase domain (DHNTPE); these enzymes have been designated folB and folX, respectively. Folate derivatives are essential cofactors in the biosynthesis of purines, pyrimidines, and amino acids, as well as formyl-tRNA. Mammalian cells are able to utilize pre-formed folates after uptake by a carrier-mediated active transport system. Most microbes and plants lack this system and must synthesize folates de novo from guanosine triphosphate. One enzyme from this pathway is DHNA which catalyses the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin in the biosynthetic pathway of tetrahydrofolate. Though it is known that DHNTPE catalyzes the epimerization of dihydroneopterin triphosphate to dihydromonapterin triphosphate, the biological role of this enzyme is still unclear. It is hypothesized that it is not an essential protein since a folX knockout in E. coli has a normal phenotype and the fact that folX is not present in H. influenza. In addition both enzymes have been shown to be able to compensate for the other's activity albeit at slower reaction rates. The functional enzyme for both is an octamer of identical subunits. Mammals lack many of the enzymes in the folate pathway including, DHNA and DHNTPE. 118 matched cddid_all.tbl CDD cd00537 cd00537 238299 MTHFR Methylenetetrahydrofolate reductase (MTHFR). 5,10-Methylenetetrahydrofolate is reduced to 5-methyltetrahydrofolate by methylenetetrahydrofolate reductase, a cytoplasmic, NAD(P)-dependent enzyme. 5-methyltetrahydrofolate is utilized by methionine synthase to convert homocysteine to methionine. The enzymatic mechanism is a ping-pong bi-bi mechanism, in which NAD(P)+ release precedes the binding of methylenetetrahydrofolate and the acceptor is free FAD. The family includes the 5,10-methylenetetrahydrofolate reductase EC:1.7.99.5 from prokaryotes and methylenetetrahydrofolate reductase EC: 1.5.1.20 from eukaryotes. The bacterial enzyme is a homotetramer and NADH is the preferred reductant while the eukaryotic enzyme is a homodimer and NADPH is the preferred reductant. In humans, there are several clinically significant mutations in MTHFR that result in hyperhomocysteinemia, which is a risk factor for the development of cardiovascular disease. 274 matched cddid_all.tbl CDD cd00538 cd00538 238300 PA PA: Protease-associated (PA) domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases including, hSPPL2a and 2b which catalyze the intramembrane proteolysis of tumor necrosis factor alpha, ii) various proteins containing a C3H2C3 RING finger including, Arabidopsis ReMembR-H2 protein and various E3 ubiquitin ligases such as human GRAIL (gene related to anergy in lymphocytes), iii) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), iv) various plant vacuolar sorting receptors such as Pisum sativum BP-80, v) glutamate carboxypeptidase II (GCPII), vi) yeast aminopeptidase Y, vii) Vibrio metschnikovii VapT, a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease, viii) lactocepin (a cell envelope-associated protease from Lactobacillus paracasei subsp. paracasei NCDO 151), ix) various subtilisin-like proteases such as melon Cucumisin, and x) human TfR (transferrin receptor) 1 and 2. 126 matched cddid_all.tbl CDD cd00539 cd00539 238301 MCR_gamma Methyl-coenzyme M reductase (MCR) gamma subunit. MCR catalyzes the terminal step of methane formation in the energy metabolism of all methanogenic archaea, in which methyl-coenzyme M and coenzyme B are converted to methane and the heterodisulfide of coenzyme M and coenzyme B (CoM-S-S-CoB). MCR is a dimer of trimers, each of which consists of one alpha, one beta, and one gamma subunit, with two identical active sites containing nickel porphinoid factor 430 (F430). 246 matched cddid_all.tbl CDD cd00540 cd00540 187726 AAG Alkyladenine DNA glycosylase catalyzes the first step in base excision repair. Alkyladenine DNA glycosylase (AAG), also known as 3-methyladenine DNA glycosylase, catalyzes the first step in base excision repair (BER) by cleaving damaged DNA bases within double-stranded DNA to produce an abasic site. AAG bends DNA by intercalating between the base pairs, causing the damaged base to flip out of the double helix and into the enzyme active site for cleavage. Although AAG represents one of six DNA glycosylase classes, it lacks the helix-hairpin-helix active site motif associated with other BER glycosylases and is structurally distinct from them. 187 matched cddid_all.tbl CDD cd00541 cd00541 238302 OMPLA The outer membrane phospholipase A (OMPLA) is an integral membrane enzyme that catalyses the hydrolysis of acylester bonds in phospholipids using calcium as a cofactor. The enzyme has a fold of transmembrane beta-barrels and is widespread among Gram-negative bacteria, both in pathogens and nonpathogens. In pathogenic bacteria such as Campylobacter coli and Helicobacter pylori OMPLA is involved in pathogenesis and virulence. In nonpathogenic bacteria the physiological function of OMPLA is less clear. The Escherichia coli enzyme is involved in the secretion of bacteriocins, antibacterial peptides that are produced in order to survive under starvation conditions. The enzyme activity of OMPLA is strictly regulated to prevent uncontrolled breakdown of the surrounding phospholipids. The activity of OMPLA can be induced by membrane perturbation and concurs with dimerization of the enzyme. 231 matched cddid_all.tbl CDD cd00542 cd00542 238303 Ntn_PVA Penicillin V acylase (PVA), also known as conjugated bile salt acid hydrolase (CBAH), catalyzes the hydrolysis of penicillin V to yield 6-amino penicillanic acid (6-APA), an important key intermediate of semisynthetic penicillins. PVA has an N-terminal nucleophilic cysteine, as do other members of the Ntn hydrolase family to which PVA belongs. This nucleophilic cysteine is exposed by post-translational prossessing of the PVA precursor. PVA forms a homotetramer. 303 matched cddid_all.tbl CDD cd00544 cd00544 410861 CobU Adenosylcobinamide kinase / adenosylcobinamide phosphate guanyltransferase (CobU). CobU is a bacterial bifunctional cobalbumin biosynthesis enzyme which display adenosylcobinamide kinase and adenosylcobinamide phosphate guanyltransferase activity and is a key participant in the final stages of cobalamin biosynthesis where it is involved in nucleotide loop assembly. CobU is a homotrimer which functions both as a kinase and as a nucleotidyl transferase. It phosphorylates of adenosylcobinamide to form adenosylcobinamide phosphate (using a variety of nucleotides as the phosphate donor) and then adds GMP to adenosylcobinamide phosphate to form adenosylcobinamide-GDP, specifically using GTP. 166 matched cddid_all.tbl CDD cd00545 cd00545 238305 MCH Methenyltetrahydromethanopterin (methenyl-H4MPT) cyclohydrolase (MCH). MCH is a cytoplasmic enzyme that has been identified in methanogenic archaea, sulfate- reducing archaea, and methylotrophic bacteria. It catalyzes the reversible formation of N(5), N(10)-methenyltetrahydromethanopterin (methenyl-H4MPT+) from N(5)-formyltetrahydromethanopterin (formyl- H4MPT), in the third step of the reaction to reduce CO2 to CH4. The protein functions as a homodimer or homotrimer, depending on the organism. 312 matched cddid_all.tbl CDD cd00546 cd00546 238306 QFR_TypeD_subunitC Quinol:fumarate reductase (QFR) Type D subfamily, 15kD hydrophobic subunit C; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine oxidoreductase (SQR). QFRs oxidize low potential quinols such as menaquinol and are involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQR and QFR share a common subunit arrangement, composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are classified as Type D as they contain two transmembrane subunits (C and D) and no heme groups. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, and the transmembrane subunit containing the electron donor (quinol). The quinone binding site resides in the transmembrane subunits. 124 matched cddid_all.tbl CDD cd00547 cd00547 238307 QFR_TypeD_subunitD Quinol:fumarate reductase (QFR) Type D subfamily, 13kD hydrophobic subunit D; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinine oxidoreductase (SQR). QFRs oxidize low potential quinols such as menaquinol and are involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQR and QFR share a common subunit arrangement, composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are classified as Type D as they contain two transmembrane subunits (C and D) and no heme groups. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, and the transmembrane subunit containing the electron donor (quinol). The quinone binding site resides in the transmembrane subunits. 115 matched cddid_all.tbl CDD cd00548 cd00548 349426 NrfA-like cytochrome c nitrite reductase and similar proteins. This family contains cytochrome c nitrite reductase (also known as cytochrome c552, or NrfA) and similar proteins. The pentaheme enzyme NrfA catalyzes the electron reduction of nitrite to ammonia in the nitrogen cycle. This enzyme can also transform nitrogen monoxide and hydroxylamine, two potential bound reaction intermediates, into ammonia. It is a homodimer, with each monomer containing four classical CXXCH type heme-binding sites along with an alternative CXXCK heme-binding motif, which is important for catalysis. This family also includes octaheme nitrite reductase (TvNiR) from the haloalkaliphilic bacterium Thioalkalivibrio paradoxus which catalyzes the reduction of nitrite and hydroxylamine to ammonia as well as the reduction of sulfite to sulfide. 370 matched cddid_all.tbl CDD cd00551 cd00551 200451 AmyAc_family Alpha amylase catalytic domain family. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; and C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost this catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 260 matched cddid_all.tbl CDD cd00552 cd00552 238308 RaiA "RaiA (""ribosome-associated inhibitor A"", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site. RaiA is also thought to counteract miscoding at the A site thus reducing translation errors. The RaiA fold structurally resembles the double-stranded RNA-binding domain (dsRBD)." 93 matched cddid_all.tbl CDD cd00553 cd00553 467484 NAD_synthase NAD(+) synthase. NAD(+) synthase (EC 6.3.5.1), a homodimer, catalyzes the final step in the de novo nicotinamide adenine dinucleotide (NAD(+)) biosynthesis, an amide transfer from either ammonia or glutamine to nicotinic acid adenine dinucleotide (NaAD). The conversion of NaAD to NAD(+) occurs via a NAD-adenylate intermediate and requires ATP and Mg(2+). The intermediate is subsequently cleaved into NAD(+) and AMP. In many prokaryotes, such as Escherichia coli, NAD synthase consists of a single domain and is strictly ammonia dependent. In contrast, eukaryotes and other prokaryotes have an additional N-terminal amidohydrolase domain that prefer glutamine. Interestingly, NAD(+) synthases in these prokaryotes, can also utilize ammonia as an amide source. 248 matched cddid_all.tbl CDD cd00554 cd00554 100025 MECDP_synthase MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis. This pathway is present in bacteria, plants and some protozoa but is distinct from that used by mammals and Archaea. MECDP_synthase forms a homotrimer, carrying three active sites, each of which is formed in a cleft between pairs of subunits. 153 matched cddid_all.tbl CDD cd00555 cd00555 238310 Maf Nucleotide binding protein Maf. Maf has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea, but homologs in B.subtilis and S.cerevisiae are nonessential for cell division. Maf has been predicted to be a nucleotide- or nucleic acid-binding protein with structural similarity to the hypoxanthine/xanthine NTP pyrophosphatase Ham1 from Methanococcus jannaschii, RNase H from Escherichia coli, and some other nucleotide or RNA-binding proteins. 180 matched cddid_all.tbl CDD cd00556 cd00556 238311 Thioesterase_II Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP) domains, respectively. TEII has two tandem asymmetric hot dog folds that are structurally similar to one found in PaaI thioesterase, 4-hydroxybenzoyl-CoA thioesterase (4HBT) and beta-hydroxydecanoyl-ACP dehydratase and thus, the TEII monomer is equivalent to the homodimeric form of the latter three enzymes. Human TEII is expressed in T cells and has been shown to bind the product of the HIV-1 Nef gene. 99 matched cddid_all.tbl CDD cd00557 cd00557 238312 Translocase_SecB Preprotein translocase subunit SecB. SecB is a cytoplasmic component of the multisubunit membrane-bound enzyme termed Sec protein translocase, which is the main constituent of the General Secretory (type II) Pathway involved in translocation of nascent polypeptides across the cytoplasmic membrane. SecB has been shown to function as export-specific molecular chaperone that selectively binds preproteins, maintains them in a translocation competent state and delivers them to SecA, the membrane-bound ATPase, that drives the translocation reaction. In solution, SecB exists as homotetramer, which is organized as a dimer of dimers. 131 matched cddid_all.tbl CDD cd00559 cd00559 238313 Cyanase_C Cyanase C-terminal domain. Cyanase (Cyanate lyase) is responsible for the hydrolysis of cyanate. It catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. This allows organisms that possess the enzyme to overcome the toxicity of environmental cyanate and to use cyanate as a source of nitrogen for growth. This enzyme is a homodecamer, formed by five dimers. Each monomer is composed of two domains, an N-terminal helix-turn-helix and this structurally unique C-terminal domain. 69 matched cddid_all.tbl CDD cd00560 cd00560 185673 PanC Pantoate-beta-alanine ligase. PanC Pantoate-beta-alanine ligase, also known as pantothenate synthase, catalyzes the formation of pantothenate from pantoate and alanine. PanC belongs to a large superfamily of nucleotidyltransferases that includes , ATP sulfurylase (ATPS), phosphopantetheine adenylyltransferase (PPAT), and the amino-acyl tRNA synthetases. The enzymes of this family are structurally similar and share a dinucleotide-binding domain. 277 matched cddid_all.tbl CDD cd00561 cd00561 410862 CobA_ACA CobA-type ATP:corrinoid adenosyltransferase. CobA-ATP:corrinoid adenosyltransferase is one of three sequence and structurally unrelated groups of ATP:corrinoid adenosyltransferase, PduO and EutT being the other two. CobA has been shown to be involved in cobalamin (vitamin B12) biosynthesis and scavenging of incomplete corrinoids. This enzyme is a homodimer, which catalyzes the adenosylation reaction: ATP + cob(I)alamin + H2O 170 matched cddid_all.tbl CDD cd00562 cd00562 238315 NifX_NifB This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This domain is a predicted small-molecule-binding domain (SMBD) with an alpha/beta fold that is present either as a stand-alone domain (e.g. NifX and NifY) or fused to another conserved domain (e.g. NifB) however, its function is still undetermined.The SCOP database suggests that this domain is most similar to structures within the ribonuclease H superfamily. This conserved domain is represented in two of the three major divisions of life (bacteria and archaea). 102 matched cddid_all.tbl CDD cd00563 cd00563 238316 Dtyr_deacylase D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not in archea; beta barrel-like fold structure; forms homodimers in which two surface cavities serve as the active site for tRNA binding 145 matched cddid_all.tbl CDD cd00564 cd00564 238317 TMP_TenI Thiamine monophosphate synthase (TMP synthase)/TenI. TMP synthase catalyzes an important step in the thiamine biosynthesis pathway, the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl) thiazole phosphate to yield thiamine phosphate. TenI is a enzymatically inactive regulatory protein involved in the regulation of several extracellular enzymes. This superfamily also contains other enzymatically inactive proteins with unknown functions. 196 matched cddid_all.tbl CDD cd00565 cd00565 340451 Ubl_ThiS ubiquitin-like (Ubl) domain found in sulfur carrier protein ThiS. ThiS, also termed Thiamine biosynthesis protein (ThiaminS), is a sulfur carrier protein involved in thiamin biosynthesis in prokaryotes. It has the beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin (Ub), and is activated in an ATP-dependent manner by sulfurtransferases, similar to the activation mechanism of Ub-activating enzyme E1. ThiS has common evolutionary origin with Ub-related protein modifiers in eukaryotes, a beta-grasp fold as Ub, and is closely related to proteins MoaD and Urm1. 64 matched cddid_all.tbl CDD cd00567 cd00567 173838 ACAD Acyl-CoA dehydrogenase. Both mitochondrial acyl-CoA dehydrogenases (ACAD) and peroxisomal acyl-CoA oxidases (AXO) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. In contrast, AXO catalyzes a different oxidative half-reaction, in which the reduced FAD is reoxidized by molecular oxygen. The ACAD family includes the eukaryotic beta-oxidation enzymes, short (SCAD), medium (MCAD), long (LCAD) and very-long (VLCAD) chain acyl-CoA dehydrogenases. These enzymes all share high sequence similarity, but differ in their substrate specificities. The ACAD family also includes amino acid catabolism enzymes such as Isovaleryl-CoA dehydrogenase (IVD), short/branched chain acyl-CoA dehydrogenases(SBCAD), Isobutyryl-CoA dehydrogenase (IBDH), glutaryl-CoA deydrogenase (GCD) and Crotonobetainyl-CoA dehydrogenase. The mitochondrial ACAD's are generally homotetramers, except for VLCAD, which is a homodimer. Related enzymes include the SOS adaptive reponse proten aidB, Naphthocyclinone hydroxylase (NcnH), and and Dibenzothiophene (DBT) desulfurization enzyme C (DszC) 327 matched cddid_all.tbl CDD cd00568 cd00568 238318 TPP_enzymes Thiamine pyrophosphate (TPP) enzyme family, TPP-binding module; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. These enzymes include, among others, the E1 components of the pyruvate, the acetoin and the branched chain alpha-keto acid dehydrogenase complexes. 168 matched cddid_all.tbl CDD cd00569 cd00569 259851 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins. This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain. 42 matched cddid_all.tbl CDD cd00570 cd00570 238319 GST_N_family Glutathione S-transferase (GST) family, N-terminal domain; a large, diverse group of cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. In addition, GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. This family, also referred to as soluble GSTs, is the largest family of GSH transferases and is only distantly related to the mitochondrial GSTs (GSTK subfamily, a member of the DsbA family). Soluble GSTs bear no structural similarity to microsomal GSTs (MAPEG family) and display additional activities unique to their group, such as catalyzing thiolysis, reduction and isomerization of certain compounds. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. Based on sequence similarity, different classes of GSTs have been identified, which display varying tissue distribution, substrate specificities and additional specific activities. In humans, GSTs display polymorphisms which may influence individual susceptibility to diseases such as cancer, arthritis, allergy and sclerosis. Some GST family members with non-GST functions include glutaredoxin 2, the CLIC subfamily of anion channels, prion protein Ure2p, crystallins, metaxin 2 and stringent starvation protein A. 71 matched cddid_all.tbl CDD cd00571 cd00571 238320 UreE UreE urease accessory protein. UreE is a metallochaperone assisting the insertion of a Ni2+ ion in the active site of urease, an important step in the in vivo assembly of urease, an enzyme that hydrolyses urea into ammonia and carbamic acid. The C-terminal region of UreE contains a histidine rich nickel binding site. 136 matched cddid_all.tbl CDD cd00575 cd00575 238321 NOS_oxygenase Nitric oxide synthase (NOS) produces nitric oxide (NO) by catalyzing a five-electron heme-based oxidation of a guanidine nitrogen of L-arginine to L-citrulline via two successive monooxygenation reactions producing N(omega)-hydroxy-L-arginine (NHA) as an intermediate. In mammals, there are three distinct NOS isozymes: neuronal (nNOS or NOS-1), cytokine-inducible (iNOS or NOS-2) and endothelial (eNOS or NOS-3) . Nitric oxide synthases are homodimers. In eukaryotes, each monomer has an N-terminal oxygenase domain which binds to the substrate L-Arg, zinc, and to the cofactors heme and 5.6.7.8-(6R)-tetrahydrobiopterin (BH4) . Eukaryotic NOSs also have a C-terminal electron supplying reductase region, which is homologous to cytochrome P450 reductase and binds NADH, FAD and FMN. While prokaryotes can produce NO as a byproduct of denitrification, using a completely different set of enzymes than NOS, a few prokaryotes also have a NOS which consists solely of the NOS oxygenase domain. Prokaryotic NOS binds to the substrate L-Arg, zinc, and to the cofactors heme and tetrahydrofolate. 356 matched cddid_all.tbl CDD cd00576 cd00576 153083 RNR_PFL Ribonucleotide reductase and Pyruvate formate lyase. Ribonucleotide reductase (RNR) and pyruvate formate lyase (PFL) are believed to have diverged from a common ancestor. They have a structurally similar ten-stranded alpha-beta barrel domain that hosts the active site, and are radical enzymes. RNRs are found in all organisms and provide the only mechanism by which nucleotides are converted to deoxynucleotides. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs use a diiron-tyrosyl radical while Class II RNRs use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. PFL, an essential enzyme in anaerobic bacteria, catalyzes the conversion of pyruvate and CoA to acteylCoA and formate in a mechanism that uses a glycyl radical. 401 matched cddid_all.tbl CDD cd00577 cd00577 238322 PCNA Proliferating Cell Nuclear Antigen (PCNA) domain found in eukaryotes and archaea. These polymerase processivity factors play a role in DNA replication and repair. PCNA encircles duplex DNA in its central cavity, providing a DNA-bound platform for the attachment of the polymerase. The trimeric PCNA ring is structurally similar to the dimeric ring formed by the DNA polymerase processivity factors in bacteria (beta subunit DNA polymerase III holoenzyme) and in bacteriophages (catalytic subunits in T4 and RB69). This structural correspondence further substantiates the mechanistic connection between eukaryotic and prokaryotic DNA replication that has been suggested on biochemical grounds. PCNA is also involved with proteins involved in cell cycle processes such as DNA repair and apoptosis. Many of these proteins contain a highly conserved motif known as the PIP-box (PCNA interacting protein box) which contains the sequence Qxx[LIM]xxF[FY]. 248 matched cddid_all.tbl CDD cd00578 cd00578 238323 L-fuc_L-ara-isomerases L-fucose isomerase (FucIase) and L-arabinose isomerase (AI) family; composed of FucIase, AI and similar proteins. FucIase converts L-fucose, an aldohexose, to its ketose form, which prepares it for aldol cleavage (similar to the isomerization of glucose in glycolysis). L-fucose (or 6-deoxy-L-galactose) is found in various oligo- and polysaccharides in mammals, bacteria and plants. AI catalyzes the isomerization of L-arabinose to L-ribulose, the first reaction in its conversion to D-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway, which allows L-arabinose to be used as a carbon source. AI can also convert D-galactose to D-tagatose at elevated temperatures in the presence of divalent metal ions. D-tagatose, rarely found in nature, is of commercial interest as a low-calorie sugar substitute. 452 matched cddid_all.tbl CDD cd00580 cd00580 238324 CHMI 5-carboxymethyl-2-hydroxymuconate isomerase (CHMI) is a trimeric enzyme catalyzing the isomerization of the unsaturated ketone 5-(carboxymethyl)-2-hydroxymuconate to 5-(carboxymethyl)-2-oxo-3-hexene-1,6-dionate. This is one step in the homoprotocatechuate pathway, one of the microbial meta-fission pathways that degrade aromatic carbon sources to citric acid cycle intermediates. Despite the structural similarity of CHMI with 4-oxalocrotonate tautomerase (4-OT) and macrophage migration inhibitory factor (MIF), there is no significant sequence similarity among these protein families, and therefore, they are not combined in one hierarchy. 113 matched cddid_all.tbl CDD cd00581 cd00581 238325 QFR_TypeB_TM Quinol:fumarate reductase (QFR) Type B subfamily, transmembrane subunit; QFR couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, the opposite reaction to that catalyzed by the related protein, succinate:quinone oxidoreductase (SQR). QFRs oxidize low potential quinols such as menaquinol and rhodoquinol and are involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQR and QFR share a common subunit arrangement, composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are classified as Type B as they contain one transmembrane subunit and two heme groups. The heme and quinone binding sites reside in the transmembrane subunit. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, and the transmembrane subunit containing the electron donor (quinol). The Type B enzyme from Desulfovibrio gigas is capable of fumarate reduction and succinate oxidation. 206 matched cddid_all.tbl CDD cd00583 cd00583 411704 MutH-like Restriction endonuclease MutH and similar endonucleases. MutH is a 28kD endonuclease involved in methyl-directed DNA mismatch repair in gram negative bacteria. MutH is both sequence-specific and methylation-specific, introducing a nick in the unmethylated strand of a hemi-methylated d(GATC) DNA duplex. MutH is homologous to the type II restriction endonuclease Sau3AI which also recognizes the d(GATC) sequence however, Sau3AI cleaves both strands regardless of their methylation state. The active form of MutH is monomeric while that of Sau3AI is homodimeric. In addition to MutH, MutS, involved in mismatch recognition, and MutL, involved in mediating the interactions between MutH and MutS, are essential in initiating mismatch repair in Escherichia coli. 208 matched cddid_all.tbl CDD cd00584 cd00584 467468 Prefoldin_alpha Prefoldin alpha subunit. Alpha subunits of prefoldin, a hexameric molecular chaperone complex, found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils. 121 matched cddid_all.tbl CDD cd00585 cd00585 238328 Peptidase_C1B Peptidase C1B subfamily (MEROPS database nomenclature); composed of eukaryotic bleomycin hydrolases (BH) and bacterial aminopeptidases C (pepC). The proteins of this subfamily contain a large insert relative to the C1A peptidase (papain) subfamily. BH is a cysteine peptidase that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. Bleomycin, a glycopeptide derived from the fungus Streptomyces verticullus, is an effective anticancer drug due to its ability to induce DNA strand breaks. Human BH is the major cause of tumor cell resistance to bleomycin chemotherapy, and is also genetically linked to Alzheimer's disease. In addition to its peptidase activity, the yeast BH (Gal6) binds DNA and acts as a repressor in the Gal4 regulatory system. BH forms a hexameric ring barrel structure with the active sites imbedded in the central channel. The bacterial homolog of BH, called pepC, is a cysteine aminopeptidase possessing broad specificity. Although its crystal structure has not been solved, biochemical analysis shows that pepC also forms a hexamer. 437 matched cddid_all.tbl CDD cd00586 cd00586 238329 4HBT 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites. There is no evidence to suggest that 4HBT is related to the type I thioesterases functioning in primary or secondary metabolic pathways. Each subunit of the 4HBT tetramer adopts a so-called hot-dog fold similar to those of beta-hydroxydecanoyl-ACP dehydratase, (R)-specific enoyl-CoA hydratase, and type II, thioesterase (TEII). 110 matched cddid_all.tbl CDD cd00587 cd00587 238330 HCP_like The HCP family of iron-sulfur proteins includes hybrid cluster protein (HCP), acetyl-CoA synthase (ACS), and carbon monoxide dehydrogenase (CODH), all of which contain [Fe4-S4] metal clusters at their active sites. These proteins have a conserved alpha-beta rossman fold domain. HCP, formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. Acetyl-CoA synthase (ACS), is found in acetogenic and methanogenic organisms and is responsible for the synthesis and breakdown of acetyl-CoA. ACS forms a heterotetramer with carbon monoxide dehydrogenase (CODH) consisting of two ACS and two CODH subunits. CODH reduces carbon dioxide to carbon monoxide and ACS then synthesizes acetyl-CoA from carbon monoxide and CoA. 258 matched cddid_all.tbl CDD cd00588 cd00588 238331 CheW_like CheW-like domain. CheW proteins are part of the chemotaxis signalling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and other related proteins that are involved in chemotaxis. The CheW-like regulatory domain in the chemotaxis associated histidine kinase CheA binds to CheW, suggesting that these domains can interact with each other. 136 matched cddid_all.tbl CDD cd00590 cd00590 409669 RRM_SF RNA recognition motif (RRM) superfamily. RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs). 72 matched cddid_all.tbl CDD cd00591 cd00591 259852 HU_IHF DNA sequence specific (IHF) and non-specific (HU) domains. This family includes integration host factor (IHF) and HU, also called type II DNA-binding proteins (DNABII), which are small dimeric proteins that specifically bind the DNA minor groove, inducing large bends in the DNA and serving as architectural factors in a variety of cellular processes such as recombination, initiation of replication/transcription and gene regulation. IHF binds DNA in a sequence specific manner while HU displays little or no sequence preference. IHF homologs are usually heterodimers, while HU homologs are typically homodimers (except HU heterodimers from E. coli and other enterobacteria). HU is highly basic and contributes to chromosomal compaction and maintenance of negative supercoiling, thus often referred to as histone-like protein. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). Bacillus phage SPO1-encoded transcription factor 1 (TF1) is another related type II DNA-binding protein. Like IHF, TF1 binds DNA specifically and bends DNA sharply. 85 matched cddid_all.tbl CDD cd00592 cd00592 133378 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. 100 matched cddid_all.tbl CDD cd00593 cd00593 238333 RIBOc RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing. 133 matched cddid_all.tbl CDD cd00594 cd00594 238334 KU Ku-core domain; includes the central DNA-binding beta-barrels, polypeptide rings, and the C-terminal arm of Ku proteins. The Ku protein consists of two tightly associated homologous subunits, Ku70 and Ku80, and was originally identified as an autoantigen recognized by the sera of patients with an autoimmunity disease. In eukaryotes, the Ku heterodimer contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by non-homologous end-joining. The bacterial Ku homologs does not contain the conserved N-terminal extension that is present in the eukaryotic Ku protein. 272 matched cddid_all.tbl CDD cd00595 cd00595 238335 NDPk Nucleoside diphosphate kinases (NDP kinases, NDPks): NDP kinases, responsible for the synthesis of nucleoside triphosphates (NTPs), are involved in numerous regulatory processes associated with proliferation, development, and differentiation. They are vital for DNA/RNA synthesis, cell division, macromolecular metabolism and growth. The enzymes generate NTPs or their deoxy derivatives by terminal (gamma) phosphotransfer from an NTP such as ATP or GTP to any nucleoside diphosphate (NDP) or its deoxy derivative. The sequence of NDPk has been highly conserved through evolution. There is a single histidine residue conserved in all known NDK isozymes, which is involved in the catalytic mechanism. The first confirmed metastasis suppressor gene was the NDP kinase protein encoded by the nm23 gene. Unicellular organisms generally possess only one gene encoding NDP kinase, while most multicellular organisms possess not only an ortholog that provides most of the NDP kinase enzymatic activity but also multiple divergent paralogous genes. The human genome codes for at least nine NDP kinases and can be classified into two groups, Groups I and II, according to their genomic architecture and distinct enzymatic activity. Group I isoforms (A-D) are well-conserved, catalytically active, and share 58-88% identity between each other, while Group II are more divergent, with only NDPk6 shown to be active. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. The hexamer can be viewed as trimer of dimers, while tetramers are dimers of dimers, with the dimerization interface conserved. 133 matched cddid_all.tbl CDD cd00596 cd00596 349427 Peptidase_M14_like M14 family of metallocarboxypeptidases and related proteins. The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism. 216 matched cddid_all.tbl CDD cd00598 cd00598 119349 GH18_chitinase-like The GH18 (glycosyl hydrolase, family 18) type II chitinases hydrolyze chitin, an abundant polymer of beta-1,4-linked N-acetylglucosamine (GlcNAc) which is a major component of the cell wall of fungi and the exoskeleton of arthropods. Chitinases have been identified in viruses, bacteria, fungi, protozoan parasites, insects, and plants. The structure of the GH18 domain is an eight-stranded beta/alpha barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel. The GH18 family includes chitotriosidase, chitobiase, hevamine, zymocin-alpha, narbonin, SI-CLP (stabilin-1 interacting chitinase-like protein), IDGF (imaginal disc growth factor), CFLE (cortical fragment-lytic enzyme) spore hydrolase, the type III and type V plant chitinases, the endo-beta-N-acetylglucosaminidases, and the chitolectins. The GH85 (glycosyl hydrolase, family 85) ENGases (endo-beta-N-acetylglucosaminidases) are closely related to the GH18 chitinases and are included in this alignment model. 210 matched cddid_all.tbl CDD cd00599 cd00599 119373 GH25_muramidase Endo-N-acetylmuramidases (muramidases) are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues. This family of muramidases contains a glycosyl hydrolase family 25 (GH25) catalytic domain and is found in bacteria, fungi, slime molds, round worms, protozoans and bacteriophages. The bacteriophage members are referred to as endolysins which are involved in lysing the host cell at the end of the replication cycle to allow release of mature phage particles. Endolysins are typically modular enzymes consisting of a catalytically active domain that hydrolyzes the peptidoglycan cell wall and a cell wall-binding domain that anchors the protein to the cell wall. Endolysins generally have narrow substrate specificities with either intra-species or intra-genus bacteriolytic activity. 186 matched cddid_all.tbl CDD cd00600 cd00600 212462 Sm_like Sm and related proteins. The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes. 63 matched cddid_all.tbl CDD cd00602 cd00602 238336 IPT_TF IPT domain of eukaryotic transcription factors NF-kappaB/Rel, nuclear factor of activated Tcells (NFAT), and recombination signal J-kappa binding protein (RBP-Jkappa). The IPT domains in these proteins are involved in DNA binding. Most NF-kappaB/Rel proteins form homo- and heterodimers, while NFAT proteins are largely monomeric (with TonEBP being an exception). While the majority of sequence-specific DNA binding elements are found in the N-terminal domain, several are found in the IPT domain in loops adjacent to, and including, the linker region. 101 matched cddid_all.tbl CDD cd00603 cd00603 238337 IPT_PCSR IPT domain of Plexins and Cell Surface Receptors (PCSR) and related proteins . This subgroup contains IPT domains of plexins, receptors, like the plasminogen-related growth factor receptors, the hepatocyte growth factor-scatter factors, and the macrophage-stimulating receptors and of fibrocystin. Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT_PCSR domain present preceeded by SEMA (semaphorin) and PSI (plexin, semaphorin, integrin) domains. 90 matched cddid_all.tbl CDD cd00604 cd00604 238338 IPT_CGTD IPT domain (domain D) of cyclodextrin glycosyltransferase (CGTase) and similar enzymes. These enzymes are involved in the enzymatic hydrolysis of alpha-1,4 linkages of starch polymers and belong to the glycosyl hydrolase family 13. Most consist of three domains (A,B,C) but CGTase is more complex and has two additional domains (D,E). The function of the IPT/D domain is unknown. 81 matched cddid_all.tbl CDD cd00606 cd00606 238339 fungal_RNase fungal type ribonuclease. Ribonucleases (RNAses) cleave phosphodiester bonds in RNA and are essential for both non-specific RNA degradation and for numerous forms of RNA processing. The members of this CD belong to the superfamily of microbial ribonucleases which are predominantly guanyl specific nucleases. Guanyl specific RNAses are endonucleases which split RNA phosphodiester bonds at the 3' oxygen end of guanosine residues to yield oligonucleotides with the guanosine-2',3'-cyclophosphate at the 3' end and the hydroxyl group at the 5' end. The terminal guanosine-2,3'-cyclophosphate is hydrolysed by guanyl RNAses to give guanosine-3'-phosphate. The alignment also contains ribotoxins, a fungal group of cytotoxins, specifically cleaving the sarcin/ricin loop (SRL) structure of the 23-28S rRNA and therefore being very potent inhibitors of protein synthesis. 100 matched cddid_all.tbl CDD cd00607 cd00607 238340 RNase_Sa RNase_Sa. Ribonucleases first isolated from Streptomyces aureofaciens. In general, ribonucleases cleave phosphodiester bonds in RNA and are essential for both non-specific RNA degradation and for numerous forms of RNA processing. RNAse Sa is a guanylate specific endoribonuclease which belongs to the superfamily of microbial ribonucleases. Typical of this sub-family, the enzyme hydrolyses the phosphodiester bonds of RNA at the 3' oxygen end of guanosine residues to yield oligonucleotides with the guanosine-2',3'-cyclophosphate at the 3' end and the hydroxyl group at the 5' end. The terminal guanosine-2,3'-cyclophosphate is hydrolysed by guanyl RNAses to give guanosine-3'-phosphate. 95 matched cddid_all.tbl CDD cd00608 cd00608 238341 GalT Galactose-1-phosphate uridyl transferase (GalT): This enzyme plays a key role in galactose metabolism by catalysing the transfer of a uridine 5'-phosphoryl group from UDP-galactose 1-phosphate. The structure of E.coli GalT reveals that the enzyme contains two identical subunits. It also demonstrates that the active site is formed by amino acid residues from both subunits of the dimer. 329 matched cddid_all.tbl CDD cd00609 cd00609 99734 AAT_like Aspartate aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Pyridoxal phosphate combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. The major groups in this CD corresponds to Aspartate aminotransferase a, b and c, Tyrosine, Alanine, Aromatic-amino-acid, Glutamine phenylpyruvate, 1-Aminocyclopropane-1-carboxylate synthase, Histidinol-phosphate, gene products of malY and cobC, Valine-pyruvate aminotransferase and Rhizopine catabolism regulatory protein. 350 matched cddid_all.tbl CDD cd00610 cd00610 99735 OAT_like Acetyl ornithine aminotransferase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to ornithine aminotransferase, acetylornithine aminotransferase, alanine-glyoxylate aminotransferase, dialkylglycine decarboxylase, 4-aminobutyrate aminotransferase, beta-alanine-pyruvate aminotransferase, adenosylmethionine-8-amino-7-oxononanoate aminotransferase, and glutamate-1-semialdehyde 2,1-aminomutase. All the enzymes belonging to this family act on basic amino acids and their derivatives are involved in transamination or decarboxylation. 413 matched cddid_all.tbl CDD cd00611 cd00611 99736 PSAT_like Phosphoserine aminotransferase (PSAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major group in this CD corresponds to phosphoserine aminotransferase (PSAT). PSAT is active as a dimer and catalyzes the conversion of phosphohydroxypyruvate to phosphoserine. 355 matched cddid_all.tbl CDD cd00613 cd00613 99737 GDC-P Glycine cleavage system P-protein, alpha- and beta-subunits. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1.2.10 (GDC) also annotated as glycine cleavage system or glycine synthase. GDC consists of four proteins P, H, L and T. The reaction catalysed by this protein is: Glycine + lipoylprotein <=> S-aminomethyldihydrolipoylprotein + CO2. Alpha-beta-type dimers associate to form an alpha(2)beta(2) tetramer, where the alpha- and beta-subunits are structurally similar and appear to have arisen by gene duplication and subsequent divergence with a loss of one active site. The members of this CD are widely dispersed among all three forms of cellular life. 398 matched cddid_all.tbl CDD cd00614 cd00614 99738 CGS_like CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of antimicrobials and herbicides. This subgroup also includes cystathionine gamma-lyases (CGL), O-acetylhomoserine sulfhydrylases and O-acetylhomoserine thiol lyases. CGL's are very similar to CGS's. Members of this group are widely distributed among all three forms of life. 369 matched cddid_all.tbl CDD cd00615 cd00615 99739 Orn_deC_like Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine decarboxylase (LDC). ODC is a dodecamer composed of six homodimers and catalyzes the decarboxylation of tryptophan. ADC catalyzes the decarboxylation of arginine and LDC catalyzes the decarboxylation of lysine. Members of this family are widely found in all three forms of life. 294 matched cddid_all.tbl CDD cd00616 cd00616 99740 AHBA_syn 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary metabolites. Some well studied proteins in this CD are AHBA_synthase, protein product of pleiotropic regulatory gene degT, Arnb aminotransferase and pilin glycosylation protein. The prototype of this family, the AHBA_synthase, is a dimeric PLP dependent enzyme. AHBA_syn is the terminal enzyme of 3-amino-5-hydroxybenzoic acid (AHBA) formation which is involved in the biosynthesis of ansamycin antibiotics, including rifamycin B. Some members of this CD are involved in 4-amino-6-deoxy-monosaccharide D-perosamine synthesis. Perosamine is an important element in the glycosylation of several cell products, such as antibiotics and lipopolysaccharides of gram-positive and gram-negative bacteria. The pilin glycosylation protein encoded by gene pglA, is a galactosyltransferase involved in pilin glycosylation. Additionally, this CD consists of ArnB (PmrH) aminotransferase, a 4-amino-4-deoxy-L-arabinose lipopolysaccharide-modifying enzyme. This CD also consists of several predicted pyridoxal phosphate-dependent enzymes apparently involved in regulation of cell wall biogenesis. The catalytic lysine which is present in all characterized PLP dependent enzymes is replaced by histidine in some members of this CD. 352 matched cddid_all.tbl CDD cd00617 cd00617 99741 Tnase_like Tryptophanase family (Tnase). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to tryptophanase (Tnase) and tyrosine phenol-lyase (TPL). Tnase and TPL are active as tetramers and catalyze beta-elimination reactions. Tnase catalyzes degradation of L-tryptophan to yield indole, pyruvate and ammonia and TPL catalyzes degradation of L-tyrosine to yield phenol, pyruvate and ammonia. 431 matched cddid_all.tbl CDD cd00618 cd00618 153092 PLA2_like PLA2_like: Phospholipase A2, a super-family of secretory and cytosolic enzymes; the latter are either Ca dependent or Ca independent. PLA2 cleaves the sn-2 position of the glycerol backbone of phospholipids (PC or phosphatidylethanolamine), usually in a metal-dependent reaction, to generate lysophospholipid (LysoPL) and a free fatty acid (FA). The resulting products are either dietary or used in synthetic pathways for leukotrienes and prostaglandins. Often, arachidonic acid is released as a free fatty acid and acts as second messenger in signaling networks. Secreted PLA2s have also been found to specifically bind to a variety of soluble and membrane proteins in mammals, including receptors. As a toxin, PLA2 is a potent presynaptic neurotoxin which blocks nerve terminals by binding to the nerve membrane and hydrolyzing stable membrane lipids. The products of the hydrolysis (LysoPL and FA) cannot form bilayers leading to a change in membrane conformation and ultimately to a block in the release of neurotransmitters. PLA2 may form dimers or oligomers. 83 matched cddid_all.tbl CDD cd00619 cd00619 238342 Terminator_NusB Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation. 130 matched cddid_all.tbl CDD cd00620 cd00620 238343 Methyltransferase_Sun N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine transferase Sun, also known as RrmB or Fmu shares the RNA-binding non-catalytic domain with the transcription termination factor NusB. The precise biological role of this domain in Sun is unknown, although it is likely to be involved in sequence-specific RNA binding. The C-terminal methyltransferase domain of Sun has been shown to catalyze formation of m5C at position 967 of 16S rRNA in Escherichia coli. 126 matched cddid_all.tbl CDD cd00622 cd00622 143482 PLPDE_III_ODC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase. This subfamily is composed mainly of eukaryotic ornithine decarboxylases (ODC, EC 4.1.1.17) and ODC-like enzymes from prokaryotes represented by Vibrio vulnificus LysineOrnithine decarboxylase. These are fold type III PLP-dependent enzymes that differ from most bacterial ODCs which are fold type I PLP-dependent enzymes. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. Members of this subfamily contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity. Also members of this subfamily are proteins with homology to ODC but do not possess any catalytic activity, the Antizyme inhibitor (AZI) and ODC-paralogue (ODC-p). AZI binds to the regulatory protein Antizyme with a higher affinity than ODC and prevents ODC degradation. ODC-p is a novel ODC-like protein, present only in mammals, that is specifically exressed in the brain and testes. ODC-p may function as a tissue-specific antizyme inhibitory protein. 362 matched cddid_all.tbl CDD cd00625 cd00625 238344 ArsB_NhaD_permease Anion permease ArsB/NhaD. These permeases have been shown to translocate sodium, arsenate, antimonite, sulfate and organic anions across biological membranes in all three kingdoms of life. A typical anion permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump. 396 matched cddid_all.tbl CDD cd00630 cd00630 132719 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain. RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria. 158 matched cddid_all.tbl CDD cd00632 cd00632 467469 Prefoldin_beta Prefoldin beta subunit. Beta subunits of prefoldin, a hexameric molecular chaperone complex, found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils. 78 matched cddid_all.tbl CDD cd00633 cd00633 238346 Secretoglobin Secretoglobins are relatively small, secreted, disulphide-bridged dimeric proteins with encoding genes sharing substantial sequence similarity. Their family subunits may be grouped into five subfamilies, A-E. Uteroglobin (subfamily A), which is identical to Clara cell protein (CC10), forms a globular shaped homodimer with a large hydrophobic pocket located between the two dimers. The uteroglobin monomer structure is composed of four alpha helices that do not form a canonical four helix-bundle motif but rather a boomerang-shaped structure in which helices H1, H3, and H4 are able to bind a homodimeric partner. The hydrophobic pocket binds steroids, particularly progesterone, with high specificity. However, the true biological function of uteroglobin is poorly understood. In mammals, uteroglobin has immunosuppressive and anti-inflammatory properties through the inhibition of phospholipase A2. The other four main subfamilies of secretoglobins are found in heterodimeric combinations, with B and C subfamilies disulphide-bridged to the E and D subfamilies, respectively. [See review by Laukaitis C.M. & Karn R.C. (2005). Biological Journal of the Linnean Society 84, 493]. These include rat prostatic steroid-binding protein (PBP or prostatein), human mammaglobin (or heteroglobin), lipophilins, major cat allergen Fel dI, the hamster Harderian gland proteins and mouse salivary androgen-binding protein (ABP). Example of such a heterodimer: ABPalpha-like sequences are closely related to cat Fel dI chain 1, whereas ABPbeta-gamma-like sequences are closely related to Fel dI chain 2. Thus, the heterodimeric structure of ABPalpha-beta and ABPalpha-gamma is recapitulated by the sequence-similar Fel dI chains 1 and 2. This conservation of primary and quaternary structure indicates that the genome of the eutherian common ancestor of cats, rodents, and primates contained a similar gene pair. 67 matched cddid_all.tbl CDD cd00635 cd00635 143483 PLPDE_III_YBL036c_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, YBL036c-like proteins. This family contains mostly uncharacterized proteins, widely distributed among eukaryotes, bacteria and archaea, that bear similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain monomeric protein with a typical TIM barrel fold. It binds the PLP cofactor and has been shown to exhibit amino acid racemase activity. The YBL036c structure is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. The lack of a second domain in YBL036c may explain limited D- to L-alanine racemase or non-specific racemase activity. 222 matched cddid_all.tbl CDD cd00636 cd00636 238347 TroA-like Helical backbone metal receptor (TroA-like domain). These proteins have been shown to function in the ABC transport of ferric siderophores and metal ions such as Mn2+, Fe3+, Cu2+ and/or Zn2+. Their ligand binding site is formed in the interface between two globular domains linked by a single helix. Many of these proteins also possess a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence). The TroA-like proteins differ in their fold and ligand-binding mechanism from the PBPI and PBPII proteins, but are structurally similar, however, to the beta-subunit of the nitrogenase molybdenum-iron protein MoFe. Most TroA-like proteins are encoded by ABC-type operons and appear to function as periplasmic components of ABC transporters in metal ion uptake. 148 matched cddid_all.tbl CDD cd00637 cd00637 410626 7tm_classA_rhodopsin-like rhodopsin receptor-like class A family of the seven-transmembrane G protein-coupled receptor superfamily. Class A rhodopsin-like receptors constitute about 90% of all GPCRs. The class A GPCRs include the light-sensitive rhodopsin as well as receptors for biogenic amines, lipids, nucleotides, odorants, peptide hormones, and a variety of other ligands. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. Based on sequence similarity, GPCRs can be divided into six major classes: class A (rhodopsin-like family), class B (Methuselah-like, adhesion and secretin-like receptor family), class C (metabotropic glutamate receptor family), class D (fungal mating pheromone receptors), class E (cAMP receptor family), and class F (frizzled/smoothened receptor family). Nearly 800 human GPCR genes have been identified and are involved essentially in all major physiological processes. Approximately 40% of clinically marketed drugs mediate their effects through modulation of GPCR function for the treatment of a variety of human diseases including bacterial infections. 275 matched cddid_all.tbl CDD cd00640 cd00640 107202 Trp-synth-beta_II Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine. 244 matched cddid_all.tbl CDD cd00641 cd00641 238348 GTP_cyclohydro2 GTP cyclohydrolase II (RibA). GTP cyclohydrolase II catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5' phosphate, formate, pyrophosphate (APy), and GMP in the biosynthetic pathway of riboflavin. Riboflavin is the precursor molecule for the synthesis of the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which are essential to cell metabolism. The enzyme is present in plants and numerous pathogenic bacteria, especially gram negative organisms, who are dependent on endogenous synthesis of the vitamin because they lack an appropriate uptake system. For animals and humans, which lack this biosynthetic pathway, riboflavin is the essential vitamin B2. GTP cyclohydrolase II requires magnesium ions for activity and has a bound catalytic zinc. The functionally active form is thought to be a homodimer. A paralogous protein is encoded in the genome of Streptomyces coelicolor, which converts GTP to 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (FAPy), an activity that has otherwise been reported for unrelated GTP cyclohydrolases III. 193 matched cddid_all.tbl CDD cd00642 cd00642 238349 GTP_cyclohydro1 GTP cyclohydrolase I (GTP-CH-I) catalyzes the conversion of GTP into dihydroneopterin triphosphate. The enzyme product is the precursor of tetrahydrofolate in eubacteria, fungi, and plants and of the folate analogs in methanogenic bacteria. In vertebrates and insects it is the biosynthtic precursor of tetrahydrobiopterin (BH4) which is involved in the formation of catacholamines, nitric oxide, and the stimulation of T lymphocytes. The biosynthetic reaction of BH4 is controlled by a regulatory protein GFRP which mediates feedback inhibition of GTP-CH-I by BH4. This inhibition is reversed by phenylalanine. The decameric GTP-CH-I forms a complex with two pentameric GFRP in the presence of phenylalanine or a combination of GTP and BH4, respectively. 185 matched cddid_all.tbl CDD cd00643 cd00643 153081 HMG-CoA_reductase_classI Class I hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR). Hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR), class I enzyme, homotetramer. Catalyzes the synthesis of coenzyme A and mevalonate in isoprenoid synthesis. In mammals this is the rate limiting committed step in cholesterol biosynthesis. Class I enzymes are found predominantly in eukaryotes and contain N-terminal membrane regions. With the exception of Archaeoglobus fulgidus, most archeae are assigned to class I, based on sequence similarity of the active site, even though they lack membrane regions. Yeast and human HMGR are divergent in their N-terminal regions, but are conserved in their active site. In contrast, human and bacterial HMGR differ in their active site architecture. 403 matched cddid_all.tbl CDD cd00644 cd00644 153082 HMG-CoA_reductase_classII Class II hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR). Hydroxymethylglutaryl-coenzyme A (HMG-CoA) reductase (HMGR), class II, prokaryotic enzyme is a homodimer. Class II enzymes are found primarily in prokaryotes and Archaeoglobus fulgidus and are soluble as they lack the membrane region. Enzymes catalyze the synthesis of coenzyme A and mevalonate in isoprenoid synthesis. Bacteria, such as Pseudomonas mevalonii, which rely solely on mevalonate for their carbon source, catalyze the reverse reaction, using an NAD-dependent HMGR to deacetylate mevalonate into 3-hydroxy-3-methylglutaryl-CoA. Human and bacterial HMGR differ in their active site architecture. 417 matched cddid_all.tbl CDD cd00645 cd00645 238350 AsnA Asparagine synthetase (aspartate-ammonia ligase) (AsnA) catalyses the conversion of L-aspartate to L-asparagine in the presence of ATP and ammonia. AsnA is a homodimeric enzyme which is structurally similiar to the catalytic core domain of class II aminoacyl-tRNA synthetases. Ammonia-dependent AsnA is not homologous to the glutamine-dependent asparagine synthetase AsnB. 309 matched cddid_all.tbl CDD cd00648 cd00648 270214 Periplasmic_Binding_Protein_Type_2 Type 2 periplasmic binding fold superfamily. This evolutionary model and hierarchy represent the ligand-binding domains found in solute binding proteins that serve as initial receptors in the transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1 (PBP1), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The origin of PBP module can be traced across the distant phyla, including eukaryotes, archebacteria, and prokaryotes. The majority of PBP2 proteins are involved in the uptake of a variety of soluble substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. The substrate binding domain of the LysR transcriptional regulators and the oligopeptide-like transport systems also contain the type 2 periplasmic binding fold and thus they are significantly homologous to that of the PBP2; however, these two families are grouped into a separate hierarchy of the PBP2 superfamily due to the large number of protein sequences. 196 matched cddid_all.tbl CDD cd00649 cd00649 173824 catalase_peroxidase_1 N-terminal catalytic domain of catalase-peroxidases. This is a subgroup of heme-dependent peroxidases of the plant superfamily that share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Catalase-peroxidases can exhibit both catalase and broad-spectrum peroxidase activities depending on the steady-state concentration of hydrogen peroxide. These enzymes are found in many archaeal and bacterial organisms, where they neutralize potentially lethal hydrogen peroxide molecules generated during photosynthesis or stationary phase. Along with related intracellular fungal and plant peroxidases, catalase-peroxidases belong to class I of the plant peroxidase superfamily. Unlike the eukaryotic enzymes, they are typically comprised of two homologous domains that probably arose via a single gene duplication event. The heme binding motif is present only in the N-terminal domain; the function of the C-terminal domain is not clear. 409 matched cddid_all.tbl CDD cd00650 cd00650 133419 LDH_MDH_like NAD-dependent, lactate dehydrogenase-like, 2-hydroxycarboxylate dehydrogenase family. Members of this family include ubiquitous enzymes like L-lactate dehydrogenases (LDH), L-2-hydroxyisocaproate dehydrogenases, and some malate dehydrogenases (MDH). LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH/MDH-like proteins are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. 263 matched cddid_all.tbl CDD cd00651 cd00651 238351 TFold Tunnelling fold (T-fold). The five known T-folds are found in five different enzymes with different functions: dihydroneopterin-triphosphate epimerase (DHNTPE), dihydroneopterin aldolase (DHNA) , GTP cyclohydrolase I (GTPCH-1), 6-pyrovoyl tetrahydropterin synthetase (PTPS), and uricase (UO,uroate/urate oxidase). They bind to substrates belonging to the purine or pterin families, and share a fold-related binding site with a glutamate or glutamine residue anchoring the substrate and a lot of conserved interactions. They also share a similar oligomerization mode: several T-folds join together to form a beta(2n)alpha(n) barrel, then two barrels join together in a head-to-head fashion to made up the native enzymes. The functional enzyme is a tetramer for UO, a hexamer for PTPS, an octamer for DHNA/DHNTPE and a decamer for GTPCH-1. The substrate is located in a deep and narrow pocket at the interface between monomers. In PTPS, the active site is located at the interface of three monomers, two from one trimer and one from the other trimer. In GTPCH-1, it is also located at the interface of three subunits, two from one pentamer and one from the other pentamer. There are four equivalent active sites in UO, six in PTPS, eight in DHNA/DHNTPE and ten in GTPCH-1. Each globular multimeric enzyme encloses a tunnel which is lined with charged residues for DHNA and UO, and with basic residues in PTPS. The N and C-terminal ends are located on one side of the T-fold while the residues involved in the catalytic activity are located at the opposite side. In PTPS, UO and DHNA/DHNTPE, the N and C-terminal extremities of the enzyme are located on the exterior side of the functional multimeric enzyme. In GTPCH-1, the extra C-terminal helix places the extremity inside the tunnel. 122 matched cddid_all.tbl CDD cd00652 cd00652 238352 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many equivalent positions, suggesting similar structure. However, TLFs contain distinct, conserved amino acids at several positions that distinguish them from TBP. 174 matched cddid_all.tbl CDD cd00653 cd00653 238353 RNA_pol_B_RPB2 RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation. 866 matched cddid_all.tbl CDD cd00655 cd00655 238354 RNAP_Rpb7_N_like RNAP_Rpb7_N_like: This conserved domain represents the N-terminal ribonucleoprotein (RNP) domain of the Rpb7 subunit of eukaryotic RNA polymerase (RNAP) II and its homologs, Rpa43 of eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and RpoE (subunit E) of archaeal RNAP. These proteins have, in addition to their N-terminal RNP domain, a C-terminal oligonucleotide-binding (OB) domain. Each of these subunits heterodimerizes with another RNAP subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, RpoE to RpoF, and Rpa43 to Rpa14). The heterodimer is thought to tether the RNAP to a given promoter via its interactions with a promoter-bound transcription factor.The heterodimer is also thought to bind and position nascent RNA as it exits the polymerase complex. 80 matched cddid_all.tbl CDD cd00656 cd00656 259791 Zn-ribbon C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit. The homologous C-terminal zinc ribbon domains of subunits A12.2, Rpb9, and C11 in RNA Polymerases (Pol) I, II, and III, respectively are required for intrinsic transcript cleavage. TFS is a related archaeal protein that is involved in RNA cleavage by archaeal polymerase. These proteins have two zinc-binding beta-ribbon domains, N-terminal zinc ribbon (N-ribbon) and C-terminal zinc ribbon (C-ribbon). Transcription Factor IIS (TFIIS) domain III is homologous to the C-ribbon domain that stimulates the weak cleavage activity of Rpb9 for Pol II. 45 matched cddid_all.tbl CDD cd00657 cd00657 153097 Ferritin_like Ferritin-like superfamily of diiron-containing four-helix-bundle proteins. Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterioferritin, ferritin, rubrerythrin, aromatic and alkene monooxygenase hydroxylases (AAMH), ribonucleotide reductase R2 (RNRR2), acyl-ACP-desaturases (Acyl_ACP_Desat), manganese (Mn) catalases, demethoxyubiquinone hydroxylases (DMQH), DNA protecting proteins (DPS), and ubiquinol oxidases (AOX), and the aerobic cyclase system, Fe-containing subunit (ACSF). 130 matched cddid_all.tbl CDD cd00659 cd00659 271176 Topo_IB_C DNA topoisomerase IB, C-terminal catalytic domain. Topoisomerase I promotes the relaxation of both positive and negative DNA superhelical tension by introducing a transient single-stranded break in duplex DNA. This function is vital for the processes of replication, transcription, and recombination. Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. The type IB family of DNA topoisomerases includes eukaryotic nuclear topoisomerase I, topoisomerases of poxviruses, and bacterial versions of Topo IB. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their C-terminal catalytic domain and the overall reaction mechanism with tyrosine recombinases. The C-terminal catalytic domain in topoisomerases is linked to a divergent N-terminal domain that shows no sequence or structure similarity to the N-terminal domains of tyrosine recombinases. 210 matched cddid_all.tbl CDD cd00660 cd00660 238356 Topoisomer_IB_N Topoisomer_IB_N: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I differ from human topo I in their sensitivity to CPTs and other classical topo I inhibitors. Trypanosomatid topos I play putative roles in organizing the kinetoplast DNA network unique to these parasites. This family may represent more than one structural domain. 215 matched cddid_all.tbl CDD cd00667 cd00667 238357 ring_hydroxylating_dioxygenases_beta Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the substrate by nonheme iron-containing dioxygenases. These enzymes consist of two or three soluble proteins that interact to form an electron-transport chain that transfers electrons from reduced nucleotides (NADH) via flavin and [2Fe-2S] redox centers to a terminal dioxygenase. Aromatic-ring-hydroxylating dioxygenases oxidize aromatic hydrocarbons and related compounds to cis-arene diols. These enzymes utilize a mononuclear non-heme iron center to catalyze the addition of dioxygen to their respective substrates. The active site of these enzymes however is in the alpha sub-unit. No functional role has been attributed to the beta sub-unit except for a structural role. 160 matched cddid_all.tbl CDD cd00668 cd00668 185674 Ile_Leu_Val_MetRS_core catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases. Catalytic core domain of isoleucyl, leucyl, valyl and methioninyl tRNA synthetases. These class I enzymes are all monomers. However, in some species, MetRS functions as a homodimer, as a result of an additional C-terminal domain. These enzymes aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. Enzymes in this subfamily share an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. MetRS has a significantly shorter insertion, which lacks the editing function. 312 matched cddid_all.tbl CDD cd00669 cd00669 238358 Asp_Lys_Asn_RS_core Asp_Lys_Asn_tRNA synthetase class II core domain. This domain is the core catalytic domain of class II aminoacyl-tRNA synthetases of the subgroup containing aspartyl, lysyl, and asparaginyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. Nearly all class II tRNA synthetases are dimers and enzymes in this subgroup are homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA. 269 matched cddid_all.tbl CDD cd00670 cd00670 238359 Gly_His_Pro_Ser_Thr_tRS_core Gly_His_Pro_Ser_Thr_tRNA synthetase class II core domain. This domain is the core catalytic domain of tRNA synthetases of the subgroup containing glycyl, histidyl, prolyl, seryl and threonyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. These enzymes belong to class II aminoacyl-tRNA synthetases (aaRS) based upon their structure and the presence of three characteristic sequence motifs in the core domain. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ and the accessory subunit of mitochondrial polymerase gamma (Pol gamma b) . Most class II tRNA synthetases are dimers, with this subgroup consisting of mostly homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA. 235 matched cddid_all.tbl CDD cd00671 cd00671 185675 ArgRS_core catalytic core domain of arginyl-tRNA synthetases. Arginyl tRNA synthetase (ArgRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. There are at least three subgroups of ArgRS. One type contains both characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The second subtype lacks the KMSKS motif; however, it has a lysine N-terminal to the HIGH motif, which serves as the functional counterpart to the second lysine of the KMSKS motif. A third group, which is found primarily in archaea and a few bacteria, lacks both the KMSKS motif and the HIGH loop lysine. 212 matched cddid_all.tbl CDD cd00672 cd00672 173899 CysRS_core catalytic core domain of cysteinyl tRNA synthetase. Cysteinyl tRNA synthetase (CysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. 213 matched cddid_all.tbl CDD cd00673 cd00673 238360 AlaRS_core Alanyl-tRNA synthetase (AlaRS) class II core catalytic domain. AlaRS is a homodimer. It is responsible for the attachment of alanine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its predicted structure and the presence of three characteristic sequence motifs. 232 matched cddid_all.tbl CDD cd00674 cd00674 173900 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity. 353 matched cddid_all.tbl CDD cd00677 cd00677 238361 S15_NS1_EPRS_RNA-bind S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism. 46 matched cddid_all.tbl CDD cd00680 cd00680 176852 RHO_alpha_C C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases. C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenase (RHO) family. RHOs, also known as aromatic ring hydroxylating dioxygenases, utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ring, an initial step in the oxidative degradation of aromatic compounds. RHOs are composed of either two or three protein components, and are comprised of an electron transport chain (ETC), and an oxygenase. The ETC transfers reducing equivalents from the electron donor to the oxygenase component, which in turn transfers electrons to the oxygen molecules. The oxygenase components are oligomers, either (alpha)n or (alpha)n(beta)n. The alpha subunits are the catalytic components and have an N-terminal domain, which binds a Rieske-like 2Fe-2S cluster, and a C-terminal domain which binds the non-heme Fe(II). The Fe(II) is co-ordinated by conserved His and Asp residues. Oxygenases belonging to this family include the alpha subunits of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase, Stenotrophomonas maltophilia dicamba O-demethylase, Ralstonia sp. U2 salicylate-5-hydroxylase, Cycloclasticus sp. strain A5 polycyclic aromatic hydrocarbon dioxygenase, toluene 2,3-dioxygenase from Pseudomonas putida F1, dioxin dioxygenase of Sphingomonas sp. Strain RW1, plant choline monooxygenase, and the polycyclic aromatic hydrocarbon (PAH)-degrading ring-hydroxylating dioxygenase from Sphingomonas CHY-1. This group also includes the C-terminal catalytic domains of MupW, part of the mupirocin biosynthetic gene cluster in Pseudomonas fluorescens, and Pseudomonas aeruginosa GbcA (glycine betaine catabolism A). This family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. 188 matched cddid_all.tbl CDD cd00683 cd00683 173831 Trans_IPPS_HH Trans-Isoprenyl Diphosphate Synthases, head-to-head. These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze a head-to-head (HH) (1'-1) condensation reaction. This CD includes squalene and phytoene synthases which catalyze the 1'-1 condensation of two 15-carbon (farnesyl) and 20-carbon (geranylgeranyl) isoprenyl diphosphates, respectively. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DXXXD) located on opposite walls. These residues mediate binding of prenyl phosphates. A two-step reaction has been proposed for squalene synthase (farnesyl-diphosphate farnesyltransferase) in which, two molecules of FPP react to form a stable cyclopropylcarbinyl diphosphate intermediate, and then the intermediate undergoes heterolysis, isomerization, and reduction with NADPH to form squalene, a precursor of cholestrol. The carotenoid biosynthesis enzyme, phytoene synthase (CrtB), catalyzes the condensation reaction of two molecules of geranylgeranyl diphosphate to produce phytoene, a precursor of beta-carotene. These enzymes produce the triterpene and tetraterpene precursors for many diverse sterol and carotenoid end products and are widely distributed among eukareya, bacteria, and archaea. 265 matched cddid_all.tbl CDD cd00684 cd00684 173832 Terpene_cyclase_plant_C1 Plant Terpene Cyclases, Class 1. This CD includes a diverse group of monomeric plant terpene cyclases (Tspa-Tspf) that convert the acyclic isoprenoid diphosphates, geranyl diphosphate (GPP), farnesyl diphosphate (FPP), or geranylgeranyl diphosphate (GGPP) into cyclic monoterpenes, diterpenes, or sesquiterpenes, respectively; a few form acyclic species. Terpnoid cyclases are soluble enzymes localized to the cytosol (sesquiterpene synthases) or plastids (mono- and diterpene synthases). All monoterpene and diterpene synthases have restrict substrate specificity, however, some sesquiterpene synthases can accept both FPP and GPP. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl diphosphates, via bridging Mg2+ ions (K+ preferred by gymnosperm cyclases), inducing conformational changes such that an N-terminal region forms a cap over the catalytic core. Loss of diphosphate from the enzyme-bound substrate (GPP, FPP, or GGPP) results in an allylic carbocation that electrophilically attacks a double bond further down the terpene chain to effect the first ring closure. Unlike monoterpene, sesquiterene, and macrocyclic diterpenes synthases, which undergo substrate ionization by diphosphate ester scission, Tpsc-like diterpene synthases catalyze cyclization reactions by an initial protonation step producing a copalyl diphosphate intermediate. These enzymes lack the aspartate-rich sequences mentioned above. Most diterpene synthases have an N-terminal, internal element (approx 210 aa) whose function is unknown. 542 matched cddid_all.tbl CDD cd00685 cd00685 173833 Trans_IPPS_HT Trans-Isoprenyl Diphosphate Synthases, head-to-tail. These trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) catalyze head-to-tail (HT) (1'-4) condensation reactions. This CD includes all-trans (E)-isoprenyl diphosphate synthases which synthesize various chain length (C10, C15, C20, C25, C30, C35, C40, C45, and C50) linear isoprenyl diphosphates from precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). They catalyze the successive 1'-4 condensation of the 5-carbon IPP to allylic substrates geranyl-, farnesyl-, or geranylgeranyl-diphosphate. Isoprenoid chain elongation reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions (DDXX(XX)D) located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, protecting and stabilizing reactive carbocation intermediates. Farnesyl diphosphate synthases produce the precursors of steroids, cholesterol, sesquiterpenes, farnsylated proteins, heme, and vitamin K12; and geranylgeranyl diphosphate and longer chain synthases produce the precursors of carotenoids, retinoids, diterpenes, geranylgeranylated chlorophylls, ubiquinone, and archaeal ether linked lipids. Isoprenyl diphosphate synthases are widely distributed among archaea, bacteria, and eukareya. 259 matched cddid_all.tbl CDD cd00686 cd00686 173834 Terpene_cyclase_cis_trans_C1 Cis, Trans, Terpene Cyclases, Class 1. This CD includes the terpenoid cyclase, trichodiene synthase, which catalyzes the cyclization of farnesyl diphosphate (FPP) to trichodiene using a cis-trans pathway, and is the first committed step in the biosynthesis of trichothecene toxins and antibiotics. As with other enzymes with the 'terpenoid synthase fold', this enzyme has two conserved metal binding motifs that coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function as homodimers and are found in several genera of fungi. 357 matched cddid_all.tbl CDD cd00687 cd00687 173835 Terpene_cyclase_nonplant_C1 Non-plant Terpene Cyclases, Class 1. This CD includes terpenoid cyclases such as pentalenene synthase and aristolochene synthase which, using an all-trans pathway, catalyze the ionization of farnesyl diphosphate, followed by the formation of a macrocyclic intermediate by bond formation between C1 with either C10 (aristolochene synthase) or C11 (pentalenene synthase), resulting in production of tricyclic hydrocarbon pentalenene or bicyclic hydrocarbon aristolochene. As with other enzymes with the 'terpenoid synthase fold', they have two conserved metal binding motifs, proposed to coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP to the enzymes. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function in the monomeric form and are found in fungi, bacteria and Dictyostelium. 303 matched cddid_all.tbl CDD cd00688 cd00688 238362 ISOPREN_C2_like This group contains class II terpene cyclases, protein prenyltransferases beta subunit, two broadly specific proteinase inhibitors alpha2-macroglobulin (alpha (2)-M) and pregnancy zone protein (PZP) and, the C3 C4 and C5 components of vertebrate complement. Class II terpene cyclases include squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY), these integral membrane proteins catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds. The protein prenyltransferases include protein farnesyltransferase (FTase) and geranylgeranyltransferase types I and II (GGTase-I and GGTase-II) which catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. Alpha (2)-M is a major carrier protein in serum and involved in the immobilization and entrapment of proteases. PZP is a pregnancy associated protein. Alpha (2)-M and PZP are known to bind to and, may modulate, the activity of placental protein-14 in T-cell growth and cytokine production thereby protecting the allogeneic fetus from attack by the maternal immune system. 300 matched cddid_all.tbl CDD cd00691 cd00691 173825 ascorbate_peroxidase Ascorbate peroxidases and cytochrome C peroxidases. Ascorbate peroxidases are a subgroup of heme-dependent peroxidases of the plant superfamily that share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Along with related catalase-peroxidases, ascorbate peroxidases belong to class I of the plant superfamily. Ascorbate peroxidases are found in the chloroplasts and/or cytosol of algae and plants, where they have been shown to control the concentration of lethal hydrogen peroxide molecules. The yeast cytochrome c peroxidase is a divergent member of the family; it forms a complex with cytochrome c to catalyze the reduction of hydrogen peroxide to water. 253 matched cddid_all.tbl CDD cd00692 cd00692 173826 ligninase Ligninase and other manganese-dependent fungal peroxidases. Ligninases and related extracellular fungal peroxidases belong to class II of the plant heme-dependent peroxidase superfamily. All members of the superfamily share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Class II peroxidases are fungal glycoproteins that have been implicated in the oxidative breakdown of lignin, the main cell wall component of woody plants. They contain four conserved disulphide bridges and two conserved calcium binding sites. 328 matched cddid_all.tbl CDD cd00693 cd00693 173827 secretory_peroxidase Horseradish peroxidase and related secretory plant peroxidases. Secretory peroxidases belong to class III of the plant heme-dependent peroxidase superfamily. All members of the superfamily share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Class III peroxidases are found in the extracellular space or in the vacuole in plants where they have been implicated in hydrogen peroxide detoxification, auxin catabolism and lignin biosynthesis, and stress response. Class III peroxidases contain four conserved disulphide bridges and two conserved calcium binding sites. 298 matched cddid_all.tbl CDD cd00704 cd00704 133420 MDH Malate dehydrogenase. Malate dehydrogenase (MDH) is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. MDHs belong to the NAD-dependent, lactate dehydrogenase (LDH)-like, 2-hydroxycarboxylate dehydrogenase family, which also includes the GH4 family of glycoside hydrolases. They are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. 323 matched cddid_all.tbl CDD cd00707 cd00707 238363 Pancreat_lipase_like "Pancreatic lipase-like enzymes. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is ""interfacial activation,"" the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure. A ""lid"" or ""flap"" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site." 275 matched cddid_all.tbl CDD cd00710 cd00710 100039 LbH_gamma_CA Gamma carbonic anhydrases (CA): Carbonic anhydrases are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism, involving the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three distinct groups of carbonic anhydrases - alpha, beta and gamma - which show no significant sequence identity or structural similarity. Gamma CAs are homotrimeric enzymes, with each subunit containing a left-handed parallel beta helix (LbH) structural domain. 167 matched cddid_all.tbl CDD cd00712 cd00712 238364 AsnB Glutamine amidotransferases class-II (GATase) asparagine synthase_B type. Asparagine synthetase B catalyses the ATP-dependent conversion of aspartate to asparagine. This enzyme is a homodimer, with each monomer composed of a glutaminase domain and a synthetase domain. The N-terminal glutaminase domain hydrolyzes glutamine to glutamic acid and ammonia. 220 matched cddid_all.tbl CDD cd00713 cd00713 238365 GltS Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The N-terminal glutaminase domain catalyzes the hydrolysis of glutamine to glutamic acid and ammonia, and has a fold similar to that of other glutamine amidotransferases such as glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), and beta lactam synthetase (beta-LS), as well as the Ntn hydrolase folds of the proteasomal alpha and beta subunits. 413 matched cddid_all.tbl CDD cd00714 cd00714 238366 GFAT Glutamine amidotransferases class-II (Gn-AT)_GFAT-type. This domain is found at the N-terminus of glucosamine-6P synthase (GlmS, or GFAT in humans). The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. In humans, GFAT catalyzes the first and rate-limiting step of hexosamine metabolism, the conversion of D-fructose-6P (Fru6P) into D-glucosamine-6P using L-glutamine as a nitrogen source. The end product of this pathway, UDP-N-acetyl glucosamine, is a major building block of the bacterial peptidoglycan and fungal chitin. 215 matched cddid_all.tbl CDD cd00715 cd00715 238367 GPATase_N Glutamine amidotransferases class-II (GN-AT)_GPAT- type. This domain is found at the N-terminus of glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase) . The glutaminase domain catalyzes amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. GPATase catalyzes the first step in purine biosynthesis, an amide transfer from glutamine to PRPP, resulting in phosphoribosylamine, pyrophosphate and glutamate. GPATase crystalizes as a homotetramer, but can also exist as a homdimer. 252 matched cddid_all.tbl CDD cd00716 cd00716 153076 creatine_kinase_like Phosphagen (guanidino) kinases such as creatine kinase and similar enzymes. Eukaryotic creatine kinase-like phosphagen (guanidino) kinases are enzymes that transphosphorylate a high energy phosphoguanidino compound, like phosphocreatine (PCr) in the case of creatine kinase (CK), which is used as an energy-storage and -transport metabolite, to ADP, thereby creating ATP. The substrate binding site is located in the cleft between the N and C-terminal domains, but most of the catalytic residues are found in the larger C-terminal domain. In higher eukaryotes, CKs are found as tissue-specific (muscle, brain), as well as compartment-specific (mitochondrial, cytosolic, and flagellar) isoforms. Mitochondrial and cytoplasmic CKs are dimeric or octameric, while the flagellar isoforms are trimers with three CD domains fused as a single protein chain. CKs are either coupled to glycolysis (cytosolic form) or oxidative phosphorylation (mitochondrial form). Besides CK, one of the most studied members of this family, this model also represents other phosphagen kinases with different substrate specificities, like glycocyamine kinase (GK), lombricine kinase (LK), taurocyamine kinase (TK), and echinoderm arginine kinase (AK). 357 matched cddid_all.tbl CDD cd00717 cd00717 238368 URO-D Uroporphyrinogen decarboxylase (URO-D) is a dimeric cytosolic enzyme that decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, without requiring any prosthetic groups or cofactors. This reaction is located at the branching point of the tetrapyrrole biosynthetic pathway, leading to the biosynthesis of heme, chlorophyll or bacteriochlorophyll. URO-D deficiency is responsible for the human genetic diseases familial porphyria cutanea tarda (fPCT) and hepatoerythropoietic porphyria (HEP). 335 matched cddid_all.tbl CDD cd00719 cd00719 198380 GIY-YIG_SF GIY-YIG nuclease domain superfamily. The GIY-YIG nuclease domain superfamily includes a large and diverse group of proteins involved in many cellular processes, such as class I homing GIY-YIG family endonucleases, prokaryotic nucleotide excision repair proteins UvrC and Cho, type II restriction enzymes, the endonuclease/reverse transcriptase of eukaryotic retrotransposable elements, and a family of eukaryotic enzymes that repair stalled replication forks. All of these members contain a conserved GIY-YIG nuclease domain that may serve as a scaffold for the coordination of a divalent metal ion required for catalysis of the phosphodiester bond cleavage. By combining with different specificity, targeting, or other domains, the GIY-YIG nucleases may perform different functions. 69 matched cddid_all.tbl CDD cd00727 cd00727 238369 malate_synt_A Malate synthase A (MSA), present in some bacteria, plants and fungi. Prokaryotic MSAs tend to be monomeric, whereas eukaryotic enzymes are homomultimers. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA, which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms, like plants and fungi, to derive their carbon requirements from two-carbon compounds, by bypassing the two carboxylation steps of the citric acid cycle. 511 matched cddid_all.tbl CDD cd00728 cd00728 238370 malate_synt_G Malate synthase G (MSG), monomeric enzyme present in some bacteria. In general, malate synthase catalyzes the Claisen condensation of glyoxylate and acetyl-CoA to malyl-CoA , which hydrolyzes to malate and CoA. This reaction is part of the glyoxylate cycle, which allows certain organisms to derive their carbon requirements from two-carbon compounds, by bypassing the two carboxylation steps of the citric acid cycle. 712 matched cddid_all.tbl CDD cd00729 cd00729 238371 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity. 34 matched cddid_all.tbl CDD cd00730 cd00730 238372 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer. 50 matched cddid_all.tbl CDD cd00731 cd00731 238373 CheA_reg CheA regulatory domain; CheA is a histidine protein kinase present in bacteria and archea. Activated by the chemotaxis receptor a histidine phosphoryl group from CheA is passed directly to an aspartate in the response regulator CheY. This signalling mechanism is modulated by the methyl accepting chemotaxis proteins (MCPs). MCPs form a highly interconnected, tightly packed array within the membrane that is organized, at least in part, through interactions with CheW and CheA. The CheA regulatory domain belongs to the family of CheW_like proteins and has been proposed to mediate interaction with the kinase regulator CheW. 132 matched cddid_all.tbl CDD cd00732 cd00732 238374 CheW CheW, a small regulator protein, unique to the chemotaxis signalling in prokaryotes and archea. CheW interacts with the histidine kinase CheA, most likely with the related regulatory domain of CheA. CheW is proposed to form signalling arrays together with CheA and the methyl-accepting chemotaxis proteins (MCPs), which are involved in response modulation. 140 matched cddid_all.tbl CDD cd00733 cd00733 238375 GlyRS_alpha_core Class II Glycyl-tRNA synthetase (GlyRS) alpha subunit core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes and in arabidopsis. It is responsible for the attachment of glycine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. This alignment contains only sequences from the GlyRS form which heterotetramerizes. The homodimer form of GlyRS is in a different family of class II aaRS. Class II assignment is based upon structure and the presence of three characteristic sequence motifs. 279 matched cddid_all.tbl CDD cd00735 cd00735 381597 T4-like_lys bacteriophage T4-like lysozymes. Bacteriophage T4-like lysozymes hydrolyze the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) in peptidoglycan heteropolymers of prokaryotic cell walls. Members include a variety of bacteriophages (T4, RB49, RB69, Aeh1), as well as Dictyostelium. 146 matched cddid_all.tbl CDD cd00736 cd00736 381598 lambda_lys-like Bacteriophage lambda lysozyme and similar proteins. Lysozyme from bacteriophage lambda hydrolyzes the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc), as do other lysozymes. However, unlike other lysozymes, bacteriophage lambda does not produce a reducing end upon cleavage of the peptidoglycan, but rather uses the 6-OH of the same MurNAc residue to produce a 1,6-anhydromuramic acid terminal residue and is therefore a lytic transglycosylase. An identical 1,6-anhydro bond is formed in bacterial peptidoglycans by the action of the lytic transglycosylases of E. coli, though they differ structurally. 141 matched cddid_all.tbl CDD cd00737 cd00737 381599 lyz_endolysin_autolysin endolysin and autolysin. The dsDNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell walls. Similarly, bacteria produce autolysins to facilitate the biosynthesis of its cell wall heteropolymer peptidoglycan and cell division. Endolysins and autolysins are found in viruses and bacteria, respectively. Both endolysin and autolysin enzymes cleave the glycosidic beta 1,4-bonds between the N-acetylmuramic acid and the N-acetylglucosamine of the peptidoglycan. 136 matched cddid_all.tbl CDD cd00738 cd00738 238379 HGTP_anticodon HGTP anticodon binding domain, as found at the C-terminus of histidyl, glycyl, threonyl and prolyl tRNA synthetases, which are classified as a group of class II aminoacyl-tRNA synthetases (aaRS). In aaRSs, the anticodon binding domain is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. This domain is also found in the accessory subunit of mitochondrial polymerase gamma (Pol gamma b). 94 matched cddid_all.tbl CDD cd00739 cd00739 238380 DHPS DHPS subgroup of Pterin binding enzymes. DHPS (dihydropteroate synthase), a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and protein biosynthesis. Prokaryotes (and some lower eukaryotes) must synthesize folate de novo, while higher eukaryotes are able to utilize dietary folate and therefore lack DHPS. Sulfonamide drugs, which are substrate analogs of pABA, target DHPS. 257 matched cddid_all.tbl CDD cd00740 cd00740 238381 MeTr MeTr subgroup of pterin binding enzymes. This family includes cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). Cobalamin-dependent methyltransferases catalyze the transfer of a methyl group via a methyl- cob(III)amide intermediate. These include MeTr, a functional heterodimer, and the folate binding domain of MetH. 252 matched cddid_all.tbl CDD cd00741 cd00741 238382 Lipase "Lipase. Lipases are esterases that can hydrolyze long-chain acyl-triglycerides into di- and monoglycerides, glycerol, and free fatty acids at a water/lipid interface. A typical feature of lipases is ""interfacial activation"", the process of becoming active at the lipid/water interface, although several examples of lipases have been identified that do not undergo interfacial activation . The active site of a lipase contains a catalytic triad consisting of Ser - His - Asp/Glu, but unlike most serine proteases, the active site is buried inside the structure. A ""lid"" or ""flap"" covers the active site, making it inaccessible to solvent and substrates. The lid opens during the process of interfacial activation, allowing the lipid substrate access to the active site." 153 matched cddid_all.tbl CDD cd00742 cd00742 381183 FABP intracellular fatty acid-binding protein family. Members of this family are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner. They protect and shuttle fatty acids within the cell and are involved in acquisition and removal of fatty acids from intracellular sites. They include cellular retinol-binding proteins (CRBPs) which participate in the cellular uptake of vitamin A in the form of free retinol, cellular retinoic acid-binding proteins (CRABPs) which participate in the metabolism of vitamin A and retinoic acid, and bind all trans retinoic acid, but not retinol, and FABPs similar to FABP3 which plays an important role in fatty acid transportation, cell growth, cell signaling, and gene transcription. 129 matched cddid_all.tbl CDD cd00743 cd00743 381184 lipocalin_RBP_like retinol-binding protein 4 and similar proteins. Retinol-Binding Protein 4 (RBP4) is a plasma protein that transports retinol (vitamin A) from the liver stores to the peripheral tissues. The RBP4-retinol complex interacts with transthyretin (TTR - transports thyroxine and retinol) which protects it from renal excretion. In addition to retinol, other endogenous and synthetic retinoids bind RBP4, including all-trans and 13-cis retinoic acid, retinyl acetate, N-(ethyl)retinamide, and fenretinide. This group also includes purpurin, a retinol-specific protein that plays a role in neural retina cell adhesion during development of the chicken retina; it also binds retinol and may participate in retinol transporter in the retina. This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 171 matched cddid_all.tbl CDD cd00751 cd00751 238383 thiolase Thiolase are ubiquitous enzymes that catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. They are found in prokaryotes and eukaryotes (cytosol, microbodies and mitochondria). There are 2 functional different classes: thiolase-I (3-ketoacyl-CoA thiolase) and thiolase-II (acetoacetyl-CoA thiolase). Thiolase-I can cleave longer fatty acid molecules and plays an important role in the beta-oxidative degradation of fatty acids. Thiolase-II has a high substrate specificity. Although it can cleave acetoacyl-CoA, its main function is the synthesis of acetoacyl-CoA from two molecules of acetyl-CoA, which gives it importance in several biosynthetic pathways. 386 matched cddid_all.tbl CDD cd00754 cd00754 340452 Ubl_MoaD ubiquitin-like (Ubl) domain found in molybdenum cofactor biosynthesis protein D (MoaD) and similar proteins. MoaD, also termed molybdopterin synthase sulfur carrier subunit, or MPT synthase subunit 1, or MPT synthase small subunit, or molybdopterin-converting factor small subunit, or molybdopterin-converting factor subunit 1, is a conserved small sulfur carrier protein that has beta-grasp ubiquitin-like (Ubl) fold involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor of a diverse group of redox enzymes. MoaD is activated in an ATP-dependent manner by sulfurtransferases similar to the activation mechanism of ubiquitin-activating enzyme E1. 79 matched cddid_all.tbl CDD cd00755 cd00755 238384 YgdL_like Family of activating enzymes (E1) of ubiquitin-like proteins related to the E.coli hypothetical protein ygdL. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like substrate, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of the substrate. The exact function of this family is unknown. 231 matched cddid_all.tbl CDD cd00756 cd00756 238385 MoaE MoaE family. Members of this family are involved in biosynthesis of the molybdenum cofactor (Moco), an essential cofactor for a diverse group of redox enzymes. Moco biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), which carries the cis-dithiolene group responsible for molybdenum ligation. This dithiolene group is generated by MPT synthase in the second major step in Moco biosynthesis. MPT synthase is a heterotetramer consisting of two large (MoaE) and two small (MoaD) subunits. 124 matched cddid_all.tbl CDD cd00757 cd00757 238386 ThiF_MoeB_HesA_family ThiF_MoeB_HesA. Family of E1-like enzymes involved in molybdopterin and thiamine biosynthesis family. The common reaction mechanism catalyzed by MoeB and ThiF, like other E1 enzymes, begins with a nucleophilic attack of the C-terminal carboxylate of MoaD and ThiS, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS. MoeB, as the MPT synthase (MoaE/MoaD complex) sulfurase, is involved in the biosynthesis of the molybdenum cofactor, a derivative of the tricyclic pterin, molybdopterin (MPT). ThiF catalyzes the adenylation of ThiS, as part of the biosynthesis pathway of thiamin pyrophosphate (vitamin B1). 228 matched cddid_all.tbl CDD cd00758 cd00758 238387 MoCF_BD MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin. 133 matched cddid_all.tbl CDD cd00761 cd00761 132997 Glyco_tranf_GTA_type Glycosyltransferase family A (GT-A) includes diverse families of glycosyl transferases with a common GT-A type structural fold. Glycosyltransferases (GTs) are enzymes that synthesize oligosaccharides, polysaccharides, and glycoconjugates by transferring the sugar moiety from an activated nucleotide-sugar donor to an acceptor molecule, which may be a growing oligosaccharide, a lipid, or a protein. Based on the stereochemistry of the donor and acceptor molecules, GTs are classified as either retaining or inverting enzymes. To date, all GT structures adopt one of two possible folds, termed GT-A fold and GT-B fold. This hierarchy includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. The majority of the proteins in this superfamily are Glycosyltransferase family 2 (GT-2) proteins. But it also includes families GT-43, GT-6, GT-8, GT13 and GT-7; which are evolutionarily related to GT-2 and share structure similarities. 156 matched cddid_all.tbl CDD cd00762 cd00762 133442 NAD_bind_malic_enz NAD(P) binding domain of malic enzyme. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. 254 matched cddid_all.tbl CDD cd00763 cd00763 238388 Bacterial_PFK Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include bacterial ATP-dependent phosphofructokinases. These are allosrterically regulated homotetramers; the subunits are of about 320 amino acids. 317 matched cddid_all.tbl CDD cd00764 cd00764 238389 Eukaryotic_PFK Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include eukaryotic ATP-dependent phosphofructokinases. These have evolved from the bacterial PFKs by gene duplication and fusion events and exhibit complex allosteric behavior. 762 matched cddid_all.tbl CDD cd00765 cd00765 238390 Pyrophosphate_PFK Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include pyrophosphate-dependent phosphofructokinases. These are found in bacteria as well as plants. These may be dimeric nonallosteric enzymes as in bacteria or allosteric heterotetramers as in plants. 550 matched cddid_all.tbl CDD cd00768 cd00768 238391 class_II_aaRS-like_core Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial ATP phosphoribosyltransferase regulatory subunit HisZ. 211 matched cddid_all.tbl CDD cd00769 cd00769 238392 PheRS_beta_core Phenylalanyl-tRNA synthetase (PheRS) beta chain core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer. While the alpha chain contains a catalytic core domain, the beta chain has a non-catalytic core domain. 198 matched cddid_all.tbl CDD cd00770 cd00770 238393 SerRS_core Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. SerRS synthetase is a homodimer. 297 matched cddid_all.tbl CDD cd00771 cd00771 238394 ThrRS_core Threonyl-tRNA synthetase (ThrRS) class II core catalytic domain. ThrRS is a homodimer. It is responsible for the attachment of threonine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. 298 matched cddid_all.tbl CDD cd00772 cd00772 238395 ProRS_core Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. 264 matched cddid_all.tbl CDD cd00773 cd00773 238396 HisRS-like_core Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ. HisZ along with HisG catalyze the first reaction in histidine biosynthesis. HisZ is found only in a subset of bacteria and differs from HisRS in lacking a C-terminal anti-codon binding domain. 261 matched cddid_all.tbl CDD cd00774 cd00774 238397 GlyRS-like_core Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP binding and hydrolysis. This alignment contains only sequences from the GlyRS form which homodimerizes. The heterotetramer glyQ is in a different family of class II aaRS. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. This domain is also found at the N-terminus of the accessory subunit of mitochondrial polymerase gamma (Pol gamma b). Pol gamma b stimulates processive DNA synthesis and is functional as a homodimer, which can associate with the catalytic subunit Pol gamma alpha to form a heterotrimer. Despite significant both structural and sequence similarity with GlyRS, Pol gamma b lacks conservation of several class II functional residues. 254 matched cddid_all.tbl CDD cd00775 cd00775 238398 LysRS_core Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three characteristic sequence motifs in the core domain. It is found in eukaryotes as well as some prokaryotes and archaea. However, LysRS belongs to class I aaRS's in some prokaryotes and archaea. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. 329 matched cddid_all.tbl CDD cd00776 cd00776 238399 AsxRS_core Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as a subgroup of AspRS. AsnRS and AspRS are homodimers, which attach either asparagine or aspartate to the 3'OH group of ribose of the appropriate tRNA. While archaea lack asnRS, they possess a non-discriminating aspRS, which can mischarge Asp-tRNA with Asn. Subsequently, a tRNA-dependent aspartate amidotransferase converts the bound aspartate to asparagine. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. 322 matched cddid_all.tbl CDD cd00777 cd00777 238400 AspRS_core Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the appropriate tRNA. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. AspRS in this family differ from those found in the AsxRS family by a GAD insert in the core domain. 280 matched cddid_all.tbl CDD cd00778 cd00778 238401 ProRS_core_arch_euk Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from archaea, the cytoplasm of eukaryotes and some bacteria. 261 matched cddid_all.tbl CDD cd00779 cd00779 238402 ProRS_core_prok Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from prokaryotes and from the mitochondria of eukaryotes. 255 matched cddid_all.tbl CDD cd00780 cd00780 238403 NTF2 Nuclear transport factor 2 (NTF2) domain plays an important role in the trafficking of macromolecules, ions and small molecules between the cytoplasm and nucleus. This bi-directional transport of macromolecules across the nuclear envelope requires many soluble factors that includes GDP-binding protein Ran (RanGDP). RanGDP is required for both import and export of proteins and poly(A) RNA. RanGDP also has been implicated in cell cycle control, specifically in mitotic spindle assembly. In interphase cells, RanGDP is predominately nuclear and thought to be GTP bound, but it is also present in the cytoplasm, probably in the GDP-bound state. NTF2 mediates the nuclear import of RanGDP. NTF2 binds to both RanGDP and FxFG repeat-containing nucleoporins. 119 matched cddid_all.tbl CDD cd00781 cd00781 238404 ketosteroid_isomerase ketosteroid isomerase: Many biological reactions proceed by enzymatic cleavage of a C-H bond adjacent to carbonyl or a carboxyl group, leading to an enol or a enolate intermediate that is subsequently re-protonated at the same or an adjacent carbon. Ketosteroid isomerases are important members of this class of enzymes which are the most proficient of all enzymes known and have served as a paradigm for enzymatic enolizations since its discovery in 1954. This CD includes members of this class that calalyze the isomerization of various beta,gamma-unsaturated isomers at nearly a diffusion-controlled rate. These enzymes are widely distributed in bacteria. 122 matched cddid_all.tbl CDD cd00782 cd00782 238405 MutL_Trans MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to human MLH1, hPMS2, hPMS1, hMLH3 and E. coli MutL, MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot syndrome (HNPCC variant). Mutation in hPMS2 causes predisposition to HPNCC and Turcot syndrome. Mutation in hMLH1 accounts for a large fraction of HNPCC families. There is no convincing evidence to support hPMS1 having a role in HNPCC predisposition. It has been suggested that hMLH3 may be a low risk gene for colorectal cancer; however there is little evidence to support it having a role in classical HNPCC. It has been suggested that during initiation of DNA mismatch repair in E. coli, the mismatch recognition protein MutS recruits MutL in the presence of ATP. The MutS(ATP)-MutL ternary complex formed, then recruits the latent endonuclease MutH. 122 matched cddid_all.tbl CDD cd00786 cd00786 238406 cytidine_deaminase-like Cytidine and deoxycytidylate deaminase zinc-binding region. The family contains cytidine deaminases, nucleoside deaminases, deoxycytidylate deaminases and riboflavin deaminases. Also included are the apoBec family of mRNA editing enzymes. All members are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. 96 matched cddid_all.tbl CDD cd00788 cd00788 238407 KU70 Ku-core domain, Ku70 subfamily; Ku70 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination. The mechanism underlying the regulation of all the diverse functions of Ku is still unclear, although it seems that Ku is a multifunctional protein that works in the nuclei. In mammalian cells, the Ku heterodimer recruits the catalytic subunit of DNA-dependent protein kinase (DNA-PK), which is dependent on its association with the Ku70/80 heterodimer bound to DNA for its protein kinase activity. 287 matched cddid_all.tbl CDD cd00789 cd00789 238408 KU_like Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku. The alignment includes the core domain shared by the prokaryotic YkoV-like proteins and the eukaryotic Ku70 and Ku80. The prokaryotic Ku homologs are predicted to form homodimers. It is proposed that the Ku homologs are functionally associated with ATP-dependent DNA ligase and the eukaryotic-type primase, probably as components of a double-strand break repair system. 256 matched cddid_all.tbl CDD cd00794 cd00794 238409 NOS_oxygenase_prok Nitric oxide synthase (NOS) prokaryotic oxygenase domain. NOS produces nitric oxide (NO) by catalyzing a five-electron heme-based oxidation of a guanidine nitrogen of L-arginine to L-citrulline via two successive monooxygenation reactions producing N(omega)-hydroxy-L-arginine (NHA) as an intermediate. Nitric oxide synthases are homodimers. Most prokaryotes produce NO as a byproduct of denitrification, using a completely different set of enzymes than NOS. However, a few prokaryotes also have a NOS, consisting solely of the NOS oxygenase domain. Prokaryotic NOS binds to the substrate L-Arg, zinc, and to the cofactors heme and tetrahydrofolate. 353 matched cddid_all.tbl CDD cd00795 cd00795 238410 NOS_oxygenase_euk Nitric oxide synthase (NOS) eukaryotic oxygenase domain. NOS produces nitric oxide (NO) by catalyzing a five-electron heme-based oxidation of a guanidine nitrogen of L-arginine to L-citrulline via two successive monooxygenation reactions producing N(omega)-hydroxy-L-arginine (NHA) as an intermediate. In mammals, there are three distinct NOS isozymes: neuronal (nNOS or NOS-1), cytokine-inducible (iNOS or NOS-2) and endothelial (eNOS or NOS-3) . Nitric oxide synthases are homodimers. In eukaryotes, each monomer has an N-terminal oxygenase domain, which binds to the substrate L-Arg, zinc, and to the cofactors heme and 5.6.7.8-(6R)-tetrahydrobiopterin (BH4) . Eukaryotic NOS's also have a C-terminal electron supplying reductase region, which is homologous to cytochrome P450 reductase and binds NADH, FAD and FMN. 412 matched cddid_all.tbl CDD cd00796 cd00796 271177 INT_Rci_Hp1_C Shufflon-specific DNA recombinase Rci and Bacteriophage Hp1_like integrase, C-terminal catalytic domain. Rci protein is a tyrosine recombinase specifically involved in Shufflon type of DNA rearrangement in bacteria. The shufflon of plasmid R64 consists of four invertible DNA segments which are separated and flanked by seven 19-bp repeat sequences. RCI recombinase facilitates the site-specific recombination between any inverted repeats results in an inversion of the DNA segment(s) either independently or in groups. HP1 integrase promotes site-specific recombination of the HP1 genome into that of Haemophilus influenza. Bacteriophage Hp1_like integrases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. 162 matched cddid_all.tbl CDD cd00797 cd00797 271178 INT_RitB_C_like C-terminal catalytic domain of recombinase RitB, a component of the recombinase trio. Recombinases belonging to the RitA (also known as pAE1 due to its presence in the deletion prone region of plasmid pAE1 of Alcaligenes eutrophus H1), RitB, and RitC families are associated in a complex referred to as a Recombinase in Trio (RIT) element. These RIT elements consist of three adjacent and unidirectional overlapping genes, one from each family (ritABC in order of transcription). All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not yet fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. 198 matched cddid_all.tbl CDD cd00798 cd00798 271179 INT_XerDC_C XerD and XerC integrases, C-terminal catalytic domains. XerDC-like integrases are involved in the site-specific integration and excision of lysogenic bacteriophage genomes, transposition of conjugative transposons, termination of chromosomal replication, and stable plasmid inheritance. They share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism with the DNA breaking-rejoining enzyme superfamily. In Escherichia coli, the Xer site-specific recombination system acts to convert dimeric chromosomes, which are formed by homologous recombination to monomers. Two related recombinases, XerC and XerD, bind cooperatively to a recombination site present in the E. coli chromosome. Each recombinase catalyzes the exchange of one pair of DNA strand in a reaction that proceeds through a Holliday junction intermediate. These enzymes can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves, and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites. 172 matched cddid_all.tbl CDD cd00799 cd00799 271180 INT_Cre_C C-terminal catalytic domain of Cre recombinase (also called integrase). Cre-like recombinases are tyrosine based site specific recombinases. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The bacteriophage P1 Cre recombinase maintains the circular phage replicon in a monomeric state by catalyzing a site-specific recombination between two loxP sites. The catalytic core domain of Cre recombinase is linked to a more divergent helical N-terminal domain, which interacts primarily with the DNA major groove proximal to the crossover region. 188 matched cddid_all.tbl CDD cd00800 cd00800 271181 INT_Lambda_C C-terminal catalytic domain of Lambda integrase, a tyrosine-based site-specific recombinase. Lambda-type integrases catalyze site-specific integration and excision of temperate bacteriophages and other mobile genetic elements to and from the bacterial host chromosome. They are tyrosine-based site-specific recombinase and belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The phage lambda integrase can bridge two different and well-separated DNA sequences called arm- and core-sites. The C-terminal domain binds, cleaves and re-ligates DNA strands at the core-sites, while the N-terminal domain is largely responsible for high-affinity binding to the arm-type sites. 161 matched cddid_all.tbl CDD cd00801 cd00801 271182 INT_P4_C Bacteriophage P4 integrase, C-terminal catalytic domain. P4-like integrases are found in temperate bacteriophages, integrative plasmids, pathogenicity and symbiosis islands, and other mobile genetic elements. The P4 integrase mediates integrative and excisive site-specific recombination between two sites, called attachment sites, located on the phage genome and the bacterial chromosome. The phage attachment site is often found adjacent to the integrase gene, while the host attachment sites are typically situated near tRNA genes. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. 180 matched cddid_all.tbl CDD cd00802 cd00802 173901 class_I_aaRS_core catalytic core domain of class I amino acyl-tRNA synthetase. Class I amino acyl-tRNA synthetase (aaRS) catalytic core domain. These enzymes are mostly monomers which aminoacylate the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. 143 matched cddid_all.tbl CDD cd00805 cd00805 173902 TyrRS_core catalytic core domain of tyrosinyl-tRNA synthetase. Tyrosinyl-tRNA synthetase (TyrRS) catalytic core domain. TyrRS is a homodimer which attaches Tyr to the appropriate tRNA. TyrRS is a class I tRNA synthetases, so it aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formationof the enzyme bound aminoacyl-adenylate. It contains the class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding. 269 matched cddid_all.tbl CDD cd00806 cd00806 173903 TrpRS_core catalytic core domain of tryptophanyl-tRNA synthetase. Tryptophanyl-tRNA synthetase (TrpRS) catalytic core domain. TrpRS is a homodimer which attaches Tyr to the appropriate tRNA. TrpRS is a class I tRNA synthetases, so it aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains class I characteristic HIGH and KMSKS motifs, which are involved in ATP binding 280 matched cddid_all.tbl CDD cd00807 cd00807 185676 GlnRS_core "catalytic core domain of glutaminyl-tRNA synthetase. Glutaminyl-tRNA synthetase (GlnRS) cataytic core domain. These enzymes attach Gln to the appropriate tRNA. Like other class I tRNA synthetases, they aminoacylate the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. GlnRS contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. These enzymes function as monomers. Archaea and most bacteria lack GlnRS. In these organisms, the ""non-discriminating"" form of GluRS aminoacylates both tRNA(Glu) and tRNA(Gln) with Glu, which is converted to Gln when appropriate by a transamidation enzyme." 238 matched cddid_all.tbl CDD cd00808 cd00808 173905 GluRS_core catalytic core domain of discriminating glutamyl-tRNA synthetase. Discriminating Glutamyl-tRNA synthetase (GluRS) catalytic core domain . The discriminating form of GluRS is only found in bacteria and cellular organelles. GluRS is a monomer that attaches Glu to the appropriate tRNA. Like other class I tRNA synthetases, GluRS aminoacylates the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. 239 matched cddid_all.tbl CDD cd00812 cd00812 173906 LeuRS_core catalytic core domain of leucyl-tRNA synthetases. Leucyl tRNA synthetase (LeuRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. In Aquifex aeolicus, the gene encoding LeuRS is split in two, just before the KMSKS motif. Consequently, LeuRS is a heterodimer, which likely superimposes with the LeuRS monomer found in most other organisms. LeuRS has an insertion in the core domain, which is subject to both deletions and rearrangements and thus differs between prokaryotic LeuRS and archaeal/eukaryotic LeuRS. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. 314 matched cddid_all.tbl CDD cd00814 cd00814 173907 MetRS_core catalytic core domain of methioninyl-tRNA synthetases. Methionine tRNA synthetase (MetRS) catalytic core domain. This class I enzyme aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. MetRS, which consists of the core domain and an anti-codon binding domain, functions as a monomer. However, in some species the anti-codon binding domain is followed by an EMAP domain. In this case, MetRS functions as a homodimer. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. As a result of a deletion event, MetRS has a significantly shorter core domain insertion than IleRS, ValRS, and LeuR. Consequently, the MetRS insertion lacks the editing function. 319 matched cddid_all.tbl CDD cd00817 cd00817 185677 ValRS_core catalytic core domain of valyl-tRNA synthetases. Valine amino-acyl tRNA synthetase (ValRS) catalytic core domain. This enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. ValRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. 382 matched cddid_all.tbl CDD cd00818 cd00818 173909 IleRS_core catalytic core domain of isoleucyl-tRNA synthetases. Isoleucine amino-acyl tRNA synthetases (IleRS) catalytic core domain . This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. IleRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. 338 matched cddid_all.tbl CDD cd00819 cd00819 238417 PEPCK_GTP Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity, this model describes the GTP-dependent group. 579 matched cddid_all.tbl CDD cd00820 cd00820 238418 PEPCK_HprK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups).HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of HPr and its dephosphorylation by phosphorolysis. PEPCK and the C-terminal catalytic domain of HprK/P are structurally similar with conserved active site residues suggesting that these two phosphotransferases have related functions. 107 matched cddid_all.tbl CDD cd00821 cd00821 275388 PH Pleckstrin homology (PH) domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 92 matched cddid_all.tbl CDD cd00822 cd00822 238419 TopoII_Trans_DNA_gyrase TopoIIA_Trans_DNA_gyrase: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to the B subunits of E. coli DNA gyrase and E. coli Topoisomerase IV which are heterodimers composed of two subunits. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes. All type IIA topoisomerases are related to each other at amino acid sequence level, though their oligomeric organization sometimes differs. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. TopoIIA enzymes also catenate/ decatenate duplex rings. E.coli DNA gyrase is a heterodimer composed of two subunits. E. coli DNA gyrase B subunit is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. 172 matched cddid_all.tbl CDD cd00823 cd00823 238420 TopoIIB_Trans TopoIIB_Trans: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIB family of DNA topoisomerases similar to Sulfolobus shibatae topoisomerase VI (topoVI). The sole representative of the Type IIB family is topo VI. Topo VI enzymes are heterotetramers found in archaea and plants. S. shibatae topoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. 151 matched cddid_all.tbl CDD cd00825 cd00825 238421 decarbox_cond_enzymes decarboxylating condensing enzymes; Family of enzymes that catalyze the formation of a new carbon-carbon bond by a decarboxylating Claisen-like condensation reaction. Members are involved in the synthesis of fatty acids and polyketides, a diverse group of natural products. Both pathways are an iterative series of additions of small carbon units, usually acetate, to a nascent acyl group. There are 2 classes of decarboxylating condensing enzymes, which can be distinguished by sequence similarity, type of active site residues and type of primer units (acetyl CoA or acyl carrier protein (ACP) linked units). 332 matched cddid_all.tbl CDD cd00826 cd00826 238422 nondecarbox_cond_enzymes nondecarboxylating condensing enzymes; In general, thiolases catalyze the reversible thiolytic cleavage of 3-ketoacyl-CoA into acyl-CoA and acetyl-CoA, a 2-step reaction involving a covalent intermediate formed with a catalytic cysteine. There are 2 functional different classes: thiolase-I (3-ketoacyl-CoA thiolase) and thiolase-II (acetoacetyl-CoA thiolase). Thiolase-I can cleave longer fatty acid molecules and plays an important role in the beta-oxidative degradation of fatty acids. Thiolase-II has a high substrate specificity. Although it can cleave acetoacyl-CoA, its main function is the synthesis of acetoacyl-CoA from two molecules of acetyl-CoA, which gives it importance in several biosynthetic pathways. 393 matched cddid_all.tbl CDD cd00827 cd00827 238423 init_cond_enzymes """initiating"" condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type III and polyketide synthases, type III, which include chalcone synthase and related enzymes. They are characterized by the utlization of CoA substrate primers, as well as the nature of their active site residues." 324 matched cddid_all.tbl CDD cd00828 cd00828 238424 elong_cond_enzymes """elongating"" condensing enzymes are a subclass of decarboxylating condensing enzymes, including beta-ketoacyl [ACP] synthase, type I and II and polyketide synthases.They are characterized by the utlization of acyl carrier protein (ACP) thioesters as primer substrates, as well as the nature of their active site residues." 407 matched cddid_all.tbl CDD cd00829 cd00829 238425 SCP-x_thiolase Thiolase domain associated with sterol carrier protein (SCP)-x isoform and related proteins; SCP-2 has multiple roles in intracellular lipid circulation and metabolism. The N-terminal presequence in the SCP-x isoform represents a peroxisomal 3-ketacyl-Coa thiolase specific for branched-chain acyl CoAs, which is proteolytically cleaved from the sterol carrier protein. 375 matched cddid_all.tbl CDD cd00830 cd00830 238426 KAS_III Ketoacyl-acyl carrier protein synthase III (KASIII) initiates the elongation in type II fatty acid synthase systems. It is found in bacteria and plants. Elongation of fatty acids in the type II systems occurs by Claisen condensation of malonyl-acyl carrier protein (ACP) with acyl-ACP. KASIII initiates this process by specifically using acetyl-CoA over acyl-CoA. 320 matched cddid_all.tbl CDD cd00831 cd00831 238427 CHS_like Chalcone and stilbene synthases; plant-specific polyketide synthases (PKS) and related enzymes, also called type III PKSs. PKS generate an array of different products, dependent on the nature of the starter molecule. They share a common chemical strategy, after the starter molecule is loaded onto the active site cysteine, a carboxylative condensation reation extends the polyketide chain. Plant-specific PKS are dimeric iterative PKSs, using coenzyme A esters to deliver substrate to the active site, but they differ in the choice of starter molecule and the number of condensation reactions. 361 matched cddid_all.tbl CDD cd00832 cd00832 238428 CLF Chain-length factor (CLF) is a factor required for polyketide chain initiation of aromatic antibiotic-producing polyketide synthases (PKSs) of filamentous bacteria. CLFs have been shown to have decarboxylase activity towards malonyl-acyl carrier protein (ACP). CLFs are similar to other elongation ketosynthase domains, but their active site cysteine is replaced by a conserved glutamine. 399 matched cddid_all.tbl CDD cd00833 cd00833 238429 PKS polyketide synthases (PKSs) polymerize simple fatty acids into a large variety of different products, called polyketides, by successive decarboxylating Claisen condensations. PKSs can be divided into 2 groups, modular type I PKSs consisting of one or more large multifunctional proteins and iterative type II PKSs, complexes of several monofunctional subunits. 421 matched cddid_all.tbl CDD cd00834 cd00834 238430 KAS_I_II Beta-ketoacyl-acyl carrier protein (ACP) synthase (KAS), type I and II. KASs are responsible for the elongation steps in fatty acid biosynthesis. KASIII catalyses the initial condensation and KAS I and II catalyze further elongation steps by Claisen condensation of malonyl-acyl carrier protein (ACP) with acyl-ACP. 406 matched cddid_all.tbl CDD cd00835 cd00835 269907 RanBD_family Ran-binding domain. The RanBD is present in RanBP1, RanBP2, RanBP3, Nuc2, and Nuc50. Most of these proteins have a single RanBD, with the exception of RanBP2 which has 4 RanBDs. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran. The Ran-binding domain is found in multiple copies in Nuclear pore complex proteins. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity. The RanBD proteins of the nuclear pore complex (NPC): nucleoporin 1 (NUP1), NUP2, NUP61, and Nuclear Pore complex Protein 9 (npp-9) are present in the parent, but specific models were not made due to lineage. To date there been no reports of inositol phosphate or phosphoinositide binding by Ran-binding proteins. 118 matched cddid_all.tbl CDD cd00836 cd00836 275389 FERM_C-lobe FERM domain C-lobe. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 93 matched cddid_all.tbl CDD cd00837 cd00837 269909 EVH1_family EVH1 (Drosophila Enabled (Ena)/Vasodilator-stimulated phosphoprotein (VASP) homology 1) domain. The EVH1 domains are part of the PH domain superfamily. EVH1 subfamilies include Enables/VASP, Homer/Vesl, WASP, and Spred. Ligands are known for three of the EVH1 subfamilies, all of which bind proline-rich sequences: the Enabled/VASP family binds to FPPPP peptides, the Homer/Vesl family binds PPxxF peptides, and the WASP family binds LPPPEP peptides. EVH1 has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains. 103 matched cddid_all.tbl CDD cd00838 cd00838 277317 MPP_superfamily metallophosphatase superfamily, metallophosphatase domain. Metallophosphatases (MPPs), also known as metallophosphoesterases, phosphodiesterases (PDEs), binuclear metallophosphoesterases, and dimetal-containing phosphoesterases (DMPs), represent a diverse superfamily of enzymes with a conserved domain containing an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. This superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 130 matched cddid_all.tbl CDD cd00839 cd00839 277318 MPP_PAPs purple acid phosphatases of the metallophosphatase superfamily, metallophosphatase domain. Purple acid phosphatases (PAPs) belong to a diverse family of binuclear metallohydrolases that have been identified and characterized in plants, animals, and fungi. PAPs contain a binuclear metal center and their characteristic pink or purple color derives from a charge-transfer transition between a tyrosine residue and a chromophoric ferric ion within the binuclear center. PAPs catalyze the hydrolysis of a wide range of activated phosphoric acid mono- and di-esters and anhydrides. PAPs are distinguished from the other phosphatases by their insensitivity to L-(+) tartrate inhibition and are therefore also known as tartrate resistant acid phosphatases (TRAPs). While only a few copies of PAP-like genes are present in mammalian and fungal genomes, multiple copies are present in plant genomes. PAPs belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 296 matched cddid_all.tbl CDD cd00840 cd00840 277319 MPP_Mre11_N Mre11 nuclease, N-terminal metallophosphatase domain. Mre11 (also known as SbcD in Escherichia coli) is a subunit of the MRX protein complex. This complex includes: Mre11, Rad50, and Xrs2/Nbs1, and plays a vital role in several nuclear processes including DNA double-strand break repair, telomere length maintenance, cell cycle checkpoint control, and meiotic recombination, in eukaryotes. During double-strand break repair, the MRX complex is required to hold the two ends of a broken chromosome together. In vitro studies show that Mre11 has 3'-5' exonuclease activity on dsDNA templates and endonuclease activity on dsDNA and ssDNA templates. In addition to the N-terminal phosphatase domain, the eukaryotic MRE11 members of this family have a C-terminal DNA binding domain (not included in this alignment model). MRE11-like proteins are found in prokaryotes and archaea was well as in eukaryotes. Mre11 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 186 matched cddid_all.tbl CDD cd00841 cd00841 277320 MPP_YfcE Escherichia coli YfcE and related proteins, metallophosphatase domain. YfcE is a manganase-dependent metallophosphatase, found in bacteria and archaea, that cleaves bis-p-nitrophenyl phosphate, thymidine 5'-monophosphate-p-nitrophenyl ester, and p-nitrophenyl phosphorylcholine, but is unable to hydrolyze 2',3 ' or 3',5' cyclic nucleic phosphodiesters, and various phosphomonoesters, including p-nitrophenyl phosphate. This family also includes the Bacilus subtilis YsnB and Methanococcus jannaschii MJ0936 proteins. This domain family belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 156 matched cddid_all.tbl CDD cd00842 cd00842 277321 MPP_ASMase acid sphingomyelinase and related proteins, metallophosphatase domain. Acid sphingomyelinase (ASMase) is a ubiquitously expressed phosphodiesterase which hydrolyzes sphingomyelin in acid pH conditions to form ceramide, a bioactive second messenger, as part of the sphingomyelin signaling pathway. ASMase is localized at the noncytosolic leaflet of biomembranes (for example the luminal leaflet of endosomes, lysosomes and phagosomes, and the extracellular leaflet of plasma membranes). ASMase-deficient humans develop Niemann-Pick disease. This disease is characterized by lysosomal storage of sphingomyelin in all tissues. Although ASMase-deficient mice are resistant to stress-induced apoptosis, they have greater susceptibility to bacterial infection. The latter correlates with defective phagolysosomal fusion and antibacterial killing activity in ASMase-deficient macrophages. ASMase belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: the phosphoprotein phosphatases (PPPs), Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 294 matched cddid_all.tbl CDD cd00844 cd00844 277322 MPP_Dbr1_N Dbr1 RNA lariat debranching enzyme, N-terminal metallophosphatase domain. Dbr1 is an RNA lariat debranching enzyme that hydrolyzes 2'-5' phosphodiester bonds at the branch points of excised intron lariats. This alignment model represents the N-terminal metallophosphatase domain of Dbr1. This domain belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 271 matched cddid_all.tbl CDD cd00845 cd00845 277323 MPP_UshA_N_like Escherichia coli UshA-like family, N-terminal metallophosphatase domain. This family includes the bacterial enzyme UshA, and related enzymes including SoxB, CpdB, YhcR, and CD73. All members have a similar domain architecture which includes an N-terminal metallophosphatase domain and a C-terminal nucleotidase domain. The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 255 matched cddid_all.tbl CDD cd00851 cd00851 238431 MTH1175 This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This domain is a predicted small-molecule-binding domain (SMBD) with an alpha/beta fold that is present either as a stand-alone domain (e.g. NifX and NifY) or fused to another conserved domain (e.g. NifB) however, its function is still undetermined.The SCOP database suggests that this domain is most similar to structures within the ribonuclease H superfamily. This conserved domain is represented in two of the three major divisions of life (bacteria and archaea). 103 matched cddid_all.tbl CDD cd00852 cd00852 238432 NifB NifB belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme as part of nitrogen fixation in bacteria. This domain is sometimes found fused to a N-terminal domain (the Radical SAM domain) in nifB-like proteins. 106 matched cddid_all.tbl CDD cd00853 cd00853 238433 NifX NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein is part of the nitrogen fixation gene cluster in nitrogen-fixing bacteria and has sequence similarity to other members of the cluster. 102 matched cddid_all.tbl CDD cd00854 cd00854 238434 NagA N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of N-acetyl-glucosamine-6-phosphate (GlcNAc-6-P) to glucosamine 6-phosphate and acetate. This is the first committed step in the biosynthetic pathway to amino-sugar-nucleotides, which is needed for cell wall peptidoglycan and teichoic acid biosynthesis. Deacetylation of N-acetylglucosamine is also important in lipopolysaccharide synthesis and cell wall recycling. 374 matched cddid_all.tbl CDD cd00855 cd00855 349487 SWIB-MDM2 SWIB/MDM2 domain family. The SWIB/MDM2 protein domain, short for SWI/SNF complex B/MDM2, has been found in both SWI/SNF complex B (SWIB) and the negative regulator of the p53 tumor suppressor MDM2, which are homologous and share a common fold. The SWIB domain is a conserved region found within proteins in the SWI/SNF (SWItch/Sucrose Non-Fermentable) family of complexes. SWI/SNF complex proteins display helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). MDM2 is an inhibitor of p53 tumor repressor. It binds to the transactivation domain and down-regulates the ability of p53 to activate transcription. This family corresponds to the SWIB domain and the p53 binding domain of MDM2. 69 matched cddid_all.tbl CDD cd00858 cd00858 238435 GlyRS_anticodon GlyRS Glycyl-anticodon binding domain. GlyRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. 121 matched cddid_all.tbl CDD cd00859 cd00859 238436 HisRS_anticodon HisRS Histidyl-anticodon binding domain. HisRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. 91 matched cddid_all.tbl CDD cd00860 cd00860 238437 ThrRS_anticodon ThrRS Threonyl-anticodon binding domain. ThrRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. 91 matched cddid_all.tbl CDD cd00861 cd00861 238438 ProRS_anticodon_short ProRS Prolyl-anticodon binding domain, short version found predominantly in bacteria. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only. 94 matched cddid_all.tbl CDD cd00862 cd00862 238439 ProRS_anticodon_zinc ProRS Prolyl-anticodon binding domain, long version found predominantly in eukaryotes and archaea. ProRS belongs to class II aminoacyl-tRNA synthetases (aaRS). This alignment contains the anticodon binding domain, which is responsible for specificity in tRNA-binding, so that the activated amino acid is transferred to a ribose 3' OH group of the appropriate tRNA only, and an additional C-terminal zinc-binding domain specific to this subfamily of aaRSs. 202 matched cddid_all.tbl CDD cd00864 cd00864 238440 PI3Ka Phosphoinositide 3-kinase family, accessory domain (PIK domain); PIK domain is conserved in PI3 and PI4-kinases. Its role is unclear, but it has been suggested to be involved in substrate presentation. Phosphoinositide 3-kinases play an important role in a variety of fundamental cellular processes and can be divided into three main classes, defined by their substrate specificity and domain architecture. 152 matched cddid_all.tbl CDD cd00865 cd00865 176643 PEBP_bact_arch PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in bacteria and archaea. PhosphatidylEthanolamine-Binding Proteins (PEBPs) are represented in all three major phylogenetic divisions (eukaryotes, bacteria, archaea). The members in this subgroup are present in bacterial and archaea. Members here include Escherichia coli YBHB and YBCL which are thought to regulate protein phosphorylation as well as Sulfolobus solfataricus SsCEI which inhibits serine proteases alpha-chymotrypsin and elastase. Although their overall structures are similar, the members of the PEBP family have very different substrates and oligomerization states (monomer/dimer/tetramer). In a few of the bacterial members present here the dimerization interface is proposed to form the ligand binding site, unlike in other PEBP members. 150 matched cddid_all.tbl CDD cd00866 cd00866 176644 PEBP_euk PhosphatidylEthanolamine-Binding Protein (PEBP) domain present in eukaryotes. PhosphatidylEthanolamine-Binding Proteins (PEBPs) are represented in all three major phylogenetic divisions (eukaryotes, bacteria, archaea). The members in this subgroup are present in eukaryotes. Members here include those in plants such as Arabidopsis thaliana FLOWERING LOCUS (FT) and TERMINAL FLOWER1 (FT1) which function as a promoter and a repressor of the floral transitions, respectively as well as the mammalian Raf kinase inhibitory protein (RKIP) which inhibits MAP kinase (Raf-MEK-ERK), G protein-coupled receptor (GPCR) kinase and NFkappaB signaling cascades. Although their overall structures are similar, the members of the PEBP family have very different substrates and oligomerization states (monomer/dimer/tetramer). 154 matched cddid_all.tbl CDD cd00867 cd00867 173836 Trans_IPPS Trans-Isoprenyl Diphosphate Synthases. Trans-Isoprenyl Diphosphate Synthases (Trans_IPPS) of class 1 isoprenoid biosynthesis enzymes which either synthesis geranyl/farnesyl diphosphates (GPP/FPP) or longer chained products from isoprene precursors, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), or use geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate as substrate. These enzymes produce a myriad of precursors for such end products as steroids, cholesterol, sesquiterpenes, heme, carotenoids, retinoids, diterpenes, ubiquinone, and archaeal ether linked lipids; and are widely distributed among archaea, bacteria, and eukareya. The enzymes in this family share the same 'isoprenoid synthase fold' and include the head-to-tail (HT) IPPS which catalyze the successive 1'-4 condensation of the 5-carbon IPP to the growing isoprene chain to form linear, all-trans, C10-, C15-, C20- C25-, C30-, C35-, C40-, C45-, or C50-isoprenoid diphosphates. The head-to-head (HH) IPPS catalyze the successive 1'-1 condensation of 2 farnesyl or 2 geranylgeranyl isoprenoid diphosphates. Isoprenoid chain elongation reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, stabilizing reactive carbocation intermediates. Mechanistically and structurally distinct, cis-IPPS are not included in this CD. 236 matched cddid_all.tbl CDD cd00868 cd00868 173837 Terpene_cyclase_C1 Terpene cyclases, Class 1. Terpene cyclases, Class 1 (C1) of the class 1 family of isoprenoid biosynthesis enzymes, which share the 'isoprenoid synthase fold' and convert linear, all-trans, isoprenoids, geranyl (C10)-, farnesyl (C15)-, or geranylgeranyl (C20)-diphosphate into numerous cyclic forms of monoterpenes, diterpenes, and sesquiterpenes. Also included in this CD are the cis-trans terpene cyclases such as trichodiene synthase. The class I terpene cyclization reactions proceed via electrophilic alkylations in which a new carbon-carbon single bond is generated through interaction between a highly reactive electron-deficient allylic carbocation and an electron-rich carbon-carbon double bond. The catalytic site consists of a large central cavity formed by mostly antiparallel alpha helices with two aspartate-rich regions located on opposite walls. These residues mediate binding of prenyl phosphates via bridging Mg2+ ions, inducing proposed conformational changes that close the active site to solvent, stabilizing reactive carbocation intermediates. Mechanistically and structurally distinct, class II terpene cyclases and cis-IPPS are not included in this CD. Taxonomic distribution includes bacteria, fungi and plants. 284 matched cddid_all.tbl CDD cd00869 cd00869 238441 PI3Ka_II Phosphoinositide 3-kinase (PI3K) class II, accessory domain (PIK domain); PIK domain is conserved in all PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation. In general, class II PI3-kinases phosphorylate phosphoinositol (PtdIns), PtdIns(4)-phosphate, but not PtdIns(4,5)-bisphosphate. They are larger, having a C2 domain at the C-terminus. 169 matched cddid_all.tbl CDD cd00870 cd00870 238442 PI3Ka_III Phosphoinositide 3-kinase (PI3K) class III, accessory domain (PIK domain); PIK domain is conserved in all PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation. In general, PI3Ks class III phosphorylate phosphoinositol (PtdIns) only. The prototypical PI3K class III, yeast Vps34, is involved in trafficking proteins from Golgi to the vacuole. 166 matched cddid_all.tbl CDD cd00871 cd00871 238443 PI4Ka Phosphoinositide 4-kinase(PI4K), accessory domain (PIK domain); PIK domain is conserved in PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation. PI4K phosphorylates hydroxylgroup at position 4 on the inositol ring of phosphoinositide, the first commited step in the phosphatidylinositol cycle. 175 matched cddid_all.tbl CDD cd00872 cd00872 238444 PI3Ka_I Phosphoinositide 3-kinase (PI3K) class I, accessory domain ; PIK domain is conserved in all PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation. In general, PI3K class I prefer phosphoinositol (4,5)-bisphosphate as a substrate. Mammalian members interact with active Ras. They form heterodimers with adapter molecules linking them to different signaling pathways. 171 matched cddid_all.tbl CDD cd00873 cd00873 238445 KU80 Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination. The mechanism underlying the regulation of all the diverse functions of Ku is still unclear, although it seems that Ku is a multifunctional protein that works in nuclei. In mammalian cells, the Ku heterodimer recruits the catalytic subunit of DNA-dependent protein kinase (DNA-PK), which is dependent on its association with the Ku70/80 heterodimer bound to DNA for its protein kinase activity. 300 matched cddid_all.tbl CDD cd00874 cd00874 238446 RNA_Cyclase_Class_II RNA 3' phosphate cyclase domain (class II). These proteins function as RNA cyclase to catalyze the ATP-dependent conversion of 3'-phosphate to a 2'.3'-cyclic phosphodiester at the end of RNA molecule. A conserved catalytic histidine residue is found in all members of this subfamily. 326 matched cddid_all.tbl CDD cd00875 cd00875 238447 RNA_Cyclase_Class_I RNA 3' phosphate cyclase domain (class I) This subfamily of cyclase-like proteins are encoded in eukaryotic genomes. They lack a conserved catalytic histidine residue required for cyclase activity, so probably do not function as cyclases. They are believed to play a role in ribosomal RNA processing and assembly. 341 matched cddid_all.tbl CDD cd00876 cd00876 206642 Ras Rat sarcoma (Ras) family of small guanosine triphosphatases (GTPases). The Ras family of the Ras superfamily includes classical N-Ras, H-Ras, and K-Ras, as well as R-Ras, Rap, Ral, Rheb, Rhes, ARHI, RERG, Rin/Rit, RSR1, RRP22, Ras2, Ras-dva, and RGK proteins. Ras proteins regulate cell growth, proliferation and differentiation. Ras is activated by guanine nucleotide exchange factors (GEFs) that release GDP and allow GTP binding. Many RasGEFs have been identified. These are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active GTP-bound Ras interacts with several effector proteins: among the best characterized are the Raf kinases, phosphatidylinositol 3-kinase (PI3K), RalGEFs and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 160 matched cddid_all.tbl CDD cd00877 cd00877 206643 Ran Ras-related nuclear proteins (Ran)/TC4 family of small GTPases. Ran GTPase is involved in diverse biological functions, such as nuclear transport, spindle formation during mitosis, DNA replication, and cell division. Among the Ras superfamily, Ran is a unique small G protein. It does not have a lipid modification motif at the C-terminus to bind to the membrane, which is often observed within the Ras superfamily. Ran may therefore interact with a wide range of proteins in various intracellular locations. Like other GTPases, Ran exists in GTP- and GDP-bound conformations that interact differently with effectors. Conversion between these forms and the assembly or disassembly of effector complexes requires the interaction of regulator proteins. The intrinsic GTPase activity of Ran is very low, but it is greatly stimulated by a GTPase-activating protein (RanGAP1) located in the cytoplasm. By contrast, RCC1, a guanine nucleotide exchange factor that generates RanGTP, is bound to chromatin and confined to the nucleus. Ran itself is mobile and is actively imported into the nucleus by a mechanism involving NTF-2. Together with the compartmentalization of its regulators, this is thought to produce a relatively high concentration of RanGTP in the nucleus. 166 matched cddid_all.tbl CDD cd00878 cd00878 206644 Arf_Arl ADP-ribosylation factor(Arf)/Arf-like (Arl) small GTPases. Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thus, despite their significant sequence homologies, Arf family proteins may regulate unrelated functions. 158 matched cddid_all.tbl CDD cd00879 cd00879 206645 Sar1 Sar1 is an essential component of COPII vesicle coats. Sar1 is an essential component of COPII vesicle coats involved in export of cargo from the ER. The GTPase activity of Sar1 functions as a molecular switch to control protein-protein and protein-lipid interactions that direct vesicle budding from the ER. Activation of the GDP to the GTP-bound form of Sar1 involves the membrane-associated guanine nucleotide exchange factor (GEF) Sec12. Sar1 is unlike all Ras superfamily GTPases that use either myristoyl or prenyl groups to direct membrane association and function, in that Sar1 lacks such modification. Instead, Sar1 contains a unique nine-amino-acid N-terminal extension. This extension contains an evolutionarily conserved cluster of bulky hydrophobic amino acids, referred to as the Sar1-N-terminal activation recruitment (STAR) motif. The STAR motif mediates the recruitment of Sar1 to ER membranes and facilitates its interaction with mammalian Sec12 GEF leading to activation. 191 matched cddid_all.tbl CDD cd00880 cd00880 206646 Era_like E. coli Ras-like protein (Era)-like GTPase. The Era (E. coli Ras-like protein)-like family includes several distinct subfamilies (TrmE/ThdF, FeoB, YihA (EngB), Era, and EngA/YfgK) that generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. TrmE is ubiquitous in bacteria and is a widespread mitochondrial protein in eukaryotes, but is absent from archaea. The yeast member of TrmE family, MSS1, is involved in mitochondrial translation; bacterial members are often present in translation-related operons. FeoB represents an unusual adaptation of GTPases for high-affinity iron (II) transport. YihA (EngB) family of GTPases is typified by the E. coli YihA, which is an essential protein involved in cell division control. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain. EngA and its orthologs are composed of two GTPase domains and, since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. 161 matched cddid_all.tbl CDD cd00881 cd00881 206647 GTP_translation_factor GTP translation factor family primarily contains translation initiation, elongation and release factors. The GTP translation factor family consists primarily of translation initiation, elongation, and release factors, which play specific roles in protein translation. In addition, the family includes Snu114p, a component of the U5 small nuclear riboprotein particle which is a component of the spliceosome and is involved in excision of introns, TetM, a tetracycline resistance gene that protects the ribosome from tetracycline binding, and the unusual subfamily CysN/ATPS, which has an unrelated function (ATP sulfurylase) acquired through lateral transfer of the EF1-alpha gene and development of a new function. 183 matched cddid_all.tbl CDD cd00882 cd00882 206648 Ras_like_GTPase Rat sarcoma (Ras)-like superfamily of small guanosine triphosphatases (GTPases). Ras-like GTPase superfamily. The Ras-like superfamily of small GTPases consists of several families with an extremely high degree of structural and functional similarity. The Ras superfamily is divided into at least four families in eukaryotes: the Ras, Rho, Rab, and Sar1/Arf families. This superfamily also includes proteins like the GTP translation factors, Era-like GTPases, and G-alpha chain of the heterotrimeric G proteins. Members of the Ras superfamily regulate a wide variety of cellular functions: the Ras family regulates gene expression, the Rho family regulates cytoskeletal reorganization and gene expression, the Rab and Sar1/Arf families regulate vesicle trafficking, and the Ran family regulates nucleocytoplasmic transport and microtubule organization. The GTP translation factor family regulates initiation, elongation, termination, and release in translation, and the Era-like GTPase family regulates cell division, sporulation, and DNA replication. Members of the Ras superfamily are identified by the GTP binding site, which is made up of five characteristic sequence motifs, and the switch I and switch II regions. 161 matched cddid_all.tbl CDD cd00883 cd00883 238448 beta_CA_cladeA Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. CAs are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionarily distinct families of CAs (the alpha-, beta-, and gamma-CAs) which show no significant sequence identity or structural similarity. Within the beta-CA family there are four evolutionarily distinct clades (A through D). The beta-CAs are multimeric enzymes (forming dimers,tetramers,hexamers and octamers) which are present in higher plants, algae, fungi, archaea and prokaryotes. 182 matched cddid_all.tbl CDD cd00884 cd00884 238449 beta_CA_cladeB Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. CAs are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionarily distinct families of CAs (the alpha-, beta-, and gamma-CAs) which show no significant sequence identity or structural similarity. Within the beta-CA family there are four evolutionarily distinct clades (A through D). The beta-CAs are multimeric enzymes (forming dimers,tetramers,hexamers and octamers) which are present in higher plants, algae, fungi, archaea and prokaryotes. 190 matched cddid_all.tbl CDD cd00885 cd00885 238450 cinA Competence-damaged protein. CinA is the first gene in the competence- inducible (cin) operon and is thought to be specifically required at some stage in the process of transformation. This domain is closely related to a domain, found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, where the domain is presumed to bind molybdopterin. 170 matched cddid_all.tbl CDD cd00886 cd00886 238451 MogA_MoaB MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea, and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT). MogA, together with MoeA, is responsible for the metal incorporation into MPT, the third step in MoCF biosynthesis. The plant homolog Cnx1 is a MoeA-MogA fusion protein. The mammalian homolog gephyrin is a MogA-MoeA fusion protein, that plays a critical role in postsynaptic anchoring of inhibitory glycine receptors and major GABAa receptor subtypes. In contrast, MoaB shows high similarity to MogA, but little is known about its physiological role. All well studied members of this family form highly stable trimers. 152 matched cddid_all.tbl CDD cd00887 cd00887 238452 MoeA MoeA family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF), an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT). MoeA, together with MoaB, is responsible for the metal incorporation into MPT, the third step in MoCF biosynthesis. The plant homolog Cnx1 is a MoeA-MogA fusion protein. The mammalian homolog gephyrin is a MogA-MoeA fusion protein, that plays a critical role in postsynaptic anchoring of inhibitory glycine receptors and major GABAa receptor subtypes. 394 matched cddid_all.tbl CDD cd00890 cd00890 467470 Prefoldin prefoldin. Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits; the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes, there are two or more paralogous genes encoding each subunit, adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils. 79 matched cddid_all.tbl CDD cd00891 cd00891 270624 PI3Kc Catalytic domain of Phosphoinositide 3-kinase. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class I PI3Ks are the only enzymes capable of converting PtdIns(4,5)P2 to the critical second messenger PtdIns(3,4,5)P3. Class I enzymes are heterodimers and exist in multiple isoforms consisting of one catalytic subunit (out of four isoforms) and one of several regulatory subunits. Class II PI3Ks comprise three catalytic isoforms that do not associate with any regulatory subunits. They selectively use PtdIns as a susbtrate to produce PtsIns(3)P. The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 334 matched cddid_all.tbl CDD cd00892 cd00892 270625 PIKKc_ATR Catalytic domain of Ataxia telangiectasia and Rad3-related proteins. ATR is also referred to as Mei-41 (Drosophila), Esr1/Mec1p (Saccharomyces cerevisiae), Rad3 (Schizosaccharomyces pombe), and FRAP-related protein (human). ATR contains a UME domain of unknown function, a FAT (FRAP, ATM and TRRAP) domain, a catalytic domain, and a FATC domain at the C-terminus. Together with its downstream effector kinase, Chk1, ATR plays a central role in regulating the replication checkpoint. ATR stabilizes replication forks by promoting the association of DNA polymerases with the fork. Preventing fork collapse is essential in preserving genomic integrity. ATR also plays a role in normal cell growth and in response to DNA damage. ATR is a member of the phosphoinositide 3-kinase-related protein kinase (PIKK) subfamily. PIKKs have intrinsic serine/threonine kinase activity and are distinguished from other PKs by their unique catalytic domain, similar to that of lipid PI3K, and their large molecular weight (240-470 kDa). The ATR catalytic domain subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 237 matched cddid_all.tbl CDD cd00893 cd00893 270626 PI4Kc_III Catalytic domain of Type III Phosphoinositide 4-kinase. PI4Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 4-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) to generate PtdIns(4)P, the major precursor in the synthesis of other phosphoinositides including PtdIns(4,5)P2, PtdIns(3,4)P2, and PtdIns(3,4,5)P3. There are two types of PI4Ks, types II and III. Type II PI4Ks lack the characteristic catalytic kinase domain present in PI3Ks and type III PI4Ks, and are excluded from this family. Two isoforms of type III PI4K, alpha and beta, exist in most eukaryotes. The PI4K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 286 matched cddid_all.tbl CDD cd00894 cd00894 270627 PI3Kc_IB_gamma Catalytic domain of Class IB Phosphoinositide 3-kinase gamma. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. PI3Kgamma signaling controls diverse immune and vascular functions including cell recruitment, mast cell activation, platelet aggregation, and smooth muscle contractility. It associates with one of two regulatory subunits, p101 and p84, and is activated by G-protein-coupled receptors (GPCRs) by direct binding to their betagamma subunits. It contains an N-terminal Ras binding domain, a lipid binding C2 domain, a PI3K homology domain of unknown function, and a C-terminal ATP-binding cataytic domain. PI3Ks can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class I PI3Ks are the only enzymes capable of converting PtdIns(4,5)P2 to the critical second messenger PtdIns(3,4,5)P3. Class I enzymes are heterodimers and exist in multiple isoforms consisting of one catalytic subunit (out of four isoforms) and one of several regulatory subunits. They are further classified into class IA (alpha, beta and delta) and IB (gamma). The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 367 matched cddid_all.tbl CDD cd00895 cd00895 119421 PI3Kc_C2_beta Catalytic domain of Class II Phosphoinositide 3-kinase beta. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. The class II beta isoform, PI3K-C2beta, contributes to the migration and survival of cancer cells. It regulates Rac activity and impacts membrane ruffling, cell motility, and cadherin-mediated cell-cell adhesion. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class II PI3Ks preferentially use PtdIns as a substrate to produce PtdIns(3)P, but can also phosphorylate PtdIns(4)P. They function as monomers and do not associate with any regulatory subunits. Class II enzymes contain an N-terminal Ras binding domain, a lipid binding C2 domain, a PI3K homology domain of unknown function, an ATP-binding cataytic domain, a Phox homology (PX) domain, and a second C2 domain at the C-terminus. The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 354 matched cddid_all.tbl CDD cd00896 cd00896 270628 PI3Kc_III Catalytic domain of Class III Phosphoinositide 3-kinase. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. Class III PI3Ks, also called Vps34 (vacuolar protein sorting 34), contain an N-terminal lipid binding C2 domain, a PI3K homology domain of unknown function, and a C-terminal ATP-binding cataytic domain. They phosphorylate only the substrate PtdIns. They interact with a regulatory subunit, Vps15, to form a membrane-associated complex. Class III PI3Ks are involved in protein and vesicular trafficking and sorting, autophagy, trimeric G-protein signaling, and phagocytosis. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 346 matched cddid_all.tbl CDD cd00897 cd00897 132998 UGPase_euk Eukaryotic UGPase catalyses the synthesis of UDP-Glucose. UGPase (UDP-Glucose Pyrophosphorylase) catalyzes the reversible production of UDP-Glucose and pyrophosphate (PPi) from Glucose-1-phosphate and UTP. UDP-glucose plays pivotal roles in galactose utilization, in glycogen synthesis, and in the synthesis of the carbohydrate moieties of glycolipids, glycoproteins, and proteoglycans. UGPase is found in both prokaryotes and eukaryotes. Interestingly, while the prokaryotic and eukaryotic forms of UGPase catalyze the same reaction, they share low sequence similarity. This family consists of mainly eukaryotic UTP-glucose-1-phosphate uridylyltransferases. 300 matched cddid_all.tbl CDD cd00899 cd00899 132999 b4GalT Beta-4-Galactosyltransferase is involved in the formation of the poly-N-acetyllactosamine core structures present in glycoproteins and glycosphingolipids. Beta-4-Galactosyltransferase transfers galactose from uridine diphosphogalactose to the terminal beta-N-acetylglucosamine residues, hereby forming the poly-N-acetyllactosamine core structures present in glycoproteins and glycosphingolipids. At least seven homologous beta-4-galactosyltransferase isoforms have been identified that use different types of glycoproteins and glycolipids as substrates. Of the seven identified members of the beta-1,4-galactosyltransferase subfamily (beta1,4-Gal-T1 to -T7), b1,4-Gal-T1 is most characterized (biochemically). It is a Golgi-resident type II membrane enzyme with a cytoplasmic domain, membrane spanning region, and a stem region and catalytic domain facing the lumen. 219 matched cddid_all.tbl CDD cd00900 cd00900 275390 PH-like Pleckstrin homology-like domain. The PH-like family includes the PH domain, both the Shc-like and IRS-like PTB domains, the ran-binding domain, the EVH1 domain, a domain in neurobeachin and the third domain of FERM. All of these domains have a PH fold, but lack significant sequence similarity. They are generally involved in targeting to protein to the appropriate cellular location or interacting with a binding partner. This domain family possesses multiple functions including the ability to bind inositol phosphates and to other proteins. 89 matched cddid_all.tbl CDD cd00904 cd00904 153098 Ferritin Ferritin iron storage proteins. Ferritins are the primary iron storage proteins of most living organisms and members of a broad superfamily of ferritin-like diiron-carboxylate proteins. The iron-free (apoferritin) ferritin molecule is a protein shell composed of 24 protein chains arranged in 432 symmetry. Iron storage involves the uptake of iron (II) at the protein shell, its oxidation by molecular oxygen at the dinuclear ferroxidase centers, and the movement of iron (III) into the cavity for deposition as ferrihydrite; the protein shell can hold up to 4500 iron atoms. In vertebrates, two types of chains (subunits) have been characterized, H or M (fast) and L (slow), which differ in rates of iron uptake and mineralization. Bacterial non-heme ferritins are composed only of H chains. Fe(II) oxidation in the H/M subunits take place initially at the ferroxidase center, a carboxylate-bridged diiron center, located within the subunit four-helix bundle. In a complementary role, negatively charged residues on the protein shell inner surface of the L subunits promote ferrihydrite nucleation. Most plant ferritins combine both oxidase and nucleation functions in one chain: they have four interior glutamate residues as well as seven ferroxidase center residues. 160 matched cddid_all.tbl CDD cd00907 cd00907 153099 Bacterioferritin Bacterioferritin, ferritin-like diiron-binding domain. Bacterioferritins, also known as cytochrome b1, are members of a broad superfamily of ferritin-like diiron-carboxylate proteins. Similar to ferritin in architecture, Bfr forms an oligomer of 24 subunits that assembles to form a hollow sphere with 432 symmetry. Up to 12 heme cofactor groups (iron protoporphyrin IX or coproporphyrin III) are bound between dimer pairs. The role of the heme is unknown, although it may be involved in mediating iron-core reduction and iron release. Each subunit is composed of a four-helix bundle which carries a diiron ferroxidase center; it is here that initial oxidation of ferrous iron by molecular oxygen occurs, facilitating the detoxification of iron, protection against dioxygen and radical products, and storage of ferric-hydroxyphosphate at the core. Some bacterioferritins are composed of two subunit types, one conferring heme-binding ability (alpha) and the other (beta) bestowing ferroxidase activity. 153 matched cddid_all.tbl CDD cd00912 cd00912 238454 ML The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2 and several proteins of unknown function in plants, animals and fungi. These single-domain proteins form two anti-parallel beta-pleated sheets stabilized by three disulfide bonds and with an accessible central hydrophobic cavity, and are predicted to mediate diverse biological functions through interaction with specific lipids. 127 matched cddid_all.tbl CDD cd00913 cd00913 238455 PCD_DCoH_subfamily_a PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein). 76 matched cddid_all.tbl CDD cd00914 cd00914 238456 PCD_DCoH_subfamily_b PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein). Two DCoH proteins have been identifed in humans: DCoH1 and DCoH2. Mutations in human DCoH1 cause hyperphenylalaninemia. Loss of enzymic activity of DCoH in humans is associated with the depigmentation disorder vitiligo. DCoH1 has been reported to be overexpessed in colon cancer carcinomas and in malignant melanomas. 76 matched cddid_all.tbl CDD cd00915 cd00915 238457 MD-1_MD-2 MD-1 and MD-2 are cofactors required for LPS signaling through cell surface receptors. MD-2 and its binding partner, Toll-like receptor 4 (TLR4), are essential for the innate immune responses of mammalian cells to bacterial lipopolysaccharide (LPS); MD-2 directly binds the lipid A moiety of LPS. The TLR4-like receptor, RP105, which mediates LPS-induced lymphocyte proliferation, interacts with MD-1; MD-1 enhances RP105-mediated LPS-induced growth of B cells. These proteins belong to the ML domain family. 130 matched cddid_all.tbl CDD cd00916 cd00916 238458 Npc2_like Niemann-Pick type C2 (Npc2) is a lysosomal protein in which a mutation in the gene causes a rare form of Niemann-Pick type C disease, an autosomal recessive lipid storage disorder characterized by accumulation of low-density lipoprotein-derived cholesterol in lysosomes. Although Npc2 is known to bind cholesterol, the function of this protein is unknown. These proteins belong to the ML domain family. 123 matched cddid_all.tbl CDD cd00917 cd00917 238459 PG-PI_TP The phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP) has been shown to bind phosphatidylglycerol and phosphatidylinositol, but the biological significance of this is still obscure. These proteins belong to the ML domain family. 122 matched cddid_all.tbl CDD cd00918 cd00918 238460 Der-p2_like Several group 2 allergen proteins belong to the ML domain family. They include Dermatophagoides pteronyssinus, group 2 (Der p 2) and D. farinae, group 2 (Der f 2) allergens. These house dust mites cause heavy atopic diseases such as asthma and dermatitis. Although the allergenic properties of these proteins have been well characterized, their biological function in mites is unknown. 120 matched cddid_all.tbl CDD cd00919 cd00919 238461 Heme_Cu_Oxidase_I Heme-copper oxidase subunit I. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is diverse in terms of electron donors, subunit composition, and heme types. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. It has been proposed that Archaea acquired heme-copper oxidases through gene transfer from Gram-positive bacteria. Membership in the superfamily is defined by subunit I, which contains a heme-copper binuclear center (the active site where O2 is reduced to water) formed by a high-spin heme and a copper ion. It also contains a low-spin heme, believed to participate in the transfer of electrons to the binuclear center. Only subunit I is common to the entire superfamily. For every reduction of an O2 molecule, eight protons are taken from the inside aqueous compartment and four electrons are taken from the electron donor on the opposite side of the membrane. The four electrons and four of the protons are used in the reduction of O2; the four remaining protons are pumped across the membrane. This charge separation of four charges contributes to the electrochemical gradient used for ATP synthesis. Two proton channels, the D-pathway and K-pathway, leading to the binuclear center have been identified in subunit I of cytochrome c oxidase (CcO) and ubiquinol oxidase. A well-defined pathway for the transfer of pumped protons beyond the binuclear center has not been identified. Electron transfer occurs in two segments: from the electron donor to the low-spin heme, and from the low-spin heme to the binuclear center. The first segment can be a multi-step process and varies among the different families, while the second segment, a direct transfer, is consistent throughout the superfamily. 463 matched cddid_all.tbl CDD cd00920 cd00920 259860 Cupredoxin Cupredoxin superfamily. Cupredoxins contain type I copper centers and are involved in inter-molecular electron transfer reactions. Cupredoxins are blue copper proteins, having an intense blue color due to the presence of a mononuclear type 1 (T1) copper site. Structurally, the cupredoxin-like fold consists of a beta-sandwich with 7 strands in 2 beta-sheets, which is arranged in a Greek-key beta-barrel. Some of these proteins have lost the ability to bind copper. The majority of family members contain multiple cupredoxin domain repeats: ceruloplasmin and the coagulation factors V/VIII have six repeats; laccase, ascorbate oxidase, spore coat protein A, and multicopper oxidase CueO contain three repeats; and nitrite reductase has two repeats. Others are mono-domain cupredoxins, such as plastocyanin, pseudoazurin, plantacyanin, azurin, rusticyanin, stellacyanin, quinol oxidase, and the periplasmic domain of cytochrome c oxidase subunit II. 110 matched cddid_all.tbl CDD cd00922 cd00922 238462 Cyt_c_Oxidase_IV Cytochrome c oxidase subunit IV. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit IV is the largest of the nuclear-encoded subunits. It binds ATP at the matrix side, leading to an allosteric inhibition of enzyme activity at high intramitochondrial ATP/ADP ratios. In mammals, subunit IV has a lung-specific isoform and a ubiquitously expressed isoform. 136 matched cddid_all.tbl CDD cd00923 cd00923 238463 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios. 103 matched cddid_all.tbl CDD cd00924 cd00924 238464 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly. 97 matched cddid_all.tbl CDD cd00925 cd00925 238465 Cyt_c_Oxidase_VIa Cytochrome c oxidase subunit VIa. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit VIa is expressed in two tissue-specific isoforms in mammals but not fish. VIa-H is the heart and skeletal muscle isoform; VIa-L is the liver or non-muscle isoform. Mammalian VIa-H induces a slip in CcO (decrease in proton/electron stoichiometry) at high intramitochondrial ATP/ADP ratios, while VIa-L induces a permanent slip in CcO, depending on the presence of cardiolipin and palmitate. 86 matched cddid_all.tbl CDD cd00926 cd00926 238466 Cyt_c_Oxidase_VIb Cytochrome c oxidase subunit VIb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit VIb is one of three mammalian subunits that lacks a transmembrane region. It is located on the cytosolic side of the membrane and helps form the dimer interface with the corresponding subunit on the other monomer complex. 75 matched cddid_all.tbl CDD cd00927 cd00927 438621 CcO_VIc-like Cytochrome c oxidase subunit VIc-like. Cytochrome c oxidase subunit VIc-like proteins are subunits of the cytochrome c oxidase (CcO, also called complex IV or CIV), the terminal oxidase in the mitochondrial electron transport chain which drives oxidative phosphorylation. CcO is a multi-chain transmembrane protein complex located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 14 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 11 subunits are encoded within the nuclear genome. The VIc subunit-like proteins are single-pass membrane proteins found only in eukaryotes and their specific function remains unclear. 50 matched cddid_all.tbl CDD cd00928 cd00928 238468 Cyt_c_Oxidase_VIIa Cytochrome c oxidase subunit VIIa. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit VIIa has two tissue-specific isoforms that are expressed in a developmental manner. VIIa-H is expressed in heart and skeletal muscle but not smooth muscle. VIIa-L is expressed in liver and non-muscle tissues. 55 matched cddid_all.tbl CDD cd00929 cd00929 238469 Cyt_c_Oxidase_VIIc Cytochrome c oxidase subunit VIIc. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. The VIIc subunit is found only in eukaryotes and its specific function remains unclear. Peroxide inactivation of bovine CcO coincides with the direct oxidation of tryptophan (W19) within subunit VIIc, along with other structural changes in other subunits. 46 matched cddid_all.tbl CDD cd00930 cd00930 238470 Cyt_c_Oxidase_VIII Cytochrome oxidase c subunit VIII. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit VIII is the smallest of the nuclear-encoded subunits. It exists in muscle-specific and non-muscle-specific isoforms that are differently expressed in different species, suggesting species-specific regulation of energy metabolism. 43 matched cddid_all.tbl CDD cd00933 cd00933 238471 barnase Barnase, a member of the family of homologous microbial ribonucleases, catalyses the cleavage of single-stranded RNA via a two-step mechanism thought to be similar to that of pancreatic ribonuclease. The mechanism involves a transesterification to give a 2', 3'-cyclic phosphate intermediate, followed by hydrolysis to yield a 3' nucleotide. The active site residues His and Glu act as general acid-base groups during catalysis, while the Arg and Lys residues are important in binding the reactive phosphate, the latter probably binding the phosphate in the transition state. Barstar, a small 89 residue intracellular protein is a natural inhibitor of Barnase. 107 matched cddid_all.tbl CDD cd00934 cd00934 269911 PTB Phosphotyrosine-binding (PTB) PH-like fold. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to bind peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. 120 matched cddid_all.tbl CDD cd00935 cd00935 238472 GlyRS_RNA GlyRS_RNA binding domain. This short RNA-binding domain is found at the N-terminus of GlyRS in several higher eukaryote aminoacyl-tRNA synthetases (aaRSs). This domain consists of a helix-turn-helix structure , which is similar to other RNA-binding proteins. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions, which are important for the formation of aaRSs into multienzyme complexes. 51 matched cddid_all.tbl CDD cd00936 cd00936 238473 WEPRS_RNA WEPRS_RNA binding domain. This short RNA-binding domain is found in several higher eukaryote aminoacyl-tRNA synthetases (aaRSs). It is found in multiple copies in eukaryotic bifunctional glutamyl-prolyl-tRNA synthetases (EPRS) in a region that separates the N-terminal glutamyl-tRNA synthetase (GluRS) from the C-terminal prolyl-tRNA synthetase (ProRS). It is also found at the N-terminus of vertebrate tryptophanyl-tRNA synthetases (TrpRS). This domain consists of a helix-turn-helix structure, which is similar to other RNA-binding proteins. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions, which are important for the formation of aaRSs into multienzyme complexes. 50 matched cddid_all.tbl CDD cd00938 cd00938 238474 HisRS_RNA HisRS_RNA binding domain. This short RNA-binding domain is found at the N-terminus of HisRS in several higher eukaryote aminoacyl-tRNA synthetases (aaRSs). This domain consists of a helix- turn- helix structure, which is similar to other RNA-binding proteins. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions, which are important for the formation of aaRSs into multienzyme complexes. 45 matched cddid_all.tbl CDD cd00939 cd00939 238475 MetRS_RNA MetRS_RNA binding domain. This short RNA-binding domain is found at the C-terminus of MetRS in several higher eukaryote aminoacyl-tRNA synthetases (aaRSs). It is repeated in Drosophila MetRS. This domain consists of a helix-turn-helix structure, which is similar to other RNA-binding proteins. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions, which are important for the formation of aaRSs into multienzyme complexes. 45 matched cddid_all.tbl CDD cd00941 cd00941 411993 FokI_N N-terminal DNA recognition domain of restriction endonuclease FokI and similar proteins. Restriction endonuclease FokI (EC3.1.21.4), also called R.FokI, or endonuclease FokI, is a type IIS restriction enzyme that require only divalent metals (such as Mg2+ or Mn2+) as cofactors to catalyze the hydrolysis of DNA. FokI recognizes the double-stranded sequence 5'-GGATG-3'/3'-CATCC-5' and cleaves 14 bases after G-1 and 13 bases before C-1, respectively. It contains an N-terminal DNA recognition domain and a C-terminal endonuclease domain. This model describes the DNA recognition domain. The family also includes endonuclease StsI, a type IIS restriction endonuclease found in Streptococcus sanguinis 54. It recognizes the same sequence as FokI but cleaves at different positions. 373 matched cddid_all.tbl CDD cd00942 cd00942 411705 BamHI-like Restriction endonuclease BamHI and similar proteins. Restriction endonuclease BamHI (EC 3.1.21.4), also termed R.BamHI, or endonuclease BamHI, is a type II restriction enzyme that require only divalent metals (such as Mg2+ or Mn2+) as cofactors to catalyze the hydrolysis of DNA. BamHI recognizes the double-stranded sequence GGATCC and cleaves after G-1. It shows striking resemblance to the structure of EcoRI, but lacks sequence similarity between them. The family also includes a BamHI isoschizomer, OkrAI endonuclease, which recognizes and cleaves the same DNA sequence (TATGGATCCATA) as BamHI. However, OkrAI does not have the equivalent of N- and C-terminal helices of BamHI, and it has higher star activity compared to BamHI. 196 matched cddid_all.tbl CDD cd00943 cd00943 411706 EcoRI-like "Restriction endonuclease EcoRI and similar proteins. Restriction endonuclease EcoRI (EC 3.1.21.4), also termed R.EcoRI, or endonuclease EcoRI, is a type II restriction enzyme that require only divalent metals (such as Mg2+ or Mn2+) as cofactors to catalyze the hydrolysis of DNA. EcoRI recognizes the double-stranded sequence GAATTC and cleaves after G-1. The family also includes an EcoRI isoschizomer, RsrI endonuclease, which also catalyzes the cleavage of duplex DNA and oligodeoxyribonucleotides between the first two residues of the sequence GAATTC. RsrI differs from EcoRI in its N-terminal amino acid sequence, susceptibility to inhibition by antibodies, sensitivity to N-ethylmaleimide, isoelectric point, state of aggregation at high concentrations, temperature lability, and conditions for optimal reaction. It displays a reduction of specificity (""star activity"") under conditions that also relax the specificity of EcoRI." 254 matched cddid_all.tbl CDD cd00945 cd00945 188634 Aldolase_Class_I Class I aldolases. Class I aldolases. The class I aldolases use an active-site lysine which stabilizes a reaction intermediates via Schiff base formation, and have TIM beta/alpha barrel fold. The members of this family include 2-keto-3-deoxy-6-phosphogluconate (KDPG) and 2-keto-4-hydroxyglutarate (KHG) aldolases, transaldolase, dihydrodipicolinate synthase sub-family, Type I 3-dehydroquinate dehydratase, DeoC and DhnA proteins, and metal-independent fructose-1,6-bisphosphate aldolase. Although structurally similar, the class II aldolases use a different mechanism and are believed to have an independent evolutionary origin. 201 matched cddid_all.tbl CDD cd00946 cd00946 238476 FBP_aldolase_IIA Class II Type A, Fructose-1,6-bisphosphate (FBP) aldolases. The enzyme catalyses the zinc-dependent, reversible aldol condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to form fructose-1,6-bisphosphate. FBP aldolase is homodimeric and used in gluconeogenesis and glycolysis. The type A and type B Class II FBPA's differ in the presence and absence of distinct indels in the sequence that result in differing loop lengths in the structures. 345 matched cddid_all.tbl CDD cd00947 cd00947 238477 TBP_aldolase_IIB Tagatose-1,6-bisphosphate (TBP) aldolase and related Type B Class II aldolases. TBP aldolase is a tetrameric class II aldolase that catalyzes the reversible condensation of dihydroxyacetone phosphate with glyceraldehyde 3-phsophate to produce tagatose 1,6-bisphosphate. There is an absolute requirement for a divalent metal ion, usually zinc, and in addition the enzymes are activated by monovalent cations such as Na+. The type A and type B Class II FBPA's differ in the presence and absence of distinct indels in the sequence that result in differing loop lengths in the structures. 276 matched cddid_all.tbl CDD cd00948 cd00948 188635 FBP_aldolase_I_a Fructose-1,6-bisphosphate aldolase. Fructose-1,6-bisphosphate aldolase. The enzyme catalyzes the cleavage of fructose 1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). This family includes proteins found in vertebrates, plants, and bacterial plant pathogens. Mutations in the aldolase genes in humans cause hemolytic anemia and hereditary fructose intolerance. The enzyme is a member of the class I aldolase family, which utilizes covalent catalysis through a Schiff base formed between a lysine residue of the enzyme and ketose substrates. 330 matched cddid_all.tbl CDD cd00949 cd00949 188636 FBP_aldolase_I_bact Fructose-1.6-bisphosphate aldolase found in gram +/- bacteria. Fructose-1.6-bisphosphate aldolase found in gram +/- bacteria. The enzyme catalyzes the cleavage of fructose 1,6-bisphosphate to glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). The enzyme is member of the class I aldolase family, which utilizes covalent catalysis through a Schiff base formed between a lysine residue of the enzyme and ketose substrates. 292 matched cddid_all.tbl CDD cd00950 cd00950 188637 DHDPS Dihydrodipicolinate synthase (DHDPS). Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways. 284 matched cddid_all.tbl CDD cd00951 cd00951 188638 KDGDH 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH). 5-dehydro-4-deoxyglucarate dehydratase, also called 5-keto-4-deoxy-glucarate dehydratase (KDGDH), which is member of dihydrodipicolinate synthase (DHDPS) family that comprises several pyruvate-dependent class I aldolases. The enzyme is involved in glucarate metabolism, and its mechanism presumbly involves a Schiff-base intermediate similar to members of DHDPS family. While in the case of Pseudomonas sp. 5-dehydro-4-deoxy-D-glucarate is degraded by KDGDH to 2,5-dioxopentanoate, in certain species of Enterobacteriaceae it is degraded instead to pyruvate and glycerate. 289 matched cddid_all.tbl CDD cd00952 cd00952 188639 CHBPH_aldolase Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase (HBPHA) and trans-2'-carboxybenzalpyruvate hydratase-aldolase (CBPHA). Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase (HBPHA) and trans-2'-carboxybenzalpyruvate hydratase-aldolase (CBPHA). HBPHA catalyzes HBP to salicyaldehyde and pyruvate. This reaction is part of the degradative pathways for naphthalene and naphthalenesulfonates by bacteria. CBPHA is homologous to HBPHA and catalyzes the cleavage of CBP to 2-carboxylbenzaldehyde and pyruvate during the degradation of phenanthrene. They are member of the DHDPS family of Schiff-base-dependent class I aldolases. 309 matched cddid_all.tbl CDD cd00953 cd00953 188640 KDG_aldolase KDG (2-keto-3-deoxygluconate) aldolases found in archaea. KDG (2-keto-3-deoxygluconate) aldolases found in archaea. This subfamily of enzymes is adapted for high thermostability and shows specificity for non-phosphorylated substrates. The enzyme catalyses the reversible aldol cleavage of 2-keto-3-dexoygluconate to pyruvate and glyceraldehyde, the third step of a modified non-phosphorylated Entner-Doudoroff pathway of glucose oxidation. KDG aldolase shows no significant sequence similarity to microbial 2-keto-3-deoxyphosphogluconate (KDPG) aldolases, and the enzyme shows no activity with glyceraldehyde 3-phosphate as substrate. The enzyme is a tetramer and a member of the DHDPS family of Schiff-base-dependent class I aldolases. 279 matched cddid_all.tbl CDD cd00954 cd00954 188641 NAL N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL). N-Acetylneuraminic acid aldolase, also called N-acetylneuraminate lyase (NAL), which catalyses the reversible aldol reaction of N-acetyl-D-mannosamine and pyruvate to give N-acetyl-D-neuraminic acid (D-sialic acid). It has a widespread application as biocatalyst for the synthesis of sialic acid and its derivatives. This enzyme has been shown to be quite specific for pyruvate as the donor, but flexible to a variety of D- and, to some extent, L-hexoses and pentoses as acceptor substrates. NAL is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases. 288 matched cddid_all.tbl CDD cd00955 cd00955 188642 Transaldolase_like Transaldolase-like proteins from plants and bacteria. Transaldolase-like proteins from plants and bacteria. Transaldolase is found in the non-oxidative branch of the pentose phosphate pathway, that catalyze the reversible transfer of a dihydroxyacetone group from fructose-6-phosphate to erythrose-4-phosphate yielding sedoheptulose-7-phosphate and glyceraldehyde-3-phosphate. They are members of the class I aldolases, who are characterized by using a Schiff-base mechanism for stabilization of the reaction intermediates. 338 matched cddid_all.tbl CDD cd00956 cd00956 188643 Transaldolase_FSA Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea. Transaldolase-like fructose-6-phosphate aldolases (FSA) found in bacteria and archaea, which are member of the MipB/TalC subfamily of class I aldolases. FSA catalyze an aldol cleavage of fructose 6-phosphate and do not utilize fructose, fructose 1-phosphate, fructose 1,6-phosphate, or dihydroxyacetone phosphate. The enzymes belong to the transaldolase family that serves in transfer reactions in the pentose phosphate cycle, and are more distantly related to fructose 1,6-bisphosphate aldolase. 211 matched cddid_all.tbl CDD cd00957 cd00957 188644 Transaldolase_TalAB Transaldolases including both TalA and TalB. Transaldolases including both TalA and TalB. The enzyme catalyses the reversible transfer of a dyhydroxyacetone moiety, derived from fructose-6-phosphate to erythrose-4-phosphate yielding sedoheptulose-7-phosphate and glyceraldehyde-3-phosphate. The catalytic mechanism is similar to other class I aldolases. The enzyme is found in the non-oxidative branch of the pentose phosphate pathway and forms a dimer in solution. 313 matched cddid_all.tbl CDD cd00958 cd00958 188645 DhnA Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs). Class I fructose-1,6-bisphosphate (FBP) aldolases of the archaeal type (DhnA homologs) found in bacteria and archaea. Catalysis of the enzymes proceeds via a Schiff-base mechanism like other class I aldolases, although this subfamily is clearly divergent based on sequence similarity to other class I and class II (metal dependent) aldolase subfamilies. 235 matched cddid_all.tbl CDD cd00959 cd00959 188646 DeoC 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family. 2-deoxyribose-5-phosphate aldolase (DERA) of the DeoC family. DERA belongs to the class I aldolases and catalyzes a reversible aldol reaction between acetaldehyde and glyceraldehyde 3-phosphate to generate 2-deoxyribose 5-phosphate. DERA is unique in catalyzing the aldol reaction between two aldehydes, and its broad substrate specificity confers considerable utility as a biocatalyst, offering an environmentally benign alternative to chiral transition metal catalysis of the asymmetric aldol reaction. 203 matched cddid_all.tbl CDD cd00974 cd00974 238478 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)]. 34 matched cddid_all.tbl CDD cd00978 cd00978 381600 chitosanase_GH46 chitosanase belonging to the glycosyl hydrolase 46 family. This family is composed of the chitosanase enzymes which hydrolyzes chitosan, a biopolymer of beta (1,4)-linked-D-glucosamine (GlcN) residues produced by partial or full deacetylation of chitin. Chitosanases play a role in defense against pathogens such as fungi and are found in microorganisms, fungi, viruses, and plants. Microbial chitosanases can be divided into 3 subclasses based on the specificity of the cleavage positions for partial acetylated chitosan. Subclass I chitosanases such as N174 can split GlcN-GlcN and GlcNAc-GlcN linkages, whereas subclass II chitosanases such as Bacillus sp. no. 7-M can cleave only GlcN-GlcN linkages. Subclass III chitosanases such as MH-K1 chitosanase are the most versatile and can split both GlcN-GlcN and GlcN-GlcNAc linkages. 222 matched cddid_all.tbl CDD cd00980 cd00980 238480 FwdC/FmdC FwdC/FmdC. This domain of unknown function is found in the subunit C of formylmethanofuran dehydrogenase, an enzyme that catalyzes the first step in methane formation from CO2 in methanogenic archaea, hyperthermophiles and bacteria. There are two isoenzymes, a tungsten-containing isoenzyme (Fwd) and a molybdenum-containing isoenzyme (Fmd). The subunits C of both isoenzymes (FwdC/FmdC) are characterized by a repeated GXXGXXXG motif. 203 matched cddid_all.tbl CDD cd00981 cd00981 238481 arch_gltB Archaeal-type gltB domain. This domain shares sequence similarity with a region of unknown function found in the large subunit of glutamate synthase, which is encoded by gltB and found in most bacteria and eukaryotes. It is predicted to be homologous to the C-terminal domain of glutamate synthase based upon sequence similarity coupled with genome organization data, showing that this domain is found in a gene cluster with other domains of Glts, which are annotated. This domain is found primarily in archaea, but is also present in a few bacteria, likely as a result of lateral gene transfer. 232 matched cddid_all.tbl CDD cd00982 cd00982 238482 gltB_C gltb_C. This domain is found at the C-terminus of the large subunit (gltB) of glutamate synthase (GltS). GltS encodes a complex iron-sulfur flavoprotein that catalyzes the synthesis of L-glutamate from L-glutamine and 2-oxoglutarate. It requires the transfer of ammonia and electrons among three distinct active centers that carry out L-Gln hydrolysis, conversion of 2-oxoglutarate into L-Glu, and electron uptake from a donor. These catalytic sites appear to occur in other domains within the protein, and not the domain in this CD. This particular domain has no known function, but it likely has a structural role as it interacts with the amidotransferase and FMN-binding domains of gltS. 251 matched cddid_all.tbl CDD cd00983 cd00983 410863 RecA recombinase A. RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange. 235 matched cddid_all.tbl CDD cd00984 cd00984 410864 DnaB_C C-terminal domain of DnaB helicase. DnaB helicase C-terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. 256 matched cddid_all.tbl CDD cd00985 cd00985 238485 Maf_Ham1 Maf_Ham1. Maf, a nucleotide binding protein, has been implicated in inhibition of septum formation in eukaryotes, bacteria and archaea. A Ham1-related protein from Methanococcus jannaschii is a novel NTPase that has been shown to hydrolyze nonstandard nucleotides, such as hypoxanthine/xanthine NTP, but not standard nucleotides. 131 matched cddid_all.tbl CDD cd00990 cd00990 467618 cpPDZ_AtDEGP1-like circularly permuted PDZ domain of Arabidopsis thaliana DEGP1, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Arabidopsis thaliana DEGP1 (also known as protease Do-like 1, chloroplastic, protein DEGRADATION OF PERIPLASMIC PROTEINS 1, DEGP PROTEASE 1 and DEG1), and related domains. DEGP1 is a serine protease that is required at high temperature and may be involved in the degradation of damaged proteins. This family also includes Arabidopsis protease DEGP8/Do-like 8 (chloroplastic), a probable serine protease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This AtDEGP-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus. 102 matched cddid_all.tbl CDD cd00993 cd00993 270215 PBP2_ModA_like Substrate binding domain of molybdate-binding proteins, the type 2 periplasmic binding protein fold. Molybdate binding domain ModA. Molybdate transport system is comprised of a periplasmic binding protein, an integral membrane protein, and an energizer protein. These three proteins are coded by modA, modB, and modC genes, respectively. ModA proteins serve as initial receptors in the ABC transport of molybdate mostly in eubacteria and archaea. Bacteria and archaea import molybdenum and tungsten from the environment in the form of the oxyanions molybdate (MoO(4) (2-)) and tungstate (WO(4) (2-)). After binding molybdate with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. In contrast to the structure of the two ModA homologs from Escherichia coli and Azotobacter vinelandii, where the oxygen atoms are tetrahedrally arranged around the metal center, the structure of Pyrococcus furiosus ModA/WtpA (PfModA) has revealed a binding site for molybdate and tungstate where the central metal atom is in a hexacoordinate configuration. This octahedral geometry was rather unexpected. The ModA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 225 matched cddid_all.tbl CDD cd00994 cd00994 270216 PBP2_GlnH Glutamine binding domain of ABC-type transporter; the type 2 periplasmic binding protein fold. This periplasmic substrate-binding component serves as an initial receptor in the ABC transport of glutamine in bacteria and eukaryota. GlnH belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 218 matched cddid_all.tbl CDD cd00995 cd00995 173853 PBP2_NikA_DppA_OppA_like The substrate-binding domain of an ABC-type nickel/oligopeptide-like import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel/dipeptide/oligopeptide transport systems, which function in the import of nickel and peptides, and other closely related proteins. The oligopeptide-binding protein OppA is a periplasmic component of an ATP-binding cassette (ABC) transport system OppABCDEF consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Similar to the ABC-type dipeptide and oligopeptide import systems, nickel transporter is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, which is the initial nickel receptor that controls the chemotactic response away from nickel. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand binding domains of ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 466 matched cddid_all.tbl CDD cd00996 cd00996 270217 PBP2_AatB_like Polar amino acids-binding domain of ATP-binding cassette transporter-like systems that belong to the type 2 periplasmic binding fold protein superfamily. This subfamily includes periplasmic binding domain of ATP-binding cassette transporter-like systems that serve as initial receptors in the ABC transport of amino acids and their derivatives in eubacteria. After binding their ligand with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically-located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The Abp proteins belong to the PBPI superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 227 matched cddid_all.tbl CDD cd00997 cd00997 270218 PBP2_GluR0 Bacterial GluR0 ligand-binding domain; the type 2 periplasmic binding protein fold. Glutamate receptor domain GluR0. These domains are found in the GluR0 proteins that have been shown to function as prokaryotic L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. The GluR0 proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 218 matched cddid_all.tbl CDD cd00998 cd00998 270219 PBP2_iGluR_ligand_binding The ligand-binding domain of ionotropic glutamate receptor family, a member of the periplasmic binding protein type II superfamily. This subfamily represents the ligand binding of ionotropic glutamate receptors. iGluRs are heterotetrameric ion channels that comprises of three functionally distinct subtypes based on their pharmacology and structural similarities: AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid), NMDA (N-methyl-D-aspartate), and kainate receptors. All three types of channels are also activated by the physiological neurotransmitter, glutamate. iGluRs are concentrated at postsynaptic sites, where they exert a variety of different functions. While this ligand-binding domain of iGluRs is structurally homologous to the periplasmic binding fold type II superfamily, the N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain belongs to the periplasmic-binding fold type I. 243 matched cddid_all.tbl CDD cd00999 cd00999 270220 PBP2_ArtJ The solute binding domain of ArtJ protein, a member of the type 2 periplasmic binding fold protein superfamily. An arginine-binding protein found in Chlamydiae trachomatis (CT-ArtJ) and pneumoniae (CPn-ArtJ) and its closely related proteins. CT- and CPn-ArtJ are shown to have different immunogenic properties despite a high sequence similarity. The ArtJ proteins display the type 2 periplasmic binding fold organized in two alpha-beta domains with arginine-binding region at their interface. 223 matched cddid_all.tbl CDD cd01000 cd01000 270221 PBP2_Cys_DEBP_like Substrate-binding domain of cysteine- and aspartate/glutamate-binding proteins; the type 2 periplasmic-binding protein fold. This family comprises of the periplasmic-binding protein component of ABC transporters specific for cysteine and carboxylic amino acids, as well as their closely related proteins. The cysteine and aspartate-glutamate binding domains belong to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 228 matched cddid_all.tbl CDD cd01001 cd01001 270222 PBP2_HisJ_LAO_like Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporters and related proteins; the type 2 periplasmic-binding protein fold. This family comprises the periplasmic substrate-binding proteins, including the lysine-, arginine-, ornithine-binding protein (LAO) and the histidine-binding protein (HisJ), which serve as initial receptors for active transport. HisJ and LAO proteins belong to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 228 matched cddid_all.tbl CDD cd01002 cd01002 270223 PBP2_Ehub_like Substrate binding domain of ectoine/hydroxyectoine specific ABC transport system; the type 2 periplasmic binding protein fold. This family represents the periplasmic substrate-binding component of ABC transport systems that involved in uptake of osmoprotectants (also termed compatible solutes) such as ectoine and hydroxyectoine. To counteract the efflux of water, bacteria and archaea accumulate the compatible solutes for a sustained adjustment to high osmolarity surroundings. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 242 matched cddid_all.tbl CDD cd01003 cd01003 270224 PBP2_YckB Substrate binding domain of an ABC cystine transporter; the type 2 periplasmic binding protein fold. Periplasmic cystine-binding domain (YckB) of an ATP-binding cassette (ABC) transporter from Bacillus subtilis and its related proteins. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Likewise, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 229 matched cddid_all.tbl CDD cd01004 cd01004 270225 PBP2_MidA_like Mimosine binding domain of ABC-type transporter MidA and similar proteins; the type 2 periplasmic binding protein fold. This subgroup includes the periplasmic binding component of ABC transporter involved in uptake of mimosine MidA and its similar proteins. This periplasmic binding domain belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 230 matched cddid_all.tbl CDD cd01005 cd01005 270226 PBP2_CysP Substrate binding domain of an active sulfate transporter, a member of the type 2 periplasmic binding fold superfamily. This family contains sulfate binding domain of CysP proteins that serve as initial receptors in the ABC transport of sulfate and thiosulfate in eubacteria. After binding the ligand, CysP interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The CysP proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 307 matched cddid_all.tbl CDD cd01006 cd01006 270227 PBP2_phosphate_binding Substrate binding domain of ABC-type phosphate transporter, a member of the type 2 periplasmic-binding fold superfamily. This phosphate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 253 matched cddid_all.tbl CDD cd01007 cd01007 270228 PBP2_BvgS_HisK_like The type 2 periplasmic ligand-binding protein domain of the sensor-kinase BvgS and histidine kinase receptors, and related proteins. This family comprises the periplasmic sensor domain of the two-component sensor-kinase systems, such as the sensor protein BvgS of Bordetella pertussis and histidine kinase receptors (HisK), and uncharacterized related proteins. Typically, the two-component system consists of a membrane spanning sensor-kinase and a cytoplasmic response regulator. It serves as a stimulus-response coupling mechanism to enable microorganisms to sense and respond to changes in environmental conditions. The N-terminal sensing domain of the sensor kinase detects extracellular signals, such as small molecule ligands and ions, which then modulate the catalytic activity of the cytoplasmic kinase domain through a phosphorylation cascade. The periplasmic sensor domain belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 220 matched cddid_all.tbl CDD cd01008 cd01008 270229 PBP2_NrtA_SsuA_CpmA_like Substrate binding domain of ABC-type nitrate/sulfonate/bicarbonate transporters, a member of the type 2 periplasmic binding fold superfamily. This family represents the periplasmic binding proteins involved in nitrate, alkanesulfonate, and bicarbonate transport. These domains are found in eubacterial perisplamic-binding proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates. Other closest homologs involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB) are also included in this family. After binding their ligand with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. These binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 212 matched cddid_all.tbl CDD cd01009 cd01009 270230 PBP2_YfhD_N The solute binding domain of YfhD proteins, a member of the type 2 periplasmic binding fold protein superfamily. This subfamily includes the solute binding domain YfhD_N. These domains are found in the YfhD proteins that are predicted to function as lytic transglycosylases that cleave the glycosidic bond between N-acetylmuramic acid and N-acetylglucosamin in peptidoglycan, while the YfhD_N domain might act as an auxiliary or regulatory subunit. In addition to periplasmic solute binding domain, they have an SLT domain, typically found in soluble lytic transglycosylases, and a C-terminal low complexity domain. The YfhD proteins might have been recruited to create localized cell wall openings required for transport of large substrates such as DNA. They belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 223 matched cddid_all.tbl CDD cd01011 cd01011 238493 nicotinamidase Nicotinamidase/pyrazinamidase (PZase). Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is also called pyrazinamidase, because in converts the tuberculosis drug pyrazinamide (PZA) into its active form pyrazinoic acid (POA). 196 matched cddid_all.tbl CDD cd01012 cd01012 238494 YcaC_related YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them. Multimerisation interface seems not to be conserved in all members. 157 matched cddid_all.tbl CDD cd01013 cd01013 238495 isochorismatase Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase, catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of a vinyl ether, an uncommon reaction in biological systems. Isochorismatase is part of the phenazine biosynthesis pathway. Phenazines are antimicrobial compounds that provide the competitive advantage for certain bacteria. 203 matched cddid_all.tbl CDD cd01014 cd01014 238496 nicotinamidase_related Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia. 155 matched cddid_all.tbl CDD cd01015 cd01015 238497 CSHase N-carbamoylsarcosine amidohydrolase (CSHase) hydrolyzes N-carbamoylsarcosine to sarcosine, carbon dioxide and ammonia. CSHase is involved in one of the two alternative pathways for creatinine degradation to glycine in microorganisms.This CSHase-containing pathway degrades creatinine via N-methylhydantoin N-carbamoylsarcosine and sarcosine to glycine. Enzymes of this pathway are used in the diagnosis for renal disfunction, for determining creatinine levels in urine and serum. 179 matched cddid_all.tbl CDD cd01016 cd01016 238498 TroA Metal binding protein TroA. These proteins have been shown to function as initial receptors in ABC transport of Zn2+ and possibly Fe3+ in many eubacterial species. The TroA proteins belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence). 276 matched cddid_all.tbl CDD cd01017 cd01017 238499 AdcA Metal binding protein AdcA. These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion. The AdcA proteins belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and they bind their ligand in the cleft between these domains. In addition, many of these proteins have a low complexity region containing metal binding histidine-rich motif (repetitive HDH sequence). 282 matched cddid_all.tbl CDD cd01018 cd01018 238500 ZntC Metal binding protein ZntC. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and bind their specific ligands in the cleft between these domains. In addition, many of these proteins possess a metal-binding histidine-rich motif (repetitive HDH sequence). 266 matched cddid_all.tbl CDD cd01019 cd01019 238501 ZnuA Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a single helix and bind their specific ligands in the cleft between these domains. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence). 286 matched cddid_all.tbl CDD cd01020 cd01020 238502 TroA_b Metal binding protein TroA_b. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence). 264 matched cddid_all.tbl CDD cd01021 cd01021 381601 GEWL Goose egg-white lysozyme. Eukaryotic goose-type or G-type lysozyme (goose egg-white lysozyme; GEWL) catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc). Mammals have two lysozymes. This family corresponds to human and mouse lysozyme G-like protein 2. 174 matched cddid_all.tbl CDD cd01022 cd01022 212096 GH57N_like N-terminal catalytic domain of heat stable retaining glycoside hydrolase family 57. Glycoside hydrolase family 57(GH57) is a chiefly prokaryotic family with the majority of thermostable enzymes coming from extremophiles (many of these are archaeal hyperthermophiles), which exhibit the enzyme specificities of alpha-amylase (EC 3.2.1.1), 4-alpha-glucanotransferase (EC 2.4.1.25), amylopullulanase (EC 3.2.1.1/41), and alpha-galactosidase (EC 3.2.1.22). This family also includes many hypothetical proteins with uncharacterized activity and specificity. GH57s cleave alpha-glycosidic bonds by employing a retaining mechanism, which involves a glycosyl-enzyme intermediate, allowing transglycosylation. 313 matched cddid_all.tbl CDD cd01025 cd01025 173775 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). In RecR sequences this glutamate in the first turn of the TOPRIM domain is semiconserved, the DXD motif is not conserved. 112 matched cddid_all.tbl CDD cd01026 cd01026 173776 TOPRIM_OLD TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as RNase activity, consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain; the nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. Functional details on OLD are scant and further experimentation is required to define the relationship between the ATPase and Toprim nuclease domains. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. 97 matched cddid_all.tbl CDD cd01027 cd01027 173777 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. 81 matched cddid_all.tbl CDD cd01028 cd01028 173778 TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. 142 matched cddid_all.tbl CDD cd01029 cd01029 173779 TOPRIM_primases TOPRIM_primases: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme. 79 matched cddid_all.tbl CDD cd01030 cd01030 173780 TOPRIM_TopoIIA_like TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. 115 matched cddid_all.tbl CDD cd01031 cd01031 238504 EriC ClC chloride channel EriC. This domain is found in the EriC chloride transporters that mediate the extreme acid resistance response in eubacteria and archaea. This response allows bacteria to survive in the acidic environments by decarboxylation-linked proton utilization. As shown for Escherichia coli EriC, these channels can counterbalance the electric current produced by the outwardly directed virtual proton pump linked to amino acid decarboxylation. The EriC proteins belong to the ClC superfamily of chloride ion channels, which share a unique double-barreled architecture and voltage-dependent gating mechanism. The voltage-dependent gating is conferred by the permeating anion itself, acting as the gating charge. In Escherichia coli EriC, a glutamate residue that protrudes into the pore is thought to participate in gating by binding to a Cl- ion site within the selectivity filter. 402 matched cddid_all.tbl CDD cd01033 cd01033 238505 ClC_like Putative ClC chloride channel. Clc proteins are putative halogen ion (Cl-, Br- and I-) transporters found in eubacteria. They belong to the ClC superfamily of halogen ion channels, which share a unique double-barreled architecture and voltage-dependent gating mechanism. This superfamily lacks any structural or sequence similarity to other known ion channels and exhibit unique properties of ion permeation and gating. The voltage-dependent gating is conferred by the permeating anion itself, acting as the gating charge. 388 matched cddid_all.tbl CDD cd01034 cd01034 238506 EriC_like ClC chloride channel family. These protein sequences, closely related to the ClC Eric family, are putative halogen ion (Cl-, Br- and I-) transport proteins found in eubacteria. They belong to the ClC superfamily of chloride ion channels, which share a unique double-barreled architecture and voltage-dependent gating mechanism. This superfamily lacks any structural or sequence similarity to other known ion channels and exhibit unique properties of ion permeation and gating. The voltage-dependent gating is conferred by the permeating anion itself, acting as the gating charge. 390 matched cddid_all.tbl CDD cd01036 cd01036 238507 ClC_euk Chloride channel, ClC. These domains are found in the eukaryotic halogen ion (Cl-, Br- and I-) channel proteins that perform a variety of functions including cell volume regulation, membrane potential stabilization, charge compensation necessary for the acidification of intracellular organelles, signal transduction and transepithelial transport. They are also involved in many pathophysiological processes and are responsible for a number of human diseases. These proteins belong to the ClC superfamily of chloride ion channels, which share the unique double-barreled architecture and voltage-dependent gating mechanism. The gating is conferred by the permeating anion itself, acting as the gating charge. Some proteins possess long C-terminal cytoplasmic regions containing two CBS (cystathionine beta synthase) domains of putative regulatory function. 416 matched cddid_all.tbl CDD cd01037 cd01037 411707 PDDEXK_nuclease-like PDDEXK family nucleases. Superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 83 matched cddid_all.tbl CDD cd01038 cd01038 411708 Endonuclease_DUF559 Putative endonuclease. Domain of unknown function 559 (DUF559) is a putative endonuclease of unknown function, belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 97 matched cddid_all.tbl CDD cd01040 cd01040 381254 Mb-like myoglobin-like; M family globin domain. This family includes chimeric (FHbs/flavohemoglobins) and single-domain globins: FHbs, Ngbs/neuroglobins, Cygb/cytoglobins, GbE/avian eye specific globin E, GbX/globin X, amphibian GbY/globin Y, Mb/myoglobin, HbA/hemoglobin-alpha, HbB/hemoglobin-beta, SDgbs/single-domain globins related to FHbs, and Adgb/androglobin. The M family exhibits the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments (named A through H). In Adgbs, the globin domain is split into two: helices C-H are followed by helices A-B and the two parts are separated by the IQ motif. Although rearranged, the globin domain of most Adgbs contains a number of conserved residues which play critical roles in heme-coordination and gas ligand binding. Adgbs have been omitted from this A-H helix cd. 133 matched cddid_all.tbl CDD cd01041 cd01041 153100 Rubrerythrin Rubrerythrin, ferritin-like diiron-binding domain. Rubrerythrin domain is a nonheme iron binding domain found in many air-sensitive bacteria and archaea and member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The homodimeric rubrerythrin protein contains a binuclear metal center located within a four helix bundle. Many, but not all, rubrerythrin proteins have a second domain with a rubredoxin-like hexacoordinated iron center. Rubrerythrin is thought to reduce hydrogen peroxide as part of an oxidative stress protection system but its function is still poorly understood. 134 matched cddid_all.tbl CDD cd01042 cd01042 153101 DMQH Demethoxyubiquinone hydroxylase, ferritin-like diiron-binding domain. Demethoxyubiquinone hydroxylases (DMQH) are members of the ferritin-like, diiron-carboxylate family which are present in eukaryotes (the CLK-1/CAT5 family) and prokaryotes (the Coq7 family). DMQH participates in one of the last steps of ubiquinone biosysnthesis and is responsible for DMQ hydroxylation, resulting in the formation of hydroxyubiquinone, a precursor of ubiquinone. CLK-1 is a mitochondrial inner membrane protein and Coq7 is a proposed interfacial integral membrane protein. Mutations in the Caenorhabditis elegans gene clk-1 affect biological timing and extend longevity. The conserved residues of a diiron center are present in this domain. 165 matched cddid_all.tbl CDD cd01043 cd01043 153102 DPS DPS protein, ferritin-like diiron-binding domain. DPS (DNA Protecting protein under Starved conditions) domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Some DPS proteins nonspecifically bind DNA, protecting it from cleavage caused by reactive oxygen species such as the hydroxyl radicals produced during oxidation of Fe(II) by hydrogen peroxide. These proteins assemble into dodecameric structures, some form DPS-DNA co-crystalline complexes, and possess iron and H2O2 detoxification capabilities. Expression of DPS is induced by oxidative or nutritional stress, including metal ion starvation. Members of the DPS family are homopolymers formed by 12 four-helix bundle subunits that assemble with 23 symmetry into a hollow shell. The DPS ferroxidase site is unusual in that it is not located in a four-helix bundle as in ferritin, but is shared by 2-fold symmetry-related subunits providing the iron ligands. Many DPS sequences (e.g., E. coli) display an N-terminal extension of variable length that contains two or three positively charged lysine residues that extends into the solvent and is thought to play an important role in the stabilization of the complex with DNA. DPS Listeria Flp, Bacillus anthracis Dlp-1 and Dlp-2, and Helicobacter pylori HP-NAP which lack the N-terminal extension, do not bind DNA. DPS proteins from Helicobacter pylori, Treponema pallidum, and Borrelia burgdorferi are highly immunogenic. 139 matched cddid_all.tbl CDD cd01044 cd01044 153103 Ferritin_CCC1_N Ferritin-CCC1, N-terminal ferritin-like diiron-binding domain. Ferritin-like N-terminal domain present in an uncharacterized family of proteins found in bacteria and archaea. These proteins also have a C-terminal CCC1-like transmembrane domain and are thought to be involved in iron and/or manganese transport. This domain has the conserved residues of a diiron center found in other ferritin-like proteins. 125 matched cddid_all.tbl CDD cd01045 cd01045 153104 Ferritin_like_AB Uncharacterized family of ferritin-like proteins found in archaea and bacteria. Ferritin-like domain found in archaea and bacteria (Ferritin_like_AB). This uncharacterized domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins whose function is unknown. This family includes unknown or hypothetical proteins which were sequenced from mostly anaerobic or microaerophilic metal-metabolizing and/or nitrogen-fixing microbes. The family includes sequences from ferric-, sulfate-, and arsenic-reducing bacteria, Geobacter, Magnetospirillum, Desulfovibrio, and Desulfitobacterium. Also included are several nitrogen-fixing endosymbiotic bacteria, Rhizobium, Mesorhizobium, and Bradyrhizobium; also phototrophic purple nonsulfur bacteria, Rhodobacter and Rhodopseudomonas, as well as, obligate thermophiles, Thermotoga, Thermoanaerobacter, and Pyrococcus. The conserved residues of a diiron center are present in this uncharacterized domain. 139 matched cddid_all.tbl CDD cd01046 cd01046 153105 Rubrerythrin_like rubrerythrin-like, diiron-binding domain. Rubrerythrin-like domain, similar to rubrerythrin, a nonheme iron binding domain found in many air-sensitive bacteria and archaea, and member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Rubrerythrin is thought to reduce hydrogen peroxide as part of an oxidative stress protection system. The rubrerythrin protein has two domains, a binuclear metal center located within a four-helix bundle of the rubrerythrin domain, and a rubredoxin domain. The Rubrerythrin-like domains in this CD are singular domains (no C-terminus rubredoxin domain) and are phylogenetically distinct from rubrerythrin domains of rubrerythrin-rubredoxin proteins. 123 matched cddid_all.tbl CDD cd01047 cd01047 153106 ACSF Aerobic Cyclase System Fe-containing subunit (ACSF), ferritin-like diiron-binding domain. Aerobic Cyclase System, Fe-containing subunit (ACSF) is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. Rubrivivax gelatinosus acsF codes for a conserved, putative binuclear iron-cluster-containing protein involved in aerobic oxidative cyclization of Mg-protoporphyrin IX monomethyl ester. AcsF and homologs have a leucine zipper and two copies of the conserved glutamate and histidine residues predicted to act as ligands for iron in the Ex(29-35)DExRH motifs. Several homologs of AcsF are found in a wide range of photosynthetic organisms, including Chlamydomonas reinhardtii Crd1 and Pharbitis nil PNZIP, suggesting that this aerobic oxidative cyclization mechanism is conserved from bacteria to plants. 323 matched cddid_all.tbl CDD cd01048 cd01048 153107 Ferritin_like_AB2 Uncharacterized family of ferritin-like proteins found in archaea and bacteria. Ferritin-like domain found in archaea and bacteria, subgroup 2 (Ferritin_like_AB2). This uncharacterized domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins whose function is unknown. The conserved residues of a diiron center are present within the putative active site. 135 matched cddid_all.tbl CDD cd01049 cd01049 153108 RNRR2 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain. Ribonucleotide Reductase, R2/beta subunit (RNRR2) is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in all eukaryotes, many prokaryotes, several viruses, and few archaea. The catalytically active form of RNR is a proposed alpha2-beta2 tetramer. The homodimeric alpha subunit (R1) contains the active site and redox active cysteines as well as the allosteric binding sites. The beta subunit (R2) contains a diiron cluster that, in its reduced state, reacts with dioxygen to form a stable tyrosyl radical and a diiron(III) cluster. This essential tyrosyl radical is proposed to generate a thiyl radical, located on a cysteine residue in the R1 active site that initiates ribonucleotide reduction. The beta subunit is composed of 10-13 helices, the 8 longest helices form an alpha-helical bundle; some have 2 addition beta strands. Yeast is unique in that it assembles both homodimers and heterodimers of RNRR2. The yeast heterodimer, Y2Y4, contains R2 (Y2) and a R2 homolog (Y4) that lacks the diiron center and is proposed to only assist in cofactor assembly, and perhaps stabilize R1 (Y1) in its active conformation. 288 matched cddid_all.tbl CDD cd01050 cd01050 153109 Acyl_ACP_Desat Acyl ACP desaturase, ferritin-like diiron-binding domain. Acyl-Acyl Carrier Protein Desaturase (Acyl_ACP_Desat) is a mu-oxo-bridged diiron-carboxylate enzyme, which belongs to a broad superfamily of ferritin-like proteins and catalyzes the NADPH and O2-dependent formation of a cis-double bond in acyl-ACPs. Acyl-ACP desaturases are found in higher plants and a few bacterial species (Mycobacterium tuberculosis, M. leprae, M. avium and Streptomyces avermitilis, S. coelicolor). In plants, Acyl-ACP desaturase is a plastid-localized, covalently ACP linked, soluble desaturase that introduces the first double bound into saturated fatty acids, resulting in the corresponding monounsaturated fatty acid. Members of this class of soluble desaturases are specific for a particular substrate chain length and introduce the double bond between specific carbon atoms. For example, delta 9 stearoyl-ACP is specific for stearic acid and introduces a double bond between carbon 9 and 10 to yield oleic acid in the ACP-bound form. The enzymatic reaction requires molecular oxygen, NAD(P)H, NAD(P)H ferredoxin oxido-reductase and ferredoxin. The enzyme is active in the homodimeric form; the monomer consists mainly of alpha-helices with the catalytic diiron center buried within a four-helix bundle. Integral membrane fatty acid desaturases that introduce double bonds into fatty acid chains, acyl-CoA desaturases of animals, yeasts, and fungi, and acyl-lipid desaturases of cyanobacteria and higher plants, are distinct from soluble acyl-ACP desaturases, lack diiron centers, and are not included in this CD. 297 matched cddid_all.tbl CDD cd01051 cd01051 153110 Mn_catalase Manganese catalase, ferritin-like diiron-binding domain. Manganese (Mn) catalase is a member of a broad superfamily of ferritin-like diiron enzymes. While many diiron enzymes catalyze dioxygen-dependent reactions, manganese catalase performs peroxide-dependent oxidation-reduction. Catalases are important antioxidant metalloenzymes that catalyze disproportionation of hydrogen peroxide, forming dioxygen and water. Manganese catalase, a nonheme type II catalase, contains a binuclear manganese cluster that catalyzes the redox dismutation of hydrogen peroxide, interconverting between dimanganese(II) [(2,2)] and dimanganese(III) [(3,3)] oxidation states during turnover. Mn catalases are found in a broad range of microorganisms in microaerophilic environments, including the mesophilic lactic acid bacteria (e.g., Lactobacillus plantarum) and bacterial and archaeal thermophiles (e.g., Thermus thermophilus and Pyrobaculum caldifontis). L. plantarum and T. thermophilus holoenzymes are homohexameric structures; each subunit contains a dimanganese active site. The manganese ions are linked by a mu 1,3-bridging glutamate carboxylate and two mu-bridging solvent oxygens that electronically couple the metal centers. Several members of this CD lack the C-terminal strands that pack against the neighboring catalytic domains as seen in L. plantarum. One such sequence, Bacillus subtilis CotJC, is known to be a component of the inner spore coat that interacts with spore coat protein, CotJA. It has been suggested that CotJC could modulate the degree of Mn SodA-dependent cross-linking of an outer coat component, or the two enzymes could serve to protect specific cellular structures during the developmental process. 156 matched cddid_all.tbl CDD cd01052 cd01052 153111 DPSL DPS-like protein, ferritin-like diiron-binding domain. DPSL (DPS-like). DPSL is a phylogenetically distinct class within the ferritin-like superfamily, and similar in many ways to the DPS (DNA Protecting protein under Starved conditions) proteins. Like DPS, these proteins are expressed in response to oxidative stress, form dodecameric cage-like particles, preferentially utilize hydrogen peroxide in the controlled oxidation of iron, and possess a short N-terminal extension implicated in stabilizing cellular DNA. This domain is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. These proteins are distantly related to bacterial ferritins which assemble 24 monomers, each of which have a four-helix bundle with a fifth shorter helix at the C terminus and a diiron (ferroxidase) center. Ferritins contain a center where oxidation of ferrous iron by molecular oxygen occurs, facilitating the detoxification of iron, protection against dioxygen and radical products, and storage of iron in the ferric form. Many of the conserved residues of a diiron center are present in this domain. 148 matched cddid_all.tbl CDD cd01053 cd01053 153112 AOX Alternative oxidase, ferritin-like diiron-binding domain. Alternative oxidase (AOX) is a mitochondrial ubiquinol oxidase found in plants and some fungi and protists. AOX is a member of the ferritin-like diiron-carboxylate superfamily. The plant mitochondrial protein alternative oxidase catalyses dioxygen dependent ubiquinol oxidation to yield ubiquinone and water. AOX is a cyanide-resistant, salicylhydroxamic acid-sensitive oxidase that transfers electrons from ubiquinol to oxygen, bypassing the cytochrome chain. AOX has been proposed to contain a hydroxo-bridged diiron center within a four-helix bundle and a proximal redox-active tyrosine residue. AOX is proposed to be peripherally associated with the matrix side of the inner mitochondrial membrane. Fungal and protozoan AOXs generally exist as monomers. In plants, AOX is dimeric. Pyruvate is an allosteric activator of plant AOX involved in the reversible inactivation of the enzyme though the formation of an intermolecular disulfide bridge between monomeric subunits. The enzyme is non-proton-motive and does not contribute to the conservation of energy. The heat that dissipates from AOX activity is used in thermogenic plants to volatilize primary amines to attract pollinating insects. Other functions have been proposed: i) that the alternative oxidase allows Krebs-cycle turnover when the energy charge of the cell is high, and ii) that the enzyme protects against oxidative stress. The expression of AOX is induced when plants are exposed to a variety of stresses including chilling, pathogen attack, senescence and fruit ripening. 168 matched cddid_all.tbl CDD cd01055 cd01055 153113 Nonheme_Ferritin nonheme-containing ferritins. Nonheme Ferritin domain, found in archaea and bacteria, is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The ferritin protein shell is composed of 24 protein subunits arranged in 432 symmetry. Each protein subunit, a four-helix bundle with a fifth short terminal helix, contains a dinuclear ferroxidase center (H type). Unique to this group of proteins is a third metal site in the ferroxidase center. Iron storage involves the uptake of iron (II) at the protein shell, its oxidation by molecular oxygen at the ferroxidase centers, and the movement of iron (III) into the cavity for deposition as ferrihydrite. 156 matched cddid_all.tbl CDD cd01056 cd01056 153114 Euk_Ferritin eukaryotic ferritins. Eukaryotic Ferritin (Euk_Ferritin) domain. Ferritins are the primary iron storage proteins of most living organisms and members of a broad superfamily of ferritin-like diiron-carboxylate proteins. The iron-free (apoferritin) ferritin molecule is a protein shell composed of 24 protein chains arranged in 432 symmetry. Iron storage involves the uptake of iron (II) at the protein shell, its oxidation by molecular oxygen at the dinuclear ferroxidase centers, and the movement of iron (III) into the cavity for deposition as ferrihydrite; the protein shell can hold up to 4500 iron atoms. In vertebrates, two types of chains (subunits) have been characterized, H or M (fast) and L (slow), which differ in rates of iron uptake and mineralization. Fe(II) oxidation in the H/M subunits take place initially at the ferroxidase center, a carboxylate-bridged diiron center, located within the subunit four-helix bundle. In a complementary role, negatively charged residues on the protein shell inner surface of the L subunits promote ferrihydrite nucleation. Most plant ferritins combine both oxidase and nucleation functions in one chain: they have four interior glutamate residues as well as seven ferroxidase center residues. 161 matched cddid_all.tbl CDD cd01057 cd01057 153115 AAMH_A Aromatic and Alkene Monooxygenase Hydroxylase, subunit A, ferritin-like diiron-binding domain. Aromatic and Alkene Monooxygenase Hydroxylases, subunit A (AAMH_A). Subunit A of the soluble hydroxylase of multicomponent, aromatic and alkene monooxygenases are members of a superfamily of ferritin-like iron-storage proteins. AAMH exists as a hexamer (an alpha2-beta2-gamma2 homodimer) with each alpha-subunit housing one nonheme diiron center embedded in a four-helix bundle. The N-terminal domain of the alpha- and noncatalytic beta-subunits possess nearly identical folds, however, the beta-subunit lacks critical diiron ligands and a C-terminal domain found in the alpha-subunit. Methane monooxygenase is a multicomponent enzyme found in methanotrophic bacteria that catalyzes the hydroxylation of methane and higher alkenes (as large as octane). Phenol monooxygenase, found in a diverse group of bacteria, catalyses the hydroxylation of phenol, chloro- and methyl-phenol and naphthol. Both enzyme systems consist of three components: the hydroxylase, a coupling protein and a reductase. In the MMO hydroxylase, dioxygen and substrate interact with the diiron center in a hydrophobic cavity at the active site. The reductase component and protein coupling factor provide electrons from NADH for reducing the oxidized binuclear iron-oxo cluster to its reduced form. Reaction with dioxygen produces a peroxy-bridged complex and dehydration leads to the formation of complex Q, which is thought to be the oxygenating species that carries out the insertion of an oxygen atom into a C-H bond of the substrate. The toluene monooxygenase systems, toluene 2-, 3-, and 4-monooxygenase, are similar to MMO but with an additional component, a Rieske-type ferredoxin. The alkene monooxygenase from Xanthobacter strain Py2 is closely related to aromatic monooxygenases and catalyzes aromatic monohydroxylation of benzene, toluene, and phenol. Alkane omega-hydroxylase (AlkB) and xylene monooxygenase are members of a distinct class of integral membrane diiron proteins and are not included in this CD. 465 matched cddid_all.tbl CDD cd01058 cd01058 153116 AAMH_B Aromatic and Alkene Monooxygenase Hydroxylase, subunit B, ferritin-like diiron-binding domain. Aromatic and Alkene Monooxygenase Hydroxylases, subunit B (AAMH_B). Subunit B (beta) of the soluble hydroxylase of multicomponent, aromatic and alkene monooxygenases are members of a superfamily of ferritin-like iron-storage proteins. AAMH exists as a hexamer (an alpha2-beta2-gamma2 homodimer) with each alpha-subunit housing one nonheme diiron center embedded in a four-helix bundle. The N-terminal domain of the alpha- and noncatalytic beta-subunits possess nearly identical folds; the beta-subunit lacks the C-terminal domain found in the alpha-subunit. Methane monooxygenase is a multicomponent enzyme found in methanotrophic bacteria that catalyzes the hydroxylation of methane and higher alkenes (as large as octane). Phenol monooxygenase, found in a diverse group of bacteria, catalyses the hydroxylation of phenol, chloro- and methyl-phenol and naphthol. Both enzyme systems consist of three components: the hydroxylase, a coupling protein and a reductase. In the MMO hydroxylase, dioxygen and substrate interact with the diiron center in a hydrophobic cavity at the active site. The reductase component and protein coupling factor provide electrons from NADH for reducing the oxidized binuclear iron-oxo cluster to its reduced form. Reaction with dioxygen produces a peroxy-bridged complex and dehydration leads to the formation of complex Q, which is thought to be the oxygenating species that carries out the insertion of an oxygen atom into a C-H bond of the substrate. The toluene monooxygenase systems, toluene 2-, 3-, and 4-monooxygenase, are similar to MMO but with an additional component, a Rieske-type ferredoxin. The alkene monooxygenase from Xanthobacter strain Py2 is closely related to aromatic monooxygenases and catalyzes aromatic monohydroxylation of benzene, toluene, and phenol. Alkane omega-hydroxylase (AlkB) and xylene monooxygenase are members of a distinct class of integral membrane diiron proteins and are not included in this CD. 304 matched cddid_all.tbl CDD cd01059 cd01059 153121 CCC1_like CCC1-related family of proteins. CCC1_like: This protein family includes the proteins related to CCC1, a yeast vacuole transmembrane protein responsible for the iron and manganese transport from the cytosol into vacuole. It also includes the proteins similar to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. 143 matched cddid_all.tbl CDD cd01060 cd01060 238511 Membrane-FADS-like The membrane fatty acid desaturase (Membrane_FADS)-like CD includes membrane FADSs, alkane hydroxylases, beta carotene ketolases (CrtW-like), hydroxylases (CrtR-like), and other related proteins. They are present in all groups of organisms with the exception of archaea. Membrane FADSs are non-heme, iron-containing, oxygen-dependent enzymes involved in regioselective introduction of double bonds in fatty acyl aliphatic chains. They play an important role in the maintenance of the proper structure and functioning of biological membranes. Alkane hydroxylases are bacterial, integral-membrane di-iron enzymes that share a requirement for iron and oxygen for activity similar to that of membrane FADSs, and are involved in the initial oxidation of inactivated alkanes. Beta-carotene ketolase and beta-carotene hydroxylase are carotenoid biosynthetic enzymes for astaxanthin and zeaxanthin, respectively. This superfamily domain has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of these sequences also reveals three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXX(X)H, HXX(X)HH, and HXXHH (an additional conserved histidine residue is seen between clusters 2 and 3). Spectroscopic and genetic evidence point to a nitrogen-rich coordination environment located in the cytoplasm with as many as eight histidines coordinating the two iron ions and a carboxylate residue bridging the two metals in the Pseudomonas oleovorans alkane hydroxylase (AlkB). In addition, the eight histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the rat stearoyl CoA delta-9 desaturase. 122 matched cddid_all.tbl CDD cd01061 cd01061 238512 RNase_T2_euk "Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases). Plant T2 RNases are expressed during leaf senescence in order to scavenge phosphate from ribonucleotides. They are also expressed in response to wounding or pathogen invasion. S-RNases are thought to prevent self-fertilization by acting as selective cytotoxins of ""self"" pollen. Generally, RNases have two distinct binding sites: the primary site (B1 site) and the subsite (B2 site), for nucleotides located at the 5'- and 3'- terminal ends of the sessil bond, respectively. This CD includes the eukaryotic RNase T2 family members." 195 matched cddid_all.tbl CDD cd01062 cd01062 238513 RNase_T2_prok "Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases). Plant T2 RNases are expressed during leaf senescence in order to scavenge phosphate from ribonucleotides. They are also expressed in response to wounding or pathogen invasion. S-RNases are thought to prevent self-fertilization by acting as selective cytotoxins of ""self"" pollen. Generally, RNases have two distinct binding sites: the primary site (B1 site) and the subsite (B2 site), for nucleotides located at the 5'- and 3'- terminal ends of the sessil bond, respectively. This CD includes the prokaryotic RNase T2 family members." 184 matched cddid_all.tbl CDD cd01065 cd01065 133443 NAD_bind_Shikimate_DH NAD(P) binding domain of Shikimate dehydrogenase. Shikimate dehydrogenase (DH) is an amino acid DH family member. Shikimate pathway links metabolism of carbohydrates to de novo biosynthesis of aromatic amino acids, quinones and folate. It is essential in plants, bacteria, and fungi but absent in mammals, thus making enzymes involved in this pathway ideal targets for broad spectrum antibiotics and herbicides. Shikimate DH catalyzes the reduction of 3-hydroshikimate to shikimate using the cofactor NADH. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DHs, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. 155 matched cddid_all.tbl CDD cd01066 cd01066 238514 APP_MetAP A family including aminopeptidase P, aminopeptidase M, and prolidase. Also known as metallopeptidase family M24. This family of enzymes is able to cleave amido-, imido- and amidino-containing bonds. Members exibit relatively narrow substrate specificity compared to other metallo-aminopeptidases, suggesting they play roles in regulation of biological processes rather than general protein degradation. 207 matched cddid_all.tbl CDD cd01067 cd01067 381255 Globin-like Globin-like protein superfamily. This globin-like domain superfamily contains a wide variety of all-helical proteins that bind porphyrins, phycobilins, and other non-heme cofactors, and play various roles in all three kingdoms of life, including sensors or transporters of oxygen. It includes the M/myoglobin-like, S/sensor globin, and T/truncated globin (TrHb) families, and the phycobiliproteins (PBPs). The M family includes chimeric (FHbs/flavohemoglobins) and single-domain globins: FHbs, Ngbs/neuroglobins, Cygb/cytoglobins, GbE/avian eye specific globin E, GbX/globin X, amphibian GbY/globin Y, Mb/myoglobin, HbA/hemoglobin-alpha, HbB/hemoglobin-beta, SDgbs/single-domain globins related to FHbs, and Adgb/androglobin. The S family includes GCS/globin-coupled sensors, Pgbs/protoglobins, and SSDgbs/sensor single domain globins. The T family is classified into three main groups: TrHb1s (N), TrHb2s (O) and TrHb3s (P). The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments (named A through H). For M family Adgbs, this globin domain is permuted, such that C-H are followed by A-B. The T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. PBPs bind the linear tetrapyrrole chromophore, phycobilin, a prosthetic group chemically and metabolically related to iron protoporphyrin IX/protoheme. Examples of other globin-like domains which bind non-heme cofactors include those of the Bacillus anthracis sporulation inhibitors pXO1-118 and pXO2-61 which bind fatty acid and halide in vitro, and the globin-like domain of Bacillus subtilis RsbRA which is presumed to channel sensory input to the C-terminal sulfate transporter/ anti-sigma factor antagonist (STAT) domain. RsbRA is a component of the sigma B-activating stressosome, and a regulator of the RNA polymerase sigma factor subunit sigma (B). 119 matched cddid_all.tbl CDD cd01068 cd01068 381256 globin_sensor Globin sensor domain of globin-coupled-sensors (GCSs), protoglobins (Pgbs), and sensor single-domain globins (SSDgbs); S family. This family includes sensor domains which binds porphyrins, and other non-heme cofactors. GCSs have an N-terminal sensor domain coupled to a functional domain. For heme-bound oxygen sensing/binding globin domains, O2 binds to/dissociates from the heme iron complex inducing a structural change in the sensor domain, which is then transduced to the functional domain, switching on (or off) the function of the latter. Functional domains include DGC/GGDEF, EAL, histidine kinase, MCP, PAS, and GAF domains. Characterized members include Bacillus subtilis heme-based aerotaxis transducer (HemAT-Bs) which has a sensor domain coupled to an MCP domain. HemAT-Bs mediates an aerophilic response, and may control the movement direction of bacteria and archaea. Its MCP domain interacts with the CheA histidine kinase, a component of the CheA/CheY signal transduction system that regulates the rotational direction of flagellar motors. Another GCS having the sensor domain coupled to an MCP domain is Caulobacter crescentus McpB. McpB is encoded by a gene which lies adjacent to the major chemotaxis operon. Like McpA (encoded on this operon), McpB has three potential methylation sites, a C-terminal CheBR docking motif, and a motif needed for proteolysis via a ClpX-dependent pathway during the swarmer-to-stalked cell transition. Also included is Geobacter sulfurreducens GCS, a GCS of unknown function, in which the sensor domain is coupled to a transmembrane signal-transduction domain. Pgbs are single-domain globins of unknown function. Methanosarcina acetivorans Pgbs is dimeric and has an N-terminal extension, which together with other Pgb-specific loops, buries the heme within the protein; small ligand molecules gain access to the heme via two orthogonal apolar tunnels. Pgbs and other single-domain globins can function as sensors, when coupled to an appropriate regulator domain. 146 matched cddid_all.tbl CDD cd01069 cd01069 270231 PBP2_PheC Cyclohexadienyl dehydratase, a member of the type 2 periplasmic binding fold protein superfamily. This subfamily includes cyclohexadienyl dehydratase PheC. These proteins catalyze the decarboxylation of prephenate to phenylpyruvate in the alternative phenylalanine biosynthesis pathway in some proteobacteria and archaea. The PheC proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. Since they the PheC proteins are so similar to periplasmic binding proteins, (PBP), it is evolutionarily plausible that several pre-existing PBP proteins might have been recruited to perform the enzymatic function. 232 matched cddid_all.tbl CDD cd01071 cd01071 270232 PBP2_PhnD_like Substrate binding domain of phosphonate uptake system-like, a member of the type 2 periplasmic-binding fold superfamily. This family includes alkylphosphonate binding domain PhnD. These domains are found in PhnD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. PhnD is the periplasmic binding component of an ABC-type phosphonate uptake system (PhnCDE) that recognizes and binds phosphonate. PhnD belongs to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. The PBP2 have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 253 matched cddid_all.tbl CDD cd01072 cd01072 270233 PBP2_SMa0082_like The substrate-binding domain of putatuve amino acid transporter; the type 2 periplasmic binding protein fold. This group includes the periplamic-binding protein component of a putative amino acid ABC transporter from Sinorhizobium meliloti and its related proteins. The putative SMa0082-like domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 238 matched cddid_all.tbl CDD cd01075 cd01075 133444 NAD_bind_Leu_Phe_Val_DH NAD(P) binding domain of leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. For example, leucine DH catalyzes the reversible oxidative deamination of L-leucine and several other straight or branched chain amino acids to the corresponding 2-oxoacid derivative. Amino acid DH -like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. 200 matched cddid_all.tbl CDD cd01076 cd01076 133445 NAD_bind_1_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 1. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha -beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. 227 matched cddid_all.tbl CDD cd01078 cd01078 133446 NAD_bind_H4MPT_DH NADP binding domain of methylene tetrahydromethanopterin dehydrogenase. Methylene Tetrahydromethanopterin Dehydrogenase (H4MPT DH) NADP binding domain. NADP-dependent H4MPT DH catalyzes the dehydrogenation of methylene- H4MPT and methylene-tetrahydrofolate (H4F) with NADP+ as cofactor. H4F and H4MPT are both cofactors that carry the one-carbon units between the formyl and methyl oxidation level. H4F and H4MPT are structurally analogous to each other with respect to the pterin moiety, but each has distinct side chain. H4MPT is present only in anaerobic methanogenic archaea and aerobic methylotrophic proteobacteria. H4MPT seems to have evolved independently from H4F and functions as a distinct carrier in C1 metabolism. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. 194 matched cddid_all.tbl CDD cd01079 cd01079 133447 NAD_bind_m-THF_DH NAD binding domain of methylene-tetrahydrofolate dehydrogenase. The NAD-binding domain of methylene-tetrahydrofolate dehydrogenase (m-THF DH). M-THF is a versatile carrier of activated one-carbon units. The major one-carbon folate donors are N-5 methyltetrahydrofolate, N5,N10-m-THF, and N10-formayltetrahydrofolate. The oxidation of metabolic intermediate m-THF to m-THF requires the enzyme m-THF DH. M-THF DH is a component of an unusual monofunctional enzyme; in eukaryotes, m-THF DH is typically found as part of a multifunctional protein. NADP-dependent m-THF DHs in mammals, birds and yeast are components of a trifunctional enzyme with DH, cyclohydrolase, and synthetase activities. Certain eukaryotic cells also contain homodimeric bifunctional DH/cyclodrolase form. In bacteria, monofunctional DH, as well as bifunctional DH/cyclodrolase are found. In addition, yeast (S. cerevisiae) also express an monofunctional DH. This family contains only the monofunctional DHs from S. cerevisiae and certain bacteria. M-THF DH, like other amino acid DH-like NAD(P)-binding domains, is a member of the Rossmann fold superfamily which includes glutamate, leucine, and phenylalanine DHs, m-THF DH, methylene-tetrahydromethanopterin DH, m-THF DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. 197 matched cddid_all.tbl CDD cd01080 cd01080 133448 NAD_bind_m-THF_DH_Cyclohyd NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase. NADP binding domain of the Methylene-Tetrahydrofolate Dehydrogenase/cyclohydrolase (m-THF DH/cyclohydrolase) bifunctional enzyme. Tetrahydrofolate is a versatile carrier of activated one-carbon units. The major one-carbon folate donors are N-5 methyltetrahydrofolate, N5,N10-m-THF, and N10-formayltetrahydrofolate. The oxidation of metabolic intermediate m-THF to m-THF requires the enzyme m-THF DH. In addition, most DHs also have an associated cyclohydrolase activity which catalyzes its hydrolysis to N10-formyltetrahydrofolate. m-THF DH is typically found as part of a multifunctional protein in eukaryotes. NADP-dependent m-THF DH in mammals, birds and yeast are components of a trifunctional enzyme with DH, cyclohydrolase, and synthetase activities. Certain eukaryotic cells also contain homodimeric bifunctional DH/cyclodrolase form. In bacteria, monofucntional DH, as well as bifunctional m-THF m-THF DHm-THF DHDH/cyclodrolase are found. In addition, yeast (S. cerevisiae) also express an monofunctional DH. This family contains the bifunctional DH/cyclohydrolase. M-THF DH, like other amino acid DH-like NAD(P)-binding domains, is a member of the Rossmann fold superfamily which includes glutamate, leucine, and phenylalanine DHs, m-THF DH, methylene-tetrahydromethanopterin DH, m-THF DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. 168 matched cddid_all.tbl CDD cd01081 cd01081 185695 Aldose_epim aldose 1-epimerase superfamily. Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism; they catalyze the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate and the histidine as the active site acid to protonate the C-5 ring oxygen. 284 matched cddid_all.tbl CDD cd01083 cd01083 238517 GAG_Lyase Glycosaminoglycan (GAG) polysaccharide lyase family. This family consists of a group of secreted bacterial lyase enzymes capable of acting on glycosaminoglycans, such as hyaluronan and chondroitin, in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen. These are broad-specificity glycosaminoglycan lyases which recognize uronyl residues in polysaccharides and cleave their glycosidic bonds via a beta-elimination reaction to form a double bond between C-4 and C-5 of the non-reducing terminal uronyl residues of released products. Substrates include chondroitin, chondroitin 4-sulfate, chondroitin 6-sulfate, and hyaluronic acid. Family members include chondroitin AC lyase, chondroitin abc lyase, xanthan lyase, and hyalurate lyase. 693 matched cddid_all.tbl CDD cd01085 cd01085 238518 APP X-Prolyl Aminopeptidase 2. E.C. 3.4.11.9. Also known as X-Pro aminopeptidase, proline aminopeptidase, aminopeptidase P, and aminoacylproline aminopeptidase. Catalyses release of any N-terminal amino acid, including proline, that is linked with proline, even from a dipeptide or tripeptide. 224 matched cddid_all.tbl CDD cd01086 cd01086 238519 MetAP1 Methionine Aminopeptidase 1. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and Peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides. 238 matched cddid_all.tbl CDD cd01087 cd01087 238520 Prolidase Prolidase. E.C. 3.4.13.9. Also known as Xaa-Pro dipeptidase, X-Pro dipeptidase, proline dipeptidase., imidodipeptidase, peptidase D, gamma-peptidase. Catalyses hydrolysis of Xaa-Pro dipeptides; also acts on aminoacyl-hydroxyproline analogs. No action on Pro-Pro. 243 matched cddid_all.tbl CDD cd01088 cd01088 238521 MetAP2 Methionine Aminopeptidase 2. E.C. 3.4.11.18. Also known as methionyl aminopeptidase and peptidase M. Catalyzes release of N-terminal amino acids, preferentially methionine, from peptides and arylamides. 291 matched cddid_all.tbl CDD cd01089 cd01089 238522 PA2G4-like Related to aminopepdidase M, this family contains proliferation-associated protein 2G4. Family members have been implicated in cell cycle control. 228 matched cddid_all.tbl CDD cd01090 cd01090 238523 Creatinase Creatine amidinohydrolase. E.C.3.5.3.3. Hydrolyzes creatine to sarcosine and urea. 228 matched cddid_all.tbl CDD cd01091 cd01091 238524 CDC68-like Related to aminopeptidase P and aminopeptidase M, a member of this domain family is present in cell division control protein 68, a transcription factor. 243 matched cddid_all.tbl CDD cd01092 cd01092 238525 APP-like Similar to Prolidase and Aminopeptidase P. The members of this subfamily presumably catalyse hydrolysis of Xaa-Pro dipeptides and/or release of any N-terminal amino acid, including proline, that is linked with proline. 208 matched cddid_all.tbl CDD cd01093 cd01093 238526 CRIB_PAK_like PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. This subgroup of CRIB/PBD-domains is found N-terminal of Serine/Threonine kinase domains in PAK and PAK-like proteins. 46 matched cddid_all.tbl CDD cd01094 cd01094 238527 Alkanesulfonate_monoxygenase Alkanesulfonate monoxygenase is the monoxygenase of a two-component system that catalyzes the conversion of alkanesulfonates to the corresponding aldehyde and sulfite. Alkanesulfonate monoxygenase (SsuD) has an absolute requirement for reduced flavin mononucleotide (FMNH2), which is provided by the NADPH-dependent FMN oxidoreductase (SsuE). 244 matched cddid_all.tbl CDD cd01095 cd01095 238528 Nitrilotriacetate_monoxgenase nitrilotriacetate monoxygenase oxidizes nitrilotriacetate utilizing reduced flavin mononucleotide (FMNH2) and oxygen. The FMNH2 is provided by an NADH:flavin mononucleotide (FMN) oxidorductase that uses NADH to reduce FMN to FMNH2. 358 matched cddid_all.tbl CDD cd01096 cd01096 238529 Alkanal_monooxygenase Alkanal monooxygenase are flavin monoxygenases. Molecular oxygen is activated by reaction with reduced flavin mononucleotide (FMNH2) and reacts with an aldehyde to yield the carboxylic acid, oxidized flavin (FMN) and a blue-green light. Bacterial luciferases are heterodimers made of alpha and beta subunits which are homologous. The single activer center is on the alpha subunit. The alpha subunit has a stretch of 30 amino acid residues that is not present in the beta subunit. The beta subunit does not contain the active site and is required for the formation of the fully active heterodimer. The beta subunit does not contribute anything directly to the active site. Its role is probably to stabilize the high quantum yield conformation of the alpha subunit through interactionbs across the subunit interface. 315 matched cddid_all.tbl CDD cd01097 cd01097 238530 Tetrahydromethanopterin_reductase N5,N10-methylenetetrahydromethanopterin reductase (Mer) catalyzes the reduction of N5,N10-methylenetetrahydromethanopterin with reduced coenzyme F420 to N5-methyltetrahydromethanopterin and oxidized coenzyme F420. 202 matched cddid_all.tbl CDD cd01098 cd01098 238531 PAN_AP_plant Plant PAN/APPLE-like domain; present in plant S-receptor protein kinases and secreted glycoproteins. PAN/APPLE domains fulfill diverse biological functions by mediating protein-protein or protein-carbohydrate interactions. S-receptor protein kinases and S-locus glycoproteins are involved in sporophytic self-incompatibility response in Brassica, one of probably many molecular mechanisms, by which hermaphrodite flowering plants avoid self-fertilization. 84 matched cddid_all.tbl CDD cd01099 cd01099 238532 PAN_AP_HGF Subfamily of PAN/APPLE-like domains; present in N-terminal (N) domains of plasminogen/hepatocyte growth factor proteins, and various proteins found in Bilateria, such as leech anti-platelet proteins. PAN/APPLE domains fulfill diverse biological functions by mediating protein-protein or protein-carbohydrate interactions. 80 matched cddid_all.tbl CDD cd01100 cd01100 238533 APPLE_Factor_XI_like Subfamily of PAN/APPLE-like domains; present in plasma prekallikrein/coagulation factor XI, microneme antigen proteins, and a few prokaryotic proteins. PAN/APPLE domains fulfill diverse biological functions by mediating protein-protein or protein-carbohydrate interactions. 73 matched cddid_all.tbl CDD cd01102 cd01102 238534 Link_Domain The link domain is a hyaluronan (HA)-binding domain. It functions to mediate adhesive interactions during inflammatory leukocyte homing and tumor metastasis. It is found in the CD44 receptor and in human TSG-6. TSG-6 is the protein product of the tumor necrosis factor-stimulated gene-6. TSG-6 has a strong anti-inflammatory effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. This group also contains the link domains of the chondroitin sulfate proteoglycan core proteins (CSPG) including aggrecan, versican, neurocan, and brevican and the link domains of the vertebrate HAPLN (HA and proteoglycan binding link) protein family. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates in which other CSPGs substitute for aggregan might contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN gene family are physically linked adjacent to CSPG genes. TSG-6 contains a single link module which supports high affinity binding with HA. The functional HA-binding domain of CD44 is an extended domain comprised of a link module flanked with N-and C- extensions. These extensions are essential for folding and functional activity. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of the CSPG aggrecan are involved in interaction with HA. Aggrecan in addition contains a second globular domain (G2) which contains link modules 3 and 4 which lack HA-binding activity. HAPLNs contain two contiguous link modules. 92 matched cddid_all.tbl CDD cd01104 cd01104 133379 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins. 68 matched cddid_all.tbl CDD cd01105 cd01105 133380 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. 88 matched cddid_all.tbl CDD cd01106 cd01106 133381 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Unique to this family, is a TipAL-like, lineage specific Bacilli subgroup, which has five conserved cysteines in the C-terminus of the protein. 103 matched cddid_all.tbl CDD cd01107 cd01107 133382 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. 108 matched cddid_all.tbl CDD cd01108 cd01108 133383 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. 127 matched cddid_all.tbl CDD cd01109 cd01109 133384 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. 113 matched cddid_all.tbl CDD cd01110 cd01110 133385 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center. 139 matched cddid_all.tbl CDD cd01111 cd01111 133386 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs, and organic substrates. 107 matched cddid_all.tbl CDD cd01115 cd01115 238535 SLC13_permease Permease SLC13 (solute carrier 13). The sodium/dicarboxylate cotransporter NaDC-1 has been shown to translocate Krebs cycle intermediates such as succinate, citrate, and alpha-ketoglutarate across plasma membranes rabbit, human, and rat kidney. It is related to renal and intestinal Na+/sulfate cotransporters and a few putative bacterial permeases. The SLC13-type proteins belong to the ArsB/NhaD superfamily of permeases that translocate sodium and various anions across biological membranes in all three kingdoms of life. A typical ArsB/NhaD permease is composed of 8-13 transmembrane helices. 382 matched cddid_all.tbl CDD cd01116 cd01116 238536 P_permease Permease P (pink-eyed dilution). Mutations in the human melanosomal P gene were responsible for classic phenotype of oculocutaneous albinism type 2 (OCA2). Although the precise function of the P protein is unknown, it was predicted to regulate the intraorganelle pH, together with the ATP-driven proton pump. It shows significant sequence similarity to the Na+/H+ antiporter NhaD from Vibrio parahaemolyticus. Both proteins belong to ArsB/NhaD superfamily of permeases that translocate sodium, arsenate, sulfate, and organic anions across biological membranes in all three kingdoms of life. A typical ArsB/NhaD permease contains 8-13 transmembrane domains. 413 matched cddid_all.tbl CDD cd01117 cd01117 238537 YbiR_permease Putative anion permease YbiR. Based on sequence similarity, YbiR proteins are predicted to function as anion translocating permeases in eubacteria, archaea and plants. They belong to ArsB/NhaD superfamily of permeases that have been shown to translocate sodium, sulfate, arsenite and organic anions. A typical ArsB/NhaD permease is composed of 8-13 transmembrane domains. 384 matched cddid_all.tbl CDD cd01118 cd01118 238538 ArsB_permease Anion permease ArsB. These permeases have been shown to export arsenate and antimonite in eubacteria and archaea. A typical ArsB permease contains 8-13 transmembrane helices and can function either independently as a chemiosmotic transporter or as a channel-forming subunit of an ATP-driven anion pump (ArsAB). The ArsAB complex is similar in many ways to ATP-binding cassette transporters, which have two groups of six transmembrane-spanning helical segments and two nucleotide-binding domains. The ArsB proteins belong to the ArsB/NhaD superfamily of permeases that translocate sodium, arsenate, sulfate, and organic anions across biological membranes in all three kingdoms of life. 416 matched cddid_all.tbl CDD cd01119 cd01119 238539 Chemokine_CC_DCCL Chemokine_CC_DCCL: subgroup of the Chemokine_CC subgroup based on the presence of a DCCL motif involving the two N-terminal cysteine residues; includes a number of small inducible cytokines capable of reversibly inhibiting normal hematopoietic progenitor proliferation by blocking progression through the cell cycle; DCCL subgroup contains Exodus-1 (also known as CCL20, MIP-3alpha, LARC, ST38 (mouse)), Exodus-2 (also known as CCL21, SLC, 6-Ckine, TCA4, CKbeta9), and Exodus-3 (also known as CCL-19, ELC, MIP-3beta, CKbeta11). Exodus-3 was shown to inhibit the growth of human breast cancer cells in vivo in a mouse model; Exodus-1, -2, and -3 were all shown to significantly inhibit chronic myelogenous leukemia progenitor cell proliferation; Exodus-2 and -3 show potent immunotherapeutic activity toward solid tumors; chemotatic for T cells, B cells, dendritic cells, macrophage progenitor cells, and NK cells; exist as monomers and dimers, but are believed to be functional as monomers; found only in vertebrates. See CDs: Chemokine_CC (cd00272) for the entire CC subgroup, Chemokine (cd00169) for the general alignment of chemokines, or Chemokine_CXC (cd00273), Chemokine_C (cd00271), and Chemokine_CX3C (cd00274) for the additional chemokine subgroups. 61 matched cddid_all.tbl CDD cd01120 cd01120 410865 RecA-like_superfamily RecA-like_NTPases. RecA-like NTPases. This superfamily includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 119 matched cddid_all.tbl CDD cd01121 cd01121 410866 RadA_SMS_N bacterial RadA DNA repair protein. Sms or bacterial RadA is a DNA repair protein that plays a role in recombination and recombinational repair of DNA damaged by UV radiation, X-rays, and chemical agent and is responsible for the stabilization or processing of branched DNA molecules. 268 matched cddid_all.tbl CDD cd01122 cd01122 410867 Twinkle_C C-terminal domain of Twinkle. Twinkle ( T7 gp4-like protein with intramitochondrial nucleoid localization, also known as C10orf2, PEO1, SCA8, ATXN8, IOSCA, PEOA3 or SANDO) is a homohexameric DNA helicases which unwinds short stretches of double-stranded DNA in the 5' to 3' direction and, along with mitochondrial single-stranded DNA binding protein and mtDNA polymerase gamma, is thought to play a key role in mtDNA replication. Mutations in the human gene cause infantile onset spinocerebellar ataxia (IOSCA) and progressive external ophthalmoplegia (PEO) and are also associated with several mitochondrial depletion syndromes. This group also contains viral GP4-like and related bacterial helicases. 266 matched cddid_all.tbl CDD cd01123 cd01123 410868 Rad51_DMC1_archRadA recombinase Rad51, DMC1, and archaeal RadA. This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal protein RadA. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 . 234 matched cddid_all.tbl CDD cd01124 cd01124 410869 KaiC-like Circadian Clock Protein KaiC. KaiC is a circadian clock protein, most studied in cyanobacteria. KaiC, an autokinase, autophosphatase, and ATPase, is part of the core oscillator, composed of three proteins: KaiA, KaiB, and KaiC. The circadian oscillation is regulated via KaiC phosphorylation. 222 matched cddid_all.tbl CDD cd01125 cd01125 410870 RepA_RSF1010_like Hexameric Replicative Helicase RepA of plasmid RSF1010 and related proteins. This family includes the homo-hexameric replicative helicase RepA encoded by plasmid RSF1010. RSF1010 is found in most Gram-negative bacteria and some Gram-positive bacteria . The RepA protein of Plasmid RSF1010 is a 5'-3' DNA helicase which can utilize ATP, dATP, GTP and dGTP (and CTP and dCTP to a lesser extent). 238 matched cddid_all.tbl CDD cd01127 cd01127 410871 TrwB_TraG_TraD_VirD4 TrwB/TraG/TraD/VirD4 family of bacterial conjugation proteins. The TraG/TraD/VirD4 family are bacterial conjugation proteins involved in type IV secretion (T4S) systems, versatile bacterial secretion systems mediating transport of protein and/or DNA. They are present in gram-negative and gram-positive bacteria, as well as archaea. They form hexameric rings and belong to the RecA-like NTPases superfamily, which also includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. 144 matched cddid_all.tbl CDD cd01128 cd01128 410872 rho_factor_C C-terminal ATP binding domain of transcription termination factor rho. Transcription termination factor rho is a bacterial ATP-dependent RNA/DNA helicase. It is a homohexamer. Each monomer consists of an N-terminal oligonucleotide/oligosaccharide binding fold (OB-fold) domain which binds cysteine-rich nucleotides, and a C-terminal ATP binding domain. This alignment is of the C-terminal ATP binding domain. 249 matched cddid_all.tbl CDD cd01129 cd01129 410873 PulE-GspE-like PulE-GspE family. PulE and General secretory pathway protein GspE are ATPases of the type II secretory pathway, the main terminal branch of the general secretory pathway (GSP). PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PilB, a type IV pilus assembly ATPase, DotB, an ATPase of the type IVb secretion system, also known as the dot/icm system, Escherichia coli IncI plasmid-encoded conjugative transfer ATPase TraJ, and HofB. 159 matched cddid_all.tbl CDD cd01130 cd01130 410874 VirB11-like_ATPase Type IV secretory pathway component VirB11-like. Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir (virulence) proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the bacterial Ti (tumor-inducing)-plasmid into plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11-related ATPases include Sulfolobus acidocaldarius FlaI, which plays key roles in archaellum (archaeal flagellum) assembly and motility functions, and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase. 177 matched cddid_all.tbl CDD cd01131 cd01131 410875 PilT Pilus retraction ATPase PilT. Pilus retraction ATPase PilT is a nucleotide-binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility. 223 matched cddid_all.tbl CDD cd01132 cd01132 410876 F1-ATPase_alpha_CD F1 ATP synthase alpha subunit, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The mitochondrial extrinsic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic. Alpha and beta subunits form the globular catalytic moiety, a hexameric ring of alternating alpha and beta subunits. Gamma, delta and epsilon subunits form a stalk, connecting F1 to F0, the integral membrane proton-translocating domain. 274 matched cddid_all.tbl CDD cd01133 cd01133 410877 F1-ATPase_beta_CD F1 ATP synthase beta subunit, central domain. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The mitochondrial extrinsic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic. Alpha and beta subunits form the globular catalytic moiety, a hexameric ring of alternating alpha and beta subunits. Gamma, delta and epsilon subunits form a stalk, connecting F1 to F0, the integral membrane proton-translocating domain. 277 matched cddid_all.tbl CDD cd01134 cd01134 410878 V_A-ATPase_A V/A-type ATP synthase catalytic subunit A. V/A-type ATP synthase catalytic subunit A. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. Vacuolar (V-type) ATPases play major roles in endomembrane and plasma membrane proton transport in eukaryotes. They are found in multiple intracellular membranes including vacuoles, endosomes, lysosomes, Golgi-derived vesicles, secretory vesicles, as well as the plasma membrane. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. 288 matched cddid_all.tbl CDD cd01135 cd01135 410879 V_A-ATPase_B V/A-type ATP synthase subunit B. V/A-type ATP synthase (non-catalytic) subunit B. These ATPases couple ATP hydrolysis to the build up of a H+ gradient, but V-type ATPases do not catalyze the reverse reaction. Vacuolar (V-type) ATPases play major roles in endomembrane and plasma membrane proton transport in eukaryotes. They are found in multiple intracellular membranes including vacuoles, endosomes, lysosomes, Golgi-derived vesicles, secretory vesicles, as well as the plasma membrane. Archaea have a protein which is similar in sequence to V-ATPases, but functions like an F-ATPase (called A-ATPase). A similar protein is also found in a few bacteria. This subfamily consists of the non-catalytic beta subunit. 282 matched cddid_all.tbl CDD cd01136 cd01136 410880 ATPase_flagellum-secretory_path_III Flagellum-specific ATPase/type III secretory pathway virulence-related protein. Flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The bacterial flagellar motor is similar to the F0F1-ATPase, in that they both are proton-driven rotary molecular devices. However, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway. 265 matched cddid_all.tbl CDD cd01137 cd01137 238557 PsaA Metal binding protein PsaA. These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence). 287 matched cddid_all.tbl CDD cd01138 cd01138 238558 FeuA Periplasmic binding protein FeuA. These proteins have predicted to function as initial receptors in ABC transport of metal ions in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains. 248 matched cddid_all.tbl CDD cd01139 cd01139 238559 TroA_f Periplasmic binding protein TroA_f. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains. 342 matched cddid_all.tbl CDD cd01140 cd01140 238560 FatB Siderophore binding protein FatB. These proteins have been shown to function as ABC-type initial receptors in the siderophore-mediated iron uptake in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains. 270 matched cddid_all.tbl CDD cd01141 cd01141 238561 TroA_d Periplasmic binding protein TroA_d. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains. 186 matched cddid_all.tbl CDD cd01142 cd01142 238562 TroA_e Periplasmic binding protein TroA_e. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains. 289 matched cddid_all.tbl CDD cd01143 cd01143 238563 YvrC Periplasmic binding protein YvrC. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria and archaea. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. 195 matched cddid_all.tbl CDD cd01144 cd01144 238564 BtuF Cobalamin binding protein BtuF. These proteins have been shown to function as initial receptors in ABC transport of vitamin B12 (cobalamin) in eubacterial and some archaeal species. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence). 245 matched cddid_all.tbl CDD cd01145 cd01145 238565 TroA_c Periplasmic binding protein TroA_c. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains. 203 matched cddid_all.tbl CDD cd01146 cd01146 238566 FhuD Fe3+-siderophore binding domain FhuD. These proteins have been shown to function as initial receptors in ABC transport of Fe3+-siderophores in many eubacterial species. They belong to the TroA-like superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA-like protein is comprised of two globular subdomains connected by a long alpha helix and binds its specific ligands in the cleft between these domains. 256 matched cddid_all.tbl CDD cd01147 cd01147 238567 HemV-2 Metal binding protein HemV-2. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence). 262 matched cddid_all.tbl CDD cd01148 cd01148 238568 TroA_a Metal binding protein TroA_a. These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. 284 matched cddid_all.tbl CDD cd01149 cd01149 238569 HutB Hemin binding protein HutB. These proteins have been shown to function as initial receptors in ABC transport of hemin and hemoproteins in many eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. 235 matched cddid_all.tbl CDD cd01150 cd01150 173839 AXO Peroxisomal acyl-CoA oxidase. Peroxisomal acyl-CoA oxidases (AXO) catalyze the first set in the peroxisomal fatty acid beta-oxidation, the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. In a second oxidative half-reaction, the reduced FAD is reoxidized by molecular oxygen. AXO is generally a homodimer, but it has been reported to form a different type of oligomer in yeast. There are several subtypes of AXO's, based on substrate specificity. Palmitoyl-CoA oxidase acts on straight-chain fatty acids and prostanoids; whereas, the closely related Trihydroxycoprostanoly-CoA oxidase has the greatest activity for 2-methyl branched side chains of bile precursors. Pristanoyl-CoA oxidase, acts on 2-methyl branched fatty acids. AXO has an additional domain, C-terminal to the region with similarity to acyl-CoA dehydrogenases, which is included in this alignment. 610 matched cddid_all.tbl CDD cd01151 cd01151 173840 GCD Glutaryl-CoA dehydrogenase. Glutaryl-CoA dehydrogenase (GCD). GCD is an acyl-CoA dehydrogenase, which catalyzes the oxidative decarboxylation of glutaryl-CoA to crotonyl-CoA and carbon dioxide in the catabolism of lysine, hydroxylysine, and tryptophan. It uses electron transfer flavoprotein (ETF) as an electron acceptor. GCD is a homotetramer. GCD deficiency leads to a severe neurological disorder in humans. 386 matched cddid_all.tbl CDD cd01152 cd01152 173841 ACAD_fadE6_17_26 Putative acyl-CoA dehydrogenases similar to fadE6, fadE17, and fadE26. Putative acyl-CoA dehydrogenases (ACAD). Mitochondrial acyl-CoA dehydrogenases (ACAD) catalyze the alpha, beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. The ACD family includes the eukaryotic beta-oxidation, as well as amino acid catabolism enzymes. These enzymes share high sequence similarity, but differ in their substrate specificities. The mitochondrial ACD's are generally homotetramers and have an active site glutamate at a conserved position. 380 matched cddid_all.tbl CDD cd01153 cd01153 173842 ACAD_fadE5 Putative acyl-CoA dehydrogenases similar to fadE5. Putative acyl-CoA dehydrogenase (ACAD). Mitochondrial acyl-CoA dehydrogenases (ACAD) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. The ACD family includes the eukaryotic beta-oxidation, as well as amino acid catabolism enzymes. These enzymes share high sequence similarity, but differ in their substrate specificities. The mitochondrial ACD's are generally homotetramers and have an active site glutamate at a conserved position. 407 matched cddid_all.tbl CDD cd01154 cd01154 173843 AidB Proteins involved in DNA damage response, similar to the AidB gene product. AidB is one of several genes involved in the SOS adaptive response to DNA alkylation damage, whose expression is activated by the Ada protein. Its function has not been entirely elucidated; however, it is similar in sequence and function to acyl-CoA dehydrogenases. It has been proposed that aidB directly destroys DNA alkylating agents such as nitrosoguanidines (nitrosated amides) or their reaction intermediates. 418 matched cddid_all.tbl CDD cd01155 cd01155 173844 ACAD_FadE2 Acyl-CoA dehydrogenases similar to fadE2. FadE2-like Acyl-CoA dehydrogenase (ACAD). Acyl-CoA dehydrogenases (ACAD) catalyze the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. The ACAD family includes the eukaryotic beta-oxidation, as well as amino acid catabolism enzymes. These enzymes share high sequence similarity, but differ in their substrate specificities. ACAD's are generally homotetramers and have an active site glutamate at a conserved position. 394 matched cddid_all.tbl CDD cd01156 cd01156 173845 IVD Isovaleryl-CoA dehydrogenase. Isovaleryl-CoA dehydrogenase (IVD) is an is an acyl-CoA dehydrogenase, which catalyzes the third step in leucine catabolism, the conversion of isovaleryl-CoA (3-methylbutyryl-CoA) into 3-methylcrotonyl-CoA. IVD is a homotetramer and has the greatest affinity for small branched chain substrates. 376 matched cddid_all.tbl CDD cd01157 cd01157 173846 MCAD Medium chain acyl-CoA dehydrogenase. MCADs are mitochondrial beta-oxidation enzymes, which catalyze the alpha,beta dehydrogenation of the corresponding medium chain acyl-CoA by FAD, which becomes reduced. The reduced form of MCAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. MCAD is a homotetramer. 378 matched cddid_all.tbl CDD cd01158 cd01158 173847 SCAD_SBCAD Short chain acyl-CoA dehydrogenases and eukaryotic short/branched chain acyl-CoA dehydrogenases. Short chain acyl-CoA dehydrogenase (SCAD). SCAD is a mitochondrial beta-oxidation enzyme. It catalyzes the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of SCAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. This subgroup also contains the eukaryotic short/branched chain acyl-CoA dehydrogenase(SBCAD), the bacterial butyryl-CoA dehydorgenase(BCAD) and 2-methylbutyryl-CoA dehydrogenase, which is involved in isoleucine catabolism. These enzymes are homotetramers. 373 matched cddid_all.tbl CDD cd01159 cd01159 173848 NcnH Naphthocyclinone hydroxylase. Naphthocyclinone is an aromatic polyketide and an antibiotic, which is active against Gram-positive bacteria. Polyketides are secondary metabolites, which have important biological functions such as antitumor, immunosupressive or antibiotic activities. NcnH is a hydroxylase involved in the biosynthesis of naphthocyclinone and possibly other polyketides. 370 matched cddid_all.tbl CDD cd01160 cd01160 173849 LCAD Long chain acyl-CoA dehydrogenase. LCAD is an acyl-CoA dehydrogenases (ACAD), which is found in the mitochondria of eukaryotes and in some prokaryotes. It catalyzes the alpha, beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of LCAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. LCAD acts as a homodimer. 372 matched cddid_all.tbl CDD cd01161 cd01161 173850 VLCAD Very long chain acyl-CoA dehydrogenase. VLCAD is an acyl-CoA dehydrogenase (ACAD), which is found in the mitochondria of eukaryotes and in some bacteria. It catalyzes the alpha,beta dehydrogenation of the corresponding trans-enoyl-CoA by FAD, which becomes reduced. The reduced form of ACAD is reoxidized in the oxidative half-reaction by electron-transferring flavoprotein (ETF), from which the electrons are transferred to the mitochondrial respiratory chain coupled with ATP synthesis. VLCAD acts as a homodimer. 409 matched cddid_all.tbl CDD cd01162 cd01162 173851 IBD Isobutyryl-CoA dehydrogenase. Isobutyryl-CoA dehydrogenase (IBD) catalyzes the alpha, beta- dehydrogenation of short branched chain acyl-CoA intermediates in valine catabolism. It is predicted to be a homotetramer. 375 matched cddid_all.tbl CDD cd01163 cd01163 173852 DszC Dibenzothiophene (DBT) desulfurization enzyme C. DszC is a flavin reductase dependent enzyme, which catalyzes the first two steps of DBT desulfurization in mesophilic bacteria. DszC converts DBT to DBT-sulfoxide, which is then converted to DBT-sulfone. Bacteria with this enzyme are candidates for the removal of organic sulfur compounds from fossil fuels, which pollute the environment. An equivalent enzyme tdsC, is found in thermophilic bacteria. This alignment also contains a closely related uncharacterized subgroup. 377 matched cddid_all.tbl CDD cd01164 cd01164 238570 FruK_PfkB_like 1-phosphofructokinase (FruK), minor 6-phosphofructokinase (pfkB) and related sugar kinases. FruK plays an important role in the predominant pathway for fructose utilisation.This group also contains tagatose-6-phophate kinase, an enzyme of the tagatose 6-phosphate pathway, which responsible for breakdown of the galactose moiety during lactose metabolism by bacteria such as L. lactis. 289 matched cddid_all.tbl CDD cd01165 cd01165 349496 BTB_POZ BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily. Proteins in this superfamily are characterized by the presence of a common protein-protein interaction motif of about 100 amino acids, known as the BTB/POZ domain. Members include transcription factors, oncogenic proteins, ion channel proteins, and potassium channel tetramerization domain (KCTD) proteins. They have been identified in poxviruses and many eukaryotes, and have diverse functions, such as transcriptional regulation, chromatin remodeling, protein degradation and cytoskeletal regulation. Many BTB/POZ proteins contain one or two additional domains, such as kelch repeats, zinc-finger domains, FYVE (Fab1, YOTB, Vac1, and EEA1) fingers, or ankyrin repeats, among others. These special additional domains or interaction partners provide unique characteristics and functions to BTB/POZ proteins. In ion channel proteins and KCTD proteins, the BTB/POZ domain is also called the tetramerization (T1) domain. 79 matched cddid_all.tbl CDD cd01166 cd01166 238571 KdgK 2-keto-3-deoxygluconate kinase (KdgK) phosphorylates 2-keto-3-deoxygluconate (KDG) to form 2-keto-3-deoxy-6-phosphogluconate (KDGP). KDG is the common intermediate product, that allows organisms to channel D-glucuronate and/or D-galacturinate into the glycolysis and therefore use polymers, like pectin and xylan as carbon sources. 294 matched cddid_all.tbl CDD cd01167 cd01167 238572 bac_FRK Fructokinases (FRKs) mainly from bacteria and plants are enzymes with high specificity for fructose, as are all FRKs, but they catalyzes the conversion of fructose to fructose-6-phosphate, which is an entry point into glycolysis via conversion into glucose-6-phosphate. This is in contrast to FRKs [or ketohexokinases (KHKs)] from mammalia and halophilic archaebacteria, which phosphorylate fructose to fructose-1-phosphate. 295 matched cddid_all.tbl CDD cd01168 cd01168 238573 adenosine_kinase Adenosine kinase (AK) catalyzes the phosphorylation of ribofuranosyl-containing nucleoside analogues at the 5'-hydroxyl using ATP or GTP as the phosphate donor.The physiological function of AK is associated with the regulation of extracellular adenosine levels and the preservation of intracellular adenylate pools. Adenosine kinase is involved in the purine salvage pathway. 312 matched cddid_all.tbl CDD cd01169 cd01169 238574 HMPP_kinase 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate kinase (HMPP-kinase) catalyzes two consecutive phosphorylation steps in the thiamine phosphate biosynthesis pathway, leading to the synthesis of vitamin B1. The first step is the phosphorylation of the hydroxyl group of HMP to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine phosphate (HMP-P) and then the phophorylation of HMP-P to form 4-amino-5-hydroxymethyl-2-methyl-pyrimidine pyrophosphate (HMP-PP), which is the substrate for the thiamine synthase coupling reaction. 242 matched cddid_all.tbl CDD cd01170 cd01170 238575 THZ_kinase 4-methyl-5-beta-hydroxyethylthiazole (Thz) kinase catalyzes the phosphorylation of the hydroxylgroup of Thz. A reaction that allows cells to recycle Thz into the thiamine biosynthesis pathway, as an alternative to its synthesis from cysteine, tyrosine and 1-deoxy-D-xylulose-5-phosphate. 242 matched cddid_all.tbl CDD cd01171 cd01171 238576 YXKO-related B.subtilis YXKO protein of unknown function and related proteins. Based on the conservation of the ATP binding site, the substrate binding site and the Mg2+binding site and structural homology this group is a member of the ribokinase-like superfamily. 254 matched cddid_all.tbl CDD cd01172 cd01172 238577 RfaE_like RfaE encodes a bifunctional ADP-heptose synthase involved in the biosynthesis of the lipopolysaccharide (LPS) core precursor ADP-L-glycero-D-manno-heptose. LPS plays an important role in maintaining the structural integrity of the bacterial outer membrane of gram-negative bacteria. RfaE consists of two domains, a sugar kinase domain, represented here, and a domain belonging to the cytidylyltransferase superfamily. 304 matched cddid_all.tbl CDD cd01173 cd01173 238578 pyridoxal_pyridoxamine_kinase Pyridoxal kinase plays a key role in the synthesis of the active coenzyme pyridoxal-5'-phosphate (PLP), by catalyzing the phosphorylation of the precursor vitamin B6 in the presence of Zn2+ and ATP. Mammals are unable to synthesize PLP de novo and require its precursors in the form of vitamin B6 (pyridoxal, pyridoxine, and pyridoxamine) from their diet. Pyridoxal kinase encoding genes are also found in many other species including yeast and bacteria. 254 matched cddid_all.tbl CDD cd01174 cd01174 238579 ribokinase Ribokinase catalyses the phosphorylation of ribose to ribose-5-phosphate using ATP. This reaction is the first step in the ribose metabolism. It traps ribose within the cell after uptake and also prepares the sugar for use in the synthesis of nucleotides and histidine, and for entry into the pentose phosphate pathway. Ribokinase is dimeric in solution. 292 matched cddid_all.tbl CDD cd01175 cd01175 238580 IPT_COE IPT domain of the COE family (Col/Olf-1/EBF) of non-basic, helix-loop-helix (HLH)-containing transcription factors. COE family proteins are all transcription factors and play an important role in variety of developmental processes. Mouse EBF is involved in the regulation of the early stages of B-cell differentiation, Drosophila collier is a regulator of the head patterning, and a related protein in Xenopus is involved in primary neurogenesis. All COE family members have a well conserved DNA binding domain that contains an atypical Zn finger motif. The function of the IPT domain is unknown. 85 matched cddid_all.tbl CDD cd01176 cd01176 238581 IPT_RBP-Jkappa IPT domain of the recombination signal Jkappa binding protein (RBP-Jkappa). RBP-J kappa, was initially considered to be involved in V(D)J recombination because of its DNA binding specificity and structural similarity to site-specific recombinases known as the integrase family. Further studies indicated that RBP-J kappa functions as a repressor of transcription, via destabilization of the general transcription factor IID and recruitment of histone deacetylase complexes. 97 matched cddid_all.tbl CDD cd01177 cd01177 238582 IPT_NFkappaB IPT domain of the transcription factor NFkappaB and related transcription factors. NFkappaB is considered a central regulator of stress responses, activated by different stressful conditions, including physical stress, oxidative stress, and exposure to certain chemicals. NFkappaB blocking cell apoptosis in several cell types, gives it an important role in cell proliferation and differentiation. 102 matched cddid_all.tbl CDD cd01178 cd01178 238583 IPT_NFAT IPT domain of the NFAT family of transcription factors. NFAT transcription complexes are a target of calcineurin, a calcium dependent phosphatase, and activate genes mainly involved in cell-cell-interaction. 101 matched cddid_all.tbl CDD cd01179 cd01179 238584 IPT_plexin_repeat2 Second repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present preceeded by SEMA (semaphorin) and PSI (plexin, semaphorin, integrin) domains. 85 matched cddid_all.tbl CDD cd01180 cd01180 238585 IPT_plexin_repeat1 First repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present preceeded by SEMA (semaphorin) and PSI (plexin, semaphorin, integrin) domains. 94 matched cddid_all.tbl CDD cd01181 cd01181 238586 IPT_plexin_repeat3 Third repeat of the IPT domain of Plexins and Cell Surface Receptors (PCSR) . Plexins are involved in the regulation of cell proliferation and of cellular adhesion and repulsion receptors. In general, there are three copies of the IPT domain present preceeded by SEMA (semaphorin) and PSI (plexin, semaphorin, integrin) domains. 99 matched cddid_all.tbl CDD cd01182 cd01182 271183 INT_RitC_C_like C-terminal catalytic domain of recombinase RitC, a component of the recombinase trio. Recombinases belonging to the RitA (also known as pAE1 due to its presence in the deletion prone region of plasmid pAE1 of Alcaligenes eutrophus H1), RitB, and RitC families are associated in a complex referred to as a Recombinase in Trio (RIT) element. These RIT elements consist of three adjacent and unidirectional overlapping genes, one from each family (ritABC in order of transcription). All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not yet fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. 186 matched cddid_all.tbl CDD cd01184 cd01184 271184 INT_C_like_1 Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain. Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain containing six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity. 180 matched cddid_all.tbl CDD cd01185 cd01185 271185 INTN1_C_like Integrase IntN1 of Bacteroides mobilizable transposon NBU1 and similar proteins, C-terminal catalytic domain. IntN1 is a tyrosine recombinase for the integration and excision of Bacteroides mobilizable transposon NBU1 from the host chromosome. IntN1 does not require strict homology between the recombining sites seen with other tyrosine recombinases. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. 161 matched cddid_all.tbl CDD cd01186 cd01186 271186 INT_tnpA_C_Tn554 Putative Transposase A from transposon Tn554, C-terminal catalytic domain. This family includes putative Transposase A from transposon Tn554. It belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity. 184 matched cddid_all.tbl CDD cd01187 cd01187 271187 INT_tnpB_C_Tn554 Putative Transposase B from transposon Tn554, C-terminal catalytic domain. This family includes putative Transposase B from transposon Tn554. It belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain containing six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity. 142 matched cddid_all.tbl CDD cd01188 cd01188 271188 INT_RitA_C_like C-terminal catalytic domain of recombinase RitA, a component of the recombinase trio. Recombinases RitA (also known as pAE1), RitB, and RitC are encoded by three adjacent and overlapping genes. Collectively they are known as the Recombinase in Trio (RIT). This RitA family includes various bacterial integrases and integrases from the deletion-prone region of plasmid pAE1 of Alcaligenes eutrophus H1. All three integrases contain a catalytic motif, suggesting that they are all active enzymes. However, their specific roles are not fully understood. All three families belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism is essentially identical and involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. 179 matched cddid_all.tbl CDD cd01189 cd01189 271189 INT_ICEBs1_C_like C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons. This family of tyrosine based site-specific integrases is has origins in bacterial phages and conjugate transposons. One member is the integrase from Bacillus subtilis conjugative transposon ICEBs1. ICEBs1 can be excised and transfered to various recipients in response to DNA damage or high concentrations of potential mating partners. The family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. 147 matched cddid_all.tbl CDD cd01190 cd01190 271190 INT_StrepXerD_C_like Putative XerD in Streptococcus pneumonia and similar proteins, C-terminal catalytic domain. This family includes a putative XerD recombinase in Streptococcus pneumonia and similar tyrosine recombinases. However, the members of this family contain unusual active site motifs from the XerD from Escherichia coli. E. coli XerD and homologous enzymes show four conserved amino acids R-H-R-H that are spaced along the C-terminal domain. The putative S. pneumoniae XerD contains three unique replacements at the conserved positions resulting in L-Q-R-L. Severe growth defects in a loss-of-function xerD mutant demonstrate an important in vivo function of the S. pneumoniae XerD protein. This family belongs to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their catalytic domain and the overall reaction mechanism. The catalytic domain contains six conserved active site residues. Their overall reaction mechanism involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. 150 matched cddid_all.tbl CDD cd01191 cd01191 271191 INT_C_like_2 Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain. Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity. 176 matched cddid_all.tbl CDD cd01192 cd01192 271192 INT_C_like_3 Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain. Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity. 178 matched cddid_all.tbl CDD cd01193 cd01193 271193 INT_IntI_C Integron integrase and similar protiens, C-terminal catalytic domain. Integron integrases mediate site-specific DNA recombination between a proximal primary site (attI) and a secondary target site (attC) found within mobile gene cassettes encoding resistance or virulence factors. Unlike other site specific recombinases, the attC sites lack sequence conservation. Integron integrase exhibits broader DNA specificity by recognizing the non-conserved attC sites. The structure shows that DNA target site recognition are not dependent on canonical DNA but on the position of two flipped-out bases that interact in cis and in trans with the integrase. Integron-integrases are present in many natural occurring mobile elements, including transposons and conjugative plasmids. Vibrio, Shewanella, Xanthomonas, and Pseudomonas species harbor chromosomal super-integrons. All integron-integrases carry large inserts unlike the TnpF ermF-like proteins also seen in this group. 176 matched cddid_all.tbl CDD cd01194 cd01194 271194 INT_C_like_4 Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain. Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity. 174 matched cddid_all.tbl CDD cd01195 cd01195 271195 INT_C_like_5 Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain. Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity. 170 matched cddid_all.tbl CDD cd01196 cd01196 271196 INT_C_like_6 Uncharacterized site-specific tyrosine recombinase, C-terminal catalytic domain. Tyrosine recombinase (integrase) belongs to a DNA breaking-rejoining enzyme superfamily. The catalytic domain contains six conserved active site residues. The recombination reaction involves cleavage of a single strand of a DNA duplex by nucleophilic attack of a conserved tyrosine to give a 3' phosphotyrosyl protein-DNA adduct. In the second rejoining step, a terminal 5' hydroxyl attacks the covalent adduct to release the enzyme and generate duplex DNA. Many DNA breaking-rejoining enzymes also have N-terminal domains, which show little sequence or structure similarity. 183 matched cddid_all.tbl CDD cd01197 cd01197 271197 INT_FimBE_like FimB and FimE and related proteins, integrase/recombinases. This CD includes proteins similar to E.coli FimE and FimB and Proteus mirabilis MrpI. FimB and FimE are the regulatory proteins during expression of type 1 fimbriae in Escherichia coli. The fimB and fimE proteins direct the phase switch into the 'on' and 'off' position. MrpI is the regulatory protein of proteus mirabilis fimbriae expression. This family belongs to the integrase/recombinase superfamily. 181 matched cddid_all.tbl CDD cd01200 cd01200 238605 WHEPGMRS_RNA EPRS-like_RNA binding domain. This short RNA-binding domain is found in several higher eukaryote aminoacyl-tRNA synthetases (aaRSs). It is found in three copies in the mammalian bifunctional EPRS in a region that separates the N-terminal GluRS from the C-terminal ProRS. In the Drosophila EPRS, this domain is repeated six times. It is found at the N-terminus of TrpRS, HisRS and GlyR and at the C-terminus of MetRS. This domain consists of a helix- turn- helix structure, which is similar to other RNA-binding proteins. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions, which are important for the formation of aaRSs into multienzyme complexes. 42 matched cddid_all.tbl CDD cd01201 cd01201 275391 PH_BEACH Pleckstrin homology domain in BEACH domain containing proteins. The BEACH domain is present in several eukaroyotic proteins CHS, neurobeachin (Nbea), LRBA (also called BGL, beige-like, or CDC4L), FAN, KIAA1607, and LvsA-LvsF. CHS is a rare, autosomal recessive disorder that can cause severe immunodeficiency and albinism in mammals and beige is the name for the CHS disease in mice. The CHS disease is associated with the presence of giant, perinuclear vesicles (lysosomes, melanosomes, and others) and CHS protein is thought to play an important role in the fusion, fission, or trafficking of these vesicles. All BEACH proteins contain the following domains: PH, BEACH, and WD40. The WD40 domain is involved in mediating protein-protein interactions involved in targeting proteins to subcellular compartments. The combined PH-BEACH motifs may present a single continuous structural unit involved in protein binding. Some members have an additional N-terminal Laminin G-like (LamG) domains Ca++ mediated receptors or an additional C-terminal FYVE zinc-binding domain which targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 112 matched cddid_all.tbl CDD cd01202 cd01202 269913 PTB_FRS2 Fibroblast growth factor receptor substrate 2 phosphotyrosine-binding domain. FRS2 (also called Suc1-associated neurotrophic factor (SNT)-induced tyrosine-phosphorylated target) proteins are membrane-anchored adaptor proteins. They are composed of an N-terminal myristoylation site followed by a phosphotyrosine binding (PTB) domain, which has a PH-like fold, and a C-terminal effector domain containing multiple tyrosine and serine/threonine phosphorylation site. The FRS2/SNT proteins show increased tyrosine phosphorylation by activated receptors, such as fibroblast growth factor receptor (FGFR) and TrkA, recruit SH2 domain containing proteins such as Grb2, and mediate signals from activated receptors to a variety of downstream pathways. The PTB domains of the SNT proteins directly interact with the canonical NPXpY motif of TrkA in a phosphorylationdependent manner, they directly bind to the juxtamembrane region of FGFR in a phosphorylation-independent manner. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the IRS-like subgroup. 92 matched cddid_all.tbl CDD cd01203 cd01203 269914 PTB_DOK1_DOK2_DOK3 Downstream of tyrosine kinase 1, 2, and 3 proteins phosphotyrosine-binding domain (PTBi). The Dok family adapters are phosphorylated by different protein tyrosine kinases. Dok proteins are involved in processes such as modulation of cell differentiation and proliferation, as well as in control of the cell spreading and migration The Dok protein contains an N-terminal pleckstrin homology (PH) domain followed by a central phosphotyrosine binding (PTB) domain, which has a PH-like fold, and a proline- and tyrosine-rich C-terminal tail. The PH domain is binds to acidic phospholids and localizes proteins to the plasma membrane, while the PTB domain mediates protein-protein interactions by binding to phosphotyrosine-containing motifs. The C-terminal part of Dok contains multiple tyrosine phosphorylation sites that serve as potential docking sites for Src homology 2-containing proteins such as ras GTPase-activating protein and Nck, leading to inhibition of ras signaling pathway activation and the c-Jun N-terminal kinase (JNK) and c-Jun activation, respectively. There are 7 mammalian Dok members: Dok-1 to Dok-7. Dok-1 and Dok-2 act as negative regulators of the Ras-Erk pathway downstream of many immunoreceptor-mediated signaling systems, and it is believed that recruitment of p120 rasGAP by Dok-1 and Dok-2 is critical to their negative regulation. Dok-3 is a negative regulator of the activation of JNK and mobilization of Ca2+ in B-cell receptor-mediated signaling, interacting with SHIP-1 and Grb2. Dok-4- 6 play roles in protein tyrosine kinase(PTK)-mediated signaling in neural cells and Dok-7 is the key cytoplasmic activator of MuSK (Muscle-Specific Protein Tyrosine Kinase). PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the IRS-like subgroup. 99 matched cddid_all.tbl CDD cd01204 cd01204 269915 PTB_IRS Insulin receptor substrate phosphotyrosine-binding domain (PTBi). Insulin receptor substrate (IRS) molecules are mediators in insulin signaling and play a role in maintaining basic cellular functions such as growth and metabolism. They act as docking proteins between the insulin receptor and a complex network of intracellular signaling molecules containing Src homology 2 (SH2) domains. Four members (IRS-1, IRS-2, IRS-3, IRS-4) of this family have been identified that differ as to tissue distribution, subcellular localization, developmental expression, binding to the insulin receptor, and interaction with SH2 domain-containing proteins. IRS molecules have an N-terminal PH domain, followed by an IRS-like PTB domain which has a PH-like fold. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the IRS-like subgroup. 106 matched cddid_all.tbl CDD cd01205 cd01205 269916 EVH1_WASP-like WASP family proteins EVH1 domain. The Wiskott-Aldrich Syndrome Protein (WASP; also called Bee1p) and its homolog N (neuronal)-WASP are signal transduction proteins that promote actin polymerization in response to upstream intracellular signals. WAS is an X-linked recessive disease, characterized by eczema, immunodeficiency, and thrombocytopenia. The majority of patients with WAS, or a milder version of the disorder, X-linked thrombocytopenia (XLT), have point mutations in the EVH1 domain of WASP. WASP is an actin regulatory protein consisting of an N-terminal EVH1 domain called WH1 which binds LPPPEP peptides, a basic region (B), a GTP binding domain (GBP), a proline rich region, a WH2 domain, and a verprolin-cofilin-acidic motif (VCA) which activates the actin-related protein (Arp)2/3 actin nucleating complex. The B, GBD, and the proline-rich region are involved in autoinhibitory interactions that repress or block the activity of the VCA. Yeast members lack the GTP binding domain. The EVH1 domains are part of the PH domain superamily. There are 5 EVH1 subfamilies: Enables/VASP, Homer/Vesl, WASP, Dcp1, and Spred. Ligands are known for three of the EVH1 subfamilies, all of which bind proline-rich sequences: the Enabled/VASP family binds to FPPPP peptides, the Homer/Vesl family binds PPxxF peptides, and the WASP family binds LPPPEP peptides. EVH1 has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains. 101 matched cddid_all.tbl CDD cd01206 cd01206 269917 EVH1_Homer_Vesl Homer/Vesl family proteins EVH1 domain. Homer/Vesl proteins are synaptic scaffolding proteins, required for long-term potentiation, a form of synaptic plasticity thought to underlie memory formation. They contains an N-terminal EVH1 domain and bind to both neurotransmitter receptors, such as the metabotropic group 1 glutamate receptor (mGluR) and to other scaffolding proteins via PPXXF motifs, in order to target them to the synaptic junction. These mGluRs possess a long C-terminal intracellular tail that may be important for subcellular localization of the receptor. The C-terminus is also the site of binding by the immediate early gene (IEG), Homer 1a. In contrast to Homer 1a, other Homer members additionally encode a C-terminal coiled-coil (CC) domain and form multivalent complexes that bind group 1 mGluRs. Homer 1a competes with constitutively expressed CC-Homers to modify the association of group 1 mGluRs with CC-Homer complexes. Since Homer proteins are strikingly enriched at the postsynaptic density (PSD), these observations suggest a role for the Homer family in regulating synaptic metabotropic receptor function. PSD-Zip45 (also named Homer 1c/Vesl-1L) has an EVH1 domain with a longer alpha-helix and its linking part included in the conserved region of Homer 1 (CRH1) interacts with the EVH1 domain of the neighbour CRH1 molecule in the crystal, suggesting that the EVH1 domain recognizes the PPXXF motif found in the binding partners, and the SPLTP sequence (P-motif) in the linking region of the CRH1. The two types of binding are partly overlapped in the EVH1 domain, implying a mechanism to regulate multimerization of Homer 1 family proteins. Homer 2 and Homer 3 are negative regulators of T cell activation. They bind the nuclear factor of activated T cells (NFAT) and compete with calcineurin binding. NFAT plays a critical role in calcium-dependent signaling in other cell types, including muscle and neurons. Homer-NFAT binding is also antagonized by active serine-threonine kinase AKT, enhancing TCR signaling via calcineurin-dependent dephosphorylation of NFAT resulting in changes in cytokine expression and an increase in effector-memory T cell populations in Homer-deficient mice. The EVH1 domains are part of the PH domain superamily. There are 5 EVH1 subfamilies: Enables/VASP, Homer/Vesl, WASP, Dcp1, and Spred. Ligands are known for three of the EVH1 subfamilies, all of which bind proline-rich sequences: the Enabled/VASP family binds to FPPPP peptides, the Homer/Vesl family binds PPxxF peptides, and the WASP family binds LPPPEP peptides. EVH1 has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains. 109 matched cddid_all.tbl CDD cd01207 cd01207 269918 EVH1_Ena_VASP-like Enabled/VASP family EVH1 domain. Ena/VASP family includes proteins such as: Vasodilator-stimulated phosphoprotein (VASP), enabled gene product from Drosophila (Ena), mammalian enabled (Mena) and Ena/VASP-Like protein (EVL) localize to focal adhesions and to sites of actin filament dynamics. These proteins share a common modular organization with a highly conserved N- and C-terminal domains, termed Ena/VASP homology domains 1 and 2 (EVH1 and EVH2), that are separated by a central proline-rich domain. The EVH1 domain binds to other proteins at proline rich sequences. The majority of Ena-VASP type EVH1 domains recognize FPPPP motifs such as in the focal adhesion proteins zyxin and vinculin, and the ActA surface protein of Listeria monocytogenes, however the LIM3 domain of Tes lacks the FPPPP motif but still binds the EVH1 domain of Mena. It has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains. EVH2 mediates oligomerization within the family. The proline-rich region binds SH3 and WW domains as well as profilin, a protein that regulates actin filament dynamics. The EVH1 domains are part of the PH domain superamily. There are 5 EVH1 subfamilies: Enables/VASP, Homer/Vesl, WASP, Dcp1, and Spred. Ligands are known for three of the EVH1 subfamilies, all of which bind proline-rich sequences: the Enabled/VASP family binds to FPPPP peptides, the Homer/Vesl family binds PPxxF peptides, and the WASP family binds LPPPEP peptides. EVH1 has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains. 108 matched cddid_all.tbl CDD cd01208 cd01208 269919 PTB_X11 X11-like Phosphotyrosine-binding (PTB) domain. The function of the neuronal protein X11 is unknown to date. X11 has a PTB domain followed by two PDZ domains. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Dab-like subgroup. 161 matched cddid_all.tbl CDD cd01209 cd01209 269920 PTB_Shc Shc-like phosphotyrosine-binding (PTB) domain. Shc is a substrate for receptor tyrosine kinases, which can interact with phosphoproteins at NPXY motifs. Shc contains an PTB domain followed by an SH2 domain. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Shc-like subgroup. 170 matched cddid_all.tbl CDD cd01210 cd01210 269921 PTB_EPS8 Epidermal growth factor receptor kinase substrate (EPS8)-like Phosphotyrosine-binding (PTB) domain. EPS8 is a regulator of Rac signaling. It consists of a PTB and an SH3 domain. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Dab-like subgroup. 131 matched cddid_all.tbl CDD cd01211 cd01211 269922 PTB_Rab6GAP GTPase activating protein for Rab 6 Phosphotyrosine-binding (PTB) domain. GAPCenA is a centrosome-associated GTPase activating protein (GAP) for Rab 6. It consists of an N-terminal PTB domain and a C-terminal TBC domain. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Dab-like subgroup. 129 matched cddid_all.tbl CDD cd01212 cd01212 269923 PTB_JIP JNK-interacting protein-like (JIP) Phosphotyrosine-binding (PTB) domain. JIP is a mitogen-activated protein kinase scaffold protein. JIP consists of a C-terminal SH3 domain, followed by a PTB domain. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Dab-like subgroup. 149 matched cddid_all.tbl CDD cd01213 cd01213 269924 PTB_tensin Tensin Phosphotyrosine-binding (PTB) domain. Tensin is a a focal adhesion protein, which contains a C-terminal SH2 domain followed by a PTB domain. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Dab-like subgroup. 136 matched cddid_all.tbl CDD cd01214 cd01214 269925 PTB_FAM43A Family with sequence similarity 43, member A (FAM43A) Phosphotyrosine-binding (PTB) domain. The function of FAM43A is currently unknown. Human FAM43A is located on chromosome 3 at location 3q29. It encodes a 3182 base pair mRNA which possesses one Pleckstrin homology-like domain. The mRNA translates into LOC131583, a hydrophilic protein that is predicted to localize in the nucleus. The FAM43A gene is conserved through a broad range of vertebrates. It is highly conserved from chimpanzees to zebrafish. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. 125 matched cddid_all.tbl CDD cd01215 cd01215 269926 PTB_Dab Disabled (Dab) Phosphotyrosine-binding domain. Dab is a cystosolic adaptor protein, which binds to the cytoplasmic tails of lipoprotein receptors, such as ApoER2 and VLDLR, via its PTB domain. The dab PTB domain has a preference for unphosphorylated tyrosine within an NPxY motif. Additionally, the Dab PTB domain, which is structurally similar to PH domains, binds to phosphatidlyinositol phosphate 4,5 bisphosphate in a manner characteristic of phosphoinositide binding PH domains. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Dab-like subgroup. 147 matched cddid_all.tbl CDD cd01217 cd01217 241252 PTB_CG12581 CG12581 Phosphotyrosine-binding (PTB) domain. The function of CG12581 and its related proteins are unknown to date. Members here contain a single N-terminal PTB domain. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Dab-like subgroup. 166 matched cddid_all.tbl CDD cd01218 cd01218 269927 PH_Phafin2-like Phafin2 (also called EAPF, FLJ13187, ZFYVE18 or PLEKHF2) Pleckstrin Homology (PH) domain. Phafin2 is differentially expressed in the liver cancer cell and regulates the structure and function of the endosomes through Rab5-dependent processes. Phafin2 modulates the cell's response to extracellular stimulation by modulating the receptor density on the cell surface. Phafin2 contains a PH domain and a FYVE domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 123 matched cddid_all.tbl CDD cd01219 cd01219 275392 PH1_FGD1 FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 1, N-terminal Pleckstrin homology (PH) domain. In general, FGDs have a RhoGEF (DH) domain, followed by an N-terminal PH domain, a FYVE domain and a C-terminal PH domain. All FGDs are guanine nucleotide exchange factors that activates the Rho GTPase Cdc42, an important regulator of membrane trafficking. The RhoGEF domain is responsible for GEF catalytic activity, while the N-terminal PH domain is involved in intracellular targeting of the DH domain. Mutations in the FGD1 gene are responsible for the X-linked disorder known as faciogenital dysplasia (FGDY). Both FGD1 and FGD3 are targeted by the ubiquitin ligase SCF(FWD1/beta-TrCP) upon phosphorylation of two serine residues in its DSGIDS motif and subsequently degraded by the proteasome. However, FGD1 and FGD3 induced significantly different morphological changes in HeLa Tet-Off cells and while FGD1 induced long finger-like protrusions, FGD3 induced broad sheet-like protrusions when the level of GTP-bound Cdc42 was significantly increased by the inducible expression of FGD3. They also reciprocally regulated cell motility in inducibly expressed in HeLa Tet-Off cells, FGD1 stimulated cell migration while FGD3 inhibited it. FGD1 and FGD3 therefore play different roles to regulate cellular functions, even though their intracellular levels are tightly controlled by the same destruction pathway through SCF(FWD1/beta-TrCP). PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 108 matched cddid_all.tbl CDD cd01220 cd01220 269928 PH1_FARP1-like FERM, RhoGEF and pleckstrin domain-containing protein 1 and related proteins Pleckstrin Homology (PH) domain, repeat 1. Members here include FARP1 (also called Chondrocyte-derived ezrin-like protein; PH domain-containing family C member 2), FARP2 (also called FIR/FERM domain including RhoGEF; FGD1-related Cdc42-GEF/FRG), and FARP6 (also called Zinc finger FYVE domain-containing protein 24). They are members of the Dbl family guanine nucleotide exchange factors (GEFs) which are upstream positive regulators of Rho GTPases. Little is known about FARP1 and FARP6, though FARP1 has increased expression in differentiated chondrocytes. FARP2 is thought to regulate neurite remodeling by mediating the signaling pathways from membrane proteins to Rac. It is found in brain, lung, and testis, as well as embryonic hippocampal and cortical neurons. FARP1 and FARP2 are composed of a N-terminal FERM domain, a proline-rich (PR) domain, Dbl-homology (DH), and two C-terminal PH domains. FARP6 is composed of Dbl-homology (DH), and two C-terminal PH domains separated by a FYVE domain. This hierarchy contains the first PH repeat. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 109 matched cddid_all.tbl CDD cd01221 cd01221 269929 PH_ephexin Ephexin Pleckstrin homology (PH) domain. Ephexin-1 (also called NGEF/ neuronal guanine nucleotide exchange factor) plays a role in the homeostatic modulation of presynaptic neurotransmitter release. Specific functions are still unknown for Ephexin-2 (also called RhoGEF19) and Ephexin-3 (also called Rho guanine nucleotide exchange factor 5/RhoGEF5, Transforming immortalized mammary oncogene/p60 TIM, and NGEF/neuronalGEF). Ephexin-4 (also called RhoGEF16) acts downstream of EphA2 to promote ligand-independent breast cancer cell migration and invasion toward epidermal growth factor through activation of RhoG. This in turn results in the activation of RhoG which recruits ELMO2 and Dock4 to form a complex with EphA2 at the tips of cortactin-rich protrusions in migrating breast cancer cells. Ephexin-5 is the specific GEF for RhoA activation and the regulation of vascular smooth muscle contractility. It interacts with EPHA4 PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. The members of the Ephexin family contains a RhoGEF (DH) followed by a PH domain and an SH3 domain. The ephexin PH domain is believed to act with the DH domain in mediating protein-protein interactions. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 131 matched cddid_all.tbl CDD cd01223 cd01223 269930 PH_Vav Vav pleckstrin homology (PH) domain. Vav acts as a guanosine nucleotide exchange factor (GEF) for Rho/Rac proteins. They control processes including T cell activation, phagocytosis, and migration of cells. The Vav subgroup of Dbl GEFs consists of three family members (Vav1, Vav2, and Vav3) in mammals. Vav1 is preferentially expressed in the hematopoietic system, while Vav2 and Vav3 are described by broader expression patterns. Mammalian Vav proteins consist of a calponin homology (CH) domain, an acidic region, a catalytic Dbl homology (DH) domain, a PH domain, a zinc finger cysteine rich domain (C1/CRD), and an SH2 domain, flanked by two SH3 domains. In invertebrates such as Drosophila and C. elegans, Vav is missing the N-terminal SH3 domain. The DH domain is involved in RhoGTPase recognition and selectivity and stimulates the reorganization of the switch regions for GDP/GTP exchange. The PH domain is implicated in directing membrane localization, allosteric regulation of guanine nucleotide exchange activity, and as a phospholipid- dependent regulator of GEF activity. Vavs bind RhoGTPases including Rac1, RhoA, RhoG, and Cdc42, while other members of the GEF family are specific for a single RhoGTPase. This promiscuity is thought to be a result of its CRD. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but only a few (less than 10%) display strong specificity in binding inositol phosphates. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinases, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, cytoskeletal associated molecules, and in lipid associated enzymes. 127 matched cddid_all.tbl CDD cd01224 cd01224 269931 PH_Collybistin_ASEF Collybistin/APC-stimulated guanine nucleotide exchange factor pleckstrin homology (PH) domain. Collybistin (also called PEM2) is homologous to the Dbl proteins ASEF (also called ARHGEF4/RhoGEF4) and SPATA13 (Spermatogenesis-associated protein 13; also called ASEF2). It activates CDC42 specifically and not any other Rho-family GTPases. Collybistin consists of an SH3 domain, followed by a RhoGEF/DH and PH domain. In Dbl proteins, the DH and PH domains catalyze the exchange of GDP for GTP in Rho GTPases, allowing them to signal to downstream effectors. It induces submembrane clustering of the receptor-associated peripheral membrane protein gephyrin, which is thought to form a scaffold underneath the postsynaptic membrane linking receptors to the cytoskeleton. It also acts as a tumor suppressor that links adenomatous polyposis coli (APC) protein, a negative regulator of the Wnt signaling pathway and promotes the phosphorylation and degradation of beta-catenin, to Cdc42. Autoinhibition of collybistin is accomplished by the binding of its SH3 domain with both the RhoGEF and PH domains to block access of Cdc42 to the GTPase-binding site. Inactivation promotes cancer progression. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 138 matched cddid_all.tbl CDD cd01225 cd01225 269932 PH_Cool_Pix Cloned out of library/PAK-interactive exchange factor pleckstrin homology (PH) domain. There are two forms of Pix proteins: alpha Pix (also called Rho guanine nucleotide exchange factor (GEF) 6/90Cool-2) and beta Pix (GEF7/p85Cool-1). betaPix contains an N-terminal SH3 domain, a RhoGEF/DH domain, a PH domain, a GIT1 binding domain (GBD), and a C-terminal coiled-coil (CC) domain. alphaPix differs in that it contains a calponin homology (CH) domain, which interacts with beta-parvin, N-terminal to the SH3 domain. alphaPix is an exchange factor for Rac1 and Cdc42 and mediates Pak activation on cell adhesion to fibronectin. Mutations in alphaPix can cause X-linked mental retardation. alphaPix also interacts with Huntington's disease protein (htt), and enhances the aggregation of mutant htt (muthtt) by facilitating SDS-soluble muthtt-muthtt interactions. The DH-PH domain of a Pix was required for its binding to htt. In the majority of Rho GEF proteins, the DH-PH domain is responsible for the exchange activity. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 100 matched cddid_all.tbl CDD cd01226 cd01226 269933 PH_RalBD_exo84 Exocyst complex 84-kDa subunit Ral-binding domain/Pleckstrin Homology (PH) domain. The Sec6/8 complex, also called the exocyst complex, forms an octameric protein (Sec3, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70 and Exo84) involved in the tethering of secretory vesicles to specific regions on the plasma membrane. The regulation of Sec6/8 complex differs between mammals and yeast. Mamalian Exo84 and Sec5 are effector targets for active Ral GTPases which are not present in yeast. Ral GTPases are members of the Ras superfamily, and as such cycle between an active GTP-bound state and an inactive GDP-bound state. The Exo84 Ral-binding domain adopts a PH domain fold. Mammalian Exo84 and Sec5 competitively bind to active RalA. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 115 matched cddid_all.tbl CDD cd01227 cd01227 269934 PH_Dbs DBL's big sister protein pleckstrin homology (PH) domain. Dbs (also called MCF2-transforming sequence-like protein 2) is a guanine nucleotide exchange factor (GEF), which contains spectrin repeats, a rhoGEF (DH) domain and a PH domain. The Dbs PH domain participates in binding to both the Cdc42 and RhoA GTPases. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 126 matched cddid_all.tbl CDD cd01228 cd01228 269935 PH_BCR-related Breakpoint Cluster Region-related pleckstrin homology (PH) domain. The BCR gene is one of the two genes in the BCR-ABL complex, which is associated with the Philadelphia chromosome, a product of a reciprocal translocation between chromosomes 22 and 9. BCR is a GTPase-activating protein (GAP) for RAC1 (primarily) and CDC42. The Dbl region of BCR has the most RhoGEF activity for Cdc42, and less activity towards Rac and Rho. Since BCR possesses both GAP and GEF activities, it may function to temporally regulate the activity of these GTPases. It also displays serine/threonine kinase activity. The BCR protein contains multiple domains including an N-terminal kinase domain, a RhoGEF domain, a PH domain, a C1 domain, a C2 domain, and a C-terminal RhoGAP domain. ABR, a related smaller protein, is structurally similar to BCR, but lacks the N-terminal kinase domain and has GAP activity for both Rac and Cdc42. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 166 matched cddid_all.tbl CDD cd01229 cd01229 269936 PH_Ect2 Epithelial cell transforming 2 (Ect2) pleckstrin homology (PH) domain. Ect2, a mammalian ortholog of Drosophila pebble, plays a role in neuronal differentiation and brain development. Pebble and Ect2 have been identified as Rho-family guanine nucleotide exchange factors (GEF) that mediate activation of Rho during cytokinesis, but are proposed to play slightly different roles. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 180 matched cddid_all.tbl CDD cd01230 cd01230 269937 PH1_Tiam1_2 T-lymphoma invasion and metastasis 1 and 2 Pleckstrin Homology (PH) domain, N-terminal domain. Tiam1 activates Rac GTPases to induce membrane ruffling and cell motility while Tiam2 (also called STEF (SIF (still life) and Tiam1 like-exchange factor) contributes to neurite growth. Tiam1/2 are Dbl-family of GEFs that possess a Dbl(DH) domain with a PH domain in tandem. DH-PH domain catalyzes the GDP/GTP exchange reaction in the GTPase cycle and facillitating the switch between inactive GDP-bound and active GTP-bound states. Tiam1/2 possess two PH domains, which are often referred to as PHn and PHc domains. The DH-PH tandem domain is made up of the PHc domain while the PHn is part of a novel N-terminal PHCCEx domain which is made up of the PHn domain, a coiled coil region(CC), and an extra region (Ex). PHCCEx mediates binding to plasma membranes and signalling proteins in the activation of Rac GTPases. The PH domain resembles the beta-spectrin PH domain, suggesting non-canonical phosphatidylinositol binding. CC and Ex form a positively charged surface for protein binding. There are 2 motifs in Tiam1/2-interacting proteins that bind to the PHCCEx domain: Motif-I in CD44, ephrinBs, and the NMDA receptor and Motif-II in Par3 and JIP2.Neither of these fall in the PHn domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 127 matched cddid_all.tbl CDD cd01231 cd01231 269938 PH_SH2B_family SH2B adapter protein 1, 2, and 3 Pleckstrin homology (PH) domain. SH2B family/APS proteins are a family of intracellular adaptor proteins that influences a variety of signaling pathways mediated by Janus kinase (JAK) and receptor tyrosine kinases (RTKs) including receptors for insulin, insulin-like growth factor-1, Janus kinase 2 (Jak2), platelet derived growth factor, fibroblast growth factor and nerve growth factor. They function in glucose homeostasis, energy metabolism, hematopoesis and reproduction. Mutations in human SH2B orthologs are associated with metabolic disregulation and obesity. There are several SH2B members in mammals: SH2B1 (splice variants: SH2B1alpha, SH2B1beta, SH2B1gamma, and SH2B1delta), SH2B2 (APS) and SH2B3 (Lnk). They contain a PH domain, a SH2 domain, a proline rich region, multiple consensus sites for tyrosine and serine/threonine phosphorylation and a highly conserved c-Cbl recognition motif. These domains function as protein-protein interaction motifs which allows SH2B proteins to integrate and transduce intracellular signals from multiple signaling networks in the absence of intrinsic catalytic activity. SH2B proteins bind via their SH2 domains to phosphotyrosine residues within the intracellular tails of several activated RTKs thereby contributing to receptor activation. SH2B proteins have been shown to interact with insulin receptor substrates IRS1 and IRS2, Grb2, Shc and c-Cbl which may or may not require RTK-stimulated tyrosine phosphorylation of SH2B. positively and negatively regulating RTK signaling. Understanding the physiological functions of SH2B proteins in mammals has been complicated by the presence of multiple SH2B isoforms and conflicting data. Both SH2-Bbeta and APS associate with JAKs, but the former facilitates JAK/STAT signaling while the latter inhibits it. Lnk plays a role in cell growth and proliferation with mutations resulting in growth reduction, developmental delay and female sterility. Recently Lnk Drosophila has been shown to be an important regulator of the insulin/insulin-like growth factor (IGF)-1 signaling (IIS) pathway during growth. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 115 matched cddid_all.tbl CDD cd01233 cd01233 269939 PH_KIFIA_KIFIB KIFIA and KIFIB protein pleckstrin homology (PH) domain. The kinesin-3 family motors KIFIA (Caenorhabditis elegans homolog unc-104) and KIFIB transport synaptic vesicle precursors that contain synaptic vesicle proteins, such as synaptophysin, synaptotagmin and the small GTPase RAB3A, but they do not transport organelles that contain plasma membrane proteins. They have a N-terminal motor domain, followed by a coiled-coil domain, and a C-terminal PH domain. KIF1A adopts a monomeric form in vitro, but acts as a processive dimer in vivo. KIF1B has alternatively spliced isoforms distinguished by the presence or absence of insertion sequences in the conserved amino-terminal region of the protein; this results in their different motor activities. KIF1A and KIF1B bind to RAB3 proteins through the adaptor protein mitogen-activated protein kinase (MAPK) -activating death domain (MADD; also calledDENN), which was first identified as a RAB3 guanine nucleotide exchange factor (GEF). PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 103 matched cddid_all.tbl CDD cd01234 cd01234 269940 PH_CADPS Ca2+-dependent activator protein (also called CAPS) Pleckstrin homology (PH) domain. CADPS/CAPS consists of two members, CAPS1 which regulates catecholamine release from neuroendocrine cells and CAPS2 which is involved in the release of two neurotrophins, brain-derived neurotrophic factor (BDNF) and neurotrophin-3 (NT-3) from cerebellar granule cells. CADPS plays an important role in vesicle exocytosis in neurons and endocrine cells where it functions to prime the exocytic machinery for Ca2+-triggered fusion. Priming involves the assembly of trans SNARE complexes. The initial interaction of vesicles with target membranes is mediated by diverse stage-specific tethering factors or multi-subunit tethering complexes. CADPS and Munc13 proteins are proposed to be the functional homologs of the stage-specific tethering factors that prime membrane fusion. Interestingly, regions in the C-terminal half of CADPS are similar to the C-terminal region of Munc13-1 that was reported to bind syntaxin-1. CADPS has independent interactions with each of the SNARE proteins (Q-SNARE and R-SNARE) required for vesicle fusion. CADPS interacts with Q-SNARE proteins syntaxin-1 (H3 SNARE) and SNAP-25 (SN1) and might promote Q-SNARE heterodimer formation. Through its N-terminal R-SNARE VAMP-2 interactions, CADPS bound to heterodimeric Q-SNARE complexes could be involved in catalyzing the zippering of VAMP-2 into recipient complexes. It also contains a central PH domain that binds to phosphoinositide 4,5 bisphosphate containing liposomes. Membrane association may also be mediated by binding to phosphatidlyserine via general electrostatic interactions. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 122 matched cddid_all.tbl CDD cd01235 cd01235 269941 PH_Sbf1_hMTMR5 Set binding factor 1 (also called Human MTMR5) Pleckstrin Homology (PH) domain. Sbf1 is a myotubularin-related pseudo-phosphatase. Both Sbf1 and myotubularin interact with the SET domains of Hrx and other epigenetic regulatory proteins, but Sbf1 lacks phosphatase activity due to several amino acid changes in its structurally preserved catalytic pocket. It contains pleckstrin (PH), GEF, and myotubularin homology domains that are thought to be responsible for signaling and growth control. Sbf1 functions as an inhibitor of cellular growth. The N-terminal GEF homology domain serves to inhibit the transforming effects of Sbf1. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 106 matched cddid_all.tbl CDD cd01236 cd01236 269942 PH_RIP Rho-Interacting Protein Pleckstrin homology (PH) domain. RIP1-RhoGDI2 was obtained in a screen for proteins that bind to wild-type RhoA. RIP2, RIP3, and RIP4 were isolated from cDNA libraries with constitutively active V14RhoA (containing the C190R mutation). RIP2 represents a novel GDP/GTP exchange factor (RhoGEF), while RIP3 (p116Rip) and RIP4 are thought to be structural proteins. RhoGEF contains a Dbl(DH)/PH region, a a zinc finger motif, a leucine-rich domain, and a coiled-coil region. The last 2 domains are thought to be involved in mediating protein-protein interactions. RIP3 is a negative regulator of RhoA signaling that inhibits, either directly or indirectly, RhoA-stimulated actomyosin contractility. In plants RIP3 is localized at microtubules and interacts with the kinesin-13 family member AtKinesin-13A, suggesting a role for RIP3 in microtubule reorganization and a possible function in Rho proteins of plants (ROP)-regulated polar growth. It has a PH domain, two proline-rich regions which are putative binding sites for SH3 domains, and a COOH-terminal coiled-coil region which overlaps with the RhoA-binding region. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 136 matched cddid_all.tbl CDD cd01237 cd01237 269943 PH_fermitin Fermitin family pleckstrin homology (PH) domain. Fermitin functions as a mediator of integrin inside-out signalling. The recruitment of Fermitin proteins and Talin to the membrane mediates the terminal event of integrin signalling, via interaction with integrin beta subunits. Fermatin has FERM domain interrupted with a pleckstrin homology (PH) domain. Fermitin family homologs (Fermt1, 2, and 3, also known as Kindlins) are each encoded by a different gene. In mammalian studies, Fermt1 is generally expressed in epithelial cells, Fermt2 is expressed inmuscle tissues, and Fermt3 is expressed in hematopoietic lineages. Specifically Fermt2 is expressed in smooth and striated muscle tissues in mice and in the somites (a trunk muscle precursor) and neural crest in Xenopus embryos. As such it has been proposed that Fermt2 plays a role in cardiomyocyte and neural crest differentiation. Expression of mammalian Fermt3 is associated with hematopoietic lineages: the anterior ventral blood islands, vitelline veins, and early myeloid cells. In Xenopus embryos this expression, also include the notochord and cement gland. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 125 matched cddid_all.tbl CDD cd01238 cd01238 269944 PH_Btk Bruton's tyrosine kinase pleckstrin homology (PH) domain. Btk is a member of the Tec family of cytoplasmic protein tyrosine kinases that includes BMX, IL2-inducible T-cell kinase (Itk) and Tec. Btk plays a role in the maturation of B cells. Tec proteins general have an N-terminal PH domain, followed by a Tek homology (TH) domain, a SH3 domain, a SH2 domain and a kinase domain. The Btk PH domain binds phosphatidylinositol 3,4,5-trisphosphate and responds to signalling via phosphatidylinositol 3-kinase. The PH domain is also involved in membrane anchoring which is confirmed by the discovery of a mutation of a critical arginine residue in the BTK PH domain. This results in severe human immunodeficiency known as X-linked agammaglobulinemia (XLA) in humans and a related disorder is mice.PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 140 matched cddid_all.tbl CDD cd01239 cd01239 269945 PH_PKD Protein kinase D (PKD/PKCmu) pleckstrin homology (PH) domain. Protein Kinase C family is composed of three members, PKD1 (PKCmu), PKD2 and PKD3 (PKCnu). Like the C-type protein kinases (PKCs), PKDs are activated by diacylglycerol (DAG). They are involved in vesicular transport, cell proliferation, survival, migration and immune responses. PKD consists of tandem C1 domains, followed by a PH domain and a kinase domain. While the PKD PH domain has not been shown to bind phosphorylated inositol lipids and is not required for membrane translocation, it is required for nuclear export. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 127 matched cddid_all.tbl CDD cd01240 cd01240 269946 PH_GRK2_subgroup G Protein-Coupled Receptor Kinase 2 subgroup pleckstrin homology (PH) domain. GRKs are a family of serine-threonine kinases which phosphorylates activated G-protein coupled receptors leading to the release of the previously bound heterotrimeric G protein agonist and thus signal termination. There are seven mammalian GRKs (GRK1-7) grouped into three subfamilies: GRK1 (GRK1 and 7), GRK2 (GRK2 and 3), and GRK4 (GRK4-6). GRKs have three functional components: an N-terminal Regulators of G-protein signaling (RGS) which interacts with the seven-trans-membrane helical receptor protein and/or other membrane targets, a central catalytic protein kinase C (PKc) domain, and a C-terminal section containing a autophosphorylation region and a variable region that mediates membrane association. In both GRK2 (also known as beta-adrenergic receptor kinase-1) and GRK3 (beta-adrenergic receptor kinase-2), the C-terminal variable region contains a PH domain which gives binding specificity to Gbetagamma proteins. The GRK2 PH domain has an extended C-terminal helix, which mediates interactions with G beta gamma subunits. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 118 matched cddid_all.tbl CDD cd01241 cd01241 269947 PH_PKB Protein Kinase B-like pleckstrin homology (PH) domain. PKB (also called Akt), a member of the AGC kinase family, is a phosphatidylinositol 3'-kinase (PI3K)-dependent Ser/Thr kinase which alters the activity of the targeted protein. The name AGC is based on the three proteins that it is most similar to cAMP-dependent protein kinase 1 (PKA; also known as PKAC), cGMP-dependent protein kinase (PKG; also known as CGK1) and protein kinase C (PKC). Human Akt has three isoforms derived for distinct genes: Akt1/PKBalpha, Akt2/PKBbeta, and Akt3/PKBgamma. All Akts have an N-terminal PH domain with an activating Thr phosphorylation site, a kinase domain, and a short C-terminal regulatory tail with an activating Ser phosphorylation site. The PH domain recruits Akt to the plasma membrane by binding to phosphoinositides (PtdIns-3,4-P2) and is required for activation. The phosphorylation of Akt at its Thr and Ser phosphorylation sites leads to increased Akt activity toward forkhead transcription factors, the mammalian target of rapamycin (mTOR), and the Bcl-xL/Bcl-2-associated death promoter (BAD), all of which possess a consensus motif R-X-R-XX-ST-B (X = amino acid, B = bulky hydrophobic residue) for Akt phosphorylation. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 107 matched cddid_all.tbl CDD cd01242 cd01242 269948 PH_ROCK Rho-associated coiled-coil containing protein kinase pleckstrin homology (PH) domain. ROCK is a serine/threonine kinase that binds GTP-Rho. It consists of a kinase domain, a coiled coil region and a PH domain. The ROCK PH domain is interrupted by a C1 domain. ROCK plays a role in cellular functions, such as contraction, adhesion, migration, and proliferation and in the regulation of apoptosis. There are two ROCK isoforms, ROCK1 and ROCK2. In ROCK2 the Rho Binding Domain (RBD) and the PH domain work together in membrane localization with RBD receiving the RhoA signal and the PH domain receiving the phospholipid signal. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 110 matched cddid_all.tbl CDD cd01243 cd01243 269949 PH_MRCK MRCK (myotonic dystrophy-related Cdc42-binding kinase) pleckstrin homology (PH) domain. MRCK is thought to be coincidence detector of signaling by Cdc42 and phosphoinositides. It has been shown to promote cytoskeletal reorganization, which affects many biological processes. There are 2 members of this family: MRCKalpha and MRCKbeta. MRCK consists of a serine/threonine kinase domain, a cysteine rich (C1) region, a PH domain and a p21 binding motif. The MRCK PH domain is responsible for its targeting to cell to cell junctions. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 135 matched cddid_all.tbl CDD cd01244 cd01244 269950 PH_GAP1-like RAS p21 protein activator (GTPase activating protein) family pleckstrin homology (PH) domain. RASAL1, GAP1(m), GAP1(IP4BP), and CAPRI are all members of the GAP1 family of GTPase-activating proteins. They contain N-terminal SH2-SH3-SH2 domains, followed by two C2 domains, a PH domain, a RasGAP domain, and a BTK domain. With the notable exception of GAP1(m), they all possess an arginine finger-dependent GAP activity on the Ras-related protein Rap1. They act as a suppressor of RAS enhancing the weak intrinsic GTPase activity of RAS proteins resulting in the inactive GDP-bound form of RAS, allowing control of cellular proliferation and differentiation. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 107 matched cddid_all.tbl CDD cd01247 cd01247 269951 PH_FAPP1_FAPP2 Four phosphate adaptor protein 1 and 2 Pleckstrin homology (PH) domain. Human FAPP1 (also called PLEKHA3/Pleckstrin homology domain-containing, family A member 3) regulates secretory transport from the trans-Golgi network to the plasma membrane. It is recruited through binding of PH domain to phosphatidylinositol 4-phosphate (PtdIns(4)P) and a small GTPase ADP-ribosylation factor 1 (ARF1). These two binding sites have little overlap the FAPP1 PH domain to associate with both ligands simultaneously and independently. FAPP1 has a N-terminal PH domain followed by a short proline-rich region. FAPP1 is a member of the oxysterol binding protein (OSBP) family which includes OSBP, OSBP-related proteins (ORP), and Goodpasture antigen binding protein (GPBP). They have a wide range of purported functions including sterol transport, cell cycle control, pollen development and vessicle transport from Golgi recognize both PI lipids and ARF proteins. FAPP2 (also called PLEKHA8/Pleckstrin homology domain-containing, family A member 8), a member of the Glycolipid lipid transfer protein(GLTP) family has an N-terminal PH domain that targets the TGN and C-terminal GLTP domain. FAPP2 functions to traffic glucosylceramide (GlcCer) which is made in the Golgi. It's interaction with vesicle-associated membrane protein-associated protein (VAP) could be a means of regulation. Some FAPP2s share the FFAT-like motifs found in GLTP. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 100 matched cddid_all.tbl CDD cd01248 cd01248 269952 PH_PLC_ELMO1 Phospholipase C and Engulfment and cell motility protein 1 pleckstrin homology domain. The C-terminal region of ELMO1, the PH domain and Pro-rich sequences, binds the SH3-containing region of DOCK2 forming a intermolecular five-helix bundle allowing for DOCK mediated Rac1 activation. ELMO1, a mammalian homolog of C. elegans CED-12, contains an N-terminal RhoG-binding region, a ELMO domain, a PH domain, and a C-terminal sequence with three PxxP motifs. Specificaly, PLCs catalyze the cleavage of phosphatidylinositol-4,5-bisphosphate (PIP2) and result in the release of 1,2-diacylglycerol (DAG) and inositol 1,4,5-triphosphate (IP3). These products trigger the activation of protein kinase C (PKC) and the release of Ca2+ from intracellular stores. There are fourteen kinds of mammalian phospholipase C which are are classified into six isotypes (beta, gamma, delta, epsilon, zeta, eta). All PLCs, except for PLCzeta, have a PH domain which is for most part N-terminally located, though lipid binding specificity is not conserved between them. In addition PLC gamma contains a split PH domain within its catalytic domain that is separated by 2 SH2 domains and a single SH3 domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 108 matched cddid_all.tbl CDD cd01249 cd01249 269953 BAR-PH_GRAF_family GTPase Regulator Associated with Focal adhesion and related proteins Pleckstrin homology (PH) domain. This hierarchy contains GRAF family members: OPHN1/oligophrenin1, GRAF1 (also called ARHGAP26/Rho GTPase activating protein 26), GRAF2 (also called ARHGAP10/ARHGAP42), AK057372, and LOC129897, all of which are members of the APPL family. OPHN1 is a RhoGAP involved in X-linked mental retardation, epilepsy, rostral ventricular enlargement, and cerebellar hypoplasia. Affected individuals have morphological abnormalities of their brain with enlargement of the cerebral ventricles and cerebellar hypoplasia. OPHN1 negatively regulates RhoA, Cdc42, and Rac1 in neuronal and non-neuronal cells. GRAF1 sculpts the endocytic membranes of the CLIC/GEEC (clathrin-independent carriers/GPI-enriched early endosomal compartments) endocytic pathway. It strongly interacts with dynamin and inhibition of dynamin abolishes CLIC/GEEC endocytosis. GRAF2, GRAF3 and oligophrenin are likely to play similar roles during clathrin-independent endocytic events. GRAF1 mutations are linked to leukaemia. All members are composed of a N-terminal BAR-PH domain, followed by a RhoGAP domain, a proline rich region, and a C-terminal SH3 domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 105 matched cddid_all.tbl CDD cd01250 cd01250 241281 PH_AGAP Arf-GAP with GTPase, ANK repeat and PH domain-containing protein Pleckstrin homology (PH) domain. AGAP (also called centaurin gamma; PIKE/Phosphatidylinositol-3-kinase enhancer) reside mainly in the nucleus and are known to activate phosphoinositide 3-kinase, a key regulator of cell proliferation, motility and vesicular trafficking. There are 3 isoforms of AGAP (PIKE-A, PIKE-L, and PIKE-S) the longest of which PIKE-L consists of N-terminal proline rich domains (PRDs), followed by a GTPase domain, a split PH domain (PHN and PHC), an ArfGAP domain and two ankyrin repeats. PIKE-S terminates after the PHN domain and PIKE-A is missing the PRD region. Centaurin binds phosphatidlyinositol (3,4,5)P3. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 114 matched cddid_all.tbl CDD cd01251 cd01251 241282 PH2_ADAP ArfGAP with dual PH domains Pleckstrin homology (PH) domain, repeat 2. ADAP (also called centaurin alpha) is a phophatidlyinositide binding protein consisting of an N-terminal ArfGAP domain and two PH domains. In response to growth factor activation, PI3K phosphorylates phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 1 is recruited to the plasma membrane following growth factor stimulation by specific binding of its PH domain to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 2 is constitutively bound to the plasma membrane since it binds phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate with equal affinity. This cd contains the second PH domain repeat. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 105 matched cddid_all.tbl CDD cd01252 cd01252 269954 PH_GRP1-like General Receptor for Phosphoinositides-1-like Pleckstrin homology (PH) domain. GRP1/cytohesin3 and the related proteins ARNO (ARF nucleotide-binding site opener)/cytohesin-2 and cytohesin-1 are ARF exchange factors that contain a pleckstrin homology (PH) domain thought to target these proteins to cell membranes through binding polyphosphoinositides. The PH domains of all three proteins exhibit relatively high affinity for PtdIns(3,4,5)P3. Within the Grp1 family, diglycine (2G) and triglycine (3G) splice variants, differing only in the number of glycine residues in the PH domain, strongly influence the affinity and specificity for phosphoinositides. The 2G variants selectively bind PtdIns(3,4,5)P3 with high affinity,the 3G variants bind PtdIns(3,4,5)P3 with about 30-fold lower affinity and require the polybasic region for plasma membrane targeting. These ARF-GEFs share a common, tripartite structure consisting of an N-terminal coiled-coil domain, a central domain with homology to the yeast protein Sec7, a PH domain, and a C-terminal polybasic region. The Sec7 domain is autoinhibited by conserved elements proximal to the PH domain. GRP1 binds to the DNA binding domain of certain nuclear receptors (TRalpha, TRbeta, AR, ER, but not RXR), and can repress thyroid hormone receptor (TR)-mediated transactivation by decreasing TR-complex formation on thyroid hormone response elements. ARNO promotes sequential activation of Arf6, Cdc42 and Rac1 and insulin secretion. Cytohesin acts as a PI 3-kinase effector mediating biological responses including cell spreading and adhesion, chemotaxis, protein trafficking, and cytoskeletal rearrangements, only some of which appear to depend on their ability to activate ARFs. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 119 matched cddid_all.tbl CDD cd01253 cd01253 269955 PH_ARHGAP21-like ARHGAP21 and related proteins pleckstrin homology (PH) domain. ARHGAP family genes encode Rho/Rac/Cdc42-like GTPase activating proteins with a RhoGAP domain. These proteins functions as a GTPase-activating protein (GAP) for RHOA and CDC42. ARHGAP21 controls the Arp2/3 complex and F-actin dynamics at the Golgi complex by regulating the activity of the small GTPase Cdc42. It is recruited to the Golgi by to GTPase, ARF1, through its PH domain and its helical motif. It is also required for CTNNA1 recruitment to adherens junctions. ARHGAP21 and it related proteins all contains a PH domain and a RhoGAP domain. Some of the members have additional N-terminal domains including PDZ, SH3, and SPEC. The ARHGAP21 PH domain interacts with the GTPbound forms of both ARF1 and ARF6 ARF-binding domain/ArfBD. The members here include: ARHGAP15, ARHGAP21, and ARHGAP23. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 113 matched cddid_all.tbl CDD cd01254 cd01254 269956 PH_PLD Phospholipase D pleckstrin homology (PH) domain. PLD hydrolyzes phosphatidylcholine to phosphatidic acid (PtdOH), which can bind target proteins. PLD contains a PH domain, a PX domain and four conserved PLD signature domains. The PLD PH domain is specific for bisphosphorylated inositides. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 136 matched cddid_all.tbl CDD cd01255 cd01255 269957 PH2_Tiam1_2 T-lymphoma invasion and metastasis 1 and 2 Pleckstrin Homology (PH) domain, C-terminal domain. Tiam1 activates Rac GTPases to induce membrane ruffling and cell motility while Tiam2 (also called STEF (SIF (still life) and Tiam1 like-exchange factor) contributes to neurite growth. Tiam1/2 are Dbl-family of GEFs that possess a Dbl(DH) domain with a PH domain in tandem. DH-PH domain catalyzes the GDP/GTP exchange reaction in the GTPase cycle and facillitating the switch between inactive GDP-bound and active GTP-bound states. The DH domain of Tiam1 interacts with Switch regions 1 and 2 of Rac1 which blocks magnesium binding and GDP is released. Tiam1/2 possess two PH domains, which are often referred to as PHn and PHc domains. The DH-PH tandem domain is made up of the PHc domain while the PHn is part of a novel N-terminal PHCCEx domain which is made up of the PHn domain, a coiled coil region(CC), and an extra region (Ex). PHCCEx mediates binding to plasma membranes and signalling proteins in the activation of Rac GTPases. The PH domain resembles the beta-spectrin PH domain, suggesting non-canonical phosphatidylinositol binding. CC and Ex form a positively charged surface for protein binding. There are 2 motifs in Tiam1/2-interacting proteins that bind to the PHCCEx domain: Motif-I in CD44, ephrinBs, and the NMDA receptor and Motif-II in Par3 and JIP2. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 172 matched cddid_all.tbl CDD cd01256 cd01256 269958 PH_dynamin Dynamin pleckstrin homology (PH) domain. Dynamin is a GTPase that regulates endocytic vesicle formation. It has an N-terminal GTPase domain, followed by a PH domain, a GTPase effector domain and a C-terminal proline arginine rich domain. Dynamin-like proteins, which are found in metazoa, plants and yeast have the same domain architecture as dynamin, but lack the PH domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 112 matched cddid_all.tbl CDD cd01257 cd01257 269959 PH_IRS Insulin receptor substrate (IRS) pleckstrin homology (PH) domain. Insulin receptor substrate (IRS) molecules are mediators in insulin signaling and play a role in maintaining basic cellular functions such as growth and metabolism. They act as docking proteins between the insulin receptor and a complex network of intracellular signaling molecules containing Src homology 2 (SH2) domains. Four members (IRS-1, IRS-2, IRS-3, IRS-4) of this family have been identified that differ as to tissue distribution, subcellular localization, developmental expression, binding to the insulin receptor, and interaction with SH2 domain-containing proteins. IRS molecules have an N-terminal PH domain, followed by an IRS-like PTB domain which has a PH-like fold. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.cytoskeletal associated molecules, and in lipid associated enzymes. 106 matched cddid_all.tbl CDD cd01258 cd01258 269960 PHsplit_syntrophin Syntrophin Split Pleckstrin homology (PH) domain. Syntrophins are scaffold proteins that associate with associate with the Duchenne muscular dystrophy protein dystrophin and the dystrophin-related proteins, utrophin and dystrobrevin to form the dystrophin glycoprotein complex (DGC). There are 5 members: alpha, beta1, beta2, gamma1, and gamma2) all of which contains a split (also called joined) PH domain and a PDZ domain (PHN-PDZ-PHC). The split PH domain of alpha-syntrophin adopts a canonical PH domain fold and together with PDZ forms a supramodule functioning synergistically in binding to inositol phospholipids. The alpha-syntrophin PH-PDZ supramodule showed strong binding to phosphoinositides PI(3,5)P2 and PI(5)P, modest binding to PI(3,4)P2 and PI(4,5)P2, and weak binding to PI(3)P, PI(4)P, and PI(3,4,5)P. There are a large number of signaling proteins that bind to the PDZ domain of syntrophins: nitric oxide synthase (nNOS), aquaporin-4, voltage-gated sodium channels, potassium channels, serine/threonine protein kinases, and the ATP-binding cassette transporter A1. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 89 matched cddid_all.tbl CDD cd01259 cd01259 269961 PH_APBB1IP Amyloid beta (A4) Precursor protein-Binding, family B, member 1 Interacting Protein pleckstrin homology (PH) domain. APBB1IP consists of a Ras-associated (RA) domain, a PH domain, a family-specific BPS region, and a C-terminal SH2 domain. Grb7, Grb10 and Grb14 are paralogs that are also present in this hierarchy. These adapter proteins bind a variety of receptor tyrosine kinases, including the insulin and insulin-like growth factor-1 (IGF1) receptors. Grb10 and Grb14 are important tissue-specific negative regulators of insulin and IGF1 signaling based and may contribute to type 2 (non-insulin-dependent) diabetes in humans. RA-PH function as a single structural unit and is dimerized via a helical extension of the PH domain. The PH domain here are proposed to bind phosphoinositides non-cannonically ahd are unlikely to bind an activated GTPase. The tandem RA-PH domains are present in a second adapter-protein family, MRL proteins, Caenorhabditis elegans protein MIG-1012, the mammalian proteins RIAM and lamellipodin and the Drosophila melanogaster protein Pico12, all of which are Ena/VASP-binding proteins involved in actin-cytoskeleton rearrangement. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 124 matched cddid_all.tbl CDD cd01260 cd01260 269962 PH_CNK_mammalian-like Connector enhancer of KSR (Kinase suppressor of ras) (CNK) pleckstrin homology (PH) domain. CNK family members function as protein scaffolds, regulating the activity and the subcellular localization of RAS activated RAF. There is a single CNK protein present in Drosophila and Caenorhabditis elegans in contrast to mammals which have 3 CNK proteins (CNK1, CNK2, and CNK3). All of the CNK members contain a sterile a motif (SAM), a conserved region in CNK (CRIC) domain, and a PSD-95/DLG-1/ZO-1 (PDZ) domain, and, with the exception of CNK3, a PH domain. A CNK2 splice variant CNK2A also has a PDZ domain-binding motif at its C terminus and Drosophila CNK (D-CNK) also has a domain known as the Raf-interacting region (RIR) that mediates binding of the Drosophila Raf kinase. This cd contains CNKs from mammals, chickens, amphibians, fish, and crustacea. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 114 matched cddid_all.tbl CDD cd01261 cd01261 269963 PH_SOS Son of Sevenless (SOS) Pleckstrin homology (PH) domain. SOS is a Ras guanine nucleotide exchange factor. SOS is thought to transmit signals from activated receptor tyrosine kinases to the Ras signaling pathway. SOS contains a histone domain, Dbl-homology (DH), a PH domain, Rem domain, Cdc25 domain, and a Grb2 binding domain. The SOS PH domain binds to phosphatidylinositol-4,5-bisphosphate (PIP2) and phosphatidic acid (PA). SOS is dependent on Ras binding to the allosteric site via its histone domain for both a lower level of activity (Ras GDP) and maximal activity (Ras GTP). The DH domain blocks the allosteric Ras binding site in SOS. The PH domain is closely associated with the DH domain and the action of the DH-PH unit gates a reciprocal interaction between Ras and SOS. The C-terminal proline-rich domain of SOS binds to the adapter protein Grb2 which localizes the Sos protein to the plasma membrane and diminishes the negative effect of the C-terminal domain on the guanine nucleotide exchange activity of the CDC25-homology domain of SOS. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 109 matched cddid_all.tbl CDD cd01262 cd01262 241293 PH_PDK1 3-Phosphoinositide dependent protein kinase 1 (PDK1) pleckstrin homology (PH) domain. PDK1 plays an important role in insulin and growth factor signalling cascades. It phosphorylates and activates many AGC (cAMP-dependent, cGMP-dependent, protein kinase C (PKC)) family of protein kinases members, including protein kinase B (PKB, also known as Akt), p70 ribosomal S6-kinase (S6K), serum and glucocorticoid responsive kinase (SGK), p90 ribosomal S6 kinase (RSK), and PKC. PDK1 contains an N-terminal serine/threonine kinase domain followed by a PH domain. Following binding of the PH domain to PtdIns(3,4,5)P3 and PtdIns(3,4)P2, PDK1 activates these enzymes by phosphorylating a Ser/Thr residue in their activation loop. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 107 matched cddid_all.tbl CDD cd01263 cd01263 269964 PH_anillin Anillin Pleckstrin homology (PH) domain. Anillin (Rhotekin/RTKN; also called PLEKHK/Pleckstrin homology domain-containing family K) is an actin binding protein involved in cytokinesis. It interacts with GTP-bound Rho proteins and results in the inhibition of their GTPase activity. Dysregulation of the Rho signal transduction pathway has been implicated in many forms of cancer. Anillin proteins have a N-terminal HRI domain/ACC (anti-parallel coiled-coil) finger domain or Rho-binding domain binds small GTPases from the Rho family. The C-terminal PH domain helps target anillin to ectopic septin containing foci. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 121 matched cddid_all.tbl CDD cd01264 cd01264 269965 PH_MELT_VEPH1 Melted pleckstrin homology (PH) domain. The melted protein (also called Ventricular zone expressed PH domain-containing protein homolog 1) is expressed in the developing central nervous system of vertebrates. It contains a single C-terminal PH domain that is required for membrane targeting. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 105 matched cddid_all.tbl CDD cd01265 cd01265 269966 PH_TBC1D2A TBC1 domain family member 2A pleckstrin homology (PH) domain. TBC1D2A (also called PARIS-1/Prostate antigen recognized and identified by SEREX 1 and ARMUS) contains a PH domain and a TBC-type GTPase catalytic domain. TBC1D2A integrates signaling between Arf6, Rac1, and Rab7 during junction disassembly. Activated Rac1 recruits TBC1D2A to locally inactivate Rab7 via its C-terminal TBC/RabGAP domain and facilitate E-cadherin degradation in lysosomes. The TBC1D2A PH domain mediates localization at cell-cell contacts and coprecipitates with cadherin complexes. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 102 matched cddid_all.tbl CDD cd01266 cd01266 241297 PH_Gab1_Gab2 Grb2-associated binding proteins 1 and 2 pleckstrin homology (PH) domain. The Gab subfamily includes several Gab proteins, Drosophila DOS and C. elegans SOC-1. They are scaffolding adaptor proteins, which possess N-terminal PH domains and a C-terminus with proline-rich regions and multiple phosphorylation sites. Following activation of growth factor receptors, Gab proteins are tyrosine phosphorylated and activate PI3K, which generates 3-phosphoinositide lipids. By binding to these lipids via the PH domain, Gab proteins remain in proximity to the receptor, leading to further signaling. While not all Gab proteins depend on the PH domain for recruitment, it is required for Gab activity. The members in this cd include the Gab1 and Gab2 proteins. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 123 matched cddid_all.tbl CDD cd01268 cd01268 241298 PTB_Numb Numb Phosphotyrosine-binding (PTB) domain. Numb is a membrane associated adaptor protein which plays critical roles in cell fate determination. Numb proteins are involved in control of asymmetric cell division and cell fate choice, endocytosis, cell adhesion, cell migration, ubiquitination of specific substrates and a number of signaling pathways (Notch, Hedgehog, p53). Mutations in Numb plays a critical role in disease (cancer). Numb has an N-terminal PTB domain and a C-terminal NumbF domain. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Dab-like subgroup. 135 matched cddid_all.tbl CDD cd01269 cd01269 269967 PTB_TBC1D1_like TBC1 domain family member 1 and related proteins Phosphotyrosine-binding (PTB) domain. The TBC1D1-like members here include TBC1D1, TBC1D4 (also called Akt substrate of 160 kDa or AS160), and pollux (PLX), a calmodulin-binding protein, and are thought to have a role in regulating cell growth and differentiation. These proteins are thought to function as GTPase-activating protein for Rab family protein(s). They may play a role in the cell cycle and differentiation of various tissues. They all contain an N-terminal PTB domain, a calmodulin CBD domain, and a C-terminal TBC domain which is thought to be a GTPase activator protein of Rab-like small GTPases. Recently, TBC1D1 and TBC1D4 were recognized to potentially link the proximal signalling of insulin and/or exercise with GLUT4. TBC1D4 is thought to be involved in contraction-stimulated glucose uptake, but TBC1D4-independent mechanisms (potentially involving TBC1D1) are likely to be essential for most of the contraction's effect. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Dab-like subgroup. 143 matched cddid_all.tbl CDD cd01270 cd01270 269968 PTB_CAPON-like Carboxyl-terminal PDZ ligand of neuronal nitric oxide synthase protein (CAPON) Phosphotyrosine-binding (PTB) domain. CAPON (also known as Nitric oxide synthase 1 adaptor protein, NOS1AP, encodes a cytosolic protein that binds to the signaling molecule, neuronal NOS (nNOS). It contains a N-terminal PTB domain that binds to the small monomeric G protein, Dexras1 and a C-terminal PDZ-binding domain that mediates interactions with nNOS. Included in this cd are C. elegan proteins dystrobrevin, DYB-1, which controls neurotransmitter release and muscle Ca(2+) transients by localizing BK channels and DYstrophin-like phenotype and CAPON related,DYC-1, which is functionally related to dystrophin homolog, DYS-1. Mutations in the dystrophin gene causes Duchenne muscular dystrophy. DYS-1 shares sequence similarity, including key motifs, with their mammalian counterparts. These CAPON-like proteins all have a single PTB domain. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Dab-like subgroup. 179 matched cddid_all.tbl CDD cd01271 cd01271 269969 PTB2_Fe65 Fe65 C-terminal Phosphotyrosine-binding (PTB) domain. The neuronal adaptor protein Fe65 is involved in brain development, Alzheimer disease amyloid precursor protein (APP) signaling, and proteolytic processing of APP. It contains three protein-protein interaction domains, one WW domain, and a unique tandem array of phosphotyrosine-binding (PTB) domains. The C-terminal PTB domain is responsible for APP binding. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Dab-like subgroup. 127 matched cddid_all.tbl CDD cd01272 cd01272 269970 PTB1_Fe65 Fe65 N-terminal Phosphotyrosine-binding (PTB) domain. The neuronal adaptor protein Fe65 is involved in brain development, Alzheimer disease amyloid precursor protein (APP) signaling, and proteolytic processing of APP. It contains three protein-protein interaction domains, one WW domain, and a unique tandem array of phosphotyrosine-binding (PTB) domains. The N-terminal PTB domain was shown to interact with a variety of proteins, including the low density lipoprotein receptor-related protein (LRP-1), the ApoEr2 receptor, and the histone acetyltransferase Tip60. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Dab-like subgroup. 138 matched cddid_all.tbl CDD cd01273 cd01273 269971 PTB_CED-6 Cell death protein 6 homolog (CED-6/GULP1) Phosphotyrosine-binding (PTB) domain. CED6 (also known as GULP1: engulfment adaptor PTB domain containing 1) is an adaptor protein involved in the specific recognition and engulfment of apoptotic cells. CED6 has been shown to interact with the cytoplasmic tail of another protein involved in the engulfment of apoptotic cells, CED1. CED6 has a C-terminal PTB domain, which can bind to NPXY motifs. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Dab-like subgroup. 144 matched cddid_all.tbl CDD cd01274 cd01274 269972 PTB_Anks Ankyrin repeat and sterile alpha motif (SAM) domain-containing (Anks) protein family Phosphotyrosine-binding (PTB) domain. Both AIDA-1b (AbetaPP intracellular domain-associated protein 1b) and Odin (also known as ankyrin repeat and sterile alpha motif domain-containing 1A; ANKS1A) belong to the Anks protein family. Both of these family members interacts with the EphA8 receptor. Ank members consists of ankyrin repeats, a SAM domain and a C-terminal PTB domain which is crucial for interaction with the juxtamembrane (JM) region of EphA8. PTB domains are classified into three groups, namely, phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains of which the Anks PTB is a member. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Dab-like subgroup. 146 matched cddid_all.tbl CDD cd01275 cd01275 238606 FHIT FHIT (fragile histidine family): FHIT proteins, related to the HIT family carry a motif HxHxH/Qxx (x, is a hydrophobic amino acid), On the basis of sequence, substrate specificity, structure, evolution and mechanism, HIT proteins are classified into three branches: the Hint branch, which consists of adenosine 5' -monophosphoramide hydrolases, the Fhit branch, that consists of diadenosine polyphosphate hydrolases, and the GalT branch consisting of specific nucloside monophosphate transferases. Fhit plays a very important role in the development of tumours. Infact, Fhit deletions are among the earliest and most frequent genetic alterations in the development of tumours. 126 matched cddid_all.tbl CDD cd01276 cd01276 238607 PKCI_related Protein Kinase C Interacting protein related (PKCI): PKCI and related proteins belong to the ubiquitous HIT family of hydrolases that act on alpha-phosphates of ribonucleotides. The members of this subgroup have a conserved HxHxHxx motif (x is a hydrophobic residue) that is a signature for this family. No enzymatic activity has been reported however, for PKCI and its related members. 104 matched cddid_all.tbl CDD cd01277 cd01277 238608 HINT_subgroup HINT (histidine triad nucleotide-binding protein) subgroup: Members of this CD belong to the superfamily of histidine triad hydrolases that act on alpha-phosphate of ribonucleotides. This subgroup includes members from all three forms of cellular life. Although the biochemical function has not been characterised for many of the members of this subgroup, the proteins from Yeast have been shown to be involved in secretion, peroxisome formation and gene expression. 103 matched cddid_all.tbl CDD cd01278 cd01278 238609 aprataxin_related aprataxin related: Aprataxin, a HINT family hydrolase is mutated in ataxia oculomotor apraxia syndrome. All the members of this subgroup have the conserved HxHxHxx (where x is a hydrophobic residue) signature motif. Members of this subgroup are predominantly eukaryotic in origin. 104 matched cddid_all.tbl CDD cd01279 cd01279 133387 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. 98 matched cddid_all.tbl CDD cd01282 cd01282 133388 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. 112 matched cddid_all.tbl CDD cd01283 cd01283 238610 cytidine_deaminase Cytidine deaminase zinc-binding domain. These enzymes are Zn dependent. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. Cytidine deaminases catalyze the deamination of cytidine to uridine and are important in the pyrimadine salvage pathway in many cell types, from bacteria to humans. This family also includes the apoBec proteins, which are a mammal specific expansion of RNA editing enzymes, and the closely related phorbolins, and the AID (activation-induced) enzymes. 112 matched cddid_all.tbl CDD cd01284 cd01284 238611 Riboflavin_deaminase-reductase Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the biosynthesis of riboflavin.The ribG gene of Bacillus subtilis and the ribD gene of E. coli are bifunctional and contain this deaminase domain and a reductase domain which catalyzes the subsequent reduction of the ribosyl side chain. 115 matched cddid_all.tbl CDD cd01285 cd01285 238612 nucleoside_deaminase Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia and is a member of the pyrimidine salvage pathway. Cytosine deaminase is found in bacteria and fungi but is not present in mammals; for this reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protein synthesis. Other members of the family are guanine deaminases which deaminate guanine to xanthine as part of the utilization of guanine as a nitrogen source. 109 matched cddid_all.tbl CDD cd01286 cd01286 238613 deoxycytidylate_deaminase Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the enzyme is allosterically regulated by the ratio of dCTP to dTTP not only in eukaryotic cells but also in T-even phage-infected Escherichia coli, with dCTP acting as an activator and dTTP as an inhibitor. 131 matched cddid_all.tbl CDD cd01287 cd01287 238614 FabA FabA, beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase: Bacterial protein of the type II, fatty acid synthase system that binds ACP and catalyzes both dehydration and isomerization reactions, apparently in the same active site. The FabA structure is a homodimer with two independent active sites located at the dimer interface. Each active site is tunnel-shaped and completely inaccessible to solvent. No metal ions or cofactors are required for ligand binding or catalysis. 150 matched cddid_all.tbl CDD cd01288 cd01288 238615 FabZ FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid biosynthesis pathway. 131 matched cddid_all.tbl CDD cd01289 cd01289 238616 FabA_like Domain of unknown function, appears to be related to a diverse group of beta-hydroxydecanoyl ACP dehydratases (FabA) and beta-hydroxyacyl ACP dehydratases (FabZ). This group appears to lack the conserved active site histidine of FabA and FabZ. 138 matched cddid_all.tbl CDD cd01291 cd01291 211324 PseudoU_synth Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Pseudouridine synthases contains the RsuA/RluD, TruA, TruB and TruD families. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases. Some psi sites such as psi55,13,38 and 39 in tRNA are highly conserved, being in the same position in eubacteria, archeabacteria and eukaryotes. Other psi sites occur in a more restricted fashion, for example psi2604in 23S RNA made by E.coli RluF has only been detected in E.coli. Human dyskerin with the help of guide RNAs makes the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA). 87 matched cddid_all.tbl CDD cd01292 cd01292 238617 metallo-dependent_hydrolases Superfamily of metallo-dependent hydrolases (also called amidohydrolase superfamily) is a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The family includes urease alpha, adenosine deaminase, phosphotriesterase dihydroorotases, allantoinases, hydantoinases, AMP-, adenine and cytosine deaminases, imidazolonepropionase, aryldialkylphosphatase, chlorohydrolases, formylmethanofuran dehydrogenases and others. 275 matched cddid_all.tbl CDD cd01293 cd01293 238618 Bact_CD Bacterial cytosine deaminase and related metal-dependent hydrolases. Cytosine deaminases (CDs) catalyze the deamination of cytosine, producing uracil and ammonia. They play an important role in pyrimidine salvage. CDs are present in prokaryotes and fungi, but not mammalian cells. The bacterial enzymes, but not the fungal enzymes, are related to the adenosine deaminases (ADA). The bacterial enzymes are iron dependent and hexameric. 398 matched cddid_all.tbl CDD cd01294 cd01294 238619 DHOase Dihydroorotase (DHOase) catalyzes the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in the pyrimidine biosynthesis. In contrast to the large polyfunctional CAD proteins of higher organisms, this group of DHOases is monofunctional and mainly dimeric. 335 matched cddid_all.tbl CDD cd01295 cd01295 238620 AdeC Adenine deaminase (AdeC) directly deaminates adenine to form hypoxanthine. This reaction is part of one of the adenine salvage pathways, as well as the degradation pathway. It is important for adenine utilization as a purine, as well as a nitrogen source in bacteria and archea. 422 matched cddid_all.tbl CDD cd01296 cd01296 238621 Imidazolone-5PH Imidazolonepropionase/imidazolone-5-propionate hydrolase (Imidazolone-5PH) catalyzes the third step in the histidine degradation pathway, the hydrolysis of (S)-3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate to N-formimidoyl-L-glutamate. In bacteria, the enzyme is part of histidine utilization (hut) operon. 371 matched cddid_all.tbl CDD cd01297 cd01297 238622 D-aminoacylase D-aminoacylases (N-acyl-D-Amino acid amidohydrolases) catalyze the hydrolysis of N-acyl-D-amino acids to produce the corresponding D-amino acids, which are used as intermediates in the synthesis of pesticides, bioactive peptides, and antibiotics. 415 matched cddid_all.tbl CDD cd01298 cd01298 238623 ATZ_TRZ_like TRZ/ATZ family contains enzymes from the atrazine degradation pathway and related hydrolases. Atrazine, a chlorinated herbizide, can be catabolized by a variety of different bacteria. The first three steps of the atrazine dehalogenation pathway are catalyzed by atrazine chlorohydrolase (AtzA), hydroxyatrazine ethylaminohydrolase (AtzB), and N-isopropylammelide N-isopropylaminohydrolase (AtzC). All three enzymes belong to the superfamily of metal dependent hydrolases. AtzA and AtzB, beside other related enzymes are represented in this CD. 411 matched cddid_all.tbl CDD cd01299 cd01299 238624 Met_dep_hydrolase_A Metallo-dependent hydrolases, subgroup A is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The function of this subgroup is unknown. 342 matched cddid_all.tbl CDD cd01300 cd01300 238625 YtcJ_like YtcJ_like metal dependent amidohydrolases. YtcJ is a Bacillus subtilis ORF of unknown function. The Arabidopsis homolog LAF3 has been identified as a factor required for phytochrome A signalling. 479 matched cddid_all.tbl CDD cd01301 cd01301 238626 rDP_like renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics. Although the biological function of the enzyme is still unknown, it has been suggested to play a role in the renal glutathione metabolism. 309 matched cddid_all.tbl CDD cd01302 cd01302 238627 Cyclic_amidohydrolases Cyclic amidohydrolases, including hydantoinase, dihydropyrimidinase, allantoinase, and dihydroorotase, are involved in the metabolism of pyrimidines and purines, sharing the property of hydrolyzing the cyclic amide bond of each substrate to the corresponding N-carbamyl amino acids. Allantoinases catalyze the degradation of purines, while dihydropyrimidinases and hydantoinases, a microbial counterpart of dihydropyrimidinase, are involved in pyrimidine degradation. Dihydroorotase participates in the de novo synthesis of pyrimidines. 337 matched cddid_all.tbl CDD cd01303 cd01303 238628 GDEase Guanine deaminase (GDEase). Guanine deaminase is an aminohydrolase responsible for the conversion of guanine to xanthine and ammonia, the first step to utilize guanine as a nitrogen source. This reaction also removes the guanine base from the pool and therefore can play a role in the regulation of cellular GTP and the guanylate nucleotide pool. 429 matched cddid_all.tbl CDD cd01304 cd01304 238629 FMDH_A Formylmethanofuran dehydrogenase (FMDH) subunit A; Methanogenic bacteria and archea derive the energy for autotrophic growth from methanogenesis, the reduction of CO2 with molecular hydrogen as the electron donor. FMDH catalyzes the first step in methanogenesis, the formyl-methanofuran synthesis. In this step, CO2 is bound to methanofuran and subsequently reduced to the formyl state with electrons derived from hydrogen. 541 matched cddid_all.tbl CDD cd01305 cd01305 238630 archeal_chlorohydrolases Predicted chlorohydrolases. These metallo-dependent hydrolases from archea are part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. They have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. Some members of this subgroup are predicted to be chlorohyrolases. 263 matched cddid_all.tbl CDD cd01306 cd01306 238631 PhnM PhnM is believed to be a subunit of the membrane associated C-P lyase complex. C-P lyase is thought to catalyze the direct cleavage of inactivated C-P bonds to yield inorganic phosphate and the corresponding hydrocarbons. It is responsible for cleavage of alkylphosphonates, which are utilized as sole phosphorus sources by many bacteria. 325 matched cddid_all.tbl CDD cd01307 cd01307 238632 Met_dep_hydrolase_B Metallo-dependent hydrolases, subgroup B is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The function of this subgroup is unknown. 338 matched cddid_all.tbl CDD cd01308 cd01308 238633 Isoaspartyl-dipeptidase Isoaspartyl dipeptidase hydrolyzes the beta-L-isoaspartyl linkages in dipeptides, as part of the degradative pathway to eliminate proteins with beta-L-isoaspartyl peptide bonds, bonds whereby the beta-group of an aspartate forms the peptide link with the amino group of the following amino acid. Formation of this bond is a spontaneous nonenzymatic reaction in nature and can profoundly effect the function of the protein. Isoaspartyl dipeptidase is an octameric enzyme that contains a binuclear zinc center in the active site of each subunit and shows a strong preference of hydrolyzing Asp-Leu dipeptides. 387 matched cddid_all.tbl CDD cd01309 cd01309 238634 Met_dep_hydrolase_C Metallo-dependent hydrolases, subgroup C is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The function of this subgroup is unknown. 359 matched cddid_all.tbl CDD cd01310 cd01310 238635 TatD_DNAse TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity. 251 matched cddid_all.tbl CDD cd01311 cd01311 238636 PDC_hydrolase 2-pyrone-4,6-dicarboxylic acid (PDC) hydrolase hydrolyzes PDC to yield 4-oxalomesaconic acid (OMA) or its tautomer, 4-carboxy-2-hydroxymuconic acid (CHM). This reaction is part of the protocatechuate (PCA) 4,5-cleavage pathway. PCA is one of the most important intermediate metabolites in the bacterial pathways for various phenolic compounds, including lignin, which is the most abundant aromatic material in nature. 263 matched cddid_all.tbl CDD cd01312 cd01312 238637 Met_dep_hydrolase_D Metallo-dependent hydrolases, subgroup D is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The function of this subgroup is unknown. 381 matched cddid_all.tbl CDD cd01313 cd01313 238638 Met_dep_hydrolase_E Metallo-dependent hydrolases, subgroup D is part of the superfamily of metallo-dependent hydrolases, a large group of proteins that show conservation in their 3-dimensional fold (TIM barrel) and in details of their active site. The vast majority of the members have a conserved metal binding site, involving four histidines and one aspartic acid residue. In the common reaction mechanism, the metal ion (or ions) deprotonate a water molecule for a nucleophilic attack on the substrate. The function of this subgroup is unknown. 418 matched cddid_all.tbl CDD cd01314 cd01314 238639 D-HYD D-hydantoinases (D-HYD) also called dihydropyrimidases (DHPase) and related proteins; DHPases are a family of enzymes that catalyze the reversible hydrolytic ring opening of the amide bond in five- or six-membered cyclic diamides, like dihydropyrimidine or hydantoin. The hydrolysis of dihydropyrimidines is the second step of reductive catabolism of pyrimidines in human. The hydrolysis of 5-substituted hydantoins in microorganisms leads to enantiomerically pure N-carbamyl amino acids, which are used for the production of antibiotics, peptide hormones, pyrethroids, and pesticides. HYDs are classified depending on their stereoselectivity. This family also includes collapsin response regulators (CRMPs), cytosolic proteins involved in neuronal differentiation and axonal guidance which have strong homology to DHPases, but lack most of the active site residues. 447 matched cddid_all.tbl CDD cd01315 cd01315 238640 L-HYD_ALN L-Hydantoinases (L-HYDs) and Allantoinase (ALN); L-Hydantoinases are a member of the dihydropyrimidinase family, which catalyzes the reversible hydrolytic ring opening of dihydropyrimidines and hydantoins (five-membered cyclic diamides used in biotechnology). But L-HYDs differ by having an L-enantio specificity and by lacking activity on possible natural substrates such as dihydropyrimidines. Allantoinase catalyzes the hydrolytic cleavage of the five-member ring of allantoin (5-ureidohydantoin) to form allantoic acid. 447 matched cddid_all.tbl CDD cd01316 cd01316 238641 CAD_DHOase The eukaryotic CAD protein is a trifunctional enzyme of carbamoylphosphate synthetase-aspartate transcarbamoylase-dihydroorotase, which catalyzes the first three steps of de novo pyrimidine nucleotide biosynthesis. Dihydroorotase (DHOase) catalyzes the third step, the reversible interconversion of carbamoyl aspartate to dihydroorotate. 344 matched cddid_all.tbl CDD cd01317 cd01317 238642 DHOase_IIa Dihydroorotase (DHOase), subgroup IIa; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This subgroup also contains proteins that lack the active site, like unc-33, a C.elegans protein involved in axon growth. 374 matched cddid_all.tbl CDD cd01318 cd01318 238643 DHOase_IIb Dihydroorotase (DHOase), subgroup IIb; DHOases catalyze the reversible interconversion of carbamoyl aspartate to dihydroorotate, a key reaction in pyrimidine biosynthesis. This group contains the archeal members of the DHOase family. 361 matched cddid_all.tbl CDD cd01319 cd01319 238644 AMPD AMP deaminase (AMPD) catalyzes the hydrolytic deamination of adensosine monophosphate (AMP) at position 6 of the adenine nucleotide ring. AMPD is a diverse and highly regulated eukaryotic key enzyme of the adenylate catabolic pathway. 496 matched cddid_all.tbl CDD cd01320 cd01320 238645 ADA Adenosine deaminase (ADA) is a monomeric zinc dependent enzyme which catalyzes the irreversible hydrolytic deamination of both adenosine, as well as desoxyadenosine, to ammonia and inosine or desoxyinosine, respectively. ADA plays an important role in the purine pathway. Low, as well as high levels of ADA activity have been linked to several diseases. 325 matched cddid_all.tbl CDD cd01321 cd01321 238646 ADGF Adenosine deaminase-related growth factors (ADGF), a novel family of secreted growth-factors with sequence similarty to adenosine deaminase. 345 matched cddid_all.tbl CDD cd01324 cd01324 238647 cbb3_Oxidase_CcoQ Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. Found exclusively in proteobacteria, cbb3 is believed to be a modern enzyme that has evolved independently to perform a specialized function in microaerobic energy metabolism. The cbb3 operon contains four genes (ccoNOQP or fixNOQP), with ccoN coding for subunit I. Instead of a CuA-containing subunit II analogous to other cytochrome oxidases, cbb3 utilizes subunits ccoO and ccoP, which contain one and two hemes, respectively, to transfer electrons to the binuclear center. ccoQ, the fourth subunit, is a single transmembrane helix protein. It has been shown to protect the core complex from proteolytic degradation by serine proteases. See cd00919, cd01322, or cd01323 for more information on cbb3 oxidase. 48 matched cddid_all.tbl CDD cd01327 cd01327 238648 KAZAL_PSTI Kazal-type pancreatic secretory trypsin inhibitors (PSTI) and related proteins, including the second domain of the ovomucoid turkey inhibitor and the C-terminal domain of the esophagus cancer-related gene-2 protein (ECRG-2), are members of the superfamily of kazal-type proteinase inhibitors and follistatin-like proteins. 45 matched cddid_all.tbl CDD cd01328 cd01328 238649 FSL_SPARC Follistatin-like SPARC (secreted protein, acidic, and rich in cysteines) domain; SPARC/BM-40/osteonectin is a multifunctional glycoprotein which modulates cellular interaction with the extracellular matrix by its binding to structural matrix proteins such as collagen and vitronectin. The protein it composed of an N-terminal acidic region, a follistatin (FS) domain and an EF-hand calcium binding domain. The FS domain consists of an N-terminal beta hairpin (FOLN/EGF-like domain) and a small hydrophobic core of alpha/beta structure (Kazal domain) and has five disulfide bonds and a conserved N-glycosylation site. The FSL_SPARC domain is a member of the superfamily of kazal-like proteinase inhibitors and follistatin-like proteins. 86 matched cddid_all.tbl CDD cd01330 cd01330 238650 KAZAL_SLC21 The kazal-type serine protease inhibitor domain has been detected in an extracellular loop region of solute carrier 21 (SLC21) family members (organic anion transporters) , which may regulate the specificity of anion uptake. The KAZAL_SLC21 domain is a member of the superfamily of kazal-like proteinase inhibitors and follistatin-like proteins. 54 matched cddid_all.tbl CDD cd01334 cd01334 176461 Lyase_I Lyase class I family; a group of proteins which catalyze similar beta-elimination reactions. The Lyase class I family contains class II fumarase, aspartase, adenylosuccinate lyase (ASL), argininosuccinate lyase (ASAL), prokaryotic-type 3-carboxy-cis,cis-muconate cycloisomerase (pCMLE), and related proteins. It belongs to the Lyase_I superfamily. Proteins of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. 325 matched cddid_all.tbl CDD cd01335 cd01335 100105 Radical_SAM Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin. 204 matched cddid_all.tbl CDD cd01336 cd01336 133421 MDH_cytoplasmic_cytosolic Cytoplasmic and cytosolic Malate dehydrogenases. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. Members of this subfamily are eukaryotic MDHs localized to the cytoplasm and cytosol. MDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. 325 matched cddid_all.tbl CDD cd01337 cd01337 133422 MDH_glyoxysomal_mitochondrial Glyoxysomal and mitochondrial malate dehydrogenases. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. Members of this subfamily are localized to the glycosome and mitochondria. MDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. 310 matched cddid_all.tbl CDD cd01338 cd01338 133423 MDH_chloroplast-like Chloroplast-like malate dehydrogenases. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. Members of this subfamily are bacterial MDHs, and plant MDHs localized to the chloroplasts. MDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. 322 matched cddid_all.tbl CDD cd01339 cd01339 133424 LDH-like_MDH L-lactate dehydrogenase-like malate dehydrogenase proteins. Members of this subfamily have an LDH-like structure and an MDH enzymatic activity. Some members, like MJ0490 from Methanococcus jannaschii, exhibit both MDH and LDH activities. Tetrameric MDHs, including those from phototrophic bacteria, are more similar to LDHs than to other MDHs. LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH-like MDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. 300 matched cddid_all.tbl CDD cd01341 cd01341 238651 ADP_ribosyl ADP_ribosylating enzymes catalyze the transfer of ADP_ribose from NAD+ to substrates. Bacterial toxins are cytoplasmic and catalyze the transfer of a single ADP_ribose unit to eukaryotic elongation factor 2, halting protein synthesis and killing the cell. Poly(ADP-ribose) polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length in part through poy(ADP_ribosylation) of telomere repeat binding factor 1 (TRF1). Poly(ADP-ribose) polymerase catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active. 137 matched cddid_all.tbl CDD cd01342 cd01342 293888 Translation_Factor_II_like Domain II of Elongation factor Tu (EF-Tu)-like proteins. Elongation factor Tu consists of three structural domains. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought to be involved in binding of E. coli IF-2 to 30S subunits. 80 matched cddid_all.tbl CDD cd01343 cd01343 238653 PL1_Passenger_AT Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 1, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of Neisseria and Haemophilus IgA1 proteases, SPATEs (serine protease autotransporters secreted by Enterobacteriaceae), Bordetella pertacins, and nonprotease autotransporters, TibA and similar AIDA-like proteins. 233 matched cddid_all.tbl CDD cd01344 cd01344 238654 PL2_Passenger_AT Pertactin-like passenger domains (virulence factors), C-terminal, subgroup 2, of autotransporter proteins of the type V secretion system of Gram-negative bacteria. This subgroup includes the passenger domains of the nonprotease autotransporters, Ag43, AIDA-1 and IcsA, as well as, the less characterized ShdA, MisL, and BapA autotransporters. 188 matched cddid_all.tbl CDD cd01345 cd01345 238655 OM_channels Porin superfamily. These outer membrane channels share a beta-barrel structure that differ in strand and shear number. Classical (gram-negative ) porins are non-specific channels for small hydrophillic molecules and form 16 beta-stranded barrels (16,20), which associate as trimers. Maltoporin-like channels have specificities for various sugars and form 18 beta-stranded barrels (18,22), which associate as trimers. Ligand-gated protein channels cooperate with a TonB associated inner membrane complex to actively transport ligands via the proton motive force and they form monomeric, (22,24) barrels. The 150-200 N-terminal residues form a plug that blocks the channel from the periplasmic end. 253 matched cddid_all.tbl CDD cd01346 cd01346 238656 Maltoporin-like The Maltoporin-like channels (LamB porin) form a trimeric structure which facilitate the diffusion of maltodextrins and other sugars across the outer membrane of Gram-negative bacteria. The membrane channel is formed by an 18-strand antiparallel beta-barrel (18,22). Loop 3 folds into the core to constrict pore size. Long irregular loops are found on the extracelllular side, while short turns are in the periplasm.Tightly-bound water molecules are found in the eyelet of the passage, and only substrates that can displace and replace the broken hydrogen bonds are likely to enter the pore. In the MPR structure, loops 4,6, and 9 have the greatest mobility and are highly variable; these are postulated to attract maltodextrins. 392 matched cddid_all.tbl CDD cd01347 cd01347 238657 ligand_gated_channel TonB dependent/Ligand-Gated channels are created by a monomeric 22 strand (22,24) anti-parallel beta-barrel. Ligands apparently bind to the large extracellular loops. The N-terminal 150-200 residues form a plug from the periplasmic end of barrel. Energy (proton-motive force) and TonB-dependent conformational alteration of channel (parts of plug, and loops 7 and 8) allow passage of ligand. FepA residues 12-18 form the TonB box, which mediates the interaction with the TonB-containing inner membrane complex. TonB preferentially interacts with ligand-bound receptors. Transport thru the channel may resemble passage thru an air lock. In this model, ligand binding leads to closure of the extracellular end of pore, then a TonB-mediated signal facillitates opening of the interior side of pore, deforming the N-terminal plug and allowing passage of the ligand to the periplasm. Such a mechanism would prevent the free diffusion of small molecules thru the pore. 635 matched cddid_all.tbl CDD cd01351 cd01351 153129 Aconitase Aconitase catalytic domain; Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. Aconitase catalytic domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. Cis-aconitate is formed as an intermediate product during the course of the reaction. In eukaryotes two isozymes of aconitase are known to exist: one found in the mitochondrial matrix and the other found in the cytoplasm. Aconitase, in its active form, contains a 4Fe-4S iron-sulfur cluster; three cysteine residues have been shown to be ligands of the 4Fe-4S cluster. This is the Aconitase core domain, including structural domains 1, 2 and 3, which binds the Fe-S cluster. The aconitase family also contains the following proteins: - Iron-responsive element binding protein (IRE-BP), a cytosolic protein that binds to iron-responsive elements (IREs). IREs are stem-loop structures found in the 5'UTR of ferritin, and delta aminolevulinic acid synthase mRNAs, and in the 3'UTR of transferrin receptor mRNA. IRE-BP also express aconitase activity. - 3-isopropylmalate dehydratase (isopropylmalate isomerase), the enzyme that catalyzes the second step in the biosynthesis of leucine. - Homoaconitase (homoaconitate hydratase), an enzyme that participates in the alpha-aminoadipate pathway of lysine biosynthesis and that converts cis-homoaconitate into homoisocitric acid. 389 matched cddid_all.tbl CDD cd01355 cd01355 153130 AcnX Putative Aconitase X catalytic domain. Putative Aconitase X catalytic domain. It is predicted by comparative genomic analysis. The proteins are mainly found in archaea and proteobacteria. They are distantly related to Aconitase family of proteins by sequence similarity and seconary structure prediction. The functions have not yet been experimentally characterized. Thus, the prediction should be treated with caution. 389 matched cddid_all.tbl CDD cd01356 cd01356 238658 AcnX_swivel Putative Aconitase X swivel domain. It is predicted by comparative genomic analysis. The proteins are mainly found in archaea and proteobacteria. They are distantly related to Aconitase family of proteins by sequence similarity and seconary structure prediction. The functions have not yet been experimentally characterized. Thus, the prediction should be treated with caution. 123 matched cddid_all.tbl CDD cd01357 cd01357 176462 Aspartase Aspartase. This subgroup contains Escherichia coli aspartase (L-aspartate ammonia-lyase), Bacillus aspartase and related proteins. It is a member of the Lyase class I family, which includes both aspartase (L-aspartate ammonia-lyase) and fumarase class II enzymes. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. Aspartase catalyzes the reversible deamination of aspartic acid. 450 matched cddid_all.tbl CDD cd01359 cd01359 176463 Argininosuccinate_lyase Argininosuccinate lyase (argininosuccinase, ASAL). This group contains ASAL and related proteins. It is a member of the Lyase class I family. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. ASAL is a cytosolic enzyme which catalyzes the reversible breakdown of argininosuccinate to arginine and fumarate during arginine biosynthesis. In ureotelic species ASAL also catalyzes a reaction involved in the production of urea. Included in this group are the major soluble avian eye lens proteins from duck, delta 1 and delta 2 crystallin. Of these two isoforms only delta 2 has retained ASAL activity. These crystallins may have evolved by, gene recruitment of ASAL followed by gene duplication. In humans, mutations in ASAL result in the autosomal recessive disorder argininosuccinic aciduria. 435 matched cddid_all.tbl CDD cd01360 cd01360 176464 Adenylsuccinate_lyase_1 Adenylsuccinate lyase (ASL)_subgroup 1. This subgroup contains bacterial and archeal proteins similar to ASL, a member of the Lyase class I family. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. ASL catalyzes two steps in the de novo purine biosynthesis: the conversion of 5-aminoimidazole-(N-succinylocarboxamide) ribotide (SAICAR) into 5-aminoimidazole-4-carboxamide ribotide (AICAR) and, the conversion of adenylsuccinate (SAMP) into adenosine monophosphate (AMP). 387 matched cddid_all.tbl CDD cd01362 cd01362 176465 Fumarase_classII Class II fumarases. This subgroup contains Escherichia coli fumarase C, human mitochondrial fumarase, and related proteins. It is a member of the Lyase class I family. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. Fumarase catalyzes the reversible hydration/dehydration of fumarate to L-malate during the Krebs cycle. 455 matched cddid_all.tbl CDD cd01363 cd01363 276814 Motor_domain Myosin and Kinesin motor domain. Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes. Some of the names do not match with what is given in the sequence list. This is because they are based on the current nomenclature by Kollmar/Sebe-Pedros. 170 matched cddid_all.tbl CDD cd01364 cd01364 276815 KISc_BimC_Eg5 Kinesin motor domain, BimC/Eg5 spindle pole proteins. Kinesin motor domain, BimC/Eg5 spindle pole proteins, participate in spindle assembly and chromosome segregation during cell division. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type), N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. 353 matched cddid_all.tbl CDD cd01365 cd01365 276816 KISc_KIF1A_KIF1B Kinesin motor domain, KIF1_like proteins. Kinesin motor domain, KIF1_like proteins. KIF1A (Unc104) transports synaptic vesicles to the nerve terminal, KIF1B has been implicated in transport of mitochondria. Both proteins are expressed in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. In contrast to the majority of dimeric kinesins, most KIF1A/Unc104 kinesins are monomeric motors. A lysine-rich loop in KIF1A binds to the negatively charged C-terminus of tubulin and compensates for the lack of a second motor domain, allowing KIF1A to move processively. 361 matched cddid_all.tbl CDD cd01366 cd01366 276817 KISc_C_terminal Kinesin motor domain, KIFC2/KIFC3/ncd-like carboxy-terminal kinesins. Kinesin motor domain, KIFC2/KIFC3/ncd-like carboxy-terminal kinesins. Ncd is a spindle motor protein necessary for chromosome segregation in meiosis. KIFC2/KIFC3-like kinesins have been implicated in motility of the Golgi apparatus as well as dentritic and axonal transport in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this subgroup the motor domain is found at the C-terminus (C-type). C-type kinesins are (-) end-directed motors, i.e. they transport cargo towards the (-) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. 329 matched cddid_all.tbl CDD cd01367 cd01367 276818 KISc_KIF2_like Kinesin motor domain, KIF2-like group. Kinesin motor domain, KIF2-like group. KIF2 is a protein expressed in neurons, which has been associated with axonal transport and neuron development; alternative splice forms have been implicated in lysosomal translocation. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this subgroup the motor domain is found in the middle (M-type) of the protein chain. M-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second (KIF2 may be slower). To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. 328 matched cddid_all.tbl CDD cd01368 cd01368 276819 KISc_KIF23_like Kinesin motor domain, KIF23-like subgroup. Kinesin motor domain, KIF23-like subgroup. Members of this group may play a role in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. 345 matched cddid_all.tbl CDD cd01369 cd01369 276820 KISc_KHC_KIF5 Kinesin motor domain, kinesin heavy chain (KHC) or KIF5-like subgroup. Kinesin motor domain, kinesin heavy chain (KHC) or KIF5-like subgroup. Members of this group have been associated with organelle transport. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. 325 matched cddid_all.tbl CDD cd01370 cd01370 276821 KISc_KIP3_like Kinesin motor domain, KIP3-like subgroup. Kinesin motor domain, KIP3-like subgroup. The yeast kinesin KIP3 plays a role in positioning the mitotic spindle. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. 345 matched cddid_all.tbl CDD cd01371 cd01371 276822 KISc_KIF3 Kinesin motor domain, kinesins II or KIF3_like proteins. Kinesin motor domain, kinesins II or KIF3_like proteins. Subgroup of kinesins, which form heterotrimers composed of 2 kinesins and one non-motor accessory subunit. Kinesins II play important roles in ciliary transport, and have been implicated in neuronal transport, melanosome transport, the secretory pathway, and mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this group the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. 334 matched cddid_all.tbl CDD cd01372 cd01372 276823 KISc_KIF4 Kinesin motor domain, KIF4-like subfamily. Kinesin motor domain, KIF4-like subfamily. Members of this group seem to perform a variety of functions, and have been implicated in neuronal organelle transport and chromosome segregation during mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. 341 matched cddid_all.tbl CDD cd01373 cd01373 276824 KISc_KLP2_like Kinesin motor domain, KIF15-like subgroup. Kinesin motor domain, KIF15-like subgroup. Members of this subgroup seem to play a role in mitosis and meiosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. 347 matched cddid_all.tbl CDD cd01374 cd01374 276825 KISc_CENP_E Kinesin motor domain, CENP-E/KIP2-like subgroup. Kinesin motor domain, CENP-E/KIP2-like subgroup, involved in chromosome movement and/or spindle elongation during mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. 321 matched cddid_all.tbl CDD cd01375 cd01375 276826 KISc_KIF9_like Kinesin motor domain, KIF9-like subgroup. Kinesin motor domain, KIF9-like subgroup; might play a role in cell shape remodeling. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. 334 matched cddid_all.tbl CDD cd01376 cd01376 276827 KISc_KID_like Kinesin motor domain, KIF22/Kid-like subgroup. Kinesin motor domain, KIF22/Kid-like subgroup. Members of this group might play a role in regulating chromosomal movement along microtubules in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. 319 matched cddid_all.tbl CDD cd01377 cd01377 276951 MYSc_class_II "class II myosins, motor domain. Myosin motor domain in class II myosins. Class II myosins, also called conventional myosins, are the myosin type responsible for producing actomyosin contraction in metazoan muscle and non-muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. Thus, myosin II has two heads. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. " 662 matched cddid_all.tbl CDD cd01378 cd01378 276829 MYSc_Myo1 class I myosin, motor domain. Myosin I generates movement at the leading edge in cell motility, and class I myosins have been implicated in phagocytosis and vesicle transport. Myosin I, an unconventional myosin, does not form dimers. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. There are 5 myosin subclasses with subclasses c/h, d/g, and a/b have an IQ domain and a TH1 domain. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 652 matched cddid_all.tbl CDD cd01379 cd01379 276830 MYSc_Myo3 class III myosin, motor domain. Myosin III has been shown to play a role in the vision process in insects and in hearing in mammals. Myosin III, an unconventional myosin, does not form dimers. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. They are characterized by an N-terminal protein kinase domain and several IQ domains. Some members also contain WW, SH2, PH, and Y-phosphatase domains. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 633 matched cddid_all.tbl CDD cd01380 cd01380 276831 MYSc_Myo5 class V myosin, motor domain. Myo5, also called heavy chain 12, myoxin, are dimeric myosins that transport a variety of intracellular cargo processively along actin filaments, such as melanosomes, synaptic vesicles, vacuoles, and mRNA. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. It also contains a IQ domain and a globular DIL domain. Myosin V is a class of actin-based motor proteins involved in cytoplasmic vesicle transport and anchorage, spindle-pole alignment and mRNA translocation. The protein encoded by this gene is abundant in melanocytes and nerve cells. Mutations in this gene cause Griscelli syndrome type-1 (GS1), Griscelli syndrome type-3 (GS3) and neuroectodermal melanolysosomal disease, or Elejalde disease. Multiple alternatively spliced transcript variants encoding different isoforms have been reported, but the full-length nature of some variants has not been determined. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. Note that the Dictyostelium myoVs are not contained in this child group. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 629 matched cddid_all.tbl CDD cd01381 cd01381 276832 MYSc_Myo7 class VII myosin, motor domain. These monomeric myosins have been associated with functions in sensory systems such as vision and hearing. Mammalian myosin VII has a tail with 2 MyTH4 domains, 2 FERM domains, and a SH3 domain. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 648 matched cddid_all.tbl CDD cd01382 cd01382 276833 MYSc_Myo6 class VI myosin, motor domain. Myosin VI is a monomeric myosin, which moves towards the minus-end of actin filaments, in contrast to most other myosins which moves towards the plus-end of actin filaments. It is thought that myosin VI, unlike plus-end directed myosins, does not use a pure lever arm mechanism, but instead steps with a mechanism analogous to the kinesin neck-linker uncoupling model. It has been implicated in a myriad of functions including: the transport of cytoplasmic organelles, maintenance of normal Golgi morphology, endocytosis, secretion, cell migration, border cell migration during development, and in cancer metastasis playing roles in deafness and retinal development among others. While how this is accomplished is largely unknown there are several interacting proteins that have been identified such as disabled homolog 2 (DAB2), GIPC1, synapse-associated protein 97 (SAP97; also known as DLG1) and optineurin, which have been found to target myosin VI to different cellular compartments. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the minus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 649 matched cddid_all.tbl CDD cd01383 cd01383 276834 MYSc_Myo8 class VIII myosin, motor domain. These plant-specific type VIII myosins has been associated with endocytosis, cytokinesis, cell-to-cell coupling and gating at plasmodesmata. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. It also contains IQ domains Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 647 matched cddid_all.tbl CDD cd01384 cd01384 276835 MYSc_Myo11 class XI myosin, motor domain. These plant-specific type XI myosin are involved in organelle transport. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. 647 matched cddid_all.tbl CDD cd01385 cd01385 276836 MYSc_Myo9 class IX myosin, motor domain. Myosin IX is a processive single-headed motor, which might play a role in signalling. It has a N-terminal RA domain, an IQ domain, a C1_1 domain, and a RhoGAP domain. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 690 matched cddid_all.tbl CDD cd01386 cd01386 276837 MYSc_Myo18 class XVIII myosin, motor domain. Many members of this class contain a N-terminal PDZ domain which is commonly found in proteins establishing molecular complexes. The motor domain itself does not exhibit ATPase activity, suggesting that it functions as an actin tether protein. It also has two IQ domains that probably bind light chains or related calmodulins and a C-terminal tail with two sections of coiled-coil domains, which are thought to mediate homodimerization. The function of these myosins are largely unknown. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 689 matched cddid_all.tbl CDD cd01387 cd01387 276838 MYSc_Myo15 class XV mammal-like myosin, motor domain. The class XV myosins are monomeric. In vertebrates, myosin XV appears to be expressed in sensory tissue and play a role in hearing. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. C-terminal to the head domain are 2 MyTH4 domain, a FERM domain, and a SH3 domain. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 657 matched cddid_all.tbl CDD cd01388 cd01388 438790 HMG-box_SoxB high mobility group (HMG)-box found in group B SRY-related high-mobility group (HMG) box (Sox) transcription factors. SoxB transcription factors play critical roles in the regulation of neurogenesis. They can be divided into two main subgroups, SoxB1 (Sox-1/Sox-2/Sox-3) and SoxB2 (SOX-14/SOX-21). SoxB1 proteins suppress neurogenesis by maintaining neural cells in an undifferentiated state. SoxB2 proteins may have the opposite activity and promote neuronal differentiation. SOX-1 is involved in the regulation of embryonic development and cell fate determination. It also acts as a tumor suppressor that plays an anti-tumorigenicity role in different cells and its expression is inhibited in a variety of cancers. SOX-2 plays an important role in various phases of embryonic development, including cell fate and differentiation. Its overexpression and gene amplification may be associated with tumor aggression and metastasis in various cancer types, including breast, prostate, lung, ovarian and colon cancer. SOX-3 is required during the formation of the hypothalamic-pituitary axis. It plays a role in both normal neural development and carcinogenesis. SOX-14, also called SOX-28, acts as a negative regulator of transcription. It is mainly involved in the regulation of neural development. It can also promote proliferation and invasion capacity of cervical cancer cells by activating the Wnt/beta-catenin pathway. SOX-21, also called SOX-A, or SOX-25, promotes the progression of vertebrate neurogenesis. 80 matched cddid_all.tbl CDD cd01389 cd01389 438791 HMG-box_ROX1-like high mobility group (HMG)-box found in Saccharomyces cerevisiae repressor ROX1 and similar proteins. This family includes class I members of the HMG-box superfamily of DNA-binding proteins, including Saccharomyces cerevisiae repressor ROX1, Schizosaccharomyces pombe mating-type M-specific polypeptide Mc (mat-Mc), Schizosaccharomyces pombe transcription factor ste11, Podospora anserina MAT+ sexual cell fertilization-promoting factor (FPR1), Podospora anserina sporulation minus regulator 2 (SMR2) and Candida albicans repressor of filamentous growth 1 (RFG1). These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. ROX1, also called heme-dependent repression factor, or hypoxic function repressor, is a transcription factor that represses the expression of HEM13, COX5B, ANB1, CYC7 or AAC3. It binds to the DNA sequence 5'-RRRTAACAAGAG-3'. mat-Mc belongs to the mating type protein family, which contains sequence specific DNA-binding proteins that act as master switches in yeast differentiation by controlling gene expression in a cell type-specific fashion. mat-Mc is a positive regulator of MFM genes and is required for conjugation and efficient meiosis. Its HMG box recognizes the DNA sequence 5'-AACAAAG-3'. Ste11 is a key transcription factor for sexual development. It activates the transcription of the matp, matm, mei2, mfm, ste6 and rgs1 genes. It binds specifically to a DNA fragment carrying a 10-base motif 5'-TTCTTTGTTY-3'. FPR1 controls fertilization, probably by determining the mating type. SMR2 is a transcription factor that is required for post-fertilization events. It is required for the developmental events that occur in the female organ after fertilization. RFG1 is a transcription regulator that functions in both the positive and negative regulation of filamentous growth, depending upon environmental conditions. 72 matched cddid_all.tbl CDD cd01390 cd01390 438792 HMG-box_NHP6-like high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone chromosomal proteins NHP6A, NHP6B and similar proteins. This subfamily includes Saccharomyces cerevisiae high-mobility-group proteins NHP6A and its closely related paralog NHP6B. NHP6A and NHP6B seem to be functionally redundant. They are DNA-binding proteins that induce severe bending of DNA and are required for DNA-binding by the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. They augment the fidelity of transcription by RNA polymerase III independently of any role in the FACT complex. They may also play essential roles in transcriptional initiation fidelity of some but not all tRNA genes. 81 matched cddid_all.tbl CDD cd01391 cd01391 380477 Periplasmic_Binding_Protein_type1 Type 1 periplasmic binding fold superfamily. Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins, the ligands are monosaccharides, including lactose, ribose, fructose, xylose, arabinose, galactose/glucose and other sugars, with a few exceptions. Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The core structures of periplasmic binding proteins are classified into two types, and they differ in number and order of beta strands: type 1 has six beta strands while type 2 has five beta strands per sub-domain. These two structural folds are thought to be distantly related via a common ancestor. Notably, while the N-terminal LIVBP-like domain of iGluRs belongs to the type 1 periplasmic-binding fold protein superfamily, the glutamate-binding domain of the iGluR is structurally similar to the type 2 periplasmic-binding fold. 280 matched cddid_all.tbl CDD cd01392 cd01392 143331 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repressor binds its ligand, it undergoes a conformational change which affects the DNA-binding affinity of the repressor. In Escherichia coli, LacI represses transcription by binding with high affinity to the lac operon at a specific operator DNA sequence until it interacts with the physiological inducer allolactose or a non-degradable analog IPTG (isopropyl-beta-D-thiogalactopyranoside). Induction of the repressor lowers its affinity for the operator sequence, thereby allowing transcription of the lac operon structural genes (lacZ, lacY, and LacA). The lac repressor occurs as a tetramer made up of two functional dimers. Thus, two DNA binding domains of a dimer are required to bind the inverted repeat sequences of the operator DNA binding sites. 52 matched cddid_all.tbl CDD cd01393 cd01393 410881 RecA-like RecA family. RecA is a bacterial enzyme which has roles in homologous recombination, DNA repair, and the induction of the SOS response. RecA couples ATP hydrolysis to DNA strand exchange. While prokaryotes have a single RecA protein, eukaryotes have multiple RecA homologs such as Rad51, DMC1 and Rad55/57. Archaea have the RecA-like homologs RadA and RadB. 185 matched cddid_all.tbl CDD cd01394 cd01394 410882 archRadB archaeal RadB. The archaeal protein RadB shares similarity RadA, the archaeal functional homologue to the bacterial RecA. The precise function of RadB is unclear. 216 matched cddid_all.tbl CDD cd01395 cd01395 238689 HMT_MBD Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated transcriptional repression. SETDB1 and other proteins in this group have a similar domain architecture. SETDB1 is a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. 60 matched cddid_all.tbl CDD cd01396 cd01396 238690 MeCP2_MBD MeCP2, MBD1, MBD2, MBD3, and MBD4 are members of a protein family that share the methyl-CpG-binding domain (MBD). The MBD, consists of about 70 residues and is defined as the minimal region required for binding to methylated DNA by a methyl-CpG-binding protein which binds specifically to methylated DNA. The MBD can recognize a single symmetrically methylated CpG either as naked DNA or within chromatin. MeCP2, MBD1 and MBD2 (and likely MBD3) form complexes with histone deacetylase and are involved in histone deacetylase-dependent repression of transcription. MBD4 is an endonuclease that forms a complex with the DNA mismatch-repair protein MLH1. 77 matched cddid_all.tbl CDD cd01397 cd01397 238691 HAT_MBD Methyl-CpG binding domains (MBD) present in putative chromatin remodelling factor such as BAZ2A; BAZ2A contains a MBD, DDT, PHD-type zinc finger and Bromo domain suggesting that BAZ2A might be associated with histone acetyltransferase (HAT) activity. The Drosophila melanogaster toutatis protein, a putative subunit of the chromatin-remodeling complex, and other such proteins in this group share a similar domain architecture with BAZ2A, as does the Caenorhabditis elegans flectin homolog. 73 matched cddid_all.tbl CDD cd01398 cd01398 238692 RPI_A RPI_A: Ribose 5-phosphate isomerase type A (RPI_A) subfamily; RPI catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate, the first step of the non-oxidative branch of the pentose phosphate pathway. This reaction leads to the conversion of phosphosugars into glycolysis intermediates, which are precursors for the synthesis of amino acids, vitamins, nucleotides, and cell wall components. In plants, RPI is part of the Calvin cycle as ribulose 5-phosphate is the carbon dioxide receptor in the first dark reaction of photosynthesis. There are two unrelated types of RPIs (A and B), which catalyze the same reaction, at least one type of RPI is present in an organism. RPI_A is more widely distributed than RPI_B in bacteria, eukaryotes, and archaea. 213 matched cddid_all.tbl CDD cd01399 cd01399 238693 GlcN6P_deaminase GlcN6P_deaminase: Glucosamine-6-phosphate (GlcN6P) deaminase subfamily; GlcN6P deaminase catalyzes the reversible conversion of GlcN6P to D-fructose-6-phosphate (Fru6P) and ammonium. The reaction is an aldo-keto isomerization coupled with an amination or deamination. It is the last step of the metabolic pathway of N-acetyl-D-glucosamine-6-phosphate (GlcNAc6P). GlcN6P deaminase is a hexameric enzyme that is allosterically activated by GlcNAc6P. 232 matched cddid_all.tbl CDD cd01400 cd01400 238694 6PGL 6PGL: 6-Phosphogluconolactonase (6PGL) subfamily; 6PGL catalyzes the second step of the oxidative phase of the pentose phosphate pathway, the hydrolyzation of 6-phosphoglucono-1,5-lactone (delta form) to 6-phosphogluconate. 6PGL is thought to guard against the accumulation of the delta form of the lactone, which may be toxic through its reaction with endogenous cellular nucleophiles. 219 matched cddid_all.tbl CDD cd01401 cd01401 238695 PncB_like Nicotinate phosphoribosyltransferase (NAPRTase), related to PncB. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products. This subgroup is present in bacteria, archea and funghi. 377 matched cddid_all.tbl CDD cd01403 cd01403 238696 Cyt_c_Oxidase_VIIb Cytochrome C oxidase chain VIIb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. The VIIb subunit is found only in eukaryotes and its specific function remains unclear. A rare polymorphism of the CcO VIIb gene may be associated with the high risk of nasopharyngeal carcinoma in a Cantonese family. 51 matched cddid_all.tbl CDD cd01406 cd01406 238697 SIR2-like Sir2-like: Prokaryotic group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines; and are members of the SIR2 superfamily of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. 242 matched cddid_all.tbl CDD cd01407 cd01407 238698 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. 218 matched cddid_all.tbl CDD cd01408 cd01408 238699 SIRT1 SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The nuclear SIRT1 has been shown to target the p53 tumor suppressor protein for deacetylation to suppress DNA damage, and the cytoplasmic SIRT2 homolog has been shown to target alpha-tubulin for deacetylation for the maintenance of cell integrity. 235 matched cddid_all.tbl CDD cd01409 cd01409 238700 SIRT4 SIRT4: Eukaryotic and prokaryotic group (class2) which includes human sirtuin SIRT4 and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. 260 matched cddid_all.tbl CDD cd01410 cd01410 238701 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. 206 matched cddid_all.tbl CDD cd01411 cd01411 238702 SIR2H SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. 225 matched cddid_all.tbl CDD cd01412 cd01412 238703 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity. 224 matched cddid_all.tbl CDD cd01413 cd01413 238704 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression. 222 matched cddid_all.tbl CDD cd01414 cd01414 133469 SAICAR_synt_Sc non-metazoan 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase. Eukaryotic, bacterial, and archaeal group of SAICAR synthetases represented by the Saccharomyces cerevisiae (Sc) enzyme, mostly absent in metazoans. SAICAR synthetase catalyzes the seventh step of the de novo biosynthesis of purine nucleotides (also reported as eighth step). It converts 5-aminoimidazole-4-carboxyribonucleotide (CAIR), ATP, and L-aspartate into 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR), ADP, and phosphate. 279 matched cddid_all.tbl CDD cd01415 cd01415 133470 SAICAR_synt_PurC bacterial and archaeal 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase. A subfamily of SAICAR synthetases represented by the Thermotoga maritima (Tm) enzyme and E. coli PurC. SAICAR synthetase catalyzes the seventh step of the de novo biosynthesis of purine nucleotides (also reported as eighth step). It converts 5-aminoimidazole-4-carboxyribonucleotide (CAIR), ATP, and L-aspartate into 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR), ADP, and phosphate. 230 matched cddid_all.tbl CDD cd01416 cd01416 133471 SAICAR_synt_Ade5 Ade5_like 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR) synthase. Eukaryotic group of SAICAR synthetases represented by the Drosophila melanogaster, N-terminal, SAICAR synthetase domain of bifunctional Ade5. The Ade5 gene product (CAIR-SAICARs) catalyzes the sixth and seventh steps of the de novo biosynthesis of purine nucleotides (also reported as seventh and eighth steps). SAICAR synthetase converts 5-aminoimidazole-4-carboxyribonucleotide (CAIR), ATP, and L-aspartate into 5-aminoimidazole-4-(N-succinylcarboxamide) ribonucleotide (SAICAR), ADP, and phosphate. 252 matched cddid_all.tbl CDD cd01417 cd01417 238705 Ribosomal_L19e_E Ribosomal protein L19e, eukaryotic. L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small subunit. The other exposed end is involved in forming the translocon binding site, along with L22, L23, L24, L29, and L31e subunits. 164 matched cddid_all.tbl CDD cd01418 cd01418 238706 Ribosomal_L19e_A Ribosomal protein L19e, archaeal. L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small subunit. The other exposed end is involved in forming the translocon binding site, along with L22, L23, L24, L29, and L31e subunits. 145 matched cddid_all.tbl CDD cd01419 cd01419 238707 MoaC_A MoaC family, archaeal. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor Z by inserting the carbon-8 of the purine between the 2' and 3' ribose carbon atoms, which is the first of three phases of Moco biosynthesis. 141 matched cddid_all.tbl CDD cd01420 cd01420 238708 MoaC_PE MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor Z by inserting the carbon-8 of the purine between the 2' and 3' ribose carbon atoms, which is the first of three phases of Moco biosynthesis. 140 matched cddid_all.tbl CDD cd01421 cd01421 238709 IMPCH Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates 5-aminoimidazole-4-carboxamide-ribonucleotide. The IMPCH domain then converts the formyl-5-aminoimidazole-4-carboxamide-ribonucleotide to inosine monophosphate. This is the final step in de novo purine production. 187 matched cddid_all.tbl CDD cd01422 cd01422 238710 MGS Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to form an ene-diolate phosphate intermediate. In MGS, the second catalytic step is characterized by the elimination of phosphate and collapse of the enediolate to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate, as in TIM. This is the first reaction in the methylglyoxal bypass of the Embden-Myerhoff glycolytic pathway and is believed to provide physiological benefits under non-ideal growth conditions in bacteria. 115 matched cddid_all.tbl CDD cd01423 cd01423 238711 MGS_CPS_I_III Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain. 116 matched cddid_all.tbl CDD cd01424 cd01424 238712 MGS_CPS_II Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding allosteric effector molecules, including UMP and ornithine. 110 matched cddid_all.tbl CDD cd01425 cd01425 100106 RPS2 Ribosomal protein S2 (RPS2), involved in formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome. It has been shown that in Escherichia coli RPS2 is essential for the binding of ribosomal protein S1 to the 30s ribosomal subunit. In humans, most likely in all vertebrates, and perhaps in all metazoans, the protein also functions as the 67 kDa laminin receptor (LAMR1 or 67LR), which is formed from a 37 kDa precursor, and is overexpressed in many tumors. 67LR is a cell surface receptor which interacts with a variety of ligands, laminin-1 and others. It is assumed that the ligand interactions are mediated via the conserved C-terminus, which becomes extracellular as the protein undergoes conformational changes which are not well understood. Specifically, a conserved palindromic motif, LMWWML, may participate in the interactions. 67LR plays essential roles in the adhesion of cells to the basement membrane and subsequent signalling events, and has been linked to several diseases. Some evidence also suggests that the precursor of 67LR, 37LRP is also present in the nucleus in animals, where it appears associated with histones. 193 matched cddid_all.tbl CDD cd01426 cd01426 349738 ATP-synt_F1_V1_A1_AB_FliI_N ATP synthase, alpha/beta subunits of F1/V1/A1 complex, flagellum-specific ATPase FliI, N-terminal domain. The alpha and beta (or A and B) subunits are primarily found in the F1, V1, and A1 complexes of the F-, V- and A-type family of ATPases with rotary motors. These ion-transporting rotary ATPases are composed of two linked multi-subunit complexes: the F1, V1, or A1 complex which contains three copies each of the alpha and beta subunits that form the soluble catalytic core involved in ATP synthesis/hydrolysis, and the Fo, Vo, or Ao complex which forms the membrane-embedded proton pore. The F-ATP synthases (also called FoF1-ATPases) are found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts, or in the plasma membranes of bacteria. F-ATPases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. The A-ATP synthases (AoA1-ATPases), a different class of proton-translocating ATP synthases, are found in archaea and function like F-ATP synthases. Structurally, however, the A-ATP synthases are more closely related to the V-ATP synthases (vacuolar VoV1-ATPases), which are a proton-translocating ATPase responsible for acidification of eukaryotic intracellular compartments and for ATP synthesis in archaea and some eubacteria. Collectively, F-, V-, and A-type synthases can function in both ATP synthesis and hydrolysis modes. This family also includes the flagellum-specific ATPase/type III secretory pathway virulence-related protein, which shows extensive similarity to the alpha and beta subunits of F1-ATP synthase. 73 matched cddid_all.tbl CDD cd01427 cd01427 319763 HAD_like Haloacid dehalogenase-like hydrolases. The haloacid dehalogenase-like (HAD) superfamily includes L-2-haloacid dehalogenase, epoxide hydrolase, phosphoserine phosphatase, phosphomannomutase, phosphoglycolate phosphatase, P-type ATPase, and many others. This superfamily includes a variety of enzymes that catalyze the cleavage of substrate C-Cl, P-C, and P-OP bonds via nucleophilic substitution pathways. All of which use a nucleophilic aspartate in their phosphoryl transfer reaction. They catalyze nucleophilic substitution reactions at phosphorus or carbon centers, using a conserved Asp carboxylate in covalent catalysis. All members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. Members of this superfamily are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 106 matched cddid_all.tbl CDD cd01428 cd01428 238713 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates. 194 matched cddid_all.tbl CDD cd01429 cd01429 349744 ATP-synt_F1_V1_A1_AB_FliI_C ATP synthase, alpha/beta subunits of F1/V1/A1 complex, flagellum-specific ATPase FliI, C-terminal domain. The alpha and beta (also called A and B) subunits are primarily found in the F1, V1, and A1 complexes of F-, V- and A-type family of ATPases with rotary motors. These ion-transporting rotary ATPases are composed of two linked multi-subunit complexes: the F1, V1, and A1 complexes contain three copies each of the alpha and beta subunits that form the soluble catalytic core, which is involved in ATP synthesis/hydrolysis, and the Fo, Vo, or Ao complex that forms the membrane-embedded proton pore. The F-ATP synthases (also called FoF1-ATPases) are found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts, or in the plasma membranes of bacteria. F-ATPases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. The A-ATP synthases (AoA1-ATPases), a different class of proton-translocating ATP synthases, are found in archaea and function like F-ATP synthases. Structurally, however, the A-ATP synthases are more closely related to the V-ATP synthases (vacuolar VoV1-ATPases), which are a proton-translocating ATPase responsible for acidification of eukaryotic intracellular compartments and for ATP synthesis in archaea and some eubacteria. Collectively, F-, V-, and A-type synthases can function in both ATP synthesis and hydrolysis modes. This family also includes the flagellum-specific ATPase/type III secretory pathway virulence-related protein, which shows extensive similarity to the alpha and beta subunits of F1-ATP synthase. 70 matched cddid_all.tbl CDD cd01431 cd01431 319764 P-type_ATPases ATP-dependent membrane-bound cation and aminophospholipid transporters. The P-type ATPases, are a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids. They are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. A general characteristic of P-type ATPases is a bundle of transmembrane helices which make up the transport path, and three domains on the cytoplasmic side of the membrane. Members include pumps that transport various light metal ions, such as H(+), Na(+), K(+), Ca(2+), and Mg(2+), pumps that transport indispensable trace elements, such as Zn(2+) and Cu(2+), pumps that remove toxic heavy metal ions, such as Cd(2+), and pumps such as aminophospholipid translocases which transport phosphatidylserine and phosphatidylethanolamine. 319 matched cddid_all.tbl CDD cd01433 cd01433 238714 Ribosomal_L16_L10e Ribosomal_L16_L10e: L16 is an essential protein in the large ribosomal subunit of bacteria, mitochondria, and chloroplasts. Large subunits that lack L16 are defective in peptidyl transferase activity, peptidyl-tRNA hydrolysis activity, association with the 30S subunit, binding of aminoacyl-tRNA and interaction with antibiotics. L16 is required for the function of elongation factor P (EF-P), a protein involved in peptide bond synthesis through the stimulation of peptidyl transferase activity by the ribosome. Mutations in L16 and the adjoining bases of 23S rRNA confer antibiotic resistance in bacteria, suggesting a role for L16 in the formation of the antibiotic binding site. The GTPase RbgA (YlqF) is essential for the assembly of the large subunit, and it is believed to regulate the incorporation of L16. L10e is the archaeal and eukaryotic cytosolic homolog of bacterial L16. L16 and L10e exhibit structural differences at the N-terminus. 112 matched cddid_all.tbl CDD cd01434 cd01434 238715 EFG_mtEFG1_IV EFG_mtEFG1_IV: domains similar to domain IV of the bacterial translational elongation factor (EF) EF-G. Included in this group is a domain of mitochondrial Elongation factor G1 (mtEFG1) proteins homologous to domain IV of EF-G. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG2s are not present in this group. 116 matched cddid_all.tbl CDD cd01435 cd01435 259844 RNAP_I_RPA1_N Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain. RPA1 is the largest subunit of the eukaryotic RNA polymerase I (RNAP I). RNAP I is a multi-subunit protein complex responsible for the synthesis of rRNA precursors. RNAP I consists of at least 14 different subunits, the largest being homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. The yeast member of this family is known as Rpb190. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site. It makes up the head and core of one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between RPA1 and Rpb1 suggests a similar functional and structural role. 779 matched cddid_all.tbl CDD cd01436 cd01436 238716 Dipth_tox_like Mono-ADP-ribosylating toxins catalyze the transfer of ADP_ribose from NAD+ to eukaryotic Elongation Factor 2, halting protein synthesis. A single molecule of delivered toxin is sufficient to kill a cell. These toxins share mono-ADP-ribosylating activity with a variety of bacterial toxins, such as cholera toxin and pertussis toxin. The structural core is homologous to the poly-ADP ribosylating enzymes such as the PARP enzymes and Tankyrase. Diphtheria toxin is encoded by a lysogenic bacteriophage. Both diphtheria toxin and Pseudomonas aeruginosa exotoxin A are multi-domain proteins. These domains provide a EF2 ADP_ribosylating, receptor-binding, and intracellular trafficking/transmembrane functions . 147 matched cddid_all.tbl CDD cd01437 cd01437 238717 parp_like Poly(ADP-ribose) polymerase (parp) catalytic domain catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active. Poly(ADP-ribose)-like polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length through interactions with telomere repeat binding factor 1. 347 matched cddid_all.tbl CDD cd01438 cd01438 238718 tankyrase_like Tankyrases interact with the telomere reverse transcriptase complex (TERT). Tankyrase 1 poly-ADP-ribosylates Telomere Repeat Binding Factor 1 (TRF1) while Tankyrase 2 can poly-ADP-ribosylate itself or TRF1. The tankyrases also contain multiple ankyrin repeats that mediate protein-protein interaction (binding TRF1 and insulin-responsive aminopeptidase) and may function as a complex. Overexpression of Tank1 promotes increased telomere length when overexpressed, while overexpressed Tank2 has been shown to promote PARP cleavage- independent cell death (necrosis). 223 matched cddid_all.tbl CDD cd01439 cd01439 238719 TCCD_inducible_PARP_like Poly(ADP-ribose) polymerases catalyse the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) causes pleotropic effects in mammalian species through modulating gene expression. TCCD indicible PARP (TiPARP) is a target of TCDD that may contribute to multiple responses to TCDD by modulating protein function through poly ADP-ribosylation 121 matched cddid_all.tbl CDD cd01443 cd01443 238720 Cdc25_Acr2p Cdc25 enzymes are members of the Rhodanese Homology Domain (RHOD) superfamily. Also included in this CD are eukaryotic arsenate resistance proteins such as Saccharomyces cerevisiae Acr2p and similar proteins. Cdc25 phosphatases activate the cell division kinases throughout the cell cycle progression. Cdc25 phosphatases dephosphorylate phosphotyrosine and phosphothreonine residues, in order to activate their Cdk/cyclin substrates. The Cdc25 and Acr2p RHOD domains have the signature motif (H/YCxxxxxR). 113 matched cddid_all.tbl CDD cd01444 cd01444 238721 GlpE_ST GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily. Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a catalytically active cysteine. 96 matched cddid_all.tbl CDD cd01445 cd01445 238722 TST_Repeats Thiosulfate sulfurtransferases (TST) contain 2 copies of the Rhodanese Homology Domain. Only the second repeat contains the catalytically active Cys residue. The role of the 1st repeat is uncertain, but believed to be involved in protein interaction. This CD aligns the 1st and 2nd repeats. 138 matched cddid_all.tbl CDD cd01446 cd01446 238723 DSP_MapKP N-terminal regulatory rhodanese domain of dual specificity phosphatases (DSP), such as Mapk Phosphatase. This domain is believed to determine substrate specificity by binding the substrate, such as ERK2, and activating the C-terminal catalytic domain by inducing a conformational change. This domain has homology to the Rhodanese Homology Domain. 132 matched cddid_all.tbl CDD cd01447 cd01447 238724 Polysulfide_ST Polysulfide-sulfurtransferase - Rhodanese Homology Domain. This domain is believed to serve as a polysulfide binding and transferase domain in anaerobic gram-negative bacteria, functioning in oxidative phosphorylation with polysulfide-sulfur as a terminal electron acceptor. The active site contains the same conserved cysteine that is the catalytic residue in other Rhodanese Homology Domain proteins. 103 matched cddid_all.tbl CDD cd01448 cd01448 238725 TST_Repeat_1 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it is believed to be involved in protein interaction. 122 matched cddid_all.tbl CDD cd01449 cd01449 238726 TST_Repeat_2 Thiosulfate sulfurtransferase (TST), C-terminal, catalytic domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the second repeat. Only the second repeat contains the catalytically active Cys residue. 118 matched cddid_all.tbl CDD cd01450 cd01450 238727 vWFA_subfamily_ECM Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains 161 matched cddid_all.tbl CDD cd01451 cd01451 238728 vWA_Magnesium_chelatase Magnesium chelatase: Mg-chelatase catalyses the insertion of Mg into protoporphyrin IX (Proto). In chlorophyll biosynthesis, insertion of Mg2+ into protoporphyrin IX is catalysed by magnesium chelatase in an ATP-dependent reaction. Magnesium chelatase is a three sub-unit (BchI, BchD and BchH) enzyme with a novel arrangement of domains: the C-terminal helical domain is located behind the nucleotide binding site. The BchD domain contains a AAA domain at its N-terminus and a VWA domain at its C-terminus. The VWA domain has been speculated to be involved in mediating protein-protein interactions. 178 matched cddid_all.tbl CDD cd01452 cd01452 238729 VWA_26S_proteasome_subunit 26S proteasome plays a major role in eukaryotic protein breakdown, especially for ubiquitin-tagged proteins. It is an ATP-dependent protease responsible for the bulk of non-lysosomal proteolysis in eukaryotes, often using covalent modification of proteins by ubiquitylation. It consists of a 20S proteolytic core particle (CP) and a 19S regulatory particle (RP). The CP is an ATP independent peptidase consisting of hydrolyzing activities. One or both ends of CP carry the RP that confers both ubiquitin and ATP dependence to the 26S proteosome. The RP's proposed functions include recognition of substrates and translocation of these to CP for proteolysis. The RP can dissociate into a stable lid and base subcomplexes. The base is composed of three non-ATPase subunits (Rpn 1, 2 and 10). A single residue in the vWA domain of Rpn10 has been implicated to be responsible for stabilizing the lid-base association. 187 matched cddid_all.tbl CDD cd01453 cd01453 238730 vWA_transcription_factor_IIH_type Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair, and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear, but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group. 183 matched cddid_all.tbl CDD cd01454 cd01454 238731 vWA_norD_type norD type: Denitrifying bacteria contain both membrane bound and periplasmic nitrate reductases. Denitrification plays a major role in completing the nitrogen cycle by converting nitrate or nitrite to nitrogen gas. The pathway for microbial denitrification has been established as NO3- ------> NO2- ------> NO -------> N2O ---------> N2. This reaction generally occurs under oxygen limiting conditions. Genetic and biochemical studies have shown that the first srep of the biochemical pathway is catalyzed by periplasmic nitrate reductases. This family is widely present in proteobacteria and firmicutes. This version of the domain is also present in some archaeal members. The function of the vWA domain in this sub-group is not known. Members of this subgroup have a conserved MIDAS motif. 174 matched cddid_all.tbl CDD cd01455 cd01455 238732 vWA_F11C1-5a_type Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains. Not much is known about the functions of the members of this subgroup. The members of this subgroup are fused to the ancient AAA domain. 191 matched cddid_all.tbl CDD cd01456 cd01456 238733 vWA_ywmD_type VWA ywmD type:Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains. Not much is known about the function of the members of this subgroup. All members of this subgroup however have a conserved MIDAS motif. 206 matched cddid_all.tbl CDD cd01457 cd01457 238734 vWA_ORF176_type VWA ORF176 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses. In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains. The members of this subgroup are Eubacterial in origin and have a conserved MIDAS motif. Not much is known about the biochemistry of these. 199 matched cddid_all.tbl CDD cd01458 cd01458 238735 vWA_ku Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks (DSB) in a preferred orientation. DSB's are repaired by either homologues recombination or non-homologues end joining and facilitate repair by the non-homologous end-joining pathway (NHEJ). The Ku heterodimer is required for accurate process that tends to preserve the sequence at the junction. Ku78 is found in all three kingdoms of life. However, only the eukaryotic proteins have a vWA domain fused to them at their N-termini. The vWA domain is not involved in DNA binding but may very likey mediate Ku78's interactions with other proteins. Members of this subgroup lack the conserved MIDAS motif. 218 matched cddid_all.tbl CDD cd01459 cd01459 238736 vWA_copine_like VWA Copine: Copines are phospholipid-binding proteins originally identified in paramecium. They are found in human and orthologues have been found in C. elegans and Arabidopsis Thaliana. None have been found in D. Melanogaster or S. Cereviciae. Phylogenetic distribution suggests that copines have been lost in some eukaryotes. No functional properties have been assigned to the VWA domains present in copines. The members of this subgroup contain a functional MIDAS motif based on their preferential binding to magnesium and manganese. However, the MIDAS motif is not totally conserved, in most cases the MIDAS consists of the sequence DxTxS instead of the motif DxSxS that is found in most cases. The C2 domains present in copines mediate phospholipid binding. 254 matched cddid_all.tbl CDD cd01460 cd01460 238737 vWA_midasin VWA_Midasin: Midasin is a member of the AAA ATPase family. The proteins of this family are unified by their common archetectural organization that is based upon a conserved ATPase domain. The AAA domain of midasin contains six tandem AAA protomers. The AAA domains in midasin is followed by a D/E rich domain that is following by a VWA domain. The members of this subgroup have a conserved MIDAS motif. The function of this domain is not exactly known although it has been speculated to play a crucial role in midasin function. 266 matched cddid_all.tbl CDD cd01461 cd01461 238738 vWA_interalpha_trypsin_inhibitor vWA_interalpha trypsin inhibitor (ITI): ITI is a glycoprotein composed of three polypeptides- two heavy chains and one light chain (bikunin). Bikunin confers the protease-inhibitor function while the heavy chains are involved in rendering stability to the extracellular matrix by binding to hyaluronic acid. The heavy chains carry the VWA domain with a conserved MIDAS motif. Although the exact role of the VWA domains remains unknown, it has been speculated to be involved in mediating protein-protein interactions with the components of the extracellular matrix. 171 matched cddid_all.tbl CDD cd01462 cd01462 238739 VWA_YIEM_type VWA YIEM type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains. Members of this subgroup have a conserved MIDAS motif, however, their biochemical function is not well characterised. 152 matched cddid_all.tbl CDD cd01463 cd01463 238740 vWA_VGCC_like VWA Voltage gated Calcium channel like: Voltage-gated calcium channels are a complex of five proteins: alpha 1, beta 1, gamma, alpha 2 and delta. The alpha 2 and delta subunits result from proteolytic processing of a single gene product and carries at its N-terminus the VWA and cache domains, The alpha 2 delta gene family has orthologues in D. melanogaster and C. elegans but none have been detected in aither A. thaliana or yeast. The exact biochemical function of the VWA domain is not known but the alpha 2 delta complex has been shown to regulate various functional properties of the channel complex. 190 matched cddid_all.tbl CDD cd01464 cd01464 238741 vWA_subfamily VWA subfamily: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains. Members of this subgroup have no assigned function. This subfamily is typified by the presence of a conserved MIDAS motif. 176 matched cddid_all.tbl CDD cd01465 cd01465 238742 vWA_subgroup VWA subgroup: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains. Not much is known about the function of the VWA domain in these proteins. The members do have a conserved MIDAS motif. The biochemical function however is not known. 170 matched cddid_all.tbl CDD cd01466 cd01466 238743 vWA_C3HC4_type VWA C3HC4-type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains. Membes of this subgroup belong to Zinc-finger family as they are found fused to RING finger domains. The MIDAS motif is not conserved in all the members of this family. The function of vWA domains however is not known. 155 matched cddid_all.tbl CDD cd01467 cd01467 238744 vWA_BatA_type VWA BatA type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses. In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains. Members of this subgroup are bacterial in origin. They are typified by the presence of a MIDAS motif. 180 matched cddid_all.tbl CDD cd01468 cd01468 238745 trunk_domain trunk domain. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is known as the trunk domain and has an alpha/beta vWA fold and forms the dimer interface. Some members of this family possess a partial MIDAS motif that is a characteristic feature of most vWA domain proteins. 239 matched cddid_all.tbl CDD cd01469 cd01469 238746 vWA_integrins_alpha_subunit Integrins are a class of adhesion receptors that link the extracellular matrix to the cytoskeleton and cooperate with growth factor receptors to promote celll survival, cell cycle progression and cell migration. Integrins consist of an alpha and a beta sub-unit. Each sub-unit has a large extracellular portion, a single transmembrane segment and a short cytoplasmic domain. The N-terminal domains of the alpha and beta subunits associate to form the integrin headpiece, which contains the ligand binding site, whereas the C-terminal segments traverse the plasma membrane and mediate interaction with the cytoskeleton and with signalling proteins.The VWA domains present in the alpha subunits of integrins seem to be a chordate specific radiation of the gene family being found only in vertebrates. They mediate protein-protein interactions. 177 matched cddid_all.tbl CDD cd01470 cd01470 238747 vWA_complement_factors Complement factors B and C2 are two critical proteases for complement activation. They both contain three CCP or Sushi domains, a trypsin-type serine protease domain and a single VWA domain with a conserved metal ion dependent adhesion site referred commonly as the MIDAS motif. Orthologues of these molecules are found from echinoderms to chordates. During complement activation, the CCP domains are cleaved off, resulting in the formation of an active protease that cleaves and activates complement C3. Complement C2 is in the classical pathway and complement B is in the alternative pathway. The interaction of C2 with C4 and of factor B with C3b are both dependent on Mg2+ binding sites within the VWA domains and the VWA domain of factor B has been shown to mediate the binding of C3. This is consistent with the common inferred function of VWA domains as magnesium-dependent protein interaction domains. 198 matched cddid_all.tbl CDD cd01471 cd01471 238748 vWA_micronemal_protein Micronemal proteins: The Toxoplasma lytic cycle begins when the parasite actively invades a target cell. In association with invasion, T. gondii sequentially discharges three sets of secretory organelles beginning with the micronemes, which contain adhesive proteins involved in parasite attachment to a host cell. Deployed as protein complexes, several micronemal proteins possess vertebrate-derived adhesive sequences that function in binding receptors. The VWA domain likely mediates the protein-protein interactions of these with their interacting partners. 186 matched cddid_all.tbl CDD cd01472 cd01472 238749 vWA_collagen von Willebrand factor (vWF) type A domain; equivalent to the I-domain of integrins. This domain has a variety of functions including: intermolecular adhesion, cell migration, signalling, transcription, and DNA repair. In integrins these domains form heterodimers while in vWF it forms homodimers and multimers. There are different interaction surfaces of this domain as seen by its complexes with collagen with either integrin or human vWFA. In integrins collagen binding occurs via the metal ion-dependent adhesion site (MIDAS) and involves three surface loops located on the upper surface of the molecule. In human vWFA, collagen binding is thought to occur on the bottom of the molecule and does not involve the vestigial MIDAS motif. 164 matched cddid_all.tbl CDD cd01473 cd01473 238750 vWA_CTRP CTRP for CS protein-TRAP-related protein: Adhesion of Plasmodium to host cells is an important phenomenon in parasite invasion and in malaria associated pathology.CTRP encodes a protein containing a putative signal sequence followed by a long extracellular region of 1990 amino acids, a transmembrane domain, and a short cytoplasmic segment. The extracellular region of CTRP contains two separated adhesive domains. The first domain contains six 210-amino acid-long homologous VWA domain repeats. The second domain contains seven repeats of 87-60 amino acids in length, which share similarities with the thrombospondin type 1 domain found in a variety of adhesive molecules. Finally, CTRP also contains consensus motifs found in the superfamily of haematopoietin receptors. The VWA domains in these proteins likely mediate protein-protein interactions. 192 matched cddid_all.tbl CDD cd01474 cd01474 238751 vWA_ATR ATR (Anthrax Toxin Receptor): Anthrax toxin is a key virulence factor for Bacillus anthracis, the causative agent of anthrax. ATR is the cellular receptor for the anthrax protective antigen and facilitates entry of the toxin into cells. The VWA domain in ATR contains the toxin binding site and mediates interaction with protective antigen. The binding is mediated by divalent cations that binds to the MIDAS motif. These proteins are a family of vertebrate ECM receptors expressed by endothelial cells. 185 matched cddid_all.tbl CDD cd01475 cd01475 238752 vWA_Matrilin VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity. Some members of the matrilin family are expressed specifically in developing cartilage rudiments. The matrilin family consists of at least four members. All the members of the matrilin family contain VWA domains, EGF-like domains and a heptad repeat coiled-coiled domain at the carboxy terminus which is responsible for the oligomerization of the matrilins. The VWA domains have been shown to be essential for matrilin network formation by interacting with matrix ligands. 224 matched cddid_all.tbl CDD cd01476 cd01476 238753 VWA_integrin_invertebrates VWA_integrin (invertebrates): Integrins are a family of cell surface receptors that have diverse functions in cell-cell and cell-extracellular matrix interactions. Because of their involvement in many biologically important adhesion processes, integrins are conserved across a wide range of multicellular animals. Integrins from invertebrates have been identified from six phyla. There are no data to date to suggest any immunological functions for the invertebrate integrins. The members of this sub-group have the conserved MIDAS motif that is charateristic of this domain suggesting the involvement of the integrins in the recognition and binding of multi-ligands. 163 matched cddid_all.tbl CDD cd01477 cd01477 238754 vWA_F09G8-8_type VWA F09G8.8 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains. The members of this subgroup lack the MIDAS motif. This subgroup is found only in C. elegans and the members identified thus far are always found fused to a C-Lectin type domain. Biochemical function thus far has not be attributed to any of the members of this subgroup. 193 matched cddid_all.tbl CDD cd01478 cd01478 238755 Sec23-like Sec23-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 23 is very similar to Sec24. The Sec23 and Sec24 polypeptides fold into five distinct domains: a beta-barrel, a zinc finger, a vWA or trunk, an all helical region and a carboxy Gelsolin domain. The members of this subgroup lack the consensus MIDAS motif but have the overall Para-Rossmann type fold that is characteristic of this superfamily. 267 matched cddid_all.tbl CDD cd01479 cd01479 238756 Sec24-like Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes of vesicular carriers within the endocytic and the biosynthetic pathways are COP- and clathrin-coated vesicles. Formation of COPII vesicles requires the ordered assembly of the coat built from several cytosolic components GTPase Sar1, complexes of Sec23-Sec24 and Sec13-Sec31. The process is initiated by the conversion of GDP to GTP by the GTPase Sar1 which then recruits the heterodimeric complex of Sec23 and Sec24. This heterodimeric complex generates the pre-budding complex. The final step leading to membrane deformation and budding of COPII-coated vesicles is carried by the heterodimeric complex Sec13-Sec31. The members of this CD belong to the Sec23-like family. Sec 24 is very similar to Sec23. The Sec23 and Sec24 polypeptides fold into five distinct domains: a beta-barrel, a zinc finger, a vWA or trunk, an all helical region and a carboxy Gelsolin domain. The members of this subgroup carry a partial MIDAS motif and have the overall Para-Rossmann type fold that is characteristic of this superfamily. 244 matched cddid_all.tbl CDD cd01480 cd01480 238757 vWA_collagen_alpha_1-VI-type VWA_collagen alpha(VI) type: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions. 186 matched cddid_all.tbl CDD cd01481 cd01481 238758 vWA_collagen_alpha3-VI-like VWA_collagen alpha 3(VI) like: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions. 165 matched cddid_all.tbl CDD cd01482 cd01482 238759 vWA_collagen_alphaI-XII-like Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different collagen types identified thus far. Collagens are centrally involved in the formation of fibrillar and microfibrillar networks of the extracellular matrix, basement membranes as well as other structures of the extracellular matrix. Some collagens have about 15-18 vWA domains in them. The VWA domains present in these collagens mediate protein-protein interactions. 164 matched cddid_all.tbl CDD cd01483 cd01483 238760 E1_enzyme_family Superfamily of activating enzymes (E1) of the ubiquitin-like proteins. This family includes classical ubiquitin-activating enzymes E1, ubiquitin-like (ubl) activating enzymes and other mechanistic homologes, like MoeB, Thif1 and others. The common reaction mechanism catalyzed by MoeB, ThiF and the E1 enzymes begins with a nucleophilic attack of the C-terminal carboxylate of MoaD, ThiS and ubiquitin, respectively, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of MoaD and ThiS. 143 matched cddid_all.tbl CDD cd01484 cd01484 238761 E1-2_like Ubiquitin activating enzyme (E1), repeat 2-like. E1, a highly conserved small protein present universally in eukaryotic cells, is part of cascade to attach ubiquitin (Ub) covalently to substrate proteins. This cascade consists of activating (E1), conjugating (E2), and/or ligating (E3) enzymes and then targets them for degradation by the 26S proteasome. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and ubiquitin's C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. A set of novel molecules with a structural similarity to Ub, called Ub-like proteins (Ubls), have similar conjugation cascades. In contrast to ubiquitin-E1, which is a single-chain protein with a weakly conserved two-fold repeat, many of the Ubls-E1are a heterodimer where each subunit corresponds to one half of a single-chain E1. This CD represents the family homologous to the second repeat of Ub-E1. 234 matched cddid_all.tbl CDD cd01485 cd01485 238762 E1-1_like Ubiquitin activating enzyme (E1), repeat 1-like. E1, a highly conserved small protein present universally in eukaryotic cells, is part of cascade to attach ubiquitin (Ub) covalently to substrate proteins. This cascade consists of activating (E1), conjugating (E2), and/or ligating (E3) enzymes and then targets them for degradation by the 26S proteasome. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and ubiquitin's C-terminus. The E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. A set of novel molecules with a structural similarity to Ub, called Ub-like proteins (Ubls), have similar conjugation cascades. In contrast to ubiquitin-E1, which is a single-chain protein with a weakly conserved two-fold repeat, many of the Ubls-E1are a heterodimer where each subunit corresponds to one half of a single-chain E1. This CD represents the family homologous to the first repeat of Ub-E1. 198 matched cddid_all.tbl CDD cd01486 cd01486 238763 Apg7 Apg7 is an E1-like protein, that activates two different ubiquitin-like proteins, Apg12 and Apg8, and assigns them to specific E2 enzymes, Apg10 and Apg3, respectively. This leads to the covalent conjugation of Apg8 with phosphatidylethanolamine, an important step in autophagy. Autophagy is a dynamic membrane phenomenon for bulk protein degradation in the lysosome/vacuole. 307 matched cddid_all.tbl CDD cd01487 cd01487 238764 E1_ThiF_like E1_ThiF_like. Member of superfamily of activating enzymes (E1) of the ubiquitin-like proteins. The common reaction mechanism catalyzed by E1-like enzymes begins with a nucleophilic attack of the C-terminal carboxylate of the ubiquitin-like substrate, on the alpha-phosphate of an ATP molecule bound at the active site of the activating enzymes, leading to the formation of a high-energy acyladenylate intermediate and subsequently to the formation of a thiocarboxylate at the C termini of the substrate. The exact function of this family is unknown. 174 matched cddid_all.tbl CDD cd01488 cd01488 238765 Uba3_RUB Ubiquitin activating enzyme (E1) subunit UBA3. UBA3 is part of the heterodimeric activating enzyme (E1), specific for the Rub family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins. consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin(-like) by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by Rub family of ubiquitin-like proteins (Ublps) activates SCF ubiquitin ligases and is involved in cell cycle control, signaling and embryogenesis. UBA3 contains both the nucleotide-binding motif involved in adenylation and the catalytic cysteine involved in the thioester intermediate and Ublp transfer to E2. 291 matched cddid_all.tbl CDD cd01489 cd01489 238766 Uba2_SUMO Ubiquitin activating enzyme (E1) subunit UBA2. UBA2 is part of the heterodimeric activating enzyme (E1), specific for the SUMO family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. The E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by SUMO family of ubiquitin-like proteins (Ublps) is involved in cell division, nuclear transport, the stress response and signal transduction. UBA2 contains both the nucleotide-binding motif involved in adenylation and the catalytic cysteine involved in the thioester intermediate and Ublp transfer to E2. 312 matched cddid_all.tbl CDD cd01490 cd01490 238767 Ube1_repeat2 Ubiquitin activating enzyme (E1), repeat 2. E1, a highly conserved small protein present universally in eukaryotic cells, is part of cascade to attach ubiquitin (Ub) covalently to substrate proteins. This cascade consists of activating (E1), conjugating (E2), and/or ligating (E3) enzymes and then targets them for degradation by the 26S proteasome. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and ubiquitin's C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Ubiquitin-E1 is a single-chain protein with a weakly conserved two-fold repeat. This CD represents the second repeat of Ub-E1. 435 matched cddid_all.tbl CDD cd01491 cd01491 238768 Ube1_repeat1 Ubiquitin activating enzyme (E1), repeat 1. E1, a highly conserved small protein present universally in eukaryotic cells, is part of cascade to attach ubiquitin (Ub) covalently to substrate proteins. This cascade consists of activating (E1), conjugating (E2), and/or ligating (E3) enzymes and then targets them for degradation by the 26S proteasome. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and ubiquitin's C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Ubiquitin-E1 is a single-chain protein with a weakly conserved two-fold repeat. This CD represents the first repeat of Ub-E1. 286 matched cddid_all.tbl CDD cd01492 cd01492 238769 Aos1_SUMO Ubiquitin activating enzyme (E1) subunit Aos1. Aos1 is part of the heterodimeric activating enzyme (E1), specific for the SUMO family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. The E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by SUMO family of ubiquitin-like proteins (Ublps) is involved in cell division, nuclear transport, the stress response and signal transduction. Aos1 contains part of the adenylation domain. 197 matched cddid_all.tbl CDD cd01493 cd01493 238770 APPBP1_RUB Ubiquitin activating enzyme (E1) subunit APPBP1. APPBP1 is part of the heterodimeric activating enzyme (E1), specific for the Rub family of ubiquitin-like proteins (Ubls). E1 enzymes are part of a conjugation cascade to attach Ub or Ubls, covalently to substrate proteins consisting of activating (E1), conjugating (E2), and/or ligating (E3) enzymes. E1 activates ubiquitin(-like) by C-terminal adenylation, and subsequently forms a highly reactive thioester bond between its catalytic cysteine and Ubls C-terminus. E1 also associates with E2 and promotes ubiquitin transfer to the E2's catalytic cysteine. Post-translational modification by Rub family of ubiquitin-like proteins (Ublps) activates SCF ubiquitin ligases and is involved in cell cycle control, signaling and embryogenesis. ABPP1 contains part of the adenylation domain. 425 matched cddid_all.tbl CDD cd01494 cd01494 99742 AAT_I Aspartate aminotransferase (AAT) superfamily (fold type I) of pyridoxal phosphate (PLP)-dependent enzymes. PLP combines with an alpha-amino acid to form a compound called a Schiff base or aldimine intermediate, which depending on the reaction, is the substrate in four kinds of reactions (1) transamination (movement of amino groups), (2) racemization (redistribution of enantiomers), (3) decarboxylation (removing COOH groups), and (4) various side-chain reactions depending on the enzyme involved. Pyridoxal phosphate (PLP) dependent enzymes were previously classified into alpha, beta and gamma classes, based on the chemical characteristics (carbon atom involved) of the reaction they catalyzed. The availability of several structures allowed a comprehensive analysis of the evolutionary classification of PLP dependent enzymes, and it was found that the functional classification did not always agree with the evolutionary history of these enzymes. Structure and sequence analysis has revealed that the PLP dependent enzymes can be classified into four major groups of different evolutionary origin: aspartate aminotransferase superfamily (fold type I), tryptophan synthase beta superfamily (fold type II), alanine racemase superfamily (fold type III), and D-amino acid superfamily (fold type IV) and Glycogen phophorylase family (fold type V). 170 matched cddid_all.tbl CDD cd01513 cd01513 275447 Translation_factor_III Domain III of Elongation factor (EF) Tu (EF-TU) and related proteins. Elongation factor (EF) EF-Tu participates in the elongation phase during protein biosynthesis on the ribosome. Its functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Experimental findings indicate an essential contribution of domain III to activation of GTP hydrolysis. This domain III, which is distinct from the domain III in EFG and related elongation factors, is found in several eukaryotic translation factors, like peptide chain release factors RF3, elongation factor 1, selenocysteine (Sec)-specific elongation factor, and in GT-1 family of GTPase (GTPBP1). 102 matched cddid_all.tbl CDD cd01514 cd01514 238772 Elongation_Factor_C Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of elongation factors (EFs) bacterial EF-G, eukaryotic and archeal EF-2 and eukaryotic mitochondrial mtEFG1s and mtEFG2s. This group also includes proteins similar to the ribosomal protection proteins Tet(M) and Tet(O), BipA, LepA and, spliceosomal proteins: human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and yeast counterpart Snu114p. This domain adopts a ferredoxin-like fold consisting of an alpha-beta sandwich with anti-parallel beta-sheets, resembling the topology of domain III found in the elongation factors EF-G and eukaryotic EF-2, with which it forms the C-terminal block. The two domains however are not superimposable and domain III lacks some of the characteristics of this domain. EF-2/EF-G in complex with GTP, promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome. Tet(M) and Tet(O) mediate Tc resistance. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. Yeast Snu114p is essential for cell viability and for splicing in vivo. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. The function of LepA proteins is unknown. 79 matched cddid_all.tbl CDD cd01515 cd01515 238773 Arch_FBPase_1 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family (FBPase class IV). These are Mg++ dependent phosphatases. Members in this family may have both fructose-1,6-bisphosphatase and inositol-monophosphatase activity. In hyperthermophilic archaea, inositol monophosphatase is thought to play a role in the biosynthesis of di-myo-inositol-1,1'-phosphate, an osmolyte unique to hyperthermophiles. 257 matched cddid_all.tbl CDD cd01516 cd01516 238774 FBPase_glpX Bacterial fructose-1,6-bisphosphatase, glpX-encoded. A dimeric enzyme dependent on Mg(2+). glpX-encoded FPBase (FBPase class II) differs from other members of the inositol-phosphatase superfamily by permutation of secondary structure elements. The core structure around the active site is well preserved. In E. coli, FBPase II is part of the glp regulon, which mediates growth on glycerol or sn-glycerol 3-phosphate as the sole carbon source. 309 matched cddid_all.tbl CDD cd01517 cd01517 238775 PAP_phosphatase PAP-phosphatase_like domains. PAP-phosphatase is a member of the inositol monophosphatase family, and catalyses the hydrolysis of 3'-phosphoadenosine-5'-phosphate (PAP) to AMP. In Saccharomyces cerevisiae, HAL2 (MET22) is involved in methionine biosynthesis and provides increased salt tolerance when over-expressed. Bacterial members of this domain family may differ in their substrate specificity and dephosphorylate different targets, as the substrate binding site does not appear to be conserved in that sub-set. 274 matched cddid_all.tbl CDD cd01518 cd01518 238776 RHOD_YceA Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins. 101 matched cddid_all.tbl CDD cd01519 cd01519 238777 RHOD_HSP67B2 Member of the Rhodanese Homology Domain superfamily. This CD includes the heat shock protein 67B2 of Drosophila melanogaster and other similar proteins, many of which are uncharacterized. 106 matched cddid_all.tbl CDD cd01520 cd01520 238778 RHOD_YbbB Member of the Rhodanese Homology Domain superfamily. This CD includes several putative ATP /GTP binding proteins including E. coli YbbB. 128 matched cddid_all.tbl CDD cd01521 cd01521 238779 RHOD_PspE2 Member of the Rhodanese Homology Domain superfamily. This CD includes the putative rhodanese-like protein, Psp2, of Yersinia pestis biovar Medievalis and other similar uncharacterized proteins. 110 matched cddid_all.tbl CDD cd01522 cd01522 238780 RHOD_1 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins. 117 matched cddid_all.tbl CDD cd01523 cd01523 238781 RHOD_Lact_B Member of the Rhodanese Homology Domain superfamily. This CD includes predicted proteins with rhodanese-like domains found N-terminal of the metallo-beta-lactamase domain. 100 matched cddid_all.tbl CDD cd01524 cd01524 238782 RHOD_Pyr_redox Member of the Rhodanese Homology Domain superfamily. Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar rhodanese-like domains found C-terminal of the pyridine nucleotide-disulphide oxidoreductase (Pyr-redox) domain and the Pyr-redox dimerization domain. 90 matched cddid_all.tbl CDD cd01525 cd01525 238783 RHOD_Kc Member of the Rhodanese Homology Domain superfamily. Included in this CD are the rhodanese-like domains found C-terminal of the serine/threonine protein kinases catalytic (S_TKc) domain and the Tre-2, BUB2p, Cdc16p (TBC) domain. The putative active site Cys residue is not present in this CD. 105 matched cddid_all.tbl CDD cd01526 cd01526 238784 RHOD_ThiF Member of the Rhodanese Homology Domain superfamily. This CD includes several putative molybdopterin synthase sulfurylases including the molybdenum cofactor biosynthetic protein (CnxF) of Aspergillus nidulans and the molybdenum cofactor synthesis protein 3 (MOCS3) of Homo sapiens. These rhodanese-like domains are found C-terminal of the ThiF and MoeZ_MoeB domains. 122 matched cddid_all.tbl CDD cd01527 cd01527 238785 RHOD_YgaP Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YgaP, and similar uncharacterized putative rhodanese-related sulfurtransferases. 99 matched cddid_all.tbl CDD cd01528 cd01528 238786 RHOD_2 Member of the Rhodanese Homology Domain superfamily, subgroup 2. Subgroup 2 includes uncharacterized putative rhodanese-related domains. 101 matched cddid_all.tbl CDD cd01529 cd01529 238787 4RHOD_Repeats Member of the Rhodanese Homology Domain superfamily. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. Only the second and most of the fourth repeats contain the putative catalytic Cys residue. This CD aligns the 1st , 2nd, 3rd, and 4th repeats. 96 matched cddid_all.tbl CDD cd01530 cd01530 238788 Cdc25 Cdc25 phosphatases are members of the Rhodanese Homology Domain superfamily. They activate the cell division kinases throughout the cell cycle progression. Cdc25 phosphatases dephosphorylate phosphotyrosine and phosphothreonine residues, in order to activate their Cdk/cyclin substrates. Cdc25A phosphatase functions to regulate S phase entry and Cdc25B is required for G2/M phase transition of the cell cycle. The Cdc25 domain binds oxyanions at the catalytic site and has the signature motif (H/YCxxxxxR). 121 matched cddid_all.tbl CDD cd01531 cd01531 238789 Acr2p Eukaryotic arsenate resistance proteins are members of the Rhodanese Homology Domain superfamily. Included in this CD is the Saccharomyces cerevisiae arsenate reductase protein, Acr2p, and other yeast and plant homologs. 113 matched cddid_all.tbl CDD cd01532 cd01532 238790 4RHOD_Repeat_1 Member of the Rhodanese Homology Domain superfamily, repeat 1. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 1st repeat which does not contain the putative catalytic Cys residue. 92 matched cddid_all.tbl CDD cd01533 cd01533 238791 4RHOD_Repeat_2 Member of the Rhodanese Homology Domain superfamily, repeat 2. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 2nd repeat which does contain the putative catalytic Cys residue. 109 matched cddid_all.tbl CDD cd01534 cd01534 238792 4RHOD_Repeat_3 Member of the Rhodanese Homology Domain superfamily, repeat 3. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 3rd repeat which does not contain the putative catalytic Cys residue. 95 matched cddid_all.tbl CDD cd01535 cd01535 238793 4RHOD_Repeat_4 Member of the Rhodanese Homology Domain superfamily, repeat 4. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 4th repeat which, in general, contains the putative catalytic Cys residue. 145 matched cddid_all.tbl CDD cd01536 cd01536 380478 PBP1_ABC_sugar_binding-like periplasmic sugar-binding domain of active transport systems that are members of the type 1 periplasmic binding protein (PBP1) superfamily. Periplasmic sugar-binding domain of active transport systems that are members of the type 1 periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2) receptors such as LsrB and LuxP which are highly homologous to periplasmic pentose/hexose sugar-binding proteins. 268 matched cddid_all.tbl CDD cd01537 cd01537 380479 PBP1_repressor_sugar_binding-like Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems. Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type 1 periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain. The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type 1, which has six beta strands, and type 2, which has five beta strands. These two distinct structural arrangements may have originated from a common ancestor. 265 matched cddid_all.tbl CDD cd01538 cd01538 380480 PBP1_ABC_xylose_binding-like periplasmic xylose-like sugar-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily. Periplasmic xylose-like sugar-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. 283 matched cddid_all.tbl CDD cd01539 cd01539 380481 PBP1_GGBP periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic GGBP is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. 302 matched cddid_all.tbl CDD cd01540 cd01540 380482 PBP1_arabinose_binding periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such as LacI and GalR. 294 matched cddid_all.tbl CDD cd01541 cd01541 380483 PBP1_AraR ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for arabinose (AraR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of AraR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 274 matched cddid_all.tbl CDD cd01542 cd01542 380484 PBP1_TreR-like ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor specific for trehalose (TreR) which is a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of TreR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 259 matched cddid_all.tbl CDD cd01543 cd01543 380485 PBP1_XylR ligand-binding domain of DNA transcription repressor specific for xylose (XylR). Ligand-binding domain of DNA transcription repressor specific for xylose (XylR), a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of XylR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 265 matched cddid_all.tbl CDD cd01544 cd01544 380486 PBP1_GalR ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand-binding domain of DNA transcription repressor GalR which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalR is a dimeric protein like GalS and is exclusively involved in the regulation of galactose permease, the low-affinity galactose transporter. GalS is involved in regulating expression of the high-affinity galactose transporter encoded by the mgl operon. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type 1 periplasmic binding protein-like fold. Hence, they are structurally homologous to the periplasmic sugar binding of ABC-type transport systems. 269 matched cddid_all.tbl CDD cd01545 cd01545 380487 PBP1_SalR ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 270 matched cddid_all.tbl CDD cd01553 cd01553 238794 EPT_RTPC-like This domain family includes the Enolpyruvate transferase (EPT) family and the RNA 3' phosphate cyclase family (RTPC). These 2 families differ in that EPT is formed by 3 repeats of an alpha-beta structural domain while RTPC has 3 similar repeats with a 4th slightly different domain inserted between the 2nd and 3rd repeat. They evidently share the same active site location, although the catalytic residues differ. 211 matched cddid_all.tbl CDD cd01554 cd01554 238795 EPT-like Enol pyruvate transferases family includes EPSP synthases and UDP-N-acetylglucosamine enolpyruvyl transferase. Both enzymes catalyze the reaction of enolpyruvyl transfer. 408 matched cddid_all.tbl CDD cd01555 cd01555 238796 UdpNAET UDP-N-acetylglucosamine enolpyruvyl transferase catalyzes enolpyruvyl transfer as part of the first step in the biosynthesis of peptidoglycan, a component of the bacterial cell wall. The reaction is phosphoenolpyruvate + UDP-N-acetyl-D-glucosamine = phosphate + UDP-N-acetyl-3-(1-carboxyvinyl)-D-glucosamine. This enzyme is of interest as a potential target for anti-bacterial agents. The only other known enolpyruvyl transferase is the related 5-enolpyruvylshikimate-3-phosphate synthase. 400 matched cddid_all.tbl CDD cd01556 cd01556 238797 EPSP_synthase EPSP synthase domain. 3-phosphoshikimate 1-carboxyvinyltransferase (5-enolpyruvylshikimate-3-phosphate synthase) (EC 2.5.1.19) catalyses the reaction between shikimate-3-phosphate (S3P) and phosphoenolpyruvate (PEP) to form 5-enolpyruvylshkimate-3-phosphate (EPSP), an intermediate in the shikimate pathway leading to aromatic amino acid biosynthesis. The reaction is phosphoenolpyruvate + 3-phosphoshikimate = phosphate + 5-O-(1-carboxyvinyl)-3-phosphoshikimate. It is found in bacteria and plants but not animals. The enzyme is the target of the widely used herbicide glyphosate, which has been shown to occupy the active site. In bacteria and plants, it is a single domain protein, while in fungi, the domain is found as part of a multidomain protein with functions that are all part of the shikimate pathway. 409 matched cddid_all.tbl CDD cd01557 cd01557 238798 BCAT_beta_family BCAT_beta_family: Branched-chain aminotransferase catalyses the transamination of the branched-chain amino acids leusine, isoleucine and valine to their respective alpha-keto acids, alpha-ketoisocaproate, alpha-keto-beta-methylvalerate and alpha-ketoisovalerate. The enzyme requires pyridoxal 5'-phosphate (PLP) as a cofactor to catalyze the reaction. It has been found that mammals have two foms of the enzyme - mitochondrial and cytosolic forms while bacteria contain only one form of the enzyme. The mitochondrial form plays a significant role in skeletal muscle glutamine and alanine synthesis and in interorgan nitrogen metabolism.Members of this subgroup are widely distributed in all three forms of life. 279 matched cddid_all.tbl CDD cd01558 cd01558 238799 D-AAT_like D-Alanine aminotransferase (D-AAT_like): D-amino acid aminotransferase catalyzes transamination between D-amino acids and their respective alpha-keto acids. It plays a major role in the synthesis of bacterial cell wall components like D-alanine and D-glutamate in addition to other D-amino acids. The enzyme like other members of this superfamily requires PLP as a cofactor. Members of this subgroup are found in all three forms of life. 270 matched cddid_all.tbl CDD cd01559 cd01559 238800 ADCL_like ADCL_like: 4-Amino-4-deoxychorismate lyase: is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate. Based on the information available from the crystal structure, most members of this subgroup are likely to function as dimers. The enzyme from E.Coli, the structure of which is available, is a homodimer that is folded into a small and a larger domain. The coenzyme pyridoxal 5; -phosphate resides at the interface of the two domains that is linked by a flexible loop. Members of this subgroup are found in Eukaryotes and bacteria. 249 matched cddid_all.tbl CDD cd01560 cd01560 107203 Thr-synth_2 Threonine synthase catalyzes the final step of threonine biosynthesis. The conversion of O-phosphohomoserine into threonine and inorganic phosphate is pyridoxal 5'-phosphate dependent. The Thr-synth_1 CD includes members from higher plants, cyanobacteria, archaebacteria and eubacterial groups. This CD, Thr-synth_2, includes enzymes from fungi and eubacterial groups, as well as, metazoan threonine synthase-like proteins. 460 matched cddid_all.tbl CDD cd01561 cd01561 107204 CBS_like CBS_like: This subgroup includes Cystathionine beta-synthase (CBS) and Cysteine synthase. CBS is a unique heme-containing enzyme that catalyzes a pyridoxal 5'-phosphate (PLP)-dependent condensation of serine and homocysteine to give cystathionine. Deficiency of CBS leads to homocystinuria, an inherited disease of sulfur metabolism characterized by increased levels of the toxic metabolite homocysteine. Cysteine synthase on the other hand catalyzes the last step of cysteine biosynthesis. This subgroup also includes an O-Phosphoserine sulfhydrylase found in hyperthermophilic archaea which produces L-cysteine from sulfide and the more thermostable O-phospho-L-serine. 291 matched cddid_all.tbl CDD cd01562 cd01562 107205 Thr-dehyd Threonine dehydratase: The first step in amino acid degradation is the removal of nitrogen. Although the nitrogen atoms of most amino acids are transferred to alpha-ketoglutarate before removal, the alpha-amino group of threonine can be directly converted into NH4+. The direct deamination is catalyzed by threonine dehydratase, in which pyridoxal phosphate (PLP) is the prosthetic group. Threonine dehydratase is widely distributed in all three major phylogenetic divisions. 304 matched cddid_all.tbl CDD cd01563 cd01563 107206 Thr-synth_1 Threonine synthase is a pyridoxal phosphate (PLP) dependent enzyme that catalyses the last reaction in the synthesis of threonine from aspartate. It proceeds by converting O-phospho-L-homoserine (OPH) into threonine and inorganic phosphate. In plants, OPH is an intermediate between the methionine and threonine/isoleucine pathways. Thus threonine synthase competes for OPH with cystathionine-gamma-synthase, the first enzyme in the methionine pathway. These enzymes are in general dimers. Members of this CD, Thr-synth_1, are widely distributed in bacteria, archaea and higher plants. 324 matched cddid_all.tbl CDD cd01567 cd01567 238801 NAPRTase_PncB Nicotinate phosphoribosyltransferase (NAPRTase) family. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products. 343 matched cddid_all.tbl CDD cd01568 cd01568 238802 QPRTase_NadC Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide. QPRTase functions as a homodimer with two active sites, each formed by the C-terminal region of one subunit and the N-terminal region of the other. 269 matched cddid_all.tbl CDD cd01569 cd01569 238803 PBEF_like pre-B-cell colony-enhancing factor (PBEF)-like. The mammalian members of this group of nicotinate phosphoribosyltransferases (NAPRTases) were originally identified as genes whose expression is upregulated upon activation in lymphoid cells. In general, nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. 407 matched cddid_all.tbl CDD cd01570 cd01570 238804 NAPRTase_A Nicotinate phosphoribosyltransferase (NAPRTase), subgroup A. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products. This subgroup is present in bacteria and eukaryota (except funghi). 327 matched cddid_all.tbl CDD cd01571 cd01571 238805 NAPRTase_B Nicotinate phosphoribosyltransferase (NAPRTase), subgroup B. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products. 302 matched cddid_all.tbl CDD cd01572 cd01572 238806 QPRTase Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase), also called nicotinate-nucleotide pyrophosphorylase, is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide. QPRTase functions as a homodimer with two active sites, each formed by the C-terminal region of one subunit and the N-terminal region of the other. 268 matched cddid_all.tbl CDD cd01573 cd01573 238807 modD_like ModD; Quinolinate phosphoribosyl transferase (QAPRTase or QPRTase) present in some modABC operons in bacteria, which are involved in molybdate transport. In general, QPRTases are part of the de novo synthesis pathway of NAD in both prokaryotes and eukaryotes. They catalyse the reaction of quinolinic acid (QA) with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to produce nicotinic acid mononucleotide (NAMN), pyrophosphate and carbon dioxide. 272 matched cddid_all.tbl CDD cd01574 cd01574 380488 PBP1_LacI ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor LacI specific for lactose, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of LacI is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 265 matched cddid_all.tbl CDD cd01575 cd01575 380489 PBP1_GntR ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. This group represents the ligand-binding domain of DNA transcription repressor GntR specific for gluconate, a member of the LacI-GalR family of bacterial transcription regulators. The ligand-binding domain of GntR is structurally homologous to the periplasmic sugar-binding domain of ABC-type transporters and both domains contain the type 1 periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type 1 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding, which in turn changes the DNA binding affinity of the repressor. 269 matched cddid_all.tbl CDD cd01576 cd01576 238808 AcnB_Swivel Aconitase B swivel domain. Aconitate hydratase B is involved in energy metabolism as part of the TCA cycle. It catalyses the formation of cis-aconitate from citrate. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme mechanism. The domain structure of Aconitase B is different from other Aconitases in that he swivel domain that is found at N-terminus of B family is normally found at C-terminus for other Aconitases. In most members of the family, there is also a HEAT domain before domain 4, which is believed to play a role in protein-protein interaction. 131 matched cddid_all.tbl CDD cd01577 cd01577 238809 IPMI_Swivel Aconatase-like swivel domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate 3-isopropylmalate. IPMI is involved in fungal and bacterial leucine biosynthesis and is also found in eukaryotes. This is the aconitase-like swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism. 91 matched cddid_all.tbl CDD cd01578 cd01578 238810 AcnA_Mitochon_Swivel Mitochondrial aconitase A swivel domain. Aconitase (also known as aconitate hydratase and citrate hydro-lyase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme mechanism. In eukaryotes two isozymes of aconitase are known to exist: one found in the mitochondrial matrix and the other found in the cytoplasm. This is the mitochondrial form. The mitochondrial product is coded by a nuclear gene. Most members of this subfamily are mitochondrial but there are some bacterial members. 149 matched cddid_all.tbl CDD cd01579 cd01579 238811 AcnA_Bact_Swivel Bacterial Aconitase-like swivel domain. Aconitase (aconitate hydratase or citrate hydrolyase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. Cis-aconitate is formed as an intermediate product during the course of the reaction. This is the aconitase-like swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism. This distinct subfamily is found only in bacteria and archea. Its exact characteristics are not known. 121 matched cddid_all.tbl CDD cd01580 cd01580 238812 AcnA_IRP_Swivel Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group also includes sequences that have been shown to act as an iron-responsive element (IRE) binding protein in animals and may have the same role in other eukaryotes. This is the aconitase-like swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism. 171 matched cddid_all.tbl CDD cd01581 cd01581 153131 AcnB Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle. Aconitase B catalytic domain. Aconitate hydratase B catalyses the formation of cis-aconitate from citrate as part of the TCA cycle. Aconitase has an active (4FE-4S) and an inactive (3FE-4S) form. The active cluster is part of the catalytic site that interconverts citrate, cis-aconitase and isocitrate. The domain architecture of aconitase B is different from other aconitases in that the catalytic domain is normally found at C-terminus for other aconitases, but it is at N-terminus for B family. It also has a HEAT domain before domain 4 which plays a role in protein-protein interaction. This alignment is the core domain including domains 1,2 and 3. 436 matched cddid_all.tbl CDD cd01582 cd01582 153132 Homoaconitase Homoaconitase and other uncharacterized proteins of the Aconitase family. Homoaconitase catalytic domain. Homoaconitase and other uncharacterized proteins of the Aconitase family. Homoaconitase is part of an unusual lysine biosynthesis pathway found only in filamentous fungi, in which lysine is synthesized via the alpha-aminoadipate pathway. In this pathway, homoaconitase catalyzes the conversion of cis-homoaconitic acid into homoisocitric acid. The reaction mechanism is believed to be similar to that of other aconitases. 363 matched cddid_all.tbl CDD cd01583 cd01583 153133 IPMI 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate. Aconatase-like catalytic domain of 3-isopropylmalate dehydratase and related uncharacterized proteins. 3-isopropylmalate dehydratase catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate 3-isopropylmalate. IPMI is involved in fungal and bacterial leucine biosynthesis and is also found in eukaryotes. 382 matched cddid_all.tbl CDD cd01584 cd01584 153134 AcnA_Mitochondrial Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. Mitochondrial aconitase A catalytic domain. Aconitase (also known as aconitate hydratase and citrate hydro-lyase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. Cis-aconitate is formed as an intermediary product during the course of the reaction. In eukaryotes two isozymes of aconitase are known to exist: one found in the mitochondrial matrix and the other found in the cytoplasm. This is the mitochondrial form. The mitochondrial product is coded by a nuclear gene. Most members of this subfamily are mitochondrial but there are some bacterial members. 412 matched cddid_all.tbl CDD cd01585 cd01585 153135 AcnA_Bact Aconitase catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. Bacterial Aconitase-like catalytic domain. Aconitase (aconitate hydratase or citrate hydrolyase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. Cis-aconitate is formed as an intermediate product during the course of the reaction. This distinct subfamily is found only in bacteria and Archaea. Its exact characteristics are not known. 380 matched cddid_all.tbl CDD cd01586 cd01586 153136 AcnA_IRP Aconitase A catalytic domain. Aconitase A catalytic domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydrolyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group also includes sequences that have been shown to act as an iron-responsive element (IRE) binding protein in animals and may have the same role in other eukaryotes. 404 matched cddid_all.tbl CDD cd01594 cd01594 176466 Lyase_I_like Lyase class I_like superfamily: contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase, which catalyze similar beta-elimination reactions. Lyase class I_like superfamily of enzymes that catalyze beta-elimination reactions and are active as homotetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. This superfamily contains the lyase class I family, histidine ammonia-lyase and phenylalanine ammonia-lyase. The lyase class I family comprises proteins similar to class II fumarase, aspartase, adenylosuccinate lyase, argininosuccinate lyase, and 3-carboxy-cis, cis-muconate lactonizing enzyme which, for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. Histidine or phenylalanine ammonia-lyase catalyze a beta-elimination of ammonia from histidine and phenylalanine, respectively. 231 matched cddid_all.tbl CDD cd01595 cd01595 176467 Adenylsuccinate_lyase_like Adenylsuccinate lyase (ASL)_like. This group contains ASL, prokaryotic-type 3-carboxy-cis,cis-muconate cycloisomerase (pCMLE), and related proteins. These proteins are members of the Lyase class I family. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. ASL catalyzes two steps in the de novo purine biosynthesis: the conversion of 5-aminoimidazole-(N-succinylocarboxamide) ribotide (SAICAR) into 5-aminoimidazole-4-carboxamide ribotide (AICAR) and; the conversion of adenylsuccinate (SAMP) into adenosine monophosphate (AMP). pCMLE catalyzes the cyclization of 3-carboxy-cis,cis-muconate (3CM) to 4-carboxy-muconolactone, in the beta-ketoadipate pathway. ASL deficiency has been linked to several pathologies including psychomotor retardation with autistic features, epilepsy and muscle wasting. 381 matched cddid_all.tbl CDD cd01596 cd01596 176468 Aspartase_like aspartase (L-aspartate ammonia-lyase) and fumarase class II enzymes. This group contains aspartase (L-aspartate ammonia-lyase), fumarase class II enzymes, and related proteins. It is a member of the Lyase class I family. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. Aspartase catalyzes the reversible deamination of aspartic acid. Fumarase catalyzes the reversible hydration/dehydration of fumarate to L-malate during the Krebs cycle. 450 matched cddid_all.tbl CDD cd01597 cd01597 176469 pCLME prokaryotic 3-carboxy-cis,cis-muconate cycloisomerase (CMLE)_like. This subgroup contains pCLME and related proteins, and belongs to the Lyase class I family. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. CMLE catalyzes the cyclization of 3-carboxy-cis,cis-muconate (3CM) to 4-carboxy-muconolactone in the beta-ketoadipate pathway. This pathway is responsible for the catabolism of a variety of aromatic compounds into intermediates of the citric cycle in prokaryotic and eukaryotic micro-organisms. 437 matched cddid_all.tbl CDD cd01598 cd01598 176470 PurB PurB_like adenylosuccinases (adenylosuccinate lyase, ASL). This subgroup contains EcASL, the product of the purB gene in Escherichia coli, and related proteins. It is a member of the Lyase class I family of the Lyase_I superfamily. Members of the Lyase class I family function as homotetramers to catalyze similar beta-elimination reactions in which a Calpha-N or Calpha-O bond is cleaved with the subsequent release of fumarate as one of the products. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. ASL catalyzes two non-sequential steps in the de novo purine biosynthesis pathway: the conversion of 5-aminoimidazole-(N-succinylocarboxamide) ribotide (SAICAR) into 5-aminoimidazole-4-carboxamide ribotide (AICAR) and; the conversion of adenylosuccinate (SAMP) into adenosine monophosphate (AMP). 425 matched cddid_all.tbl CDD cd01609 cd01609 259845 RNAP_beta'_N "Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain. Beta' is the largest subunit of bacterial DNA-dependent RNA polymerase (RNAP). This family also includes the eukaryotic plastid-encoded RNAP beta' subunit. Bacterial RNAP is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. Structure studies suggest that RNA polymerase complexes from different organisms share a crab-claw-shaped structure with two ""pincers"" defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. Beta' contains part of the active site and binds two zinc ions that have a structural role in the formation of the active polymerase." 659 matched cddid_all.tbl CDD cd01610 cd01610 238813 PAP2_like PAP2_like proteins, a super-family of histidine phosphatases and vanadium haloperoxidases, includes type 2 phosphatidic acid phosphatase or lipid phosphate phosphatase (LPP), Glucose-6-phosphatase, Phosphatidylglycerophosphatase B and bacterial acid phosphatase, vanadium chloroperoxidases, vanadium bromoperoxidases, and several other mostly uncharacterized subfamilies. Several members of this superfamily have been predicted to be transmembrane proteins. 122 matched cddid_all.tbl CDD cd01611 cd01611 340453 Ubl_Autophagy_like ubiquitin-like (Ubl) domain found in autophagy-related ubiquitin-like protein. Autophagy is an essential intracellular process that targets large protein complexes, bacterial pathogens, and organelles for degradation. The autophagy-related ubiquitin-like proteins, such as Saccharomyces cerevisiae Atg8p, undergo a unique ubiquitin-like (Ubl) conjugation, a process essential for autophagosome formation. Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. The ubiquitination process comprises a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. ATG8 family proteins undergo multistep modifications by the E1-like (ubiquitin activating) enzyme ATG7, and the E2-like (ubiquitin conjugating) enzyme ATG3. The mammalian ATG8 family is classified into three subfamilies: i) MAP1LC3 (microtubule associated protein 1 light chain 3) which includes MAP1LC3A, MAP1LC3B, MAP1LC3B2, and MAP1LC3C, ii) GABARAP (GABA type A receptor associated protein) which includes GABARAP, GABARAPL1, and GABARAPL3, and iii) GABARAPL2 (GABA type A receptor associated protein like 2), also known as GATE-16 (golgi-associated adenosine triphosphatase enhancer of 16 kDa). 84 matched cddid_all.tbl CDD cd01612 cd01612 340454 Ubl_ATG12 ubiquitin-like (Ubl) domain found in autophagy-related protein 12 (ATG12). Autophagy is an essential intracellular process that targets large protein complexes, bacterial pathogens, and organelles for degradation. The autophagy-related ubiquitin-like (Ubl) proteins such as ATG12 protein have a conserved Ubl fold structure and undergo a unique Ubl conjugation, a process essential for autophagosome formation. ATG12 is conjugated to ATG5 by multistep modifications of the E1-like (ubiquitin activating) enzyme ATG7, and the E2-like (ubiquitin conjugating) enzyme ATG10. The ATG12-ATG5 conjugate facilitates the lipidation of ATG8 and directs its correct subcellular localization. ATG12 is localized at the developing autophagosome. 86 matched cddid_all.tbl CDD cd01614 cd01614 133473 EutN_CcmL Ethanolamine utilisation protein and carboxysome structural protein domain family. Beside the Escherichia coli ethanolamine utilization protein EutN and the Synechocystis sp. carboxysome (beta-type) structural protein CcmL, this family also includes alpha-type carboxysome structural proteins CsoS4A and CsoS4B (previously known as OrfA and OrfB), propanediol utilizationprotein PduN, and some hypothetical homologous of various bacterial microcompartments. The carboxysome, a polyhedral organelle, participates in carbon fixation by sequestering enzymes. It is the prototypical bacterial microcompartment. Its enzymatic components, ribulose bisphosphate carboxylase/oxygenase(RuBisCO) and carbonic anhydrase (CA), are surrounded by a polyhedral protein shell. Similarly, the ethanolamine utilization (eut) microcompartment, and the 1,2-propanediol utilization (pdu) microcompartment encapsulate the enzymes necessary for the process of cobalamin-dependent ethanolamine degradation, and coenzyme B12-dependent degradation of 1,2-propanediol, respectively, within its polyhedral protein shells. It is interesting that both carboxysome structural proteins CcmL and CsoS4A assemble as pentamers in the crystal structures, which might constitute the twelve pentameric vertices of a regular icosahedral carboxysome. However, the reported EutN structure is hexameric rather than pentameric. The absence of pentamers in Eut microcompartments might lead to less-regular icosahedral shell shapes. Due to the lack of structure evidence, the functional roles of the CsoS4A adjacent paralog, CsoS4B, and propanediol utilization protein PduN are not yet clear. 83 matched cddid_all.tbl CDD cd01615 cd01615 119367 CIDE_N CIDE_N domain, found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins, as well as CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of ICAD/DFF45, and the CAD/DFF40 and CIDE nucleases during apoptosis. The CIDE-N domain is also found in the FSP27/CIDE-C protein. 78 matched cddid_all.tbl CDD cd01616 cd01616 340455 TGS TGS (ThrRS, GTPase and SpoT) domain structurally similar to a beta-grasp ubiquitin-like fold. This family includes eukaryotic and some bacterial threonyl-tRNA synthetases (ThrRSs), a distinct Obg family GTPases, and guanosine polyphosphate hydrolase (SpoT) and synthetase (RelA), which are involved in stringent response in bacteria, as well as uridine kinase (UDK) from Thermotogales. All family members contain a TGS domain named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs. It is a small domain with a beta-grasp ubiquitin-like fold, a common structure involved in protein-protein interactions. The functions of the TGS domain remains unclear, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, with a regulatory role. 61 matched cddid_all.tbl CDD cd01617 cd01617 340456 DCX Dublecortin-like domain structurally similar to a beta-grasp ubiquitin-like fold. Dublecortin (DCX) is a microtubule-associated protein (MAP) with a stable ubiquitin-like tertiary fold. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Microtubules are key components of the cytoskeleton that are involved in cell movement, shape determination, division and transport. The DCX gene family consists of eleven paralogs in human and mouse, and its DCX protein domains can occur in double tandem or as single DCX repeats. Proteins with DCX tandem domains in general have roles in microtubule (MT) regulation and signal transduction such as X-linked doublecortin (DCX), retinitis pigmentosa-1 (RP1) and doublecortin-like kinase (DCLK). Single DCX repeat proteins are normally localized to actin-rich subcellular structures, or the nucleus such as DCDC2. DCX is not only a unique MAP in terms of structure, it also interacts with multiple additional proteins. Mutations in human DCX genes are associated with abnormal neuronal migration, epilepsy, and mental retardation. 73 matched cddid_all.tbl CDD cd01619 cd01619 240620 LDH_like D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains. D-Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate, and is a member of the 2-hydroxyacid dehydrogenase family. LDH is homologous to D-2-Hydroxyisocaproic acid dehydrogenase (D-HicDH) and shares the 2 domain structure of formate dehydrogenase. D-HicDH is a NAD-dependent member of the hydroxycarboxylate dehydrogenase family, and shares the Rossmann fold typical of many NAD binding proteins. D-HicDH from Lactobacillus casei forms a monomer and catalyzes the reaction R-CO-COO(-) + NADH + H+ to R-COH-COO(-) + NAD+. Similar to the structurally distinct L-HicDH, D-HicDH exhibits low side-chain R specificity, accepting a wide range of 2-oxocarboxylic acid side chains. (R)-2-hydroxyglutarate dehydrogenase (HGDH) catalyzes the NAD-dependent reduction of 2-oxoglutarate to (R)-2-hydroxyglutarate. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. 323 matched cddid_all.tbl CDD cd01620 cd01620 240621 Ala_dh_like Alanine dehydrogenase and related dehydrogenases. Alanine dehydrogenase/Transhydrogenase, such as the hexameric L-alanine dehydrogenase of Phormidium lapideum, contain 2 Rossmann fold-like domains linked by an alpha helical region. Related proteins include Saccharopine Dehydrogenase (SDH), bifunctional lysine ketoglutarate reductase /saccharopine dehydrogenase enzyme, N(5)-(carboxyethyl)ornithine synthase, and Rubrum transdehydrogenase. Alanine dehydrogenase (L-AlaDH) catalyzes the NAD-dependent conversion of pyrucate to L-alanine via reductive amination. Transhydrogenases found in bacterial and inner mitochondrial membranes link NAD(P)(H)-dependent redox reactions to proton translocation. The energy of the proton electrochemical gradient (delta-p), generated by the respiratory electron transport chain, is consumed by transhydrogenase in NAD(P)+ reduction. Transhydrogenase is likely involved in the regulation of the citric acid cycle. Rubrum transhydrogenase has 3 components, dI, dII, and dIII. dII spans the membrane while dI and dIII protrude on the cytoplasmic/matirx side. DI contains 2 domains with Rossmann folds, linked by a long alpha helix, and contains a NAD binding site. Two dI polypeptides (represented in this sub-family) spontaneously form a heterotrimer with one dIII in the absence of dII. In the heterotrimer, both dI chains may bind NAD, but only one is well-ordered. dIII also binds a well-ordered NADP, but in a different orientation than classical Rossmann domains. 317 matched cddid_all.tbl CDD cd01624 cd01624 319765 HAD_VSP_like vegetative storage proteins and related proteins, similar to soybean VSPalpha and VSPbeta proteins; belongs to the haloacid dehalogenase-like superfamily. Soybean [Glycine max (L.) Merr.] vegetative storage protein VSPalpha and VSPbeta levels were identified as storage proteins due to their abundance and pattern of expression in plant tissues, they accumulate to almost one-half the amount of soluble leaf protein when soybean plants are continually depodded. They possess acid phosphatase activity which appears to be low compared to several other plant acid phosphatases; it increases in the leaves of depodded soybean plants, but to no more than 0.1% of the total acid phosphatase activity in these leaves. This acid phosphatase activity has maximal activity at pH 5.0 - 5.5, and can liberate Pi from different substrates such as napthyl acid phosphate, carboxyphenyl phosphate, sugar-phosphates, glyceraldehyde 3-phosphate, dihydroxyacetone phosphate, phosphoenolpyruvate, ATP, ADP, PPi, and short chain polyphosphates; they cleave phosphoenolpyruvate, ATP, ADP, PPI, and polyphosphates most efficiently. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Soybean VSPalpha and VSPbeta lack this active site aspartate, other members of this family have this aspartate and may be more active. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 160 matched cddid_all.tbl CDD cd01625 cd01625 319766 HAD_PNP polynucleotide 3'-phosphatase domain similar to the phosphatase domain of the bifunctional enzyme polynucleotide 5'-kinase/3'-phosphatase. Polynucleotide 3'-phosphatase (PNP) domain. This domain dephosphorylates single-stranded as well as double-stranded 3'-phospho termini. It is found in bifunctional enzyme polynucleotide kinase/phosphatase (PNKP) which contain both kinase and phosphatase domains. PNKP plays a key role in both base excision repair and non-homologous end-joining DNA repair pathway. DNA strand breaks can result from DNA damage by ionizing radiation and chemical agents, such as alkylating agents or anticancer agents. Such DNA damage often results in DNA strands with 5'-hydroxyl and 3'-phosphate termini. However, the repair of DNA damage by DNA polymerases and ligases requires 5'-phosphate and 3'-hydroxyl termini. PNKP acts as a 5'-kinase/3'-phosphatase to create 5'-phosphate/3'-hydroxyl termini, which are a necessary prerequisite for ligation during repair. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 154 matched cddid_all.tbl CDD cd01627 cd01627 319767 HAD_TPP trehalose-phosphate phosphatase similar to Escherichia coli trehalose-6-phosphate phosphatase OtsB and Saccharomyces cerevisiae trehalose-phosphatase TPS2. Trehalose biosynthesis in bacteria is known through three pathways - OtsAB, TreYZ and TreS. The OtsAB pathway, also known as the trehalose 6-phosphate synthase (TSP)/ Trehalose-6-phosphate phosphatase (TPP) pathway, is the most common route known to be involved in the stress response of Escherichia coli. It involves converting glucose-6-phosphate and UDP-glucose to form trehalose-6-phosphate (T6P), catalyzed by TPS, the product of the otsA gene, this step is followed by the dephosphorylation of T6P to yield trehalose and inorganic phosphate, catalyzed by a specific TPP, the product of otsB gene. This OtsAB (or TSP/TPP) pathway, is also the most common route known to be involved in the stress response of yeast In Saccharomyces cerevisiae, the corresponding enzymes, TPS1p and TPS2p, form a multimeric synthase complex together with additional regulatory subunits encoded by Tsl1 and Tps3. Trehalose is a common disaccharide accumulated by organisms as a reservation of carbohydrate and in response to unfavorable growth conditions. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 228 matched cddid_all.tbl CDD cd01629 cd01629 319768 HAD_EP Enolase-phosphatase similar to human enolase-phosphatase E1 and and Xanthomonas oryzae pv. Oryzae enolase-phosphatase Xep. Enolase-phosphatase E1 (also called MASA) is a bifunctional enolase- phosphatase which promotes the conversion of 2,3-diketo-5-methylthio-1-phosphopentane to 1,2-dihydroxy-3-keto-5-methylthiopentene anion (an aci-reductone) in the methionine salvage pathway. The catalytic reaction is carried out continuously by enolization and dephosphorylation, and the enolase activity cannot be classified as typical enzymatic enolization. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 204 matched cddid_all.tbl CDD cd01630 cd01630 319769 HAD_KDO-like haloacid dehalogenase-like (HAD) hydrolase, similar to Escherichia coli 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) phosphatase KdsC, and rainbow trout N-acylneuraminate cytidylyltransferase. KDO 8-P phosphatase catalyzes the hydrolysis of KDO 8-P to KDO (3-deoxy-D-manno-octulosonate) and inorganic phosphate and is the last enzyme in the KDO biosynthetic pathway. KDO is an 8-carbon sugar that links the lipid A and polysaccharide moieties of the lipopolysaccharide region in Gram-negative bacteria. An interruption in KDO biosynthesis leads to the accumulation of lipid A precursors and subsequent arrest in cell growth. The KDO biosynthesis pathway involves five sequential enzymatic reactions. This family also includes rainbow trout CMP-sialic acid synthetase which effectively converts both deaminoneuraminic acid (KDN, 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid) and N-acetylneuraminic acid (Neu5Ac) to CMP-KDN and CMP-Neu5Ac, respectively. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 146 matched cddid_all.tbl CDD cd01635 cd01635 340816 Glycosyltransferase_GTB-type glycosyltransferase family 1 and related proteins with GTB topology. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. The structures of the formed glycoconjugates are extremely diverse, reflecting a wide range of biological functions. The members of this family share a common GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. 235 matched cddid_all.tbl CDD cd01636 cd01636 238814 FIG FIG, FBPase/IMPase/glpX-like domain. A superfamily of metal-dependent phosphatases with various substrates. Fructose-1,6-bisphospatase (both the major and the glpX-encoded variant) hydrolyze fructose-1,6,-bisphosphate to fructose-6-phosphate in gluconeogenesis. Inositol-monophosphatases and inositol polyphosphatases play vital roles in eukaryotic signalling, as they participate in metabolizing the messenger molecule Inositol-1,4,5-triphosphate. Many of these enzymes are inhibited by Li+. 184 matched cddid_all.tbl CDD cd01637 cd01637 238815 IMPase_like Inositol-monophosphatase-like domains. This family of phosphatases is dependent on bivalent metal ions such as Mg++, and many members are inhibited by Li+ (which is thought to displace a bivalent ion in the active site). Substrates include fructose-1,6-bisphosphate, inositol poly- and monophosphates, PAP and PAPS, sedoheptulose-1,7-bisphosphate and probably others. 238 matched cddid_all.tbl CDD cd01638 cd01638 238816 CysQ CysQ, a 3'-Phosphoadenosine-5'-phosphosulfate (PAPS) 3'-phosphatase, is a bacterial member of the inositol monophosphatase family. It has been proposed that CysQ helps control intracellular levels of PAPS, which is an intermediate in cysteine biosynthesis (a principal route of sulfur assimilation). 242 matched cddid_all.tbl CDD cd01639 cd01639 238817 IMPase IMPase, inositol monophosphatase and related domains. A family of Mg++ dependent phosphatases, inhibited by lithium, many of which may act on inositol monophosphate substrate. They dephosphorylate inositol phosphate to generate inositol, which may be recycled into inositol lipids; in eukaryotes IMPase plays a vital role in intracellular signaling. IMPase is one of the proposed targets of Li+ therapy in manic-depressive illness. This family contains some bacterial members of the inositol monophosphatase family classified as SuhB-like. E. coli SuhB has been suggested to participate in posstranscriptional control of gene expression, and its inositol monophosphatase activity doesn't appear to be sufficient for its cellular function. It has been proposed, that SuhB plays a role in the biosynthesis of phosphatidylinositol in mycobacteria. 244 matched cddid_all.tbl CDD cd01640 cd01640 238818 IPPase IPPase; Inositol polyphosphate-1-phosphatase, a member of the Mg++ dependent family of inositol monophosphatase-like domains, hydrolyzes the 1' position phosphate from inositol 1,3,4-trisphosphate and inositol 1,4-bisphosphate. Members in this group may also exhibit 3'-phosphoadenosine 5'-phosphate phosphatase activity, and they all appear to be inhibited by lithium. IPPase is one of the proposed targets of Li+ therapy in manic-depressive illness. 293 matched cddid_all.tbl CDD cd01641 cd01641 238819 Bacterial_IMPase_like_1 Predominantly bacterial family of Mg++ dependend phosphatases, related to inositol monophosphatases. These enzymes may dephosphorylate fructose-1,6-bisphosphate, inositol monophospate, 3'-phosphoadenosine-5'-phosphate, or similar substrates. 248 matched cddid_all.tbl CDD cd01642 cd01642 238820 Arch_FBPase_2 Putative fructose-1,6-bisphosphatase or related enzymes of inositol monophosphatase family. These are Mg++ dependent phosphatases. Members in this family may have fructose-1,6-bisphosphatase and/or inositol-monophosphatase activity. Fructose-1,6-bisphosphatase catalyzes the hydrolysis of fructose-1,6-biphosphate into fructose-6-phosphate and is critical in gluconeogenesis pathway. 244 matched cddid_all.tbl CDD cd01643 cd01643 238821 Bacterial_IMPase_like_2 Bacterial family of Mg++ dependent phosphatases, related to inositol monophosphatases. These enzymes may dephosphorylate inositol monophosphate or similar substrates. 242 matched cddid_all.tbl CDD cd01644 cd01644 238822 RT_pepA17 RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements. 213 matched cddid_all.tbl CDD cd01645 cd01645 238823 RT_Rtv "RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or ""jumps"", are required to generate the LTRs." 213 matched cddid_all.tbl CDD cd01646 cd01646 238824 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome. 158 matched cddid_all.tbl CDD cd01647 cd01647 238825 RT_LTR RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses. 177 matched cddid_all.tbl CDD cd01648 cd01648 238826 TERT TERT: Telomerase reverse transcriptase (TERT). Telomerase is a ribonucleoprotein (RNP) that synthesizes telomeric DNA repeats. The telomerase RNA subunit provides the template for synthesis of these repeats. The catalytic subunit of RNP is known as telomerase reverse transcriptase (TERT). The reverse transcriptase (RT) domain is located in the C-terminal region of the TERT polypeptide. Single amino acid substitutions in this region lead to telomere shortening and senescence. Telomerase is an enzyme that, in certain cells, maintains the physical ends of chromosomes (telomeres) during replication. In somatic cells, replication of the lagging strand requires the continual presence of an RNA primer approximately 200 nucleotides upstream, which is complementary to the template strand. Since there is a region of DNA less than 200 base pairs from the end of the chromosome where this is not possible, the chromosome is continually shortened. However, a surplus of repetitive DNA at the chromosome ends protects against the erosion of gene-encoding DNA. Telomerase is not normally expressed in somatic cells. It has been suggested that exogenous TERT may extend the lifespan of, or even immortalize, the cell. However, recent studies have shown that telomerase activity can be induced by a number of oncogenes. Conversely, the oncogene c-myc can be activated in human TERT immortalized cells. Sequence comparisons place the telomerase proteins in the RT family but reveal hallmarks that distinguish them from retroviral and retrotransposon relatives. 119 matched cddid_all.tbl CDD cd01650 cd01650 238827 RT_nLTR_like RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities. 220 matched cddid_all.tbl CDD cd01651 cd01651 238828 RT_G2_intron RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs). 226 matched cddid_all.tbl CDD cd01653 cd01653 153210 GATase1 Type 1 glutamine amidotransferase (GATase1)-like domain. Type 1 glutamine amidotransferase (GATase1)-like domain. This group includes proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA. and, the A4 beta-galactosidase middle domain. The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site. Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase, cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. 115 matched cddid_all.tbl CDD cd01657 cd01657 100099 Ribosomal_L7_archeal_euk Ribosomal protein L7, which is found in archaea and eukaryotes but not in prokaryotes, binds domain II of the 23S rRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome. The eukaryotic L7 members have an N-terminal extension not found in the archeal L7 orthologs. L7 is closely related to the ribosomal L30 protein found in eukaryotes and prokaryotes. 159 matched cddid_all.tbl CDD cd01658 cd01658 100100 Ribosomal_L30 Ribosomal protein L30, which is found in eukaryotes and prokaryotes but not in archaea, is one of the smallest ribosomal proteins with a molecular mass of about 7kDa. L30 binds the 23SrRNA as well as the 5S rRNA and is one of five ribosomal proteins that mediate the interactions 5S rRNA makes with the ribosome. The eukaryotic L30 members have N- and/or C-terminal extensions not found in their prokaryotic orthologs. L30 is closely related to the ribosomal L7 protein found in eukaryotes and archaea. 54 matched cddid_all.tbl CDD cd01659 cd01659 238829 TRX_superfamily Thioredoxin (TRX) superfamily; a large, diverse group of proteins containing a TRX-fold. Many members contain a classic TRX domain with a redox active CXXC motif. They function as protein disulfide oxidoreductases (PDOs), altering the redox state of target proteins via the reversible oxidation of their active site dithiol. The PDO members of this superfamily include TRX, protein disulfide isomerase (PDI), tlpA-like, glutaredoxin, NrdH redoxin, and the bacterial Dsb (DsbA, DsbC, DsbG, DsbE, DsbDgamma) protein families. Members of the superfamily that do not function as PDOs but contain a TRX-fold domain include phosducins, peroxiredoxins and glutathione (GSH) peroxidases, SCO proteins, GSH transferases (GST, N-terminal domain), arsenic reductases, TRX-like ferredoxins and calsequestrin, among others. 69 matched cddid_all.tbl CDD cd01660 cd01660 238830 ba3-like_Oxidase_I ba3-like heme-copper oxidase subunit I. The ba3 family of heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and some archaea which catalyze the reduction of O2 and simultaneously pump protons across the membrane. It has been proposed that Archaea acquired heme-copper oxidases through gene transfer from Gram-positive bacteria. The ba3 family contains oxidases that lack the conserved residues that form the D- and K-pathways in CcO and ubiquinol oxidase. Instead they contain a potential alternative K-pathway. Additional proton channels have been proposed for this family of oxidases but none have been identified definitively. For general information on the heme-copper oxidase superfamily, please see cd00919. 473 matched cddid_all.tbl CDD cd01661 cd01661 238831 cbb3_Oxidase_I Cytochrome cbb3 oxidase subunit I. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. Found mainly in proteobacteria, cbb3 is believed to be a modern enzyme that has evolved independently to perform a specialized function in microaerobic energy metabolism. Subunit I contains a heme-copper binuclear center (the active site where O2 is reduced to water) formed by a high-spin heme and a copper ion. It also contains a low-spin heme, believed to participate in the transfer of electrons to the binuclear center. The cbb3 operon contains four genes (ccoNOQP or fixNOQP), with ccoN coding for subunit I. Instead of a CuA-containing subunit II analogous to other cytochrome oxidases, cbb3 utilizes subunits ccoO and ccoP, which contain one and two hemes, respectively, to transfer electrons to the binuclear center. The fourth subunit (ccoQ) has been shown to protect the core complex from proteolytic degradation by serine proteases. For every reduction of an O2 molecule, eight protons are taken from the inside aqueous compartment and four electrons are taken from cytochrome c on the opposite side of the membrane. The four electrons and four of the protons are used in the reduction of O2; the four remaining protons are pumped across the membrane. This charge separation of four charges contributes to the electrochemical gradient used for ATP synthesis. The polar residues that form the D- and K-pathways in subunit I of other cytochrome c and ubiquinol oxidases are absent in cbb3. The proton pathways remain undefined. A pathway for the transfer of pumped protons beyond the binuclear center also remains undefined. It is believed that electrons are passed from cytochrome c (the electron donor) to the low-spin heme via ccoP and ccoO, respectively, and directly from the low-spin heme to the binuclear center. 493 matched cddid_all.tbl CDD cd01662 cd01662 238832 Ubiquinol_Oxidase_I Ubiquinol oxidase subunit I. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits in ubiquinol oxidase varies from two to five. Subunit I contains a heme-copper binuclear center (the active site where O2 is reduced to water) formed by a high-spin heme and a copper ion. It also contains a low-spin heme, believed to participate in the transfer of electrons from ubiquinol to the binuclear center. For every reduction of an O2 molecule, eight protons are taken from the inside aqueous compartment and four electrons are taken from ubiquinol on the opposite side of the membrane. The four electrons and four of the protons are used in the reduction of O2; the four remaining protons are pumped across the membrane. This charge separation of four charges contributes to the electrochemical gradient used for ATP synthesis. Two proton channels, the D-pathway and K-pathway, leading to the binuclear center have been identified in subunit I. It is generally believed that the channels contain water molecules that act as 'proton wires' to transfer the protons. A well-defined pathway for the transfer of pumped protons beyond the binuclear center has not been identified. Electrons are believed to be transferred directly from ubiquinol (the electron donor) to the low-spin heme, and directly from the low-spin heme to the binuclear center. 501 matched cddid_all.tbl CDD cd01663 cd01663 238833 Cyt_c_Oxidase_I Cytochrome C oxidase subunit I. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Only subunits I and II are essential for function, but subunit III, which is also conserved, may play a role in assembly or oxygen delivery to the active site. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Subunit I contains a heme-copper binuclear center (the active site where O2 is reduced to water) formed by a high-spin heme (heme a3) and a copper ion (CuB). It also contains a low-spin heme (heme a), believed to participate in the transfer of electrons to the binuclear center. For every reduction of an O2 molecule, eight protons are taken from the inside aqueous compartment and four electrons are taken from cytochrome c on the opposite side of the membrane. The four electrons and four of the protons are used in the reduction of O2; the four remaining protons are pumped across the membrane. This charge separation of four charges contributes to the electrochemical gradient used for ATP synthesis. Two proton channels, the D-pathway and K-pathway, leading to the binuclear center have been identified in subunit I. A well-defined pathway for the transfer of pumped protons beyond the binuclear center has not been identified. Electrons are transferred from cytochrome c (the electron donor) to heme a via the CuA binuclear site in subunit II, and directly from heme a to the binuclear center. 488 matched cddid_all.tbl CDD cd01665 cd01665 238834 Cyt_c_Oxidase_III "Cytochrome c oxidase subunit III. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. CcO catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Only subunits I and II are essential for function, but subunit III, which is also conserved, is believed to play a role in assembly of the multimer complex. Rhodobacter CcO subunit III stabilizes the integrity of the binuclear center in subunit I. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Subunit III contains bound phospholipids in several crystal structures and is proposed to contain a ""lipid pool."" These phospholipids are believed to intrinsic constituents similar to cofactors of the enzyme." 243 matched cddid_all.tbl CDD cd01666 cd01666 340457 TGS_DRG TGS (ThrRS, GTPase and SpoT) domain found in developmentally regulated GTP binding protein (DRG) family. DRG-1 and DRG-2 comprise a highly conserved DRG subfamily of GTP-binding proteins found in archaea, plants, fungi and animals. The exact function of DRG proteins is unknown, although phylogenetic and biochemical fraction studies have linked them to translation, differentiation and growth. Their abnormal expressions may trigger cell transformation or cell cycle arrest. DRG-1 and DRG-2 bind to DFRP1 (DRG family regulatory protein 1) and DFRP2, respectively. Both DRG-1 and DRG-2 contain a domain of characteristic Obg-type G-motifs that may be the core of GTPase activity, as well as the C-terminal TGS (ThrRS, GTPase and SpoT) domain, which has a predominantly beta-grasp ubiquitin-like fold and may be related to RNA binding. DRG subfamily belongs to the Obg family of GTPases. 77 matched cddid_all.tbl CDD cd01667 cd01667 340458 TGS_ThrRS TGS (ThrRS, GTPase and SpoT) domain found in threonyl-tRNA synthetase (ThrRS) and similar proteins. ThrRS, also termed cytoplasmic threonine--tRNA ligase, is a class II aminoacyl-tRNA synthetase (aaRS) that plays an essential role in protein synthesis by catalyzing the aminoacylation of tRNA(Thr), generating aminoacyl-tRNA, and editing misacylation. In addition to its catalytic and anticodon-binding domains, ThrRS has an N-terminal TGS domain, named after the ThrRS, GTPase, and SpoT/RelA proteins where it occurs. TGS is a small domain with a beta-grasp ubiquitin-like fold, a common structure involved in protein-protein interactions. 65 matched cddid_all.tbl CDD cd01668 cd01668 340459 TGS_RSH TGS (ThrRS, GTPase and SpoT) domain found in the RelA/SpoT homolog (RSH) family. The RelA/SpoT homolog (RSH) family consists of long RSH proteins and short RSH proteins. Long RSH proteins have been characterized as containing an N-terminal region and a C-terminal region. The N-terminal region contains a pseudo-hydrolase (inactive-hydrolase) domain and a (p)ppGpp synthetase domain. The C-terminal region contains a ubiquitin-like TGS (ThrRS, GTPase and SpoT) domain, a conserved cysteine domain (CC), helical and ACT (aspartate kinase, chorismate mutase, TyrA domain) domains connected by a linker region. Short RSH proteins have a truncated C-terminal region without ACT domain. The RSH family includes two classes of enzyme: i) monofunctional (p)ppGpp synthetase I, RelA, and ii) bifunctional (p)ppGpp synthetase II/hydrolase, SpoT (also called Rel). Both classes are capable of synthesizing (p)ppGpp but only bifunctional enzymes are capable of (p)ppGpp hydrolysis. SpoT is a ribosome-associated protein that is activated during amino acid starvation and thought to mediate the stringent response. The function of the TGS domain of SpoT is in transcription of survival and virulence genes in respond to environmental stress. RelA is an ATP:GTP(GDP) pyrophosphate transferase that is recruited to stalled ribosomes and activated to synthesize (p)ppGpp, which acts as a pleiotropic secondary messenger. 59 matched cddid_all.tbl CDD cd01669 cd01669 340460 TGS_MJ1332_like TGS (ThrRS, GTPase and SpoT) domain found in Methanocaldococcus jannaschii uncharacterized GTP-binding protein MJ1332 and similar proteins. This family includes a group of uncharacterized GTP-binding proteins from archaea, which belong to the Obg family of GTPases. The family members contain a domain of characteristic Obg-type G-motifs that may be the core of GTPase activity, as well as a C-terminal TGS (ThrRS, GTPase and SpoT) domain that has a predominantly beta-grasp ubiquitin-like fold. 78 matched cddid_all.tbl CDD cd01670 cd01670 260017 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in animal cells. 79 matched cddid_all.tbl CDD cd01671 cd01671 260018 CARD Caspase activation and recruitment domain: a protein-protein interaction domain. Caspase activation and recruitment domains (CARDs) are death domains (DDs) found associated with caspases. Caspases are aspartate-specific cysteine proteases with functions in apoptosis, immune signaling, inflammation, and host-defense mechanisms. In addition to caspases, proteins containing CARDs include adaptor proteins such as RAIDD, CARD9, and RIG-I-like helicases, which can form multiprotein complexes and play important roles in mediating the signals to induce immune and inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 79 matched cddid_all.tbl CDD cd01672 cd01672 238835 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP). 200 matched cddid_all.tbl CDD cd01673 cd01673 238836 dNK Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key enzymes in the salvage of deoxyribonucleosides originating from extra- or intracellular breakdown of DNA. 193 matched cddid_all.tbl CDD cd01674 cd01674 238837 Homoaconitase_Swivel Homoaconitase swivel domain. This family includes homoaconitase and other uncharacterized proteins of the Aconitase family. Homoaconitase is part of an unusual lysine biosynthesis pathway found only in filamentous fungi, in which lysine is synthesized via the alpha-aminoadipate pathway. In this pathway, homoaconitase catalyzes the conversion of cis-homoaconitic acid into homoisocitric acid. The reaction mechanism is believed to be similar to that of other aconitases. This is the swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism. 129 matched cddid_all.tbl CDD cd01675 cd01675 153084 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit which contains the active and allosteric sites. 555 matched cddid_all.tbl CDD cd01676 cd01676 153085 RNR_II_monomer Class II ribonucleotide reductase, monomeric form. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). Class II RNRs are found in bacteria that can live under both aerobic and anaerobic conditions. Many, but not all members of this class, are found to be homodimers. This particular subfamily is found to be active as a monomer. Adenosylcobalamin interacts directly with an active site cysteine to form the reactive cysteine radical. 658 matched cddid_all.tbl CDD cd01677 cd01677 153086 PFL2_DhaB_BssA Pyruvate formate lyase 2 and related enzymes. This family includes pyruvate formate lyase 2 (PFL2), B12-independent glycerol dehydratase (DhaB) and the alpha subunit of benzylsuccinate synthase (BssA), all of which have a highly conserved ten-stranded alpha/beta barrel domain, which is similar to those of PFL1 (pyruvate formate lyase 1) and RNR (ribonucleotide reductase). Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, the conversion of pyruvate and CoenzymeA to formate and acetylCoA. DhaB catalyzes the first step in the conversion of glycerol to 1,3-propanediol while BssA catalyzes the first step in the anaerobic mineralization of both toluene and m-xylene. 781 matched cddid_all.tbl CDD cd01678 cd01678 153087 PFL1 Pyruvate formate lyase 1. Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, the conversion of pyruvate and CoenzymeA to formate and acetylCoA. The PFL mechanism involves an unusual radical cleavage of pyruvate in which two cysteines and one glycine form radicals that are required for catalysis. PFL has a ten-stranded alpha/beta barrel domain that is structurally similar to those of all three ribonucleotide reductase (RNR) classes as well as benzylsuccinate synthase and B12-independent glycerol dehydratase. 738 matched cddid_all.tbl CDD cd01679 cd01679 153088 RNR_I Class I ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and many viruses, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in anaerobic bacteria, bacteriophages, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). Class I RNR is oxygen-dependent and can be subdivided into classes Ia (eukaryotes, prokaryotes, viruses and phages) and Ib (which is found in prokaryotes only). It is a tetrameric enzyme of two alpha and two beta subunits; this model covers the major part of the alpha or large subunit, called R1 in class Ia and R1E in class Ib. 460 matched cddid_all.tbl CDD cd01680 cd01680 238838 EFG_like_IV Elongation Factor G-like domain IV. This family includes the translational elongation factor termed EF-2 (for Archaea and Eukarya) and EF-G (for Bacteria), ribosomal protection proteins that mediate tetracycline resistance and, an evolutionarily conserved U5 snRNP-specific protein (U5-116kD). In complex with GTP, EF-G/EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site of the small subunit of ribosome and the mRNA is shifted one codon relative to the ribosome. It has been shown that EF-G/EF-2_IV domain mimics the shape of anticodon arm of the tRNA in the structurally homologous ternary complex of Petra, EF-Tu (another transcriptional elongation factor) and GTP analog. The tip portion of this domain is found in a position that overlaps the anticodon arm of the A-site tRNA, implying that EF-G/EF-2 displaces the A-site tRNA to the P-site by physical interaction with the anticodon arm. 116 matched cddid_all.tbl CDD cd01681 cd01681 238839 aeEF2_snRNP_like_IV This family represents domain IV of archaeal and eukaryotic elongation factor 2 (aeEF-2) and of an evolutionarily conserved U5 snRNP-specific protein. U5 snRNP is a GTP-binding factor closely related to the ribosomal translocase EF-2. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site of the small subunit of ribosome and the mRNA is shifted one codon relative to the ribosome. It has been shown that EF-2_IV domain mimics the shape of anticodon arm of the tRNA in the structurally homologous ternary complex of Phe-tRNA, EF-1 (another transcriptional elongation factor) and GTP analog. The tip portion of this domain is found in a position that overlaps the anticodon arm of the A-site tRNA, implying that EF-2 displaces the A-site tRNA to the P-site by physical interaction with the anticodon arm. 177 matched cddid_all.tbl CDD cd01683 cd01683 238840 EF2_IV_snRNP EF-2_domain IV_snRNP domain is a part of 116kD U5-specific protein of the U5 small nucleoprotein (snRNP) particle, essential component of the spliceosome. The protein is structurally closely related to the eukaryotic translational elongation factor EF2. This domain has been also identified in 114kD U5-specific protein of Saccharomyces cerevisiae and may play an important role either in splicing process itself or the recycling of spliceosomal snRNP. 178 matched cddid_all.tbl CDD cd01684 cd01684 238841 Tet_like_IV EF-G_domain IV_RPP domain is a part of bacterial ribosomal protected proteins (RPP) family. RPPs such as tetracycline resistance proteins Tet(M) and Tet(O) mediate tetracycline resistance in both gram-positive and -negative species. Tetracyclines inhibit the accommodation of aminoacyl-tRNA into ribosomal A site and therefore prevent the addition of new amino acids to the growing polypeptide. RPPs Tet(M) confer tetracycline resistance by releasing tetracycline from the ribosome and thereby freeing the ribosome from inhibitory effects of the drug, such that aa-tRNA can bind to the A site and protein synthesis can continue. 115 matched cddid_all.tbl CDD cd01693 cd01693 238842 mtEFG2_like_IV mtEF-G2 domain IV. This subfamily is a part the of mitochondrial transcriptional elongation factor, mtEF-G2. Mitochondrial translation is crucial for maintaining mitochondrial function and mutations in this system lead to a breakdown in the respiratory chain-oxidative phosphorylation system and to impaired maintenance of mitochondrial DNA. In complex with GTP, EF-G promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site of the small subunit of ribosome and the mRNA is shifted one codon relative to the ribosome. 120 matched cddid_all.tbl CDD cd01699 cd01699 238843 RNA_dep_RNAP RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage. RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D structure of the catalytic center of a wide range of RdRps, including those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing a number of conserved amino acid residues. This subfamily represents the RNA-dependent RNA polymerases from all positive-strand RNA eukaryotic viruses with no DNA stage. 278 matched cddid_all.tbl CDD cd01700 cd01700 176454 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V. umuC subunit of Pol V. Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol V, RecA, single stranded DNA-binding protein, beta sliding clamp, and gamma clamp loading complex are responsible for inducing the SOS response in bacteria to repair UV-induced DNA damage. 344 matched cddid_all.tbl CDD cd01701 cd01701 176455 PolY_Rev1 DNA polymerase Rev1. Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. Enzymatically, it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment. 404 matched cddid_all.tbl CDD cd01702 cd01702 176456 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA. 359 matched cddid_all.tbl CDD cd01703 cd01703 176457 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides. 379 matched cddid_all.tbl CDD cd01709 cd01709 238844 RT_like_1 RT_like_1: A subfamily of reverse transcriptases (RTs). An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. 346 matched cddid_all.tbl CDD cd01712 cd01712 467485 PPase_ThiI pyrophosphatase domain of thiamine biosynthesis protein ThiI. ThiI is required for thiazole synthesis in the thiamine biosynthesis pathway. ThiI is also responsible for the 4-thiouridine (S4U) modification at position 8 in some prokaryotic tRNAs. ThiI contains a PP-loop pyrophosphatase domain which binds ATP and activates tRNA by adenylation. The PP-loop pyrophosphatase catalytic domain of ThiI proteins is always accompanied by a THUMP domain towards the N terminus. THUMP domains are predicted to bind RNA and are widespread in bacteria, archaea, and eukaryotes. The acronym was derived from the names of RNA-modifying enzymes in which this domain is found, namely, thiouridine synthases (ThiI), methylases, and archaeal pseudouridine synthases. ThiI proteins from gamma-proteobacteria and from archaea of the genus Thermoplasma also contain a C-terminal extension of approximately 100 amino acid residues which accepts sulfur in the form of a persulfide on a cysteine residue. This persulfide is responsible for a nucleophilic attack of the adenylated tRNA substrate, completing the sulfur insertion forming a disulfide-bridge between the rhodanese-like domain and a second cysteine residue located in the PP-loop domain. The reaction releases AMP and modified tRNA, and leaves the enzyme in an oxidized state. The disulfide is then reductively cleaved to complete the enzymatic cycle. The pyrophosphatase domain of ThiI belongs to the adenine nucleotide hydrolase (AANH) superfamily and it binds to adenosine nucleotide. 185 matched cddid_all.tbl CDD cd01713 cd01713 467486 CTU1-like cytoplasmic tRNA 2-thiolation protein 1 and similar proteins. This subfamily includes human cytoplasmic tRNA 2-thiolation protein 1, also called cytosolic thiouridylase subunit 1 (CTU1), ATP-binding domain-containing protein 3 (ATPBD3), cancer-associated gene protein, or cytoplasmic tRNA adenylyltransferase 1. CTU1 plays a central role in 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of tRNA(Lys), tRNA(Glu) and tRNA(Gln). It directly binds tRNAs and probably acts by catalyzing adenylation of tRNAs, an intermediate required for 2-thiolation. The CTU1-like subfamily belongs to the nucleotide alpha hydrolase (AANH) superfamily that includes N-type ATP PPases and ATP sulfurylases. It forms an alpha/beta/alpha fold which binds to the adenosine group. 208 matched cddid_all.tbl CDD cd01714 cd01714 467487 ETF_beta electron transfer flavoprotein (ETF) beta. The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is a heterodimer, consisting of an alpha and a beta subunit, which binds one molecule of FAD per dimer. A similar system also exists in some bacteria. The homologous pair of proteins (FixA/FixB) are essential for nitrogen fixation. The beta subunit is distantly related to and forms a heterodimer with the alpha subunit. 210 matched cddid_all.tbl CDD cd01715 cd01715 467488 ETF_alpha electron transfer flavoprotein (ETF) alpha. The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is a heterodimer, consisting of an alpha and a beta subunit, which binds one molecule of FAD per dimer. A similar system also exists in some bacteria. The homologous pair of proteins (FixA/FixB) are essential for nitrogen fixation. The alpha subunit of ETF is structurally related to the bacterial nitrogen fixation protein fixB which could play a role in a redox process and feed electrons to ferredoxin. 171 matched cddid_all.tbl CDD cd01716 cd01716 212463 Hfq bacterial Hfq-like. Hfq, an abundant, ubiquitous RNA-binding protein, functions as a pleiotropic regulator of RNA metabolism in prokaryotes, required for transcription of some transcripts and degradation of others. Hfq binds small RNA molecules called riboregulators that modulate the stability or translation efficiency of RNA transcripts. Hfq binds preferentially to unstructured A/U-rich RNA sequences and is similar to the eukaryotic Sm proteins in both sequence and structure. Hfq forms a homo-hexameric ring similar to the heptameric ring of the Sm proteins. 60 matched cddid_all.tbl CDD cd01717 cd01717 212464 Sm_B Sm protein B. The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. 80 matched cddid_all.tbl CDD cd01718 cd01718 212465 Sm_E Sm protein E. The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. 79 matched cddid_all.tbl CDD cd01719 cd01719 212466 Sm_G Sm protein G. The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure. 70 matched cddid_all.tbl CDD cd01720 cd01720 212467 Sm_D2 Sm protein D2. The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits. 89 matched cddid_all.tbl CDD cd01721 cd01721 212468 Sm_D3 Sm protein D3. The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. 70 matched cddid_all.tbl CDD cd01722 cd01722 212469 Sm_F Sm protein F. The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers. 69 matched cddid_all.tbl CDD cd01723 cd01723 212470 LSm4 Like-Sm protein 4. The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. 76 matched cddid_all.tbl CDD cd01724 cd01724 212471 Sm_D1 Sm protein D1. The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. 92 matched cddid_all.tbl CDD cd01725 cd01725 212472 LSm2 Like-Sm protein 2. The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. 89 matched cddid_all.tbl CDD cd01726 cd01726 212473 LSm6 Like-Sm protein 6. The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. 68 matched cddid_all.tbl CDD cd01727 cd01727 212474 LSm8 Like-Sm protein 8. The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. 91 matched cddid_all.tbl CDD cd01728 cd01728 212475 LSm1 Like-Sm protein 1. The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. Accumulation of uridylated RNAs in an lsm1 mutant suggests an involvement of the LSm1-7 complex in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm1-7, together with Pat1, are also called the decapping activator. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. 74 matched cddid_all.tbl CDD cd01729 cd01729 212476 LSm7 Like-Sm protein 7. The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. 89 matched cddid_all.tbl CDD cd01730 cd01730 212477 LSm3 Like-Sm protein 3. The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. 82 matched cddid_all.tbl CDD cd01731 cd01731 212478 archaeal_Sm1 archaeal Sm protein 1. The archaeal Sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal LSm proteins are likely to represent the ancestral Sm domain. 69 matched cddid_all.tbl CDD cd01732 cd01732 212479 LSm5 Like-Sm protein 5. The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. 76 matched cddid_all.tbl CDD cd01733 cd01733 212480 LSm10 Like-Sm protein 10. The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-membered ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing. 78 matched cddid_all.tbl CDD cd01734 cd01734 212481 YlxS_C Bacillus subtilis YxlS-like, C-terminal domain. YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3. 72 matched cddid_all.tbl CDD cd01735 cd01735 212482 LSm12_N Like-Sm protein 12, N-terminal domain. LSm12 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm12 has a novel methyltransferase domain. 61 matched cddid_all.tbl CDD cd01736 cd01736 212483 LSm14_N Like-Sm protein 14, N-terminal domain. LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles. 74 matched cddid_all.tbl CDD cd01737 cd01737 212484 LSm16_N Like-Sm protein 16, N-terminal domain. LSm16 (also known as enhancer of decapping-3 or EDC3) has been shown to be associated with an mRNA-decapping complex Dcp1-Dcp2, required for removal of the 5-prime cap from mRNA prior to its degradation from the 5-prime end. EDC3 is believed to be a scaffold for decapping complex formation. It belongs to a family of Sm-like proteins that associate with RNA to form complexes involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type Rossmann fold domain of unknown function. 65 matched cddid_all.tbl CDD cd01739 cd01739 212485 LSm11_M Like-Sm protein 11, middle domain. The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm11 is an SmD2-like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-membered ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing. 63 matched cddid_all.tbl CDD cd01740 cd01740 153211 GATase1_FGAR_AT Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase. Type 1 glutamine amidotransferase (GATase1)-like domain found in Formylglycinamide ribonucleotide amidotransferase (FGAR-AT). FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP, Pi, and glutamate in the fourth step of the purine biosynthetic pathway. FGAR-AT is a glutamine amidotransferase. Glutamine amidotransferase activity catalyses the transfer of ammonia from the amide side chain of glutamine to an acceptor substrate. FGAR-AT belongs to the triad family of amidotransferases having a conserved Cys-His-Glu catalytic triad in the glutaminase active site 238 matched cddid_all.tbl CDD cd01741 cd01741 153212 GATase1_1 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain. This group contains a subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain. GATase activity catalyses the transfer of ammonia from the amide side chain of glutamine to an acceptor substrate. Glutamine amidotransferases (GATase) includes the triad family of amidotransferases which have a conserved Cys-His-Glu catalytic triad in the glutaminase active site. In this subgroup this triad is conserved. GATase activity can be found in a range of biosynthetic enzymes, including: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase , anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase, cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. Glutamine amidotransferase (GATase) domains can occur either as single polypeptides, as in glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. 188 matched cddid_all.tbl CDD cd01742 cd01742 153213 GATase1_GMP_Synthase Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase. Type 1 glutamine amidotransferase (GATase1) domain found in GMP synthetase. GMP synthetase is a glutamine amidotransferase from the de novo purine biosynthetic pathway. Glutamine amidotransferase (GATase) activity catalyse the transfer of ammonia from the amide side chain of glutamine to an acceptor substrate. GMP synthetase catalyses the amination of the nucleotide precursor xanthosine 5'-monophosphate to form GMP. GMP synthetase belongs to the triad family of amidotransferases having a conserved Cys-His-Glu catalytic triad in the glutaminase active site. 181 matched cddid_all.tbl CDD cd01743 cd01743 153214 GATase1_Anthranilate_Synthase Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase. Type 1 glutamine amidotransferase (GATase1) domain found in Anthranilate synthase (ASase). This group contains proteins similar to para-aminobenzoate (PABA) synthase and ASase. These enzymes catalyze similar reactions and produce similar products, PABA and ortho-aminobenzoate (anthranilate). Each enzyme is composed of non-identical subunits: a glutamine amidotransferase subunit (component II) and a subunit that produces an aminobenzoate products (component I). ASase catalyses the synthesis of anthranilate from chorismate and glutamine and is a tetrameric protein comprising two copies each of components I and II. Component II of ASase belongs to the family of triad GTases which hydrolyze glutamine and transfer nascent ammonia between the active sites. In some bacteria, such as Escherichia coli, component II can be much larger than in other organisms, due to the presence of phosphoribosyl-anthranilate transferase (PRTase) activity. PRTase catalyses the second step in tryptophan biosynthesis and results in the addition of 5-phosphoribosyl-1-pyrophosphate to anthranilate to create N-5'-phosphoribosyl-anthranilate. In E.coli, the first step in the conversion of chorismate to PABA involves two proteins: PabA and PabB which co-operate to transfer the amide nitrogen of glutamine to chorismate forming 4-amino-4 deoxychorismate (ADC). PabA acts as a glutamine amidotransferase, supplying an amino group to PabB, which carries out the amination reaction. A third protein PabC then mediates elimination of pyruvate and aromatization to give PABA. Several organisms have bipartite proteins containing fused domains homologous to PabA and PabB commonly called PABA synthases. These hybrid PABA synthases may produce ADC and not PABA. 184 matched cddid_all.tbl CDD cd01744 cd01744 153215 GATase1_CPSase Small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II. This group of sequences represents the small chain of the glutamine-dependent form of carbamoyl phosphate synthase, CPSase II. CPSase II catalyzes the production of carbomyl phosphate (CP) from bicarbonate, glutamine and two molecules of MgATP. The reaction is believed to proceed by a series of four biochemical reactions involving a minimum of three discrete highly reactive intermediates. The synthesis of CP is critical for the initiation of two separate biosynthetic pathways. In one CP is coupled to aspartate, its carbon and nitrogen nuclei ultimately incorporated into the aromatic moieties of pyrimidine nucleotides. In the second pathway CP is condensed with ornithine at the start of the urea cycle and is utilized for the detoxification of ammonia and biosynthesis of arginine. CPSases may be encoded by one or by several genes, depending on the species. The E.coli enzyme is a heterodimer consisting of two polypeptide chains referred to as the small and large subunit. Ammonia an intermediate during the biosynthesis of carbomyl phosphate produced by the hydrolysis of glutamine in the small subunit of the enzyme is delivered via a molecular tunnel between the remotely located carboxyphosphate active site in the large subunit. CPSase IIs belong to the triad family of amidotransferases having a conserved Cys-His-Glu catalytic triad in the glutaminase active site. This group also contains the sequence from the mammalian urea cycle form which has lost the active site Cys, resulting in an ammonia-dependent form, CPSase I. 178 matched cddid_all.tbl CDD cd01745 cd01745 153216 GATase1_2 Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain. This group contains a subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain. GATase activity catalyses the transfer of ammonia from the amide side chain of glutamine to an acceptor substrate. Glutamine amidotransferases (GATase) includes the triad family of amidotransferases which have a conserved Cys-His-Glu catalytic triad in the glutaminase active site. In this subgroup this triad is conserved. GATase activity can be found in a range of biosynthetic enzymes, including: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase , anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase, cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. Glutamine amidotransferase (GATase) domains can occur either as single polypeptides, as in glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. 189 matched cddid_all.tbl CDD cd01746 cd01746 153217 GATase1_CTP_Synthase Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase. Type 1 glutamine amidotransferase (GATase1) domain found in Cytidine Triphosphate Synthetase (CTP). CTP is involved in pyrimidine ribonucleotide/ribonucleoside metabolism. CTPs produce CTP from UTP and glutamine and regulate intracellular CTP levels through interactions with four ribonucleotide triphosphates. The enzyme exists as a dimer of identical chains that aggregates as a tetramer. CTP is derived form UTP in three separate steps involving two active sites. In one active site, the UTP O4 oxygen is activated by Mg-ATP-dependent phosphorylation, followed by displacement of the resulting 4-phosphate moiety by ammonia. At a separate site, ammonia is generated via rate limiting glutamine hydrolysis (glutaminase) activity. A gated channel that spans between the glutamine hydrolysis and amidoligase active sites provides a path for ammonia diffusion. CTPs belong to the triad family of amidotransferases having a conserved Cys-His-Glu catalytic triad in the glutaminase active site. 235 matched cddid_all.tbl CDD cd01747 cd01747 153218 GATase1_Glutamyl_Hydrolase Type 1 glutamine amidotransferase (GATase1) domain found in gamma-Glutamyl Hydrolase. Type 1 glutamine amidotransferase (GATase1) domain found in gamma-Glutamyl Hydrolase. gamma-Glutamyl Hydrolase catalyzes the cleavage of the gamma-glutamyl chain of folylpoly-gamma-glutamyl substrates and is a central enzyme in folyl and antifolyl poly-gamma-glutamate metabolism. GATase activity involves the removal of the ammonia group from a glutamate molecule and its subsequent transfer to a specific substrate, thus creating a new carbon-nitrogen group on the substrate. gamma-Glutamyl hydrolases belong to the triad family of amidotransferases having a conserved Cys-His-Glu catalytic triad in the glutaminase active site. 273 matched cddid_all.tbl CDD cd01748 cd01748 153219 GATase1_IGP_Synthase Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS). Type 1 glutamine amidotransferase (GATase1) domain found in imidazole glycerol phosphate synthase (IGPS). IGPS incorporates ammonia derived from glutamine into N1-[(5'-phosphoribulosyl)-formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to form 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR) and imidazole glycerol phosphate (IGP). The glutamine amidotransferase domain generates the ammonia nucleophile which is channeled from the glutaminase active site to the PRFAR active site. IGPS belong to the triad family of amidotransferases having a conserved Cys-His-Glu catalytic triad in the glutaminase active site. 198 matched cddid_all.tbl CDD cd01749 cd01749 153220 GATase1_PB Glutamine Amidotransferase (GATase_I) involved in pyridoxine biosynthesis. Glutamine Amidotransferase (GATase_I) involved in pyridoxine biosynthesis. Glutamine amidotransferase (GATase) activity involves the removal of the ammonia group from a glutamate molecule and its subsequent transfer to a specific substrate, thus creating a new carbon-nitrogen group on the substrate. This group contains proteins like Bacillus subtilus YaaE and Plasmodium falciparum Pdx2 which are members of the triad glutamine aminotransferase family and function in a pathway for the biosynthesis of vitamin B6. 183 matched cddid_all.tbl CDD cd01750 cd01750 153221 GATase1_CobQ Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ). Type 1 glutamine amidotransferase (GATase1) domain found in Cobyric Acid Synthase (CobQ). CobQ plays a role in cobalamin biosythesis. CobQ catalyses amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide in the biosynthesis of cobalamin. CobQ belongs to the triad family of amidotransferases. Two of the three residues of the catalytic triad that are involved in glutamine binding, hydrolysis and transfer of the resulting ammonia to the acceptor substrate in other triad aminodotransferases are conserved in CobQ. 194 matched cddid_all.tbl CDD cd01751 cd01751 238849 PLAT_LH2 PLAT/ LH2 domain of plant lipoxygenase related proteins. Lipoxygenases are nonheme, nonsulfur iron dioxygenases that act on lipid substrates containing one or more (Z,Z)-1,4-pentadiene moieties. In plants, the immediate products are involved in defense mechanisms against pathogens and may be precursors of metabolic regulators. The generally proposed function of PLAT/LH2 domains is to mediate interaction with lipids or membrane bound proteins. 137 matched cddid_all.tbl CDD cd01752 cd01752 238850 PLAT_polycystin PLAT/LH2 domain of polycystin-1 like proteins. Polycystins are a large family of membrane proteins composed of multiple domains, present in fish, invertebrates, mammals, and humans that are widely expressed in various cell types and whose biological functions remain poorly defined. In human, mutations in polycystin-1 (PKD1) and polycystin-2 (PKD2) have been shown to be the cause for autosomal dominant polycystic kidney disease (ADPKD). The generally proposed function of PLAT/LH2 domains is to mediate interaction with lipids or membrane bound proteins. 120 matched cddid_all.tbl CDD cd01753 cd01753 238851 PLAT_LOX PLAT domain of 12/15-lipoxygenase. As a unique subfamily of the mammalian lipoxygenases, they catalyze enzymatic lipid peroxidation in complex biological structures via direct dioxygenation of phospholipids and cholesterol esters of biomembranes and plasma lipoproteins. Both types of enzymes are cytosolic but need this domain to access their sequestered membrane or micelle bound substrates. 113 matched cddid_all.tbl CDD cd01754 cd01754 238852 PLAT_plant_stress PLAT/LH2 domain of plant-specific single domain protein family with unknown function. Many of its members are stress induced. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins. 129 matched cddid_all.tbl CDD cd01755 cd01755 238853 PLAT_lipase PLAT/ LH2 domain present in connection with a lipase domain. This family contains two major subgroups, the lipoprotein lipase (LPL) and the pancreatic triglyceride lipase. LPL is a key enzyme in catabolism of plasma lipoprotein triglycerides (TGs). The central role of triglyceride lipases is in energy production. In general, PLAT/LH2 domain's proposed function is to mediate interaction with lipids or membrane bound proteins. 120 matched cddid_all.tbl CDD cd01756 cd01756 238854 PLAT_repeat PLAT/LH2 domain repeats of family of proteins with unknown function. In general, PLAT/LH2 consists of an eight stranded beta-barrel and it's proposed function is to mediate interaction with lipids or membrane bound proteins. 120 matched cddid_all.tbl CDD cd01757 cd01757 238855 PLAT_RAB6IP1 PLAT/LH2 domain present in RAB6 interacting protein 1 (Rab6IP1)_like family. PLAT/LH2 domains consists of an eight stranded beta-barrel. In RabIP1 this domain may participate in lipid-mediated modulation of Rab6IP1's function via it's generally proposed function of mediating interaction with lipids or membrane bound proteins. 114 matched cddid_all.tbl CDD cd01758 cd01758 238856 PLAT_LPL PLAT/ LH2 domain present in lipoprotein lipase (LPL). LPL is a key enzyme in catabolism of plasma lipoprotein triglycerides (TGs) and has therefeore has a profound influence on triglyceride and high-density lipoprotein (HDL) cholesterol levels in the blood. In general, PLAT/LH2 domain's proposed function is to mediate interaction with lipids or membrane bound proteins. 137 matched cddid_all.tbl CDD cd01759 cd01759 238857 PLAT_PL PLAT/LH2 domain of pancreatic triglyceride lipase. Lipases hydrolyze phospholipids and triglycerides to generate fatty acids for energy production or for storage and to release inositol phosphates that act as second messengers. The central role of triglyceride lipases is in energy production. The proposed function of PLAT/LH2 domains is to mediate interaction with lipids or membrane bound proteins. 113 matched cddid_all.tbl CDD cd01760 cd01760 340461 RBD Ras-binding domain (RBD), structurally similar to a beta-grasp ubiquitin-like fold. The RBD of the serine/threonine kinase Raf is structurally similar to the beta-grasp fold of ubiquitin, a common structure involved in protein-protein interactions. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. A Raf-like RBD is also present in Regulator of G protein Signaling (RGS12 and RGS14) members of GTPase activating proteins. 71 matched cddid_all.tbl CDD cd01763 cd01763 340462 Ubl_SUMO_like "ubiquitin-like (Ubl) domain found in small ubiquitin-related modifier (SUMO) and similar proteins. SUMO (also known as ""Smt3"" and ""sentrin"" in other organisms) resembles ubiquitin (Ub) in structure, ligation to other proteins, and the mechanism of ligation. Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of Ub and the epsilon-amino group of a substrate lysine. SUMOs, like Ub, are covalently conjugated to lysine residues in a wide variety of target proteins in eukaryotic cells and regulate numerous cellular processes, such as transcription, epigenetic gene control, genomic instability, and protein degradation. The mammalian SUMOs have four paralogs, SUMO1 through SUMO4, which all regulate different cellular functions by conjugating to different proteins. SUMO2-4 are more closely related to each other than to SUMO1." 72 matched cddid_all.tbl CDD cd01764 cd01764 340463 Ubl_Urm1 ubiquitin-like (Ubl) domain found in ubiquitin-related modifier 1 (Urm1). Urm1 acts as a sulfur carrier in the thiolation of eukaryotic tRNA via a mechanism that requires the formation of a thiocarboxylated Urm1, which is similar to that of prokaryotic sulfur carrier proteins such as ThiS and MoaD, containing the beta-grasp ubiquitin-like (Ubl) fold. Urm1 can be covalently conjugated to lysine residues of other proteins through a mechanism involving the E1-like protein Uba4. Urm1 is involved in yeast bioprocesses such as budding, nutrient sensing, high temperature sensitivity, antioxidant stress response and post-translation modification of the elongator subunit. 94 matched cddid_all.tbl CDD cd01765 cd01765 340464 FERM_F0_F1 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F0 sub-domain and F1 sub-domain, found in FERM (Four.1/Ezrin/Radixin/Moesin) family proteins. FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain is present at the N-terminus of a large and diverse group of proteins that mediate linkage of the cytoskeleton to the plasma membrane. FERM-containing proteins are ubiquitous components of the cytocortex and are involved in cell transport, cell structure and signaling functions. The FERM domain is made up of three sub-domains, F1, F2, and F3. The family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N), which is structurally similar to ubiquitin. 80 matched cddid_all.tbl CDD cd01766 cd01766 340465 Ubl_UFM1 ubiquitin-like (Ubl) domain found in ubiquitin fold modifier 1 (UFM1). UFM1 belongs to the ubiquitin-like protein family with similar ubiquitin beta-grasp folds and mechanism of ligation to other proteins. UFM1 is present in nearly all eukaryotic organisms except fungi. Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. The UNF1 cascade has been implicated in endoplasmic reticulum functions, cell cycle control and cell differentiation. The involvement of the UFM1 cascade in diseases is diverse; reports include its involvement in ischemic heart diseases, diabetes, gastric lesions, schizophrenia, hip dysplasia and cancer. 75 matched cddid_all.tbl CDD cd01767 cd01767 340466 UBX Ubiquitin regulatory domain X (UBX) structurally similar to a beta-grasp ubiquitin-like fold. The UBXD family of proteins contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. Members in this family function as cofactors of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. Based on domain composition, UBXD proteins can be divided into two main groups, with and without ubiquitin-associated (UBA) domain. 74 matched cddid_all.tbl CDD cd01768 cd01768 340467 RA_FERM_F0_F1_like Ras-associating (RA) domain, FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F0/F1 sub-domain, structurally similar to a beta-grasp ubiquitin-like fold. RA domain-containing proteins function by interacting, directly or indirectly, with Ras proteins and are involved in several different functions ranging from tumor suppression to being oncoproteins. Ras protein is a small GTPase that is involved in cellular signal transduction. The RA domain has the beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin (Ub). Ub is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. RA-containing proteins include RalGDS, AF6, RIN, RASSF1, SNX27, CYR1, STE50, and phospholipase C epsilon. The FERM domain is present at the N-terminus of a large and diverse group of proteins that mediate linkage of the cytoskeleton to the plasma membrane. FERM-containing proteins are ubiquitous components of the cytocortex and are involved in cell transport, cell structure and signaling. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, also known as the N-terminal Ubl-like structural domain of the FERM domain (FERM_N), which is structurally similar to Ub. Some FERM domain-containing proteins contain an N-terminal region, which also has the beta-grasp Ub-like fold, precedes the FERM domain and has been referred to as the F0 domain. 110 matched cddid_all.tbl CDD cd01770 cd01770 340468 UBX_UBXN2 Ubiquitin regulatory domain X (UBX) found in UBX domain-containing proteins UBXN2A, UBXN2B, NSFL1C/UBXN2C, and similar proteins. This family includes UBX domain-containing proteins UBXN2A, UBXN2B, and NSFL1C/UBXN2C, which contain a SEP (Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47) domain, and a ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold at the C-terminus. UBX domain participates broadly in the regulation of protein degradation. UBXN2A, UBXN2B, and UBXN2C function as the adaptor proteins of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. 71 matched cddid_all.tbl CDD cd01771 cd01771 340469 UBX_UBXN3A Ubiquitin regulatory domain X (UBX) found in FAS associated factor 1 (FAF1, also known as UBXN3A) and similar proteins. UBX domain-containing protein 3A (UBXN3A),also termed UBX domain-containing protein 12 (UBXD12), or FAF1, belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. In addition, FAF1 contains two tandem ubiquitin-like (Ubl) domains, which shows high structural similarity with UBX domain. FAF1 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. The FAF1-p97 complex inhibits the proteasomal protein degradation in which p97 acts as a co-chaperone. Moreover, FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF1 is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kappaB (NF-kappaB) by interfering with the nuclear translocation of the p65 subunit. Although the precise role of FAF1 in the ubiquitination pathway remains unclear, FAF1 interacts with valosin-containing protein (VCP), which is involved in the ubiquitin-proteosome pathway. This family corresponds to UBX domain. 80 matched cddid_all.tbl CDD cd01772 cd01772 340470 UBX_UBXN1 Ubiquitin regulatory domain X (UBX) found in UBX domain protein 1 (UBXN1) and similar proteins. UBXN1, also termed SAPK substrate protein 1 (SAKS1), UBA/UBX 33.3 kDa protein (Y33K), or UBXD10, is a widely expressed protein containing an N-terminal ubiquitin-associated (UBA) domain, a coiled-coil region, and a C-terminal ubiquitin-like (Ubl or UBX) domain that has a beta-grasp ubiquitin-like fold without the C-terminal double glycine motif. UBXN1 has been identified as a substrate for stress-activated protein kinases (SAPKs). It binds polyubiquitin and valosin-containing protein (VCP), suggesting a role as an adaptor that directs VCP to polyubiquitinated proteins facilitating its destruction by the proteasome. In addition, UBXN1 specifically binds to Homer2b. It may also interact with ubiquitin (Ub) and be involved in the Ub-proteasome proteolytic pathways. UBXN1 can also associate with autoubiquitinated BRCA1 tumor suppressor and inhibit its enzymatic function through its UBA domains. 81 matched cddid_all.tbl CDD cd01773 cd01773 340471 UBX_UBXN7 Ubiquitin regulatory domain X (UBX) found in UBX domain protein 7 (UBXN7) and similar proteins. UBXN7, also termed UBX domain-containing protein 7 (UBXD7), belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. UBXN7 functions as a ubiquitin-binding adaptor that mediates the interaction between the AAA+ ATPase p97 (also known as VCP or Cdc48) and the transcription factor HIF1-alpha. It binds only to the active, NEDD8- or Rub1-modified form of cullins. In addition to having a UBX domain, UBXD7 contains a ubiquitin-associated (UBA), ubiquitin-associating (UAS), and ubiquitin-interacting motif (UIM) domains. Either UBA or UIM could serve as a docking site for neddylated-cullins. UBA domain is required for binding ubiquitylated-protein substrates, while the UIM motif is responsible for the binding to cullin RING ligases (CRLs), and the UBX domain is essential for p97 binding. 76 matched cddid_all.tbl CDD cd01774 cd01774 340472 UBX_UBXN8 Ubiquitin regulatory domain X (UBX) found in UBX domain protein 8 (UBXN8) and similar proteins. UBXN8, also termed reproduction 8 protein (Rep8), or UBX domain-containing protein 6 (UBXD6), or D8S2298E, belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. UBXN8 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. UBXN8 is a transmembrane protein that localizes to the endoplasmic reticulum (ER) membrane with its UBX domain facing the cytoplasm. It facilitates efficient ER-associated degradation (ERAD) by tethering p97 to the ER membrane. 76 matched cddid_all.tbl CDD cd01775 cd01775 340473 RA_PHLPP_like Ras-associating (RA) domain found in PH domain leucine-rich repeat-containing protein phosphatases, fungal adenylate cyclase, and similar proteins. PHLPP represents a novel family of Ser/Thr protein phosphatases, which is involved in two key signaling pathways, the phosphatidylinositol 3-kinase and diacylglycerol signaling pathways, by directly dephosphorylating and inactivating Akt serine-threonine kinases (Akt1, Akt2, Akt3) and protein kinase C (PKC) isoforms. PHLPP contains a putative Ras-associating (RA) domain followed by a pleckstrin homology (PH) domain, a series of leucine-rich repeats and a protein phosphatase 2C (PP2C) domain. Fungal adenylate cyclase regulates developmental processes such as hyphal growth, biofilm formation, and phenotypic switching. It plays an essential role in regulation of cellular metabolism by catalyzing the synthesis of a second messenger, cAMP. Fungal adenylate cyclase has at least four domains, including an N-terminal adenylate cyclase G-alpha binding domain, a Ras-associating (RA) domain, a middle leucine-rich repeat region, and a catalytic domain. The RA domain of adenylate cyclase post-translationally modifies a small GTPase called Ras, which is involved in cellular signal transduction. The activity of adenylate cyclase is stimulated directly by regulatory proteins (Ras1 and Gpa2), peptidoglycan fragments and carbon dioxide. 99 matched cddid_all.tbl CDD cd01776 cd01776 340474 RA_Rin Ras-associating (RA) domain of Ras and Rab interactor (Rin) protein family. Family of Ras-interaction/interference (Rin) proteins, also known as Ras and Rab interactors, is composed of Rin1, Rin2, and Rin3, which have multifunctional domains, including SH2 and proline-rich domains in the N-terminal region, and RH, VPS9, and RA domains in the C-terminal region. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and are involved in several different functions ranging from tumor suppression to being oncoproteins. Ras proteins are small GTPases that are involved in cellular signal transduction. The RA domain has the beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin; ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. The RA domains of Rin1, Rin2, and Rin3 are well conserved and they all have Ras binding characteristics. 90 matched cddid_all.tbl CDD cd01777 cd01777 340475 FERM_F1_SNX27 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in sorting nexin protein 27 (SNX27). SNX27 is a member of the family of cytoplasmic sorting nexin adaptor proteins that regulate endosomal trafficking of cell surface proteins. In addition to a PX (Phox homology) domain that regulates its endosomal localization, SNX27 has a unique PDZ (Psd-95/Dlg/ZO1) domain and an atypical FERM (4.1, ezrin, radixin, moesin) domain that both function to bind short peptide sequence motifs in the cytoplasmic domains of the cargo receptors. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 92 matched cddid_all.tbl CDD cd01778 cd01778 340476 RA_RASSF1_like Ras-associating (RA) domain found in Ras-association domain family members, RASSF1, RASSF3, and RASSF5. The RASSF family of proteins shares a conserved RalGDS/AF6 Ras association (RA) domain which is located either at the C-terminus (RASSF1-6, the classical group) or at the N-terminus (RASSF7-10). RASSF1-6 contains a conserved SARAH (Salvador/RASSF/Hpo) motif adjacent to the RA domain that functions in scaffolding and regulatory interactions. The RA domain of the classical RASSF proteins has a beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. Classical RASSF members interact either directly or indirectly with activated Ras. Ras proteins are small GTPases that are involved in cellular signal transduction. The classical RASSF proteins seem to modulate some of the growth inhibitory responses mediated by Ras and may serve as tumor suppressor genes. This family contains RASSF1, RASSF3, and RASSF5. 130 matched cddid_all.tbl CDD cd01779 cd01779 340477 RA_Myosin-IX Ras-associating (RA) domain found in Myosin-IX. Myosins IX (Myo9) is a class of unique motor proteins with a common structure of an N-terminal extension preceding a myosin head homologous to the Ras-association (RA) domain, a head (motor) domain, a neck with IQ motifs that bind light chains and a C-terminal tail containing a Rho-GTPase activating protein (RhoGAP) domain. The RA domain is located at its head domain and has the beta-grasp ubiquitin-like fold with unknown function. There are two genes for myosins IX in humans, IXa and IXb, that are different in their expression and localization. IXa is expressed abundantly in brain and testis and IXb is expressed abundantly in tissues of the immune system. 97 matched cddid_all.tbl CDD cd01780 cd01780 340478 RA2_PLC-epsilon Ras-associating (RA) domain 2 found in Phosphatidylinositide-specific phospholipase C (PLC)-epsilon. PLC is a signaling enzyme that hydrolyzes membrane phospholipids to generate inositol triphosphate. PLC-epsilon represents a novel forth class of PLC that has a PLC catalytic core domain, a CDC25 guanine nucleotide exchange factor domain and two RA (Ras-association) domains. RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. Although PLC RA1 and RA2 have homologous ubiquitin-like folds only RA2 can bind Ras and activate it. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and involve in several different functions ranging from tumor suppression to being oncoproteins. Ras proteins are small GTPases that are involved in cellular signal transduction. This family corresponds to the second RA domain of PLC-epsilon. 102 matched cddid_all.tbl CDD cd01781 cd01781 340479 RA2_Afadin Ras-associating (RA) domain 2 found in Afadin. Afadin, also termed ALL1-fused gene from chromosome 6 protein (AF-6), or canoe, is involved in many fundamental signaling cascades in cells. In addition, it is involved in oncogenesis and metastasis. Afadin has multiple domains: from the N-terminus to the C-terminus it has two Ras-associated (RA) domains, a forkhead-associated domain, a dilute domain, a PDZ domain, three proline-rich domains, and an F-actin binding domain. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and are involved in several different functions ranging from tumor suppression to being oncoproteins. Ras proteins are small GTPases that are involved in cellular signal transduction. The RA domain has a beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin (Ub). Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. Afadin is abundant at cadherin-based adherens junctions in epithelial cells, endothelial cells, and fibroblasts. This family corresponds to the second RA domain of afadin. 102 matched cddid_all.tbl CDD cd01782 cd01782 340480 RA1_Afadin Ras-associating (RA) domain 1 found in Afadin. Afadin, also termed ALL1-fused gene from chromosome 6 protein (AF-6), or canoe, is involved in many fundamental signaling cascades in cells. In addition, it is involved in oncogenesis and metastasis. Afadin has multiple domains: from the N-terminus to the C-terminus it has two Ras-associated (RA) domains, a forkhead-associated domain, a dilute domain, a PDZ domain, three proline-rich domains, and an F-actin-binding domain. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and are involved in several different functions ranging from tumor suppression to being oncoproteins. Ras proteins are small GTPases that are involved in cellular signal transduction. The RA domain has a beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin (Ub). Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. Afadin is abundant at cadherin-based adherens junctions in epithelial cells, endothelial cells, and fibroblasts. This family corresponds to the first RA domain of afadin, which mediates its self-association. 112 matched cddid_all.tbl CDD cd01783 cd01783 340481 RA2_DAGK-theta Ras-associating (RA) domain 2 found in diacylgylcerol kinase theta (DAGK-theta) and similar proteins. DAGK phosphorylates the second messenger diacylglycerol to phosphatidic acid as part of a protein kinase C pathway. DAGK-theta is characterized as a type V DAGK that has three cysteine-rich domains (all other isoforms have two), a proline/glycine-rich domain at its N-terminal, and a proposed Ras-associating (RA) domain. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and are involved in several different functions ranging from tumor suppression to being oncoproteins. Ras proteins are small GTPases that are involved in cellular signal transduction. The RA domain has a beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin (Ub). Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. There are ten mammalian isoforms of DAGK have been identified to date, these are organized into five categories based on the domain architecture. DAGK-theta also contains a pleckstrin homology (PH) domain. The subcellular localization and the activity of DAGK-theta are regulated in a complex (stimulation- and cell type-dependent) manner. This family corresponds to the second RA domain of DAGK-theta. 95 matched cddid_all.tbl CDD cd01784 cd01784 340482 RA_RASSF2_like Ras-associating (RA) domain found in Ras-association domain family members, RASSF2, RASSF4, and RASSF6. The RASSF family of proteins shares a conserved RalGDS/AF6 RA domain either in the C-terminus (RASSF1-6) or N-terminus (RASSF7-10). The classical family members (RASSF1-6) contain a conserved SARAH (Salvador/RASSF/Hpo) motif adjacent to the RA domain that functions as scaffolding and regulatory interactions. The RA domain of the classical RASSF protein family has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. Classical RASSF members interact either directly or indirectly with activated Ras. Ras proteins are small GTPases that are involved in cellular signal transduction. The classical RASSF protein family seem to modulate some of the growth inhibitory responses mediated by Ras and may serve as tumor suppressor genes. This family contains RASSF2, RASSF4, and RASSF6. 87 matched cddid_all.tbl CDD cd01785 cd01785 340483 RA_PDZ-GEF1 Ras-associating (RA) domain found in PDZ domain-containing guanine nucleotide exchange factor 1 (PDZ-GEF1) and similar proteins. PDZ-GEF1, also termed Rap guanine nucleotide exchange factor 2, or cyclic nucleotide ras GEF (CNrasGEF), or neural RAP guanine nucleotide exchange protein (nRap GEP), or Ras/Rap1-associating GEF-1 (RA-GEF-1), is a Rap-specific guanine nucleotide exchange factor (GEF) that has a PSD-95/DlgA/ZO-1 (PDZ) domain, a RA domain and a region related to a cyclic nucleotide binding domain (RCBD). The RA domain of PDZ-GEF interacts with Rap1 and also contributes to the membrane localization of PDZ-GEF. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and involve in several different functions ranging from tumor suppression to being oncoproteins. Ras proteins are small GTPases that are involved in cellular signal transduction. RA domain has the beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin (Ub). Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. 85 matched cddid_all.tbl CDD cd01786 cd01786 340484 RA_STE50 Ras-associating (RA) domain found in the fungal adaptor protein STE50. The fungal adaptor protein STE50 is an essential component of three MAPK-mediated signaling pathways that control the mating response, invasive/filamentous growth and osmotolerance (HOG pathway), respectively. STE50 functions in cell signaling between the activated G protein and STE11. The domain architecture of STE50 includes an amino-terminal SAM (sterile alpha motif) domain in addition to the carboxy-terminal ubiquitin-like RA (RAS-associated) domain. RA domain of STE50 interacts with the small GTPase Cdc42p, a member of Rho type of the Ras superfamily. This interaction activates Ste11p/Ste7p/Kss1pMAP kinase cascade that controls filamentous growth. RA domain has the beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin (Ub). Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. 101 matched cddid_all.tbl CDD cd01787 cd01787 340485 RA_MRL Ras-associating (RA) domain of Mig10/RIAM/Lpd (MRL) family. MRL proteins share a common structural architecture, including a central structural unit consisting of a Ras-associating (RA) domain and a pleckstrin homology (PH) domain, an upstream coiled-coil region, and a number of polyproline motifs. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and are involved in several different functions ranging from tumor suppression to being oncoproteins. Ras proteins are small GTPases that are involved in cellular signal transduction. RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin (Ub). Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. RA and PH form a tandem domain pair (RA-PH), and serve tightly coordinated functions in both Ras GTPase signaling via the RA domain and membrane translocalization via the PH domain. MRL proteins have distinct functions in cell migration and adhesion, signaling, and in cell growth. 85 matched cddid_all.tbl CDD cd01788 cd01788 340486 Ubl_ElonginB ubiquitin-like (Ubl) domain found in transcription elongation factor B (Elongin B) and similar proteins. Elongin B, also termed Elongin 18 kDa subunit, or EloB, or RNA polymerase II transcription factor SIII subunit B (SIII p18), is part of an E3 ubiquitin ligase complex called VEC that activates ubiquitination by the E2 ubiquitin-conjugating enzyme Ubc5. VEC is composed of von Hippel-Lindau tumor suppressor protein (pVHL), elongin C, cullin 2, NEDD8, and Rbx1. ElonginB binds elonginC to form the elonginBC complex which is a positive regulator of RNA polymerase II elongation factor Elongin A. The BC complex then binds VHL (von Hippel-Lindau) tumor suppressor protein to form a VCB ternary complex. Elongin B has a ubiquitin-like (Ubl) domain. Ub has a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. Ub is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. 101 matched cddid_all.tbl CDD cd01789 cd01789 340487 Ubl_TBCB ubiquitin-like (Ubl) domain found in tubulin-folding cofactor B (TBCB) and similar proteins. TBCB, also termed cytoskeleton-associated protein 1, or cytoskeleton-associated protein CKAPI, or tubulin-specific chaperone B, is one of protein cofactors A through E that is required for the folding of tubulins prior to their incorporation into microtubules and heterodimer assembly. TBCB comprises an N-terminal ubiquitin-like (Ubl) domain and a C-terminal cytoskeleton-associated protein with glycine-rich segment (CAP-Gly) domain. The Ubl domain of TBCB is essential for proper folding and assembly of tubulin alpha. It has a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. TBC-A through E are necessary for the biogenesis of microtubules and for cell viability. 80 matched cddid_all.tbl CDD cd01790 cd01790 340488 Ubl_HERP ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress protein HERP. HERP is an endoplasmic reticulum (ER) integral membrane protein containing an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. The Ubl domain is required for the degradation of HERP itself as well as for HERP-mediated anti-apoptotic effects. HERP is induced by the ER stress response pathway and is involved in improving the balance of folding capacity and protein loads in the ER. There are two types of HERP, HERP1 and HERP2, which are encoded by the HERPUD1 and HERPUD2 genes, respectively. 78 matched cddid_all.tbl CDD cd01791 cd01791 340489 Ubl_UBL5 ubiquitin-like (Ubl) domain found in ubiquitin-like protein 5 (UBL5) and similar proteins. UBL5, known as Hub1 in yeast, is an atypical ubiquitin-like (Ubl) post-translational modifier that contains a conserved Ubl domain with a beta-grasp Ubl fold. At the C-terminal end of its Ubl fold is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other Ubl modifiers, and thus UBL5 does not form covalent conjugates with cellular proteins. The yeast Hub1p binds non-covalently to the HIND element of spliceosomal protein Snu66p (Snu66p is termed SART1 in mammals) and modifies the spliceosome by this unconventional Ubl modifier. In higher eukaryotes, UBL5/Hub1 plays a role in modulating pre-mRNA splicing. It also is required for signaling in the mitochondrial unfolded protein response, through interaction with the transcription factor DVE-1 and upregulation of chaperone genes in response to mitochondrial stress. Moreover, UBL5 functions as a factor that directly binds to and stabilizes FANCI, and promotes the functionality of the Fanconi anemia (FA) DNA repair pathway. 71 matched cddid_all.tbl CDD cd01792 cd01792 340490 Ubl1_ISG15 ubiquitin-like (Ubl) domain 1 found in interferon-stimulated gene 15 (ISG15) and similar proteins. ISG15, also termed interferon-induced 15 kDa protein, or interferon-induced 17 kDa protein (IP17), or ubiquitin cross-reactive protein (UCRP), is an antiviral interferon-induced ubiquitin-like protein (Ubl) that upon viral infection, modifies cellular and viral proteins by mechanisms similar to ubiquitination. Although ISG15 has properties similar to those of other Ubl molecules, it is a unique member of the Ubl superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system. ISG15 contains two tandem Ubl domains with a beta-grasp Ubl fold. This family corresponds to the first Ubl domain. 75 matched cddid_all.tbl CDD cd01793 cd01793 340491 Ubl_FUBI ubiquitin-like (Ubl) domain found in ubiquitin-like protein FUBI and similar proteins. FUBI is a pro-apoptotic regulatory gene FAU encoding ubiquitin-like protein with ribosomal protein S30 as a C-terminal extension. FUBI functions as a tumor suppressor protein that may be involved in the ATP-dependent proteolytic activity of ubiquitin. The N-terminal ubiquitin-like (Ubl) domain of FUBI has the beta-grasp Ubl fold, and it may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8. 74 matched cddid_all.tbl CDD cd01794 cd01794 340492 Ubl_UBTD ubiquitin-like (Ubl) domain found in ubiquitin domain-containing proteins UBTD1, UBTD2, and similar proteins. This family represents a group of ubiquitin-like (Ubl) domain-containing proteins evolutionarily conserved and found in metazoa, fungi, and plants. They may regulate the activity and/or specificity of E2 ubiquitin conjugating enzymes belonging to the UBE2D family. Members in this family contain an N-terminal ubiquitin binding domain (UBD) and a C-terminal Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. 69 matched cddid_all.tbl CDD cd01795 cd01795 340493 Ubl_USP48 ubiquitin-like (Ubl) domain found in ubiquitin-specific-processing protease 48 (USP48) and similar proteins. USP48, also termed USP31, or deubiquitinating enzyme 48, or ubiquitin thioesterase 48, or ubiquitin carboxyl-terminal hydrolase 48, belongs to the ubiquitin specific protease (USP) family that is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin (Ub)and ubiquitin-like (Ubl) adducts. While the USP proteins have a conserved catalytic core domain, USP48 differs in its domain architecture. It contains an N-terminal USP domain, three DUSP (domain present in ubiquitin-specific protease) domains, and a C-terminal Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. USP48 is a deubiquitinating enzyme that interacts with TNF receptor-associated factor 2 (TRAF2) and has been implicated in activation of nuclear factor-kappaB (NF-kappaB). Moreover, as a nuclear deubiquitinase regulated by casein kinase 2 (CK2), USP48 controls the ubiquitin/proteasome-system (UPS)-dependent turnover of activated NF-kappaB/RelA in the nucleus together with the COP9 signalosome, suggesting a role of USP48 in a timely control of immune responses. 99 matched cddid_all.tbl CDD cd01796 cd01796 340494 Ubl_Ddi1_like ubiquitin-like (Ubl) domain found in the eukaryotic Ddi1 family. The eukaryotic Ddi1 family, including yeast aspartyl protease DNA-damage inducible 1 (Ddi1) and Ddi1-like proteins from vertebrates and other eukaryotes, has been characterized by containing an N-terminal ubiquitin-like (Ubl) domain and a conserved retroviral aspartyl-protease-like domain (RVP) that is important in cell-cycle control. Yeast Ddi1 and many family members also contain a C-terminal ubiquitin-association (UBA) domain, however, Ddi1-like proteins from all vertebrates lack the UBA domain. Ddi1, also termed v-SNARE-master 1 (Vsm1), is an ubiquitin receptor involved in the cell cycle and late secretory pathway in Saccharomyces cerevisiae. It functions as an UBA-Ubl shuttle protein that is required for the proteasome to enable ubiquitin-dependent degradation of its ligands. For instance, Ddi1 plays an essential role in the final stages of proteasomal degradation of Ho endonuclease and of its cognate FBP, Ufo1. Moreover, Ddi1 and its associated protein Rad23p play a cooperative role as negative regulators in yeast PHO pathway. This family also includes mammalian regulatory solute carrier protein family 1 member 1 (RSC1A1), also termed transporter regulator RS1 (RS1), which mediates transcriptional and post-transcriptional regulation of Na(+)-D-glucose cotransporter SGLT1. Ddi1-like proteins play a significant role in cell cycle control, growth control, and trafficking in yeast and may play a crucial role in embryogenesis in higher eukaryotes. 73 matched cddid_all.tbl CDD cd01797 cd01797 340495 Ubl_UHRF ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing proteins, UHRF1 and UHRF2, and similar proteins. UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma, gastric cancer, esophageal squamous cell carcinoma, colorectal cancer, prostate cancer, and breast cancer. UHRF1 can acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumor suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (Ubl), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a set- and ring-associated (SRA) domain, and a C-terminal RING finger. 74 matched cddid_all.tbl CDD cd01798 cd01798 340496 Ubl_parkin ubiquitin-like (Ubl) domain found in parkin and similar proteins. Parkin, also termed Parkinson juvenile disease protein 2, is a RBR-type E3 ubiquitin-protein ligase that is associated with recessive early onset Parkinson's disease (PD), and exerts a protective effect against dopamine-induced alpha-synuclein-dependent cell toxicity. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Parkin functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, RHOT1/MIRO1, MFN1, MFN2, STUB1, SNCAIP, SEPT5, TOMM20, USP30, ZNF746 and AIMP2. It mediates monoubiquitination as well as Lys-6-, Lys-11-, Lys-48- and Lys-63-linked polyubiquitination of substrates depending on the context. Parkin may enhance cell viability and protects dopaminergic neurons from oxidative stress-mediated death by regulating mitochondrial function. It also limits the production of reactive oxygen species (ROS), and regulates cyclin-E during neuronal apoptosis. Moreover, parkin displays a ubiquitin ligase-independent function in transcriptional repression of p53. Parkin contains an N-terminal ubiquitin-like (Ubl) domain and a C-terminal RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain use an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. 74 matched cddid_all.tbl CDD cd01799 cd01799 340497 Ubl_HOIL1 ubiquitin-like (Ubl) domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins. HOIL-1, also termed RBCK1, or HOIL-1L, or RanBP-type and C3HC4-type zinc finger-containing protein 1, HBV-associated factor 4, or Hepatitis B virus X-associated protein 4, or RING finger protein 54 (RNF54), or ubiquitin-conjugating enzyme 7-interacting protein 3, or UbcM4-interacting protein 28 (UIP28), together with E3 ubiquitin-protein ligase RNF31 (also known as HOIP) and SHANK-associated RH domain interacting protein (SHARPIN), forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis through conjugation of linear polyubiquitin chains to NF-kappaB essential modulator (also known as NEMO or IKBKG). HOIL-1 plays a crucial role in TNF-alpha-mediated NF-kappaB activation. It also functions as an ubiquitin-protein ligase E3 that interacts with not only PKCbeta but also PKCzeta. It can recognize heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. HOIL-1 contains an N-terminal ubiqutin-like (UBL) domain and an Npl4 zinc-finger (NZF) domain, which regulate the interaction with the LUBAC subunit RNF31 and ubiquitin, respectively. The NZF domain belongs to RanBP2-type zinc finger (zf-RanBP2) domain superfamily. In addition, HOIL-1 has a RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain use an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. 81 matched cddid_all.tbl CDD cd01800 cd01800 340498 Ubl_SF3a120 ubiquitin-like (Ubl) domain found in splicing factor 3A 120kDa subunit (SF3a120) and similar proteins. Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit SF3a120, also termed splicing factor 3A subunit 1 (SF3A1), or spliceosome-associated protein 114 (SAP114), is the U2 snRNP-specific protein that is critical for spliceosome assembly and normal splicing events. During splicing, SF3a120, together with the U2 snRNP and other proteins, are recruited to the 3' splicing site to generate the splicing complex A after the recognition of the 3' splicing site. SF3a120 contains two N-terminal SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, as well as a C-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. 84 matched cddid_all.tbl CDD cd01801 cd01801 340499 Ubl_TECR_like ubiquitin-like (Ubl) domain found in trans-2,3-enoyl-CoA reductase (TECR) and similar proteins. This family includes TECR and many TECR-like proteins, such as TECRL. TECR, also termed very-long-chain enoyl-CoA reductase, or synaptic glycoprotein SC2, or TER, or GPSN2, is a synaptic glycoprotein that catalyzes the fourth reaction in the synthesis of very long-chain fatty acids (VLCFA) which is the reduction step of the microsomal fatty acyl-elongation process. Diseases involving perturbations to normal synthesis and degradation of VLCFA (e.g. adrenoleukodystrophy and Zellweger syndrome) have significant neurological consequences. The mammalian TECR P182L mutation causes nonsyndromic mental retardation. Deletion of the yeast TECR (TSC13) homolog is lethal. TECR contains an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions, as well as a C-terminal catalytic domain. TECRL, also termed steroid 5-alpha-reductase 2-like 2 protein (SRD5A2L2), is associated with life-threatening inherited arrhythmias displaying features of both long QT syndrome (LQTS) and catecholaminergic polymorphic ventricular tachycardia (CPVT). Both TECR and TECRL contain an N-terminal Ubl domain with a beta-grasp Ubl fold, and a C-terminal catalytic domain. 77 matched cddid_all.tbl CDD cd01802 cd01802 340500 Ubl_ZFAND4 ubiquitin-like (Ubl) domain found in AN1-type zinc finger protein 4 (ZFAND4) and similar proteins. ZFAND4, also termed AN1-type zinc finger and ubiquitin domain-containing protein-like 1 (ANUBL1), may function as an oncogene that promotes proliferation and regulates relevant tumor suppressor genes in gastric cancer, suggesting a role in gastric cancer initiation and progression. ZFAND4contains an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions, as well as a C-terminal AN1-type zinc finger. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal Ubl domain of ZFAND4 does not undergo proteolytic processing. 74 matched cddid_all.tbl CDD cd01803 cd01803 340501 Ubl_ubiquitin ubiquitin-like (Ubl) domain found in ubiquitin. Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. Ubiquitin-like (Ubl) proteins have similar ubiquitin beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ubiquitin (Ub)and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Ub includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains. 76 matched cddid_all.tbl CDD cd01804 cd01804 340502 Ubl_midnolin ubiquitin-like (Ubl) domain found in midnolin and similar proteins. Midnolin, also termed midbrain nucleolar protein, is a nucleolar protein that may be involved in regulation of genes related to neurogenesis in the nucleolus. It is strongly expressed at the mesencephalon (midbrain) of the embryo in day 12.5 (E12.5) mice and its expression is developmentally regulated. Midnolin plays a role in cellular signaling of adult tissues and regulates glucokinase enzyme activity in pancreatic beta cells. It can also control development via regulation of mRNA transport in cells. Midnolin contains an N-terminal conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. 70 matched cddid_all.tbl CDD cd01805 cd01805 340503 Ubl_Rad23 ubiquitin-like (Ubl) domain found in the Rad23 protein family. The Rad23 family includes the yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe), their mammalian orthologs HR23A and HR23B, and putative DNA repair proteins from plants. Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ubiquitinylated proteins and participate in translocating polyubiquitinated proteins to the proteasome. Rad23 proteins carry an ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. The Ubl domain is responsible for the binding to proteasome. The UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates, which suggests Rad23 proteins might be involved in certain pathways of Ub metabolism. Both the Ubl domain and the XPC-binding domain are necessary for efficient NER function of Rad23 proteins. 72 matched cddid_all.tbl CDD cd01806 cd01806 340504 Ubl_NEDD8 ubiquitin-like (Ubl) domain found in neural precursor cell expressed developmentally down-regulated protein 8 (NEDD8) and similar proteins. NEDD8, also termed Neddylin, or RELATED TO UBIQUITIN (RUB/Rub1p) in plant and yeast, is a ubiquitin-like protein that conjugates to nuclear proteins in a manner analogous to ubiquitination and sentrinization. It modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. NEDD8 deamidation and its inhibition of Cullin-RING ubiquitin ligases (CRLs) activity are responsible for Cycle-inhibiting factor (Cif)/Cif homolog in Burkholderia pseudomallei (CHBP)-induced cytopathic effect. NEDD8 contains a single conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. Polyubiquitination, signals for a diverse set of cellular events via different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the epsilon-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. Ubl NEDD8, contains many of the same lysines (K6, K11, K27, K33, K48) as Ub, where K27 has an role (other than conjugation) in the mechanism of protein neddylation. 74 matched cddid_all.tbl CDD cd01807 cd01807 340505 Ubl_UBL4A_like ubiquitin-like (Ubl) domain found in ubiquitin-like proteins UBL4A and similar proteins. UBL4A, also termed GdX, is a ubiquitously expressed ubiquitin-like (Ubl) protein that forms a complex with partner proteins and participates in the protein processing through endoplasmic reticulum (ER), acting as a chaperone. As a key component of the BCL2-associated athanogene 6 (BAG6) chaperone complex, UBL4A plays a role in mediating DNA damage signaling and cell death. UBL4A also regulates insulin-induced Akt plasma membrane translocation through promotion of Arp2/3-dependent actin branching. Moreover, UBL4A specifically stabilizes the TC45/STAT3 association and promotes dephosphorylation of STAT3 to repress tumorigenesis. UBL4B is testis-specific, and encoded by an X-derived retrogene Ubl4b, which is specifically expressed in post-meiotic germ cells in mammals. As a germ cell-specific cytoplasmic protein, UBL4B is not present in somatic cells. Moreover, UBL4B is present in elongated spermatids, but not in spermatocytes and round spermatids, suggesting its function is restricted to late spermiogenesis. The function of UBL4A may be compensated by either UBL4B or other Ubl proteins in normal conditions. Both UBL4A and UBL4B contain a conserved Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. 72 matched cddid_all.tbl CDD cd01808 cd01808 340506 Ubl_PLICs ubiquitin-like (Ubl) domain found in eukaryotic protein linking integrin-associated protein (IAP, also known as CD47) with cytoskeleton (PLIC) proteins. The PLIC proteins (or ubiquilins) family contains human homologs of the yeast ubiquitin-like (Ubl) Dsk2 protein, PLIC-1 (also termed ubiquilin-1), PLIC-2 (also termed ubiquilin-2, or Chap1), PLIC-3 (also termed ubiquilin-3) and PLIC-4 (also termed ubiquilin-4, ataxin-1 interacting ubiquitin-like protein, A1Up, connexin43-interacting protein of 75 kDa, or CIP75), and mouse PLIC proteins. They are ubiquitin (Ub)-binding adaptor proteins involved in all protein degradation pathways through delivering ubiquitinated substrates to proteasomes. They also promote autophagy-dependent cell survival during nutrient starvation. PLIC-1 regulates the function of the thrombospondin receptor CD47 and G protein signaling. It plays a role in TLR4-mediated signaling through interacting with the Toll/interleukin-1 receptor (TIR) domain of TLR4. It also inhibits the TLR3-Trif antiviral pathway by reducing the abundance of Trif. Moreover, PLIC-1 binds to gamma-aminobutyric acid receptors (GABAARs) and modulates the Ub-dependent, proteasomal degradation of GABAARs. Furthermore, PLIC-1 acts as a molecular chaperone regulating amyloid precursor protein (APP) biosynthesis, trafficking, and degradation by stimulating K63-linked polyubiquitination of lysine 688 in the APP intracellular domain. In addition, PLIC-1 is involved in the protein aggregation-stress pathway via associating with the Ub-interacting motif (UIM) proteins ataxin 3, HSJ1a, and epidermal growth factor substrate 15 (EPS15). PLIC-2 is a protein that binds the ATPase domain of the HSP70-like Stch protein. It functions as a negative regulator of G protein-coupled receptor (GPCR) endocytosis. It also involved in amyotrophic lateral sclerosis (ALS)-related dementia. PLIC-3 is encoded by UbiquilinN3, a testis-specific gene. It shows high sequence similarity with the Xenopus protein XDRP1, a nuclear phosphoprotein that binds to the N-terminus of cyclin A and inhibits Ca2+-induced degradation of cyclin A, but not cyclin B. PLIC-4 is an ubiquitin-like (Ubl) nuclear protein that interacts with ataxin-1 and further links ataxin-1 with the chaperone and Ub-proteasome pathways. It also binds to the non-ubiquitinated gap junction protein connexin43 (Cx43) and regulates the turnover of Cx43 through the proteasomal pathway. PLIC proteins contain an N-terminal Ubl domain that is responsible for the binding of Ub-interacting motifs (UIMs) expressed by proteasomes and endocytic adaptors, and C-terminal Ub-associated (UBA) domain that interacts with Ub chains present on proteins destined for proteasomal degradation. In addition, mammalian PLIC2 proteins have an extra collagen-like motif region, which is absent in other PLIC proteins and the yeast Dsk2 protein. 73 matched cddid_all.tbl CDD cd01809 cd01809 340507 Ubl_BAG6 ubiquitin-like (Ubl) domain found in BCL2-associated athanogene 6 (BAG6) and similar proteins. BAG6, also termed large proline-rich protein BAG6, or BAG family molecular chaperone regulator 6, or HLA-B-associated transcript 3 (Bat3), or protein Scythe, or protein G3, is a nucleo-cytoplasmic shuttling chaperone protein that is highly conserved in eukaryotes. It functions in two distinct biological pathways, ubiquitin-mediated protein degradation of defective polypeptides and tail-anchored transmembrane protein biogenesis in mammals. BAG6 is a component of the heterotrimeric BAG6 sortase complex composed of BAG6, transmembrane recognition complex 35 (TRC35) and ubiquitin-like protein 4A (UBL4A). The BAG6 complex together with the cochaperone small, glutamine-rich, tetratricopeptide repeat-containing, protein alpha (SGTA) plays a role in the biogenesis of tail-anchored membrane proteins and subsequently shown to regulate the ubiquitination and proteasomal degradation of mislocalized proteins. Moreover, BAG6 acts as an apoptotic regulator that binds reaper, a potent apoptotic inducer. BAG6/reaper is thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules. It is also likely a key regulator of the molecular chaperone Heat Shock Protein A2 (HSPA2) stability/function in human germ cells. Furthermore, aspartyl protease-mediated cleavage of BAG6 is necessary for autophagy and fungal resistance in plants. BAG6 contains a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, which provides a platform for discriminating substrates with shorter hydrophobicity stretches as a signal for defective proteins. 71 matched cddid_all.tbl CDD cd01810 cd01810 340508 Ubl2_ISG15 ubiquitin-like (Ubl) domain 2 found in interferon-stimulated gene 15 (ISG15) and similar proteins. ISG15, also termed interferon-induced 15 kDa protein, or interferon-induced 17 kDa protein (IP17), or ubiquitin cross-reactive protein (UCRP), is an antiviral interferon-induced ubiquitin-like protein that upon viral infection it modifies cellular and viral proteins by mechanisms similar to ubiquitination. Although ISG15 has properties similar to those of other ubiquitin-like (Ubl) molecules, it is a unique member of the Ubl superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system. ISG15 contains two tandem Ubl domains with a beta-grasp Ubl fold. This family corresponds to the second Ubl domain. 74 matched cddid_all.tbl CDD cd01811 cd01811 340509 Ubl1_OASL ubiquitin-like (Ubl) domain 1 found in 2'-5'-oligoadenylate synthase-like protein (OASL) and similar proteins. OASL, also termed 2'-5'-OAS-related protein (2'-5'-OAS-RP), or 59 kDa 2'-5'-oligoadenylate synthase-like protein, or thyroid receptor-interacting protein 14, or TR-interacting protein 14 (TRIP-14), or p59 OASL (p59OASL), is an interferon (IFN)-induced antiviral protein that plays an important role in the IFNs-mediated antiviral signaling pathway. It inhibits respiratory syncytial virus replication and is targeted by the viral nonstructural protein 1 (NS1). It also displays antiviral activity against encephalomyocarditis virus (EMCV) and hepatitis C virus (HCV) via an alternative antiviral pathway independent of RNase L. Moreover, OASL does not have 2'-5'-OAS activity, but can bind double-stranded RNA (dsRNA) to enhance RIG-I signaling. OASL belongs to the 2'-5' oligoadenylate synthase (OAS) family. While each member of this family has a conserved N-terminal OAS catalytic domain, only OASL has two tandem C-terminal ubiquitin-like (Ubl) repeats, which is required for its antiviral activity. This family corresponds to the first Ubl domain. 75 matched cddid_all.tbl CDD cd01812 cd01812 340510 Ubl_BAG1 ubiquitin-like (Ubl) domain found in BAG family molecular chaperone regulator 1 (BAG1) and similar proteins. BAG1, also termed Bcl-2-associated athanogene 1, or HAP, is a multifunctional protein involved in a variety of cellular functions such as apoptosis, transcription, and proliferative pathways, as well as in cell signaling and differentiation. It delivers chaperone-recognized unfolded substrates to the proteasome for degradation. BAG1 functions as a co-chaperone for Hsp70/Hsc70 to increase Hsp70 foldase activity. It also suppresses apoptosis and enhances neuronal differentiation. As an anti-apoptotic factor, BAG1 interacts with tau and regulates its proteasomal degradation. It also binds to BCR-ABL with a high affinity, and directly routes immature BCR-ABL for proteasomal degradation. It acts as a potential therapeutic target in Parkinson's disease. It also modulates huntingtin toxicity, aggregation, degradation, and subcellular distribution, suggesting a role in Huntington's disease. There are at least four isoforms of Bag1 protein that are formed by alternative initiation of translation within a common mRNA. BAG1 contains an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, and a C-terminal BAG domain. 77 matched cddid_all.tbl CDD cd01813 cd01813 340511 Ubl_UBLCP1 ubiquitin-like (Ubl) domain found in ubiquitin-like domain-containing CTD phosphatase 1 (UBLCP1) and similar proteins. UBLCP1 is a 26S proteasome phosphatase that regulates nuclear proteasome activity. It is localized in the nucleus and it contains conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, which directly interacts with the proteasome. Knockdown of UBLCP1 in cells promotes 26S proteasome assembly and selectively enhances nuclear proteasome activity. UBLCP1 may also play a role in the regulation of phosphorylation state of RNA polymerase II C-terminal domain, a key event during mRNA metabolism. 74 matched cddid_all.tbl CDD cd01814 cd01814 340512 Ubl_MUBs_plant ubiquitin-like (Ubl) domain found in plant membrane-anchored ubiquitin-fold proteins (MUBs). The plant MUBs belong to a family of ubiquitin-fold proteins that are plasma membrane-anchored by prenylation. They may serve as docking site to facilitate the association of specific E2s to the plasma membrane. MUBs contain a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. 89 matched cddid_all.tbl CDD cd01815 cd01815 340513 Ubl_UBL7 ubiquitin-like (Ubl) domain found in ubiquitin-like protein 7 (UBL7) and similar proteins. UBL7, also termed bone marrow stromal cell ubiquitin-like (Ubl)protein (BMSC-UbP), or ubiquitin-like protein SB132, is a novel Ubl protein that may play roles in regulation of bone marrow stromal cell (BMSC) function or cell differentiation via an evocator-associated and cell-specific pattern. UBL7 contains an N-terminal Ubl domain with a beta-grasp Ubl fold, and a C-terminal ubiquitin-associated (UBA) domain. The Ubl domain interacts with 26S proteasome-dependent degradation, and the UBA domain links cellular processes and the ubiquitin system. 92 matched cddid_all.tbl CDD cd01816 cd01816 340514 RBD_RAF Ras-binding domain (RBD) found in RAF family serine/threonine kinases. The RAF family includes three RAF serine/threonine kinases ARAF, BRAF, and RAF1/CRAF. These are encoded by proto-oncogenes, and activate the mitogen-activated protein kinase/extracellular-signal-regulated kinase (MAPK/ERK) cascade downstream of RAS. They share a common structure consisting of an N-terminal regulatory domain and a C-terminal kinase domain. There are three conserved regions (CR1-3) in the regulatory domain, CR1 contains a Ras-binding domain (RBD) and a cysteine-rich domain (CRD), CR2 is a serine/threonine-rich domain, and CR3 encodes the kinase domain required for RAF. The RBD of RAF has a beta-grasp ubiquitin-like fold, a common structure involved in protein-protein interactions. 71 matched cddid_all.tbl CDD cd01817 cd01817 340515 RBD1_RGS12_like Ras-binding domain (RBD) 1 of regulator of G protein signaling 12 (RGS12) and similar proteins. Regulator of G protein signaling (RGS) proteins belong to a large family of GTpase-accelerating proteins (GAPs) which act as key inhibitors of G-protein-mediated cell responses in eukaryotes. This RGS12-like subfamily is composed of RGS12 and RGS14, with multidomain architectures including a RGS domain, two tandem Ras-binding domains (RBDs), and a second Galpha interacting domain, the GoLoco motif. The RBD is structurally similar to the beta-grasp fold of ubiquitin, a common structure involved in protein-protein interactions. Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. 70 matched cddid_all.tbl CDD cd01819 cd01819 132836 Patatin_and_cPLA2 "Patatins and Phospholipases. Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. This family also includes the catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both ""closed lid"" and ""open lid"" forms." 155 matched cddid_all.tbl CDD cd01820 cd01820 238858 PAF_acetylesterase_like PAF_acetylhydrolase (PAF-AH)_like subfamily of SGNH-hydrolases. Platelet-activating factor (PAF) and PAF-AH are key players in inflammation and in atherosclerosis. PAF-AH is a calcium independent phospholipase A2 which exhibits strong substrate specificity towards PAF, hydrolyzing an acetyl ester at the sn-2 position. PAF-AH also degrades a family of oxidized PAF-like phospholipids with short sn-2 residues. In addition, PAF and PAF-AH are associated with neural migration and mammalian reproduction. 214 matched cddid_all.tbl CDD cd01821 cd01821 238859 Rhamnogalacturan_acetylesterase_like Rhamnogalacturan_acetylesterase_like subgroup of SGNH-hydrolases. Rhamnogalacturan acetylesterase removes acetyl esters from rhamnogalacturonan substrates, and renders them susceptible to degradation by rhamnogalacturonases. Rhamnogalacturonans are highly branched regions in pectic polysaccharides, consisting of repeating -(1,2)-L-Rha-(1,4)-D-GalUA disaccharide units, with many rhamnose residues substituted by neutral oligosaccharides such as arabinans, galactans and arabinogalactans. Extracellular enzymes participating in the degradation of plant cell wall polymers, such as Rhamnogalacturonan acetylesterase, would typically be found in saprophytic and plant pathogenic fungi and bacteria. 198 matched cddid_all.tbl CDD cd01822 cd01822 238860 Lysophospholipase_L1_like Lysophospholipase L1-like subgroup of SGNH-hydrolases. The best characterized member in this family is TesA, an E. coli periplasmic protein with thioesterase, esterase, arylesterase, protease and lysophospholipase activity. 177 matched cddid_all.tbl CDD cd01823 cd01823 238861 SEST_like SEST_like. A family of secreted SGNH-hydrolases similar to Streptomyces scabies esterase (SEST), a causal agent of the potato scab disease, which hydrolyzes a specific ester bond in suberin, a plant lipid. The tertiary fold of this enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles two of the three components of typical Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxylic acid. 259 matched cddid_all.tbl CDD cd01824 cd01824 238862 Phospholipase_B_like Phospholipase-B_like. This subgroup of the SGNH-family of lipolytic enzymes may have both esterase and phospholipase-A/lysophospholipase activity. It's members may be involved in the conversion of phosphatidylcholine to fatty acids and glycerophosphocholine, perhaps in the context of dietary lipid uptake. Members may be membrane proteins. The tertiary fold of the SGNH-hydrolases is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; Its active site closely resembles two of the three components of typical Ser-His-Asp(Glu) triad from other serine hydrolases. 288 matched cddid_all.tbl CDD cd01825 cd01825 238863 SGNH_hydrolase_peri1 SGNH_peri1; putative periplasmic member of the SGNH-family of hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. 189 matched cddid_all.tbl CDD cd01826 cd01826 238864 acyloxyacyl_hydrolase_like Acyloxyacyl-hydrolase like subfamily of the SGNH-hydrolase family. Acyloxyacyl-hydrolase is a leukocyte-secreted enzyme that deacetylates bacterial lipopolysaccharides. 305 matched cddid_all.tbl CDD cd01827 cd01827 238865 sialate_O-acetylesterase_like1 sialate O-acetylesterase_like family of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. 188 matched cddid_all.tbl CDD cd01828 cd01828 238866 sialate_O-acetylesterase_like2 sialate_O-acetylesterase_like subfamily of the SGNH-hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. 169 matched cddid_all.tbl CDD cd01829 cd01829 238867 SGNH_hydrolase_peri2 SGNH_peri2; putative periplasmic member of the SGNH-family of hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. 200 matched cddid_all.tbl CDD cd01830 cd01830 238868 XynE_like SGNH_hydrolase subfamily, similar to the putative arylesterase/acylhydrolase from the rumen anaerobe Prevotella bryantii XynE. The P. bryantii XynE gene is located in a xylanase gene cluster. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. 204 matched cddid_all.tbl CDD cd01831 cd01831 238869 Endoglucanase_E_like Endoglucanase E-like members of the SGNH hydrolase family; Endoglucanase E catalyzes the endohydrolysis of 1,4-beta-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans. 169 matched cddid_all.tbl CDD cd01832 cd01832 238870 SGNH_hydrolase_like_1 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid. Myxobacterial members of this subfamily have been reported to be involved in adventurous gliding motility. 185 matched cddid_all.tbl CDD cd01833 cd01833 238871 XynB_like SGNH_hydrolase subfamily, similar to Ruminococcus flavefaciens XynB. Most likely a secreted hydrolase with xylanase activity. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. 157 matched cddid_all.tbl CDD cd01834 cd01834 238872 SGNH_hydrolase_like_2 SGNH_hydrolase subfamily. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. 191 matched cddid_all.tbl CDD cd01835 cd01835 238873 SGNH_hydrolase_like_3 SGNH_hydrolase subfamily. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. 193 matched cddid_all.tbl CDD cd01836 cd01836 238874 FeeA_FeeB_like SGNH_hydrolase subfamily, FeeA, FeeB and similar esterases/lipases. FeeA and FeeB are part of a biosynthetic gene cluster and may participate in the biosynthesis of long-chain N-acyltyrosines by providing saturated and unsaturated fatty acids, which it turn are loaded onto the acyl carrier protein FeeL. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. 191 matched cddid_all.tbl CDD cd01837 cd01837 238875 SGNH_plant_lipase_like SGNH_plant_lipase_like, a plant specific subfamily of the SGNH-family of hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. 315 matched cddid_all.tbl CDD cd01838 cd01838 238876 Isoamyl_acetate_hydrolase_like Isoamyl-acetate hydrolyzing esterase-like proteins. SGNH_hydrolase subfamily similar to the Saccharomyces cerevisiae IAH1. IAH1 may be the major esterase that hydrolyses isoamyl acetate in sake mash. The SGNH-family of hydrolases is a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases 199 matched cddid_all.tbl CDD cd01839 cd01839 238877 SGNH_arylesterase_like SGNH_hydrolase subfamily, similar to arylesterase (7-aminocephalosporanic acid-deacetylating enzyme) of A. tumefaciens. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. 208 matched cddid_all.tbl CDD cd01840 cd01840 238878 SGNH_hydrolase_yrhL_like yrhL-like subfamily of SGNH-hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. Most members of this sub-family appear to co-occur with N-terminal acyltransferase domains. Might be involved in lipid metabolism. 150 matched cddid_all.tbl CDD cd01841 cd01841 238879 NnaC_like NnaC (CMP-NeuNAc synthetase) _like subfamily of SGNH_hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles two of the three components of typical Ser-His-Asp(Glu) triad from other serine hydrolases. E. coli NnaC appears to be involved in polysaccharide synthesis. 174 matched cddid_all.tbl CDD cd01842 cd01842 238880 SGNH_hydrolase_like_5 SGNH_hydrolase subfamily. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. 183 matched cddid_all.tbl CDD cd01844 cd01844 238881 SGNH_hydrolase_like_6 SGNH_hydrolase subfamily. SGNH hydrolases are a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. 177 matched cddid_all.tbl CDD cd01846 cd01846 238882 fatty_acyltransferase_like Fatty acyltransferase-like subfamily of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. Might catalyze fatty acid transfer between phosphatidylcholine and sterols. 270 matched cddid_all.tbl CDD cd01847 cd01847 238883 Triacylglycerol_lipase_like Triacylglycerol lipase-like subfamily of the SGNH hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases. Members of this subfamily might hydrolyze triacylglycerol into diacylglycerol and fatty acid anions. 281 matched cddid_all.tbl CDD cd01849 cd01849 206746 YlqF_related_GTPase Circularly permuted YlqF-related GTPases. These proteins are found in bacteria, eukaryotes, and archaea. They all exhibit a circular permutation of the GTPase signature motifs so that the order of the conserved G box motifs is G4-G5-G1-G2-G3, with G4 and G5 being permuted from the C-terminal region of proteins in the Ras superfamily to the N-terminus of YlqF-related GTPases. 146 matched cddid_all.tbl CDD cd01850 cd01850 206649 CDC_Septin CDC/Septin GTPase family. Septins are a conserved family of GTP-binding proteins associated with diverse processes in dividing and non-dividing cells. They were first discovered in the budding yeast S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and CDC12) required for normal bud morphology. Septins are also present in metazoan cells, where they are required for cytokinesis in some systems, and implicated in a variety of other processes involving organization of the cell cortex and exocytosis. In humans, 12 septin genes generate dozens of polypeptides, many of which comprise heterooligomeric complexes. Since septin mutants are commonly defective in cytokinesis and formation of the neck formation of the neck filaments/septin rings, septins have been considered to be the primary constituents of the neck filaments. Septins belong to the GTPase superfamily for their conserved GTPase motifs and enzymatic activities. 275 matched cddid_all.tbl CDD cd01851 cd01851 206650 GBP Guanylate-binding protein (GBP) family (N-terminal domain). Guanylate-binding protein (GBP), N-terminal domain. Guanylate-binding proteins (GBPs) define a group of proteins that are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. Furthermore, two unique regions around the base and the phosphate-binding areas, the guanine and the phosphate caps, respectively, give the nucleotide-binding site a unique appearance not found in the canonical GTP-binding proteins. The phosphate cap, which constitutes the region analogous to switch I, completely shields the phosphate-binding site from solvent such that a potential GTPase-activating protein (GAP) cannot approach. 224 matched cddid_all.tbl CDD cd01852 cd01852 206651 AIG1 AvrRpt2-Induced Gene 1 (AIG1). This group represents Arabidoposis protein AIG1 (avrRpt2-induced gene 1) that appears to be involved in plant resistance to bacteria. The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 exhibits RPS2- and avrRpt1-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2. This subfamily also includes IAN-4 protein, which has GTP-binding activity and shares sequence homology with a novel family of putative GTP-binding proteins: the immuno-associated nucleotide (IAN) family. The evolutionary conservation of the IAN family provides a unique example of a plant pathogen response gene conserved in animals. The IAN/IMAP subfamily has been proposed to regulate apoptosis in vertebrates and angiosperm plants, particularly in relation to cancer, diabetes, and infections. The human IAN genes were renamed GIMAP (GTPase of the immunity associated proteins). 201 matched cddid_all.tbl CDD cd01853 cd01853 206652 Toc34_like Translocon at the Outer-envelope membrane of Chloroplasts 34-like (Toc34-like). The Toc34-like (Translocon at the Outer-envelope membrane of Chloroplasts) family contains several Toc proteins, including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125, and Toc90. The Toc complex at the outer envelope membrane of chloroplasts is a molecular machine of ~500 kDa that contains a single Toc159 protein, four Toc75 molecules, and four or five copies of Toc34. Toc64 and Toc12 are associated with the translocon, but do not appear to be part of the core complex. The Toc translocon initiates the import of nuclear-encoded preproteins from the cytosol into the organelle. Toc34 and Toc159 are both GTPases, while Toc75 is a beta-barrel integral membrane protein. Toc159 is equally distributed between a soluble cytoplasmic form and a membrane-inserted form, suggesting that assembly of the Toc complex is dynamic. Toc34 and Toc75 act sequentially to mediate docking and insertion of Toc159 resulting in assembly of the functional translocon. 248 matched cddid_all.tbl CDD cd01854 cd01854 206747 YjeQ_EngC Ribosomal interacting GTPase YjeQ/EngC, a circularly permuted subfamily of the Ras GTPases. YjeQ (YloQ in Bacillus subtilis) is a ribosomal small subunit-dependent GTPase; hence also known as RsgA. YjeQ is a late-stage ribosomal biogenesis factor involved in the 30S subunit maturation, and it represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. 211 matched cddid_all.tbl CDD cd01855 cd01855 206748 YqeH Circularly permuted YqeH GTPase. YqeH is an essential GTP-binding protein. Depletion of YqeH induces an excess initiation of DNA replication, suggesting that it negatively controls initiation of chromosome replication. The YqeH subfamily is common in eukaryotes and sporadically present in bacteria with probable acquisition by plants from chloroplasts. Proteins of the YqeH family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. 191 matched cddid_all.tbl CDD cd01856 cd01856 206749 YlqF Circularly permuted YlqF GTPase. Proteins of the YlqF family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. The YlqF subfamily is represented in all eukaryotes as well as a phylogenetically diverse array of bacteria (including gram-positive bacteria, proteobacteria, Synechocystis, Borrelia, and Thermotoga). 171 matched cddid_all.tbl CDD cd01857 cd01857 206750 HSR1_MMR1 A circularly permuted subfamily of the Ras GTPases. Human HSR1 is localized to the human MHC class I region and is highly homologous to a putative GTP-binding protein, MMR1 from mouse. These proteins represent a new subfamily of GTP-binding proteins that has only eukaryote members. This subfamily shows a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with sequence NKXD) are relocated to the N-terminus. 140 matched cddid_all.tbl CDD cd01858 cd01858 206751 NGP_1 A novel nucleolar GTP-binding protein, circularly permuted subfamily of the Ras GTPases. Autoantigen NGP-1 (Nucleolar G-protein gene 1) has been shown to localize in the nucleolus and nucleolar organizers in all cell types analyzed, which is indicative of a function in ribosomal assembly. NGP-1 and its homologs show a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with NKXD motif) are relocated to the N terminus. 157 matched cddid_all.tbl CDD cd01859 cd01859 206752 MJ1464 An uncharacterized, circularly permuted subfamily of the Ras GTPases. This family represents archaeal GTPase typified by the protein MJ1464 from Methanococcus jannaschii. The members of this family show a circular permutation of the GTPase signature motifs so that C-terminal strands 5, 6, and 7 (strands 6 contain the NKxD motif) are relocated to the N terminus. 157 matched cddid_all.tbl CDD cd01860 cd01860 206653 Rab5_related Rab-related GTPase family includes Rab5 and Rab22; regulates early endosome fusion. The Rab5-related subfamily includes Rab5 and Rab22 of mammals, Ypt51/Ypt52/Ypt53 of yeast, and RabF of plants. The members of this subfamily are involved in endocytosis and endocytic-sorting pathways. In mammals, Rab5 GTPases localize to early endosomes and regulate fusion of clathrin-coated vesicles to early endosomes and fusion between early endosomes. In yeast, Ypt51p family members similarly regulate membrane trafficking through prevacuolar compartments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 163 matched cddid_all.tbl CDD cd01861 cd01861 206654 Rab6 Rab GTPase family 6 (Rab6). Rab6 is involved in microtubule-dependent transport pathways through the Golgi and from endosomes to the Golgi. Rab6A of mammals is implicated in retrograde transport through the Golgi stack, and is also required for a slow, COPI-independent, retrograde transport pathway from the Golgi to the endoplasmic reticulum (ER). This pathway may allow Golgi residents to be recycled through the ER for scrutiny by ER quality-control systems. Yeast Ypt6p, the homolog of the mammalian Rab6 GTPase, is not essential for cell viability. Ypt6p acts in endosome-to-Golgi, in intra-Golgi retrograde transport, and possibly also in Golgi-to-ER trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 161 matched cddid_all.tbl CDD cd01862 cd01862 206655 Rab7 Rab GTPase family 7 (Rab7). Rab7 subfamily. Rab7 is a small Rab GTPase that regulates vesicular traffic from early to late endosomal stages of the endocytic pathway. The yeast Ypt7 and mammalian Rab7 are both involved in transport to the vacuole/lysosome, whereas Ypt7 is also required for homotypic vacuole fusion. Mammalian Rab7 is an essential participant in the autophagic pathway for sequestration and targeting of cytoplasmic components to the lytic compartment. Mammalian Rab7 is also proposed to function as a tumor suppressor. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 172 matched cddid_all.tbl CDD cd01863 cd01863 206656 Rab18 Rab GTPase family 18 (Rab18). Rab18 subfamily. Mammalian Rab18 is implicated in endocytic transport and is expressed most highly in polarized epithelial cells. However, trypanosomal Rab, TbRAB18, is upregulated in the BSF (Blood Stream Form) stage and localized predominantly to elements of the Golgi complex. In human and mouse cells, Rab18 has been identified in lipid droplets, organelles that store neutral lipids. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 161 matched cddid_all.tbl CDD cd01864 cd01864 133267 Rab19 Rab GTPase family 19 (Rab19). Rab19 subfamily. Rab19 proteins are associated with Golgi stacks. Similarity analysis indicated that Rab41 is closely related to Rab19. However, the function of these Rabs is not yet characterized. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 165 matched cddid_all.tbl CDD cd01865 cd01865 206657 Rab3 Rab GTPase family 3 contains Rab3A, Rab3B, Rab3C and Rab3D. The Rab3 subfamily contains Rab3A, Rab3B, Rab3C, and Rab3D. All four isoforms were found in mouse brain and endocrine tissues, with varying levels of expression. Rab3A, Rab3B, and Rab3C localized to synaptic and secretory vesicles; Rab3D was expressed at high levels only in adipose tissue, exocrine glands, and the endocrine pituitary, where it is localized to cytoplasmic secretory granules. Rab3 appears to control Ca2+-regulated exocytosis. The appropriate GDP/GTP exchange cycle of Rab3A is required for Ca2+-regulated exocytosis to occur, and interaction of the GTP-bound form of Rab3A with effector molecule(s) is widely believed to be essential for this process. Functionally, most studies point toward a role for Rab3 in the secretion of hormones and neurotransmitters. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 165 matched cddid_all.tbl CDD cd01866 cd01866 206658 Rab2 Rab GTPase family 2 (Rab2). Rab2 is localized on cis-Golgi membranes and interacts with Golgi matrix proteins. Rab2 is also implicated in the maturation of vesicular tubular clusters (VTCs), which are microtubule-associated intermediates in transport between the ER and Golgi apparatus. In plants, Rab2 regulates vesicle trafficking between the ER and the Golgi bodies and is important to pollen tube growth. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 168 matched cddid_all.tbl CDD cd01867 cd01867 206659 Rab8_Rab10_Rab13_like Rab GTPase families 8, 10, 13 (Rab8, Rab10, Rab13). Rab8/Sec4/Ypt2 are known or suspected to be involved in post-Golgi transport to the plasma membrane. It is likely that these Rabs have functions that are specific to the mammalian lineage and have no orthologs in plants. Rab8 modulates polarized membrane transport through reorganization of actin and microtubules, induces the formation of new surface extensions, and has an important role in directed membrane transport to cell surfaces. The Ypt2 gene of the fission yeast Schizosaccharomyces pombe encodes a member of the Ypt/Rab family of small GTP-binding proteins, related in sequence to Sec4p of Saccharomyces cerevisiae but closer to mammalian Rab8. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 167 matched cddid_all.tbl CDD cd01868 cd01868 206660 Rab11_like Rab GTPase family 11 (Rab11)-like includes Rab11a, Rab11b, and Rab25. Rab11a, Rab11b, and Rab25 are closely related, evolutionary conserved Rab proteins that are differentially expressed. Rab11a is ubiquitously synthesized, Rab11b is enriched in brain and heart and Rab25 is only found in epithelia. Rab11/25 proteins seem to regulate recycling pathways from endosomes to the plasma membrane and to the trans-Golgi network. Furthermore, Rab11a is thought to function in the histamine-induced fusion of tubulovesicles containing H+, K+ ATPase with the plasma membrane in gastric parietal cells and in insulin-stimulated insertion of GLUT4 in the plasma membrane of cardiomyocytes. Overexpression of Rab25 has recently been observed in ovarian cancer and breast cancer, and has been correlated with worsened outcomes in both diseases. In addition, Rab25 overexpression has also been observed in prostate cancer, transitional cell carcinoma of the bladder, and invasive breast tumor cells. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 165 matched cddid_all.tbl CDD cd01869 cd01869 206661 Rab1_Ypt1 Rab GTPase family 1 includes the yeast homolog Ypt1. Rab1/Ypt1 subfamily. Rab1 is found in every eukaryote and is a key regulatory component for the transport of vesicles from the ER to the Golgi apparatus. Studies on mutations of Ypt1, the yeast homolog of Rab1, showed that this protein is necessary for the budding of vesicles of the ER as well as for their transport to, and fusion with, the Golgi apparatus. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 166 matched cddid_all.tbl CDD cd01870 cd01870 206662 RhoA_like Ras homology family A (RhoA)-like includes RhoA, RhoB and RhoC. The RhoA subfamily consists of RhoA, RhoB, and RhoC. RhoA promotes the formation of stress fibers and focal adhesions, regulating cell shape, attachment, and motility. RhoA can bind to multiple effector proteins, thereby triggering different downstream responses. In many cell types, RhoA mediates local assembly of the contractile ring, which is necessary for cytokinesis. RhoA is vital for muscle contraction; in vascular smooth muscle cells, RhoA plays a key role in cell contraction, differentiation, migration, and proliferation. RhoA activities appear to be elaborately regulated in a time- and space-dependent manner to control cytoskeletal changes. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. RhoA and RhoC are observed only in geranylgeranylated forms; however, RhoB can be present in palmitoylated, farnesylated, and geranylgeranylated forms. RhoA and RhoC are highly relevant for tumor progression and invasiveness; however, RhoB has recently been suggested to be a tumor suppressor. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 175 matched cddid_all.tbl CDD cd01871 cd01871 206663 Rac1_like Ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rac1)-like consists of Rac1, Rac2 and Rac3. The Rac1-like subfamily consists of Rac1, Rac2, and Rac3 proteins, plus the splice variant Rac1b that contains a 19-residue insertion near switch II relative to Rac1. While Rac1 is ubiquitously expressed, Rac2 and Rac3 are largely restricted to hematopoietic and neural tissues respectively. Rac1 stimulates the formation of actin lamellipodia and membrane ruffles. It also plays a role in cell-matrix adhesion and cell anoikis. In intestinal epithelial cells, Rac1 is an important regulator of migration and mediates apoptosis. Rac1 is also essential for RhoA-regulated actin stress fiber and focal adhesion complex formation. In leukocytes, Rac1 and Rac2 have distinct roles in regulating cell morphology, migration, and invasion, but are not essential for macrophage migration or chemotaxis. Rac3 has biochemical properties that are closely related to Rac1, such as effector interaction, nucleotide binding, and hydrolysis; Rac2 has a slower nucleotide association and is more efficiently activated by the RacGEF Tiam1. Both Rac1 and Rac3 have been implicated in the regulation of cell migration and invasion in human metastatic breast cancer. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 174 matched cddid_all.tbl CDD cd01873 cd01873 133275 RhoBTB RhoBTB protein is an atypical member of the Rho family of small GTPases. Members of the RhoBTB subfamily of Rho GTPases are present in vertebrates, Drosophila, and Dictyostelium. RhoBTB proteins are characterized by a modular organization, consisting of a GTPase domain, a proline rich region, a tandem of two BTB (Broad-Complex, Tramtrack, and Bric a brac) domains, and a C-terminal region of unknown function. RhoBTB proteins may act as docking points for multiple components participating in signal transduction cascades. RhoBTB genes appeared upregulated in some cancer cell lines, suggesting a participation of RhoBTB proteins in the pathogenesis of particular tumors. Note that the Dictyostelium RacA GTPase domain is more closely related to Rac proteins than to RhoBTB proteins, where RacA actually belongs. Thus, the Dictyostelium RacA is not included here. Most Rho proteins contain a lipid modification site at the C-terminus; however, RhoBTB is one of few Rho subfamilies that lack this feature. 195 matched cddid_all.tbl CDD cd01874 cd01874 206664 Cdc42 cell division cycle 42 (Cdc42) is a small GTPase of the Rho family. Cdc42 is an essential GTPase that belongs to the Rho family of Ras-like GTPases. These proteins act as molecular switches by responding to exogenous and/or endogenous signals and relaying those signals to activate downstream components of a biological pathway. Cdc42 transduces signals to the actin cytoskeleton to initiate and maintain polarized growth and to mitogen-activated protein morphogenesis. In the budding yeast Saccharomyces cerevisiae, Cdc42 plays an important role in multiple actin-dependent morphogenetic events such as bud emergence, mating-projection formation, and pseudohyphal growth. In mammalian cells, Cdc42 regulates a variety of actin-dependent events and induces the JNK/SAPK protein kinase cascade, which leads to the activation of transcription factors within the nucleus. Cdc42 mediates these processes through interactions with a myriad of downstream effectors, whose number and regulation we are just starting to understand. In addition, Cdc42 has been implicated in a number of human diseases through interactions with its regulators and downstream effectors. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 175 matched cddid_all.tbl CDD cd01875 cd01875 133277 RhoG Ras homolog family, member G (RhoG) of small guanosine triphosphatases (GTPases). RhoG is a GTPase with high sequence similarity to members of the Rac subfamily, including the regions involved in effector recognition and binding. However, RhoG does not bind to known Rac1 and Cdc42 effectors, including proteins containing a Cdc42/Rac interacting binding (CRIB) motif. Instead, RhoG interacts directly with Elmo, an upstream regulator of Rac1, in a GTP-dependent manner and forms a ternary complex with Dock180 to induce activation of Rac1. The RhoG-Elmo-Dock180 pathway is required for activation of Rac1 and cell spreading mediated by integrin, as well as for neurite outgrowth induced by nerve growth factor. Thus RhoG activates Rac1 through Elmo and Dock180 to control cell morphology. RhoG has also been shown to play a role in caveolar trafficking and has a novel role in signaling the neutrophil respiratory burst stimulated by G protein-coupled receptor (GPCR) agonists. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. 191 matched cddid_all.tbl CDD cd01876 cd01876 206665 YihA_EngB YihA (EngB) GTPase family. The YihA (EngB) subfamily of GTPases is typified by the E. coli YihA, an essential protein involved in cell division control. YihA and its orthologs are small proteins that typically contain less than 200 amino acid residues and consists of the GTPase domain only (some of the eukaryotic homologs contain an N-terminal extension of about 120 residues that might be involved in organellar targeting). Homologs of yihA are found in most Gram-positive and Gram-negative pathogenic bacteria, with the exception of Mycobacterium tuberculosis. The broad-spectrum nature of YihA and its essentiality for cell viability in bacteria make it an attractive antibacterial target. 170 matched cddid_all.tbl CDD cd01878 cd01878 206666 HflX HflX GTPase family. HflX subfamily. A distinct conserved domain with a glycine-rich segment N-terminal of the GTPase domain characterizes the HflX subfamily. The E. coli HflX has been implicated in the control of the lambda cII repressor proteolysis, but the actual biological functions of these GTPases remain unclear. HflX is widespread, but not universally represented in all three superkingdoms. 204 matched cddid_all.tbl CDD cd01879 cd01879 206667 FeoB Ferrous iron transport protein B (FeoB) family. Ferrous iron transport protein B (FeoB) subfamily. E. coli has an iron(II) transport system, known as feo, which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent. 159 matched cddid_all.tbl CDD cd01881 cd01881 206668 Obg_like Obg-like family of GTPases consist of five subfamilies: Obg, DRG, YyaF/YchF, Ygr210, and NOG1. The Obg-like subfamily consists of five well-delimited, ancient subfamilies, namely Obg, DRG, YyaF/YchF, Ygr210, and NOG1. Four of these groups (Obg, DRG, YyaF/YchF, and Ygr210) are characterized by a distinct glycine-rich motif immediately following the Walker B motif (G3 box). Obg/CgtA is an essential gene that is involved in the initiation of sporulation and DNA replication in the bacteria Caulobacter and Bacillus, but its exact molecular role is unknown. Furthermore, several OBG family members possess a C-terminal RNA-binding domain, the TGS domain, which is also present in threonyl-tRNA synthetase and in bacterial guanosine polyphosphatase SpoT. Nog1 is a nucleolar protein that might function in ribosome assembly. The DRG and Nog1 subfamilies are ubiquitous in archaea and eukaryotes, the Ygr210 subfamily is present in archaea and fungi, and the Obg and YyaF/YchF subfamilies are ubiquitous in bacteria and eukaryotes. The Obg/Nog1 and DRG subfamilies appear to form one major branch of the Obg family and the Ygr210 and YchF subfamilies form another branch. No GEFs, GAPs, or GDIs for Obg have been identified. 167 matched cddid_all.tbl CDD cd01882 cd01882 206669 BMS1 Bms1, an essential GTPase, promotes assembly of preribosomal RNA processing complexes. Bms1 is an essential, evolutionarily conserved, nucleolar protein. Its depletion interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits. Bms1, the putative endonuclease Rc11, and the essential U3 small nucleolar RNA form a stable subcomplex that is believed to control an early step in the formation of the 40S subumit. The C-terminal domain of Bms1 contains a GTPase-activating protein (GAP) that functions intramolecularly. It is believed that Rc11 activates Bms1 by acting as a guanine-nucleotide exchange factor (GEF) to promote GDP/GTP exchange, and that activated (GTP-bound) Bms1 delivers Rc11 to the preribosomes. 231 matched cddid_all.tbl CDD cd01883 cd01883 206670 EF1_alpha Elongation Factor 1-alpha (EF1-alpha) protein family. EF1 is responsible for the GTP-dependent binding of aminoacyl-tRNAs to the ribosomes. EF1 is composed of four subunits: the alpha chain which binds GTP and aminoacyl-tRNAs, the gamma chain that probably plays a role in anchoring the complex to other cellular components and the beta and delta (or beta') chains. This subfamily is the alpha subunit, and represents the counterpart of bacterial EF-Tu for the archaea (aEF1-alpha) and eukaryotes (eEF1-alpha). eEF1-alpha interacts with the actin of the eukaryotic cytoskeleton and may thereby play a role in cellular transformation and apoptosis. EF-Tu can have no such role in bacteria. In humans, the isoform eEF1A2 is overexpressed in 2/3 of breast cancers and has been identified as a putative oncogene. This subfamily also includes Hbs1, a G protein known to be important for efficient growth and protein synthesis under conditions of limiting translation initiation in yeast, and to associate with Dom34. It has been speculated that yeast Hbs1 and Dom34 proteins may function as part of a complex with a role in gene expression. 219 matched cddid_all.tbl CDD cd01884 cd01884 206671 EF_Tu Elongation Factor Tu (EF-Tu) GTP-binding proteins. EF-Tu subfamily. This subfamily includes orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts. It is one of several GTP-binding translation factors found in the larger family of GTP-binding elongation factors. The eukaryotic counterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this family. EF-Tu is one of the most abundant proteins in bacteria, as well as, one of the most highly conserved, and in a number of species the gene is duplicated with identical function. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors. Transfer RNA is carried to the ribosome in these complexes for protein translation. 195 matched cddid_all.tbl CDD cd01885 cd01885 206672 EF2 Elongation Factor 2 (EF2) in archaea and eukarya. Translocation requires hydrolysis of a molecule of GTP and is mediated by EF-G in bacteria and by eEF2 in eukaryotes. The eukaryotic elongation factor eEF2 is a GTPase involved in the translocation of the peptidyl-tRNA from the A site to the P site on the ribosome. The 95-kDa protein is highly conserved, with 60% amino acid sequence identity between the human and yeast proteins. Two major mechanisms are known to regulate protein elongation and both involve eEF2. First, eEF2 can be modulated by reversible phosphorylation. Increased levels of phosphorylated eEF2 reduce elongation rates presumably because phosphorylated eEF2 fails to bind the ribosomes. Treatment of mammalian cells with agents that raise the cytoplasmic Ca2+ and cAMP levels reduce elongation rates by activating the kinase responsible for phosphorylating eEF2. In contrast, treatment of cells with insulin increases elongation rates by promoting eEF2 dephosphorylation. Second, the protein can be post-translationally modified by ADP-ribosylation. Various bacterial toxins perform this reaction after modification of a specific histidine residue to diphthamide, but there is evidence for endogenous ADP ribosylase activity. Similar to the bacterial toxins, it is presumed that modification by the endogenous enzyme also inhibits eEF2 activity. 218 matched cddid_all.tbl CDD cd01886 cd01886 206673 EF-G Elongation factor G (EF-G) family involved in both the elongation and ribosome recycling phases of protein synthesis. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group contains both eukaryotic and bacterial members. 270 matched cddid_all.tbl CDD cd01887 cd01887 206674 IF2_eIF5B Initiation Factor 2 (IF2)/ eukaryotic Initiation Factor 5B (eIF5B) family. IF2/eIF5B contribute to ribosomal subunit joining and function as GTPases that are maximally activated by the presence of both ribosomal subunits. As seen in other GTPases, IF2/IF5B undergoes conformational changes between its GTP- and GDP-bound states. Eukaryotic IF2/eIF5Bs possess three characteristic segments, including a divergent N-terminal region followed by conserved central and C-terminal segments. This core region is conserved among all known eukaryotic and archaeal IF2/eIF5Bs and eubacterial IF2s. 169 matched cddid_all.tbl CDD cd01888 cd01888 206675 eIF2_gamma Gamma subunit of initiation factor 2 (eIF2 gamma). eIF2 is a heterotrimeric translation initiation factor that consists of alpha, beta, and gamma subunits. The GTP-bound gamma subunit also binds initiator methionyl-tRNA and delivers it to the 40S ribosomal subunit. Following hydrolysis of GTP to GDP, eIF2:GDP is released from the ribosome. The gamma subunit has no intrinsic GTPase activity, but is stimulated by the GTPase activating protein (GAP) eIF5, and GDP/GTP exchange is stimulated by the guanine nucleotide exchange factor (GEF) eIF2B. eIF2B is a heteropentamer, and the epsilon chain binds eIF2. Both eIF5 and eIF2B-epsilon are known to bind strongly to eIF2-beta, but have also been shown to bind directly to eIF2-gamma. It is possible that eIF2-beta serves simply as a high-affinity docking site for eIF5 and eIF2B-epsilon, or that eIF2-beta serves a regulatory role. eIF2-gamma is found only in eukaryotes and archaea. It is closely related to SelB, the selenocysteine-specific elongation factor from eubacteria. The translational factor components of the ternary complex, IF2 in eubacteria and eIF2 in eukaryotes are not the same protein (despite their unfortunately similar names). Both factors are GTPases; however, eubacterial IF-2 is a single polypeptide, while eIF2 is heterotrimeric. eIF2-gamma is a member of the same family as eubacterial IF2, but the two proteins are only distantly related. This family includes translation initiation, elongation, and release factors. 197 matched cddid_all.tbl CDD cd01889 cd01889 206676 SelB_euk SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome. SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryotes, they do share a common feature. Unlike in E. coli, these SECIS elements are located in the 3' UTRs. This group contains eukaryotic SelBs and some from archaea. 192 matched cddid_all.tbl CDD cd01890 cd01890 206677 LepA LepA also known as Elongation Factor 4 (EF4). LepA (also known as elongation factor 4, EF4) belongs to the GTPase family and exhibits significant homology to the translation factors EF-G and EF-Tu, indicating its possible involvement in translation and association with the ribosome. LepA is ubiquitous in bacteria and eukaryota (e.g. yeast GUF1p), but is missing from archaea. This pattern of phyletic distribution suggests that LepA evolved through a duplication of the EF-G gene in bacteria, followed by early transfer into the eukaryotic lineage, most likely from the promitochondrial endosymbiont. Yeast GUF1p is not essential and mutant cells did not reveal any marked phenotype. 179 matched cddid_all.tbl CDD cd01891 cd01891 206678 TypA_BipA Tyrosine phosphorylated protein A (TypA)/BipA family belongs to ribosome-binding GTPases. BipA is a protein belonging to the ribosome-binding family of GTPases and is widely distributed in bacteria and plants. BipA was originally described as a protein that is induced in Salmonella typhimurium after exposure to bactericidal/permeability-inducing protein (a cationic antimicrobial protein produced by neutrophils), and has since been identified in E. coli as well. The properties thus far described for BipA are related to its role in the process of pathogenesis by enteropathogenic E. coli. It appears to be involved in the regulation of several processes important for infection, including rearrangements of the cytoskeleton of the host, bacterial resistance to host defense peptides, flagellum-mediated cell motility, and expression of K5 capsular genes. It has been proposed that BipA may utilize a novel mechanism to regulate the expression of target genes. In addition, BipA from enteropathogenic E. coli has been shown to be phosphorylated on a tyrosine residue, while BipA from Salmonella and from E. coli K12 strains is not phosphorylated under the conditions assayed. The phosphorylation apparently modifies the rate of nucleotide hydrolysis, with the phosphorylated form showing greatly increased GTPase activity. 194 matched cddid_all.tbl CDD cd01892 cd01892 206679 Miro2 Mitochondrial Rho family 2 (Miro2), C-terminal. Miro2 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the putative GTPase domain in the C terminus of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature. 180 matched cddid_all.tbl CDD cd01893 cd01893 206680 Miro1 Mitochondrial Rho family 1 (Miro1), N-terminal. Miro1 subfamily. Miro (mitochondrial Rho) proteins have tandem GTP-binding domains separated by a linker region containing putative calcium-binding EF hand motifs. Genes encoding Miro-like proteins were found in several eukaryotic organisms. This CD represents the N-terminal GTPase domain of Miro proteins. These atypical Rho GTPases have roles in mitochondrial homeostasis and apoptosis. Most Rho proteins contain a lipid modification site at the C-terminus; however, Miro is one of few Rho subfamilies that lack this feature. 168 matched cddid_all.tbl CDD cd01894 cd01894 206681 EngA1 EngA1 GTPase contains the first domain of EngA. This EngA1 subfamily CD represents the first GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability. 157 matched cddid_all.tbl CDD cd01895 cd01895 206682 EngA2 EngA2 GTPase contains the second domain of EngA. This EngA2 subfamily CD represents the second GTPase domain of EngA and its orthologs, which are composed of two adjacent GTPase domains. Since the sequences of the two domains are more similar to each other than to other GTPases, it is likely that an ancient gene duplication, rather than a fusion of evolutionarily distinct GTPases, gave rise to this family. Although the exact function of these proteins has not been elucidated, studies have revealed that the E. coli EngA homolog, Der, and Neisseria gonorrhoeae EngA are essential for cell viability. A recent report suggests that E. coli Der functions in ribosome assembly and stability. 174 matched cddid_all.tbl CDD cd01896 cd01896 206683 DRG Developmentally Regulated GTP-binding protein (DRG). The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins. GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. In view of their widespread expression in various tissues and high conservation among distantly related species in eukaryotes and archaea, DRG proteins may regulate fundamental cellular processes. It is proposed that the DRG subfamily proteins play their physiological roles through RNA binding. 233 matched cddid_all.tbl CDD cd01897 cd01897 206684 NOG Nucleolar GTP-binding protein (NOG). NOG1 is a nucleolar GTP-binding protein present in eukaryotes ranging from trypanosomes to humans. NOG1 is functionally linked to ribosome biogenesis and found in association with the nuclear pore complexes and identified in many preribosomal complexes. Thus, defects in NOG1 can lead to defects in 60S biogenesis. The S. cerevisiae NOG1 gene is essential for cell viability, and mutations in the predicted G motifs abrogate function. It is a member of the ODN family of GTP-binding proteins that also includes the bacterial Obg and DRG proteins. 167 matched cddid_all.tbl CDD cd01898 cd01898 206685 Obg Obg GTPase. The Obg nucleotide binding protein subfamily has been implicated in stress response, chromosome partitioning, replication initiation, mycelium development, and sporulation. Obg proteins are among a large group of GTP binding proteins conserved from bacteria to humans. The E. coli homolog, ObgE is believed to function in ribosomal biogenesis. Members of the subfamily contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain. 170 matched cddid_all.tbl CDD cd01899 cd01899 206686 Ygr210 Ygr210 GTPase. Ygr210 is a member of Obg-like family and present in archaea and fungi. They are characterized by a distinct glycine-rich motif immediately following the Walker B motif. The Ygr210 and YyaF/YchF subfamilies appear to form one major branch of the Obg-like family. Among eukaryotes, the Ygr210 subfamily is represented only in fungi. These fungal proteins form a tight cluster with their archaeal orthologs, which suggests the possibility of horizontal transfer from archaea to fungi. 318 matched cddid_all.tbl CDD cd01900 cd01900 206687 YchF YchF GTPase. YchF is a member of the Obg family, which includes four other subfamilies of GTPases: Obg, DRG, Ygr210, and NOG1. Obg is an essential gene that is involved in DNA replication in C. crescentus and Streptomyces griseus and is associated with the ribosome. Several members of the family, including YchF, possess the TGS domain related to the RNA-binding proteins. Experimental data and genomic analysis suggest that YchF may be part of a nucleoprotein complex and may function as a GTP-dependent translational factor. 274 matched cddid_all.tbl CDD cd01901 cd01901 238884 Ntn_hydrolase The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either the nucleophilic hydroxyl in a Ser or Thr residue or the nucleophilic thiol in a Cys residue. The position of the N-terminal nucleophile in the active site and the mechanism of catalysis are conserved in this family, despite considerable variation in the protein sequences. 164 matched cddid_all.tbl CDD cd01902 cd01902 238885 Ntn_CGH Choloylglycine hydrolase (CGH) is a bile salt-modifying enzyme that hydrolyzes non-peptide carbon-nitrogen bonds in choloylglycine and choloyltaurine, both of which are present in bile. CGH is present in a number of probiotic microbial organisms that inhabit the gut. CGH has an N-terminal nucleophilic cysteine, as do other members of the Ntn hydrolase family to which CGH belongs. 291 matched cddid_all.tbl CDD cd01903 cd01903 238886 Ntn_AC_NAAA "AC_NAAA This conserved domain includes two closely related proteins, acid ceramidase (AC, also known as N-acylsphingosine amidohydrolase), and N-acylethanolamine-hydrolyzing acid amidase (NAAA). AC catalyzes the hydrolysis of ceramide to sphingosine and fatty acid. Ceramide is required for the biosynthesis of most sphingolipids and plays an important role in many signal transduction pathways by inducing apoptosis and/or arresting cell growth. An inherited deficiency of AC activity leads to the lysosomal storage disorder known as Farber disease. AC is considered a ""rheostat"" important for maintaining the proper intracellular levels of these lipids since hydrolysis of ceramide is the only source of sphingosine in cells. NAAA is a eukaryotic glycoprotein that hydrolyzes bioactive N-acylethanolamines, including anandamide (an endocannabinoid) and N-palmitoylethanolamine (an anti-inflammatory and neuroprotective substance), to fatty acids and ethanolamine at acidic pH. NAAA shows structural and functional similarity to acid ceramidase, but lacks the ceramide-hydrolyzing activity of AC." 231 matched cddid_all.tbl CDD cd01906 cd01906 238887 proteasome_protease_HslV proteasome_protease_HslV. This group contains the eukaryotic proteosome alpha and beta subunits and the prokaryotic protease hslV subunit. Proteasomes are large multimeric self-compartmentalizing proteases, involved in the clearance of misfolded proteins, the breakdown of regulatory proteins, and the processing of proteins such as the preparation of peptides for immune presentation. Two main proteasomal types are distinguished by their different tertiary structures: the eukaryotic/archeal 20S proteasome and the prokaryotic proteasome-like heat shock protein encoded by heat shock locus V, hslV. The proteasome core particle is a highly conserved cylindrical structure made up of non-identical subunits that have their active sites on the inner walls of a large central cavity. The proteasome subunits of bacteria, archaea, and eukaryotes all share a conserved Ntn (N terminal nucleophile) hydrolase fold and a catalytic mechanism involving an N-terminal nucleophilic threonine that is exposed by post-translational processing of an inactive propeptide. 182 matched cddid_all.tbl CDD cd01907 cd01907 238888 GlxB Glutamine amidotransferases class-II (Gn-AT)_GlxB-type. GlxB is a glutamine amidotransferase-like protein of unknown function found in bacteria and archaea. GlxB has a structural fold similar to that of other class II glutamine amidotransferases including glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), beta lactam synthetase (beta-LS) and glutamate synthase (GltS). The GlxB fold is also somewhat similar to the Ntn (N-terminal nucleophile) hydrolase fold of the proteasomal alpha and beta subunits. 249 matched cddid_all.tbl CDD cd01908 cd01908 238889 YafJ Glutamine amidotransferases class-II (Gn-AT)_YafJ-type. YafJ is a glutamine amidotransferase-like protein of unknown function found in prokaryotes, eukaryotes and archaea. YafJ has a conserved structural fold similar to those of other class II glutamine amidotransferases including glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), beta lactam synthetase (beta-LS) and glutamate synthase (GltS). The YafJ fold is also somewhat similar to the Ntn (N-terminal nucleophile) hydrolase fold of the proteasomal alpha and beta subunits. 257 matched cddid_all.tbl CDD cd01909 cd01909 238890 betaLS_CarA_N Glutamine amidotransferases class-II (GATase) asparagine synthase_betaLS-type. Carbapenam synthetase (CarA) is an ATP/Mg2+-dependent enzyme that catalyzes the formation of the beta-lactam ring in (5R)-carbapenem-3-carboxylic acid biosynthesis. CarA is homologous to beta-lactam synthetase (beta-LS), which is involved in the biosynthesis of clavulanic acid, a clinically important beta-lactamase inhibitor. CarA and beta-LS each have two distinct domains, an N-terminal Ntn hydrolase domain and a C-terminal synthetase domain, a domain architecture similar to that of the class-B asparagine synthetases (AS-B's). The N-terminal domain of these enzymes hydrolyzes glutamine to glutamate and ammonia. CarA forms a homotetramer while betaLS forms a heterodimer. The N-terminal folds of CarA and beta-LS are similar to those of other class II glutamine amidotransferases including lucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), and glutamate synthase (GltS). This fold is also somwhat similar to the Ntn (N-terminal nucleophile) hydrolase fold of the proteasomal alpha and beta subunits. 199 matched cddid_all.tbl CDD cd01910 cd01910 238891 Wali7 This domain is present in Wali7, a protein of unknown function, expressed in wheat and induced by aluminum. Wali7 has a single domain similar to the glutamine amidotransferase domain of glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), beta lactam synthetase (beta-LS) and glutamate synthase (GltS). The Wali7 domain is also somewhat similar to the Ntn hydrolase fold of the proteasomal alph and beta subunits. 224 matched cddid_all.tbl CDD cd01911 cd01911 238892 proteasome_alpha proteasome alpha subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 different alpha and 10 different beta proteasome subunit genes while archaea have one of each. 209 matched cddid_all.tbl CDD cd01912 cd01912 238893 proteasome_beta proteasome beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. 189 matched cddid_all.tbl CDD cd01913 cd01913 238894 protease_HslV Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the interior walls of the cavity. HslV shares significant sequence and structural similarity with the proteasomal beta-subunit and both are members of the Ntn-family of hydrolases. HslV has a nucleophilic threonine residue at its N-terminus that is exposed after processing of the propeptide and is directly involved in active site catalysis. 171 matched cddid_all.tbl CDD cd01914 cd01914 238895 HCP Hybrid cluster protein (HCP), formerly known as prismane, is thought to play a role in nitrogen metabolism but its specific function is unknown. HCP has three structural domains, an N-terminal alpha-helical domain, and two similar domains comprising a central beta-sheet flanked by alpha-helices. HCP contains two iron-sulfur clusters, one of which is a [Fe4-S4] cubane cluster similar to that of carbon monoxide dehydrogenase (CODH). The second cluster, referred to as the hybrid cluster, is a hybrid [Fe4-S2-O2] center located at the interface of the three domains. Although the hybrid cluster is buried within the protein, it is accessible through a large hydrophobic cavity. 423 matched cddid_all.tbl CDD cd01915 cd01915 238896 CODH Carbon monoxide dehydrogenase (CODH) is found in acetogenic and methanogenic organisms and is responsible for the synthesis and breakdown of acetyl-CoA, respectively. CODH has two types of metal clusters, a cubane [Fe4-S4] center (B-cluster) similar to that of hybrid cluster protein (HCP) and a Ni-Fe-S center (C-cluster) where carbon monoxide oxidation occurs. Bifunctional CODH forms a heterotetramer with acetyl-CoA synthase (ACS) consisting of two CODH and two ACS subunits while monofunctional CODH forms a homodimer. Bifunctional CODH reduces carbon dioxide to carbon monoxide and ACS then synthesizes acetyl-CoA from carbon monoxide, CoA, and a methyl group donated by another protein (CoFeSP), while monofunctional CODH oxidizes carbon monoxide to carbon dioxide. CODH and ACS each have a metal cluster referred to as the C- and A-clusters, respectively. 613 matched cddid_all.tbl CDD cd01916 cd01916 238897 ACS_1 Acetyl-CoA synthase (ACS), also known as acetyl-CoA decarbonylase, is found in acetogenic and methanogenic organisms and is responsible for the synthesis and breakdown of acetyl-CoA. ACS forms a heterotetramer with carbon monoxide dehydrogenase (CODH) consisting of two ACS and two CODH subunits. CODH reduces carbon dioxide to carbon monoxide and ACS then synthesizes acetyl-CoA from carbon monoxide, CoA, and a methyl group donated by another protein (CoFeSP). ACS has three structural domains, an N-terminal rossman fold domain with a helical region at its N-terminus which interacts with CODH, and two alpha + beta fold domains. A Ni-Fe-S center referred to as the A-cluster is located in the C-terminal domain. A large cavity exists between the three domains which may bind CoA. 731 matched cddid_all.tbl CDD cd01917 cd01917 238898 ACS_2 Acetyl-CoA synthase (ACS), also known as acetyl-CoA decarbonylase, is found in acetogenic and methanogenic organisms and is responsible for the synthesis and breakdown of acetyl-CoA. ACS forms a heterotetramer with carbon monoxide dehydrogenase (CODH) consisting of two ACS and two CODH subunits. CODH reduces carbon dioxide to carbon monoxide and ACS then synthesizes acetyl-CoA from carbon monoxide, CoA, and a methyl group donated by another protein (CoFeSP). ACS has three structural domains, an N-terminal rossman fold domain with a helical region at its N-terminus which interacts with CODH, and two alpha + beta fold domains. A Ni-Fe-S center referred to as the A-cluster is located in the C-terminal domain. A large cavity exists between the three domains which may bind CoA. 287 matched cddid_all.tbl CDD cd01918 cd01918 238899 HprK_C HprK/P, the bifunctional histidine-containing protein kinase/phosphatase, controls the phosphorylation state of the phosphocarrier protein HPr and regulates the utilization of carbon sources by gram-positive bacteria. It catalyzes both the ATP-dependent phosphorylation of Ser-46 of HPr and its dephosphorylation by phosphorolysis. The latter reaction uses inorganic phosphate as substrate and produces pyrophosphate. Phosphoenolpyruvate carboxykinase (PEPCK) and the C-terminal catalytic domain of HprK/P are structurally similar with conserved active site residues suggesting these two phosphotransferases have related functions. The HprK/P N-terminal domain is structurally similar to the N-terminal domains of the MurE and MurF amino acid ligases. 149 matched cddid_all.tbl CDD cd01919 cd01919 238900 PEPCK Phosphoenolpyruvate carboxykinase (PEPCK), a critical gluconeogenic enzyme, catalyzes the first committed step in the diversion of tricarboxylic acid cycle intermediates toward gluconeogenesis. It catalyzes the reversible decarboxylation and phosphorylation of oxaloacetate to yield phosphoenolpyruvate and carbon dioxide, using a nucleotide molecule (ATP or GTP) for the phosphoryl transfer, and has a strict requirement for divalent metal ions for activity. PEPCK's separate into two phylogenetic groups based on their nucleotide substrate specificity (the ATP-, and GTP-dependent groups). 515 matched cddid_all.tbl CDD cd01920 cd01920 238901 cyclophilin_EcCYP_like cyclophilin_EcCYP_like: cyclophilin-type A-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to the cytosolic E. coli cyclophilin A and Streptomyces antibioticus SanCyp18. Compared to the archetypal cyclophilin Human cyclophilin A, these have reduced affinity for cyclosporin A. E. coli cyclophilin A has a similar peptidylprolyl cis- trans isomerase activity to the human cyclophilin A. Most members of this subfamily contain a phenylalanine residue at the position equivalent to Human cyclophilin W121, where a tyrptophan has been shown to be important for cyclophilin binding. 155 matched cddid_all.tbl CDD cd01921 cd01921 238902 cyclophilin_RRM cyclophilin_RRM: cyclophilin-type peptidylprolyl cis- trans isomerase domain occuring with a C-terminal RNA recognition motif domain (RRM). This subfamily of the cyclophilin domain family contains a number of eukaryotic cyclophilins having the RRM domain including the nuclear proteins: human hCyP-57, Arabidopsis thaliana AtCYP59, Caenorhabditis elegans CeCyP-44 and Paramecium tetrurelia Kin241. The Kin241 protein has been shown to have a role in cell morphogenesis. 166 matched cddid_all.tbl CDD cd01922 cd01922 238903 cyclophilin_SpCYP2_like cyclophilin_SpCYP2_like: cyclophilin 2-like peptidylprolyl cis- trans isomerase (PPIase) domain similar to Schizosaccharomyces pombe cyp-2. These proteins bind their respective SNW chromatin binding protein in autologous systems, in a CsA independent manner indicating interaction with a surface outside the PPIase active site. SNW proteins play a basic and broad range role in signaling. 146 matched cddid_all.tbl CDD cd01923 cd01923 238904 cyclophilin_RING cyclophilin_RING: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a modified RING finger domain. This group includes the nuclear proteins, Human hCyP-60 and Caenorhabditis elegans MOG-6 which, compared to the archetypal cyclophilin Human cyclophilin A exhibit reduced peptidylprolyl cis- trans isomerase activity and lack a residue important for cyclophilin binding. Human hCyP-60 has been shown to physically interact with the proteinase inhibitor peptide eglin c and; C. elegans MOG-6 to physically interact with MEP-1, a nuclear zinc finger protein. MOG-6 has been shown to function in germline sex determination. 159 matched cddid_all.tbl CDD cd01924 cd01924 238905 cyclophilin_TLP40_like cyclophilin_TLP40_like: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) similar ot the Spinach thylakoid lumen protein TLP40. Compared to the archetypal cyclophilin Human cyclophilin A, these proteins have similar peptidylprolyl cis- trans isomerase activity and reduced affinity for cyclosporin A. Spinach TLP40 has been shown to have a dual function as a folding catalyst and regulator of dephosphorylation. 176 matched cddid_all.tbl CDD cd01925 cd01925 238906 cyclophilin_CeCYP16-like cyclophilin_CeCYP16-like: cyclophilin-type peptidylprolyl cis- trans isomerase) (PPIase) domain similar to Caenorhabditis elegans cyclophilin 16. C. elegans CeCYP-16, compared to the archetypal cyclophilin Human cyclophilin A has, a reduced peptidylprolyl cis- trans isomerase activity, is cyclosporin insensitive and shows an altered substrate preference favoring, hydrophobic, acidic or amide amino acids. Most members of this subfamily have a glutamate residue in the active site at the position equivalent to a tryptophan (W121 in Human cyclophilin A), which has been shown to be important for cyclophilin binding. 171 matched cddid_all.tbl CDD cd01926 cd01926 238907 cyclophilin_ABH_like cyclophilin_ABH_like: Cyclophilin A, B and H-like cyclophilin-type peptidylprolyl cis- trans isomerase (PPIase) domain. This family represents the archetypal cystolic cyclophilin similar to human cyclophilins A, B and H. PPIase is an enzyme which accelerates protein folding by catalyzing the cis-trans isomerization of the peptide bonds preceding proline residues. These enzymes have been implicated in protein folding processes which depend on catalytic /chaperone-like activities. As cyclophilins, Human hCyP-A, human cyclophilin-B (hCyP-19), S. cerevisiae Cpr1 and C. elegans Cyp-3, are inhibited by the immunosuppressive drug cyclopsporin A (CsA). CsA binds to the PPIase active site. Cyp-3. S. cerevisiae Cpr1 interacts with the Rpd3 - Sin3 complex and in addition is a component of the Set3 complex. S. cerevisiae Cpr1 has also been shown to have a role in Zpr1p nuclear transport. Human cyclophilin H associates with the [U4/U6.U5] tri-snRNP particles of the splicesome. 164 matched cddid_all.tbl CDD cd01927 cd01927 238908 cyclophilin_WD40 cyclophilin_WD40: cyclophilin-type peptidylprolyl cis- trans isomerases (cyclophilins) having a WD40 domain. This group consists of several hypothetical and putative eukaryotic and bacterial proteins which have a cyclophilin domain and a WD40 domain. Function of the protein is not known. 148 matched cddid_all.tbl CDD cd01928 cd01928 238909 Cyclophilin_PPIL3_like Cyclophilin_PPIL3_like. Proteins similar to Human cyclophilin-like peptidylprolyl cis- trans isomerase (PPIL3). Members of this family lack a key residue important for cyclosporin binding: the tryptophan residue corresponding to W121 in human hCyP-18a; most members have a histidine at this position. The exact function of the protein is not known. 153 matched cddid_all.tbl CDD cd01935 cd01935 238910 Ntn_CGH_like Choloylglycine hydrolase (CGH)_like. This family of choloylglycine hydrolase-like proteins includes conjugated bile acid hydrolase (CBAH), penicillin V acylase (PVA), acid ceramidase (AC), and N-acylethanolamine-hydrolyzing acid amidase (NAAA) which cleave non-peptide carbon-nitrogen bonds in bile salt constituents. These enzymes have an N-terminal nucleophilic cysteine, as do other members of the Ntn hydrolase family to which they belong. This nucleophilic cysteine is exposed by post-translational prossessing of the precursor protein. 229 matched cddid_all.tbl CDD cd01936 cd01936 238911 Ntn_CA Cephalosporin acylase (CA) belongs to a family of beta-lactam acylases that includes penicillin G acylase (PGA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and 7-aminocephalosporanic acid (7-ACA), which can be used to synthesize semi-synthetic penicillins and cephalosporins, respectively. While both PGA and CA have a conserved Ntn (N-terminal nucleophile) hydrolase fold and the structural similarity at their active sites is very high, their sequence similarity to other Ntn's is low. 469 matched cddid_all.tbl CDD cd01937 cd01937 238912 ribokinase_group_D Ribokinase-like subgroup D. Found in bacteria and archaea, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time. 254 matched cddid_all.tbl CDD cd01938 cd01938 238913 ADPGK_ADPPFK ADP-dependent glucokinase (ADPGK) and phosphofructokinase (ADPPFK). ADPGK and ADPPFK are proteins that rely on ADP rather than ATP to donate a phosphoryl group. They are found in certain hyperthermophilic archaea and in higher eukaryotes. A functional ADPGK has been characterized in mouse and is assumed to be desirable during ischemia/hypoxia. ADPGK and ADPPFK contain a large and a small domain with the binding site located in a groove between the domains. Partial domain closing is seen when ADP is bound, and further domain closing is observed when glucose is also bound. The oligomerization state apparently varies depending on the species, with some existing as monomers, some as dimers, and some as tetramers. 445 matched cddid_all.tbl CDD cd01939 cd01939 238914 Ketohexokinase Ketohexokinase (fructokinase, KHK) catalyzes the phosphorylation of fructose to fructose-1-phosphate (F1P), the first step in the metabolism of dietary fructose. KHK can also phosphorylate several other furanose sugars. It is found in higher eukaryotes where it is believed to function as a dimer and requires K(+) and ATP to be active. In humans, hepatic KHK deficiency causes fructosuria, a benign inborn error of metabolism. 290 matched cddid_all.tbl CDD cd01940 cd01940 238915 Fructoselysine_kinase_like Fructoselysine kinase-like. Fructoselysine is a fructoseamine formed by glycation, a non-enzymatic reaction of glucose with a primary amine followed by an Amadori rearrangement, resulting in a protein that is modified at the amino terminus and at the lysine side chains. Fructoseamines are typically metabolized by fructoseamine-3-kinase, especially in higher eukaryotes. In E. coli, fructoselysine kinase has been shown in vitro to catalyze the phosphorylation of fructoselysine. It is proposed that fructoselysine is released from glycated proteins during human digestion and is partly metabolized by bacteria in the hind gut using a protein such as fructoselysine kinase. This family is found only in bacterial sequences, and its oligomeric state is currently unknown. 264 matched cddid_all.tbl CDD cd01941 cd01941 238916 YeiC_kinase_like YeiC-like sugar kinase. Found in eukaryotes and bacteria, YeiC-like kinase is part of the ribokinase/pfkB sugar kinase superfamily. Its oligomerization state is unknown at this time. 288 matched cddid_all.tbl CDD cd01942 cd01942 238917 ribokinase_group_A Ribokinase-like subgroup A. Found in bacteria and archaea, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time. 279 matched cddid_all.tbl CDD cd01943 cd01943 238918 MAK32 MAK32 kinase. MAK32 is a protein found primarily in fungi that is necessary for the structural stability of L-A particles. The L-A virus particule is a specialized compartment for the transcription and replication of double-stranded RNA, known to infect yeast and other fungi. MAK32 is part of the host machinery used by the virus to multiply. 328 matched cddid_all.tbl CDD cd01944 cd01944 238919 YegV_kinase_like YegV-like sugar kinase. Found only in bacteria, YegV-like kinase is part of the ribokinase/pfkB sugar kinase superfamily. Its oligomerization state is unknown at this time. 289 matched cddid_all.tbl CDD cd01945 cd01945 238920 ribokinase_group_B Ribokinase-like subgroup B. Found in bacteria and plants, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time. . 284 matched cddid_all.tbl CDD cd01946 cd01946 238921 ribokinase_group_C Ribokinase-like subgroup C. Found only in bacteria, this subgroup is part of the ribokinase/pfkB superfamily. Its oligomerization state is unknown at this time. 277 matched cddid_all.tbl CDD cd01947 cd01947 238922 Guanosine_kinase_like Guanosine kinase-like sugar kinases. Found in bacteria and archaea, the guanosine kinase-like group is part of the ribokinase/pfkB sugar kinase superfamily. Its oligomerization state is unknown at this time. 265 matched cddid_all.tbl CDD cd01948 cd01948 238923 EAL EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues and is also known as domain of unknown function 2 (DUF2). The EAL domain has been shown to stimulate degradation of a second messenger, cyclic di-GMP, and is a good candidate for a diguanylate phosphodiesterase function. Together with the GGDEF domain, EAL might be involved in regulating cell surface adhesiveness in bacteria. 240 matched cddid_all.tbl CDD cd01949 cd01949 143635 GGDEF Diguanylate-cyclase (DGC) or GGDEF domain. Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as a domain of unknown function 1 (DUF1). This domain is widely present in bacteria, linked to a wide range of non-homologous domains in a variety of cell signaling proteins. The domain shows homology to the adenylyl cyclase catalytic domain. This correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. Together with the EAL domain, GGDEF might be involved in regulating cell surface adhesion in bacteria. 158 matched cddid_all.tbl CDD cd01951 cd01951 173886 lectin_L-type "legume lectins. The L-type (legume-type) lectins are a highly diverse family of carbohydrate binding proteins that generally display no enzymatic activity toward the sugars they bind. This family includes arcelin, concanavalinA, the lectin-like receptor kinases, the ERGIC-53/VIP36/EMP46 type1 transmembrane proteins, and an alpha-amylase inhibitor. L-type lectins have a dome-shaped beta-barrel carbohydrate recognition domain with a curved seven-stranded beta-sheet referred to as the ""front face"" and a flat six-stranded beta-sheet referred to as the ""back face"". This domain homodimerizes so that adjacent back sheets form a contiguous 12-stranded sheet and homotetramers occur by a back-to-back association of these homodimers. Though L-type lectins exhibit both sequence and structural similarity to one another, their carbohydrate binding specificities differ widely." 223 matched cddid_all.tbl CDD cd01958 cd01958 238924 HPS_like HPS_like: Hydrophobic Protein from Soybean (HPS)-like subfamily; composed of proteins with similarity to HPS, a small hydrophobic protein with unknown function related to cereal-type alpha-amylase inhibitors and lipid transfer proteins. In addition to HPS, members of this subfamily include a hybrid proline-rich protein (HyPRP) from maize, a dark-inducible protein (LeDI-2) from Lithospermum erythrorhizon, maize ZRP3 protein, and rice RcC3 protein. HyPRP is an embryo-specific protein that contains an N-terminal proline-rich domain and a C-terminal HPS-like cysteine-rich domain. It has been suggested that HyPRP may be involved in the stability and defense of the developing embryo. LeDI-2 is a root-specific protein that may be involved in regulating the biosynthesis of shikonin derivatives in L. erythrorhizon. Maize ZRP3 and rice RcC3 are root-specific proteins whose functions are yet to be determined. It has been reported that ZRP3 largely accumulates in a distinct subset of cortical cells. 85 matched cddid_all.tbl CDD cd01959 cd01959 238925 nsLTP2 nsLTP2: Non-specific lipid-transfer protein type 2 (nsLTP2) subfamily; Plant nsLTPs are small, soluble proteins that facilitate the transfer of fatty acids, phospholipids, glycolipids, and steroids between membranes. In addition to lipid transport and assembly, nsLTPs also play a key role in the defense of plants against pathogens. There are two closely-related types of nsLTPs, types 1 and 2, which differ in protein sequence, molecular weight, and biological properties. nsLTPs contain an internal hydrophobic cavity, which serves as the binding site for lipids. nsLTP2 can bind lipids and sterols. Structure studies of rice nsLTPs show that the plasticity of the hydrophobic cavity is an important factor in ligand binding. The flexibility of the sLTP2 cavity allows its binding to rigid sterol molecules, whereas nsLTP1 cannot bind sterols despite its larger cavity size. The resulting nsLTP2/sterol complexes may bind to receptors that trigger defense responses. nsLTP2 gene expression has been observed in barley and rice developing seeds, during Zinnia elegans cell differentiation, and under abiotic stress conditions in barley roots. The nsLTP2 of Brassica rapa has also been identified as a potent allergen. 66 matched cddid_all.tbl CDD cd01960 cd01960 238926 nsLTP1 nsLTP1: Non-specific lipid-transfer protein type 1 (nsLTP1) subfamily; Plant nsLTPs are small, soluble proteins that facilitate the transfer of fatty acids, phospholipids, glycolipids, and steroids between membranes. In addition to lipid transport and assembly, nsLTPs also play a key role in the defense of plants against pathogens. There are two closely-related types of nsLTPs, types 1 and 2, which differ in protein sequence, molecular weight, and biological properties. nsLTPs contain an internal hydrophobic cavity, which serves as the binding site for lipids. The hydrophobic cavity accommodates various fatty acid ligands containing from ten to 18 carbon atoms. In general, the cavity is larger in nsLTP1 than in nsLTP2. nsLTP1 proteins are located in extracellular layers and in vacuolar structures. They may be involved in the formation of cutin layers on plant surfaces by transporting cutin monomers. Many nsLTP1 proteins have been characterized as allergens in humans. 89 matched cddid_all.tbl CDD cd01965 cd01965 238927 Nitrogenase_MoFe_beta_like Nitrogenase_MoFe_beta_like: Nitrogenase MoFe protein, beta subunit_like. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia. This group contains the beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent nitrogenase (Mo-nitrogenase), a vanadium-dependent nitrogenase (V-nitrogenase), and an iron-only nitrogenase (Fe-nitrogenase). These nitrogenase systems consist of component 1 (MoFe protein, VFe protein or, FeFe protein respectively) and, component 2 (Fe protein). The most widespread and best characterized of these systems is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer, the alternative nitrogenases are alpha2beta2delta2 hexamers having alpha and beta subunits similar to the alpha and beta subunits of MoFe. For MoFe, each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (FeMoco) contained within the alpha subunit. The Fe protein contains, a single [4Fe-4S] cluster from which electrons are transferred to the P-cluster of the MoFe and in turn, to FeMoCo, the site of substrate reduction. The V-nitrogenase requires an iron-vanadium cofactor (FeVco), the iron only-nitrogenase an iron only cofactor (FeFeco). These cofactors are analogous to the FeMoco. The V-nitrogenase has P clusters identical to those of MoFe. In addition to N2, nitrogenase also catalyzes the reduction of a variety of other substrates such as acetylene The V-nitrogenase differs from the Mo-nitrogenase in that it produces free hydrazine, as a minor product during N2-reduction and, ethane as a minor product during acetylene reduction 428 matched cddid_all.tbl CDD cd01966 cd01966 238928 Nitrogenase_NifN_1 Nitrogenase_nifN1: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE. NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The nifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this nifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco). 417 matched cddid_all.tbl CDD cd01967 cd01967 238929 Nitrogenase_MoFe_alpha_like Nitrogenase_MoFe_alpha_like: Nitrogenase MoFe protein, alpha subunit_like. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to ammonia. Three genetically distinct types of nitrogenase systems are known to exist: a molybdenum-dependent nitrogenase (Mo-nitrogenase), a vanadium dependent nitrogenase (V-nitrogenase), and an iron-only nitrogenase (Fe-nitrogenase). These nitrogenase systems consist of component 1 (MoFe protein, VFe protein or, FeFe protein respectively) and, component 2 (Fe protein). This group contains the alpha subunit of component 1 of all three different forms. The most widespread and best characterized of these systems is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer, the alternative nitrogenases are alpha2beta2delta2 hexamers having alpha and beta subunits similar to the alpha and beta subunits of MoFe. The role of the delta subunit is unknown. For MoFe, each alphabeta pair of subunits contains one P-cluster (located at the alphabeta interface) and, one molecule of iron molybdenum cofactor (FeMoco) contained within the alpha subunit. The Fe protein is a homodimer which contains, a single [4Fe-4S] cluster from which electrons are transferred to the P-cluster of the MoFe and in turn, to FeMoCo the site of substrate reduction. The V-nitrogenase requires an iron-vanadium cofactor (FeVco), the iron only-nitrogenase an iron only cofactor (FeFeco). These cofactors are analogous to the FeMoco. The V-nitrogenase has P clusters identical to those of MoFe. In addition to N2, nitrogenase also catalyzes the reduction of a variety of other substrates such as acetylene The V-nitrogenase differs from the Mo- nitrogenase in that it produces free hydrazine, as a minor product during dinitrogen reduction and, ethane as a minor product during acetylene reduction. 406 matched cddid_all.tbl CDD cd01968 cd01968 238930 Nitrogenase_NifE_I Nitrogenase_NifE_I: a subgroup of the NifE subunit of the NifEN complex: NifE forms an alpha2beta2 tetramer with NifN. NifE and NifN are structurally homologous to nitrogenase MoFe protein alpha and beta subunits respectively. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The NifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this NifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco). 410 matched cddid_all.tbl CDD cd01971 cd01971 238931 Nitrogenase_VnfN_like Nitrogenase_vnfN_like: VnfN subunit of the VnfEN complex-like. This group in addition to VnfN contains a subset of the beta subunit of the nitrogenase MoFe protein and NifN-like proteins. The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of MoFe protein of the molybdenum(Mo)-nitrogenase. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to NifEN where it is further processed to FeMoco. VnfEN may similarly be a scaffolding protien for the iron-vanadium cofactor (FeVco) of the vanadium-dependent (V)-nitrogenase. NifE and NifN are essential for the Mo-nitrogenase, VnfE and VnfN are not essential for the V-nitrogenase. NifE and NifN can substitute when the vnfEN genes are inactivated. 427 matched cddid_all.tbl CDD cd01972 cd01972 238932 Nitrogenase_VnfE_like Nitrogenase_VnfE_like: VnfE subunit of the VnfEN complex_like. This group in addition to VnfE contains a subset of the alpha subunit of the nitrogenase MoFe protein and NifE-like proteins. The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of MoFe protein of the molybdenum(Mo)-nitrogenase. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to NifEN where it is further processed to FeMoco. VnfEN may similarly be a scaffolding protein for the iron-vanadium cofactor (FeVco) of the vanadium-dependent (V)-nitrogenase. NifE and NifN are essential for the Mo-nitrogenase, VnfE and VnfN are not essential for the V-nitrogenase. NifE and NifN can substitute when the vnfEN genes are inactivated. 426 matched cddid_all.tbl CDD cd01973 cd01973 238933 Nitrogenase_VFe_beta_like Nitrogenase_VFe_beta -like: Nitrogenase VFe protein, beta subunit like. This group contains proteins similar to the beta subunits of the VFe protein of the vanadium-dependent (V-) nitrogenase. Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia. In addition to V-nitrogenase there is a molybdenum (Mo)-dependent nitrogenase and an iron only (Fe-) nitrogenase. The Mo-nitrogenase is the most widespread and best characterized of these systems. These systems consist of component 1 (VFe protein, FeFe protein or, MoFe protein respectively) and, component 2 (Fe protein). MoFe is an alpha2beta2 tetramer, V-and Fe- nitrogenases are alpha2beta2delta2 hexamers. The alpha and beta subunits of VFe and FeFe are similar to the alpha and beta subunits of MoFe. For MoFe each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (FeMoco) contained within the alpha subunit. The Fe protein which has a practically identical structure in all three systems, it contains a single [4Fe-4S] cluster. Electrons are transferred from the [4Fe-4S] cluster of the Fe protein to the P-cluster of the MoFe and in turn to FeMoCo, the site of substrate reduction. The V-nitrogenase requires an iron-vanadium cofactor (FeVco), the iron only-nitrogenase an iron only cofactor (FeFeco). These cofactors are analogous to the FeMoco. The V-nitrogenase has P clusters identical to those of MoFe. In addition to N2, nitrogenase also catalyzes the reduction of a variety of other substrates such as acetylene The V-nitrogenase differs from the Mo-nitrogenase in that it produces free hydrazine, as a minor product during dinitrogen reduction and, ethane as a minor product during acetylene reduction. 454 matched cddid_all.tbl CDD cd01974 cd01974 238934 Nitrogenase_MoFe_beta Nitrogenase_MoFe_beta: Nitrogenase MoFe protein, beta subunit. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to ammonia. The Molybdenum (Mo-) nitrogenase is the most widespread and best characterized of these systems. Mo-nitrogenase consists of the MoFe protein (component 1) and the Fe protein (component 2). MoFe is an alpha2beta2 tetramer. This group contains the beta subunit of the MoFe protein. Each alphabeta pair of MoFe contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (FeMoco) contained within the alpha subunit. The Fe protein contains a single [4Fe-4S] cluster. Electrons are transferred from the [4Fe-4S] cluster of the Fe protein to the P-cluster of the MoFe and in turn to FeMoCo, the site of substrate reduction. 435 matched cddid_all.tbl CDD cd01976 cd01976 238935 Nitrogenase_MoFe_alpha Nitrogenase_MoFe_alpha_II: Nitrogenase MoFe protein, beta subunit. A group of proteins similar to the alpha subunit of the MoFe protein of the molybdenum (Mo-) nitrogenase. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to ammonia. The Mo-nitrogenase is the most widespread and best characterized of these systems. Mo-nitrogenase consists of the MoFe protein (component 1) and the Fe protein (component 2). MoFe is an alpha2beta2 tetramer. Each alphabeta pair of MoFe contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (FeMoco) contained within the alpha subunit. The Fe protein contains a single [4Fe-4S] cluster. Electrons are transferred from the [4Fe-4S] cluster of the Fe protein to the P-cluster of the MoFe and in turn to FeMoCo, the site of substrate reduction. 421 matched cddid_all.tbl CDD cd01977 cd01977 238936 Nitrogenase_VFe_alpha Nitrogenase_VFe_alpha -like: Nitrogenase VFe protein, alpha subunit like. This group contains proteins similar to the alpha subunits of, the VFe protein of the vanadium-dependent (V-) nitrogenase and the FeFe protein of the iron only (Fe-) nitrogenase Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia. In addition to V- and Fe- nitrogenases there is a molybdenum (Mo)-dependent nitrogenase which is the most widespread and best characterized of these systems. These systems consist of component 1 (VFe protein, FeFe protein or, MoFe protein respectively) and, component 2 (Fe protein). MoFe is an alpha2beta2 tetramer, V-and Fe- nitrogenases are alpha2beta2delta2 hexamers. The alpha and beta subunits of VFe and FeFe are similar to the alpha and beta subunits of MoFe. For MoFe each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (FeMoco) contained within the alpha subunit. The Fe protein which has a practically identical structure in all three systems, it contains a single [4Fe-4S] cluster. Electrons are transferred from the [4Fe-4S] cluster of the Fe protein to the P-cluster of the MoFe and in turn to FeMoCo, the site of substrate reduction. The V-nitrogenase requires an iron-vanadium cofactor (FeVco), the iron only-nitrogenase an iron only cofactor (FeFeco). These cofactors are analogous to the FeMoco. The V-nitrogenase has P clusters identical to those of MoFe. In addition to N2, nitrogenase also catalyzes the reduction of a variety of other substrates such as acetylene The V-nitrogenase differs from the Mo-nitrogenase in that it produces free hydrazine, as a minor product during dinitrogen reduction and, ethane as a minor product during acetylene reduction. 415 matched cddid_all.tbl CDD cd01979 cd01979 238937 Pchlide_reductase_N Pchlide_reductase_N: N protein of the NB protein complex of Protochlorophyllide (Pchlide)_reductase. Pchlide reductase catalyzes the reductive formation of chlorophyllide (chlide) from protochlorophyllide (pchlide) during biosynthesis of chlorophylls and bacteriochlorophylls. This group contains both the light-independent Pchlide reductase (DPOR) and light-dependent Pchlide reductase (LPOR). Angiosperms contain only LPOR, cyanobacteria, algae and gymnosperms contain both DPOR and LPOR, primitive anoxygenic photosynthetic bacteria contain only DPOR. NB is structurally similar to the FeMo protein of nitrogenase, forming an N2B2 heterotetramer. N and B are homologous to the FeMo alpha and beta subunits respectively. Also in common with nitrogenase in vitro DPOR activity requires ATP hydrolysis and dithoionite or ferredoxin as electron donor. The NB protein complex may serve as a catalytic site for Pchlide reduction similar to MoFe for nitrogen reduction. 396 matched cddid_all.tbl CDD cd01980 cd01980 238938 Chlide_reductase_Y Chlide_reductase_Y : Y subunit of chlorophyllide (chlide) reductase (BchY). Chlide reductase participates in photosynthetic pigment synthesis playing a role in the conversion of chlorophylls(Chl) into bacteriochlorophylls (BChl). Chlide reductase catalyzes the reduction of the B-ring of the tetrapyrolle. Chlide reductase is a three subunit enzyme (subunits are designated BchX, BchY and BchZ). The similarity between these three subunits and the subunits for nitrogenase suggests that BchX serves as an electron donor for the BchY-BchY catalytic subunits. 416 matched cddid_all.tbl CDD cd01981 cd01981 238939 Pchlide_reductase_B Pchlide_reductase_B: B protein of the NB protein complex of Protochlorophyllide (Pchlide)_reductase. Pchlide reductase catalyzes the reductive formation of chlorophyllide (chlide) from protochlorophyllide (pchlide) during biosynthesis of chlorophylls and bacteriochlorophylls. This group contains both the light-independent Pchlide reductase (DPOR) and light-dependent Pchlide reductase (LPOR). Angiosperms contain only LPOR, cyanobacteria, algae and gymnosperms contain both DPOR and LPOR, primitive anoxygenic photosynthetic bacteria contain only DPOR. NB is structurally similar to the FeMo protein of nitrogenase, forming an N2B2 heterotetramer. N and B are homologous to the FeMo alpha and beta subunits respectively. Also in common with nitrogenase in vitro DPOR activity requires ATP hydrolysis and dithoionite or ferredoxin as electron donor. The NB protein complex may serve as a catalytic site for Pchlide reduction similar to MoFe for nitrogen reduction. 430 matched cddid_all.tbl CDD cd01982 cd01982 238940 Chlide_reductase_Z Chlide_reductase_Z : Z subunit of chlorophyllide (chlide) reductase (BchZ). Chlide reductase participates in photosynthetic pigment synthesis playing a role in the conversion of chlorophylls(Chl) into bacteriochlorophylls (BChl). Chlide reductase catalyzes the reduction of the B-ring of the tetrapyrolle. Chlide reductase is a three subunit enzyme (subunits are designated BchX, BchY and BchZ). The similarity between these three subunits and the subunits for nitrogenase suggests that BchX serves as an electron donor for the BchY-BchY catalytic subunits. 412 matched cddid_all.tbl CDD cd01983 cd01983 349751 SIMIBI SIMIBI (signal recognition particle, MinD and BioD)-class NTPases. SIMIBI (after signal recognition particle, MinD, and BioD), consists of signal recognition particle (SRP) GTPases, the assemblage of MinD-like ATPases, which are involved in protein localization, chromosome partitioning, and membrane transport, and a group of metabolic enzymes with kinase or related phosphate transferase activity. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion. 107 matched cddid_all.tbl CDD cd01984 cd01984 467489 AANH_superfamily Adenine nucleotide alpha hydrolase (AANH) superfamily. The adenine nucleotide alpha hydrolase (AANH) superfamily includes N-type ATP PPases, ATP sulfurylases, universal stress response proteins (USPs), and electron transfer flavoproteins (ETFs). The domain forms an alpha/beta/alpha fold which binds to adenosine nucleotide. 56 matched cddid_all.tbl CDD cd01986 cd01986 467490 AANH-like adenine nucleotide alpha hydrolase (AANH)-like proteins. This group of adenine nucleotide alpha hydrolase (AANH)-like proteins includes N-type ATP PPases and ATP sulfurylases. The domain forms an alpha/beta/alpha fold which binds to adenosine nucleotide. 74 matched cddid_all.tbl CDD cd01987 cd01987 467491 USP_KdpD-like "USP domain of the osmosensitive K+ channel histidine kinase family. The KdpDE two component system is widespread in bacteria and archaea; it controls potassium homeostasis and virulence by regulating the transcription of multiple genes, including a kdpFABC operon, which encodes a high-affinity P-type ATPase transporter. The KdpD histidine kinase (HK, EC:2.7.13.3) contain an N-terminal sensory cytoplasmic region (NTR) composed of KdpD' and universal stress protein (USP) domains, a canonical transmembrane domain, and a cytoplasmic C-terminal region with a transmitter GAF domain and an EnvZ-like catalytic HK domain. Proteins containing the USP domain are induced by many environmental stressors such as nutrient starvation, drought, extreme temperatures, high salinity, and the presence of uncouplers, antibiotics, and metals. It enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general ""stress endurance"" activity." 124 matched cddid_all.tbl CDD cd01988 cd01988 467492 USP_NhaS5_C "C-terminal USP domain(s) of Na(+)/H(+) antiporter NhaS5 and similar proteins. Na(+)/H(+) exchange proteins eject protons from cells, effectively eliminating excess acid from actively metabolizing cells. Na(+)/H(+) exchange activity is also crucial for the regulation of cell volume, and for the reabsorption of NaCl across renal, intestinal, and other epithelia. These antiporters exchange Na(+) for H(+) in an electroneutral manner, and this activity is carried out by a family of Na(+)/H(+) exchangers, or NHEs, which are known to be present in both prokaryotic and eukaryotic cells. These exchangers are highly-regulated (glyco)phosphoproteins, which, based on their primary structure, appear to contain 10-12 membrane-spanning regions (M) at the N-terminus and a large cytoplasmic region at the C-terminus. The transmembrane regions M3-M12 share identity with other members of the family. The M6 and M7 regions are highly conserved. This is thought to be the region that is involved in the transport of sodium and hydrogen ions. The C-terminal region contains one or two domains that show homology with universal stress protein (USP), a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. USP enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general ""stress endurance"" activity." 125 matched cddid_all.tbl CDD cd01989 cd01989 467493 USP_STK_Ubox_N N-terminal USP domain of serine threonine kinases (STK) and U-box domain proteins. This model represents the N-terminal domain found in some plant serine threonine kinases (STK, EC 2.7.11.-) and U-box domain-containing proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. They play a role in the regulation of cell proliferation, programmed cell death (apoptosis), cell differentiation, and embryonic development. These enzymes belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. U-box domain-containing proteins function as E3 ubiquitin ligases (EC 2.3.2.27), mediating the ubiquitination of target proteins by bringing the ubiquitin-charged E2 ubiquitin-conjugating enzyme and the acceptor protein together to enable the direct transfer of ubiquitin. The N-terminal domain of these proteins is homologous to the universal stress protein (USP) family which has an ATP binding fold. The N-terminal domain is predicted to be involved in ATP binding. 154 matched cddid_all.tbl CDD cd01990 cd01990 467494 LarE-like Lactate racemization operon protein LarE and similar proteins. This subfamily includes Lactiplantibacillus plantarum LarE, a sacrificial sulfur insertase of the N-type ATP pyrophosphatase family. LarE is part of the lar operon, encoding five Lar proteins (LarA-E) that collaboratively synthesize and incorporate a niacin-derived Ni-containing cofactor into LarA, an Ni-dependent lactate racemase. It catalyzes successive thiolation reactions by donating the sulfur atom of their exclusive cysteine residues to the substrate. The LarE-like subfamily belongs to the nucleotide alpha hydrolase (AANH) superfamily that includes N-type ATP PPases and ATP sulfurylases. It forms an alpha/beta/alpha fold which binds to the adenosine group. Proteins from this subfamily probably binds ATP. This domain is about 200 amino acids long with a strongly conserved motif SGGxDS at the N-terminus. 222 matched cddid_all.tbl CDD cd01991 cd01991 467495 Asn_synthase_B_C C-terminal domain of asparagine synthase B. The C-terminal domain of asparagine synthase (or synthetase) B is always associated with an N-terminal amidotransferase domain. Family members that contain this domain catalyze the conversion of aspartate to asparagine. Asparagine synthase B catalyzes the synthesis of asparagine from aspartate, Mg(2+)ATP, and glutamine. The three-dimensional architecture of the N-terminal domain of asparagine synthetase B is similar to that observed for glutamine phosphoribosylpyrophosphate amidotransferase while the molecular motif of the C-domain is reminiscent to that observed for GMP synthetase. 224 matched cddid_all.tbl CDD cd01992 cd01992 467496 TilS_N N-terminal domain of tRNA(Ile)-lysidine synthase and similar proteins. tRNA(Ile)-lysidine synthase (EC 6.3.4.19), also called tRNA(Ile)-2-lysyl-cytidine synthase or tRNA(Ile)-lysidine synthetase, catalyzes the ligation of lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine. This subfamily belongs to the adenine nucleotide alpha hydrolase superfamily that also includes N-type ATP PPases and ATP sulfurylases. It forms an alpha/beta/alpha fold which binds to adenosine group. This domain has a strongly conserved motif SGGXD at the N-terminus. 185 matched cddid_all.tbl CDD cd01993 cd01993 467497 TtuA-like tRNA-5-methyluridine(54) 2-sulfurtransferase and similar proteins. tRNA-5-methyluridine(54) 2-sulfurtransferase, also called tRNA thiouridine synthetase TtuA, catalyzes the ATP-dependent 2-thiolation of 5-methyluridine residue at position 54 in the T loop of tRNAs, leading to 5-methyl-2-thiouridine (m(5)s(2)U or s(2)T). TtuA belongs to the adenine nucleotide alpha hydrolase superfamily (AANH) that includes N-type ATP PPases and ATP sulfurylases. It forms an alpha/beta/alpha fold which binds to the adenosine group. This domain has a strongly conserved motif SGGKD at the N-terminus. 190 matched cddid_all.tbl CDD cd01994 cd01994 467498 AANH_PF0828-like putative ATP pyrophosphatase PF0828 and similar proteins. This subfamily includes Pyrococcus furiosus putative ATP pyrophosphatase PF0828 and Pyrococcus horikoshii PH1257. They belong to the adenine nucleotide alpha hydrolase (AANH) superfamily that also includes other N-type ATP PPases and ATP sulfurylases. It forms an alpha/beta/alpha fold which binds to the adenosine group. This subfamily of proteins is predicted to bind ATP. This domain has a strongly conserved motif SGGKD at the N-terminus. 211 matched cddid_all.tbl CDD cd01995 cd01995 467499 QueC-like 7-cyano-7-deazaguanine synthase QueC and similar proteins. 7-cyano-7-deazaguanine synthase (EC 6.3.4.20) is also called 7-cyano-7-carbaguanine synthase, preQ(0) synthase, or queuosine biosynthesis protein QueC. It catalyzes the ATP-dependent conversion of 7-carboxy-7-deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0)), as part of the biosynthesis pathway of queuosine (Q). Q is one of the most complex modifications occurring at the wobble position of tRNAs with GUN anticodons, and is implicated in a number of biological activities, including accuracy of decoding, virulence, and cellular differentiation. This subfamily belongs to the adenine nucleotide alpha hydrolase (AANH) superfamily that also includes other N-type ATP PPases and ATP sulfurylases. It forms an alpha/beta/alpha fold which binds to the adenosine group. 208 matched cddid_all.tbl CDD cd01996 cd01996 467500 AANH_WbpG-like Rhizobium leguminosarum WbpG protein and similar proteins. This subfamily includes Rhizobium leguminosarum WbpG and Campylobacter jejuni PseA proteins. They belong to the of adenine nucleotide alpha hydrolase (AANH) superfamily that also includes N-type ATP PPases and ATP sulfurylases. It forms an alpha/beta/alpha fold which binds to adenosine group. This subfamily of proteins is predicted to bind ATP. This domain has a strongly conserved motif SGGKD at the N-terminus. 158 matched cddid_all.tbl CDD cd01997 cd01997 467501 GMP_synthase_C C-terminal domain of GMP synthetase (glutamine-hydrolyzing). The C-terminal domain of GMP synthetase (glutamine-hydrolyzing, EC 6.3.5.2) contains two subdomains: the ATP pyrophosphatase domain at the N-terminal and the dimerization domain at the C-terminal end. The ATP-PPase domain is a twisted, five-stranded parallel beta-sheet sandwiched between helical layers. It has a signature nucleotide-binding motif, or PP-loop, at the end of the first-beta strand. GMP synthetase is a homodimer, but in some archaea, it is a heterodimer made up of ATP pyrophosphatase (ATP-PPase) and a GATase subunit. In eukaryotes and bacteria, the two catalytic units are encoded by a single gene producing a two-domain-type GMP with a GATase domain in the N-terminus and an ATP-PPase domain in the C-terminus. 311 matched cddid_all.tbl CDD cd01998 cd01998 467502 MnmA_TRMU-like MnmA/TRMU family 2-thiouridylases and similar proteins. This family is composed of bacterial tRNA-specific 2-thiouridylase MnmA (EC 2.8.1.13) and mitochondrial tRNA-specific 2-thiouridylase 1 (TRMU or MTU1, EC 2.8.1.14). MnmA catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34. TRMU/MTU1 catalyzes the 2-thiolation of uridine at the wobble position (U34) of mitochondrial tRNA(Lys), tRNA(Glu) and tRNA(Gln); this is required for the formation of 5-taurinomethyl-2-thiouridine (tm5s2U) of mitochondrial tRNA(Lys), tRNA(Glu), and tRNA(Gln) at the wobble position. This family belongs to the adenine nucleotide alpha hydrolase (AANH) superfamily that also includes other N-type ATP PPases and ATP sulfurylases. It forms an alpha/beta/alpha fold which binds to the adenosine group. 349 matched cddid_all.tbl CDD cd01999 cd01999 467503 ASS argininosuccinate_synthase (ASS). Argininosuccinate synthase (ASS; EC 6.3.4.5) is a urea cycle enzyme that catalyzes the penultimate step in arginine biosynthesis: the ATP-dependent ligation of citrulline to aspartate to form argininosuccinate, AMP and pyrophosphate. In humans, a defect in the ASS gene causes citrullinemia, a genetic disease characterized by severe vomiting spells and mental retardation. ASS is a homotetrameric enzyme of about 400 amino-acid residues. An arginine residue seems to be important for the enzyme's catalytic mechanism. The sequences of ASS from various prokaryotes, archaeabacteria and eukaryotes show significant similarity. 386 matched cddid_all.tbl CDD cd02000 cd02000 238958 TPP_E1_PDC_ADC_BCADC Thiamine pyrophosphate (TPP) family, E1 of PDC_ADC_BCADC subfamily, TPP-binding module; composed of proteins similar to the E1 components of the human pyruvate dehydrogenase complex (PDC), the acetoin dehydrogenase complex (ADC) and the branched chain alpha-keto acid dehydrogenase/2-oxoisovalerate dehydrogenase complex (BCADC). PDC catalyzes the irreversible oxidative decarboxylation of pyruvate to produce acetyl-CoA in the bridging step between glycolysis and the citric acid cycle. ADC participates in the breakdown of acetoin while BCADC participates in the breakdown of branched chain amino acids. BCADC catalyzes the oxidative decarboxylation of 4-methyl-2-oxopentanoate, 3-methyl-2-oxopentanoate and 3-methyl-2-oxobutanoate (branched chain 2-oxo acids derived from the transamination of leucine, valine and isoleucine). 293 matched cddid_all.tbl CDD cd02001 cd02001 238959 TPP_ComE_PpyrDC Thiamine pyrophosphate (TPP) family, ComE and PpyrDC subfamily, TPP-binding module; composed of proteins similar to sulfopyruvate decarboxylase beta subunit (ComE) and phosphonopyruvate decarboxylase (Ppyr decarboxylase). Methanococcus jannaschii sulfopyruvate decarboxylase (ComDE) is a dodecamer of six alpha (D) subunits and six (E) beta subunits which, catalyzes the decarboxylation of sulfopyruvic acid to sulfoacetaldehyde in the coenzyme M pathway. Ppyr decarboxylase is a homotrimeric enzyme which functions in the biosynthesis of C-P compounds such as bialaphos tripeptide in Streptomyces hygroscopicus. Ppyr decarboxylase and ComDE require TPP and divalent metal cation cofactors. 157 matched cddid_all.tbl CDD cd02002 cd02002 238960 TPP_BFDC Thiamine pyrophosphate (TPP) family, BFDC subfamily, TPP-binding module; composed of proteins similar to Pseudomonas putida benzoylformate decarboxylase (BFDC). P. putida BFDC plays a role in the mandelate pathway, catalyzing the conversion of benzoylformate to benzaldehyde and carbon dioxide. This enzyme is dependent on TPP and a divalent metal cation as cofactors. 178 matched cddid_all.tbl CDD cd02003 cd02003 238961 TPP_IolD Thiamine pyrophosphate (TPP) family, IolD subfamily, TPP-binding module; composed of proteins similar to Rhizobium leguminosarum bv. viciae IolD. IolD plays an important role in myo-inositol catabolism. 205 matched cddid_all.tbl CDD cd02004 cd02004 238962 TPP_BZL_OCoD_HPCL Thiamine pyrophosphate (TPP) family, BZL_OCoD_HPCL subfamily, TPP-binding module; composed of proteins similar to benzaldehyde lyase (BZL), oxalyl-CoA decarboxylase (OCoD) and 2-hydroxyphytanoyl-CoA lyase (2-HPCL). Pseudomonas fluorescens biovar I BZL cleaves the acyloin linkage of benzoin producing 2 molecules of benzaldehyde and enabling the Pseudomonas to grow on benzoin as the sole carbon and energy source. OCoD has a role in the detoxification of oxalate, catalyzing the decarboxylation of oxalyl-CoA to formate. 2-HPCL is a peroxisomal enzyme which plays a role in the alpha-oxidation of 3-methyl-branched fatty acids, catalyzing the cleavage of 2-hydroxy-3-methylacyl-CoA into formyl-CoA and a 2-methyl-branched fatty aldehyde. All these enzymes depend on Mg2+ and TPP for activity. 172 matched cddid_all.tbl CDD cd02005 cd02005 238963 TPP_PDC_IPDC Thiamine pyrophosphate (TPP) family, PDC_IPDC subfamily, TPP-binding module; composed of proteins similar to pyruvate decarboxylase (PDC) and indolepyruvate decarboxylase (IPDC). PDC, a key enzyme in alcoholic fermentation, catalyzes the conversion of pyruvate to acetaldehyde and CO2. It is able to utilize other 2-oxo acids as substrates. In plants and various plant-associated bacteria, IPDC plays a role in the indole-3-pyruvic acid (IPA) pathway, a tryptophan-dependent biosynthetic route to indole-3-acetaldehyde (IAA). IPDC catalyzes the decarboxylation of IPA to IAA. Both PDC and IPDC depend on TPP and Mg2+ as cofactors. 183 matched cddid_all.tbl CDD cd02006 cd02006 238964 TPP_Gcl Thiamine pyrophosphate (TPP) family, Gcl subfamily, TPP-binding module; composed of proteins similar to Escherichia coli glyoxylate carboligase (Gcl). E. coli glyoxylate carboligase, plays a key role in glyoxylate metabolism where it catalyzes the condensation of two molecules of glyoxylate to give tartronic semialdehyde and carbon dioxide. This enzyme requires TPP, magnesium ion and FAD as cofactors. 202 matched cddid_all.tbl CDD cd02007 cd02007 238965 TPP_DXS Thiamine pyrophosphate (TPP) family, DXS subfamily, TPP-binding module; 1-Deoxy-D-xylulose-5-phosphate synthase (DXS) is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis. Terpeniods are plant natural products with important pharmaceutical activity. DXS catalyzes a transketolase-type condensation of pyruvate with D-glyceraldehyde-3-phosphate to form 1-deoxy-D-xylulose-5-phosphate (DXP) and carbon dioxide. The formation of DXP leads to the formation of the terpene precursor IPP (isopentyl diphosphate) and to the formation of thiamine (vitamin B1) and pyridoxal (vitamin B6). 195 matched cddid_all.tbl CDD cd02008 cd02008 238966 TPP_IOR_alpha Thiamine pyrophosphate (TPP) family, IOR-alpha subfamily, TPP-binding module; composed of proteins similar to indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as indolepyruvate or phenylpyruvate, which are generated by the transamination of aromatic amino acids, to the corresponding aryl acetyl-CoA. 178 matched cddid_all.tbl CDD cd02009 cd02009 238967 TPP_SHCHC_synthase Thiamine pyrophosphate (TPP) family, SHCHC synthase subfamily, TPP-binding module; composed of proteins similar to Escherichia coli 2-succinyl-6-hydroxyl-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) synthase (also called MenD). SHCHC synthase plays a key role in the menaquinone biosynthetic pathway, converting isochorismate and 2-oxoglutarate to SHCHC, pyruvate and carbon dioxide. The enzyme requires TPP and a divalent metal cation for activity. 175 matched cddid_all.tbl CDD cd02010 cd02010 238968 TPP_ALS Thiamine pyrophosphate (TPP) family, Acetolactate synthase (ALS) subfamily, TPP-binding module; composed of proteins similar to Klebsiella pneumoniae ALS, a catabolic enzyme required for butanediol fermentation. ALS catalyzes the conversion of 2 molecules of pyruvate to acetolactate and carbon dioxide. ALS does not contain FAD, and requires TPP and a divalent metal cation for activity. 177 matched cddid_all.tbl CDD cd02011 cd02011 238969 TPP_PK Thiamine pyrophosphate (TPP) family, Phosphoketolase (PK) subfamily, TPP-binding module; PK catalyzes the conversion of D-xylulose 5-phosphate and phosphate to acetyl phosphate, D-glyceraldehyde-3-phosphate and H2O. This enzyme requires divalent magnesium ions and TPP for activity. 227 matched cddid_all.tbl CDD cd02012 cd02012 238970 TPP_TK Thiamine pyrophosphate (TPP) family, Transketolase (TK) subfamily, TPP-binding module; TK catalyzes the transfer of a two-carbon unit from ketose phosphates to aldose phosphates. In heterotrophic organisms, TK provides a link between glycolysis and the pentose phosphate pathway and provides precursors for nucleotide, aromatic amino acid and vitamin biosynthesis. In addition, the enzyme plays a central role in the Calvin cycle in plants. Typically, TKs are homodimers. They require TPP and divalent cations, such as magnesium ions, for activity. 255 matched cddid_all.tbl CDD cd02013 cd02013 238971 TPP_Xsc_like Thiamine pyrophosphate (TPP) family, Xsc-like subfamily, TPP-binding module; composed of proteins similar to Alcaligenes defragrans sulfoacetaldehyde acetyltransferase (Xsc). Xsc plays a key role in the degradation of taurine, catalyzing the desulfonation of 2-sulfoacetaldehyde into sulfite and acetyl phosphate. This enzyme requires TPP and divalent metal ions for activity. 196 matched cddid_all.tbl CDD cd02014 cd02014 238972 TPP_POX Thiamine pyrophosphate (TPP) family, Pyruvate oxidase (POX) subfamily, TPP-binding module; composed of proteins similar to Lactobacillus plantarum POX, which plays a key role in controlling acetate production under aerobic conditions. POX decarboxylates pyruvate, producing hydrogen peroxide and the energy-storage metabolite acetylphosphate. It requires FAD in addition to TPP and a divalent cation as cofactors. 178 matched cddid_all.tbl CDD cd02015 cd02015 238973 TPP_AHAS Thiamine pyrophosphate (TPP) family, Acetohydroxyacid synthase (AHAS) subfamily, TPP-binding module; composed of proteins similar to the large catalytic subunit of AHAS. AHAS catalyzes the condensation of two molecules of pyruvate to give the acetohydroxyacid, 2-acetolactate. 2-Acetolactate is the precursor of the branched chain amino acids, valine and leucine. AHAS also catalyzes the condensation of pyruvate and 2-ketobutyrate to form 2-aceto-2-hydroxybutyrate in isoleucine biosynthesis. In addition to requiring TPP and a divalent metal ion as cofactors, AHAS requires FAD. 186 matched cddid_all.tbl CDD cd02016 cd02016 238974 TPP_E1_OGDC_like Thiamine pyrophosphate (TPP) family, E1 of OGDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the 2-oxoglutarate dehydrogenase multienzyme complex (OGDC). OGDC catalyzes the oxidative decarboxylation of 2-oxoglutarate to succinyl-CoA and carbon dioxide, a key reaction of the tricarboxylic acid cycle. 265 matched cddid_all.tbl CDD cd02017 cd02017 238975 TPP_E1_EcPDC_like Thiamine pyrophosphate (TPP) family, E1 of E. coli PDC-like subfamily, TPP-binding module; composed of proteins similar to the E1 component of the Escherichia coli pyruvate dehydrogenase multienzyme complex (PDC). PDC catalyzes the oxidative decarboxylation of pyruvate and the subsequent acetylation of coenzyme A to acetyl-CoA. The E1 component of PDC catalyzes the first step of the multistep process, using TPP and a divalent cation as cofactors. E. coli PDC is a homodimeric enzyme. 386 matched cddid_all.tbl CDD cd02018 cd02018 238976 TPP_PFOR Thiamine pyrophosphate (TPP family), Pyruvate ferredoxin/flavodoxin oxidoreductase (PFOR) subfamily, TPP-binding module; PFOR catalyzes the oxidative decarboxylation of pyruvate to form acetyl-CoA, a crucial step in many metabolic pathways. Archaea, anaerobic bacteria and eukaryotes that lack mitochondria (and therefore pyruvate dehydrogenase) use PFOR to oxidatively decarboxylate pyruvate, with ferredoxin or flavodoxin as the electron acceptor. PFORs can be homodimeric, heterodimeric, or heterotetrameric, depending on the organism. These enzymes are dependent on TPP and a divalent metal cation as cofactors. 237 matched cddid_all.tbl CDD cd02019 cd02019 238977 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate. 69 matched cddid_all.tbl CDD cd02020 cd02020 238978 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor. 147 matched cddid_all.tbl CDD cd02021 cd02021 238979 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits. 150 matched cddid_all.tbl CDD cd02022 cd02022 238980 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis. 179 matched cddid_all.tbl CDD cd02023 cd02023 238981 UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine. 198 matched cddid_all.tbl CDD cd02024 cd02024 238982 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+). This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside. 187 matched cddid_all.tbl CDD cd02025 cd02025 238983 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis. 220 matched cddid_all.tbl CDD cd02026 cd02026 238984 PRK Phosphoribulokinase (PRK) is an enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. This enzyme catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis. 273 matched cddid_all.tbl CDD cd02027 cd02027 238985 APSK "Adenosine 5'-phosphosulfate kinase (APSK) catalyzes the phosphorylation of adenosine 5'-phosphosulfate to form 3'-phosphoadenosine 5'-phosphosulfate (PAPS). The end-product PAPS is a biologically ""activated"" sulfate form important for the assimilation of inorganic sulfate." 149 matched cddid_all.tbl CDD cd02028 cd02028 238986 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK). 179 matched cddid_all.tbl CDD cd02029 cd02029 238987 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis. 277 matched cddid_all.tbl CDD cd02030 cd02030 238988 NDUO42 NADH:Ubiquinone oxioreductase, 42 kDa (NDUO42) is a family of proteins that are highly similar to deoxyribonucleoside kinases (dNK). Members of this family have been identified as one of the subunits of NADH:Ubiquinone oxioreductase (complex I), a multi-protein complex located in the inner mitochondrial membrane. The main function of the complex is to transport electrons from NADH to ubiquinone, which is accompanied by the translocation of protons from the mitochondrial matrix to the inter membrane space. 219 matched cddid_all.tbl CDD cd02032 cd02032 349752 Bchl-like L-subunit of protochlorophyllide reductase. This family of proteins contains BchL and ChlL. Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. Three genes, bchL, bchN and bchB, are involved in light-independent protochlorophyllide reduction in bacteriochlorophyll biosynthesis. In cyanobacteria, algae, and gymnosperms, three similar genes, chlL, chlN and chlB are involved in protochlorophyllide reduction during chlorophylls biosynthesis. BchL/chlL, bchN/chlN and bchB/chlB exhibit significant sequence similarity to the nifH, nifD and nifK subunits of nitrogenase, respectively. Nitrogenase catalyzes the reductive formation of ammonia from dinitrogen. 267 matched cddid_all.tbl CDD cd02033 cd02033 349753 BchX X-subunit of protochlorophyllide reductase. Chlorophyllide reductase converts chlorophylls into bacteriochlorophylls by reducing the chlorin B-ring. This family contains the X subunit of this three-subunit enzyme. Sequence and structure similarity between bchX, protochlorophyllide reductase L subunit (bchL and chlL) and nitrogenase Fe protein (nifH gene) suggest their functional similarity. Members of the BchX family serve as the unique electron donors to their respective catalytic subunits (bchN-bchB, bchY-bchZ and nitrogenase component 1). Mechanistically, they hydrolyze ATP and transfer electrons through a Fe4-S4 cluster. 329 matched cddid_all.tbl CDD cd02034 cd02034 349754 CooC1 accessory protein CooC1. The accessory protein CooC1, a nickel-binding ATPase, participates in the incorporation of nickel into the complex active site ([Ni-4Fe-4S]) cluster of Ni,Fe-dependent carbon monoxide dehydrogenase (CODH). CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function. 249 matched cddid_all.tbl CDD cd02035 cd02035 349755 ArsA Arsenical pump-driving ATPase ArsA. ArsA ATPase functions as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces resistance to the toxic agents. The pump is composed of two subunits, the catalytic ArsA subunit and the membrane subunit ArsB, which are encoded by arsA and arsB genes, respectively. Arsenic efflux in bacteria is catalyzed by either ArsB alone or by ArsAB complex. The ATP-coupled pump, however, is more efficient. ArsA is composed of two homologous halves, A1 and A2, connected by a short linker sequence. 250 matched cddid_all.tbl CDD cd02036 cd02036 349756 MinD septum site-determining protein MinD. Septum site-determining protein MinD is part of the operon MinCDE that determines the site of the formation of a septum at mid-cell, an important part of bacterial cell division. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal role, selecting the mid-cell over other sites through the activation and regulation of MinC and MinE. MinD is a membrane-associated ATPase, related to nitrogenase iron protein. 236 matched cddid_all.tbl CDD cd02037 cd02037 349757 Mrp_NBP35 Mrp/NBP35 ATP-binding protein family. Mrp/NBP35 ATP-binding family protein are typically iron-sulfur (FeS) cluster scaffolds that function to assemble nascent FeS clusters for transfer to FeS-requiring enzymes. Members include the eukaryotic nucleotide-binding protein 1 (NUBP1) which is a component of the cytosolic iron-sulfur (Fe/S) protein assembly (CIA) machinery and the archael [NiFe] hydrogenase maturation protein HypB which is required for nickel insertion into [NiFe] hydrogenase. 213 matched cddid_all.tbl CDD cd02038 cd02038 349758 FlhG-like MinD-like ATPase FlhG. FlhG is a member of the SIMIBI superfamily. FlhG (also known as YlxH) is a major determinant for a variety of flagellation patterns. It effects location and number of bacterial flagella during C-ring assembly. 230 matched cddid_all.tbl CDD cd02039 cd02039 185678 cytidylyltransferase_like Cytidylyltransferase-like domain. Cytidylyltransferase-like domain. Many of these proteins are known to use CTP or ATP and release pyrophosphate. Protein families that contain at least one copy of this domain include citrate lyase ligase, pantoate-beta-alanine ligase, glycerol-3-phosphate cytidyltransferase, ADP-heptose synthase, phosphocholine cytidylyltransferase, lipopolysaccharide core biosynthesis protein KdtB, the bifunctional protein NadR, and a number whose function is unknown. 143 matched cddid_all.tbl CDD cd02040 cd02040 349759 NifH nitrogenase component II NifH. NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia. 265 matched cddid_all.tbl CDD cd02042 cd02042 349760 ParAB_family partition proteins ParAB family. ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in Rhizobium etli symbiotic plasmid. This operon is involved in the plasmid replication and partition. 130 matched cddid_all.tbl CDD cd02043 cd02043 381001 serpinP_plants serpin family P, plant serpins. Plant SERine Proteinase INhibitors (serpins) are potent inhibitors of a range of mammalian serine proteases in vitro, and at least seven serpin genes are expressed in Arabidopsis. Serpins from plants display a wide range of functions including protection of storage protein degradation by exogenous proteases and seed survival within the herbivore digestive tract. Comparison between Arabidopsis AtSerpin1 and other serpins reveals several distinguishing features including a plant-specific insertion between s2B and s3B, with a plant-specific motif YXXGXDXRXF and the presence of a beta-bulge in strand s2C. The conserved Asp-230 and Arg-232 in the motif form a network of hydrogen bonds stabilize a loop region, which is otherwise disordered in many other serpin structures. AtSerpin1 is targeted to the secretory pathway and was shown to interact with cysteine protease RD21 (RESPONSIVE TO DESICCATION-21). RD21 accepts peptides and ligates them to the N termini of acceptor proteins so it has been proposed that AtSerpin1 functions to curb this activity. This subgroup corresponds to clade P of the serpin superfamily. In general, serpins exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 382 matched cddid_all.tbl CDD cd02045 cd02045 381002 serpinC1_AT3 serpin family C member 1, antithrombin III. Antithrombin III (AT3/ATIII) is a non-vitamin K-dependent serine protease that inhibits coagulation by neutralizing the enzymatic activity of thrombin (factors IIa, IXa, Xa). It is the most important anticoagulant molecule in mammalian circulation systems, controlled by its interaction with the cofactor, heparin, which accelerates its interaction with target proteases. This subgroup corresponds to clade C of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants can cause blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 395 matched cddid_all.tbl CDD cd02046 cd02046 381003 serpinH1_CBP1 serpin family H member 1, collagen-binding protein 1. Collagen-binding protein 1 (CBP1, also called heat shock protein 47/hsp47 or colligin), because of its collagen binding ability, is a chaperone specific protein for the correct folding of types I-V procollagen in the endoplasmic reticulum (ER). It is induced under stress conditions through heat shock element-heat shock factor interaction and has been shown to be essential for collagen biosynthesis. Hsp47 transiently binds to procollagen in the ER, dissociates in the cis-Golgi or ER-Golgi intermediate compartment, and is then transported back to the ER via its RDEL retention sequence. Hsp47 recognizes collagenous (Gly-Xaa-Arg) repeats on triple-helical procollagen and can prevent local unfolding and/or aggregate formation of procollagen. Hsp47 is a non-inhibitory member of the SERPIN superfamily and corresponds to clade H. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants can cause blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 382 matched cddid_all.tbl CDD cd02047 cd02047 381004 serpinD1_HCF2 serpin family D member 1, Heparin cofactor II. Heparin cofactor II (HCF2/HC-II, also called protease inhibitor leuserpin-2/hLS2) is a protein encoded by the SERPIND1 gene that inhibits thrombin, the final protease of the coagulation cascade. HCII is allosterically activated by binding to cell surface glycosaminoglycans (GAGs). The specificity of HCII for thrombin is conferred by a highly acidic hirudin-like N-terminal tail, which becomes available after GAG binding for interaction with the anion-binding exosite I of thrombin. HCII deficiency can lead to increased thrombin generation and a hypercoagulable state. This subgroup corresponds to clade D of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 449 matched cddid_all.tbl CDD cd02048 cd02048 381005 serpinI1_NSP serpin family I member 1, neuroserpin. Neuroserpin (NSP, also called proteinase inhibitor 12/PI-12) is an inhibitory member of the serpin family that reacts preferentially with tissue-type plasminogen activator (tPA). It is located in neurons in regions of the brain where tPA is also found, suggesting that neuroserpin is the selective inhibitor of tPA in the central nervous system (CNS). This subgroup corresponds to clade I of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 372 matched cddid_all.tbl CDD cd02050 cd02050 381006 serpinG1_C1-INH serpin family G member 1, plasma proteinase C1 inhibitor. Plasma proteinase C1 inhibitor (C1-INH/C1IN) is a protease inhibitor of the serpin family. It plays a pivotal role in regulating the activation of the classical complement pathway and of the contact system, via regulating bradykinin formation, inhibiting factor XII and kallikrein of the contact system, and via acting on factor XI in the coagulation cascade. This subgroup corresponds to clade G of the serpin superfamily. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 362 matched cddid_all.tbl CDD cd02051 cd02051 381007 serpinE1_PAI-1 serpin family E member 1, plasminogen activator inhibitor-1. Plasminogen activator inhibitor-1 (PAI-1/PLANH1, also called endothelial PAI) is the primary, fast-acting inhibitor of plasminogen activators. It is often bound to vitronectin, an abundant component of the extracellular matrix in many tissues. PAI1 deficiency is a rare bleeding disorder that causes excessive or prolonged bleeding due to blood clots being broken down too early. PAI-1 is a member of the serpin superfamily and belongs to clade E. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 374 matched cddid_all.tbl CDD cd02052 cd02052 381008 serpinF1_PEDF serpin family F member 1, Pigment epithelium-derived factor (PEDF). Pigment epithelium-derived factor (PEDF, also called capsin or EPC-1) is an extracellular component of the retinal interphotoreceptor matrix, vitreous humor, and aqueous humor of the adult eye. PEDF is non-inhibitory member of the serpin superfamily. It exhibits neurotrophic, neuroprotective and antiangiogenic properties and is widely expressed in the developing and adult nervous systems. This subgroup corresponds to clade F1 of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 373 matched cddid_all.tbl CDD cd02053 cd02053 381009 serpinF2_A2AP serpin family F member 2, alpha2-antiplasmin inhibitor. Alpha2-antiplasmin inhibitor (A2AP/API, also called plasmin inhibitor/PLI or alpha-2-antiplasmin) is the primary inhibitor of plasmin, a proteinase that digests fibrin, the main component of blood clots. Alpha2AP forms an inactive 1:1 stoichiometric complex with plasmin. It also rapidly crosslinks to fibrin during blood clotting by activated coagulation factor XIII, and as a consequence fibrin becomes more resistant to fibrinolysis. Therefore alpha2AP is important in modulating the effectiveness and persistence of fibrin with respect to its susceptibility to digestion and removal by plasmin. This subgroup corresponds to clade F2 of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 363 matched cddid_all.tbl CDD cd02054 cd02054 381010 serpinA8_AGT serpin family A member 8, angiotensinogen. Angiotensinogen (AGT) is part of the renin-angiotensin system (RAS), which plays an important role in blood pressure regulation, renal hemodynamics, as well as fluid and electrolyte homeostasis. It is also involved in normal and abnormal growth processes. The growth promoting actions of angiotensin have been shown in a variety of cells and tissues. This subgroup represents clade A8 of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 446 matched cddid_all.tbl CDD cd02055 cd02055 381011 serpinA10_PZI serpin family A member 10, protein Z-dependent protease inhibitor. Protein Z-dependent protease inhibitor (ZPI) is a member of the serpin superfamily of proteinase inhibitors (clade A10). ZPI inhibits coagulation factor Xa, dependent on protein Z (PZ), a vitamin K-dependent plasma protein. ZPI also inhibits factor XIa in a process that does not require PZ. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 380 matched cddid_all.tbl CDD cd02056 cd02056 381012 serpinA1_A1AT serpin family A member 1, alpha-1-antitrypsin. Alpha-1-antitrypsin (also called A1AT, A1A, AAT, alpha1-proteinase inhibitor/A1PI, alpha1-antiproteinase/A1AP, proteinase inhibitor/PI, and serum trypsin inhibitor) is a protease inhibitor that belongs to the serpin superfamily. It is encoded in humans by the SERPINA1 gene. When the blood contains inadequate amounts of A1AT or functionally defective A1AT (such as in alpha-1 antitrypsin deficiency), neutrophil elastase is excessively free to break down elastin, degrading the elasticity of the lungs, which results in respiratory complications, such as chronic obstructive pulmonary disease. Normally, A1AT leaves its site of origin, the liver, and joins the systemic circulation; defective A1AT fails to do so, building up in the liver, which results in cirrhosis. This family contains other A1AT-like members of clade A of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 368 matched cddid_all.tbl CDD cd02057 cd02057 381013 serpinB5_maspin serpin family B member 5, mammary serine proteinase inhibitor. Mammary serine proteinase inhibitor (maspin, also known as proteinase inhibitor 5/PI5), a member of the serpin superfamily, is related to the ov-serpins, with a multitude of effects on cells and tissues at an assortment of developmental stages. Maspin has tumor suppressing activity against breast and prostate cancer. All true inhibitory serpins rely on an exposed reactive center loop (RCL) to inhibit their target proteinase, in which the proteinase cleaves the RCL and becomes incorporated into a serpin-proteinase complex. Maspin differs from other serpins in that its RCL is necessary for activity, but it is not cleaved or rearranged. The ovalbumin family of serpins (ov-serpins) is a family of closely related proteins, whose members can be secreted (ovalbumin), cytosolic (leukocyte elastase inhibitor, LEI), or targeted to both compartments (plasminogen activator inhibitor 2, PAI-2). It also characterized by N- and C-terminal extensions, the absence of a signal peptide, and a Ser rather than an Asn residue at the penultimate position. The ov-serpins corresponds to clade B of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants can cause blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 375 matched cddid_all.tbl CDD cd02058 cd02058 381014 serpinB_MENT-like serpin family B, Myeloid and Erythroid Nuclear Termination stage-specific protein (MENT) and similar proteins. Gallus gallus Myeloid and Erythroid Nuclear Termination stage-specific protein (MENT) is a nonhistone heterochromatin-associated serpin that is an effective inhibitor of cathepsin L as well as the papain-like cysteine proteases cathepsins K, L, and V in vitro. It's reactive center loop, which is essential for chromatin bridging, is able to mediate formation of a loop-sheet oligomer. It also contains an M-loop which contains two critical functional motifs: a classical nuclear localization signal (NLS) that is required for nuclear import and an AT-hook motif that is involved in chromatin and DNA binding. MENT belongs to the clade B of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants can cause blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 406 matched cddid_all.tbl CDD cd02059 cd02059 381015 serpinB14_OVA serpin family B member 14, ovalbumin. The chicken protein ovalbumin (OVA3), a storage protein from egg white, lacking a loop insertion mechanism and therefore protease inhibitory activity, is a historical member of the serpin superfamily and the founding member of the subgroup known as ov-serpins (ovalbumin-related serpins). It has several modifications, including N-terminal acetylation, phosphorylation, and glycosylation. Ovalbumin is secreted from the cell, targeted by an internal signal sequence, rather than the N-terminal signal sequence commonly found in other secreted proteins. The ovalbumin family of serpins (ov-serpins) is a family of closely related proteins, whose members can be secreted (ovalbumin), cytosolic (leukocyte elastase inhibitor, LEI), or targeted to both compartments (plasminogen activator inhibitor 2, PAI-2). It also characterized by N- and C-terminal extensions, the absence of a signal peptide, and a Ser rather than an Asn residue at the penultimate position. The ov-serpins corresponds to clade B of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants can cause blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 385 matched cddid_all.tbl CDD cd02062 cd02062 380311 Nitro_FMN_reductase nitroreductase family protein. Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are described as NAD(P)H:FMN oxidoreductases, oxygen-insensitive nitroreductase, flavin reductase P, dihydropteridine reductase, NADH oxidase or NADH dehydrogenase. 139 matched cddid_all.tbl CDD cd02064 cd02064 185679 FAD_synthetase_N FAD synthetase, N-terminal domain of the bifunctional enzyme. FAD synthetase_N. N-terminal domain of the bifunctional riboflavin biosynthesis protein riboflavin kinase/FAD synthetase. These enzymes have both ATP:riboflavin 5'-phosphotransferase and ATP:FMN-adenylyltransferase activities. The N-terminal domain is believed to play a role in the adenylylation reaction of FAD synthetases. The C-terminal domain is thought to have kinase activity. FAD synthetase is present among all kingdoms of life. However, the bifunctional enzyme is not found in mammals, which use separate enzymes for FMN and FAD formation. 180 matched cddid_all.tbl CDD cd02065 cd02065 239016 B12-binding_like B12 binding domain (B12-BD). Most of the members bind different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide. This domain is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins. Not all members of this family contain the conserved binding motif. 125 matched cddid_all.tbl CDD cd02066 cd02066 239017 GRX_family Glutaredoxin (GRX) family; composed of GRX, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH -> GSH reductase -> GSH -> GRX -> protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known including human GRX1 and GRX2, as well as E. coli GRX1 and GRX3, which are members of this family. E. coli GRX2, however, is a 24-kDa protein that belongs to the GSH S-transferase (GST) family. 72 matched cddid_all.tbl CDD cd02067 cd02067 239018 B12-binding B12 binding domain (B12-BD). This domain binds different cobalamid derivates, like B12 (adenosylcobamide) or methylcobalamin or methyl-Co(III) 5-hydroxybenzimidazolylcobamide, it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. Cobalamin undergoes a conformational change on binding the protein; the dimethylbenzimidazole group, which is coordinated to the cobalt in the free cofactor, moves away from the corrin and is replaced by a histidine contributed by the protein. The sequence Asp-X-His-X-X-Gly, which contains this histidine ligand, is conserved in many cobalamin-binding proteins. 119 matched cddid_all.tbl CDD cd02068 cd02068 239019 radical_SAM_B12_BD B12 binding domain_like associated with radical SAM domain. This domain shows similarity with B12 (adenosylcobamide) binding domains found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase, but it lacks the signature motif Asp-X-His-X-X-Gly, which contains the histidine that acts as a cobalt ligand. The function of this domain remains unclear. 127 matched cddid_all.tbl CDD cd02069 cd02069 239020 methionine_synthase_B12_BD B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy). 213 matched cddid_all.tbl CDD cd02070 cd02070 239021 corrinoid_protein_B12-BD B12 binding domain of corrinoid proteins. A family of small methanogenic corrinoid proteins that bind methyl-Co(III) 5-hydroxybenzimidazolylcobamide as a cofactor. They play a role on the methanogenesis from trimethylamine, dimethylamine or monomethylamine, which is initiated by a series of corrinoid-dependent methyltransferases. 201 matched cddid_all.tbl CDD cd02071 cd02071 239022 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation. 122 matched cddid_all.tbl CDD cd02072 cd02072 239023 Glm_B12_BD B12 binding domain of glutamate mutase (Glm). Glutamate mutase catalysis the conversion of (S)-glutamate with (2S,3S)-3-methylaspartate. The rearrangement reaction is initiated by the extraction of a hydrogen from the protein-bound substrate by a 5'-desoxyadenosyl radical, which is generated by the homolytic cleavage of the organometallic bond of the cofactor B12. Glm is a heterotetrameric molecule consisting of two alpha and two epsilon polypeptide chains. 128 matched cddid_all.tbl CDD cd02073 cd02073 319770 P-type_ATPase_APLT_Dnf-like Aminophospholipid translocases (APLTs), similar to Saccharomyces cerevisiae Dnf1-3p, Drs2p, and human ATP8A2, -10D, -11B, -11C. Aminophospholipid translocases (APLTs), also known as type 4 P-type ATPases, act as flippases, and translocate specific phospholipids from the exoplasmic leaflet to the cytoplasmic leaflet of biological membranes. Yeast Dnf1 and Dnf2 mediate the transport of phosphatidylethanolamine, phosphatidylserine, and phosphatidylcholine from the outer to the inner leaflet of the plasma membrane. This subfamily includes mammalian flippases such as ATP11C which may selectively transports PS and PE from the outer leaflet of the plasma membrane to the inner leaflet. It also includes Arabidopsis phospholipid flippases including ALA1, and Caenorhabditis elegans flippases, including TAT-1, the latter has been shown to facilitate the inward transport of phosphatidylserine. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 836 matched cddid_all.tbl CDD cd02076 cd02076 319771 P-type_ATPase_H plant and fungal plasma membrane H(+)-ATPases, and related bacterial and archaeal putative H(+)-ATPases. This subfamily includes eukaryotic plasma membrane H(+)-ATPase which transports H(+) from the cytosol to the extracellular space, thus energizing the plasma membrane for the uptake of ions and nutrients, and is expressed in plants and fungi. This H(+)-ATPase consists of four domains: a transmembrane domain and three cytosolic domains: nucleotide-binding domain, phosphorylation domain and actuator domain, and belongs to the P-type ATPase type III subfamily. This subfamily also includes the putative P-type H(+)-ATPase, MJ1226p of the anaerobic hyperthermophilic archaea Methanococcus jannaschii. The P-type ATPases, are a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 781 matched cddid_all.tbl CDD cd02077 cd02077 319772 P-type_ATPase_Mg magnesium transporting ATPase (MgtA), similar to Escherichia coli MgtA and Salmonella typhimurium MgtA. MgtA is a membrane protein which actively transports Mg(2+) into the cytosol with its electro-chemical gradient rather than against the gradient as other cation transporters do. It may act both as a transporter and as a sensor for Mg(2+). In Salmonella typhimurium and Escherichia coli, the two-component system PhoQ/PhoP regulates the transcription of the mgtA gene by sensing Mg(2+) concentrations in the periplasm. MgtA is activated by cardiolipin and it highly sensitive to free magnesium in vitro. It consists of a transmembrane domain and three cytosolic domains: nucleotide-binding domain, phosphorylation domain and actuator domain, and belongs to the P-type ATPase type III subfamily. The P-type ATPases, are a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 768 matched cddid_all.tbl CDD cd02078 cd02078 319773 P-type_ATPase_K potassium-transporting ATPase ATP-binding subunit, KdpB, a subunit of the prokaryotic high-affinity potassium uptake system KdpFABC; similar to Escherichia coli KdpB. KdpFABC is a prokaryotic high-affinity potassium uptake system. It is expressed under K(+) limiting conditions when the other potassium transport systems are not able to provide a sufficient flow of K(+) into the bacteria. The KdpB subunit represents the catalytic subunit performing ATP hydrolysis. KdpB is comprised of four domains: the transmembrane domain, the nucleotide-binding domain, the phosphorylation domain, and the actuator domain. The P-type ATPases, are a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 667 matched cddid_all.tbl CDD cd02079 cd02079 319774 P-type_ATPase_HM P-type heavy metal-transporting ATPase. Heavy metal-transporting ATPases (Type IB ATPases) transport heavy metal ions (Cu(+), Cu(2+), Zn(2+), Cd(2+), Co(2+), etc.) across biological membranes. These ATPases include mammalian copper-transporting ATPases, ATP7A and ATP7B, Bacillus subtilis CadA which transports cadmium, zinc and cobalt out of the cell, Bacillus subtilis ZosA/PfeT which transports copper, and perhaps also zinc and ferrous iron, Archaeoglobus fulgidus CopA and CopB, Staphylococcus aureus plasmid pI258 CadA, a cadmium-efflux ATPase, and Escherichia coli ZntA which is selective for Pb(2+), Zn(2+), and Cd(2+). The characteristic N-terminal heavy metal associated (HMA) domain of this group is essential for the binding of metal ions. This family belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 617 matched cddid_all.tbl CDD cd02080 cd02080 319775 P-type_ATPase_cation P-type cation-transporting ATPase similar to Exiguobacterium aurantiacum Mna, an Na(+)-ATPase, and Synechocystis sp. PCC 6803 PMA1, a putative Ca(2+)-ATPase. This subfamily includes the P-type Na(+)-ATPase of an alkaliphilic bacterium Exiguobacterium aurantiacum Mna and cyanobacterium Synechocystis sp. PCC 6803 PMA1, a cation-transporting ATPase which may translocate calcium. The P-type ATPases, are a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 819 matched cddid_all.tbl CDD cd02081 cd02081 319776 P-type_ATPase_Ca_PMCA-like animal plasma membrane Ca2(+)-ATPases (PMCA), similar to human ATP2B1-4/PMCA1-4, and related Ca2(+)-ATPases including Saccharomyces cerevisiae vacuolar PMC1. Animal PMCAs function to export Ca(2+) from cells and play a role in regulating Ca(2+) signals following stimulus induction and in preventing calcium toxicity. Many PMCA pump variants exist due to alternative splicing of transcripts. PMCAs are regulated by the binding of calmodulin or by kinase-mediated phosphorylation. Saccharomyces cerevisiae vacuolar transporter Pmc1p facilitates the accumulation of Ca2+ into vacuoles. Pmc1p is not regulated by direct calmodulin binding but responds to the calmodulin/calcineurin-signaling pathway and is controlled by the transcription factor complex Tcn1p/Crz1p. Similarly, the expression of the gene for Dictyostelium discoideum Ca(2+)-ATPase PAT1, patA, is under the control of a calcineurin-dependent transcription factor. Plant vacuolar Ca(2+)-ATPases, are regulated by direct-calmodulin binding. Plant Ca(2+)-ATPases are present at various cellular locations including the plasma membrane, endoplasmic reticulum, chloroplast and vacuole. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 721 matched cddid_all.tbl CDD cd02082 cd02082 319777 P-type_ATPase_cation P-type cation-transporting ATPases, similar to human ATPase type 13A1-A4 (ATP13A1-A4) proteins and Saccharomyces cerevisiae Ypk9p and Spf1p. Saccharomyces cerevisiae Yph9p localizes to the yeast vacuole and may play a role in sequestering heavy metal ions, its deletion confers sensitivity for growth for cadmium, manganese, nickel or selenium. Saccharomyces 1 Spf1p may mediate manganese transport into the endoplasmic reticulum. Human ATP13A2 (PARK9/CLN12) is a lysosomal transporter with zinc as the possible substrate. Mutation in the ATP13A2 gene has been linked to Parkinson's disease and Kufor-Rakeb syndrome, and to neuronal ceroid lipofuscinoses. ATP13A3/AFURS1 is a candidate gene for oculo auriculo vertebral spectrum (OAVS), being one of nine genes included in a 3q29 microduplication in a patient with OAVS. Mutation in the human ATP13A4 may be involved in a speech-language disorder. The expression of ATP13A1 has been followed during mouse development, ATP13A1 transcript expression showed an increase as development progressed, with the highest expression at the peak of neurogenesis. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 786 matched cddid_all.tbl CDD cd02083 cd02083 319778 P-type_ATPase_SERCA sarco/endoplasmic reticulum Ca(2+)-ATPase (SERCA), similar to mammalian ATP2A1-3/SERCA1-3. SERCA is a transmembrane (Ca2+)-ATPase and a major regulator of Ca(2+) homeostasis and contractility in cardiac and skeletal muscle. It re-sequesters cytoplasmic Ca(2+) to the sarco/endoplasmic reticulum store, thereby also terminating Ca(2+)-induced signaling such as in muscle contraction. Three genes (ATP2A1-3/SERCA1-3) encode SERCA pumps in mammals, further isoforms exist due to alternative splicing of transcripts. The activity of SERCA is regulated by two small membrane proteins called phospholamban and sarcolipin. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 979 matched cddid_all.tbl CDD cd02085 cd02085 319779 P-type_ATPase_SPCA golgi-associated secretory pathway Ca(2+) transport ATPases, similar to human ATPase secretory pathway Ca(2+) transporting 1/hSPCA1 and Saccharomyces cerevisiae Ca(2+)/Mn(2+)-transporting P-type ATPase, Pmr1p. SPCAs are Ca(2+) pumps important for the golgi-associated secretion pathway, in addition some function as Mn(2+) pumps in Mn(2+) detoxification. Saccharomyces cerevisiae Pmr1p is a high affinity Ca(2+)/Mn(2+) ATPase which transports Ca(2+) and Mn(2+) from the cytoplasm into the Golgi. Pmr1p also contributes to Cd(2+) detoxification. This subfamily includes human SPCA1 and SPCA2, encoded by the ATP2C1 and ATP2C2 genes; autosomal dominant Hailey-Hailey disease is caused by mutations in the human ATP2C1 gene. It also includes Strongylocentrotus purpuratus testis secretory pathway calcium transporting ATPase SPCA which plays an important role in fertilization. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 804 matched cddid_all.tbl CDD cd02086 cd02086 319780 P-type_ATPase_Na_ENA fungal-type Na(+)-ATPase, similar to the plasma membrane sodium transporters Saccharomyces cerevisiae Ena1p, Ena2p and Ustilago maydis Ena1, and the endoplasmic reticulum sodium transporter Ustilago maydis Ena2. Fungal-type Na(+)-ATPase (also called ENA ATPases). This subfamily includes the Saccharomyces cerevisiae plasma membrane transporters: Na(+)/Li(+)-exporting ATPase Ena1p which may also extrudes K(+), and Na(+)-exporting P-type ATPase Ena2p. It also includes Ustilago maydis plasma membrane Ena1, an K(+)/Na(+)-ATPase whose chief role is to pump Na(+) and K(+) out of the cytoplasm, especially at high pH values, and endoplasmic reticulum Ena2 ATPase which mediates Na(+) or K(+) fluxes in the ER or in other endomembranes. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 920 matched cddid_all.tbl CDD cd02089 cd02089 319781 P-type_ATPase_Ca_prok prokaryotic P-type Ca(2+)-ATPase similar to Synechococcus elongatus sp. strain PCC 7942 PacL and Listeria monocytogenes LMCA1. Ca(2+) transport ATPase is a plasma membrane protein which pumps Ca(2+) ion out of the cytoplasm. This prokaryotic subfamily includes the Ca(2+)-ATPase Synechococcus elongatus PacL, Listeria monocytogenes Ca(2+)-ATPase 1 (LMCA1) which has a low Ca(2+) affinity and a high pH optimum (pH about 9) and may remove Ca(2+) from the microorganism in environmental conditions when e.g. stressed by high Ca(2+) and alkaline pH, and the Bacillus subtilis putative P-type Ca(2+)-transport ATPase encoded by the yloB gene, which is expressed during sporulation. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 674 matched cddid_all.tbl CDD cd02092 cd02092 319782 P-type_ATPase_FixI-like Rhizobium meliloti FixI and related proteins; belongs to P-type heavy metal-transporting ATPase subfamily. FixI may be a pump of a specific cation involved in symbiotic nitrogen fixation. The Rhizobium fixI gene is part of an operon conserved among rhizobia, fixGHIS. FixG, FixH, FixI, and FixS may participate in a membrane-bound complex coupling the FixI cation pump with a redox process catalyzed by FixG, an iron-sulfur protein. This subclass of P-type ATPase is also referred to as CPx-type ATPases because their amino acid sequences contain a characteristic CPC or CPH motif associated with a stretch of hydrophobic amino acids and N-terminal ion-binding sequences. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 605 matched cddid_all.tbl CDD cd02094 cd02094 319783 P-type_ATPase_Cu-like P-type heavy metal-transporting ATPase, similar to human copper-transporting ATPases, ATP7A and ATP7B. The mammalian copper-transporting P-type ATPases, ATP7A and ATP7B are key molecules required for the regulation and maintenance of copper homeostasis. Menkes and Wilson diseases are caused by mutation in ATP7A and ATP7B respectively. This subfamily includes other copper-transporting ATPases such as: Bacillus subtilis CopA , Archeaoglobus fulgidus CopA, and Saccharomyces cerevisiae Ccc2p. This subclass of P-type ATPase is also referred to as CPx-type ATPases because their amino acid sequences contain a characteristic CPC or CPH motif associated with a stretch of hydrophobic amino acids and N-terminal ion-binding sequences. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 647 matched cddid_all.tbl CDD cd02106 cd02106 259797 SPFH_like core domain of the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model summarizes proteins similar to stomatin, prohibitin, flotillin, HflK/C (SPFH) and podocin. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Many superfamily members are associated with lipid rafts. Individual proteins of the SPFH superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions. Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins. Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons, and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins. Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease, and in cancer invasion and metastasis. Mutations in the podocin gene give rise to autosomal recessive steroid resistant nephritic syndrome. 110 matched cddid_all.tbl CDD cd02107 cd02107 239025 YedY_like_Moco YedY_like molybdopterin cofactor (Moco) binding domain, a subgroup of the sulfite oxidase (SO) family of molybdopterin binding domains. Escherichia coli YedY has been proposed to form a heterodimer, consisting of a soluble catalytic subunit termed YedY, which is likely membrane-anchored by a heme-containing trans-membrane subunit YedZ. Preliminary results indicate that YedY may represent a new type of membrane-associated bacterial reductase. Common features of all known members of this family are that they contain one single pterin cofactor and part of the coordination of the metal (Mo) is a cysteine ligand of the protein and that they catalyze the transfer of an oxygen to or from a lone pair of electrons on the substrate. 218 matched cddid_all.tbl CDD cd02108 cd02108 239026 bact_SO_family_Moco bacterial subgroup of the sulfite oxidase (SO) family of molybdopterin binding domains. This domain is found in a variety of oxidoreductases. Common features of all known members of this family, like sulfite oxidase and nitrite reductase, are that they contain one single pterin cofactor and part of the coordination of the metal (Mo) is a cysteine ligand of the protein and that they catalyze the transfer of an oxygen to or from a lone pair of electrons on the substrate. The specific function of this subgroup is unknown. 185 matched cddid_all.tbl CDD cd02109 cd02109 239027 arch_bact_SO_family_Moco bacterial and archael members of the sulfite oxidase (SO) family of molybdopterin binding domains. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). Common features of all known members of this family are that they contain one single pterin cofactor and part of the coordination of the metal (Mo) is a cysteine ligand of the protein and that they catalyze the transfer of an oxygen to or from a lone pair of electrons on the substrate. The specific function of this subgroup is unknown. 180 matched cddid_all.tbl CDD cd02110 cd02110 239028 SO_family_Moco_dimer Subgroup of sulfite oxidase (SO) family molybdopterin binding domains that contains conserved dimerization domain. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). 317 matched cddid_all.tbl CDD cd02111 cd02111 239029 eukary_SO_Moco molybdopterin binding domain of sulfite oxidase (SO). SO catalyzes the terminal reaction in the oxidative degradation of the sulfur-containing amino acids cysteine and methionine. Common features of all known members of the sulfite oxidase (SO) family of molybdopterin binding domains are that they contain one single pterin cofactor and part of the coordination of the metal (Mo) is a cysteine ligand of the protein and that they catalyze the transfer of an oxygen to or from a lone pair of electrons on the substrate. 365 matched cddid_all.tbl CDD cd02112 cd02112 239030 eukary_NR_Moco molybdopterin binding domain of eukaryotic nitrate reductase (NR). Assimilatory NRs catalyze the reduction of nitrate to nitrite which is subsequently converted to NH4+ by nitrite reductase. Eukaryotic assimilatory nitrate reductases are cytosolic homodimeric enzymes with three prosthetic groups, flavin adenine dinucleotide (FAD), cytochrome b557, and Mo cofactor, which are located in three functional domains. Common features of all known members of the sulfite oxidase (SO) family of molybdopterin binding domains are that they contain one single pterin cofactor and part of the coordination of the metal (Mo) is a cysteine ligand of the protein and that they catalyze the transfer of an oxygen to or from a lone pair of electrons on the substrate. 386 matched cddid_all.tbl CDD cd02113 cd02113 239031 bact_SoxC_Moco bacterial SoxC is a member of the sulfite oxidase (SO) family of molybdopterin binding domains. SoxC is involved in oxidation of sulfur compounds during chemolithothrophic growth. Together with SoxD, a small c-type heme containing subunit, it forms a hetrotetrameric sulfite dehydrogenase. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). Common features of all known members of this family are that they contain one single pterin cofactor and part of the coordination of the metal (Mo) is a cysteine ligand of the protein and that they catalyze the transfer of an oxygen to or from a lone pair of electrons on the substrate. 326 matched cddid_all.tbl CDD cd02114 cd02114 239032 bact_SorA_Moco sulfite:cytochrome c oxidoreductase subunit A (SorA), molybdopterin binding domain. SorA is involved in oxidation of sulfur compounds during chemolithothrophic growth. Together with SorB, a small c-type heme containing subunit, it forms a hetrodimer. It is a member of the sulfite oxidase (SO) family of molybdopterin binding domains. This molybdopterin cofactor (Moco) binding domain is found in a variety of oxidoreductases, main members of this family are nitrate reductase (NR) and sulfite oxidase (SO). Common features of all known members of this family are that they contain one single pterin cofactor and part of the coordination of the metal (Mo) is a cysteine ligand of the protein and that they catalyze the transfer of an oxygen to or from a lone pair of electrons on the substrate. 367 matched cddid_all.tbl CDD cd02115 cd02115 239033 AAK Amino Acid Kinases (AAK) superfamily, catalytic domain; present in such enzymes like N-acetylglutamate kinase (NAGK), carbamate kinase (CK), aspartokinase (AK), glutamate-5-kinase (G5K) and UMP kinase (UMPK). The AAK superfamily includes kinases that phosphorylate a variety of amino acid substrates. These kinases catalyze the formation of phosphoric anhydrides, generally with a carboxylate, and use ATP as the source of the phosphoryl group; are involved in amino acid biosynthesis. Some of these kinases control the process via allosteric feed-back inhibition. 248 matched cddid_all.tbl CDD cd02116 cd02116 153139 ACT ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has been detected in a number of diverse proteins; some of these proteins are involved in amino acid and purine biosynthesis, phenylalanine hydroxylation, regulation of bacterial metabolism and transcription, and many remain to be characterized. ACT domain-containing enzymes involved in amino acid and purine synthesis are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of D-3-phosphoglycerate dehydrogenase and the bifunctional chorismate mutase-prephenate dehydratase enzyme (P-protein), respectively. Aspartokinases typically consist of two C-terminal ACT domains in a tandem repeat, but the second ACT domain is inserted within the first, resulting in, what is normally the terminal beta strand of ACT2, formed from a region N-terminal of ACT1. ACT domain repeats have been shown to have nonequivalent ligand-binding sites with complex regulatory patterns such as those seen in the bifunctional enzyme, aspartokinase-homoserine dehydrogenase (ThrA). In other enzymes, such as phenylalanine hydroxylases, the ACT domain appears to function as a flexible small module providing allosteric regulation via transmission of conformational changes, these conformational changes are not necessarily initiated by regulatory ligand binding at the ACT domain itself. ACT domains are present either singularly, N- or C-terminal, or in pairs present C-terminal or between two catalytic domains. Unique to cyanobacteria are four ACT domains C-terminal to an aspartokinase domain. A few proteins are composed almost entirely of ACT domain repeats as seen in the four ACT domain protein, the ACR protein, found in higher plants; and the two ACT domain protein, the glycine cleavage system transcriptional repressor (GcvR) protein, found in some bacteria. Also seen are single ACT domain proteins similar to the Streptococcus pneumoniae ACT domain protein (uncharacterized pdb structure 1ZPV) found in both bacteria and archaea. Purportedly, the ACT domain is an evolutionarily mobile ligand binding regulatory module that has been fused to different enzymes at various times. 60 matched cddid_all.tbl CDD cd02117 cd02117 349761 NifH-like NifH family. This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the protochlorophyllide reductase, and the BchX subunit of the Chlorophyllide reductase. Members of this family use energy from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for substrate reduction 266 matched cddid_all.tbl CDD cd02120 cd02120 239035 PA_subtilisin_like PA_subtilisin_like: Protease-associated domain containing subtilisin-like proteases. This group contains various PA domain-containing subtilisin-like proteases including melon cucumisin, Arabidopsis thaliana Ara12, a nodule specific serine protease from Alnus glutinosa ag12, members of the tomato P69 family, and tomato LeSBT2. These proteins belong to the peptidase S8 family. Cucumisin from the juice of melon fruits is a thermostable serine peptidase, with a broad substrate specificity for oligopeptides and proteins. A. thaliana Ara12 is a thermostable, extracellular serine protease, found chiefly in silique tissue and stem tissue. Ara12 is stimulated by Ca2+ ions. A. glutinosa ag12 is expressed at high levels in the nodules, and at low levels in the shoot tips; it is implicated in both symbiotic and non-symbiotic processes in plant development. The tomato P69 protease family is comprised of various protein isoforms of approximately 69KDa. These isoforms accumulate extracellularly. Some of the P69 genes are tightly regulated in a tissue specific fashion, and by environmental and developmental signals. For example: infection with avirulent bacteria activates transcription of the genes for the P69 B and C isoforms, the P69 E transcript was detected only in roots, and the P69F transcript only in hydathodes. The Tomato LeSBT2 subtilase transcript was not detected in flowers and roots, but was present in cotyledons and leaves. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. 126 matched cddid_all.tbl CDD cd02121 cd02121 239036 PA_GCPII_like PA_GCPII_like: Protease-associated domain containing protein, glutamate carboxypeptidase II (GCPII)-like. This group contains various PA domain-containing proteins similar to GCPII including, GCPIII (NAALADase2) and NAALADase L. These proteins belong to the peptidase M28 family. GCPII is also known N-acetylated-alpha-linked acidic dipeptidase (NAALDase1), folate hydrolase or prostate-specific membrane antigen (PSMA). GCPII is found in various human tissues including prostate, small intestine, and the central nervous system. In the brain, GCPII is known as NAALDase1, it functions as a NAALDase hydrolyzing the neuropeptide N-acetyl-L-aspartyl-L-glutamate (alpha-NAAG), to release free glutamate. In the small intestine, GCPII releases the terminal glutamate from poly-gamma-glutamated folates. GCPII (PSMA) is a useful cancer marker; its expression is markedly increased in prostate cancer and in tumor-associated neovasculature. GCPIII hydrolyzes alpha-NAAG with a lower efficiency than does GCPII; NAALADase L is not able to hydrolyze alpha-NAAG. The GCPII PA domain (referred to as the apical domain) participates in substrate binding and may act as a protein-protein interaction domain. 220 matched cddid_all.tbl CDD cd02122 cd02122 239037 PA_GRAIL_like PA _GRAIL_like: Protease-associated (PA) domain GRAIL-like. This group includes PA domain containing E3 (ubiquitin ligases) similar to human GRAIL (gene related to anergy in lymphocytes) protein. Proteins in this group contain a C3H2C3 RING finger. E3 ubiquitin ligase is part of an enzymic cascade, the end result of which is the ubiquitination of proteins. In this cascade, E1 activates the ubiquitin, the activated ubiquitin is carried by E2, and E3 recognizes the acceptor protein as well as catalyzes the transfer of the activated ubiquitin from E2 to this acceptor. GRAIL, a transmembrane protein localized in the endosomes, controls the development of T cell clonal anergy, and may ubiquitinate membrane-associated targets for T cell activation. GRAIL1 is associated with, and regulated by, two isoforms of otubain 1 (the ubiquitin-specific protease). Additional E3s belonging to this group include human (h)Goliath and Xenopus GREUL1 (Goliath Related E3 Ubiquitin Ligase 1). hGoliath and GRAIL both have the property of self-ubiquitination. hGoliath is expressed in leukocytes; its expression and localization is not modified in leukemia. GREUL1 may play a role in the generation of anterior ectoderm. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. 138 matched cddid_all.tbl CDD cd02123 cd02123 239038 PA_C_RZF_like PA_C-RZF_ like: Protease-associated (PA) domain C_RZF-like. This group includes various PA domain-containing proteins similar to C-RZF (chicken embryo RING zinc finger) protein. These proteins contain a C3H2C3 RING finger. C-RZF is expressed in embryo cells and is restricted mainly to brain and heart, it is localized to both the nucleus and endosomes. Additional C3H2C3 RING finger proteins belonging to this group, include Arabidopsis ReMembR-H2 protein and mouse sperizin. ReMembR-H2 is likely to be an integral membrane protein, and to traffic through the endosomal pathway. Sperizin is expressed in haploid germ cells and localized in the cytoplasm, it may participate in spermatogenesis. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. 153 matched cddid_all.tbl CDD cd02124 cd02124 239039 PA_PoS1_like PA_PoS1_like: Protease-associated (PA) domain PoS1-like. This group includes various PA domain-containing proteins similar to Pleurotus ostreatus (Po)S1. PoSl, the main extracellular protease in P. ostreatus is a subtilisin-like serine protease belonging to the peptidase S8 family. Ca2+ and Mn2+ both stimulate the protease activity of (Po)S1. Ca2+ protects PoS1 from autolysis. PoS1 is a monomeric glycoprotein, which may play a role in the regulation of laccases in lignin formation. (Po)S1 participates in the degradation of POXA1b, and in the activation of POXA3, (POXA1b and POXA3 are laccase isoenzymes), but its effect may be indirect. The significance of the PA domain to PoS1 has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. 129 matched cddid_all.tbl CDD cd02125 cd02125 239040 PA_VSR PA_VSR: Protease-associated (PA) domain-containing plant vacuolar sorting receptor (VSR). This group includes various PA domain-containing VSRs such as garden pea BP-80, pumpkin PV72, and various Arabidopsis VSRs including AtVSR1. In contrast to most eukaryotes, which only have one or two VSRs, plants have several. This may in part be a reflection of having a more complex vacuolar system with both lytic vacuoles and storage vacuoles. The lytic vacuole is thought to be equivalent to the mammalian lysosome and the yeast vacuole. Pea BP-80 is a type 1 transmembrane protein, involved in the targeting of proteins to the lytic vacuole; it has been suggested that this protein also mediates targeting to the storage vacuole. PV72 and AtVSR1 may mediate transport of seed storage proteins to protein storage vacuoles. The significance of the PA domain to VSRs has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. 127 matched cddid_all.tbl CDD cd02126 cd02126 239041 PA_EDEM3_like PA_EDEM3_like: protease associated domain (PA) domain-containing EDEM3-like proteins. This group contains various PA domain-containing proteins similar to mouse EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein). EDEM3 contains a region, similar to Class I alpha-mannosidases (gylcosyl hydrolase family 47), N-terminal to the PA domain. EDEM3 accelerates glycoprotein ERAD (ER-associated degradation). In transfected mammalian cells, overexpression of EDEM3 enhances the mannose trimming from the N-glycans, of a model misfolded protein [alpha1-antitrypsin null (Hong Kong)] as well as, from total glycoproteins. Mannose trimming appears to be involved in the selection of ERAD substrates. EDEM3 has a different specificity of trimming than ER alpha-mannosidase 1. The significance of the PA domain to EDEM3 has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. 126 matched cddid_all.tbl CDD cd02127 cd02127 239042 PA_hPAP21_like PA_hPAP21_like: Protease-associated domain containing proteins like the human secreted glycoprotein hPAP21 (human protease-associated domain-containing protein, 21kDa). This group contains various PA domain-containing proteins similar to hPAP21. Complex N-glycosylation may be required for the secretion of hPAP21. The significance of the PA domain to hPAP21 has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. 118 matched cddid_all.tbl CDD cd02128 cd02128 239043 PA_TfR PA_TfR: Protease-associated domain containing proteins like transferrin receptor (TfR). This group contains various PA domain-containing proteins similar to human TfR1 and TfR2. TfR1 and TfR2 are type II membrane proteins, belonging to the peptidase M28 family. TfR1 is homodimeric, widely expressed, and a key player in the uptake of iron-loaded transferrin (Tf) into cells. The TfR1 homodimer binds two molecules of Tf and this complex is internalized. In addition to its role in iron uptake, TfR1 may participate in cell growth and proliferation. TfR2 also binds Tf but with a significantly lower affinity than does TfR1. TfR2 is expressed chiefly in hepatocytes, hematopoietic cells, and duodenal crypt cells; its expression overlaps with that of hereditary hemochromatosis protein (HFE). TfR2 is involved in iron homeostasis. HFE and TfR2 interact in cells. By one model for serum iron sensing, at low or basal iron concentrations, HFE and TFR1 form a complex at the plasma membrane; at increased Tf, Tf competes with HFE for binding of TfR1, resulting in HFE disassociating from TfR1 and associating with TfR2 . The TfR1-TfR2 association might initiate a signal cascade leading to the induction of hepcidin (a small peptide hormone that controls systemic iron levels). Human mutations in TfR2 are associated with a form of hemochromatosis (HFE3). The significance of the PA domain to TfRs has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. 183 matched cddid_all.tbl CDD cd02129 cd02129 239044 PA_hSPPL_like PA_hSPPL_like: Protease-associated domain containing human signal peptide peptidase-like (hSPPL)-like. This group contains various PA domain-containing proteins similar to hSPPL2a and 2b. These SPPLs are GxGD aspartic proteases. SPPL2a is sorted to the late endosomes, SPPL2b to the plasma membrane. In activated dendritic cells, hSPPL2a and 2b catalyze the intramembrane proteolysis of tumor necrosis factor alpha triggering IL-12 production. hSPPL2a and 2b may have a broad substrate spectrum. The significance of the PA domain to these SPPLs has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. 120 matched cddid_all.tbl CDD cd02130 cd02130 239045 PA_ScAPY_like PA_ScAPY_like: Protease-associated domain containing proteins like Saccharomyces cerevisiae aminopeptidase Y (ScAPY). This group contains various PA domain-containing proteins similar to the S. cerevisiae APY, including Trichophyton rubrum leucine aminopeptidase 1(LAP1). Proteins in this group belong to the peptidase M28 family. ScAPY hydrolyzes amino acid-4-methylcoumaryl-7-amides (MCAs). ScAPY more rapidly hydrolyzes dipeptidyl-MCAs. Hydrolysis of amino acid-MCAs or dipeptides is stimulated by Co2+ while the hydrolysis of dipeptidyl-MCAs, tripeptides, and longer peptides is inhibited by Co2+. ScAPY is vacuolar and is activated by proteolytic processing. LAP1 is a secreted leucine aminopeptidase. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. 122 matched cddid_all.tbl CDD cd02131 cd02131 239046 PA_hNAALADL2_like PA_hNAALADL2_like: Protease-associated domain containing proteins like human N-acetylated alpha-linked acidic dipeptidase-like 2 protein (hNAALADL2). This group contains various PA domain-containing proteins similar to hNAALADL2. The function of hNAALADL2 is unknown. This gene has been mapped to a chromosomal region associated with Cornelia de Lange syndrome. The significance of the PA domain to hNAALADL2 has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. 153 matched cddid_all.tbl CDD cd02132 cd02132 239047 PA_GO-like PA_GO-like: Protease-associated domain containing proteins like Arabidopsis thaliana growth-on protein GRO10. This group contains various PA domain-containing proteins similar to the functionally uncharacterized Arabidopsis GRO10. The PA domain may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. 139 matched cddid_all.tbl CDD cd02133 cd02133 239048 PA_C5a_like PA_C5a_like: Protease-associated domain containing proteins like Streptococcus pyogenes C5a peptidase. This group contains various PA domain-containing proteins similar to S. pyogenes C5a, including, i) Vpr, a minor extracellular serine protease from Bacillus subtilis, ii) a large molecular mass collagenolytic protease from Geobacillus collagenovorans MO-1, and iii) PrtS, a cell envelope protease from Streptococcus thermophilus CNRZ 385. Proteins in this group belong to the peptidase S8 family. C5a peptidase is a cell surface serine protease which specifically inactivates C5a [a chemotactic peptide, which attracts polymorphonuclear leukocytes (PMNs)], by cleaving it to release a 7-residue carboxy-terminal fragment which contains the PMN binding site. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. 143 matched cddid_all.tbl CDD cd02134 cd02134 411779 KH-II_NusA_rpt1 first type II K-homology (KH) RNA-binding domain found in transcription termination/antitermination protein NusA and similar proteins. NusA, also called N utilization substance protein A or transcription termination/antitermination L factor, is an essential multifunctional transcription elongation factor that participates in both transcription termination and antitermination. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNA polymerase pausing provides a mechanism for synchronizing transcription and translation. In prokaryotes, the N-terminal RNA polymerase-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, the S1 and two K-homology (KH), KH1 and KH2. The KH domains of NusA belong to the type II KH RNA-binding domain superfamily. This model corresponds to the first KH domain of NusA and similar proteins. 76 matched cddid_all.tbl CDD cd02135 cd02135 380312 YdjA-like nitroreductase family protein similar to Escherichia coli YdjA. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase YdjA from Escherichia coli. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase. 162 matched cddid_all.tbl CDD cd02136 cd02136 380313 PnbA_NfnB-like nitroreductase similar to Mycobacterium smegmatis NfnB. Members of this family utilize FMN as a cofactor and catalyze reduction of a variety of nitroaromatic compounds, including nitrofurans, nitrobenzens, nitrophenol, nitrobenzoate and quinones by using either NADH or NADPH as a source of reducing equivalents in an obligatory two-election transfer mechanism. The enzyme is typically a homodimer. Mycobacterium smegmatis nitroreductase NfnB plays a role in resistance to benzothiazinone. 152 matched cddid_all.tbl CDD cd02137 cd02137 380314 MhqN-like nitroreductase family protein similar to the NAD(P)H nitroreductase MhqN. A diverse subfamily of the nitroreductase family containing uncharacterized proteins; includes nitroreductases MhqN, YodC, YdgI, DrgA. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. 147 matched cddid_all.tbl CDD cd02138 cd02138 380315 TdsD-like nitroreductase similar to Burkholderia pseudomallei TdsD. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to Burkholderia pseudomallei TdsD, may be involved in the processing of organosulfur compounds. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. 174 matched cddid_all.tbl CDD cd02139 cd02139 380316 nitroreductase nitroreductase family protein. A subfamily of the nitroreductase family containing uncharacterized proteins. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. 165 matched cddid_all.tbl CDD cd02140 cd02140 380317 Frm2-like nitroreductase family protein. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. Members of this family are also called NADH dehydrogenase, oxygen-insensitive NAD(P)H nitrogenase or dihydropteridine reductase. 192 matched cddid_all.tbl CDD cd02142 cd02142 380318 McbC_SagB-like_oxidoreductase oxidase similar to the microcin B17 processing protein McbC. This family is the oxidase domain of NRPS (non-ribosomal peptide synthetase) and other systems that modify polypeptides by cyclizing a thioester to form a ring. These include EpoB, part of the epothilone biosynthesis pathway; TubD, part of the tubulysin biosynthesis pathway, MtsD, part of the myxothiozol biosynthesis pathway; IndC, part of the indigoidine biosynthesis pathway and TfxB, part of the trifitoxin processing pathway. All are FMN-dependent and oxidize the product of the cyclization of thioesters in short polypeptides. 200 matched cddid_all.tbl CDD cd02143 cd02143 380319 nitroreductase_FeS-like nitroreductases with an N-terminal iron-sulfur cluster-binding domain. Members of this family utilize FMN as a cofactor. This family may be involved in the reduction of flavin or nitroaromatic compounds via an obligatory two-electron transfer. Nitroreductase is homodimer. Each subunit contains one FMN molecule. 187 matched cddid_all.tbl CDD cd02144 cd02144 380320 iodotyrosine_dehalogenase iodotyrosine dehalogenase. Iodotyrosine dehalogenase catalyzes the removal of iodine from the 3, 5 positions of L-tyosine in thyroid, liver and kidney, using NADPH as electron donor. This enzyme is a homolog of the nitroreductase family. These enzymes are usually homodimers. 192 matched cddid_all.tbl CDD cd02145 cd02145 380321 BluB 5,6-dimethylbenzimidazole synthase. BluB catalyzes the O2-dependent conversion of FMNH2 to 5,6-dimethylbenzimidazole (DMB), a component of vitamin B12; is is a subfamily of the nitroreductase family; nitroreductases typically reduce their substrates by using NAD(P)H as electron donor and often use FMN as a cofactor. 196 matched cddid_all.tbl CDD cd02146 cd02146 380322 NfsA-like nitroreductase similar to Escherichia coli NfsA. This family contains NADPH-dependent flavin reductase and oxygen-insensitive nitroreductase. These enzymes are homodimeric flavoproteins that contain one FMN per monomer as a cofactor. Flavin reductase catalyzes the reduction of flavin by using NADPH as an electron donor. Oxygen-insensitive nitroreductase, such as NfsA protein in Escherichia coli, catalyzes reduction of nitrocompounds using NADPH as electron donor. 229 matched cddid_all.tbl CDD cd02148 cd02148 380323 RutE-like nitroreductase similar to Escherichia coli RutE. A subfamily of the nitroreductase family containing uncharacterized proteins that are similar to nitroreductase. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. RutE is involved in the utilization of uracil as the sole nitrogen source; it appears to have the same function as YdfG, which reduces malonic semialdehyde to 3-hydroxypropionic acid. 186 matched cddid_all.tbl CDD cd02149 cd02149 380324 NfsB-like nitroreductase similar to Escherichia coli NfsB. NAD(P)H:FMN oxidoreductase family. This domain catalyzes the reduction of flavin, nitrocompound, quinones and azo compounds using NADH or NADPH as an electron donor. The enzyme is a homodimer, and each monomer binds a FMN as co-factor. This family includes FRase I in Vibrio fischeri, wihich reduces FMN into FMNH2 as part of the bioluminescent reaction. The family also includes oxygen-insensitive nitroreductases that use NADH or NADPH as an electron donor in the ping pong bi bi mechanism. This type of nitroreductase can be used in cancer chemotherapy to activate a range of prodrugs. 156 matched cddid_all.tbl CDD cd02150 cd02150 380325 nitroreductase nitroreductase family protein. A subfamily of the nitroreductase family containing uncharacterized proteins. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer.often found to be homodimers. 156 matched cddid_all.tbl CDD cd02151 cd02151 380326 nitroreductase nitroreductase family protein. A subfamily of the nitroreductase family containing uncharacterized proteins. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer.often found to be homodimers.. 157 matched cddid_all.tbl CDD cd02152 cd02152 239065 OAT Ornithine acetyltransferase (OAT) family; also referred to as ArgJ. OAT catalyzes the first and fifth steps in arginine biosynthesis, coupling acetylation of glutamate with deacetylation of N-acetylornithine, which allows recycling of the acetyl group in the arginine biosynthetic pathway. Members of this family may experience feedback inhibition by L-arginine. The active enzyme is a heterotetramer of two alpha and two beta chains, where the alpha and beta chains are the result of autocatalytic cleavage. OATs found in the clavulanic acid biosynthesis gene cluster catalyze the fifth step only, and may utilize acetyl acceptors other than glutamate. 390 matched cddid_all.tbl CDD cd02153 cd02153 239066 tRNA_bindingDomain The tRNA binding domain is also known as the Myf domain in literature. This domain is found in a diverse collection of tRNA binding proteins, including prokaryotic phenylalanyl tRNA synthetases (PheRS), methionyl-tRNA synthetases (MetRS), human tyrosyl-tRNA synthetase(hTyrRS), Saccharomyces cerevisiae Arc1p, Thermus thermophilus CsaA, Aquifex aeolicus Trbp111, human p43 and human EMAP-II. PheRS, MetRS and hTyrRS aminoacylate their cognate tRNAs. Arc1p is a transactivator of yeast methionyl-tRNA and glutamyl-tRNA synthetases. The molecular chaperones Trbp111 and CsaA also contain this domain. CsaA has export related activities; Trbp111 is structure-specific recognizing the L-shape of the tRNA fold. This domain has general tRNA binding properties. In a subset of this family this domain has the added capability of a cytokine. For example the p43 component of the Human aminoacyl-tRNA synthetase complex is cleaved to release EMAP-II cytokine. EMAP-II has multiple activities during apoptosis, angiogenesis and inflammation and participates in malignant transformation. An EMAP-II-like cytokine is released from hTyrRS upon cleavage. The active cytokine heptapeptide locates to this domain. For homodimeric members of this group which include CsaA, Trbp111 and Escherichia coli MetRS this domain acts as a dimerization domain. 99 matched cddid_all.tbl CDD cd02156 cd02156 173912 nt_trans nucleotidyl transferase superfamily. nt_trans (nucleotidyl transferase) This superfamily includes the class I amino-acyl tRNA synthetases, pantothenate synthetase (PanC), ATP sulfurylase, and the cytidylyltransferases, all of which have a conserved dinucleotide-binding domain. 105 matched cddid_all.tbl CDD cd02163 cd02163 173914 PPAT Phosphopantetheine adenylyltransferase. Phosphopantetheine adenylyltransferase (PPAT). PPAT is an essential enzyme in bacteria, responsible for catalyzing the rate-limiting step in coenzyme A (CoA) biosynthesis. The dinucleotide-binding fold of PPAT is homologous to class I aminoacyl-tRNA synthetases. CoA has been shown to inhibit PPAT and competes with ATP, PhP, and dPCoA. PPAT is a homohexamer in E. coli. 153 matched cddid_all.tbl CDD cd02164 cd02164 173915 PPAT_CoAS phosphopantetheine adenylyltransferase domain of eukaryotic and archaeal bifunctional enzymes. The PPAT domain of the bifunctional enzyme with PPAT and DPCK functions. The final two steps of the CoA biosynthesis pathway are catalyzed by phosphopantetheine adenylyltransferase (PPAT) and dephospho-CoA (dPCoA) kinase (DPCK). The PPAT reaction involves the reversible adenylation of 4'-phosphopantetheine to form 3'-dPCoA and PPi, and DPCK catalyses phosphorylation of the 3'-hydroxy group of the ribose moiety of dPCoA. In eukaryotes the two enzymes are part of a large multienzyme complex . Studies in Corynebacterium ammoniagenes suggested that separate enzymes were present, and this was confirmed through identification of the bacterial PPAT/CoAD. 143 matched cddid_all.tbl CDD cd02165 cd02165 185680 NMNAT Nicotinamide/nicotinate mononucleotide adenylyltransferase. Nicotinamide/nicotinate mononucleotide (NMN/ NaMN)adenylyltransferase (NMNAT). NMNAT represents the primary bacterial and eukaryotic adenylyltransferases for nicotinamide-nucleotide and for the deamido form, nicotinate nucleotide. It is an indispensable enzyme in the biosynthesis of NAD(+) and NADP(+). Nicotinamide-nucleotide adenylyltransferase synthesizes NAD via the salvage pathway, while nicotinate-nucleotide adenylyltransferase synthesizes the immediate precursor of NAD via the de novo pathway. Human NMNAT displays unique dual substrate specificity toward both NMN and NaMN, and can participate in both de novo and salvage pathways of NAD synthesis. 192 matched cddid_all.tbl CDD cd02166 cd02166 173917 NMNAT_Archaea Nicotinamide/nicotinate mononucleotide adenylyltransferase, archaeal. This family of archaeal proteins exhibits nicotinamide-nucleotide adenylyltransferase (NMNAT) activity utilizing the salvage pathway to synthesize NAD. In some cases, the enzyme was tested and found also to have the activity of nicotinate-nucleotide adenylyltransferase an enzyme of NAD de novo biosynthesis, although with a higher Km. In some archaeal species, a number of proteins which are uncharacterized with respect to activity, are also present. 163 matched cddid_all.tbl CDD cd02167 cd02167 173918 NMNAT_NadR Nicotinamide/nicotinate mononucleotide adenylyltransferase of bifunctional NadR-like proteins. NMNAT domain of NadR protein. The NadR protein (NadR) is a bifunctional enzyme possessing both NMN adenylytransferase (NMNAT) and ribosylnicotinamide kinase (RNK) activities. Its function is essential for the growth and survival of H. influenzae and thus may present a new highly specific anti-infectious drug target. The N-terminal domain that hosts the NMNAT activity is closely related to archaeal NMNAT. The bound NAD at the active site of the NMNAT domain reveals several critical interactions between NAD and the protein.The NMNAT domain of hiNadR defines yet another member of the pyridine nucleotide adenylyltransferase 158 matched cddid_all.tbl CDD cd02168 cd02168 173919 NMNAT_Nudix Nicotinamide/nicotinate mononucleotide adenylyltransferase of bifunctional proteins, also containing a Nudix hydrolase domain. N-terminal NMNAT (Nicotinamide/nicotinate mononucleotide adenylyltransferase) domain of a novel bifunctional enzyme endowed with NMN adenylyltransferase and Nudix hydrolase activities. This domain is highly homologous to the archeal NMN adenyltransferase that catalyzes NAD synthesis from NMN and ATP. NMNAT is an essential enzyme in the biosynthesis of NAD(+) and NADP(+). Nicotinamide-nucleotide adenylyltransferase synthesizes NAD via the salvage pathway, while nicotinate-nucleotide adenylyltransferase synthesizes the immediate precursor of NAD via the de novo pathway. The C-terminal domain of this enzyme shares homology with the archaeal ADP-ribose pyrophosphatase, a member of the 'Nudix' hydrolase family. 181 matched cddid_all.tbl CDD cd02169 cd02169 173920 Citrate_lyase_ligase Citrate lyase ligase. Citrate lyase ligase, also known as [Citrate (pro-3S)-lyase] ligase, is responsible for acetylation of the (2-(5''-phosphoribosyl)-3'-dephosphocoenzyme-A) prosthetic group of the gamma subunit of citrate lyase, converting the inactive thiol form of this enzyme to the active form. The acetylation of 1 molecule of deacetyl-citrate lyase to enzymatically active citrate lyase requires 6 molecules of ATP. The Adenylylyltranferase activity of the enzyme involves the formation of AMP and and pyrophosphate in the acetylation reaction. 297 matched cddid_all.tbl CDD cd02170 cd02170 173921 cytidylyltransferase cytidylyltransferase. The cytidylyltransferase family includes cholinephosphate cytidylyltransferase (CCT), glycerol-3-phosphate cytidylyltransferase, RafE and phosphoethanolamine cytidylyltransferase (ECT). All enzymes catalyze the transfer of a cytidylyl group from CTP to various substrates. 136 matched cddid_all.tbl CDD cd02171 cd02171 173922 G3P_Cytidylyltransferase glycerol-3-phosphate cytidylyltransferase. Glycerol-3-phosphate cytidylyltransferase,(CDP-glycerol pyrophosphorylase). Glycerol-3-phosphate cytidyltransferase acts in pathways of teichoic acid biosynthesis. Teichoic acids are substituted polymers, linked by phosphodiester bonds, of glycerol, ribitol, etc. An example is poly(glycerol phosphate), the major teichoic acid of the Bacillus subtilis cell wall. Most, but not all, species encoding proteins in this family are Gram-positive bacteria. A closely related protein assigned a different function experimentally is a human ethanolamine-phosphate cytidylyltransferase. 129 matched cddid_all.tbl CDD cd02172 cd02172 173923 RfaE_N N-terminal domain of RfaE. RfaE is a protein involved in the biosynthesis of ADP-L-glycero-D-manno-heptose, a precursor for LPS inner core biosynthesis. RfaE is a bifunctional protein in Escherichia coli, and separate proteins in other organisms. Domain I is suggested to act in D-glycero-D-manno-heptose 1-phosphate biosynthesis, while domain II (this family) adds ADP to yield ADP-D-glycero-D-manno-heptose . 144 matched cddid_all.tbl CDD cd02173 cd02173 173924 ECT CTP:phosphoethanolamine cytidylyltransferase (ECT). CTP:phosphoethanolamine cytidylyltransferase (ECT) catalyzes the conversion of phosphoethanolamine to CDP-ethanolamine as part of the CDP-ethanolamine biosynthesis pathway. ECT expression in hepatocytes is localized predominantly to areas of the cytoplasm that are rich in rough endoplasmic reticulum. Several ECTs, including yeast and human ECT, have large repetitive sequences located within their N- and C-termini. 152 matched cddid_all.tbl CDD cd02174 cd02174 173925 CCT CTP:phosphocholine cytidylyltransferase. CTP:phosphocholine cytidylyltransferase (CCT) catalyzes the condensation of CTP and phosphocholine to form CDP-choline as the rate-limiting and regulatory step in the CDP-choline pathway. CCT is unique in that its enzymatic activity is regulated by the extent of its association with membrane structures. A current model posts that the elastic stress of the bilayer curvature is sensed by CCT and this governs the degree of membrane association, thus providing a mechanism for both positive and negative regulation of activity. 150 matched cddid_all.tbl CDD cd02175 cd02175 185684 GH16_lichenase lichenase, member of glycosyl hydrolase family 16. Lichenase, also known as 1,3-1,4-beta-glucanase, is a member of glycosyl hydrolase family 16, that specifically cleaves 1,4-beta-D-glucosidic bonds in mixed-linked beta glucans that also contain 1,3-beta-D-glucosidic linkages. Natural substrates of beta-glucanase are beta-glucans from grain endosperm cell walls or lichenan from the Islandic moss, Cetraria islandica. This protein is found not only in bacteria but also in anaerobic fungi. This domain includes two seven-stranded antiparallel beta-sheets that are adjacent to one another forming a compact, jellyroll beta-sandwich structure. 212 matched cddid_all.tbl CDD cd02176 cd02176 185685 GH16_XET Xyloglucan endotransglycosylase, member of glycosyl hydrolase family 16. Xyloglucan endotransglycosylases (XETs) cleave and religate xyloglucan polymers in plant cell walls via a transglycosylation mechanism. Xyloglucan is a soluble hemicellulose with a backbone of beta-1,4-linked glucose units, partially substituted with alpha-1,6-linked xylopyranose branches. It binds noncovalently to cellulose, cross-linking the adjacent cellulose microfibrils, giving it a key structural role as a matrix polymer. Therefore, XET plays an important role in all plant processes that require cell wall remodeling. 263 matched cddid_all.tbl CDD cd02177 cd02177 185686 GH16_kappa_carrageenase Kappa-carrageenase, member of glycosyl hydrolase family 16. Kappa-carrageenase is a glycosyl hydrolase family 16 (GH16) member that hydrolyzes the internal beta-1,4-linkage of kappa-carrageenans, a hydrophilic polysaccharide found in the cell wall of Rhodophyceaea, marine red algae. Carrageenans are linear chains of galactose units linked by alternating D-alpha-1,3- and D-beta-1,4-linkages that are additionally modified by a 3,6-anhydro-bridge. Depending on the position and number of sulfate ester modifications they are subdivided into kappa-, iota-, and lambda-carrageenases, kappa being modified once. Carrageenans form thermo-reversible gels widely used for industrial applications. Kappa-carrageenases exist in bacteria belonging to at least three phylogenetically distant branches, including pseudoalteromonas, planctomycetes, and baceroidetes. This domain adopts a curved beta-sandwich conformation, with a tunnel-shaped active site cavity, referred to as a jellyroll fold. 269 matched cddid_all.tbl CDD cd02178 cd02178 185687 GH16_beta_agarase Beta-agarase, member of glycosyl hydrolase family 16. Beta-agarase is a glycosyl hydrolase family 16 (GH16) member that hydrolyzes the internal beta-1,4-linkage of agarose, a hydrophilic polysaccharide found in the cell wall of Rhodophyceaea, marine red algae. Agarose is a linear chain of galactose units linked by alternating L-alpha-1,3- and D-beta-1,4-linkages that are additionally modified by a 3,6-anhydro-bridge. Agarose forms thermo-reversible gels that are widely used in the food industry or as a laboratory medium. While beta-agarases are also found in two other families derived from the sequence-based classification of glycosyl hydrolases (GH50, and GH86) the GH16 members are most abundant. This domain adopts a curved beta-sandwich conformation, with a tunnel-shaped active site cavity, referred to as a jellyroll fold. 258 matched cddid_all.tbl CDD cd02179 cd02179 185688 GH16_beta_GRP beta-1,3-glucan recognition protein, member of glycosyl hydrolase family 16. Beta-GRP (beta-1,3-glucan recognition protein) is one of several pattern recognition receptors (PRRs), also referred to as biosensor proteins, that complexes with pathogen-associated beta-1,3-glucans and then transduces signals necessary for activation of an appropriate innate immune response. They are present in insects and lack all catalytic residues. This subgroup also contains related proteins of unknown function that still contain the active site. Their structures adopt a jelly roll fold with a deep active site channel harboring the catalytic residues, like those of other glycosyl hydrolase family 16 members. 321 matched cddid_all.tbl CDD cd02180 cd02180 185689 GH16_fungal_KRE6_glucanase Saccharomyces cerevisiae KRE6 and related glucanses, member of glycosyl hydrolase family 16. KRE6 is a Saccharomyces cerevisiae glucanase that participates in the synthesis of beta-1,6-glucan, a major structural component of the cell wall. It is a golgi membrane protein required for normal beta-1,6-glucan levels in the cell wall. KRE6 is closely realted to laminarinase, a glycosyl hydrolase family 16 member that hydrolyzes 1,3-beta-D-glucosidic linkages in 1,3-beta-D-glucans such as laminarins, curdlans, paramylons, and pachymans, with very limited action on mixed-link (1,3-1,4-)-beta-D-glucans. 295 matched cddid_all.tbl CDD cd02181 cd02181 185690 GH16_fungal_Lam16A_glucanase fungal 1,3(4)-beta-D-glucanases, similar to Phanerochaete chrysosporium laminarinase 16A. Group of fungal 1,3(4)-beta-D-glucanases, similar to Phanerochaete chrysosporium laminarinase 16A. Lam16A belongs to the 'nonspecific' 1,3(4)-beta-glucanase subfamily, although beta-1,6 branching and beta-1,4 bonds specifically define where Lam16A hydrolyzes its substrates, like curdlan (beta-1,3-glucan), lichenin (beta-1,3-1,4-mixed linkage glucan), and laminarin (beta-1,6-branched-1,3-glucan). 293 matched cddid_all.tbl CDD cd02182 cd02182 185691 GH16_Strep_laminarinase_like Streptomyces laminarinase-like, member of glycosyl hydrolase family 16. Proteins similar to Streptomyces sioyaensis beta-1,3-glucanase (laminarinase) present in Actinomycetales as well as Peziomycotina. Laminarinases belong to glycosyl hydrolase family 16 and hydrolyze the glycosidic bond of the 1,3-beta-linked glucan, a major component of fungal and plant cell walls and the structural and storage polysaccharides (laminarin) of marine macro-algae. Members of the GH16 family have a conserved jelly roll fold with an active site channel. 259 matched cddid_all.tbl CDD cd02183 cd02183 185692 GH16_fungal_CRH1_transglycosylase glycosylphosphatidylinositol-glucanosyltransferase. Group of fungal GH16 members related to Saccharomyces cerevisiae Crh1p. Chr1p and Crh2p are transglycosylases that are required for the linkage of chitin to beta(1-3)glucose branches of beta(1-6)glucan, an important step in the assembly of new cell wall. Both have been shown to be glycosylphosphatidylinositol (GPI)-anchored. A third homologous protein, Crr1p, functions in the formation of the spore wall. They belongs to the family 16 of glycosyl hydrolases that includes lichenase, xyloglucan endotransglycosylase (XET), beta-agarase, kappa-carrageenase, endo-beta-1,3-glucanase, endo-beta-1,3-1,4-glucanase, and endo-beta-galactosidase, all of which have a conserved jelly roll fold with a deep active site channel harboring the catalytic residues. 203 matched cddid_all.tbl CDD cd02185 cd02185 100026 AroH Chorismate mutase (AroH) is one of at least five chorismate-utilizing enzymes present in microorganisms that catalyze the rearrangement of chorismate to prephenic acid, the first committed step in the biosynthesis of aromatic amino acids. In prokaryotes, chorismate mutase may be fused to prephenate dehydratase, prephenate dehydrogenase, or 3-deoxy-D-arabino-heptulosonat-7-phosphate (DAHP) as part of a bifunctional enzyme. The AroH domain forms a homotrimer with three-fold symmetry. 117 matched cddid_all.tbl CDD cd02186 cd02186 276955 alpha_tubulin The alpha-tubulin family. The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The alpha- and beta-tubulins are the major components of microtubules, while gamma-tubulin plays a major role in the nucleation of microtubule assembly. The delta- and epsilon-tubulins are widespread but unlike the alpha, beta, and gamma-tubulins they are not ubiquitous among eukaryotes. The alpha/beta-tubulin heterodimer is the structural subunit of microtubules. The alpha- and beta-tubulins share 40% amino-acid sequence identity, exist in several isotype forms, and undergo a variety of posttranslational modifications. The structures of alpha- and beta-tubulin are basically identical: each monomer is formed by a core of two beta-sheets surrounded by alpha-helices. The monomer structure is very compact, but can be divided into three regions based on function: the amino-terminal nucleotide-binding region, an intermediate taxol-binding region and the carboxy-terminal region which probably constitutes the binding surface for motor proteins. 434 matched cddid_all.tbl CDD cd02187 cd02187 276956 beta_tubulin The beta-tubulin family. The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The alpha- and beta-tubulins are the major components of microtubules, while gamma-tubulin plays a major role in the nucleation of microtubule assembly. The delta- and epsilon-tubulins are widespread but unlike the alpha, beta, and gamma-tubulins they are not ubiquitous among eukaryotes. The alpha/beta-tubulin heterodimer is the structural subunit of microtubules. The alpha- and beta-tubulins share 40% amino-acid sequence identity, exist in several isotype forms, and undergo a variety of posttranslational modifications. The structures of alpha- and beta-tubulin are basically identical: each monomer is formed by a core of two beta-sheets surrounded by alpha-helices. The monomer structure is very compact, but can be divided into three regions based on function: the amino-terminal nucleotide-binding region, an intermediate taxol-binding region and the carboxy-terminal region which probably constitutes the binding surface for motor proteins. 425 matched cddid_all.tbl CDD cd02188 cd02188 276957 gamma_tubulin The gamma-tubulin family. Gamma-tubulin is a ubiquitous phylogenetically conserved member of tubulin superfamily. Gamma is a low abundance protein present within the cells in both various types of microtubule-organizing centers and cytoplasmic protein complexes. Gamma-tubulin recruits the alpha/beta-tubulin dimers that form the minus ends of microtubules and is thought to be involved in microtubule nucleation and capping. 430 matched cddid_all.tbl CDD cd02189 cd02189 276958 delta_zeta_tubulin-like The delta- and zeta-tubulin families. The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The alpha- and beta-tubulins are the major components of microtubules, while gamma-tubulin plays a major role in the nucleation of microtubule assembly. The delta- and epsilon-tubulins are widespread but unlike the alpha, beta, and gamma-tubulins they are not ubiquitous among eukaryotes. Delta-tubulin plays an essential role in forming the triplet microtubules of centrioles and basal bodies. 433 matched cddid_all.tbl CDD cd02190 cd02190 276959 epsilon_tubulin The epsilon-tubulin family. The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The epsilon-tubulins which are widespread but not ubiquitous among eukaryotes play a role in basal body/centriole morphogenesis. 449 matched cddid_all.tbl CDD cd02191 cd02191 276960 FtsZ_CetZ-like Subfamily of FitZ and Cell-structure-related euryarchaeota tubulin/FtsZ homolog-like. FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. CetZ-like proteins are related to tubulin and FtsZ and co-exists with FtsZ in many archaea. However, a recent study found that Cetz proteins (formerly annotated FtsZ type 2) are not required for cell division. Instead, CetZ proteins are shown to be involved in controlling archaeal cell shape dynamics. The results from inactivation studies of CetZ proteins in Haloferax volcanii suggest that CetZ1 is essential for normal swimming motility and rod-cell development. 308 matched cddid_all.tbl CDD cd02192 cd02192 100028 PurM-like3 AIR synthase (PurM) related protein, subgroup 3 of unknown function. The family of PurM related proteins includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM synthase and Selenophosphate synthetase (SelD). They all contain two conserved domains and seem to dimerize. The N-terminal domain forms the dimer interface and is a putative ATP binding domain. 283 matched cddid_all.tbl CDD cd02193 cd02193 100029 PurL Formylglycinamide ribonucleotide amidotransferase (FGAR-AT) catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP, phosphate, and glutamate in the fourth step of the purine biosynthetic pathway. In eukaryotes and Gram-negative bacteria, FGAR-AT is encoded by the purL gene as a multidomain protein with a molecular mass of about 140 kDa. In Gram-positive bacteria and archaea FGAR-AT is a complex of three proteins: PurS, PurL, and PurQ. PurL itself contains two tandem N- and C-terminal domains (four domains altogether). The N-terminal domains bind ATP and are related to the ATP-binding domains of HypE, ThiL, SelD and PurM. 272 matched cddid_all.tbl CDD cd02194 cd02194 100030 ThiL ThiL (Thiamine-monophosphate kinase) plays a dual role in de novo biosynthesis and in salvage of exogenous thiamine. Thiamine salvage occurs in two steps, with thiamine kinase catalyzing the formation of thiamine phosphate, and ThiL catalyzing the conversion of this intermediate to thiamine pyrophosphate. The N-terminal domain of ThiL binds ATP and is related to the ATP-binding domains of hydrogen expression/formation protein HypE, the AIR synthases, FGAM synthase and selenophosphate synthetase (SelD). 291 matched cddid_all.tbl CDD cd02195 cd02195 100031 SelD Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The N-terminal domain of SelD is related to the ATP-binding domains of hydrogen expression/formation protein HypE, the AIR synthases, and FGAM synthase and is thought to bind ATP. 287 matched cddid_all.tbl CDD cd02196 cd02196 100032 PurM PurM (Aminoimidazole Ribonucleotide [AIR] synthetase), one of eleven enzymes required for purine biosynthesis, catalyzes the conversion of formylglycinamide ribonucleotide (FGAM) and ATP to AIR, ADP, and Pi, the fifth step in de novo purine biosynthesis. The N-terminal domain of PurM is related to the ATP-binding domains of hydrogen expression/formation protein HypE, the AIR synthases, selenophosphate synthetase (SelD), and FGAM synthase and is thought to bind ATP. 297 matched cddid_all.tbl CDD cd02197 cd02197 100033 HypE HypE (Hydrogenase expression/formation protein). HypE is involved in Ni-Fe hydrogenase biosynthesis. HypE dehydrates its own carbamoyl moiety in an ATP-dependent process to yield the enzyme thiocyanate. The N-terminal domain of HypE is related to the ATP-binding domains of the AIR synthases, selenophosphate synthetase (SelD), and FGAM synthase and is thought to bind ATP. 293 matched cddid_all.tbl CDD cd02198 cd02198 100005 YjgH_like YjgH belongs to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site. 111 matched cddid_all.tbl CDD cd02199 cd02199 100006 YjgF_YER057c_UK114_like_1 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site. 142 matched cddid_all.tbl CDD cd02201 cd02201 276961 FtsZ_type1 Filamenting temperature sensitive mutant Z, type 1. FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells. 303 matched cddid_all.tbl CDD cd02202 cd02202 276962 CetZ_tubulin-like Cell-structure-related euryarchaeota tubulin/FtsZ homologs. CetZ proteins comprise a distinct tubulin/FtsZ family. The crystal structures of CetZ contain the FtsZ/tubulin superfamily fold and its family members have mosaic of tubulin-like and FtsZ-like amino acid residues. However, a recent study found that CetZ proteins (formerly annotated FtsZ type 2) are not required for cell division, whereas FtsZ proteins play an important role. Instead, CetZ proteins are shown to be involved in controlling archaeal cell shape dynamics. The results from inactivation studies of CetZ proteins in Haloferax volcanii suggest that CetZ1 is essential for normal swimming motility and rod-cell development. 357 matched cddid_all.tbl CDD cd02203 cd02203 100034 PurL_repeat1 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), first repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP, phosphate, and glutamate in the fourth step of the purine biosynthetic pathway. In eukaryotes and Gram-negative bacteria, FGAR-AT is encoded by the purL gene as a multidomain protein with a molecular mass of about 140 kDa. In Gram-positive bacteria and archaea FGAR-AT is a complex of three proteins: PurS, PurL, and PurQ. PurL itself contains two tandem N- and C-terminal domains (four domains altogether). The N-terminal domains bind ATP and are related to the ATP-binding domains of HypE, ThiL, SelD and PurM. 313 matched cddid_all.tbl CDD cd02204 cd02204 100035 PurL_repeat2 PurL subunit of the formylglycinamide ribonucleotide amidotransferase (FGAR-AT), second repeat. FGAR-AT catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP, phosphate, and glutamate in the fourth step of the purine biosynthetic pathway. In eukaryotes and Gram-negative bacteria, FGAR-AT is encoded by the purL gene as a multidomain protein with a molecular mass of about 140 kDa. In Gram-positive bacteria and archaea FGAR-AT is a complex of three proteins: PurS, PurL, and PurQ. PurL itself contains two tandem N- and C-terminal domains (four domains altogether). The N-terminal domains bind ATP and are related to the ATP-binding domains of HypE, ThiL, SelD and PurM. 264 matched cddid_all.tbl CDD cd02205 cd02205 341358 CBS_pair_SF Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains superfamily. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 113 matched cddid_all.tbl CDD cd02208 cd02208 380338 cupin_RmlC-like RmlC-like cupin superfamily. This superfamily contains proteins similar to the RmlC (dTDP (deoxythymidine diphosphates)-4-dehydrorhamnose 3,5-epimerase)-like cupins. RmlC is a dTDP-sugar isomerase involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. Cupins are a functionally diverse superfamily originally discovered based on the highly conserved motif found in germin and germin-like proteins. This conserved motif forms a beta-barrel fold found in all of the cupins, giving rise to the name cupin ('cupa' is the Latin term for small barrel). The active site of members of this superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. The different functional classes in this superfamily include single domain bacterial isomerases and epimerases involved in the modification of cell wall carbohydrates, two domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain nuclear transcription factors involved in legume root nodulation. 73 matched cddid_all.tbl CDD cd02209 cd02209 380339 cupin_XRE_C "XRE (Xenobiotic Response Element) family transcriptional regulators, C-terminal cupin domain. This family contains transcriptional regulators containing an N-terminal XRE (Xenobiotic Response Element) family helix-turn-helix (HTH) DNA-binding domain and a C-terminal cupin domain. Included in this family is Escherichia coli transcription factor SutR (YdcN) that plays a regulatory role in sulfur utilization; it regulates a set of genes involved in the generation of sulfate and its reduction, the synthesis of cysteine, the synthesis of enzymes containing Fe-S as cofactors, and the modification of tRNA with use of sulfur-containing substrates. This family belongs to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 90 matched cddid_all.tbl CDD cd02210 cd02210 380340 cupin_BLR2406-like "Bradyrhizobium japonicum BLR2406 and related proteins, cupin domain. This family includes bacterial and fungal proteins homologous to BLR2406, a Bradyrhizobium japonicum protein of unknown function with a cupin beta barrel domain. Proteins in this subfamily appear to align closest to RmlC carbohydrate epimerase which is involved in dTDP-L-rhamnose production, and belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 98 matched cddid_all.tbl CDD cd02211 cd02211 380341 cupin_UGlyAH_N "(S)-ureidoglycine aminohydrolase and related proteins, N-terminal cupin domain. This family includes the N-terminal cupin domain of (S)-ureidoglycine aminohydrolase (UGlyAH), an enzyme that converts (S)-ureidoglycine into (S)-ureidoglycolate and ammonia, providing the final substrate to the ureide pathway. The ureide pathway has recently been identified as the metabolic route of purine catabolism in plants and some bacteria where, uric acid, which is a major product of the early stage of purine catabolism, is degraded into glyoxylate and ammonia via stepwise reactions by seven different enzymes. Thus, this pathway has a possible physiological role in mobilization of purine ring nitrogen for further assimilation. This enzyme from Arabidopsis thaliana(AtUGlyAH) has been shown to bind a Mn2+ ion, via the C-terminal cupin domain, which acts as a molecular anchor to bind (S)-ureidoglycine, and its binding mode dictates the enantioselectivity of the reaction. The structure of AtUGlyAH shows a bi-cupin fold with a conserved ""jelly roll-like"" beta-barrel fold and an octameric functional unit. Several structural homologs of UGlyAH, including the Escherichia coli ortholog YlbA (also known as GlxB6), also exhibit similar features." 117 matched cddid_all.tbl CDD cd02212 cd02212 380342 cupin_UGlyAH_C "(S)-ureidoglycine aminohydrolase and related proteins, C-terminal cupin domain. This family includes the C-terminal cupin domain of (S)-Ureidoglycine aminohydrolase (UGlyAH), an enzyme that converts (S)-ureidoglycine into (S)-ureidoglycolate and ammonia, providing the final substrate to the ureide pathway. The ureide pathway has recently been identified as the metabolic route of purine catabolism in plants and some bacteria where, uric acid, which is a major product of the early stage of purine catabolism, is degraded into glyoxylate and ammonia via stepwise reactions by seven different enzymes. Thus, this pathway has a possible physiological role in mobilization of purine ring nitrogen for further assimilation. This enzyme from Arabidopsis thaliana(AtUGlyAH) has been shown to bind a Mn2+ ion,via the C-terminal cupin domain, which acts as a molecular anchor to bind (S)-ureidoglycine, and its binding mode dictates the enantioselectivity of the reaction. The structure of AtUGlyAH shows a bi-cupin fold with a conserved ""jelly roll-like"" beta-barrel fold and an octameric functional unit. Several structural homologs of UGlyAH, including the Escherichia coli ortholog YlbA (also known as GlxB6), also exhibit similar features." 92 matched cddid_all.tbl CDD cd02213 cd02213 380343 cupin_PMI_typeII_C Phosphomannose isomerase type II, C-terminal cupin domain. This family includes the C-terminal cupin domain of mannose-6-phosphate isomerases (MPIs) which have been classified broadly into two groups, type I and type II, based on domain organization. This family contains type II phosphomannose isomerase (also known as PMI-GDP, phosphomannose isomerase/GDP-D-mannose pyrophosphorylase), a bifunctional enzyme with two domains that catalyze the first and third steps in the GDP-mannose pathway in which fructose 6-phosphate is converted to GDP-D-mannose. The N-terminal domain catalyzes the first and rate-limiting step, the isomerization from D-fructose-6-phosphate to D-mannose-6-phosphate, while the C-terminal cupin domain (represented in this alignment model) converts mannose 1-phosphate to GDP-D-mannose in the final step of the reaction. Although these two domains occur together in one protein in most organisms, they occur as separate proteins in certain cyanobacterial organisms. Also, although type I and type II MPIs have no overall sequence similarity, they share a conserved catalytic motif. 126 matched cddid_all.tbl CDD cd02214 cd02214 380344 cupin_MJ1618 Methanocaldococcus jannaschii MJ1618 and related proteins, cupin domain. This family includes bacterial and archaeal proteins homologous to MJ1618, a Methanocaldococcus jannaschii protein of unknown function with a cupin beta barrel domain. The active site of members of the cupin superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. 100 matched cddid_all.tbl CDD cd02215 cd02215 380345 cupin_QDO_N_C quercetinase, N- and C-terminal cupin domains. This family contains quercetinase (also known as quercetin 2,3-dioxygenase, 2,3QD, QDO and YxaG; EC 1.13.11.24), a mononuclear copper-dependent dioxygenase that catalyzes the cleavage of the flavonol quercetin (5,7,3',4'-tetrahydroxyflavonol) heterocyclic ring to produce 2-protocatechuoyl-phloroglucinol carboxylic acid and carbon monoxide. Bacillus subtilis quercetin 2,3-dioxygenase (QDO) is a homodimer that shows oxygenase activity with several divalent metals such as Mn2+, Co2+, Fe2+, and Cu2+, although the preferred one appears to be Mn2+. The dioxygen binds to the metal ion of the Cu-QDO-quercetin complex, yielding a Cu2+-superoxo quercetin radical intermediate, which then forms a Cu2+-alkylperoxo complex which then evolves into endoperoxide intermediate that decomposes to the product. Quercetinase is a bicupin with two tandem cupin beta-barrel domains, both of which are included in this alignment model. The pirins, which also belong to the cupin domain family, have been shown to catalyze a reaction involving quercetin and may have a function similar to that of quercetinase. 122 matched cddid_all.tbl CDD cd02216 cd02216 380346 cupin_GDO-like_N gentisate 1,2-dioxygenase, 1-hydroxy-2-naphthoate dioxygenase, and salicylate 1,2-dioxygenase, N-terminal cupin domain. This family includes the N-terminal cupin domains of three closely related bicupin aromatic ring-cleaving dioxygenases: gentisate 1,2-dioxygenase (GDO), salicylate 1,2-dioxygenase (SDO), and 1-hydroxy-2-naphthoate dioxygenase (NDO). GDO catalyzes the cleavage of the gentisate (2,5-dihydroxybenzoate) aromatic ring, a key step in the gentisate degradation pathway allowing soil bacteria to utilize 2,5-xylenol, 3,5-xylenol, and m-cresol as sole carbon and energy sources. NDO catalyzes the cleavage of 1-hydroxy-2-naphthoate as part of the bacterial phenanthrene degradation pathway. SDO is a ring cleavage dioxygenase from Pseudaminobacter salicylatoxidans that oxidizes salicylate to 2-oxohepta-3,5-dienedioic acid via a novel ring fission mechanism. SDO differs from other known GDOs and NDOs in its unique ability to oxidatively cleave many different salicylate, gentisate and 1-hydroxy-2-naphthoate substrates with high catalytic efficiency. The active site of these enzymes is located in the N-terminal domain but could be influenced by changes in the C-terminal domain, which lacks the strictly conserved metal-binding residues found in other cupin domains and is thought to be an inactive vestigial remnant. 108 matched cddid_all.tbl CDD cd02218 cd02218 380347 cupin_PGI cupin-type phosphoglucose isomerase. The cupin-type phosphoglucose isomerase (also called cupin-like glucose-6-phosphate isomerase or cPGI; EC 5.3.1.9) family is found in archaea and certain prokaryotes where they catalyze the reversible aldose-ketose isomerization of glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P) as part of a unique variation of the Embden-Meyerhof glycolytic pathway. Cupin-PGIs represent a separate lineage in the evolution of phosphoglucose isomerases. Pyrococcus furiosus phosphoglucose isomerase (PfPGI) has been shown to be a metal-containing enzyme which catalyzes the interconversion of glucose 6-phosphate (G6P) and fructose 6-phosphate (F6P). These domains have a cupin beta-barrel fold capable of homodimerization. 168 matched cddid_all.tbl CDD cd02219 cd02219 380348 cupin_YjlB-like Bacillus subtilis YjlB and related proteins, cupin domain. This family includes bacterial and fungal proteins homologous to YjlB, a Bacillus subtilis protein of unknown function with a cupin beta barrel fold. The active site of members of the cupin superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. The different functional classes in this superfamily include single domain bacterial isomerases and epimerases involved in the modification of cell wall carbohydrates, two-domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain nuclear transcription factors involved in legume root nodulation. 154 matched cddid_all.tbl CDD cd02220 cd02220 380349 cupin_ABP1 auxin-binding protein 1, cupin domain. Auxin-binding protein 1 (ABP1) is a soluble glycoprotein receptor that binds the plant hormone auxin, indole-3-acetic acid (IAA). ABP1 belongs to the ancient and functionally diverse germin/seed storage 7S protein superfamily. It is an important mediator of auxin action in plants and is essential for cell cycle control. Cellular auxin responses typically depend on auxin concentrations that mainly result from intercellular auxin transport and auxin biosynthesis, as well as metabolism. The functional inactivation of ABP1 results in cell cycle arrest, showing that ABP1 plays a critical role in cell cycle regulation, acting at both the G1/S and G2/M checkpoints. ABP1 is ubiquitous among green plants, found mainly within the endoplasmic reticulum (ER) and in smaller quantities at the cell surface associated with the plasma membrane. In Arabidopsis thaliana, ABP1 null mutations result in embryonic lethality while decreased ABP1 expression leads to severe retardation of leaf growth. 151 matched cddid_all.tbl CDD cd02221 cd02221 380350 cupin_TM1287-like "Thermotoga maritima TM1287 decarboxylase, cupin domain. This family includes bacterial proteins homologous to TM1287 decarboxylase, a Thermotoga maritima manganese-containing cupin thought to catalyze the conversion of oxalate to formate and carbon dioxide, due to its similarity to oxalate decarboxylase (OXDC) from Bacillus subtilis. TM1287 shows a cupin fold with a conserved ""jelly roll-like"" beta-barrel fold and forms a homodimer." 93 matched cddid_all.tbl CDD cd02222 cd02222 380351 cupin_TM1459-like "Thermotoga maritima TM1459 and related proteins, cupin domain. This family includes bacterial and archaeal proteins homologous to Thermotoga maritima TM1459, a manganese-containing cupin that has been shown to cleave C=C bonds in the presence of alkylperoxide as oxidant in vitro. Its biological function is still unknown. This family also includes Halorhodospira halophila Hhal_0468. Structures of these proteins show a cupin fold with a conserved ""jelly roll-like"" beta-barrel fold that form a homodimer." 91 matched cddid_all.tbl CDD cd02223 cd02223 380352 cupin_Bh2720-like Bacillus halodurans Bh2720 and related proteins, cupin domain. This family includes bacterial, archaeal, and eukaryotic proteins similar to Bh2720, a Bacillus halodurans protein of unknown function with a cupin beta-barrel fold. 98 matched cddid_all.tbl CDD cd02224 cd02224 380353 cupin_SPO2919-like "Silicibacter pomeroyi SPO2919 and related proteins, uncharacterized sugar phosphate isomerase with a cupin domain. This family includes proteins similar to sugar phosphate isomerase SPO2919 from Silicibacter pomeroyi and Afe_0303 from Acidithiobacillus ferrooxidans, but are as yet uncharacterized. Structures of these proteins show a cupin fold with a conserved ""jelly roll-like"" beta-barrel fold that form a homodimer." 105 matched cddid_all.tbl CDD cd02225 cd02225 380354 cupin_PA3510-like Pseudomonas aeruginosa PA3510 and related proteins, cupin domain. This family includes bacterial proteins homologous to PA3510, a Pseudomonas aeruginosa protein of unknown function with a beta-barrel fold that belongs to the cupin superfamily. 150 matched cddid_all.tbl CDD cd02226 cd02226 380355 cupin_YdbB-like "Bacillus subtilis YdbB and related proteins, cupin domain. This family includes bacterial proteins homologous to YdbB, a Bacillus subtilis protein of unknown function. It also includes protein Nmb1881 From Neisseria meningitidis, also of unknown function. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 94 matched cddid_all.tbl CDD cd02227 cd02227 380356 cupin_TM1112-like "Thermotoga maritima TM1112 and related proteins, cupin domain. This family includes bacterial and plant proteins homologous to TM1112, a Thermotoga maritima protein of unknown function with a cupin beta barrel domain. TM1112 (also known as DUF861) is a subfamily of RmlC-like cupins with a conserved ""jelly roll-like"" beta-barrel fold; structures indicate that a monomer is the biologically-relevant form." 69 matched cddid_all.tbl CDD cd02228 cd02228 380357 cupin_EutQ "Clostridium difficile EutQ and related proteins, cupin domain. This family includes bacterial and fungal proteins homologous to ethanolamine utilization protein EutQ found in Clostridium difficile, as well as in other bacteria, including the enteric pathogens Salmonella enterica and Enterococcus faecalis. EutQ is encoded by the eutQ gene which is part of the eut (ethanolamine utilization) operon found to be essential during anoxic growth of S. enterica on ethanolamine and tetrathionate. In C. difficile, inability to utilize ethanolamine results in greater virulence and a shorter time to morbidity in the animal model, suggesting that, in contrast to other intestinal pathogens, the metabolism of ethanolamine can delay the onset of disease. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization. In contrast to the metal-binding catalytic cupins, the EutQ family does not possess the histidine residues that are responsible for metal coordination in the oxidoreductase and epimerase classes of cupins." 84 matched cddid_all.tbl CDD cd02230 cd02230 380358 cupin_HP0902-like Helicobacter pylori HP0902 and related proteins, cupin domain. This family includes prokaryotic and archaeal proteins homologous to HP0902, a functionally uncharacterized protein from Helicobacter pylori and Spy1581, a protein of unknown function from Streptococcus pyogenes. These proteins demonstrate all-beta cupin folds that cannot bind metal ions due to the absence of a metal-binding histidine that is conserved in many metallo-cupins. HP0902 is able to bind bacterial endotoxin lipopolysaccharides (LPS) through its surface-exposed loops, where metal-binding sites are usually found in other metallo-cupins, and thus may have a putative role in H. pylori pathogenicity. 83 matched cddid_all.tbl CDD cd02231 cd02231 380359 cupin_BLL6423-like "Bradyrhizobium japonicum BLL6423 and related proteins, cupin domain. This family includes bacterial and fungal proteins homologous to BLL6423, a Bradyrhizobium japonicum protein of unknown function; it includes a structure of an uncharacterized protein from Novosphingobium aromaticivorans. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 108 matched cddid_all.tbl CDD cd02232 cd02232 380360 cupin_ARD "acireductone dioxygenase (ARD), cupin domain. Acireductone dioxygenase (ARD; also known as 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase) catalyzes the oxidation of 1,2-dihydroxy-3-keto-5-methylthiopentene to yield two different products depending on which active site metal is present (Fe2+ or Ni2+) as part of the methionine salvage pathway. The ARD apo-enzyme, obtained after the metal is removed, is catalytically inactive. The Fe(II)-ARD reaction yields an alpha-keto acid and formic acid, while Ni(II)-ARD instead catalyzes a shunt out of the methionine salvage pathway, yielding methylthiocarboxylic acid, formic acid, and CO. ARD belongs to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization" 134 matched cddid_all.tbl CDD cd02233 cd02233 380361 cupin_HNL-like "Granulicella tundricola hydroxynitrile lyase (GtHNL) and related proteins, cupin domain. This family includes archaeal, eukaryotic, and bacterial proteins homologous to hydroxynitrile lyase from Granulicella tundricola (GtHNL), a novel class of HNLs that does not show any sequence or structural similarity to any other HNL and does not contain conserved motifs typical of HNLs. HNLs comprise a diverse group of enzymes that vary in terms of their substrate specificity, enantioselectivity and the need for a co-factor. In plants, they catalyze the reversible cleavage of cyanohydrins, yielding HCN and aldehydes or ketones. Also included in this family is TM1010 from Thermotoga maritima, a protein of unknown function. Some but not all members of this family have N- or C-terminal carboxymuconolactone decarboxylase domains in addition to the cupin domain. Members of this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 106 matched cddid_all.tbl CDD cd02234 cd02234 380362 cupin_BLR7677-like "Bradyrhizobium japonicum BLR7677 and related proteins, cupin domain. This family includes bacterial and fungal proteins homologous to BLR7677, a Bradyrhizobium japonicum protein of unknown function. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 103 matched cddid_all.tbl CDD cd02235 cd02235 380363 cupin_BLL4011-like "Bradyrhizobium diazoefficiens BLL4011 and related proteins, cupin domain. This family includes bacterial and fungal proteins homologous to BLL4011, a Bradyrhizobium diazoefficiens protein of unknown function. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 100 matched cddid_all.tbl CDD cd02236 cd02236 380364 cupin_CV2614-like "Chromobacterium violaceum CV2614 and related proteins, cupin domain. This family includes mostly bacterial proteins homologous to CV2614, a Chromobacterium violaceum protein of unknown function. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 102 matched cddid_all.tbl CDD cd02237 cd02237 380365 cupin_DAD_ChrR "2,4'-Dihydroxyacetophenone dioxygenase (DAD) and anti-sigma factor ChrR, and similar proteins; cupin domain. This family includes the proteins 2,4'-Dihydroxyacetophenone dioxygenase (DAD) and anti-sigma factor ChrR. DAD catalyzes the oxidation of 2,4'-dihydroxyacetophenone to 4-hydroxybenzoate and formate as part of the 4-hydroxyacetophenone catabolic pathway. The enzyme is a homotetramer containing one iron per molecule of enzyme. Anti-sigma factor ChrR is a member of the ZAS (Zn2+ anti-sigma) subfamily of group IV anti-sigmas. It inhibits transcriptional activity by binding to the Rsp extra cytoplasmic function (ECF) sigma factor E (sigmaE). Some ChrR members contain tandem repeats of two distinct homologous functional domains. Members of this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 82 matched cddid_all.tbl CDD cd02238 cd02238 380366 cupin_KdgF "pectin degradation protein KdgF and related proteins, cupin domain. This family includes bacterial and archaeal pectin degradation protein KdgF that catalyzes the linearization of unsaturated uronates from both pectin and alginate, which are polysaccharides found in the cell walls of plants and brown algae, respectively, and represent an important source of carbon. These polysaccharides, mostly consisting of chains of uronates, can be metabolized by bacteria through a pathway of enzymatic steps to the key metabolite 2-keto-3-deoxygluconate (KDG). Pectin degradation is used by many plant-pathogenic bacteria during infection, and also, pectin and alginate can both represent abundant sources of carbohydrate for the production of biofuels. These proteins belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 104 matched cddid_all.tbl CDD cd02240 cd02240 380367 cupin_OxDC "Oxalate decarboxylase (OxDC), cupin domain. Oxalate decarboxylase (OxDC; EC 4.1.1.2) is a manganese-dependent bicupin that catalyzes the conversion of oxalate to formate and carbon dioxide, utilizing dioxygen as a cofactor. It is evolutionarily related to oxalate oxidase (OxOx or germin; EC 1.2.3.4) which, in contrast, converts oxalate and dioxygen to carbon dioxide and hydrogen peroxide. OxDC is classified as a bicupin because it contains two cupin folds and both domains are included in this alignment. Each OxDC cupin domain contains one manganese binding site, with four manganese binding residues (three histidines and one glutamate) conserved as well as a number of hydrophobic residues. Members of this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 145 matched cddid_all.tbl CDD cd02241 cd02241 380368 cupin_OxOx "Oxalate oxidase (germin), cupin domain. Oxalate oxidase (OxOx, also known as germin; EC 1.2.3.4) catalyzes the manganese-dependent oxidative decarboxylation of oxalate to carbon dioxide and hydrogen peroxide (H2O2). It is widespread in fungi and various plant tissues and may play a role in plant signaling and defense. This enzyme has been employed in a widely used assay for detecting urinary oxalate levels. Also, the gene encoding OxOx from barley roots has been expressed in oilseed rape in order to provide a defense against externally supplied oxalic acid. In germin, the predominant protein produced during the early phase of wheat germination, it is believed that H2O2 production is employed as a defense mechanism in response to infection by pathogens. Germin is also a marker of growth onset in cell walls in germinating cereals. The H2O2 produced by OxOx, together with the Ca2+ released by degradation of calcium oxalate, are thought to mediate cell wall cross-linking at high concentrations. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 191 matched cddid_all.tbl CDD cd02242 cd02242 380369 cupin_11S_legumin_N "11S legumin seed storage globulin, N-terminal cupin domain. This family contains the N-terminal domains of 11S legumin seed storage proteins that supply nutrition for seed germination, such as glycinin and legumin, including many common food allergens such as the peanut major allergen Ara h 3, almond allergen Pru du 6, Pecan allergen Car i 4, hazelnut nut allergen Cor a 9, Brazil nut allergen Ber e 2, cashew allergen Ana o 2, pistachio allergen Pis v 2/5, and walnut allergen Jug n/r 4. These plant seed storage globulins have tandem cupin-like beta-barrel folds (referred to as a bicupin). They are synthesized as propeptides in the endoplasmic reticulum and transported to the secretory vesicles as a homotrimer. The propeptides are processed as they are sorted in the secretory vesicles. The homotrimer binds another homotrimer to form a homohexamer with 32-point symmetry formed by a face-to-face stacking of the two trimers. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 209 matched cddid_all.tbl CDD cd02243 cd02243 380370 cupin_11S_legumin_C "11S legumin seed storage globulin, C-terminal cupin domain. This family contains the C-terminal domains of 11S legumin seed storage proteins that supply nutrition for seed germination, such as glycinin and legumin, including many common food allergens such as the peanut major allergen Ara h 3, almond allergen Pru du 6, Pecan allergen Car i 4, hazelnut nut allergen Cor a 9, Brazil nut allergen Ber e 2, cashew allergen Ana o 2, pistachio allergen Pis v 2/5, and walnut allergen Jug n/r 4. These plant seed storage globulins have tandem cupin-like beta-barrel folds (referred to as a bicupin). They are synthesized as propeptides in the endoplasmic reticulum and transported to the secretory vesicles as a homotrimer. The propeptides are processed as they are sorted in the secretory vesicles. The homotrimer binds another homotrimer to form a homohexamer with 32-point symmetry formed by a face-to-face stacking of the two trimers. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 155 matched cddid_all.tbl CDD cd02244 cd02244 380371 cupin_7S_vicilin-like_N "7S vicilin seed storage globulin, N-terminal cupin domain. This family contains the N-terminal domains of plant 7S seed storage proteins such as vicilin, and includes beta-conglycinin, phaseolin, canavalin, conglutin-beta, a chromatin protein in Pisum sativum called P54, and a sucrose binding protein in soybean called SBP. These 7S globulins also include soybean allergen beta-conglycinin, peanut allergen conarachin (Ara h 1), walnut allergen Jug r 2, and lentil allergen Len c 1. Proteins in this family perform various functions, including a role in sucrose binding, desiccation, defense against microbes and oxidative stress. The vicilin peptides formed by trypsin or chymotrypsin digestion exhibit antihypertensive effects. These plant seed storage globulins have tandem cupin-like beta-barrel folds (referred to as a bicupin). Storage proteins are the cause of well-known allergic reactions to peanuts and cereals. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 178 matched cddid_all.tbl CDD cd02245 cd02245 380372 cupin_7S_vicilin-like_C "7S vicilin seed storage globulin, C-terminal cupin domain. This family contains C-terminal domain of plant 7S seed storage protein such as vicilin and includes beta-conglycinin, phaseolin, canavalin, conglutin-beta, a chromatin protein in Pisum sativum called P54, and a sucrose binding protein in soybean called SBP. These 7S globulins also include soybean allergen beta-conglycinin, peanut allergen conarachin (Ara h 1), walnut allergen Jug r 2 and lentil allergen Len c 1. Proteins in this family perform various functions, including a role in sucrose binding, desiccation, defense against microbes and oxidative stress. The vicilin peptides formed by trypsin or chymotrypsin digestion exhibit antihypertensive effects. These plant seed storage globulins have tandem cupin-like beta-barrel folds (referred to as a bicupin). Storage proteins are the cause of well-known allergic reactions to peanuts and cereals. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 166 matched cddid_all.tbl CDD cd02247 cd02247 380373 cupin_pirin_C "pirin, C-terminal cupin domain. This family contains the C-terminal domain of pirin, a nuclear protein that is highly conserved among mammals, plants, fungi, and prokaryotes. It is widely expressed in dot-like subnuclear structures in human tissues such as liver and heart. Pirin functions as both a transcriptional cofactor and an apoptosis-related protein in mammals and is involved in seed germination and seedling development in plants. The pirins have been assigned as a subfamily of the cupin superfamily based on structure and sequence similarity. The pirins have two tandem cupin-like folds but the C-terminal cupin fold has diverged considerably and does not have a metal binding site. The exact functions of pirins are unknown but they have quercitinase activity in Escherichia coli and are thought to play important roles in transcription and apoptosis. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 76 matched cddid_all.tbl CDD cd02248 cd02248 239068 Peptidase_C1A Peptidase C1A subfamily (MEROPS database nomenclature); composed of cysteine peptidases (CPs) similar to papain, including the mammalian CPs (cathepsins B, C, F, H, L, K, O, S, V, X and W). Papain is an endopeptidase with specific substrate preferences, primarily for bulky hydrophobic or aromatic residues at the S2 subsite, a hydrophobic pocket in papain that accommodates the P2 sidechain of the substrate (the second residue away from the scissile bond). Most members of the papain subfamily are endopeptidases. Some exceptions to this rule can be explained by specific details of the catalytic domains like the occluding loop in cathepsin B which confers an additional carboxydipeptidyl activity and the mini-chain of cathepsin H resulting in an N-terminal exopeptidase activity. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds. Parasitic CPs act extracellularly to help invade tissues and cells, to hatch or to evade the host immune system. Mammalian CPs are primarily lysosomal enzymes with the exception of cathepsin W, which is retained in the endoplasmic reticulum. They are responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. In addition to its inhibitory role, the propeptide is required for proper folding of the newly synthesized enzyme and its stabilization in denaturing pH conditions. Residues within the propeptide region also play a role in the transport of the proenzyme to lysosomes or acidified vesicles. Also included in this subfamily are proteins classified as non-peptidase homologs, which lack peptidase activity or have missing active site residues. 210 matched cddid_all.tbl CDD cd02249 cd02249 239069 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins. 46 matched cddid_all.tbl CDD cd02252 cd02252 239070 nylC_like nylC-like family; composed of proteins with similarity to Flavobacterium endo-type 6-aminohexanoate-oligomer hydrolase (EIII), the product of the nylon oligomer degradation gene, nylC. EIII is an amide hydrolase that catalyzes the degradation of highly-polymerized 6-aminohexanoate oligomers. Together with other nylon degradation enzymes, such as 6-aminohexanoate cyclic dimer hydrolase (EI) and 6-aminohexanoate dimer hydrolase (EII), EIII plays a role in the detoxification and biological removal of the synthetic by-products of nylon manufacture. EIII shows sequence similarity to L-aminopeptidase D-amidase/D-esterase (DmpA), an aminopeptidase that releases N-terminal D and L amino acids from peptide substrates. Like DmpA, EIII undergoes autocatalytic cleavage in front of a nucleophile to form a heterodimer. DmpA shows similarity in catalytic mechanism to N-terminal nucleophile (Ntn) hydrolases, which are enzymes that catalyze the cleavage of amide bonds through the nucleophilic attack of the side chain of an N-terminal serine, threonine, or cysteine. 260 matched cddid_all.tbl CDD cd02253 cd02253 239071 DmpA L-Aminopeptidase D-amidase/D-esterase (DmpA) family; DmpA catalyzes the release of N-terminal D and L amino acids from peptide susbtrates. DmpA is synthesized as a single polypeptide precursor, which is autocatalytically cleaved to the active heterodimeric form. The cleavage results in two polypeptide chains, with one chain containing an N-terminal nucleophile. This group represents one of the rare aminopeptidases that are not metalloenzymes. DmpA shows similarity in catalytic mechanism to N-terminal nucleophile (Ntn) hydrolases, which are enzymes that catalyze the cleavage of amide bonds through the nucleophilic attack of the side chain of an N-terminal serine, threonine, or cysteine. 339 matched cddid_all.tbl CDD cd02255 cd02255 187736 Peptidase_C12 Cysteine peptidase C12 contains ubiquitin carboxyl-terminal hydrolase (UCH) families L1, L3, L5 and BAP1. The ubiquitin C-terminal hydrolase (UCH; ubiquitinyl hydrolase; ubiquitin thiolesterase) family of deubiquitinating enzymes (DUBs) consists of four members to date: UCH-L1, UCH-L3, UCH-L5 (UCH37) and BRCA1-associated protein-1 (BAP1), all containing a conserved catalytic domain with cysteine peptidase activity. UCH-L1 hydrolyzes carboxyl terminal esters and amides of ubiquitin (Ub). Dysfunction of this hydrolase activity can lead to an accumulation of alpha-synuclein, which is linked to Parkinson's disease (PD) and neurofibrillary tangles, linked to Alzheimer's disease (AD). UCH-L1, in its dimeric form, has additional enzymatic activity as a ubiquitin ligase. UCH-L3 hydrolyzes isopeptide bonds at the C-terminal glycine of either Ub or Nedd8, a ubiquitin-like protein. UCH-L3 can also interact with Lys48-linked Ub dimers to protect it from degradation while inhibiting its hydrolase activity at the same time. UCH-L1 and UCH-L3 are the most closely related of the UCH members. UCH-L5 (UCH37) is involved in the deubiquitinating activity in the 19S proteasome regulatory complex. It is also associated with the human Ino80 chromatin-remodeling complex (hINO80) in the nucleus. BAP1 binds to the wild-type BRCA1 RING finger domain, localized in the nucleus. It consists of the N-terminal UCH domain and two predicted nuclear localization signals (NLSs), only one of which is functional. The full-length human BRCA1 is a ubiquitin ligase. However, BAP1 does not appear to function in the deubiquitination of autoubiquitinated BRCA1. There is growing evidence that UCH enzymes and human malignancies are closely correlated. Studies show that UCH enzymes play a crucial role in some signaling pathways and in cell-cycle regulation. 222 matched cddid_all.tbl CDD cd02257 cd02257 239072 Peptidase_C19 Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. 255 matched cddid_all.tbl CDD cd02258 cd02258 199210 Peptidase_C25_N Peptidase C25 family N-terminal domain, found in Arg-gingipain (Rgp), Lys-gingipain (Kgp) and related proteins. Peptidase family C25 is a unique class of cysteine proteases, exemplified by gingipain, which is produced by Porphyromonas gingivalis. P. gingivalis is one of the primary gram-negative pathogens that causes periodontitis, a disease that is also associated with other diseases such as diabetes and cardiovascular disease. Gingipains are a group of extracellular Arg- and Lys-specific proteinases called Arg-gingipain (Rgp) and Lys-gingipain (Kgp); RgpA and RgpB are homologous Arg-specific gingipains encoded by two closely related genes, rgpA and rgpB, while Lys-specific gingipain is encoded by the single kgp gene. Mutant studies have shown that, among the large quantities of proteolytic enzymes produced by P. gingivalis, these three proteases are major virulence factors of this bacterium. All three genes encode an N-terminal pre-pro fragment, followed by the protease domain; however, rgpA and kgp also encode additional C-terminal HA (hemaglutinin/adhesion) subunits which consist of several sequence-related adhesion domains. Although unique, their cysteine protease active site residues (His and Cys) forming the catalytic dyad are well-conserved, cleaving the C-terminal peptide bond with Arg or Lys residues. Gingipains are evolutionarily related to other highly specific proteases including caspases, clostripain, legumains, and separase. Gingipains function by dysregulating host defense and inflammatory responses, and degrading host proteins, e.g. tissue, cells, matrix, plasma and immunological proteins. They are proposed to enhance gingival crevicular fluid (GCF) production through activation of the kallikrein/kinin pathways, thus increasing vascular permeability and causing gingival inflammation, a distinctive feature of periodontitis. RgpA and RgpB are also able to cleave and activate coagulation factors IX and X in order to activate prothrombin to produce thrombin, which in turn increases production of GCF. The gingipains also play a pivotal role in the survival of P. gingivalis in the host by attacking the host defense system through cleavage of several immunological molecules, while at the same time evading the host-immune response by dysregulating the cytokine network. 382 matched cddid_all.tbl CDD cd02259 cd02259 239073 Peptidase_C39_like "Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the ""double-glycine"" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in all sub-families. " 122 matched cddid_all.tbl CDD cd02266 cd02266 187535 SDR Short-chain dehydrogenases/reductases (SDR). SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human prostaglandin dehydrogenase (PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107, PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase (KR) domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type KRs have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 186 matched cddid_all.tbl CDD cd02270 cd02270 467610 meso-DAPDH_N N-terminal NAD(P)-binding domain of meso-diaminopimelate D-dehydrogenase (meso-DAPDH) and similar proteins. Meso-DAPDH (EC 1.4.1.16), also called diaminopimelate dehydrogenase, or meso-DAP dehydrogenase, probably plays a role in lysine biosynthesis. It catalyzes the reversible NADP(H)-dependent reductive amination of L-2-amino-6-oxopimelate, the acyclic form of L-tetrahydrodipicolinate, to generate the meso compound, D,L-2,6-diaminopimelate. DAPDH is a homodimer which is highly specific for meso-DAP and NADP(+) as substrates. Members of this family contain an N-terminal Rossmann fold NAD(P)-binding domain and a C-terminal dimerization domain. 151 matched cddid_all.tbl CDD cd02274 cd02274 467611 DHDPR_N N-terminal NAD(P)-binding domain of dihydrodipicolinate reductase (DHDPR) and similar proteins. DHDPR (EC 1.17.1.8), also called 4-hydroxy-tetrahydrodipicolinate reductase, or HTPA reductase, is a product of an essential gene referred to as dapB. It catalyzes the NAD(P)H-dependent reduction of 2,3-dihydrodipicolinate (DHDP) to 2,3,4,5-tetrahydrodipicolinate (THDP). DHDPR could also function as a dehydratase in addition to the role of a nucleotide dependent reductase. DHDPR is a component of the biosynthetic pathway that generates meso-diaminopimelate, a component of bacterial cell walls, and the amino acid L-lysine in various bacteria, archaea, cyanobacteria and higher plants. The enzyme is a homotetramer where each monomer is composed of two domains, an N-terminal NAD(P)-binding domain which forms a Rossmann fold, and a C-terminal substrate-binding domain that forms an open, mixed alpha-beta sandwich. 139 matched cddid_all.tbl CDD cd02278 cd02278 467612 GAPDH_II_N N-terminal NAD(P)-binding domain of type II glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and similar proteins. GAPDH plays an important role in glycolysis and gluconeogenesis by reversibly catalyzing the oxidation and phosphorylation of D-glyceraldehyde-3-phosphate to 1,3-diphospho-glycerate. It has been implicated in varied activities including regulating mRNA stability, the regulation of gene expression, induction of apoptosis, intracellular membrane trafficking, iron uptake and transport (via secreted GAPDH), heme metabolism, the maintenance of genomic integrity, and nuclear tRNA export. GAPDH contains an N-terminal NAD(P)-binding domain and a C-terminal catalytic domain. The N-terminal NAD(P)-binding domain contains a Rossmann fold which combines with the catalytic cysteine-containing C-terminus to form a catalytic cleft. Phosphatidyl-serine, RNA, and glutathione binding sites have been identified in the N-terminus. Different forms of GAPDH exist which utilize NAD (EC 1.2.1.12), NADP (EC 1.2.1.13) or either (EC 1.2.1.59). The family corresponds to type II NADP+ utilizing GAPDHs mainly from archaea. 171 matched cddid_all.tbl CDD cd02280 cd02280 467515 AGPR_N N-terminal NAD(P)-binding domain of N-acetyl-gamma-glutamyl-phosphate reductase (AGPR) and similar proteins. AGPR (EC 1.2.1.38), also called N-acetyl-glutamate semialdehyde dehydrogenase, or NAGSA dehydrogenase, catalyzes the third step in the biosynthesis of arginine from glutamate, the NADPH-dependent reduction of N-acetyl-5-glutamyl phosphate into N-acetylglutamate 5-semialdehyde. In bacteria it is a monofunctional protein of 35 to 38kDa (gene argC), while in fungi it is part of a bifunctional mitochondrial enzyme (gene ARG5,6, arg11 or arg-6) which contains a N-terminal acetylglutamate kinase (EC 2.7.2.8) domain and a C-terminal AGPR domain. There are two related families (type 1 and type 2) of N-acetyl-gamma-glutamyl-phosphate reductase, which differ by phylogeny, similarity clustering, and gap architecture in a multiple sequence alignment. This family also includes LysY (LysW-L-2-aminoadipate/LysW-L-glutamate phosphate reductase, EC 1.2.1.103/EC 1.2.1.106), which is involved in both the arginine and lysine biosynthetic pathways. Members in this family contain an N-terminal Rossmann fold NAD(P)-binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like domain. 160 matched cddid_all.tbl CDD cd02281 cd02281 467516 ASADH_AGPR_N N-terminal NAD(P)-binding domain of aspartate-beta-semialdehyde dehydrogenase (ASADH) and N-acetyl-gamma-glutamyl-phosphate reductase (AGPR). Aspartate-beta-semialdehyde dehydrogenase (ASADH, EC 1.2.1.11), also called ASA dehydrogenase (ASD), or aspartate-beta-semialdehyde dehydrogenase, catalyzes the second step of the aspartate biosynthetic pathway, an essential enzyme found in bacteria, fungi, and higher plants. ASADH catalyses the formation of L-aspartate-beta-semialdehyde (ASA) by the reductive dephosphorylation of L-beta-aspartyl phosphate (BAP), utilizing the reducing power of NADPH. ASA can either be further reduced to homoserine, which leads to methionine, threonine, or isoleucine, or it can be condensed with pyruvate and cyclized into dihydrodipicolinate, and then converted into diaminopimelate, a component of bacterial cell walls, and finally decarboxylated to produce lysine. N-acetyl-gamma-glutamyl-phosphate reductase (AGPR, EC 1.2.1.38), also called N-acetyl-glutamate semialdehyde dehydrogenase, or NAGSA dehydrogenase, reversibly catalyses the NADPH-dependent reduction of N-acetyl-gamma-glutamyl phosphate; the third step of arginine biosynthesis. ASADH and AGPR proteins contain an N-terminal Rossmann fold NAD(P)H binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like domain. 145 matched cddid_all.tbl CDD cd02314 cd02314 467517 VcASADH1_like_N N-terminal NAD(P)-binding domain of Vibrio cholerae aspartate beta-semialdehyde dehydrogenase 1 (ASADH1) and similar proteins. The family corresponds to a branch of bacterial ASADH enzymes mainly found from proteobacteria, such as Escherichia coli, Haemophilus influenzae, Pseudomonas aeruginosa and Vibrio cholerae. The first isoform of ASADH in Vibrio cholerae is one of the prototypes of this family. They have similar overall folds and domain organizations but sharing less sequence homology with fungal and archaeal ASADHs. ASADH (EC 1.2.1.11), also called ASA dehydrogenase (ASD), or aspartate-beta-semialdehyde dehydrogenase, catalyzes the NADPH-dependent formation of L-aspartate-semialdehyde (ASA) by the reductive dephosphorylation of L-aspartyl-4-phosphate, which is the second step of the aspartate biosynthetic pathway. ASA can either be further reduced to homoserine, which leads to methionine, threonine, or isoleucine, or it can be condensed with pyruvate and cyclized into dihydrodipicolinate, and then converted into diaminopimelate, a component of bacterial cell walls, and finally decarboxylated to produce lysine. ASADH contains an N-terminal Rossmann fold NAD(P) binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like catalytic domain. 150 matched cddid_all.tbl CDD cd02315 cd02315 467518 ScASADH_like_N N-terminal NAD(P)-binding domain of Saccharomyces cerevisiae aspartate beta-semialdehyde dehydrogenase (ASADH) and similar proteins. The family corresponds to a new branch of ASADH enzymes that has a similar overall fold and domain organization but sharing very little sequence homology with the typical bacterial ASADHs. They are mainly from archaea and fungi. ASADH (EC 1.2.1.11), also called ASA dehydrogenase (ASD), or aspartate-beta-semialdehyde dehydrogenase, catalyzes the NADPH-dependent formation of L-aspartate-semialdehyde (ASA) by the reductive dephosphorylation of L-aspartyl-4-phosphate, which is the second step of the aspartate biosynthetic pathway. ASA can either be further reduced to homoserine, which leads to methionine, threonine, or isoleucine, or it can be condensed with pyruvate and cyclized into dihydrodipicolinate, and then converted into diaminopimelate, a component of bacterial cell walls, and finally decarboxylated to produce lysine. ASADH contains an N-terminal Rossmann fold NAD(P) binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like catalytic domain. Family also includes NADP-dependent malonyl-CoA reductase (MCR, EC 1.2.1.75), which catalyzes the reduction of malonyl-CoA to malonate semialdehyde, a key step in the 3-hydroxypropanoate and the 3-hydroxypropanoate/4-hydroxybutyrate cycles. It can also use succinyl-CoA and succinate semialdehyde as substrates but at a lower rate than malonyl-CoA. 162 matched cddid_all.tbl CDD cd02316 cd02316 467519 VcASADH2_like_N N-terminal NAD(P)-binding domain of Vibrio cholerae aspartate beta-semialdehyde dehydrogenase 2 (ASADH2) and similar proteins. The family corresponds to a new branch of bacterial ASADH enzymes that has a similar overall fold and domain organization but sharing less sequence homology with the other bacterial ASADHs. The second isoform of ASADH in Vibrio cholerae is one of the prototypes of this family. It also includes ASADHs from Streptococcus pneumoniae, Mycobacterium tuberculosis, Thermus thermophilus, as well as from eukaryotes. ASADH (EC 1.2.1.11), also called ASA dehydrogenase (ASD), or aspartate-beta-semialdehyde dehydrogenase, catalyzes the NADPH-dependent formation of L-aspartate-semialdehyde (ASA) by the reductive dephosphorylation of L-aspartyl-4-phosphate, which is the second step of the aspartate biosynthetic pathway. ASA can either be further reduced to homoserine, which leads to methionine, threonine, or isoleucine, or it can be condensed with pyruvate and cyclized into dihydrodipicolinate, and then converted into diaminopimelate, a component of bacterial cell walls, and finally decarboxylated to produce lysine. ASADH contains an N-terminal Rossmann fold NAD(P) binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like catalytic domain. 142 matched cddid_all.tbl CDD cd02325 cd02325 100064 R3H R3H domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. R3H domains are found in proteins together with ATPase domains, SF1 helicase domains, SF2 DEAH helicase domains, Cys-rich repeats, ring-type zinc fingers, and KH domains. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner. 59 matched cddid_all.tbl CDD cd02334 cd02334 239074 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan. 49 matched cddid_all.tbl CDD cd02335 cd02335 239075 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. 49 matched cddid_all.tbl CDD cd02336 cd02336 239076 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding. 45 matched cddid_all.tbl CDD cd02337 cd02337 239077 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear. 41 matched cddid_all.tbl CDD cd02338 cd02338 239078 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination. 49 matched cddid_all.tbl CDD cd02339 cd02339 239079 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster. 45 matched cddid_all.tbl CDD cd02340 cd02340 239080 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain. 43 matched cddid_all.tbl CDD cd02341 cd02341 239081 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. 48 matched cddid_all.tbl CDD cd02342 cd02342 239082 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding. 43 matched cddid_all.tbl CDD cd02343 cd02343 239083 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. 48 matched cddid_all.tbl CDD cd02344 cd02344 239084 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. 45 matched cddid_all.tbl CDD cd02345 cd02345 239085 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila. 49 matched cddid_all.tbl CDD cd02393 cd02393 411803 KH-I_PNPase type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase (PNPase) and similar proteins. PNPase, also called polynucleotide phosphorylase, is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. It is also involved, along with RNase II, in tRNA processing. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. The model corresponds to the KH domain. 70 matched cddid_all.tbl CDD cd02394 cd02394 411804 KH-I_Vigilin_rpt6 sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins. Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one. 68 matched cddid_all.tbl CDD cd02395 cd02395 411805 KH-I_BBP type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) and similar proteins. Yeast BBP, also called mud synthetic-lethal 5 protein, or splicing factor 1, or zinc finger protein BBP, is a mammalian splicing factor SF1 ortholog. It is involved in protein-protein interactions that bridge the 3' and 5' splice-site ends of the intron during the early steps of yeast pre-mRNA splicing. BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC. 92 matched cddid_all.tbl CDD cd02396 cd02396 411806 KH-I_PCBP_rpt2 second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs). The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one. 72 matched cddid_all.tbl CDD cd02406 cd02406 239090 CRS2 Chloroplast RNA splicing 2 (CRS2) is a nuclear-encoded protein required for the splicing of group II introns in the chloroplast. CRS2 forms stable complexes with two CRS2-associated factors, CAF1 and CAF2, which are required for the splicing of distinct subsets of CRS2-dependent introns. CRS2 is closely related to bacterial peptidyl-tRNA hydrolases (PTH). 191 matched cddid_all.tbl CDD cd02407 cd02407 239091 PTH2_family Peptidyl-tRNA hydrolase, type 2 (PTH2)_like . Peptidyl-tRNA hydrolase activity releases tRNA from the premature translation termination product peptidyl-tRNA. Two structurally different enzymes have been reported to encode such activity, Pth present in bacteria and eukaryotes and Pth2 present in archaea and eukaryotes. 115 matched cddid_all.tbl CDD cd02409 cd02409 411780 KH-II_SF "type II K-homology (KH) RNA-binding domain superfamily. The K-homology (KH) domain binds single-stranded RNA or DNA, and is found in a wide variety of proteins including ribosomal proteins, transcription factors, and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but share a single ""minimal KH motif"" which is folded into a beta-alpha-alpha-beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension while type I KH domains (e.g. hnRNP K) contain a C-terminal extension, connected to the KH motif by variable loops that are different in different KH domains, whether they are type I or type II. KH-II superfamily members contain one or two KH domains, most of which are canonical type II KH domains that have the signature motif GXXG (where X represents any amino acid). The first KH domain found in archaeal cleavage and polyadenylation specificity factors (CPSFs) is a non-canonical type II KH domain that lacks the GXXG motif. Some others have mutated GXXG motifs which may or may not have nucleic acid binding ability." 67 matched cddid_all.tbl CDD cd02410 cd02410 411781 KH-II_CPSF_arch_rpt2 second type II K-homology (KH) RNA-binding domain found in archaeal cleavage and polyadenylation specificity factor (CPSF) and similar proteins. The archaeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup of enzymes within the metallo-beta-lactamase fold. Within the CPSF family, all archaeal genomes contain one member with two N-terminal type II K-homology (KH) domains and one without. This family includes the CPSF homologs from archaea possessing N-terminal KH domains. This model corresponds to the second KH domain of CPSF, which is a canonical type II KH domain that contains the signature motif GXXG (where X represents any amino acid). 76 matched cddid_all.tbl CDD cd02411 cd02411 411782 KH-II_30S_S3_arch type II K-homology (KH) RNA-binding domain found in archaeal 30S ribosomal protein S3 and similar proteins. 30S ribosomal protein S3, also called small ribosomal subunit protein uS3, is part of the head region of the 30S ribosomal subunit and binds to the lower part of the 30S subunit head. It is believed to interact with mRNA as it threads its way from the latch into the channel. Members of this family are mainly from archaea and contain only one canonical type II K-homology (KH) domain that has the signature motif GXXG (where X represents any amino acid). 87 matched cddid_all.tbl CDD cd02412 cd02412 411783 KH-II_30S_S3 type II K-homology (KH) RNA-binding domain found in 30S ribosomal protein S3 and similar proteins. 30S ribosomal protein S3, also called small ribosomal subunit protein uS3, is part of the head region of the 30S ribosomal subunit and binds to the lower part of the 30S subunit head. It may also bind mRNA in the 70S ribosome, positioning it for translation. S3 protein is believed to interact with mRNA as it threads its way from the latch into the channel. Members of this family contain only one canonical type II K-homology (KH) domain that has the signature motif GXXG (where X represents any amino acid). 108 matched cddid_all.tbl CDD cd02413 cd02413 411784 KH-II_40S_S3 type II K-homology (KH) RNA-binding domain found in 40S ribosomal protein S3 and similar proteins. 40S ribosomal protein S3, also called small ribosomal subunit protein uS3, is part of the head region of the 40S ribosomal subunit and is involved in translation. It is believed to interact with mRNA as it threads its way from the latch into the channel. 40S ribosomal protein S3 has endonuclease activity and plays a role in repair of damaged DNA. It cleaves phosphodiester bonds of DNAs containing altered bases with broad specificity and cleaves supercoiled DNA more efficiently than relaxed DNA. Members of this family are mainly from prokaryotes and contain only one canonical type II K-homology (KH) domain that has the signature motif GXXG (where X represents any amino acid). 91 matched cddid_all.tbl CDD cd02414 cd02414 411785 KH-II_Jag type II K-homology (KH) RNA-binding domain found in protein Jag and similar proteins. Protein Jag, also called SpoIIIJ-associated protein, is associated with SpoIIIJ and is necessary for the third stage of sporulation. Members of this family are mainly from bacteria and contain only one canonical type II K-homology (KH) domain that has the signature motif GXXG (where X represents any amino acid). 79 matched cddid_all.tbl CDD cd02417 cd02417 239098 Peptidase_C39_likeA "A sub-family of peptidase C39 which contains Cyclolysin and Hemolysin processing peptidases. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the ""double-glycine"" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this sub-family." 121 matched cddid_all.tbl CDD cd02418 cd02418 239099 Peptidase_C39B "A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the ""double-glycine"" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family." 136 matched cddid_all.tbl CDD cd02419 cd02419 239100 Peptidase_C39C "A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the ""double-glycine"" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family." 127 matched cddid_all.tbl CDD cd02420 cd02420 239101 Peptidase_C39D "A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the ""double-glycine"" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family." 125 matched cddid_all.tbl CDD cd02421 cd02421 239102 Peptidase_C39_likeD "A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the ""double-glycine"" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this sub-family." 124 matched cddid_all.tbl CDD cd02423 cd02423 239103 Peptidase_C39G "A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the ""double-glycine"" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are lacking the nucleotide-binding transporter signature." 129 matched cddid_all.tbl CDD cd02424 cd02424 239104 Peptidase_C39E "A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the ""double-glycine"" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family, which contains Colicin V perocessing peptidase." 129 matched cddid_all.tbl CDD cd02425 cd02425 239105 Peptidase_C39F "A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the ""double-glycine"" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family." 126 matched cddid_all.tbl CDD cd02426 cd02426 239106 Pol_gamma_b_Cterm C-terminal domain of mitochondrial DNA polymerase gamma B subunit, which is required for processivity. Polymerase gamma replicates and repairs mitochondrial DNA. The c-terminal domain of its B subunit is strikingly similar to the anticodon-binding domain of glycyl tRNA synthetase. 128 matched cddid_all.tbl CDD cd02429 cd02429 239107 PTH2_like Peptidyl-tRNA hydrolase, type 2 (PTH2)_like . Peptidyl-tRNA hydrolase activity releases tRNA from the premature translation termination product peptidyl-tRNA. Two structurally different enzymes have been reported to encode such activity, Pth present in bacteria and eukaryotes and Pth2 present in archaea and eukaryotes. There is no functional information for this eukaryote-specific subgroup. 116 matched cddid_all.tbl CDD cd02430 cd02430 239108 PTH2 Peptidyl-tRNA hydrolase, type 2 (PTH2). Peptidyl-tRNA hydrolase (PTH) activity releases tRNA from the premature translation termination product peptidyl-tRNA, therefore allowing the tRNA and peptide to be reused in protein synthesis. PTH2 is present in archaea and eukaryotes. 115 matched cddid_all.tbl CDD cd02431 cd02431 153122 Ferritin_CCC1_C CCC1-related domain of ferritin. Ferritin_CCC1_like_C: The proteins of this family contain two domains. This is the C-terminal domain that is closely related to the CCC1, a vacuole transmembrane protein functioning as an iron and manganese transporter. The N-terminal domain is similar to ferritin-like diiron-carboxylate proteins, which are involved in a variety of iron ion related functions, such as iron storage and regulation, mono-oxygenation, and reactive radical production. This family may be unique to certain bacteria and archaea. 149 matched cddid_all.tbl CDD cd02432 cd02432 153123 Nodulin-21_like_1 Nodulin-21 and CCC1-related protein family. Nodulin-21_like_1: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter. 218 matched cddid_all.tbl CDD cd02433 cd02433 153124 Nodulin-21_like_2 Nodulin-21 and CCC1-related protein family. Nodulin-21_like_2: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter. 234 matched cddid_all.tbl CDD cd02434 cd02434 153125 Nodulin-21_like_3 Nodulin-21 and CCC1-related protein family. Nodulin-21_like_3: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter. 225 matched cddid_all.tbl CDD cd02435 cd02435 153126 CCC1 CCC1. CCC1: This domain is present in the CCC1, an iron and manganese transporter of Saccharomyces cerevisiae. CCC1 is a transmembrane protein that is located in the vacuole and transfers the iron and manganese ions from the cytosol to the vacuole. This domain may be unique to certain fungi and plants. 241 matched cddid_all.tbl CDD cd02436 cd02436 153127 Nodulin-21 Nodulin-21. Nodulin-21: This is a family of proteins that may be unique to certain plants. The family member in soybean is found to be nodule-specific and is abundant during nodule development. The proteins of this family thus may play a role in symbiotic nitrogen fixation. 152 matched cddid_all.tbl CDD cd02437 cd02437 153128 CCC1_like_1 CCC1-related protein family. CCC1_like_1: This is a protein family closely related to CCC1, a family of proteins involved in iron and manganese transport. Yeast CCC1 is a vacuole transmembrane protein responsible for the iron and manganese accumulation in vacuole. 175 matched cddid_all.tbl CDD cd02439 cd02439 143332 DMB-PRT_CobT Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT. Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT/CobT, not to be confused with the CobT subunit of cobaltochelatase, which does not belong to this group) catalyzes the synthesis of alpha-ribazole-5'-phosphate, from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB). This function is essential to the anaerobic biosynthesis pathway of cobalamin (vitamin B12), which is the largest and most complex cofactor in a number of enzyme-catalyzed reactions in bacteria, archaea and eukaryotes. Only eubacteria and archaebacteria can synthesize vitamin B12; multicellular organisms have lost this ability during evolution. DMB-PRT/CobT works sequentially with CobC (a phosphatase) to couple the lower ligand of cobalamin to a ribosyl moiety. DMB is the most common lower ligand of cobamides; other lower ligands include adenine, 5-methoxybenzimidazole or phenol. It has been suggested that earlier metabolic or enzymatic steps may control which lower ligand is available to DMB-PRT/CobT. In Salmonella enterica, for example, the lower ligand is DMB under aerobic conditions and adenine or 2-methyladenine under anaerobic conditions. Salmonella enterica DMB-PRT/CobT is a homodimer with two active sites, each active site is comprised of residues from both monomers. This group includes two distinct subfamilies, one archaeal-like, the other comprised of bacterial sequences. 315 matched cddid_all.tbl CDD cd02440 cd02440 100107 AdoMet_MTases S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.). 107 matched cddid_all.tbl CDD cd02503 cd02503 133000 MobA MobA catalyzes the formation of molybdopterin guanine dinucleotide. The prokaryotic enzyme molybdopterin-guanine dinucleotide biosynthesis protein A (MobA). All mononuclear molybdoenzymes bind molybdenum in complex with an organic cofactor termed molybdopterin (MPT). In many bacteria, including Escherichia coli, molybdopterin can be further modified by attachment of a GMP group to the terminal phosphate of molybdopterin to form molybdopterin guanine dinucleotide (MGD). This GMP attachment step is catalyzed by MobA, by linking a guanosine 5'-phosphate to MPT forming molybdopterin guanine dinucleotide. This reaction requires GTP, MgCl2, and the MPT form of the cofactor. It is a reaction unique to prokaryotes, and therefore may represent a potential drug target. 181 matched cddid_all.tbl CDD cd02507 cd02507 133001 eIF-2B_gamma_N_like The N-terminal of eIF-2B_gamma_like is predicted to have glycosyltransferase activity. N-terminal domain of eEIF-2B epsilon and gamma, subunits of eukaryotic translation initiators, is a subfamily of glycosyltranferase 2 and is predicted to have glycosyltranferase activity. eIF-2B is a guanine nucleotide-exchange factor which mediates the exchange of GDP (bound to initiation factor eIF2) for GTP, generating active eIF2.GTP complex. EIF2B is a complex multimeric protein consisting of five subunits named alpha, beta, gamma, delta and epsilon. Subunit epsilon shares sequence similarity with gamma subunit, and with a family of bifunctional nucleotide-binding enzymes such as ADP-glucose pyrophosphorylase, suggesting that epsilon subunit may play roles in nucleotide binding activity. In yeast, eIF2B gamma enhances the activity of eIF2B-epsilon leading to the idea that these subunits form the catalytic subcomplex. 216 matched cddid_all.tbl CDD cd02508 cd02508 133002 ADP_Glucose_PP ADP-glucose pyrophosphorylase is involved in the biosynthesis of glycogen or starch. ADP-glucose pyrophosphorylase (glucose-1-phosphate adenylyltransferase) catalyzes a very important step in the biosynthesis of alpha 1,4-glucans (glycogen or starch) in bacteria and plants: synthesis of the activated glucosyl donor, ADP-glucose, from glucose-1-phosphate and ATP. ADP-glucose pyrophosphorylase is a tetrameric allosterically regulated enzyme. While a homotetramer in bacteria, in plant chloroplasts and amyloplasts, it is a heterotetramer of two different, yet evolutionary related, subunits. There are a number of conserved regions in the sequence of bacterial and plant ADP-glucose pyrophosphorylase subunits. It is a subfamily of a very diverse glycosy transferase family 2. 200 matched cddid_all.tbl CDD cd02509 cd02509 133003 GDP-M1P_Guanylyltransferase GDP-M1P_Guanylyltransferase catalyzes the formation of GDP-Mannose. GDP-mannose-1-phosphate guanylyltransferase, also called GDP-mannose pyrophosphorylase (GDP-MP), catalyzes the formation of GDP-Mannose from mannose-1-phosphate and GTP. Mannose is a key monosaccharide for glycosylation of proteins and lipids. GDP-Mannose is the activated donor for mannosylation of various biomolecules. This enzyme is known to be bifunctional, as both mannose-6-phosphate isomerase and mannose-1-phosphate guanylyltransferase. This CD covers the N-terminal GDP-mannose-1-phosphate guanylyltransferase domain, whereas the isomerase function is located at the C-terminal half. GDP-MP is a member of the nucleotidyltransferase family of enzymes. 274 matched cddid_all.tbl CDD cd02510 cd02510 133004 pp-GalNAc-T pp-GalNAc-T initiates the formation of mucin-type O-linked glycans. UDP-GalNAc: polypeptide alpha-N-acetylgalactosaminyltransferases (pp-GalNAc-T) initiate the formation of mucin-type, O-linked glycans by catalyzing the transfer of alpha-N-acetylgalactosamine (GalNAc) from UDP-GalNAc to hydroxyl groups of Ser or Thr residues of core proteins to form the Tn antigen (GalNAc-a-1-O-Ser/Thr). These enzymes are type II membrane proteins with a GT-A type catalytic domain and a lectin domain located on the lumen side of the Golgi apparatus. In human, there are 15 isozymes of pp-GalNAc-Ts, representing the largest of all glycosyltransferase families. Each isozyme has unique but partially redundant substrate specificity for glycosylation sites on acceptor proteins. 299 matched cddid_all.tbl CDD cd02511 cd02511 133005 Beta4Glucosyltransferase UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide. UDP-glucose: lipooligosaccharide (LOS) beta-1-4-glucosyltransferase catalyzes the addition of the first residue, glucose, of the lacto-N-neotetrase structure to HepI of the LOS inner core. LOS is the major constituent of the outer leaflet of the outer membrane of gram-positive bacteria. It consists of a short oligosaccharide chain of variable composition (alpha chain) attached to a branched inner core which is lined in turn to lipid A. Beta 1,4 glucosyltransferase is required to attach the alpha chain to the inner core. 229 matched cddid_all.tbl CDD cd02513 cd02513 133006 CMP-NeuAc_Synthase CMP-NeuAc_Synthase activates N-acetylneuraminic acid by adding CMP moiety. CMP-N-acetylneuraminic acid synthetase (CMP-NeuAc synthetase) or acylneuraminate cytidylyltransferase catalyzes the transfer the CMP moiety of CTP to the anomeric hydroxyl group of NeuAc in the presence of Mg++. It is the second to last step in the sialylation of the oligosaccharide component of glycoconjugates by providing the activated sugar-nucleotide cytidine 5'-monophosphate N-acetylneuraminic acid (CMP-Neu5Ac), the substrate for sialyltransferases. Eukaryotic CMP-NeuAc synthetases are predominantly located in the nucleus. The activated CMP-Neu5Ac diffuses from the nucleus into the cytoplasm. 223 matched cddid_all.tbl CDD cd02514 cd02514 133007 GT13_GLCNAC-TI GT13_GLCNAC-TI is involved in an essential step in the synthesis of complex or hybrid-type N-linked oligosaccharides. Alpha-1,3-mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransferase (GLCNAC-T I , GNT-I) transfers N-acetyl-D-glucosamine from UDP to high-mannose glycoprotein N-oligosaccharide, an essential step in the synthesis of complex or hybrid-type N-linked oligosaccharides. The enzyme is an integral membrane protein localized to the Golgi apparatus. The catalytic domain is located at the C-terminus. These proteins are members of the glycosy transferase family 13. 334 matched cddid_all.tbl CDD cd02515 cd02515 133008 Glyco_transf_6 Glycosyltransferase family 6 comprises enzymes responsible for the production of the human ABO blood group antigens. Glycosyltransferase family 6, GT_6, comprises enzymes with three known activities: alpha-1,3-galactosyltransferase, alpha-1,3 N-acetylgalactosaminyltransferase, and alpha-galactosyltransferase. UDP-galactose:beta-galactosyl alpha-1,3-galactosyltransferase (alpha3GT) catalyzes the transfer of galactose from UDP-alpha-d-galactose into an alpha-1,3 linkage with beta-galactosyl groups in glycoconjugates. The enzyme exists in most mammalian species but is absent from humans, apes, and old world monkeys as a result of the mutational inactivation of the gene. The alpha-1,3 N-acetylgalactosaminyltransferase and alpha-galactosyltransferase are responsible for the production of the human ABO blood group antigens. A N-acetylgalactosaminyltransferases use a UDP-GalNAc donor to convert the H-antigen acceptor to the A antigen, whereas a galactosyltransferase uses a UDP-galactose donor to convert the H-antigen acceptor to the B antigen. Alpha-1,3 N-acetylgalactosaminyltransferase and alpha-galactosyltransferase differ only in the identity of four critical amino acid residues. 271 matched cddid_all.tbl CDD cd02516 cd02516 133009 CDP-ME_synthetase CDP-ME synthetase is involved in mevalonate-independent isoprenoid production. 4-diphosphocytidyl-2-methyl-D-erythritol synthase (CDP-ME), also called 2C-methyl-d-erythritol 4-phosphate cytidylyltransferase catalyzes the third step in the alternative (non-mevalonate) pathway of Isopentenyl diphosphate (IPP) biosynthesis: the formation of 4-diphosphocytidyl-2C-methyl-D-erythritol from CTP and 2C-methyl-D-erythritol 4-phosphate. This mevalonate independent pathway that utilizes pyruvate and glyceraldehydes 3-phosphate as starting materials for production of IPP occurs in a variety of bacteria, archaea and plant cells, but is absent in mammals. Thus, CDP-ME synthetase is an attractive targets for the structure-based design of selective antibacterial, herbicidal and antimalarial drugs. 218 matched cddid_all.tbl CDD cd02517 cd02517 133010 CMP-KDO-Synthetase CMP-KDO synthetase catalyzes the activation of KDO which is an essential component of the lipopolysaccharide. CMP-KDO Synthetase: 3-Deoxy-D-manno-octulosonate cytidylyltransferase (CMP-KDO synthetase) catalyzes the conversion of CTP and 3-deoxy-D-manno-octulosonate into CMP-3-deoxy-D-manno-octulosonate (CMP-KDO) and pyrophosphate. KDO is an essential component of the lipopolysaccharide found in the outer surface of gram-negative eubacteria. It is also a constituent of the capsular polysaccharides of some gram-negative eubacteria. Its presence in the cell wall polysaccharides of green algae and plant were also discovered. However, they have not been found in yeast and animals. The absence of the enzyme in mammalian cells makes it an attractive target molecule for drug design. 239 matched cddid_all.tbl CDD cd02518 cd02518 133011 GT2_SpsF SpsF is a glycosyltrnasferase implicated in the synthesis of the spore coat. Spore coat polysaccharide biosynthesis protein F (spsF) is a glycosyltransferase implicated in the synthesis of the spore coat in a variety of bacteria challenged by stress as starvation. The spsF gene is expressed in the late stage of coat development responsible for a terminal step in coat formation that involves the glycosylation of the coat. SpsF gene mutation resulted in spores that appeared normal. But, the spores tended to aggregate and had abnormal adsorption properties, indicating a surface alteration. 233 matched cddid_all.tbl CDD cd02520 cd02520 133012 Glucosylceramide_synthase Glucosylceramide synthase catalyzes the first glycosylation step of glycosphingolipid synthesis. UDP-glucose:N-acylsphingosine D-glucosyltransferase (glucosylceramide synthase or ceramide glucosyltransferase) catalyzes the first glycosylation step of glycosphingolipid synthesis. Its product, glucosylceramide, serves as the core of more than 300 glycosphingolipids (GSL). GSLs are a group of membrane components that have the lipid portion embedded in the outer plasma membrane leaflet and the sugar chains extended to the outer environment. Several lines of evidence suggest the importance of GSLs in various cellular processes such as differentiation, adhesion, proliferation, and cell-cell recognition. In pathogenic fungus Cryptococcus neoformans, glucosylceramide serves as an antigen that elicits an antibody response in patients and it is essential for fungal growth in host extracellular environment. 196 matched cddid_all.tbl CDD cd02522 cd02522 133013 GT_2_like_a GT_2_like_a represents a glycosyltransferase family-2 subfamily with unknown function. Glycosyltransferase family 2 (GT-2) subfamily of unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families. 221 matched cddid_all.tbl CDD cd02523 cd02523 133014 PC_cytidylyltransferase Phosphocholine cytidylyltransferases catalyze the synthesis of CDP-choline. This family contains proteins similar to prokaryotic phosphocholine (P-cho) cytidylyltransferases. Phosphocholine (PC) cytidylyltransferases catalyze the transfer of a cytidine monophosphate from CTP to phosphocholine to form CDP-choline. PC is the most abundant phospholipid in eukaryotic membranes and it is also important in prokaryotic membranes. For pathogenic prokaryotes, the cell surface PC facilitates the interaction with host surface and induces attachment and invasion. In addition cell wall PC serves as scaffold for a group of choline-binding proteins that are secreted from the cells. Phosphocholine (PC) cytidylyltransferase is a key enzyme in the prokaryotic choline metabolism pathway. It has been hypothesized to consist of a choline transport system, a choline kinase, CTP:phosphocholine cytidylyltransferase, and a choline phosphotransferase that transfers P-Cho from CDP-Cho to either lipoteichoic acid or lipopolysaccharide. 229 matched cddid_all.tbl CDD cd02524 cd02524 133015 G1P_cytidylyltransferase G1P_cytidylyltransferase catalyzes the production of CDP-D-Glucose. Alpha-D-Glucose-1-phosphate Cytidylyltransferase catalyzes the production of CDP-D-Glucose from alpha-D-Glucose-1-phosphate and MgCTP as substrate. CDP-D-Glucose is the precursor for synthesizing four of the five naturally occurring 3,6-dideoxy sugars-abequose (3,6-dideoxy-D-Xylo-hexose), ascarylose (3,6-dideoxy-L-arabino-hexose), paratose (3,6-dideoxy-D-ribohexose), and tyvelose (3,6-dideoxy-D-arabino-hexose. Deoxysugars are ubiquitous in nature where they function in a variety of biological processes, including cell adhesion, immune response, determination of ABO blood groups, fertilization, antibiotic function, and microbial pathogenicity. 253 matched cddid_all.tbl CDD cd02525 cd02525 133016 Succinoglycan_BP_ExoA ExoA is involved in the biosynthesis of succinoglycan. Succinoglycan Biosynthesis Protein ExoA catalyzes the formation of a beta-1,3 linkage of the second sugar (glucose) of the succinoglycan with the galactose on the lipid carrie. Succinoglycan is an acidic exopolysaccharide that is important for invasion of the nodules. Succinoglycan is a high-molecular-weight polymer composed of repeating octasaccharide units. These units are synthesized on membrane-bound isoprenoid lipid carriers, beginning with galactose followed by seven glucose molecules, and modified by the addition of acetate, succinate, and pyruvate. ExoA is a membrane protein with a transmembrance domain at c-terminus. 249 matched cddid_all.tbl CDD cd02526 cd02526 133017 GT2_RfbF_like RfbF is a putative dTDP-rhamnosyl transferase. Shigella flexneri RfbF protein is a putative dTDP-rhamnosyl transferase. dTDP rhamnosyl transferases of Shigella flexneri add rhamnose sugars to N-acetyl-glucosamine in the O-antigen tetrasaccharide repeat. Lipopolysaccharide O antigens are important virulence determinants for many bacteria. The variations of sugar composition, the sequence of the sugars and the linkages in the O antigen provide structural diversity of the O antigen. 237 matched cddid_all.tbl CDD cd02537 cd02537 133018 GT8_Glycogenin Glycogenin belongs the GT 8 family and initiates the biosynthesis of glycogen. Glycogenin initiates the biosynthesis of glycogen by incorporating glucose residues through a self-glucosylation reaction at a Tyr residue, and then acts as substrate for chain elongation by glycogen synthase and branching enzyme. It contains a conserved DxD motif and an N-terminal beta-alpha-beta Rossmann-like fold that are common to the nucleotide-binding domains of most glycosyltransferases. The DxD motif is essential for coordination of the catalytic divalent cation, most commonly Mn2+. Glycogenin can be classified as a retaining glycosyltransferase, based on the relative anomeric stereochemistry of the substrate and product in the reaction catalyzed. It is placed in glycosyltransferase family 8 which includes lipopolysaccharide glucose and galactose transferases and galactinol synthases. 240 matched cddid_all.tbl CDD cd02538 cd02538 133019 G1P_TT_short G1P_TT_short is the short form of glucose-1-phosphate thymidylyltransferase. This family is the short form of glucose-1-phosphate thymidylyltransferase. Glucose-1-phosphate thymidylyltransferase catalyses the formation of dTDP-glucose, from dTTP and glucose 1-phosphate. It is the first enzyme in the biosynthesis of dTDP-L-rhamnose, a cell wall constituent and a feedback inhibitor of the enzyme.There are two forms of Glucose-1-phosphate thymidylyltransferase in bacteria and archeae; short form and long form. The homotetrameric, feedback inhibited short form is found in numerous bacterial species that produce dTDP-L-rhamnose. The long form, which has an extra 50 amino acids c-terminal, is found in many species for which it serves as a sugar-activating enzyme for antibiotic biosynthesis and or other, unknown pathways, and in which dTDP-L-rhamnose is not necessarily produced. 240 matched cddid_all.tbl CDD cd02540 cd02540 133020 GT2_GlmU_N_bac N-terminal domain of bacterial GlmU. The N-terminal domain of N-Acetylglucosamine-1-phosphate uridyltransferase (GlmU). GlmU is an essential bacterial enzyme with both an acetyltransferase and an uridyltransferase activity which have been mapped to the C-terminal and N-terminal domains, respectively. This family represents the N-terminal uridyltransferase. GlmU performs the last two steps in the synthesis of UDP-N-acetylglucosamine (UDP-GlcNAc), which is an essential precursor in both the peptidoglycan and the lipopolysaccharide metabolic pathways in Gram-positive and Gram-negative bacteria, respectively. 229 matched cddid_all.tbl CDD cd02541 cd02541 133021 UGPase_prokaryotic Prokaryotic UGPase catalyses the synthesis of UDP-glucose. Prokaryotic UDP-Glucose Pyrophosphorylase (UGPase) catalyzes a reversible production of UDP-Glucose and pyrophosphate (PPi) from glucose-1-phosphate and UTP. UDP-glucose plays pivotal roles in galactose utilization, in glycogen synthesis, and in the synthesis of the carbohydrate moieties of glycolipids , glycoproteins , and proteoglycans. UGPase is found in both prokaryotes and eukaryotes, although prokaryotic and eukaryotic forms of UGPase catalyze the same reaction, they share low sequence similarity. 267 matched cddid_all.tbl CDD cd02549 cd02549 239109 Peptidase_C39A "A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the ""double-glycine"" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family of proteins with a single peptidase domain, which are lacking the nucleotide-binding transporter signature or have different domain architectures." 141 matched cddid_all.tbl CDD cd02550 cd02550 211325 PseudoU_synth_Rsu_Rlu_like Pseudouridine synthase, Rsu/Rlu family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli. 154 matched cddid_all.tbl CDD cd02552 cd02552 211326 PseudoU_synth_TruD_like Pseudouridine synthase, TruD family. This group consists of eukaryotic, bacterial and archeal pseudouridine synthases similar to Escherichia coli TruD and Saccharomyces cerevisiae Pus7. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruD and S. cerevisiae Pus7 make psi13 in cytoplasmic tRNAs. In addition S. cerevisiae Pus7 makes psi35 in U2 small nuclear RNA (U2 snRNA) and psi35 in pre-tRNATyr. Psi35 in U2 snRNA and psi13 in tRNAs are highly phylogenetically conserved. Psi34 is the mammalian U2 snRNA counterpart of yeast U2 snRNA psi35. 232 matched cddid_all.tbl CDD cd02553 cd02553 211327 PseudoU_synth_RsuA Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RsuA makes psi516 in 16S RNA. Psi at this position is not generally conserved in other organisms. 167 matched cddid_all.tbl CDD cd02554 cd02554 211328 PseudoU_synth_RluF Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site. 164 matched cddid_all.tbl CDD cd02555 cd02555 211329 PSSA_1 Pseudouridine synthase, a subgroup of the RsuA family. This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The TruA family is comprised of proteins related to Escherichia coli RsuA. 177 matched cddid_all.tbl CDD cd02556 cd02556 211330 PseudoU_synth_RluB Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site. 167 matched cddid_all.tbl CDD cd02557 cd02557 211331 PseudoU_synth_ScRIB2 Pseudouridine synthases similar to Saccharomyces cerevisiae RIB2. Pseudouridine synthase, Saccharomyces cerevisiae RIB2_like. This group is comprised of eukaryotic and bacterial proteins similar to Saccharomyces cerevisiae RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S. cerevisiae RIB2 displays two distinct catalytic activities. The N-terminal domain of RIB2 is RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs. Psi32 is highly phylogenetically conserved. The C-terminal domain of RIB2 has a DRAP deaminase activity which catalyses the formation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione 5'-phosphate from 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate during riboflavin biosynthesis. S. cerevisiae Pus6p makes the psi31 of cytoplasmic and mitochondrial tRNAs. 213 matched cddid_all.tbl CDD cd02558 cd02558 211332 PSRA_1 Pseudouridine synthase, a subgroup of the RluA family. This group is comprised of bacterial proteins assigned to the RluA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The RluA family is comprised of proteins related to Escherichia coli RluA. 246 matched cddid_all.tbl CDD cd02563 cd02563 211333 PseudoU_synth_TruC tRNA pseudouridine isomerase C. Pseudouridine synthases catalyze the isomerization of specific uridines in an tRNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. TruC makes psi65 in tRNAs. This psi residue is not universally conserved. 223 matched cddid_all.tbl CDD cd02566 cd02566 211334 PseudoU_synth_RluE Pseudouridine synthase, Escherichia coli RluE. This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. Escherichia coli RluE makes psi2457 in 23S RNA. psi2457 is not universally conserved. 168 matched cddid_all.tbl CDD cd02568 cd02568 211335 PseudoU_synth_PUS1_PUS2 Pseudouridine synthase, PUS1/ PUS2 like. This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus1p, S. cerevisiae Pus2p, Caenorhabditis elegans Pus1p and human PUS1. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus1p catalyzes the formation of psi34 and psi36 in the intron-containing tRNAIle, psi35 in the intron-containing tRNATyr, psi27 and/or psi28 in several yeast cytoplasmic tRNAs and, psi44 in U2 small nuclear RNA (U2 snRNA). The presence of the intron is required for the formation of psi 34, 35 and 36. In addition S. cerevisiae PUS1 makes are psi 26, 65 and 67. C. elegans Pus1p does not modify psi44 in U2 snRNA. Mouse Pus1p makes psi27/28 in pre- tRNASer , tRNAVal and tRNAIle, psi 34/36 in tRNAIle and, psi 32 and potentially 67 in tRNAVal. Psi44 in U2 snRNA and psi32 in tRNAs are highly phylogenetically conserved. Psi 26,27,28,34,35,36,65 and 67 in tRNAs are less highly conserved. Mouse Pus1p regulates nuclear receptor activity through pseudouridylation of Steroid Receptor RNA Activator. Missense mutation in human PUS1 causes mitochondrial myopathy and sideroblastic anemia (MLASA). 245 matched cddid_all.tbl CDD cd02569 cd02569 211336 PseudoU_synth_ScPus3 Pseudouridine synthase, Saccharomyces cerevisiae Pus3 like. This group consists of eukaryotic pseudouridine synthases similar to S. cerevisiae Pus3p, mouse Pus3p and, human PUS2. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. S. cerevisiae Pus3p makes psi38 and psi39 in tRNAs. Mouse Pus3p has been shown to makes psi38 and, possibly also psi 39, in tRNAs. Psi38 and psi39 are highly conserved in tRNAs from eubacteria, archea and eukarya. 256 matched cddid_all.tbl CDD cd02570 cd02570 211337 PseudoU_synth_EcTruA Eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA. This group consists of eukaryotic and bacterial pseudouridine synthases similar to E. coli TruA, Pseudomonas aeruginosa truA and human pseudouridine synthase-like 1 (PUSL1). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E. coli TruA makes psi38/39 and/or 40 in tRNA. psi38 and psi39 in tRNAs are highly phylogenetically conserved. P. aeruginosa truA is required for induction of type III secretory genes and may act through modifying tRNAs critical for the expression of type III genes or their regulators. 239 matched cddid_all.tbl CDD cd02572 cd02572 211338 PseudoU_synth_hDyskerin Pseudouridine synthase, human dyskerin like. This group consists of eukaryotic and archeal pseudouridine synthases similar to human dyskerin, Saccharomyces cerevisiae Cbf5, and Drosophila melanogaster Mfl (minifly protein). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactor is required. S. cerevisiae Cbf5 and human dyskerin are nucleolar proteins that, with the help of guide RNAs, make the hundreds of psueudouridnes present in rRNA and small nuclear RNAs (snRNAs). Cbf5/Dyskerin is the catalytic subunit of eukaryotic box H/ACA small nucleolar ribonucleoprotein (snoRNP) particles. D. melanogaster mfl hosts in its fourth intron, a box H/AC snoRNA gene. In addition dyskerin is likely to have a structural role in the telomerase complex. Mutations in human dyskerin cause X-linked dyskeratosis congenitas. Mutations in Drosophila Mfl results in miniflies that suffer abnormalities. 182 matched cddid_all.tbl CDD cd02573 cd02573 211339 PseudoU_synth_EcTruB Pseudouridine synthase, Escherichia coli TruB like. This group consists of bacterial pseudouridine synthases similar to E. coli TruB and Mycobacterium tuberculosis TruB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruB and M. tuberculosis TruB make psi55 in the T loop of tRNAs. Psi55 is nearly universally conserved. E. coli TruB is not inhibited by RNA containing 5-fluorouridine. 213 matched cddid_all.tbl CDD cd02575 cd02575 211340 PseudoU_synth_EcTruD Pseudouridine synthase, similar to Escherichia coli TruD. This group consists of bacterial pseudouridine synthases similar to Escherichia coli TruD. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). E. coli TruD makes the highly phylogenetically conserved psi13 in tRNAs. 253 matched cddid_all.tbl CDD cd02576 cd02576 211341 PseudoU_synth_ScPUS7 Pseudouridine synthase, TruD family. This group consists of eukaryotic pseudouridine synthases similar to Saccharomyces cerevisiae Pus7. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). Saccharomyces cerevisiae Pus7 makes psi35 in U2 small nuclear RNA (U2 snRNA), psi13 in cytoplasmic tRNAs and psi35 in pre-tRNATyr. Psi35 in yeast U2 snRNA and psi13 in tRNAs are highly phylogenetically conserved. Psi34 is the mammalian U2 snRNA counterpart of yeast U2 snRNA psi35. 371 matched cddid_all.tbl CDD cd02577 cd02577 211342 PSTD1 Pseudouridine synthase, a subgroup of the TruD family. This group consists of several hypothetical archeal pseudouridine synthases assigned to the TruD family of psuedouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). The TruD family is comprised of proteins related to Escherichia coli TruD. 319 matched cddid_all.tbl CDD cd02582 cd02582 259846 RNAP_archeal_A' A' subunit of archaeal RNA polymerase (RNAP). A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins. 861 matched cddid_all.tbl CDD cd02583 cd02583 259847 RNAP_III_RPC1_N Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain. Rpc1 (C160) subunit forms part of the active site region of RNAP III. RNAP III is one of the three distinct classes of nuclear RNAP in eukaryotes that is responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA genes, and some others. RNAP III is the largest nuclear RNA polymerase with 17 subunits. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site, making up the head and core of the one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between Rpc1 and Rpb1 suggests a similar functional and structural role. 816 matched cddid_all.tbl CDD cd02584 cd02584 132720 RNAP_II_Rpb1_C Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain. RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures. 410 matched cddid_all.tbl CDD cd02585 cd02585 319784 HAD_PMM phosphomannomutase, similar to human PMM1 and PMM2, Saccharomyces Sec53p, and Arabidopsis thaliana PMM. PMM catalyzes the interconversion of mannose-6-phosphate (M6P) to mannose-1-phosphate (M1P); the conversion of M6P to M1P is an essential step in mannose activation and the biosynthesis of glycoconjugates in all eukaryotes. M1P is the substrate for the synthesis of GDP-mannose, which is an intermediate for protein glycosylation, protein sorting and secretion, and maintaining a functional endomembrane system in eukaryotic cells. Proteins in this family contains a conserved phosphorylated motif DxDx(T/V) shared with some other phosphotransferases. This family contains two human homologs, PMM1 and PMM2; PMM2 deficiency causes congenital disorder of glycosylation type I-a, also known as Jaeken syndrome. PMM1 can also act as glucose-1,6-bisphosphatase in the brain after stimulation with inosine monophosphate; PMM2 on the other hand, is insensitive to IMP and demonstrates low glucose-1,6-bisphosphatase activity. Arabidopsis thaliana PMM converted M1P into M6P and glucose-1-phosphate into glucose-6-phosphate, with the latter reaction being less efficient. Arabidopsis thaliana and Nicotiana benthamian PPMs are involved in ascorbic acid biosynthesis. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 238 matched cddid_all.tbl CDD cd02586 cd02586 319785 HAD_PHN Phosphonoacetaldehyde hydrolase (phosphonatase); similar to Bacillus cereus phosphonatase. Degradation of the ubiquitous natural phosphonate 2-aminoethylphosphonate (AEP) into useable forms of nitrogen, carbon, and phosphorus is a two-step metabolic pathway. The first step, catalyzed by AEP transaminase, involves the transfer of NH3 from AEP to pyruvate, yielding phosphonoacetaldehyde (P-Ald) and alanine. In the second step, phosphonatase catalyzes the hydrolytic P-C bond cleavage of P-Ald to form orthophosphate and acetaldehyde. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 242 matched cddid_all.tbl CDD cd02587 cd02587 319786 HAD_5-3dNT 5'(3')-deoxyribonucleotidase. This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) and mitochondrial 5'(3')-deoxyribonucleotidase (mdN). cdN and mdN specifically dephosphorylate the deoxyribo form of nucleoside monophosphates helps maintain homeostasis of deoxynucleosides required for mitochondrial DNA synthesis. Their preferred substrates are dUMP and dTMP. cdN also dephosphorylates dGMP and dIMP efficiently. They can also dephosphorylate the 5'- or 3'-phosphates of pyrimidine ribonucleotides. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 161 matched cddid_all.tbl CDD cd02588 cd02588 319787 HAD_L2-DEX L-2-haloacid dehalogenase. L-2-Haloacid dehalogenase catalyzes the hydrolytic dehalogenation of L-2-haloacids to produce the corresponding D-2-hydroxyacids with an inversion of the C2-configuration. 2-haloacid dehalogenases are of interest for their potential to degrade recalcitrant halogenated environmental pollutants and their use in the synthesis of industrial chemicals. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 216 matched cddid_all.tbl CDD cd02598 cd02598 319788 HAD_BPGM beta-phosphoglucomutase, similar to Lactococcus lactis beta-phosphoglucomutase (beta-PGM). Lactococcus lactis beta-PGM catalyzes the interconversion of beta-D-glucose 1-phosphate (G1P) and D-glucose 6-phosphate (G6P), forming beta-D-glucose 1,6-(bis)phosphate as an intermediate. In the forward G6P-forming direction, this reaction links polysaccharide phosphorolysis to glycolysis, in the reverse direction, the reaction provides G1P for the biosynthesis of exo-polysaccharides. This subfamily belongs to the beta-phosphoglucomutase-like family whose other members include Saccharomyces cerevisiae phosphatases GPP1 and GPP2 that dephosphorylate DL-glycerol-3-phosphate and DOG1 and DOG2 that dephosphorylate 2-deoxyglucose-6-phosphate, and Escherichia coli 6-phosphogluconate phosphatase YieH. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 174 matched cddid_all.tbl CDD cd02601 cd02601 319789 HAD_Eya protein tyrosine phosphatase domain of the nuclear transcription factor of Eyes absent (Eya) and related phosphatase domains. Eyes absent (Eya) is a transcriptional coactivator, and an aspartyl-based protein tyrosine phosphatase. Eya and Six operate as a composite transcription factor, within a conserved network of transcription factors called the retinal determination (RD) network. The RD network interacts with a broad variety of signaling pathways to regulate the development and homeostasis of organs and tissues such as eye, muscle, kidney and ear. To date it is not clear what the physiologically relevant substrates of the Eya protein tyrosine phosphatase are, or whether this phosphatase activity plays a role in transcription. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 271 matched cddid_all.tbl CDD cd02603 cd02603 319790 HAD_sEH-N_like N-terminal lipase phosphatase domain of human soluble epoxide hydrolase, Escherichia coli YihX/HAD4 alpha-D-glucose 1-phosphate phosphatase, and related domains, may be inactive. This family includes the N-terminal phosphatase domain of human soluble epoxide hydrolase (sEH). sEH is a bifunctional enzyme with two distinct enzyme activities, the C-terminal domain has epoxide hydrolysis activity and the N-terminal domain (Ntermphos), which belongs to this family, has lipid phosphatase activity. The latter prefers mono-phosphate esters, and lysophosphatidic acids (LPAs) are the best natural substrates found to date. In addition this family includes Gallus gallus sEH and Xenopus sEH which appears to lack phosphatase activity, and Escherichia coli YihX/HAD4 which selectively hydrolyzes alpha-Glucose-1-P, phosphatase, has significant phosphatase activity against pyridoxal phosphate, and has low beta phosphoglucomutase activity. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 195 matched cddid_all.tbl CDD cd02604 cd02604 319791 HAD_5NT haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to Saccharomyces cerevisiae Phm8p and Sdt1p. This family includes Saccharomyces cerevisiae Phm8p (phosphate metabolism protein 8) and Sdt1p (Suppressor of disruption of TFIIS). Phm8p participates in the ribose salvage pathway, it catalyzes the dephosphorylation of nucleotide monophosphates to nucleosides, its preferred substrates are nucleotide monophosphates AMP, GMP, CMP, and UMP. Phm8p is also a lysophosphatidic acid phosphatase, dephosphorylating lysophosphatidic acids (LPAs) to monoacylglycerol in response to phosphate starvation. Sdt1p is a pyrimidine and pyridine-specific 5'-nucleotidase; it is an NMN/NaMN 5'-nucleotidases involved in the production of nicotinamide riboside and nicotinic acid riboside, and is a pyrimidine 5'-nucleotidase with high specificity for UMP and CMP. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 182 matched cddid_all.tbl CDD cd02605 cd02605 319792 HAD_SPP sucrose-phosphatase, similar to Synechocystis sp PCC 6803 SPP. Sucrose-phosphatase (SPP; EC 3.1.3.24) catalyzes the dephosphorylation of sucrose-6(F)-phosphate (Suc6P)-the final step in the pathway of sucrose biosynthesis in plants and cyanobacteria. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 245 matched cddid_all.tbl CDD cd02607 cd02607 319793 HAD_ThrH_like bifunctional phosphoserine phosphatase/phosphoserine:homoserine phosphotransferase, similar to Pseudomonas aeruginosa ThrH. This family includes Pseudomonas aeruginosa ThrH which is a duel activity enzyme having both phosphoserine phosphatase and phosphoserine:homoserine phosphotransferase activities, i.e. it can dephosphorylate phosphoserine, and can transfer phosphate from phosphoserine to homoserine. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 195 matched cddid_all.tbl CDD cd02608 cd02608 319794 P-type_ATPase_Na-K_like alpha-subunit of Na(+)/K(+)-ATPases and of gastric H(+)/K(+)-ATPase, similar to the human Na(+)/K(+)-ATPase alpha subunits 1-4. This subfamily includes the alpha subunit of Na(+)/K(+)-ATPase a heteromeric transmembrane protein composed of an alpha- and beta-subunit and an optional third subunit belonging to the FXYD proteins which are more tissue specific regulatory subunits of the enzyme. The alpha-subunit is the catalytic subunit responsible for transport activities of the enzyme. This subfamily includes all four isotopes of the human alpha subunit: (alpha1-alpha4, encoded by the ATP1A1- ATP1A4 genes). Na(+)/K(+)-ATPase functions chiefly as an ion pump, hydrolyzing one molecule of ATP to pump three Na(+) out of the cell in exchange for two K(+)entering the cell per pump cycle. In addition Na(+)/K(+)-ATPase acts as a signal transducer. This subfamily also includes Oreochromis mossambicus (tilapia) Na(+)/K(+)-ATPase alpha 1 and alpha 3 subunits, and gastric H(+)/K(+)-ATPase which exchanges hydronium ion with potassium and is responsible for gastric acid secretion. Gastric H(+)/K(+)-ATPase is an alpha,beta-heterodimeric enzyme. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 905 matched cddid_all.tbl CDD cd02609 cd02609 319795 P-type_ATPase uncharacterized subfamily of P-type ATPase transporter, similar to uncharacterized Streptococcus pneumoniae exported protein 7, Exp7. This subfamily contains P-type ATPase transporters of unknown function, similar to Streptococcus pneumoniae Exp7. The P-type ATPases, are a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids. They are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. A general characteristic of P-type ATPases is a bundle of transmembrane helices which make up the transport path, and three domains on the cytoplasmic side of the membrane. Members include pumps that transport various light metal ions, such as H(+), Na(+), K(+), Ca(2+), and Mg(2+), pumps that transport indispensable trace elements, such as Zn(2+) and Cu(2+), pumps that remove toxic heavy metal ions, such as Cd(2+), and pumps such as aminophospholipid translocases which transport phosphatidylserine and phosphatidylethanolamine. 661 matched cddid_all.tbl CDD cd02612 cd02612 319796 HAD_PGPPase phosphatidylglycerol-phosphate phosphatase, similar to Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C. This family includes Escherichia coli K-12 phosphatidylglycerol-phosphate phosphatase C, PgpC (previously named yfhB) which catalyzes the dephosphorylation of phosphatidylglycerol-phosphate (PGP) to phosphatidylglycerol (PG). This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 195 matched cddid_all.tbl CDD cd02616 cd02616 319797 HAD_PPase pyrophosphatase similar to Bacillus subtilis PpaX. This family includes Bacillus subtilis PpaX which hydrolyzes pyrophosphate formed during serine-46-phosphorylated HPr (P-Ser-HPr) dephosphorylation by the bifunctional enzyme HPr kinase/phosphorylase. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 207 matched cddid_all.tbl CDD cd02619 cd02619 239110 Peptidase_C1 C1 Peptidase family (MEROPS database nomenclature), also referred to as the papain family; composed of two subfamilies of cysteine peptidases (CPs), C1A (papain) and C1B (bleomycin hydrolase). Papain-like enzymes are mostly endopeptidases with some exceptions like cathepsins B, C, H and X, which are exopeptidases. Papain-like CPs have different functions in various organisms. Plant CPs are used to mobilize storage proteins in seeds while mammalian CPs are primarily lysosomal enzymes responsible for protein degradation in the lysosome. Papain-like CPs are synthesized as inactive proenzymes with N-terminal propeptide regions, which are removed upon activation. Bleomycin hydrolase (BH) is a CP that detoxifies bleomycin by hydrolysis of an amide group. It acts as a carboxypeptidase on its C-terminus to convert itself into an aminopeptidase and peptide ligase. BH is found in all tissues in mammals as well as in many other eukaryotes. It forms a hexameric ring barrel structure with the active sites imbedded in the central channel. Some members of the C1 family are proteins classified as non-peptidase homologs which lack peptidase activity or have missing active site residues. 223 matched cddid_all.tbl CDD cd02620 cd02620 239111 Peptidase_C1A_CathepsinB Cathepsin B group; composed of cathepsin B and similar proteins, including tubulointerstitial nephritis antigen (TIN-Ag). Cathepsin B is a lysosomal papain-like cysteine peptidase which is expressed in all tissues and functions primarily as an exopeptidase through its carboxydipeptidyl activity. Together with other cathepsins, it is involved in the degradation of proteins, proenzyme activation, Ag processing, metabolism and apoptosis. Cathepsin B has been implicated in a number of human diseases such as cancer, rheumatoid arthritis, osteoporosis and Alzheimer's disease. The unique carboxydipeptidyl activity of cathepsin B is attributed to the presence of an occluding loop in its active site which favors the binding of the C-termini of substrate proteins. Some members of this group do not possess the occluding loop. TIN-Ag is an extracellular matrix basement protein which was originally identified as a target Ag involved in anti-tubular basement membrane antibody-mediated interstitial nephritis. It plays a role in renal tubulogenesis and is defective in hereditary tubulointerstitial disorders. TIN-Ag is exclusively expressed in kidney tissues. 236 matched cddid_all.tbl CDD cd02621 cd02621 239112 Peptidase_C1A_CathepsinC Cathepsin C; also known as Dipeptidyl Peptidase I (DPPI), an atypical papain-like cysteine peptidase with chloride dependency and dipeptidyl aminopeptidase activity, resulting from its tetrameric structure which limits substrate access. Each subunit of the tetramer is composed of three peptides: the heavy and light chains, which together adopts the papain fold and forms the catalytic domain; and the residual propeptide region, which forms a beta barrel and points towards the substrate's N-terminus. The subunit composition is the result of the unique characteristic of procathepsin C maturation involving the cleavage of the catalytic domain and the non-autocatalytic excision of an activation peptide within its propeptide region. By removing N-terminal dipeptide extensions, cathepsin C activates granule serine peptidases (granzymes) involved in cell-mediated apoptosis, inflammation and tissue remodelling. Loss-of-function mutations in cathepsin C are associated with Papillon-Lefevre and Haim-Munk syndromes, rare diseases characterized by hyperkeratosis and early-onset periodontitis. Cathepsin C is widely expressed in many tissues with high levels in lung, kidney and placenta. It is also highly expressed in cytotoxic lymphocytes and mature myeloid cells. 243 matched cddid_all.tbl CDD cd02636 cd02636 100065 R3H_sperm-antigen R3H domain of a group of metazoan proteins that is related to the sperm-associated antigen 7. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner. 61 matched cddid_all.tbl CDD cd02637 cd02637 100066 R3H_PARN R3H domain of Poly(A)-specific ribonuclease (PARN). PARN is a poly(A)-specific 3' exonuclease from the RNase D family that, in Xenopus, deadenylates a specific class of maternal mRNAs which results in their translational repression. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA. 65 matched cddid_all.tbl CDD cd02638 cd02638 100067 R3H_unknown_1 R3H domain of a group of eukaryotic proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner. 62 matched cddid_all.tbl CDD cd02639 cd02639 100068 R3H_RRM R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner. 60 matched cddid_all.tbl CDD cd02640 cd02640 100069 R3H_NRF R3H domain of the NF-kappaB-repression factor (NRF). NRF is a nuclear inhibitor of NF-kappaB proteins that can silence the IFNbeta promoter via binding to a negative regulatory element (NRE). Beside R3H NRF also contains a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner. 60 matched cddid_all.tbl CDD cd02641 cd02641 100070 R3H_Smubp-2_like R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA. 60 matched cddid_all.tbl CDD cd02642 cd02642 100071 R3H_encore_like R3H domain of encore-like and DIP1-like proteins. Drosophila encore is involved in the germline exit after four mitotic divisions, by facilitating SCF-ubiquitin-proteasome-dependent proteolysis. Maize DBF1-interactor protein 1 (DIP1) containing an R3H domain is a potential regulator of DBF1 activity in stress responses. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner. 63 matched cddid_all.tbl CDD cd02643 cd02643 100072 R3H_NF-X1 R3H domain of the X1 box binding protein (NF-X1) and related proteins. Human NF-X1 is a transcription factor that regulates the expression of class II major histocompatibility complex (MHC) genes. The Drosophila homolog shuttle craft (STC) has been shown to be a DNA- or RNA-binding protein required for proper axon guidance in the central nervous system and, the yeast homolog FAP1 encodes a dosage suppressor of rapamycin toxicity. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner. 74 matched cddid_all.tbl CDD cd02644 cd02644 100073 R3H_jag R3H domain found in proteins homologous to Bacillus subtilus Jag, which is associated with SpoIIIJ. SpoIIIJ is necessary for the third stage of sporulation. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner. 67 matched cddid_all.tbl CDD cd02645 cd02645 100074 R3H_AAA R3H domain of a group of proteins with unknown function, who also contain a AAA-ATPase (AAA) domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA or ssRNA in a sequence-specific manner. 60 matched cddid_all.tbl CDD cd02646 cd02646 100075 R3H_G-patch R3H domain of a group of fungal and plant proteins with unknown function, who also contain a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the R3H domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner. 58 matched cddid_all.tbl CDD cd02647 cd02647 239113 nuc_hydro_TvIAG nuc_hydro_ TvIAG: Nucleoside hydrolases similar to the Inosine-adenosine-guanosine-preferring nucleoside hydrolase from Trypanosoma vivax. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. Nucleoside hydrolases vary in their substrate specificity. This group contains eukaryotic and bacterial proteins similar to the purine specific inosine-adenosine-guanosine-preferring nucleoside hydrolase (IAG-NH) from T. vivax. T. vivax IAG-NH is of the order of a thousand to ten thousand fold more specific towards the naturally occurring purine nucleosides, than towards the pyrimidine nucleosides. 312 matched cddid_all.tbl CDD cd02648 cd02648 239114 nuc_hydro_1 NH_1: A subgroup of nucleoside hydrolases. This group contains fungal proteins similar to nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity. 367 matched cddid_all.tbl CDD cd02649 cd02649 239115 nuc_hydro_CeIAG nuc_hydro_CeIAG: Nucleoside hydrolases similar to the inosine-adenosine-guanosine-preferring nucleoside hydrolase from Caenorhabditis elegans. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity. This group contains eukaryotic, bacterial and archeal proteins similar to the purine-preferring nucleoside hydrolase (IAG-NH) from C. elegans and the salivary purine nucleosidase from Aedes aegypti. C. elegans IAG-NH exhibits a high affinity for the substrate analogue p-nitrophenylriboside (p-NPR). 306 matched cddid_all.tbl CDD cd02650 cd02650 239116 nuc_hydro_CaPnhB NH_hydro_CaPnhB: A subgroup of nucleoside hydrolases similar to Corynebacterium ammoniagenes Purine/pyrimidine nucleoside hydrolase (pnhB). Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity. 304 matched cddid_all.tbl CDD cd02651 cd02651 239117 nuc_hydro_IU_UC_XIUA nuc_hydro_IU_UC_XIUA: inosine-uridine preferring, xanthosine-inosine-uridine-adenosine-preferring and, uridine-cytidine preferring nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity. This group contains proteins similar to nucleoside hydrolases which hydrolyze both pyrimidine and purine ribonucleosides: the inosine-uridine preferring nucleoside hydrolase from Crithidia fasciculata, the inosine-uridine-xanthosine preferring nucleoside hydrolase RihC from Escherichia coli and the xanthosine-inosine-uridine-adenosine-preferring nucleoside hydrolase RihC from Salmonella enterica serovar Typhimurium. This group also contains proteins similar to the pyrimidine-specific uridine-cytidine preferring nucleoside hydrolases URH1 from Saccharomyces cerevisiae, E. coli RihA and E. coli RihB. E. coli RihA is equally efficient with uridine and cytidine, E. coli RihB prefers cytidine over uridine. S. cerevisiae URH1 prefers uridine over cytidine. 302 matched cddid_all.tbl CDD cd02652 cd02652 239118 nuc_hydro_2 NH_2: A subgroup of nucleoside hydrolases. This group contains eukaryotic and bacterial proteins similar to nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity. 293 matched cddid_all.tbl CDD cd02653 cd02653 239119 nuc_hydro_3 NH_3: A subgroup of nucleoside hydrolases. This group contains eukaryotic and bacterial proteins similar to nucleoside hydrolases. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity. 320 matched cddid_all.tbl CDD cd02654 cd02654 239120 nuc_hydro_CjNH nuc_hydro_CjNH. Nucleoside hydrolases similar to Campylobacter jejuni nucleoside hydrolase. This group contains eukaryotic and bacterial proteins similar to C. jejuni nucleoside hydrolase. Nucleoside hydrolases cleave the N-glycosidic bond in nucleosides generating ribose and the respective base. These enzymes vary in their substrate specificity. C. jejuni nucleoside hydrolase is inactive against natural nucleosides or against common nucleoside analogues. 318 matched cddid_all.tbl CDD cd02655 cd02655 132721 RNAP_beta'_C "Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain. Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta"" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations." 204 matched cddid_all.tbl CDD cd02656 cd02656 239121 MIT MIT: domain contained within Microtubule Interacting and Trafficking molecules. The MIT domain is found in sorting nexins, the nuclear thiol protease PalBH, the AAA protein spastin and archaebacterial proteins with similar domain architecture, vacuolar sorting proteins and others. The molecular function of the MIT domain is unclear. 75 matched cddid_all.tbl CDD cd02657 cd02657 239122 Peptidase_C19A A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. 305 matched cddid_all.tbl CDD cd02658 cd02658 239123 Peptidase_C19B A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. 311 matched cddid_all.tbl CDD cd02659 cd02659 239124 peptidase_C19C A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. 334 matched cddid_all.tbl CDD cd02660 cd02660 239125 Peptidase_C19D A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. 328 matched cddid_all.tbl CDD cd02661 cd02661 239126 Peptidase_C19E A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. 304 matched cddid_all.tbl CDD cd02662 cd02662 239127 Peptidase_C19F A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. 240 matched cddid_all.tbl CDD cd02663 cd02663 239128 Peptidase_C19G A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. 300 matched cddid_all.tbl CDD cd02664 cd02664 239129 Peptidase_C19H A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. 327 matched cddid_all.tbl CDD cd02665 cd02665 239130 Peptidase_C19I A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. 228 matched cddid_all.tbl CDD cd02666 cd02666 239131 Peptidase_C19J A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. 343 matched cddid_all.tbl CDD cd02667 cd02667 239132 Peptidase_C19K A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. 279 matched cddid_all.tbl CDD cd02668 cd02668 239133 Peptidase_C19L A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. 324 matched cddid_all.tbl CDD cd02669 cd02669 239134 Peptidase_C19M A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. 440 matched cddid_all.tbl CDD cd02670 cd02670 239135 Peptidase_C19N A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. 241 matched cddid_all.tbl CDD cd02671 cd02671 239136 Peptidase_C19O A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. 332 matched cddid_all.tbl CDD cd02672 cd02672 239137 Peptidase_C19P A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. 268 matched cddid_all.tbl CDD cd02673 cd02673 239138 Peptidase_C19Q A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. 245 matched cddid_all.tbl CDD cd02674 cd02674 239139 Peptidase_C19R A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome. 230 matched cddid_all.tbl CDD cd02675 cd02675 259861 Ephrin_ectodomain Ectodomain of Ephrins. Ephrins and their receptors EphR play an important role in cell communication in normal physiology, as well as in disease pathogenesis. Binding of the ephrin (Eph) ligand to EphR requires cell-cell contact, since both molecules are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling, depending on Eph kinase activity) and ephrin-expressing cells (reverse signaling). Eph signaling controls cell morphology, adhesion, migration and invasion. Ephrins can be subdivided into 2 groups, A and B, depending on their respective receptors EphA or EphB. The nine human EphA receptors bind to five GPI-linked ephrin-A ligands and the five EphB receptors bind to three transmembrane ephrin-B ligands. Interactions are promiscuous within each class, and some Eph receptors can also bind to ephrins of the other class. All ephrins contain a highly conserved ectodomain for receptor binding, which is characterized by this domain hierarchy. 136 matched cddid_all.tbl CDD cd02677 cd02677 239140 MIT_SNX15 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in sorting nexin 15 and related proteins. The molecular function of the MIT domain is unclear. 75 matched cddid_all.tbl CDD cd02678 cd02678 239141 MIT_VPS4 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in intracellular protein transport proteins of the AAA-ATPase family. The molecular function of the MIT domain is unclear. 75 matched cddid_all.tbl CDD cd02679 cd02679 239142 MIT_spastin MIT: domain contained within Microtubule Interacting and Trafficking molecules. This MIT domain sub-family is found in the AAA protein spastin, a probable ATPase involved in the assembly or function of nuclear protein complexes; spastins might also be involved in microtubule dynamics. The molecular function of the MIT domain is unclear. 79 matched cddid_all.tbl CDD cd02680 cd02680 239143 MIT_calpain7_2 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in the nuclear thiol protease PalBH. The molecular function of the MIT domain is unclear. 75 matched cddid_all.tbl CDD cd02681 cd02681 239144 MIT_calpain7_1 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in the nuclear thiol protease PalBH. The molecular function of the MIT domain is unclear. 76 matched cddid_all.tbl CDD cd02682 cd02682 239145 MIT_AAA_Arch MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in mostly archaebacterial AAA-ATPases. The molecular function of the MIT domain is unclear. 75 matched cddid_all.tbl CDD cd02683 cd02683 239146 MIT_1 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in proteins with unknown function, co-occuring with an as yet undescribed domain. The molecular function of the MIT domain is unclear. 77 matched cddid_all.tbl CDD cd02684 cd02684 239147 MIT_2 MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in proteins with an n-terminal serine/threonine kinase domain. The molecular function of the MIT domain is unclear. 75 matched cddid_all.tbl CDD cd02685 cd02685 239148 MIT_C MIT_C; domain found C-terminal to MIT (contained within Microtubule Interacting and Trafficking molecules) domains, as well as in some bacterial proteins. The function of this domain is unknown. 148 matched cddid_all.tbl CDD cd02688 cd02688 199878 E_set "Early set domain associated with the catalytic domain of sugar utilizing enzymes at either the N or C terminus. The E or ""early"" set domains of sugar utilizing enzymes are associated with different types of catalytic domains at either the N-terminal or C-terminal end. These domains may be related to the immunoglobulin and/or fibronectin type III superfamilies. Members of this family include alpha amylase, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase. A subset of these members were recently identified as members of the CBM48 (Carbohydrate Binding Module 48) family. Members of the CBM48 family include pullulanase, maltooligosyl trehalose synthase, starch branching enzyme, glycogen branching enzyme, glycogen debranching enzyme, isoamylase, and the beta subunit of AMP-activated protein kinase." 82 matched cddid_all.tbl CDD cd02690 cd02690 349868 M28 M28 Zn-peptidases include aminopeptidases and carboxypeptidases. Peptidase M28 family (also called aminopeptidase Y family) contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Plasma glutamate carboxypeptidase (PGCP) and glutamate carboxypeptidase II (NAALADase) hydrolyze dipeptides. Several members of the M28 peptidase family have PA domain inserts which may participate in substrate binding and/or in promoting conformational changes, which influence the stability and accessibility of the site to substrate. These include prostate-specific membrane antigen (PSMA), yeast aminopeptidase S (SGAP), human transferrin receptors (TfR1 and TfR2), plasma glutamate carboxypeptidase (PGCP) and several predicted aminopeptidases where relatively little is known about them. Also included in the M28 family are glutaminyl cyclases (QC), which are involved in N-terminal glutamine cyclization of many endocrine peptides. Nicastrin and nicalin belong to this family but lack the amino-acid conservation required for catalytically active aminopeptidases. 202 matched cddid_all.tbl CDD cd02691 cd02691 100036 PurM-like2 AIR synthase (PurM) related protein, archaeal subgroup 2 of unknown function. The family of PurM related proteins includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM synthase and Selenophosphate synthetase (SelD). They all contain two conserved domains and seem to dimerize. The N-terminal domain forms the dimer interface and is a putative ATP binding domain. 346 matched cddid_all.tbl CDD cd02696 cd02696 119407 MurNAc-LAA N-acetylmuramoyl-L-alanine amidase or MurNAc-LAA (also known as peptidoglycan aminohydrolase, NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan amidase; EC 3.5.1.28) is an autolysin that hydrolyzes the amide bond between N-acetylmuramoyl and L-amino acids in certain cell wall glycopeptides. These proteins are Zn-dependent peptidases with highly conserved residues involved in cation co-ordination. MurNAc-LAA in this family is one of several peptidoglycan hydrolases (PGHs) found in bacterial and bacteriophage or prophage genomes that are involved in the degradation of the peptidoglycan. In Escherichia coli, there are five MurNAc-LAAs present: AmiA, AmiB, AmiC and AmiD that are periplasmic, and AmpD that is cytoplasmic. Three of these (AmiA, AmiB and AmiC) belong to this family, the other two (AmiD and AmpD) do not. E. coli AmiA, AmiB and AmiC play an important role in cleaving the septum to release daughter cells after cell division. In general, bacterial MurNAc-LAAs are members of the bacterial autolytic system and carry a signal peptide in their N-termini that allows their transport across the cytoplasmic membrane. However, the bacteriophage MurNAc-LAAs are endolysins since these phage-encoded enzymes break down bacterial peptidoglycan at the terminal stage of the phage reproduction cycle. As opposed to autolysins, almost all endolysins have no signal peptides and their translocation through the cytoplasmic membrane is thought to proceed with the help of phage-encoded holin proteins. The amidase catalytic module is fused to another functional module (cell wall binding module or CWBM) either at the N- or C-terminus, which is responsible for high affinity binding of the protein to the cell wall. 172 matched cddid_all.tbl CDD cd02697 cd02697 349869 M20_like M20 Zn-peptidases include exopeptidases. Peptidase M20 family; uncharacterized subfamily. These hypothetical proteins have been inferred by homology to be exopeptidases: carboxypeptidases, dipeptidases and a specialized aminopeptidase. In general, the peptidase hydrolyzes the late products of protein degradation in order to complete the conversion of proteins to free amino acids. Members of this subfamily may bind metal ions such as zinc. 394 matched cddid_all.tbl CDD cd02698 cd02698 239149 Peptidase_C1A_CathepsinX Cathepsin X; the only papain-like lysosomal cysteine peptidase exhibiting carboxymonopeptidase activity. It can also act as a carboxydipeptidase, like cathepsin B, but has been shown to preferentially cleave substrates through a monopeptidyl carboxypeptidase pathway. The propeptide region of cathepsin X, the shortest among papain-like peptidases, is covalently attached to the active site cysteine in the inactive form of the enzyme. Little is known about the biological function of cathepsin X. Some studies point to a role in early tumorigenesis. A more recent study indicates that cathepsin X expression is restricted to immune cells suggesting a role in phagocytosis and the regulation of the immune response. 239 matched cddid_all.tbl CDD cd02699 cd02699 341048 M4_M36 Peptidase M4 family (includes thermolysin, aureolysin, neutral protease and bacillolysin) and Peptidase M36 family (also known as fungalysin). This family includes the peptidases M4 as well as M36, both belonging to the Gluzincin family. The M4 peptidase family includes numerous zinc-dependent metallopeptidases that hydrolyze peptide bonds, such as thermolysin (EC 3.4.24.27), pseudolysin (the extracellullar elastase of Pseudomonas aeruginosa), aureolysin (the extracellular metalloproteinase from Staphylococcus aureus), neutral protease from Bacillus cereus, as well as bacillolysin (EC 3.4.24.28). The M36 family also known as fungalysin (elastinolytic metalloproteinase) family, includes endopeptidases from pathogenic fungi. Both M4 and M36 families have similar folds and contain the Zn-binding site and the active site HEXXH motif. The eukaryotic M36 and bacterial M4 families of metalloproteases also share a conserved domain in their propeptides called FTP (fungalysin/thermolysin propeptide). 313 matched cddid_all.tbl CDD cd02733 cd02733 259848 RNAP_II_RPB1_N Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain. The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II. 751 matched cddid_all.tbl CDD cd02735 cd02735 132722 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain. RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role. 309 matched cddid_all.tbl CDD cd02736 cd02736 132723 RNAP_III_Rpc1_C Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain. Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role. 300 matched cddid_all.tbl CDD cd02737 cd02737 132724 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain. Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena. 381 matched cddid_all.tbl CDD cd02742 cd02742 119331 GH20_hexosaminidase Beta-N-acetylhexosaminidases of glycosyl hydrolase family 20 (GH20) catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides. These enzymes are broadly distributed in microorganisms, plants and animals, and play roles in various key physiological and pathological processes. These processes include cell structural integrity, energy storage, cellular signaling, fertilization, pathogen defense, viral penetration, the development of carcinomas, inflammatory events and lysosomal storage disorders. The GH20 enzymes include the eukaryotic beta-N-acetylhexosaminidases A and B, the bacterial chitobiases, dispersin B, and lacto-N-biosidase. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by the solvent or the enzyme, but by the substrate itself. 303 matched cddid_all.tbl CDD cd02749 cd02749 394871 Macro_SF "macrodomain superfamily. Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Macrodomains include the yeast macrodomain Poa1 which is a phosphatase of ADP-ribose-1""-phosphate, a by-product of tRNA splicing. Some macrodomains have ADPr-unrelated binding partners such as the coronavirus SUD-N (N-terminal subdomain) and SUD-M (middle subdomain) of the SARS-unique domain (SUD) which bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). Macrodomains regulate a wide variety of cellular and organismal processes, including DNA damage repair, signal transduction, and immune response." 121 matched cddid_all.tbl CDD cd02750 cd02750 239151 MopB_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. Members of the MopB_Nitrate-R-NarG-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins. 461 matched cddid_all.tbl CDD cd02751 cd02751 239152 MopB_DMSOR-like The MopB_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. Members of the MopB_DMSOR-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins. 609 matched cddid_all.tbl CDD cd02752 cd02752 239153 MopB_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. Members of the MopB_Formate-Dh-Na-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins. 649 matched cddid_all.tbl CDD cd02753 cd02753 239154 MopB_Formate-Dh-H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. Members of the MopB_Formate-Dh-H CD belong to the molybdopterin_binding (MopB) superfamily of proteins. 512 matched cddid_all.tbl CDD cd02754 cd02754 239155 MopB_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. Members of the MopB_Nitrate-R-NapA CD belong to the molybdopterin_binding (MopB) superfamily of proteins. 565 matched cddid_all.tbl CDD cd02755 cd02755 239156 MopB_Thiosulfate-R-like The MopB_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Members of the MopB_Thiosulfate-R-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins. 454 matched cddid_all.tbl CDD cd02756 cd02756 239157 MopB_Arsenite-Ox Arsenite oxidase (Arsenite-Ox) oxidizes arsenite to the less toxic arsenate; it transfers the electrons obtained from the oxidation of arsenite towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin. Arsenite oxidase is a heterodimeric enzyme containing a large and a small subunit. The large catalytic subunit harbors the molybdopterin cofactor and the [3Fe-4S] cluster; and the small subunit belongs to the structural class of the Rieske proteins. The small subunit is not included in this alignment. Members of MopB_Arsenite-Ox CD belong to the molybdopterin_binding (MopB) superfamily of proteins. 676 matched cddid_all.tbl CDD cd02757 cd02757 239158 MopB_Arsenate-R This CD includes the respiratory arsenate reductase, As(V), catalytic subunit (ArrA) and other related proteins. These members belong to the molybdopterin_binding (MopB) superfamily of proteins. 523 matched cddid_all.tbl CDD cd02758 cd02758 239159 MopB_Tetrathionate-Ra The MopB_Tetrathionate-Ra CD contains tetrathionate reductase, subunit A, (TtrA) and other related proteins. The Salmonella enterica tetrathionate reductase catalyses the reduction of trithionate but not sulfur or thiosulfate. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins. 735 matched cddid_all.tbl CDD cd02759 cd02759 239160 MopB_Acetylene-hydratase The MopB_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins. 477 matched cddid_all.tbl CDD cd02760 cd02760 239161 MopB_Phenylacetyl-CoA-OR The MopB_Phenylacetyl-CoA-OR CD contains the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), and other related proteins. The phenylacetyl-CoA:acceptor oxidoreductase has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins. 760 matched cddid_all.tbl CDD cd02761 cd02761 239162 MopB_FmdB-FwdB The MopB_FmdB-FwdB CD contains the molybdenum/tungsten formylmethanofuran dehydrogenases, subunit B (FmdB/FwdB), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea and some eubacteria. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins. 415 matched cddid_all.tbl CDD cd02762 cd02762 239163 MopB_1 The MopB_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins. 539 matched cddid_all.tbl CDD cd02763 cd02763 239164 MopB_2 The MopB_2 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins 679 matched cddid_all.tbl CDD cd02764 cd02764 239165 MopB_PHLH The MopB_PHLH CD includes a group of related uncharacterized putative hydrogenase-like homologs (PHLH) of molybdopterin binding (MopB) proteins. This CD is of the PHLH region homologous to the catalytic molybdopterin-binding subunit of MopB homologs. 524 matched cddid_all.tbl CDD cd02765 cd02765 239166 MopB_4 The MopB_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins 567 matched cddid_all.tbl CDD cd02766 cd02766 239167 MopB_3 The MopB_3 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins 501 matched cddid_all.tbl CDD cd02767 cd02767 239168 MopB_ydeP The MopB_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins. 574 matched cddid_all.tbl CDD cd02768 cd02768 239169 MopB_NADH-Q-OR-NuoG2 MopB_NADH-Q-OR-NuoG2: The NuoG/Nad11/75-kDa subunit (second domain) of the NADH-quinone oxidoreductase (NADH-Q-OR)/respiratory complex I/NADH dehydrogenase-1 (NDH-1). The NADH-Q-OR is the first energy-transducting complex in the respiratory chains of many prokaryotes and eukaryotes. Mitochondrial complex I and its bacterial counterpart, NDH-1, function as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. The atomic structure of complex I is not known and the mechanisms of electron transfer and proton pumping are not established. The nad11 gene codes for the largest (75-kDa) subunit of the mitochondrial NADH:ubiquinone oxidoreductase, it constitutes the electron input part of the enzyme, or the so-called NADH dehydrogenase fragment. In Escherichia coli, this subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the 'minimal' functional enzyme. The nad11 gene is nuclear-encoded in animals, plants, and fungi, but is still encoded in the mitochondrial genome of some protists. The Nad11/NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain (this CD), is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Although only vestigial sequence evidence remains of a molybdopterin binding site, this protein domain family belongs to the molybdopterin_binding (MopB) superfamily of proteins. Bacterial type II NADH-quinone oxidoreductases and NQR-type sodium-motive NADH-quinone oxidoreductases are not homologs of this domain family. 386 matched cddid_all.tbl CDD cd02769 cd02769 239170 MopB_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Members of this CD belong to the molybdopterin_binding (MopB) superfamily of proteins. 609 matched cddid_all.tbl CDD cd02770 cd02770 239171 MopB_DmsA-EC This CD (MopB_DmsA-EC) includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins. 617 matched cddid_all.tbl CDD cd02771 cd02771 239172 MopB_NDH-1_NuoG2-N7 MopB_NDH-1_NuoG2-N7: The second domain of the NuoG subunit (with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain (this CD), is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Unique to this group, compared to the other prokaryotic and eukaryotic groups in this domain protein family (NADH-Q-OR-NuoG2), is an N-terminal [4Fe-4S] cluster (N7/N1c) present in the second domain. Although only vestigial sequence evidence remains of a molybdopterin binding site, this protein domain belongs to the molybdopterin_binding (MopB) superfamily of proteins. 472 matched cddid_all.tbl CDD cd02772 cd02772 239173 MopB_NDH-1_NuoG2 MopB_NDH-1_NuoG2: The second domain of the NuoG subunit of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1), found in beta- and gammaproteobacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain (this CD), is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Although only vestigial sequence evidence remains of a molybdopterin binding site, this protein domain belongs to the molybdopterin_binding (MopB) superfamily of proteins. 414 matched cddid_all.tbl CDD cd02773 cd02773 239174 MopB_Res-Cmplx1_Nad11 MopB_Res_Cmplx1_Nad11: The second domain of the Nad11/75-kDa subunit of the NADH-quinone oxidoreductase/respiratory complex I/NADH dehydrogenase-1(NDH-1) of eukaryotes and the Nqo3/G subunit of alphaproteobacteria NDH-1. The NADH-quinone oxidoreductase is the first energy-transducting complex in the respiratory chains of many prokaryotes and eukaryotes. Mitochondrial complex I and its bacterial counterpart, NDH-1, function as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. The nad11 gene codes for the largest (75 kDa) subunit of the mitochondrial NADH:ubiquinone oxidoreductase, it constitutes the electron input part of the enzyme, or the so-called NADH dehydrogenase fragment. In Paracoccus denitrificans, this subunit is encoded by the nqo3 gene, and is part of the 14 distinct subunits constituting the 'minimal' functional enzyme. The Nad11/Nqo3 subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain (this CD), is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Although only vestigial sequence evidence remains of a molybdopterin binding site, this protein domain belongs to the molybdopterin_binding (MopB) superfamily of proteins. 375 matched cddid_all.tbl CDD cd02774 cd02774 239175 MopB_Res-Cmplx1_Nad11-M MopB_Res_Cmplx1_Nad11_M: Mitochondrial-encoded NADH-quinone oxidoreductase/respiratory complex I, the second domain of the Nad11/75-kDa subunit of some protists. NADH-quinone oxidoreductase is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. The nad11 gene codes for the largest (75-kDa) subunit of the mitochondrial NADH-quinone oxidoreductase, it constitutes the electron input part of the enzyme, or the so-called NADH dehydrogenase fragment. The Nad11 subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain (this CD), is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Although only vestigial sequence evidence remains of a molybdopterin binding site, this protein domain belongs to the molybdopterin_binding (MopB) superfamily of proteins. 366 matched cddid_all.tbl CDD cd02775 cd02775 239176 MopB_CT Molybdopterin-Binding, C-terminal (MopB_CT) domain of the MopB superfamily of proteins, a large, diverse, heterogeneous superfamily of enzymes that, in general, bind molybdopterin as a cofactor. The MopB domain is found in a wide variety of molybdenum- and tungsten-containing enzymes, including formate dehydrogenase-H (Fdh-H) and -N (Fdh-N), several forms of nitrate reductase (Nap, Nas, NarG), dimethylsulfoxide reductase (DMSOR), thiosulfate reductase, formylmethanofuran dehydrogenase, and arsenite oxidase. Molybdenum is present in most of these enzymes in the form of molybdopterin, a modified pterin ring with a dithiolene side chain, which is responsible for ligating the Mo. In many bacterial and archaeal species, molybdopterin is in the form of a dinucleotide, with two molybdopterin dinucleotide units per molybdenum. These proteins can function as monomers, heterodimers, or heterotrimers, depending on the protein and organism. Also included in the MopB superfamily is the eukaryotic/eubacterial protein domain family of the 75-kDa subunit/Nad11/NuoG (second domain) of respiratory complex 1/NADH-quinone oxidoreductase which is postulated to have lost an ancestral formate dehydrogenase activity and only vestigial sequence evidence remains of a molybdopterin binding site. This hierarchy is of the conserved MopB_CT domain present in many, but not all, MopB homologs. 101 matched cddid_all.tbl CDD cd02776 cd02776 239177 MopB_CT_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. This CD (MopB_CT_Nitrate-R-NarG-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. 141 matched cddid_all.tbl CDD cd02777 cd02777 239178 MopB_CT_DMSOR-like The MopB_CT_DMSOR-like CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO. Also included in this group is the pyrogallol-phloroglucinol transhydroxylase from Pelobacter acidigallici. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. 127 matched cddid_all.tbl CDD cd02778 cd02778 239179 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. 123 matched cddid_all.tbl CDD cd02779 cd02779 239180 MopB_CT_Arsenite-Ox This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of Arsenite oxidase (Arsenite-Ox) and related proteins. Arsenite oxidase oxidizes arsenite to the less toxic arsenate; it transfers the electrons obtained from the oxidation of arsenite towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin. 115 matched cddid_all.tbl CDD cd02780 cd02780 239181 MopB_CT_Tetrathionate_Arsenate-R This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of tetrathionate reductase, subunit A, (TtrA); respiratory arsenate As(V) reductase, catalytic subunit (ArrA); and other related proteins. 143 matched cddid_all.tbl CDD cd02781 cd02781 239182 MopB_CT_Acetylene-hydratase The MopB_CT_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. 130 matched cddid_all.tbl CDD cd02782 cd02782 239183 MopB_CT_1 The MopB_CT_1 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. 129 matched cddid_all.tbl CDD cd02783 cd02783 239184 MopB_CT_2 The MopB_CT_2 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. 156 matched cddid_all.tbl CDD cd02784 cd02784 239185 MopB_CT_PHLH The MopB_CT_PHLH CD includes a group of related uncharacterized putative hydrogenase-like homologs (PHLH) of molybdopterin binding proteins. This CD is of the PHLH region homologous to the conserved molybdopterin-binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. 137 matched cddid_all.tbl CDD cd02785 cd02785 239186 MopB_CT_4 The MopB_CT_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. 124 matched cddid_all.tbl CDD cd02786 cd02786 239187 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. 116 matched cddid_all.tbl CDD cd02787 cd02787 239188 MopB_CT_ydeP The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. 112 matched cddid_all.tbl CDD cd02788 cd02788 239189 MopB_CT_NDH-1_NuoG2-N7 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain, is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Unique to this group, compared to the other prokaryotic and eukaryotic groups in this domain protein family (NADH-Q-OR-NuoG2), is an N-terminal [4Fe-4S] cluster (N7/N1c) present in the second domain and a C-terminal region (this CD) homologous to the formate dehydrogenase C-terminal molybdopterin_binding (MopB) region. 96 matched cddid_all.tbl CDD cd02789 cd02789 239190 MopB_CT_FmdC-FwdD The MopB_FmdC-FwdD CD includes the C-terminus of subunit C of molybdenum formylmethanofuran dehydrogenase (FmdC) and subunit D of tungsten formylmethanofuran dehydrogenase (FwdD), and other related proteins. Formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea and some eubacteria. Members of this CD belong to the molybdopterin_binding superfamily of proteins. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. 106 matched cddid_all.tbl CDD cd02790 cd02790 239191 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. 116 matched cddid_all.tbl CDD cd02791 cd02791 239192 MopB_CT_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. This CD (MopB_CT_Nitrate-R-Nap) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs 122 matched cddid_all.tbl CDD cd02792 cd02792 239193 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. 122 matched cddid_all.tbl CDD cd02793 cd02793 239194 MopB_CT_DMSOR-BSOR-TMAOR The MopB_DMSOR-BSOR-TMAOR CD contains dimethylsulfoxide reductase (DMSOR), biotin sulfoxide reductase (BSOR), trimethylamine N-oxide reductase (TMAOR) and other related proteins. DMSOR always catalyzes the reduction of DMSO to dimethylsulfide, but its cellular location and oligomerization state are organism-dependent. For example, in Rhodobacter sphaeriodes and Rhodobacter capsulatus, it is an 82-kDa monomeric soluble protein found in the periplasmic space; in E. coli, it is membrane-bound and exists as a heterotrimer. BSOR catalyzes the reduction of biotin sulfixode to biotin, and is unique among Mo enzymes because no additional auxiliary proteins or cofactors are required. TMAOR is similar to DMSOR, but its only natural substrate is TMAO.This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. 129 matched cddid_all.tbl CDD cd02794 cd02794 239195 MopB_CT_DmsA-EC The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs. 121 matched cddid_all.tbl CDD cd02795 cd02795 271143 CBM6-CBM35-CBM36_like Carbohydrate Binding Module 6 (CBM6) and CBM35_like superfamily. Carbohydrate binding module family 6 (CBM6, family 6 CBM), also known as cellulose binding domain family VI (CBD VI), and related CBMs (CBM35 and CBM36). These are non-catalytic carbohydrate binding domains found in a range of enzymes that display activities against a diverse range of carbohydrate targets, including mannan, xylan, beta-glucans, cellulose, agarose, and arabinans. These domains facilitate the strong binding of the appended catalytic modules to their dedicated, insoluble substrates. Many of these CBMs are associated with glycoside hydrolase (GH) domains. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold. CBM36s are calcium-dependent xylan binding domains. CBM35s display conserved specificity through extensive sequence similarity, but divergent function through their appended catalytic modules. This alignment model also contains the C-terminal domains of bacterial insecticidal toxins, where they may be involved in determining insect specificity through carbohydrate binding functionality. 124 matched cddid_all.tbl CDD cd02796 cd02796 239196 tRNA_bind_bactPheRS tRNA-binding-domain-containing prokaryotic phenylalanly tRNA synthetase (PheRS) beta chain. PheRS aminoacylate phenylalanine transfer RNAs (tRNAphe). PheRSs belong structurally to class II aminoacyl tRNA synthetases (aaRSs) but, as they aminoacylate the 2'OH of the terminal ribose of tRNA they belong functionally to class 1 aaRSs. This domain has general tRNA binding properties and is believed to direct tRNAphe to the active site of the enzyme. 103 matched cddid_all.tbl CDD cd02798 cd02798 239197 tRNA_bind_CsaA tRNA-binding-domain-containing CsaA-like proteins. CsaA is a molecular chaperone with export related activities. CsaA has a putative tRNA binding activity. The functional unit of CsaA is a homodimer and this domain acts as a dimerization domain. 107 matched cddid_all.tbl CDD cd02799 cd02799 239198 tRNA_bind_EMAP-II_like tRNA-binding-domain-containing EMAP2-like proteins. This family contains a diverse fraction of tRNA binding proteins, including Caenorhabditis elegans methionyl-tRNA synthetase (CeMetRS), human tyrosyl- tRNA synthetase (hTyrRS), Saccharomyces cerevisiae Arc1p, human p43 and EMAP2. CeMetRS and hTyrRS aminoacylate their cognate tRNAs. Arc1p is a transactivator of yeast methionyl-tRNA and glutamyl-tRNA synthetases. This domain has general tRNA binding properties. In a subset of this family this domain has the added capability of a cytokine. For example the p43 component of the Human aminoacyl-tRNA synthetase complex is cleaved to release EMAP-II cytokine. EMAP-II has multiple activities during apoptosis, angiogenesis and inflammation and participates in malignant transformation. A EMAP-II-like cytokine also is released from hTyrRS upon cleavage. The active cytokine heptapeptide locates to this domain. 105 matched cddid_all.tbl CDD cd02800 cd02800 239199 tRNA_bind_EcMetRS_like tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins. This family includes EcMetRS and Aquifex aeolicus Trbp111 (AaTrbp111). This domain has general tRNA binding properties. MetRS aminoacylates methionine transfer RNAs (tRNAmet). AaTrbp111 is structure-specific molecular chaperone recognizing the L-shape of the tRNA fold. AaTrbp111 plays a role in nuclear trafficking of tRNAs. The functional unit of EcMetRs and AaTrbp111 is a homodimer, this domain acts as the dimerization domain. 105 matched cddid_all.tbl CDD cd02801 cd02801 239200 DUS_like_FMN Dihydrouridine synthase-like (DUS-like) FMN-binding domain. Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archaea. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. 1VHN, a putative flavin oxidoreductase, has high sequence similarity to DUS. The enzymatic mechanism of 1VHN is not known at the present. 231 matched cddid_all.tbl CDD cd02803 cd02803 239201 OYE_like_FMN_family Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase. 327 matched cddid_all.tbl CDD cd02808 cd02808 239202 GltS_FMN Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast and bacterial pathway for ammonia assimilation. It is a multifunctional enzyme that functions through three distinct active centers, carrying out L-glutamine hydrolysis, conversion of 2-oxoglutarate into L-glutamate, and electron uptake from an electron donor. 392 matched cddid_all.tbl CDD cd02809 cd02809 239203 alpha_hydroxyacid_oxid_FMN Family of homologous FMN-dependent alpha-hydroxyacid oxidizing enzymes. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate dehydrogenase (MDH), and long chain hydroxyacid oxidase (LCHAO). In green plants, glycolate oxidase is one of the key enzymes in photorespiration where it oxidizes glycolate to glyoxylate. LMO catalyzes the oxidation of L-lactate to acetate and carbon dioxide. MDH oxidizes (S)-mandelate to phenylglyoxalate. It is an enzyme in the mandelate pathway that occurs in several strains of Pseudomonas which converts (R)-mandelate to benzoate. 299 matched cddid_all.tbl CDD cd02810 cd02810 239204 DHOD_DHPD_FMN Dihydroorotate dehydrogenase (DHOD) and Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass its homodimeric interface twice. Two of the Fe-S clusters show a hitherto unobserved coordination involving a glutamine residue. 289 matched cddid_all.tbl CDD cd02811 cd02811 239205 IDI-2_FMN Isopentenyl-diphosphate:dimethylallyl diphosphate isomerase type 2 (IDI-2) FMN-binding domain. Two types of IDIs have been characterized at present. The long known IDI-1 is only dependent on divalent metals for activity, whereas IDI-2 requires a metal, FMN and NADPH. IDI-2 catalyzes the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) in the mevalonate pathway. 326 matched cddid_all.tbl CDD cd02812 cd02812 239206 PcrB_like PcrB_like proteins. One member of this family, a protein from Archaeoglobus fulgidus, has been characterized as a (S)-3-O-geranylgeranylglyceryl phosphate synthase (AfGGGPS). AfGGGPS catalyzes the formation of an ether linkage between sn-glycerol-1-phosphate (G1P) and geranylgeranyl diphosphate (GGPP), the committed step in archaeal lipid biosynthesis. Therefore, it has been proposed that PcrB-like proteins are either prenyltransferases or are involved in lipoteichoic acid biosynthesis although the exact function is still unknown. 219 matched cddid_all.tbl CDD cd02825 cd02825 239207 PAZ PAZ domain, named PAZ after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. This parent model also contains structures of an archaeal PAZ domain. 115 matched cddid_all.tbl CDD cd02826 cd02826 239208 Piwi-like Piwi-like: PIWI domain. Domain found in proteins involved in RNA silencing. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The central component of the RNA-induced silencing complex (RISC) and related complexes is Argonaute. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing. This domain is also found in closely related proteins, including the Piwi subfamily, where it is believed to perform a crucial role in germline cells, via a similar mechanism. 393 matched cddid_all.tbl CDD cd02843 cd02843 239209 PAZ_dicer_like PAZ domain, dicer_like subfamily. Dicer is an RNAse involved in cleaving dsRNA in the RNA interference pathway. It generates dsRNAs which are approximately 20 bp long (siRNAs), which in turn target hydrolysis of homologous RNAs. PAZ domains are named after the proteins Piwi Argonaut and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. 122 matched cddid_all.tbl CDD cd02844 cd02844 239210 PAZ_CAF_like PAZ domain, CAF_like subfamily. CAF (for carpel factory) is a plant homolog of Dicer. CAF has been implicated in flower morphogenesis and in early Arabidopsis development and might function through posttranscriptional regulation of specific mRNA molecules. PAZ domains are named after the proteins Piwi, Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic-acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. 135 matched cddid_all.tbl CDD cd02845 cd02845 239211 PAZ_piwi_like PAZ domain, Piwi_like subfamily. In multi-cellular organisms, the Piwi protein appears to be essential for the maintenance of germline stem cells. In the Drosophila male germline, Piwi was shown to be involved in the silencing of retrotransposons in the male gametes. The Piwi proteins share their domain architecture with other members of the argonaute family. The PAZ domain has been named after the proteins Piwi, Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. 117 matched cddid_all.tbl CDD cd02846 cd02846 239212 PAZ_argonaute_like PAZ domain, argonaute_like subfamily. Argonaute is part of the RNA-induced silencing complex (RISC), and is an endonuclease that plays a key role in the RNA interference pathway. The PAZ domain has been named after the proteins Piwi,Argonaut, and Zwille. PAZ is found in two families of proteins that are essential components of RNA-mediated gene-silencing pathways, including RNA interference, the Piwi and Dicer families. PAZ functions as a nucleic acid binding domain, with a strong preference for single-stranded nucleic acids (RNA or DNA) or RNA duplexes with single-stranded 3' overhangs. It has been suggested that the PAZ domain provides a unique mode for the recognition of the two 3'-terminal nucleotides in single-stranded nucleic acids and buries the 3' OH group, and that it might recognize characteristic 3' overhangs in siRNAs within RISC (RNA-induced silencing) and other complexes. 114 matched cddid_all.tbl CDD cd02847 cd02847 199879 E_set_Chitobiase_C "C-terminal Early set domain associated with the catalytic domain of chitobiase (also called N-acetylglucosaminidase). E or ""early"" set domains are associated with the catalytic domain of chitobiase at the C-terminus. Chitobiase digests the beta, 1-4 glycosidic bonds of the N-acetylglucosamine (NAG) oligomers found in chitin, an important structural element of fungal cell wall and arthropod exoskeletons. It is thought to proceed through an acid-base reaction mechanism, in which one protein carboxylate acts as the catalytic acid, while the nucleophile is the polar acetamido group of the sugar in a substrate-assisted reaction with retention of the anomeric configuration. The C-terminus of chitobiase may be related to the immunoglobulin and/or fibronectin type III superfamilies. E set domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase, among others." 62 matched cddid_all.tbl CDD cd02848 cd02848 199880 E_set_Chitinase_N "N-terminal Early set domain associated with the catalytic domain of chitinase. E or ""early"" set domains are associated with the catalytic domain of chitinase at the N-terminal end. Chitinases hydrolyze the abundant natural biopolymer chitin, producing smaller chito-oligosaccharides. Chitin consists of multiple N-acetyl-D-glucosamine (NAG) residues connected via beta-1,4-glycosidic linkages and is an important structural element of fungal cell wall and arthropod exoskeletons. On the basis of the mode of chitin hydrolysis, chitinases are classified as random, endo-, and exo-chitinases and belong to families 18 and 19 of glycosyl hydrolases based on sequence criteria. The N-terminal domain of chitinase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase, among others." 105 matched cddid_all.tbl CDD cd02850 cd02850 199881 E_set_Cellulase_N "N-terminal Early set domain associated with the catalytic domain of cellulase. E or ""early"" set domains are associated with the catalytic domain of cellulases at the N-terminal end. Cellulases are O-glycosyl hydrolases (GHs) that hydrolyze beta 1-4 glucosidic bonds in cellulose. They are usually categorized into either exoglucanases, which sequentially release terminal sugar units from the cellulose chain, or endoglucanases, which also attack the chain internally. The N-terminal domain of cellulase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase, among others." 86 matched cddid_all.tbl CDD cd02851 cd02851 199882 E_set_GO_C "C-terminal Early set domain associated with the catalytic domain of galactose oxidase. E or ""early"" set domains are associated with the catalytic domain of galactose oxidase at the C-terminal end. Galactose oxidase is an extracellular monomeric enzyme which catalyzes the stereospecific oxidation of a broad range of primary alcohol substrates and possesses a unique mononuclear copper site essential for catalyzing a two-electron transfer reaction during the oxidation of primary alcohols to corresponding aldehydes. The second redox active center necessary for the reaction was found to be situated at a tyrosine residue. The C-terminal domain of galactose oxidase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase, among others." 103 matched cddid_all.tbl CDD cd02853 cd02853 199883 E_set_MTHase_like_N "N-terminal Early set domain associated with the catalytic domain of Maltooligosyl trehalose trehalohydrolase (also called Glycosyltrehalose trehalohydrolase) and similar proteins. E or ""early"" set domains are associated with the catalytic domain of Maltooligosyl trehalose trehalohydrolase (MTHase) and similar proteins at the N-terminal end. This subfamily also includes bacterial alpha amylases and 1,4-alpha-glucan branching enzymes which are highly similar to MTHase. Maltooligosyl trehalose synthase (MTSase) and MTHase work together to produce trehalose. MTSase is responsible for converting the alpha-1,4-glucosidic linkage to an alpha,alpha-1,1-glucosidic linkage at the reducing end of the maltooligosaccharide through an intramolecular transglucosylation reaction, while MTHase hydrolyzes the penultimate alpha-1,4 linkage of the reducing end, resulting in the release of trehalose. The N-terminal domain of MTHase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase, among others." 84 matched cddid_all.tbl CDD cd02854 cd02854 199884 E_set_GBE_euk_N "N-terminal Early set domain associated with the catalytic domain of eukaryotic glycogen branching enzyme (also called 1,4 alpha glucan branching enzyme). This subfamily is composed of predominantly eukaryotic 1,4 alpha glucan branching enzymes, also called glycogen branching enzymes or starch binding enzymes in plants. E or ""early"" set domains are associated with the catalytic domain of the 1,4 alpha glucan branching enzymes at the N-terminal end. These enzymes catalyze the formation of alpha-1,6 branch points in either glycogen or starch by cleavage of the alpha-1,4 glucosidic linkage, yielding a non-reducing end oligosaccharide chain, as well as the subsequent attachment of short glucosyl chains to the alpha-1,6 position. Starch is composed of two types of glucan polymer: amylose and amylopectin. Amylose is mainly composed of linear chains of alpha-1,4 linked glucose residues and amylopectin consists of shorter alpha-1,4 linked chains connected by alpha-1,6 linkages. Amylopectin is synthesized from linear chains by starch branching enzyme. The N-terminal domains of the branching enzyme proteins may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase, among others." 95 matched cddid_all.tbl CDD cd02855 cd02855 199885 E_set_GBE_prok_N "N-terminal Early set domain associated with the catalytic domain of prokaryotic glycogen branching enzyme. This subfamily is composed of predominantly prokaryotic 1,4 alpha glucan branching enzymes, also called glycogen branching enzymes. E or ""early"" set domains are associated with the catalytic domain of glycogen branching enzymes at the N-terminal end. Glycogen branching enzyme catalyzes the formation of alpha-1,6 branch points in either glycogen or starch by cleavage of the alpha-1,4 glucosidic linkage, yielding a non-reducing end oligosaccharide chain, as well as the subsequent attachment of short glucosyl chains to the alpha-1,6 position. By increasing the number of non-reducing ends, glycogen is more reactive to synthesis and digestion as well as being more soluble. The N-terminal domain of the 1,4 alpha glucan branching enzyme may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase, among others." 105 matched cddid_all.tbl CDD cd02856 cd02856 199886 E_set_GDE_Isoamylase_N "N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase). E or ""early"" set domains are associated with the catalytic domain of the glycogen debranching enzyme at the N-terminal end. Glycogen debranching enzymes have both 4-alpha-glucanotransferase and amylo-1,6-glucosidase activities. As a transferase, it transfers a segment of the 1,4-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose or another 1,4-alpha-D-glucan. As a glucosidase, it catalyzes the endohydrolysis of 1,6-alpha-D-glucoside linkages at points of branching in chains of 1,4-linked alpha-D-glucose residues. Bacterial isoamylases are also included in this subfamily. Isoamylase is one of the starch-debranching enzymes that catalyze the hydrolysis of alpha-1,6-glucosidic linkages specific in alpha-glucans such as amylopectin or glycogen. Isoamylase contains a bound calcium ion, but this is not in the same position as the conserved calcium ion that has been reported in other alpha-amylase family enzymes. The N-terminal domain of glycogen debranching enzyme may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase, among others." 130 matched cddid_all.tbl CDD cd02857 cd02857 199887 E_set_CDase_PDE_N "N-terminal Early set domain associated with the catalytic domain of cyclomaltodextrinase and pullulan-degrading enzymes. E or ""early"" set domains are associated with the catalytic domain of the cyclomaltodextrinase (CDase) and pullulan-degrading enzymes at the N-terminal end. Members of this subgroup include CDase, maltogenic amylase, and neopullulanase, all of which are capable of hydrolyzing all or two of the following three types of substrates: cyclomaltodextrins (CDs), pullulan, and starch. These enzymes hydrolyze CDs and starch to maltose and pullulan to panose by cleavage of alpha-1,4 glycosidic bonds whereas alpha-amylases essentially lack activity on CDs and pullulan. They also catalyze transglycosylation of oligosaccharides to the C3-, C4- or C6-hydroxyl groups of various acceptor sugar molecules. The N-terminal domain of the CDase and pullulan-degrading enzymes may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase, among others." 109 matched cddid_all.tbl CDD cd02858 cd02858 199888 E_set_Esterase_N "N-terminal Early set domain associated with the catalytic domain of esterase. E or ""early"" set domains are associated with the catalytic domain of esterase at the N-terminal end. Esterases catalyze the hydrolysis of organic esters to release an alcohol or thiol and acid. The term esterase can be applied to enzymes that hydrolyze carboxylate, phosphate and sulphate esters, but is more often restricted to the first class of substrate. The N-terminal domain of esterase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase, among others." 78 matched cddid_all.tbl CDD cd02859 cd02859 199889 E_set_AMPKbeta_like_N "N-terminal Early set domain, a glycogen binding domain, associated with the catalytic domain of AMP-activated protein kinase beta subunit. E or ""early"" set domains are associated with the catalytic domain of AMP-activated protein kinase beta subunit glycogen binding domain at the N-terminal end. AMPK is a metabolic stress sensing protein that senses AMP/ATP and has recently been found to act as a glycogen sensor as well. The protein functions as an alpha-beta-gamma heterotrimer. This N-terminal domain is the glycogen binding domain of the beta subunit. This domain is also a member of the CBM48 (Carbohydrate Binding Module 48) family whose members include pullulanase, maltooligosyl trehalose synthase, starch branching enzyme, glycogen branching enzyme, glycogen debranching enzyme, and isoamylase." 80 matched cddid_all.tbl CDD cd02860 cd02860 199890 E_set_Pullulanase "Early set domain associated with the catalytic domain of pullulanase (also called dextrinase and alpha-dextrin endo-1,6-alpha glucosidase). E or ""early"" set domains are associated with the catalytic domain of pullulanase at either the N-terminal or C-terminal end, and in a few instances at both ends. Pullulanase is an enzyme with activity similar to that of isoamylase; it cleaves 1,6-alpha-glucosidic linkages in pullulan, amylopectin, and glycogen, and in alpha-and beta-amylase limit-dextrins of amylopectin and glycogen. The E set domain of pullulanase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase. This domain is also a member of the CBM48 (Carbohydrate Binding Module 48) family whose members include maltooligosyl trehalose synthase, starch branching enzyme, glycogen branching enzyme, glycogen debranching enzyme, isoamylase, and the beta subunit of AMP-activated protein kinase." 97 matched cddid_all.tbl CDD cd02861 cd02861 199891 E_set_pullulanase_like "Early set domain associated with the catalytic domain of pullulanase-like proteins. E or ""early"" set domains are associated with the catalytic domain of pullulanase at either the N-terminal or C-terminal end, and in a few instances at both ends. Pullulanase (also called dextrinase or alpha-dextrin endo-1,6-alpha glucosidase) is an enzyme with action similar to that of isoamylase; it cleaves 1,6-alpha-glucosidic linkages in pullulan, amylopectin, and glycogen, and in alpha-and beta-amylase limit-dextrins of amylopectin and glycogen. The E set domain of pullulanase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase. This domain is also a member of the CBM48 (Carbohydrate Binding Module 48) family whose members include maltooligosyl trehalose synthase, starch branching enzyme, glycogen branching enzyme, glycogen debranching enzyme, isoamylase, and the beta subunit of AMP-activated protein kinase." 88 matched cddid_all.tbl CDD cd02862 cd02862 239213 NorE_like NorE_like subfamily of heme-copper oxidase subunit III. Heme-copper oxidases include cytochrome c and ubiquinol oxidases. Alcaligenes faecalis norE is found in a gene cluster containing norCB. norCB encodes the cytochrome c and cytochrome b subunits of nitric oxide reductase (NOR). Based on this and on its similarity to subunit III of cytochrome c oxidase (CcO) and ubiquinol oxidase, NorE has been speculated to be a subunit of NOR. 186 matched cddid_all.tbl CDD cd02863 cd02863 239214 Ubiquinol_oxidase_III Ubiquinol oxidase subunit III subfamily. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. Ubiquinol oxidases feature four subunits in contrast to the 13 subunit bovine cytochrome c oxidase (CcO). Subunits I, II, and III of bovine CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Subunits I, II and III of ubiquinol oxidase are homologous to the corresponding subunits in bovine CcO. Although not required for catalytic activity, subunit III appears to be involved in assembly of the multimer complex. 186 matched cddid_all.tbl CDD cd02864 cd02864 239215 Heme_Cu_Oxidase_III_1 Heme-copper oxidase subunit III subfamily. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The heme-copper oxidase superfamily is diverse in terms of electron donors, subunit composition, and heme types. This superfamily includes cytochrome c and ubiquinol oxidases. Bacterial oxidases typically contain 3 or 4 subunits in contrast to the 13 subunit bovine cytochrome c oxidase (CcO). Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Subunits I, II and III of ubiquinol oxidase are homologous to the corresponding subunits in CcO. Although not required for catalytic activity, subunit III is believed to play a role in assembly of the multimer complex. Rhodobacter CcO subunit III stabilizes the integrity of the binuclear center in subunit I. It has been proposed that Archaea acquired heme-copper oxidases through gene transfer from Gram-positive bacteria. 202 matched cddid_all.tbl CDD cd02865 cd02865 239216 Heme_Cu_Oxidase_III_2 Heme-copper oxidase subunit III subfamily. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which couple the reduction of molecular oxygen to water to, proton pumping across the membrane. The heme-copper oxidase superfamily is diverse in terms of electron donors, subunit composition, and heme types. This superfamily includes cytochrome c and ubiquinol oxidases. Bacterial oxidases typically contain 3 or 4 subunits in contrast to the 13 subunit bovine cytochrome c oxidase (CcO). Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Subunits I, II and III of ubiquinol oxidase are homologous to the corresponding subunits in CcO. Although not required for catalytic activity, subunit III is believed to play a role in assembly of the multimer complex. Rhodobacter CcO subunit III stabilizes the integrity of the binuclear center in subunit I. It has been proposed that Archaea acquired heme-copper oxidases through gene transfer from Gram-positive bacteria. 184 matched cddid_all.tbl CDD cd02866 cd02866 211343 PseudoU_synth_TruA_Archea Archeal pseudouridine synthases. This group consists of archeal pseudouridine synthases.Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. This group of proteins make Psedouridine in tRNAs. 219 matched cddid_all.tbl CDD cd02867 cd02867 211344 PseudoU_synth_TruB_4 Pseudouridine synthase homolog 4. This group consists of Eukaryotic TruB proteins similar to Saccharomyces cerevisiae Pus4. S. cerevisiae Pus4, makes psi55 in the T loop of both cytoplasmic and mitochondrial tRNAs. Psi55 is almost universally conserved. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). 312 matched cddid_all.tbl CDD cd02868 cd02868 211345 PseudoU_synth_hTruB2_like Pseudouridine synthase, humanTRUB2_like. This group consists of eukaryotic pseudouridine synthases similar to human TruB pseudouridine synthase homolog 2 (TRUB2). Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). 226 matched cddid_all.tbl CDD cd02869 cd02869 211346 PseudoU_synth_RluA_like Pseudouridine synthase, RluA family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli. 185 matched cddid_all.tbl CDD cd02870 cd02870 211347 PseudoU_synth_RsuA_like Pseudouridine synthases, RsuA subfamily. Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins. 146 matched cddid_all.tbl CDD cd02871 cd02871 119350 GH18_chitinase_D-like GH18 domain of Chitinase D (ChiD). ChiD, a chitinase found in Bacillus circulans, hydrolyzes the 1,4-beta-linkages of N-acetylglucosamine in chitin and chitodextrins. The domain architecture of ChiD includes a catalytic glycosyl hydrolase family 18 (GH18) domain, a chitin-binding domain, and a fibronectin type III domain. The chitin-binding and fibronectin type III domains are located either N-terminal or C-terminal to the catalytic domain. This family includes exochitinase Chi36 from Bacillus cereus. 312 matched cddid_all.tbl CDD cd02872 cd02872 119351 GH18_chitolectin_chitotriosidase This conserved domain family includes a large number of catalytically inactive chitinase-like lectins (chitolectins) including YKL-39, YKL-40 (HCGP39), YM1, oviductin, and AMCase (acidic mammalian chitinase), as well as catalytically active chitotriosidases. The conserved domain is an eight-stranded alpha/beta barrel fold belonging to the family 18 glycosyl hydrolases. The fold has a pronounced active-site cleft at the C-terminal end of the beta-barrel. The chitolectins lack a key active site glutamate (the proton donor required for hydrolytic activity) but retain highly conserved residues involved in oligosaccharide binding. Chitotriosidase is a chitinolytic enzyme expressed in maturing macrophages, which suggests that it plays a part in antimicrobial defense. Chitotriosidase hydrolyzes chitotriose, as well as colloidal chitin to yield chitobiose and is therefore considered an exochitinase. Chitotriosidase occurs in two major forms, the large form being converted to the small form by either RNA or post-translational processing. Although the small form, containing the chitinase domain alone, is sufficient for the chitinolytic activity, the additional C-terminal chitin-binding domain of the large form plays a role in processing colloidal chitin. The chitotriosidase gene is nonessential in humans, as about 35% of the population are heterozygous and 6% homozygous for an inactivated form of the gene. HCGP39 is a 39-kDa human cartilage glycoprotein thought to play a role in connective tissue remodeling and defense against pathogens. 362 matched cddid_all.tbl CDD cd02873 cd02873 119352 GH18_IDGF The IDGF's (imaginal disc growth factors) are a family of growth factors identified in insects that include at least five members, some of which are encoded by genes in a tight cluster. The IDGF's have an eight-stranded alpha/beta barrel fold and are related to the glycosyl hydrolase family 18 (GH18) chitinases, but they have an amino acid substitution known to abolish chitinase catalytic activity. IDGFs may have evolved from chitinases to gain new functions as growth factors, interacting with cell surface glycoproteins involved in growth-promoting processes. 413 matched cddid_all.tbl CDD cd02874 cd02874 119353 GH18_CFLE_spore_hydrolase Cortical fragment-lytic enzyme (CFLE) is a peptidoglycan hydrolase involved in bacterial endospore germination. CFLE is expressed as an inactive preprotein (called SleB) in the forespore compartment of sporulating cells. SleB translocates across the forespore inner membrane and is deposited as a mature enzyme in the cortex layer of the spore. As part of a sensory mechanism capable of initiating germination, CFLE degrades a spore-specific peptidoglycan constituent called muramic-acid delta-lactam that comprises the outer cortex. CFLE has a C-terminal glycosyl hydrolase family 18 (GH18) catalytic domain as well as two N-terminal LysM peptidoglycan-binding domains. In addition to SleB, this family includes YaaH, YdhD, and YvbX from Bacillus subtilis. 313 matched cddid_all.tbl CDD cd02875 cd02875 119354 GH18_chitobiase Chitobiase (also known as di-N-acetylchitobiase) is a lysosomal glycosidase that hydrolyzes the reducing-end N-acetylglucosamine from the chitobiose core of oligosaccharides during the ordered degradation of asparagine-linked glycoproteins in eukaryotes. Chitobiase can only do so if the asparagine that joins the oligosaccharide to protein is previously removed by a glycosylasparaginase. Chitobiase is therefore the final step in the lysosomal degradation of the protein/carbohydrate linkage component of asparagine-linked glycoproteins. The catalytic domain of chitobiase is an eight-stranded alpha/beta barrel fold similar to that of other family 18 glycosyl hydrolases such as hevamine and chitotriosidase. 358 matched cddid_all.tbl CDD cd02876 cd02876 119355 GH18_SI-CLP Stabilin-1 interacting chitinase-like protein (SI-CLP) is a eukaryotic chitinase-like protein of unknown function that interacts with the endocytic/sorting transmembrane receptor stabilin-1 and is secreted from the lysosome. SI-CLP has a glycosyl hydrolase family 18 (GH18) domain but lacks a chitin-binding domain. The catalytic amino acids of the GH18 domain are not conserved in SI-CLP, similar to the chitolectins YKL-39, YKL-40, and YM1/2. Human SI-CLP is sorted to late endosomes and secretory lysosomes in alternatively activated macrophages. 318 matched cddid_all.tbl CDD cd02877 cd02877 119356 GH18_hevamine_XipI_class_III This conserved domain family includes xylanase inhibitor Xip-I, and the class III plant chitinases such as hevamine, concanavalin B, and PPL2, all of which have a glycosyl hydrolase family 18 (GH18) domain. Hevamine is a class III endochitinase that hydrolyzes the linear polysaccharide chains of chitin and peptidoglycan and is important for defense against pathogenic bacteria and fungi. PPL2 (Parkia platycephala lectin 2) is a class III chitinase from Parkia platycephala seeds that hydrolyzes beta(1-4) glycosidic bonds linking 2-acetoamido-2-deoxy-beta-D-glucopyranose units in chitin. 280 matched cddid_all.tbl CDD cd02878 cd02878 119357 GH18_zymocin_alpha Zymocin, alpha subunit. Zymocin is a heterotrimeric enzyme that inhibits yeast cell cycle progression. The zymocin alpha subunit has a chitinase activity that is essential for holoenzyme action from the cell exterior while the gamma subunit contains the intracellular toxin responsible for G1 phase cell cycle arrest. The zymocin alpha and beta subunits are thought to act from the cell's exterior by docking to the cell wall-associated chitin, thus mediating gamma-toxin translocation. The alpha subunit has an eight-stranded TIM barrel fold similar to that of family 18 glycosyl hydrolases such as hevamine, chitolectin, and chitobiase. 345 matched cddid_all.tbl CDD cd02879 cd02879 119358 GH18_plant_chitinase_class_V The class V plant chitinases have a glycosyl hydrolase family 18 (GH18) domain, but lack the chitin-binding domain present in other GH18 enzymes. The GH18 domain of the class V chitinases has endochitinase activity in some cases and no catalytic activity in others. Included in this family is a lectin found in black locust (Robinia pseudoacacia) bark, which binds chitin but lacks chitinase activity. Also included is a chitinase-related receptor-like kinase (CHRK1) from tobacco (Nicotiana tabacum), with an N-terminal GH18 domain and a C-terminal kinase domain, which is thought to be part of a plant signaling pathway. The GH18 domain of CHRK1 is expressed extracellularly where it binds chitin but lacks chitinase activity. 299 matched cddid_all.tbl CDD cd02883 cd02883 467528 NUDIX_Hydrolase "NUDIX hydrolase superfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 106 matched cddid_all.tbl CDD cd02885 cd02885 467529 NUDIX_IPP_Isomerase Isopentenyl diphosphate isomerase. Isopentenyl diphosphate (IPP) isomerase, a member of the NUDIX hydrolase superfamily, is a key enzyme in the isoprenoid biosynthetic pathway. Isoprenoids comprise a large family of natural products including sterols, carotenoids, dolichols and prenylated proteins. These compounds are synthesized from two precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). IPP isomerase catalyzes the interconversion of IPP and DMAPP by a stereoselective antarafacial transposition of hydrogen. The enzyme requires one Mn2+ or Mg2+ ion in its active site to fold into an active conformation and also contains the NUDIX motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. The metal binding site is present within the active site and plays structural and catalytical roles. IPP isomerase is well represented in several bacteria, archaebacteria and eukaryotes, including fungi, mammals and plants. Despite sequence variations (mainly at the N-terminus), the core structure is highly conserved. 162 matched cddid_all.tbl CDD cd02888 cd02888 153089 RNR_II_dimer Class II ribonucleotide reductase, dimeric form. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). Class II RNRs are found in bacteria that can live under both aerobic and anaerobic conditions. Many, but not all members of this class are found to be homodimers. Adenosylcobalamin interacts directly with an active site cysteine to form the reactive cysteine radical. 464 matched cddid_all.tbl CDD cd02889 cd02889 239219 SQCY Squalene cyclase (SQCY) domain; found in class II terpene cyclases that have an alpha 6 - alpha 6 barrel fold. Squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY) are integral membrane proteins that catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds. Bacterial SQCY catalyzes the convertion of squalene to hopene or diplopterol. Eukaryotic OSQCY transforms the 2,3-epoxide of squalene to compounds such as, lanosterol (a metabolic precursor of cholesterol and steroid hormones) in mammals and fungi or, cycloartenol in plants. Deletion of a single glycine residue of Alicyclobacillus acidocaldarius SQCY alters its substrate specificity into that of eukaryotic OSQCY. Both enzymes have a second minor domain, which forms an alpha-alpha barrel that is inserted into the major domain. This group also contains SQCY-like archael sequences and some bacterial SQCY's which lack this minor domain. 348 matched cddid_all.tbl CDD cd02890 cd02890 239220 PTase "Protein prenyltransferase (PTase) domain, beta subunit (alpha 6 - alpha 6 barrel fold). The protein prenyltransferase family of lipid-modifying enzymes includes protein farnesyltransferase (FTase) and geranylgeranyltransferase types I and II (GGTase-I and GGTase-II). They catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. Prenyltransferases employ a Zn2+ ion to alkylate a thiol group catalyzing the formation of thioether linkages between the C1 atom of farnesyl (15-carbon by FTase) or geranylgeranyl (20-carbon by GGTase-I, II) isoprenoid lipids and cysteine residues at or near the C-terminus of protein acceptors. FTase and GGTase-I prenylate the cysteine in the terminal sequence, ""CAAX""; and GGTase-II prenylates both cysteines in the ""CC"" (or ""CXC"") terminal sequence. These enzymes are heterodimeric with both alpha and beta subunits required for catalytic activity. In contrast to other prenyltransferases, GGTase-II does not recognize its protein acceptor directly but requires Rab to complex with REP (Rab escort protein) before prenylation can occur. These enzymes are found exclusively in eukaryotes." 286 matched cddid_all.tbl CDD cd02891 cd02891 239221 A2M_like Proteins similar to alpha2-macroglobulin (alpha (2)-M). Alpha (2)-M is a major carrier protein in serum. It is a broadly specific proteinase inhibitor. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of proteases. This group contains another broadly specific proteinase inhibitor: pregnancy zone protein (PZP). PZP is a trace protein in the plasma of non-pregnant females and males which is elevated in pregnancy. Alpha (2)-M and PZ bind to placental protein-14 and may modulate its activity in T-cell growth and cytokine production thereby protecting the allogeneic fetus from attack by the maternal immune system. This group also contains C3, C4 and C5 of vertebrate complement. The vertebrate complement is an effector of both the acquired and innate immune systems The point of convergence of the classical, alternative and lectin pathways of the complement system is the proteolytic activation of C3. C4 plays a key role in propagating the classical and lectin pathways. C5 participates in the classical and alternative pathways. The thioester bond located within the structure of C3 and C4 is central to the function of complement. C5 does not contain an active thioester bond. 282 matched cddid_all.tbl CDD cd02892 cd02892 239222 SQCY_1 Squalene cyclase (SQCY) domain subgroup 1; found in class II terpene cyclases that have an alpha 6 - alpha 6 barrel fold. Squalene cyclase (SQCY) and 2,3-oxidosqualene cyclase (OSQCY) are integral membrane proteins that catalyze a cationic cyclization cascade converting linear triterpenes to fused ring compounds. This group contains bacterial SQCY which catalyzes the convertion of squalene to hopene or diplopterol and eukaryotic OSQCY which transforms the 2,3-epoxide of squalene to compounds such as, lanosterol in mammals and fungi or, cycloartenol in plants. Deletion of a single glycine residue of Alicyclobacillus acidocaldarius SQCY alters its substrate specificity into that of eukaryotic OSQCY. Both enzymes have a second minor domain, which forms an alpha-alpha barrel that is inserted into the major domain. 634 matched cddid_all.tbl CDD cd02893 cd02893 239223 FTase Protein farnesyltransferase (FTase)_like proteins containing the protein prenyltransferase (PTase) domain, beta subunit (alpha 6 - alpha 6 barrel fold). FTases are a subgroup of PTase family of lipid-modifying enzymes. PTases catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. These proteins are heterodimers of alpha and beta subunits. Both subunits are required for catalytic activity. Prenyltransferases employ a Zn2+ ion to alkylate a thiol group catalyzing the formation of thioether linkages between cysteine residues at or near the C-terminus of protein acceptors and the C1 atom of isoprenoid lipids. Ftase attaches a 15-carbon farnesyl group to the cysteine within the C-terminal CaaX motif of substrate proteins when X is Ala, Met, Ser, Cys or Gln. Protein farnesylation has been shown to play critical roles in a variety of cellular processes including Ras/mitogen activated protein kinase signaling pathways in mammals and, abscisic acid signal transduction in Arabidopsis. 299 matched cddid_all.tbl CDD cd02894 cd02894 239224 GGTase-II "Geranylgeranyltransferase type II (GGTase-II)_like proteins containing the protein prenyltransferase (PTase) domain, beta subunit (alpha 6 - alpha 6 barrel fold). GGTase-IIs are a subgroup of the protein prenyltransferase family of lipid-modifying enzymes. PTases catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. Prenyltransferases employ a Zn2+ ion to alkylate a thiol group catalyzing the formation of thioether linkages between cysteine residues at or near the C-terminus of protein acceptors and the C1 atom of isoprenoid lipids (geranylgeranyl (20-carbon) in the case of GGTase-II ). GGTase-II catalyzes alkylation of both cysteine residues in Rab proteins containing carboxy-terminal ""CC"", ""CXCX"" or ""CXC"" motifs. PTases are heterodimeric with both alpha and beta subunits required for catalytic activity. In contrast to other prenyltransferases, GGTas-II requires an escort protein to bring the substrate protein to the catalytic heterodimer and to escort the geryanylgeranylated product to the membrane." 287 matched cddid_all.tbl CDD cd02895 cd02895 239225 GGTase-I "Geranylgeranyltransferase types I (GGTase-I)-like proteins containing the protein prenyltransferase (PTase) domain, beta subunit (alpha 6 - alpha 6 barrel fold). GGTase-I s are a subgroup of the protein prenyltransferase family of lipid-modifying enzymes PTases catalyze the carboxyl-terminal lipidation of Ras, Rab, and several other cellular signal transduction proteins, facilitating membrane associations and specific protein-protein interactions. Prenyltransferases employ a Zn2+ ion to alkylate a thiol group catalyzing the formation of thioether linkages between cysteine residues at or near the C-terminus of protein acceptors and the C1 atom of isoprenoid lipids (geranylgeranyl (20-carbon) in the case of GGTase-I ). GGTase-I prenylates the cysteine in the terminal sequence, ""CAAX"" when X is Leu or Phe. Substrates for GTTase-I include the gamma subunit of neural G-proteins and several Ras-related G-proteins. PTases are heterodimeric with both alpha and beta subunits required for catalytic activity." 307 matched cddid_all.tbl CDD cd02896 cd02896 239226 complement_C3_C4_C5 Proteins similar to C3, C4 and C5 of vertebrate complement. The vertebrate complement system, comprised of a large number of distinct plasma proteins, is an effector of both the acquired and innate immune systems. The point of convergence of the classical, alternative and lectin pathways of the complement system is the proteolytic activation of C3. C4 plays a key role in propagating the classical and lectin pathways. C5 participates in the classical and alternative pathways. The thioester bond located within the structure of C3 and C4 is central to the function of complement. C5 does not contain an active thioester bond. 297 matched cddid_all.tbl CDD cd02897 cd02897 239227 A2M_2 Proteins similar to alpha2-macroglobulin (alpha (2)-M). This group also contains the pregnancy zone protein (PZP). Alpha(2)-M and PZP are broadly specific proteinase inhibitors. Alpha (2)-M is a major carrier protein in serum. The structural thioester of alpha (2)-M, is involved in the immobilization and entrapment of proteases. PZP is a trace protein in the plasma of non-pregnant females and males which is elevated in pregnancy. Alpha (2)-M and PZ bind to placental protein-14 and may modulate its activity in T-cell growth and cytokine production contributing to fetal survival. It has been suggested that thioester bond cleavage promotes the binding of PZ and alpha (2)-M to the CD91 receptor clearing them from circulation. 292 matched cddid_all.tbl CDD cd02899 cd02899 239228 PLAT_SR Scavenger receptor protein. A subfamily of PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates. This subfamily contains Toxoplasma gondii Scavenger protein TgSR1. 109 matched cddid_all.tbl CDD cd02900 cd02900 394872 Macro_Appr_pase "macrodomain, Appr-1""-pase family. Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. The yeast protein Ymx7 and related proteins in this family contain a stand-alone macrodomain and may be specific phosphatases catalyzing the conversion of ADP-ribose-1""-monophosphate (Appr-1""-p) to ADP-ribose. Appr-1""-p is an intermediate in a metabolic pathway involved in pre-tRNA splicing." 195 matched cddid_all.tbl CDD cd02901 cd02901 394873 Macro_Poa1p-like "macrodomain, Poa1p-like family. Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Members of this family show similarity to the yeast protein Poa1p, reported to be a phosphatase specific for Appr-1""-p, a tRNA splicing metabolite. Poa1p may play a role in tRNA splicing regulation." 135 matched cddid_all.tbl CDD cd02903 cd02903 394874 Macro_BAL-like macrodomain, B-aggressive lymphoma (BAL)-like family. Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Members of this family show similarity to BAL (B-aggressive lymphoma) proteins, which contain one to three macrodomains. Most BAL family macrodomains belong to this family except for the most N-terminal domain in multiple-domain containing proteins. This family includes the second and third macrodomains of mono-ADP-ribosyltransferase PARP14 (PARP-14, also known as ADP-ribosyltransferase diphtheria toxin-like 8, ATRD8, B aggressive lymphoma protein 2, or BAL2). Most BAL proteins also contain a C-terminal PARP active site and are also named as PARPs. Human BAL1 (or PARP-9) was originally identified as a risk-related gene in diffuse large B-cell lymphoma that promotes malignant B-cell migration. Some BAL family proteins exhibit PARP activity. Poly (ADP-ribosyl)ation is an immediate DNA-damage-dependent post-translational modification of histones and other nuclear proteins. BAL proteins may also function as transcriptional repressors. 175 matched cddid_all.tbl CDD cd02904 cd02904 394875 Macro_H2A-like macrodomain, macroH2A-like family. Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Members of this family are similar to macroH2A, a variant of the major-type core histone H2A, which contains an N-terminal H2A domain and a C-terminal nonhistone macrodomain. Histone macroH2A is enriched on the inactive X chromosome of mammalian female cells. It does not bind poly ADP-ribose, but does bind the monomeric SirT1 metabolite O-acetyl-ADP-ribose (OAADPR) with high affinity through its macrodomain. This family also includes the ADP-ribose binding macrodomain of the macroH2A variant, macroH2A1.1. The macroH2A1.1 isoform inhibits PARP1-dependent DNA-damage induced chromatin dynamics. The putative ADP-ribose binding pocket of the human macroH2A2 macrodomain exhibits marked structural differences compared with the macroH2A1.1 variant. 188 matched cddid_all.tbl CDD cd02905 cd02905 394876 Macro_GDAP2-like macrodomain, GDAP2-like family. Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. This family contains proteins similar to human GDAP2, the ganglioside induced differentiation associated protein 2, whose gene is expressed at a higher level in differentiated Neuro2a cells compared with non-differentiated cells. GDAP2 contains an N-terminal macrodomain and a C-terminal Sec14p-like lipid binding domain. It is specifically expressed in brain and testis. 169 matched cddid_all.tbl CDD cd02907 cd02907 394877 Macro_Af1521_BAL-like "macrodomain, Af1521-like family. Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. The macrodomains in this family show similarity to Af1521, a protein from Archaeoglobus fulgidus containing a stand-alone macrodomain. Af1521 binds ADP-ribose and exhibits phosphatase activity toward ADP-ribose-1""-monophosphate (Appr-1""-p). Also included in this family are the N-terminal (or first) macrodomains of BAL (B-aggressive lymphoma) proteins which contain multiple macrodomains, such as the first macrodomain of mono-ADP-ribosyltransferase PARP14 (PARP-14, also known as ADP-ribosyltransferase diphtheria toxin-like 8, ATRD8, B aggressive lymphoma protein 2, or BAL2). Most BAL proteins also contain a C-terminal PARP active site and are also named as PARPs. Human BAL1 (or PARP-9) was originally identified as a risk-related gene in diffuse large B-cell lymphoma that promotes malignant B-cell migration. Some BAL family proteins exhibit PARP activity. Poly (ADP-ribosyl)ation is an immediate DNA-damage-dependent post-translational modification of histones and other nuclear proteins. BAL proteins may also function as transcriptional repressors." 158 matched cddid_all.tbl CDD cd02908 cd02908 438955 Macro_OAADPr_deacetylase macrodomain, O-acetyl-ADP-ribose (OAADPr) family. Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. This family includes eukaryotic macrodomain proteins such as human MacroD1 and MacroD2, and bacterial proteins such as Escherichia coli YmdB; these have been shown to be O-acetyl-ADP-ribose (OAADPr) deacetylases that efficiently catalyze the hydrolysis of OAADPr to produce ADP-ribose and free acetate. OAADPr is a sirtuin reaction product generated from the NAD+-dependent protein deacetylation reactions and has been implicated as a signaling molecule. By acting on mono-ADP-ribosylated substrates, OAADPr deacetylases may reverse cellular ADP-ribosylation. 166 matched cddid_all.tbl CDD cd02909 cd02909 380374 cupin_pirin_N "pirin, N-terminal cupin domain. This family contains the N-terminal domain of pirin, a nuclear protein that is highly conserved among mammals, plants, fungi, and prokaryotes. It is widely expressed in dot-like subnuclear structures in human tissues such as liver and heart. Pirin functions as both a transcriptional cofactor and an apoptosis-related protein in mammals and is involved in seed germination and seedling development in plants. The pirins have been assigned as a subfamily of the cupin superfamily based on structure and sequence similarity. The pirins have two tandem cupin-like folds but the C-terminal cupin fold has diverged considerably and does not have a metal binding site. The exact functions of pirins are unknown but they have quercitinase activity in Escherichia coli and are thought to play important roles in transcription and apoptosis. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold generally capable of homodimerization." 104 matched cddid_all.tbl CDD cd02910 cd02910 380375 cupin_Yhhw_N "Escherichia coli YhhW and YhaK and related proteins, pirin-like bicupin, N-terminal cupin domain. This family includes the N-terminal cupin domains of YhhW and YhaK, Escherichia coli pirin-like proteins with unknown function. YhhW is structurally similar not only to human pirin but also to quercitin 2,3-dioxygenase (quercitinase). Although the function of YhhW is not completely understood, YhhW and its human ortholog have quercitinase activity and are likely to play an important role in transcription and apoptosis. This N-terminal cupin domain of YhhW has a metal coordination site and is thought to have catalytic activity while the C-terminal cupin-like domain has diverged considerably and has closer alignment with C-terminal pirin. YhaK is found in low abundance in the cytosol of E. coli and is strongly up-regulated by nitroso-glutathione (GSNO). There are major structural differences at the N-terminus of YhaK compared with YhhW; YhaK lacks the canonical cupin metal-binding residues of pirins and may be involved in chloride binding and/or sensing of oxidative stress in enterobacteria. YhaK showed no quercetinase and peroxidase activity; however, reduced YhaK was very sensitive to reactive oxygen species (ROS). Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 119 matched cddid_all.tbl CDD cd02911 cd02911 239237 arch_FMN Archeal FMN-binding domain. This family of archaeal proteins are part of the NAD(P)H-dependent flavin oxidoreductase (oxidored) FMN-binding family that reduce a range of alternative electron acceptors. Most use FAD/FMN as a cofactor and NAD(P)H as electron donor. Some contain 4Fe-4S cluster to transfer electron from FAD to FMN. The specific function of this group is unknown. 233 matched cddid_all.tbl CDD cd02922 cd02922 239238 FCB2_FMN Flavocytochrome b2 (FCB2) FMN-binding domain. FCB2 (AKA L-lactate:cytochrome c oxidoreductase) is a respiratory enzyme located in the intermembrane space of fungal mitochondria which catalyzes the oxidation of L-lactate to pyruvate. FCB2 also participates in a short electron-transport chain involving cytochrome c and cytochrome oxidase which ultimately directs the reducing equivalents gained from L-lactate oxidation to oxygen, yielding one molecule of ATP for every L-lactate molecule consumed. FCB2 is composed of 2 domains: a C-terminal flavin-binding domain, which includes the active site for lacate oxidation, and an N-terminal b2-cytochrome domain, required for efficient cytochrome c reduction. FCB2 is a homotetramer and contains two noncovalently bound cofactors, FMN and heme per subunit. 344 matched cddid_all.tbl CDD cd02929 cd02929 239239 TMADH_HD_FMN Trimethylamine dehydrogenase (TMADH) and histamine dehydrogenase (HD) FMN-binding domain. TMADH is an iron-sulfur flavoprotein that catalyzes the oxidative demethylation of trimethylamine to form dimethylamine and formaldehyde. The protein forms a symetrical dimer with each subunit containing one 4Fe-4S cluster and one FMN cofactor. It contains a unique flavin, in the form of a 6-S-cysteinyl FMN which is bent by ~25 degrees along the N5-N10 axis of the flavin isoalloxazine ring. This modification of the conformation of the flavin is thought to facilitate catalysis.The closely related histamine dehydrogenase catalyzes oxidative deamination of histamine. 370 matched cddid_all.tbl CDD cd02930 cd02930 239240 DCR_FMN 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the flavin and iron-sulfur cofactors. Metabolism of unsaturated fatty acids requires auxiliary enzymes in addition to those used in b-oxidation. After a given number of cycles through the b-oxidation pathway, those unsaturated fatty acyl-CoAs with double bonds at even-numbered carbon positions contain 2-trans, 4-cis double bonds that can not be modified by enoyl-CoA hydratase. DCR utilizes NADPH to remove the C4-C5 double bond. DCR can catalyze the reduction of both natural fatty acids with cis double bonds, as well as substrates containing trans double bonds. The reaction is initiated by hybrid transfer from NADPH to FAD, which in turn transfers electrons, one at a time, to FMN via the 4Fe-4S cluster. The fully reduced FMN provides a hydrid ion to the C5 atom of substrate, and Tyr and His are proposed to form a catalytic dyad that protonates the C4 atom of the substrate and completes the reaction. 353 matched cddid_all.tbl CDD cd02931 cd02931 239241 ER_like_FMN Enoate reductase (ER)-like FMN-binding domain. Enoate reductase catalyzes the NADH-dependent reduction of carbon-carbon double bonds of several molecules, including nonactivated 2-enoates, alpha,beta-unsaturated aldehydes, cyclic ketones, and methylketones. ERs are similar to 2,4-dienoyl-CoA reductase from E. coli and to the old yellow enzyme from Saccharomyces cerevisiae. 382 matched cddid_all.tbl CDD cd02932 cd02932 239242 OYE_YqiM_FMN Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent. The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs. 336 matched cddid_all.tbl CDD cd02933 cd02933 239243 OYE_like_FMN Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Members of OYE family include 12-oxophytodienoate reductase, pentaerythritol tetranitrate reductase, morphinone reductase, and related enzymes. 338 matched cddid_all.tbl CDD cd02940 cd02940 239244 DHPD_FMN Dihydropyrimidine dehydrogenase (DHPD) FMN-binding domain. DHPD catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. DHPD contains two FAD, two FMN, and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass the dimer interface twice. Two of the Fe-S clusters show a hitherto unobserved coordination involving a glutamine residue. 299 matched cddid_all.tbl CDD cd02947 cd02947 239245 TRX_family TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox state of target proteins via the reversible oxidation of an active site dithiol, present in a CXXC motif, partially exposed at the protein's surface. TRX reduces protein disulfide bonds, resulting in a disulfide bond at its active site. Oxidized TRX is converted to the active form by TRX reductase, using reducing equivalents derived from either NADPH or ferredoxins. By altering their redox state, TRX regulates the functions of at least 30 target proteins, some of which are enzymes and transcription factors. It also plays an important role in the defense against oxidative stress by directly reducing hydrogen peroxide and certain radicals, and by serving as a reductant for peroxiredoxins. At least two major types of functional TRXs have been reported in most organisms; in eukaryotes, they are located in the cytoplasm and the mitochondria. Higher plants contain more types (at least 20 TRX genes have been detected in the genome of Arabidopsis thaliana), two of which (types f amd m) are located in the same compartment, the chloroplast. Also included in the alignment are TRX-like domains which show sequence homology to TRX but do not contain the redox active CXXC motif. Group II proteins, in addition to either a redox active TRX or a TRX-like domain, also contain additional domains, which may or may not possess homology to known proteins. 93 matched cddid_all.tbl CDD cd02948 cd02948 239246 TRX_NDPK TRX domain, TRX and NDP-kinase (NDPK) fusion protein family; most members of this group are fusion proteins which contain one redox active TRX domain containing a CXXC motif and three NDPK domains, and are characterized as intermediate chains (ICs) of axonemal outer arm dynein. Dyneins are molecular motors that generate force against microtubules to produce cellular movement, and are divided into two classes: axonemal and cytoplasmic. They are supramolecular complexes consisting of three protein groups classified according to size: dynein heavy, intermediate and light chains. Axonemal dyneins form two structures, the inner and outer arms, which are attached to doublet microtubules throughout the cilia and flagella. The human homolog is the sperm-specific Sptrx-2, presumed to be a component of the human sperm axoneme architecture. Included in this group is another human protein, TRX-like protein 2, a smaller fusion protein containing one TRX and one NDPK domain, which is also associated with microtubular structures. The other members of this group are hypothetical insect proteins containing a TRX domain and outer arm dynein light chains (14 and 16kDa) of Chlamydomonas reinhardtii. Using standard assays, the fusion proteins have shown no TRX enzymatic activity. 102 matched cddid_all.tbl CDD cd02949 cd02949 239247 TRX_NTR TRX domain, novel NADPH thioredoxin reductase (NTR) family; composed of fusion proteins found only in oxygenic photosynthetic organisms containing both TRX and NTR domains. The TRX domain functions as a protein disulfide reductase via the reversible oxidation of an active center dithiol present in a CXXC motif, while the NTR domain functions as a reductant to oxidized TRX. The fusion protein is bifunctional, showing both TRX and NTR activities, but it is not an independent NTR/TRX system. In plants, the protein is found exclusively in shoots and mature leaves and is localized in the chloroplast. It is involved in plant protection against oxidative stress. 97 matched cddid_all.tbl CDD cd02950 cd02950 239248 TxlA TRX-like protein A (TxlA) family; TxlA was originally isolated from the cyanobacterium Synechococcus. It is found only in oxygenic photosynthetic organisms. TRX is a small enzyme that participate in redox reactions, via the reversible oxidation of an active site dithiol present in a CXXC motif. Disruption of the txlA gene suggests that the protein is involved in the redox regulation of the structure and function of photosynthetic apparatus. The plant homolog (designated as HCF164) is localized in the chloroplast and is involved in the assembly of the cytochrome b6f complex, which takes a central position in photosynthetic electron transport. 142 matched cddid_all.tbl CDD cd02951 cd02951 239249 SoxW SoxW family; SoxW is a bacterial periplasmic TRX, containing a redox active CXXC motif, encoded by a genetic locus (sox operon) involved in thiosulfate oxidation. Sulfur bacteria oxidize sulfur compounds to provide reducing equivalents for carbon dioxide fixation during autotrophic growth and the respiratory electron transport chain. It is unclear what the role of SoxW is, since it has been found to be dispensable in the oxidation of thiosulfate to sulfate. SoxW is specifically kept in the reduced state by SoxV, which is essential in thiosulfate oxidation. 125 matched cddid_all.tbl CDD cd02952 cd02952 239250 TRP14_like Human TRX-related protein 14 (TRP14)-like family; composed of proteins similar to TRP14, a 14kD cytosolic protein that shows disulfide reductase activity in vitro with a different substrate specificity compared with another human cytosolic protein, TRX1. TRP14 catalyzes the reduction of small disulfide-containing peptides but does not reduce disulfides of ribonucleotide reductase, peroxiredoxin and methionine sulfoxide reductase, which are TRX1 substrates. TRP14 also plays a role in tumor necrosis factor (TNF)-alpha signaling pathways, distinct from that of TRX1. Its depletion promoted TNF-alpha induced activation of c-Jun N-terminal kinase and mitogen-activated protein kinases. 119 matched cddid_all.tbl CDD cd02953 cd02953 239251 DsbDgamma DsbD gamma family; DsbD gamma is the C-terminal periplasmic domain of the bacterial protein DsbD. It contains a CXXC motif in a TRX fold and shuttles the reducing potential from the membrane domain (DsbD beta) to the N-terminal periplasmic domain (DsbD alpha). DsbD beta, a transmembrane domain comprising of eight helices, acquires its reducing potential from the cytoplasmic thioredoxin. DsbD alpha transfers the acquired reducing potential from DsbD gamma to target proteins such as the periplasmic protein disulphide isomerases, DsbC and DsbG. This flow of reducing potential from the cytoplasm through DsbD allows DsbC and DsbG to act as isomerases in the oxidizing environment of the bacterial periplasm. DsbD also transfers reducing potential from the cytoplasm to specific reductases in the periplasm which are involved in the maturation of cytochromes. 104 matched cddid_all.tbl CDD cd02954 cd02954 239252 DIM1 Dim1 family; Dim1 is also referred to as U5 small nuclear ribonucleoprotein particle (snRNP)-specific 15kD protein. It is a component of U5 snRNP, which pre-assembles with U4/U6 snRNPs to form a [U4/U6:U5] tri-snRNP complex required for pre-mRNA splicing. Dim1 interacts with multiple splicing-associated proteins, suggesting that it functions at multiple control points in the splicing of pre-mRNA as part of a large spliceosomal complex involving many protein-protein interactions. U5 snRNP contains seven core proteins (common to all snRNPs) and nine U5-specific proteins, one of which is Dim1. Dim1 adopts a thioredoxin fold but does not contain the redox active CXXC motif. It is essential for G2/M phase transition, as a consequence to its role in pre-mRNA splicing. 114 matched cddid_all.tbl CDD cd02955 cd02955 239253 SSP411 TRX domain, SSP411 protein family; members of this family are highly conserved proteins present in eukaryotes, bacteria and archaea, about 600-800 amino acids in length, which contain a TRX domain with a redox active CXXC motif. The human/rat protein, called SSP411, is specifically expressed in the testis in an age-dependent manner. The SSP411 mRNA is increased during spermiogenesis and is localized in round and elongated spermatids, suggesting a function in fertility regulation. 124 matched cddid_all.tbl CDD cd02956 cd02956 239254 ybbN ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria. 96 matched cddid_all.tbl CDD cd02957 cd02957 239255 Phd_like Phosducin (Phd)-like family; composed of Phd and Phd-like proteins (PhLP), characterized as cytosolic regulators of G protein functions. Phd and PhLPs specifically bind G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane and impeding G protein-mediated signal transduction by inhibiting the formation of a functional G protein trimer (G protein alphabetagamma). Phd also inhibits the GTPase activity of G protein alpha. Phd can be phosphorylated by protein kinase A and G protein-coupled receptor kinase 2, leading to its inactivation. Phd was originally isolated from the retina, where it is highly expressed and has been implicated to play an important role in light adaptation. It is also found in the pineal gland, liver, spleen, striated muscle and the brain. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain. Also included in this family is a PhLP characterized as a viral inhibitor of apoptosis (IAP)-associated factor, named VIAF, that functions in caspase activation during apoptosis. 113 matched cddid_all.tbl CDD cd02958 cd02958 239256 UAS UAS family; UAS is a domain of unknown function. Most members of this family are uncharacterized proteins with similarity to FAS-associated factor 1 (FAF1) and ETEA because of the presence of a UAS domain N-terminal to a ubiquitin-associated UBX domain. FAF1 is a longer protein, compared to the other members of this family, having additional N-terminal domains, a ubiquitin-associated UBA domain and a nuclear targeting domain. FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. ETEA is the protein product of a highly expressed gene in T-cells and eosinophils of atopic dermatitis patients. The presence of the ubiquitin-associated UBX domain in the proteins of this family suggests the possibility of their involvement in ubiquitination. Recently, FAF1 has been shown to interact with valosin-containing protein (VCP), which is involved in the ubiquitin-proteosome pathway. Some members of this family are uncharacterized proteins containing only a UAS domain. 114 matched cddid_all.tbl CDD cd02959 cd02959 239257 ERp19 Endoplasmic reticulum protein 19 (ERp19) family; ERp19 is also known as ERp18, a protein located in the ER containing one redox active TRX domain. Denaturation studies indicate that the reduced form is more stable than the oxidized form, suggesting that the protein is involved in disulfide bond formation. In vitro, ERp19 has been shown to possess thiol-disulfide oxidase activity which is dependent on the presence of both active site cysteines. Although described as protein disulfide isomerase (PDI)-like, the protein does not complement for PDI activity. ERp19 shows a wide tissue distribution but is most abundant in liver, testis, heart and kidney. 117 matched cddid_all.tbl CDD cd02960 cd02960 239258 AGR Anterior Gradient (AGR) family; members of this family are similar to secreted proteins encoded by the cement gland-specific genes XAG-1 and XAG-2, expressed in the anterior region of dorsal ectoderm of Xenopus. They are implicated in the formation of the cement gland and the induction of forebrain fate. The human homologs, hAG-2 and hAG-3, are secreted proteins associated with estrogen-positive breast tumors. Yeast two-hybrid studies identified the metastasis-associated C4.4a protein and dystroglycan as binding partners, indicating possible roles in the development and progression of breast cancer. hAG-2 has also been implicated in prostate cancer. Its gene was cloned as an androgen-inducible gene and it was shown to be overexpressed in prostate cancer cells at the mRNA and protein levels. AGR proteins contain one conserved cysteine corresponding to the first cysteine in the CXXC motif of TRX. They show high sequence similarity to ERp19. 130 matched cddid_all.tbl CDD cd02961 cd02961 239259 PDI_a_family Protein Disulfide Isomerase (PDIa) family, redox active TRX domains; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants. Members of this family include PDI and PDI-related proteins like ERp72, ERp57 (or ERp60), ERp44, P5, PDIR, ERp46 and the transmembrane PDIs. PDI, ERp57, ERp72, P5, PDIR and ERp46 are all oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. These proteins usually contain multiple copies of a redox active TRX (a) domain containing a CXXC motif, and may also contain one or more redox inactive TRX-like (b) domains. Only one a domain is required for the oxidase function but multiple copies are necessary for the isomerase function. The different types of PDIs may show different substrate specificities and tissue-specific expression, or may be induced by stress. PDIs are in their reduced form at steady state and are oxidized to the active form by Ero1, which is localized in the ER through ERp44. Some members of this family also contain a DnaJ domain in addition to the redox active a domains; examples are ERdj5 and Pfj2. Also included in the family is the redox inactive N-terminal TRX-like domain of ERp29. 101 matched cddid_all.tbl CDD cd02962 cd02962 239260 TMX2 TMX2 family; composed of proteins similar to human TMX2, a 372-amino acid TRX-related transmembrane protein, identified and characterized through the cloning of its cDNA from a human fetal library. It contains a TRX domain but the redox active CXXC motif is replaced with SXXC. Sequence analysis predicts that TMX2 may be a Type I membrane protein, with its C-terminal half protruding on the luminal side of the endoplasmic reticulum (ER). In addition to the TRX domain, transmembrane region and ER-retention signal, TMX2 also contains a Myb DNA-binding domain repeat signature and a dileucine motif in the tail. 152 matched cddid_all.tbl CDD cd02963 cd02963 239261 TRX_DnaJ TRX domain, DnaJ domain containing protein family; composed of uncharacterized proteins of about 500-800 amino acids, containing an N-terminal DnaJ domain followed by one redox active TRX domain. DnaJ is a member of the 40 kDa heat-shock protein (Hsp40) family of molecular chaperones, which regulate the activity of Hsp70s. TRX is involved in the redox regulation of many protein substrates through the reduction of disulfide bonds. TRX has been implicated to catalyse the reduction of Hsp33, a chaperone holdase that binds to unfolded protein intermediates. The presence of DnaJ and TRX domains in members of this family suggests that they could be involved in a redox-regulated chaperone network. 111 matched cddid_all.tbl CDD cd02964 cd02964 239262 TryX_like_family Tryparedoxin (TryX)-like family; composed of TryX and related proteins including nucleoredoxin (NRX), rod-derived cone viability factor (RdCVF) and the nematode homolog described as a 16-kD class of TRX. Most members of this family, except RdCVF, are protein disulfide oxidoreductases containing an active site CXXC motif, similar to TRX. 132 matched cddid_all.tbl CDD cd02965 cd02965 239263 HyaE HyaE family; HyaE is also called HupG and HoxO. They are proteins serving a critical role in the assembly of multimeric [NiFe] hydrogenases, the enzymes that catalyze the oxidation of molecular hydrogen to enable microorganisms to utilize hydrogen as the sole energy source. The E. coli HyaE protein is a chaperone that specifically interacts with the twin-arginine translocation (Tat) signal peptide of the [NiFe] hydrogenase-1 beta subunit precursor. Tat signal peptides target precursor proteins to the Tat protein export system, which facilitates the transport of fully folded proteins across the inner membrane. HyaE may be involved in regulating the traffic of [NiFe] hydrogenase-1 on the Tat transport pathway. 111 matched cddid_all.tbl CDD cd02966 cd02966 239264 TlpA_like_family TlpA-like family; composed of TlpA, ResA, DsbE and similar proteins. TlpA, ResA and DsbE are bacterial protein disulfide reductases with important roles in cytochrome maturation. They are membrane-anchored proteins with a soluble TRX domain containing a CXXC motif located in the periplasm. The TRX domains of this family contain an insert, approximately 25 residues in length, which correspond to an extra alpha helix and a beta strand when compared with TRX. TlpA catalyzes an essential reaction in the biogenesis of cytochrome aa3, while ResA and DsbE are essential proteins in cytochrome c maturation. Also included in this family are proteins containing a TlpA-like TRX domain with domain architectures similar to E. coli DipZ protein, and the N-terminal TRX domain of PilB protein from Neisseria which acts as a disulfide reductase that can recylce methionine sulfoxide reductases. 116 matched cddid_all.tbl CDD cd02967 cd02967 239265 mauD Methylamine utilization (mau) D family; mauD protein is the translation product of the mauD gene found in methylotrophic bacteria, which are able to use methylamine as a sole carbon source and a nitrogen source. mauD is an essential accessory protein for the biosynthesis of methylamine dehydrogenase (MADH), the enzyme that catalyzes the oxidation of methylamine and other primary amines. MADH possesses an alpha2beta2 subunit structure; the alpha subunit is also referred to as the large subunit. Each beta (small) subunit contains a tryptophan tryptophylquinone (TTQ) prosthetic group. Accessory proteins are essential for the proper transport of MADH to the periplasm, TTQ synthesis and the formation of several structural disulfide bonds. Bacterial mutants containing an insertion on the mauD gene were unable to grow on methylamine as a sole carbon source, were found to lack the MADH small subunit and had decreased amounts of the MADH large subunit. 114 matched cddid_all.tbl CDD cd02968 cd02968 239266 SCO SCO (an acronym for Synthesis of Cytochrome c Oxidase) family; composed of proteins similar to Sco1, a membrane-anchored protein possessing a soluble domain with a TRX fold. Members of this family are required for the proper assembly of cytochrome c oxidase (COX). They contain a metal binding motif, typically CXXXC, which is located in a flexible loop. COX, the terminal enzyme in the respiratory chain, is imbedded in the inner mitochondrial membrane of all eukaryotes and in the plasma membrane of some prokaryotes. It is composed of two subunits, COX I and COX II. It has been proposed that Sco1 specifically delivers copper to the CuA site, a dinuclear copper center, of the COX II subunit. Mutations in human Sco1 and Sco2 cause fatal infantile hepatoencephalomyopathy and cardioencephalomyopathy, respectively. Both disorders are associated with severe COX deficiency in affected tissues. More recently, it has been argued that the redox sensitivity of the copper binding properties of Sco1 implies that it participates in signaling events rather than functioning as a chaperone that transfers copper to COX II. 142 matched cddid_all.tbl CDD cd02969 cd02969 239267 PRX_like1 Peroxiredoxin (PRX)-like 1 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a conserved cysteine that aligns to the first cysteine in the CXXC motif of TRX. This does not correspond to the peroxidatic cysteine found in PRXs, which aligns to the second cysteine in the CXXC motif of TRX. In addition, these proteins do not contain the other two conserved residues of the catalytic triad of PRX. PRXs confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. 171 matched cddid_all.tbl CDD cd02970 cd02970 239268 PRX_like2 Peroxiredoxin (PRX)-like 2 family; hypothetical proteins that show sequence similarity to PRXs. Members of this group contain a CXXC motif, similar to TRX. The second cysteine in the motif corresponds to the peroxidatic cysteine of PRX, however, these proteins do not contain the other two residues of the catalytic triad of PRX. PRXs confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. TRXs alter the redox state of target proteins by catalyzing the reduction of their disulfide bonds via the CXXC motif using reducing equivalents derived from either NADPH or ferredoxins. 149 matched cddid_all.tbl CDD cd02971 cd02971 239269 PRX_family Peroxiredoxin (PRX) family; composed of the different classes of PRXs including many proteins originally known as bacterioferritin comigratory proteins (BCP), based on their electrophoretic mobility before their function was identified. PRXs are thiol-specific antioxidant (TSA) proteins also known as TRX peroxidases and alkyl hydroperoxide reductase C22 (AhpC) proteins. They confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either TRX, glutathione, trypanothione and AhpF. They are distinct from other peroxidases in that they have no cofactors such as metals or prosthetic groups. The first step of catalysis, common to all PRXs, is the nucleophilic attack by the catalytic cysteine (also known as the peroxidatic cysteine) on the peroxide leading to cleavage of the oxygen-oxygen bond and the formation of a cysteine sulfenic acid intermediate. The second step of the reaction, the resolution of the intermediate, distinguishes the different types of PRXs. The presence or absence of a second cysteine (the resolving cysteine) classifies PRXs as either belonging to the 2-cys or 1-cys type. The resolving cysteine of 2-cys PRXs is either on the same chain (atypical) or on the second chain (typical) of a functional homodimer. Structural and motif analysis of this growing family supports the need for a new classification system. The peroxidase activity of PRXs is regulated in vivo by irreversible cysteine over-oxidation into a sulfinic acid, phosphorylation and limited proteolysis. 140 matched cddid_all.tbl CDD cd02972 cd02972 239270 DsbA_family DsbA family; consists of DsbA and DsbA-like proteins, including DsbC, DsbG, glutathione (GSH) S-transferase kappa (GSTK), 2-hydroxychromene-2-carboxylate (HCCA) isomerase, an oxidoreductase (FrnE) presumed to be involved in frenolicin biosynthesis, a 27-kDa outer membrane protein, and similar proteins. Members of this family contain a redox active CXXC motif (except GSTK and HCCA isomerase) imbedded in a TRX fold, and an alpha helical insert of about 75 residues (shorter in DsbC and DsbG) relative to TRX. DsbA is involved in the oxidative protein folding pathway in prokaryotes, catalyzing disulfide bond formation of proteins secreted into the bacterial periplasm. DsbC and DsbG function as protein disulfide isomerases and chaperones to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins. 98 matched cddid_all.tbl CDD cd02973 cd02973 239271 TRX_GRX_like Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All members contain a redox-active CXXC motif and may function as PDOs. The archaeal proteins Mj0307 and Mt807 show structures more similar to GRX, but activities more similar to TRX. Some members of the family are similar to PfPDO in that they contain a second CXXC motif located in a second TRX-fold subdomain at the N-terminus; the superimposable N- and C-terminal TRX subdomains form a compact structure. PfPDO is postulated to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI). The C-terminal CXXC motif of PfPDO is required for its oxidase, reductase and isomerase activities. Also included in the family is the C-terminal TRX-fold subdomain of the N-terminal domain (NTD) of bacterial AhpF, which has a similar fold as PfPDO with two TRX-fold subdomains but without the second CXXC motif. 67 matched cddid_all.tbl CDD cd02974 cd02974 239272 AhpF_NTD_N Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) family, N-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which in turn catalyzes the reduction of hydrogen peroxide and organic hydroperoxides. AhpF contains an NTD forming two contiguous TRX-fold subdomain similar to Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). It also contains a catalytic core similar to TRX reductase containing FAD and NADH binding domains with an active site disulfide. The proposed mechanism of action of AhpF is similar to a TRX/TRX reductase system. The flow of reducing equivalents goes from NADH -> catalytic core of AhpF -> NTD of AhpF -> AhpC -> peroxide substrates. The N-terminal TRX-fold subdomain of AhpF NTD is redox inactive, but is proposed to contain an important residue that aids in the catalytic function of the redox-active CXXC motif contained in the C-terminal TRX-fold subdomain. 94 matched cddid_all.tbl CDD cd02975 cd02975 239273 PfPDO_like_N Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO)-like family, N-terminal TRX-fold subdomain; composed of proteins with similarity to PfPDO, a redox active thermostable protein believed to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI), which are both involved in oxidative protein folding. PfPDO contains two redox active CXXC motifs in two contiguous TRX-fold subdomains. The active site in the N-terminal TRX-fold subdomain is required for isomerase but not for reductase activity of PfPDO. The exclusive presence of PfPDO-like proteins in extremophiles may suggest that they have a special role in adaptation to extreme conditions. 113 matched cddid_all.tbl CDD cd02976 cd02976 239274 NrdH NrdH-redoxin (NrdH) family; NrdH is a small monomeric protein with a conserved redox active CXXC motif within a TRX fold, characterized by a glutaredoxin (GRX)-like sequence and TRX-like activity profile. In vitro, it displays protein disulfide reductase activity that is dependent on TRX reductase, not glutathione (GSH). It is part of the NrdHIEF operon, where NrdEF codes for class Ib ribonucleotide reductase (RNR-Ib), an efficient enzyme at low oxygen levels. Under these conditions when GSH is mostly conjugated to spermidine, NrdH can still function and act as a hydrogen donor for RNR-Ib. It has been suggested that the NrdHEF system may be the oldest RNR reducing system, capable of functioning in a microaerophilic environment, where GSH was not yet available. NrdH from Corynebacterium ammoniagenes can form domain-swapped dimers, although it is unknown if this happens in vivo. Domain-swapped dimerization, which results in the blocking of the TRX reductase binding site, could be a mechanism for regulating the oxidation state of the protein. 73 matched cddid_all.tbl CDD cd02977 cd02977 239275 ArsC_family Arsenate Reductase (ArsC) family; composed of TRX-fold arsenic reductases and similar proteins including the transcriptional regulator, Spx. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX), through a single catalytic cysteine. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases. Spx is a general regulator that exerts negative and positive control over transcription initiation by binding to the C-terminal domain of the alpha subunit of RNA polymerase. 105 matched cddid_all.tbl CDD cd02978 cd02978 239276 KaiB_like KaiB-like family; composed of the circadian clock proteins, KaiB and the N-terminal KaiB-like sensory domain of SasA. KaiB is an essential protein in maintaining circadian rhythm. It was originally discovered from the cyanobacterium Synechococcus as part of the circadian clock gene cluster, kaiABC. KaiB attenuates KaiA-enhanced KaiC autokinase activity by interacting with KaiA-KaiC complexes in a circadian fashion. KaiB is membrane-associated as well as cytosolic. The amount of membrane-associated protein peaks in the evening (at circadian time (CT) 12-16) while the cytosolic form peaks later (at CT 20). The rhythmic localization of KaiB may function in regulating the formation of Kai complexes. SasA is a sensory histidine kinase which associates with KaiC. Although it is not an essential oscillator component, it is important in enhancing kaiABC expression and is important in metabolic growth control under day/night cycle conditions. SasA contains an N-terminal sensory domain with a TRX fold which is involved in the SasA-KaiC interaction. This domain shows high sequence similarity with KaiB. However, the KaiB structure does not show a classical TRX fold. The N-terminal half of KaiB shares the same beta-alpha-beta topology as TRX, but the topology of its C-terminal half diverges. 72 matched cddid_all.tbl CDD cd02979 cd02979 239277 PHOX_C FAD-dependent Phenol hydoxylase (PHOX) family, C-terminal TRX-fold domain; composed of proteins similar to PHOX from the aerobic topsoil yeast Trichosporon cutaneum. PHOX is a flavoprotein monooxygenase that catalyzes the hydroxylation of phenol and simple phenol derivatives in the ortho position with the consumption of NADPH and oxygen. This is the first step in the biodegradation and detoxification of phenolic compounds. PHOX contains three domains. The substrate and FAD/NAD(P) binding sites are contained in the first two domains, which adopt a complicated folding pattern. The third or C-terminal domain contains a TRX fold and is involved in dimerization. The functional unit of PHOX is a dimer, although active tetramers of the recombinant enzyme can be isolated when overproduced in bacteria. 167 matched cddid_all.tbl CDD cd02980 cd02980 239278 TRX_Fd_family Thioredoxin (TRX)-like [2Fe-2S] Ferredoxin (Fd) family; composed of [2Fe-2S] Fds with a TRX fold (TRX-like Fds) and proteins containing domains similar to TRX-like Fd including formate dehydrogenases, NAD-reducing hydrogenases and the subunit E of NADH:ubiquinone oxidoreductase (NuoE). TRX-like Fds are soluble low-potential electron carriers containing a single [2Fe-2S] cluster. The exact role of TRX-like Fd is still unclear. It has been suggested that it may be involved in nitrogen fixation. Its homologous domains in large redox enzymes (such as Nuo and hydrogenases) function as electron carriers. 77 matched cddid_all.tbl CDD cd02981 cd02981 239279 PDI_b_family Protein Disulfide Isomerase (PDIb) family, redox inactive TRX-like domain b; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants. Members of this family include PDI, calsequestrin and other PDI-related proteins like ERp72, ERp57, ERp44 and PDIR. PDI, ERp57 (or ERp60), ERp72 and PDIR are all oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. These proteins contain multiple copies of a redox active TRX (a) domain containing a CXXC motif, and one or more redox inactive TRX-like (b) domains. The molecular structure of PDI is abb'a'. Also included in this family is the PDI-related protein ERp27, which contains only redox-inactive TRX-like (b and b') domains. The redox inactive b domains are implicated in substrate recognition. 97 matched cddid_all.tbl CDD cd02982 cd02982 239280 PDI_b'_family Protein Disulfide Isomerase (PDIb') family, redox inactive TRX-like domain b'; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants. Members of this family include PDI, calsequestrin and other PDI-related proteins like ERp72, ERp57 (or ERp60), ERp44, P5 and PDIR. PDI, ERp57, ERp72, P5 and PDIR are all oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. These proteins contain multiple copies of a redox active TRX (a) domain containing a CXXC motif, and one or more redox inactive TRX-like (b) domains. The molecular structure of PDI is abb'a'. Also included in this family is the PDI-related protein ERp27, which contains only redox-inactive TRX-like (b and b') domains. The redox inactive domains are implicated in substrate recognition with the b' domain serving as the primary substrate binding site. Only the b' domain is necessary for the binding of small peptide substrates. In addition to the b' domain, other domains are required for the binding of larger polypeptide substrates. The b' domain is also implicated in chaperone activity. 103 matched cddid_all.tbl CDD cd02983 cd02983 239281 P5_C P5 family, C-terminal redox inactive TRX-like domain; P5 is a protein disulfide isomerase (PDI)-related protein with a domain structure of aa'b (where a and a' are redox active TRX domains and b is a redox inactive TRX-like domain). Like PDI, P5 is located in the endoplasmic reticulum (ER) and displays both isomerase and chaperone activities, which are independent of each other. Compared to PDI, the isomerase and chaperone activities of P5 are lower. The first cysteine in the CXXC motif of both redox active domains in P5 is necessary for isomerase activity. The P5 gene was first isolated as an amplified gene from a hydroxyurea-resistant hamster cell line. The zebrafish P5 homolog has been implicated to play a critical role in establishing left/right asymmetries in the embryonic midline. The C-terminal domain is likely involved in substrate binding, similar to the b and b' domains of PDI. 130 matched cddid_all.tbl CDD cd02984 cd02984 239282 TRX_PICOT TRX domain, PICOT (for PKC-interacting cousin of TRX) subfamily; PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes. PICOT contains an N-terminal TRX-like domain, which does not contain the catalytic CXXC motif, followed by one to three glutaredoxin domains. The TRX-like domain is required for interaction with PKC theta. PICOT inhibits the activation of c-Jun N-terminal kinase and the transcription factors, AP-1 and NF-kB, induced by PKC theta or T-cell activating stimuli. 97 matched cddid_all.tbl CDD cd02985 cd02985 239283 TRX_CDSP32 TRX family, chloroplastic drought-induced stress protein of 32 kD (CDSP32); CDSP32 is composed of two TRX domains, a C-terminal TRX domain which contains a redox active CXXC motif and an N-terminal TRX-like domain which contains an SXXS sequence instead of the redox active motif. CDSP32 is a stress-inducible TRX, i.e., it acts as a TRX by reducing protein disulfides and is induced by environmental and oxidative stress conditions. It plays a critical role in plastid defense against oxidative damage, a role related to its function as a physiological electron donor to BAS1, a plastidic 2-cys peroxiredoxin. Plants lacking CDSP32 exhibit decreased photosystem II photochemical efficiencies and chlorophyll retention compared to WT controls, as well as an increased proportion of BAS1 in its overoxidized monomeric form. 103 matched cddid_all.tbl CDD cd02986 cd02986 239284 DLP Dim1 family, Dim1-like protein (DLP) subfamily; DLP is a novel protein which shares 38% sequence identity to Dim1. Like Dim1, it is also implicated in pre-mRNA splicing and cell cycle progression. DLP is located in the nucleus and has been shown to interact with the U5 small nuclear ribonucleoprotein particle (snRNP)-specific 102kD protein (or Prp6). Dim1 protein, also known as U5 snRNP-specific 15kD protein is a component of U5 snRNP, which pre-assembles with U4/U6 snRNPs to form a [U4/U6:U5] tri-snRNP complex required for pre-mRNA splicing. Dim1 adopts a thioredoxin fold but does not contain the redox active CXXC motif. 114 matched cddid_all.tbl CDD cd02987 cd02987 239285 Phd_like_Phd Phosducin (Phd)-like family, Phd subfamily; Phd is a cytosolic regulator of G protein functions. It specifically binds G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane. This impedes the formation of a functional G protein trimer (G protein alphabetagamma), thereby inhibiting G protein-mediated signal transduction. Phd also inhibits the GTPase activity of G protein alpha. Phd can be phosphorylated by protein kinase A and G protein-coupled receptor kinase 2, leading to its inactivation. Phd was originally isolated from the retina, where it is highly expressed and has been implicated to play an important role in light adaptation. It is also found in the pineal gland, liver, spleen, striated muscle and the brain. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain. 175 matched cddid_all.tbl CDD cd02988 cd02988 239286 Phd_like_VIAF Phosducin (Phd)-like family, Viral inhibitor of apoptosis (IAP)-associated factor (VIAF) subfamily; VIAF is a Phd-like protein that functions in caspase activation during apoptosis. It was identified as an IAP binding protein through a screen of a human B-cell library using a prototype IAP. VIAF lacks a consensus IAP binding motif and while it does not function as an IAP antagonist, it still plays a regulatory role in the complete activation of caspases. VIAF itself is a substrate for IAP-mediated ubiquitination, suggesting that it may be a target of IAPs in the prevention of cell death. The similarity of VIAF to Phd points to a potential role distinct from apoptosis regulation. Phd functions as a cytosolic regulator of G protein by specifically binding to G protein betagamma (Gbg)-subunits. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain. 192 matched cddid_all.tbl CDD cd02989 cd02989 239287 Phd_like_TxnDC9 Phosducin (Phd)-like family, Thioredoxin (TRX) domain containing protein 9 (TxnDC9) subfamily; composed of predominantly uncharacterized eukaryotic proteins, containing a TRX-like domain without the redox active CXXC motif. The gene name for the human protein is TxnDC9. The two characterized members are described as Phd-like proteins, PLP1 of Saccharomyces cerevisiae and PhLP3 of Dictyostelium discoideum. Gene disruption experiments show that both PLP1 and PhLP3 are non-essential proteins. Unlike Phd and most Phd-like proteins, members of this group do not contain the Phd N-terminal helical domain which is implicated in binding to the G protein betagamma subunit. 113 matched cddid_all.tbl CDD cd02990 cd02990 239288 UAS_FAF1 UAS family, FAS-associated factor 1 (FAF1) subfamily; FAF1 contains a UAS domain of unknown function N-terminal to a ubiquitin-associated UBX domain. FAF1 also contains ubiquitin-associated UBA and nuclear targeting domains, N-terminal to the UAS domain. FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. It is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kB (NF-kB) by interfering with the nuclear translocation of the p65 subunit. FAF1 also interacts with valosin-containing protein (VCP), which is involved in the ubiquitin-proteosome pathway. 136 matched cddid_all.tbl CDD cd02991 cd02991 239289 UAS_ETEA UAS family, ETEA subfamily; composed of proteins similar to human ETEA protein, the translation product of a highly expressed gene in the T-cells and eosinophils of atopic dermatitis patients compared with those of normal individuals. ETEA shows homology to Fas-associated factor 1 (FAF1); both containing UAS and UBX (ubiquitin-associated) domains. Compared to FAF1, however, ETEA lacks the ubiquitin-associated UBA domain and a nuclear targeting domain. The function of ETEA is still unknown. A yeast two-hybrid assay showed that it can interact with Fas. Because of its homology to FAF1, it is postulated that ETEA could be involved in modulating Fas-mediated apoptosis of T-cells and eosinophils of atopic dermatitis patients, making them more resistant to apoptosis. 116 matched cddid_all.tbl CDD cd02992 cd02992 239290 PDI_a_QSOX PDIa family, Quiescin-sulfhydryl oxidase (QSOX) subfamily; QSOX is a eukaryotic protein containing an N-terminal redox active TRX domain, similar to that of PDI, and a small C-terminal flavin adenine dinucleotide (FAD)-binding domain homologous to the yeast ERV1p protein. QSOX oxidizes thiol groups to disulfides like PDI, however, unlike PDI, this oxidation is accompanied by the reduction of oxygen to hydrogen peroxide. QSOX is localized in high concentrations in cells with heavy secretory load and prefers peptides and proteins as substrates, not monothiols like glutathione. Inside the cell, QSOX is found in the endoplasmic reticulum and Golgi. The flow of reducing equivalents in a QSOX-catalyzed reaction goes from the dithiol substrate -> dithiol of the QSOX TRX domain -> dithiols of the QSOX ERV1p domain -> FAD -> oxygen. 114 matched cddid_all.tbl CDD cd02993 cd02993 239291 PDI_a_APS_reductase PDIa family, 5'-Adenylylsulfate (APS) reductase subfamily; composed of plant-type APS reductases containing a C-terminal redox active TRX domain and an N-terminal reductase domain which is part of a superfamily that includes N type ATP PPases. APS reductase catalyzes the reduction of activated sulfate to sulfite, a key step in the biosynthesis of sulfur-containing metabolites. Sulfate is first activated by ATP sulfurylase, forming APS, which can be phosphorylated to 3'-phosphoadenosine-5'-phosphosulfate (PAPS). Depending on the organism, either APS or PAPS can be used for sulfate reduction. Prokaryotes and fungi use PAPS, whereas plants use both APS and PAPS. Since plant-type APS reductase uses glutathione (GSH) as its electron donor, the C-terminal domain may function like glutaredoxin, a GSH-dependent member of the TRX superfamily. The flow of reducing equivalents goes from GSH -> C-terminal TRX domain -> N-terminal reductase domain -> APS. Plant-type APS reductase shows no homology to that of dissimilatory sulfate-reducing bacteria, which is an iron-sulfur flavoenzyme. Also included in the alignment is EYE2 from Chlamydomonas reinhardtii, a protein required for eyespot assembly. 109 matched cddid_all.tbl CDD cd02994 cd02994 239292 PDI_a_TMX PDIa family, TMX subfamily; composed of proteins similar to the TRX-related human transmembrane protein, TMX. TMX is a type I integral membrane protein; the N-terminal redox active TRX domain is present in the endoplasmic reticulum (ER) lumen while the C-terminus is oriented towards the cytoplasm. It is expressed in many cell types and its active site motif (CPAC) is unique. In vitro, TMX reduces interchain disulfides of insulin and renatures inactive RNase containing incorrect disulfide bonds. The C. elegans homolog, DPY-11, is expressed only in the hypodermis and resides in the cytoplasm. It is required for body and sensory organ morphogeneis. Another uncharacterized TRX-related transmembrane protein, human TMX4, is included in the alignment. The active site sequence of TMX4 is CPSC. 101 matched cddid_all.tbl CDD cd02995 cd02995 239293 PDI_a_PDI_a'_C "PDIa family, C-terminal TRX domain (a') subfamily; composed of the C-terminal redox active a' domains of PDI, ERp72, ERp57 (or ERp60) and EFP1. PDI, ERp72 and ERp57 are endoplasmic reticulum (ER)-resident eukaryotic proteins involved in oxidative protein folding. They are oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. PDI and ERp57 have the abb'a' domain structure (where a and a' are redox active TRX domains while b and b' are redox inactive TRX-like domains). PDI also contains an acidic region (c domain) after the a' domain that is absent in ERp57. ERp72 has an additional a domain at the N-terminus (a""abb'a' domain structure). ERp57 interacts with the lectin chaperones, calnexin and calreticulin, and specifically promotes the oxidative folding of glycoproteins, while PDI shows a wider substrate specificity. ERp72 associates with several ER chaperones and folding factors to form complexes in the ER that bind nascent proteins. EFP1 is a binding partner protein of thyroid oxidase, which is responsible for the generation of hydrogen peroxide, a crucial substrate of thyroperoxidase, which functions to iodinate thyroglobulin and synthesize thyroid hormones." 104 matched cddid_all.tbl CDD cd02996 cd02996 239294 PDI_a_ERp44 PDIa family, endoplasmic reticulum protein 44 (ERp44) subfamily; ERp44 is an ER-resident protein, induced during stress, involved in thiol-mediated ER retention. It contains an N-terminal TRX domain, similar to that of PDIa, with a CXFS motif followed by two redox inactive TRX-like domains, homologous to the b and b' domains of PDI. The CXFS motif in the N-terminal domain allows ERp44 to form stable reversible mixed disulfides with its substrates. Through this activity, ERp44 mediates the ER localization of Ero1alpha, a protein that oxidizes protein disulfide isomerases into their active form. ERp44 also prevents the secretion of unassembled cargo protein with unpaired cysteines. It also modulates the activity of inositol 1,4,5-triphosphate type I receptor (IP3R1), an intracellular channel protein that mediates calcium release from the ER to the cytosol. 108 matched cddid_all.tbl CDD cd02997 cd02997 239295 PDI_a_PDIR PDIa family, PDIR subfamily; composed of proteins similar to human PDIR (for Protein Disulfide Isomerase Related). PDIR is composed of three redox active TRX (a) domains and an N-terminal redox inactive TRX-like (b) domain. Similar to PDI, it is involved in oxidative protein folding in the endoplasmic reticulum (ER) through its isomerase and chaperone activities. These activities are lower compared to PDI, probably due to PDIR acting only on a subset of proteins. PDIR is preferentially expressed in cells actively secreting proteins and its expression is induced by stress. Similar to PDI, the isomerase and chaperone activities of PDIR are independent; CXXC mutants lacking isomerase activity retain chaperone activity. 104 matched cddid_all.tbl CDD cd02998 cd02998 239296 PDI_a_ERp38 PDIa family, endoplasmic reticulum protein 38 (ERp38) subfamily; composed of proteins similar to the P5-like protein first isolated from alfalfa, which contains two redox active TRX (a) domains at the N-terminus, like human P5, and a C-terminal domain with homology to the C-terminal domain of ERp29, unlike human P5. The cDNA clone of this protein (named G1) was isolated from an alfalfa cDNA library by screening with human protein disulfide isomerase (PDI) cDNA. The G1 protein is constitutively expressed in all major organs of the plant and its expression is induced by treatment with tunicamycin, indicating that it may be a glucose-regulated protein. The G1 homolog in the eukaryotic social amoeba Dictyostelium discoideum is also described as a P5-like protein, which is located in the endoplasmic reticulum (ER) despite the absence of an ER-retrieval signal. G1 homologs from Aspergillus niger and Neurospora crassa have also been characterized, and are named TIGA and ERp38, respectively. Also included in the alignment is an atypical PDI from Leishmania donovani containing a single a domain, and the C-terminal a domain of a P5-like protein from Entamoeba histolytica. 105 matched cddid_all.tbl CDD cd02999 cd02999 239297 PDI_a_ERp44_like PDIa family, endoplasmic reticulum protein 44 (ERp44)-like subfamily; composed of uncharacterized PDI-like eukaryotic proteins containing only one redox active TRX (a) domain with a CXXS motif, similar to ERp44. CXXS is still a redox active motif; however, the mixed disulfide formed with the substrate is more stable than those formed by CXXC motif proteins. PDI-related proteins are usually involved in the oxidative protein folding in the ER by acting as catalysts and folding assistants. ERp44 is involved in thiol-mediated retention in the ER. 100 matched cddid_all.tbl CDD cd03000 cd03000 239298 PDI_a_TMX3 PDIa family, TMX3 subfamily; composed of eukaryotic proteins similar to human TMX3, a TRX related transmembrane protein containing one redox active TRX domain at the N-terminus and a classical ER retrieval sequence for type I transmembrane proteins at the C-terminus. The TMX3 transcript is found in a variety of tissues with the highest levels detected in skeletal muscle and the heart. In vitro, TMX3 showed oxidase activity albeit slightly lower than that of protein disulfide isomerase. 104 matched cddid_all.tbl CDD cd03001 cd03001 239299 PDI_a_P5 PDIa family, P5 subfamily; composed of eukaryotic proteins similar to human P5, a PDI-related protein with a domain structure of aa'b (where a and a' are redox active TRX domains and b is a redox inactive TRX-like domain). Like PDI, P5 is located in the endoplasmic reticulum (ER) and displays both isomerase and chaperone activities, which are independent of each other. Compared to PDI, the isomerase and chaperone activities of P5 are lower. The first cysteine in the CXXC motif of both redox active domains in P5 is necessary for isomerase activity. The P5 gene was first isolated as an amplified gene from a hydroxyurea-resistant hamster cell line. The zebrafish P5 homolog has been implicated to play a critical role in establishing left/right asymmetries in the embryonic midline. Some members of this subfamily are P5-like proteins containing only one redox active TRX domain. 103 matched cddid_all.tbl CDD cd03002 cd03002 239300 PDI_a_MPD1_like PDI family, MPD1-like subfamily; composed of eukaryotic proteins similar to Saccharomyces cerevisiae MPD1 protein, which contains a single redox active TRX domain located at the N-terminus, and an ER retention signal at the C-terminus indicative of an ER-resident protein. MPD1 has been shown to suppress the maturation defect of carboxypeptidase Y caused by deletion of the yeast PDI1 gene. Other characterized members of this subfamily include the Aspergillus niger prpA protein and Giardia PDI-1. PrpA is non-essential to strain viability, however, its transcript level is induced by heterologous protein expression suggesting a possible role in oxidative protein folding during high protein production. Giardia PDI-1 has the ability to refold scrambled RNase and exhibits transglutaminase activity. 109 matched cddid_all.tbl CDD cd03003 cd03003 239301 PDI_a_ERdj5_N PDIa family, N-terminal ERdj5 subfamily; ERdj5, also known as JPDI and macrothioredoxin, is a protein containing an N-terminal DnaJ domain and four redox active TRX domains. This subfamily is comprised of the first TRX domain of ERdj5 located after the DnaJ domain at the N-terminal half of the protein. ERdj5 is a ubiquitous protein localized in the endoplasmic reticulum (ER) and is abundant in secretory cells. It's transcription is induced during ER stress. It interacts with BiP through its DnaJ domain in an ATP-dependent manner. BiP, an ER-resident member of the Hsp70 chaperone family, functions in ER-associated degradation and protein translocation. 101 matched cddid_all.tbl CDD cd03004 cd03004 239302 PDI_a_ERdj5_C PDIa family, C-terminal ERdj5 subfamily; ERdj5, also known as JPDI and macrothioredoxin, is a protein containing an N-terminal DnaJ domain and four redox active TRX domains. This subfamily is composed of the three TRX domains located at the C-terminal half of the protein. ERdj5 is a ubiquitous protein localized in the endoplasmic reticulum (ER) and is abundant in secretory cells. It's transcription is induced during ER stress. It interacts with BiP through its DnaJ domain in an ATP-dependent manner. BiP, an ER-resident member of the Hsp70 chaperone family, functions in ER-associated degradation and protein translocation. Also included in the alignment is the single complete TRX domain of an uncharacterized protein from Tetraodon nigroviridis, which also contains a DnaJ domain at its N-terminus. 104 matched cddid_all.tbl CDD cd03005 cd03005 239303 PDI_a_ERp46 PDIa family, endoplasmic reticulum protein 46 (ERp46) subfamily; ERp46 is an ER-resident protein containing three redox active TRX domains. Yeast complementation studies show that ERp46 can substitute for protein disulfide isomerase (PDI) function in vivo. It has been detected in many tissues, however, transcript and protein levels do not correlate in all tissues, suggesting regulation at a posttranscriptional level. An identical protein, named endoPDI, has been identified as an endothelial PDI that is highly expressed in the endothelium of tumors and hypoxic lesions. It has a protective effect on cells exposed to hypoxia. 102 matched cddid_all.tbl CDD cd03006 cd03006 239304 PDI_a_EFP1_N PDIa family, N-terminal EFP1 subfamily; EFP1 is a binding partner protein of thyroid oxidase (ThOX), also called Duox. ThOX proteins are responsible for the generation of hydrogen peroxide, a crucial substrate of thyroperoxidase, which functions to iodinate thyroglobulin and synthesize thyroid hormones. EFP1 was isolated through a yeast two-hybrid method using the EF-hand fragment of dog Duox1 as a bait. It could be one of the partners in the assembly of a multiprotein complex constituting the thyroid hydrogen peroxide generating system. EFP1 contains two TRX domains related to the redox active TRX domains of protein disulfide isomerase (PDI). This subfamily is composed of the N-terminal TRX domain of EFP1, which contains a CXXS sequence in place of the typical CXXC motif, similar to ERp44. The CXXS motif allows the formation of stable mixed disulfides, crucial for the ER-retention function of ERp44. 113 matched cddid_all.tbl CDD cd03007 cd03007 239305 PDI_a_ERp29_N PDIa family, endoplasmic reticulum protein 29 (ERp29) subfamily; ERp29 is a ubiquitous ER-resident protein expressed in high levels in secretory cells. It forms homodimers and higher oligomers in vitro and in vivo. It contains a redox inactive TRX-like domain at the N-terminus, which is homologous to the redox active TRX (a) domains of PDI, and a C-terminal helical domain similar to the C-terminal domain of P5. The expression profile of ERp29 suggests a role in secretory protein production distinct from that of PDI. It has also been identified as a member of the thyroglobulin folding complex. The Drosophila homolog, Wind, is the product of windbeutel, an essential gene in the development of dorsal-ventral patterning. Wind is required for correct targeting of Pipe, a Golgi-resident type II transmembrane protein with homology to 2-O-sulfotransferase. 116 matched cddid_all.tbl CDD cd03008 cd03008 239306 TryX_like_RdCVF Tryparedoxin (TryX)-like family, Rod-derived cone viability factor (RdCVF) subfamily; RdCVF is a thioredoxin (TRX)-like protein specifically expressed in photoreceptors. RdCVF was isolated and identified as a factor that supports cone survival in retinal cultures. Cone photoreceptor loss is responsible for the visual handicap resulting from the inherited disease, retinitis pigmentosa. RdCVF shows 33% similarity to TRX but does not exhibit any detectable thiol oxidoreductase activity. 146 matched cddid_all.tbl CDD cd03009 cd03009 239307 TryX_like_TryX_NRX Tryparedoxin (TryX)-like family, TryX and nucleoredoxin (NRX) subfamily; TryX and NRX are thioredoxin (TRX)-like protein disulfide oxidoreductases that alter the redox state of target proteins via the reversible oxidation of an active center CXXC motif. TryX is involved in the regulation of oxidative stress in parasitic trypanosomatids by reducing TryX peroxidase, which in turn catalyzes the reduction of hydrogen peroxide and organic hydroperoxides. TryX derives reducing equivalents from reduced trypanothione, a polyamine peptide conjugate unique to trypanosomatids, which is regenerated by the NADPH-dependent flavoprotein trypanothione reductase. Vertebrate NRX is a 400-amino acid nuclear protein with one redox active TRX domain containing a CPPC active site motif followed by one redox inactive TRX-like domain. Mouse NRX transcripts are expressed in all adult tissues but is restricted to the nervous system and limb buds in embryos. Plant NRX, longer than the vertebrate NRX by about 100-200 amino acids, is a nuclear protein containing a redox inactive TRX-like domain between two redox active TRX domains. Both vertebrate and plant NRXs show thiol oxidoreductase activity in vitro. Their localization in the nucleus suggests a role in the redox regulation of nuclear proteins such as transcription factors. 131 matched cddid_all.tbl CDD cd03010 cd03010 239308 TlpA_like_DsbE TlpA-like family, DsbE (also known as CcmG and CycY) subfamily; DsbE is a membrane-anchored, periplasmic TRX-like reductase containing a CXXC motif that specifically donates reducing equivalents to apocytochrome c via CcmH, another cytochrome c maturation (Ccm) factor with a redox active CXXC motif. Assembly of cytochrome c requires the ligation of heme to reduced thiols of the apocytochrome. In bacteria, this assembly occurs in the periplasm. The reductase activity of DsbE in the oxidizing environment of the periplasm is crucial in the maturation of cytochrome c. 127 matched cddid_all.tbl CDD cd03011 cd03011 239309 TlpA_like_ScsD_MtbDsbE TlpA-like family, suppressor for copper sensitivity D protein (ScsD) and actinobacterial DsbE homolog subfamily; composed of ScsD, the DsbE homolog of Mycobacterium tuberculosis (MtbDsbE) and similar proteins, all containing a redox-active CXXC motif. The Salmonella typhimurium ScsD is a thioredoxin-like protein which confers copper tolerance to copper-sensitive mutants of E. coli. MtbDsbE has been characterized as an oxidase in vitro, catalyzing the disulfide bond formation of substrates like hirudin. The reduced form of MtbDsbE is more stable than its oxidized form, consistent with an oxidase function. This is in contrast to the function of DsbE from gram-negative bacteria which is a specific reductase of apocytochrome c. 123 matched cddid_all.tbl CDD cd03012 cd03012 239310 TlpA_like_DipZ_like TlpA-like family, DipZ-like subfamily; composed uncharacterized proteins containing a TlpA-like TRX domain. Some members show domain architectures similar to that of E. coli DipZ protein (also known as DsbD). The only eukaryotic members of the TlpA family belong to this subfamily. TlpA is a disulfide reductase known to have a crucial role in the biogenesis of cytochrome aa3. 126 matched cddid_all.tbl CDD cd03013 cd03013 239311 PRX5_like Peroxiredoxin (PRX) family, PRX5-like subfamily; members are similar to the human protein, PRX5, a homodimeric TRX peroxidase, widely expressed in tissues and found cellularly in mitochondria, peroxisomes and the cytosol. The cellular location of PRX5 suggests that it may have an important antioxidant role in organelles that are major sources of reactive oxygen species (ROS), as well as a role in the control of signal transduction. PRX5 has been shown to reduce hydrogen peroxide, alkyl hydroperoxides and peroxynitrite. As with all other PRXs, the N-terminal peroxidatic cysteine of PRX5 is oxidized into a sulfenic acid intermediate upon reaction with peroxides. Human PRX5 is able to resolve this intermediate by forming an intramolecular disulfide bond with its C-terminal cysteine (the resolving cysteine), which can then be reduced by TRX, just like an atypical 2-cys PRX. This resolving cysteine, however, is not conserved in other members of the subfamily. In such cases, it is assumed that the oxidized cysteine is directly resolved by an external small-molecule or protein reductant, typical of a 1-cys PRX. In the case of the H. influenza PRX5 hybrid, the resolving glutaredoxin domain is on the same protein chain as PRX. PRX5 homodimers show an A-type interface, similar to atypical 2-cys PRXs. 155 matched cddid_all.tbl CDD cd03014 cd03014 239312 PRX_Atyp2cys Peroxiredoxin (PRX) family, Atypical 2-cys PRX subfamily; composed of PRXs containing peroxidatic and resolving cysteines, similar to the homodimeric thiol specific antioxidant (TSA) protein also known as TRX-dependent thiol peroxidase (Tpx). Tpx is a bacterial periplasmic peroxidase which differs from other PRXs in that it shows substrate specificity toward alkyl hydroperoxides over hydrogen peroxide. As with all other PRXs, the peroxidatic cysteine (N-terminal) of Tpx is oxidized into a sulfenic acid intermediate upon reaction with peroxides. Tpx is able to resolve this intermediate by forming an intramolecular disulfide bond with a conserved C-terminal cysteine (the resolving cysteine), which can then be reduced by thioredoxin. This differs from the typical 2-cys PRX which resolves the oxidized cysteine by forming an intermolecular disulfide bond with the resolving cysteine from the other subunit of the homodimer. Atypical 2-cys PRX homodimers have a loop-based interface (A-type for alternate), in contrast with the B-type interface of typical 2-cys and 1-cys PRXs. 143 matched cddid_all.tbl CDD cd03015 cd03015 239313 PRX_Typ2cys Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides. The functional unit of typical 2-cys PRX is a homodimer. A unique intermolecular redox-active disulfide center is utilized for its activity. Upon reaction with peroxides, its peroxidatic cysteine is oxidized into a sulfenic acid intermediate which is resolved by bonding with the resolving cysteine from the other subunit of the homodimer. This intermolecular disulfide bond is then reduced by thioredoxin, tryparedoxin or AhpF. Typical 2-cys PRXs, like 1-cys PRXs, form decamers which are stabilized by reduction of the active site cysteine. Typical 2-cys PRX interacts through beta strands at one edge of the monomer (B-type interface) to form the functional homodimer, and uses an A-type interface (similar to the dimeric interface in atypical 2-cys PRX and PRX5) at the opposite end of the monomer to form the stable decameric (pentamer of dimers) structure. 173 matched cddid_all.tbl CDD cd03016 cd03016 239314 PRX_1cys Peroxiredoxin (PRX) family, 1-cys PRX subfamily; composed of PRXs containing only one conserved cysteine, which serves as the peroxidatic cysteine. They are homodimeric thiol-specific antioxidant (TSA) proteins that confer a protective role in cells by reducing and detoxifying hydrogen peroxide, peroxynitrite, and organic hydroperoxides. As with all other PRXs, a cysteine sulfenic acid intermediate is formed upon reaction of 1-cys PRX with its substrates. Having no resolving cysteine, the oxidized enzyme is resolved by an external small-molecule or protein reductant such as thioredoxin or glutaredoxin. Similar to typical 2-cys PRX, 1-cys PRX forms a functional dimeric unit with a B-type interface, as well as a decameric structure which is stabilized in the reduced form of the enzyme. Other oligomeric forms, tetramers and hexamers, have also been reported. Mammalian 1-cys PRX is localized cellularly in the cytosol and is expressed at high levels in brain, eye, testes and lung. The seed-specific plant 1-cys PRXs protect tissues from reactive oxygen species during desiccation and are also called rehydrins. 203 matched cddid_all.tbl CDD cd03017 cd03017 239315 PRX_BCP Peroxiredoxin (PRX) family, Bacterioferritin comigratory protein (BCP) subfamily; composed of thioredoxin-dependent thiol peroxidases, widely expressed in pathogenic bacteria, that protect cells against toxicity from reactive oxygen species by reducing and detoxifying hydroperoxides. The protein was named BCP based on its electrophoretic mobility before its function was known. BCP shows substrate selectivity toward fatty acid hydroperoxides rather than hydrogen peroxide or alkyl hydroperoxides. BCP contains the peroxidatic cysteine but appears not to possess a resolving cysteine (some sequences, not all, contain a second cysteine but its role is still unknown). Unlike other PRXs, BCP exists as a monomer. The plant homolog of BCP is PRX Q, which is expressed only in leaves and is cellularly localized in the chloroplasts and the guard cells of stomata. Also included in this subfamily is the fungal nuclear protein, Dot5p (for disrupter of telomere silencing protein 5), which functions as an alkyl-hydroperoxide reductase during post-diauxic growth. 140 matched cddid_all.tbl CDD cd03018 cd03018 239316 PRX_AhpE_like Peroxiredoxin (PRX) family, AhpE-like subfamily; composed of proteins similar to Mycobacterium tuberculosis AhpE. AhpE is described as a 1-cys PRX because of the absence of a resolving cysteine. The structure and sequence of AhpE, however, show greater similarity to 2-cys PRXs than 1-cys PRXs. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. The first step of catalysis is the nucleophilic attack by the peroxidatic cysteine on the peroxide leading to the formation of a cysteine sulfenic acid intermediate. The absence of a resolving cysteine suggests that functional AhpE is regenerated by an external reductant. The solution behavior and crystal structure of AhpE show that it forms dimers and octamers. 149 matched cddid_all.tbl CDD cd03019 cd03019 239317 DsbA_DsbA DsbA family, DsbA subfamily; DsbA is a monomeric thiol disulfide oxidoreductase protein containing a redox active CXXC motif imbedded in a TRX fold. It is involved in the oxidative protein folding pathway in prokaryotes, and is the strongest thiol oxidant known, due to the unusual stability of the thiolate anion form of the first cysteine in the CXXC motif. The highly unstable oxidized form of DsbA directly donates disulfide bonds to reduced proteins secreted into the bacterial periplasm. This rapid and unidirectional process helps to catalyze the folding of newly-synthesized polypeptides. To regain catalytic activity, reduced DsbA is then reoxidized by the membrane protein DsbB, which generates its disulfides from oxidized quinones, which in turn are reoxidized by the electron transport chain. 178 matched cddid_all.tbl CDD cd03020 cd03020 239318 DsbA_DsbC_DsbG DsbA family, DsbC and DsbG subfamily; V-shaped homodimeric proteins containing a redox active CXXC motif imbedded in a TRX fold. They function as protein disulfide isomerases and chaperones in the bacterial periplasm to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins. DsbC and DsbG are kept in their reduced state by the cytoplasmic membrane protein DsbD, which utilizes the TRX/TRX reductase system in the cytosol as a source of reducing equivalents. DsbG differ from DsbC in that it has a more limited substrate specificity, and it may preferentially act later in the folding process to catalyze disulfide rearrangements in folded or partially folded proteins. Also included in the alignment is the predicted protein TrbB, whose gene was sequenced from the enterohemorrhagic E. coli type IV pilus gene cluster, which is required for efficient plasmid transfer. 197 matched cddid_all.tbl CDD cd03021 cd03021 239319 DsbA_GSTK DsbA family, Glutathione (GSH) S-transferase Kappa (GSTK) subfamily; GSTK is a member of the GST family of enzymes which catalyzes the transfer of the thiol of GSH to electrophilic substrates. It is specifically located in the mitochondria and peroxisomes, unlike other members of the canonical GST family, which are mainly cytosolic. The biological substrates of GSTK are not yet known. It is presumed to have a protective role during respiration when large amounts of reactive oxygen species are generated. GSTK has the same general fold as DsbA, consisting of a thioredoxin domain interrupted by an alpha-helical domain and its biological unit is a homodimer. GSTK is closely related to the bacterial enzyme, 2-hydroxychromene-2-carboxylate (HCCA) isomerase. It shows little sequence similarity to the other members of the GST family. 209 matched cddid_all.tbl CDD cd03022 cd03022 239320 DsbA_HCCA_Iso DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1,2-dihydroxynapthalene by a dioxygenase, into cis-o-hydroxybenzylidenepyruvate (cHBPA). This is the fourth reaction in a six-step pathway that converts napthalene into salicylate. HCCA isomerase is unique to bacteria that degrade polycyclic aromatic compounds. It is closely related to the eukaryotic protein, GSH transferase kappa (GSTK). 192 matched cddid_all.tbl CDD cd03023 cd03023 239321 DsbA_Com1_like DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown. 154 matched cddid_all.tbl CDD cd03024 cd03024 239322 DsbA_FrnE DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins. 201 matched cddid_all.tbl CDD cd03025 cd03025 239323 DsbA_FrnE_like DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins. 193 matched cddid_all.tbl CDD cd03026 cd03026 239324 AhpF_NTD_C TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then reduces hydrogen peroxide and organic hydroperoxides. AhpF contains an NTD containing two contiguous TRX-fold subdomains similar to Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). It also contains a catalytic core similar to TRX reductase containing FAD and NADH binding domains with an active site disulfide. The proposed mechanism of action of AhpF is similar to a TRX/TRX reductase system. The flow of reducing equivalents goes from NADH -> catalytic core of AhpF -> NTD of AhpF -> AhpC -> peroxide substrates. The catalytic CXXC motif of the NTD of AhpF is contained in its C-terminal TRX subdomain. 89 matched cddid_all.tbl CDD cd03027 cd03027 239325 GRX_DEP Glutaredoxin (GRX) family, Dishevelled, Egl-10, and Pleckstrin (DEP) subfamily; composed of uncharacterized proteins containing a GRX domain and additional domains DEP and DUF547, both of which have unknown functions. GRX is a glutathione (GSH) dependent reductase containing a redox active CXXC motif in a TRX fold. It has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. By altering the redox state of target proteins, GRX is involved in many cellular functions. 73 matched cddid_all.tbl CDD cd03028 cd03028 239326 GRX_PICOT_like Glutaredoxin (GRX) family, PKC-interacting cousin of TRX (PICOT)-like subfamily; composed of PICOT and GRX-PICOT-like proteins. The non-PICOT members of this family contain only the GRX-like domain, whereas PICOT contains an N-terminal TRX-like domain followed by one to three GRX-like domains. It is interesting to note that PICOT from plants contain three repeats of the GRX-like domain, metazoan proteins (except for insect) have two repeats, while fungal sequences contain only one copy of the domain. PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes. PICOT inhibits the activation of c-Jun N-terminal kinase and the transcription factors, AP-1 and NF-kB, induced by PKC theta or T-cell activating stimuli. Both GRX and TRX domains of PICOT are required for its activity. Characterized non-PICOT members of this family include CXIP1, a CAX-interacting protein in Arabidopsis thaliana, and PfGLP-1, a GRX-like protein from Plasmodium falciparum. 90 matched cddid_all.tbl CDD cd03029 cd03029 239327 GRX_hybridPRX5 Glutaredoxin (GRX) family, PRX5 hybrid subfamily; composed of hybrid proteins containing peroxiredoxin (PRX) and GRX domains, which is found in some pathogenic bacteria and cyanobacteria. PRXs are thiol-specific antioxidant (TSA) proteins that confer a protective antioxidant role in cells through their peroxidase activity in which hydrogen peroxide, peroxynitrate, and organic hydroperoxides are reduced and detoxified using reducing equivalents derived from either thioredoxin, glutathione, trypanothione and AhpF. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins. PRX-GRX hybrid proteins from Haemophilus influenza and Neisseria meningitis exhibit GSH-dependent peroxidase activity. The flow of reducing equivalents in the catalytic cycle of the hybrid protein goes from NADPH -> GSH reductase -> GSH -> GRX domain of hybrid -> PRX domain of hybrid -> peroxide substrate. 72 matched cddid_all.tbl CDD cd03030 cd03030 239328 GRX_SH3BGR Glutaredoxin (GRX) family, SH3BGR (SH3 domain binding glutamic acid-rich protein) subfamily; a recently-identified subfamily composed of SH3BGR and similar proteins possessing significant sequence similarity to GRX, but without a redox active CXXC motif. The SH3BGR gene was cloned in an effort to identify genes mapping to chromosome 21, which could be involved in the pathogenesis of congenital heart disease affecting Down syndrome newborns. Several human SH3BGR-like (SH3BGRL) genes have been identified since, mapping to different locations in the chromosome. Of these, SH3BGRL3 was identified as a tumor necrosis factor (TNF) alpha inhibitory protein and was also named TIP-B1. Upregulation of expression of SH3BGRL3 is associated with differentiation. It has been suggested that it functions as a regulator of differentiation-related signal transduction pathways. 92 matched cddid_all.tbl CDD cd03031 cd03031 239329 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive. 147 matched cddid_all.tbl CDD cd03032 cd03032 239330 ArsC_Spx Arsenate Reductase (ArsC) family, Spx subfamily; Spx is a unique RNA polymerase (RNAP)-binding protein present in bacilli and some mollicutes. It inhibits transcription by binding to the C-terminal domain of the alpha subunit of RNAP, disrupting complex formation between RNAP and certain transcriptional activator proteins like ResD and ComA. In response to oxidative stress, Spx can also activate transcription, making it a general regulator that exerts both positive and negative control over transcription initiation. Spx has been shown to exert redox-sensitive transcriptional control over genes like trxA (TRX) and trxB (TRX reductase), genes that function in thiol homeostasis. This redox-sensitive activity is dependent on the presence of a CXXC motif, present in some members of the Spx subfamily, that acts as a thiol/disulfide switch. Spx has also been shown to repress genes in a sulfate-dependent manner independent of the presence of the CXXC motif. 115 matched cddid_all.tbl CDD cd03033 cd03033 239331 ArsC_15kD Arsenate Reductase (ArsC) family, 15kD protein subfamily; composed of proteins of unknown function with similarity to thioredoxin-fold arsenic reductases, ArsC. It is encoded by an ORF present in a gene cluster associated with nitrogen fixation that also encodes dinitrogenase reductase ADP-ribosyltransferase (DRAT) and dinitrogenase reductase activating glycohydrolase (DRAG). ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via glutaredoxin, through a single catalytic cysteine. 113 matched cddid_all.tbl CDD cd03034 cd03034 239332 ArsC_ArsC Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the detoxification of arsenic, using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX). ArsC contains a single catalytic cysteine, within a thioredoxin fold, that forms a covalent thiolate-As(V) intermediate, which is reduced by GRX through a mixed GSH-arsenate intermediate. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases. 112 matched cddid_all.tbl CDD cd03035 cd03035 239333 ArsC_Yffb Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine suggest that it is likely to function as a glutathione (GSH)-dependent thiol reductase. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from GSH via glutaredoxin, through a single catalytic cysteine. 105 matched cddid_all.tbl CDD cd03036 cd03036 239334 ArsC_like Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC. Proteins containing a redox active CXXC motif like TRX and glutaredoxin (GRX) function as protein disulfide oxidoreductases, altering the redox state of target proteins via the reversible oxidation of the active site dithiol. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via GRX, through a single catalytic cysteine. 111 matched cddid_all.tbl CDD cd03037 cd03037 239335 GST_N_GRX2 GST_N family, Glutaredoxin 2 (GRX2) subfamily; composed of bacterial proteins similar to E. coli GRX2, an atypical GRX with a molecular mass of about 24kD, compared with other GRXs which are 9-12kD in size. GRX2 adopts a GST fold containing an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain. It contains a redox active CXXC motif located in the N-terminal domain but is not able to reduce ribonucleotide reductase like other GRXs. However, it catalyzes GSH-dependent protein disulfide reduction of other substrates efficiently. GRX2 is thought to function primarily in catalyzing the reversible glutathionylation of proteins in cellular redox regulation including stress responses. 71 matched cddid_all.tbl CDD cd03038 cd03038 239336 GST_N_etherase_LigE GST_N family, Beta etherase LigE subfamily; composed of proteins similar to Sphingomonas paucimobilis beta etherase, LigE, a GST-like protein that catalyzes the cleavage of the beta-aryl ether linkages present in low-moleculer weight lignins using GSH as the hydrogen donor. This reaction is an essential step in the degradation of lignin, a complex phenolic polymer that is the most abundant aromatic material in the biosphere. The beta etherase activity of LigE is enantioselective and it complements the activity of the other GST family beta etherase, LigF. 84 matched cddid_all.tbl CDD cd03039 cd03039 239337 GST_N_Sigma_like GST_N family, Class Sigma_like; composed of GSTs belonging to class Sigma and similar proteins, including GSTs from class Mu, Pi and Alpha. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. Vertebrate class Sigma GSTs are characterized as GSH-dependent hematopoietic prostaglandin (PG) D synthases and are responsible for the production of PGD2 by catalyzing the isomerization of PGH2. The functions of PGD2 include the maintenance of body temperature, inhibition of platelet aggregation, bronchoconstriction, vasodilation and mediation of allergy and inflammation. Other class Sigma members include the class II insect GSTs, S-crystallins from cephalopods and 28-kDa GSTs from parasitic flatworms. Drosophila GST2 is associated with indirect flight muscle and exhibits preference for catalyzing GSH conjugation to lipid peroxidation products, indicating an anti-oxidant role. S-crystallin constitutes the major lens protein in cephalopod eyes and is responsible for lens transparency and proper refractive index. The 28-kDa GST from Schistosoma is a multifunctional enzyme, exhibiting GSH transferase, GSH peroxidase and PGD2 synthase activities, and may play an important role in host-parasite interactions. Also members are novel GSTs from the fungus Cunninghamella elegans, designated as class Gamma, and from the protozoan Blepharisma japonicum, described as a light-inducible GST. 72 matched cddid_all.tbl CDD cd03040 cd03040 239338 GST_N_mPGES2 GST_N family; microsomal Prostaglandin E synthase Type 2 (mPGES2) subfamily; mPGES2 is a membrane-anchored dimeric protein containing a CXXC motif which catalyzes the isomerization of PGH2 to PGE2. Unlike cytosolic PGE synthase (cPGES) and microsomal PGES Type 1 (mPGES1), mPGES2 does not require glutathione (GSH) for its activity, although its catalytic rate is increased two- to four-fold in the presence of DTT, GSH or other thiol compounds. PGE2 is widely distributed in various tissues and is implicated in the sleep/wake cycle, relaxation/contraction of smooth muscle, excretion of sodium ions, maintenance of body temperature and mediation of inflammation. mPGES2 contains an N-terminal hydrophobic domain which is membrane associated, and a C-terminal soluble domain with a GST-like structure. 77 matched cddid_all.tbl CDD cd03041 cd03041 239339 GST_N_2GST_N GST_N family, 2 repeats of the N-terminal domain of soluble GSTs (2 GST_N) subfamily; composed of uncharacterized proteins. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. 77 matched cddid_all.tbl CDD cd03042 cd03042 239340 GST_N_Zeta GST_N family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. Class Zeta GSTs, also known as maleylacetoacetate (MAA) isomerases, catalyze the isomerization of MAA to fumarylacetoacetate, the penultimate step in tyrosine/phenylalanine catabolism, using GSH as a cofactor. They show little GSH-conjugating activity towards traditional GST substrates but display modest GSH peroxidase activity. They are also implicated in the detoxification of the carcinogen dichloroacetic acid by catalyzing its dechlorination to glyoxylic acid. 73 matched cddid_all.tbl CDD cd03043 cd03043 239341 GST_N_1 GST_N family, unknown subfamily 1; composed of uncharacterized proteins, predominantly from bacteria, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. 73 matched cddid_all.tbl CDD cd03044 cd03044 239342 GST_N_EF1Bgamma GST_N family, Gamma subunit of Elongation Factor 1B (EFB1gamma) subfamily; EF1Bgamma is part of the eukaryotic translation elongation factor-1 (EF1) complex which plays a central role in the elongation cycle during protein biosynthesis. EF1 consists of two functionally distinct units, EF1A and EF1B. EF1A catalyzes the GTP-dependent binding of aminoacyl-tRNA to the ribosomal A site concomitant with the hydrolysis of GTP. The resulting inactive EF1A:GDP complex is recycled to the active GTP form by the guanine-nucleotide exchange factor EF1B, a complex composed of at least two subunits, alpha and gamma. Metazoan EFB1 contain a third subunit, beta. The EF1B gamma subunit contains a GST fold consisting of an N-terminal TRX-fold domain and a C-terminal alpha helical domain. The GST-like domain of EF1Bgamma is believed to mediate the dimerization of the EF1 complex, which in yeast is a dimer of the heterotrimer EF1A:EF1Balpha:EF1Bgamma. In addition to its role in protein biosynthesis, EF1Bgamma may also display other functions. The recombinant rice protein has been shown to possess GSH conjugating activity. The yeast EF1Bgamma binds membranes in a calcium dependent manner and is also part of a complex that binds to the msrA (methionine sulfoxide reductase) promoter suggesting a function in the regulation of its gene expression. 75 matched cddid_all.tbl CDD cd03045 cd03045 239343 GST_N_Delta_Epsilon GST_N family, Class Delta and Epsilon subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. The class Delta and Epsilon subfamily is made up primarily of insect GSTs, which play major roles in insecticide resistance by facilitating reductive dehydrochlorination of insecticides or conjugating them with GSH to produce water-soluble metabolites that are easily excreted. They are also implicated in protection against cellular damage by oxidative stress. 74 matched cddid_all.tbl CDD cd03046 cd03046 239344 GST_N_GTT1_like GST_N family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GTT1, a homodimer, exhibits GST activity with standard substrates and associates with the endoplasmic reticulum. Its expression is induced after diauxic shift and remains high throughout the stationary phase. S. pombe GST-III is implicated in the detoxification of various metals. 76 matched cddid_all.tbl CDD cd03047 cd03047 239345 GST_N_2 GST_N family, unknown subfamily 2; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. The sequence from Burkholderia cepacia was identified as part of a gene cluster involved in the degradation of 2,4,5-trichlorophenoxyacetic acid. Some GSTs (e.g. Class Zeta and Delta) are known to catalyze dechlorination reactions. 73 matched cddid_all.tbl CDD cd03048 cd03048 239346 GST_N_Ure2p_like GST_N family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p and related GSTs. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources when rich sources are available. A transmissible conformational change of Ure2p results in a prion called [Ure3], an inactive, self-propagating and infectious amyloid. Ure2p displays a GST fold containing an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. The N-terminal TRX-fold domain is sufficient to induce the [Ure3] phenotype and is also called the prion domain of Ure2p. In addition to its role in nitrogen regulation, Ure2p confers protection to cells against heavy metal ion and oxidant toxicity, and shows glutathione (GSH) peroxidase activity. Characterized GSTs in this subfamily include Aspergillus fumigatus GSTs 1 and 2, and Schizosaccharomyces pombe GST-I. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of GSH with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. 81 matched cddid_all.tbl CDD cd03049 cd03049 239347 GST_N_3 GST_N family, unknown subfamily 3; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. 73 matched cddid_all.tbl CDD cd03050 cd03050 239348 GST_N_Theta GST_N family, Class Theta subfamily; composed of eukaryotic class Theta GSTs and bacterial dichloromethane (DCM) dehalogenase. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. Mammalian class Theta GSTs show poor GSH conjugating activity towards the standard substrates, CDNB and ethacrynic acid, differentiating them from other mammalian GSTs. GSTT1-1 shows similar cataytic activity as bacterial DCM dehalogenase, catalyzing the GSH-dependent hydrolytic dehalogenation of dihalomethanes. This is an essential process in methylotrophic bacteria to enable them to use chloromethane and DCM as sole carbon and energy sources. The presence of polymorphisms in human GSTT1-1 and its relationship to the onset of diseases including cancer is subject of many studies. Human GSTT2-2 exhibits a highly specific sulfatase activity, catalyzing the cleavage of sulfate ions from aralkyl sufate esters, but not from aryl or alkyl sulfate esters. 76 matched cddid_all.tbl CDD cd03051 cd03051 239349 GST_N_GTT2_like GST_N family, Saccharomyces cerevisiae GTT2-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT2. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GTT2, a homodimer, exhibits GST activity with standard substrates. Strains with deleted GTT2 genes are viable but exhibit increased sensitivity to heat shock. 74 matched cddid_all.tbl CDD cd03052 cd03052 239350 GST_N_GDAP1 GST_N family, Ganglioside-induced differentiation-associated protein 1 (GDAP1) subfamily; GDAP1 was originally identified as a highly expressed gene at the differentiated stage of GD3 synthase-transfected cells. More recently, mutations in GDAP1 have been reported to cause both axonal and demyelinating autosomal-recessive Charcot-Marie-Tooth (CMT) type 4A neuropathy. CMT is characterized by slow and progressive weakness and atrophy of muscles. Sequence analysis of GDAP1 shows similarities and differences with GSTs; it appears to contain both N-terminal TRX-fold and C-terminal alpha helical domains of GSTs, however, it also contains additional C-terminal transmembrane domains unlike GSTs. GDAP1 is mainly expressed in neuronal cells and is localized in the mitochondria through its transmembrane domains. It does not exhibit GST activity using standard substrates. 73 matched cddid_all.tbl CDD cd03053 cd03053 239351 GST_N_Phi GST_N family, Class Phi subfamily; composed of plant-specific class Phi GSTs and related fungal and bacterial proteins. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. The class Phi GST subfamily has experience extensive gene duplication. The Arabidopsis and Oryza genomes contain 13 and 16 Phi GSTs, respectively. They are primarily responsible for herbicide detoxification together with class Tau GSTs, showing class specificity in substrate preference. Phi enzymes are highly reactive toward chloroacetanilide and thiocarbamate herbicides. Some Phi GSTs have other functions including transport of flavonoid pigments to the vacuole, shoot regeneration and GSH peroxidase activity. 76 matched cddid_all.tbl CDD cd03054 cd03054 239352 GST_N_Metaxin GST_N family, Metaxin subfamily; composed of metaxins and related proteins. Metaxin 1 is a component of a preprotein import complex of the mitochondrial outer membrane. It extends to the cytosol and is anchored to the mitochondrial membrane through its C-terminal domain. In mice, metaxin is required for embryonic development. In humans, alterations in the metaxin gene may be associated with Gaucher disease. Metaxin 2 binds to metaxin 1 and may also play a role in protein translocation into the mitochondria. Genome sequencing shows that a third metaxin gene also exists in zebrafish, Xenopus, chicken and mammals. Sequence analysis suggests that all three metaxins share a common ancestry and that they possess similarity to GSTs. Also included in the subfamily are uncharacterized proteins with similarity to metaxins, including a novel GST from Rhodococcus with toluene o-monooxygenase and glutamylcysteine synthetase activities. 72 matched cddid_all.tbl CDD cd03055 cd03055 239353 GST_N_Omega GST_N family, Class Omega subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. Class Omega GSTs show little or no GSH-conjugating activity towards standard GST substrates. Instead, they catalyze the GSH dependent reduction of protein disulfides, dehydroascorbate and monomethylarsonate, activities which are more characteristic of glutaredoxins. They contain a conserved cysteine equivalent to the first cysteine in the CXXC motif of glutaredoxins, which is a redox active residue capable of reducing GSH mixed disulfides in a monothiol mechanism. Polymorphisms of the class Omega GST genes may be associated with the development of some types of cancer and the age-at-onset of both Alzheimer's and Parkinson's diseases. 89 matched cddid_all.tbl CDD cd03056 cd03056 239354 GST_N_4 GST_N family, unknown subfamily 4; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. 73 matched cddid_all.tbl CDD cd03057 cd03057 239355 GST_N_Beta GST_N family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. Unlike mammalian GSTs which detoxify a broad range of compounds, the bacterial class Beta GSTs exhibit limited GSH conjugating activity with a narrow range of substrates. In addition to GSH conjugation, they also bind antibiotics and reduce the antimicrobial activity of beta-lactam drugs. The structure of the Proteus mirabilis enzyme reveals that the cysteine in the active site forms a covalent bond with GSH. 77 matched cddid_all.tbl CDD cd03058 cd03058 239356 GST_N_Tau GST_N family, Class Tau subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. The plant-specific class Tau GST subfamily has undergone extensive gene duplication. The Arabidopsis and Oryza genomes contain 28 and 40 Tau GSTs, respectively. They are primarily responsible for herbicide detoxification together with class Phi GSTs, showing class specificity in substrate preference. Tau enzymes are highly efficient in detoxifying diphenylether and aryloxyphenoxypropionate herbicides. In addition, Tau GSTs play important roles in intracellular signalling, biosynthesis of anthocyanin, responses to soil stresses and responses to auxin and cytokinin hormones. 74 matched cddid_all.tbl CDD cd03059 cd03059 239357 GST_N_SspA GST_N family, Stringent starvation protein A (SspA) subfamily; SspA is a RNA polymerase (RNAP)-associated protein required for the lytic development of phage P1 and for stationary phase-induced acid tolerance of E. coli. It is implicated in survival during nutrient starvation. SspA adopts the GST fold with an N-terminal TRX-fold domain and a C-terminal alpha helical domain, but it does not bind glutathione (GSH) and lacks GST activity. SspA is highly conserved among gram-negative bacteria. Related proteins found in Neisseria (called RegF), Francisella and Vibrio regulate the expression of virulence factors necessary for pathogenesis. 73 matched cddid_all.tbl CDD cd03060 cd03060 239358 GST_N_Omega_like GST_N family, Omega-like subfamily; composed of uncharacterized proteins with similarity to class Omega GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. Class Omega GSTs show little or no GSH-conjugating activity towards standard GST substrates. Instead, they catalyze the GSH dependent reduction of protein disulfides, dehydroascorbate and monomethylarsonate, activities which are more characteristic of glutaredoxins. Like Omega enzymes, proteins in this subfamily contain a conserved cysteine equivalent to the first cysteine in the CXXC motif of glutaredoxins, which is a redox active residue capable of reducing GSH mixed disulfides in a monothiol mechanism. 71 matched cddid_all.tbl CDD cd03061 cd03061 239359 GST_N_CLIC GST_N family, Chloride Intracellular Channel (CLIC) subfamily; composed of CLIC1-5, p64, parchorin and similar proteins. They are auto-inserting, self-assembling intracellular anion channels involved in a wide variety of functions including regulated secretion, cell division and apoptosis. They can exist in both water-soluble and membrane-bound states, and are found in various vesicles and membranes. Biochemical studies of the C. elegans homolog, EXC-4, show that the membrane localization domain is present in the N-terminal part of the protein. The structure of soluble human CLIC1 reveals that it is monomeric and it adopts a fold similar to GSTs, containing an N-terminal domain with a TRX fold and a C-terminal alpha helical domain. Upon oxidation, the N-terminal domain of CLIC1 undergoes a structural change to form a non-covalent dimer stabilized by the formation of an intramolecular disulfide bond between two cysteines that are far apart in the reduced form. The CLIC1 dimer bears no similarity to GST dimers. The redox-controlled structural rearrangement exposes a large hydrophobic surface, which is masked by dimerization in vitro. In vivo, this surface may represent the docking interface of CLIC1 in its membrane-bound state. The two cysteines in CLIC1 that form the disulfide bond in oxidizing conditions are essential for dimerization and chloride channel activity, however, in other subfamily members, the second cysteine is not conserved. 91 matched cddid_all.tbl CDD cd03062 cd03062 239360 TRX_Fd_Sucrase TRX-like [2Fe-2S] Ferredoxin (Fd) family, Sucrase subfamily; composed of proteins with similarity to a novel plant enzyme, isolated from potato, which contains a Fd-like domain and exhibits sucrolytic activity. The putative active site of the Fd-like domain of the enzyme contains two cysteines and two histidines for possible binding to iron-sulfur clusters, compared to four cysteines present in the active site of Fd. 97 matched cddid_all.tbl CDD cd03063 cd03063 239361 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH beta subunit contains a NADH:ubiquinone oxidoreductase (Nuo) F domain C-terminal to a Fd-like domain without the active site cysteines. The absence of conserved metal-binding residues in the putative active site suggests that members of this subfamily have lost the ability to bind iron-sulfur clusters in the N-terminal Fd-like domain. The C-terminal NuoF domain is a component of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. NuoF contains one [4Fe-4S] cluster and binds NADH and FMN. 92 matched cddid_all.tbl CDD cd03064 cd03064 239362 TRX_Fd_NuoE TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily; Nuo, also called respiratory chain Complex 1, is the entry point for electrons into the respiratory chains of bacteria and the mitochondria of eukaryotes. It is a multisubunit complex with at least 14 core subunits. It catalyzes the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane, providing the proton motive force required for energy-consuming processes. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE core subunit, also called the 24 kD subunit of Complex 1. This subfamily also include formate dehydrogenases, NiFe hydrogenases and NAD-reducing hydrogenases, that contain a NuoE domain. A subset of these proteins contain both NuoE and NuoF in a single chain. NuoF, also called the 51 kD subunit of Complex 1, contains one [4Fe-4S] cluster and also binds the NADH substrate and FMN. 80 matched cddid_all.tbl CDD cd03065 cd03065 239363 PDI_b_Calsequestrin_N PDIb family, Calsequestrin subfamily, N-terminal TRX-fold domain; Calsequestrin is the major calcium storage protein in the sarcoplasmic reticulum (SR) of skeletal and cardiac muscle. It stores calcium ions in sufficient quantities (up to 20 mM) to allow repetitive contractions and is essential to maintain movement, respiration and heart beat. A missense mutation in human cardiac calsequestrin is associated with catecholamine-induced polymorphic ventricular tachycardia (CPVT), a rare disease characterized by seizures or sudden death in response to physiologic or emotional stress. Calsequestrin is a highly acidic protein with up to 50 calcium binding sites formed simply by the clustering of two or more acidic residues. The monomer contains three redox inactive TRX-fold domains. Calsequestrin is condensed as a linear polymer in the SR lumen and is membrane-anchored through binding with intra-membrane proteins triadin, junctin and ryanodine receptor (RyR) Ca2+ release channel. In addition to its role as a calcium ion buffer, calsequestrin also regulates the activity of the RyR channel, coordinating the release of calcium ions from the SR with the loading of the calcium store. The N-terminal TRX-fold domain (or domain I) mediates front-to-front dimer interaction, an important feature in the formation of calsequestrin polymers. 120 matched cddid_all.tbl CDD cd03066 cd03066 239364 PDI_b_Calsequestrin_middle PDIb family, Calsequestrin subfamily, Middle TRX-fold domain; Calsequestrin is the major calcium storage protein in the sarcoplasmic reticulum (SR) of skeletal and cardiac muscle. It stores calcium ions in sufficient quantities (up to 20 mM) to allow repetitive contractions and is essential to maintain movement, respiration and heart beat. A missense mutation in human cardiac calsequestrin is associated with catecholamine-induced polymorphic ventricular tachycardia (CPVT), a rare disease characterized by seizures or sudden death in response to physiologic or emotional stress. Calsequestrin is a highly acidic protein with up to 50 calcium binding sites formed simply by the clustering of two or more acidic residues. The monomer contains three redox inactive TRX-fold domains. Calsequestrin is condensed as a linear polymer in the SR lumen and is membrane-anchored through binding with intra-membrane proteins triadin, junctin and ryanodine receptor (RyR) Ca2+ release channel. In addition to its role as a calcium ion buffer, calsequestrin also regulates the activity of the RyR channel, coordinating the release of calcium ions from the SR with the loading of the calcium store. 102 matched cddid_all.tbl CDD cd03067 cd03067 239365 PDI_b_PDIR_N PDIb family, PDIR subfamily, N-terminal TRX-like b domain; composed of proteins similar to human PDIR (for Protein Disulfide Isomerase Related). PDIR is composed of three redox active TRX (a) domains and an N-terminal redox inactive TRX-like (b) domain. Similar to PDI, it is involved in oxidative protein folding in the endoplasmic reticulum (ER) through its isomerase and chaperone activities. These activities are lower compared to PDI, probably due to PDIR acting only on a subset of proteins. PDIR is preferentially expressed in cells actively secreting proteins and its expression is induced by stress. Similar to PDI, the isomerase and chaperone activities of PDIR are independent; CXXC mutants lacking isomerase activity retain chaperone activity. The TRX-like b domain of PDIR is critical for its chaperone activity. 112 matched cddid_all.tbl CDD cd03068 cd03068 239366 PDI_b_ERp72 "PDIb family, ERp72 subfamily, first redox inactive TRX-like domain b; ERp72 exhibits both disulfide oxidase and reductase functions like PDI, by catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER and acting as isomerases to correct any non-native disulfide bonds. It also displays chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. ERp72 contains three redox-active TRX (a) domains and two redox inactive TRX-like (b) domains. Its molecular structure is a""abb'a', compared to the abb'a' structure of PDI. ERp72 associates with several ER chaperones and folding factors to form complexes in the ER that bind nascent proteins. Similar to PDI, the b domain of ERp72 is likely involved in binding to substrates." 107 matched cddid_all.tbl CDD cd03069 cd03069 239367 PDI_b_ERp57 PDIb family, ERp57 subfamily, first redox inactive TRX-like domain b; ERp57 (or ERp60) exhibits both disulfide oxidase and reductase functions like PDI, by catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER and acting as isomerases to correct any non-native disulfide bonds. It also displays chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. ERp57 contains two redox-active TRX (a) domains and two redox inactive TRX-like (b) domains. It shares the same domain arrangement of abb'a' as PDI, but lacks the C-terminal acid-rich region (c domain) that is present in PDI. ERp57 interacts with the lectin chaperones, calnexin and calreticulin, and specifically promotes the oxidative folding of glycoproteins. Similar to PDI, the b domain of ERp57 is likely involved in binding to substrates. 104 matched cddid_all.tbl CDD cd03070 cd03070 239368 PDI_b_ERp44 PDIb family, ERp44 subfamily, first redox inactive TRX-like domain b; ERp44 is an endoplasmic reticulum (ER)-resident protein, induced during stress, involved in thiol-mediated ER retention. It contains an N-terminal TRX domain with a CXFS motif followed by two redox inactive TRX-like domains, homologous to the b and b' domains of PDI. Through the formation of reversible mixed disulfides, ERp44 mediates the ER localization of Ero1alpha, a protein that oxidizes protein disulfide isomerases into their active form. ERp44 also prevents the secretion of unassembled cargo protein with unpaired cysteines. ERp44 also modulates the activity of inositol 1,4,5-triphosphate type I receptor (IP3R1), an intracellular channel protein that mediates calcium release from the ER to the cytosol. Similar to PDI, the b domain of ERp44 is likely involved in binding to substrates. 91 matched cddid_all.tbl CDD cd03071 cd03071 239369 PDI_b'_NRX PDIb' family, NRX subgroup, redox inactive TRX-like domain b'; composed of vertebrate nucleoredoxins (NRX). NRX is a 400-amino acid nuclear protein with one redox active TRX domain followed by one redox inactive TRX-like domain homologous to the b' domain of PDI. In vitro studies show that NRX has thiol oxidoreductase activity and that it may be involved in the redox regulation of transcription, in a manner different from that of TRX or glutaredoxin. NRX enhances the activation of NF-kB by TNFalpha, as well as PMA-1 induced AP-1 and FK-induced CREB activation. Mouse NRX transcripts are expressed in all adult tissues but is restricted to the nervous system and limb buds in embryos. The mouse NRX gene is implicated in streptozotocin-induced diabetes. Similar to PDI, the b' domain of NRX is likely involved in substrate recognition. 116 matched cddid_all.tbl CDD cd03072 cd03072 239370 PDI_b'_ERp44 PDIb' family, ERp44 subfamily, second redox inactive TRX-like domain b'; ERp44 is an endoplasmic reticulum (ER)-resident protein, induced during stress, involved in thiol-mediated ER retention. It contains an N-terminal TRX domain with a CXFS motif followed by two redox inactive TRX-like domains, homologous to the b and b' domains of PDI. Through the formation of reversible mixed disulfides, ERp44 mediates the ER localization of Ero1alpha, a protein that oxidizes protein disulfide isomerases into their active form. ERp44 also prevents the secretion of unassembled cargo protein with unpaired cysteines. ERp44 also modulates the activity of inositol 1,4,5-triphosphate type I receptor (IP3R1), an intracellular channel protein that mediates calcium release from the ER to the cytosol. Similar to PDI, the b' domain of ERp44 is likely involved in substrate recognition and may be the primary binding site. 111 matched cddid_all.tbl CDD cd03073 cd03073 239371 PDI_b'_ERp72_ERp57 "PDIb' family, ERp72 and ERp57 subfamily, second redox inactive TRX-like domain b'; ERp72 and ER57 are involved in oxidative protein folding in the ER, like PDI. They exhibit both disulfide oxidase and reductase functions, by catalyzing the formation of disulfide bonds of newly synthesized polypeptides and acting as isomerases to correct any non-native disulfide bonds. They also display chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. ERp57 contains two redox-active TRX (a) domains and two redox inactive TRX-like (b) domains. It shares the same domain arrangement of abb'a' as PDI, but lacks the C-terminal acid-rich region (c domain) that is present in PDI. ERp72 contains one additional redox-active TRX (a) domain at the N-terminus with a molecular structure of a""abb'a'. ERp57 interacts with the lectin chaperones, calnexin and calreticulin, and specifically promotes the oxidative folding of glycoproteins. ERp72 associates with several ER chaperones and folding factors to form complexes in the ER that bind nascent proteins. The b' domain of ERp57 is the primary binding site and is adapted for ER lectin association. Similarly, the b' domain of ERp72 is likely involved in substrate recognition." 111 matched cddid_all.tbl CDD cd03074 cd03074 239372 PDI_b'_Calsequestrin_C Protein Disulfide Isomerase (PDIb') family, Calsequestrin subfamily, C-terminal TRX-fold domain; Calsequestrin is the major calcium storage protein in the sarcoplasmic reticulum (SR) of skeletal and cardiac muscle. It stores calcium ions in sufficient quantities (up to 20 mM) to allow repetitive contractions and is essential to maintain movement, respiration and heart beat. A missense mutation in human cardiac calsequestrin is associated with catecholamine-induced polymorphic ventricular tachycardia (CPVT), a rare disease characterized by seizures or sudden death in response to physiologic or emotional stress. Calsequestrin is a highly acidic protein with up to 50 calcium binding sites formed simply by the clustering of two or more acidic residues. The monomer contains three redox inactive TRX-fold domains. Calsequestrin is condensed as a linear polymer in the SR lumen and is membrane-anchored through binding with intra-membrane proteins triadin, junctin and ryanodine receptor (RyR) Ca2+ release channel. In addition to its role as a calcium ion buffer, calsequestrin also regulates the activity of the RyR channel, coordinating the release of calcium ions from the SR with the loading of the calcium store. The C-terminal TRX-fold domain (or domain III) mediates back-to-back dimer interaction and also contriubutes to the front-to-front dimer interface, both of which are important features in the formation of calsequestrin polymers. 120 matched cddid_all.tbl CDD cd03075 cd03075 239373 GST_N_Mu GST_N family, Class Mu subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. The class Mu subfamily is composed of eukaryotic GSTs. In rats, at least six distinct class Mu subunits have been identified, with homologous genes in humans for five of these subunits. Class Mu GSTs can form homodimers and heterodimers, giving a large number of possible isoenzymes that can be formed, all with overlapping activities but different substrate specificities. They are the most abundant GSTs in human liver, skeletal muscle and brain, and are believed to provide protection against diseases including cancer and neurodegenerative disorders. Some isoenzymes have additional specific functions. Human GST M1-1 acts as an endogenous inhibitor of ASK1 (apoptosis signal-regulating kinase 1), thereby suppressing ASK1-mediated cell death. Human GSTM2-2 and 3-3 have been identified as prostaglandin E2 synthases in the brain and may play crucial roles in temperature and sleep-wake regulation. 82 matched cddid_all.tbl CDD cd03076 cd03076 239374 GST_N_Pi GST_N family, Class Pi subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. Class Pi GST is a homodimeric eukaryotic protein. The human GSTP1 is mainly found in erythrocytes, kidney, placenta and fetal liver. It is involved in stress responses and in cellular proliferation pathways as an inhibitor of JNK (c-Jun N-terminal kinase). Following oxidative stress, monomeric GSTP1 dissociates from JNK and dimerizes, losing its ability to bind JNK and causing an increase in JNK activity, thereby promoting apoptosis. GSTP1 is expressed in various tumors and is the predominant GST in a wide range of cancer cells. It has been implicated in the development of multidrug-resistant tumours. 73 matched cddid_all.tbl CDD cd03077 cd03077 239375 GST_N_Alpha GST_N family, Class Alpha subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal TRX-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. The class Alpha subfamily is composed of eukaryotic GSTs which can form homodimer and heterodimers. There are at least six types of class Alpha GST subunits in rats, four of which have human counterparts, resulting in many possible isoenzymes with different activities, tissue distribution and substrate specificities. Human GSTA1-1 and GSTA2-2 show high GSH peroxidase activity. GSTA3-3 catalyzes the isomerization of intermediates in steroid hormone biosynthesis. GSTA4-4 preferentially catalyzes the GSH conjugation of alkenals. 79 matched cddid_all.tbl CDD cd03078 cd03078 239376 GST_N_Metaxin1_like GST_N family, Metaxin subfamily, Metaxin 1-like proteins; composed of metaxins 1 and 3, and similar proteins including Tom37 from fungi. Mammalian metaxin (or metaxin 1) and the fungal protein Tom37 are components of preprotein import complexes of the mitochondrial outer membrane. Metaxin extends to the cytosol and is anchored to the mitochondrial membrane through its C-terminal domain. In mice, metaxin is required for embryonic development. Like the murine gene, the human metaxin gene is located downstream to the glucocerebrosidase (GBA) pseudogene and is convergently transcribed. Inherited deficiency of GBA results in Gaucher disease, which presents many diverse clinical phenotypes. Alterations in the metaxin gene, in addition to GBA mutations, may be associated with Gaucher disease. Genome sequencing shows that a third metaxin gene also exists in zebrafish, Xenopus, chicken and mammals. 73 matched cddid_all.tbl CDD cd03079 cd03079 239377 GST_N_Metaxin2 GST_N family, Metaxin subfamily, Metaxin 2; a metaxin 1 binding protein identified through a yeast two-hybrid system using metaxin 1 as the bait. Metaxin 2 shares sequence similarity with metaxin 1 but does not contain a C-terminal mitochondrial outer membrane signal-anchor domain. It associates with mitochondrial membranes through its interaction with metaxin 1, which is a component of the mitochondrial preprotein import complex of the outer membrane. The biological function of metaxin 2 is unknown. It is likely that it also plays a role in protein translocation into the mitochondria. However, this has not been experimentally validated. In a recent proteomics study, it has been shown that metaxin 2 is overexpressed in response to lipopolysaccharide-induced liver injury. 74 matched cddid_all.tbl CDD cd03080 cd03080 239378 GST_N_Metaxin_like GST_N family, Metaxin subfamily, Metaxin-like proteins; a heterogenous group of proteins, predominantly uncharacterized, with similarity to metaxins and GSTs. Metaxin 1 is a component of a preprotein import complex of the mitochondrial outer membrane. It extends to the cytosol and is anchored to the mitochondrial membrane through its C-terminal domain. In mice, metaxin is required for embryonic development. In humans, alterations in the metaxin gene may be associated with Gaucher disease. One characterized member of this subgroup is a novel GST from Rhodococcus with toluene o-monooxygenase and gamma-glutamylcysteine synthetase activities. Also members are the cadmium-inducible lysosomal protein CDR-1 and its homologs from C. elegans, and the failed axon connections (fax) protein from Drosophila. CDR-1 is an integral membrane protein that functions to protect against cadmium toxicity and may also have a role in osmoregulation to maintain salt balance in C. elegans. The fax gene of Drosophila was identified as a genetic modifier of Abelson (Abl) tyrosine kinase. The fax protein is localized in cellular membranes and is expressed in embryonic mesoderm and axons of the central nervous system. 75 matched cddid_all.tbl CDD cd03081 cd03081 239379 TRX_Fd_NuoE_FDH_gamma TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, NAD-dependent formate dehydrogenase (FDH) gamma subunit; composed of proteins similar to the gamma subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD+ to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH gamma subunit is closely related to NuoE, which is part of a multisubunit complex (Nuo) catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster present in NuoE. Similarly, the FDH gamma subunit is hypothesized to be involved in an electron transport chain involving other FDH subunits, upon the oxidation of formate. 80 matched cddid_all.tbl CDD cd03082 cd03082 239380 TRX_Fd_NuoE_W_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E family, Tungsten-containing formate dehydrogenase (W-FDH) beta subunit; composed of proteins similar to the W-FDH beta subunit of Methylobacterium extorquens. W-FDH is a heterodimeric NAD-dependent enzyme catalyzing the conversion of formate to carbon dioxide. The beta subunit is a fusion protein containing an N-terminal NuoE domain and a C-terminal NuoF domain. NuoE and NuoF are components of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster in NuoE and the [4Fe-4S] cluster in NuoF. In addition, NuoF is also the NADH- and FMN-binding subunit. Similarly, the beta subunit of W-FDH is most likely involved in the electron transport chain during the NAD-dependent oxidation of formate. 72 matched cddid_all.tbl CDD cd03083 cd03083 239381 TRX_Fd_NuoE_hoxF TRX-like [2Fe-2S] Ferredoxin (Fd) family, NADH:ubiquinone oxidoreductase (Nuo) subunit E subfamily, hoxF; composed of proteins similar to the NAD-reducing hydrogenase (hoxS) alpha subunit of Alcaligenes eutrophus H16. HoxS is a cytoplasmic hydrogenase catalyzing the oxidation of molecular hydrogen accompanied by the reduction of NAD. It is composed of four structural subunits encoded by the genes hoxF, hoxU, hoxY and hoxH. The hoxF protein (or alpha subunit) is a fusion protein containing an N-terminal NuoE-like domain and a C-terminal NuoF domain. NuoE and NuoF are components of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. Electrons are transferred from NADH to quinone through a chain of iron-sulfur clusters in Nuo, including the [2Fe-2S] cluster in NuoE and the [4Fe-4S] cluster in NuoF. In addition, NuoF is also the NADH- and FMN-binding subunit. HoxF may be involved in the electron transport chain during the NAD-dependent oxidation of hydrogen through its NuoF domain. The NuoE-like domain of hoxF contains only one conserved cysteine in its putative active site, compared to four cysteines in NuoE, and may have lost the ability to bind [2Fe-2S] clusters. 80 matched cddid_all.tbl CDD cd03084 cd03084 100086 phosphohexomutase The alpha-D-phosphohexomutase superfamily includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this family include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). These enzymes play important and diverse roles in carbohydrate metabolism in organisms from bacteria to humans. Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model. 355 matched cddid_all.tbl CDD cd03085 cd03085 100087 PGM1 Phosphoglucomutase 1 (PGM1) catalyzes the bidirectional interconversion of glucose-1-phosphate (G-1-P) and glucose-6-phosphate (G-6-P) via a glucose 1,6-diphosphate intermediate, an important metabolic step in prokaryotes and eukaryotes. In one direction, G-1-P produced from sucrose catabolism is converted to G-6-P, the first intermediate in glycolysis. In the other direction, conversion of G-6-P to G-1-P generates a substrate for synthesis of UDP-glucose which is required for synthesis of a variety of cellular constituents including cell wall polymers and glycoproteins. The PGM1 family also includes a non-enzymatic PGM-related protein (PGM-RP) thought to play a structural role in eukaryotes, as well as pp63/parafusin, a phosphoglycoprotein that plays an important role in calcium-regulated exocytosis in ciliated protozoans. PGM1 belongs to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model. 548 matched cddid_all.tbl CDD cd03086 cd03086 100088 PGM3 PGM3 (phosphoglucomutase 3), also known as PAGM (phosphoacetylglucosamine mutase) and AGM1 (N-acetylglucosamine-phosphate mutase), is an essential enzyme found in eukaryotes that reversibly catalyzes the conversion of GlcNAc-6-phosphate into GlcNAc-1-phosphate as part of the UDP-N-acetylglucosamine (UDP-GlcNAc) biosynthetic pathway. UDP-GlcNAc is an essential metabolite that serves as the biosynthetic precursor of many glycoproteins and mucopolysaccharides. AGM1 is a member of the alpha-D-phosphohexomutase superfamily, which catalyzes the intramolecular phosphoryl transfer of sugar substrates. The alpha-D-phosphohexomutases have four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model. 513 matched cddid_all.tbl CDD cd03087 cd03087 100089 PGM_like1 This archaeal PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this superfamily include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model. 439 matched cddid_all.tbl CDD cd03088 cd03088 100090 ManB ManB is a bacterial phosphomannomutase (PMM) that catalyzes the conversion of mannose 6-phosphate to mannose-1-phosphate in the second of three steps in the GDP-mannose pathway, in which GDP-D-mannose is synthesized from fructose-6-phosphate. In Mycobacterium tuberculosis, the causative agent of tuberculosis, PMM is involved in the biosynthesis of mannosylated lipoglycans that participate in the association of mycobacteria with host macrophage phagocytic receptors. ManB belongs to the the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model. 459 matched cddid_all.tbl CDD cd03089 cd03089 100091 PMM_PGM The phosphomannomutase/phosphoglucomutase (PMM/PGM) bifunctional enzyme catalyzes the reversible conversion of 1-phospho to 6-phospho-sugars (e.g. between mannose-1-phosphate and mannose-6-phosphate or glucose-1-phosphate and glucose-6-phosphate) via a bisphosphorylated sugar intermediate. The reaction involves two phosphoryl transfers, with an intervening 180 degree reorientation of the reaction intermediate during catalysis. Reorientation of the intermediate occurs without dissociation from the active site of the enzyme and is thus, a simple example of processivity, as defined by multiple rounds of catalysis without release of substrate. Glucose-6-phosphate and glucose-1-phosphate are known to be utilized for energy metabolism and cell surface construction, respectively. PMM/PGM belongs to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the phosphoglucomutases (PGM1 and PGM2). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model. 443 matched cddid_all.tbl CDD cd03108 cd03108 349762 AdSS adenylosuccinate synthetase. Adenylosuccinate synthetase (AdSS) catalyzes the first step in the de novo biosynthesis of AMP. IMP and L-aspartate are conjugated in a two-step reaction accompanied by the hydrolysis of GTP to GDP in the presence of Mg2+. In the first step, the r-phosphate group of GTP is transferred to the 6-oxygen atom of IMP. An aspartate then displaces this 6-phosphate group to form the product adenylosuccinate. Because of its critical role in purine biosynthesis, AdSS is a target of antibiotics, herbicides and antitumor drugs. 316 matched cddid_all.tbl CDD cd03109 cd03109 349763 DTBS dethiobiotin synthetase. Dethiobiotin synthetase (DTBS) is the penultimate enzyme in the biotin biosynthesis pathway in Escherichia coli and other microorganisms. The enzyme catalyzes formation of the ureido ring of dethiobiotin from (7R,8S)-7,8-diaminononanoic acid (DAPA) and carbon dioxide. The enzyme utilizes carbon dioxide instead of hydrogen carbonate as substrate and is dependent on ATP and divalent metal ions as cofactors. 189 matched cddid_all.tbl CDD cd03110 cd03110 349764 SIMIBI_bact_arch bacterial and archaeal subfamily of SIMIBI. Uncharacterized bacterial and archaeal subfamily of SIMIBI superfamily. Proteins in this superfamily contain an ATP-binding domain and use energy from hydrolysis of ATP to transfer electron or ion. The specific function of this family is unknown. 246 matched cddid_all.tbl CDD cd03111 cd03111 349765 CpaE-like pilus assembly ATPase CpaE. This protein family consists of proteins similar to the cpaE protein of the Caulobacter pilus assembly and the orf4 protein of Actinobacillus pilus formation gene cluster. The function of these proteins are unkown. The Caulobacter pilus assembly contains 7 genes: pilA, cpaA, cpaB, cpaC, cpaD, cpaE and cpaF. These genes are clustered together on chromosome. 235 matched cddid_all.tbl CDD cd03112 cd03112 349766 CobW-like cobalamin synthesis protein CobW. The function of this protein family is unknown. The amino acid sequence of YjiA protein in E. coli contains several conserved motifs that characterizes it as a P-loop GTPase. YijA gene is among the genes significantly induced in response to DNA-damage caused by mitomycin. YijA gene is a homologue of the CobW gene which encodes the cobalamin synthesis protein/P47K. 198 matched cddid_all.tbl CDD cd03113 cd03113 349767 CTPS_N N-terminal domain of cytidine 5'-triphosphate synthase. Cytidine 5'-triphosphate synthase (CTPS) is a two-domain protein, which consists of an N-terminal synthetase domain and C-terminal glutaminase domain. The enzymes hydrolyze the amide bond of glutamine to ammonia and glutamate at the glutaminase domains and transfer nascent ammonia to the acceptor substrate at the synthetase domain to form an aminated product. 261 matched cddid_all.tbl CDD cd03114 cd03114 349768 MMAA-like methylmalonic aciduria associated protein. Methylmalonyl Co-A mutase-associated GTPase MeaB and its human homolog, methylmalonic aciduria associated protein (MMAA) are metallochaperones that function as a G-protein chaperone that assists AdoCbl cofactor delivery to the methylmalonyl-CoA mutase (MCM) and reactivation of the enzyme during catalysis. A member of the family, Escherichia coli ArgK, was previously thought to be a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems. 252 matched cddid_all.tbl CDD cd03115 cd03115 349769 SRP_G_like GTPase domain similar to the signal recognition particle subunit 54. The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal signal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognate receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain. 193 matched cddid_all.tbl CDD cd03116 cd03116 349770 MobB molybdopterin-guanine dinucleotide biosynthesis protein B. Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In Escherichia coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin. 157 matched cddid_all.tbl CDD cd03117 cd03117 239391 alpha_CA_IV_XV_like Carbonic anhydrase alpha, CA_IV, CA_XV, like isozymes. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues. This subgroup, restricted to animals, contains isozyme IV and similar proteins such as mouse CA XV. Isozymes IV is attached to membranes via a glycosylphosphatidylinositol (GPI) tail. In mammals, Isozyme IV plays crucial roles in kidney and lung function, amongst others. This subgroup also contains the dual domain CA from the giant clam, Tridacna gigas. T. gigas CA plays a role in the movement of inorganic carbon from the surrounding seawater to the symbiotic algae found in the clam's tissues. CA XV is expressed in several species but not in humans or chimps. Similar to isozyme CA IV, CA XV attaches to membranes via a GPI tail. 234 matched cddid_all.tbl CDD cd03118 cd03118 239392 alpha_CA_V Carbonic anhydrase alpha, CA isozyme V_like subgroup. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidines. This vertebrate subgroup comprises isozyme V. CA V is the mitochondrial isozyme, which may play a role in gluconeogenesis and ureagenesis and possibly also in lipogenesis. 236 matched cddid_all.tbl CDD cd03119 cd03119 239393 alpha_CA_I_II_III_XIII Carbonic anhydrase alpha, isozymes I, II, and III and XIII. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidines. This vertebrate subgroup comprises isozymes I, II, and III, which are cytoplasmic enzymes. CA I, for example, is expressed in erythrocyes of many vertebrates; CA II is the most active cytosolic isozyme; while it is being expressed nearly ubiquitously, it comprises 95% of the renal carbonic anhydrase and is required for renal acidification; CA III has been implicated in protection from the damaging effect of oxidizing agents in hepatocytes. CAXIII may play important physiological roles in several organs. 259 matched cddid_all.tbl CDD cd03120 cd03120 239394 alpha_CARP_VIII Carbonic anhydrase alpha related protein, group VIII. Carbonic anhydrase related proteins (CARPs) are sequence similar to carbonic anhydrases. Carbonic anhydrases are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism. CARPs have lost conserved histidines involved in zinc binding and consequently their catalytic activity. CARP VIII may play roles in various biological processes of the central nervous system, and could be involved in protein-protein interactions. CARP VIII has been shown to bind inositol 1,4,5-triphosphate (IP3) receptor type I (IP3RI), reducing the affinity of the receptor for IP3. IP3RI is an intracellular IP3-gated Ca2+ channel located on intracellular Ca2+ stores. IP3RI converts IP3 signaling into Ca2+ signaling thereby participating in a variety of cell functions. 256 matched cddid_all.tbl CDD cd03121 cd03121 239395 alpha_CARP_X_XI_like Carbonic anhydrase alpha related protein: groups X, XI and related proteins. This subgroup contains carbonic anhydrase related proteins (CARPs) X and XI, which have been implicated in various biological processes of the central nervous system. CARPs are sequence similar to carbonic anhydrases. Carbonic anhydrases are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism. CARPs have lost conserved histidines involved in zinc binding and consequently their catalytic activity. CARP XI plays a role in the development of gastrointestinal stromal tumors. 256 matched cddid_all.tbl CDD cd03122 cd03122 239396 alpha_CARP_receptor_like Carbonic anhydrase alpha related protein, receptor_like subfamily. Carbonic anhydrase related proteins (CARPs) are sequence similar to carbonic anhydrases. Carbonic anhydrases are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism. CARPs have lost conserved histidines involved in zinc binding and consequently their catalytic activity. This sub-family of carbonic anhydrase-related domains found in tyrosine phosphatase receptors may play a role in cell adhesion. 253 matched cddid_all.tbl CDD cd03123 cd03123 239397 alpha_CA_VI_IX_XII_XIV Carbonic anhydrase alpha, isozymes VI, IX, XII and XIV. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Alpha CAs are mostly monomeric enzymes. The zinc ion is complexed by three histidine residues. This sub-family comprises the secreted CA VI, which is found in saliva, for example, and the membrane proteins CA IX, XII, and XIV. 248 matched cddid_all.tbl CDD cd03124 cd03124 239398 alpha_CA_prokaryotic_like Carbonic anhydrase alpha, prokaryotic-like subfamily. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidines. This sub-family includes bacterial carbonic anhydrase alpha, as well as plant enzymes such as tobacco nectarin III and yam dioscorin and, carbonic anhydrases from molluscs, such as nacrein, which are part of the organic matrix layer in shells. Other members of this family may be involved in maintaining pH balance, in facilitating transport of carbon dioxide or carbonic acid, or in sensing carbon dioxide levels in the environment. Dioscorin is the major storage protein of yam tubers and may play a role as an antioxidant. Tobacco Nectarin may play a role in the maintenace of pH and oxidative balance in nectar. Mollusc nacrein may participate in calcium carbonate crystal formation of the nacreous layer. This subfamily also includes three alpha carbonic anhydrases from Chlamydomonas reinhardtii (CAH 1-3). CAHs1-2 are localized in the periplasmic space. CAH1 faciliates the movement of carbon dioxide across the plasma membrane when the medium is alkaline. CAH3 is localized to the thylakoid lumen and provides CO2 to Rubisco. 216 matched cddid_all.tbl CDD cd03125 cd03125 239399 alpha_CA_VI Carbonic anhydrase alpha, isozyme VI. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues. This sub-family comprises the secreted CA VI, which is found in saliva. 249 matched cddid_all.tbl CDD cd03126 cd03126 239400 alpha_CA_XII_XIV Carbonic anhydrase alpha, isozymes XII and XIV. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidine residues. This sub-family comprises the membrane proteins CA XII and XIV. 249 matched cddid_all.tbl CDD cd03127 cd03127 239401 tetraspanin_LEL "Tetraspanin, extracellular domain or large extracellular loop (LEL). Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. The tetraspanin family contains CD9, CD63, CD37, CD53, CD82, CD151, and CD81, amongst others. Tetraspanins are involved in diverse processes such as cell activation and proliferation, adhesion and motility, differentiation, cancer, and others. Their various functions may relate to their ability to act as molecular facilitators, grouping specific cell-surface proteins and affecting formation and stability of signaling complexes. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the ""tetraspanin web"", which may also include integrins." 90 matched cddid_all.tbl CDD cd03128 cd03128 153222 GAT_1 Type 1 glutamine amidotransferase (GATase1)-like domain. Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to Class I glutamine amidotransferases, the intracellular PH1704 from Pyrococcus horikoshii, the C-terminal of the large catalase: Escherichia coli HP-II, Sinorhizobium meliloti Rm1021 ThuA, the A4 beta-galactosidase middle domain and peptidase E. The majority of proteins in this group have a reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. For Class I glutamine amidotransferases proteins which transfer ammonia from the amide side chain of glutamine to an acceptor substrate, this Cys forms a Cys-His-Glu catalytic triad in the active site. Glutamine amidotransferases activity can be found in a range of biosynthetic enzymes included in this cd: glutamine amidotransferase, formylglycinamide ribonucleotide, GMP synthetase, anthranilate synthase component II, glutamine-dependent carbamoyl phosphate synthase (CPSase), cytidine triphosphate synthetase, gamma-glutamyl hydrolase, imidazole glycerol phosphate synthase and, cobyric acid synthase. For Pyrococcus horikoshii PH1704, the Cys of the nucleophile elbow together with a different His and, a Glu from an adjacent monomer form a catalytic triad different from the typical GATase1 triad. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad of typical GATase1 domains, by having a Ser in place of the reactive Cys at the nucleophile elbow. The E. coli HP-II C-terminal domain, S. meliloti Rm1021 ThuA and the A4 beta-galactosidase middle domain lack the catalytic triad typical GATaseI domains. GATase1-like domains can occur either as single polypeptides, as in Class I glutamine amidotransferases, or as domains in a much larger multifunctional synthase protein, such as CPSase. Peptidase E has a circular permutation in the common core of a typical GTAse1 domain. 92 matched cddid_all.tbl CDD cd03129 cd03129 153223 GAT1_Peptidase_E_like Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E_like proteins. Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E_like proteins. This group contains proteins similar to the aspartyl dipeptidases Salmonella typhimurium peptidase E and Xenopus laevis peptidase E and, extracellular cyanophycinases from Pseudomonas anguilliseptica BI (CphE) and Synechocystis sp. PCC 6803 CphB. In bacteria peptidase E is believed to play a role in degrading peptides generated by intracellular protein breakdown or imported into the cell as nutrient sources. Peptidase E uniquely hydrolyses only Asp-X dipeptides (where X is any amino acid), and one tripeptide Asp-Gly-Gly. Cyanophycinases are intracellular exopeptidases which hydrolyze the polymer cyanophycin (multi L-arginyl-poly-L-aspartic acid) to the dipeptide beta-Asp-Arg. Peptidase E and cyanophycinases are thought to have a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad typical of GATase1 domains by having a Ser in place of the reactive Cys at the nucleophile elbow. Xenopus peptidase E is developmentally regulated in response to thyroid hormone and, it is thought to play a role in apoptosis during tail reabsorption. 210 matched cddid_all.tbl CDD cd03130 cd03130 153224 GATase1_CobB Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase. Type 1 glutamine amidotransferase (GATase1) domain found in Cobyrinic Acid a,c-Diamide Synthase. CobB plays a role in cobalamin biosythesis catalyzing the conversion of cobyrinic acid to cobyrinic acid a,c-diamide. CobB belongs to the triad family of amidotransferases. Two of the three residues of the catalytic triad that are involved in glutamine binding, hydrolysis and transfer of the resulting ammonia to the acceptor substrate in other triad aminodotransferases are conserved in CobB. 198 matched cddid_all.tbl CDD cd03131 cd03131 153225 GATase1_HTS Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS). Type 1 glutamine amidotransferase (GATase1)-like domain found in homoserine trans-succinylase (HTS). HTS, the first enzyme in methionine biosynthesis in Escherichia coli, transfers a succinyl group from succinyl-CoA to homoserine forming succinyl homoserine. It has been suggested that the succinyl group of succinyl-CoA is initially transferred to an enzyme nucleophile before subsequent transfer to homoserine. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, in common with GATase1 domains a reactive cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. It has been proposed that this cys is in the active site of the molecule. However, as succinyl has been found bound to a conserved lysine residue, this conserved cys may play a role in dimer formation. HTS activity is tightly regulated by several mechanisms including feedback inhibition and proteolysis. It represents a critical control point for cell growth and viability. 175 matched cddid_all.tbl CDD cd03132 cd03132 153226 GATase1_catalase Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases. Type 1 glutamine amidotransferase (GATase1)-like domain found in at the C-terminal of several large catalases. Catalase catalyzes the dismutation of hydrogen peroxide (H2O2) to water and oxygen. This group includes the large catalases: Neurospora crassa Catalase-1 and Catalase-3 and, Escherichia coli HP-II. This GATase1-like domain has an essential role in HP-II catalase activity. However, it lacks enzymatic activity and the catalytic triad typical of GATase1 domains. Catalase-1 and -3 are homotetrameric, HP-II is homohexameric. It has been proposed that this domain may facilitate the folding and oligomerization process. The interface between this GATase1-like domain of HP-II and the core of the subunit forms part of a channel which provides access to the deeply buried catalase active sites of HPII. Catalase-1 is associated with non-growing cells; Catalase-3 is associated with growing conditions. HP-II is produced in stationary phase. Catalase-1 is induced by ethanol and heat shock. Catalase-3 is induced under stress conditions such a hydrogen peroxide, paraquat, cadmium, heat shock, uric acid and nitrate treatment. 142 matched cddid_all.tbl CDD cd03133 cd03133 153227 GATase1_ES1 Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1. Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1. This group includes, proteins similar to ES1, Escherichia coli enhancing lycopene biosynthesis protein 2, Azospirillum brasilense iaaC and, human HES1. The catalytic triad typical of GATase1domains is not conserved in this GATase1-like domain. However, in common with GATase1domains a reactive cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. Zebrafish ES1 is expressed specifically in adult photoreceptor cells and appears to be a cytoplasmic protein. A. brasilense iaaC is involved in controlling IAA biosynthesis. 213 matched cddid_all.tbl CDD cd03134 cd03134 153228 GATase1_PfpI_like A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus. A type 1 glutamine amidotransferase (GATase1)-like domain found in PfpI from Pyrococcus furiosus. This group includes proteins similar to PfpI from P. furiosus. and PH1704 from Pyrococcus horikoshii. These enzymes are ATP-independent intracellular proteases and may hydrolyze small peptides to provide a nutritional source. Only Cys of the catalytic triad typical of GATase1 domains is conserved in this group. This Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. For PH1704, it is believed that this Cys together with a different His in one monomer and Glu (from an adjacent monomer) forms a different catalytic triad from the typical GATase1domain. PfpI is homooligomeric. Protease activity is only found for oligomeric forms of PH1704. 165 matched cddid_all.tbl CDD cd03135 cd03135 153229 GATase1_DJ-1 Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1. Type 1 glutamine amidotransferase (GATase1)-like domain found in Human DJ-1. DJ-1 is involved in multiple physiological processes including cancer, Parkinson's disease and male fertility. It is unclear how DJ-1 functions in these. DJ-1 has been shown to possess chaperone activity. DJ-1 is preferentially expressed in the testis and moderately in other tissues; it is induced together with genes involved in oxidative stress response. The Drosophila homologue (DJ-1A) plays an essential role in oxidative stress response and neuronal maintenance. Inhibition of DJ-1A function through RNAi, results in the cellular accumulation of reactive oxygen species, organismal hypersensitivity to oxidative stress, and dysfunction and degeneration of dopaminergic and photoreceptor neurons. DJ-1 has lacks enzymatic activity and the catalytic triad of typical GATase1 domains, however it does contain the highly conserved cysteine located at the nucelophile elbow region typical of these domains. This cysteine been proposed to be a site of regulation of DJ-1 activity by oxidation. DJ-1 is a dimeric enzyme. 163 matched cddid_all.tbl CDD cd03136 cd03136 153230 GATase1_AraC_ArgR_like AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain. A subgroup of AraC transcriptional regulators having an N-terminal Type 1 glutamine amidotransferase (GATase1)-like domain. This group contains proteins similar to the Pseudomonas aeruginosa ArgR regulator. ArgR functions in the control of expression of certain genes of arginine biosynthesis and catabolism. AraC regulators are defined by a AraC-type helix-turn-helix DNA binding domain at their C-terminal. AraC family transcriptional regulators are widespread among bacteria and are involved in regulating diverse and important biological functions, including carbon metabolism, stress responses and virulence in different microorganisms. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, in common with typical GATase1domains a reactive cys residue is found in some sequences in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. 185 matched cddid_all.tbl CDD cd03137 cd03137 153231 GATase1_AraC_1 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain. A subgroup of AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain. AraC regulators are defined by a AraC-type helix-turn-helix DNA binding domain at their C-terminal. AraC family transcriptional regulators are widespread among bacteria and are involved in regulating diverse and important biological functions, including carbon metabolism, stress responses and virulence in different microorganisms. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, in common with typical GATase1domains a reactive cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. 187 matched cddid_all.tbl CDD cd03138 cd03138 153232 GATase1_AraC_2 AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain. A subgroup of AraC transcriptional regulators having a Type 1 glutamine amidotransferase (GATase1)-like domain. AraC regulators are defined by a AraC-type helix-turn-helix DNA binding domain at their C-terminal. AraC family transcriptional regulators are widespread among bacteria and are involved in regulating diverse and important biological functions, including carbon metabolism, stress responses and virulence in different microorganisms. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, in common with typical GATase1domains a reactive cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. 195 matched cddid_all.tbl CDD cd03139 cd03139 153233 GATase1_PfpI_2 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. PfpI is an ATP-independent intracellular proteases which may hydrolyze small peptides to provide a nutritional source. Only Cys of the catalytic triad typical of GATase1 domains is conserved in this group. This Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. 183 matched cddid_all.tbl CDD cd03140 cd03140 153234 GATase1_PfpI_3 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. PfpI is an ATP-independent intracellular proteases which may hydrolyze small peptides to provide a nutritional source. Only Cys of the catalytic triad typical of GATase1 domains is conserved in this group. This Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. 170 matched cddid_all.tbl CDD cd03141 cd03141 153235 GATase1_Hsp31_like Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein. Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein (EcHsp31). This group includes EcHsp31 and Saccharomyces cerevisiae Ydr533c protein. EcHsp31 has chaperone activity. Ydr533c is upregulated in response to various stress conditions along with the heat shock family. EcHsp31 coordinates a metal ion using a 2-His-1-carboxylate motif present in various ions that use iron as a cofactor such as Carboxypeptidase A. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, in common with a typical GATase1 domain, a reactive Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. For EcHsp31, this Cys together with a different His and, an Asp (rather than a Glu) residue form a different catalytic triad from the typical GATase1 domain. For Ydr533c a catalytic triad forms from the conserved Cys together with a different His and Glu from that of the typical GATase1domain. Ydr533c protein and EcHsp31 are homodimers. 221 matched cddid_all.tbl CDD cd03142 cd03142 153236 GATase1_ThuA Type 1 glutamine amidotransferase (GATase1)-like domain found in Sinorhizobium meliloti Rm1021 ThuA (SmThuA). Type 1 glutamine amidotransferase (GATase1)-like domain found in Sinorhizobium meliloti Rm1021 ThuA (SmThuA). This group includes proteins similar to SmThuA which plays a role in a major pathway for trehalose catabolism. SmThuA is induced by trehalose but not by related structurally similar disaccharides like sucrose or maltose. Proteins in this group lack the catalytic triad of typical GATase1 domains: a His replaces the reactive Cys found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. S. meliloti Rm1021 thuA mutants are impaired in competitive colonization of Medicago sativa roots but are more competitive than the wild-type Rml021 in infecting alfalfa roots and forming nitrogen-fixing nodules. 215 matched cddid_all.tbl CDD cd03143 cd03143 153237 A4_beta-galactosidase_middle_domain A4 beta-galactosidase middle domain: a type 1 glutamine amidotransferase (GATase1)-like domain. A4 beta-galactosidase middle domain: a type 1 glutamine amidotransferase (GATase1)-like domain. This group includes proteins similar to beta-galactosidase from Thermus thermophilus. Beta-Galactosidase hydrolyzes the beta-1,4-D-galactosidic linkage of lactose, as well as those of related chromogens, o-nitrophenyl-beta-D-galactopyranoside (ONP-Gal) and 5-bromo-4-chloro-3-indolyl-beta-D-galactoside (X-gal). This A4 beta-galactosidase middle domain lacks the catalytic triad of typical GATase1 domains. The reactive Cys residue found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow in typical GATase1 domains is not conserved in this group. 154 matched cddid_all.tbl CDD cd03144 cd03144 153238 GATase1_ScBLP_like Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP). Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Saccharomyces cerevisiae biotin-apoprotein ligase (ScBLP). Biotin-apoprotein ligase modifies proteins by covalently attaching biotin. ScBLP is known to biotinylate acety-CoA carboxylase and pyruvate carboxylase. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, the Cys residue found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow in a typical GATase1 domain is conserved. 114 matched cddid_all.tbl CDD cd03145 cd03145 153239 GAT1_cyanophycinase Type 1 glutamine amidotransferase (GATase1)-like domain found in cyanophycinase. Type 1 glutamine amidotransferase (GATase1)-like domain found in cyanophycinase. This group contains proteins similar to the extracellular cyanophycinases from Pseudomonas anguilliseptica BI (CphE) and Synechocystis sp. PCC 6803 CphB. Cyanophycinases are intracellular exopeptidases which hydrolyze the polymer cyanophycin (multi L-arginyl-poly-L-aspartic acid) to the dipeptide beta-Asp-Arg. Cyanophycinase is believed to be a serine-type exopeptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad typical of GATase1 domains by having a Ser in place of the reactive Cys at the nucleophile elbow. 217 matched cddid_all.tbl CDD cd03146 cd03146 153240 GAT1_Peptidase_E Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E. Type 1 glutamine amidotransferase (GATase1)-like domain found in peptidase E. This group contains proteins similar to the aspartyl dipeptidases Salmonella typhimurium peptidase E and Xenopus laevis peptidase E. In bacteria peptidase E is believed to play a role in degrading peptides generated by intracellular protein breakdown or imported into the cell as nutrient sources. Peptidase E uniquely hydrolyses only Asp-X dipeptides (where X is any amino acid), and one tripeptide Asp-Gly-Gly. Peptidase E is believed to be a serine peptidase having a Ser-His-Glu catalytic triad which differs from the Cys-His-Glu catalytic triad typical of GATase1 domains by having a Ser in place of the reactive Cys at the nucleophile elbow. Xenopus PepE is developmentally regulated in response to thyroid hormone and, it is thought to play a role in apoptosis during tail reabsorption. 212 matched cddid_all.tbl CDD cd03147 cd03147 153241 GATase1_Ydr533c_like Type 1 glutamine amidotransferase (GATase1)-like domain found in Saccharomyces cerevisiae Ydr533c protein. Type 1 glutamine amidotransferase (GATase1)-like domain found in Saccharomyces cerevisiae Ydr533c protein. This group includes proteins similar to S. cerevisiae Ydr533c. Ydr533c is upregulated in response to various stress conditions along with the heat shock family. The catalytic triad typical of GATase1domains is not conserved in this GATase1-like domain. However, in common with a typical GATase1domain, a reactive Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. This Cys together with a different His and Glu residue form a different catalytic triad from the typical GATase1domain. Ydr533c protein is a homodimer. 231 matched cddid_all.tbl CDD cd03148 cd03148 153242 GATase1_EcHsp31_like Type 1 glutamine amidotransferase (GATase1)-like domain found in Escherichia coli Hsp31 protein (EcHsp31). Type 1 glutamine amidotransferase (GATase1)-like domain found in Escherichia coli Hsp31 protein (EcHsp31). This group includes proteins similar to EcHsp31. EcHsp31 has chaperone activity. EcHsp31 coordinates a metal ion using a 2-His-1-carboxylate motif present in various ions that use iron as a cofactor such as Carboxypeptidase A. The catalytic triad typical of GATase1 domains is not conserved in this GATase1-like domain. However, in common with a typical GATase1domain, a reactive Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. This Cys together with a different His and, an Asp (rather than a Glu) residue form a different catalytic triad from the typical GATase1 domain. EcHsp31 is a homodimer. 232 matched cddid_all.tbl CDD cd03149 cd03149 239402 alpha_CA_VII Carbonic anhydrase alpha, CA isozyme VII_like subgroup. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. Most alpha CAs are monomeric enzymes. The zinc ion is complexed by three histidines. This vertebrate subgroup comprises isozyme VII. CA VII is the most active cytosolic enzyme after CA II, and may be highly expressed in the brain. Human CA VII may be a target of antiepileptic sulfonamides/sulfamates. 236 matched cddid_all.tbl CDD cd03150 cd03150 239403 alpha_CA_IX Carbonic anhydrase alpha, isozyme IX. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Alpha CAs are strictly monomeric enzymes. The zinc ion is complexed by three histidine residues. This sub-family comprises the membrane protein CA IX. CA IX is functionally implicated in tumor growth and survival. CA IX is mainly present in solid tumors and its expression in normal tissues is limited to the mucosa of alimentary tract. CA IX is a transmembrane protein with two extracellular domains: carbonic anhydrase and, a proteoglycan-like segment mediating cell-cell adhesion. There is evidence for an involvement of the MAPK pathway in the regulation of CA9 expression. 247 matched cddid_all.tbl CDD cd03151 cd03151 239404 CD81_like_LEL "Tetraspanin, extracellular domain or large extracellular loop (LEL), CD81_like subfamily. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the ""tetraspanin web"". CD81, also referred to as Target for anti-proliferative antigen-1, TAPA-1, is found in virtually all tissues, may be involved in regulation of cell growth and has been described as a member of the CD19/CD21/Leu-13 signal transduction complex identified on B cells (the B-Cell co-receptor)." 84 matched cddid_all.tbl CDD cd03152 cd03152 239405 CD9_LEL "Tetraspanin, extracellular domain or large extracellular loop (LEL), CD9 family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the ""tetraspanin web"". CD9 is found in virtually all tissues and is potentially involved in developmental processes. It associates with the tetraspanins CD81 and CD63, as well as with some integrin, and has been shown to be involved in a variety of activation, adhesion, and cell motility functions, as well as cell-cell interactions - such as during fertilization." 84 matched cddid_all.tbl CDD cd03153 cd03153 239406 PHEMX_like_LEL "Tetraspanin, extracellular domain or large extracellular loop (LEL), PHEMX_like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the ""tetraspanin web"". Phemx (pan hematopoietic expression) or TSSC6 may play a role in hematopoietic cell function." 87 matched cddid_all.tbl CDD cd03154 cd03154 239407 TM4SF3_like_LEL "Tetraspanin, extracellular domain or large extracellular loop (LEL), TM4SF3_like subfamily. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the ""tetraspanin web"". This subfamily contaions transmembrane 4 superfamily 3 (TM4SF3) or D6.1a and related proteins. D6.1a associates with alpha6beta4 integrin and supports cell motility, it has been ascribed a role in tumor progression and metastasis." 100 matched cddid_all.tbl CDD cd03155 cd03155 239408 CD151_like_LEL "Tetraspanin, extracellular domain or large extracellular loop (LEL), CD151_Like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the ""tetraspanin web"". CD151strongly associates with integrins, especially alpha3beta1, alpha6beta1, alpha7beta1, and alpha6beta4; it may play roles in cell-cell adhesion, cell migration, platelet aggregation, and angiogenesis. For example, CD151 is is involved in regulation of migration of neutrophils, endothelial cells, and various tumor cell lines; it associates specifically with laminin-binding integrins and strengthens alpha6beta1 integrin-mediated adhesion to laminin-1; CD151 also specifically attenuates adhesion-dependent activation of Ras and correspdonding downstream effects, and is involved in epithelial cell-cell adhesion as a modulator of PKC- and Cdc42-dependent actin cytoskeletal reorganization." 110 matched cddid_all.tbl CDD cd03156 cd03156 239409 uroplakin_I_like_LEL "Tetraspanin, extracellular domain or large extracellular loop (LEL), uroplakin_I_like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the ""tetraspanin web"". Uroplakin Ia and Ib are components of the 16nm protein particles, which are packed hexagonally to form 2D crystals of asymmetric unit membranes, and cover the apical surface of mammalian urothelium, contributing to the urinay bladder's permeability barrier function. Uroplakins Ia and Ib are maturation facilitators. They trigger conformational changes in their single-transmembrane-domain binding partner proteins uroplakin II and IIIa, which in turn may lead to ER-exit, stabilization, and cell-surface expression." 114 matched cddid_all.tbl CDD cd03157 cd03157 239410 TM4SF12_like_LEL "Tetraspanin, extracellular domain or large extracellular loop (LEL), TM4SF12_like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the ""tetraspanin web"". This sub-family contains proteins similar to human transmembrane 4 superfamily member 12 (TM4SF12)." 103 matched cddid_all.tbl CDD cd03158 cd03158 239411 penumbra_like_LEL "Tetraspanin, extracellular domain or large extracellular loop (LEL), penumbra_like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the ""tetraspanin web"". Human Penumbra exhibits growth-suppressive activity in vitro and has been associated with myeloid malignancies." 119 matched cddid_all.tbl CDD cd03159 cd03159 239412 TM4SF9_like_LEL "Tetraspanin, extracellular domain or large extracellular loop (LEL), TM4SF9_like subfamily. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the ""tetraspanin web"". This subfamily contaions transmembrane 4 superfamily 9 (TM4SF9) or Tetraspanin-5 and related proteins. TM4SF9 is strongly expressed witin the central nervous system, and expression levels appear to correlate with differentiation status of particular neurons, hinting at a role in neuronal maturation." 121 matched cddid_all.tbl CDD cd03160 cd03160 239413 CD37_CD82_like_LEL "Tetraspanin, extracellular domain or large extracellular loop (LEL), CD37_CD82_Like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the ""tetraspanin web"". CD37 is a leukocyte-specific protein, and its restricted expression pattern suggests a role in the immune system. A regulatory role in T-cell proliferation has been suggested. CD82 is a metastasis suppressor implicated in biological processes ranging from fusion, adhesion, and migration to apoptosis and alterations of cell morphology." 117 matched cddid_all.tbl CDD cd03161 cd03161 239414 TM4SF2_6_like_LEL "Tetraspanin, extracellular domain or large extracellular loop (LEL), TM4SF2_6_like subfamily. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the ""tetraspanin web"". This subfamily contaions transmembrane 4 superfamily 2 (TM4SF2) or Tspan-7, transmembrane 4 superfamily 6 (TM4SF6) or Tspan-6, and related proteins. TM4SF2 has been identified as involved in some forms of X-linked mental retardation." 104 matched cddid_all.tbl CDD cd03162 cd03162 239415 peripherin_like_LEL "Tetraspanin, extracellular domain or large extracellular loop (LEL), peripherin_like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the ""tetraspanin web"". Peripherin, or RDS (retinal degradation slow) is a glycoprotein expressed in vertebrate photoreceptors, located at the rim of the disc membranes of the photoreceptor outer segments. RDS is thought to play a major role in folding and stacking of the discs. Mutations in RDS have been linked to hereditary retinal dystrophies, which typically exhibit a wide phenotypic spectrum." 143 matched cddid_all.tbl CDD cd03163 cd03163 239416 TM4SF8_like_LEL "Tetraspanin, extracellular domain or large extracellular loop (LEL), TM4SF8_like subfamily. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the ""tetraspanin web"". This subfamily contaions transmembrane 4 superfamily 8 (TM4SF8) or Tspan-3 and related proteins. Tspan-3 has been reported to form a complex with integrin beta1 and OSP/claudin-11, which may be involved in oligodendrocyte proliferation and migration." 105 matched cddid_all.tbl CDD cd03164 cd03164 239417 CD53_like_LEL "Tetraspanin, extracellular domain or large extracellular loop (LEL), CD53_Like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the ""tetraspanin web"". CD53 is a tetraspanin of the lymphoid-myeloid lineage and has been implicated in apoptosis protection. It associates with integrin alpha4beta1. Some of the cellular responses modulated by CD53 may be mediated by JNK activation and/or via the AKT pathway." 86 matched cddid_all.tbl CDD cd03165 cd03165 239418 NET-5_like_LEL "Tetraspanin, extracellular domain or large extracellular loop (LEL), NET-5_like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the ""tetraspanin web"". This sub-family contains proteins similar to human tetraspan NET-5." 98 matched cddid_all.tbl CDD cd03166 cd03166 239419 CD63_LEL "Tetraspanin, extracellular domain or large extracellular loop (LEL), CD63 family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the ""tetraspanin web"". CD63 is present in platelets, neutrophils, and endothelial cells, amongst others. In platelets it associates with the integrin alphaIIBbeta3 and may modulate alphaIIbbeta3-dependent cytoskeletal reorganization." 99 matched cddid_all.tbl CDD cd03167 cd03167 239420 oculospanin_like_LEL "Tetraspanin, extracellular domain or large extracellular loop (LEL), oculospanin_like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the ""tetraspanin web"". This subfamily contains sequences similar to oculospanin, which is found to be expressed in retinal pigment epithelium, iris, ciliary body, and retinal ganglion cells." 120 matched cddid_all.tbl CDD cd03169 cd03169 153243 GATase1_PfpI_1 Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. Type 1 glutamine amidotransferase (GATase1)-like domain found in a subgroup of proteins similar to PfpI from Pyrococcus furiosus. PfpI is an ATP-independent intracellular proteases which may hydrolyze small peptides to provide a nutritional source. Only Cys of the catalytic triad typical of GATase1 domains is conserved in this group. This Cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. 180 matched cddid_all.tbl CDD cd03171 cd03171 239421 SORL_Dfx_classI Superoxide reductase-like (SORL) domain, class I; SORL-domains are present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals as a defense mechanism against reactive oxygen species and are found in anaerobic bacteria and archeae, and microaerophilic Treponema pallidum. Desulfoferrodoxin (class I) is a homodimeric protein, with each protomer comprised of two domains, the N-terminal desulforedoxin (DSRD) domain and C-terminal SORL domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)]. 78 matched cddid_all.tbl CDD cd03172 cd03172 239422 SORL_classII Superoxide reductase-like (SORL) domain, class II; SORL-domains are present in a family of mononuclear non-heme iron proteins that includes superoxide reductase and desulfoferrodoxin. Superoxide reductase-like proteins scavenge superoxide anion radicals as a defense mechanism against reactive oxygen species and are found in anaerobic bacteria and archeae, and microaerophilic Treponema pallidum. The SORL domain contains an active iron site, Fe[His4Cys(Glu)], which in the reduced state loses the glutamate ligand. Superoxide reductase (class II) forms a homotetramer with four Fe[His4Cys(Glu)] centers. 104 matched cddid_all.tbl CDD cd03173 cd03173 176264 DUF619-like DUF619 domain of various N-acetylglutamate Kinases and N-acetylglutamate Synthases. DUF619-like: This family includes the DUF619 domain of various N-acetylglutamate synthases (NAGS) of the urea cycle found in humans and fish, the DUF619 domain of the NAGS of the fungal arginine-biosynthetic pathway (FABP), as well as the DUF619 domain present C-terminal of a NAG kinase-like domain in a limited number of predicted NAGSs found in bacteria and Dictyostelium. Ureogenic NAGS is a mitochondrial enzyme catalyzing the formation of NAG from acetylcoenzyme A and L-glutamate. NAGS is an essential allosteric activator of carbamylphosphate synthase I, the first and rate limiting enzyme of the urea cycle. Domain architecture of ureogenic and fungal NAGS consists of an N-terminal NAG kinase-like domain and a C-terminal DUF619 domain. This subgroup also includes the DUF619 domain of the FABP N-acetylglutamate kinase (NAGK), the enzyme that catalyzes the second reaction of arginine biosynthesis; the phosphorylation of the gamma-carboxyl group of NAG to produce N-acetylglutamylphosphate (NAGP) which is subsequently converted to ornithine in two more steps. The nuclear-encoded, mitochondrial polyprotein precursor (ARG5,6) consists of an N-terminal NAGK (ArgB) domain, a central DUF619 domain, and a C-terminal reductase domain (ArgC, N-acetylglutamate phosphate reductase). The DUF619 domain function has yet to be characterized. 98 matched cddid_all.tbl CDD cd03174 cd03174 163674 DRE_TIM_metallolyase "DRE-TIM metallolyase superfamily. The DRE-TIM metallolyase superfamily includes 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name ""DRE-TIM""." 265 matched cddid_all.tbl CDD cd03177 cd03177 198287 GST_C_Delta_Epsilon C-terminal, alpha helical domain of Class Delta and Epsilon Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, Class Delta and Epsilon subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. The class Delta and Epsilon subfamily is made up primarily of insect GSTs, which play major roles in insecticide resistance by facilitating reductive dehydrochlorination of insecticides or conjugating them with GSH to produce water-soluble metabolites that are easily excreted. They are also implicated in protection against cellular damage by oxidative stress. 117 matched cddid_all.tbl CDD cd03178 cd03178 198288 GST_C_Ure2p_like C-terminal, alpha helical domain of Ure2p and related Glutathione S-transferase-like proteins. Glutathione S-transferase (GST) C-terminal domain family, Ure2p-like subfamily; composed of the Saccharomyces cerevisiae Ure2p, YfcG and YghU from Escherichia coli, and related GST-like proteins. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources when rich sources are available. A transmissible conformational change of Ure2p results in a prion called [Ure3], an inactive, self-propagating and infectious amyloid. Ure2p displays a GST fold containing an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain. The N-terminal thioredoxin-fold domain is sufficient to induce the [Ure3] phenotype and is also called the prion domain of Ure2p. In addition to its role in nitrogen regulation, Ure2p confers protection to cells against heavy metal ion and oxidant toxicity, and shows glutathione (GSH) peroxidase activity. YfcG and YghU are two of the nine GST homologs in the genome of Escherichia coli. They display very low or no GSH transferase, but show very good disulfide bond oxidoreductase activity. YghU also shows modest organic hydroperoxide reductase activity. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of GSH with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST active site is located in a cleft between the N- and C-terminal domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. 110 matched cddid_all.tbl CDD cd03180 cd03180 198289 GST_C_2 C-terminal, alpha helical domain of an unknown subfamily 2 of Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, unknown subfamily 2; composed of uncharacterized bacterial proteins, with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. 110 matched cddid_all.tbl CDD cd03181 cd03181 198290 GST_C_EF1Bgamma_like Glutathione S-transferase C-terminal-like, alpha helical domain of the Gamma subunit of Elongation Factor 1B and similar proteins. Glutathione S-transferase (GST) C-terminal domain family, Gamma subunit of Elongation Factor 1B (EF1Bgamma) subfamily; EF1Bgamma is part of the eukaryotic translation elongation factor-1 (EF1) complex which plays a central role in the elongation cycle during protein biosynthesis. EF1 consists of two functionally distinct units, EF1A and EF1B. EF1A catalyzes the GTP-dependent binding of aminoacyl-tRNA to the ribosomal A site concomitant with the hydrolysis of GTP. The resulting inactive EF1A:GDP complex is recycled to the active GTP form by the guanine-nucleotide exchange factor EF1B, a complex composed of at least two subunits, alpha and gamma. Metazoan EFB1 contain a third subunit, beta. The EF1B gamma subunit contains a GST fold consisting of an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain. The GST-like domain of EF1Bgamma is believed to mediate the dimerization of the EF1 complex, which in yeast is a dimer of the heterotrimer EF1A:EF1Balpha:EF1Bgamma. In addition to its role in protein biosynthesis, EF1Bgamma may also display other functions. The recombinant rice protein has been shown to possess GSH conjugating activity. The yeast EF1Bgamma binds to membranes in a calcium dependent manner and is also part of a complex that binds to the msrA (methionine sulfoxide reductase) promoter suggesting a function in the regulation of its gene expression. Also included in this subfamily is the GST_C-like domain at the N-terminus of human valyl-tRNA synthetase (ValRS) and its homologs. Metazoan ValRS forms a stable complex with Elongation Factor-1H (EF-1H), and together, they catalyze consecutive steps in protein biosynthesis, tRNA aminoacylation and its transfer to EF. 123 matched cddid_all.tbl CDD cd03182 cd03182 198291 GST_C_GTT2_like C-terminal, alpha helical domain of GTT2-like Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, Saccharomyces cerevisiae GTT2-like subfamily; composed of predominantly uncharacterized proteins with similarity to the Saccharomyces cerevisiae GST protein, GTT2. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. GTT2, a homodimer, exhibits GST activity with standard substrates. Strains with deleted GTT2 genes are viable but exhibit increased sensitivity to heat shock. 116 matched cddid_all.tbl CDD cd03183 cd03183 198292 GST_C_Theta C-terminal, alpha helical domain of Class Theta Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, Class Theta subfamily; composed of eukaryotic class Theta GSTs and bacterial dichloromethane (DCM) dehalogenase. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Mammalian class Theta GSTs show poor GSH conjugating activity towards the standard substrates, CDNB and ethacrynic acid, differentiating them from other mammalian GSTs. GSTT1-1 shows similar cataytic activity as bacterial DCM dehalogenase, catalyzing the GSH-dependent hydrolytic dehalogenation of dihalomethanes. This is an essential process in methylotrophic bacteria to enable them to use chloromethane and DCM as sole carbon and energy sources. The presence of polymorphisms in human GSTT1-1 and its relationship to the onset of diseases including cancer is the subject of many studies. Human GSTT2-2 exhibits a highly specific sulfatase activity, catalyzing the cleavage of sulfate ions from aralkyl sufate esters, but not from the aryl or alkyl sulfate esters. 126 matched cddid_all.tbl CDD cd03184 cd03184 198293 GST_C_Omega C-terminal, alpha helical domain of Class Omega Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, Class Omega subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Class Omega GSTs show little or no GSH-conjugating activity towards standard GST substrates. Instead, they catalyze the GSH dependent reduction of protein disulfides, dehydroascorbate and monomethylarsonate, activities which are more characteristic of glutaredoxins. They contain a conserved cysteine equivalent to the first cysteine in the CXXC motif of glutaredoxins, which is a redox active residue capable of reducing GSH mixed disulfides in a monothiol mechanism. Polymorphisms of the class Omega GST genes may be associated with the development of some types of cancer and the age-at-onset of both Alzheimer's and Parkinson's diseases. 124 matched cddid_all.tbl CDD cd03185 cd03185 198294 GST_C_Tau C-terminal, alpha helical domain of Class Tau Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, Class Tau subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. The plant-specific class Tau GST subfamily has undergone extensive gene duplication. The Arabidopsis and Oryza genomes contain 28 and 40 Tau GSTs, respectively. They are primarily responsible for herbicide detoxification together with class Phi GSTs, showing class specificity in substrate preference. Tau enzymes are highly efficient in detoxifying diphenylether and aryloxyphenoxypropionate herbicides. In addition, Tau GSTs play important roles in intracellular signalling, biosynthesis of anthocyanin, responses to soil stresses and responses to auxin and cytokinin hormones. 127 matched cddid_all.tbl CDD cd03186 cd03186 198295 GST_C_SspA C-terminal, alpha helical domain of Stringent starvation protein A. Glutathione S-transferase (GST) C-terminal domain family, Stringent starvation protein A (SspA) subfamily; SspA is a RNA polymerase (RNAP)-associated protein required for the lytic development of phage P1 and for stationary phase-induced acid tolerance of E. coli. It is implicated in survival during nutrient starvation. SspA adopts the GST fold with an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, but it does not bind glutathione (GSH) and lacks GST activity. SspA is highly conserved among gram-negative bacteria. Related proteins found in Neisseria (called RegF), Francisella and Vibrio regulate the expression of virulence factors necessary for pathogenesis. 108 matched cddid_all.tbl CDD cd03187 cd03187 198296 GST_C_Phi C-terminal, alpha helical domain of Class Phi Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, Class Phi subfamily; composed of plant-specific class Phi GSTs and related fungal and bacterial proteins. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. The class Phi GST subfamily has experience extensive gene duplication. The Arabidopsis and Oryza genomes contain 13 and 16 Tau GSTs, respectively. They are primarily responsible for herbicide detoxification together with class Tau GSTs, showing class specificity in substrate preference. Phi enzymes are highly reactive toward chloroacetanilide and thiocarbamate herbicides. Some Phi GSTs have other functions including transport of flavonoid pigments to the vacuole, shoot regeneration and GSH peroxidase activity. 118 matched cddid_all.tbl CDD cd03188 cd03188 198297 GST_C_Beta C-terminal, alpha helical domain of Class Beta Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, Class Beta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Unlike mammalian GSTs which detoxify a broad range of compounds, the bacterial class Beta GSTs exhibit GSH conjugating activity with a narrow range of substrates. In addition to GSH conjugation, they are involved in the protection against oxidative stress and are able to bind antibiotics and reduce the antimicrobial activity of beta-lactam drugs, contributing to antibiotic resistance. The structure of the Proteus mirabilis enzyme reveals that the cysteine in the active site forms a covalent bond with GSH. One member of this subfamily is a GST from Burkholderia xenovorans LB400 that is encoded by the bphK gene and is part of the biphenyl catabolic pathway. 113 matched cddid_all.tbl CDD cd03189 cd03189 198298 GST_C_GTT1_like C-terminal, alpha helical domain of GTT1-like Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, Saccharomyces cerevisiae GTT1-like subfamily; composed of predominantly uncharacterized proteins with similarity to the S. cerevisiae GST protein, GTT1, and the Schizosaccharomyces pombe GST-III. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. GTT1, a homodimer, exhibits GST activity with standard substrates and associates with the endoplasmic reticulum. Its expression is induced after diauxic shift and remains high throughout the stationary phase. S. pombe GST-III is implicated in the detoxification of various metals. 123 matched cddid_all.tbl CDD cd03190 cd03190 198299 GST_C_Omega_like C-terminal, alpha helical domain of Class Omega-like Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, Saccharomyces cerevisiae Omega-like subfamily; composed of three Saccharomyces cerevisiae GST omega-like (Gto) proteins, Gto1p, Gto2p (also known as Extracellular mutant protein 4 or ECM4p), and Gto3p, as well as similar uncharacterized proteins from fungi and bacteria. The three Saccharomyces cerevisiae Gto proteins are omega-class GSTs with low or no GST activity against standard substrates, but have glutaredoxin/thiol oxidoreductase and dehydroascorbate reductase activity through a single cysteine residue in the active site. Gto1p is located in the peroxisomes while Gto2p and Gto3p are cytosolic. The gene encoding Gto2p, called ECM4, is involved in cell surface biosynthesis and architecture. S. cerevisiae ECM4 mutants show increased amounts of the cell wall hexose, N-acetylglucosamine. More recently, global gene expression analysis shows that ECM4 is upregulated during genotoxic conditions and together with the expression profiles of 18 other genes could potentially differentiate between genotoxic and cytotoxic insults in yeast. 142 matched cddid_all.tbl CDD cd03191 cd03191 198300 GST_C_Zeta C-terminal, alpha helical domain of Class Zeta Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, Class Zeta subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Class Zeta GSTs, also known as maleylacetoacetate (MAA) isomerases, catalyze the isomerization of MAA to fumarylacetoacetate, the penultimate step in tyrosine/phenylalanine catabolism, using GSH as a cofactor. They show little GSH-conjugating activity towards traditional GST substrates, but display modest GSH peroxidase activity. They are also implicated in the detoxification of the carcinogen dichloroacetic acid by catalyzing its dechlorination to glyoxylic acid. 121 matched cddid_all.tbl CDD cd03192 cd03192 198301 GST_C_Sigma_like C-terminal, alpha helical domain of Class Sigma-like Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, Class Sigma_like; composed of GSTs belonging to class Sigma and similar proteins, including GSTs from class Mu, Pi, and Alpha. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Vertebrate class Sigma GSTs are characterized as GSH-dependent hematopoietic prostaglandin (PG) D synthases and are responsible for the production of PGD2 by catalyzing the isomerization of PGH2. The functions of PGD2 include the maintenance of body temperature, inhibition of platelet aggregation, bronchoconstriction, vasodilation, and mediation of allergy and inflammation. Other class Sigma-like members include the class II insect GSTs, S-crystallins from cephalopods, nematode-specific GSTs, and 28-kDa GSTs from parasitic flatworms. Drosophila GST2 is associated with indirect flight muscle and exhibits preference for catalyzing GSH conjugation to lipid peroxidation products, indicating an anti-oxidant role. S-crystallin constitutes the major lens protein in cephalopod eyes and is responsible for lens transparency and proper refractive index. The 28-kDa GST from Schistosoma is a multifunctional enzyme, exhibiting GSH transferase, GSH peroxidase, and PGD2 synthase activities, and may play an important role in host-parasite interactions. Members also include novel GSTs from the fungus Cunninghamella elegans, designated as class Gamma, and from the protozoan Blepharisma japonicum, described as a light-inducible GST. 104 matched cddid_all.tbl CDD cd03193 cd03193 198302 GST_C_Metaxin C-terminal, alpha helical domain of Metaxin and related proteins. Glutathione S-transferase (GST) C-terminal domain family, Metaxin subfamily; composed of metaxins and related proteins. Metaxin 1 is a component of a preprotein import complex of the mitochondrial outer membrane. It extends to the cytosol and is anchored to the mitochondrial membrane through its C-terminal domain. In mice, metaxin is required for embryonic development. In humans, alterations in the metaxin gene may be associated with Gaucher disease. Metaxin 2 binds to metaxin 1 and may also play a role in protein translocation into the mitochondria. Genome sequencing shows that a third metaxin gene also exists in zebrafish, Xenopus, chicken, and mammals. Sequence analysis suggests that all three metaxins share a common ancestry and that they possess similarity to GSTs. Also included in the subfamily are uncharacterized proteins with similarity to metaxins, including a novel GST from Rhodococcus with toluene o-monooxygenase and glutamylcysteine synthetase activities. Other members are the cadmium-inducible lysosomal protein CDR-1 and its homologs from C. elegans, and the failed axon connections (fax) protein from Drosophila. CDR-1 is an integral membrane protein that functions to protect against cadmium toxicity and may also have a role in osmoregulation to maintain salt balance in C. elegans. The fax gene of Drosophila was identified as a genetic modifier of Abelson (Abl) tyrosine kinase. The fax protein is localized in cellular membranes and is expressed in embryonic mesoderm and axons of the central nervous system. 88 matched cddid_all.tbl CDD cd03194 cd03194 198303 GST_C_3 C-terminal, alpha helical domain of an unknown subfamily 3 of Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, unknown subfamily 3; composed of uncharacterized proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. 115 matched cddid_all.tbl CDD cd03195 cd03195 198304 GST_C_4 C-terminal, alpha helical domain of an unknown subfamily 4 of Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, unknown subfamily 4; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. 114 matched cddid_all.tbl CDD cd03196 cd03196 198305 GST_C_5 C-terminal, alpha helical domain of an unknown subfamily 5 of Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, unknown subfamily 5; composed of uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. 115 matched cddid_all.tbl CDD cd03197 cd03197 198306 GST_C_mPGES2 C-terminal, alpha helical domain of microsomal Prostaglandin E synthase Type 2. Glutathione S-transferase (GST) C-terminal domain family, microsomal Prostaglandin E synthase Type 2 (mPGES2) subfamily; mPGES2 is a membrane-anchored dimeric protein containing a CXXC motif which catalyzes the isomerization of PGH2 to PGE2. Unlike cytosolic PGE synthase (cPGES) and microsomal PGES Type 1 (mPGES1), mPGES2 does not require glutathione (GSH) for its activity, although its catalytic rate is increased two- to four-fold in the presence of DTT, GSH, or other thiol compounds. PGE2 is widely distributed in various tissues and is implicated in the sleep/wake cycle, relaxation/contraction of smooth muscle, excretion of sodium ions, maintenance of body temperature, and mediation of inflammation. mPGES2 contains an N-terminal hydrophobic domain which is membrane associated and a C-terminal soluble domain with a GST-like structure. The C-terminal GST-like domain contains two structural domains, an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain. The GST active site is located in a cleft between the two structural domains. 149 matched cddid_all.tbl CDD cd03198 cd03198 198307 GST_C_CLIC C-terminal, alpha helical domain of Chloride Intracellular Channels. Glutathione S-transferase (GST) C-terminal domain family, Chloride Intracellular Channel (CLIC) subfamily; composed of CLICs (CLIC1-6 in vertebrates), p64, parchorin, and similar proteins. They are auto-inserting, self-assembling intracellular anion channels involved in a wide variety of functions including regulated secretion, cell division, and apoptosis. They can exist in both water-soluble and membrane-bound states and are found in various vesicles and membranes, and they may play roles in the maintenance of these intracellular membranes. Biochemical studies of the Caenorhabditis elegans homolog, EXC-4, show that the membrane localization domain is present in the N-terminal part of the protein. CLICs display structural plasticity, with CLIC1 adopting two soluble conformations. The structure of soluble human CLIC1 reveals that it is monomeric and adopts a fold similar to GSTs, containing an N-terminal domain with a thioredoxin fold and a C-terminal alpha helical domain. Upon oxidation, the N-terminal domain of CLIC1 undergoes a structural change to form a non-covalent dimer stabilized by the formation of an intramolecular disulfide bond between two cysteines that are far apart in the reduced form. The CLIC1 dimer bears no similarity to GST dimers. The redox-controlled structural rearrangement exposes a large hydrophobic surface, which is masked by dimerization in vitro. In vivo, this surface may represent the docking interface of CLIC1 in its membrane-bound state. The two cysteines in CLIC1 that form the disulfide bond in oxidizing conditions are essential for dimerization and chloride channel activity, however, in other subfamily members, the second cysteine is not conserved. 119 matched cddid_all.tbl CDD cd03199 cd03199 198308 GST_C_GRX2 C-terminal, alpha helical domain of Glutaredoxin 2. Glutathione S-transferase (GST) C-terminal domain family, Glutaredoxin 2 (GRX2) subfamily; composed of Escherichia coli GRX2 and similar proteins. Escherichia coli GRX2 is an atypical GRX with a molecular mass of about 24kD (most GRXs range from 9-12kD). It adopts a GST fold containing an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain. It contains a redox active CXXC motif located in the N-terminal domain, but is not able to reduce ribonucleotide reductase like other GRXs. However, it catalyzes GSH-dependent protein disulfide reduction of other substrates efficiently. GRX2 is thought to function primarily in catalyzing the reversible glutathionylation of proteins in cellular redox regulation including stress responses. 128 matched cddid_all.tbl CDD cd03200 cd03200 198309 GST_C_AIMP2 Glutathione S-transferase C-terminal-like, alpha helical domain of Aminoacyl tRNA synthetase complex-Interacting Multifunctional Protein 2. Glutathione S-transferase (GST) C-terminal domain family, Aminoacyl tRNA synthetase complex-Interacting Multifunctional Protein (AIMP) 2 subfamily; AIMPs are non-enzymatic cofactors that play critical roles in the assembly and formation of a macromolecular multi-tRNA synthetase protein complex that functions as a molecular hub to coordinate protein synthesis. There are three AIMPs, named AIMP1-3, which play diverse regulatory roles. AIMP2, also called p38 or JTV-1, contains a C-terminal domain with similarity to the C-terminal alpha helical domain of GSTs. It plays an important role in the control of cell fate via antiproliferative (by enhancing the TGF-beta signal) and proapoptotic (activation of p53 and TNF-alpha) activities. Its roles in the control of cell proliferation and death suggest that it is a potent tumor suppressor. AIMP2 heterozygous mice with lower than normal expression of AIMP2 show high susceptibility to tumorigenesis. AIMP2 is also a substrate of Parkin, an E3 ubiquitin ligase that is involved in the ubiquitylation and proteasomal degradation of its substrates. Mutations in the Parkin gene is found in 50% of patients with autosomal-recessive early-onset parkinsonism. The accumulation of AIMP2, due to impaired Parkin function, may play a role in the pathogenesis of Parkinson's disease. 96 matched cddid_all.tbl CDD cd03201 cd03201 198310 GST_C_DHAR C-terminal, alpha helical domain of Dehydroascorbate Reductase. Glutathione S-transferase (GST) C-terminal domain family, Dehydroascorbate Reductase (DHAR) subfamily; composed of plant-specific DHARs, which are monomeric enzymes catalyzing the reduction of DHA into ascorbic acid (AsA) using glutathione as the reductant. DHAR allows plants to recycle oxidized AsA before it is lost. AsA serves as a cofactor of violaxanthin de-epoxidase in the xanthophyll cycle and as an antioxidant in the detoxification of reactive oxygen species. Because AsA is the major reductant in plants, DHAR serves to regulate their redox state. It has been suggested that a significant portion of DHAR activity is plastidic, acting to reduce the large amounts of ascorbate oxidized during hydrogen peroxide scavenging by ascorbate peroxidase. DHAR contains a conserved cysteine in its active site and in addition to its reductase activity, shows thiol transferase activity similar to glutaredoxins. 121 matched cddid_all.tbl CDD cd03202 cd03202 198311 GST_C_etherase_LigE C-terminal, alpha helical domain of Beta etherase LigE. Glutathione S-transferase (GST) C-terminal domain family, Beta etherase LigE subfamily; composed of proteins similar to Sphingomonas paucimobilis beta etherase, LigE, a GST-like protein that catalyzes the cleavage of the beta-aryl ether linkages present in low-moleculer weight lignins using GSH as the hydrogen donor. This reaction is an essential step in the degradation of lignin, a complex phenolic polymer that is the most abundant aromatic material in the biosphere. The beta etherase activity of LigE is enantioselective and it complements the activity of the other GST family beta etherase, LigF. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. 124 matched cddid_all.tbl CDD cd03203 cd03203 198312 GST_C_Lambda C-terminal, alpha helical domain of Class Lambda Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, Class Lambda subfamily; composed of plant-specific class Lambda GSTs. GSTs are cytosolic, usually dimeric, proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. The class Lambda subfamily was recently discovered, together with dehydroascorbate reductases (DHARs), as two outlying groups of the GST superfamily in Arabidopsis thaliana, which contain conserved active site cysteines. Characterization of recombinant A. thaliana proteins show that Lambda class GSTs are monomeric, similar to DHARs. They do not exhibit GSH conjugating or DHAR activities, but are active as thiol transferases, similar to glutaredoxins. Members of this subfamily were originally identified as encoded proteins of the In2-1 gene, which can be induced by treatment with herbicide safeners. 120 matched cddid_all.tbl CDD cd03204 cd03204 198313 GST_C_GDAP1_like C-terminal, alpha helical domain of Ganglioside-induced differentiation-associated protein 1-like proteins. Glutathione S-transferase (GST) C-terminal domain family, Ganglioside-induced differentiation-associated protein 1 (GDAP1)-like subfamily; GDAP1 was originally identified as a highly expressed gene at the differentiated stage of GD3 synthase-transfected cells. More recently, mutations in GDAP1 have been reported to cause both axonal and demyelinating autosomal-recessive Charcot-Marie-Tooth (CMT) type 4A neuropathy. CMT is characterized by slow and progressive weakness and atrophy of muscles. Sequence analysis of GDAP1 shows similarities and differences with GSTs; it appears to contain both N-terminal thioredoxin-fold and C-terminal alpha helical domains of GSTs, however, it also contains additional C-terminal transmembrane domains unlike GSTs. GDAP1 is mainly expressed in neuronal cells and is localized in the mitochondria through its transmembrane domains. It does not exhibit GST activity using standard substrates. 111 matched cddid_all.tbl CDD cd03205 cd03205 198314 GST_C_6 C-terminal, alpha helical domain of an unknown subfamily 6 of Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, unknown subfamily 6; composed of uncharacterized bacterial proteins with similarity to GSTs, including Pseudomonas fluorescens GST with a known three-dimensional structure. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Though the three-dimensional structure of Pseudomonas fluorescens GST has been determined, there is no information on its functional characterization. 109 matched cddid_all.tbl CDD cd03206 cd03206 198315 GST_C_7 C-terminal, alpha helical domain of an unknown subfamily 7 of Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, unknown subfamily 7; composed of uncharacterized proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. 100 matched cddid_all.tbl CDD cd03207 cd03207 198316 GST_C_8 C-terminal, alpha helical domain of an unknown subfamily 8 of Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, unknown subfamily 8; composed of Agrobacterium tumefaciens GST and other uncharacterized bacterial proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. The three-dimensional structure of Agrobacterium tumefaciens GST has been determined but there is no information on its functional characterization. 101 matched cddid_all.tbl CDD cd03208 cd03208 198317 GST_C_Alpha C-terminal, alpha helical domain of Class Alpha Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, Class Alpha subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. The class Alpha subfamily is composed of vertebrate GSTs which can form homodimer and heterodimers. There are at least six types of class Alpha GST subunits in rats, four of which have human counterparts, resulting in many possible isoenzymes with different activities, tissue distribution and substrate specificities. Human GSTA1-1 and GSTA2-2 show high GSH peroxidase activity. GSTA3-3 catalyzes the isomerization of intermediates in steroid hormone biosynthesis. GSTA4-4 preferentially catalyzes the GSH conjugation of alkenals. 135 matched cddid_all.tbl CDD cd03209 cd03209 198318 GST_C_Mu C-terminal, alpha helical domain of Class Mu Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, Class Mu subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. The class Mu subfamily is composed of eukaryotic GSTs. In rats, at least six distinct class Mu subunits have been identified, with homologous genes in humans for five of these subunits. Class Mu GSTs can form homodimers and heterodimers, giving a large number of possible isoenzymes that can be formed, all with overlapping activities but different substrate specificities. They are the most abundant GSTs in human liver, skeletal muscle and brain, and are believed to provide protection against diseases including cancer and neurodegenerative disorders. Some isoenzymes have additional specific functions. Human GST M1-1 acts as an endogenous inhibitor of ASK1 (apoptosis signal-regulating kinase 1) thereby suppressing ASK1-mediated cell death. Human GSTM2-2 and 3-3 have been identified as prostaglandin E2 synthases in the brain and may play crucial roles in temperature and sleep-wake regulation. 121 matched cddid_all.tbl CDD cd03210 cd03210 198319 GST_C_Pi C-terminal, alpha helical domain of Class Pi Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, Class Pi subfamily; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Class Pi GST is a homodimeric eukaryotic protein. The human GSTP1 is mainly found in erythrocytes, kidney, placenta and fetal liver. It is involved in stress responses and in cellular proliferation pathways as an inhibitor of JNK (c-Jun N-terminal kinase). Following oxidative stress, monomeric GSTP1 dissociates from JNK and dimerizes, losing its ability to bind JNK and causing an increase in JNK activity, thereby promoting apoptosis. GSTP1 is expressed in various tumors and is the predominant GST in a wide range of cancer cells. It has been implicated in the development of multidrug-resistant tumors. 126 matched cddid_all.tbl CDD cd03211 cd03211 198320 GST_C_Metaxin2 C-terminal, alpha helical domain of Metaxin 2. Glutathione S-transferase (GST) C-terminal domain family, Metaxin subfamily, Metaxin 2; a metaxin 1 binding protein identified through a yeast two-hybrid system using metaxin 1 as the bait. Metaxin 2 shares sequence similarity with metaxin 1 but does not contain a C-terminal mitochondrial outer membrane signal-anchor domain. It associates with mitochondrial membranes through its interaction with metaxin 1, which is a component of the mitochondrial preprotein import complex of the outer membrane. The biological function of metaxin 2 is unknown. It is likely that it also plays a role in protein translocation into the mitochondria. However, this has not been experimentally validated. In a recent proteomics study, it has been shown that metaxin 2 is overexpressed in response to lipopolysaccharide-induced liver injury. 126 matched cddid_all.tbl CDD cd03212 cd03212 198321 GST_C_Metaxin1_3 C-terminal, alpha helical domain of Metaxin 1, Metaxin 3, and similar proteins. Glutathione S-transferase (GST) C-terminal domain family, Metaxin subfamily, Metaxin 1-like proteins; composed of metaxins 1 and 3, and similar proteins. Mammalian metaxin (or metaxin 1) is a component of the preprotein import complex of the mitochondrial outer membrane. Metaxin extends to the cytosol and is anchored to the mitochondrial membrane through its C-terminal domain. In mice, metaxin is required for embryonic development. Like the murine gene, the human metaxin gene is located downstream to the glucocerebrosidase (GBA) pseudogene and is convergently transcribed. Inherited deficiency of GBA results in Gaucher disease, which presents many diverse clinical phenotypes. Alterations in the metaxin gene, in addition to GBA mutations, may be associated with Gaucher disease. Genome sequencing shows that a third metaxin gene also exists in zebrafish, Xenopus, chicken, and mammals. 137 matched cddid_all.tbl CDD cd03213 cd03213 213180 ABCG_EPDR Eye pigment and drug resistance transporter subfamily G of the ATP-binding cassette superfamily. ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR). DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus. 194 matched cddid_all.tbl CDD cd03214 cd03214 213181 ABC_Iron-Siderophores_B12_Hemin ATP-binding component of iron-siderophores, vitamin B12 and hemin transporters and related proteins. ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea. Only very few species lack representatives of the siderophore family transporters. The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake. The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA. The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme. A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters. 180 matched cddid_all.tbl CDD cd03215 cd03215 213182 ABC_Carb_Monos_II Second domain of the ATP-binding cassette component of monosaccharide transport system. This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. In members of Carb_Monos family the single hydrophobic gene product forms a homodimer, while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter. 182 matched cddid_all.tbl CDD cd03216 cd03216 213183 ABC_Carb_Monos_I First domain of the ATP-binding cassette component of monosaccharide transport system. This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos). The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter. 163 matched cddid_all.tbl CDD cd03217 cd03217 213184 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component. Biosynthesis of iron-sulfur clusters (Fe-S) depends on multi-protein systems. The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions. The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet. 200 matched cddid_all.tbl CDD cd03218 cd03218 213185 ABC_YhbG ATP-binding cassette component of YhbG transport system. The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids. The genes yhbG and yhbN are located in a single operon and may function together in cell envelope during biogenesis. YhbG is the putative ATP-binding cassette component and YhbN is the putative periplasmic-binding protein. Depletion of each gene product leads to growth arrest, irreversible cell damage and loss of viability in E. coli. The YhbG homolog (NtrA) is essential in Rhizobium meliloti, a symbiotic nitrogen-fixing bacterium. 232 matched cddid_all.tbl CDD cd03219 cd03219 213186 ABC_Mj1267_LivG_branched ATP-binding cassette component of branched chain amino acids transport system. The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine. MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E. coli branched-chain amino acid transporter. MJ1267 contains an insertion from residues 114 to 123 characteristic of LivG (Leucine-Isoleucine-Valine) homologs. The branched-chain amino acid transporter from E. coli comprises a heterodimer of ABCs (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ). 236 matched cddid_all.tbl CDD cd03220 cd03220 213187 ABC_KpsT_Wzt ATP-binding cassette component of polysaccharide transport system. The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export. Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and teichoic acids have been shown to be exported by ABC transporters. A typical system is made of a conserved integral membrane and an ABC. In addition to these proteins, capsular polysaccharide exporter systems require two 'accessory' proteins to perform their function: a periplasmic (E.coli) or a lipid-anchored outer membrane protein called OMA (Neisseria meningitidis and Haemophilus influenza) and a cytoplasmic membrane protein MPA2. 224 matched cddid_all.tbl CDD cd03221 cd03221 213188 ABCF_EF-3 ATP-binding cassette domain of elongation factor 3, subfamily F. Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions. 144 matched cddid_all.tbl CDD cd03222 cd03222 213189 ABC_RNaseL_inhibitor ATP-binding cassette domain of RNase L inhibitor. The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology. 177 matched cddid_all.tbl CDD cd03223 cd03223 213190 ABCD_peroxisomal_ALDP ATP-binding cassette domain of peroxisomal transporter, subfamily D. Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asymptomatic). 166 matched cddid_all.tbl CDD cd03224 cd03224 213191 ABC_TM1139_LivF_branched ATP-binding cassette domain of branched-chain amino acid transporter. LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. 222 matched cddid_all.tbl CDD cd03225 cd03225 213192 ABC_cobalt_CbiO_domain1 First domain of the ATP-binding cassette component of cobalt transport system. Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems. 211 matched cddid_all.tbl CDD cd03226 cd03226 213193 ABC_cobalt_CbiO_domain2 Second domain of the ATP-binding cassette component of cobalt transport system. Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems. 205 matched cddid_all.tbl CDD cd03227 cd03227 213194 ABC_Class2 ATP-binding cassette domain of non-transporter proteins. ABC-type Class 2 contains systems involved in cellular processes other than transport. These families are characterized by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins. 162 matched cddid_all.tbl CDD cd03228 cd03228 213195 ABCC_MRP_Like ATP-binding cassette domain of multidrug resistance protein-like transporters. The MRP (Multidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export. They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 171 matched cddid_all.tbl CDD cd03229 cd03229 213196 ABC_Class3 ATP-binding cassette domain of the binding protein-dependent transport systems. This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 178 matched cddid_all.tbl CDD cd03230 cd03230 213197 ABC_DR_subfamily_A ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A. This family of ATP-binding proteins belongs to a multi-subunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryotic systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 173 matched cddid_all.tbl CDD cd03231 cd03231 213198 ABC_CcmA_heme_exporter Cytochrome c biogenesis ATP-binding export protein. CcmA, the ATP-binding component of the bacterial CcmAB transporter. The CCM family is involved in bacterial cytochrome c biogenesis. Cytochrome c maturation in E. coli requires the ccm operon, which encodes eight membrane proteins (CcmABCDEFGH). CcmE is a periplasmic heme chaperon that binds heme covalently and transfers it onto apocytochrome c in the presence of CcmF, CcmG, and CcmH. The CcmAB proteins represent an ABC transporter and the CcmCD proteins participate in heme transfer to CcmE. 201 matched cddid_all.tbl CDD cd03232 cd03232 213199 ABCG_PDR_domain2 Second domain of the pleiotropic drug resistance-like (PDR) subfamily G of ATP-binding cassette transporters. The pleiotropic drug resistance (PDR) is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 192 matched cddid_all.tbl CDD cd03233 cd03233 213200 ABCG_PDR_domain1 First domain of the pleiotropic drug resistance-like subfamily G of ATP-binding cassette transporters. The pleiotropic drug resistance (PDR) is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes. This PDR subfamily represents domain I of its (ABC-IM)2 organization. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 202 matched cddid_all.tbl CDD cd03234 cd03234 213201 ABCG_White White pigment protein homolog of ABCG transporter subfamily. The White subfamily represents ABC transporters homologous to the Drosophila white gene, which acts as a dimeric importer for eye pigment precursors. The eye pigmentation of Drosophila is developed from the synthesis and deposition in the cells of red pigments, which are synthesized from guanine, and brown pigments, which are synthesized from tryptophan. The pigment precursors are encoded by the white, brown, and scarlet genes, respectively. Evidence from genetic and biochemical studies suggest that the White and Brown proteins function as heterodimers to import guanine, while the White and Scarlet proteins function to import tryptophan. However, a recent study also suggests that White may be involved in the transport of a metabolite, such as 3-hydroxykynurenine, across intracellular membranes. Mammalian ABC transporters belonging to the White subfamily (ABCG1, ABCG5, and ABCG8) have been shown to be involved in the regulation of lipid-trafficking mechanisms in macrophages, hepatocytes, and intestinal mucosa cells. ABCG1 (ABC8), the human homolog of the Drosophila white gene is induced in monocyte-derived macrophages during cholesterol influx mediated by acetylated low-density lipoprotein. It is possible that human ABCG1 forms heterodimers with several heterologous partners. 226 matched cddid_all.tbl CDD cd03235 cd03235 213202 ABC_Metallic_Cations ATP-binding cassette domain of the metal-type transporters. This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-siderophore uptake family suggesting that they share a common ancestor. The best characterized metal-type ABC transporters are the YfeABCD system of Y. pestis, the SitABCD system of Salmonella enterica serovar Typhimurium, and the SitABCD transporter of Shigella flexneri. Moreover other uncharacterized homologs of these metal-type transporters are mainly found in pathogens like Haemophilus or enteroinvasive E. coli isolates. 213 matched cddid_all.tbl CDD cd03236 cd03236 213203 ABC_RNaseL_inhibitor_domain1 The ATP-binding cassette domain 1 of RNase L inhibitor. The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI s are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLIs have an N-terminal Fe-S domain and two nucleotide binding domains which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology. 255 matched cddid_all.tbl CDD cd03237 cd03237 213204 ABC_RNaseL_inhibitor_domain2 The ATP-binding cassette domain 2 of RNase L inhibitor. The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity of more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology. 246 matched cddid_all.tbl CDD cd03238 cd03238 213205 ABC_UvrA ATP-binding cassette domain of the excision repair protein UvrA. Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases. 176 matched cddid_all.tbl CDD cd03239 cd03239 213206 ABC_SMC_head The SMC head domain belongs to the ATP-binding cassette superfamily. The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair, and epigenetic silencing of gene expression. 178 matched cddid_all.tbl CDD cd03240 cd03240 213207 ABC_Rad50 ATP-binding cassette domain of Rad50. The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains. The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence. 204 matched cddid_all.tbl CDD cd03241 cd03241 213208 ABC_RecN ATP-binding cassette domain of RecN. RecN ATPase involved in DNA repair; similar to ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 276 matched cddid_all.tbl CDD cd03242 cd03242 213209 ABC_RecF ATP-binding cassette domain of RecF. RecF is a recombinational DNA repair ATPase that maintains replication in the presence of DNA damage. When replication is prematurely disrupted by DNA damage, several recF pathway gene products play critical roles processing the arrested replication fork, allowing it to resume and complete its task. This CD represents the nucleotide binding domain of RecF. RecF belongs to a large superfamily of ABC transporters involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases with a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 270 matched cddid_all.tbl CDD cd03243 cd03243 213210 ABC_MutS_homologs ATP-binding cassette domain of MutS homologs. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. 202 matched cddid_all.tbl CDD cd03244 cd03244 213211 ABCC_MRP_domain2 ATP-binding cassette domain 2 of multidrug resistance-associated protein. The ABC subfamily C is also known as MRP (multidrug resistance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate. 221 matched cddid_all.tbl CDD cd03245 cd03245 213212 ABCC_bacteriocin_exporters ATP-binding cassette domain of bacteriocin exporters, subfamily C. Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two glycine residues in positions -1 and -2. A dedicated ATP-binding cassette (ABC) transporter is responsible for the proteolytic cleavage of the leader peptides and subsequent translocation of the bacteriocins across the cytoplasmic membrane. 220 matched cddid_all.tbl CDD cd03246 cd03246 213213 ABCC_Protease_Secretion ATP-binding cassette domain of PrtD, subfamily C. This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain. They export degradative enzymes by using a type I protein secretion system and lack an N-terminal signal peptide, but contain a C-terminal secretion signal. The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP). For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli. The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior. HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels. The spectrum of transport substrates ranges from inorganic ions, nutrients such as amino acids, sugars, or peptides, hydrophobic drugs, to large polypeptides, such as HlyA. 173 matched cddid_all.tbl CDD cd03247 cd03247 213214 ABCC_cytochrome_bd ATP-binding cassette domain of CydCD, subfamily C. The CYD subfamily implicated in cytochrome bd biogenesis. The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes. CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space. In Bacillus subtilis, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism. 178 matched cddid_all.tbl CDD cd03248 cd03248 213215 ABCC_TAP ATP-binding cassette domain of the Transporter Associated with Antigen Processing, subfamily C. TAP (Transporter Associated with Antigen Processing) is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules. Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells. Subsequently, virus-infected or malignantly transformed cells can be eliminated. TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes. 226 matched cddid_all.tbl CDD cd03249 cd03249 213216 ABC_MTABC3_MDL1_MDL2 ATP-binding cassette domain of a mitochondrial protein MTABC3 and related proteins. MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1. In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD. MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another. 238 matched cddid_all.tbl CDD cd03250 cd03250 213217 ABCC_MRP_domain1 ATP-binding cassette domain 1 of multidrug resistance-associated protein, subfamily C. This subfamily is also known as MRP (multidrug resistance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate. 204 matched cddid_all.tbl CDD cd03251 cd03251 213218 ABCC_MsbA ATP-binding cassette domain of the bacterial lipid flippase and related proteins, subfamily C. MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 234 matched cddid_all.tbl CDD cd03252 cd03252 213219 ABCC_Hemolysin ATP-binding cassette domain of hemolysin B, subfamily C. The ABC-transporter hemolysin B is a central component of the secretion machinery that translocates the toxin, hemolysin A, in a Sec-independent fashion across both membranes of E. coli. The hemolysin A (HlyA) transport machinery is composed of the ATP-binding cassette (ABC) transporter HlyB located in the inner membrane, hemolysin D (HlyD), also anchored in the inner membrane, and TolC, which resides in the outer membrane. HlyD apparently forms a continuous channel that bridges the entire periplasm, interacting with TolC and HlyB. This arrangement prevents the appearance of periplasmic intermediates of HlyA during substrate transport. Little is known about the molecular details of HlyA transport, but it is evident that ATP-hydrolysis by the ABC-transporter HlyB is a necessary source of energy. 237 matched cddid_all.tbl CDD cd03253 cd03253 213220 ABCC_ATM1_transporter ATP-binding cassette domain of iron-sulfur clusters transporter, subfamily C. ATM1 is an ABC transporter that is expressed in the mitochondria. Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to mitochondrial DNA, and decreased levels of cytosolic heme proteins. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 236 matched cddid_all.tbl CDD cd03254 cd03254 213221 ABCC_Glucan_exporter_like ATP-binding cassette domain of glucan transporter and related proteins, subfamily C. Glucan exporter ATP-binding protein. In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virulence factor. This subfamily belongs to the MRP-like family and is involved in drug, peptide, and lipid export. The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains each composed of six transmembrane (TM) helices and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 229 matched cddid_all.tbl CDD cd03255 cd03255 213222 ABC_MJ0796_LolCDE_FtsE ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and Cell division ATP-binding protein FtsE. This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of lipoproteins from the cytoplasmic membrane (LolCDE). They are clustered together phylogenetically. MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all. The FtsEX complex resembles an ABC transporter, where FtsE is the ATPase and the membrane subunit FtsX resembles a permease subunit. But rather than transporting any substrate, the complex acts in cell division by undergoing conformational changes that alter the activity of cell wall hydrolases located outside the plasma membrane. The complex is widely conserved in bacteria, but also extremely divergent in sequence between different lineages. The LolCDE complex catalyzes the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane. 218 matched cddid_all.tbl CDD cd03256 cd03256 213223 ABC_PhnC_transporter ATP-binding cassette domain of the binding protein-dependent phosphonate transport system. Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only prokaryotic microorganisms are able to cleave this bond. Certain bacteria such as E. coli can use alkylphosphonates as a phosphorus source. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 241 matched cddid_all.tbl CDD cd03257 cd03257 213224 ABC_NikE_OppD_transporters ATP-binding cassette domain of nickel/oligopeptides specific transporters. The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE). The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis. The molecular mechanism of nickel uptake in many bacteria and most archaea is not known. Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides. The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF. 228 matched cddid_all.tbl CDD cd03258 cd03258 213225 ABC_MetN_methionine_transporter ATP-binding cassette domain of methionine transporter. MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport. Other members of this system include the MetP permease and the MetQ substrate binding protein. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 233 matched cddid_all.tbl CDD cd03259 cd03259 213226 ABC_Carb_Solutes_like ATP-binding cassette domain of the carbohydrate and solute transporters-like. This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 213 matched cddid_all.tbl CDD cd03260 cd03260 213227 ABC_PstB_phosphate_transporter ATP-binding cassette domain of the phosphate transport system. Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient. The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes. The PstS protein is a phosphate-binding protein located in the periplasmic space. PstA and PstC are hydrophobic and they form the transmembrane portion of the Pst system. PstB is the catalytic subunit, which couples the energy of ATP hydrolysis to the import of phosphate across cellular membranes through the Pst system, often referred as ABC-protein. PstB belongs to one of the largest superfamilies of proteins characterized by a highly conserved adenosine triphosphate (ATP) binding cassette (ABC), which is also a nucleotide binding domain (NBD). 227 matched cddid_all.tbl CDD cd03261 cd03261 213228 ABC_Org_Solvent_Resistant ATP-binding cassette transport system involved in resistance to organic solvents. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 235 matched cddid_all.tbl CDD cd03262 cd03262 213229 ABC_HisP_GlnQ ATP-binding cassette domain of the histidine and glutamine transporters. HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, respectively. Histidine permease is a multi-subunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP. HisP has properties intermediate between those of integral and peripheral membrane proteins and is accessible from both sides of the membrane, presumably by its interaction with HisQ and HisM. The two HisP subunits form a homodimer within the complex. The domain structure of the amino acid uptake systems is typical for prokaryotic extracellular solute binding protein-dependent uptake systems. All of the amino acid uptake systems also have at least one, and in a few cases, two extracellular solute binding proteins located in the periplasm of Gram-negative bacteria, or attached to the cell membrane of Gram-positive bacteria. The best-studied member of the PAAT (polar amino acid transport) family is the HisJQMP system of S. typhimurium, where HisJ is the extracellular solute binding proteins and HisP is the ABC protein. 213 matched cddid_all.tbl CDD cd03263 cd03263 213230 ABC_subfamily_A ATP-binding cassette domain of the lipid transporters, subfamily A. The ABCA subfamily mediates the transport of a variety of lipid compounds. Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders. The ABCA1 protein is involved in disorders of cholesterol transport and high-density lipoprotein (HDL) biosynthesis. The ABCA4 (ABCR) protein transports vitamin A derivatives in the outer segments of photoreceptor cells, and therefore, performs a crucial step in the visual cycle. The ABCA genes are not present in yeast. However, evolutionary studies of ABCA genes indicate that they arose as transporters that subsequently duplicated and that certain sets of ABCA genes were lost in different eukaryotic lineages. 220 matched cddid_all.tbl CDD cd03264 cd03264 213231 ABC_drug_resistance_like ABC-type multidrug transport system, ATPase component. The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 211 matched cddid_all.tbl CDD cd03265 cd03265 213232 ABC_DrrA Daunorubicin/doxorubicin resistance ATP-binding protein. DrrA is the ATP-binding protein component of a bacterial exporter complex that confers resistance to the antibiotics daunorubicin and doxorubicin. In addition to DrrA, the complex includes an integral membrane protein called DrrB. DrrA belongs to the ABC family of transporters and shares sequence and functional similarities with a protein found in cancer cells called P-glycoprotein. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 220 matched cddid_all.tbl CDD cd03266 cd03266 213233 ABC_NatA_sodium_exporter ATP-binding cassette domain of the Na+ transporter. NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled proton or K+ uptake. NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilis, NatAB is inducible by agents such as ethanol and protonophores, which lower the proton-motive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunorubicin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of a single ATP-binding protein and a single integral membrane protein. 218 matched cddid_all.tbl CDD cd03267 cd03267 213234 ABC_NatA_like ATP-binding cassette domain of an uncharacterized transporter similar in sequence to NatA. NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled to proton or K+ uptake. NatB possess six putative membrane spanning regions at its C-terminus. In B. subtilis, NatAB is inducible by agents such as ethanol and protonophores, which lower the proton-motive force across the membrane. The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunorubicin- and doxorubicin-efflux system. Hence, the functional NatAB is presumably assembled with two copies of the single ATP-binding protein and the single integral membrane protein. 236 matched cddid_all.tbl CDD cd03268 cd03268 213235 ABC_BcrA_bacitracin_resist ATP-binding cassette domain of the bacitracin-resistance transporter. The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance. Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis. The synthesis of bacitracin is non-ribosomally catalyzed by a multi-enzyme complex BcrABC. Bacitracin has potent antibiotic activity against gram-positive bacteria. The inhibition of peptidoglycan biosynthesis is the best characterized bacterial effect of bacitracin. The bacitracin resistance of B. licheniformis is mediated by the ABC transporter Bcr which is composed of two identical BcrA ATP-binding subunits and one each of the integral membrane proteins, BcrB and BcrC. B. subtilis cells carrying bcr genes on high-copy number plasmids develop collateral detergent sensitivity, a similar phenomenon in human cells with overexpressed multi-drug resistance P-glycoprotein. 208 matched cddid_all.tbl CDD cd03269 cd03269 213236 ABC_putative_ATPase ATP-binding cassette domain of an uncharacterized transporter. This subgroup is related to the subfamily A transporters involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity. In eubacteria and archaea, the typical organization consists of one ABC and one or two integral membranes. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 210 matched cddid_all.tbl CDD cd03270 cd03270 213237 ABC_UvrA_I ATP-binding cassette domain I of the excision repair protein UvrA. Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases. 226 matched cddid_all.tbl CDD cd03271 cd03271 213238 ABC_UvrA_II ATP-binding cassette domain II of the excision repair protein UvrA. Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion. Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins. Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins and UvrB having one ATP binding site that is structurally related to that of helicases. 261 matched cddid_all.tbl CDD cd03272 cd03272 213239 ABC_SMC3_euk ATP-binding cassette domain of eukaryotic SMC3 proteins. The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18). 243 matched cddid_all.tbl CDD cd03273 cd03273 213240 ABC_SMC2_euk ATP-binding cassette domain of eukaryotic SMC2 proteins. The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18). 251 matched cddid_all.tbl CDD cd03274 cd03274 213241 ABC_SMC4_euk ATP-binding cassette domain of eukaryotic SMC4 proteins. The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18). 212 matched cddid_all.tbl CDD cd03275 cd03275 213242 ABC_SMC1_euk ATP-binding cassette domain of eukaryotic SMC1 proteins. The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18). 247 matched cddid_all.tbl CDD cd03276 cd03276 213243 ABC_SMC6_euk ATP-binding cassette domain of eukaryotic SM6 proteins. The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18). 198 matched cddid_all.tbl CDD cd03277 cd03277 213244 ABC_SMC5_euk ATP-binding cassette domain of eukaryotic SMC5 proteins. The structural maintenance of chromosomes (SMC) proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18). 213 matched cddid_all.tbl CDD cd03278 cd03278 213245 ABC_SMC_barmotin ATP-binding cassette domain of barmotin, a member of the SMC protein family. Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18). 197 matched cddid_all.tbl CDD cd03279 cd03279 213246 ABC_sbcCD ATP-binding cassette domain of sbcCD. SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini. 213 matched cddid_all.tbl CDD cd03280 cd03280 213247 ABC_MutS2 ATP-binding cassette domain of MutS2. MutS2 homologs in bacteria and eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. 200 matched cddid_all.tbl CDD cd03281 cd03281 213248 ABC_MSH5_euk ATP-binding cassette domain of eukaryotic MutS5 homolog. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. 213 matched cddid_all.tbl CDD cd03282 cd03282 213249 ABC_MSH4_euk ATP-binding cassette domain of eukaryotic MutS4 homolog. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. 204 matched cddid_all.tbl CDD cd03283 cd03283 213250 ABC_MutS-like ATP-binding cassette domain of MutS-like homolog. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. 199 matched cddid_all.tbl CDD cd03284 cd03284 213251 ABC_MutS1 ATP-binding cassette domain of MutS1 homolog. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. 216 matched cddid_all.tbl CDD cd03285 cd03285 213252 ABC_MSH2_euk ATP-binding cassette domain of eukaryotic MutS2 homolog. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. 222 matched cddid_all.tbl CDD cd03286 cd03286 213253 ABC_MSH6_euk ATP-binding cassette domain of eukaryotic MutS6 homolog. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. 218 matched cddid_all.tbl CDD cd03287 cd03287 213254 ABC_MSH3_euk ATP-binding cassette domain of eukaryotic MutS3 homolog. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. 222 matched cddid_all.tbl CDD cd03288 cd03288 213255 ABCC_SUR2 ATP-binding cassette domain 2 of the sulfonylurea receptor SUR. The SUR domain 2. The sulfonylurea receptor SUR is an ATP binding cassette (ABC) protein of the ABCC/MRP family. Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel. Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism. It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity. 257 matched cddid_all.tbl CDD cd03289 cd03289 213256 ABCC_CFTR2 ATP-binding cassette domain 2 of CFTR,subfamily C. The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2. 275 matched cddid_all.tbl CDD cd03290 cd03290 213257 ABCC_SUR1_N ATP-binding cassette domain of the sulfonylurea receptor, subfamily C. The SUR domain 1. The sulfonylurea receptor SUR is an ATP transporter of the ABCC/MRP family with tandem ATPase binding domains. Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel. Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism. It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity. 218 matched cddid_all.tbl CDD cd03291 cd03291 213258 ABCC_CFTR1 ATP-binding cassette domain of the cystic fibrosis transmembrane regulator, subfamily C. The CFTR subfamily domain 1. The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia. Use of the term assembly of a functional ion channel implies the coming together of subunits, or at least smaller not-yet functional components of the active whole. In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells. CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2. 282 matched cddid_all.tbl CDD cd03292 cd03292 213259 ABC_FtsE Cell division ATP-binding protein FtsE. The FtsEX complex resembles an ABC transporter, where FtsE is the ATPase and the membrane subunit FtsX resembles a permease subunit. But rather than transporting any substrate, the complex acts in cell division by undergoing conformational changes that alter the activity of cell wall hydrolases located outside the plasma membrane. The complex is widely conserved in bacteria, but also extremely divergent in sequence between different lineages 214 matched cddid_all.tbl CDD cd03293 cd03293 213260 ABC_NrtD_SsuB_transporters ATP-binding cassette domain of the nitrate and sulfonate transporters. NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 220 matched cddid_all.tbl CDD cd03294 cd03294 213261 ABC_Pro_Gly_Betaine ATP-binding cassette domain of the osmoprotectant proline/glycine betaine uptake system. This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporters is the obligatory coupling of ATP hydrolysis to substrate translocation. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 269 matched cddid_all.tbl CDD cd03295 cd03295 213262 ABC_OpuCA_Osmoprotection ATP-binding cassette domain of the osmoprotectant transporter. OpuCA is a the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment. ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition, to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 242 matched cddid_all.tbl CDD cd03296 cd03296 213263 ABC_CysA_sulfate_importer ATP-binding cassette domain of the sulfate transporter. Part of the ABC transporter complex cysAWTP involved in sulfate import. Responsible for energy coupling to the transport system. The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a solute-binding protein (cysP). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 239 matched cddid_all.tbl CDD cd03297 cd03297 213264 ABC_ModC_molybdenum_transporter ATP-binding cassette domain of the molybdenum transport system. ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 214 matched cddid_all.tbl CDD cd03298 cd03298 213265 ABC_ThiQ_thiamine_transporter ATP-binding cassette domain of the thiamine transport system. Part of the binding-protein-dependent transport system tbpA-thiPQ for thiamine and TPP. Probably responsible for the translocation of thiamine across the membrane. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 211 matched cddid_all.tbl CDD cd03299 cd03299 213266 ABC_ModC_like ATP-binding cassette domain similar to the molybdate transporter. Archaeal protein closely related to ModC. ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 235 matched cddid_all.tbl CDD cd03300 cd03300 213267 ABC_PotA_N ATP-binding cassette domain of the polyamine transporter. PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D. PotA has two domains with the N-terminal domain containing the ATPase activity and the residues required for homodimerization with PotA and heterdimerization with PotB. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. 232 matched cddid_all.tbl CDD cd03301 cd03301 213268 ABC_MalK_N The N-terminal ATPase domain of the maltose transporter, MalK. ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles. ABC transporters contain two transmembrane-spanning domains (TMDs) or subunits and two nucleotide binding domains (NBDs) or subunits that couple transport to the hydrolysis of ATP. In the maltose transport system, the periplasmic maltose binding protein (MBP) stimulates the ATPase activity of the membrane-associated transporter, which consists of two transmembrane subunits, MalF and MalG, and two copies of the ATP binding subunit, MalK, and becomes tightly bound to the transporter in the catalytic transition state, ensuring that maltose is passed to the transporter as ATP is hydrolyzed. 213 matched cddid_all.tbl CDD cd03302 cd03302 176471 Adenylsuccinate_lyase_2 Adenylsuccinate lyase (ASL)_subgroup 2. This subgroup contains mainly eukaryotic proteins similar to ASL, a member of the Lyase class I family. Members of this family for the most part catalyze similar beta-elimination reactions in which a C-N or C-O bond is cleaved with the release of fumarate as one of the products. These proteins are active as tetramers. The four active sites of the homotetrameric enzyme are each formed by residues from three different subunits. ASL catalyzes two steps in the de novo purine biosynthesis: the conversion of 5-aminoimidazole-(N-succinylocarboxamide) ribotide (SAICAR) into 5-aminoimidazole-4-carboxamide ribotide (AICAR) and, the conversion of adenylsuccinate (SAMP) into adenosine monophosphate (AMP). ASL deficiency has been linked to several pathologies including psychomotor retardation with autistic features, epilepsy and muscle wasting. 436 matched cddid_all.tbl CDD cd03307 cd03307 239423 Mta_CmuA_like MtaA_CmuA_like family. MtaA/CmuA, also MtsA, or methyltransferase 2 (MT2) MT2-A and MT2-M isozymes, are methylcobamide:Coenzyme M methyltransferases, which play a role in metabolic pathways of methane formation from various substrates, such as methylated amines and methanol. Coenzyme M, 2-mercaptoethylsulfonate or CoM, is methylated during methanogenesis in a reaction catalyzed by three proteins. A methyltransferase methylates the corrinoid cofactor, which is bound to a second polypeptide, a corrinoid protein. The methylated corrinoid protein then serves as a substrate for MT2-A and related enzymes, which methylate CoM. 326 matched cddid_all.tbl CDD cd03308 cd03308 239424 CmuA_CmuC_like CmuA_CmuC_like: uncharacterized protein family similar to uroporphyrinogen decarboxylase (URO-D) and the methyltransferases CmuA and CmuC. 378 matched cddid_all.tbl CDD cd03309 cd03309 239425 CmuC_like CmuC_like. Proteins similar to the putative corrinoid methyltransferase CmuC. Its function has been inferred from sequence similarity to the methyltransferases CmuA and MtaA. Mutants of Methylobacterium sp. disrupted in cmuC and purU appear deficient in some step of chloromethane metabolism. 321 matched cddid_all.tbl CDD cd03310 cd03310 239426 CIMS_like CIMS - Cobalamine-independent methonine synthase, or MetE. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to L-homocysteine without using an intermediate methyl carrier. The active enzyme has a dual (beta-alpha)8-barrel structure, and this model covers both the N-and C-terminal barrel, and some single-barrel sequences, mostly from Archaea. It is assumed that the homologous N-terminal barrel has evolved from the C-terminus via gene duplication and has subsequently lost binding sites, and it seems as if the two barrels forming the active enzyme may sometimes reside on different polypeptides. The C-terminal domain incorporates the Zinc ion, which binds and activates homocysteine. Side chains from both barrels contribute to the binding of the folate substrate. 321 matched cddid_all.tbl CDD cd03311 cd03311 239427 CIMS_C_terminal_like CIMS - Cobalamine-independent methonine synthase, or MetE, C-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to L-homocysteine without using an intermediate methyl carrier. The active enzyme has a dual (beta-alpha)8-barrel structure, and this model covers the C-terminal barrel, and a few single-barrel sequences most similar to the C-terminal barrel. It is assumed that the homologous N-terminal barrel has evolved from the C-terminus via gene duplication and has subsequently lost binding sites, and it seems as if the two barrels forming the active enzyme may sometimes reside on different polypeptides. The C-terminal domain incorporates the Zinc ion, which binds and activates homocysteine. Sidechains from both barrels contribute to the binding of the folate substrate. 332 matched cddid_all.tbl CDD cd03312 cd03312 239428 CIMS_N_terminal_like CIMS - Cobalamine-independent methonine synthase, or MetE, N-terminal domain_like. Many members have been characterized as 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferases, EC:2.1.1.14, mostly from bacteria and plants. This enzyme catalyses the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to L-homocysteine without using an intermediate methyl carrier. The active enzyme has a dual (beta-alpha)8-barrel structure, and this model covers the N-terminal barrel, and a few single-barrel sequences most similar to the N-terminal barrel. It is assumed that the homologous N-terminal barrel has evolved from the C-terminus via gene duplication and has subsequently lost binding sites, and it seems as if the two barrels forming the active enzyme may sometimes reside on different polypeptides. The C-terminal domain incorporates the Zinc ion, which binds and activates homocysteine. Side chains from both barrels contribute to the binding of the folate substrate. 360 matched cddid_all.tbl CDD cd03313 cd03313 239429 enolase Enolase: Enolases are homodimeric enzymes that catalyse the reversible dehydration of 2-phospho-D-glycerate to phosphoenolpyruvate as part of the glycolytic and gluconeogenesis pathways. The reaction is facilitated by the presence of metal ions. 408 matched cddid_all.tbl CDD cd03314 cd03314 239430 MAL Methylaspartate ammonia lyase (3-methylaspartase, MAL) is a homodimeric enzyme, catalyzing the magnesium-dependent reversible alpha,beta-elimination of ammonia from L-threo-(2S,3S)-3-methylaspartic acid to mesaconic acid. This reaction is part of the main catabolic pathway for glutamate. MAL belongs to the enolase superfamily of enzymes, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. 369 matched cddid_all.tbl CDD cd03315 cd03315 239431 MLE_like Muconate lactonizing enzyme (MLE) like subgroup of the enolase superfamily. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and residues that can function as general acid/base catalysts, a Lys-X-Lys motif and another conserved lysine. Despite these conserved residues, the members of the MLE subgroup, like muconate lactonizing enzyme, o-succinylbenzoate synthase (OSBS) and N-acylamino acid racemase (NAAAR), catalyze different reactions. 265 matched cddid_all.tbl CDD cd03316 cd03316 239432 MR_like Mandelate racemase (MR)-like subfamily of the enolase superfamily. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues, a Lys-X-Lys motif and a conserved histidine-aspartate dyad. Members of the MR subgroup are mandelate racemase, D-glucarate/L-idarate dehydratase (GlucD), D-altronate/D-mannonate dehydratase , D-galactonate dehydratase (GalD) , D-gluconate dehydratase (GlcD), and L-rhamnonate dehydratase (RhamD). 357 matched cddid_all.tbl CDD cd03317 cd03317 239433 NAAAR N-acylamino acid racemase (NAAAR), an octameric enzyme that catalyzes the racemization of N-acylamino acids. NAAARs act on a broad range of N-acylamino acids rather than amino acids. Enantiopure amino acids are of industrial interest as chiral building blocks for antibiotics, herbicides, and drugs. NAAAR is a member of the enolase superfamily, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. 354 matched cddid_all.tbl CDD cd03318 cd03318 239434 MLE Muconate Lactonizing Enzyme (MLE), an homooctameric enzyme, catalyses the conversion of cis,cis-muconate (CCM) to muconolactone (ML) in the catechol branch of the beta-ketoadipate pathway. This pathway is used in soil microbes to breakdown lignin-derived aromatics, catechol and protocatechuate, to citric acid cycle intermediates. Some bacterial species are also capable of dehalogenating chloroaromatic compounds by the action of chloromuconate lactonizing enzymes (Cl-MLEs). MLEs are members of the enolase superfamily characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and that is stabilized by coordination to the essential Mg2+ ion. 365 matched cddid_all.tbl CDD cd03319 cd03319 239435 L-Ala-DL-Glu_epimerase L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism of the murein peptide of peptidoglycan, of which L-Ala-D-Glu is a component. L-Ala-D/L-Glu epimerase is a member of the enolase-superfamily, which is characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. 316 matched cddid_all.tbl CDD cd03320 cd03320 239436 OSBS o-Succinylbenzoate synthase (OSBS) catalyzes the conversion of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 4-(2'-carboxyphenyl)-4-oxobutyrate (o-succinylbenzoate or OSB), a reaction in the menaquinone biosynthetic pathway. Menaquinone is an essential cofactor for anaerobic growth in eubacteria and some archaea. OSBS belongs to the enolase superfamily of enzymes, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. 263 matched cddid_all.tbl CDD cd03321 cd03321 239437 mandelate_racemase Mandelate racemase (MR) catalyzes the Mg2+-dependent 1,1-proton transfer reaction that interconverts the enantiomers of mandelic acid. MR is the first enzyme in the bacterial pathway that converts mandelic acid to benzoic acid and allows this pathway to utilize either enantiomer of mandelate. MR belongs to the enolase superfamily of enzymes, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. 355 matched cddid_all.tbl CDD cd03322 cd03322 239438 RspA The starvation sensing protein RspA from E.coli and its homologs are lactonizing enzymes whose putative targets are homoserine lactone (HSL)-derivative. They are part of the mandelate racemase (MR)-like subfamily of the enolase superfamily. Enzymes of this subfamily share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and catalytic residues, a partially conserved Lys-X-Lys motif and a conserved histidine-aspartate dyad. 361 matched cddid_all.tbl CDD cd03323 cd03323 239439 D-glucarate_dehydratase D-Glucarate dehydratase (GlucD) catalyzes the dehydration of both D-glucarate and L-idarate to form 5-keto-4-deoxy-D-glucarate (5-KDG) , the initial reaction of the catabolic pathway for (D)-glucarate. GlucD belongs to the enolase superfamily of enzymes, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and that is stabilized by coordination to the essential Mg2+ ion. 395 matched cddid_all.tbl CDD cd03324 cd03324 239440 rTSbeta_L-fuconate_dehydratase Human rTS beta is encoded by the rTS gene which, through alternative RNA splicing, also encodes rTS alpha whose mRNA is complementary to thymidylate synthase mRNA. rTS beta expression is associated with the production of small molecules that appear to mediate the down-regulation of thymidylate synthase protein by a novel intercellular signaling mechanism. A member of this family, from Xanthomonas, has been characterized to be a L-fuconate dehydratase. rTS beta belongs to the enolase superfamily of enzymes, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. 415 matched cddid_all.tbl CDD cd03325 cd03325 239441 D-galactonate_dehydratase D-galactonate dehydratase catalyses the dehydration of galactonate to 2-keto-3-deoxygalactonate (KDGal), as part of the D-galactonate nonphosphorolytic catabolic Entner-Doudoroff pathway. D-galactonate dehydratase belongs to the enolase superfamily of enzymes, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion. 352 matched cddid_all.tbl CDD cd03326 cd03326 239442 MR_like_1 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 1. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues, a Lys-X-Lys motif and a conserved histidine-aspartate dyad. This subgroup's function is unknown. 385 matched cddid_all.tbl CDD cd03327 cd03327 239443 MR_like_2 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 2. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues, a Lys-X-Lys motif and a conserved histidine-aspartate dyad. This subgroup's function is unknown. 341 matched cddid_all.tbl CDD cd03328 cd03328 239444 MR_like_3 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 3. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues, a Lys-X-Lys motif and a conserved histidine-aspartate dyad. This subgroup's function is unknown. 352 matched cddid_all.tbl CDD cd03329 cd03329 239445 MR_like_4 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 4. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues, a Lys-X-Lys motif and a conserved histidine-aspartate dyad. This subgroup's function is unknown. 368 matched cddid_all.tbl CDD cd03330 cd03330 394879 Macro_Ttha0132-like "Macrodomain, uncharacterized family similar to Thermus thermophilus hypothetical protein Ttha0132. Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Macrodomains include the yeast macrodomain Poa1 which is a phosphatase of ADP-ribose-1""-phosphate, a by-product of tRNA splicing. Some macrodomains have ADPr-unrelated binding partners such as the coronavirus SUD-N (N-terminal subdomain) and SUD-M (middle subdomain) of the SARS-unique domain (SUD) which bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). Macrodomains regulate a wide variety of cellular and organismal processes, including DNA damage repair, signal transduction, and immune response. This family is composed of uncharacterized proteins containing a stand-alone macrodomain, similar to Thermus thermophilus hypothetical protein Ttha0132." 147 matched cddid_all.tbl CDD cd03331 cd03331 394880 Macro_Poa1p-like_SNF2 "macrodomain, Poa1p-like family, SNF2 subfamily. Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Members of this subfamily contain a C-terminal macrodomain that show similarity to the yeast protein Poa1p, reported to be a phosphatase specific for Appr-1""-p, a tRNA splicing metabolite. In addition, they also contain an SNF2 domain, defined by the presence of seven motifs with sequence similarity to DNA helicases. SNF2 proteins have the capacity to use the energy released by their DNA-dependent ATPase activity to stabilize or perturb protein-DNA interactions and play important roles in transcriptional regulation, maintenance of chromosome integrity and DNA repair." 152 matched cddid_all.tbl CDD cd03332 cd03332 239448 LMO_FMN L-Lactate 2-monooxygenase (LMO) FMN-binding domain. LMO is a FMN-containing enzyme that catalyzes the conversion of L-lactate and oxygen to acetate, carbon dioxide, and water. LMO is a member of the family of alpha-hydroxy acid oxidases. It is thought to be a homooctamer with two- and four- fold axes in the center of the octamer. 383 matched cddid_all.tbl CDD cd03333 cd03333 239449 chaperonin_like chaperonin_like superfamily. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. There are 2 main chaperonin groups. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). The symmetry of type II is eight- or nine-fold and they are found in archea (thermosome), thermophilic bacteria (TF55) and in the eukaryotic cytosol (CTT). Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. This superfamily also contains related domains from Fab1-like phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinases that only contain the intermediate and apical domains. 209 matched cddid_all.tbl CDD cd03334 cd03334 239450 Fab1_TCP TCP-1 like domain of the eukaryotic phosphatidylinositol 3-phosphate (PtdIns3P) 5-kinase Fab1. Fab1p is important for vacuole size regulation, presumably by modulating PtdIns(3,5)P2 effector activity. In the human homolog p235/PIKfyve deletion of this domain leads to loss of catalytic activity. However no exact function this domain has been defined. In general, chaperonins are involved in productive folding of proteins. 261 matched cddid_all.tbl CDD cd03335 cd03335 239451 TCP1_alpha TCP-1 (CTT or eukaryotic type II) chaperonin family, alpha subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin. 527 matched cddid_all.tbl CDD cd03336 cd03336 239452 TCP1_beta TCP-1 (CTT or eukaryotic type II) chaperonin family, beta subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin. 517 matched cddid_all.tbl CDD cd03337 cd03337 239453 TCP1_gamma TCP-1 (CTT or eukaryotic type II) chaperonin family, gamma subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin. 480 matched cddid_all.tbl CDD cd03338 cd03338 239454 TCP1_delta TCP-1 (CTT or eukaryotic type II) chaperonin family, delta subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin. 515 matched cddid_all.tbl CDD cd03339 cd03339 239455 TCP1_epsilon TCP-1 (CTT or eukaryotic type II) chaperonin family, epsilon subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin. 526 matched cddid_all.tbl CDD cd03340 cd03340 239456 TCP1_eta TCP-1 (CTT or eukaryotic type II) chaperonin family, eta subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin. 522 matched cddid_all.tbl CDD cd03341 cd03341 239457 TCP1_theta TCP-1 (CTT or eukaryotic type II) chaperonin family, theta subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin. 472 matched cddid_all.tbl CDD cd03342 cd03342 239458 TCP1_zeta TCP-1 (CTT or eukaryotic type II) chaperonin family, zeta subunit. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. In contrast to bacterial group I chaperonins (GroEL), each ring of the eukaryotic cytosolic chaperonin (CTT) consists of eight different, but homologous subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. The best studied in vivo substrates of CTT are actin and tubulin. 484 matched cddid_all.tbl CDD cd03343 cd03343 239459 cpn60 cpn60 chaperonin family. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings. Archaeal cpn60 (thermosome), together with TF55 from thermophilic bacteria and the eukaryotic cytosol chaperonin (CTT), belong to the type II group of chaperonins. Cpn60 consists of two stacked octameric rings, which are composed of one or two different subunits. Their common function is to sequester nonnative proteins inside their central cavity and promote folding by using energy derived from ATP hydrolysis. 517 matched cddid_all.tbl CDD cd03344 cd03344 239460 GroEL GroEL_like type I chaperonin. Chaperonins are involved in productive folding of proteins. They share a common general morphology, a double toroid of 2 stacked rings, each composed of 7-9 subunits. The symmetry of type I is seven-fold and they are found in eubacteria (GroEL) and in organelles of eubacterial descent (hsp60 and RBP). With the aid of cochaperonin GroES, GroEL encapsulates non-native substrate proteins inside the cavity of the GroEL-ES complex and promotes folding by using energy derived from ATP hydrolysis. 520 matched cddid_all.tbl CDD cd03345 cd03345 239461 eu_TyrOH Eukaryotic tyrosine hydroxylase (TyrOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH) and eukaryotic tryptophan hydroxylase (TrpOH). TyrOH catalyzes the conversion of tyrosine to L-dihydroxyphenylalanine (L-DOPA), the rate-limiting step in the biosynthesis of the catecholamines dopamine, noradrenaline, and adrenaline. 298 matched cddid_all.tbl CDD cd03346 cd03346 239462 eu_TrpOH Eukaryotic tryptophan hydroxylase (TrpOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes prokaryotic and eukaryotic phenylalanine-4-hydroxylase (PheOH) and eukaryotic tyrosine hydroxylase (TyrOH). TrpOH oxidizes L-tryptophan to 5-hydroxy-L-tryptophan, the rate-limiting step in the biosynthesis of serotonin (5-hydroxytryptamine), a widely distributed hormone and neurotransmitter. 287 matched cddid_all.tbl CDD cd03347 cd03347 239463 eu_PheOH Eukaryotic phenylalanine-4-hydroxylase (eu_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes prokaryotic phenylalanine-4-hydroxylase (pro_PheOH), eukaryotic tyrosine hydroxylase (TyrOH) and eukaryotic tryptophan hydroxylase (TrpOH). PheOH catalyzes the first and rate-limiting step in the metabolism of the amino acid L-phenylalanine (L-Phe), the hydroxylation of L-Phe to L-tyrosine (L-Tyr). It uses (6R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH4) as the physiological electron donor. The catalytic activity of the tetrameric enzyme is tightly regulated by the binding of L-Phe and BH4 as well as by phosphorylation. Mutations in the human enzyme are linked to a severe variant of phenylketonuria. 306 matched cddid_all.tbl CDD cd03348 cd03348 239464 pro_PheOH Prokaryotic phenylalanine-4-hydroxylase (pro_PheOH); a member of the biopterin-dependent aromatic amino acid hydroxylase family of non-heme, iron(II)-dependent enzymes that also includes the eukaryotic proteins, phenylalanine-4-hydroxylase (eu_PheOH), tyrosine hydroxylase (TyrOH) and tryptophan hydroxylase (TrpOH). PheOH catalyzes the hydroxylation of L-Phe to L-tyrosine (L-Tyr). It uses (6R)-L-erythro-5,6,7,8-tetrahydrobiopterin (BH4) as the physiological electron donor. 228 matched cddid_all.tbl CDD cd03349 cd03349 100040 LbH_XAT Xenobiotic acyltransferase (XAT): The XAT class of hexapeptide acyltransferases is composed of a large number of microbial enzymes that catalyze the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and streptogramin, among others. Members of this class of enzymes include Enterococcus faecium streptogramin A acetyltransferase and Pseudomonas aeruginosa chloramphenicol acetyltransferase. They contain repeated copies of a six-residue hexapeptide repeat sequence motif (X-[STAV]-X-[LIV]-[GAED]-X) and adopt a left-handed parallel beta helix (LbH) structure. The active enzyme is a trimer with CoA and substrate binding sites at the interface of two separate LbH subunits. XATs are implicated in inactivating xenobiotics leading to xenobiotic resistance in patients. 145 matched cddid_all.tbl CDD cd03350 cd03350 100041 LbH_THP_succinylT 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (also called THP succinyltransferase): THDP N-succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA. It is the committed step in the succinylase pathway by which bacteria synthesize L-lysine and meso-diaminopimelate, a component of peptidoglycan. The enzyme is homotrimeric and each subunit contains an N-terminal region with alpha helices and hairpin loops, as well as a C-terminal region with a left-handed parallel alpha-helix (LbH) structural motif encoded by hexapeptide repeat motifs. 139 matched cddid_all.tbl CDD cd03351 cd03351 100042 LbH_UDP-GlcNAc_AT UDP-N-acetylglucosamine O-acyltransferase (UDP-GlcNAc acyltransferase): Proteins in this family catalyze the transfer of (R)-3-hydroxymyristic acid from its acyl carrier protein thioester to UDP-GlcNAc. It is the first enzyme in the lipid A biosynthetic pathway and is also referred to as LpxA. Lipid A is essential for the growth of Escherichia coli and related bacteria. It is also essential for maintaining the integrity of the outer membrane. UDP-GlcNAc acyltransferase is a homotrimer of left-handed parallel beta helix (LbH) subunits. Each subunit contains an N-terminal LbH region with 9 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X), and a C-terminal alpha-helical region. 254 matched cddid_all.tbl CDD cd03352 cd03352 100043 LbH_LpxD UDP-3-O-acyl-glucosamine N-acyltransferase (LpxD): The enzyme catalyzes the transfer of 3-hydroxymyristic acid or 3-hydroxy-arachidic acid, depending on the organism, from the acyl carrier protein (ACP) to UDP-3-O-acyl-glucosamine to produce UDP-2,3-diacyl-GlcNAc. This constitutes the third step in the lipid A biosynthetic pathway in Gram-negative bacteria. LpxD is a homotrimer, with each subunit consisting of a novel combination of an N-terminal uridine-binding domain, a core lipid-binding left-handed parallel beta helix (LbH) domain, and a C-terminal alpha-helical extension. The LbH domain contains 9 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). 205 matched cddid_all.tbl CDD cd03353 cd03353 100044 LbH_GlmU_C N-acetyl-glucosamine-1-phosphate uridyltransferase (GlmU), C-terminal left-handed beta-helix (LbH) acetyltransferase domain: GlmU is also known as UDP-N-acetylglucosamine pyrophosphorylase. It is a bifunctional bacterial enzyme that catalyzes two consecutive steps in the formation of UDP-N-acetylglucosamine (UDP-GlcNAc), an important precursor in bacterial cell wall formation. The two enzymatic activities, uridyltransferase and acetyltransferase, are carried out by two independent domains. The C-terminal LbH domain possesses the acetyltransferase activity. It catalyzes the CoA-dependent acetylation of GlcN-1-phosphate to GlcNAc-1-phosphate. The LbH domain contains 10 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X. The acetyltransferase active site is located at the interface between two subunits of the active LbH trimer. 193 matched cddid_all.tbl CDD cd03354 cd03354 100045 LbH_SAT Serine acetyltransferase (SAT): SAT catalyzes the CoA-dependent acetylation of the side chain hydroxyl group of L-serine to form O-acetylserine, as the first step of a two-step biosynthetic pathway in bacteria and plants leading to the formation of L-cysteine. This reaction represents a key metabolic point of regulation for the cysteine biosynthetic pathway due to its feedback inhibition by cysteine. The enzyme is a 175 kDa homohexamer, composed of a dimer of homotrimers. Each subunit contains an N-terminal alpha helical region and a C-terminal left-handed beta-helix (LbH) subdomain with 5 turns, each containing a hexapeptide repeat motif characteristic of the acyltransferase superfamily of enzymes. The trimer interface mainly involves the C-terminal LbH subdomain while the dimer (of trimers) interface is mediated by the N-terminal alpha helical subdomain. 101 matched cddid_all.tbl CDD cd03356 cd03356 100046 LbH_G1P_AT_C_like Left-handed parallel beta-Helix (LbH) domain of a group of proteins with similarity to glucose-1-phosphate adenylyltransferase: Included in this family are glucose-1-phosphate adenylyltransferase, mannose-1-phosphate guanylyltransferase, and the eukaryotic translation initiation factor eIF-2B subunits, epsilon and gamma. Most members of this family contains an N-terminal catalytic domain that resembles a dinucleotide-binding Rossmann fold, followed by a LbH fold domain with at least 4 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). eIF-2B epsilon contains an additional domain of unknown function at the C-terminus. Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity. 79 matched cddid_all.tbl CDD cd03357 cd03357 100047 LbH_MAT_GAT Maltose O-acetyltransferase (MAT) and Galactoside O-acetyltransferase (GAT): MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively at the C6 position of the nonreducing end glucosyl moiety. GAT specifically acetylates galactopyranosides. Furthermore, MAT shows higher affinity toward artificial substrates containing an alkyl or hydrophobic chain as well as a glucosyl unit. Active MAT and GAT are homotrimers, with each subunit consisting of an N-terminal alpha-helical region and a C-terminal left-handed parallel alpha-helix (LbH) subdomain with 6 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). 169 matched cddid_all.tbl CDD cd03358 cd03358 100048 LbH_WxcM_N_like WcxM-like, Left-handed parallel beta-Helix (LbH) N-terminal domain: This group is composed of Xanthomonas campestris WcxM and proteins with similarity to the WcxM N-terminal domain. WcxM is thought to be bifunctional, catalyzing both the isomerization and transacetylation reactions of keto-hexoses. It contains an N-terminal LbH domain responsible for the transacetylation function and a C-terminal isomerase domain. The LbH domain contains imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X), typical of enzymes with acyltransferase activity. 119 matched cddid_all.tbl CDD cd03359 cd03359 100049 LbH_Dynactin_5 Dynactin 5 (or subunit p25); Dynactin is a major component of the activator complex that stimulates dynein-mediated vesicle transport. Dynactin is a heterocomplex of at least eight subunits, including a 150,000-MW protein called Glued, the actin-capping protein Arp1, and dynamatin. In vitro binding experiments show that dynactin enhances dynein-dependent motility, possibly through interaction with microtubules and vesicles. Subunit p25 is part of the pointed-end subcomplex in dynactin that also includes p26, p27, and Arp11. This subcomplex interacts with membranous cargoes. p25 and p27 contain imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X), indicating a left-handed parallel beta helix (LbH) structural domain. Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity. 161 matched cddid_all.tbl CDD cd03360 cd03360 100050 LbH_AT_putative Putative Acyltransferase (AT), Left-handed parallel beta-Helix (LbH) domain; This group is composed of mostly uncharacterized proteins containing an N-terminal helical subdomain followed by a LbH domain. The alignment contains 6 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity. A few members are identified as NeuD, a sialic acid (Sia) O-acetyltransferase that is required for Sia synthesis and surface polysaccharide sialylation. 197 matched cddid_all.tbl CDD cd03361 cd03361 173781 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. 170 matched cddid_all.tbl CDD cd03362 cd03362 173782 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. 151 matched cddid_all.tbl CDD cd03363 cd03363 173783 TOPRIM_TopoIA_TopoI TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TOPRIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. 123 matched cddid_all.tbl CDD cd03364 cd03364 173784 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme. 79 matched cddid_all.tbl CDD cd03365 cd03365 173785 TOPRIM_TopoIIA TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. 120 matched cddid_all.tbl CDD cd03366 cd03366 173786 TOPRIM_TopoIIA_GyrB TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings. DNA gyrase is more effective at relaxing supercoils than decatentating DNA. DNA gyrase in addition inserts negative supercoils in the presence of ATP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. 114 matched cddid_all.tbl CDD cd03367 cd03367 239465 Ribosomal_S23 S12-like family, 40S ribosomal protein S23 subfamily; S23 is located at the interface of the large and small ribosomal subunits of eukaryotes, adjacent to the decoding center. It interacts with domain III of the eukaryotic elongation factor 2 (eEF2), which catalyzes the translocation of the growing peptidyl-tRNA to the P site to make room for the next aminoacyl-tRNA at the A (acceptor) site. Through its interaction with eEF2, S23 may play an important role in translocation. Also members of this subfamily are the archaeal 30S ribosomal S12 proteins. Prokaryotic S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as control element for the rRNA- and tRNA-driven movements of translocation. S12 and S23 are also implicated in translation accuracy. Antibiotics such as streptomycin bind S12/S23 and cause the ribosome to misread the genetic code. 115 matched cddid_all.tbl CDD cd03368 cd03368 239466 Ribosomal_S12 S12-like family, 30S ribosomal protein S12 subfamily; S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria, where it plays an important role in both tRNA and ribosomal subunit interactions. S12 is essential for maintenance of a pretranslocation state and, together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation. Antibiotics such as streptomycin bind S12 and cause the ribosome to misread the genetic code. 108 matched cddid_all.tbl CDD cd03369 cd03369 213269 ABCC_NFT1 ATP-binding cassette domain 2 of NFT1, subfamily C. Domain 2 of NFT1 (New full-length MRP-type transporter 1). NFT1 belongs to the MRP (multidrug resistance-associated protein) family of ABC transporters. Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate. 207 matched cddid_all.tbl CDD cd03370 cd03370 380327 nitroreductase uncharacterized nitroreductase family proteins. Nitroreductase family containing Thermus thermophilus NADH oxidase and other, uncharacterized proteins. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer. 191 matched cddid_all.tbl CDD cd03371 cd03371 239468 TPP_PpyrDC Thiamine pyrophosphate (TPP) family, PpyrDC subfamily, TPP-binding module; composed of proteins similar to phosphonopyruvate decarboxylase (PpyrDC) proteins. PpyrDC is a homotrimeric enzyme which functions in the biosynthesis of C-P compounds such as bialaphos tripeptide in Streptomyces hygroscopicus. These proteins require TPP and divalent metal cation cofactors. 188 matched cddid_all.tbl CDD cd03372 cd03372 239469 TPP_ComE Thiamine pyrophosphate (TPP) family, ComE subfamily, TPP-binding module; composed of proteins similar to Methanococcus jannaschii sulfopyruvate decarboxylase beta subunit (ComE). M. jannaschii sulfopyruvate decarboxylase (ComDE) is a dodecamer of six alpha (D) subunits and six (E) beta subunits, which catalyzes the decarboxylation of sulfopyruvic acid to sulfoacetaldehyde in the coenzyme M pathway. ComDE requires TPP and divalent metal cation cofactors. 179 matched cddid_all.tbl CDD cd03375 cd03375 239470 TPP_OGFOR Thiamine pyrophosphate (TPP family), 2-oxoglutarate ferredoxin oxidoreductase (OGFOR) subfamily, TPP-binding module; OGFOR catalyzes the oxidative decarboxylation of 2-oxo-acids, with ferredoxin acting as an electron acceptor. In the TCA cycle, OGFOR catalyzes the oxidative decarboxylation of 2-oxoglutarate to succinyl-CoA. In the reductive tricarboxylic acid cycle found in the anaerobic autotroph Hydrogenobacter thermophilus, OGFOR catalyzes the reductive carboxylation of succinyl-CoA to produce 2-oxoglutarate. Thauera aromatica OGFOR has been shown to provide reduced ferredoxin to benzoyl-CoA reductase, a key enzyme in the anaerobic metabolism of aromatic compounds. OGFOR is dependent on TPP and a divalent metal cation for activity. 193 matched cddid_all.tbl CDD cd03376 cd03376 239471 TPP_PFOR_porB_like Thiamine pyrophosphate (TPP family), PFOR porB-like subfamily, TPP-binding module; composed of proteins similar to the beta subunit (porB) of the Helicobacter pylori four-subunit pyruvate ferredoxin oxidoreductase (PFOR), which are also found in archaea and some hyperthermophilic bacteria. PFOR catalyzes the oxidative decarboxylation of pyruvate to form acetyl-CoA, a crucial step in many metabolic pathways. Archaea, anaerobic bacteria and eukaryotes that lack mitochondria (and therefore pyruvate dehydrogenase) use PFOR to oxidatively decarboxylate pyruvate, with ferredoxin or flavodoxin as the electron acceptor. The 36-kDa porB subunit contains the binding sites for the cofactors, TPP and a divalent metal cation, which are required for activity. 235 matched cddid_all.tbl CDD cd03377 cd03377 239472 TPP_PFOR_PNO Thiamine pyrophosphate (TPP family), PFOR_PNO subfamily, TPP-binding module; composed of proteins similar to the single subunit pyruvate ferredoxin oxidoreductase (PFOR) of Desulfovibrio Africanus, present in bacteria and amitochondriate eukaryotes. This subfamily also includes proteins characterized as pyruvate NADP+ oxidoreductase (PNO). These enzymes are dependent on TPP and a divalent metal cation as cofactors. PFOR and PNO catalyze the oxidative decarboxylation of pyruvate to form acetyl-CoA, a crucial step in many metabolic pathways. Archaea, anaerobic bacteria and eukaryotes that lack mitochondria (and therefore pyruvate dehydrogenase) use PFOR to oxidatively decarboxylate pyruvate, with ferredoxin or flavodoxin as the electron acceptor. The PFOR from cyanobacterium Anabaena (NifJ) is required for the transfer of electrons from pyruvate to flavodoxin, which reduces nitrogenase. The facultative anaerobic mitochondrion of the photosynthetic protist Euglena gracilis oxidizes pyruvate with PNO. 365 matched cddid_all.tbl CDD cd03378 cd03378 239473 beta_CA_cladeC Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. CAs are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionarily distinct families of CAs (the alpha-, beta-, and gamma-CAs) which show no significant sequence identity or structural similarity. Within the beta-CA family there are four evolutionarily distinct clades (A through D). The beta-CAs are multimeric enzymes (forming dimers,tetramers,hexamers and octamers) which are present in higher plants, algae, fungi, archaea and prokaryotes. 154 matched cddid_all.tbl CDD cd03379 cd03379 239474 beta_CA_cladeD Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. CAs are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionarily distinct families of CAs (the alpha-, beta-, and gamma-CAs) which show no significant sequence identity or structural similarity. Within the beta-CA family there are four evolutionarily distinct clades (A through D). The beta-CAs are multimeric enzymes (forming dimers,tetramers,hexamers and octamers) which are present in higher plants, algae, fungi, archaea and prokaryotes. 142 matched cddid_all.tbl CDD cd03380 cd03380 239475 PAP2_like_1 PAP2_like_1 proteins, a sub-family of PAP2, containing bacterial acid phosphatase, vanadium chloroperoxidases and vanadium bromoperoxidases. 209 matched cddid_all.tbl CDD cd03381 cd03381 239476 PAP2_glucose_6_phosphatase PAP2_like proteins, glucose-6-phosphatase subfamily. Glucose-6-phosphatase converts glucose-6-phosphate into free glucose and is active in the lumen of the endoplasmic reticulum, where it is bound to the membrane. The generation of free glucose is an important control point in metabolism, and stands at the end of gluconeogenesis and the release of glucose from glycogen. Deficiency of glucose-6-phosphatase leads to von Gierke's disease. 235 matched cddid_all.tbl CDD cd03382 cd03382 239477 PAP2_dolichyldiphosphatase PAP2_like proteins, dolichyldiphosphatase subfamily. Dolichyldiphosphatase is a membrane-associated protein located in the endoplasmic reticulum and hydrolyzes dolichyl pyrophosphate, as well as dolichylmonophosphate at a low rate. The enzyme is necessary for maintaining proper levels of dolichol-linked oligosaccharides and protein N-glycosylation, and might play a role in re-utilization of the glycosyl carrier lipid for additional rounds of lipid intermediate biosynthesis after its release during protein N-glycosylation reactions. 159 matched cddid_all.tbl CDD cd03383 cd03383 239478 PAP2_diacylglycerolkinase PAP2_like proteins, diacylglycerol_kinase like sub-family. In some prokaryotes, PAP2_like phosphatase domains appear fused to E. coli DAGK-like trans-membrane diacylglycerol kinase domains. The cellular function of these architectures remains to be determined. 109 matched cddid_all.tbl CDD cd03384 cd03384 239479 PAP2_wunen PAP2, wunen subfamily. Most likely a family of membrane associated phosphatidic acid phosphatases. Wunen is a drosophila protein expressed in the central nervous system, which provides repellent activity towards primordial germ cells (PGCs), controls the survival of PGCs and is essential in the migration process of these cells towards the somatic gonadal precursors. 150 matched cddid_all.tbl CDD cd03385 cd03385 239480 PAP2_BcrC_like PAP2_like proteins, BcrC_like subfamily. Several members of this family have been annotated as bacitracin transport permeases, as it was suspected that they form the permease component of an ABC transporter system. It was shown, however, that BcrC from Bacillus subtilis posesses undecaprenyl pyrophosphate (UPP) phospatase activity, and it is hypothesized that it competes with bacitracin for UPP, increasing the cell's resistance to bacitracin. 144 matched cddid_all.tbl CDD cd03386 cd03386 239481 PAP2_Aur1_like PAP2_like proteins, Aur1_like subfamily. Yeast Aur1p or Ipc1p is necessary for the addition of inositol phosphate to ceramide, an essential step in yeast sphingolipid synthesis, and is the target of several antifungal compounds such as aureobasidin. 186 matched cddid_all.tbl CDD cd03388 cd03388 239482 PAP2_SPPase1 PAP2_like proteins, sphingosine-1-phosphatase subfamily. Sphingosine-1-phosphatase is an intracellular enzyme located in the endoplasmic reticulum, which regulates the level of sphingosine-1-phosphate (S1P), a bioactive lipid. S1P acts as a second messenger in the cell, and extracellularly by binding to G-protein coupled receptors of the endothelial differentiation gene family. 151 matched cddid_all.tbl CDD cd03389 cd03389 239483 PAP2_lipid_A_1_phosphatase PAP2_like proteins, Lipid A 1-phosphatase subfamily. Lipid A 1-phosphatase, or LpxE from Francisella novicida selectively dephosphorylates lipid A at the 1-position. Lipid A is the membrane-anchor component of lipopolysaccharides (LPS), the major constituents of the outer membrane in many gram-negative bacteria. 186 matched cddid_all.tbl CDD cd03390 cd03390 239484 PAP2_containing_1_like PAP2, subfamily similar to human phosphatidic_acid_phosphatase_type_2_domain_containing_1. Most likely membrane-associated phosphatidic acid phosphatases. Plant members of this group are constitutively expressed in many tissues and exhibit both diacylglycerol pyrophosphate phosphatase activity as well as phosphatidate (PA) phosphatase activity, they may have a more generic housekeeping role in lipid metabolism. 193 matched cddid_all.tbl CDD cd03391 cd03391 239485 PAP2_containing_2_like PAP2, subfamily similar to human phosphatidic_acid_phosphatase_type_2_domain_containing_2. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to eukaryota, lacks functional characterization and may act as a membrane-associated phosphatidic acid phosphatase. 159 matched cddid_all.tbl CDD cd03392 cd03392 239486 PAP2_like_2 PAP2_like_2 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase. 182 matched cddid_all.tbl CDD cd03393 cd03393 239487 PAP2_like_3 PAP2_like_3 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria and archaea, lacks functional characterization and may act as a membrane-associated lipid phosphatase. 125 matched cddid_all.tbl CDD cd03394 cd03394 239488 PAP2_like_5 PAP2_like_5 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase. 106 matched cddid_all.tbl CDD cd03395 cd03395 239489 PAP2_like_4 PAP2_like_4 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which is specific to bacteria, lacks functional characterization and may act as a membrane-associated lipid phosphatase. 177 matched cddid_all.tbl CDD cd03396 cd03396 239490 PAP2_like_6 PAP2_like_6 proteins. PAP2 is a super-family of phosphatases and haloperoxidases. This subgroup, which mainly contains bacterial proteins, lacks functional characterization and may act as a membrane-associated lipid phosphatase. 197 matched cddid_all.tbl CDD cd03397 cd03397 239491 PAP2_acid_phosphatase PAP2, bacterial acid phosphatase or class A non-specific acid phosphatases. These enzymes catalyze phosphomonoester hydrolysis, with optimal activity in low pH conditions. They are secreted into the periplasmic space, and their physiological role remains to be determined. 232 matched cddid_all.tbl CDD cd03398 cd03398 239492 PAP2_haloperoxidase PAP2, haloperoxidase_like subfamily. Haloperoxidases catalyze the oxidation of halides such as bromide or chloride by hydrogen peroxide, which results in subsequent halogenation of organic substrates, or halide-assisted disproportionation of hydrogen peroxide forming dioxygen. They are likely to participate in the biosynthesis of halogenated natural products, such as volatile halogenated hydrocarbons, chiral halogenated terpenes, acetogenins and indoles. 232 matched cddid_all.tbl CDD cd03399 cd03399 259798 SPFH_flotillin Flotillin or reggie family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. The flotillin (reggie) like proteins are lipid raft-associated. Individual proteins of this SPFH family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. In addition, microdomains formed from flotillin proteins may be dynamic units with their own regulatory functions. Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and interact with a variety of proteins. They may play a role in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and in cancer invasion, and metastasis. 145 matched cddid_all.tbl CDD cd03401 cd03401 259799 SPFH_prohibitin Prohibitin family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model characterizes proteins similar to prohibitin (a lipid raft-associated integral membrane protein). Individual proteins of the SPFH (band 7) domain superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. These microdomains, in addition to being stable scaffolds, may also be dynamic units with their own regulatory functions. Prohibitin is a mitochondrial inner-membrane protein which may act as a chaperone for the stabilization of mitochondrial proteins. Human prohibitin forms a hetero-oligomeric complex with Bap-37 (prohibitin 2, an SPFH domain carrying homolog). This complex may protect non-assembled membrane proteins against proteolysis by the m-AAA protease. Prohibitin and Bap-37 yeast homologs have been implicated in yeast longevity and in the maintenance of mitochondrial morphology. 195 matched cddid_all.tbl CDD cd03402 cd03402 259800 SPFH_like_u2 Uncharacterized family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model summarizes an uncharacterized family of proteins similar to stomatin, prohibitin, flotillin, HflK/C (SPFH) and podocin. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Many superfamily members are associated with lipid rafts. Individual proteins of the SPFH superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions. Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins. Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins. Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease, and in cancer invasion and metastasis. Mutations in the podocin gene give rise to autosomal recessive steroid resistant nephritic syndrome. 231 matched cddid_all.tbl CDD cd03403 cd03403 259801 SPFH_stomatin Stomatin, a subgroup of the stomatin-like proteins (slipins) family; belonging to the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. Stomatin (or band 7) is widely expressed and, highly expressed in red blood cells. It localizes predominantly to the plasma membrane and to intracellular vesicles of the endocytic pathway, where it is present in higher order homo-oligomeric complexes (of between 9 and 12 monomers). Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and, is implicated in trafficking of Glut1 glucose transporters. This subgroup found in animals, also contains proteins similar to Caenorhabditis elegans MEC-2. MEC-2 interacts with MEC-4, which is part of the degenerin channel complex required for response to gentle body touch. 202 matched cddid_all.tbl CDD cd03404 cd03404 259802 SPFH_HflK High frequency of lysogenization K (HflK) family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model characterizes proteins similar to prokaryotic HflK (High frequency of lysogenization K). Although many members of the SPFH (or band 7) superfamily are lipid raft associated, prokaryote plasma membranes lack cholesterol and are unlikely to have lipid raft domains. Individual proteins of this SPFH domain superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Escherichia coli HflK is an integral membrane protein which may localize to the plasma membrane. HflK associates with another SPFH superfamily member (HflC) to form an HflKC complex. HflKC interacts with FtsH in a large complex termed the FtsH holo-enzyme. FtsH is an AAA ATP-dependent protease which exerts progressive proteolysis against membrane-embedded and soluble substrate proteins. HflKC can modulate the activity of FtsH. HflKC plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. 266 matched cddid_all.tbl CDD cd03405 cd03405 259803 SPFH_HflC High frequency of lysogenization C (HflC) family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model characterizes proteins similar to prokaryotic HflC (High frequency of lysogenization C). Although many members of the SPFH (or band 7) superfamily are lipid raft associated, prokaryote plasma membranes lack cholesterol and are unlikely to have lipid raft domains. Individual proteins of this SPFH domain superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Escherichia coli HflC is an integral membrane protein which may localize to the plasma membrane. HflC associates with another SPFH superfamily member (HflK) to form an HflKC complex. HflKC interacts with FtsH in a large complex termed the FtsH holo-enzyme. FtsH is an AAA ATP-dependent protease which exerts progressive proteolysis against membrane-embedded and soluble substrate proteins. HflKC can modulate the activity of FtsH. HflKC plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. 249 matched cddid_all.tbl CDD cd03406 cd03406 259804 SPFH_like_u3 Uncharacterized family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model summarizes an uncharacterized family of proteins similar to stomatin, prohibitin, flotillin, HflK/C (SPFH) and podocin. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Many superfamily members are associated with lipid rafts. Individual proteins of the SPFH superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions. Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins. Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins. Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podocin gene give rise to autosomal recessive steroid resistant nephritic syndrome. 293 matched cddid_all.tbl CDD cd03407 cd03407 259805 SPFH_like_u4 Uncharacterized family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model summarizes an uncharacterized family of proteins similar to stomatin, prohibitin, flotillin, HflK/C (SPFH) and podocin. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Many superfamily members are associated with lipid rafts. Individual proteins of the SPFH superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions. Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins. Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins. Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podocin gene give rise to autosomal recessive steroid resistant nephritic syndrome. 269 matched cddid_all.tbl CDD cd03408 cd03408 259806 SPFH_like_u1 Uncharacterized family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model summarizes an uncharacterized family of proteins similar to stomatin, prohibitin, flotillin, HflK/C (SPFH) and podocin. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Many superfamily members are associated with lipid rafts. Individual proteins of the SPFH superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Microdomains formed from flotillin proteins may in addition be dynamic units with their own regulatory functions. Flotillins have been implicated in signal transduction, vesicle trafficking, cytoskeleton rearrangement and are known to interact with a variety of proteins. Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Prohibitin may act as a chaperone for the stabilization of mitochondrial proteins. Prokaryotic HflK/C plays a role in the decision between lysogenic and lytic cycle growth during lambda phage infection. Flotillins have been implicated in the progression of prion disease, in the pathogenesis of neurodegenerative diseases such as Parkinson's and Alzheimer's disease and, in cancer invasion and metastasis. Mutations in the podocin gene give rise to autosomal recessive steroid resistant nephritic syndrome. 217 matched cddid_all.tbl CDD cd03409 cd03409 239503 Chelatase_Class_II Class II Chelatase: a family of ATP-independent monomeric or homodimeric enzymes that catalyze the insertion of metal into protoporphyrin rings. This family includes protoporphyrin IX ferrochelatase (HemH), sirohydrochlorin ferrochelatase (SirB) and the cobaltochelatases, CbiK and CbiX. HemH and SirB are involved in heme and siroheme biosynthesis, respectively, while the cobaltochelatases are associated with cobalamin biosynthesis. Excluded from this family are the ATP-dependent heterotrimeric chelatases (class I) and the multifunctional homodimeric enzymes with dehydrogenase and chelatase activities (class III). 101 matched cddid_all.tbl CDD cd03411 cd03411 239504 Ferrochelatase_N Ferrochelatase, N-terminal domain: Ferrochelatase (protoheme ferrolyase or HemH) is the terminal enzyme of the heme biosynthetic pathway. It catalyzes the insertion of ferrous iron into the protoporphyrin IX ring yielding protoheme. This enzyme is ubiquitous in nature and widely distributed in bacteria and eukaryotes. Recently, some archaeal members have been identified. The oligomeric state of these enzymes varies depending on the presence of a dimerization motif at the C-terminus. 159 matched cddid_all.tbl CDD cd03412 cd03412 239505 CbiK_N Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), N-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the second step of the anaerobic branch of vitamin B12 biosynthesis. CbiK belongs to the class II family of chelatases and is a homomeric enzyme that does not require ATP for its enzymatic activity. 127 matched cddid_all.tbl CDD cd03413 cd03413 239506 CbiK_C Anaerobic cobalamin biosynthetic cobalt chelatase (CbiK), C-terminal domain. CbiK is part of the cobalt-early path for cobalamin biosynthesis. It catalyzes the insertion of cobalt into the oxidized form of precorrin-2, factor II (sirohydrochlorin), the second step of the anaerobic branch of vitamin B12 biosynthesis. CbiK belongs to the class II family of chelatases, and is a homomeric enzyme that does not require ATP for its enzymatic activity. 103 matched cddid_all.tbl CDD cd03414 cd03414 239507 CbiX_SirB_C Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), C-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase, responsible for the chelation of Co2+ into sirohydrochlorin, an important step in the vitamin B12 biosynthetic pathway. CbiX often contains a C-terminal histidine-rich region that may be important for metal delivery and/or storage, and may also contain an iron-sulfur center. Both CbiX and SirB are found in a wide range of bacteria. 117 matched cddid_all.tbl CDD cd03415 cd03415 239508 CbiX_CbiC Archaeal sirohydrochlorin cobalt chelatase (CbiX) single domain. Proteins in this subgroup contain a single CbiX domain N-terminal to a precorrin-8X methylmutase (CbiC) domain. CbiX is a cobaltochelatase, responsible for the chelation of Co2+ into sirohydrochlorin, while CbiC catalyzes the conversion of cobalt-precorrin 8 to cobyrinic acid by methyl rearrangement. Both CbiX and CbiC are involved in vitamin B12 biosynthesis. 125 matched cddid_all.tbl CDD cd03416 cd03416 239509 CbiX_SirB_N Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain. SirB catalyzes the ferro-chelation of sirohydrochlorin to siroheme, the prosthetic group of sulfite and nitrite reductases. CbiX is a cobaltochelatase, responsible for the chelation of Co2+ into sirohydrochlorin, an important step in the vitamin B12 biosynthetic pathway. CbiX often contains a C-terminal histidine-rich region that may be important for metal delivery and/or storage, and may also contain an iron-sulfur center. Both are found in a wide range of bacteria. This subgroup also contains single domain proteins from archaea and bacteria which may represent the ancestral form of class II chelatases before domain duplication occurred. 101 matched cddid_all.tbl CDD cd03418 cd03418 239510 GRX_GRXb_1_3_like Glutaredoxin (GRX) family, GRX bacterial class 1 and 3 (b_1_3)-like subfamily; composed of bacterial GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH -> GSH reductase -> GSH -> GRX -> protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known including E. coli GRX1 and GRX3, which are members of this subfamily. 75 matched cddid_all.tbl CDD cd03419 cd03419 239511 GRX_GRXh_1_2_like Glutaredoxin (GRX) family, GRX human class 1 and 2 (h_1_2)-like subfamily; composed of proteins similar to human GRXs, approximately 10 kDa in size, and proteins containing a GRX or GRX-like domain. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins such as ribonucleotide reductase. It contains a redox active CXXC motif in a TRX fold and uses a similar dithiol mechanism employed by TRXs for intramolecular disulfide bond reduction of protein substrates. Unlike TRX, GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. The flow of reducing equivalents in the GRX system goes from NADPH -> GSH reductase -> GSH -> GRX -> protein substrates. By altering the redox state of target proteins, GRX is involved in many cellular functions including DNA synthesis, signal transduction and the defense against oxidative stress. Different classes are known including human GRX1 and GRX2, which are members of this subfamily. Also included in this subfamily are the N-terminal GRX domains of proteins similar to human thioredoxin reductase 1 and 3. 82 matched cddid_all.tbl CDD cd03420 cd03420 239512 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3. 69 matched cddid_all.tbl CDD cd03421 cd03421 239513 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding. 67 matched cddid_all.tbl CDD cd03422 cd03422 239514 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding. 69 matched cddid_all.tbl CDD cd03423 cd03423 239515 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding. 69 matched cddid_all.tbl CDD cd03424 cd03424 467530 NUDIX_ADPRase_Nudt5_UGPPase_Nudt14 ADP-ribose pyrophosphatase, UDP-glucose pyrophosphatase, and similar proteins. ADP-ribose pyrophosphatase (ADPRase) ( NUDIX (Nucleoside diphosphate-linked moiety X)) motif 5; Nudt5) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. In humans, there are four distinct ADPRase activities, three putative cytosolic enzymes (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). Human ADPRase-II is also referred to as NUDT5. It lacks the N-terminal target sequence unique to mitochondrial ADPRase. The different cytosolic types are distinguished by their specificities for substrate and specific requirement for metal ions. NUDT5 forms a homodimer. It also contains a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the NUDIX motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. UDP-glucose pyrophosphatase (UGPPase) (EC 3.6.1.45; also known as nucleoside diphosphate-linked moiety X)) motif 14; Nudt14) hydrolyzes the pyrophosphate of the nucleoside diphosphate sugar to generate glucose-1-P and UMP. In mammals, UDP-glucose is the glucosyl donor for the synthesis of the storage polysaccharide glycogen. UGPPase, as a regulator of UDP-glucose, could play a regulatory role, but it has been shown to prefer ADP-ribose over UDP-glucose. Like other members of the NUDIX hydrolase superfamily, it requires a divalent cation, such as Mg2+, for its activity. It also contains a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. 134 matched cddid_all.tbl CDD cd03425 cd03425 467531 NUDIX_MutT_NudA_like MutT pyrophosphohydrolase. The MutT pyrophosphohydrolase is a prototypical NUDIX hydrolase that catalyzes the hydrolysis of nucleoside and deoxynucleoside triphosphates (NTPs and dNTPs) by substitution at a beta-phosphorus to yield a nucleotide monophosphate (NMP) and inorganic pyrophosphate (PPi). This enzyme requires two divalent cations for activity; one coordinates the phosphoryl groups of the NTP/dNTP substrate, and the other coordinates to the enzyme. It also contains the NUDIX motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as metal binding and catalytic site. MutT pyrophosphohydrolase is important in preventing errors in DNA replication by hydrolyzing mutagenic nucleotides such as 8-oxo-dGTP (a product of oxidative damage), which can mispair with template adenine during DNA replication, to guanine nucleotides. 123 matched cddid_all.tbl CDD cd03426 cd03426 467532 NUDIX_CoAse_Nudt7 coenzyme A pyrophosphatase and similar proteins. Coenzyme A pyrophosphatase (CoAse; EC 3.6.1.1), also called nucleoside diphosphate-linked moiety X)) motif 7, is a member of the NUDIX hydrolase superfamily, functions to catalyze the elimination of oxidized inactive CoA, which can inhibit CoA-utilizing enzymes. The need of CoAses mainly arises under conditions of oxidative stress. CoAse has a conserved NUDIX fold and requires a single divalent cation for catalysis. In addition to a signature NUDIX motif G[X5]E[X7]REUXEEXGU, where U is Ile, Leu, or Val, CoAse contains an additional motif upstream called the NuCoA motif (LLTXT(SA)X3RX3GX3FPGG) which is postulated to be involved in CoA recognition. CoA plays a central role in lipid metabolism. It is involved in the initial steps of fatty acid sythesis in the cytosol, in the oxidation of fatty acids and the citric acid cycle in the mitochondria, and in the oxidation of long-chain fatty acids in peroxisomes. CoA has the important role of activating fatty acids for further modification into key biological signalling molecules. 158 matched cddid_all.tbl CDD cd03427 cd03427 467533 NUDIX_MTH1_Nudt1 MutT homolog-1 (MTH1). MutT homolog-1 (MTH1; EC 3.6.1.- ), also called nucleoside diphosphate-linked moiety X)) motif 1 (Nudt1), is a member of the NUDIX hydrolase superfamily. MTH1, the mammalian counterpart of MutT, hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to monophosphates, thereby preventing the incorporation of such oxygen radicals during replication. This is an important step in the repair mechanism in genomic and mitochondrial DNA. Like other members of the NUDIX family, it requires a divalent cation, such as Mg2+ or Mn2+, for activity, and contain the NUDIX motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. MTH1 is predominantly localized in the cytoplasm and mitochondria. Structurally, this enzyme adopts a similar fold to MutT despite low sequence similarity outside the conserved NUDIX motif. The most distinctive structural difference between MutT and MTH1 is the presence of a beta-hairpin, which is absent in MutT. This results in a much deeper and narrower substrate binding pocket. Mechanistically, MTH1 contains dual specificity for nucleotides that contain 2-OH-adenine bases and those that contain 8-oxo-guanine bases. 136 matched cddid_all.tbl CDD cd03428 cd03428 467534 NUDIX_Ap4A_Nudt2 diadenosine tetraphosphate. Diadenosine tetraphosphate (Ap4A; EC 3.6.1.17), also called NUDIX (nucleoside diphosphate-linked moiety X)) motif 2/Nudt2, is a member of the NUDIX hydrolase superfamily. Ap4A hydrolases are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant enzymes fall into one subfamily and fungi/animals/archaea enzymes, represented by this subfamily, fall into another. Bacterial enzymes are found in both subfamilies. Ap4A is a potential by-product of aminoacyl tRNA synthesis, and accumulation of Ap4A has been implicated in a range of biological events, such as DNA replication, cellular differentiation, heat shock, metabolic stress, and apoptosis. Ap4A hydrolase cleaves Ap4A asymmetrically into ATP and AMP. It is important in the invasive properties of bacteria and thus presents a potential target for inhibition of such invasive bacteria. Besides the signature NUDIX motif (G[X5]E[X7]REUXEEXGU, where U is Ile, Leu, or Val) that functions as a metal binding and catalytic site, and a required divalent cation, Ap4A hydrolase is structurally similar to the other members of the NUDIX hydrolase superfamily with some degree of variation. Several regions in the sequences are poorly defined and substrate and metal binding sites are only predicted based on kinetic studies. 132 matched cddid_all.tbl CDD cd03429 cd03429 467535 NUDIX_NADH_pyrophosphatase_Nudt13 NADH pyrophosphatase. NADH pyrophosphatase, also known as NUDIX (nucleoside diphosphate linked moiety X)) motif 13/Nudt13, is thought to have NADH pyrophosphatase activity, be involved in NADH metabolic process and NADP catabolic process, catalyzing the cleavage of NADH into reduced nicotinamide mononucleotide (NMNH) and AMP, and located in mitochondrion. Like other members of the NUDIX family, it requires a divalent cation, such as Mg2+ or Mn2+, for activity. Members of this family are also recognized by the NUDIX motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. A block of 8 conserved amino acids downstream of the NUDIX motif is thought to give NADH pyrophosphatase its specificity for NADH. NADH pyrophosphatase forms a dimer. 126 matched cddid_all.tbl CDD cd03430 cd03430 467536 NUDIX_GDPMH_NudD GDP-mannose glycosyl hydrolase. GDP-mannose glycosyl hydrolase, also known as GDP-mannose mannosyl hydrolase/GDPMH, is a member of the NUDIX hydrolase superfamily. This class of enzymes is unique from other members of the superfamily in two aspects. First, it contains a modified NUDIX signature sequence. The slight changes to the conserved sequence motif, GX5EX7REUXEEXGU, where U = I, L or V), are believed to contribute to the removal of all magnesium binding sites but one, retaining only the metal site that coordinates the pyrophosphate of the substrate. Secondly, it is not a pyrophosphatase that substitutes at a phosphorus; instead, it hydrolyzes nucleotide sugars such as GDP-mannose to GDP and mannose, cleaving the phosphoglycosyl bond by substituting at a carbon position. GDP-mannose provides mannosyl components for cell wall synthesis and is required for the synthesis of other glycosyl donors (such as GDP-fucose and colitose) for the cell wall. The importance of GDP-sugar hydrolase activities is thus closely related to the regulation of cell wall biosynthesis. Enzymes in this family are believed to regulate the concentration of GDP-mannose and GDP-glucose in the bacterial cell wall. 146 matched cddid_all.tbl CDD cd03431 cd03431 467537 NUDIX_DNA_Glycosylase_C-MutY C-terminal domain of DNA glycosylase. DNA glycosylase (MutY in bacteria and hMYH in humans) is responsible for repairing misread A*oxoG residues to C*G by removing the inappropriately paired adenine base from the DNA backbone. It belongs to the NUDIX hydrolase superfamily and is important for the repair of various genotoxic lesions. Enzymes belonging to this superfamily requires a divalent cation, such as Mg2+ or Mn2+ for their activity. They are also recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V). However, DNA glycosylase does not seem to contain this signature motif. DNA glycosylase consists of 2 domains: the N-terminal domain contains the catalytic properties of the enzyme and the C-terminal domain affects substrate (oxoG) binding and enzymatic turnover. The C-terminal domain is highly similar to MutT, based on secondary structure and topology, despite low sequence identity. MutT sanitizes the nucleotide precursor pool by hydrolyzing oxo-dGTP to oxo-dGMO and inorganic pyrophosphate. The similarity strongly suggests that the two proteins share a common evolutionary origin. 118 matched cddid_all.tbl CDD cd03440 cd03440 239524 hot_dog The hotdog fold was initially identified in the E. coli FabA (beta-hydroxydecanoyl-acyl carrier protein (ACP)-dehydratase) structure and subsequently in 4HBT (4-hydroxybenzoyl-CoA thioesterase) from Pseudomonas. A number of other seemingly unrelated proteins also share the hotdog fold. These proteins have related, but distinct, catalytic activities that include metabolic roles such as thioester hydrolysis in fatty acid metabolism, and degradation of phenylacetic acid and the environmental pollutant 4-chlorobenzoate. This superfamily also includes the PaaI-like protein FapR, a non-catalytic bacterial homolog involved in transcriptional regulation of fatty acid biosynthesis. 100 matched cddid_all.tbl CDD cd03441 cd03441 239525 R_hydratase_like (R)-hydratase [(R)-specific enoyl-CoA hydratase]. Catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. The structure of the monomer includes a five-strand antiparallel beta-sheet wrapped around a central alpha helix, referred to as a hot dog fold. The active site lies within a substrate-binding tunnel formed by the homodimer. Other enzymes with this fold include MaoC dehydratase, Hydratase-Dehydrogenase-Epimerase protein (HDE), and the fatty acid synthase beta subunit. 127 matched cddid_all.tbl CDD cd03442 cd03442 239526 BFIT_BACH Brown fat-inducible thioesterase (BFIT). Brain acyl-CoA hydrolase (BACH). These enzymes deacylate long-chain fatty acids by hydrolyzing acyl-CoA thioesters to free fatty acids and CoA-SH. Eukaryotic members of this family are expressed in brain, testis, and brown adipose tissues. The archeal and eukaryotic members of this family have two tandem copies of the conserved hot dog fold, while most bacterial members have only one copy. 123 matched cddid_all.tbl CDD cd03443 cd03443 239527 PaaI_thioesterase PaaI_thioesterase is a tetrameric acyl-CoA thioesterase with a hot dog fold and one of several proteins responsible for phenylacetic acid (PA) degradation in bacteria. Although orthologs of PaaI exist in archaea and eukaryotes, their function has not been determined. Sequence similarity between PaaI, E. coli medium chain acyl-CoA thioesterase II, and human thioesterase III suggests they all belong to the same thioesterase superfamily. The conserved fold present in these thioesterases is referred to as an asymmetric hot dog fold, similar to those of 4-hydroxybenzoyl-CoA thioesterase (4HBT) and the beta-hydroxydecanoyl-ACP dehydratases (FabA/FabZ). 113 matched cddid_all.tbl CDD cd03444 cd03444 239528 Thioesterase_II_repeat1 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP) domains, respectively. TEII has two tandem asymmetric hot dog folds that are structurally similar to one found in PaaI thioesterase, 4-hydroxybenzoyl-CoA thioesterase (4HBT) and beta-hydroxydecanoyl-ACP dehydratase and thus, the TEII monomer is equivalent to the homodimeric form of the latter three enzymes. Human TEII is expressed in T cells and has been shown to bind the product of the HIV-1 Nef gene. 104 matched cddid_all.tbl CDD cd03445 cd03445 239529 Thioesterase_II_repeat2 Thioesterase II (TEII) is thought to regenerate misprimed nonribosomal peptide synthetases (NRPSs) as well as modular polyketide synthases (PKSs) by hydrolyzing acetyl groups bound to the peptidyl carrier protein (PCP) and acyl carrier protein (ACP) domains, respectively. TEII has two tandem asymmetric hot dog folds that are structurally similar to one found in PaaI thioesterase, 4-hydroxybenzoyl-CoA thioesterase (4HBT) and beta-hydroxydecanoyl-ACP dehydratase and thus, the TEII monomer is equivalent to the homodimeric form of the latter three enzymes. Human TEII is expressed in T cells and has been shown to bind the product of the HIV-1 Nef gene. 94 matched cddid_all.tbl CDD cd03446 cd03446 239530 MaoC_like MoaC_like Similar to the MaoC (monoamine oxidase C) dehydratase regulatory protein but without the N-terminal PutA domain. This protein family has a hot-dog fold similar to that of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. 140 matched cddid_all.tbl CDD cd03447 cd03447 239531 FAS_MaoC FAS_MaoC, the MaoC-like hot dog fold of the fatty acid synthase, beta subunit. Other enzymes with this fold include MaoC dehydratase, Hydratase-Dehydrogenase-Epimerase protein (HDE), and 17-beta-hydroxysteriod dehydrogenase (HSD). 126 matched cddid_all.tbl CDD cd03448 cd03448 239532 HDE_HSD HDE_HSD The R-hydratase-like hot dog fold of the 17-beta-hydroxysteriod dehydrogenase (HSD), and Hydratase-Dehydrogenase-Epimerase (HDE) proteins. Other enzymes with this fold include MaoC dehydratase, and the fatty acid synthase beta subunit. 122 matched cddid_all.tbl CDD cd03449 cd03449 239533 R_hydratase (R)-hydratase [(R)-specific enoyl-CoA hydratase] catalyzes the hydration of trans-2-enoyl CoA to (R)-3-hydroxyacyl-CoA as part of the PHA (polyhydroxyalkanoate) biosynthetic pathway. (R)-hydratase contains a hot-dog fold similar to those of thioesterase II, and beta-hydroxydecanoyl-ACP dehydratase, MaoC dehydratase, Hydratase-Dehydrogenase-Epimerase protein (HDE), and the fatty acid synthase beta subunit. The active site lies within a substrate-binding tunnel formed by the (R)-hydratase homodimer. A subset of the bacterial (R)-hydratases contain a C-terminal phosphotransacetylase (PTA) domain. 128 matched cddid_all.tbl CDD cd03450 cd03450 239534 NodN NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their legume hosts, a symbiotic process that requires production of Nod factors, which are signal molecules involved in root hair deformation and meristematic cell division. The nodulation gene products, including NodN, are involved in producing the Nod factors, however the role played by NodN is unclear. 149 matched cddid_all.tbl CDD cd03451 cd03451 239535 FkbR2 FkbR2 is a Streptomyces hygroscopicus protein with a hot dog fold that belongs to a conserved family of proteins found in prokaryotes and archaea but not in eukaryotes. FkbR2 has sequence similarity to (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. The function of FkbR2 is unknown. 146 matched cddid_all.tbl CDD cd03452 cd03452 239536 MaoC_C MaoC_C The C-terminal hot dog fold of the MaoC (monoamine oxidase C) dehydratase regulatory protein. Orthologs of MaoC include PaaZ [Escherichia coli] and PaaN [Pseudomonas putida], which are putative ring-opening enzymes involved in phenylacetic acid degradation. The C-terminal domain of MaoC has sequence similarity to (R)-specific enoyl-CoA hydratase,Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. MaoC also has an N-terminal PutA domain like that found in the E. coli PutA proline dehydrogenase and other members of the aldehyde dehydrogenase family. 142 matched cddid_all.tbl CDD cd03453 cd03453 239537 SAV4209_like SAV4209_like. Similar in sequence to the Streptomyces avermitilis SAV4209 protein, with a hot dog fold that is similar to those of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. 127 matched cddid_all.tbl CDD cd03454 cd03454 239538 YdeM YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function. YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase. Other enzymes with this fold include the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. 140 matched cddid_all.tbl CDD cd03455 cd03455 239539 SAV4209 SAV4209 is a Streptomyces avermitilis protein with a hot dog fold that is similar to those of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. The alpha- and gamma-proteobacterial members of this CD have, in addition to a hot dog fold, an N-terminal extension. 123 matched cddid_all.tbl CDD cd03457 cd03457 239540 intradiol_dioxygenase_like Intradiol dioxygenase supgroup. Intradiol dioxygenases catalyze the critical ring-cleavage step in the conversion of catecholate derivatives to citric acid cycle intermediates. They break the catechol C1-C2 bond and utilize Fe3+, as opposed to the extradiol-cleaving enzymes which break the C2-C3 or C1-C6 bond and utilize Fe2+ and Mn+. The family contains catechol 1,2-dioxygenases and protocatechuate 3,4-dioxygenases. The specific function of this subgroup is unknown. 188 matched cddid_all.tbl CDD cd03458 cd03458 239541 Catechol_intradiol_dioxygenases Catechol intradiol dioxygenases can be divided into several subgroups according to their substrate specificity for catechol, chlorocatechols and hydroxyquinols. Almost all members of this family are homodimers containing one ferric ion (Fe3+) per monomer. They belong to the intradiol dioxygenase family, a family of mononuclear non-heme iron intradiol-cleaving enzymes that catalyze the oxygenation of catecholates to aliphatic acids via the cleavage of aromatic rings. 256 matched cddid_all.tbl CDD cd03459 cd03459 239542 3,4-PCD Protocatechuate 3,4-dioxygenase (3,4-PCD) catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and beta-subunit and an Fe3+ ion bound in the beta-subunit at the alpha-beta-subunit interface. 3,4-PCD is a member of the aromatic dioxygenases which are non-heme iron intradiol-cleaving enzymes that break the C1-C2 bond and utilize Fe3+. 158 matched cddid_all.tbl CDD cd03460 cd03460 239543 1,2-CTD Catechol 1,2 dioxygenase (1,2-CTD) catalyzes an intradiol cleavage reaction of catechol to form cis,cis-muconate. 1,2-CTDs is homodimers with one catalytic non-heme ferric ion per monomer. They belong to the aromatic dioxygenase family, a family of mononuclear non-heme iron intradiol-cleaving enzymes that catalyze the oxygenation of catecholates to aliphatic acids via the cleavage of aromatic rings. 282 matched cddid_all.tbl CDD cd03461 cd03461 239544 1,2-HQD Hydroxyquinol 1,2-dioxygenase (1,2-HQD) catalyzes the ring cleavage of hydroxyquinol (1,2,4-trihydroxybenzene), a intermediate in the degradation of a large variety of aromatic compounds including some polychloro- and nitroaromatic pollutants, to form 3-hydroxy-cis,cis-muconates. 1,2-HQD blongs to the aromatic dioxygenase family, a family of mononuclear non-heme intradiol-cleaving enzymes. 277 matched cddid_all.tbl CDD cd03462 cd03462 239545 1,2-CCD chlorocatechol 1,2-dioxygenases (1,2-CCDs) (type II enzymes) are homodimeric intradiol dioxygenases that degrade chlorocatechols via the addition of molecular oxygen and the subsequent cleavage between two adjacent hydroxyl groups. This reaction is part of the modified ortho-cleavage pathway which is a central oxidative bacterial pathway that channels chlorocatechols, derived from the degradation of chlorinated benzoic acids, phenoxyacetic acids, phenols, benzenes, and other aromatics into the energy-generating tricarboxylic acid pathway. 247 matched cddid_all.tbl CDD cd03463 cd03463 239546 3,4-PCD_alpha Protocatechuate 3,4-dioxygenase (3,4-PCD) , alpha subunit. 3,4-PCD catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and beta-subunit and an Fe3+ ion bound in the beta-subunit at the alpha-subunit-beta-subunit interface. 3,4-PCD is a member of the aromatic dioxygenases which are non-heme iron intradiol-cleaving enzymes that break the C1-C2 bond and utilize Fe3+. 185 matched cddid_all.tbl CDD cd03464 cd03464 239547 3,4-PCD_beta Protocatechuate 3,4-dioxygenase (3,4-PCD) , beta subunit. 3,4-PCD catalyzes the oxidative ring cleavage of 3,4-dihydroxybenzoate to produce beta-carboxy-cis,cis-muconate. 3,4-PCDs are large aggregates of 12 protomers, each composed of an alpha- and beta-subunit and an Fe3+ ion bound in the beta-subunit at the alpha-subunit-beta-subunit interface. 3,4-PCD is a member of the aromatic dioxygenases which are non-heme iron intradiol-cleaving enzymes that break the C1-C2 bond and utilize Fe3+. 220 matched cddid_all.tbl CDD cd03465 cd03465 239548 URO-D_like The URO-D _like protein superfamily includes bacterial and eukaryotic uroporphyrinogen decarboxylases (URO-D), coenzyme M methyltransferases and other putative bacterial methyltransferases. Uroporphyrinogen decarboxylase (URO-D) decarboxylates the four acetate side chains of uroporphyrinogen III (uro-III) to create coproporphyrinogen III, an important branching point of the tetrapyrrole biosynthetic pathway. The methyltransferases represented here are important for ability of methanogenic organisms to use other compounds than carbon dioxide for reduction to methane. 330 matched cddid_all.tbl CDD cd03466 cd03466 239549 Nitrogenase_NifN_2 Nitrogenase_nifN_2: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE. NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively. NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein. NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The nifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this nifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco). This group also contains the Clostidium fused NifN-NifB protein. 429 matched cddid_all.tbl CDD cd03467 cd03467 239550 Rieske Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis. 98 matched cddid_all.tbl CDD cd03468 cd03468 176458 PolY_like DNA Polymerase Y-family. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion. Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention. 335 matched cddid_all.tbl CDD cd03469 cd03469 239551 Rieske_RO_Alpha_N Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The oxygenase component may contain alpha and beta subunits, with the beta subunit having a purely structural function. Some oxygenase components contain only an alpha subunit. The oxygenase alpha subunit has two domains, an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from the reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Reduced pyridine nucleotide is used as the initial source of two electrons for dioxygen activation. 118 matched cddid_all.tbl CDD cd03470 cd03470 239552 Rieske_cytochrome_bc1 Iron-sulfur protein (ISP) component of the bc(1) complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The bc(1) complex is a multisubunit enzyme found in many different organisms including uni- and multi-cellular eukaryotes, plants (in their mitochondria) and bacteria. The cytochrome bc(1) and b6f complexes are central components of the respiratory and photosynthetic electron transport chains, respectively, which carry out similar core electron and proton transfer steps. The bc(1) and b6f complexes share a common core structure of three catalytic subunits: cyt b, the Rieske ISP, and either a cyt c1 in the bc(1) complex or cyt f in the b6f complex, which are arranged in an integral membrane-bound dimeric complex. While the core of the b6f complex is similar to that of the bc(1) complex, the domain arrangement outside the core and the complement of prosthetic groups are strikingly different. 126 matched cddid_all.tbl CDD cd03471 cd03471 239553 Rieske_cytochrome_b6f Iron-sulfur protein (ISP) component of the b6f complex family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The cytochrome b6f complex from Mastigocladus laminosus, a thermophilic cyanobacterium, contains four large subunits, including cytochrome f, cytochrome b6, the Rieske ISP, and subunit IV; as well as four small hydrophobic subunits, PetG, PetL, PetM, and PetN. Rieske ISP, one of the large subunits of the cytochrome bc-type complexes, is involved in respiratory and photosynthetic electron transfer. The core of the chloroplast b6f complex is similar to the analogous respiratory cytochrome bc(1) complex, but the domain arrangement outside the core and the complement of prosthetic groups are strikingly different. 126 matched cddid_all.tbl CDD cd03472 cd03472 239554 Rieske_RO_Alpha_BPDO_like Rieske non-heme iron oxygenase (RO) family, Biphenyl dioxygenase (BPDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of BPDO and similar proteins including cumene dioxygenase (CumDO), nitrobenzene dioxygenase (NBDO), alkylbenzene dioxygenase (AkbDO) and dibenzofuran 4,4a-dioxygenase (DFDO). ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. BPDO degrades biphenyls and polychlorinated biphenyls (PCB's) while CumDO degrades cumene (isopropylbenzene), an aromatic hydrocarbon that is intermediate in size between ethylbenzene and biphenyl. NBDO catalyzes the initial reaction in nitrobenzene degradation, oxidizing the aromatic rings of mono- and dinitrotoluenes to form catechol and nitrite. NBDO belongs to the naphthalene subfamily of ROs. AkbDO is involved in alkylbenzene catabolism, converting o-xylene to 2,3- and 3,4-dimethylphenol and ethylbenzene to cis-dihydrodiol. DFDO is involved in dibenzofuran degradation. 128 matched cddid_all.tbl CDD cd03473 cd03473 239555 Rieske_CMP_Neu5Ac_hydrolase_N Cytidine monophosphate-N-acetylneuraminic acid (CMP Neu5Ac) hydroxylase family, N-terminal Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. CMP Neu5Ac hydroxylase is the key enzyme for the synthesis of N-glycolylneuraminic acid (NeuGc) from N-acetylneuraminic acid (Neu5Ac), NeuGc and Neu5Ac are members of a family of cell surface sugars called sialic acids. All mammals except humans have both NeuGc variants on their cell surfaces. In humans, the gene encoding CMP Neu5Ac hydroxylase has a mutation within its coding region that abolishes NeuGc production. 107 matched cddid_all.tbl CDD cd03474 cd03474 239556 Rieske_T4moC Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. T4mo is a four-protein complex that catalyzes the NADH- and O2-dependent hydroxylation of toluene to form p-cresol. T4mo consists of an NADH oxidoreductase (T4moF), a diiron hydroxylase (T4moH), a catalytic effector protein (T4moD), and a Rieske ferredoxin (T4moC). T4moC contains a Rieske domain and functions as an obligate electron carrier between T4moF and T4moH. Rieske ferredoxins are found as subunits of membrane oxidase complexes, cis-dihydrodiol-forming aromatic dioxygenases, bacterial assimilatory nitrite reductases, and arsenite oxidase. Rieske ferredoxins are also found as soluble electron carriers in bacterial dioxygenase and monooxygenase complexes. 108 matched cddid_all.tbl CDD cd03475 cd03475 239557 Rieske_SoxF_SoxL SoxF and SoxL family, Rieske domain; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. SoxF is a subunit of the terminal oxidase supercomplex SoxM in the plasma membrane of Sulfolobus acidocaldarius that combines features of a cytochrome bc(1) complex and a cytochrome. The Rieske domain of SoxF has a 12 residue insertion which is not found in eukaryotic and bacterial Rieske proteins and is thought to influence the redox properties of the iron-sulfur cluster. SoxL is a Rieske protein which may be part of an archaeal bc-complex homologue whose physiological function is still unknown. SoxL has two features not seen in other Rieske proteins; (i) a significantly greater distance between the two cluster-binding sites and (ii) an unexpected Pro -> Asp substitution at one of the cluster binding sites. SoxF and SoxL are found in archaea and in bacteria. 171 matched cddid_all.tbl CDD cd03476 cd03476 239558 Rieske_ArOX_small Small subunit of Arsenite oxidase (ArOX) family, Rieske domain; ArOX is a molybdenum/iron protein involved in the detoxification of arsenic, oxidizing it to arsenate. It consists of two subunits, a large subunit similar to members of the DMSO reductase family of molybdenum enzymes and a small subunit with a Rieske-type [2Fe-2S] cluster. The large subunit of ArOX contains the molybdenum site at which the oxidation of arsenite occurs. The small subunit contains a domain homologous to the Rieske domains of the cytochrome bc(1) and cytochrome b6f complexes as well as naphthalene 1,2-dioxygenase. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. 126 matched cddid_all.tbl CDD cd03477 cd03477 239559 Rieske_YhfW_C YhfW family, C-terminal Rieske domain; YhfW is a protein of unknown function with an N-terminal DadA-like (glycine/D-amino acid dehydrogenase) domain and a C-terminal Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. It is commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. YhfW is found in bacteria, some eukaryotes and archaea. 91 matched cddid_all.tbl CDD cd03478 cd03478 239560 Rieske_AIFL_N AIFL (apoptosis-inducing factor like) family, N-terminal Rieske domain; members of this family show similarity to human AIFL, containing an N-terminal Rieske domain and a C-terminal pyridine nucleotide-disulfide oxidoreductase domain (Pyr_redox). The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. AIFL shares 35% homology with human AIF (apoptosis-inducing factor), mainly in the Pyr_redox domain. AIFL is predominantly localized to the mitochondria. AIFL induces apoptosis in a caspase-dependent manner. 95 matched cddid_all.tbl CDD cd03479 cd03479 239561 Rieske_RO_Alpha_PhDO_like Rieske non-heme iron oxygenase (RO) family, Phthalate 4,5-dioxygenase (PhDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of PhDO and similar proteins including 3-chlorobenzoate 3,4-dioxygenase (CBDO), phenoxybenzoate dioxygenase (POB-dioxygenase) and 3-nitrobenzoate oxygenase (MnbA). ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. PhDO and CBDO are two-component RO systems, containing oxygenase and reductase components. PhDO catalyzes the dihydroxylation of phthalate to form the 4,5-dihydro-cis-dihydrodiol of phthalate (DHD). CBDO, together with CbaC dehydrogenase, converts the environmental pollutant 3CBA to protocatechuate (PCA) and 5-Cl-PCA, which are then metabolized by the chromosomal PCA meta (extradiol) ring fission pathway. POB-dioxygenase catalyzes the initial catabolic step in the angular dioxygenation of phenoxybenzoate, converting mono- and dichlorinated phenoxybenzoates to protocatechuate and chlorophenols. These phenoxybenzoates are metabolic products formed during the degradation of pyrethroid insecticides. 144 matched cddid_all.tbl CDD cd03480 cd03480 239562 Rieske_RO_Alpha_PaO Rieske non-heme iron oxygenase (RO) family, Pheophorbide a oxygenase (PaO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of a small subfamily of enzymes found in plants as well as oxygenic cyanobacterial photosynthesizers including LLS1 (lethal leaf spot 1, also known as PaO) and ACD1 (accelerated cell death 1). ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. PaO expression increases upon physical wounding of plant leaves and is thought to catalyze a key step in chlorophyll degradation. The Arabidopsis-accelerated cell death gene ACD1 is involved in oxygenation of PaO. 138 matched cddid_all.tbl CDD cd03481 cd03481 239563 TopoIIA_Trans_ScTopoIIA TopoIIA_Trans_ScTopoIIA: Transducer domain, having a ribosomal S5 domain 2-like fold, of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topo IIA. S. cerevisiae Topo IIA is a homodimer encoded by a single gene. The type IIA enzymes are the predominant form of topoisomerase and are found in some bacteriophages, viruses and archaea, and in all bacteria and eukaryotes. All type IIA topoisomerases are related to each other at amino acid sequence level, though their oligomeric organization sometimes differs. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA. These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. TopoIIA enzymes also catenate/ decatenate duplex rings. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. 153 matched cddid_all.tbl CDD cd03482 cd03482 239564 MutL_Trans_MutL MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from the ATP-binding site to the DNA breakage/reunion regions of the enzymes. It has been suggested that during initiation of DNA mismatch repair in E. coli, the mismatch recognition protein MutS recruits MutL in the presence of ATP. The MutS(ATP)-MutL ternary complex formed, then recruits the latent endonuclease MutH. Prokaryotic MutS and MutL are homodimers. 123 matched cddid_all.tbl CDD cd03483 cd03483 239565 MutL_Trans_MLH1 MutL_Trans_MLH1: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH1 (MutL homologue 1). This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking hMLH1 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot syndrome (HNPCC variant). Mutation in hMLH1 accounts for a large fraction of HNPCC families. 127 matched cddid_all.tbl CDD cd03484 cd03484 239566 MutL_Trans_hPMS_2_like MutL_Trans_hPMS2_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM2 (hPSM2). hPSM2 belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to yeast PMS1. The yeast MLH1-PMS1 and the human MLH1-PMS2 heterodimers play a role in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Cells lacking hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hPMS2 causes predisposition to HPNCC and Turcot syndrome. 142 matched cddid_all.tbl CDD cd03485 cd03485 239567 MutL_Trans_hPMS_1_like MutL_Trans_hPMS1_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM1 (hPSM1) and yeast MLH2. hPSM1 and yMLH2 are members of the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. PMS1 forms a heterodimer with MLH1. The MLH1-PMS1 complex functions in meiosis. Loss of yMLH2 results in a small but significant decrease in spore viability and a significant increase in gene conversion frequencies. A role for hMLH1-hPMS1 in DNA mismatch repair has not been established. Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families, however there is no convincing evidence to support hPMS1 having a role in HNPCC predisposition. 132 matched cddid_all.tbl CDD cd03486 cd03486 239568 MutL_Trans_MLH3 MutL_Trans_MLH3: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH3 (MutL homologue 3). MLH3 belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. MLH1 forms heterodimers with MLH3. The MLH1-MLH3 complex plays a role in meiosis. A role for hMLH1-hMLH3 in DNA mismatch repair (MMR) has not been established. It has been suggested that hMLH3 may be a low risk gene for colorectal cancer; however there is little evidence to support it having a role in classical HNPCC. 141 matched cddid_all.tbl CDD cd03487 cd03487 239569 RT_Bac_retron_II RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome. 214 matched cddid_all.tbl CDD cd03488 cd03488 239570 Topoisomer_IB_N_htopoI_like Topoisomer_IB_N_htopoI_like : N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the monomeric yeast and human topo I. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. This family may represent more than one structural domain. 215 matched cddid_all.tbl CDD cd03489 cd03489 239571 Topoisomer_IB_N_LdtopoI_like Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB proteins similar to the heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit re-ligation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topo I differ from human topo I in their sensitivity to CPTs and other classical topo I inhibitors. Trypanosomatid topo I play putative roles in organizing the kinetoplast DNA network unique to these parasites. This family may represent more than one structural domain. 212 matched cddid_all.tbl CDD cd03490 cd03490 239572 Topoisomer_IB_N_1 Topoisomer_IB_N_1: A subgroup of the N-terminal DNA binding fragment found in eukaryotic DNA topoisomerase (topo) IB. Topo IB proteins include the monomeric yeast and human topo I and heterodimeric topo I from Leishmania donvanni. Topo I enzymes are divided into: topo type IA (bacterial) and type IB (eukaryotic). Topo I relaxes superhelical tension in duplex DNA by creating a single-strand nick, the broken strand can then rotate around the unbroken strand to remove DNA supercoils and, the nick is religated, liberating topo I. These enzymes regulate the topological changes that accompany DNA replication, transcription and other nuclear processes. Human topo I is the target of a diverse set of anticancer drugs including camptothecins (CPTs). CPTs bind to the topo I-DNA complex and inhibit religation of the single-strand nick, resulting in the accumulation of topo I-DNA adducts. In addition to differences in structure and some biochemical properties, Trypanosomatid parasite topos I differ from human topo I in their sensitivity to CPTs and other classical topo I inhibitors. Trypanosomatid topos I have putative roles in organizing the kinetoplast DNA network unique to these parasites. This family may represent more than one structural domain. 217 matched cddid_all.tbl CDD cd03493 cd03493 239573 SQR_QFR_TM Succinate:quinone oxidoreductase (SQR) and Quinol:fumarate reductase (QFR) family, transmembrane subunits; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol, while QFR catalyzes the reverse reaction. SQR, also called succinate dehydrogenase or Complex II, is part of the citric acid cycle and the aerobic respiratory chain, while QFR is involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQRs may reduce either high or low potential quinones while QFRs oxidize only low potential quinols. SQR and QFR share a common subunit arrangement, composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, and the transmembrane subunit(s) containing the electron donor/acceptor (quinol or quinone). The reversible reduction of quinone is an essential feature of respiration, allowing the transfer of electrons between respiratory complexes. SQRs and QFRs can be classified into five types (A-E) according to the number of their hydrophobic subunits and heme groups. This classification is consistent with the characteristics and phylogeny of the catalytic and iron-sulfur subunits. Type E proteins, e.g. non-classical archael SQRs, contain atypical transmembrane subunits and are not included in this hierarchy. The heme and quinone binding sites reside in the transmembrane subunits. Although succinate oxidation and fumarate reduction are carried out by separate enzymes in most organisms, some bifunctional enzymes that exhibit both SQR and QFR activities exist. 98 matched cddid_all.tbl CDD cd03494 cd03494 239574 SQR_TypeC_SdhD Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. E. coli SQR, a member of this subfamily, reduces the high potential quinine, ubiquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are classified as Type C SQRs because they contain two transmembrane subunits and one heme group. SdhD and SdhC are the two transmembrane proteins of bacterial SQRs. They contain heme and quinone binding sites. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the membrane anchor subunits via electron transport through FAD and three iron-sulfur centers. The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes. 99 matched cddid_all.tbl CDD cd03495 cd03495 239575 SQR_TypeC_SdhD_like Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase D (SdhD) subunit-like; composed of predominantly uncharacterized bacterial proteins with similarity to the E. coli SdhD subunit. One characterized protein is the respiratory Complex II SdhD subunit of the only eukaryotic member, Reclinomonas americana. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. It is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. E. coli SQR is classified as Type C SQRs because it contains two transmembrane subunits and one heme group. The SdhD and SdhC subunits are membrane anchor subunits containing heme and quinone binding sites. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the membrane anchor subunits via electron transport through FAD and three iron-sulfur centers. The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes. 100 matched cddid_all.tbl CDD cd03496 cd03496 239576 SQR_TypeC_CybS SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Eukaryotic SQRs reduce high potential quinones such as ubiquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are classified as Type C SQRs because they contain two transmembrane subunits and one heme group. CybS and CybL are the two transmembrane proteins of eukaryotic SQRs. They contain heme and quinone binding sites. CybS is the eukaryotic homolog of the bacterial SdhD subunit. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the transmembrane subunits via electron transport through FAD and three iron-sulfur centers. The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes. Mutations in human Complex II result in various physiological disorders including hereditary paraganglioma and pheochromocytoma tumors. The gene encoding for the SdhD subunit is classified as a tumor suppressor gene. 104 matched cddid_all.tbl CDD cd03497 cd03497 239577 SQR_TypeB_1_TM Succinate:quinone oxidoreductase (SQR) Type B subfamily 1, transmembrane subunit; composed of proteins similar to Bacillus subtilis SQR. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Bacillus subtilis SQR reduces low potential quinones such as menaquinone. SQR is also called succinate dehydrogenase (Sdh) or Complex II and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are classified as Type B as they contain one transmembrane subunit and two heme groups. The heme and quinone binding sites reside on the transmembrane subunit. The transmembrane subunit of Bacillus subtilis SQR is also called Sdh cytochrome b558 subunit. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, and the transmembrane subunit containing the electron acceptor (quinone). The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes. 207 matched cddid_all.tbl CDD cd03498 cd03498 239578 SQR_TypeB_2_TM Succinate:quinone oxidoreductase (SQR)-like Type B subfamily 2, transmembrane subunit; composed of proteins with similarity to the SQRs of Geobacter metallireducens and Corynebacterium glutamicum. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. C. glutamicum SQR reduces low potential quinones such as menaquinone. SQR is also called succinate dehydrogenase (Sdh) or Complex II and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are classified as Type B as they contain one transmembrane subunit and two heme groups. The heme and quinone binding sites reside in the transmembrane subunit. The transmembrane subunit of members of this subfamily is also called Sdh cytochrome b558 subunit based on the Bacillus subtilis protein. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, and the transmembrane subunit containing the electron acceptor (quinone). The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes. Proteins in this subfamily from G. metallireducens and G. sulfurreducens are bifunctional enzymes with SQR and QFR activities. 209 matched cddid_all.tbl CDD cd03499 cd03499 239579 SQR_TypeC_SdhC Succinate:quinone oxidoreductase (SQR) Type C subfamily, Succinate dehydrogenase C (SdhC) subunit; composed of bacterial SdhC and eukaryotic large cytochrome b binding (CybL) proteins. SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Members of this family reduce high potential quinones such as ubiquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Proteins in this subfamily are classified as Type C SQRs because they contain two transmembrane subunits and one heme group. The heme and quinone binding sites reside in the transmembrane subunits. The SdhC or CybL protein is one of the two transmembrane subunits of bacterial and eukaryotic SQRs. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the membrane anchor subunits via electron transport through FAD and three iron-sulfur centers. The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes. 117 matched cddid_all.tbl CDD cd03500 cd03500 239580 SQR_TypeA_SdhD_like Succinate:quinone oxidoreductase (SQR) Type A subfamily, Succinate dehydrogenase D (SdhD)-like subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Members of this subfamily reduce low potential quinones such as menaquinone and thermoplasmaquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are similar to the Thermoplasma acidophilum SQR and are classified as Type A because they contain two transmembrane subunits as well as two heme groups. Although there are no structures available for this subfamily, the presence of two hemes has been proven spectroscopically for T. acidophilum. The two membrane anchor subunits are similar to the SdhD and SdhC subunits of bacterial SQRs, which contain heme and quinone binding sites. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the membrane anchor subunits via electron transport through FAD and three iron-sulfur centers. The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes. 106 matched cddid_all.tbl CDD cd03501 cd03501 239581 SQR_TypeA_SdhC_like Succinate:quinone oxidoreductase (SQR) Type A subfamily, Succinate dehydrogenase C (SdhC)-like subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol. Members of this subfamily reduce low potential quinones such as menaquinone and thermoplasmaquinone. SQR is also called succinate dehydrogenase or Complex II, and is part of the citric acid cycle and the aerobic respiratory chain. SQR is composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Members of this subfamily are similar to the Thermoplasma acidophilum SQR and are classified as Type A because they contain two transmembrane subunits as well as two heme groups. Although there are no structures available for this subfamily, the presence of two hemes has been proven spectroscopically for T. acidophilum. The two membrane anchor subunits are similar to the SdhD and SdhC subunits of bacterial SQRs, which contain heme and quinone binding sites. The two-electron oxidation of succinate in the flavoprotein active site is coupled to the two-electron reduction of quinone in the membrane anchor subunits via electron transport through FAD and three iron-sulfur centers. The reversible reduction of quinone is an essential feature of respiration, allowing transfer of electrons between respiratory complexes. 101 matched cddid_all.tbl CDD cd03505 cd03505 239582 Delta9-FADS-like The Delta9 Fatty Acid Desaturase (Delta9-FADS)-like CD includes the delta-9 and delta-11 acyl CoA desaturases found in various eukaryotes including vertebrates, insects, higher plants, and fungi. The delta-9 acyl-lipid desaturases are found in a wide range of bacteria. These enzymes play essential roles in fatty acid metabolism and the regulation of cell membrane fluidity. Acyl-CoA desaturases are the enzymes involved in the CoA-bound desaturation of fatty acids. Mammalian stearoyl-CoA delta-9 desaturase is a key enzyme in the biosynthesis of monounsaturated fatty acids, and in yeast, the delta-9 acyl-CoA desaturase (OLE1) reaction accounts for all de nova unsaturated fatty acid production in Saccharomyces cerevisiae. These non-heme, iron-containing, ER membrane-bound enzymes are part of a three-component enzyme system involving cytochrome b5, cytochrome b5 reductase, and the delta-9 fatty acid desaturase. This complex catalyzes the NADH- and oxygen-dependent insertion of a cis double bond between carbons 9 and 10 of the saturated fatty acyl substrates, palmitoyl (16:0)-CoA or stearoyl (18:0)-CoA, yielding the monoenoic products palmitoleic (16:l) or oleic (18:l) acids, respectively. In cyanobacteria, the biosynthesis of unsaturated fatty acids is initiated by delta 9 acyl-lipid desaturase (DesC) which introduces the first double bond at the delta-9 position of a saturated fatty acid that has been esterified to a glycerolipid. This domain family has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of sequences also reveals the existence of three regions of conserved histidine cluster motifs that contain the residues: HXXXXH, HXXHH, and H/QXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the rat stearoyl CoA delta-9 desaturase. Some eukaryotic (Fungi, Euglenozoa, Mycetozoa, Rhodophyta) desaturase domains have an adjacent C-terminal cytochrome b5-like domain. 178 matched cddid_all.tbl CDD cd03506 cd03506 239583 Delta6-FADS-like The Delta6 Fatty Acid Desaturase (Delta6-FADS)-like CD includes the integral-membrane enzymes: delta-4, delta-5, delta-6, delta-8, delta-8-sphingolipid, and delta-11 desaturases found in vertebrates, higher plants, fungi, and bacteria. These desaturases are required for the synthesis of highly unsaturated fatty acids (HUFAs), which are mainly esterified into phospholipids and contribute to maintaining membrane fluidity. While HUFAs may be required for cold tolerance in bacteria, plants and fish, the primary role of HUFAs in mammals is cell signaling. These enzymes are described as front-end desaturases because they introduce a double bond between the pre-exiting double bond and the carboxyl (front) end of the fatty acid. Various substrates are involved, with both acyl-coenzyme A (CoA) and acyl-lipid desaturases present in this CD. Acyl-lipid desaturases are localized in the membranes of cyanobacterial thylakoid, plant endoplasmic reticulum (ER), and plastid; and acyl-CoA desaturases are present in ER membrane. ER-bound plant acyl-lipid desaturases and acyl-CoA desaturases require cytochrome b5 as an electron donor. Most of the eukaryotic desaturase domains have an adjacent N-terminal cytochrome b5-like domain. This domain family has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of sequences also reveals the existence of three regions of conserved histidine cluster motifs that contain the residues: HXXXH, HXX(X)HH, and Q/HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the homolog, stearoyl CoA desaturase. 204 matched cddid_all.tbl CDD cd03507 cd03507 239584 Delta12-FADS-like The Delta12 Fatty Acid Desaturase (Delta12-FADS)-like CD includes the integral-membrane enzymes, delta-12 acyl-lipid desaturases, oleate 12-hydroxylases, omega3 and omega6 fatty acid desaturases, and other related proteins, found in a wide range of organisms including higher plants, green algae, diatoms, nematodes, fungi, and bacteria. The expression of these proteins appears to be temperature dependent: decreases in temperature result in increased levels of fatty acid desaturation within membrane lipids subsequently altering cell membrane fluidity. An important enzyme for the production of polyunsaturates in plants is the oleate delta-12 desaturase (Arabidopsis FAD2) of the endoplasmic reticulum. This enzyme accepts l-acyl-2-oleoyl-sn-glycero-3-phosphocholine as substrate and requires NADH:cytochrome b oxidoreductase, cytochrome b, and oxygen for activity. FAD2 converts oleate(18:1) to linoleate (18:2) and is closely related to oleate 12-hydroxylase which catalyzes the hydroxylation of oleate to ricinoleate. Plastid-bound desaturases (Arabidopsis delta-12 desaturase (FAD6), omega-3 desaturase (FAD8), omega-6 desaturase (FAD6)), as well as, the cyanobacterial thylakoid-bound FADSs require oxygen, ferredoxin, and ferredoxin oxidoreductase for activity. As in higher plants, the cyanobacteria delta-12 (DesA) and omega-3 (DesB) FADSs desaturate oleate (18:1) to linoleate (18:2) and linoleate (18:2) to linolenate (18:3), respectively. Omega-3 (DesB/FAD8) and omega-6 (DesD/FAD6) desaturases catalyze reactions that introduce a double bond between carbons three and four, and carbons six and seven, respectively, from the methyl end of fatty acids. As with other members of this superfamily, this domain family has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of sequences also reveals the existence of three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXX(X)HH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the homologue, stearoyl CoA desaturase. Mutation of any one of four of these histidines in the Synechocystis delta-12 acyl-lipid desaturase resulted in complete inactivity. 222 matched cddid_all.tbl CDD cd03508 cd03508 239585 Delta4-sphingolipid-FADS-like The Delta4-sphingolipid Fatty Acid Desaturase (Delta4-sphingolipid-FADS)-like CD includes the integral-membrane enzymes, dihydroceramide Delta-4 desaturase, involved in the synthesis of sphingosine; and the human membrane fatty acid (lipid) desaturase (MLD), reported to modulate biosynthesis of the epidermal growth factor receptor; and other related proteins. These proteins are found in various eukaryotes including vertebrates, higher plants, and fungi. Studies show that MLD is localized to the endoplasmic reticulum. As with other members of this superfamily, this domain family has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of sequences also reveals the existence of three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXXHH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the homolog, stearoyl CoA desaturase. 289 matched cddid_all.tbl CDD cd03509 cd03509 239586 DesA_FADS-like Fatty acid desaturase protein family subgroup, a delta-12 acyl-lipid desaturase-like, DesA-like, yet uncharacterized subgroup of membrane fatty acid desaturase proteins found in alpha-, beta-, and gamma-proteobacteria. Sequences of this domain family appear to be structurally related to membrane fatty acid desaturases and alkane hydroxylases. They all share in common extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of these sequences also reveals three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXXHH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within homologs, stearoyl CoA desaturase and alkane hydroxylase. 288 matched cddid_all.tbl CDD cd03510 cd03510 239587 Rhizobitoxine-FADS-like This CD includes the dihydrorhizobitoxine fatty acid desaturase (RtxC) characterized in Bradyrhizobium japonicum USDA110, and other related proteins. Dihydrorhizobitoxine desaturase is reported to be involved in the final step of rhizobitoxine biosynthesis. This domain family appears to be structurally related to the membrane fatty acid desaturases and the alkane hydroxylases. They all share in common extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of sequences also reveals the existence of three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXX(X)HH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within homologs, stearoyl CoA desaturase and alkane hydroxylase. 175 matched cddid_all.tbl CDD cd03511 cd03511 239588 Rhizopine-oxygenase-like This CD includes the putative hydrocarbon oxygenase, MocD, a bacterial rhizopine (3-O-methyl-scyllo-inosamine, 3-O-MSI) oxygenase, and other related proteins. It has been proposed that MocD, MocE (Rieske-like ferredoxin), and MocF (ferredoxin reductase) under the regulation of MocR, act in concert to form a ferredoxin oxygenase system that demethylates 3-O-MSI to form scyllo-inosamine. This domain family appears to be structurally related to the membrane fatty acid desaturases and the alkane hydroxylases. They all share in common extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of sequences also reveals the existence of three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXXHH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within homologs, stearoyl CoA desaturase and alkane hydroxylase. 285 matched cddid_all.tbl CDD cd03512 cd03512 239589 Alkane-hydroxylase Alkane hydroxylase is a bacterial, integral-membrane di-iron enzyme that shares a requirement for iron and oxygen for activity similar to that of the non-heme integral-membrane acyl coenzyme A (CoA) desaturases and acyl lipid desaturases. The alk genes in Pseudomonas oleovorans encode conversion of alkanes to acyl CoA. The alkane omega-hydroxylase (AlkB) system is responsible for the initial oxidation of inactivated alkanes. It is a three-component system comprising a soluble NADH-rubredoxin reductase (AlkT), a soluble rubredoxin (AlkG), and the integral membrane oxygenase (AlkB). AlkB utilizes the oxygen rebound mechanism to hydroxylate alkanes. This mechanism involves homolytic cleavage of the C-H bond by an electrophilic metal-oxo intermediate to generate a substrate-based radical. As with other members of this superfamily, this domain family has extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. The active site structure of AlkB is not known, however, spectroscopic and genetic evidence points to a nitrogen-rich coordination environment located in the cytoplasm with as many as eight histidines coordinating the two iron ions and a carboxylate residue bridging the two metals. Like all other members of this superfamily, there are eight conserved histidines seen in the histidine cluster motifs: HXXXH, HXXXHH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within the homolog, stearoyl CoA desaturase. Also included in this CD are terminal alkane hydroxylases (AlkM), xylene monooxygenase hydroxylases (XylM), p-cymene monooxygenase hydroxylases (CymAa), and other related proteins. 314 matched cddid_all.tbl CDD cd03513 cd03513 239590 CrtW_beta-carotene-ketolase Beta-carotene ketolase/oxygenase (CrtW, also known as CrtO), the carotenoid astaxanthin biosynthetic enzyme, initially catalyzes the addition of two keto groups to carbons C4 and C4' of beta-carotene. Carotenoids are important natural pigments produced by many microorganisms and plants. Astaxanthin is reported to be an antioxidant, an anti-cancer agent, and an immune system stimulant. A number of bacteria and green algae can convert beta-carotene into astaxanthin by using several ketocarotenoids as intermediates and CrtW and a beta-carotene hydroxylase (CrtZ). CrtW initially converts beta-carotene to canthaxanthin via echinenone, and CrtZ initially mediates the conversion of beta-carotene to zeaxanthin via beta-cryptoxanthin. After a few more intermediates are formed, CrtW and CrtZ act in combination to produce astaxanthin. Sequences of this domain family appear to be structurally related to membrane fatty acid desaturases and alkane hydroxylases. They all share in common extensive hydrophobic regions that are capable of spanning the membrane bilayer at least twice. Comparison of these sequences also reveals three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXXHH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within homologs, stearoyl CoA desaturase and alkane hydroxylase. 225 matched cddid_all.tbl CDD cd03514 cd03514 239591 CrtR_beta-carotene-hydroxylase Beta-carotene hydroxylase (CrtR), the carotenoid zeaxanthin biosynthetic enzyme catalyzes the addition of hydroxyl groups to the beta-ionone rings of beta-carotene to form zeaxanthin and is found in bacteria and red algae. Carotenoids are important natural pigments; zeaxanthin and lutein are the only dietary carotenoids that accumulate in the macular region of the retina and lens. It is proposed that these carotenoids protect ocular tissues against photooxidative damage. CrtR does not show overall amino acid sequence similarity to the beta-carotene hydroxylases similar to CrtZ, an astaxanthin biosynthetic beta-carotene hydroxylase. However, CrtR does show sequence similarity to the green alga, Haematococcus pluvialis, beta-carotene ketolase (CrtW), which converts beta-carotene to canthaxanthin. Sequences of the CrtR_beta-carotene-hydroxylase domain family, as well as, the CrtW_beta-carotene-ketolase domain family appear to be structurally related to membrane fatty acid desaturases and alkane hydroxylases. They all share in common extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of these sequences also reveals three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXXHH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within homologs, stearoyl CoA desaturase and alkane hydroxylase. 207 matched cddid_all.tbl CDD cd03515 cd03515 239592 Link_domain_TSG_6_like This is the extracellular link domain of the type found in human TSG-6. The link domain is a hyaluronan (HA)-binding domain. TSG-6 is the protein product of tumor necrosis factor-stimulated gene-6. TSG-6 is up-regulated in inflammatory lesions and in the ovary during ovulation. It has a strong anti-inflammatory and chondroprotective effect in models of acute inflammation and autoimmune arthritis and plays an essential role in female fertility. Also included in this group are the stabilins: stabilin-1 (FEEL-1, CLEVER-1) and stabilin-2 (FEEL-2). Stabilin-2 functions as the major liver and lymph node-scavenging receptor for HA and related glycosaminoglycans. Stabilin-2 is a scavenger receptor with a broad range of ligands including advanced glycation end (AGE) products, acetylated low density lipoprotein and procollagen peptides. In contrast, stabilin-1 does not bind HA, but binds acetylated low density lipoprotein and AGEs with lower affinity. As AGEs accumulate in vascular tissues during aging and diabetes, these receptors may be implicated in the pathologies of these states. Both stabilins are present in the early endocytic pathway in hepatic sinusoidal epithelium associating with clathrin/AP-2. Stabilin-1 is expressed in macrophages. Stabilin-2 is absent from the latter. In macrophages: stabilin-1 is involved in trafficking between early/sorting endosomes and the trans-Golgi network. Stabilin-1 has also been implicated in angiogenesis and possibly leucocyte trafficking. Both stabilins bind gram-positive and gram-negative bacteria. TSG-6 and stabilins contain a single link module which supports high affinity binding to HA. 93 matched cddid_all.tbl CDD cd03516 cd03516 239593 Link_domain_CD44_like This domain is a hyaluronan (HA)-binding domain. It is found in CD44 receptor and mediates adhesive interactions during inflammatory leukocyte homing and tumor metastasis. It also plays an important role in arteriogenesis. The functional HA-binding domain of CD44 is an extended domain comprised of a single link module flanked with N-and C- extensions. These extensions are essential for folding and for functional activity. This group also contains the cell surface retention sequence (CRS) binding protein-1 (CRSBP-1) and lymph vessel endothelial receptor-1 (LYVE-1). CRSBP-1 is a cell surface binding protein for the CRS motif of PDGF-BB (platelet-derived growth factor-BB) and is responsible for the cell surface retention of PDGF-BB in SSV-transformed cells. CRSBP-1 may play a role in autocrine regulation of cell growth mediated by CRS containing growth regulators. LYVE-1 is preferentially expressed on the lymphatic endothelium and is used as a molecular marker for the detection and characterization of lymphatic vessels in tumors. 144 matched cddid_all.tbl CDD cd03517 cd03517 239594 Link_domain_CSPGs_modules_1_3 Link_domain_CSPGs_modules_1_3; this extracellular link domain is found in the first and third link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan. In addition, it is found in the first link module of three other CSPGs: versican, neurocan, and brevican. The link domain is a hyaluronan (HA)-binding domain. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of aggrecan are involved in interaction with HA. In addition, aggrecan contains a second globular domain (G2) which contains link modules 3 and 4. G2 appears to lack HA-binding activity. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes. 95 matched cddid_all.tbl CDD cd03518 cd03518 239595 Link_domain_HAPLN_module_1 Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding domain. HAPLNs contain two contiguous link modules. Both link modules of cartilage link protein are involved in interaction with HA. In cartilage, a chondroitin sulfate proteoglycan core protein (CSPG) aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates with other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HAPLN gene family are physically linked adjacent to CSPG genes. 95 matched cddid_all.tbl CDD cd03519 cd03519 239596 Link_domain_HAPLN_module_2 Link_domain_HAPLN_module_2; this link domain is found in the second link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding domain. HAPLNs contain two contiguous link modules. Both link modules of cartilage link protein are involved in interaction with HA. In cartilage, a chondroitin sulfate proteoglycan core protein (CSPG) aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates with other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HAPLN gene family are physically linked adjacent to CSPG genes. 91 matched cddid_all.tbl CDD cd03520 cd03520 239597 Link_domain_CSPGs_modules_2_4 Link_domain_CSPGs_modules_2_4; this link domain is found in the second and fourth link modules of the chondroitin sulfate proteoglycan core protein (CSPG) aggrecan and, in the second link module of three other CSPGs: versican, neurocan, and brevican. The link domain is a hyaluronan (HA)-binding domain. CSPGs are characterized by an N-terminal globular domain (G1 domain) containing two contiguous link modules (modules 1 and 2). Both link modules of the G1 domain of aggrecan are involved in interaction with HA. Aggrecan in addition contains a second globular domain (G2) having link modules 3 and 4 which lack HA-binding activity. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggregan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes. 96 matched cddid_all.tbl CDD cd03521 cd03521 239598 Link_domain_KIAA0527_like Link_domain_KIAA0527_like; this domain is found in the human protein KIAA0527. Sequence-wise, it is highly similar to the link domain. The link domain is a hyaluronan-binding (HA) domain. KIAA0527 contains a single link module. The KIAA0527 gene was originally cloned from human brain tissue. 95 matched cddid_all.tbl CDD cd03522 cd03522 239599 MoeA_like MoeA_like. This domain is similar to a domain found in a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. There this domain is presumed to bind molybdopterin. The exact function of this subgroup is unknown. 312 matched cddid_all.tbl CDD cd03523 cd03523 239600 NTR_like NTR_like domain; a beta barrel with an oligosaccharide/oligonucleotide-binding fold found in netrins, complement proteins, tissue inhibitors of metalloproteases (TIMP), and procollagen C-proteinase enhancers (PCOLCE), amongst others. In netrins, the domain plays a role in controlling axon branching in neural development, while the common function of these modules in TIMPs appears to be binding to metzincins. A subset of this family is also known as the C345C domain because it occurs as a C-terminal domain in complement C3, C4 and C5. In C5, the domain interacts with various partners during the formation of the membrane attack complex. 105 matched cddid_all.tbl CDD cd03524 cd03524 239601 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyrococcus abyssi DNA polymerase II (Pol II) small subunit, Sulfolobus solfataricus SSB, and Bacillus subtilis YhaM (a 3'-to-5'exoribonuclease). It also includes the OB folds of breast cancer susceptibility gene 2 protein (BRCA2), Oxytricha nova telomere end binding protein (TEBP), Saccharomyces cerevisiae telomere-binding protein (Cdc13), and human protection of telomeres 1 protein (POT1). 75 matched cddid_all.tbl CDD cd03526 cd03526 239602 SQR_QFR_TypeB_TM Succinate:quinone oxidoreductase (SQR) and Quinol:fumarate reductase (QFR) Type B subfamily, transmembrane subunit; SQR catalyzes the oxidation of succinate to fumarate coupled to the reduction of quinone to quinol, while QFR catalyzes the reverse reaction. SQR, also called succinate dehydrogenase or Complex II, is part of the citric acid cycle and the aerobic respiratory chain, while QFR is involved in anaerobic respiration with fumarate as the terminal electron acceptor. SQR and QFR share a common subunit arrangement, composed of a flavoprotein catalytic subunit, an iron-sulfur protein and one or two hydrophobic transmembrane subunits. Type B proteins contain one transmembrane subunit and two heme groups. The heme and quinone binding sites reside in the transmembrane subunits. The structural arrangement allows efficient electron transfer between the catalytic subunit, through iron-sulfur centers, and the transmembrane subunit containing the electron donor/acceptor (quinol or quinone). The reversible reduction of quinone is an essential feature of respiration, allowing the transfer of electrons between respiratory complexes. 199 matched cddid_all.tbl CDD cd03527 cd03527 239603 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits. 99 matched cddid_all.tbl CDD cd03528 cd03528 239604 Rieske_RO_ferredoxin Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The ferredoxin component contains either a plant-type or Rieske-type [2Fe-2S] cluster. The Rieske ferredoxin component in this family carries an electron from the RO reductase component to the terminal RO oxygenase component. BPDO degrades biphenyls and polychlorinated biphenyls. BPDO ferredoxin (BphF) has structural features consistent with a minimal and perhaps archetypical Rieske protein in that the insertions that give other Rieske proteins unique structural features are missing. CARDO catalyzes dihydroxylation at the C1 and C9a positions of carbazole. Rieske ferredoxins are found as subunits of membrane oxidase complexes, cis-dihydrodiol-forming aromatic dioxygenases, bacterial assimilatory nitrite reductases, and arsenite oxidase. Rieske ferredoxins are also found as soluble electron carriers in bacterial dioxygenase and monooxygenase complexes. 98 matched cddid_all.tbl CDD cd03529 cd03529 239605 Rieske_NirD Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while fungal proteins have a C-terminal Rieske domain in addition to several other domains. The fungal NirD is involved in nutrient acquisition, functioning at the soil/fungus interface to control nutrient exchange between the fungus and the host plant. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The Rieske [2Fe-2S] cluster is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In this family, only a few members contain these residues. Other members may have lost the ability to bind the Rieske [2Fe-2S] cluster. 103 matched cddid_all.tbl CDD cd03530 cd03530 239606 Rieske_NirD_small_Bacillus Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. 98 matched cddid_all.tbl CDD cd03531 cd03531 239607 Rieske_RO_Alpha_KSH The alignment model represents the N-terminal rieske iron-sulfur domain of KshA, the oxygenase component of 3-ketosteroid 9-alpha-hydroxylase (KSH). The terminal oxygenase component of KSH is a key enzyme in the microbial steroid degradation pathway, catalyzing the 9 alpha-hydroxylation of 4-androstene-3,17-dione (AD) and 1,4-androstadiene-3,17-dione (ADD). KSH is a two-component class IA monooxygenase, with terminal oxygenase (KshA) and oxygenase reductase (KshB) components. KSH activity has been found in many actino- and proteo- bacterial genera including Rhodococcus, Nocardia, Arthrobacter, Mycobacterium, and Burkholderia. 115 matched cddid_all.tbl CDD cd03532 cd03532 239608 Rieske_RO_Alpha_VanA_DdmC Rieske non-heme iron oxygenase (RO) family, Vanillate-O-demethylase oxygenase (VanA) and dicamba O-demethylase oxygenase (DdmC) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Vanillate-O-demethylase is a heterodimeric enzyme consisting of a terminal oxygenase (VanA) and reductase (VanB) components. This enzyme reductively catalyzes the conversion of vanillate into protocatechuate and formaldehyde. Protocatechuate and vanillate are important intermediate metabolites in the degradation pathway of lignin-derived compounds such as ferulic acid and vanillin by soil microbes. DDmC is the oxygenase component of a three-component dicamba O-demethylase found in Pseudomonas maltophila, that catalyzes the conversion of a widely used herbicide called herbicide dicamba (2-methoxy-3,6-dichlorobenzoic acid) to DCSA (3,6-dichlorosalicylic acid). 116 matched cddid_all.tbl CDD cd03535 cd03535 239609 Rieske_RO_Alpha_NDO Rieske non-heme iron oxygenase (RO) family, Nathphalene 1,2-dioxygenase (NDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. NDO is a three-component RO system consisting of a reductase, a ferredoxin, and a hetero-hexameric alpha-beta subunit oxygenase component. NDO catalyzes the oxidation of naphthalene to cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene (naphthalene cis-dihydrodiol) with the consumption of O2 and NAD(P)H. NDO has a relaxed substrate specificity and can oxidize almost 100 substrates. Included in its varied activities are the enantiospecific cis-dihydroxylation of polycyclic aromatic hydrocarbons and benzocycloalkenes, benzylic hydroxylation, N- and O-dealkylation, sulfoxidation and desaturation reactions. 123 matched cddid_all.tbl CDD cd03536 cd03536 239610 Rieske_RO_Alpha_DTDO This alignment model represents the N-terminal rieske domain of the oxygenase alpha subunit (DitA) of diterpenoid dioxygenase (DTDO). DTDO is a novel aromatic-ring-hydroxylating dioxygenase found in Pseudomonas and other proteobacteria that degrades dehydroabietic acid (DhA). Specifically, DitA hydroxylates 7-oxodehydroabietic acid to 7-oxo-11,12-dihydroxy-8, 13-abietadien acid. The ditA1 and ditA2 genes encode the alpha and beta subunits of the oxygenase component of DTDO while the ditA3 gene encodes the ferredoxin component of DTDO. The organization of the genes encoding the various diterpenoid dioxygenase components, the phylogenetic distinctiveness of both the alpha subunit and the ferredoxin component, and the unusual iron-sulfur cluster of the ferredoxin all suggest that this enzyme belongs to a new class of aromatic ring-hydroxylating dioxygenases. 123 matched cddid_all.tbl CDD cd03537 cd03537 239611 Rieske_RO_Alpha_PrnD This alignment model represents the N-terminal rieske domain of the oxygenase alpha subunit of aminopyrrolnitrin oxygenase (PrnD). PrnD is a novel Rieske N-oxygenase that catalyzes the final step in the pyrrolnitrin biosynthetic pathway, the oxidation of the amino group in aminopyrrolnitrin to a nitro group, forming the antibiotic pyrrolnitrin. The biosynthesis of pyrrolnitrin is one of the best examples of enzyme-catalyzed arylamine oxidation. Although arylamine oxygenases are widely distributed within the microbial world and used in a variety of metabolic reactions, PrnD represents one of only two known examples of arylamine oxygenases or N-oxygenases involved in arylnitro group formation, the other being AurF involved in aureothin biosynthesis. 123 matched cddid_all.tbl CDD cd03538 cd03538 239612 Rieske_RO_Alpha_AntDO Rieske non-heme iron oxygenase (RO) family, Anthranilate 1,2-dioxygenase (AntDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. AntDO converts anthranilate to catechol, a naturally occurring compound formed through tryptophan degradation and an important intermediate in the metabolism of many N-heterocyclic compounds such as indole, o-nitrobenzoate, carbazole, and quinaldine. 146 matched cddid_all.tbl CDD cd03539 cd03539 239613 Rieske_RO_Alpha_S5H This alignment model represents the N-terminal rieske iron-sulfur domain of the oxygenase alpha subunit (NagG) of salicylate 5-hydroxylase (S5H). S5H converts salicylate (2-hydroxybenzoate), a metabolic intermediate of phenanthrene, to gentisate (2,5-dihydroxybenzoate) as part of an alternate pathway for naphthalene catabolism. S5H is a multicomponent enzyme made up of NagGH (the oxygenase components), NagAa (the ferredoxin reductase component), and NagAb (the ferredoxin component). The oxygenase component is made up of alpha (NagG) and beta (NagH) subunits. 129 matched cddid_all.tbl CDD cd03541 cd03541 239614 Rieske_RO_Alpha_CMO Rieske non-heme iron oxygenase (RO) family, Choline monooxygenase (CMO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. CMO is a novel RO found in certain plants which catalyzes the first step in betaine synthesis. CMO is not found in animals or bacteria. In these organisms, the first step in betaine synthesis is catalyzed by either the membrane-bound choline dehydrogenase (CDH) or the soluble choline oxidase (COX). 118 matched cddid_all.tbl CDD cd03542 cd03542 239615 Rieske_RO_Alpha_HBDO Rieske non-heme iron oxygenase (RO) family, 2-Halobenzoate 1,2-dioxygenase (HBDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. HBDO catalyzes the double hydroxylation of 2-halobenzoates with concomitant release of halogenide and carbon dioxide, yielding catechol. 123 matched cddid_all.tbl CDD cd03545 cd03545 239616 Rieske_RO_Alpha_OHBDO_like Rieske non-heme iron oxygenase (RO) family, Ortho-halobenzoate-1,2-dioxygenase (OHBDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of OHBDO, salicylate 5-hydroxylase (S5H), terephthalate 1,2-dioxygenase system (TERDOS) and similar proteins. ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. OHBDO converts 2-chlorobenzoate (2-CBA) to catechol as well as 2,4-dCBA and 2,5-dCBA to 4-chlorocatechol, as part of the chlorobenzoate degradation pathway. Although ortho-substituted chlorobenzoates appear to be particularly recalcitrant to biodegradation, several strains utilize 2-CBA and the dCBA derivatives as a sole carbon and energy source. S5H converts salicylate (2-hydroxybenzoate), a metabolic intermediate of phenanthrene, to gentisate (2,5-dihydroxybenzoate) as part of an alternate pathway for naphthalene catabolism. S5H is a multicomponent enzyme made up of NagGH (the oxygenase components), NagAa (the ferredoxin reductase component), and NagAb (the ferredoxin component). The oxygenase component is made up of alpha (NagG) and beta (NagH) subunits. TERDOS is present in gram-positive bacteria and proteobacteria where it converts terephthalate (1,4-dicarboxybenzene) to protocatechuate as part of the terephthalate degradation pathway. The oxygenase component of TERDOS, called TerZ, is a hetero-hexamer with 3 alpha (TerZalpha) and 3 beta (TerZbeta) subunits. 150 matched cddid_all.tbl CDD cd03548 cd03548 239617 Rieske_RO_Alpha_OMO_CARDO Rieske non-heme iron oxygenase (RO) family, 2-Oxoquinoline 8-monooxygenase (OMO) and Carbazole 1,9a-dioxygenase (CARDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. OMO catalyzes the NADH-dependent oxidation of the N-heterocyclic aromatic compound 2-oxoquinoline to 8-hydroxy-2-oxoquinoline, the second step in the bacterial degradation of quinoline. OMO consists of a reductase component (OMR) and an oxygenase component (OMO) that together function to shuttle electrons from the reduced pyridine nucleotide to the active site of OMO, where O2 activation and 2-oxoquinoline hydroxylation occurs. CARDO, which contains oxygenase (CARDO-O), ferredoxin (CARDO-F) and ferredoxin reductase (CARDO-R) components, catalyzes the dihydroxylation at the C1 and C9a positions of carbazole. The oxygenase component of OMO and CARDO contain only alpha subunits arranged in a trimeric structure. 136 matched cddid_all.tbl CDD cd03556 cd03556 239618 L-fucose_isomerase L-fucose isomerase (FucIase); FucIase converts L-fucose, an aldohexose, to its ketose form, which prepares it for aldol cleavage (similar to the isomerization of glucose during glycolysis). L-fucose (or 6-deoxy-L-galactose) is found in blood group determinants as well as in various oligo- and polysaccharides, and glycosides in mammals, bacteria and plants. 584 matched cddid_all.tbl CDD cd03557 cd03557 239619 L-arabinose_isomerase L-Arabinose isomerase (AI) catalyzes the isomerization of L-arabinose to L-ribulose, the first reaction in its conversion into D-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway, which allows L-arabinose to be used as a carbon source. AI can also convert D-galactose to D-tagatose at elevated temperatures in the presence of divalent metal ions. D-tagatose, rarely found in nature, is of commercial interest as a low-calorie sugar substitute. 484 matched cddid_all.tbl CDD cd03558 cd03558 349787 LGIC_ECD extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels (also known as ligand-gated ion channel (LGIC)). This superfamily contains the extracellular domain (ECD) of Cys-loop neurotransmitter-gated ion channels, which include nicotinic acetylcholine receptor (nAChR), serotonin 5-hydroxytryptamine receptor (5-HT3), type-A gamma-aminobutyric acid receptor (GABAAR) and glycine receptor (GlyR). These ligand-gated ion channels (LGICs) are found across metazoans and have close homologs in bacteria. They are vital for communication throughout the nervous system. GABAAR and GlyR are anionic channels, both mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR receptor pore, resulting in hyperpolarization of the neuron. nAChR is a non-selective cation channel that is permeable to Na+ and K+, and some subunit combinations are also permeable to Ca2+. Na+ enters and K+ exits to allow net flow of positively charged ions inward. 5-HT3, a cation-selective channel, binds serotonin and is permeable to Na+, K+, and Ca2+. It mediates neuronal depolarization and excitation within the central and peripheral nervous systems. These ligand-gated chloride channels are critical not only for maintaining appropriate neuronal activity, but have long been important therapeutic targets: benzodiazepines, barbiturates, some intravenous and volatile anaesthetics, alcohol, strychnine, picrotoxin, and ivermectin all derive their biological activity from acting on the inhibitory half of the Cys-loop receptor family. The ECD contains the ligand binding sites for these receptors. 179 matched cddid_all.tbl CDD cd03559 cd03559 349850 LGIC_TM transmembrane domain of Cys-loop neurotransmitter-gated ion channels. This superfamily contains the transmembrane domain of Cys-loop neurotransmitter-gated ion channels, which include nicotinic acetylcholine receptor (nAChR), serotonin 5-hydroxytryptamine receptor (5-HT3), type-A gamma-aminobutyric acid receptor (GABAAR), and glycine receptor (GlyR). These ligand-gated ion channels (LGICs) are found across metazoans and have close homologs in bacteria. They are vital for communication throughout the nervous system where the sign of synaptic connections (excitatory or inhibitory) is determined by the charge of the ions that flow through these channels. In general, channels that conduct positive ions are excitatory, whereas channels that conduct negative ions are inhibitory. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. GABAAR and GlyR are anionic channels, both mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR receptor pore, resulting in hyperpolarization of the neuron. nAChR is a non-selective cation channel that is permeable to Na+ and K+, and some subunit combinations are also permeable to Ca2+. Na+ enters and K+ exits to allow net flow of positively charged ions inward. 5-HT3, a cation-selective channel, binds serotonin and is permeable to Na+, K+, and Ca2+. It mediates neuronal depolarization and excitation within the central and peripheral nervous systems. These ligand-gated chloride channels are critical not only for maintaining appropriate neuronal activity, but have long been important therapeutic targets: benzodiazepines, barbiturates, some intravenous and volatile anaesthetics, alcohol, strychnine, picrotoxin, and ivermectin all derive their biological activity from acting on the inhibitory half of the Cys-loop receptor family. 116 matched cddid_all.tbl CDD cd03561 cd03561 340765 VHS VHS (Vps27/Hrs/STAM) domain family. The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family, which has the domain composition of VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition of VHS-GAT (GGA and TOM)-GAE (Gamma-Adaptin Ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general membrane targeting/cargo recognition role in vesicular trafficking. 131 matched cddid_all.tbl CDD cd03562 cd03562 340766 CID CID (CTD-Interacting Domain) family. The CTD-Interacting Domain (CID) is present in several eukaryotic RNA-processing factors including yeast proteins, Pcf11 and Nrd1, and vertebrate proteins, CTD-associated factors 8 (SCAF8) and Regulation of nuclear pre-mRNA domain-containing proteins (such as RPRD1 and RPRD2). Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices. 123 matched cddid_all.tbl CDD cd03564 cd03564 340767 ANTH_N ANTH (AP180 N-Terminal Homology) domain family, N-terminal region. The ANTH (AP180 N-Terminal Homology) domain family is composed of Adaptor Protein 180 (AP180), Clathrin Assembly Lymphoid Myeloid Leukemia protein (CALM), and similar proteins. ANTH domains bind both inositol phospholipids and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the Trans-Golgi Network, which suggests that the ANTH domain is a universal component of the machinery for clathrin-mediated membrane budding. The ANTH domain is a unique module whose N-terminal half is structurally similar to the Epsin N-Terminal Homology (ENTH) and Vps27/Hrs/STAM (VHS) domains, containing a superhelix of eight alpha helices. In addition, it contains a coiled-coil C-terminal half with strutural similarity to spectrin repeats. It binds phosphoinositide PtdIns(4,5)P2 at a short conserved motif K[X]9[K/R][H/Y] between helices 1 and 2. This model describes the N-terminal region of ANTH domains. 120 matched cddid_all.tbl CDD cd03565 cd03565 340768 VHS_Tom1_like VHS (Vps27/Hrs/STAM) domain of Tom1 subfamily. This subfamily is composed of Tom1 (Target of myb1 - retroviral oncogene) protein, Tom1L1 (Tom1-like1), Tom1L2 (Tom1-like2), and similar proteins. Proteins belonging to this subfamily are characterized by the presence of a VHS (Vps27p/Hrs/Stam) domain in the N-terminal portion followed by a GAT (GGA and Tom) domain. They are novel regulators for post-Golgi trafficking and signaling. Yeast do not contain homologous proteins of the Tom1 subfamily, suggesting these proteins have evolved to accommodate more complex cellular processes. Tom1 is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. 138 matched cddid_all.tbl CDD cd03567 cd03567 340769 VHS_GGA_metazoan VHS (Vps27/Hrs/STAM) domain of metazoan GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) proteins. GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprises a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins involved in membrane trafficking between the Trans-Golgi Network (TGN) and endosomes. Jawed vertebrates contain as many as three GGA proteins: GGA1, GGA2, and GGA3. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (Gamma-Adaptin Ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the Trans-Golgi Network and the endosomal system. 139 matched cddid_all.tbl CDD cd03568 cd03568 340770 VHS_STAM VHS (Vps27/Hrs/STAM) domain of the STAM (Signal Transducing Adaptor Molecule) subfamily. STAM (Signal Transducing Adaptor Molecule) subfamily members have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a Ubiquitin-Interacting Motif (UIM) and a SH3 (Src Homology 3) domain, which is a well-established protein-protein interaction domain, and a GAT (GGA and TOM) domain. At the C-termini of most vertebrate STAMs, an Immunoreceptor Tyrosine-based Activation Motif (ITAM) is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries. STAM is a component of the ESCRT (Endosomal Sorting Complex Required for Transport)-0 machinery and together with Hrs, functions to bind and sequester cargoes for downstream sorting into intralumenal vesicles. Jawed vertebrates have two STAM subfamily members, STAM1 and STAM2. 132 matched cddid_all.tbl CDD cd03569 cd03569 340771 VHS_Hrs VHS (Vps27/Hrs/STAM) domain of Hepatocyte growth factor-regulated tyrosine kinase substrate, Hrs. Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) plays a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane. Together with STAM or STAM2, it comprises the ESCRT (Endosomal Sorting Complex Required for Transport)-0 machinery, which functions to bind and sequester cargoes for downstream sorting into intralumenal vesicles. Hrs contains an N-terminal VHS domain, which has a superhelical structure similar to the structure of ARM (Armadillo) repeats, a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain, a Double Ubiquitin-Interacting Motif (DUIM), a P(S/T)XP motif that recruit ESCRT-I, a GAT (GGA and TOM) domain, and a short peptide motif near the C-terminus that recruits clathrin. 138 matched cddid_all.tbl CDD cd03571 cd03571 340772 ENTH Epsin N-Terminal Homology (ENTH) domain family. The Epsin N-Terminal Homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. ENTH domain is highly similar to the N-terminal region of the AP180 N-Terminal Homology (ANTH_N) domain. ENTH and ANTH_N domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. ENTH domains bind both, inositol phospholipids with preference for PtdIns(4,5)P2, and proteins, contributing to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. ENTH and ANTH (E/ANTH)-containing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the Trans-Golgi Network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding. 117 matched cddid_all.tbl CDD cd03572 cd03572 340773 ENTH_like_Tepsin Epsin N-Terminal Homology (ENTH)-like domain of AP-4 complex accessory subunit Tepsin and similar domains. This family is composed of proteins containing an ENTH-like domain including vertebrate AP-4 complex accessory subunit Tepsin and Arabidopsis thaliana VHS domain-containing protein At3g16270. Tepsin is also called ENTH Domain-containing protein 2 (ENTHD2), Epsin for AP-4, or Tetra-epsin. It associates with the adapter-like complex 4 (AP-4), a heterotetramer composed of two large adaptins (epsilon and beta), a medium adaptin (mu) and a small adaptin (sigma), which forms a non-clathrin coat on vesicles departing the Trans-Golgi Network. The Epsin N-Terminal Homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. ENTH domain is highly similar to the N-terminal region of the AP180 N-Terminal Homology (ANTH_N) domain. ENTH and ANTH_N domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. ENTH domains bind both, inositol phospholipids with preference for PtdIns(4,5)P2, and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. ENTH and ANTH (E/ANTH)-containing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the Trans-Golgi Network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding. 119 matched cddid_all.tbl CDD cd03574 cd03574 239629 NTR_complement_C345C NTR/C345C domain; The NTR domains that are found in the C-termini of complement C3, C4 and C5, are also called C345C domains. In C5, the domain interacts with various partners during the formation of the membrane attack complex, a fundamental process in the mammalian defense against infection. It's role in component C3 and C4 is not well understood. 147 matched cddid_all.tbl CDD cd03575 cd03575 239630 NTR_WFIKKN NTR domain, WFIKKN subfamily; WFIKKN proteins contain a C-terminal NTR domain and are putative secreted proteins which may be multivalent protease inhibitors that act on serine proteases as well as metalloproteases. Human WFIKKN and a related protein sharing the same domain architecture were observed to have distinct tissue expression patterns. WFIKKN is also referred to as growth and differentiation factor-associated serum protein-1 (GASP-1). It inhibits the activity of mature myostatin, a specific regulator of skeletal muscle mass and a member of the TGFbeta superfamily. 109 matched cddid_all.tbl CDD cd03576 cd03576 239631 NTR_PCOLCE NTR domain, PCOLCE subfamily; Procollagen C-endopeptidase enhancers (PCOLCEs) are extracellular matrix proteins that enhance the activity of procollagen C-proteases, by binding to the procollagen I C-peptide. They contain a C-terminal NTR domain, which have been suggested to possess inhibitory functions towards specific serine proteases but not towards metzincins, which are inhibited by the related TIMPs. 124 matched cddid_all.tbl CDD cd03577 cd03577 239632 NTR_TIMP_like NTR domain, TIMP-like subfamily; TIMPs, or tissue inibitors of metalloproteases, are essential regulators of extracellular matrix turnover and remodeling. They form complexes with matrix metalloproteases (MMPs) and inactivate them irreversibly by non-covalently binding their active zinc-binding sites. This group contains domains similar to the TIMP NTR domain, which binds MMPs. Members of this group may or may not function as MMP inhibitors. 116 matched cddid_all.tbl CDD cd03578 cd03578 239633 NTR_netrin-4_like NTR domain, Netrin-4-like subfamily; composed of the C-terminal NTR domains of netrin-4 (beta netrin) and similar proteins. Netrins are secreted proteins that function as tropic cues in the direction of axon growth and cell migration during neural development. Netrin-4 is a basement membrane component that is important in neural, kidney and vascular development. It may also be involved in regulating the outgrowth and shape of epithelial cells during lung branching morphogenesis. 111 matched cddid_all.tbl CDD cd03579 cd03579 239634 NTR_netrin-1_like NTR domain, Netrin-1-like subfamily; The C-terminal NTR domain of netrins is also called domain C in the context of C. elegans netrin UNC-6. Netrins are secreted proteins that function as tropic cues in the direction of axon growth and cell migration during neural development. These proteins may be chemoattractive to some neurons and chemorepellant for others. In the case of netrin-1, attraction and repulsion responses are mediated by the DCC and UNC-5 receptor families. The biological activities of C. elegans UNC-6, which may either attract or repel migrating cells or axons, are mediated by its different domains. The C-terminal NTR domain of UNC-6 has been shown to inhibit axon branching activity. 115 matched cddid_all.tbl CDD cd03580 cd03580 239635 NTR_Sfrp1_like NTR domain, Secreted frizzled-related protein (Sfrp) 1-like subfamily; composed of proteins similar to human Sfrp1, Sfrp2 and Sfrp5. Sfrps are soluble proteins containing an NTR domain C-terminal to a cysteine-rich Frizzled domain. They show diverse functions and are thought to work in Wnt signaling indirectly, as modulators or antagonists by binding Wnt ligands, and directly, via the Wnt receptor, Frizzled. They participate in regulating the patterning along the anteroposterior axis in vertebrates. Human Sfrp1 has been found frequently to be downregulated in breast cancer and is associated with disease progression and poor prognosis. 126 matched cddid_all.tbl CDD cd03581 cd03581 239636 NTR_Sfrp3_like NTR domain, Secreted frizzled-related protein (Sfrp) 3-like subfamily; composed of proteins similar to human Sfrp3 and Sfrp4. Sfrps are soluble proteins containing an NTR domain C-terminal to a cysteine-rich Frizzled domain. They show diverse functions and are thought to work in Wnt signaling indirectly, as modulators or antagonists by binding Wnt ligands, and directly, via the Wnt receptor, Frizzled. They participate in regulating the patterning along the anteroposterior axis in vertebrates. Human Sfrp3 may suppress the growth and invasiveness of androgen-independent prostate cancer cells. 111 matched cddid_all.tbl CDD cd03582 cd03582 239637 NTR_complement_C5 NTR/C345C domain, complement C5 subfamily; The NTR domain found in complement C5 is also known as C345C because it occurs at the C-terminus of complement C3, C4 and C5. Complement C5 is activated by C5 convertase, which itself is a complex between C3b and C3 convertase. The small cleavage fragment, C5a, is the most important small peptide mediator of inflammation, and the larger active fragment, C5b, initiates late events of complement activation. The NTR/C345C domain is important in the function of C5 as it interacts with enzymes that convert C5 to the active form, C5b. The domain has also been found to bind to complement components C6 and C7, and may specifically interact with their factor I modules. 150 matched cddid_all.tbl CDD cd03583 cd03583 239638 NTR_complement_C3 NTR/C345C domain, complement C3 subfamily; The NTR domain found in complement C3 is also known as the C345C domain because it occurs at the C-terminus of complement C3, C4 and C5. Complement C3 plays a pivotal role in the activation of the complement systems, as all pathways (classical, alternative, and lectin) result in the processing of C3 by C3 convertase. The larger fragment, activated C3b, contains the NTR/C345C domain and binds covalently, via a reactive thioester, to cell surface carbohydrates including components of bacterial cell walls and immune aggregates. The smaller cleavage product, C3a, acts independently as a diffusible signal to mediate local inflammatory processes. The structure of C3 shows that the NTR/C345C domain is located in an exposed position relative to the rest of the molecule. The function of the domain in complement C3 is poorly understood. 149 matched cddid_all.tbl CDD cd03584 cd03584 239639 NTR_complement_C4 NTR/C345C domain, complement C4 subfamily; The NTR domain found in complement C4 is also known as the C345C domain because it occurs at the C-terminus of complement C3, C4 and C5. Complement C4 is a key player in the activation of the component classical pathway. C4 is cleaved by activated C1 to yield C4a anaphylatoxin, and the larger fragment C4b, an essential component of the C3- and C5-convertase enzymes. C4b binds covalently to the surface of pathogens through a reactive thioester. The role of the NTR/C345C domain in C4 (C4b) is unclear. 153 matched cddid_all.tbl CDD cd03585 cd03585 239640 NTR_TIMP NTR domain, TIMP subfamily; TIMPs, or tissue inibitors of metalloproteases, are essential regulators of extracellular matrix turnover and remodeling. They form complexes with matrix metalloproteases (MMPs) and inactivate them irreversibly by non-covalently binding their active zinc-binding sites. The levels of activated membrane-type MMPs, MMPs, and free TIMPs determine the balance between matrix degradation and matrix formation or stabilization. Consequently, TIMPs play roles in processes that require the remodeling and degradation of connective tissue, such as development, morphogenesis, wound healing, as well as in various diseases and pathological states such as tumor cell metastasis, arthritis, and artherosclerosis. Most TIMPs bind to a variety of MMPs. TIMP-1 and TIMP-2 appear to be multifunctional proteins with diverse biological action. They may exhibit growth factor-like activity and can inhibit angiogenesis. TIMP-3 has been implicated in apoptosis. 183 matched cddid_all.tbl CDD cd03586 cd03586 176459 PolY_Pol_IV_kappa "DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the ""N-clasp"" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a higher error rate than other Y-family polymerases." 334 matched cddid_all.tbl CDD cd03587 cd03587 239641 SOCS SOCS (suppressors of cytokine signaling) box. The SOCS box is found in the C-terminal region of CIS/SOCS family proteins (in combination with a SH2 domain), ASBs (ankyrin repeat-containing proteins with a SOCS box), SSBs (SPRY domain-containing proteins with a SOCS box), and WSBs (WD40 repeat-containing proteins with a SOCS box), as well as, other miscellaneous proteins. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 41 matched cddid_all.tbl CDD cd03588 cd03588 153058 CLECT_CSPGs C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins. CLECT_CSPGs: C-type lectin-like domain (CTLD) of the type found in chondroitin sulfate proteoglycan core proteins (CSPGs) in human and chicken aggrecan, frog brevican, and zebra fish dermacan. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Xenopus brevican is expressed in the notochord and the brain during early embryogenesis. Zebra fish dermacan is expressed in dermal bones and may play a role in dermal bone development. CSPGs do contain LINK domain(s) which bind HA. These LINK domains are considered by one classification system to be a variety of CTLD, but are omitted from this hierarchical classification based on insignificant sequence similarity. 124 matched cddid_all.tbl CDD cd03589 cd03589 153059 CLECT_CEL-1_like C-type lectin-like domain (CTLD) of the type found in CEL-1 from Cucumaria echinata and Echinoidin from Anthocidaris crassispina. CLECT_CEL-1_like: C-type lectin-like domain (CTLD) of the type found in CEL-1 from Cucumaria echinata and Echinoidin from Anthocidaris crassispina. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. The CEL-1 CTLD binds three calcium ions and has a high specificity for N-acteylgalactosamine (GalNAc). CEL-1 exhibits strong cytotoxicity which is inhibited by GalNAc. This protein may play a role as a toxin defending against predation. Echinoidin is found in the coelomic fluid of the sea urchin and is specific for GalBeta1-3GalNAc. Echinoidin has a cell adhesive activity towards human cancer cells which is not mediated through the CTLD. Both CEL-1 and Echinoidin are multimeric proteins comprised of multiple dimers linked by disulfide bonds. 137 matched cddid_all.tbl CDD cd03590 cd03590 153060 CLECT_DC-SIGN_like C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR). CLECT_DC-SIGN_like: C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) and the related receptor, DC-SIGN receptor (DC-SIGNR). This group also contains proteins similar to hepatic asialoglycoprotein receptor (ASGP-R) and langerin in human. These proteins are type II membrane proteins with a CTLD ectodomain. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. DC-SIGN is thought to mediate the initial contact between dendritic cells and resting T cells, and may also mediate the rolling of DCs on epithelium. DC-SIGN and DC-SIGNR bind to oligosaccharides present on human tissues, as well as, on pathogens including parasites, bacteria, and viruses. DC-SIGN and DC-SIGNR bind to HIV enhancing viral infection of T cells. DC-SIGN and DC-SIGNR are homotetrameric, and contain four CTLDs stabilized by a coiled coil of alpha helices. The hepatic ASGP-R is an endocytic recycling receptor which binds and internalizes desialylated glycoproteins having a terminal galactose or N-acetylgalactosamine residues on their N-linked carbohydrate chains, via the clathrin-coated pit mediated endocytic pathway, and delivers them to lysosomes for degradation. It has been proposed that glycoproteins bearing terminal Sia (sialic acid) alpha2, 6GalNAc and Sia alpha2, 6Gal are endogenous ligands for ASGP-R and that ASGP-R participates in regulating the relative concentration of serum glycoproteins bearing alpha 2,6-linked Sia. The human ASGP-R is a hetero-oligomer composed of two subunits, both of which are found within this group. Langerin is expressed in a subset of dendritic leukocytes, the Langerhans cells (LC). Langerin induces the formation of Birbeck Granules (BGs) and associates with these BGs following internalization. Langerin binds, in a calcium-dependent manner, to glyco-conjugates containing mannose and related sugars mediating their uptake and degradation. Langerin molecules oligomerize as trimers with three CTLDs held together by a coiled-coil of alpha helices. 126 matched cddid_all.tbl CDD cd03591 cd03591 153061 CLECT_collectin_like C-type lectin-like domain (CTLD) of the type found in human collectins including lung surfactant proteins A and D, mannose- or mannan binding lectin (MBL), and CL-L1 (collectin liver 1). CLECT_collectin_like: C-type lectin-like domain (CTLD) of the type found in human collectins including lung surfactant proteins A and D, mannose- or mannan binding lectin (MBL), and CL-L1 (collectin liver 1). CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. The CTLDs of these collectins bind carbohydrates on surfaces (e.g. pathogens, allergens, necrotic, or apoptotic cells) and mediate functions associated with killing and phagocytosis. MBPs recognize high mannose oligosaccharides in a calcium dependent manner, bind to a broad range of pathogens, and trigger cell killing by activating the complement pathway. MBP also acts directly as an opsonin. SP-A and SP-D in addition to functioning as host defense components, are components of pulmonary surfactant which play a role in surfactant homeostasis. Pulmonary surfactant is a phospholipid-protein complex which reduces the surface tension within the lungs. SP-A binds the major surfactant lipid: dipalmitoylphosphatidylcholine (DPPC). SP-D binds two minor components of surfactant that contain sugar moieties: glucosylceramide and phosphatidylinositol (PI). MBP and SP-A, -D monomers are homotrimers with an N-terminal collagen region and three CTLDs. Multiple homotrimeric units associate to form supramolecular complexes. MBL deficiency results in an increased susceptibility to a large number of different infections and to inflammatory disease, such as rheumatoid arthritis. 114 matched cddid_all.tbl CDD cd03592 cd03592 153062 CLECT_selectins_like C-type lectin-like domain (CTLD) of the type found in the type 1 transmembrane proteins: P(platlet)-, E(endothelial)-, and L(leukocyte)- selectins (sels). CLECT_selectins_like: C-type lectin-like domain (CTLD) of the type found in the type 1 transmembrane proteins: P(platlet)-, E(endothelial)-, and L(leukocyte)- selectins (sels). CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. P- E- and L-sels are cell adhesion receptors that mediate the initial attachment, tethering, and rolling of lymphocytes on inflamed vascular walls enabling subsequent lymphocyte adhesion and transmigration. L- sel is expressed constitutively on most leukocytes. P-sel is stored in the Weibel-Palade bodies of endothelial cells and in the alpha granules of platlets. E- sels are present on endothelial cells. Following platelet and/or endothelial cell activation P- sel is rapidly translocated to the cell surface and E-sel expression is induced. The initial step in leukocyte migration involves interactions of selectins with fucosylated, sialylated, and sulfated carbohydrate moieties on target ligands displayed on glycoprotein scaffolds on endothelial cells and leucocytes. A major ligand of P- E- and L-sels is PSGL-1 (P-sel glycoprotein ligand). Interactions of E- and P- sels with tumor cells may promote extravasation of cancer cells. Regulation of L-sel and P-sel function includes proteolytic shedding of the most extracellular portion (containing the CTLD) from the cell surface. Increased levels of the soluble form of P-sel in the plasma have been found in a number of diseases including coronary disease and diabetes. E- and P- sel also play roles in the development of synovial inflammation in inflammatory arthritis. Platelet P-sel, but not endothelial P-sel, plays a role in the inflammatory response and neointimal formation after arterial injury. Selectins may also function as signal-transducing receptors. 115 matched cddid_all.tbl CDD cd03593 cd03593 153063 CLECT_NK_receptors_like C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs). CLECT_NK_receptors_like: C-type lectin-like domain (CTLD) of the type found in natural killer cell receptors (NKRs), including proteins similar to oxidized low density lipoprotein (OxLDL) receptor (LOX-1), CD94, CD69, NKG2-A and -D, osteoclast inhibitory lectin (OCIL), dendritic cell-associated C-type lectin-1 (dectin-1), human myeloid inhibitory C-type lectin-like receptor (MICL), mast cell-associated functional antigen (MAFA), killer cell lectin-like receptors: subfamily F, member 1 (KLRF1) and subfamily B, member 1 (KLRB1), and lys49 receptors. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. NKRs are variously associated with activation or inhibition of natural killer (NK) cells. Activating NKRs stimulate cytolysis by NK cells of virally infected or transformed cells; inhibitory NKRs block cytolysis upon recognition of markers of healthy self cells. Most Lys49 receptors are inhibitory; some are stimulatory. OCIL inhibits NK cell function via binding to the receptor NKRP1D. Murine OCIL in addition to inhibiting NK cell function inhibits osteoclast differentiation. MAFA clusters with the type I Fc epsilon receptor (FcepsilonRI) and inhibits the mast cells secretory response to FcepsilonRI stimulus. CD72 is a negative regulator of B cell receptor signaling. NKG2D is an activating receptor for stress-induced antigens; human NKG2D ligands include the stress induced MHC-I homologs, MICA, MICB, and ULBP family of glycoproteins Several NKRs have a carbohydrate-binding capacity which is not mediated through calcium ions (e.g. OCIL binds a range of high molecular weight sulfated glycosaminoglycans including dextran sulfate, fucoidan, and gamma-carrageenan sugars). Dectin-1 binds fungal beta-glucans and in involved in the innate immune responses to fungal pathogens. MAFA binds saccharides having terminal alpha-D mannose residues in a calcium-dependent manner. LOX-1 is the major receptor for OxLDL in endothelial cells and thought to play a role in the pathology of atherosclerosis. Some NKRs exist as homodimers (e.g.Lys49, NKG2D, CD69, LOX-1) and some as heterodimers (e.g. CD94/NKG2A). Dectin-1 can function as a monomer in vitro. 116 matched cddid_all.tbl CDD cd03594 cd03594 153064 CLECT_REG-1_like C-type lectin-like domain (CTLD) of the type found in Human REG-1 (lithostathine), REG-4, and avian eggshell-specific proteins: ansocalcin, structhiocalcin-1(SCA-1), and -2(SCA-2). CLECT_REG-1_like: C-type lectin-like domain (CTLD) of the type found in Human REG-1 (lithostathine), REG-4, and avian eggshell-specific proteins: ansocalcin, structhiocalcin-1(SCA-1), and -2(SCA-2). CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. REG-1 is a proliferating factor which participates in various kinds of tissue regeneration including pancreatic beta-cell regeneration, regeneration of intestinal mucosa, regeneration of motor neurons, and perhaps in tissue regeneration of damaged heart. REG-1 may play a role on the pathophysiology of Alzheimer's disease and in the development of gastric cancers. Its expression is correlated with reduced survival from early-stage colorectal cancer. REG-1 also binds and aggregates several bacterial strains from the intestinal flora and it has been suggested that it is involved in the control of the intestinal bacterial ecosystem. Rat lithostathine has calcium carbonate crystal inhibitor activity in vitro. REG-IV is unregulated in pancreatic, gastric, hepatocellular, and prostrate adenocarcinomas. REG-IV activates the EGF receptor/Akt/AP-1 signaling pathway in colorectal carcinoma. Ansocalcin, SCA-1 and -2 are found at high concentration in the calcified egg shell layer of goose and ostrich, respectively and tend to form aggregates. Ansocalcin nucleates calcite crystal aggregates in vitro. 129 matched cddid_all.tbl CDD cd03595 cd03595 153065 CLECT_chondrolectin_like C-type lectin-like domain (CTLD) of the type found in the human type-1A transmembrane proteins chondrolectin (CHODL) and layilin. CLECT_chondrolectin_like: C-type lectin-like domain (CTLD) of the type found in the human type-1A transmembrane proteins chondrolectin (CHODL) and layilin. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. CHODL is predominantly expressed in muscle cells and is associated with T-cell maturation. Various alternatively spliced isoforms have been of CHODL have been identified. The transmembrane form of CHODL is localized in the ER-Golgi apparatus. Layilin is widely expressed in different cell types. The extracellular CTLD of layilin binds hyaluronan (HA), a major constituent of the extracellular matrix (ECM). The cytoplasmic tail of layilin binds various members of the band 4.1/ERM superfamily (talin, radixin, and merlin). The ERM proteins are cytoskeleton-membrane linker molecules which link actin to receptors in the plasma membrane. Layilin co-localizes in with talin in membrane ruffles and may mediate signals from the ECM to the cell cytoskeleton. 149 matched cddid_all.tbl CDD cd03596 cd03596 153066 CLECT_tetranectin_like C-type lectin-like domain (CTLD) of the type found in the tetranectin (TN), cartilage derived C-type lectin (CLECSF1), and stem cell growth factor (SCGF). CLECT_tetranectin_like: C-type lectin-like domain (CTLD) of the type found in the tetranectin (TN), cartilage derived C-type lectin (CLECSF1), and stem cell growth factor (SCGF). CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. TN binds to plasminogen and stimulates activation of plasminogen, playing a key role in the regulation of proteolytic processes. The TN CTLD binds two calcium ions. Its calcium free form binds to various kringle-like protein ligands. Two residues involved in the coordination of calcium are critical for the binding of TN to the fourth kringle (K4) domain of plasminogen (Plg K4). TN binds the kringle 1-4 form of angiostatin (AST K1-4). AST K1-4 is a fragment of Plg, commonly found in cancer tissues. TN inhibits the binding of Plg and AST K1-4 to the extracellular matrix (EMC) of endothelial cells and counteracts the antiproliferative effects of AST K1-4 on these cells. TN also binds the tenth kringle domain of apolipoprotein (a). In addition, TN binds fibrin and complex polysaccharides in a Ca2+ dependent manner. The binding site for complex sulfated polysaccharides is N-terminal to the CTLD. TN is homotrimeric; N-terminal to the CTLD is an alpha helical domain responsible for trimerization of monomeric units. TN may modulate angiogenesis through interactions with angiostatin and coagulation through interaction with fibrin. TN may play a role in myogenesis and in bone development. Mice having a deletion in the TN gene exhibit a kyphotic spine abnormality. TN is a useful prognostic marker of certain cancer types. CLECSF1 is expressed in cartilage tissue, which is primarily intracellular matrix (ECM), and is a candidate for organizing ECM. SCGF is strongly expressed in bone marrow and is a cytokine for primitive hematopoietic progenitor cells. 129 matched cddid_all.tbl CDD cd03597 cd03597 153067 CLECT_attractin_like C-type lectin-like domain (CTLD) of the type found in human and mouse attractin (AtrN) and attractin-like protein (ALP). CLECT_attractin_like: C-type lectin-like domain (CTLD) of the type found in human and mouse attractin (AtrN) and attractin-like protein (ALP). CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. Mouse AtrN (the product of the mahogany gene) has been shown to bind Agouti protein and to function in agouti-induced pigmentation and obesity. Mutations in AtrN have also been shown to cause spongiform encephalopathy and hypomyelination in rats and hamsters. The cytoplasmic region of mouse ALP has been shown to binds to melanocortin receptor (MCR4). Signaling through MCR4 plays a role in appetite suppression. Attractin may have therapeutic potential in the treatment of obesity. Human attractin (hAtrN) has been shown to be expressed on activated T cells and released extracellularly. The circulating serum attractin induces the spreading of monocytes that become the focus of the clustering of non-proliferating T cells. 129 matched cddid_all.tbl CDD cd03598 cd03598 153068 CLECT_EMBP_like C-type lectin-like domain (CTLD) of the type found in the human proteins, eosinophil major basic protein (EMBP) and prepro major basic protein homolog (MBPH). CLECT_EMBP_like: C-type lectin-like domain (CTLD) of the type found in the human proteins, eosinophil major basic protein (EMBP) and prepro major basic protein homolog (MBPH). CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. Eosinophils and basophils carry out various functions in allergic, parasitic, and inflammatory diseases. EMBP is stored in eosinophil crystalloid granules and is released upon degranulation. EMBP is also expressed in basophils. The proform of EMBP is expressed in placental X cells and breast tissue and increases significantly during human pregnancy. EMBP has cytotoxic properties and damages bacteria and mammalian cells, in vitro, as well as, helminth parasites. EMBP deposition has been observed in the inflamed tissue of allergy patients in a variety of diseases including asthma, atopic dermatitis, and rhinitis. In addition to its cytotoxic functions, EMBP activates cells and stimulates cytokine production. EMBP has been shown to bind the proteoglycan heparin. The binding site is similar to the carbohydrate binding site of other classical CTLD, such as mannose-binding protein (MBP1), however, heparin binding to EMBP is calcium ion independent. MBPH has reduced potency in cytotoxic and cytostimulatory assays compared with EMBP. 117 matched cddid_all.tbl CDD cd03599 cd03599 153069 CLECT_DGCR2_like C-type lectin-like domain (CTLD) of the type found in DGCR2, an integral membrane protein deleted in DiGeorge Syndrome (DGS). CLECT_DGCR2_like: C-type lectin-like domain (CTLD) of the type found in DGCR2, an integral membrane protein deleted in DiGeorge Syndrome (DGS). CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. DGS is also known velo-cardio-facial syndrome (VCFS). DGS is a genetic abnormality that results in malformations of the heart, face, and limbs and is associated with schizophrenia and depressive disorders. DGCR2 is a candidate for involvement in the pathogenesis of DGS since the DGCR2 gene lies within the minimal DGS critical region (MDGRC) of 22q11, which when deleted gives rise to DGS, and the DGCR2 gene is in close proximity to the balanced translocation breakpoint in a DGS patient having a balanced translocation. 153 matched cddid_all.tbl CDD cd03600 cd03600 153070 CLECT_thrombomodulin_like C-type lectin-like domain (CTLD) of the type found in human thrombomodulin(TM), Endosialin, C14orf27, and C1qR. CLECT_thrombomodulin_like: C-type lectin-like domain (CTLD) of the type found in human thrombomodulin(TM), Endosialin, C14orf27, and C1qR. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. In these thrombomodulin-like proteins the residues involved in coordinating Ca2+ in the classical MBP-A CTLD are not conserved. TM exerts anti-fibrinolytic and anti-inflammatory activity. TM also regulates blood coagulation in the anticoagulant protein C pathway. In this pathway, the procoagulant properties of thrombin (T) are lost when it binds TM. TM also plays a key role in tumor biology. It is expressed on endothelial cells and on several type of tumor cell including squamous cell carcinoma. Loss of TM expression correlates with advanced stage and poor prognosis. Loss of function of TM function may be associated with arterial or venous thrombosis and with late fetal loss. Soluble molecules of TM retaining the CTLD are detected in human plasma and urine where higher levels indicate injury and/or enhanced turnover of the endothelium. C1qR is expressed on endothelial cells and stem cells. It is also expressed on monocots and neutrophils, where it is subject to ectodomain shedding. Soluble forms of C1qR retaining the CTLD is detected in human plasma. C1qR modulates the phagocytosis of apoptotic cells in vivo. C1qR-deficient mice are defective in clearance of apoptotic cells in vivo. The cytoplasmic tail of C1qR, C-terminal to the CTLD of CD93, contains a PDZ binding domain which interacts with the PDZ domain-containing adaptor protein, GIPC. The juxtamembrane region of this tail interacts with the ezrin/radixin/moesin family. Endosialin functions in the growth and progression of abdominal tumors and is expressed in the stroma of several tumors. 141 matched cddid_all.tbl CDD cd03601 cd03601 153071 CLECT_TC14_like C-type lectin-like domain (CTLD) of the type found in lectins TC14, TC14-2, TC14-3, and TC14-4 from the budding tunicate Polyandrocarpa misakiensis and PfG6 from the Acorn worm. CLECT_TC14_like: C-type lectin-like domain (CTLD) of the type found in lectins TC14, TC14-2, TC14-3, and TC14-4 from the budding tunicate Polyandrocarpa misakiensis and PfG6 from the Acorn worm. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. TC14 is homodimeric. The CTLD of TC14 binds D-galactose and D-fucose. TC14 is expressed constitutively by multipotent epithelial and mesenchymal cells and plays in role during budding, in inducing the aggregation of undifferentiated mesenchymal cells to give rise to epithelial forming tissue. TC14-2 and TC14-3 shows calcium-dependent galactose binding activity. TC14-3 is a cytostatic factor which blocks cell growth and dedifferentiation of the atrial epithelium during asexual reproduction. It may also act as a differentiation inducing factor. Galactose inhibits the cytostatic activity of TC14-3. The gene for Acorn worm PfG6 is gill-specific; PfG6 may be a secreted protein. 119 matched cddid_all.tbl CDD cd03602 cd03602 153072 CLECT_1 C-type lectin (CTL)/C-type lectin-like (CTLD) domain subgroup 1; a subgroup of protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. CLECT_1: C-type lectin (CTL)/C-type lectin-like (CTLD) domain subgroup 1; a subgroup of protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces including CaCO3 and ice. Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose. CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers from which ligand-binding sites project in different orientations. In some CTLDs a loop extends to the adjoining domain to form a loop-swapped dimer. 108 matched cddid_all.tbl CDD cd03603 cd03603 153073 CLECT_VCBS A bacterial subgroup of the C-type lectin-like (CTLD) domain; a subgroup of bacterial protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. CLECT_VCBS: A bacterial subgroup of the C-type lectin-like (CTLD) domain; a subgroup of bacterial protein domains homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins. Many CTLDs are calcium-dependent carbohydrate binding modules; other CTLDs bind protein ligands, lipids, and inorganic surfaces including CaCO3 and ice. Bacterial CTLDs within this group are functionally uncharacterized. Animal C-type lectins are involved in such functions as extracellular matrix organization, endocytosis, complement activation, pathogen recognition, and cell-cell interactions. CTLDs may bind a variety of carbohydrate ligands including mannose, N-acetylglucosamine, galactose, N-acetylgalactosamine, and fucose. CTLDs associate with each other through several different surfaces to form dimers, trimers, or tetramers from which ligand-binding sites project in different orientations. In some CTLDs a loop extends to the adjoining domain to form a loop-swapped dimer. 118 matched cddid_all.tbl CDD cd03670 cd03670 467538 NUDIX_ADPRase_Nudt9 ADP-ribose pyrophosphatase. ADP-ribose pyrophosphatase (ADPRase;EC 3.6.1.13, also known as NUDIX (nucleoside diphosphate-linked moiety X)) motif 9/Nudt9, catalyzes the hydrolysis of ADP-ribose to AMP and ribose-5-P. Like other members of the NUDIX hydrolase superfamily of enzymes, it is thought to require a divalent cation, such as Mg2+, for its activity. It also contains a 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the NUDIX motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. In humans, there are four distinct ADPRase activities, three putative cytosolic (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). ADPRase-m is also known as NUDT9. It can be distinugished from the cytosolic ADPRase by a N-terminal target sequence unique to mitochondrial ADPRase. NUDT9 functions as a monomer. 179 matched cddid_all.tbl CDD cd03671 cd03671 467539 NUDIX_Ap4A_hydrolase_plant_like plant diadenosine tetraphosphate (Ap4A) hydrolase and similar proteins. Diadenosine tetraphosphate (Ap4A) hydrolase is a member of the NUDIX hydrolase superfamily. Members of this family are well represented in a variety of prokaryotic and eukaryotic organisms. Phylogenetic analysis reveals two distinct subgroups where plant enzymes fall into one group (represented by this subfamily) and fungi/animals/archaea enzymes fall into another. Bacterial enzymes are found in both subfamilies. Ap4A is a potential by-product of aminoacyl tRNA synthesis, and accumulation of Ap4A has been implicated in a range of biological events, such as DNA replication, cellular differentiation, heat shock, metabolic stress, and apoptosis. Ap4A hydrolase cleaves Ap4A asymmetrically into ATP and AMP. It is important in the invasive properties of bacteria and thus presents a potential target for the inhibition of such invasive bacteria. Besides the signature NUDIX motif (G[X5]E[X7]REUXEEXGU where U is Ile, Leu, or Val), Ap4A hydrolase is structurally similar to the other members of the NUDIX hydrolase superfamily with some degree of variations. Several regions in the sequences are poorly defined and substrate and metal binding sites are only predicted based on kinetic studies. 147 matched cddid_all.tbl CDD cd03672 cd03672 467540 NUDIX_Dcp2p_Nudt20 mRNA decapping enzyme 2. mRNA decapping enzyme 2 (Dcp2p; EC 3.6.1.62), nucleoside diphosphate linked moiety X))-type motif 20/Nudt20, is required for degradation of mRNAs, both in normal mRNA turnover, and in nonsense-mediated mRNA decay (NMD). Its catalytic subunit, and Dcp1p are the two components of the decapping enzyme complex. Decapping is a key step in both general and nonsense-mediated 5'->3' mRNA-decay pathways. Dcp2p contains an all-alpha helical N-terminal domain and a C-terminal domain which has the NUDIX fold. While decapping is not dependent on the N-terminus of Dcp2p, it does affect its efficiency. Dcp1p binds the N-terminal domain of Dcp2p stimulating the decapping activity of Dcp2p. Decapping permits the degradation of the transcript and is a site of numerous control inputs. It is responsible for nonsense-mediated decay as well as AU-rich element (ARE)-mediated decay. In addition, it may also play a role in the levels of mRNA. Enzymes belonging to the NUDIX hydrolase superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V). 144 matched cddid_all.tbl CDD cd03673 cd03673 467541 NUDIX_Ap6A_hydrolase diadenosine hexaphosphate (Ap6A) hydrolase. Diadenosine hexaphosphate (Ap6A) hydrolase is a member of the NUDIX hydrolase superfamily. Ap6A hydrolase specifically hydrolyzes diadenosine polyphosphates, but not ATP or diadenosine triphosphate, and it generates ATP as the product. Ap6A, the most preferred substrate, hydrolyzes to produce two ATP molecules, which is a novel hydrolysis mode for Ap6A. These results indicate that Ap6A hydrolase is a diadenosine polyphosphate hydrolase. It requires the presence of a divalent cation, such as Mn2+, Mg2+, Zn2+, and Co2+, for activity. Members of the NUDIX hydrolase superfamily are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. 131 matched cddid_all.tbl CDD cd03674 cd03674 467542 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 130 matched cddid_all.tbl CDD cd03675 cd03675 467543 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. Contains a crystal structure of the NUDIX hydrolase from Nitrosomonas europaea, which has an unknown function. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 138 matched cddid_all.tbl CDD cd03676 cd03676 467544 NUDIX_Tnr3_like "thiamine diphosphokinase Tnr3 from Schizosaccharomyces pombe and similar proteins. Tnr3 is a bifunctional enzyme composed of a C-terminal thiamine pyrophosphokinase domain, which transfers pyrophosphate from ATP to thiamine and an N-terminal NUDIX hydrolase domain that converts oxidized derivatives of thiamine diphosphate (oxothiamine and oxythiamine) to their respective monophosphates. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belong to this superfamily requires a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & ""house-cleaning"" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required." 153 matched cddid_all.tbl CDD cd03677 cd03677 239649 MM_CoA_mutase_beta Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Beta subunit-like subfamily; contains bacterial proteins similar to the beta subunit of MCMs from Propionbacterium shermanni and Streptomyces cinnamonensis, which are alpha/beta heterodimers. For P. shermanni MCM, it is known that only the alpha subunit binds coenzyme B12 and substrates. The role of the beta subunit is unclear. MCM catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA. The reaction proceeds via radical intermediates beginning with a substrate-induced homolytic cleavage of the Co-C bond of coenzyme B12 to produce cob(II)alamin and the deoxyadenosyl radical. MCM plays an important role in the conversion of propionyl-CoA to succinyl-CoA during the degradation of propionate for the Krebs cycle. Methylobacterium extorquens MCM participates in the glyoxylate regeneration pathway. In M. extorquens, MCM forms a complex with MeaB; MeaB may protect MCM from irreversible inactivation. In some bacteria, MCM is involved in the reverse metabolic reaction, the rearrangement of succinyl-CoA to methylmalonyl-CoA. Examples include P. shermanni MCM during propionic acid fermentation and Streptomyces MCM in polyketide biosynthesis. 424 matched cddid_all.tbl CDD cd03678 cd03678 239650 MM_CoA_mutase_1 Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, unknown subfamily 1; composed of uncharacterized bacterial proteins containing a C-terminal MCM domain. MCM catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA. The reaction proceeds via radical intermediates beginning with a substrate-induced homolytic cleavage of the Co-C bond of coenzyme B12 to produce cob(II)alamin and the deoxyadenosyl radical. MCM plays an important role in the conversion of propionyl-CoA to succinyl-CoA during the degradation of propionate for the Krebs cycle. In some bacteria, MCM is involved in the reverse metabolic reaction, the rearrangement of succinyl-CoA to methylmalonyl-CoA. Members of this subfamily also contain an N-terminal coenzyme B12 binding domain followed by a domain similar to the E. coli ArgK membrane ATPase. 495 matched cddid_all.tbl CDD cd03679 cd03679 239651 MM_CoA_mutase_alpha_like Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, Alpha subunit-like subfamily; contains proteins similar to the alpha subunit of Propionbacterium shermanni MCM, as well as human and E. coli MCM. Members of this subfamily contain an N-terminal MCM domain and a C-terminal coenzyme B12 binding domain. MCM catalyzes the isomerization of methylmalonyl-CoA to succinyl-CoA. The reaction proceeds via radical intermediates beginning with a substrate-induced homolytic cleavage of the Co-C bond of coenzyme B12 to produce cob(II)alamin and the deoxyadenosyl radical. MCM plays an important role in the conversion of propionyl-CoA to succinyl-CoA during the degradation of propionate for the Krebs cycle. In higher animals, MCM is involved in the breakdown of odd-chain fatty acids, several amino acids, and cholesterol. Methylobacterium extorquens MCM participates in the glyoxylate regeneration pathway. In M. extorquens, MCM forms a complex with MeaB; MeaB may protect MCM from irreversible inactivation. In some bacteria, MCM is involved in the reverse metabolic reaction, the rearrangement of succinyl-CoA to methylmalonyl-CoA. Examples include P. shermanni MCM during propionic acid fermentation, E.coli MCM in a pathway for the conversion of succinate to propionate and Streptomyces MCM in polyketide biosynthesis. Sinorhizobium meliloti strain SU47 MCM plays a role in the polyhydroxyalkanoate degradation pathway. P. shermanni and Streptomyces cinnamonensis MCMs are alpha/beta heterodimers. It has been shown for P. shermanni MCM that only the alpha subunit binds coenzyme B12 and substrates. Human MCM is a homodimer with two active sites. Mouse and E.coli MCMs are also homodimers. In humans, impaired activity of MCM results in methylmalonic aciduria, a disorder of propionic acid metabolism. 536 matched cddid_all.tbl CDD cd03680 cd03680 239652 MM_CoA_mutase_ICM_like Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, isobutyryl-CoA mutase (ICM)-like subfamily; contains archaeal and bacterial proteins similar to the large subunit of Streptomyces cinnamonensis coenzyme B12-dependent ICM. ICM from S. cinnamonensis is comprised of a large and a small subunit. The holoenzyme appears to be an alpha2beta2 heterotetramer with up to 2 molecules of coenzyme B12 bound. The small subunit binds coenzyme B12. ICM catalyzes the reversible rearrangement of n-butyryl-CoA to isobutyryl-CoA, intermediates in fatty acid and valine catabolism, which in S. cinnamonensis can be converted to methylmalonyl-CoA and used in polyketide synthesis. 538 matched cddid_all.tbl CDD cd03681 cd03681 239653 MM_CoA_mutase_MeaA Coenzyme B12-dependent-methylmalonyl coenzyme A (CoA) mutase (MCM) family, MeaA-like subfamily; contains various methylmalonyl coenzyme A (CoA) mutase (MCM)-like proteins similar to the Streptomyces cinnamonensis MeaA, Methylobacterium extorquens MeaA and Streptomyces collinus B12-dependent mutase. Members of this subfamily contain an N-terminal MCM domain and a C-terminal coenzyme B12 binding domain. S. cinnamonensis MeaA is a putative B12-dependent mutase which provides methylmalonyl-CoA precursors for the biosynthesis of the monensin polyketide via an unknown pathway. S. collinus B12-dependent mutase may be involved in a pathway for acetate assimilation. 407 matched cddid_all.tbl CDD cd03682 cd03682 239654 ClC_sycA_like ClC sycA-like chloride channel proteins. This ClC family presents in bacteria, where it facilitates acid resistance in acidic soil. Mutation of this gene (sycA) in Rhizobium tropici CIAT899 causes serious deficiencies in nodule development, nodulation competitiveness, and N2 fixation on Phaseolus vulgaris plants, due to its reduced ability for acid resistance. This family is part of the ClC chloride channel superfamiy. These proteins catalyse the selective flow of Cl- ions across cell membranes and Cl-/H+ exchange transport. These proteins share two characteristics that are apparently inherent to the entire ClC chloride channel superfamily: a unique double-barreled architecture and voltage-dependent gating mechanism. The gating is conferred by the permeating anion itself, acting as the gating charge. 378 matched cddid_all.tbl CDD cd03683 cd03683 239655 ClC_1_like ClC-1-like chloride channel proteins. This CD includes isoforms ClC-0, ClC-1, ClC-2 and ClC_K. ClC-1 is expressed in skeletal muscle and its mutation leads to both recessively and dominantly-inherited forms of muscle stiffness or myotonia. ClC-K is exclusively expressed in kidney. Similarly, mutation of ClC-K leads to nephrogenic diabetes insipidus in mice and Bartter's syndrome in human. These proteins belong to the ClC superfamily of chloride ion channels, which share the unique double-barreled architecture and voltage-dependent gating mechanism. The gating is conferred by the permeating anion itself, acting as the gating charge. This domain is found in the eukaryotic halogen ion (Cl-, Br- and I-) channel proteins, that perform a variety of functions including cell volume regulation, regulation of intracelluar chloride concentration, membrane potential stabilization, charge compensation necessary for the acidification of intracellular organelles and transepithelial chloride transport. 426 matched cddid_all.tbl CDD cd03684 cd03684 239656 ClC_3_like ClC-3-like chloride channel proteins. This CD includes ClC-3, ClC-4, ClC-5 and ClC-Y1. ClC-3 was initially cloned from rat kidney. Expression of ClC-3 produces outwardly-rectifying Cl currents that are inhibited by protein kinase C activation. It has been suggested that ClC-3 may be a ubiquitous swelling-activated Cl channel that has very similar characteristics to those of native volume-regulated Cl currents. The function of ClC-4 is unclear. Studies of human ClC-4 have revealed that it gives rise to Cl currents that rapidly activate at positive voltages, and are sensitive to extracellular pH, with currents decreasing when pH falls below 6.5. ClC-4 is broadly distributed, especially in brain and heart. ClC-5 is predominantly expressed in the kidney, but can be found in the brain and liver. Mutations in the ClC-5 gene cause certain hereditary diseases, including Dent's disease, an X-chromosome linked syndrome characterised by proteinuria, hypercalciuria, and kidney stones (nephrolithiasis), leading to progressive renal failure. These proteins belong to the ClC superfamily of chloride ion channels, which share the unique double-barreled architecture and voltage-dependent gating mechanism. The gating is conferred by the permeating anion itself, acting as the gating charge. This domain is found in the eukaryotic halogen ion (Cl- and I-) channel proteins, that perform a variety of functions including cell volume regulation, the membrane potential stabilization, transepithelial chloride transport and charge compensation necessary for the acidification of intracellular organelles. 445 matched cddid_all.tbl CDD cd03685 cd03685 239657 ClC_6_like ClC-6-like chloride channel proteins. This CD includes ClC-6, ClC-7 and ClC-B, C, D in plants. Proteins in this family are ubiquitous in eukarotes and their functions are unclear. They are expressed in intracellular organelles membranes. This family belongs to the ClC superfamily of chloride ion channels, which share the unique double-barreled architecture and voltage-dependent gating mechanism. The gating is conferred by the permeating anion itself, acting as the gating charge. ClC chloride ion channel superfamily perform a variety of functions including cellular excitability regulation, cell volume regulation, membrane potential stabilization, acidification of intracellular organelles, signal transduction, and transepithelial transport in animals. 466 matched cddid_all.tbl CDD cd03687 cd03687 239658 Dehydratase_LU Dehydratase large subunit. This family contains the large (alpha) subunit of B12-dependent glycerol dehydratases (GDHs) and B12-dependent diol dehydratases (DDHs). GDH is isofunctional with DDH. These enzymes can each catalyze the conversion of 1,2-propanediol, glycerol, and 1,2-ethanediol to the corresponding aldehydes via a coenzyme B12 (adenosylcobalamin)-dependent radical mechanism. Both enzymes exhibit a subunit composition of alpha2beta2gamma2. The enzymes differ in substrate specificity; glycerol is the preferred substrate for GDH and 1,2-propanediol for DDH. GDH shows almost equal affinity for both (R) and (S)-isomers while DDH prefers the (S) isomer. GDH plays a key role in the dihydroxyacetone (DHA) pathway and DDH in the anaerobic degradation of 1,2-diols. The radical mechanism has been well studied for Klebsiella oxytoca DDH and involves binding of 1,2-propanediol to the enzyme to induce hemolytic cleavage of the Co-C5' bond of the coenzyme to form cob(II)alamin and the adenosyl radical. Hydrogen abstraction from the substrate follows producing a substrate generated radical and 5'-deoxyadenosine. Rearrangement to the product radical is then followed by abstraction of a hydrogen atom from 5'-deoxyadenosine to produce the hydrated propionaldehyde and regenerate the adenosyl radical. After the Co-C5' bond is reformed and the hydrated aldehyde dehydrated, the process is complete. GDH has a higher affinity for coenzyme B12 than DDH. Both GDH and DDH are activated by various monovalent cations with K+, NH4+, and Rb+ being the most effective. However, DDH differs from GDH in that it is partially active with Cs+ and Na+. In general, the alpha and beta subunits for both enzymes are on different chains. However, for a subset of the GDHs, alpha and beta subunits appear to be on a single chain. 545 matched cddid_all.tbl CDD cd03688 cd03688 293889 eIF2_gamma_II Domain II of the gamma subunit of eukaryotic translation initiation factor 2. This subfamily represents domain II of the gamma subunit of eukaryotic translation initiation factor 2 (eIF2-gamma) found in eukaryota and archaea. eIF2 is a G protein that delivers the methionyl initiator tRNA to the small ribosomal subunit and releases it upon GTP hydrolysis after the recognition of the initiation codon. eIF2 is composed of three subunits, alpha, beta and gamma. Subunit gamma shows strongest conservation, and it confers both tRNA binding and GTP/GDP binding. 113 matched cddid_all.tbl CDD cd03689 cd03689 293890 RF3_II Domain II of bacterial Release Factor 3. This subfamily represents domain II of bacterial Release Factor 3 (RF3). Termination of protein synthesis by the ribosome requires two release factor (RF) classes. The class II RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the ribosome after release of the nascent polypeptide. RF3 in the GDP state binds to the ribosomal class I RF complex, followed by an exchange of GDP for GTP and release of the class I RF. Sequence comparison of class II release factors with elongation factors shows that prokaryotic RF3 is more similar to EF-G whereas eukaryotic eRF3 is more similar to eEF1A, implying that their precise function may differ. 87 matched cddid_all.tbl CDD cd03690 cd03690 293891 Tet_II Domain II of ribosomal protection proteins Tet(M) and Tet(O). This subfamily represents domain II of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to domain II of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA. 86 matched cddid_all.tbl CDD cd03691 cd03691 293892 BipA_TypA_II Domain II of BipA. BipA (also called TypA) is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion. The domain II of BipA shows similarity to the domain II of the elongation factors (EFs) EF-G and EF-Tu. 94 matched cddid_all.tbl CDD cd03692 cd03692 293893 mtIF2_IVc C2 subdomain of domain IV in mitochondrial translation initiation factor 2. This model represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor EF-Tu. The C-terminal part of mtIF2 contains the entire fMet-tRNAfmet binding site of IF-2 and is resistant to proteolysis. This C-terminal portion consists of two domains, IF2 C1 and IF2 C2. IF2 C2 has been shown to contain all molecular determinants necessary and sufficient for the recognition and binding of fMet-tRNAfMet. Like IF2 from certain prokaryotes such as Thermus thermophilus, mtIF2lacks domain II which is thought to be involved in binding of E.coli IF-2 to 30S subunits. 84 matched cddid_all.tbl CDD cd03693 cd03693 293894 EF1_alpha_II Domain II of elongation factor 1-alpha. This family represents domain II of elongation factor 1-alpha (EF-1A) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF-1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF-1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression. 91 matched cddid_all.tbl CDD cd03694 cd03694 293895 GTPBP_II Domain II of the GTPBP family of GTP binding proteins. This group includes proteins similar to GTPBP1 and GTPBP2. GTPBP1 is structurally related to elongation factor 1 alpha, a key component of the protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution. 87 matched cddid_all.tbl CDD cd03695 cd03695 293896 CysN_NodQ_II Domain II of the large subunit of ATP sulfurylase. This subfamily represents domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction, APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sulfation of a nodulation factor. In Rhizobium meliloti, the heterodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, archaea, and eukaryotes use a different ATP sulfurylase, which shows no amino acid sequence similarity to CysN or NodQ. CysN and the N-terminal portion of NodQ show similarity to GTPases involved in translation, in particular, EF-Tu and EF-1alpha. 81 matched cddid_all.tbl CDD cd03696 cd03696 293897 SelB_II Domain II of elongation factor SelB. This subfamily represents the domain of elongation factor SelB that is homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. 83 matched cddid_all.tbl CDD cd03697 cd03697 293898 EFTU_II Domain II of elongation factor Tu. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven alpha helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Both non-catalytic domains are composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA; and an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher affinity for GDP than for GTP. 87 matched cddid_all.tbl CDD cd03698 cd03698 293899 eRF3_II_like Domain II of the eukaryotic class II release factor-like proteins. This model represents the domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribosome. eRF3 is a GTPase, which enhances termination efficiency by stimulating eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF-1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-like protein with the property of aggregating into polymer-like fibrils. This group also contains proteins similar to S. cerevisiae Hbs1, a G protein known to be important for efficient growth and protein synthesis under conditions of limiting translation initiation and to associate with Dom34. It has been speculated that yeast Hbs1 and Dom34 proteins may function as part of a complex with a role in gene expression. 84 matched cddid_all.tbl CDD cd03699 cd03699 293900 EF4_II Domain II of Elongation Factor 4 (EF4). Elongation factor 4 (EF4 or LepA) is a highly conserved guanosine triphosphatase found in bacteria and eukaryotic mitochondria and chloroplasts. EF4 functions as a translation factor, which promotes back-translocation of tRNAs on posttranslocational ribosome complexes and competes with elongation factor G for interaction with pretranslocational ribosomes, inhibiting the elongation phase of protein synthesis. 86 matched cddid_all.tbl CDD cd03700 cd03700 293901 EF2_snRNP_like_II Domain II of elongation factor 2 and C-terminal domain of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein. This subfamily represents domain II of elongation factor (EF) EF-2 found in eukaryotes and archaea, and the C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and its yeast counterpart Snu114p. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. This translocation step is catalyzed by EF-2_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of U5-116 kD/Snu114p. 95 matched cddid_all.tbl CDD cd03701 cd03701 293902 IF2_IF5B_II Domain II of prokaryotic Initiation Factor 2 and archaeal and eukaryotic Initiation Factor 5. This family represents domain II of prokaryotic Initiation Factor 2 (IF2) and its archaeal and eukaryotic homologue aeIF5B. IF2, the largest initiation factor, is an essential GTP binding protein. In E. coli, three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of the 60S ribosomal subunit. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains in EF1A, eEF1A and aeIF2gamma. 96 matched cddid_all.tbl CDD cd03702 cd03702 293903 IF2_mtIF2_II Domain II of bacterial and mitochondrial Initiation Factor 2. This family represents domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homolog mtIF2. IF2, the largest initiation factor, is an essential GTP binding protein. In E. coli, three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2 is structurally and functionally related to eukaryotic mitochondrial mtIF-2. 96 matched cddid_all.tbl CDD cd03703 cd03703 293904 aeIF5B_II Domain II of archaeal and eukaryotic Initiation Factor 5. This family represents domain II of archaeal and eukaryotic IF5B. aIF5B and eIF5B are homologs of prokaryotic Initiation Factor 2 (IF2). Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of joining of 60S subunits. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains of EF1A, eEF1A and aeIF2gamma. 111 matched cddid_all.tbl CDD cd03704 cd03704 294003 eRF3_C_III C-terminal domain of eRF3. This model represents the eEF1alpha-like C-terminal region of eRF3, which is homologous to the domain III of EF-Tu. eRF3 is a GTPase which enhances termination efficiency by stimulating eRF1 activity in a GTP-dependent manner. The C-terminal region is responsible for translation termination activity and is essential for viability. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions: N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-like protein with the property of aggregating into polymer-like fibrils. 108 matched cddid_all.tbl CDD cd03705 cd03705 294004 EF1_alpha_III Domain III of Elongation Factor 1. Eukaryotic elongation factor 1 (EF-1) is responsible for the GTP-dependent binding of aminoacyl-tRNAs to ribosomes. EF-1 is composed of four subunits: the alpha chain, which binds GTP and aminoacyl-tRNAs; the gamma chain that probably plays a role in anchoring the complex to other cellular components; and the beta and delta (or beta') chains. This model represents the alpha subunit, which is the counterpart of bacterial EF-Tu for archaea (aEF-1 alpha) and eukaryotes (eEF-1 alpha). 104 matched cddid_all.tbl CDD cd03706 cd03706 294005 mtEFTU_III Domain III of mitochondrial EF-TU (mtEF-TU). mtEF-TU is highly conserved and is 55-60% identical to bacterial EF-TU. The overall structure is similar to that observed in the Escherichia coli and Thermus aquaticus EF-TU. However, compared with that observed in prokaryotic EF-TU, the nucleotide-binding domain (domain I) of mtEF-TU is in a different orientation relative to the rest of the structure. Furthermore, domain III is followed by a short 11-amino acid extension that forms one helical turn. This extension seems to be specific to the mitochondrial factors and has not been observed in any of the prokaryotic factors. 93 matched cddid_all.tbl CDD cd03707 cd03707 294006 EFTU_III "Domain III of Elongation Factor (EF) Tu. EF-Tu consists of three structural domains, designated I, II, and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and to elongation factor Ts (EF-Ts). EF-Ts is the guanine-nucleotide-exchange factor for EF-Tu. EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Crystallographic studies revealed structural similarities (""molecular mimicry"") between tertiary structures of EF-G and the EF-Tu-aminoacyl-tRNA ternary complex. Domains III, IV, and V of EF-G mimic the tRNA structure in the EF-Tu ternary complex; domains III, IV and V can be related to the acceptor stem, anticodon helix and T stem of tRNA respectively." 90 matched cddid_all.tbl CDD cd03708 cd03708 294007 GTPBP_III Domain III of the GP-1 family of GTPases. This family includes proteins similar to GTPBP1 and GTPBP2. GTPBP1 is structurally related to elongation factor 1 alpha, a key component of the protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in the cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution. 87 matched cddid_all.tbl CDD cd03709 cd03709 239680 lepA_C lepA_C: This family represents the C-terminal region of LepA, a GTP-binding protein localized in the cytoplasmic membrane. LepA is ubiquitous in Bacteria and Eukaryota (e.g. Saccharomyces cerevisiae GUF1p), but is missing from Archaea. LepA exhibits significant homology to elongation factors (EFs) Tu and G. The function(s) of the proteins in this family are unknown. The N-terminal domain of LepA is homologous to a domain of similar size found in initiation factor 2 (IF2), and in EF-Tu and EF-G (factors required for translation in Escherichia coli). Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including S. cerevisiae GUF1) originated within the bacterial LepA family. LepA has never been observed in archaea, and eukaryl LepA is organellar. LepA is therefore a true bacterial GTPase, found only in the bacterial lineage. 80 matched cddid_all.tbl CDD cd03710 cd03710 239681 BipA_TypA_C BipA_TypA_C: a C-terminal portion of BipA or TypA having homology to the C terminal domains of the elongation factors EF-G and EF-2. A member of the ribosome binding GTPase superfamily, BipA is widely distributed in bacteria and plants. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion. 79 matched cddid_all.tbl CDD cd03711 cd03711 239682 Tet_C Tet_C: C-terminus of ribosomal protection proteins Tet(M) and Tet(O). This domain has homology to the C terminal domains of the elongation factors EF-G and EF-2. Tet(M) and Tet(O) catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA. 78 matched cddid_all.tbl CDD cd03713 cd03713 239683 EFG_mtEFG_C EFG_mtEFG_C: domains similar to the C-terminal domain of the bacterial translational elongation factor (EF) EF-G. Included in this group is the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2) proteins. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. No clear phenotype has been found for mutants in the yeast homologue of mtEFG2, MEF2. 78 matched cddid_all.tbl CDD cd03714 cd03714 239684 RT_DIRS1 RT_DIRS1: Reverse transcriptases (RTs) occurring in the DIRS1 group of retransposons. Members of the subfamily include the Dictyostelium DIRS-1, Volvox carteri kangaroo, and Panagrellus redivivus PAT elements. These elements differ from LTR and conventional non-LTR retrotransposons. They contain split direct repeat (SDR) termini, and have been proposed to integrate via double-stranded closed-circle DNA intermediates assisted by an encoded recombinase which is similar to gamma-site-specific integrase. 119 matched cddid_all.tbl CDD cd03715 cd03715 239685 RT_ZFREV_like RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses. 210 matched cddid_all.tbl CDD cd03716 cd03716 239686 SOCS_ASB_like SOCS (suppressors of cytokine signaling) box of ASB (ankyrin repeat and SOCS box) and SSB (SPRY domain-containing SOCS box proteins) protein families. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence of a variable number of repeats. SSB proteins contain a central SPRY domain and a C-terminal SOCS. Recently, it has been shown that all four SSB proteins interact with the MET, the receptor protein-tyrosine kinase for hepatocyte growth factor (HGF), and that SSB-1, SSB-2, and SSB-4 interact with prostate apoptosis response protein-4. Both types of interactions are mediated through the SPRY domain. 42 matched cddid_all.tbl CDD cd03717 cd03717 239687 SOCS_SOCS_like SOCS (suppressors of cytokine signaling) box of SOCS-like proteins. The CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. These intracellular proteins regulate the responses of immune cells to cytokines. Identified as negative regulators of the cytokine-JAK-STAT pathway, they seem to play a role in many immunological and pathological processes. The function of the SOCS box is the recruitment of the ubiquitin-transferase system. Related SOCS boxes are also present in Rab40-like proteins and insect proteins of unknown function that also contain a NEUZ (domain in neuralized proteins) domain. 39 matched cddid_all.tbl CDD cd03718 cd03718 239688 SOCS_SSB1_4 SOCS (suppressors of cytokine signaling) box of SSB1 and SSB4 (SPRY domain-containing SOCS box proteins)-like proteins. SSB proteins contain a central SPRY domain and a C-terminal SOCS. SSB1 and SSB4 has been shown to bind to MET, the receptor protein-tyrosine kinase for hepatocyte growth factor (HGF) and also interacts with prostate apoptosis response protein-4. Both types of interactions are mediated through the SPRY domain. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 42 matched cddid_all.tbl CDD cd03719 cd03719 239689 SOCS_SSB2 SOCS (suppressors of cytokine signaling) box of SSB2 (SPRY domain-containing SOCS box proteins)-like proteins. SSB proteins contain a central SPRY domain and a C-terminal SOCS. SSB2 has been shown to bind to MET, the receptor protein-tyrosine kinase for hepatocyte growth factor (HGF). SSB2, like SSB4 and SSB1, also interacts with prostate apoptosis response protein-4. Both types of interactions are mediated through the SPRY domain. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 42 matched cddid_all.tbl CDD cd03720 cd03720 239690 SOCS_ASB1 SOCS (suppressors of cytokine signaling) box of ASB1-like proteins. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 42 matched cddid_all.tbl CDD cd03721 cd03721 239691 SOCS_ASB2 SOCS (suppressors of cytokine signaling) box of ASB2-like proteins. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence. ASB2 targets specific proteins to destruction by the proteasome in leukemia cells that have been induced to differentiate. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 45 matched cddid_all.tbl CDD cd03722 cd03722 239692 SOCS_ASB3 SOCS (suppressors of cytokine signaling) box of ASB3-like proteins. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence. ABS3 has been shown to be negative regulator of TNF-R2-mediated cellular responses to TNF-alpha by direct targeting of tumor necrosis factor receptor II (TNF-R2) for ubiquitination and proteasome-mediated degradation. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 51 matched cddid_all.tbl CDD cd03723 cd03723 239693 SOCS_ASB4_ASB18 SOCS (suppressors of cytokine signaling) box of ASB4 and ASB18 proteins. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence. Asb4 was identified as imprinted gene in mice. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 48 matched cddid_all.tbl CDD cd03724 cd03724 239694 SOCS_ASB5 SOCS (suppressors of cytokine signaling) box of ASB5-like proteins. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence. ASB5 has been implicated in the initiation of arteriogenesis. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 42 matched cddid_all.tbl CDD cd03725 cd03725 239695 SOCS_ASB6 SOCS (suppressors of cytokine signaling) box of ASB6-like proteins. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence. ASB6 interacts with the adaptor protein APS and recruits elongin B/C to the insulin receptor signaling complex. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 44 matched cddid_all.tbl CDD cd03726 cd03726 239696 SOCS_ASB7 SOCS (suppressors of cytokine signaling) box of ASB7-like proteins. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 45 matched cddid_all.tbl CDD cd03727 cd03727 239697 SOCS_ASB8 SOCS (suppressors of cytokine signaling) box of ASB8-like proteins. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence. Human ASB8 is highly transcribed in skeletal muscle and in lung carcinoma cell lines. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 43 matched cddid_all.tbl CDD cd03728 cd03728 239698 SOCS_ASB_9_11 SOCS (suppressors of cytokine signaling) box of ASB9 and 11 proteins. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 42 matched cddid_all.tbl CDD cd03729 cd03729 239699 SOCS_ASB13 SOCS (suppressors of cytokine signaling) box of ASB13-like proteins. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 42 matched cddid_all.tbl CDD cd03730 cd03730 239700 SOCS_ASB14 SOCS (suppressors of cytokine signaling) box of ASB14-like proteins. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 57 matched cddid_all.tbl CDD cd03731 cd03731 239701 SOCS_ASB15 SOCS (suppressors of cytokine signaling) box of ASB15-like proteins. ASB family members have a C-terminal SOCS box and an N-terminal ankyrin-related sequence. Human ASB15 is expressed predominantly in skeletal muscle and participates in the regulation of protein turnover and muscle cell development by stimulating protein synthesis and regulating differentiation of muscle cells. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 56 matched cddid_all.tbl CDD cd03733 cd03733 239702 SOCS_WSB_SWIP SOCS (suppressors of cytokine signaling) box of WSB/SWiP-like proteins. This subfamily contains WSB-1 (SOCS-box-containing WD-40 protein), part of an E3 ubiquitin ligase for the thyroid-hormone-activating type 2 iodothyronine deiodinase (D2), and SWiP-1 (SOCS box and WD-repeats in Protein), a WD40-containing protein that is expressed in embryonic structures of chickens and regulated by Sonic Hedgehog (Shh), as well as, their isoforms WSB-2 and SWiP-2. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 39 matched cddid_all.tbl CDD cd03734 cd03734 239703 SOCS_CIS1 SOCS (suppressors of cytokine signaling) box of CIS (cytokine-inducible SH2 protein) 1-like proteins. Together with the SOCS proteins, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. CIS1, like SOCS1 and SOCS3, is involved in the down-regulation of the JAK/STAT pathway. CIS1 binds to cytokine receptors at STAT5-docking sites, which prohibits recruitment of STAT5 to the receptor signaling complex and results in the down-regulation of activation by STAT5. 41 matched cddid_all.tbl CDD cd03735 cd03735 239704 SOCS_SOCS1 SOCS (suppressors of cytokine signaling) box of SOCS1-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. SOCS1, like CIS1 and SOCS3, is involved in the down-regulation of the JAK/STAT pathway. SOCS1 has a dual function as a direct potent JAK kinase inhibitor and as a component of an E3 ubiquitin-ligase complex recruiting substrates to the protein degradation machinery. 43 matched cddid_all.tbl CDD cd03736 cd03736 239705 SOCS_SOCS2 SOCS (suppressors of cytokine signaling) box of SOCS2-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. SOCS2 has recently been shown to regulate neuronal differentiation by controlling expression of a neurogenic transcription factor, Neurogenin-1. SOCS2 binds to GH receptors and inhibits the activation of STAT5b induced by GH. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 41 matched cddid_all.tbl CDD cd03737 cd03737 239706 SOCS_SOCS3 SOCS (suppressors of cytokine signaling) box of SOCS3-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. SOCS3, like CIS1 and SOCS1, is involved in the down-regulation of the JAK/STAT pathway. SOCS3 inhibits JAK activity indirectly through recruitment to the cytokine receptors. SOCS3 has been shown to play an essential role in placental development and a non-essential role in embryo development. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 42 matched cddid_all.tbl CDD cd03738 cd03738 239707 SOCS_SOCS4 SOCS (suppressors of cytokine signaling) box of SOCS4-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 56 matched cddid_all.tbl CDD cd03739 cd03739 239708 SOCS_SOCS5 SOCS (suppressors of cytokine signaling) box of SOCS5-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. SOCS5 inhibits Th2 differentiation by inhibiting IL-4 signaling. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 57 matched cddid_all.tbl CDD cd03740 cd03740 239709 SOCS_SOCS6 SOCS (suppressors of cytokine signaling) box of SOCS6-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 41 matched cddid_all.tbl CDD cd03741 cd03741 239710 SOCS_SOCS7 SOCS (suppressors of cytokine signaling) box of SOCS7-like proteins. Together with CIS1, the CIS/SOCS family of proteins is characterized by the presence of a C-terminal SOCS box and a central SH2 domain. SOCS7 is important in the functioning of neuronal cells. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 49 matched cddid_all.tbl CDD cd03742 cd03742 239711 SOCS_Rab40 SOCS (suppressors of cytokine signaling) box of Rab40-like proteins. Rab40 is part of the Rab family of small GTP-binding proteins that form the largest family within the Ras superfamily. Rab proteins regulate vesicular trafficking pathways, behaving as membrane-associated molecular switches. Rab40 is characterized by a SOCS box c-terminal to the GTPase domain. The SOCS boxes interact with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 43 matched cddid_all.tbl CDD cd03743 cd03743 239712 SOCS_SSB4 SOCS (suppressors of cytokine signaling) box of SSB4 (SPRY domain-containing SOCS box proteins)-like proteins. SSB proteins contain a central SPRY domain and a C-terminal SOCS. SSB4 has been shown to bind to MET, the receptor protein-tyrosine kinase for hepatocyte growth factor (HGF). SSB4, like SSB2 and SSB1, also interacts with prostate apoptosis response protein-4. Both types of interactions are mediated through the SPRY domain. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 42 matched cddid_all.tbl CDD cd03744 cd03744 239713 SOCS_SSB1 SOCS (suppressors of cytokine signaling) box of SSB1 (SPRY domain-containing SOCS box proteins)-like proteins. SSB proteins contain a central SPRY domain and a C-terminal SOCS. SSB1 has been shown to bind to MET, the receptor protein-tyrosine kinase for hepatocyte growth factor (HGF), both the absence and the presence of HGF and enhances the HGF-MET-induced mitogen-activated protein kinases Erk-transcription factor Elk-1-serum response elements (SRE) pathway. SSB1, like SSB2 and SSB4, also interacts with prostate apoptosis response protein-4. Both types of interactions are mediated through the SPRY domain. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 42 matched cddid_all.tbl CDD cd03745 cd03745 239714 SOCS_WSB2_SWIP2 SOCS (suppressors of cytokine signaling) box of WSB2/SWiP2-like proteins. This family consists of WSB-2 (SOCS-box-containing WD-40 protein) and SWiP-2 (SOCS box and WD-repeats in Protein). No functional information is available for WSB2 or SWiP-2, but limited information is available for the isoforms WSB-1 and SWiP-1. The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 39 matched cddid_all.tbl CDD cd03746 cd03746 239715 SOCS_WSB1_SWIP1 SOCS (suppressors of cytokine signaling) box of WSB1/SWiP1-like proteins. This subfamily contains WSB-1 (SOCS-box-containing WD-40 protein), part of an E3 ubiquitin ligase for the thyroid-hormone-activating type 2 iodothyronine deiodinase (D2) and SWiP-1 (SOCS box and WD-repeats in Protein), a WD40-containing protein that is expressed in embryonic structures of chickens and regulated by Sonic Hedgehog (Shh). The general function of the SOCS box is the recruitment of the ubiquitin-transferase system. The SOCS box interacts with Elongins B and C, Cullin-5 or Cullin-2, Rbx-1, and E2. Therefore, SOCS-box-containing proteins probably function as E3 ubiquitin ligases and mediate the degradation of proteins associated through their N-terminal regions. 40 matched cddid_all.tbl CDD cd03747 cd03747 239716 Ntn_PGA_like Penicillin G acylase (PGA) belongs to a family of beta-lactam acylases that includes cephalosporin acylase (CA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and 7-aminocephalosporanic acid (7-ACA), which can be used to synthesize semi-synthetic penicillins and cephalosporins, respectively. While both PGA and CA have a conserved Ntn (N-terminal nucleophile) hydrolase fold and the structural similarity at their active sites is very high, their sequence similarity is low. 312 matched cddid_all.tbl CDD cd03748 cd03748 239717 Ntn_PGA Penicillin G acylase (PGA) is the key enzyme in the industrial production of beta-lactam antibiotics. PGA hydrolyzes the side chain of penicillin G and related beta-lactam antibiotics releasing 6-amino penicillanic acid (6-APA), a building block in the production of semisynthetic penicillins. PGA is widely distributed among microorganisms, including bacteria, yeast and filamentous fungi but it's in vivo role remains unclear. 488 matched cddid_all.tbl CDD cd03749 cd03749 239718 proteasome_alpha_type_1 proteasome_alpha_type_1. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. 211 matched cddid_all.tbl CDD cd03750 cd03750 239719 proteasome_alpha_type_2 proteasome_alpha_type_2. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. 227 matched cddid_all.tbl CDD cd03751 cd03751 239720 proteasome_alpha_type_3 proteasome_alpha_type_3. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. 212 matched cddid_all.tbl CDD cd03752 cd03752 239721 proteasome_alpha_type_4 proteasome_alpha_type_4. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. 213 matched cddid_all.tbl CDD cd03753 cd03753 239722 proteasome_alpha_type_5 proteasome_alpha_type_5. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. 213 matched cddid_all.tbl CDD cd03754 cd03754 239723 proteasome_alpha_type_6 proteasome_alpha_type_6. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. 215 matched cddid_all.tbl CDD cd03755 cd03755 239724 proteasome_alpha_type_7 proteasome_alpha_type_7. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. 207 matched cddid_all.tbl CDD cd03756 cd03756 239725 proteasome_alpha_archeal proteasome_alpha_archeal. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. 211 matched cddid_all.tbl CDD cd03757 cd03757 239726 proteasome_beta_type_1 proteasome beta type-1 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. 212 matched cddid_all.tbl CDD cd03758 cd03758 239727 proteasome_beta_type_2 proteasome beta type-2 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis.Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. 193 matched cddid_all.tbl CDD cd03759 cd03759 239728 proteasome_beta_type_3 proteasome beta type-3 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. 195 matched cddid_all.tbl CDD cd03760 cd03760 239729 proteasome_beta_type_4 proteasome beta type-4 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis.Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. 197 matched cddid_all.tbl CDD cd03761 cd03761 239730 proteasome_beta_type_5 proteasome beta type-5 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. 188 matched cddid_all.tbl CDD cd03762 cd03762 239731 proteasome_beta_type_6 proteasome beta type-6 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. 188 matched cddid_all.tbl CDD cd03763 cd03763 239732 proteasome_beta_type_7 proteasome beta type-7 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. 189 matched cddid_all.tbl CDD cd03764 cd03764 239733 proteasome_beta_archeal Archeal proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme for non-lysosomal protein degradation in both the cytosol and the nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are both members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. 188 matched cddid_all.tbl CDD cd03765 cd03765 239734 proteasome_beta_bacterial Bacterial proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each. 236 matched cddid_all.tbl CDD cd03766 cd03766 239735 Gn_AT_II_novel Gn_AT_II_novel. This asparagine synthase-related domain is present in eukaryotes but its function has not yet been determined. The glutaminase domain catalyzes an amide nitrogen transfer from glutamine to the appropriate substrate. In this process, glutamine is hydrolyzed to glutamic acid and ammonia. This domain is related to members of the Ntn (N-terminal nucleophile) hydrolase superfamily and is found at the N-terminus of enzymes such as glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), beta lactam synthetase (beta-LS) and glutamate synthase (GltS). GLMS catalyzes the formation of glucosamine 6-phosphate from fructose 6-phosphate and glutamine in amino sugar synthesis. GPATase catalyzes the first step in purine biosynthesis, an amide transfer from glutamine to PRPP, resulting in phosphoribosylamine, pyrophosphate and glutamate. Asparagine synthetase B synthesizes asparagine from aspartate and glutamine. Beta-LS catalyzes the formation of the beta-lactam ring in the beta-lactamase inhibitor clavulanic acid. GltS synthesizes L-glutamate from 2-oxoglutarate and L-glutamine. These enzymes are generally dimers, but GPATase also exists as a homotetramer. 181 matched cddid_all.tbl CDD cd03767 cd03767 239736 SR_Res_par Serine recombinase (SR) family, Partitioning (par)-Resolvase subfamily, catalytic domain; Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. This subgroup is composed of proteins similar to the E. coli resolvase found in the par region of the RP4 plasmid, which encodes a highly efficient partitioning system. This protein is part of a complex stabilization system involved in the resolution of plasmid dimers during cell division. Similar to Tn3 and other resolvases, members of this family may contain a C-terminal DNA binding domain. 146 matched cddid_all.tbl CDD cd03768 cd03768 239737 SR_ResInv Serine Recombinase (SR) family, Resolvase and Invertase subfamily, catalytic domain; members contain a C-terminal DNA binding domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. Resolvases and invertases affect resolution or inversion and comprise a major phylogenic group. Resolvases (e.g. Tn3, gamma-delta, and Tn5044) normally recombine two sites in direct repeat causing deletion of the DNA between the sites. Invertases (e.g. Gin and Hin) recombine sites in inverted repeat to invert the DNA between the sites. Cointegrate resolution with gamma-delta resolvase requires the formation of a synaptosome of three resolvase dimers bound to each of two res sites on the DNA. Also included in this subfamily are some putative integrases including a sequence from bacteriophage phi-FC1. 126 matched cddid_all.tbl CDD cd03769 cd03769 239738 SR_IS607_transposase_like Serine Recombinase (SR) family, IS607-like transposase subfamily, catalytic domain; members contain a DNA binding domain with homology to MerR/SoxR located N-terminal to the catalytic domain. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. This subfamily is composed of proteins that catalyze the transposition of insertion sequence (IS) elements such as IS607 from Helicobacter and IS1535 from Mycobacterium, and similar proteins from other bacteria and several archaeal species. IS elements are DNA segments that move to new sites in prokaryotic and eukaryotic genomes causing insertion mutations and gene rearrangements. 134 matched cddid_all.tbl CDD cd03770 cd03770 239739 SR_TndX_transposase Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms. 140 matched cddid_all.tbl CDD cd03771 cd03771 239740 MATH_Meprin Meprin family, MATH domain; Meprins are multidomain, highly glycosylated extracellular metalloproteases, which are either anchored to the membrane or secreted into extracellular spaces. They are expressed in renal and intestinal brush border membranes, leukocytes, and cancer cells, and are capable of cleaving growth factors, cytokines, extracellular matrix proteins, and biologically active peptides. Meprin proteases are composed of two related subunits, alpha and beta, which form homo- or hetro-complexes where the basic unit is a disulfide-linked dimer. Despite their similarity, the two subunits differ in their ability to self-associate, in proteolytic processing during biosynthesis and in substrate specificity. Both subunits are synthesized as membrane spanning proteins, however, the alpha subunit is cleaved during biosynthesis and loses its transmembrane domain. Meprin beta forms homodimers or heterotetramers while meprin alpha oligomerizes into large complexes containing 10-100 subunits. Both alpha and beta subunits contain a catalytic astacin (M12 family) protease domain followed by the adhesion or interaction domains MAM, MATH and AM. The MATH and MAM domains provide symmetrical intersubunit disulfide bonds necessary for the dimerization of meprin subunits. The MATH domain may also be required for folding of an activable zymogen. 167 matched cddid_all.tbl CDD cd03772 cd03772 239741 MATH_HAUSP Herpesvirus-associated ubiquitin-specific protease (HAUSP, also known as USP7) family, N-terminal MATH (TRAF-like) domain; composed of proteins similar to human HAUSP, an enzyme that specifically catalyzes the deubiquitylation of p53 and MDM2, hence playing an important role in the p53-MDM2 pathway. It contains an N-terminal TRAF-like domain and a C-terminal catalytic protease (C19 family) domain. The tumor suppressor p53 protein is a transcription factor that responds to many cellular stress signals and is regulated primarily through ubiquitylation and subsequent degradation. MDM2 is a RING-finger E3 ubiquitin ligase that promotes p53 ubiquitinylation. p53 and MDM2 bind to the same site in the N-terminal TRAF-like domain of HAUSP in a mutually exclusive manner. HAUSP also interacts with the Epstein-Barr nuclear antigen 1 (EBNA1) protein of the Epstein-Barr virus (EBV), which efficiently immortalizes infected cells predisposing the host to a variety of cancers. EBNA1 plays several important roles in EBV latent infection and cellular transformation. It binds the same pocket as p53 in the HAUSP TRAF-like domain. Through interactions with p53, MDM2 and EBNA1, HAUSP plays a role in cell proliferation, apoptosis and EBV-mediated immortalization. 137 matched cddid_all.tbl CDD cd03773 cd03773 239742 MATH_TRIM37 Tripartite motif containing protein 37 (TRIM37) family, MATH domain; TRIM37 is a peroxisomal protein and is a member of the tripartite motif (TRIM) protein subfamily, also known as the RING-B-box-coiled-coil (RBCC) subfamily of zinc-finger proteins. Mutations in the human TRIM37 gene (also known as MUL) cause Mulibrey (muscle-liver-brain-eye) nanism, a rare growth disorder of prenatal onset characterized by dysmorphic features, pericardial constriction and hepatomegaly. TRIM37, similar to other TRIMs, contains a cysteine-rich, zinc-binding RING-finger domain followed by another cysteine-rich zinc-binding domain, the B-box, and a coiled-coil domain. TRIM37 is autoubiquitinated in a RING domain-dependent manner, indicating that it functions as an ubiquitin E3 ligase. In addition to the tripartite motif, TRIM37 also contains a MATH domain C-terminal to the coiled-coil domain. The MATH domain of TRIM37 has been shown to interact with the TRAF domain of six known TRAFs in vitro, however, it is unclear whether this is physiologically relevant. Eleven TRIM37 mutations have been associated with Mulibrey nanism so far. One mutation, Gly322Val, is located in the MATH domain and is the only mutation that does not affect the length of the protein. It results in the incorrect subcellular localization of TRIM37. 132 matched cddid_all.tbl CDD cd03774 cd03774 239743 MATH_SPOP Speckle-type POZ protein (SPOP) family, MATH domain; composed of proteins with similarity to human SPOP. SPOP was isolated as a novel antigen recognized by serum from a scleroderma patient, whose overexpression in COS cells results in a discrete speckled pattern in the nuclei. It contains an N-terminal MATH domain and a C-terminal BTB (also called POZ) domain. Together with Cul3, SPOP constitutes an ubiquitin E3 ligase which is able to ubiquitinate the PcG protein BMI1, the variant histone macroH2A1 and the death domain-associated protein Daxx. Therefore, SPOP may be involved in the regulation of these proteins and may play a role in transcriptional regulation, apoptosis and X-chromosome inactivation. Cul3 binds to the BTB domain of SPOP whereas Daxx and the macroH2A1 nonhistone region have been shown to bind to the MATH domain. Both MATH and BTB domains are necessary for the nuclear speckled accumulation of SPOP. There are many proteins, mostly uncharacterized, containing both MATH and BTB domains from C. elegans and plants which are excluded from this family. 139 matched cddid_all.tbl CDD cd03775 cd03775 239744 MATH_Ubp21p Ubiquitin-specific protease 21 (Ubp21p) family, MATH domain; composed of fungal proteins with similarity to Ubp21p of fission yeast. Ubp21p is a deubiquitinating enzyme that may be involved in the regulation of the protein kinase Prp4p, which controls the formation of active spliceosomes. Members of this family are similar to human HAUSP (Herpesvirus-associated ubiquitin-specific protease) in that they contain an N-terminal MATH domain and a C-terminal catalytic protease (C19 family) domain. HAUSP is also an ubiquitin-specific protease that specifically catalyzes the deubiquitylation of p53 and MDM2. The MATH domain of HAUSP contains the binding site for p53 and MDM2. Similarly, the MATH domain of members in this family may be involved in substrate binding. 134 matched cddid_all.tbl CDD cd03776 cd03776 239745 MATH_TRAF6 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF6 subfamily, TRAF domain, C-terminal MATH subdomain; composed of proteins with similarity to human TRAF6, including the Drosophila protein DTRAF2. TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF6 is the most divergent in its TRAF domain among the mammalian TRAFs. In addition to mediating TNFR family signaling, it is also an essential signaling molecule of the interleukin-1/Toll-like receptor superfamily. Whereas other TRAF molecules display similar and overlapping TNFR-binding specificities, TRAF6 binds completely different sites on receptors such as CD40 and RANK. TRAF6 serves as a molecular bridge between innate and adaptive immunity and plays a central role in osteoimmunology. DTRAF2, as an activator of nuclear factor-kappaB, plays a pivotal role in Drosophila development and innate immunity. TRAF6 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors. 147 matched cddid_all.tbl CDD cd03777 cd03777 239746 MATH_TRAF3 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF3 subfamily, TRAF domain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF3 was first described as a molecule that binds the cytoplasmic tail of CD40. However, it is not required for CD40 signaling. More recently, TRAF3 has been identified as a key regulator of type I interferon (IFN) production and the mammalian innate antiviral immunity. It mediates IFN responses in Toll-like receptor (TLR)-dependent as well as TLR-independent viral recognition pathways. It is also a key element in immunological homeostasis through its regulation of the anti-inflammatory cytokine interleukin-10. TRAF3 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors. 186 matched cddid_all.tbl CDD cd03778 cd03778 239747 MATH_TRAF2 Tumor Necrosis Factor Receptor (TNFR) Associated Factor (TRAF) family, TRAF2 subfamily, TRAF domain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF2 associates with the receptors TNFR-1, TNFR-2, RANK (which mediates differentiation and maturation of osteoclasts) and CD40 (which is important for the proliferation and activation of B cells), among others. It regulates distinct pathways that lead to the activation of nuclear factor-kappaB and Jun NH2-terminal kinases. TRAF2 also indirectly associates with death receptors through its interaction with TRADD (TNFR-associated death domain protein). It is involved in regulating oxidative stress or ROS-induced cell death and in the preconditioning of cells by sublethal stress for protection from subsequent injury. TRAF2 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors. 164 matched cddid_all.tbl CDD cd03779 cd03779 239748 MATH_TRAF1 Tumor Necrosis Factor Receptor (TNFR) Associated Factor (TRAF) family, TRAF1 subfamily, TRAF domain, C-terminal MATH subdomain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF1 expression is the most restricted among the TRAFs. It is found exclusively in activated lymphocytes, dendritic cells and certain epithelia. TRAF1 associates, directly or indirectly through heterodimerization with TRAF2, with the TNFR family receptors TNFR-2, CD30, RANK, CD40 and LMP1, among others. It also binds the intracellular proteins TRADD, TANK, TRIP, RIP1, RIP2 and FLIP. TRAF1 is unique among the TRAFs in that it lacks a RING domain, which is critical for the activation of nuclear factor-kappaB and Jun NH2-terminal kinase. Studies on TRAF1-deficient mice suggest that TRAF1 has a negative regulatory role in TNFR-mediated signaling events. TRAF1 contains one zinc finger and one TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors. 147 matched cddid_all.tbl CDD cd03780 cd03780 239749 MATH_TRAF5 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF5 subfamily, TRAF domain, C-terminal MATH subdomain; TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF5 was identified as an activator of nuclear factor-kappaB and a regulator of lymphotoxin-beta receptor and CD40 signaling. Its interaction with CD40 is indirect, involving hetero-oligomerization with TRAF3. In addition, TRAF5 has been shown to associate with other TNFRs including CD27, CD30, OX40 and GITR (glucocorticoid-induced TNFR). It plays a role in modulating Th2 immune responses (driven by OX40 costimulation) and T-cell activation (triggered by GITR). It is also involved in osteoclastogenesis. TRAF5 contains a RING finger domain, five zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors. 148 matched cddid_all.tbl CDD cd03781 cd03781 239750 MATH_TRAF4 Tumor Necrosis Factor Receptor (TNFR)-Associated Factor (TRAF) family, TRAF4 subfamily, TRAF domain, C-terminal MATH subdomain; composed of proteins with similarity to human TRAF4, including the Drosophila protein DTRAF1. TRAF molecules serve as adapter proteins that link TNFRs and downstream kinase cascades resulting in the activation of transcription factors and the regulation of cell survival, proliferation and stress responses. TRAF4 is highly expressed during embryogenesis, especially in the central and peripheral nervous system. Studies using TRAF4-deficient mice show that TRAF4 is required for neurogenesis, as well as the development of the trachea and the axial skeleton. In addition, TRAF4 augments nuclear factor-kappaB activation triggered by GITR (glucocorticoid-induced TNFR), a receptor expressed in T-cells, B-cells and macrophages. It also participates in counteracting the signaling mediated by Toll-like receptors through its association with TRAF6 and TRIF. DTRAF1 plays a pivotal role in the development of eye imaginal discs and photosensory neuron arrays in Drosophila. TRAF4 contains a RING finger domain, seven zinc finger domains, and a TRAF domain. The TRAF domain can be divided into a more divergent N-terminal alpha helical region (TRAF-N), and a highly conserved C-terminal MATH subdomain (TRAF-C) with an eight-stranded beta-sandwich structure. TRAF-N mediates trimerization while TRAF-C interacts with receptors. 154 matched cddid_all.tbl CDD cd03782 cd03782 239751 MATH_Meprin_Beta Meprin family, Beta subunit, MATH domain; Meprins are multidomain extracellular metalloproteases capable of cleaving growth factors, cytokines, extracellular matrix proteins, and biologically active peptides. They are composed of two related subunits, alpha and beta, which form homo- or hetro-complexes where the basic unit is a disulfide-linked dimer. The beta subunit is a type I membrane protein, which forms homodimers or heterotetramers (alpha2beta2 or alpha3beta). Meprin beta shows preference for acidic residues at the P1 and P1' sites of its substrate. Among its best substrates are growth factors and chemokines such as gastrin and osteopontin. Both alpha and beta subunits contain a catalytic astacin (M12 family) protease domain followed by the adhesion or interaction domains MAM, MATH and AM. The MATH and MAM domains provide symmetrical intersubunit disulfide bonds necessary for the dimerization of meprin subunits. The MATH domain may also be required for folding of an activable zymogen. 167 matched cddid_all.tbl CDD cd03783 cd03783 239752 MATH_Meprin_Alpha Meprin family, Alpha subunit, MATH domain; Meprins are multidomain extracellular metalloproteases capable of cleaving growth factors, cytokines, extracellular matrix proteins, and biologically active peptides. They are composed of two related subunits, alpha and beta, which form homo- or hetro-complexes where the basic unit is a disulfide-linked dimer. The alpha subunit is synthesized as a membrane spanning protein, however, it is cleaved during biosynthesis and loses its transmembrane domain. It oligomerizes into large complexes, containing 10-100 subunits (dimers that associate noncovalently), which are secreted as latent proteases and can move through extracellular spaces in a nondestructive manner. This allows delivery of the concentrated protease to sites containing activating enzymes, such as sites of inflammation, infection or cancerous growth. Meprin alpha shows preference for small or hydrophobic residues at the P1 and P1' sites of its substrate. Both alpha and beta subunits contain a catalytic astacin (M12 family) protease domain followed by the adhesion or interaction domains MAM, MATH and AM. The MATH and MAM domains provide symmetrical intersubunit disulfide bonds necessary for the dimerization of meprin subunits. The MATH domain may also be required for folding of an activable zymogen. 167 matched cddid_all.tbl CDD cd03784 cd03784 340817 GT1_Gtf-like UDP-glycosyltransferases and similar proteins. This family includes the Gtfs, a group of homologous glycosyltransferases involved in the final stages of the biosynthesis of antibiotics vancomycin and related chloroeremomycin. Gtfs transfer sugar moieties from an activated NDP-sugar donor to the oxidatively cross-linked heptapeptide core of vancomycin group antibiotics. The core structure is important for the bioactivity of the antibiotics. 404 matched cddid_all.tbl CDD cd03785 cd03785 340818 GT28_MurG undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase. MurG (EC 2.4.1.227) is an N-acetylglucosaminyltransferase, the last enzyme involved in the intracellular phase of peptidoglycan biosynthesis. It transfers N-acetyl-D-glucosamine (GlcNAc) from UDP-GlcNAc to the C4 hydroxyl of a lipid-linked N-acetylmuramoyl pentapeptide (NAM). The resulting disaccharide is then transported across the cell membrane, where it is polymerized into NAG-NAM cell-wall repeat structure. MurG belongs to the GT-B structural superfamily of glycoslytransferases, which have characteristic N- and C-terminal domains, each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. 350 matched cddid_all.tbl CDD cd03786 cd03786 340819 GTB_UDP-GlcNAc_2-Epimerase UDP-N-acetylglucosamine 2-epimerase and similar proteins. Bacterial members of the UDP-N-Acetylglucosamine (GlcNAc) 2-Epimerase family (EC 5.1.3.14) are known to catalyze the reversible interconversion of UDP-GlcNAc and UDP-N-acetylmannosamine (UDP-ManNAc). The enzyme serves to produce an activated form of ManNAc residues (UDP-ManNAc) for use in the biosynthesis of a variety of cell surface polysaccharides; The mammalian enzyme is bifunctional, catalyzing both the inversion of stereochemistry at C-2 and the hydrolysis of the UDP-sugar linkage to generate free ManNAc. It also catalyzes the phosphorylation of ManNAc to generate ManNAc 6-phosphate, a precursor to salic acids. In mammals, sialic acids are found at the termini of oligosaccharides in a large variety of cell surface glycoconjugates and are key mediators of cell-cell recognition events. Mutations in human members of this family have been associated with Sialuria, a rare disease caused by the disorders of sialic acid metabolism. This family belongs to the GT-B structural superfamily of glycoslytransferases, which have characteristic N- and C-terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. 365 matched cddid_all.tbl CDD cd03788 cd03788 340820 GT20_TPS trehalose-6-phosphate synthase. Trehalose-6-Phosphate Synthase (TPS, EC 2.4.1.15) is a glycosyltransferase that catalyses the synthesis of alpha,alpha-1,1-trehalose-6-phosphate from glucose-6-phosphate using a UDP-glucose donor. It is a key enzyme in the trehalose synthesis pathway. Trehalose is a nonreducing disaccharide present in a wide variety of organisms and may serve as a source of energy and carbon. It is characterized most notably in insect, plant, and microbial cells. Its production is often associated with a variety of stress conditions, including desiccation, dehydration, heat, cold, and oxidation. This family represents the catalytic domain of the TPS. Some members of this domain family coexist with a C-terminal trehalose phosphatase domain. 463 matched cddid_all.tbl CDD cd03789 cd03789 340821 GT9_LPS_heptosyltransferase lipopolysaccharide heptosyltransferase and similar proteins. Lipopolysaccharide heptosyltransferase (2.4.99.B6) is involved in the biosynthesis of lipooligosaccharide (LOS). Lipopolysaccharide (LPS) is a major component of the outer membrane of gram-negative bacteria. LPS heptosyltransferase transfers heptose molecules from ADP-heptose to 3-deoxy-D-manno-octulosonic acid (KDO), a part of the inner core component of LPS. This family also contains lipopolysaccharide 1,2-N-acetylglucosaminetransferase EC 2.4.1.56 and belongs to the GT-B structural superfamily of glycoslytransferases, which have characteristic N- and C-terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. 277 matched cddid_all.tbl CDD cd03791 cd03791 340822 GT5_Glycogen_synthase_DULL1-like Glycogen synthase GlgA and similar proteins. This family is most closely related to the GT5 family of glycosyltransferases. Glycogen synthase (EC:2.4.1.21) catalyzes the formation and elongation of the alpha-1,4-glucose backbone using ADP-glucose, the second and key step of glycogen biosynthesis. This family includes starch synthases of plants, such as DULL1 in Zea mays and glycogen synthases of various organisms. 474 matched cddid_all.tbl CDD cd03792 cd03792 340823 GT4_trehalose_phosphorylase trehalose phosphorylase and similar proteins. Trehalose phosphorylase (TP) reversibly catalyzes trehalose synthesis and degradation from alpha-glucose-1-phosphate (alpha-Glc-1-P) and glucose. The catalyzing activity includes the phosphorolysis of trehalose, which produce alpha-Glc-1-P and glucose, and the subsequent synthesis of trehalose. This family is most closely related to the GT4 family of glycosyltransferases. 378 matched cddid_all.tbl CDD cd03793 cd03793 340824 GT3_GSY2-like glycogen synthase GSY2 and similar proteins. Glycogen synthase, which is most closely related to the GT3 family of glycosyltransferases, catalyzes the transfer of a glucose molecule from UDP-glucose to a terminal branch of a glycogen molecule, a rate-limit step of glycogen biosynthesis. GSY2, the member of this family in S. cerevisiae, has been shown to possess glycogen synthase activity. 590 matched cddid_all.tbl CDD cd03794 cd03794 340825 GT4_WbuB-like Escherichia coli WbuB and similar proteins. This family is most closely related to the GT1 family of glycosyltransferases. WbuB in E. coli is involved in the biosynthesis of the O26 O-antigen. It has been proposed to function as an N-acetyl-L-fucosamine (L-FucNAc) transferase. 391 matched cddid_all.tbl CDD cd03795 cd03795 340826 GT4_WfcD-like Escherichia coli alpha-1,3-mannosyltransferase WfcD and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP-linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. The members of this family are found mainly in bacteria and eukaryotes. 355 matched cddid_all.tbl CDD cd03796 cd03796 340827 GT4_PIG-A-like phosphatidylinositol N-acetylglucosaminyltransferase subunit A and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. Phosphatidylinositol glycan-class A (PIG-A), an X-linked gene in humans, is necessary for the synthesis of N-acetylglucosaminyl-phosphatidylinositol, a very early intermediate in glycosyl phosphatidylinositol (GPI)-anchor biosynthesis. The GPI-anchor is an important cellular structure that facilitates the attachment of many proteins to cell surfaces. Somatic mutations in PIG-A have been associated with Paroxysmal Nocturnal Hemoglobinuria (PNH), an acquired hematological disorder. 398 matched cddid_all.tbl CDD cd03798 cd03798 340828 GT4_WlbH-like Bordetella parapertussis WlbH and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. Staphylococcus aureus CapJ may be involved in capsule polysaccharide biosynthesis. WlbH in Bordetella parapertussis has been shown to be required for the biosynthesis of a trisaccharide that, when attached to the B. pertussis lipopolysaccharide (LPS) core (band B), generates band A LPS. 376 matched cddid_all.tbl CDD cd03799 cd03799 340829 GT4_AmsK-like Erwinia amylovora AmsK and similar proteins. This is a family of GT4 glycosyltransferases found specifically in certain bacteria. AmsK in Erwinia amylovora, has been reported to be involved in the biosynthesis of amylovoran, a exopolysaccharide acting as a virulence factor. 350 matched cddid_all.tbl CDD cd03800 cd03800 340830 GT4_sucrose_synthase sucrose-phosphate synthase and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. The sucrose-phosphate synthases in this family may be unique to plants and photosynthetic bacteria. This enzyme catalyzes the synthesis of sucrose 6-phosphate from fructose 6-phosphate and uridine 5'-diphosphate-glucose, a key regulatory step of sucrose metabolism. The activity of this enzyme is regulated by phosphorylation and moderated by the concentration of various metabolites and light. 398 matched cddid_all.tbl CDD cd03801 cd03801 340831 GT4_PimA-like phosphatidyl-myo-inositol mannosyltransferase. This family is most closely related to the GT4 family of glycosyltransferases and named after PimA in Propionibacterium freudenreichii, which is involved in the biosynthesis of phosphatidyl-myo-inositol mannosides (PIM) which are early precursors in the biosynthesis of lipomannans (LM) and lipoarabinomannans (LAM), and catalyzes the addition of a mannosyl residue from GDP-D-mannose (GDP-Man) to the position 2 of the carrier lipid phosphatidyl-myo-inositol (PI) to generate a phosphatidyl-myo-inositol bearing an alpha-1,2-linked mannose residue (PIM1). Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. The members of this family are found mainly in certain bacteria and archaea. 366 matched cddid_all.tbl CDD cd03802 cd03802 340832 GT4_AviGT4-like UDP-Glc:tetrahydrobiopterin alpha-glucosyltransferase and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. aviGT4 in Streptomyces viridochromogenes has been shown to be involved in biosynthesis of oligosaccharide antibiotic avilamycin A. Inactivation of aviGT4 resulted in a mutant that accumulated a novel avilamycin derivative lacking the terminal eurekanate residue. 333 matched cddid_all.tbl CDD cd03804 cd03804 340833 GT4_WbaZ-like mannosyltransferase WbaZ and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. WbaZ in Salmonella enterica has been shown to possess mannosyltransferase activity. 356 matched cddid_all.tbl CDD cd03805 cd03805 340834 GT4_ALG2-like alpha-1,3/1,6-mannosyltransferase ALG2 and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. ALG2, a 1,3-mannosyltransferase, in yeast catalyzes the mannosylation of Man(2)GlcNAc(2)-dolichol diphosphate and Man(1)GlcNAc(2)-dolichol diphosphate to form Man(3)GlcNAc(2)-dolichol diphosphate. A deficiency of this enzyme causes an abnormal accumulation of Man1GlcNAc2-PP-dolichol and Man2GlcNAc2-PP-dolichol, which is associated with a type of congenital disorders of glycosylation (CDG), designated CDG-Ii, in humans. 392 matched cddid_all.tbl CDD cd03806 cd03806 340835 GT4_ALG11-like alpha-1,2-mannosyltransferase ALG11 and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. ALG11 in yeast is involved in adding the final 1,2-linked Man to the Man5GlcNAc2-PP-Dol synthesized on the cytosolic face of the ER. The deletion analysis of ALG11 was shown to block the early steps of core biosynthesis that takes place on the cytoplasmic face of the ER and lead to a defect in the assembly of lipid-linked oligosaccharides. 419 matched cddid_all.tbl CDD cd03807 cd03807 340836 GT4_WbnK-like Shigella dysenteriae WbnK and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. WbnK in Shigella dysenteriae has been shown to be involved in the type 7 O-antigen biosynthesis. 362 matched cddid_all.tbl CDD cd03808 cd03808 340837 GT4_CapM-like capsular polysaccharide biosynthesis glycosyltransferase CapM and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. CapM in Staphylococcus aureus is required for the synthesis of type 1 capsular polysaccharides. 358 matched cddid_all.tbl CDD cd03809 cd03809 340838 GT4_MtfB-like glycosyltransferases MtfB, WbpX, and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. MtfB (mannosyltransferase B) in E. coli has been shown to direct the growth of the O9-specific polysaccharide chain. It transfers two mannoses into the position 3 of the previously synthesized polysaccharide. 362 matched cddid_all.tbl CDD cd03811 cd03811 340839 GT4_GT28_WabH-like family 4 and family 28 glycosyltransferases similar to Klebsiella WabH. This family is most closely related to the GT1 family of glycosyltransferases. WabH in Klebsiella pneumoniae has been shown to transfer a GlcNAc residue from UDP-GlcNAc onto the acceptor GalUA residue in the cellular outer core. 351 matched cddid_all.tbl CDD cd03812 cd03812 340840 GT4_CapH-like capsular polysaccharide biosynthesis glycosyltransferase CapH and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. capH in Staphylococcus aureus has been shown to be required for the biosynthesis of the type 1 capsular polysaccharide (CP1). 357 matched cddid_all.tbl CDD cd03813 cd03813 340841 GT4-like glycosyltransferase family 4 proteins. This family is most closely related to the GT4 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. The members of this family are found mainly in bacteria, while some of them are also found in Archaea and eukaryotes. 474 matched cddid_all.tbl CDD cd03814 cd03814 340842 GT4-like glycosyltransferase family 4 proteins. This family is most closely related to the GT4 family of glycosyltransferases and includes a sequence annotated as alpha-D-mannose-alpha(1-6)phosphatidyl myo-inositol monomannoside transferase from Bacillus halodurans. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. The members of this family are found mainly in bacteria and eukaryotes. 365 matched cddid_all.tbl CDD cd03816 cd03816 340843 GT33_ALG1-like chitobiosyldiphosphodolichol beta-mannosyltransferase and similar proteins. This family is most closely related to the GT33 family of glycosyltransferases. The yeast gene ALG1 has been shown to function as a mannosyltransferase that catalyzes the formation of dolichol pyrophosphate (Dol-PP)-GlcNAc2Man from GDP-Man and Dol-PP-Glc-NAc2, and participates in the formation of the lipid-linked precursor oligosaccharide for N-glycosylation. In humans ALG1 has been associated with the congenital disorders of glycosylation (CDG) designated as subtype CDG-Ik. 411 matched cddid_all.tbl CDD cd03817 cd03817 340844 GT4_UGDG-like UDP-Glc:1,2-diacylglycerol 3-a-glucosyltransferase and similar proteins. This family is most closely related to the GT1 family of glycosyltransferases. UDP-glucose-diacylglycerol glucosyltransferase (EC 2.4.1.337, UGDG; also known as 1,2-diacylglycerol 3-glucosyltransferase) catalyzes the transfer of glucose from UDP-glucose to 1,2-diacylglycerol forming 3-D-glucosyl-1,2-diacylglycerol. 372 matched cddid_all.tbl CDD cd03818 cd03818 340845 GT4_ExpC-like Rhizobium meliloti ExpC and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. ExpC in Rhizobium meliloti has been shown to be involved in the biosynthesis of galactoglucan (exopolysaccharide II). 396 matched cddid_all.tbl CDD cd03819 cd03819 340846 GT4_WavL-like Vibrio cholerae WavL and similar sequences. This family is most closely related to the GT4 family of glycosyltransferases. WavL in Vibrio cholerae has been shown to be involved in the biosynthesis of the lipopolysaccharide core. 345 matched cddid_all.tbl CDD cd03820 cd03820 340847 GT4_AmsD-like amylovoran biosynthesis glycosyltransferase AmsD and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. AmSD in Erwinia amylovora has been shown to be involved in the biosynthesis of amylovoran, the acidic exopolysaccharide acting as a virulence factor. This enzyme may be responsible for the formation of galactose alpha-1,6 linkages in amylovoran. 351 matched cddid_all.tbl CDD cd03821 cd03821 340848 GT4_Bme6-like Brucella melitensis Bme6 and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. Bme6 in Brucella melitensis has been shown to be involved in the biosynthesis of a polysaccharide. 377 matched cddid_all.tbl CDD cd03822 cd03822 340849 GT4_mannosyltransferase-like mannosyltransferases of glycosyltransferase family 4 and similar proteins. This family is most closely related to the GT1 family of glycosyltransferases. ORF704 in E. coli has been shown to be involved in the biosynthesis of O-specific mannose homopolysaccharides. 370 matched cddid_all.tbl CDD cd03823 cd03823 340850 GT4_ExpE7-like glycosyltransferase ExpE7 and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. ExpE7 in Sinorhizobium meliloti has been shown to be involved in the biosynthesis of galactoglucans (exopolysaccharide II). 357 matched cddid_all.tbl CDD cd03825 cd03825 340851 GT4_WcaC-like putative colanic acid biosynthesis glycosyl transferase WcaC and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. Escherichia coli WcaC has been predicted to function in colanic acid biosynthesis. WcfI in Bacteroides fragilis has been shown to be involved in the capsular polysaccharide biosynthesis. 364 matched cddid_all.tbl CDD cd03829 cd03829 239753 Sina Seven in absentia (Sina) protein family, C-terminal substrate binding domain; composed of the Drosophila Sina protein, the mammalian Sina homolog (Siah), the plant protein SINAT5, and similar proteins. Sina, Siah and SINAT5 are RING-containing proteins that function as E3 ubiquitin ligases, acting either as single proteins or as a part of multiprotein complexes. Sina is expressed in many cells in the developing eye but is essential specifically for R7 photoreceptor cell development. Sina cooperates with Phyllopod (Phyl), Ebi and the E2 ubiquitin-conjugating enzyme Ubcd1 to catalyze the ubiquitination and subsequent degradation of Tramtrack (Ttk88); Ttk88 is a transcriptional repressor that blocks photoreceptor differentiation. Similarly, the mammalian homologue Siah1 cooperates with SIP (Siah-interacting protein), Ebi and the adaptor protein Skp1, to target beta-catenin for ubiquitination and degradation via a p53-dependent mechanism. SINAT5 targets NAC1 for ubiquitin-mediated degradation resulting in the downregulation of auxin, a hormone that controls many aspects of plant development. Other targets of Sina family proteins include c-Myb, synaptophysin, group 1 glutamate receptors, promyelocytic leukemia protein, alpha-synuclein, synphilin-1 and alpha-ketoglutarate dehydrogenase, among others. Sina proteins also bind proteins that are not targets for ubiquitination such as Phyl, adenomatous polyposis coli, VAV, BAG-1 and Dab-1. Siah binds to a consensus motif, PXAXVXP, which is present in Siah-binding proteins. Siah is a dimeric protein consisting of an N-terminal RING domain, two zinc finger motifs and a C-terminal substrate-binding domain (SBD); this SBD contains an eight-stranded antiparallel beta-sandwich fold similar to the MATH (meprin and TRAF-C homology) domain. 127 matched cddid_all.tbl CDD cd03855 cd03855 349428 M14_ASTE Peptidase M14 Succinylglutamate desuccinylase (ASTE) subfamily. Peptidase M14 Succinylglutamate desuccinylase (ASTE, also known as N-succinyl-L-glutamate amidohydrolase, N2-succinylglutamate desuccinylase, and SGDS; EC 3.5.1.96) belongs to the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily of the M14 family of metallocarboxypeptidases. This group includes succinylglutamate desuccinylase that catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway. It hydrolyzes N-succinyl-L-glutamate to succinate and L-glutamate. 239 matched cddid_all.tbl CDD cd03856 cd03856 349429 M14_Nna1-like Peptidase M14-like domain of ATP/GTP binding proteins, cytosolic carboxypeptidases and related proteins. Peptidase M14-like domain of Nna-1 (Nervous system Nuclear protein induced by Axotomy), also known as ATP/GTP binding protein (AGTPBP-1) and cytosolic carboxypeptidase (CCP), and related proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. This subfamily includes the human AGTPBP-1 and AGBL -2, -3, -4, and -5, and the mouse Nna1/CCP-1 and CCP -2 through -6. Nna1-like proteins are active metallopeptidases that are thought to act on cytosolic proteins such as alpha-tubulin, to remove a C-terminal tyrosine. Nna1 is widely expressed in the developing and adult nervous systems, including cerebellar Purkinje and granule neurons, miral cells of the olfactory bulb and retinal photoreceptors. Nna1 is also induced in axotomized motor neurons. Mutations in Nna1 cause Purkinje cell degeneration (pcd). The Nna1 CP domain is required to prevent the retinal photoreceptor loss and cerebellar ataxia phenotypes of pcd mice, and a functional zinc-binding domain is needed for Nna-1 to support neuron survival in these mice. Nna1-like proteins from the different phyla are highly diverse, but they all contain a characteristic N-terminal conserved domain right before the CP domain. It has been suggested that this N-terminal domain might act as a folding domain. 252 matched cddid_all.tbl CDD cd03857 cd03857 349430 M14-like Peptidase M14-like domain; uncharacterized subfamily. Peptidase M14-like domain of a functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism. 203 matched cddid_all.tbl CDD cd03858 cd03858 349431 M14_CP_N-E_like Peptidase M14 carboxypeptidase subfamily N/E-like. Carboxypeptidase (CP) N/E-like subfamily of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. The N/E subfamily includes eight members, of which five (CPN, CPE, CPM, CPD, CPZ) are considered enzymatically active, while the other three are non-active (CPX1, PCX2, ACLP/AEBP1) and lack the critical active site and substrate-binding residues considered necessary for CP activity. These non-active members may function as binding proteins or display catalytic activity towards other substrates. Unlike the A/B CP subfamily, enzymes belonging to the N/E subfamily are not produced as inactive precursors that require proteolysis to produce the active form; rather, they rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavages that would otherwise damage the cell. In addition, all members of the N/E subfamily contain an extra C-terminal domain that is not present in the A/B subfamily. This domain has structural homology to transthyretin and other proteins and has been proposed to function as a folding domain. The active N/E enzymes fulfill a variety of cellular functions, including prohormone processing, regulation of peptide hormone activity, alteration of protein-protein or protein-cell interactions and transcriptional regulation. 292 matched cddid_all.tbl CDD cd03859 cd03859 349432 M14_CPT Peptidase M14 Carboxypeptidase T subfamily. Peptidase M14-like domain of carboxypeptidase (CP) T (CPT), CPT belongs to the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPT has moderate similarity to CPA and CPB, and exhibits dual-substrate specificity by cleaving C-terminal hydrophobic amino acid residues like CPA and C-terminal positively charged residues like CPB. CPA and CPB are M14 family peptidases but do not belong to this CPT group. The substrate specificity difference between CPT and CPA and CPB is ascribed to a few amino acid substitutions at the substrate-binding pocket while the spatial organization of the binding site remains the same as in all Zn-CPs. CPT has increased thermal stability in presence of Ca2+ ions, and two disulfide bridges which give an additional stabilization factor. 292 matched cddid_all.tbl CDD cd03860 cd03860 349433 M14_CP_A-B_like Peptidase M14 carboxypeptidase subfamily A/B-like. The Peptidase M14 Carboxypeptidase (CP) A/B subfamily is one of two main M14 CP subfamilies defined by sequence and structural homology, the other being the N/E subfamily. CPs hydrolyze single, C-terminal amino acids from polypeptide chains. They have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by a globular N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. There are nine members in the A/B family: CPA1, CPA2, CPA3, CPA4, CPA5, CPA6, CPB, CPO and CPU. CPA1, CPA2 and CPB are produced by the pancreas. The A forms have slightly different specificities, with CPA1 preferring aliphatic and small aromatic residues, and CPA2 preferring the bulkier aromatic side chains. CPA3 is found in secretory granules of mast cells and functions in inflammatory processes. CPA4 is detected in hormone-regulated tissues, and is thought to play a role in prostate cancer. CPA5 is present in discrete regions of pituitary and other tissues, and cleaves aliphatic C-terminal residues. CPA6 is highly expressed in embryonic brain and optic muscle, suggesting that it may play a specific role in cell migration and axonal guidance. CPU (also called CPB2) is produced and secreted by the liver as the inactive precursor, PCPU, commonly referred to as thrombin-activatable fibrinolysis inhibitor (TAFI). Little is known about CPO but it has been suggested to have specificity for acidic residues. 300 matched cddid_all.tbl CDD cd03862 cd03862 349434 M14-like Peptidase M14-like domain; uncharacterized subfamily. A functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavages. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism. 245 matched cddid_all.tbl CDD cd03863 cd03863 349435 M14_CPD_II Peptidase M14 carboxypeptidase subfamily N/E-like; Carboxypeptidase D, domain II subgroup. The second carboxypeptidase (CP)-like domain of Carboxypeptidase D (CPD; EC 3.4.17.22), domain II. CPD differs from all other metallocarboxypeptidases in that it contains multiple CP-like domains. CPD belongs to the N/E-like subfamily of the M14 family of metallocarboxypeptidases (MCPs).The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPD is a single-chain protein containing a signal peptide, three tandem repeats of CP-like domains separated by short bridge regions, followed by a transmembrane domain, and a C-terminal cytosolic tail. The first two CP-like domains of CPD contain all of the essential active site and substrate-binding residues, while the third CP-like domain lacks critical residues necessary for enzymatic activity and is inactive towards standard CP substrates. Domain I is optimally active at pH 6.3-7.5 and prefers substrates with C-terminal Arg, whereas domain II is active at pH 5.0-6.5 and prefers substrates with C-terminal Lys. CPD functions in the processing of proteins that transit the secretory pathway, and is present in all vertebrates as well as Drosophila. It is broadly distributed in all tissue types. Within cells, CPD is present in the trans-Golgi network and immature secretory vesicles, but is excluded from mature vesicles. It is thought to play a role in the processing of proteins that are initially processed by furin or related endopeptidases present in the trans-Golgi network, such as growth factors and receptors. CPD is implicated in the pathogenesis of lupus erythematosus (LE), it is regulated by TGF-beta in various cell types of murine and human origin and is significantly down-regulated in CD14 positive cells isolated from patients with LE. As down -regulation of CPD leads to down-modulation of TGF-beta, CPD may have a role in a positive feedback loop. 296 matched cddid_all.tbl CDD cd03864 cd03864 349436 M14_CPN Peptidase M14 carboxypeptidase subfamily N/E-like; Carboxypeptidase N subgroup. Peptidase M14 Carboxypeptidase N (CPN, also known as kininase I, creatine kinase conversion factor, plasma carboxypeptidase B, arginine carboxypeptidase, and protaminase; EC 3.4.17.3) is an extracellular glycoprotein synthesized in the liver and released into the blood, where it is present in high concentrations. CPN belongs to the N/E subfamily of the M14 family of metallocarboxypeptidases (MCPs).The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPN plays an important role in protecting the body from excessive buildup of potentially deleterious peptides that normally act as local autocrine or paracrine hormones. It specifically removes C-terminal basic residues. As CPN can cleave lysine more avidly than arginine residues it is also called lysine carboxypeptidase. CPN substrates include peptides found in the bloodstream, such as kinins (e.g. bradykinin, kalinin, met-lys-bradykinin), complement anaphylatoxins and creatine kinase MM (CK-MM). By removing just one amino acid, CPN can alter peptide activity and receptor binding. For example Bradykinin, a nine-residue peptide released from kiningen in response to tissue injury which is inactivated by CPN, anaphylatoxins which are regulated by CPN by the cleaving and removal of their C-terminal arginines resulting in a reduction in their biological activities of 10-100-fold, and creatine kinase MM, a cytosolic enzyme that catalyzes the reversible transfer of a phosphate group from ATP to creatine, and is regulated by CPN by the cleavage of C-terminal lysines. Like the other N/E subfamily members, two surface loops surrounding the active-site groove restrict access to the catalytic center, thus restricting larger protein carboxypeptidase inhibitors from inhibiting CPN. 313 matched cddid_all.tbl CDD cd03865 cd03865 349437 M14_CPE Peptidase M14 carboxypeptidase subfamily N/E-like; Carboxypeptidase E subgroup. Peptidase M14 Carboxypeptidase (CP) E (CPE, also known as carboxypeptidase H, and enkephalin convertase; EC 3.4.17.10) belongs to the N/E subfamily of the M14 family of metallocarboxypeptidases (MCPs).The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPE is an important enzyme responsible for the proteolytic processing of prohormone intermediates (such as pro-insulin, pro-opiomelanocortin, or pro-gonadotropin-releasing hormone) by specifically removing C-terminal basic residues. In addition, it has been proposed that the regulated secretory pathway (RSP) of the nervous and endocrine systems utilizes membrane-bound CPE as a sorting receptor. A naturally occurring point mutation in CPE reduces the stability of the enzyme and causes its degradation, leading to an accumulation of numerous neuroendocrine peptides that result in obesity and hyperglycemia. Reduced CPE enzyme and receptor activity could underlie abnormal placental phenotypes from the observation that CPE is down-regulated in enlarged placentas of interspecific hybrid (interspecies hybrid placental dysplasia, IHPD) and cloned mice. 319 matched cddid_all.tbl CDD cd03866 cd03866 349438 M14_CPM Peptidase M14 carboxypeptidase subfamily N/E-like; Carboxypeptidase M subgroup. Peptidase M14 Carboxypeptidase (CP) M (CPM) belongs to the N/E subfamily of the M14 family of metallocarboxypeptidases (MCPs).The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPM is an extracellular glycoprotein, bound to cell membranes via a glycosyl-phosphatidylinositol on the C-terminus of the protein. It specifically removes C-terminal basic residues such as lysine and arginine from peptides and proteins. The highest levels of CPM have been found in human lung and placenta, but significant amounts are present in kidney, blood vessels, intestine, brain, and peripheral nerves. CPM has also been found in soluble form in various body fluids, including amniotic fluid, seminal plasma and urine. Due to its wide distribution in a variety of tissues, it is believed that it plays an important role in the control of peptide hormones and growth factor activity on the cell surface and in the membrane-localized degradation of extracellular proteins, for example it hydrolyses the C-terminal arginine of epidermal growth factor (EGF) resulting in des-Arg-EGF which binds to the EGF receptor (EGFR) with an equal or greater affinity than native EGF. CPM is a required processing enzyme that generates specific agonists for the B1 receptor. 289 matched cddid_all.tbl CDD cd03867 cd03867 349439 M14_CPZ Peptidase M14 carboxypeptidase subfamily N/E-like; Carboxypeptidase Z subgroup. Peptidase M14-like domain of carboxypeptidase (CP) Z (CPZ), CPZ belongs to the N/E subfamily of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPZ is a secreted Zn-dependent enzyme whose biological function is largely unknown. Unlike other members of the N/E subfamily, CPZ has a bipartite structure, which consists of an N-terminal cysteine-rich domain (CRD) whose sequence is similar to Wnt-binding proteins, and a C-terminal CP catalytic domain that removes C-terminal Arg residues from substrates. CPZ is enriched in the extracellular matrix and is widely distributed during early embryogenesis. That the CRD of CPZ can bind to Wnt4 suggests that CPZ plays a role in Wnt signaling. 315 matched cddid_all.tbl CDD cd03868 cd03868 349440 M14_CPD_I Peptidase M14 carboxypeptidase subfamily N/E-like; Carboxypeptidase D, domain I subgroup. The first carboxypeptidase (CP)-like domain of Carboxypeptidase D (CPD; EC 3.4.17.22), domain I. CPD differs from all other metallocarboxypeptidases in that it contains multiple CP-like domains. CPD belongs to the N/E-like subfamily of the M14 family of metallocarboxypeptidases (MCPs).The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPD is a single-chain protein containing a signal peptide, three tandem repeats of CP-like domains separated by short bridge regions, followed by a transmembrane domain, and a C-terminal cytosolic tail. The first two CP-like domains of CPD contain all of the essential active site and substrate-binding residues, the third CP-like domain lacks critical residues necessary for enzymatic activity and is inactive towards standard CP substrates. Domain I is optimally active at pH 6.3-7.5 and prefers substrates with C-terminal Arg, whereas domain II is active at pH 5.0-6.5 and prefers substrates with C-terminal Lys. This Domain I family contains two contiguous surface cysteines that may become palmitoylated and target the enzyme to membranes, thus regulating intracellular trafficking. CPD functions in the processing of proteins that transit the secretory pathway, and is present in all vertebrates as well as Drosophila. It is broadly distributed in all tissue types. Within cells, CPD is present in the trans Golgi network and immature secretory vesicles, but is excluded from mature vesicles. It is thought to play a role in the processing of proteins that are initially processed by furin or related endopeptidases present in the trans Golgi network, such as growth factors and receptors. CPD is implicated in the pathogenesis of lupus erythematosus (LE), it is regulated by TGF-beta in various cell types of murine and human origin and is significantly down-regulated in CD14 positive cells isolated from patients with LE. As down-regulation of CPD leads to down-modulation of TGF-beta, CPD may have a role in a positive feedback loop. In D. melanogaster, the CPD variant 1B short (DmCPD1Bs) is necessary and sufficient for viability of the fruit fly. 294 matched cddid_all.tbl CDD cd03869 cd03869 349441 M14_CPX_like Peptidase M14 carboxypeptidase subfamily N/E-like; Carboxypeptidase X subgroup. Peptidase M14-like domain of carboxypeptidase (CP)-like protein X (CPX), CPX forms a distinct subgroup of the N/E subfamily of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Proteins belonging to this subgroup include CP-like protein X1 (CPX1), CP-like protein X2 (CPX2), and aortic CP-like protein (ACLP) and its isoform adipocyte enhancer binding protein-1 (AEBP1). AEBP1 is a truncated form of ACLP, which may arise from alternative splicing of the gene. These proteins are inactive towards standard CP substrates because they lack one or more critical active site and substrate-binding residues that are necessary for activity. They may function as binding proteins rather than as active CPs or display catalytic activity toward other substrates. Proteins in this subgroup also contain an N-terminal discoidin domain. The CP domain is important for the function of AEBP1 as a transcriptional repressor. AEBP1 is involved in several biological processes including adipogenesis, macrophage cholesterol homeostasis, and inflammation. In macrophages, AEBP1 promotes the expression of IL-6, TNF-alpha, MCP-1, and iNOS whose expression is tightly regulated by NF-kappaB activity. ACLP, a secreted protein that associates with the extracellular matrix, is essential for abdominal wall development and contributes to dermal wound healing. 322 matched cddid_all.tbl CDD cd03870 cd03870 349442 M14_CPA Peptidase M14 carboxypeptidase subfamily A/B-like; Carboxypeptidase A subgroup. Peptidase M14 Carboxypeptidase (CP) A (CPA) belongs to the A/B subfamily of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPA enzymes generally favor hydrophobic residues. A/B subfamily enzymes are normally synthesized as inactive precursors containing preceding signal peptide, followed by a globular N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The procarboxypeptidase A (PCPA) is produced by the exocrine pancreas and stored as a stable zymogen in the pancreatic granules until secretion into the digestive tract occurs. This subfamily includes CPA1, CPA2 and CPA4 forms. Within these A forms, there are slightly different specificities, with CPA1 preferring aliphatic and small aromatic residues, and CPA2 preferring the bulkier aromatic side chains. CPA4, detected in hormone-regulated tissues, is thought to play a role in prostate cancer. 301 matched cddid_all.tbl CDD cd03871 cd03871 349443 M14_CPB Peptidase M14 carboxypeptidase subfamily A/B-like; Carboxypeptidase B subgroup. Peptidase M14 Carboxypeptidase B (CPB) belongs to the carboxypeptidase A/B subfamily of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Carboxypeptidase B (CPB) enzymes only cleave the basic residues lysine or arginine. A/B subfamily enzymes are normally synthesized as inactive precursors containing preceding signal peptide, followed by a globular N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The procarboxypeptidase B (PCPB) is produced by the exocrine pancreas and stored as stable zymogen in the pancreatic granules until secretion into the digestive tract occurs. PCPB has been reported to be a good serum marker for the diagnosis of acute pancreatitis and graft rejection in pancreas transplant recipients. this subfamily also includes thrombin activatable fibrinolysis inhibitor (TAFIa), a carboxypeptidase that stabilizes fibrin clots by removing C-terminal arginines and lysines from partially degraded fibrin. Inhibition of TAFIa stimulates the degradation of fibrin clots and may help in prevention of thrombosis. 300 matched cddid_all.tbl CDD cd03872 cd03872 349444 M14_CPA6 Peptidase M14 carboxypeptidase subfamily A/B-like; Carboxypeptidase A6 subgroup. Carboxypeptidase (CP) A6 (CPA6, also known as CPAH; EC 3.4.17.1), belongs to the carboxypeptidase A/B subfamily of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPA6 prefers large hydrophobic C-terminal amino acids as well as histidine, while peptides with a penultimate glycine or proline are very poorly cleaved. Several neuropeptides are processed by CPA6, including Met- and Leu-enkephalin, angiotensin I, and neurotensin. CPA6 converts enkephalin and neurotensin into forms known to be inactive toward their receptors, but converts inactive angiotensin I into the biologically active angiotensin II. Thus, CPA6 plays a possible role in the regulation of neuropeptides in the extracellular environment within the olfactory bulb where it is highly expressed. It is also broadly expressed in embryonic tissue, being found in neuronal tissues, bone, skin as well as the lateral rectus eye muscle. A disruption in the CPA6 gene is linked to Duane syndrome, a defect in the abducens nerve/lateral rectus muscle connection. 300 matched cddid_all.tbl CDD cd03873 cd03873 349870 Zinc_peptidase_like Zinc peptidases M18, M20, M28, and M42. Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This hierarchy contains zinc peptidases that correspond to the MH clan in the MEROPS database, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a non-specific eukaryotic dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carboxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metallo-aminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacyl-peptidase activity (i.e. hydrolysis of acylated N-terminal residues). 200 matched cddid_all.tbl CDD cd03874 cd03874 349871 M28_PMSA_TfR_like M28 Zn-peptidase Transferrin Receptor-like family. Peptidase M28 family; Transferrin Receptor (TfR) and prostate-specific membrane antigen (PSMA, also called glutamate carboxypeptidase or GCP-II) subfamily. TfR and PSMA are homodimeric type II transmembrane proteins containing three distinct domains: protease-like, apical or protease-associated (PA) and helical domains. The protease-like domain is a large extracellular portion (ectodomain). In TfR, it contains a binding site for the transferrin molecule and has 28% identity to membrane glutamate carboxypeptidase II (mGCP-II or PSMA). The PA domain is inserted between the first and second strands of the central beta sheet in the protease-like domain. TfR1 is widely expressed, and is a key player in the uptake of iron-loaded transferrin (Tf) into cells. The TfR1 homodimer binds two molecules of Tf and the complex is then internalized. TfR1 may also participate in cell growth and proliferation. TfR2 binds Tf but with a significantly lower affinity than TfR1. It is expressed chiefly in hepatocytes, hematopoietic cells, and duodenal crypt cells; its expression overlaps with that of hereditary hemochromatosis protein (HFE). TfR2 is involved in iron homeostasis; in humans, mutations in TfR2 are associated with a form of hemochromatosis (HFE3). PSMA is over-expressed predominantly in prostate cancer (PCa) as well as in the neovasculature of most solid tumors, but not in the vasculature of normal tissues. PSMA is considered a biomarker for PCa and possibly for use as an imaging and therapeutic target. The extracellular domain of PSMA possesses two unique enzymatic functions: N-acetylated, alpha-linked acidic dipeptidase (NAALADase) which cleaves terminal glutamate from the neurodipeptide N-acetyl-aspartyl-glutamate (NAAG), and folate hydrolase (FOLH) which cleaves the terminal glutamates from gamma-linked polyglutamates (carboxypeptidase). A mutation in this gene may be associated with impaired intestinal absorption of dietary folates, resulting in low blood folate levels and consequent hyperhomocysteinemia. Expression of this protein in the brain may be involved in a number of pathological conditions associated with glutamate excitotoxicity. This gene likely arose from a duplication event of a nearby chromosomal region. Alternative splicing gives rise to multiple transcript variants. While related in sequence to peptidase M28 GCP-II, TfR lacks the metal ion coordination centers and protease activity. 278 matched cddid_all.tbl CDD cd03875 cd03875 349872 M28_Fxna_like M28 Zn-peptidase Endoplasmic reticulum metallopeptidase 1. Peptidase family M28; Endoplasmic reticulum metallopeptidase 1 (ERMP1; Felix-ina, FXNA or Fxna peptidase; KIAA1815) subfamily. ERMP1 is a multi-pass membrane protein located in the endoplasmic reticulum membrane. In humans, Fxna may play a crucial role in processing proteins required for the organization of somatic cells and oocytes into discrete follicular structures, although which proteins are hydrolyzed has not yet been determined. Another member of this subfamily is the 24-kDa vacuolar protein (VP24) which is probably involved in the formation of intravacuolar pigmented globules (cyanoplasts) in highly anthocyanin-containing vacuoles; however, the biological function of the C-terminal region which includes the putative transmembrane metallopeptidase domain is unknown. 307 matched cddid_all.tbl CDD cd03876 cd03876 349873 M28_SGAP_like M28 Zn-peptidase Streptomyces griseus aminopeptidase and similar proteins. Peptidase family M28; Streptomyces griseus Aminopeptidase (SGAP, Leucine aminopeptidase (LAP), aminopeptidase S, Mername-AA022 peptidase) subfamily. SGAP is a di-zinc exopeptidase with high preference towards large hydrophobic amino-terminal residues, with Leu being the most efficiently cleaved. It can accommodate all except Pro and Glu residues in the P1' position. It is a monomeric (30 kDa), calcium-activated and calcium-stabilized enzyme; its activation by calcium correlates with substrate specificity and it has thermal stability only in the presence of calcium. Although SGAP contains a calcium binding site, it is not conserved in many members of this subfamily. SGAP is present in the extracellular fluid of S. griseus cultures. 289 matched cddid_all.tbl CDD cd03877 cd03877 349874 M28_like M28 Zn-peptidase, many containing a protease-associated (PA) domain insert. Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. This subfamily is composed of uncharacterized proteins, many of which contain a protease-associated (PA) domain insert which may participate in substrate binding and/or promote conformational changes, influencing the stability and accessibility of the site to substrate. Some proteins in this subfamily are also associated with the PDZ domain, a widespread protein module that has been recruited to serve multiple functions during the course of evolution. 206 matched cddid_all.tbl CDD cd03879 cd03879 349875 M28_AAP M28 Zn-peptidase Aeromonas (Vibrio) proteolytica aminopeptidase. Peptidase family M28; Aeromonas (Vibrio) proteolytica aminopeptidase (AAP; leucine aminopeptidase from Vibrio proteolyticus; Bacterial leucyl aminopeptidase; E.C. 3.4.11.10) subfamily. AAP is a small (32kDa), heat stable leucine aminopeptidase and is active as a monomer. Similar forms of the enzyme have been isolated from Escherichia coli and Staphylococcus thermophilus. Leucine aminopeptidases, in general, play important roles in many biological processes such as protein catabolism, hormone degradation, regulation of migration and cell proliferation, as well as HIV infection and proliferation. AAP is a broad-specificity enzyme, utilizing two zinc(II) ions in its active site to remove N-terminal amino acids, with preference for large hydrophobic amino acids in the P1 position of the substrate, Leu being the most efficiently cleaved. It can accommodate all residues, except Pro, Asp and Glu in the P1' position. 286 matched cddid_all.tbl CDD cd03880 cd03880 349876 M28_QC_like M28 Zn-peptidase glutaminyl cyclase. Peptidase M28 family, glutaminyl cyclase (QC; EC 2.3.2.5) subfamily. QC is involved in N-terminal glutamine cyclization of many endocrine peptides and is typically abundant in brain tissue. N-terminal glutamine residue cyclization is an important post-translational event in the processing of numerous bioactive proteins, including neuropeptides, hormones, and cytokines during their maturation in the secretory pathway. The N-terminal pGlu protects them from exopeptidase degradation and/or enables them to have proper conformation for binding to their receptors. QCs are highly conserved from yeast to human. In humans, several genetic diseases, such as osteoporosis, appear to result from mutations of the QC gene. N-terminal glutamate cyclization into pyroglutamate (pGlu) is a reaction that may be related to the formation of several plaque-forming peptides, such as amyloid-(A) peptides and collagen-like Alzheimer amyloid plaque component, which play a pivotal role in Alzheimer's disease. 305 matched cddid_all.tbl CDD cd03881 cd03881 349877 M28_Nicastrin M28 Zn-peptidase nicastrin, a main component of gamma-secretase complex. Peptidase M28 family, nicastrin subfamily. Nicastrin is a main component of the gamma-secretase complex, which also contains presenilin, Pen-2 and Aph-1. Its extracellular domain sequence resembles aminopeptidases, but certain catalytic residues are not conserved. It is mainly localized to the endoplasmic reticulum and Golgi. It is highly glycosylated (Mr 120 kDa) and is essential for substrate recognition of the N-terminus of gamma-secretase substrates derived from APP and Notch. Nicastrin facilitates substrate cleavage by the catalytic presenilin subunit in the gamma-secretase complex. One conserved glutamate is especially important, probably because this residue forms an ion pair with the amino terminus of the substrate. This substrate-binding domain is often called the DAP domain (named after DYIGS, the amino acid stretch that modulates amyloid precursor protein (APP) processing, and Peptidase homologous region). The sequence of the substrate N-terminus is apparently not critical for the interaction, but a free amino group is. Thus, nicastrin can be considered a kind of gatekeeper for the gamma-secretase complex: type I membrane proteins that have not shed their ectodomains cannot interact properly with nicastrin and do not gain access to the active site. Dysfunction of gamma-secretase is thought to cause Alzheimer's disease, with most mutations derived from Alzheimer's disease mapping to the catalytic subunit presenilin 1 (PS1). 519 matched cddid_all.tbl CDD cd03882 cd03882 349878 M28_nicalin_like M28 Zn-Peptidase Nicalin, Nicastrin-like protein. Peptidase M28 family, Nicalin (nicastrin-like protein) subfamily. Nicalin is distantly related to Nicastrin, a component of the Alzheimer's disease-associated gamma-secretase, and forms a complex with Nomo (nodal modulator) pM5. Similar to Nicastrin, Nicalin lacks the amino-acid conservation required for catalytically active aminopeptidases. Functional studies in zebrafish embryos and cultured human cells reveal that nicalin and Nomo collaborate to antagonize the Nodal/TGFbeta signaling pathway. Thus, nicastrin and nicalin are both associated with protein complexes involved in cell fate decisions during early embryonic development. 296 matched cddid_all.tbl CDD cd03883 cd03883 349879 M28_Pgcp_like M28 Zn-Peptidase Plasma glutamate carboxypeptidase. Peptidase M28 family; Plasma glutamate carboxypeptidase (PGCP; blood plasma glutamate carboxypeptidase; EC 3.4.17.21) subfamily. PGCP is a 56kDa glutamate carboxypeptidase that is mainly produced in mammalian placenta and kidney, the majority of which is thought to be secreted into the bloodstream. Similar proteins are also found in other species, including bacteria. These proteins contain protease-associated (PA) domain inserts between the first and second strands of the central beta sheet in the protease-like domain. The PA domains may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. The exact physiological substrates of PGCP are unknown, although this enzyme may play an important role in the hydrolysis of circulating peptides. Its closest homolog encodes an important brain glutamate carboxypeptidase II (NAALADase) identical to the prostate-specific membrane antigen (PSMA), which serves as a marker for prostatic cancer metastasis. Hypermethylation of PGCP gene has been associated with human bronchial epithelial (HBE) cell immortalization and lung cancer. PGCP also provides an attractive target for serological analysis in hepatitis C virus (HCV)-induced hepatocellular carcinoma (HCC) patients. 425 matched cddid_all.tbl CDD cd03884 cd03884 349880 M20_bAS M20 Peptidase beta-alanine synthase, an amidohydrolase. Peptidase M20 family, beta-alanine synthase (bAS; N-carbamoyl-beta-alanine amidohydrolase and beta-ureidopropionase; EC 3.5.1.6) subfamily. bAS is an amidohydrolase and is the final enzyme in the pyrimidine catabolic pathway, which is involved in the regulation of the cellular pyrimidine pool. bAS catalyzes the irreversible hydrolysis of the N-carbamylated beta-amino acids to beta-alanine or aminoisobutyrate with the release of carbon dioxide and ammonia. Also included in this subfamily is allantoate amidohydrolase (allantoate deiminase), which catalyzes the conversion of allantoate to (S)-ureidoglycolate, one of the crucial alternate steps in purine metabolism. It is possible that these two enzymes arose from the same ancestral peptidase that evolved into two structurally related enzymes with distinct catalytic properties and biochemical roles within the cell. Downstream enzyme (S)-ureidoglycolate amidohydrolase (UAH) is homologous in structure and sequence with AAH and catalyzes the conversion of (S)-ureidoglycolate into glyoxylate, releasing two molecules of ammonia as by-products. Yeast requires beta-alanine as a precursor of pantothenate and coenzyme A biosynthesis, but generates it mostly via degradation of spermine. Disorders in pyrimidine degradation and beta-alanine metabolism caused by beta-ureidopropionase deficiency (UPB1 gene) in humans are normally associated with neurological disorders. 398 matched cddid_all.tbl CDD cd03885 cd03885 349881 M20_CPDG2 M20 Peptidase Glutamate carboxypeptidase, a periplasmic enzyme. Peptidase M20 family, Glutamate carboxypeptidase (carboxypeptidase G; carboxypeptidase G1; carboxypeptidase G2; CPDG2; CPG2; Folate hydrolase G2; Pteroylmonoglutamic acid hydrolase G2; Glucarpidase; E.C. 3.4.17.11) subfamily. CPDG2 is a periplasmic enzyme that is synthesized with a signal peptide. It is a dimeric zinc-dependent exopeptidase, with two domains, a catalytic domain, which provides the ligands for the two zinc ions in the active site, and a dimerization domain. CPDG2 cleaves the C-terminal glutamate moiety from a wide range of N-acyl groups, including peptidyl, aminoacyl, benzoyl, benzyloxycarbonyl, folyl, and pteroyl groups to release benzoic acid, phenol, and aniline mustards. It is used clinically to treat methotrexate toxicity by hydrolyzing it to inactive and non-toxic metabolites. It is also proposed for use in antibody-directed enzyme prodrug therapy; for example, glutamate can be cleaved from glutamated benzoyl nitrogen mustards, producing nitrogen mustards with effective cytotoxicity against tumor cells. 362 matched cddid_all.tbl CDD cd03886 cd03886 349882 M20_Acy1 M20 Peptidase Aminoacylase 1 family. Peptidase M20 family, Aminoacylase 1 (ACY1; hippuricase; acylase I; amido acid deacylase; IAA-amino acid hydrolase; dehydropeptidase II; N-acyl-L-amino-acid amidohydrolase; EC 3.5.1.14) subfamily. ACY1 is the most abundant of the aminoacylases, a class of zinc binding homodimeric enzymes involved in the hydrolysis of N-acetylated proteins. It is encoded by the aminoacylase 1 gene (Acy1) on chromosome 3p21 that comprises 15 exons. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in the protection and stability of proteins. Several types of aminoacylases can be distinguished on the basis of substrate specificity; substrates include indoleacetic acid (IAA) N-conjugates of amino acids, N-acetyl-L-amino acids and aminobenzoylglutamate. ACY1 breaks down cytosolic aliphatic N-acyl-alpha-amino acids (except L-aspartate), especially N-acetyl-methionine and acetyl-glutamate into L-amino acids and an acyl group. However, ACY1 can also catalyze the reverse reaction, the synthesis of acetylated amino acids. ACY1 may also play a role in xenobiotic bioactivation as well as the inter-organ processing of amino acid-conjugated xenobiotic derivatives (S-substituted-N-acetyl-L-cysteine). ACY1 appears to physically interact with Sphingosine kinase type 1 (SphK1) and may influence its physiological functions; SphK1 and its product sphingosine-1-phosphate have been shown to promote cell growth and inhibit apoptosis of tumor cells. Strong expression of the human gene and its mouse ortholog Acy1 in brain, liver, and kidney, suggest a role of the enzyme in amino acid metabolism of these organs. Defects in ACY1 are the cause of aminoacylase-1 deficiency (ACY1D), resulting in a metabolic disorder manifesting encephalopathy and psychomotor delay. 371 matched cddid_all.tbl CDD cd03887 cd03887 349883 M20_Acy1L2 M20 Peptidase Aminoacylase 1-like protein 2, amidohydrolase family. Peptidase M20 family, Aminoacylase 1-like protein 2 (ACY1L2; amidohydrolase) subfamily. This group contains many uncharacterized proteins predicted as amidohydrolases, including gene products of abgA and abgB that catalyze the cleavage of p-aminobenzoyl-glutamate, a folate catabolite in Escherichia coli, to p-aminobenzoate and glutamate. p-Aminobenzoyl-glutamate utilization is catalyzed by the abg region gene product, AbgT. Aminoacylase 1 (ACY1) proteins are a class of zinc binding homodimeric enzymes involved in hydrolysis of N-acetylated proteins. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in the protection and stability of proteins. Several types of aminoacylases can be distinguished on the basis of substrate specificity. ACY1 breaks down cytosolic aliphatic N-acyl-alpha-amino acids (except L-aspartate), especially N-acetyl-methionine and acetyl-glutamate into L-amino acids and an acyl group. However, ACY1 can also catalyze the reverse reaction, the synthesis of acetylated amino acids. ACY1 may also play a role in xenobiotic bioactivation as well as the inter-organ processing of amino acid-conjugated xenobiotic derivatives (S-substituted-N-acetyl-L-cysteine). 360 matched cddid_all.tbl CDD cd03888 cd03888 349884 M20_PepV M20 Peptidase Xaa-His dipeptidase (PepV) degrades hydrophobic dipeptides. Peptidase M20 family, Peptidase V (Xaa-His dipeptidase; PepV g.p. (Lactobacillus lactis); X-His dipeptidase; beta-Ala-His dipeptidase; carnosinase) subfamily. The PepV group of proteins is widely distributed in lactic acid bacteria. PepV, along with PepT, functions at the end of the proteolytic processing system. PepV is a monomeric metalloenzyme that preferentially degrades hydrophobic dipeptides. The Streptococcus gordonii PepV gene is homologous to the PepV gene family from Lactobacillus and Lactococcus spp. PepV recognizes and fixes the dipeptide backbone, while the side chains are not specifically probed and can vary, rendering it a nonspecific dipeptidase. It has been shown that Lactococcus lactis subspecies lactis (L9) PepV does not hydrolyze dipeptides containing Pro or D-amino acids at the C-terminus, while PepV from Lactobaccilus has been shown to have L-carnosine hydrolyzing activity. The mammalian PepV also acts on anserine and homocarnosine (but not on homoanserine), and to a lesser extent on some other aminoacyl-L-histidine dipeptides. Also included is the Staphylococcus aureus metallopeptidase, Sapep, a Mn(2+)-dependent dipeptidase where large interdomain movements could potentially regulate the activity of this enzyme. 449 matched cddid_all.tbl CDD cd03890 cd03890 349885 M20_pepD M20 Peptidase D has specificity for beta-alanyl-L-histidine dipeptide. Peptidase M20 family, Peptidase D (PepD, Xaa-His dipeptidase; X-His dipeptidase; aminoacylhistidine dipeptidase; dipeptidase D; Beta-alanyl-histidine dipeptidase; pepD g.p. (Escherichia coli); EC 3.4.13.3) subfamily. PepD is a cytoplasmic enzyme family characterized by its unusual specificity for the dipeptides beta-alanyl-L-histidine (L-carnosine or beta-Ala-His) and gamma-aminobutyryl histidine (L-homocarnosine or gamma-amino-butyl-His). Homocarnosine has been suggested as a precursor for the neurotransmitter gamma-aminobutyric acid (GABA), acting as a GABA reservoir, and may mediate anti-seizure effects of GABAergic therapies. It has also been reported that glucose metabolism could be influenced by L-carnosine. PepD also includes a lid domain that forms a homodimer; however, the physiological function of this extra domain remains unclear. 474 matched cddid_all.tbl CDD cd03891 cd03891 349886 M20_DapE_proteobac M20 Peptidase proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase. Peptidase M20 family, proteobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE; aspartyl dipeptidase; succinyl-diaminopimelate desuccinylase) subfamily. DapE catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelate (L,L-SDAP) to L,L-diaminopimelate and succinate. It has been shown that DapE is essential for cell growth and proliferation. DapEs have been purified from Escherichia coli and Haemophilus influenzae, while the genes that encode for DapEs have been sequenced from several bacterial sources such as Corynebacterium glutamicum, Helicobacter pylori, Neisseria meningitidis and Mycobacterium tuberculosis. DapE is a small, dimeric enzyme that requires two zinc atoms per molecule for full enzymatic activity. All of the amino acids that function as metal binding ligands are strictly conserved in DapE. 366 matched cddid_all.tbl CDD cd03892 cd03892 349887 M20_peptT M20 Peptidase T specifically cleaves tripeptides. Peptidase M20 family, Peptidase T (peptT; tripeptide aminopeptidase; tripeptidase) subfamily. PepT acts only on tripeptide substrates, and is thus called a tripeptidase. It catalyzes the release of N-terminal amino acids with hydrophobic side chains from tripeptides with high specificity; dipeptides, tetrapeptides or tripeptides with the N-terminus blocked are not cleaved. Tripeptidases are known to function at the final stage of proteolysis in lactococcal bacteria and release amino acids from tripeptides produced during the digestion of milk proteins such as casein. 400 matched cddid_all.tbl CDD cd03893 cd03893 349888 M20_Dipept_like M20 Dipeptidases. Peptidase M20 family, dipeptidase-like subfamily. This group contains a large variety of enzymes, including cytosolic nonspecific dipeptidase (CNDP), Xaa-methyl-His dipeptidase (anserinase), canosinase, DUG2 type proteins, as well as many proteins inferred by homology to be dipeptidases. These enzymes have been shown to act on a wide range of dipeptides, but not larger peptides. For example, anserinase mainly catalyzes the hydrolysis of N-alpha-acetylhistidine while carnosinase degrades beta-alanyl-L-histidine. Substrates of CNDP are varied and not limited to Xaa-His dipeptides. DUG2 proteins contain a metallopeptidase domain and a large N-terminal WD40 repeat region, and are involved in the alternative pathway of glutathione degradation. 426 matched cddid_all.tbl CDD cd03894 cd03894 349889 M20_ArgE M20 Peptidase acetylornithine deacetylase. Peptidase M20 family, acetylornithine deacetylase (ArgE, Acetylornithinase, AO, N2-acetyl-L-ornithine amidohydrolase, EC 3.5.1.16) subfamily. ArgE catalyzes the conversion of N-acetylornithine to ornithine, which can then be incorporated into the urea cycle for the final stage of arginine synthesis. The substrate specificity of ArgE is quite broad; several alpha-N-acyl-L-amino acids can be hydrolyzed, including alpha-N-acetylmethionine and alpha-N-formylmethionine. ArgE shares significant sequence homology and biochemical features, and possibly a common origin, with glutamate carboxypeptidase (CPG2) and succinyl-diaminopimelate desuccinylase (DapE), and aminoacylase I (ACY1), having all metal ligand binding residues conserved. 367 matched cddid_all.tbl CDD cd03895 cd03895 349890 M20_ArgE_DapE-like M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases. Peptidase M20 family, uncharacterized protein subfamily with similarity to acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE) subfamily. ArgE/DapE enzymes catalyze analogous reactions and share a common activator, the metal ion (usually Co2+ or Zn2+). ArgE catalyzes a broad range of substrates, including N-acetylornithine, alpha-N-acetylmethionine and alpha-N-formylmethionine, while DapE catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelate (L,L-SDAP) to L,L-diaminopimelate and succinate. Proteins in this subfamily are mostly bacterial, and have been inferred by homology as being related to both ArgE and DapE. 400 matched cddid_all.tbl CDD cd03896 cd03896 349891 M20_PAAh_like M20 Peptidases, Poly(aspartic acid) hydrolase-like proteins. Peptidase M20 family, Poly(aspartic acid) hydrolase (PAA hydrolase)-like subfamily. PAA hydrolase enzymes are involved in alpha,beta-poly(D,L-aspartic acid) (tPAA) biodegradation. PAA is being extensively studied as a replacement for commercial polycarboxylate components since it can be degraded by enzymes from isolated tPAA degrading bacteria. Thus far, two types of PAA degrading bacteria (Sphingomonas sp. KT-1 and Pedobacter sp. KP-2) have been investigated in detail; the former can completely degrade tPAA of low-molecular weights below 5000, while the latter can degrade high molecular weight tPAA to release oligo(aspartic acid) (OAA) as a product, suggesting two kinds of PAA degrading enzymes. It has been shown that PAA hydrolase-1 from Sphingomonas sp. KT-1 hydrolyzes beta,beta-aspartic acid units in tPAA to produce OAA, and it is suggested that PAA hydrolase-2 hydrolyzes OAA to aspartic acid. Also included in this family is Bradyrhizobium 5-nitroanthranilic acid (5NAA)-aminohydrolase (5NAA-A), a biodegradation enzyme that converts 5NAA to 5-nitrosalicylic acid; 5NAA is a metabolite secreted by Streptomyces scabies, the bacterium responsible for potato scab, and metabolized by Bradyrhizobium species strain JS329. 357 matched cddid_all.tbl CDD cd04009 cd04009 175976 C2B_Munc13-like C2 domain second repeat in Munc13 (mammalian uncoordinated)-like proteins. C2-like domains are thought to be involved in phospholipid binding in a Ca2+ independent manner in both Unc13 and Munc13. Caenorabditis elegans Unc13 has a central domain with sequence similarity to PKC, which includes C1 and C2-related domains. Unc13 binds phorbol esters and DAG with high affinity in a phospholipid manner. Mutations in Unc13 results in abnormal neuronal connections and impairment in cholinergic neurotransmission in the nematode. Munc13 is the mammalian homolog which are expressed in the brain. There are 3 isoforms (Munc13-1, -2, -3) and are thought to play a role in neurotransmitter release and are hypothesized to be high-affinity receptors for phorbol esters. Unc13 and Munc13 contain both C1 and C2 domains. There are two C2 related domains present, one central and one at the carboxyl end. Munc13-1 contains a third C2-like domain. Munc13 interacts with syntaxin, synaptobrevin, and synaptotagmin suggesting a role for these as scaffolding proteins. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the third C2 repeat, C2C, and has a type-II topology. 133 matched cddid_all.tbl CDD cd04010 cd04010 175977 C2B_RasA3 C2 domain second repeat present in RAS p21 protein activator 3 (RasA3). RasA3 are members of GTPase activating protein 1 (GAP1), a Ras-specific GAP, which suppresses Ras function by enhancing the GTPase activity of Ras proteins resulting in the inactive GDP-bound form of Ras. In this way it can control cellular proliferation and differentiation. RasA3 contains an N-terminal C2 domain, a Ras-GAP domain, a plextrin homology (PH)-like domain, and a Bruton's Tyrosine Kinase (BTK) zinc binding domain. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-I topology. 148 matched cddid_all.tbl CDD cd04011 cd04011 175978 C2B_Ferlin C2 domain second repeat in Ferlin. Ferlins are involved in vesicle fusion events. Ferlins and other proteins, such as Synaptotagmins, are implicated in facilitating the fusion process when cell membranes fuse together. There are six known human Ferlins: Dysferlin (Fer1L1), Otoferlin (Fer1L2), Myoferlin (Fer1L3), Fer1L4, Fer1L5, and Fer1L6. Defects in these genes can lead to a wide range of diseases including muscular dystrophy (dysferlin), deafness (otoferlin), and infertility (fer-1, fertilization factor-1). Structurally they have 6 tandem C2 domains, designated as (C2A-C2F) and a single C-terminal transmembrane domain, though there is a new study that disputes this and claims that there are actually 7 tandem C2 domains with another C2 domain inserted between C2D and C2E. In a subset of them (Dysferlin, Myoferlin, and Fer1) there is an additional conserved domain called DysF. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-II topology. 111 matched cddid_all.tbl CDD cd04012 cd04012 175979 C2A_PI3K_class_II C2 domain first repeat present in class II phosphatidylinositol 3-kinases (PI3Ks). There are 3 classes of PI3Ks based on structure, regulation, and specificity. All classes contain a N-terminal C2 domain, a PIK domain, and a kinase catalytic domain. Unlike class I and class III, class II PI3Ks have additionally a PX domain and a C-terminal C2 domain containing a nuclear localization signal both of which bind phospholipids though in a slightly different fashion. Class II PIK3s act downstream of receptors for growth factors, integrins, and chemokines. PI3Ks (AKA phosphatidylinositol (PtdIns) 3-kinases) regulate cell processes such as cell growth, differentiation, proliferation, and motility. PI3Ks work on phosphorylation of phosphatidylinositol, phosphatidylinositide (4)P (PtdIns (4)P),2 or PtdIns(4,5)P2. Specifically they phosphorylate the D3 hydroxyl group of phosphoinositol lipids on the inositol ring. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-I topology. 171 matched cddid_all.tbl CDD cd04013 cd04013 175980 C2_SynGAP_like C2 domain present in Ras GTPase activating protein (GAP) family. SynGAP, GAP1, RasGAP, and neurofibromin are all members of the Ras-specific GAP (GTPase-activating protein) family. SynGAP regulates the MAP kinase signaling pathway and is critical for cognition and synapse function. Mutations in this gene causes mental retardation in humans. SynGAP contains a PH-like domain, a C2 domain, and a Ras-GAP domain. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 146 matched cddid_all.tbl CDD cd04014 cd04014 175981 C2_PKC_epsilon C2 domain in Protein Kinase C (PKC) epsilon. A single C2 domain is found in PKC epsilon. The PKC family of serine/threonine kinases regulates apoptosis, proliferation, migration, motility, chemo-resistance, and differentiation. There are 3 groups: group 1 (alpha, betaI, beta II, gamma) which require phospholipids and calcium, group 2 (delta, epsilon, theta, eta) which do not require calcium for activation, and group 3 (xi, iota/lambda) which are atypical and can be activated in the absence of diacylglycerol and calcium. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. Members here have a type-II topology. 132 matched cddid_all.tbl CDD cd04015 cd04015 175982 C2_plant_PLD C2 domain present in plant phospholipase D (PLD). PLD hydrolyzes terminal phosphodiester bonds in diester glycerophospholipids resulting in the degradation of phospholipids. In vitro PLD transfers phosphatidic acid to primary alcohols. In plants PLD plays a role in germination, seedling growth, phosphatidylinositol metabolism, and changes in phospholipid composition. There is a single Ca(2+)/phospholipid-binding C2 domain in PLD. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 158 matched cddid_all.tbl CDD cd04016 cd04016 175983 C2_Tollip C2 domain present in Toll-interacting protein (Tollip). Tollip is a part of the Interleukin-1 receptor (IL-1R) signaling pathway. Tollip is proposed to link serine/threonine kinase IRAK to IL-1Rs as well as inhibiting phosphorylation of IRAK. There is a single C2 domain present in Tollip. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 121 matched cddid_all.tbl CDD cd04017 cd04017 175984 C2D_Ferlin C2 domain fourth repeat in Ferlin. Ferlins are involved in vesicle fusion events. Ferlins and other proteins, such as Synaptotagmins, are implicated in facilitating the fusion process when cell membranes fuse together. There are six known human Ferlins: Dysferlin (Fer1L1), Otoferlin (Fer1L2), Myoferlin (Fer1L3), Fer1L4, Fer1L5, and Fer1L6. Defects in these genes can lead to a wide range of diseases including muscular dystrophy (dysferlin), deafness (otoferlin), and infertility (fer-1, fertilization factor-1). Structurally they have 6 tandem C2 domains, designated as (C2A-C2F) and a single C-terminal transmembrane domain, though there is a new study that disputes this and claims that there are actually 7 tandem C2 domains with another C2 domain inserted between C2D and C2E. In a subset of them (Dysferlin, Myoferlin, and Fer1) there is an additional conserved domain called DysF. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the fourth C2 repeat, C2D, and has a type-II topology. 135 matched cddid_all.tbl CDD cd04018 cd04018 175985 C2C_Ferlin C2 domain third repeat in Ferlin. Ferlins are involved in vesicle fusion events. Ferlins and other proteins, such as Synaptotagmins, are implicated in facilitating the fusion process when cell membranes fuse together. There are six known human Ferlins: Dysferlin (Fer1L1), Otoferlin (Fer1L2), Myoferlin (Fer1L3), Fer1L4, Fer1L5, and Fer1L6. Defects in these genes can lead to a wide range of diseases including muscular dystrophy (dysferlin), deafness (otoferlin), and infertility (fer-1, fertilization factor-1). Structurally they have 6 tandem C2 domains, designated as (C2A-C2F) and a single C-terminal transmembrane domain, though there is a new study that disputes this and claims that there are actually 7 tandem C2 domains with another C2 domain inserted between C2D and C2E. In a subset of them (Dysferlin, Myoferlin, and Fer1) there is an additional conserved domain called DysF. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the third C2 repeat, C2C, and has a type-II topology. 151 matched cddid_all.tbl CDD cd04019 cd04019 175986 C2C_MCTP_PRT_plant C2 domain third repeat found in Multiple C2 domain and Transmembrane region Proteins (MCTP); plant subset. MCTPs are involved in Ca2+ signaling at the membrane. Plant-MCTPs are composed of a variable N-terminal sequence, four C2 domains, two transmembrane regions (TMRs), and a short C-terminal sequence. It is one of four protein classes that are anchored to membranes via a transmembrane region; the others being synaptotagmins, extended synaptotagmins, and ferlins. MCTPs are the only membrane-bound C2 domain proteins that contain two functional TMRs. MCTPs are unique in that they bind Ca2+ but not phospholipids. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the third C2 repeat, C2C, and has a type-II topology. 150 matched cddid_all.tbl CDD cd04020 cd04020 175987 C2B_SLP_1-2-3-4 C2 domain second repeat present in Synaptotagmin-like proteins 1-4. All Slp members basically share an N-terminal Slp homology domain (SHD) and C-terminal tandem C2 domains (named the C2A domain and the C2B domain) with the SHD and C2 domains being separated by a linker sequence of various length. Slp1/JFC1 and Slp2/exophilin 4 promote granule docking to the plasma membrane. Additionally, their C2A domains are both Ca2+ independent, unlike the case in Slp3 and Slp4/granuphilin in which their C2A domains are Ca2+ dependent. It is thought that SHD (except for the Slp4-SHD) functions as a specific Rab27A/B-binding domain. In addition to Slps, rabphilin, Noc2, and Munc13-4 also function as Rab27-binding proteins. It has been demonstrated that Slp3 and Slp4/granuphilin promote dense-core vesicle exocytosis. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-I topology. 162 matched cddid_all.tbl CDD cd04021 cd04021 175988 C2_E3_ubiquitin_ligase C2 domain present in E3 ubiquitin ligase. E3 ubiquitin ligase is part of the ubiquitylation mechanism responsible for controlling surface expression of membrane proteins. The sequential action of several enzymes are involved: ubiquitin-activating enzyme E1, ubiquitin-conjugating enzyme E2, and ubiquitin-protein ligase E3 which is responsible for substrate recognition and promoting the transfer of ubiquitin to the target protein. E3 ubiquitin ligase is composed of an N-terminal C2 domain, 4 WW domains, and a HECTc domain. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 125 matched cddid_all.tbl CDD cd04022 cd04022 175989 C2A_MCTP_PRT_plant C2 domain first repeat found in Multiple C2 domain and Transmembrane region Proteins (MCTP); plant subset. MCTPs are involved in Ca2+ signaling at the membrane. Plant-MCTPs are composed of a variable N-terminal sequence, four C2 domains, two transmembrane regions (TMRs), and a short C-terminal sequence. It is one of four protein classes that are anchored to membranes via a transmembrane region; the others being synaptotagmins, extended synaptotagmins, and ferlins. MCTPs are the only membrane-bound C2 domain proteins that contain two functional TMRs. MCTPs are unique in that they bind Ca2+ but not phospholipids. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-II topology. 127 matched cddid_all.tbl CDD cd04024 cd04024 175990 C2A_Synaptotagmin-like C2 domain first repeat present in Synaptotagmin-like proteins. Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-I topology. 128 matched cddid_all.tbl CDD cd04025 cd04025 175991 C2B_RasA1_RasA4 C2 domain second repeat present in RasA1 and RasA4. RasA1 and RasA4 are GAP1s (GTPase activating protein 1s ), Ras-specific GAP members, which suppresses Ras function by enhancing the GTPase activity of Ras proteins resulting in the inactive GDP-bound form of Ras. In this way it can control cellular proliferation and differentiation. Both proteins contain two C2 domains, a Ras-GAP domain, a plextrin homology (PH)-like domain, and a Bruton's Tyrosine Kinase (BTK) zinc binding domain. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-I topology. 123 matched cddid_all.tbl CDD cd04026 cd04026 175992 C2_PKC_alpha_gamma C2 domain in Protein Kinase C (PKC) alpha and gamma. A single C2 domain is found in PKC alpha and gamma. The PKC family of serine/threonine kinases regulates apoptosis, proliferation, migration, motility, chemo-resistance, and differentiation. There are 3 groups: group 1(alpha, betaI, beta II, gamma) which require phospholipids and calcium, group 2 (delta, epsilon, theta, eta) which do not require calcium for activation, and group 3 (xi, iota/lambda) which are atypical and can be activated in the absence of diacylglycerol and calcium. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. Members here have a type-I topology. 131 matched cddid_all.tbl CDD cd04027 cd04027 175993 C2B_Munc13 C2 domain second repeat in Munc13 (mammalian uncoordinated) proteins. C2-like domains are thought to be involved in phospholipid binding in a Ca2+ independent manner in both Unc13 and Munc13. Caenorabditis elegans Unc13 has a central domain with sequence similarity to PKC, which includes C1 and C2-related domains. Unc13 binds phorbol esters and DAG with high affinity in a phospholipid manner. Mutations in Unc13 results in abnormal neuronal connections and impairment in cholinergic neurotransmission in the nematode. Munc13 is the mammalian homolog which are expressed in the brain. There are 3 isoforms (Munc13-1, -2, -3) and are thought to play a role in neurotransmitter release and are hypothesized to be high-affinity receptors for phorbol esters. Unc13 and Munc13 contain both C1 and C2 domains. There are two C2 related domains present, one central and one at the carboxyl end. Munc13-1 contains a third C2-like domain. Munc13 interacts with syntaxin, synaptobrevin, and synaptotagmin suggesting a role for these as scaffolding proteins. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-II topology. 127 matched cddid_all.tbl CDD cd04028 cd04028 175994 C2B_RIM1alpha C2 domain second repeat contained in Rab3-interacting molecule (RIM) proteins. RIMs are believed to organize specialized sites of the plasma membrane called active zones. They also play a role in controlling neurotransmitter release, plasticity processes, as well as memory and learning. RIM contains an N-terminal zinc finger domain, a PDZ domain, and two C-terminal C2 domains (C2A, C2B). C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. Members here have a type-I topology and do not bind Ca2+. 146 matched cddid_all.tbl CDD cd04029 cd04029 175995 C2A_SLP-4_5 C2 domain first repeat present in Synaptotagmin-like proteins 4 and 5. All Slp members basically share an N-terminal Slp homology domain (SHD) and C-terminal tandem C2 domains (named the C2A domain and the C2B domain) with the SHD and C2 domains being separated by a linker sequence of various length. SHD of Slp (except for the Slp4-SHD) function as a specific Rab27A/B-binding domain. In addition to Slp, rabphilin, Noc2, and Munc13-4 also function as Rab27-binding proteins. It has been demonstrated that Slp4/granuphilin promotes dense-core vesicle exocytosis. The C2A domain of Slp4 is Ca2+ dependent. Slp5 mRNA has been shown to be restricted to human placenta and liver suggesting a role in Rab27A-dependent membrane trafficking in specific tissues. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-I topology. 125 matched cddid_all.tbl CDD cd04030 cd04030 175996 C2C_KIAA1228 C2 domain third repeat present in uncharacterized human KIAA1228-like proteins. KIAA proteins are uncharacterized human proteins. They were compiled by the Kazusa mammalian cDNA project which identified more than 2000 human genes. They are identified by 4 digit codes that precede the KIAA designation. Many KIAA genes are still functionally uncharacterized including KIAA1228. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the third C2 repeat, C2C, and has a type-II topology. 127 matched cddid_all.tbl CDD cd04031 cd04031 175997 C2A_RIM1alpha C2 domain first repeat contained in Rab3-interacting molecule (RIM) proteins. RIMs are believed to organize specialized sites of the plasma membrane called active zones. They also play a role in controlling neurotransmitter release, plasticity processes, as well as memory and learning. RIM contains an N-terminal zinc finger domain, a PDZ domain, and two C-terminal C2 domains (C2A, C2B). C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. Members here have a type-I topology and do not bind Ca2+. 125 matched cddid_all.tbl CDD cd04032 cd04032 175998 C2_Perforin C2 domain of Perforin. Perforin contains a single copy of a C2 domain in its C-terminus and plays a role in lymphocyte-mediated cytotoxicity. Mutations in perforin leads to familial hemophagocytic lymphohistiocytosis type 2. The function of perforin is calcium dependent and the C2 domain is thought to confer this binding to target cell membranes. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 127 matched cddid_all.tbl CDD cd04033 cd04033 175999 C2_NEDD4_NEDD4L C2 domain present in the Human neural precursor cell-expressed, developmentally down-regulated 4 (NEDD4) and NEDD4-like (NEDD4L/NEDD42). Nedd4 and Nedd4-2 are two of the nine members of the Human Nedd4 family. All vertebrates appear to have both Nedd4 and Nedd4-2 genes. They are thought to participate in the regulation of epithelial Na+ channel (ENaC) activity. They also have identical specificity for ubiquitin conjugating enzymes (E2). Nedd4 and Nedd4-2 are composed of a C2 domain, 2-4 WW domains, and a ubiquitin ligase Hect domain. Their WW domains can bind PPxY (PY) or LPSY motifs, and in vitro studies suggest that WW3 and WW4 of both proteins bind PY motifs in the key substrates, with WW3 generally exhibiting higher affinity. Most Nedd4 family members, especially Nedd4-2, also have multiple splice variants, which might play different roles in regulating their substrates. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 133 matched cddid_all.tbl CDD cd04035 cd04035 176000 C2A_Rabphilin_Doc2 C2 domain first repeat present in Rabphilin and Double C2 domain. Rabphilin is found neurons and in neuroendrocrine cells, while Doc2 is found not only in the brain but in tissues, including mast cells, chromaffin cells, and osteoblasts. Rabphilin and Doc2s share highly homologous tandem C2 domains, although their N-terminal structures are completely different: rabphilin contains an N-terminal Rab-binding domain (RBD),7 whereas Doc2 contains an N-terminal Munc13-1-interacting domain (MID). C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-I topology. 123 matched cddid_all.tbl CDD cd04036 cd04036 176001 C2_cPLA2 C2 domain present in cytosolic PhosphoLipase A2 (cPLA2). A single copy of the C2 domain is present in cPLA2 which releases arachidonic acid from membranes initiating the biosynthesis of potent inflammatory mediators such as prostaglandins, leukotrienes, and platelet-activating factor. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. Members of this cd have a type-II topology. 119 matched cddid_all.tbl CDD cd04037 cd04037 176002 C2E_Ferlin C2 domain fifth repeat in Ferlin. Ferlins are involved in vesicle fusion events. Ferlins and other proteins, such as Synaptotagmins, are implicated in facilitating the fusion process when cell membranes fuse together. There are six known human Ferlins: Dysferlin (Fer1L1), Otoferlin (Fer1L2), Myoferlin (Fer1L3), Fer1L4, Fer1L5, and Fer1L6. Defects in these genes can lead to a wide range of diseases including muscular dystrophy (dysferlin), deafness (otoferlin), and infertility (fer-1, fertilization factor-1). Structurally they have 6 tandem C2 domains, designated as (C2A-C2F) and a single C-terminal transmembrane domain, though there is a new study that disputes this and claims that there are actually 7 tandem C2 domains with another C2 domain inserted between C2D and C2E. In a subset of them (Dysferlin, Myoferlin, and Fer1) there is an additional conserved domain called DysF. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the fifth C2 repeat, C2E, and has a type-II topology. 124 matched cddid_all.tbl CDD cd04038 cd04038 176003 C2_ArfGAP C2 domain present in Arf GTPase Activating Proteins (GAP). ArfGAP is a GTPase activating protein which regulates the ADP ribosylation factor Arf, a member of the Ras superfamily of GTP-binding proteins. The GTP-bound form of Arf is involved in Golgi morphology and is involved in recruiting coat proteins. ArfGAP is responsible for the GDP-bound form of Arf which is necessary for uncoating the membrane and allowing the Golgi to fuse with an acceptor compartment. These proteins contain an N-terminal ArfGAP domain containing the characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) and C-terminal C2 domain. C2 domains were first identified in Protein Kinase C (PKC). C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 145 matched cddid_all.tbl CDD cd04039 cd04039 176004 C2_PSD C2 domain present in Phosphatidylserine decarboxylase (PSD). PSD is involved in the biosynthesis of aminophospholipid by converting phosphatidylserine (PtdSer) to phosphatidylethanolamine (PtdEtn). There is a single C2 domain present and it is thought to confer PtdSer binding motif that is common to PKC and synaptotagmin. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 108 matched cddid_all.tbl CDD cd04040 cd04040 176005 C2D_Tricalbin-like C2 domain fourth repeat present in Tricalbin-like proteins. 5 to 6 copies of the C2 domain are present in Tricalbin, a yeast homolog of Synaptotagmin, which is involved in membrane trafficking and sorting. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the fifth C2 repeat, C2E, and has a type-II topology. 115 matched cddid_all.tbl CDD cd04041 cd04041 176006 C2A_fungal C2 domain first repeat; fungal group. C2 domains were first identified in Protein Kinase C (PKC). C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 111 matched cddid_all.tbl CDD cd04042 cd04042 176007 C2A_MCTP_PRT C2 domain first repeat found in Multiple C2 domain and Transmembrane region Proteins (MCTP). MCTPs are involved in Ca2+ signaling at the membrane. MCTP is composed of a variable N-terminal sequence, three C2 domains, two transmembrane regions (TMRs), and a short C-terminal sequence. It is one of four protein classes that are anchored to membranes via a transmembrane region; the others being synaptotagmins, extended synaptotagmins, and ferlins. MCTPs are the only membrane-bound C2 domain proteins that contain two functional TMRs. MCTPs are unique in that they bind Ca2+ but not phospholipids. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-II topology. 121 matched cddid_all.tbl CDD cd04043 cd04043 176008 C2_Munc13_fungal C2 domain in Munc13 (mammalian uncoordinated) proteins; fungal group. C2-like domains are thought to be involved in phospholipid binding in a Ca2+ independent manner in both Unc13 and Munc13. Caenorabditis elegans Unc13 has a central domain with sequence similarity to PKC, which includes C1 and C2-related domains. Unc13 binds phorbol esters and DAG with high affinity in a phospholipid manner. Mutations in Unc13 results in abnormal neuronal connections and impairment in cholinergic neurotransmission in the nematode. Munc13 is the mammalian homolog which are expressed in the brain. There are 3 isoforms (Munc13-1, -2, -3) and are thought to play a role in neurotransmitter release and are hypothesized to be high-affinity receptors for phorbol esters. Unc13 and Munc13 contain both C1 and C2 domains. There are two C2 related domains present, one central and one at the carboxyl end. Munc13-1 contains a third C2-like domain. Munc13 interacts with syntaxin, synaptobrevin, and synaptotagmin suggesting a role for these as scaffolding proteins. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-II topology. 126 matched cddid_all.tbl CDD cd04044 cd04044 176009 C2A_Tricalbin-like C2 domain first repeat present in Tricalbin-like proteins. 5 to 6 copies of the C2 domain are present in Tricalbin, a yeast homolog of Synaptotagmin, which is involved in membrane trafficking and sorting. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-II topology. 124 matched cddid_all.tbl CDD cd04045 cd04045 176010 C2C_Tricalbin-like C2 domain third repeat present in Tricalbin-like proteins. 5 to 6 copies of the C2 domain are present in Tricalbin, a yeast homolog of Synaptotagmin, which is involved in membrane trafficking and sorting. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the third C2 repeat, C2C, and has a type-II topology. 120 matched cddid_all.tbl CDD cd04046 cd04046 176011 C2_Calpain C2 domain present in Calpain proteins. A single C2 domain is found in calpains (EC 3.4.22.52, EC 3.4.22.53), calcium-dependent, non-lysosomal cysteine proteases. Caplains are classified as belonging to Clan CA by MEROPS and include six families: C1, C2, C10, C12, C28, and C47. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 126 matched cddid_all.tbl CDD cd04047 cd04047 176012 C2B_Copine C2 domain second repeat in Copine. There are 2 copies of the C2 domain present in copine, a protein involved in membrane trafficking, protein-protein interactions, and perhaps even cell division and growth. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-I topology. 110 matched cddid_all.tbl CDD cd04048 cd04048 176013 C2A_Copine C2 domain first repeat in Copine. There are 2 copies of the C2 domain present in copine, a protein involved in membrane trafficking, protein-protein interactions, and perhaps even cell division and growth. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-I topology. 120 matched cddid_all.tbl CDD cd04049 cd04049 176014 C2_putative_Elicitor-responsive_gene C2 domain present in the putative elicitor-responsive gene. In plants elicitor-responsive proteins are triggered in response to specific elicitor molecules such as glycolproteins, peptides, carbohydrates and lipids. A host of defensive responses are also triggered resulting in localized cell death. Antimicrobial secondary metabolites, such as phytoalexins, or defense-related proteins, including pathogenesis-related (PR) proteins are also produced. There is a single C2 domain present here. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. Members have a type-II topology. 124 matched cddid_all.tbl CDD cd04050 cd04050 176015 C2B_Synaptotagmin-like C2 domain second repeat present in Synaptotagmin-like proteins. Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-I topology. 105 matched cddid_all.tbl CDD cd04051 cd04051 176016 C2_SRC2_like C2 domain present in Soybean genes Regulated by Cold 2 (SRC2)-like proteins. SRC2 production is a response to pathogen infiltration. The initial response of increased Ca2+ concentrations are coupled to downstream signal transduction pathways via calcium binding proteins. SRC2 contains a single C2 domain which localizes to the plasma membrane and is involved in Ca2+ dependent protein binding. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 125 matched cddid_all.tbl CDD cd04052 cd04052 176017 C2B_Tricalbin-like C2 domain second repeat present in Tricalbin-like proteins. 5 to 6 copies of the C2 domain are present in Tricalbin, a yeast homolog of Synaptotagmin, which is involved in membrane trafficking and sorting. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-II topology. 111 matched cddid_all.tbl CDD cd04054 cd04054 176018 C2A_Rasal1_RasA4 C2 domain first repeat present in RasA1 and RasA4. Rasal1 and RasA4 are both members of GAP1 (GTPase activating protein 1). Rasal1 responds to repetitive Ca2+ signals by associating with the plasma membrane and deactivating Ras. RasA4 suppresses Ras function by enhancing the GTPase activity of Ras proteins resulting in the inactive GDP-bound form of Ras. In this way it can control cellular proliferation and differentiation. Both of these proteins contains two C2 domains, a Ras-GAP domain, a plextrin homology (PH)-like domain, and a Bruton's Tyrosine Kinase (BTK) zinc binding domain. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-I topology. 121 matched cddid_all.tbl CDD cd04056 cd04056 173788 Peptidases_S53 Peptidase domain in the S53 family. Members of the peptidases S53 (sedolisin) family include endopeptidases and exopeptidases sedolisin, kumamolysin, and (PSCP) Pepstatin-insensitive Carboxyl Proteinase. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of Asn in subtilisin. The stability of these enzymes may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. Characterized sedolisins include Kumamolisin, an extracellular calcium-dependent thermostable endopeptidase from Bacillus. The enzyme is synthesized with a 188 amino acid N-terminal preprotein region which is cleaved after the extraction into the extracellular space with low pH. One kumamolysin paralog, kumamolisin-As, is believed to be a collagenase. TPP1 is a serine protease that functions as a tripeptidyl exopeptidase as well as an endopeptidase. Less is known about PSCP from Pseudomonas which is thought to be an aspartic proteinase. 361 matched cddid_all.tbl CDD cd04059 cd04059 173789 Peptidases_S8_Protein_convertases_Kexins_Furin-like Peptidase S8 family domain in Protein convertases. Protein convertases, whose members include furins and kexins, are members of the peptidase S8 or Subtilase clan of proteases. They have an Asp/His/Ser catalytic triad that is not homologous to trypsin. Kexins are involved in the activation of peptide hormones, growth factors, and viral proteins. Furin cleaves cell surface vasoactive peptides and proteins involved in cardiovascular tissue remodeling in the TGN, at cell surface, or in endosomes but rarely in the ER. Furin also plays a key role in blood pressure regulation though the activation of transforming growth factor (TGF)-beta. High specificity is seen for cleavage after dibasic (Lys-Arg or Arg-Arg) or multiple basic residues in protein convertases. There is also strong sequence conservation. 297 matched cddid_all.tbl CDD cd04077 cd04077 173790 Peptidases_S8_PCSK9_ProteinaseK_like Peptidase S8 family domain in ProteinaseK-like proteins. The peptidase S8 or Subtilase clan of proteases have a Asp/His/Ser catalytic triad that is not homologous to trypsin. This CD contains several members of this clan including: PCSK9 (Proprotein convertase subtilisin/kexin type 9), Proteinase_K, Proteinase_T, and other subtilisin-like serine proteases. PCSK9 posttranslationally regulates hepatic low-density lipoprotein receptors (LDLRs) by binding to LDLRs on the cell surface, leading to their degradation. The binding site of PCSK9 has been localized to the epidermal growth factor-like repeat A (EGF-A) domain of the LDLR. Characterized Proteinases K are secreted endopeptidases with a high degree of sequence conservation. Proteinases K are not substrate-specific and function in a wide variety of species in different pathways. It can hydrolyze keratin and other proteins with subtilisin-like specificity. The number of calcium-binding motifs found in these differ. Proteinase T is a novel proteinase from the fungus Tritirachium album Limber. The amino acid sequence of proteinase T as deduced from the nucleotide sequence is about 56% identical to that of proteinase K. 255 matched cddid_all.tbl CDD cd04078 cd04078 271144 CBM36_xylanase-like Carbohydrate Binding Module family 36 (CBM36); appended mainly to glycoside hydrolase family 11 (GH11) domains; xylan binding. This family includes carbohydrate binding module family 36 (CBM36) most of which appear appended to glycoside hydrolase family 11 (GH11) domains. These CBMs are non-catalytic carbohydrate binding domains that facilitate the strong binding of the GH11 catalytic modules with their dedicated, insoluble substrates. GH11 domains have xylanase (endo-1,4-beta-xylanase) activity which catalyzes the hydrolysis of beta-1,4 bonds of xylan, the major component of hemicelluloses, to generate xylooligosaccharides and xylose. This family includes XynB from Dictyoglomus thermophilum Rt46B.1 and Xyn11A from Pseudobutyrivibrio xylanivorans Mz5T. Xyn11A is a multicatalytic enzyme with an N-terminal GH11 domain, a CBM36 domain, and a C-terminal putative NodB-like polysaccharide deacetylase which is predicted to be an acetyl esterase involved in debranching activity in the xylan backbone. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold. Consistent with its structural and sequence similarity to CBM6, CBM36 binds xylan, but only at binding site I, and in a calcium-dependent manner; the latter suggests its potential application in affinity labeling. 119 matched cddid_all.tbl CDD cd04079 cd04079 271145 CBM6_agarase-like Carbohydrate Binding Module 6 (CBM6); appended mainly to glycoside hydrolase (GH) family 16 alpha- and beta agarases. This family includes carbohydrate binding module 6 (CBM6) domains that are appended mainly to glycoside hydrolase (GH) family 16 agarases. These CBM6s are non-catalytic carbohydrate binding domains that facilitate the activity of alpha- and beta-agarase catalytic modules which are involved in the hydrolysis of 1,4-beta-D-galactosidic linkages. These CBM6s bind specifically to the non-reducing end of agarose chains, recognizing only the first repeat of the disaccharide, and directing the appended catalytic modules to areas of the plant cell wall attacked by beta-agarases. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold. This family includes three tandem CBM6s from the Saccharophagus degradans agarase Aga86E, and three tandem CBM6s from Vibrio sp. strain PO-303 AgaA; in both these proteins these are appended to a GH16 domain. Vibrio AgaA also contains a Big-2-like protein-protein interaction domain. This family also includes two tandem CBM6s from an endo-type beta-agarase from a deep-sea Microbulbifer-like isolate, which are appended to a GH16 domain, and two of three CBM6s of Alteromonas agarilytica AgaA alpha-agarase, which are appended to a GH96 domain. 134 matched cddid_all.tbl CDD cd04080 cd04080 271146 CBM6_cellulase-like Carbohydrate Binding Module 6 (CBM6); appended to glycoside hydrolase (GH) domains, including GH5 (cellulase). This family includes carbohydrate binding module 6 (CBM6) domains that are appended to several glycoside hydrolase (GH) domains, including GH5 (cellulase) and GH16, as well as to coagulation factor 5/8 carbohydrate-binding domains. CBM6s are non-catalytic carbohydrate binding domains that facilitate the strong binding of the GH catalytic modules with their dedicated, insoluble substrates. The CBM6s are appended to GHs that display a diversity of substrate specificities. For some members of this family information is available about the specific substrates of the appended GH domains. It includes the CBM domains of various enzymes involved in cell wall degradation including, an extracellular beta-1,3-glucanase from Lysobacter enzymogenes encoded by the gluC gene (its catalytic domain belongs to the GH16 family), the tandem CBM domains of Pseudomonas sp. PE2 beta-1,3(4)-glucanase A (its catalytic domain also belongs to GH16), and a family 6 CBM from Cellvibrio mixtus Endoglucanase 5A (CmCBM6) which binds to the beta1,4-beta1,3-mixed linked glucans lichenan, and barley beta-glucan, cello-oligosaccharides, insoluble forms of cellulose, the beta1,3-glucan laminarin, and xylooligosaccharides, and the CBM6 of Fibrobacter succinogenes S85 XynD xylanase, appended to a GH10 domain, and Cellvibrio japonicas Cel5G appended to a GH5 (cellulase) domain. GH5 (cellulase) family includes enzymes with several known activities such as endoglucanase, beta-mannanase, and xylanase, which are involved in the degradation of cellulose and xylans. GH16 family includes enzymes with lichenase, xyloglucan endotransglycosylase (XET), and beta-agarase activities. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold. For CmCBM6 it has been shown that these two binding sites have different ligand specificities. 144 matched cddid_all.tbl CDD cd04081 cd04081 271147 CBM35_galactosidase-like Carbohydrate Binding Module family 35 (CBM35); appended mainly to enzymes that bind alpha-D-galactose (CBM35-Gal), including glycoside hydrolase (GH) families GH27 and GH43. This family includes carbohydrate binding module family 35 (CBM35); these are non-catalytic carbohydrate binding domains that are appended mainly to enzymes that bind alpha-D-galactose (CBM35-Gal), including glycoside hydrolase (GH) families GH27 and GH43. Examples of proteins which contain CBM35s belonging to this family includes the CBM35 of an exo-beta-1,3-galactanase from Phanerochaete chrysosporium 9 (Pc1,3Gal43A) which is appended to a GH43 domain, and the CBM35 domain of two bifunctional proteins with beta-L-arabinopyranosidase/alpha-D-galactopyranosidase activities from Fusarium oxysporum 12S, Foap1 and Foap2 (Fo/AP1 and Fo/AP2), that are appended to GH27 domains. CBM35s are unique in that they display conserved specificity through extensive sequence similarity but divergent function through their appended catalytic modules. They are known to bind alpha-D-galactose (Gal), mannan (Man), xylan, glucuronic acid (GlcA), a beta-polymer of mannose, and possibly glucans, forming four subfamilies based on general ligand specificities (galacto, urono, manno, and gluco configurations). Some CBM35s bind their ligands in a calcium-dependent manner. In contrast to most CBMs that are generally rigid proteins, CBM35 undergoes significant conformational change upon ligand binding. GH43 includes beta-xylosidases and beta-xylanases, using aryl-glycosides as substrates, while family GH27 includes alpha-galactosidases, alpha-N-acetylgalactosaminidases, and isomaltodextranases. 125 matched cddid_all.tbl CDD cd04082 cd04082 271148 CBM35_pectate_lyase-like Carbohydrate Binding Module family 35 (CBM35), pectate lyase-like; appended mainly to enzymes that bind mannan (Man), xylan, glucuronic acid (GlcA) and possibly glucans. This family includes carbohydrate binding module family 35 (CBM35) domains that are non-catalytic carbohydrate binding domains that are appended mainly to enzymes that bind mannan (Man), xylan, glucuronic acid (GlcA) and possibly glucans. Included in this family are CBM35s of pectate lyases, including pectate lyase 10A from Cellvibrio japonicas, these enzymes release delta-4,5-anhydrogalaturonic acid (delta4,5-GalA) from pectin, thus identifying a signature molecule for plant cell wall degradation. CBM35s are unique in that they display conserved specificity through extensive sequence similarity but divergent function through their appended catalytic modules. They are known to bind alpha-D-galactose (Gal), mannan (Man), xylan, glucuronic acid (GlcA), a beta-polymer of mannose, and possibly glucans, forming four subfamilies based on general ligand specificities (galacto, urono, manno, and gluco configurations). In contrast to most CBMs that are generally rigid proteins, CBM35 undergoes significant conformational change upon ligand binding. Some CBM35s bind their ligands in a calcium-dependent manner, especially those binding uronic acids. 124 matched cddid_all.tbl CDD cd04083 cd04083 271149 CBM35_Lmo2446-like Carbohydrate Binding Module 35 (CBM35) domains similar to Lmo2446. This family includes carbohydrate binding module 35 (CBM35) domains that are appended to several carbohydrate binding enzymes. Some CBM35 domains belonging to this family are appended to glycoside hydrolase (GH) family domains, including glycoside hydrolase family 31 (GH31), for example the CBM35 domain of Lmo2446, an uncharacterized protein from Listeria monocytogenes EGD-e. These CBM35s are non-catalytic carbohydrate binding domains that facilitate the strong binding of the GH catalytic modules with their dedicated, insoluble substrates. GH31 has a wide range of hydrolytic activities such as alpha-glucosidase, alpha-xylosidase, 6-alpha-glucosyltransferase, or alpha-1,4-glucan lyase, cleaving a terminal carbohydrate moiety from a substrate that may be a starch or a glycoprotein. Most characterized GH31 enzymes are alpha-glucosidases. 125 matched cddid_all.tbl CDD cd04084 cd04084 271150 CBM6_xylanase-like Carbohydrate Binding Module 6 (CBM6); many are appended to glycoside hydrolase (GH) family 11 and GH43 xylanase domains. This family includes carbohydrate binding module 6 (CBM6) domains that are appended mainly to glycoside hydrolase (GH) family domains, including GH3, GH11, and GH43 domains. These CBM6s are non-catalytic carbohydrate binding domains that facilitate the strong binding of the GH catalytic modules with their dedicated, insoluble substrates. Examples of proteins having CMB6s belonging to this family are Microbispora bispora GghA, a 1,4-beta-D-glucan glucohydrolase (GH3); Clostridium thermocellum xylanase U (GH11), and Penicillium purpurogenum ABF3, a bifunctional alpha-L-arabinofuranosidase/xylobiohydrolase (GH43). GH3 comprises enzymes with activities including beta-glucosidase (hydrolyzes beta-galactosidase) and beta-xylosidase (hydrolyzes 1,4-beta-D-xylosidase). GH11 family comprises enzymes with xylanase (endo-1,4-beta-xylanase) activity which catalyze the hydrolysis of beta-1,4 bonds of xylan, the major component of hemicelluloses, to generate xylooligosaccharides and xylose. GH43 includes beta-xylosidases and beta-xylanases, using aryl-glycosides as substrates. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold. 123 matched cddid_all.tbl CDD cd04085 cd04085 271151 delta_endotoxin_C delta-endotoxin C-terminal domain may be associated with carbohydrate binding functionality. Delta-endotoxin C-terminal domain (delta endotoxin domain III) is part of the activated region of delta endotoxins, which are insecticidal toxins produced during sporulation by Bacillus species of bacteria. The activated endotoxin binds to the gut epithelium and causes cell lysis leading to death. This activated region of the delta endotoxin is composed of three structural domains. The N-terminal helical domain (I) is involved in membrane insertion and pore formation, while the second and third domains (II and III) are involved in receptor binding. Domain III structurally resembles the carbohydrate binding domain 6 (CBM6) and it is possible that insect specificity is determined by protein-protein or protein-carbohydrate interactions mediated by both domains II and III of the toxin. Delta-endotoxins are of great interest for development of new bioinsecticides and in the control of mosquitoes. 152 matched cddid_all.tbl CDD cd04086 cd04086 271152 CBM35_mannanase-like Carbohydrate Binding Module 35 (CBM35); appended to several carbohydrate binding enzymes, including several glycoside hydrolase (GH) family 26 mannanase domains. This family includes carbohydrate binding module 35 (CBM35) domains that are appended to several carbohydrate binding enzymes, including periplasmic component of ABC-type sugar transport system involved in carbohydrate transport and metabolism, and several glycoside hydrolase (GH) domains, including GH26. These CBM6s are non-catalytic carbohydrate binding domains that facilitate the strong binding of the GH catalytic modules with their dedicated, insoluble substrates. Examples of proteins having CMB35s belonging to this family are mannanase A from Clostridium thermocellum (GH26), Man26B from Paenibacillus sp. BME-14 (GH26), and the multifunctional Cel44C-Man26A from Paenibacillus polymyxa GS01 (which has two GH domains, GH44 and GH26). GH26 mainly includes mannan endo-1,4-beta-mannosidase which hydrolyzes 1,4-beta-D-linkages in mannans, galacto-mannans, glucomannans, and galactoglucomannans, but displays little activity towards other plant cell wall polysaccharides. A few proteins belonging to this family have additional CBM3 domains; these CBM3s are not found in the CBM6-CBM35-CBM36_like superfamily. 119 matched cddid_all.tbl CDD cd04087 cd04087 239754 PTPA Phosphotyrosyl phosphatase activator (PTPA) is also known as protein phosphatase 2A (PP2A) phosphatase activator. PTPA is an essential, well conserved protein that stimulates the tyrosyl phosphatase activity of PP2A. It also reactivates the serine/threonine phosphatase activity of an inactive form of PP2A. Together, PTPA and PP2A constitute an ATPase. It has been suggested that PTPA alters the relative specificity of PP2A from phosphoserine/phosphothreonine substrates to phosphotyrosine substrates in an ATP-hydrolysis-dependent manner. Basal expression of PTPA is controlled by the transcription factor Yin Yang1 (YY1). PTPA has been suggested to play a role in the insertion of metals to the PP2A catalytic subunit (PP2Ac) active site, to act as a chaperone, and more recently, to have peptidyl prolyl cis/trans isomerase activity that specifically targets human PP2Ac. 266 matched cddid_all.tbl CDD cd04088 cd04088 293905 EFG_mtEFG_II Domain II of bacterial elongation factor G and C-terminal domain of mitochondrial Elongation factors G1 and G2. This family represents the domain II of bacterial Elongation factor G (EF-G)and mitochondrial Elongation factors G1 (mtEFG1) and G2 (mtEFG2). During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. mtEFG1 and mtEFG2 show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. No clear phenotype has been found for mutants in the yeast homolog of mtEFG2, MEF2. 83 matched cddid_all.tbl CDD cd04089 cd04089 293906 eRF3_II Domain II of the eukaryotic class II release factor. In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribosome. eRF3 is a GTPase, which enhances termination efficiency by stimulating eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF-1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-like protein with the property of aggregating into polymer-like fibrils. 82 matched cddid_all.tbl CDD cd04090 cd04090 293907 EF2_II_snRNP Domain II of the spliceosomal 116kD U5 small nuclear ribonucleoprotein (snRNP) component. This subfamily includes domain II of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and its yeast counterpart Snu114p. This domain is homologous to domain II of the eukaryotic translational elongation factor EF-2. U5-116 kD is a GTPase which is a component of the spliceosome complex which processes precursor mRNAs to produce mature mRNAs. 94 matched cddid_all.tbl CDD cd04091 cd04091 293908 mtEFG1_II_like Domain II of mitochondrial elongation factor G1-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s); mtEFG2s are not present in this group. 81 matched cddid_all.tbl CDD cd04092 cd04092 293909 mtEFG2_II_like Domain II of mitochondrial elongation factor G2-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. No clear phenotype has been found for mutants in the yeast homolog of mtEFG2, MEF2. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s); mtEFG1s are not present in this group. 83 matched cddid_all.tbl CDD cd04093 cd04093 294008 HBS1_C_III C-terminal domain of Hsp70 subfamily B suppressor 1 (HBS1). This model represents the C-terminal domain of Hsp70 subfamily B suppressor 1 (HBS1), which is homologous to the domain III of EF-1alpha. This group contains proteins similar to yeast Hbs1, which together with Dom34, promotes the No-go decay (NGD) of mRNA. The NGD targets mRNAs whose elongation stalled for degradation initiated by endonucleolytic cleavage in the vicinity of the stalled ribosome. 109 matched cddid_all.tbl CDD cd04094 cd04094 294009 eSelB_III Domain III of eukaryotic and archaeal elongation factor SelB. This model represents the domain III of archaeal and eukaryotic selenocysteine (Sec)-specific eukaryotic elongation factor (eEFSec or eSelB), which is homologous to domain III of EF-Tu. SelB is a specialized translation elongation factor responsible for the co-translational incorporation of selenocysteine into proteins by recoding of a UGA stop codon in the presence of a downstream mRNA hairpin loop, called Sec insertion sequence (SECIS) element. 114 matched cddid_all.tbl CDD cd04095 cd04095 294010 CysN_NoDQ_III Domain III of the large subunit of ATP sulfurylase (ATPS). This model represents domain III of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and is homologous to domain III of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sulfation of a nodulation factor. In Rhizobium meliloti, the heterodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N- and C-termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, archaea, and eukaryotes use a different ATP sulfurylase, which shows no amino acid sequence similarity to CysN or NodQ. CysN and the N-terminal portion of NodQ show similarity to GTPases involved in translation, in particular, EF-Tu and EF-1alpha. 103 matched cddid_all.tbl CDD cd04096 cd04096 239763 eEF2_snRNP_like_C eEF2_snRNP_like_C: this family represents a C-terminal domain of eukaryotic elongation factor 2 (eEF-2) and a homologous domain of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome. 80 matched cddid_all.tbl CDD cd04097 cd04097 239764 mtEFG1_C mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals (designated mtEFG1s and mtEFG2s) mtEFG2s are not present in this group. 78 matched cddid_all.tbl CDD cd04098 cd04098 239765 eEF2_C_snRNP eEF2_C_snRNP: This family includes a C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. This domain is homologous to the C-terminal domain of the eukaryotic translational elongation factor EF-2. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome. 80 matched cddid_all.tbl CDD cd04100 cd04100 239766 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like AspRSs which are non-discriminating and can charge both tRNAAsp and tRNAAsn. E. coli cells have two isoforms of LysRSs (LysS and LysU) encoded by two distinct genes, which are differentially regulated. The cytoplasmic and the mitochondrial isoforms of human LysRS are encoded by a single gene. Yeast cytoplasmic and mitochondrial LysRSs participate in mitochondrial import of cytoplasmic tRNAlysCUU. In addition to their housekeeping role, human LysRS may function as a signaling molecule that activates immune cells. Tomato LysRS may participate in a process possibly connected to conditions of oxidative-stress conditions or heavy metal uptake. It is known that human tRNAlys and LysRS are specifically packaged into HIV-1 suggesting a role for LysRS in tRNA packaging. AsnRS is immunodominant antigen of the filarial nematode Brugia malayai and is of interest as a target for anti-parasitic drug design. Human AsnRS has been shown to be a pro-inflammatory chemokine which interacts with CCR3 chemokine receptors on T cells, immature dendritic cells and macrophages. 85 matched cddid_all.tbl CDD cd04101 cd04101 206688 RabL4 Rab GTPase-like family 4 (Rab-like4). RabL4 (Rab-like4) subfamily. RabL4s are novel proteins that have high sequence similarity with Rab family members, but display features that are distinct from Rabs, and have been termed Rab-like. As in other Rab-like proteins, RabL4 lacks a prenylation site at the C-terminus. The specific function of RabL4 remains unknown. 167 matched cddid_all.tbl CDD cd04102 cd04102 206689 RabL3 Rab GTPase-like family 3 (Rab-like3). RabL3 (Rab-like3) subfamily. RabL3s are novel proteins that have high sequence similarity with Rab family members, but display features that are distinct from Rabs, and have been termed Rab-like. As in other Rab-like proteins, RabL3 lacks a prenylation site at the C-terminus. The specific function of RabL3 remains unknown. 204 matched cddid_all.tbl CDD cd04103 cd04103 133303 Centaurin_gamma Centaurin gamma (CENTG) GTPase. The centaurins (alpha, beta, gamma, and delta) are large, multi-domain proteins that all contain an ArfGAP domain and ankyrin repeats, and in some cases, numerous additional domains. Centaurin gamma contains an additional GTPase domain near its N-terminus. The specific function of this GTPase domain has not been well characterized, but centaurin gamma 2 (CENTG2) may play a role in the development of autism. Centaurin gamma 1 is also called PIKE (phosphatidyl inositol (PI) 3-kinase enhancer) and centaurin gamma 2 is also known as AGAP (ArfGAP protein with a GTPase-like domain, ankyrin repeats and a Pleckstrin homology domain) or GGAP. Three isoforms of PIKE have been identified. PIKE-S (short) and PIKE-L (long) are brain-specific isoforms, with PIKE-S restricted to the nucleus and PIKE-L found in multiple cellular compartments. A third isoform, PIKE-A was identified in human glioblastoma brain cancers and has been found in various tissues. GGAP has been shown to have high GTPase activity due to a direct intramolecular interaction between the N-terminal GTPase domain and the C-terminal ArfGAP domain. In human tissue, AGAP mRNA was detected in skeletal muscle, kidney, placenta, brain, heart, colon, and lung. Reduced expression levels were also observed in the spleen, liver, and small intestine. 158 matched cddid_all.tbl CDD cd04104 cd04104 206690 p47_IIGP_like p47 GTPase family includes IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1. The p47 GTPase family consists of several highly homologous proteins, including IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1. They are found in higher eukaryotes where they play a role in immune resistance against intracellular pathogens. p47 proteins exist at low resting levels in mouse cells, but are strongly induced by Type II interferon (IFN-gamma). ITGP is critical for resistance to Toxoplasma gondii infection and in involved in inhibition of Coxsackievirus-B3-induced apoptosis. TGTP was shown to limit vesicular stomatitis virus (VSV) infection of fibroblasts in vitro. IRG-47 is involved in resistance to T. gondii infection. LRG-47 has been implicated in resistance to T. gondii, Listeria monocytogenes, Leishmania, and mycobacterial infections. IIGP1 has been shown to localize to the ER and to the Golgi membranes in IFN-induced cells and inflamed tissues. In macrophages, IIGP1 interacts with hook3, a microtubule binding protein that participates in the organization of the cis-Golgi compartment. 197 matched cddid_all.tbl CDD cd04105 cd04105 206691 SR_beta Signal recognition particle receptor, beta subunit (SR-beta), together with SR-alpha, forms the heterodimeric signal recognition particle (SRP). Signal recognition particle receptor, beta subunit (SR-beta). SR-beta and SR-alpha form the heterodimeric signal recognition particle (SRP or SR) receptor that binds SRP to regulate protein translocation across the ER membrane. Nascent polypeptide chains are synthesized with an N-terminal hydrophobic signal sequence that binds SRP54, a component of the SRP. SRP directs targeting of the ribosome-nascent chain complex (RNC) to the ER membrane via interaction with the SR, which is localized to the ER membrane. The RNC is then transferred to the protein-conducting channel, or translocon, which facilitates polypeptide translation across the ER membrane or integration into the ER membrane. SR-beta is found only in eukaryotes; it is believed to control the release of the signal sequence from SRP54 upon binding of the ribosome to the translocon. High expression of SR-beta has been observed in human colon cancer, suggesting it may play a role in the development of this type of cancer. 202 matched cddid_all.tbl CDD cd04106 cd04106 133306 Rab23_like Rab GTPase family 23 (Rab23)-like. Rab23-like subfamily. Rab23 is a member of the Rab family of small GTPases. In mouse, Rab23 has been shown to function as a negative regulator in the sonic hedgehog (Shh) signaling pathway. Rab23 mediates the activity of Gli2 and Gli3, transcription factors that regulate Shh signaling in the spinal cord, primarily by preventing Gli2 activation in the absence of Shh ligand. Rab23 also regulates a step in the cytoplasmic signal transduction pathway that mediates the effect of Smoothened (one of two integral membrane proteins that are essential components of the Shh signaling pathway in vertebrates). In humans, Rab23 is expressed in the retina. Mice contain an isoform that shares 93% sequence identity with the human Rab23 and an alternative splicing isoform that is specific to the brain. This isoform causes the murine open brain phenotype, indicating it may have a role in the development of the central nervous system. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 162 matched cddid_all.tbl CDD cd04107 cd04107 206692 Rab32_Rab38 Rab GTPase families 18 (Rab18) and 32 (Rab32). Rab38/Rab32 subfamily. Rab32 and Rab38 are members of the Rab family of small GTPases. Human Rab32 was first identified in platelets but it is expressed in a variety of cell types, where it functions as an A-kinase anchoring protein (AKAP). Rab38 has been shown to be melanocyte-specific. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. 201 matched cddid_all.tbl CDD cd04108 cd04108 206693 Rab36_Rab34 Rab GTPase families 34 (Rab34) and 36 (Rab36). Rab34/Rab36 subfamily. Rab34, found primarily in the Golgi, interacts with its effector, Rab-interacting lysosomal protein (RILP). This enables its participation in microtubular dynenin-dynactin-mediated repositioning of lysosomes from the cell periphery to the Golgi. A Rab34 (Rah) isoform that lacks the consensus GTP-binding region has been identified in mice. This isoform is associated with membrane ruffles and promotes macropinosome formation. Rab36 has been mapped to human chromosome 22q11.2, a region that is homozygously deleted in malignant rhabdoid tumors (MRTs). However, experimental assessments do not implicate Rab36 as a tumor suppressor that would enable tumor formation through a loss-of-function mechanism. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. 170 matched cddid_all.tbl CDD cd04109 cd04109 206694 Rab28 Rab GTPase family 28 (Rab28). Rab28 subfamily. First identified in maize, Rab28 has been shown to be a late embryogenesis-abundant (Lea) protein that is regulated by the plant hormone abcisic acid (ABA). In Arabidopsis, Rab28 is expressed during embryo development and is generally restricted to provascular tissues in mature embryos. Unlike maize Rab28, it is not ABA-inducible. Characterization of the human Rab28 homolog revealed two isoforms, which differ by a 95-base pair insertion, producing an alternative sequence for the 30 amino acids at the C-terminus. The two human isoforms are presumably the result of alternative splicing. Since they differ at the C-terminus but not in the GTP-binding region, they are predicted to be targeted to different cellular locations. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. 213 matched cddid_all.tbl CDD cd04110 cd04110 133310 Rab35 Rab GTPase family 35 (Rab35). Rab35 is one of several Rab proteins to be found to participate in the regulation of osteoclast cells in rats. In addition, Rab35 has been identified as a protein that interacts with nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) in human cells. Overexpression of NPM-ALK is a key oncogenic event in some anaplastic large-cell lymphomas; since Rab35 interacts with N|PM-ALK, it may provide a target for cancer treatments. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. 199 matched cddid_all.tbl CDD cd04111 cd04111 133311 Rab39 Rab GTPase family 39 (Rab39). Found in eukaryotes, Rab39 is mainly found in epithelial cell lines, but is distributed widely in various human tissues and cell lines. It is believed to be a novel Rab protein involved in regulating Golgi-associated vesicular transport during cellular endocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. 211 matched cddid_all.tbl CDD cd04112 cd04112 206695 Rab26 Rab GTPase family 26 (Rab26). Rab26 subfamily. First identified in rat pancreatic acinar cells, Rab26 is believed to play a role in recruiting mature granules to the plasma membrane upon beta-adrenergic stimulation. Rab26 belongs to the Rab functional group III, which are considered key regulators of intracellular vesicle transport during exocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. 191 matched cddid_all.tbl CDD cd04113 cd04113 206696 Rab4 Rab GTPase family 4 (Rab4). Rab4 subfamily. Rab4 has been implicated in numerous functions within the cell. It helps regulate endocytosis through the sorting, recycling, and degradation of early endosomes. Mammalian Rab4 is involved in the regulation of many surface proteins including G-protein-coupled receptors, transferrin receptor, integrins, and surfactant protein A. Experimental data implicate Rab4 in regulation of the recycling of internalized receptors back to the plasma membrane. It is also believed to influence receptor-mediated antigen processing in B-lymphocytes, in calcium-dependent exocytosis in platelets, in alpha-amylase secretion in pancreatic cells, and in insulin-induced translocation of Glut4 from internal vesicles to the cell surface. Rab4 is known to share effector proteins with Rab5 and Rab11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 161 matched cddid_all.tbl CDD cd04114 cd04114 133314 Rab30 Rab GTPase family 30 (Rab30). Rab30 subfamily. Rab30 appears to be associated with the Golgi stack. It is expressed in a wide variety of tissue types and in humans maps to chromosome 11. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 169 matched cddid_all.tbl CDD cd04115 cd04115 133315 Rab33B_Rab33A Rab GTPase family 33 includes Rab33A and Rab33B. Rab33B/Rab33A subfamily. Rab33B is ubiquitously expressed in mouse tissues and cells, where it is localized to the medial Golgi cisternae. It colocalizes with alpha-mannose II. Together with the other cisternal Rabs, Rab6A and Rab6A', it is believed to regulate the Golgi response to stress and is likely a molecular target in stress-activated signaling pathways. Rab33A (previously known as S10) is expressed primarily in the brain and immune system cells. In humans, it is located on the X chromosome at Xq26 and its expression is down-regulated in tuberculosis patients. Experimental evidence suggests that Rab33A is a novel CD8+ T cell factor that likely plays a role in tuberculosis disease processes. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 170 matched cddid_all.tbl CDD cd04116 cd04116 206697 Rab9 Rab GTPase family 9 (Rab9). Rab9 is found in late endosomes, together with mannose 6-phosphate receptors (MPRs) and the tail-interacting protein of 47 kD (TIP47). Rab9 is a key mediator of vesicular transport from late endosomes to the trans-Golgi network (TGN) by redirecting the MPRs. Rab9 has been identified as a key component for the replication of several viruses, including HIV1, Ebola, Marburg, and measles, making it a potential target for inhibiting a variety of viruses. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 170 matched cddid_all.tbl CDD cd04117 cd04117 206698 Rab15 Rab GTPase family 15 (Rab15). Rab15 colocalizes with the transferrin receptor in early endosome compartments, but not with late endosomal markers. It codistributes with Rab4 and Rab5 on early/sorting endosomes, and with Rab11 on pericentriolar recycling endosomes. It is believed to function as an inhibitory GTPase that regulates distinct steps in early endocytic trafficking. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 164 matched cddid_all.tbl CDD cd04118 cd04118 133318 Rab24 Rab GTPase family 24 (Rab24). Rab24 is distinct from other Rabs in several ways. It exists primarily in the GTP-bound state, having a low intrinsic GTPase activity; it is not efficiently geranyl-geranylated at the C-terminus; it does not form a detectable complex with Rab GDP-dissociation inhibitors (GDIs); and it has recently been shown to undergo tyrosine phosphorylation when overexpressed in vitro. The specific function of Rab24 still remains unknown. It is found in a transport route between ER-cis-Golgi and late endocytic compartments. It is putatively involved in an autophagic pathway, possibly directing misfolded proteins in the ER to degradative pathways. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. 193 matched cddid_all.tbl CDD cd04119 cd04119 133319 RJL Rab GTPase family J-like (RabJ-like). RJLs are found in many protists and as chimeras with C-terminal DNAJ domains in deuterostome metazoa. They are not found in plants, fungi, and protostome metazoa, suggesting a horizontal gene transfer between protists and deuterostome metazoa. RJLs lack any known membrane targeting signal and contain a degenerate phosphate/magnesium-binding 3 (PM3) motif, suggesting an impaired ability to hydrolyze GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. 168 matched cddid_all.tbl CDD cd04120 cd04120 206699 Rab12 Rab GTPase family 12 (Rab12). Rab12 was first identified in canine cells, where it was localized to the Golgi complex. The specific function of Rab12 remains unknown, and inconsistent results about its cellular localization have been reported. More recent studies have identified Rab12 associated with post-Golgi vesicles, or with other small vesicle-like structures but not with the Golgi complex. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. 202 matched cddid_all.tbl CDD cd04121 cd04121 133321 Rab40 Rab GTPase family 40 (Rab40) contains Rab40a, Rab40b and Rab40c. The Rab40 subfamily contains Rab40a, Rab40b, and Rab40c, which are all highly homologous. In rat, Rab40c is localized to the perinuclear recycling compartment (PRC), and is distributed in a tissue-specific manor, with high expression in brain, heart, kidney, and testis, low expression in lung and liver, and no expression in spleen and skeletal muscle. Rab40c is highly expressed in differentiated oligodendrocytes but minimally expressed in oligodendrocyte progenitors, suggesting a role in the vesicular transport of myelin components. Unlike most other Ras-superfamily proteins, Rab40c was shown to have a much lower affinity for GTP, and an affinity for GDP that is lower than for GTP. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. 189 matched cddid_all.tbl CDD cd04122 cd04122 133322 Rab14 Rab GTPase family 14 (Rab14). Rab14 GTPases are localized to biosynthetic compartments, including the rough ER, the Golgi complex, and the trans-Golgi network, and to endosomal compartments, including early endosomal vacuoles and associated vesicles. Rab14 is believed to function in both the biosynthetic and recycling pathways between the Golgi and endosomal compartments. Rab14 has also been identified on GLUT4 vesicles, and has been suggested to help regulate GLUT4 translocation. In addition, Rab14 is believed to play a role in the regulation of phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 166 matched cddid_all.tbl CDD cd04123 cd04123 133323 Rab21 Rab GTPase family 21 (Rab21). The localization and function of Rab21 are not clearly defined, with conflicting data reported. Rab21 has been reported to localize in the ER in human intestinal epithelial cells, with partial colocalization with alpha-glucosidase, a late endosomal/lysosomal marker. More recently, Rab21 was shown to colocalize with and affect the morphology of early endosomes. In Dictyostelium, GTP-bound Rab21, together with two novel LIM domain proteins, LimF and ChLim, has been shown to regulate phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 162 matched cddid_all.tbl CDD cd04124 cd04124 133324 RabL2 Rab GTPase-like family 2 (Rab-like2). RabL2 (Rab-like2) subfamily. RabL2s are novel Rab proteins identified recently which display features that are distinct from other Rabs, and have been termed Rab-like. RabL2 contains RabL2a and RabL2b, two very similar Rab proteins that share > 98% sequence identity in humans. RabL2b maps to the subtelomeric region of chromosome 22q13.3 and RabL2a maps to 2q13, a region that suggests it is also a subtelomeric gene. Both genes are believed to be expressed ubiquitously, suggesting that RabL2s are the first example of duplicated genes in human proximal subtelomeric regions that are both expressed actively. Like other Rab-like proteins, RabL2s lack a prenylation site at the C-terminus. The specific functions of RabL2a and RabL2b remain unknown. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. 161 matched cddid_all.tbl CDD cd04126 cd04126 133326 Rab20 Rab GTPase family 20 (Rab20). Rab20 is one of several Rab proteins that appear to be restricted in expression to the apical domain of murine polarized epithelial cells. It is expressed on the apical side of polarized kidney tubule and intestinal epithelial cells, and in non-polarized cells. It also localizes to vesico-tubular structures below the apical brush border of renal proximal tubule cells and in the apical region of duodenal epithelial cells. Rab20 has also been shown to colocalize with vacuolar H+-ATPases (V-ATPases) in mouse kidney cells, suggesting a role in the regulation of V-ATPase traffic in specific portions of the nephron. It was also shown to be one of several proteins whose expression is upregulated in human myelodysplastic syndrome (MDS) patients. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. 220 matched cddid_all.tbl CDD cd04127 cd04127 206700 Rab27A Rab GTPase family 27a (Rab27a). The Rab27a subfamily consists of Rab27a and its highly homologous isoform, Rab27b. Unlike most Rab proteins whose functions remain poorly defined, Rab27a has many known functions. Rab27a has multiple effector proteins, and depending on which effector it binds, Rab27a has different functions as well as tissue distribution and/or cellular localization. Putative functions have been assigned to Rab27a when associated with the effector proteins Slp1, Slp2, Slp3, Slp4, Slp5, DmSlp, rabphilin, Dm/Ce-rabphilin, Slac2-a, Slac2-b, Slac2-c, Noc2, JFC1, and Munc13-4. Rab27a has been associated with several human diseases, including hemophagocytic syndrome (Griscelli syndrome or GS), Hermansky-Pudlak syndrome, and choroidermia. In the case of GS, a rare, autosomal recessive disease, a Rab27a mutation is directly responsible for the disorder. When Rab27a is localized to the secretory granules of pancreatic beta cells, it is believed to mediate glucose-stimulated insulin secretion, making it a potential target for diabetes therapy. When bound to JFC1 in prostate cells, Rab27a is believed to regulate the exocytosis of prostate- specific markers. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 180 matched cddid_all.tbl CDD cd04128 cd04128 206701 Spg1 Septum-promoting GTPase (Spg1). Spg1p. Spg1p (septum-promoting GTPase) was first identified in the fission yeast S. pombe, where it regulates septum formation in the septation initiation network (SIN) through the cdc7 protein kinase. Spg1p is an essential gene that localizes to the spindle pole bodies. When GTP-bound, it binds cdc7 and causes it to translocate to spindle poles. Sid4p (septation initiation defective) is required for localization of Spg1p to the spindle pole body, and the ability of Spg1p to promote septum formation from any point in the cell cycle depends on Sid4p. Spg1p is negatively regulated by Byr4 and cdc16, which form a two-component GTPase activating protein (GAP) for Spg1p. The existence of a SIN-related pathway in plants has been proposed. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. 182 matched cddid_all.tbl CDD cd04129 cd04129 206702 Rho2 Ras homology family 2 (Rho2) of small guanosine triphosphatases (GTPases). Rho2 is a fungal GTPase that plays a role in cell morphogenesis, control of cell wall integrity, control of growth polarity, and maintenance of growth direction. Rho2 activates the protein kinase C homolog Pck2, and Pck2 controls Mok1, the major (1-3) alpha-D-glucan synthase. Together with Rho1 (RhoA), Rho2 regulates the construction of the cell wall. Unlike Rho1, Rho2 is not an essential protein, but its overexpression is lethal. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for proper intracellular localization via membrane attachment. As with other Rho family GTPases, the GDP/GTP cycling is regulated by GEFs (guanine nucleotide exchange factors), GAPs (GTPase-activating proteins) and GDIs (guanine nucleotide dissociation inhibitors). 190 matched cddid_all.tbl CDD cd04130 cd04130 133330 Wrch_1 Wnt-1 responsive Cdc42 homolog (Wrch-1) is a Rho family GTPase similar to Cdc42. Wrch-1 (Wnt-1 responsive Cdc42 homolog) is a Rho family GTPase that shares significant sequence and functional similarity with Cdc42. Wrch-1 was first identified in mouse mammary epithelial cells, where its transcription is upregulated in Wnt-1 transformation. Wrch-1 contains N- and C-terminal extensions relative to cdc42, suggesting potential differences in cellular localization and function. The Wrch-1 N-terminal extension contains putative SH3 domain-binding motifs and has been shown to bind the SH3 domain-containing protein Grb2, which increases the level of active Wrch-1 in cells. Unlike Cdc42, which localizes to the cytosol and perinuclear membranes, Wrch-1 localizes extensively with the plasma membrane and endosomes. The membrane association, localization, and biological activity of Wrch-1 indicate an atypical model of regulation distinct from other Rho family GTPases. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 173 matched cddid_all.tbl CDD cd04131 cd04131 206703 Rnd Rho family GTPase subfamily Rnd includes Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8. The Rnd subfamily contains Rnd1/Rho6, Rnd2/Rho7, and Rnd3/RhoE/Rho8. These novel Rho family proteins have substantial structural differences compared to other Rho members, including N- and C-terminal extensions relative to other Rhos. Rnd3/RhoE is farnesylated at the C-terminal prenylation site, unlike most other Rho proteins that are geranylgeranylated. In addition, Rnd members are unable to hydrolyze GTP and are resistant to GAP activity. They are believed to exist only in the GTP-bound conformation, and are antagonists of RhoA activity. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 176 matched cddid_all.tbl CDD cd04132 cd04132 206704 Rho4_like Ras homology family 4 (Rho4) of small guanosine triphosphatases (GTPases)-like. Rho4 is a GTPase that controls septum degradation by regulating secretion of Eng1 or Agn1 during cytokinesis. Rho4 also plays a role in cell morphogenesis. Rho4 regulates septation and cell morphology by controlling the actin cytoskeleton and cytoplasmic microtubules. The localization of Rho4 is modulated by Rdi1, which may function as a GDI, and by Rga9, which is believed to function as a GAP. In S. pombe, both Rho4 deletion and Rho4 overexpression result in a defective cell wall, suggesting a role for Rho4 in maintaining cell wall integrity. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. 197 matched cddid_all.tbl CDD cd04133 cd04133 206705 Rop_like Rho-related protein from plants (Rop)-like. The Rop (Rho-related protein from plants) subfamily plays a role in diverse cellular processes, including cytoskeletal organization, pollen and vegetative cell growth, hormone responses, stress responses, and pathogen resistance. Rops are able to regulate several downstream pathways to amplify a specific signal by acting as master switches early in the signaling cascade. They transmit a variety of extracellular and intracellular signals. Rops are involved in establishing cell polarity in root-hair development, root-hair elongation, pollen-tube growth, cell-shape formation, responses to hormones such as abscisic acid (ABA) and auxin, responses to abiotic stresses such as oxygen deprivation, and disease resistance and disease susceptibility. An individual Rop can have a unique function or an overlapping function shared with other Rop proteins; in addition, a given Rop-regulated function can be controlled by one or multiple Rop proteins. For example, Rop1, Rop3, and Rop5 are all involved in pollen-tube growth; Rop2 plays a role in response to low-oxygen environments, cell-morphology, and root-hair development; root-hair development is also regulated by Rop4 and Rop6; Rop6 is also responsible for ABA response, and ABA response is also regulated by Rop10. Plants retain some of the regulatory mechanisms that are shared by other members of the Rho family, but have also developed a number of unique modes for regulating Rops. Unique RhoGEFs have been identified that are exclusively active toward Rop proteins, such as those containing the domain PRONE (plant-specific Rop nucleotide exchanger). Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 173 matched cddid_all.tbl CDD cd04134 cd04134 206706 Rho3 Ras homology family 3 (Rho3) of small guanosine triphosphatases (GTPases). Rho3 is a member of the Rho family found only in fungi. Rho3 is believed to regulate cell polarity by interacting with the diaphanous/formin family protein For3 to control both the actin cytoskeleton and microtubules. Rho3 is also believed to have a direct role in exocytosis that is independent of its role in regulating actin polarity. The function in exocytosis may be two-pronged: first, in the transport of post-Golgi vesicles from the mother cell to the bud, mediated by myosin (Myo2); second, in the docking and fusion of vesicles to the plasma membrane, mediated by an exocyst (Exo70) protein. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. 185 matched cddid_all.tbl CDD cd04135 cd04135 206707 Tc10 Rho GTPase TC10 (Tc10). TC10 is a Rho family protein that has been shown to induce microspike formation and neurite outgrowth in vitro. Its expression changes dramatically after peripheral nerve injury, suggesting an important role in promoting axonal outgrowth and regeneration. TC10 regulates translocation of insulin-stimulated GLUT4 in adipocytes and has also been shown to bind directly to Golgi COPI coat proteins. GTP-bound TC10 in vitro can bind numerous potential effectors. Depending on its subcellular localization and distinct functional domains, TC10 can differentially regulate two types of filamentous actin in adipocytes. TC10 mRNAs are highly expressed in three types of mouse muscle tissues: leg skeletal muscle, cardiac muscle, and uterus; they were also present in brain, with higher levels in adults than in newborns. TC10 has also been shown to play a role in regulating the expression of cystic fibrosis transmembrane conductance regulator (CFTR) through interactions with CFTR-associated ligand (CAL). The GTP-bound form of TC10 directs the trafficking of CFTR from the juxtanuclear region to the secretory pathway toward the plasma membrane, away from CAL-mediated DFTR degradation in the lysosome. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 174 matched cddid_all.tbl CDD cd04136 cd04136 206708 Rap_like Rap-like family consists of Rap1, Rap2 and RSR1. The Rap subfamily consists of the Rap1, Rap2, and RSR1. Rap subfamily proteins perform different cellular functions, depending on the isoform and its subcellular localization. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and microsomal membrane of the pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. Rap1 localizes in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres. Rap2 is involved in multiple functions, including activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton and activation of the Wnt/beta-catenin signaling pathway in embryonic Xenopus. A number of effector proteins for Rap2 have been identified, including isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK), and the RalGEFs RalGDS, RGL, and Rlf, which also interact with Rap1 and Ras. RSR1 is the fungal homolog of Rap1 and Rap2. In budding yeasts, it is involved in selecting a site for bud growth, which directs the establishment of cell polarization. The Rho family GTPase Cdc42 and its GEF, Cdc24, then establish an axis of polarized growth. It is believed that Cdc42 interacts directly with RSR1 in vivo. In filamentous fungi such as Ashbya gossypii, RSR1 is a key regulator of polar growth in the hypha. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 164 matched cddid_all.tbl CDD cd04137 cd04137 206709 RheB Ras Homolog Enriched in Brain (RheB) is a small GTPase. Rheb (Ras Homolog Enriched in Brain) subfamily. Rheb was initially identified in rat brain, where its expression is elevated by seizures or by long-term potentiation. It is expressed ubiquitously, with elevated levels in muscle and brain. Rheb functions as an important mediator between the tuberous sclerosis complex proteins, TSC1 and TSC2, and the mammalian target of rapamycin (TOR) kinase to stimulate cell growth. TOR kinase regulates cell growth by controlling nutrient availability, growth factors, and the energy status of the cell. TSC1 and TSC2 form a dimeric complex that has tumor suppressor activity, and TSC2 is a GTPase activating protein (GAP) for Rheb. The TSC1/TSC2 complex inhibits the activation of TOR kinase through Rheb. Rheb has also been shown to induce the formation of large cytoplasmic vacuoles in a process that is dependent on the GTPase cycle of Rheb, but independent of the TOR kinase, suggesting Rheb plays a role in endocytic trafficking that leads to cell growth and cell-cycle progression. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. 180 matched cddid_all.tbl CDD cd04138 cd04138 133338 H_N_K_Ras_like Ras GTPase family containing H-Ras,N-Ras and K-Ras4A/4B. H-Ras/N-Ras/K-Ras subfamily. H-Ras, N-Ras, and K-Ras4A/4B are the prototypical members of the Ras family. These isoforms generate distinct signal outputs despite interacting with a common set of activators and effectors, and are strongly associated with oncogenic progression in tumor initiation. Mutated versions of Ras that are insensitive to GAP stimulation (and are therefore constitutively active) are found in a significant fraction of human cancers. Many Ras guanine nucleotide exchange factors (GEFs) have been identified. They are sequestered in the cytosol until activation by growth factors triggers recruitment to the plasma membrane or Golgi, where the GEF colocalizes with Ras. Active (GTP-bound) Ras interacts with several effector proteins that stimulate a variety of diverse cytoplasmic signaling activities. Some are known to positively mediate the oncogenic properties of Ras, including Raf, phosphatidylinositol 3-kinase (PI3K), RalGEFs, and Tiam1. Others are proposed to play negative regulatory roles in oncogenesis, including RASSF and NORE/MST1. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 162 matched cddid_all.tbl CDD cd04139 cd04139 206710 RalA_RalB Ral (Ras-like) family containing highly homologous RalA and RalB. The Ral (Ras-like) subfamily consists of the highly homologous RalA and RalB. Ral proteins are believed to play a crucial role in tumorigenesis, metastasis, endocytosis, and actin cytoskeleton dynamics. Despite their high sequence similarity (>80% sequence identity), nonoverlapping and opposing functions have been assigned to RalA and RalBs in tumor migration. In human bladder and prostate cancer cells, RalB promotes migration while RalA inhibits it. A Ral-specific set of GEFs has been identified that are activated by Ras binding. This RalGEF activity is enhanced by Ras binding to another of its target proteins, phosphatidylinositol 3-kinase (PI3K). Ral effectors include RLIP76/RalBP1, a Rac/cdc42 GAP, and the exocyst (Sec6/8) complex, a heterooctomeric protein complex that is involved in tethering vesicles to specific sites on the plasma membrane prior to exocytosis. In rat kidney cells, RalB is required for functional assembly of the exocyst and for localizing the exocyst to the leading edge of migrating cells. In human cancer cells, RalA is required to support anchorage-independent proliferation and RalB is required to suppress apoptosis. RalA has been shown to localize to the plasma membrane while RalB is localized to the intracellular vesicles. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 163 matched cddid_all.tbl CDD cd04140 cd04140 206711 ARHI_like A Ras homolog member I (ARHI). ARHI (A Ras homolog member I) is a member of the Ras family with several unique structural and functional properties. ARHI is expressed in normal human ovarian and breast tissue, but its expression is decreased or eliminated in breast and ovarian cancer. ARHI contains an N-terminal extension of 34 residues (human) that is required to retain its tumor suppressive activity. Unlike most other Ras family members, ARHI is maintained in the constitutively active (GTP-bound) state in resting cells and has modest GTPase activity. ARHI inhibits STAT3 (signal transducers and activators of transcription 3), a latent transcription factor whose abnormal activation plays a critical role in oncogenesis. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 165 matched cddid_all.tbl CDD cd04141 cd04141 206712 Rit_Rin_Ric Ras-like protein in all tissues (Rit), Ras-like protein in neurons (Rin) and Ras-related protein which interacts with calmodulin (Ric). Rit (Ras-like protein in all tissues), Rin (Ras-like protein in neurons) and Ric (Ras-related protein which interacts with calmodulin) form a subfamily with several unique structural and functional characteristics. These proteins all lack a the C-terminal CaaX lipid-binding motif typical of Ras family proteins, and Rin and Ric contain calmodulin-binding domains. Rin, which is expressed only in neurons, induces neurite outgrowth in rat pheochromocytoma cells through its association with calmodulin and its activation of endogenous Rac/cdc42. Rit, which is ubiquitously expressed in mammals, inhibits growth-factor withdrawl-mediated apoptosis and induces neurite extension in pheochromocytoma cells. Rit and Rin are both able to form a ternary complex with PAR6, a cell polarity-regulating protein, and Rac/cdc42. This ternary complex is proposed to have physiological function in processes such as tumorigenesis. Activated Ric is likely to signal in parallel with the Ras pathway or stimulate the Ras pathway at some upstream point, and binding of calmodulin to Ric may negatively regulate Ric activity. 172 matched cddid_all.tbl CDD cd04142 cd04142 133342 RRP22 Ras-related protein on chromosome 22 (RRP22) family. RRP22 (Ras-related protein on chromosome 22) subfamily consists of proteins that inhibit cell growth and promote caspase-independent cell death. Unlike most Ras proteins, RRP22 is down-regulated in many human tumor cells due to promoter methylation. RRP22 localizes to the nucleolus in a GTP-dependent manner, suggesting a novel function in modulating transport of nucleolar components. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Like most Ras family proteins, RRP22 is farnesylated. 198 matched cddid_all.tbl CDD cd04143 cd04143 133343 Rhes_like Ras homolog enriched in striatum (Rhes) and activator of G-protein signaling 1 (Dexras1/AGS1). This subfamily includes Rhes (Ras homolog enriched in striatum) and Dexras1/AGS1 (activator of G-protein signaling 1). These proteins are homologous, but exhibit significant differences in tissue distribution and subcellular localization. Rhes is found primarily in the striatum of the brain, but is also expressed in other areas of the brain, such as the cerebral cortex, hippocampus, inferior colliculus, and cerebellum. Rhes expression is controlled by thyroid hormones. In rat PC12 cells, Rhes is farnesylated and localizes to the plasma membrane. Rhes binds and activates PI3K, and plays a role in coupling serpentine membrane receptors with heterotrimeric G-protein signaling. Rhes has recently been shown to be reduced under conditions of dopamine supersensitivity and may play a role in determining dopamine receptor sensitivity. Dexras1/AGS1 is a dexamethasone-induced Ras protein that is expressed primarily in the brain, with low expression levels in other tissues. Dexras1 localizes primarily to the cytoplasm, and is a critical regulator of the circadian master clock to photic and nonphotic input. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. 247 matched cddid_all.tbl CDD cd04144 cd04144 133344 Ras2 Rat sarcoma (Ras) family 2 of small guanosine triphosphatases (GTPases). The Ras2 subfamily, found exclusively in fungi, was first identified in Ustilago maydis. In U. maydis, Ras2 is regulated by Sql2, a protein that is homologous to GEFs (guanine nucleotide exchange factors) of the CDC25 family. Ras2 has been shown to induce filamentous growth, but the signaling cascade through which Ras2 and Sql2 regulate cell morphology is not known. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. 190 matched cddid_all.tbl CDD cd04145 cd04145 133345 M_R_Ras_like R-Ras2/TC21, M-Ras/R-Ras3. The M-Ras/R-Ras-like subfamily contains R-Ras2/TC21, M-Ras/R-Ras3, and related members of the Ras family. M-Ras is expressed in lympho-hematopoetic cells. It interacts with some of the known Ras effectors, but appears to also have its own effectors. Expression of mutated M-Ras leads to transformation of several types of cell lines, including hematopoietic cells, mammary epithelial cells, and fibroblasts. Overexpression of M-Ras is observed in carcinomas from breast, uterus, thyroid, stomach, colon, kidney, lung, and rectum. In addition, expression of a constitutively active M-Ras mutant in murine bone marrow induces a malignant mast cell leukemia that is distinct from the monocytic leukemia induced by H-Ras. TC21, along with H-Ras, has been shown to regulate the branching morphogenesis of ureteric bud cell branching in mice. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 164 matched cddid_all.tbl CDD cd04146 cd04146 206713 RERG_RasL11_like Ras-related and Estrogen-Regulated Growth inhibitor (RERG) and Ras-like 11 (RasL11)-like families. RERG (Ras-related and Estrogen- Regulated Growth inhibitor) and Ras-like 11 are members of a novel subfamily of Ras that were identified based on their behavior in breast and prostate tumors, respectively. RERG expression was decreased or lost in a significant fraction of primary human breast tumors that lack estrogen receptor and are correlated with poor clinical prognosis. Elevated RERG expression correlated with favorable patient outcome in a breast tumor subtype that is positive for estrogen receptor expression. In contrast to most Ras proteins, RERG overexpression inhibited the growth of breast tumor cells in vitro and in vivo. RasL11 was found to be ubiquitously expressed in human tissue, but down-regulated in prostate tumors. Both RERG and RasL11 lack the C-terminal CaaX prenylation motif, where a = an aliphatic amino acid and X = any amino acid, and are localized primarily in the cytoplasm. Both are believed to have tumor suppressor activity. 166 matched cddid_all.tbl CDD cd04147 cd04147 206714 Ras_dva Ras - dorsal-ventral anterior localization (Ras-dva) family. Ras-dva subfamily. Ras-dva (Ras - dorsal-ventral anterior localization) subfamily consists of a set of proteins characterized only in Xenopus leavis, to date. In Xenopus Ras-dva expression is activated by the transcription factor Otx2 and begins during gastrulation throughout the anterior ectoderm. Ras-dva expression is inhibited in the anterior neural plate by factor Xanf1. Downregulation of Ras-dva results in head development abnormalities through the inhibition of several regulators of the anterior neural plate and folds patterning, including Otx2, BF-1, Xag2, Pax6, Slug, and Sox9. Downregulation of Ras-dva also interferes with the FGF-8a signaling within the anterior ectoderm. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. 197 matched cddid_all.tbl CDD cd04148 cd04148 206715 RGK Rem, Rem2, Rad, Gem/Kir (RGK) subfamily of Ras GTPases. RGK subfamily. The RGK (Rem, Rem2, Rad, Gem/Kir) subfamily of Ras GTPases are expressed in a tissue-specific manner and are dynamically regulated by transcriptional and posttranscriptional mechanisms in response to environmental cues. RGK proteins bind to the beta subunit of L-type calcium channels, causing functional down-regulation of these voltage-dependent calcium channels, and either termination of calcium-dependent secretion or modulation of electrical conduction and contractile function. Inhibition of L-type calcium channels by Rem2 may provide a mechanism for modulating calcium-triggered exocytosis in hormone-secreting cells, and has been proposed to influence the secretion of insulin in pancreatic beta cells. RGK proteins also interact with and inhibit the Rho/Rho kinase pathway to modulate remodeling of the cytoskeleton. Two characteristics of RGK proteins cited in the literature are N-terminal and C-terminal extensions beyond the GTPase domain typical of Ras superfamily members. The N-terminal extension is not conserved among family members; the C-terminal extension is reported to be conserved among the family and lack the CaaX prenylation motif typical of membrane-associated Ras proteins. However, a putative CaaX motif has been identified in the alignment of the C-terminal residues of this CD. 219 matched cddid_all.tbl CDD cd04149 cd04149 206716 Arf6 ADP ribosylation factor 6 (Arf6). Arf6 subfamily. Arf6 (ADP ribosylation factor 6) proteins localize to the plasma membrane, where they perform a wide variety of functions. In its active, GTP-bound form, Arf6 is involved in cell spreading, Rac-induced formation of plasma membrane ruffles, cell migration, wound healing, and Fc-mediated phagocytosis. Arf6 appears to change the actin structure at the plasma membrane by activating Rac, a Rho family protein involved in membrane ruffling. Arf6 is required for and enhances Rac formation of ruffles. Arf6 can regulate dendritic branching in hippocampal neurons, and in yeast it localizes to the growing bud, where it plays a role in polarized growth and bud site selection. In leukocytes, Arf6 is required for chemokine-stimulated migration across endothelial cells. Arf6 also plays a role in down-regulation of beta2-adrenergic receptors and luteinizing hormone receptors by facilitating the release of sequestered arrestin to allow endocytosis. Arf6 is believed to function at multiple sites on the plasma membrane through interaction with a specific set of GEFs, GAPs, and effectors. Arf6 has been implicated in breast cancer and melanoma cell invasion, and in actin remodelling at the invasion site of Chlamydia infection. 168 matched cddid_all.tbl CDD cd04150 cd04150 206717 Arf1_5_like ADP-ribosylation factor-1 (Arf1) and ADP-ribosylation factor-5 (Arf5). The Arf1-Arf5-like subfamily contains Arf1, Arf2, Arf3, Arf4, Arf5, and related proteins. Arfs1-5 are soluble proteins that are crucial for assembling coat proteins during vesicle formation. Each contains an N-terminal myristoylated amphipathic helix that is folded into the protein in the GDP-bound state. GDP/GTP exchange exposes the helix, which anchors to the membrane. Following GTP hydrolysis, the helix dissociates from the membrane and folds back into the protein. A general feature of Arf1-5 signaling may be the cooperation of two Arfs at the same site. Arfs1-5 are generally considered to be interchangeable in function and location, but some specific functions have been assigned. Arf1 localizes to the early/cis-Golgi, where it is activated by GBF1 and recruits the coat protein COPI. It also localizes to the trans-Golgi network (TGN), where it is activated by BIG1/BIG2 and recruits the AP1, AP3, AP4, and GGA proteins. Humans, but not rodents and other lower eukaryotes, lack Arf2. Human Arf3 shares 96% sequence identity with Arf1 and is believed to generally function interchangeably with Arf1. Human Arf4 in the activated (GTP-bound) state has been shown to interact with the cytoplasmic domain of epidermal growth factor receptor (EGFR) and mediate the EGF-dependent activation of phospholipase D2 (PLD2), leading to activation of the activator protein 1 (AP-1) transcription factor. Arf4 has also been shown to recognize the C-terminal sorting signal of rhodopsin and regulate its incorporation into specialized post-Golgi rhodopsin transport carriers (RTCs). There is some evidence that Arf5 functions at the early-Golgi and the trans-Golgi to affect Golgi-associated alpha-adaptin homology Arf-binding proteins (GGAs). 159 matched cddid_all.tbl CDD cd04151 cd04151 206718 Arl1 ADP ribosylation factor 1 (Arf1). Arl1 subfamily. Arl1 (Arf-like 1) localizes to the Golgi complex, where it is believed to recruit effector proteins to the trans-Golgi network. Like most members of the Arf family, Arl1 is myristoylated at its N-terminal helix and mutation of the myristoylation site disrupts Golgi targeting. In humans, the Golgi-localized proteins golgin-97 and golgin-245 have been identified as Arl1 effectors. Golgins are large coiled-coil proteins found in the Golgi, and these golgins contain a C-terminal GRIP domain, which is the site of Arl1 binding. Additional Arl1 effectors include the GARP (Golgi-associated retrograde protein)/VFT (Vps53) vesicle-tethering complex and Arfaptin 2. Arl1 is not required for exocytosis, but appears necessary for trafficking from the endosomes to the Golgi. In Drosophila zygotes, mutation of Arl1 is lethal, and in the host-bloodstream form of Trypanosoma brucei, Arl1 is essential for viability. 158 matched cddid_all.tbl CDD cd04152 cd04152 206719 Arl4_Arl7 Arf-like 4 (Arl4) and 7 (Arl7) GTPases. Arl4 (Arf-like 4) is highly expressed in testicular germ cells, and is found in the nucleus and nucleolus. In mice, Arl4 is developmentally expressed during embryogenesis, and a role in somite formation and central nervous system differentiation has been proposed. Arl7 has been identified as the only Arf/Arl protein to be induced by agonists of liver X-receptor and retinoid X-receptor and by cholesterol loading in human macrophages. Arl7 is proposed to play a role in transport between a perinuclear compartment and the plasma membrane, apparently linked to the ABCA1-mediated cholesterol secretion pathway. Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily. 183 matched cddid_all.tbl CDD cd04153 cd04153 133353 Arl5_Arl8 Arf-like 5 (Arl5) and 8 (Arl8) GTPases. Arl5/Arl8 subfamily. Arl5 (Arf-like 5) and Arl8, like Arl4 and Arl7, are localized to the nucleus and nucleolus. Arl5 is developmentally regulated during embryogenesis in mice. Human Arl5 interacts with the heterochromatin protein 1-alpha (HP1alpha), a nonhistone chromosomal protein that is associated with heterochromatin and telomeres, and prevents telomere fusion. Arl5 may also play a role in embryonic nuclear dynamics and/or signaling cascades. Arl8 was identified from a fetal cartilage cDNA library. It is found in brain, heart, lung, cartilage, and kidney. No function has been assigned for Arl8 to date. 174 matched cddid_all.tbl CDD cd04154 cd04154 206720 Arl2 Arf-like 2 (Arl2) GTPase. Arl2 (Arf-like 2) GTPases are members of the Arf family that bind GDP and GTP with very low affinity. Unlike most Arf family proteins, Arl2 is not myristoylated at its N-terminal helix. The protein PDE-delta, first identified in photoreceptor rod cells, binds specifically to Arl2 and is structurally very similar to RhoGDI. Despite the high structural similarity between Arl2 and Rho proteins and between PDE-delta and RhoGDI, the interactions between the GTPases and their effectors are very different. In its GTP bound form, Arl2 interacts with the protein Binder of Arl2 (BART), and the complex is believed to play a role in mitochondrial adenine nucleotide transport. In its GDP bound form, Arl2 interacts with tubulin- folding Cofactor D; this interaction is believed to play a role in regulation of microtubule dynamics that impact the cytoskeleton, cell division, and cytokinesis. 173 matched cddid_all.tbl CDD cd04155 cd04155 206721 Arl3 Arf-like 3 (Arl3) GTPase. Arl3 (Arf-like 3) is an Arf family protein that differs from most Arf family members in the N-terminal extension. In is inactive, GDP-bound form, the N-terminal extension forms an elongated loop that is hydrophobically anchored into the membrane surface; however, it has been proposed that this region might form a helix in the GTP-bound form. The delta subunit of the rod-specific cyclic GMP phosphodiesterase type 6 (PDEdelta) is an Arl3 effector. Arl3 binds microtubules in a regulated manner to alter specific aspects of cytokinesis via interactions with retinitis pigmentosa 2 (RP2). It has been proposed that RP2 functions in concert with Arl3 to link the cell membrane and the cytoskeleton in photoreceptors as part of the cell signaling or vesicular transport machinery. In mice, the absence of Arl3 is associated with abnormal epithelial cell proliferation and cyst formation. 174 matched cddid_all.tbl CDD cd04156 cd04156 133356 ARLTS1 Arf-like tumor suppressor gene 1 (ARLTS1 or Arl11). ARLTS1 (Arf-like tumor suppressor gene 1), also known as Arl11, is a member of the Arf family of small GTPases that is believed to play a major role in apoptotic signaling. ARLTS1 is widely expressed and functions as a tumor suppressor gene in several human cancers. ARLTS1 is a low-penetrance suppressor that accounts for a small percentage of familial melanoma or familial chronic lymphocytic leukemia (CLL). ARLTS1 inactivation seems to occur most frequently through biallelic down-regulation by hypermethylation of the promoter. In breast cancer, ARLTS1 alterations were typically a combination of a hypomorphic polymorphism plus loss of heterozygosity. In a case of thyroid adenoma, ARLTS1 alterations were polymorphism plus promoter hypermethylation. The nonsense polymorphism Trp149Stop occurs with significantly greater frequency in familial cancer cases than in sporadic cancer cases, and the Cys148Arg polymorphism is associated with an increase in high-risk familial breast cancer. 160 matched cddid_all.tbl CDD cd04157 cd04157 206722 Arl6 Arf-like 6 (Arl6) GTPase. Arl6 (Arf-like 6) forms a subfamily of the Arf family of small GTPases. Arl6 expression is limited to the brain and kidney in adult mice, but it is expressed in the neural plate and somites during embryogenesis, suggesting a possible role for Arl6 in early development. Arl6 is also believed to have a role in cilia or flagella function. Several proteins have been identified that bind Arl6, including Arl6 interacting protein (Arl6ip), and SEC61beta, a subunit of the heterotrimeric conducting channel SEC61p. Based on Arl6 binding to these effectors, Arl6 is also proposed to play a role in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation. At least three specific homozygous Arl6 mutations in humans have been found to cause Bardet-Biedl syndrome, a disorder characterized by obesity, retinopathy, polydactyly, renal and cardiac malformations, learning disabilities, and hypogenitalism. Older literature suggests that Arl6 is a part of the Arl4/Arl7 subfamily, but analyses based on more recent sequence data place Arl6 in its own subfamily. 162 matched cddid_all.tbl CDD cd04158 cd04158 206723 ARD1 (ADP-ribosylation factor domain protein 1 (ARD1). ARD1 (ADP-ribosylation factor domain protein 1) is an unusual member of the Arf family. In addition to the C-terminal Arf domain, ARD1 has an additional 46-kDa N-terminal domain that contains a RING finger domain, two predicted B-Boxes, and a coiled-coil protein interaction motif. This domain belongs to the TRIM (tripartite motif) or RBCC (RING, B-Box, coiled-coil) family. Like most Arfs, the ARD1 Arf domain lacks detectable GTPase activity. However, unlike most Arfs, the full-length ARD1 protein has significant GTPase activity due to the GAP (GTPase-activating protein) activity exhibited by the 46-kDa N-terminal domain. The GAP domain of ARD1 is specific for its own Arf domain and does not bind other Arfs. The rate of GDP dissociation from the ARD1 Arf domain is slowed by the adjacent 15 amino acids, which act as a GDI (GDP-dissociation inhibitor) domain. ARD1 is ubiquitously expressed in cells and localizes to the Golgi and to the lysosomal membrane. Two Tyr-based motifs in the Arf domain are responsible for Golgi localization, while the GAP domain controls lysosomal localization. 169 matched cddid_all.tbl CDD cd04159 cd04159 206724 Arl10_like Arf-like 9 (Arl9) and 10 (Arl10) GTPases. Arl10-like subfamily. Arl9/Arl10 was identified from a human cancer-derived EST dataset. No functional information about the subfamily is available at the current time, but crystal structures of human Arl10b and Arl10c have been solved. 159 matched cddid_all.tbl CDD cd04160 cd04160 206725 Arfrp1 Arf-related protein 1 (Arfrp1). Arfrp1 (Arf-related protein 1), formerly known as ARP, is a membrane-associated Arf family member that lacks the N-terminal myristoylation motif. Arfrp1 is mainly associated with the trans-Golgi compartment and the trans-Golgi network, where it regulates the targeting of Arl1 and the GRIP domain-containing proteins, golgin-97 and golgin-245, onto Golgi membranes. It is also involved in the anterograde transport of the vesicular stomatitis virus G protein from the Golgi to the plasma membrane, and in the retrograde transport of TGN38 and Shiga toxin from endosomes to the trans-Golgi network. Arfrp1 also inhibits Arf/Sec7-dependent activation of phospholipase D. Deletion of Arfrp1 in mice causes embryonic lethality at the gastrulation stage and apoptosis of mesodermal cells, indicating its importance in development. 168 matched cddid_all.tbl CDD cd04161 cd04161 133361 Arl2l1_Arl13_like Arl2-like protein 1 (Arl2l1) and Arl13. Arl2l1 (Arl2-like protein 1) and Arl13 form a subfamily of the Arf family of small GTPases. Arl2l1 was identified in human cells during a search for the gene(s) responsible for Bardet-Biedl syndrome (BBS). Like Arl6, the identified BBS gene, Arl2l1 is proposed to have cilia-specific functions. Arl13 is found on the X chromosome, but its expression has not been confirmed; it may be a pseudogene. 167 matched cddid_all.tbl CDD cd04162 cd04162 133362 Arl9_Arfrp2_like Arf-like 9 (Arl9)/Arfrp2-like GTPase. Arl9/Arfrp2-like subfamily. Arl9 (Arf-like 9) was first identified as part of the Human Cancer Genome Project. It maps to chromosome 4q12 and is sometimes referred to as Arfrp2 (Arf-related protein 2). This is a novel subfamily identified in human cancers that is uncharacterized to date. 164 matched cddid_all.tbl CDD cd04163 cd04163 206726 Era E. coli Ras-like protein (Era) is a multifunctional GTPase. Era (E. coli Ras-like protein) is a multifunctional GTPase found in all bacteria except some eubacteria. It binds to the 16S ribosomal RNA (rRNA) of the 30S subunit and appears to play a role in the assembly of the 30S subunit, possibly by chaperoning the 16S rRNA. It also contacts several assembly elements of the 30S subunit. Era couples cell growth with cytokinesis and plays a role in cell division and energy metabolism. Homologs have also been found in eukaryotes. Era contains two domains: the N-terminal GTPase domain and a C-terminal domain KH domain that is critical for RNA binding. Both domains are important for Era function. Era is functionally able to compensate for deletion of RbfA, a cold-shock adaptation protein that is required for efficient processing of the 16S rRNA. 168 matched cddid_all.tbl CDD cd04164 cd04164 206727 trmE trmE is a tRNA modification GTPase. TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes. It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes. TrmE contains a GTPase domain that forms a canonical Ras-like fold. It functions a molecular switch GTPase, and apparently uses a conformational change associated with GTP hydrolysis to promote the tRNA modification reaction, in which the conserved cysteine in the C-terminal domain is thought to function as a catalytic residue. In bacteria that are able to survive in extremely low pH conditions, TrmE regulates glutamate-dependent acid resistance. 159 matched cddid_all.tbl CDD cd04165 cd04165 206728 GTPBP1_like GTP binding protein 1 (GTPBP1)-like family includes GTPBP2. Mammalian GTP binding protein 1 (GTPBP1), GTPBP2, and nematode homologs AGP-1 and CGP-1 are GTPases whose specific functions remain unknown. In mouse, GTPBP1 is expressed in macrophages, in smooth muscle cells of various tissues and in some neurons of the cerebral cortex; GTPBP2 tissue distribution appears to overlap that of GTPBP1. In human leukemia and macrophage cell lines, expression of both GTPBP1 and GTPBP2 is enhanced by interferon-gamma (IFN-gamma). The chromosomal location of both genes has been identified in humans, with GTPBP1 located in chromosome 22q12-13.1 and GTPBP2 located in chromosome 6p21-12. Human glioblastoma multiforme (GBM), a highly-malignant astrocytic glioma and the most common cancer in the central nervous system, has been linked to chromosomal deletions and a translocation on chromosome 6. The GBM translocation results in a fusion of GTPBP2 and PTPRZ1, a protein involved in oligodendrocyte differentiation, recovery, and survival. This fusion product may contribute to the onset of GBM. 224 matched cddid_all.tbl CDD cd04166 cd04166 206729 CysN_ATPS CysN, together with protein CysD, forms the ATP sulfurylase (ATPS) complex. CysN_ATPS subfamily. CysN, together with protein CysD, form the ATP sulfurylase (ATPS) complex in some bacteria and lower eukaryotes. ATPS catalyzes the production of ATP sulfurylase (APS) and pyrophosphate (PPi) from ATP and sulfate. CysD, which catalyzes ATP hydrolysis, is a member of the ATP pyrophosphatase (ATP PPase) family. CysN hydrolysis of GTP is required for CysD hydrolysis of ATP; however, CysN hydrolysis of GTP is not dependent on CysD hydrolysis of ATP. CysN is an example of lateral gene transfer followed by acquisition of new function. In many organisms, an ATPS exists which is not GTP-dependent and shares no sequence or structural similarity to CysN. 209 matched cddid_all.tbl CDD cd04167 cd04167 206730 Snu114p Snu114p, a spliceosome protein, is a GTPase. Snu114p subfamily. Snu114p is one of several proteins that make up the U5 small nuclear ribonucleoprotein (snRNP) particle. U5 is a component of the spliceosome, which catalyzes the splicing of pre-mRNA to remove introns. Snu114p is homologous to EF-2, but typically contains an additional N-terminal domain not found in Ef-2. This protein is part of the GTP translation factor family and the Ras superfamily, characterized by five G-box motifs. 213 matched cddid_all.tbl CDD cd04168 cd04168 206731 TetM_like Tet(M)-like family includes Tet(M), Tet(O), Tet(W), and OtrA, containing tetracycline resistant proteins. Tet(M), Tet(O), Tet(W), and OtrA are tetracycline resistance genes found in Gram-positive and Gram-negative bacteria. Tetracyclines inhibit protein synthesis by preventing aminoacyl-tRNA from binding to the ribosomal acceptor site. This subfamily contains tetracycline resistance proteins that function through ribosomal protection and are typically found on mobile genetic elements, such as transposons or plasmids, and are often conjugative. Ribosomal protection proteins are homologous to the elongation factors EF-Tu and EF-G. EF-G and Tet(M) compete for binding on the ribosomes. Tet(M) has a higher affinity than EF-G, suggesting these two proteins may have overlapping binding sites and that Tet(M) must be released before EF-G can bind. Tet(M) and Tet(O) have been shown to have ribosome-dependent GTPase activity. These proteins are part of the GTP translation factor family, which includes EF-G, EF-Tu, EF2, LepA, and SelB. 237 matched cddid_all.tbl CDD cd04169 cd04169 206732 RF3 Release Factor 3 (RF3) protein involved in the terminal step of translocation in bacteria. Peptide chain release factor 3 (RF3) is a protein involved in the termination step of translation in bacteria. Termination occurs when class I release factors (RF1 or RF2) recognize the stop codon at the A-site of the ribosome and activate the release of the nascent polypeptide. The class II release factor RF3 then initiates the release of the class I RF from the ribosome. RF3 binds to the RF/ribosome complex in the inactive (GDP-bound) state. GDP/GTP exchange occurs, followed by the release of the class I RF. Subsequent hydrolysis of GTP to GDP triggers the release of RF3 from the ribosome. RF3 also enhances the efficiency of class I RFs at less preferred stop codons and at stop codons in weak contexts. 268 matched cddid_all.tbl CDD cd04170 cd04170 206733 EF-G_bact Elongation factor G (EF-G) family. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group contains only bacterial members. 268 matched cddid_all.tbl CDD cd04171 cd04171 206734 SelB SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome. SelB is an elongation factor needed for the co-translational incorporation of selenocysteine. Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin. In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu). It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons. In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence). The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation. Archaeal and animal mechanisms of selenocysteine incorporation are more complex. Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryotes, they do share a common feature. Unlike in E. coli, these SECIS elements are located in the 3' UTRs. This group contains bacterial SelBs, as well as, one from archaea. 170 matched cddid_all.tbl CDD cd04172 cd04172 206735 Rnd3_RhoE_Rho8 Rnd3/RhoE/Rho8 GTPases. Rnd3/RhoE/Rho8 subfamily. Rnd3/RhoE/Rho8 is a member of the novel Rho subfamily Rnd, together with Rnd1/Rho6 and Rnd2/Rho7. Rnd3/RhoE is known to bind the serine-threonine kinase ROCK I. Unphosphorylated Rnd3/RhoE associates primarily with membranes, but ROCK I-phosphorylated Rnd3/RhoE localizes in the cytosol. Phosphorylation of Rnd3/RhoE correlates with its activity in disrupting RhoA-induced stress fibers and inhibiting Ras-induced fibroblast transformation. In cells that lack stress fibers, such as macrophages and monocytes, Rnd3/RhoE induces a redistribution of actin, causing morphological changes in the cell. In addition, Rnd3/RhoE has been shown to inhibit cell cycle progression in G1 phase at a point upstream of the pRb family pocket protein checkpoint. Rnd3/RhoE has also been shown to inhibit Ras- and Raf-induced fibroblast transformation. In mammary epithelial tumor cells, Rnd3/RhoE regulates the assembly of the apical junction complex and tight junction formation. Rnd3/RhoE is underexpressed in prostate cancer cells both in vitro and in vivo; re-expression of Rnd3/RhoE suppresses cell cycle progression and increases apoptosis, suggesting it may play a role in tumor suppression. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 182 matched cddid_all.tbl CDD cd04173 cd04173 206736 Rnd2_Rho7 Rnd2/Rho7 GTPases. Rnd2/Rho7 is a member of the novel Rho subfamily Rnd, together with Rnd1/Rho6 and Rnd3/RhoE/Rho8. Rnd2/Rho7 is transiently expressed in radially migrating cells in the brain while they are within the subventricular zone of the hippocampus and cerebral cortex. These migrating cells typically develop into pyramidal neurons. Cells that exogenously expressed Rnd2/Rho7 failed to migrate to upper layers of the brain, suggesting that Rnd2/Rho7 plays a role in the radial migration and morphological changes of developing pyramidal neurons, and that Rnd2/Rho7 degradation is necessary for proper cellular migration. The Rnd2/Rho7 GEF Rapostlin is found primarily in the brain and together with Rnd2/Rho7 induces dendrite branching. Unlike Rnd1/Rho6 and Rnd3/RhoE/Rho8, which are RhoA antagonists, Rnd2/Rho7 binds the GEF Pragmin and significantly stimulates RhoA activity and Rho-A mediated cell contraction. Rnd2/Rho7 is also found to be expressed in spermatocytes and early spermatids, with male-germ-cell Rac GTPase-activating protein (MgcRacGAP), where it localizes to the Golgi-derived pro-acrosomal vesicle. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. 221 matched cddid_all.tbl CDD cd04174 cd04174 206737 Rnd1_Rho6 Rnd1/Rho6 GTPases. Rnd1/Rho6 is a member of the novel Rho subfamily Rnd, together with Rnd2/Rho7 and Rnd3/RhoE/Rho8. Rnd1/Rho6 binds GTP but does not hydrolyze it to GDP, indicating that it is constitutively active. In rat, Rnd1/Rho6 is highly expressed in the cerebral cortex and hippocampus during synapse formation, and plays a role in spine formation. Rnd1/Rho6 is also expressed in the liver and in endothelial cells, and is upregulated in uterine myometrial cells during pregnancy. Like Rnd3/RhoE/Rho8, Rnd1/Rho6 is believed to function as an antagonist to RhoA. Most Rho proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Rho proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 232 matched cddid_all.tbl CDD cd04175 cd04175 133375 Rap1 Rap1 family GTPase consists of Rap1a and Rap1b isoforms. The Rap1 subgroup is part of the Rap subfamily of the Ras family. It can be further divided into the Rap1a and Rap1b isoforms. In humans, Rap1a and Rap1b share 95% sequence homology, but are products of two different genes located on chromosomes 1 and 12, respectively. Rap1a is sometimes called smg p21 or Krev1 in the older literature. Rap1 proteins are believed to perform different cellular functions, depending on the isoform, its subcellular localization, and the effector proteins it binds. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules. Rap1 has also been shown to localize in the Golgi of rat fibroblasts, zymogen granules, plasma membrane, and the microsomal membrane of pancreatic acini, as well as in the endocytic compartment of skeletal muscle cells and fibroblasts. High expression of Rap1 has been observed in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines; interestingly, in the SCCs, the active GTP-bound form localized to the nucleus, while the inactive GDP-bound form localized to the cytoplasm. Rap1 plays a role in phagocytosis by controlling the binding of adhesion receptors (typically integrins) to their ligands. In yeast, Rap1 has been implicated in multiple functions, including activation and silencing of transcription and maintenance of telomeres. Rap1a, which is stimulated by T-cell receptor (TCR) activation, is a positive regulator of T cells by directing integrin activation and augmenting lymphocyte responses. In murine hippocampal neurons, Rap1b determines which neurite will become the axon and directs the recruitment of Cdc42, which is required for formation of dendrites and axons. In murine platelets, Rap1b is required for normal homeostasis in vivo and is involved in integrin activation. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 164 matched cddid_all.tbl CDD cd04176 cd04176 133376 Rap2 Rap2 family GTPase consists of Rap2a, Rap2b, and Rap2c. The Rap2 subgroup is part of the Rap subfamily of the Ras family. It consists of Rap2a, Rap2b, and Rap2c. Both isoform 3 of the human mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) and Traf2- and Nck-interacting kinase (TNIK) are putative effectors of Rap2 in mediating the activation of c-Jun N-terminal kinase (JNK) to regulate the actin cytoskeleton. In human platelets, Rap2 was shown to interact with the cytoskeleton by binding the actin filaments. In embryonic Xenopus development, Rap2 is necessary for the Wnt/beta-catenin signaling pathway. The Rap2 interacting protein 9 (RPIP9) is highly expressed in human breast carcinomas and correlates with a poor prognosis, suggesting a role for Rap2 in breast cancer oncogenesis. Rap2b, but not Rap2a, Rap2c, Rap1a, or Rap1b, is expressed in human red blood cells, where it is believed to be involved in vesiculation. A number of additional effector proteins for Rap2 have been identified, including the RalGEFs RalGDS, RGL, and Rlf, which also interact with Rap1 and Ras. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. 163 matched cddid_all.tbl CDD cd04177 cd04177 133377 RSR1 RSR1/Bud1p family GTPase. RSR1/Bud1p is a member of the Rap subfamily of the Ras family that is found in fungi. In budding yeasts, RSR1 is involved in selecting a site for bud growth on the cell cortex, which directs the establishment of cell polarization. The Rho family GTPase cdc42 and its GEF, cdc24, then establish an axis of polarized growth by organizing the actin cytoskeleton and secretory apparatus at the bud site. It is believed that cdc42 interacts directly with RSR1 in vivo. In filamentous fungi, polar growth occurs at the tips of hypha and at novel growth sites along the extending hypha. In Ashbya gossypii, RSR1 is a key regulator of hyphal growth, localizing at the tip region and regulating in apical polarization of the actin cytoskeleton. Most Ras proteins contain a lipid modification site at the C-terminus, with a typical sequence motif CaaX, where a = an aliphatic amino acid and X = any amino acid. Lipid binding is essential for membrane attachment, a key feature of most Ras proteins. 168 matched cddid_all.tbl CDD cd04178 cd04178 206753 Nucleostemin_like A circularly permuted subfamily of the Ras GTPases. Nucleostemin (NS) is a nucleolar protein that functions as a regulator of cell growth and proliferation in stem cells and in several types of cancer cells, but is not expressed in the differentiated cells of most mammalian adult tissues. NS shuttles between the nucleolus and nucleoplasm bidirectionally at a rate that is fast and independent of cell type. Lowering GTP levels decreases the nucleolar retention of NS, and expression of NS is abruptly down-regulated during differentiation prior to terminal cell division. Found only in eukaryotes, NS consists of an N-terminal basic domain, a coiled-coil domain, a GTP-binding domain, an intermediate domain, and a C-terminal acidic domain. Experimental evidence indicates that NS uses its GTP-binding property as a molecular switch to control the transition between the nucleolus and nucleoplasm, and this process involves interaction between the basic, GTP-binding, and intermediate domains of the protein. 171 matched cddid_all.tbl CDD cd04179 cd04179 133022 DPM_DPG-synthase_like DPM_DPG-synthase_like is a member of the Glycosyltransferase 2 superfamily. DPM1 is the catalytic subunit of eukaryotic dolichol-phosphate mannose (DPM) synthase. DPM synthase is required for synthesis of the glycosylphosphatidylinositol (GPI) anchor, N-glycan precursor, protein O-mannose, and C-mannose. In higher eukaryotes,the enzyme has three subunits, DPM1, DPM2 and DPM3. DPM is synthesized from dolichol phosphate and GDP-Man on the cytosolic surface of the ER membrane by DPM synthase and then is flipped onto the luminal side and used as a donor substrate. In lower eukaryotes, such as Saccharomyces cerevisiae and Trypanosoma brucei, DPM synthase consists of a single component (Dpm1p and TbDpm1, respectively) that possesses one predicted transmembrane region near the C terminus for anchoring to the ER membrane. In contrast, the Dpm1 homologues of higher eukaryotes, namely fission yeast, fungi, and animals, have no transmembrane region, suggesting the existence of adapter molecules for membrane anchoring. This family also includes bacteria and archaea DPM1_like enzymes. However, the enzyme structure and mechanism of function are not well understood. The UDP-glucose:dolichyl-phosphate glucosyltransferase (DPG_synthase) is a transmembrane-bound enzyme of the endoplasmic reticulum involved in protein N-linked glycosylation. This enzyme catalyzes the transfer of glucose from UDP-glucose to dolichyl phosphate. This protein family belongs to Glycosyltransferase 2 superfamily. 185 matched cddid_all.tbl CDD cd04180 cd04180 133023 UGPase_euk_like Eukaryotic UGPase-like includes UDPase and UDPGlcNAc pyrophosphorylase enzymes. This family includes UDP-Glucose Pyrophosphorylase (UDPase) and UDPGlcNAc pyrophosphorylase enzymes. The two enzymes share significant sequence and structure similarity. UDP-Glucose Pyrophosphorylase catalyzes a reversible production of UDP-Glucose and pyrophosphate (PPi) from Glucose-1-phosphate and UTP. UDP-glucose plays pivotal roles in galactose utilization, in glycogen synthesis, and in the synthesis of the carbohydrate moieties of glycolipids , glycoproteins , and proteoglycans . UDP-N-acetylglucosamine (UDPGlcNAc) pyrophosphorylase (UAP) (also named GlcNAc1P uridyltransferase), catalyzes the reversible conversion of UTP and GlcNAc1P from PPi and UDPGlcNAc, which is a key precursor of N- and O-linked glycosylations and is essential for the synthesis of chitin (a major component of the fungal cell wall) and of the glycosylphosphatidylinositol (GPI) linker anchoring a variety of cell surface proteins to the plasma membrane. In bacteria, UDPGlcNAc represents an essential precursor for both peptidoglycan and lipopolysaccharide biosynthesis. 266 matched cddid_all.tbl CDD cd04181 cd04181 133024 NTP_transferase NTP_transferases catalyze the transfer of nucleotides onto phosphosugars. Nucleotidyltransferases transfer nucleotides onto phosphosugars. The enzyme family includes Alpha-D-Glucose-1-Phosphate Cytidylyltransferase, Mannose-1-phosphate guanyltransferase, and Glucose-1-phosphate thymidylyltransferase. The products are activated sugars that are precursors for synthesis of lipopolysaccharide, glycolipids and polysaccharides. 217 matched cddid_all.tbl CDD cd04182 cd04182 133025 GT_2_like_f GT_2_like_f is a subfamily of the glycosyltransferase family 2 (GT-2) with unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families. 186 matched cddid_all.tbl CDD cd04183 cd04183 133026 GT2_BcE_like GT2_BcbE_like is likely involved in the biosynthesis of the polysaccharide capsule. GT2_BcbE_like: The bcbE gene is one of the genes in the capsule biosynthetic locus of Pasteurella multocida. Its deducted product is likely involved in the biosynthesis of the polysaccharide capsule, which is found on surface of a wide range of bacteria. It is a subfamily of Glycosyltransferase Family GT2, which includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. 231 matched cddid_all.tbl CDD cd04184 cd04184 133027 GT2_RfbC_Mx_like Myxococcus xanthus RfbC like proteins are required for O-antigen biosynthesis. The rfbC gene encodes a predicted protein of 1,276 amino acids, which is required for O-antigen biosynthesis in Myxococcus xanthus. It is a subfamily of Glycosyltransferase Family GT2, which includes diverse families of glycosyl transferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. 202 matched cddid_all.tbl CDD cd04185 cd04185 133028 GT_2_like_b Subfamily of Glycosyltransferase Family GT2 of unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families. 202 matched cddid_all.tbl CDD cd04186 cd04186 133029 GT_2_like_c Subfamily of Glycosyltransferase Family GT2 of unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families. 166 matched cddid_all.tbl CDD cd04187 cd04187 133030 DPM1_like_bac Bacterial DPM1_like enzymes are related to eukaryotic DPM1. A family of bacterial enzymes related to eukaryotic DPM1; Although the mechanism of eukaryotic enzyme is well studied, the mechanism of the bacterial enzymes is not well understood. The eukaryotic DPM1 is the catalytic subunit of eukaryotic Dolichol-phosphate mannose (DPM) synthase. DPM synthase is required for synthesis of the glycosylphosphatidylinositol (GPI) anchor, N-glycan precursor, protein O-mannose, and C-mannose. The enzyme has three subunits, DPM1, DPM2 and DPM3. DPM is synthesized from dolichol phosphate and GDP-Man on the cytosolic surface of the ER membrane by DPM synthase and then is flipped onto the luminal side and used as a donor substrate. This protein family belongs to Glycosyltransferase 2 superfamily. 181 matched cddid_all.tbl CDD cd04188 cd04188 133031 DPG_synthase DPG_synthase is involved in protein N-linked glycosylation. UDP-glucose:dolichyl-phosphate glucosyltransferase (DPG_synthase) is a transmembrane-bound enzyme of the endoplasmic reticulum involved in protein N-linked glycosylation. This enzyme catalyzes the transfer of glucose from UDP-glucose to dolichyl phosphate. 211 matched cddid_all.tbl CDD cd04189 cd04189 133032 G1P_TT_long G1P_TT_long represents the long form of glucose-1-phosphate thymidylyltransferase. This family is the long form of Glucose-1-phosphate thymidylyltransferase. Glucose-1-phosphate thymidylyltransferase catalyses the formation of dTDP-glucose, from dTTP and glucose 1-phosphate. It is the first enzyme in the biosynthesis of dTDP-L-rhamnose, a cell wall constituent and a feedback inhibitor of the enzyme.There are two forms of Glucose-1-phosphate thymidylyltransferase in bacteria and archeae; short form and long form. The long form, which has an extra 50 amino acids c-terminal, is found in many species for which it serves as a sugar-activating enzyme for antibiotic biosynthesis and or other, unknown pathways, and in which dTDP-L-rhamnose is not necessarily produced.The long from enzymes also have a left-handed parallel helix domain at the c-terminus, whereas, th eshort form enzymes do not have this domain. The homotetrameric, feedback inhibited short form is found in numerous bacterial species that produce dTDP-L-rhamnose. 236 matched cddid_all.tbl CDD cd04190 cd04190 133033 Chitin_synth_C C-terminal domain of Chitin Synthase catalyzes the incorporation of GlcNAc from substrate UDP-GlcNAc into chitin. Chitin synthase, also called UDP-N-acetyl-D-glucosamine:chitin 4-beta-N-acetylglucosaminyltransferase, catalyzes the incorporation of GlcNAc from substrate UDP-GlcNAc into chitin, which is a linear homopolymer of GlcNAc residues formed by covalent beta-1,4 linkages. Chitin is an important component of the cell wall of fungi and bacteria and it is synthesized on the cytoplasmic surface of the cell membrane by membrane bound chitin synthases. Studies with fungi have revealed that most of them contain more than one chitin synthase gene. At least five subclasses of chitin synthases have been identified. 244 matched cddid_all.tbl CDD cd04191 cd04191 133034 Glucan_BSP_MdoH Glucan_BSP_MdoH catalyzes the elongation of beta-1,2 polyglucose chains of glucan. Periplasmic Glucan Biosynthesis protein MdoH is a glucosyltransferase that catalyzes the elongation of beta-1,2 polyglucose chains of glucan, requiring a beta-glucoside as a primer and UDP-glucose as a substrate. Glucans are composed of 5 to 10 units of glucose forming a highly branched structure, where beta-1,2-linked glucose constitutes a linear backbone to which branches are attached by beta-1,6 linkages. In Escherichia coli, glucans are located in the periplasmic space, functioning as regulator of osmolarity. It is synthesized at a maximum when cells are grown in a medium with low osmolarity. It has been shown to span the cytoplasmic membrane. 254 matched cddid_all.tbl CDD cd04192 cd04192 133035 GT_2_like_e Subfamily of Glycosyltransferase Family GT2 of unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families. 229 matched cddid_all.tbl CDD cd04193 cd04193 133036 UDPGlcNAc_PPase UDPGlcNAc pyrophosphorylase catalayzes the synthesis of UDPGlcNAc. UDP-N-acetylglucosamine (UDPGlcNAc) pyrophosphorylase (UAP) (also named GlcNAc1P uridyltransferase), catalyzes the reversible conversion of UTP and GlcNAc1 to PPi and UDPGlcNAc. UDP-N-acetylglucosamine (UDPGlcNAc), the activated form of GlcNAc, is a key precursor of N- and O-linked glycosylations. It is essential for the synthesis of chitin (a major component of the fungal cell wall) and of the glycosylphosphatidylinositol (GPI) linker which anchors a variety of cell surface proteins to the plasma membrane. In bacteria, UDPGlcNAc represents an essential precursor for both peptidoglycan and lipopolysaccharide biosynthesis. Human UAP has two isoforms, resulting from alternative splicing of a single gene and differing by the presence or absence of 17 amino acids. UDPGlcNAc pyrophosphorylase shares significant sequence and structure conservation with UDPglucose pyrophosphorylase. 323 matched cddid_all.tbl CDD cd04194 cd04194 133037 GT8_A4GalT_like A4GalT_like proteins catalyze the addition of galactose or glucose residues to the lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of the bacterial cell surface. The members of this family of glycosyltransferases catalyze the addition of galactose or glucose residues to the lipooligosaccharide (LOS) or lipopolysaccharide (LPS) of the bacterial cell surface. The enzymes exhibit broad substrate specificities. The known functions found in this family include: Alpha-1,4-galactosyltransferase, LOS-alpha-1,3-D-galactosyltransferase, UDP-glucose:(galactosyl) LPS alpha1,2-glucosyltransferase, UDP-galactose: (glucosyl) LPS alpha1,2-galactosyltransferase, and UDP-glucose:(glucosyl) LPS alpha1,2-glucosyltransferase. Alpha-1,4-galactosyltransferase from N. meningitidis adds an alpha-galactose from UDP-Gal (the donor) to a terminal lactose (the acceptor) of the LOS structure of outer membrane. LOSs are virulence factors that enable the organism to evade the immune system of host cells. In E. coli, the three alpha-1,2-glycosyltransferases, that are involved in the synthesis of the outer core region of the LPS, are all members of this family. The three enzymes share 40 % of sequence identity, but have different sugar donor or acceptor specificities, representing the structural diversity of LPS. 248 matched cddid_all.tbl CDD cd04195 cd04195 133038 GT2_AmsE_like GT2_AmsE_like is involved in exopolysaccharide amylovora biosynthesis. AmsE is a glycosyltransferase involved in exopolysaccharide amylovora biosynthesis in Erwinia amylovora. Amylovara is one of the three exopolysaccharide produced by E. amylovora. Amylovara-deficient mutants are non-pathogenic. It is a subfamily of Glycosyltransferase Family GT2, which includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. 201 matched cddid_all.tbl CDD cd04196 cd04196 133039 GT_2_like_d Subfamily of Glycosyltransferase Family GT2 of unknown function. GT-2 includes diverse families of glycosyltransferases with a common GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families. 214 matched cddid_all.tbl CDD cd04197 cd04197 133040 eIF-2B_epsilon_N The N-terminal domain of epsilon subunit of the eIF-2B is a subfamily of glycosyltransferase 2. N-terminal domain of epsilon subunit of the eukaryotic translation initiation factor 2B (eIF-2B): eIF-2B is a guanine nucleotide-exchange factor which mediates the exchange of GDP (bound to initiation factor eIF2) for GTP, generating active eIF2.GTP complex. EIF2B is a complex multimeric protein consisting of five subunits named alpha, beta, gamma, delta and epsilon. Subunit epsilon shares sequence similarity with gamma subunit, and with a family of bifunctional nucleotide-binding enzymes such as ADP-glucose pyrophosphorylase, suggesting that epsilon subunit may play roles in nucleotide binding activity. In yeast, eIF2B gamma enhances the activity of eIF2B-epsilon leading to the idea that these subunits form the catalytic subcomplex. 217 matched cddid_all.tbl CDD cd04198 cd04198 133041 eIF-2B_gamma_N The N-terminal domain of gamma subunit of the eIF-2B is a subfamily of glycosyltransferase 2. N-terminal domain of gamma subunit of the eukaryotic translation initiation factor 2B (eIF-2B): eIF-2B is a guanine nucleotide-exchange factor which mediates the exchange of GDP (bound to initiation factor eIF2) for GTP, generating active eIF2.GTP complex. EIF2B is a complex multimeric protein consisting of five subunits named alpha, beta, gamma, delta and epsilon. Subunit gamma shares sequence similarity with epsilon subunit, and with a family of bifunctional nucleotide-binding enzymes such as ADP-glucose pyrophosphorylase, suggesting that epsilon subunit may play roles in nucleotide binding activity. In yeast, eIF2B gamma enhances the activity of eIF2B-epsilon leading to the idea that these subunits form the catalytic subcomplex. 214 matched cddid_all.tbl CDD cd04199 cd04199 259862 CuRO_1_ceruloplasmin_like Cupredoxin domains 1, 3, and 5 of ceruloplasmin and similar proteins. This family includes the first, third, and fifth cupredoxin domains of ceruloplasmin and similar proteins including the first, third and fifth cupredoxin domains of unprocessed coagulation factors V and VIII. Ceruloplasmin (ferroxidase) is a multicopper oxidase essential for normal iron homeostasis. It functions in copper transport, amine oxidation and as an antioxidant preventing free radicals in serum. The protein has 6 cupredoxin domains and exhibits internal sequence homology that appears to have evolved from the triplication of a sequence unit composed of two tandem cupredoxin domains. Human Factor VIII facilitates blood clotting by acting as a cofactor for factor IXa. Factor VIII and IXa forms a complex in the presence of Ca+2 and phospholipids that converts factor X to the activated form Xa. 177 matched cddid_all.tbl CDD cd04200 cd04200 259863 CuRO_2_ceruloplasmin_like Cupredoxin domains 2, 4, and 6 of ceruloplasmin and similar proteins. This family includes the second, fourth and sixth cupredoxin domains of ceruloplasmin and similar proteins, including the second, fourth, and sixth cupredoxin domains of unprocessed coagulation factors V and VIII. Ceruloplasmin (ferroxidase) is a multicopper oxidase essential for normal iron homeostasis. Ceruloplasmin also functions in copper transport, amine oxidase and as an antioxidant preventing free radicals in serum. The protein has 6 cupredoxin domains and exhibits internal sequence homology that appears to have evolved from the triplication of a sequence unit composed of two tandem cupredoxin domains. Human Factor VIII facilitates blood clotting by acting as a cofactor for factor IXa Factor VIII and IXa forms a complex in the presence of Ca+2 and phospholipids that converts factor X to the activated form Xa. 141 matched cddid_all.tbl CDD cd04201 cd04201 259864 CuRO_1_CuNIR_like Cupredoxin domain 1 of Copper-containing nitrite reductase and two-domain laccase. Copper-containing nitrite reductase (CuNIR), which catalyzes the reduction of NO2- to NO, is the key enzyme in the denitrification process in denitrifying bacteria. CuNIR contains at least one type 1 copper center and a type 2 copper center, which serves as the active site of the enzyme. A histidine, bound to the Type 2 Cu center, is responsible for binding and reducing nitrite. A Cys-His bridge plays an important role in facilitating rapid electron transfer from the type 1 center to the type 2 center. A reduced type I blue copper protein (pseudoazurin) was found to be a specific electron transfer donor for the copper-containing NIR in bacteria Alcaligenes faecalis. The two-domain laccase (small laccase) in this family differs significantly from all laccases. It resembles two domain nitrite reductase in both sequence homology and structure similarity. It consists of two domains and forms trimers and hence resembles the quaternary structure of nitrite reductases more than that of larger laccases. 120 matched cddid_all.tbl CDD cd04202 cd04202 259865 CuRO_D2_2dMcoN_like The second cupredoxin domain of bacterial two domain multicopper oxidase McoN and similar proteins. This family includes bacterial two domain multicopper oxidases (2dMCOs) represented by the McoN from Nitrosomonas europaea. McoN is a trimeric type C blue copper oxidase. Each subunit houses a type 1 copper site in domain 1 and a type 2/type 3 trinuclear copper cluster at the subunit-subunit interface. The 2dMCO is proposed to be a key intermediate in the evolution of three domain MCOs. The biological function of McoN has not been characterized. Multicopper oxidases couple oxidation of substrates with reduction of dioxygen to water. These MCOs are capable of oxidizing a vast range of substrates, varying from aromatic to inorganic compounds such as metals. 138 matched cddid_all.tbl CDD cd04203 cd04203 259866 Cupredoxin_like_3 Uncharacterized subfamiy of Cupredoxin. Cupredoxins contain type I copper centers and are involved in inter-molecular electron transfer reactions. Cupredoxins are blue copper proteins, having an intense blue color due to the presence of a mononuclear type 1 (T1) copper site. Structurally, the cupredoxin-like fold consists of a beta-sandwich with 7 strands in 2 beta-sheets, which is arranged in a Greek-key beta-barrel. Some of these proteins have lost the ability to bind copper. Majority of family members contain multiple cupredoxin domain repeats: ceruloplamin and coagulation factors V/VIII have six repeats; laccase, ascorbate oxidase, and spore coat protein A, and multicopper oxidase CueO contain three repeats; and nitrite reductase has two repeats. Others are mono-domain cupredoxins, such as plastocyanin, pseudoazurin, plantacyanin, azurin, rusticyanin, stellacyanin, quinol oxidase and the periplasmic domain of cytochrome c oxidase subunit II. Proteins of this uncharacterized subfamily contain a single cupredoxin domain. 84 matched cddid_all.tbl CDD cd04204 cd04204 259867 Pseudoazurin_like Small blue copper proteins including pseudocyanin, plastocyanin, halocyanin and amicyanin. The Pseudocyanin-like family of copper-binding proteins (or blue (type 1) copper domain) is a family of small proteins that bind a single copper atom and are characterized by an intense electronic absorption band near 600 nm. Pseudoazurin (PAz) has been identified as a electron donor in the denitrification pathway. For example, PAz acts as an electron donor to cytochrome c peroxidase and N2OR from Paracoccus pantotrophus (Pp), and to the copper containing nitrite reductase (NiR) that catalyzes the second step of denitrification. Plastocyanin is found in cyanobacteria, higher plants, and some algae where it plays a role in photosynthesis. Plastocyanin is responsible for transporting electrons from PSII to PSI. This family also includes halocyanins found in halophilic archaea such as Natronomonas pharaonis (Natronobacterium pharaonis) and amicyanin found in bacteria Paracoccus denitrificans. 92 matched cddid_all.tbl CDD cd04205 cd04205 259868 CuRO_2_LCC_like Cupredoxin domain 2 of laccase-like multicopper oxidases; including laccase, CueO, spore coat protein A, ascorbate oxidase and similar proteins. Laccase-like multicopper oxidases (MCOs) are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 152 matched cddid_all.tbl CDD cd04206 cd04206 259869 CuRO_1_LCC_like Cupredoxin domain 1 of laccase-like multicopper oxidases; including laccase, CueO, spore coat protein A, ascorbate oxidase and similar proteins. Laccase-like multicopper oxidases (MCOs) in this family contain three cupredoxin domains. They are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs are capable of oxidizing a vast range of substrates, varying from aromatic to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites; Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. Also included in this family are cupredoxin domains 1, 3, and 5 of the 6-domain MCO ceruloplasmin and similar proteins. 120 matched cddid_all.tbl CDD cd04207 cd04207 259870 CuRO_3_LCC_like Cupredoxin domain 3 of laccase-like multicopper oxidases; including laccase, CueO, spore coat protein A, ascorbate oxidase and similar proteins. Laccase-like multicopper oxidases (MCOs) in this family contain three cupredoxin domains. They are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs are capable of oxidizing a vast range of substrates, varying from aromatic to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites; Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. Also included in this family are cupredoxin domains 2, 4, and 6 of the 6-domain MCO ceruloplasmin and similar proteins. 132 matched cddid_all.tbl CDD cd04208 cd04208 259871 CuRO_2_CuNIR Cupredoxin domain 2 of Copper-containing nitrite reductase. Copper-containing nitrite reductase (CuNIR), which catalyzes the reduction of NO2- to NO, is the key enzyme in the denitrification process in denitrifying bacteria. CuNIR contains at least one type 1 copper center and a type 2 copper center in the protein. The type 2 copper center of a copper nitrite reductase is the active site of the enzyme. A histidine, bound to the Type 2 Cu center, is responsible for binding and reducing nitrite. A Cys-His bridge plays an important role in facilitating rapid electron transfer from the type 1 center to the type 2 center. A reduced type I blue copper protein (pseudoazurin) was found to be a specific electron transfer donor for the copper-containing NIR in bacteria Alcaligenes faecalis. 143 matched cddid_all.tbl CDD cd04210 cd04210 259872 Cupredoxin_like_1 Uncharacterized Cupredoxin-like subfamily. Cupredoxins contain type I copper centers and are involved in inter-molecular electron transfer reactions. Cupredoxins are blue copper proteins because they have an intense blue color due to the presence of a mononuclear type 1 (T1) copper site. Structurally, the cupredoxin-like fold consists of a beta-sandwich with 7 strands in 2 beta-sheets, which is arranged in a Greek-key beta-barrel. Some of these proteins have lost the ability to bind copper. Majority of family members contain multiple cupredoxin domain repeats; ceruloplasmin and coagulation factors V/VIII have six repeats; Laccase, ascorbate oxidase, and spore coat protein A, and multicopper oxidase CueO contain three repeats; and nitrite reductase has two repeats. Others are mono-domain cupredoxins, such as plastocyanin, pseudoazurin, plantacyanin, azurin, rusticyanin, stellacyanin, quinol oxidase and the periplasmic domain of cytochrome c oxidase subunit II. 111 matched cddid_all.tbl CDD cd04211 cd04211 259873 Cupredoxin_like_2 Uncharacterized Cupredoxin-like subfamily. Cupredoxins contain type I copper centers and are involved in inter-molecular electron transfer reactions. Cupredoxins are blue copper proteins because they have an intense blue color due to the presence of a mononuclear type 1 (T1) copper site. Structurally, the cupredoxin-like fold consists of a beta-sandwich with 7 strands in 2 beta-sheets, which is arranged in a Greek-key beta-barrel. Some of these proteins have lost the ability to bind copper. Majority of family members contain multiple cupredoxin domain repeats; ceruloplasmin and coagulation factors V/VIII have six repeats; Laccase, ascorbate oxidase, and spore coat protein A, and multicopper oxidase CueO contain three repeats; and nitrite reductase has two repeats. Others are mono-domain cupredoxins, such as plastocyanin, pseudoazurin, plantacyanin, azurin, rusticyanin, stellacyanin, quinol oxidase and the periplasmic domain of cytochrome c oxidase subunit II. 110 matched cddid_all.tbl CDD cd04212 cd04212 259874 CuRO_UO_II The cupredoxin domain of Ubiquinol oxidase subunit II. Ubiquinol oxidase, the terminal oxidase in the respiratory chains of aerobic bacteria, is a multi-chain transmembrane protein located in the cell membrane. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits in ubiquinol oxidase varies from two to five. Although subunit II of ubiquinol oxidase lacks the binuclear CuA site found in cytochrome c oxidases, the structure is conserved. 99 matched cddid_all.tbl CDD cd04213 cd04213 259875 CuRO_CcO_Caa3_II The cupredoxin domain of Caa3 type Cytochrome c oxidase subunit II. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of most bacteria, is a multi-chain transmembrane protein located in the inner membrane the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. Caa3 type of CcO Subunit II contains a copper-copper binuclear site called CuA, which is believed to be involved in electron transfer from cytochrome c to the cytochromes a, a3 and CuB active site in subunit I. 103 matched cddid_all.tbl CDD cd04214 cd04214 259876 PAD_N N-terminal non-catalytic domain of protein-arginine deiminase. The N-terminal non-catalytic domain of protein-arginine deiminase has a cupredoxin-like fold, but lacks the Cu binding site. PAD (protein-arginine deiminase) and protein L-arginine iminohydrolase catalyze the conversion of protein arginine residues to citrulline residues post-translationally in a process called citrullination. The modification plays crucial regulatory roles in development and cell differentiation. 108 matched cddid_all.tbl CDD cd04215 cd04215 259877 Nitrosocyanin Nitrosocyanin (NC) is a mononuclear red copper protein. Nitrosocyanin (NC) is isolated from the ammonia oxidizing bacterium Nitrosomonas europaea. Nitrosocyanin exhibits remote sequence homology to classic blue copper proteins; its spectroscopic and electrochemical properties are different. The structure of NC is a trimer of single domain cupredoxins. Nitroscocyanin may mediate electron transfer. It could have a novel role as a nitric oxide dehydrogenase or a nitric oxide reductase in the oxidation of ammonia. 107 matched cddid_all.tbl CDD cd04216 cd04216 259878 Phytocyanin Phytocyanins are plant blue or type I copper proteins. Phytocyanins are plant blue or type I copper proteins. They are involved in electron transfer reactions with the Cu center transitioning between the oxidized Cu(II) form and the reduced Cu(I) form. Phytocyanins are classified into four groups: stellacyanin, plantacyanin, uclacyanin and early nodulin groups. Stellacyanin appears to be associated with the plant cell wall; it may be involved in oxidative reactions to build polymeric material making up the cell wall. Plantacyanin is shown to play a role in reproduction in Arabidopsis. Plantacyanins may also be stress-related proteins and may be involved in plant defense responses. The early nodulin-like protein (OsENODL1) from Oryza sativa is expressed specifically at the late developmental stage of the seeds. 98 matched cddid_all.tbl CDD cd04217 cd04217 259879 Cupredoxin_Fibrocystin-L_like Cupredoxin domain of PKHDL1, a homolog of the autosomal recessive polycystic kidney disease protein. One member of this family is Fibrocystin-L, a homolog of the autosomal recessive polycystic kidney disease protein PKHD1. Human fibrocystin-L is predicted to be a large receptor protein (466 kDa) with a signal peptide, a single transmembrane domain and a short cytoplasmic tail. Fibrocystin-L is widely expressed at a low level in most tissues but is up-regulated specifically in T lymphocytes following activation signals. It may play roles in immunity. 86 matched cddid_all.tbl CDD cd04218 cd04218 259880 Pseudoazurin Pseudoazurin (Paz) is a type I blue copper electron-transfer protein. Pseudoazurin (PAz) has been identified as an electron donor to the denitrification pathway. For example, PAz acts as an electron donor to cytochrome c peroxidase and N2OR from Paracoccus pantotrophus (Pp), and to the copper containing nitrite reductase (NiR) that catalyzes the second step of denitrification. It has been shown that pseudoazurin dramatically enhances the reaction profile of nitrite reduction by Paracoccus pantotrophus cytochrome cd1 and facilitates release of the product nitric oxide. The ability of this small redox protein to interact with a multitude of structurally different partners has been attributed to the hydrophobic character of the binding surface. 117 matched cddid_all.tbl CDD cd04219 cd04219 259881 Plastocyanin Plastocyanin is a type I copper protein and functions in the electron transfer from PSII to PSI. Plastocyanin is a small copper-containing protein found in cyanobacteria, higher plants, and some algae, where it plays a role in photosynthesis. The two photosystems that are primarily responsible for photosynthesis are photosystem I (PSI) and photosystem II (PSII). The flow of electrons begins in PSII, which acts as a proton pump. Plastocyanin is responsible for transporting electrons from PSII to PSI. 97 matched cddid_all.tbl CDD cd04220 cd04220 259882 Halocyanin Halocyanin is an archaea blue (type I) copper redox protein. Halocyanins are blue (type I) copper redox proteins found in halophilic archaea such as Natronomonas pharaonis (Natronobacterium pharaonis). Halocyanin may serve as a mobile electron carrier at a peripheral membrane protein. The copper-binding domain is present only once in some halocyanins and is duplicated in others. 92 matched cddid_all.tbl CDD cd04221 cd04221 259883 MauL Methylamine utilization protein MauL. MauL is one of the products from the methylamine utilization gene cluster in Methylobacterium extorquens AM1. Mutants generated by insertions in mauL were not able to grow on methylamine or any other primary amine as carbon sources. MauL belongs to the blue or type I copper protein family. They are involved in electron transfer reactions with the Cu center transitioning between the oxidized Cu(II) form and the reduced Cu(I) form. 83 matched cddid_all.tbl CDD cd04222 cd04222 259884 CuRO_1_ceruloplasmin The first cupredoxin domain of Ceruloplasmin. Ceruloplasmin is a multicopper oxidase essential for normal iron homeostasis and copper transport in blood. It also functions in amine oxidation and as an antioxidant preventing free radicals in serum. The protein has 6 cupredoxin domains with six copper centers; three mononuclear sites in domain 2, 4 and 6 and three in the form of trinuclear clusters at the interface of domains 1 and 6. Ceruloplasmin exhibits internal sequence homology that appears to have evolved from the triplication of a sequence unit composed of two tandem cupredoxin domains. This model represents the first cupredoxin domain of ceruloplasmin. 183 matched cddid_all.tbl CDD cd04223 cd04223 259885 N2OR_C The C-terminal cupredoxin domain of Nitrous-oxide reductase. Nitrous-oxide reductase participates in nitrogen metabolism and catalyzes the last step in dissimilatory nitrate reduction, the two-electron reduction of N2O to N2. It contains copper ions as cofactors in the form of a binuclear CuA center at the site of electron entry and a tetranuclear CuZ centre at the active site. The C-terminus of Nitrous-oxide reductase is a cupredoxin domain. 95 matched cddid_all.tbl CDD cd04224 cd04224 259886 CuRO_3_ceruloplasmin The third cupredoxin domain of Ceruloplasmin. Ceruloplasmin is a multicopper oxidase essential for normal iron homeostasis and copper transport in blood. It also functions in amine oxidation and as an antioxidant preventing free radicals in serum. The protein has 6 cupredoxin domains with six copper centers; three mononuclear sites in domain 2, 4 and 6 and three in the form of trinuclear clusters at the interface of domains 1 and 6. Ceruloplasmin exhibits internal sequence homology that appears to have evolved from the triplication of a sequence unit composed of two tandem cupredoxin domains. This model represents the third cupredoxin domain of ceruloplasmin. 197 matched cddid_all.tbl CDD cd04225 cd04225 259887 CuRO_5_ceruloplasmin The fifth cupredoxin domain of Ceruloplasmin. Ceruloplasmin is a multicopper oxidase essential for normal iron homeostasis and copper transport in blood. It also functions in amine oxidation and as an antioxidant preventing free radicals in serum. The protein has 6 cupredoxin domains with six copper centers; three mononuclear sites in domain 2, 4 and 6 and three in the form of trinuclear clusters at the interface of domains 1 and 6. Ceruloplasmin exhibits internal sequence homology that appears to have evolved from the triplication of a sequence unit composed of two tandem cupredoxin domains. This model represents the fifth cupredoxin domain of ceruloplasmin. 171 matched cddid_all.tbl CDD cd04226 cd04226 259888 CuRO_1_FV_like The first cupredoxin domain of coagulation factor VIII and similar proteins. Factor V is an essential coagulation protein with both pro- and anti-coagulant functions. Aberrant expression of human factor V can lead to bleeding or thromboembolic disease, which may be life-threatening. Bovine factor Va serves as the cofactor in the prothrombinase complex that results in a 300,000-fold increase in the rate of thrombin generation. Factor V is synthesized as a single polypeptide with six cupredoxin domains and a domain structure of 1-2-3-4-B-5-6-C1-C2, where 1-6 are cupredoxin domains, B is a domain with no known structural homologs and is dispensible for coagulant activity, and C are domains distantly related to discoidin protein-fold family members. Factor V has little activity prior to proteolytic cleavage by thrombin or FXa upon secretion. The resulting Factor Va is a heterodimer consisting of a heavy chain (1-2-3-4) and a light chain (5-6-C1-C2). This model represents the cupredoxin domain 1 of unprocessed Factor V or the heavy chain of Factor Va, and similar proteins including pseutarin C non-catalytic subunit. Pseutarin C is a prothrombin activator from Pseudonaja textilis venom. 165 matched cddid_all.tbl CDD cd04227 cd04227 259889 CuRO_3_FVIII_like The third cupredoxin domain of coagulation factor VIII and similar proteins. Factor VIII functions in the factor X-activating complex of the intrinsic coagulation pathway. It facilitates blood clotting by acting as a cofactor for factor IXa. In the presence of Ca2+ and phospholipids, Factor VIII and IXa form a complex that converts factor X to the activated form Xa. A variety of mutations in the Factor VIII gene can cause hemophilia A, which typically requires replacement therapy with purified protein. Factor VIII is synthesized as a single polypeptide with six cupredoxin domains and a domain structure of 1-2-3-4-B-5-6-C1-C2, where 1-6 are cupredoxin domains, B is a domain with no known structural homologs and is dispensible for coagulant activity, and C are domains distantly related to discoidin protein-fold family members. Factor VIII is initially processed through proteolysis to generate a heterodimer consisting of a heavy chain (1-2-3-4) and a light chain (5-6-C1-C2), which circulates in a tight complex with von Willebrand factor (VWF). Further processing of the heavy chain produces activated factor VIIIa, a heterotrimer composed of polypeptides (1-2), (3-4), and the light chain. This model represents the cupredoxin domain 3 of unprocessed Factor VIII or the heavy chain of circulating Factor VIII, and similar proteins. 177 matched cddid_all.tbl CDD cd04228 cd04228 259890 CuRO_5_FVIII_like The fifth cupredoxin domain of coagulation factor VIII and similar proteins. Factor VIII functions in the factor X-activating complex of the intrinsic coagulation pathway. It facilitates blood clotting by acting as a cofactor for factor IXa. In the presence of Ca2+ and phospholipids, Factor VIII and IXa form a complex that converts factor X to the activated form Xa. A variety of mutations in the Factor VIII gene can cause hemophilia A, which typically requires replacement therapy with purified protein. Factor VIII is synthesized as a single polypeptide with six cupredoxin domains and a domain structure of 1-2-3-4-B-5-6-C1-C2, where 1-6 are cupredoxin domains, B is a domain with no known structural homologs and is dispensible for coagulant activity, and C are domains distantly related to discoidin protein-fold family members. Factor VIII is initially processed through proteolysis to generate a heterodimer consisting of a heavy chain (1-2-3-4) and a light chain (5-6-C1-C2), which circulates in a tight complex with von Willebrand factor (VWF). Further processing of the heavy chain produces activated factor VIIIa, a heterotrimer composed of polypeptides (1-2), (3-4), and the light chain. This model represents the cupredoxin domain 5 of unprocessed Factor VIII or the first cupredoxin domain of the light chain of circulating Factor VIII, and similar proteins. 169 matched cddid_all.tbl CDD cd04229 cd04229 259891 CuRO_1_Ceruloplasmin_like_1 cupredoxin domain of ceruloplasmin homologs. Uncharacterized subfamily of ceruloplasmin homologous proteins. Ceruloplasmin (ferroxidase) is a multicopper oxidase essential for normal iron homeostasis. Ceruloplasmin also functions in copper transport, amine oxidase and as an antioxidant preventing free radicals in serum. The protein has 6 cupredoxin domains and exhibits internal sequence homology that appears to have evolved from the triplication of a sequence unit composed of two tandem cupredoxin domains. This model represents the first domain of the triplicated units. 175 matched cddid_all.tbl CDD cd04230 cd04230 259892 Sulfocyanin Sulfocyanin is a blue copper protein in archaebacterium Sulfolobus acidocaldarius. Sulfocyanin is a blue copper protein with a putative membrane anchoring hydrophobic motif at the N-terminus. It may substitute for cytochrome C in electron transfer reactions in archaea. 143 matched cddid_all.tbl CDD cd04231 cd04231 259893 Rusticyanin Rusticyanin is a cupredoxin in archaea and proteobacteria. Rusticyanin is a copper-containing protein which is involved in electron-transfer. The members of this family are found in archaea and proteobacteria. It is a cupredoxin, or blue-copper protein due to its color. Rusticyanin, extracted from the bacteria Thiobacillus ferrooxidans is redox active down to PH 2.0 and the acid-stable cytochrome c is the primary acceptor of the electron. This organism can grow on Fe2+ as its sole energy source. Rusticyanin is thought to be a principal component in the iron respiratory electron transport chain of T. ferrooxidans. 127 matched cddid_all.tbl CDD cd04232 cd04232 259894 CuRO_1_CueO_FtsP The first Cupredoxin domain of the multicopper oxidase CueO, the cell division protein FtsP, and similar proteins. CueO is a multicopper oxidase (MCO) that is part of the copper-regulatory cue operon, which employs a cytosolic metalloregulatory protein CueR that induces expression of CopA and CueO under copper stress conditions. CueO is a periplasmic multicopper oxidase that is stimulated by exogenous copper(II). FtsP (also named SufI) is a component of the cell division apparatus. It is involved in protecting or stabilizing the assembly of divisomes under stress conditions. FtsP belongs to the multicopper oxidase superfamily but lacks metal cofactors. The protein is localized at septal rings and may serve as a scaffolding function. Members of this subfamily contain three cupredoxin domains and this model represents the first domain. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. FtsP does not contain any copper binding sites. 120 matched cddid_all.tbl CDD cd04233 cd04233 259895 Auracyanin Auracyanins A and B and similar proteins. This subfamily includes both auracyanins A and B from the photosynthetic bacterium Chloroflexus aurantiacus and similar proteins. Auracyanins A and B are very similar blue copper proteins with 38% sequence identity and are homologous to the bacterial redox protein Azurin. However, auracyanin A is expressed only when C. aurantiacus cells are grown in light, whereas auracyanin B is expressed in both dark and light conditions. Thus, auracyanin A may function as a redox partner in photosynthesis, while auracyanin B may function in aerobic respiration. 121 matched cddid_all.tbl CDD cd04234 cd04234 239767 AAK_AK AAK_AK: Amino Acid Kinase Superfamily (AAK), Aspartokinase (AK); this CD includes the N-terminal catalytic domain of aspartokinase (4-L-aspartate-4-phosphotransferase;). AK is the first enzyme in the biosynthetic pathway of the aspartate family of amino acids (lysine, threonine, methionine, and isoleucine) and the bacterial cell wall component, meso-diaminopimelate. It also catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. One mechanism for the regulation of this pathway is by the production of several isoenzymes of aspartokinase with different repressors and allosteric inhibitors. Pairs of ACT domains are proposed to specifically bind amino acids leading to allosteric regulation of the enzyme. In Escherichia coli, three different aspartokinase isoenzymes are regulated specifically by lysine, methionine, and threonine. AK-HSDHI (ThrA) and AK-HSDHII (MetL) are bifunctional enzymes that consist of an N-terminal AK and a C-terminal homoserine dehydrogenase (HSDH). ThrA and MetL are involved in threonine and methionine biosynthesis, respectively. The third isoenzyme, AKIII (LysC), is monofunctional and is involved in lysine synthesis. The three Bacillus subtilis isoenzymes, AKI (DapG), AKII (LysC), and AKIII (YclM), are feedback-inhibited by meso-diaminopimelate, lysine, and lysine plus threonine, respectively. The E. coli lysine-sensitive AK is described as a homodimer, whereas, the B. subtilis lysine-sensitive AK is described as a heterodimeric complex of alpha- and beta- subunits that are formed from two in-frame overlapping genes. A single AK enzyme type has been described in Pseudomonas, Amycolatopsis, and Corynebacterium. The fungal aspartate pathway is regulated at the AK step, with L-Thr being an allosteric inhibitor of the Saccharomyces cerevisiae AK (Hom3). At least two distinct AK isoenzymes can occur in higher plants, one is a monofunctional lysine-sensitive isoenzyme, which is involved in the overall regulation of the pathway and can be synergistically inhibited by S-adenosylmethionine. The other isoenzyme is a bifunctional, threonine-sensitive AK-HSDH protein. Also included in this CD is the catalytic domain of the Methylomicrobium alcaliphilum ectoine AK, the first enzyme of the ectoine biosynthetic pathway, found in this bacterium, and several other halophilic/halotolerant bacteria. 227 matched cddid_all.tbl CDD cd04235 cd04235 239768 AAK_CK AAK_CK: Carbamate kinase (CK) catalyzes both the ATP-phosphorylation of carbamate and carbamoyl phosphate (CP) utilization with the production of ATP from ADP and CP. Both CK (this CD) and nonhomologous CP synthetase synthesize carbamoyl phosphate, an essential precursor of arginine and pyrimidine bases, in the presence of ATP, bicarbonate, and ammonia. CK is a homodimer of 33 kDa subunits and is a member of the Amino Acid Kinase Superfamily (AAK). 308 matched cddid_all.tbl CDD cd04236 cd04236 239769 AAK_NAGS-Urea AAK_NAGS-Urea: N-acetylglutamate (NAG) kinase-like domain of the NAG Synthase (NAGS) of the urea cycle found in animals. Ureogenic NAGS is a mitochondrial enzyme catalyzing the formation of NAG from acetylcoenzyme A and L-glutamate; NAG is an essential allosteric activator of carbamylphosphate synthase I, the first and rate limiting enzyme of the urea cycle. Ureogenic NAGS activity is dependent on the concentration of glutamate (substrate) and arginine (activator). Domain architecture of ureogenic NAGS consists of an N-terminal NAG kinase-like (ArgB) domain (this CD) and a C-terminal DUF619 domain. Members of this CD belong to the protein superfamily, the Amino Acid Kinase Family (AAKF). 271 matched cddid_all.tbl CDD cd04237 cd04237 239770 AAK_NAGS-ABP AAK_NAGS-ABP: N-acetylglutamate (NAG) kinase-like domain of the NAG Synthase (NAGS) of the arginine-biosynthesis pathway (ABP) found in gamma- and beta-proteobacteria and higher plant chloroplasts. Domain architecture of these NAGS consisted of an N-terminal NAG kinase-like (ArgB) domain (this CD) and a C-terminal NAG synthase, acetyltransferase (ArgA) domain. Both bacterial and plant sequences in this CD have a conserved N-terminal extension; a similar sequence in the NAG kinases of the cyclic arginine-biosynthesis pathway has been implicated in feedback inhibition sensing. Plant sequences also have an N-terminal chloroplast transit peptide and an insert (approx. 70 residues) in the C-terminal region of ArgB. Members of this CD belong to the Amino Acid Kinase Superfamily (AAK). 280 matched cddid_all.tbl CDD cd04238 cd04238 239771 AAK_NAGK-like AAK_NAGK-like: N-Acetyl-L-glutamate kinase (NAGK)-like . Included in this CD are the Escherichia coli and Pseudomonas aeruginosa type NAGKs which catalyze the phosphorylation of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in bacteria and photosynthetic organisms using either the acetylated, noncyclic (NC), or non-acetylated, cyclic (C) route of ornithine biosynthesis. Also included in this CD is a distinct group of uncharacterized (UC) bacterial and archeal NAGKs. Members of this CD belong to the Amino Acid Kinase Superfamily (AAK). 256 matched cddid_all.tbl CDD cd04239 cd04239 239772 AAK_UMPK-like AAK_UMPK-like: UMP kinase (UMPK)-like, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis. Regulation of this process is via feed-back control and via gene repression of carbamoyl phosphate synthetase (the first enzyme of the pyrimidine biosynthesis pathway). The UMP kinases of E. coli (Ec) and Pyrococcus furiosus (Pf) are known to function as homohexamers, with GTP and UTP being allosteric effectors. Like other related enzymes (carbamate kinase, aspartokinase, and N-acetylglutamate kinase) the E. coli and most bacterial UMPKs have a conserved, N-terminal, lysine residue proposed to function in the catalysis of the phosphoryl group transfer, whereas most archaeal UMPKs appear to lack this residue and the Pyrococcus furiosus structure has an additional Mg ion bound to the ATP molecule which is proposed to function as the catalysis instead. Also included in this CD are the alpha and beta subunits of the Mo storage protein (MosA and MosB) characterized as an alpha4-beta4 octamer containing an ATP-dependent, polynuclear molybdenum-oxide cluster. These and related sequences in this CD are members of the Amino Acid Kinase Superfamily (AAK). 229 matched cddid_all.tbl CDD cd04240 cd04240 239773 AAK_UC AAK_UC: Uncharacterized (UC) amino acid kinase-like proteins found mainly in archaea and a few bacteria. Sequences in this CD are members of the Amino Acid Kinase (AAK) superfamily. 203 matched cddid_all.tbl CDD cd04241 cd04241 239774 AAK_FomA-like AAK_FomA-like: This CD includes a fosfomycin biosynthetic gene product, FomA, and similar proteins found in a wide range of organisms. Together, the fomA and fomB genes in the fosfomycin biosynthetic gene cluster of Streptomyces wedmorensis confer high-level fosfomycin resistance. FomA and FomB proteins converted fosfomycin to fosfomycin monophosphate and fosfomycin diphosphate in the presence of ATP and a magnesium ion, indicating that FomA and FomB catalyzed phosphorylations of fosfomycin and fosfomycin monophosphate, respectively. FomA and related sequences in this CD are members of the Amino Acid Kinase Superfamily (AAK). 252 matched cddid_all.tbl CDD cd04242 cd04242 239775 AAK_G5K_ProB AAK_G5K_ProB: Glutamate-5-kinase (G5K) catalyzes glutamate-dependent ATP cleavage; G5K transfers the terminal phosphoryl group of ATP to the gamma-carboxyl group of glutamate, in the first and controlling step of proline (and, in mammals, ornithine) biosynthesis. G5K is subject to feedback allosteric inhibition by proline or ornithine. In microorganisms and plants, proline plays an important role as an osmoprotectant and, in mammals, ornithine biosynthesis is crucial for proper ammonia detoxification, since a G5K mutation has been shown to cause human hyperammonaemia. Microbial G5K generally consists of two domains: a catalytic G5K domain and one PUA (pseudo uridine synthases and archaeosine-specific transglycosylases) domain, and some lack the PUA domain. G5K requires free Mg for activity, it is tetrameric, and it aggregates to higher forms in a proline-dependent way. G5K lacking the PUA domain remains tetrameric, active, and proline-inhibitable, but the Mg requirement and the proline-triggered aggregation are greatly diminished and abolished, respectively, and more proline is needed for inhibition. Although plant and animal G5Ks are part of a bifunctional polypeptide, delta 1-pyrroline-5-carboxylate synthetase (P5CS), composed of an N-terminal G5K (ProB) and a C-terminal glutamyl 5- phosphate reductase (G5PR; ProA); bacterial and yeast G5Ks are monofunctional single-polypeptide enzymes. In this CD, all three domain architectures are present: G5K, G5K+PUA, and G5K+G5PR. 251 matched cddid_all.tbl CDD cd04243 cd04243 239776 AAK_AK-HSDH-like AAK_AK-HSDH-like: Amino Acid Kinase Superfamily (AAK), AK-HSDH-like; this family includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK- homoserine dehydrogenase (HSDH). These aspartokinases are found in such bacteria as E. coli (AKI-HSDHI, ThrA and AKII-HSDHII, MetL) and in higher plants (Z. mays AK-HSDH). AK and HSDH are the first and third enzymes in the biosynthetic pathway of the aspartate family of amino acids. AK catalyzes the phosphorylation of Asp to P-aspartyl phosphate. HSDH catalyzes the NADPH-dependent conversion of Asp 3-semialdehyde to homoserine. ThrA and MetL are involved in threonine and methionine biosynthesis, respectively. In E. coli, ThrA is subject to allosteric regulation by the end product L-threonine and the native enzyme is reported to be tetrameric. As with bacteria, plant AK and HSDH are feedback inhibited by pathway end products. Maize AK-HSDH is a Thr-sensitive 180-kD enzyme. Arabidopsis AK-HSDH is an alanine-activated, threonine-sensitive enzyme whose ACT domains, located C-terminal to the AK catalytic domain, were shown to be involved in allosteric activation. Also included in this CD is the catalytic domain of the aspartokinase (AK) of the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme (LysC) found in some bacteria such as E. coli. In E. coli, LysC is reported to be a homodimer of 50 kD subunits. Also included in this CD is the catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK - DAP decarboxylase (DapDC) found in some bacteria. DapDC, which is the lysA gene product, catalyzes the decarboxylation of DAP to lysine. 293 matched cddid_all.tbl CDD cd04244 cd04244 239777 AAK_AK-LysC-like AAK_AK-LysC-like: Amino Acid Kinase Superfamily (AAK), AK-LysC-like; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive AK isoenzyme found in higher plants. The lysine-sensitive AK isoenzyme is a monofunctional protein. It is involved in the overall regulation of the aspartate pathway and can be synergistically inhibited by S-adenosylmethionine. Also included in this CD is an uncharacterized LysC-like AK found in Euryarchaeota and some bacteria. AK catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. 298 matched cddid_all.tbl CDD cd04245 cd04245 239778 AAK_AKiii-YclM-BS AAK_AKiii-YclM-BS: Amino Acid Kinase Superfamily (AAK), AKiii-YclM-BS; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. In Bacillus subtilis (BS), YclM is reported to be a single polypeptide of 50 kD. The Bacillus subtilis 168 AKIII is induced by lysine and repressed by threonine, and it is synergistically inhibited by lysine and threonine. 288 matched cddid_all.tbl CDD cd04246 cd04246 239779 AAK_AK-DapG-like AAK_AK-DapG-like: Amino Acid Kinase Superfamily (AAK), AK-DapG-like; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the diaminopimelate-sensitive aspartokinase isoenzyme AKI (DapG), a monofunctional enzymes found in Bacilli (Bacillus subtilis 168), Clostridia, and Actinobacteria bacterial species, as well as, the catalytic AK domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related isoenzymes. In Bacillus subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive aspartokinase isoenzymes. The role of the AKI isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulation. The B. subtilis 168 AKII is induced by methionine, and repressed and inhibited by lysine. In Corynebacterium glutamicum and other various Gram-positive bacteria, the DAP-lysine pathway is feedback regulated by the concerted action of lysine and threonine. Also included in this CD are the aspartokinases of the extreme thermophile, Thermus thermophilus HB27, the Gram-negative obligate methylotroph, Methylophilus methylotrophus AS1, and those single aspartokinase isoenzyme types found in Pseudomonas, C. glutamicum, and Amycolatopsis lactamdurans. The B. subtilis AKI is tetrameric consisting of two alpha and two beta subunits; the alpha (43 kD) and beta (17 kD) subunit formed by two in-phase overlapping genes. The alpha subunit contains the AK catalytic domain and two ACT domains. The beta subunit contains two ACT domains. The B. subtilis 168 AKII aspartokinase is also described as tetrameric consisting of two alpha and two beta subunits. Some archeal aspartokinases in this group lack recognizable ACT domains. 239 matched cddid_all.tbl CDD cd04247 cd04247 239780 AAK_AK-Hom3 AAK_AK-Hom3: Amino Acid Kinase Superfamily (AAK), AK-Hom3; this CD includes the N-terminal catalytic domain of the aspartokinase HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae and other related AK domains. Aspartokinase, the first enzyme in the aspartate metabolic pathway, catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and in fungi, is responsible for the production of threonine, isoleucine and methionine. S. cerevisiae has a single aspartokinase isoenzyme type, which is regulated by feedback, allosteric inhibition by L-threonine. Recent studies show that the allosteric transition triggered by binding of threonine to AK involves a large change in the conformation of the native hexameric enzyme that is converted to an inactive one of different shape and substantially smaller hydrodynamic size. 306 matched cddid_all.tbl CDD cd04248 cd04248 239781 AAK_AK-Ectoine AAK_AK-Ectoine: Amino Acid Kinase Superfamily (AAK), AK-Ectoine; this CD includes the N-terminal catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and other various halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinase and L-aspartate-semialdehyde dehydrogenase. The M. alcaliphilum and the V. cholerae aspartokinases are encoded on the ectABCask operon. 304 matched cddid_all.tbl CDD cd04249 cd04249 239782 AAK_NAGK-NC AAK_NAGK-NC: N-Acetyl-L-glutamate kinase - noncyclic (NAGK-NC) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of microbial arginine biosynthesis using the acetylated, noncyclic route of ornithine biosynthesis. There are two variants of this pathway. In one, typified by the pathway in Escherichia coli, glutamate is acetylated by acetyl-CoA and acetylornithine is deacylated hydrolytically. In this pathway, feedback inhibition by arginine occurs at the initial acetylation of glutamate and not at the phosphorylation of NAG by NAGK. Homodimeric NAGK-NC are members of the Amino Acid Kinase Superfamily (AAK). 252 matched cddid_all.tbl CDD cd04250 cd04250 239783 AAK_NAGK-C AAK_NAGK-C: N-Acetyl-L-glutamate kinase - cyclic (NAGK-C) catalyzes the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of arginine biosynthesis found in some bacteria and photosynthetic organisms using the non-acetylated, cyclic route of ornithine biosynthesis. In this pathway, glutamate is first N-acetylated and then phosphorylated by NAGK to give phosphoryl NAG, which is converted to NAG-ornithine. There are two variants of this pathway. In one, typified by the pathway in Thermotoga maritima and Pseudomonas aeruginosa, the acetyl group is recycled by reversible transacetylation from acetylornithine to glutamate. The phosphorylation of NAG by NAGK is feedback inhibited by arginine. In photosynthetic organisms, NAGK is the target of the nitrogen-signaling protein PII. Hexameric formation of NAGK domains appears to be essential to both arginine inhibition and NAGK-PII complex formation. NAGK-C are members of the Amino Acid Kinase Superfamily (AAK). 279 matched cddid_all.tbl CDD cd04251 cd04251 239784 AAK_NAGK-UC AAK_NAGK-UC: N-Acetyl-L-glutamate kinase - uncharacterized (NAGK-UC). This domain is similar to Escherichia coli and Pseudomonas aeruginosa NAGKs which catalyze the phosphorylation of the gamma-COOH group of N-acetyl-L-glutamate (NAG) by ATP in the second step of microbial arginine biosynthesis. These uncharacterized domain sequences are found in some bacteria (Deinococci and Chloroflexi) and archea and belong to the Amino Acid Kinase Superfamily (AAK). 257 matched cddid_all.tbl CDD cd04252 cd04252 239785 AAK_NAGK-fArgBP AAK_NAGK-fArgBP: N-Acetyl-L-glutamate kinase (NAGK) of the fungal arginine-biosynthetic pathway (fArgBP). The nuclear-encoded, mitochondrial polyprotein precursor with an N-terminal NAGK (ArgB) domain (this CD), a central DUF619 domain, and a C-terminal reductase domain (ArgC, N-Acetylglutamate Phosphate Reductase, NAGPR). The precursor is cleaved in the mitochondria into two distinct enzymes (NAGK-DUF619 and NAGPR). Native molecular weights of these proteins indicate that the kinase is an octamer whereas the reductase is a dimer. This CD also includes some gamma-proteobacteria (Xanthomonas and Xylella) NAG kinases with an N-terminal NAGK (ArgB) domain (this CD) and a C-terminal DUF619 domain. The DUF619 domain is described as a putative distant homolog of the acetyltransferase, ArgA, predicted to function in NAG synthase association in fungi. Eukaryotic sequences have an N-terminal mitochondrial transit peptide. Members of this NAG kinase domain CD belong to the Amino Acid Kinase Superfamily (AAK). 248 matched cddid_all.tbl CDD cd04253 cd04253 239786 AAK_UMPK-PyrH-Pf AAK_UMPK-PyrH-Pf: UMP kinase (UMPK)-Pf, the mostly archaeal uridine monophosphate kinase (uridylate kinase) enzymes that catalyze UMP phosphorylation and play a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and via gene repression of carbamoyl phosphate synthetase (the first enzyme of the pyrimidine biosynthesis pathway). The UMP kinase of Pyrococcus furiosus (Pf) is known to function as a homohexamer, with GTP and UTP being allosteric effectors. Like other related enzymes (carbamate kinase, aspartokinase, and N-acetylglutamate kinase) the E. coli and most bacterial UMPKs have a conserved, N-terminal, lysine residue proposed to function in the catalysis of the phosphoryl group transfer, whereas most archaeal UMPKs (this CD) appear to lack this residue and the Pyrococcus furiosus structure has an additional Mg ion bound to the ATP molecule which is proposed to function as the catalysis instead. Members of this CD belong to the Amino Acid Kinase Superfamily (AAK). 221 matched cddid_all.tbl CDD cd04254 cd04254 239787 AAK_UMPK-PyrH-Ec UMP kinase (UMPK)-Ec, the microbial/chloroplast uridine monophosphate kinase (uridylate kinase) enzyme that catalyzes UMP phosphorylation and plays a key role in pyrimidine nucleotide biosynthesis; regulation of this process is via feed-back control and via gene repression of carbamoyl phosphate synthetase (the first enzyme of the pyrimidine biosynthesis pathway). The UMP kinase of E. coli (Ec) is known to function as a homohexamer, with GTP and UTP being allosteric effectors. Like other related enzymes (carbamate kinase, aspartokinase, and N-acetylglutamate kinase) the E. coli and most bacterial and chloroplast UMPKs (this CD) have a conserved, N-terminal, lysine residue proposed to function in the catalysis of the phosphoryl group transfer, whereas most archaeal UMPKs appear to lack this residue and the Pyrococcus furiosus structure has an additional Mg ion bound to the ATP molecule which is proposed to function as the catalysis instead. Members of this CD belong to the Amino Acid Kinase Superfamily (AAK). 231 matched cddid_all.tbl CDD cd04255 cd04255 239788 AAK_UMPK-MosAB AAK_UMPK-MosAB: This CD includes the alpha and beta subunits of the Mo storage protein (MosA and MosB) which are related to uridine monophosphate kinase (UMPK) enzymes that catalyze the phosphorylation of UMP by ATP, yielding UDP, and playing a key role in pyrimidine nucleotide biosynthesis. The Mo storage protein from the nitrogen-fixing bacterium, Azotobacter vinelandii, is characterized as an alpha4-beta4 octamer containing a polynuclear molybdenum-oxide cluster which is ATP-dependent to bind Mo and pH-dependent to release Mo. These and related bacterial sequences in this CD are members of the Amino Acid Kinase Superfamily (AAK). 262 matched cddid_all.tbl CDD cd04256 cd04256 239789 AAK_P5CS_ProBA AAK_P5CS_ProBA: Glutamate-5-kinase (G5K) domain of the bifunctional delta 1-pyrroline-5-carboxylate synthetase (P5CS), composed of an N-terminal G5K (ProB) and a C-terminal glutamyl 5- phosphate reductase (G5PR, ProA), the first and second enzyme catalyzing proline (and, in mammals, ornithine) biosynthesis. G5K transfers the terminal phosphoryl group of ATP to the gamma-carboxyl group of glutamate, and is subject to feedback allosteric inhibition by proline or ornithine. In plants, proline plays an important role as an osmoprotectant and, in mammals, ornithine biosynthesis is crucial for proper ammonia detoxification, since a G5K mutation has been shown to cause human hyperammonaemia. 284 matched cddid_all.tbl CDD cd04257 cd04257 239790 AAK_AK-HSDH AAK_AK-HSDH: Amino Acid Kinase Superfamily (AAK), AK-HSDH; this CD includes the N-terminal catalytic domain of aspartokinase (AK) of the bifunctional enzyme AK - homoserine dehydrogenase (HSDH). These aspartokinases are found in bacteria (E. coli AKI-HSDHI, ThrA and E. coli AKII-HSDHII, MetL) and higher plants (Z. mays AK-HSDH). AK and HSDH are the first and third enzymes in the biosynthetic pathway of the aspartate family of amino acids. AK catalyzes the phosphorylation of Asp to P-aspartyl phosphate. HSDH catalyzes the NADPH-dependent conversion of Asp 3-semialdehyde to homoserine. ThrA and MetL are involved in threonine and methionine biosynthesis, respectively. In E. coli, ThrA is subject to allosteric regulation by the end product L-threonine and the native enzyme is reported to be tetrameric. As with bacteria, plant AK and HSDH are feedback inhibited by pathway end products. Maize AK-HSDH is a Thr-sensitive 180-kD enzyme. Arabidopsis AK-HSDH is an alanine-activated, threonine-sensitive enzyme whose ACT domains, located C-terminal to the AK catalytic domain, were shown to be involved in allosteric activation. 294 matched cddid_all.tbl CDD cd04258 cd04258 239791 AAK_AKiii-LysC-EC AAK_AKiii-LysC-EC: Amino Acid Kinase Superfamily (AAK), AKiii-LysC-EC: this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKIII. AKIII is a monofunctional class enzyme (LysC) found in some bacteria such as E. coli. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. In E. coli, LysC is reported to be a homodimer of 50 kD subunits. 292 matched cddid_all.tbl CDD cd04259 cd04259 239792 AAK_AK-DapDC AAK_AK-DapDC: Amino Acid Kinase Superfamily (AAK), AK-DapDC; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the bifunctional enzyme AK - DAP decarboxylase (DapDC) found in some bacteria. Aspartokinase is the first enzyme in the aspartate metabolic pathway, catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. DapDC, which is the lysA gene product, catalyzes the decarboxylation of DAP to lysine. 295 matched cddid_all.tbl CDD cd04260 cd04260 239793 AAK_AKi-DapG-BS AAK_AKi-DapG-BS: Amino Acid Kinase Superfamily (AAK), AKi-DapG; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the diaminopimelate-sensitive aspartokinase isoenzyme AKI (DapG), a monofunctional class enzyme found in Bacilli (Bacillus subtilis 168), Clostridia, and Actinobacteria bacterial species. In Bacillus subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive aspartokinase isoenzymes. AKI activity is invariant during the exponential and stationary phases of growth and is not altered by addition of amino acids to the growth medium. The role of this isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulation. The B. subtilis AKI is tetrameric consisting of two alpha and two beta subunits; the alpha (43 kD) and beta (17 kD) subunit formed by two in-phase overlapping genes. The alpha subunit contains the AK catalytic domain and two ACT domains. The beta subunit contains two ACT domains. 244 matched cddid_all.tbl CDD cd04261 cd04261 239794 AAK_AKii-LysC-BS AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis 168, the regulation of the diaminopimelate (Dap)-lysine biosynthetic pathway involves dual control by Dap and lysine, effected through separate Dap- and lysine-sensitive aspartokinase isoenzymes. The B. subtilis 168 AKII is induced by methionine, and repressed and inhibited by lysine. Although Corynebacterium glutamicum is known to contain a single aspartokinase isoenzyme type, both the succinylase and dehydrogenase variant pathways of DAP-lysine synthesis operate simultaneously in this organism. In this organism and other various Gram-positive bacteria, the DAP-lysine pathway is feedback regulated by the concerted action of lysine and theronine. Also included in this CD are the aspartokinases of the extreme thermophile, Thermus thermophilus HB27, the Gram-negative obligate methylotroph, Methylophilus methylotrophus AS1, and those single aspartokinases found in Pseudomons, C. glutamicum, and Amycolatopsis lactamdurans. B. subtilis 168 AKII, and the C. glutamicum, Streptomyces clavuligerus and A. lactamdurans aspartokinases are described as tetramers consisting of two alpha and two beta subunits; the alpha (44 kD) and beta (18 kD) subunits formed by two in-phase overlapping polypeptides. 239 matched cddid_all.tbl CDD cd04263 cd04263 176265 DUF619-NAGK-FABP DUF619 domain of N-acetylglutamate kinase (NAGK) of the fungal arginine-biosynthetic pathway. DUF619-NAGK-FABP: DUF619 domain of N-acetylglutamate kinase (NAGK) of the fungal arginine-biosynthetic pathway (FABP). The nuclear-encoded, mitochondrial polyprotein precursor (ARG5,6) consists of an N-terminal NAGK (ArgB) domain, a central DUF619 domain, and a C-terminal reductase domain (ArgC, N-Acetylglutamate Phosphate Reductase, NAGPR). The precursor is cleaved into two distinct enzymes (NAGK-DUF619 and NAGPR) in the mitochondria. Native molecular weights of these proteins indicate that the kinase is an octamer whereas the reductase is a dimer. Arg5,6 catalyzes the second reaction of arginine biosynthesis; the phosphorylation of the gamma-carboxyl group of NAG to produce N-acetylglutamylphosphate (NAGP) which is subsequently converted to ornithine in two more steps. It also binds and regulates the promoters of nuclear and mitochondrial genes, and may possibly regulate precursor mRNA metabolism. The DUF619 domain function has yet to be characterized. 98 matched cddid_all.tbl CDD cd04264 cd04264 176266 DUF619-NAGS DUF619 domain of various N-acetylglutamate Synthases of the fungal arginine-biosynthetic pathway and urea cycle found in humans and fish. DUF619-NAGS: This family includes the DUF619 domain of various N-acetylglutamate synthases (NAGS) of the urea cycle found in humans and fish, the DUF619 domain of the NAGS of the fungal arginine-biosynthetic pathway (FABP), as well as the DUF619 domain present in C-terminal of a NAG kinase-like domain in a limited number of predicted NAGSs found in bacteria and Dictyostelium. Ureogenic NAGS is a mitochondrial enzyme catalyzing the formation of NAG from acetylcoenzyme A and L-glutamate. NAGS is an essential allosteric activator of carbamylphosphate synthase I, the first and rate limiting enzyme of the urea cycle. Domain architecture of ureogenic and fungal NAGS consists of an N-terminal NAG kinase-like domain and a C-terminal DUF619 domain. The DUF619 domain function has yet to be characterized. 99 matched cddid_all.tbl CDD cd04265 cd04265 176267 DUF619-NAGS-U DUF619 domain of various N-acetylglutamate Synthases (NAGS) of the urea (U) cycle of humans and fish. This family includes the DUF619 domain of various N-acetylglutamate synthases (NAGS) of the urea cycle found in humans and fish, the DUF619 domain of the NAGS of the fungal arginine-biosynthetic pathway (FABP), as well as the DUF619 domain present in C-terminal of a NAG kinase-like domain in a limited number of predicted NAGSs found in bacteria and Dictyostelium. Ureogenic NAGS is a mitochondrial enzyme catalyzing the formation of NAG from acetylcoenzyme A and L-glutamate. NAGS is an essential allosteric activator of carbamylphosphate synthase I, the first and rate limiting enzyme of the urea cycle. Domain architecture of ureogenic and fungal NAGS consists of an N-terminal NAG kinase-like domain and a C-terminal DUF619 domain. The DUF619 domain function has yet to be characterized. 99 matched cddid_all.tbl CDD cd04266 cd04266 176268 DUF619-NAGS-FABP DUF619 domain of N-acetylglutamate Synthase of the fungal arginine-biosynthetic pathway. DUF619-NAGS-FABP: This family includes the DUF619 domain of N-acetylglutamate synthase (NAGS) of the fungal arginine-biosynthetic pathway (FABP). This NAGS (also known as arginine-requiring protein 2 or ARG2) consists of an N-terminal NAG kinase-like domain and a C-terminal DUF619 domain. NAGS catalyzes the formation of NAG from acetylcoenzyme A and L-glutamate. The DUF619 domain, yet to be characterized, is predicted to function in NAGS association in fungi. 108 matched cddid_all.tbl CDD cd04267 cd04267 239795 ZnMc_ADAM_like Zinc-dependent metalloprotease, ADAM_like or reprolysin_like subgroup. The adamalysin_like or ADAM family of metalloproteases contains proteolytic domains from snake venoms, proteases from the mammalian reproductive tract, and the tumor necrosis factor alpha convertase, TACE. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions. 192 matched cddid_all.tbl CDD cd04268 cd04268 239796 ZnMc_MMP_like Zinc-dependent metalloprotease, MMP_like subfamily. This group contains matrix metalloproteinases (MMPs), serralysins, and the astacin_like family of proteases. 165 matched cddid_all.tbl CDD cd04269 cd04269 239797 ZnMc_adamalysin_II_like Zinc-dependent metalloprotease; adamalysin_II_like subfamily. Adamalysin II is a snake venom zinc endopeptidase. This subfamily contains other snake venom metalloproteinases, as well as membrane-anchored metalloproteases belonging to the ADAM family. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions. 194 matched cddid_all.tbl CDD cd04270 cd04270 239798 ZnMc_TACE_like Zinc-dependent metalloprotease; TACE_like subfamily. TACE, the tumor-necrosis factor-alpha converting enzyme, releases soluble TNF-alpha from transmembrane pro-TNF-alpha. 244 matched cddid_all.tbl CDD cd04271 cd04271 239799 ZnMc_ADAM_fungal Zinc-dependent metalloprotease, ADAM_fungal subgroup. The adamalysin_like or ADAM (A Disintegrin And Metalloprotease) family of metalloproteases are integral membrane proteases acting on a variety of extracellular targets. They are involved in shedding soluble peptides or proteins from the cell surface. This subfamily contains fungal ADAMs, whose precise function has yet to be determined. 228 matched cddid_all.tbl CDD cd04272 cd04272 239800 ZnMc_salivary_gland_MPs Zinc-dependent metalloprotease, salivary_gland_MPs. Metalloproteases secreted by the salivary glands of arthropods. 220 matched cddid_all.tbl CDD cd04273 cd04273 239801 ZnMc_ADAMTS_like Zinc-dependent metalloprotease, ADAMTS_like subgroup. ADAMs (A Disintegrin And Metalloprotease) are glycoproteins, which play roles in cell signaling, cell fusion, and cell-cell interactions. This particular subfamily represents domain architectures that combine ADAM-like metalloproteinases with thrombospondin type-1 repeats. ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) proteinases are inhibited by TIMPs (tissue inhibitors of metalloproteinases), and they play roles in coagulation, angiogenesis, development and progression of arthritis. They hydrolyze the von Willebrand factor precursor and various components of the extracellular matrix. 207 matched cddid_all.tbl CDD cd04275 cd04275 239802 ZnMc_pappalysin_like Zinc-dependent metalloprotease, pappalysin_like subfamily. The pregnancy-associated plasma protein A (PAPP-A or pappalysin-1) cleaves insulin-like growth factor-binding proteins 4 and 5, thereby promoting cell growth by releasing bound growth factor. This model includes pappalysins and related metalloprotease domains from all three kingdoms of life. The three-dimensional structure of an archaeal representative, ulilysin, has been solved. 225 matched cddid_all.tbl CDD cd04276 cd04276 239803 ZnMc_MMP_like_2 Zinc-dependent metalloprotease; MMP_like sub-family 2. A group of bacterial metalloproteinase domains similar to matrix metalloproteinases and astacin. 197 matched cddid_all.tbl CDD cd04277 cd04277 239804 ZnMc_serralysin_like Zinc-dependent metalloprotease, serralysin_like subfamily. Serralysins and related proteases are important virulence factors in pathogenic bacteria. They may be secreted into the medium via a mechanism found in gram-negative bacteria, that does not require n-terminal signal sequences which are cleaved after the transmembrane translocation. A calcium-binding domain c-terminal to the metalloprotease domain, which contains multiple tandem repeats of a nine-residue motif including the pattern GGxGxD, and which forms a parallel beta roll may be involved in the translocation mechanism and/or substrate binding. Serralysin family members may have a broad spectrum of substrates each, including host immunoglobulins, complement proteins, cell matrix and cytoskeletal proteins, as well as antimicrobial peptides. 186 matched cddid_all.tbl CDD cd04278 cd04278 239805 ZnMc_MMP Zinc-dependent metalloprotease, matrix metalloproteinase (MMP) sub-family. MMPs are responsible for a great deal of pericellular proteolysis of extracellular matrix and cell surface molecules, playing crucial roles in morphogenesis, cell fate specification, cell migration, tissue repair, tumorigenesis, gain or loss of tissue-specific functions, and apoptosis. In many instances, they are anchored to cell membranes via trans-membrane domains, and their activity is controlled via TIMPs (tissue inhibitors of metalloproteinases). 157 matched cddid_all.tbl CDD cd04279 cd04279 239806 ZnMc_MMP_like_1 Zinc-dependent metalloprotease; MMP_like sub-family 1. A group of bacterial, archaeal, and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin. 156 matched cddid_all.tbl CDD cd04280 cd04280 239807 ZnMc_astacin_like Zinc-dependent metalloprotease, astacin_like subfamily or peptidase family M12A, a group of zinc-dependent proteolytic enzymes with a HExxH zinc-binding site/active site. Members of this family may have an amino terminal propeptide, which is cleaved to yield the active protease domain, which is consequently always found at the N-terminus in multi-domain architectures. This family includes: astacin, a digestive enzyme from Crayfish; meprin, a multiple domain membrane component that is constructed from a homologous alpha and beta chain, proteins involved in (bone) morphogenesis, tolloid from drosophila, and the sea urchin SPAN protein, which may also play a role in development. 180 matched cddid_all.tbl CDD cd04281 cd04281 239808 ZnMc_BMP1_TLD Zinc-dependent metalloprotease; BMP1/TLD-like subfamily. BMP1 (Bone morphogenetic protein 1) and TLD (tolloid)-like metalloproteases play vital roles in extracellular matrix formation, by cleaving precursor proteins such as enzymes, structural proteins, and proteins involved in the mineralization of the extracellular matrix. The drosophila protein tolloid and its Xenopus homologue xolloid cleave and inactivate Sog and chordin, respectively, which are inhibitors of Dpp (the Drosophila decapentaplegic gene product) and its homologue BMP4, involved in dorso-ventral patterning. 200 matched cddid_all.tbl CDD cd04282 cd04282 239809 ZnMc_meprin Zinc-dependent metalloprotease, meprin_like subfamily. Meprins are membrane-bound or secreted extracellular proteases, which cleave a variety of targets, including peptides such as parathyroid hormone, gastrin, and cholecystokinin, cytokines such as osteopontin, and proteins such as collagen IV, fibronectin, casein and gelatin. Meprins may also be able to release proteins from the cell surface. Closely related meprin alpha- and beta-subunits form homo- and hetero-oligomers; these complexes are found on epithelial cells of the intestine, for example, and are also expressed in certain cancer cells. 230 matched cddid_all.tbl CDD cd04283 cd04283 239810 ZnMc_hatching_enzyme Zinc-dependent metalloprotease, hatching enzyme-like subfamily. Hatching enzymes are secreted by teleost embryos to digest the egg envelope or chorion. In some teleosts, the hatching enzyme may be a system consisting of two evolutionary related metalloproteases, high choriolytic enzyme and low choriolytic enzyme (HCE and LCE), which may have different substrate specificities and cooperatively digest the chorion. 182 matched cddid_all.tbl CDD cd04299 cd04299 340852 GT35_Glycogen_Phosphorylase-like proteins similar to glycogen phosphorylase. This family is most closely related to the oligosaccharide phosphorylase domain family and other unidentified sequences. Oligosaccharide phosphorylase catalyzes the breakdown of oligosaccharides into glucose-1-phosphate units. They are important allosteric enzymes in carbohydrate metabolism. 776 matched cddid_all.tbl CDD cd04300 cd04300 340853 GT35_Glycogen_Phosphorylase glycogen phosphorylase and similar proteins. This is a family of oligosaccharide phosphorylases. It includes yeast and mammalian glycogen phosphorylases, plant starch/glucan phosphorylase, as well as the maltodextrin phosphorylases of bacteria. The members of this family catalyze the breakdown of oligosaccharides into glucose-1-phosphate units. They are important allosteric enzymes in carbohydrate metabolism. The allosteric control mechanisms of yeast and mammalian members of this family are different from that of bacterial members. The members of this family belong to the GT-B structural superfamily of glycoslytransferases, which have characteristic N- and C-terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. 795 matched cddid_all.tbl CDD cd04301 cd04301 173926 NAT_SF N-Acyltransferase superfamily: Various enzymes that characteristically catalyze the transfer of an acyl group to a substrate. NAT (N-Acyltransferase) is a large superfamily of enzymes that mostly catalyze the transfer of an acyl group to a substrate and are implicated in a variety of functions, ranging from bacterial antibiotic resistance to circadian rhythms in mammals. Members include GCN5-related N-Acetyltransferases (GNAT) such as Aminoglycoside N-acetyltransferases, Histone N-acetyltransferase (HAT) enzymes, and Serotonin N-acetyltransferase, which catalyze the transfer of an acetyl group to a substrate. The kinetic mechanism of most GNATs involves the ordered formation of a ternary complex: the reaction begins with Acetyl Coenzyme A (AcCoA) binding, followed by binding of substrate, then direct transfer of the acetyl group from AcCoA to the substrate, followed by product and subsequent CoA release. Other family members include Arginine/ornithine N-succinyltransferase, Myristoyl-CoA: protein N-myristoyltransferase, and Acyl-homoserinelactone synthase which have a similar catalytic mechanism but differ in types of acyl groups transferred. Leucyl/phenylalanyl-tRNA-protein transferase and FemXAB nonribosomal peptidyltransferases which catalyze similar peptidyltransferase reactions are also included. 65 matched cddid_all.tbl CDD cd04302 cd04302 319798 HAD_5NT haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to the Pseudomonas aeruginosa PA0065. 5'-nucleotidases dephosphorylate nucleoside 5'-monophosphates to nucleosides and inorganic phosphate. Purified Pseudomonas aeruginosa PA0065 displayed high activity toward 5'-UMP and 5'-IMP, significant activity against 5'-XMP and 5'-TMP, and low activity against 5'-CMP. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 209 matched cddid_all.tbl CDD cd04303 cd04303 319799 HAD_PGPase phosphoglycolate phosphatase, similar to Synechococcus elongates phosphoglycolate phosphatase PGP/CbbZ. Phosphoglycolate phosphatase catalyzes the dephosphorylation of phosphoglycolate; its activity requires divalent cations, especially Mg++. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 201 matched cddid_all.tbl CDD cd04305 cd04305 319800 HAD_Neu5Ac-Pase_like human N-acetylneuraminate-9-phosphate phosphatase, Escherichia coli house-cleaning phosphatase YjjG, and related phosphatases. N-acetylneuraminate-9- phosphatase (Neu5Ac-9-Pase; E.C. 3.1.3.29) catalyzes the dephosphorylation of N-acylneuraminate 9-phosphate during the synthesis of N-acetylneuraminate; Escherichia coli nucleotide phosphatase YjjG has a broad pyrimidine nucleotide activity spectrum and functions as an in vivo house-cleaning phosphatase for noncanonical pyrimidine nucleotides. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 109 matched cddid_all.tbl CDD cd04309 cd04309 319801 HAD_PSP_eu phosphoserine phosphatase eukaryotic-like, similar to human phosphoserine phosphatase. Human PSP, EC 3.1.3.3, catalyzes the third and final of the L-serine biosynthesis pathway, the Mg2+-dependent hydrolysis of phospho-L-serine to L-serine and inorganic phosphate, L-serine is a precursor for the biosynthesis of glycine. HPSP regulates the levels of glycine and D-serine (converted from L-serine), the putative co-agonists for the glycine site of the NMDA receptor in the brain. Plant 3-PSP catalyzes the conversion of 3-phosphoserine to serine in the last step of the plastidic pathway of serine biosynthesis. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 202 matched cddid_all.tbl CDD cd04316 cd04316 239811 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes. 108 matched cddid_all.tbl CDD cd04317 cd04317 239812 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS. These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, whereas the other exclusively with mitochondrial protein synthesis. Human mtAspRS participates in mitochondrial biosynthesis; this enzyme been shown to charge E.coli native tRNAsp in addition to in vitro transcribed human mitochondrial tRNAsp. T. thermophilus is rare among bacteria in having both a D_AspRS and a ND_AspRS. H.pylori ND-AspRS can charge both tRNAASp and tRNAAsn, it is fractionally more efficient at aminoacylating tRNAAsp over tRNAAsn. The H.pylori genome does not contain AsnRS. 135 matched cddid_all.tbl CDD cd04318 cd04318 239813 EcAsnRS_like_N "EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. S. cerevisiae mtAsnRS can charge E.coli tRNA with asparagines. Mutations in the gene for S. cerevisiae mtAsnRS has been found to induce a ""petite"" phenotype typical for a mutation in a nuclear gene that results in a non-functioning mitochondrial protein synthesis system." 82 matched cddid_all.tbl CDD cd04319 cd04319 239814 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The archeal enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. 103 matched cddid_all.tbl CDD cd04320 cd04320 239815 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. 102 matched cddid_all.tbl CDD cd04321 cd04321 239816 ScAspRS_mt_like_N "ScAspRS_mt_like_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae mitochondrial (mt) aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this fungal group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Mutations in the gene for S. cerevisiae mtAspRS result in a ""petite"" phenotype typical for a mutation in a nuclear gene that results in a non-functioning mitochondrial protein synthesis system." 86 matched cddid_all.tbl CDD cd04322 cd04322 239817 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Saccharomyces cerevisiae cytoplasmic and mitochondrial LysRSs have been shown to participate in the mitochondrial import of the only nuclear-encoded tRNA of S. cerevisiae (tRNAlysCUU). The gene for human LysRS encodes both the cytoplasmic and the mitochondrial isoforms of LysRS. In addition to their housekeeping role, human lysRS may function as a signaling molecule that activates immune cells and tomato LysRS may participate in a root-specific process possibly connected to conditions of oxidative-stress conditions or heavy metal uptake. It is known that human tRNAlys and LysRS are specifically packaged into HIV-1 suggesting a role for LysRS in tRNA packaging. 108 matched cddid_all.tbl CDD cd04323 cd04323 239818 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, whereas the other exclusively with mitochondrial protein synthesis. AsnRS is immunodominant antigen of the filarial nematode B. malayai and of interest as a target for anti-parasitic drug design. Human AsnRS has been shown to be a pro-inflammatory chemokine which interacts with CCR3 chemokine receptors on T cells, immature dendritic cells and macrophages. 84 matched cddid_all.tbl CDD cd04327 cd04327 239819 ZnMc_MMP_like_3 Zinc-dependent metalloprotease; MMP_like sub-family 3. A group of bacterial and fungal metalloproteinase domains similar to matrix metalloproteinases and astacin. 198 matched cddid_all.tbl CDD cd04328 cd04328 239820 RNAP_I_Rpa43_N RNAP_I_Rpa43_N: Rpa43, N-terminal ribonucleoprotein (RNP) domain. Rpa43 is a subunit of eukaryotic RNA polymerase (RNAP) I that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNP III, and RpoE of archaeal RNAP. Rpa43 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Rpa43 heterodimerizes with Rpa14 and this heterodimer has genetic and biochemical characteristics similar to those of the Rpb7/Rpb4 heterodimer of RNAP II. In addition, the Rpa43/Rpa14 heterodimer binds single-stranded RNA, as is the case for the Rpb7/Rpb4 and the archaeal E/F complexes. The position of Rpa43/Rpa14 in the three-dimensional structure of RNAP I is similar to that of Rpb4/Rpb7, which forms an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. Rpb43 binds Rrn3, an rDNA-specific transcription factor, functionally equivalent to TFIIB, involved in recruiting RNAP I to the pol I promoter. 89 matched cddid_all.tbl CDD cd04329 cd04329 239821 RNAP_II_Rpb7_N RNAP_II_Rpb7_N: Rpb7, N-terminal ribonucleoprotein (RNP) domain. Rpb7 is a subunit of eukaryotic RNA polymerase (RNAP) II that is homologous to Rpc25 of RNAP III, RpoE of archaeal RNAP, and Rpa43 of eukaryotic RNAP I. Rpb7 heterodimerizes with Rpb4 and this heterodimer binds the 10-subunit core of RNAP II, forming part of the floor of the DNA-binding cleft. Rpb7 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which bind single-stranded RNA. Rpb7 is thought to interact with the nascent RNA strand as it exits the RNAP II complex during transcription elongation. The Rpb7/Rpb4 heterodimer is also thought to serve as an upstream interface between the C-terminal domain of Rpb1 and the transcription factor IIB (TFIIB), recruiting pol II to the pol II promoter. 80 matched cddid_all.tbl CDD cd04330 cd04330 239822 RNAP_III_Rpc25_N RNAP_III_Rpc25_N: Rpc25, N-terminal ribonucleoprotein (RNP) domain. Rpc25 is a subunit of eukaryotic RNA polymerase (RNAP) III and is homologous to Rpa43 of eukaryotic RNAP I, Rpb7 of eukaryotic RNAP II, and RpoE of archaeal RNAP. Rpc25 has two domains, an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain, both of which are thought to bind single-stranded RNA. Rpc25 heterodimerizes with Rpc17 and plays an important role in transcription initiation. RNAP III transcribes diverse structural and catalytic RNAs including 5S ribosomal RNAs, tRNAs, and a small number of snRNAs involved in RNA and protein synthesis. 80 matched cddid_all.tbl CDD cd04331 cd04331 239823 RNAP_E_N RNAP_E_N: RpoE, N-terminal ribonucleoprotein (RNP) domain. RpoE (subunit E) is a subunit of the archaeal RNA polymerase (RNAP) that is homologous to Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNAP III, and Rpa43 of eukaryotic RNAP I. RpoE heterodimerizes with RpoF, another RNA polymerase subunit. RpoE has an elongated two-domain structure that includes an N-terminal RNP domain and a C-terminal oligonucleotide-binding (OB) domain. Both domains of RpoE bind single-stranded RNA. 80 matched cddid_all.tbl CDD cd04332 cd04332 239824 YbaK_like YbaK-like. The YbaK family of deacylase domains includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, ProX, and PrdX. The primary function of INS is to hydrolyze mischarged cysteinyl-tRNA(Pro)'s, thus helping ensure the fidelity of translation. Organisms whose ProRS lacks the INS domain express an INS homolog in trans (e.g. YbaK, ProX, or PrdX). 136 matched cddid_all.tbl CDD cd04333 cd04333 239825 ProX_deacylase This CD, composed mainly of bacterial single-domain proteins, includes the Thermus thermophilus (Tt) YbaK-like protein, a homolog of the trans-acting Escherichia coli YbaK Cys-tRNA(Pro) deacylase and the Agrobacterium tumefaciens ProX Ala-tRNA(Pro) deacylase and also the cis-acting prolyl-tRNA synthetase-editing domain (ProRS-INS). While ProX and ProRS-INS hydrolyze misacylated Ala-tRNA(Pro), the E. coli YbaK hydrolyzes misacylated Cys-tRNA(Pro). A few CD members are N-terminal, YbaK-ProX-like domains of an uncharacterized protein with a C-terminal, predicted Fe-S protein domain. 148 matched cddid_all.tbl CDD cd04334 cd04334 239826 ProRS-INS INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and single-celled parasites. ProRS catalyzes the attachment of proline to tRNA(Pro); proline is first activated by ATP, and then transferred to the acceptor end of tRNA(Pro). ProRS can inadvertently process noncognate amino acids such as alanine and cysteine, and to avoid such errors, in post-transfer editing, the INS domain deacylates mischarged Ala-tRNA(Pro), thus ensuring the fidelity of translation. Misacylated Cys-tRNA(Pro) is not edited by ProRS. In addition to the INS editing domain, the prokaryote-like ProRS protein contains catalytic and anticodon-binding domains which form a dimeric interface. 160 matched cddid_all.tbl CDD cd04335 cd04335 239827 PrdX_deacylase This CD includes bacterial (Agrobacterium tumefaciens and Caulobacter crescentus ProX, and Clostridium sticklandii PrdX) and eukaryotic (Plasmodium falciparum N-terminal ProRS editing domain) sequences. The C. sticklandii PrdX protein, a homolog of the YbaK and ProX proteins, and the prolyl-tRNA synthetase-editing domain (ProRS-INS), specifically hydrolyzes Ala-tRNA(Pro). In this CD, many of the eukaryotic editing domains are N-terminal and cis-acting, expressed from a multidomain ProRS, however, similar to the bacterial PrdX, the mammalian, amphibian, and echinoderm PrdX-like proteins are trans-acting, single-domain proteins. 156 matched cddid_all.tbl CDD cd04336 cd04336 239828 YeaK YeaK is an uncharacterized Echerichia coli protein with a YbaK-like domain of unknown function. The YbaK-like domain family includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, and ProX. The primary function of INS is to hydrolyze mischarged cysteinyl-tRNA(Pro)'s, thus helping ensure the fidelity of translation. Organisms whose ProRS lacks the INS domain express a single-domain INS homolog such as YbaK, ProX, or PrdX which supplies the function of INS in trans. 153 matched cddid_all.tbl CDD cd04337 cd04337 239829 Rieske_RO_Alpha_Cao Cao (chlorophyll a oxygenase) is a rieske non-heme iron-sulfur protein located within the plastid-envelope inner and thylakoid membranes, that catalyzes the conversion of chlorophyllide a to chlorophyllide b. CAO is found not only in plants but also in chlorophytes and prochlorophytes. This domain represents the N-terminal rieske domain of the oxygenase alpha subunit. ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Cao is closely related to several other plant RO's including Tic 55, a 55 kDa protein associated with protein transport through the inner chloroplast membrane; Ptc 52, a novel 52 kDa protein isolated from chloroplasts; and LLS1/Pao (Lethal-leaf spot 1/pheophorbide a oxygenase). 129 matched cddid_all.tbl CDD cd04338 cd04338 239830 Rieske_RO_Alpha_Tic55 Tic55 is a 55kDa LLS1-related non-heme iron oxygenase associated with protein transport through the plant inner chloroplast membrane. This domain represents the N-terminal Rieske domain of the Tic55 oxygenase alpha subunit. Tic55 is closely related to the oxygenase alpha subunits of a small subfamily of enzymes found in plants as well as oxygenic cyanobacterial photosynthesizers including LLS1 (lethal leaf spot 1, also known as PaO), Ptc52, and ACD1 (accelerated cell death 1). ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. 134 matched cddid_all.tbl CDD cd04365 cd04365 239831 IlGF_relaxin_like "IlGF_like family, relaxin_like subgroup, specific to vertebrates. Members include a number of active peptides including (pro)relaxin, mammalian Leydig cell-specific insulin-like peptide (gene INSL3), early placenta insulin-like peptide (ELIP; gene INSL4), and insulin-like peptides 5 (INSL5) and 6 (INSL6). Members of this subgroup are widely expressed in testes (INSL3, INSL6), decidua, placenta, prostate, corpus luteum, brain (various relaxins), GI tract, and kidney (INSL5) where they serve a variety of functions in parturition and development. Typically, the active forms of these peptide hormones are composed of two chains (A and B) linked by two disulfide bonds; the arrangement of four cysteines is conserved in the ""A"" chain: Cys1 is linked by a disulfide bond to Cys3, Cys2 and Cys4 are linked by interchain disulfide bonds to cysteines in the ""B"" chain. This alignment contains both chains, plus the intervening linker region, arranged as found in the propeptide form. Propeptides are cleaved to yield two separate chains linked covalently by the two disulfide bonds." 59 matched cddid_all.tbl CDD cd04366 cd04366 239832 IlGF_insulin_bombyxin_like "IlGF_like family, insulin_bombyxin_like subgroup. Members include a number of peptides including insulin, insulin-like growth factors I and II, insect prothoracicotropic hormone (bombyxin), locust insulin-related peptide (LIRP), molluscan insulin-related peptides 1 to 5 (MIP), and C. elegans insulin-like peptides. With the exception of insulin-like growth factors, the active forms of these peptide hormones are composed of two chains (A and B) linked by two disulfide bonds; the arrangement of four cysteines is conserved in the ""A"" chain: Cys1 is linked by a disulfide bond to Cys3, Cys2 and Cys4 are linked by interchain disulfide bonds to cysteines in the ""B"" chain. This alignment contains both chains, plus the intervening linker region, arranged as found in the propeptide form. Propeptides are cleaved to yield two separate chains linked covalently by the two disulfide bonds." 42 matched cddid_all.tbl CDD cd04367 cd04367 239833 IlGF_insulin_like "IlGF_like family, insulin_like subgroup, specific to vertebrates. Members include a number of peptides including insulin and insulin-like growth factors I and II, which play a variety of roles in controlling processes such as metabolism, growth and differentiation, and reproduction. On a cellular level they affect cell cycle, apoptosis, cell migration, and differentiation. With the exception of the insulin-like growth factors, the active forms of these peptide hormones are composed of two chains (A and B) linked by two disulfide bonds; the arrangement of four cysteines is conserved in the ""A"" chain: Cys1 is linked by a disulfide bond to Cys3, Cys2 and Cys4 are linked by interchain disulfide bonds to cysteines in the ""B"" chain. This alignment contains both chains, plus the intervening linker region, arranged as found in the propeptide form. Propeptides are cleaved to yield two separate chains linked covalently by the two disulfide bonds." 79 matched cddid_all.tbl CDD cd04368 cd04368 239834 IlGF IlGF, insulin_like growth factors; specific to vertebrates. Members include a number of peptides including insulin-like growth factors I and II, which play a variety of roles in controlling processes such as growth, differentiation, and reproduction. On a cellular level they affect cell cycle, apoptosis, cell migration, proliferation, and differentiation. Typically, the active forms of these peptide hormones are single chains cross-linked by three disulfide bonds. 67 matched cddid_all.tbl CDD cd04369 cd04369 99922 Bromodomain Bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine. 99 matched cddid_all.tbl CDD cd04370 cd04370 239835 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions. 123 matched cddid_all.tbl CDD cd04371 cd04371 239836 DEP DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction. 81 matched cddid_all.tbl CDD cd04372 cd04372 239837 RhoGAP_chimaerin RhoGAP_chimaerin: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of chimaerins. Chimaerins are a family of phorbolester- and diacylglycerol-responsive GAPs specific for the Rho-like GTPase Rac. Chimaerins exist in two alternative splice forms that each contain a C-terminal GAP domain, and a central C1 domain which binds phorbol esters, inducing a conformational change that activates the protein; one splice form is lacking the N-terminal Src homology-2 (SH2) domain. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 194 matched cddid_all.tbl CDD cd04373 cd04373 239838 RhoGAP_p190 RhoGAP_p190: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of p190-like proteins. p190, also named RhoGAP5, plays a role in neuritogenesis and axon branch stability. p190 shows a preference for Rho, over Rac and Cdc42, and consists of an N-terminal GTPase domain and a C-terminal GAP domain. The central portion of p190 contains important regulatory phosphorylation sites. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 185 matched cddid_all.tbl CDD cd04374 cd04374 239839 RhoGAP_Graf RhoGAP_Graf: GTPase-activator protein (GAP) domain for Rho-like GTPases found in GRAF (GTPase regulator associated with focal adhesion kinase); Graf is a multi-domain protein, containing SH3 and PH domains, that binds focal adhesion kinase and influences cytoskeletal changes mediated by Rho proteins. Graf exhibits GAP activity toward RhoA and Cdc42, but only weakly activates Rac1. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 203 matched cddid_all.tbl CDD cd04375 cd04375 239840 RhoGAP_DLC1 RhoGAP_DLC1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of DLC1-like proteins. DLC1 shows in vitro GAP activity towards RhoA and CDC42. Beside its C-terminal GAP domain, DLC1 also contains a SAM (sterile alpha motif) and a START (StAR-related lipid transfer action) domain. DLC1 has tumor suppressor activity in cell culture. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 220 matched cddid_all.tbl CDD cd04376 cd04376 239841 RhoGAP_ARHGAP6 RhoGAP_ARHGAP6: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP6-like proteins. ArhGAP6 shows GAP activity towards RhoA, but not towards Cdc42 and Rac1. ArhGAP6 is often deleted in microphthalmia with linear skin defects syndrome (MLS); MLS is a severe X-linked developmental disorder. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 206 matched cddid_all.tbl CDD cd04377 cd04377 239842 RhoGAP_myosin_IX RhoGAP_myosin_IX: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in class IX myosins. Class IX myosins contain a characteristic head domain, a neck domain, a tail domain which contains a C6H2-zinc binding motif and a RhoGAP domain. Class IX myosins are single-headed, processive myosins that are partly cytoplasmic, and partly associated with membranes and the actin cytoskeleton. Class IX myosins are implicated in the regulation of neuronal morphogenesis and function of sensory systems, like the inner ear. There are two major isoforms, myosin IXA and IXB with several splice variants, which are both expressed in developing neurons. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 186 matched cddid_all.tbl CDD cd04378 cd04378 239843 RhoGAP_GMIP_PARG1 RhoGAP_GMIP_PARG1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of GMIP (Gem interacting protein) and PARG1 (PTPL1-associated RhoGAP1). GMIP plays important roles in neurite growth and axonal guidance, and interacts with Gem, a member of the RGK subfamily of the Ras small GTPase superfamily, through the N-terminal half of the protein. GMIP contains a C-terminal RhoGAP domain. GMIP inhibits RhoA function, but is inactive towards Rac1 and Cdc41. PARG1 interacts with Rap2, also a member of the Ras small GTPase superfamily whose exact function is unknown, and shows strong preference for Rho. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 203 matched cddid_all.tbl CDD cd04379 cd04379 239844 RhoGAP_SYD1 RhoGAP_SYD1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in SYD-1_like proteins. Syd-1, first identified and best studied in C.elegans, has been shown to play an important role in neuronal development by specifying axonal properties. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 207 matched cddid_all.tbl CDD cd04380 cd04380 239845 RhoGAP_OCRL1 RhoGAP_OCRL1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in OCRL1-like proteins. OCRL1 (oculocerebrorenal syndrome of Lowe 1)-like proteins contain two conserved domains: a central inositol polyphosphate 5-phosphatase domain and a C-terminal Rho GAP domain, this GAP domain lacks the catalytic residue and therefore maybe inactive. OCRL-like proteins are type II inositol polyphosphate 5-phosphatases that can hydrolyze lipid PI(4,5)P2 and PI(3,4,5)P3 and soluble Ins(1,4,5)P3 and Ins(1,3,4,5)P4, but their individual specificities vary. The functionality of the RhoGAP domain is still unclear. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 220 matched cddid_all.tbl CDD cd04381 cd04381 239846 RhoGap_RalBP1 RhoGap_RalBP1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in RalBP1 proteins, also known as RLIP, RLIP76 or cytocentrin. RalBP1 plays an important role in endocytosis during interphase. During mitosis, RalBP1 transiently associates with the centromere and has been shown to play an essential role in the proper assembly of the mitotic apparatus. RalBP1 is an effector of the Ral GTPase which itself is an effector of Ras. RalBP1 contains a RhoGAP domain, which shows weak activity towards Rac1 and Cdc42, but not towards Ral, and a Ral effector domain binding motif. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 182 matched cddid_all.tbl CDD cd04382 cd04382 239847 RhoGAP_MgcRacGAP RhoGAP_MgcRacGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in MgcRacGAP proteins. MgcRacGAP plays an important dual role in cytokinesis: i) it is part of centralspindlin-complex, together with the mitotic kinesin MKLP1, which is critical for the structure of the central spindle by promoting microtuble bundling. ii) after phosphorylation by aurora B MgcRacGAP becomes an effective regulator of RhoA and plays an important role in the assembly of the contractile ring and the initiation of cytokinesis. MgcRacGAP-like proteins contain a N-terminal C1-like domain, and a C-terminal RhoGAP domain. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 193 matched cddid_all.tbl CDD cd04383 cd04383 239848 RhoGAP_srGAP RhoGAP_srGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in srGAPs. srGAPs are components of the intracellular part of Slit-Robo signalling pathway that is important for axon guidance and cell migration. srGAPs contain an N-terminal FCH domain, a central RhoGAP domain and a C-terminal SH3 domain; this SH3 domain interacts with the intracellular proline-rich-tail of the Roundabout receptor (Robo). This interaction with Robo then activates the rhoGAP domain which in turn inhibits Cdc42 activity. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 188 matched cddid_all.tbl CDD cd04384 cd04384 239849 RhoGAP_CdGAP RhoGAP_CdGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of CdGAP-like proteins; CdGAP contains an N-terminal RhoGAP domain and a C-terminal proline-rich region, and it is active on both Cdc42 and Rac1 but not RhoA. CdGAP is recruited to focal adhesions via the interaction with the scaffold protein actopaxin (alpha-parvin). Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 195 matched cddid_all.tbl CDD cd04385 cd04385 239850 RhoGAP_ARAP RhoGAP_ARAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in ARAPs. ARAPs (also known as centaurin deltas) contain, besides the RhoGAP domain, an Arf GAP, ankyrin repeat ras-associating, and PH domains. Since their ArfGAP activity is PIP3-dependent, ARAPs are considered integration points for phosphoinositide, Arf and Rho signaling. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 184 matched cddid_all.tbl CDD cd04386 cd04386 239851 RhoGAP_nadrin RhoGAP_nadrin: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of Nadrin-like proteins. Nadrin, also named Rich-1, has been shown to be involved in the regulation of Ca2+-dependent exocytosis in neurons and recently has been implicated in tight junction maintenance in mammalian epithelium. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 203 matched cddid_all.tbl CDD cd04387 cd04387 239852 RhoGAP_Bcr RhoGAP_Bcr: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of Bcr (breakpoint cluster region protein)-like proteins. Bcr is a multidomain protein with a variety of enzymatic functions. It contains a RhoGAP and a Rho GEF domain, a Ser/Thr kinase domain, an N-terminal oligomerization domain, and a C-terminal PDZ binding domain, in addition to PH and C2 domains. Bcr is a negative regulator of: i) RacGTPase, via the Rho GAP domain, ii) the Ras-Raf-MEK-ERK pathway, via phosphorylation of the Ras binding protein AF-6, and iii) the Wnt signaling pathway through binding beta-catenin. Bcr can form a complex with beta-catenin and Tcf1. The Wnt signaling pathway is involved in cell proliferation, differentiation, and cell renewal. Bcr was discovered as a fusion partner of Abl. The Bcr-Abl fusion is characteristic for a large majority of chronic myelogenous leukemias (CML). Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 196 matched cddid_all.tbl CDD cd04388 cd04388 239853 RhoGAP_p85 RhoGAP_p85: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in the p85 isoforms of the regulatory subunit of the class IA PI3K (phosphatidylinositol 3'-kinase). This domain is also called Bcr (breakpoint cluster region protein) homology (BH) domain. Class IA PI3Ks are heterodimers, containing a regulatory subunit (p85) and a catalytic subunit (p110) and are activated by growth factor receptor tyrosine kinases (RTKs); this activation is mediated by the p85 subunit. p85 isoforms, alpha and beta, contain a C-terminal p110-binding domain flanked by two SH2 domains, an N-terminal SH3 domain, and a RhoGAP domain flanked by two proline-rich regions. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 200 matched cddid_all.tbl CDD cd04389 cd04389 239854 RhoGAP_KIAA1688 RhoGAP_KIAA1688: GTPase-activator protein (GAP) domain for Rho-like GTPases found in KIAA1688-like proteins; KIAA1688 is a protein of unknown function that contains a RhoGAP domain and a myosin tail homology 4 (MyTH4) domain. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 187 matched cddid_all.tbl CDD cd04390 cd04390 239855 RhoGAP_ARHGAP22_24_25 RhoGAP_ARHGAP22_24_25: GTPase-activator protein (GAP) domain for Rho-like GTPases found in ARHGAP22, 24 and 25-like proteins; longer isoforms of these proteins contain an additional N-terminal pleckstrin homology (PH) domain. ARHGAP25 (KIA0053) has been identified as a GAP for Rac1 and Cdc42. Short isoforms (without the PH domain) of ARHGAP24, called RC-GAP72 and p73RhoGAP, and of ARHGAP22, called p68RacGAP, has been shown to be involved in angiogenesis and endothelial cell capillary formation. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 199 matched cddid_all.tbl CDD cd04391 cd04391 239856 RhoGAP_ARHGAP18 RhoGAP_ARHGAP18: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP18-like proteins. The function of ArhGAP18 is unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 216 matched cddid_all.tbl CDD cd04392 cd04392 239857 RhoGAP_ARHGAP19 RhoGAP_ARHGAP19: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP19-like proteins. The function of ArhGAP19 is unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 208 matched cddid_all.tbl CDD cd04393 cd04393 239858 RhoGAP_FAM13A1a RhoGAP_FAM13A1a: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of FAM13A1, isoform a-like proteins. The function of FAM13A1a is unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by up several orders of magnitude. 189 matched cddid_all.tbl CDD cd04394 cd04394 239859 RhoGAP-ARHGAP11A RhoGAP-ARHGAP11A: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP11A-like proteins. The mouse homolog of human ArhGAP11A has been detected as a gene exclusively expressed in immature ganglion cells, potentially playing a role in retinal development. The exact function of ArhGAP11A is unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 202 matched cddid_all.tbl CDD cd04395 cd04395 239860 RhoGAP_ARHGAP21 RhoGAP_ARHGAP21: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP21-like proteins. ArhGAP21 is a multi-domain protein, containing RhoGAP, PH and PDZ domains, and is believed to play a role in the organization of the cell-cell junction complex. It has been shown to function as a GAP of Cdc42 and RhoA, and to interact with alpha-catenin and Arf6. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 196 matched cddid_all.tbl CDD cd04396 cd04396 239861 RhoGAP_fSAC7_BAG7 RhoGAP_fSAC7_BAG7: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of fungal SAC7 and BAG7-like proteins. Both proteins are GTPase activating proteins of Rho1, but differ functionally in vivo: SAC7, but not BAG7, is involved in the control of Rho1-mediated activation of the PKC-MPK1 pathway. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 225 matched cddid_all.tbl CDD cd04397 cd04397 239862 RhoGAP_fLRG1 RhoGAP_fLRG1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of fungal LRG1-like proteins. Yeast Lrg1p is required for efficient cell fusion, and mother-daughter cell separation, possibly through acting as a RhoGAP specifically regulating 1,3-beta-glucan synthesis. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 213 matched cddid_all.tbl CDD cd04398 cd04398 239863 RhoGAP_fRGD1 RhoGAP_fRGD1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of fungal RGD1-like proteins. Yeast Rgd1 is a GAP protein for Rho3 and Rho4 and plays a role in low-pH response. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 192 matched cddid_all.tbl CDD cd04399 cd04399 239864 RhoGAP_fRGD2 RhoGAP_fRGD2: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of fungal RGD2-like proteins. Yeast Rgd2 is a GAP protein for Cdc42 and Rho5. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 212 matched cddid_all.tbl CDD cd04400 cd04400 239865 RhoGAP_fBEM3 RhoGAP_fBEM3: RhoGAP (GTPase-activator [GAP] protein for Rho-like small GTPases) domain of fungal BEM3-like proteins. Bem3 is a GAP protein of Cdc42, and is specifically involved in the control of the initial assembly of the septin ring in yeast bud formation. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 190 matched cddid_all.tbl CDD cd04401 cd04401 239866 RhoGAP_fMSB1 RhoGAP_fMSB1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of fungal MSB1-like proteins. Msb1 was originally identified as a multicopy suppressor of temperature sensitive cdc42 mutation. Msb1 is a positive regulator of the Pkc1p-MAPK pathway and 1,3-beta-glucan synthesis, both pathways involve Rho1 regulation. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 198 matched cddid_all.tbl CDD cd04402 cd04402 239867 RhoGAP_ARHGAP20 RhoGAP_ARHGAP20: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP20-like proteins. ArhGAP20, also known as KIAA1391 and RA-RhoGAP, contains a RhoGAP, a RA, and a PH domain, and ANXL repeats. ArhGAP20 is activated by Rap1 and induces inactivation of Rho, which in turn leads to neurite outgrowth. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 192 matched cddid_all.tbl CDD cd04403 cd04403 239868 RhoGAP_ARHGAP27_15_12_9 RhoGAP_ARHGAP27_15_12_9: GTPase-activator protein (GAP) domain for Rho-like GTPases found in ARHGAP27 (also called CAMGAP1), ARHGAP15, 12 and 9-like proteins; This subgroup of ARHGAPs are multidomain proteins that contain RhoGAP, PH, SH3 and WW domains. Most members that are studied show GAP activity towards Rac1, some additionally show activity towards Cdc42. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 187 matched cddid_all.tbl CDD cd04404 cd04404 239869 RhoGAP-p50rhoGAP RhoGAP-p50rhoGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of p50RhoGAP-like proteins; p50RhoGAP, also known as RhoGAP-1, contains a C-terminal RhoGAP domain and an N-terminal Sec14 domain which binds phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3). It is ubiquitously expressed and preferentially active on Cdc42. This subgroup also contains closely related ARHGAP8. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 195 matched cddid_all.tbl CDD cd04405 cd04405 239870 RhoGAP_BRCC3-like RhoGAP_BRCC3-like: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of BRCC3-like proteins. This subgroup also contains two groups of closely related proteins, BRCC3 and DEPDC7, which both contain a C-terminal RhoGAP-like domain and an N-terminal DEP (Disheveled, Egl-10, and Pleckstrin) domain. The function(s) of BRCC3 and DEPDC7 are unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 235 matched cddid_all.tbl CDD cd04406 cd04406 239871 RhoGAP_myosin_IXA RhoGAP_myosin_IXA: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in myosins IXA. Class IX myosins contain a characteristic head domain, a neck domain and a tail domain which contains a C6H2-zinc binding motif and a Rho-GAP domain. Class IX myosins are single-headed, processive myosins that are partly cytoplasmic, and partly associated with membranes and the actin cytoskeleton. Class IX myosins are implicated in the regulation of neuronal morphogenesis and function of sensory systems, like the inner ear. There are two major isoforms, myosin IXA and IXB with several splice variants, which are both expressed in developing neurons. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 186 matched cddid_all.tbl CDD cd04407 cd04407 239872 RhoGAP_myosin_IXB RhoGAP_myosin_IXB: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in myosins IXB. Class IX myosins contain a characteristic head domain, a neck domain and a tail domain which contains a C6H2-zinc binding motif and a Rho-GAP domain. Class IX myosins are single-headed, processive myosins that are partly cytoplasmic, and partly associated with membranes and the actin cytoskeleton. Class IX myosins are implicated in the regulation of neuronal morphogenesis and function of sensory systems, like the inner ear. There are two major isoforms, myosin IXA and IXB with several splice variants, which are both expressed in developing neurons Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 186 matched cddid_all.tbl CDD cd04408 cd04408 239873 RhoGAP_GMIP RhoGAP_GMIP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of GMIP (Gem interacting protein). GMIP plays important roles in neurite growth and axonal guidance, and interacts with Gem, a member of the RGK subfamily of the Ras small GTPase superfamily, through the N-terminal half of the protein. GMIP contains a C-terminal RhoGAP domain. GMIP inhibits RhoA function, but is inactive towards Rac1 and Cdc41. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 200 matched cddid_all.tbl CDD cd04409 cd04409 239874 RhoGAP_PARG1 RhoGAP_PARG1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of PARG1 (PTPL1-associated RhoGAP1). PARG1 was originally cloned as an interaction partner of PTPL1, an intracellular protein-tyrosine phosphatase. PARG1 interacts with Rap2, also a member of the Ras small GTPase superfamily whose exact function is unknown, and shows strong preference for Rho. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. 211 matched cddid_all.tbl CDD cd04410 cd04410 319870 DMSOR_beta-like Beta subunit of the DMSO Reductase (DMSOR) family. This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system. 136 matched cddid_all.tbl CDD cd04411 cd04411 100108 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have two copies each of P1 and P2 (two heterodimers). Bacteria may have four or six copies (two or three homodimers), depending on the species. As in bacteria, the stalk is crucial for binding of initiation, elongation, and release factors in eukaryotes and archaea. 105 matched cddid_all.tbl CDD cd04412 cd04412 239875 NDPk7B Nucleoside diphosphate kinase 7 domain B (NDPk7B): The nm23-H7 class of nucleoside diphosphate kinase (NDPk7) consists of an N-terminal DM10 domain and two functional catalytic NDPk modules, NDPk7A and NDPk7B. The function of the DM10 domain, which also occurs in multiple copies in other proteins, is unknown. NDPk7 is predominantly expressed in testes, although appreciable amount are also found in liver, heart, brain, ovary, small intestine and spleen. The nm23-H7 gene is located in or near the hereditary prostrate cancer susceptibility locus. Nm23-H7 may be involved in the development of colon and gastric carcinoma, the latter possibly in a type-specific manner. 134 matched cddid_all.tbl CDD cd04413 cd04413 239876 NDPk_I Nucleoside diphosphate kinase Group I (NDPk_I)-like: NDP kinase domains are present in a large family of structurally and functionally conserved proteins from bacteria to humans that generally catalyze the transfer of gamma-phosphates of a nucleoside triphosphate (NTP) donor onto a nucleoside diphosphate (NDP) acceptor through a phosphohistidine intermediate. The mammalian nm23/NDP kinase gene family can be divided into two distinct groups. The group I genes encode proteins that generally have highly homologous counterparts in other organisms and possess the classic enzymatic activity of a kinase. This group includes vertebrate NDP kinases A-D (Nm23- H1 to -H4), and its counterparts in bacteria, archea and other eukaryotes. NDP kinases exist in two different quaternary structures; all known eukaryotic enzymes are hexamers, while some bacterial enzymes are tetramers, as in Myxococcus. They possess the NDP kinase active site motif (NXXH[G/A]SD) and the nine residues that are most essential for catalysis. 130 matched cddid_all.tbl CDD cd04414 cd04414 239877 NDPk6 Nucleoside diphosphate kinase 6 (NDP kinase 6, NDPk6, NM23-H6; NME6; Inhibitor of p53-induced apoptosis-alpha, IPIA-alpha): The nm23-H6 gene encoding NDPk6 is expressed mainly in mitochondria, but also found at a lower level in most tissues. NDPk6 has all nine residues considered crucial for enzyme structure and activity, and has been found to have NDP kinase activity. It may play a role in cell growth and cell cycle progression. The nm23-H6 gene locus has been implicated in a variety of malignant tumors. 135 matched cddid_all.tbl CDD cd04415 cd04415 239878 NDPk7A Nucleoside diphosphate kinase 7 domain A (NDPk7A): The nm23-H7 class of nucleoside diphosphate kinase (NDPk7) consists of an N-terminal DM10 domain and two functional catalytic NDPk modules, NDPk7A and NDPk7B. The function of the DM10 domain, which also occurs in multiple copies in other proteins, is unknown. NDPk7 is predominantly expressed in testes, although appreciable amount are also found in liver, heart, brain, ovary, small intestine and spleen. The nm23-H7 gene is located in or near the hereditary prostrate cancer susceptibility locus. Nm23-H7 may be involved in the development of colon and gastric carcinoma, the latter possibly in a type-specific manner. 131 matched cddid_all.tbl CDD cd04416 cd04416 239879 NDPk_TX NDP kinase domain of thioredoxin domain-containing proteins (TXNDC3 and TXNDC6): Txl-2 (TXNDC6) and Sptrx-2 (TXNDC3) are fusion proteins of Group II N-terminal thioredoxin domains followed by one or three NDP kinase domains, respectively. Sptrx-2, which has a tissue specific distribution in human testis, has been considered as a member of the nm23 family (nm23-H8) and exhibits a high homology with sea urchin IC1 (intermediate chain-1) protein, a component of the sperm axonemal outer dynein arm complex. Txl-2 is mainly represented in close association with microtubules within tissues with cilia and flagella such as seminiferous epithelium (spermatids) and lung airway epithelium, suggesting possible role in control of microtubule stability and maintenance. 132 matched cddid_all.tbl CDD cd04418 cd04418 239880 NDPk5 Nucleoside diphosphate kinase homolog 5 (NDP kinase homolog 5, NDPk5, NM23-H5; Inhibitor of p53-induced apoptosis-beta, IPIA-beta): In human, mRNA for NDPk5 is almost exclusively found in testis, especially in the flagella of spermatids and spermatozoa, in association with axoneme microtubules, and may play a role in spermatogenesis by increasing the ability of late-stage spermatids to eliminate reactive oxygen species. It belongs to the nm23 Group II genes and appears to differ from the other human NDPks in that it lacks two important catalytic site residues, and thus does not appear to possess NDP kinase activity. NDPk5 confers protection from cell death by Bax and alters the cellular levels of several antioxidant enzymes, including glutathione peroxidase 5 (Gpx5). 132 matched cddid_all.tbl CDD cd04433 cd04433 341228 AFD_class_I Adenylate forming domain, Class I, also known as the ANL superfamily. This family is known as the ANL (acyl-CoA synthetases, the NRPS adenylation domains, and the Luciferase enzymes) superfamily. It includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases.The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain. 336 matched cddid_all.tbl CDD cd04434 cd04434 271198 LanC_like Cyclases involved in the biosynthesis of lantibiotics, and similar proteins. LanC is the cyclase enzyme of the lanthionine synthetase. Lanthionine is a lantibiotic, a unique class of peptide antibiotics. They are ribosomally synthesized as a precursor peptide and then post-translationally modified to contain thioether cross-links called lanthionines (Lans) or methyllanthionines (MeLans), in addition to 2,3-didehydroalanine (Dha) and (Z)-2,3-didehydrobutyrine (Dhb). These unusual amino acids are introduced by the dehydration of serine and threonine residues, followed by thioether formation via addition of cysteine thiols, catalysed by LanB and LanC or LanM. LanC, the cyclase component, is a zinc metalloprotein, whose bound metal has been proposed to activate the thiol substrate for nucleophilic addition. A related domain is also present in LanM and other pro- and eukaryotic proteins with poorly characterized functions. 351 matched cddid_all.tbl CDD cd04435 cd04435 239882 DEP_fRom2 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) Rom2-like proteins. Rom2-like proteins share a common domain architecture, containing, beside the RhoGEF domain, a DEP, a PH (pleckstrin homology) and a CNH domain. Rom2, a yeast GEF for Rho1 and Rho2, is involved in mediating stress response via the Ras-cAMP pathway and also plays a role in mediating resistance to sphingolipid disturbances. 82 matched cddid_all.tbl CDD cd04436 cd04436 239883 DEP_fRgd2 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGAP (GTPase-activator protein) Rgd2-like proteins. Rgd2-like proteins share a common domain architecture, containing, beside the RhoGAP domain, a DEP and a FCH (Fes/CIP4 homology) domain. Yeast Rgd2 is a GAP protein for Cdc42 and Rho5. 84 matched cddid_all.tbl CDD cd04437 cd04437 239884 DEP_Epac DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in Epac-like proteins. Epac (exchange proteins directly activated by cAMP) proteins are GEFs (guanine-nucleotide-exchange factors) for the small GTPases, Rap1 and Rap2. They are directly regulated by cyclic AMP, a second messenger that plays a role in the control of diverse cellular processes, such as cell adhesion and insulin secretion. Epac-like proteins share a common domain architecture, containing RasGEF, DEP and CAP-effector (cAMP binding) domains. The DEP domain is involved in membrane localization. 125 matched cddid_all.tbl CDD cd04438 cd04438 239885 DEP_dishevelled DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in dishevelled-like proteins. Dishevelled-like proteins play a key role in the transduction of the Wnt signal from the cell surface to the nucleus, which in turn is an important regulatory pathway for cellular development and growth. They contain an N-terminal DIX domain, a central PDZ domain, and a C-terminal DEP domain. 84 matched cddid_all.tbl CDD cd04439 cd04439 239886 DEP_1_P-Rex DEP (Dishevelled, Egl-10, and Pleckstrin) domain 1 found in P-Rex-like proteins. The P-Rex family is the guanine-nucleotide exchange factor (GEF) for the small GTPase Rac that contains an N-terminal RhoGEF domain, two DEP and PDZ domains. Rac-GEF activity is stimulated by phosphatidylinositol (3,4,5)-trisphosphate (PtdIns(3,4,5)P3), a lipid second messenger, and by the G beta-gamma subunits of heterotrimeric G proteins. The DEP domains are not involved in mediating these stimuli, but may be of importance for basal and stimulated levels Rac-GEF activity. 81 matched cddid_all.tbl CDD cd04440 cd04440 239887 DEP_2_P-Rex DEP (Dishevelled, Egl-10, and Pleckstrin) domain 2 found in P-Rex-like proteins. The P-Rex family is the guanine-nucleotide exchange factor (GEF) for the small GTPase Rac that contains an N-terminal RhoGEF domain, two DEP and PDZ domains. Rac-GEF activity is stimulated by phosphatidylinositol (3,4,5)-trisphosphate (PtdIns(3,4,5)P3), a lipid second messenger, and the G beta-gamma subunits of heterotrimeric G proteins. The DEP domains are not involved in mediating these stimuli, but may be of importance for basal and stimulated levels Rac-GEF activity. 93 matched cddid_all.tbl CDD cd04441 cd04441 239888 DEP_2_DEP6 DEP (Dishevelled, Egl-10, and Pleckstrin) domain 2 found in DEP6-like proteins. DEP6 proteins contain two DEP and a PDZ domain. Their function is unknown. 85 matched cddid_all.tbl CDD cd04442 cd04442 239889 DEP_1_DEP6 DEP (Dishevelled, Egl-10, and Pleckstrin) domain 1 found in DEP6-like proteins. DEP6 proteins contain two DEP and a PDZ domain. Their function is unknown. 82 matched cddid_all.tbl CDD cd04443 cd04443 239890 DEP_GPR155 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in GPR155-like proteins. GRP155-like proteins, also known as PGR22, contain an N-terminal permease domain, a central transmembrane region and a C-terminal DEP domain. They are orphan receptors of the class B G protein-coupled receptors. Their function is unknown. 83 matched cddid_all.tbl CDD cd04444 cd04444 239891 DEP_PLEK2 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in pleckstrin 2-like proteins. Pleckstrin 2 is found in a wide variety of cell types, which suggest a more general role in signaling than pleckstrin 1. Pleckstrin-like proteins contain a central DEP domain, flanked by 2 PH (pleckstrin homology) domains. 109 matched cddid_all.tbl CDD cd04445 cd04445 239892 DEP_PLEK1 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in pleckstrin 1-like proteins. Pleckstrin 1 plays a role in cell spreading and reorganization of actin cytoskeleton in platelets and leukocytes. Its activity is highly regulated by phosphorylation, mainly by protein kinase C. Pleckstrin-like proteins contain a central DEP domain, flanked by 2 PH (pleckstrin homology) domains. 99 matched cddid_all.tbl CDD cd04446 cd04446 239893 DEP_DEPDC4 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC4-like proteins. DEPDC4 is a DEP domain containing protein of unknown function. 95 matched cddid_all.tbl CDD cd04447 cd04447 239894 DEP_BRCC3 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in BBRC3-like proteins. BBRC3, also known as DEPDC1B, is a DEP containing protein of unknown function. 92 matched cddid_all.tbl CDD cd04448 cd04448 239895 DEP_PIKfyve DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) PIKfyve-like proteins. PIKfyve contains N-terminal Fyve finger and DEP domains, a central chaperonin-like domain and a C-terminal PIPK (phosphatidylinositol phosphate kinase) domain. PIKfyve-like proteins are important phosphatidylinositol (3)-monophosphate (PtdIns(3)P)-5-kinases, producing PtdIns(3,5)P2, which plays a major role in multivesicular body (MVB) sorting and control of retrograde traffic from the vacuole back to the endosome and/or Golgi. PIKfyve itself has been shown to be play a role in regulating early-endosome-to-trans-Golgi network (TGN) retrograde trafficking. 81 matched cddid_all.tbl CDD cd04449 cd04449 239896 DEP_DEPDC5-like DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC5-like proteins. DEPDC5, in human also known as KIAA0645, is a DEP domain containing protein of unknown function. 83 matched cddid_all.tbl CDD cd04450 cd04450 239897 DEP_RGS7-like DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in RGS (regulator of G-protein signaling) proteins of the subfamily R7. This subgroup contains RGS7, RGS6, RGS9 and RGS11. They share a common domain architecture, containing, beside the RGS domain, a DEP domain and a GGL (G-protein gamma subunit-like ) domain. RGS proteins are GTPase-activating (GAP) proteins of heterotrimeric G proteins by increasing the rate of GTP hydrolysis of the alpha subunit. The fungal homologs, like yeast Sst2, share a related common domain architecture, containing RGS and DEP domains. Sst2 has been identified as the principal regulator of mating pheromone signaling and recently the DEP domain of Sst2 has been shown to be necessary and sufficient to mediate receptor interaction. 88 matched cddid_all.tbl CDD cd04451 cd04451 239898 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of the mRNA. 64 matched cddid_all.tbl CDD cd04452 cd04452 239899 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to complete the initiation complex, which is competent to begin translation. The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue. This alpha subunit is well conserved in eukaryotes and archaea but is not present in bacteria. IF2 is a cold-shock-inducible protein. 76 matched cddid_all.tbl CDD cd04453 cd04453 239900 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain that is highly homologous to that of RNase E. RNase G not only shares sequence similarity with RNase E, but also functionally overlaps with RNase E. In Escherichia coli, RNase G is involved in the maturation of the 5' end of the 16S rRNA. RNase G plays a secondary role in mRNA decay. 88 matched cddid_all.tbl CDD cd04454 cd04454 239901 S1_Rrp4_like "S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the ""S1 pore structure""." 82 matched cddid_all.tbl CDD cd04455 cd04455 239902 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible. 67 matched cddid_all.tbl CDD cd04456 cd04456 239903 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea. 78 matched cddid_all.tbl CDD cd04457 cd04457 239904 S1_S28E S1_S28E: S28E, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. S28E protein is a component of the 30S ribosomal subunit. S28E is highly conserved among archaea and eukaryotes. S28E may control precursor RNA splicing and turnover in mRNA maturation process but its function in the ribosome is largely unknown. The structure contains an OB-fold found in many oligosaccharide and nucleic acid binding proteins. This implies that S28E might be involved in protein synthesis. 60 matched cddid_all.tbl CDD cd04458 cd04458 239905 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription. 65 matched cddid_all.tbl CDD cd04459 cd04459 239906 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer. 68 matched cddid_all.tbl CDD cd04460 cd04460 239907 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core. 99 matched cddid_all.tbl CDD cd04461 cd04461 239908 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea. 83 matched cddid_all.tbl CDD cd04462 cd04462 239909 S1_RNAPII_Rpb7 S1_RNAPII_Rpb7: Eukaryotic RNA polymerase II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a heterodimer that associate with the RNAPII core. Rpb7 is a homolog of the Rpc25 of RNA polymerase III, RpoE of the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA polymerase I. Rpb7 has two domains, an N-terminal ribonucleoprotein (RNP) domain and a C-terminal S1 domain, both of which bind single-stranded RNA. It is possible that the S1 domain interacts with the nascent RNA transcript, assisted by the RNP domain. In yeast, Rpb4/Rpb7 is necessary for promoter-directed transcription initiation. They also play a role in regulating transcription-coupled repair in the Rad26-dependent pathway, in efficient mRNA export, and in transcription termination. 88 matched cddid_all.tbl CDD cd04463 cd04463 239910 S1_EF_like S1_EF_like: EF-like, S1-like RNA-binding domain. The EF-like superfamily contains the bacterial translation elongation factor P and its archeal and eukaryotic homologs, aIF5A and eIF5A. All proteins in this superfamily contain an S1 domain, which binds RNA or single-stranded DNA and often interacts with the ribosome. Hex-1, the SI-like domain of which is also found in this group, is structurally homologous to eIF5A and might have evolved from an ancestral eIF5A through gene duplication. 55 matched cddid_all.tbl CDD cd04465 cd04465 239911 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. 67 matched cddid_all.tbl CDD cd04466 cd04466 239912 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain. 68 matched cddid_all.tbl CDD cd04467 cd04467 239913 S1_aIF5A S1_aIF5A: Archaeal translation Initiation Factor 5A (aIF5A), S1-like RNA-binding domain. aIF5A is a homolog of eukaryotic eIF5A. IF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is a post-translationally modified lysine and is essential for IF5A function. In yeast, eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the cold-shock domain which binds RNA. Moreover, IF5A prefers binding to the actively translating ribosome. This evidence suggests that IF5A plays a role in translation elongation instead of translation initiation as previously proposed. 57 matched cddid_all.tbl CDD cd04468 cd04468 239914 S1_eIF5A S1_eIF5A: Eukaryotic translation Initiation Factor 5A (eIF5A), S1-like RNA-binding domain. eIF5A is an evolutionarily conserved protein found in eukaryotes. eIF5A is the only protein known to have the unusual amino acid hypusine. Hypusine is essential for eIF5A function and is a post-translationally modified lysine. eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) in a hypusine-dependent manner. This C-terminal S1 domain resembles the oligonucleotides-binding fold (OB fold) which binds RNA. Moreover, eIF5A prefers binding to the actively translating ribosome. This evidence suggests that eIF5A plays a role in translation elongation instead of translation initiation as previously proposed. 69 matched cddid_all.tbl CDD cd04469 cd04469 239915 S1_Hex1 S1_Hex1: Hex1, S1-like RNA-binding domain. Hex1 protein is the major component of the Woronin body in filamentous fungi. The Woronin body is a dense vesicle and plays a vital role in filamentous fungi cell integrity. When cell damage occurs, Woronin bodies seal the septal pore to prevent further cytoplasmic bleeding. Hex1 protein self-assembles to form the solid core of the Woronin body vesicle. The Hex1 sequence and structure are similar to eukaryotic initiation factor 5A (eIF5A), suggesting they share a common ancestor during evolution. All members of the EF superfamily to which Hex1 belongs, contain an S1 domain, which has been shown to bind RNA or single-stranded DNA and often interacts with the ribosome. 75 matched cddid_all.tbl CDD cd04470 cd04470 239916 S1_EF-P_repeat_1 S1_EF-P_repeat_1: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P has 3 domains (domains I, II, and III). Domains II and III are S1-like domains. This CD includes domain II (the first S1 domain of EF_P). Domains II and III have structural homology to the eIF5A domain C, suggesting that domains II and III evolved by duplication. 61 matched cddid_all.tbl CDD cd04471 cd04471 239917 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA. 83 matched cddid_all.tbl CDD cd04472 cd04472 239918 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo. 68 matched cddid_all.tbl CDD cd04473 cd04473 239919 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair. 77 matched cddid_all.tbl CDD cd04474 cd04474 239920 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functionally. Antibodies to hRPA do not cross-react with ScRPA, and null mutations in the ScRPA subunits are not complemented by corresponding human genes. Also, ScRPA cannot support Simian virus 40 (SV40) DNA replication in vitro, whereas human RPA can. 104 matched cddid_all.tbl CDD cd04475 cd04475 239921 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ functionally. Antibodies to hRPA do not cross-react with ScRPA, and null mutations in the ScRPA subunits are not complemented by corresponding human genes. Also, ScRPA cannot support Simian virus 40 (SV40) DNA replication in vitro, whereas human RPA can. 101 matched cddid_all.tbl CDD cd04476 cd04476 239922 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding function of this domain. It appears that zinc itself may not be required for ssDNA binding. 166 matched cddid_all.tbl CDD cd04477 cd04477 239923 RPA1N RPA1N: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA1N is known to specifically interact with the p53 tumor suppressor, DNA polymerase alpha, and transcription factors. In addition to RPA1N, RPA1 contains three other OB folds: ssDNA-binding domain (DBD)-A, DBD-B, and DBD-C. 97 matched cddid_all.tbl CDD cd04478 cd04478 239924 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA damage. RPA2 interacts physically with menin; the gene encoding menin is a tumor suppressor gene disrupted in multiple endocrine neoplasia type I. This subfamily also includes RPA2 from Cryptosporidium parvum (CpRPA2). CpRPA2 is an SSB, which can be phosphorylated by DNA-PK in vitro. 95 matched cddid_all.tbl CDD cd04479 cd04479 239925 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer. 101 matched cddid_all.tbl CDD cd04480 cd04480 239926 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. 86 matched cddid_all.tbl CDD cd04481 cd04481 239927 RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity to the third OB fold, the ssDNA-binding domain (DBD)-B, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. 106 matched cddid_all.tbl CDD cd04482 cd04482 239928 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA damage. 91 matched cddid_all.tbl CDD cd04483 cd04483 239929 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization. 92 matched cddid_all.tbl CDD cd04484 cd04484 239930 polC_OBF polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis. 82 matched cddid_all.tbl CDD cd04485 cd04485 239931 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis. 84 matched cddid_all.tbl CDD cd04486 cd04486 239932 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall. 78 matched cddid_all.tbl CDD cd04487 cd04487 239933 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function. 73 matched cddid_all.tbl CDD cd04488 cd04488 239934 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched chain substrates. 75 matched cddid_all.tbl CDD cd04489 cd04489 239935 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis. 78 matched cddid_all.tbl CDD cd04490 cd04490 239936 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit. PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain. 79 matched cddid_all.tbl CDD cd04491 cd04491 239937 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating the DNA helicase activity of MCM. 82 matched cddid_all.tbl CDD cd04492 cd04492 239938 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases. 83 matched cddid_all.tbl CDD cd04493 cd04493 239939 BRCA2DBD_OB1 BRCA2DBD_OB1: A subfamily of OB folds corresponding to the first OB fold (OB1) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA). BRCA2DBD OB1 binds DNA weakly. 100 matched cddid_all.tbl CDD cd04494 cd04494 239940 BRCA2DBD_OB2 BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA). 251 matched cddid_all.tbl CDD cd04495 cd04495 239941 BRCA2DBD_OB3 BRCA2DBD_OB3: A subfamily of OB folds corresponding to the third OB fold (OB3) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA). 100 matched cddid_all.tbl CDD cd04496 cd04496 239942 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart at forks that have stalled at sites of DNA damage. It also plays a role in the assembly of primosome during replication initiation at the bacteriophage phiX174 origin. PriB physically interacts with SSB and binds ssDNA with high affinity. 100 matched cddid_all.tbl CDD cd04497 cd04497 239943 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. A second OB fold has not been predicted in S. pombe POT1. OnTEBP binds the extreme 3-prime end of telomeric DNA. It is heterodimeric and contains four OB folds - three in the alpha subunit (two in the N-terminal domain and one in the C-terminal domain) and one in the beta subunit. OB1Nalpha, together with the second OB fold of the N-terminal domain of OnTEBP alpha subunit and the beta subunit OB fold, forms a deep cleft that binds ssDNA. 138 matched cddid_all.tbl CDD cd04498 cd04498 239944 hPOT1_OB2 hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. hPOT1 is implicated in telomere length regulation. 123 matched cddid_all.tbl CDD cd04501 cd04501 239945 SGNH_hydrolase_like_4 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid. 183 matched cddid_all.tbl CDD cd04502 cd04502 239946 SGNH_hydrolase_like_7 Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid. 171 matched cddid_all.tbl CDD cd04506 cd04506 239947 SGNH_hydrolase_YpmR_like Members of the SGNH-hydrolase superfamily, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad from other serine hydrolases, but may lack the carboxlic acid. This subfamily contains sequences similar to Bacillus YpmR. 204 matched cddid_all.tbl CDD cd04508 cd04508 410449 Tudor_SF Tudor domain superfamily. The Tudor domain is a conserved structural domain, originally identified in the Tudor protein of Drosophila, that adopts a beta-barrel-like core structure containing four short beta-strands followed by an alpha-helical region. It binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Tudor domain-containing proteins may mediate protein-protein interactions required for various DNA-templated biological processes, such as RNA metabolism, as well as histone modification and the DNA damage response. Members of this superfamily contain one or more copies of the Tudor domain. 47 matched cddid_all.tbl CDD cd04509 cd04509 380490 PBP1_ABC_transporter_GPCR_C-like Family C of G-protein coupled receptors and their close homologs, the type 1 periplasmic-binding proteins of ATP-binding cassette transporter-like systems. This CD includes members of the family C of G-protein coupled receptors and their close homologs, the type 1 periplasmic-binding proteins of ATP-binding cassette transporter-like systems. The family C GPCR includes glutamate/glycine-gated ion channels such as the NMDA receptor, G-protein-coupled receptors, metabotropic glutamate, GABA-B, calcium sensing, pheromone receptors, and atrial natriuretic peptide-guanylate cyclase receptors. The glutamate receptors that form cation-selective ion channels, iGluR, can be classified into three different subgroups according to their binding-affinity for the agonists NMDA (N-methyl-D-asparate), AMPA (alpha-amino-3-dihydro-5-methyl-3-oxo-4-isoxazolepropionic acid), and kainate. L-glutamate is a major neurotransmitter in the brain of vertebrates and acts through either mGluRs or iGluRs. mGluRs subunits possess seven transmembrane segments and a large N-terminal extracellular domain. ABC-type leucine-isoleucine-valine binding protein (LIVBP) is a bacterial periplasmic binding protein that has homology with the amino-terminal domain of the glutamate-receptor ion channels (iGluRs). The extracellular regions of iGluRs are made of two PBP-like domains in tandem, a LIVBP-like domain that constitutes the N terminus (included in this model) followed by a domain related to lysine-arginine-ornithine-binding protein (LAOBP) that belongs to the type 2 periplasmic binding fold protein superfamily. The uncharacterized periplasmic components of various ABC-type transport systems are also included in this family. 306 matched cddid_all.tbl CDD cd04511 cd04511 467545 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 123 matched cddid_all.tbl CDD cd04512 cd04512 271334 Ntn_Asparaginase_2_like L-Asparaginase type 2-like enzymes of the NTN-hydrolase superfamily. This family includes Glycosylasparaginase, Taspase 1, and L-Asparaginase type 2 enzymes. Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked glycoprotein. Taspase1 catalyzes the cleavage of the Mix Lineage Leukemia (MLL) nuclear protein and transcription factor TFIIA. L-Asparaginase type 2 hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzymes of this family undergo autoproteolytic cleavage before a threonine to generate alpha and beta subunits. The threonine becomes the N-terminal residue of the beta subunit and is the catalytic residue. The family is circularly permuted relative to other NTN-hydrolase families. 249 matched cddid_all.tbl CDD cd04513 cd04513 271335 Glycosylasparaginase Glycosylasparaginase and similar proteins. Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked glycoproteins. This enzyme is an amidase located inside lysosomes. Mutation of this gene in humans causes a genetic disorder known as aspartylglycosaminuria (AGU). The glycosylasparaginase precursor undergoes autoproteolysis through an N-O or N-S acyl rearrangement of the peptide bond, which leads to the cleavage of a peptide bond between an Asp and a Thr. This proteolysis step generates an exposed N-terminal catalytic threonine and activates the enzyme. 294 matched cddid_all.tbl CDD cd04514 cd04514 271336 Taspase1_like Taspase 1 (threonine aspartase 1) and similar proteins. Taspase1 catalyzes the cleavage of the mix lineage leukemia (MLL) nuclear protein and transcription factor TFIIA. Taspase1 is a threonine aspartase, a member of the Ntn hydrolase superfamily and the type 2 asparaginase family. A threonine residue acts as the active site nucleophile in both endopeptidease and protease activities to cleave polypeptide substrates after an aspartate residue. The Taspase1 proenzyme undergoes autoproteolysis into alpha and beta subunits. The N-terminal residue of the beta subunit is a threonine which is the active catalytic residue. The active enzyme is a heterotetramer. 313 matched cddid_all.tbl CDD cd04515 cd04515 341214 Alpha_kinase Alpha kinase family. The alpha kinase family is a novel family of eukaryotic protein kinase catalytic domains, which have no detectable similarity to conventional serine/threonine protein kinases. The family contains myosin heavy chain kinases, elongation factor-2 kinases, and bifunctional ion channel kinases. These kinases are implicated in a large variety of cellular processes such as protein translation, Mg2+/Ca2+ homeostasis, intracellular transport, cell migration, adhesion, and proliferation. The alpha-kinase family was named after the unique mode of substrate recognition by its initial members, the Dictyostelium heavy chain kinases, which targeted protein sequences that adopt an alpha-helical conformation. More recently, alpha-kinases were found to also target residues in non-helical regions. 213 matched cddid_all.tbl CDD cd04516 cd04516 239952 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. 174 matched cddid_all.tbl CDD cd04517 cd04517 239953 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters. 174 matched cddid_all.tbl CDD cd04518 cd04518 239954 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. 174 matched cddid_all.tbl CDD cd04519 cd04519 213328 RasGAP Ras GTPase Activating Domain. RasGAP functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Proteins having a RasGAP domain include p120GAP, IQGAP, Rab5-activating protein 6, and Neurofibromin, among others. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP exhibit no similarity at their amino acid sequence level. RasGTPases function as molecular switches in a large number of signaling pathways. They are in the on state when bound to GTP, and in the off state when bound to GDP. The RasGAP domain speeds up the hydrolysis of GTP in Ras-like proteins acting as a negative regulator. 256 matched cddid_all.tbl CDD cd04582 cd04582 341359 CBS_pair_ABC_OpuCA_assoc Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains found associated with the ABC transporter OpuCA. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains found in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment but the function of the CBS domains in OpuCA remains unknown. In the related ABC transporter, OpuA, the tandem CBS domains have been shown to function as sensors for ionic strength, whereby they control the transport activity through an electronic switching mechanism. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. They are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 111 matched cddid_all.tbl CDD cd04583 cd04583 341360 CBS_pair_ABC_OpuCA_assoc Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains found associated with the ABC transporter OpuCA. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains found in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment but the function of the CBS domains in OpuCA remains unknown. In the related ABC transporter, OpuA, the tandem CBS domains have been shown to function as sensors for ionic strength, whereby they control the transport activity through an electronic switching mechanism. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. They are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 110 matched cddid_all.tbl CDD cd04584 cd04584 341361 CBS_pair_AcuB_like Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the ACT domain. The putative Acetoin Utilization Protein (Acub) from Vibrio Cholerae contains a CBS pair domain. The acetoin utilization protein plays a role in growth and sporulation on acetoin or butanediol for use as a carbon source. Acetoin is an important physiological metabolite excreted by many microorganisms. It is used as an external energy store by a number of fermentive bacteria. Acetoin is produced by the decarboxylation of alpha-acetolactate. Once superior carbon sources are exhausted, and the culture enters stationary phase, acetoin can be utilised in order to maintain the culture density. The conversion of acetoin into acetyl-CoA or 2,3-butanediol is catalysed by the acetoin dehydrogenase complex and acetoin reductase/2,3-butanediol dehydrogenase, respectively. Acetoin utilization proteins, acetylpolyamine amidohydrolases, and histone deacetylases are members of an ancient protein superfamily.This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the acetoin utilization proteins in bacteria. Acetoin is a product of fermentative metabolism in many prokaryotic and eukaryotic microorganisms. They produce acetoin as an external carbon storage compound and then later reuse it as a carbon and energy source during their stationary phase and sporulation. In addition these CBS domains are associated with a downstream ACT (aspartate kinase/chorismate mutase/TyrA) domain, which is linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 130 matched cddid_all.tbl CDD cd04586 cd04586 341362 CBS_pair_BON_assoc Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the BON (bacterial OsmY and nodulation domain) domain. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the BON (bacterial OsmY and nodulation domain) domain. BON is a putative phospholipid-binding domain found in a family of osmotic shock protection proteins. It is also found in some secretins and a group of potential haemolysins. Its likely function is attachment to phospholipid membranes. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 137 matched cddid_all.tbl CDD cd04587 cd04587 341363 CBS_pair_CAP-ED_NT_Pol-beta-like_DUF294_assoc Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the bacterial CAP_ED (cAMP receptor protein effector domain) family of transcription factors, the NT (Nucleotidyltransferase) Pol-beta-like domain, and the DUF294 domain. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the bacterial CAP_ED (cAMP receptor protein effector domain) family of transcription factors, the NT_Pol-beta-like domain, and the DUF294 domain. Members of CAP_ED, include CAP which binds cAMP, FNR (fumarate and nitrate reductase) which uses an iron-sulfur cluster to sense oxygen, and CooA a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. The NT_Pol-beta-like domain includes the Nucleotidyltransferase (NT) domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of class I and class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. DUF294 is a putative nucleotidyltransferase with a conserved DxD motif. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 114 matched cddid_all.tbl CDD cd04588 cd04588 341364 CBS_pair_archHTH_assoc Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains found in archaea and associated with helix turn helix domain. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key role in the regulation of cell proliferation and differentiation. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 111 matched cddid_all.tbl CDD cd04589 cd04589 341365 CBS_pair_CAP-ED_NT_Pol-beta-like_DUF294_assoc Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the bacterial CAP_ED (cAMP receptor protein effector domain) family of transcription factors, the NT (Nucleotidyltransferase) Pol-beta-like domain, and the DUF294 domain. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the bacterial CAP_ED (cAMP receptor protein effector domain) family of transcription factors, the NT_Pol-beta-like domain, and the DUF294 domain. Members of CAP_ED, include CAP which binds cAMP, FNR (fumarate and nitrate reductase) which uses an iron-sulfur cluster to sense oxygen, and CooA a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. The NT_Pol-beta-like domain includes the Nucleotidyltransferase (NT) domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of class I and class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. DUF294 is a putative nucleotidyltransferase with a conserved DxD motif. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 113 matched cddid_all.tbl CDD cd04590 cd04590 341366 CBS_pair_CorC_HlyC_assoc Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains the majority of which are associated with the CorC_HlyC domain. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains the majority of which are associated with the CorC_HlyC domain. CorC_HlyC is a transporter associated domain. This small domain is found in Na+/H+ antiporters, in proteins involved in magnesium and cobalt efflux, and in association with some proteins of unknown function. The function of the CorC_HlyC domain is uncertain but it might be involved in modulating transport of ion substrates. These CBS domains are found in highly conserved proteins that either have unknown function or are puported to be hemolysins, exotoxins involved in lysis of red blood cells in vitro. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 119 matched cddid_all.tbl CDD cd04591 cd04591 341367 CBS_pair_voltage-gated_CLC_euk_bac Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC (chloride channel) in eukaryotes and bacteria. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC voltage-gated chloride channel. The CBS pairs here are found in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the CIC-type chloride channel are double-barreled: two proteins forming homodimers at a broad interface formed by four helices from each protein. The two pores are not found at this interface, but are completely contained within each subunit, as deduced from the mutational analyses, unlike many other channels, in which four or five identical or structurally related subunits jointly form one pore. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 114 matched cddid_all.tbl CDD cd04592 cd04592 341368 CBS_pair_voltage-gated_CLC_euk_bac Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC (chloride channel) in eukaryotes and bacteria. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC voltage-gated chloride channel. The CBS pairs here are found in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the CIC-type chloride channel are double-barreled: two proteins forming homodimers at a broad interface formed by four helices from each protein. The two pores are not found at this interface, but are completely contained within each subunit, as deduced from the mutational analyses, unlike many other channels, in which four or five identical or structurally related subunits jointly form one pore. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 128 matched cddid_all.tbl CDD cd04594 cd04594 341369 CBS_pair_voltage-gated_CLC_archaea Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC (chloride channel) in archaea. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC voltage-gated chloride channel. The CBS pairs here are found in the EriC CIC-type chloride channels in archaea. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the CIC-type chloride channel are double-barreled: two proteins forming homodimers at a broad interface formed by four helices from each protein. The two pores are not found at this interface, but are completely contained within each subunit, as deduced from the mutational analyses, unlike many other channels, in which four or five identical or structurally related subunits jointly form one pore. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 107 matched cddid_all.tbl CDD cd04595 cd04595 341370 CBS_pair_DHH_polyA_Pol_assoc Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the DHH and nucleotidyltransferase (NT) domains. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with an upstream DHH domain which performs a phosphoesterase function and a downstream nucleotidyltransferase (NT) domain of family X DNA polymerases. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 110 matched cddid_all.tbl CDD cd04596 cd04596 341371 CBS_pair_DRTGG_assoc Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the DRTGG domain. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with a DRTGG domain upstream. The function of the DRTGG domain, named after its conserved residues, is unknown. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 108 matched cddid_all.tbl CDD cd04597 cd04597 341372 CBS_pair_inorgPPase Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with family II inorganic pyrophosphatase. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with a subgroup of family II inorganic pyrophosphatases (PPases) that also contain a DRTGG domain. The homolog from Clostridium has been shown to be inhibited by AMP and activated by a novel effector, diadenosine 5',5-P1,P4-tetraphosphate (AP(4)A), which has been shown to bind to the CBS domain. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. 106 matched cddid_all.tbl CDD cd04598 cd04598 341373 CBS_pair_GGDEF_EAL Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and is thought to be involved in regulating cell surface adhesiveness in bacteria. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 121 matched cddid_all.tbl CDD cd04599 cd04599 341374 CBS_pair_GGDEF_assoc Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the GGDEF (DiGuanylate-Cyclase (DGC)) domain. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and is thought to be involved in regulating cell surface adhesiveness in bacteria. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 107 matched cddid_all.tbl CDD cd04600 cd04600 341375 CBS_pair_HPP_assoc Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. These proteins are integral membrane proteins with four transmembrane spanning helices. The function of these proteins is uncertain, but they are thought to be transporters. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 133 matched cddid_all.tbl CDD cd04601 cd04601 341376 CBS_pair_IMPDH Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the inosine 5' monophosphate dehydrogenase (IMPDH) protein. IMPDH is an essential enzyme that catalyzes the first step unique to GTP synthesis, playing a key role in the regulation of cell proliferation and differentiation. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 110 matched cddid_all.tbl CDD cd04603 cd04603 341377 CBS_pair_KefB_assoc Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the KefB (Kef-type K+ transport systems) domain. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the KefB (Kef-type K+ transport systems) domain which is involved in inorganic ion transport and metabolism. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 112 matched cddid_all.tbl CDD cd04604 cd04604 341378 CBS_pair_SIS_assoc Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the with the SIS (Sugar ISomerase) domain. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the SIS (Sugar ISomerase) domain in the API [A5P (D-arabinose 5-phosphate) isomerase] protein KpsF/GutQ. These APIs catalyze the conversion of the pentose pathway intermediate D-ribulose 5-phosphate into A5P, a precursor of 3-deoxy-D-manno-octulosonate, which is an integral carbohydrate component of various glycolipids coating the surface of the outer membrane of Gram-negative bacteria, including lipopolysaccharide and many group 2 K-antigen capsules. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 124 matched cddid_all.tbl CDD cd04605 cd04605 341379 CBS_pair_arch_MET2_assoc Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the MET2 domain. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the MET2 domain. Met2 is a key enzyme in the biosynthesis of methionine. It encodes a homoserine transacetylase involved in converting homoserine to O-acetyl homoserine. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 116 matched cddid_all.tbl CDD cd04606 cd04606 341380 CBS_pair_Mg_transporter Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the magnesium transporter, MgtE. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other divalent cations into the cell via two highly conserved aspartates. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 121 matched cddid_all.tbl CDD cd04607 cd04607 341381 CBS_pair_NTP_transferase_assoc Two tandem repeats of the cystathionine beta-synthase (CBS pair) domain associated with the NTP (Nucleotidyl transferase) domain. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain associated with the NTP (Nucleotidyl transferase) domain downstream. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 112 matched cddid_all.tbl CDD cd04608 cd04608 341382 CBS_pair_CBS Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the pyridoxal-phosphate (PALP) dependent enzyme domain. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the pyridoxal-phosphate (PALP) dependent enzyme domain upstream. Cystathionine beta-synthase (CBS ) contains, besides the C-terminal regulatory CBS-pair, an N-terminal heme-binding module, followed by a pyridoxal phosphate (PLP) domain, which houses the active site. It is the first enzyme in the transsulfuration pathway, catalyzing the conversion of serine and homocysteine to cystathionine and water. In general, CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 120 matched cddid_all.tbl CDD cd04610 cd04610 341383 CBS_pair_ParBc_assoc Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with a ParBc (ParB-like nuclease) domain. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with a ParBc (ParB-like nuclease) domain downstream. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 108 matched cddid_all.tbl CDD cd04611 cd04611 341384 CBS_pair_GGDEF_PAS_repeat2 Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains found in diguanylate cyclase/phosphodiesterase proteins with PAS sensors, repeat 2. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains found in diguanylate cyclase/phosphodiesterase proteins with PAS sensors. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and is thought to be involved in regulating cell surface adhesiveness in bacteria. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 131 matched cddid_all.tbl CDD cd04613 cd04613 341385 CBS_pair_voltage-gated_CLC_bac Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC (chloride channel) in bacteria. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC voltage-gated chloride channel. The CBS pairs here are found in the EriC CIC-type chloride channels in bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the CIC-type chloride channel are double-barreled: two proteins forming homodimers at a broad interface formed by four helices from each protein. The two pores are not found at this interface, but are completely contained within each subunit, as deduced from the mutational analyses, unlike many other channels, in which four or five identical or structurally related subunits jointly form one pore. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 119 matched cddid_all.tbl CDD cd04614 cd04614 341386 CBS_pair_arch2_repeat2 Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in archaea, repeat 2. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains found in Inosine monophosphate (IMP) dehydrogenases and related proteins including IMP dehydrogenase IX from Methanothermobacter. IMP dehydrogenase is an essential enzyme in the de novo biosynthesis of Guanosine monophosphate (GMP), catalyzing the NAD-dependent oxidation of IMP to xanthosine monophosphate (XMP). The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 150 matched cddid_all.tbl CDD cd04617 cd04617 341387 CBS_pair_CcpN Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains of CcpN repressor. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 125 matched cddid_all.tbl CDD cd04618 cd04618 341388 CBS_euAMPK_gamma-like_repeat1 Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains found in AMP-activated protein kinase gamma-like proteins, repeat 1. AMP-activated protein kinase (AMPK) plays multiple roles in the body's overall metabolic balance and response to exercise, nutritional stress, hormonal stimulation, and the glucose-lowering drugs metformin and rosiglitazone. AMPK consists of a catalytic alpha subunit and two non-catalytic subunits, beta and gamma, each with multiple isoforms that form active 1:1:1 heterotrimers. This cd contains 2 tandem repeats of the CBS domains found in the gamma subunits of AMPK. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 138 matched cddid_all.tbl CDD cd04620 cd04620 341389 CBS_two-component_sensor_histidine_kinase_repeat1 2 tandem repeats of the CBS domain in the two-component sensor histidine kinase and related-proteins, repeat 1. This cd contains 2 tandem repeats of the CBS domain in the two-component sensor histidine kinase and related-proteins. Two-component regulation is the predominant form of signal recognition and response coupling mechanism used by bacteria to sense and respond to diverse environmental stresses and cues ranging from common environmental stimuli to host signals recognized by pathogens and bacterial cell-cell communication signals. The structures of both sensors and regulators are modular, and numerous variations in domain architecture and composition have evolved to tailor to specific needs in signal perception and signal transduction. The simplest histidine kinase sensors consists of only sensing and kinase domains. The more complex hybrid sensors contain an additional REC domain typical of two-component regulators and in some cases a C-terminal histidine phosphotransferase (HPT) domain. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 136 matched cddid_all.tbl CDD cd04622 cd04622 341390 CBS_pair_HRP1_like CBS pair domain found in Hypoxic Response Protein 1 (HRP1) -like proteinds. Mycobacterium tuberculosis adapts to cellular stresses by upregulation of the dormancy survival regulon. Hypoxic response protein 1 (HRP1) is encoded by one of the most strongly upregulated genes in the dormancy survival regulon. HRP1 is a 'CBS-domain-only protein; however unlike other CBS containing proteins it does not appear to bind AMP. The biological function of the protein remains unclear, but is thought to contribute to the modulation of the host immune response. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 115 matched cddid_all.tbl CDD cd04623 cd04623 341391 CBS_pair_bac_euk Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in bacteria and eukaryotes. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 113 matched cddid_all.tbl CDD cd04629 cd04629 341392 CBS_pair_bac Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in bacteria. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 116 matched cddid_all.tbl CDD cd04630 cd04630 341393 CBS_pair_bac Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in bacteria. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 120 matched cddid_all.tbl CDD cd04631 cd04631 341394 CBS_archAMPK_gamma-repeat2 CBS pair domains found in archeal 5'-AMP-activated protein kinase gamma subunit-like proteins. Archeal gamma-subunit of 5'-AMP-activated protein kinase (AMPK) contains four CBS domains in tandem repeats, similar to eukaryotic homologs. AMPK is an important regulator of metabolism and of energy homeostasis. It is a heterotrimeric protein composed of a catalytic serine/threonine kinase subunit (alpha) and two regulatory subunits (beta and gamma). The gamma subunit senses the intracellular energy status by competitively binding AMP and ATP and is believed to be responsible for allosteric regulation of the whole complex. In humans mutations in gamma- subunit of AMPK are associated with hypertrophic cardiomiopathy, Wolff-Parkinson-White syndrome and glycogen storage in the skeletal muscle. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. 130 matched cddid_all.tbl CDD cd04632 cd04632 341395 CBS_pair_arch1_repeat2 Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in archaea, repeat 2. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 127 matched cddid_all.tbl CDD cd04638 cd04638 341396 CBS_pair_arch2_repeat1 Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in archaea, repeat 1. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 109 matched cddid_all.tbl CDD cd04639 cd04639 341397 CBS_pair_peptidase_M50 Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains found in the metalloprotease peptidase M50. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in peptidase M50. Members of the M50 metallopeptidase family include mammalian sterol-regulatory element binding protein (SREBP) site 2 proteases and various hypothetical bacterial homologues. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 120 matched cddid_all.tbl CDD cd04640 cd04640 341398 CBS_pair_proteobact Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in proteobacteria. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 133 matched cddid_all.tbl CDD cd04641 cd04641 341399 CBS_euAMPK_gamma-like_repeat2 CBS pair domain found in 5'-AMP (adenosine monophosphate)-activated protein kinase. The 5'-AMP (adenosine monophosphate)-activated protein kinase (AMPK) coordinates metabolic function with energy availability by responding to changes in intracellular ATP (adenosine triphosphate) and AMP concentrations. Most of the members of this cd contain two Bateman domains, each of which is composed of a tandem pair of cystathionine beta-synthase (CBS) motifs. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 124 matched cddid_all.tbl CDD cd04643 cd04643 341400 CBS_pair_bac Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in bacteria. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 130 matched cddid_all.tbl CDD cd04645 cd04645 100051 LbH_gamma_CA_like Gamma carbonic anhydrase-like: This family is composed of gamma carbonic anhydrase (CA), Ferripyochelin Binding Protein (FBP), E. coli paaY protein, and similar proteins. CAs are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism, involving the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Gamma CAs are trimeric enzymes with left-handed parallel beta helix (LbH) structural domain. 153 matched cddid_all.tbl CDD cd04646 cd04646 100052 LbH_Dynactin_6 Dynactin 6 (or subunit p27): Dynactin is a major component of the activator complex that stimulates dynein-mediated vesicle transport. Dynactin is a heterocomplex of at least eight subunits, including a 150,000-MW protein called Glued, the actin-capping protein Arp1, and dynamatin. In vitro binding experiments show that dynactin enhances dynein-dependent motility, possibly through interaction with microtubules and vesicles. Subunit p27 is part of the pointed-end subcomplex in dynactin that also includes p25, p26, and Arp11. This subcomplex interacts with membranous cargoes. p25 and p27 contain the imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X), indicating a left-handed parallel beta helix (LbH) structural domain. Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity. 164 matched cddid_all.tbl CDD cd04647 cd04647 100053 LbH_MAT_like Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins. MAT and GAT catalyze the CoA-dependent acetylation of the 6-hydroxyl group of their respective sugar substrates. MAT acetylates maltose and glucose exclusively while GAT specifically acetylates galactopyranosides. XAT catalyzes the CoA-dependent acetylation of a variety of hydroxyl-bearing acceptors such as chloramphenicol and streptogramin, among others. XATs are implicated in inactivating xenobiotics leading to xenobiotic resistance in patients. Members of this family contain a a left-handed parallel beta-helix (LbH) domain with at least 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). They are trimeric in their active form. 109 matched cddid_all.tbl CDD cd04649 cd04649 100054 LbH_THP_succinylT_putative Putative 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate (THDP) N-succinyltransferase (THP succinyltransferase), C-terminal left-handed parallel alpha-helix (LbH) domain: This group is composed of mostly uncharacterized proteins containing an N-terminal domain of unknown function and a C-terminal LbH domain with similarity to THP succinyltransferase LbH. THP succinyltransferase catalyzes the conversion of tetrahydrodipicolinate and succinyl-CoA to N-succinyltetrahydrodipicolinate and CoA. It is the committed step in the succinylase pathway by which bacteria synthesize L-lysine and meso-diaminopimelate, a component of peptidoglycan. The enzyme is trimeric and displays the left-handed parallel alpha-helix (LbH) structural motif encoded by the hexapeptide repeat motif. 147 matched cddid_all.tbl CDD cd04650 cd04650 100055 LbH_FBP Ferripyochelin Binding Protein (FBP): FBP is an outer membrane protein which plays a role in iron acquisition. It binds iron when it is complexed with pyochelin. It adopts the left-handed parallel beta-helix (LbH) structure, and contains imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity. Acyltransferase activity has not been observed in this group. 154 matched cddid_all.tbl CDD cd04651 cd04651 100056 LbH_G1P_AT_C Glucose-1-phosphate adenylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Glucose-1-phosphate adenylyltransferase is also known as ADP-glucose synthase or ADP-glucose pyrophosphorylase. It catalyzes the first committed and rate-limiting step in starch biosynthesis in plants and glycogen biosynthesis in bacteria. It is the enzymatic site for regulation of storage polysaccharide accumulation in plants and bacteria. The enzyme is a homotetramer, with each subunit containing an N-terminal catalytic domain that resembles a dinucleotide-binding Rossmann fold and a C-terminal LbH fold domain with at 5 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). The LbH domain is involved in cooperative allosteric regulation and oligomerization. 104 matched cddid_all.tbl CDD cd04652 cd04652 100057 LbH_eIF2B_gamma_C eIF-2B gamma subunit, C-terminal Left-handed parallel beta-Helix (LbH) domain: eIF-2B is a eukaryotic translation initiator, a guanine nucleotide exchange factor (GEF) composed of five different subunits (alpha, beta, gamma, delta and epsilon). eIF2B is important for regenerating GTP-bound eIF2 during the initiation process. This event is obligatory for eIF2 to bind initiator methionyl-tRNA, forming the ternary initiation complex. The eIF-2B gamma subunit contains an N-terminal domain that resembles a dinucleotide-binding Rossmann fold and a C-terminal LbH domain with 4 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). The epsilon and gamma subunits form the catalytic subcomplex of eIF-2B, which binds eIF2 and catalyzes guanine nucleotide exchange. 81 matched cddid_all.tbl CDD cd04657 cd04657 240015 Piwi_ago-like Piwi_ago-like: PIWI domain, Argonaute-like subfamily. Argonaute is the central component of the RNA-induced silencing complex (RISC) and related complexes. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing. 426 matched cddid_all.tbl CDD cd04658 cd04658 240016 Piwi_piwi-like_Euk Piwi_piwi-like_Euk: PIWI domain, Piwi-like subfamily found in eukaryotes. This domain is found in Piwi and closely related proteins, where it is believed to perform a crucial role in germline cells, via RNA silencing. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The mechanism in Piwi is believed to be similar to that in Argonaute, the central component of the RNA-induced silencing complex (RISC). The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing. 448 matched cddid_all.tbl CDD cd04659 cd04659 240017 Piwi_piwi-like_ProArk Piwi_piwi-like_ProArk: PIWI domain, Piwi-like subfamily found in Archaea and Bacteria. RNA silencing refers to a group of related gene-silencing mechanisms mediated by short RNA molecules, including siRNAs, miRNAs, and heterochromatin-related guide RNAs. The central component of the RNA-induced silencing complex (RISC) and related complexes is Argonaute. The PIWI domain is the C-terminal portion of Argonaute and consists of two subdomains, one of which provides the 5' anchoring of the guide RNA and the other, the catalytic site for slicing. This domain is also found in closely related proteins, including the Piwi subfamily, where it is believed to perform a crucial role in germline cells, via a similar mechanism. 404 matched cddid_all.tbl CDD cd04660 cd04660 240018 nsLTP_like nsLTP_like: Non-specific lipid-transfer protein (nsLTP)-like subfamily; composed of predominantly uncharacterized proteins with similarity to nsLTPs, including Medicago truncatula MtN5, the root-specific Phaseolus vulgaris PVR3, Antirrhinum majus FIL1, and Lilium longiflorum LIM3. Plant nsLTPs are small, soluble proteins that facilitate the transfer of fatty acids, phospholipids, glycolipids, and steroids between membranes. The MtN5 gene is induced during root nodule development. FIL1 is thought to be important in petal and stamen formation. The LIM3 gene is induced during the early prophase stage of meiosis in lily microsporocytes. 73 matched cddid_all.tbl CDD cd04661 cd04661 467546 NUDIX_MRP_L46 Mitochondrial ribosomal protein L46. Mitochondrial ribosomal protein L46 (MRP L46) is a component of the large subunit (39S) of the mammalian mitochondrial ribosome and a member of the NUDIX hydrolase superfamily. MRPs are thought to be involved in the maintenance of the mitochondrial DNA. In general, members of the NUDIX hydrolase superfamily require a divalent cation, such as Mg2+ or Mn2+, for activity and contain the NUDIX motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. MRP L46 appears to contain a modified NUDIX motif. 142 matched cddid_all.tbl CDD cd04662 cd04662 467547 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 147 matched cddid_all.tbl CDD cd04663 cd04663 467548 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 132 matched cddid_all.tbl CDD cd04664 cd04664 467549 NUDIX_DHNTPase_like "dihydroneopterin hydrolase. DHNTP pyrophosphatase (DHNTPase) catalyzes the hydrolysis of dihydroneopterin triphosphate (DHNTP) to dihydroneopterin monophosphate (DHNMP) and pyrophosphate,the second step in the pterin branch of the folate synthesis pathway in bacteria. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & ""house-cleaning"" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required." 132 matched cddid_all.tbl CDD cd04665 cd04665 467550 NUDIX_RppH "RNA pyrophosphohydrolase. The initiation of mRNA degradation often requires deprotection of its 5' end. In eukaryotes, the 5'-methylguanosine (cap) structure is principally removed by the NUDIX family decapping enzyme Dcp2, yielding a 5'-monophosphorylated RNA that is a substrate for 5' exoribonucleases. In bacteria, the 5'-triphosphate group of primary transcripts is also converted to a 5' monophosphate by a NUDIX protein called RNA pyrophosphohydrolase (RppH), allowing access to both endo- and 5' exoribonucleases. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 121 matched cddid_all.tbl CDD cd04666 cd04666 467551 NUDIX_DIPP2_like_Nudt4 "diadenosine 5',5'''-P1,P6-hexaphosphate hydrolase type 2 and similar proteins. Diadenosine 5',5'''-P1,P6-hexaphosphate hydrolase type 2 (DIPP2), also known as NUDIX (nucleoside diphosphate-linked moiety X)) motif 4; Nudt4, and other proteins including DIPP1/Nudt3, DIPP3a;APS2/Nudt10 and DIPP3beta;APS1/Nudt11. DIPP regulates the turnover of diphosphoinositol polyphosphates. The turnover of these high-energy diphosphoinositol polyphosphates represents a molecular switching activity with important regulatory consequences. Molecular switching by diphosphoinositol polyphosphates may contribute to regulating intracellular trafficking. Several alternatively spliced transcript variants have been described, but the full-length nature of some variants has not been determined. Isoforms DIPP2alpha and DIPP2beta are distinguishable from each other solely by DIPP2beta possessing one additional amino acid due to intron boundary skidding in alternate splicing. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & ""house-cleaning"" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required." 128 matched cddid_all.tbl CDD cd04667 cd04667 467552 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 117 matched cddid_all.tbl CDD cd04669 cd04669 467553 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 120 matched cddid_all.tbl CDD cd04670 cd04670 467554 NUDIX_ASFGF2_Nudt6 "Antisense Basic Fibroblast Growth Factor. Antisense Basic Fibroblast Growth Factor (ASFGF2; EC 3.6.1.-), also known as nucleoside diphosphate-linked moiety X)) motif 6/Nudt6, and similar proteins including peroxisomal coenzyme A diphosphatase/Nudt7 and mitochondrial coenzyme A diphosphatase/Nudt8. The Nudt6 gene overlaps and lies on the opposite strand from FGF2 gene, and is thought to be the FGF2 antisense gene. The two genes are independently transcribed, and their expression shows an inverse relationship, suggesting that this antisense transcript may regulate FGF2 expression. This gene has also been shown to have hormone-regulatory and antiproliferative actions in the pituitary that are independent of FGF2 expression. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & ""house-cleaning"" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required." 131 matched cddid_all.tbl CDD cd04671 cd04671 467555 NUDIX_8DGDPP_Nudt18 "8-oxo-DGDP phosphatase. 8-oxo-DGDP phosphatase (8DGDPP; EC 3.6.1.55), also known as NUDIX (nucleoside diphosphate-linked moiety X)) motif 18/Nudt18; 2-hydroxy-DADP phosphatase; 7,8-dihydro-8-oxoguanine phosphatase, hydrolyzes 8-oxo-7,8-dihydroguanine (8-oxo-Gua)-containing deoxyribo- and ribonucleoside diphosphates to the monophosphates. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & ""house-cleaning"" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required." 130 matched cddid_all.tbl CDD cd04672 cd04672 467556 NUDIX_CDP-Chase_like "CDP-Choline Pyrophosphatase and similar proteins. Members include: CDP-Choline Pyrophosphatase, ADP-ribose pyrophosphatase, and UDP-X diphosphatase. CDP-choline pyrophosphatase catalyzes the hydrolysis of CDP-choline to produce CMP and phosphocholine. ADP-ribose pyrophosphatase catalyzes the hydrolysis of ADP-ribose to AMP and ribose-5-P. UDP-X diphosphatase hydrolyzes UDP-N-acetylmuramic acid and UDP-N-acetylmuramoyl-L-alanine. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & ""house-cleaning"" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required." 128 matched cddid_all.tbl CDD cd04673 cd04673 467557 NUDIX_ADPRase ADP-ribose pyrophosphatase. ADP-ribose pyrophosphatase (ADPRase; EC 3.6.1.13) catalyzes the hydrolysis of ADP-ribose to AMP and ribose-5-P. Like other members of the NUDIX hydrolase superfamily of enzymes, it is thought to require a divalent cation, such as Mg2+, for its activity. It also contains a 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the NUDIX motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. In humans, there are four distinct ADPRase activities, three putative cytosolic (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). ADPRase-m is also known as NUDT9. It can be distinugished from the cytosolic ADPRase by a N-terminal target sequence unique to mitochondrial ADPRase. NUDT9 functions as a monomer. 128 matched cddid_all.tbl CDD cd04674 cd04674 467558 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 118 matched cddid_all.tbl CDD cd04676 cd04676 467559 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 144 matched cddid_all.tbl CDD cd04677 cd04677 467560 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 137 matched cddid_all.tbl CDD cd04678 cd04678 467561 NUDIX_MTH2_Nudt15 "MutT homolog 2. MutT Homolog 2 (MTH2; EC 3.6.1.9), also known as NUDIX (nucleoside diphosphate-linked moiety X)) motif 15/Nudt15, may catalyze the hydrolysis of nucleoside diphosphates, triphosphates including dGTP, dTTP, dCTP, their oxidized forms like 8-oxo-dGTP, and prodrug thiopurine derivatives 6-thio-dGTP and 6-thio-GTP. MTH2 may also play a role in DNA synthesis and cell cycle progression by stabilizing PCNA. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & ""house-cleaning"" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required." 128 matched cddid_all.tbl CDD cd04679 cd04679 467562 NUDIX_MutT_Nudt1 MutT homolog-1 and similar proteins. MutT homolog-1 (MTH1), also known as NUDIX (nucleoside diphosphate-linked moiety X)) motif 1/Nudt1, is a member of the NUDIX hydrolase superfamily. MTH1, the mammalian counterpart of MutT, hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to monophosphates, thereby preventing the incorporation of such oxygen radicals during replication. This is an important step in the repair mechanism in genomic and mitochondrial DNA. Like other members of the NUDIX family, it requires a divalent cation, such as Mg2+ or Mn2+, for activity, and contain the NUDIX motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. MTH1 is predominantly localized in the cytoplasm and mitochondria. Structurally, this enzyme adopts a similar fold to MutT despite low sequence similarity outside the conserved NUDIX motif. The most distinctive structural difference between MutT and MTH1 is the presence of a beta-hairpin, which is absent in MutT. This results in a much deeper and narrower substrate binding pocket. Mechanistically, MTH1 contains dual specificity for nucleotides that contain 2-OH-adenine bases and those that contain 8-oxo-guanine bases. 126 matched cddid_all.tbl CDD cd04680 cd04680 467563 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 121 matched cddid_all.tbl CDD cd04681 cd04681 467564 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 135 matched cddid_all.tbl CDD cd04682 cd04682 467565 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 123 matched cddid_all.tbl CDD cd04683 cd04683 467566 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 137 matched cddid_all.tbl CDD cd04684 cd04684 467567 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. Contains a crystal structure of the NUDIX hydrolase from Enterococcus faecalis, which has an unknown function. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 140 matched cddid_all.tbl CDD cd04685 cd04685 467568 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 138 matched cddid_all.tbl CDD cd04686 cd04686 467569 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 130 matched cddid_all.tbl CDD cd04688 cd04688 467570 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 130 matched cddid_all.tbl CDD cd04689 cd04689 467571 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 145 matched cddid_all.tbl CDD cd04690 cd04690 467572 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 123 matched cddid_all.tbl CDD cd04691 cd04691 467573 NUDIX_ADPRase ADP-ribose pyrophosphatase and similar proteins. ADP-ribose pyrophosphatase (ADPRase; EC 3.6.1.13) catalyzes the hydrolysis of ADP-ribose to AMP and ribose-5-P. Like other members of the NUDIX hydrolase superfamily of enzymes, it is thought to require a divalent cation, such as Mg2+, for its activity. It also contains a 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the NUDIX motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. In humans, there are four distinct ADPRase activities, three putative cytosolic (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). ADPRase-m is also known as NUDT9. It can be distinugished from the cytosolic ADPRase by a N-terminal target sequence unique to mitochondrial ADPRase. NUDT9 functions as a monomer. 122 matched cddid_all.tbl CDD cd04692 cd04692 467574 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 142 matched cddid_all.tbl CDD cd04693 cd04693 467575 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 157 matched cddid_all.tbl CDD cd04694 cd04694 467576 NUDIX_Nudt17 "nucleoside diphosphate-linked moiety X)) motif 17. Nucleoside diphosphate-linked moiety X)) motif 17 (EC 3.6.1.-) encoded by the NUDT17 gene on chromosome 1q21.1 and encodes an enzyme thought to hydrolyse some nucleoside diphosphate derivatives. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & ""house-cleaning"" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required." 135 matched cddid_all.tbl CDD cd04696 cd04696 467577 NUDIX_NudI "NUDIX hydrolase subfamily. Nucleoside triphosphatase NudI catalyzes the hydrolysis of nucleoside triphosphates, with a preference for pyrimidine deoxynucleoside triphosphates (dUTP, dTTP and dCTP). It is a members of the NUDIX hydrolase superfamily which catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & ""house-cleaning"" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required." 134 matched cddid_all.tbl CDD cd04697 cd04697 467578 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 157 matched cddid_all.tbl CDD cd04699 cd04699 467579 NUDIX_MutT_Nudt1 MutT homolog-1 and similar proteins. MutT homolog-1 (MTH1), also known as NUDIX (nucleoside diphosphate-linked moiety X)) motif 1/Nudt1, is a member of the NUDIX hydrolase superfamily. MTH1, the mammalian counterpart of MutT, hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to monophosphates, thereby preventing the incorporation of such oxygen radicals during replication. This is an important step in the repair mechanism in genomic and mitochondrial DNA. Like other members of the NUDIX family, it requires a divalent cation, such as Mg2+ or Mn2+, for activity, and contain the NUDIX motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. MTH1 is predominantly localized in the cytoplasm and mitochondria. Structurally, this enzyme adopts a similar fold to MutT despite low sequence similarity outside the conserved NUDIX motif. The most distinctive structural difference between MutT and MTH1 is the presence of a beta-hairpin, which is absent in MutT. This results in a much deeper and narrower substrate binding pocket. Mechanistically, MTH1 contains dual specificity for nucleotides that contain 2-OH-adenine bases and those that contain 8-oxo-guanine bases. 118 matched cddid_all.tbl CDD cd04700 cd04700 467580 NUDIX_DR1025_like "DR1025 and similar proteins. DR1025 from Deinococcus radiodurans, a member of the NUDIX hydrolase superfamily, show nucleoside triphosphatase and dinucleoside polyphosphate pyrophosphatase activities. Like other enzymes belonging to this superfamily, it requires a divalent cation, in this case Mg2+, for its activity. It also contains a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. In general, substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & ""house-cleaning"" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required." 147 matched cddid_all.tbl CDD cd04701 cd04701 271337 Asparaginase_2 Bacterial/fungal L-Asparaginase type 2. L-Asparaginase hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzyme undergoes an autoproteolytic cleavage into alpha and beta subunits to expose a threonine residue which becomes the N-terminal residue of the beta subunit. The threonine residue plays a central role in hydrolase activity. Some asparaginases can also hydrolyze L-glutamine and are termed glutaminase-asparaginase. This is a member of the Ntn-hydrolase superfamily, and this subfamily covers mostly bacterial and fungal enzymes. 264 matched cddid_all.tbl CDD cd04702 cd04702 271338 ASRGL1_like Metazoan L-Asparaginase type 2. ASRGL1 and similar proteins constitute a subfamily of the L-Asparaginase type 2-like enzymes. The wider family includes Glycosylasparaginase, Taspase 1, and L-Asparaginase type 2 enzymes. The proenzymes undergo autoproteolytic cleavage before a threonine to generate alpha and beta subunits. The threonine becomes the N-terminal residue of the beta subunit and is the catalytic residue. ASRGL1, or asparaginase-like 1, has been cloned from mammalian testis cDNA libraries. It has been identified as a sperm antigen that may induce the production of autoantibodies following obstruction of the male reproductive tract, e.g. vasectomy. 289 matched cddid_all.tbl CDD cd04703 cd04703 271339 Asparaginase_2_like_1 Uncharacterized subfamily of the L-Asparaginase type 2-like enzymes, an Ntn-hydrolase family. The wider family of Asparaginase 2-like enzymes includes Glycosylasparaginase, Taspase 1, and L-Asparaginase type 2. Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked glycoprotein. Taspase1 catalyzes the cleavage of the Mix Lineage Leukemia (MLL) nuclear protein and transcription factor TFIIA. L-Asparaginase type 2 hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzymes of this family undergo autoproteolytic cleavage before a threonine to generate alpha and beta subunits. The threonine becomes the N-terminal residue of the beta subunit and is the catalytic residue. 243 matched cddid_all.tbl CDD cd04704 cd04704 153093 PLA2_bee_venom_like PLA2_bee_venom_like: A sub-family of Phospholipase A2, similar to bee venom PLA2. PLA2 is a super-family of secretory and cytosolic enzymes; the latter are either Ca dependent or Ca independent. Enzymatically active PLA2 cleaves the sn-2 position of the glycerol backbone of phospholipids; secreted PLA2s have also been found to specifically bind to a variety of soluble and membrane proteins in mammals, including receptors. As a toxin, PLA2 is a potent presynaptic neurotoxin which blocks nerve terminals by binding to the nerve membrane and hydrolyzing stable membrane lipids. The products of the hydrolysis cannot form bilayers leading to a change in membrane conformation and ultimately to a block in the release of neurotransmitters. PLA2 may form dimers or oligomers. Bee venom PLA2 has fewer conserved disulfide bridges than most canonical PLA2s. 97 matched cddid_all.tbl CDD cd04705 cd04705 153094 PLA2_group_III_like PLA2_group_III_like: A sub-family of Phospholipase A2, similar to human group III PLA2. PLA2 is a super-family of secretory and cytosolic enzymes; the latter are either Ca dependent or Ca independent. Enzymatically active PLA2 cleaves the sn-2 position of the glycerol backbone of phospholipids; secreted PLA2s have also been found to specifically bind to a variety of soluble and membrane proteins in mammals, including receptors. As a toxin, PLA2 is a potent presynaptic neurotoxin which blocks nerve terminals by binding to the nerve membrane and hydrolyzing stable membrane lipids. The products of the hydrolysis cannot form bilayers leading to a change in membrane conformation and ultimately to a block in the release of neurotransmitters. PLA2 may form dimers or oligomers. 100 matched cddid_all.tbl CDD cd04706 cd04706 153095 PLA2_plant PLA2_plant: Plant-specific sub-family of Phospholipase A2, a super-family of secretory and cytosolic enzymes; the latter are either Ca dependent or Ca independent. Enzymatically active PLA2 cleaves the sn-2 position of the glycerol backbone of phospholipids; secreted PLA2s have also been found to specifically bind to a variety of soluble and membrane proteins in mammals, including receptors. As a toxin, PLA2 is a potent presynaptic neurotoxin which blocks nerve terminals by binding to the nerve membrane and hydrolyzing stable membrane lipids. The products of the hydrolysis cannot form bilayers leading to a change in membrane conformation and ultimately to a block in the release of neurotransmitters. PLA2 may form dimers or oligomers. This sub-family does not appear to have a conserved active site and metal-binding loop. 117 matched cddid_all.tbl CDD cd04707 cd04707 153096 otoconin_90 otoconin_90: Phospholipase A2-like domains present in otoconin-90 and otoconin-95, mammal proteins that are principal matrix proteins of calcitic otoconia. Interactions involving otoconin-90 may trigger or constitute key events in otoconia formation. The PLA2-like domains in otoconins may have lost their metal-binding sites. 117 matched cddid_all.tbl CDD cd04708 cd04708 240059 BAH_plantDCM_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. 202 matched cddid_all.tbl CDD cd04709 cd04709 240060 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. 164 matched cddid_all.tbl CDD cd04710 cd04710 240061 BAH_fungalPHD BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. 135 matched cddid_all.tbl CDD cd04711 cd04711 240062 BAH_Dnmt1_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. 137 matched cddid_all.tbl CDD cd04712 cd04712 240063 BAH_DCM_I BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. 130 matched cddid_all.tbl CDD cd04713 cd04713 240064 BAH_plant_3 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. 146 matched cddid_all.tbl CDD cd04714 cd04714 240065 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. 121 matched cddid_all.tbl CDD cd04715 cd04715 240066 BAH_Orc1p_like BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins. Orc1 is part of the Yeast Sir1-origin recognition complex, the Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. 159 matched cddid_all.tbl CDD cd04716 cd04716 240067 BAH_plantDCM_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. 122 matched cddid_all.tbl CDD cd04717 cd04717 240068 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. 121 matched cddid_all.tbl CDD cd04718 cd04718 240069 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. 148 matched cddid_all.tbl CDD cd04719 cd04719 240070 BAH_Orc1p_animal BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces cerevisiae Orc1p. Orc1 is part of the Yeast Sir1-origin recognition complex. The Orc1p BAH doman functions in epigenetic silencing. In vertebrates, a similar ORC protein complex exists, which has been shown essential for DNA replication in Xenopus laevis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. 128 matched cddid_all.tbl CDD cd04720 cd04720 240071 BAH_Orc1p_Yeast BAH, or Bromo Adjacent Homology domain, as present in Orc1p, which again is part of the Saccharomyces cerevisiae Sir1-origin recognition complex, and as present in Sir3p. The Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. 179 matched cddid_all.tbl CDD cd04721 cd04721 240072 BAH_plant_1 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. 130 matched cddid_all.tbl CDD cd04722 cd04722 240073 TIM_phosphate_binding TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN. 200 matched cddid_all.tbl CDD cd04723 cd04723 240074 HisA_HisF Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase (HisA) and the cyclase subunit of imidazoleglycerol phosphate synthase (HisF). The ProFAR isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''-phospho-ribosyl)-4-imidazolecarboxamide). In bacteria and archaea, ProFAR isomerase is encoded by the HisA gene. The Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion involves two tightly coupled reactions in distinct active sites of IGPS. The two catalytic domains can be fused, like in fungi and plants, or peformed by a heterodimer (HisH-glutaminase and HisF-cyclase), like in bacteria. 233 matched cddid_all.tbl CDD cd04724 cd04724 240075 Tryptophan_synthase_alpha Ttryptophan synthase (TRPS) alpha subunit (TSA). TPRS is a bifunctional tetrameric enzyme (2 alpha and 2 beta subunits) that catalyzes the last two steps of L-tryptophan biosynthesis. Alpha and beta subunit catalyze two distinct reactions which are both strongly stimulated by the formation of the complex. The alpha subunit catalyzes the cleavage of indole 3-glycerol phosphate (IGP) to indole and d-glyceraldehyde 3-phosphate (G3P). Indole is then channeled to the active site of the beta subunit, a PLP-dependent enzyme that catalyzes a replacement reaction to convert L-serine into L-tryptophan. 242 matched cddid_all.tbl CDD cd04725 cd04725 240076 OMP_decarboxylase_like Orotidine 5'-phosphate decarboxylase (ODCase) is a dimeric enzyme that decarboxylates orotidine 5'-monophosphate (OMP) to form uridine 5'-phosphate (UMP), an essential step in the pyrimidine biosynthetic pathway. In mammals, UMP synthase contains two domains: the orotate phosphoribosyltransferase (OPRTase) domain that catalyzes the transfer of phosphoribosyl 5'-pyrophosphate (PRPP) to orotate to form OMP, and the orotidine-5'-phosphate decarboxylase (ODCase) domain that decarboxylates OMP to form UMP. 216 matched cddid_all.tbl CDD cd04726 cd04726 240077 KGPDC_HPS 3-Keto-L-gulonate 6-phosphate decarboxylase (KGPDC) and D-arabino-3-hexulose-6-phosphate synthase (HPS). KGPDC catalyzes the formation of L-xylulose 5-phosphate and carbon dioxide from 3-keto-L-gulonate 6-phosphate as part of the anaerobic pathway for L-ascorbate utilization in some eubacteria. HPS catalyzes the formation of D-arabino-3-hexulose-6-phosphate from D-ribulose 5-phosphate and formaldehyde in microorganisms that can use formaldehyde as a carbon source. Both catalyze reactions that involve the Mg2+-assisted formation and stabilization of 1,2-enediolate reaction intermediates. 202 matched cddid_all.tbl CDD cd04727 cd04727 240078 pdxS PdxS is a subunit of the pyridoxal 5'-phosphate (PLP) synthase, an important enzyme in deoxyxylulose 5-phosphate (DXP)-independent pathway for de novo biosynthesis of PLP, present in some eubacteria, in archaea, fungi, plants, plasmodia, and some metazoa. Together with PdxT, PdxS forms the PLP synthase, a heteromeric glutamine amidotransferase (GATase), whereby PdxT produces ammonia from glutamine and PdxS combines ammonia with five- and three-carbon phosphosugars to form PLP. PLP is the biologically active form of vitamin B6, an essential cofactor in many biochemical processes. PdxS subunits form two hexameric rings. 283 matched cddid_all.tbl CDD cd04728 cd04728 240079 ThiG Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes the formation of thiazole from 1-deoxy-D-xylulose 5-phosphate (DXP) and dehydroglycine, with the help of the sulfur carrier protein ThiS that carries the sulfur needed for thiazole assembly on its carboxy terminus (ThiS-COSH). 248 matched cddid_all.tbl CDD cd04729 cd04729 240080 NanE N-acetylmannosamine-6-phosphate epimerase (NanE) converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate. This reaction is part of the pathway that allows the usage of sialic acid as a carbohydrate source. Sialic acids are a family of related sugars that are found as a component of glycoproteins, gangliosides, and other sialoglycoconjugates. 219 matched cddid_all.tbl CDD cd04730 cd04730 240081 NPD_like 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase family that reduce a range of alternative electron acceptors. Most use FAD/FMN as a cofactor and NAD(P)H as electron donor. Some contain 4Fe-4S cluster to transfer electron from FAD to FMN. 236 matched cddid_all.tbl CDD cd04731 cd04731 240082 HisF The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion involves two tightly coupled reactions in distinct active sites of IGPS. The two catalytic domains can be fused, like in fungi and plants, or peformed by a heterodimer (HisH-glutaminase and HisF-cyclase), like in bacteria. 243 matched cddid_all.tbl CDD cd04732 cd04732 240083 HisA HisA. Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''-phospho-ribosyl)-4-imidazolecarboxamide). In bacteria and archaea, ProFAR isomerase is encoded by the HisA gene. 234 matched cddid_all.tbl CDD cd04733 cd04733 240084 OYE_like_2_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 2. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase. 338 matched cddid_all.tbl CDD cd04734 cd04734 240085 OYE_like_3_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 3. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase. One member of this subgroup, the Sinorhizobium meliloti stachydrine utilization protein stcD, has been idenified as a putative N-methylproline demethylase. 343 matched cddid_all.tbl CDD cd04735 cd04735 240086 OYE_like_4_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 4. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase. 353 matched cddid_all.tbl CDD cd04736 cd04736 240087 MDH_FMN Mandelate dehydrogenase (MDH)-like FMN-binding domain. MDH is part of a widespread family of homologous FMN-dependent a-hydroxy acid oxidizing enzymes that oxidizes (S)-mandelate to phenylglyoxalate. MDH is an enzyme in the mandelate pathway that occurs in several strains of Pseudomonas which converts (R)-mandelate to benzoate. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate dehydrogenase (MDH), and long chain hydroxyacid oxidase (LCHAO). 361 matched cddid_all.tbl CDD cd04737 cd04737 240088 LOX_like_FMN L-Lactate oxidase (LOX) FMN-binding domain. LOX is a member of the family of FMN-containing alpha-hydroxyacid oxidases and catalyzes the oxidation of l-lactate using molecular oxygen to generate pyruvate and H2O2. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate dehydrogenase (MDH), and long chain hydroxyacid oxidase (LCHAO). 351 matched cddid_all.tbl CDD cd04738 cd04738 240089 DHOD_2_like Dihydroorotate dehydrogenase (DHOD) class 2. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences, their cellular location and their natural electron acceptor used to reoxidize the flavin group. Members of class 1 are cytosolic enzymes and multimers, while class 2 enzymes are membrane associated, monomeric and use respiratory quinones as their physiological electron acceptors. 327 matched cddid_all.tbl CDD cd04739 cd04739 240090 DHOD_like Dihydroorotate dehydrogenase (DHOD) like proteins. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. This subgroup has the conserved FMN binding site, but lacks some catalytic residues and may therefore be inactive. 325 matched cddid_all.tbl CDD cd04740 cd04740 240091 DHOD_1B_like Dihydroorotate dehydrogenase (DHOD) class 1B FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. 296 matched cddid_all.tbl CDD cd04741 cd04741 240092 DHOD_1A_like Dihydroorotate dehydrogenase (DHOD) class 1A FMN-binding domain. DHOD catalyzes the oxidation of (S)-dihydroorotate to orotate. This is the fourth step and the only redox reaction in the de novo biosynthesis of UMP, the precursor of all pyrimidine nucleotides. DHOD requires FMN as co-factor. DHOD divides into class 1 and class 2 based on their amino acid sequences and cellular location. Members of class 1 are cytosolic enzymes and multimers while class 2 enzymes are membrane associated and monomeric. The class 1 enzymes can be further divided into subtypes 1A and 1B which are homodimers and heterotetrameric proteins, respectively. 294 matched cddid_all.tbl CDD cd04742 cd04742 240093 NPD_FabD 2-Nitropropane dioxygenase (NPD)-like domain, associated with the (acyl-carrier-protein) S-malonyltransferase FabD. NPD is part of the nitroalkaneoxidizing enzyme family, that catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDPs are members of the NAD(P)H-dependent flavin oxidoreductase family that reduce a range of alternative electron acceptors. Most use FAD/FMN as a cofactor and NAD(P)H as electron donor. Some contain 4Fe-4S cluster to transfer electron from FAD to FMN. 418 matched cddid_all.tbl CDD cd04743 cd04743 240094 NPD_PKS 2-Nitropropane dioxygenase (NPD)-like domain, associated with polyketide synthases (PKS). NPD is part of the nitroalkaneoxidizing enzyme family, that catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDPs are members of the NAD(P)H-dependent flavin oxidoreductase family that reduce a range of alternative electron acceptors. Most use FAD/FMN as a cofactor and NAD(P)H as electron donor. Some contain 4Fe-4S cluster to transfer electron from FAD to FMN. 320 matched cddid_all.tbl CDD cd04745 cd04745 100058 LbH_paaY_like paaY-like: This group is composed by uncharacterized proteins with similarity to the protein product of the E. coli paaY gene, which is part of the paa gene cluster responsible for phenylacetic acid degradation. Proteins in this group are expected to adopt the left-handed parallel beta-helix (LbH) structure. They contain imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Similarity to gamma carbonic anhydrase and Ferripyochelin Binding Protein (FBP) may suggest metal binding capacity. 155 matched cddid_all.tbl CDD cd04747 cd04747 240095 OYE_like_5_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 5. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase. 361 matched cddid_all.tbl CDD cd04748 cd04748 240096 Commd COMM_Domain, a family of domains found at the C-terminus of HCarG, the copper metabolism gene MURR1 product, and related proteins. Presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been identified as a regulator of the human delta epithelial sodium channel. HCaRG, a nuclear protein that might be involved in cell proliferation, is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals. 87 matched cddid_all.tbl CDD cd04749 cd04749 240097 Commd1_MURR1 COMM_Domain containing protein 1, also called Murr1. Murr1/Commd1 is a protein involved in copper homeostasis, which has also been identified as a regulator of the human delta epithelial sodium channel. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. 174 matched cddid_all.tbl CDD cd04750 cd04750 240098 Commd2 COMM_Domain containing protein 2. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. 166 matched cddid_all.tbl CDD cd04751 cd04751 240099 Commd3 COMM_Domain containing protein 3. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. 95 matched cddid_all.tbl CDD cd04752 cd04752 240100 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. 174 matched cddid_all.tbl CDD cd04753 cd04753 240101 Commd5_HCaRG COMM_Domain containing protein 5, also called HCaRG (hypertension-related, calcium-regulated gene). HCaRG is a nuclear protein that might be involved in cell proliferation; it is negatively regulated by extracellular calcium concentration, and its basal mRNA levels are higher in hypertensive animals. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. 110 matched cddid_all.tbl CDD cd04754 cd04754 240102 Commd6 COMM_Domain containing protein 6. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. 86 matched cddid_all.tbl CDD cd04755 cd04755 240103 Commd7 COMM_Domain containing protein 7. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. 180 matched cddid_all.tbl CDD cd04756 cd04756 240104 Commd8 COMM_Domain containing protein 8. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. 176 matched cddid_all.tbl CDD cd04757 cd04757 240105 Commd9 COMM_Domain containing protein 9. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. 108 matched cddid_all.tbl CDD cd04758 cd04758 240106 Commd10 COMM_Domain containing protein 10. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB. 186 matched cddid_all.tbl CDD cd04759 cd04759 212498 Rib_hydrolase ADP-ribosyl cyclase, also known as cyclic ADP-ribose hydrolase or CD38. ADP-ribosyl cyclase (EC:3.2.2.5) synthesizes the second messenger cyclic-ADP ribose (cADPR), which in turn releases calcium from internal stores. Mammals possess two membrane proteins, CD38 and BST-1/CD157, which exhibit ADP-ribosyl cyclase activity, as well as intracellular soluble ADP-ribose cyclases. CD38 is involved in differentiation, adhesion, and cell proliferation, and has been implicated in diseases such as AIDS, diabetes, and B-cell chronic lymphocytic leukemia. The extramembrane domain of CD38 acts as a multifunctional enzyme, and can synthesize cADPR from NAD+, hydrolyze NAD+ and cADPR to ADPR, as well as catalyze the exchange of the nicotinamide group of NADP+ with nicotinic acid under acidic conditions, to yield NAADP+ (nicotinic acid-adenine dinucleotide phosphate), a metabolite involved in Ca2+ mobilization from acidic stores. 244 matched cddid_all.tbl CDD cd04760 cd04760 240107 BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions. 124 matched cddid_all.tbl CDD cd04761 cd04761 133389 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. 49 matched cddid_all.tbl CDD cd04762 cd04762 133390 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles. 49 matched cddid_all.tbl CDD cd04763 cd04763 133391 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins. 68 matched cddid_all.tbl CDD cd04764 cd04764 133392 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins. 67 matched cddid_all.tbl CDD cd04765 cd04765 133393 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. 99 matched cddid_all.tbl CDD cd04766 cd04766 133394 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. 91 matched cddid_all.tbl CDD cd04767 cd04767 133395 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. 120 matched cddid_all.tbl CDD cd04768 cd04768 133396 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. 96 matched cddid_all.tbl CDD cd04769 cd04769 133397 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. 116 matched cddid_all.tbl CDD cd04770 cd04770 133398 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. 123 matched cddid_all.tbl CDD cd04772 cd04772 133399 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins. 99 matched cddid_all.tbl CDD cd04773 cd04773 133400 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins. 108 matched cddid_all.tbl CDD cd04774 cd04774 133401 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. 96 matched cddid_all.tbl CDD cd04775 cd04775 133402 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. 102 matched cddid_all.tbl CDD cd04776 cd04776 133403 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. 118 matched cddid_all.tbl CDD cd04777 cd04777 133404 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. 107 matched cddid_all.tbl CDD cd04778 cd04778 133405 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. 219 matched cddid_all.tbl CDD cd04779 cd04779 133406 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. 134 matched cddid_all.tbl CDD cd04780 cd04780 133407 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. 95 matched cddid_all.tbl CDD cd04781 cd04781 133408 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. 120 matched cddid_all.tbl CDD cd04782 cd04782 133409 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. 97 matched cddid_all.tbl CDD cd04783 cd04783 133410 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. 126 matched cddid_all.tbl CDD cd04784 cd04784 133411 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. 127 matched cddid_all.tbl CDD cd04785 cd04785 133412 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. 126 matched cddid_all.tbl CDD cd04786 cd04786 133413 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. 131 matched cddid_all.tbl CDD cd04787 cd04787 133414 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the conserved, metal-binding cysteines seen in the MerR1 group. 133 matched cddid_all.tbl CDD cd04788 cd04788 133415 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. 96 matched cddid_all.tbl CDD cd04789 cd04789 133416 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. 102 matched cddid_all.tbl CDD cd04790 cd04790 133417 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates. 172 matched cddid_all.tbl CDD cd04791 cd04791 271199 LanC_SerThrkinase Lanthionine synthetase C-like domain associated with serine/threonine kinases. Some members of this subgroup lack the zinc binding site and the active site residues, and therefore are most likely inactive. The function of this domain is unknown. 327 matched cddid_all.tbl CDD cd04792 cd04792 271200 LanM-like Cyclases involved in the biosynthesis of class II lantibiotics, and similar proteins. LanM-like proteins. LanM is a bifunctional enzyme, involved in the synthesis of class II lantibiotics. It is responsible for both the dehydration and the cyclization of the precursor-peptide during lantibiotic synthesis. The C-terminal domain shows similarity to LanC, the cyclase component of the lan operon, but the N terminus seems to be unrelated to the dehydratase, LanB. 836 matched cddid_all.tbl CDD cd04793 cd04793 271201 LanC Cyclases involved in the biosynthesis of lantibiotics. LanC is the cyclase enzyme of the lanthionine synthetase. Lanthinoine is a lantibiotic, a unique class of peptide antibiotics. They are ribosomally synthesized as precursor peptides and then post-translationally modified to contain thioether cross-links called lanthionines (Lans) or methyllanthionines (MeLans) in addition to 2,3-didehydroalanine (Dha) and (Z)-2,3-didehydrobutyrine (Dhb). These unusual amino acids are introduced by the dehydration of serine and threonine residues, followed by thioether formation via addition of cysteine thiols, catalysed by LanB and LanC or LanM. LanC, the cyclase component, is a zinc metalloprotein, whose bound metal has been proposed to activate the thiol substrate for nucleophilic addition. Also contains SpaC (the cyclase involved in the biosynthesis of subtilin), NisC, and homologs. 377 matched cddid_all.tbl CDD cd04794 cd04794 271202 euk_LANCL Eukaryotic Lanthionine synthetase C-like protein. This family contains the lanthionine synthetase C-like proteins 1 and 2 which are related to the bacterial lanthionine synthetase components C (LanC). LANCL1 and LANCL2 (testes-specific adriamycin sensitivity protein) were thought to be peptide-modifying enzyme components in eukaryotic cells. Both proteins are produced in large quantities in the brain and testes and may have role in the immune surveillance of these organs. More recently, they have been associated with signal transduction processes and insulin sensitization. In particular, LANCL2 has been shown to bind abscisic acid (ABA), and this interaction may play a role in signaling pathways triggered by ABA, such as in human granulocytes and rat insulinoma cells. This eukaryotic LANCL family also includes Arabidopsis GCR2. 349 matched cddid_all.tbl CDD cd04795 cd04795 240112 SIS SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars. 87 matched cddid_all.tbl CDD cd04801 cd04801 341401 CBS_pair_peptidase_M50 Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains found in the metalloprotease peptidase M50. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in peptidase M50. Members of the M50 metallopeptidase family include mammalian sterol-regulatory element binding protein (SREBP) site 2 proteases and various hypothetical bacterial homologues. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 113 matched cddid_all.tbl CDD cd04813 cd04813 240117 PA_1 PA_1: Protease-associated (PA) domain subgroup 1. A subgroup of PA-domain containing proteins. Proteins in this subgroup contain a RING-finger (Really Interesting New Gene) domain C-terminal to this PA domain. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins in this group contain a C-terminal RING-finger domain. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases: such as hSPPL2a and 2b, ii) various E3 ubiquitin ligases similar to human GRAIL (gene related to anergy in lymphocytes) protein, iii) various proteins containing a RING finger motif such as Arabidopsis ReMembR-H2 protein, iv) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), v) various plant vacuolar sorting receptors such as Pisum sativum BP-80, vi) prostate-specific membrane antigen (PSMA), vii) yeast aminopeptidase Y viii) Vibrio metschnikovii VapT, a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease, ix) various subtilisin-like proteases such as Cucumisin from the juice of melon fruits, and x) human TfR (transferrin receptor) 1 and human TfR2. The proteins listed above belong to other subgroups; relatively little is known about proteins in this subgroup. 117 matched cddid_all.tbl CDD cd04814 cd04814 240118 PA_M28_1 PA_M28_1: Protease-associated (PA) domain, peptidase family M28, subfamily-1. A subfamily of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subfamilies, relatively little is known about proteins in this subfamily. 142 matched cddid_all.tbl CDD cd04815 cd04815 240119 PA_M28_2 PA_M28_2: Protease-associated (PA) domain, peptidase family M28, subfamily-2. A subfamily of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subfamilies; relatively little is known about proteins in this subfamily. 134 matched cddid_all.tbl CDD cd04816 cd04816 240120 PA_SaNapH_like PA_SaNapH_like: Protease-associated domain containing proteins like Streptomyces anulatus N-acetylpuromycin N-acetylhydrolase (SaNapH).This group contains various PA domain-containing proteins similar SaNapH. Proteins in this group belong to the peptidase M28 family. NapH is a terminal enzyme in the puromycin biosynthetic pathway; NapH hydrolyzes N-acetylpuromycin to the active antibiotic. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. 122 matched cddid_all.tbl CDD cd04817 cd04817 240121 PA_VapT_like PA_VapT_like: Protease-associated domain containing proteins like VapT from Vibrio metschnikovii strain RH530. This group contains various PA domain-containing proteins similar to V. metschnikovii VapT, including the serine alkaline protease SapSh from the psychotroph Shewanella strain Ac10 and the Apa1 protease from the psychrotroph Pseudoalteromonas Sp. As-11. VapT is a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease showing high activity over a broad pH range and temperature. SapSh has a high level of protease activity at low temperatures. Apa1 is also cold-adapted. The significance of the PA domain to these proteins has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. 139 matched cddid_all.tbl CDD cd04818 cd04818 240122 PA_subtilisin_1 PA_subtilisin_1: Protease-associated domain containing subtilisin-like proteases, subgroup 1. A subgroup of PA domain-containing subtilisin-like proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following subtilisin-like proteases: i) melon cucumisin, ii) Arabidopsis thaliana Ara12, iii) Alnus glutinosa ag12, iv) members of the tomato P69 family, and v) tomato LeSBT2. However, these proteins belong to other subtilisin-like subgroups. Relatively little is known about proteins in this subgroup. 118 matched cddid_all.tbl CDD cd04819 cd04819 240123 PA_2 PA_2: Protease-associated (PA) domain subgroup 2. A subgroup of PA-domain containing proteins. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins in this group contain a C-terminal RING-finger domain. Proteins into which the PA domain is inserted include the following: i) various signal peptide peptidases: such as hSPPL2a and 2b, ii) various E3 ubiquitin ligases similar to human GRAIL (gene related to anergy in lymphocytes) protein, iii) various proteins containing a RING finger motif such as Arabidopsis ReMembR-H2 protein, iv) EDEM3 (ER-degradation-enhancing mannosidase-like 3 protein), v) various plant vacuolar sorting receptors such as Pisum sativum BP-80, vi) prostate-specific membrane antigen (PSMA), vii) yeast aminopeptidase Y viii) Vibrio metschnikovii VapT, a sodium dodecyl sulfate (SDS) resistant extracellular alkaline serine protease, ix) various subtilisin-like proteases such as Cucumisin from the juice of melon fruits, and x) human TfR (transferrin receptor) 1 and human TfR2. The proteins listed above belong to other subgroups; relatively little is known about proteins in this subgroup. 127 matched cddid_all.tbl CDD cd04820 cd04820 240124 PA_M28_1_1 PA_M28_1_1: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 1. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subgroups; relatively little is known about proteins in this subgroup. 137 matched cddid_all.tbl CDD cd04821 cd04821 240125 PA_M28_1_2 PA_M28_1_2: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 2. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subgroups; relatively little is known about proteins in this subgroup. 157 matched cddid_all.tbl CDD cd04822 cd04822 240126 PA_M28_1_3 PA_M28_1_3: Protease-associated (PA) domain, peptidase family M28, subfamily-1, subgroup 3. A subgroup of PA-domain containing proteins belonging to the peptidase family M28. Family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. The PA domain is an insert domain in a diverse fraction of proteases. The significance of the PA domain to many of the proteins in which it is inserted is undetermined. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate. Proteins into which the PA domain is inserted include the following members of the peptidase family M28: i) prostate-specific membrane antigen (PSMA), ii) yeast aminopeptidase Y, and ii) human TfR (transferrin receptor)1 and human TfR2. The proteins listed above belong to other subgroups; relatively little is known about proteins in this subgroup. 151 matched cddid_all.tbl CDD cd04823 cd04823 240127 ALAD_PBGS_aspartate_rich Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between the substrate and the enzyme. PBGSs are metalloenzymes, some of which have a second, allosteric metal binding site, beside the metal ion binding site in their active site. Although PBGS is a family of homologous enzymes, its metal ion utilization at catalytic site varies between zinc and magnesium and/or potassium. PBGS can be classified into two groups based on differences in their active site metal binding site. All of PBGS_aspartate_rich contain an aspartate rich metal binding site with the general sequence DXALDX(Y/F)X3G(H/Q)DG. They also contain an allosteric magnesium binding sequence RX~164DX~65EXXXD and are activated by magnesium and/or potassium, but not by zinc. PBGSs_aspartate_rich are found in some bacterial species and photosynthetic organisms such as vascular plants, mosses and algae, but not in archaea. 320 matched cddid_all.tbl CDD cd04824 cd04824 240128 eu_ALAD_PBGS_cysteine_rich Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between the substrate and the enzyme. PBGSs are metalloenzymes, some of which have a second, allosteric metal binding site, beside the metal ion binding site in their active site. Although PBGS is a family of homologous enzymes, its metal ion utilization at catalytic site varies between zinc and magnesium and/or potassium. PBGS can be classified into two groups based on differences in their active site metal binding site. The eukaryotic PBGSs represented by this model, which contain a cysteine-rich zinc binding motif (DXCXCX(Y/F)X3G(H/Q)CG), require zinc for their activity, they do not contain an additional allosteric metal binding site and do not bind magnesium. 320 matched cddid_all.tbl CDD cd04842 cd04842 173791 Peptidases_S8_Kp43_protease Peptidase S8 family domain in Kp43 proteases. Kp43 proteases are members of the peptidase S8 or Subtilase clan of proteases. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure (an example of convergent evolution). Kp43 is topologically similar to kexin and furin both of which are proprotein convertases, but differ in amino acids sequence and the position of its C-terminal barrel. Kp43 has 3 Ca2+ binding sites that differ from the corresponding sites in the other known subtilisin-like proteases. KP-43 protease is known to be an oxidation-resistant protease when compared with the other subtilisin-like proteases 293 matched cddid_all.tbl CDD cd04843 cd04843 173792 Peptidases_S8_11 Peptidase S8 family domain, uncharacterized subfamily 11. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 277 matched cddid_all.tbl CDD cd04847 cd04847 173793 Peptidases_S8_Subtilisin_like_2 Peptidase S8 family domain in Subtilisin-like proteins. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 291 matched cddid_all.tbl CDD cd04848 cd04848 173794 Peptidases_S8_Autotransporter_serine_protease_like Peptidase S8 family domain in Autotransporter serine proteases. Autotransporter serine proteases belong to Peptidase S8 or Subtilase family. Subtilases, or subtilisin-like serine proteases, have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure (an example of convergent evolution). Autotransporters are a superfamily of outer membrane/secreted proteins of gram-negative bacteria. The presence of these subtilisin-like domains in these autotransporters are may enable them to be auto-catalytic and may also serve to allow them to act as a maturation protease cleaving other outer membrane proteins at the cell surface. 267 matched cddid_all.tbl CDD cd04852 cd04852 173795 Peptidases_S8_3 Peptidase S8 family domain, uncharacterized subfamily 3. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 307 matched cddid_all.tbl CDD cd04857 cd04857 173796 Peptidases_S8_Tripeptidyl_Aminopeptidase_II Peptidase S8 family domain in Tripeptidyl aminopeptidases_II. Tripeptidyl aminopeptidases II are member of the peptidase S8 or Subtilase family. Subtilases, or subtilisin-like serine proteases, have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure (an example of convergent evolution). Tripeptidyl aminopeptidase II removes tripeptides from the free N terminus of oligopeptides as well as having endoproteolytic activity. Some tripeptidyl aminopeptidases have been shown to cleave tripeptides and small peptides, e.g. angiotensin II and glucagon, while others are believed to be involved in MHC I processing. 412 matched cddid_all.tbl CDD cd04859 cd04859 240129 Prim_Pol Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases from archaeal plasmids, including ORF904 protein of the crenarchaeal plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol). These primpol domains belong to the archaeal/eukaryal primase (AEP) superfamily. This group includes archaeal plasmids and bacteriophage AEPs. The ORF904 protein is a multifunctional protein having ATPase, primase and DNA polymerase activity, and may play a role in the replication of the archaeal plasmid. The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. For pRN1 primpol, the primase activity prefers dNTPs to rNTPs; incorporation of dNTPs requires rNTP as cofactor. The pRN1 primpol contains an unusual zinc-binding stem, which is not conserved in other members of this group. 152 matched cddid_all.tbl CDD cd04860 cd04860 240130 AE_Prim_S AE_Prim_S: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In addition to its catalytic role in replication, DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. The function of the larger primase subunit is unclear. Included in this group are Pfu41 and Pfu46, these two proteins comprise the primase complex of the archaea Pyrococcus furiosus; Pfu41 and Pfu46 have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the primase activity of Pfu41. 232 matched cddid_all.tbl CDD cd04861 cd04861 240131 LigD_Pol_like LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. Mycobacterium tuberculosis (Mt)LigD, also found in this group, is monomeric and contains the same modules but these are arranged differently: an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nucleotide additions to blunt-end duplex DNA; it preferentially adds single ribonucleotides at blunt DNA ends. PaeLigD Pol adds a correctly paired rNTP to the DNA primer termini more rapidly than it does a correctly paired dNTP; it has higher infidelity as an RNA polymerase than it does as a DNA polymerase, which is in keeping with the mutagenic property of NHEJ-mediated DNA DSB repair. The MtLigD Pol domain similarly is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates containing a 5'-phosphate group at the gap. 227 matched cddid_all.tbl CDD cd04862 cd04862 240132 PaeLigD_Pol_like PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nucleotide additions to blunt-end duplex DNA; it preferentially adds single ribonucleotides at blunt DNA ends. PaeLigD Pol adds a correctly paired rNTP to the DNA primer termini more rapidly than it does a correctly paired dNTP; it has higher infidelity as an RNA polymerase than it does as a DNA polymerase, which is in keeping with the mutagenic property of NHEJ-mediated DNA DSB repair. 227 matched cddid_all.tbl CDD cd04863 cd04863 240133 MtLigD_Pol_like MtLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Mycobacterium tuberculosis (Mt)LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. MtLigD is monomeric and contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates containing a 5'-phosphate group at the gap. 231 matched cddid_all.tbl CDD cd04864 cd04864 240134 LigD_Pol_like_1 LigD_Pol_like_1: Polymerase (Pol) domain of mostly bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 1. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization. 228 matched cddid_all.tbl CDD cd04865 cd04865 240135 LigD_Pol_like_2 LigD_Pol_like_2: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization. 228 matched cddid_all.tbl CDD cd04866 cd04866 240136 LigD_Pol_like_3 LigD_Pol_like_3: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 3. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated repair DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization. 223 matched cddid_all.tbl CDD cd04867 cd04867 340516 TGS_YchF_OLA1 TGS (ThrRS, GTPase and SpoT) domain found in the YchF/OLA1 family proteins. The YchF/Ola1 family includes bacterial ribosome-binding ATPase YchF as well as its human homolog Obg-like ATPase 1 (OLA1), both of which belong to the Obg family of GTPases, and are novel ATPases that bind and hydrolyze ATP more efficiently than GTP. They have been associated with various cellular processes and pathologies, including DNA repair, tumorigenesis, and apoptosis, in addition to the regulation of the oxidative stress response. OLA1 is also termed DNA damage-regulated overexpressed in cancer 45 (DOC45), or GTP-binding protein 9 (GTPBP9). It is over-expressed in several human malignancies, including cancers of the colon, rectum, ovary, lung, stomach, and uterus. It is linked to the cellular stress response and tumorigenesis, and may also serve as a valuable tumor marker. Members in this family contain a central Obg-type G (guanine nucleotide-binding) domain, flanked by a coiled-coil domain and this TGS (ThrRS, GTPase, SpoT) domain of unknown function. 85 matched cddid_all.tbl CDD cd04868 cd04868 153140 ACT_AK-like ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). This CD includes each of two ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). Typically, AK consists of two ACT domains in a tandem repeat, but the second ACT domain is inserted within the first, resulting in, what is normally the terminal beta strand of ACT2, formed from a region N-terminal of ACT1. AK catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Aspartokinase is the first enzyme in the pathway of the biosynthesis of the aspartate family of amino acids (lysine, threonine, methionine, and isoleucine) and the bacterial cell wall component, meso-diaminopimelate. One mechanism for the regulation of this pathway is by the production of several isoenzymes of aspartokinase with different repressors and allosteric inhibitors. Pairs of ACT domains are proposed to specifically bind amino acids leading to allosteric regulation of the enzyme. In Escherichia coli (EC), three different aspartokinase isoenzymes are regulated specifically by lysine, methionine, and threonine. AK-HSDHI (ThrA) and AK-HSDHII (MetL) are bifunctional enzymes that consist of an N-terminal AK and a C-terminal homoserine dehydrogenase (HSDH). ThrA and MetL are involved in threonine and methionine biosynthesis, respectively. The third isoenzyme, AKIII (LysC), is monofunctional and is involved in lysine synthesis. The three Bacillus subtilis (BS) isoenzymes, AKI (DapG), AKII (LysC), and AKIII (YclM), are feedback inhibited by meso-diaminopimelate, lysine, and lysine plus threonine, respectively. The E. coli lysine-sensitive AK is described as a homodimer, whereas, the B. subtilis lysine-sensitive AK is described as is a heterodimeric complex of alpha- and beta- subunits that are formed from two in-frame overlapping genes. A single AK enzyme type has been described in Pseudomonas, Amycolatopsis, and Corynebacterium, and apparently, unique to cyanobacteria, are aspartokinases with two tandem pairs of ACT domains, C-terminal to the catalytic domain. The fungal aspartate pathway is regulated at the AK step, with L-Thr being an allosteric inhibitor of the Saccharomyces cerevisiae AK (Hom3). At least two distinct AK isoenzymes can occur in higher plants, a monofunctional lysine-sensitive isoenzyme, which is involved in the overall regulation of the pathway and can be synergistically inhibited by S-adenosylmethionine. The other isoenzyme is a bifunctional, threonine-sensitive AK-HSDH protein. Also included in this AK family CD are the ACT domains of the Methylomicrobium alcaliphilum AK; the first enzyme of the ectoine biosynthetic pathway found in this bacterium and several other halophilic/halotolerant bacteria. Members of this CD belong to the superfamily of ACT regulatory domains. 60 matched cddid_all.tbl CDD cd04869 cd04869 153141 ACT_GcvR_2 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the second of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR interacts directly with GcvA rather than binding to DNA to cause repression. Members of this CD belong to the superfamily of ACT regulatory domains. 81 matched cddid_all.tbl CDD cd04870 cd04870 153142 ACT_PSP_1 CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). The ACT_PSP_1 CD includes the first of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Members of this CD belong to the superfamily of ACT regulatory domains. 75 matched cddid_all.tbl CDD cd04871 cd04871 153143 ACT_PSP_2 ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). The ACT_PSP_2 CD includes the second of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Members of this CD belong to the superfamily of ACT regulatory domains 84 matched cddid_all.tbl CDD cd04872 cd04872 153144 ACT_1ZPV ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein. This CD, ACT_1ZPV, includes those single ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein (pdb structure 1ZPV). Members of this CD belong to the superfamily of ACT regulatory domains. 88 matched cddid_all.tbl CDD cd04873 cd04873 153145 ACT_UUR-ACR-like ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD. This ACT domain family, ACT_UUR_ACR-like, includes the two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the four ACT domains of a novel protein composed almost entirely of ACT domain repeats (the ACR protein) and like proteins. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. This CD also includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein and related domains, as well as, the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted tyrosine kinase. Members of this CD belong to the superfamily of ACT regulatory domains. 70 matched cddid_all.tbl CDD cd04874 cd04874 153146 ACT_Af1403 N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, and related domains. This CD includes the N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, from Archaeoglobus fulgidus and other related archeal ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains. 72 matched cddid_all.tbl CDD cd04875 cd04875 153147 ACT_F4HF-DF N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase). This CD includes the N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase) which catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate. Formyl-FH4 hydrolase generates the formate that is used by purT-encoded 5'-phosphoribosylglycinamide transformylase for step three of de novo purine nucleotide synthesis. Formyl-FH4 hydrolase, a hexamer which is activated by methionine and inhibited by glycine, is proposed to regulate the balance FH4 and C1-FH4 in response to changing growth conditions. Members of this CD belong to the superfamily of ACT regulatory domains. 74 matched cddid_all.tbl CDD cd04876 cd04876 153148 ACT_RelA-SpoT ACT domain found C-terminal of the RelA/SpoT domains. ACT_RelA-SpoT: the ACT domain found C-terminal of the RelA/SpoT domains. Enzymes of the Rel/Spo family enable bacteria to survive prolonged periods of nutrient limitation by controlling guanosine-3'-diphosphate-5'-(tri)diphosphate ((p)ppGpp) production and subsequent rRNA repression (stringent response). Both the synthesis of (p)ppGpp from ATP and GDP(GTP), and its hydrolysis to GDP(GTP) and pyrophosphate, are catalyzed by Rel/Spo proteins. In Escherichia coli and its close relatives, the metabolism of (p)ppGpp is governed by two homologous proteins, RelA and SpoT. The RelA protein catalyzes (p)ppGpp synthesis in a reaction requiring its binding to ribosomes bearing codon-specified uncharged tRNA. The major role of the SpoT protein is the breakdown of (p)ppGpp by a manganese-dependent (p)ppGpp pyrophosphohydrolase activity. Although the stringent response appears to be tightly regulated by these two enzymes in E. coli, a bifunctional Rel/Spo protein has been discovered in most gram-positive organisms studied so far. These bifunctional Rel/Spo homologs (rsh) appear to modulate (p)ppGpp levels through two distinct active sites that are controlled by a reciprocal regulatory mechanism ensuring inverse coupling of opposing activities. In studies with the Streptococcus equisimilis Rel/Spo homolog, the C-terminal domain appears to be involved in this reciprocal regulation of the two opposing catalytic activities present in the N-terminal domain, ensuring that both synthesis and degradation activities are not coinduced. Members of this CD belong to the superfamily of ACT regulatory domains. 71 matched cddid_all.tbl CDD cd04877 cd04877 153149 ACT_TyrR N-terminal ACT domain of the TyrR protein. ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence of cofactors or in the presence of phenylalanine alone, the TyrR protein exists as a dimer. However, in the presence of ATP and tyrosine the TyrR protein self-aggregates to form a hexamer. Members of this CD belong to the superfamily of ACT regulatory domains. 74 matched cddid_all.tbl CDD cd04878 cd04878 153150 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of this CD belong to the superfamily of ACT regulatory domains. 72 matched cddid_all.tbl CDD cd04879 cd04879 153151 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-exposed active site cleft. This CD also includes the C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillus, and Treponema species. LSD enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in E. coli, and other Enterobacteriales, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains. 71 matched cddid_all.tbl CDD cd04880 cd04880 153152 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mechanisms of regulation. One commonality is that all three eukaryotic enzymes appear to be regulated, in part, by the phosphorylation of serine residues N-terminal of the ACT domain. Also included in this CD are the C-terminal ACT domains of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme found in plants, fungi, bacteria, and archaea. The P-protein of Escherichia coli (CM-PDT) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe binding. L-Phe binds with positive cooperativity; with this binding, there is a shift in the protein to less active tetrameric and higher oligomeric forms from a more active dimeric form. Members of this CD belong to the superfamily of ACT regulatory domains. 75 matched cddid_all.tbl CDD cd04881 cd04881 153153 ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains. The ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) encoded by the hom gene of Bacillus subtilis and other related sequences. HSDH reduces aspartate semi-aldehyde to the amino acid homoserine, one that is required for the biosynthesis of Met, Thr, and Ile from Asp. Neither the enzyme nor the aspartate pathway is found in the animal kingdom. This mostly bacterial HSDH group has a C-terminal ACT domain and is believed to be involved in enzyme regulation. A C-terminal deletion in the Corynebacterium glutamicum HSDH abolished allosteric inhibition by L-threonine. Members of this CD belong to the superfamily of ACT regulatory domains. 79 matched cddid_all.tbl CDD cd04882 cd04882 153154 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains. 65 matched cddid_all.tbl CDD cd04883 cd04883 153155 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains. 72 matched cddid_all.tbl CDD cd04884 cd04884 153156 ACT_CBS C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria. This CD includes the C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria. This protein has two N-terminal tandem CBS domains and a single C-terminal ACT domain. The CBS domain is found in a wide range of proteins, often in tandem arrangements and together with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Members of this CD belong to the superfamily of ACT regulatory domains. 72 matched cddid_all.tbl CDD cd04885 cd04885 153157 ACT_ThrD-I Tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes each of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains. 68 matched cddid_all.tbl CDD cd04886 cd04886 153158 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains. 73 matched cddid_all.tbl CDD cd04887 cd04887 153159 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains. 74 matched cddid_all.tbl CDD cd04888 cd04888 153160 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains. 76 matched cddid_all.tbl CDD cd04889 cd04889 153161 ACT_PDH-BS-like C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate. Included in this CD is the C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Also included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains. 56 matched cddid_all.tbl CDD cd04890 cd04890 153162 ACT_AK-like_1 ACT domains found C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). This CD includes the first of two ACT domains found C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). AK catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and is the first enzyme in the pathway of the biosynthesis of the aspartate family of amino acids, lysine, threonine, methionine, and isoleucine. This CD, includes the first ACT domain of the Escherichia coli (EC) isoenzyme, AKIII (LysC) and the Arabidopsis isoenzyme, asparate kinase 1, both enzymes monofunctional and involved in lysine synthesis, as well as the the first ACT domain of Bacillus subtilis (BS) isoenzyme, AKIII (YclM), and of the Saccharomyces cerevisiae AK (Hom3). Also included are the first ACT domains of the Methylomicrobium alcaliphilum AK, the first enzyme of the ectoine biosynthetic pathway. Members of this CD belong to the superfamily of ACT regulatory domains. 62 matched cddid_all.tbl CDD cd04891 cd04891 153163 ACT_AK-LysC-DapG-like_1 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII and related proteins. This CD includes the N-terminal of the two ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, as well as, the first and third, of four, ACT domains present in cyanobacteria AK. Also included are the N-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase isoenzyme AKI found in Bacilli (Bacillus subtilis strain 168), Clostridia, and Actinobacteria bacterial species. Members of this CD belong to the superfamily of ACT regulatory domains. 61 matched cddid_all.tbl CDD cd04892 cd04892 153164 ACT_AK-like_2 ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). This CD includes the second of two ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). The exception in this group, is the inclusion of the first ACT domain of the bifunctional aspartokinase - homoserine dehydrogenase-like enzyme group (ACT_AKi-HSDH-ThrA-like_1) which includes the monofunctional, threonine-sensitive, aspartokinase found in Methanococcus jannaschii and other related archaeal species. AK catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. AK is the first enzyme in the pathway of the biosynthesis of the aspartate family of amino acids (lysine, threonine, methionine, and isoleucine) and the bacterial cell wall component, meso-diaminopimelate. One mechanism for the regulation of this pathway is by the production of several isoenzymes of AK with different repressors and allosteric inhibitors. Pairs of ACT domains are proposed to specifically bind amino acids leading to allosteric regulation of the enzyme. In Escherichia coli (EC), three different AK isoenzymes are regulated specifically by lysine, methionine, and threonine. AK-HSDHI (ThrA) and AK-HSDHII (MetL) are bifunctional enzymes that consist of an N-terminal AK and a C-terminal homoserine dehydrogenase (HSDH). ThrA and MetL are involved in threonine and methionine biosynthesis, respectively. The third isoenzyme, AKIII (LysC), is monofunctional and is involved in lysine synthesis. The three Bacillus subtilis (BS) isoenzymes, AKI (DapG), AKII (LysC), and AKIII (YclM), are feedback inhibited by meso-diaminopimelate, lysine, and lysine plus threonine, respectively. The E. coli lysine-sensitive AK is described as a homodimer, whereas, the B. subtilis lysine-sensitive AK is described as is a heterodimeric complex of alpha- and beta- subunits that are formed from two in-frame overlapping genes. A single AK enzyme type has been described in Pseudomonas, Amycolatopsis, and Corynebacterium, and apparently, unique to cyanobacteria, are AKs with two tandem pairs of ACT domains, C-terminal to the catalytic domain. The fungal aspartate pathway is regulated at the AK step, with L-Thr being an allosteric inhibitor of the Saccharomyces cerevisiae AK (Hom3). At least two distinct AK isoenzymes can occur in higher plants, a monofunctional lysine-sensitive isoenzyme, which is involved in the overall regulation of the pathway and can be synergistically inhibited by S-adenosylmethionine. The other isoenzyme is a bifunctional, threonine-sensitive AK-HSDH protein. Also included in this CD are the ACT domains of the Methylomicrobium alcaliphilum AK; the first enzyme of the ectoine biosynthetic pathway found in this bacterium and several other halophilic/halotolerant bacteria. Members of this CD belong to the superfamily of ACT regulatory domains. 65 matched cddid_all.tbl CDD cd04893 cd04893 153165 ACT_GcvR_1 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR interacts directly with GcvA rather than binding to DNA to cause repression. Members of this CD belong to the superfamily of ACT regulatory domains. 77 matched cddid_all.tbl CDD cd04894 cd04894 153166 ACT_ACR-like_1 "ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the ""ACR"" protein). This CD includes the N-terminal ACT domain of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the ""ACR"" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains." 69 matched cddid_all.tbl CDD cd04895 cd04895 153167 ACT_ACR_1 "ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the ""ACR"" protein). This CD includes the N-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the ""ACR"" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains." 72 matched cddid_all.tbl CDD cd04896 cd04896 153168 ACT_ACR-like_3 "ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the ""ACR"" protein). This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the ""ACR"" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains." 75 matched cddid_all.tbl CDD cd04897 cd04897 153169 ACT_ACR_3 "ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the ""ACR"" protein). This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the ""ACR"" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains." 75 matched cddid_all.tbl CDD cd04898 cd04898 153170 ACT_ACR-like_4 "ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the ""ACR"" protein). This CD includes the C-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the ""ACR"" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains." 77 matched cddid_all.tbl CDD cd04899 cd04899 153171 ACT_ACR-UUR-like_2 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains. This ACT domain family, ACT_ACR-UUR-like_2, includes the second of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the second and fourth ACT domains of a novel protein composed almost entirely of ACT domain repeats, the ACR protein. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. Members of this CD belong to the superfamily of ACT regulatory domains. 70 matched cddid_all.tbl CDD cd04900 cd04900 153172 ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains. This ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD is the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted tyrosine kinase. Members of this CD belong to the superfamily of ACT regulatory domains. 73 matched cddid_all.tbl CDD cd04901 cd04901 153173 ACT_3PGDH C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. The C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In Escherichia coli, the SerA 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. In the homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-exposed active site cleft. Members of this CD belong to the superfamily of ACT regulatory domains. 69 matched cddid_all.tbl CDD cd04902 cd04902 153174 ACT_3PGDH-xct C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between identical domains in the asymmetric unit. How this asymmetry influences the mechanism of effector inhibition is still unknown. Members of this CD belong to the superfamily of ACT regulatory domains. 73 matched cddid_all.tbl CDD cd04903 cd04903 153175 ACT_LSD C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit. The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains. 71 matched cddid_all.tbl CDD cd04904 cd04904 153176 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxytryptamine (serotonin) and the first reaction in the synthesis of melatonin. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains (this CD) and differ in their mechanisms of regulation. One commonality is that all three eukaryotic enzymes are regulated in part by the phosphorylation of serine residues N-terminal of the ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains. 74 matched cddid_all.tbl CDD cd04905 cd04905 153177 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe binding. L-Phe binds with positive cooperativity; with this binding, there is a shift in the protein to less active tetrameric and higher oligomeric forms from a more active dimeric form. Members of this CD belong to the superfamily of ACT regulatory domains. 80 matched cddid_all.tbl CDD cd04906 cd04906 153178 ACT_ThrD-I_1 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains. 85 matched cddid_all.tbl CDD cd04907 cd04907 153179 ACT_ThrD-I_2 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains. 81 matched cddid_all.tbl CDD cd04908 cd04908 153180 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains. 66 matched cddid_all.tbl CDD cd04909 cd04909 153181 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains. 69 matched cddid_all.tbl CDD cd04910 cd04910 153182 ACT_AK-Ectoine_1 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinase and L-aspartate-semialdehyde dehydrogenase. The M. alcaliphilum and the V. cholerae aspartokinases are encoded on the ectABCask operon. Members of this CD belong to the superfamily of ACT regulatory domains. 71 matched cddid_all.tbl CDD cd04911 cd04911 153183 ACT_AKiii-YclM-BS_1 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Bacillus subtilis YclM is reported to be a single polypeptide of 50 kD. AKIII from Bacillus subtilis strain 168 is induced by lysine and repressed by threonine and it is synergistically inhibited by lysine and threonine. Members of this CD belong to the superfamily of ACT regulatory domains. 76 matched cddid_all.tbl CDD cd04912 cd04912 153184 ACT_AKiii-LysC-EC-like_1 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in bacteria (Escherichia coli (EC) LysC) and plants, (Zea mays Ask1, Ask2, and Arabidopsis thaliana AK1). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Like the A. thaliana AK1 (AK1-AT), the E. coli AKIII (LysC) has two bound feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. The lysine-sensitive plant isoenzyme is synergistically inhibited by S-adenosylmethionine. A homolog of this group appears to be the Saccharomyces cerevisiae AK (Hom3) which clusters with this group as well. Members of this CD belong to the superfamily of ACT regulatory domains. 75 matched cddid_all.tbl CDD cd04913 cd04913 153185 ACT_AKii-LysC-BS-like_1 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins. This CD includes the N-terminal of the two ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis 168, the regulation of the diaminopimelate (Dap)-lysine biosynthetic pathway involves dual control by Dap and lysine, effected through separate Dap- and lysine-sensitive aspartokinase isoenzymes. The B. subtilis 168 AKII is induced by methionine and repressed and inhibited by lysine. Although Corynebacterium glutamicum is known to contain a single aspartokinase, both the succinylase and dehydrogenase variant pathways of DAP-lysine synthesis operate simultaneously in this organism. In corynebacteria and other various Gram-positive bacteria, the DAP-lysine pathway is feedback regulated by the concerted action of lysine and threonine. Conserved residues in the ACT domains have been shown to be involved in this concerted feedback inhibition. Also included in this CD are the aspartokinases of the extreme thermophile, Thermus thermophilus HB27, the Gram-negative obligate methylotroph, Methylophilus methylotrophus AS1, and those single aspartokinases found in Pseudomonas aeruginosa, C. glutamicum, and Amycolatopsis lactamdurans. B. subtilis 168 AKII, and the C. glutamicum, Streptomyces clavuligerus and A. lactamdurans aspartokinases are described as tetramers consisting of two alpha and two beta subunits; the alpha (44 kD) and beta (18 kD) subunits formed by two in-phase overlapping polypeptides. This CD includes the first ACT domain C-terminal to the AK catalytic domain of the alpha subunit and the first ACT domain of the beta subunit that lacks the AK catalytic domain. Unlike the C. glutamicum AK beta subunit, which is involved in feedback regulation, the B. subtilis AKII beta subunit is not. Cyanobacteria aspartokinases are unique to this CD and they have a unique domain architecture with two tandem pairs of ACT domains, C-terminal to the catalytic AK domain. In this CD, the first and third cyanobacteria AK ACT domains are present. Members of this CD belong to the superfamily of ACT regulatory domains. 75 matched cddid_all.tbl CDD cd04914 cd04914 153186 ACT_AKi-DapG-BS_1 ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI. This CD includes the N-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) strain 168), Clostridia, and Actinobacteria, bacterial species. In B. subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive aspartokinase isoenzymes. AKI activity is invariant during the exponential and stationary phases of growth and is not altered by addition of amino acids to the growth medium. The role of this isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulation. The B. subtilis AKI is tetrameric consisting of two alpha and two beta subunits; the alpha (43 kD) and beta (17 kD) subunit formed by two in-phase overlapping genes. The alpha subunit contains the AK catalytic domain and two ACT domains. The beta subunit contains two ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains. 67 matched cddid_all.tbl CDD cd04915 cd04915 153187 ACT_AK-Ectoine_2 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinase and L-aspartate-semialdehyde dehydrogenase. The M. alcaliphilum and the V. cholerae aspartokinases are encoded on the ectABCask operon. Members of this CD belong to the superfamily of ACT regulatory domains. 66 matched cddid_all.tbl CDD cd04916 cd04916 153188 ACT_AKiii-YclM-BS_2 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. B. subtilis YclM is reported to be a single polypeptide of 50 kD. AKIII from B. subtilis strain 168 is induced by lysine and repressed by threonine and it is synergistically inhibited by lysine and threonine. Members of this CD belong to the superfamily of ACT regulatory domains. 66 matched cddid_all.tbl CDD cd04917 cd04917 153189 ACT_AKiii-LysC-EC_2 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in bacteria (Escherichia coli (EC) LysC). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The E. coli AKIII (LysC) binds two feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. The second ACT domain (ACT2), this CD, is not involved in the binding of heterotrophic effectors. Members of this CD belong to the superfamily of ACT regulatory domains. 64 matched cddid_all.tbl CDD cd04918 cd04918 153190 ACT_AK1-AT_2 ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1). This CD includes the second of two ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1), which can be synergistically inhibited by S-adenosylmethionine (SAM). This isoenzyme is found in higher plants, Arabidopsis thaliana (AT) and Zea mays, and also in Chlorophyta. In its inactive state, Arabidopsis AK1 binds the effectors lysine and SAM (two molecules each) at the interface of two ACT1 domain subunits. The second ACT domain (ACT2), this CD, does not interact with an effector. Members of this CD belong to the superfamily of ACT regulatory domains. 65 matched cddid_all.tbl CDD cd04919 cd04919 153191 ACT_AK-Hom3_2 ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae, and other related ACT domains. AK is the first enzyme in the aspartate metabolic pathway, catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and in fungi, is responsible for the production of threonine, isoleucine and methionine. S. cerevisiae has a single AK, which is regulated by feedback, allosteric inhibition by L-threonine. Recent studies shown that the allosteric transition triggered by binding of threonine to AK involves a large change in the conformation of the native hexameric enzyme that is converted to an inactive one of different shape and substantially smaller hydrodynamic size. Members of this CD belong to the superfamily of ACT regulatory domains. 66 matched cddid_all.tbl CDD cd04920 cd04920 153192 ACT_AKiii-DAPDC_2 ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC). This CD includes the second of two ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. Aspartokinase (AK) is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The lysA gene encodes the enzyme DAPDC, a pyridoxal-5'-phosphate (PLP)-dependent enzyme which catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine. Tandem ACT domains are positioned centrally with the AK catalytic domain N-terminal and the DAPDC domains C-terminal. Members of this CD belong to the superfamily of ACT regulatory domains. 63 matched cddid_all.tbl CDD cd04921 cd04921 153193 ACT_AKi-HSDH-ThrA-like_1 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). This CD includes the first of two ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). The ACT domains are positioned between the N-terminal catalytic domain of AK and the C-terminal HSDH domain found in bacteria (Escherichia coli (EC) ThrA) and higher plants (Zea mays AK-HSDH). AK and HSDH are the first and third enzymes in the biosynthetic pathway of the aspartate family of amino acids. AK catalyzes the phosphorylation of Asp to P-aspartyl phosphate. HSDH catalyzes the NADPH-dependent conversion of Asp 3-semialdehyde to homoserine. HSDH is the first committed reaction in the branch of the pathway that leads to Thr and Met. In E. coli, ThrA is subject to allosteric regulation by the end product L-threonine and the native enzyme is reported to be tetrameric. As with bacteria, plant AK and HSDH are feedback inhibited by pathway end products. Maize AK-HSDH is a Thr-sensitive 180-kD enzyme. Arabidopsis AK-HSDH is an alanine-activated, threonine-sensitive enzyme whose ACT domains were shown to be involved in allosteric activation. Also included in this CD is the first of two ACT domains of a tetrameric, monofunctional, threonine-sensitive, AK found in Methanococcus jannaschii and other related archaeal species. Members of this CD belong to the superfamily of ACT regulatory domains. 80 matched cddid_all.tbl CDD cd04922 cd04922 153194 ACT_AKi-HSDH-ThrA_2 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). This CD includes the second of two ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). The ACT domains are positioned between the N-terminal catalytic domain of AK and the C-terminal HSDH domain found in bacteria (Escherichia coli (EC) ThrA) and higher plants (Zea mays AK-HSDH). AK and HSDH are the first and third enzymes in the biosynthetic pathway of the aspartate family of amino acids. AK catalyzes the phosphorylation of Asp to P-aspartyl phosphate. HSDH catalyzes the NADPH-dependent conversion of Asp 3-semialdehyde to homoserine. HSDH is the first committed reaction in the branch of the pathway that leads to Thr and Met. In E. coli, ThrA is subject to allosteric regulation by the end product L-threonine and the native enzyme is reported to be tetrameric. As with bacteria, plant AK and HSDH are feedback inhibited by pathway end products. Maize AK-HSDH is a Thr-sensitive 180-kD enzyme. Arabidopsis AK-HSDH is an alanine-activated, threonine-sensitive enzyme whose ACT domains were shown to be involved in allosteric activation. Members of this CD belong to the superfamily of ACT regulatory domains. 66 matched cddid_all.tbl CDD cd04923 cd04923 153195 ACT_AK-LysC-DapG-like_2 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains. This CD includes the C-terminal of the two ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, as well as, the second and fourth, of four, ACT domains present in cyanobacteria AK. Also included are the C-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase isoenzyme AKI found in Bacilli (B. subtilis strain 168), Clostridia, and Actinobacteria bacterial species. Members of this CD belong to the superfamily of ACT regulatory domains. 63 matched cddid_all.tbl CDD cd04924 cd04924 153196 ACT_AK-Arch_2 ACT domains of a monofunctional aspartokinase found mostly in Archaea species (ACT_AK-Arch_2). Included in this CD is the second of two ACT domains of a monofunctional aspartokinase found mostly in Archaea species (ACT_AK-Arch_2). The first or N-terminal ACT domain of these proteins cluster with the ThrA-like ACT 1 domains (ACT_AKi-HSDH-ThrA-like_1) which includes the threonine-sensitive archaeal Methanococcus jannaschii aspartokinase ACT 1 domain. Members of this CD belong to the superfamily of ACT regulatory domains. 66 matched cddid_all.tbl CDD cd04925 cd04925 153197 ACT_ACR_2 "ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the ""ACR"" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the ""ACR"" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains." 74 matched cddid_all.tbl CDD cd04926 cd04926 153198 ACT_ACR_4 "C-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the ""ACR"" protein). This CD includes the C-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the ""ACR"" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains." 72 matched cddid_all.tbl CDD cd04927 cd04927 153199 ACT_ACR-like_2 "Second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the ""ACR"" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the ""ACR"" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains." 76 matched cddid_all.tbl CDD cd04928 cd04928 153200 ACT_TyrKc Uncharacterized, N-terminal ACT domain of an Arabidopsis/Oryza predicted tyrosine kinase and other related ACT domains. This CD includes a novel, yet uncharacterized, N-terminal ACT domain of an Arabidopsis/Oryza predicted tyrosine kinase and other related ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains. 68 matched cddid_all.tbl CDD cd04929 cd04929 153201 ACT_TPH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxytryptamine (serotonin) and the first reaction in the synthesis of melatonin. Very little is known about the role of the ACT domain in TPH, which appears to be regulated by phosphorylation but not by its substrate or cofactor. Members of this CD belong to the superfamily of ACT regulatory domains. 74 matched cddid_all.tbl CDD cd04930 cd04930 153202 ACT_TH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines (dopamine, noradrenaline and adrenaline), functioning as hormones and neurotransmitters. The enzyme is not regulated by its amino acid substrate, but instead by phosphorylation at several serine residues located N-terminal of the ACT domain, and by feedback inhibition by catecholamines at the active site. Members of this CD belong to the superfamily of ACT regulatory domains. 115 matched cddid_all.tbl CDD cd04931 cd04931 153203 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains. 90 matched cddid_all.tbl CDD cd04932 cd04932 153204 ACT_AKiii-LysC-EC_1 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in bacteria (Escherichia coli (EC) LysC). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The E. coli AKIII (LysC) binds two feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. Members of this CD belong to the superfamily of ACT regulatory domains. 75 matched cddid_all.tbl CDD cd04933 cd04933 153205 ACT_AK1-AT_1 ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1). This CD includes the first of two ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1), which can be synergistically inhibited by S-adenosylmethionine. This isoenzyme is found in higher plants, Arabidopsis thaliana (AT) and Zea mays, and also in Chlorophyta. Like the Escherichia coli AKIII (LysC), Arabidopsis AK1 binds two feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. A loop in common is involved in the binding of both Lys and S-adenosylmethionine providing an explanation for the synergistic inhibition by these effectors. Members of this CD belong to the superfamily of ACT regulatory domains. 78 matched cddid_all.tbl CDD cd04934 cd04934 153206 ACT_AK-Hom3_1 CT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae, and other related ACT domains. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae, and other related ACT domains. AK is the first enzyme in the aspartate metabolic pathway, catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and in fungi, is responsible for the production of threonine, isoleucine and methionine. S. cerevisiae has a single AK, which is regulated by feedback, allosteric inhibition by L-threonine. Recent studies shown that the allosteric transition triggered by binding of threonine to AK involves a large change in the conformation of the native hexameric enzyme that is converted to an inactive one of different shape and substantially smaller hydrodynamic size. Members of this CD belong to the superfamily of ACT regulatory domains. 73 matched cddid_all.tbl CDD cd04935 cd04935 153207 ACT_AKiii-DAPDC_1 ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. This CD includes the first of two ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. Aspartokinase (AK) is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The lysA gene encodes the enzyme DAPDC, a pyridoxal-5'-phosphate (PLP)-dependent enzyme which catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine. Tandem ACT domains are positioned centrally with the AK catalytic domain N-terminal and the DAPDC domains C-terminal. Members of this CD belong to the superfamily of ACT regulatory domains. 75 matched cddid_all.tbl CDD cd04936 cd04936 153208 ACT_AKii-LysC-BS-like_2 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains. This CD includes the C-terminal of the two ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis strain 168, the regulation of the diaminopimelate (Dap)-lysine biosynthetic pathway involves dual control by Dap and lysine, effected through separate Dap- and lysine-sensitive AK isoenzymes. The B. subtilis strain 168 AKII is induced by methionine and repressed and inhibited by lysine. Although C. glutamicum is known to contain a single AK, both the succinylase and dehydrogenase variant pathways of DAP-lysine synthesis operate simultaneously in this organism. In corynebacteria and other various Gram-positive bacteria, the DAP-lysine pathway is feedback regulated by the concerted action of lysine and threonine. Conserved residues in the ACT domains have been shown to be involved in this concerted feedback inhibition. Also included in this CD are the AKs of the extreme thermophile, Thermus thermophilus HB27, the Gram-negative obligate methylotroph, Methylophilus methylotrophus AS1, and those single AKs found in Pseudomons, C. glutamicum, and Amycolatopsis lactamdurans. B. subtilis strain 168 AKII, and the C. glutamicum, Streptomyces clavuligerus and A. lactamdurans AKs are described as tetramers consisting of two alpha and two beta subunits; the alpha (44 kD) and beta (18 kD) subunits formed by two in-phase overlapping polypeptides. This CD includes the second ACT domain C-terminal to the AK catalytic domain of the alpha subunit and the second ACT domain of the beta subunit that lacks the AK catalytic domain. Unlike the C. glutamicum AK beta subunit, which is involved in feedback regulation, the B. subtilis AKII beta subunit is not. Cyanobacteria AKs are unique to this CD and they have a unique domain architecture with two tandem pairs of ACT domains, C-terminal to the catalytic AK domain. In this CD, the second and fourth cyanobacteria AK ACT domains are present. Members of this CD belong to the superfamily of ACT regulatory domains. 63 matched cddid_all.tbl CDD cd04937 cd04937 153209 ACT_AKi-DapG-BS_2 ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI. This CD includes the C-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) strain 168), Clostridia, and Actinobacteria bacterial species. In B. subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive AK isoenzymes. AKI activity is invariant during the exponential and stationary phases of growth and is not altered by addition of amino acids to the growth medium. The role of this isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulation. The BS AKI is tetrameric consisting of two alpha and two beta subunits; the alpha (43 kD) and beta (17 kD) subunit formed by two in-phase overlapping genes. The alpha subunit contains the AK catalytic domain and two ACT domains. The beta subunit contains two ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains. 64 matched cddid_all.tbl CDD cd04938 cd04938 340517 TGS_Obg TGS (ThrRS, GTPase and SpoT) domain found in the Obg protein family. The Obg family of GTPases function has been implicated in cellular processes as diverse as sporulation, stress response, control of DNA replication, and ribosome assembly. It consists of several subfamilies such as DRG and YchF with TGS domain. The TGS domain is named after the various RNA-binding multidomain ThrRS, GTPase, and SpoT/RelA proteins in which this domain occurs. The TGS domain of Obg-like GTPases such as those present in DRG (developmentally regulated GTP-binding protein), and GTP-binding proteins Ygr210 and YchF has a beta-grasp ubiquitin-like fold, a common structure involved in protein-protein interactions. 77 matched cddid_all.tbl CDD cd04939 cd04939 240137 PA2301 PA2301 is an uncharacterized Pseudomonas aeruginosa protein with a YbaK-like domain of unknown function. The YbaK-like domain family includes the INS amino acid-editing domain of the bacterial class II prolyl tRNA synthetase (ProRS), and it's trans-acting homologs, YbaK, and ProX. The primary function of INS is to hydrolyze mischarged cysteinyl-tRNA(Pro)'s, thus helping ensure the fidelity of translation. Organisms whose ProRS lacks the INS domain express a single-domain INS homolog such as YbaK, ProX, or PrdX which supplies the function of INS in trans. 139 matched cddid_all.tbl CDD cd04946 cd04946 340854 GT4_AmsK-like amylovoran biosynthesis glycosyltransferase AmsK and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases. AmsK is involved in the biosynthesis of amylovoran, which functions as a virulence factor. It functions as a glycosyl transferase which transfers galactose from UDP-galactose to a lipid-linked amylovoran-subunit precursor. The members of this family are found mainly in bacteria and Archaea. 401 matched cddid_all.tbl CDD cd04949 cd04949 340855 GT4_GtfA-like accessory Sec system glycosyltransferase GtfA and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases and is named after gtfA in Streptococcus gordonii, where it plays a role in the O-linked glycosylation of GspB, a cell surface glycoprotein involved in platelet binding. In general glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. The members of this family are found in bacteria. 328 matched cddid_all.tbl CDD cd04950 cd04950 340856 GT4_TuaH-like teichuronic acid biosynthesis glycosyltransferase TuaH and similar proteins. Members of this family may function in teichuronic acid biosynthesis/cell wall biogenesis. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. 373 matched cddid_all.tbl CDD cd04951 cd04951 340857 GT4_WbdM_like LPS/UnPP-GlcNAc-Gal a-1,4-glucosyltransferase WbdM and similar proteins. This family is most closely related to the GT4 family of glycosyltransferases and is named after WbdM in Escherichia coli. In general glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. The members of this family are found in bacteria. 360 matched cddid_all.tbl CDD cd04955 cd04955 340858 GT4-like glycosyltransferase family 4 proteins. This family is most closely related to the GT4 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. The members of this family are found in certain bacteria and Archaea. 379 matched cddid_all.tbl CDD cd04962 cd04962 340859 GT4_BshA-like N-acetyl-alpha-D-glucosaminyl L-malate synthase BshA and similar proteins. This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. The members of this family are found mainly in bacteria, while some of them are also found in Archaea and eukaryotes. 370 matched cddid_all.tbl CDD cd04967 cd04967 409356 IgI_1_Contactin First immunoglobulin (Ig) domain of contactin; member of the I-set of (Ig) superfamily domains. The members here are composed of the first immunoglobulin (Ig) domain of contactins. Contactins are neural cell adhesion molecules and are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. The first four Ig domains form the intermolecular binding fragment, which arranges as a compact U-shaped module via contacts between Ig domains 1 and 4, and between Ig domains 2 and 3. Contactin-2 (TAG-1, axonin-1) may play a part in the neuronal processes of neurite outgrowth, axon guidance and fasciculation, and neuronal migration. This group also includes contactin-1 and contactin-5. The different contactins show different expression patterns in the central nervous system. During development and in adulthood, contactin-2 is transiently expressed in subsets of central and peripheral neurons. Contactin-5 is expressed specifically in the rat postnatal nervous system, peaking at about 3 weeks postnatal, and a lack of contactin-5 (NB-2) results in an impairment of neuronal activity in the rat auditory system. Contactin-5 is highly expressed in the adult human brain in the occipital lobe and in the amygdala. Contactin-1 is differentially expressed in tumor tissues and may, through a RhoA mechanism, facilitate invasion and metastasis of human lung adenocarcinoma. This group belongs to the I-set of IgSF domains. 96 matched cddid_all.tbl CDD cd04968 cd04968 409357 IgI_3_Contactin Third immunoglobulin (Ig) domain of contactin; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the third immunoglobulin (Ig) domain of contactins. Contactins are neural cell adhesion molecules and are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. The first four Ig domains form the intermolecular binding fragment, which arranges as a compact U-shaped module via contacts between Ig domains 1 and 4, and between Ig domains 2 and 3. Contactin-2 (TAG-1, axonin-1) may play a part in the neuronal processes of neurite outgrowth, axon guidance and fasciculation, and neuronal migration. This group also includes contactin-1 and contactin-5. The different contactins show different expression patterns in the central nervous system. During development and in adulthood, contactin-2 is transiently expressed in subsets of central and peripheral neurons. Contactin-5 is expressed specifically in the rat postnatal nervous system, peaking at about 3 weeks postnatal, and a lack of contactin-5 (NB-2) results in an impairment of neuronal activity in the rat auditory system. Contactin-5 is highly expressed in the adult human brain in the occipital lobe and in the amygdala. Contactin-1 is differentially expressed in tumor tissues and may, through a RhoA mechanism, facilitate invasion and metastasis of human lung adenocarcinoma. This group belongs to the I-set of IgSF domains. 88 matched cddid_all.tbl CDD cd04969 cd04969 409358 Ig5_Contactin Fifth immunoglobulin (Ig) domain of contactin. The members here are composed of the fifth immunoglobulin (Ig) domain of contactins. Contactins are neural cell adhesion molecules and are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. The first four Ig domains form the intermolecular binding fragment, which arranges as a compact U-shaped module via contacts between Ig domains 1 and 4, and between Ig domains 2 and 3. Contactin-2 (TAG-1, axonin-1) may play a part in the neuronal processes of neurite outgrowth, axon guidance and fasciculation, and neuronal migration. This group also includes contactin-1 and contactin-5. The different contactins show different expression patterns in the central nervous system. During development and in adulthood, contactin-2 is transiently expressed in subsets of central and peripheral neurons. Contactin-5 is expressed specifically in the rat postnatal nervous system, peaking at about 3 weeks postnatal, and a lack of contactin-5 (NB-2) results in an impairment of neuronal activity in the rat auditory system. Contactin-5 is highly expressed in the adult human brain in the occipital lobe and in the amygdala. Contactin-1 is differentially expressed in tumor tissues and may, through a RhoA mechanism, facilitate invasion and metastasis of human lung adenocarcinoma. 89 matched cddid_all.tbl CDD cd04970 cd04970 409359 Ig6_Contactin Sixth immunoglobulin (Ig) domain of contactin. The members here are composed of the sixth immunoglobulin (Ig) domain of contactins. Contactins are neural cell adhesion molecules and are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. The first four Ig domains form the intermolecular binding fragment, which arranges as a compact U-shaped module via contacts between Ig domains 1 and 4, and between Ig domains 2 and 3. Contactin-2 (TAG-1, axonin-1) may play a part in the neuronal processes of neurite outgrowth, axon guidance and fasciculation, and neuronal migration. This group also includes contactin-1 and contactin-5. The different contactins show different expression patterns in the central nervous system. During development and in adulthood, contactin-2 is transiently expressed in subsets of central and peripheral neurons. Contactin-5 is expressed specifically in the rat postnatal nervous system, peaking at about 3 weeks postnatal, and a lack of contactin-5 (NB-2) results in an impairment of neuronal activity in the rat auditory system. Contactin-5 is highly expressed in the adult human brain in the occipital lobe and in the amygdala. Contactin-1 is differentially expressed in tumor tissues and may, through a RhoA mechanism, facilitate invasion and metastasis of human lung adenocarcinoma. 102 matched cddid_all.tbl CDD cd04971 cd04971 409360 IgI_TrKABC_d5 Fifth domain (immunoglobulin-like) of Trk receptors TrkA, TrkB, and TrkC; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the fifth domain of Trk receptors TrkA, TrkB, and TrkC, an immunoglobulin (Ig)-like domain which binds to neurotrophin. The Trk family of receptors are tyrosine kinase receptors. They are activated by dimerization, leading to autophosphorylation of intracellular tyrosine residues, and triggering the signal transduction pathway. TrkA, TrkB, and TrkC share significant sequence homology and domain organization. The first three domains are leucine-rich domains while the fourth and fifth domains are Ig-like domains playing a part in ligand binding. TrkA, TrkB, and TrkC mediate the trophic effects of the neurotrophin Nerve Growth Factor (NGF) family. TrkA is recognized by NGF. TrkB is recognized by brain-derived neurotrophic factor (BDNF) and neurotrophin (NT)-4. TrkC is recognized by NT-3. NT-3 is promiscuous as in some cell systems it activates TrkA and TrkB receptors. TrkA is a receptor found in all major NGF targets, including the sympathetic, trigeminal, and dorsal root ganglia, cholinergic neurons of the basal forebrain, and the striatum. TrKB transcripts are found throughout multiple structures of the central and peripheral nervous systems. The TrkC gene is expressed throughout the mammalian nervous system. This group belongs to the I-set of IgSF domains. 96 matched cddid_all.tbl CDD cd04972 cd04972 409361 Ig_TrkABC_d4 Fourth domain (immunoglobulin-like) of Trk receptors TrkA, TrkB, and TrkC. The members here are composed of the fourth domain of Trk receptors TrkA, TrkB, and TrkC, an immunoglobulin (Ig)-like domain which binds to neurotrophin. The Trk family of receptors are tyrosine kinase receptors. They are activated by dimerization, leading to autophosphorylation of intracellular tyrosine residues, and triggering the signal transduction pathway. TrkA, TrkB, and TrkC share significant sequence homology and domain organization. The first three domains are leucine-rich domains while the fourth and fifth domains are Ig-like domains playing a part in ligand binding. TrkA, TrkB, and TrkC mediate the trophic effects of the neurotrophin Nerve Growth Factor (NGF) family. TrkA is recognized by NGF. TrKB is recognized by brain-derived neurotrophic factor (BDNF) and neurotrophin (NT)-4. TrkC is recognized by NT-3. NT-3 is promiscuous as in some cell systems it activates TrkA and TrkB receptors. TrkA is a receptor found in all major NGF targets, including the sympathetic, trigeminal, and dorsal root ganglia, cholinergic neurons of the basal forebrain, and the striatum. TrKB transcripts are found throughout multiple structures of the central and peripheral nervous systems. The TrkC gene is expressed throughout the mammalian nervous system. 88 matched cddid_all.tbl CDD cd04973 cd04973 409362 IgI_1_FGFR First immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR); member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the first immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR). Fibroblast growth factors (FGFs) participate in morphogenesis, development, angiogenesis, and wound healing. These FGF-stimulated processes are mediated by four FGFR tyrosine kinases (FGRF1-4). FGFRs are comprised of an extracellular portion consisting of three Ig-like domains, a transmembrane helix, and a cytoplasmic portion having protein tyrosine kinase activity. The highly conserved Ig-like domains 2 and 3, and the linker region between D2 and D3 define a general binding site for all FGFs. 94 matched cddid_all.tbl CDD cd04974 cd04974 409363 IgI_3_FGFR "Third immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR); member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the third immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR). Fibroblast growth factors (FGFs) participate in morphogenesis, development, angiogenesis, and wound healing. These FGF-stimulated processes are mediated by four FGFR tyrosine kinases (FGRF1-4). FGFRs are comprised of an extracellular portion consisting of three Ig-like domains, a transmembrane helix, and a cytoplasmic portion having protein tyrosine kinase activity. The highly conserved Ig-like domains 2 and 3, and the linker region between D2 and D3 define a general binding site for FGFs. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 102 matched cddid_all.tbl CDD cd04975 cd04975 409364 IgI_4_SCFR_like "Fourth immunoglobulin (Ig)-like domain of stem cell factor receptor (SCFR), and similar domains; member of the I-set of IgSF domains. The members here are composed of the fourth immunoglobulin (Ig)-like domain of stem cell factor receptor (SCFR). In addition to SCFR, this group also includes the fourth Ig domain of macrophage colony stimulating factor receptor (M-CSF-R). SCFR, also called receptor tyrosine kinase KIT or proto-oncogene c-Kit, contains an extracellular component having five Ig-like domains, a transmembrane segment, and a cytoplasmic portion having protein tyrosine kinase activity. SCFR and its ligand SCF are critical for normal hematopoiesis, mast cell development, melanocytes, and gametogenesis. SCF binds to the second and third Ig-like domains of SCFR, this fourth Ig-like domain participates in SCFR dimerization, which follows ligand binding. Deletion of this fourth SCFR Ig-like domain abolishes the ligand-induced dimerization of SCFR and completely inhibits signal transduction. M-CSF-R, also called proto-oncogene c-Fms, acts as cell-surface receptor for CSF1 and IL34 and plays an essential role in the regulation of survival, proliferation and differentiation of hematopoietic precursor cells, such as macrophages and monocytes. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 101 matched cddid_all.tbl CDD cd04976 cd04976 409365 IgI_VEGFR "Immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor (VEGFR); member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor (VEGFR). The VEGFRs have an extracellular component with seven Ig-like domains, a transmembrane segment, and an intracellular tyrosine kinase domain interrupted by a kinase-insert domain. The VEGFR family consists of three members, VEGFR-1 (Flt-1), VEGFR-2 (KDR/Flk-1), and VEGFR-3 (Flt-4). VEGFRs bind VEGFs with high affinity at the Ig-like domains. VEGF-A is important to the growth and maintenance of vascular endothelial cells and to the development of new blood- and lymphatic-vessels in physiological and pathological states. VEGFR-2 is a major mediator of the mitogenic, angiogenic, and microvascular permeability-enhancing effects of VEGF-A. VEGFR-1 may play an inhibitory part in these processes by binding VEGF and interfering with its interaction with VEGFR-2. VEGFR-1 has a signaling role in mediating monocyte chemotaxis. VEGFR-1 and VEGFR-2 may mediate a chemotactic and a survival signal in hematopoietic stem cells or leukemia cells. VEGFR-3 has been shown to be involved in tumor angiogenesis and growth. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 90 matched cddid_all.tbl CDD cd04977 cd04977 409366 IgI_1_NCAM-1_like "First immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-1, and similar domains; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the first immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-1. NCAM-1 plays important roles in the development and regeneration of the central nervous system, in synaptogenesis and neural migration. NCAM mediates cell-cell and cell-substratum recognition and adhesion via homophilic (NCAM-NCAM) and heterophilic (NCAM-nonNCAM) interactions. NCAM is expressed as three major isoforms having different intracellular extensions. The extracellular portion of NCAM has five N-terminal Ig-like domains and two fibronectin type III domains. The double zipper adhesion complex model for NCAM homophilic binding involves the Ig1, Ig2, and Ig3 domains. By this model, Ig1 and Ig2 mediate dimerization of NCAM molecules situated on the same cell surface (cis interactions), and Ig3 domains mediate interactions between NCAM molecules expressed on the surface of opposing cells (trans interactions), through binding to the Ig1 and Ig2 domains. The adhesive ability of NCAM is modulated by the addition of polysialic acid chains to the fifth Ig-like domain. Also included in this group is NCAM-2 (also known as OCAM/mamFas II and RNCAM). NCAM-2 is differentially expressed in the developing and mature olfactory epithelium (OE). This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 95 matched cddid_all.tbl CDD cd04978 cd04978 409367 Ig4_L1-NrCAM_like Fourth immunoglobulin (Ig)-like domain of L1, Ng-CAM (Neuron-glia CAM cell adhesion molecule), and NrCAM (Ng-CAM-related). The members here are composed of the fourth immunoglobulin (Ig)-like domain of L1, Ng-CAM (Neuron-glia CAM cell adhesion molecule), and NrCAM (Ng-CAM-related). These proteins belong to the L1 subfamily of cell adhesion molecules (CAMs) and are comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region and an intracellular domain. These molecules are primarily expressed in the nervous system. L1 is associated with an X-linked recessive disorder, X-linked hydrocephalus, MASA syndrome, or spastic paraplegia type 1, that involves abnormalities of axonal growth. 89 matched cddid_all.tbl CDD cd04979 cd04979 409368 Ig_Semaphorin_C Immunoglobulin (Ig)-like domain at the C-terminus of semaphorins. The members here are composed of the immunoglobulin (Ig)-like domain in semaphorins. Semaphorins are transmembrane protein that have important roles in a variety of tissues. Functionally, semaphorins were initially characterized for their importance in the development of the nervous system and in axonal guidance. Later they have been found to be important for the formation and functioning of the cardiovascular, endocrine, gastrointestinal, hepatic, immune, musculoskeletal, renal, reproductive, and respiratory systems. Semaphorins function through binding to their receptors and transmembrane semaphorins also serves as receptors themselves. Although molecular mechanism of semaphorins is poorly understood, the Ig-like domains may be involved in ligand binding or dimerization. 88 matched cddid_all.tbl CDD cd04980 cd04980 409369 IgV_L_kappa "Immunoglobulin (Ig) light chain, kappa type, variable (V) domain. The members here are composed of the immunoglobulin (Ig) light chain, kappa type, variable (V) domain. This group contains the standard Ig superfamily V-set AGFCC'C""/DEB domain topology. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains." 106 matched cddid_all.tbl CDD cd04981 cd04981 409370 IgV_H "Immunoglobulin (Ig) heavy chain (H), variable (V) domain. The members here are composed of the immunoglobulin (Ig) heavy chain (H), variable (V) domain. This group contains the standard Ig superfamily V-set AGFCC'C""/DEB domain topology. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains." 118 matched cddid_all.tbl CDD cd04982 cd04982 409371 IgV_TCR_gamma "Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain. The members here are composed of the immunoglobulin (Ig) variable (V) domain of the gamma chain of gamma/delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha/beta TCRs, but a small subset contain gamma/delta TCRs. Alpha/beta TCRs recognize antigens as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize MHC independently of the bound peptide. Gamma/delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain the standard Ig superfamily V-set AGFCC'C""/DEB domain topology." 117 matched cddid_all.tbl CDD cd04983 cd04983 409372 IgV_TCR_alpha "Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar proteins. The members here are composed of the immunoglobulin (Ig) variable domain of the alpha chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta polypeptide chains with variable (V) and constant (C) regions. This group represents the variable domain of the alpha chain of TCRs and also includes the variable domain of delta chains of TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize MHC independently of the bound peptide. Members of this group contain standard Ig superfamily V-set AGFCC'C""/DEB domain topology." 109 matched cddid_all.tbl CDD cd04984 cd04984 409373 IgV_L_lambda "Immunoglobulin (Ig) lambda light chain variable (V) domain. The members here are composed of the immunoglobulin (Ig) light chain, lambda type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains. Members of this group contain standard Ig superfamily V-set AGFCC'C""/DEB domain topology." 105 matched cddid_all.tbl CDD cd04985 cd04985 409374 IgC1_CH1_IgADEGM CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, epsilon, gamma, and mu chains; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the first immunoglobulin constant-1 set domain of alpha, delta, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors. 98 matched cddid_all.tbl CDD cd04986 cd04986 409375 IgC1_CH2_IgA CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the second immunoglobulin constant-1 set domain (IgC) of alpha heavy chains. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors. 96 matched cddid_all.tbl CDD cd05005 cd05005 240138 SIS_PHI Hexulose-6-phosphate isomerase (PHI). PHI is a member of the SIS (Sugar ISomerase domain) superfamily. In the ribulose monophosphate pathway of formaldehyde fixation, hexulose-6-phosphate synthase catalyzes the condensation of ribulose-5-phosphate with formadelhyde to become hexulose-6-phosphate, which is then isomerized to fructose-6-phosphate by PHI. 179 matched cddid_all.tbl CDD cd05006 cd05006 240139 SIS_GmhA Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of gram-negative bacteria inner core lipopolysaccharide precursor, L-glycero-D-mannoheptose (Gmh). 177 matched cddid_all.tbl CDD cd05007 cd05007 240140 SIS_Etherase N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate. 257 matched cddid_all.tbl CDD cd05008 cd05008 240141 SIS_GlmS_GlmD_1 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source. The glutaminase domain hydrolyzes glutamine to glutamate and ammonia. Ammonia is transferred through a channel to the isomerase domain for glucosamine 6-phosphate synthesis. The end product of the pathway is N-acetylglucosamine, which plays multiple roles in eukaryotic cells including being a building block of bacterial and fungal cell walls. In the absence of glutamine, GlmS catalyzes the isomerization of fructose 6-phosphate into glucose 6- phosphate (PGI-like activity). Glucosamine-6-phosphate deaminase (GlmD) contains two SIS domains and catalyzes the deamination and isomerization of glucosamine-6-phosphate into fructose-6-phosphate with the release of ammonia; in presence of high ammonia concentration, GlmD can catalyze the reverse reaction. 126 matched cddid_all.tbl CDD cd05009 cd05009 240142 SIS_GlmS_GlmD_2 SIS (Sugar ISomerase) domain repeat 2 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source. The glutaminase domain hydrolyzes glutamine to glutamate and ammonia. Ammonia is transferred through a channel to the isomerase domain for glucosamine 6-phosphate synthesis. The end product of the pathway is N-acetylglucosamine, which plays multiple roles in eukaryotic cells including being a building block of bacterial and fungal cell walls. In the absence of glutamine, GlmS catalyzes the isomerization of fructose 6-phosphate into glucose 6- phosphate (PGI-like activity). Glucosamine-6-phosphate deaminase (GlmD) contains two SIS domains and catalyzes the deamination and isomerization of glucosamine-6-phosphate into fructose-6-phosphate with the release of ammonia; in presence of high ammonia concentration, GlmD can catalyze the reverse reaction. 153 matched cddid_all.tbl CDD cd05010 cd05010 240143 SIS_AgaS_like AgaS-like protein. AgaS contains a SIS (Sugar ISomerase) domain which is found in many phosphosugar isomerases and phosphosugar binding proteins. AgaS is a putative isomerase in Escherichia coli. It is similar to the glucosamine-6-phosphate synthases (GlmS) which catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source. 151 matched cddid_all.tbl CDD cd05013 cd05013 240144 SIS_RpiR RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate isomerases that catalyze the reversible reactions of ribose 5-phosphate into ribulose 5-phosphate. 139 matched cddid_all.tbl CDD cd05014 cd05014 240145 SIS_Kpsf KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-phosphate to arabinose 5-phosphate. This is the second step in the CMP-Kdo biosynthesis pathway. 128 matched cddid_all.tbl CDD cd05015 cd05015 240146 SIS_PGI_1 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the first SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of glucose 6-phosphate to fructose 6-phosphate. As an extracellular protein, PGI also has functions equivalent to neuroleukin (NLK), autocrine motility factor (AMF), and maturation factor (MF). Evidence suggests that PGI, NLK, AMF, and MF are closely related or identical. NLK is a neurotrophic growth factor that promotes regeneration and survival of neurons. The dimeric form of NLK has isomerase function, whereas its monomeric form carries out neurotrophic activity. AMF is a cytokine that stimulates cell migration and metastasis. MF mediates the differentiation of human myeloid leukemic HL-60 cells to terminal monocytic cells. 158 matched cddid_all.tbl CDD cd05016 cd05016 240147 SIS_PGI_2 Phosphoglucose isomerase (PGI) contains two SIS (Sugar ISomerase) domains. This classification is based on the alignment of the second SIS domain. PGI is a multifunctional enzyme which as an intracellular dimer catalyzes the reversible isomerization of glucose 6-phosphate to fructose 6-phosphate. As an extracellular protein, PGI also has functions equivalent to neuroleukin (NLK), autocrine motility factor (AMF), and maturation factor (MF). Evidence suggests that PGI, NLK, AMF, and MF are closely related or identical. NLK is a neurotrophic growth factor that promotes regeneration and survival of neurons. The dimeric form of NLK has isomerase function, whereas its monomeric form carries out neurotrophic activity. AMF is a cytokine that stimulates cell migration and metastasis. MF mediates the differentiation of human myeloid leukemic HL-60 cells to terminal monocytic cells. 164 matched cddid_all.tbl CDD cd05017 cd05017 240148 SIS_PGI_PMI_1 The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions. These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the first SIS domain. 119 matched cddid_all.tbl CDD cd05018 cd05018 176853 CoxG Carbon monoxide dehydrogenase subunit G (CoxG). CoxG has been shown, in Oligotropha carboxidovorans, to anchor the carbon monoxide (CO) dehydrogenase to the cytoplasmic membrane. The gene encoding CoxG is part of the Cox cluster (coxBCMSLDEFGHIK) located on a low-copy-number, circular, megaplasmid pHCG3. This cluster includes genes encoding subunits of CO dehydrogenase and several accessory components involved in the utilization of CO. This family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. 144 matched cddid_all.tbl CDD cd05022 cd05022 240149 S-100A13 S-100A13: S-100A13 domain found in proteins similar to S100A13. S100A13 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A13 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100A13 is involved in the cellular export of interleukin-1 (IL-1) and of fibroblast growth factor-1 (FGF-1), which plays an important role in angiogenesis and tissue regeneration. Export is based on the CuII-dependent formation of multiprotein complexes containing the S100A13 protein. Assembly of these complexes occurs near the inner surface of the plasma membrane. Binding of two Ca(II) ions per monomer triggers key conformational changes leading to the creation of two identical and symmetrical Cu(II)-binding sites on the surface of the protein, close to the interface between the two monomers. These Cu(II)-binding sites are unique among the S100 proteins, which are reported to bind Cu(II) or Zn(II) ions in addition to Ca(II) ions. In addition, the three-dimensional structure of S100A13 differs significantly from those of other S100 proteins; the hydrophobic pocket that largely contributes to protein-protein interactions in other S100 proteins is absent in S100A13. The structure of S100A13 contains a large patch of negatively charged residues flanked by dense cationic clusters, formed mostly from positively charged residues from the C-terminal end, which plays major role in binding FGF-1. 89 matched cddid_all.tbl CDD cd05023 cd05023 240150 S-100A11 S-100A11: S-100A11 domain found in proteins similar to S100A11. S100A11 is a member of the S-100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A11 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100 proteins have also been associated with a variety of pathological events, including neoplastic transformation and neurodegenerative diseases such as Alzheimer's, usually via over expression of the protein. S100A11 is expressed in smooth muscle and other tissues and involves in calcium-dependent membrane aggregation, which is important for cell vesiculation . As is the case for many other S100 proteins, S100A11 is homodimer, which is able to form a heterodimer with S100B through subunit exchange. Ca2+ binding to S100A11 results in a conformational change in the protein, exposing a hydrophobic surface that interacts with target proteins. In addition to binding to annexin A1 and A6 S100A11 also interacts with actin and transglutaminase. 89 matched cddid_all.tbl CDD cd05024 cd05024 240151 S-100A10 S-100A10: A subgroup of the S-100A10 domain found in proteins similar to S100A10. S100A10 is a member of the S100 family of EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A10 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. A unique feature of S100A10 is that it contains mutation in both of the calcium binding sites, making it calcium insensitive. S100A10 has been detected in brain, heart, gastrointestinal tract, kidney, liver, lung, spleen, testes, epidermis, aorta, and thymus. Structural data supports the homo- and hetero-dimeric as well as hetero-tetrameric nature of the protein. S100A10 has multiple binding partners in its calcium free state and is therefore involved in many diverse biological functions. 91 matched cddid_all.tbl CDD cd05025 cd05025 240152 S-100A1 S-100A1: S-100A1 domain found in proteins similar to S100A1. S100A1 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A1 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. As is the case with many other members of S100 protein family, S100A1 is implicated in intracellular and extracellular regulatory activities, including interaction with myosin-associated twitchin kinase, actin-capping protein CapZ, sinapsin I, and tubulin. Structural data suggests that S100A1 proteins exist within cells as antiparallel homodimers, while heterodimers with S100A4 and S100B also has been reported. Upon binding calcium S100A1 changes conformation to expose a hydrophobic cleft which is the interaction site of S100A1 with its more that 20 known target proteins. 92 matched cddid_all.tbl CDD cd05026 cd05026 240153 S-100Z S-100Z: S-100Z domain found in proteins similar to S100Z. S100Z is a member of the S100 domain family within the EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100Z group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately.S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control. S100Z is normally expressed in various tissues, with its highest level of expression being in spleen and leukocytes. The function of S100Z remains unclear. Preliminary structural data suggests that S100Z is homodimer, however a heterodimer with S100P has been reported. S100Z is capable of binding calcium ions. When calcium binds to S110Z, the protein experiences a conformational change, which exposes hydrophobic surfaces on the protein. In comparison with their normal tissue counterparts, S100Z gene expression appears to be deregulated in some tumor tissues. 93 matched cddid_all.tbl CDD cd05027 cd05027 240154 S-100B S-100B: S-100B domain found in proteins similar to S100B. S100B is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100B group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100B is most abundant in glial cells of the central nervous system, predominately in astrocytes. S100B is involved in signal transduction via the inhibition of protein phoshorylation, regulation of enzyme activity and by affecting the calcium homeostasis. Upon calcium binding the S100B homodimer changes conformation to expose a hydrophobic cleft, which represents the interaction site of S100B with its more than 20 known target proteins. These target proteins include several cellular architecture proteins such as tubulin and GFAP; S100B can inhibit polymerization of these oligomeric molecules. Furthermore, S100B inhibits the phosphorylation of multiple kinase substrates including the Alzheimer protein tau and neuromodulin (GAP-43) through a calcium-sensitive interaction with the protein substrates. 88 matched cddid_all.tbl CDD cd05029 cd05029 240155 S-100A6 S-100A6: S-100A6 domain found in proteins similar to S100A6. S100A6 is a member of the S100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A6 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100A6 is normally expressed in the G1 phase of the cell cycle in neuronal cells. The function of S100A6 remains unclear, but evidence suggests that it is involved in cell cycle regulation and exocytosis. S100A6 may also be involved in tumorigenesis; the protein is overexpressed in several tumors. Ca2+ binding to S100A6 leads to a conformational change in the protein, which exposes a hydrophobic surface for interaction with target proteins. Several such proteins have been identified: glyceraldehyde-3-phosphate dehydrogenase , annexins 2, 6 and 11 and Calcyclin-Binding Protein (CacyBP). 88 matched cddid_all.tbl CDD cd05030 cd05030 240156 calgranulins Calgranulins: S-100 domain found in proteins belonging to the Calgranulin subgroup of the S100 family of EF-hand calcium-modulated proteins, including S100A8, S100A9, and S100A12 . Note that the S-100 hierarchy, to which this Calgranulin group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. These proteins are expressed mainly in granulocytes, and are involved in inflammation, allergy, and neuritogenesis, as well as in host-parasite response. Calgranulins are modulated not only by calcium, but also by other metals such as zinc and copper. Structural data suggested that calgranulins may exist in multiple structural forms, homodimers, as well as hetero-oligomers. For example, the S100A8/S100A9 complex called calprotectin plays important roles in the regulation of inflammatory processes, wound repair, and regulating zinc-dependent enzymes as well as microbial growth. 88 matched cddid_all.tbl CDD cd05031 cd05031 240157 S-100A10_like S-100A10_like: S-100A10 domain found in proteins similar to S100A10. S100A10 is a member of the S100 family of EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A1_like group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. A unique feature of S100A10 is that it contains mutation in both of the calcium binding sites, making it calcium insensitive. S100A10 has been detected in brain, heart, gastrointestinal tract, kidney, liver, lung, spleen, testes, epidermis, aorta, and thymus. Structural data supports the homo- and hetero-dimeric as well as hetero-tetrameric nature of the protein. S100A10 has multiple binding partners in its calcium free state and is therefore involved in many diverse biological functions. 94 matched cddid_all.tbl CDD cd05032 cd05032 173625 PTKc_InsR_like Catalytic domain of Insulin Receptor-like Protein Tyrosine Kinases. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. The InsR subfamily is composed of InsR, Insulin-like Growth Factor-1 Receptor (IGF-1R), and similar proteins. InsR and IGF-1R are receptor PTKs (RTKs) composed of two alphabeta heterodimers. Binding of the ligand (insulin, IGF-1, or IGF-2) to the extracellular alpha subunit activates the intracellular tyr kinase domain of the transmembrane beta subunit. Receptor activation leads to autophosphorylation, stimulating downstream kinase activities, which initiate signaling cascades and biological function. InsR and IGF-1R, which share 84% sequence identity in their kinase domains, display physiologically distinct yet overlapping functions in cell growth, differentiation, and metabolism. InsR activation leads primarily to metabolic effects while IGF-1R activation stimulates mitogenic pathways. In cells expressing both receptors, InsR/IGF-1R hybrids are found together with classical receptors. Both receptors can interact with common adaptor molecules such as IRS-1 and IRS-2. The InsR-like subfamily is part of a larger superfamily that includes the catalytic domains of serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 277 matched cddid_all.tbl CDD cd05033 cd05033 270629 PTKc_EphR Catalytic domain of Ephrin Receptor Protein Tyrosine Kinases. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. EphRs comprise the largest subfamily of receptor PTKs (RTKs). They can be classified into two classes (EphA and EphB), according to their extracellular sequences, which largely correspond to binding preferences for either GPI-anchored ephrin-A ligands or transmembrane ephrin-B ligands. Vertebrates have ten EphA and six EphB receptors, which display promiscuous ligand interactions within each class. EphRs contain an ephrin binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyr kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. This allows ephrin/EphR dimers to form, leading to the activation of the intracellular tyr kinase domain. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). The main effect of ephrin/EphR interaction is cell-cell repulsion or adhesion. Ephrin/EphR signaling is important in neural development and plasticity, cell morphogenesis and proliferation, cell-fate determination, embryonic development, tissue patterning, and angiogenesis.The EphR subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 266 matched cddid_all.tbl CDD cd05034 cd05034 270630 PTKc_Src_like Catalytic domain of Src kinase-like Protein Tyrosine Kinases. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Src subfamily members include Src, Lck, Hck, Blk, Lyn, Fgr, Fyn, Yrk, and Yes. Src (or c-Src) proteins are cytoplasmic (or non-receptor) PTKs which are anchored to the plasma membrane. They contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). Src proteins are involved in signaling pathways that regulate cytokine and growth factor responses, cytoskeleton dynamics, cell proliferation, survival, and differentiation. They were identified as the first proto-oncogene products, and they regulate cell adhesion, invasion, and motility in cancer cells and tumor vasculature, contributing to cancer progression and metastasis. Src kinases are overexpressed in a variety of human cancers, making them attractive targets for therapy. They are also implicated in acute inflammatory responses and osteoclast function. Src, Fyn, Yes, and Yrk are widely expressed, while Blk, Lck, Hck, Fgr, and Lyn show a limited expression pattern. The Src-like subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 248 matched cddid_all.tbl CDD cd05035 cd05035 270631 PTKc_TAM Catalytic Domain of TAM (Tyro3, Axl, Mer) Protein Tyrosine Kinases. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. The TAM subfamily consists of Tyro3 (or Sky), Axl, Mer (or Mertk), and similar proteins. TAM subfamily members are receptor tyr kinases (RTKs) containing an extracellular ligand-binding region with two immunoglobulin-like domains followed by two fibronectin type III repeats, a transmembrane segment, and an intracellular catalytic domain. Binding to their ligands, Gas6 and protein S, leads to receptor dimerization, autophosphorylation, activation, and intracellular signaling. TAM proteins are implicated in a variety of cellular effects including survival, proliferation, migration, and phagocytosis. They are also associated with several types of cancer as well as inflammatory, autoimmune, vascular, and kidney diseases. The TAM subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 273 matched cddid_all.tbl CDD cd05036 cd05036 270632 PTKc_ALK_LTK Catalytic domain of the Protein Tyrosine Kinases, Anaplastic Lymphoma Kinase and Leukocyte Tyrosine Kinase. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyr residues in protein substrates. ALK and LTK are orphan receptor PTKs (RTKs) whose ligands are not yet well-defined. ALK appears to play an important role in mammalian neural development as well as visceral muscle differentiation in Drosophila. ALK is aberrantly expressed as fusion proteins, due to chromosomal translocations, in about 60% of anaplastic large cell lymphomas (ALCLs). ALK fusion proteins are also found in rare cases of diffuse large B cell lymphomas (DLBCLs). LTK is mainly expressed in B lymphocytes and neuronal tissues. It is important in cell proliferation and survival. Transgenic mice expressing TLK display retarded growth and high mortality rate. In addition, a polymorphism in mouse and human LTK is implicated in the pathogenesis of systemic lupus erythematosus. RTKs contain an extracellular ligand-binding domain, a transmembrane region, and an intracellular tyr kinase domain. They are usually activated through ligand binding, which causes dimerization and autophosphorylation of the intracellular tyr kinase catalytic domain. The ALK/LTK subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 277 matched cddid_all.tbl CDD cd05037 cd05037 270633 PTK_Jak_rpt1 Pseudokinase (repeat 1) domain of the Protein Tyrosine Kinases, Janus kinases. The Jak subfamily is composed of Jak1, Jak2, Jak3, TYK2, and similar proteins. They are cytoplasmic (or nonreceptor) PTKs containing an N-terminal FERM domain, followed by a Src homology 2 (SH2) domain, a pseudokinase domain, and a C-terminal catalytic tyr kinase domain. The pseudokinase domain shows similarity to tyr kinases but lacks crucial residues for catalytic activity and ATP binding. It modulates the kinase activity of the C-terminal catalytic domain. In the case of Jak2, the presumed pseudokinase (repeat 1) domain exhibits dual-specificity kinase activity, phosphorylating two negative regulatory sites in Jak2: Ser523 and Tyr570. Most Jaks are expressed in a wide variety of tissues, except for Jak3, which is expressed only in hematopoietic cells. Jaks are crucial for cytokine receptor signaling. They are activated by autophosphorylation upon cytokine-induced receptor aggregation, and subsequently trigger downstream signaling events such as the phosphorylation of signal transducers and activators of transcription (STATs). Jaks are also involved in regulating the surface expression of some cytokine receptors. The Jak-STAT pathway is involved in many biological processes including hematopoiesis, immunoregulation, host defense, fertility, lactation, growth, and embryogenesis. The Jak subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 259 matched cddid_all.tbl CDD cd05038 cd05038 270634 PTKc_Jak_rpt2 Catalytic (repeat 2) domain of the Protein Tyrosine Kinases, Janus kinases. The Jak subfamily is composed of Jak1, Jak2, Jak3, TYK2, and similar proteins. They are PTKs, catalyzing the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Jaks are cytoplasmic (or nonreceptor) PTKs containing an N-terminal FERM domain, followed by a Src homology 2 (SH2) domain, a pseudokinase domain, and a C-terminal tyr kinase catalytic domain. Most Jaks are expressed in a wide variety of tissues, except for Jak3, which is expressed only in hematopoietic cells. Jaks are crucial for cytokine receptor signaling. They are activated by autophosphorylation upon cytokine-induced receptor aggregation, and subsequently trigger downstream signaling events such as the phosphorylation of signal transducers and activators of transcription (STATs). Jaks are also involved in regulating the surface expression of some cytokine receptors. The Jak-STAT pathway is involved in many biological processes including hematopoiesis, immunoregulation, host defense, fertility, lactation, growth, and embryogenesis. The Jak subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 284 matched cddid_all.tbl CDD cd05039 cd05039 270635 PTKc_Csk_like Catalytic domain of C-terminal Src kinase-like Protein Tyrosine Kinases. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. This subfamily is composed of Csk, Chk, and similar proteins. They are cytoplasmic (or nonreceptor) PTKs containing the Src homology domains, SH3 and SH2, N-terminal to the catalytic tyr kinase domain. They negatively regulate the activity of Src kinases that are anchored to the plasma membrane. To inhibit Src kinases, Csk and Chk are translocated to the membrane via binding to specific transmembrane proteins, G-proteins, or adaptor proteins near the membrane. Csk catalyzes the tyr phosphorylation of the regulatory C-terminal tail of Src kinases, resulting in their inactivation. Chk inhibit Src kinases using a noncatalytic mechanism by simply binding to them. As negative regulators of Src kinases, Csk and Chk play important roles in cell proliferation, survival, and differentiation, and consequently, in cancer development and progression. The Csk-like subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd05040 cd05040 270636 PTKc_Ack_like Catalytic domain of the Protein Tyrosine Kinase, Activated Cdc42-associated kinase. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. This subfamily includes Ack1, thirty-eight-negative kinase 1 (Tnk1), and similar proteins. They are cytoplasmic (or nonreceptor) PTKs containing an N-terminal catalytic domain, an SH3 domain, a Cdc42-binding CRIB domain, and a proline-rich region. They are mainly expressed in brain and skeletal tissues and are involved in the regulation of cell adhesion and growth, receptor degradation, and axonal guidance. Ack1 is also associated with androgen-independent prostate cancer progression. Tnk1 regulates TNFalpha signaling and may play an important role in cell death. The Ack-like subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 258 matched cddid_all.tbl CDD cd05041 cd05041 270637 PTKc_Fes_like Catalytic domain of Fes-like Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family; Fes subfamily; catalytic (c) domain. Fes subfamily members include Fes (or Fps), Fer, and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Fes subfamily proteins are cytoplasmic (or nonreceptor) tyr kinases containing an N-terminal region with FCH (Fes/Fer/CIP4 homology) and coiled-coil domains, followed by a SH2 domain, and a C-terminal catalytic domain. The genes for Fes (feline sarcoma) and Fps (Fujinami poultry sarcoma) were first isolated from tumor-causing retroviruses. The viral oncogenes encode chimeric Fes proteins consisting of Gag sequences at the N-termini, resulting in unregulated tyr kinase activity. Fes and Fer kinases play roles in haematopoiesis, inflammation and immunity, growth factor signaling, cytoskeletal regulation, cell migration and adhesion, and the regulation of cell-cell interactions. Fes and Fer show redundancy in their biological functions. 251 matched cddid_all.tbl CDD cd05042 cd05042 270638 PTKc_Aatyk Catalytic domain of the Protein Tyrosine Kinases, Apoptosis-associated tyrosine kinases. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. The Aatyk subfamily is also referred to as the lemur tyrosine kinase (Lmtk) subfamily. It consists of Aatyk1 (Lmtk1), Aatyk2 (Lmtk2, Brek), Aatyk3 (Lmtk3), and similar proteins. Aatyk proteins are mostly receptor PTKs (RTKs) containing a transmembrane segment and a long C-terminal cytoplasmic tail with a catalytic domain. Aatyk1 does not contain a transmembrane segment and is a cytoplasmic (or nonreceptor) kinase. Aatyk proteins are classified as PTKs based on overall sequence similarity and the phylogenetic tree. However, analysis of catalytic residues suggests that Aatyk proteins may be multispecific kinases, functioning also as serine/threonine kinases. They are involved in neural differentiation, nerve growth factor (NGF) signaling, apoptosis, and spermatogenesis. The Aatyk subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 269 matched cddid_all.tbl CDD cd05043 cd05043 270639 PTK_Ryk Pseudokinase domain of Ryk (Receptor related to tyrosine kinase). Ryk is a receptor tyr kinase (RTK) containing an extracellular region with two leucine-rich motifs, a transmembrane segment, and an intracellular inactive pseudokinase domain, which shows similarity to tyr kinases but lacks crucial residues for catalytic activity and ATP binding. The extracellular region of Ryk shows homology to the N-terminal domain of Wnt inhibitory factor-1 (WIF) and serves as the ligand (Wnt) binding domain of Ryk. Ryk is expressed in many different tissues both during development and in adults, suggesting a widespread function. It acts as a chemorepulsive axon guidance receptor of Wnt glycoproteins and is responsible for the establishment of axon tracts during the development of the central nervous system. In addition, studies in mice reveal that Ryk is essential in skeletal, craniofacial, and cardiac development. Thus, it appears Ryk is involved in signal transduction despite its lack of kinase activity. Ryk may function as an accessory protein that modulates the signals coming from catalytically active partner RTKs such as the Eph receptors. The Ryk subfamily is part of a larger superfamily that includes other pseudokinases and the catalytic domains of active kinases including PTKs, protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 279 matched cddid_all.tbl CDD cd05044 cd05044 270640 PTKc_c-ros Catalytic domain of the Protein Tyrosine Kinase, C-ros. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. This subfamily contains c-ros, Sevenless, and similar proteins. The proto-oncogene c-ros encodes an orphan receptor PTK (RTK) with an unknown ligand. RTKs contain an extracellular ligand-binding domain, a transmembrane region, and an intracellular tyr kinase domain. RTKs are usually activated through ligand binding, which causes dimerization and autophosphorylation of the intracellular tyr kinase catalytic domain. C-ros is expressed in embryonic cells of the kidney, intestine and lung, but disappears soon after birth. It persists only in the adult epididymis. Male mice bearing inactive mutations of c-ros lack the initial segment of the epididymis and are infertile. The Drosophila protein, Sevenless, is required for the specification of the R7 photoreceptor cell during eye development. The c-ros subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 268 matched cddid_all.tbl CDD cd05045 cd05045 173631 PTKc_RET Catalytic domain of the Protein Tyrosine Kinase, REarranged during Transfection protein. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. RET is a receptor PTK (RTK) containing an extracellular region with four cadherin-like repeats, a calcium-binding site, and a cysteine-rich domain, a transmembrane segment, and an intracellular catalytic domain. It is part of a multisubunit complex that binds glial-derived neurotropic factor (GDNF) family ligands (GFLs) including GDNF, neurturin, artemin, and persephin. GFLs bind RET along with four GPI-anchored coreceptors, bringing two RET molecules together, leading to autophosphorylation, activation, and intracellular signaling. RET is essential for the development of the sympathetic, parasympathetic and enteric nervous systems, and the kidney. RET disruption by germline mutations causes diseases in humans including congenital aganglionosis of the gastrointestinal tract (Hirschsprung's disease) and three related inherited cancers: multiple endocrine neoplasia type 2A (MEN2A), MEN2B, and familial medullary thyroid carcinoma. The RET subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 290 matched cddid_all.tbl CDD cd05046 cd05046 133178 PTK_CCK4 Pseudokinase domain of the Protein Tyrosine Kinase, Colon Carcinoma Kinase 4. CCK4, also called protein tyrosine kinase 7 (PTK7), is an orphan receptor PTK (RTK) containing an extracellular region with seven immunoglobulin domains, a transmembrane segment, and an intracellular inactive pseudokinase domain, which shows similarity to tyr kinases but lacks crucial residues for catalytic activity and ATP binding. Studies in mice reveal that CCK4 is essential for neural development. Mouse embryos containing a truncated CCK4 die perinatally and display craniorachischisis, a severe form of neural tube defect. The mechanism of action of the CCK4 pseudokinase is still unknown. Other pseudokinases such as HER3 rely on the activity of partner RTKs. The CCK4 subfamily is part of a larger superfamily that includes other pseudokinases and the catalytic domains of active kinases including PTKs, protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 275 matched cddid_all.tbl CDD cd05047 cd05047 270641 PTKc_Tie Catalytic domain of Tie Protein Tyrosine Kinases. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Tie proteins, consisting of Tie1 and Tie2, are receptor PTKs (RTKs) containing an extracellular region, a transmembrane segment, and an intracellular catalytic domain. The extracellular region contains an immunoglobulin (Ig)-like domain, three epidermal growth factor (EGF)-like domains, a second Ig-like domain, and three fibronectin type III repeats. Tie receptors are specifically expressed in endothelial cells and hematopoietic stem cells. The angiopoietins (Ang-1 to Ang-4) serve as ligands for Tie2, while no specific ligand has been identified for Tie1. The binding of Ang-1 to Tie2 leads to receptor autophosphorylation and activation, promoting cell migration and survival. In contrast, Ang-2 binding to Tie2 does not result in the same response, suggesting that Ang-2 may function as an antagonist. In vivo studies of Tie1 show that it is critical in vascular development. The Tie subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 270 matched cddid_all.tbl CDD cd05048 cd05048 270642 PTKc_Ror Catalytic Domain of the Protein Tyrosine Kinases, Receptor tyrosine kinase-like Orphan Receptors. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. The Ror subfamily consists of Ror1, Ror2, and similar proteins. Ror proteins are orphan receptor PTKs (RTKs) containing an extracellular region with immunoglobulin-like, cysteine-rich, and kringle domains, a transmembrane segment, and an intracellular catalytic domain. Ror RTKs are unrelated to the nuclear receptor subfamily called retinoid-related orphan receptors (RORs). RTKs are usually activated through ligand binding, which causes dimerization and autophosphorylation of the intracellular tyr kinase catalytic domain. Ror kinases are expressed in many tissues during development. They play important roles in bone and heart formation. Mutations in human Ror2 result in two different bone development genetic disorders, recessive Robinow syndrome and brachydactyly type B. Drosophila Ror is expressed only in the developing nervous system during neurite outgrowth and neuronal differentiation, suggesting a role for Drosophila Ror in neural development. More recently, mouse Ror1 and Ror2 have also been found to play an important role in regulating neurite growth in central neurons. Ror1 and Ror2 are believed to have some overlapping and redundant functions. The Ror subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 283 matched cddid_all.tbl CDD cd05049 cd05049 270643 PTKc_Trk Catalytic domain of the Protein Tyrosine Kinases, Tropomyosin Related Kinases. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. The Trk subfamily consists of TrkA, TrkB, TrkC, and similar proteins. They are receptor PTKs (RTKs) containing an extracellular region with arrays of leucine-rich motifs flanked by two cysteine-rich clusters followed by two immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. Binding to their ligands, the nerve growth factor (NGF) family of neutrotrophins, leads to Trk receptor oligomerization and activation of the catalytic domain. Trk receptors are mainly expressed in the peripheral and central nervous systems. They play important roles in cell fate determination, neuronal survival and differentiation, as well as in the regulation of synaptic plasticity. Altered expression of Trk receptors is associated with many human diseases. The Trk subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 280 matched cddid_all.tbl CDD cd05050 cd05050 133181 PTKc_Musk Catalytic domain of the Protein Tyrosine Kinase, Muscle-specific kinase. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Musk is a receptor PTK (RTK) containing an extracellular region with four immunoglobulin-like domains and a cysteine-rich cluster, a transmembrane segment, and an intracellular catalytic domain. Musk is expressed and concentrated in the postsynaptic membrane in skeletal muscle. It is essential for the establishment of the neuromuscular junction (NMJ), a peripheral synapse that conveys signals from motor neurons to muscle cells. Agrin, a large proteoglycan released from motor neurons, stimulates Musk autophosphorylation and activation, leading to the clustering of acetylcholine receptors (AChRs). To date, there is no evidence to suggest that agrin binds directly to Musk. Mutations in AChR, Musk and other partners are responsible for diseases of the NMJ, such as the autoimmune syndrome myasthenia gravis. The Musk subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 288 matched cddid_all.tbl CDD cd05051 cd05051 270644 PTKc_DDR Catalytic domain of the Protein Tyrosine Kinases, Discoidin Domain Receptors. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. The DDR subfamily consists of homologs of mammalian DDR1, DDR2, and similar proteins. They are receptor PTKs (RTKs) containing an extracellular discoidin homology domain, a transmembrane segment, an extended juxtamembrane region, and an intracellular catalytic domain. The binding of the ligand, collagen, to DDRs results in a slow but sustained receptor activation. DDRs regulate cell adhesion, proliferation, and extracellular matrix remodeling. They have been linked to a variety of human cancers including breast, colon, ovarian, brain, and lung. There is no evidence showing that DDRs act as transforming oncogenes. They are more likely to play a role in the regulation of tumor growth and metastasis. The DDR subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 297 matched cddid_all.tbl CDD cd05052 cd05052 270645 PTKc_Abl Catalytic domain of the Protein Tyrosine Kinase, Abelson kinase. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Abl (or c-Abl) is a ubiquitously-expressed cytoplasmic (or nonreceptor) PTK that contains SH3, SH2, and tyr kinase domains in its N-terminal region, as well as nuclear localization motifs, a putative DNA-binding domain, and F- and G-actin binding domains in its C-terminal tail. It also contains a short autoinhibitory cap region in its N-terminus. Abl function depends on its subcellular localization. In the cytoplasm, Abl plays a role in cell proliferation and survival. In response to DNA damage or oxidative stress, Abl is transported to the nucleus where it induces apoptosis. In chronic myelogenous leukemia (CML) patients, an aberrant translocation results in the replacement of the first exon of Abl with the BCR (breakpoint cluster region) gene. The resulting BCR-Abl fusion protein is constitutively active and associates into tetramers, resulting in a hyperactive kinase sending a continuous signal. This leads to uncontrolled proliferation, morphological transformation and anti-apoptotic effects. BCR-Abl is the target of selective inhibitors, such as imatinib (Gleevec), used in the treatment of CML. Abl2, also known as ARG (Abelson-related gene), is thought to play a cooperative role with Abl in the proper development of the nervous system. The Tel-ARG fusion protein, resulting from reciprocal translocation between chromosomes 1 and 12, is associated with acute myeloid leukemia (AML). The TEL gene is a frequent fusion partner of other tyr kinase oncogenes, including Tel/Abl, Tel/PDGFRbeta, and Tel/Jak2, found in patients with leukemia and myeloproliferative disorders. The Abl subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 263 matched cddid_all.tbl CDD cd05053 cd05053 270646 PTKc_FGFR Catalytic domain of the Protein Tyrosine Kinases, Fibroblast Growth Factor Receptors. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. The FGFR subfamily consists of FGFR1, FGFR2, FGFR3, FGFR4, and similar proteins. They are receptor PTKs (RTKs) containing an extracellular ligand-binding region with three immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of FGFRs to their ligands, the FGFs, and to heparin/heparan sulfate (HS) results in the formation of a ternary complex, which leads to receptor dimerization and activation, and intracellular signaling. There are at least 23 FGFs and four types of FGFRs. The binding of FGFs to FGFRs is promiscuous, in that a receptor may be activated by several ligands and a ligand may bind to more that one type of receptor. FGF/FGFR signaling is important in the regulation of embryonic development, homeostasis, and regenerative processes. Depending on the cell type and stage, FGFR signaling produces diverse cellular responses including proliferation, growth arrest, differentiation, and apoptosis. Aberrant signaling leads to many human diseases such as skeletal, olfactory, and metabolic disorders, as well as cancer. The FGFR subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase . 294 matched cddid_all.tbl CDD cd05054 cd05054 270647 PTKc_VEGFR Catalytic domain of the Protein Tyrosine Kinases, Vascular Endothelial Growth Factor Receptors. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. The VEGFR subfamily consists of VEGFR1 (Flt1), VEGFR2 (Flk1), VEGFR3 (Flt4), and similar proteins. VEGFR subfamily members are receptor PTKss (RTKs) containing an extracellular ligand-binding region with seven immunoglobulin (Ig)-like domains, a transmembrane segment, and an intracellular catalytic domain. In VEGFR3, the fifth Ig-like domain is replaced by a disulfide bridge. The binding of VEGFRs to their ligands, the VEGFs, leads to receptor dimerization, activation, and intracellular signaling. There are five VEGF ligands in mammals, which bind, in an overlapping pattern to the three VEGFRs, which can form homo or heterodimers. VEGFRs regulate the cardiovascular system. They are critical for vascular development during embryogenesis and blood vessel formation in adults. They induce cellular functions common to other growth factor receptors such as cell migration, survival, and proliferation. The VEGFR subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 298 matched cddid_all.tbl CDD cd05055 cd05055 133186 PTKc_PDGFR Catalytic domain of the Protein Tyrosine Kinases, Platelet Derived Growth Factor Receptors. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. The PDGFR subfamily consists of PDGFR alpha, PDGFR beta, KIT, CSF-1R, the mammalian FLT3, and similar proteins. They are receptor PTKs (RTKs) containing an extracellular ligand-binding region with five immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. PDGFR kinase domains are autoinhibited by their juxtamembrane regions containing tyr residues. The binding to their ligands leads to receptor dimerization, trans phosphorylation and activation, and intracellular signaling. PDGFR subfamily receptors are important in the development of a variety of cells. PDGFRs are expressed in a many cells including fibroblasts, neurons, endometrial cells, mammary epithelial cells, and vascular smooth muscle cells. PDGFR signaling is critical in normal embryonic development, angiogenesis, and wound healing. Kit is important in the development of melanocytes, germ cells, mast cells, hematopoietic stem cells, the interstitial cells of Cajal, and the pacemaker cells of the GI tract. CSF-1R signaling is critical in the regulation of macrophages and osteoclasts. Mammalian FLT3 plays an important role in the survival, proliferation, and differentiation of stem cells. The PDGFR subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase . 302 matched cddid_all.tbl CDD cd05056 cd05056 133187 PTKc_FAK Catalytic domain of the Protein Tyrosine Kinase, Focal Adhesion Kinase. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. FAK is a cytoplasmic (or nonreceptor) PTK that contains an autophosphorylation site and a FERM domain at the N-terminus, a central tyr kinase domain, proline-rich regions, and a C-terminal FAT (focal adhesion targeting) domain. FAK activity is dependent on integrin-mediated cell adhesion, which facilitates N-terminal autophosphorylation. Full activation is achieved by the phosphorylation of its two adjacent A-loop tyrosines. FAK is important in mediating signaling initiated at sites of cell adhesions and at growth factor receptors. Through diverse molecular interactions, FAK functions as a biosensor or integrator to control cell motility. It is a key regulator of cell survival, proliferation, migration and invasion, and thus plays an important role in the development and progression of cancer. Src binds to autophosphorylated FAK forming the FAK-Src dual kinase complex, which is activated in a wide variety of tumor cells and generates signals promoting growth and metastasis. FAK is being developed as a target for cancer therapy. The FAK subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 270 matched cddid_all.tbl CDD cd05057 cd05057 270648 PTKc_EGFR_like Catalytic domain of Epidermal Growth Factor Receptor-like Protein Tyrosine Kinases. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. EGFR (HER, ErbB) subfamily members include EGFR (HER1, ErbB1), HER2 (ErbB2), HER3 (ErbB3), HER4 (ErbB4), and similar proteins. They are receptor PTKs (RTKs) containing an extracellular EGF-related ligand-binding region, a transmembrane helix, and a cytoplasmic region with a tyr kinase domain and a regulatory C-terminal tail. Unlike other PTKs, phosphorylation of the activation loop of EGFR proteins is not critical to their activation. Instead, they are activated by ligand-induced dimerization, resulting in the phosphorylation of tyr residues in the C-terminal tail, which serve as binding sites for downstream signaling molecules. Collectively, they can recognize a variety of ligands including EGF, TGFalpha, and neuregulins, among others. All four subfamily members can form homo- or heterodimers. HER3 contains an impaired kinase domain and depends on its heterodimerization partner for activation. EGFR subfamily members are involved in signaling pathways leading to a broad range of cellular responses including cell proliferation, differentiation, migration, growth inhibition, and apoptosis. Gain of function alterations, through their overexpression, deletions, or point mutations in their kinase domains, have been implicated in various cancers. These receptors are targets of many small molecule inhibitors and monoclonal antibodies used in cancer therapy. The EGFR subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 279 matched cddid_all.tbl CDD cd05058 cd05058 270649 PTKc_Met_Ron Catalytic domain of the Protein Tyrosine Kinases, Met and Ron. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Met and Ron are receptor PTKs (RTKs) composed of an alpha-beta heterodimer. The extracellular alpha chain is disulfide linked to the beta chain, which contains an extracellular ligand-binding region with a sema domain, a PSI domain and four IPT repeats, a transmembrane segment, and an intracellular catalytic domain. Binding to their ligands leads to receptor dimerization, autophosphorylation, activation, and intracellular signaling. Met binds to the ligand, hepatocyte growth factor/scatter factor (HGF/SF), and is also called the HGF receptor. HGF/Met signaling plays a role in growth, transformation, cell motility, invasion, metastasis, angiogenesis, wound healing, and tissue regeneration. Aberrant expression of Met through mutations or gene amplification is associated with many human cancers including hereditary papillary renal and gastric carcinomas. The ligand for Ron is macrophage stimulating protein (MSP). Ron signaling is important in regulating cell motility, adhesion, proliferation, and apoptosis. Aberrant Ron expression is implicated in tumorigenesis and metastasis. The Met/Ron subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 262 matched cddid_all.tbl CDD cd05059 cd05059 173637 PTKc_Tec_like Catalytic domain of Tec-like Protein Tyrosine Kinases. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. The Tec-like subfamily is composed of Tec, Btk, Bmx (Etk), Itk (Tsk, Emt), Rlk (Txk), and similar proteins. They are cytoplasmic (or nonreceptor) PTKs with similarity to Src kinases in that they contain Src homology protein interaction domains (SH3, SH2) N-terminal to the catalytic tyr kinase domain. Unlike Src kinases, most Tec subfamily members except Rlk also contain an N-terminal pleckstrin homology (PH) domain, which binds the products of PI3K and allows membrane recruitment and activation. In addition, some members contain the Tec homology (TH) domain, which contains proline-rich and zinc-binding regions. Tec kinases form the second largest subfamily of nonreceptor PTKs and are expressed mainly by haematopoietic cells, although Tec and Bmx are also found in endothelial cells. B-cells express Btk and Tec, while T-cells express Itk, Txk, and Tec. Collectively, Tec kinases are expressed in a variety of myeloid cells such as mast cells, platelets, macrophages, and dendritic cells. Each Tec kinase shows a distinct cell-type pattern of expression. Tec kinases play important roles in the development, differentiation, maturation, regulation, survival, and function of B-cells and T-cells. Mutations in Btk cause the severe B-cell immunodeficiency, X-linked agammaglobulinaemia (XLA). The Tec-like subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd05060 cd05060 270650 PTKc_Syk_like Catalytic domain of Spleen Tyrosine Kinase-like Protein Tyrosine Kinases. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. The Syk-like subfamily is composed of Syk, ZAP-70, Shark, and similar proteins. They are cytoplasmic (or nonreceptor) PTKs containing two Src homology 2 (SH2) domains N-terminal to the catalytic tyr kinase domain. They are involved in the signaling downstream of activated receptors (including B-cell, T-cell, and Fc receptors) that contain ITAMs (immunoreceptor tyr activation motifs), leading to processes such as cell proliferation, differentiation, survival, adhesion, migration, and phagocytosis. Syk is important in B-cell receptor signaling, while Zap-70 is primarily expressed in T-cells and NK cells, and is a crucial component in T-cell receptor signaling. Syk also plays a central role in Fc receptor-mediated phagocytosis in the adaptive immune system. Shark is exclusively expressed in ectodermally derived epithelia, and is localized preferentially to the apical surface of the epithelial cells, it may play a role in a signaling pathway for epithelial cell polarity. The Syk-like subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 257 matched cddid_all.tbl CDD cd05061 cd05061 133192 PTKc_InsR Catalytic domain of the Protein Tyrosine Kinase, Insulin Receptor. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. InsR is a receptor PTK (RTK) that is composed of two alphabeta heterodimers. Binding of the insulin ligand to the extracellular alpha subunit activates the intracellular tyr kinase domain of the transmembrane beta subunit. Receptor activation leads to autophosphorylation, stimulating downstream kinase activities, which initiate signaling cascades and biological function. InsR signaling plays an important role in many cellular processes including glucose homeostasis, glycogen synthesis, lipid and protein metabolism, ion and amino acid transport, cell cycle and proliferation, cell differentiation, gene transcription, and nitric oxide synthesis. Insulin resistance, caused by abnormalities in InsR signaling, has been described in diabetes, hypertension, cardiovascular disease, metabolic syndrome, heart failure, and female infertility. The InsR subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 288 matched cddid_all.tbl CDD cd05062 cd05062 133193 PTKc_IGF-1R Catalytic domain of the Protein Tyrosine Kinase, Insulin-like Growth Factor-1 Receptor. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. IGF-1R is a receptor PTK (RTK) that is composed of two alphabeta heterodimers. Binding of the ligand (IGF-1 or IGF-2) to the extracellular alpha subunit activates the intracellular tyr kinase domain of the transmembrane beta subunit. Receptor activation leads to autophosphorylation, which stimulates downstream kinase activities and biological function. IGF-1R signaling is important in the differentiation, growth, and survival of normal cells. In cancer cells, where it is frequently overexpressed, IGF-1R is implicated in proliferation, the suppression of apoptosis, invasion, and metastasis. IGF-1R is being developed as a therapeutic target in cancer treatment. The IGF-1R subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 277 matched cddid_all.tbl CDD cd05063 cd05063 133194 PTKc_EphR_A2 Catalytic domain of the Protein Tyrosine Kinase, Ephrin Receptor A2. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. The EphA2 receptor is overexpressed in tumor cells and tumor blood vessels in a variety of cancers including breast, prostate, lung, and colon. As a result, it is an attractive target for drug design since its inhibition could affect several aspects of tumor progression. EphRs comprise the largest subfamily of receptor PTKs (RTKs). Class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. EphRs contain an ephrin binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyr kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). Ephrin/EphR interaction mainly results in cell-cell repulsion or adhesion, making it important in neural development and plasticity, cell morphogenesis, cell-fate determination, embryonic development, tissue patterning, and angiogenesis. The EphA2 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). 268 matched cddid_all.tbl CDD cd05064 cd05064 133195 PTKc_EphR_A10 Catalytic domain of the Protein Tyrosine Kinase, Ephrin Receptor A10. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. EphA10, which contains an inactive tyr kinase domain, may function to attenuate signals of co-clustered active receptors. EphA10 is mainly expressed in the testis. Ephrin/EphR interaction results in cell-cell repulsion or adhesion, making it important in neural development and plasticity, cell morphogenesis, cell-fate determination, embryonic development, tissue patterning, and angiogenesis. EphRs comprise the largest subfamily of receptor tyr kinases (RTKs). In general, class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. EphRs contain an ephrin binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyr kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). The EphA10 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 266 matched cddid_all.tbl CDD cd05065 cd05065 173638 PTKc_EphR_B Catalytic domain of the Protein Tyrosine Kinases, Class EphB Ephrin Receptors. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Class EphB receptors bind to transmembrane ephrin-B ligands. There are six vertebrate EphB receptors (EphB1-6), which display promiscuous interactions with three ephrin-B ligands. One exception is EphB2, which also interacts with ephrin A5. EphB receptors play important roles in synapse formation and plasticity, spine morphogenesis, axon guidance, and angiogenesis. In the intestinal epithelium, EphBs are Wnt signaling target genes that control cell compartmentalization. They function as suppressors of colon cancer progression. EphRs comprise the largest subfamily of receptor PTKs (RTKs). They contain an ephrin-binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyr kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). Ephrin/EphR interaction mainly results in cell-cell repulsion or adhesion. The EphB subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 269 matched cddid_all.tbl CDD cd05066 cd05066 270651 PTKc_EphR_A Catalytic domain of the Protein Tyrosine Kinases, Class EphA Ephrin Receptors. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. This subfamily is composed of most class EphA receptors including EphA3, EphA4, EphA5, and EphA7, but excluding EphA1, EphA2 and EphA10. Class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. One exception is EphA4, which also binds ephrins-B2/B3. EphA receptors and ephrin-A ligands are expressed in multiple areas of the developing brain, especially in the retina and tectum. They are part of a system controlling retinotectal mapping. EphRs comprise the largest subfamily of receptor PTKs (RTKs). EphRs contain an ephrin-binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyr kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). Ephrin/EphR interaction mainly results in cell-cell repulsion or adhesion, making it important in neural development and plasticity, cell morphogenesis, cell-fate determination, embryonic development, tissue patterning, and angiogenesis. The EphA subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 267 matched cddid_all.tbl CDD cd05067 cd05067 270652 PTKc_Lck_Blk Catalytic domain of the Protein Tyrosine Kinases, Lymphocyte-specific kinase and Blk. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Lck and Blk are members of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) PTKs. Lck is expressed in T-cells and natural killer cells. It plays a critical role in T-cell maturation, activation, and T-cell receptor (TCR) signaling. Lck phosphorylates ITAM (immunoreceptor tyr activation motif) sequences on several subunits of TCRs, leading to the activation of different second messenger cascades. Phosphorylated ITAMs serve as binding sites for other signaling factor such as Syk and ZAP-70, leading to their activation and propagation of downstream events. In addition, Lck regulates drug-induced apoptosis by interfering with the mitochondrial death pathway. The apototic role of Lck is independent of its primary function in T-cell signaling. Blk is expressed specifically in B-cells. It is involved in pre-BCR (B-cell receptor) signaling. Src kinases contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). The Lck/Blk subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 264 matched cddid_all.tbl CDD cd05068 cd05068 270653 PTKc_Frk_like Catalytic domain of Fyn-related kinase-like Protein Tyrosine Kinases. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Frk and Srk are members of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) PTKs. Frk, also known as Rak, is specifically expressed in liver, lung, kidney, intestine, mammary glands, and the islets of Langerhans. Rodent homologs were previously referred to as GTK (gastrointestinal tyr kinase), BSK (beta-cell Src-like kinase), or IYK (intestinal tyr kinase). Studies in mice reveal that Frk is not essential for viability. It plays a role in the signaling that leads to cytokine-induced beta-cell death in Type I diabetes. It also regulates beta-cell number during embryogenesis and early in life. Src kinases contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). The Frk-like subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 267 matched cddid_all.tbl CDD cd05069 cd05069 270654 PTKc_Yes Catalytic domain of the Protein Tyrosine Kinase, Yes. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Yes (or c-Yes) is a member of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) PTKs. c-Yes kinase is the cellular homolog of the oncogenic protein (v-Yes) encoded by the Yamaguchi 73 and Esh sarcoma viruses. It displays functional overlap with other Src subfamily members, particularly Src. It also shows some unique functions such as binding to occludins, transmembrane proteins that regulate extracellular interactions in tight junctions. Yes also associates with a number of proteins in different cell types that Src does not interact with, like JAK2 and gp130 in pre-adipocytes, and Pyk2 in treated pulmonary vein endothelial cells. Although the biological function of Yes remains unclear, it appears to have a role in regulating cell-cell interactions and vesicle trafficking in polarized cells. Src kinases contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). The Yes subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). 279 matched cddid_all.tbl CDD cd05070 cd05070 270655 PTKc_Fyn Catalytic domain of the Protein Tyrosine Kinase, Fyn. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Fyn and Yrk are members of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) PTKs. Fyn, together with Lck, plays a critical role in T-cell signal transduction by phosphorylating ITAM (immunoreceptor tyr activation motif) sequences on T-cell receptors, ultimately leading to the proliferation and differentiation of T-cells. In addition, Fyn is involved in the myelination of neurons, and is implicated in Alzheimer's and Parkinson's diseases. Src kinases contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). The Fyn/Yrk subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase. 274 matched cddid_all.tbl CDD cd05071 cd05071 270656 PTKc_Src Catalytic domain of the Protein Tyrosine Kinase, Src. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Src (or c-Src) is a cytoplasmic (or non-receptor) PTK, containing an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region with a conserved tyr. It is activated by autophosphorylation at the tyr kinase domain, and is negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). c-Src is the vertebrate homolog of the oncogenic protein (v-Src) from Rous sarcoma virus. Together with other Src subfamily proteins, it is involved in signaling pathways that regulate cytokine and growth factor responses, cytoskeleton dynamics, cell proliferation, survival, and differentiation. Src also play a role in regulating cell adhesion, invasion, and motility in cancer cells and tumor vasculature, contributing to cancer progression and metastasis. Elevated levels of Src kinase activity have been reported in a variety of human cancers. Several inhibitors of Src have been developed as anti-cancer drugs. Src is also implicated in acute inflammatory responses and osteoclast function. The Src subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 277 matched cddid_all.tbl CDD cd05072 cd05072 270657 PTKc_Lyn Catalytic domain of the Protein Tyrosine Kinase, Lyn. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Lyn is a member of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) PTKs. Lyn is expressed in B lymphocytes and myeloid cells. It exhibits both positive and negative regulatory roles in B cell receptor (BCR) signaling. Lyn, as well as Fyn and Blk, promotes B cell activation by phosphorylating ITAMs (immunoreceptor tyr activation motifs) in CD19 and in Ig components of BCR. It negatively regulates signaling by its unique ability to phosphorylate ITIMs (immunoreceptor tyr inhibition motifs) in cell surface receptors like CD22 and CD5. Lyn also plays an important role in G-CSF receptor signaling by phosphorylating a variety of adaptor molecules. Src kinases contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). The Lyn subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 272 matched cddid_all.tbl CDD cd05073 cd05073 270658 PTKc_Hck Catalytic domain of the Protein Tyrosine Kinase, Hematopoietic cell kinase. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Hck is a member of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) PTKs. Hck is present in myeloid and lymphoid cells that play a role in the development of cancer. It may be important in the oncogenic signaling of the protein Tel-Abl, which induces a chronic myelogenous leukemia (CML)-like disease. Hck also acts as a negative regulator of G-CSF-induced proliferation of granulocytic precursors, suggesting a possible role in the development of acute myeloid leukemia (AML). In addition, Hck is essential in regulating the degranulation of polymorphonuclear leukocytes. Genetic polymorphisms affect the expression level of Hck, which affects PMN mediator release and influences the development of chronic obstructive pulmonary disease (COPD). Src kinases contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). The Hck subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 265 matched cddid_all.tbl CDD cd05074 cd05074 270659 PTKc_Tyro3 Catalytic domain of the Protein Tyrosine Kinase, Tyro3. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Tyro3 (or Sky) is predominantly expressed in the central nervous system and the brain, and functions as a neurotrophic factor. It is also expressed in osteoclasts and has a role in bone resorption. Tyro3 is a member of the TAM subfamily, composed of receptor PTKs (RTKs) containing an extracellular ligand-binding region with two immunoglobulin-like domains followed by two fibronectin type III repeats, a transmembrane segment, and an intracellular catalytic domain. Binding to their ligands, Gas6 and protein S, leads to receptor dimerization, autophosphorylation, activation, and intracellular signaling. The Tyro3 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 284 matched cddid_all.tbl CDD cd05075 cd05075 270660 PTKc_Axl Catalytic domain of the Protein Tyrosine Kinase, Axl. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Axl is widely expressed in a variety of organs and cells including epithelial, mesenchymal, hematopoietic, as well as non-transformed cells. It is important in many cellular functions such as survival, anti-apoptosis, proliferation, migration, and adhesion. Axl was originally isolated from patients with chronic myelogenous leukemia and a chronic myeloproliferative disorder. It is overexpressed in many human cancers including colon, squamous cell, thyroid, breast, and lung carcinomas. Axl is a member of the TAM subfamily, composed of receptor PTKs (RTKs) containing an extracellular ligand-binding region with two immunoglobulin-like domains followed by two fibronectin type III repeats, a transmembrane segment, and an intracellular catalytic domain. Binding to its ligands, Gas6 and protein S, leads to receptor dimerization, autophosphorylation, activation, and intracellular signaling. The Axl subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 277 matched cddid_all.tbl CDD cd05076 cd05076 270661 PTK_Tyk2_rpt1 Pseudokinase (repeat 1) domain of the Protein Tyrosine Kinase, Tyrosine kinase 2. Tyk2 is widely expressed in many tissues. It is involved in signaling via the cytokine receptors IFN-alphabeta, IL-6, IL-10, IL-12, IL-13, and IL-23. It mediates cell surface urokinase receptor (uPAR) signaling and plays a role in modulating vascular smooth muscle cell (VSMC) functional behavior in response to injury. Tyk2 is also important in dendritic cell function and T helper (Th)1 cell differentiation. A homozygous mutation of Tyk2 was found in a patient with hyper-IgE syndrome (HIES), a primary immunodeficiency characterized by recurrent skin abscesses, pneumonia, and elevated serum IgE. This suggests that Tyk2 may play important roles in multiple cytokine signaling involved in innate and adaptive immunity. Tyk2 is a member of the Janus kinase (Jak) subfamily of proteins, which are cytoplasmic (or nonreceptor) PTKs containing an N-terminal FERM domain, followed by a Src homology 2 (SH2) domain, a pseudokinase domain, and a C-terminal tyr kinase domain. The pseudokinase domain shows similarity to tyr kinases but lacks crucial residues for catalytic activity and ATP binding. It modulates the kinase activity of the C-terminal catalytic domain. The Tyk2 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 273 matched cddid_all.tbl CDD cd05077 cd05077 270662 PTK_Jak1_rpt1 Pseudokinase (repeat 1) domain of the Protein Tyrosine Kinase, Janus kinase 1. Jak1 is widely expressed in many tissues. Many cytokines are dependent on Jak1 for signaling, including those that use the shared receptor subunits, common gamma chain (IL-2, IL-4, IL-7, IL-9, IL-15, IL-21) and gp130 (IL-6, IL-11, oncostatin M, G-CSF, and IFNs, among others). The many varied interactions of Jak1 and its ubiquitous expression suggest many biological roles. Jak1 is important in neurological development, as well as in lymphoid development and function. It also plays a role in the pathophysiology of cardiac hypertrophy and heart failure. A mutation in the ATP-binding site of Jak1 was identified in a human uterine leiomyosarcoma cell line, resulting in defective cytokine induction and antigen presentation, thus allowing the tumor to evade the immune system. Jak1 is a cytoplasmic (or nonreceptor) PTK containing an N-terminal FERM domain, followed by a Src homology 2 (SH2) domain, a pseudokinase domain, and a C-terminal tyr kinase domain. The pseudokinase domain shows similarity to tyr kinases but lacks crucial residues for catalytic activity and ATP binding. It modulates the kinase activity of the C-terminal catalytic domain. The Jak1 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 266 matched cddid_all.tbl CDD cd05078 cd05078 270663 PTK_Jak2_rpt1 Pseudokinase (repeat 1) domain of the Protein Tyrosine Kinase, Janus kinase 2. Jak2 is widely expressed in many tissues. It is essential for the signaling of hormone-like cytokines such as growth hormone, erythropoietin, thrombopoietin, and prolactin, as well as some IFNs and cytokines that signal through the IL-3 and gp130 receptors. Disruption of Jak2 in mice results in an embryonic lethal phenotype with multiple defects including erythropoietic and cardiac abnormalities. It is the only Jak gene that results in a lethal phenotype when disrupted in mice. A mutation in the pseudokinase domain of Jak2, V617F, is present in many myeloproliferative diseases, including almost all patients with polycythemia vera, and 50% of patients with essential thrombocytosis and myelofibrosis. Jak2 is a cytoplasmic (or nonreceptor) PTK containing an N-terminal FERM domain, followed by a Src homology 2 (SH2) domain, a pseudokinase domain, and a C-terminal tyr kinase domain. The pseudokinase domain shows similarity to tyr kinases but lacks crucial residues for catalytic activity and ATP binding. Despite this, the presumed pseudokinase (repeat 1) domain of Jak2 exhibits dual-specificity kinase activity, phosphorylating two negative regulatory sites in Jak2: Ser523 and Tyr570. Inactivation of the repeat 1 domain increased Jak2 basal activity, suggesting that it modulates the kinase activity of the C-terminal catalytic (repeat 2) domain. The Jak2 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 262 matched cddid_all.tbl CDD cd05079 cd05079 173644 PTKc_Jak1_rpt2 Catalytic (repeat 2) domain of the Protein Tyrosine Kinase, Janus kinase 1. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Jak1 is widely expressed in many tissues. Many cytokines are dependent on Jak1 for signaling, including those that use the shared receptor subunits common gamma chain (IL-2, IL-4, IL-7, IL-9, IL-15, IL-21) and gp130 (IL-6, IL-11, oncostatin M, G-CSF, and IFNs, among others). The many varied interactions of Jak1 and its ubiquitous expression suggest many biological roles. Jak1 is important in neurological development, as well as in lymphoid development and function. It also plays a role in the pathophysiology of cardiac hypertrophy and heart failure. A mutation in the ATP-binding site of Jak1 was identified in a human uterine leiomyosarcoma cell line, resulting in defective cytokine induction and antigen presentation, thus allowing the tumor to evade the immune system. Jak1 is a member of the Janus kinase (Jak) subfamily of proteins, which are cytoplasmic (or nonreceptor) PTKs containing an N-terminal FERM domain, followed by a Src homology 2 (SH2) domain, a pseudokinase domain, and a C-terminal tyr kinase domain. Jaks are crucial for cytokine receptor signaling. They are activated by autophosphorylation upon cytokine-induced receptor aggregation, and subsequently trigger downstream signaling events such as the phosphorylation of signal transducers and activators of transcription (STATs). The Jak1 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 284 matched cddid_all.tbl CDD cd05080 cd05080 270664 PTKc_Tyk2_rpt2 Catalytic (repeat 2) domain of the Protein Tyrosine Kinase, Tyrosine kinase 2. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Tyk2 is widely expressed in many tissues. It is involved in signaling via the cytokine receptors IFN-alphabeta, IL-6, IL-10, IL-12, IL-13, and IL-23. It mediates cell surface urokinase receptor (uPAR) signaling and plays a role in modulating vascular smooth muscle cell (VSMC) functional behavior in response to injury. Tyk2 is also important in dendritic cell function and T helper (Th)1 cell differentiation. A homozygous mutation of Tyk2 was found in a patient with hyper-IgE syndrome (HIES), a primary immunodeficiency characterized by recurrent skin abscesses, pneumonia, and elevated serum IgE. This suggests that Tyk2 may play important roles in multiple cytokine signaling involved in innate and adaptive immunity. Tyk2 is a member of the Janus kinase (Jak) subfamily of proteins, which are cytoplasmic (or nonreceptor) PTKs containing an N-terminal FERM domain, followed by a Src homology 2 (SH2) domain, a pseudokinase domain, and a C-terminal tyr kinase catalytic domain. Jaks are crucial for cytokine receptor signaling. They are activated by autophosphorylation upon cytokine-induced receptor aggregation, and subsequently trigger downstream signaling events such as the phosphorylation of signal transducers and activators of transcription (STATs). The Tyk2 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 283 matched cddid_all.tbl CDD cd05081 cd05081 270665 PTKc_Jak3_rpt2 Catalytic (repeat 2) domain of the Protein Tyrosine Kinase, Janus kinase 3. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Jak3 is expressed only in hematopoietic cells. It binds the shared receptor subunit common gamma chain and thus, is essential in the signaling of cytokines that use it such as IL-2, IL-4, IL-7, IL-9, IL-15, and IL-21. Jak3 is important in lymphoid development and myeloid cell differentiation. Inactivating mutations in Jak3 have been reported in humans with severe combined immunodeficiency (SCID). Jak3 is a member of the Janus kinase (Jak) subfamily of proteins, which are cytoplasmic (or nonreceptor) PTKs containing an N-terminal FERM domain, followed by a Src homology 2 (SH2) domain, a pseudokinase domain, and a C-terminal catalytic tyr kinase domain. Jaks are crucial for cytokine receptor signaling. They are activated by autophosphorylation upon cytokine-induced receptor aggregation, and subsequently trigger downstream signaling events such as the phosphorylation of signal transducers and activators of transcription (STATs). The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 283 matched cddid_all.tbl CDD cd05082 cd05082 133213 PTKc_Csk Catalytic domain of the Protein Tyrosine Kinase, C-terminal Src kinase. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Csk catalyzes the tyr phosphorylation of the regulatory C-terminal tail of Src kinases, resulting in their inactivation. Csk is expressed in a wide variety of tissues. As a negative regulator of Src, Csk plays a role in cell proliferation, survival, and differentiation, and consequently, in cancer development and progression. Csk is a cytoplasmic (or nonreceptor) PTK containing the Src homology domains, SH3 and SH2, N-terminal to the catalytic tyr kinase domain. To inhibit Src kinases, Csk is translocated to the membrane via binding to specific transmembrane proteins, G-proteins, or adaptor proteins near the membrane. In addition, Csk also shows Src-independent functions. It is a critical component in G-protein signaling, and plays a role in cytoskeletal reorganization and cell migration. The Csk subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd05083 cd05083 270666 PTKc_Chk Catalytic domain of the Protein Tyrosine Kinase, Csk homologous kinase. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Chk is also referred to as megakaryocyte-associated tyrosine kinase (Matk). Chk inhibits Src kinases using a noncatalytic mechanism by simply binding to them. As a negative regulator of Src kinases, Chk may play important roles in cell proliferation, survival, and differentiation, and consequently, in cancer development and progression. Chk is expressed in brain and hematopoietic cells. Like Csk, it is a cytoplasmic (or nonreceptor) tyr kinase containing the Src homology domains, SH3 and SH2, N-terminal to the catalytic tyr kinase domain. To inhibit Src kinases that are anchored to the plasma membrane, Chk is translocated to the membrane via binding to specific transmembrane proteins, G-proteins, or adaptor proteins near the membrane. Studies in mice reveal that Chk is not functionally redundant with Csk and that it plays an important role as a regulator of immune responses. Chk also plays a role in neural differentiation in a manner independent of Src by enhancing Mapk activation via Ras-mediated signaling. The Chk subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 254 matched cddid_all.tbl CDD cd05084 cd05084 270667 PTKc_Fes Catalytic domain of the Protein Tyrosine Kinase, Fes. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Fes (or Fps) is a cytoplasmic (or nonreceptor) PTK containing an N-terminal region with FCH (Fes/Fer/CIP4 homology) and coiled-coil domains, followed by a SH2 domain, and a C-terminal catalytic domain. The genes for Fes (feline sarcoma) and Fps (Fujinami poultry sarcoma) were first isolated from tumor-causing retroviruses. The viral oncogenes encode chimeric Fes proteins consisting of Gag sequences at the N-termini, resulting in unregulated PTK activity. Fes kinase is expressed in myeloid, vascular endothelial, epithelial, and neuronal cells. It plays important roles in cell growth and differentiation, angiogenesis, inflammation and immunity, and cytoskeletal regulation. A recent study implicates Fes kinase as a tumor suppressor in colorectal cancer. The Fes subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 252 matched cddid_all.tbl CDD cd05085 cd05085 270668 PTKc_Fer Catalytic domain of the Protein Tyrosine Kinase, Fer. Protein Tyrosine Kinase (PTK) family; Fer kinase; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Fer kinase is a member of the Fes subfamily of proteins which are cytoplasmic (or nonreceptor) tyr kinases containing an N-terminal region with FCH (Fes/Fer/CIP4 homology) and coiled-coil domains, followed by a SH2 domain, and a C-terminal catalytic domain. Fer kinase is expressed in a wide variety of tissues, and is found to reside in both the cytoplasm and the nucleus. It plays important roles in neuronal polarization and neurite development, cytoskeletal reorganization, cell migration, growth factor signaling, and the regulation of cell-cell interactions mediated by adherens junctions and focal adhesions. Fer kinase also regulates cell cycle progression in malignant cells. 251 matched cddid_all.tbl CDD cd05086 cd05086 270669 PTKc_Aatyk2 Catalytic domain of the Protein Tyrosine Kinase, Apoptosis-associated tyrosine kinase 2. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Aatyk2 is a member of the Aatyk subfamily of proteins, which are receptor kinases containing a transmembrane segment and a long C-terminal cytoplasmic tail with a catalytic domain. Aatyk2 is also called lemur tyrosine kinase 2 (Lmtk2) or brain-enriched kinase (Brek). It is expressed at high levels in early postnatal brain, and has been shown to play a role in nerve growth factor (NGF) signaling. Studies with knockout mice reveal that Aatyk2 is essential for late stage spermatogenesis. Although it is classified as a PTK based on sequence similarity and the phylogenetic tree, Aatyk2 has been functionally characterized as a serine/threonine kinase. The Aatyk2 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 271 matched cddid_all.tbl CDD cd05087 cd05087 270670 PTKc_Aatyk1 Catalytic domain of the Protein Tyrosine Kinases, Apoptosis-associated tyrosine kinase 1. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Aatyk1 (or simply Aatyk) is also called lemur tyrosine kinase 1 (Lmtk1). It is a cytoplasmic (or nonreceptor) kinase containing a long C-terminal region. The expression of Aatyk1 is upregulated during growth arrest and apoptosis in myeloid cells. Aatyk1 has been implicated in neural differentiation, and is a regulator of the Na-K-2Cl cotransporter, a membrane protein involved in cell proliferation and survival, epithelial transport, and blood pressure control. The Aatyk1 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 271 matched cddid_all.tbl CDD cd05088 cd05088 133219 PTKc_Tie2 Catalytic domain of the Protein Tyrosine Kinase, Tie2. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Tie2 is a receptor PTK (RTK) containing an extracellular region, a transmembrane segment, and an intracellular catalytic domain. The extracellular region contains an immunoglobulin (Ig)-like domain, three epidermal growth factor (EGF)-like domains, a second Ig-like domain, and three fibronectin type III repeats. Tie2 is expressed mainly in endothelial cells and hematopoietic stem cells. It is also found in a subset of tumor-associated monocytes and eosinophils. The angiopoietins (Ang-1 to Ang-4) serve as ligands for Tie2. The binding of Ang-1 to Tie2 leads to receptor autophosphorylation and activation, promoting cell migration and survival. In contrast, Ang-2 binding to Tie2 does not result in the same response, suggesting that Ang-2 may function as an antagonist. Tie2 signaling plays key regulatory roles in vascular integrity and quiescence, and in inflammation. The Tie2 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 303 matched cddid_all.tbl CDD cd05089 cd05089 270671 PTKc_Tie1 Catalytic domain of the Protein Tyrosine Kinase, Tie1. Protein Tyrosine Kinase (PTK) family; Tie1; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Tie1 is a receptor tyr kinase (RTK) containing an extracellular region, a transmembrane segment, and an intracellular catalytic domain. The extracellular region contains an immunoglobulin (Ig)-like domain, three epidermal growth factor (EGF)-like domains, a second Ig-like domain, and three fibronectin type III repeats. Tie receptors are specifically expressed in endothelial cells and hematopoietic stem cells. No specific ligand has been identified for Tie1, although the angiopoietin, Ang-1, binds to Tie1 through integrins at high concentrations. In vivo studies of Tie1 show that it is critical in vascular development. 297 matched cddid_all.tbl CDD cd05090 cd05090 270672 PTKc_Ror1 Catalytic domain of the Protein Tyrosine Kinase, Receptor tyrosine kinase-like Orphan Receptor 1. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Ror kinases are expressed in many tissues during development. Avian Ror1 was found to be involved in late limb development. Studies in mice reveal that Ror1 is important in the regulation of neurite growth in central neurons, as well as in respiratory development. Loss of Ror1 also enhances the heart and skeletal abnormalities found in Ror2-deficient mice. Ror proteins are orphan receptor PTKs (RTKs) containing an extracellular region with immunoglobulin-like, cysteine-rich, and kringle domains, a transmembrane segment, and an intracellular catalytic domain. Ror RTKs are unrelated to the nuclear receptor subfamily called retinoid-related orphan receptors (RORs). RTKs are usually activated through ligand binding, which causes dimerization and autophosphorylation of the intracellular tyr kinase catalytic domain. The Ror1 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 283 matched cddid_all.tbl CDD cd05091 cd05091 270673 PTKc_Ror2 Catalytic domain of the Protein Tyrosine Kinase, Receptor tyrosine kinase-like Orphan Receptor 2. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Ror2 plays important roles in skeletal and heart formation. Ror2-deficient mice show widespread bone abnormalities, ventricular defects in the heart, and respiratory dysfunction. Mutations in human Ror2 result in two different bone development genetic disorders, recessive Robinow syndrome and brachydactyly type B. Ror2 is also implicated in neural development. Ror proteins are orphan receptor PTKs (RTKs) containing an extracellular region with immunoglobulin-like, cysteine-rich, and kringle domains, a transmembrane segment, and an intracellular catalytic domain. Ror RTKs are unrelated to the nuclear receptor subfamily called retinoid-related orphan receptors (RORs). RTKs are usually activated through ligand binding, which causes dimerization and autophosphorylation of the intracellular tyr kinase catalytic domain. The Ror2 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 284 matched cddid_all.tbl CDD cd05092 cd05092 270674 PTKc_TrkA Catalytic domain of the Protein Tyrosine Kinase, Tropomyosin Related Kinase A. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. TrkA is a receptor PTK (RTK) containing an extracellular region with arrays of leucine-rich motifs flanked by two cysteine-rich clusters followed by two immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. Binding of TrkA to its ligand, nerve growth factor (NGF), results in receptor oligomerization and activation of the catalytic domain. TrkA is expressed mainly in neural-crest-derived sensory and sympathetic neurons of the peripheral nervous system, and in basal forebrain cholinergic neurons of the central nervous system. It is critical for neuronal growth, differentiation and survival. Alternative TrkA splicing has been implicated as a pivotal regulator of neuroblastoma (NB) behavior. Normal TrkA expression is associated with better NB prognosis, while the hypoxia-regulated TrkAIII splice variant promotes NB pathogenesis and progression. Aberrant TrkA expression has also been demonstrated in non-neural tumors including prostate, breast, lung, and pancreatic cancers. The TrkA subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 280 matched cddid_all.tbl CDD cd05093 cd05093 270675 PTKc_TrkB Catalytic domain of the Protein Tyrosine Kinase, Tropomyosin Related Kinase B. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. TrkB is a receptor PTK (RTK) containing an extracellular region with arrays of leucine-rich motifs flanked by two cysteine-rich clusters followed by two immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. Binding of TrkB to its ligands, brain-derived neurotrophic factor (BDNF) or neurotrophin 4 (NT4), results in receptor oligomerization and activation of the catalytic domain. TrkB is broadly expressed in the nervous system and in some non-neural tissues. It plays important roles in cell proliferation, differentiation, and survival. BDNF/Trk signaling plays a key role in regulating activity-dependent synaptic plasticity. TrkB also contributes to protection against gp120-induced neuronal cell death. TrkB overexpression is associated with poor prognosis in neuroblastoma (NB) and other human cancers. It acts as a suppressor of anoikis (detachment-induced apoptosis) and contributes to tumor metastasis. The TrkB subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 288 matched cddid_all.tbl CDD cd05094 cd05094 270676 PTKc_TrkC Catalytic domain of the Protein Tyrosine Kinase, Tropomyosin Related Kinase C. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. TrkC is a receptor PTK (RTK) containing an extracellular region with arrays of leucine-rich motifs flanked by two cysteine-rich clusters followed by two immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. Binding of TrkC to its ligand, neurotrophin 3 (NT3), results in receptor oligomerization and activation of the catalytic domain. TrkC is broadly expressed in the nervous system and in some non-neural tissues including the developing heart. NT3/TrkC signaling plays an important role in the innervation of the cardiac conducting system and the development of smooth muscle cells. Mice deficient with NT3 and TrkC have multiple heart defects. NT3/TrkC signaling is also critical for the development and maintenance of enteric neurons that are important for the control of gut peristalsis. The TrkC subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 287 matched cddid_all.tbl CDD cd05095 cd05095 270677 PTKc_DDR2 Catalytic domain of the Protein Tyrosine Kinase, Discoidin Domain Receptor 2. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. DDR2 is a receptor PTK (RTK) containing an extracellular discoidin homology domain, a transmembrane segment, an extended juxtamembrane region, and an intracellular catalytic domain. The binding of the ligand, collagen, to DDR2 results in a slow but sustained receptor activation. DDR2 binds mostly to fibrillar collagens as well as collagen X. DDR2 is widely expressed in many tissues with the highest levels found in skeletal muscle, skin, kidney and lung. It is important in cell proliferation and development. Mice, with a deletion of DDR2, suffer from dwarfism and delayed healing of epidermal wounds. DDR2 also contributes to collagen (type I) regulation by inhibiting fibrillogenesis and altering the morphology of collagen fibers. It is also expressed in immature dendritic cells (DCs), where it plays a role in DC activation and function. The DDR2 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). 297 matched cddid_all.tbl CDD cd05096 cd05096 133227 PTKc_DDR1 Catalytic domain of the Protein Tyrosine Kinase, Discoidin Domain Receptor 1. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. DDR1 is a receptor PTK (RTK) containing an extracellular discoidin homology domain, a transmembrane segment, an extended juxtamembrane region, and an intracellular catalytic domain. The binding of the ligand, collagen, to DDR1 results in a slow but sustained receptor activation. DDR1 binds to all collagens tested to date (types I-IV). It is widely expressed in many tissues. It is abundant in the brain and is also found in keratinocytes, colonic mucosa epithelium, lung epithelium, thyroid follicles, and the islets of Langerhans. During embryonic development, it is found in the developing neuroectoderm. DDR1 is a key regulator of cell morphogenesis, differentiation and proliferation. It is important in the development of the mammary gland, the vasculator and the kidney. DDR1 is also found in human leukocytes, where it facilitates cell adhesion, migration, maturation, and cytokine production. The DDR1 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 304 matched cddid_all.tbl CDD cd05097 cd05097 133228 PTKc_DDR_like Catalytic domain of Discoidin Domain Receptor-like Protein Tyrosine Kinases. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. DDR-like proteins are members of the DDR subfamily, which are receptor PTKs (RTKs) containing an extracellular discoidin homology domain, a transmembrane segment, an extended juxtamembrane region, and an intracellular catalytic domain. The binding of the ligand, collagen, to DDRs results in a slow but sustained receptor activation. DDRs regulate cell adhesion, proliferation, and extracellular matrix remodeling. They have been linked to a variety of human cancers including breast, colon, ovarian, brain, and lung. There is no evidence showing that DDRs act as transforming oncogenes. They are more likely to play a role in the regulation of tumor growth and metastasis. The DDR-like subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 295 matched cddid_all.tbl CDD cd05098 cd05098 270678 PTKc_FGFR1 Catalytic domain of the Protein Tyrosine Kinase, Fibroblast Growth Factor Receptor 1. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Alternative splicing of FGFR1 transcripts produces a variety of isoforms, which are differentially expressed in cells. FGFR1 binds the ligands, FGF1 and FGF2, with high affinity and has also been reported to bind FGF4, FGF6, and FGF9. FGFR1 signaling is critical in the control of cell migration during embryo development. It promotes cell proliferation in fibroblasts. Nuclear FGFR1 plays a role in the regulation of transcription. Mutations, insertions or deletions of FGFR1 have been identified in patients with Kallman's syndrome (KS), an inherited disorder characterized by hypogonadotropic hypogonadism and loss of olfaction. Aberrant FGFR1 expression has been found in some human cancers including 8P11 myeloproliferative syndrome (EMS), breast cancer, and pancreatic adenocarcinoma. FGFR1 is part of the FGFR subfamily, which are receptor PTKs (RTKs) containing an extracellular ligand-binding region with three immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of FGFRs to their ligands, the FGFs, results in receptor dimerization and activation, and intracellular signaling. The binding of FGFs to FGFRs is promiscuous, in that a receptor may be activated by several ligands and a ligand may bind to more that one type of receptor. The FGFR1 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 302 matched cddid_all.tbl CDD cd05099 cd05099 133230 PTKc_FGFR4 Catalytic domain of the Protein Tyrosine Kinase, Fibroblast Growth Factor Receptor 4. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Unlike other FGFRs, there is only one splice form of FGFR4. It binds FGF1, FGF2, FGF6, FGF19, and FGF23. FGF19 is a selective ligand for FGFR4. Although disruption of FGFR4 in mice causes no obvious phenotype, in vivo inhibition of FGFR4 in cultured skeletal muscle cells resulted in an arrest of muscle progenitor differentiation. FGF6 and FGFR4 are uniquely expressed in myofibers and satellite cells. FGF6/FGFR4 signaling appears to play a key role in the regulation of muscle regeneration. A polymorphism in FGFR4 is found in head and neck squamous cell carcinoma. FGFR4 is part of the FGFR subfamily, which are receptor PTKs (RTKs) containing an extracellular ligand-binding region with three immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of FGFRs to their ligands, the FGFs, results in receptor dimerization and activation, and intracellular signaling. The binding of FGFs to FGFRs is promiscuous, in that a receptor may be activated by several ligands and a ligand may bind to more that one type of receptor. The FGFR4 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 314 matched cddid_all.tbl CDD cd05100 cd05100 173652 PTKc_FGFR3 Catalytic domain of the Protein Tyrosine Kinase, Fibroblast Growth Factor Receptor 3. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Many FGFR3 splice variants have been reported with the IIIb and IIIc isoforms being the predominant forms. FGFR3 IIIc is the isoform expressed in chondrocytes, the cells affected in dwarfism, while IIIb is expressed in epithelial cells. FGFR3 ligands include FGF1, FGF2, FGF4, FGF8, FGF9, and FGF23. It is a negative regulator of long bone growth. In the cochlear duct and in the lens, FGFR3 is involved in differentiation while it appears to have a role in cell proliferation in epithelial cells. Germline mutations in FGFR3 are associated with skeletal disorders including several forms of dwarfism. Some missense mutations are associated with multiple myeloma and carcinomas of the bladder and cervix. Overexpression of FGFR3 is found in thyroid carcinoma. FGFR3 is part of the FGFR subfamily, which are receptor PTKs (RTKs) containing an extracellular ligand-binding region with three immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of FGFRs to their ligands, the FGFs, results in receptor dimerization and activation, and intracellular signaling. The binding of FGFs to FGFRs is promiscuous, in that a receptor may be activated by several ligands and a ligand may bind to more that one type of receptor. The FGFR3 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 334 matched cddid_all.tbl CDD cd05101 cd05101 270679 PTKc_FGFR2 Catalytic domain of the Protein Tyrosine Kinase, Fibroblast Growth Factor Receptor 2. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. There are many splice variants of FGFR2 which show differential expression and binding to FGF ligands. Disruption of either FGFR2 or FGFR2b is lethal in mice, due to defects in the placenta or severe impairment of tissue development including lung, limb, and thyroid, respectively. Disruption of FGFR2c in mice results in defective bone and skull development. Genetic alterations of FGFR2 are associated with many human skeletal disorders including Apert syndrome, Crouzon syndrome, Jackson-Weiss syndrome, and Pfeiffer syndrome. FGFR2 is part of the FGFR subfamily, which are receptor PTKs (RTKs) containing an extracellular ligand-binding region with three immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of FGFRs to their ligands, the FGFs, results in receptor dimerization and activation, and intracellular signaling. The binding of FGFs to FGFRs is promiscuous, in that a receptor may be activated by several ligands and a ligand may bind to more that one type of receptor. The FGFR2 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 313 matched cddid_all.tbl CDD cd05102 cd05102 270680 PTKc_VEGFR3 Catalytic domain of the Protein Tyrosine Kinase, Vascular Endothelial Growth Factor Receptor 3. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. VEGFR3 (or Flt4) preferentially binds the ligands VEGFC and VEGFD. VEGFR3 is essential for lymphatic endothelial cell (EC) development and function. It has been shown to regulate adaptive immunity during corneal transplantation. VEGFR3 is upregulated on blood vascular ECs in pathological conditions such as vascular tumors and the periphery of solid tumors. It plays a role in cancer progression and lymph node metastasis. Missense mutations in the VEGFR3 gene are associated with primary human lymphedema. VEGFR3 is a member of the VEGFR subfamily of proteins, which are receptor PTKs (RTKs) containing an extracellular ligand-binding region with seven immunoglobulin (Ig)-like domains, a transmembrane segment, and an intracellular catalytic domain. In VEGFR3, the fifth Ig-like domain is replaced by a disulfide bridge. The binding of VEGFRs to their ligands, the VEGFs, leads to receptor dimerization, activation, and intracellular signaling. The VEGFR3 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 336 matched cddid_all.tbl CDD cd05103 cd05103 270681 PTKc_VEGFR2 Catalytic domain of the Protein Tyrosine Kinase, Vascular Endothelial Growth Factor Receptor 2. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. VEGFR2 (or Flk1) binds the ligands VEGFA, VEGFC, VEGFD and VEGFE. VEGFR2 signaling is implicated in all aspects of normal and pathological vascular endothelial cell biology. It induces a variety of cellular effects including migration, survival, and proliferation. It is critical in regulating embryonic vascular development and angiogenesis. VEGFR2 is the major signal transducer in pathological angiogenesis including cancer and diabetic retinopathy, and is a target for inhibition in cancer therapy. The carboxyl terminus of VEGFR2 plays an important role in its autophosphorylation and activation. VEGFR2 is a member of the VEGFR subfamily of proteins, which are receptor PTKs (RTKs) containing an extracellular ligand-binding region with seven immunoglobulin (Ig)-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of VEGFRs to their ligands, the VEGFs, leads to receptor dimerization, activation, and intracellular signaling. The VEGFR2 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 343 matched cddid_all.tbl CDD cd05104 cd05104 270682 PTKc_Kit Catalytic domain of the Protein Tyrosine Kinase, Kit. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Kit is important in the development of melanocytes, germ cells, mast cells, hematopoietic stem cells, the interstitial cells of Cajal, and the pacemaker cells of the GI tract. Kit signaling is involved in major cellular functions including cell survival, proliferation, differentiation, adhesion, and chemotaxis. Mutations in Kit, which result in constitutive ligand-independent activation, are found in human cancers such as gastrointestinal stromal tumor (GIST) and testicular germ cell tumor (TGCT). The aberrant expression of Kit and/or SCF is associated with other tumor types such as systemic mastocytosis and cancers of the breast, neurons, lung, prostate, colon, and rectum. Although the structure of the human Kit catalytic domain is known, it is excluded from this specific alignment model because it contains a deletion in its sequence. Kit is a member of the Platelet Derived Growth Factor Receptor (PDGFR) subfamily of proteins, which are receptor PTKs (RTKs) containing an extracellular ligand-binding region with five immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of Kit to its ligand, the stem-cell factor (SCF), leads to receptor dimerization, trans phosphorylation and activation, and intracellular signaling. The Kit subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 375 matched cddid_all.tbl CDD cd05105 cd05105 173653 PTKc_PDGFR_alpha Catalytic domain of the Protein Tyrosine Kinase, Platelet Derived Growth Factor Receptor alpha. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. PDGFR alpha is a receptor PTK (RTK) containing an extracellular ligand-binding region with five immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding to its ligands, the PDGFs, leads to receptor dimerization, trans phosphorylation and activation, and intracellular signaling. PDGFR alpha forms homodimers or heterodimers with PDGFR beta, depending on the nature of the PDGF ligand. PDGF-AA, PDGF-AB, and PDGF-CC induce PDGFR alpha homodimerization. PDGFR signaling plays many roles in normal embryonic development and adult physiology. PDGFR alpha signaling is important in the formation of lung alveoli, intestinal villi, mesenchymal dermis, and hair follicles, as well as in the development of oligodendrocytes, retinal astrocytes, neural crest cells, and testicular cells. Aberrant PDGFR alpha expression is associated with some human cancers. Mutations in PDGFR alpha have been found within a subset of gastrointestinal stromal tumors (GISTs). An active fusion protein FIP1L1-PDGFR alpha, derived from interstitial deletion, is associated with idiopathic hypereosinophilic syndrome and chronic eosinophilic leukemia. The PDGFR alpha subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 400 matched cddid_all.tbl CDD cd05106 cd05106 133237 PTKc_CSF-1R Catalytic domain of the Protein Tyrosine Kinase, Colony-Stimulating Factor-1 Receptor. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. CSF-1R, also called c-Fms, is a member of the Platelet Derived Growth Factor Receptor (PDGFR) subfamily of proteins, which are receptor PTKs (RTKs) containing an extracellular ligand-binding region with five immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of CSF-1R to its ligand, CSF-1, leads to receptor dimerization, trans phosphorylation and activation, and intracellular signaling. CSF-1R signaling is critical in the regulation of macrophages and osteoclasts. It leads to increases in gene transcription and protein translation, and induces cytoskeletal remodeling. CSF-1R signaling leads to a variety of cellular responses including survival, proliferation, and differentiation of target cells. It plays an important role in innate immunity, tissue development and function, and the pathogenesis of some diseases including atherosclerosis and cancer. CSF-1R signaling is also implicated in mammary gland development during pregnancy and lactation. Aberrant CSF-1/CSF-1R expression correlates with tumor cell invasiveness, poor clinical prognosis, and bone metastasis in breast cancer. Although the structure of the human CSF-1R catalytic domain is known, it is excluded from this specific alignment model because it contains a deletion in its sequence. The CSF-1R subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 374 matched cddid_all.tbl CDD cd05107 cd05107 133238 PTKc_PDGFR_beta Catalytic domain of the Protein Tyrosine Kinase, Platelet Derived Growth Factor Receptor beta. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. PDGFR beta is a receptor PTK (RTK) containing an extracellular ligand-binding region with five immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding to its ligands, the PDGFs, leads to receptor dimerization, trans phosphorylation and activation, and intracellular signaling. PDGFR beta forms homodimers or heterodimers with PDGFR alpha, depending on the nature of the PDGF ligand. PDGF-BB and PDGF-DD induce PDGFR beta homodimerization. PDGFR signaling plays many roles in normal embryonic development and adult physiology. PDGFR beta signaling leads to a variety of cellular effects including the stimulation of cell growth and chemotaxis, as well as the inhibition of apoptosis and GAP junctional communication. It is critical in normal angiogenesis as it is involved in the recruitment of pericytes and smooth muscle cells essential for vessel stability. Aberrant PDGFR beta expression is associated with some human cancers. The continuously-active fusion proteins of PDGFR beta with COL1A1 and TEL are associated with dermatofibrosarcoma protuberans (DFSP) and a subset of chronic myelomonocytic leukemia (CMML), respectively. The PDGFR beta subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 401 matched cddid_all.tbl CDD cd05108 cd05108 270683 PTKc_EGFR Catalytic domain of the Protein Tyrosine Kinase, Epidermal Growth Factor Receptor. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. EGFR (HER1, ErbB1) is a receptor PTK (RTK) containing an extracellular EGF-related ligand-binding region, a transmembrane helix, and a cytoplasmic region with a tyr kinase domain and a regulatory C-terminal tail. Unlike other PTKs, phosphorylation of the activation loop of EGFR proteins is not critical to their activation. Instead, they are activated by ligand-induced dimerization, leading to the phosphorylation of tyr residues in the C-terminal tail, which serve as binding sites for downstream signaling molecules. Ligands for EGFR include EGF, heparin binding EGF-like growth factor (HBEGF), epiregulin, amphiregulin, TGFalpha, and betacellulin. Upon ligand binding, EGFR can form homo- or heterodimers with other EGFR subfamily members. The EGFR signaling pathway is one of the most important pathways regulating cell proliferation, differentiation, survival, and growth. Overexpression and mutation in the kinase domain of EGFR have been implicated in the development and progression of a variety of cancers. A number of monoclonal antibodies and small molecule inhibitors have been developed that target EGFR, including the antibodies Cetuximab and Panitumumab, which are used in combination with other therapies for the treatment of colorectal cancer and non-small cell lung carcinoma (NSCLC). The small molecule inhibitors Gefitinib (Iressa) and Erlotinib (Tarceva), already used for NSCLC, are undergoing clinical trials for other types of cancer including gastrointestinal, breast, head and neck, and bladder. The EGFR subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 313 matched cddid_all.tbl CDD cd05109 cd05109 270684 PTKc_HER2 Catalytic domain of the Protein Tyrosine Kinase, HER2. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. HER2 (ErbB2, HER2/neu) is a member of the EGFR (HER, ErbB) subfamily of proteins, which are receptor PTKs (RTKs) containing an extracellular EGF-related ligand-binding region, a transmembrane helix, and a cytoplasmic region with a tyr kinase domain and a regulatory C-terminal tail. Unlike other PTKs, phosphorylation of the activation loop of EGFR proteins is not critical to their activation. Instead, they are activated by ligand-induced dimerization, leading to the phosphorylation of tyr residues in the C-terminal tail, which serve as binding sites for downstream signaling molecules. HER2 does not bind to any known EGFR subfamily ligands, but contributes to the kinase activity of all possible heterodimers. It acts as the preferred partner of other ligand-bound EGFR proteins and functions as a signal amplifier, with the HER2-HER3 heterodimer being the most potent pair in mitogenic signaling. HER2 plays an important role in cell development, proliferation, survival and motility. Overexpression of HER2 results in its activation and downstream signaling, even in the absence of ligand. HER2 overexpression, mainly due to gene amplification, has been shown in a variety of human cancers. Its role in breast cancer is especially well-documented. HER2 is up-regulated in about 25% of breast tumors and is associated with increases in tumor aggressiveness, recurrence and mortality. HER2 is a target for monoclonal antibodies and small molecule inhibitors, which are being developed as treatments for cancer. The first humanized antibody approved for clinical use is Trastuzumab (Herceptin), which is being used in combination with other therapies to improve the survival rates of patients with HER2-overexpressing breast cancer. The HER2 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 279 matched cddid_all.tbl CDD cd05110 cd05110 173655 PTKc_HER4 Catalytic domain of the Protein Tyrosine Kinase, HER4. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. HER4 (ErbB4) is a member of the EGFR (HER, ErbB) subfamily of proteins, which are receptor PTKs (RTKs) containing an extracellular EGF-related ligand-binding region, a transmembrane helix, and a cytoplasmic region with a tyr kinase domain and a regulatory C-terminal tail. Unlike other PTKs, phosphorylation of the activation loop of EGFR proteins is not critical to their activation. Instead, they are activated by ligand-induced dimerization, leading to the phosphorylation of tyr residues in the C-terminal tail, which serve as binding sites for downstream signaling molecules. Ligands that bind HER4 fall into two groups, the neuregulins (or heregulins) and some EGFR (HER1) ligands including betacellulin, HBEGF, and epiregulin. All four neuregulins (NRG1-4) interact with HER4. Upon ligand binding, HER4 forms homo- or heterodimers with other HER proteins. HER4 is essential in embryonic development. It is implicated in mammary gland, cardiac, and neural development. As a postsynaptic receptor of NRG1, HER4 plays an important role in synaptic plasticity and maturation. The impairment of NRG1/HER4 signaling may contribute to schizophrenia. The HER4 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 303 matched cddid_all.tbl CDD cd05111 cd05111 173656 PTK_HER3 Pseudokinase domain of the Protein Tyrosine Kinase, HER3. HER3 (ErbB3) is a member of the EGFR (HER, ErbB) subfamily of proteins, which are receptor PTKs (RTKs) containing an extracellular EGF-related ligand-binding region, a transmembrane helix, and a cytoplasmic region with a tyr kinase domain and a regulatory C-terminal tail. Unlike other PTKs, phosphorylation of the activation loop of EGFR proteins is not critical to their activation. Instead, they are activated by ligand-induced dimerization, leading to the phosphorylation of tyr residues in the C-terminal tail, which serve as binding sites for downstream signaling molecules. HER3 contains an impaired tyr kinase domain, which lacks crucial residues for catalytic activity against exogenous substrates but is still able to bind ATP and autophosphorylate. HER3 binds the neuregulin ligands, NRG1 and NRG2, and it relies on its heterodimerization partners for activity following ligand binding. The HER2-HER3 heterodimer constitutes a high affinity co-receptor capable of potent mitogenic signaling. HER3 participates in a signaling pathway involved in the proliferation, survival, adhesion, and motility of tumor cells. The HER3 subfamily is part of a larger superfamily that includes other pseudokinases and the the catalytic domains of active kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 279 matched cddid_all.tbl CDD cd05112 cd05112 133243 PTKc_Itk Catalytic domain of the Protein Tyrosine Kinase, Interleukin-2-inducible T-cell Kinase. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Itk, also known as Tsk or Emt, is a member of the Tec-like subfamily of proteins, which are cytoplasmic (or nonreceptor) PTKs with similarity to Src kinases in that they contain Src homology protein interaction domains (SH3, SH2) N-terminal to the catalytic tyr kinase domain. Unlike Src kinases, most Tec subfamily members except Rlk also contain an N-terminal pleckstrin homology (PH) domain, which binds the products of PI3K and allows membrane recruitment and activation. In addition, Itk contains the Tec homology (TH) domain containing one proline-rich region and a zinc-binding region. Itk is expressed in T-cells and mast cells, and is important in their development and differentiation. Of the three Tec kinases expressed in T-cells, Itk plays the predominant role in T-cell receptor (TCR) signaling. It is activated by phosphorylation upon TCR crosslinking and is involved in the pathway resulting in phospholipase C-gamma1 activation and actin polymerization. It also plays a role in the downstream signaling of the T-cell costimulatory receptor CD28, the T-cell surface receptor CD2, and the chemokine receptor CXCR4. In addition, Itk is crucial for the development of T-helper(Th)2 effector responses. The Itk subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd05113 cd05113 173657 PTKc_Btk_Bmx Catalytic domain of the Protein Tyrosine Kinases, Bruton's tyrosine kinase and Bone marrow kinase on the X chromosome. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Btk and Bmx (also named Etk) are members of the Tec-like subfamily of proteins, which are cytoplasmic (or nonreceptor) PTKs with similarity to Src kinases in that they contain Src homology protein interaction domains (SH3, SH2) N-terminal to the catalytic tyr kinase domain. Unlike Src kinases, most Tec subfamily members except Rlk also contain an N-terminal pleckstrin homology (PH) domain, which binds the products of PI3K and allows membrane recruitment and activation. In addition, Btk contains the Tec homology (TH) domain with proline-rich and zinc-binding regions. Btk is expressed in B-cells, and a variety of myeloid cells including mast cells, platelets, neutrophils, and dendrictic cells. It interacts with a variety of partners, from cytosolic proteins to nuclear transcription factors, suggesting a diversity of functions. Stimulation of a diverse array of cell surface receptors, including antigen engagement of the B-cell receptor, leads to PH-mediated membrane translocation of Btk and subsequent phosphorylation by Src kinase and activation. Btk plays an important role in the life cycle of B-cells including their development, differentiation, proliferation, survival, and apoptosis. Mutations in Btk cause the primary immunodeficiency disease, X-linked agammaglobulinaemia (XLA) in humans. Bmx is primarily expressed in bone marrow and the arterial endothelium, and plays an important role in ischemia-induced angiogenesis. It facilitates arterial growth, capillary formation, vessel maturation, and bone marrow-derived endothelial progenitor cell mobilization. The Btk/Bmx subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd05114 cd05114 270685 PTKc_Tec_Rlk Catalytic domain of the Protein Tyrosine Kinases, Tyrosine kinase expressed in hepatocellular carcinoma and Resting lymphocyte kinase. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Tec and Rlk (also named Txk) are members of the Tec-like subfamily of proteins, which are cytoplasmic (or nonreceptor) PTKs with similarity to Src kinases in that they contain Src homology protein interaction domains (SH3, SH2) N-terminal to the catalytic tyr kinase domain. Unlike Src kinases, most Tec subfamily members except Rlk also contain an N-terminal pleckstrin homology (PH) domain, which binds the products of PI3K and allows membrane recruitment and activation. Instead of PH, Rlk contains an N-terminal cysteine-rich region. In addition to PH, Tec also contains the Tec homology (TH) domain with proline-rich and zinc-binding regions. Tec kinases are expressed mainly by haematopoietic cells. Tec is more widely-expressed than other Tec-like subfamily kinases. It is found in endothelial cells, both B- and T-cells, and a variety of myeloid cells including mast cells, erythroid cells, platelets, macrophages and neutrophils. Rlk is expressed in T-cells and mast cell lines. Tec and Rlk are both key components of T-cell receptor (TCR) signaling. They are important in TCR-stimulated proliferation, IL-2 production and phopholipase C-gamma1 activation. The Tec/Rlk subfamily is part of a larger superfamily, that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 260 matched cddid_all.tbl CDD cd05115 cd05115 270686 PTKc_Zap-70 Catalytic domain of the Protein Tyrosine Kinase, Zeta-chain-associated protein of 70kDa. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Zap-70 is a cytoplasmic (or nonreceptor) PTK containing two Src homology 2 (SH2) domains N-terminal to the catalytic tyr kinase domain. Zap-70 is primarily expressed in T-cells and NK cells, and is a crucial component in T-cell receptor (TCR) signaling. Zap-70 binds the phosphorylated ITAM (immunoreceptor tyr activation motif) sequences of the activated TCR zeta-chain through its SH2 domains, leading to its phosphorylation and activation. It then phosphorylates target proteins, which propagate the signals to downstream pathways. Zap-70 is hardly detected in normal peripheral B-cells, but is present in some B-cell malignancies. It is used as a diagnostic marker for chronic lymphocytic leukemia (CLL) as it is associated with the more aggressive subtype of the disease. The Zap-70 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 269 matched cddid_all.tbl CDD cd05116 cd05116 133247 PTKc_Syk Catalytic domain of the Protein Tyrosine Kinase, Spleen tyrosine kinase. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Syk is a cytoplasmic (or nonreceptor) PTK containing two Src homology 2 (SH2) domains N-terminal to the catalytic tyr kinase domain. Syk was first cloned from the spleen, and its function in hematopoietic cells is well-established. It is involved in the signaling downstream of activated receptors (including B-cell and Fc receptors) that contain ITAMs (immunoreceptor tyr activation motifs), leading to processes such as cell proliferation, differentiation, survival, adhesion, migration, and phagocytosis. More recently, Syk expression has been detected in other cell types (including epithelial cells, vascular endothelial cells, neurons, hepatocytes, and melanocytes), suggesting a variety of biological functions in non-immune cells. Syk plays a critical role in maintaining vascular integrity and in wound healing during embryogenesis. It also regulates Vav3, which is important in osteoclast function including bone development. In breast epithelial cells, where Syk acts as a negative regulator for EGFR signaling, loss of Syk expression is associated with abnormal proliferation during cancer development suggesting a potential role as a tumor suppressor. In mice, Syk has been shown to inhibit malignant transformation of mammary epithelial cells induced with murine mammary tumor virus (MMTV). The Syk subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 257 matched cddid_all.tbl CDD cd05117 cd05117 270687 STKc_CAMK The catalytic domain of CAMK family Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CaMKs are multifunctional calcium and calmodulin (CaM) stimulated STKs involved in cell cycle regulation. There are several types of CaMKs including CaMKI, CaMKII, and CaMKIV. CaMKI proteins are monomeric and they play pivotal roles in the nervous system, including long-term potentiation, dendritic arborization, neurite outgrowth, and the formation of spines, synapses, and axons. CaMKII is a signaling molecule that translates upstream calcium and reactive oxygen species (ROS) signals into downstream responses that play important roles in synaptic function and cardiovascular physiology. CAMKIV is implicated in regulating several transcription factors like CREB, MEF2, and retinoid orphan receptors, as well as in T-cell development and signaling. The CAMK family also consists of other related kinases including the Phosphorylase kinase Gamma subunit (PhKG), the C-terminal kinase domains of Ribosomal S6 kinase (RSK) and Mitogen and stress-activated kinase (MSK), Doublecortin-like kinase (DCKL), and the MAPK-activated protein kinases MK2, MK3, and MK5, among others. The CAMK family is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 258 matched cddid_all.tbl CDD cd05118 cd05118 270688 STKc_CMGC Catalytic domain of CMGC family Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The CMGC family consists of Cyclin-Dependent protein Kinases (CDKs), Mitogen-activated protein kinases (MAPKs) such as Extracellular signal-regulated kinase (ERKs), c-Jun N-terminal kinases (JNKs), and p38, and other kinases. CDKs belong to a large subfamily of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. MAPKs serve as important mediators of cellular responses to extracellular signals. They control critical cellular functions including differentiation, proliferation, migration, and apoptosis. They are also implicated in the pathogenesis of many diseases including multiple types of cancer, stroke, diabetes, and chronic inflammation. Other members of the CMGC family include casein kinase 2 (CK2), Dual-specificity tYrosine-phosphorylated and -Regulated Kinase (DYRK), Glycogen Synthase Kinase 3 (GSK3), among many others. The CMGC family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 249 matched cddid_all.tbl CDD cd05119 cd05119 270689 RIO Catalytic domain of the atypical protein serine kinases, RIO kinases. RIO kinases are atypical protein serine kinases present in archaea, bacteria and eukaryotes. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. RIO kinases contain a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. Most organisms contain at least two RIO kinases, RIO1 and RIO2. A third protein, RIO3, is present in multicellular eukaryotes. In yeast, RIO1 and RIO2 are essential for survival. They function as non-ribosomal factors necessary for late 18S rRNA processing. RIO1 is also required for proper cell cycle progression and chromosome maintenance. The biological substrates for RIO kinases are still unknown. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). 192 matched cddid_all.tbl CDD cd05120 cd05120 270690 APH_ChoK_like Aminoglycoside 3'-phosphotransferase and Choline Kinase family. This family is composed of APH, ChoK, ethanolamine kinase (ETNK), macrolide 2'-phosphotransferase (MPH2'), an unusual homoserine kinase, and uncharacterized proteins with similarity to the N-terminal domain of acyl-CoA dehydrogenase 10 (ACAD10). The members of this family catalyze the transfer of the gamma-phosphoryl group from ATP (or CTP) to small molecule substrates such as aminoglycosides, macrolides, choline, ethanolamine, and homoserine. Phosphorylation of the antibiotics, aminoglycosides and macrolides, leads to their inactivation and to bacterial antibiotic resistance. Phosphorylation of choline, ethanolamine, and homoserine serves as precursors to the synthesis of important biological compounds, such as the major phospholipids, phosphatidylcholine and phosphatidylethanolamine and the amino acids, threonine, methionine, and isoleucine. The APH/ChoK family is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). 158 matched cddid_all.tbl CDD cd05121 cd05121 270691 ABC1_ADCK3-like Activator of bc1 complex (ABC1) kinases (also called aarF domain containing kinase 3) and similar proteins. This family is composed of the atypical yeast protein kinase Abc1p, its human homolog ADCK3 (also called CABC1), and similar proteins. Abc1p (also called Coq8p) is required for the biosynthesis of Coenzyme Q (ubiquinone or Q), which is an essential lipid component in respiratory electron and proton transport. It is necessary for the formation of a multi-subunit Q-biosynthetic complex and may also function in the regulation of Q synthesis. Human ADCK3 is able to rescue defects in Q synthesis and the phosphorylation state of Coq proteins in yeast Abc1 (or Coq8) mutants. Mutations in ADCK3 cause progressive cerebellar ataxia and atrophy due to Q10 deficiency. Eukaryotes contain at least two more ABC1/ADCK3-like proteins: in humans, these are the putative atypical protein kinases named ADCK1 and ADCK2. In algae and higher plants, ABC1 kinases have proliferated to more than 15 subfamilies, most of which are located in plastids or mitochondria. Eight of these plant ABC1 kinase subfamilies (ABC1K1-8) are specific for photosynthetic organisms. ABC1 kinases are not related to the ATP-binding cassette (ABC) membrane transporter family. 247 matched cddid_all.tbl CDD cd05122 cd05122 270692 PKc_STE Catalytic domain of STE family Protein Kinases. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (ST) or tyrosine residues on protein substrates. This family is composed of STKs, and some dual-specificity PKs that phosphorylate both threonine and tyrosine residues of target proteins. Most members are kinases involved in mitogen-activated protein kinase (MAPK) signaling cascades, acting as MAPK kinases (MAPKKs), MAPKK kinases (MAPKKKs), or MAPKKK kinases (MAP4Ks). The MAPK signaling pathways are important mediators of cellular responses to extracellular signals. The pathways involve a triple kinase core cascade comprising of the MAPK, which is phosphorylated and activated by a MAPKK, which itself is phosphorylated and activated by a MAPKKK. Each MAPK cascade is activated either by a small GTP-binding protein or by an adaptor protein, which transmits the signal either directly to a MAPKKK to start the triple kinase core cascade or indirectly through a mediator kinase, a MAP4K. Other STE family members include p21-activated kinases (PAKs) and class III myosins, among others. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. Class III myosins are motor proteins containing an N-terminal kinase catalytic domain and a C-terminal actin-binding domain, which can phosphorylate several cytoskeletal proteins, conventional myosin regulatory light chains, as well as autophosphorylate the C-terminal motor domain. They play an important role in maintaining the structural integrity of photoreceptor cell microvilli. The STE family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 254 matched cddid_all.tbl CDD cd05123 cd05123 270693 STKc_AGC Catalytic domain of AGC family Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. AGC kinases regulate many cellular processes including division, growth, survival, metabolism, motility, and differentiation. Many are implicated in the development of various human diseases. Members of this family include cAMP-dependent Protein Kinase (PKA), cGMP-dependent Protein Kinase (PKG), Protein Kinase C (PKC), Protein Kinase B (PKB), G protein-coupled Receptor Kinase (GRK), Serum- and Glucocorticoid-induced Kinase (SGK), and 70 kDa ribosomal Protein S6 Kinase (p70S6K or S6K), among others. AGC kinases share an activation mechanism based on the phosphorylation of up to three sites: the activation loop (A-loop), the hydrophobic motif (HM) and the turn motif. Phosphorylation at the A-loop is required of most AGC kinases, which results in a disorder-to-order transition of the A-loop. The ordered conformation results in the access of substrates and ATP to the active site. A subset of AGC kinases with C-terminal extensions containing the HM also requires phosphorylation at this site. Phosphorylation at the HM allows the C-terminal extension to form an ordered structure that packs into the hydrophobic pocket of the catalytic domain, which then reconfigures the kinase into an active bi-lobed state. In addition, growth factor-activated AGC kinases such as PKB, p70S6K, RSK, MSK, PKC, and SGK, require phosphorylation at the turn motif (also called tail or zipper site), located N-terminal to the HM at the C-terminal extension. The AGC family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and Phosphoinositide 3-Kinase. 250 matched cddid_all.tbl CDD cd05124 cd05124 270694 AFK Catalytic domain of Actin-Fragmin Kinase. AFK is found in slime molds, ciliates, and flowering plants. It catalyzes the transfer of the gamma-phosphoryl group from ATP specifically to threonine residues in the actin-fragmin complex. The phosphorylation sites are located at a minor contact site for DNase I and at an actin-actin contact site. Fragmin is an actin-binding protein that functions as a regulator of the microfilament system. It interferes with the growth of F-actin by severing actin filaments and capping their ends. The phosphorylation of the actin-fragmin complex inhibits its nucleation activity and results in calcium-dependent capping activity. Thus, AFK plays a role in regulating actin polymerization. The AFK catalytic domain is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 240 matched cddid_all.tbl CDD cd05125 cd05125 240161 Mth938_2P1-like Mth938_2P1-like domain. This model contains sequences that are similar to 2P1, a partially characterized nuclear protein, which is homologous to E3-3 from rat and known to be alternatively spliced. Its function is unknown. This family is part of the Mth938 family, for which structures, but no functional data are available. 114 matched cddid_all.tbl CDD cd05126 cd05126 240162 Mth938 Mth938 domain. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. The function of the protein has not been determined. 117 matched cddid_all.tbl CDD cd05127 cd05127 213329 RasGAP_IQGAP_like Ras-GTPase Activating Domain of IQ motif containing GTPase activating proteins. This family represents IQ motif containing GTPase activating protein (IQGAP) which associated with the Ras GTP-binding protein. A primary function of IQGAP proteins is to modulate cytoskeletal architecture. There are three known IQGAP family members: IQGAP1, IQGAP2 and IQGAP3. Human IQGAP1 and IQGAP2 share 62% identity. IQGAPs are multi-domain molecules having a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeats, a single WW domain, four IQ motifs that mediate interactions with calmodulin, and a RasGAP related domain that binds active Rho family GTPases. IQGAP is an essential regulator of cytoskeletal function. IQGAP1 negatively regulates Ras family GTPases by stimulating their intrinsic GTPase activity, the protein actually lacks GAP activity. Both IQGAP1 and IQGAP2 specifically bind to Cdc42 and Rac1, but not to RhoA. Despite of their similarities to part of the sequence of RasGAP, neither IQGAP1 nor IQGAP2 interacts with Ras. IQGAP3, only present in mammals, regulates the organization of the cytoskeleton under the regulation of Rac1 and Cdc42 in neuronal cells. The depletion of IQGAP3 is shown to impair neurite or axon outgrowth in neuronal cells with disorganized cytoskeleton. 331 matched cddid_all.tbl CDD cd05128 cd05128 213330 RasGAP_GAP1_like Ras-GTPase Activating Domain of GAP1 and similar proteins. The GAP1 family of Ras GTPase-activating proteins includes GAP1(m) (or RASA2), GAP1_IP4BP (or RASA3), Ca2+ -promoted Ras inactivator (CAPRI, or RASAL4), and Ras GTPase activating-like proteins (RASAL) or RASAL1. The members are characterized by a conserved domain structure comprising N-terminal tandem C2 domains, a highly conserved central RasGAP domain, and a C-terminal pleckstrin homology domain that is associated with a Bruton's tyrosine kinase motif. While this domain structure is conserved, a small change in the function of each individual domain and the interaction between domains has a marked effect on the regulation of each protein. 269 matched cddid_all.tbl CDD cd05129 cd05129 213331 RasGAP_RAP6 Ras-GTPase Activating Domain of Rab5-activating protein 6. Rab5-activating protein 6 (RAP6) is an endosomal protein with a role in the regulation of receptor-mediated endocytosis. RAP6 contains a Vps9 domain, which is involved in the activation of Rab5, and a Ras GAP domain (RGD). Rab5 is a small GTPase required for the control of the endocytic route, and its activity is regulated by guanine nucleotide exchange factor, such as Rabex5, and GAPs, such as RN-tre. Human Rap6 protein is localized on the plasma membrane and on the endosome. RAP6 binds to Rab5 and Ras through the Vps9 and RGD domains, respectively. 365 matched cddid_all.tbl CDD cd05130 cd05130 213332 RasGAP_Neurofibromin Ras-GTPase Activating Domain of neurofibromin. Neurofibromin is the product of the neurofibromatosis type 1 gene (NF1) and shares a region of similarity with catalytic domain of the mammalian p120RasGAP protein and an extended similarity with the Saccharomyces cerevisiae RasGAP proteins Ira1 and Ira2. Neurofibromin has been shown to function as a GAP (GTPase-activating protein) which inhibits low molecular weight G proteins such as Ras by stimulating their intrinsic GTPase activity. NF1 is a common genetic disorder characterized by various symptoms ranging from predisposition for the development of tumors to learning disability or mental retardation. Loss of neurofibromin activity can be correlated to the increase in Ras-GTP concentration in neurofibromas of NF1 of patients, supporting the notion that unregulated Ras signaling may contribute to their development. 332 matched cddid_all.tbl CDD cd05131 cd05131 213333 RasGAP_IQGAP2 Ras-GTPase Activating Domain of IQ motif containing GTPase activating protein 2. IQGAP2 is a member of the IQGAP family that contains a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeat, a single WW domain, four IQ motifs which mediate interactions with calmodulin, and a Ras-GTPase-activating protein (GAP)-related domain that binds Rho family GTPases. IQGAP2 and IQGAP3 play important roles in the regulation of the cytoskeleton for axon outgrowth in hippocampal neurons and are thought to stay in a common regulatory pathway. The results of RNA interference studies indicated that IQGAP3 partially compensates functions of IQGAP2, but has lesser ability than IQGAP2 to promote axon outgrowth in hippocampal neuron. Moreover, IQGAP2 is required for the cadherin-mediated cell-to-cell adhesion in Xenopus laevis embryos. 359 matched cddid_all.tbl CDD cd05132 cd05132 213334 RasGAP_GAPA Ras-GTPase Activating Domain of GAPA. GAPA is an IQGAP-related protein and is predicted to bind to small GTPases, which are yet to be identified. IQGAP proteins are integral components of cytoskeletal regulation. Results from truncated GAPAs indicated that almost the entire region of GAPA homologous to IQGAP is required for cytokinesis in Dictyostelium. More members of the IQGAP family are emerging, and evidence suggests that there are both similarities and differences in their function. 352 matched cddid_all.tbl CDD cd05133 cd05133 213335 RasGAP_IQGAP1 Ras-GTPase Activating Domain of IQ motif containing GTPase activating protein 1. IQGAP1 is a homodimeric protein that is widely expressed among vertebrate cell types from early embryogenesis. Mammalian IQGAP1 protein is the best characterized member of the IQGAP family, and contains several protein-interacting domains. Human IQGAP1 is most similar to mouse Iqgap1 (94% identity) and has 62% identity to human IQGAP2. IQGAP1 binds and cross-links actin filaments in vitro and has been implicated in Ca2+/calmodulin signaling, E-cadherin-dependent cell adhesion, cell motility, and invasion. Yeast IQGAP homologs have a role in the recruitment of actin filaments, are components of the spindle pole body, and are required for actomyosin ring assembly and cytokinesis. Furthermore, IQGAP1 over-expression has also been detected in gastric and colorectal carcinomas and gastric cancer cell lines. 380 matched cddid_all.tbl CDD cd05134 cd05134 213336 RasGAP_RASA3 Ras-GTPase Activating Domain of RASA3. RASA3 (or GAP1_IP4BP) is a member of the GAP1 family and has been shown to specifically bind 1,3,4,5-tetrakisphosphate (IP4). Thus, RASA3 may function as an IP4 receptor. The members of GAP1 family are characterized by a conserved domain structure comprising N-terminal tandem C2 domains, a highly conserved central RasGAP domain, and a C-terminal pleckstrin-homology domain that is associated with a Bruton's tyrosine kinase motif. Purified RASA3 stimulates GAP activity on Ras with about a five-fold lower potency than p120RasGAP, but shows no GAP-stimulating activity at all against Rac or Rab3A. 269 matched cddid_all.tbl CDD cd05135 cd05135 213337 RasGAP_RASAL Ras-GTPase Activating Domain of RASAL1 and similar proteins. Ras GTPase activating-like protein (RASAL) or RASAL1 is a member of the GAP1 family, and a Ca2+ sensor responding in-phase to repetitive Ca2+ signals by associating with the plasma membrane and deactivating Ras. It contains a conserved domain structure comprising N-terminal tandem C2 domains, a highly conserved central RasGAP domain, and a C-terminal pleckstrin-homology domain that is associated with a Bruton's tyrosine kinase motif. RASAL, like Ca2+ -promoted Ras inactivator (CAPRI, or RASAL4), is a cytosolic protein that undergoes a rapid translocation to the plasma membrane in response to receptor-mediated elevation in the concentration of intracellular free Ca2+, a translocation that activates its ability to function as a RasGAP. However, unlike RASAL4, RASAL undergoes an oscillatory translocation to the plasma membrane that occurs in synchrony with repetitive Ca2+ spikes. 287 matched cddid_all.tbl CDD cd05136 cd05136 213338 RasGAP_DAB2IP Ras-GTPase Activating Domain of DAB2IP and similar proteins. The DAB2IP family of Ras GTPase-activating proteins includes DAB2IP, nGAP, and Syn GAP. Disabled 2 interactive protein, (DAB2IP; also known as ASK-interacting protein 1 (AIP1)), is a member of the GTPase-activating proteins, down-regulates Ras-mediated signal pathways, and mediates TNF-induced activation of ASK1-JNK signaling pathways. The mechanism by which TNF signaling is coupled to DAB2IP is not known. 324 matched cddid_all.tbl CDD cd05137 cd05137 213339 RasGAP_CLA2_BUD2 Ras-GTPase Activating Domain of CLA2/BUD2. CLA2/BUD2 functions as a GTPase-activating protein (GAP) for BUD1/RSR1 and is necessary for proper bud-site selection in yeast. BUD2 has sequence similarity to the catalytic domain of RasGAPs, and stimulates the hydrolysis of BUD1-GTP to BUD1-GDP. Elimination of Bud2p activity by mutation causes a random budding pattern with no growth defect. Overproduction of Bud2p also alters the budding pattern. 356 matched cddid_all.tbl CDD cd05140 cd05140 240163 Barstar_AU1054-like Barstar_AU1054-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor AU1054 found in Burkholderia cenocepacia. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it thus inhibiting its potentially lethal RNase activity inside the cell. Barstar also binds and inhibits a ribonuclease called RNase Sa (produced by Streptomyces aureofaciens) which belongs to the same enzyme family as does barnase. 86 matched cddid_all.tbl CDD cd05141 cd05141 240164 Barstar_evA4336-like Barstar_evA4336-like contains uncharacterized sequences similar to the uncharacterized, predicted RNAase inhibitor evA4336 found in Azoarcus sp. EvN1. This is a subfamily of the Barstar family of RNAase inhibitors. Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it thus inhibiting its potentially lethal RNase activity inside the cell. Barstar also binds and inhibits a ribonuclease called RNase Sa (produced by Streptomyces aureofaciens) which belongs to the same enzyme family as does barnase. 81 matched cddid_all.tbl CDD cd05142 cd05142 240165 Barstar Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it thus inhibiting its potentially lethal RNase activity inside the cell. Barstar also binds and inhibits a ribonuclease called RNase Sa (produced by Streptomyces aureofaciens) which belongs to the same enzyme family as does barnase. 87 matched cddid_all.tbl CDD cd05143 cd05143 240166 Barstar_SaI14_like Barstar_SaI14_like contains sequences that are similar to SaI14, an RNAase inhibitor, which are members of the Barstar family. Barstar is an intracellular inhibitor of barnase, an extracellular ribonuclease of Bacillus amyloliquefaciens. Barstar binds tightly to the barnase active site and sterically blocks it thus inhibiting its potentially lethal RNase activity inside the cell. The sequences in this subfamily are mostly uncharacterized, but believed to have a similar function and role. 88 matched cddid_all.tbl CDD cd05144 cd05144 270695 RIO2_C C-terminal catalytic domain of the atypical protein serine kinase, RIO2 kinase. RIO2 is present in archaea and eukaryotes. It contains an N-terminal winged helix (wHTH) domain and a C-terminal RIO kinase catalytic domain. The wHTH domain is primarily seen in DNA-binding proteins, although some wHTH domains may be involved in RNA recognition. RIO2 is essential for survival and is necessary for rRNA cleavage during 40S ribosomal subunit maturation. RIO kinases are atypical protein serine kinases containing a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. The RIO2 kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). 183 matched cddid_all.tbl CDD cd05145 cd05145 270696 RIO1_like Catalytic domain of the atypical protein serine kinases, RIO1 and RIO3 kinases and similar proteins. RIO1 is present in archaea, bacteria and eukaryotes. In addition, RIO3 is present in multicellular eukaryotes. Both RIO1 and RIO3 are associated with precursors of 40S ribosomal subunits, just like RIO2. RIO1 is essential for survival and is required for 18S rRNA processing, proper cell cycle progression and chromosome maintenance. Although depletion of either RIO1 and RIO2 results in similar effects, the two kinases are not fully interchangeable. The specific function of RIO3 is unknown. RIO kinases are atypical protein serine kinases containing a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). 189 matched cddid_all.tbl CDD cd05146 cd05146 270697 RIO3_euk Catalytic domain of the atypical protein serine kinase, RIO3 kinase. RIO3 is present only in multicellular eukaryotes. It is associated with precursors of 40S ribosomal subunits, just like RIO1 and RIO2. Its specific function is still unknown. Like RIO1 and RIO2, it may be involved in ribosomal subunit processing and maturation. RIO kinases are atypical protein serine kinases containing a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. The RIO3 kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). 196 matched cddid_all.tbl CDD cd05147 cd05147 270698 RIO1_euk Catalytic domain of the atypical protein serine kinase, Eukaryotic RIO1 kinase. RIO1 is present in archaea, bacteria and eukaryotes. This subfamily is composed of RIO1 proteins from eukaryotes. RIO1 is essential for survival and is required for 18S rRNA processing, proper cell cycle progression and chromosome maintenance. It is associated with precursors of 40S ribosomal subunits, just like RIO2. Although depletion of either RIO1 and RIO2 results in similar effects, the two kinases are not fully interchangeable. RIO kinases are atypical protein serine kinases containing a kinase catalytic signature, but otherwise show very little sequence similarity to typical PKs. Serine kinases catalyze the transfer of the gamma-phosphoryl group from ATP to serine residues in protein substrates. The RIO catalytic domain is truncated compared to the catalytic domains of typical PKs, with deletions of the loops responsible for substrate binding. The RIO kinase catalytic domain family is part of a larger superfamily, that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). 190 matched cddid_all.tbl CDD cd05148 cd05148 133248 PTKc_Srm_Brk Catalytic domain of the Protein Tyrosine Kinases, Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristylation sites (Srm) and Breast tumor kinase (Brk). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Srm and Brk (also called protein tyrosine kinase 6) are members of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) PTKs. Brk has been found to be overexpressed in a majority of breast tumors. Src kinases in general contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr; they are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). Srm and Brk however, lack the N-terminal myristylation sites. Src proteins are involved in signaling pathways that regulate cytokine and growth factor responses, cytoskeleton dynamics, cell proliferation, survival, and differentiation. The Srm/Brk subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 261 matched cddid_all.tbl CDD cd05150 cd05150 270699 APH Aminoglycoside 3'-phosphotransferase. APH catalyzes the transfer of the gamma-phosphoryl group from ATP to aminoglycoside antibiotics such as kanamycin, streptomycin, neomycin, and gentamicin, among others. The aminoglycoside antibiotics target the 30S ribosome and promote miscoding, leading to the production of defective proteins which insert into the bacterial membrane, resulting in membrane damage and the ultimate demise of the bacterium. Phosphorylation of the aminoglycoside antibiotics results in their inactivation, leading to bacterial antibiotic resistance. The APH gene is found on transposons and plasmids and is thought to have originated as a self-defense mechanism used by microorganisms that produce the antibiotics. The APH subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). 244 matched cddid_all.tbl CDD cd05151 cd05151 270700 ChoK-like Choline Kinase and similar proteins. This subfamily is composed of bacterial and eukaryotic choline kinases, as well as eukaryotic ethanolamine kinase. ChoK catalyzes the transfer of the gamma-phosphoryl group from ATP (or CTP) to its substrate, choline, producing phosphorylcholine (PCho), a precursor to the biosynthesis of two major membrane phospholipids, phosphatidylcholine (PC), and sphingomyelin (SM). Although choline is the preferred substrate, ChoK also shows substantial activity towards ethanolamine and its N-methylated derivatives. Bacterial ChoK is also referred to as licA protein. ETNK catalyzes the transfer of the gamma-phosphoryl group from CTP to ethanolamine (Etn), the first step in the CDP-Etn pathway for the formation of the major phospholipid, phosphatidylethanolamine (PtdEtn). Unlike ChoK, ETNK shows specific activity for its substrate and displays negligible activity towards N-methylated derivatives of Etn. ChoK plays an important role in cell signaling pathways and the regulation of cell growth. The ChoK subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). 152 matched cddid_all.tbl CDD cd05152 cd05152 270701 MPH2' Macrolide 2'-Phosphotransferase. MPH2' catalyzes the transfer of the gamma-phosphoryl group from ATP to the 2'-hydroxyl of macrolide antibiotics such as erythromycin, clarithromycin, and azithromycin, among others. Macrolides penetrate the bacterial cell and bind to ribosomes, where it interrupts protein elongation, leading ultimately to the demise of the bacterium. Phosphorylation of macrolides leads to their inactivation. Based on substrate specificity and amino acid sequence, MPH2' is divided into types I and II, encoded by mphA and mphB genes, respectively. MPH2'I inactivates 14-membered ring macrolides while MPH2'II inactivates both 14- and 16-membered ring macrolides. Enzymatic inactivation of macrolides has been reported as a mechanism for bacterial resistance in clinical samples. MPH2' is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). 276 matched cddid_all.tbl CDD cd05153 cd05153 270702 HomoserineK_II Type II Homoserine Kinase. This subfamily is composed of unusual homoserine kinases, from a subset of bacteria, which have a Protein Kinase fold. These proteins do not bear any similarity to the GHMP family homoserine kinases present in most bacteria and eukaryotes. Homoserine kinase catalyzes the transfer of the gamma-phosphoryl group from ATP to L-homoserine producing L-homoserine phosphate, an intermediate in the production of the amino acids threonine, methionine, and isoleucine. The Type II homoserine kinase subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). 300 matched cddid_all.tbl CDD cd05154 cd05154 270703 ACAD10_11_N-like N-terminal domain of Acyl-CoA dehydrogenase (ACAD) 10 and 11, and similar proteins. This subfamily is composed of the N-terminal domains of vertebrate ACAD10 and ACAD11, and similar uncharacterized bacterial and eukaryotic proteins. ACADs are a family of flavoproteins that are involved in the beta-oxidation of fatty acyl-CoA derivatives. ACAD deficiency can cause metabolic disorders including muscle fatigue, hypoglycemia, and hepatic lipidosis. There are at least 11 distinct ACADs, some of which show distinct substrate specificities to either straight-chain or branched-chain fatty acids. ACAD10 is widely expressed in human tissues and highly expressed in liver, kidney, pancreas, and spleen. ACAD10 and ACAD11 are both significantly expressed in human brain tissues. They contain a long N-terminal domain with similarity to phosphotransferases with a Protein Kinase fold, which is absent in other ACADs. They may exhibit multiple functions in acyl-CoA oxidation pathways. ACAD11 utilizes substrates with carbon chain lengths of 20 to 26, with optimal activity towards C22CoA. ACAD10 may be associated with an increased risk in type II diabetes. The ACAD10/11-like subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). 254 matched cddid_all.tbl CDD cd05155 cd05155 270704 APH_ChoK_like_1 Uncharacterized bacterial proteins with similarity to Aminoglycoside 3'-phosphotransferase and Choline kinase. This subfamily is composed of uncharacterized bacterial proteins with similarity to APH and ChoK. Other APH/ChoK-like proteins include ethanolamine kinase (ETNK), macrolide 2'-phosphotransferase (MPH2'), an unusual homoserine kinase, and uncharacterized proteins with similarity to the N-terminal domain of acyl-CoA dehydrogenase 10 (ACAD10). These proteins catalyze the transfer of the gamma-phosphoryl group from ATP (or CTP) to small molecule substrates, such as aminoglycosides, macrolides, choline, ethanolamine, and homoserine. Phosphorylation of the antibiotics, aminoglycosides, and macrolides leads to their inactivation and to bacterial antibiotic resistance. Phosphorylation of choline, ethanolamine, and homoserine serves as precursors to the synthesis of important biological compounds, such as the major phospholipids, phosphatidylcholine and phosphatidylethanolamine and the amino acids, threonine, methionine, and isoleucine. The APH/ChoK-like subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). 234 matched cddid_all.tbl CDD cd05156 cd05156 270705 ChoK_euk Euykaryotic Choline Kinase. ChoK catalyzes the transfer of the gamma-phosphoryl group from ATP (or CTP) to its substrate, choline, producing phosphorylcholine (PCho), a precursor to the biosynthesis of two major membrane phospholipids, phosphatidylcholine (PC) and sphingomyelin (SM). Although choline is the preferred substrate, ChoK also shows substantial activity towards ethanolamine and its N-methylated derivatives. ChoK plays an important role in cell signaling pathways and the regulation of cell growth. Along with PCho, it is involved in malignant transformation through Ras oncogenes in various human cancers such as breast, lung, colon, prostate, neuroblastoma, and hepatic lymphoma. In mammalian cells, there are three ChoK isoforms (A-1, A-2, and B) which are active in homo- or heterodimeric forms. The ChoK subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). 326 matched cddid_all.tbl CDD cd05157 cd05157 270706 ETNK_euk Euykaryotic Ethanolamine kinase. ETNK catalyzes the transfer of the gamma-phosphoryl group from CTP to ethanolamine (Etn), the first step in the CDP-Etn pathway for the formation of the major phospholipid, phosphatidylethanolamine (PtdEtn). Unlike ChoK, ETNK shows specific activity for its substrate, and displays negligible activity towards N-methylated derivatives of Etn. The Drosophila ETNK is implicated in development and neuronal function. Mammals contain two ETNK proteins, ETNK1 and ETNK2. ETNK1 selectively increases Etn uptake and phosphorylation, as well as PtdEtn synthesis. ETNK2 is found primarily in the liver and reproductive tissues. It plays a critical role in regulating placental hemostasis to support late embryonic development. It may also have a role in testicular maturation. ETNK is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). 307 matched cddid_all.tbl CDD cd05160 cd05160 176646 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon and zeta), and eukaryotic viral and plasmid-borne enzymes. Nuclear DNA polymerases alpha and zeta lack the four conserved acidic metal-binding residues. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair. 199 matched cddid_all.tbl CDD cd05162 cd05162 438958 PWWP PWWP (Pro-Trp-Trp-Pro) domain. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids and is composed of a five-stranded antiparallel beta-barrel followed by a helical region. It is found in numerous proteins that are involved in cell division, growth, and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. PWWP domains specifically recognize DNA and histone methylated lysines at the level of the nucleosome. Based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors. 86 matched cddid_all.tbl CDD cd05163 cd05163 270707 PIKK_TRRAP Pseudokinase domain of TRansformation/tRanscription domain-Associated Protein. TRRAP belongs to the the phosphoinositide 3-kinase-related protein kinase (PIKK) subfamily. It contains a FATC (FRAP, ATM and TRRAP, C-terminal) domain and has a large molecular weight. Unlike most PIKK proteins, however, it contains an inactive PI3K-like pseudokinase domain, which lacks the conserved residues necessary for ATP binding and catalytic activity. TRRAP also contains many motifs that may be critical for protein-protein interactions. TRRAP is a common component of many histone acetyltransferase (HAT) complexes, and is responsible for the recruitment of these complexes to chromatin during transcription, replication, and DNA repair. TRRAP also exists in non-HAT complexes such as the p400 and MRN complexes, which are implicated in ATP-dependent remodeling and DNA repair, respectively. The TRRAP pseudokinase domain subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 252 matched cddid_all.tbl CDD cd05164 cd05164 270708 PIKKc Catalytic domain of Phosphoinositide 3-kinase-related protein kinases. PIKK subfamily members include ATM (Ataxia telangiectasia mutated), ATR (Ataxia telangiectasia and Rad3-related), TOR (Target of rapamycin), SMG-1 (Suppressor of morphogenetic effect on genitalia-1), and DNA-PK (DNA-dependent protein kinase). PIKKs have intrinsic serine/threonine kinase activity and are distinguished from other PKs by their unique catalytic domain, similar to that of lipid PI3K, and their large molecular weight (240-470 kDa). They show strong preference for phosphorylating serine/threonine residues followed by a glutamine and are also referred to as (S/T)-Q-directed kinases. They all contain a FATC (FRAP, ATM and TRRAP, C-terminal) domain. PIKKs have diverse functions including cell-cycle checkpoints, genome surveillance, mRNA surveillance, and translation control. The PIKK catalytic domain subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 222 matched cddid_all.tbl CDD cd05165 cd05165 270709 PI3Kc_I Catalytic domain of Class I Phosphoinositide 3-kinase. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. Class I PI3Ks are the only enzymes capable of converting PtdIns(4,5)P2 to the critical second messenger PtdIns(3,4,5)P3. In vitro, they can also phosphorylate the substrates PtdIns and PtdIns(4)P. Class I enzymes are heterodimers and exist in multiple isoforms consisting of one catalytic subunit (out of four isoforms) and one of several regulatory subunits. They are further classified into class IA (alpha, beta and delta) and IB (gamma). PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 363 matched cddid_all.tbl CDD cd05166 cd05166 270710 PI3Kc_II Catalytic domain of Class II Phosphoinositide 3-kinase. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class II PI3Ks preferentially use PtdIns as a substrate to produce PtdIns(3)P, but can also phosphorylate PtdIns(4)P. They function as monomers and do not associate with any regulatory subunits. Class II enzymes contain an N-terminal Ras binding domain, a lipid binding C2 domain, a PI3K homology domain of unknown function, an ATP-binding cataytic domain, a Phox homology (PX) domain, and a second C2 domain at the C-terminus. They are activated by a variety of stimuli including chemokines, cytokines, lysophosphatidic acid (LPA), insulin, and tyrosine kinase receptors. The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 352 matched cddid_all.tbl CDD cd05167 cd05167 270711 PI4Kc_III_alpha Catalytic domain of Type III Phosphoinositide 4-kinase alpha. PI4Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 4-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) to generate PtdIns(4)P, the major precursor in the synthesis of other phosphoinositides including PtdIns(4,5)P2, PtdIns(3,4)P2, and PtdIns(3,4,5)P3. Two isoforms of type III PI4K, alpha and beta, exist in most eukaryotes. PI4KIIIalpha is a 220 kDa protein found in the plasma membrane and the endoplasmic reticulum (ER). The role of PI4KIIIalpha in the ER remains unclear. In the plasma membrane, it provides PtdIns(4)P, which is then converted by PI5Ks to PtdIns(4,5)P2, an important signaling molecule. Vertebrate PI4KIIIalpha is also part of a signaling complex associated with P2X7 ion channels. The yeast homolog, Stt4p, is also important in regulating the conversion of phosphatidylserine to phosphatidylethanolamine at the ER and Golgi interface. Mammalian PI4KIIIalpha is highly expressed in the nervous system. The PI4K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 307 matched cddid_all.tbl CDD cd05168 cd05168 270712 PI4Kc_III_beta Catalytic domain of Type III Phosphoinositide 4-kinase beta. PI4Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 4-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) to generate PtdIns(4)P, the major precursor in the synthesis of other phosphoinositides including PtdIns(4,5)P2, PtdIns(3,4)P2, and PtdIns(3,4,5)P3. Two isoforms of type III PI4K, alpha and beta, exist in most eukaryotes. PI4KIIIbeta (also called Pik1p in yeast) is a 110 kDa protein that is localized to the Golgi and the nucleus. It is required for maintaining the structural integrity of the Golgi complex (GC), and is a key regulator of protein transport from the GC to the plasma membrane. PI4KIIIbeta also functions in the genesis, transport, and exocytosis of synaptic vesicles. The Drosophila PI4KIIIbeta is essential for cytokinesis during spermatogenesis. The PI4K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 292 matched cddid_all.tbl CDD cd05169 cd05169 270713 PIKKc_TOR Catalytic domain of Target of Rapamycin. TOR contains a rapamycin binding domain, a catalytic domain, and a FATC (FRAP, ATM and TRRAP, C-terminal) domain at the C-terminus. It is also called FRAP (FK506 binding protein 12-rapamycin associated protein). TOR is a central component of the eukaryotic growth regulatory network. It controls the expression of many genes transcribed by all three RNA polymerases. It associates with other proteins to form two distinct complexes, TORC1 and TORC2. TORC1 is involved in diverse growth-related functions including protein synthesis, nutrient use and transport, autophagy and stress responses. TORC2 is involved in organizing cytoskeletal structures. TOR is a member of the phosphoinositide 3-kinase-related protein kinase (PIKK) subfamily. PIKKs have intrinsic serine/threonine kinase activity and are distinguished from other PKs by their unique catalytic domain, similar to that of lipid PI3K, and their large molecular weight (240-470 kDa). The TOR catalytic domain subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 279 matched cddid_all.tbl CDD cd05170 cd05170 270714 PIKKc_SMG1 Catalytic domain of Suppressor of Morphogenetic effect on Genitalia-1. SMG-1 plays a critical role in the mRNA surveillance mechanism known as non-sense mediated mRNA decay (NMD). NMD protects the cells from the accumulation of aberrant mRNAs with premature termination codons (PTCs) generated by genome mutations and by errors during transcription and splicing. SMG-1 phosphorylates Upf1, another central component of NMD, at the C-terminus upon recognition of PTCs. The phosphorylation/dephosphorylation cycle of Upf1 is essential for promoting NMD. In addition to its catalytic domain, SMG-1 contains a FATC (FRAP, ATM and TRRAP, C-terminal) domain at the C-terminus. SMG-1 is a member of the phosphoinositide 3-kinase-related protein kinase (PIKK) subfamily. PIKKs have intrinsic serine/threonine kinase activity and are distinguished from other PKs by their unique catalytic domain, similar to that of lipid PI3K, and their large molecular weight (240-470 kDa). The SMG-1 catalytic domain subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 304 matched cddid_all.tbl CDD cd05171 cd05171 270715 PIKKc_ATM Catalytic domain of Ataxia Telangiectasia Mutated. ATM is critical in the response to DNA double strand breaks (DSBs) caused by radiation. It is activated at the site of a DSB and phosphorylates key substrates that trigger pathways that regulate DNA repair and cell cycle checkpoints at the G1/S, S phase, and G2/M transition. Patients with the human genetic disorder Ataxia telangiectasia (A-T), caused by truncating mutations in ATM, show genome instability, increased cancer risk, immunodeficiency, compromised mobility, and neurodegeneration. A-T displays clinical heterogeneity, which is correlated to the degree of retained ATM activity. ATM contains a FAT (FRAP, ATM and TRRAP) domain, a catalytic domain, and a FATC domain at the C-terminus. It is a member of the phosphoinositide 3-kinase-related protein kinase (PIKK) subfamily. PIKKs have intrinsic serine/threonine kinase activity and are distinguished from other PKs by their unique catalytic domain, similar to that of lipid PI3K, and their large molecular weight (240-470 kDa). The ATM catalytic domain subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 282 matched cddid_all.tbl CDD cd05172 cd05172 270716 PIKKc_DNA-PK Catalytic domain of DNA-dependent protein kinase. DNA-PK is comprised of a regulatory subunit, containing the Ku70/80 subunit, and a catalytic subunit, which contains a NUC194 domain of unknown function, a FAT (FRAP, ATM and TRRAP) domain, a catalytic domain, and a FATC domain at the C-terminus. It is part of a multi-component system involved in non-homologous end joining (NHEJ), a process of repairing double strand breaks (DSBs) by joining together two free DNA ends of little homology. DNA-PK functions as a molecular sensor for DNA damage that enhances the signal via phosphorylation of downstream targets. It may also act as a protein scaffold that aids the localization of DNA repair proteins to the site of DNA damage. DNA-PK also plays a role in the maintenance of telomeric stability and the prevention of chromosomal end fusion. DNA-PK is a member of the phosphoinositide 3-kinase-related protein kinase (PIKK) subfamily. PIKKs have intrinsic serine/threonine kinase activity and are distinguished from other PKs by their unique catalytic domain, similar to that of lipid PI3K, and their large molecular weight (240-470 kDa). The DNA-PK catalytic domain subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 235 matched cddid_all.tbl CDD cd05173 cd05173 270717 PI3Kc_IA_beta Catalytic domain of Class IA Phosphoinositide 3-kinase beta. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. PI3Kbeta can be activated by G-protein-coupled receptors. Deletion of PI3Kbeta in mice results in early lethality at around day three of development. PI3Kbeta plays an important role in regulating sustained integrin activation and stable platelet agrregation, especially under conditions of high shear stress. PI3Ks can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class I PI3Ks are the only enzymes capable of converting PtdIns(4,5)P2 to the critical second messenger PtdIns(3,4,5)P3. Class I enzymes are heterodimers and exist in multiple isoforms consisting of one catalytic subunit (out of four isoforms) and one of several regulatory subunits. They are further classified into class IA (alpha, beta and delta) and IB (gamma). Class IA enzymes contain an N-terminal p85 binding domain, a Ras binding domain, a lipid binding C2 domain, a PI3K homology domain of unknown function, and a C-terminal ATP-binding cataytic domain. They associate with a regulatory subunit of the p85 family and are activated by tyrosine kinase receptors. The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 362 matched cddid_all.tbl CDD cd05174 cd05174 270718 PI3Kc_IA_delta Catalytic domain of Class IA Phosphoinositide 3-kinase delta. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. PI3Kdelta is mainly expressed in immune cells and plays an important role in cellular and humoral immunity. It plays a major role in antigen receptor signaling in B-cells, T-cells, and mast cells. It regulates the differentiation of peripheral helper T-cells and controls the development and function of regulatory T-cells. PI3Ks can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class I PI3Ks are the only enzymes capable of converting PtdIns(4,5)P2 to the critical second messenger PtdIns(3,4,5)P3. Class I enzymes are heterodimers and exist in multiple isoforms consisting of one catalytic subunit (out of four isoforms) and one of several regulatory subunits. They are further classified into class IA (alpha, beta and delta) and IB (gamma). Class IA enzymes contain an N-terminal p85 binding domain, a Ras binding domain, a lipid binding C2 domain, a PI3K homology domain of unknown function, and a C-terminal ATP-binding cataytic domain. They associate with a regulatory subunit of the p85 family and are activated by tyrosine kinase receptors. The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 366 matched cddid_all.tbl CDD cd05175 cd05175 270719 PI3Kc_IA_alpha Catalytic domain of Class IA Phosphoinositide 3-kinase alpha. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. PI3Kalpha plays an important role in insulin signaling. It also mediates physiologic heart growth and provides protection from stress. Activating mutations of PI3Kalpha is associated with diverse forms of cancer at high frequency. PI3Ks can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class I PI3Ks are the only enzymes capable of converting PtdIns(4,5)P2 to the critical second messenger PtdIns(3,4,5)P3. Class I enzymes are heterodimers and exist in multiple isoforms consisting of one catalytic subunit (out of four isoforms) and one of several regulatory subunits. They are further classified into class IA (alpha, beta and delta) and IB (gamma). Class IA enzymes contain an N-terminal p85 binding domain, a Ras binding domain, a lipid binding C2 domain, a PI3K homology domain of unknown function, and a C-terminal ATP-binding cataytic domain. They associate with a regulatory subunit of the p85 family and are activated by tyrosine kinase receptors. The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 370 matched cddid_all.tbl CDD cd05176 cd05176 270720 PI3Kc_C2_alpha Catalytic domain of Class II Phosphoinositide 3-kinase alpha. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. The class II alpha isoform, PI3K-C2alpha, plays key roles in clathrin assembly and clathrin-mediated membrane trafficking, insulin signaling, vascular smooth muscle contraction, and the priming of neurosecretory granule exocytosis. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class II PI3Ks preferentially use PtdIns as a substrate to produce PtdIns(3)P, but can also phosphorylate PtdIns(4)P. They function as monomers and do not associate with any regulatory subunits. Class II enzymes contain an N-terminal Ras binding domain, a lipid binding C2 domain, a PI3K homology domain of unknown function, an ATP-binding cataytic domain, a Phox homology (PX) domain, and a second C2 domain at the C-terminus. The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 353 matched cddid_all.tbl CDD cd05177 cd05177 270721 PI3Kc_C2_gamma Catalytic domain of Class II Phosphoinositide 3-kinase gamma. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. The class II gamma isoform, PI3K-C2gamma, is expressed in the liver, breast, and prostate. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class II PI3Ks preferentially use PtdIns as a substrate to produce PtdIns(3)P, but can also phosphorylate PtdIns(4)P. They function as monomers and do not associate with any regulatory subunits. Class II enzymes contain an N-terminal Ras binding domain, a lipid binding C2 domain, a PI3K homology domain of unknown function, an ATP-binding cataytic domain, a Phox homology (PX) domain, and a second C2 domain at the C-terminus. It's biological function remains unknown. The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. 354 matched cddid_all.tbl CDD cd05188 cd05188 176178 MDR Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family. The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc. 271 matched cddid_all.tbl CDD cd05191 cd05191 133449 NAD_bind_amino_acid_DH NAD(P) binding domain of amino acid dehydrogenase-like proteins. Amino acid dehydrogenase(DH)-like NAD(P)-binding domains are members of the Rossmann fold superfamily and are found in glutamate, leucine, and phenylalanine DHs (DHs), methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. 86 matched cddid_all.tbl CDD cd05192 cd05192 467613 GAPDH-like_N N-terminal NAD(P)-binding domain of the glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like family. The GAPDH-like family includes glyceraldehyde-3-phosphate dehydrogenase (GAPDH), native NAD(P)H-dependent amine dehydrogenases (nat-AmDHs), 2,4-diaminopentanoate dehydrogenase (DAPDH), meso-diaminopimelate D-dehydrogenase (meso-DAPDH), and dihydrodipicolinate reductase (DHDPR). GAPDH plays an important role in glycolysis and gluconeogenesis by reversibly catalyzing the oxidation and phosphorylation of D-glyceraldehyde-3-phosphate to 1,3-diphospho-glycerate. nat-AmDHs catalyze the reductive amination of ketone and aldehyde substrates using NAD(P)H as the hydride source. They play important roles in the efficient asymmetric synthesis of alpha-chiral amines. DAPDH is involved in the ornithine fermentation pathway. It catalyzes the oxidative deamination of (2R,4S)-2,4-diaminopentanoate ((2R,4S)-DAP) to yield 2-amino-4-ketopentanoate (AKP). DHDPR catalyzes the NAD(P)H-dependent reduction of 2,3-dihydrodipicolinate (DHDP) to 2,3,4,5-tetrahydrodipicolinate (THDP). It could also function as a dehydratase in addition to the role of a nucleotide dependent reductase. The model corresponds to the N-terminal NAD(P)-binding domain of GAPDH-like family proteins. It contains a Rossmann fold which combines with the catalytic cysteine-containing C-terminus to form a catalytic cleft. 109 matched cddid_all.tbl CDD cd05193 cd05193 187536 AR_like_SDR_e aldehyde reductase, flavonoid reductase, and related proteins, extended (e) SDRs. This subgroup contains aldehyde reductase and flavonoid reductase of the extended SDR-type and related proteins. Proteins in this subgroup have a complete SDR-type active site tetrad and a close match to the canonical extended SDR NADP-binding motif. Aldehyde reductase I (aka carbonyl reductase) is an NADP-binding SDR; it catalyzes the NADP-dependent reduction of ethyl 4-chloro-3-oxobutanoate to ethyl (R)-4-chloro-3-hydroxybutanoate. The related flavonoid reductases act in the NADP-dependent reduction of flavonoids, ketone-containing plant secondary metabolites. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 295 matched cddid_all.tbl CDD cd05195 cd05195 176179 enoyl_red enoyl reductase of polyketide synthase. Putative enoyl reductase of polyketide synthase. Polyketide synthases produce polyketides in step by step mechanism that is similar to fatty acid synthesis. Enoyl reductase reduces a double to single bond. Erythromycin is one example of a polyketide generated by 3 complex enzymes (megasynthases). 2-enoyl thioester reductase (ETR) catalyzes the NADPH-dependent dependent conversion of trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl thioester reductase activity has been linked in Candida tropicalis as essential in maintaining mitiochondrial respiratory function. This ETR family is a part of the medium chain dehydrogenase/reductase family, but lack the zinc coordination sites characteristic of the alcohol dehydrogenases in this family. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site, and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains, at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. 293 matched cddid_all.tbl CDD cd05197 cd05197 133425 GH4_glycoside_hydrolases Glycoside Hydrases Family 4. Glycoside hydrolases cleave glycosidic bonds to release smaller sugars from oligo- or polysaccharides. Some bacteria simultaneously translocate and phosphorylate disaccharides via the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS). After translocation, these phospho-disaccharides may be hydrolyzed by GH4 glycoside hydrolases. Other organisms (such as archaea and Thermotoga maritima) lack the PEP-PTS system, but have several enzymes normally associated with the PEP-PTS operon. GH4 family members include 6-phospho-beta-glucosidases, 6-phospho-alpha-glucosidases, alpha-glucosidases/alpha-glucuronidases (only from Thermotoga), and alpha-galactosidases. They require two cofactors, NAD+ and a divalent metal (Mn2+, Ni2+, Mg2+), for activity. Some also require reducing conditions. GH4 glycoside hydrolases are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. 425 matched cddid_all.tbl CDD cd05198 cd05198 240622 formate_dh_like Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxy acid dehydrogenase family. Formate dehydrogenase, D-specific 2-hydroxy acid dehydrogenase, Phosphoglycerate Dehydrogenase, Lactate dehydrogenase, Thermostable Phosphite Dehydrogenase, and Hydroxy(phenyl)pyruvate reductase, among others, share a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases. FDHs are found in all methylotrophic microorganisms in energy production and in the stress responses of plants. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine Hydrolase, among others. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 302 matched cddid_all.tbl CDD cd05199 cd05199 240623 SDH_like Saccharopine Dehydrogenase like proteins. Saccharopine Dehydrogenase (SDH) and related proteins, including bifunctional lysine ketoglutarate reductase/SDH enzymes and N(5)-(carboxyethyl)ornithine synthases. SDH catalyzes the final step in the reversible NAD-dependent oxidative deamination of saccharopine to alpha-ketoglutarate and lysine, in the alpha-aminoadipate pathway of L-lysine biosynthesis. SDH is structurally related to formate dehydrogenase and similar enzymes, having a 2-domain structure in which a Rossmann-fold NAD(P)-binding domain is inserted within the linear sequence of a catalytic domain of related structure. Bifunctional lysine ketoglutarate reductase/SDH protein is a pair of enzymes linked on a single polypeptide chain that catalyze the initial, consecutive steps of lysine degradation. These proteins are related to the 2-domain saccharopine dehydrogenases. 319 matched cddid_all.tbl CDD cd05211 cd05211 133450 NAD_bind_Glu_Leu_Phe_Val NAD(P) binding domain of glutamate dehydrogenase, leucine dehydrogenase, phenylalanine dehydrogenase, and valine dehydrogenase. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NAD(P)+. This subfamily includes glutamate, leucine, phenylalanine, and valine DHs. Glutamate DH is a multi-domain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. As in other NAD+-dependent DHs, monomers in this family have 2 domains separated by a deep cleft. Here the c-terminal domain contains a modified NAD-binding Rossmann fold with 7 rather than the usual 6 beta strands and one strand anti-parrallel to the others. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. 217 matched cddid_all.tbl CDD cd05212 cd05212 133451 NAD_bind_m-THF_DH_Cyclohyd_like NAD(P) binding domain of methylene-tetrahydrofolate dehydrogenase and methylene-tetrahydrofolate dehydrogenase/cyclohydrolase. NAD(P) binding domains of methylene-tetrahydrofolate dehydrogenase (m-THF DH) and m-THF DH/cyclohydrolase bifunctional enzymes (m-THF DH/cyclohydrolase). M-THF is a versatile carrier of activated one-carbon units. The major one-carbon folate donors are N-5 methyltetrahydrofolate, N5,N10-m-THF, and N10-formayltetrahydrofolate. The oxidation of metabolic intermediate m-THF to m-THF requires the enzyme m-THF DH. In addition, most DHs also have an associated cyclohydrolase activity which catalyzes its hydrolysis to N10-formyltetrahydrofolate. m-THF DH is typically found as part of a multifunctional protein in eukaryotes. NADP-dependent m-THF DH in mammals, birds and yeast are components of a trifunctional enzyme with DH, cyclohydrolase, and synthetase activities. Certain eukaryotic cells also contain homodimeric bifunctional DH/cyclodrolase form. In bacteria, mono-functional DH, as well as bifunctional DH/cyclodrolase are found. In addition, yeast (S. cerevisiae) also express a monofunctional DH. M-THF DH, like other amino acid DH-like NAD(P)-binding domains, is a member of the Rossmann fold superfamily which includes glutamate, leucine, and phenylalanine DHs, m-THF DH, methylene-tetrahydromethanopterin DH, m-THF DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. 140 matched cddid_all.tbl CDD cd05213 cd05213 133452 NAD_bind_Glutamyl_tRNA_reduct NADP-binding domain of glutamyl-tRNA reductase. Glutamyl-tRNA reductase catalyzes the conversion of glutamyl-tRNA to glutamate-1-semialdehyde, initiating the synthesis of tetrapyrrole. Whereas tRNAs are generally associated with peptide bond formation in protein translation, here the tRNA activates glutamate in the initiation of tetrapyrrole biosynthesis in archaea, plants and many bacteria. In the first step, activated glutamate is reduced to glutamate-1-semi-aldehyde via the NADPH dependent glutamyl-tRNA reductase. Glutamyl-tRNA reductase forms a V-shaped dimer. Each monomer has 3 domains: an N-terminal catalytic domain, a classic nucleotide binding domain, and a C-terminal dimerization domain. Although the representative structure 1GPJ lacks a bound NADPH, a theoretical binding pocket has been described. (PMID 11172694). Amino acid dehydrogenase (DH)-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. 311 matched cddid_all.tbl CDD cd05214 cd05214 467614 GAPDH_I_N N-terminal NAD(P)-binding domain of type I glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and similar proteins. GAPDH plays an important role in glycolysis and gluconeogenesis by reversibly catalyzing the oxidation and phosphorylation of D-glyceraldehyde-3-phosphate to 1,3-diphospho-glycerate. It has been implicated in varied activities including regulating mRNA stability, the regulation of gene expression, induction of apoptosis, intracellular membrane trafficking, iron uptake and transport (via secreted GAPDH), heme metabolism, the maintenance of genomic integrity, and nuclear tRNA export. GAPDH contains an N-terminal NAD(P)-binding domain and a C-terminal catalytic domain. The N-terminal NAD(P)-binding domain contains a Rossmann fold which combines with the catalytic cysteine-containing C-terminus to form a catalytic cleft. Phosphatidyl-serine, RNA, and glutathione binding sites have been identified in the N-terminus. Different forms of GAPDH exist which utilize NAD (EC 1.2.1.12), NADP (EC 1.2.1.13) or either (EC 1.2.1.59). The family corresponds to the ubiquitous NAD+ or NADP+ utilizing type I GAPDH and a small clade of dehydrogenases, called erythrose-4-phosphate dehydrogenase (E4PDH) proteins, which utilize NAD+ to oxidize erythrose-4-phosphate (E4P) to 4-phospho-erythronate, a precursor for the de novo synthesis of pyridoxine via 4-hydroxythreonine and D-1-deoxyxylulose. 164 matched cddid_all.tbl CDD cd05226 cd05226 187537 SDR_e_a Extended (e) and atypical (a) SDRs. Extended or atypical short-chain dehydrogenases/reductases (SDRs, aka tyrosine-dependent oxidoreductases) are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 176 matched cddid_all.tbl CDD cd05227 cd05227 187538 AR_SDR_e aldehyde reductase, extended (e) SDRs. This subgroup contains aldehyde reductase of the extended SDR-type and related proteins. Aldehyde reductase I (aka carbonyl reductase) is an NADP-binding SDR; it has an NADP-binding motif consensus that is slightly different from the canonical SDR form and lacks the Asn of the extended SDR active site tetrad. Aldehyde reductase I catalyzes the NADP-dependent reduction of ethyl 4-chloro-3-oxobutanoate to ethyl (R)-4-chloro-3-hydroxybutanoate. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 301 matched cddid_all.tbl CDD cd05228 cd05228 187539 AR_FR_like_1_SDR_e uncharacterized subgroup of aldehyde reductase and flavonoid reductase related proteins, extended (e) SDRs. This subgroup contains proteins of unknown function related to aldehyde reductase and flavonoid reductase of the extended SDR-type. Aldehyde reductase I (aka carbonyl reductase) is an NADP-binding SDR; it has an NADP-binding motif consensus that is slightly different from the canonical SDR form and lacks the Asn of the extended SDR active site tetrad. Aldehyde reductase I catalyzes the NADP-dependent reduction of ethyl 4-chloro-3-oxobutanoate to ethyl (R)-4-chloro-3-hydroxybutanoate. The related flavonoid reductases act in the NADP-dependent reduction of flavonoids, ketone-containing plant secondary metabolites. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 318 matched cddid_all.tbl CDD cd05229 cd05229 187540 SDR_a3 atypical (a) SDRs, subgroup 3. These atypical SDR family members of unknown function have a glycine-rich NAD(P)-binding motif consensus that is very similar to the extended SDRs, GXXGXXG. Generally, this group has poor conservation of the active site tetrad, However, individual sequences do contain matches to the YXXXK active site motif, and generally Tyr or Asn in place of the upstream Ser found in most SDRs. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 302 matched cddid_all.tbl CDD cd05230 cd05230 187541 UGD_SDR_e UDP-glucuronate decarboxylase (UGD) and related proteins, extended (e) SDRs. UGD catalyzes the formation of UDP-xylose from UDP-glucuronate; it is an extended-SDR, and has the characteristic glycine-rich NAD-binding pattern, TGXXGXXG, and active site tetrad. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 305 matched cddid_all.tbl CDD cd05231 cd05231 187542 NmrA_TMR_like_1_SDR_a NmrA (a transcriptional regulator) and triphenylmethane reductase (TMR) like proteins, subgroup 1, atypical (a) SDRs. Atypical SDRs related to NMRa, TMR, and HSCARG (an NADPH sensor). This subgroup resembles the SDRs and has a partially conserved characteristic [ST]GXXGXXG NAD-binding motif, but lacks the conserved active site residues. NmrA is a negative transcriptional regulator of various fungi, involved in the post-translational modulation of the GATA-type transcription factor AreA. NmrA lacks the canonical GXXGXXG NAD-binding motif and has altered residues at the catalytic triad, including a Met instead of the critical Tyr residue. NmrA may bind nucleotides but appears to lack any dehydrogenase activity. HSCARG has been identified as a putative NADP-sensing molecule, and redistributes and restructures in response to NADPH/NADP ratios. Like NmrA, it lacks most of the active site residues of the SDR family, but has an NAD(P)-binding motif similar to the extended SDR family, GXXGXXG. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Atypical SDRs are distinct from classical SDRs. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 259 matched cddid_all.tbl CDD cd05232 cd05232 187543 UDP_G4E_4_SDR_e UDP-glucose 4 epimerase, subgroup 4, extended (e) SDRs. UDP-glucose 4 epimerase (aka UDP-galactose-4-epimerase), is a homodimeric extended SDR. It catalyzes the NAD-dependent conversion of UDP-galactose to UDP-glucose, the final step in Leloir galactose synthesis. This subgroup is comprised of bacterial proteins, and includes the Staphylococcus aureus capsular polysaccharide Cap5N, which may have a role in the synthesis of UDP-N-acetyl-d-fucosamine. This subgroup has the characteristic active site tetrad and NAD-binding motif of the extended SDRs. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 303 matched cddid_all.tbl CDD cd05233 cd05233 212491 SDR_c classical (c) SDRs. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human prostaglandin dehydrogenase (PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107, PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 234 matched cddid_all.tbl CDD cd05234 cd05234 187545 UDP_G4E_2_SDR_e UDP-glucose 4 epimerase, subgroup 2, extended (e) SDRs. UDP-glucose 4 epimerase (aka UDP-galactose-4-epimerase), is a homodimeric extended SDR. It catalyzes the NAD-dependent conversion of UDP-galactose to UDP-glucose, the final step in Leloir galactose synthesis. This subgroup is comprised of archaeal and bacterial proteins, and has the characteristic active site tetrad and NAD-binding motif of the extended SDRs. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 305 matched cddid_all.tbl CDD cd05235 cd05235 187546 SDR_e1 extended (e) SDRs, subgroup 1. This family consists of an SDR module of multidomain proteins identified as putative polyketide sythases fatty acid synthases (FAS), and nonribosomal peptide synthases, among others. However, unlike the usual ketoreductase modules of FAS and polyketide synthase, these domains are related to the extended SDRs, and have canonical NAD(P)-binding motifs and an active site tetrad. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 290 matched cddid_all.tbl CDD cd05236 cd05236 187547 FAR-N_SDR_e fatty acyl CoA reductases (FARs), extended (e) SDRs. SDRs are Rossmann-fold NAD(P)H-binding proteins, many of which may function as fatty acyl CoA reductases (FAR), acting on medium and long chain fatty acids, and have been reported to be involved in diverse processes such as biosynthesis of insect pheromones, plant cuticular wax production, and mammalian wax biosynthesis. In Arabidopsis thaliana, proteins with this particular architecture have also been identified as the MALE STERILITY 2 (MS2) gene product, which is implicated in male gametogenesis. Mutations in MS2 inhibit the synthesis of exine (sporopollenin), rendering plants unable to reduce pollen wall fatty acids to corresponding alcohols. This N-terminal domain shares the catalytic triad (but not the upstream Asn) and characteristic NADP-binding motif of the extended SDR family. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 320 matched cddid_all.tbl CDD cd05237 cd05237 187548 UDP_invert_4-6DH_SDR_e UDP-Glcnac (UDP-linked N-acetylglucosamine) inverting 4,6-dehydratase, extended (e) SDRs. UDP-Glcnac inverting 4,6-dehydratase was identified in Helicobacter pylori as the hexameric flaA1 gene product (FlaA1). FlaA1 is hexameric, possesses UDP-GlcNAc-inverting 4,6-dehydratase activity, and catalyzes the first step in the creation of a pseudaminic acid derivative in protein glycosylation. Although this subgroup has the NADP-binding motif characteristic of extended SDRs, its members tend to have a Met substituted for the active site Tyr found in most SDR families. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 287 matched cddid_all.tbl CDD cd05238 cd05238 187549 Gne_like_SDR_e Escherichia coli Gne (a nucleoside-diphosphate-sugar 4-epimerase)-like, extended (e) SDRs. Nucleoside-diphosphate-sugar 4-epimerase has the characteristic active site tetrad and NAD-binding motif of the extended SDR, and is related to more specifically defined epimerases such as UDP-glucose 4 epimerase (aka UDP-galactose-4-epimerase), which catalyzes the NAD-dependent conversion of UDP-galactose to UDP-glucose, the final step in Leloir galactose synthesis. This subgroup includes Escherichia coli 055:H7 Gne, a UDP-GlcNAc 4-epimerase, essential for O55 antigen synthesis. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 305 matched cddid_all.tbl CDD cd05239 cd05239 187550 GDP_FS_SDR_e GDP-fucose synthetase, extended (e) SDRs. GDP-fucose synthetase (aka 3, 5-epimerase-4-reductase) acts in the NADP-dependent synthesis of GDP-fucose from GDP-mannose. Two activities have been proposed for the same active site: epimerization and reduction. Proteins in this subgroup are extended SDRs, which have a characteristic active site tetrad and an NADP-binding motif, [AT]GXXGXXG, that is a close match to the archetypical form. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 300 matched cddid_all.tbl CDD cd05240 cd05240 187551 UDP_G4E_3_SDR_e UDP-glucose 4 epimerase (G4E), subgroup 3, extended (e) SDRs. Members of this bacterial subgroup are identified as possible sugar epimerases, such as UDP-glucose 4 epimerase. However, while the NAD(P)-binding motif is fairly well conserved, not all members retain the canonical active site tetrad of the extended SDRs. UDP-glucose 4 epimerase (aka UDP-galactose-4-epimerase), is a homodimeric extended SDR. It catalyzes the NAD-dependent conversion of UDP-galactose to UDP-glucose, the final step in Leloir galactose synthesis. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 306 matched cddid_all.tbl CDD cd05241 cd05241 187552 3b-HSD-like_SDR_e 3beta-hydroxysteroid dehydrogenases (3b-HSD)-like, extended (e) SDRs. Extended SDR family domains belonging to this subgroup have the characteristic active site tetrad and a fairly well-conserved NAD(P)-binding motif. 3b-HSD catalyzes the NAD-dependent conversion of various steroids, such as pregnenolone to progesterone, or androstenediol to testosterone. This subgroup includes an unusual bifunctional 3b-HSD/C-4 decarboxylase from Arabidopsis thaliana, and Saccharomyces cerevisiae ERG26, a 3b-HSD/C-4 decarboxylase, involved in the synthesis of ergosterol, the major sterol of yeast. It also includes human 3 beta-HSD/HSD3B1 and C(27) 3beta-HSD/ [3beta-hydroxy-delta(5)-C(27)-steroid oxidoreductase; HSD3B7]. C(27) 3beta-HSD/HSD3B7 is a membrane-bound enzyme of the endoplasmic reticulum, that catalyzes the isomerization and oxidation of 7alpha-hydroxylated sterol intermediates, an early step in bile acid biosynthesis. Mutations in the human NSDHL (NAD(P)H steroid dehydrogenase-like protein) cause CHILD syndrome (congenital hemidysplasia with ichthyosiform nevus and limb defects), an X-linked dominant, male-lethal trait. Mutations in the human gene encoding C(27) 3beta-HSD underlie a rare autosomal recessive form of neonatal cholestasis. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid sythase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 331 matched cddid_all.tbl CDD cd05242 cd05242 187553 SDR_a8 atypical (a) SDRs, subgroup 8. This subgroup contains atypical SDRs of unknown function. Proteins in this subgroup have a glycine-rich NAD(P)-binding motif consensus that resembles that of the extended SDRs, (GXXGXXG or GGXGXXG), but lacks the characteristic active site residues of the SDRs. A Cys often replaces the usual Lys of the YXXXK active site motif, while the upstream Ser is generally present and Arg replaces the usual Asn. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 296 matched cddid_all.tbl CDD cd05243 cd05243 187554 SDR_a5 atypical (a) SDRs, subgroup 5. This subgroup contains atypical SDRs, some of which are identified as putative NAD(P)-dependent epimerases, one as a putative NAD-dependent epimerase/dehydratase. Atypical SDRs are distinct from classical SDRs. Members of this subgroup have a glycine-rich NAD(P)-binding motif that is very similar to the extended SDRs, GXXGXXG, and binds NADP. Generally, this subgroup has poor conservation of the active site tetrad; however, individual sequences do contain matches to the YXXXK active site motif, the upstream Ser, and there is a highly conserved Asp in place of the usual active site Asn throughout the subgroup. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 203 matched cddid_all.tbl CDD cd05244 cd05244 187555 BVR-B_like_SDR_a biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs. Human BVR-B catalyzes pyridine nucleotide-dependent production of bilirubin-IX beta during fetal development; in the adult BVR-B has flavin and ferric reductase activities. Human BVR-B catalyzes the reduction of FMN, FAD, and riboflavin. Recognition of flavin occurs mostly by hydrophobic interactions, accounting for the broad substrate specificity. Atypical SDRs are distinct from classical SDRs. BVR-B does not share the key catalytic triad, or conserved tyrosine typical of SDRs. The glycine-rich NADP-binding motif of BVR-B is GXXGXXG, which is similar but not identical to the pattern seen in extended SDRs. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 207 matched cddid_all.tbl CDD cd05245 cd05245 187556 SDR_a2 atypical (a) SDRs, subgroup 2. This subgroup contains atypical SDRs, one member is identified as Escherichia coli protein ybjT, function unknown. Atypical SDRs are distinct from classical SDRs. Members of this subgroup have a glycine-rich NAD(P)-binding motif consensus that generally matches the extended SDRs, TGXXGXXG, but lacks the characteristic active site residues of the SDRs. This subgroup has basic residues (HXXXR) in place of the active site motif YXXXK, these may have a catalytic role. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 293 matched cddid_all.tbl CDD cd05246 cd05246 187557 dTDP_GD_SDR_e dTDP-D-glucose 4,6-dehydratase, extended (e) SDRs. This subgroup contains dTDP-D-glucose 4,6-dehydratase and related proteins, members of the extended-SDR family, with the characteristic Rossmann fold core region, active site tetrad and NAD(P)-binding motif. dTDP-D-glucose 4,6-dehydratase is closely related to other sugar epimerases of the SDR family. dTDP-D-dlucose 4,6,-dehydratase catalyzes the second of four steps in the dTDP-L-rhamnose pathway (the dehydration of dTDP-D-glucose to dTDP-4-keto-6-deoxy-D-glucose) in the synthesis of L-rhamnose, a cell wall component of some pathogenic bacteria. In many gram negative bacteria, L-rhamnose is an important constituent of lipopoylsaccharide O-antigen. The larger N-terminal portion of dTDP-D-Glucose 4,6-dehydratase forms a Rossmann fold NAD-binding domain, while the C-terminus binds the sugar substrate. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 315 matched cddid_all.tbl CDD cd05247 cd05247 187558 UDP_G4E_1_SDR_e UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs. UDP-glucose 4 epimerase (aka UDP-galactose-4-epimerase), is a homodimeric extended SDR. It catalyzes the NAD-dependent conversion of UDP-galactose to UDP-glucose, the final step in Leloir galactose synthesis. This subgroup has the characteristic active site tetrad and NAD-binding motif of the extended SDRs. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 323 matched cddid_all.tbl CDD cd05248 cd05248 187559 ADP_GME_SDR_e ADP-L-glycero-D-mannoheptose 6-epimerase (GME), extended (e) SDRs. This subgroup contains ADP-L-glycero-D-mannoheptose 6-epimerase, an extended SDR, which catalyzes the NAD-dependent interconversion of ADP-D-glycero-D-mannoheptose and ADP-L-glycero-D-mannoheptose. This subgroup has the canonical active site tetrad and NAD(P)-binding motif. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 317 matched cddid_all.tbl CDD cd05250 cd05250 187560 CC3_like_SDR_a CC3(TIP30)-like, atypical (a) SDRs. Atypical SDRs in this subgroup include CC3 (also known as TIP30) which is implicated in tumor suppression. Atypical SDRs are distinct from classical SDRs. Members of this subgroup have a glycine rich NAD(P)-binding motif that resembles the extended SDRs, and have an active site triad of the SDRs (YXXXK and upstream Ser), although the upstream Asn of the usual SDR active site is substituted with Asp. For CC3, the Tyr of the triad is displaced compared to the usual SDRs and the protein is monomeric, both these observations suggest that the usual SDR catalytic activity is not present. NADP appears to serve an important role as a ligand, and may be important in the interaction with other macromolecules. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 214 matched cddid_all.tbl CDD cd05251 cd05251 187561 NmrA_like_SDR_a NmrA (a transcriptional regulator) and HSCARG (an NADPH sensor) like proteins, atypical (a) SDRs. NmrA and HSCARG like proteins. NmrA is a negative transcriptional regulator of various fungi, involved in the post-translational modulation of the GATA-type transcription factor AreA. NmrA lacks the canonical GXXGXXG NAD-binding motif and has altered residues at the catalytic triad, including a Met instead of the critical Tyr residue. NmrA may bind nucleotides but appears to lack any dehydrogenase activity. HSCARG has been identified as a putative NADP-sensing molecule, and redistributes and restructures in response to NADPH/NADP ratios. Like NmrA, it lacks most of the active site residues of the SDR family, but has an NAD(P)-binding motif similar to the extended SDR family, GXXGXXG. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Atypical SDRs are distinct from classical SDRs. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 242 matched cddid_all.tbl CDD cd05252 cd05252 187562 CDP_GD_SDR_e CDP-D-glucose 4,6-dehydratase, extended (e) SDRs. This subgroup contains CDP-D-glucose 4,6-dehydratase, an extended SDR, which catalyzes the conversion of CDP-D-glucose to CDP-4-keto-6-deoxy-D-glucose. This subgroup has the characteristic active site tetrad and NAD-binding motif of the extended SDRs. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 336 matched cddid_all.tbl CDD cd05253 cd05253 187563 UDP_GE_SDE_e UDP glucuronic acid epimerase, extended (e) SDRs. This subgroup contains UDP-D-glucuronic acid 4-epimerase, an extended SDR, which catalyzes the conversion of UDP-alpha-D-glucuronic acid to UDP-alpha-D-galacturonic acid. This group has the SDR's canonical catalytic tetrad and the TGxxGxxG NAD-binding motif of the extended SDRs. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 332 matched cddid_all.tbl CDD cd05254 cd05254 187564 dTDP_HR_like_SDR_e dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs. dTDP-6-deoxy-L-lyxo-4-hexulose reductase, an extended SDR, synthesizes dTDP-L-rhamnose from alpha-D-glucose-1-phosphate, providing the precursor of L-rhamnose, an essential cell wall component of many pathogenic bacteria. This subgroup has the characteristic active site tetrad and NADP-binding motif. This subgroup also contains human MAT2B, the regulatory subunit of methionine adenosyltransferase (MAT); MAT catalyzes S-adenosylmethionine synthesis. The human gene encoding MAT2B encodes two major splicing variants which are induced in human cell liver cancer and regulate HuR, an mRNA-binding protein which stabilizes the mRNA of several cyclins, to affect cell proliferation. Both MAT2B variants include this extended SDR domain. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 280 matched cddid_all.tbl CDD cd05255 cd05255 187565 SQD1_like_SDR_e UDP_sulfoquinovose_synthase (Arabidopsis thaliana SQD1 and related proteins), extended (e) SDRs. Arabidopsis thaliana UDP-sulfoquinovose-synthase ( SQD1), an extended SDR, catalyzes the transfer of SO(3)(-) to UDP-glucose in the biosynthesis of plant sulfolipids. Members of this subgroup share the conserved SDR catalytic residues, and a partial match to the characteristic extended-SDR NAD-binding motif. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 382 matched cddid_all.tbl CDD cd05256 cd05256 187566 UDP_AE_SDR_e UDP-N-acetylglucosamine 4-epimerase, extended (e) SDRs. This subgroup contains UDP-N-acetylglucosamine 4-epimerase of Pseudomonas aeruginosa, WbpP, an extended SDR, that catalyzes the NAD+ dependent conversion of UDP-GlcNAc and UDPGalNA to UDP-Glc and UDP-Gal. This subgroup has the characteristic active site tetrad and NAD-binding motif of the extended SDRs. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 304 matched cddid_all.tbl CDD cd05257 cd05257 187567 Arna_like_SDR_e Arna decarboxylase_like, extended (e) SDRs. Decarboxylase domain of ArnA. ArnA, is an enzyme involved in the modification of outer membrane protein lipid A of gram-negative bacteria. It is a bifunctional enzyme that catalyzes the NAD-dependent decarboxylation of UDP-glucuronic acid and N-10-formyltetrahydrofolate-dependent formylation of UDP-4-amino-4-deoxy-l-arabinose; its NAD-dependent decaboxylating activity is in the C-terminal 360 residues. This subgroup belongs to the extended SDR family, however the NAD binding motif is not a perfect match and the upstream Asn of the canonical active site tetrad is not conserved. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 316 matched cddid_all.tbl CDD cd05258 cd05258 187568 CDP_TE_SDR_e CDP-tyvelose 2-epimerase, extended (e) SDRs. CDP-tyvelose 2-epimerase is a tetrameric SDR that catalyzes the conversion of CDP-D-paratose to CDP-D-tyvelose, the last step in tyvelose biosynthesis. This subgroup is a member of the extended SDR subfamily, with a characteristic active site tetrad and NAD-binding motif. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 337 matched cddid_all.tbl CDD cd05259 cd05259 187569 PCBER_SDR_a phenylcoumaran benzylic ether reductase (PCBER) like, atypical (a) SDRs. PCBER and pinoresinol-lariciresinol reductases are NADPH-dependent aromatic alcohol reductases, and are atypical members of the SDR family. Other proteins in this subgroup are identified as eugenol synthase. These proteins contain an N-terminus characteristic of NAD(P)-binding proteins and a small C-terminal domain presumed to be involved in substrate binding, but they do not have the conserved active site Tyr residue typically found in SDRs. Numerous other members have unknown functions. The glycine rich NADP-binding motif in this subgroup is of 2 forms: GXGXXG and G[GA]XGXXG; it tends to be atypical compared with the forms generally seen in classical or extended SDRs. The usual SDR active site tetrad is not present, but a critical active site Lys at the usual SDR position has been identified in various members, though other charged and polar residues are found at this position in this subgroup. Atypical SDR-related proteins retain the Rossmann fold of the SDRs, but have limited sequence identity and generally lack the catalytic properties of the archetypical members. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 282 matched cddid_all.tbl CDD cd05260 cd05260 187570 GDP_MD_SDR_e GDP-mannose 4,6 dehydratase, extended (e) SDRs. GDP-mannose 4,6 dehydratase, a homodimeric SDR, catalyzes the NADP(H)-dependent conversion of GDP-(D)-mannose to GDP-4-keto, 6-deoxy-(D)-mannose in the fucose biosynthesis pathway. These proteins have the canonical active site triad and NAD-binding pattern, however the active site Asn is often missing and may be substituted with Asp. A Glu residue has been identified as an important active site base. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 316 matched cddid_all.tbl CDD cd05261 cd05261 187571 CAPF_like_SDR_e capsular polysaccharide assembling protein (CAPF) like, extended (e) SDRs. This subgroup of extended SDRs, includes some members which have been identified as capsular polysaccharide assembling proteins, such as Staphylococcus aureus Cap5F which is involved in the biosynthesis of N-acetyl-l-fucosamine, a constituent of surface polysaccharide structures of S. aureus. This subgroup has the characteristic active site tetrad and NAD-binding motif of extended SDRs. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 248 matched cddid_all.tbl CDD cd05262 cd05262 187572 SDR_a7 atypical (a) SDRs, subgroup 7. This subgroup contains atypical SDRs of unknown function. Members of this subgroup have a glycine-rich NAD(P)-binding motif consensus that matches the extended SDRs, TGXXGXXG, but lacks the characteristic active site residues of the SDRs. This subgroup has basic residues (HXXXR) in place of the active site motif YXXXK, these may have a catalytic role. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 291 matched cddid_all.tbl CDD cd05263 cd05263 187573 MupV_like_SDR_e Pseudomonas fluorescens MupV-like, extended (e) SDRs. This subgroup of extended SDR family domains have the characteristic active site tetrad and a well-conserved NAD(P)-binding motif. This subgroup is not well characterized, its members are annotated as having a variety of putative functions. One characterized member is Pseudomonas fluorescens MupV a protein involved in the biosynthesis of Mupirocin, a polyketide-derived antibiotic. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 293 matched cddid_all.tbl CDD cd05264 cd05264 187574 UDP_G4E_5_SDR_e UDP-glucose 4-epimerase (G4E), subgroup 5, extended (e) SDRs. This subgroup partially conserves the characteristic active site tetrad and NAD-binding motif of the extended SDRs, and has been identified as possible UDP-glucose 4-epimerase (aka UDP-galactose 4-epimerase), a homodimeric member of the extended SDR family. UDP-glucose 4-epimerase catalyzes the NAD-dependent conversion of UDP-galactose to UDP-glucose, the final step in Leloir galactose synthesis. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 300 matched cddid_all.tbl CDD cd05265 cd05265 187575 SDR_a1 atypical (a) SDRs, subgroup 1. Atypical SDRs in this subgroup are poorly defined and have been identified putatively as isoflavones reductase, sugar dehydratase, mRNA binding protein etc. Atypical SDRs are distinct from classical SDRs. Members of this subgroup retain the canonical active site triad (though not the upstream Asn found in most SDRs) but have an unusual putative glycine-rich NAD(P)-binding motif, GGXXXXG, in the usual location. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 250 matched cddid_all.tbl CDD cd05266 cd05266 187576 SDR_a4 atypical (a) SDRs, subgroup 4. Atypical SDRs in this subgroup are poorly defined, one member is identified as a putative NAD-dependent epimerase/dehydratase. Atypical SDRs are distinct from classical SDRs. Members of this subgroup have a glycine-rich NAD(P)-binding motif that is related to, but is different from, the archetypical SDRs, GXGXXG. This subgroup also lacks most of the characteristic active site residues of the SDRs; however, the upstream Ser is present at the usual place, and some potential catalytic residues are present in place of the usual YXXXK active site motif. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 251 matched cddid_all.tbl CDD cd05267 cd05267 187577 SDR_a6 atypical (a) SDRs, subgroup 6. These atypical SDR family members of unknown function have only a partial match to a prototypical glycine-rich NAD(P)-binding motif consensus, GXXG, which conserves part of the motif of extended SDR. Furthermore, they lack the characteristic active site residues of the SDRs. This subgroup is related to phenylcoumaran benzylic ether reductase, an NADPH-dependent aromatic alcohol reductase. One member is identified as a putative NAD-dependent epimerase/dehydratase. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 203 matched cddid_all.tbl CDD cd05269 cd05269 187578 TMR_SDR_a triphenylmethane reductase (TMR)-like proteins, NMRa-like, atypical (a) SDRs. TMR is an atypical NADP-binding protein of the SDR family. It lacks the active site residues of the SDRs but has a glycine rich NAD(P)-binding motif that matches the extended SDRs. Proteins in this subgroup however, are more similar in length to the classical SDRs. TMR was identified as a reducer of triphenylmethane dyes, important environmental pollutants. This subgroup also includes Escherichia coli NADPH-dependent quinine oxidoreductase (QOR2), which catalyzes two-electron reduction of quinone; but is unlikely to play a major role in protecting against quinone cytotoxicity. Atypical SDRs are distinct from classical SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 272 matched cddid_all.tbl CDD cd05271 cd05271 187579 NDUFA9_like_SDR_a NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, subunit 9, 39 kDa, (NDUFA9) -like, atypical (a) SDRs. This subgroup of extended SDR-like proteins are atypical SDRs. They have a glycine-rich NAD(P)-binding motif similar to the typical SDRs, GXXGXXG, and have the YXXXK active site motif (though not the other residues of the SDR tetrad). Members identified include NDUFA9 (mitochondrial) and putative nucleoside-diphosphate-sugar epimerase. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 273 matched cddid_all.tbl CDD cd05272 cd05272 187580 TDH_SDR_e L-threonine dehydrogenase, extended (e) SDRs. This subgroup contains members identified as L-threonine dehydrogenase (TDH). TDH catalyzes the zinc-dependent formation of 2-amino-3-ketobutyrate from L-threonine via NAD(H)-dependent oxidation. This group is distinct from TDHs that are members of the medium chain dehydrogenase/reductase family. This group has the NAD-binding motif and active site tetrad of the extended SDRs. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 308 matched cddid_all.tbl CDD cd05273 cd05273 187581 GME-like_SDR_e Arabidopsis thaliana GDP-mannose-3',5'-epimerase (GME)-like, extended (e) SDRs. This subgroup of NDP-sugar epimerase/dehydratases are extended SDRs; they have the characteristic active site tetrad, and an NAD-binding motif: TGXXGXX[AG], which is a close match to the canonical NAD-binding motif. Members include Arabidopsis thaliana GDP-mannose-3',5'-epimerase (GME) which catalyzes the epimerization of two positions of GDP-alpha-D-mannose to form GDP-beta-L-galactose. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 328 matched cddid_all.tbl CDD cd05274 cd05274 187582 KR_FAS_SDR_x ketoreductase (KR) and fatty acid synthase (FAS), complex (x) SDRs. Ketoreductase, a module of the multidomain polyketide synthase (PKS), has 2 subdomains, each corresponding to a SDR family monomer. The C-terminal subdomain catalyzes the NADPH-dependent reduction of the beta-carbonyl of a polyketide to a hydroxyl group, a step in the biosynthesis of polyketides, such as erythromycin. The N-terminal subdomain, an interdomain linker, is a truncated Rossmann fold which acts to stabilizes the catalytic subdomain. Unlike typical SDRs, the isolated domain does not oligomerize but is composed of 2 subdomains, each resembling an SDR monomer. The active site resembles that of typical SDRs, except that the usual positions of the catalytic Asn and Tyr are swapped, so that the canonical YXXXK motif changes to YXXXN. Modular PKSs are multifunctional structures in which the makeup recapitulates that found in (and may have evolved from) FAS. In some instances, such as porcine FAS, an enoyl reductase (ER) module is inserted between the sub-domains. Fatty acid synthesis occurs via the stepwise elongation of a chain (which is attached to acyl carrier protein, ACP) with 2-carbon units. Eukaryotic systems consist of large, multifunctional synthases (type I) while bacterial, type II systems, use single function proteins. Fungal fatty acid synthase uses a dodecamer of 6 alpha and 6 beta subunits. In mammalian type FAS cycles, ketoacyl synthase forms acetoacetyl-ACP which is reduced by the NADP-dependent beta-KR, forming beta-hydroxyacyl-ACP, which is in turn dehydrated by dehydratase to a beta-enoyl intermediate, which is reduced by NADP-dependent beta-ER. Polyketide synthesis also proceeds via the addition of 2-carbon units as in fatty acid synthesis. The complex SDR NADP-binding motif, GGXGXXG, is often present, but is not strictly conserved in each instance of the module. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human prostaglandin dehydrogenase (PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107, PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type KRs have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 375 matched cddid_all.tbl CDD cd05276 cd05276 176180 p53_inducible_oxidoreductase PIG3 p53-inducible quinone oxidoreductase. PIG3 p53-inducible quinone oxidoreductase, a medium chain dehydrogenase/reductase family member, acts in the apoptotic pathway. PIG3 reduces ortho-quinones, but its apoptotic activity has been attributed to oxidative stress generation, since overexpression of PIG3 accumulates reactive oxygen species. PIG3 resembles the MDR family member quinone reductases, which catalyze the reduction of quinone to hydroxyquinone. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site, and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 323 matched cddid_all.tbl CDD cd05278 cd05278 176181 FDH_like Formaldehyde dehydrogenases. Formaldehyde dehydrogenase (FDH) is a member of the zinc-dependent/medium chain alcohol dehydrogenase family. Formaldehyde dehydrogenase (aka ADH3) may be the ancestral form of alcohol dehydrogenase, which evolved to detoxify formaldehyde. This CD contains glutathione dependant FDH, glutathione independent FDH, and related alcohol dehydrogenases. FDH converts formaldehyde and NAD(P) to formate and NAD(P)H. The initial step in this process the spontaneous formation of a S-(hydroxymethyl)glutathione adduct from formaldehyde and glutathione, followed by FDH-mediated oxidation (and detoxification) of the adduct to S-formylglutathione. Unlike typical FDH, Pseudomonas putida aldehyde-dismutating FDH (PFDH) is glutathione-independent. The medium chain alcohol dehydrogenase family (MDR) have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. 347 matched cddid_all.tbl CDD cd05279 cd05279 176182 Zn_ADH1 Liver alcohol dehydrogenase and related zinc-dependent alcohol dehydrogenases. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. There are 7 vertebrate ADH 7 classes, 6 of which have been identified in humans. Class III, glutathione-dependent formaldehyde dehydrogenase, has been identified as the primordial form and exists in diverse species, including plants, micro-organisms, vertebrates, and invertebrates. Class I, typified by liver dehydrogenase, is an evolving form. Gene duplication and functional specialization of ADH into ADH classes and subclasses created numerous forms in vertebrates. For example, the A, B and C (formerly alpha, beta, gamma) human class I subunits have high overall structural similarity, but differ in the substrate binding pocket and therefore in substrate specificity. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine (His-51), the ribose of NAD, a serine (Ser-48), then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of an beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. 365 matched cddid_all.tbl CDD cd05280 cd05280 176183 MDR_yhdh_yhfp Yhdh and yhfp-like putative quinone oxidoreductases. Yhdh and yhfp-like putative quinone oxidoreductases (QOR). QOR catalyzes the conversion of a quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR actin the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens protein in some vertebrates (e.g. zeta-crystalin). QOR reduces quinones through a semi-quinone intermediate via a NAD(P)H-dependent single electron transfer. QOR is a member of the medium chain dehydrogenase/reductase family, but lacks the zinc-binding sites of the prototypical alcohol dehydrogenases of this group. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 325 matched cddid_all.tbl CDD cd05281 cd05281 176184 TDH Threonine dehydrogenase. L-threonine dehydrogenase (TDH) catalyzes the zinc-dependent formation of 2-amino-3-ketobutyrate from L-threonine via NAD(H)- dependent oxidation. THD is a member of the zinc-requiring, medium chain NAD(H)-dependent alcohol dehydrogenase family (MDR). MDRs have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria) and have 2 tightly bound zinc atoms per subunit. Sorbitol and aldose reductase are NAD(+) binding proteins of the polyol pathway, which interconverts glucose and fructose. 341 matched cddid_all.tbl CDD cd05282 cd05282 176645 ETR_like 2-enoyl thioester reductase-like. 2-enoyl thioester reductase (ETR) catalyzes the NADPH-dependent conversion of trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl thioester reductase activity has been linked in Candida tropicalis as essential in maintaining mitiochondrial respiratory function. This ETR family is a part of the medium chain dehydrogenase/reductase family, but lack the zinc coordination sites characteristic of the alcohol dehydrogenases in this family. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. Candida tropicalis enoyl thioester reductase (Etr1p) catalyzes the NADPH-dependent reduction of trans-2-enoyl thioesters in mitochondrial fatty acid synthesis. Etr1p forms homodimers with each subunit containing a nucleotide-binding Rossmann fold domain and a catalytic domain. 323 matched cddid_all.tbl CDD cd05283 cd05283 176186 CAD1 Cinnamyl alcohol dehydrogenases (CAD). Cinnamyl alcohol dehydrogenases (CAD), members of the medium chain dehydrogenase/reductase family, reduce cinnamaldehydes to cinnamyl alcohols in the last step of monolignal metabolism in plant cells walls. CAD binds 2 zinc ions and is NADPH- dependent. CAD family members are also found in non-plant species, e.g. in yeast where they have an aldehyde reductase activity. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 337 matched cddid_all.tbl CDD cd05284 cd05284 176187 arabinose_DH_like D-arabinose dehydrogenase. This group contains arabinose dehydrogenase (AraDH) and related alcohol dehydrogenases. AraDH is a member of the medium chain dehydrogenase/reductase family and catalyzes the NAD(P)-dependent oxidation of D-arabinose and other pentoses, the initial step in the metabolism of d-arabinose into 2-oxoglutarate. Like the alcohol dehydrogenases, AraDH binds a zinc in the catalytic cleft as well as a distal structural zinc. AraDH forms homotetramers as a dimer of dimers. AraDH replaces a conserved catalytic His with replace with Arg, compared to the canonical ADH site. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 340 matched cddid_all.tbl CDD cd05285 cd05285 176188 sorbitol_DH Sorbitol dehydrogenase. Sorbitol and aldose reductase are NAD(+) binding proteins of the polyol pathway, which interconverts glucose and fructose. Sorbitol dehydrogenase is tetrameric and has a single catalytic zinc per subunit. Aldose reductase catalyzes the NADP(H)-dependent conversion of glucose to sorbital, and SDH uses NAD(H) in the conversion of sorbitol to fructose. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. The medium chain alcohol dehydrogenase family (MDR) have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. 343 matched cddid_all.tbl CDD cd05286 cd05286 176189 QOR2 Quinone oxidoreductase (QOR). Quinone oxidoreductase (QOR) and 2-haloacrylate reductase. QOR catalyzes the conversion of a quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR actin the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens protein in some vertebrates (e.g. zeta-crystalin). QOR reduces quinones through a semi-quinone intermediate via a NAD(P)H-dependent single electron transfer. QOR is a member of the medium chain dehydrogenase/reductase family, but lacks the zinc-binding sites of the prototypical alcohol dehydrogenases of this group. 2-haloacrylate reductase, a member of this subgroup, catalyzes the NADPH-dependent reduction of a carbon-carbon double bond in organohalogen compounds. Although similar to QOR, Burkholderia 2-haloacrylate reductase does not act on the quinones 1,4-benzoquinone and 1,4-naphthoquinone. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 320 matched cddid_all.tbl CDD cd05288 cd05288 176190 PGDH Prostaglandin dehydrogenases. Prostaglandins and related eicosanoids are metabolized by the oxidation of the 15(S)-hydroxyl group of the NAD+-dependent (type I 15-PGDH) 15-prostaglandin dehydrogenase (15-PGDH) followed by reduction by NADPH/NADH-dependent (type II 15-PGDH) delta-13 15-prostaglandin reductase (13-PGR) to 15-keto-13,14,-dihydroprostaglandins. 13-PGR is a bifunctional enzyme, since it also has leukotriene B(4) 12-hydroxydehydrogenase activity. These 15-PGDH and related enzymes are members of the medium chain dehydrogenase/reductase family. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. 329 matched cddid_all.tbl CDD cd05289 cd05289 176191 MDR_like_2 alcohol dehydrogenase and quinone reductase-like medium chain degydrogenases/reductases. Members identified as zinc-dependent alcohol dehydrogenases and quinone oxidoreductase. QOR catalyzes the conversion of a quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR actin the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens protein in some vertebrates (e.g. zeta-crystalin). QOR reduces quinones through a semi-quinone intermediate via a NAD(P)H-dependent single electron transfer. QOR is a member of the medium chain dehydrogenase/reductase family, but lacks the zinc-binding sites of the prototypical alcohol dehydrogenases of this group. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 309 matched cddid_all.tbl CDD cd05290 cd05290 133426 LDH_3 A subgroup of L-lactate dehydrogenases. L-lactate dehydrogenases (LDH) are tetrameric enzymes catalyzing the last step of glycolysis in which pyruvate is converted to L-lactate. This subgroup is composed of some bacterial LDHs from firmicutes, gammaproteobacteria, and actinobacteria. Vertebrate LDHs are non-allosteric, but some bacterial LDHs are activated by an allosteric effector such as fructose-1,6-bisphosphate. LDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenase, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. 307 matched cddid_all.tbl CDD cd05291 cd05291 133427 HicDH_like L-2-hydroxyisocapronate dehydrogenases and some bacterial L-lactate dehydrogenases. L-2-hydroxyisocapronate dehydrogenase (HicDH) catalyzes the conversion of a variety of 2-oxo carboxylic acids with medium-sized aliphatic or aromatic side chains. This subfamily is composed of HicDHs and some bacterial L-lactate dehydrogenases (LDH). LDHs catalyze the last step of glycolysis in which pyruvate is converted to L-lactate. Bacterial LDHs can be non-allosteric or may be activated by an allosteric effector such as fructose-1,6-bisphosphate. Members of this subfamily with known structures such as the HicDH of Lactobacillus confusus, the non-allosteric LDH of Lactobacillus pentosus, and the allosteric LDH of Bacillus stearothermophilus, show that they exist as homotetramers. The HicDH-like subfamily is part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. 306 matched cddid_all.tbl CDD cd05292 cd05292 133428 LDH_2 A subgroup of L-lactate dehydrogenases. L-lactate dehydrogenases (LDH) are tetrameric enzymes catalyzing the last step of glycolysis in which pyruvate is converted to L-lactate. This subgroup is composed predominantly of bacterial LDHs and a few fungal LDHs. Bacterial LDHs may be non-allosteric or may be activated by an allosteric effector such as fructose-1,6-bisphosphate. LDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. 308 matched cddid_all.tbl CDD cd05293 cd05293 133429 LDH_1 A subgroup of L-lactate dehydrogenases. L-lactate dehydrogenases (LDH) are tetrameric enzymes catalyzing the last step of glycolysis in which pyruvate is converted to L-lactate. This subgroup is composed of eukaryotic LDHs. Vertebrate LDHs are non-allosteric. This is in contrast to some bacterial LDHs that are activated by an allosteric effector such as fructose-1,6-bisphosphate. LDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. 312 matched cddid_all.tbl CDD cd05294 cd05294 133430 LDH-like_MDH_nadp A lactate dehydrogenases-like structure with malate dehydrogenase enzymatic activity. The LDH-like MDH proteins have a lactate dehyhydrogenase-like (LDH-like) structure and malate dehydrogenase (MDH) enzymatic activity. This subgroup is composed of some archaeal LDH-like MDHs that prefer NADP(H) rather than NAD(H) as a cofactor. One member, MJ0490 from Methanococcus jannaschii, has been observed to form dimers and tetramers during crystalization, although it is believed to exist primarilly as a tetramer in solution. In addition to its MDH activity, MJ0490 also possesses fructose-1,6-bisphosphate-activated LDH activity. Members of this subgroup have a higher sequence similarity to LDHs than to other MDHs. LDH catalyzes the last step of glycolysis in which pyruvate is converted to L-lactate. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. The LDH-like MDHs are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)- binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenase, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. 309 matched cddid_all.tbl CDD cd05295 cd05295 133431 MDH_like Malate dehydrogenase-like. These MDH-like proteins are related to other groups in the MDH family but do not have conserved substrate and cofactor binding residues. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. Members of this subgroup are uncharacterized MDH-like proteins from animals. They are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. 452 matched cddid_all.tbl CDD cd05296 cd05296 133432 GH4_P_beta_glucosidase Glycoside Hydrolases Family 4; Phospho-beta-glucosidase. Some bacteria simultaneously translocate and phosphorylate disaccharides via the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS). After translocation, these phospho-disaccharides may be hydrolyzed by the GH4 glycoside hydrolases such as the phospho-beta-glucosidases. Other organisms (such as archaea and Thermotoga maritima ) lack the PEP-PTS system, but have several enzymes normally associated with the PEP-PTS operon. The 6-phospho-beta-glucosidase from Thermotoga maritima hydrolylzes cellobiose 6-phosphate (6P) into glucose-6P and glucose, in an NAD+ and Mn2+ dependent fashion. The Escherichia coli 6-phospho-beta-glucosidase (also called celF) hydrolyzes a variety of phospho-beta-glucosides including cellobiose-6P, salicin-6P, arbutin-6P, and gentobiose-6P. Phospho-beta-glucosidases are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. 419 matched cddid_all.tbl CDD cd05297 cd05297 133433 GH4_alpha_glucosidase_galactosidase Glycoside Hydrolases Family 4; Alpha-glucosidases and alpha-galactosidases. linked to 3D####ucture 423 matched cddid_all.tbl CDD cd05298 cd05298 133434 GH4_GlvA_pagL_like Glycoside Hydrolases Family 4; GlvA- and pagL-like glycosidases. Bacillus subtilis GlvA and Clostridium acetobutylicum pagL are 6-phospho-alpha-glucosidase, catalyzing the hydrolysis of alpha-glucopyranoside bonds to release glucose from oligosaccharides. The substrate specificities of other members of this subgroup are unknown. Some bacteria simultaneously translocate and phosphorylate disaccharides via the phosphoenolpyruvate-dependent phosphotransferase system (PEP_PTS). After translocation, these phospho-disaccharides may be hydrolyzed by the GH4 glycoside hydrolases, which include 6-phospho-beta-glucosidases, 6-phospho-alpha-glucosidases, alpha-glucosidases/alpha-glucuronidases (only from Thermotoga), and alpha-galactosidases. Members of this subfamily are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. 437 matched cddid_all.tbl CDD cd05299 cd05299 240624 CtBP_dh C-terminal binding protein (CtBP), D-isomer-specific 2-hydroxyacid dehydrogenases related repressor. The transcriptional corepressor CtBP is a dehydrogenase with sequence and structural similarity to the d2-hydroxyacid dehydrogenase family. CtBP was initially identified as a protein that bound the PXDLS sequence at the adenovirus E1A C terminus, causing the loss of CR-1-mediated transactivation. CtBP binds NAD(H) within a deep cleft, undergoes a conformational change upon NAD binding, and has NAD-dependent dehydrogenase activity. 312 matched cddid_all.tbl CDD cd05300 cd05300 240625 2-Hacid_dh_1 Putative D-isomer specific 2-hydroxyacid dehydrogenase. 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomains but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of the hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases. FDHs are found in all methylotrophic microorganisms in energy production and in the stress responses of plants. 313 matched cddid_all.tbl CDD cd05301 cd05301 240626 GDH D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH). D-glycerate dehydrogenase (GDH, also known as hydroxypyruvate reductase, HPR) catalyzes the reversible reaction of (R)-glycerate + NAD+ to hydroxypyruvate + NADH + H+. In humans, HPR deficiency causes primary hyperoxaluria type 2, characterized by over-excretion of L-glycerate and oxalate in the urine, possibly due to an imbalance in competition with L-lactate dehydrogenase, another formate dehydrogenase (FDH)-like enzyme. GDH, like FDH and other members of the D-specific hydroxyacid dehydrogenase family that also includes L-alanine dehydrogenase and S-adenosylhomocysteine hydrolase, typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann-fold NAD+ binding form, despite often low sequence identity. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 309 matched cddid_all.tbl CDD cd05302 cd05302 240627 FDH NAD-dependent Formate Dehydrogenase (FDH). NAD-dependent formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of a formate anion to carbon dioxide coupled with the reduction of NAD+ to NADH. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxy acid dehydrogenase family have 2 highly similar subdomains of the alpha/beta form, with NAD binding occurring in the cleft between subdomains. NAD contacts are primarily to the Rossmann-fold NAD-binding domain which is inserted within the linear sequence of the more diverse flavodoxin-like catalytic subdomain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of the hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases. FDHs are found in all methylotrophic microorganisms in energy production from C1 compounds such as methanol, and in the stress responses of plants. NAD-dependent FDH is useful in cofactor regeneration in asymmetrical biocatalytic reduction processes, where FDH irreversibly oxidizes formate to carbon dioxide, while reducing the oxidized form of the cofactor to the reduced form. 348 matched cddid_all.tbl CDD cd05303 cd05303 240628 PGDH_2 Phosphoglycerate dehydrogenase (PGDH) NAD-binding and catalytic domains. Phosphoglycerate dehydrogenase (PGDH) catalyzes the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDH comes in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases. PGDH in E. coli and Mycobacterium tuberculosis form tetramers, with subunits containing a Rossmann-fold NAD binding domain. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine Hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. 301 matched cddid_all.tbl CDD cd05304 cd05304 240629 Rubrum_tdh Rubrum transdehydrogenase NAD-binding and catalytic domains. Transhydrogenases found in bacterial and inner mitochondrial membranes link NAD(P)(H)-dependent redox reactions to proton translocation. The energy of the proton electrochemical gradient (delta-p), generated by the respiratory electron transport chain, is consumed by transhydrogenase in NAD(P)+ reduction. Transhydrogenase is likely involved in the regulation of the citric acid cycle. Rubrum transhydrogenase has 3 components, dI, dII, and dIII. dII spans the membrane while dI and dIII protrude on the cytoplasmic/matrix side. DI contains 2 domains in Rossmann-like folds, linked by a long alpha helix, and contains a NAD binding site. Two dI polypeptides (represented in this sub-family) spontaneously form a heterotrimer with dIII in the absence of dII. In the heterotrimer, both dI chains may bind NAD, but only one is well-ordered. dIII also binds a well-ordered NADP, but in a different orientation than a classical Rossmann domain. 363 matched cddid_all.tbl CDD cd05305 cd05305 240630 L-AlaDH Alanine dehydrogenase NAD-binding and catalytic domains. Alanine dehydrogenase (L-AlaDH) catalyzes the NAD-dependent conversion of pyruvate to L-alanine via reductive amination. Like formate dehydrogenase and related enzymes, L-AlaDH is comprised of 2 domains connected by a long alpha helical stretch, each resembling a Rossmann fold NAD-binding domain. The NAD-binding domain is inserted within the linear sequence of the more divergent catalytic domain. Ligand binding and active site residues are found in the cleft between the subdomains. L-AlaDH is typically hexameric and is critical in carbon and nitrogen metabolism in micro-organisms. 359 matched cddid_all.tbl CDD cd05311 cd05311 133453 NAD_bind_2_malic_enz NAD(P) binding domain of malic enzyme (ME), subgroup 2. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. This subfamily consists primarily of archaeal and bacterial ME. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. 226 matched cddid_all.tbl CDD cd05312 cd05312 133454 NAD_bind_1_malic_enz NAD(P) binding domain of malic enzyme (ME), subgroup 1. Malic enzyme (ME), a member of the amino acid dehydrogenase (DH)-like domain family, catalyzes the oxidative decarboxylation of L-malate to pyruvate in the presence of cations (typically Mg++ or Mn++) with the concomitant reduction of cofactor NAD+ or NADP+. ME has been found in all organisms, and plays important roles in diverse metabolic pathways such as photosynthesis and lipogenesis. This enzyme generally forms homotetramers. The conversion of malate to pyruvate by ME typically involves oxidation of malate to produce oxaloacetate, followed by decarboxylation of oxaloacetate to produce pyruvate and CO2. This subfamily consists of eukaryotic and bacterial ME. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. 279 matched cddid_all.tbl CDD cd05313 cd05313 133455 NAD_bind_2_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 2. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia asimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha -beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts. 254 matched cddid_all.tbl CDD cd05322 cd05322 187583 SDH_SDR_c_like Sorbitol 6-phosphate dehydrogenase (SDH), classical (c) SDRs. Sorbitol 6-phosphate dehydrogenase (SDH, aka glucitol 6-phosphate dehydrogenase) catalyzes the NAD-dependent interconversion of D-fructose 6-phosphate to D-sorbitol 6-phosphate. SDH is a member of the classical SDRs, with the characteristic catalytic tetrad, but without a complete match to the typical NAD-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 257 matched cddid_all.tbl CDD cd05323 cd05323 187584 ADH_SDR_c_like insect type alcohol dehydrogenase (ADH)-like, classical (c) SDRs. This subgroup contains insect type ADH, and 15-hydroxyprostaglandin dehydrogenase (15-PGDH) type I; these proteins are classical SDRs. ADH catalyzes the NAD+-dependent oxidation of alcohols to aldehydes/ketones. This subgroup is distinct from the zinc-dependent alcohol dehydrogenases of the medium chain dehydrogenase/reductase family, and evolved in fruit flies to allow the digestion of fermenting fruit. 15-PGDH catalyzes the NAD-dependent interconversion of (5Z,13E)-(15S)-11alpha,15-dihydroxy-9-oxoprost-13-enoate and (5Z,13E)-11alpha-hydroxy-9,15-dioxoprost-13-enoate, and has a typical SDR glycine-rich NAD-binding motif, which is not fully present in ADH. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 244 matched cddid_all.tbl CDD cd05324 cd05324 187585 carb_red_PTCR-like_SDR_c Porcine testicular carbonyl reductase (PTCR)-like, classical (c) SDRs. PTCR is a classical SDR which catalyzes the NADPH-dependent reduction of ketones on steroids and prostaglandins. Unlike most SDRs, PTCR functions as a monomer. This subgroup also includes human carbonyl reductase 1 (CBR1) and CBR3. CBR1 is an NADPH-dependent SDR with broad substrate specificity and may be responsible for the in vivo reduction of quinones, prostaglandins, and other carbonyl-containing compounds. In addition it includes poppy NADPH-dependent salutaridine reductase which catalyzes the stereospecific reduction of salutaridine to 7(S)-salutaridinol in the biosynthesis of morphine, and Arabidopsis SDR1,a menthone reductase, which catalyzes the reduction of menthone to neomenthol, a compound with antimicrobial activity; SDR1 can also carry out neomenthol oxidation. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 225 matched cddid_all.tbl CDD cd05325 cd05325 187586 carb_red_sniffer_like_SDR_c carbonyl reductase sniffer-like, classical (c) SDRs. Sniffer is an NADPH-dependent carbonyl reductase of the classical SDR family. Studies in Drosophila melanogaster implicate Sniffer in the prevention of neurodegeneration due to aging and oxidative-stress. This subgroup also includes Rhodococcus sp. AD45 IsoH, which is an NAD-dependent 1-hydroxy-2-glutathionyl-2-methyl-3-butene dehydrogenase involved in isoprene metabolism, Aspergillus nidulans StcE encoded by a gene which is part of a proposed sterigmatocystin biosynthesis gene cluster, Bacillus circulans SANK 72073 BtrF encoded by a gene found in the butirosin biosynthesis gene cluster, and Aspergillus parasiticus nor-1 involved in the biosynthesis of aflatoxins. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 233 matched cddid_all.tbl CDD cd05326 cd05326 187587 secoisolariciresinol-DH_like_SDR_c secoisolariciresinol dehydrogenase (secoisolariciresinol-DH)-like, classical (c) SDRs. Podophyllum secoisolariciresinol-DH is a homo tetrameric, classical SDR that catalyzes the NAD-dependent conversion of (-)-secoisolariciresinol to (-)-matairesinol via a (-)-lactol intermediate. (-)-Matairesinol is an intermediate to various 8'-lignans, including the cancer-preventive mammalian lignan, and those involved in vascular plant defense. This subgroup also includes rice momilactone A synthase which catalyzes the conversion of 3beta-hydroxy-9betaH-pimara-7,15-dien-19,6beta-olide into momilactone A, Arabidopsis ABA2 which during abscisic acid (ABA) biosynthesis, catalyzes the conversion of xanthoxin to abscisic aldehyde and, maize Tasselseed2 which participate in the maize sex determination pathway. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 249 matched cddid_all.tbl CDD cd05327 cd05327 212492 retinol-DH_like_SDR_c_like retinol dehydrogenase (retinol-DH), Light dependent Protochlorophyllide (Pchlide) OxidoReductase (LPOR) and related proteins, classical (c) SDRs. Classical SDR subgroup containing retinol-DHs, LPORs, and related proteins. Retinol is processed by a medium chain alcohol dehydrogenase followed by retinol-DHs. Pchlide reductases act in chlorophyll biosynthesis. There are distinct enzymes that catalyze Pchlide reduction in light or dark conditions. Light-dependent reduction is via an NADP-dependent SDR, LPOR. Proteins in this subfamily share the glycine-rich NAD-binding motif of the classical SDRs, have a partial match to the canonical active site tetrad, but lack the typical active site Ser. This subgroup includes the human proteins: retinol dehydrogenase -12, -13 ,and -14, dehydrogenase/reductase SDR family member (DHRS)-12 , -13 and -X (a DHRS on chromosome X), and WWOX (WW domain-containing oxidoreductase), as well as a Neurospora crassa SDR encoded by the blue light inducible bli-4 gene. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 269 matched cddid_all.tbl CDD cd05328 cd05328 187589 3alpha_HSD_SDR_c alpha hydroxysteroid dehydrogenase (3alpha_HSD), classical (c) SDRs. Bacterial 3-alpha_HSD, which catalyzes the NAD-dependent oxidoreduction of hydroxysteroids, is a dimeric member of the classical SDR family. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 250 matched cddid_all.tbl CDD cd05329 cd05329 187590 TR_SDR_c tropinone reductase-I and II (TR-1, and TR-II)-like, classical (c) SDRs. This subgroup includes TR-I and TR-II; these proteins are members of the SDR family. TRs catalyze the NADPH-dependent reductions of the 3-carbonyl group of tropinone, to a beta-hydroxyl group. TR-I and TR-II produce different stereoisomers from tropinone, TR-I produces tropine (3alpha-hydroxytropane), and TR-II, produces pseudotropine (sigma-tropine, 3beta-hydroxytropane). SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 251 matched cddid_all.tbl CDD cd05330 cd05330 187591 cyclohexanol_reductase_SDR_c cyclohexanol reductases, including levodione reductase, classical (c) SDRs. Cyloclohexanol reductases,including (6R)-2,2,6-trimethyl-1,4-cyclohexanedione (levodione) reductase of Corynebacterium aquaticum, catalyze the reversible oxidoreduction of hydroxycyclohexanone derivatives. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 257 matched cddid_all.tbl CDD cd05331 cd05331 187592 DH-DHB-DH_SDR_c 2,3 dihydro-2,3 dihydrozybenzoate dehydrogenases, classical (c) SDRs. 2,3 dihydro-2,3 dihydrozybenzoate dehydrogenase shares the characteristics of the classical SDRs. This subgroup includes Escherichai coli EntA which catalyzes the NAD+-dependent oxidation of 2,3-dihydro-2,3-dihydroxybenzoate to 2,3-dihydroxybenzoate during biosynthesis of the siderophore Enterobactin. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 244 matched cddid_all.tbl CDD cd05332 cd05332 187593 11beta-HSD1_like_SDR_c 11beta-hydroxysteroid dehydrogenase type 1 (11beta-HSD1)-like, classical (c) SDRs. Human 11beta_HSD1 catalyzes the NADP(H)-dependent interconversion of cortisone and cortisol. This subgroup also includes human dehydrogenase/reductase SDR family member 7C (DHRS7C) and DHRS7B. These proteins have the GxxxGxG nucleotide binding motif and S-Y-K catalytic triad characteristic of the SDRs, but have an atypical C-terminal domain that contributes to homodimerization contacts. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 257 matched cddid_all.tbl CDD cd05333 cd05333 187594 BKR_SDR_c beta-Keto acyl carrier protein reductase (BKR), involved in Type II FAS, classical (c) SDRs. This subgroup includes the Escherichai coli K12 BKR, FabG. BKR catalyzes the NADPH-dependent reduction of ACP in the first reductive step of de novo fatty acid synthesis (FAS). FAS consists of four elongation steps, which are repeated to extend the fatty acid chain through the addition of two-carbo units from malonyl acyl-carrier protein (ACP): condensation, reduction, dehydration, and a final reduction. Type II FAS, typical of plants and many bacteria, maintains these activities on discrete polypeptides, while type I FAS utilizes one or two multifunctional polypeptides. BKR resembles enoyl reductase, which catalyzes the second reduction step in FAS. SDRs are a functionally diverse family of oxidoreductases that have a single domain with structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet) NAD(P)(H) binding region and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H) binding pattern: TGxxxGxG in classical SDRs. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P) binding motif and an altered active site motif (YXXXN). Fungal type type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P) binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr-151 and Lys-155, and well as Asn-111 (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 240 matched cddid_all.tbl CDD cd05334 cd05334 187595 DHPR_SDR_c_like dihydropteridine reductase (DHPR), classical (c) SDRs. Dihydropteridine reductase is an NAD-binding protein related to the SDRs. It converts dihydrobiopterin into tetrahydrobiopterin, a cofactor necessary in catecholamines synthesis. Dihydropteridine reductase has the YXXXK of these tyrosine-dependent oxidoreductases, but lacks the typical upstream Asn and Ser catalytic residues. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 221 matched cddid_all.tbl CDD cd05337 cd05337 187596 BKR_1_SDR_c putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR), subgroup 1, classical (c) SDR. This subgroup includes Escherichia coli CFT073 FabG. The Escherichai coli K12 BKR, FabG, belongs to a different subgroup. BKR catalyzes the NADPH-dependent reduction of ACP in the first reductive step of de novo fatty acid synthesis (FAS). FAS consists of four elongation steps, which are repeated to extend the fatty acid chain through the addition of two-carbo units from malonyl acyl-carrier protein (ACP): condensation, reduction, dehydration, and a final reduction. Type II FAS, typical of plants and many bacteria, maintains these activities on discrete polypeptides, while type I FAS utilizes one or two multifunctional polypeptides. BKR resembles enoyl reductase, which catalyzes the second reduction step in FAS. SDRs are a functionally diverse family of oxidoreductases that have a single domain with structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet) NAD(P)(H) binding region and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H) binding pattern: TGxxxGxG in classical SDRs. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P) binding motif and an altered active site motif (YXXXN). Fungal type type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P) binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr-151 and Lys-155, and well as Asn-111 (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 255 matched cddid_all.tbl CDD cd05338 cd05338 187597 DHRS1_HSDL2-like_SDR_c human dehydrogenase/reductase (SDR family) member 1 (DHRS1) and human hydroxysteroid dehydrogenase-like protein 2 (HSDL2), classical (c) SDRs. This subgroup includes human DHRS1 and human HSDL2 and related proteins. These are members of the classical SDR family, with a canonical Gly-rich NAD-binding motif and the typical YXXXK active site motif. However, the rest of the catalytic tetrad is not strongly conserved. DHRS1 mRNA has been detected in many tissues, liver, heart, skeletal muscle, kidney and pancreas; a longer transcript is predominantly expressed in the liver , a shorter one in the heart. HSDL2 may play a part in fatty acid metabolism, as it is found in peroxisomes. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 246 matched cddid_all.tbl CDD cd05339 cd05339 187598 17beta-HSDXI-like_SDR_c human 17-beta-hydroxysteroid dehydrogenase XI-like, classical (c) SDRs. 17-beta-hydroxysteroid dehydrogenases (17betaHSD) are a group of isozymes that catalyze activation and inactivation of estrogen and androgens. 17betaHSD type XI, a classical SDR, preferentially converts 3alpha-Adiol to androsterone but not numerous other tested steroids. This subgroup of classical SDRs also includes members identified as retinol dehydrogenases, which convert retinol to retinal, a property that overlaps with 17betaHSD activity. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 243 matched cddid_all.tbl CDD cd05340 cd05340 187599 Ycik_SDR_c Escherichia coli K-12 YCIK-like, classical (c) SDRs. Escherichia coli K-12 YCIK and related proteins have a canonical classical SDR nucleotide-binding motif and active site tetrad. They are predicted oxoacyl-(acyl carrier protein/ACP) reductases. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 236 matched cddid_all.tbl CDD cd05341 cd05341 187600 3beta-17beta-HSD_like_SDR_c 3beta17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs. This subgroup includes members identified as 3beta17beta hydroxysteroid dehydrogenase, 20beta hydroxysteroid dehydrogenase, and R-alcohol dehydrogenase. These proteins exhibit the canonical active site tetrad and glycine rich NAD(P)-binding motif of the classical SDRs. 17beta-dehydrogenases are a group of isozymes that catalyze activation and inactivation of estrogen and androgens, and include members of the SDR family. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 247 matched cddid_all.tbl CDD cd05343 cd05343 187601 Mgc4172-like_SDR_c human Mgc4172-like, classical (c) SDRs. Human Mgc4172-like proteins, putative SDRs. These proteins are members of the SDR family, with a canonical active site tetrad and a typical Gly-rich NAD-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 250 matched cddid_all.tbl CDD cd05344 cd05344 187602 BKR_like_SDR_like putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR)-like, SDR. This subgroup resembles the SDR family, but does not have a perfect match to the NAD-binding motif or the catalytic tetrad characteristic of the SDRs. It includes the SDRs, Q9HYA2 from Pseudomonas aeruginosa PAO1 and APE0912 from Aeropyrum pernix K1. BKR catalyzes the NADPH-dependent reduction of ACP in the first reductive step of de novo fatty acid synthesis (FAS). FAS consists of four elongation steps, which are repeated to extend the fatty acid chain through the addition of two-carbo units from malonyl acyl-carrier protein (ACP): condensation, reduction, dehydration, and a final reduction. Type II FAS, typical of plants and many bacteria, maintains these activities on discrete polypeptides, while type I FAS utilizes one or two multifunctional polypeptides. BKR resembles enoyl reductase, which catalyzes the second reduction step in FAS. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 253 matched cddid_all.tbl CDD cd05345 cd05345 187603 BKR_3_SDR_c putative beta-ketoacyl acyl carrier protein [ACP] reductase (BKR), subgroup 3, classical (c) SDR. This subgroup includes the putative Brucella melitensis biovar Abortus 2308 BKR, FabG, Mesorhizobium loti MAFF303099 FabG, and other classical SDRs. BKR, a member of the SDR family, catalyzes the NADPH-dependent reduction of acyl carrier protein in the first reductive step of de novo fatty acid synthesis (FAS). FAS consists of 4 elongation steps, which are repeated to extend the fatty acid chain thru the addition of two-carbo units from malonyl acyl-carrier protein (ACP): condensation, reduction, dehydration, and final reduction. Type II FAS, typical of plants and many bacteria, maintains these activities on discrete polypeptides, while type I Fas utilizes one or 2 multifunctional polypeptides. BKR resembles enoyl reductase, which catalyzes the second reduction step in FAS. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 248 matched cddid_all.tbl CDD cd05346 cd05346 187604 SDR_c5 classical (c) SDR, subgroup 5. These proteins are members of the classical SDR family, with a canonical active site tetrad and a typical Gly-rich NAD-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 249 matched cddid_all.tbl CDD cd05347 cd05347 187605 Ga5DH-like_SDR_c gluconate 5-dehydrogenase (Ga5DH)-like, classical (c) SDRs. Ga5DH catalyzes the NADP-dependent conversion of carbon source D-gluconate and 5-keto-D-gluconate. This SDR subgroup has a classical Gly-rich NAD(P)-binding motif and a conserved active site tetrad pattern. However, it has been proposed that Arg104 (Streptococcus suis Ga5DH numbering), as well as an active site Ca2+, play a critical role in catalysis. In addition to Ga5DHs this subgroup contains Erwinia chrysanthemi KduD which is involved in pectin degradation, and is a putative 2,5-diketo-3-deoxygluconate dehydrogenase. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107,15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 248 matched cddid_all.tbl CDD cd05348 cd05348 187606 BphB-like_SDR_c cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB)-like, classical (c) SDRs. cis-biphenyl-2,3-dihydrodiol-2,3-dehydrogenase (BphB) is a classical SDR, it is of particular importance for its role in the degradation of biphenyl/polychlorinated biphenyls(PCBs); PCBs are a significant source of environmental contamination. This subgroup also includes Pseudomonas putida F1 cis-biphenyl-1,2-dihydrodiol-1,2-dehydrogenase (aka cis-benzene glycol dehydrogenase, encoded by the bnzE gene), which participates in benzene metabolism. In addition it includes Pseudomonas sp. C18 putative 1,2-dihydroxy-1,2-dihydronaphthalene dehydrogenase (aka dibenzothiophene dihydrodiol dehydrogenase, encoded by the doxE gene) which participates in an upper naphthalene catabolic pathway. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 257 matched cddid_all.tbl CDD cd05349 cd05349 187607 BKR_2_SDR_c putative beta-ketoacyl acyl carrier protein [ACP]reductase (BKR), subgroup 2, classical (c) SDR. This subgroup includes Rhizobium sp. NGR234 FabG1. The Escherichai coli K12 BKR, FabG, belongs to a different subgroup. BKR catalyzes the NADPH-dependent reduction of ACP in the first reductive step of de novo fatty acid synthesis (FAS). FAS consists of four elongation steps, which are repeated to extend the fatty acid chain through the addition of two-carbo units from malonyl acyl-carrier protein (ACP): condensation, reduction, dehydration, and a final reduction. Type II FAS, typical of plants and many bacteria, maintains these activities on discrete polypeptides, while type I FAS utilizes one or two multifunctional polypeptides. BKR resembles enoyl reductase, which catalyzes the second reduction step in FAS. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 246 matched cddid_all.tbl CDD cd05350 cd05350 187608 SDR_c6 classical (c) SDR, subgroup 6. These proteins are members of the classical SDR family, with a canonical active site tetrad and a fairly well conserved typical Gly-rich NAD-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 239 matched cddid_all.tbl CDD cd05351 cd05351 187609 XR_like_SDR_c xylulose reductase-like, classical (c) SDRs. Members of this subgroup include proteins identified as L-xylulose reductase (XR) and carbonyl reductase; they are members of the SDR family. XR, catalyzes the NADP-dependent reduction of L-xyulose and other sugars. Tetrameric mouse carbonyl reductase is involved in the metabolism of biogenic and xenobiotic carbonyl compounds. This subgroup also includes tetrameric chicken liver D-erythrulose reductase, which catalyzes the reduction of D-erythrulose to D-threitol. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). 244 matched cddid_all.tbl CDD cd05352 cd05352 187610 MDH-like_SDR_c mannitol dehydrogenase (MDH)-like, classical (c) SDRs. NADP-mannitol dehydrogenase catalyzes the conversion of fructose to mannitol, an acyclic 6-carbon sugar. MDH is a tetrameric member of the SDR family. This subgroup also includes various other tetrameric SDRs, including Pichia stipitis D-arabinitol dehydrogenase (aka polyol dehydrogenase), Candida albicans Sou1p, a sorbose reductase, and Candida parapsilosis (S)-specific carbonyl reductase (SCR, aka S-specific alcohol dehydrogenase) which catalyzes the enantioselective reduction of 2-hydroxyacetophenone into (S)-1-phenyl-1,2-ethanediol. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). 252 matched cddid_all.tbl CDD cd05353 cd05353 187611 hydroxyacyl-CoA-like_DH_SDR_c-like (3R)-hydroxyacyl-CoA dehydrogenase-like, classical(c)-like SDRs. Beta oxidation of fatty acids in eukaryotes occurs by a four-reaction cycle, that may take place in mitochondria or in peroxisomes. (3R)-hydroxyacyl-CoA dehydrogenase is part of rat peroxisomal multifunctional MFE-2, it is a member of the NAD-dependent SDRs, but contains an additional small C-terminal domain that completes the active site pocket and participates in dimerization. The atypical, additional C-terminal extension allows for more extensive dimerization contact than other SDRs. MFE-2 catalyzes the second and third reactions of the peroxisomal beta oxidation cycle. Proteins in this subgroup have a typical catalytic triad, but have a His in place of the usual upstream Asn. This subgroup also contains members identified as 17-beta-hydroxysteroid dehydrogenases, including human peroxisomal 17-beta-hydroxysteroid dehydrogenase type 4 (17beta-HSD type 4, aka MFE-2, encoded by HSD17B4 gene) which is involved in fatty acid beta-oxidation and steroid metabolism. This subgroup also includes two SDR domains of the Neurospora crassa and Saccharomyces cerevisiae multifunctional beta-oxidation protein (MFP, aka Fox2). SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 250 matched cddid_all.tbl CDD cd05354 cd05354 187612 SDR_c7 classical (c) SDR, subgroup 7. These proteins are members of the classical SDR family, with a canonical active site triad (and also an active site Asn) and a typical Gly-rich NAD-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 235 matched cddid_all.tbl CDD cd05355 cd05355 187613 SDR_c1 classical (c) SDR, subgroup 1. These proteins are members of the classical SDR family, with a canonical active site tetrad and a typical Gly-rich NAD-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 270 matched cddid_all.tbl CDD cd05356 cd05356 187614 17beta-HSD1_like_SDR_c 17-beta-hydroxysteroid dehydrogenases (17beta-HSDs) types -1, -3, and -12, -like, classical (c) SDRs. This subgroup includes various 17-beta-hydroxysteroid dehydrogenases and 3-ketoacyl-CoA reductase, these are members of the SDR family, and contain the canonical active site tetrad and glycine-rich NAD-binding motif of the classical SDRs. 3-ketoacyl-CoA reductase (KAR, aka 17beta-HSD type 12, encoded by HSD17B12) acts in fatty acid elongation; 17beta- hydroxysteroid dehydrogenases are isozymes that catalyze activation and inactivation of estrogen and androgens, and include members of the SDR family. 17beta-estradiol dehydrogenase (aka 17beta-HSD type 1, encoded by HSD17B1) converts estrone to estradiol. Estradiol is the predominant female sex hormone. 17beta-HSD type 3 (aka testosterone 17-beta-dehydrogenase 3, encoded by HSD17B3) catalyses the reduction of androstenedione to testosterone, it also accepts estrogens as substrates. This subgroup also contains a putative steroid dehydrogenase let-767 from Caenorhabditis elegans, mutation in which results in hypersensitivity to cholesterol limitation. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 239 matched cddid_all.tbl CDD cd05357 cd05357 187615 PR_SDR_c pteridine reductase (PR), classical (c) SDRs. Pteridine reductases (PRs), members of the SDR family, catalyzes the NAD-dependent reduction of folic acid, dihydrofolate and related compounds. In Leishmania, pteridine reductase (PTR1) acts to circumvent the anti-protozoan drugs that attack dihydrofolate reductase activity. Proteins in this subgroup have an N-terminal NAD-binding motif and a YxxxK active site motif, but have an Asp instead of the usual upstream catalytic Ser. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 234 matched cddid_all.tbl CDD cd05358 cd05358 187616 GlcDH_SDR_c glucose 1 dehydrogenase (GlcDH), classical (c) SDRs. GlcDH, is a tetrameric member of the SDR family, it catalyzes the NAD(P)-dependent oxidation of beta-D-glucose to D-glucono-delta-lactone. GlcDH has a typical NAD-binding site glycine-rich pattern as well as the canonical active site tetrad (YXXXK motif plus upstream Ser and Asn). SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 253 matched cddid_all.tbl CDD cd05359 cd05359 187617 ChcA_like_SDR_c 1-cyclohexenylcarbonyl_coenzyme A_reductase (ChcA)_like, classical (c) SDRs. This subgroup contains classical SDR proteins, including members identified as 1-cyclohexenylcarbonyl coenzyme A reductase. ChcA of Streptomyces collinus is implicated in the final reduction step of shikimic acid to ansatrienin. ChcA shows sequence similarity to the SDR family of NAD-binding proteins, but it lacks the conserved Tyr of the characteristic catalytic site. This subgroup also contains the NADH-dependent enoyl-[acyl-carrier-protein(ACP)] reductase FabL from Bacillus subtilis. This enzyme participates in bacterial fatty acid synthesis, in type II fatty-acid synthases and catalyzes the last step in each elongation cycle. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 242 matched cddid_all.tbl CDD cd05360 cd05360 187618 SDR_c3 classical (c) SDR, subgroup 3. These proteins are members of the classical SDR family, with a canonical active site triad (and also active site Asn) and a typical Gly-rich NAD-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 233 matched cddid_all.tbl CDD cd05361 cd05361 187619 haloalcohol_DH_SDR_c-like haloalcohol dehalogenase, classical (c) SDRs. Dehalogenases cleave carbon-halogen bonds. Haloalcohol dehalogenase show low sequence similarity to short-chain dehydrogenases/reductases (SDRs). Like the SDRs, haloalcohol dehalogenases have a conserved catalytic triad (Ser-Tyr-Lys/Arg), and form a Rossmann fold. However, the normal classical SDR NAD(P)-binding motif (TGXXGXG) and NAD-binding function is replaced with a halide binding site, allowing the enzyme to catalyze a dehalogenation reaction. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 242 matched cddid_all.tbl CDD cd05362 cd05362 187620 THN_reductase-like_SDR_c tetrahydroxynaphthalene/trihydroxynaphthalene reductase-like, classical (c) SDRs. 1,3,6,8-tetrahydroxynaphthalene reductase (4HNR) of Magnaporthe grisea and the related 1,3,8-trihydroxynaphthalene reductase (3HNR) are typical members of the SDR family containing the canonical glycine rich NAD(P)-binding site and active site tetrad, and function in fungal melanin biosynthesis. This subgroup also includes an SDR from Norway spruce that may function to protect against both biotic and abitoic stress. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 243 matched cddid_all.tbl CDD cd05363 cd05363 187621 SDH_SDR_c Sorbitol dehydrogenase (SDH), classical (c) SDR. This bacterial subgroup includes Rhodobacter sphaeroides SDH, and other SDHs. SDH preferentially interconverts D-sorbitol (D-glucitol) and D-fructose, but also interconverts L-iditol/L-sorbose and galactitol/D-tagatose. SDH is NAD-dependent and is a dimeric member of the SDR family. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 254 matched cddid_all.tbl CDD cd05364 cd05364 187622 SDR_c11 classical (c) SDR, subgroup 11. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 253 matched cddid_all.tbl CDD cd05365 cd05365 187623 7_alpha_HSDH_SDR_c 7 alpha-hydroxysteroid dehydrogenase (7 alpha-HSDH), classical (c) SDRs. This bacterial subgroup contains 7 alpha-HSDHs, including Escherichia coli 7 alpha-HSDH. 7 alpha-HSDH, a member of the SDR family, catalyzes the NAD+ -dependent dehydrogenation of a hydroxyl group at position 7 of the steroid skeleton of bile acids. In humans the two primary bile acids are cholic and chenodeoxycholic acids, these are formed from cholesterol in the liver. Escherichia coli 7 alpha-HSDH dehydroxylates these bile acids in the human intestine. Mammalian 7 alpha-HSDH activity has been found in livers. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 242 matched cddid_all.tbl CDD cd05366 cd05366 187624 meso-BDH-like_SDR_c meso-2,3-butanediol dehydrogenase-like, classical (c) SDRs. 2,3-butanediol dehydrogenases (BDHs) catalyze the NAD+ dependent conversion of 2,3-butanediol to acetonin; BDHs are classified into types according to their stereospecificity as to substrates and products. Included in this subgroup are Klebsiella pneumonia meso-BDH which catalyzes meso-2,3-butanediol to D(-)-acetonin, and Corynebacterium glutamicum L-BDH which catalyzes lX+)-2,3-butanediol to L(+)-acetonin. This subgroup is comprised of classical SDRs with the characteristic catalytic triad and NAD-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 257 matched cddid_all.tbl CDD cd05367 cd05367 187625 SPR-like_SDR_c sepiapterin reductase (SPR)-like, classical (c) SDRs. Human SPR, a member of the SDR family, catalyzes the NADP-dependent reduction of sepiaptern to 7,8-dihydrobiopterin (BH2). In addition to SPRs, this subgroup also contains Bacillus cereus yueD, a benzil reductase, which catalyzes the stereospecific reduction of benzil to (S)-benzoin. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 241 matched cddid_all.tbl CDD cd05368 cd05368 187626 DHRS6_like_SDR_c human DHRS6-like, classical (c) SDRs. Human DHRS6, and similar proteins. These proteins are classical SDRs, with a canonical active site tetrad and a close match to the typical Gly-rich NAD-binding motif. Human DHRS6 is a cytosolic type 2 (R)-hydroxybutyrate dehydrogenase, which catalyses the conversion of (R)-hydroxybutyrate to acetoacetate. Also included in this subgroup is Escherichia coli UcpA (upstream cys P). Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. Note: removed : needed to make this chiodl smaller when drew final trees: rmeoved text form description: Other proteins in this subgroup include Thermoplasma acidophilum aldohexose dehydrogenase, which has high dehydrogenase activity against D-mannose, Bacillus subtilis BacC involved in the biosynthesis of the dipeptide bacilysin and its antibiotic moiety anticapsin, Sphingomonas paucimobilis strain B90 LinC, involved in the degradation of hexachlorocyclohexane isomers...... P). 241 matched cddid_all.tbl CDD cd05369 cd05369 187627 TER_DECR_SDR_a Trans-2-enoyl-CoA reductase (TER) and 2,4-dienoyl-CoA reductase (DECR), atypical (a) SDR. TTER is a peroxisomal protein with a proposed role in fatty acid elongation. Fatty acid synthesis is known to occur in the both endoplasmic reticulum and mitochondria; peroxisomal TER has been proposed as an additional fatty acid elongation system, it reduces the double bond at C-2 as the last step of elongation. This system resembles the mitochondrial system in that acetyl-CoA is used as a carbon donor. TER may also function in phytol metabolism, reducting phytenoyl-CoA to phytanoyl-CoA in peroxisomes. DECR processes double bonds in fatty acids to increase their utility in fatty acid metabolism; it reduces 2,4-dienoyl-CoA to an enoyl-CoA. DECR is active in mitochondria and peroxisomes. This subgroup has the Gly-rich NAD-binding motif of the classical SDR family, but does not display strong identity to the canonical active site tetrad, and lacks the characteristic Tyr at the usual position. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 249 matched cddid_all.tbl CDD cd05370 cd05370 187628 SDR_c2 classical (c) SDR, subgroup 2. Short-chain dehydrogenases/reductases (SDRs, aka Tyrosine-dependent oxidoreductases) are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 228 matched cddid_all.tbl CDD cd05371 cd05371 187629 HSD10-like_SDR_c 17hydroxysteroid dehydrogenase type 10 (HSD10)-like, classical (c) SDRs. HSD10, also known as amyloid-peptide-binding alcohol dehydrogenase (ABAD), was previously identified as a L-3-hydroxyacyl-CoA dehydrogenase, HADH2. In fatty acid metabolism, HADH2 catalyzes the third step of beta-oxidation, the conversion of a hydroxyl to a keto group in the NAD-dependent oxidation of L-3-hydroxyacyl CoA. In addition to alcohol dehydrogenase and HADH2 activites, HSD10 has steroid dehydrogenase activity. Although the mechanism is unclear, HSD10 is implicated in the formation of amyloid beta-petide in the brain (which is linked to the development of Alzheimer's disease). Although HSD10 is normally concentrated in the mitochondria, in the presence of amyloid beta-peptide it translocates into the plasma membrane, where it's action may generate cytotoxic aldehydes and may lower estrogen levels through its use of 17-beta-estradiol as a substrate. HSD10 is a member of the SRD family, but differs from other SDRs by the presence of two insertions of unknown function. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 252 matched cddid_all.tbl CDD cd05372 cd05372 187630 ENR_SDR Enoyl acyl carrier protein (ACP) reductase (ENR), divergent SDR. This bacterial subgroup of ENRs includes Escherichia coli ENR. ENR catalyzes the NAD(P)H-dependent reduction of enoyl-ACP in the last step of fatty acid biosynthesis. De novo fatty acid biosynthesis is catalyzed by the fatty acid synthetase complex, through the serial addition of 2-carbon subunits. In bacteria and plants,ENR catalyzes one of six synthetic steps in this process. Oilseed rape ENR, and also apparently the NADH-specific form of Escherichia coli ENR, is tetrameric. Although similar to the classical SDRs, this group does not have the canonical catalytic tetrad, nor does it have the typical Gly-rich NAD-binding pattern. Such so-called divergent SDRs have a GXXXXXSXA NAD-binding motif and a YXXMXXXK (or YXXXMXXXK) active site motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 250 matched cddid_all.tbl CDD cd05373 cd05373 187631 SDR_c10 classical (c) SDR, subgroup 10. This subgroup resembles the classical SDRs, but has an incomplete match to the canonical glycine rich NAD-binding motif and lacks the typical active site tetrad (instead of the critical active site Tyr, it has Phe, but contains the nearby Lys). SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 238 matched cddid_all.tbl CDD cd05374 cd05374 187632 17beta-HSD-like_SDR_c 17beta hydroxysteroid dehydrogenase-like, classical (c) SDRs. 17beta-hydroxysteroid dehydrogenases are a group of isozymes that catalyze activation and inactivation of estrogen and androgens. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 248 matched cddid_all.tbl CDD cd05379 cd05379 349398 CAP_bacterial Bacterial CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain proteins. Little is known about bacterial and archaeal members of the CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain family. The wider family of CAP domain containing proteins includes plant pathogenesis-related protein 1 (PR-1), cysteine-rich secretory proteins (CRISPs), and allergen 5 from vespid venom, among others. Studies of eukaryotic proteins show that CAP domains have several functions, including the binding of cholesterol, lipids and heparan sulfate. This group includes Borrelia burgdorferi outer surface protein BB0689, which does not bind to cholesterol, lipids, or heparan sulfate, and whose function is unknown. 120 matched cddid_all.tbl CDD cd05380 cd05380 349399 CAP_euk Eukaryotic CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain proteins. The CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain is found mainly in eukaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), cysteine-rich secretory proteins (CRISPs), glioma pathogenesis-related 1 (GLIPR1), Golgi associated pathogenesis related-1 (GAPR1) proteins, peptidase inhibitor 15 (PI15), peptidase inhibitor 16 (PI16), CRISP LCCL domain containing 1 (CRISPLD1), CRISP LCCL domain containing 2 (CRISPLD2), and allergen 5 from vespid venom. 144 matched cddid_all.tbl CDD cd05381 cd05381 349400 CAP_PR-1 CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain of pathogenesis-related protein 1 (PR-1) family proteins. Members of pathogenesis-related protein 1 (PR-1) family are among the most abundantly produced proteins in plants on pathogen attack. They are considered hallmarks of hypersensitive response/defense pathways and may act as anti-fungal agents or be involved in cell wall loosening. 136 matched cddid_all.tbl CDD cd05382 cd05382 349401 CAP_GAPR1-like CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain of Golgi-associated plant pathogenesis-related protein 1 and similar proteins. Golgi-associated plant pathogenesis related protein 1 (GAPR1), also called Golgi-associated PR-1 protein or glioma pathogenesis-related protein 2 (GLIPR-2), forms amyloid-like fibrils in the presence of liposomes containing acidic phospholipids. It has been identified in mice as an up-regulated protein in kidney fibrosis, and is involved in epithelial to mesenchymal transition and in generating a pool of myofibroblasts contributing to fibrosis. The wider family of CAP domain containing proteins includes plant pathogenesis-related protein 1 (PR-1), cysteine-rich secretory proteins (CRISPs), and allergen 5 from vespid venom, among others. 132 matched cddid_all.tbl CDD cd05383 cd05383 349402 CAP_CRISP CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain of cysteine-rich secretory proteins. Cysteine-rich secretory proteins (CRISPs) are two-domain proteins with an evolutionary diverse and structurally conserved N-terminal CAP domain and a C-terminal cysteine-rich domain, which is comprised of a hinge and an ICR (ion channel regulator) region. CRISPs are involved in response to pathogens, fertilization, and sperm maturation. One member, Tex31 from the venom duct of Conus textile, has been shown to possess proteolytic activity sensitive to serine protease inhibitors. CRISP-1 has been shown to mediate gamete fusion by binding to the egg surface. Other members of the CRISP family secreted in the testis (CRISP2), epididymis (CRISP3-4), or during ejaculation (CRISP3), are also involved in sperm-egg interaction, supporting the existence of a functional redundancy and cooperation between homolog proteins ensuring the success of fertilization. The wider family of CAP domain containing proteins includes plant pathogenesis-related protein 1 (PR-1) and allergen 5 from vespid venom, among others. 139 matched cddid_all.tbl CDD cd05384 cd05384 349403 CAP_PRY1-like CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain of pathogen-related yeast 1 (PRY1) protein and similar fungal proteins. PRY1, also called pathogenesis-related protein 1, is a yeast protein that is up-regulated in core ESCRT mutants. It is a secreted protein required for efficient export of lipids such as acetylated sterols, and acts in detoxification of hydrophobic compounds. This PRY1-like group also contains fruiting body proteins SC7/14 from Schizophyllum commune. The wider family of CAP domain containing proteins includes plant pathogenesis-related protein 1 (PR-1), cysteine-rich secretory proteins (CRISPs), and allergen 5 from vespid venom, among others. 129 matched cddid_all.tbl CDD cd05385 cd05385 349404 CAP_GLIPR1-like CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain of glioma pathogenesis-related protein 1 and similar proteins. Glioma pathogenesis-related protein 1 (GLIPR1) is also called related to testes-specific, vespid, and pathogenesis protein 1 (RTVP-1). The GLIPR1 gene has been identified as a p53 target gene and was shown to be methylated and down-regulated in prostate cancer. It is a novel broad-spectrum tumor suppressor whose proapoptotic properties are exerted in part through ROS-JNK signaling. GLIPR1 is composed of a signal peptide that directs its secretion, a CAP domain, and a transmembrane domain. The wider family of CAP domain containing proteins includes plant pathogenesis-related protein 1 (PR-1), cysteine-rich secretory proteins (CRISPs), and allergen 5 from vespid venom, among others. 148 matched cddid_all.tbl CDD cd05386 cd05386 349771 TraL transfer origin protein TraL. The transfer origin protein TraL is member of the SIMIBI superfamily which contains a ATP-binding domain. Proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion. The specific function of TraL protein is unknown. 155 matched cddid_all.tbl CDD cd05387 cd05387 349772 BY-kinase bacterial tyrosine-kinase. Bacterial tyrosine (BY)-kinases catalyze the autophosphorylation on a C-terminal tyrosine cluster and also phosphorylate endogenous protein substrates by using ATP as phosphoryl donor. Besides their capacity to function as tyrosine kinase, most of these proteins are also involved in the production and transport of exopolysaccharides. BY-kinases are involved in a number of physiological processes ranging from stress resistance to pathogenicity. 190 matched cddid_all.tbl CDD cd05388 cd05388 349773 CobB_N N-terminal domain of cobyrinic acid a,c-diamide synthase. Cobyrinic acid a,c-diamide synthase (CobB, CbiA). Biosynthesis of cobalamin (vitamin B12) requires more than two dozen different enzymes. CobB catalyzes the ATP-dependent amidation of the two carboxylate groups at positions a and c of cobyrinic acid, via the formation of a phosphorylated intermediate, using glutamine or ammonia as the nitrogen source. CobB is comprised of two protein domains: the C-terminal glutaminase domain and the N-terminal ATP-binding domain. The glutaminase domain catalyzes the hydrolysis of glutamine to glutamate and ammonia. It belongs to the triad class of glutamine amidotransferases. This classification is based on the N-terminal domain which catalyzes the ultimate synthesis of the diamide product by using energy from the hydrolysis of ATP and ammonia transferred from the C-terminal domain. 193 matched cddid_all.tbl CDD cd05389 cd05389 349774 CobQ_N N-terminal domain of cobyric acid synthase. Cobyric acid synthase (CobQ, CbiP) N-terminal domain. CobQ plays a role in the cobalamin (vitamin B12) biosynthesis pathway. CobQ catalyzes the ATP-dependent amidation of adenosyl-cobyrinic acid a,c-diamide at carboxylates positions b, d, e, and g to produce cobyric acid using glutamine or ammonia as the nitrogen source. The C-terminal glutaminase domain catalyzes the hydrolysis of glutamine to glutamate and ammonia. Ammonia is translocated via an intramolecular tunnel to the N-terminal domain for the synthesis of cobyric acid. 223 matched cddid_all.tbl CDD cd05390 cd05390 349775 HypB nickel incorporation protein HypB. HypB is one of numerous accessory proteins required for the maturation of nickel-dependent hydrogenases, like carbon monoxide dehydrogenase or urease. HypB is a GTP-binding protein and has GTP hyrolase activity. It forms homodimer and is capable of binding two nickel ions and two zinc ions. The active site is located on the dimer interface. Energy from hydrolysis of GTP is used to insert nickels into hydrogenases. 203 matched cddid_all.tbl CDD cd05391 cd05391 213340 RasGAP_p120GAP Ras-GTPase Activating Domain of p120. p120GAP is a negative regulator of Ras that stimulates hydrolysis of bound GTP to GDP. Once the Ras regulator p120GAP, a member of the GAP protein family, is recruited to the membrane, it is transiently immobilized to interact with Ras-GTP. The down-regulation of Ras by p120GAP is a critical step in the regulation of many cellular processes, which is disrupted in approximately 30% of human cancers. p120GAP contains SH2, SH3, PH, calcium- and lipid-binding domains, suggesting its involvement in a complex network of cellular interactions in vivo. 328 matched cddid_all.tbl CDD cd05392 cd05392 213341 RasGAP_Neurofibromin_like Ras-GTPase Activating Domain of proteins similar to neurofibromin. Neurofibromin-like proteins include the Saccharomyces cerevisiae RasGAP proteins Ira1 and Ira2, the closest homolog of neurofibromin, which is responsible for the human autosomal dominant disease neurofibromatosis type I (NF1). The RasGAP Ira1/2 proteins are negative regulators of the Ras-cAMP signaling pathway and conserved from yeast to human. In yeast Ras proteins are activated by GEFs, and inhibited by two GAPs, Ira1 and Ira2. Ras proteins activate the cAMP/protein kinase A (PKA) pathway, which controls metabolism, stress resistance, growth, and meiosis. Recent studies showed that the kelch proteins Gpb1 and Gpb2 inhibit Ras activity via association with Ira1 and Ira2. Gpb1/2 bind to a conserved C-terminal domain of Ira1/2, and loss of Gpb1/2 results in a destabilization of Ira1 and Ira2, leading to elevated levels of Ras2-GTP and uninhibited cAMP-PKA signaling. Since the Gpb1/2 binding domain on Ira1/2 is conserved in the human neurofibromin protein, the studies suggest that an analogous signaling mechanism may contribute to the neoplastic development of NF1. 317 matched cddid_all.tbl CDD cd05394 cd05394 213342 RasGAP_RASA2 Ras-GTPase Activating Domain of RASA2. RASA2 (or GAP1(m)) is a member of the GAP1 family of Ras GTPase-activating proteins that includes GAP1_IP4BP (or RASA3), CAPRI, and RASAL. In vitro, RASA2 has been shown to bind inositol 1,3,4,5-tetrakisphosphate (IP4), the water soluble inositol head group of the lipid second messenger phosphatidylinositol 3,4,5-trisphosphate (PIP3). In vivo studies also demonstrated that RASA2 binds PIP3, and it is recruited to the plasma membrane following agonist stimulation of PI 3-kinase. Furthermore, the membrane translocation is a consequence of the ability of its pleckstrin homology (PH) domain to bind PIP3. 272 matched cddid_all.tbl CDD cd05395 cd05395 213343 RasGAP_RASA4 Ras-GTPase Activating Domain of RASA4. Ras GTPase activating-like 4 protein (RASAL4), also known as Ca2+ -promoted Ras inactivator (CAPRI), is a member of the GAP1 family. Members of the GAP1 family are characterized by a conserved domain structure comprising N-terminal tandem C2 domains, a highly conserved central RasGAP domain, and a C-terminal pleckstrin-homology domain that is associated with a Bruton's tyrosine kinase motif. RASAL4, like RASAL, is a cytosolic protein that undergoes a rapid translocation to the plasma membrane in response to a receptor-mediated elevation in the concentration of intracellular free Ca2+ ([Ca2+]i). However, unlike RASAL, RASAL4 does not sense oscillations in [Ca2+]i. 287 matched cddid_all.tbl CDD cd05396 cd05396 188647 An_peroxidase_like Animal heme peroxidases and related proteins. A diverse family of enzymes, which includes prostaglandin G/H synthase, thyroid peroxidase, myeloperoxidase, linoleate diol synthase, lactoperoxidase, peroxinectin, peroxidasin, and others. Despite its name, this family is not restricted to metazoans: members are found in fungi, plants, and bacteria as well. 370 matched cddid_all.tbl CDD cd05397 cd05397 143387 NT_Pol-beta-like Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins. This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are involved in a two-metal ion mechanism of nucleotide addition. Two of the three catalytic carboxylates are found in Rel-Spo enzymes, with the second carboxylate of the DXD motif missing. Evidence supports a single-cation synthetase mechanism for Rel-Spo enzymes. 49 matched cddid_all.tbl CDD cd05398 cd05398 143388 NT_ClassII-CCAase Nucleotidyltransferase (NT) domain of ClassII CCA-adding enzymes. CCA-adding enzymes add the sequence [cytidine(C)-cytidine-adenosine (A)], one nucleotide at a time, onto the 3' end of tRNA, in a template-independent reaction. This Class II group is comprised mainly of eubacterial and eukaryotic enzymes and includes Bacillus stearothermophilus CCAase, Escherichia coli poly(A) polymerase I, human mitochondrial CCAase, and Saccharomyces cerevisiae CCAase (CCA1). CCA-adding enzymes have a single catalytic pocket, which recognizes both ATP and CTP substrates. Included in this subgroup are CC- and A-adding enzymes from various ancient species of bacteria such as Aquifex aeolicus; these enzymes collaborate to add CCA to tRNAs. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are fairly well conserved in this family. Escherichia coli CCAase is related to this group but has not been included in this alignment as this enzyme lacks the N-terminal helix conserved in the remainder of the NT superfamily. 139 matched cddid_all.tbl CDD cd05399 cd05399 143389 NT_Rel-Spo_like Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases. This family includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydrolase domain (TGS). Some Rel-Spo proteins also have a C-terminal regulatory ACT domain. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition.Two of the three catalytic carboxylates are found in Rel-Spo enzymes, with the second carboxylate of the DXD motif missing. Evidence supports a single-cation synthetase mechanism. 129 matched cddid_all.tbl CDD cd05400 cd05400 143390 NT_2-5OAS_ClassI-CCAase Nucleotidyltransferase (NT) domain of 2'5'-oligoadenylate (2-5A)synthetase (2-5OAS) and class I CCA-adding enzyme. In vertebrates, 2-5OASs are induced by interferon during the innate immune response to protect against RNA virus infections. In the presence of an RNA activator, 2-5OASs catalyze the oligomerization of ATP into 2-5A. 2-5A activates endoribonuclease L, which leads to degradation of the viral RNA. 2-5OASs are also implicated in cell growth control, differentiation, and apoptosis. This family includes human OAS1, -2, -3, and OASL. CCA-adding enzymes add the sequence [cytidine(C)-cytidine-adenosine (A)], one nucleotide at a time, onto the 3' end of tRNA, in a template-independent reaction. This class I group includes the archaeal Sulfolobus shibatae and Archeoglobus fulgidus CCA-adding enzymes. It belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are conserved in this family. 143 matched cddid_all.tbl CDD cd05401 cd05401 143391 NT_GlnE_GlnD_like Nucleotidyltransferase (NT) domain of Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), and similar proteins. Escherichia coli GlnD and -E participate in the Glutamine synthetase (GS)/Glutamate synthase (GOGAT) pathway for the assimilation of ammonium nitrogen. In nitrogen sufficiency, GlnE adenylates GS, reducing GS activity; when nitrogen is limiting, GlnE deadenylates GS-AMP, restoring GS activity. When nitrogen is limiting, GlnD uridylylates the nitrogen regulatory protein PII to PII-UTP, and in nitrogen sufficiency, it removes the modifying groups. The activity of Escherichia coli GlnE is modulated by PII-proteins. PII-UMP promotes GlnE deadenylation activity, and PII promotes GlnE adenylation activity. Escherichia coli GlnE has two separate NT domains. The N-terminal NT domain catalyzes the deadenylylation of GS, and the C-terminal NT domain the adenylylation reaction. The majority of proteins in this family contain a C-terminal NT domain which is associated with a cystathionine beta-synthase (CBS) domain pair and a CAP_ED (cAMP receptor protein effector ) domain. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxylate residues are conserved. 172 matched cddid_all.tbl CDD cd05402 cd05402 143392 NT_PAP_TUTase Nucleotidyltransferase (NT) domain of poly(A) polymerases and terminal uridylyl transferases. Poly(A) polymerases (PAPs) catalyze mRNA poly(A) tail synthesis, and terminal uridylyl transferases (TUTases) uridylate RNA. PAPs in this subgroup include human PAP alpha, mouse testis-specific cytoplasmic PAP beta, human nuclear PAP gamma, Saccharomyces cerevisiae PAP1, TRF4 and-5, Schizosaccharomyces pombe caffeine-induced death proteins -1, and -14, Caenorhabditis elegans Germ Line Development-2, and Chlamydomonas reinhardtii MUT68. This family also includes human U6 snRNA-specific TUTase1, and Trypanosoma brucei 3'-TUTase-1,-2, and 4. This family belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. For the majority of proteins in this family, these carboxylate residues are conserved. 114 matched cddid_all.tbl CDD cd05403 cd05403 143393 NT_KNTase_like Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. S. aureus KNTase is a plasmid encoded enzyme which confers resistance to a wide range of aminoglycoside antibiotics which have a 4'- or 4''-hydroxyl group in the equatorial position, such as kanamycin A. This enzyme transfers a nucleoside monophosphate group from a nucleotide (ATP,GTP, or UTP) to the 4'-hydroxyl group of kanamycin A. This enzyme is a homodimer, having two NT active sites. The nucleotide and antibiotic binding sites of each active site include residues from each monomer. Included in this subgroup is Escherichia coli AadA5 which confers resistance to the antibiotic spectinomycin and is a putative aminoglycoside-3'-adenylyltransferase. It is part of the aadA5 cassette of a class 1 integron. This subgroup also includes Haemophilus influenzae HI0073 which forms a 2:2 heterotetramer with an unrelated protein HI0074. Structurally HI0074 is related to the substrate-binding domain of S. aureus KNTase. The genes encoding HI0073 and HI0074 form an operon. Little is known about the substrate specificity or function of two-component NTs. The characterized members of this subgroup may not be representive of the function of this subgroup. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, co-ordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are conserved in this subgroup. 93 matched cddid_all.tbl CDD cd05466 cd05466 176102 PBP2_LTTR_substrate The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily. This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, oxidative stress responses, nodule formation of nitrogen-fixing bacteria, synthesis of virulence factors, toxin production, attachment and secretion, to name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 197 matched cddid_all.tbl CDD cd05467 cd05467 119437 CBM20 The family 20 carbohydrate-binding module (CBM20), also known as the starch-binding domain, is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch. 96 matched cddid_all.tbl CDD cd05468 cd05468 176472 pVHL von Hippel-Landau (pVHL) tumor suppressor protein. von Hippel-Landau (pVHL) protein, the gene product of VHL, is a critical regulator of the ubiquitous oxygen-sensing pathway. It is conserved throughout evolution, as its homologs are found in organisms ranging from mammals to the Drosophila melanogaster, Anopheles gambiae insects and the Caenorhabditis elegans nematode. pVHL acts as the substrate recognition component of an E3 ubiquitin ligase complex. Several proteins have been identified as pVHL-binding proteins that are subject to ubiquitin-mediated proteolysis; the best characterized putative substrates are the alpha subunits of the hypoxia-inducible factor (HIF1alpha, HIF2alpha, and HIF3alpha). In addition to HIF degradation, pVHL has been implicated to be involved in HIF independent cellular processes. Germline VHL mutations cause renal cell carcinomas, hemangioblastomas and pheochromocytomas in humans. pVHL can bind to and direct the proper deposition of fibronectin and collagen IV within the extracellular matrix. It works to stabilize microtubules and foster the maintenance of primary cilium. It also has been reported to promote the stabilization and activation of p53 in a HIF-independent manner and, in neuronal cells, promote apoptosis by down-regulation of Jun-B. 141 matched cddid_all.tbl CDD cd05469 cd05469 100112 Transthyretin_like Transthyretin_like. This domain is present in the transthyretin-like protein (TLP) family which includes transthyretin (TTR) and a transthyretin-related protein called 5-hydroxyisourate hydrolase (HIUase). TTR and HIUase are homotetrameric proteins with each subunit consisting of eight beta-strands arranged in two sheets and a short alpha-helix. The central channel of the tetramer contains two independent binding sites, each located between a pair of subunits. TTR transports thyroid hormones and retinol in the blood serum of vertebrates while HIUase catalyzes the second step in a three-step ureide pathway. TTRs are highly conserved and found only in vertebrates while the HIUases are found in a wide range of bacterial, plant, fungal, slime mold and vertebrate organisms. 113 matched cddid_all.tbl CDD cd05470 cd05470 133137 pepsin_retropepsin_like Cellular and retroviral pepsin-like aspartate proteases. This family includes both cellular and retroviral pepsin-like aspartate proteases. The cellular pepsin and pepsin-like enzymes are twice as long as their retroviral counterparts. The cellular pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, rennin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (rennin, cathepsin D and E, pepsin) or commercially (chymosin) important. The eukaryotic pepsin-like proteases contain two domains possessing similar topological features. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except in the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The eukaryotic pepsin-like proteases have two active site ASP residues with each N- and C-terminal lobe contributing one residue. While the fungal and mammalian pepsins are bilobal proteins, retropepsins function as dimers and the monomer resembles structure of the N- or C-terminal domains of eukaryotic enzyme. The active site motif (Asp-Thr/Ser-Gly-Ser) is conserved between the retroviral and eukaryotic proteases and between the N-and C-terminal of eukaryotic pepsin-like proteases. The retropepsin-like family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements; as well as eukaryotic DNA-damage-inducible proteins (DDIs), and bacterial aspartate peptidases. Retropepsin is synthesized as part of the POL polyprotein that contains an aspartyl-protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A) and A2 (retropepsin family). 109 matched cddid_all.tbl CDD cd05471 cd05471 133138 pepsin_like Pepsin-like aspartic proteases, bilobal enzymes that cleave bonds in peptides at acidic pH. Pepsin-like aspartic proteases are found in mammals, plants, fungi and bacteria. These well known and extensively characterized enzymes include pepsins, chymosin, renin, cathepsins, and fungal aspartic proteases. Several have long been known to be medically (renin, cathepsin D and E, pepsin) or commercially (chymosin) important. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Aspartate residue, with an extended active site cleft localized between the two lobes of the molecule. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. Most members of the pepsin family specifically cleave bonds in peptides that are at least six residues in length, with hydrophobic residues in both the P1 and P1' positions. The active site is located at the groove formed by the two lobes, with an extended loop projecting over the cleft to form an 11-residue flap, which encloses substrates and inhibitors in the active site. Specificity is determined by nearest-neighbor hydrophobic residues surrounding the catalytic aspartates, and by three residues in the flap.The enzymes are mostly secreted from cells as inactive proenzymes that activate autocatalytically at acidic pH. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA). 283 matched cddid_all.tbl CDD cd05472 cd05472 133139 cnd41_like Chloroplast Nucleoids DNA-binding Protease, catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase. Chloroplast Nucleoids DNA-binding Protease catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in senescent leaves of tobacco. Antisense tobacco with reduced amount of CND41 maintained green leaves and constant protein levels, especially Rubisco. CND41 has DNA-binding as well as aspartic protease activities. The pepsin-like aspartic protease domain is located at the C-terminus of the protein. The enzyme is characterized by having two aspartic protease catalytic site motifs, the Asp-Thr-Gly-Ser in the N-terminal and Asp-Ser-Gly-Ser in the C-terminal region. Aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe may be evolved from the other through ancient gene-duplication event. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA). 299 matched cddid_all.tbl CDD cd05473 cd05473 133140 beta_secretase_like Beta-secretase, aspartic-acid protease important in the pathogenesis of Alzheimer's disease. Beta-secretase also called BACE (beta-site of APP cleaving enzyme) or memapsin-2. Beta-secretase is an aspartic-acid protease important in the pathogenesis of Alzheimer's disease, and in the formation of myelin sheaths in peripheral nerve cells. It cleaves amyloid precursor protein (APP) to reveal the N-terminus of the beta-amyloid peptides. The beta-amyloid peptides are the major components of the amyloid plaques formed in the brain of patients with Alzheimer's disease (AD). Since BACE mediates one of the cleavages responsible for generation of AD, it is regarded as a potential target for pharmacological intervention in AD. Beta-secretase is a member of pepsin family of aspartic proteases. Same as other aspartic proteases, beta-secretase is a bilobal enzyme, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The enzymes specifically cleave bonds in peptides which have at least six residues in length with hydrophobic residues in both the P1 and P1' positions. The active site is located at the groove formed by the two lobes, with an extended loop projecting over the cleft to form an 11-residue flap, which encloses substrates and inhibitors in the active site. Specificity is determined by nearest-neighbor hydrophobic residues surrounding the catalytic aspartates, and by three residues in the flap. The enzymes are mostly secreted from cells as inactive proenzymes that activate autocatalytically at acidic pH. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA). 364 matched cddid_all.tbl CDD cd05474 cd05474 133141 SAP_like SAPs, pepsin-like proteinases secreted from pathogens to degrade host proteins. SAPs (Secreted aspartic proteinases) are secreted from a group of pathogenic fungi, predominantly Candida species. They are secreted from the pathogen to degrade host proteins. SAP is one of the most significant extracellular hydrolytic enzymes produced by C. albicans. SAP proteins, encoded by a family of 10 SAP genes. All 10 SAP genes of C. albicans encode preproenzymes, approximately 60 amino acid longer than the mature enzyme, which are processed when transported via the secretory pathway. The mature enzymes contain sequence motifs typical for all aspartyl proteinases, including the two conserved aspartate residues other active site and conserved cysteine residues implicated in the maintenance of the three-dimensional structure. Most Sap proteins contain putative N-glycosylation sites, but it remains to be determined which Sap proteins are glycosylated. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA). The overall structure of Sap protein conforms to the classical aspartic proteinase fold typified by pepsin. SAP is a bilobal enzyme, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe may be evolved from the other through ancient gene-duplication event. More recently evolved enzymes have similar three-dimensional structures, however their amino acid sequences are more divergent except for the conserved catalytic site motif. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA). 295 matched cddid_all.tbl CDD cd05475 cd05475 133142 nucellin_like Nucellins, plant aspartic proteases specifically expressed in nucellar cells during degradation. Nucellins are important regulators of nucellar cell's progressive degradation after ovule fertilization. This degradation is a characteristic of programmed cell death. Nucellins are plant aspartic proteases specifically expressed in nucellar cells during degradation. The enzyme is characterized by having two aspartic protease catalytic site motifs, the Asp-Thr-Gly-Ser in the N-terminal and Asp-Ser-Gly-Ser in the C-terminal region, and two other regions nearly identical to two regions of plant aspartic proteases. Aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe may be evolved from the other through ancient gene-duplication event. Although the three-dimensional structures of the two lobes are very similar, the amino acid sequences are more divergent, except for the conserved catalytic site motif. 273 matched cddid_all.tbl CDD cd05476 cd05476 133143 pepsin_A_like_plant Chroloplast Nucleoids DNA-binding Protease and Nucellin, pepsin-like aspartic proteases from plants. This family contains pepsin like aspartic proteases from plants including Chloroplast Nucleoids DNA-binding Protease and Nucellin. Chloroplast Nucleoids DNA-binding Protease catalyzes the degradation of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) in senescent leaves of tobacco and Nucellins are important regulators of nucellar cell's progressive degradation after ovule fertilization. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The enzymes specifically cleave bonds in peptides which have at least six residues in length with hydrophobic residues in both the P1 and P1' positions. The active site is located at the groove formed by the two lobes, with an extended loop projecting over the cleft to form an 11-residue flap, which encloses substrates and inhibitors in the active site. Specificity is determined by nearest-neighbor hydrophobic residues surrounding the catalytic aspartates, and by three residues in the flap. The enzymes are mostly secreted from cells as inactive proenzymes that activate autocatalytically at acidic pH. 265 matched cddid_all.tbl CDD cd05477 cd05477 133144 gastricsin Gastricsins, asparate proteases produced in gastric mucosa. Gastricsin is also called pepsinogen C. Gastricsins are produced in gastric mucosa of mammals. It is synthesized by the chief cells in the stomach as an inactive zymogen. It is self-converted to a mature enzyme under acidic conditions. Human gastricsin is distributed throughout all parts of the stomach. Gastricsin is synthesized as an inactive progastricsin that has an approximately 40 residue prosequence. It is self-converting to a mature enzyme being triggered by a drop in pH from neutrality to acidic conditions. Like other aspartic proteases, gastricsin are characterized by two catalytic aspartic residues at the active site, and display optimal activity at acidic pH. Mature enzyme has a pseudo-2-fold symmetry that passes through the active site between the catalytic aspartate residues. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic aspartate residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe may be evolved from the other through ancient gene-duplication event. Although the three-dimensional structures of the two lobes are very similar, the amino acid sequences are more divergent, except for the conserved catalytic site motif. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA). 318 matched cddid_all.tbl CDD cd05478 cd05478 133145 pepsin_A Pepsin A, aspartic protease produced in gastric mucosa of mammals. Pepsin, a well-known aspartic protease, is produced by the human gastric mucosa in seven different zymogen isoforms, subdivided into two types: pepsinogen A and pepsinogen C. The prosequence of the zymogens are self cleaved under acidic pH. The mature enzymes are called pepsin A and pepsin C, correspondingly. The well researched porcine pepsin is also in this pepsin A family. Pepsins play an integral role in the digestion process of vertebrates. Pepsins are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe may be evolved from the other through ancient gene-duplication event. More recently evolved enzymes have similar three-dimensional structures, however their amino acid sequences are more divergent except for the conserved catalytic site motif. Pepsins specifically cleave bonds in peptides which have at least six residues in length with hydrophobic residues in both the P1 and P1' positions. The active site is located at the groove formed by the two lobes, with an extended loop projecting over the cleft to form an 11-residue flap, which encloses substrates and inhibitors in the active site. Specificity is determined by nearest-neighbor hydrophobic residues surrounding the catalytic aspartates, and by three residues in the flap. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA). 317 matched cddid_all.tbl CDD cd05479 cd05479 133146 RP_DDI RP_DDI; retropepsin-like domain of DNA damage inducible protein. The family represents the retropepsin-like domain of DNA damage inducible protein. DNA damage inducible protein has a retropepsin-like domain and an amino-terminal ubiquitin-like domain and/or a UBA (ubiquitin-associated) domain. This CD represents the retropepsin-like domain of DDI. 124 matched cddid_all.tbl CDD cd05480 cd05480 133147 NRIP_C NRIP_C; putative nuclear receptor interacting protein. Proteins in this family have been described as probable nuclear receptor interacting proteins. The C-terminal domain of this family is homologous to the retroviral aspartyl protease domain. The domain is structurally related to one lobe of the pepsin molecule. The conserved active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A. 103 matched cddid_all.tbl CDD cd05481 cd05481 133148 retropepsin_like_LTR_1 Retropepsins_like_LTR; pepsin-like aspartate protease from retrotransposons with long terminal repeats. Retropepsin of retrotransposons with long terminal repeats are pepsin-like aspartate proteases. While fungal and mammalian pepsins are bilobal proteins with structurally related N and C-terminals, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A. 93 matched cddid_all.tbl CDD cd05482 cd05482 133149 HIV_retropepsin_like Retropepsins, pepsin-like aspartate proteases. This is a subfamily of retropepsins. The family includes pepsin-like aspartate proteases from retroviruses, retrotransposons and retroelements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A. 87 matched cddid_all.tbl CDD cd05483 cd05483 133150 retropepsin_like_bacteria Bacterial aspartate proteases, retropepsin-like protease family. This family of bacteria aspartate proteases is a subfamily of retropepsin-like protease family, which includes enzymes from retrovirus and retrotransposons. While fungal and mammalian pepsin-like aspartate proteases are bilobal proteins with structurally related N- and C-termini, this family of bacteria aspartate proteases is half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate proteases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A. 96 matched cddid_all.tbl CDD cd05484 cd05484 133151 retropepsin_like_LTR_2 Retropepsins_like_LTR, pepsin-like aspartate proteases. Retropepsin of retrotransposons with long terminal repeats are pepsin-like aspartate proteases. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A. 91 matched cddid_all.tbl CDD cd05485 cd05485 133152 Cathepsin_D_like Cathepsin_D_like, pepsin family of proteinases. Cathepsin D is the major aspartic proteinase of the lysosomal compartment where it functions in protein catabolism. It is a member of the pepsin family of proteinases. This enzyme is distinguished from other members of the pepsin family by two features that are characteristic of lysosomal hydrolases. First, mature Cathepsin D is found predominantly in a two-chain form due to a posttranslational cleavage event. Second, it contains phosphorylated, N-linked oligosaccharides that target the enzyme to lysosomes via mannose-6-phosphate receptors. Cathepsin D preferentially attacks peptide bonds flanked by bulky hydrophobic amino acids and its pH optimum is between pH 2.8 and 4.0. Two active site aspartic acid residues are essential for the catalytic activity of aspartic proteinases. Like other aspartic proteinases, Cathepsin D is a bilobed molecule; the two evolutionary related lobes are mostly made up of beta-sheets and flank a deep active site cleft. Each of the two related lobes contributes one active site aspartic acid residue and contains a single carbohydrate group. Cathepsin D is an essential enzyme. Mice deficient for proteinase cathepsin D, generated by gene targeting, develop normally during the first 2 weeks, stop thriving in the third week and die in a state of anorexia in the fourth week. The mice develop atrophy of ileal mucosa followed by other degradation of intestinal organs. In these knockout mice, lysosomal proteolysis was normal. These results suggest that vital functions of cathepsin D are exerted by limited proteolysis of proteins regulating cell growth and/or tissue homeostasis, while its contribution to bulk proteolysis in lysosomes appears to be non-critical. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA). 329 matched cddid_all.tbl CDD cd05486 cd05486 133153 Cathespin_E Cathepsin E, non-lysosomal aspartic protease. Cathepsin E is an intracellular, non-lysosomal aspartic protease expressed in a variety of cells and tissues. The protease has proposed physiological roles in antigen presentation by the MHC class II system, in the biogenesis of the vasoconstrictor peptide endothelin, and in neurodegeneration associated with brain ischemia and aging. Cathepsin E is the only A1 aspartic protease that exists as a homodimer with a disulfide bridge linking the two monomers. Like many other aspartic proteases, it is synthesized as a zymogen which is catalytically inactive towards its natural substrates at neutral pH and which auto-activates in an acidic environment. The overall structure follows the general fold of aspartic proteases of the A1 family, it is composed of two structurally similar beta barrel lobes, each lobe contributing an aspartic acid residue to form a catalytic dyad that acts to cleave the substrate peptide bond. The catalytic Asp residues are contained in an Asp-Thr-Gly-Ser/thr motif in both N- and C-terminal lobes of the enzyme. The aspartic acid residues act together to allow a water molecule to attack the peptide bond. One aspartic acid residue (in its deprotonated form) activates the attacking water molecule, whereas the other aspartic acid residue (in its protonated form) polarizes the peptide carbonyl, increasing its susceptibility to attack. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA). 316 matched cddid_all.tbl CDD cd05487 cd05487 133154 renin_like Renin stimulates production of angiotensin and thus affects blood pressure. Renin, also known as angiotensinogenase, is a circulating enzyme that participates in the renin-angiotensin system that mediates extracellular volume, arterial vasoconstriction, and consequently mean arterial blood pressure. The enzyme is secreted by the kidneys from specialized juxtaglomerular cells in response to decreases in glomerular filtration rate (a consequence of low blood volume), diminished filtered sodium chloride and sympathetic nervous system innervation. The enzyme circulates in the blood stream and hydrolyzes angiotensinogen secreted from the liver into the peptide angiotensin I. Angiotensin I is further cleaved in the lungs by endothelial bound angiotensin converting enzyme (ACE) into angiotensin II, the final active peptide. Renin is a member of the aspartic protease family. Structurally, aspartic proteases are bilobal enzymes, each lobe contributing a catalytic Aspartate residue, with an extended active site cleft localized between the two lobes of the molecule. The N- and C-terminal domains, although structurally related by a 2-fold axis, have only limited sequence homology except the vicinity of the active site. This suggests that the enzymes evolved by an ancient duplication event. The active site is located at the groove formed by the two lobes, with an extended loop projecting over the cleft to form an 11-residue flap, which encloses substrates and inhibitors in the active site. Specificity is determined by nearest-neighbor hydrophobic residues surrounding the catalytic aspartates, and by three residues in the flap. The enzymes are mostly secreted from cells as inactive proenzymes that activate autocatalytically at acidic pH. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA). 326 matched cddid_all.tbl CDD cd05488 cd05488 133155 Proteinase_A_fungi Fungal Proteinase A , aspartic proteinase superfamily. Fungal Proteinase A, a proteolytic enzyme distributed among a variety of organisms, is a member of the aspartic proteinase superfamily. In Saccharomyces cerevisiae, targeted to the vacuole as a zymogen, activation of proteinases A at acidic pH can occur by two different pathways: a one-step process to release mature proteinase A, involving the intervention of proteinase B, or a step-wise pathway via the auto-activation product known as pseudo-proteinase A. Once active, S. cerevisiae proteinase A is essential to the activities of other yeast vacuolar hydrolases, including proteinase B and carboxypeptidase Y. The mature enzyme is bilobal, with each lobe providing one of the two catalytically essential aspartic acid residues in the active site. The crystal structure of free proteinase A shows that flap loop is atypically pointing directly into the S(1) pocket of the enzyme. Proteinase A preferentially hydrolyzes hydrophobic residues such as Phe, Leu or Glu at the P1 position and Phe, Ile, Leu or Ala at P1'. Moreover, the enzyme is inhibited by IA3, a natural and highly specific inhibitor produced by S. cerevisiae. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA). 320 matched cddid_all.tbl CDD cd05489 cd05489 133156 xylanase_inhibitor_I_like TAXI-I inhibits degradation of xylan in the cell wall. Xylanase inhibitor-I (TAXI-I) is a member of potent TAXI-type inhibitors of fungal and bacterial family 11 xylanases. Plants developed a diverse battery of defense mechanisms in response to continual challenges by a broad spectrum of pathogenic microorganisms. Their defense arsenal includes inhibitors of cell wall-degrading enzymes, which hinder a possible invasion and colonization by antagonists. Xylanases of fungal and bacterial pathogens are the key enzymes in the degradation of xylan in the cell wall. Plants secrete proteins that inhibit these degradation glycosidases, including xylanase. Surprisingly, TAXI-I displays structural homology with the pepsin-like family of aspartic proteases but is proteolytically nonfunctional, because one or more residues of the essential catalytic triad are absent. The structure of the TAXI-inhibitor, Aspergillus niger xylanase I complex, illustrates the ability of tight binding and inhibition with subnanomolar affinity and indicates the importance of the C-terminal end for the differences in xylanase specificity among different TAXI-type inhibitors. This family also contains pepsin-like aspartic proteinases homologous to TAXI-I. Unlike TAXI-I, they have active site aspartates and are functionally active. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA). 362 matched cddid_all.tbl CDD cd05490 cd05490 133157 Cathepsin_D2 Cathepsin_D2, pepsin family of proteinases. Cathepsin D is the major aspartic proteinase of the lysosomal compartment where it functions in protein catabolism. It is a member of the pepsin family of proteinases. This enzyme is distinguished from other members of the pepsin family by two features that are characteristic of lysosomal hydrolases. First, mature Cathepsin D is found predominantly in a two-chain form due to a posttranslational cleavage event. Second, it contains phosphorylated, N-linked oligosaccharides that target the enzyme to lysosomes via mannose-6-phosphate receptors. Cathepsin D preferentially attacks peptide bonds flanked by bulky hydrophobic amino acids and its pH optimum is between pH 2.8 and 4.0. Two active site aspartic acid residues are essential for the catalytic activity of aspartic proteinases. Like other aspartic proteinases, Cathepsin D is a bilobed molecule; the two evolutionary related lobes are mostly made up of beta-sheets and flank a deep active site cleft. Each of the two related lobes contributes one active site aspartic acid residue and contains a single carbohydrate group. Cathepsin D is an essential enzyme. Mice deficient for proteinase cathepsin D, generated by gene targeting, develop normally during the first 2 weeks, stop thriving in the third week and die in a state of anorexia in the fourth week. The mice develop atrophy of ileal mucosa followed by other degradation of intestinal organs. In these knockout mice, lysosomal proteolysis was normal. These results suggest that vital functions of cathepsin D are exerted by limited proteolysis of proteins regulating cell growth and/or tissue homeostasis, while its contribution to bulk proteolysis in lysosomes appears to be non-critical. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA). 325 matched cddid_all.tbl CDD cd05491 cd05491 99923 Bromo_TBP7_like Bromodomain; TBP7_like subfamily, limited to fungi. TBP7, or TAT-binding protein homolog 7, is a yeast protein of unknown function that contains AAA-superfamily ATP-ase domains and a bromodomain. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine. 119 matched cddid_all.tbl CDD cd05492 cd05492 99924 Bromo_ZMYND11 Bromodomain; ZMYND11_like sub-family. ZMYND11 or BS69 is a ubiquitously expressed nuclear protein that has been shown to associate with chromatin. It interacts with chromatin remodeling factors and might play a role in chromatin remodeling and gene expression. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 109 matched cddid_all.tbl CDD cd05493 cd05493 99925 Bromo_ALL-1 Bromodomain, ALL-1 like proteins. ALL-1 is a vertebrate homologue of Drosophila trithorax and is often affected in chromosomal rearrangements that are linked to acute leukemias, such as acute lymphocytic leukemia (ALL). Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine. 131 matched cddid_all.tbl CDD cd05494 cd05494 99926 Bromodomain_1 Bromodomain; uncharacterized subfamily. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine. 114 matched cddid_all.tbl CDD cd05495 cd05495 99927 Bromo_cbp_like Bromodomain, cbp_like subfamily. Cbp (CREB binding protein or CREBBP) is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CREBBP binds specifically to phosphorylated CREB protein and augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 108 matched cddid_all.tbl CDD cd05496 cd05496 99928 Bromo_WDR9_II Bromodomain; WDR9 repeat II_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 119 matched cddid_all.tbl CDD cd05497 cd05497 99929 Bromo_Brdt_I_like Bromodomain, Brdt_like subfamily, repeat I. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 107 matched cddid_all.tbl CDD cd05498 cd05498 99930 Bromo_Brdt_II_like Bromodomain, Brdt_like subfamily, repeat II. Human Brdt is a testis-specific member of the BET subfamily of bromodomain proteins; the first bromodomain in Brdt has been shown to be essential for male germ cell differentiation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 102 matched cddid_all.tbl CDD cd05499 cd05499 99931 Bromo_BDF1_2_II Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat II. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 102 matched cddid_all.tbl CDD cd05500 cd05500 99932 Bromo_BDF1_2_I Bromodomain. BDF1/BDF2 like subfamily, restricted to fungi, repeat I. BDF1 and BDF2 are yeast transcription factors involved in the expression of a wide range of genes, including snRNAs; they are required for sporulation and DNA repair and protect histone H4 from deacetylation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 103 matched cddid_all.tbl CDD cd05501 cd05501 99933 Bromo_SP100C_like Bromodomain, SP100C_like subfamily. The SP100C protein is a splice variant of SP100, a major component of PML-SP100 nuclear bodies (NBs), which are poorly understood. It is covalently modified by SUMO-1 and may play a role in processes at the chromatin level. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 102 matched cddid_all.tbl CDD cd05502 cd05502 99934 Bromo_tif1_like Bromodomain; tif1_like subfamily. Tif1 (transcription intermediary factor 1) is a member of the tripartite motif (TRIM) protein family, which is characterized by a particular domain architecture. It functions by recruiting coactivators and/or corepressors to modulate transcription. Vertebrate Tif1-gamma, also labeled E3 ubiquitin-protein ligase TRIM33, plays a role in the control of hematopoiesis. Its homologue in Xenopus laevis, Ectodermin, has been shown to function in germ-layer specification and control of cell growth during embryogenesis. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 109 matched cddid_all.tbl CDD cd05503 cd05503 99935 Bromo_BAZ2A_B_like Bromodomain, BAZ2A/BAZ2B_like subfamily. Bromo adjacent to zinc finger 2A (BAZ2A) and 2B (BAZ2B) were identified as a novel human bromodomain gene by cDNA library screening. BAZ2A is also known as Tip5 (Transcription termination factor I-interacting protein 5) and hWALp3. The proteins may play roles in transcriptional regulation. Human Tip5 is part of a complex termed NoRC (nucleolar remodeling complex), which induces nucleosome sliding and may play a role in the regulation of the rDNA locus. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 97 matched cddid_all.tbl CDD cd05504 cd05504 99936 Bromo_Acf1_like Bromodomain; Acf1_like or BAZ1A_like subfamily. Bromo adjacent to zinc finger 1A (BAZ1A) was identified as a novel human bromodomain gene by cDNA library screening. The Drosophila homologue, Acf1, is part of the CHRAC (chromatin accessibility complex) and regulates ISWI-induced nucleosome remodeling. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 115 matched cddid_all.tbl CDD cd05505 cd05505 99937 Bromo_WSTF_like Bromodomain; Williams syndrome transcription factor-like subfamily (WSTF-like). The Williams-Beuren syndrome deletion transcript 9 is a putative transcriptional regulator. WSTF was found to play a role in vitamin D-mediated transcription as part of two chromatin remodeling complexes, WINAC and WICH. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 97 matched cddid_all.tbl CDD cd05506 cd05506 99938 Bromo_plant1 Bromodomain, uncharacterized subfamily specific to plants. Might function as a global transcription factor. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 99 matched cddid_all.tbl CDD cd05507 cd05507 99939 Bromo_brd8_like Bromodomain, brd8_like subgroup. In mammals, brd8 (bromodomain containing 8) interacts with the thyroid hormone receptor in a ligand-dependent fashion and enhances thyroid hormone-dependent activation from thyroid response elements. Brd8 is thought to be a nuclear receptor coactivator. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 104 matched cddid_all.tbl CDD cd05508 cd05508 99940 Bromo_RACK7 Bromodomain, RACK7_like subfamily. RACK7 (also called human protein kinase C-binding protein) was identified as a potential tumor suppressor genes, it shares domain architecture with BS69/ZMYND11; both have been implicated in the regulation of cellular proliferation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 99 matched cddid_all.tbl CDD cd05509 cd05509 99941 Bromo_gcn5_like Bromodomain; Gcn5_like subfamily. Gcn5p is a histone acetyltransferase (HAT) which mediates acetylation of histones at lysine residues; such acetylation is generally correlated with the activation of transcription. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 101 matched cddid_all.tbl CDD cd05510 cd05510 99942 Bromo_SPT7_like Bromodomain; SPT7_like subfamily. SPT7 is a yeast protein that functions as a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA, and SLIK. SAGA is involved in the RNA polymerase II-dependent transcriptional regulation of about 10% of all yeast genes. The SPT7 bromodomain has been shown to weakly interact with acetylated histone H3, but not H4. The human representative of this subfamily is cat eye syndrome critical region protein 2 (CECR2). Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 112 matched cddid_all.tbl CDD cd05511 cd05511 99943 Bromo_TFIID Bromodomain, TFIID-like subfamily. Human TAFII250 (or TAF250) is the largest subunit of TFIID, a large multi-domain complex, which initiates the assembly of the transcription machinery. TAFII250 contains two bromodomains that specifically bind to acetylated histone H4. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 112 matched cddid_all.tbl CDD cd05512 cd05512 99944 Bromo_brd1_like Bromodomain; brd1_like subfamily. BRD1 is a mammalian gene which encodes for a nuclear protein assumed to be a transcriptional regulator. BRD1 has been implicated with brain development and susceptibility to schizophrenia and bipolar affective disorder. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 98 matched cddid_all.tbl CDD cd05513 cd05513 99945 Bromo_brd7_like Bromodomain, brd7_like subgroup. The BRD7 gene encodes a nuclear protein that has been shown to inhibit cell growth and the progression of the cell cycle by regulating cell-cycle genes at the transcriptional level. BRD7 has been identified as a gene involved in nasopharyngeal carcinoma. The protein interacts with acetylated histone H3 via its bromodomain. Bromodomains are 110 amino acid long domains that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 98 matched cddid_all.tbl CDD cd05515 cd05515 99946 Bromo_polybromo_V Bromodomain, polybromo repeat V. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine. 105 matched cddid_all.tbl CDD cd05516 cd05516 99947 Bromo_SNF2L2 Bromodomain, SNF2L2-like subfamily, specific to animals. SNF2L2 (SNF2-alpha) or SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 2 is a global transcriptional activator, which cooperates with nuclear hormone receptors to boost transcriptional activation. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 107 matched cddid_all.tbl CDD cd05517 cd05517 99948 Bromo_polybromo_II Bromodomain, polybromo repeat II. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine. 103 matched cddid_all.tbl CDD cd05518 cd05518 99949 Bromo_polybromo_IV Bromodomain, polybromo repeat IV. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine. 103 matched cddid_all.tbl CDD cd05519 cd05519 99950 Bromo_SNF2 Bromodomain, SNF2-like subfamily, specific to fungi. SNF2 is a yeast protein involved in transcriptional activation, it is the catalytic component of the SWI/SNF ATP-dependent chromatin remodeling complex. The protein is essential for the regulation of gene expression (both positive and negative) of a large number of genes. The SWI/SNF complex changes chromatin structure by altering DNA-histone contacts within the nucleosome, which results in a re-positioning of the nucleosome and facilitates or represses the binding of gene-specific transcription factors. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 103 matched cddid_all.tbl CDD cd05520 cd05520 99951 Bromo_polybromo_III Bromodomain, polybromo repeat III. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine. 103 matched cddid_all.tbl CDD cd05521 cd05521 99952 Bromo_Rsc1_2_I Bromodomain, repeat I in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 106 matched cddid_all.tbl CDD cd05522 cd05522 99953 Bromo_Rsc1_2_II Bromodomain, repeat II in Rsc1/2_like subfamily, specific to fungi. Rsc1 and Rsc2 are components of the RSC complex (remodeling the structure of chromatin), are essential for transcriptional control, and have a specific domain architecture including two bromodomains. The RSC complex has also been linked to homologous recombination and nonhomologous end-joining repair of DNA double strand breaks. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 104 matched cddid_all.tbl CDD cd05524 cd05524 99954 Bromo_polybromo_I Bromodomain, polybromo repeat I. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine. 113 matched cddid_all.tbl CDD cd05525 cd05525 99955 Bromo_ASH1 Bromodomain; ASH1_like sub-family. ASH1 (absent, small, or homeotic 1) is a member of the trithorax-group in Drosophila melanogaster, an epigenetic transcriptional regulator of HOX genes. Drosophila ASH1 has been shown to methylate specific lysines in histones H3 and H4. Mammalian ASH1 has been shown to methylate histone H3. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 106 matched cddid_all.tbl CDD cd05526 cd05526 99956 Bromo_polybromo_VI Bromodomain, polybromo repeat VI. Polybromo is a nuclear protein of unknown function, which contains 6 bromodomains. The human ortholog BAF180 is part of a SWI/SNF chromatin-remodeling complex, and it may carry out the functions of Yeast Rsc-1 and Rsc-2. It was shown that polybromo bromodomains bind to histone H3 at specific acetyl-lysine positions. Bromodomains are found in many chromatin-associated proteins and in nuclear histone acetyltransferases. They interact specifically with acetylated lysine, but not all the bromodomains in polybromo may bind to acetyl-lysine. 110 matched cddid_all.tbl CDD cd05528 cd05528 99957 Bromo_AAA Bromodomain; sub-family co-occurring with AAA domains. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. The structure(2DKW) in this alignment is an uncharacterized protein predicted from analysis of cDNA clones from human fetal liver 112 matched cddid_all.tbl CDD cd05529 cd05529 99958 Bromo_WDR9_I_like Bromodomain; WDR9 repeat I_like subfamily. WDR9 is a human gene located in the Down Syndrome critical region-2 of chromosome 21. It encodes for a nuclear protein containing WD40 repeats and two bromodomains, which may function as a transcriptional regulator involved in chromatin remodeling and play a role in embryonic development. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 128 matched cddid_all.tbl CDD cd05530 cd05530 99913 POLBc_B1 DNA polymerase type-B B1 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. 372 matched cddid_all.tbl CDD cd05531 cd05531 99914 POLBc_B2 DNA polymerase type-B B2 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaeal members also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. 352 matched cddid_all.tbl CDD cd05532 cd05532 99915 POLBc_alpha DNA polymerase type-B alpha subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. In most organisms no specific repair role, other than check point control, has been assigned to this enzyme. Pol alpha contains both polymerase and exonuclease domains, but lacks exonuclease activity suggesting that the exonuclease domain may be for structural purposes only. 400 matched cddid_all.tbl CDD cd05533 cd05533 99916 POLBc_delta DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. 393 matched cddid_all.tbl CDD cd05534 cd05534 99917 POLBc_zeta DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. 451 matched cddid_all.tbl CDD cd05535 cd05535 99918 POLBc_epsilon DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) epsilon has been proposed to play a role in elongation of the leading strand during DNA replication. Pol epsilon might also have a role in DNA repair. The structure of pol epsilon is characteristic of this family with the exception that it contains a large c-terminal domain with an unclear function. Phylogenetic analyses indicate that Pol epsilon is the ortholog to the archaeal Pol B3 rather than to Pol alpha, delta, or zeta. This might be because pol epsilon is ancestral to both archaea and eukaryotes DNA polymerases type B. 621 matched cddid_all.tbl CDD cd05536 cd05536 99919 POLBc_B3 DNA polymerase type-B B3 subfamily catalytic domain. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some members of the archaea also possess multiple family B DNA polymerases (B1, B2 and B3). So far there is no specific function(s) has been assigned for different members of the archaea type B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B DNA polymerases are support independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Structural comparison of the thermostable DNA polymerase type B to its mesostable homolog suggests several adaptations to high temperature such as shorter loops, disulfide bridges, and increasing electrostatic interaction at subdomain interfaces. 371 matched cddid_all.tbl CDD cd05537 cd05537 99920 POLBc_Pol_II DNA polymerase type-II subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proven by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication. 371 matched cddid_all.tbl CDD cd05538 cd05538 99921 POLBc_Pol_II_B DNA polymerase type-II B subfamily catalytic domain. Bacteria contain five DNA polymerases (I, II, III, IV and V). DNA polymerase II (Pol II) is a prototype for the B-family of polymerases. The role of Pol II in a variety of cellular activities, such as repair of DNA damaged by UV irradiation or oxidation has been proved by genetic studies. DNA polymerase III is the main enzyme responsible for replication of the bacterial chromosome; however, In vivo studies have also shown that Pol II is able to participate in chromosomal DNA replication with larger role in lagging-strand replication. 347 matched cddid_all.tbl CDD cd05540 cd05540 349776 UreG urease accessory protein UreG. UreG is one of the four accessory proteins of urease. Urease is an enzyme which catalyzes the decomposition of urea to form ammonia and carbon dioxide. Bacterial urease is a trimer of three subunits which are encoded by genes ureA, ureB, and ureC. Up to four accessory proteins (ureD, ureE, ureF, and ureG) are required for urease catalytical function. UreG may play an important role in nickel incorporation of the urease metallocenter. UreG is a member of the Fer4_NifH superfamily which contains an ATP-binding domain. Proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion. 191 matched cddid_all.tbl CDD cd05559 cd05559 349405 CAP_PI16_HrTT-1 CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain of peptidase inhibitor 16 and HrTT-1 protein. Human peptidase inhibitor 16 (PI16) is also called cysteine-rich secretory protein 9 (CRISP-9) or PSP94-binding protein. Mouse PI16 is also called cysteine-rich protease inhibitor. PI16 is predominantly expressed by cardiac fibroblasts and is exposed to the interstitium via a glycophosphatidylinositol (-GPI) membrane anchor. It suppresses the activation of the chemokine chemerin in the myocardium, which may be a part of the cardiac stress response. At high endothelial shear stress, PI16 is an inflammation-regulated inhibitor of matrix metalloproteinase 2 (MMP2). Also included in this subfamily is the HrTT-1 protein, a tail-tip epidermis marker in ascidians. The wider family of CAP domain containing proteins includes plant pathogenesis-related protein 1 (PR-1), cysteine-rich secretory proteins (CRISPs), and allergen 5 from vespid venom, among others. 134 matched cddid_all.tbl CDD cd05560 cd05560 240187 Xcc1710_like Xcc1710_like family, specific to proteobacteria. Xcc1710 is a hypothetical protein from Xanthomonas campestris pv. campestris str. ATCC 33913, similar to Mth938, a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. Their three-dimensional structures have been determined, but their functions are unknown. 109 matched cddid_all.tbl CDD cd05561 cd05561 173797 Peptidases_S8_4 Peptidase S8 family domain, uncharacterized subfamily 4. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 239 matched cddid_all.tbl CDD cd05562 cd05562 173798 Peptidases_S53_like Peptidase domain in the S53 family. Members of the peptidase S53 (sedolisin) family include endopeptidases and exopeptidases. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of Asn in subtilisin. The stability of these enzymes may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. Characterized sedolisins include Kumamolisin, an extracellular calcium-dependent thermostable endopeptidase from Bacillus. The enzyme is synthesized with a 188 amino acid N-terminal preprotein region which is cleaved after the extraction into the extracellular space with low pH. One kumamolysin paralog, kumamolisin-As, is believed to be a collagenase. TPP1 is a serine protease that functions as a tripeptidyl exopeptidase as well as an endopeptidase. Less is known about PSCP from Pseudomonas which is thought to be an aspartic proteinase. 275 matched cddid_all.tbl CDD cd05563 cd05563 99905 PTS_IIB_ascorbate PTS_IIB_ascorbate: subunit IIB of enzyme II (EII) of the L-ascorbate-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is an L-ascorbate-specific permease with two cytoplasmic subunits (IIA and IIB) and a transmembrane channel IIC subunit. Subunits IIA, IIB, and IIC are encoded by the sgaA, sgaB, and sgaT genes of the E. coli sgaTBA operon. In some bacteria, the IIB (SgaB) domain is fused C-terminal to the IIA (SgaT) domain. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include ascorbate, chitobiose/lichenan, lactose, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system. 86 matched cddid_all.tbl CDD cd05564 cd05564 99906 PTS_IIB_chitobiose_lichenan PTS_IIB_chitobiose_lichenan: subunit IIB of enzyme II (EII) of the N,N-diacetylchitobiose-specific and lichenan-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In these systems, EII is either a lichenan- or an N,N-diacetylchitobiose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. In the chitobiose system, these subunits are expressed as separate proteins from chbA, chbB, and chbC of the chb operon (formerly the cel (cellulose) operon). In the lichenan system, these subunits are expressed from licA, licB, and licC of the lic operon. The lic operon of Bacillus subtilis is required for the transport and degradation of oligomeric beta-glucosides, which are produced by extracellular enzymes on substrates such as lichenan or barley glucan. The lic operon is transcribed from a gammaA-dependent promoter and is inducible by lichenan, lichenan hydrolysate, and cellobiose. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include chitobiose/lichenan, ascorbate, lactose, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system. 96 matched cddid_all.tbl CDD cd05565 cd05565 99907 PTS_IIB_lactose PTS_IIB_lactose: subunit IIB of enzyme II (EII) of the lactose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) found in Firmicutes as well as Actinobacteria. In this system, EII is a lactose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIC and IIB domains are expressed as a single protein from the lac operon. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include lactose, chitobiose/lichenan, ascorbate, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system. 99 matched cddid_all.tbl CDD cd05566 cd05566 99908 PTS_IIB_galactitol PTS_IIB_galactitol: subunit IIB of enzyme II (EII) of the galactitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a galactitol-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain that are expressed on three distinct polypeptide chains, in contrast to other PTS sugar transporters. The three genes encoding these subunits (gatA, gatB, and gatC) comprise the gatCBA operon. Galactitol PTS permease takes up exogenous galactitol, releasing the phosphate ester into the cytoplasm in preparation for oxidation and further metabolism via a modified glycolytic pathway called the tagatose-6-phosphate glycolytic pathway. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include galactitol, chitobiose/lichenan, ascorbate, lactose, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system. 89 matched cddid_all.tbl CDD cd05567 cd05567 99909 PTS_IIB_mannitol PTS_IIB_mannitol: subunit IIB of enzyme II (EII) of the mannitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII is a mannitol-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIA, IIB, and IIC domains are expressed from the mtlA gene as a single protein, also known as the mannitol PTS permease, the mtl transporter, or MtlA. MtlA is only functional as a dimer with the dimer contacts occuring between the IIC domains. MtlA takes up exogenous mannitol releasing the phosphate ester into the cytoplasm in preparation for oxidation to fructose-6-phosphate by the NAD-dependent mannitol-P dehydrogenase (MtlD). The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include mannitol, chitobiose/lichenan, ascorbate, lactose, galactitol, fructose, and a sensory system with similarity to the bacterial bgl system. 87 matched cddid_all.tbl CDD cd05568 cd05568 99910 PTS_IIB_bgl_like PTS_IIB_bgl_like: the PTS (phosphotransferase system) IIB domain of a family of sensory systems composed of a membrane-bound sugar-sensor (similar to BglF) and a transcription antiterminator (similar to BglG) which regulate expression of genes involved in sugar utilization. The domain architecture of the IIB-containing protein includes a region N-terminal to the IIB domain which is homologous to the BglG transcription antiterminator with an RNA-binding domain followed by two homologous domains, PRD1 and PRD2 (PTS Regulation Domains). C-terminal to the IIB domain is a domain similar to the PTS IIA domain. In this system, the BglG-like region and the IIB and IIA-like domains are all expressed together as a single multidomain protein. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include this sensory system with similarity to the bacterial bgl system, chitobiose/lichenan, ascorbate, lactose, galactitol, mannitol, and fructose systems. 85 matched cddid_all.tbl CDD cd05569 cd05569 99911 PTS_IIB_fructose PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and FruB) each containing 3 domains. The FruA protein contains two tandem nonidentical IIB domains and a C-terminal IIC transmembrane domain. Both IIB domains of FruA are included in this alignment. The FruB protein (also referred to as diphosphoryl transfer protein) contains a IIA domain, a domain of unknown function, and an Hpr-like domain called FPr (fructose-inducible HPr). This familiy also includes the IIB domains of several fructose-like PTS permeases including the Frv permease encoded by the frvABXR operon, the Frw permease encoded by the frwACBD operon, the Frx permease encoded by the hrsA gene, and the Fry permease encoded by the fryABC (ypdDGH) operon. FruAB takes up exogenous fructose, releasing the 1-phosphate ester in to the cytoplasm in preparation for metabolism primarily via glycolysis. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include fructose, chitobiose/lichenan, ascorbate, lactose, galactitol, mannitol, and a sensory system with similarity to the bacterial bgl system. 96 matched cddid_all.tbl CDD cd05570 cd05570 270722 STKc_PKC Catalytic domain of the Serine/Threonine Kinase, Protein Kinase C. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. PKCs undergo three phosphorylations in order to take mature forms. In addition, classical PKCs depend on calcium, DAG (1,2-diacylglycerol), and in most cases, phosphatidylserine (PS) for activation. Novel PKCs are calcium-independent, but require DAG and PS for activity, while atypical PKCs only require PS. PKCs phosphorylate and modify the activities of a wide variety of cellular proteins including receptors, enzymes, cytoskeletal proteins, transcription factors, and other kinases. They play a central role in signal transduction pathways that regulate cell migration and polarity, proliferation, differentiation, and apoptosis. Also included in this subfamily are the PKC-like proteins, called PKNs. The PKC subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 318 matched cddid_all.tbl CDD cd05571 cd05571 270723 STKc_PKB Catalytic domain of the Serine/Threonine Kinase, Protein Kinase B. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. There are three PKB isoforms from different genes, PKB-alpha (or Akt1), PKB-beta (or Akt2), and PKB-gamma (or Akt3). PKB contains an N-terminal pleckstrin homology (PH) domain and a C-terminal catalytic domain. It is activated downstream of phosphoinositide 3-kinase (PI3K) and plays important roles in diverse cellular functions including cell survival, growth, proliferation, angiogenesis, motility, and migration. PKB also has a central role in a variety of human cancers, having been implicated in tumor initiation, progression, and metastasis. The PKB subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and PI3K. 322 matched cddid_all.tbl CDD cd05572 cd05572 270724 STKc_cGK Catalytic domain of the Serine/Threonine Kinase, cGMP-dependent protein kinase (cGK or PKG). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Mammals have two cGK isoforms from different genes, cGKI and cGKII. cGKI exists as two splice variants, cGKI-alpha and cGKI-beta. cGK consists of an N-terminal regulatory domain containing a dimerization and an autoinhibitory pseudosubstrate region, two cGMP-binding domains, and a C-terminal catalytic domain. Binding of cGMP to both binding sites releases the inhibition of the catalytic center by the pseudosubstrate region, allowing autophosphorylation and activation of the kinase. cGKI is a soluble protein expressed in all smooth muscles, platelets, cerebellum, and kidney. It is also expressed at lower concentrations in other tissues. cGKII is a membrane-bound protein that is most abundantly expressed in the intestine. It is also present in the brain nuclei, adrenal cortex, kidney, lung, and prostate. cGKI is involved in the regulation of smooth muscle tone, smooth cell proliferation, and platelet activation. cGKII plays a role in the regulation of secretion, such as renin secretion by the kidney and aldosterone secretion by the adrenal. It also regulates bone growth and the circadian rhythm. The cGK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 262 matched cddid_all.tbl CDD cd05573 cd05573 270725 STKc_ROCK_NDR_like Catalytic domain of Rho-associated coiled-coil containing protein kinase (ROCK)- and Nuclear Dbf2-Related (NDR)-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Members of this subfamily include ROCK and ROCK-like proteins such as DMPK, MRCK, and CRIK, as well as NDR and NDR-like proteins such as LATS, CBK1 and Sid2p. ROCK and CRIK are effectors of the small GTPase Rho, while MRCK is an effector of the small GTPase Cdc42. NDR and NDR-like kinases contain an N-terminal regulatory (NTR) domain and an insert within the catalytic domain that contains an auto-inhibitory sequence. Proteins in this subfamily are involved in regulating many cellular functions including contraction, motility, division, proliferation, apoptosis, morphogenesis, and cytokinesis. The ROCK/NDR-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 350 matched cddid_all.tbl CDD cd05574 cd05574 270726 STKc_phototropin_like Catalytic domain of Phototropin-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Phototropins are blue-light receptors that control responses such as phototropism, stromatal opening, and chloroplast movement in order to optimize the photosynthetic efficiency of plants. They are light-activated STKs that contain an N-terminal photosensory domain and a C-terminal catalytic domain. The N-terminal domain contains two LOV (Light, Oxygen or Voltage) domains that binds FMN. Photoexcitation of the LOV domains results in autophosphorylation at multiple sites and activation of the catalytic domain. In addition to plant phototropins, included in this subfamily are predominantly uncharacterized fungal STKs whose catalytic domains resemble the phototropin kinase domain. One protein from Neurospora crassa is called nrc-2, which plays a role in growth and development by controlling entry into the conidiation program. The phototropin-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 316 matched cddid_all.tbl CDD cd05575 cd05575 270727 STKc_SGK Catalytic domain of the Serine/Threonine Kinase, Serum- and Glucocorticoid-induced Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. SGKs are activated by insulin and growth factors via phosphoinositide 3-kinase and PDK1. They activate ion channels, ion carriers, and the Na-K-ATPase, as well as regulate the activity of enzymes and transcription factors. SGKs play important roles in transport, hormone release, neuroexcitability, cell proliferation, and apoptosis. There are three isoforms of SGK, named SGK1, SGK2, and SGK3 (also called cytokine-independent survival kinase CISK). The SGK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 323 matched cddid_all.tbl CDD cd05576 cd05576 270728 STKc_RPK118_like Catalytic domain of the Serine/Threonine Kinase, RPK118, and similar proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. RPK118 contains an N-terminal Phox homology (PX) domain, a Microtubule Interacting and Trafficking (MIT) domain, and a kinase domain containing a long uncharacterized insert. Also included in the family is human RPK60 (or ribosomal protein S6 kinase-like 1), which also contains MIT and kinase domains but lacks a PX domain. RPK118 binds sphingosine kinase, a key enzyme in the synthesis of sphingosine 1-phosphate (SPP), a lipid messenger involved in many cellular events. RPK118 may be involved in transmitting SPP-mediated signaling. RPK118 also binds the antioxidant peroxiredoxin-3. RPK118 may be involved in the transport of PRDX3 from the cytoplasm to its site of function in the mitochondria. The RPK118-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 265 matched cddid_all.tbl CDD cd05577 cd05577 270729 STKc_GRK Catalytic domain of the Serine/Threonine Kinase, G protein-coupled Receptor Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. GRKs phosphorylate and regulate G protein-coupled receptors (GPCRs), the largest superfamily of cell surface receptors, which regulate some part of nearly all physiological functions. Phosphorylated GPCRs bind to arrestins, which prevents further G protein signaling despite the presence of activating ligand. GRKs play important roles in the cardiovascular, immune, respiratory, skeletal, and nervous systems. They contain a central catalytic domain, flanked by N- and C-terminal extensions. The N-terminus contains an RGS (regulator of G protein signaling) homology (RH) domain and several motifs. The C-terminus diverges among different groups of GRKs. There are seven types of GRKs, named GRK1 to GRK7, which are subdivided into three main groups: visual (GRK1/7); beta-adrenergic receptor kinases (GRK2/3); and GRK4-like (GRK4/5/6). Expression of GRK2/3/5/6 is widespread while GRK1/4/7 show a limited tissue distribution. The substrate spectrum of the widely expressed GRKs partially overlaps. The GRK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 278 matched cddid_all.tbl CDD cd05578 cd05578 270730 STKc_Yank1 Catalytic domain of the Serine/Threonine Kinase, Yank1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily contains uncharacterized STKs with similarity to the human protein designated as Yank1 or STK32A. The Yank1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 257 matched cddid_all.tbl CDD cd05579 cd05579 270731 STKc_MAST_like Catalytic domain of Microtubule-associated serine/threonine (MAST) kinase-like proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily includes MAST kinases, MAST-like (MASTL) kinases (also called greatwall kinase or Gwl), and fungal kinases with similarity to Saccharomyces cerevisiae Rim15 and Schizosaccharomyces pombe cek1. MAST kinases contain an N-terminal domain of unknown function, a central catalytic domain, and a C-terminal PDZ domain that mediates protein-protein interactions. MASTL kinases carry only a catalytic domain which contains a long insert relative to other kinases. The fungal kinases in this subfamily harbor other domains in addition to a central catalytic domain, which like in MASTL, also contains an insert relative to MAST kinases. Rim15 contains a C-terminal signal receiver (REC) domain while cek1 contains an N-terminal PAS domain. MAST kinases are cytoskeletal associated kinases of unknown function that are also expressed at neuromuscular junctions and postsynaptic densities. MASTL/Gwl is involved in the regulation of mitotic entry, mRNA stabilization, and DNA checkpoint recovery. The fungal proteins Rim15 and cek1 are involved in the regulation of meiosis and mitosis, respectively. The MAST-like kinase subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 272 matched cddid_all.tbl CDD cd05580 cd05580 270732 STKc_PKA_like Catalytic subunit of the Serine/Threonine Kinases, cAMP-dependent protein kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of the cAMP-dependent protein kinases, PKA and PRKX, and similar proteins. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis. PRKX is also reulated by the R subunit and is is present in many tissues including fetal and adult brain, kidney, and lung. It is implicated in granulocyte/macrophage lineage differentiation, renal cell epithelial migration, and tubular morphogenesis in the developing kidney. The PKA-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 290 matched cddid_all.tbl CDD cd05581 cd05581 270733 STKc_PDK1 Catalytic domain of the Serine/Threonine Kinase, Phosphoinositide-dependent kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PDK1 carries an N-terminal catalytic domain and a C-terminal pleckstrin homology (PH) domain that binds phosphoinositides. It phosphorylates the activation loop of AGC kinases that are regulated by PI3K such as PKB, SGK, and PKC, among others, and is crucial for their activation. Thus, it contributes in regulating many processes including metabolism, growth, proliferation, and survival. PDK1 also has the ability to autophosphorylate and is constitutively active in mammalian cells. It is essential for normal embryo development and is important in regulating cell volume. The PDK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 278 matched cddid_all.tbl CDD cd05582 cd05582 270734 STKc_RSK_N N-terminal catalytic domain of the Serine/Threonine Kinase, 90 kDa ribosomal protein S6 kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. RSKs contain an N-terminal kinase domain (NTD) from the AGC family and a C-terminal kinase domain (CTD) from the CAMK family. They are activated by signaling inputs from extracellular regulated kinase (ERK) and phosphoinositide dependent kinase 1 (PDK1). ERK phosphorylates and activates the CTD of RSK, serving as a docking site for PDK1, which phosphorylates and activates the NTD, which in turn phosphorylates all known RSK substrates. RSKs act as downstream effectors of mitogen-activated protein kinase (MAPK) and play key roles in mitogen-activated cell growth, differentiation, and survival. Mammals possess four RSK isoforms (RSK1-4) from distinct genes. RSK proteins are also referred to as MAP kinase-activated protein kinases (MAPKAPKs), p90-RSKs, or p90S6Ks. The RSK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 317 matched cddid_all.tbl CDD cd05583 cd05583 270735 STKc_MSK_N N-terminal catalytic domain of the Serine/Threonine Kinase, Mitogen and stress-activated kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MSKs contain an N-terminal kinase domain (NTD) from the AGC family and a C-terminal kinase domain (CTD) from the CAMK family. MSKs are activated by two major signaling cascades, the Ras-MAPK and p38 stress kinase pathways, in response to various stimuli such as growth factors, hormones, neurotransmitters, cellular stress, and pro-inflammatory cytokines. This triggers phosphorylation in the activation loop (A-loop) of the CTD of MSK. The active CTD phosphorylates the hydrophobic motif (HM) in the C-terminal extension of NTD, which facilitates the phosphorylation of the A-loop and activates the NTD, which in turn phosphorylates downstream targets. MSKs are predominantly nuclear proteins. They are widely expressed in many tissues including heart, brain, lung, liver, kidney, and pancreas. There are two isoforms of MSK, called MSK1 and MSK2. The MSK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 268 matched cddid_all.tbl CDD cd05584 cd05584 270736 STKc_p70S6K Catalytic domain of the Serine/Threonine Kinase, 70 kDa ribosomal protein S6 kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. p70S6K (or S6K) contains only one catalytic kinase domain, unlike p90 ribosomal S6 kinases (RSKs). It acts as a downstream effector of the STK mTOR (mammalian Target of Rapamycin) and plays a role in the regulation of the translation machinery during protein synthesis. p70S6K also plays a pivotal role in regulating cell size and glucose homeostasis. Its targets include S6, the translation initiation factor eIF3, and the insulin receptor substrate IRS-1, among others. Mammals contain two isoforms of p70S6K, named S6K1 and S6K2 (or S6K-beta). The p70S6K subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 323 matched cddid_all.tbl CDD cd05585 cd05585 270737 STKc_YPK1_like Catalytic domain of Yeast Protein Kinase 1-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of fungal proteins with similarity to the AGC STKs, Saccharomyces cerevisiae YPK1 and Schizosaccharomyces pombe Gad8p. YPK1 is required for cell growth and acts as a downstream kinase in the sphingolipid-mediated signaling pathway of yeast. It also plays a role in efficient endocytosis and in the maintenance of cell wall integrity. Gad8p is a downstream target of Tor1p, the fission yeast homolog of mTOR. It plays a role in cell growth and sexual development. The YPK1-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 313 matched cddid_all.tbl CDD cd05586 cd05586 270738 STKc_Sck1_like Catalytic domain of Suppressor of loss of cAMP-dependent protein kinase-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of Schizosaccharomyces pombe Sck1 and similar fungal proteins. Sck1 plays a role in trehalase activation triggered by glucose and a nitrogen source. Trehalase catalyzes the cleavage of the disaccharide trehalose to glucose. Trehalose, as a carbohydrate reserve and stress metabolite, plays an important role in the response of yeast to environmental changes. The Sck1-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 330 matched cddid_all.tbl CDD cd05587 cd05587 270739 STKc_cPKC Catalytic domain of the Serine/Threonine Kinase, Classical (or Conventional) Protein Kinase C. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. cPKCs are potent kinases for histones, myelin basic protein, and protamine. They depend on calcium, DAG (1,2-diacylglycerol), and in most cases, phosphatidylserine (PS) for activation. cPKCs contain a calcium-binding C2 region in their regulatory domain. There are four cPKC isoforms, named alpha, betaI, betaII, and gamma. PKC-gamma is mainly expressed in neuronal tissues. It plays a role in protection from ischemia. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. The cPKC subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 320 matched cddid_all.tbl CDD cd05588 cd05588 270740 STKc_aPKC Catalytic domain of the Serine/Threonine Kinase, Atypical Protein Kinase C. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. aPKCs only require phosphatidylserine (PS) for activation. They contain a C2-like region, instead of a calcium-binding (C2) region found in classical PKCs, in their regulatory domain. There are two aPKC isoforms, zeta and iota. aPKCs are involved in many cellular functions including proliferation, migration, apoptosis, polarity maintenance and cytoskeletal regulation. They also play a critical role in the regulation of glucose metabolism and in the pathogenesis of type 2 diabetes. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. The aPKC subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 328 matched cddid_all.tbl CDD cd05589 cd05589 270741 STKc_PKN Catalytic domain of the Serine/Threonine Kinase, Protein Kinase N. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PKN has a C-terminal catalytic domain that is highly homologous to PKCs. Its unique N-terminal regulatory region contains antiparallel coiled-coil (ACC) domains. In mammals, there are three PKN isoforms from different genes (designated PKN-alpha, beta, and gamma), which show different enzymatic properties, tissue distribution, and varied functions. PKN can be activated by the small GTPase Rho, and by fatty acids such as arachidonic and linoleic acids. It is involved in many biological processes including cytokeletal regulation, cell adhesion, vesicle transport, glucose transport, regulation of meiotic maturation and embryonic cell cycles, signaling to the nucleus, and tumorigenesis. The PKN subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 326 matched cddid_all.tbl CDD cd05590 cd05590 270742 STKc_nPKC_eta Catalytic domain of the Serine/Threonine Kinase, Novel Protein Kinase C eta. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PKC-eta is predominantly expressed in squamous epithelia, where it plays a crucial role in the signaling of cell-type specific differentiation. It is also expressed in pro-B cells and early-stage thymocytes, and acts as a key regulator in early B-cell development. PKC-eta increases glioblastoma multiforme (GBM) proliferation and resistance to radiation, and is being developed as a therapeutic target for the management of GBM. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. nPKCs are calcium-independent, but require DAG (1,2-diacylglycerol) and phosphatidylserine (PS) for activity. The nPKC-eta subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 323 matched cddid_all.tbl CDD cd05591 cd05591 270743 STKc_nPKC_epsilon Catalytic domain of the Serine/Threonine Kinase, Novel Protein Kinase C epsilon. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PKC-epsilon has been shown to behave as an oncoprotein. Its overexpression contributes to neoplastic transformation depending on the cell type. It contributes to oncogenesis by inducing disordered cell growth and inhibiting cell death. It also plays a role in tumor invasion and metastasis. PKC-epsilon has also been found to confer cardioprotection against ischemia and reperfusion-mediated damage. Other cellular functions include the regulation of gene expression, cell adhesion, and cell motility. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. nPKCs are calcium-independent, but require DAG (1,2-diacylglycerol) and phosphatidylserine (PS) for activity. The nPKC-epsilon subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 321 matched cddid_all.tbl CDD cd05592 cd05592 270744 STKc_nPKC_theta_like Catalytic domain of the Serine/Threonine Kinases, Novel Protein Kinase C theta, delta, and similar proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PKC-theta is selectively expressed in T-cells and plays an important and non-redundant role in several aspects of T-cell biology. PKC-delta plays a role in cell cycle regulation and programmed cell death in many cell types. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. nPKCs are calcium-independent, but require DAG (1,2-diacylglycerol) and phosphatidylserine (PS) for activity. There are four nPKC isoforms, delta, epsilon, eta, and theta. The nPKC-theta-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 320 matched cddid_all.tbl CDD cd05593 cd05593 270745 STKc_PKB_gamma Catalytic domain of the Serine/Threonine Kinase, Protein Kinase B gamma (also called Akt3). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PKB-gamma is predominantly expressed in neuronal tissues. Mice deficient in PKB-gamma show a reduction in brain weight due to the decreases in cell size and cell number. PKB-gamma has also been shown to be upregulated in estrogen-deficient breast cancer cells, androgen-independent prostate cancer cells, and primary ovarian tumors. It acts as a key mediator in the genesis of ovarian cancer. PKB contains an N-terminal pleckstrin homology (PH) domain and a C-terminal catalytic domain. The PKB-gamma subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 348 matched cddid_all.tbl CDD cd05594 cd05594 270746 STKc_PKB_alpha Catalytic domain of the Serine/Threonine Kinase, Protein Kinase B alpha (also called Akt1). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PKB-alpha is predominantly expressed in endothelial cells. It is critical for the regulation of angiogenesis and the maintenance of vascular integrity. It also plays a role in adipocyte differentiation. Mice deficient in PKB-alpha exhibit perinatal morbidity, growth retardation, reduction in body weight accompanied by reduced sizes of multiple organs, and enhanced apoptosis in some cell types. PKB-alpha activity has been reported to be frequently elevated in breast and prostate cancers. In some cancer cells, PKB-alpha may act as a suppressor of metastasis. PKB contains an N-terminal pleckstrin homology (PH) domain and a C-terminal catalytic domain. The PKB-alpha subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 356 matched cddid_all.tbl CDD cd05595 cd05595 173686 STKc_PKB_beta Catalytic domain of the Serine/Threonine Kinase, Protein Kinase B beta (also called Akt2). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PKB-beta is the predominant PKB isoform expressed in insulin-responsive tissues. It plays a critical role in the regulation of glucose homeostasis. It is also implicated in muscle cell differentiation. Mice deficient in PKB-beta display normal growth weights but exhibit severe insulin resistance and diabetes, accompanied by lipoatrophy and B-cell failure. PKB contains an N-terminal pleckstrin homology (PH) domain and a C-terminal catalytic domain.The PKB-beta subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 323 matched cddid_all.tbl CDD cd05596 cd05596 270747 STKc_ROCK Catalytic domain of the Serine/Threonine Kinase, Rho-associated coiled-coil containing protein kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. ROCK is also referred to as Rho-associated kinase or simply as Rho kinase. It contains an N-terminal extension, a catalytic kinase domain, and a long C-terminal extension, which contains a coiled-coil region encompassing a Rho-binding domain (RBD) and a pleckstrin homology (PH) domain. ROCK is auto-inhibited by the RBD and PH domain interacting with the catalytic domain. It is activated via interaction with Rho GTPases and is involved in many cellular functions including contraction, adhesion, migration, motility, proliferation, and apoptosis. The ROCK subfamily consists of two isoforms, ROCK1 and ROCK2, which may be functionally redundant in some systems, but exhibit different tissue distributions. Both isoforms are ubiquitously expressed in most tissues, but ROCK2 is more prominent in brain and skeletal muscle while ROCK1 is more pronounced in the liver, testes, and kidney. Studies in knockout mice result in different phenotypes, suggesting that the two isoforms do not compensate for each other during embryonic development. The ROCK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 352 matched cddid_all.tbl CDD cd05597 cd05597 270748 STKc_DMPK_like Catalytic domain of Myotonic Dystrophy protein kinase (DMPK)-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The DMPK-like subfamily is composed of DMPK and DMPK-related cell division control protein 42 (Cdc42) binding kinase (MRCK). DMPK is expressed in skeletal and cardiac muscles, and in central nervous tissues. The functional role of DMPK is not fully understood. It may play a role in the signal transduction and homeostasis of calcium. The DMPK gene is implicated in myotonic dystrophy 1 (DM1), an inherited multisystemic disorder with symptoms that include muscle hyperexcitability, progressive muscle weakness and wasting, cataract development, testicular atrophy, and cardiac conduction defects. The genetic basis for DM1 is the mutational expansion of a CTG repeat in the 3'-UTR of DMPK. MRCK is activated via interaction with the small GTPase Cdc42. MRCK/Cdc42 signaling mediates myosin-dependent cell motility. Three isoforms of MRCK are known, named alpha, beta and gamma. MRCKgamma is expressed in heart and skeletal muscles, unlike MRCKalpha and MRCKbeta, which are expressed ubiquitously. The DMPK-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 331 matched cddid_all.tbl CDD cd05598 cd05598 270749 STKc_LATS Catalytic domain of the Serine/Threonine Kinase, Large Tumor Suppressor. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. LATS was originally identified in Drosophila using a screen for genes whose inactivation led to overproliferation of cells. In tetrapods, there are two LATS isoforms, LATS1 and LATS2. Inactivation of LATS1 in mice results in the development of various tumors, including sarcomas and ovarian cancer. LATS functions as a tumor suppressor and is implicated in cell cycle regulation. The LATS subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 333 matched cddid_all.tbl CDD cd05599 cd05599 270750 STKc_NDR_like Catalytic domain of Nuclear Dbf2-Related kinase-like Protein Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. NDR kinases regulate mitosis, cell growth, embryonic development, and neurological processes. They are also required for proper centrosome duplication. Higher eukaryotes contain two NDR isoforms, NDR1 and NDR2. This subfamily also contains fungal NDR-like kinases. NDR kinase contains an N-terminal regulatory (NTR) domain and an insert within the catalytic domain that contains an auto-inhibitory sequence. Like many other AGC kinases, NDR kinase requires phosphorylation at two sites, the activation loop (A-loop) and the hydrophobic motif (HM), for activity. The NDR kinase subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 324 matched cddid_all.tbl CDD cd05600 cd05600 270751 STKc_Sid2p_like Catalytic domain of Fungal Sid2p-like Protein Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This group contains fungal kinases including Schizosaccharomyces pombe Sid2p and Saccharomyces cerevisiae Dbf2p. Group members show similarity to NDR kinases in that they contain an N-terminal regulatory (NTR) domain and an insert within the catalytic domain that contains an auto-inhibitory sequence. Sid2p plays a crucial role in the septum initiation network (SIN) and in the initiation of cytokinesis. Dbf2p is important in regulating the mitotic exit network (MEN) and in cytokinesis. The Sid2p-like group is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 386 matched cddid_all.tbl CDD cd05601 cd05601 270752 STKc_CRIK Catalytic domain of the Serine/Threonine Kinase, Citron Rho-interacting kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CRIK (also called citron kinase) is an effector of the small GTPase Rho. It plays an important function during cytokinesis and affects its contractile process. CRIK-deficient mice show severe ataxia and epilepsy as a result of abnormal cytokinesis and massive apoptosis in neuronal precursors. A Down syndrome critical region protein TTC3 interacts with CRIK and inhibits CRIK-dependent neuronal differentiation and neurite extension. CRIK contains a catalytic domain, a central coiled-coil domain, and a C-terminal region containing a Rho-binding domain (RBD), a zinc finger, and a pleckstrin homology (PH) domain, in addition to other motifs. The CRIK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 328 matched cddid_all.tbl CDD cd05602 cd05602 270753 STKc_SGK1 Catalytic domain of the Protein Serine/Threonine Kinase, Serum- and Glucocorticoid-induced Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. SGK1 is ubiquitously expressed and is under transcriptional control of numerous stimuli including cell stress (cell shrinkage), serum, hormones (gluco- and mineralocorticoids), gonadotropins, growth factors, interleukin-6, and other cytokines. It plays roles in sodium retention and potassium elimination in the kidney, nutrient transport, salt sensitivity, memory consolidation, and cardiac repolarization. A common SGK1 variant is associated with increased blood pressure and body weight. SGK1 may also contribute to tumor growth, neurodegeneration, fibrosing disease, and ischemia. The SGK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 339 matched cddid_all.tbl CDD cd05603 cd05603 270754 STKc_SGK2 Catalytic domain of the Serine/Threonine Kinase, Serum- and Glucocorticoid-induced Kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. SGK2 shows a more restricted distribution than SGK1 and is most abundantly expressed in epithelial tissues including kidney, liver, pancreas, and the choroid plexus of the brain. In vitro cellular assays show that SGK2 can stimulate the activity of ion channels, the glutamate transporter EEAT4, and the glutamate receptors, GluR6 and GLUR1. The SGK2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 321 matched cddid_all.tbl CDD cd05604 cd05604 270755 STKc_SGK3 Catalytic domain of the Protein Serine/Threonine Kinase, Serum- and Glucocorticoid-induced Kinase 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. SGK3 (also called cytokine-independent survival kinase or CISK) is expressed in most tissues and is most abundant in the embryo and adult heart and spleen. It was originally discovered in a screen for antiapoptotic genes. It phosphorylates and inhibits the proapoptotic proteins, Bad and FKHRL1. SGK3 also regulates many transporters, ion channels, and receptors. It plays a critical role in hair follicle morphogenesis and hair cycling. The SGK3 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 326 matched cddid_all.tbl CDD cd05605 cd05605 270756 STKc_GRK4_like Catalytic domain of G protein-coupled Receptor Kinase 4-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Members of the GRK4-like group include GRK4, GRK5, GRK6, and similar GRKs. They contain an N-terminal RGS homology (RH) domain and a catalytic domain, but lack a G protein betagamma-subunit binding domain. They are localized to the plasma membrane through post-translational lipid modification or direct binding to PIP2. GRKs phosphorylate and regulate G protein-coupled receptors (GPCRs), the largest superfamily of cell surface receptors which regulate some part of nearly all physiological functions. Phosphorylated GPCRs bind to arrestins, which prevents further G protein signaling despite the presence of activating ligand. The GRK4-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 285 matched cddid_all.tbl CDD cd05606 cd05606 270757 STKc_beta_ARK Catalytic domain of the Serine/Threonine Kinase, beta-adrenergic receptor kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The beta-ARK group is composed of GRK2, GRK3, and similar proteins. GRK2 and GRK3 are both widely expressed in many tissues, although GRK2 is present at higher levels. They contain an N-terminal RGS homology (RH) domain, a central catalytic domain, and C-terminal pleckstrin homology (PH) domain that mediates PIP2 and G protein betagamma-subunit translocation to the membrane. GRK2 (also called beta-ARK or beta-ARK1) is important in regulating several cardiac receptor responses. It plays a role in cardiac development and in hypertension. Deletion of GRK2 in mice results in embryonic lethality, caused by hypoplasia of the ventricular myocardium. GRK2 also plays important roles in the liver (as a regulator of portal blood pressure), in immune cells, and in the nervous system. Altered GRK2 expression has been reported in several disorders including major depression, schizophrenia, bipolar disorder, and Parkinsonism. GRKs phosphorylate and regulate G protein-coupled receptors (GPCRs), the largest superfamily of cell surface receptors which regulate some part of nearly all physiological functions. Phosphorylated GPCRs bind to arrestins, which prevents further G protein signaling despite the presence of activating ligand. The beta-ARK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 279 matched cddid_all.tbl CDD cd05607 cd05607 270758 STKc_GRK7 Catalytic domain of the Protein Serine/Threonine Kinase, G protein-coupled Receptor Kinase 7. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. GRK7 (also called iodopsin kinase) belongs to the visual group of GRKs. It is primarily found in the retina and plays a role in the regulation of opsin light receptors. GRK7 is located in retinal cone outer segments and plays an important role in regulating photoresponse of the cones. GRKs phosphorylate and regulate G protein-coupled receptors (GPCRs), the largest superfamily of cell surface receptors, which regulate some part of nearly all physiological functions. Phosphorylated GPCRs bind to arrestins, which prevents further G protein signaling despite the presence of activating ligand. The GRK7 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 286 matched cddid_all.tbl CDD cd05608 cd05608 270759 STKc_GRK1 Catalytic domain of the Serine/Threonine Kinase, G protein-coupled Receptor Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. GRK1 (also called rhodopsin kinase) belongs to the visual group of GRKs and is expressed in retinal cells. It phosphorylates rhodopsin in rod cells, which leads to termination of the phototransduction cascade. Mutations in GRK1 are associated to a recessively inherited form of stationary nightblindness called Oguchi disease. GRKs phosphorylate and regulate G protein-coupled receptors (GPCRs), the largest superfamily of cell surface receptors, which regulate some part of nearly all physiological functions. Phosphorylated GPCRs bind to arrestins, which prevents further G protein signaling despite the presence of activating ligand. The GRK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 288 matched cddid_all.tbl CDD cd05609 cd05609 270760 STKc_MAST Catalytic domain of the Protein Serine/Threonine Kinase, Microtubule-associated serine/threonine kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MAST kinases contain an N-terminal domain of unknown function, a central catalytic domain, and a C-terminal PDZ domain that mediates protein-protein interactions. There are four mammalian MAST kinases, named MAST1-MAST4. MAST1 is also called syntrophin-associated STK (SAST) while MAST2 is also called MAST205. MAST kinases are cytoskeletal associated kinases of unknown function that are also expressed at neuromuscular junctions and postsynaptic densities. MAST1, MAST2, and MAST3 bind and phosphorylate the tumor suppressor PTEN, and may contribute to the regulation and stabilization of PTEN. MAST2 is involved in the regulation of the Fc-gamma receptor of the innate immune response in macrophages, and may also be involved in the regulation of the Na+/H+ exchanger NHE3. The MAST kinase subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 280 matched cddid_all.tbl CDD cd05610 cd05610 270761 STKc_MASTL Catalytic domain of the Serine/Threonine Kinase, Microtubule-associated serine/threonine-like kinase (also called greatwall kinase). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The MASTL kinases in this group carry only a catalytic domain, which contains a long insertion relative to MAST kinases. MASTL, also called greatwall kinase (Gwl), is involved in the regulation of mitotic entry, which is controlled by the coordinated activities of protein kinases and opposing protein phosphatases (PPs). The cyclin B/CDK1 complex induces entry into M-phase while PP2A-B55 shows anti-mitotic activity. MASTL/Gwl is activated downstream of cyclin B/CDK1 and indirectly inhibits PP2A-B55 by phosphorylating the small protein alpha-endosulfine (Ensa) or the cAMP-regulated phosphoprotein 19 (Arpp19), resulting in M-phase progression. Gwl kinase may also play roles in mRNA stabilization and DNA checkpoint recovery. The human MASTL gene has also been named FLJ14813; a missense mutation in FLJ14813 is associated with autosomal dominant thrombocytopenia. The MASTL kinase subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 349 matched cddid_all.tbl CDD cd05611 cd05611 270762 STKc_Rim15_like Catalytic domain of fungal Rim15-like Protein Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Members of this group include Saccharomyces cerevisiae Rim15, Schizosaccharomyces pombe cek1, and similar fungal proteins. They contain a central catalytic domain, which contains an insert relative to MAST kinases. In addition, Rim15 contains a C-terminal signal receiver (REC) domain while cek1 contains an N-terminal PAS domain. Rim15 (or Rim15p) functions as a regulator of meiosis. It acts as a downstream effector of PKA and regulates entry into stationary phase (G0). Thus, it plays a crucial role in regulating yeast proliferation, differentiation, and aging. Cek1 may facilitate progression of mitotic anaphase. The Rim15-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 263 matched cddid_all.tbl CDD cd05612 cd05612 270763 STKc_PRKX_like Catalytic domain of PRKX-like Protein Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Members of this group include human PRKX (X chromosome-encoded protein kinase), Drosophila DC2, and similar proteins. PRKX is present in many tissues including fetal and adult brain, kidney, and lung. The PRKX gene is located in the Xp22.3 subregion and has a homolog called PRKY on the Y chromosome. An abnormal interchange between PRKX aand PRKY leads to the sex reversal disorder of XX males and XY females. PRKX is implicated in granulocyte/macrophage lineage differentiation, renal cell epithelial migration, and tubular morphogenesis in the developing kidney. The PRKX-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 292 matched cddid_all.tbl CDD cd05613 cd05613 270764 STKc_MSK1_N N-terminal catalytic domain of the Serine/Threonine Kinase, Mitogen and stress-activated kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MSK1 plays a role in the regulation of translational control and transcriptional activation. It phosphorylates the transcription factors, CREB and NFkB. It also phosphorylates the nucleosomal proteins H3 and HMG-14. Increased phosphorylation of MSK1 is associated with the development of cerebral ischemic/hypoxic preconditioning. MSKs contain an N-terminal kinase domain (NTD) from the AGC family and a C-terminal kinase domain (CTD) from the CAMK family. MSKs are activated by two major signaling cascades, the Ras-MAPK and p38 stress kinase pathways, which trigger phosphorylation in the activation loop (A-loop) of the CTD of MSK. The active CTD phosphorylates the hydrophobic motif (HM) of NTD, which facilitates the phosphorylation of the A-loop and activates the NTD, which in turn phosphorylates downstream targets. The MSK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 290 matched cddid_all.tbl CDD cd05614 cd05614 270765 STKc_MSK2_N N-terminal catalytic domain of the Serine/Threonine Kinase, Mitogen and stress-activated kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MSK2 and MSK1 play nonredundant roles in activating histone H3 kinases, which play pivotal roles in compaction of the chromatin fiber. MSK2 is the required H3 kinase in response to stress stimuli and activation of the p38 MAPK pathway. MSK2 also plays a role in the pathogenesis of psoriasis. MSKs contain an N-terminal kinase domain (NTD) from the AGC family and a C-terminal kinase domain (CTD) from the CAMK family, similar to 90 kDa ribosomal protein S6 kinases (RSKs). MSKs are activated by two major signaling cascades, the Ras-MAPK and p38 stress kinase pathways, which trigger phosphorylation in the activation loop (A-loop) of the CTD of MSK. The active CTD phosphorylates the hydrophobic motif (HM) of NTD, which facilitates the phosphorylation of the A-loop and activates the NTD, which in turn phosphorylates downstream targets. The MSK2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 332 matched cddid_all.tbl CDD cd05615 cd05615 270766 STKc_cPKC_alpha Catalytic domain of the Serine/Threonine Kinase, Classical Protein Kinase C alpha. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PKC-alpha is expressed in many tissues and is associated with cell proliferation, apoptosis, and cell motility. It plays a role in the signaling of the growth factors PDGF, VEGF, EGF, and FGF. Abnormal levels of PKC-alpha have been detected in many transformed cell lines and several human tumors. In addition, PKC-alpha is required for HER2 dependent breast cancer invasion. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. PKCs undergo three phosphorylations in order to take mature forms. In addition, cPKCs depend on calcium, DAG (1,2-diacylglycerol), and in most cases, phosphatidylserine (PS) for activation. The cPKC-alpha subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 341 matched cddid_all.tbl CDD cd05616 cd05616 270767 STKc_cPKC_beta Catalytic domain of the Serine/Threonine Kinase, Classical Protein Kinase C beta. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The PKC beta isoforms (I and II), generated by alternative splicing of a single gene, are preferentially activated by hyperglycemia-induced DAG (1,2-diacylglycerol) in retinal tissues. This is implicated in diabetic microangiopathy such as ischemia, neovascularization, and abnormal vasodilator function. PKC-beta also plays an important role in VEGF signaling. In addition, glucose regulates proliferation in retinal endothelial cells via PKC-betaI. PKC-beta is also being explored as a therapeutic target in cancer. It contributes to tumor formation and is involved in the tumor host mechanisms of inflammation and angiogenesis. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. PKCs undergo three phosphorylations in order to take mature forms. In addition, cPKCs depend on calcium, DAG, and in most cases, phosphatidylserine (PS) for activation. The cPKC-beta subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 323 matched cddid_all.tbl CDD cd05617 cd05617 270768 STKc_aPKC_zeta Catalytic domain of the Serine/Threonine Kinase, Atypical Protein Kinase C zeta. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PKC-zeta plays a critical role in activating the glucose transport response. It is activated by glucose, insulin, and exercise through diverse pathways. PKC-zeta also plays a central role in maintaining cell polarity in yeast and mammalian cells. In addition, it affects actin remodeling in muscle cells. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. aPKCs only require phosphatidylserine (PS) for activation. The aPKC-zeta subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 357 matched cddid_all.tbl CDD cd05618 cd05618 270769 STKc_aPKC_iota Catalytic domain of the Serine/Threonine Kinase, Atypical Protein Kinase C iota. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PKC-iota is directly implicated in carcinogenesis. It is critical to oncogenic signaling mediated by Ras and Bcr-Abl. The PKC-iota gene is the target of tumor-specific gene amplification in many human cancers, and has been identified as a human oncogene. In addition to its role in transformed growth, PKC-iota also promotes invasion, chemoresistance, and tumor cell survival. Expression profiling of PKC-iota is a prognostic marker of poor clinical outcome in several human cancers. PKC-iota also plays a role in establishing cell polarity, and has critical embryonic functions. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. aPKCs only require phosphatidylserine (PS) for activation. The aPKC subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 364 matched cddid_all.tbl CDD cd05619 cd05619 270770 STKc_nPKC_theta Catalytic domain of the Serine/Threonine Kinase, Novel Protein Kinase C theta. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PKC-theta is selectively expressed in T-cells and plays an important and non-redundant role in several aspects of T-cell biology. Although T-cells also express other PKC isoforms, PKC-theta is unique in that upon antigen stimulation, it is translocated to the plasma membrane at the immunological synapse, where it mediates signals essential for T-cell activation. It is essential for TCR-induced proliferation, cytokine production, T-cell survival, and the differentiation and effector function of T-helper (Th) cells, particularly Th2 and Th17. PKC-theta is being developed as a therapeutic target for Th2-mediated allergic inflammation and Th17-mediated autoimmune diseases. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. nPKCs are calcium-independent, but require DAG (1,2-diacylglycerol) and phosphatidylserine (PS) for activity. The nPKC subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 331 matched cddid_all.tbl CDD cd05620 cd05620 173710 STKc_nPKC_delta Catalytic domain of the Serine/Threonine Kinase, Novel Protein Kinase C delta. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PKC-delta plays a role in cell cycle regulation and programmed cell death in many cell types. It slows down cell proliferation, inducing cell cycle arrest and enhancing cell differentiation. PKC-delta is also involved in the regulation of transcription as well as immune and inflammatory responses. It plays a central role in the genotoxic stress response that leads to DNA damaged-induced apoptosis. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. nPKCs are calcium-independent, but require DAG (1,2-diacylglycerol) and phosphatidylserine (PS) for activity. The nPKC-delta subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 316 matched cddid_all.tbl CDD cd05621 cd05621 270771 STKc_ROCK2 Catalytic domain of the Serine/Threonine Kinase, Rho-associated coiled-coil containing protein kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. ROCK2 was the first identified target of activated RhoA, and was found to play a role in stress fiber and focal adhesion formation. It is prominently expressed in the brain, heart, and skeletal muscles. It is implicated in vascular and neurological disorders, such as hypertension and vasospasm of the coronary and cerebral arteries. ROCK2 is also activated by caspase-2 cleavage, resulting in thrombin-induced microparticle generation in response to cell activation. Mice deficient in ROCK2 show intrauterine growth retardation and embryonic lethality because of placental dysfunction. ROCK contains an N-terminal extension, a catalytic kinase domain, and a C-terminal extension, which contains a coiled-coil region encompassing a Rho-binding domain (RBD) and a pleckstrin homology (PH) domain. ROCK is auto-inhibited by the RBD and PH domain interacting with the catalytic domain, and is activated via interaction with Rho GTPases. The ROCK2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 379 matched cddid_all.tbl CDD cd05622 cd05622 270772 STKc_ROCK1 Catalytic domain of the Serine/Threonine Kinase, Rho-associated coiled-coil containing protein kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. ROCK1 is preferentially expressed in the liver, lung, spleen, testes, and kidney. It mediates signaling from Rho to the actin cytoskeleton. It is implicated in the development of cardiac fibrosis, cardiomyocyte apoptosis, and hyperglycemia. Mice deficient with ROCK1 display eyelids open at birth (EOB) and omphalocele phenotypes due to the disorganization of actin filaments in the eyelids and the umbilical ring. ROCK contains an N-terminal extension, a catalytic kinase domain, and a C-terminal extension, which contains a coiled-coil region encompassing a Rho-binding domain (RBD) and a pleckstrin homology (PH) domain. ROCK is auto-inhibited by the RBD and PH domain interacting with the catalytic domain, and is activated via interaction with Rho GTPases. The ROCK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 405 matched cddid_all.tbl CDD cd05623 cd05623 270773 STKc_MRCK_alpha Catalytic domain of the Serine/Threonine Kinase, DMPK-related cell division control protein 42 binding kinase (MRCK) alpha. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MRCK-alpha is expressed ubiquitously in many tissues. It plays a role in the regulation of peripheral actin reorganization and neurite outgrowth. It may also play a role in the transferrin iron uptake pathway. MRCK is activated via interaction with the small GTPase Cdc42. MRCK/Cdc42 signaling mediates myosin-dependent cell motility. The MRCK-alpha subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. This alignment model includes the dimerization domain. 409 matched cddid_all.tbl CDD cd05624 cd05624 270774 STKc_MRCK_beta Catalytic domain of the Protein Serine/Threonine Kinase, DMPK-related cell division control protein 42 binding kinase (MRCK) beta. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MRCK-beta is expressed ubiquitously in many tissues. MRCK is activated via interaction with the small GTPase Cdc42. MRCK/Cdc42 signaling mediates myosin-dependent cell motility. The MRCK-beta subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. This alignment model includes the dimerization domain. 409 matched cddid_all.tbl CDD cd05625 cd05625 270775 STKc_LATS1 Catalytic domain of the Serine/Threonine Kinase, Large Tumor Suppressor 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. LATS1 functions as a tumor suppressor and is implicated in cell cycle regulation. Inactivation of LATS1 in mice results in the development of various tumors, including sarcomas and ovarian cancer. Promoter methylation, loss of heterozygosity, and missense mutations targeting the LATS1 gene have also been found in human sarcomas and ovarian cancers. In addition, decreased expression of LATS1 is associated with an aggressive phenotype and poor prognosis. LATS1 induces G2 arrest and promotes cytokinesis. It may be a component of the mitotic exit network in higher eukaryotes. The LATS1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 382 matched cddid_all.tbl CDD cd05626 cd05626 173715 STKc_LATS2 Catalytic domain of the Protein Serine/Threonine Kinase, Large Tumor Suppressor 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. LATS2 is an essential mitotic regulator responsible for coordinating accurate cytokinesis completion and governing the stabilization of other mitotic regulators. It is also critical in the maintenance of proper chromosome number, genomic stability, mitotic fidelity, and the integrity of centrosome duplication. Downregulation of LATS2 is associated with poor prognosis in acute lymphoblastic leukemia and breast cancer. The LATS2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 381 matched cddid_all.tbl CDD cd05627 cd05627 270776 STKc_NDR2 Catalytic domain of the Serine/Threonine Kinase, Nuclear Dbf2-Related kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. NDR2 (also called STK38-like) plays a role in proper centrosome duplication. In addition, it is involved in regulating neuronal growth and differentiation, as well as in facilitating neurite outgrowth. NDR2 is also implicated in fear conditioning as it contributes to the coupling of neuronal morphological changes with fear-memory consolidation. NDR kinase contains an N-terminal regulatory (NTR) domain and an insert within the catalytic domain that contains an auto-inhibitory sequence. Like many other AGC kinases, NDR kinase requires phosphorylation at two sites, the activation loop (A-loop) and the hydrophobic motif (HM), for activity. The NDR2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 366 matched cddid_all.tbl CDD cd05628 cd05628 270777 STKc_NDR1 Catalytic domain of the Serine/Threonine Kinase, Nuclear Dbf2-Related kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. NDR1 (also called STK38) plays a role in proper centrosome duplication. It is highly expressed in thymus, muscle, lung and spleen. It is not an essential protein because mice deficient of NDR1 remain viable and fertile. However, these mice develop T-cell lymphomas and appear to be hypersenstive to carcinogenic treatment. NDR1 appears to also act as a tumor suppressor. NDR kinase contains an N-terminal regulatory (NTR) domain and an insert within the catalytic domain that contains an auto-inhibitory sequence. Like many other AGC kinases, NDR kinase requires phosphorylation at two sites, the activation loop (A-loop) and the hydrophobic motif (HM), for activity. The NDR1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 376 matched cddid_all.tbl CDD cd05629 cd05629 270778 STKc_NDR_like_fungal Catalytic domain of Fungal Nuclear Dbf2-Related kinase-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This group is composed of fungal NDR-like proteins including Saccharomyces cerevisiae CBK1 (or CBK1p), Schizosaccharomyces pombe Orb6 (or Orb6p), Ustilago maydis Ukc1 (or Ukc1p), and Neurospora crassa Cot1. Like NDR kinase, group members contain an N-terminal regulatory (NTR) domain and an insert within the catalytic domain that contains an auto-inhibitory sequence. CBK1 is an essential component in the RAM (regulation of Ace2p activity and cellular morphogenesis) network. CBK1 and Orb6 play similar roles in coordinating cell morphology with cell cycle progression. Ukc1 is involved in morphogenesis, pathogenicity, and pigment formation. Cot1 plays a role in polar tip extension.The fungal NDR subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 377 matched cddid_all.tbl CDD cd05630 cd05630 270779 STKc_GRK6 Catalytic domain of the Serine/Threonine Kinase, G protein-coupled Receptor Kinase 6. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. GRK6 is widely expressed in many tissues and is expressed as multiple splice variants with different domain architectures. It is post-translationally palmitoylated and localized in the membrane. GRK6 plays important roles in the regulation of dopamine, M3 muscarinic, opioid, and chemokine receptor signaling. It also plays maladaptive roles in addiction and Parkinson's disease. GRK6-deficient mice exhibit altered dopamine receptor regulation, decreased lymphocyte chemotaxis, and increased acute inflammation and neutrophil chemotaxis. GRKs phosphorylate and regulate G protein-coupled receptors (GPCRs), the largest superfamily of cell surface receptors which regulate some part of nearly all physiological functions. Phosphorylated GPCRs bind to arrestins, which prevents further G protein signaling despite the presence of activating ligand. The GRK6 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 285 matched cddid_all.tbl CDD cd05631 cd05631 173720 STKc_GRK4 Catalytic domain of the Serine/Threonine Kinase, G protein-coupled Receptor Kinase 4. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. GRK4 has a limited tissue distribution. It is mainly found in the testis, but is also present in the cerebellum and kidney. It is expressed as multiple splice variants with different domain architectures and is post-translationally palmitoylated and localized in the membrane. GRK4 polymorphisms are associated with hypertension and salt sensitivity, as they cause hyperphosphorylation, desensitization, and internalization of the dopamine 1 (D1) receptor while increasing the expression of the angiotensin II type 1 receptor. GRK4 plays a crucial role in the D1 receptor regulation of sodium excretion and blood pressure. GRKs phosphorylate and regulate G protein-coupled receptors (GPCRs), the largest superfamily of cell surface receptors which regulate some part of nearly all physiological functions. Phosphorylated GPCRs bind to arrestins, which prevents further G protein signaling despite the presence of activating ligand. The GRK4 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 285 matched cddid_all.tbl CDD cd05632 cd05632 270780 STKc_GRK5 Catalytic domain of the Serine/Threonine Kinase, G protein-coupled Receptor Kinase 5. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. GRK5 is widely expressed in many tissues. It associates with the membrane though an N-terminal PIP2 binding domain and also binds phospholipids via its C-terminus. GRK5 deficiency is associated with early Alzheimer's disease in humans and mouse models. GRK5 also plays a crucial role in the pathogenesis of sporadic Parkinson's disease. It participates in the regulation and desensitization of PDGFRbeta, a receptor tyrosine kinase involved in a variety of downstream cellular effects including cell growth, chemotaxis, apoptosis, and angiogenesis. GRK5 also regulates Toll-like receptor 4, which is involved in innate and adaptive immunity. GRKs phosphorylate and regulate G protein-coupled receptors (GPCRs), the largest superfamily of cell surface receptors which regulate some part of nearly all physiological functions. Phosphorylated GPCRs bind to arrestins, which prevents further G protein signaling despite the presence of activating ligand. The GRK5 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 313 matched cddid_all.tbl CDD cd05633 cd05633 270781 STKc_GRK3 Catalytic domain of the Serine/Threonine Kinase, G protein-coupled Receptor Kinase 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. GRK3, also called beta-adrenergic receptor kinase 2 (beta-ARK2), is widely expressed in many tissues. It is involved in modulating the cholinergic response of airway smooth muscles, and also plays a role in dopamine receptor regulation. GRK3-deficient mice show a lack of olfactory receptor desensitization and altered regulation of the M2 muscarinic airway. GRK3 promoter polymorphisms may also be associated with bipolar disorder. GRK3 contains an N-terminal RGS homology (RH) domain, a central catalytic domain, and C-terminal pleckstrin homology (PH) domain that mediates PIP2 and G protein betagamma-subunit translocation to the membrane. GRKs phosphorylate and regulate G protein-coupled receptors (GPCRs), the largest superfamily of cell surface receptors which regulate some part of nearly all physiological functions. Phosphorylated GPCRs bind to arrestins, which prevents further G protein signaling despite the presence of activating ligand. The GRK3 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 346 matched cddid_all.tbl CDD cd05635 cd05635 100059 LbH_unknown Uncharacterized proteins, Left-handed parallel beta-Helix (LbH) domain: Members in this group are uncharacterized bacterial proteins containing a LbH domain with multiple turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity. 101 matched cddid_all.tbl CDD cd05636 cd05636 100060 LbH_G1P_TT_C_like Putative glucose-1-phosphate thymidylyltransferase, C-terminal Left-handed parallel beta-Helix (LbH) domain: Proteins in this family show simlarity to glucose-1-phosphate adenylyltransferases in that they contain N-terminal catalytic domains that resemble a dinucleotide-binding Rossmann fold and C-terminal LbH fold domains. Members in this family are predicted to be glucose-1-phosphate thymidylyltransferases, which are involved in the dTDP-L-rhamnose biosynthetic pathway. Glucose-1-phosphate thymidylyltransferase catalyzes the synthesis of deoxy-thymidine di-phosphate (dTDP)-L-rhamnose, an important component of the cell wall of many microorganisms. The C-terminal LbH domain contains multiple turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity. 163 matched cddid_all.tbl CDD cd05637 cd05637 240188 SIS_PGI_PMI_2 The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions. These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the second SIS domain. 132 matched cddid_all.tbl CDD cd05638 cd05638 193517 M42 M42 Peptidases, also known as glutamyl aminopeptidase family. Peptidase M42 family proteins, also known as glutamyl aminopeptidases (GAP), are co-catalytic metallopeptidases, found in archaea and bacteria. They typically bind two zinc or cobalt atoms and include cellulase and endo-1,4-beta-glucanase (endoglucanase). Some of the enzymes exhibit typical aminopeptidase specificity, whereas others are also capable of N-terminal deblocking activity, i.e. hydrolyzing acylated N-terminal residues. GAP removes glutamyl residues from the N-terminus of peptide substrates, but is also effective against aspartyl and, to a lesser extent, seryl residues. Lactococcus lactis glutamyl aminopeptidase (PepA; aminopeptidase A) has high thermal stability and aids growth of the organism in milk. Pyrococcus horikoshii contain a thermostable de-blocking aminopeptidase member of this family, used commercially for N-terminal protein sequencing. 332 matched cddid_all.tbl CDD cd05639 cd05639 349892 M18 M18 peptidase aminopeptidase family. Peptidase M18 aminopeptidase family is widely distributed in bacteria and eukaryotes, but only the yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized to date. Yeast aminopeptidase I is active only in its dodecameric form with broad substrate specificity, acting on N-terminal leucine and most other amino acids. In contrast, the mammalian aspartyl aminopeptidase is highly selective for hydrolysis of N-terminal Asp or Glu residues from peptides. These enzymes have two catalytic zinc ions at the active site. 430 matched cddid_all.tbl CDD cd05640 cd05640 349893 M28_like M28 Zn-peptidase; uncharacterized subfamily. Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. 281 matched cddid_all.tbl CDD cd05642 cd05642 349894 M28_like M28 Zn-peptidase-like; uncharacterized subfamily. Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. 347 matched cddid_all.tbl CDD cd05643 cd05643 349895 M28_like M28 Zn-peptidase-like. Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They typically have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. This protein subfamily conserves some of the metal-coordinating residues of the typically co-catalytic M28 family which might suggest binding of a single metal ion. 290 matched cddid_all.tbl CDD cd05644 cd05644 381731 M28_like M28 Zn-peptidase-like, uncharacterized subfamily. Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They typically have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. Proteins in this subfamily conserve some of the metal-coordinating residues of the typically co-catalytic M28 family, and appear to bind a single metal (Zn) ion. 340 matched cddid_all.tbl CDD cd05645 cd05645 349897 M20_peptidase_T M20 Peptidase T specifically cleaves tripeptides. Peptidase M20 family, Peptidase T (PepT; tripeptide aminopeptidase; tripeptidase) subfamily and similar proteins. PepT acts only on tripeptide substrates, and is thus termed a tripeptidase. It catalyzes the release of N-terminal amino acids with hydrophobic side chains from tripeptides with high specificity; dipeptides, tetrapeptides or tripeptides with the N-terminus blocked are not cleaved. Tripeptidases are known to function at the final stage of proteolysis in lactococcal bacteria and release amino acids from tripeptides produced during the digestion of milk proteins such as casein. 400 matched cddid_all.tbl CDD cd05646 cd05646 349898 M20_AcylaseI_like M20 Aminoacylase-I like subfamily. Peptidase M20 family, aminoacylase-I like (AcyI-like; acylase I; N-acyl-L-amino-acid amidohydrolase; EC 3.5.1.14) subfamily. Acylase I is involved in the hydrolysis of N-acylated or N-acetylated amino acids (except L-aspartate) and is considered as a potential target of antimicrobial agents. Porcine AcyI is also shown to deacetylate certain quorum-sensing N-acylhomoserine lactones, while the rat enzyme has been implicated in degradation of chemotactic peptides of commensal bacteria. Prokaryotic arginine synthesis usually involves the transfer of an acetyl group to glutamate by ornithine acetyltransferase in order to form ornithine. However, Escherichia coli acetylornithine deacetylase (acetylornithinase, ArgE) (EC 3.5.1.16) catalyzes the deacylation of N2-acetyl-L-ornithine to yield ornithine and acetate. Phylogenetic evidence suggests that the clustering of the arg genes in one continuous sequence pattern arose in an ancestor common to Enterobacteriaceae and Vibrionaceae, where ornithine acetyltransferase was lost and replaced by a deacylase. Elevated levels of serum aminoacylase-1 autoantibody have been seen in the disease progression of chronic hepatitis B (CHB), making ACY1 autoantibody a valuable serum biomarker for discriminating hepatitis B virus (HBV) related liver cirrhosis from CHB. 391 matched cddid_all.tbl CDD cd05647 cd05647 349899 M20_DapE_actinobac M20 Peptidase actinobacterial DapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase. Peptidase M20 family, actinobacterial dapE encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE) subfamily. This group is composed of predominantly actinobacterial DapE proteins. DapE catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelate (L,L-SDAP) to L,L-diaminopimelate and succinate. It has been shown that DapE is essential for cell growth and proliferation. DapEs have been purified from proteobacteria such as Escherichia coli and Haemophilus influenzae, while genes that encode for DapEs have been sequenced from several bacterial sources such as the actinobacteria Corynebacterium glutamicum and Mycobacterium tuberculosis. DapE is a small, dimeric enzyme (41.6 kDa per subunit) that requires 2 atoms of zinc per molecule of polypeptide for full enzymatic activity. All of the amino acids that function as metal binding ligands are strictly conserved in DapE. 347 matched cddid_all.tbl CDD cd05649 cd05649 349900 M20_ArgE_DapE-like M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases. Peptidase M20 family, uncharacterized protein subfamily with similarity to acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE) subfamily. This group includes the hypothetical protein ygeY from Escherichia coli, a putative deacetylase, but many in this subfamily are classified as unassigned peptidases. ArgE/DapE enzymes catalyze analogous reactions and share a common activator, the metal ion (usually Co2+ or Zn2+). ArgE catalyzes a broad range of substrates, including N-acetylornithine, alpha-N-acetylmethionine and alpha-N-formylmethionine, while DapE catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelate (L,L-SDAP) to L,L-diaminopimelate and succinate. Proteins in this subfamily are mostly bacterial and archaeal, and have been inferred by homology as being related to both ArgE and DapE. 381 matched cddid_all.tbl CDD cd05650 cd05650 349901 M20_ArgE_DapE-like M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases. Peptidase M20 family, uncharacterized protein subfamily with similarity to acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE) subfamily. ArgE/DapE enzymes catalyze analogous reactions and share a common activator, the metal ion (usually Co2+ or Zn2+). ArgE catalyzes a broad range of substrates, including N-acetylornithine, alpha-N-acetylmethionine and alpha-N-formylmethionine, while DapE catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelate (L,L-SDAP) to L,L-diaminopimelate and succinate. Proteins in this subfamily are mostly bacterial and archaeal, and have been inferred by homology as being related to both ArgE and DapE. 389 matched cddid_all.tbl CDD cd05651 cd05651 349902 M20_ArgE_DapE-like M20 peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases. Peptidase M20 family, uncharacterized protein subfamily with similarity to acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE) subfamily. ArgE/DapE enzymes catalyze analogous reactions and share a common activator, the metal ion (usually Co2+ or Zn2+). ArgE catalyzes a broad range of substrates, including N-acetylornithine, alpha-N-acetylmethionine and alpha-N-formylmethionine, while DapE catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelate (L,L-SDAP) to L,L-diaminopimelate and succinate. Proteins in this subfamily are bacterial, and have been inferred by homology as being related to both ArgE and DapE. 341 matched cddid_all.tbl CDD cd05652 cd05652 349903 M20_ArgE_DapE-like_fungal M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases. Peptidase M20 family, uncharacterized protein subfamily with similarity to acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE) subfamily. ArgE/DapE enzymes catalyze analogous reactions and share a common activator, the metal ion (usually Co2+ or Zn2+). ArgE catalyzes a broad range of substrates, including N-acetylornithine, alpha-N-acetylmethionine and alpha-N-formylmethionine, while DapE catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelate (L,L-SDAP) to L,L-diaminopimelate and succinate. Proteins in this subfamily are mostly fungal, and have been inferred by similarity as being related to both ArgE and DapE. 340 matched cddid_all.tbl CDD cd05653 cd05653 349904 M20_ArgE_LysK M20 Peptidase acetylornithine deacetylase/acetyl-lysine deacetylase. Peptidase M20 family, acetylornithine deacetylase (ArgE)/acetyl-lysine deacetylase (LysK) subfamily. Proteins in this subfamily are mainly archaeal with related bacterial species and are deacetylases with specificity for both N-acetyl-ornithine and N-acetyl-lysine found within a lysine biosynthesis operon. ArgE catalyzes the conversion of N-acetylornithine to ornithine, while LysK, a homolog of ArgE, has deacetylating activities for both N-acetyllysine and N-acetylornithine at almost equal efficiency. These results suggest that LysK which may share an ancestor with ArgE functions not only for lysine biosynthesis, but also for arginine biosynthesis in species such as Thermus thermophilus. The substrate specificity of ArgE is quite broad in that several alpha-N-acyl-L-amino acids can be hydrolyzed, including alpha-N-acetylmethionine and alpha-N-formylmethionine. ArgE shares significant sequence homology and biochemical features, and possibly a common origin, with glutamate carboxypeptidase (CPG2) and succinyl-diaminopimelate desuccinylase (DapE), and aminoacylase I (ACY1), having all metal ligand binding residues conserved. 343 matched cddid_all.tbl CDD cd05654 cd05654 349905 M20_ArgE_RocB M20 Peptidase arginine utilization protein, RocB. Peptidase M20 family, ArgE RocB (arginine utilization protein, RocB; arginine degradation protein, RocB) subfamily. This group of proteins is possibly related to acetylornithine deacetylase (ArgE) and may be involved in the arginine and/or ornithine degradation pathway. In Bacillus subtilis, RocB is one of the three genes found in the rocABC operon, which is sigma L dependent and induced by arginine. The function of members of this family is as yet unknown, although they are predicted as deacetylases. 534 matched cddid_all.tbl CDD cd05656 cd05656 349906 M42_Frv M42 Peptidase, endoglucanases. Peptidase M42 family, Frv (Frv Operon Protein; Endo-1 4-Beta-Glucanase; Cellulase Protein; Endoglucanase; Endo-1 4-Beta-Glucanase Homolog; Glucanase; EC. 3.2.1.4) subfamily. Frv is a co-catalytic metallopeptidase, found in archaea and bacteria, including Pyrococcus horikoshii tetrahedral shaped phTET1 (DAPPh1; FrvX; PhDAP aminopeptidase; PhTET aminopeptidase; deblocking aminopeptidase), phTET2 (DAPPh2) and phTET3 (DAPPh3), Haloarcula marismortui TET (HmTET) as well as Bacillus subtilis YsdC. All of these exhibit aminopeptidase and deblocking activities. The HmTET is a broad substrate aminopeptidase capable of degrading large peptides. PhTET2, which shares 24% identity with HmTET, is a cobalt-activated peptidase and possibly a deblocking aminopeptidase, assembled as a 12-subunit tetrahedral dodecamer, while PhTET1 can be alternatively assembled as a tetrahedral dodecamer or as an octahedral tetracosameric structure. The active site in such a self-compartmentalized complex is located on the inside such that substrate sizes are limited, indicating function as possible peptide scavengers. PhTET2 cleaves polypeptides by a nonprocessive mechanism, preferring N-terminal hydrophobic or uncharged polar amino acids. Streptococcus pneumoniae PepA (SpPepA) also forms dodecamer with tetrahedral architecture, and exhibits selective substrate specificity to acidic amino acids with the preference to glutamic acid, with the substrate binding S1 pocket containing an Arg allows electrostatic interactions with the N-terminal acidic residue in the substrate. The YsdC gene is conserved in a number of thermophiles, archaea and pathogenic bacterial species; the closest structural homolog is Thermotoga maritima FrwX (34% identity), which is annotated as either a cellulase or an endoglucanase, and is possibly involved in polysaccharide biosynthesis or degradation. 337 matched cddid_all.tbl CDD cd05657 cd05657 349907 M42_glucanase_like M42 Peptidase, endoglucanase-like subfamily. Peptidase M42 family, glucanase (endo-1,4-beta-glucanase or endoglucanase)-like subfamily. Proteins in this subfamily are co-catalytic metallopeptidases, found in archaea and bacteria. They show similarity to cellulase and endo-1,4-beta-glucanase (endoglucanase) which typically bind two zinc or cobalt atoms. Some of the enzymes exhibit typical aminopeptidase specificity, whereas others are also capable of N-terminal deblocking activity, i.e. hydrolyzing acylated N-terminal residues. Many of these enzymes are assembled either as tetrahedral dodecamers or as octahedral tetracosameric structures, with the active site located on the inside such that substrate sizes are limited, indicating function as possible peptide scavengers. 337 matched cddid_all.tbl CDD cd05658 cd05658 349908 M18_DAP M18 peptidase aspartyl aminopeptidase. Peptidase M18 family, aspartyl aminopeptidase (DAP; EC 3.4.11.21) subfamily, is widely distributed in bacteria and eukaryotes. DAP cleaves only unblocked N-terminal acidic amino-acid residues. It is a cytosolic enzyme and is highly conserved; for example, the human enzyme has 51% identity to an aspartyl aminopeptidase-like protein in Arabidopsis thaliana. The mammalian DAP is highly selective for hydrolysis of N-terminal aspartate or glutamate residues from peptides. Unlike glutamyl aminopeptidase (M42), DAP does not cleave simple aminoaryl-arylamide substrates. Although there is lack of understanding of the function of this enzyme, it is thought to act in concert with other aminopeptidases to facilitate protein turnover because of their restricted specificities for the N-terminal aspartic and glutamic acid, which cannot be cleaved by any other aminopeptidases. The mammalian aspartyl aminopeptidase is possibly contributing to the catabolism of peptides, including those produced by the proteasome. It may also trim the N-terminus of peptides that are intended for the MHC class I system. In humans, DAP has been implicated in the specific function of converting angiotensin II to the vasoactive angiotensin III within the brain. Saccharomyces cerevisiae aminopeptidase I (Ape1) is involved in protein degradation in vacuoles (the yeast lysosomes) where it is transported by the unique cytoplasm-to-vacuole targeting (Cvt) pathway under vegetative growth conditions and by the autophagy pathway during starvation. Its N-terminal propeptide region, which mediates higher-order complex formation, serves as a scaffolding cargo critical for the assembly of the Cvt vesicle for vacuolar delivery. Pseudomonas aeruginosa aminopeptidase (PaAP) shows that its activity is dependent on Co2+ rather than Zn2+, and is thus a cocatalytic cobalt peptidase rather than a zinc-dependent peptidase. 439 matched cddid_all.tbl CDD cd05659 cd05659 349909 M18_API M18 peptidase aminopeptidase I. Peptidase M18 family, aminopeptidase I (vacuolar aminopeptidase I; polypeptidase; Leucine aminopeptidase IV; LAPIV; aminopeptidase III; aminopeptidase yscI; EC 3.4.11.22) subfamily. Aminopeptidase I is widely distributed in bacteria and eukaryotes, but only the yeast enzyme has been characterized to date. It is a vacuolar enzyme, synthesized as a cytosolic proform, and proteolytically matured upon arrival in the vacuole. The pro-aminopeptidase I (proAPI) does not enter the vacuole via the secretory pathway. In non-starved cells, it uses the cytoplasm to vacuole targeting (cvt) pathway and in cells starved for nitrogen, it is targeted to the vacuole via autophagy. Yeast aminopeptidase I is active only in its dodecameric form with broad substrate specificity, acting on all aminoacyl and peptidyl derivatives that contain a free alpha-amino group; this is in contrast to the highly selective M18 mammalian aspartyl aminopeptidase. N-terminal leucine and most other hydrophobic amino acid residues are the best substrates while glycine and charged amino acid residues in P1 position are cleaved much more slowly. This enzyme is strongly and specifically activated by zinc (Zn2+) and chloride (Cl-) ions. 446 matched cddid_all.tbl CDD cd05660 cd05660 349910 M28_like_PA M28 Zn-peptidase containing a protease-associated (PA) domain insert. Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. This subfamily is composed of uncharacterized proteins containing a protease-associated (PA) domain insert which may participate in substrate binding and/or promote conformational changes, influencing the stability and accessibility of the site to substrate. 290 matched cddid_all.tbl CDD cd05661 cd05661 349911 M28_like_PA M28 Zn-peptidase containing a PA domain insert. Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. This subfamily is composed of uncharacterized proteins containing a protease-associated (PA) domain insert which may participate in substrate binding and/or promote conformational changes, influencing the stability and accessibility of the site to substrate. 262 matched cddid_all.tbl CDD cd05662 cd05662 349912 M28_like M28 Zn-Peptidases. Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. This subfamily is composed of uncharacterized proteins that do not contain a protease-associated (PA) domain. 268 matched cddid_all.tbl CDD cd05663 cd05663 349913 M28_like_PA_PDZ_associated M28 Zn-peptidase containing a protease-associated (PA) domain insert and associated with a PDZ domain. Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. This subfamily is composed of uncharacterized proteins, many of which contain a protease-associated (PA) domain insert which may participate in substrate binding and/or promote conformational changes, influencing the stability and accessibility of the site to substrate. Proteins in this subfamily are also associated with the PDZ domain, a widespread protein module that has been recruited to serve multiple functions during the course of evolution. 266 matched cddid_all.tbl CDD cd05664 cd05664 349914 M20_Acy1-like M20 Peptidase aminoacylase 1 subfamily. Peptidase M20 family, Uncharacterized subfamily of proteins predicted as putative amidohydrolases or hippurate hydrolases. These are a class of zinc binding homodimeric enzymes involved in the hydrolysis of N-acetylated proteins. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in the protection and stability of proteins. Several types of aminoacylases can be distinguished on the basis of substrate specificity. Aminoacylase 1 (ACY1) breaks down cytosolic aliphatic N-acyl-alpha-amino acids (except L-aspartate), especially N-acetyl-methionine and acetyl-glutamate into L-amino acids and an acyl group. However, ACY1 can also catalyze the reverse reaction, the synthesis of acetylated amino acids. ACY1 may also play a role in xenobiotic bioactivation as well as in the inter-organ processing of amino acid-conjugated xenobiotic derivatives (S-substituted-N-acetyl-L-cysteine). 399 matched cddid_all.tbl CDD cd05665 cd05665 349915 M20_Acy1_IAAspH M20 Peptidases aminoacyclase-1 indole-3-acetic-L-aspartic acid hydrolase. Peptidase M20 family, bacterial and archaeal aminoacyclase-1 indole-3-acetic-L-aspartic acid hydrolase (IAA-Asp hydrolase; IAAspH; IAAH; IAA amidohydrolase; EC 3.5.1.-) subfamily. IAAspH hydrolyzes indole-3-acetyl-N-aspartic acid (IAA or auxin) to indole-3-acetic acid. Genes encoding IAA-amidohydrolases were first cloned from Arabidopsis; ILR1, IAR3, ILL1 and ILL2 encode active IAA- amino acid hydrolases, and three additional amidohydrolase-like genes (ILL3, ILL5, ILL6) have been isolated. In higher plants, the growth regulator indole-3-acetic acid (IAA or auxin) is found both free and conjugated via amide bonding to a variety of amino acids and peptides, and via an ester linkage to carbohydrates. IAA-Asp conjugates are involved in homeostatic control, protection, storing and subsequent use of free IAA. IAA-Asp is also found in some plants as a unique intermediate for entering into IAA non-decarboxylative oxidative pathway. IAA amidohydrolase cleaves the amide bond between the auxin and the conjugated amino acid. Enterobacter agglomerans IAAspH has very strong enzyme activity and substrate specificity towards IAA-Asp, although its substrate affinity is weaker compared to Arabidopsis enzymes of the ILR1 gene family. Enhanced IAA-hydrolase activity has been observed during clubroot disease in Chinese cabbage. 415 matched cddid_all.tbl CDD cd05666 cd05666 349916 M20_Acy1-like M20 Peptidase aminoacylase 1 subfamily. Peptidase M20 family, uncharacterized subfamily of bacterial proteins predicted as putative amidohydrolases or hippurate hydrolases. These are a class of zinc binding homodimeric enzymes involved in hydrolysis of N-acetylated proteins. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in protection and stability of proteins. Several types of aminoacylases can be distinguished on the basis of substrate specificity. Aminoacylase 1 (ACY1) breaks down cytosolic aliphatic N-acyl-alpha-amino acids (except L-aspartate), especially N-acetyl-methionine and acetyl-glutamate into L-amino acids and an acyl group. However, ACY1 can also catalyze the reverse reaction, the synthesis of acetylated amino acids. ACY1 may also play a role in xenobiotic bioactivation as well as the inter-organ processing of amino acid-conjugated xenobiotic derivatives (S-substituted-N-acetyl-L-cysteine). 373 matched cddid_all.tbl CDD cd05667 cd05667 349917 M20_Acy1-like M20 Peptidase aminoacylase 1 subfamily. Peptidase M20 family, uncharacterized subfamily of bacterial proteins that have been predicted as N-acyl-L-amino acid amidohydrolase (amaA), thermostable carboxypeptidase (cpsA-1, cpsA-2 in Sulfolobus solfataricus) and abgB (aminobenzoyl-glutamate utilization protein B), and generally are involved in the urea cycle and metabolism of amino groups. Aminoacylases 1 (ACY1s) comprise a class of zinc binding homodimeric enzymes involved in the hydrolysis of N-acetylated proteins. N-terminal acetylation of proteins is a widespread and is a highly conserved process that is involved in the protection and stability of proteins. Several types of aminoacylases can be distinguished on the basis of substrate specificity. ACY1 breaks down cytosolic aliphatic N-acyl-alpha-amino acids (except L-aspartate), especially N-acetyl-methionine and acetyl-glutamate into L-amino acids and an acyl group. However, ACY1 can also catalyze the reverse reaction, the synthesis of acetylated amino acids. ACY1 may also play a role in xenobiotic bioactivation as well as the inter-organ processing of amino acid-conjugated xenobiotic derivatives (S-substituted-N-acetyl-L-cysteine). 403 matched cddid_all.tbl CDD cd05668 cd05668 349918 M20_Acy1-like M20 Peptidase aminoacylase 1 subfamily. Peptidase M20 family, uncharacterized subfamily of bacterial uncharacterized proteins predicted as putative amidohydrolases. These are a class of zinc binding homodimeric enzymes involved in hydrolysis of N-acetylated proteins. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in protection and stability of proteins. Several types of aminoacylases can be distinguished on the basis of substrate specificity. Aminoacylase 1 (ACY1) breaks down cytosolic aliphatic N-acyl-alpha-amino acids (except L-aspartate), especially N-acetyl-methionine and acetyl-glutamate into L-amino acids and an acyl group. However, ACY1 can also catalyze the reverse reaction, the synthesis of acetylated amino acids. ACY1 may also play a role in xenobiotic bioactivation as well as the inter-organ processing of amino acid-conjugated xenobiotic derivatives (S-substituted-N-acetyl-L-cysteine). 371 matched cddid_all.tbl CDD cd05669 cd05669 349919 M20_Acy1_YxeP-like M20 Peptidase aminoacyclase-1 YxeP-like proteins, including YxeP, YtnL, YjiB and HipO2. Peptidase M20 family, aminoacyclase-1 YxeP-like subfamily including YxeP, YtnL, YjiB and HipO2, most of which have not been well characterized to date. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in the protection and stability of proteins. Several types of aminoacylases can be distinguished on the basis of substrate specificity; substrates include indoleacetic acid (IAA) N-conjugates of amino acids, N-acetyl-L-amino acids and aminobenzoylglutamate. ACY1 breaks down cytosolic aliphatic N-acyl-alpha-amino acids (except L-aspartate), especially N-acetyl-methionine and acetyl-glutamate into L-amino acids and an acyl group. However, ACY1 can also catalyze the reverse reaction, the synthesis of acetylated amino acids. ACY1 may also play a role in xenobiotic bioactivation as well as in the inter-organ processing of amino acid-conjugated xenobiotic derivatives (S-substituted-N-acetyl-L-cysteine). ACY1 appears to physically interact with Sphingosine kinase type 1 (SphK1) and may influence its physiological functions; SphK1 and its product sphingosine-1-phosphate have been shown to promote cell growth and inhibit apoptosis of tumor cells. Strong expression of the human gene and its mouse ortholog Acy1 in brain, liver, and kidney suggest a role of the enzyme in amino acid metabolism of these organs. 371 matched cddid_all.tbl CDD cd05670 cd05670 349920 M20_Acy1_YkuR-like M20 Peptidase aminoacyclase-1 YkuR-like proteins, including YkuR and Ama/HipO/HyuC proteins. Peptidase M20 family, aminoacyclase-1 YkuR-like subfamily including YkuR and Ama/HipO/HyuC proteins, most of which have not been well characterized to date. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in the protection and stability of proteins. Several types of aminoacylases can be distinguished on the basis of substrate specificity; substrates include indoleacetic acid (IAA) N-conjugates of amino acids, N-acetyl-L-amino acids and aminobenzoylglutamate. ACY1 breaks down cytosolic aliphatic N-acyl-alpha-amino acids (except L-aspartate), especially N-acetyl-methionine and acetyl-glutamate into L-amino acids and an acyl group. However, ACY1 can also catalyze the reverse reaction, the synthesis of acetylated amino acids. ACY1 may also play a role in xenobiotic bioactivation as well as in the inter-organ processing of amino acid-conjugated xenobiotic derivatives (S-substituted-N-acetyl-L-cysteine). ACY1 appears to physically interact with Sphingosine kinase type 1 (SphK1) and may influence its physiological functions; SphK1 and its product sphingosine-1-phosphate have been shown to promote cell growth and inhibit apoptosis of tumor cells. Strong expression of the human gene and its mouse ortholog Acy1 in brain, liver, and kidney suggest a role of the enzyme in amino acid metabolism of these organs. 367 matched cddid_all.tbl CDD cd05672 cd05672 349921 M20_ACY1L2-like M20 Peptidase aminoacylase 1-like protein 2-like, amidohydrolase subfamily. Peptidase M20 family, aminoacylase 1-like protein 2 (ACY1L2; amidohydrolase)-like subfamily. This group contains many uncharacterized proteins predicted as amidohydrolases, including gene products of abgA and abgB that catalyze the cleavage of p-aminobenzoyl-glutamate, a folate catabolite in Escherichia coli, to p-aminobenzoate and glutamate. p-Aminobenzoyl-glutamate utilization is catalyzed by the abg region gene product, AbgT. This subfamily includes Staphylococcus aureus antibiotic resistance factor HmrA that has been shown to participate in methicillin resistance mechanisms in vivo in the presence of beta-lactams. Aminoacylase 1 (ACY1) proteins are a class of zinc binding homodimeric enzymes involved in hydrolysis of N-acetylated proteins. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in the protection and stability of proteins. Several types of aminoacylases can be distinguished on the basis of substrate specificity. ACY1 breaks down cytosolic aliphatic N-acyl-alpha-amino acids (except L-aspartate), especially N-acetyl-methionine and acetyl-glutamate into L-amino acids and an acyl group. However, ACY1 can also catalyze the reverse reaction, the synthesis of acetylated amino acids. ACY1 may also play a role in xenobiotic bioactivation as well as the inter-organ processing of amino acid-conjugated xenobiotic derivatives (S-substituted-N-acetyl-L-cysteine). 360 matched cddid_all.tbl CDD cd05673 cd05673 349922 M20_Acy1L2_AbgB M20 Peptidase Aminoacylase 1-like protein 2 aminobenzoyl-glutamate utilization protein B subfamily. Peptidase M20 family, ACY1L2 aminobenzoyl-glutamate utilization protein B (AbgB) subfamily. This group contains mostly bacterial amidohydrolases, including gene products of abgB that catalyze the cleavage of p-aminobenzoyl-glutamate, a folate catabolite in Escherichia coli, to p-aminobenzoate and glutamate. p-Aminobenzoyl-glutamate is a natural end product of folate catabolism, and its utilization is initiated by the abg region gene product, AbgT, by enabling uptake of its into the cell in a concentration-dependent, saturable manner. It is subsequently cleaved by AbgA and AbgB (sometimes referred to as AbgAB). 437 matched cddid_all.tbl CDD cd05674 cd05674 349923 M20_yscS M20 Peptidase, carboxypeptidase yscS. Peptidase M20 family, yscS (GlyX-carboxypeptidase, CPS1, carboxypeptidase S, carboxypeptidase a, carboxypeptidase yscS, glycine carboxypeptidase)-like subfamily. This group mostly contains proteins that have been uncharacterized to date, but also includes vacuolar proteins involved in nitrogen metabolism which are essential for use of certain peptides that are sole nitrogen sources. YscS releases a C-terminal amino acid from a peptide that has glycine as the penultimate residue. It is synthesized as one polypeptide chain precursor which yields two active precursor molecules after carbohydrate modification in the secretory pathway. The proteolytically unprocessed forms are associated with the membrane, whereas the mature forms of the enzyme are soluble. Enzymes in this subfamily may also cleave intracellularly generated peptides in order to recycle amino acids for protein synthesis. Also included in this subfamily is peptidase M20 domain containing 1 (PM20D1), that is enriched in uncoupling protein 1, UCP1(+) versus UCP1(-) adipocytes is a bidirectional enzyme in vitro, catalyzing both the condensation of fatty acids and amino acids to generate N-acyl amino acids and also the reverse hydrolytic reaction; N-acyl amino acids directly bind mitochondria and function as endogenous uncouplers of UCP1-independent respiration. Mice studies show increased circulating PM20D1 augments respiration and increases N-acyl amino acids in blood, and administration of N-acyl amino acids improves glucose homeostasis and increases energy expenditure. 471 matched cddid_all.tbl CDD cd05675 cd05675 349924 M20_yscS_like M20 Peptidase, carboxypeptidase yscS-like. Peptidase M20 family, yscS (GlyX-carboxypeptidase, CPS1, carboxypeptidase S, carboxypeptidase a, carboxypeptidase yscS, glycine carboxypeptidase)-like subfamily. This group contains proteins that have been uncharacterized to date with similarity to vacuolar proteins involved in nitrogen metabolism which are essential for use of certain peptides that are sole nitrogen sources. YscS releases a C-terminal amino acid from a peptide that has glycine as the penultimate residue. It is synthesized as one polypeptide chain precursor which yields two active precursor molecules after carbohydrate modification in the secretory pathway. The proteolytically unprocessed forms are associated with the membrane, whereas the mature forms of the enzyme are soluble. Enzymes in this subfamily may also cleave intracellularly generated peptides in order to recycle amino acids for protein synthesis. 431 matched cddid_all.tbl CDD cd05676 cd05676 349925 M20_dipept_like_CNDP M20 cytosolic nonspecific dipeptidases including anserinase and serum carnosinase. Peptidase M20 family, CNDP (cytosolic nonspecific dipeptidase) subfamily including anserinase (Xaa-methyl-His dipeptidase, EC 3.4.13.5), 'serum' carnosinase (beta-alanyl-L-histidine dipeptidase; EC 3.4.13.20), and some uncharacterized proteins. Two genes, CN1 and CN2, coding for proteins that degrade carnosine (beta-alanyl-L-histidine) and homocarnosine (gamma-aminobutyric acid-L-histidine), two naturally occurring dipeptides with potential neuroprotective and neurotransmitter functions, have been identified. CN1 encodes for serum carnosinase and has narrow substrate specificity for Xaa-His dipeptides, where Xaa can be beta-alanine (carnosine), N-methyl beta-alanine, alanine, glycine and gamma-aminobutyric acid (homocarnosine). CN2 corresponds to the cytosolic nonspecific dipeptidase (CNDP; EC 3.4.13.18) and is not limited to Xaa-His dipeptides. CNDP requires Mn(2+) for full activity and does not hydrolyze homocarnosine. Anserinase is a dipeptidase that mainly catalyzes the hydrolysis of N-alpha-acetylhistidine. 467 matched cddid_all.tbl CDD cd05677 cd05677 349926 M20_dipept_like_DUG2_type "M20 Defective in Utilization of Glutathione-type peptidases containing WD repeats. Peptidase M20 family, Defective in Utilization of Glutathione (DUG2) subfamily. DUG2-type proteins are metallopeptidases containing WD repeats at the N-terminus. DUG2 proteins are involved in the alternative pathway of glutathione (GSH) degradation. GSH, the major low-molecular-weight thiol compound in most eukaryotic cells, is normally degraded through the gamma-glutamyl cycle initiated by gamma-glutamyl transpeptidase. However, a novel pathway for the degradation of GSH has been characterized; it requires the participation of three genes identified in Saccharomyces cerevisiae as ""defective in utilization of glutathione"" genes including DUG1, DUG2, and DUG3. DUG1 encodes a probable di- or tri-peptidase identified as M20 metallopeptidase, DUG2 gene encodes a protein with a metallopeptidase domain and a large N-terminal WD40 repeat region, while DUG3 encodes a protein with a glutamine amidotransferase domain. Although dipeptides and tripeptides with a normal peptide bond, such as cys-gly or glu-cys-gly, can be hydrolyzed by the DUG1 protein, the presence of an unusual peptide bond, like in GSH, requires the participation of the DUG2 and DUG3 proteins as well. These three proteins form a GSH degradosomal complex." 436 matched cddid_all.tbl CDD cd05678 cd05678 349927 M20_dipept_like uncharacterized M20 dipeptidase. Peptidase M20 family, unknown dipeptidase-like subfamily (inferred by homology to be dipeptidases). M20 dipeptidases include a large variety of bacterial enzymes including cytosolic nonspecific dipeptidase (CNDP), Xaa-methyl-His dipeptidase (anserinase),and canosinase. These dipeptidases have been shown to act on a wide range of dipeptides, but not larger peptides. For example, anserinase mainly catalyzes the hydrolysis of N-alpha-acetylhistidine while carnosinase degrades beta-alanyl-L-histidine. 466 matched cddid_all.tbl CDD cd05679 cd05679 349928 M20_dipept_like uncharacterized M20 dipeptidase. Peptidase M20 family, unknown dipeptidase-like subfamily (inferred by homology to be dipeptidases). M20 dipeptidases include a large variety of bacterial enzymes including cytosolic nonspecific dipeptidase (CNDP), Xaa-methyl-His dipeptidase (anserinase),and canosinase. These dipeptidases have been shown to act on a wide range of dipeptides, but not larger peptides. For example, anserinase mainly catalyzes the hydrolysis of N-alpha-acetylhistidine while carnosinase degrades beta-alanyl-L-histidine. 448 matched cddid_all.tbl CDD cd05680 cd05680 349929 M20_dipept_like uncharacterized M20 dipeptidase. Peptidase M20 family, unknown dipeptidase-like subfamily (inferred by homology to be dipeptidases). M20 dipeptidases include a large variety of bacterial enzymes including cytosolic nonspecific dipeptidase (CNDP), Xaa-methyl-His dipeptidase (anserinase),and canosinase. These dipeptidases have been shown to act on a wide range of dipeptides, but not larger peptides. For example, anserinase mainly catalyzes the hydrolysis of N-alpha-acetylhistidine while carnosinase degrades beta-alanyl-L-histidine. 437 matched cddid_all.tbl CDD cd05681 cd05681 349930 M20_dipept_Sso-CP2 uncharacterized M20 dipeptidase. Peptidase M20 family, unknown dipeptidase-like subfamily (inferred by homology to be dipeptidases). M20 dipeptidases include a large variety of bacterial enzymes including cytosolic nonspecific dipeptidase (CNDP), Xaa-methyl-His dipeptidase (anserinase),and canosinase. These dipeptidases have been shown to act on a wide range of dipeptides, but not larger peptides. For example, anserinase mainly catalyzes the hydrolysis of N-alpha-acetylhistidine while carnosinase degrades beta-alanyl-L-histidine. This family includes Sso-CP2 from Sulfolobus solfataricus. 429 matched cddid_all.tbl CDD cd05682 cd05682 349931 M20_dipept_dapE uncharacterized M20 dipeptidase. Peptidase M20 family, unknown dipeptidase-like subfamily (inferred by homology to be dipeptidases). M20 dipeptidases include a large variety of bacterial enzymes including cytosolic nonspecific dipeptidase (CNDP), Xaa-methyl-His dipeptidase (anserinase),and canosinase. These dipeptidases have been shown to act on a wide range of dipeptides, but not larger peptides. For example, anserinase mainly catalyzes the hydrolysis of N-alpha-acetylhistidine while carnosinase degrades beta-alanyl-L-histidine. This family includes dapE (Lpg0809) from Legionella pneumophila. 451 matched cddid_all.tbl CDD cd05683 cd05683 349932 M20_peptT_like M20 Peptidase T like enzymes specifically cleave tripeptides. Peptidase M20 family, PeptT (tripeptide aminopeptidase; tripeptidase)-like subfamily. This group includes bacterial tripeptidases as well as predicted tripeptidases. Peptidase T acts only on tripeptide substrates, and is thus called a tripeptidase. It catalyzes the release of N-terminal amino acids with hydrophobic side chains from tripeptides with high specificity; dipeptides, tetrapeptides or tripeptides with the N-terminus blocked are not cleaved. Tripeptidases are known to function at the final stage of proteolysis in lactococcal bacteria and release amino acids from tripeptides produced during the digestion of milk proteins such as casein. 368 matched cddid_all.tbl CDD cd05684 cd05684 240189 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae. 79 matched cddid_all.tbl CDD cd05685 cd05685 240190 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea. 68 matched cddid_all.tbl CDD cd05686 cd05686 240191 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis. 73 matched cddid_all.tbl CDD cd05687 cd05687 240192 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. 70 matched cddid_all.tbl CDD cd05688 cd05688 240193 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. 68 matched cddid_all.tbl CDD cd05689 cd05689 240194 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. 72 matched cddid_all.tbl CDD cd05690 cd05690 240195 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. 69 matched cddid_all.tbl CDD cd05691 cd05691 240196 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. 73 matched cddid_all.tbl CDD cd05692 cd05692 240197 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog. 69 matched cddid_all.tbl CDD cd05693 cd05693 240198 S1_Rrp5_repeat_hs1_sc1 S1_Rrp5_repeat_hs1_sc1: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 1 (hs1) and S. cerevisiae S1 repeat 1 (sc1). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. 100 matched cddid_all.tbl CDD cd05694 cd05694 240199 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. 74 matched cddid_all.tbl CDD cd05695 cd05695 240200 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. 66 matched cddid_all.tbl CDD cd05696 cd05696 240201 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. 71 matched cddid_all.tbl CDD cd05697 cd05697 240202 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. 69 matched cddid_all.tbl CDD cd05698 cd05698 240203 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. 70 matched cddid_all.tbl CDD cd05699 cd05699 240204 S1_Rrp5_repeat_hs7 S1_Rrp5_repeat_hs7: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 7 (hs7). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. 72 matched cddid_all.tbl CDD cd05700 cd05700 240205 S1_Rrp5_repeat_hs9 S1_Rrp5_repeat_hs9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes Homo sapiens S1 repeat 9 (hs9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. 65 matched cddid_all.tbl CDD cd05701 cd05701 240206 S1_Rrp5_repeat_hs10 S1_Rrp5_repeat_hs10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 10 (hs10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. 69 matched cddid_all.tbl CDD cd05702 cd05702 240207 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. 70 matched cddid_all.tbl CDD cd05703 cd05703 240208 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. 73 matched cddid_all.tbl CDD cd05704 cd05704 240209 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. 72 matched cddid_all.tbl CDD cd05705 cd05705 240210 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. 74 matched cddid_all.tbl CDD cd05706 cd05706 240211 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. 73 matched cddid_all.tbl CDD cd05707 cd05707 240212 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. 68 matched cddid_all.tbl CDD cd05708 cd05708 240213 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea. 77 matched cddid_all.tbl CDD cd05709 cd05709 100078 S2P-M50 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. The domain core structure appears to contain at least three transmembrane helices with a catalytic zinc atom coordinated by three conserved residues contained within the consensus sequence HExxH, together with a conserved aspartate residue. The S2P/M50 family of RIP proteases is widely distributed; in eukaryotic cells, they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum (ER) stress responses. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of sterol regulatory element-binding proteins (SREBPs) from membranes of the ER. These domains translocate into the nucleus, where they activate genes of cholesterol and fatty acid biosynthesis. It is the second proteolytic step that is carried out by the SREBP Site-2 protease (S2P) which is present in this CD superfamily. Prokaryotic S2P/M50 homologs have been shown to regulate stress responses, sporulation, cell division, and cell differentiation. In Escherichia coli, the S2P homolog RseP is involved in the sigmaE pathway of extracytoplasmic stress responses, and in Bacillus subtilis, the S2P homolog SpoIVFB is involved in the pro-sigmaK pathway of spore formation. Some of the subfamilies within this hierarchy contain one or two PDZ domain insertions, with putative regulatory roles, such as the inhibition of substrate cleavage as seen by the RseP PDZ domain. 180 matched cddid_all.tbl CDD cd05710 cd05710 240214 SIS_1 A subgroup of the SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars. 120 matched cddid_all.tbl CDD cd05711 cd05711 409376 IgC2_D2_LILR_KIR_like Second immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors, Natural killer inhibitory receptors (KIRs) and similar domains; member of Immunoglobulin Constant-2 set of IgSF domains. The members here are composed of the second immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILRs), Natural killer inhibitory receptors (KIRs, also known as also known as cluster of differentiation (CD) 158), and similar proteins. This group includes LILRB1 (also known as LIR-1), LILRA5 (also known as LIR9), an activating natural cytotoxicity receptor NKp46, the immune-type receptor glycoprotein VI (GPVI), and the IgA-specific receptor Fc-alphaRI (also known as cluster of differentiation (CD) 89). LILRs are a family of immunoreceptors expressed on expressed on T and B cells, on monocytes, dendritic cells, and subgroups of natural killer (NK) cells. The human LILR family contains nine proteins (LILRA1-3, and 5, and LILRB1-5). From functional assays, and as the cytoplasmic domains of various LILRs, for example LILRB1, LILRB2 (also known as LIR-2), and LILRB3 (also known as LIR-3) contain immunoreceptor tyrosine-based inhibitory motifs (ITIMs), it is thought that LIR proteins are inhibitory receptors. Of the eight LIR family proteins, only LILRB1, and LILRB2, show detectable binding to class I MHC molecules; ligands for the other members have yet to be determined. The extracellular portions of the different LIR proteins contain different numbers of Ig-like domains for example, four in the case of LILRB1, and LILRB2, and two in the case of LILRB4 (also known as LIR-5). The activating natural cytotoxicity receptor NKp46 is expressed in natural killer cells, and is organized as an extracellular portion having two Ig-like extracellular domains, a transmembrane domain, and a small cytoplasmic portion. GPVI, which also contains two Ig-like domains, participates in the processes of collagen-mediated platelet activation and arterial thrombus formation. Fc-alphaRI is expressed on monocytes, eosinophils, neutrophils, and macrophages; it mediates IgA-induced immune effector responses such as phagocytosis, antibody-dependent cell-mediated cytotoxicity and respiratory burst. Killer cell immunoglobulin-like receptors (KIRs; also known as CD158 for human KIR) are transmembrane glycoproteins expressed by natural killer cells and subsets of T cells. KIRs are a family of highly polymorphic activating and inhibitory receptors that serve as key regulators of human NK cell function. The KIR proteins are classified by the number of extracellular immunoglobulin domains (2D or 3D) and by whether they have a long (L) or short (S) cytoplasmic domain. KIR proteins with the long cytoplasmic domain transduce inhibitory signals upon ligand binding via an immune tyrosine-based inhibitory motif (ITIM), while KIR proteins with the short cytoplasmic domain lack the ITIM motif and instead associate with the TYRO protein tyrosine kinase binding protein to transduce activating signals. The major ligands for KIR are MHC class I (HLA-A, -B or -C) molecules. 90 matched cddid_all.tbl CDD cd05712 cd05712 409377 IgV_CD33 Immunoglobulin Variable (IgV) domain at the N-terminus of CD33 and related Siglecs (sialic acid-binding Ig-like lectins). The members here are composed of the immunoglobulin (Ig) domain at the N-terminus of Cluster of Differentiation (CD) 33 and related Siglecs (sialic acid-binding Ig-like lectins). Siglec refers to a structurally related protein family that specifically recognizes sialic acid in oligosaccharide chains of glycoproteins and glycolipids. Siglecs are type I transmembrane proteins, organized as an extracellular module composed of Ig-like domains, an N-terminal variable set of Ig-like carbohydrate recognition domains, and 1 to 16 constant Ig-like domains, followed by transmembrane and short cytoplasmic domains. Human Siglecs are classified into two subgroups, one subgroup is comprised of sialoadhesin (Siglec-1), CD22 (Siglec-2), and MAG, the other subgroup is comprised of CD33-related Siglecs which include CD33 (Siglec-3) and human Siglecs 5-11. 119 matched cddid_all.tbl CDD cd05713 cd05713 409378 IgV_MOG_like Immunoglobulin (Ig)-like domain of myelin oligodendrocyte glycoprotein (MOG). The members here are composed of the immunoglobulin (Ig)-like domain of myelin oligodendrocyte glycoprotein (MOG). MOG, a minor component of the myelin sheath, is an important CNS-specific autoantigen, linked to the pathogenesis of multiple sclerosis (MS) and experimental autoimmune encephalomyelitis (EAE). It is a transmembrane protein having an extracellular Ig domain. MOG is expressed in the CNS on the outermost lamellae of the myelin sheath, and on the surface of oligodendrocytes, and may participate in the completion, compaction, and/or maintenance of myelin. This group also includes butyrophilin (BTN). BTN is the most abundant protein in bovine milk-fat globule membrane (MFGM). 114 matched cddid_all.tbl CDD cd05714 cd05714 409379 Ig_CSPGs_LP_like Immunoglobulin (Ig)-like domain of chondroitin sulfate proteoglycans (CSPGs), human cartilage link protein (LP), and similar domains. The members here are composed of the immunoglobulin (Ig)-like domain similar to that found in chondroitin sulfate proteoglycans (CSPGs) and human cartilage link protein (LP). Included in this group are the CSPGs aggrecan, versican, and neurocan. In CSPGs, this Ig-like domain is followed by hyaluronan (HA)-binding tandem repeats, and a C-terminal region with epidermal growth factor-like, lectin-like, and complement regulatory protein-like domains. Separating these N- and C-terminal regions is a nonhomologous glycosaminoglycan attachment region. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggrecan and versican have a wide distribution in connective tissue and extracellular matrices. Neurocan is localized almost exclusively in nervous tissue. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. There is considerable evidence that HA-binding CSPGs are involved in developmental processes in the central nervous system. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes. 123 matched cddid_all.tbl CDD cd05715 cd05715 409380 IgV_P0-like Immunoglobulin (Ig)-like domain of protein zero (P0) and similar proteins. The members here are composed of the immunoglobulin (Ig) domain of protein zero (P0), a myelin membrane adhesion molecule. P0 accounts for over 50% of the total protein in peripheral nervous system (PNS) myelin. P0 is a single-pass transmembrane glycoprotein with a highly basic intracellular domain and an extracellular Ig domain. The extracellular domain of P0 (P0-ED) is similar to the Ig variable domain, carrying one acceptor sequence for N-linked glycosylation. P0 plays a role in membrane adhesion in the spiral wraps of the myelin sheath. The intracellular domain is thought to mediate membrane apposition of the cytoplasmic faces and may, through electrostatic interactions, interact directly with lipid headgroups. It is thought that homophilic interactions of the P0 extracellular domain mediate membrane juxtaposition in the extracellular space of PNS myelin. This group also contains the Ig domain of sodium channel subunit beta-2 (SCN2B), and of epithelial V-like antigen 1 (EVA). EVA, also known as myelin protein zero-like 2, is an adhesion molecule, which may play a role in structural organization of the thymus and early lymphocyte development. SCN2B subunits play a role in determining sodium channel density and function in neurons,and in control of electrical excitability in the brain. 117 matched cddid_all.tbl CDD cd05716 cd05716 409381 IgV_pIgR_like Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins. The members here are composed of the immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins. pIgR delivers dimeric IgA and pentameric IgM to mucosal secretions. Polymeric immunoglobulin (pIgs) are the first defense against pathogens and toxins. IgA and IgM can form polymers via an 18-residue extension at their C-termini referred to as the tailpiece. pIgR transports pIgs across mucosal epithelia into mucosal secretions. Human pIgR is a glycosylated type I transmembrane protein, comprised of a 620-residue extracellular region, a 23-residue transmembrane region, and a 103-residue cytoplasmic tail. The extracellular region contains five domains that share sequence similarity with Ig variable (v) regions. This group also contains the Ig-like extracellular domains of other receptors such as NK cell receptor Nkp44 and myeloid receptors, among others. 100 matched cddid_all.tbl CDD cd05717 cd05717 409382 IgV_1_Necl_like First (N-terminal) immunoglobulin (Ig)-like domain of the nectin-like molecules; member of the V-set of Ig superfamily (IgSF) domains. The members here are composed of the N-terminal immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 (also known as cell adhesion molecule 3 (CADM3)), Necl-2 (CADM1), Necl-3 (CADM2), and similar proteins. At least five nectin-like molecules have been identified (Necl-1 to Necl-5). They all have an extracellular region containing three Ig-like domains, a transmembrane region, and a cytoplasmic region. The N-terminal Ig-like domain of the extracellular region belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-1, Necl-2, and Necl-3 have Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-1 is specifically expressed in neural tissue, and is important to the formation of synapses, axon bundles, and myelinated axons. Necl-2 is expressed in a wide variety of tissues and is a putative tumour suppressor gene which is downregulated in aggressive neuroblastoma. Necl-3 accumulates in central and peripheral nervous system tissue and has been shown to selectively interact with oligodendrocytes. This group also contains Class-I MHC-restricted T-cell-associated molecule (CRTAM), whose expression pattern is consistent with its expression in Class-I MHC-restricted T-cells. 94 matched cddid_all.tbl CDD cd05718 cd05718 409383 IgV_1_PVR_like "First immunoglobulin variable (IgV) domain of poliovirus receptor (PVR, also known as CD155 and necl-5), and similar domains. The members here are composed of the first immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155 and nectin-like protein 5 (necl-5)). Poliovirus (PV) binds to its cellular receptor (PVR/CD155) to initiate infection. CD155 is a membrane-anchored, single-span glycoprotein; its extracellular region has three Ig-like domains. There are four different isotypes of CD155 (referred to as alpha, beta, gamma, and delta), that result from alternate splicing of the CD155 mRNA, and have identical extracellular domains. CD155-beta and CD155-gamma are secreted; CD155-alpha and CD155-delta are membrane-bound and function as PV receptors. The virus recognition site is contained in the amino-terminal domain, D1. Having the virus attachment site on the receptor distal from the plasma membrane may be important for successful initiation of infection of cells by the virus. CD155 binds in the poliovirus ""canyon"" with a footprint similar to that of the intercellular adhesion molecule-1 receptor on human rhinoviruses. This group also includes the first Ig-like domain of nectin-1 (also known as poliovirus receptor related protein(PVRL)1; CD111), nectin-3 (also known as PVRL 3), nectin-4 (also known as PVRL4; LNIR receptor)and DNAX accessory molecule 1 (DNAM-1; CD226)." 113 matched cddid_all.tbl CDD cd05719 cd05719 409384 IgC1_2_PVR_like "Second immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155 and Necl-5), and similar domains; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the second immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155 and nectin-like protein 5 (Necl-5)) and similar proteins. Poliovirus (PV) binds to its cellular receptor (PVR/CD155) to initiate infection. CD155 is a membrane-anchored, single-span glycoprotein; its extracellular region has three Ig-like domains. There are four different isotypes of CD155 (referred to as alpha, beta, gamma, and delta), these result from alternate splicing of the CD155 mRNA, and have identical extracellular domains. CD155-beta and CD155-gamma are secreted, while CD155-alpha and CD155-delta are membrane-bound and function as PV receptors. The virus recognition site is contained in the amino-terminal domain, D1. Having the virus attachment site on the receptor distal from the plasma membrane may be important for successful initiation of infection of cells by the virus. CD155 binds in the poliovirus ""canyon"" and has a footprint similar to that of the intercellular adhesion molecule-1 receptor on human rhinoviruses. This group also includes the second Ig-like domain of nectin-1, also known as poliovirus receptor related protein(PVRL)1 or CD111." 96 matched cddid_all.tbl CDD cd05720 cd05720 409385 IgV_CD8_alpha "Immunoglobulin (Ig)-like variable (V) domain of Cluster of Differentiation (CD) 8 alpha chain. The members here are composed of the immunoglobulin (Ig)-like variable domain of the Cluster of Differentiation (CD) 8 alpha. The CD8 glycoprotein plays an essential role in the control of T-cell selection, maturation, and the T-cell receptor (TCR)-mediated response to peptide antigen. CD8 is comprised of alpha and beta subunits and is expressed as either an alpha/alpha or alpha/beta dimer. Both dimeric isoforms can serve as a coreceptor for T cell activation and differentiation, however they have distinct physiological roles, different cellular distributions, unique binding partners, etc. Each CD8 subunit is comprised of an extracellular domain containing a V-type Ig-like domain, a single pass transmembrane portion, and a short intracellular domain. The Ig domain of CD8 alpha binds to antibodies. Members of this group contain standard Ig superfamily V-set AGFCC'C""/DEB domain topology." 110 matched cddid_all.tbl CDD cd05721 cd05721 409386 IgV_CTLA-4 Immunoglobulin Variable (IgV) domain of cytotoxic T lymphocyte-associated antigen 4 (CTLA-4). The members here are composed of the variable(v)-type immunoglobulin (Ig) domain found in cytotoxic T lymphocyte-associated antigen 4 (CTLA-4). CTLA-4 is involved in the regulation of T cell response, acting as an inhibitor of intracellular signaling. CTLA-4 is similar to CD28, a T cell co-receptor protein that recognizes the B7 proteins (CD80 and CD86). CD28 binding of the B7 proteins occurs after the presentation of antigen to the T cell receptor (TCR) via the peptide-MHC complex on the surface of an antigen presenting cell (APC). CTLA-4 also binds the B7 molecules with a higher affinity than does CD28. The B7/CTLA-4 interaction generates inhibitory signals down-regulating the response, and may prevent T cell activation by weak TCR signals. CD28 and CTLA-4 then elicit opposing signals in the regulation of T cell responsiveness and homeostasis. T cell activation leads to increased CTLA-4 gene expression and trafficking of CTLA-4 protein to the cell surface. CTLA-4 is not detected on the T-cell surface until 24 hours after activation. Covalent dimerization of CTLA-4 has been shown to be required for its high binding avidity, although each CTLA-4 monomer contains a binding site for CD80 and CD86. 115 matched cddid_all.tbl CDD cd05722 cd05722 409387 IgI_1_Neogenin_like "First immunoglobulin (Ig)-like domain in neogenin, and similar domains; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the first immunoglobulin (Ig)-like domain in neogenin and related proteins. Neogenin is a cell surface protein which is expressed in the developing nervous system of vertebrate embryos in the growing nerve cells. It is also expressed in other embryonic tissues and may play a general role in developmental processes such as cell migration, cell-cell recognition, and tissue growth regulation. Included in this group is the tumor suppressor protein DCC which is deleted in colorectal carcinoma. DCC and neogenin each have four Ig-like domains followed by six fibronectin type III domains, a transmembrane domain, and an intracellular domain. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 97 matched cddid_all.tbl CDD cd05723 cd05723 409388 IgI_4_Neogenin_like "Fourth immunoglobulin (Ig)-like domain in neogenin, and similar domains; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the fourth immunoglobulin (Ig)-like domain in neogenin and related proteins. Neogenin is a cell surface protein which is expressed in the developing nervous system of vertebrate embryos in the growing nerve cells. It is also expressed in other embryonic tissues, and may play a general role in developmental processes such as cell migration, cell-cell recognition, and tissue growth regulation. Included in this group is the tumor suppressor protein DCC which is deleted in colorectal carcinoma. DCC and neogenin each have four Ig-like domains followed by six fibronectin type III domains, a transmembrane domain, and an intracellular domain. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 84 matched cddid_all.tbl CDD cd05724 cd05724 409389 IgI_2_Robo "Second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of the Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (Robo1, Robo2, and Robo3), and three mammalian Slit homologs (Slit-1,Slit-2, Slit-3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. Robo1, Robo2, and Robo3 are expressed by commissural neurons in the vertebrate spinal cord and Slit-1, Slit-2, Slit-3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of Slit responsiveness, antagonizes Slit responsiveness in precrossing axons. The Slit-Robo interaction is mediated by the second leucine-rich repeat (LRR) domain of Slit and the two N-terminal Ig domains of Robo, Ig1 and Ig2. The primary Robo binding site for Slit-2 has been shown by surface plasmon resonance experiments and mutational analysis to be the Ig1 domain, while the Ig2 domain has been proposed to harbor a weak secondary binding site. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 87 matched cddid_all.tbl CDD cd05725 cd05725 409390 IgI_3_Robo "Third immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the third immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (Robo1, Robo2, Robo3), and three mammalian Slit homologs (Slit-1,Slit-2, Slit-3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. Robo1, Robo2, and Robo3 are expressed by commissural neurons in the vertebrate spinal cord and Slit-1, Slit-2, and Slit-3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of Slit responsiveness, antagonizes Slit responsiveness in precrossing axons. The Slit-Robo interaction is mediated by the second leucine-rich repeat (LRR) domain of Slit and the two N-terminal Ig domains of Robo, Ig1 and Ig2. The primary Robo binding site for Slit2 has been shown by surface plasmon resonance experiments and mutational analysis to be the Ig1 domain, while the Ig2 domain has been proposed to harbor a weak secondary binding site. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 83 matched cddid_all.tbl CDD cd05726 cd05726 409391 IgI_4_Robo "Fourth immunoglobulin (Ig)-like domain in Robo (roundabout) receptors; member of the I-set of Ig superfamily (IgSF) domains. Members here are composed the fourth immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (Robo1, Robo2, Robo3), and three mammalian Slit homologs (Slit-1, Slit-2, Slit-3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. Robo1, Robo2, and Robo3 are expressed by commissural neurons in the vertebrate spinal cord and Slit-1, Slit-2, and Slit-3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of Slit responsiveness, antagonizes Slit responsiveness in precrossing axons. The Slit-Robo interaction is mediated by the second leucine-rich repeat (LRR) domain of Slit and the two N-terminal Ig domains of Robo, Ig1 and Ig2. The primary Robo binding site for Slit2 has been shown by surface plasmon resonance experiments and mutational analysis to be the Ig1 domain, while the Ig2 domain has been proposed to harbor a weak secondary binding site. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 98 matched cddid_all.tbl CDD cd05727 cd05727 409392 Ig2_Contactin-2-like Second Ig domain of the neural cell adhesion molecule contactin-2, and similar domains. The members here are composed of the second Ig domain of the neural cell adhesion molecule contactin-2. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. Contactin-2 (also called TAG-1, axonin-1) facilitates cell adhesion by homophilic binding between molecules in apposed membranes. The first four Ig domains form the intermolecular binding fragment which arranges as a compact U-shaped module by contacts between Ig domains 1 and 4, and domains 2 and 3. It has been proposed that a linear zipper-like array forms, from contactin-2 molecules alternatively provided by the two apposed membranes. 88 matched cddid_all.tbl CDD cd05728 cd05728 143205 Ig4_Contactin-2-like Fourth Ig domain of the neural cell adhesion molecule contactin-2, and similar domains. The members here are composed of the fourth Ig domain of the neural cell adhesion molecule contactin-2. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. Contactin-2 (also called TAG-1, axonin-1) facilitates cell adhesion by homophilic binding between molecules in apposed membranes. The first four Ig domains form the intermolecular binding fragment which arranges as a compact U-shaped module by contacts between Ig domains 1 and 4, and domains 2 and 3. It has been proposed that a linear zipper-like array forms, from contactin-2 molecules alternatively provided by the two apposed membranes. 85 matched cddid_all.tbl CDD cd05729 cd05729 409393 IgI_2_FGFR_like Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor, and similar domains; member of the I-set of IgSF domains. The members here are composed of the second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor. FGF receptors bind FGF signaling polypeptides. FGFs participate in multiple processes such as morphogenesis, development, and angiogenesis. FGFs bind to four FGF receptor tyrosine kinases (FGFR1, FGFR2, FGFR3, FGFR4). Receptor diversity is controlled by alternative splicing producing splice variants with different ligand binding characteristics and different expression patterns. FGFRs have an extracellular region comprised of three Ig-like domains, a single transmembrane helix, and an intracellular tyrosine kinase domain. Ligand binding and specificity reside in the Ig-like domains 2 and 3, and the linker region that connects these two. FGFR activation and signaling depend on FGF-induced dimerization, a process involving cell surface heparin or heparin sulfate proteoglycans. This group also contains fibroblast growth factor (FGF) receptor like-1(FGFRL1). FGFRL1 does not have a protein tyrosine kinase domain at its C-terminus; neither does its cytoplasmic domain appear to interact with a signaling partner. It has been suggested that FGFRL1 may not have any direct signaling function, but instead acts as a decoy receptor trapping FGFs and preventing them from binding other receptors. 95 matched cddid_all.tbl CDD cd05730 cd05730 143207 IgI_3_NCAM-1 Third immunoglobulin (Ig)-like domain of Neural Cell Adhesion Molecule 1 (NCAM-1); member of the I-set of IgSF domains. The members here are composed of the third immunoglobulin (Ig)-like domain of Neural Cell Adhesion Molecule (NCAM-1). NCAM plays important roles in the development and regeneration of the central nervous system, in synaptogenesis and neural migration. NCAM mediates cell-cell and cell-substratum recognition and adhesion via homophilic (NCAM-NCAM), and heterophilic (NCAM-non-NCAM), interactions. NCAM is expressed as three major isoforms having different intracellular extensions. The extracellular portion of NCAM has five N-terminal Ig-like domains and two fibronectin type III domains. The double zipper adhesion complex model for NCAM homophilic binding involves Ig1, Ig2, and Ig3. By this model, Ig1 and Ig2 mediate dimerization of NCAM molecules situated on the same cell surface (cis interactions), and Ig3 domains mediate interactions between NCAM molecules expressed on the surface of opposing cells (trans interactions) through binding to the Ig1 and Ig2 domains. The adhesive ability of NCAM is modulated by the addition of polysialic acid chains to the fifth Ig-like domain. 95 matched cddid_all.tbl CDD cd05731 cd05731 409394 Ig3_L1-CAM_like Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM), and similar domains. The members here are composed of the third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). L1 belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region and an intracellular domain. L1 is primarily expressed in the nervous system and is involved in its development and function. L1 is associated with an X-linked recessive disorder, X-linked hydrocephalus, MASA syndrome, and spastic paraplegia type 1, that involves abnormalities of axonal growth. This group also contains the chicken neuron-glia cell adhesion molecule, Ng-CAM and human neurofascin. 83 matched cddid_all.tbl CDD cd05732 cd05732 409395 IgI_NCAM-1_like "Immunoglobulin (Ig)-like I-set domain of Neural Cell Adhesion Molecule 1 (NCAM-1) and similar proteins. The members here are composed of the fourth immunoglobulin (Ig)-like domain of Neural Cell Adhesion Molecule (NCAM-1). NCAM plays important roles in the development and regeneration of the central nervous system, in synaptogenesis and neural migration. NCAM mediates cell-cell and cell-substratum recognition and adhesion via homophilic (NCAM-NCAM), and heterophilic (NCAM-non-NCAM), interactions. NCAM is expressed as three major isoforms having different intracellular extensions. The extracellular portion of NCAM has five N-terminal Ig-like domains and two fibronectin type III domains. The double zipper adhesion complex model for NCAM homophilic binding involves Ig1, Ig2, and Ig3. By this model, Ig1 and Ig2 mediate dimerization of NCAM molecules situated on the same cell surface (cis interactions), and Ig3 domains mediate interactions between NCAM molecules expressed on the surface of opposing cells (trans interactions), through binding to the Ig1 and Ig2 domains. The adhesive ability of NCAM is modulated by the addition of polysialic acid chains to the fifth Ig-like domain. Also included in this group is NCAM-2 (also known as OCAM/mamFas II and RNCAM) NCAM-2 is differentially expressed in the developing and mature olfactory epithelium (OE). One of the unique features of I-set domains is the lack of a C"" strand. The structures of this group show that the Ig domain lacks this strand and thus is a member of the I-set of Ig domains." 96 matched cddid_all.tbl CDD cd05733 cd05733 409396 IgI_L1-CAM_like "Immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM) and similar proteins; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the first immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). L1 belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region and an intracellular domain. L1 is primarily expressed in the nervous system and is involved in its development and function. L1 is associated with an X-linked recessive disorder, X-linked hydrocephalus, MASA syndrome, or spastic paraplegia type 1, that involves abnormalities of axonal growth. This group also contains NrCAM [Ng(neuronglia)CAM-related cell adhesion molecule], which is primarily expressed in the nervous system, and human neurofascin. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lacks a C"" strand." 94 matched cddid_all.tbl CDD cd05734 cd05734 409397 Ig_DSCAM Immunoglobulin (Ig)-like domain of Down Syndrome Cell Adhesion molecule (DSCAM). The members here are composed of the immunoglobulin (Ig)-like domain of Down Syndrome Cell Adhesion molecule (DSCAM). DSCAM is a cell adhesion molecule expressed largely in the developing nervous system. The gene encoding DSCAM is located at human chromosome 21q22, the locus associated with the intellectual disability phenotype of Down Syndrome. DSCAM is predicted to be the largest member of the IG superfamily. It has been demonstrated that DSCAM can mediate cation-independent homophilic intercellular adhesion. 97 matched cddid_all.tbl CDD cd05735 cd05735 409398 Ig_DSCAM Immunoglobulin (Ig) domain of Down Syndrome Cell Adhesion molecule (DSCAM). The members here are composed of the immunoglobulin (Ig) domain of Down Syndrome Cell Adhesion molecule (DSCAM). DSCAM is a cell adhesion molecule expressed largely in the developing nervous system. The gene encoding DSCAM is located at human chromosome 21q22, the locus associated with the intellectual disability phenotype of Down Syndrome. DSCAM is predicted to be the largest member of the IG superfamily. It has been demonstrated that DSCAM can mediate cation-independent homophilic intercellular adhesion. 101 matched cddid_all.tbl CDD cd05736 cd05736 409399 IgI_2_Follistatin_like Second immunoglobulin (Ig)-like domain of a Follistatin-related protein 5, and similar domains; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the second immunoglobulin (Ig)-like domain found in human Follistatin-related protein 5 (FSTL5) and a follistatin-like molecule encoded by the CNS-related Mahya gene. Mahya genes have been retained in certain Bilaterian branches during evolution. They are conserved in Hymenoptera and Deuterostomes, but are absent from other metazoan species such as fruit fly and nematode. Mahya proteins are secretory, with a follistatin-like domain (Kazal-type serine/threonine protease inhibitor domain and EF-hand calcium-binding domain), two Ig-like domains, and a novel C-terminal domain. Mahya may be involved in learning and memory and in processing of sensory information in Hymenoptera and vertebrates. Follistatin is a secreted, multidomain protein that binds activins with high affinity and antagonizes their signaling. 93 matched cddid_all.tbl CDD cd05737 cd05737 319300 IgI_Myomesin_like_C C-terminal immunoglobulin (Ig)-like domain of myomesin and M-protein; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the C-terminal immunoglobulin (Ig)-like domain of myomesin and M-protein (also known as myomesin-2). Myomesin and M-protein are both structural proteins localized to the M-band, a transverse structure in the center of the sarcomere, and are candidates for M-band bridges. Both proteins are modular, consisting mainly of repetitive Ig-like and fibronectin type III (FnIII) domains. Myomesin is expressed in all types of vertebrate striated muscle; M-protein has a muscle-type specific expression pattern. Myomesin is present in both slow and fast fibers; M-protein is present only in fast fibers. It has been suggested that myomesin acts as a molecular spring with alternative splicing as a means of modifying its elasticity. 92 matched cddid_all.tbl CDD cd05738 cd05738 409400 IgI_2_RPTP_IIa_LAR_like Second immunoglobulin (Ig)-like domain of the receptor protein tyrosine phosphatase (RPTP)-F; member of the I-set of IgSF domains. The members here are composed of the second immunoglobulin (Ig)-like domain found in the receptor protein tyrosine phosphatase (RPTP)-F, also known as LAR. LAR belongs to the RPTP type IIa subfamily. Members of this subfamily are cell adhesion molecule-like proteins involved in central nervous system (CNS) development. They have large extracellular portions comprised of multiple Ig-like domains and two to nine fibronectin type III (FNIII) domains and a cytoplasmic portion having two tandem phosphatase domains. 91 matched cddid_all.tbl CDD cd05739 cd05739 409401 IgI_3_RPTP_IIa_LAR_like Third immunoglobulin (Ig)-like domain of the receptor protein tyrosine phosphatase (RPTP)-F (also known as LAR), type IIa; member of the I-set of IgSF domains. The members here are composed of the third immunoglobulin (Ig)-like domain found in the receptor protein tyrosine phosphatase (RPTP)-F, also known as LAR. LAR belongs to the RPTP type IIa subfamily. Members of this subfamily are cell adhesion molecule-like proteins involved in central nervous system (CNS) development. They have large extracellular portions comprised of multiple Ig-like domains and two to nine fibronectin type III (FNIII) domains and a cytoplasmic portion having two tandem phosphatase domains. Included in this group is Drosophila LAR (DLAR). 82 matched cddid_all.tbl CDD cd05740 cd05740 409402 IgI_hCEACAM_2_4_6_like Immunoglobulin (Ig)-like domain of human carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) domains 2, 4, and 6, and similar domains. The members here are composed of the second, fourth, and sixth immunoglobulin (Ig)-like domains in human carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) protein subfamily. The CEA family is a group of anchored or secreted glycoproteins expressed by epithelial cells, leukocytes, endothelial cells, and placenta. The CEA family is divided into the CEACAM and pregnancy-specific glycoprotein (PSG) subfamilies. This group represents the CEACAM subfamily. CEACAM1 has many important cellular functions; it is a cell adhesion molecule and a signaling molecule that regulates the growth of tumor cells, an angiogenic factor, and a receptor for bacterial and viral pathogens, including mouse hepatitis virus (MHV). In mice, four isoforms of CEACAM1 generated by alternative splicing have either two [D1, D4] or four [D1-D4] Ig-like domains on the cell surface. 89 matched cddid_all.tbl CDD cd05741 cd05741 409403 IgV_CEACAM_like Immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins. The members here are composed of the immunoglobulin (Ig)-like domain in carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and related domains. The CEA family is a group of anchored or secreted glycoproteins, expressed by epithelial cells, leukocytes, endothelial cells and placenta. The CEA family is divided into the CEACAM and pregnancy-specific glycoprotein (PSG) subfamilies. This group represents the CEACAM subfamily. CEACAM1 has many important cellular functions: it is a cell adhesion molecule and a signaling molecule that regulates the growth of tumor cells, an angiogenic factor, and a receptor for bacterial and viral pathogens, including mouse hepatitis virus (MHV). In mice, four isoforms of CEACAM1 generated by alternative splicing have either two (D1, D4) or four (D1-D4) Ig-like domains on the cell surface. This family corresponds to the D1 Ig-like domain. Also belonging to this group is the N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family, CD84-like family. The SLAM family is a group of immune-cell specific receptors that can regulate both adaptive and innate immune responses. SLAM family proteins are organized as an extracellular domain with having two or four Ig-like domains, a single transmembrane segment, and a cytoplasmic region having Tyr-based motifs. The extracellular domain is organized as a membrane-distal Ig variable (IgV) domain that is responsible for ligand recognition and a membrane-proximal truncated Ig constant-2 (IgC2) domain. 102 matched cddid_all.tbl CDD cd05742 cd05742 409404 IgI_VEGFR_like Immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor (R) and similar proteins; member of the I-set of IgSF domains. The members here are composed of the immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor (R) and related proteins. The VEGFRs have an extracellular component with seven Ig-like domains, a transmembrane segment, and an intracellular tyrosine kinase domain interrupted by a kinase-insert domain. The VEGFR family consists of three members: VEGFR-1 (Flt-1), VEGFR-2 (KDR/Flk-1) and VEGFR-3 (Flt-4). VEGF-A interacts with both VEGFR-1 and VEGFR-2. VEGFR-1 binds strongest to VEGF; VEGF-2 binds more weakly. VEGFR-3 appears not to bind VEGF, but binds other members of the VEGF family (VEGF-C and -D). VEGFRs bind VEGFs with high affinity with the IG-like domains. VEGF-A is important to the growth and maintenance of vascular endothelial cells and to the development of new blood- and lymphatic-vessels in physiological and pathological states. VEGFR-2 is a major mediator of the mitogenic, angiogenic, and microvascular permeability-enhancing effects of VEGF-A. VEGFR-1 may play an inhibitory part in these processes by binding VEGF and interfering with its interaction with VEGFR-2. VEGFR-1 has a signaling role in mediating monocyte chemotaxis. VEGFR-1 and VEGFR-2 may mediate a chemotactic and a survival signal in hematopoietic stem cells or leukemia cells. VEGFR-3 has been shown to be involved in tumor angiogenesis and growth. This group also contains alpha-type platelet-derived growth factor receptor precursor (PDGFR)-alpha (CD140a), and PDGFR-beta (CD140b). PDGFRs alpha and beta have an extracellular component with five Ig-like domains, a transmembrane segment, and a cytoplasmic portion that has protein tyrosine kinase activity. 102 matched cddid_all.tbl CDD cd05743 cd05743 143220 Ig_Perlecan_like Immunoglobulin (Ig)-like domain of the human basement membrane heparan sulfate proteoglycan perlecan and similar proteins. The members here are composed of the immunoglobulin (Ig)-like domain of the human basement membrane heparan sulfate proteoglycan perlecan, also known as HSPG2, and similar proteins. Perlecan consists of five domains: domain I has three putative heparan sulfate attachment sites, domain II has four LDL receptor-like repeats, and one Ig-like repeat, domain III resembles the short arm of laminin chains, domain IV has multiple Ig-like repeats (21 repeats in human perlecan), and domain V resembles the globular G domain of the laminin A chain and internal repeats of EGF. Perlecan may participate in a variety of biological functions including cell binding, LDL-metabolism, basement membrane assembly and selective permeability, calcium binding, and growth- and neurite-promoting activities. 78 matched cddid_all.tbl CDD cd05744 cd05744 409405 IgI_Myotilin_C_like "Immunoglobulin (Ig)-like domain of myotilin, palladin, and myopalladin; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin (Ig)-like domain in myotilin, palladin, and myopalladin. Myotilin, palladin, and myopalladin function as scaffolds that regulate actin organization. Myotilin and myopalladin are most abundant in skeletal and cardiac muscle; palladin is ubiquitously expressed in the organs of developing vertebrates and plays a key role in cellular morphogenesis. The three family members each interact with specific molecular partners with all three binding to alpha-actinin; In addition, palladin also binds to vasodilator-stimulated phosphoprotein (VASP) and ezrin, myotilin binds to filamin and actin, and myopalladin also binds to nebulin and cardiac ankyrin repeat protein (CARP). This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 91 matched cddid_all.tbl CDD cd05745 cd05745 143222 Ig3_Peroxidasin Third immunoglobulin (Ig)-like domain of peroxidasin. The members here are composed of the third immunoglobulin (Ig)-like domain in peroxidasin. Peroxidasin has a peroxidase domain and interacting extracellular motifs containing four Ig-like domains. It has been suggested that peroxidasin is secreted and has functions related to the stabilization of the extracellular matrix. It may play a part in various other important processes such as removal and destruction of cells which have undergone programmed cell death and protection of the organism against non-self. 74 matched cddid_all.tbl CDD cd05746 cd05746 143223 Ig4_Peroxidasin Fourth immunoglobulin (Ig)-like domain of peroxidasin. The members here are composed of the fourth immunoglobulin (Ig)-like domain in peroxidasin. Peroxidasin has a peroxidase domain and interacting extracellular motifs containing four Ig-like domains. It has been suggested that peroxidasin is secreted, and has functions related to the stabilization of the extracellular matrix. It may play a part in various other important processes such as removal and destruction of cells which have undergone programmed cell death and protection of the organism against non-self. 69 matched cddid_all.tbl CDD cd05747 cd05747 143224 IgI_Titin_like "Immunoglobulin (Ig)-like domain of human titin C terminus and similar proteins; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the fifth immunoglobulin (Ig)-like domain from the C-terminus of human titin x and similar proteins. Titin (also called connectin) is a fibrous sarcomeric protein specifically found in vertebrate striated muscle. Titin is gigantic; depending on isoform composition it ranges from 2970 to 3700 kDa, and is of a length that spans half a sarcomere. Titin largely consists of multiple repeats of Ig-like and fibronectin type 3 (FN-III)-like domains. Titin connects the ends of myosin thick filaments to Z disks and extends along the thick filament to the H zone and appears to function similar to an elastic band, keeping the myosin filaments centered in the sarcomere during muscle contraction or stretching. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 92 matched cddid_all.tbl CDD cd05748 cd05748 409406 Ig_Titin_like Immunoglobulin (Ig)-like domain of titin and similar proteins. The members here are composed of the immunoglobulin (Ig)-like domain found in titin-like proteins and similar proteins. Titin (also called connectin) is a fibrous sarcomeric protein specifically found in vertebrate striated muscle. Titin is a giant protein; depending on isoform composition, it ranges from 2970 to 3700 kDa, and is of a length that spans half a sarcomere. Titin largely consists of multiple repeats of Ig-like and fibronectin type 3 (FN-III)-like domains. Titin connects the ends of myosin thick filaments to Z disks and extends along the thick filament to the H zone. It appears to function similarly to an elastic band, keeping the myosin filaments centered in the sarcomere during muscle contraction or stretching. Within the sarcomere, titin is also attached to or is associated with myosin binding protein C (MyBP-C). MyBP-C appears to contribute to the generation of passive tension by titin and like titin has repeated Ig-like and FN-III domains. Also included in this group are worm twitchin and insect projectin, thick filament proteins of invertebrate muscle which also have repeated Ig-like and FN-III domains. 82 matched cddid_all.tbl CDD cd05749 cd05749 409407 IgI_2_Axl_Tyro3_like Second immunoglobulin (Ig)-like domain of Axl/Tyro3 family receptor tyrosine kinases (RTKs); member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the second immunoglobulin (Ig)-like domain in the Axl/Tyro3 family of receptor tyrosine kinases (RTKs). This family includes Axl (also known as Ark, Ufo, and Tyro7), Tyro3 (also known as Sky, Rse, Brt, Dtk, and Tif), and Mer (also known as Nyk, c-Eyk, and Tyro12). Axl/Tyro3 family receptors have an extracellular portion with two Ig-like domains followed by two fibronectin-types III (FNIII) domains, a membrane-spanning single helix, and a cytoplasmic tyrosine kinase domain. Axl, Tyro3, and Mer are widely expressed in adult tissues, though they show higher expression in the brain, lymphatic and vascular systems, and testis. Axl, Tyro3, and Mer bind the vitamin K dependent protein Gas6 with high affinity, and in doing so activate their tyrosine kinase activity. Axl/Gas6 signaling may play a part in cell adhesion processes, prevention of apoptosis, and cell proliferation. 82 matched cddid_all.tbl CDD cd05750 cd05750 409408 Ig_Pro_neuregulin Immunoglobulin (Ig)-like domain in neuregulins. The members here are composed of the immunoglobulin (Ig)-like domain in neuregulins (NRGs). NRGs are signaling molecules which participate in cell-cell interactions in the nervous system, breast, heart, and other organ systems, and are implicated in the pathology of diseases including schizophrenia, multiple sclerosis, and breast cancer. There are four members of the neuregulin gene family (NRG-1, NRG-2, NRG-3, and NRG-4). The NRG-1 protein, binds to and activates the tyrosine kinases receptors ErbB3 and ErbB4, initiating signaling cascades. The other NRGs proteins bind one or the other or both of these ErbBs. NRG-1 has multiple functions: in the brain it regulates various processes such as radial glia formation and neuronal migration, dendritic development, and expression of neurotransmitters receptors, while in the peripheral nervous system NRG-1 regulates processes such as target cell differentiation, and Schwann cell survival. There are many NRG-1 isoforms which arise from the alternative splicing of mRNA. Less is known of the functions of the other NRGs. NRG-2 and NRG-3 are expressed predominantly in the nervous system. NRG-2 is expressed by motor neurons and terminal Schwann cells, and is concentrated near synaptic sites and may be a signal that regulates synaptic differentiation. NRG-4 has been shown to direct pancreatic islet cell development towards the delta-cell lineage. 92 matched cddid_all.tbl CDD cd05751 cd05751 409409 IgC2_D1_LILR_KIR_like First immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILRs), Natural killer inhibitory receptors (KIRs) and similar domains; member of Immunoglobulin Constant-2 set of IgSF domains. The members here are composed of the first immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors (LILRs) and Natural killer inhibitory receptors (KIRs, also known as also known as cluster of differentiation (CD) 158), and similar proteins. This group includes LILRB1 (also known as LIR-1), LILRA5 (also known as LIR9), an activating natural cytotoxicity receptor NKp46, the immune-type receptor glycoprotein VI (GPVI), and the IgA-specific receptor Fc-alphaRI (also known as cluster of differentiation (CD) 89). LILRs are a family of immunoreceptors expressed on expressed on T and B cells, on monocytes, dendritic cells, and subgroups of natural killer (NK) cells. The human LILR family contains nine proteins (LILRA1-3, and 5, and LILRB1-5). From functional assays, and as the cytoplasmic domains of various LILRs, for example LILRB1, LILRB2 (also known as LIR-2), and LILRB3 (also known as LIR-3) contain immunoreceptor tyrosine-based inhibitory motifs (ITIMs), it is thought that LIR proteins are inhibitory receptors. Of the eight LIR family proteins, only LILRB1, and LILRB2, show detectable binding to class I MHC molecules; ligands for the other members have yet to be determined. The extracellular portions of the different LIR proteins contain different numbers of Ig-like domains for example, four in the case of LILRB1, and LILRB2, and two in the case of LILRB4 (also known as LIR-5). The activating natural cytotoxicity receptor NKp46 is expressed in natural killer cells, and is organized as an extracellular portion having two Ig-like extracellular domains, a transmembrane domain, and a small cytoplasmic portion. GPVI, which also contains two Ig-like domains, participates in the processes of collagen-mediated platelet activation and arterial thrombus formation. Fc-alphaRI is expressed on monocytes, eosinophils, neutrophils, and macrophages; it mediates IgA-induced immune effector responses such as phagocytosis, antibody-dependent cell-mediated cytotoxicity and respiratory burst. Killer cell immunoglobulin-like receptors (KIRs; also known as CD158 for human KIR) are transmembrane glycoproteins expressed by natural killer cells and subsets of T cells. KIRs are a family of highly polymorphic activating and inhibitory receptors that serve as key regulators of human NK cell function. The KIR proteins are classified by the number of extracellular immunoglobulin domains (2D or 3D) and by whether they have a long (L) or short (S) cytoplasmic domain. KIR proteins with the long cytoplasmic domain transduce inhibitory signals upon ligand binding via an immune tyrosine-based inhibitory motif (ITIM), while KIR proteins with the short cytoplasmic domain lack the ITIM motif and instead associate with the TYRO protein tyrosine kinase binding protein to transduce activating signals. The major ligands for KIR are MHC class I (HLA-A, -B or -C) molecules. 88 matched cddid_all.tbl CDD cd05752 cd05752 409410 Ig1_FcgammaR_like First immunoglobulin (Ig)-like domain of Fcgamma-receptors (FcgammaRs), and similar domains. The members here are composed of the first immunoglobulin (Ig)-like domain of Fcgamma-receptors (FcgammaRs). Interactions between IgG and FcgammaR are important to the initiation of cellular and humoral response. IgG binding to FcgammaR leads to a cascade of signals and ultimately to functions such as antibody-dependent-cellular-cytotoxicity (ADCC), endocytosis, phagocytosis, release of inflammatory mediators, etc. FcgammaR has two Ig-like domains. This group also contains FcepsilonRI which binds IgE with high affinity. 79 matched cddid_all.tbl CDD cd05753 cd05753 409411 Ig2_FcgammaR_like Second immunoglobulin (Ig)-like domain of Fcgamma-receptors (FcgammaRs), and similar domains. The members here are composed of the second immunoglobulin (Ig)-like domain of Fcgamma-receptors (FcgammaRs). Interactions between IgG and FcgammaR are important to the initiation of cellular and humoral response. IgG binding to FcgammaR leads to a cascade of signals and ultimately to functions such as antibody-dependent-cellular-cytotoxicity (ADCC), endocytosis, phagocytosis, release of inflammatory mediators, etc. FcgammaR has two Ig-like domains. This group also contains FcepsilonRI which binds IgE with high affinity. 83 matched cddid_all.tbl CDD cd05754 cd05754 409412 IgI_Perlecan_like "Immunoglobulin (Ig)-like domain found in Perlecan and similar proteins; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the third immunoglobulin (Ig)-like domain found in Perlecan. Perlecan is a large multi-domain heparin sulfate proteoglycan, important in tissue development and organogenesis. Perlecan can be represented as 5 major portions; its fourth major portion (domain IV) is a tandem repeat of immunoglobulin-like domains (Ig2-Ig15) which can vary in size due to alternative splicing. Perlecan binds many cellular and extracellular ligands. Its domain IV region has many binding sites. Some of these have been mapped at the level of individual Ig-like domains, including a site restricted to the Ig5 domain for heparin/sulfatide, a site restricted to the Ig3 domain for nidogen-1 and nidogen-2, a site restricted to Ig4-5 for fibronectin, and sites restricted to Ig2 and to Ig13-15 for fibulin-2. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 85 matched cddid_all.tbl CDD cd05755 cd05755 409413 IgC2_2_ICAM-1_like Second immunoglobulin (Ig)-like C2-set domain of intercellular cell adhesion molecule 1 (ICAM-1), and similar domains. The members here are composed of the second immunoglobulin (Ig)-like domain of intercellular cell adhesion molecule 1 (ICAM-1; also known as domain of cluster of differentiation (CD) 54) and similar proteins. During the inflammation process, these molecules recruit leukocytes onto the vascular endothelium before extravasation to the injured tissues. ICAM-1 may be involved in organ targeted tumor metastasis. The interaction of ICAM-1 with leukocyte function-associated antigen-1 (LFA-1) plays a part in leukocyte-endothelial cell recognition. This group also contains ICAM-2 which also interacts with LFA-1. Transmigration of immature dendritic cells across resting endothelium is dependent on the interaction of ICAM-2 with, yet unidentified, ligand(s) on the dendritic cells. ICAM-1 has five Ig-like domains and ICAM-2 has two. ICAM-1 may also act as host receptor for viruses and parasites. The structures of this group show that the second Ig domain lacks a D strand and thus belonging to the C2-set of the IgSF 101 matched cddid_all.tbl CDD cd05756 cd05756 409414 Ig1_IL1R_like First immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R), and similar domains. The members here are composed of the first immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R; also known as cluster of differentiation (CD) 121). IL-1 alpha and IL-1 beta are cytokines which participate in the regulation of inflammation, immune responses, and hematopoiesis. These cytokines bind to the IL-1 receptor type 1 (IL1R1), which is activated on additional association with interleukin-1 receptor accessory protein (IL1RAP). IL-1 also binds a second receptor designated type II (IL1R2). Mature IL1R1 consists of three Ig-like domains, a transmembrane domain, and a large cytoplasmic domain. Mature IL1R2 is organized similarly except that it has a short cytoplasmic domain. The latter does not initiate signal transduction. A naturally occurring cytokine IL-1RA (IL-1 receptor antagonist) is widely expressed and binds to IL-1 receptors, inhibiting the binding of IL-1 alpha and IL-1 beta. 96 matched cddid_all.tbl CDD cd05757 cd05757 409415 Ig2_IL1R-like Second immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R), and similar domains. The members here are composed of the second immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R; also known as cluster of differentiation (CD) 121). IL-1 alpha and IL-1 beta are cytokines which participate in the regulation of inflammation, immune responses, and hematopoiesis. These cytokines bind to the IL-1 receptor type 1 (IL1R1), which is activated on additional association with interleukin-1 receptor accessory protein (IL1RAP). IL-1 also binds a second receptor designated type II (IL1R2). Mature IL1R1 consists of three IG-like domains, a transmembrane domain, and a large cytoplasmic domain. Mature IL1R2 is organized similarly except that it has a short cytoplasmic domain. The latter does not initiate signal transduction. A naturally occurring cytokine IL-1RA (IL-1 receptor antagonist) is widely expressed and binds to IL-1 receptors, inhibiting the binding of IL-1 alpha and IL-1 beta. This group also contains ILIR-like 1 (IL1R1L) which maps to the same chromosomal location as IL1R1 and IL1R2. 92 matched cddid_all.tbl CDD cd05758 cd05758 319310 IgI_5_KIRREL3-like Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3, and similar domains; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2). This protein has five Ig-like domains, one transmembrane domain, and a cytoplasmic tail. Included in this group is mammalian Kirrel (also known as Neph1), Kirrel2 (also known as Neph3), and Drosophila RST (also known as irregular chiasm C-roughest) protein. These proteins contain multiple Ig domains, have properties of cell adhesion molecules, and are important in organ development. 98 matched cddid_all.tbl CDD cd05759 cd05759 409416 IgI_2_KIRREL3-like Second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3, and similar domains; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the second immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 (also known as Neph2). This protein has five Ig-like domains, one transmembrane domain, and a cytoplasmic tail. Included in this group is mammalian Kirrel (Neph1), Kirrel2 (Neph3), and Drosophila RST (irregular chiasm C-roughest) protein. These proteins contain multiple Ig domains, have properties of cell adhesion molecules, and are important in organ development. 98 matched cddid_all.tbl CDD cd05760 cd05760 409417 Ig2_PTK7 Second immunoglobulin (Ig)-like domain of protein tyrosine kinase (PTK) 7. The members here are composed of the second immunoglobulin (Ig)-like domain in protein tyrosine kinase (PTK) 7, also known as CCK4. PTK7 is a subfamily of the receptor protein tyrosine kinase family, and is referred to as an RPTK-like molecule. RPTKs transduce extracellular signals across the cell membrane and play important roles in regulating cell proliferation, migration, and differentiation. PTK7 is organized as an extracellular portion having seven Ig-like domains, a single transmembrane region, and a cytoplasmic tyrosine kinase-like domain. PTK7 is considered a pseudokinase as it has several unusual residues in some of the highly conserved tyrosine kinase (TK) motifs; it is predicted to lack TK activity. PTK7 may function as a cell-adhesion molecule. PTK7 mRNA is expressed at high levels in placenta, melanocytes, liver, lung, pancreas, and kidney. PTK7 is overexpressed in several cancers, including melanoma and colon cancer lines. 95 matched cddid_all.tbl CDD cd05761 cd05761 409418 IgI_2_Necl-1-4 Second immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 - Necl-4; member of the I-set of Ig superfamily domains. The members here are composed of the second immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 (also known as cell adhesion molecule 3 or CADM3), Necl-2 (also known as CADM1), Necl-3 (also known as CADM2) and Necl-4 (also known as CADM4). These nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 through Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one cytoplasmic region. The N-terminal Ig-like domain of the extracellular region belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-1 and Necl-2 have Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-1 is specifically expressed in neural tissue and is important to the formation of synapses, axon bundles, and myelinated axons. Necl-2 is expressed in a wide variety of tissues, and is a putative tumour suppressor gene, which is downregulated in aggressive neuroblastoma. Necl-3 has been shown to accumulate in tissues of the central and peripheral nervous system, where it is expressed in ependymal cells and myelinated axons. It is observed at the interface between the axon shaft and the myelin sheath. Necl-4 is expressed on Schwann cells, and plays a key part in initiating peripheral nervous system (PNS) myelination. Necl-4 participates in cell-cell adhesion and is proposed to play a role in tumor suppression. 102 matched cddid_all.tbl CDD cd05762 cd05762 409419 IgI_8_hMLCK_like Eighth immunoglobulin (Ig)-like domain of human myosin light-chain kinase (MLCK) and similar protein; member of the I-set of IgSF domains. The members here are composed of the eighth immunoglobulin (Ig)-like domain of human myosin light-chain kinase (MLCK) and similar proteins. Myosin light-chain kinase (MLCK) is a key regulator of different forms of cell motility involving actin and myosin II. Agonist stimulation of smooth muscle cells increases cytosolic Ca2+ which binds calmodulin. This Ca2+-calmodulin complex in turn binds to and activates MLCK. Activated MLCK leads to the phosphorylation of the 20 kDa myosin regulatory light chain (RLC) of myosin II and the stimulation of actin-activated myosin MgATPase activity. MLCK is widely present in vertebrate tissues; it phosphorylates the 20 kDa RLC of both smooth and nonmuscle myosin II. Phosphorylation leads to the activation of the myosin motor domain and altered structural properties of myosin II. In smooth muscle MLCK it is involved in initiating contraction. In nonmuscle cells, MLCK may participate in cell division and cell motility; it has been suggested MLCK plays a role in cardiomyocyte differentiation and contraction through regulation of nonmuscle myosin II. 99 matched cddid_all.tbl CDD cd05763 cd05763 409420 IgI_LRIG1-like "Immunoglobulin (Ig)-like ectodomain of the LRIG1 (Leucine-rich Repeats And Immunoglobulin-like Domains Protein 1) and similar proteins; member of the I-set of IgSF domains. The members here are composed of subgroup of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. The ectodomain of LRIG1 has two distinct regions: the proposed 15 LRRs and three Ig-like domains closer to the membrane. LRIG1 has been reported to interact with many receptor tyrosine kinases, GDNF/c-Ret, E-cadherin, JAK/STAT, c-Met, and the EGFR family signaling systems. Immunoglobulin Superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The structure of the LRIG1 extracellular Ig domain lacks a C"" strand and thus is better described as a member of the I-set of IgSF domains." 91 matched cddid_all.tbl CDD cd05764 cd05764 409421 IgI_SALM5_like "Immunoglobulin domain of human Synaptic Adhesion-Like Molecule 5 (SALM5) and similar proteins; member of the I-set of IgSF domains. This group contains the immunoglobulin domain of human Synaptic Adhesion-Like Molecule 5 (SALM5) and similar proteins. The SALM (for synaptic adhesion-like molecules; also known as Lrfn for leucine-rich repeat and fibronectin type III domain containing) family of adhesion molecules consists of five known members: SALM1/Lrfn2, SALM2/Lrfn1, SALM3/Lrfn4, SALM4/Lrfn3, and SALM5/Lrfn5. SALMs share a similar domain structure, containing leucine-rich repeats (LRRs), an immunoglobulin (Ig) domain, and a fibronectin III (FNIII) domain, followed by a transmembrane domain and a C-terminal PDZ-binding motif. SALM5 is implicated in autism spectrum disorders (ASDs) and schizophrenia, induces presynaptic differentiation in contacting axons. SALM5 interacts with the Ig domains of LAR (Leukocyte common Antigen-Related) family receptor protein tyrosine phosphatases (LAR-RPTPs; LAR, PTPdelta, and PTPsigma). In addition, PTPdelta is implicated in ASDs, ADHD, bipolar disorder, and restless leg syndrome. Studies have shown that LAR-RPTPs are novel and splicing-dependent presynaptic ligands for SALM5, and that they mediate SALM5-dependent presynaptic differentiation. Furthermore, SALM5 maintains AMPA receptor (AMPAR)-mediated excitatory synaptic transmission through mechanisms involving the interaction of SALM5 with LAR-RPTPs. This group belongs to the I-set of immunoglobulin superfamily (IgSF) domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C"" strand." 88 matched cddid_all.tbl CDD cd05765 cd05765 409422 IgI_3_WFIKKN-like "Third immunoglobulin-like domain of the human WFIKKN (WAP, follistatin, immunoglobulin, Kunitz and NTR domain-containing protein), and similar domains; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the third immunoglobulin-like domain of the human WFIKKN (WAP, follistatin, immunoglobulin, Kunitz and NTR domain-containing protein) and similar proteins. WFIKKN is a secreted protein that consists of multiple types of protease inhibitory modules, including two tandem Kunitz-type protease inhibitor-domains. The Ig superfamily is a heterogenous group of proteins built on a common fold comprised of a sandwich of two beta sheets. Members of the Ig superfamily are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 95 matched cddid_all.tbl CDD cd05766 cd05766 409423 IgC1_MHC_II_beta Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II beta chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes and they are also expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain has two globular domains (N- and C-terminal) and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure. 96 matched cddid_all.tbl CDD cd05767 cd05767 409424 IgC1_MHC_II_alpha Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin (Ig) domain of the major histocompatibility complex (MHC) class II alpha chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are also expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure. 95 matched cddid_all.tbl CDD cd05768 cd05768 409425 IgC1_CH3_IgAGD_CH4_IgAEM CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, and delta chains, and CH4 domain (fourth constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, epsilon, and mu chains; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the third and fourth immunoglobulin constant domain (IgC) of alpha, delta, gamma and alpha, epsilon, and mu heavy chains, respectively. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. 105 matched cddid_all.tbl CDD cd05769 cd05769 409426 IgC1_TCR_beta T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the T cell receptor (TCR) beta chain constant immunoglobulin domain. TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group includes the variable domain of the beta chain. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The antigen binding site is formed by the variable domains of the alpha and beta chains, located at the N-terminus of each chain. Alpha/beta TCRs recognize antigens differently from gamma/delta TCRs. 116 matched cddid_all.tbl CDD cd05770 cd05770 409427 IgC1_beta2m Class I major histocompatibility complex (MHC) beta-2-microglobulin; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin-like domain in beta-2-microglobulin (beta2m). Beta2m is the non-covalently bound light chain of the human class I major histocompatibility complex (MHC-I). Beta2m is structured as a beta-sandwich domain composed of two facing beta-sheets (four stranded and three stranded), that is typical of the C-type immunoglobulin superfamily. This structure is stabilized by an intramolecular disulfide bridge connecting two Cys residues in the facing beta-sheets. In vivo, MHC-I continuously exposes beta2m on the cell surface, where it may be released to plasmatic fluids, transported to the kidneys, degraded, and finally excreted. 94 matched cddid_all.tbl CDD cd05771 cd05771 409428 IgC1_Tapasin_R Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin-like domain on Tapasin-R. Tapasin is a V-C1 (variable-constant) immunoglobulin superfamily molecule present in the endoplasmic reticulum (ER), where it links MHC class I molecules to the transporter associated with antigen processing (TAP). Tapasin-R is a tapasin-related protein that contains similar structural motifs to Tapasin, with some marked differences, especially in the V domain, transmembrane and cytoplasmic regions. The majority of Tapasin-R is located within the ER; however, there may be some expression of Tapasin-R at the cell surface. Tapasin-R lacks an obvious ER retention signal. 100 matched cddid_all.tbl CDD cd05772 cd05772 409429 IgC1_SIRP_domain_2 "Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin (Ig)-like domain in Signal-Regulatory Protein (SIRP), domain 2 (C1 repeat 1). The SIRPs belong to the ""paired receptors"" class of membrane proteins that comprise several genes coding for proteins with similar extracellular regions, but very different transmembrane/cytoplasmic regions with different (activating or inhibitory) signaling potentials. They are commonly on NK cells, but are also on many myeloid cells. Their extracellular region contains three Immunoglobulin superfamily domains, a single V-set and two C1-set IgSF domains. Their cytoplasmic tails contain either ITIMs or transmembrane regions that have positively charged residues that allow an association with adaptor proteins, such as DAP12/KARAP, containing ITAMs. There are 3 distinct SIRP members: alpha, beta, and gamma. SIRP alpha (also known as CD172a or SRC homology 2 domain-containing protein tyrosine phosphatase substrate 1/Shps-1) is a membrane receptor that interacts with a ligand CD47 expressed on many cells and gives an inhibitory signal through immunoreceptor tyrosine-based inhibition motifs in the cytoplasmic region that interact with phosphatases SHP-1 and SHP-2. SIRP beta has a short cytoplasmic region and associates with a transmembrane adapter protein DAP12 containing immunoreceptor tyrosine-based activation motifs to give an activating signal. SIRP gamma contains a very short cytoplasmic region lacking obvious signaling motifs, but also binds CD47, but with much less affinity." 102 matched cddid_all.tbl CDD cd05773 cd05773 143250 IgC1_hNephrin_like Immunoglobulin-like domain of human nephrin and similar proteins; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin-like domain in human nephrin and similar proteins. Nephrin is an integral component of the slit diaphragm and is a central component of the glomerular ultrafilter. Nephrin plays a structural role and has a role in signaling. Nephrin is a transmembrane protein having a short intracellular portion, an extracellular portion comprised of eight Ig-like domains, and one fibronectin type III-like domain. The extracellular portions of nephrin from neighboring foot processes of separate podocyte cells may interact with each other, and in association with other components of the slit diaphragm form a porous molecular sieve within the slit pore. The intracellular portion of nephrin is associated with linker proteins, which connect nephrin to the actin cytoskeleton. The intracellular portion is tyrosine phosphorylated, and mediates signaling from the slit diaphragm into the podocytes. 109 matched cddid_all.tbl CDD cd05774 cd05774 409430 IgV_CEACAM_D1 First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM). The members here are composed of the immunoglobulin (Ig)-like domain 1 in carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) proteins. The CEA family is a group of anchored or secreted glycoproteins, expressed by epithelial cells, leukocytes, endothelial cells, and placenta. The CEA family is divided into the CEACAM and pregnancy-specific glycoprotein (PSG) subfamilies. This group represents the CEACAM subfamily. CEACAM1 has many important cellular functions: it is a cell adhesion molecule and a signaling molecule that regulates the growth of tumor cells, an angiogenic factor, and a receptor for bacterial and viral pathogens, including mouse hepatitis virus (MHV). In mice, four isoforms of CEACAM1 generated by alternative splicing have either two (D1, D4) or four (D1-D4) Ig-like domains on the cell surface. 105 matched cddid_all.tbl CDD cd05775 cd05775 409431 IgV_CD2_like_N N-terminal immunoglobulin (Ig)-like domain of T-cell surface antigen CD2, and similar domains. The members here are composed of the N-terminal immunoglobulin (Ig)-like domain (or domain 1) of T-cell surface antigen Clusters of Differentiation (CD) 2 and similar proteins. CD2 is a T-cell specific surface glycoprotein and is critically important for mediating adhesion between T cells and antigen-presenting cells or between cytolytic T cells and target cells. CD2 is located on chromosome 1 at 1p13 in humans and on chromosome 3 in mice. CD2 contains an extracellular domain with two or Ig-like domains, a single transmembrane segment, and a cytoplasmic region rich in proline and basic residues. 98 matched cddid_all.tbl CDD cd05776 cd05776 99819 DNA_polB_alpha_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase alpha. DNA polymerase alpha is a family-B DNA polymerase with a catalytic subunit that contains a DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (delta and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase alpha is almost exclusively required for the initiation of DNA replication and the priming of Okazaki fragments during elongation. It associates with DNA primase and is the only enzyme able to start DNA synthesis de novo. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis. This explains why in most organisms, that no specific repair role, other than check point control, has been assigned to this enzyme. The exonuclease domain may have a structural role. 234 matched cddid_all.tbl CDD cd05777 cd05777 99820 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues necessary for metal binding and catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. 230 matched cddid_all.tbl CDD cd05778 cd05778 99821 DNA_polB_zeta_exo inactive DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase zeta. DNA polymerase zeta is a family-B DNA polymerase which is distantly related to DNA polymerase delta. It plays a major role in translesion replication and the production of either spontaneous or induced mutations. In addition, DNA polymerase zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen. The catalytic subunit contains both polymerase and 3'-5' exonuclease domains, but only exhibits polymerase activity. The DnaQ-like 3'-5' exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, without the four conserved acidic residues that are crucial for metal binding and catalysis. 231 matched cddid_all.tbl CDD cd05779 cd05779 99822 DNA_polB_epsilon_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase epsilon. DNA polymerase epsilon is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and delta are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase epsilon plays a role in elongating the leading strand during DNA replication. It is also involved in DNA repair. The catalytic subunit contains both polymerase and 3'-5' exonuclease activities. The N-terminal exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. DNA polymerase epsilon also carries a unique large C-terminal domain with an unknown function. Phylogenetic analyses indicate that it is orthologous to the archaeal DNA polymerase B3 rather than to the eukaryotic alpha, delta, or zeta polymerases. The exonuclease domain of family-B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation 204 matched cddid_all.tbl CDD cd05780 cd05780 99823 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show similarity to eukaryotic DNA polymerases involved in DNA replication. Some archaea possess multiple family-B DNA polymerases. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family-B DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases. 195 matched cddid_all.tbl CDD cd05781 cd05781 99824 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replication are similar to those from eukaryotes. Some archaea possess multiple family-B DNA polymerases. B3 is mainly found in crenarchaea. Phylogenetic analyses of eubacterial, archaeal, and eukaryotic family B-DNA polymerases support independent gene duplications during the evolution of archaeal and eukaryotic family-B DNA polymerases. 188 matched cddid_all.tbl CDD cd05782 cd05782 99825 DNA_polB_like1_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair. 208 matched cddid_all.tbl CDD cd05783 cd05783 99826 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B1displays thermostable polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family-B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Family-B DNA polymerases from thermophilic archaea are unique in that they are able to recognize the presence of uracil in the template strand, leading to the stalling of DNA synthesis. This is an additional safeguard mechanism against increased levels of deaminated bases during genome duplication at high temperatures. S. solfataricus B1 also interacts with DNA polymerase Y and may contribute to genome stability mechanisms. 204 matched cddid_all.tbl CDD cd05784 cd05784 99827 DNA_polB_II_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase II and similar bacterial family-B DNA polymerases. The 3'-5' exonuclease domain of Escherichia coli DNA polymerase II (Pol II) and similar bacterial proteins. Pol II is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain has a fundamental role in the proofreading activity of polII. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Pol II is involved in a variety of cellular activities, such as the repair of DNA damaged by UV irradiation or oxidation. It plays a pivotal role in replication-restart, a process that bypasses DNA damage in an error-free manner. Pol II is also involved in lagging strand synthesis. 193 matched cddid_all.tbl CDD cd05785 cd05785 99828 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair. 207 matched cddid_all.tbl CDD cd05787 cd05787 100061 LbH_eIF2B_epsilon eIF-2B epsilon subunit, central Left-handed parallel beta-Helix (LbH) domain: eIF-2B is a eukaryotic translation initiator, a guanine nucleotide exchange factor (GEF) composed of five different subunits (alpha, beta, gamma, delta and epsilon). eIF2B is important for regenerating GTP-bound eIF2 during the initiation process. This event is obligatory for eIF2 to bind initiator methionyl-tRNA, forming the ternary initiation complex. The eIF-2B epsilon subunit contains an N-terminal domain that resembles a dinucleotide-binding Rossmann fold, a central LbH domain containing 4 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X), and a C-terminal domain of unknown function that is present in eIF-4 gamma, eIF-5, and eIF-2B epsilon. The epsilon and gamma subunits form the catalytic subcomplex of eIF-2B, which binds eIF2 and catalyzes guanine nucleotide exchange. 79 matched cddid_all.tbl CDD cd05789 cd05789 240215 S1_Rrp4 "S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the ""S1 pore structure""." 86 matched cddid_all.tbl CDD cd05790 cd05790 240216 S1_Rrp40 "S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the ""S1 pore structure""." 86 matched cddid_all.tbl CDD cd05791 cd05791 240217 S1_CSL4 "S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the ""S1 pore structure""." 92 matched cddid_all.tbl CDD cd05792 cd05792 240218 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. 78 matched cddid_all.tbl CDD cd05793 cd05793 240219 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea. 77 matched cddid_all.tbl CDD cd05794 cd05794 240220 S1_EF-P_repeat_2 S1_EF-P_repeat_2: Translation elongation factor P (EF-P), S1-like RNA-binding domain, repeat 1. EF-P stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome. EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively. EF-P has 3 domains (domains I, II, and III). Domains II and III are S1-like domains. This CD includes domain III (the second S1 domain of EF_P). Domains II and III of have structural homology to the eIF5A domain C, suggesting that domains II and III evolved by duplication. 56 matched cddid_all.tbl CDD cd05795 cd05795 240221 Ribosomal_P0_L10e Ribosomal protein L10 family, P0 and L10e subfamily; composed of eukaryotic 60S ribosomal protein P0 and the archaeal P0 homolog, L10e. P0 or L10e forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). These eukaryotic and archaeal P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2. 175 matched cddid_all.tbl CDD cd05796 cd05796 240222 Ribosomal_P0_like Ribosomal protein L10 family, P0-like protein subfamily; composed of uncharacterized eukaryotic proteins with similarity to the 60S ribosomal protein P0, including the Saccharomyces cerevisiae protein called mRNA turnover protein 4 (MRT4). MRT4 may be involved in mRNA decay. P0 forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. It occupies the L7/L12 stalk of the ribosome. The stalk is known to contain the binding site for elongation factors EF-G and EF-Tu; however, there is disagreement as to whether or not P0 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, P0 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). Some eukaryotic P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2. 163 matched cddid_all.tbl CDD cd05797 cd05797 240223 Ribosomal_L10 Ribosomal protein L10 family, L10 subfamily; composed of bacterial 50S ribosomal protein and eukaryotic mitochondrial 39S ribosomal protein, L10. L10 occupies the L7/L12 stalk of the ribosome. The N-terminal domain (NTD) of L10 interacts with L11 protein and forms the base of the L7/L12 stalk, while the extended C-terminal helix binds to two or three dimers of the NTD of L7/L12 (L7 and L12 are identical except for an acetylated N-terminus). The L7/L12 stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). These bacteria and eukaryotic sequences have no additional C-terminal domain, present in other eukaryotic and archaeal orthologs. 157 matched cddid_all.tbl CDD cd05798 cd05798 240224 SIS_TAL_PGI SIS_TAL_PGI: Transaldolase (TAL)/ Phosphoglucose isomerase (PGI). This group represents the SIS (Sugar ISomerase) PGI domain, of a multifunctional protein (TAL-PGI ) having both TAL and PGI activities. TAL_PGI contains an N-terminal TAL domain and a C-terminal PGI domain. TAL catalyzes the reversible conversion of sedoheptulose-7-phosphate (S7P) and glyceraldehyde-3-phosphate (G3P), to fructose-6-phosphate (F6P) and erythrose-4-phosphate (E4P). PGI catalyzes the reversible isomerization of F6P to glucose-6-phosphate (G6P). It has been suggested for Gluconobacter oxydans TAL_PGI that this enzyme generates E4P and G6P directly from S7P and G3P. G. oxydans TAL_PGI contributes to increased xylitol production from D-arabitol. As xylitol is an alternative natural sweetner to sucrose, the microbial conversion of D-arabitol to xylitol is of interest to food and pharmaceutical industries. 129 matched cddid_all.tbl CDD cd05799 cd05799 100092 PGM2 This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1). The mammalian PGM2 is thought to be a phosphopentomutase that catalyzes the conversion of the nucleoside breakdown products, ribose-1-phosphate and deoxyribose-1-phosphate to the corresponding 5-phosphopentoses. PGM2L1 is thought to catalyze the 1,3-bisphosphoglycerate-dependent synthesis of glucose 1,6-bisphosphate and other aldose-bisphosphates that serve as cofactors for several sugar phosphomutases and possibly also as regulators of glycolytic enzymes. PGM2 and PGM2L1 belong to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model. 487 matched cddid_all.tbl CDD cd05800 cd05800 100093 PGM_like2 This PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily and is found in both archaea and bacteria. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four structural domains (subdomains) with a centrally located active site formed by four loops, one from each subdomain. All four subdomains are included in this alignment model. 461 matched cddid_all.tbl CDD cd05801 cd05801 100094 PGM_like3 This bacterial PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model. 522 matched cddid_all.tbl CDD cd05802 cd05802 100095 GlmM GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of UDP-N-acetylglucosamine, an essential precursor to components of the cell envelope. In order to be active, GlmM must be phosphorylated, which can occur via autophosphorylation or by the Ser/Thr kinase StkP. GlmM functions in a classical ping-pong bi-bi mechanism with glucosamine-1,6-diphosphate as an intermediate. Other members of the alpha-D-phosphohexomutase superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model. 434 matched cddid_all.tbl CDD cd05803 cd05803 100096 PGM_like4 This PGM-like (phosphoglucomutase-like) domain is located C-terminal to a mannose-1-phosphate guanyltransferase domain in a protein of unknown function that is found in both prokaryotes and eukaryotes. This domain belongs to the alpha-D-phosphohexomutase superfamily which includes several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this superfamily include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model. 445 matched cddid_all.tbl CDD cd05804 cd05804 100115 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure. 355 matched cddid_all.tbl CDD cd05805 cd05805 100097 MPG1_transferase GTP-mannose-1-phosphate guanyltransferase (MPG1 transferase), also known as GDP-mannose pyrophosphorylase, is a bifunctional enzyme with both phosphomannose isomerase (PMI) activity and GDP-mannose phosphorylase (GMP) activity. The protein contains an N-terminal NTP transferase domain, an L-beta-H domain, and a C-terminal PGM-like domain that belongs to the alpha-D-phosphohexomutase superfamily. This subfamily is limited to bacteria and archaea. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this group appear to lack conserved residues necessary for metal binding and catalytic activity. Other members of this superfamily include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model. 441 matched cddid_all.tbl CDD cd05806 cd05806 99881 CBM20_laforin Laforin protein tyrosine phosphatase, N-terminal CBM20 (carbohydrate-binding module, family 20) domain. Laforin, encoded by the EPM2A gene, is a dual-specificity phosphatase that dephosphorylates complex carbohydrates. Mutations in the gene encoding laforin result in Lafora disease, a fatal autosomal recessive neurodegenerative disorder characterized by the presence of intracellular deposits of insoluble, abnormally branched, glycogen-like polymers, known as Lafora bodies, in neurons, muscle, liver, and other tissues. The molecular basis for the formation of these Lafora bodies is unknown. Laforin is one of the only phosphatases that contains a carbohydrate-binding module. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch. 112 matched cddid_all.tbl CDD cd05807 cd05807 99882 CBM20_CGTase CGTase, C-terminal CBM20 (carbohydrate-binding module, family 20) domain. CGTase, also known as cyclodextrin glycosyltransferase and cyclodextrin glucanotransferase, catalyzes the formation of various cyclodextrins (alpha-1,4-glucans) from starch. CGTase has, in addition to its C-terminal CBM20 domain, an N-terminal catalytic domain belonging to glycosyl hydrolase family 13 and an IPT domain of unknown function. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch. 101 matched cddid_all.tbl CDD cd05808 cd05808 99883 CBM20_alpha_amylase Alpha-amylase, C-terminal CBM20 (carbohydrate-binding module, family 20) domain. This domain is found in several bacterial and fungal alpha-amylases including the maltopentaose-forming amylases (G5-amylases). Most alpha-amylases have, in addition to the C-terminal CBM20 domain, an N-terminal catalytic domain belonging to glycosyl hydrolase family 13, which hydrolyzes internal alpha-1,4-glucosidic bonds in starch and related saccharides, yielding maltotriose and maltose. Two types of soluble substrates are used by alpha-amylases including long substrates (e.g. amylose) and short substrates (e.g. maltodextrins or maltooligosaccharides). The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch. 95 matched cddid_all.tbl CDD cd05809 cd05809 99884 CBM20_beta_amylase Beta-amylase, C-terminal CBM20 (carbohydrate-binding module, family 20) domain. Beta-amylase has, in addition to its C-terminal CBM20 domain, an N-terminal catalytic domain belonging to glycosyl hydrolase family 14, which hydrolyzes the alpha-1,4-glucosidic bonds of starch, yielding beta-maltose from the nonreducing end of the substrate. Beta-amylase is found in both plants and microorganisms, however the plant members lack a C-terminal CBM20 domain and are not included in this group. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch. 99 matched cddid_all.tbl CDD cd05810 cd05810 99885 CBM20_alpha_MTH Glucan 1,4-alpha-maltotetraohydrolase (alpha-MTH), C-terminal CBM20 (carbohydrate-binding module, family 20) domain. Alpha-MTH, also known as maltotetraose-forming exo-amylase or G4-amylase, is an exo-amylase found in bacteria that degrades starch from its non-reducing end. Most alpha-MTHs have, in addition to the C-terminal CBM20 domain, an N-terminal glycosyl hydrolase family 13 catalytic domain. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch. 97 matched cddid_all.tbl CDD cd05811 cd05811 99886 CBM20_glucoamylase "Glucoamylase (glucan1,4-alpha-glucosidase), C-terminal CBM20 (carbohydrate-binding module, family 20) domain. Glucoamylases are inverting, exo-acting starch hydrolases that hydrolyze starch and related polysaccharides by releasing the nonreducing end glucose. They are mainly active on alpha-1,4-glycosidic bonds but also have some activity towards 1,6-glycosidic bonds occurring in natural oligosaccharides. The ability of glucoamylases to cleave 1-6-glycosidic binds is called ""debranching activity"" and is of importance in industrial applications, where complete degradation of starch to glucose is needed. Most glucoamylases are multidomain proteins containing an N-terminal catalytic domain, a C-terminal CBM20 domain, and a highly O-glycosylated linker region that connects the two. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch." 106 matched cddid_all.tbl CDD cd05813 cd05813 99887 CBM20_genethonin_1 Genethonin-1, C-terminal CBM20 (carbohydrate-binding module, family 20) domain. Genethonin-1 is a human skeletal muscle protein with no known function. It contains a C-terminal CBM20 domain. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch. 95 matched cddid_all.tbl CDD cd05814 cd05814 99888 CBM20_Prei4 Prei4, N-terminal CBM20 (carbohydrate-binding module, family 20) domain. Preimplantation protein 4 (Prei4) is a protein of unknown function that is expressed during mouse preimplantation embryogenesis. In addition to the N-terminal CBM20 domain, Prei4 contains a C-terminal glycerophosphoryl diester phosphodiesterase (GDPD) domain. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch. 120 matched cddid_all.tbl CDD cd05815 cd05815 99889 CBM20_DPE2_repeat1 Disproportionating enzyme 2 (DPE2), N-terminal CBM20 (carbohydrate-binding module, family 20) domain, repeat 1. DPE2 is a transglucosidase that is essential for the cytosolic metabolism of maltose in plant leaves at night. Maltose is an intermediate on the pathway from starch to sucrose and DPE2 is thought to metabolize the maltose that is exported from the chloroplast. DPE2 has two N-terminal CBM20 starch binding domains as well as a C-terminal amylomaltase (4-alpha-glucanotransferase) catalytic domain. DPE1, the plastid version of this enzyme, has a transglucosidase domain that is similar to that of DPE2 but lacks the N-terminal carbohydrate-binding domains. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch. 101 matched cddid_all.tbl CDD cd05816 cd05816 99890 CBM20_DPE2_repeat2 Disproportionating enzyme 2 (DPE2), N-terminal CBM20 (carbohydrate-binding module, family 20) domain, repeat 2. DPE2 is a transglucosidase that is essential for the cytosolic metabolism of maltose in plant leaves at night. Maltose is an intermediate on the pathway from starch to sucrose and DPE2 is thought to metabolize the maltose that is exported from the chloroplast. DPE2 has two N-terminal CBM20 domains as well as a C-terminal amylomaltase (4-alpha-glucanotransferase) catalytic domain. DPE1, the plastid version of this enzyme, has a transglucosidase domain that is similar to that of DPE2 but lacks the N-terminal CBM20 domains. Included in this group are PDE2-like proteins from Dictyostelium, Entamoeba, and Bacteroides. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch. 99 matched cddid_all.tbl CDD cd05817 cd05817 99891 CBM20_DSP Dual-specificity phosphatase (DSP), N-terminal CBM20 (carbohydrate-binding module, family 20) domain. This CBM20 domain is located at the N-terminus of a protein tyrosine phosphatase of unknown function found in slime molds and ciliated protozoans. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch. 100 matched cddid_all.tbl CDD cd05818 cd05818 99892 CBM20_water_dikinase Phosphoglucan water dikinase (also known as alpha-glucan water dikinase), N-terminal CBM20 (carbohydrate-binding module, family 20) domain. This domain is found in the chloroplast-encoded phosphoglucan water dikinase, one of two enzymes involved in the phosphorylation of plant starches. In addition to the CBM20 domain, phosphoglucan water dikinase contains a C-terminal pyruvate binding domain. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch. 92 matched cddid_all.tbl CDD cd05819 cd05819 271320 NHL NHL repeat unit of beta-propeller proteins. The NHL(NCL-1, HT2A and LIN-41)-repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. The repeats have a catalytic activity in Peptidyl-glycine alpha-amidating monooxygenase; proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localized to the repeats. Tripartite motif-containing protein 32 interacts with the activation domain of Tat. This interaction is mediated by the NHL repeats. 269 matched cddid_all.tbl CDD cd05820 cd05820 99893 CBM20_novamyl Novamyl (also known as acarviose transferase, ATase, maltogenic alpha-amylase, glucan 1,4-alpha-maltohydrolase, and AcbD), C-terminal CBM20 (carbohydrate-binding module, family 20) domain. Novamyl has a five-domain structure similar to that of cyclodextrin glucanotransferase (CGTase). Novamyl has a substrate-binding surface with an open groove which can accommodate both cyclodextrins and linear substrates. The CBM20 domain is found in a large number of starch degrading enzymes including alpha-amylase, beta-amylase, glucoamylase, and CGTase (cyclodextrin glucanotransferase). CBM20 is also present in proteins that have a regulatory role in starch metabolism in plants (e.g. alpha-amylase) or glycogen metabolism in mammals (e.g. laforin). CBM20 folds as an antiparallel beta-barrel structure with two starch binding sites. These two sites are thought to differ functionally with site 1 acting as the initial starch recognition site and site 2 involved in the specific recognition of appropriate regions of starch. 103 matched cddid_all.tbl CDD cd05821 cd05821 100113 TLP_Transthyretin Transthyretin (TTR) is a 55 kDa protein responsible for the transport of thyroid hormones and retinol in vertebrates. TTR distributes the two thyroid hormones T3 (3,5,3'-triiodo-L-thyronine) and T4 (Thyroxin, or 3,5,3',5'-tetraiodo-L-thyronine), as well as retinol (vitamin A) through the formation of a macromolecular complex that includes each of these as well as retinol-binding protein. Misfolded forms of TTR are implicated in the amyloid diseases familial amyloidotic polyneuropathy and senile systemic amyloidosis. TTR forms a homotetramer with each subunit consisting of eight beta-strands arranged in two sheets and a short alpha-helix. The central channel of the tetramer contains two independent binding sites, each located between a pair of subunits, which differ in their ligand binding affinity. A negative cooperativity has been observed for the binding of T4 and other TTR ligands. A fraction of plasma TTR is carried in high density lipoproteins by binding to apolipoprotein AI (apoA-I). TTR is able to proteolytically process apoA-I by cleaving its C-terminus; therefore TTR has protease activity in addition to its function in protein transport. 121 matched cddid_all.tbl CDD cd05822 cd05822 100114 TLP_HIUase HIUase (5-hydroxyisourate hydrolase) catalyzes the second step in a three-step ureide pathway in which 5-hydroxyisourate (HIU), a product of the uricase (urate oxidase) reaction, is hydrolyzed to 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (OHCU). HIUase has high sequence similarity with transthyretins and is a member of the transthyretin-like protein (TLP) family. HIUase is distinguished from transthyretins by a conserved signature motif at its C-terminus that forms part of the active site. In HIUase, this motif is YRGS, while transthyretins have a conserved TAVV sequence in the same location. Most HIUases are cytosolic but in plants and slime molds, they are peroxisomal based on the presence of N-terminal periplasmic localization sequences. HIUase forms a homotetramer with each subunit consisting of eight beta-strands arranged in two sheets and a short alpha-helix. The central channel of the tetramer contains two independent binding sites, each located between a pair of subunits. 112 matched cddid_all.tbl CDD cd05824 cd05824 100062 LbH_M1P_guanylylT_C Mannose-1-phosphate guanylyltransferase, C-terminal Left-handed parallel beta helix (LbH) domain: Mannose-1-phosphate guanylyltransferase is also known as GDP-mannose pyrophosphorylase. It catalyzes the synthesis of GDP-mannose from GTP and mannose-1-phosphate, and is involved in the maintenance of cell wall integrity and glycosylation. Similar to ADP-glucose pyrophosphorylase, it contains an N-terminal catalytic domain that resembles a dinucleotide-binding Rossmann fold and a C-terminal LbH fold domain, presumably with 4 turns, each containing three imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity. 80 matched cddid_all.tbl CDD cd05825 cd05825 100063 LbH_wcaF_like wcaF-like: This group is composed of the protein product of the E. coli wcaF gene and similar proteins. WcaF is part of the gene cluster responsible for the biosynthesis of the extracellular polysaccharide colanic acid. The wcaF protein is predicted to contain a left-handed parallel beta-helix (LbH) domain encoded by imperfect tandem repeats of a hexapeptide repeat motif (X-[STAV]-X-[LIV]-[GAED]-X). Proteins containing hexapeptide repeats are often enzymes showing acyltransferase activity. Many are trimeric in their active forms. 107 matched cddid_all.tbl CDD cd05826 cd05826 320675 Sortase_B Sortase domain found in class B sortases. Class B sortases are membrane-bound cysteine transpeptidases broadly distributed in Gram-positive bacteria (mainly present in Firmicutes and Actinobacteria). They can have radically distinct functions. Some members of this group attach haemoproteins to the peptidoglycan of the cell wall, while others assemble pili, which are multi-subunit hair-like fibres that extend from the cell surface to promote microbial adhesion and biofilm formation. In transpeptidation reaction, the surface protein substrate is cleaved at a conserved cell wall-sorting signal (Class B sortases normally recognize the consensus NP[Q/K][T/S][N/G/S][D/A] motif), and covalently linked to peptidoglycan for display on the bacterial surface. The prototypical sortase B protein from Staphylococcus aureus (named Sa-SrtB) cleaves surface protein precursors between threonine and asparagine at a conserved NPQTN motif with subsequent covalent linkage to pentaglycine cross-bridges. It is required for anchoring the heme-iron binding surface protein IsdC to the cell wall envelope. SrtB contains an N-terminal hydrophobic region that functions as a signal peptide/transmembrane domain. At the C terminus, it contains an essential cysteine residue within the catalytic TLXTC signature sequence, where X is usually a serine. Genes encoding SrtB and its targets are generally clustered in the same locus. The prototypical class B sortase involved in pilus biogenesis is pilus-specific sortase C2 from Streptococcus pyogenes (named Sp-SrtC2) that anchors a surface protein containing a QVPTGV motif to the cell wall, as well as polymerizes the major pilin subunit Tee3/FctA and attaches the minor tip pilin Cpa. The linkage of Cpa to Tee3 by SrtC2 requires the VPPTG motif in the cell wall-sorting signal of Cpa. The family also includes SrtB enzymes from Bacillus anthracis (named Ba-SrtB) and Clostridium difficile (named Cd-SrtB). Ba-SrtB is thought to recognize the NPKTG motif, and attaches surface proteins to meso-diaminopimelic acid (mDAP) cross-bridges. Cd-SrtB does not play an essential role in pathogenesis. It cleaves short [SP]PXTG motif-containing peptides between the threonine and glycine residues and then covalently anchors the threonine residue to a nucleophile such as glycine or mDAP, but not to the peptidoglycan of C. difficile, suggesting a novel association of sortase activity with cyclic diGMP (c-diGMP)-mediated regulation to control levels of cell wall anchoring and secretion of putative adhesion molecules. 170 matched cddid_all.tbl CDD cd05827 cd05827 320676 Sortase_C Sortase domain found in class C sortases. Class C sortases are membrane-bound cysteine transpeptidases broadly distributed in Gram-positive bacteria (mainly present in Firmicutes and Actinobacteria). They function as pilin polymerases responsible for the assembly of pili, which are multi-subunit hair-like fibres that extend from the cell surface to promote microbial adhesion and biofilm formation. First, one or more class C sortases form the long thin shaft of the pilus through linking together pilin subunits via isopeptide bonds. The base of the pilus is then anchored to the cell wall by a housekeeping sortase or, in some cases, the class C sortase itself. Depending upon the organism both the number and type of sortase enzymes involved varies, and in some cases, accessory factors appear to be needed. In three-component spaA pilus from Corynebacterium diphtheriae, the prototypical class C sortase (named Cd-SrtA) catalyzes polymerization of the SpaA-type pilus, consisting of the shaft pilin SpaA, tip pilin SpaC and minor pilin SpaB. The pilus shaft is then attached to the cell wall by a housekeeping class E sortase, Cd-SrtF. In the absence of Cd-SrtF, Cd-SrtA attaches the pilus to the cell wall, albeit at a reduced rate. Cd-SrtA can recognize two distinct sorting signals (LPLTG in SpaA and SpaC, and LAFTG in SpaB) and it can employ lysine residues that originate from different proteins (either Lys190 within the pilin motif of SpaA or Lys139 in SpaB). However, Cd-SrtA cannot be able to polymerize the major pilin subunit SpaH, even though it contains LPLTG motif. In two-component pili of prototypical Bacillus cereus, the class C sortase (named Bc-SrtD) cleaves related sorting signals within a major pilin protein BcpA (LPVTG) and a minor tip pilin BcpB (IPNTG), and catalyzes a transpeptidation that joins the threonine residues in each signal to the side-chain of Lys162 in BcpA (located within a pilin motif). Unlike the SpaA pilus in C. diphtheriae, in B. cereus Bc-SrtD is unable to covalently attach the pilus to the cell wall without the help of the housekeeping sortase. 131 matched cddid_all.tbl CDD cd05828 cd05828 320677 Sortase_D_1 Sortase domain found in subfamily 1 of the class D family of sortases. Class D sortases are cysteine transpeptidases distributed in Gram-positive bacteria (mainly present in Firmicutes). The prototypical subfamily 1 of class D sortase from Bacillus anthracis (named Ba-SrtC) covalently attaches proteins bearing a noncanonical LPNTA sorting signal, such as the BasH and BasI proteins, to the peptidoglycan of the cell wall that facilitate sporulation. BasH is exclusively anchored to the forespore cell wall envelope, while BasI is attached to the diaminopimelic acid moiety of the peptidoglycan of predivisional cells. Ba-SrtC lacks the N-terminal signal peptide and membrane anchor. The family also includes many class D sortase homologs from Gram-negative bacteria, but the functions of these enzymes are unknown. 127 matched cddid_all.tbl CDD cd05829 cd05829 320678 Sortase_F Sortase domain found in the class F family of sortases. Class F sortases are mainly present in Actinobacteria, Chlorobacteria and Firmicutes. Their functions are largely unknown. 144 matched cddid_all.tbl CDD cd05830 cd05830 320679 Sortase_E Sortase domain found in the class E family of sortases. Class E sortases are membrane-bound cysteine transpeptidases distributed in Gram-positive bacteria (mainly present in Actinobacteria). Genes encoding class A and E sortases are never found in the same organism, and similar to class A sortases, the genes encoding class E sortases are not positioned adjacent to genes encoding potential protein substrates, suggesting a housekeeping sortase function of class E sortases in some high G + C Gram-positive bacteria. Similar to class A sortase, class E sortases are capable of anchoring a large number of functionally distinct surface proteins containing a cell wall sorting signal to an amino group located on the bacterial cell wall. They recognize an LAXTG sorting signal, instead of the canonical LPXTG motif processed by class A sortases. The prototypical class E sortase from Corynebacterium diphtheria (named Cd-SrtF) is a non-polymerization sortase that is not required for pilus polymerization, and proceeds to complete the assembly process by anchoring the polymer to the cell wall peptidoglycan. Moreover, in Streptomyces coelicolor, one or both of Staphylococcus aureus SrtA homologs may function as class E sortase responsible for the cell wall anchoring of the long chaplin proteins (ChpA-C) containing an LAXTG sorting signal, which presumably mediate aerial hyphae formation. The family also includes some class E sortase homologs from Gram-negative and Archaebacterial species, but the functions of these enzymes are unknown. 135 matched cddid_all.tbl CDD cd05831 cd05831 100109 Ribosomal_P1 Ribosomal protein P1. This subfamily represents the eukaryotic large ribosomal protein P1. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P1 is located in the L12 stalk, with proteins P2, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers) and bacteria may have four or six copies (two or three homodimers), depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2A, and P2B, which form P1A/P2B and P1B/P2A heterodimers. Some plant species have a third P-protein, called P3, which is not homologous to P1 and P2. In humans, P1 and P2 are strongly autoimmunogenic. They play a significant role in the etiology and pathogenesis of systemic lupus erythema (SLE). In addition, the ribosome-inactivating protein trichosanthin (TCS) interacts with human P0, P1, and P2, with its primary binding site located in the C-terminal region of P2. TCS inactivates the ribosome by depurinating a specific adenine in the sarcin-ricin loop of 28S rRNA. 103 matched cddid_all.tbl CDD cd05832 cd05832 100110 Ribosomal_L12p Ribosomal protein L12p. This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly interact with rRNA. Archaeal L12p is believed to function in a similar fashion. However, hybrid ribosomes containing the large subunit from E. coli with an archaeal stalk are able to bind archaeal and eukaryotic elongation factors but not bacterial elongation factors. In several mesophilic and thermophilic archaeal species, the binding of 23S rRNA to protein L11 and to the L10/L12p pentameric complex was found to be temperature-dependent and cooperative. 106 matched cddid_all.tbl CDD cd05833 cd05833 100111 Ribosomal_P2 Ribosomal protein P2. This subfamily represents the eukaryotic large ribosomal protein P2. Eukaryotic P1 and P2 are functionally equivalent to the bacterial protein L7/L12, but are not homologous to L7/L12. P2 is located in the L12 stalk, with proteins P1, P0, L11, and 28S rRNA. P1 and P2 are the only proteins in the ribosome to occur as multimers, always appearing as sets of heterodimers. Recent data indicate that eukaryotes have four copies (two heterodimers), while most archaeal species contain six copies of L12p (three homodimers). Bacteria may have four or six copies of L7/L12 (two or three homodimers) depending on the species. Experiments using S. cerevisiae P1 and P2 indicate that P1 proteins are positioned more internally with limited reactivity in the C-terminal domains, while P2 proteins seem to be more externally located and are more likely to interact with other cellular components. In lower eukaryotes, P1 and P2 are further subdivided into P1A, P1B, P2A, and P2B, which form P1A/P2B and P1B/P2A heterodimers. Some plants have a third P-protein, called P3, which is not homologous to P1 and P2. In humans, P1 and P2 are strongly autoimmunogenic. They play a significant role in the etiology and pathogenesis of systemic lupus erythema (SLE). In addition, the ribosome-inactivating protein trichosanthin (TCS) interacts with human P0, P1, and P2, with its primary binding site in the C-terminal region of P2. TCS inactivates the ribosome by depurinating a specific adenine in the sarcin-ricin loop of 28S rRNA. 109 matched cddid_all.tbl CDD cd05834 cd05834 438959 PWWP_HRP PWWP domain found in hepatoma-derived growth factor (HDGF)-related protein (HRP) family. The HRP family includes hepatoma-derived growth factor (HDGF), and HDGF-related proteins (HRPs). HDGF, also called high mobility group protein 1-like 2 (HMG-1L2), is a heparin-binding protein that acts as a transcriptional repressor with mitogenic activity for fibroblasts. It is a prognostic factor in several types of cancer. HDGFL1 is also called PWWP domain-containing protein 1 (PWWP1). Its biological function remains unclear. HDGFL2, also called HDGF-related protein 2 (HRP-2), or hepatoma-derived growth factor 2 (HDGF-2), is involved in cellular growth control, through the regulation of cyclin D1 expression. HDGFL3, also called HDGF-related protein 3 (HRP-3), enhances DNA synthesis and may play a role in cell proliferation. The family also includes PC4 and SFRS1-interacting protein (PSIP) and similar proteins. PSIP, also called CLL-associated antigen KW-7, dense fine speckles 70 kDa protein (DFS 70), lens epithelium-derived growth factor (LEDGF), or transcriptional coactivator p75/p52, acts as a transcriptional coactivator involved in neuroepithelial stem cell differentiation and neurogenesis. Members of the HRP family contains a PWWP domain, which is necessary for DNA binding. 82 matched cddid_all.tbl CDD cd05835 cd05835 438960 PWWP_DNMT3 PWWP domain found in the DNA (cytosine-5)-methyltransferase 3 (DNMT3) family. The DNMT3 family includes DNMT3A and DNMT3B, which are required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNMT3A, also called DNA methyltransferase HsaIIIA, DNA MTase HsaIIIA, or M.HsaIIIA, modifies DNA in a non-processive manner and also methylates non-CpG sites. It may preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. DNMT3A is recruited to trimethylated 'Lys-36' of histone H3 (H3K36me3) sites. DNMT3B, also called DNA methyltransferase HsaIIIB, DNA MTase HsaIIIB, or M.HsaIIIB, may preferentially methylate nucleosomal DNA within the nucleosome core region. DNMT3B may function as a transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Members of this family contains a PWWP domain that is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by DNMT3B is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of DNMT3B has been identified in patients with ICF (immunodeficiency, centromeric instability, and facial anomalie) syndrome , a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA. 89 matched cddid_all.tbl CDD cd05836 cd05836 438961 PWWP_GLYR1 PWWP domain found in glyoxylate reductase 1 (GLYR1) and similar proteins. GLYR1, also called 3-hydroxyisobutyrate dehydrogenase-like protein, cytokine-like nuclear factor N-PAC, nuclear protein NP60, or nuclear protein of 60 kDa, is a putative oxidoreductase that is recruited on chromatin and promotes KDM1B demethylase activity. It recognizes and binds trimethylated 'Lys-36' of histone H3 (H3K36me3). GLYR1 enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In addition to the PWWP domain, GLYR1 also contains an AT-hook and a C-terminal NAD-binding domain. The PWWP domain specifically recognizes DNA and histone methylated lysines. 86 matched cddid_all.tbl CDD cd05837 cd05837 438962 PWWP_MSH6 PWWP domain found in DNA mismatch repair protein MSH6 and similar proteins. MSH6, also called G/T mismatch-binding protein (GTBP or GTMBP), MutS protein homolog 6, or MutS-alpha 160 kDa subunit (p160), is a mismatch repair protein homologous to bacterial MutS. It is a component of the post-replicative DNA mismatch repair system (MMR). It heterodimerizes with MSH2 to form MutS alpha, which binds to DNA mismatches thereby initiating DNA repair. When bound, MutS alpha bends the DNA helix and shields approximately 20 base pairs, and recognizes single base mismatches and dinucleotide insertion-deletion loops (IDL) in the DNA. After mismatch binding, it forms a ternary complex with the MutL alpha heterodimer, which is thought to be responsible for directing the downstream MMR events, including strand discrimination, excision, and resynthesis. Mutations in MSH6 have been linked to increased cancer susceptibility, particularly in hereditary nonpolyposis colorectal cancer in humans. MSH6 contains a PWWP domain, but its role in MSH6 remains unclear. MSH6 orthologs found in Saccharomyces cerevisiae, Caenorhabditis elegans, and Arabidopsis thaliana lack the PWWP domain. PWWP domains typically recognize DNA and histone methylated lysines. 103 matched cddid_all.tbl CDD cd05838 cd05838 438963 PWWP_NSD_rpt2 second PWWP domain found in nuclear receptor-binding SET domain-containing (NSD) proteins. The nuclear receptor binding SET domain (NSD) protein family consists of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising in suppressing cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play nonredundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (C5HCH). This model corresponds to the second PWWP domain. The family also includes Drosophila melanogaster maternal-effect sterile 4 (dMes4) that may act as a histone-lysine N-methyltransferase required for wing morphogenesis. The PWWP domain specifically recognizes DNA and histone methylated lysines. 96 matched cddid_all.tbl CDD cd05839 cd05839 438964 PWWP_BRPF PWWP domain found in the bromodomain and PHD finger-containing (BRPF) protein family. The BRPF family of proteins includes BRPF1, BRD1/BRPF2, and BRPF3. They are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties. 106 matched cddid_all.tbl CDD cd05840 cd05840 438965 PWWP_ScIOC4-like PWWP domain found in Saccharomyces cerevisiae ISWI one complex protein 4 (ScIOC4) and similar proteins. ScIOC4 functions as a component of the ISW1B complex, which acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA. The ISW1B complex acts within coding regions to control the amount of RNA polymerase II released into productive elongation and to coordinate elongation with termination and pre-mRNA processing. The family also includes Schizosaccharomyces pombe PWWP domain-containing proteins 1 and 2 (SpPDP1 and SpPDP2). SpPDP1 associates with Set9 to regulate its chromatin localization and methyltransferase activity towards H4K20. Members of this family contain a PWWP domain. The PWWP domain specifically recognizes DNA and histone methylated lysines. 94 matched cddid_all.tbl CDD cd05841 cd05841 438966 PWWP_BS69-like PWWP domain found in protein BS69, protein kinase C-binding protein 1 (PRKCBP1) and similar proteins. Protein BS69, also called zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. BS69 is a multi-domain protein, containing bromo, plant homeodomain (PHD), proline-tryptophan-tryptophan-proline (PWWP), and MYeloid translocation protein 8, Nervy and DEAF-1 (MYND) domains. The specific role of the PWWP domain within BS69 is not clearly identified, but BS69 functions in chromatin remodeling, consistent with other PWWP-containing proteins. PRKCBP1, also called cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor. They form a RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a PHD finger, a bromodomain, and a PWWP domain. The PWWP domain specifically recognizes DNA and histone methylated lysines. 89 matched cddid_all.tbl CDD cd05843 cd05843 320682 Peptidase_M48_M56 Peptidases M48 (Ste24 endopeptidase or htpX homolog) and M56 (in MecR1 and BlaR1), integral membrane metallopeptidases. This family contains peptidase M48 (also known as Ste24 peptidase, Ste24p, Ste24 endopeptidase, a-factor converting enzyme, AFC1), M56 (also known as BlaR1 peptidase) as well as a novel family called minigluzincins. Peptidase M48 belongs to Ste24 endopeptidase family. Members of this family include Ste24 protease (peptidase M48A), protease htpX homolog (peptidase M48B), or CAAX prenyl protease 1, and mitochondrial metalloendopeptidase OMA1 (peptidase M48C). They proteolytically remove the C-terminal three residues of farnesylated proteins. They are integral membrane proteins associated with the endoplasmic reticulum and golgi, binding one zinc ion per subunit. In eukaryotes, Ste24p is required for the first NH2-terminal proteolytic processing event within the a-factor precursor, which takes place after COOH-terminal CAAX modification (C is cysteine; A is usually aliphatic; X is one of several amino acids) is complete. The Ste24p contains multiple membrane spans, a zinc metalloprotease motif (HEXXH), and a COOH-terminal ER retrieval signal (KKXX). Mutation studies have shown that the HEXXH protease motif, which is extracellular but adjacent to a transmembrane domain and therefore close to the membrane surface, is critical for Ste24p activity. Ste24p has limited homology to HtpX family of prokaryotic proteins; HtpX proteins, also part of the M48 peptidase family, are smaller and homology is restricted to the C-terminal half of Ste24p. HtpX expression is controlled by the Cpx stress response system, which senses abnormal membrane proteins; HtpX then undergoes self-degradation and collaborates with FtsH to eliminate these misfolded proteins. Peptidase M56 includes zinc metalloprotease domain in MecR1 and BlaR1. MecR1 is a transmembrane beta-lactam sensor/signal transducer protein that regulates the expression of an altered penicillin-binding protein PBP2a, which resists inactivation by beta-lactam antibiotics, in methicillin-resistant Staphylococcus aureus (MRSA). BlaR1 regulates the inducible expression of a class A beta-lactamase that hydrolytically destroys certain beta-lactam antibiotics in MRSA. Also included are a novel family of related proteins that consist of the soluble minimal scaffold similar to the catalytic domains of the integral-membrane metallopeptidase M48 and M56, thus called minigluzincins. 94 matched cddid_all.tbl CDD cd05844 cd05844 340860 GT4-like glycosyltransferase family 4 proteins. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to glycosyltransferase family 4 (GT4). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. 365 matched cddid_all.tbl CDD cd05845 cd05845 409432 IgI_2_L1-CAM_like "Second immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM), and similar domains; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the second immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM) and similar proteins. L1 belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains, five fibronectin type III domains, a transmembrane region, and an intracellular domain. L1 is primarily expressed in the nervous system and is involved in its development and function. L1 is associated with an X-linked recessive disorder, X-linked hydrocephalus, MASA syndrome, or spastic paraplegia type 1 that involves abnormalities of axonal growth. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 91 matched cddid_all.tbl CDD cd05846 cd05846 409433 IgV_1_MRC-OX-2_like First immunoglobulin (Ig) variable (V) domain of rat MRC OX-2 antigen, and similar domains. The members here are composed of the first immunoglobulin (Ig) domain of rat MRC OX-2 antigen (also known as CD200) and similar proteins. MRC OX-2 is a membrane glycoprotein expressed in a variety of lymphoid and non-lymphoid cells in rats. It has a similar broad distribution pattern in humans. MRC OX-2 may regulate myeloid cell activity. The protein has an extracellular portion containing two Ig-like domains, a transmembrane portion, and a cytoplasmic portion. 108 matched cddid_all.tbl CDD cd05847 cd05847 409434 IgC1_CH2_IgE CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the second constant domain of the heavy chain of immunoglobulin E (IgE). The basic structure of immunoglobulin (Ig) molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta, and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). The different classes of antibodies vary in their heavy chains; the IgE class has the epsilon type. This domain (Cepsilon2) of IgE is in place of the flexible hinge region found in IgG. 97 matched cddid_all.tbl CDD cd05848 cd05848 409435 IgI_1_Contactin-5 First immunoglobulin (Ig) domain of contactin-5; member of the I-set of Ig superfamily domains. The members here are composed of the first immunoglobulin (Ig) domain of the neural cell adhesion molecule contactin-5. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains, anchored to the membrane by glycosylphosphatidylinositol. The different contactins show different expression patterns in the central nervous system. In rats, a lack of contactin-5 (NB-2) results in an impairment of the neuronal activity in the auditory system. Contactin-5 is expressed specifically in the postnatal nervous system, peaking at about 3 weeks postnatal. Contactin-5 is highly expressed in the adult human brain in the occipital lobe and in the amygdala; lower levels of expression have been detected in the corpus callosum, caudate nucleus, and spinal cord. This group belongs to the I-set of IgSF domains. 96 matched cddid_all.tbl CDD cd05849 cd05849 409436 IgI_1_Contactin-1 First immunoglobulin (Ig) domain of contactin-1; member of the I-set of Ig superfamily domains. The members here are composed of the first immunoglobulin (Ig) domain of the neural cell adhesion molecule contactin-1. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. Contactin-1 is differentially expressed in tumor tissues and may, through a RhoA mechanism, facilitate invasion and metastasis of human lung adenocarcinoma. This group belongs to the I-set of IgSF domains. 95 matched cddid_all.tbl CDD cd05850 cd05850 409437 IgI_1_Contactin-2 First immunoglobulin (Ig) domain of contactin-2; member of the I-set of Ig superfamily domains. The members here are composed of the first immunoglobulin (Ig) domain of the neural cell adhesion molecule contactin-2-like. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. Contactin-2 (TAG-1, axonin-1) facilitates cell adhesion by homophilic binding between molecules in apposed membranes. It may play a part in the neuronal processes of neurite outgrowth, axon guidance and fasciculation, and neuronal migration. The first four Ig domains form the intermolecular binding fragment, which arranges as a compact U-shaped module by contacts between IG domains 1 and 4, and domains 2 and 3. The different contactins show different expression patterns in the central nervous system. During development and in adulthood, contactin-2 is transiently expressed in subsets of central and peripheral neurons. Contactin-2 is also expressed in retinal amacrine cells in the developing chick retina, corresponding to the period of formation and maturation of AC processes. This group belongs to the I-set of IgSF domains. 97 matched cddid_all.tbl CDD cd05851 cd05851 143259 IgI_3_Contactin-1 Third immunoglobulin (Ig) domain of contactin-1; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the third immunoglobulin (Ig) domain of the neural cell adhesion molecule contactin-1. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. Contactin-1 is differentially expressed in tumor tissues and may through a RhoA mechanism, facilitate invasion and metastasis of human lung adenocarcinoma. This group belongs to the I-set of IgSF domains. 88 matched cddid_all.tbl CDD cd05852 cd05852 409438 Ig5_Contactin-1 Fifth immunoglobulin (Ig) domain of contactin-1. The members here are composed of the fifth immunoglobulin (Ig) domain of the neural cell adhesion molecule contactin-1. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. Contactin-1 is differentially expressed in tumor tissues and may through a RhoA mechanism, facilitate invasion and metastasis of human lung adenocarcinoma. 89 matched cddid_all.tbl CDD cd05853 cd05853 409439 Ig6_Contactin-4 Sixth immunoglobulin (Ig) domain of contactin-4. The members here are composed of the sixth immunoglobulin (Ig) domain of the neural cell adhesion molecule contactin-4. Contactins are neural cell adhesion molecules, and are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. The different contactins show different expression patterns in the central nervous system. Highest expression of contactin-4 is in testes, thyroid, small intestine, uterus, and brain. Contactin-4 plays a role in the response of neuroblastoma cells to differentiating agents, such as retinoids. The contactin 4 gene is associated with cerebellar degeneration in spinocerebellar ataxia type 16. 102 matched cddid_all.tbl CDD cd05854 cd05854 409440 Ig6_Contactin-2 Sixth immunoglobulin (Ig) domain of contactin-2. The members here are composed of the sixth immunoglobulin (Ig) domain of the neural cell adhesion molecule contactin-2-like. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. Contactin-2 (TAG-1, axonin-1) facilitates cell adhesion by homophilic binding between molecules in apposed membranes. It may play a part in the neuronal processes of neurite outgrowth, axon guidance and fasciculation, and neuronal migration. The first four Ig domains form the intermolecular binding fragment, which arranges as a compact U-shaped module by contacts between IG domains 1 and 4, and domains 2 and 3. The different contactins show different expression patterns in the central nervous system. During development and in adulthood, contactin-2 is transiently expressed in subsets of central and peripheral neurons. Contactin-2 is also expressed in retinal amacrine cells (AC) in the developing chick retina, corresponding to the period of formation and maturation of AC processes. 102 matched cddid_all.tbl CDD cd05855 cd05855 409441 IgI_TrkB_d5 Fifth domain (immunoglobulin-like) of Trk receptor TrkB; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the fifth domain of Trk receptor, TrkB, an immunoglobulin (Ig)-like domain which binds to neurotrophin. The Trk family of receptors are tyrosine kinase receptors, which mediate the trophic effects of the neurotrophin Nerve Growth Factor (NGF) family. Trks are activated by dimerization, leading to autophosphorylation of intracellular tyrosine residues, and triggering the signal transduction pathway. TrkB shares significant sequence homology and domain organization with TrkA and TrkC. The first three domains are leucine-rich domains while the fourth and fifth domains are Ig-like domains playing a part in ligand binding. TrKB is recognized by brain-derived neurotrophic factor (BDNF) and neurotrophin (NT)-4. In some cell systems NT-3 can activate TrkA and TrkB receptors. TrKB transcripts are found throughout multiple structures of the central and peripheral nervous systems. This group belongs to the I-set of IgSF domains 94 matched cddid_all.tbl CDD cd05856 cd05856 409442 IgI_2_FGFRL1-like Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor_like-1(FGFRL1); member of the I-set of IgSF domains. The members here are composed of the second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor like-1(FGFRL1). FGFRL1 is comprised of a signal peptide, three extracellular Ig-like modules, a transmembrane segment, and a short intracellular domain. FGFRL1 is expressed preferentially in skeletal tissues. Similar to FGF receptors, the expressed protein interacts specifically with heparin and with FGF2. FGFRL1 does not have a protein tyrosine kinase domain at its C-terminus; neither does its cytoplasmic domain appear to interact with a signaling partner. It has been suggested that FGFRL1 may not have any direct signaling function, but instead acts as a decoy receptor trapping FGFs and preventing them from binding other receptors. 92 matched cddid_all.tbl CDD cd05857 cd05857 409443 IgI_2_FGFR Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor; member of the I-set of IgSF domains. The members here are composed of the second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor. FGF receptors bind FGF signaling polypeptides. FGFs participate in multiple processes such as morphogenesis, development, and angiogenesis. FGFs bind to four FGF receptor tyrosine kinases (FGFR1, FGFR2, FGFR3, FGFR4). Receptor diversity is controlled by alternative splicing producing splice variants with different ligand binding characteristics and different expression patterns. FGFRs have an extracellular region comprised of three IG-like domains, a single transmembrane helix, and an intracellular tyrosine kinase domain. Ligand binding and specificity reside in the Ig-like domains 2 and 3, and the linker region that connects these two. FGFR activation and signaling depend on FGF-induced dimerization, a process involving cell surface heparin or heparin sulfate proteoglycans. 95 matched cddid_all.tbl CDD cd05858 cd05858 409444 IgI_3_FGFR2 "Third immunoglobulin (Ig)-like domain of fibroblast growth factor receptor 2 (FGFR2); member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the third immunoglobulin (Ig)-like domain of human fibroblast growth factor receptor 2 (FGFR2). Fibroblast growth factors (FGFs) participate in morphogenesis, development, angiogenesis, and wound healing. These FGF-stimulated processes are mediated by four FGFR tyrosine kinases (FGRF1-4). FGFRs are comprised of an extracellular portion consisting of three Ig-like domains, a transmembrane helix, and a cytoplasmic portion having protein tyrosine kinase activity. The highly conserved Ig-like domains 2 and 3, and the linker region between D2 and D3 define a general binding site for FGFs. FGFR2 is required for male sex determination. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 105 matched cddid_all.tbl CDD cd05859 cd05859 409445 Ig4_PDGFR Fourth immunoglobulin (Ig)-like domain of platelet-derived growth factor receptor (PDGFR). The members here are composed of the fourth immunoglobulin (Ig)-like domain of platelet-derived growth factor receptor (PDGFR; also known as cluster of differentiation (CD) 140a) alpha and beta. PDGF is a potent mitogen for connective tissue cells. PDGF-stimulated processes are mediated by three different PDGFs (PDGF-A,PDGF-B, and PDGF-C). PDGFR alpha binds to all three PDGFs, whereas the PDGFR beta binds only to PDGF-B. PDGF alpha is organized as an extracellular component having five Ig-like domains, a transmembrane segment, and a cytoplasmic portion having protein tyrosine kinase activity. In mice, PDGFR alpha and PDGFR beta are essential for normal development. 101 matched cddid_all.tbl CDD cd05860 cd05860 409446 IgI_4_SCFR "Fourth immunoglobulin (Ig)-like domain of stem cell factor receptor (SCFR); member of the I-set of IgSF domains. The members here are composed of the fourth Immunoglobulin (Ig)-like domain in stem cell factor receptor (SCFR). SCFR is organized as an extracellular component having five IG-like domains, a transmembrane segment, and a cytoplasmic portion having protein tyrosine kinase activity. SCFR and its ligand SCF are critical for normal hematopoiesis, mast cell development, melanocytes, and gametogenesis. SCF binds to the second and third Ig-like domains of SCFR. This fourth Ig-like domain participates in SCFR dimerization, which follows ligand binding. Deletion of this fourth domain abolishes the ligand-induced dimerization of SCFR and completely inhibits signal transduction. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 101 matched cddid_all.tbl CDD cd05861 cd05861 409447 IgI_PDGFR-alphabeta Immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha and beta; member of the I-set of IgSF domains. The members here are composed of the immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha (also known as cluster of differentiation (CD) 140a), and beta (also known as CD140b). PDGF is a potent mitogen for connective tissue cells. PDGF-stimulated processes are mediated by three different PDGFs (PDGF-A,PDGF-B, and PDGF-C). PDGFRalpha binds to all three PDGFs, whereas the PDGFRbeta binds only to PDGF-B. PDGFRs alpha and beta have similar organization: an extracellular component with five Ig-like domains, a transmembrane segment, and a cytoplasmic portion having protein tyrosine kinase activity. In mice, PDGFRalpha and PDGFRbeta are essential for normal development. 99 matched cddid_all.tbl CDD cd05862 cd05862 409448 IgI_VEGFR Immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor(R); member of the I-set of IgSF domains. The members here are composed of the immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor(R). The VEGFRs have an extracellular component with seven Ig-like domains, a transmembrane segment, and an intracellular tyrosine kinase domain interrupted by a kinase-insert domain. The VEGFR family consists of three members, VEGFR-1 (also known as Flt-1), VEGFR-2 (also known as KDR or Flk-1) and VEGFR-3 (also known as Flt-4). VEGF_A interacts with both VEGFR-1 and VEGFR-2. VEGFR-1 binds strongest to VEGF, VEGF-2 binds more weakly. VEGFR-3 appears not to bind VEGF, but binds other members of the VEGF family (VEGF-C and -D). VEGFRs bind VEGFs with high affinity with the IG-like domains. VEGF-A is important to the growth and maintenance of vascular endothelial cells and to the development of new blood- and lymphatic-vessels in physiological and pathological states. VEGFR-2 is a major mediator of the mitogenic, angiogenic and microvascular permeability-enhancing effects of VEGF-A. VEGFR-1 may play an inhibitory part in these processes by binding VEGF and interfering with its interaction with VEGFR-2. VEGFR-1 has a signaling role in mediating monocyte chemotaxis. VEGFR-2 and -1 may mediate a chemotactic and a survival signal in hematopoietic stem cells or leukemia cells. VEGFR-3 has been shown to be involved in tumor angiogenesis and growth. 102 matched cddid_all.tbl CDD cd05863 cd05863 409449 IgI_VEGFR-3 "Immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor 3 (VEGFR-3); member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor 3 (VEGFR-3). The VEGFRs have an extracellular component with seven Ig-like domains, a transmembrane segment, and an intracellular tyrosine kinase domain interrupted by a kinase-insert domain. VEGFRs bind VEGFs with high affinity at the Ig-like domains. VEGFR-3 (Flt-4) binds two members of the VEGF family (VEGF-C and VEGF-D) and is involved in tumor angiogenesis and growth. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 88 matched cddid_all.tbl CDD cd05864 cd05864 409450 IgI_VEGFR-2 "Immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor 2 (VEGFR-2); member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor 2 (VEGFR-2). The VEGFRs have an extracellular component with seven Ig-like domains, a transmembrane segment, and an intracellular tyrosine kinase domain interrupted by a kinase-insert domain. VEGFRs bind VEGFs with high affinity at the Ig-like domains. VEGFR-2 (KDR/Flk-1) is a major mediator of the mitogenic, angiogenic and microvascular permeability-enhancing effects of VEGF-A; VEGF-A is important to the growth and maintenance of vascular endothelial cells and to the development of new blood- and lymphatic-vessels in physiological and pathological states. VEGF-A also interacts with VEGFR-1, which it binds more strongly than VEGFR-2. VEGFR-1 and VEGFR-2 may mediate a chemotactic and a survival signal in hematopoietic stem cells or leukemia cells. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 89 matched cddid_all.tbl CDD cd05865 cd05865 409451 IgI_1_NCAM-1 "First immunoglobulin (Ig)-like domain of neural cell adhesion molecule (NCAM-1); member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the first immunoglobulin (Ig)-like domain of neural cell adhesion molecule (NCAM-1). NCAM-1 plays important roles in the development and regeneration of the central nervous system, in synaptogenesis and neural migration. NCAM mediates cell-cell and cell-substratum recognition and adhesion via homophilic (NCAM-NCAM), and heterophilic (NCAM-nonNCAM), interactions. NCAM is expressed as three major isoforms having different intracellular extensions. The extracellular portion of NCAM has five N-terminal Ig-like domains and two fibronectin type III domains. The double zipper adhesion complex model for NCAM homophilic binding involves the Ig1, Ig2, and Ig3 domains. By this model, Ig1 and Ig2 mediate dimerization of NCAM molecules situated on the same cell surface (cis interactions), and Ig3 domains mediate interactions between NCAM molecules expressed on the surface of opposing cells (trans interactions), through binding to the Ig1 and Ig2 domains. The adhesive ability of NCAM is modulated by the addition of polysialic acid chains to the fifth Ig-like domain. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 97 matched cddid_all.tbl CDD cd05866 cd05866 409452 IgI_1_NCAM-2 "First immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-2; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the first immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-2 (OCAM/mamFas II, RNCAM). NCAM-2 is organized similarly to NCAM-1, including five N-terminal Ig-like domains and two fibronectin type III domains. NCAM-2 is differentially expressed in the developing and mature olfactory epithelium (OE), and may function like NCAM, as an adhesion molecule. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 93 matched cddid_all.tbl CDD cd05867 cd05867 409453 Ig4_L1-CAM_like Fourth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). The members here are composed of the fourth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). L1 is comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region, and an intracellular domain. L1 is primarily expressed in the nervous system and is involved in its development and function. L1 is associated with an X-linked recessive disorder, X-linked hydrocephalus, MASA syndrome, and spastic paraplegia type 1, that involves abnormalities of axonal growth. This group also contains the chicken neuron-glia cell adhesion molecule, Ng-CAM. 89 matched cddid_all.tbl CDD cd05868 cd05868 409454 Ig4_NrCAM Fourth immunoglobulin (Ig)-like domain of NrCAM (NgCAM-related cell adhesion molecule). The members here are composed of the fourth immunoglobulin (Ig)-like domain of NrCAM (NgCAM-related cell adhesion molecule). NrCAM belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six IG-like domains and five fibronectin type III domains, a transmembrane region, and an intracellular domain. NrCAM is primarily expressed in the nervous system. 89 matched cddid_all.tbl CDD cd05869 cd05869 143277 IgI_NCAM-1 "Immunoglobulin (Ig)-like I-set domain of Neural Cell Adhesion Molecule 1 (NCAM-1). The members here are composed of the fourth Ig domain of Neural Cell Adhesion Molecule 1(NCAM-1). NCAM plays important roles in the development and regeneration of the central nervous system, in synaptogenesis and neural migration. NCAM mediates cell-cell and cell-substratum recognition and adhesion via homophilic (NCAM-NCAM) and heterophilic (NCAM-non-NCAM) interactions. NCAM is expressed as three major isoforms having different intracellular extensions. The extracellular portion of NCAM has five N-terminal Ig-like domains and two fibronectin type III domains. The double zipper adhesion complex model for NCAM homophilic binding involves Ig1, Ig2, and Ig3. By this model, Ig1 and Ig2 mediate dimerization of NCAM molecules situated on the same cell surface (cis interactions), and Ig3 domains mediate interactions between NCAM molecules expressed on the surface of opposing cells (trans interactions), through binding to the Ig1 and Ig2 domains. The adhesive ability of NCAM is modulated by the addition of polysialic acid chains to the fifth Ig-like domain. One of the unique features of I-set domains is the lack of a C"" strand. The structures of this group show that the Ig domain lacks this strand and thus is a member of the I-set of Ig domains." 97 matched cddid_all.tbl CDD cd05870 cd05870 143278 IgI_NCAM-2 "Immunoglobulin (Ig)-like I-set domain of Neural Cell Adhesion Molecule 2 (NCAM-2). The members here are composed of the fourth Ig domain of Neural Cell Adhesion Molecule NCAM-2 (also known as OCAM/mamFas II and RNCAM). NCAM-2 is organized similarly to NCAM, including five N-terminal Ig-like domains and two fibronectin type III domains. NCAM-2 is differentially expressed in the developing and mature olfactory epithelium (OE), and may function like NCAM, as an adhesion molecule. One of the unique features of I-set domains is the lack of a C"" strand. The structures of this group show that the Ig domain lacks this strand and thus is a member of the I-set of Ig domains." 98 matched cddid_all.tbl CDD cd05871 cd05871 409455 Ig_Sema3 Immunoglobulin (Ig)-like domain of class III semaphorin Sema3. The members here are composed of the immunoglobulin (Ig)-like domain of Sema3 and similar proteins. Semaphorins are classified based on structural features additional to the Sema domain. Sema3 is a Class III semaphorin that is secreted. It is a vertebrate class having a Sema domain, an Ig domain, a short basic domain. They have been shown to be axonal guidance cues and have a part in the regulation of the cardiovascular, immune, and respiratory systems. Sema3A, the prototype member of this class III subfamily, induces growth cone collapse and is an inhibitor of axonal sprouting. In perinatal rat cortex, it acts as a chemoattractant and functions to direct the orientated extension of apical dendrites. It may play a role, prior to the development of apical dendrites, in signaling the radial migration of newborn cortical neurons towards the upper layers. Sema3A selectively inhibits vascular endothelial growth factor receptor (VEGF)-induced angiogenesis and induces microvascular permeability. This group also includes Sema3B, -C, -D, -E, -G. 92 matched cddid_all.tbl CDD cd05872 cd05872 409456 Ig_Sema4B_like Immunoglobulin (Ig)-like domain of the class IV semaphorin Sema4B. The members here are composed of the immunoglobulin (Ig)-like domain of Sema4B and similar proteins. Sema4B is a Class IV semaphorin. Semaphorins are classified based on structural features additional to the Sema domain. Sema4B has extracellular Sema and Ig domains, a transmembrane domain, and a short cytoplasmic domain. Sema4B has been shown to preferentially regulate the development of the postsynaptic specialization at the glutamatergic synapses. This cytoplasmic domain includes a PDZ-binding motif upon which the synaptic localization of Sem4B is dependent. Sema4B is a ligand of CLCP1. CLCP1 was identified in an expression profiling analysis, which compared a highly metastic lung cancer subline with its low metastic parental line. Sema4B was shown to promote CLCP1 endocytosis and their interaction is a potential target for therapeutic intervention of metastasis. 86 matched cddid_all.tbl CDD cd05873 cd05873 409457 Ig_Sema4D_like Immunoglobulin (Ig)-like domain of semaphorin 4D (Sema4D) and similar proteins. The members here are composed of the immunoglobulin (Ig)-like domain of semaphorin 4D (Sema4D) and similar proteins. Sema4D is a Class IV semaphorin. Semaphorins are classified based on structural features additional to the Sema domain. Sema4D has extracellular Sema and Ig domains, a transmembrane domain, and a short cytoplasmic domain. Sema4D plays a part in the development of GABAergic synapses. Sema4D in addition is an immune semaphorin. It is abundant on resting T cells; its expression is weak on resting B cells and antigen presenting cells (APCs), but is upregulated by various stimuli. The receptor used by Sema4D in the immune system is CD72. Sem4D enhances the activation of B cells and DCs through binding CD72, perhaps by reducing CD72s inhibitory signals. The receptor used by Sema4D in the non-lymphatic tissues is plexin-B1. Sem4D is anchored to the cell surface but its extracellular domain can be released from the cell surface by a metalloprotease-dependent process. Sem4D may mediate its effects in its membrane-bound form and/or its cleaved form. 87 matched cddid_all.tbl CDD cd05874 cd05874 409458 IgI_NrCAM Immunoglobulin (Ig)-like domain of NrCAM (Ng (neuronglia) CAM-related cell adhesion molecule); member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the first immunoglobulin (Ig)-like domain of NrCAM (Ng (neuronglia) CAM-related cell adhesion molecule). NrCAM belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region, and an intracellular domain. NrCAM is primarily expressed in the nervous system. 95 matched cddid_all.tbl CDD cd05875 cd05875 409459 IgI_hNeurofascin_like "Immunoglobulin (Ig)-like domain of human neurofascin (NF); member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the first immunoglobulin (Ig)-like domain of human neurofascin (NF). NF belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region, and a cytoplasmic domain. NF has many alternatively spliced isoforms having different temporal expression patterns during development. NF participates in axon subcellular targeting and synapse formation, however little is known of the functions of the different isoforms. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lacks a C"" strand." 95 matched cddid_all.tbl CDD cd05876 cd05876 409460 Ig3_L1-CAM Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). The members here are composed of the third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). L1 belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains, five fibronectin type III domains, a transmembrane region and an intracellular domain. L1 is primarily expressed in the nervous system and is involved in its development and function. L1 is associated with an X-linked recessive disorder, X-linked hydrocephalus, MASA syndrome, or spastic paraplegia type 1, that involves abnormalities of axonal growth. This group also contains the chicken neuron-glia cell adhesion molecule, Ng-CAM. 83 matched cddid_all.tbl CDD cd05877 cd05877 409461 Ig_LP_like Immunoglobulin (Ig)-like domain of human cartilage link protein (LP), and similar domains. The members here are composed of the immunoglobulin (Ig)-like domain similar to that found in human cartilage link protein (LP; also called hyaluronan and proteoglycan link protein). In cartilage, chondroitin-keratan sulfate proteoglycan (CSPG), aggrecan, forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes. 117 matched cddid_all.tbl CDD cd05878 cd05878 409462 Ig_Aggrecan_like Immunoglobulin (Ig)-like domain of the aggrecan-like chondroitin sulfate proteoglycan core protein (CSPG). The members here are composed of the immunoglobulin (Ig)-like domain of the aggrecan-like chondroitin sulfate proteoglycan core proteins (CSPGs). Included in this group are the Ig domains of other CSPGs: versican, and neurocan. In CSPGs, this Ig-like domain is followed by hyaluronan (HA)-binding tandem repeats, and a C-terminal region with epidermal growth factor-like, lectin-like, and complement regulatory protein-like domains. Separating these N- and C-terminal regions is a nonhomologous glycosaminoglycan attachment region. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggrecan and versican have a wide distribution in connective tissue and extracellular matrices. Neurocan is localized almost exclusively in nervous tissue. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes. 125 matched cddid_all.tbl CDD cd05879 cd05879 409463 IgV_P0 Immunoglobulin (Ig)-like domain of protein zero (P0). The members here are composed of the immunoglobulin (Ig) domain of protein zero (P0), a myelin membrane adhesion molecule. P0 accounts for over 50% of the total protein in peripheral nervous system (PNS) myelin. P0 is a single-pass transmembrane glycoprotein with a highly basic intracellular domain and an Ig domain. The extracellular domain of P0 (P0-ED) is similar to the Ig variable domain, carrying one acceptor sequence for N-linked glycosylation. P0 plays a role in membrane adhesion in the spiral wraps of the myelin sheath. The intracellular domain is thought to mediate membrane apposition of the cytoplasmic faces and may, through electrostatic interactions, interact directly with lipid headgroups. It is thought that homophilic interactions of the P0 extracellular domain mediate membrane juxtaposition in the extracellular space of PNS myelin. 117 matched cddid_all.tbl CDD cd05880 cd05880 409464 IgV_EVA1 Immunoglobulin (Ig)-like domain of epithelial V-like antigen (EVA) 1. The members here are composed of the immunoglobulin (Ig) domain of epithelial V-like antigen 1 (EVA 1). EVA is also known as myelin protein zero-like 2. EVA is an adhesion molecule and may play a role in the structural organization of the thymus and early lymphocyte development. 116 matched cddid_all.tbl CDD cd05881 cd05881 409465 IgV_1_Necl-2 First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule 2; member of the V-set of Ig superfamily (IgSF) domains. The members here are composed of the N-terminal immunoglobulin (Ig)-like domain of nectin-like molecule-2, Necl-2 (also known as cell adhesion molecule 1 (CADM1), SynCAM1, IGSF4A, Tslc1, sgIGSF, and RA175). Nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 - Necl-5). They all have an extracellular region containing three Ig-like domains, a transmembrane region, and a cytoplasmic region. The N-terminal Ig-like domain of the extracellular region, belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-2 has Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-2 is expressed in a wide variety of tissues and is a putative tumour suppressor gene, which is downregulated in aggressive neuroblastoma. 94 matched cddid_all.tbl CDD cd05882 cd05882 143290 IgV_1_Necl-1 First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule-1 (Necl-1); member of the V-set of Ig superfamily (IgSF) domains. The members here are composed of the N-terminal immunoglobulin (Ig)-like domain of nectin-like molecule-1, Necl-1 (also known as celll adhesion molecule 3 (CADM3), SynCAM2, or IGSF4). Nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 - Necl-5). They all have an extracellular region containing three Ig-like domains, a transmembrane region, and a cytoplasmic region. The N-terminal Ig-like domain of the extracellular region belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-1 has Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-1 is specifically expressed in neural tissue and is important to the formation of synapses, axon bundles, and myelinated axons. 95 matched cddid_all.tbl CDD cd05883 cd05883 409466 IgI_2_Necl-2 Second immunoglobulin (Ig)-like domain of nectin-like molecule 2 (Necl-2); member of the I-set of Ig superfamily domains. The members here are composed of the second immunoglobulin (Ig)-like domain of nectin-like molecule 2 (Necl-2; also known as cell adhesion molecule 1 (CADM1)). Nectin-like molecules (Necls) have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 through Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one cytoplasmic region. Necl-2 has Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-1 is expressed in a wide variety of tissues and is a putative tumour suppressor gene which is downregulated in aggressive neuroblastoma. Ig domains are likely to participate in ligand binding and recognition. 99 matched cddid_all.tbl CDD cd05884 cd05884 409467 IgI_2_Necl-3 Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3); member of the I-set of Ig superfamily domains. The members here are composed of the second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3; also known as cell adhesion molecule 2 (CADM2)). Nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 through Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one cytoplasmic region. Necl-3 has been shown to accumulate in tissues of the central and peripheral nervous system where it is expressed in ependymal cells and myelinated axons. It is observed at the interface between the axon shaft and the myelin sheath. Ig domains are likely to participate in ligand binding and recognition. 104 matched cddid_all.tbl CDD cd05885 cd05885 409468 IgI_2_Necl-4 Second immunoglobulin (Ig)-like domain of nectin-like molecule-4 (Necl-4); member of the I-set of Ig superfamily domains. The members here are composed of the second immunoglobulin (Ig)-like domain of nectin-like molecule-4 (Necl-4; also known as cell adhesion molecule 4 (CADM4)). Nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1-Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one cytoplasmic region. Ig domains are likely to participate in ligand binding and recognition. Necl-4 is expressed on Schwann cells, and plays a key part in initiating peripheral nervous system (PNS) myelination. In injured peripheral nerve cells, the mRNA signal for both Necl-4 and Necl-5 was observed to be elevated. Necl-4 participates in cell-cell adhesion and is proposed to play a role in tumor suppression. 100 matched cddid_all.tbl CDD cd05886 cd05886 409469 IgV_1_Nectin-1_like First immunoglobulin variable (IgV) domain of nectin-1, and similar domains. The members here are composed of the first immunoglobulin (Ig) domain of nectin-1 (also known as poliovirus receptor related protein 1 (PVRL1) or cluster of differentiation (CD) 111). Nectin-1 belongs to the nectin family comprised of four transmembrane glycoproteins (nectins-1 through -4). Nectins are synaptic cell adhesion molecules (CAMs) which facilitate adhesion and signaling at various intracellular junctions. Nectins form homophilic cis-dimers, followed by homophilic and heterophilic trans-dimers involved in cell-cell adhesion. In addition nectins heterophilically trans-interact with other CAMs such as nectin-like molecules (Necls), nectin-1 for example, has been shown to trans-interact with Necl-1. Nectins also interact with various other proteins, including the actin filament (F-actin)-binding protein, afadin. Mutation in the human nectin-1 gene is associated with cleft lip/palate ectodermal dysplasia syndrome (CLPED1). Nectin-1 is a major receptor for herpes simplex virus through interaction with the viral envelope glycoprotein D. 113 matched cddid_all.tbl CDD cd05887 cd05887 409470 IgV_1_Nectin-3_like First immunoglobulin variable (IgV) domain of nectin-3 (also known as poliovirus receptor related protein 3), and similar domains. The members here are composed of the first immunoglobulin (Ig) domain of nectin-3 (also known as poliovirus receptor related protein 3 (PVRL3) or cluster of differentiation (CD) 113). Nectin-3 belongs to the nectin family comprised of four transmembrane glycoproteins (nectins-1 through -4). Nectins are synaptic cell adhesion molecules (CAMs) which participate in adhesion and signaling at various intracellular junctions. Nectins form homophilic cis-dimers, followed by homophilic and heterophilic trans-dimers involved in cell-cell adhesion. For example, during spermatid development, the nectin-3,-2 trans-interaction is required for the formation of Sertoli cell-spermatid junctions in testis, and during morphogenesis of the ciliary body, the nectin-3,-1 trans-interaction is important for apex-apex adhesion between the pigment and non-pigment layers of the ciliary epithelia. Nectins also heterophilically trans-interact with other CAMs such as nectin-like molecules (Necls); nectin-3 for example, trans-interacts with Necl-5, regulating cell movement and proliferation. Other proteins with which nectin-3 interacts include the actin filament-binding protein, afadin, integrin alpha-beta3, Par-3, and PDGF receptor; its interaction with PDGF receptor regulates the latter's signaling for anti-apoptosis. 110 matched cddid_all.tbl CDD cd05888 cd05888 409471 IgV_1_Nectin-4_like First immunoglobulin (Ig) domain of nectin-4, and similar domains. The members here are composed of the first immunoglobulin (Ig) domain of nectin-4 (also known as poliovirus receptor related protein 4 or LNIR receptor). Nectin-4 belongs to the nectin family, which is comprised of four transmembrane glycoproteins (nectins-1 through -4). Nectins are synaptic cell adhesion molecules (CAMs) which participate in adhesion and signaling at various intracellular junctions. Nectins form homophilic cis-dimers, followed by homophilic and heterophilic trans-dimers involved in cell-cell adhesion. For example nectin-4 trans-interacts with nectin-1. Nectin-4 has also been shown to interact with the actin filament-binding protein, afadin. Unlike the other nectins, which are widely expressed in adult tissues, nectin-4 is mainly expressed during embryogenesis, and is not detected in normal adult tissue or in serum. Nectin-4 is re-expressed in breast carcinoma, and patients having metastatic breast cancer have a circulating form of nectin-4 formed from the ectodomain 108 matched cddid_all.tbl CDD cd05889 cd05889 409472 IgV_1_DNAM-1_like First immunoglobulin variable (IgV) domain of DNAX accessory molecule 1, and similar domains. The members here are composed of the first immunoglobulin (Ig) domain of DNAX accessory molecule 1 (DNAM-1, also known as CD226). DNAM-1 is a transmembrane protein having two Ig-like domains. It is an adhesion molecule which plays a part in tumor-directed cytotoxicity and adhesion in natural killer (NK) cells and T lymphocytes. It has been shown to regulate the NK cell killing of several tumor types, including myeloma cells and ovarian carcinoma cells. DNAM-1 interacts specifically with poliovirus receptor (PVR; CD155) and nectin -2 (CD211), other members of the Ig superfamily. DNAM-1 is expressed in most peripheral T cells, NK cells, monocytes and a subset of B lymphocytes. 111 matched cddid_all.tbl CDD cd05890 cd05890 143298 IgC1_2_Nectin-1_like Second immunoglobulin (Ig) domain of nectin-1, and similar domains; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the second immunoglobulin (Ig) domain of nectin-1 (also known as poliovirus receptor related protein 1, or cluster of differentiation (CD) 111). Nectin-1 belongs to the nectin family comprised of four transmembrane glycoproteins (nectin-1 through -4). Nectins are synaptic cell adhesion molecules (CAMs) which facilitate adhesion and signaling at various intracellular junctions. Nectins form homophilic cis-dimers, followed by homophilic and heterophilic trans-dimers involved in cell-cell adhesion. Nectins also heterophilically trans-interact with other CAMs such as nectin-like molecules (Necls); nectin-1 for example, has been shown to trans-interact with Necl-1. Nectins also interact with various other proteins, including the actin filament (F-actin)-binding protein, afadin. Mutation in the human nectin-1 gene is associated with cleft lip/palate ectodermal dysplasia syndrome (CLPED1). Nectin-1 is a major receptor for herpes simplex virus through interaction with the viral envelope glycoprotein D. 98 matched cddid_all.tbl CDD cd05891 cd05891 143299 IgI_M-protein_C C-terminal immunoglobulin (Ig)-like domain of M-protein; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the C-terminal immunoglobulin (Ig)-like domain of M-protein (also known as myomesin-2). M-protein is a structural protein localized to the M-band, a transverse structure in the center of the sarcomere, and is a candidate for M-band bridges. M-protein is modular consisting mainly of repetitive IG-like and fibronectin type III (FnIII) domains and has a muscle-type specific expression pattern. M-protein is present in fast fibers. 92 matched cddid_all.tbl CDD cd05892 cd05892 409473 IgI_Myotilin_C "C-terminal immunoglobulin (Ig)-like domain of myotilin; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the C-terminal immunoglobulin (Ig)-like domain of myotilin. Mytolin belongs to the palladin-myotilin-myopalladin family. Proteins belonging to the latter family contain multiple Ig-like domains and function as scaffolds, modulating the actin cytoskeleton. Myotilin is most abundant in skeletal and cardiac muscle and is involved in maintaining sarcomere integrity. It binds to alpha-actinin, filamin, and actin. Mutations in myotilin lead to muscle disorders. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 92 matched cddid_all.tbl CDD cd05893 cd05893 409474 IgI_1_Palladin_C "First C-terminal immunoglobulin (Ig)-like domain of palladin; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the C-terminal immunoglobulin (Ig)-like domain of palladin. Palladin belongs to the palladin-myotilin-myopalladin family. Proteins belonging to this family contain multiple Ig-like domains and function as scaffolds, modulating actin cytoskeleton. Palladin binds to alpha-actinin ezrin, vasodilator-stimulated phosphoprotein VASP, SPIN90 (also known as DIP or mDia interacting protein), and Src. Palladin also binds F-actin directly, via its Ig3 domain. Palladin is expressed as several alternatively spliced isoforms, having various combinations of Ig-like domains, in a cell-type-specific manner. It has been suggested that palladin's different Ig-like domains may be specialized for distinct functions. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 92 matched cddid_all.tbl CDD cd05894 cd05894 409475 Ig_C5_MyBP-C C5 immunoglobulin (Ig) domain of cardiac myosin binding protein C (MyBP-C). The members here are composed of the C5 immunoglobulin (Ig) domain of cardiac myosin binding protein C (MyBP-C). MyBP-C consists of repeated domains, Ig and fibronectin type 3, and various linkers. Three isoforms of MYBP-C exist: slow-skeletal (ssMyBP-C), fast-skeletal (fsMyBP-C), and cardiac (cMyBP-C). cMYBP-C has insertions between and inside domains and an additional cardiac-specific Ig domain at the N-terminus. For cMYBP_C an interaction has been demonstrated between this C5 domain and the Ig C8 domain. 86 matched cddid_all.tbl CDD cd05895 cd05895 409476 Ig_Pro_neuregulin-1 Immunoglobulin (Ig)-like domain found in neuregulin (NRG)-1. The members here are composed of the immunoglobulin (Ig)-like domain found in neuregulin (NRG)-1. There are many NRG-1 isoforms which arise from the alternative splicing of mRNA. NRG-1 belongs to the neuregulin gene family which is comprised of four genes. This group represents NRG-1. NRGs are signaling molecules which participate in cell-cell interactions in the nervous system, breast, and heart, and other organ systems, and are implicated in the pathology of diseases including schizophrenia, multiple sclerosis, and breast cancer. The NRG-1 protein binds to and activates the tyrosine kinases receptors ErbB3 and ErbB4, initiating signaling cascades. NRG-1 has multiple functions, for example, in the brain it regulates various processes such as radial glia formation and neuronal migration, dendritic development, and expression of neurotransmitters receptors in the peripheral nervous system NRG-1 regulates processes such as target cell differentiation, and Schwann cell survival. 93 matched cddid_all.tbl CDD cd05896 cd05896 409477 Ig1_IL1RAPL-1_like First immunoglobulin (Ig)-like domain of X-linked interleukin-1 receptor accessory protein-like 1 (IL1RAPL-1), and similar domains. The members here are composed of the first immunoglobulin (Ig)-like domain of X-linked interleukin-1 receptor accessory protein-like 1 (IL1RAPL-1). IL-1 alpha and IL-1 beta are cytokines which participate in the regulation of inflammation, immune responses, and hematopoiesis. These cytokines bind to the IL-1 receptor type 1 (IL1R1), which is activated on additional association with interleukin-1 receptor accessory protein (IL1RAP). IL-1 also binds a second receptor designated type II (IL1R2). Mature IL1R1 consists of three Ig-like domains, a transmembrane domain, and a large cytoplasmic domain. Mature IL1R2 is organized similarly except that it has a short cytoplasmic domain. The latter does not initiate signal transduction. A naturally occurring cytokine IL-1RA (IL-1 receptor antagonist) is widely expressed and binds to IL-1 receptors, inhibiting the binding of IL-1 alpha and IL-1 beta. IL1RAPL is encoded by a gene on the X-chromosome, this gene is wholly or partially deleted in multiple cases of non-syndromic intellectual disability. This group also contains IL1RAPL-2 which is also encoded by a gene on the X-chromosome and is a candidate for another non-syndromic intellectual disability loci. 105 matched cddid_all.tbl CDD cd05897 cd05897 409478 Ig2_IL1R2_like Second immunoglobulin (Ig)-like domain of interleukin-1 receptor-2 (IL1R2), and similar domains. The members here are composed of the second immunoglobulin (Ig)-like domain of interleukin-1 receptor-2 (IL1R2). IL-1 alpha and IL-1 beta are cytokines which participate in the regulation of inflammation, immune responses, and hematopoiesis. These cytokines bind to the IL-1 receptor type 1 (IL1R1), which is activated on additional association with interleukin-1 receptor accessory protein (IL1RAP). IL-1 also binds the IL-1 receptor, type II (IL1R2) represented in this group. Mature IL1R2 consists of three IG-like domains, a transmembrane domain, and a short cytoplasmic domain. It lacks the large cytoplasmic domain of mature IL1R1 and does not initiate signal transduction. A naturally occurring cytokine IL-1RA (IL-1 receptor antagonist) is widely expressed and binds to IL-1 receptors, inhibiting the binding of IL-1 alpha and IL-1 beta. 95 matched cddid_all.tbl CDD cd05898 cd05898 409479 IgI_5_KIRREL3 Fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the fifth immunoglobulin (Ig)-like domain of Kirrel (kin of irregular chiasm-like) 3 protein (also known as Neph2). This protein has five Ig-like domains, one transmembrane domain, and a cytoplasmic tail. Included in this group is mammalian Kirrel (Neph1). These proteins contain multiple Ig domains, have properties of cell adhesion molecules, and are important in organ development. Neph1 and 2 may mediate axonal guidance and synapse formation in certain areas of the CNS. In the kidney they participate in the formation of the slit diaphragm. 98 matched cddid_all.tbl CDD cd05899 cd05899 409480 IgV_TCR_beta "Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain. The members here are composed of the immunoglobulin (Ig) variable domain of the beta chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group includes the variable domain of the alpha chain of alpha/beta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize MHC independently of the bound peptide. Members of this group contain standard Ig superfamily V-set AGFCC'C""/DEB domain topology." 110 matched cddid_all.tbl CDD cd05900 cd05900 409481 Ig_Aggrecan Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), aggrecan. The members here are composed of the immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), aggrecan. In CSPGs, the Ig-like domain is followed by hyaluronan (HA)-binding tandem repeats, and a C-terminal region with epidermal growth factor-like, lectin-like, and complement regulatory protein-like domains. Separating these N- and C-terminal regions is a nonhomologous glycosaminoglycan attachment region. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Aggrecan has a wide distribution in connective tissue and extracellular matrices. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes. 123 matched cddid_all.tbl CDD cd05901 cd05901 409482 Ig_Versican Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican. The members here are composed of the immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), versican. In CSPGs, the Ig-like domain is followed by hyaluronan (HA)-binding tandem repeats, and a C-terminal region with epidermal growth factor-like, lectin-like, and complement regulatory protein-like domains. Separating these N- and C-terminal regions is a nonhomologous glycosaminoglycan attachment region. In cartilage, the CSPG aggrecan (not included in this group) forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Like aggrecan, versican has a wide distribution in connective tissue and extracellular matrices. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes. 128 matched cddid_all.tbl CDD cd05902 cd05902 409483 Ig_Neurocan Immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), neurocan. The members here are composed of the immunoglobulin (Ig)-like domain of the chondroitin sulfate proteoglycan core protein (CSPG), neurocan. In CSPGs, the Ig-like domain is followed by hyaluronan (HA)-binding tandem repeats, and a C-terminal region with epidermal growth factor-like, lectin-like, and complement regulatory protein-like domains. Separating these N- and C-terminal regions is a nonhomologous glycosaminoglycan attachment region. In cartilage, the CSPG aggrecan (not included in this group) forms cartilage link protein stabilized aggregates with HA. These aggregates contribute to the tissue's load bearing properties. Unlike aggrecan which is widely distributed in connective tissue and extracellular matrices, neurocan is localized almost exclusively in nervous tissue. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes. 121 matched cddid_all.tbl CDD cd05903 cd05903 341229 CHC_CoA_lg Cyclohexanecarboxylate-CoA ligase (also called cyclohex-1-ene-1-carboxylate:CoA ligase). Cyclohexanecarboxylate-CoA ligase activates the aliphatic ring compound, cyclohexanecarboxylate, for degradation. It catalyzes the synthesis of cyclohexanecarboxylate-CoA thioesters in a two-step reaction involving the formation of cyclohexanecarboxylate-AMP anhydride, followed by the nucleophilic substitution of AMP by CoA. 437 matched cddid_all.tbl CDD cd05904 cd05904 341230 4CL 4-Coumarate-CoA Ligase (4CL). 4-Coumarate:coenzyme A ligase is a key enzyme in the phenylpropanoid metabolic pathway for monolignol and flavonoid biosynthesis. It catalyzes the synthesis of hydroxycinnamate-CoA thioesters in a two-step reaction, involving the formation of hydroxycinnamate-AMP anhydride and the nucleophilic substitution of AMP by CoA. The phenylpropanoid pathway is one of the most important secondary metabolism pathways in plants and hydroxycinnamate-CoA thioesters are the precursors of lignin and other important phenylpropanoids. 505 matched cddid_all.tbl CDD cd05905 cd05905 341231 Dip2 Disco-interacting protein 2 (Dip2). Dip2 proteins show sequence similarity to other members of the adenylate forming enzyme family, including insect luciferase, acetyl CoA ligases and the adenylation domain of nonribosomal peptide synthetases (NRPS). However, its function may have diverged from other members of the superfamily. In mouse embryo, Dip2 homolog A plays an important role in the development of both vertebrate and invertebrate nervous systems. Dip2A appears to regulate cell growth and the arrangement of cells in organs. Biochemically, Dip2A functions as a receptor of FSTL1, an extracellular glycoprotein, and may play a role as a cardiovascular protective agent. 571 matched cddid_all.tbl CDD cd05906 cd05906 341232 A_NRPS_TubE_like The adenylation domain (A domain) of a family of nonribosomal peptide synthetases (NRPSs) synthesizing toxins and antitumor agents. The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino)-acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. This family includes NRPSs that synthesize toxins and antitumor agents; for example, TubE for Tubulysine, CrpA for cryptophycin, TdiA for terrequinone A, KtzG for kutzneride, and Vlm1/Vlm2 for Valinomycin. Nonribosomal peptide synthetases are large multifunctional enzymes which synthesize many therapeutically useful peptides. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and, in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. 540 matched cddid_all.tbl CDD cd05907 cd05907 341233 VL_LC_FACS_like "Long-chain fatty acid CoA synthetases and Bubblegum-like very long-chain fatty acid CoA synthetases. This family includes long-chain fatty acid (C12-C20) CoA synthetases and Bubblegum-like very long-chain (>C20) fatty acid CoA synthetases. FACS catalyzes the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, and the formation of a fatty acyl-CoA. Eukaryotes generally have multiple isoforms of LC-FACS genes with multiple splice variants. For example, nine genes are found in Arabidopsis and six genes are expressed in mammalian cells. Drosophila melanogaster mutant bubblegum (BGM) have elevated levels of very-long-chain fatty acids (VLCFA) caused by a defective gene later named bubblegum. The human homolog (hsBG) of bubblegum has been characterized as a very long chain fatty acid CoA synthetase that functions specifically in the brain; hsBG may play a central role in brain VLCFA metabolism and myelinogenesis. Free fatty acids must be ""activated"" to their CoA thioesters before participating in most catabolic and anabolic reactions." 452 matched cddid_all.tbl CDD cd05908 cd05908 341234 A_NRPS_MycA_like The adenylation domain of nonribosomal peptide synthetases (NRPS) similar to mycosubtilin synthase subunit A (MycA). The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as (amino)-acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. This family includes NRPS similar to mycosubtilin synthase subunit A (MycA). Mycosubtilin, which is characterized by a beta-amino fatty acid moiety linked to the circular heptapeptide Asn-Tyr-Asn-Gln-Pro-Ser-Asn, belongs to the iturin family of lipopeptide antibiotics. The mycosubtilin synthase subunit A (MycA) combines functional domains derived from peptide synthetases, amino transferases, and fatty acid synthases. Nonribosomal peptide synthetases are large multifunction enzymes that synthesize many therapeutically useful peptides. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and, in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. 499 matched cddid_all.tbl CDD cd05909 cd05909 341235 AAS_C C-terminal domain of the acyl-acyl carrier protein synthetase (also called 2-acylglycerophosphoethanolamine acyltransferase, Aas). Acyl-acyl carrier protein synthase (Aas) is a membrane protein responsible for a minor pathway of incorporating exogenous fatty acids into membrane phospholipids. Its in vitro activity is characterized by the ligation of free fatty acids between 8 and 18 carbons in length to the acyl carrier protein sulfydryl group (ACP-SH) in the presence of ATP and Mg2+. However, its in vivo function is as a 2-acylglycerophosphoethanolamine (2-acyl-GPE) acyltransferase. The reaction occurs in two steps: the acyl chain is first esterified to acyl carrier protein (ACP) via a thioester bond, followed by a second step where the acyl chain is transferred to a 2-acyllysophospholipid, thus completing the transacylation reaction. This model represents the C-terminal domain of the enzyme, which belongs to the class I adenylate-forming enzyme family, including acyl-CoA synthetases. 490 matched cddid_all.tbl CDD cd05910 cd05910 341236 FACL_like_1 Uncharacterized subfamily of fatty acid CoA ligase (FACL). Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. 457 matched cddid_all.tbl CDD cd05911 cd05911 341237 Firefly_Luc_like Firefly luciferase of light emitting insects and 4-Coumarate-CoA Ligase (4CL). This family contains insect firefly luciferases that share significant sequence similarity to plant 4-coumarate:coenzyme A ligases, despite their functional diversity. Luciferase catalyzes the production of light in the presence of MgATP, molecular oxygen, and luciferin. In the first step, luciferin is activated by acylation of its carboxylate group with ATP, resulting in an enzyme-bound luciferyl adenylate. In the second step, luciferyl adenylate reacts with molecular oxygen, producing an enzyme-bound excited state product (Luc=O*) and releasing AMP. This excited-state product then decays to the ground state (Luc=O), emitting a quantum of visible light. 486 matched cddid_all.tbl CDD cd05912 cd05912 341238 OSB_CoA_lg O-succinylbenzoate-CoA ligase (also known as O-succinylbenzoate-CoA synthase, OSB-CoA synthetase, or MenE). O-succinylbenzoic acid-CoA synthase catalyzes the coenzyme A (CoA)- and ATP-dependent conversion of o-succinylbenzoic acid to o-succinylbenzoyl-CoA. The reaction is the fourth step of the biosynthesis pathway of menaquinone (vitamin K2). In certain bacteria, menaquinone is used during fumarate reduction in anaerobic respiration. In cyanobacteria, the product of the menaquinone pathway is phylloquinone (2-methyl-3-phytyl-1,4-naphthoquinone), a molecule used exclusively as an electron transfer cofactor in Photosystem 1. In green sulfur bacteria and heliobacteria, menaquinones are used as loosely bound secondary electron acceptors in the photosynthetic reaction center. 411 matched cddid_all.tbl CDD cd05913 cd05913 341239 PaaK Phenylacetate-CoA ligase (also known as PaaK). PaaK catalyzes the first step in the aromatic degradation pathway, by converting phenylacetic acid (PA) into phenylacetyl-CoA (PA-CoA). Phenylacetate-CoA ligase has been found in proteobacteria as well as gram positive prokaryotes. The enzyme is specifically induced after aerobic growth in a chemically defined medium containing PA or phenylalanine (Phe) as the sole carbon source. PaaKs are members of the adenylate-forming enzyme (AFE) family. However, sequence comparison reveals divergent features of PaaK with respect to the superfamily, including a novel N-terminal sequence. 425 matched cddid_all.tbl CDD cd05914 cd05914 341240 LC_FACL_like "Uncharacterized subfamily of fatty acid CoA ligase (FACL). The members of this family are bacterial long-chain fatty acid CoA synthetase, most of which are as yet uncharacterized. LC-FACS catalyzes the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, and the formation of a fatty acyl-CoA. Free fatty acids must be ""activated"" to their CoA thioesters before participating in most catabolic and anabolic reactions." 463 matched cddid_all.tbl CDD cd05915 cd05915 213283 ttLC_FACS_like Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles. This family includes fatty acyl-CoA synthetases that can activate medium-chain to long-chain fatty acids. They catalyze the ATP-dependent acylation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. Fatty acyl-CoA synthetases are responsible for fatty acid degradation as well as physiological regulation of cellular functions via the production of fatty acyl-CoA esters. The fatty acyl-CoA synthetase from Thermus thermophiles in this family has been shown to catalyze the long-chain fatty acid, myristoyl acid, while another member in this family, the AlkK protein identified in Pseudomonas oleovorans, targets medium chain fatty acids. This family also includes an uncharacterized subgroup of FACS. 509 matched cddid_all.tbl CDD cd05917 cd05917 341241 FACL_like_2 Uncharacterized subfamily of fatty acid CoA ligase (FACL). Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. 349 matched cddid_all.tbl CDD cd05918 cd05918 341242 A_NRPS_SidN3_like The adenylation (A) domain of siderophore-synthesizing nonribosomal peptide synthetases (NRPS). The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. This family of siderophore-synthesizing NRPS includes the third adenylation domain of SidN from the endophytic fungus Neotyphodium lolii, ferrichrome siderophore synthetase, HC-toxin synthetase, and enniatin synthase. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. 481 matched cddid_all.tbl CDD cd05919 cd05919 341243 BCL_like Benzoate CoA ligase (BCL) and similar adenylate forming enzymes. This family contains benzoate CoA ligase (BCL) and related ligases that catalyze the acylation of benzoate derivatives, 2-aminobenzoate and 4-hydroxybenzoate. Aromatic compounds represent the second most abundant class of organic carbon compounds after carbohydrates. Xenobiotic aromatic compounds are also a major class of man-made pollutants. Some bacteria use benzoate as the sole source of carbon and energy through benzoate degradation. Benzoate degradation starts with its activation to benzoyl-CoA by benzoate CoA ligase. The reaction catalyzed by benzoate CoA ligase proceeds via a two-step process; the first ATP-dependent step forms an acyl-AMP intermediate, and the second step forms the acyl-CoA ester with release of the AMP. 436 matched cddid_all.tbl CDD cd05920 cd05920 341244 23DHB-AMP_lg 2,3-dihydroxybenzoate-AMP ligase. 2,3-dihydroxybenzoate-AMP ligase activates 2,3-dihydroxybenzoate (DHB) by ligation of AMP from ATP with the release of pyrophosphate. However, it can also catalyze the ATP-PPi exchange for 2,3-DHB analogs, such as salicyclic acid (o-hydrobenzoate), as well as 2,4-DHB and 2,5-DHB, but with less efficiency. Proteins in this family are the stand-alone adenylation components of non-ribosomal peptide synthases (NRPSs) involved in the biosynthesis of siderophores, which are low molecular weight iron-chelating compounds synthesized by many bacteria to aid in the acquisition of this vital trace elements. In Escherichia coli, the 2,3-dihydroxybenzoate-AMP ligase is called EntE, the adenylation component of the enterobactin NRPS system. 482 matched cddid_all.tbl CDD cd05921 cd05921 341245 FCS Feruloyl-CoA synthetase (FCS). Feruloyl-CoA synthetase is an essential enzyme in the feruloyl acid degradation pathway and enables some proteobacteria to grow on media containing feruloyl acid as the sole carbon source. It catalyzes the transfer of CoA to the carboxyl group of ferulic acid, which then forms feruloyl-CoA in the presence of ATP and Mg2. The resulting feruloyl-CoA is further degraded to vanillin and acetyl-CoA. Feruloyl-CoA synthetase (FCS) is a subfamily of the adenylate-forming enzymes superfamily. 561 matched cddid_all.tbl CDD cd05922 cd05922 341246 FACL_like_6 Uncharacterized subfamily of fatty acid CoA ligase (FACL). Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. 457 matched cddid_all.tbl CDD cd05923 cd05923 341247 CBAL 4-Chlorobenzoate-CoA ligase (CBAL). CBAL catalyzes the conversion of 4-chlorobenzoate (4-CB) to 4-chlorobenzoyl-coenzyme A (4-CB-CoA) by the two-step adenylation and thioester-forming reactions. 4-Chlorobenzoate (4-CBA) is an environmental pollutant derived from microbial breakdown of aromatic pollutants, such as polychlorinated biphenyls (PCBs), DDT, and certain herbicides. The 4-CBA degrading pathway converts 4-CBA to the metabolite 4-hydroxybezoate (4-HBA), allowing some soil-dwelling microbes to utilize 4-CBA as an alternate carbon source. This pathway consists of three chemical steps catalyzed by 4-CBA-CoA ligase, 4-CBA-CoA dehalogenase, and 4HBA-CoA thioesterase in sequential reactions. 493 matched cddid_all.tbl CDD cd05924 cd05924 341248 FACL_like_5 Uncharacterized subfamily of fatty acid CoA ligase (FACL). Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. 364 matched cddid_all.tbl CDD cd05926 cd05926 341249 FACL_fum10p_like Subfamily of fatty acid CoA ligase (FACL) similar to Fum10p of Gibberella moniliformis. FACL catalyzes the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, followed by the formation of a fatty acyl-CoA. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. Fum10p is a fatty acid CoA ligase involved in the synthesis of fumonisin, a polyketide mycotoxin, in Gibberella moniliformis. 493 matched cddid_all.tbl CDD cd05927 cd05927 341250 LC-FACS_euk Eukaryotic long-chain fatty acid CoA synthetase (LC-FACS). The members of this family are eukaryotic fatty acid CoA synthetases that activate fatty acids with chain lengths of 12 to 20. LC-FACS catalyzes the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, and the formation of a fatty acyl-CoA. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. Organisms tend to have multiple isoforms of LC-FACS genes with multiple splice variants. For example, nine genes are found in Arabidopsis and six genes are expressed in mammalian cells. 545 matched cddid_all.tbl CDD cd05928 cd05928 341251 MACS_euk Eukaryotic Medium-chain acyl-CoA synthetase (MACS or ACSM). MACS catalyzes the two-step activation of medium chain fatty acids (containing 4-12 carbons). The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. The acyl-CoA is a key intermediate in many important biosynthetic and catabolic processes. MACS enzymes are localized to mitochondria. Two murine MACS family proteins are found in liver and kidney. In rodents, a MACS member is detected particularly in the olfactory epithelium and is called O-MACS. O-MACS demonstrates substrate preference for the fatty acid lengths of C6-C12. 530 matched cddid_all.tbl CDD cd05929 cd05929 341252 BACL_like Bacterial Bile acid CoA ligases and similar proteins. Bile acid-Coenzyme A ligase catalyzes the formation of bile acid-CoA conjugates in a two-step reaction: the formation of a bile acid-AMP molecule as an intermediate, followed by the formation of a bile acid-CoA. This ligase requires a bile acid with a free carboxyl group, ATP, Mg2+, and CoA for synthesis of the final bile acid-CoA conjugate. The bile acid-CoA ligation is believed to be the initial step in the bile acid 7alpha-dehydroxylation pathway in the intestinal bacterium Eubacterium sp. 473 matched cddid_all.tbl CDD cd05930 cd05930 341253 A_NRPS The adenylation domain of nonribosomal peptide synthetases (NRPS). The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester bond to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. 444 matched cddid_all.tbl CDD cd05931 cd05931 341254 FAAL Fatty acyl-AMP ligase (FAAL). FAAL belongs to the class I adenylate forming enzyme family and is homologous to fatty acyl-coenzyme A (CoA) ligases (FACLs). However, FAALs produce only the acyl adenylate and are unable to perform the thioester-forming reaction, while FACLs perform a two-step catalytic reaction; AMP ligation followed by CoA ligation using ATP and CoA as cofactors. FAALs have insertion motifs between the N-terminal and C-terminal subdomains that distinguish them from the FACLs. This insertion motif precludes the binding of CoA, thus preventing CoA ligation. It has been suggested that the acyl adenylates serve as substrates for multifunctional polyketide synthases to permit synthesis of complex lipids such as phthiocerol dimycocerosate, sulfolipids, mycolic acids, and mycobactin. 547 matched cddid_all.tbl CDD cd05932 cd05932 341255 LC_FACS_bac "Bacterial long-chain fatty acid CoA synthetase (LC-FACS), including Marinobacter hydrocarbonoclasticus isoprenoid Coenzyme A synthetase. The members of this family are bacterial long-chain fatty acid CoA synthetase. Marinobacter hydrocarbonoclasticus isoprenoid Coenzyme A synthetase in this family is involved in the synthesis of isoprenoid wax ester storage compounds when grown on phytol as the sole carbon source. LC-FACS catalyzes the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, and the formation of a fatty acyl-CoA. Free fatty acids must be ""activated"" to their CoA thioesters before participating in most catabolic and anabolic reactions." 508 matched cddid_all.tbl CDD cd05933 cd05933 341256 ACSBG_like "Bubblegum-like very long-chain fatty acid CoA synthetase (VL-FACS). This family of very long-chain fatty acid CoA synthetase is named bubblegum because Drosophila melanogaster mutant bubblegum (BGM) has elevated levels of very-long-chain fatty acids (VLCFA) caused by a defective gene of this family. The human homolog (hsBG) has been characterized as a very long chain fatty acid CoA synthetase that functions specifically in the brain; hsBG may play a central role in brain VLCFA metabolism and myelinogenesis. VL-FACS is involved in the first reaction step of very long chain fatty acid degradation. It catalyzes the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, and the formation of a fatty acyl-CoA. Free fatty acids must be ""activated"" to their CoA thioesters before participating in most catabolic and anabolic reactions." 596 matched cddid_all.tbl CDD cd05934 cd05934 341257 FACL_DitJ_like Uncharacterized subfamily of fatty acid CoA ligase (FACL). Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. Members of this family include DitJ from Pseudomonas and similar proteins. 422 matched cddid_all.tbl CDD cd05935 cd05935 341258 LC_FACS_like Putative long-chain fatty acid CoA ligase. The members of this family are putative long-chain fatty acyl-CoA synthetases, which catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. Fatty acyl-CoA synthetases are responsible for fatty acid degradation as well as physiological regulation of cellular functions via the production of fatty acyl-CoA esters. 430 matched cddid_all.tbl CDD cd05936 cd05936 341259 FC-FACS_FadD_like Prokaryotic long-chain fatty acid CoA synthetases similar to Escherichia coli FadD. This subfamily of the AMP-forming adenylation family contains Escherichia coli FadD and similar prokaryotic fatty acid CoA synthetases. FadD was characterized as a long-chain fatty acid CoA synthetase. The gene fadD is regulated by the fatty acid regulatory protein FadR. Fatty acid CoA synthetase catalyzes the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, followed by the formation of a fatty acyl-CoA. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. 468 matched cddid_all.tbl CDD cd05937 cd05937 341260 FATP_chFAT1_like Uncharacterized subfamily of bifunctional fatty acid transporter/very-long-chain acyl-CoA synthetase in fungi. Fatty acid transport protein (FATP) transports long-chain or very-long-chain fatty acids across the plasma membrane. FATPs also have fatty acid CoA synthetase activity, thus playing dual roles as fatty acid transporters and its activation enzymes. FATPs are the key players in the trafficking of exogenous fatty acids into the cell and in intracellular fatty acid homeostasis. Members of this family are fungal FATPs, including FAT1 from Cochliobolus heterostrophus. 468 matched cddid_all.tbl CDD cd05938 cd05938 341261 hsFATP2a_ACSVL_like Fatty acid transport proteins (FATP) including hsFATP2, hsFATP5, and hsFATP6, and similar proteins. Fatty acid transport proteins (FATP) of this family transport long-chain or very-long-chain fatty acids across the plasma membrane. At least five copies of FATPs are identified in mammalian cells. This family includes hsFATP2, hsFATP5, and hsFATP6, and similar proteins. Each FATP has unique patterns of tissue distribution. These FATPs also have fatty acid CoA synthetase activity, thus playing dual roles as fatty acid transporters and its activation enzymes. The hsFATP proteins exist in two splice variants; the b variant, lacking exon 3, has no acyl-CoA synthetase activity. FATPs are key players in the trafficking of exogenous fatty acids into the cell and in intracellular fatty acid homeostasis. 537 matched cddid_all.tbl CDD cd05939 cd05939 341262 hsFATP4_like Fatty acid transport proteins (FATP), including FATP4 and FATP1, and similar proteins. Fatty acid transport protein (FATP) transports long-chain or very-long-chain fatty acids across the plasma membrane. At least five copies of FATPs are identified in mammalian cells. This family includes FATP4, FATP1, and homologous proteins. Each FATP has unique patterns of tissue distribution. FATP4 is mainly expressed in the brain, testis, colon and kidney. FATPs also have fatty acid CoA synthetase activity, thus playing dual roles as fatty acid transporters and its activation enzymes. FATPs are the key players in the trafficking of exogenous fatty acids into the cell and in intracellular fatty acid homeostasis. 474 matched cddid_all.tbl CDD cd05940 cd05940 341263 FATP_FACS Fatty acid transport proteins (FATP) play dual roles as fatty acid transporters and its activation enzymes. Fatty acid transport protein (FATP) transports long-chain or very-long-chain fatty acids across the plasma membrane. FATPs also have fatty acid CoA synthetase activity, thus playing dual roles as fatty acid transporters and its activation enzymes. At least five copies of FATPs are identified in mammalian cells. This family also includes prokaryotic FATPs. FATPs are the key players in the trafficking of exogenous fatty acids into the cell and in intracellular fatty acid homeostasis. 449 matched cddid_all.tbl CDD cd05941 cd05941 341264 MCS Malonyl-CoA synthetase (MCS). MCS catalyzes the formation of malonyl-CoA in a two-step reaction consisting of the adenylation of malonate with ATP, followed by malonyl transfer from malonyl-AMP to CoA. Malonic acid and its derivatives are the building blocks of polyketides and malonyl-CoA serves as the substrate of polyketide synthases. Malonyl-CoA synthetase has broad substrate tolerance and can activate a variety of malonyl acid derivatives. MCS may play an important role in biosynthesis of polyketides, the important secondary metabolites with therapeutic and agrochemical utility. 442 matched cddid_all.tbl CDD cd05943 cd05943 341265 AACS Acetoacetyl-CoA synthetase (acetoacetate-CoA ligase, AACS). AACS is a cytosolic ligase that specifically activates acetoacetate to its coenzyme A ester by a two-step reaction. Acetoacetate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is the first step of the mevalonate pathway of isoprenoid biosynthesis via isopentenyl diphosphate. Isoprenoids are a large class of compounds found in all living organisms. AACS is widely distributed in bacteria, archaea and eukaryotes. In bacteria, AACS is known to exhibit an important role in the metabolism of poly-b-hydroxybutyrate, an intracellular reserve of organic carbon and chemical energy by some microorganisms. In mammals, AACS influences the rate of ketone body utilization for the formation of physiologically important fatty acids and cholesterol. 629 matched cddid_all.tbl CDD cd05944 cd05944 341266 FACL_like_4 Uncharacterized subfamily of fatty acid CoA ligase (FACL). Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. 359 matched cddid_all.tbl CDD cd05945 cd05945 341267 DltA D-alanine:D-alanyl carrier protein ligase (DltA) and similar proteins. This family includes D-alanyl carrier protein ligase DltA and aliphatic beta-amino acid adenylation enzymes IdnL1 and CmiS6. DltA incorporates D-ala in techoic acids in gram-positive bacteria via a two-step process, starting with adenylation of D-alanine that transfers D-alanine to the D-alanyl carrier protein. IdnL1, a short-chain aliphatic beta-amino acid adenylation enzyme, recognizes 3-aminobutanoic acid, and is involved in the synthesis of the macrolactam antibiotic incednine. CmiS6 is a medium-chain beta-amino acid adenylation enzyme that recognizes 3-aminononanoic acid, and is involved in the synthesis of cremimycin, also a macrolactam antibiotic. The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester bond to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. 449 matched cddid_all.tbl CDD cd05958 cd05958 341268 ABCL 2-aminobenzoate-CoA ligase (ABCL). ABCL catalyzes the initial step in the 2-aminobenzoate aerobic degradation pathway by activating 2-aminobenzoate to 2-aminobenzoyl-CoA. The reaction is carried out via a two-step process; the first step is ATP-dependent and forms a 2-aminobenzoyl-AMP intermediate, and the second step forms the 2-aminobenzoyl-CoA ester and releases the AMP. 2-Aminobenzoyl-CoA is further converted to 2-amino-5-oxo-cyclohex-1-ene-1-carbonyl-CoA catalyzed by 2-aminobenzoyl-CoA monooxygenase/reductase. ABCL has been purified from cells aerobically grown with 2-aminobenzoate as sole carbon, energy, and nitrogen source, and has been characterized as a monomer. 439 matched cddid_all.tbl CDD cd05959 cd05959 341269 BCL_4HBCL Benzoate CoA ligase (BCL) and 4-Hydroxybenzoate-Coenzyme A Ligase (4-HBA-CoA ligase). Benzoate CoA ligase and 4-hydroxybenzoate-coenzyme A ligase catalyze the first activating step for benzoate and 4-hydroxybenzoate catabolic pathways, respectively. Although these two enzymes share very high sequence homology, they have their own substrate preference. The reaction proceeds via a two-step process; the first ATP-dependent step forms the substrate-AMP intermediate, while the second step forms the acyl-CoA ester, releasing the AMP. Aromatic compounds represent the second most abundant class of organic carbon compounds after carbohydrates. Some bacteria can use benzoic acid or benzenoid compounds as the sole source of carbon and energy through degradation. Benzoate CoA ligase and 4-hydroxybenzoate-Coenzyme A ligase are key enzymes of this process. 508 matched cddid_all.tbl CDD cd05966 cd05966 341270 ACS Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme). Acetyl-CoA synthetase (ACS, EC 6.2.1.1, acetate#CoA ligase or acetate:CoA ligase (AMP-forming)) catalyzes the formation of acetyl-CoA from acetate, CoA, and ATP. Synthesis of acetyl-CoA is carried out in a two-step reaction. In the first step, the enzyme catalyzes the synthesis of acetyl-AMP intermediate from acetate and ATP. In the second step, acetyl-AMP reacts with CoA to produce acetyl-CoA. This enzyme is widely present in all living organisms. The activity of this enzyme is crucial for maintaining the required levels of acetyl-CoA, a key intermediate in many important biosynthetic and catabolic processes. Acetyl-CoA is used in the biosynthesis of glucose, fatty acids, and cholesterol. It can also be used in the production of energy in the citric acid cycle. Eukaryotes typically have two isoforms of acetyl-CoA synthetase, a cytosolic form involved in biosynthetic processes and a mitochondrial form primarily involved in energy generation. 608 matched cddid_all.tbl CDD cd05967 cd05967 341271 PrpE Propionyl-CoA synthetase (PrpE). EC 6.2.1.17: propanoate:CoA ligase (AMP-forming) or propionate#CoA ligase (PrpE) catalyzes the first step of the 2-methylcitric acid cycle for propionate catabolism. It activates propionate to propionyl-CoA in a two-step reaction, which proceeds through a propionyl-AMP intermediate and requires ATP and Mg2+. In Salmonella enterica, the PrpE protein is required for growth of Salmonella enterica on propionate and can substitute for the acetyl-CoA synthetase (Acs) enzyme during growth on acetate. PrpE can also activate acetate, 3HP, and butyrate to their corresponding CoA-thioesters, although with less efficiency. 617 matched cddid_all.tbl CDD cd05968 cd05968 341272 AACS_like Uncharacterized acyl-CoA synthetase subfamily similar to Acetoacetyl-CoA synthetase. This uncharacterized acyl-CoA synthetase family (EC 6.2.1.16, or acetoacetate#CoA ligase or acetoacetate:CoA ligase (AMP-forming)) is highly homologous to acetoacetyl-CoA synthetase. However, the proteins in this family exist in only bacteria and archaea. AACS is a cytosolic ligase that specifically activates acetoacetate to its coenzyme A ester by a two-step reaction. Acetoacetate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is the first step of the mevalonate pathway of isoprenoid biosynthesis via isopentenyl diphosphate. Isoprenoids are a large class of compounds found in all living organisms. 610 matched cddid_all.tbl CDD cd05969 cd05969 341273 MACS_like_4 Uncharacterized subfamily of Acetyl-CoA synthetase like family (ACS). This family is most similar to acetyl-CoA synthetase. Acetyl-CoA synthetase (ACS) catalyzes the formation of acetyl-CoA from acetate, CoA, and ATP. Synthesis of acetyl-CoA is carried out in a two-step reaction. In the first step, the enzyme catalyzes the synthesis of acetyl-AMP intermediate from acetate and ATP. In the second step, acetyl-AMP reacts with CoA to produce acetyl-CoA. This enzyme is only present in bacteria. 442 matched cddid_all.tbl CDD cd05970 cd05970 341274 MACS_AAE_MA_like Medium-chain acyl-CoA synthetase (MACS) of AAE_MA like. MACS catalyzes the two-step activation of medium chain fatty acids (containing 4-12 carbons). The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This family of MACS enzymes is found in archaea and bacteria. It is represented by the acyl-adenylating enzyme from Methanosarcina acetivorans (AAE_MA). AAE_MA is most active with propionate, butyrate, and the branched analogs: 2-methyl-propionate, butyrate, and pentanoate. The specific activity is weaker for smaller or larger acids. 537 matched cddid_all.tbl CDD cd05971 cd05971 341275 MACS_like_3 Uncharacterized subfamily of medium-chain acyl-CoA synthetase (MACS). MACS catalyzes the two-step activation of medium chain fatty acids (containing 4-12 carbons). The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. MACS enzymes are localized to mitochondria. 439 matched cddid_all.tbl CDD cd05972 cd05972 341276 MACS_like Medium-chain acyl-CoA synthetase (MACS or ACSM). MACS catalyzes the two-step activation of medium chain fatty acids (containing 4-12 carbons). The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. The acyl-CoA is a key intermediate in many important biosynthetic and catabolic processes. 428 matched cddid_all.tbl CDD cd05973 cd05973 341277 MACS_like_2 Uncharacterized subfamily of medium-chain acyl-CoA synthetase (MACS). MACS catalyzes the two-step activation of medium chain fatty acids (containing 4-12 carbons). The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. MACS enzymes are localized to mitochondria. 437 matched cddid_all.tbl CDD cd05974 cd05974 341278 MACS_like_1 Uncharacterized subfamily of medium-chain acyl-CoA synthetase (MACS). MACS catalyzes the two-step activation of medium chain fatty acids (containing 4-12 carbons). The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. MACS enzymes are localized to mitochondria. 432 matched cddid_all.tbl CDD cd05992 cd05992 99716 PB1 The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. 81 matched cddid_all.tbl CDD cd06006 cd06006 100076 R3H_unknown_2 R3H domain of a group of fungal proteins with unknown function. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner. 59 matched cddid_all.tbl CDD cd06007 cd06007 100077 R3H_DEXH_helicase R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner. 59 matched cddid_all.tbl CDD cd06008 cd06008 100116 NF-X1-zinc-finger Presumably a zinc binding domain, which has been shown to bind to DNA in the human nuclear transcriptional repressor NF-X1. The zinc finger can be characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The NF-X1 zinc finger co-occurs with atypical RING-finger and R3H domains. Human NF-X1 is involved in the transcriptional repression of major histocompatibility complex class II genes. The drosophila homolog encoded by stc (shuttle craft) plays a role in embryonic development, and the Arabidopsis homologue AtNFXL1 has been shown to function in the response to trichothecene and other defense mechanisms. 49 matched cddid_all.tbl CDD cd06059 cd06059 276963 Tubulin The tubulin superfamily and related homologs. The tubulin superfamily includes five distinct families, the alpha-, beta-, gamma-, delta-, and epsilon-tubulins and a sixth family (zeta-tubulin) which is present only in kinetoplastid protozoa. The alpha- and beta-tubulins are the major components of microtubules, while gamma-tubulin plays a major role in the nucleation of microtubule assembly. The delta- and epsilon-tubulins are widespread but unlike the alpha, beta, and gamma-tubulins they are not ubiquitous among eukaryotes. The alpha/beta-tubulin heterodimer is the structural subunit of microtubules. The alpha- and beta-tubulins share 40% amino-acid sequence identity, exist in several isotype forms, and undergo a variety of posttranslational modifications. The structures of alpha- and beta-tubulin are basically identical: each monomer is formed by a core of two beta-sheets surrounded by alpha-helices. The monomer structure is very compact, but can be divided into three regions based on function: the amino-terminal nucleotide-binding region, an intermediate taxol-binding region and the carboxy-terminal region which probably constitutes the binding surface for motor proteins. Also included in this group is the mitochondrial Misato/DML1 protein family, involved in mitochondrial fusion and in mitochondrial distribution and morphology. 387 matched cddid_all.tbl CDD cd06060 cd06060 276964 misato Misato segment II tubulin-like domain. Human Misato shows similarity with Tubulin/FtsZ family of GTPases and is localized to the the outer membrane of mitochondria. It has a role in mitochondrial fusion and in mitochondrial distribution and morphology. Mutations in its Drosophila homolog (misato) lead to irregular chromosome segregation during mitosis. Deletion of the budding yeast homolog DML1 is lethal and unregulate expression of DML1 leads to mitochondrial dispersion and abnormalities in cell morphology. The Misato/DML1 protein family is conserved from yeast to human, but its exact function is still unknown. 539 matched cddid_all.tbl CDD cd06061 cd06061 100037 PurM-like1 AIR synthase (PurM) related protein, subgroup 1 of unknown function. The family of PurM related proteins includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM synthase and Selenophosphate synthetase (SelD). They all contain two conserved domains and seem to dimerize. The N-terminal domain forms the dimer interface and is a putative ATP binding domain. 298 matched cddid_all.tbl CDD cd06062 cd06062 99873 H2MP_MemB-H2up Endopeptidases belonging to membrane-bound hydrogenases group. These hydrogenases transfer electrons from H2 to a cytochrome that is bound to a membrane-located complex coupling electron transfer to transmembrane proton translocation. Endopeptidase HybD from E. coli is well studied in this group. Maturation of [NiFe] hydrogenases include proteolytic processing of large subunit, assembly with other subunits, and formation of the nickel metallocenter. Hydrogenase maturation endopeptidase (HybD) cleaves a short C-terminal peptide after a His or an Arg residue in the large subunit (pre-HybC) of hydrogenase 2 (hyb operon) in E. coli. This cleavage is nickel dependent. A variety of endopeptidases belong to this group that are similar in function and sequence homology. They include such proteins as HynC, HoxM, and HupD. 146 matched cddid_all.tbl CDD cd06063 cd06063 99874 H2MP_Cyano-H2up This group of endopeptidases include HupW enzymes that are specific to the cyanobacterial hydrogenase and are involved in the C-terminal cleavage of the hydrogenase large subunit precursor protein. Cyanobacterial nickel-iron (NiFe)-hydrogenases are found exclusively in the N2-fixing strains and are encoded by hup (hydrogen uptake) genes. These uptake hydrogenases are heterodimers with a large (hupL) and small subunit (hupS) and catalyze the consumption of the H2 produced during N2 fixation. Sequence similarity shows that the putative metal-binding resides are well conserved in this group of hydrogen maturation proteases. This group also includes such proteins as the hydrogenase III from Aquifex aeolicus. 146 matched cddid_all.tbl CDD cd06064 cd06064 99875 H2MP_F420-Reduc Endopeptidases belonging to F420-reducing hydrogenases group. These hydrogenases from methanogens are encoded by the fru, frc, or frh genes. Sequence comparison indicates that fruD and frcD gene products from Methanococcus voltae are similar to HycI protease of Escherichia coli and are putatively involved in the C-terminal processing of large subunits (FruA and FrcA respectively). FrhD (F420 reducing hydrogenase delta subunit) enzyme belongs to the gene cluster of 8-hydroxy-5-deazaflavin (F420) reducing hydrogenase (FRH) from the thermophilic methanogen Methanobacterium thermoautotrophicum delta H. FrhD subunit is putatively involved in the processing of the coenzyme F420 hydrogenase-processing. It is similar to those frhD genes found in Methanomicrobia and Methanobacteria. It is different from the FrhD conserved domain found in methyl viologen-reducing hydrogenase and F420-non-reducing hydrogenase iron-sulfur subunit D. 150 matched cddid_all.tbl CDD cd06066 cd06066 99876 H2MP_NAD-link-bidir Endopeptidases that belong to the bidirectional NAD-linked hydrogenase group. This group of endopeptidases are highly specific carboxyl-terminal protease (HoxW protease) which releases a 24-amino-acid peptide from HoxH prior to progression of subunit assembly. These bidirectional hydrogenases are heteropentamers encoded by the hox (hydrogen oxidation) genes, in which complex HoxEFU shows the diaphorase activity, and HoxYH constitutes the NiFe-hydrogenase. 139 matched cddid_all.tbl CDD cd06067 cd06067 99877 H2MP_MemB-H2evol Endopeptidases belonging to membrane-bound hydrogen evolving hydrogenase group. In hydrogenase 3 from E coli, the maturation of the large subunit (HycE) requires the cleavage of a C-terminal peptide by the endopeptidase HycI, before the final formation of the [NiFe] metallocenter. HycI protease is a monomer and lacks characteristic signature motifs of serine, zinc, cysteine, or acid proteases and thus its cleavage reaction is not inhibited by conventional inhibitors of serine and metalloproteases. Such hydrogenases as those from Methanosarcina barkeri (EchCE) and Rhodospirillum rubrum (CooLH) also belong to this group of membrane-bound hydrogen evolving hydrogenase. Sequence comparison of the large subunits from related hydrogenase indicates that in contrast to EchE (358 amino acids) and CooH (361 amino acids), the large subunit HycE (569 amino acids) contains an extra carboxy-terminal stretch of 32 amino acids that is cleaved during the maturation process. In the absence of this C-terminal stretch, there is no homolog of endopeptidase HycI found in these two related hydrogenase. 136 matched cddid_all.tbl CDD cd06068 cd06068 99878 H2MP_like-1 Putative [NiFe] hydrogenase-specific C-terminal protease. Sequence comparison shows similarity to hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE (the large subunit of hydrogenases 3). This cleavage is nickel dependent. 144 matched cddid_all.tbl CDD cd06070 cd06070 99879 H2MP_like-2 Putative [NiFe] hydrogenase-specific C-terminal protease. Sequence comparison shows similarity to hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved in processing of HypE (the large subunit of hydrogenases 3). This cleavage is nickel dependent. 140 matched cddid_all.tbl CDD cd06071 cd06071 100117 Beach BEACH (Beige and Chediak-Higashi) domains, implicated in membrane trafficking, are present in a family of proteins conserved throughout eukaryotes. This group contains human lysosomal trafficking regulator (LYST), LPS-responsive and beige-like anchor (LRBA) and neurobeachin. Disruption of LYST leads to Chediak-Higashi syndrome, characterized by severe immunodeficiency, albinism, poor blood coagulation and neurologic problems. Neurobeachin is a candidate gene linked to autism. LBRA seems to be upregulated in several cancer types. It has been shown that the BEACH domain itself is important for the function of these proteins. 275 matched cddid_all.tbl CDD cd06080 cd06080 438967 PWWP_MUM1-like PWWP domain found in mutated melanoma-associated antigen 1 (MUM-1) and similar proteins. MUM-1, also called PWWP domain-containing DNA repair factor 3A (PWWP3A), or protein expandere (EXPAND1), is a melanoma-associated antigen (MAA) that belongs to the mutated or aberrantly expressed type of MAAs, along with antigens such as CDK4, beta-catenin, gp100-in4, p15, and N-acetylglucosaminyltransferase V. It is highly expressed in several types of human cancers and involved in the DNA damage response pathway by contributing to the maintenance of chromatin architecture. MUM-1 is recruited to the vicinity of DNA breaks by TP53BP1 and plays an accessory role to facilitate damage-induced chromatin changes and promoting chromatin relaxation. It is required for efficient DNA repair and cell survival following DNA damage. This subfamily also includes mutated melanoma-associated antigen 1-like protein 1 (MUM1L1), also called MUM1-like protein 1, or PWWP domain-containing DNA repair factor 3B (PWWP3B). Its biological function remains unclear. The PWWP domain specifically recognizes DNA and histone methylated lysines. 90 matched cddid_all.tbl CDD cd06081 cd06081 240505 KOW_Spt5_1 KOW domain of Spt5, repeat 1. Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases. 38 matched cddid_all.tbl CDD cd06082 cd06082 240506 KOW_Spt5_2 KOW domain of Spt5, repeat 2. Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases. 51 matched cddid_all.tbl CDD cd06083 cd06083 240507 KOW_Spt5_3 KOW domain of Spt5, repeat 3. Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases. 51 matched cddid_all.tbl CDD cd06084 cd06084 240508 KOW_Spt5_4 KOW domain of Spt5, repeat 4. Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases. 43 matched cddid_all.tbl CDD cd06085 cd06085 240509 KOW_Spt5_5 KOW domain of Spt5, repeat 5. Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases. 52 matched cddid_all.tbl CDD cd06086 cd06086 240510 KOW_Spt5_6 KOW domain of Spt5, repeat 6. Spt5, an eukaryotic ortholog of NusG, contains multiple KOW motifs at its C-terminus. Spt5 is involved in transcription elongation and termination. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW_Spt5 domains play critical roles in recruitment of multiple other eukaryotic transcription elongation and RNA biogenesis factors and additionally are involved in the binding of the eukaryotic Spt5 proteins to RNA polymerases. 58 matched cddid_all.tbl CDD cd06087 cd06087 240511 KOW_RPS4 KOW motif of Ribosomal Protein S4 (RPS4). RPS4 plays a critical role in the core assembly of the small ribosomal subunit with a KOW motif at its C-terminal. RPS4 also acts as a general transcription antiterminator factor and regulates ribosomal RNA expression level. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. RPS4 deficiency in human has been associated with Turner syndrome. Archeae RPS4 (RPS4e) showed substantial identity to the eukaryotic equivalents RPS4, but the archaeal proteins formed a different complex from the eukaryotic proteins. 55 matched cddid_all.tbl CDD cd06088 cd06088 240512 KOW_RPL14 KOW motif of Ribosomal Protein L14. RPL14 is a component of the large ribosomal subunit in both archaea and eukaryotes with KOW motif at its N terminal. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. Auto-antibodies to RPL14 in humans have been associated with systemic lupus erythematosus . Although RPL14 is well conserved, it is not found in all archaea, and therefore it is presumably not essential. 76 matched cddid_all.tbl CDD cd06089 cd06089 240513 KOW_RPL26 KOW motif of Ribosomal Protein L26. RPL26 and its bacterial paralogs RPL24 have a KOW motif at their N terminal. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. RPL26 makes a very minor contributions to the biogenesis, structure, and function of 60s ribosomal subunits. However, RPL24 is essential to generate the first intermediate during 50s ribosomal subunits assembly. RPL26 have an extra-ribosomal function to enhances p53 translation after DNA damage. 65 matched cddid_all.tbl CDD cd06090 cd06090 240514 KOW_RPL27 KOW motif of eukaryotic Ribosomal Protein L27. RPL27e has a KOW motif at its N terminal. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. 83 matched cddid_all.tbl CDD cd06091 cd06091 240515 KOW_NusG NusG contains an NGN domain at its N-terminus and KOW motif at its C-terminus. KOW_NusG motif is one of the two domains of N-Utilization Substance G (NusG) a transcription elongation and Rho-termination factor in bacteria and archaea. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. The eukaryotic ortholog of NusG is Spt5 with multiple KOW motifs at its C-terminus. 56 matched cddid_all.tbl CDD cd06093 cd06093 132768 PX_domain The Phox Homology domain, a phosphoinositide binding module. The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to membranes. Proteins containing PX domains interact with PIs and have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. Many members of this superfamily bind phosphatidylinositol-3-phosphate (PI3P) but in some cases, other PIs such as PI4P or PI(3,4)P2, among others, are the preferred substrates. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction, as in the cases of p40phox, p47phox, and some sorting nexins (SNXs). The PX domain is conserved from yeast to humans and is found in more than 100 proteins. The majority of PX domain-containing proteins are SNXs, which play important roles in endosomal sorting. 106 matched cddid_all.tbl CDD cd06094 cd06094 133158 RP_Saci_like RP_Saci_like, retropepsin family. Retropepsin on retrotransposons with long terminal repeats (LTR) including Saci-1, -2 and -3 of Schistosoma mansoni. Retropepsins are related to fungal and mammalian pepsins. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A. 89 matched cddid_all.tbl CDD cd06095 cd06095 133159 RP_RTVL_H_like Retropepsin of the RTVL_H family of human endogenous retrovirus-like elements. This family includes aspartate proteases from retroelements with LTR (long terminal repeats) including the RTVL_H family of human endogenous retrovirus-like elements. While fungal and mammalian pepsins are bilobal proteins with structurally related N- and C-termini, retropepsins are half as long as their fungal and mammalian counterparts. The monomers are structurally related to one lobe of the pepsin molecule and retropepsins function as homodimers. The active site aspartate occurs within a motif (Asp-Thr/Ser-Gly), as it does in pepsin. Retroviral aspartyl protease is synthesized as part of the POL polyprotein that contains an aspartyl protease, a reverse transcriptase, RNase H, and an integrase. The POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. In aspartate peptidases, Asp residues are ligands of an activated water molecule in all examples where catalytic residues have been identified. This group of aspartate peptidases is classified by MEROPS as the peptidase family A2 (retropepsin family, clan AA), subfamily A2A. 86 matched cddid_all.tbl CDD cd06096 cd06096 133160 Plasmepsin_5 Plasmepsins are a class of aspartic proteinases produced by the plasmodium parasite. The family contains a group of aspartic proteinases homologous to plasmepsin 5. Plasmepsins are a class of at least 10 enzymes produced by the plasmodium parasite. Through their haemoglobin-degrading activity, they are an important cause of symptoms in malaria sufferers. This family of enzymes is a potential target for anti-malarial drugs. Plasmepsins are aspartic acid proteases, which means their active site contains two aspartic acid residues. These two aspartic acid residue act respectively as proton donor and proton acceptor, catalyzing the hydrolysis of peptide bond in proteins. Aspartic proteinases are composed of two structurally similar beta barrel lobes, each lobe contributing an aspartic acid residue to form a catalytic dyad that acts to cleave the substrate peptide bond. The catalytic Asp residues are contained in an Asp-Thr-Gly-Ser/thr motif in both N- and C-terminal lobes of the enzyme. There are four types of plasmepsins, closely related but varying in the specificity of cleavage site. The name plasmepsin may come from plasmodium (the organism) and pepsin (a common aspartic acid protease with similar molecular structure). This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA). 326 matched cddid_all.tbl CDD cd06097 cd06097 133161 Aspergillopepsin_like Aspergillopepsin_like, aspartic proteases of fungal origin. The members of this family are aspartic proteases of fungal origin, including aspergillopepsin, rhizopuspepsin, endothiapepsin, and rodosporapepsin. The various fungal species in this family may be the most economically important genus of fungi. They may serve as virulence factors or as industrial aids. For example, Aspergillopepsin from A. fumigatus is involved in invasive aspergillosis owing to its elastolytic activity and Aspergillopepsins from the mold A. saitoi are used in fermentation industry. Aspartic proteinases are a group of proteolytic enzymes in which the scissile peptide bond is attacked by a nucleophilic water molecule activated by two aspartic residues in a DT(S)G motif at the active site. They have a similar fold composed of two beta-barrel domains. Between the N-terminal and C-terminal domains, each of which contributes one catalytic aspartic residue, there is an extended active-site cleft capable of interacting with multiple residues of a substrate. Although members of the aspartic protease family of enzymes have very similar three-dimensional structures and catalytic mechanisms, each has unique substrate specificity. The members of this family has an optimal acidic pH (5.5) and cleaves protein substrates with similar specificity to that of porcine pepsin A, preferring hydrophobic residues at P1 and P1' in the cleave site. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA). 278 matched cddid_all.tbl CDD cd06098 cd06098 133162 phytepsin Phytepsin, a plant homolog of mammalian lysosomal pepsins. Phytepsin, a plant homolog of mammalian lysosomal pepsins, resides in grains, roots, stems, leaves and flowers. Phytepsin may participate in metabolic turnover and in protein processing events. In addition, it highly expressed in several plant tissues undergoing apoptosis. Phytepsin contains an internal region consisting of about 100 residues not present in animal or microbial pepsins. This region is thus called a plant specific insert. The insert is highly similar to saponins, which are lysosomal sphingolipid-activating proteins in mammalian cells. The saponin-like domain may have a role in the vacuolar targeting of phytepsin. Phytepsin, as its animal counterparts, possesses a topology typical of all aspartic proteases. They are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. This family of aspartate proteases is classified by MEROPS as the peptidase family A1 (pepsin A, clan AA). 317 matched cddid_all.tbl CDD cd06099 cd06099 99853 CS_ACL-C_CCL Citrate synthase (CS), citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) from citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. Some CS proteins function as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. CCL cleaves citryl-CoA (CiCoA) to AcCoA and OAA. ACLs catalyze an ATP- and a CoA- dependant cleavage of citrate to form AcCoA and OAA; they do this in a multistep reaction, the final step of which is likely to involve the cleavage of CiCoA to generate AcCoA and OAA. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate CiCoA, and c) the hydrolysis of CiCoA to produce citrate and CoA. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site. Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). Some type II CSs are strongly and specifically inhibited by NADH through an allosteric mechanism. In fungi, yeast, plants, and animals ACL is cytosolic and generates AcCoA for lipogenesis. In several groups of autotrophic prokaryotes and archaea, ACL carries out the citrate-cleavage reaction of the reductive tricarboxylic acid (rTCA) cycle. In the family Aquificaceae this latter reaction in the rTCA cycle is carried out via a two enzyme system the second enzyme of which is CCL. 213 matched cddid_all.tbl CDD cd06100 cd06100 99854 CCL_ACL-C Citryl-CoA lyase (CCL), the C-terminal portion of the single-subunit type ATP-citrate lyase (ACL) and the C-terminal portion of the large subunit of the two-subunit type ACL. CCL cleaves citryl-CoA (CiCoA) to acetyl-CoA (AcCoA) and oxaloacetate (OAA). ACL catalyzes an ATP- and a CoA- dependant cleavage of citrate to form AcCoA and OAA in a multistep reaction, the final step of which is likely to involve the cleavage of CiCoA to generate AcCoA and OAA. In fungi, yeast, plants, and animals ACL is cytosolic and generates AcCoA for lipogenesis. ACL may be required for fruiting body maturation in the filamentous fungus Sordaria macrospore. In several groups of autotrophic prokaryotes and archaea, ACL carries out the citrate-cleavage reaction of the reductive tricarboxylic acid (rTCA) cycle. In the family Aquificaceae this latter reaction in the rTCA cycle is carried out via a two enzyme system the second enzyme of which is CCL; the first enzyme is citryl-CoA synthetase (CCS) which is not included in this group. Chlorobium limicola ACL is an example of a two-subunit type ACL. It is comprised of a large and a small subunit; it has been speculated that the large subunit arose from a fusion of the small subunit of the two subunit CCS with CCL. The small ACL subunit is a homolog of the larger CCS subunit. Mammalian ACL is of the single-subunit type and may have arisen from the two-subunit ACL by another gene fusion. Mammalian ACLs are homotetramers; the ACLs of C. limicola and Arabidopsis are a heterooctomers (alpha4beta4). In cancer cells there is a shift in energy metabolism to aerobic glycolysis, the glycolytic end product pyruvate enters a truncated TCA cycle generating citrate which is cleaved in the cytosol by ACL. Inhibiting ACL limits the in-vitro proliferation and survival of these cancer cells, reduces in vivo tumor growth, and induces differentiation. 227 matched cddid_all.tbl CDD cd06101 cd06101 99855 citrate_synt Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and form homodimers with both subunits participating in the active site. Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). Some type II CSs are strongly and specifically inhibited by NADH through an allosteric mechanism. This subgroup includes both gram-positive and gram-negative bacteria. 265 matched cddid_all.tbl CDD cd06102 cd06102 99856 citrate_synt_like_2 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site. Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). Some type II CSs are strongly and specifically inhibited by NADH through an allosteric mechanism. This subgroup includes both gram-positive and gram-negative bacteria. 282 matched cddid_all.tbl CDD cd06103 cd06103 99857 ScCS-like Saccharomyces cerevisiae (Sc) citrate synthase (CS)-like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) with oxaloacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). Some CS proteins function as 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site. Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). This group includes three S. cerevisiae CS proteins, ScCit1,-2,-3. ScCit1 is a nuclear-encoded mitochondrial CS with highly specificity for AcCoA; in addition to having activity with AcCoA, it plays a part in the construction of the TCA cycle metabolon. Yeast cells deleted for Cit1 are hyper-susceptible to apoptosis induced by heat and aging stress. ScCit2 is a peroxisomal CS involved in the glyoxylate cycle; in addition to having activity with AcCoA, it may have activity with PrCoA. ScCit3 is a mitochondrial CS and functions in the metabolism of PrCoA; it is a dual specificity CS and 2MCS, having similar catalytic efficiency with both AcCoA and PrCoA. The pattern of expression of the ScCIT3 gene follows that of the ScCIT1 gene and its expression is increased in the presence of a ScCIT1 deletion. Included in this group is the Tetrahymena 14 nm filament protein which functions as a CS in mitochondria and as a cytoskeletal component in cytoplasm and Geobacter sulfurreducens (GSu) CS. GSuCS is dimeric and eukaryotic-like; it lacks 2MCS activity and is inhibited by ATP. In contrast to eukaryotic and other prokaryotic CSs, GSuCIT is not stimulated by K+ ions. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. 426 matched cddid_all.tbl CDD cd06105 cd06105 99858 ScCit1-2_like Saccharomyces cerevisiae (Sc) citrate synthases Cit1-2_like. Citrate synthases (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) with oxaloacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). Some CS proteins function as 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site. Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). ScCit1 is a nuclear-encoded mitochondrial CS with highly specificity for AcCoA. In addition to its CS function, ScCit1 plays a part in the construction of the TCA cycle metabolon. Yeast cells deleted for Cit1 are hyper-susceptible to apoptosis induced by heat and aging stress. ScCit2 is a peroxisomal CS involved in the glyoxylate cycle; in addition to having activity with AcCoA, it may have activity with PrCoA. Chicken and pig heart CS, two Arabidopsis thaliana (Ath) CSs, CSY4 and -5, and Aspergillus niger (An) CS also belong to this group. Ath CSY4 has a mitochondrial targeting sequence; AthCSY5 has no identifiable targeting sequence. AnCS encoded by the citA gene has both an N-terminal mitochondrial import signal and a C-terminal peroxisiomal target sequence; it is not known if both these signals are functional in vivo. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. 427 matched cddid_all.tbl CDD cd06106 cd06106 99859 ScCit3_like Saccharomyces cerevisiae (Sc) 2-methylcitrate synthase Cit3-like. 2-methylcitrate synthase (2MCS) catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxaloacetate (OAA) to form 2-methylcitrate and CoA. Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) with OAA to form citrate and CoA, the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site. Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). ScCit3 is mitochondrial and functions in the metabolism of PrCoA; it is a dual specificity CS and 2MCS, having similar catalytic efficiency with both AcCoA and PrCoA. The pattern of expression of the ScCIT3 gene follows that of the major mitochondrial CS gene (CIT1, not included in this group) and its expression is increased in the presence of a CIT1 deletion. This group also contains Aspergillus nidulans 2MCS; a deletion of the gene encoding this protein results in a strain unable to grow on propionate. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. 428 matched cddid_all.tbl CDD cd06107 cd06107 99860 EcCS_AthCS-per_like Escherichia coli (Ec) citrate synthase (CS) gltA and Arabidopsis thaliana (Ath) peroxisomal (Per) CS_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site. Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). Some type II CSs, including EcCS, are strongly and specifically inhibited by NADH through an allosteric mechanism. Included in this group is an NADH-insensitive type II Acetobacter acetii CS which has retained many of the residues used by EcCS for NADH binding. C. aurantiacus is a gram-negative thermophilic green gliding bacterium; its CS belonging to this group may be a type I CS. It is not inhibited by NADH or 2-oxoglutarate and is inhibited by ATP. Both gram-positive and gram-negative bacteria are found in this group. This group also contains three Arabidopsis peroxisomal CS proteins, CYS-1, -2, and -3 which participate in the glyoxylate cycle. AthCYS1, in addition to a peroxisomal targeting sequence, has a predicted secretory signal peptide; it may be targeted to both the secretory pathway and the peroxisomes and perhaps is located in the extracellular matrix. AthCSY1 is expressed only in siliques and specifically in developing seeds. AthCSY2 and 3 are active during seed germination and seedling development and are thought to participate in the beta-oxidation of fatty acids. 382 matched cddid_all.tbl CDD cd06108 cd06108 99861 Ec2MCS_like Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and OAA to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). This group contains proteins similar to the E. coli 2MCS, EcPrpC. EcPrpC is one of two CS isozymes in the gram-negative E. coli. EcPrpC is a dimeric (type I ) CS; it is induced during growth on propionate and prefers PrCoA as a substrate though it has partial CS activity with AcCoA. This group also includes Salmonella typhimurium PrpC and Ralstonia eutropha (Re) 2-MCS1 which are also induced during growth on propionate and prefer PrCoA as substrate, but can also use AcCoA. Re 2-MCS1 can use butyryl-CoA and valeryl-CoA at a lower rate. A second Ralstonia eutropha 2MCS, Re 2-MCS2, which is induced on propionate is also found in this group. This group may include proteins which may function exclusively as a CS, those which may function exclusively as a 2MCS, or those with dual specificity which functions as both a CS and a 2MCS. 363 matched cddid_all.tbl CDD cd06109 cd06109 99862 BsCS-I_like Bacillus subtilis (Bs) citrate synthase CS-I_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. This group contains proteins similar to BsCS-I, one of two CS isozymes in the gram-positive B. subtilis. The majority of CS activity in B. subtilis is provided by the other isozyme, BsCS-II (not included in this group). BsCS-I has a lower catalytic activity than BsCS-II, and has a Glu in place of a key catalytic Asp residue. This change is conserved in other members of this group. For E. coli CS (not included in this group), site directed mutagenesis of the key Asp residue to a Glu converts the enzyme into citryl-CoA lyase which cleaves citryl-CoA to AcCoA and OAA. A null mutation in the gene encoding BsCS-I (citA) had little effect on B. subtilis CS activity or on sporulation. However, disruption of the citA gene in a strain null for the gene encoding BsCS-II resulted in a sporulation deficiency, a characteristic of strains defective in the Krebs cycle. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. Many of the gram-negative species represented in this group have a second CS isozyme which is in another group. 349 matched cddid_all.tbl CDD cd06110 cd06110 99863 BSuCS-II_like Bacillus subtilis (Bs) citrate synthase (CS)-II_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. This group contains proteins similar to BsCS-II, the major CS of the gram-positive bacterium Bacillus subtilis. A mutation in the gene which encodes BsCS-II (citZ gene) has been described which resulted in a significant loss of CS activity, partial glutamate auxotrophy, and a sporulation deficiency, all of which are characteristic of strains defective in the Krebs cycle. Streptococcus mutans CS, found in this group, may participate in a pathway for the anaerobic biosynthesis of glutamate. This group also contains functionally uncharacterized CSs of various gram-negative bacteria. Some of the gram-negative species represented in this group have a second CS isozyme found in another group. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. 356 matched cddid_all.tbl CDD cd06111 cd06111 99864 DsCS_like Cold-active citrate synthase (CS) from an Antarctic bacterial strain DS2-3R (Ds)-like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). 2-methylcitrate synthase (2MCS) catalyzes the condensation of propionyl-coenzyme A (PrCoA) and OAA to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. The overall CS reaction is thought to proceed through three partial reactions: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. DsCS, compared with CS from the hyperthermophile Pyrococcus furiosus (not included in this group), has an increase in the size of surface loops, a higher proline content in the loop regions, a more accessible active site, and a higher number of intramolecular ion pairs. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. For example, included in this group are Corynebacterium glutamicum (Cg) PrpC1 and -2, which are only synthesized during growth on propionate-containing medium, can use PrCoA, AcCoA and butyryl-CoA as substrates, and have comparable catalytic activity with AcCoA as the major CgCS (GltA, not included in this group). 362 matched cddid_all.tbl CDD cd06112 cd06112 99865 citrate_synt_like_1_1 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site. Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). Some type II CSs are strongly and specifically inhibited by NADH through an allosteric mechanism. 373 matched cddid_all.tbl CDD cd06113 cd06113 99866 citrate_synt_like_1_2 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) a carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) hydrolysis of citryl-CoA to produce citrate and CoA. CSs are found in two structural types: type I (homodimeric) and type II CSs (homohexameric). Type II CSs are unique to gram-negative bacteria. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria. Type I CS is active as a homodimer, both subunits participating in the active site. Type II CS is a hexamer of identical subunits (approximated as a trimer of dimers). Some type II CSs are strongly and specifically inhibited by NADH through an allosteric mechanism. This subgroup includes both gram-positive and gram-negative bacteria. 406 matched cddid_all.tbl CDD cd06114 cd06114 99867 EcCS_like Escherichia coli (Ec) citrate synthase (CS) GltA_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site. Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). Some type II CSs including EcCS are strongly and specifically inhibited by NADH through an allosteric mechanism. Included in this group is an NADH-insensitive type II Acetobacter acetii CS which has retained many of the residues used by EcCS for NADH binding. 400 matched cddid_all.tbl CDD cd06115 cd06115 99868 AthCS_per_like Arabidopsis thaliana (Ath) peroxisomal (Per) CS_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. This group contains three Arabidopsis peroxisomal CS proteins, CYS1, -2, and -3 which are involved in the glyoxylate cycle. AthCYS1, in addition to a peroxisomal targeting sequence, has a predicted secretory signal peptide; it may be targeted to both the secretory pathway and the peroxisomes and is thought to be located in the extracellular matrix. AthCSY1 is expressed only in siliques and specifically in developing seeds. AthCSY2 and 3 are active during seed germination and seedling development and are thought to participate in the beta-oxidation of fatty acids. 410 matched cddid_all.tbl CDD cd06116 cd06116 99869 CaCS_like Chloroflexus aurantiacus (Ca) citrate synthase (CS)_like. CS catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). This group is similar to gram-negative Escherichia coli (Ec) CS (type II, gltA) and Arabidopsis thaliana (Ath) peroxisomal (Per) CS. However EcCS and AthPerCS are not found in this group. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site. Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). Some type II CSs are strongly and specifically inhibited by NADH through an allosteric mechanism. C. aurantiacus is a gram-negative thermophilic green gliding bacterium, its CS belonging to this group may be a type I CS; it is not inhibited by NADH or 2-oxoglutarate and is inhibited by ATP. Both gram-positive and gram-negative bacteria are found in this group. 384 matched cddid_all.tbl CDD cd06117 cd06117 99870 Ec2MCS_like_1 Subgroup of Escherichia coli (Ec) 2-methylcitrate synthase (2MCS)_like. 2MCS catalyzes the condensation of propionyl-coenzyme A (PrCoA) and oxalacetate (OAA) to form 2-methylcitrate and coenzyme A (CoA) during propionate metabolism. Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and OAA to form citrate and coenzyme A (CoA), the first step in the citric acid cycle (TCA or Krebs cycle). This group contains proteins similar to the E. coli 2MCS, EcPrpC. EcPrpC is one of two CS isozymes in the gram-negative E. coli. EcPrpC is a dimeric (type I ) CS; it is induced during growth on propionate and prefers PrCoA as a substrate, but has a partial CS activity with AcCoA. This group also includes Salmonella typhimurium PrpC and Ralstonia eutropha (Re) 2-MCS1 which are also induced during growth on propionate, prefer PrCoA as substrate, but can also can use AcCoA. Re 2-MCS1 at a low rate can use butyryl-CoA and valeryl-CoA. A second Ralstonia eutropha 2MCS is also found in this group, Re 2-MCS2, which is induced on propionate. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. 366 matched cddid_all.tbl CDD cd06118 cd06118 99871 citrate_synt_like_1 Citrate synthase (CS) catalyzes the condensation of acetyl coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate and coenzyme A (CoA), the first step in the oxidative citric acid cycle (TCA or Krebs cycle). Peroxisomal CS is involved in the glyoxylate cycle. This group also includes CS proteins which functions as a 2-methylcitrate synthase (2MCS). 2MCS catalyzes the condensation of propionyl-CoA (PrCoA) and OAA to form 2-methylcitrate and CoA during propionate metabolism. This group contains proteins which functions exclusively as either a CS or a 2MCS, as well as those with relaxed specificity which have dual functions as both a CS and a 2MCS. The overall CS reaction is thought to proceed through three partial reactions and involves both closed and open conformational forms of the enzyme: a) the carbanion or equivalent is generated from AcCoA by base abstraction of a proton, b) the nucleophilic attack of this carbanion on OAA to generate citryl-CoA, and c) the hydrolysis of citryl-CoA to produce citrate and CoA. There are two types of CSs: type I CS and type II CSs. Type I CSs are found in eukarya, gram-positive bacteria, archaea, and in some gram-negative bacteria and are homodimers with both subunits participating in the active site. Type II CSs are unique to gram-negative bacteria and are homohexamers of identical subunits (approximated as a trimer of dimers). Some type II CSs are strongly and specifically inhibited by NADH through an allosteric mechanism. 358 matched cddid_all.tbl CDD cd06121 cd06121 380376 cupin_YML079wp "Saccharomyces cerevisiae YML079wp and related proteins, cupin domain. This family includes eukaryotic, bacterial, and archaeal proteins homologous to YML079wp, a Saccharomyces cerevisiae cupin-like protein of unknown function that structurally resembles plant seed storage and ligand-binding proteins (canavalin, glycinin, auxin binding protein) as well as the bacterial RmlC epimerase. YML079wp is non-essential in yeast and localizes to the nucleus and cytoplasm. The presence of a hydrophobic ligand within a well-conserved binding pocket inside the cupin beta-barrel and sequence similarity with bacterial epimerases suggests a possible biochemical function for YML079wp and its homologs. Also included in this family are Shewanella oneidensis So0799, Agrobacterium fabrum Atu3615 and Branchiostoma belcheri Bbduf985. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold and forms a homodimer." 153 matched cddid_all.tbl CDD cd06122 cd06122 380377 cupin_TTHA0104 Thermus thermophilus TTHA0104 and related proteins, cupin domain. This family contains bacterial proteins including TTHA0104 (also called TT1209), a putative antibiotic synthesis protein from Thermus thermophilus. TTHA0104 is a cupin-like protein. The cupins are a functionally diverse superfamily originally discovered based on the highly conserved motif found in germin and germin-like proteins. This conserved motif forms a beta-barrel fold found in all of the cupins, giving rise to the name cupin (cupa is the Latin term for small barrel). 102 matched cddid_all.tbl CDD cd06123 cd06123 380378 cupin_HAO "3-Hydroxyanthranilate-3,4-dioxygenase, cupin domain. 3-Hydroxyanthranilate-3,4-dioxygenase (HAO or 3HAO) is a non-heme iron-dependent extradiol dioxygenase that catalyzes the oxidative ring opening of 3-hydroxyanthranilate (3-HAA) in the final enzymatic step of the kynurenine biosynthetic pathway in which tryptophan is converted to quinolinate, an endogenous neurotoxin, making HAO a target for pharmacological downregulation. Quinolate is also the universal de novo precursor to the pyridine ring of nicotinamide adenine dinucleotide. The enzyme forms homodimers, with two metal binding sites per molecule. One of the bound metal ions occupies the proposed ferrous-coordinated active site, which is located in a conserved double-strand beta-helix domain. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 153 matched cddid_all.tbl CDD cd06124 cd06124 380379 cupin_NimR-like_N "AraC/XylS family transcriptional regulators similar to NimR, N-terminal cupin domain. This family contains mostly bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included in this family is Escherichia coli HTH-type transcriptional regulator NimR (also called YeaM) that negatively regulates expression of the nimT operon and its own expression. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 95 matched cddid_all.tbl CDD cd06125 cd06125 176647 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy or DEDDh exonucleases depending on the variation of motif III as YX(3)D or HX(4)D, respectively. The significance of the motif differences is still unclear. Almost all RNase families in this superfamily are present only in eukaryotes and bacteria, but not in archaea, suggesting a later origin, which in some cases are accompanied by horizontal gene transfer. 96 matched cddid_all.tbl CDD cd06127 cd06127 176648 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others. 159 matched cddid_all.tbl CDD cd06128 cd06128 176649 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Pol I resemble the fold of the 3'-5' exonuclease domain of KF without the proofreading activity of KF. The four critical metal-binding residues are not conserved in BF Pol I and Taq Pol I, and they are unable to bind metals necessary for exonuclease activity. 151 matched cddid_all.tbl CDD cd06129 cd06129 176650 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Egl is a component of an mRNA-binding complex which is required for oocyte specification. The Egl subfamily does not possess a completely conserved YX(3)D pattern at the ExoIII motif. 161 matched cddid_all.tbl CDD cd06130 cd06130 99834 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex. 156 matched cddid_all.tbl CDD cd06131 cd06131 99835 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon subunit of Pol III also functions as a stabilizer of the holoenzyme complex. 167 matched cddid_all.tbl CDD cd06133 cd06133 99836 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional homolog of either ERI-1 or 3'hExo. 176 matched cddid_all.tbl CDD cd06134 cd06134 99837 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site. 189 matched cddid_all.tbl CDD cd06135 cd06135 99838 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling. 173 matched cddid_all.tbl CDD cd06136 cd06136 99839 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TREX2 that point to different biological roles for these proteins. The main difference is the presence of about 70 amino acids at the C-terminus of TREX1. In addition, TREX1 has a nonrepetitive proline-rich region that is not present in the TREX2 protein. Furthermore, TREX2 contains a conserved DNA binding loop positioned adjacent to the active site that has a sequence distinct from the corresponding loop in TREX1. Truncations in the C-terminus of human TREX1 cause autosomal dominant retinal vasculopathy with cerebral leukodystrophy (RVCL), a neurovascular syndrome featuring a progressive loss of visual acuity combined with a variable neurological picture. 177 matched cddid_all.tbl CDD cd06137 cd06137 99840 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong preference for single-stranded RNA. 161 matched cddid_all.tbl CDD cd06138 cd06138 99841 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site. 183 matched cddid_all.tbl CDD cd06139 cd06139 176651 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair. 193 matched cddid_all.tbl CDD cd06140 cd06140 176652 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases. Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases. 178 matched cddid_all.tbl CDD cd06141 cd06141 176653 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability. 170 matched cddid_all.tbl CDD cd06142 cd06142 176654 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein. 178 matched cddid_all.tbl CDD cd06143 cd06143 99846 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. 174 matched cddid_all.tbl CDD cd06144 cd06144 99847 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherchia coli RNase T. 152 matched cddid_all.tbl CDD cd06145 cd06145 99848 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T. 150 matched cddid_all.tbl CDD cd06146 cd06146 176655 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs, termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. 193 matched cddid_all.tbl CDD cd06147 cd06147 99850 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome. 192 matched cddid_all.tbl CDD cd06148 cd06148 99851 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins. The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif. 197 matched cddid_all.tbl CDD cd06149 cd06149 99852 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and replication. It may carry out its function by degrading viral RNAs as part of the IFN-regulated antiviral response. 157 matched cddid_all.tbl CDD cd06150 cd06150 100007 YjgF_YER057c_UK114_like_2 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site. 105 matched cddid_all.tbl CDD cd06151 cd06151 100008 YjgF_YER057c_UK114_like_3 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site. 126 matched cddid_all.tbl CDD cd06152 cd06152 100009 YjgF_YER057c_UK114_like_4 YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site. 114 matched cddid_all.tbl CDD cd06153 cd06153 100010 YjgF_YER057c_UK114_like_5 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site. 114 matched cddid_all.tbl CDD cd06154 cd06154 100011 YjgF_YER057c_UK114_like_6 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site. 119 matched cddid_all.tbl CDD cd06155 cd06155 100012 eu_AANH_C_1 A group of hypothetical eukaryotic proteins, characterized by the presence of an adenine nucleotide alpha hydrolase (AANH)-like domain located N-terminal to two distinctly different YjgF-YER057c-UK114-like domains. This CD contains the first of these domains. The YjgF-YER057c-UK114 protein family is a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site. 101 matched cddid_all.tbl CDD cd06156 cd06156 100013 eu_AANH_C_2 A group of hypothetical eukaryotic proteins, characterized by the presence of an adenine nucleotide alpha hydrolase (AANH)-like domain located N-terminal to two distinctly different YjgF-YER057c-UK114-like domains. This CD contains the second of these domains. The YjgF-YER057c-UK114 protein family is a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site. 118 matched cddid_all.tbl CDD cd06157 cd06157 132726 NR_LBD The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators. Ligand-binding domain (LBD) of nuclear receptor (NR): Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 168 matched cddid_all.tbl CDD cd06158 cd06158 100079 S2P-M50_like_1 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with a minimal core protein and no PDZ domains. 181 matched cddid_all.tbl CDD cd06159 cd06159 100080 S2P-M50_PDZ_Arch Uncharacterized Archaeal homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group appears to be limited to Archaeal S2P/M50s homologs with additional putative N-terminal transmembrane spanning regions, relative to the core protein, and either one or two PDZ domains present. 263 matched cddid_all.tbl CDD cd06160 cd06160 100081 S2P-M50_like_2 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with additional putative N- and C-terminal transmembrane spanning regions, relative to the core protein, and no PDZ domains. 183 matched cddid_all.tbl CDD cd06161 cd06161 100082 S2P-M50_SpoIVFB SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. 208 matched cddid_all.tbl CDD cd06162 cd06162 100083 S2P-M50_PDZ_SREBP Sterol regulatory element-binding protein (SREBP) Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50A), regulates intramembrane proteolysis (RIP) of SREBP and is part of a signal transduction mechanism involved in sterol and lipid metabolism. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of SREBPs from membranes of the endoplasmic reticulum (ER). These domains translocate into the nucleus, where they activate genes of cholesterol and fatty acid biosynthesis. The first cleavage occurs at Site-1 within the ER lumen to generate an intermediate that is subsequently released from the membrane by cleavage at Site-2, which lies within the first transmembrane domain. It is the second proteolytic step that is carried out by the SREBP Site-2 protease (S2P) which is present in this CD family. This group appears to be limited to eumetazoan proteins and contains one PDZ domain. 277 matched cddid_all.tbl CDD cd06163 cd06163 100084 S2P-M50_PDZ_RseP-like RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog RseP is involved in the sigmaE pathway of extracytoplasmic stress responses. Also included in this group are such homologs as Bacillus subtilis YluC, Mycobacterium tuberculosis Rv2869c S2P, and Bordetella bronchiseptica HurP. Rv2869c S2P appears to have a role in the regulation of prokaryotic lipid biosynthesis and membrane composition and YluC of Bacillus has a role in transducing membrane stress. This group includes bacterial and eukaryotic S2P/M50s homologs with either one or two PDZ domains present. PDZ domains are believed to have a regulatory role. The RseP PDZ domain is required for the inhibitory reaction that prevents cleavage of its substrate, RseA. 182 matched cddid_all.tbl CDD cd06164 cd06164 100085 S2P-M50_SpoIVFB_CBS SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. In this subgroup, SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. 227 matched cddid_all.tbl CDD cd06165 cd06165 320680 Sortase_A Sortase domain found in class A sortases. Class A sortases are membrane-bound cysteine transpeptidases distributed in Gram-positive bacteria (mainly present in Firmicutes). They perform a housekeeping role in the cell as members of this group are capable of anchoring a large number of functionally distinct surface proteins containing a cell wall sorting signal to an amino group located on the bacterial cell wall. They do so by catalyzing a transpeptidation reaction in which the surface protein substrate is cleaved at a conserved cell wall-sorting signal (Class A sortases recognize a canonical LPXTG motif, X can be any amino acid), and covalently linked to peptidoglycan for display on the bacterial surface. The prototypical sortase A protein from Staphylococcus aureus (named Sa-SrtA) cleaves the amide bond between threonine and glycine residues of the canonical LPXTG motif in a wide range of protein substrates with diverse functions that can promote bacterial adhesion, nutrient acquisition, host cell invasion, and immune evasion. Next, it catalyzes a transpeptidation reaction by which the proteins are covalently linked to the peptidoglycan precursor lipid II. SrtA is therefore affects the ability of a pathogen to establish successful infection. SrtA contains an N-terminal hydrophobic segment, a linker region and an extra-cellular C-terminal catalytic domain. The hydrophobic segment functions as both a signal peptide for secretion and a stop-transfer signal for membrane anchoring. The catalytic domain contains the catalytic TLXTC signature sequence where X is usually a valine, isoleucine or a threonine. The gene encoding SrtA is generally not located in the same gene cluster as its substrates while the gene encoding SrtB is usually clustered in the same locus as its substrate. 127 matched cddid_all.tbl CDD cd06166 cd06166 320681 Sortase_D_2 Sortase domain found in subfamily 2 of the class D family of sortases. Class D sortases are cysteine transpeptidases distributed in Gram-positive bacteria (mainly present in Firmicutes). They anchor surface proteins bearing a cell wall sorting signal to peptidoglycans of the bacterial cell wall envelope, which is responsible for spore formation under anaerobic conditions. This involves a transpeptidation reaction in which the surface protein substrate is cleaved at the cell wall sorting signal and covalently linked to peptidoglycan for display on the bacterial surface. The prototypical subfamily 2 of class D sortase from Clostridium perfringens (named Cp-SrtD) recognizes the LPQTGS signal motif for transpeptidation. Its catalytic activity is in a metal cation- and temperature- dependent manner. The presence of magnesium appears to enhance Cp-SrtD catalysis towards the LPQTGS signal motif. 127 matched cddid_all.tbl CDD cd06167 cd06167 350201 PIN_LabA-like PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins. The LabA-like PIN domain family includes Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression. This family also includes the N-terminal domain of limkain b1, a human autoantigen associated with cytoplasmic vesicles. Other members are the LabA-like PIN domains of human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into this family. 113 matched cddid_all.tbl CDD cd06168 cd06168 212486 LSMD1 LSM domain containing 1. The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSMD1 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes, forming heptameric and hexameric ring structures similar to those found in eukaryotes. 73 matched cddid_all.tbl CDD cd06169 cd06169 132884 BMC Bacterial Micro-Compartment (BMC) domain. Bacterial micro-compartments are primitive protein-based organelles that sequester specific metabolic pathways in bacterial cells. The prototypical bacterial microcompartment is the carboxysome shell, a bacterial polyhedral organelle which increase the efficiency of CO2 fixation by encapsulating RuBisCO and carbonic anhydrase. They can be divided into two types: alpha-type carboxysomes (alpha-cyanobacteria and proteobacteria) and beta-type carboxysomes (beta-cyanobacteria). In addition to these proteins there are several homologous shell proteins including those found in pdu organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol and eut organelles involved in the cobalamin-dependent degradation of ethanolamine. Structure evidence shows that several carboxysome shell proteins and their homologs (Csos1A, CcmK1,2,4, and PduU) exist as hexamers which might further assemble into extended, tightly packed layers hypothesized to represent the flat facets of the polyhedral organelles outer shell. Although it has been suggested that other homologous proteins in this family might also form hexamers and play similar functional roles in the construction of their corresponding organelle outer shell at present no experimental evidence directly supports this view. 62 matched cddid_all.tbl CDD cd06170 cd06170 99777 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp. 57 matched cddid_all.tbl CDD cd06171 cd06171 100119 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP). 55 matched cddid_all.tbl CDD cd06172 cd06172 340862 MFS_LacY LacY proton/sugar symporter family of the Major Facilitator Superfamily of transporters. LacY proton/sugar family (also called LacY/RafB family) symporters are integral membrane proteins responsible for the transport of specific beta-glucosides into the cell accompanied by the import of a proton. Members include lactose permease (LacY), raffinose permease (RafB), and sucrose permease, which facilitate the transport of beta-galactosides, raffinose, and sucrose, respectively. The prototypical member, LacY, contains 12 transmembrane helices connected by hydrophilic loops with both N and C termini on the cytoplasmic face. The LacY/RafB permease family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 389 matched cddid_all.tbl CDD cd06173 cd06173 340863 MFS_MefA_like Macrolide efflux protein A and similar proteins of the Major Facilitator Superfamily of transporters. This family is composed of Streptococcus pyogenes macrolide efflux protein A (MefA) and similar transporters, many of which remain uncharacterized. Some members may be multidrug resistance (MDR) transporters, which are drug/H+ antiporters (DHAs) that mediate the efflux of a variety of drugs and toxic compounds, conferring resistance to these compounds. MefA confers resistance to 14-membered macrolides including erythromycin and to 15-membered macrolides. It functions as an efflux pump to regulate intracellular macrolide levels. The MefA-like family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 383 matched cddid_all.tbl CDD cd06174 cd06174 349949 MFS Major Facilitator Superfamily. The Major Facilitator Superfamily (MFS) is a large and diverse group of secondary transporters that includes uniporters, symporters, and antiporters. MFS proteins facilitate the transport across cytoplasmic or internal membranes of a variety of substrates including ions, sugar phosphates, drugs, neurotransmitters, nucleosides, amino acids, and peptides. They do so using the electrochemical potential of the transported substrates. Uniporters transport a single substrate, while symporters and antiporters transport two substrates in the same or in opposite directions, respectively, across membranes. MFS proteins are typically 400 to 600 amino acids in length, and the majority contain 12 transmembrane alpha helices (TMs) connected by hydrophilic loops. The N- and C-terminal halves of these proteins display weak similarity and may be the result of a gene duplication/fusion event. Based on kinetic studies and the structures of a few bacterial superfamily members, GlpT (glycerol-3-phosphate transporter), LacY (lactose permease), and EmrD (multidrug transporter), MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. Bacterial members function primarily for nutrient uptake, and as drug-efflux pumps to confer antibiotic resistance. Some MFS proteins have medical significance in humans such as the glucose transporter Glut4, which is impaired in type II diabetes, and glucose-6-phosphate transporter (G6PT), which causes glycogen storage disease when mutated. 378 matched cddid_all.tbl CDD cd06175 cd06175 340865 MFS_POT Proton-coupled oligopeptide transporter (POT) family of the Major Facilitator Superfamily of transporters. The Proton-coupled oligopeptide transporter (POT) family is present across all major kingdoms of life and is known by a variety of names. It is referred to as the Nitrate transporter/Peptide transporter (NRT1/PTR) family (NPF) in plants, and in addition to POT, it is also known as the Peptide transporter (PepT/PTR) or Solute Carrier 15 (SLC15) family in animals. Members of this family are proton-driven symporters involved in nitrogen acquisition in the form of di- and tripeptides. Plant members transport other nitrogenous ligands including nitrate, the plant hormone auxin, and glucosinolate compounds that are important for seed defense. POT proteins exhibit substrate multispecificity, with one transporter able to recognize as many as 8,400 types of di/tripeptides and certain peptide-like drugs. The POT family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 422 matched cddid_all.tbl CDD cd06176 cd06176 349950 MFS_BCD_PucC-like Bacteriochlorophyll delivery (BCD) family, also called PucC family, of the Major Facilitator Superfamily. The bacteriochlorophyll delivery (BCD) family, also called PucC family, is composed of the PucC protein and related proteins including LhaA (also called ORF477 and F1696) and bacteriochlorophyll synthase 44.5 kDa chain (also called ORF428). These proteins are found in photosynthetic organisms. Rhodobacter capsulatus LhaA and PucC are implicated in light-harvesting complex 1 and 2 (LH1 and LH2) assembly. PucC may function to shepherd or sequester LH2 alpha and beta proteins to facilitate proper assembly, as well as deliver bacteriochlorophyll a to nascent LH2 complexes. The BCD family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 409 matched cddid_all.tbl CDD cd06177 cd06177 340866 MFS_NHS Nucleoside:H(+) symporter family of the Major Facilitator Superfamily of transporters. The prototypical members of the Nucleoside:H(+) symporter (NHS) family are Escherichia coli nucleoside permease NupG and xanthosine permease. Nucleoside:H(+) symporters are proton-driven transporters that facilitate the import of nucleosides across the cytoplasmic membrane. NupG is a broad-specificity transporter of purine and pyrimidine nucleosides. Xanthosine permease is involved in the uptake of xanthosine and other nucleosides such as inosine, adenosine, cytidine, uridine and thymidine. The NHS family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 386 matched cddid_all.tbl CDD cd06178 cd06178 340867 MFS_unc93-like Uncharacterized Unc-93-like proteins of the Major Facilitator Superfamily of transporters. This subfamily consists of uncharacterized proteins, mainly from fungi and plants, with similarity to Caenorhabditis elegans uncoordinated protein 93 (also called putative potassium channel regulatory protein unc-93). Unc-93 acts as a regulatory subunit of a multi-subunit potassium channel complex that may function in coordinating muscle contraction in C. elegans. The unc93-like subfamily belongs to the Unc-93 family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 415 matched cddid_all.tbl CDD cd06179 cd06179 340868 MFS_TRI12_like Fungal trichothecene efflux pump (TRI12) of the Major Facilitator Superfamily of transporters. This family includes Fusarium sporotrichioides trichothecene efflux pump (TRI12), which may play a role in F. sporotrichioides self-protection against trichothecenes. TRI12 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 518 matched cddid_all.tbl CDD cd06180 cd06180 340869 MFS_YjiJ Uncharacterized protein YjiJ and similar proteins of the Major Facilitator Superfamily of transporters. This family is composed of Escherichia coli YjiJ and other uncharacterized proteins. They belong to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 371 matched cddid_all.tbl CDD cd06181 cd06181 198409 BI-1-like BAX inhibitor (BI)-1/YccA-like protein family. Mammalian members of the BAX inhibitor (BI)-1 like family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. Their broad tissue distribution and high degree of conservation suggests an important regulatory role. This superfamily also contains the lifeguard(LFG)-like proteins and other subfamilies which appear to be related by common descent and also function as inhibitors of apoptosis. In plants, BI-1 like proteins play a role in pathogen resistance. A prokaryotic member, Escherichia coli YccA, has been shown to interact with ATP-dependent protease FtsH, which degrades abnormal membrane proteins as part of a quality control mechanism to keep the integrity of biological membranes. 202 matched cddid_all.tbl CDD cd06182 cd06182 99779 CYPOR_like NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. CYPOR has a C-terminal ferredoxin reducatase (FNR)- like FAD and NAD binding module, an FMN-binding domain, and an additional conecting domain (inserted within the FAD binding region) that orients the FNR and FMN binding domains. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria and participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2, which then transfers two electrons and a proton to NADP+ to form NADPH. 267 matched cddid_all.tbl CDD cd06183 cd06183 99780 cyt_b5_reduct_like Cytochrome b5 reductase catalyzes the reduction of 2 molecules of cytochrome b5 using NADH as an electron donor. Like ferredoxin reductases, these proteins have an N-terminal FAD binding subdomain and a C-terminal NADH binding subdomain, separated by a cleft, which accepts FAD. The NADH-binding moiety interacts with part of the FAD and resembles a Rossmann fold. However, NAD is bound differently than in canonical Rossmann fold proteins. Nitrate reductases, flavoproteins similar to pyridine nucleotide cytochrome reductases, catalyze the reduction of nitrate to nitrite. The enzyme can be divided into three functional fragments that bind the cofactors molybdopterin, heme-iron, and FAD/NADH. 234 matched cddid_all.tbl CDD cd06184 cd06184 99781 flavohem_like_fad_nad_binding FAD_NAD(P)H binding domain of flavohemoglobin. Flavohemoglobins have a globin domain containing a B-type heme fused with a ferredoxin reductase-like FAD/NAD-binding domain. Flavohemoglobins detoxify nitric oxide (NO) via an NO dioxygenase reaction. The hemoglobin domain adopts a globin fold with an embedded heme molecule. Flavohemoglobins also have a C-terminal reductase domain with bindiing sites for FAD and NAD(P)H. This domain catalyzes the conversion of NO + O2 + NAD(P)H to NO3- + NAD(P)+. Instead of the oxygen transport function of hemoglobins, flavohemoglobins seem to act in NO dioxygenation and NO signalling. 247 matched cddid_all.tbl CDD cd06185 cd06185 99782 PDR_like Phthalate dioxygenase reductase (PDR) is an FMN-dependent reductase that mediates electron transfer from NADH to FMN to an iron sulfur cluster. PDR has an an N-terminal ferrredoxin reductase (FNR)-like NAD(H) binding domain and a C-terminal iron-sulfur [2Fe-2S] cluster domain. Although structurally homologous to FNR, PDR binds FMN rather than FAD in it's FNR-like domain. Electron transfer between pyrimidines and iron-sulfur clusters (Rieske center [2Fe-2S]) or heme groups is mediated by flavins in respiration, photosynthesis, and oxygenase systems. Type I dioxygenase systems, including the hydroxylate phthalate system, have 2 components, a monomeric reductase consisting of a flavin and a 2Fe-2S center and a multimeric oxygenase. In contrast to other Rieske dioxygenases the ferredoxin like domain is C-, not N-terminal. 211 matched cddid_all.tbl CDD cd06186 cd06186 99783 NOX_Duox_like_FAD_NADP NADPH oxidase (NOX) catalyzes the generation of reactive oxygen species (ROS) such as superoxide and hydrogen peroxide. ROS were originally identified as bactericidal agents in phagocytes, but are now also implicated in cell signaling and metabolism. NOX has a 6-alpha helix heme-binding transmembrane domain fused to a flavoprotein with the nucleotide binding domain located in the cytoplasm. Duox enzymes link a peroxidase domain to the NOX domain via a single transmembrane and EF-hand Ca2+ binding sites. The flavoprotein module has a ferredoxin like FAD/NADPH binding domain. In classical phagocytic NOX2, electron transfer occurs from NADPH to FAD to the heme of cytb to oxygen leading to superoxide formation. 210 matched cddid_all.tbl CDD cd06187 cd06187 99784 O2ase_reductase_like The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons using oxygen as the oxidant. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S] ferredoxin center (fused to the FAD/NADH domain and/or discrete) to the oxygenase. Dioxygenases add both atoms of oxygen to the substrate, while mono-oxygenases (aka mixed oxygenases) add one atom to the substrate and one atom to water. In dioxygenases, Class I enzymes are 2 component, containing a reductase with Rieske type [2Fe-2S] redox centers and an oxygenase. Class II are 3 component, having discrete flavin and ferredoxin proteins and an oxygenase. Class III have 2 [2Fe-2S] centers, one fused to the flavin domain and the other separate. 224 matched cddid_all.tbl CDD cd06188 cd06188 99785 NADH_quinone_reductase Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) FAD/NADH binding domain. (Na+-NQR) provides a means of storing redox reaction energy via the transmembrane translocation of Na2+ ions. The C-terminal domain resembles ferredoxin:NADP+ oxidoreductase, and has NADH and FAD binding sites. (Na+-NQR) is distinct from H+-translocating NADH:quinone oxidoreductases and noncoupled NADH:quinone oxidoreductases. The NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal domain of this group typically contains an iron-sulfur cluster binding domain. 283 matched cddid_all.tbl CDD cd06189 cd06189 99786 flavin_oxioreductase NAD(P)H dependent flavin oxidoreductases use flavin as a substrate in mediating electron transfer from iron complexes or iron proteins. Structurally similar to ferredoxin reductases, but with only 15% sequence identity, flavin reductases reduce FAD, FMN, or riboflavin via NAD(P)H. Flavin is used as a substrate, rather than a tightly bound prosthetic group as in flavoenzymes; weaker binding is due to the absence of a binding site for the AMP moeity of FAD. 224 matched cddid_all.tbl CDD cd06190 cd06190 99787 T4MO_e_transfer_like Toluene-4-monoxygenase electron transfer component of Pseudomonas mendocina hydroxylates toluene and forms p-cresol as part of a three component toluene-4-monoxygenase system. Electron transfer is from NADH to an NADH:ferredoxin oxidoreductase (TmoF in P. mendocina) to ferredoxin to an iron-containing oxygenase. TmoF is homologous to other mono- and dioxygenase systems within the ferredoxin reductase family. 232 matched cddid_all.tbl CDD cd06191 cd06191 99788 FNR_iron_sulfur_binding Iron-sulfur binding Ferredoxin Reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with a C-terminal iron-sulfur binding cluster domain. FNR was intially identified as a chloroplast reductase activity catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methnae assimilation in a variety of organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one- electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and 2 electron carriers. FNR has a strong preference for NADP(H) vs NAD(H). 231 matched cddid_all.tbl CDD cd06192 cd06192 99789 DHOD_e_trans_like FAD/NAD binding domain (electron transfer subunit) of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is co-expressed with pyrK and both gene products are required for full activity, as well as NAD binding. NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal domain may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The flavoprotein Ferredoxin-NADP+ reductase transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) which then transfers a hydride ion to convert NADP+ to NADPH. 243 matched cddid_all.tbl CDD cd06193 cd06193 99790 siderophore_interacting Siderophore interacting proteins share the domain structure of the ferredoxin reductase like family. Siderophores are produced in various bacteria (and some plants) to extract iron from hosts. Binding constants are high, so iron can be pilfered from transferrin and lactoferrin for bacterial uptake, contributing to pathogen virulence. Ferredoxin reductase (FNR), an FAD and NAD(P) binding protein, was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and has a variety of physiological functions including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation in a variety of organisms. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one-electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and two electron carriers. FNR has a strong preference for NADP(H) vs NAD(H). 235 matched cddid_all.tbl CDD cd06194 cd06194 99791 FNR_N-term_Iron_sulfur_binding Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an N-terminal Iron-Sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH. 222 matched cddid_all.tbl CDD cd06195 cd06195 99792 FNR1 Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH. 241 matched cddid_all.tbl CDD cd06196 cd06196 99793 FNR_like_1 Ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which varies in orientation with respect to the NAD(P) binding domain. The N-terminal region may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The flavoprotein Ferredoxin-NADP+ reductase transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) which then transfers a hydride ion to convert NADP+ to NADPH. 218 matched cddid_all.tbl CDD cd06197 cd06197 99794 FNR_like_2 FAD/NAD(P) binding domain of ferredoxin reductase-like proteins. Ferredoxin reductase (FNR) was intially identified as a chloroplast reductase activity, catalyzing the electron transfer from reduced iron-sulfur protein ferredoxin to NADP+ as the final step in the electron transport mechanism of photosystem I. FNR transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) and then transfers a hydride ion to convert NADP+ to NADPH. FNR has since been shown to utilize a variety of electron acceptors and donors and have a variety of physiological functions in a variety of organisms including nitrogen assimilation, dinitrogen fixation, steroid hydroxylation, fatty acid metabolism, oxygenase activity, and methane assimilation. FNR has an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) flavin sub-domain which varies in orientation with respect to the NAD(P) binding domain. The N-terminal moeity may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Because flavins such as FAD can exist in oxidized, semiquinone (one-electron reduced), or fully reduced hydroquinone forms, FNR can interact with one and two electron carriers. FNR has a strong preference for NADP(H) vs NAD(H). 220 matched cddid_all.tbl CDD cd06198 cd06198 99795 FNR_like_3 NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding sub-domain of the alpha/beta class and a discrete (usually N-terminal) domain, which varies in orientation with respect to the NAD(P) binding domain. The N-terminal domain may contain a flavin prosthetic group (as in flavoenzymes) or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The flavoprotein Ferredoxin-NADP+ reductase transfers electrons from reduced ferredoxin to FAD (forming FADH2 via a semiquinone intermediate) which then transfers a hydride ion to convert NADP+ to NADPH. 216 matched cddid_all.tbl CDD cd06199 cd06199 99796 SiR Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ gene) are of the cytochrome p450 (CyPor) family having FAD and FMN as prosthetic groups and utilizing NADPH. Cypor (including cyt -450 reductase, nitric oxide synthase, and methionine synthase reductase) are ferredoxin reductase (FNR)-like proteins with an additional N-terminal FMN domain and a connecting sub-domain inserted within the flavin binding portion of the FNR-like domain. The connecting domain orients the N-terminal FMN domain with the C-terminal FNR domain. 360 matched cddid_all.tbl CDD cd06200 cd06200 99797 SiR_like1 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ gene) are of the cytochrome p450 (CyPor) family having FAD and FMN as prosthetic groups and utilizing NADPH. Cypor (including cyt -450 reductase, nitric oxide synthase, and methionine synthase reductase) are ferredoxin reductase (FNR)-like proteins with an additional N-terminal FMN domain and a connecting sub-domain inserted within the flavin binding portion of the FNR-like domain. The connecting domain orients the N-terminal FMN domain with the C-terminal FNR domain. NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues, and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule, which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH. 245 matched cddid_all.tbl CDD cd06201 cd06201 99798 SiR_like2 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide. Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ gene) are of the cytochrome p450 (CyPor) family having FAD and FMN as prosthetic groups and utilizing NADPH. Cypor (including cyt -450 reductase, nitric oxide synthase, and methionine synthase reductase) are ferredoxin reductase (FNR)-like proteins with an additional N-terminal FMN domain and a connecting sub-domain inserted within the flavin binding portion of the FNR-like domain. The connecting domain orients the N-terminal FMN domain with the C-terminal FNR domain. NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH. 289 matched cddid_all.tbl CDD cd06202 cd06202 99799 Nitric_oxide_synthase The ferredoxin-reductase (FNR) like C-terminal domain of the nitric oxide synthase (NOS) fuses with a heme-containing N-terminal oxidase domain. The reductase portion is similar in structure to NADPH dependent cytochrome-450 reductase (CYPOR), having an inserted connecting sub-domain within the FAD binding portion of FNR. NOS differs from CYPOR in a requirement for the cofactor tetrahydrobiopterin and unlike most CYPOR is dimeric. Nitric oxide synthase produces nitric oxide in the conversion of L-arginine to L-citruline. NOS has been implicated in a variety of processes including cytotoxicity, anti-inflamation, neurotransmission, and vascular smooth muscle relaxation. 406 matched cddid_all.tbl CDD cd06203 cd06203 99800 methionine_synthase_red Human methionine synthase reductase (MSR) restores methionine sythase which is responsible for the regeneration of methionine from homocysteine, as well as the coversion of methyltetrahydrofolate to tetrahydrofolate. In MSR, electrons are transferred from NADPH to FAD to FMN to cob(II)alamin. MSR resembles proteins of the cytochrome p450 family including nitric oxide synthase, the alpha subunit of sulfite reductase, but contains an extended hinge region. NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. CYPORs resemble ferredoxin reductase (FNR) but have a connecting subdomain inserted within the flavin binding region, which helps orient the FMN binding doamin with the FNR module. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH. 398 matched cddid_all.tbl CDD cd06204 cd06204 99801 CYPOR NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH. 416 matched cddid_all.tbl CDD cd06206 cd06206 99802 bifunctional_CYPOR These bifunctional proteins fuse N-terminal cytochrome p450 with a cytochrome p450 reductase (CYPOR). NADPH cytochrome p450 reductase serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH. 384 matched cddid_all.tbl CDD cd06207 cd06207 99803 CyPoR_like NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH. 382 matched cddid_all.tbl CDD cd06208 cd06208 99804 CYPOR_like_FNR These ferredoxin reductases are related to the NADPH cytochrome p450 reductases (CYPOR), but lack the FAD-binding region connecting sub-domain. Ferredoxin-NADP+ reductase (FNR) is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins, such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap between the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2, which then transfers two electrons and a proton to NADP+ to form NADPH. CYPOR serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases, sulfite reducatase, and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via FAD and FMN. CYPOR has a C-terminal FNR-like FAD and NAD binding module, an FMN-binding domain, and an additional connecting domain (inserted within the FAD binding region) that orients the FNR and FMN -binding domains. The C-terminal domain contains most of the NADP(H) binding residues, and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule, which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH. 286 matched cddid_all.tbl CDD cd06209 cd06209 99805 BenDO_FAD_NAD Benzoate dioxygenase reductase (BenDO) FAD/NAD binding domain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. As a Class I bacterial dioxygenases, benzoate dioxygenase like proteins combine an [2Fe-2S] cluster containing N-terminal ferredoxin at the end fused to an FAD/NADP(P) domain. In dioxygenase FAD/NAD(P) binding domain, the reductase transfers 2 electrons from NAD(P)H to the oxygenase which insert into an aromatic substrate, an initial step in microbial aerobic degradation of aromatic rings. Flavin oxidoreductases use flavins as substrates, unlike flavoenzymes which have a flavin prosthetic group. 228 matched cddid_all.tbl CDD cd06210 cd06210 99806 MMO_FAD_NAD_binding Methane monooxygenase (MMO) reductase of methanotrophs catalyzes the NADH-dependent hydroxylation of methane to methanol. This multicomponent enzyme mediates electron transfer via a hydroxylase (MMOH), a coupling protein, and a reductase which is comprised of an N-terminal [2Fe-2S] ferredoxin domain, an FAD binding subdomain, and an NADH binding subdomain. Oxygenases oxidize hydrocarbons using dioxygen as the oxidant. Dioxygenases add both atom of oxygen to the substrate, while mono-oxygenases add one atom to the substrate and one atom to water. 236 matched cddid_all.tbl CDD cd06211 cd06211 99807 phenol_2-monooxygenase_like Phenol 2-monooxygenase (phenol hydroxylase) is a flavoprotein monooxygenase, able to use molecular oxygen as a substrate in the microbial degredation of phenol. This protein is encoded by a single gene and uses a tightly bound FAD cofactor in the NAD(P)H dependent conversion of phenol and O2 to catechol and H2O. This group is related to the NAD binding ferredoxin reductases. 238 matched cddid_all.tbl CDD cd06212 cd06212 99808 monooxygenase_like The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons. These flavoprotein monooxygenases use molecular oxygen as a substrate and require reduced FAD. One atom of oxygen is incorportated into the aromatic compond, while the other is used to form a molecule of water. In contrast dioxygenases add both atoms of oxygen to the substrate. 232 matched cddid_all.tbl CDD cd06213 cd06213 99809 oxygenase_e_transfer_subunit The oxygenase reductase FAD/NADH binding domain acts as part of the multi-component bacterial oxygenases which oxidize hydrocarbons. Electron transfer is from NADH via FAD (in the oxygenase reductase) and an [2FE-2S] ferredoxin center (fused to the FAD/NADH domain and/or discrete) to the oxygenase. Dioxygenases add both atoms of oxygen to the substrate while mono-oxygenases add one atom to the substrate and one atom to water. In dioxygenases, Class I enzymes are 2 component, containing a reductase with Rieske type [2Fe-2S] redox centers and an oxygenase. Class II are 3 component, having discrete flavin and ferredoxin proteins and an oxygenase. Class III have 2 [2Fe-2S] centers, one fused to the flavin domain and the other separate. 227 matched cddid_all.tbl CDD cd06214 cd06214 99810 PA_degradation_oxidoreductase_like NAD(P) binding domain of ferredoxin reductase like phenylacetic acid (PA) degradation oxidoreductase. PA oxidoreductases of E. coli hydroxylate PA-CoA in the second step of PA degradation. Members of this group typically fuse a ferredoxin reductase-like domain with an iron-sulfur binding cluster domain. Ferredoxins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal portion may contain a flavin prosthetic group, as in flavoenzymes, or use flavin as a substrate. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria and participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH. 241 matched cddid_all.tbl CDD cd06215 cd06215 99811 FNR_iron_sulfur_binding_1 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal portion of the FAD/NAD binding domain contains most of the NADP(H) binding residues and the N-terminal sub-domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. In this ferredoxin like sub-group, the FAD/NAD sub-domains is typically fused to a C-terminal iron-sulfur binding domain. Iron-sulfur proteins play an important role in electron transfer processes and in various enzymatic reactions. The family includes plant and algal ferredoxins which act as electron carriers in photosynthesis and ferredoxins which participate in redox chains from bacteria to mammals. Ferredoxin reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH. 231 matched cddid_all.tbl CDD cd06216 cd06216 99812 FNR_iron_sulfur_binding_2 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap betweed the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH. 243 matched cddid_all.tbl CDD cd06217 cd06217 99813 FNR_iron_sulfur_binding_3 Iron-sulfur binding ferredoxin reductase (FNR) proteins combine the FAD and NAD(P) binding regions of FNR with an iron-sulfur binding cluster domain. Ferredoxin-NADP+ (oxido)reductase is an FAD-containing enzyme that catalyzes the reversible electron transfer between NADP(H) and electron carrier proteins such as ferredoxin and flavodoxin. Isoforms of these flavoproteins (i.e. having a non-covalently bound FAD as a prosthetic group) are present in chloroplasts, mitochondria, and bacteria in which they participate in a wide variety of redox metabolic pathways. The C-terminal domain contains most of the NADP(H) binding residues and the N-terminal domain interacts non-covalently with the isoalloxazine rings of the flavin molecule which lies largely in a large gap between the two domains. Ferredoxin-NADP+ reductase first accepts one electron from reduced ferredoxin to form a flavin semiquinone intermediate. The enzyme then accepts a second electron to form FADH2 which then transfers two electrons and a proton to NADP+ to form NADPH. 235 matched cddid_all.tbl CDD cd06218 cd06218 99814 DHOD_e_trans FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is co-expressed with pyrK and both gene products are required for full activity, as well as 3 cofactors: FMN, FAD, and an [2Fe-2S] cluster. 246 matched cddid_all.tbl CDD cd06219 cd06219 99815 DHOD_e_trans_like1 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is co-expressed with pyrK and both gene products are required for full activity, as well as NAD binding. NAD(P) binding domain of ferredoxin reductase-like proteins catalyze electron transfer between an NAD(P)-binding domain of the alpha/beta class and a discrete (usually N-terminal) domain which vary in orientation with respect to the NAD(P) binding domain. The N-terminal domain may contain a flavin prosthetic group, as in flavoenzymes, or use flavin as a substrate. Ferredoxin is reduced in the final stage of photosystem I. The flavoprotein Ferredoxin-NADP+ reductase transfers electrons from reduced ferredoxin to FAD, forming FADH2 via a semiquinone intermediate, and then transfers a hydride ion to convert NADP+ to NADPH. 248 matched cddid_all.tbl CDD cd06220 cd06220 99816 DHOD_e_trans_like2 FAD/NAD binding domain in the electron transfer subunit of dihydroorotate dehydrogenase-like proteins. Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+. In L. lactis, DHOD B (encoded by pyrDa) is co-expressed with pyrK and both gene products are required for full activity, as well as 3 cofactors: FMN, FAD, and an [2Fe-2S] cluster. 233 matched cddid_all.tbl CDD cd06221 cd06221 99817 sulfite_reductase_like Anaerobic sulfite reductase contains an FAD and NADPH binding module with structural similarity to ferredoxin reductase and sequence similarity to dihydroorotate dehydrogenases. Clostridium pasteurianum inducible dissimilatory type sulfite reductase is linked to ferredoxin and reduces NH2OH and SeO3 at a lesser rate than it's normal substate SO3(2-). Dihydroorotate dehydrogenases (DHODs) catalyze the only redox reaction in pyrimidine de novo biosynthesis. They catalyze the oxidation of (S)-dihydroorotate to orotate coupled with the reduction of NAD+. 253 matched cddid_all.tbl CDD cd06222 cd06222 259998 RNase_H_like Ribonuclease H-like superfamily, including RNase H, HI, HII, HIII, and RNase-like domain IV of spliceosomal protein Prp8. Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as anti-HIV drug targets since RNase H inactivation inhibits reverse transcription. This model also includes the Prp8 domain IV, which adopts the RNase fold but shows low sequence homology; domain IV is implicated in key spliceosomal interactions. 121 matched cddid_all.tbl CDD cd06223 cd06223 206754 PRTases_typeI Phosphoribosyl transferase (PRT)-type I domain. Phosphoribosyl transferase (PRT) domain. The type I PRTases are identified by a conserved PRPP binding motif which features two adjacent acidic residues surrounded by one or more hydrophobic residue. PRTases catalyze the displacement of the alpha-1'-pyrophosphate of 5-phosphoribosyl-alpha1-pyrophosphate (PRPP) by a nitrogen-containing nucleophile. The reaction products are an alpha-1 substituted ribose-5'-phosphate and a free pyrophosphate (PP). PRPP, an activated form of ribose-5-phosphate, is a key metabolite connecting nucleotide synthesis and salvage pathways. The type I PRTase family includes a range of diverse phosphoribosyl transferase enzymes and regulatory proteins of the nucleotide synthesis and salvage pathways, including adenine phosphoribosyltransferase EC:2.4.2.7., hypoxanthine-guanine-xanthine phosphoribosyltransferase, hypoxanthine phosphoribosyltransferase EC:2.4.2.8., ribose-phosphate pyrophosphokinase EC:2.7.6.1., amidophosphoribosyltransferase EC:2.4.2.14., orotate phosphoribosyltransferase EC:2.4.2.10., uracil phosphoribosyltransferase EC:2.4.2.9., and xanthine-guanine phosphoribosyltransferase EC:2.4.2.22. 130 matched cddid_all.tbl CDD cd06224 cd06224 100121 REM Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal domain (RasGef_N), also called REM domain (Ras exchanger motif). This domain is common in nucleotide exchange factors for Ras-like small GTPases and is typically found immediately N-terminal to the RasGef (Cdc25-like) domain. REM contacts the GTPase and is assumed to participate in the catalytic activity of the exchange factor. Proteins with the REM domain include Sos1 and Sos2, which relay signals from tyrosine-kinase mediated signalling to Ras, RasGRP1-4, RasGRF1,2, CNrasGEF, and RAP-specific nucleotide exchange factors, to name a few. 122 matched cddid_all.tbl CDD cd06225 cd06225 381743 HAMP Histidine kinase, Adenylyl cyclase, Methyl-accepting protein, and Phosphatase (HAMP) domain. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The structure of the Af1503 HAMP dimer from Archaeoglobus fulgidus has been solved using nuclear magnetic resonance, revealing a parallel four-helix bundle; this structure has been confirmed by cross-linking analysis of HAMP domains from the Escherichia coli aerotaxis receptor Aer. It has been suggested that the four-helix arrangement can rotate between the unusually packed conformation observed in the NMR structure and a canonical coiled-coil arrangement. Such rotation may coincide with signal transduction, but a common mechanism by which HAMP domains relay a variety of input signals has yet to be established. 45 matched cddid_all.tbl CDD cd06226 cd06226 349445 M14_CPT_like Peptidase M14-like domain of an uncharacterized group of Peptidase M14 Carboxypeptidase T (CPT)-like proteins. Peptidase M14-like domain of an uncharacterized group of Peptidase M14 Carboxypeptidase T (CPT)-like proteins. This group belongs to the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPT exhibits dual-substrate specificity by cleaving C-terminal hydrophobic amino acid residues and C-terminal positively charged residues. However, CPT does not belong to this CPT-like group. 267 matched cddid_all.tbl CDD cd06227 cd06227 349446 M14-CPA-like Peptidase M14 carboxypeptidase A-like domain; uncharacterized subfamily. A functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavages. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism. 224 matched cddid_all.tbl CDD cd06228 cd06228 349447 M14-like Peptidase M14-like domain; uncharacterized subfamily. A functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavages. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism. 294 matched cddid_all.tbl CDD cd06229 cd06229 349448 M14_Endopeptidase_I Peptidase M14 carboxypeptidase family-like domain of Endopeptidase I. Peptidase M14-like domain of Gamma-D-glutamyl-L-diamino acid endopeptidase 1 (also known as Gamma-D-glutamyl-meso-diaminopimelate peptidase I, and Endopeptidase I (ENP1); EC 3.4.19.11). ENP1 is a member of the M14 family of metallocarboxypeptidases (MCPs), and is classified as belonging to subfamily C. However it has an exceptional type of activity of hydrolyzing the gamma-D-Glu-(L)meso-diaminopimelic acid (gamma-D-Glu-Dap) bond of L-Ala-gamma-D-Glu-(L)meso-diaminopimelic acid and L-Ala-gamma-D-Glu-(L)meso-diaminopimelic acid(L)-D-Ala peptides. ENP1 has a different substrate specificity and cellular role than MpaA (MpaA does not belong to this group). ENP1 hydrolyzes the gamma-D-Glu-Dap bond of MurNAc-tripeptide and MurNAc-tetrapeptide, as well as the amide bond of free tripeptide and tetrapeptide. ENP1 is active on spore cortex peptidoglycan, and is produced at stage IV of sporulation in forespore and spore integuments. 238 matched cddid_all.tbl CDD cd06230 cd06230 349449 M14_ASTE_ASPA_like Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily. The Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily belongs to the M14 family of metallocarboxypeptidases (MCPs), and includes ASTE, which catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) which cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. 177 matched cddid_all.tbl CDD cd06231 cd06231 349450 M14_REP34-like Peptidase M14-like domain similar to rapid encystment phenotype 34 (REP34). This family includes Francisella tularensis protein rapid encystment phenotype 34 (REP34) which is a zinc-containing monomeric protein demonstrating carboxypeptidase B-like activity. REP34 possesses a novel topology with its substrate binding pocket deviating from the canonical M14 peptidases with a possible catalytic role for a conserved tyrosine and distinct S1' recognition site. Thus, REP34, identified as an active carboxypeptidase and a potential key F. tularensis effector protein, may help elucidate a mechanistic understanding of F. tularensis infection of phagocytic cells. A functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavages. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism. 239 matched cddid_all.tbl CDD cd06232 cd06232 349451 M14-like Peptidase M14-like domain; uncharacterized subfamily. Peptidase M14-like domain of a functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavages. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism. 276 matched cddid_all.tbl CDD cd06233 cd06233 349452 M14-like Peptidase M14-like domain; uncharacterized subfamily. Peptidase M14-like domain of a functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavages. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism. 249 matched cddid_all.tbl CDD cd06234 cd06234 349453 M14_PaCCP-like Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases similar to Pseudomonas aerugnosa CCP (PaCCP). A bacterial subgroup of the Peptidase M14-like domain of Nna-1 (Nervous system Nuclear protein induced by Axotomy), also known as ATP/GTP binding protein (AGTPBP-1) and cytosolic carboxypeptidase (CCP)-like proteins. This subgroup includes PaCCP from Pseudomonas aeruginosa, a carboxypeptidase homologous to M14D subfamily of human CCPs. Structural complexes with well-known inhibitors of metallocarboxypeptidases indicate that PaCCP might only possess C-terminal hydrolase activity against cellular substrates of particular specificity. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Nna1-like proteins are active metallopeptidases that are thought to act on cytosolic proteins (such as alpha-tubulin in eukaryotes) to remove a C-terminal tyrosine. Nna1-like proteins from the different phyla are highly diverse, but they all contain a unique N-terminal conserved domain right before the CP domain. It has been suggested that this N-terminal domain might act as a folding domain. 256 matched cddid_all.tbl CDD cd06235 cd06235 349454 M14_AGTPBP-like Peptidase M14-like domain of human Nna1/AGTPBP-1, AGBL2 -5, and related proteins. Subgroup of the Peptidase M14-like domain of Nna-1 (Nervous system Nuclear protein induced by Axotomy), also known as ATP/GTP binding protein (AGTPBP-1) and cytosolic carboxypeptidase (CCP), and related proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. This eukaryotic subgroup includes the human Nna1/AGTPBP-1 and AGBL -2, -3, -4, and -5, and the mouse Nna1/CCP-1 and CCP -2 through -6. Nna1-like proteins are active metallopeptidases that are thought to act on cytosolic proteins such as alpha-tubulin, to remove a C-terminal tyrosine. Nna1 is widely expressed in the developing and adult nervous systems, including cerebellar Purkinje and granule neurons, miral cells of the olfactory bulb and retinal photoreceptors. Nna1 is also induced in axotomized motor neurons. Mutations in Nna1 cause Purkinje cell degeneration (pcd). The Nna1 CP domain is required to prevent the retinal photoreceptor loss and cerebellar ataxia phenotypes of pcd mice, and a functional zinc-binding domain is needed for Nna-1 to support neuron survival in these mice. Nna1-like proteins from the different phyla are highly diverse, but they all contain a unique N-terminal conserved domain right before the CP domain. It has been suggested that this N-terminal domain might act as a folding domain. 256 matched cddid_all.tbl CDD cd06236 cd06236 349455 M14_AGBL5_like Peptidase M14-like domain of ATP/GTP binding protein (AGBL)-5 and related proteins. Peptidase M14-like domain of ATP/GTP binding protein_like (AGBL)-5, and related proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. This eukaryotic subgroup includes the human AGBL5 and the mouse cytosolic carboxypeptidase (CCP)-5. ATP/GTP binding protein (AGTPBP-1/Nna1)-like proteins are active metallopeptidases that are thought to act on cytosolic proteins such as alpha-tubulin, to remove a C-terminal tyrosine. Mutations in AGTPBP-1/Nna1 cause Purkinje cell degeneration (pcd). AGTPBP-1/Nna1 however does not belong to this subgroup. AGTPBP-1/Nna1-like proteins from the different phyla are highly diverse, but they all contain a unique N-terminal conserved domain right before the CP domain. It has been suggested that this N-terminal domain might act as a folding domain. 263 matched cddid_all.tbl CDD cd06237 cd06237 349456 M14_Nna1-like Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases; uncharacterized bacterial subgroup. A bacterial subgroup of the Peptidase M14-like domain of Nna-1 (Nervous system Nuclear protein induced by Axotomy), also known as ATP/GTP binding protein (AGTPBP-1) and cytosolic carboxypeptidase (CCP),-like proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Nna1-like proteins are active metallopeptidases that are thought to act on cytosolic proteins (such as alpha-tubulin in eukaryotes) to remove a C-terminal tyrosine. Nna1-like proteins from the different phyla are highly diverse, but they all contain a unique N-terminal conserved domain right before the CP domain. It has been suggested that this N-terminal domain might act as a folding domain. 239 matched cddid_all.tbl CDD cd06238 cd06238 349457 M14-like Peptidase M14-like domain; uncharacterized subgroup. Peptidase M14-like domain of a functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism. 217 matched cddid_all.tbl CDD cd06239 cd06239 349458 M14-like Peptidase M14-like domain; uncharacterized subgroup. Peptidase M14-like domain of a functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism. 194 matched cddid_all.tbl CDD cd06240 cd06240 349459 M14-like Peptidase M14-like domain; uncharacterized subgroup. Peptidase M14-like domain of a functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavages. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism. 212 matched cddid_all.tbl CDD cd06241 cd06241 349460 M14-like Peptidase M14-like domain; uncharacterized subgroup. Peptidase M14-like domain of a functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism. 215 matched cddid_all.tbl CDD cd06242 cd06242 349461 M14-like Peptidase M14-like domain; uncharacterized subgroup. Peptidase M14-like domain of a functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavages. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism. 220 matched cddid_all.tbl CDD cd06243 cd06243 349462 M14_CP_Csd4-like Peptidase M14 carboxypeptidase Csd4 and similar proteins. This family includes peptidase M14 carboxypeptidase Csd4 from H. pylori which has been shown to be DL-carboxypeptidase with a modified zinc binding site containing a glutamine residue in place of a conserved histidine. It is an archetype of a new carboxypeptidase subfamily with a domain arrangement that differs from this family of peptide-cleaving enzymes. Csd4 plays a role in trimming uncrosslinked peptidoglycan peptide chains by cleaving the amide bond between meso-diaminopimelate and iso-D-glutamic acid in truncated peptidoglycan side chains. It acts as a cell shape determinant, similar to Campylobacter jejuni Pgp1. The M14 family of metallocarboxypeptidases (MCPs), also known as funnelins, are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavage. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism. 227 matched cddid_all.tbl CDD cd06244 cd06244 349463 M14-like Peptidase M14-like domain; uncharacterized subgroup. Peptidase M14-like domain of a functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavages. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism. 223 matched cddid_all.tbl CDD cd06245 cd06245 349464 M14_CPD_III Peptidase M14 carboxypeptidase subfamily N/E-like; Carboxypeptidase D, domain III subgroup. The third carboxypeptidase (CP)-like domain of Carboxypeptidase D (CPD; EC 3.4.17.22), domain III. CPD differs from all other metallocarboxypeptidases in that it contains multiple CP-like domains. CPD belongs to the N/E-like subfamily of the M14 family of metallocarboxypeptidases (MCPs).The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPD is a single-chain protein containing a signal peptide, three tandem repeats of CP-like domains separated by short bridge regions, followed by a transmembrane domain, and a C-terminal cytosolic tail. The first two CP-like domains of CPD contain all of the essential active site and substrate-binding residues, the third CP-like domain lacks critical residues necessary for enzymatic activity and is inactive towards standard CP substrates. Domain I is optimally active at pH 6.3-7.5 and prefers substrates with C-terminal Arg, whereas domain II is active at pH 5.0-6.5 and prefers substrates with C-terminal Lys. CPD functions in the processing of proteins that transit the secretory pathway, and is present in all vertebrates as well as Drosophila. It is broadly distributed in all tissue types. Within cells, CPD is present in the trans-Golgi network and immature secretory vesicles, but is excluded from mature vesicles. It is thought to play a role in the processing of proteins that are initially processed by furin or related endopeptidases present in the trans-Golgi network, such as growth factors and receptors. CPD is implicated in the pathogenesis of lupus erythematosus (LE), it is regulated by TGF-beta in various cell types of murine and human origin and is significantly down-regulated in CD14 positive cells isolated from patients with LE. As down -regulation of CPD leads to down-modulation of TGF-beta, CPD may have a role in a positive feedback loop. 283 matched cddid_all.tbl CDD cd06246 cd06246 349465 M14_CPB2 Peptidase M14 carboxypeptidase subfamily A/B-like; Carboxypeptidase B2 subgroup. Peptidase M14 Carboxypeptidase (CP) B2 (CPB2, also known as plasma carboxypeptidase B, carboxypeptidase U, and CPU), belongs to the carboxpeptidase A/B subfamily of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPB2 enzyme displays B-like activity; it only cleaves the basic residues lysine or arginine. It is produced and secreted by the liver as the inactive precursor, procarboxypeptidase U or PCPB2, commonly referred to as thrombin-activatable fibrinolysis inhibitor (TAFI). It circulates in plasma as a zymogen bound to plasminogen, and the active enzyme, TAFIa, inhibits fibrinolysis. It is highly regulated, increased TAFI concentrations are thought to increase the risk of thrombosis and coronary artery disease by reducing fibrinolytic activity while low TAFI levels have been correlated with chronic liver disease. 300 matched cddid_all.tbl CDD cd06247 cd06247 349466 M14_CPO Peptidase M14 carboxypeptidase subfamily A/B-like; Carboxypeptidase O subgroup. Peptidase M14 carboxypeptidase (CP) O (CPO, also known as metallocarboxypeptidase C; EC 3.4.17.) belongs to the carboxypeptidase A/B subfamily of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. CPO has not been well characterized as yet, and little is known about it. Based on modeling studies, CPO has been suggested to have specificity for acidic residues rather than aliphatic/aromatic residues as in A-like enzymes or basic residues as in B-like enzymes. It remains to be demonstrated that CPO is functional as an MCP. 298 matched cddid_all.tbl CDD cd06248 cd06248 349467 M14_CP_insect Peptidase M14 carboxypeptidase subfamily A/B-like. This family includes peptidase M14 carboxypeptidases found specifically in insects, including B-type carboxypeptidase of H. zea (CPBHz, insect gut carboxypeptidase-3) that is insensitive to potato carboxypeptidase inhibitor (PCI) in corn earworm, and midgut procarboxypeptidase A (PCPAHa, insect gut carboxypeptidase-1) from Helicoverpa armigera larva, a devastating pest of crops. PCPAHa preferentially cleaves aliphatic and aromatic residues. The peptidase M14 Carboxypeptidase (CP) A/B subfamily is one of two main M14 CP subfamilies defined by sequence and structural homology, the other being the N/E subfamily. CPs hydrolyze single, C-terminal amino acids from polypeptide chains. They have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by a globular N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. There are nine members in the A/B family: CPA1, CPA2, CPA3, CPA4, CPA5, CPA6, CPB, CPO and CPU. CPA1, CPA2 and CPB are produced by the pancreas. The A forms have slightly different specificities, with CPA1 preferring aliphatic and small aromatic residues, and CPA2 preferring the bulkier aromatic side chains. CPA3 is found in secretory granules of mast cells and functions in inflammatory processes. CPA4 is detected in hormone-regulated tissues, and is thought to play a role in prostate cancer. CPA5 is present in discrete regions of pituitary and other tissues, and cleaves aliphatic C-terminal residues. CPA6 is highly expressed in embryonic brain and optic muscle, suggesting that it may play a specific role in cell migration and axonal guidance. CPU (also called CPB2) is produced and secreted by the liver as the inactive precursor, PCPU, commonly referred to as thrombin-activatable fibrinolysis inhibitor (TAFI). Little is known about CPO but it has been suggested to have specificity for acidic residues. 297 matched cddid_all.tbl CDD cd06250 cd06250 349468 M14_PaAOTO_like Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like subfamily; subgroup includes Pseudomonas aeruginosa AotO. An uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the the M14 family of metallocarboxypeptidases. This subgroup includes Pseudomonas aeruginosa AotO and related proteins. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. The gene encoding P. aeruginosa AotO was characterized as part of an operon encoding an arginine and ornithine transport system, however it is not essential for arginine and ornithine uptake. 267 matched cddid_all.tbl CDD cd06251 cd06251 349469 M14_ASTE_ASPA-like Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup. A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. 195 matched cddid_all.tbl CDD cd06252 cd06252 349470 M14_ASTE_ASPA-like Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup. A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. 224 matched cddid_all.tbl CDD cd06253 cd06253 349471 M14_ASTE_ASPA-like Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup. A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. 211 matched cddid_all.tbl CDD cd06254 cd06254 349472 M14_ASTE_ASPA-like Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup. A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. 198 matched cddid_all.tbl CDD cd06255 cd06255 349473 M14_ASTE_ASPA-like Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup. A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. 223 matched cddid_all.tbl CDD cd06256 cd06256 349474 M14_ASTE_ASPA-like Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup. A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. 204 matched cddid_all.tbl CDD cd06257 cd06257 99751 DnaJ DnaJ domain or J-domain. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Hsp40 proteins are characterized by the presence of a J domain, which mediates the interaction with Hsp70. They may contain other domains as well, and the architectures provide a means of classification. 55 matched cddid_all.tbl CDD cd06258 cd06258 341049 M3_like "M3-like Peptidases, zincin metallopeptidases, include M2_ACE, M3A, M3B_PepF, and M32 families. The peptidase M3-like family, also called neurolysin-like family, is part of the ""zincin"" metallopeptidases, and includes the M2, M3 and M32 families of metallopeptidases. The M2 angiotensin converting enzyme (ACE, EC 3.4.15.1) is a membrane-bound, zinc-dependent dipeptidase that catalyzes the conversion of the decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. The M3 family is subdivided into two subfamilies: the widespread M3A, which comprises a number of high-molecular mass endo- and exopeptidases from bacteria, archaea, protozoa, fungi, plants and animals, and the small M3B, whose members are enzymes primarily from bacteria. Well-known mammalian/eukaryotic M3A endopeptidases are the thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (alias endopeptidase 3.4.24.16), and the mitochondrial intermediate peptidase. The first two are intracellular oligopeptidases, which act only on relatively short substrates of less than 20 amino acid residues, while the latter cleaves N-terminal octapeptides from proteins during their import into the mitochondria. The M3A subfamily also contains several bacterial endopeptidases, called oligopeptidases A, as well as a large number of bacterial carboxypeptidases, called dipeptidyl peptidases (Dcp; Dcp II; peptidyl dipeptidase; EC 3.4.15.5). M3B subfamily consists of oligopeptidase F (PepF) which hydrolyzes peptides containing 7-17 amino acid residues with fairly broad specificity. Peptidases in the M3 family contain the HEXXH motif that forms part of the active site in conjunction with a C-terminally-located Glutamic acid (Glu) residue. A single zinc ion is ligated by the side-chains of the two Histidine (His) residues, and the more C-terminal Glu. Most of the peptidases are synthesized without signal peptides or propeptides, and function intracellularly. There are similarities to the thermostable carboxypeptidases from Pyrococcus furiosus carboxypeptidase (PfuCP), and Thermus aquaticus (TaqCP), belonging to peptidase family M32. Little is known about function of this family, including carboxypeptidases Taq and Pfu." 473 matched cddid_all.tbl CDD cd06259 cd06259 99750 YdcF-like YdcF-like. YdcF-like is a large family of mainly bacterial proteins, with a few members found in fungi, plants, and archaea. Escherichia coli YdcF has been shown to bind S-adenosyl-L-methionine (AdoMet), but a biochemical function has not been idenitified. The family also includes Escherichia coli sanA and Salmonella typhimurium sfiX, which are involved in vancomycin resistance; sfiX may also be involved in murein synthesis. 150 matched cddid_all.tbl CDD cd06260 cd06260 411709 DUF820-like Uncharacterized PDDEXK family nuclease. The Domain of unknown function 820 (DUF820) family is composed of hypothetical proteins that are greatly expanded in cyanobacteria. The proteins are found sporadically in other bacteria. They have been predicted to belong to the PD-(D/E)xK superfamily of nucleases, which includes very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 155 matched cddid_all.tbl CDD cd06261 cd06261 119394 TM_PBP2 Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. For these transporters the ABCs and TMs are on independent polypeptide chains. These systems transport a diverse range of substrates. Most are specific for a single substrate or a group of related substrates; however some transporters are more promiscuous, transporting structurally diverse substrates such as the histidine/lysine and arginine transporter in Enterobacteriaceae. In the latter case, this is achieved through binding different PBPs with different specificities to the TMs. For other promiscuous transporters such as the multiple-sugar transporter Msm of Streptococcus mutans, the PBP has a wide substrate specificity. These transporters include the maltose-maltodextrin, phosphate and sulfate transporters, among others. 190 matched cddid_all.tbl CDD cd06262 cd06262 293792 metallo-hydrolase-like_MBL-fold mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain. Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily. Activities carried out by superfamily members include class B beta-lactamases which can catalyze the hydrolysis of a wide range of beta-lactam antibiotics, hydroxyacylglutathione hydrolases (also called glyoxalase II) which hydrolyze S-d-lactoylglutathione to d-lactate in the second step of the glycoxlase system, AHL lactonases which catalyze the hydrolysis and opening of the homoserine lactone rings of acyl homoserine lactones (AHLs), persulfide dioxygenase which catalyze the oxidation of glutathione persulfide to glutathione and persulfite in the mitochondria, flavodiiron proteins which catalyze the reduction of oxygen and/or nitric oxide to water or nitrous oxide respectively, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J which has both 5'-3' exoribonucleolytic and endonucleolytic activity and ribonuclease Z which catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors, cyclic nucleotide phosphodiesterases which decompose cyclic adenosine and guanosine 3', 5'-monophosphate (cAMP and cGMP) respectively, insecticide hydrolases, and proteins required for natural transformation competence. The diversity of biological roles is reflected in variations in the active site metallo-chemistry, for example classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, human persulfide dioxygenase ETHE1 is a mono-iron binding member of the superfamily; Arabidopsis thaliana hydroxyacylglutathione hydrolases incorporates iron, manganese, and zinc in its dinuclear metal binding site, and flavodiiron proteins contains a diiron site. 188 matched cddid_all.tbl CDD cd06263 cd06263 99706 MAM Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members include: type IIB receptor protein tyrosine phosphatases (such as RPTPmu), meprins (plasma membrane metalloproteases), neuropilins (receptors of secreted semaphorins), and zonadhesins (sperm-specific membrane proteins which bind to the extracellular matrix of the egg). In meprin A and neuropilin-1 and -2, MAM is involved in homo-oligomerization. In RPTPmu, it has been associated with both homophilic adhesive (trans) interactions and lateral (cis) receptor oligomerization. In a GPI-anchored protein that is expressed in cells in the embryonic chicken spinal chord, MDGA1, the MAM domain has been linked to heterophilic interactions with axon-rich region. 157 matched cddid_all.tbl CDD cd06265 cd06265 119387 RNase_A_canonical "Canonical RNase A family includes all vertebrate homologues to the bovine pancreatic ribonuclease A (RNase A) that contain the catalytic site, necessary for RNase activity. In the human genome 8 RNases , refered to as ""canonical"" RNases, have been identified, pancreatic RNase (RNase 1), Eosinophil Derived Neurotoxin (SEDN/RNASE 2), Eosinophil Cationic Protein (ECP/RNase 3), RNase 4, Angiogenin (RNase 5), RNase 6 or k6, the skin derived RNase (RNase 7) and RNase 8. The eight human genes are all located in a cluster on chromosome 14. Canonical RNase A enzymes have special biological activities; for example, some stimulate the development of vascular endothelial cells, dendritic cells, and neurons, are cytotoxic/anti-tumoral and/or anti-pathogenic. RNase A is involved in endonucleolytic cleavage of 3'-phosphomononucleotides and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates. The catalytic mechanism is a transphosphorylation of P-O 5' bonds on the 3' side of pyrimidines and subsequent hydrolysis to generate 3' phosphate groups. The canonical RNase A family proteins have a conserved catalytic triad (two histidines and one lysine). They also share 6 to 8 cysteines that form three to four disulfide bonds. Two disulfide bonds that are close to the N and C termini contribute most significantly to conformational stability. Angiogenin or RNAse 5 has been implicated in tumor-associated angiogenesis. Comparative analysis in mammals and birds indicates that the whole family may have originated from a RNase 5-like gene. This hypothesis is supported by the fact that only RNase 5-like RNases have been reported outside the mammalian class. The RNase 5 group would therefore be the most ancient form of this family, and all other members would have arisen during mammalian evolution." 115 matched cddid_all.tbl CDD cd06266 cd06266 259999 RNase_HII Ribonuclease H (RNase H) type II family (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). This family contains ribonucleases HII (RNases H2) which include bacterial RNase HII and HIII, and eukaryotic and archaeal RNase H2/HII. RNase H2 cleaves RNA sequences that are part of RNA/DNA hybrids or that are incorporated into DNA, thereby preventing genomic instability and the accumulation of aberrant nucleic acid which can induce Aicardi-Goutieres syndrome, a severe autoimmune disorder in humans. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes, but no prokaryotic genome contains the combination of only RNase HI and HIII. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype in E. coli. 193 matched cddid_all.tbl CDD cd06267 cd06267 380491 PBP1_LacI_sugar_binding-like ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI transcriptional regulator family belonging to the type 1 periplasmic-binding fold protein superfamily. In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain. 264 matched cddid_all.tbl CDD cd06268 cd06268 380492 PBP1_ABC_transporter_LIVBP-like periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type 1 periplasmic binding fold protein superfamily. Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type 1 periplasmic binding fold protein superfamily. They are mostly present in archaea and eubacteria, and are primarily involved in scavenging solutes from the environment. ABC-type transporters couple ATP hydrolysis with the uptake and efflux of a wide range of substrates across bacterial membranes, including amino acids, peptides, lipids and sterols, and various drugs. These systems are comprised of transmembrane domains, nucleotide binding domains, and in most bacterial uptake systems, periplasmic binding proteins (PBPs) which transfer the ligand to the extracellular gate of the transmembrane domains. These PBPs bind their substrates selectively and with high affinity. Members of this group include ABC-type Leucine-Isoleucine-Valine-Binding Proteins (LIVBP), which are homologous to the aliphatic amidase transcriptional repressor, AmiC, of Pseudomonas aeruginosa. The uncharacterized periplasmic components of various ABC-type transport systems are included in this group. 298 matched cddid_all.tbl CDD cd06269 cd06269 380493 PBP1_glutamate_receptors-like ligand-binding domain of family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases such as natriuretic peptide receptors (NPRs), and N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of ionotropic glutamate receptors. This CD represents the ligand-binding domain of the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases such as the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the ionotropic glutamate receptors, all of which are structurally similar and related to the periplasmic-binding fold type 1 family. The family C GPCRs consists of metabotropic glutamate receptor (mGluR), a calcium-sensing receptor (CaSR), gamma-aminobutyric acid receptor (GABAbR), the promiscuous L-alpha-amino acid receptor GPR6A, families of taste and pheromone receptors, and orphan receptors. Truncated splicing variants of the orphan receptors are not included in this CD. The family C GPCRs are activated by endogenous agonists such as amino acids, ions, and sugar based molecules. Their amino terminal ligand-binding region is homologous to the bacterial leucine-isoleucine-valine binding protein (LIVBP) and a leucine binding protein (LBP). The ionotropic glutamate receptors (iGluRs) have an integral ion channel and are subdivided into three major groups based on their pharmacology and structural similarities: NMDA receptors, AMPA receptors, and kainate receptors. The family of membrane bound guanylyl cyclases is further divided into three subfamilies: the ANP receptor (GC-A)/C-type natriuretic peptide receptor (GC-B), the heat-stable enterotoxin receptor (GC-C)/sensory organ specific membrane GCs such as retinal receptors (GC-E, GC-F), and olfactory receptors (GC-D and GC-G). 332 matched cddid_all.tbl CDD cd06270 cd06270 380494 PBP1_GalS-like ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type 1 periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar binding of ABC-type transport systems. 266 matched cddid_all.tbl CDD cd06271 cd06271 380495 PBP1_AglR_RafR-like ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 264 matched cddid_all.tbl CDD cd06272 cd06272 380496 PBP1_hexuronate_repressor-like ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and close homologs, all members of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor for the hexuronate utilization operon from Bacillus species and its close homologs from other bacteria, all of which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 266 matched cddid_all.tbl CDD cd06273 cd06273 380497 PBP1_LacI-like ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 268 matched cddid_all.tbl CDD cd06274 cd06274 380498 PBP1_FruR ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs. Ligand binding domain of DNA transcription repressor specific for fructose (FruR) and its close homologs, all of which are members of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to members of the type 1 periplasmic binding protein superfamily. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor 264 matched cddid_all.tbl CDD cd06275 cd06275 380499 PBP1_PurR ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. Ligand-binding domain of purine repressor, PurR, which functions as the master regulatory protein of de novo purine nucleotide biosynthesis in Escherichia coli. This dimeric PurR belongs to the LacI-GalR family of transcription regulators and is activated to bind to DNA operator sites by initially binding either of high affinity corepressors, hypoxanthine or guanine. PurR is composed of two functional domains: aan N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the purine transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 269 matched cddid_all.tbl CDD cd06277 cd06277 380500 PBP1_LacI-like ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 275 matched cddid_all.tbl CDD cd06278 cd06278 380501 PBP1_LacI-like ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 266 matched cddid_all.tbl CDD cd06279 cd06279 380502 PBP1_LacI-like ligand-binding domain of an uncharacterized transcription regulator from Corynebacterium glutamicum and its close homologs from other bacteria. This group includes the ligand-binding domain of an uncharacterized transcription regulator from Corynebacterium glutamicum and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding. 284 matched cddid_all.tbl CDD cd06280 cd06280 380503 PBP1_LacI-like ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus saprophyticus and its close homologs from other bacteria. This group includes the ligand-binding domain of an uncharacterized transcription regulator from Staphylococcus saprophyticus and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding. 266 matched cddid_all.tbl CDD cd06281 cd06281 380504 PBP1_LacI-like ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 270 matched cddid_all.tbl CDD cd06282 cd06282 380505 PBP1_LacI-like ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 267 matched cddid_all.tbl CDD cd06283 cd06283 380506 PBP1_RegR_EndR_KdgR-like ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR. Ligand-binding domain of DNA transcription repressor RegR and other putative regulators such as KdgR and EndR, all of which are members of the LacI-GalR family of bacterial transcription regulators. RegR regulates bacterial competence and the expression of virulence factors, including hyaluronidase. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 266 matched cddid_all.tbl CDD cd06284 cd06284 380507 PBP1_LacI-like ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group includes the ligand-binding domain of an uncharacterized transcription regulator from Actinobacillus succinogenes and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding. 267 matched cddid_all.tbl CDD cd06285 cd06285 380508 PBP1_LacI-like ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 269 matched cddid_all.tbl CDD cd06286 cd06286 380509 PBP1_CcpB-like ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. This group includes the ligand-binding domain of a novel transcription factor implicated in catabolite repression in Bacillus and Clostridium species. Catabolite control protein B (CcpB) is 30% identical in sequence to CcpA which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. Like CcpA, the DNA-binding protein CcpB exerts its catabolite-repressing effect by a mechanism dependent on the presence of HPr(Ser-P), the small phosphocarrier proteins of the phosphoenolpyruvate-sugar phosphotransferase system, but with a less significant degree. 262 matched cddid_all.tbl CDD cd06287 cd06287 380510 PBP1_LacI-like ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 268 matched cddid_all.tbl CDD cd06288 cd06288 380511 PBP1_sucrose_transcription_regulator ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of DNA-binding regulatory proteins specific to sucrose that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 268 matched cddid_all.tbl CDD cd06289 cd06289 380512 PBP1_MalI-like ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 268 matched cddid_all.tbl CDD cd06290 cd06290 380513 PBP1_LacI-like ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 267 matched cddid_all.tbl CDD cd06291 cd06291 380514 PBP1_Qymf-like ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus Metalliredigens (strain Qymf) and its close homologs. This group includes the ligand binding domain of the lacI-like transcription regulator from a novel metal-reducing bacterium Alkaliphilus metalliredigens (strain Qymf) and its close homologs. Qymf is a strict anaerobe that could be grown in the presence of borax and its cells are straight rods that produce endospores. This group is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 264 matched cddid_all.tbl CDD cd06292 cd06292 380515 PBP1_AglR_RafR-like Ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that of the repressors specific raffinose (RafR) and alpha-glucosides (AglR) which are members of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins highly similar to DNA transcription repressors specific for raffinose (RafR) and alpha-glucosides (AglR). Members of this group belong to the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 273 matched cddid_all.tbl CDD cd06293 cd06293 380516 PBP1_LacI-like ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 270 matched cddid_all.tbl CDD cd06294 cd06294 380517 PBP1_MalR-like ligand-binding domain of maltose transcription regulator MalR which is a member of the LacI-GalR family repressors. This group includes the ligand-binding domain of maltose transcription regulator MalR which is a member of the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 269 matched cddid_all.tbl CDD cd06295 cd06295 380518 PBP1_CelR ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. This group includes the ligand binding domain of a transcription regulator of cellulose genes, CelR, which is highly homologous to the LacI-GalR family of bacterial transcription regulators. The binding of CelR to the celE promoter is inhibited specifically by cellobiose. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 273 matched cddid_all.tbl CDD cd06296 cd06296 380519 PBP1_CatR-like ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 270 matched cddid_all.tbl CDD cd06297 cd06297 380520 PBP1_CcpA_TTHA0807 ligand-binding domain of TTHA0807, a CcpA regulator, from Thermus thermophilus HB8 and its close homologs. Ligand-binding domain of the uncharacterized transcription regulator TTHA0807 from the extremely thermophilic organism Thermus thermophilus HB8 and close homologs from other bacteria. Although its exact biological function is not known, the TTHA0807 belongs to the catabolite control protein A (CcpA)family of regulatory proteins. The CcpA functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators. 268 matched cddid_all.tbl CDD cd06298 cd06298 380521 PBP1_CcpA ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation. Ligand-binding domain of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators. 268 matched cddid_all.tbl CDD cd06299 cd06299 380522 PBP1_LacI-like ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum produces significant amounts of L-glutamate directly from cheap sugar and ammonia. This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 268 matched cddid_all.tbl CDD cd06300 cd06300 380523 PBP1_ABC_sugar_binding-like periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail. 302 matched cddid_all.tbl CDD cd06301 cd06301 380524 PBP1_rhizopine_binding-like periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily. 272 matched cddid_all.tbl CDD cd06302 cd06302 380525 PBP1_LsrB_Quorum_Sensing-like periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs. Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type 1 periplasmic binding protein superfamily. LsrB, which is part of the ABC transporter complex LsrABCD, binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding protein in interspecies signaling. 296 matched cddid_all.tbl CDD cd06303 cd06303 380526 PBP1_LuxPQ_Quorum_Sensing periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs. Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs from other bacteria. The members of this group are highly homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea, and that are members of the type 1 periplasmic binding protein superfamily. The Vibrio harveyi AI-2 receptor consists of two polypeptides, LuxP and LuxQ: LuxP is a periplasmic binding protein that binds AI-2 by clamping it between two domains, LuxQ is an integral membrane protein belonging to the two-component sensor kinase family. Unlike AI-2 bound to the LsrB receptor in Salmonella typhimurium, the Vibrio harveyi AI-2 signaling molecule has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LuxPQ to control light production as well as its motility behavior. 320 matched cddid_all.tbl CDD cd06304 cd06304 380527 PBP1_BmpA_Med_PnrA-like periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. These outer membrane proteins include Med, a cell-surface localized protein regulating the competence transcription factor gene comK in Bacillus subtilis, and PnrA, a periplasmic purine nucleoside binding protein of an ATP-binding cassette (ABC) transport system in Treponema pallidum. All contain the type 1 periplasmic sugar-binding protein-like fold. 262 matched cddid_all.tbl CDD cd06305 cd06305 380528 PBP1_methylthioribose_binding-like similar to methylthioribose-binding protein of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily. Proteins similar to methylthioribose-binding protein of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR. 273 matched cddid_all.tbl CDD cd06306 cd06306 380529 PBP1_TorT-like TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type 1 periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport. 269 matched cddid_all.tbl CDD cd06307 cd06307 380530 PBP1_sugar_binding periplasmic sugar-binding domain of uncharacterized transport systems. Periplasmic sugar-binding domain of uncharacterized transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily. The members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes. 275 matched cddid_all.tbl CDD cd06308 cd06308 380531 PBP1_sensor_kinase-like periplasmic binding domain of two-component sensor kinase signaling systems. Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail. 268 matched cddid_all.tbl CDD cd06309 cd06309 380532 PBP1_galactofuranose_YtfQ-like periplasmic binding domain of ABC-type galactofuranose YtfQ-like transport systems. Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally. 285 matched cddid_all.tbl CDD cd06310 cd06310 380533 PBP1_ABC_sugar_binding-like monosaccharide ABC transporter substrate-binding protein such as CUT2. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 272 matched cddid_all.tbl CDD cd06311 cd06311 380534 PBP1_ABC_sugar_binding-like periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 270 matched cddid_all.tbl CDD cd06312 cd06312 380535 PBP1_ABC_sugar_binding-like periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 272 matched cddid_all.tbl CDD cd06313 cd06313 380536 PBP1_ABC_ThpA_XypA periplasmic sugar-binding proteins (ThpA and XypA) of ABC-type transport systems. This group includes periplasmic D-threitol-binding protein ThpA and xylitol/L-sorbitol-binding protein XypA, which are part of sugar ABC-type transport systems. Both ThpA and XypA share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. 277 matched cddid_all.tbl CDD cd06314 cd06314 380537 PBP1_tmGBP periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs. Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs from other bacteria. They are members of the type 1 periplasmic binding protein superfamily which consists of two domains connected by a three-stranded hinge. TmGBP is specific for glucose and its binding pocket is buried at the interface of the two domains. TmGBP also exhibits high thermostability and the highest structural similarity to E. coli glucose binding protein (ecGBP). 271 matched cddid_all.tbl CDD cd06315 cd06315 380538 PBP1_ABC_sugar_binding-like periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 278 matched cddid_all.tbl CDD cd06316 cd06316 380539 PBP1_ABC_sugar_binding-like periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 294 matched cddid_all.tbl CDD cd06317 cd06317 380540 PBP1_ABC_sugar_binding-like periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 281 matched cddid_all.tbl CDD cd06318 cd06318 380541 PBP1_ABC_D-talitol-like periplasmic D-talitol-binding protein of an ABC transport system and similar proteins. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 282 matched cddid_all.tbl CDD cd06319 cd06319 380542 PBP1_ABC_sugar_binding-like periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 278 matched cddid_all.tbl CDD cd06320 cd06320 380543 PBP1_allose_binding periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily. Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. 283 matched cddid_all.tbl CDD cd06321 cd06321 380544 PBP1_ABC_sugar_binding-like periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 270 matched cddid_all.tbl CDD cd06322 cd06322 380545 PBP1_ABC_sugar_binding-like periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 270 matched cddid_all.tbl CDD cd06323 cd06323 380546 PBP1_ribose_binding periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis D-ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group belong to the type 1 periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability. 268 matched cddid_all.tbl CDD cd06324 cd06324 380547 PBP1_ABC_sugar_binding-like periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 317 matched cddid_all.tbl CDD cd06325 cd06325 380548 PBP1_ABC_unchar_transporter type 1 periplasmic ligand-binding domain of uncharacterized ABC-type transport systems predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This group includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); its ligand specificity has not been determined experimentally. 282 matched cddid_all.tbl CDD cd06326 cd06326 380549 PBP1_ABC_ligand_binding-like periplasmic ligand-binding domain of uncharacterized ABC-type transport systems predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This group includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); its ligand specificity has not been determined experimentally, however. 339 matched cddid_all.tbl CDD cd06327 cd06327 380550 PBP1_SBP-like periplasmic substrate-binding domain of active transport proteins (substrate binding proteins or SBPs). Periplasmic substrate-binding domain of active transport proteins found in gram-negative, gram-positive bacteria, and archaea. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids. 336 matched cddid_all.tbl CDD cd06328 cd06328 380551 PBP1_SBP-like periplasmic substrate-binding domain of active transport proteins (substrate binding proteins or SBPs). Periplasmic substrate-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids. 336 matched cddid_all.tbl CDD cd06329 cd06329 380552 PBP1_SBP-like periplasmic substrate-binding domain of active transport proteins (substrate binding proteins or SBPs). Periplasmic substrate-binding domain of active transport proteins found in bacteria and Archaea. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids. 343 matched cddid_all.tbl CDD cd06330 cd06330 380553 PBP1_As_SBP-like periplasmic substrate-binding domain of active transport proteins. Periplasmic substrate-binding domain of active transport proteins found in bacteria and Archaea that is predicted to be involved in the efflux of toxic compounds. Members of this subgroup include proteins from Herminiimonas arsenicoxydans, which is resistant to arsenic (As) and various heavy metals such as cadmium and zinc. Moreover, they show significant sequence similarity to the cluster of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. 342 matched cddid_all.tbl CDD cd06331 cd06331 380554 PBP1_AmiC-like type 1 periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF). This group includes the type 1 periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF), found in bacteria and Archaea. AmiC controls expression of the amidase operon by a ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction. In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon is induced. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two transmembrane proteins present in various hydrophobic amino acid-binding transport systems. 333 matched cddid_all.tbl CDD cd06332 cd06332 380555 PBP1_aromatic_compounds-like type 1 periplasmic binding proteins of active transport systems predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes. This group includes the type 1 periplasmic binding proteins of active transport systems that are predicted to be involved in transport of aromatic compounds such as 2-nitrobenzoic acid and alkylbenzenes; their substrate specificities are not well characterized, however. Members also exhibit close similarity to active transport systems for short chain amides and/or urea found in bacteria and archaea. 336 matched cddid_all.tbl CDD cd06333 cd06333 380556 PBP1_ABC_RPA1789-like type 1 periplasmic binding-protein component (CouP) of an ABC system (CouPSTU; RPA1789, RPA1791-1793), involved in active transport of lignin-derived aromatic substrates, and its close homologs. This group includes RPA1789 (CouP) from Rhodopseudomonas palustris and its close homologs in other bacteria. RPA1789 (CouP) is the periplasmic binding-protein component of an ABC system (CouPSTU; RPA1789, RPA1791-1793) that is involved in the active transport of lignin-derived aromatic substrates. Members of this group has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP). 342 matched cddid_all.tbl CDD cd06334 cd06334 380557 PBP1_ABC_ligand_binding-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine binding protein (LIVBP); however their ligand specificity has not been determined experimentally. 360 matched cddid_all.tbl CDD cd06335 cd06335 380558 PBP1_ABC_ligand_binding-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine binding protein (LIVBP); however their ligand specificity has not been determined experimentally. 348 matched cddid_all.tbl CDD cd06336 cd06336 380559 PBP1_ABC_ligand_binding-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems predicted to be involved in transport of amino acids, peptides, or inorganic ions. This group includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, their ligand specificity has not been determined experimentally. 345 matched cddid_all.tbl CDD cd06337 cd06337 380560 PBP1_ABC_ligand_binding-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine binding protein (LIVBP); however their ligand specificity has not been determined experimentally. 354 matched cddid_all.tbl CDD cd06338 cd06338 380561 PBP1_ABC_ligand_binding-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT); however, their ligand specificity has not been determined experimentally. 347 matched cddid_all.tbl CDD cd06339 cd06339 380562 PBP1_YraM_LppC_lipoprotein-like periplasmic binding component of lipoprotein LppC, an immunodominant antigen. This subgroup includes periplasmic binding component of lipoprotein LppC, an immunodominant antigen, whose molecular function is not characterized. Members of this subgroup are predicted to be involved in transport of lipid compounds, and they are sequence similar to the family of ABC-type hydrophobic amino acid transporters (HAAT). 331 matched cddid_all.tbl CDD cd06340 cd06340 380563 PBP1_ABC_ligand_binding-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, their ligand specificity has not been determined experimentally. 352 matched cddid_all.tbl CDD cd06341 cd06341 380564 PBP1_ABC_ligand_binding-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters such as leucine-isoleucine-valine binding protein (LIVBP); however their ligand specificity has not been determined experimentally. 340 matched cddid_all.tbl CDD cd06342 cd06342 380565 PBP1_ABC_LIVBP-like type 1 periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup includes the type 1 periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup also includes a leucine-specific binding protein (or LivK), which is very similar in sequence and structure to leucine-isoleucine-valine binding protein (LIVBP). ABC-type active transport systems are transmembrane proteins that function in the transport of diverse sets of substrates across extra- and intracellular membranes, including carbohydrates, amino acids, inorganic ions, dipeptides and oligopeptides, metabolic products, lipids and sterols, and heme, to name a few. 334 matched cddid_all.tbl CDD cd06343 cd06343 380566 PBP1_ABC_ligand_binding-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally. 355 matched cddid_all.tbl CDD cd06344 cd06344 380567 PBP1_ABC_HAAT-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of hydrophobic amino acids or peptides. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of hydrophobic amino acids or peptides. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. 332 matched cddid_all.tbl CDD cd06345 cd06345 380568 PBP1_ABC_ligand_binding-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. 356 matched cddid_all.tbl CDD cd06346 cd06346 380569 PBP1_ABC_ligand_binding-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. 314 matched cddid_all.tbl CDD cd06347 cd06347 380570 PBP1_ABC_LivK_ligand_binding-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. 334 matched cddid_all.tbl CDD cd06348 cd06348 380571 PBP1_ABC_HAAT-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids or peptides. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of amino acids or peptides. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. 342 matched cddid_all.tbl CDD cd06349 cd06349 380572 PBP1_ABC_HAAT-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids or peptides. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of amino acids or peptides. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. 338 matched cddid_all.tbl CDD cd06350 cd06350 380573 PBP1_GPCR_family_C-like ligand-binding domain of membrane-bound glutamate receptors that mediate excitatory transmission on the cellular surface through initial binding of glutamate; categorized into ionotropic glutamate receptors (iGluRs) and metabotropic glutamate receptors (mGluRs). Ligand-binding domain of membrane-bound glutamate receptors that mediate excitatory transmission on the cellular surface through initial binding of glutamate and are categorized into ionotropic glutamate receptors (iGluRs) and metabotropic glutamate receptors (mGluRs). The metabotropic glutamate receptors (mGluR) are key receptors in the modulation of excitatory synaptic transmission in the central nervous system. The mGluRs are coupled to G proteins and are thus distinct from the iGluRs which internally contain ligand-gated ion channels. The mGluR structure is divided into three regions: the extracellular region, the seven-spanning transmembrane region and the cytoplasmic region. The extracellular region is further divided into the ligand-binding domain (LBD) and the cysteine-rich domain. The LBD has sequence similarity to the LIVBP, which is a bacterial periplasmic protein (PBP), as well as to the extracellular region of both iGluR and the gamma-aminobutyric acid (GABA)b receptor. iGluRs are divided into three main subtypes based on pharmacological profile: NMDA, AMPA, and kainate receptors. All family C GPCRs have a large extracellular N terminus that contain a domain with homology to bacterial periplasmic amino acid-binding proteins. 350 matched cddid_all.tbl CDD cd06351 cd06351 380574 PBP1_iGluR_N_LIVBP-like N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NMDA, AMPA, and kainate receptor subtypes of ionotropic glutamate receptors (iGluRs). N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NMDA, AMPA, and kainate receptor subtypes of ionotropic glutamate receptors (iGluRs). While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Glutamate mediates the majority of excitatory synaptic transmission in the central nervous system via two broad classes of ionotropic receptors characterized by their response to glutamate agonists: N-methyl-aspartate (NMDA) and non-NMDA receptors. NMDA receptors have intrinsically slow kinetics, are highly permeable to Ca2+, and are blocked by extracellular Mg2+ in a voltage-dependent manner. On the other hand, non-NMDA receptors have faster kinetics, are weakly permeable to Ca2+, and are not blocked by extracellular Mg2+. While non-NMDA receptors typically mediate excitatory synaptic responses at resting membrane potentials, NMDA receptors contribute to several forms of synaptic plasticity and are suggested to play an important role in the development of synaptic pathways. 348 matched cddid_all.tbl CDD cd06352 cd06352 380575 PBP1_NPR_GC-like ligand-binding domain of membrane guanylyl-cyclase receptors. Ligand-binding domain of membrane guanylyl-cyclase receptors. Membrane guanylyl cyclases (GC) have a single membrane-spanning region and are activated by endogenous and exogenous peptides. This family can be divided into three major subfamilies: the natriuretic peptide receptors (NPRs), sensory organ-specific membrane GCs, and the enterotoxin/guanylin receptors. The binding of peptide ligands to the receptor results in the activation of the cytosolic catalytic domain. Three types of NPRs have been cloned from mammalian tissues: NPR-A/GC-A, NPR-B/ GC-B, and NPR-C. In addition, two of the GCs, GC-D and GC-G, appear to be pseudogenes in humans. Atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) are produced in the heart, and both bind to the NPR-A. NPR-C, also termed the clearance receptor, binds each of the natriuretic peptides and can alter circulating levels of these peptides. The ligand binding domain of the NPRs exhibits strong structural similarity to the type 1 periplasmic binding fold protein family. 391 matched cddid_all.tbl CDD cd06353 cd06353 380576 PBP1_Med-like periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Periplasmic binding domain of the basic membrane lipoprotein Med in Bacillus and its close homologs from other bacteria and Archaea. Med, a cell-surface localized protein, which regulates the competence transcription factor gene comK in Bacillus subtilis, lacks the DNA binding domain when compared with structures of transcription regulators from the LacI family. Nevertheless, Med has significant overall sequence homology to various periplasmic substrate-binding proteins. Moreover, the structure of Med shows a striking similarity to PnrA, a periplasmic nucleoside binding protein of an ATP-binding cassette transport system. Members of this group contain the type 1 periplasmic sugar-binding protein-like fold. 260 matched cddid_all.tbl CDD cd06354 cd06354 380577 PBP1_PrnA-like periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. The PnrA lipoprotein, also known as Tp0319 or TmpC, represents a novel family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC) transport system (pnrABCDE). It shows a striking structural similarity to another basic membrane lipoprotein Med which regulates the competence transcription factor gene, comK, in Bacillus subtilis. The members of PnrA-like subgroup are likely to have similar nucleoside-binding functions and a similar type 1 periplasmic sugar-binding protein-like fold. 268 matched cddid_all.tbl CDD cd06355 cd06355 380578 PBP1_FmdD-like periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF), found in Methylophilus methylotrophus, and its homologs from other bacteria. FmdD, a type 1 periplasmic binding protein, is induced by short-chain amides and urea and repressed by excess ammonia, while FmdE and FmdF are hydrophobic transmembrane proteins. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two transmembrane proteins present in various hydrophobic amino acid-binding transport systems. 347 matched cddid_all.tbl CDD cd06356 cd06356 380579 PBP1_amide_urea_BP-like periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the type 1 periplasmic-binding proteins that are predicted to have a function similar to that of an active transport system for short chain amides and/or urea in bacteria and Archaea, by sequence comparison and phylogenetic analysis. 334 matched cddid_all.tbl CDD cd06357 cd06357 380580 PBP1_AmiC periplasmic binding domain of amidase (AmiC) that belongs to the type 1 periplasmic binding fold protein family. This group includes the periplasmic binding domain of amidase (AmiC) that belongs to the type 1 periplasmic binding fold protein family. AmiC controls expression of the amidase operon by the ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction. In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon are induced. 357 matched cddid_all.tbl CDD cd06358 cd06358 380581 PBP1_NHase type 1 periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides. This group includes the type 1 periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides, which are subsequently converted by amidases to yield free carboxylic acids and ammonia. NHases from bacteria and fungi have been purified and characterized. In Rhodococcus sp., the nitrile hydratase operon consists of six genes encoding NHase regulator 2, NHase regulator 1, amidase, NHase alpha subunit, NHase beta subunit, and NHase activator. The operon produces a constitutive hydratase that has a broad substrate spectrum: aliphatic and aromatic nitriles, mononitriles and dinitriles, hydroxynitriles and amino-nitriles, and a constitutive amidase of equally low substrate specificity. NHases are metalloenzymes containing either cobalt or iron, and therefore can be classified into two subgroups: ferric NHases and cobalt NHases. 333 matched cddid_all.tbl CDD cd06359 cd06359 380582 PBP1_Nba-like type 1 periplasmic binding component of active transport systems predicted to be involved in 2-nitrobenzoic acid degradation pathway. This group includes the type 1 periplasmic binding component of active transport systems that are predicted to be involved in 2-nitrobenzoic acid degradation pathway; their substrate specificities are not well characterized. 333 matched cddid_all.tbl CDD cd06360 cd06360 380583 PBP1_alkylbenzenes-like type 1 periplasmic binding component of active transport systems predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene. This group includes the type 1 periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; their substrate specificity is not well characterized, however. 357 matched cddid_all.tbl CDD cd06361 cd06361 380584 PBP1_GPC6A-like ligand-binding domain of the promiscuous L-alpha-amino acid receptor GPRC6A which is a broad-spectrum amino acid-sensing receptor. This family includes the ligand-binding domain of the promiscuous L-alpha-amino acid receptor GPRC6A which is a broad-spectrum amino acid-sensing receptor, and its fish homolog, the 5.24 chemoreceptor. GPRC6A is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into cellular responses. 401 matched cddid_all.tbl CDD cd06362 cd06362 380585 PBP1_mGluR ligand binding domain of metabotropic glutamate receptors (mGluR). Ligand binding domain of the metabotropic glutamate receptors (mGluR), which are members of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into cellular responses. mGluRs bind to glutamate and function as an excitatory neurotransmitter; they are involved in learning, memory, anxiety, and the perception of pain. Eight subtypes of mGluRs have been cloned so far, and are classified into three groups according to their sequence similarities, transduction mechanisms, and pharmacological profiles. Group I is composed of mGlu1R and mGlu5R that both stimulate PLC hydrolysis. Group II includes mGlu2R and mGlu3R, which inhibit adenylyl cyclase, as do mGlu4R, mGlu6R, mGlu7R, and mGlu8R, which form group III. 460 matched cddid_all.tbl CDD cd06363 cd06363 380586 PBP1_taste_receptor ligand-binding domain of the T1R taste receptor. Ligand-binding domain of the T1R taste receptor. The T1R is a member of the family C receptors within the G-protein coupled receptor superfamily, which also includes the metabotropic glutamate receptors, GABAb receptors, the calcium-sensing receptor (CaSR), the V2R pheromone receptors, and a small group of uncharacterized orphan receptors. 418 matched cddid_all.tbl CDD cd06364 cd06364 380587 PBP1_CaSR ligand-binding domain of the CaSR calcium-sensing receptor, a member of the family C receptors within the G-protein coupled receptor superfamily. Ligand-binding domain of the CaSR calcium-sensing receptor, which is a member of the family C receptors within the G-protein coupled receptor superfamily. CaSR provides feedback control of extracellular calcium homeostasis by responding sensitively to acute fluctuations in extracellular ionized Ca2+ concentration. This ligand-binding domain has homology to the bacterial leucine-isoleucine-valine binding protein (LIVBP) and a leucine binding protein (LBP). CaSR is widely expressed in mammalian tissues and is active in tissues that are not directly involved in extracellular calcium homeostasis. Moreover, CaSR responds to aromatic, aliphatic, and polar amino acids, but not to positively charged or branched chain amino acids, which suggests that changes in plasma amino acid levels are likely to modulate whole body calcium metabolism. Additionally, the family C GPCRs includes at least two receptors with broad-spectrum amino acid-sensing properties: GPRC6A which recognizes basic and various aliphatic amino acids, its gold-fish homolog the 5.24 chemoreceptor, and a specific taste receptor (T1R) which responds to aliphatic, polar, charged, and branched amino acids, but not to aromatic amino acids. 473 matched cddid_all.tbl CDD cd06365 cd06365 380588 PBP1_pheromone_receptor Ligand-binding domain of the V2R pheromone receptor, a member of the family C receptors within the G-protein coupled receptor superfamily. Ligand-binding domain of the V2R pheromone receptor, a member of the family C receptors within the G-protein coupled receptor superfamily, which also includes the metabotropic glutamate receptor, the GABAb receptor, the calcium-sensing receptor (CaSR), the T1R taste receptor, and a small group of uncharacterized orphan receptors. 464 matched cddid_all.tbl CDD cd06366 cd06366 380589 PBP1_GABAb_receptor ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb receptor or GABAbR). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha-i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example. 404 matched cddid_all.tbl CDD cd06367 cd06367 380590 PBP1_iGluR_NMDA N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the ionotropic N-methyl-D-asparate (NMDA) subtype of glutamate receptors. N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the ionotropic N-methyl-D-asparate (NMDA) subtype of glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. The function of the NMDA subtype receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer comprising two NR1 and two NR2 (A, B, C, and D) or NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain. 357 matched cddid_all.tbl CDD cd06368 cd06368 380591 PBP1_iGluR_non_NMDA-like N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-D-aspartate) subtypes of ionotropic glutamate receptors. N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-D-asparate) subtypes of ionotropic glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Glutamate mediates the majority of excitatory synaptic transmission in the central nervous system via two broad classes of ionotropic receptors, characterized by their response to glutamate agonists: N-methyl-D-aspartate (NMDA) and non-NMDA receptors. NMDA receptors have intrinsically slow kinetics, are highly permeable to Ca2+, and are blocked by extracellular Mg2+ in a voltage-dependent manner. Non-NMDA receptors have faster kinetics, are most often only weakly permeable to Ca2+, and are not blocked by extracellular Mg2+. While non-NMDA receptors typically mediate excitatory synaptic responses at resting membrane potentials, NMDA receptors contribute several forms of synaptic plasticity and are thought to play an important role in the development of synaptic pathways. Non-NMDA receptors include alpha-amino-3-hydroxy-5-methyl-4-isoxazole proprionate (AMPA) and kainate receptors. 339 matched cddid_all.tbl CDD cd06369 cd06369 380592 PBP1_GC_C_enterotoxin_receptor ligand-binding domain of the membrane guanylyl cyclase C. Ligand-binding domain of the membrane guanylyl cyclase C (GC-C or StaR). StaR is a key receptor for the STa (Escherichia coli Heat Stable enterotoxin), a potent stimulant of intestinal chloride and bicarbonate secretion that cause acute secretory diarrhea. The catalytic domain of the STa/guanylin receptor type membrane GC is highly similar to those of the natriuretic peptide receptor (NPR) type and sensory organ-specific type membrane GCs (GC-D, GC-E and GC-F). The GC-C receptor is mainly expressed in the intestine of most vertebrates, but is also found in the kidney and other organs. Moreover, GC-C is activated by guanylin and uroguanylin, endogenous peptide ligands synthesized in the intestine and kidney. Consequently, the receptor activation results in increased cGMP levels and phosphorylation of the CFTR chloride channel and secretion. 381 matched cddid_all.tbl CDD cd06370 cd06370 380593 PBP1_SAP_GC-like Ligand-binding domain of membrane bound guanylyl cyclases. Ligand-binding domain of membrane bound guanylyl cyclases (GCs), which are known to be activated by sperm-activating peptides (SAPs), such as speract or resact. These ligand peptides are released by a range of invertebrates to stimulate the metabolism and motility of spermatozoa and are also potent chemoattractants. These GCs contain a single transmembrane segment, an extracellular ligand binding domain, and intracellular protein kinase-like and cyclase catalytic domains. GCs of insect and nematodes, which exhibit high sequence similarity to the speract receptor are also included in this model. 400 matched cddid_all.tbl CDD cd06371 cd06371 380594 PBP1_sensory_GC_DEF-like ligand-binding domain of membrane guanylyl cyclases (GC-D, GC-E, and GC-F) that are specifically expressed in sensory tissues. This group includes the ligand-binding domain of membrane guanylyl cyclases (GC-D, GC-E, and GC-F) that are specifically expressed in sensory tissues. They share a similar topology with an N-terminal extracellular ligand-binding domain, a single transmembrane domain, and a C-terminal cytosolic region that contains kinase-like and catalytic domains. GC-D is specifically expressed in a subpopulation of olfactory sensory neurons. GC-E and GC-F are colocalized within the same photoreceptor cells of the retina and have important roles in phototransduction. Unlike the other family members, GC-E and GC-F have no known extracellular ligands. Instead, they are activated under low calcium conditions by guanylyl cyclase activating proteins called GCAPs. GC-D expressing neurons have been implicated in pheromone detection and GC-D is phylogenetically more similar to the Ca2+-regulated GC-E and GC-F than to receptor GC-A, -B and -C which are activated by peptide ligands. Moreover, these olfactory GCs and retinal GCs share characteristic sequence similarity in a regulatory domain that is involved in the binding of GCAPs, suggesting GC-D activity may be regulated by an unknown extracellular ligand and intracellular Ca2+. Rodent GC-D-expressing neurons have been implicated in pheromone detection and were recently shown to respond to atmospheric CO2 which is an olfactory stimulus for many invertebrates and regulates some insect innate behavior, such as the location of food and hosts. 379 matched cddid_all.tbl CDD cd06372 cd06372 380595 PBP1_GC_G-like Ligand-binding domain of membrane guanylyl cyclase G. This group includes the ligand-binding domain of membrane guanylyl cyclase G (GC-G) which is a sperm surface receptor and might function, similar to its sea urchin counterpart, in the early signaling event that regulates the Ca2+ influx/efflux and subsequent motility response in sperm. GC-G appears to be a pseudogene in human. Furthermore, in contrast to the other orphan receptor GCs, GC-G has a broad tissue distribution in rat, including lung, intestine, kidney, and skeletal muscle. 390 matched cddid_all.tbl CDD cd06373 cd06373 380596 PBP1_NPR-like Ligand binding domain of natriuretic peptide receptor (NPR) family. Ligand binding domain of natriuretic peptide receptor (NPR) family which consists of three different subtypes: type A natriuretic peptide receptor (NPR-A, or GC-A), type B natriuretic peptide receptors (NPR-B, or GC-B), and type C natriuretic peptide receptor (NPR-C). There are three types of natriuretic peptide (NP) ligands specific to the receptors: atrial NP (ANP), brain or B-type NP (BNP), and C-type NP (CNP). The NP family is thought to have arisen through gene duplication during evolution and plays an essential role in cardiovascular and body fluid homeostasis. ANP and BNP bind mainly to NPR-A, while CNP binds specifically to NPR-B. Both NPR-A and NPR-B have guanylyl cyclase catalytic activity and produces intracellular secondary messenger cGMP in response to peptide-ligand binding. Consequently, the NPR-A activation results in vasodilation and inhibition of vascular smooth muscle cell proliferation. NPR-C acts as the receptor for all the three members of NP family, and functions as a clearance receptor. Unlike NPR-A and -B, NPR-C lacks an intracellular guanylyl cyclase domain and is thought to exert biological actions by sequestration of released natriuretic peptides and/or inhibition of adenylyl cyclase. 394 matched cddid_all.tbl CDD cd06374 cd06374 380597 PBP1_mGluR_groupI ligand binding domain of the group I metabotropic glutamate receptor. Ligand binding domain of the group I metabotropic glutamate receptor, a family containing mGlu1R and mGlu5R, all of which stimulate phospholipase C (PLC) hydrolysis. The metabotropic glutamate receptor is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into intracellular responses. The mGluRs are classified into three groups which comprise eight subtypes. 474 matched cddid_all.tbl CDD cd06375 cd06375 380598 PBP1_mGluR_groupII ligand binding domain of the group II metabotropic glutamate receptor. Ligand binding domain of the group II metabotropic glutamate receptor, a family that contains mGlu2R and mGlu3R, all of which inhibit adenylyl cyclase. The metabotropic glutamate receptor is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into intracellular responses. The mGluRs are classified into three groups which comprise eight subtypes 462 matched cddid_all.tbl CDD cd06376 cd06376 380599 PBP1_mGluR_groupIII ligand-binding domain of the group III metabotropic glutamate receptor. Ligand-binding domain of the group III metabotropic glutamate receptor, a family which contains mGlu4R, mGluR6R, mGluR7, and mGluR8; all of which inhibit adenylyl cyclase. The metabotropic glutamate receptor is a member of the family C of G-protein-coupled receptors that transduce extracellular signals into G-protein activation and ultimately into intracellular responses. The mGluRs are classified into three groups which comprise eight subtypes. 467 matched cddid_all.tbl CDD cd06377 cd06377 380600 PBP1_iGluR_NMDA_NR3 N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family. N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NR3 subunit of NMDA receptor family. The ionotropic N-methyl-D-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain. 373 matched cddid_all.tbl CDD cd06378 cd06378 380601 PBP1_iGluR_NMDA_NR2 N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NR2 subunit of NMDA receptor family. The ionotropic N-methyl-D-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain. 356 matched cddid_all.tbl CDD cd06379 cd06379 380602 PBP1_iGluR_NMDA_NR1 N-terminal leucine-isoleucine-valine-binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the NR1, an essential channel-forming subunit of the NMDA receptor. The ionotropic N-methyl-D-asparate (NMDA) subtype of glutamate receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer ccomposed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore can be classified as excitatory glycine receptors. NR1/NR3 receptors are calcium-impermeable and unaffected by ligands acting at the NR2 glutamate-binding site 364 matched cddid_all.tbl CDD cd06380 cd06380 380603 PBP1_iGluR_AMPA N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the AMPA receptor. N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor, a member of the glutamate-receptor ion channels (iGluRs). AMPA receptors are the major mediators of excitatory synaptic transmission in the central nervous system. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. AMPA receptors consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important roles in mediating the rapid excitatory synaptic current. 390 matched cddid_all.tbl CDD cd06381 cd06381 380604 PBP1_iGluR_delta-like N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of an orphan family of delta receptors, GluRdelta1 and GluRdelta2. This CD represents the N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of an orphan family of delta receptors, GluRdelta1 and GluRdelta2. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 are more homologous to non-NMDA receptors. GluRdelta2 was shown to function as an AMPA-like receptor by mutation analysis. Moreover, targeted disruption of GluRdelta2 gene caused motor coordination impairment, Purkinje cell maturation, and long-term depression of synaptic transmission. It has been suggested that GluRdelta2 is the receptor for cerebellin 1, a glycoprotein of the Clq, and the tumor necrosis factor family which is secreted from cerebellar granule cells. Furthermore, recent studies have shown that the orphan GluRdelta1 plays an essential role in high-frequency hearing and ionic homeostasis in the basal cochlea and that the locus encoding GluRdelta1 may be involved in congenial or acquired high-frequency hearing loss in humans. 401 matched cddid_all.tbl CDD cd06382 cd06382 380605 PBP1_iGluR_Kainate N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the kainate receptors. N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the kainate receptors, non-NMDA ionotropic receptors which respond to the neurotransmitter glutamate. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Kainate receptors have five subunits, GluR5, GluR6, GluR7, KA1 and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated by kainate and glutamate when expressed in heterologous systems. Kainate receptors are involved in excitatory neurotransmission by activating postsynaptic receptors and in inhibitory neurotransmission by modulating release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. Kainate receptors are closely related to AMAP receptors. In contrast of AMPA receptors, kainate receptors play only a minor role in signaling at synapses and their function is not well defined. 335 matched cddid_all.tbl CDD cd06383 cd06383 380606 PBP1_iGluR_AMPA_Like N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of uncharacterized AMPA-like receptors. N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of uncharacterized AMPA-like receptors. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. AMPA receptors consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important roles in mediating the rapid excitatory synaptic current. 379 matched cddid_all.tbl CDD cd06384 cd06384 380607 PBP1_NPR_B ligand-binding domain of type B natriuretic peptide receptor. Ligand-binding domain of type B natriuretic peptide receptor (NPR-B). NPR-B is one of three known single membrane-spanning natriuretic peptide receptors that have been identified. Natriuretic peptides are family of structurally related but genetically distinct hormones/paracrine factors that regulate blood volume, blood pressure, ventricular hypertrophy, pulmonary hypertension, fat metabolism, and long bone growth. In mammals there are three natriuretic peptides: ANP, BNP, and CNP. Like NPR-A (or GC-A), NPR-B (or GC-B) is a transmembrane guanylyl cyclase, an enzyme that catalyzes the synthesis of cGMP. NPR-B is the predominant natriuretic peptide receptor in the brain. The rank of order activation of NPR-B by natriuretic peptides is CNP>>ANP>BNP. Homozygous inactivating mutations in human NPR-B cause a form of short-limbed dwarfism known as acromesomelic dysplasia type Maroteaux. 399 matched cddid_all.tbl CDD cd06385 cd06385 380608 PBP1_NPR_A Ligand-binding domain of type A natriuretic peptide receptor. Ligand-binding domain of type A natriuretic peptide receptor (NPR-A). NPR-A is one of three known single membrane-spanning natriuretic peptide receptors that regulate blood volume, blood pressure, ventricular hypertrophy, pulmonary hypertension, fat metabolism, and long bone growth. In mammals there are three natriuretic peptides: ANP, BNP, and CNP. NPR-A is highly expressed in kidney, adrenal, terminal ileum, adipose, aortic, and lung tissues. The rank order of NPR-A activation by natriuretic peptides is ANP>BNP>>CNP. Single allele-inactivating mutations in the promoter of human NPR-A are associated with hypertension and heart failure. 408 matched cddid_all.tbl CDD cd06386 cd06386 380609 PBP1_NPR_C ligand-binding domain of type C natriuretic peptide receptor. Ligand-binding domain of type C natriuretic peptide receptor (NPR-C). NPR-C is found in atrial, mesentery, placenta, lung, kidney, venous tissue, aortic smooth muscle, and aortic endothelial cells. The affinity of NPR-C for natriuretic peptides is ANP>CNP>BNP. The extracellular domain of NPR-C is about 30% identical to NPR-A and NPR-B. However, unlike the cyclase-linked receptors, it contains only 37 intracellular amino acids and no guanylyl cyclase activity. Major function of NPR-C is to clear natriuretic peptides from the circulation or extracellular surroundings through constitutive receptor-mediated internalization and degradation. 391 matched cddid_all.tbl CDD cd06387 cd06387 380610 PBP1_iGluR_AMPA_GluR3 N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA receptor. N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR3 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs). 375 matched cddid_all.tbl CDD cd06388 cd06388 380611 PBP1_iGluR_AMPA_GluR4 N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA receptor. N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR4 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs). 373 matched cddid_all.tbl CDD cd06389 cd06389 380612 PBP1_iGluR_AMPA_GluR2 N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR2 subunit of the AMPA receptor. N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR2 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs). 372 matched cddid_all.tbl CDD cd06390 cd06390 380613 PBP1_iGluR_AMPA_GluR1 N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA receptor. N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs). 367 matched cddid_all.tbl CDD cd06391 cd06391 380614 PBP1_iGluR_delta_2 N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family. N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta2 receptor of an orphan glutamate receptor family. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 are closer related to non-NMDA receptors. GluRdelta2 was shown to function as an AMPA-like receptor by mutation analysis. Moreover, targeted disruption of GluRdelta2 gene caused motor coordination impairment, Purkinje cell maturation, and long-term depression of synaptic transmission. It has been suggested that GluRdelta2 is the receptor for cerebellin 1, a glycoprotein of the Clq and tumor necrosis factor family that is secreted from cerebellar granule cells. 402 matched cddid_all.tbl CDD cd06392 cd06392 380615 PBP1_iGluR_delta_1 N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family. N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the delta1 receptor of an orphan glutamate receptor family. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetic analysis shows that both GluRdelta1 and GluRalpha2 may be closer related to non-NMDA receptors. In contrast to GluRdelta2, GluRdelta1 is expressed in many areas in the developing CNS, including the hippocampus and the caudate putamen. Furthermore, recent studies have shown that the orphan GluRdelta1 plays an essential role in high-frequency hearing and ionic homeostasis in the basal cochlea and that the locus encoding GluRdelta1 may be involved in congenial or acquired high-frequency hearing loss in humans. 402 matched cddid_all.tbl CDD cd06394 cd06394 380616 PBP1_iGluR_Kainate_KA1_2 N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. N-terminal leucine-isoleucine-valine binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type 1 superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type 2. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated by kainate and glutamate when expressed in heterologous systems. Kainate receptors are involved in excitatory neurotransmission by activating postsynaptic receptors and in inhibitory neurotransmission by modulating release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. Kainate receptors are closely related to AMPA receptors. In contrast of AMPA receptors, kainate receptors play only a minor role in signaling at synapses and their function is not well defined. 379 matched cddid_all.tbl CDD cd06395 cd06395 99717 PB1_Map2k5 PB1 domain is essential part of the mitogen-activated protein kinase kinase 5 (Map2k5, alias MEK5) one of the key member of the signaling kinases cascade which involved in angiogenesis and early cardiovascular development. The PB1 domain of Map2k5 interacts with the PB1 domain of another members of kinase cascade MEKK2 (or MEKK3). A canonical PB1-PB1 interaction, involving heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The Map2k5 protein contains a type I PB1 domain. 91 matched cddid_all.tbl CDD cd06396 cd06396 99718 PB1_NBR1 The PB1 domain is an essential part of NBR1 protein, next to BRCA1, a scaffold protein mediating specific protein-protein interaction with both titin protein kinase and with another scaffold protein p62. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The NBR1 protein contains a type I PB1 domain. 81 matched cddid_all.tbl CDD cd06397 cd06397 99719 PB1_UP1 Uncharacterized protein 1. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. 82 matched cddid_all.tbl CDD cd06398 cd06398 99720 PB1_Joka2 The PB1 domain is present in the Nicotiana plumbaginifolia Joka2 protein which interacts with sulfur stress inducible UP9 protein. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. 91 matched cddid_all.tbl CDD cd06399 cd06399 99721 PB1_P40 The PB1 domain is essential part of the p40 adaptor protein which plays an important role in activating phagocyte NADPH oxidase during phagocytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes , such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domain of p40 represents a type I PB1 domain which interacts with the PB1 domain of oxidase activator p67 which belong to type II PB1 domain. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. 92 matched cddid_all.tbl CDD cd06401 cd06401 99722 PB1_TFG The PB1 domain found in TFG protein, an oncogenic gene product and fusion partner to nerve growth factor tyrosine kinase receptor TrkA and to the tyrosine kinase ALK. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The PB1 domains of TFG represent a type I/II PB1 domain. The physiological function of TFG remains unknown. 81 matched cddid_all.tbl CDD cd06402 cd06402 99723 PB1_p62 The PB1 domain is an essential part of p62 scaffold protein (alias sequestosome 1,SQSTM) involved in cell signaling, receptor internalization, and protein turnover. The PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. 87 matched cddid_all.tbl CDD cd06403 cd06403 99724 PB1_Par6 The PB1 domain is an essential part of Par6 protein which in complex with Par3 and aPKC proteins is crucial for establishment of apical-basal polarity of animal cells. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The Par6 protein contains a type II PB1 domain. 80 matched cddid_all.tbl CDD cd06404 cd06404 99725 PB1_aPKC PB1 domain is an essential modular domain of the atypical protein kinase C (aPKC) which in complex with Par6 and Par3 proteins is crucial for establishment of apical-basal polarity of animal cells. PB1 domain is a modular domain mediating specific protein-protein interaction which play roles in many critical cell processes. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The aPKC protein contains a type I/II PB1 domain. 83 matched cddid_all.tbl CDD cd06405 cd06405 99726 PB1_Mekk2_3 The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 which are two members of the signaling kinase cascade involved in angiogenesis and early cardiovascular development. The PB1 domain of MEKK2 (and/or MEKK3) interacts with the PB1 domain of another member of the kinase cascade Map2k5. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The MEKK2 and MEKK3 proteins contain a type II PB1 domain. 79 matched cddid_all.tbl CDD cd06406 cd06406 99727 PB1_P67 A PB1 domain is present in p67 proteins which forms a signaling complex with p40, a crucial step for activation of NADPH oxidase during phagocytosis. PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes . A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The p67 proteins contain a type II PB1 domain. 80 matched cddid_all.tbl CDD cd06407 cd06407 99728 PB1_NLP A PB1 domain is present in NIN like proteins (NLP), a key enzyme in a process of establishment of symbiosis betweeen legumes and nitrogen fixing bacteria (Rhizobium). The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes like osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. 82 matched cddid_all.tbl CDD cd06408 cd06408 99729 PB1_NoxR The PB1 domain is present in the Epichloe festucae NoxR protein (NADPH oxidase regulator), a key regulator of NADPH oxidase isoform, NoxA. NoxA is essential for growth control of the fungal endophyte in plant tissue in the process of symbiotic interaction between a fungi and its plant host. The Epichloe festucae p67(phox)-like regulator, NoxR, dispensable in culture but essential in plants for the symbiotic interaction. Plants infected with a noxR deletion mutant show severe stunting and premature senescence, whereas hyphae in the meristematic tissues show increased branching leading to increased fungal colonization of pseudostem and leaf blade tissue. The PB1 domain is a modular domain mediating specific protein-protein interactions which a play role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. 86 matched cddid_all.tbl CDD cd06409 cd06409 99730 PB1_MUG70 The MUG70 protein is a product of the meiotically up-regulated gene 70 which has a role in meiosis and harbors a PB1 domain. The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domains depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic amino acid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. 86 matched cddid_all.tbl CDD cd06410 cd06410 99731 PB1_UP2 Uncharacterized protein 2. The PB1 domain is a modular domain mediating specific protein-protein interaction which play a role in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. 97 matched cddid_all.tbl CDD cd06411 cd06411 99732 PB1_p51 The PB1 domain is present in the p51 protein, a homolog of the p67 protein. p51 plays an important role in NADPH oxidase activation during phagosytosis. The PB1 domain is a modular domain mediating specific protein-protein interaction in many critical cell processes such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. 78 matched cddid_all.tbl CDD cd06412 cd06412 119374 GH25_CH-type CH-type (Chalaropsis-type) lysozymes represent one of four functionally-defined classes of peptidoglycan hydrolases (also referred to as endo-N-acetylmuramidases) that cleave bacterial cell wall peptidoglycans. CH-type lysozymes exhibit both lysozyme (acetylmuramidase) and diacetylmuramidase activity. The first member of this family to be described was a muramidase from the fungus Chalaropsis. However, a majority of the CH-type lysozymes are found in bacteriophages and Gram-positive bacteria such as Streptomyces and Clostridium. CH-type lysozymes have a single glycosyl hydrolase family 25 (GH25) domain with an unusual beta/alpha-barrel fold in which the last strand of the barrel is antiparallel to strands beta7 and beta1. Most CH-type lysozymes appear to lack the cell wall-binding domain found in other GH25 muramidases. 199 matched cddid_all.tbl CDD cd06413 cd06413 119375 GH25_muramidase_1 Uncharacterized bacterial muramidase containing a glycosyl hydrolase family 25 (GH25) catalytic domain. Endo-N-acetylmuramidases are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues. 191 matched cddid_all.tbl CDD cd06414 cd06414 119376 GH25_LytC-like The LytC lysozyme of Streptococcus pneumoniae is a bacterial cell wall hydrolase that cleaves the beta1-4-glycosydic bond located between the N-acetylmuramoyl-N-glucosaminyl residues of the cell wall polysaccharide chains. LytC is composed of a C-terminal glycosyl hydrolase family 25 (GH25) domain and an N-terminal choline-binding module (CBM) consisting of eleven homologous repeats that specifically recognizes the choline residues of pneumococcal lipoteichoic and teichoic acids. This domain arrangement is the reverse of the major pneumococcal autolysin, LytA, and the CPL-1-like lytic enzymes of the pneumococcal bacteriophages, in which the CBM (consisting of six repeats) is at the C-terminus. This model represents the C-terminal catalytic domain of the LytC-like enzymes. 191 matched cddid_all.tbl CDD cd06415 cd06415 119377 GH25_Cpl1-like Cpl-1 lysin (also known as Cpl-9 lysozyme / muramidase) is a bacterial cell wall endolysin encoded by the pneumococcal bacteriophage Cp-1, which cleaves the glycosidic N-acetylmuramoyl-(beta1,4)-N-acetylglucosamine bonds of the pneumococcal glycan chain, thus acting as an enzymatic antimicrobial agent (an enzybiotic) against streptococcal infections. Cpl-1 belongs to the CP family of lysozymes (CPL lysozymes) which includes the Cpl-7 lysin. Cpl-1 has a glycosyl hydrolase family 25 (GH25) catalytic domain with an irregular (beta/alpha)5-beta3 barrel and a C-terminal cell wall-anchoring module formed by six similar choline-binding repeats (ChBr's). The ChBr's facilitate the anchoring of Cpl-1 to the choline-containing teichoic acid of the pneumococcal cell wall. Other members of this domain family have an N-terminal CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain similar to that of the firmicute CHAP lysins and associated with endopeptidase activity. The Cpl-7 lysin is also included here as is LysB of Lactococcus phage, and the Mur lysin of Lactobacillus phage. 196 matched cddid_all.tbl CDD cd06416 cd06416 119378 GH25_Lys1-like Lys-1 is a lysozyme encoded by the Caenorhabditis elegans lys-1 gene. This gene is one of a several lysozyme genes upregulated upon infection by the Gram-negative bacterial pathogen Serratia marcescens. Lys-1 contains a glycosyl hydrolase family 25 (GH25) catalytic domain. This family also includes Lys-5 from Caenorhabditis elegans. 196 matched cddid_all.tbl CDD cd06417 cd06417 119379 GH25_LysA-like LysA is a cell wall endolysin produced by Lactobacillus fermentum, which degrades bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues. The N-terminal glycosyl hydrolase family 25 (GH25) domain of LysA has sequence similarity with other murein hydrolase catalytic domains while the C-terminal domain has sequence similarity with putative bacterial cell wall-binding SH3b domains. This domain family also includes LysL of Lactococcus lactis. 195 matched cddid_all.tbl CDD cd06418 cd06418 119380 GH25_BacA-like BacA is a bacterial lysin from Enterococcus faecalis that degrades bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues. BacA is homologous to the YbfG and YkuG lysins of Bacillus subtilis. BacA has a C-terminal catalytic glycosyl hydrolase family 25 (GH25) domain and an N-terminal peptidoglycan-binding domain comprised of three alpha helices which is similar to a domain found in matrixins. 212 matched cddid_all.tbl CDD cd06419 cd06419 119381 GH25_muramidase_2 Uncharacterized bacterial muramidase containing a glycosyl hydrolase family 25 (GH25) catalytic domain. Endo-N-acetylmuramidases are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues. 190 matched cddid_all.tbl CDD cd06420 cd06420 133042 GT2_Chondriotin_Pol_N N-terminal domain of Chondroitin polymerase functions as a GalNAc transferase. Chondroitin polymerase is a two domain, bi-functional protein. The N-terminal domain functions as a GalNAc transferase. The bacterial chondroitin polymerase catalyzes elongation of the chondroitin chain by alternatively transferring the GlcUA and GalNAc moiety from UDP-GlcUA and UDP-GalNAc to the non-reducing ends of the chondroitin chain. The enzyme consists of N-terminal and C-terminal domains in which the two active sites catalyze the addition of GalNAc and GlcUA, respectively. Chondroitin chains range from 40 to over 100 repeating units of the disaccharide. Sulfated chondroitins are involved in the regulation of various biological functions such as central nervous system development, wound repair, infection, growth factor signaling, and morphogenesis, in addition to its conventional structural roles. In Caenorhabditis elegans, chondroitin is an essential factor for the worm to undergo cytokinesis and cell division. Chondroitin is synthesized as proteoglycans, sulfated and secreted to the cell surface or extracellular matrix. 182 matched cddid_all.tbl CDD cd06421 cd06421 133043 CESA_CelA_like CESA_CelA_like are involved in the elongation of the glucan chain of cellulose. Family of proteins related to Agrobacterium tumefaciens CelA and Gluconacetobacter xylinus BscA. These proteins are involved in the elongation of the glucan chain of cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues. They are putative catalytic subunit of cellulose synthase, which is a glycosyltransferase using UDP-glucose as the substrate. The catalytic subunit is an integral membrane protein with 6 transmembrane segments and it is postulated that the protein is anchored in the membrane at the N-terminal end. 234 matched cddid_all.tbl CDD cd06422 cd06422 133044 NTP_transferase_like_1 NTP_transferase_like_1 is a member of the nucleotidyl transferase family. This is a subfamily of nucleotidyl transferases. Nucleotidyl transferases transfer nucleotides onto phosphosugars. The activated sugars are precursors for synthesis of lipopolysaccharide, glycolipids and polysaccharides. Other subfamilies of nucleotidyl transferases include Alpha-D-Glucose-1-Phosphate Cytidylyltransferase, Mannose-1-phosphate guanyltransferase, and Glucose-1-phosphate thymidylyltransferase. 221 matched cddid_all.tbl CDD cd06423 cd06423 133045 CESA_like CESA_like is the cellulose synthase superfamily. The cellulose synthase (CESA) superfamily includes a wide variety of glycosyltransferase family 2 enzymes that share the common characteristic of catalyzing the elongation of polysaccharide chains. The members include cellulose synthase catalytic subunit, chitin synthase, glucan biosynthesis protein and other families of CESA-like proteins. Cellulose synthase catalyzes the polymerization reaction of cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues in plants, most algae, some bacteria and fungi, and even some animals. In bacteria, algae and lower eukaryotes, there is a second unrelated type of cellulose synthase (Type II), which produces acylated cellulose, a derivative of cellulose. Chitin synthase catalyzes the incorporation of GlcNAc from substrate UDP-GlcNAc into chitin, which is a linear homopolymer of beta-(1,4)-linked GlcNAc residues and Glucan Biosynthesis protein catalyzes the elongation of beta-1,2 polyglucose chains of Glucan. 180 matched cddid_all.tbl CDD cd06424 cd06424 133046 UGGPase UGGPase catalyzes the synthesis of UDP-Glucose/UDP-Galactose. UGGPase: UDP-Galactose/Glucose Pyrophosphorylase catalyzes the reversible production of UDP-Glucose/UDP-Galactose and pyrophosphate (PPi) from Glucose-1-phosphate/Galactose-1-phosphate and UTP. Its dual substrate specificity distinguishes it from the single substrate enzyme UDP-glucose pyrophosphorylase. It may play a key role in the galactose metabolism in raffinose oligosaccharide (RFO) metabolizing plants. RFO raffinose is a major photoassimilate and is a galactosylderivative of sucrose (Suc) containing a galactose (Gal) moiety. Upon arriving at the sink tissue, the Gal moieties of the RFOs are initially removed by alpha-galactosidase and then are phosphorylated to Gal-1-P. Gal-1-P is converted to UDP-Gal. The UDP-Gal is further metabolized to UDP-Glc via an epimerase reaction. The UDP-Glc can be directly utilized in cell wall metabolism or in Suc synthesis. However, for the Suc synthesis UDP-Glc must be further metabolized to Glc-1-P. This can be carried out either by the UGPase in the reverse direction or by the dual substrate PPase itself operating in the reverse direction. According to the latter possibility, the three-step pathway of Gal-1-P to Glc-1-P could be carried out by a single PPase, functioning sequentially in reverse directions separated by the epimerase reaction. 315 matched cddid_all.tbl CDD cd06425 cd06425 133047 M1P_guanylylT_B_like_N N-terminal domain of the M1P-guanylyltransferase B-isoform like proteins. GDP-mannose pyrophosphorylase (GTP: alpha-d-mannose-1-phosphate guanyltransferase) catalyzes the formation of GDP-d-mannose from GTP and alpha-d-mannose-1-Phosphate. It contains an N-terminal catalytic domain and a C-terminal Lefthanded-beta-Helix fold domain. GDP-d-mannose is the activated form of mannose for formation of cell wall lipoarabinomannan and various mannose-containing glycolipids and polysaccharides. The function of GDP-mannose pyrophosphorylase is essential for cell wall integrity, morphogenesis and viability. Repression of GDP-mannose pyrophosphorylase in yeast leads to phenotypes, such as cell lysis, defective cell wall, and failure of polarized growth and cell separation. 233 matched cddid_all.tbl CDD cd06426 cd06426 133048 NTP_transferase_like_2 NTP_trnasferase_like_2 is a member of the nucleotidyl transferase family. This is a subfamily of nucleotidyl transferases. Nucleotidyl transferases transfer nucleotides onto phosphosugars. The activated sugars are precursors for synthesis of lipopolysaccharide, glycolipids and polysaccharides. Other subfamilies of nucleotidyl transferases include Alpha-D-Glucose-1-Phosphate Cytidylyltransferase, Mannose-1-phosphate guanyltransferase, and Glucose-1-phosphate thymidylyltransferase. 220 matched cddid_all.tbl CDD cd06427 cd06427 133049 CESA_like_2 CESA_like_2 is a member of the cellulose synthase superfamily. The cellulose synthase (CESA) superfamily includes a wide variety of glycosyltransferase family 2 enzymes that share the common characteristic of catalyzing the elongation of polysaccharide chains. The members include cellulose synthase catalytic subunit, chitin synthase, Glucan Biosynthesis protein and other families of CESA-like proteins. Cellulose synthase catalyzes the polymerization reaction of cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues in plants, most algae, some bacteria and fungi, and even some animals. In bacteria, algae and lower eukaryotes, there is a second unrelated type of cellulose synthase (Type II), which produces acylated cellulose, a derivative of cellulose. Chitin synthase catalyzes the incorporation of GlcNAc from substrate UDP-GlcNAc into chitin, which is a linear homopolymer of beta-(1,4)-linked GlcNAc residues and Glucan Biosynthesis protein catalyzes the elongation of beta-1,2 polyglucose chains of glucan. 241 matched cddid_all.tbl CDD cd06428 cd06428 133050 M1P_guanylylT_A_like_N N-terminal domain of M1P_guanylyl_A_ like proteins are likely to be a isoform of GDP-mannose pyrophosphorylase. N-terminal domain of the M1P-guanylyltransferase A-isoform like proteins: The proteins of this family are likely to be a isoform of GDP-mannose pyrophosphorylase. Their sequences are highly conserved with mannose-1-phosphate guanyltransferase, but generally about 40-60 bases longer. GDP-mannose pyrophosphorylase (GTP: alpha-d-mannose-1-phosphate guanyltransferase) catalyzes the formation of GDP-d-mannose from GTP and alpha-d-mannose-1-Phosphate. It contains an N-terminal catalytic domain that resembles a dinucleotide-binding Rossmann fold and a C-terminal LbH fold domain. GDP-d-mannose is the activated form of mannose for formation of cell wall lipoarabinomannan and various mannose-containing glycolipids and polysaccharides. The function of GDP-mannose pyrophosphorylase is essential for cell wall integrity, morphogenesis and viability. Repression of GDP-mannose pyrophosphorylase in yeast leads to phenotypes including cell lysis, defective cell wall, and failure of polarized growth and cell separation. 257 matched cddid_all.tbl CDD cd06429 cd06429 133051 GT8_like_1 GT8_like_1 represents a subfamily of GT8 with unknown function. A subfamily of glycosyltransferase family 8 with unknown function: Glycosyltransferase family 8 comprises enzymes with a number of known activities; lipopolysaccharide galactosyltransferase lipopolysaccharide glucosyltransferase 1, glycogenin glucosyltransferase and inositol 1-alpha-galactosyltransferase. It is classified as a retaining glycosyltransferase, based on the relative anomeric stereochemistry of the substrate and product in the reaction catalyzed. 257 matched cddid_all.tbl CDD cd06430 cd06430 133052 GT8_like_2 GT8_like_2 represents a subfamily of GT8 with unknown function. A subfamily of glycosyltransferase family 8 with unknown function: Glycosyltransferase family 8 comprises enzymes with a number of known activities; lipopolysaccharide galactosyltransferase lipopolysaccharide glucosyltransferase 1, glycogenin glucosyltransferase and inositol 1-alpha-galactosyltransferase. It is classified as a retaining glycosyltransferase, based on the relative anomeric stereochemistry of the substrate and product in the reaction catalyzed. 304 matched cddid_all.tbl CDD cd06431 cd06431 133053 GT8_LARGE_C LARGE catalytic domain has closest homology to GT8 glycosyltransferase involved in lipooligosaccharide synthesis. The catalytic domain of LARGE is a putative glycosyltransferase. Mutations of LARGE in mouse and human cause dystroglycanopathies, a disease associated with hypoglycosylation of the membrane protein alpha-dystroglycan (alpha-DG) and consequent loss of extracellular ligand binding. LARGE needs to both physically interact with alpha-dystroglycan and function as a glycosyltransferase in order to stimulate alpha-dystroglycan hyperglycosylation. LARGE localizes to the Golgi apparatus and contains three conserved DxD motifs. While two of the motifs are indispensible for glycosylation function, one is important for localization of th eenzyme. LARGE was originally named because it covers approximately large trunck of genomic DNA, more than 600bp long. The predicted protein structure contains an N-terminal cytoplasmic domain, a transmembrane region, a coiled-coil motif, and two putative catalytic domains. This catalytic domain has closest homology to GT8 glycosyltransferase involved in lipooligosaccharide synthesis. 280 matched cddid_all.tbl CDD cd06432 cd06432 133054 GT8_HUGT1_C_like The C-terminal domain of HUGT1-like is highly homologous to the GT 8 family. C-terminal domain of glycoprotein glucosyltransferase (UGT). UGT is a large glycoprotein whose C-terminus contains the catalytic activity. This catalytic C-terminal domain is highly homologous to Glycosyltransferase Family 8 (GT 8) and contains the DXD motif that coordinates donor sugar binding, characteristic for Family 8 glycosyltransferases. GT 8 proteins are retaining enzymes based on the relative anomeric stereochemistry of the substrate and product in the reaction catalyzed. The non-catalytic N-terminal portion of the human UTG1 (HUGT1) has been shown to monitor the protein folding status and activate its glucosyltransferase activity. 248 matched cddid_all.tbl CDD cd06433 cd06433 133055 GT_2_WfgS_like WfgS and WfeV are involved in O-antigen biosynthesis. Escherichia coli WfgS and Shigella dysenteriae WfeV are glycosyltransferase 2 family enzymes involved in O-antigen biosynthesis. GT-2 enzymes have GT-A type structural fold, which has two tightly associated beta/alpha/beta domains that tend to form a continuous central sheet of at least eight beta-strands. These are enzymes that catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. Glycosyltransferases have been classified into more than 90 distinct sequence based families. 202 matched cddid_all.tbl CDD cd06434 cd06434 133056 GT2_HAS Hyaluronan synthases catalyze polymerization of hyaluronan. Hyaluronan synthases (HASs) are bi-functional glycosyltransferases that catalyze polymerization of hyaluronan. HASs transfer both GlcUA and GlcNAc in beta-(1,3) and beta-(1,4) linkages, respectively to the hyaluronan chain using UDP-GlcNAc and UDP-GlcUA as substrates. HA is made as a free glycan, not attached to a protein or lipid. HASs do not need a primer for HA synthesis; they initiate HA biosynthesis de novo with only UDP-GlcNAc, UDP-GlcUA, and Mg2+. Hyaluronan (HA) is a linear heteropolysaccharide composed of (1-3)-linked beta-D-GlcUA-beta-D-GlcNAc disaccharide repeats. It can be found in vertebrates and a few microbes and is typically on the cell surface or in the extracellular space, but is also found inside mammalian cells. Hyaluronan has several physiochemical and biological functions such as space filling, lubrication, and providing a hydrated matrix through which cells can migrate. 235 matched cddid_all.tbl CDD cd06435 cd06435 133057 CESA_NdvC_like NdvC_like proteins in this family are putative bacterial beta-(1,6)-glucosyltransferase. NdvC_like proteins in this family are putative bacterial beta-(1,6)-glucosyltransferase. Bradyrhizobium japonicum synthesizes periplasmic cyclic beta-(1,3),beta-(1,6)-D-glucans during growth under hypoosmotic conditions. Two genes (ndvB, ndvC) are involved in the beta-(1, 3), beta-(1,6)-glucan synthesis. The ndvC mutant strain resulted in synthesis of altered cyclic beta-glucans composed almost entirely of beta-(1, 3)-glycosyl linkages. The periplasmic cyclic beta-(1,3),beta-(1,6)-D-glucans function for osmoregulation. The ndvC mutation also affects the ability of the bacteria to establish a successful symbiotic interaction with host plant. Thus, the beta-glucans may function as suppressors of a host defense response. 236 matched cddid_all.tbl CDD cd06436 cd06436 133058 GlcNAc-1-P_transferase N-acetyl-glucosamine transferase is involved in the synthesis of Poly-beta-1,6-N-acetyl-D-glucosamine. N-acetyl-glucosamine transferase is responsible for the synthesis of bacteria Poly-beta-1,6-N-acetyl-D-glucosamine (PGA). Poly-beta-1,6-N-acetyl-D-glucosamine is a homopolymer that serves as an adhesion for the maintenance of biofilm structural stability in diverse eubacteria. N-acetyl-glucosamine transferase is the product of gene pgaC. Genetic analysis indicated that all four genes of the pgaABCD locus were required for the PGA production, pgaC being a glycosyltransferase. 191 matched cddid_all.tbl CDD cd06437 cd06437 133059 CESA_CaSu_A2 Cellulose synthase catalytic subunit A2 (CESA2) is a catalytic subunit or a catalytic subunit substitute of the cellulose synthase complex. Cellulose synthase (CESA) catalyzes the polymerization reaction of cellulose using UDP-glucose as the substrate. Cellulose is an aggregate of unbranched polymers of beta-1,4-linked glucose residues, which is an abundant polysaccharide produced by plants and in varying degrees by several other organisms including algae, bacteria, fungi, and even some animals. Genomes from higher plants harbor multiple CESA genes. There are ten in Arabidopsis. At least three different CESA proteins are required to form a functional complex. In Arabidopsis, CESA1, 3 and 6 and CESA4, 7 and 8, are required for cellulose biosynthesis during primary and secondary cell wall formation. CESA2 is very closely related to CESA6 and is viewed as a prime substitute for CESA6. They functionally compensate each other. The cesa2 and cesa6 double mutant plants were significantly smaller, while the single mutant plants were almost normal. 232 matched cddid_all.tbl CDD cd06438 cd06438 133060 EpsO_like EpsO protein participates in the methanolan synthesis. The Methylobacillus sp EpsO protein is predicted to participate in the methanolan synthesis. Methanolan is an exopolysaccharide (EPS), composed of glucose, mannose and galactose. A 21 genes cluster was predicted to participate in the methanolan synthesis. Gene disruption analysis revealed that EpsO is one of the glycosyltransferase enzymes involved in the synthesis of repeating sugar units onto the lipid carrier. 183 matched cddid_all.tbl CDD cd06439 cd06439 133061 CESA_like_1 CESA_like_1 is a member of the cellulose synthase (CESA) superfamily. This is a subfamily of cellulose synthase (CESA) superfamily. CESA superfamily includes a wide variety of glycosyltransferase family 2 enzymes that share the common characteristic of catalyzing the elongation of polysaccharide chains. The members of the superfamily include cellulose synthase catalytic subunit, chitin synthase, glucan biosynthesis protein and other families of CESA-like proteins. 251 matched cddid_all.tbl CDD cd06442 cd06442 133062 DPM1_like DPM1_like represents putative enzymes similar to eukaryotic DPM1. Proteins similar to eukaryotic DPM1, including enzymes from bacteria and archaea; DPM1 is the catalytic subunit of eukaryotic dolichol-phosphate mannose (DPM) synthase. DPM synthase is required for synthesis of the glycosylphosphatidylinositol (GPI) anchor, N-glycan precursor, protein O-mannose, and C-mannose. In higher eukaryotes,the enzyme has three subunits, DPM1, DPM2 and DPM3. DPM is synthesized from dolichol phosphate and GDP-Man on the cytosolic surface of the ER membrane by DPM synthase and then is flipped onto the luminal side and used as a donor substrate. In lower eukaryotes, such as Saccharomyces cerevisiae and Trypanosoma brucei, DPM synthase consists of a single component (Dpm1p and TbDpm1, respectively) that possesses one predicted transmembrane region near the C terminus for anchoring to the ER membrane. In contrast, the Dpm1 homologues of higher eukaryotes, namely fission yeast, fungi, and animals, have no transmembrane region, suggesting the existence of adapter molecules for membrane anchoring. This family also includes bacteria and archaea DPM1_like enzymes. However, the enzyme structure and mechanism of function are not well understood. This protein family belongs to Glycosyltransferase 2 superfamily. 224 matched cddid_all.tbl CDD cd06444 cd06444 176473 DNA_pol_A Family A polymerase primarily fills DNA gaps that arise during DNA repair, recombination and replication. DNA polymerase family A, 5'-3' polymerase domain. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gamma, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic polymerase I (pol I) has two functional domains located on the same polypeptide; a 5'-3' polymerase and a 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and the DNA polymerase activity to fill in the resulting gap. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains. 347 matched cddid_all.tbl CDD cd06445 cd06445 119438 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of the C-terminal domain, suggesting an important structural role for the N-terminal domain in orienting the C-terminal domain for proper catalysis. Some ATase C-terminal domain homologs are either single-domain proteins that lack an N-terminal domain, or have a tryptophan substituted in place of the acceptor cysteine (i.e. the motif PCHR is replaced by PWHR). ATase null mutant mice are viable, fertile, and have a normal lifespan. 79 matched cddid_all.tbl CDD cd06446 cd06446 107207 Trp-synth_B Tryptophan synthase-beta: Tryptophan synthase is a bifunctional enzyme that catalyses the last two steps in the biosynthesis of L-tryptophan via its alpha and beta reactions. In the alpha reaction, indole 3-glycerol phosphate is cleaved reversibly to glyceraldehyde 3-phosphate and indole at the active site of the alpha subunit. In the beta reaction, indole undergoes a PLP-dependent reaction with L-serine to form L-tryptophan at the active site of the beta subunit. Members of this CD, Trp-synth_B, are found in all three major phylogenetic divisions. 365 matched cddid_all.tbl CDD cd06447 cd06447 107208 D-Ser-dehyd D-Serine dehydratase is a pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of L- or D-serine to pyruvate and ammonia. D-serine dehydratase serves as a detoxifying enzyme in most E. coli strains where D-serine is a competitive antagonist of beta-alanine in the biosynthetic pathway to pentothenate and coenzyme A. D-serine dehydratase is different from other pyridoxal-5'-phosphate-dependent enzymes in that it catalyzes alpha, beta-elimination reactions on amino acids. 404 matched cddid_all.tbl CDD cd06448 cd06448 107209 L-Ser-dehyd Serine dehydratase is a pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of L- , D-serine, or L-threonine to pyruvate/ketobutyrate and ammonia. 316 matched cddid_all.tbl CDD cd06449 cd06449 107210 ACCD Aminocyclopropane-1-carboxylate deaminase (ACCD): Pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of 1-aminocyclopropane-L-carboxylate (ACC), a precursor of the plant hormone ethylene, to alpha-ketobutyrate and ammonia. 307 matched cddid_all.tbl CDD cd06450 cd06450 99743 DOPA_deC_like DOPA decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to DOPA/tyrosine decarboxylase (DDC), histidine decarboxylase (HDC), and glutamate decarboxylase (GDC). DDC is active as a dimer and catalyzes the decarboxylation of tyrosine. GDC catalyzes the decarboxylation of glutamate and HDC catalyzes the decarboxylation of histidine. 345 matched cddid_all.tbl CDD cd06451 cd06451 99744 AGAT_like Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT), serine-glyoxylate aminotransferase (SGAT), and 3-hydroxykynurenine transaminase (HKT). AGAT is a homodimeric protein, which catalyses the transamination of glyoxylate to glycine, and SGAT converts serine and glyoxylate to hydroxypyruvate and glycine. HKT catalyzes the PLP-dependent transamination of 3-hydroxykynurenine, a potentially toxic metabolite of the kynurenine pathway. 356 matched cddid_all.tbl CDD cd06452 cd06452 99745 SepCysS Sep-tRNA:Cys-tRNA synthase. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Cys-tRNA(Cys) is produced by O-phosphoseryl-tRNA synthetase which ligates O-phosphoserine (Sep) to tRNA(Cys), and Sep-tRNA:Cys-tRNA synthase (SepCysS) converts Sep-tRNA(Cys) to Cys-tRNA(Cys), in methanogenic archaea. SepCysS forms a dimer, each monomer is composed of a large and small domain; the larger, a typical pyridoxal 5'-phosphate (PLP)-dependent-like enzyme fold. In the active site of each monomer, PLP is covalently bound to a conserved Lys residue near the dimer interface. 361 matched cddid_all.tbl CDD cd06453 cd06453 99746 SufS_like Cysteine desulfurase (SufS)-like. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to cysteine desulfurase (SufS) and selenocysteine lyase. SufS catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L-selenocystine to produce L-alanine; and selenocysteine lyase catalyzes the decomposition of L-selenocysteine. 373 matched cddid_all.tbl CDD cd06454 cd06454 99747 KBL_like KBL_like; this family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to serine palmitoyltransferase (SPT), 5-aminolevulinate synthase (ALAS), 8-amino-7-oxononanoate synthase (AONS), and 2-amino-3-ketobutyrate CoA ligase (KBL). SPT is responsible for the condensation of L-serine with palmitoyl-CoA to produce 3-ketodihydrospingosine, the reaction of the first step in sphingolipid biosynthesis. ALAS is involved in heme biosynthesis; it catalyzes the synthesis of 5-aminolevulinic acid from glycine and succinyl-coenzyme A. AONS catalyses the decarboxylative condensation of l-alanine and pimeloyl-CoA in the first committed step of biotin biosynthesis. KBL catalyzes the second reaction step of the metabolic degradation pathway for threonine converting 2-amino-3-ketobutyrate, to glycine and acetyl-CoA. The members of this CD are widely found in all three forms of life. 349 matched cddid_all.tbl CDD cd06455 cd06455 341050 M3A_TOP Peptidase M3 thimet oligopeptidase (TOP), also includes neurolysin. Peptidase M3 Thimet oligopeptidase (TOP; PZ-peptidase; endo-oligopeptidase A; endopeptidase 24.15; soluble metallo-endopeptidase; EC 3.4.24.15) family also includes neurolysin (endopeptidase 24.16, microsomal endopeptidase, mitochondrial oligopeptidase M, neurotensin endopeptidase, soluble angiotensin II-binding protein, thimet oligopeptidase II) which hydrolyzes oligopeptides such as neurotensin, bradykinin and dynorphin A. TOP and neurolysin are neuropeptidases expressed abundantly in the testis, but are also found in the liver, lung and kidney. They are involved in the metabolism of neuropeptides under 20 amino acid residues long and cleave most bioactive peptides at the same sites, but recognize different positions on some naturally occurring and synthetic peptides; they cleave at distinct sites on the 13-residue bioactive peptide neurotensin, which modulates central dopaminergic and cholinergic circuits. TOP has been shown to degrade peptides released by the proteasome, limiting the extent of antigen presentation by major histocompatibility complex class I molecules, and has been associated with amyloid protein precursor processing. 642 matched cddid_all.tbl CDD cd06456 cd06456 341051 M3A_DCP Peptidase family M3, dipeptidyl carboxypeptidase (DCP). Peptidase family M3 dipeptidyl carboxypeptidase (DCP; Dcp II; peptidyl dipeptidase; EC 3.4.15.5). This metal-binding M3A family also includes oligopeptidase A (OpdA; EC 3.4.24.70). DCP cleaves dipeptides off the C-termini of various peptides and proteins, the smallest substrate being N-blocked tripeptides and unblocked tetrapeptides. DCP from Escherichia coli is inhibited by the anti-hypertensive drug captopril, an inhibitor of the mammalian angiotensin converting enzyme (ACE, also called peptidyl dipeptidase A). OpdA may play a specific role in the degradation of signal peptides after they are released from precursor forms of secreted proteins. It can also cleave N-acetyl-L-Ala. This family also includes Arabidopsis thaliana organellar oligopeptidase OOP (At5g65620), which plays a role in targeting peptide degradation in mitochondria and chloroplasts; it degrades peptide substrates that are between 8 to 23 amino acid residues, and shows a weak preference for hydrophobic residues (F/L) at the P1 position. 653 matched cddid_all.tbl CDD cd06457 cd06457 341052 M3A_MIP Peptidase M3 mitochondrial intermediate peptidase (MIP). Peptidase M3 mitochondrial intermediate peptidase (MIP; EC 3.4.24.59) belongs to the widespread subfamily M3A, that shows similarity to Thimet oligopeptidase (TOP). It is one of three peptidases responsible for the proteolytic processing of both nuclear and mitochondrial encoded precursor polypeptides targeted to various subcompartments of the mitochondria. It cleaves intermediate-size proteins initially processed by mitochondrial processing peptidase (MPP) to yield a processing intermediate with a typical N-terminal octapeptide that is sequentially cleaved by MIP to mature-size protein. MIP cleaves precursor proteins of respiratory components, including subunits of the electron transport chain and tri-carboxylic acid cycle enzymes, and components of the mitochondrial genetic machinery, including ribosomal proteins, translation factors, and proteins required for mitochondrial DNA metabolism. It has been suggested that the human MIP (HMIP polypeptide (gene symbol MIPEP) may be one of the loci predicted to influence the clinical manifestations of Friedreich's ataxia (FRDA), an autosomal recessive neurodegenerative disease caused by the lack of human frataxin. These proteins are enriched in cysteine residues, two of which are highly conserved, suggesting their importance to stability as well as in formation of metal binding sites, thus playing a role in MIP activity. 613 matched cddid_all.tbl CDD cd06459 cd06459 341053 M3B_PepF Peptidase family M3B, oligopeptidase F (PepF). Peptidase family M3B oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and includes oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most bacterial PepFs are cytoplasmic endopeptidases; however, the Bacillus amyloliquefaciens PepF oligopeptidase is a secreted protein and may facilitate the process of sporulation. Specifically, the yjbG gene encoding the homolog of the PepF1 and PepF2 oligoendopeptidases of Lactococcus lactis has been identified in Bacillus subtilis as an inhibitor of sporulation initiation when over-expressed from a multicopy plasmid. 539 matched cddid_all.tbl CDD cd06460 cd06460 341054 M32_Taq Peptidase family M32, which includes thermostable carboxypeptidases TaqCP, PfuCP and FisCP. Peptidase family M32 is a subclass of metallocarboxypeptidases, distributed mainly in bacteria and archaea, whose members contain a HEXXH motif that participates in coordinating a divalent cation such as Zn2+ or Co2+. It includes the thermostable carboxypeptidases (E.C. 3.4.17.19) from Thermus aquaticus (TaqCP) and Pyrococcus furiosus (PfuCP), which have broad specificities toward a wide range of C-terminal substrates that include basic, aromatic, neutral and polar amino acids. These enzymes have a similar fold to the M3 peptidases such as neurolysin and the M2 angiotensin converting enzyme (ACE). The keratin-degrading extremophilic eubacterium Fervidobacterium islandicum M32 carboxypeptidase (FisCP) plays an important role in cellular metabolism, and significantly enhances the degradation of native chicken feathers. It has been shown to mainly cleave the C-termini of peptides with a basic amino acid sequence. Novel M32 peptidases from some eukaryotes: protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, have been identified, thus making these enzymes an attractive potential target for drug development against these organisms. 484 matched cddid_all.tbl CDD cd06461 cd06461 341055 M2_ACE Peptidase family M2, angiotensin converting enzyme (ACE). Peptidase family M2 angiotensin converting enzyme (ACE, EC 3.4.15.1) is a membrane-bound, zinc-dependent dipeptidase that catalyzes the conversion of the decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II, by removing two C-terminal amino acids. There are two forms of the enzyme in humans, the ubiquitous somatic ACE and the sperm-specific germinal ACE, both encoded by the same gene through transcription from alternative promoters. Somatic ACE has two tandem active sites with distinct catalytic properties, whereas germinal ACE, the function of which is largely unknown, has just a single active site. Recently, an ACE homolog, ACE2, has been identified in humans that differs from ACE; it preferentially removes carboxy-terminal hydrophobic or basic amino acids and appears to be important in cardiac function. ACE homologs (also known as members of the M2 gluzincin family) have been found in a wide variety of species, including those that neither have a cardiovascular system nor synthesize angiotensin. ACE is well-known as a key part of the renin-angiotensin system that regulates blood pressure and ACE inhibitors are important for the treatment of hypertension. 563 matched cddid_all.tbl CDD cd06462 cd06462 119396 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the transport of proteins across membranes in all living organisms. All members in this superfamily are unique serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases. 84 matched cddid_all.tbl CDD cd06463 cd06463 107220 p23_like Proteins containing this p23_like domain include p23 and its Saccharomyces cerevisiae (Sc) homolog Sba1. Both are co-chaperones for the heat shock protein (Hsp) 90. p23 binds Hsp90 and participates in the folding of a number of Hsp90 clients, including the progesterone receptor. p23 also has a passive chaperoning activity and in addition may participate in prostaglandin synthesis. Both p23 and Sba1p can regulate telomerase activity. This group includes domains similar to the C-terminal CHORD-SGT1 (CS) domain of suppressor of G2 allele of Skp1 (Sgt1). Sgt1 interacts with multiple protein complexes and has the features of a co-chaperone. Human (h) Sgt1 interacts with both Hsp70 and Hsp90, and has been shown to bind Hsp90 through its CS domain. Saccharomyces cerevisiae (Sc) Sgt1 is a subunit of both core kinetochore and SCF (Skp1-Cul1-F-box) ubiquitin ligase complexes. Sgt1 is required for pathogen resistance in plants. This group also includes the p23_like domains of human butyrate-induced transcript 1 (hB-ind1), NUD (nuclear distribution) C, Melusin, and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR). hB-ind1 plays a role in the signaling pathway mediated by the small GTPase Rac1, NUDC is needed for nuclear movement, Melusin interacts with two splice variants of beta1 integrin, and NCB5OR plays a part in maintaining viable pancreatic beta cells. 84 matched cddid_all.tbl CDD cd06464 cd06464 107221 ACD_sHsps-like Alpha-crystallin domain (ACD) of alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. 88 matched cddid_all.tbl CDD cd06465 cd06465 107222 p23_hB-ind1_like p23_like domain found in human (h) butyrate-induced transcript 1 (B-ind1) and similar proteins. hB-ind1 participates in signaling by the small GTPase Rac1. It binds to Rac1 and enhances different Rac1 effects including activation of nuclear factor (NF) kappaB and activation of c-Jun N-terminal kinase (JNK). hB-ind1 also plays a part in the RNA replication and particle production of Hepatitis C virus (HCV) through its interaction with heat shock protein Hsp90, HCV nonstructural protein 5A (NS5A), and the immunophilin FKBP8. hB-ind1 is upregulated in the outer layer of Chinese hamster V79 cells grown as multicell spheroids, versus in the same cells grown as monolayers. This group includes the Saccharomyces cerevisiae Sba1, a co-chaperone of the Hsp90. Sba1 has been shown to be is required for telomere length maintenance, and may modulate telomerase DNA-binding activity. 108 matched cddid_all.tbl CDD cd06466 cd06466 107223 p23_CS_SGT1_like p23_like domain similar to the C-terminal CHORD-SGT1 (CS) domain of Sgt1 (suppressor of G2 allele of Skp1). Sgt1 interacts with multiple protein complexes and has the features of a cochaperone. Human (h) Sgt1 interacts with both Hsp70 and Hsp90, and has been shown to bind Hsp90 through its CS domain. Saccharomyces cerevisiae (Sc) Sgt1 is a subunit of both core kinetochore and SCF (Skp1-Cul1-F-box) ubiquitin ligase complexes. Sgt1 is required for pathogen resistance in plants. ScSgt1 is needed for the G1/S and G2/M cell-cycle transitions, and for assembly of the core kinetochore complex (CBF3) via activation of Ctf13, the F-box protein. Binding of Hsp82 (a yeast Hsp90 homologue) to ScSgt1, promotes the binding of Sgt1 to Skp1 and of Skp1 to Ctf13. Some proteins in this group have an SGT1-specific (SGS) domain at the extreme C-terminus. The ScSgt1-SGS domain binds adenylate cyclase. The hSgt1-SGS domain interacts with some S100 family proteins, and studies suggest that the interaction of hSgt1 with Hsp90 and Hsp70 may be regulated by S100A6 in a Ca2+ dependent fashion. This group also includes the p23_like domains of Melusin and NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR). Melusin is a vertebrate protein which interacts with two splice variants of beta1 integrin, and NCB5OR plays a part in maintaining viable pancreatic beta cells. 84 matched cddid_all.tbl CDD cd06467 cd06467 107224 p23_NUDC_like p23_like domain of NUD (nuclear distribution) C and similar proteins. Aspergillus nidulas (An) NUDC is needed for nuclear movement. AnNUDC is localized at the hyphal cortex, and binds NUDF at spindle pole bodies (SPBs) and in the cytoplasm at different stages in the cell cycle. At the SPBs it is part of the dynein molecular motor/NUDF complex that regulates microtubule dynamics. Mammalian(m) NUDC associates both with the dynein complex and also with an anti-inflammatory enzyme, platelet activating factor acetylhydrolase I, PAF-AH(I) complex, through binding mNUDF, the regulatory beta subunit of PAF-AH(I). mNUDC is important for cell proliferation both in normal and tumor tissues. Its expression is elevated in various cell types undergoing mitosis or stimulated to proliferate, with high expression levels observed in leukemic cells and tumors. For a leukemic cell line, human NUDC was shown to activate the thrombopoietin (TPO) receptor (Mpl) by binding to its extracellular domain, and promoting cell proliferation and differentiation. This group also includes the human broadly immunogenic tumor associated antigen, CML66, which is highly expressed in a variety of solid tumors and in leukemias. In normal tissues high expression of CML66 is limited to testis and heart. 85 matched cddid_all.tbl CDD cd06468 cd06468 107225 p23_CacyBP p23_like domain found in proteins similar to Calcyclin-Binding Protein(CacyBP)/Siah-1-interacting protein (SIP). CacyBP/SIP interacts with S100A6 (calcyclin), with some other members of the S100 family, with tubulin, and with Siah-1 and Skp-1. The latter two are components of the ubiquitin ligase that regulates beta-catenin degradation. The beta-catenin gene is an oncogene participating in tumorigenesis in many different cancers. Overexpression of CacyBP/SIP, in part through its effect on the expression of beta-catenin, inhibits the proliferation, tumorigenicity, and invasion of gastric cancer cells. CacyBP/SIP is abundant in neurons and neuroblastoma NB2a cells. An extensive re-organization of microtubules accompanies the differentiation of NB2a cells. CacyBP/SIP may contribute to NB2a cell differentiation through binding to and increasing the oligomerization of tubulin. CacyBP/SIP is also implicated in differentiation of erythroid cells, rat neonatal cardiomyocytes, in mouse endometrial events, and in thymocyte development. 92 matched cddid_all.tbl CDD cd06469 cd06469 107226 p23_DYX1C1_like p23_like domain found in proteins similar to dyslexia susceptibility 1 (DYX1) candidate 1 (C1) protein, DYX1C1. The human gene encoding this protein is a positional candidate gene for developmental dyslexia (DD), it is located on 15q21.3 by the DYX1 DD susceptibility locus (15q15-21). Independent association studies have reported conflicting results. However, association of short-term memory, which plays a role in DD, with a variant within the DYX1C1 gene has been reported. Most proteins belonging to this group contain a C-terminal tetratricopeptide repeat (TPR) protein binding region. 78 matched cddid_all.tbl CDD cd06470 cd06470 107227 ACD_IbpA-B_like Alpha-crystallin domain (ACD) found in Escherichia coli inclusion body-associated proteins IbpA and IbpB, and similar proteins. IbpA and IbpB are 16 kDa small heat shock proteins (sHsps). sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. IbpA and IbpB are produced during high-level production of various heterologous proteins, specifically human prorenin, renin and bovine insulin-like growth factor 2 (bIGF-2), and are strongly associated with inclusion bodies containing these heterologous proteins. IbpA and IbpB work as an integrated system to stabilize thermally aggregated proteins in a disaggregation competent state. The chaperone activity of IbpB is also significantly elevated as the temperature increases from normal to heat shock. The high temperature results in the disassociation of 2-3-MDa IbpB oligomers into smaller approximately 600-kDa structures. This elevated activity seen under heat shock conditions is retained for an extended period of time after the temperature is returned to normal. IbpA also forms multimers. 90 matched cddid_all.tbl CDD cd06471 cd06471 107228 ACD_LpsHSP_like Group of bacterial proteins containing an alpha crystallin domain (ACD) similar to Lactobacillus plantarum (Lp) small heat shock proteins (sHsp) HSP 18.5, HSP 18.55 and HSP 19.3. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Transcription of the genes encoding Lp HSP 18.5, 18.55 and 19.3 is regulated by a variety of stresses including heat, cold and ethanol. Early growing L. plantarum cells contain elevated levels of these mRNAs which rapidly fall of as the cells enter stationary phase. Also belonging to this group is Bifidobacterium breve (Bb) HSP20 and Oenococcus oenis (syn. Leuconostoc oenos) (Oo) HSP18. Transcription of the gene encoding BbHSP20 is strongly induced following heat or osmotic shock, and that of the gene encoding OoHSP18 following heat, ethanol or acid shock. OoHSP18 is peripherally associated with the cytoplasmic membrane. 93 matched cddid_all.tbl CDD cd06472 cd06472 107229 ACD_ScHsp26_like Alpha crystallin domain (ACD) found in Saccharomyces cerevisiae (Sc) small heat shock protein (Hsp)26 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. ScHsp26 is temperature-regulated, it switches from an inactive to a chaperone-active form upon elevation in temperature. It associates into large 24-mers storage forms which upon heat shock disassociate into dimers. These dimers initiate the interaction with non-native substrate proteins and re-assemble into large globular assemblies having one monomer of substrate bound per dimer. This group also contains Arabidopsis thaliana (Ath) Hsp15.7, a peroxisomal matrix protein which can complement the morphological phenotype of S. cerevisiae mutants deficient in Hsps26. AthHsp15.7 is minimally expressed under normal conditions and is strongly induced by heat and oxidative stress. Also belonging to this group is wheat HSP16.9 which differs in quaternary structure from the shell-type particles of ScHsp26, it assembles as a dodecameric double disc, with each disc organized as a trimer of dimers. 92 matched cddid_all.tbl CDD cd06475 cd06475 107230 ACD_HspB1_like Alpha crystallin domain (ACD) found in mammalian small (s)heat shock protein (Hsp)-27 (also denoted HspB1 in human) and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Hsp27 shows enhanced synthesis in response to stress. It is a molecular chaperone which interacts with a large number of different proteins. It is found in many types of human cells including breast, uterus, cervix, platelets and cancer cells. Hsp27 has diverse cellular functions including, chaperoning, regulation of actin polymerization, keratinocyte differentiation, regulation of inflammatory pathways in keratinocytes, and protection from oxidative stress through modulating glutathione levels. It is also a subunit of AUF1-containing protein complexes. It has been linked to several transduction pathways regulating cellular functions including differentiation, cell growth, development, and apoptosis. Its activity can be regulated by phosphorylation. Its unphosphorylated state is a high molecular weight aggregated form (100-800kDa) composed of up to 24 subunits, which forms as a result of multiple interactions within the ACD, and is required for chaperone function and resistance to oxidative stress. Upon phosphorylation these large aggregates rapidly disassociate to smaller oligomers and chaperone activity is modified. High constitutive levels of Hsp27 have been detected in various cancer cells, in particular those of carcinoma origin. Over-expression of Hsp27 has a protective effect against various diseases-processes, including Huntington's disease. Mutations in Hsp27 have been associated with a form of distal hereditary motor neuropathy type II and Charcot-Marie-Tooth disease type 2. 86 matched cddid_all.tbl CDD cd06476 cd06476 107231 ACD_HspB2_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB2/heat shock 27kDa protein 2 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB2 is preferentially and constitutively expressed in skeletal muscle and heart. HspB2 shows homooligomeric activity and forms aggregates in muscle cytosol. Although its expression is not induced by heat shock, it redistributes to the insoluble fraction in response to heat shock. In the mouse heart, HspB2 plays a role in maintaining energetic balance, by protecting cardiac energetics during ischemia/reperfusion, and allowing for increased work during acute inotropic challenge. hHspB2 [previously also known as myotonic dystrophy protein kinase (DMPK) binding protein (MKBP)] is selectively up-regulated in skeletal muscles from myotonic dystrophy patients. The ACD of hHspB2 binds the DMPK kinase domain. In vitro, hHspB2 enhances the kinase activity of DMPK and confers thermoresistance. The hHspB2 gene lies less than 1kb from the 5 prime end of the related alphaB (HspB4)-crystallin gene, with the opposite transcription direction. These two genes may share regulatory elements for their expression. 83 matched cddid_all.tbl CDD cd06477 cd06477 107232 ACD_HspB3_Like Alpha crystallin domain (ACD) found in mammalian HspB3, also known as heat-shock protein 27-like protein (HSPL27, 17-kDa) and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB3 is expressed in adult skeletal muscle, smooth muscle, and heart, and in several other fetal tissues. In muscle cells HspB3 forms an oligomeric 150 kDa complex with myotonic dystrophy protein kinase-binding protein (MKBP/ HspB2), this complex may comprise one of two independent muscle-cell specific chaperone systems. The expression of HspB3 is induced during muscle differentiation controlled by the myogenic factor MyoD. HspB3 may also interact with Hsp22 (HspB8). 83 matched cddid_all.tbl CDD cd06478 cd06478 107233 ACD_HspB4-5-6 Alpha-crystallin domain found in alphaA-crystallin (HspB4), alphaB-crystallin (HspB5), and the small heat shock protein (sHsp) HspB6, also known as Hsp20. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Alpha crystallin, an abundant protein in the mammalian lens, is a large (700 kDa) heteropolymer composed of HspB4 and HspB5, generally in a molar ratio of HspB4:HspB5 of 3:1. Only trace amounts of HspB4 are found in tissues other than the lens. HspB5 on the other hand is also expressed constitutively in other tissues including brain, heart, and type I and type IIa skeletal muscle fibers, and in several cancers including gliomas, renal cell carcinomas, basal-like and metaplastic breast carcinomas, and head and neck cancer. HspB5's functions include effects on the apoptotic pathway and on metastasis. Phosphorylation of HspB5 reduces its oligomerization and anti-apoptotic activities. HspB5 is protective in demyelinating disease such as multiple sclerosis (MS), being a negative regulator of inflammation. In early active MS lesions it is the most abundant gene transcript and an autoantigen, the immune response against it would disrupt its function and worsen inflammation and demyelination. Given as therapy for ongoing demyelinating disease it may counteract this effect. It is an autoantigen in the pathogenesis of various other inflammatory disorders including Lens-associated uveitis (LAU), and Behcet's disease. Mutations in HspB5 have been associated with diseases including dominant cataract and desmin-related myopathy. Mutations in HspB4 have been associated with Autosomal Dominant Congenital Cataract (ADCC). HspB6 (Hsp20) is ubiquitous and is involved in diverse functions including regulation of glucose transport and contraction of smooth muscle, in platelet aggregation, in cardioprotection, and in the prevention of apoptosis. It interacts with the universal scaffolding and adaptor protein 14-3-3, and also with the proapoptotic protein Bax. 83 matched cddid_all.tbl CDD cd06479 cd06479 107234 ACD_HspB7_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB7, also known as cardiovascular small heat shock protein (cvHsp), and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB7 is a 25-kDa protein, preferentially expressed in heart and skeletal muscle. It binds the cytoskeleton protein alpha-filamin (also known as actin-binding protein 280). The expression of HspB7 is increased during rat muscle aging. Its expression is also modulated in obesity implicating this protein in this and related metabolic disorders. As the human gene encoding HspB7 is mapped to chromosome 1p36.23-p34.3 it is a positional candidate for several dystrophies and myopathies. 81 matched cddid_all.tbl CDD cd06480 cd06480 107235 ACD_HspB8_like Alpha-crystallin domain (ACD) found in mammalian 21.6 KDa small heat shock protein (sHsp) HspB8, also denoted as Hsp22 in humans, and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. A chaperone complex formed of HspB8 and Bag3 stimulates degradation of protein complexes by macroautophagy. HspB8 also forms complexes with Hsp27 (HspB1), MKBP (HspB2), HspB3, alphaB-crystallin (HspB5), Hsp20 (HspB6), and cvHsp (HspB7). These latter interactions may depend on phosphorylation of the respective partner sHsp. HspB8 may participate in the regulation of cell proliferation, cardiac hypertrophy, apoptosis, and carcinogenesis. Point mutations in HspB8 have been correlated with the development of several congenital neurological diseases, including Charcot Marie tooth disease and distal motor neuropathy type II. 91 matched cddid_all.tbl CDD cd06481 cd06481 107236 ACD_HspB9_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB9 and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Human (h) HspB9 is expressed exclusively in the normal testis and in various tumor samples and is a cancer/testis antigen. hHspB9 interacts with TCTEL1 (T-complex testis expressed protein -1), a subunit of dynein. hHspB9 and TCTEL1 are co-expressed in similar cells within the testis and in tumor cells. Included in this group is Xenopus Hsp30, a developmentally-regulated heat-inducible molecular chaperone. 87 matched cddid_all.tbl CDD cd06482 cd06482 107237 ACD_HspB10 Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB10, also known as sperm outer dense fiber protein (ODFP), and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Human (h) HspB10 occurs exclusively in the axoneme of sperm cells and may have a cytoskeletal role. 87 matched cddid_all.tbl CDD cd06488 cd06488 107238 p23_melusin_like p23_like domain similar to the C-terminal (tail) domain of vertebrate Melusin and related proteins. Melusin's tail domain interacts with the cytoplasmic domain of beta1-A and beta1-D isoforms of beta1 integrin, it does not bind other integrin beta subunits. Melusin is a muscle-specific protein expressed in skeletal and cardiac muscles but not in smooth muscle or other tissues. It is needed for heart hypertrophy following mechanical overload. The integrin-binding portion of this domain appears to be sequestered in the full length melusin protein, Ca2+ may modulate the protein's conformation exposing this binding site. This group includes Chordc1, also known as Chp-1, which is conserved from vertebrates to humans. Mammalian Chordc1 interacts with the heat shock protein (HSP) Hsp90 and is implicated in circadian and/or homeostatic mechanisms in the brain. The N-terminal portions of proteins belonging to this group contain two cysteine and histidine rich domain (CHORD) domains. 87 matched cddid_all.tbl CDD cd06489 cd06489 107239 p23_CS_hSgt1_like p23_like domain similar to the C-terminal CS (CHORD-SGT1) domain of human (h) Sgt1 and related proteins. hSgt1 is a co-chaperone which has been shown to be elevated in HEp-2 cells as a result of stress conditions such as heat shock. It interacts with the heat shock proteins (HSPs) Hsp70 and Hsp90, and it expression pattern is synchronized with these two Hsps. The interaction with HSP90 has been shown to involve the hSgt1_CS domain, and appears to be required for correct kinetochore assembly and efficient cell division. Some proteins in this subgroup contain a tetratricopeptide repeat (TPR) HSP-binding domain N-terminal to this CS domain, and most proteins in this subgroup contain a Sgt1-specific (SGS) domain C-terminal to the CS domain. The SGS domain interacts with some S100 family proteins. Studies suggest that S100A6 modulates in a Ca2+ dependent manner the interactions of hSgt1 with Hsp90 and Hsp70. The yeast Sgt1 CS domain is not found in this subgroup. 84 matched cddid_all.tbl CDD cd06490 cd06490 107240 p23_NCB5OR p23_like domain found in NAD(P)H cytochrome b5 (NCB5) oxidoreductase (OR) and similar proteins. NCB5OR is widely expressed in human organs and tissues and is localized in the ER (endoplasmic reticulum). It appears to play a critical role in maintaining viable pancreatic beta cells. Mice homozygous for a targeted knockout (KO) of the gene encoding NCB5OR develop an early-onset nonautoimmune diabetes phenotype with a non-inflammatory beta-cell deficiency. The role of NCB5OR in beta cells may be in maintaining or regulating their redox status. Proteins in this group in addition contain an N-terminal cytochrome b5 domain and a C-terminal cytochrome b5 oxidoreductase domain. The gene encoding NCB5OR has been considered as a positional candidate for type II diabetes and other diabetes subtypes related to B-cell dysfunction, however variation in its coding region does not appear not to be a major contributor to the pathogenesis of these diseases. 87 matched cddid_all.tbl CDD cd06492 cd06492 107241 p23_mNUDC_like p23-like NUD (nuclear distribution) C-like domain of mammalian(m) NUDC and similar proteins. Mammalian(m) NUDC associates both with the dynein complex and also with an anti-inflammatory enzyme, platelet activating factor acetylhydrolase I, PAF-AH(I) complex, through binding mNUDF, the regulatory beta subunit of PAF-AH(I). mNUDC is important for cell proliferation both in normal and tumor tissues. Its expression is elevated in various cell types undergoing mitosis or stimulated to proliferate, with high expression levels observed in leukemic cells and tumors. For a leukemic cell line, human NUDC was shown to activate the thrombopoietin (TPO) receptor (Mpl) by binding to its extracellular domain, and promoting cell proliferation and differentiation. 87 matched cddid_all.tbl CDD cd06493 cd06493 107242 p23_NUDCD1_like p23_NUDCD1: p23-like NUD (nuclear distribution) C-like domain found in human NUD (nuclear distribution) C domain-containing protein 1, NUDCD1 (also known as CML66), and similar proteins. NUDCD1/CML66 is a broadly immunogenic tumor associated antigen, which is highly expressed in a variety of solid tumors and in leukemias. In normal tissues high expression of NUDCD1/CML66 is limited to testis and heart. 85 matched cddid_all.tbl CDD cd06494 cd06494 107243 p23_NUDCD2_like p23-like NUD (nuclear distribution) C-like found in human NUDC domain-containing protein 2 (NUDCD2) and similar proteins. Little is known about the function of the proteins in this subgroup. 93 matched cddid_all.tbl CDD cd06495 cd06495 107244 p23_NUDCD3_like p23-like NUD (nuclear distribution) C-like domain found in human NUDC domain-containing protein 3 (NUDCD3) and similar proteins. Little is known about the function of the proteins in this subgroup. 102 matched cddid_all.tbl CDD cd06497 cd06497 107245 ACD_alphaA-crystallin_HspB4 Alpha-crystallin domain found in the small heat shock protein (sHsp) alphaA-crystallin (HspB4, 20kDa). sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Alpha crystallin, an abundant protein in the mammalian lens, is a large (700 kDa) heteropolymer composed of HspB4 and HspB5, generally in a molar ratio of HspB4:HspB5 of 3:1. Only trace amounts of HspB4 are found in tissues other than the lens. HspB5 does not belong to this group. Mutations inHspB4 have been associated with Autosomal Dominant Congenital Cataract (ADCC). The chaperone-like functions of HspB4 are considered important for maintaining lens transparency and preventing cataract. 86 matched cddid_all.tbl CDD cd06498 cd06498 107246 ACD_alphaB-crystallin_HspB5 Alpha-crystallin domain found in the small heat shock protein (sHsp) alphaB-crystallin (HspB5, 20kDa). sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Alpha crystallin, an abundant protein in the mammalian lens, is a large (700 kDa) heteropolymer composed of HspB4 and HspB5, generally in a molar ratio of HspB4:HspB5 of 3:1. HspB4 does not belong to this group. HspB5 shows increased synthesis in response to stress. HspB5 is also expressed constitutively in other tissues including brain, heart, and type I and type IIa skeletal muscle fibers, and in several cancers including gliomas, renal cell carcinomas, basal-like and metaplastic breast carcinomas, and head and neck cancer. Its functions include effects on the apoptotic pathway and on metastasis. Phosphorylation of HspB5 reduces its oligomerization and anti-apoptotic activities. HspB5 is protective in demyelinating disease such as multiple sclerosis (MS), being a negative regulator of inflammation. In early active MS lesions it is the most abundant gene transcript and an autoantigen, the immune response against it would disrupt its function and worsen inflammation and demyelination. Given as therapy for ongoing demyelinating disease it may counteract this effect. It is an autoantigen in the pathogenesis of various other inflammatory disorders including Lens-associated uveitis (LAU), and Behcet's disease. Mutations in HspB5 have been associated with diseases including dominant cataract and desmin-related myopathy. 84 matched cddid_all.tbl CDD cd06499 cd06499 133460 GT_MraY-like Glycosyltransferase 4 (GT4) includes both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases. They catalyze the transfer of a D-N-acetylhexosamine 1-phosphate to a membrane-bound polyprenol phosphate, which is the initiation step of protein N-glycosylation in eukaryotes and peptidoglycan biosynthesis in bacteria. One member, D-N-acetylhexosamine 1-phosphate transferase (GPT) is a eukaryotic enzyme, which is specific for UDP-GlcNAc as donor substrate and dolichol-phosphate as the membrane bound acceptor. The bacterial members MraY, WecA, and WbpL/WbcO utilize undecaprenol phosphate as the acceptor substrate, but use different UDP-sugar donor substrates. MraY-type transferases are highly specific for UDP-N-acetylmuramate-pentapeptide, whereas WecA proteins are selective for UDP-N-acetylglucosamine (UDP-GlcNAc). The WbcO/WbpL substrate specificity has not yet been determined, but the structure of their biosynthetic endproducts implies that UDP-N-acetyl-D-fucosamine (UDP-FucNAc) and/or UDPN-acetyl-D-quinosamine (UDP-QuiNAc) are used. The eukaryotic reaction is the first step in the assembly of dolichol-linked oligosaccharide intermediates and is essential for N-glycosylation. The prokaryotic reactions lead to the formation of polyprenol-linked oligosaccharides involved in bacterial cell wall and peptidoglycan assembly. Archaeal and eukaryotic enzymes may use the same substrates and are evolutionarily closer than the bacterial enzyme. Archaea possess the same N-glycosylation pathway as eukaryotes. A glycosyl transferase gene Mv1751 in M. voltae encodes for the enzyme that carries out the first step in the pathway, the attachment of GlcNAc to a dolichol lipid carrier in the membrane. A lethal mutation in the alg7 (GPT) gene in Saccharomyces cerevisiae was successfully complemented with Mv1751, the archaea gene. 185 matched cddid_all.tbl CDD cd06502 cd06502 99748 TA_like Low-specificity threonine aldolase (TA). This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). TA catalyzes the conversion of L-threonine or L-allo-threonine to glycine and acetaldehyde in a secondary glycine biosynthetic pathway. 338 matched cddid_all.tbl CDD cd06503 cd06503 349951 ATP-synt_Fo_b F-type ATP synthase, membrane subunit b. Membrane subunit b is a component of the Fo complex of FoF1-ATP synthase. The F-type ATP synthases (FoF1-ATPase) consist of two structural domains: the F1 (assembly factor one) complex containing the soluble catalytic core, and the Fo (oligomycin sensitive factor) complex containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. F1 is composed of alpha (or A), beta (B), gamma (C), delta (D) and epsilon (E) subunits with a stoichiometry of 3:3:1:1:1, while Fo consists of the three subunits a, b, and c (1:2:10-14). An oligomeric ring of 10-14 c subunits (c-ring) make up the Fo rotor. The flux of protons through the ATPase channel (Fo) drives the rotation of the c-ring, which in turn is coupled to the rotation of the F1 complex gamma subunit rotor due to the permanent binding between the gamma and epsilon subunits of F1 and the c-ring of Fo. The F-ATP synthases are primarily found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts or in the plasma membranes of bacteria. The F-ATP synthases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. This group also includes F-ATP synthase that has also been found in the archaea Candidatus Methanoperedens. 132 matched cddid_all.tbl CDD cd06522 cd06522 119382 GH25_AtlA-like AtlA is an autolysin found in Gram-positive lactic acid bacteria that degrades bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues. This family includes the AtlA and Aml autolysins from Streptococcus mutans which have a C-terminal glycosyl hydrolase family 25 (GH25) catalytic domain as well as six tandem N-terminal repeats of the GBS (group B Streptococcus) Bsp-like peptidoglycan-binding domain. Other members of this family have one or more C-terminal peptidoglycan-binding domain(s) (SH3 or LysM) in addition to the GH25 domain. 192 matched cddid_all.tbl CDD cd06523 cd06523 119383 GH25_PlyB-like PlyB is a bacteriophage endolysin that displays potent lytic activity toward Bacillus anthracis. PlyB has an N-terminal glycosyl hydrolase family 25 (GH25) catalytic domain and a C-terminal bacterial SH3-like domain, SH3b. Both domains are required for effective catalytic activity. Endolysins are produced by bacteriophages at the end of their life cycle and participate in lysing the bacterial cell in order to release the newly formed progeny. Endolysins (also referred to as endo-N-acetylmuramidases or peptidoglycan hydrolases) degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues. 177 matched cddid_all.tbl CDD cd06524 cd06524 119384 GH25_YegX-like YegX is an uncharacterized bacterial protein with a glycosyl hydrolase family 25 (GH25) catalytic domain that is similar in sequence to the CH-type (Chalaropsis-type) lysozymes of the GH25 family of endolysins. 194 matched cddid_all.tbl CDD cd06525 cd06525 119385 GH25_Lyc-like Lyc muramidase is an autolytic lysozyme (autolysin) from Clostridium acetobutylicum encoded by the lyc gene. Lyc has a glycosyl hydrolase family 25 (GH25) catalytic domain. Endo-N-acetylmuramidases are lysozymes (also referred to as peptidoglycan hydrolases) that degrade bacterial cell walls by catalyzing the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues. 184 matched cddid_all.tbl CDD cd06526 cd06526 107247 metazoan_ACD Alpha-crystallin domain (ACD) of metazoan alpha-crystallin-type small(s) heat shock proteins (Hsps). sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, whose common feature is the Alpha-crystallin domain (ACD). sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps. 83 matched cddid_all.tbl CDD cd06528 cd06528 132725 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. 363 matched cddid_all.tbl CDD cd06529 cd06529 119397 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the protein. In the presence of single-stranded DNA, the LexA, UmuD and MucA proteins interact with RecA, activating self cleavage, thus either derepressing transcription in the case of LexA or activating the lesion-bypass polymerase in the case of UmuD and MucA. The LexA proteins are serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases. LexA sequence homologs are found in almost all of the bacterial genomes sequenced to date, covering a large number of phyla, suggesting both, an ancient origin and a widespread distribution of lexA and the SOS response. 81 matched cddid_all.tbl CDD cd06530 cd06530 119398 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa) belong to this family and they process many proteins that enter the ER for retention or for export to the Golgi apparatus, secretory vesicles, plasma membranes or vacuole. An atypical member of the S26 SPase type I family is the TraF peptidase which has the remarkable activity of producing a cyclic protein of the Pseudomonas pilin system. The type I signal peptidases are unique serine proteases that utilize a serine/lysine catalytic dyad mechanism in place of the classical serine/histidine/aspartic acid catalytic triad mechanism. 85 matched cddid_all.tbl CDD cd06532 cd06532 133474 Glyco_transf_25 Glycosyltransferase family 25 [lipooligosaccharide (LOS) biosynthesis protein] is a family of glycosyltransferases involved in LOS biosynthesis. The members include the beta(1,4) galactosyltransferases: Lgt2 of Moraxella catarrhalis, LgtB and LgtE of Neisseria gonorrhoeae and Lic2A of Haemophilus influenzae. M. catarrhalis Lgt2 catalyzes the addition of galactose (Gal) to the growing chain of LOS on the cell surface. N. gonorrhoeae LgtB and LgtE link Gal-beta(1,4) to GlcNAc (N-acetylglucosamine) and Glc (glucose), respectively. The genes encoding LgtB and LgtE are two genes of a five gene locus involved in the synthesis of gonococcal LOS. LgtE is believed to perform the first step in LOS biosynthesis. 128 matched cddid_all.tbl CDD cd06533 cd06533 119439 Glyco_transf_WecG_TagA The glycosyltransferase WecG/TagA superfamily contains Escherichia coli WecG, Bacillus subtilis TagA and related proteins. E. coli WecG is believed to be a UDP-N-acetyl-D-mannosaminuronic acid transferase, and is involved in enterobacterial common antigen (eca) synthesis. B. subtilis TagA plays a key role in the Wall Teichoic Acid (WTA) biosynthetic pathway, catalyzing the transfer of N-acetylmannosamine to the C4 hydroxyl of a membrane-anchored N-acetylglucosaminyl diphospholipid to make ManNAc-beta-(1,4)-GlcNAc-pp-undecaprenyl. This is the first committed step in this pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan. 171 matched cddid_all.tbl CDD cd06534 cd06534 143395 ALDH-SF NAD(P)+-dependent aldehyde dehydrogenase superfamily. The aldehyde dehydrogenase superfamily (ALDH-SF) of NAD(P)+-dependent enzymes, in general, oxidize a wide range of endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-L) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase. Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. The ALDH-like group is represented by such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group. 367 matched cddid_all.tbl CDD cd06535 cd06535 119368 CIDE_N_CAD CIDE_N domain of CAD nuclease. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD(DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of CAD/DFF40 and ICAD/DFF45 during apoptosis. In normal cells, DFF exists in the nucleus as a heterodimer composed of CAD/DFF40 as a latent nuclease and its chaperone and inhibitor subunit ICAD/DFF45. Apoptotic activation of caspase-3 results in the cleavage of DFF45/ICAD and the release of active DFF40/CAD nuclease. 77 matched cddid_all.tbl CDD cd06536 cd06536 119369 CIDE_N_ICAD CIDE_N domain of ICAD. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of the CAD nuclease (caspase-activated DNase/DNA fragmentation factor, DFF40) and its inhibitor, ICAD (DFF45). These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of the CAD/DFF40 and ICAD/DFF45 during apoptosis. In normal cells, DFF exists in the nucleus as a heterodimer composed of CAD/DFF40 as a latent nuclease and its chaperone and inhibitor subunit ICAD/DFF45. Apoptotic activation of caspase-3 results in the cleavage of DFF45/ICAD and release of active DFF40/CAD nuclease. 80 matched cddid_all.tbl CDD cd06537 cd06537 119370 CIDE_N_B CIDE_N domain of CIDE-B proteins. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins. These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of the CAD/DFF40, ICAD/DFF45 and CIDE nucleases during apoptosis. The CIDE protein family includes 3 members: CIDE-A, CIDE-B, and FSP27(CIDE-C). Based on sequence similarity with DFF40 and DFF45, CIDE proteins were initially characterized as mitochondrial activators of apoptosis. However, strong metabolic phenotypes of mice lacking CIDE-A and CIDE-B indicated that this family may play critical roles in energy balance. 81 matched cddid_all.tbl CDD cd06538 cd06538 119371 CIDE_N_FSP27 CIDE_N domain of FSP27 proteins. The CIDE-N (cell death-inducing DFF45-like effector, N-terminal) domain is found in the FSP27/CIDE-C protein, which has been identified as a n adipocyte lipid droplet protein that negatively regulates lipolysis and promotes triglyceride accumulation. The CIDE protein family includes 3 members: CIDE-A, CIDE-B, and FSP27(CIDE-C). Based on sequence similarity with DFF40 and DFF45, CIDE proteins were initially characterized as mitochondrial activators of apoptosis. The CIDE-N domain of FSP27 is sufficient to increase apoptosis in vitro when overexpressed. 79 matched cddid_all.tbl CDD cd06539 cd06539 119372 CIDE_N_A CIDE_N domain of CIDE-A proteins. The CIDE_N (cell death-inducing DFF45-like effector, N-terminal) domain is found at the N-terminus of the CIDE (cell death-inducing DFF45-like effector) proteins. These proteins are associated with the chromatin condensation and DNA fragmentation events of apoptosis; the CIDE_N domain is thought to regulate the activity of the CAD/DFF40, ICAD/DFF45, and CIDE nucleases during apoptosis. The CIDE protein family includes 3 members: CIDE-A, CIDE-B, and FSP27(CIDE-C). Based on sequence similarity with DFF40 and DFF45, the CIDE proteins were initially characterized as mitochondrial activators of apoptosis. However, strong metabolic phenotypes of mice lacking CIDE-A and CIDE-B indicated that this family may play critical roles in energy balance. 78 matched cddid_all.tbl CDD cd06541 cd06541 119343 ASCH ASC-1 homology or ASCH domain, a small beta-barrel domain found in all three kingdoms of life. ASCH resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery. 105 matched cddid_all.tbl CDD cd06542 cd06542 119359 GH18_EndoS-like Endo-beta-N-acetylglucosaminidases are bacterial chitinases that hydrolyze the chitin core of various asparagine (N)-linked glycans and glycoproteins. The endo-beta-N-acetylglucosaminidases have a glycosyl hydrolase family 18 (GH18) catalytic domain. Some members also have an additional C-terminal glycosyl hydrolase family 20 (GH20) domain while others have an N-terminal domain of unknown function (pfam08522). Members of this family include endo-beta-N-acetylglucosaminidase S (EndoS) from Streptococcus pyogenes, EndoF1, EndoF2, EndoF3, and EndoH from Flavobacterium meningosepticum, and EndoE from Enterococcus faecalis. EndoS is a secreted endoglycosidase from Streptococcus pyogenes that specifically hydrolyzes the glycan on human IgG between two core N-acetylglucosamine residues. EndoE is a secreted endoglycosidase, encoded by the ndoE gene in Enterococcus faecalis, that hydrolyzes the glycan on human RNase B. 255 matched cddid_all.tbl CDD cd06543 cd06543 119360 GH18_PF-ChiA-like PF-ChiA is an uncharacterized chitinase found in the hyperthermophilic archaeon Pyrococcus furiosus with a glycosyl hydrolase family 18 (GH18) catalytic domain as well as a cellulose-binding domain. Members of this domain family are found not only in archaea but also in eukaryotes and prokaryotes. PF-ChiA exhibits hydrolytic activity toward both colloidal and crystalline (beta/alpha) chitins at high temperature. 294 matched cddid_all.tbl CDD cd06544 cd06544 119361 GH18_narbonin Narbonin is a plant 2S protein from the globulin fraction of narbon bean (Vicia narbonensis L.) cotyledons with unknown function. Narbonin has a glycosyl hydrolase family 18 (GH18) domain without the conserved catalytic residues and with no known enzymatic activity. Narbonin amounts to up to 3% of the total seed globulins of mature seeds and was thought to be a storage protein but was found to degrade too slowly during germination. This family also includes the VfNOD32 nodulin from Vicia faba. 253 matched cddid_all.tbl CDD cd06545 cd06545 119362 GH18_3CO4_chitinase The Bacteroides thetaiotaomicron protein represented by pdb structure 3CO4 is an uncharacterized bacterial member of the family 18 glycosyl hydrolases with homologs found in Flavobacterium, Stigmatella, and Pseudomonas. 253 matched cddid_all.tbl CDD cd06546 cd06546 119363 GH18_CTS3_chitinase GH18 domain of CTS3 (chitinase 3), an uncharacterized protein from the human fungal pathogen Coccidioides posadasii. CTS3 has a chitinase-like glycosyl hydrolase family 18 (GH18) domain; and has homologs in bacteria as well as fungi. 256 matched cddid_all.tbl CDD cd06547 cd06547 119364 GH85_ENGase Endo-beta-N-acetylglucosaminidase (ENGase) hydrolyzes the N-N'-diacetylchitobiosyl core of N-glycosylproteins. The beta-1,4-glycosyl bond located between two N-acetylglucosamine residues is hydrolyzed such that N-acetylglucosamine 1 remains with the protein and N-acetylglucosamine 2 forms the reducing end of the released glycan. ENGase is a key enzyme in the processing of free oligosaccharides in the cytosol of eukaryotes. Oligosaccharides formed in the lumen of the endoplasmic reticulum are transported into the cytosol where they are catabolized by cytosolic ENGases and other enzymes, possibly to maximize the reutilization of the component sugars. ENGases have an eight-stranded alpha/beta barrel topology and are classified as a family 85 glycosyl hydrolase (GH85) domain. The GH85 ENGases are sequence-similar to the family 18 glycosyl hydrolases, also known as GH18 chitinases. An ENGase-like protein is also found in bacteria and is included in this alignment model. 339 matched cddid_all.tbl CDD cd06548 cd06548 119365 GH18_chitinase The GH18 (glycosyl hydrolases, family 18) type II chitinases hydrolyze chitin, an abundant polymer of N-acetylglucosamine and have been identified in bacteria, fungi, insects, plants, viruses, and protozoan parasites. The structure of this domain is an eight-stranded alpha/beta barrel with a pronounced active-site cleft at the C-terminal end of the beta-barrel. 322 matched cddid_all.tbl CDD cd06549 cd06549 119366 GH18_trifunctional GH18 domain of an uncharacterized family of bacterial proteins, which share a common three-domain architecture: an N-terminal glycosyl hydrolase family 18 (GH18) domain, a glycosyl transferase family 2 domain, and a C-terminal polysaccharide deacetylase domain. 298 matched cddid_all.tbl CDD cd06550 cd06550 119348 TM_ABC_iron-siderophores_like Transmembrane subunit (TM), of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters involved in the uptake of siderophores, heme, vitamin B12, or the divalent cations Mg2+ and Zn2+. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP which delivers it to a gated translocation pathway formed by the two TMs. The TMs are bundles of alpha helices that transverse the cytoplasmic membrane multiple times. The two ABCs bind and hydrolyze ATP and drive the transport reaction. Each TM has a prominent cytoplasmic loop which contacts an ABC and represents a conserved motif. The two TMs form either a homodimer (e.g. in the case of the BtuC subunits of the Escherichia coli BtuCD vitamin B12 transporter), a heterodimer (e.g. the TroC and TroD subunits of the Treponema pallidum general transition metal transporter, TroBCD), or a pseudo-heterodimer (e.g. the FhuB protein of the E. coli ferrichrome transporter, FhuBC). FhuB contains two tandem TMs which associate to form the pseudo-heterodimer. Both FhuB TMs are found in this hierarchy. 261 matched cddid_all.tbl CDD cd06551 cd06551 153244 LPLAT Lysophospholipid acyltransferases (LPLATs) of glycerophospholipid biosynthesis. Lysophospholipid acyltransferase (LPLAT) superfamily members are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis. These proteins catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this superfamily are LPLATs such as glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB), 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), lysophosphatidylcholine acyltransferase 1 (LPCAT-1), lysophosphatidylethanolamine acyltransferase (LPEAT, also known as, MBOAT2, membrane-bound O-acyltransferase domain-containing protein 2), lipid A biosynthesis lauroyl/myristoyl acyltransferase, 2-acylglycerol O-acyltransferase (MGAT), dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and Tafazzin (the protein product of the Barth syndrome (TAZ) gene). 187 matched cddid_all.tbl CDD cd06552 cd06552 119344 ASCH_yqfb_like ASC-1 homology domain, subfamily similar to Escherichia coli Yqfb. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. 100 matched cddid_all.tbl CDD cd06553 cd06553 119345 ASCH_Ef3133_like ASC-1 homology domain, subfamily similar to Enterococcus faecalis Ef3133. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. 127 matched cddid_all.tbl CDD cd06554 cd06554 119346 ASCH_ASC-1_like ASC-1 homology domain, ASC-1-like subfamily. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. The domain has been named after the ASC-1 protein, the activating signal cointegrator 1 or thyroid hormone receptor interactor protein 4 (TRIP4). ASC-1 is conserved in many eukaryotes and has been suggested to participate in a protein complex that interacts with RNA. It has been shown that ASC-1 mediates the interaction between various transciption factors and the basal transcriptional machinery. 113 matched cddid_all.tbl CDD cd06555 cd06555 119347 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation. 109 matched cddid_all.tbl CDD cd06556 cd06556 119341 ICL_KPHMT Members of the ICL/PEPM_KPHMT enzyme superfamily catalyze the formation and cleavage of either P-C or C-C bonds. Typical members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate lyase (ICL), 2-methylisocitrate lyase (MICL), and ketopantoate hydroxymethyltransferase (KPHMT). 240 matched cddid_all.tbl CDD cd06557 cd06557 119342 KPHMT-like Ketopantoate hydroxymethyltransferase (KPHMT) is the first enzyme in the pantothenate biosynthesis pathway. Ketopantoate hydroxymethyltransferase (KPHMT) catalyzes the first committed step in the biosynthesis of pantothenate (vitamin B5), which is a precursor to coenzyme A and is required for penicillin biosynthesis. 254 matched cddid_all.tbl CDD cd06558 cd06558 119339 crotonase-like Crotonase/Enoyl-Coenzyme A (CoA) hydratase superfamily. This superfamily contains a diverse set of enzymes including enoyl-CoA hydratase, napthoate synthase, methylmalonyl-CoA decarboxylase, 3-hydoxybutyryl-CoA dehydratase, and dienoyl-CoA isomerase. Many of these play important roles in fatty acid metabolism. In addition to a conserved structural core and the formation of trimers (or dimers of trimers), a common feature in this superfamily is the stabilization of an enolate anion intermediate derived from an acyl-CoA substrate. This is accomplished by two conserved backbone NH groups in active sites that form an oxyanion hole. 195 matched cddid_all.tbl CDD cd06559 cd06559 143472 Endonuclease_V Endonuclease_V, a DNA repair enzyme that initiates repair of nitrosative deaminated purine bases. Endonuclease_V (EndoV) is an enzyme that can initiate repair of all possible deaminated DNA bases. EndoV cleaves the DNA strand containing lesions at the second phosphodiester bond 3' to the lesion using Mg2+ as a cofactor. EndoV homologs are conserved throughout all domains of life from bacteria to humans. EndoV is encoded by the nfi gene and nfi null mutant mice have a phenotype prone to cancer. The ability of endonuclease V to recognize mismatches and abnormal replicative DNA structures suggests that the enzyme plays an important role in DNA metabolism. The details of downstream processing for the EndoV pathway remain unknown. 208 matched cddid_all.tbl CDD cd06560 cd06560 143473 PriL Archaeal/eukaryotic core primase: Large subunit, PriL. Primases synthesize the RNA primers required for DNA replication. Primases are grouped into two classes, bacteria/bacteriophage and archaeal/eukaryotic. The proteins in the two classes differ in structure and the replication apparatus components. The DNA replication machinery of archaeal organisms contains only the core primase, a simpler arrangement compared to eukaryotes. Archaeal/eukaryotic core primase is a heterodimeric enzyme consisting of a small catalytic subunit (PriS) and a large subunit (PriL). Although the catalytic activity resides within PriS, the PriL subunit is essential for primase function as disruption of the PriL gene in yeast is lethal. PriL is composed of two structural domains. Several functions have been proposed for PriL, such as the stabilization of PriS, involvement in the initiation of synthesis, the improvement of primase processivity, and the determination of product size. 166 matched cddid_all.tbl CDD cd06561 cd06561 132880 AlkD_like A new structural DNA glycosylase. This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity. 197 matched cddid_all.tbl CDD cd06562 cd06562 119332 GH20_HexA_HexB-like Beta-N-acetylhexosaminidases catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides. The hexA and hexB genes encode the alpha- and beta-subunits of the two major beta-N-acetylhexosaminidase isoenzymes, N-acetyl-beta-D-hexosaminidase A (HexA) and beta-N-acetylhexosaminidase B (HexB). Both the alpha and the beta catalytic subunits have a TIM-barrel fold and belong to the glycosyl hydrolase family 20 (GH20). The HexA enzyme is a heterodimer containing one alpha and one beta subunit while the HexB enzyme is a homodimer containing two beta-subunits. Hexosaminidase mutations cause an inability to properly hydrolyze certain sphingolipids which accumulate in lysosomes within the brain, resulting in the lipid storage disorders Tay-Sachs and Sandhoff. Mutations in the alpha subunit cause in a deficiency in the HexA enzyme and result in Tay-Sachs, mutations in the beta-subunit cause in a deficiency in both HexA and HexB enzymes and result in Sandhoff disease. In both disorders GM(2) gangliosides accumulate in lysosomes. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself. 348 matched cddid_all.tbl CDD cd06563 cd06563 119333 GH20_chitobiase-like The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. This GH20 domain family includes an N-acetylglucosamidase (GlcNAcase A) from Pseudoalteromonas piscicida and an N-acetylhexosaminidase (SpHex) from Streptomyces plicatus. SpHex lacks the C-terminal PKD (polycystic kidney disease I)-like domain found in the chitobiases. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself. 357 matched cddid_all.tbl CDD cd06564 cd06564 119334 GH20_DspB_LnbB-like Glycosyl hydrolase family 20 (GH20) catalytic domain of dispersin B (DspB), lacto-N-biosidase (LnbB) and related proteins. Dispersin B is a soluble beta-N-acetylglucosamidase found in bacteria that hydrolyzes the beta-1,6-linkages of PGA (poly-beta-(1,6)-N-acetylglucosamine), a major component of the extracellular polysaccharide matrix. Lacto-N-biosidase hydrolyzes lacto-N-biose (LNB) type I oligosaccharides at the nonreducing terminus to produce lacto-N-biose as part of the GNB/LNB (galacto-N-biose/lacto-N-biose I) degradation pathway. The lacto-N-biosidase from Bifidobacterium bifidum has this GH20 domain, a carbohydrate binding module 32, and a bacterial immunoglobulin-like domain 2, as well as a YSIRK signal peptide and a G5 membrane anchor at the N and C termini, respectively. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself. 326 matched cddid_all.tbl CDD cd06565 cd06565 119335 GH20_GcnA-like Glycosyl hydrolase family 20 (GH20) catalytic domain of N-acetyl-beta-D-glucosaminidase (GcnA, also known as BhsA) and related proteins. GcnA is an exoglucosidase which cleaves N-acetyl-beta-D-galactosamine (NAG) and N-acetyl-beta-D-galactosamine residues from 4-methylumbelliferylated (4MU) substrates, as well as cleaving NAG from chito-oligosaccharides (i.e. NAG polymers). In contrast, sulfated forms of the substrate are unable to be cleaved and act instead as mild competitive inhibitors. Additionally, the enzyme is known to be poisoned by several first-row transition metals as well as by mercury. GcnA forms a homodimer with subunits comprised of three domains, an N-terminal zincin-like domain, this central catalytic GH20 domain, and a C-terminal alpha helical domain. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself. 301 matched cddid_all.tbl CDD cd06567 cd06567 143475 Peptidase_S41 C-terminal processing peptidase family S41. Peptidase family S41 (C-terminal processing peptidase or CTPase family) contains very different subfamilies; it includes photosystem II D1 C-terminal processing protease (CTPase), interphotoreceptor retinoid-binding protein IRBP and tricorn protease (TRI). CTPase and TRI both contain the PDZ domain while IRBP, although being very similar to the tail-specific protease domain, lacks the PDZ insertion domain and hydrolytic activity. These serine proteases have distinctly different active sites: in CTPase, the active site consists of a serine/lysine catalytic dyad while in tricorn core protease, it is a tetrad (serine, histidine, serine, glutamate). CPases with different substrate specificities in different species include processing of D1 protein of the photosystem II reaction center in higher plants and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein; and others such as tricorn protease (TRI) act as a carboxypeptidase, involved in the degradation of proteasomal products. CTPase homolog IRBP, secreted by photoreceptors into the interphotoreceptor matrix, having arisen in the early evolution of the vertebrate eye, promotes the release of all-trans retinol from photoreceptors and facilitates its delivery to the retinal pigment epithelium. 224 matched cddid_all.tbl CDD cd06568 cd06568 119336 GH20_SpHex_like A subgroup of the Glycosyl hydrolase family 20 (GH20) catalytic domain found in proteins similar to the N-acetylhexosaminidase from Streptomyces plicatus (SpHex). SpHex catalyzes the hydrolysis of N-acetyl-beta-hexosaminides. An Asp residue within the active site plays a critical role in substrate-assisted catalysis by orienting the 2-acetamido group and stabilizing the transition state. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself. Proteins belonging to this subgroup lack the C-terminal PKD (polycystic kidney disease I)-like domain found in the chitobiases. 329 matched cddid_all.tbl CDD cd06569 cd06569 119337 GH20_Sm-chitobiase-like The chitobiase of Serratia marcescens is a beta-N-1,4-acetylhexosaminidase with a glycosyl hydrolase family 20 (GH20) domain that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself. 445 matched cddid_all.tbl CDD cd06570 cd06570 119338 GH20_chitobiase-like_1 A functionally uncharacterized subgroup of the Glycosyl hydrolase family 20 (GH20) catalytic domain found in proteins similar to the chitobiase of Serratia marcescens, a beta-N-1,4-acetylhexosaminidase that hydrolyzes the beta-1,4-glycosidic linkages in oligomers derived from chitin. Chitin is degraded by a two step process: i) a chitinase hydrolyzes the chitin to oligosaccharides and disaccharides such as di-N-acetyl-D-glucosamine and chitobiose, ii) chitobiase then further degrades these oligomers into monomers. This subgroup lacks the C-terminal PKD (polycystic kidney disease I)-like domain found in the chitobiases. The GH20 hexosaminidases are thought to act via a catalytic mechanism in which the catalytic nucleophile is not provided by solvent or the enzyme, but by the substrate itself. 311 matched cddid_all.tbl CDD cd06571 cd06571 119330 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step. 90 matched cddid_all.tbl CDD cd06572 cd06572 119329 Histidinol_dh Histidinol dehydrogenase, HisD, E.C 1.1.1.23. Histidinol dehydrogenase catalyzes the last two steps in the L-histidine biosynthesis pathway, which is conserved in bacteria, archaea, fungi, and plants. These last two steps are (i) the NAD-dependent oxidation of L-histidinol to L-histidinaldehyde, and (ii) the NAD-dependent oxidation of L-histidinaldehyde to L-histidine. In most fungi and in the unicellular choanoflagellate Monosiga bevicollis, the HisD domain is fused with units that catalyze the second and third biosynthesis steps in this same pathway. 390 matched cddid_all.tbl CDD cd06573 cd06573 119325 PASTA PASTA domain. This domain is found at the C-termini of several Penicillin-binding proteins (PBPs) and bacterial serine/threonine kinases. It is a small globular fold consisting of 3 beta-sheets and an alpha-helix. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain. 53 matched cddid_all.tbl CDD cd06574 cd06574 119320 TM_PBP1_branched-chain-AA_like Transmembrane subunit (TM) of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which are involved in the uptake of branched-chain amino acids (AAs), as well as TMs of transporters involved in the uptake of monosaccharides including ribose, galactose, and arabinose. These transporters generally bind type 1 PBPs. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. This group includes Escherichia coli LivM and LivH, two TMs which heterodimerize to form the translocation pathway of the E. coli branched-chain AA LIV-1/LS transporter. This transporter is comprised of two TMs (LivM and LivH), two ABCs (LivG and LivF), and one of two alternative PBPs, LivJ (LIV-BP) and LivK (LS-BP). In addition to transporting branched-chain AAs including leucine, isoleucine and valine, the E. coli LIV-1/LS transporter is involved in the uptake of the aromatic AA, phenylalanine. Included in this group are proteins from transport systems that contain a single TM which homodimerizes to generate the transmembrane pore; for example E. coli RbsC, AlsC, and MglC, the TMs of the high affinity ribose transporter, the D-allose transporter and the galactose transporter, respectively. The D-allose transporter may also to be involved in low affinity ribose transport. 266 matched cddid_all.tbl CDD cd06575 cd06575 119326 PASTA_Pbp2x-like_2 PASTA domain of PBP2x-like proteins, second repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by acylating the active site serine. PBPs catalyze key steps in the synthesis of the peptidoglycan, such as the interconnecting of glycan chains (polymers of N-glucosamine and N-acetylmuramic acid residues) and the cross-linking (transpeptidation) of short stem peptides, which are attached to glycan chains. Peptidoglycan is essential in cell division and protects bacteria from osmotic shock and lysis. PBP2x is one of the two monofunctional high molecular mass PBPs in Streptococcus pneumoniae and has been seen as the primary PBP target in beta-lactam-resistant strains. The PASTA domain is found at the C-termini of several PBPs and bacterial serine/threonine kinases. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain. 54 matched cddid_all.tbl CDD cd06576 cd06576 119327 PASTA_Pbp2x-like_1 PASTA domain of PBP2x-like proteins, first repeat. Penicillin-binding proteins (PBPs) are the major targets for beta-lactam antibiotics, like penicillins and cephalosporins. Beta-lactam antibiotics specifically inhibit transpeptidase activity by acylating the active site serine. PBPs catalyze key steps in the synthesis of the peptidoglycan, such as the interconnecting of glycan chains (polymers of N-glucosamine and N-acetylmuramic acid residues) and the cross-linking (transpeptidation) of short stem peptides, which are connected to glycan chains. Peptidoglycan is essential in cell division and protects bacteria from osmotic shock and lysis. PBP2x is one of the two monofunctional high molecular mass PBPs in Streptococcus pneumoniae and has been seen as the primary PBP target in beta-lactam-resistant strains. The PASTA domain is found at the C-termini of several PBPs and bacterial serine/threonine kinases. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain. 55 matched cddid_all.tbl CDD cd06577 cd06577 119328 PASTA_pknB PASTA domain of bacterial serine/threonine kinase pknB-like proteins. PknB is a member of a group of related transmembrane sensor kinases present in many gram positive bacteria, which has been shown to regulate cell shape in Mycobacterium tubercolosis. PknB is a receptor-like transmembrane protein with an extracellular signal sensor domain (containing multiple PASTA domains) and an intracellular, eukaryotic serine/threonine kinase-like domain. The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBPs) and bacterial serine/threonine kinases. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain. 62 matched cddid_all.tbl CDD cd06578 cd06578 119440 HemD Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in the human uroporphyrinogen-III synthase gene cause congenital erythropoietic porphyria, a recessive inborn error of metabolism also known as Gunther disease. 239 matched cddid_all.tbl CDD cd06579 cd06579 119321 TM_PBP1_transp_AraH_like Transmembrane subunit (TM) of Escherichia coli AraH and related proteins. E. coli AraH is the TM of a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of the monosaccharide arabinose. This group also contains E. coli RbsC, AlsC, and MglC, which are TMs of other monosaccharide transporters, the ribose transporter, the D-allose transporter and the galactose transporter, respectively. The D-allose transporter may also be involved in low affinity ribose transport. These transporters generally bind type 1 PBPs. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP, which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. Proteins in this subgroup have a single TM which homodimerizes to generate the transmembrane pore. 263 matched cddid_all.tbl CDD cd06580 cd06580 119322 TM_PBP1_transp_TpRbsC_like Transmembrane subunit (TM) of Treponema pallidum (Tp) RbsC-1, RbsC-2 and related proteins. This is a functionally uncharacterized subgroup of TMs which belong to a larger group of TMs of Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters, which are mainly involved in the uptake of branched-chain amino acids (AAs) or in the uptake of monosaccharides including ribose, galactose, and arabinose, and which generally bind type 1 PBPs. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP, which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. 234 matched cddid_all.tbl CDD cd06581 cd06581 119323 TM_PBP1_LivM_like Transmembrane subunit (TM) of Escherichia coli LivM and related proteins. LivM is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of branched-chain amino acids (AAs). These types of transporters generally bind type 1 PBPs. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP, which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. E. coli LivM forms a heterodimer with another TM, LivH, to generate the transmembrane pore. LivH is not included in this subgroup. The LIV-1/LS transporter is comprised of two TMs (LivM and LivH), two ABCs (LivG and LivF), and one of two alternative PBPs, LivJ (LIV-BP) or LivK (LS-BP). In addition to transporting branched-chain AAs including leucine, isoleucine and valine, the E. coli LIV-1/LS transporter is involved in the uptake of the aromatic AA, phenylalanine. 268 matched cddid_all.tbl CDD cd06582 cd06582 119324 TM_PBP1_LivH_like Transmembrane subunit (TM) of Escherichia coli LivH and related proteins. LivH is one of two TMs of the E. coli LIV-1/LS transporter, a Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporter involved in the uptake of branched-chain amino acids (AAs). These types of transporters generally bind type 1 PBPs. PBP-dependent ABC transporters consist of a PBP, two TMs, and two cytoplasmic ABCs, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP, which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. E. coli LivH forms a heterodimer with another TM, LivM, to generate the transmembrane pore. LivM is not included in this subgroup. The LIV-1/LS transporter is comprised of two TMs (LivM and LivH), two ABCs (LivG and LivF), and one of two alternative PBPs, LivJ (LIV-BP) or LivK (LS-BP). In addition to transporting branched-chain AAs including leucine, isoleucine and valine, the E. coli LIV-1/LS transporter is involved in the uptake of the aromatic AA, phenylalanine. 272 matched cddid_all.tbl CDD cd06583 cd06583 133475 PGRP Peptidoglycan recognition proteins (PGRPs) are pattern recognition receptors that bind, and in certain cases, hydrolyze peptidoglycans (PGNs) of bacterial cell walls. PGRPs have been divided into three classes: short PGRPs (PGRP-S), that are small (20 kDa) extracellular proteins; intermediate PGRPs (PGRP-I) that are 40-45 kDa and are predicted to be transmembrane proteins; and long PGRPs (PGRP-L), up to 90 kDa, which may be either intracellular or transmembrane. Several structures of PGRPs are known in insects and mammals, some bound with substrates like Muramyl Tripeptide (MTP) or Tracheal Cytotoxin (TCT). The substrate binding site is conserved in PGRP-LCx, PGRP-LE, and PGRP-Ialpha proteins. This family includes Zn-dependent N-Acetylmuramoyl-L-alanine Amidase, EC:3.5.1.28. This enzyme cleaves the amide bond between N-acetylmuramoyl and L-amino acids, preferentially D-lactyl-L-Ala, in bacterial cell walls. The structure for the bacteriophage T7 lysozyme shows that two of the conserved histidines and a cysteine are zinc binding residues. Site-directed mutagenesis of T7 lysozyme indicates that two conserved residues, a Tyr and a Lys, are important for amidase activity. 126 matched cddid_all.tbl CDD cd06586 cd06586 132915 TPP_enzyme_PYR Pyrimidine (PYR) binding domain of thiamine pyrophosphate (TPP)-dependent enzymes. Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain; found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this group. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. In the case of 2-oxoisovalerate dehydrogenase (2OXO), sulfopyruvate decarboxylase (ComDE), and the E1 component of human pyruvate dehydrogenase complex (E1- PDHc) the PYR and PP domains appear on different subunits. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. For many of these enzymes the active sites lie between PP and PYR domains on different subunits. However, for the homodimeric enzymes 1-deoxy-D-xylulose 5-phosphate synthase (DXS) and Desulfovibrio africanus pyruvate:ferredoxin oxidoreductase (PFOR), each active site lies at the interface of the PYR and PP domains from the same subunit. 154 matched cddid_all.tbl CDD cd06587 cd06587 319898 VOC vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). Type I extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into aromatic substrates, which results in the cleavage of aromatic rings. They are key enzymes in the degradation of aromatic compounds. Type I extradiol dioxygenases include class I and class II enzymes. Class I and II enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. Glyoxylase I catalyzes the glutathione-dependent inactivation of toxic methylglyoxal, requiring zinc or nickel ions for activity. The antibiotic resistance proteins in this family use a variety of mechanisms to block the function of antibiotics. Bleomycin resistance protein (BLMA) sequesters bleomycin's activity by directly binding to it. Whereas, three types of fosfomycin resistance proteins employ different mechanisms to render fosfomycin inactive by modifying the fosfomycin molecule. Although the proteins in this superfamily are functionally distinct, their structures are similar. The difference among the three dimensional structures of the three types of proteins in this superfamily is interesting from an evolutionary perspective. Both glyoxalase I and BLMA show domain swapping between subunits. However, there is no domain swapping for type 1 extradiol dioxygenases. 112 matched cddid_all.tbl CDD cd06588 cd06588 319899 PhnB_like Escherichia coli PhnB and similar proteins. The Escherichia coli phnB gene is found next to an operon of fourteen genes (phnC-to-phnP) related to the cleavage of carbon-phosphorus (C-P) bonds in unactivated alkylphosphonates, supporting bacterial growth on alkylphosphonates as the sole phosphorus source. It was originally considered part of that operon. PhnB appears to play no direct catalytic role in the usage of alkylphosphonate. Although many of the proteins in this family have been annotated as 3-demethylubiquinone-9 3-methyltransferase enzymes by automatic annotation programs, the experimental evidence for this assignment is lacking. In Escherichia coli, the gene coding 3-demethylubiquinone-9 3-methyltransferase enzyme is ubiG, which belongs to the AdoMet-MTase protein family. PhnB-like proteins adopt a structural fold similar to bleomycin resistance proteins, glyoxalase I, and type I extradiol dioxygenases. 129 matched cddid_all.tbl CDD cd06589 cd06589 269876 GH31 glycosyl hydrolase family 31 (GH31). GH31 enzymes occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite -1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed. Most characterized GH31 enzymes are alpha-glucosidases. In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as Pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively. 265 matched cddid_all.tbl CDD cd06590 cd06590 260000 RNase_HII_bacteria_HIII_like "Bacterial type 2 ribonuclease, HII and HIII-like. This family includes type 2 RNases H from several bacteria, such as Bacillus subtilis, which have two different RNases, HII and HIII. RNases HIII are distinguished by having a large (70-90 residues) N-terminal extension of unknown function. In addition, the active site of RNase HIII differs from that of other RNases H; replacing the fourth residue (aspartate) of the acidic ""DEDD"" motif with a glutamate. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes; however, no prokaryotic genomes contain the combination of both RNase HI and HIII. This mutual exclusive gene inheritance might be the result of functional redundancy of RNase HI and HIII in prokaryotes. Ribonuclease (RNase) H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, archaeal RNase HII and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication or repair." 207 matched cddid_all.tbl CDD cd06591 cd06591 269877 GH31_xylosidase_XylS xylosidase XylS-like. XylS is a glycosyl hydrolase family 31 (GH31) alpha-xylosidase found in prokaryotes, eukaryotes, and archaea, that catalyzes the release of alpha-xylose from the non-reducing terminal side of the alpha-xyloside substrate. XylS has been characterized in Sulfolobus solfataricus where it hydrolyzes isoprimeverose, the p-nitrophenyl-beta derivative of isoprimeverose, and xyloglucan oligosaccharides, and has transxylosidic activity. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. The XylS family corresponds to subgroup 3 in the Ernst et al classification of GH31 enzymes. 322 matched cddid_all.tbl CDD cd06592 cd06592 269878 GH31_NET37 glucosidase NET37. NET37 (also known as KIAA1161) is a human lamina-associated nuclear envelope transmembrane protein. A member of the glycosyl hydrolase family 31 (GH31) , it has been shown to be required for myogenic differentiation of C2C12 cells. Related proteins are found in eukaryotes and prokaryotes. Enzymes of the GH31 family possess a wide range of different hydrolytic activities including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. 364 matched cddid_all.tbl CDD cd06593 cd06593 269879 GH31_xylosidase_YicI alpha-xylosidase YicI-like. YicI alpha-xylosidase is a glycosyl hydrolase family 31 (GH31) enzyme that catalyzes the release of an alpha-xylosyl residue from the non-reducing end of alpha-xyloside substrates such as alpha-xylosyl fluoride and isoprimeverose. YicI forms a homohexamer (a trimer of dimers). All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. The YicI family corresponds to subgroup 4 in the Ernst et al classification of GH31 enzymes. 308 matched cddid_all.tbl CDD cd06594 cd06594 269880 GH31_glucosidase_YihQ alpha-glucosidase YihQ-like. YihQ is a bacterial alpha-glucosidase with a conserved glycosyl hydrolase family 31 (GH31) domain that catalyzes the release of an alpha-glucosyl residue from the non-reducing end of alpha-glucoside substrates such as alpha-glucosyl fluoride. Orthologs of YihQ that have not yet been functionally characterized are present in plants and fungi. YihQ has sequence similarity to other GH31 enzymes such as CtsZ, a 6-alpha-glucosyltransferase from Bacillus globisporus, and YicI, an alpha-xylosidase from Echerichia coli. These latter two belong to different GH31 subfamilies than YihQ. In bacteria, YihQ (along with YihO) is important for bacterial O-antigen capsule assembly and translocation. 325 matched cddid_all.tbl CDD cd06595 cd06595 269881 GH31_u1 glycosyl hydrolase family 31 (GH31); uncharacterized subgroup. This family represents an uncharacterized GH31 enzyme subgroup found in bacteria and eukaryotes. Enzymes of the GH31 family possess a wide range of different hydrolytic activities including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. 304 matched cddid_all.tbl CDD cd06596 cd06596 269882 GH31_CPE1046 Clostridium CPE1046-like. CPE1046 is an uncharacterized Clostridium perfringens protein with a glycosyl hydrolase family 31 (GH31) domain. The domain architecture of CPE1046 and its orthologs includes a C-terminal fibronectin type 3 (FN3) domain and a coagulation factor 5/8 type C domain in addition to the GH31 domain. Enzymes of the GH31 family possess a wide range of different hydrolytic activities including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase and alpha-1,4-glucan lyase. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. 334 matched cddid_all.tbl CDD cd06597 cd06597 269883 GH31_transferase_CtsY CtsY (cyclic tetrasaccharide-synthesizing enzyme Y)-like. CtsY is a bacterial 3-alpha-isomaltosyltransferase, first identified in Arthrobacter globiformis, that produces cyclic tetrasaccharides together with a closely related enzyme CtsZ. CtsY and CtsZ both have a glycosyl hydrolase family 31 (GH31) catalytic domain; CtsZ belongs to a different subfamily. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. 326 matched cddid_all.tbl CDD cd06598 cd06598 269884 GH31_transferase_CtsZ CtsZ (cyclic tetrasaccharide-synthesizing enzyme Z)-like. CtsZ is a bacterial 6-alpha-glucosyltransferase, first identified in Arthrobacter globiformis, that produces cyclic tetrasaccharides together with a closely related enzyme CtsY. CtsZ and CtsY both have a glycosyl hydrolase family 31 (GH31) catalytic domain; CtsY belongs to a different subfamily. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. 332 matched cddid_all.tbl CDD cd06599 cd06599 269885 GH31_glycosidase_Aec37 E.coli Aec37-like. Glycosyl hydrolase family 31 (GH31) domain of a bacterial protein family represented by Escherichia coli protein Aec37. The gene encoding Aec37 (aec-37) is located within a genomic island (AGI-3) isolated from the extraintestinal avian pathogenic Escherichia coli strain BEN2908. The function of Aec37 and its orthologs is unknown; however, deletion of a region of the genome that includes aec-37 affects the assimilation of seven carbohydrates, decreases growth rate of the strain in minimal medium containing galacturonate or trehalose, and attenuates the virulence of E. coli BEN2908 in chickens. All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. 319 matched cddid_all.tbl CDD cd06600 cd06600 269886 GH31_MGAM-like maltase-glucoamylase (MGAM)-like. This family includes the following closely related glycosyl hydrolase family 31 (GH31) enzymes: maltase-glucoamylase (MGAM), sucrase-isomaltase (SI), lysosomal acid alpha-glucosidase (GAA), neutral alpha-glucosidase C (GANC), the alpha subunit of neutral alpha-glucosidase AB (GANAB), and alpha-glucosidase II. MGAM is one of the two enzymes responsible for catalyzing the last glucose-releasing step in starch digestion. SI is implicated in the digestion of dietary starch and major disaccharides such as sucrose and isomaltose, while GAA degrades glycogen in the lysosome, cleaving both alpha-1,4 and alpha-1,6 glucosidic linkages. MGAM and SI are anchored to small-intestinal brush-border epithelial cells. The absence of SI from the brush border membrane or its malfunction is associated with malabsorption disorders such as congenital sucrase-isomaltase deficiency (CSID). The domain architectures of MGAM and SI include two tandem GH31 catalytic domains, an N-terminal domain found near the membrane-bound end and a C-terminal luminal domain. Both of the tandem GH31 domains of MGAM and SI are included in this family. The domain architecture of GAA includes an N-terminal TFF (trefoil factor family) domain in addition to the GH31 catalytic domain. Deficient GAA expression causes Pompe disease, an autosomal recessive genetic disorder also known as glycogen storage disease type II (GSDII). GANC and GANAB are key enzymes in glycogen metabolism that hydrolyze terminal, non-reducing 1,4-linked alpha-D-glucose residues from glycogen in the endoplasmic reticulum. Alpha-glucosidase II is a GH31 enzyme, found in bacteria and plants, which has exo-alpha-1,4-glucosidase and oligo-1,6-glucosidase activities. Alpha-glucosidase II has been characterized in Bacillus thermoamyloliquefaciens where it forms a homohexamer. This family also includes the MalA alpha-glucosidase from Sulfolobus solfataricus and the AglA alpha-glucosidase from Picrophilus torridus. MalA is part of the carbohydrate-metabolizing machinery that allows this organism to utilize carbohydrates, such as maltose, as the sole carbon and energy source. The MGAM-like family corresponds to subgroup 1 in the Ernst et al classification of GH31 enzymes. 256 matched cddid_all.tbl CDD cd06601 cd06601 269887 GH31_lyase_GLase alpha-1,4-glucan lyase. GLases (alpha-1,4-glucan lyases) are glycosyl hydrolase family 31 (GH31) enzymes that degrade alpha-1,4-glucans and maltooligosaccharides via a nonhydrolytic pathway to yield 1,5-D-anhydrofructose from the nonreducing end. GLases cleave the bond between C1 and O1 of the nonreducing sugar residue of alpha-glucans to generate a monosaccharide product with a double bond between C1 and C2. This family corresponds to subgroup 2 in the Ernst et al classification of GH31 enzymes. 347 matched cddid_all.tbl CDD cd06602 cd06602 269888 GH31_MGAM_SI_GAA maltase-glucoamylase, sucrase-isomaltase, lysosomal acid alpha-glucosidase. This subgroup includes the following three closely related glycosyl hydrolase family 31 (GH31) enzymes: maltase-glucoamylase (MGAM), sucrase-isomaltase (SI), and lysosomal acid alpha-glucosidase (GAA), also known as acid-maltase. MGAM is one of the two enzymes responsible for catalyzing the last glucose-releasing step in starch digestion. SI is implicated in the digestion of dietary starch and major disaccharides such as sucrose and isomaltose, while GAA degrades glycogen in the lysosome, cleaving both alpha-1,4 and alpha-1,6 glucosidic linkages. MGAM and SI are anchored to small-intestinal brush-border epithelial cells. The absence of SI from the brush border membrane or its malfunction is associated with malabsorption disorders such as congenital sucrase-isomaltase deficiency (CSID). The domain architectures of MGAM and SI include two tandem GH31 catalytic domains, an N-terminal domain found near the membrane-bound end, and a C-terminal luminal domain. Both of the tandem GH31 domains of MGAM and SI are included in this family. The domain architecture of GAA includes an N-terminal TFF (trefoil factor family) domain in addition to the GH31 catalytic domain. Deficient GAA expression causes Pompe disease, an autosomal recessive genetic disorder also known as glycogen storage disease type II (GSDII). 367 matched cddid_all.tbl CDD cd06603 cd06603 269889 GH31_GANC_GANAB_alpha neutral alpha-glucosidase C, neutral alpha-glucosidase AB. This subgroup includes the closely related glycosyl hydrolase family 31 (GH31) isozymes, neutral alpha-glucosidase C (GANC) and the alpha subunit of heterodimeric neutral alpha-glucosidase AB (GANAB). Initially distinguished on the basis of differences in electrophoretic mobility in starch gel, GANC and GANAB have been shown to have other differences, including those of substrate specificity. GANC and GANAB are key enzymes in glycogen metabolism that hydrolyze terminal, non-reducing 1,4-linked alpha-D-glucose residues from glycogen in the endoplasmic reticulum. The GANC/GANAB family includes the alpha-glucosidase II (ModA) from Dictyostelium discoideum as well as the alpha-glucosidase II (GLS2, or ROT2 - Reversal of TOR2 lethality protein 2) from Saccharomyces cerevisiae. 467 matched cddid_all.tbl CDD cd06604 cd06604 269890 GH31_glucosidase_II_MalA Alpha-glucosidase II-like. Alpha-glucosidase II (alpha-D-glucoside glucohydrolase) is a glycosyl hydrolase family 31 (GH31) enzyme, found in bacteria and plants, which has exo-alpha-1,4-glucosidase and oligo-1,6-glucosidase activities. Alpha-glucosidase II has been characterized in Bacillus thermoamyloliquefaciens where it forms a homohexamer. This subgroup also includes the MalA alpha-glucosidase from Sulfolobus solfataricus and the AglA alpha-glucosidase from Picrophilus torridus. MalA is part of the carbohydrate-metabolizing machinery that allows this organism to utilize carbohydrates, such as maltose, as the sole carbon and energy source. 339 matched cddid_all.tbl CDD cd06605 cd06605 270782 PKc_MAPKK Catalytic domain of the dual-specificity Protein Kinase, Mitogen-Activated Protein Kinase Kinase. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (ST) or tyrosine residues on protein substrates. MAPKKs are dual-specificity PKs that phosphorylate their downstream targets, MAPKs, at specific threonine and tyrosine residues. The MAPK signaling pathways are important mediators of cellular responses to extracellular signals. The pathways involve a triple kinase core cascade comprising the MAPK, which is phosphorylated and activated by a MAPK kinase (MAPKK or MKK or MAP2K), which itself is phosphorylated and activated by a MAPKK kinase (MAPKKK or MKKK or MAP3K). There are three MAPK subfamilies: extracellular signal-regulated kinase (ERK), c-Jun N-terminal kinase (JNK), and p38. In mammalian cells, there are seven MAPKKs (named MKK1-7) and 20 MAPKKKs. Each MAPK subfamily can be activated by at least two cognate MAPKKs and by multiple MAPKKKs. The MAPKK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 265 matched cddid_all.tbl CDD cd06606 cd06606 270783 STKc_MAPKKK Catalytic domain of the Serine/Threonine Kinase, Mitogen-Activated Protein Kinase Kinase Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MAPKKKs (MKKKs or MAP3Ks) are also called MAP/ERK kinase kinases (MEKKs) in some cases. They phosphorylate and activate MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. This subfamily is composed of the Apoptosis Signal-regulating Kinases ASK1 (or MAPKKK5) and ASK2 (or MAPKKK6), MEKK1, MEKK2, MEKK3, MEKK4, as well as plant and fungal MAPKKKs. Also included in this subfamily are the cell division control proteins Schizosaccharomyces pombe Cdc7 and Saccharomyces cerevisiae Cdc15. The MAPKKK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 258 matched cddid_all.tbl CDD cd06607 cd06607 270784 STKc_TAO Catalytic domain of the Serine/Threonine Kinases, Thousand-and-One Amino acids proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TAO proteins possess mitogen-activated protein kinase (MAPK) kinase kinase activity. They activate the MAPKs, p38 and c-Jun N-terminal kinase (JNK), by phosphorylating and activating the respective MAP/ERK kinases (MEKs, also known as MKKs or MAPKKs), MEK3/MEK6 and MKK4/MKK7. MAPK signaling cascades are important in mediating cellular responses to extracellular signals. Vertebrates contain three TAO subfamily members, named TAO1, TAO2, and TAO3. The TAO subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 258 matched cddid_all.tbl CDD cd06608 cd06608 270785 STKc_myosinIII_N_like N-terminal Catalytic domain of Class III myosin-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Class III myosins are motor proteins with an N-terminal kinase catalytic domain and a C-terminal actin-binding motor domain. Class III myosins are present in the photoreceptors of invertebrates and vertebrates and in the auditory hair cells of mammals. The kinase domain of myosin III can phosphorylate several cytoskeletal proteins, conventional myosin regulatory light chains, and can autophosphorylate the C-terminal motor domain. Myosin III may play an important role in maintaining the structural integrity of photoreceptor cell microvilli. It may also function as a cargo carrier during light-dependent translocation, in photoreceptor cells, of proteins such as transducin and arrestin. The Drosophila class III myosin, called NinaC (Neither inactivation nor afterpotential protein C), is critical in normal adaptation and termination of photoresponse. Vertebrates contain two isoforms of class III myosin, IIIA and IIIB. This subfamily also includes mammalian NIK-like embryo-specific kinase (NESK), Traf2- and Nck-interacting kinase (TNIK), and mitogen-activated protein kinase (MAPK) kinase kinase kinase 4/6. MAP4Ks are involved in some MAPK signaling pathways by activating a MAPK kinase kinase. MAPK signaling cascades are important in mediating cellular responses to extracellular signals. The class III myosin-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 275 matched cddid_all.tbl CDD cd06609 cd06609 270786 STKc_MST3_like Catalytic domain of Mammalian Ste20-like protein kinase 3-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of MST3, MST4, STK25, Schizosaccharomyces pombe Nak1 and Sid1, Saccharomyces cerevisiae sporulation-specific protein 1 (SPS1), and related proteins. Nak1 is required by fission yeast for polarizing the tips of actin cytoskeleton and is involved in cell growth, cell separation, cell morphology and cell-cycle progression. Sid1 is a component in the septation initiation network (SIN) signaling pathway, and plays a role in cytokinesis. SPS1 plays a role in regulating proteins required for spore wall formation. MST4 plays a role in mitogen-activated protein kinase (MAPK) signaling during cytoskeletal rearrangement, morphogenesis, and apoptosis. MST3 phosphorylates the STK NDR and may play a role in cell cycle progression and cell morphology. STK25 may play a role in the regulation of cell migration and polarization. The MST3-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 274 matched cddid_all.tbl CDD cd06610 cd06610 270787 STKc_OSR1_SPAK Catalytic domain of the Serine/Threonine Kinases, Oxidative stress response kinase and Ste20-related proline alanine-rich kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. SPAK is also referred to as STK39 or PASK (proline-alanine-rich STE20-related kinase). OSR1 and SPAK regulate the activity of cation-chloride cotransporters through direct interaction and phosphorylation. They are also implicated in cytoskeletal rearrangement, cell differentiation, transformation and proliferation. OSR1 and SPAK contain a conserved C-terminal (CCT) domain, which recognizes a unique motif ([RK]FX[VI]) present in their activating kinases (WNK1/WNK4) and their substrates. The OSR1 and SPAK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 267 matched cddid_all.tbl CDD cd06611 cd06611 132942 STKc_SLK_like Catalytic domain of Ste20-Like Kinase-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Members of the subfamily include SLK, STK10 (also called LOK for Lymphocyte-Oriented Kinase), SmSLK (Schistosoma mansoni SLK), and related proteins. SLK promotes apoptosis through apoptosis signal-regulating kinase 1 (ASK1) and the mitogen-activated protein kinase (MAPK) p38. It also plays a role in mediating actin reorganization. STK10 is responsible in regulating the CD28 responsive element in T cells, as well as leukocyte function associated antigen (LFA-1)-mediated lymphocyte adhesion. SmSLK is capable of activating the MAPK Jun N-terminal kinase (JNK) pathway in human embryonic kidney cells as well as in Xenopus oocytes. It may participate in regulating MAPK cascades during host-parasite interactions. The SLK-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 280 matched cddid_all.tbl CDD cd06612 cd06612 132943 STKc_MST1_2 Catalytic domain of the Serine/Threonine Kinases, Mammalian STe20-like protein kinase 1 and 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of MST1, MST2, and related proteins including Drosophila Hippo and Dictyostelium discoideum Krs1 (kinase responsive to stress 1). MST1/2 and Hippo are involved in a conserved pathway that governs cell contact inhibition, organ size control, and tumor development. MST1 activates the mitogen-activated protein kinases (MAPKs) p38 and c-Jun N-terminal kinase (JNK) through MKK7 and MEKK1 by acting as a MAPK kinase kinase kinase. Activation of JNK by MST1 leads to caspase activation and apoptosis. MST1 has also been implicated in cell proliferation and differentiation. Krs1 may regulate cell growth arrest and apoptosis in response to cellular stress. The MST1/2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd06613 cd06613 270788 STKc_MAP4K3_like Catalytic domain of Mitogen-activated protein kinase kinase kinase kinase (MAP4K) 3-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily includes MAP4K3, MAP4K1, MAP4K2, MAP4K5, and related proteins. Vertebrate members contain an N-terminal catalytic domain and a C-terminal citron homology (CNH) regulatory domain. MAP4K1, also called haematopoietic progenitor kinase 1 (HPK1), is a hematopoietic-specific STK involved in many cellular signaling cascades including MAPK, antigen receptor, apoptosis, growth factor, and cytokine signaling. It participates in the regulation of T cell receptor signaling and T cell-mediated immune responses. MAP4K2 was referred to as germinal center (GC) kinase because of its preferred location in GC B cells. MAP4K3 plays a role in the nutrient-responsive pathway of mTOR (mammalian target of rapamycin) signaling. It is required in the activation of S6 kinase by amino acids and for the phosphorylation of the mTOR-regulated inhibitor of eukaryotic initiation factor 4E. MAP4K5, also called germinal center kinase-related enzyme (GCKR), has been shown to activate the MAPK c-Jun N-terminal kinase (JNK). The MAP4K3-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 259 matched cddid_all.tbl CDD cd06614 cd06614 270789 STKc_PAK Catalytic domain of the Serine/Threonine Kinase, p21-activated kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. PAKs are implicated in the regulation of many cellular processes including growth factor receptor-mediated proliferation, cell polarity, cell motility, cell death and survival, and actin cytoskeleton organization. PAK deregulation is associated with tumor development. PAKs from higher eukaryotes are classified into two groups (I and II), according to their biochemical and structural features. Group I PAKs contain a PBD (p21-binding domain) overlapping with an AID (autoinhibitory domain), a C-terminal catalytic domain, SH3 binding sites and a non-classical SH3 binding site for PIX (PAK-interacting exchange factor). Group II PAKs contain a PBD and a catalytic domain, but lack other motifs found in group I PAKs. Since group II PAKs do not contain an obvious AID, they may be regulated differently from group I PAKs. Group I PAKs interact with the SH3 containing proteins Nck, Grb2 and PIX; no such binding has been demonstrated for group II PAKs. The PAK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 255 matched cddid_all.tbl CDD cd06615 cd06615 132946 PKc_MEK Catalytic domain of the dual-specificity Protein Kinase, Mitogen-Activated Protein (MAP)/Extracellular signal-Regulated Kinase (ERK) Kinase. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (ST) or tyrosine residues on protein substrates. MEK1 and MEK2 are MAPK kinases (MAPKKs or MKKs), and are dual-specificity PKs that phosphorylate and activate the downstream targets, ERK1 and ERK2, on specific threonine and tyrosine residues. The ERK cascade starts with extracellular signals including growth factors, hormones, and neurotransmitters, which act through receptors and ion channels to initiate intracellular signaling that leads to the activation at the MAPKKK (Raf-1 or MOS) level, which leads to the transmission of signals to MEK1/2, and finally to ERK1/2. The ERK cascade plays an important role in cell proliferation, differentiation, oncogenic transformation, and cell cycle control, as well as in apoptosis and cell survival under certain conditions. This cascade has also been implicated in synaptic plasticity, migration, morphological determination, and stress response immunological reactions. Gain-of-function mutations in genes encoding ERK cascade proteins, including MEK1/2, cause cardiofaciocutaneous (CFC) syndrome, a condition leading to multiple congenital anomalies and mental retardation in patients. The MEK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 308 matched cddid_all.tbl CDD cd06616 cd06616 270790 PKc_MKK4 Catalytic domain of the dual-specificity Protein Kinase, Mitogen-activated protein Kinase Kinase 4. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (ST) or tyrosine residues on protein substrates. MKK4 is a dual-specificity PK that phosphorylates and activates the downstream targets, c-Jun N-terminal kinase (JNK) and p38 MAPK, on specific threonine and tyrosine residues. JNK and p38 are collectively known as stress-activated MAPKs, as they are activated in response to a variety of environmental stresses and pro-inflammatory cytokines. Their activation is associated with the induction of cell death. Mice deficient in MKK4 die during embryogenesis and display anemia, severe liver hemorrhage, and abnormal hepatogenesis. MKK4 may also play roles in the immune system and in cardiac hypertrophy. It plays a major role in cancer as a tumor and metastasis suppressor. Under certain conditions, MKK4 is pro-oncogenic. The MKK4 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 291 matched cddid_all.tbl CDD cd06617 cd06617 173729 PKc_MKK3_6 Catalytic domain of the dual-specificity Protein Kinases, Mitogen-activated protein Kinase Kinases 3 and 6. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (ST) or tyrosine residues on protein substrates. MKK3 and MKK6 are dual-specificity PKs that phosphorylate and activate their downstream target, p38 MAPK, on specific threonine and tyrosine residues. MKK3/6 play roles in the regulation of cell cycle progression, cytokine- and stress-induced apoptosis, oncogenic transformation, and adult tissue regeneration. In addition, MKK6 plays a critical role in osteoclast survival in inflammatory disease while MKK3 is associated with tumor invasion, progression, and poor patient survival in glioma. The MKK3/6 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 283 matched cddid_all.tbl CDD cd06618 cd06618 270791 PKc_MKK7 Catalytic domain of the dual-specificity Protein Kinase, Mitogen-activated protein Kinase Kinase 7. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (ST) or tyrosine residues on protein substrates. MKK7 is a dual-specificity PK that phosphorylates and activates its downstream target, c-Jun N-terminal kinase (JNK), on specific threonine and tyrosine residues. Although MKK7 is capable of dual phosphorylation, it prefers to phosphorylate the threonine residue of JNK. Thus, optimal activation of JNK requires both MKK4 and MKK7. MKK7 is primarily activated by cytokines. MKK7 is essential for liver formation during embryogenesis. It plays roles in G2/M cell cycle arrest and cell growth. In addition, it is involved in the control of programmed cell death, which is crucial in oncogenesis, cancer chemoresistance, and antagonism to TNFalpha-induced killing, through its inhibition by Gadd45beta and the subsequent suppression of the JNK cascade. The MKK7 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 295 matched cddid_all.tbl CDD cd06619 cd06619 132950 PKc_MKK5 Catalytic domain of the dual-specificity Protein Kinase, Mitogen-activated protein Kinase Kinase 5. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (ST) or tyrosine residues on protein substrates. MKK5 (also called MEK5) is a dual-specificity PK that phosphorylates its downstream target, extracellular signal-regulated kinase 5 (ERK5), on specific threonine and tyrosine residues. MKK5 is activated by MEKK2 and MEKK3 in response to mitogenic and stress stimuli. The ERK5 cascade promotes cell proliferation, differentiation, neuronal survival, and neuroprotection. This cascade plays an essential role in heart development. Mice deficient in either ERK5 or MKK5 die around embryonic day 10 due to cardiovascular defects including underdevelopment of the myocardium. In addition, MKK5 is associated with metastasis and unfavorable prognosis in prostate cancer. The MKK5 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 279 matched cddid_all.tbl CDD cd06620 cd06620 270792 PKc_Byr1_like Catalytic domain of fungal Byr1-like dual-specificity Mitogen-activated protein Kinase Kinases. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (ST) or tyrosine residues on protein substrates. Members of this group include the MAPKKs Byr1 from Schizosaccharomyces pombe, FUZ7 from Ustilago maydis, and related proteins. Byr1 phosphorylates its downstream target, the MAPK Spk1, and is regulated by the MAPKK kinase Byr2. The Spk1 cascade is pheromone-responsive and is essential for sporulation and sexual differentiation in fission yeast. FUZ7 phosphorylates and activates its target, the MAPK Crk1, which is required in mating and virulence in U. maydis. MAPK signaling pathways are important mediators of cellular responses to extracellular signals. The Byr-1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 286 matched cddid_all.tbl CDD cd06621 cd06621 270793 PKc_Pek1_like Catalytic domain of fungal Pek1-like dual-specificity Mitogen-Activated Protein Kinase Kinases. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (ST) or tyrosine residues on protein substrates. Members of this group include the MAPKKs Pek1/Skh1 from Schizosaccharomyces pombe and MKK2 from Saccharomyces cerevisiae, and related proteins. Both fission yeast Pek1 and baker's yeast MKK2 are components of the cell integrity MAPK pathway. In fission yeast, Pek1 phosphorylates and activates Pmk1/Spm1 and is regulated by the MAPKK kinase Mkh1. In baker's yeast, the pathway involves the MAPK Slt2, the MAPKKs MKK1 and MKK2, and the MAPKK kinase Bck1. The cell integrity MAPK cascade is activated by multiple stress conditions, and is essential in cell wall construction, morphogenesis, cytokinesis, and ion homeostasis. MAPK signaling pathways are important mediators of cellular responses to extracellular signals. The MAPKK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 287 matched cddid_all.tbl CDD cd06622 cd06622 132953 PKc_PBS2_like Catalytic domain of fungal PBS2-like dual-specificity Mitogen-Activated Protein Kinase Kinases. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (ST) or tyrosine residues on protein substrates. Members of this group include the MAPKKs Polymyxin B resistance protein 2 (PBS2) from Saccharomyces cerevisiae, Wis1 from Schizosaccharomyces pombe, and related proteins. PBS2 and Wis1 are components of stress-activated MAPK cascades in budding and fission yeast, respectively. PBS2 is the specific activator of the MAPK Hog1, which plays a central role in the response of budding yeast to stress including exposure to arsenite and hyperosmotic environments. Wis1 phosphorylates and activates the MAPK Sty1 (also called Spc1 or Phh1), which stimulates a transcriptional response to a wide range of cellular insults through the bZip transcription factors Atf1, Pcr1, and Pap1. The PBS2 subfamily is part of a larger superfamily that includes the catalytic domains of STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 286 matched cddid_all.tbl CDD cd06623 cd06623 132954 PKc_MAPKK_plant_like Catalytic domain of Plant dual-specificity Mitogen-Activated Protein Kinase Kinases and similar proteins. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (ST) or tyrosine residues on protein substrates. Members of this group include MAPKKs from plants, kinetoplastids, alveolates, and mycetozoa. The MAPKK, LmxPK4, from Leishmania mexicana, is important in differentiation and virulence. Dictyostelium discoideum MEK1 is required for proper chemotaxis; MEK1 null mutants display severe defects in cell polarization and directional movement. Plants contain multiple MAPKKs like other eukaryotes. The Arabidopsis genome encodes for 10 MAPKKs while poplar and rice contain 13 MAPKKs each. The functions of these proteins have not been fully elucidated. There is evidence to suggest that MAPK cascades are involved in plant stress responses. In Arabidopsis, MKK3 plays a role in pathogen signaling; MKK2 is involved in cold and salt stress signaling; MKK4/MKK5 participates in innate immunity; and MKK7 regulates basal and systemic acquired resistance. The MAPKK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 264 matched cddid_all.tbl CDD cd06624 cd06624 270794 STKc_ASK Catalytic domain of the Serine/Threonine Kinase, Apoptosis signal-regulating kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Members of this subfamily are mitogen-activated protein kinase (MAPK) kinase kinases (MAPKKKs or MKKKs) and include ASK1, ASK2, and MAPKKK15. ASK1 (also called MAPKKK5) functions in the c-Jun N-terminal kinase (JNK) and p38 MAPK signaling pathways by directly activating their respective MAPKKs, MKK4/MKK7 and MKK3/MKK6. It plays important roles in cytokine and stress responses, as well as in reactive oxygen species-mediated cellular responses. ASK1 is implicated in various diseases mediated by oxidative stress including inschemic heart disease, hypertension, vessel injury, brain ischemia, Fanconi anemia, asthma, and pulmonary edema, among others. ASK2 (also called MAPKKK6) functions only in a heteromeric complex with ASK1, and can activate ASK1 by direct phosphorylation. The function of MAPKKK15 is still unknown. The ASK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 268 matched cddid_all.tbl CDD cd06625 cd06625 270795 STKc_MEKK3_like Catalytic domain of Mitogen-Activated Protein (MAP)/Extracellular signal-Regulated Kinase (ERK) Kinase Kinase 3-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of MEKK3, MEKK2, and related proteins; all contain an N-terminal PB1 domain, which mediates oligomerization, and a C-terminal catalytic domain. MEKK2 and MEKK3 are MAPK kinase kinases (MAPKKKs or MKKK) that activate MEK5 (also called MKK5), which activates ERK5. The ERK5 cascade plays roles in promoting cell proliferation, differentiation, neuronal survival, and neuroprotection. MEKK3 plays an essential role in embryonic angiogenesis and early heart development. MEKK2 and MEKK3 can also activate the MAPKs, c-Jun N-terminal kinase (JNK) and p38, through their respective MAPKKs. The MEKK3-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 260 matched cddid_all.tbl CDD cd06626 cd06626 270796 STKc_MEKK4 Catalytic domain of the Protein Serine/Threonine Kinase, Mitogen-Activated Protein (MAP)/Extracellular signal-Regulated Kinase (ERK) Kinase Kinase 4. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MEKK4 is a MAPK kinase kinase that phosphorylates and activates the c-Jun N-terminal kinase (JNK) and p38 MAPK signaling pathways by directly activating their respective MAPKKs, MKK4/MKK7 and MKK3/MKK6. JNK and p38 are collectively known as stress-activated MAPKs, as they are activated in response to a variety of environmental stresses and pro-inflammatory cytokines. MEKK4 also plays roles in the re-polarization of the actin cytoskeleton in response to osmotic stress, in the proper closure of the neural tube, in cardiovascular development, and in immune responses. The MEKK4 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 265 matched cddid_all.tbl CDD cd06627 cd06627 270797 STKc_Cdc7_like Catalytic domain of Cell division control protein 7-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Members of this subfamily include Schizosaccharomyces pombe Cdc7, Saccharomyces cerevisiae Cdc15, Arabidopsis thaliana mitogen-activated protein kinase kinase kinase (MAPKKK) epsilon, and related proteins. MAPKKKs phosphorylate and activate MAPK kinases, which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. Fission yeast Cdc7 is essential for cell division by playing a key role in the initiation of septum formation and cytokinesis. Budding yeast Cdc15 functions to coordinate mitotic exit with cytokinesis. Arabidopsis MAPKKK epsilon is required for pollen development in the plasma membrane. The Cdc7-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 254 matched cddid_all.tbl CDD cd06628 cd06628 270798 STKc_Byr2_like Catalytic domain of the Serine/Threonine Kinases, fungal Byr2-like Mitogen-Activated Protein Kinase Kinase Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Members of this group include the MAPKKKs Schizosaccharomyces pombe Byr2, Saccharomyces cerevisiae and Cryptococcus neoformans Ste11, and related proteins. They contain an N-terminal SAM (sterile alpha-motif) domain, which mediates protein-protein interaction, and a C-terminal catalytic domain. MAPKKKs phosphorylate and activate MAPK kinases, which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. Fission yeast Byr2 is regulated by Ras1. It responds to pheromone signaling and controls mating through the MAPK pathway. Budding yeast Ste11 functions in MAPK cascades that regulate mating, high osmolarity glycerol, and filamentous growth responses. The Byr2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 267 matched cddid_all.tbl CDD cd06629 cd06629 270799 STKc_Bck1_like Catalytic domain of the Serine/Threonine Kinases, fungal Bck1-like Mitogen-Activated Protein Kinase Kinase Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Members of this group include the MAPKKKs Saccharomyces cerevisiae Bck1 and Schizosaccharomyces pombe Mkh1, and related proteins. Budding yeast Bck1 is part of the cell integrity MAPK pathway, which is activated by stresses and aggressions to the cell wall. The MAPKKK Bck1, MAPKKs Mkk1 and Mkk2, and the MAPK Slt2 make up the cascade that is important in the maintenance of cell wall homeostasis. Fission yeast Mkh1 is involved in MAPK cascades regulating cell morphology, cell wall integrity, salt resistance, and filamentous growth in response to stress. MAPKKKs phosphorylate and activate MAPK kinases, which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. The Bck1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 270 matched cddid_all.tbl CDD cd06630 cd06630 270800 STKc_MEKK1 Catalytic domain of the Protein Serine/Threonine Kinase, Mitogen-Activated Protein (MAP)/Extracellular signal-Regulated Kinase (ERK) Kinase Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MEKK1 is a MAPK kinase kinase (MAPKKK or MKKK) that phosphorylates and activates activates the ERK1/2 and c-Jun N-terminal kinase (JNK) pathways by activating their respective MAPKKs, MEK1/2 and MKK4/MKK7, respectively. MEKK1 is important in regulating cell survival and apoptosis. MEKK1 also plays a role in cell migration, tissue maintenance and homeostasis, and wound healing. The MEKK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 268 matched cddid_all.tbl CDD cd06631 cd06631 270801 STKc_YSK4 Catalytic domain of the Serine/Threonine Kinase, Yeast Sps1/Ste20-related Kinase 4. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. YSK4 is a putative MAPKKK, whose mammalian gene has been isolated. MAPKKKs phosphorylate and activate MAPK kinases, which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. The YSK4 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 266 matched cddid_all.tbl CDD cd06632 cd06632 270802 STKc_MEKK1_plant Catalytic domain of the Serine/Threonine Kinase, Plant Mitogen-Activated Protein (MAP)/Extracellular signal-Regulated Kinase (ERK) Kinase Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of plant MAPK kinase kinases (MAPKKKs) including Arabidopsis thaliana MEKK1 and MAPKKK3. Arabidopsis thaliana MEKK1 activates MPK4, a MAPK that regulates systemic acquired resistance. MEKK1 also participates in the regulation of temperature-sensitive and tissue-specific cell death. MAPKKKs phosphorylate and activate MAPK kinases, which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. The plant MEKK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 259 matched cddid_all.tbl CDD cd06633 cd06633 270803 STKc_TAO3 Catalytic domain of the Serine/Threonine Kinase, Thousand-and-One Amino acids 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TAO3 is also known as JIK (c-Jun N-terminal kinase inhibitory kinase) or KFC (kinase from chicken). It specifically activates JNK, presumably by phosphorylating and activating MKK4/MKK7. In Saccharomyces cerevisiae, TAO3 is a component of the RAM (regulation of Ace2p activity and cellular morphogenesis) signaling pathway. TAO3 is upregulated in retinal ganglion cells after axotomy, and may play a role in apoptosis. TAO proteins possess mitogen-activated protein kinase (MAPK) kinase kinase activity. MAPK signaling cascades are important in mediating cellular responses to extracellular signals. The TAO3 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 313 matched cddid_all.tbl CDD cd06634 cd06634 270804 STKc_TAO2 Catalytic domain of the Serine/Threonine Kinase, Thousand-and-One Amino acids 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Human TAO2 is also known as prostate-derived Ste20-like kinase (PSK) and was identified in a screen for overexpressed RNAs in prostate cancer. TAO2 possesses mitogen-activated protein kinase (MAPK) kinase kinase activity and activates both p38 and c-Jun N-terminal kinase (JNK), by phosphorylating and activating their respective MAP/ERK kinases, MEK3/MEK6 and MKK4/MKK7. It contains a long C-terminal extension with autoinhibitory segments, and is activated by the release of this inhibition and the phosphorylation of its activation loop serine. TAO2 functions as a regulator of actin cytoskeletal and microtubule organization. In addition, it regulates the transforming growth factor-activated kinase 1 (TAK1), which is a MAPKKK that plays an essential role in the signaling pathways of tumor necrosis factor, interleukin 1, and Toll-like receptor. The TAO2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 308 matched cddid_all.tbl CDD cd06635 cd06635 270805 STKc_TAO1 Catalytic domain of the Serine/Threonine Kinase, Thousand-and-One Amino acids 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TAO1 is sometimes referred to as prostate-derived sterile 20-like kinase 2 (PSK2). TAO1 activates the p38 MAPK through direct interaction with and activation of MEK3. TAO1 is highly expressed in the brain and may play a role in neuronal apoptosis. TAO1 interacts with the checkpoint proteins BubR1 and Mad2, and plays an important role in regulating mitotic progression, which is required for both chromosome congression and checkpoint-induced anaphase delay. TAO1 may play a role in protecting genomic stability. TAO proteins possess MAPK kinase kinase activity. MAPK signaling cascades are important in mediating cellular responses to extracellular signals. The TAO1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 317 matched cddid_all.tbl CDD cd06636 cd06636 270806 STKc_MAP4K4_6_N N-terminal Catalytic domain of the Serine/Threonine Kinases, Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 and 6. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Members of this subfamily contain an N-terminal catalytic domain and a C-terminal citron homology (CNH) regulatory domain. MAP4K4 is also called Nck Interacting kinase (NIK). It facilitates the activation of the MAPKs, extracellular signal-regulated kinase (ERK) 1, ERK2, and c-Jun N-terminal kinase (JNK), by phosphorylating and activating MEKK1. MAP4K4 plays a role in tumor necrosis factor (TNF) alpha-induced insulin resistance. MAP4K4 silencing in skeletal muscle cells from type II diabetic patients restores insulin-mediated glucose uptake. MAP4K4, through JNK, also plays a broad role in cell motility, which impacts inflammation, homeostasis, as well as the invasion and spread of cancer. MAP4K4 is found to be highly expressed in most tumor cell lines relative to normal tissue. MAP4K6 (also called MINK for Misshapen/NIKs-related kinase) is activated after Ras induction and mediates activation of p38 MAPK. MAP4K6 plays a role in cell cycle arrest, cytoskeleton organization, cell adhesion, and cell motility. The MAP4K4/6 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 282 matched cddid_all.tbl CDD cd06637 cd06637 270807 STKc_TNIK Catalytic domain of the Serine/Threonine Kinase, Traf2- and Nck-Interacting Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TNIK is an effector of Rap2, a small GTP-binding protein from the Ras family. TNIK specifically activates the c-Jun N-terminal kinase (JNK) pathway and plays a role in regulating the actin cytoskeleton. The TNIK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 296 matched cddid_all.tbl CDD cd06638 cd06638 132969 STKc_myosinIIIA_N N-terminal Catalytic domain of the Serine/Threonine Kinase, Class IIIA myosin. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Class IIIA myosin is highly expressed in retina and in inner ear hair cells. It is localized to the distal ends of actin-bundled structures. Mutations in human myosin IIIA are responsible for progressive nonsyndromic hearing loss. Human myosin IIIA possesses ATPase and kinase activities, and the ability to move actin filaments in a motility assay. It may function as a cellular transporter capable of moving along actin bundles in sensory cells. Class III myosins are motor proteins containing an N-terminal kinase catalytic domain and a C-terminal actin-binding domain. Class III myosins may play an important role in maintaining the structural integrity of photoreceptor cell microvilli. In photoreceptor cells, they may also function as cargo carriers during light-dependent translocation of proteins such as transducin and arrestin. The class III myosin subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 286 matched cddid_all.tbl CDD cd06639 cd06639 270808 STKc_myosinIIIB_N N-terminal Catalytic domain of the Serine/Threonine Kinase, Class IIIB myosin. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Class IIIB myosin is expressed highly in retina. It is also present in the brain and testis. The human class IIIB myosin gene maps to a region that overlaps the locus for Bardet-Biedl syndrome, which is characterized by dysmorphic extremities, retinal dystrophy, obesity, male hypogenitalism, and renal abnormalities. Class III myosins are motor proteins containing an N-terminal kinase catalytic domain and a C-terminal actin-binding domain. They may play an important role in maintaining the structural integrity of photoreceptor cell microvilli. They may also function as cargo carriers during light-dependent translocation, in photoreceptor cells, of proteins such as transducin and arrestin. The class III myosin subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 291 matched cddid_all.tbl CDD cd06640 cd06640 132971 STKc_MST4 Catalytic domain of the Serine/Threonine Kinase, Mammalian Ste20-like protein kinase 4. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MST4 is sometimes referred to as MASK (MST3 and SOK1-related kinase). It plays a role in mitogen-activated protein kinase (MAPK) signaling during cytoskeletal rearrangement, morphogenesis, and apoptosis. It influences cell growth and transformation by modulating the extracellular signal-regulated kinase (ERK) pathway. MST4 may also play a role in tumor formation and progression. It localizes in the Golgi apparatus by interacting with the Golgi matrix protein GM130 and may play a role in cell migration. The MST4 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 277 matched cddid_all.tbl CDD cd06641 cd06641 270809 STKc_MST3 Catalytic domain of the Serine/Threonine Kinase, Mammalian Ste20-like protein kinase 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MST3 phosphorylates the STK NDR and may play a role in cell cycle progression and cell morphology. It may also regulate paxillin and consequently, cell migration. MST3 is present in human placenta, where it plays an essential role in the oxidative stress-induced apoptosis of trophoblasts in normal spontaneous delivery. Dysregulation of trophoblast apoptosis may result in pregnancy complications such as preeclampsia and intrauterine growth retardation. The MST3 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 277 matched cddid_all.tbl CDD cd06642 cd06642 270810 STKc_STK25 Catalytic domain of Serine/Threonine Kinase 25 (also called Yeast Sps1/Ste20-related kinase 1). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. STK25 is also called Ste20/oxidant stress response kinase 1 (SOK1) or yeast Sps1/Ste20-related kinase 1 (YSK1). It is localized in the Golgi apparatus through its interaction with the Golgi matrix protein GM130. It may be involved in the regulation of cell migration and polarization. STK25 binds and phosphorylates CCM3 (cerebral cavernous malformation 3), also called PCD10 (programmed cell death 10), and may play a role in apoptosis. Human STK25 is a candidate gene responsible for pseudopseudohypoparathyroidism (PPHP), a disease that shares features with the Albright hereditary osteodystrophy (AHO) phenotype. The STK25 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 277 matched cddid_all.tbl CDD cd06643 cd06643 270811 STKc_SLK Catalytic domain of the Serine/Threonine Kinase, Ste20-Like Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. SLK promotes apoptosis through apoptosis signal-regulating kinase 1 (ASK1) and the mitogen-activated protein kinase (MAPK) p38. It acts as a MAPK kinase kinase by phosphorylating ASK1, resulting in the phosphorylation of p38. SLK also plays a role in mediating actin reorganization. It is part of a microtubule-associated complex that is targeted at adhesion sites, and is required in focal adhesion turnover and in regulating cell migration. The SLK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 283 matched cddid_all.tbl CDD cd06644 cd06644 132975 STKc_STK10 Catalytic domain of the Serine/Threonine Kinase, STK10 (also called Lymphocyte-Oriented Kinase or LOK). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. STK10/LOK is also called polo-like kinase kinase 1 in Xenopus (xPlkk1). It is highly expressed in lymphocytes and is responsible in regulating leukocyte function associated antigen (LFA-1)-mediated lymphocyte adhesion. It plays a role in regulating the CD28 responsive element in T cells, and may also function as a regulator of polo-like kinase 1 (Plk1), a protein which is overexpressed in multiple tumor types. The STK10 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 292 matched cddid_all.tbl CDD cd06645 cd06645 270812 STKc_MAP4K3 Catalytic domain of the Serine/Threonine Kinase, Mitogen-activated protein kinase kinase kinase kinase 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MAP4K3 plays a role in the nutrient-responsive pathway of mTOR (mammalian target of rapamycin) signaling. MAP4K3 is required in the activation of S6 kinase by amino acids and for the phosphorylation of the mTOR-regulated inhibitor of eukaryotic initiation factor 4E. mTOR regulates ribosome biogenesis and protein translation, and is frequently deregulated in cancer. MAP4Ks are involved in MAPK signaling pathways by activating a MAPK kinase kinase. Each MAPK cascade is activated either by a small GTP-binding protein or by an adaptor protein, which transmits the signal either directly to a MAP3K to start the triple kinase core cascade or indirectly through a mediator kinase, a MAP4K. Members of this subfamily contain an N-terminal catalytic domain and a C-terminal citron homology (CNH) regulatory domain. The MAP4K3 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 272 matched cddid_all.tbl CDD cd06646 cd06646 270813 STKc_MAP4K5 Catalytic domain of the Serine/Threonine Kinase, Mitogen-activated protein kinase kinase kinase kinase 5. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MAP4K5, also called germinal center kinase-related enzyme (GCKR), has been shown to activate the MAPK c-Jun N-terminal kinase (JNK). MAP4K5 also facilitates Wnt signaling in B cells, and may therefore be implicated in the control of cell fate, proliferation, and polarity. MAP4Ks are involved in some MAPK signaling pathways by activating a MAPK kinase kinase. Each MAPK cascade is activated either by a small GTP-binding protein or by an adaptor protein, which transmits the signal either directly to a MAP3K to start the triple kinase core cascade or indirectly through a mediator kinase, a MAP4K. Members of this subfamily contain an N-terminal catalytic domain and a C-terminal citron homology (CNH) regulatory domain. The MAP4K5 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 268 matched cddid_all.tbl CDD cd06647 cd06647 270814 STKc_PAK_I Catalytic domain of the Serine/Threonine Kinase, Group I p21-activated kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Group I PAKs, also called conventional PAKs, include PAK1, PAK2, and PAK3. Group I PAKs contain a PBD (p21-binding domain) overlapping with an AID (autoinhibitory domain), a C-terminal catalytic domain, SH3 binding sites and a non-classical SH3 binding site for PIX (PAK-interacting exchange factor). They interact with the SH3 domain containing proteins Nck, Grb2 and PIX. Binding of group I PAKs to activated GTPases leads to conformational changes that destabilize the AID, allowing autophosphorylation and full activation of the kinase domain. Known group I PAK substrates include MLCK, Bad, Raf, MEK1, LIMK, Merlin, Vimentin, Myc, Stat5a, and Aurora A, among others. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. PAKs are implicated in the regulation of many cellular processes including growth factor receptor-mediated proliferation, cell polarity, cell motility, cell death and survival, and actin cytoskeleton organization. The PAK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 261 matched cddid_all.tbl CDD cd06648 cd06648 270815 STKc_PAK_II Catalytic domain of the Serine/Threonine Kinase, Group II p21-activated kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Group II PAKs, also called non-conventional PAKs, include PAK4, PAK5, and PAK6. Group II PAKs contain PBD (p21-binding domain) and catalytic domains, but lack other motifs found in group I PAKs, such as an AID (autoinhibitory domain) and SH3 binding sites. Since group II PAKs do not contain an obvious AID, they may be regulated differently from group I PAKs. While group I PAKs interact with the SH3 containing proteins Nck, Grb2 and PIX, no such binding has been demonstrated for group II PAKs. Some known substrates of group II PAKs are also substrates of group I PAKs such as Raf, BAD, LIMK and GEFH1. Unique group II substrates include MARK/Par-1 and PDZ-RhoGEF. Group II PAKs play important roles in filopodia formation, neuron extension, cytoskeletal organization, and cell survival. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. The PAK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 261 matched cddid_all.tbl CDD cd06649 cd06649 132980 PKc_MEK2 Catalytic domain of the dual-specificity Protein Kinase, Mitogen-Activated Protein (MAP)/Extracellular signal-Regulated Kinase (ERK) Kinase 2. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (ST) or tyrosine residues on protein substrates. MEK2 is a dual-specificity PK and a MAPK kinase (MAPKK or MKK) that phosphorylates and activates the downstream targets, ERK1 and ERK2, on specific threonine and tyrosine residues. The ERK cascade starts with extracellular signals including growth factors, hormones, and neurotransmitters, which act through receptors and ion channels to initiate intracellular signaling that leads to the activation at the MAPKKK (Raf-1 or MOS) level, which leads to the transmission of signals to MEK2, and finally to ERK1/2. The ERK cascade plays an important role in cell proliferation, differentiation, oncogenic transformation, and cell cycle control, as well as in apoptosis and cell survival under certain conditions. Gain-of-function mutations in genes encoding ERK cascade proteins, including MEK2, cause cardiofaciocutaneous (CFC) syndrome, a condition leading to multiple congenital anomalies and mental retardation in patients. The MEK subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 331 matched cddid_all.tbl CDD cd06650 cd06650 270816 PKc_MEK1 Catalytic domain of the dual-specificity Protein Kinase, Mitogen-Activated Protein (MAP)/Extracellular signal-Regulated Kinase (ERK) Kinase 1. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (ST) or tyrosine residues on protein substrates. MEK1 is a dual-specificity PK and a MAPK kinase (MAPKK or MKK) that phosphorylates and activates the downstream targets, ERK1 and ERK2, on specific threonine and tyrosine residues. The ERK cascade starts with extracellular signals including growth factors, hormones, and neurotransmitters, which act through receptors and ion channels to initiate intracellular signaling that leads to the activation at the MAPKKK (Raf-1 or MOS) level, which leads to the transmission of signals to MEK1, and finally to ERK1/2. The ERK cascade plays an important role in cell proliferation, differentiation, oncogenic transformation, and cell cycle control, as well as in apoptosis and cell survival under certain conditions. Gain-of-function mutations in genes encoding ERK cascade proteins, including MEK1, cause cardiofaciocutaneous (CFC) syndrome, a condition leading to multiple congenital anomalies and mental retardation in patients. MEK1 also plays a role in cell cycle control. The MEK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 319 matched cddid_all.tbl CDD cd06651 cd06651 270817 STKc_MEKK3 Catalytic domain of the Serine/Threonine Kinase, Mitogen-Activated Protein (MAP)/Extracellular signal-Regulated Kinase (ERK) Kinase Kinase 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MEKK3 is a MAPK kinase kinase (MAPKKK or MKKK), that phosphorylates and activates the MAPK kinase MEK5 (or MKK5), which in turn phosphorylates and activates ERK5. The ERK5 cascade plays roles in promoting cell proliferation, differentiation, neuronal survival, and neuroprotection. MEKK3 plays an essential role in embryonic angiogenesis and early heart development. In addition, MEKK3 is involved in interleukin-1 receptor and Toll-like receptor 4 signaling. It is also a specific regulator of the proinflammatory cytokines IL-6 and GM-CSF in some immune cells. MEKK3 also regulates calcineurin, which plays a critical role in T cell activation, apoptosis, skeletal myocyte differentiation, and cardiac hypertrophy. The MEKK3 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 271 matched cddid_all.tbl CDD cd06652 cd06652 270818 STKc_MEKK2 Catalytic domain of the Serine/Threonine Kinase, Mitogen-Activated Protein (MAP)/Extracellular signal-Regulated Kinase (ERK) Kinase Kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MEKK2 is a MAPK kinase kinase (MAPKKK or MKKK), that phosphorylates and activates the MAPK kinase MEK5 (or MKK5), which in turn phosphorylates and activates ERK5. The ERK5 cascade plays roles in promoting cell proliferation, differentiation, neuronal survival, and neuroprotection. MEKK2 also activates ERK1/2, c-Jun N-terminal kinase (JNK) and p38 through their respective MAPKKs MEK1/2, JNK-activating kinase 2 (JNKK2), and MKK3/6. MEKK2 plays roles in T cell receptor signaling, immune synapse formation, cytokine gene expression, as well as in EGF and FGF receptor signaling. The MEKK2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 264 matched cddid_all.tbl CDD cd06653 cd06653 270819 STKc_MEKK3_like_u1 Catalytic domain of an Uncharacterized subfamily of Mitogen-Activated Protein (MAP)/Extracellular signal-Regulated Kinase (ERK) Kinase Kinase 3-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of uncharacterized proteins with similarity to MEKK3, MEKK2, and related proteins; they contain an N-terminal PB1 domain, which mediates oligomerization, and a C-terminal catalytic domain. MEKK2 and MEKK3 are MAPK kinase kinases (MAPKKKs or MKKKs), proteins that phosphorylate and activate MAPK kinases (MAPKKs or MKKs), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. MEKK2 and MEKK3 activate MEK5 (also called MKK5), which activates ERK5. The ERK5 cascade plays roles in promoting cell proliferation, differentiation, neuronal survival, and neuroprotection. MEKK3 plays an essential role in embryonic angiogenesis and early heart development. MEKK2 and MEKK3 can also activate the MAPKs, c-Jun N-terminal kinase (JNK) and p38, through their respective MAPKKs. The MEKK3-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 264 matched cddid_all.tbl CDD cd06654 cd06654 270820 STKc_PAK1 Catalytic domain of the Serine/Threonine Kinase, p21-activated kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PAK1 is important in the regulation of many cellular processes including cytoskeletal dynamics, cell motility, growth, and proliferation. Although PAK1 has been regarded mainly as a cytosolic protein, recent reports indicate that PAK1 also exists in significant amounts in the nucleus, where it is involved in transcription modulation and in cell cycle regulatory events. PAK1 is also involved in transformation and tumorigenesis. Its overexpression, hyperactivation and increased nuclear accumulation is correlated to breast cancer invasiveness and progression. Nuclear accumulation is also linked to tamoxifen resistance in breast cancer cells. PAK1 belongs to the group I PAKs, which contain a PBD (p21-binding domain) overlapping with an AID (autoinhibitory domain), a C-terminal catalytic domain, SH3 binding sites and a non-classical SH3 binding site for PIX (PAK-interacting exchange factor). PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. The PAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 296 matched cddid_all.tbl CDD cd06655 cd06655 132986 STKc_PAK2 Catalytic domain of the Serine/Threonine Kinase, p21-activated kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PAK2 plays a role in pro-apoptotic signaling. It is cleaved and activated by caspases leading to morphological changes during apoptosis. PAK2 is also activated in response to a variety of stresses including DNA damage, hyperosmolarity, serum starvation, and contact inhibition, and may play a role in coordinating the stress response. PAK2 also contributes to cancer cell invasion through a mechanism distinct from that of PAK1. It belongs to the group I PAKs, which contain a PBD (p21-binding domain) overlapping with an AID (autoinhibitory domain), a C-terminal catalytic domain, SH3 binding sites and a non-classical SH3 binding site for PIX (PAK-interacting exchange factor). PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. The PAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 296 matched cddid_all.tbl CDD cd06656 cd06656 132987 STKc_PAK3 Catalytic domain of the Protein Serine/Threonine Kinase, p21-activated kinase 3. Serine/threonine kinases (STKs), p21-activated kinase (PAK) 3, catalytic (c) domain. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The PAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. PAKs from higher eukaryotes are classified into two groups (I and II), according to their biochemical and structural features. PAK3 belongs to group I. Group I PAKs contain a PBD (p21-binding domain) overlapping with an AID (autoinhibitory domain), a C-terminal catalytic domain, SH3 binding sites and a non-classical SH3 binding site for PIX (PAK-interacting exchange factor). PAK3 is highly expressed in the brain. It is implicated in neuronal plasticity, synapse formation, dendritic spine morphogenesis, cell cycle progression, neuronal migration, and apoptosis. Inactivating mutations in the PAK3 gene cause X-linked non-syndromic mental retardation, the severity of which depends on the site of the mutation. 297 matched cddid_all.tbl CDD cd06657 cd06657 132988 STKc_PAK4 Catalytic domain of the Serine/Threonine Kinase, p21-activated kinase 4. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PAK4 regulates cell morphology and cytoskeletal organization. It is essential for embryonic viability and proper neural development. Mice lacking PAK4 die due to defects in the fetal heart. In addition, their spinal cord motor neurons showed failure to differentiate and migrate. PAK4 also plays a role in cell survival and tumorigenesis. It is overexpressed in many primary tumors including colon, esophageal, and mammary tumors. PAK4 has also been implicated in viral and bacterial infection pathways. PAK4 belongs to the group II PAKs, which contain a PBD (p21-binding domain) and a C-terminal catalytic domain, but do not harbor an AID (autoinhibitory domain) or SH3 binding sites. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. The PAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 292 matched cddid_all.tbl CDD cd06658 cd06658 132989 STKc_PAK5 Catalytic domain of the Serine/Threonine Kinase, p21-activated kinase 5. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PAK5 is mainly expressed in the brain. It is not required for viability, but together with PAK6, it is required for normal levels of locomotion and activity, and for learning and memory. PAK5 cooperates with Inca (induced in neural crest by AP2) in the regulation of cell adhesion and cytoskeletal organization in the embryo and in neural crest cells during craniofacial development. PAK5 may also play a role in controlling the signaling of Raf-1, an effector of Ras, at the mitochondria. PAK5 belongs to the group II PAKs, which contain a PBD (p21-binding domain) and a C-terminal catalytic domain, but do not harbor an AID (autoinhibitory domain) or SH3 binding sites. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. The PAK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 292 matched cddid_all.tbl CDD cd06659 cd06659 270821 STKc_PAK6 Catalytic domain of the Serine/Threonine Kinase, p21-activated kinase 6. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PAK6 may play a role in stress responses through its activation by the mitogen-activated protein kinase (MAPK) p38 and MAPK kinase 6 (MKK6) pathway. PAK6 is highly expressed in the brain. It is not required for viability, but together with PAK5, it is required for normal levels of locomotion and activity, and for learning and memory. Increased expression of PAK6 is found in primary and metastatic prostate cancer. PAK6 may play a role in the regulation of motility. PAK6 belongs to the group II PAKs, which contain a PBD (p21-binding domain) and a C-terminal catalytic domain, but do not harbor an AID (autoinhibitory domain) or SH3 binding sites. PAKs are Rho family GTPase-regulated kinases that serve as important mediators in the function of Cdc42 (cell division cycle 42) and Rac. The PAK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 297 matched cddid_all.tbl CDD cd06660 cd06660 381296 AKR_SF Aldo-keto reductase (AKR) superfamily. Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance in both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits, and aflatoxin aldehyde reductases, among others. 232 matched cddid_all.tbl CDD cd06661 cd06661 119400 GGCT_like GGCT-like domains, also called AIG2-like family. Gamma-glutamyl cyclotransferase (GGCT) catalyzes the formation of pyroglutamic acid (5-oxoproline) from dipeptides containing gamma-glutamyl, and is a dimeric protein. In Homo sapiens, the protein is encoded by the gene C7orf24, and the enzyme participates in the gamma-glutamyl cycle. Hereditary defects in the gamma-glutamyl cycle have been described for some of the genes involved, but not for C7orf24. The synthesis and metabolism of glutathione (L-gamma-glutamyl-L-cysteinylglycine) ties the gamma-glutamyl cycle to numerous cellular processes; glutathione acts as a ubiquitous reducing agent in reductive mechanisms involved in protein and DNA synthesis, transport processes, enzyme activity, and metabolism. AIG2 (avrRpt2-induced gene) is an Arabidopsis protein that exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae pv maculicola strain ES4326 carrying avrRpt2. avrRpt2 is an avirulence gene that can convert virulent strains of P. syringae to avirulence on Arabidopsis thaliana, soybean, and bean. The family also includes bacterial tellurite-resistance proteins (trgB); tellurium (Te) compounds are used in industrial processes and had been used as antimicrobial agents in the past. Some members have been described proteins involved in cation transport (chaC). 99 matched cddid_all.tbl CDD cd06662 cd06662 119401 SURF1 SURF1 superfamily. Surf1/Shy1 has been implicated in the posttranslational steps of the biogenesis of the mitochondrially-encoded Cox1 subunit of cytochrome c oxidase (complex IV). Cytochrome c oxidase (complex IV), the terminal electron-transferring complex of the respiratory chain, is an assemblage of nuclear and mitochondrially-encoded subunits. Its assembly is mediated by nuclear encoded assembly factors, one of which is Surf1/Shy1. Mutations in human Surf1 are a major cause of Leigh syndrome, a severe neurodegenerative disorder. 202 matched cddid_all.tbl CDD cd06663 cd06663 133456 Biotinyl_lipoyl_domains Biotinyl_lipoyl_domains are present in biotin-dependent carboxylases/decarboxylases, the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases, and the H-protein of the glycine cleavage system (GCS). These domains transport CO2, acyl, or methylamine, respectively, between components of the complex/protein via a biotinyl or lipoyl group, which is covalently attached to a highly conserved lysine residue. 73 matched cddid_all.tbl CDD cd06664 cd06664 143480 IscU_like Iron-sulfur cluster scaffold-like proteins. IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy. 123 matched cddid_all.tbl CDD cd06665 cd06665 467154 PDZ1_PDZ3_bazooka-like PDZ domain 1 and PDZ domain 3 of Drosophila bazooka (DmPar3), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 and 3 of Drosophila bazooka (DmPar3), and related domains. The Par complex comprises atypical protein kinase C (aPKC) and two scaffolding proteins, Par3 (Bazooka (Baz) in Drosophila) and Par6; bazooka (DmPar3) has three central PDZ domains. Both PDZ1 and PDZ3 domains, but not PDZ2, in bazooka (DmPar3) engage in a canonical interaction with the PDZ domain-binding motif in Par6. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This bazooka-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 87 matched cddid_all.tbl CDD cd06667 cd06667 467155 PDZ2_MUPP1-like PDZ domain 2 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction) and similar domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of MUPP1 and PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F 80 matched cddid_all.tbl CDD cd06668 cd06668 467156 PDZ4_MUPP1-like PDZ domain 4 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction) and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of MUPP1 and PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F 88 matched cddid_all.tbl CDD cd06669 cd06669 467157 PDZ5_MUPP1-like PDZ domain 5 of multi-PDZ-domain protein 1 (MUPP1), PATJ (protein-associated tight junction) and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of MUPP1 and PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ5 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F 98 matched cddid_all.tbl CDD cd06670 cd06670 467158 PDZ6_MUPP1-like PDZ domain 6 of multi-PDZ-domain protein 1 (MUPP1) and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 6 of multi-PDZ-domain protein 1 (MUPP1). MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, PDZ9, and PDZ13. This MuPP1-like PDZ6 domain is therefore absent from PATJ. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ6 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F 87 matched cddid_all.tbl CDD cd06671 cd06671 467159 PDZ7_MUPP1-PD6_PATJ-like PDZ domain 7 of multi-PDZ-domain protein 1 (MUPP1), PDZ domain 6 of PATJ (protein-associated tight junction) and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 7 of MUPP1 and PDZ domain 6 of PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ7 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 96 matched cddid_all.tbl CDD cd06672 cd06672 467160 PDZ8_MUPP1-PDZ7_PATJ-PDZ2_INAD-like PDZ domain 8 of multi-PDZ-domain protein 1 (MUPP1), PDZ domain 7 of protein-associated tight junction (PATJ), PDZ domain 2 of Drosophila melanogaster inactivation-no-after-potential D (INAD), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 8 of MUPP1, PDZ domain 7 of PATJ, and PDZ domain 2 of Drosophila melanogaster INAD, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. INAD assembles key enzymes of the Drosophila compound eye photo-transduction pathway into a supramolecular complex, supporting efficient and fast light signaling. It contains 5 PDZ domains arranged in tandem (PDZ1-PDZ5) which independently bind various proteins. INAD PDZ2 binds eye-specific protein kinase C. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ8 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 84 matched cddid_all.tbl CDD cd06673 cd06673 467161 PDZ10_MUPP1-PDZ8_PATJ-like PDZ domain 10 of multi-PDZ-domain protein 1 (MUPP1), domain 8 of PATJ (protein-associated tight junction) and similar domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 10 of MUPP1, PDZ domain 8 of PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ10 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 86 matched cddid_all.tbl CDD cd06674 cd06674 467162 PDZ11_MUPP1-PDZ9_PATJ-like PDZ domain 11 of MUPP1 of multi-PDZ-domain protein 1 (MUPP1), domain 9 of PATJ (protein-associated tight junction) and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 11 of MUPP1, PDZ domain 9 of PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ11 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 87 matched cddid_all.tbl CDD cd06675 cd06675 467163 PDZ12_MUPP1-like PDZ domain 12 of multi-PDZ-domain protein 1 (MUPP1), PDZ domain 10 of protein-associated tight junction (PATJ, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 12 of MUPP1, PDZ domain 10 of PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like PDZ12 family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F 86 matched cddid_all.tbl CDD cd06676 cd06676 467164 PDZ13_MUPP1-like PDZ domain 13 of multi-PDZ-domain protein 1 (MUPP1) and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 13 of MUPP1. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, PDZ9, and PDZ13. This MuPP1-like PDZ13 domain is therefore absent from PATJ. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ13 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 83 matched cddid_all.tbl CDD cd06677 cd06677 467165 PDZ1_LNX1_2-like PDZ domain 1 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2) and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LNX family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 89 matched cddid_all.tbl CDD cd06678 cd06678 467166 PDZ2_LNX1_2-like PDZ domain 2 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2) and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LNX family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 82 matched cddid_all.tbl CDD cd06679 cd06679 467167 PDZ3_LNX1_2-like PDZ domain 3 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2) and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LNX family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 88 matched cddid_all.tbl CDD cd06680 cd06680 467168 PDZ4_LNX1_2-like PDZ domain 4 of human Ligand of Numb protein X 1 (LNX1) and LNX2, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of LNX1 (also known as PDZ domain-containing RING finger protein 2, PDZRN2)and LNX2 (also known as PDZ domain-containing RING finger protein 1, PDZRN1), and related domains. LNX1 and LNX2 are Ring (Really Interesting New Gene) finger and PDZ domain-containing E3 ubiquitin ligases that bind to the cell fate determinant protein NUMB and mediate its ubiquitination. LNX1 can ubiquitinate a number of other ligands including PPFIA1, KLHL11, KIF7 and ERC2. LNX1 and LNX2 each have four PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LNX family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 89 matched cddid_all.tbl CDD cd06681 cd06681 467169 PDZ2_GRIP1-2-like PDZ domain 2 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 89 matched cddid_all.tbl CDD cd06682 cd06682 467170 PDZ5_GRIP1-2-like PDZ domain 5 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family domain PDZ5 is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 85 matched cddid_all.tbl CDD cd06683 cd06683 467171 PDZ6_GRIP1-2-like PDZ domain 6 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ6 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 85 matched cddid_all.tbl CDD cd06684 cd06684 467172 PDZ3_GRIP1-2-like PDZ domain 3 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 87 matched cddid_all.tbl CDD cd06685 cd06685 467173 PDZ7_GRIP1-2-like PDZ domain 7 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ7 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 85 matched cddid_all.tbl CDD cd06686 cd06686 467174 PDZ4_GRIP1-2-like PDZ domain 4 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 99 matched cddid_all.tbl CDD cd06687 cd06687 467175 PDZ1_GRIP1-2-like PDZ domain 1 of glutamate receptor-interacting protein 1 (GRIP1) and GRIP2, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) binding proteins GRIP1 (ABP/GRIP2) and GRIP2, and related domains. GRIP1 and GRIP2 each have 7 PDZ domains. The interaction of GRIP1 and GRIP2 with GluA2/3 (AMPAR subunit) regulates AMPAR trafficking and synaptic targeting. GRIP1 has an essential role in regulating AMPAR trafficking during synaptic plasticity and learning and memory. GRIP1 and GRIP2 interact with a variety of other proteins associated with protein trafficking and internalization, for example GRIP1 also interacts with KIF5 (also known as kinesin 1), EphB receptors, scaffold protein liprin-alpha, and the rasGEF GRASP-1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GRIP family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 83 matched cddid_all.tbl CDD cd06689 cd06689 467176 PDZ1_MUPP1-like PDZ domain 1 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of MUPP1 and PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 102 matched cddid_all.tbl CDD cd06690 cd06690 467177 PDZ_Radil-like PDZ domain of Ras-associating and dilute domain-containing protein (Radil) and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Radil (also known as protein KIAA1849) and related domains. Radil is required for cell adhesion and migration of neural crest precursors during development. Radil is a component of a Rasip1-Radil-ARHGAP29 complex at endothelial cell-cell junctions. Rap1, via its effectors Radil and Rasip1 and their binding partner ArhGAP29, controls the endothelial barrier by decreasing Rho-mediated radial tension on cell-cell junctions. ArhGAP29 binds the Radil PDZ domain. The Radil PDZ domain also binds kinesin family protein 14 (KIF14); KIF14 negatively regulates Rap1-mediated inside-out integrin activation by tethering Radil on microtubules. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Radil-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 88 matched cddid_all.tbl CDD cd06691 cd06691 467178 PDZ1_Par3-like PDZ domain 1 of partitioning defective 3 (Par3), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Par3 (or PAR3 or Par-3, also known as Atypical PKC isotype-specific-interacting protein, ASIP) and related domains; Drosophila bazooka PDZ1 belongs to a different PDZ family. Par3 is a scaffold protein involved in organizing cell polarity across animals. Par3 binds numerous molecules both for its recruitment to one pole of the cell and for downstream contributions to polarized cell function. It regulates cell polarity by targeting the Par complex proteins Par6 and atypical protein kinase C (aPKC) to specific cortical sites. Physical interactions between Par3 and the Par complex include: Par-3 PDZ domain 1 binding to the Par6 PDZ domain, Par3 PDZ domain 1 and PDZ domain 3 binding the Par6's PDZ-binding motif, and an interaction with an undefined region of aPKC that requires both Par3 PDZ2 and PDZ3. The PDZ domains of Par3 have also been implicated as potential phosphoinositide signaling integrators, since its second PDZ domain binds to phosphoinositides, and the third PDZ interacts with phosphoinositide phosphatase PTEN. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Par3 family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 98 matched cddid_all.tbl CDD cd06692 cd06692 467179 PDZ1_GgSTXBP4-like PDZ1 domain of Gallus gallus uncharacterized syntaxin-binding protein 4 (STXBP4) isoform X1, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Gallus gallus uncharacterized syntaxin-binding protein 4 (STXBP4) isoform X1, and related domains. Gallus gallus STXBP4 isoform X1 contains 2 PDZ domains (PDZ1 and PDZ2). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This STXBP4-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 88 matched cddid_all.tbl CDD cd06694 cd06694 467180 PDZ1_PTPN13_FRMPD2-like PDZ domain 1 of protein tyrosine phosphatase non-receptor type 13 (PTPN13),FERM and PDZ domain-containing protein 2 (FRMPD2), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1)], FRMPD2 (also known as PDZ domain-containing protein 4; PDZ domain-containing protein 5C), and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. FRMPD2 is localized in the basolateral membranes of polarized epithelial cells and is associated with tight junction formation and immune response; it contains 3 PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 92 matched cddid_all.tbl CDD cd06695 cd06695 467181 PDZ3_PTPN13_FRMPD2-like PDZ domain 3 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), FERM and PDZ domain-containing protein 2 (FRMPD2), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1)], FRMPD2 (also known as PDZ domain-containing protein 4; PDZ domain-containing protein 5C), and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). FRMPD2 is localized in the basolateral membranes of polarized epithelial cells and is associated with tight junction formation and immune response; it contains 3 PDZ domains). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 90 matched cddid_all.tbl CDD cd06696 cd06696 467182 PDZ4_PTPN13-like PDZ domain 4 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1)] and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 85 matched cddid_all.tbl CDD cd06697 cd06697 467183 PDZ5_PTPN13-like PDZ domain 5 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), Protein-tyrosine phosphatase 1E (PTP-E1), and Protein-tyrosine phosphatase (PTPL1)] and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ5 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 87 matched cddid_all.tbl CDD cd06698 cd06698 467184 PDZ1_hSTXBP4-PDZ2_GgSTXBP4-like PDZ1 domain of human syntaxin-binding protein 4 (STXBP4), PDZ2 domain of Gallus gallus uncharacterized STXBP4 isoform X1, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of human syntaxin-binding protein 4 (STXBP4), PDZ2 domain of Gallus gallus uncharacterized STXBP4 isoform X1, and related domains. Human STXBP4 (also known as Synip) includes a single PDZ domain, a coiled-coil domain, and a WW domain (named for its two conserved tryptophans); Gallus gallus STXBP4 isoform X1 contains 2 PDZ domains (PDZ1 and PDZ2). Human STXBP4 plays a role in the translocation of transport vesicles from the cytoplasm to the plasma membrane: insulin induces the dissociation of the STXBP4 and STX4 complex liberating STX4 to interact with Vamp2, and to form the SNARE complex thereby promoting vesicle fusion. It may also play a role in the regulation of insulin release by pancreatic beta cells after stimulation by glucose. Human STXBP4 is also known to physically associate with a prominent isoform of TP63 (deltaNp63alpha 9) whose overexpression promotes squamous cell carcinoma development, and in doing so prevents degradation of this isoform by the Cdc20-APC/C complex, Itch, and RACK1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This STXBP4-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 89 matched cddid_all.tbl CDD cd06701 cd06701 467185 PDZ4_Scribble-like PDZ domain 4 of Drosophila Scribble, human Scribble homolog, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 98 matched cddid_all.tbl CDD cd06702 cd06702 467186 PDZ3_Scribble-like PDZ domain 3 of Drosophila Scribble, human Scribble homolog, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 89 matched cddid_all.tbl CDD cd06703 cd06703 467187 PDZ2_Scribble-like PDZ domain 2 of Drosophila Scribble, human Scribble homolog, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 92 matched cddid_all.tbl CDD cd06704 cd06704 467188 PDZ1_Scribble-like PDZ domain 1 of Drosophila Scribble, human Scribble homolog, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Drosophila Scribble (also known as LAP4), human Scribble homolog (also known as hScrib, LAP4, CriB1, ScrB1 and Vartul), and related domains. They belong to the LAP family, which describes proteins that contain either one or four PDZ domains and 16 LRRs (leucine-rich repeats) and function in controlling cell shape, size and subcellular protein localization. In Drosophila, the Scribble complex, comprising Scribble, discs large, and lethal giant larvae, plays a role in apico-basal cell polarity, in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Mammalian Scribble is important in many aspects of cancer development. Scribble and its homologs can be downregulated or overexpressed in cancer; they have a role in cancer beyond their function in loss of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Scribble-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 87 matched cddid_all.tbl CDD cd06705 cd06705 467189 PDZ_MAST PDZ domain of the microtubule-associated serine-threonine (MAST) protein kinase family. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MAST family kinases, including MAST1-4. These MAST proteins contain a DUF1908 domain, a serine/threonine kinase domain, a AGC-kinase C-terminal domain, and a PDZ domain; MAST family member MASTL is a shorter protein lacking the PDZ domain. The PDZ domain gives the MAST family the capacity to scaffold its own kinase activity. These kinases are implicated in the inhibition of neurite outgrowth and regeneration in cultured cells. Their binding partners include microtubules, beta2-syntrophin, TNF receptor-associated factor 6 (TRAF6), cAMP-regulated phosphoprotein (ARPP-16), and PTEN. This family also includes Caenorhabditis elegans KIN-4 MAST kinase, a key longevity factor acting through binding PTEN phosphatase, and Drosophila Drop out which regulates dynein-dependent transport during embryonic development. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAST-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 93 matched cddid_all.tbl CDD cd06706 cd06706 467190 PDZ_PTPN3-4-like PDZ domain of tyrosine-protein phosphatase non-receptor type 3 (PTPN3), tyrosine-protein phosphatase non-receptor type 4 (PTNP4), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PTPN3, PTPN4 and related domains. PTPN3 (also known as protein-tyrosine phosphatase H1, PTP-H1) has a tumor-suppressive or a tumor-promoting role in many cancers. It serves as a specific phosphatase for the MAP kinase p38gamma; the two interact via their PDZ domains and cooperate to promote Ras-induced oncogenesis. Interaction partners of the PTPN3 PDZ domain include p38gamma and human papillomavirus E6 oncoprotein. PTPN4 (also known as protein-tyrosine phosphatase MEG1) plays a role in immunity, learning, synaptic plasticity or cell homeostasis. p38gamma is also an interaction partner of the PTPN4 PDZ domain: PTPN4 regulates neuronal cell homeostasis by protecting neurons against apoptosis; binding of the C terminus of p38gamma to the PDZ domain of PTPN4, antagonizes the catalytic autoinhibition of PTPN4, leading to cell apoptosis. Other interaction partners of the PTPN4 PDZ domain include glutamate receptor subunit GluN2A, and RABV strain G protein, among others. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN3-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 90 matched cddid_all.tbl CDD cd06707 cd06707 467191 PDZ_GIPC PDZ domain of GIPC family proteins. GIPC1/GIPC (GAIP/RGS19-interacting protein), GIPC2, and GIPC3 (also known as C19orf64) constitute the GIPC family. These proteins contain an N-terminal GIPC-homology 1 (GH1) domain, a central PDZ domain, and a C-terminal GH2 domain. GIPC proteins function as adaptor molecules that assemble RTKs, GPCRs, integrins, transmembrane proteins and cytoplasmic signaling regulators as cargoes of MYO6-dependent endocytic transport. Mutations in the Gipc1 and Gipc2 genes have been linked to cancer, while mutations in the Gipc3 gene cause nonsyndromic hearing loss. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GIPC family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 89 matched cddid_all.tbl CDD cd06708 cd06708 467192 PDZ_nNOS-like PDZ domain of neuronal nitric oxide synthase (nNOS), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of nNOS, and related domains. nNOS produces a key signaling molecule, nitric oxide (NO), which has diverse functions throughout the body and acts as a neurotransmitter and intracellular signaling molecule in the central and peripheral nervous system. nNOS is concentrated at synaptic junctions in the brain and motor endplates in skeletal muscle. The PDZ domain of neuronal nitric oxide synthase (nNOS) interacts with the PDZ domain of alpha1-syntrophin (in muscle cells) and with the second PDZ domain of Disks large homolog 4 (Dlg4, also known as PSD-95), and nitric oxide synthase 1 adaptor protein NOS1AP in neurons. Dlg4 binds NMDA receptors, and nNOS, forming a complex in neurons. NOS1AP competes with Dgl4 for the nNOS PDZ domain and prevents the coupling of nNos activation with NMDA receptor-mediated calcium influx. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This nNOS-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 110 matched cddid_all.tbl CDD cd06709 cd06709 467193 PDZ_SYNJ2BP-like PDZ domain of synaptojanin-2-binding protein (SYNJ2BP), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SYNJ2BP, and related domains. SYNJ2BP (also known as mitochondrial outer membrane protein 25, OMP25) regulates endocytosis of activin type 2 receptor kinases through the Ral/RALBP1-dependent pathway and may be involved in suppression of activin-induced signal transduction. Binding partners of the SYNJ2BP PDZ domain include activin type II receptors (ActR-II), and SYNJ2. SYNJ2BP interacts with the PDZ binding motif of the Notch Delta-like ligand 1 (DLL1) and DLL4, promoting Delta-Notch signaling, and inhibiting sprouting angiogenesis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SYNJ2BP-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 86 matched cddid_all.tbl CDD cd06710 cd06710 467194 PDZ_RGS12-like PDZ domain of regulator of G-protein signaling 12 (RGS12), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of RGS12, and related domains. RGS12 downregulates GPCR signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving G-proteins into their inactive GDP-bound form. The RGS12 PDZ domain can bind selectively to C-terminal (A/S)-T-X-(L/V) motifs as found within both the CXCR2 IL-8 receptor, and the alternative 3' exon form of RGS12. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This RGS12-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 76 matched cddid_all.tbl CDD cd06711 cd06711 467195 PDZ_RGS3-like PDZ domain of regulator of G-protein signaling 3 (RGS3), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of RGS3, and related domains. RGS3 down-regulates GPCR signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving G-proteins into their inactive GDP-bound form. It downregulates G-protein-mediated release of inositol phosphates and activation of MAP kinases. In Eph/ephrin signaling, RGS3 binds via its PDZ domain to the cytoplasmic C terminus of Eph receptor tyrosine kinase EphB. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This RGS3-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 77 matched cddid_all.tbl CDD cd06712 cd06712 467196 PDZ_rhophilin-like PDZ domain of rhophilin-1, rhophilin-2, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of rhophilin-1, rhophilin-2, and related domains. Rhophilin-1 (RHPN1, also known as GTP-Rho-binding protein 1) and rhophilin-2 (RHPN2, also known as GTP-Rho-binding protein 2) are Rho-GTP binding proteins involved in cytoskeletal dynamics. Rhophilin-2 inhibits RhoA's activity to induce F-actin stress fibers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This rhophilin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 78 matched cddid_all.tbl CDD cd06713 cd06713 467197 PDZ_tamalin_CYTIP-like PDZ domain of tamalin, cytohesin-1-interacting protein (CYTIP), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of tamalin, cytohesin-1-interacting protein, and related domains. Tamalin (trafficking regulator and scaffold protein tamalin, also known as general receptor for phosphoinositides 1-associated scaffold protein, GRASP) functions to link receptors, including group 1 metabotropic glutamate receptors (mGluRs), to neuronal proteins. The tamalin PDZ domain binds the C-terminal domains of group I mGluRs; it also binds potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 (HCN2), neurotrophin-3 (NT3) TrkCT1-truncated receptor, SAP90/PSD-95-associated protein, and tamalin itself. CYTIP (cytohesin-1-interacting protein, also known as Pleckstrin homology Sec7 and coiled-coil domain-binding protein) sequesters cytohesin-1 in the cytoplasm, limiting its interaction with beta2 integrins; cytohesin-1 binds the CYTIP coiled coil domain. The CYTIP PDZ domain can bind the C-terminal peptide of protocadherin alpha-1 (PCDHA1), indicating a possible interaction between the two. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This tamalin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 91 matched cddid_all.tbl CDD cd06714 cd06714 467198 PDZ_RIM-like PDZ domain of Rab3-interacting molecule 1 (RIM), RIM2, piccolo and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of RIM, RIM2, piccolo and related domains. RIM proteins and Gallus gallus protein piccolo (also called aczonin) are involved in neurotransmitter release at presynaptic active zones, the site of vesicle fusion. A protein complex containing RIM proteins positions synaptic vesicles containing synaptotagmin at the active zone. RIM proteins simultaneously activate docking and priming of synaptic vesicles and recruit Ca2+-channels to active zones, thereby connecting primed synaptic vesicles to Ca2+-channels. RIM binding to vesicular Rab proteins (Rab3 and Rab27 isoforms) mediates vesicle docking; RIM binding to Munc13 activates vesicle priming; RIM binding to the Ca2+-channel, both directly and indirectly via RIM-BP, recruits the Ca2+-channels. The RIM PDZ domain interacts with the C-termini of N- and P/Q-type voltage-gated Ca2+-channels. RIM1, RIM2 and piccolo also participate in regulated exocytosis through binding cAMP-GEFII (cAMP-binding protein-guanidine nucleotide exchange factor II). The piccolo PDZ domain binds cAMP-GEFII. RIM2 also plays a role in dendrite formation by melanocytes. Caenorhabditis elegans RIM (also known as unc-10) may be involved in the regulation of defecation and daumone response. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This RIM-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 95 matched cddid_all.tbl CDD cd06715 cd06715 467199 PDZ1-PDZRN4-like PDZ domain 1 of PDZ domain-containing RING finger protein 4 (PDZRN4), PDZRN3-B, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PDZRN4, PDZRN3-B, and related domains. PDZRN4 (also known as ligand of numb protein X 4, and SEMACAP3-like protein) contains an N-terminal RING domain and two tandem repeat PDZ domains. It is involved in the progression of cancer, including human liver cancer and breast cancer, and may contribute to the tumorigenesis of rectal adenocarcinoma. Danio rerio PDZRN3-B may participate in neurogenesis: the first PDZ domain of Danio rerio Pdzrn3 interacts with Kidins220 (Kinase D-interacting substrate 220 kD, also named Ankyrin Repeat-Rich Membrane Spanning), a crucial mediator of signal transduction in neural tissues. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZRN4-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 92 matched cddid_all.tbl CDD cd06716 cd06716 467200 PDZ2-PDZRN4-like PDZ domain 2 of PDZ domain-containing RING finger protein 4 (PDZRN4), PDZRN3-B, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PDZRN4, PDZRN3-B, and related domains. PDZRN4 (also known as ligand of numb protein X 4, and SEMACAP3-like protein) contains an N-terminal RING domain and two tandem repeat PDZ domains. It is involved in the progression of cancer, including human liver cancer and breast cancer, and may contribute to the tumorigenesis of rectal adenocarcinoma. Danio rerio PDZRN3-B may participate in neurogenesis: the first PDZ domain of Danio rerio Pdzrn3 interacts with Kidins220 (Kinase D-interacting substrate 220 kD, also named Ankyrin Repeat-Rich Membrane Spanning), a crucial mediator of signal transduction in neural tissues. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZRN4-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 88 matched cddid_all.tbl CDD cd06717 cd06717 467201 PDZ_Dishevelled-like PDZ domain of segment polarity protein dishevelled homolog DVL1, DVL2, DVL3, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of DVL1-3, and related domains. The dishevelleds (DVL1, 2 and 3 in humans) act downstream of Frizzled (FZD) receptors in both the canonical and non-canonical WNT signaling pathway; they bind the cytoplasmic C-terminus of frizzled family members and transduce the Wnt signal to down-stream effectors. They bind to several proteins known to modulate Wnt signaling. Binding partners of the DVL1 PDZ domain include nucleoredoxin (NXN), Van Gogh-like (VANGL1), Wnt receptor RYK, Dapper 1 (DACT1), Frizzled7 (FZD7), transmembrane protein 88 (TMEM88), Daple (dishevelled-associating protein with a high frequency of leucines), also known as Ccdc88c), and cysteine-rich protein Idax. The DVL2 PDZ domain has been shown to bind the nuclear export signal sequence of the DVL2 protein. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This DVL-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 87 matched cddid_all.tbl CDD cd06718 cd06718 467202 PDZ_Par6-like PDZ domain of partitioning defective 6 (Par6), Drosophila Rho GTPase-activating protein 100F (RhoGAP100F), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Par6 (also known as PAR6 or Par-6), RhoGAP100F, and related domains. Par6 is part of a conserved machinery that directs metazoan cell polarity, a process necessary for the function of diverse cell types. Par6 forms a cell polarity-regulatory complex with atypical protein kinase C (aPKC) and Par3. Par6 can also directly associate with PALS1 (proteins associated with Lin7, also known as Stardust) providing a link between the Par3/aPKC/Par6 complex and the PALS1-PATJ (protein-associated TJ) complex. Binding partners of the Par6-PDZ domain include Par3, PALS1/Stardust; leucine-rich repeat-containing protein netrin-G ligand-2 (NGL-2), human crumbs (CRB3) involve in the morphogenesis of the tight junctions in mammalian epithelial cells, and PAR-6 co-operates with the Par6 semi-CRIB domain to bind CDC42. CDC42 regulates the Par6 PDZ domain through an allosteric CRIB-PDZ transition. Drosophila RhoGAP100F, also known as synapse defective protein 1 homolog (syd-1 homolog), is a GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound form. The RhoGAP100F-PDZ domain binds the neurexin C terminus to control synapse formation at the Drosophila neuromuscular junction. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Par6-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 84 matched cddid_all.tbl CDD cd06719 cd06719 467617 PDZ2-4_Nma111p-like second and fourth PDZ domains (PDZ2 and 4) of Saccharomyces cerevisiae pro-apoptotic serine protease Nma111p and related domains. Second and fourth PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens 1)) domains of the HtrA-type protease Saccharomyces cerevisiae Nma11p (also known as Ynm3p), and related domains. Nma111p is a nuclear serine protease which mediates apoptosis through proteolysis of the apoptotic inhibitor Bir1p. Nma111p is composed of two protease domains and four PDZ domains; its N-terminal half is comprised of a protease domain, followed by two PDZ domains, and its C-terminal half has a similar domain arrangement. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminus of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands (A-F) and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. One permutation places beta-strand A at the C-terminus, another permutation places both beta-strands A and B at the C-terminus. This Nma111p-like family PDZ2 and PDZ4 domains show similarity to permuted PDZ domains. 79 matched cddid_all.tbl CDD cd06720 cd06720 467203 PDZ1_APBA1_3-like PDZ domain 1 of amyloid-beta A4 precursor protein-binding family A member 1 (APBA1), APBA2, APBA3, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of APBA1, APBA2, APBA3, and related domains. The APBA/X11/Mint protein family includes three members: neuron specific APBA1 (also known as X11alpha and Mint1) and APBA2 (also known as X11beta and Mint2), and the ubiquitously expressed APBA3 (also known as (X12gamma and Mint3). They are involved in regulating neuronal signaling, trafficking and plasticity. They contain two PDZ domains (PDZ1 and PDZ2) which bind a variety of proteins: Arf GTPases (APBA1 and APBA2 PDZ2) and neurexin (APBA1 and APBA2 PDZ1 and 2), which are involved in vesicle docking and exocytosis; alpha1B subunit of N-type Ca2+ channel (APBA1 PDZ1) that is involved in ion channels; KIF17 (APBA1 PDZ1) that is involved in transport and traffic; and Alzheimer's disease related proteins such as APP (APBA3 PDZ2), CCS (APBA1 PDZ2), NF-kappa-B/p65 (APBA2 PDZ2), presenilin-1 (APBA1 and APBA2 PDZ1 and PDZ2). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This APBA1,2,3-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta- strand F. 86 matched cddid_all.tbl CDD cd06721 cd06721 467204 PDZ1_syntenin-like PDZ domain 1 of syntenin-1, syntenin-2, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of syntenin-1, syntenin-2, and related domains. Syntenins are implicated in various cellular processes such as trafficking, signaling, and cancer metastasis. They bind to signaling and adhesion molecules, such as syndecans, neurexins, ephrin B, and phospholipid PIP2. Through its tandem PDZ domains (PDZ1 and PDZ2), syntenin links syndecans to other cell surface receptors and kinases, such as E-cadherin and ephrin-B, establishing signaling crosstalk. During syndecan binding, syntenin PDZ2 serves as a high-affinity domain, and PDZ1, also necessary for binding, acts as a complementary, low-affinity domain; this is also the case for syntenin binding to proto-oncogene c-Src. The syntenin PDZ domain-PIP2 interaction controls Arf6-mediated syndecan recycling through endosomal compartments; both PDZ1 and PDZ2 interact with PIP2. Different binding partners and downstream regulators of syntenin1 PDZ domains, such as to proto-oncogene c-Src, mitogen-activated protein kinase (MAPK), and focal adhesion kinase (FAK), have been identified that promote the progression and invasion of a variety of cancers, such as melanoma, glioblastoma multiforme and breast cancer. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This syntenin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta- strand F. 79 matched cddid_all.tbl CDD cd06722 cd06722 467205 PDZ_PICK1-like PDZ domain of PICK1 (protein interacting with C-kinase 1) and similar domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PICK1, and related domains. PICK1 (also known as PRKCA-binding protein and protein kinase C-alpha-binding protein) plays a key role in regulating trafficking of binding partners by altering either their subcellular targeting and/or surface expression. PICK1 plays a role in synaptic plasticity by regulating the trafficking and internalization of amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) receptors; the PICK1-PDZ domain binds the AMPA receptor subunits. The PICK1 PDZ domain also binds glutamate transporters, Eph receptors, metabotropic glutamate receptors, and ASICs (acid-sensing ion channels), among others. Clustering and synaptic targeting of PICK1 requires direct interaction between the PDZ domain and lipid membranes. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PICK-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta- strand F. 84 matched cddid_all.tbl CDD cd06723 cd06723 467206 PDZ1_Dlg1-2-4-like PDZ domain 1 of human discs large homolog 1 (Dlg1), Dlg2, and Dlg4, Drosophila disc large (Dlg), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Drosophila Dlg1, human Dlg1,2, and 4 and related domains. Dlg1 (also known as synapse-associated protein Dlg197 or SAP-97), Dlg2 (also known as channel-associated protein of synapse-110, postsynaptic density protein 93, or PSD-93), Dlg4 (also known as postsynaptic density protein 95, PSD-95, synapse-associated protein 90, or SAP-90) each have 3 PDZ domains and belong to the membrane-associated guanylate kinase family. Dlg1 regulates antigen receptor signaling and cell polarity in lymphocytes, B-cell proliferation and antibody production, and TGFalpha bioavailability; its PDZ3 domain binds pro-TGFalpha, and its PDZ2 domain binds the TACE metalloprotease responsible for cleaving pro-TGFalpha to a soluble form. Dlg2 is involved in N-methyl-D-aspartate (NMDA) receptor signaling. It regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord, and it also interacts with NMDA receptor subunits and with Shaker-type K+ channel subunits to cluster into a channel complex. Dlg4 PDZ1 domain binds NMDA receptors, and its PDZ2 domain binds neuronal nitric oxide synthase (nNOS), forming a complex in neurons. The Drosophila Scribble complex (Scribble, Dlg, and lethal giant larvae) plays a role in apico-basal cell polarity, and in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Postsynaptic targeting of Drosophila DLG requires interactions mediated by the first two PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 89 matched cddid_all.tbl CDD cd06724 cd06724 467207 PDZ2_Dlg1-2-4-like PDZ domain 2 of human discs large homolog 1 (Dlg1), Dlg2, and Dlg4, Drosophila disc large (Dlg), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Drosophila Dlg1, human Dlg1,2, and 4 and related domains. Dlg1 (also known as synapse-associated protein Dlg197 or SAP-97), Dlg2 (also known as channel-associated protein of synapse-110, postsynaptic density protein 93, or PSD-93), Dlg4 (also known as postsynaptic density protein 95, PSD-95, synapse-associated protein 90, or SAP-90) each have 3 PDZ domains and belong to the membrane-associated guanylate kinase family. Dlg1 regulates antigen receptor signaling and cell polarity in lymphocytes, B-cell proliferation and antibody production, and TGFalpha bioavailability; its PDZ3 domain binds pro-TGFalpha, and its PDZ2 domain binds the TACE metalloprotease responsible for cleaving pro-TGFalpha to a soluble form. Dlg2 is involved in N-methyl-D-aspartate (NMDA) receptor signaling. It regulates surface expression of NMDA receptors in dorsal horn neurons of the spinal cord, and it also interacts with NMDA receptor subunits and with Shaker-type K+ channel subunits to cluster into a channel complex. Dlg4 PDZ1 domain binds NMDA receptors, and its PDZ2 domain binds neuronal nitric oxide synthase (nNOS), forming a complex in neurons. The Drosophila Scribble complex (Scribble, Dlg, and lethal giant larvae) plays a role in apico-basal cell polarity, and in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development. Postsynaptic targeting of Drosophila DLG requires interactions mediated by the first two PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 85 matched cddid_all.tbl CDD cd06726 cd06726 467208 PDZ_MPP-like PDZ domain of membrane palmitoylated proteins (MPPs), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MPP1-7 (also known as MAGUK p55 subfamily members 1-7), and related domains. MPPs comprise a subfamily of a larger group of multidomain proteins, namely, membrane-associated guanylate kinases (MAGUKs). MPPs form diverse protein complexes at the cell membranes, which are involved in a wide range of cellular processes, including establishing proper cell structure, polarity and cell adhesion. MPPs have only one PDZ domain. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MPP1-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 80 matched cddid_all.tbl CDD cd06727 cd06727 467209 PDZ1_ZO1-like PDZ domain 1 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of ZO-1, -2, -3 and related domains. Zonula occludens proteins (ZO-1, ZO-2, ZO-3) are multi-PDZ domain proteins involved in the maintenance and biogenesis of multi-protein networks at the cytoplasmic surface of intercellular contacts in epithelial and endothelial cells. They have three N-terminal PDZ domains, PDZ1-3, followed by a Src homology-3 (SH3) domain and a guanylate kinase (GuK)-like domain. Among protein-protein interactions for all ZO proteins is the binding of the first PDZ domain (PDZ1) to the C-termini of claudins, and the homo- and hetero-dimerization of ZO-proteins via their second PDZ domain (PDZ2), which takes place by symmetrical domain swapping of the first two beta-strands of PDZ2. At the cell level, ZO-1 and ZO-2 are involved in polarity maintenance, gene transcription, cell proliferation, and tumor cell metastasis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This ZO family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 87 matched cddid_all.tbl CDD cd06728 cd06728 467210 PDZ2_ZO1-like_ds PDZ domain 2 of Zonula Occludens-1 (ZO-1), ZO-2 and ZO-3, and related domains; form domain-swapping dimers. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of ZO-1, -2, -3 and related domains. Zonula occludens proteins (ZO-1, ZO-2, ZO-3) are multi-PDZ domain proteins involved in the maintenance and biogenesis of multi-protein networks at the cytoplasmic surface of intercellular contacts in epithelial and endothelial cells. They have three N-terminal PDZ domains, PDZ1-3, followed by a Src homology-3 (SH3) domain and a guanylate kinase (GuK)-like domain. Among protein-protein interactions for all ZO proteins is the binding of the first PDZ domain (PDZ1) to the C-termini of claudins , and the homo- and hetero-dimerization of ZO-proteins via their second PDZ domain (PDZ2), which takes place by symmetrical domain swapping of the first two beta-strands of PDZ2. At the cell level, ZO-1 and ZO-2 are involved in polarity maintenance, gene transcription, cell proliferation, and tumor cell metastasis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This ZO family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 79 matched cddid_all.tbl CDD cd06729 cd06729 467211 PDZ3_ZO1-like_domain PDZ domain 3 of Zonula Occludens-1 (ZO-1), homologs ZO-2 and ZO-3, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of ZO-1, -2, -3 and related domains. Zonula occludens proteins (ZO-1, ZO-2, ZO-3) are multi-PDZ domain proteins involved in the maintenance and biogenesis of multi-protein networks at the cytoplasmic surface of intercellular contacts in epithelial and endothelial cells. They have three N-terminal PDZ domains, PDZ1-3, followed by a Src homology-3 (SH3) domain and a guanylate kinase (GuK)-like domain. Among protein-protein interactions for all ZO proteins is the binding of the first PDZ domain (PDZ1) to the C-termini of claudins , and the homo- and hetero-dimerization of ZO-proteins via their second PDZ domain (PDZ2), which takes place by symmetrical domain swapping of the first two beta-strands of PDZ2. At the cell level, ZO-1 and ZO-2 are involved in polarity maintenance, gene transcription, cell proliferation, and tumor cell metastasis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This ZO family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 82 matched cddid_all.tbl CDD cd06730 cd06730 467212 PDZ0_MAGI-1_3-like PDZ domain 0 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 0 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ0 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, -B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 85 matched cddid_all.tbl CDD cd06731 cd06731 467213 PDZ1_MAGI-1_3-like PDZ domain 1 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, -B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 85 matched cddid_all.tbl CDD cd06732 cd06732 467214 PDZ2_MAGI-1_3-like PDZ domain 2 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, -B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 82 matched cddid_all.tbl CDD cd06733 cd06733 467215 PDZ3_MAGI-1_3-like PDZ domain 3 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, -B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 85 matched cddid_all.tbl CDD cd06734 cd06734 467216 PDZ4_MAGI-1_3-like PDZ domain 4 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, -B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 84 matched cddid_all.tbl CDD cd06735 cd06735 467217 PDZ5_MAGI-1_3-like PDZ domain 5 of membrane-associated guanylate kinase inverted 1 (MAGI-1), MAGI-2, and MAGI-3, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of MAGI1, 2, 3 (MAGI is also known as Membrane-associated guanylate kinase, WW and PDZ domain-containing protein) and related domains. MAGI proteins have been implicated in the control of cell migration and invasion through altering the activity of phosphatase and tensin homolog (PTEN) and modulating Akt signaling. Four MAGI proteins have been identified (MAGI1-3 and MAGIX). MAGI1-3 have 6 PDZ domains and bind to the C-terminus of PTEN via their PDZ2 domain. MAGIX has a single PDZ domain that is related to MAGI1-3 PDZ domain 5, and belongs to this MAGI1,2,3-like family. Other binding partners for MAGI1 include JAM4, C-terminal tail of high risk HPV-18 E6, megalin, TRAF6, Kir4.1 (basolateral K+ channel subunit), and cadherin 23; for MAGI2, include DASM1, dendrin, axin, beta- and delta-catenin, neuroligin, hyperpolarization-activated cation channels, beta1-adrenergic receptors, NMDA receptor, and TARPs; and for MAGI3 includes LPA2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAGI family PDZ5 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 84 matched cddid_all.tbl CDD cd06736 cd06736 467218 PDZ_CARD11_CARD14-like PDZ domain of caspase recruitment domain-containing protein 11 (CARD11), CARD14, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of CARD11, CARD14, and related domains. CARD11 (also known as CARD-containing MAGUK protein 1, CARMA1, Bimp3) and CARD14 (also known as CARD-containing MAGUK protein 2, CARMA2, Bimp2) belong to the CARD-containing membrane-associated guanylate kinase (MAGUK) protein family. They play several crucial biological functions, including regulation of immune response and inflammation. The CARD11-Bcl10-MALT1 (CBM) complex bridges T cell receptor signaling to the canonical IkappaB kinase (IKK)/NF-kappaB pathway. CARD14 can form an analogous biochemical complex to activate NF-kappaB during specialized immunity. The CBM complex of CARD14/CARMA2 may bind with TRAF6 and get involved in IL-17 pathways in keratinocytes. The preponderance of protein interactions occurs through the N-terminal half of CARD11 that includes the CARD, LATCH, and coiled-coil domains; the C-terminal PDZ-SH3-MAGUK region binds the adhesion and degranulation-promoting adapter protein (ADAP) and aryl hydrocarbon receptor interacting protein (AIP). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This CARD11 and CARD14-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 75 matched cddid_all.tbl CDD cd06737 cd06737 467219 PDZ1_harmonin PDZ domain 1 of harmonin isoforms a, b, and c, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of harmonin isoforms a, b, and c, and related domains. Harmonin (also known as Usher Type 1C, PDZ-73 and AIE-75) is a key organizer of the Usher (USH) protein interactome. USH syndrome is the leading cause of hereditary sensory deaf-blindness in humans; three clinically distinct types of USH have been identified, type 1 to 3. The gene encoding harmonin (USH1C) is the causative gene for the USH type 1C phenotype. There are at least 10 alternatively spliced isoforms of harmonin, which are divided into three subclasses (a, b, and c). All isoforms contain the first two PDZ domains and the first coiled-coil domain. The a and b isoforms all have a third PDZ domain. The different PDZ domains are responsible for interactions with all known Usher syndrome type 1 proteins, and most Usher syndrome type 2 proteins. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This harmonin family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 85 matched cddid_all.tbl CDD cd06738 cd06738 467220 PDZ2_harmonin PDZ domain 2 of harmonin isoforms a, b, and c, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of harmonin isoforms a, b, and c, and related domains. Harmonin (also known as Usher Type 1C, PDZ-73 and AIE-75) is a key organizer of the Usher (USH) protein interactome. USH syndrome is the leading cause of hereditary sensory deaf-blindness in humans; three clinically distinct types of USH have been identified, type 1 to 3. The gene encoding harmonin (USH1C) is the causative gene for the USH type 1C phenotype. There are at least 10 alternatively spliced isoforms of harmonin, which are divided into three subclasses (a, b, and c). All isoforms contain the first two PDZ domains and the first coiled-coil domain. The a and b isoforms all have a third PDZ domain. The different PDZ domains are responsible for interactions with all known Usher syndrome type 1 proteins, and most Usher syndrome type 2 proteins. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This harmonin family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 82 matched cddid_all.tbl CDD cd06739 cd06739 467221 PDZ3_harmonin PDZ domain 3 of harmonin isoforms a and b, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of harmonin isoforms a and b, and related domains. Harmonin (also known as Usher Type 1C, PDZ-73 and AIE-75) is a key organizer of the Usher (USH) protein interactome. USH syndrome is the leading cause of hereditary sensory deaf-blindness in humans; three clinically distinct types of USH have been identified, type 1 to 3. The gene encoding harmonin (USH1C) is the causative gene for the USH type 1C phenotype. There are at least 10 alternatively spliced isoforms of harmonin, which are divided into three subclasses (a, b, and c). All isoforms contain the first two PDZ domains and the first coiled-coil domain. The a and b isoforms all have a third PDZ domain. The different PDZ domains are responsible for interactions with all known Usher syndrome type 1 proteins, and most Usher syndrome type 2 proteins. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This harmonin family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 94 matched cddid_all.tbl CDD cd06740 cd06740 467222 PDZ1_FL-whirlin PDZ domain 1 of the full-length isoform of whirlin and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of the full-length isoform of whirlin and related domains. Whirlin is an essential protein for developmental pathways in photoreceptor cells of the retina and hair cells of the inner ear. The full-length whirlin isoform has two harmonin N-like domains, three PDZ domains, a proline-rich region, and a PDZ-binding motif. Whirlin isoforms may form different complexes at the periciliary membrane complex (PMC) in photoreceptors, and the stereociliary tip and base in inner ear hair cells. It interacts with ADGRV1 and usherin at the PMC; with SANS and RpgrORF15 at the connecting cilium in photoreceptors; with EPS8, MYO15A, p55, and CASK proteins at the stereociliary tip of inner ear hair cells; and with ADGRV1, usherin, and PDZD7 at the stereociliary base in inner ear hair cells. Mutations in the gene encoding whirlin (WHRN; also known as USH2D and DFNB31), have been found to cause either USH2 subtype (USH2D) or autosomal recessive non-syndromic deafness type 31 (DFNB31). Whirlin is the key protein in the USH2 complex (whirlin, usherin and GPR98) which recruits other USH2 causative proteins at the periciliary membrane in photoreceptors and the ankle link of the stereocilia in hair cells. Whirlin's interaction with espin, another stereociliary protein, may be important for the architecture of the USH2 complex. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This whirlin family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 82 matched cddid_all.tbl CDD cd06741 cd06741 467223 PDZ2_FL-whirlin PDZ domain 2 of the full-length isoform of whirlin and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of the full-length isoform of whirlin and related domains. Whirlin is an essential protein for developmental pathways in photoreceptor cells of the retina and hair cells of the inner ear. The full-length whirlin isoform has two harmonin N-like domains, three PDZ domains, a proline-rich region, and a PDZ-binding motif. Whirlin isoforms may form different complexes at the periciliary membrane complex (PMC) in photoreceptors, and the stereociliary tip and base in inner ear hair cells. It interacts with ADGRV1 and usherin at the PMC; with SANS and RpgrORF15 at the connecting cilium in photoreceptors; with EPS8, MYO15A, p55, and CASK proteins at the stereociliary tip of inner ear hair cells; and with ADGRV1, usherin, and PDZD7 at the stereociliary base in inner ear hair cells. Mutations in the gene encoding whirlin (WHRN; also known as USH2D and DFNB31), have been found to cause either USH2 subtype (USH2D) or autosomal recessive non-syndromic deafness type 31 (DFNB31). Whirlin is the key protein in the USH2 complex (whirlin, usherin and GPR98) which recruits other USH2 causative proteins at the periciliary membrane in photoreceptors and the ankle link of the stereocilia in hair cells. Whirlin's interaction with espin, another stereociliary protein, may be important for the architecture of the USH2 complex. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This whirlin family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 84 matched cddid_all.tbl CDD cd06742 cd06742 467224 PDZ3_FL-whirlin-like PDZ domain 3 of the full-length isoform of whirlin, PDZ domain 1 of the short isoform of whirlin, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of the full-length isoform of whirlin, PDZ domain 1 of the short isoform of whirlin, and related domains. Whirlin is an essential protein for developmental pathways in photoreceptor cells of the retina and hair cells of the inner ear. The full-length whirlin isoform has two harmonin N-like domains, three PDZ domains, a proline-rich region, and a PDZ-binding motif. Whirlin isoforms may form different complexes at the periciliary membrane complex (PMC) in photoreceptors, and the stereociliary tip and base in inner ear hair cells. It interacts with ADGRV1 and usherin at the PMC; with SANS and RpgrORF15 at the connecting cilium in photoreceptors; with EPS8, MYO15A, p55, and CASK proteins at the stereociliary tip of inner ear hair cells; and with ADGRV1, usherin, and PDZD7 at the stereociliary base in inner ear hair cells. Mutations in the gene encoding whirlin (WHRN; also known as USH2D and DFNB31), have been found to cause either USH2 subtype (USH2D) or autosomal recessive non-syndromic deafness type 31 (DFNB31). Whirlin is the key protein in the USH2 complex (whirlin, usherin and GPR98) which recruits other USH2 causative proteins at the periciliary membrane in photoreceptors and the ankle link of the stereocilia in hair cells. Whirlin's interaction with espin, another stereociliary protein, may be important for the architecture of the USH2 complex. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This whirlin family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F 91 matched cddid_all.tbl CDD cd06743 cd06743 467225 PDZ1_L-delphilin-like PDZ domain 1 of delphilin (L-delphilin isoform), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of delphilin (also known as glutamate receptor, ionotropic, delta 2-interacting protein 1, L-delphilin). Delphilin, a postsynaptic protein which is selectively expressed at cerebellar Purkinje cells, links the glutamate receptor delta 2 subunit (GluRdelta2) with the actin cytoskeleton and various signaling molecules. Two alternatively spliced isoforms of delphilin have been characterized: L-delphilin has two PDZ domains, PDZ1 and PDZ2, and S-delphilin has a single PDZ domain (PDZ2). These two isoforms are differently palmitoylated and may be involved in controlling GluRdelta2 signaling in Purkinje cells. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This delphilin-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 76 matched cddid_all.tbl CDD cd06744 cd06744 467226 PDZ2_L-delphilin-like PDZ domain 2 of delphilin (L-delphilin isoform), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of delphilin (also known as glutamate receptor, ionotropic, delta 2-interacting protein 1, L-delphilin). Delphilin, a postsynaptic protein which it is selectively expressed at cerebellar Purkinje cells, links the glutamate receptor delta 2 subunit (GluRdelta2) with the actin cytoskeleton and various signaling molecules. Two alternatively spliced isoforms of delphilin have been characterized: L-delphilin has two PDZ domains, PDZ1 and PDZ2, and S-delphilin has a single PDZ domain (PDZ2). These two isoforms are differently palmitoylated and may be involved in controlling GluRdelta2 signaling in Purkinje cells. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This delphilin-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F 75 matched cddid_all.tbl CDD cd06745 cd06745 467227 PDZ_SIPA1-like PDZ domain of signal-induced proliferation-associated protein 1 (SIPA1), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SIPA1, and related domains. The Rap-GTPase activating protein SIPA1 (also known as GTPase-activating protein Spa-1, p130 SPA1) is a metastasis promoter; a polymorphism in a region of the Sipa1 gene encoding the PDZ domain is associated with metastasis. The SIPA1 PDZ domain binds ribosomal RNA processing 1 homolog B (Rrp1b). SIPA1 also forms a complex with water channel aquaporin-2 (AQP2) and plays a role in trafficking of AQP2, targeted positioning of which strictly regulates body water homeostasis; the SIPA1 PDZ domain binds AQP2. Rrp1b or AQP2 binding inhibits the RapGAP activity of SIPA1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SIPA1-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta- strand F. 73 matched cddid_all.tbl CDD cd06746 cd06746 467228 PDZ_SHANK1_3-like PDZ domain of SH3 and multiple ankyrin repeat domains protein 1 (SHANK1), SHANK2, SHANK3, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SHANK1, SHANK2, SHANK3, and related domains. SHANK family proteins, SHANK1 (also known as somatostatin receptor-interacting protein, SSTR-interacting protein, SSTRIP), SHANK2 (also known as cortactin-binding protein 1, proline-rich synapse-associated protein 1), and SHANK3 (proline-rich synapse-associated protein 2) are synaptic scaffolding proteins which are highly enriched in the post-synaptic densities of excitatory synapses. They have been implicated in synaptic transmission, synapse formation, synaptic plasticity, and cytoskeletal remodeling, and are regulators of Cav1 calcium current and CREB target expression. Many protein ligands have been identified for the Shank PDZ domain, such as GKAP (also known as SAPAP), betaPIX (a guanine nucleotide exchange factor used by Rho GTPase family members Rac1 and Cdc42), alpha-latrotoxin, neuroligin, group I metabotropic glutamate receptors (mGluRs), and L-type calcium channels. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SHANK-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta- strand F. 101 matched cddid_all.tbl CDD cd06747 cd06747 467229 PDZ_MYO18-like PDZ domain of MYO18A protein, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MYO18 protein and related domains. MYO18 (also known as myosin XVIIIA, KIAA0216, MysPDZ), a member of the myosin superfamily, is involved in regulating cell protrusion and migration, and Golgi trafficking and morphology, and is required for myoblast adhesion and muscle integrity. The MYO18A/MRCK/LRAP35a complex regulates actomyosin retrograde flow in cell protrusion and migration; the PtdIns(4)P/GOLPH3/MYO18A/F-actin complex is a hub for signals that regulate Golgi trafficking function. The MYO18A PDZ domain binds p190Rho-guanine nucleotide exchange factor (p190RhoGEF), Golgin45, and leucine repeat adaptor protein 1 (Lurap1, also known as Lrap35a). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MYO18-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta- strand F. 90 matched cddid_all.tbl CDD cd06748 cd06748 467230 PDZ_CNK1_2_3-like PDZ domain of connector enhancer of kinase suppressor of ras 1 (CNK1), CNK2, CNK3, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of CNK1 (also known as connector enhancer of KSR 1 (CNKSR1), CNK homolog protein 1, connector enhancer of KSR-like), CNK2 (also known as CNKSR2, CNK homolog protein 2), and CNK3 (also known as CNKSR3, CNK homolog protein 3, CNKSR family member 3, maguin-like). CNK proteins modulate Ras-mediated signaling, acting downstream of Ras as a scaffold for the Raf/MEK/ERK kinase cascade. They also modulate signaling mediated via Rho family small GTPases, through interactions with various guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), and modulate the insulin signaling pathway through interactions with the Arf guanine nucleotide exchange factors. CNK proteins also regulate cell proliferation and migration by acting as scaffolds for the PI3K/Akt and JNK signaling cascades. CNK2 plays a role in the molecular processes that govern morphology of the postsynaptic density (PSD), and influences subcellular localization of the regulatory NCK-interacting kinase TNIK. TNIK binds a region of CNK2 including the PDZ and the DUF domain; this region also binds the kinase MINK1. CNK2 may also influence the membrane localization of MINK1. CNK3 plays a part in transepithelial sodium transport; it coordinates assembly of an epithelial sodium channel (ENaC)-regulatory complex. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This CNK1-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta- strand F. 81 matched cddid_all.tbl CDD cd06749 cd06749 467231 PDZ_densin_erbin-like PDZ domain of densin, erbin, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of densin, erbin, and related domains. Densin (also known as leucine-rich repeat-containing protein 7, LRRC7, densin-180, protein LAP1) and erbin (also known as densin-180-like protein, Erbb2-interacting protein, protein LAP2) belong to the LAP (leucine-rich repeat and PDZ domain) family of scaffolding proteins that play roles in the maintenance of cell shape and apical-basal polarity. Densin and erbin are components of the excitatory postsynaptic compartment and are regulators of dendritic morphology and postsynaptic structure. The densin PDZ domain binds CaV1.3 alpha1 subunit, delta-catenin, and MAGUIN-1. Binding partners of the erbin PDZ domain include ErbB receptor tyrosine kinase ErbB2, HTLV-1 Tax1, Cav1.3 Ca2+channels, and constituents of the cadherin:catenin cell adhesion complex, in particular delta-catenin, p0071 and ARVCF. The erbin PDZ domain binds Smad3, a transductor of the TGFbeta pathway, possibly by a novel interface of binding. Erbin and two other LAP proteins (scribble and lano) redundantly regulate epithelial polarity and apical adhesion complex. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This densin and erbin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 87 matched cddid_all.tbl CDD cd06750 cd06750 467232 PDZ_shroom2_3_4-like PDZ domain of shroom2, shroom3, shroom4, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of shroom2, shroom3, shroom4, and related domains. Shroom family proteins shroom2 (also known as apical-like protein; protein APXL), shroom3 (also known as shroom-related protein), and shroom4 (also known as second homolog of apical protein) are essential regulators of cell morphology during animal development; they regulate cell architecture by directing the subcellular distribution and activation of Rho kinase (ROCK), which results in the localized activation of non-muscle myosin. The interaction between shroom and ROCK is mediated by the shroom domain 2 (SD2). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This shroom2,3,4-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 82 matched cddid_all.tbl CDD cd06751 cd06751 467233 PDZ3_PDZD7-like PDZ domain 3 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of the Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa and can also form homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the third PDZ domain of the canonical isoform of PDZD7- isoform 1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD7-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 89 matched cddid_all.tbl CDD cd06752 cd06752 467234 PDZ_PDZD11-like PDZ domain of PDZ domain-containing protein 11, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PDZD11, and related domains. PDZD11 (also known as ATPase-interacting PDZ protein, plasma membrane calcium ATPase-interacting single-PDZ protein, PMCA-interacting single-PDZ protein, PISP) is involved in the dynamic assembly of apical junctions (AJs). It is recruited by PLEKHA7 to AJs to promote the efficient junctional recruitment and stabilization of nectins, and the efficient early phases of assembly of AJs in epithelial cells. The PDZD11 PDZ domain binds nectin-1 and nectin-3. PDZD11 also binds to a PDZ binding motif located in the C-terminal tail of the human sodium-dependent multivitamin transporter, to the cytoplasmic tail of the Menkes copper ATPase ATP7A, and to the cytoplasmic tail of all plasma membrane Ca2+-ATPase b-splice variants. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD11-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 83 matched cddid_all.tbl CDD cd06753 cd06753 467235 PDZ_PDLIM-like PDZ domain of PDZ-LIM family proteins, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of PDZ-LIM family proteins including PDLIM1-7, and related domains. PDZ-LIM family proteins (also known as Zasp PDZ domain proteins) are involved in the rearrangement of the actin cytoskeleton; they mediate association with the cytoskeleton through alpha-actinin as well as with other proteins involved in signal transduction pathways. Members of this family include PDLIM1 (also known as C-terminal LIM domain protein 1, elfin, LIM domain protein CLP-36), PDLIM2 (also known as PDZ-LIM protein mystique), PDLIM3 (also known as actinin-associated LIM protein, alpha-actinin-2-associated LIM protein, ALP), PDLIM4 (also known as LIM protein RIL, Reversion-induced LIM protein), PDLIM5 (also known as enigma homolog, ENH, enigma-like PDZ and LIM domains protein), PDLIM6 (also known as LIM domain-binding protein 3, ZASP, Cypher, Oracle), and PDLIM7 (also known as PDZ and LIM domain protein 7, LIM mineralization protein, LMP; protein enigma). PDLIM1 has been shown to negatively regulate NF-kappaB-mediated signaling in the cytoplasm. PDLIM7 negatively regulates p53 through binding murine double minute 2 (MDM2). The PDZ domains of PDZ-LIM family proteins PDLIM1, 2, 3, 5, 6, 7 have been shown to bind actin. Other PDZ-LIM family PDZ domain binding partners include thyroid receptor interacting protein-6 (PDLIM4-PDZ), the LIM domain of PDLIM4 (PDLIM4-PDZ), tropomyosin (PDLIM7-PDZ), myotilin and calsarcin 1 (PDLIM6-PDZ), and proteins from the myotilin and FATZ (calsarcin/myozenin) families (PDLIM1, 3, 4, 6 PDZ domains). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDLIM-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 79 matched cddid_all.tbl CDD cd06754 cd06754 467236 PDZ_LIMK-like PDZ domain of LIM Kinase (LIMK) family, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the LIMK protein family, and related domains. The LIMK family is composed of LIMK1 and LIMK2, which are common downstream effectors of several signalization pathways and function as signaling nodes that control cytoskeleton dynamics through the phosphorylation of cofilin family proteins. They also control microtubule dynamics. The LIMK1 PDZ domain binds tubulin and nischarin. LIMK1 also binds a carboxy-terminal motif of membrane type 1-matrix metalloproteinase (MT1-MMP, also known as MMP14) having features of a PDZ domain-binding site; MT1-MMP is a major protease involved in dissemination of carcinoma cells during cancer progression. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This LIMK-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 92 matched cddid_all.tbl CDD cd06755 cd06755 467237 PDZ_RapGEF2_RapGEF6-like PDZ domain of Rap guanine nucleotide exchange factor 2 and Rap guanine nucleotide exchange factor 6, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Rap guanine nucleotide exchange factor 2 (RapGEF2, also named RA-GEF-1, PDZ-GEF1, CNrasGEF and nRapGEP) and Rap guanine nucleotide exchange factor 6 (RapGEF6, also named RA-GEF-2 and PDZ-GEF2). RapGEF2 and RapGEF6 constitute a subfamily of guanine nucleotide exchange factors (GEFs) for RAP small GTPases that is characterized by the possession of the PDZ and Ras/Rap-associating domains. They activate Rap small GTPases, by catalyzing the release of GDP from the inactive GDP-bound forms, thereby accelerating GTP loading to yield the active GTP-bound forms. The PDZ domain of RapGEF6 (also known as PDZ-GEF2) binds junctional adhesion molecule A (JAM-A). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This RapGEF2 and RapGEF6 family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 83 matched cddid_all.tbl CDD cd06756 cd06756 467238 PDZ_ARHGAP21_23-like PDZ domain of ARHGAP21 and ARHGAP23, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ARHGAP21, ARHGAP23, and related domains. This subfamily includes the GAPs (GTPase activating proteins): ARHGAP21 (Rho GTPase-activating protein 21; also known as Rho GTPase-activating protein 10, Rho-type GTPase-activating protein 21) and ARHGAP23 (Rho GTPase-activating protein 23; also known as Rho-type GTPase-activating protein 23). GAPs deactivate Rho GTPases by accelerating GTP hydrolysis. ARHGAP21/23 interact with a planar cell polarity (PCP) protein Pk1 to regulate a lateral signaling pathway in migrating cells. The ARHGAP21 PDZ domain binds claudin-2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This ARHGAP21-23-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 109 matched cddid_all.tbl CDD cd06758 cd06758 467239 PDZ2_PDZD2-like PDZ domain 2 of PDZ domain containing 2 (PDZD2), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains, and is expressed at exceptionally high levels in the pancreas and certain cancer tissues such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 88 matched cddid_all.tbl CDD cd06759 cd06759 467240 PDZ3_PDZD2-PDZ1_hPro-IL-16-like PDZ domain 3 of PDZ domain containing 2 (PDZD2), PDZ domain 1 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family also includes the first PDZ domain (PDZ1) of human pro-interleukin-16 (isoform 1, also known as nPro-Il-16; 1332 amino-acid protein). Precursor IL-16 is cleaved to produce pro-IL-16 and mature IL-16 (derived from the C-terminal 121 AA). Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 87 matched cddid_all.tbl CDD cd06760 cd06760 467241 PDZ4_PDZD2-PDZ2_hPro-IL-16-like PDZ domain 4 of PDZ domain containing 2 (PDZD2), PDZ domain 2 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family also includes the second PDZ domain (PDZ2) of human pro-interleukin-16 (isoform 1, also known as nPro-Il-16; 1332 amino-acid protein). Precursor IL-16 is cleaved to produce pro-IL-16 and mature IL-16 (derived from the C-terminal 121 AA). Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 90 matched cddid_all.tbl CDD cd06761 cd06761 467242 PDZ5_PDZD2-like PDZ domain 5 of PDZ domain containing 2 (PDZD2), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ5 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F 85 matched cddid_all.tbl CDD cd06762 cd06762 467243 PDZ6_PDZD2-PDZ3_hPro-IL-16-like PDZ domain 6 of PDZ domain containing 2 (PDZD2), PDZ domain 3 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 6 of PDZD2, also known as KIAA0300, PIN-1, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family also includes the third PDZ domain (PDZ3) of human pro-interleukin-16 (isoform 1, also known as nPro-IL-16). Precursor IL-16 is cleaved to produce pro-IL-16 and C-terminal mature IL-16. Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ6 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 86 matched cddid_all.tbl CDD cd06763 cd06763 467244 PDZ7_PDZD2-PDZ4_hPro-IL-16-like PDZ domain 7 of PDZ domain containing 2 (PDZD2), PDZ domain 4 of human pro-interleukin-16 (isoform 1, 1332 AA), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 7 of PDZD2, also known as KIAA0300, PIN-1, PAPIN, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues, such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. This family include the PDZ domain of the secreted mature form of human interleukin-16 (IL-16); this is the fourth PDZ domain (PDZ4) of human pro-interleukin-16 (isoform 1, also known as nPro-Il-16). Precursor IL-16 is cleaved to produce pro-IL-16 and C-terminal mature IL-16. Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ7 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 86 matched cddid_all.tbl CDD cd06764 cd06764 467245 PDZ1_DLG5-like PDZ domain 1 of Discs Large 5 (Dlg5) and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Drosophila and mammalian Dlg5, and related domains. Dlg5 is a scaffold protein with multiple conserved functions that are independent of each other in regulating growth, cell polarity, and cell adhesion. It has a coiled-coil domain, 4 PDZ domains and a MAGUK domain (an SH3 domain next to a non-catalytically active guanylate kinase domain). Deregulation of Dlg5 has been implicated in the malignancy of several cancer types. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg5-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 95 matched cddid_all.tbl CDD cd06765 cd06765 467246 PDZ2_DLG5-like PDZ domain 2 of Discs Large 5 (Dlg5) and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Drosophila and mammalian Dlg5, and related domains. Dlg5 is a scaffold protein with multiple conserved functions that are independent of each other in regulating growth, cell polarity, and cell adhesion. It has a coiled-coil domain, 4 PDZ domains and a MAGUK domain (an SH3 domain next to a non-catalytically active guanylate kinase domain). Deregulation of Dlg5 has been implicated in the malignancy of several cancer types. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg5-like family PSZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 77 matched cddid_all.tbl CDD cd06766 cd06766 467247 PDZ4_DLG5-like PDZ domain 4 of Discs Large 5 (Dlg5) and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of Drosophila and mammalian Dlg5, and related domains. Dlg5 is a scaffold protein with multiple conserved functions that are independent of each other in regulating growth, cell polarity, and cell adhesion. It has a coiled-coil domain, 4 PDZ domains and a MAGUK domain (an SH3 domain next to a non-catalytically active guanylate kinase domain). Deregulation of Dlg5 has been implicated in the malignancy of several cancer types. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg5-like family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 81 matched cddid_all.tbl CDD cd06767 cd06767 467248 PDZ3_DLG5-like PDZ domain 3 of Discs Large 5 (Dlg5) and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of Drosophila and mammalian Dlg5, and related domains. Dlg5 is a scaffold protein with multiple conserved functions that are independent of each other in regulating growth, cell polarity, and cell adhesion. It has a coiled-coil domain, 4 PDZ domains and a MAGUK domain (an SH3 domain next to a non-catalytically active guanylate kinase domain). Deregulation of Dlg5 has been implicated in the malignancy of several cancer types. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg5-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 82 matched cddid_all.tbl CDD cd06768 cd06768 467249 PDZ_NHERF-like PDZ domains of the Na+/H+ exchange regulatory cofactor (NHERF) family (NHERF1-4), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the Na+/H+ exchange regulatory cofactor (NHERF) family of multi-PDZ-domain-containing scaffolding proteins (NHERF1-4), and related domains. The NHERF family includes NHERF1 (also known as EBP50), NHERF2 (also known as E3KARP; TKA-1; SIP-1), NHERF3 (also known as CAP70; CLAMP; Napi-Cap-1; PDZD1) and NHERF4 (also known as IKEPP; PDZK2; Napi-Cap-2). NHERF1 and NHERF2 have tandem PDZ domains (PDZ1-2); NHERF3 and NHERF4 have four PDZ domains (PDZ1-4). NHERFs are involved in the regulation of multiple receptors or transporters, such as type II sodium-phosphate cotransporter (Npt2a), purinergic P2Y1 receptor P2Y1R, the beta2-adrenergic receptor (beta2-AR), parathyroid hormone receptor type 1 (PTHR), the lysophosphatidic acid receptors (LPARs), sodium-hydrogen exchanger 3 (NHE3), and cystic fibrosis transmembrane conductance regulator (CFTR). NHERF-PDZ1 domain interaction partners include Npt2a, purinergic P2Y1 receptor, beta2-AR, CFTR, PTHR, NH3, G-protein-coupled receptor kinase 6 (GRK6A), platelet-derived growth factor receptor (PDGFR), B1 subunit of the H+ATPase, cholesterol, receptor for activated C-kinase RACK1, aquaporin 9, among others. The NHERF PDZ2 domain interacts with fewer proteins: NHERF1 PDZ2 binds Npt2a, PTHR, beta-catenin, aquaporin 9, and RACK1; NHERF2 PDZ2 binds LPA2, P2Y1R, and NHE3, cGMP-dependent protein kinase type II (cGKII). NHERF4 PDZ1 and PDZ4 bind the epithelial Ca(2+) channels TRPV5 and TRPV6. NHERF2/NHERF3 heterodimerization is mediated by PDZ domains of NHERF2 and the C-terminal PDZ domain recognition motif of NHERF3. NHERF4 regulates several transporters mediating influx of xenobiotics and nutrients in the small intestine. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This NHERF-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 80 matched cddid_all.tbl CDD cd06769 cd06769 467250 PDZ_FRMPD1_3_4-like PDZ domain of FERM and PDZ domain-containing protein 1 (FRMPD1), FRMPD3, FRMPD4, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of FRMPD1, FRMPD3, FRMPD4, and related domains. FRMPD1 (also known as FERM domain-containing protein 2, FRMD2), inhibits the malignant phenotype of lung cancer by activating the Hippo pathway via interaction with WWC3; the FRMPD1 PDZ domain binds WWC3. FRMPD3 is a target gene of the neuron-specific transcription factor NPAS4 that is involved in synaptic plasticity. FRMPD4 (also known as PDZ domain-containing protein 10, PDZD10, PDZK10, PSD-95-interacting regulator of spine morphogenesis, and Preso) regulates dendritic spine morphogenesis, and mGluR1/5 signaling; the FRMPD4 PDZ domain binds PAK-interacting exchange factor-beta (betaPix). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This FRMPD1,3,4-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 75 matched cddid_all.tbl CDD cd06775 cd06775 467619 cpPDZ_MBTPS2-like circularly permuted PDZ domain of membrane-bound transcription factor site-2 protease (MBTPS2, also known as S2P) and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MBTPS2, also known as sterol regulatory element-binding protein (SREBP) Site-2 protease (S2P), and related domains. MBTPS2 is a zinc metalloprotease (MEROPS family M50A). In the Golgi, it catalyzes the second step in the proteolytic activation of sterol regulatory element-binding proteins (SREBPs), releasing the transcriptionally active N-terminal domain of SREBP, which then enters the nucleus and activates genes encoding the low density lipoprotein (LDL) receptor and enzymes for cholesterol and fatty acid biosynthesis. MBTPS2 also mediates the second step in the proteolytic activation of the cyclic AMP-dependent transcription factor ATF6. ATF6 is a membrane-bound transcription factor that activates genes in the endoplasmic reticulum (ER) stress response. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. One permutation places beta-strand A on the C-terminus, another permutation places both beta-strands A and B on the C-terminus. 107 matched cddid_all.tbl CDD cd06777 cd06777 467620 cpPDZ_DegS circularly permuted PDZ domain of DegS serine endoprotease. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Escherichia coli DegS and related domains. DegS (also known as Site-1 protease DegS, S1P protease DegS, and Site-1-type intramembrane protease) participates in the activation of the sigma(E) extracytoplasmic stress response. Initially, there is an accumulation of misfolded membrane proteins (OMPs) in the periplasm which bind by their YXF motif to the DegS PDZ domain, activating DegS-catalyzed cleavage of the RseA periplasmic domain and making RseA a substrate for cleavage by another membrane protease RseP. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This DegS family PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus. 93 matched cddid_all.tbl CDD cd06779 cd06779 467621 cpPDZ_Deg_HtrA-like permuted PDZ domain of Deg/high-temperature requirement factor A (HtrA) family of housekeeping serine proteases and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Deg/HtrA-type serine proteases that participate in folding and degradation of aberrant proteins, and in processing and maturation of native proteins. Typically, these proteases have an N-terminal serine protease domain and at least one C-terminal PDZ domain that recognizes substrates, and in some cases activates the protease function. An exception is yeast Nma11p which has two protease domains and four PDZ domains; its N-terminal half is comprised of a protease domain, followed by two PDZ domains, and its C-terminal half has a similar domain arrangement. HtrA-type proteases include the human HtrA1-4 and MBTPS2, tricorn protease, DegS, DegP and C-terminal processing peptidase, cyanobacterial serine proteases Hhoa, HhoB, and HtrA, and yeast Nma11p. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-termini of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This Deg/HtrA family PDZ domain is a circularly permuted PDZ domain which places beta-strand A at the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus. 91 matched cddid_all.tbl CDD cd06781 cd06781 467622 cpPDZ_BsHtra-like circularly permuted PDZ domain of Bacillus subtilis HtrA-type serine proteases HtrA, HtrB, and YyxA and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Bacillus subtilis HtrA/YkdA, HtrB/YvtA and YyxA/YycK, and related domains. HtrA-type serine proteases participate in folding and degradation of aberrant proteins, and in processing and maturation of native proteins. HtrA, HtrB, and YyxA have a single transmembrane domain at the N-terminus and a PDZ domain at the C-terminus. Expression of htrA and htrB genes is induced both by heat shock and by secretion stress (by a common) mechanism; yyxA is neither heat shock nor secretion stress inducible. HtrA and HtrB may have overlapping cellular functions; YyxA may have a cellular function distinct from the other two proteases or have the same function but under different conditions. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This BsHtrA-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus. 98 matched cddid_all.tbl CDD cd06782 cd06782 467623 cpPDZ_CPP-like circularly permuted PDZ domain of C-terminal processing peptidase (CPP), a serine protease, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of CPP (also known as tail-specific protease, PRC protein, Protease Re, and Photosystem II D1 protein processing peptidase), and related domains. CPP belongs to the peptidase S41A family. It cleaves a C-terminal 11 residue peptide from the precursor form of penicillin-binding protein 3, and may have a role in protecting bacterium from thermal and osmotic stresses. In the plant chloroplast, the enzyme removes the C-terminal extension of the D1 polypeptide of photosystem II. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This CPP-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus. 88 matched cddid_all.tbl CDD cd06785 cd06785 467624 cpPDZ_HtrA-like circularly permuted PDZ domain of high-temperature requirement factor A (HtrA) family serine proteases and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of HtrA family serine proteases including human HtrA1, HtrA2 (mitochondrial), HtrA3, and HtrA4, and related domains. These proteases are key enzymes associated with pregnancy. Their diverse biological functions include cell growth proliferation, migration and apoptosis. They are also implicated in disorders including Alzheimer's, Parkinson's, arthritis and cancer. HtrA1 (also known as high-temperature requirement A serine peptidase 1, L56, and serine protease 11) substrates include extracellular matrix proteins, proteoglycans, and insulin-like growth factor (IGF)-binding proteins. HtrA1 also inhibits signaling by members of the transforming growth factor beta (TGF-beta) family. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This HtrA-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus. 98 matched cddid_all.tbl CDD cd06786 cd06786 467625 cpPDZ1_ScNma111-like circularly permuted first PDZ domain (PDZ1) of Saccharomyces cerevisiae pro-apoptotic serine protease Nma111p and related domains. First PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the HtrA-type protease Saccharomyces cerevisiae Nma111p (also known as Ynm3p), and related domains. Nma111p is a nuclear serine protease which mediates apoptosis through proteolysis of the apoptotic inhibitor Bir1p. Nma111p is composed of two protease domains and four PDZ domains; its N-terminal half is comprised of a protease domain, followed by two PDZ domains, and its C-terminal half has a similar domain arrangement. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This ScNma111-like PDZ1 domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation places both beta-strands A and B on the C-terminus. 89 matched cddid_all.tbl CDD cd06787 cd06787 467626 cpPDZ_AthDEGP7-like circularly permuted PDZ domain of Arabidopsis thaliana putative protease Do-like 7 (DEGP7) and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Arabidopsis thaliana putative protease DEGP7 (also known as DegP protease 7, DEG7), and related domains. DEGP7 belongs to the HtrA family of housekeeping proteases. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This AtDEGP7-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus. 92 matched cddid_all.tbl CDD cd06789 cd06789 467251 PDZ_AFDN-like PDZ domain of afadin (AFDN), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of afadin (AFDN, also known as ALL1-fused gene from chromosome 6 protein (AF6) and MLLT4), and related domains. AFDN belongs to the adhesion system, probably together with the E-cadherin-catenin system, that plays a role in the organization of homotypic, interneuronal, and heterotypic cell-cell adherens junctions. The AFDN PDZ domain interaction partners include poliovirus receptor-related protein PRR2/nectin, the junctional adhesion molecule (JAM), the breakpoint-cluster-region protein (BCR), connexin36 (Cx36), and a subset of Eph-related receptor tyrosine kinases; it can also bind low molecular weight ligands, in competition with a natural peptide ligand. Other AFDN-binding proteins have been identified. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This AFDN family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 89 matched cddid_all.tbl CDD cd06790 cd06790 467252 PDZ_neurabin-like PDZ domain of neurabin-1 and neurabin-2, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of neurabin-1 (also known as protein phosphatase 1 regulatory subunit 9A) and neurabin-2 (also known as spinophilin, and protein phosphatase 1 regulatory subunit 9B), and related domains. Neurabin-1 and neurabin-2 are neuronal scaffolding proteins that play important roles in the regulation of synaptic transmission through their ability to interact with and target protein phosphatase 1 (PP1) to dendritic spines where PP1 dephosphorylates and inactivates glutamate receptors. Neurabin-2 interacts with multiple other synaptic proteins, including synaptic signaling and scaffolding proteins (e.g., GluN1 and SAPAP3) and cytoskeletal proteins (e.g., neurofilament medium polypeptide, NF-M). Neurabin-1 and neurabin-2 also binds F-actin. Other binding partners of neurabin-1 include adenosine A1 receptor (A1R), SAD-1 kinase and 70 kDa ribosomal protein S6 kinase (p70-S6K). This PDZ domain is immediately C-terminal to the PP1 binding domain. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This neurabin-like PDZ domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 90 matched cddid_all.tbl CDD cd06791 cd06791 467253 PDZ3_MUPP1-like PDZ domain 3 of multi-PDZ-domain protein 1 (MUPP1) and PATJ (protein-associated tight junction) and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of MUPP1 and PATJ, and related domains. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, 9, and 13; consequently, MUPP1 PDZ7 and 8 align with PATJ PDZ6 and 7; and MUPP1 PDZ domains 10-12 align with PATJ PDZ domains 8-10. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 89 matched cddid_all.tbl CDD cd06792 cd06792 467254 PDZ2-PTPN13_FRMPD2-like PDZ domain 2 of tyrosine kinase PTPN13, FERM and PDZ domain-containing protein 2 (FRMPD2), and similar domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of human PTPN13, and related domains. PTPN13, also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1), negatively regulates FAS-mediated apoptosis and NGFR-mediated pro-apoptotic signaling, and may also regulate phosphoinositide 3-kinase (PI3K) signaling. It contains 5 PDZ domains; interaction partners of its second PDZ domain (PDZ2) include the Fas receptor (TNFRSF6) and thyroid receptor-interacting protein 6 (TRIP6). The second PDZ (PDZ2) domain, but not PDZ1 or PDZ3, of FRMPD2 binds to GluN2A and GluN2B, two subunits of N-methyl-d-aspartic acid (NMDA) receptors. Other binding partners of the FRMPDZ2 PDZ2 domain include NOD2, and catenin family members, delta catenin (CTNND2), armadillo repeat gene deleted in velo-cardio-facial syndrome (ARVCF) and p0071 (also known as plakophilin 4; PKP4). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 87 matched cddid_all.tbl CDD cd06793 cd06793 467255 PDZ2_APBA1_3-like PDZ domain 2 of amyloid-beta A4 precursor protein-binding family A member 1 (APBA1), APBA2, APBA3, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of APBA1, APBA2, APBA3, and related domains. The APBA/X11/Mint protein family includes three members: neuron specific APBA1 (also known as X11alpha and Mint1) and APBA2 (also known as X11beta and Mint2), and the ubiquitously expressed APBA3 (also known as X12gamma and Mint3). They are involved in regulating neuronal signaling, trafficking, and plasticity. They contain two PDZ domains (PDZ1 and PDZ2) which bind a variety of proteins: Arf GTPases (APBA1 and APBA2 PDZ2) and neurexin (APBA1 and APBA2 PDZ1 and 2) which are involved in vesicle docking and exocytosis; alpha1B subunit of N-type Ca2+ channel (APBA1 PDZ1) that is involved in ion channels; KIF17 (APBA1 PDZ1) that is involved in transport and traffic; and Alzheimer's disease related proteins, APP (APBA3 PDZ2), CCS (APBA1 PDZ2), NF-kappa-B/p65 (APBA2 PDZ2), presenilin-1 (APBA1 and APBA2 PDZ1 and PDZ2). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This APBA1,3-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 78 matched cddid_all.tbl CDD cd06794 cd06794 467256 PDZ2_syntenin-like PDZ domain 2 of syntenin-1, syntenin-2, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of syntenin-1, syntenin-2, and related domains. Syntenins are implicated in various cellular processes such as trafficking, signaling, and cancer metastasis. They bind to signaling and adhesion molecules, such as syndecans, neurexins, ephrin B, and phospholipid PIP2. Through its tandem PDZ domains (PDZ1 and PDZ2) syntenin links syndecans to other cell surface receptors and kinases, such as E-cadherin and ephrin-B, establishing signaling crosstalk. During syndecan binding, syntenin PDZ2 serves as a high-affinity domain, and PDZ1, also necessary for binding, acts as a complementary, low-affinity domain; this is also the case for syntenin binding to proto-oncogene c-Src. The syntenin PDZ domain-PIP2 interaction controls Arf6-mediated syndecan recycling through endosomal compartments; both PDZ1 and PDZ2 interact with PIP2. Different binding partners and downstream regulators of syntenin1 PDZ domains, such as to proto-oncogene c-Src, mitogen-activated protein kinase (MAPK), and focal adhesion kinase (FAK), have been identified that promote the progression and invasion of a variety of cancers, such as melanoma, glioblastoma multiforme, and breast cancer. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This syntenin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta- strand F. 78 matched cddid_all.tbl CDD cd06795 cd06795 467257 PDZ3_Dlg1-2-4-like PDZ domain 3 of human discs large homolog 1 (Dlg1), Dlg2, and Dlg4, Drosophila disc large (Dlg), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of Drosophila Dlg1, human Dlg1, 2, and 4 and related domains. Dlg1 (also known as synapse-associated protein Dlg197; SAP-97), Dlg2 (also known as channel-associated protein of synapse-110; postsynaptic density protein 93, PSD-93), Dlg4 (also known as postsynaptic density protein 95, PSD-95; synapse-associated protein 90, SAP-90) each have 3 PDZ domains and belong to the membrane-associated guanylate kinase family. Dlg1 regulates antigen receptor signaling and cell polarity in lymphocytes, B-cell proliferation and antibody production, and TGFalpha bioavailability; its PDZ3 domain binds pro-TGFalpha, and its PDZ2 domain binds the TACE metalloprotease responsible for cleaving pro-TGFalpha to a soluble form. Dlg2 is involved in N-methyl-D-aspartate (NMDA) receptor signaling, regulating surface expression of NMDA receptors in dorsal horn neurons of the spinal cord; it interacts with NMDA receptor subunits and with Shaker-type K+ channel subunits to cluster into a channel complex. The Dlg4 PDZ1 domain binds NMDA receptors, and its PDZ2 domain binds neuronal nitric oxide synthase (nNOS), forming a complex in neurons. The Drosophila Scribble complex (Scribble, Dlg, and lethal giant larvae) plays a role in apico-basal cell polarity, and in other forms of polarity, including regulation of the actin cytoskeleton, cell signaling and vesicular trafficking, and in tumor development; postsynaptic targeting of Drosophila DLG requires interactions mediated by the first two PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Dlg-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 91 matched cddid_all.tbl CDD cd06796 cd06796 467258 PDZ_Lin-7-like PDZ domain of protein Lin-7 and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Lin-7 (also known as LIN-7 or LIN7), and related domains. Lin-7 targets and organize protein complexes to epithelial and synaptic plasma membranes. There are three mammalian Lin-7 homologs: Lin-7A (protein lin-7 homolog A, also known as mammalian lin-seven protein 1 (MALS-1), vertebrate lin-7 homolog 1 (Veli-1), tax interaction protein 33); Lin-7B (also known as MALS-2, Veli-2); and Lin-7C (also known as MALS-3, Veli-3). Lin-7 is involved in localization of the Let-23 growth factor receptor to the basolateral membrane of epithelial cells, in tight junction localization of insulin receptor substrate p53 (IRSp53), in retaining gamma-aminobutyric (GABA) transporter (BGT-1) at the basolateral surface of epithelial cells, and in regulating recruitment of neurotransmitter receptors to the postsynaptic density (PSD). The Lin7 PDZ domain binds Let-23, BGT and beta-catenin, and NMDA (N-methyl-D-aspartate) receptor NR2B. Lin-7 also binds to the PDZ binding motif located in the C-terminal tail of Rhotekin, an effector protein for small GTPase Rho. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Lin-7-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 86 matched cddid_all.tbl CDD cd06798 cd06798 467259 PDZ_MPP5-like PDZ domain of membrane palmitoylated protein 5 (MPP5), Drosophila Stardust, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MPP5, Drosophila Stardust, and related domains. MPP5 (also known as MAGUK p55 subfamily member 1, protein associated with Lin-7 1 or PALS1) and Drosophila Stardust are membrane-associated guanylate kinase (MAGUK)-like proteins that serve as signaling and scaffolding proteins, linking different proteins critical to the formation and maintenance of tight junctions (TJ) and apical-basal polarity. Apical-basal polarity determinants cluster in complexes; in particular, the Crumbs complex (Crb, MPP5, and PATJ) and the PAR/aPKC-complex (PAR-3, PAR-6, aPKC) determine the apical plasma membrane domain. Within the Crumbs complex, Crb is stabilized in the plasma membrane by MPP5, which in turn recruits PATJ and Lin-7 to the complex. MPP5 also links the Crumbs complex with the PAR/aPKC-complex. The Drosophila homolog of the Crumbs complex is the (CRB)-Stardust (Sdt)-Discs Lost (Dlt) complex. MPP5 also acts as an interaction partner for SARS-CoV envelope protein E, which results in delayed formation of TJs and dysregulation of cell polarity. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MPP5-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 79 matched cddid_all.tbl CDD cd06799 cd06799 467260 PDZ_MPP3-MPP4-MPP7-like PDZ domain of membrane palmitoylated proteins 3 (MPP3), MPP4, and MPP7, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MPP3, MPP4, and MPP7, and related domains. MPP3 (also known as MAGUK p55 subfamily member 3, erythrocyte membrane protein p55, or EMP55), MPP4 (also known as MAGUK p55 subfamily member 4 or Discs large homolog 6), and MPP7 (also known as MAGUK p55 subfamily member 7) are membrane-associated guanylate kinase (MAGUK)-like proteins. MPP3 is part of a cell adhesion protein complex including tumor suppressor CADM1 and actin-binding protein 4.1B. Participation in the Crumbs cell polarity complex has also been demonstrated for MPP7 in epithelial cells, and for MPP3 and MPP4 in the retina. MPP4 is needed for proper localization of plasma membrane calcium ATPases and maintenance of calcium homeostasis at the rod photoreceptor synaptic terminals. Binding partners of the MPP3 PDZ domain include nectin-3, serotonin 5-hydroxytryptamine, 5-HT(2C) receptor, and a cell adhesion protein, TSLC1 (tumor suppressor in lung cancer 1); fragments of MPP4 having the PDZ domain bind CRB (PDZ-SH3-GUK) and GABA transporter GAT1 (PDZ-SH3). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MPP1-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 81 matched cddid_all.tbl CDD cd06800 cd06800 467261 PDZ_GOPC-like PDZ domain of Golgi-associated PDZ and coiled-coil motif-containing protein (GOPC), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of GOPC and related domains. GOPC, also known as PIST (PDZ domain protein interacting specifically with TC10), FIG (fused in glioblastoma), and CAL (CFTR-associated ligand), regulates the trafficking of a wide array of proteins, including small GTPases, receptors, and cell surface molecules such as cadherin 23 and CFTR. It may regulate CFTR chloride currents and acid-sensing ASIC3 currents by modulating cell surface expression of both channels, and may play a role in autophagy. Interaction partners of the GOPC PDZ domains include: FZD5, FZD8, ASIC3, CFTR, MUC3, ARFRP1, Ggamma13, neuroligin, and Stargazin. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GOPC-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 83 matched cddid_all.tbl CDD cd06801 cd06801 467262 PDZ_syntrophin-like PDZ domain of syntrophins, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of syntrophins (including alpha-1-syntrophin, beta-1-syntrophin, beta-2-syntrophin, gamma-1-syntrophin, and gamma-2-syntrophin), and related domains. Syntrophins play a role in recruiting various signaling molecules into signaling complexes and help provide appropriate spatiotemporal regulation of signaling pathways. They function in cytoskeletal organization and maintenance; as components of the dystrophin-glycoprotein complex (DGC), they help maintain structural integrity of skeletal muscle fibers. They link voltage-gated sodium channels to the actin cytoskeleton and the extracellular matrix, and control the localization and activity of the actin reorganizing proteins such as PI3K, PI(3,4)P2 and TAPP1. Through association with various cytoskeletal proteins within the cells, they are involved in processes such as regulation of focal adhesions, myogenesis, calcium homeostasis, and cell migration. They also have roles in synapse formation and in the organization of utrophin, acetylcholine receptor, and acetylcholinesterase at the neuromuscular synapse. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This syntrophin-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 83 matched cddid_all.tbl CDD cd06808 cd06808 143484 PLPDE_III Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes. The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these proteins may possess only limited D- to L-alanine racemase activity or non-specific racemase activity. 211 matched cddid_all.tbl CDD cd06810 cd06810 143485 PLPDE_III_ODC_DapDC_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Ornithine and Diaminopimelate Decarboxylases, and Related Enzymes. This family includes eukaryotic ornithine decarboxylase (ODC, EC 4.1.1.17), diaminopimelate decarboxylase (DapDC, EC 4.1.1.20), plant and prokaryotic biosynthetic arginine decarboxylase (ADC, EC 4.1.1.19), carboxynorspermidine decarboxylase (CANSDC), and ODC-like enzymes from diverse bacterial species. These proteins are fold type III PLP-dependent enzymes that catalyze essential steps in the biosynthesis of polyamine and lysine. ODC and ADC participate in alternative pathways of the biosynthesis of putrescine, which is the precursor of aliphatic polyamines in many organisms. ODC catalyzes the direct synthesis of putrescine from L-ornithine, while ADC converts L-arginine to agmatine, which is hydrolysed to putrescine by agmatinase in a pathway that exists only in plants and bacteria. DapDC converts meso-2,6-diaminoheptanedioate to L-lysine, which is the final step of lysine biosynthesis. CANSDC catalyzes the decarboxylation of carboxynorspermidine, which is the last step in the synthesis of norspermidine. The PLP-dependent decarboxylases in this family contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Prokaryotic ornithine, lysine and biodegradative arginine decarboxylases are fold type I PLP-dependent enzymes and are not included in this family. 368 matched cddid_all.tbl CDD cd06811 cd06811 143486 PLPDE_III_yhfX_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX. This subfamily is composed of the uncharacterized protein yhfX from Escherichia coli K-12 and similar bacterial proteins. These proteins are homologous to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes. 382 matched cddid_all.tbl CDD cd06812 cd06812 143487 PLPDE_III_DSD_D-TA_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 1. This subfamily is composed of uncharacterized bacterial proteins with similarity to eukaryotic D-serine dehydratases (DSD) and D-threonine aldolases (D-TA). DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. D-TA reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. DSD and D-TA are fold type III PLP-dependent enzymes, similar to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on their similarity to AR, it is possible members of this family also form dimers in solution. 374 matched cddid_all.tbl CDD cd06813 cd06813 143488 PLPDE_III_DSD_D-TA_like_2 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 2. This subfamily is composed of uncharacterized bacterial proteins with similarity to eukaryotic D-serine dehydratases (DSD) and D-threonine aldolases (D-TA). DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. D-TA reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. DSD and D-TA are fold type III PLP-dependent enzymes, similar to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on their similarity to AR, it is possible members of this family also form dimers in solution. 388 matched cddid_all.tbl CDD cd06814 cd06814 143489 PLPDE_III_DSD_D-TA_like_3 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 3. This subfamily is composed of uncharacterized bacterial proteins with similarity to eukaryotic D-serine dehydratases (DSD) and D-threonine aldolases (D-TA). DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. D-TA reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. DSD and D-TA are fold type III PLP-dependent enzymes, similar to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on their similarity to AR, it is possible members of this family also form dimers in solution. 379 matched cddid_all.tbl CDD cd06815 cd06815 143490 PLPDE_III_AR_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1. This subfamily is composed of uncharacterized bacterial proteins with similarity to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes. 353 matched cddid_all.tbl CDD cd06817 cd06817 143491 PLPDE_III_DSD Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Eukaryotic D-Serine Dehydratase. This subfamily is composed of chicken D-serine dehydratase (DSD, EC 4.3.1.18) and similar eukaryotic proteins. Chicken DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. It is a fold type III PLP-dependent enzyme with similarity to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as dimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Experimental data suggest that chicken DSD also exists as dimers. Sequence comparison and biochemical experiments show that chicken DSD is distinct from the ubiquitous bacterial DSDs coded by dsdA gene, mammalian L-serine dehydratases (LSD) and mammalian serine racemase (SerRac), which are fold type II PLP-dependent enzymes. 389 matched cddid_all.tbl CDD cd06818 cd06818 143492 PLPDE_III_cryptic_DSD Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bacterial Cryptic D-Serine Dehydratase. This subfamily is composed of Burkholderia cepacia cryptic D-serine dehydratase (cryptic DSD), which is also called D-serine deaminase, and similar bacterial proteins. Members of this subfamily are fold type III PLP-dependent enzymes with similarity to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as dimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on similarity, it is possible cryptic DSDs may also form dimers. Cryptic DSDs are distinct from the ubiquitous bacterial DSDs coded by the dsdA gene, mammalian L-serine dehydratases (LSD) and mammalian serine racemase (SerRac), which are fold type II PLP-dependent enzymes. At present, the enzymatic and biochemical properties of cryptic DSDs are still poorly understood. Typically, DSDs catalyze the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. 382 matched cddid_all.tbl CDD cd06819 cd06819 143493 PLPDE_III_LS_D-TA Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Low Specificity D-Threonine Aldolase. Low specificity D-threonine aldolase (Low specificity D-TA, EC 4.3.1.18), encoded by dtaAS gene from Arthrobacter sp. strain DK-38, is the prototype of this subfamily. Low specificity D-TAs are fold type III PLP-dependent enzymes that catalyze the interconversion between D-threonine/D-allo-threonine and glycine plus acetaldehyde. Both PLP and divalent cations (eg. Mn2+) are required for catalytic activity. Members of this subfamily show similarity to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on its similarity to AR, it is possible that low specificity D-TAs also form dimers in solution. Experimental data show that the monomeric form of low specificity D-TAs exhibit full catalytic activity. 358 matched cddid_all.tbl CDD cd06820 cd06820 143494 PLPDE_III_LS_D-TA_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Low Specificity D-Threonine Aldolase-like. This subfamily is composed of uncharacterized bacterial proteins with similarity to low specificity D-threonine aldolase (D-TA), which is a fold type III PLP-dependent enzyme that catalyzes the interconversion between D-threonine/D-allo-threonine and glycine plus acetaldehyde. Both PLP and divalent cations (eg. Mn2+) are required for catalytic activity. Low specificity D-TAs show similarity to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on its similarity to AR, it is possible that low specificity D-TAs also form dimers in solution. Experimental data show that the monomeric form of low specificity D-TAs exhibit full catalytic activity. 353 matched cddid_all.tbl CDD cd06821 cd06821 143495 PLPDE_III_D-TA Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme D-Threonine Aldolase. D-threonine aldolase (D-TA, EC 4.3.1.18) reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. Its activity is present in several genera of bacteria but not in fungi. It requires PLP and a divalent cation such as Co2+, Ni2+, Mn2+, or Mg2+ as cofactors for catalytic activity and thermal stability. Members of this subfamily show similarity to bacterial alanine racemase (AR), a fold type III PLP-dependent enzyme which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on its similarity to AR, it is possible that low specificity D-TAs also form dimers in solution. Experimental data show that the monomeric form of low specificity D-TAs exhibit full catalytic activity. 361 matched cddid_all.tbl CDD cd06822 cd06822 143496 PLPDE_III_YBL036c_euk Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Eukaryotic YBL036c-like proteins. This subfamily contains mostly uncharacterized eukaryotic proteins with similarity to the yeast hypothetical protein YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. YBL036c is a single domain monomeric protein with a typical TIM barrel fold. It binds the PLP cofactor and has been shown to exhibit amino acid racemase activity. The YBL036c structure is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. The lack of a second domain in YBL036c may explain limited D- to L-alanine racemase or non-specific racemase activity. Some members of this subfamily are also referred to as PROSC (Proline synthetase co-transcribed bacterial homolog). 227 matched cddid_all.tbl CDD cd06824 cd06824 143497 PLPDE_III_Yggs_like Pyridoxal 5-phosphate (PLP)-binding TIM barrel domain of Type III PLP-Dependent Enzymes, Yggs-like proteins. This subfamily contains mainly uncharacterized proteobacterial proteins with similarity to the hypothetical Escherichia coli protein YggS, a homolog of yeast YBL036c, which is homologous to a Pseudomonas aeruginosa gene that is co-transcribed with a known proline biosynthetic gene. Like yeast YBL036c, Yggs is a single domain monomeric protein with a typical TIM-barrel fold. Its structure, which shows a covalently-bound PLP cofactor, is similar to the N-terminal domain of the fold type III PLP-dependent enzymes, bacterial alanine racemase and eukaryotic ornithine decarboxylase, which are two-domain dimeric proteins. YggS has not been characterized extensively and its biological function is still unkonwn. 224 matched cddid_all.tbl CDD cd06825 cd06825 143498 PLPDE_III_VanT Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, VanT and similar proteins. This subfamily is composed of Enterococcus gallinarum VanT and similar proteins. VanT is a membrane-bound serine racemase (EC 5.1.1.18) that is essential for vancomycin resistance in Enterococcus gallinarum. It converts L-serine into its D-enantiomer (D-serine) for peptidoglycan synthesis. The C-terminal region of this protein contains a PLP-binding TIM-barrel domain followed by beta-sandwich domain, which is homologous to the fold type III PLP-dependent enzyme, bacterial alanine racemase (AR). AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. On the basis of this similarity, it has been suggested that dimer formation of VanT is required for its catalytic activity, and that it catalyzes the racemization of serine in a mechanistically similar manner to that of alanine by bacterial AR. Some biochemical evidence indicates that VanT also exhibits alanine racemase activity and plays a role in the racemization of L-alanine. VanT contains a unique N-terminal transmembrane domain, which may function as an L-serine transporter. VanT serine racemases are not related to eukaryotic serine racemases, which are fold type II PLP-dependent enzymes. 368 matched cddid_all.tbl CDD cd06826 cd06826 143499 PLPDE_III_AR2 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme, Alanine Racemase 2. This subfamily is composed of bacterial alanine racemases (EC 5.1.1.1) with similarity to Yersinia pestis and Vibrio cholerae alanine racemase (AR) 2. ARs catalyze the interconversion between L- and D-alanine, an essential component of the peptidoglycan layer of bacterial cell walls. These proteins are similar to other bacterial ARs and are fold type III PLP-dependent enzymes containing contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity. 365 matched cddid_all.tbl CDD cd06827 cd06827 143500 PLPDE_III_AR_proteobact Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Proteobacterial Alanine Racemases. This subfamily is composed mainly of proteobacterial alanine racemases (EC 5.1.1.1), fold type III PLP-dependent enzymes that catalyze the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. hese proteins are similar to other bacterial ARs and are fold type III PLP-dependent enzymes containing contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity. 354 matched cddid_all.tbl CDD cd06828 cd06828 143501 PLPDE_III_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Diaminopimelate Decarboxylase. Diaminopimelate decarboxylase (DapDC, EC 4.1.1.20) participates in the last step of lysine biosynthesis. It converts meso-2,6-diaminoheptanedioate to L-lysine. It is a fold type III PLP-dependent enzyme that contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. DapDC exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Homodimer formation and the presence of the PLP cofactor are required for catalytic activity. 373 matched cddid_all.tbl CDD cd06829 cd06829 143502 PLPDE_III_CANSDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Carboxynorspermidine Decarboxylase. Carboxynorspermidine decarboxylase (CANSDC) catalyzes the decarboxylation of carboxynorspermidine, the last step in the biosynthesis of norspermidine. It is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC), which are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. Based on this similarity, CANSDC may require homodimer formation and the presence of the PLP cofactor for its catalytic activity. 346 matched cddid_all.tbl CDD cd06830 cd06830 143503 PLPDE_III_ADC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Arginine Decarboxylase. This subfamily includes plants and biosynthetic prokaryotic arginine decarboxylases (ADC, EC 4.1.1.19). ADC is involved in the biosynthesis of putrescine, which is the precursor of aliphatic polyamines in many organisms. It catalyzes the decarboxylation of L-arginine to agmatine, which is then hydrolyzed to putrescine by agmatinase. ADC is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC), which are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. Homodimer formation and the presence of both PLP and Mg2+ cofactors may be required for catalytic activity. Prokaryotic ADCs (biodegradative), which are fold type I PLP-dependent enzymes, are not included in this family. 409 matched cddid_all.tbl CDD cd06831 cd06831 143504 PLPDE_III_ODC_like_AZI Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase-like Antizyme Inhibitor. Antizyme inhibitor (AZI) is homologous to the fold type III PLP-dependent enzyme ODC but does not retain any decarboxylase activity. Like ODC, AZI is presumed to exist as a homodimer. Antizyme is a regulatory protein that binds directly to the ODC monomer to block its active site, leading to its degradation by the 26S proteasome. AZI binds to Antizyme with a higher affinity than ODC, preventing the formation of the Antizyme-ODC complex. Thus, AZI blocks the ability of Antizyme to promote ODC degradation, which leads to increased ODC enzymatic activity and polyamine levels. AZI also prevents the degradation of other proteins regulated by Antizyme, such as cyclin D1. 394 matched cddid_all.tbl CDD cd06836 cd06836 143505 PLPDE_III_ODC_DapDC_like_1 Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes, Uncharacterized Proteins with similarity to Ornithine and Diaminopimelate Decarboxylases. This subfamily contains uncharacterized proteins with similarity to ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Proteins in this subfamily may function as PLP-dependent decarboxylases. Homodimer formation and the presence of the PLP cofactor may be required for catalytic activity. 379 matched cddid_all.tbl CDD cd06839 cd06839 143506 PLPDE_III_Btrk_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Btrk Decarboxylase. This subfamily is composed of Bacillus circulans BtrK decarboxylase and similar proteins. These proteins are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases, eukaryotic ornithine decarboxylases and diaminopimelate decarboxylases. BtrK is presumed to function as a PLP-dependent decarboxylase involved in the biosynthesis of the aminoglycoside antibiotic butirosin. Homodimer formation and the presence of the PLP cofactor may be required for catalytic activity. 382 matched cddid_all.tbl CDD cd06840 cd06840 143507 PLPDE_III_Bif_AspK_DapDC Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bifunctional Aspartate Kinase/Diaminopimelate Decarboxylase. Bifunctional aspartate kinase/diaminopimelate decarboxylase (AspK/DapDC, EC 4.1.1.20/EC 2.7.2.4) typically exists in bacteria. These proteins contain an N-terminal AspK region and a C-terminal DapDC region, which contains a PLP-binding TIM-barrel domain followed by beta-sandwich domain, characteristic of fold type III PLP-dependent enzymes. Members of this subfamily have not been fully characterized. Based on their sequence, these proteins may catalyze both reactions catalyzed by AspK and DapDC. AspK catalyzes the phosphorylation of L-aspartate to produce 4-phospho-L-aspartate while DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. 368 matched cddid_all.tbl CDD cd06841 cd06841 143508 PLPDE_III_MccE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme MccE. This subfamily is composed of uncharacterized proteins with similarity to Escherichia coli MccE, a hypothetical protein that is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Most members of this subfamily share the same domain architecture as ODC and DapDC. A few members, including Escherichia coli MccE, contain an additional acetyltransferase domain at the C-terminus. 379 matched cddid_all.tbl CDD cd06842 cd06842 143509 PLPDE_III_Y4yA_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Y4yA. This subfamily is composed of the hypothetical Rhizobium sp. protein Y4yA and similar uncharacterized bacterial proteins. These proteins are homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. ODC participates in the formation of putrescine by catalyzing the decarboxylation of ornithine, the first step in polyamine biosynthesis. DapDC participates in the last step of lysine biosynthesis, the conversion of meso-2,6-diaminoheptanedioate to L-lysine. Proteins in this subfamily may function as PLP-dependent decarboxylases. 423 matched cddid_all.tbl CDD cd06843 cd06843 143510 PLPDE_III_PvsE_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme PvsE. This subfamily is composed of PvsE from Vibrio parahaemolyticus and similar proteins. PvsE is a vibrioferrin biosynthesis protein which is homologous to eukaryotic ornithine decarboxylase (ODC) and diaminopimelate decarboxylase (DapDC). ODC and DapDC are fold type III PLP-dependent enzymes that contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain, similar to bacterial alanine racemases. It has been suggested that PvsE may be involved in the biosynthesis of the polycarboxylate siderophore vibrioferrin. It may catalyze the decarboxylation of serine to yield ethanolamine. PvsE may require homodimer formation and the presence of the PLP cofactor for activity. 377 matched cddid_all.tbl CDD cd06844 cd06844 132911 STAS "Sulphate Transporter and Anti-Sigma factor antagonist domain found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors. The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain is found in the C-terminal region of sulphate transporters as well as in bacterial and archaeal proteins involved in the regulation of sigma factors, like anti-anti-sigma factors and ""stressosome"" components. The sigma factor regulators are involved in protein-protein interaction which is regulated by phosphorylation." 100 matched cddid_all.tbl CDD cd06845 cd06845 132900 Bcl-2_like Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting with their BH3 regions. Interfering with this heterodimeric interaction via small-molecule inhibitors may prove effective in targeting various cancers. This family also includes the Caenorhabditis elegans Bcl-2 homolog CED-9, which binds to CED-4, the C. Elegans homolog of mammalian Apaf-1. Apaf-1, however, does not seem to be inhibited by Bcl-2 directly. 144 matched cddid_all.tbl CDD cd06846 cd06846 185704 Adenylation_DNA_ligase_like Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases. ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases including eukaryotic GRP-dependent mRNA-capping enzymes. The catalytic core contains both the active site as well as many DNA-binding residues. The RNA circularization protein from archaea and bacteria contains the minimal catalytic unit, the adenylation domain, but does not contain an OB-fold domain. This family also includes the m3G-cap binding domain of snurportin, a nuclear import adaptor that binds m3G-capped spliceosomal U small nucleoproteins (snRNPs), but doesn't have enzymatic activity. 182 matched cddid_all.tbl CDD cd06847 cd06847 467022 HFD_SUPT7L histone-fold domain found in Suppressor of Ty 7-like (SUPT7L) and similar proteins. SUPT7L, also called STAGA complex 65 subunit gamma, adenocarcinoma antigen ART1, SPTF-associated factor 65 gamma, or STAF65gamma, is the ortholog of yeast SPT7 in mammalian cells. It is highly similar to yeast SPT7 but lacks the N-terminal SPT7 bromodomain. SUPT7L is a protein component specific to STAGA (SPT3-TAF9-GCN5 Acetyltransferase)-type complexes. It plays an essential role for the integrity of the STAGA complex. 86 matched cddid_all.tbl CDD cd06848 cd06848 133457 GCS_H Glycine cleavage H-protein. Glycine cleavage H-proteins are part of the glycine cleavage system (GCS) found in bacteria, archea and the mitochondria of eukaryotes. GCS is a multienzyme complex consisting of 4 different components (P-, H-, T- and L-proteins) which catalyzes the oxidative cleavage of glycine. The H-protein shuttles the methylamine group of glycine from the P-protein (glycine dehydrogenase) to the T-protein (aminomethyltransferase) via a lipoyl group, attached to a completely conserved lysine residue. 96 matched cddid_all.tbl CDD cd06849 cd06849 133458 lipoyl_domain Lipoyl domain of the dihydrolipoyl acyltransferase component (E2) of 2-oxo acid dehydrogenases. 2-oxo acid dehydrogenase multienzyme complexes, like pyruvate dehydrogenase (PDH), 2-oxoglutarate dehydrogenase (OGDH) and branched-chain 2-oxo acid dehydrogenase (BCDH), contain at least three different enzymes, 2-oxo acid dehydrogenase (E1), dihydrolipoyl acyltransferase (E2) and dihydrolipoamide dehydrogenase (E3) and play a key role in redox regulation. E2, the central component of the complex, catalyzes the transfer of the acyl group of CoA from E1 to E3 via reductive acetylation of a lipoyl group covalently attached to a lysine residue. 74 matched cddid_all.tbl CDD cd06850 cd06850 133459 biotinyl_domain The biotinyl-domain or biotin carboxyl carrier protein (BCCP) domain is present in all biotin-dependent enzymes, such as acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranyl-CoA carboxylase, oxaloacetate decarboxylase, methylmalonyl-CoA decarboxylase, transcarboxylase and urea amidolyase. This domain functions in transferring CO2 from one subsite to another, allowing carboxylation, decarboxylation, or transcarboxylation. During this process, biotin is covalently attached to a specific lysine. 67 matched cddid_all.tbl CDD cd06851 cd06851 133461 GT_GPT_like This family includes eukaryotic UDP-GlcNAc:dolichol-P GlcNAc-1-P transferase (GPT) and archaeal GPT-like glycosyltransferases. Eukaryotic GPT catalyzes the transfer of GlcNAc-1-P from UDP-GlcNAc to dolichol-P to form GlcNAc-P-P-dolichol. The reaction is the first step in the assembly of dolichol-linked oligosaccharide intermediates and is essential for eukaryotic N-linked glycosylation. GPT activity has been identified in all eukaryotic cells examined to date. Evidence for the existence of the N-glycosylation pathway in archaea has emerged and genes responsible for the pathway have been identified. A glycosyl transferase gene Mv1751 in M. voltae encodes for the enzyme that carries out the first step in the pathway, the attachment of GlcNAc to a dolichol lipid carrier in the membrane. A lethal mutation in the alg7 (GPT) gene in Saccharomyces cerevisiae was successfully complemented with Mv1751, the archaeal gene, indicating eukaryotic and archaeal enzymes may use the same substrates and are evolutionarily closer than the bacterial enzyme, which uses a different substrate. 223 matched cddid_all.tbl CDD cd06852 cd06852 133462 GT_MraY Phospho-N-acetylmuramoyl-pentapeptide-transferase (mraY) is an enzyme responsible for the formation of the first lipid intermediate in the synthesis of bacterial cell wall peptidoglycan. It catalyzes the formation of undecaprenyl-pyrophosphoryl-N-acetylmuramoyl-pentapeptide from UDP-MurNAc-pentapeptide and undecaprenyl-phosphate. It is an integral membrane protein with possibly ten transmembrane domains. 280 matched cddid_all.tbl CDD cd06853 cd06853 133463 GT_WecA_like This subfamily contains Escherichia coli WecA, Bacillus subtilis TagO and related proteins. WecA is an UDP-N-acetylglucosamine (GlcNAc):undecaprenyl-phosphate (Und-P) GlcNAc-1-phosphate transferase that catalyzes the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate molecule and N-acetylglucosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylglucosamine precursor. WecA participates in the biosynthesis of O antigen LPS in many enteric bacteria and is also involved in the biosynthesis of enterobacterial common antigen. A conserved short sequence motif and a conserved arginine at a cytosolic loop of this integral membrane protein were shown to be critical in recognition of substrate UDP-N-acetylglucosamine. 249 matched cddid_all.tbl CDD cd06854 cd06854 133464 GT_WbpL_WbcO_like The members of this subfamily catalyze the formation of a phosphodiester bond between a membrane-associated undecaprenyl-phosphate (Und-P) molecule and N-acetylhexosamine 1-phosphate, which is usually donated by a soluble UDP-N-acetylhexosamine precursor. The WbcO/WbpL substrate specificity has not yet been determined, but the structure of their biosynthetic end products implies that UDP-N-acetyl-D-fucosamine (UDP-FucNAc) and/or UDPN-acetyl-D-quinosamine (UDP-QuiNAc) are used. The subgroup of bacterial UDP-HexNAc:polyprenol-P HexNAc-1-P transferases includes the WbcO protein from Yersinia enterocolitica and the WbpL protein from Pseudomonas aeruginosa. These transferases initiate LPS O-antigen biosynthesis. Similar to other GlcNAc/MurNAc-1-P transferase family members, WbpL is a highly hydrophobic protein possessing 11 predicted transmembrane segments. 253 matched cddid_all.tbl CDD cd06855 cd06855 133465 GT_GPT_euk UDP-GlcNAc:dolichol-P GlcNAc-1-P transferase (GPT) catalyzes the transfer of GlcNAc-1-P from UDP-GlcNAc to dolichol-P to form GlcNAc-P-P-dolichol. The reaction is the first step in the assembly of dolichol-linked oligosaccharide intermediates and is essential for eukaryotic N-glycosylation. GPT activity has been identified in all eukaryotic cells examined to date. A series of six conserved motifs designated A through F, ranging in length from 5 to 13 amino acid residues, has been identified in this family. They have been determined to be important for stable expression, substrate binding, or catalytic activities. 283 matched cddid_all.tbl CDD cd06856 cd06856 133466 GT_GPT_archaea UDP-GlcNAc:dolichol-P GlcNAc-1-P transferase (GPT)-like proteins in archaea. Eukaryotic GPT catalyzes the transfer of GlcNAc-1-P from UDP-GlcNAc to dolichol-P to form GlcNAc-P-P-dolichol. The reaction is the first step in the assembly of dolichol-linked oligosaccharide intermediates and is essential for eukaryotic N-linked glycosylation. Evidence for the existence of the N-glycosylation pathway in archaea has emerged and genes responsible for the pathway have been identified. A glycosyl transferase gene Mv1751 in M. voltae encodes for the enzyme that carries out the first step in the pathway, the attachment of GlcNAc to a dolichol lipid carrier in the membrane. A lethal mutation in the alg7 (GPT) gene in Saccharomyces cerevisiae was successfully complemented with Mv1751, the archaea gene, indicating that eukaryotic and archaeal enzymes may use the same substrates and are evolutionarily closer than the bacterial enzyme, which uses a different substrate. 280 matched cddid_all.tbl CDD cd06857 cd06857 271356 SLC5-6-like_sbd Solute carrier families 5 and 6-like; solute binding domain. This superfamily includes the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporters or solute sodium symporters), SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporters or Na+/Cl--dependent transporters), and nucleobase-cation-symport-1 (NCS1) transporters. SLC5s co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. SLC6s include Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin, dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. Members of this superfamily are important in human physiology and disease. They contain a functional core of 10 transmembrane helices (TMs): an inverted structural repeat, TMs1-5 and TMs6-10; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT. 407 matched cddid_all.tbl CDD cd06859 cd06859 132769 PX_SNX1_2_like The phosphoinositide binding Phox Homology domain of Sorting Nexins 1 and 2. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. This subfamily consists of SNX1, SNX2, and similar proteins. They harbor a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain. Both domains have been shown to determine the specific membrane-targeting of SNX1. SNX1 and SNX2 are components of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi. The retromer consists of a cargo-recognition subcomplex and a subcomplex formed by a dimer of sorting nexins (SNX1 and/or SNX2), which ensures effcient cargo sorting by facilitating proper membrane localization of the cargo-recognition subcomplex. 114 matched cddid_all.tbl CDD cd06860 cd06860 132770 PX_SNX7_30_like The phosphoinositide binding Phox Homology domain of Sorting Nexins 7 and 30. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. This subfamily consists of SNX7, SNX30, and similar proteins. They harbor a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain, similar to the sorting nexins SNX1-2, SNX4-6, SNX8, and SNX32. Both domains have been shown to determine the specific membrane-targeting of SNX1. The specific function of the sorting nexins in this subfamily has yet to be elucidated. 116 matched cddid_all.tbl CDD cd06861 cd06861 132771 PX_Vps5p The phosphoinositide binding Phox Homology domain of yeast sorting nexin Vps5p. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Vsp5p is the yeast counterpart of human SNX1 and is part of the retromer complex, which functions in the endosome-to-Golgi retrieval of vacuolar protein sorting receptor Vps10p, the Golgi-resident membrane protein A-ALP, and endopeptidase Kex2. The PX domain of Vps5p binds phosphatidylinositol-3-phosphate (PI3P). Similar to SNX1, Vps5p contains a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain. Both domains have been shown to determine the specific membrane-targeting of SNX1. 112 matched cddid_all.tbl CDD cd06862 cd06862 132772 PX_SNX9_18_like The phosphoinositide binding Phox Homology domain of Sorting Nexins 9 and 18. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. This subfamily consists of SNX9, SNX18, and similar proteins. They contain an N-terminal Src Homology 3 (SH3) domain, a PX domain, and a C-terminal Bin/Amphiphysin/Rvs (BAR) domain. SNX9 is localized to plasma membrane endocytic sites and acts primarily in clathrin-mediated endocytosis, while SNX18 is localized to peripheral endosomal structures, and acts in a trafficking pathway that is clathrin-independent but relies on AP-1 and PACS1. 125 matched cddid_all.tbl CDD cd06863 cd06863 132773 PX_Atg24p The phosphoinositide binding Phox Homology domain of yeast Atg24p, an autophagic degradation protein. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. The yeast Atg24p is a sorting nexin (SNX) which is involved in membrane fusion events at the vacuolar surface during pexophagy. This is facilitated via binding of Atg24p to phosphatidylinositol 3-phosphate (PI3P) through its PX domain. SNXs make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. 118 matched cddid_all.tbl CDD cd06864 cd06864 132774 PX_SNX4 The phosphoinositide binding Phox Homology domain of Sorting Nexin 4. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX4 is involved in recycling traffic from the sorting endosome (post-Golgi endosome) back to the late Golgi. It shows a similar domain architecture as SNX1-2, among others, containing a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain. SNX4 is implicated in the regulation of plasma membrane receptor trafficking and interacts with receptors for EGF, insulin, platelet-derived growth factor and the long form of the leptin receptor. 129 matched cddid_all.tbl CDD cd06865 cd06865 132775 PX_SNX_like The phosphoinositide binding Phox Homology domain of SNX-like proteins. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. This subfamily is composed of uncharacterized proteins, predominantly from plants, with similarity to sorting nexins. A few members show a similar domain architecture as a subfamily of sorting nexins, containing a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain. The PX-BAR structural unit is known to determine specific membrane localization. 120 matched cddid_all.tbl CDD cd06866 cd06866 132776 PX_SNX8_Mvp1p_like The phosphoinositide binding Phox Homology domain of Sorting Nexin 8 and yeast Mvp1p. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX8 and the yeast counterpart Mvp1p are involved in sorting and delivery of late-Golgi proteins, such as carboxypeptidase Y, to vacuoles. 105 matched cddid_all.tbl CDD cd06867 cd06867 132777 PX_SNX41_42 The phosphoinositide binding Phox Homology domain of fungal Sorting Nexins 41 and 42. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX41 and SNX42 (also called Atg20p) form dimers with SNX4, and are required in protein recycling from the sorting endosome (post-Golgi endosome) back to the late Golgi in yeast. 112 matched cddid_all.tbl CDD cd06868 cd06868 132778 PX_HS1BP3 The phosphoinositide binding Phox Homology domain of HS1BP3. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Hematopoietic lineage cell-specific protein-1 (HS1) binding protein 3 (HS1BP3) associates with HS1 proteins through their SH3 domains, suggesting a role in mediating signaling. It has been reported that HS1BP3 might affect the IL-2 signaling pathway in hematopoietic lineage cells. Mutations in HS1BP3 may also be associated with familial Parkinson disease and essential tremor. HS1BP3 contains a PX domain, a leucine zipper, motifs similar to immunoreceptor tyrosine-based inhibitory motif and proline-rich regions. The PX domain interacts with PIs and plays a role in targeting proteins to PI-enriched membranes. 120 matched cddid_all.tbl CDD cd06869 cd06869 132779 PX_UP2_fungi The phosphoinositide binding Phox Homology domain of uncharacterized fungal proteins. The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to PI-enriched membranes. Members in this subfamily are uncharacterized fungal proteins containing a PX domain. PX domain harboring proteins have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction. 119 matched cddid_all.tbl CDD cd06870 cd06870 132780 PX_CISK The phosphoinositide binding Phox Homology Domain of Cytokine-Independent Survival Kinase. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Cytokine-independent survival kinase (CISK), also called Serum- and Glucocorticoid-induced Kinase 3 (SGK3), plays a role in cell growth and survival. It is expressed in most tissues and is most abundant in the embryo and adult heart and spleen. It was originally discovered in a screen for antiapoptotic genes. It phosphorylates and inhibits the proapoptotic proteins, Bad and FKHRL1. CISK/SGK3 also regulates many transporters, ion channels, and receptors. It plays a critical role in hair follicle morphogenesis and hair cycling. N-terminal to a catalytic kinase domain, CISK contains a PX domain which binds highly phosphorylated PIs, directs membrane localization, and regulates the enzyme's activity. 109 matched cddid_all.tbl CDD cd06871 cd06871 132781 PX_MONaKA The phosphoinositide binding Phox Homology domain of Modulator of Na,K-ATPase. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. MONaKA (Modulator of Na,K-ATPase) binds the plasma membrane ion transporter, Na,K-ATPase, and modulates its enzymatic and ion pump activities. It modulates brain Na,K-ATPase and may be involved in regulating electrical excitability and synaptic transmission. MONaKA contains an N-terminal PX domain and a C-terminal catalytic kinase domain. The PX domain interacts with PIs and plays a role in targeting proteins to PI-enriched membranes. 120 matched cddid_all.tbl CDD cd06872 cd06872 132782 PX_SNX19_like_plant The phosphoinositide binding Phox Homology domain of uncharacterized SNX19-like plant proteins. The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to PI-enriched membranes. Members in this subfamily are uncharacterized plant proteins containing an N-terminal PXA domain, a central PX domain, and a C-terminal domain that is conserved in some sorting nexins (SNXs). This is the same domain architecture found in SNX19. SNX13 and SNX14 also contain these three domains but also contain a regulator of G protein signaling (RGS) domain in between the PXA and PX domains. SNXs make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction. 107 matched cddid_all.tbl CDD cd06873 cd06873 132783 PX_SNX13 The phosphoinositide binding Phox Homology domain of Sorting Nexin 13. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX13, also called RGS-PX1, contains an N-terminal PXA domain, a regulator of G protein signaling (RGS) domain, a PX domain, and a C-terminal domain that is conserved in some SNXs. It specifically binds to the stimulatory subunit of the heterotrimeric G protein G(alpha)s, serving as its GTPase activating protein, through the RGS domain. It preferentially binds phosphatidylinositol-3-phosphate (PI3P) through the PX domain and is localized in early endosomes. SNX13 is involved in endosomal sorting of EGFR into multivesicular bodies (MVB) for delivery to the lysosome. 120 matched cddid_all.tbl CDD cd06874 cd06874 132784 PX_KIF16B_SNX23 The phosphoinositide binding Phox Homology domain of KIF16B kinesin or Sorting Nexin 23. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. KIF16B, also called sorting nexin 23 (SNX23), is a family-3 kinesin which harbors an N-terminal kinesin motor domain containing ATP and microtubule binding sites, a ForkHead Associated (FHA) domain, and a C-terminal PX domain. The PX domain of KIF16B binds to phosphatidylinositol-3-phosphate (PI3P) in early endosomes and plays a role in the transport of early endosomes to the plus end of microtubules. By regulating early endosome plus end motility, KIF16B modulates the balance between recycling and degradation of receptors. SNXs make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. 127 matched cddid_all.tbl CDD cd06875 cd06875 132785 PX_IRAS The phosphoinositide binding Phox Homology domain of the Imidazoline Receptor Antisera-Selected. The PX domain is a phosphoinositide binding (PI) module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Imidazoline Receptor Antisera-Selected (IRAS), also called nischarin, contains an N-terminal PX domain, leucine rich repeats, and a predicted coiled coil domain. The PX domain of IRAS binds to phosphatidylinositol-3-phosphate in membranes. Together with the coiled coil domain, it is essential for the localization of IRAS to endosomes. IRAS has been shown to interact with integrin and inhibit cell migration. Its interaction with alpha5 integrin causes a redistribution of the receptor from the cell surface to endosomal structures, suggesting that IRAS may function as a sorting nexin (SNX) which regulates the endosomal trafficking of integrin. SNXs make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. 116 matched cddid_all.tbl CDD cd06876 cd06876 132786 PX_MDM1p The phosphoinositide binding Phox Homology domain of yeast MDM1p. The PX domain is a phosphoinositide binding (PI) module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Yeast MDM1p is a filament-like protein localized in punctate structures distributed throughout the cytoplasm. It plays an important role in nuclear and mitochondrial transmission to daughter buds. Members of this subfamily show similar domain architectures as some sorting nexins (SNXs). Some members are similar to SNX19 in that they contain an N-terminal PXA domain, a central PX domain, and a C-terminal domain that is conserved in some SNXs. Others are similar to SNX13 and SNX14, which also harbor these three domains as well as a regulator of G protein signaling (RGS) domain in between the PXA and PX domains. SNXs make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. 133 matched cddid_all.tbl CDD cd06877 cd06877 132787 PX_SNX14 The phosphoinositide binding Phox Homology domain of Sorting Nexin 14. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX14 may be involved in recruiting other proteins to the membrane via protein-protein and protein-ligand interaction. It is expressed in the embryonic nervous system of mice, and is co-expressed in the motoneurons and the anterior pituary with Islet-1. SNX14 shows a similar domain architecture as SNX13, containing an N-terminal PXA domain, a regulator of G protein signaling (RGS) domain, a PX domain, and a C-terminal domain that is conserved in some SNXs. 119 matched cddid_all.tbl CDD cd06878 cd06878 132788 PX_SNX25 The phosphoinositide binding Phox Homology domain of Sorting Nexin 25. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. The function of SNX25 is not yet known. It has been found in exosomes from human malignant pleural effusions. SNX25 shows the same domain architecture as SNX13 and SNX14, containing an N-terminal PXA domain, a regulator of G protein signaling (RGS) domain, a PX domain, and a C-terminal domain that is conserved in some SNXs. 127 matched cddid_all.tbl CDD cd06879 cd06879 132789 PX_UP1_plant The phosphoinositide binding Phox Homology domain of uncharacterized plant proteins. The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to PI-enriched membranes. Members in this subfamily are uncharacterized fungal proteins containing a PX domain. PX domain harboring proteins have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction. 138 matched cddid_all.tbl CDD cd06880 cd06880 132790 PX_SNX22 The phosphoinositide binding Phox Homology domain of Sorting Nexin 22. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX22 may be involved in recruiting other proteins to the membrane via protein-protein and protein-ligand interaction. The biological function of SNX22 is not yet known. 110 matched cddid_all.tbl CDD cd06881 cd06881 132791 PX_SNX15_like The phosphoinositide binding Phox Homology domain of Sorting Nexin 15-like proteins. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Members of this subfamily have similarity to sorting nexin 15 (SNX15), which contains an N-terminal PX domain and a C-terminal Microtubule Interacting and Trafficking (MIT) domain. SNXs make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNX15 plays a role in protein trafficking processes in the endocytic pathway and the trans-Golgi network. The PX domain of SNX15 interacts with the PDGF receptor and is responsible for the membrane association of the protein. Other members of this subfamily contain an additional C-terminal kinase domain, similar to human RPK118, which binds sphingosine kinase and the antioxidant peroxiredoxin-3 (PRDX3). RPK118 may be involved in the transport of proteins such as PRDX3 from the cytoplasm to its site of function in the mitochondria. 117 matched cddid_all.tbl CDD cd06882 cd06882 132792 PX_p40phox The phosphoinositide binding Phox Homology domain of the p40phox subunit of NADPH oxidase. The PX domain is a phosphoinositide binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. p40phox contains an N-terminal PX domain, a central SH3 domain that binds p47phox, and a C-terminal PB1 domain that interacts with p67phox. It is a cytosolic subunit of the phagocytic NADPH oxidase complex (also called Nox2 or gp91phox) which plays a crucial role in the cellular response to bacterial infection. NADPH oxidase catalyzes the transfer of electrons from NADPH to oxygen during phagocytosis forming superoxide and reactive oxygen species. p40phox positively regulates NADPH oxidase in both phosphatidylinositol-3-phosphate (PI3P)-dependent and PI3P-independent manner. The PX domain is a phospholipid-binding module involved in the membrane targeting of proteins. The p40phox PX domain binds to PI3P, an abundant lipid in phagosomal membranes, playing an important role in the localization of NADPH oxidase. The PX domain of p40phox is also involved in protein-protein interaction. 123 matched cddid_all.tbl CDD cd06883 cd06883 132793 PX_PI3K_C2 The phosphoinositide binding Phox Homology Domain of Class II Phosphoinositide 3-Kinases. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. The Phosphoinositide 3-Kinase (PI3K) family of enzymes catalyzes the phosphorylation of the 3-hydroxyl group of the inositol ring of phosphatidylinositol. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They are also involved in the regulation of clathrin-mediated membrane trafficking as well as ATP-dependent priming of neurosecretory granule exocytosis. PI3Ks are divided into three main classes (I, II, and III) based on their substrate specificity, regulation, and domain structure. Class II PI3Ks preferentially use PI as a substrate to produce PI3P, but can also phosphorylate PI4P to produce PI(3,4)P2. They function as monomers and do not associate with any regulatory subunits. Class II enzymes contain an N-terminal Ras binding domain, a lipid binding C2 domain, a PI3K homology domain of unknown function, an ATP-binding cataytic domain, a PX domain, and a second C2 domain at the C-terminus. Class II PI3Ks include three vertebrate isoforms (alpha, beta, and gamma), the Drosophila PI3K_68D, and similar proteins. 109 matched cddid_all.tbl CDD cd06884 cd06884 132794 PX_PI3K_C2_68D The phosphoinositide binding Phox Homology Domain of Class II Phosphoinositide 3-Kinases similar to the Drosophila PI3K_68D protein. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. The Phosphoinositide 3-Kinase (PI3K) family of enzymes catalyzes the phosphorylation of the 3-hydroxyl group of the inositol ring of phosphatidylinositol. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI3Ks are divided into three main classes (I, II, and III) based on their substrate specificity, regulation, and domain structure. Class II PI3Ks preferentially use PI as a substrate to produce PI3P, but can also phosphorylate PI4P to produce PI(3,4)P2. They function as monomers and do not associate with any regulatory subunits. Class II enzymes contain an N-terminal Ras binding domain, a lipid binding C2 domain, a PI3K homology domain of unknown function, an ATP-binding cataytic domain, a PX domain, and a second C2 domain at the C-terminus. PI3K_68D is a novel PI3K which is widely expressed throughout the Drosophila life cycle. In vitro, it has been shown to phosphorylate PI and PI4P. It is involved in signaling pathways that affect pattern formation of Drosophila wings. 111 matched cddid_all.tbl CDD cd06885 cd06885 132795 PX_SNX17_31 The phosphoinositide binding Phox Homology domain of Sorting Nexins 17 and 31. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Members of this subfamily include sorting nexin 17 (SNX17), SNX31, and similar proteins. They contain an N-terminal PX domain followed by a truncated FERM (4.1, ezrin, radixin, and moesin) domain and a unique C-terminal region. SNXs make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX17 is known to regulate the trafficking and processing of a number of proteins. It binds some members of the low-density lipoprotein receptor (LDLR) family such as LDLR, VLDLR, ApoER2, and others, regulating their endocytosis. It also binds P-selectin and may regulate its lysosomal degradation. SNX17 is highly expressed in neurons. It binds amyloid precursor protein (APP) and may be involved in its intracellular trafficking and processing to amyloid beta peptide, which plays a central role in the pathogenesis of Alzheimer's disease. The biological function of SNX31 is unknown. 104 matched cddid_all.tbl CDD cd06886 cd06886 132796 PX_SNX27 The phosphoinositide binding Phox Homology domain of Sorting Nexin 27. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX27 contains an N-terminal PDZ domain followed by a PX domain and a Ras-Associated (RA) domain. It binds G protein-gated potassium (Kir3) channels, which play a role in neuronal excitability control, through its PDZ domain. SNX27 downregulates Kir3 channels by promoting their movement in the endosome, reducing surface expression and increasing degradation. SNX27 also associates with 5-hydroxytryptamine type 4 receptor (5-HT4R), cytohesin associated scaffolding protein (CASP), and diacylglycerol kinase zeta, and may play a role in their intracellular trafficking and endocytic recycling. The SNX27 PX domain preferentially binds to phosphatidylinositol-3-phosphate (PI3P) and is important for targeting to the early endosome. 106 matched cddid_all.tbl CDD cd06887 cd06887 132797 PX_p47phox The phosphoinositide binding Phox Homology domain of the p47phox subunit of NADPH oxidase. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. p47phox is a cytosolic subunit of the phagocytic NADPH oxidase complex (also called Nox2 or gp91phox), which plays a key role in the ability of phagocytes to defend against bacterial infections. NADPH oxidase catalyzes the transfer of electrons from NADPH to oxygen during phagocytosis forming superoxide and reactive oxygen species. p47phox is required for activation of NADH oxidase and plays a role in translocation. It contains an N-terminal PX domain, two Src Homology 3 (SH3) domains, and a C-terminal domain that contains PxxP motifs for binding SH3 domains. The PX domain of p47phox is unique in that it contains two distinct basic pockets on the membrane-binding surface: one preferentially binds phosphatidylinositol-3,4-bisphosphate [PI(3,4)P2] and is analogous to the PI3P-binding pocket of p40phox, while the other binds anionic phospholipids such as phosphatidic acid or phosphatidylserine. Simultaneous binding in the two pockets results in increased membrane affinity. The PX domain of p47phox is also involved in protein-protein interaction. 118 matched cddid_all.tbl CDD cd06888 cd06888 132798 PX_FISH The phosphoinositide binding Phox Homology domain of Five SH protein. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Five SH (FISH), also called Tks5, is a scaffolding protein and Src substrate that is localized in podosomes, which are electron-dense structures found in Src-transformed fibroblasts, osteoclasts, macrophages, and some invasive cancer cells. FISH contains an N-terminal PX domain and five Src homology 3 (SH3) domains. FISH binds and regulates some members of the ADAMs family of transmembrane metalloproteases, which function as sheddases and mediators of cell and matrix interactions. It is required for podosome formation, degradation of the extracellular matrix, and cancer cell invasion. This subfamily also includes proteins with a different number of SH3 domains than FISH, such as Tks4, which contains four SH3 domains instead of five. The Tks4 adaptor protein is required for the formation of functional podosomes. It has overlapping, but not identical, functions as FISH. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. 119 matched cddid_all.tbl CDD cd06889 cd06889 132799 PX_NoxO1 The phosphoinositide binding Phox Homology domain of Nox Organizing protein 1. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Nox Organizing protein 1 (NoxO1) is a critical regulator of enzyme kinetics of the nonphagocytic NADPH oxidase Nox1, which catalyzes the transfer of electrons from NADPH to molecular oxygen to form superoxide. Nox1 is expressed in colon, stomach, uterus, prostate, and vascular smooth muscle cells. NoxO1, a homolog of the p47phox subunit of phagocytic NADPH oxidase, is involved in targeting activator subunits (such as NoxA1) to Nox1. It is co-localized with Nox1 in the membranes of resting cells and directs the subcellular localization of Nox1. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. The PX domain of NoxO1 preferentially binds phosphatidylinositol-3,5-bisphosphate [PI(3,5)P2], PI5P, and PI4P. 121 matched cddid_all.tbl CDD cd06890 cd06890 132800 PX_Bem1p The phosphoinositide binding Phox Homology domain of Bem1p. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Members of this subfamily bear similarity to Saccharomyces cerevisiae Bem1p, containing two Src Homology 3 (SH3) domains at the N-terminus, a central PX domain, and a C-terminal PB1 domain. Bem1p is a scaffolding protein that is critical for proper Cdc42p activation during bud formation in yeast. During budding and mating, Bem1p migrates to the plasma membrane where it can serve as an adaptor for Cdc42p and some other proteins. Bem1p also functions as an effector of the G1 cyclin Cln3p and the cyclin-dependent kinase Cdc28p in promoting vacuolar fusion. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. The PX domain of Bem1p specifically binds phosphatidylinositol-4-phosphate (PI4P). 112 matched cddid_all.tbl CDD cd06891 cd06891 132801 PX_Vps17p The phosphoinositide binding Phox Homology domain of yeast sorting nexin Vps17p. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Vsp17p forms a dimer with Vps5p, the yeast counterpart of human SNX1, and is part of the retromer complex that mediates the transport of the carboxypeptidase Y receptor Vps10p from endosomes to Golgi. Similar to Vps5p and SNX1, Vps17p harbors a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain. The PX-BAR structural unit helps determine specific membrane localization. 140 matched cddid_all.tbl CDD cd06892 cd06892 132802 PX_SNX5_like The phosphoinositide binding Phox Homology domain of Sorting Nexins 5 and 6. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Members of this subfamily include SNX5, SNX6, and similar proteins. They contain a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain, similar to other sorting nexins including SNX1-2. The PX-BAR structural unit helps determine the specific membrane-targeting of some SNXs. SNX5 and SNX6 may be components of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. 141 matched cddid_all.tbl CDD cd06893 cd06893 132803 PX_SNX19 The phosphoinositide binding Phox Homology domain of Sorting Nexin 19. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX19 contains an N-terminal PXA domain, a central PX domain, and a C-terminal domain that is conserved in some SNXs. These domains are also found in SNX13 and SNX14, which also contain a regulator of G protein signaling (RGS) domain in between the PXA and PX domains. SNX19 interacts with IA-2, a major autoantigen found in type-1 diabetes. It inhibits the conversion of phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2] to PI(3,4,5)P3, which leads in the decrease of protein phosphorylation in the Akt signaling pathway, resulting in apoptosis. SNX19 may also be implicated in coronary heart disease and thyroid oncocytic tumors. 132 matched cddid_all.tbl CDD cd06894 cd06894 132804 PX_SNX3_like The phosphoinositide binding Phox Homology domain of Sorting Nexin 3 and related proteins. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. This subfamily is composed of SNX3, SNX12, and fungal Grd19. Grd19 is involved in the localization of late Golgi membrane proteins in yeast. SNX3/Grp19 associates with the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, and functions as a cargo-specific adaptor for the retromer. 123 matched cddid_all.tbl CDD cd06895 cd06895 132805 PX_PLD The phosphoinositide binding Phox Homology domain of Phospholipase D. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Phospholipase D (PLD) catalyzes the hydrolysis of the phosphodiester bond of phosphatidylcholine to generate membrane-bound phosphatidic acid and choline. Members of this subfamily contain PX and Pleckstrin Homology (PH) domains in addition to the catalytic domain. PLD activity has been detected in viruses, bacteria, yeast, plants, and mammals, but the PX domain is not present in PLDs from viruses and bacteria. PLDs are implicated in many cellular functions like signaling, cytoskeletal reorganization, vesicular transport, stress responses, and the control of differentiation, proliferation, and survival. Vertebrates contain two PLD isozymes, PLD1 and PLD2. PLD1 is located mainly in intracellular membranes while PLD2 is associated with plasma membranes. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. 140 matched cddid_all.tbl CDD cd06896 cd06896 132806 PX_PI3K_C2_gamma The phosphoinositide binding Phox Homology Domain of the Gamma Isoform of Class II Phosphoinositide 3-Kinases. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. The Phosphoinositide 3-Kinase (PI3K) family of enzymes catalyzes the phosphorylation of the 3-hydroxyl group of the inositol ring of phosphatidylinositol. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI3Ks are divided into three main classes (I, II, and III) based on their substrate specificity, regulation, and domain structure. Class II PI3Ks preferentially use PI as a substrate to produce PI3P, but can also phosphorylate PI4P to produce PI(3,4)P2. They function as monomers and do not associate with any regulatory subunits. Class II enzymes contain an N-terminal Ras binding domain, a lipid binding C2 domain, a PI3K homology domain of unknown function, an ATP-binding cataytic domain, a PX domain, and a second C2 domain at the C-terminus. The class II gamma isoform, PI3K-C2gamma, is expressed in the liver, breast, and prostate. It's biological function remains unknown. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. 101 matched cddid_all.tbl CDD cd06897 cd06897 132807 PX_SNARE The phosphoinositide binding Phox Homology domain of SNARE proteins from fungi. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. This subfamily is composed of fungal proteins similar to Saccharomyces cerevisiae Vam7p. They contain an N-terminal PX domain and a C-terminal SNARE domain. The SNARE (Soluble NSF attachment protein receptor) family of proteins are integral membrane proteins that serve as key factors for vesicular trafficking. Vam7p is anchored at the vacuolar membrane through the specific interaction of its PX domain with phosphatidylinositol-3-phosphate (PI3P) present in bilayers. It plays an essential role in vacuole fusion. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. 108 matched cddid_all.tbl CDD cd06898 cd06898 132808 PX_SNX10 The phosphoinositide binding Phox Homology domain of Sorting Nexin 10. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX10 may be involved in the regulation of endosome homeostasis. Its expression induces the formation of giant vacuoles in mammalian cells. 113 matched cddid_all.tbl CDD cd06899 cd06899 173887 lectin_legume_LecRK_Arcelin_ConA "legume lectins, lectin-like receptor kinases, arcelin, concanavalinA, and alpha-amylase inhibitor. This alignment model includes the legume lectins (also known as agglutinins), the arcelin (also known as phytohemagglutinin-L) family of lectin-like defense proteins, the LecRK family of lectin-like receptor kinases, concanavalinA (ConA), and an alpha-amylase inhibitor. Arcelin is a major seed glycoprotein discovered in kidney beans (Phaseolus vulgaris) that has insecticidal properties and protects the seeds from predation by larvae of various bruchids. Arcelin is devoid of monosaccharide binding properties and lacks a key metal-binding loop that is present in other members of this family. Phytohaemagglutinin (PHA) is a lectin found in plants, especially beans, that affects cell metabolism by inducing mitosis and by altering the permeability of the cell membrane to various proteins. PHA agglutinates most mammalian red blood cell types by binding glycans on the cell surface. Medically, PHA is used as a mitogen to trigger cell division in T-lymphocytes and to activate latent HIV-1 from human peripheral lymphocytes. Plant L-type lectins are primarily found in the seeds of leguminous plants where they constitute about 10% of the total soluble protein of the seed extracts. They are synthesized during seed development several weeks after flowering and transported to the vacuole where they become condensed into specialized vesicles called protein bodies. L-type lectins have a dome-shaped beta-barrel carbohydrate recognition domain with a curved seven-stranded beta-sheet referred to as the ""front face"" and a flat six-stranded beta-sheet referred to as the ""back face"". This domain homodimerizes so that adjacent back sheets form a contiguous 12-stranded sheet and homotetramers occur by a back-to-back association of these homodimers. Though L-type lectins exhibit both sequence and structural similarity to one another, their carbohydrate binding specificities differ widely." 236 matched cddid_all.tbl CDD cd06900 cd06900 173888 lectin_VcfQ VcfQ bacterial pilus biogenesis protein, lectin domain. This family includes bacterial proteins homologous to the VcfQ (also known as MshQ) bacterial pilus biogenesis protein. VcfQ is encoded by the vcfQ gene of the type IV pilus gene cluster of Vibrio cholerae and is essential for type IV pilus assembly. VcfQ has a Laminin G-like domain as well as an L-type lectin domain. 255 matched cddid_all.tbl CDD cd06901 cd06901 173889 lectin_VIP36_VIPL "VIP36 and VIPL type 1 transmembrane proteins, lectin domain. The vesicular integral protein of 36 kDa (VIP36) is a type 1 transmembrane protein of the mammalian early secretory pathway that acts as a cargo receptor transporting high mannose type glycoproteins between the Golgi and the endoplasmic reticulum (ER). Lectins of the early secretory pathway are involved in the selective transport of newly synthesized glycoproteins from the ER to the ER-Golgi intermediate compartment (ERGIC). The most prominent cycling lectin is the mannose-binding type1 membrane protein ERGIC-53, which functions as a cargo receptor to facilitate export of glycoproteins from the ER. L-type lectins have a dome-shaped beta-barrel carbohydrate recognition domain with a curved seven-stranded beta-sheet referred to as the ""front face"" and a flat six-stranded beta-sheet referred to as the ""back face"". This domain homodimerizes so that adjacent back sheets form a contiguous 12-stranded sheet and homotetramers occur by a back-to-back association of these homodimers. Though L-type lectins exhibit both sequence and structural similarity to one another, their carbohydrate binding specificities differ widely." 248 matched cddid_all.tbl CDD cd06902 cd06902 173890 lectin_ERGIC-53_ERGL "ERGIC-53 and ERGL type 1 transmembrane proteins, N-terminal lectin domain. ERGIC-53 and ERGL, N-terminal carbohydrate recognition domain. ERGIC-53 and ERGL are eukaryotic mannose-binding type 1 transmembrane proteins of the early secretory pathway that transport newly synthesized glycoproteins from the endoplasmic reticulum (ER) to the ER-Golgi intermediate compartment (ERGIC). ERGIC-53 and ERGL have an N-terminal lectin-like carbohydrate recognition domain (represented by this alignment model) as well as a C-terminal transmembrane domain. ERGIC-53 functions as a 'cargo receptor' to facilitate the export of glycoproteins with different characteristics from the ER, while the ERGIC-53-like protein (ERGL) which may act as a regulator of ERGIC-53. In mammals, ERGIC-53 forms a complex with MCFD2 (multi-coagulation factor deficiency 2) which then recruits blood coagulation factors V and VIII. Mutations in either MCFD2 or ERGIC-53 cause a mild form of inherited hemophilia known as combined deficiency of factors V and VIII (F5F8D). In addition to the lectin and transmembrane domains, ERGIC-53 and ERGL have a short N-terminal cytoplasmic region of about 12 amino acids. ERGIC-53 forms disulphide-linked homodimers and homohexamers. ERGIC-53 and ERGL are sequence-similar to the lectins of leguminous plants. L-type lectins have a dome-shaped beta-barrel carbohydrate recognition domain with a curved seven-stranded beta-sheet referred to as the ""front face"" and a flat six-stranded beta-sheet referred to as the ""back face"". This domain homodimerizes so that adjacent back sheets form a contiguous 12-stranded sheet and homotetramers occur by a back-to-back association of these homodimers. Though L-type lectins exhibit both sequence and structural similarity to one another, their carbohydrate binding specificities differ widely." 225 matched cddid_all.tbl CDD cd06903 cd06903 173891 lectin_EMP46_EMP47 "EMP46 and EMP47 type 1 transmembrane proteins, N-terminal lectin domain. EMP46 and EMP47, N-terminal carbohydrate recognition domain. EMP46 and EMP47 are fungal type-I transmembrane proteins that cycle between the endoplasmic reticulum and the golgi apparatus and are thought to function as cargo receptors that transport newly synthesized glycoproteins. EMP47 is a receptor for EMP46 responsible for the selective transport of EMP46 by forming hetero-oligomerization between the two proteins. EMP46 and EMP47 have an N-terminal lectin-like carbohydrate recognition domain (represented by this alignment model) as well as a C-terminal transmembrane domain. EMP46 and EMP47 are 45% sequence-identical to one another and have sequence homology to a class of intracellular lectins defined by ERGIC-53 and VIP36. L-type lectins have a dome-shaped beta-barrel carbohydrate recognition domain with a curved seven-stranded beta-sheet referred to as the ""front face"" and a flat six-stranded beta-sheet referred to as the ""back face"". This domain homodimerizes so that adjacent back sheets form a contiguous 12-stranded sheet and homotetramers occur by a back-to-back association of these homodimers. Though L-type lectins exhibit both sequence and structural similarity to one another, their carbohydrate binding specificities differ widely." 215 matched cddid_all.tbl CDD cd06904 cd06904 349475 M14_MpaA-like Peptidase M14-like domain of Escherichia coli Murein Peptide Amidase A and related proteins. Peptidase M14-like domain of Escherichia coli Murein Peptide Amidase A (MpaA) and related proteins. MpaA is a member of the M14 family of metallocarboxypeptidases (MCPs), however it has an exceptional type of activity, it hydrolyzes the gamma-D-glutamyl-meso-diaminopimelic acid (gamma-D-Glu-Dap) bond in murein peptides. MpaA is specific for cleavage of the gamma-D-Glu-Dap bond of free murein tripeptide; it may also cleave murein tetrapeptide. MpaA has a different substrate specificity and cellular role than endopeptidase I, ENP1 (ENP1 does not belong to this group). MpaA works on free murein peptide in the recycling pathway. 214 matched cddid_all.tbl CDD cd06905 cd06905 349476 M14-like Peptidase M14-like domain; uncharacterized subfamily. A functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly different specificities, with Carboxypeptidase A1 (CPA1) preferring aliphatic and small aromatic residues, and CPA2 preferring the bulky aromatic side chains. Enzymes belonging to the N/E subfamily enzymes are not produced as inactive precursors and instead rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavages. They contain an extra C-terminal transthyretin-like domain, thought to be involved in folding or formation of oligomers. MCPs can also be classified based on their involvement in specific physiological processes; the pancreatic MCPs participate only in alimentary digestion and include carboxypeptidase A and B (A/B subfamily), while others, namely regulatory MCPs or the N/E subfamily, are involved in more selective reactions, mainly in non-digestive tissues and fluids, acting on blood coagulation/fibrinolysis, inflammation and local anaphylaxis, pro-hormone and neuropeptide processing, cellular response and others. Another MCP subfamily, is that of succinylglutamate desuccinylase /aspartoacylase, which hydrolyzes N-acetyl-L-aspartate (NAA), and deficiency in which is the established cause of Canavan disease. Another subfamily (referred to as subfamily C) includes an exceptional type of activity in the MCP family, that of dipeptidyl-peptidase activity of gamma-glutamyl-(L)-meso-diaminopimelate peptidase I which is involved in bacterial cell wall metabolism. 359 matched cddid_all.tbl CDD cd06906 cd06906 349477 M14_Nna1 Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases. Peptidase M14-like domain of Nna-1 (Nervous system Nuclear protein induced by Axotomy), also known as ATP/GTP binding protein (AGTPBP-1) and cytosolic carboxypeptidase (CCP), and related proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. This eukaryotic subgroup includes the mouse Nna1/CCP-1, and -4 proteins, and the human Nna1/AGTPBP-1 protein. Nna1-like proteins are active metallopeptidases that are thought to act on cytosolic proteins such as alpha-tubulin, to remove a C-terminal tyrosine. Nna1 is widely expressed in the developing and adult nervous systems, including cerebellar Purkinje and granule neurons, miral cells of the olfactory bulb and retinal photoreceptors. Nna1 is also induced in axotomized motor neurons. Mutations in Nna1 cause Purkinje cell degeneration (pcd). The Nna1 CP domain is required to prevent the retinal photoreceptor loss and cerebellar ataxia phenotypes of pcd mice, and a functional zinc-binding domain is needed for Nna-1 to support neuron survival in these mice. Nna1-like proteins from the different phyla are highly diverse, but they all contain a unique N-terminal conserved domain right before the CP domain. It has been suggested that this N-terminal domain might act as a folding domain. 271 matched cddid_all.tbl CDD cd06907 cd06907 349478 M14_AGBL2-3_like Peptidase M14-like domain of ATP/GTP binding protein AGBL-2 and AGBL-3, and related proteins. Peptidase M14-like domain of ATP/GTP binding protein_like (AGBL)-2, and related proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. This subgroup includes the human AGBL-2, and -3, and the mouse cytosolic carboxypeptidase (CCPs)-2, and -3. ATP/GTP binding protein (AGTPBP-1/Nna1)-like proteins are active metallopeptidases that are thought to act on cytosolic proteins such as alpha-tubulin, to remove a C-terminal tyrosine. Mutations in AGTPBP-1/Nna1 cause Purkinje cell degeneration (pcd). AGTPBP-1/Nna1 however does not belong to this subgroup. AGTPBP-1/Nna1-like proteins from the different phyla are highly diverse, but they all contain a unique N-terminal conserved domain right before the CP domain. It has been suggested that this N-terminal domain might act as a folding domain. 252 matched cddid_all.tbl CDD cd06908 cd06908 349479 M14_AGBL4_like Peptidase M14-like domain of ATP/GTP binding protein AGBL-4 and related proteins. Peptidase M14-like domain of ATP/GTP binding protein_like (AGBL)-4, and related proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. This eukaryotic subgroup includes the human AGBL4 and the mouse cytosolic carboxypeptidase (CCP)-6. ATP/GTP binding protein (AGTPBP-1/Nna1)-like proteins are active metallopeptidases that are thought to act on cytosolic proteins such as alpha-tubulin, to remove a C-terminal tyrosine. Mutations in AGTPBP-1/Nna1 cause Purkinje cell degeneration (pcd). AGTPBP-1/Nna1 however does not belong to this subgroup. AGTPBP-1/Nna1-like proteins from the different phyla are highly diverse, but they all contain a unique N-terminal conserved domain right before the CP domain. It has been suggested that this N-terminal domain might act as a folding domain. 254 matched cddid_all.tbl CDD cd06909 cd06909 349480 M14_ASPA Peptidase M14 Aspartoacylase (ASPA) subfamily. Aspartoacylase (ASPA) belongs to the Succinylglutamate desuccinylase/aspartoacylase subfamily of the M14 family of metallocarboxypeptidases. ASPA (also known as aminoacylase 2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. 190 matched cddid_all.tbl CDD cd06910 cd06910 349481 M14_ASTE_ASPA-like Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup. A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. 208 matched cddid_all.tbl CDD cd06911 cd06911 132874 VirB9_CagX_TrbG VirB9/CagX/TrbG, a component of the type IV secretion system. VirB9 is a component of the type IV secretion system, which is employed by pathogenic bacteria to export virulence proteins directly from the bacterial cytoplasm into the host cell. Unlike the more common type III secretion system, type IV systems evolved from the conjugative apparatus, which is used to transfer DNA between cells. VirB9 was initially identified as an essential virulence gene on the Agrobacterium tumefaciens Ti plasmid. In the pilin-like conjugative structure, VirB9 appears to form a stabilizing complex in the outer membrane, by interacting with the lipoprotein VirB7. The heterodimer has been shown to stabilize other components of the type IV system. This alignment model spans the C-terminal domain of VirB9. CagX is a component of the Helicobacter pylori cag PAI-encoded type IV secretion system. Some other members of this family are involved in conjugal transfer to T-DNA of plant cells. 86 matched cddid_all.tbl CDD cd06912 cd06912 133467 GT_MraY_like This subfamily is composed of uncharacterized bacterial glycosyltransferases in the MraY-like family. This family contains both eukaryotic and prokaryotic UDP-D-N-acetylhexosamine:polyprenol phosphate D-N-acetylhexosamine-1-phosphate transferases, which catalyze the transfer of a D-N-acetylhexosamine 1-phosphate to a membrane-bound polyprenol phosphate. This is the initiation step of protein N-glycosylation in eukaryotes and peptidoglycan biosynthesis in bacteria. The three bacterial members MraY, WecA, and WbpL/WbcO, utilize undecaprenol phosphate as the acceptor substrate, but use different UDP-sugar donor substrates. MraY-type transferases are highly specific for UDP-N-acetylmuramate-pentapeptide, whereas WecA proteins are selective for UDP-N-acetylglucosamine (UDP-GlcNAc). The WbcO/WbpL substrate specificity has not yet been determined, but the structure of their biosynthetic end products implies that UDP-N-acetyl-D-fucosamine (UDP-FucNAc) and/or UDPN-acetyl-D-quinosamine (UDP-QuiNAc) are used. The prokaryotic enzyme-catalyzed reactions lead to the formation of polyprenol-linked oligosaccharides involved in bacterial cell wall and peptidoglycan assembly. 193 matched cddid_all.tbl CDD cd06913 cd06913 133063 beta3GnTL1_like Beta 1, 3-N-acetylglucosaminyltransferase is essential for the formation of poly-N-acetyllactosamine . This family includes human Beta3GnTL1 and related eukaryotic proteins. Human Beta3GnTL1 is a putative beta-1,3-N-acetylglucosaminyltransferase. Beta3GnTL1 is expressed at various levels in most of tissues examined. Beta 1, 3-N-acetylglucosaminyltransferase has been found to be essential for the formation of poly-N-acetyllactosamine. Poly-N-acetyllactosamine is a unique carbohydrate composed of N-acetyllactosamine repeats. It is often an important part of cell-type-specific oligosaccharide structures and some functional oligosaccharides. It has been shown that the structure and biosynthesis of poly-N-acetyllactosamine display a dramatic change during development and oncogenesis. Several members of beta-1, 3-N-acetylglucosaminyltransferase have been identified. 219 matched cddid_all.tbl CDD cd06914 cd06914 133064 GT8_GNT1 GNT1 is a fungal enzyme that belongs to the GT 8 family. N-acetylglucosaminyltransferase is a fungal enzyme that catalyzes the addition of N-acetyl-D-glucosamine to mannotetraose side chains by an alpha 1-2 linkage during the synthesis of mannan. The N-acetyl-D-glucosamine moiety in mannan plays a role in the attachment of mannan to asparagine residues in proteins. The mannotetraose and its N-acetyl-D-glucosamine derivative side chains of mannan are the principle immunochemical determinants on the cell surface. N-acetylglucosaminyltransferase is a member of glycosyltransferase family 8, which are, based on the relative anomeric stereochemistry of the substrate and product in the reaction catalyzed, retaining glycosyltransferases. 278 matched cddid_all.tbl CDD cd06915 cd06915 133065 NTP_transferase_WcbM_like WcbM_like is a subfamily of nucleotidyl transferases. WcbM protein of Burkholderia mallei is involved in the biosynthesis, export or translocation of capsule. It is a subfamily of nucleotidyl transferases that transfer nucleotides onto phosphosugars. 223 matched cddid_all.tbl CDD cd06916 cd06916 143512 NR_DBD_like DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers. 72 matched cddid_all.tbl CDD cd06917 cd06917 270822 STKc_NAK1_like Catalytic domain of Fungal Nak1-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of Schizosaccharomyces pombe Nak1, Saccharomyces cerevisiae Kic1p (kinase that interacts with Cdc31p) and related proteins. Nak1 (also called N-rich kinase 1), is required by fission yeast for polarizing the tips of actin cytoskeleton and is involved in cell growth, cell separation, cell morphology and cell-cycle progression. Kic1p is required by budding yeast for cell integrity and morphogenesis. Kic1p interacts with Cdc31p, the yeast homologue of centrin, and phosphorylates substrates in a Cdc31p-dependent manner. The Nak1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 277 matched cddid_all.tbl CDD cd06919 cd06919 132994 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment model spans the precursor (or both beta and alpha chains) of aspartate decarboxylase. 111 matched cddid_all.tbl CDD cd06920 cd06920 132993 NEAT NEAr Transport domain, a component of cell surface proteins. NEAr Transporter (NEAT) domain; used by pathogenic bacteria to to scavenge heme-iron from host hemoproteins. The NEAT domain is a component of cell surface proteins (iron regulated surface determinants, or Isd, such as IsdA and IsdC) in various gram-positive bacteria, and may be arranged in tandem repeats. 117 matched cddid_all.tbl CDD cd06921 cd06921 211312 ChtBD1_GH19_hevein Hevein or Type 1 chitin binding domain subfamily co-occuring with family 19 glycosyl hydrolases or with barwin domains. This subfamily includes Hevein, a major IgE-binding allergen in natural rubber latex. ChtBD1 is a lectin domain found in proteins from plants and fungi that bind N-acetylglucosamine, plant endochitinases, wound-induced proteins, and the alpha subunit of Kluyveromyces lactis killer toxin. This domain is involved in the recognition and/or binding of chitin subunits; it typically occurs N-terminal to glycosyl hydrolase domains in chitinases, together with other carbohydrate-binding domains, or by itself in tandem-repeat arrangements. 40 matched cddid_all.tbl CDD cd06922 cd06922 211313 ChtBD1_GH18_1 Hevein or Type 1 chitin binding domain subfamily that co-occurs with family 18 glycosyl hydrolases. ChtBD1 is a lectin domain found in proteins from plants and fungi that bind N-acetylglucosamine, plant endochitinases, wound-induced proteins, and the alpha subunit of Kluyveromyces lactis killer toxin. This domain is involved in the recognition and/or binding of chitin subunits; it typically occurs N-terminal to glycosyl hydrolase domains in chitinases, together with other carbohydrate-binding domains, or by itself in tandem-repeat arrangements. 38 matched cddid_all.tbl CDD cd06923 cd06923 211314 ChtBD1_GH16 Hevein or Type 1 chitin binding domain subfamily that co-occurs with family 16 glycosyl hydrolases. This subfamily includes Saccharomyces cerevisiae Utr2p, also known as Crh2p, which participates in the cross-linking of chitin to beta(1-3)- and beta(1-6) glucan in the cell wall, and S. cerevisiae Crr1p, a putative transglycosidase which is needed for proper spore wall assembly. ChtBD1 is a lectin domain found in proteins from plants and fungi that bind N-acetylglucosamine, plant endochitinases, wound-induced proteins, and the alpha subunit of Kluyveromyces lactis killer toxin. This domain is involved in the recognition and/or binding of chitin subunits; it typically occurs N-terminal to glycosyl hydrolase domains in chitinases, together with other carbohydrate-binding domains, or by itself in tandem-repeat arrangements. 47 matched cddid_all.tbl CDD cd06926 cd06926 132902 RNAP_II_RPB11 RPB11 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB11 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. 93 matched cddid_all.tbl CDD cd06927 cd06927 132903 RNAP_L "L subunit of Archaeal RNA polymerase. The archaeal L subunit of RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A"", B'/B"" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer." 83 matched cddid_all.tbl CDD cd06928 cd06928 132904 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bacterial RNAP core enzyme consists of four subunits (beta', beta, alpha and omega). All residues in the alpha subunit that is involved in dimerization or in the interaction with other subunits are located within alphaNTD. 215 matched cddid_all.tbl CDD cd06929 cd06929 132727 NR_LBD_F1 Ligand-binding domain of nuclear receptor family 1. Ligand-binding domain (LBD) of nuclear receptor (NR) family 1: This is one of the major subfamily of nuclear receptors, including thyroid receptor, retinoid acid receptor, ecdysone receptor, farnesoid X receptor, vitamin D receptor, and other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 174 matched cddid_all.tbl CDD cd06930 cd06930 132728 NR_LBD_F2 Ligand-binding domain of nuclear receptor family 2. Ligand-binding domain (LBD) of nuclear receptor (NR) family 2: This is one of the major subfamily of nuclear receptors, including some well known nuclear receptors such as glucocorticoid receptor (GR), mineralocorticoid receptor (MR), estrogen receptor (ER), progesterone receptor (PR), and androgen receptor (AR), other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 165 matched cddid_all.tbl CDD cd06931 cd06931 132729 NR_LBD_HNF4_like The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes. The ligand binding domain of hepatocyte nuclear factor 4 (HNF4) like proteins: HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is constitutively active as a transcription activator. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, HNF4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD domain is also responsible for recruiting co-activator proteins. More than 280 nuclear receptors are found in C. ele gans, most of which are originated from an explosive burst of duplications of HNF4. 222 matched cddid_all.tbl CDD cd06932 cd06932 132730 NR_LBD_PPAR The ligand binding domain of peroxisome proliferator-activated receptors. The ligand binding domain (LBD) of peroxisome proliferator-activated receptors (PPAR): Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response element located upstream of the peroxisome proliferator responsive genes and interacts with co-activators. There are three subtypes of peroxisome proliferator activated receptors, alpha, beta (or delta), and gamma, each with a distinct tissue distribution. Several essential fatty acids, oxidized lipids and prostaglandin J derivatives can bind and activate PPAR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR has a central well conserved DNA binding domain (DBD), a variable N-terminal regulatory domain, a flexible hinge a nd a C-terminal ligand binding domain (LBD). 259 matched cddid_all.tbl CDD cd06933 cd06933 132731 NR_LBD_VDR The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily. The ligand binding domain of vitamin D receptors (VDR): VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of corepressors. Upon ligand binding, VDR forms heterodimer with the retinoid X receptor (RXR) that binds to vitamin D response elements (VDREs), recruits coactivators. This leads to the expression of a large number of genes. Approximately 200 human genes are considered to be primary targets of VDR and even more genes are regulated indirectly. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, VDR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 238 matched cddid_all.tbl CDD cd06934 cd06934 132732 NR_LBD_PXR_like The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor. The ligand binding domain of xenobiotic receptors: This xenobiotic receptor family includes pregnane X receptor (PXR), constitutive androstane receptor (CAR) and other related nuclear receptors. They function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The nuclear receptor pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. The ligand binding domain of PXR shows remarkable flexibility to accommodate both large and small molecules. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and elimination of these molecules from the cell. Constitutive androstane receptor (CAR) is a closest mammalian relative of PXR, which has also been proposed to function as a xenosensor. CAR is activated by some of the same ligands as PXR and regulates a subset of common genes. The sequence homology and functional similarity suggests that the CAR gene arose from a duplication of an ancestral PXR gene. Like other nuclear receptors, xenobiotic receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 226 matched cddid_all.tbl CDD cd06935 cd06935 132733 NR_LBD_TR The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors. The ligand binding domain (LBD) of thyroid hormone receptors: Thyroid hormone receptors are members of a superfamily of nuclear receptors. Thyroid hormone receptors (TR) mediate the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the heart to regulate heart rate and rhythm and TRbeta is active in the liver and other tissues. The unliganded TRs function as transcription repressors, by binding to thyroid hormone response elements (TRE) predominantly as homodimers, or as heterodimers with retinoid X-receptors (RXR), and being associated with a complex of proteins containing corepressor proteins. Ligand binding promotes corepressor dissociation and binding of a coactivator to activate transcription. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 243 matched cddid_all.tbl CDD cd06936 cd06936 132734 NR_LBD_Fxr The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors. The ligand binding domain (LBD) of Farnesoid X receptor: Farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily of ligand-activated transcription factors. FXR is highly expressed in the liver, the intestine, the kidney, and the adrenals. FXR plays key roles in the regulation of bile acid, cholesterol, triglyceride, and glucose metabolism. Evidences show that it also regulates liver regeneration. Upon binding of ligands, such as bile acid, an endogenous ligand, FXRs bind to FXR response elements (FXREs) either as a monomer or as a heterodimer with retinoid X receptor (RXR), and regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. There are two FXR genes (FXRalpha and FXRbeta) in mammals. A single FXRalpha gene encodes four isoforms resulting from differential use of promoters and alternative splicing. FXRbeta is a functional receptor in mice, rats, rabbits and dogs, but is a pseudogene in humans and primates. Like other members of the nuclear receptor (NR) superfamily, farnesoid X receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 221 matched cddid_all.tbl CDD cd06937 cd06937 132735 NR_LBD_RAR The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily. The ligand binding domain (LBD) of retinoic acid receptor (RAR): Retinoic acid receptors are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors. RARs mediate the biological effect of retinoids, including both naturally dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RARs function as heterodimers with retinoic X receptors by binding to specific RAR response elements (RAREs) found in the promoter regions of retinoid target genes. In the absence of ligand, the RAR-RXR heterodimer recruits the corepressor proteins NCoR or AMRT, and associated factors such as histone deacetylases or DNA-methyltransferases, leading to an inactive condensed chromatin structure, preventing transcription. Upon ligand binding, the corepressors are released, and coactivator complexes such as histone acetyltransferase or histone arginine methyltransferases are recruited to activate transcription. There are three RAR subtypes (alpha, beta, gamma), originating from three distinct genes. For each subtype, several isoforms exist that differ in their N-terminal region, allowing retinoids to exert their pleiotropic effects. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoic acid receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 231 matched cddid_all.tbl CDD cd06938 cd06938 132736 NR_LBD_EcR The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors super family. The ligand binding domain (LBD) of the ecdysone receptor: The ecdysone receptor (EcR) belongs to the superfamily of nuclear receptors (NRs) of ligand-dependent transcription factors. Ecdysone receptor is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. ECR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of ecdysone receptor are ecdysteroids#the endogenous steroidal hormones found in invertebrates. In addition, insecticide bisacylhydrazine used against pests has shown to act on EcR. EcR must be dimerised with a USP for high-affinity ligand binding to occur. The ligand binding triggers a conformational change in the C-terminal part of the EcR ligand-binding domain that leads to transcriptional activation of genes controlled by EcR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ec dysone receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 231 matched cddid_all.tbl CDD cd06939 cd06939 132737 NR_LBD_ROR_like The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily. The ligand binding domain (LBD) of Retinoid-related orphan receptors (RORs): Retinoid-related orphan receptors (RORs) are transcription factors belonging to the nuclear receptor superfamily. RORs are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. Transcription regulation by RORs is mediated through certain corepressors, as well as coactivators. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma that differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum, particularly in the regulation of the maturation and survival of Purkinje cells. RORbeta expression is largely restricted to several regions of the brain, the retina, and pineal gland. RORgamma is essential for lymph node organogenesis. Recently, it has been su ggested that cholesterol or a cholesterol derivative is the natural ligand of RORalpha. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoid-related orphan receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 241 matched cddid_all.tbl CDD cd06940 cd06940 132738 NR_LBD_REV_ERB The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily. The ligand binding domain (LBD) of REV-ERB receptors: REV-ERBs are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. The LBD domain of REV-ERB is unusual in the nuclear receptor family by lacking the AF-2 region that is responsible for coactivator interaction. REV-ERBs act as constitutive repressors because of their inability to bind coactivators. REV-ERB receptors can bind to two classes of DNA response elements as either a monomer or heterodimer, indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target gene. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, REV-ERB receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 189 matched cddid_all.tbl CDD cd06941 cd06941 132739 NR_LBD_DmE78_like The ligand binding domain of Drosophila ecdysone-induced protein 78, a member of the nuclear receptor superfamily. The ligand binding domain (LBD) of Drosophila ecdysone-induced protein 78 (E78) like: Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. Two isoforms of E78, E78A and E78B, are expressed from two nested transcription units. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. SmE78 may be involved in transduction of an ecdysone signal in S. mansoni, consistent with its function in Drosophila. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, E78-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 195 matched cddid_all.tbl CDD cd06942 cd06942 132740 NR_LBD_Sex_1_like The ligand binding domain of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein. The ligand binding domain (LBD) of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein like: Sex-1 protein of C. elegans is a transcription factor belonging to the nuclear receptor superfamily. Sex-1 plays pivotal role in sex fate of C. elegans by regulating the transcription of the sex-determination gene xol-1, which specifies male (XO) fate when active and hermaphrodite (XX) fate when inactive. The Sex-1 protein directly represses xol-1 transcription by binding to its promoter. However, the active ligand for Sex-1 protein has not yet been identified. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Sex-1 like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 191 matched cddid_all.tbl CDD cd06943 cd06943 132741 NR_LBD_RXR_like The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily. The ligand binding domain of the retinoid X receptor (RXR) and Ultraspiracle (USP): This family includes two evolutionary related nuclear receptors: retinoid X receptor (RXR) and Ultraspiracle (USP). RXR is a nuclear receptor in mammalian and USP is its counterpart in invertebrates. The native ligand of retinoid X receptor is 9-cis retinoic acid (RA). RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. RXRs can play different roles in these heterodimers. It acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear receptors. Ultraspiracle (USP) plays similar roles as DNA binding partner of other nuclear rec eptors in invertebrates. USP has no known high-affinity ligand and is thought to be a silent component in the heterodimeric complex with partner receptors. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, RXR and USP have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 207 matched cddid_all.tbl CDD cd06944 cd06944 132742 NR_LBD_Ftz-F1_like The ligand binding domain of FTZ-F1 like nuclear receptors. The ligand binding domain of FTZ-F1 like nuclear receptors: This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which required at several stages of development. Particularly, FTZ-F1 genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. SF-1 is an essential regulator of endocrine development and function and is considered a master regulator of reproduction; SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). However, the ligand for FTZ-F1 has not yet been identified. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 and SF-1 bind to DNA as a monomer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, receptors in this family have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 237 matched cddid_all.tbl CDD cd06945 cd06945 132743 NR_LBD_Nurr1_like The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear receptor superfamily. The ligand binding domain of nuclear receptor Nurr1_like: This family of nuclear receptors, including Nurr1, Nerve growth factor-induced-B (NGFI-B) and DHR38 are involved in the embryo development. Nurr1 is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of tr anscriptional initiation. Another group of receptor in this family is DHR38. DHR38 is the Drosophila homolog to the vertebrate NGFI-B-type orphan receptor. It interacts with the USP component of the ecdysone receptor complex, suggesting that DHR38 might modulate ecdysone-triggered signals in the fly, in addition to the ECR/USP pathway. Nurr1_like proteins exhibit a modular structure that is characteristic for nuclear receptors; they have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 239 matched cddid_all.tbl CDD cd06946 cd06946 132744 NR_LBD_ERR The ligand binding domain of estrogen receptor-related nuclear receptors. The ligand binding domain of estrogen receptor-related receptors (ERRs): The family of estrogen receptor-related receptors (ERRs), a subfamily of nuclear receptors, is closely related to the estrogen receptor (ER) family, but it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signaling pathway, positively or negatively. ERRs share target genes, co-regulators and promoters with the estrogen receptor (ER) family. There are three subtypes of ERRs: alpha, beta and gamma. ERRs bind at least two types of DNA sequence, the estrogen response element and another site, originally characterized as SF-1 (steroidogenic factor 1) response element. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ERR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 221 matched cddid_all.tbl CDD cd06947 cd06947 132745 NR_LBD_GR_Like Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid receptor , progesterone receptor, and androgen receptor. The ligand binding domain of GR_like nuclear receptors: This family of NRs includes four distinct, but closely related nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). These four receptors play key roles in some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family use multiple signaling pathways and share similar functional mechanisms. The dominant signaling pathway is via direct DNA binding and transcriptional regulation of target genes. Another mechanism is via protein-protein interactions, mainly with other transcription factors such as nuclear factor-kappaB and activator protein-1, to regulate gene expression patterns. Both pathways can up-regulate or down-regulate gene expression and require ligand activation of the receptor and recruitment of other cofactors such as chaperone proteins and coregulator proteins. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GR, MR, PR, and AR share the same modular structure with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 246 matched cddid_all.tbl CDD cd06948 cd06948 132746 NR_LBD_COUP-TF Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member of the nuclear receptor family. The ligand binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs): COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. In mammals two isoforms named COUP-TFI and COUP-TFII have been identified. Both genes show an exceptional homology and overlapping expression patterns, suggesting that they may serve redundant functions. Although COUP-TF was originally characterized as a transcriptional activator of the chicken ovalbumin gene, COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone receptors, such as retinoic acid receptor (RAR), thyroid hormone receptor (TR), vitamin D receptor (VDR), peroxisome proliferator activated receptor (PPAR), and hepatocyte nuclear factor 4 (HNF4). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, COUP-TFs have a central well cons erved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 236 matched cddid_all.tbl CDD cd06949 cd06949 132747 NR_LBD_ER Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen). The ligand binding domain (LBD) of Estrogen receptor (ER): Estrogen receptor, a member of nuclear receptor superfamily, is activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The C-terminal LBD also contains AF-2 activation motif, the dimerization motif, and part of the nuclear localization region. Estrogen receptor has been linked to aging, cancer, obesity and other diseases. 235 matched cddid_all.tbl CDD cd06950 cd06950 132748 NR_LBD_Tlx_PNR_like The ligand binding domain of Tailless-like proteins, orphan nuclear receptors. The ligand binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like family: This family includes photoreceptor cell-specific nuclear receptor (PNR), Tailless (TLX), and related receptors. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX and PNR have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 206 matched cddid_all.tbl CDD cd06951 cd06951 132749 NR_LBD_Dax1_like The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of DAX1-like proteins: This orphan nuclear receptor family includes DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) and the Small Heterodimer Partner (SHP). Both receptors have a typical ligand binding domain, but lack the DNA binding domain, typical to almost all of the nuclear receptors. They function as a transcriptional coregulator by directly interacting with other nuclear receptors. DAX1 and SHP can form heterodimers with each other, as well as with many other nuclear receptors. In addition, DAX1 can also form homodimers. DAX1 plays an important role in the normal development of several hormone-producing tissues. SHP has shown to regulate a variety of target genes. 222 matched cddid_all.tbl CDD cd06952 cd06952 132750 NR_LBD_TR2_like The ligand binding domain of the orphan nuclear receptors TR4 and TR2. The ligand binding domain of the TR4 and TR2 (human testicular receptor 4 and 2): TR4 and TR2 are orphan nuclear receptors. Several isoforms of TR4 and TR2 have been isolated in various tissues. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. The expression of TR2 is negatively regulated by androgen, retinoids, and radiation. The expression of both mouse TR2 and TR4 is up-regulated by neurocytokine ciliary neurotrophic factor (CNTF) in mouse. It has shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or TR4 include genes that are regulated by retinoic acid receptor, vitamin D receptor, peroxisome proliferator-activated receptor. TR4/2 binds to HREs as a dimer. Like other members of the nuclea r receptor (NR) superfamily of ligand-activated transcription factors, TR2-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 222 matched cddid_all.tbl CDD cd06953 cd06953 132751 NR_LBD_DHR4_like The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4. The ligand binding domain of Ecdysone-induced receptor DHR4: Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 213 matched cddid_all.tbl CDD cd06954 cd06954 132752 NR_LBD_LXR The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors. The ligand binding domain of Liver X receptors: Liver X receptors (LXRs) belong to a family of nuclear receptors of ligand-activated transcription factors. LXRs operate as cholesterol sensors which protect from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. Upon ligand binding a conformational change leads to recruitment of co-factors, which stimulates expression of target genes. Among the LXR target genes are several genes involved in cholesterol efflux from peripheral tissues such as the ATP-binding-cassette transporters ABCA1, ABCG1 and ApoE. There are two LXR isoforms in mammals, LXRalpha and LXRbeta. LXRalpha is expressed mainly in the liver, intestine, kidney, spleen, and adipose tissue, whereas LXRbeta is ubiquitously expressed at lower level. Both LXRalpha and LXRbeta function as heterodimers with the retinoid X receptor (RX R) which may be activated by either LXR ligands or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. LXR has typical NR modular structure with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and the ligand binding domain (LBD) at the C-terminal. 236 matched cddid_all.tbl CDD cd06955 cd06955 143513 NR_DBD_VDR DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of corepressors. Upon ligand binding, VDR forms a heterodimer with the retinoid X receptor (RXR) that binds to vitamin D response elements (VDREs), recruits coactivators. This leads to the expression of a large number of genes. Approximately 200 human genes are considered to be primary targets of VDR and even more genes are regulated indirectly. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, VDR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 107 matched cddid_all.tbl CDD cd06956 cd06956 143514 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor, or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear receptors. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, RXR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 77 matched cddid_all.tbl CDD cd06957 cd06957 143515 NR_DBD_PNR_like_2 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like is composed of two C4-type zinc fingers. The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR-like receptors have a central well-conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 82 matched cddid_all.tbl CDD cd06958 cd06958 143516 NR_DBD_COUP_TF DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. COUP-TFs homodimerize or heterodimerize with retinoid X receptor (RXR) and a few other nuclear receptors and bind to a variety of response elements that are composed of imperfect AGGTCA direct or inverted repeats with various spacings. COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone receptors such as retinoic acid receptor (RAR), thyroid hormone receptor (TR), vitamin D receptor (VDR), peroxisome proliferator activated receptor (PPAR), and hepatocyte nuclear factor 4 (HNF4). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, COUP-TFs have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 73 matched cddid_all.tbl CDD cd06959 cd06959 143517 NR_DBD_EcR_like The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: Ecdysone receptor (EcR), Liver X receptor (LXR) and Farnesoid X receptor (FXR). The DNA binding activity is regulated by their corresponding ligands. The ligands for EcR are ecdysteroids; LXR is regulated by oxidized cholesterol derivatives or oxysterols; and bile acids control FXR's activities. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 73 matched cddid_all.tbl CDD cd06960 cd06960 143518 NR_DBD_HNF4A DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is constitutively active as a transcription activator. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, HNF4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 76 matched cddid_all.tbl CDD cd06961 cd06961 143519 NR_DBD_TR DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TR interacts with the thyroid response element, which is a DNA site with direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs, upstream of target genes and modulates the rate of transcriptional initiation. Thyroid hormone receptor (TR) mediates the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the heart to regulate heart rate and rhythm and TRbeta is active in the liver and other tissues. The unliganded TRs function as transcription repressors, by binding to thyroid hormone response elements (TRE) predominantly as homodimers, or as heterodimers with retinoid X-receptors (RXR), and being associated with a complex of proteins containing corepressor proteins. Ligand binding promotes corepressor dissociation and binding of a coactivator to activate transcription. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 85 matched cddid_all.tbl CDD cd06962 cd06962 143520 NR_DBD_FXR DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. FXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. FXR is a member of the nuclear receptor family of ligand activated transcription factors. Bile acids are endogenous ligands for FXRs. Upon binding of a ligand, FXR binds to FXR response element (FXRE), which is an inverted repeat of TGACCT spaced by one nucleotide, either as a monomer or as a heterodimer with retinoid X receptor (RXR), to regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, FXR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 84 matched cddid_all.tbl CDD cd06963 cd06963 143521 NR_DBD_GR_like The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family of NRs includes four types of nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). The receptors bind to common DNA elements containing a partial palindrome of the core sequence 5'-TGTTCT-3' with a 3bp spacer. These four receptors regulate some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family have high sequence homology and share similar functional mechanisms. The dominant mechanism of function is by direct DNA binding and transcriptional regulation of target genes . The GR, MR, PR, and AR exhibit same modular structure. They have a central highly conserved DNA binding domain (DBD), a non-conserved N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 73 matched cddid_all.tbl CDD cd06964 cd06964 143522 NR_DBD_RAR DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RARs mediate the biological effect of retinoids, including both natural dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RAR function as a heterodimer with retinoic X receptor by binding to specific RAR response elements (RAREs), which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair and found in the promoter regions of retinoid target genes. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoic acid receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 85 matched cddid_all.tbl CDD cd06965 cd06965 143523 NR_DBD_Ppar DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive genes, and interacts with co-activators. Several essential fatty acids, oxidized lipids and prostaglandin J derivatives can bind and activate PPAR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR has a central well conserved DNA binding domain (DBD), a variable N-terminal regulatory domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 84 matched cddid_all.tbl CDD cd06966 cd06966 143524 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian relative of PXR and is activated by some of the same ligands as PXR and regulates a subset of common genes. The sequence homology and functional similarity suggests that the CAR gene arose from a duplication of an ancestral PXR gene. Like other nuclear receptors, CAR has a central well conserved DNA binding domain, a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain. 94 matched cddid_all.tbl CDD cd06967 cd06967 143525 NR_DBD_TR2_like DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. It has been shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or TR4 include genes that are regulated by retinoic acid receptor, vitamin D receptor, and peroxisome proliferator-activated receptor. TR4/2 binds to HREs as dimers. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TR2-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 87 matched cddid_all.tbl CDD cd06968 cd06968 143526 NR_DBD_ROR DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RORS are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum particularly in the regulation of the maturation and survival of Purkinje cells. RORbeta expression is largely restricted to several regions of the brain, the retina, and pineal gland. RORgamma is essential for lymph node organogenesis. Recently, it has been suggested that cholesterol or a cholesterol derivative are the natural ligands of RORalpha. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoid-related orphan receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 95 matched cddid_all.tbl CDD cd06969 cd06969 143527 NR_DBD_NGFI-B DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B. DNA-binding domain (DBD) of the orphan nuclear receptor, nerve growth factor-induced-B (NGFI-B) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NGFI-B interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. NGFI-B is a member of the nuclear-steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcriptional initiation. NGFI-B binds to the NGFI-B response element (NBRE) 5'-(A/T)AAAGGTCA as a monomer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, NGFI-B has a central well-conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 75 matched cddid_all.tbl CDD cd06970 cd06970 143528 NR_DBD_PNR DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of the nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 92 matched cddid_all.tbl CDD cd06971 cd06971 133477 PgpA Phosphatidylglycerophosphatase A; a bacterial membrane-associated enzyme involved in lipid metabolism. Phosphatidylglycerophosphatase A domain represents a family of bacterial membrane-associated enzymes involved in lipid metabolism. The prototype of this CD is a putative Phosphatidylglycerophosphatase A (PGPase A) from Listeria monocytogenes. PGPase A (EC: 3.1.3.27), encoded by the gene pgpA, specifically catalyzes the formation of phosphatidylglycerol from phosphatidyl glycerophosphate (PGP). It requires Mg2+ for activity and is inhibited by sulfhydryl agents and freezing/thawing. PGPase B encoded from pgpB is not included in this family, which also acts on phosphatidic acid (PA) and lysophosphatidic acid (LPA). Aside from PGPase A and B, evidence shows that there is another PGPase existing in E. coli. Thus, PGPase A is not essential for PGPase activity in E. coli. 143 matched cddid_all.tbl CDD cd06974 cd06974 132992 TerD_like Uncharacterized proteins involved in stress response, similar to tellurium resistance terD. Tellurium resistance terD like proteins. This family is composed of uncharacterized proteins involved in stress response, such as the tellurium resistance proteins, chemical-damaging agent resistance proteins, and general stress proteins from a variety of organisms. The tellurium resistance proteins are homologous terA,-D,-E,-F,-Z,-X gene products, which confer tellurium resistance mediated by plasmids. Currently, the biochemical mechanism of tellurium resistance remains unknown. The family also contains several ter gene homologues, YceC, YceD, YceE, for which there is no clear evidence for any involvement in the tellurium resistance. A putative cAMP-binding protin CABP1 shows a significant similarity to the terD protein and is also included in this family. 162 matched cddid_all.tbl CDD cd06975 cd06975 380380 cupin_BacB Bacillus subtilis bacilysin and related proteins, cupin domain. Bacilysin (BacB, also known as AerE in Microcystis aeruginosa) is a non-ribosomally synthesized dipeptide antibiotic that is produced and excreted by certain strains of Bacillus subtilis. It is an oxidase that catalyzes the synthesis of 2-oxo-3-(4-oxocyclohexa-2,5-dienyl)propanoic acid, a precursor to L-anticapsin. Each bacilysin monomer has two tandem cupin domains. It is active against a wide range of bacteria and some fungi. The antimicrobial activity of bacilysin is antagonized by glucosamine and N-acetyl glucosamine, indicating that bacilysin interferes with glucosamine synthesis, and thus, with the synthesis of microbial cell walls. AerE is thought to be involved in the formation of the 2-carboxy-6-hydroxyoctahydroindole (Choi) moiety found on all aeruginosin tetrapeptides, based on gene knock-out experiments. It is encoded by the aerE gene of the aerABCDEF aeruginosin biosynthesis gene cluster in Microcystis aeruginosa. 93 matched cddid_all.tbl CDD cd06976 cd06976 380381 cupin_MtlR-like_N "AraC/XylS family transcriptional regulators similar to MtlR, N-terminal cupin domain. MtlR is a Pseudomonas fluorescens protein that acts as a transcriptional regulator of the mannitol utilization genes. It has an N-terminal cupin domain (represented by this alignment) and a C-terminal AraC/XylS family helix-turn-helix (HTH) DNA-binding domain. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 83 matched cddid_all.tbl CDD cd06977 cd06977 380382 cupin_RhaR_RhaS-like_N "HTH-type transcriptional activator RhaR and RhaS and related proteins, N-terminal cupin domain. Members of this family contain an N-terminal cupin domain and a C-terminal AraC/XylS family helix-turn-helix (HTH) DNA-binding domain, including the HTH-type transcription activators RhaS and RhaR. RhaS and RhaR respond to the availability of L-rhamnose and activate transcription of the operons in the Escherichia coli L-rhamnose catabolic regulon. The E. coli RhaR protein activates expression of the rhaSR operon in the presence of its effector, L-rhamnose. The resulting RhaS protein (plus L-rhamnose) activates expression of the L-rhamnose catabolic operon rhaBAD as well as the transport operon rhaT. These proteins bind DNA as dimers, via their HTH motifs. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 147 matched cddid_all.tbl CDD cd06978 cd06978 380383 cupin_EctC "L-ectoine synthase, cupin domain. Ectoine synthase (EctC; also known as L-ectoine synthase or N-acetyldiaminobutyrate dehydratase; EC 4.2.1.108) is a cupin-like bacterial protein that converts N'-acetyldiaminobutyric acid to ectoine, in the last step of the L-ectoine biosynthetic pathway, via a cyclo-condensation reaction and using iron as the cofactor. Ectoines are potent microbial stress protectants, primarily synthesized by bacteria but also found in a few obligate halophilic protists and archaea, based on the ectoine biosynthetic ectABC gene. In halophilic eubacteria, the osmolytic ectoines enable the organisms to adapt to a wide range of salt concentrations by adjusting the cytoplasmic solute pool to the osmolarity of the surrounding environment. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 111 matched cddid_all.tbl CDD cd06979 cd06979 380384 cupin_RemF-like "Streptomyces resistomycificus RemF cyclase and related proteins, cupin domain. RemF cyclase is a manganese-containing polyketide cyclase present in bacteria that is involved in the biosynthesis of resistomycin, the aromatic pentacyclic metabolite in Streptomyces resistomycificus. Structure of this enzyme shows a cupin fold with a conserved ""jelly roll-like"" beta-barrel fold that forms a homodimer. It contains an unusual octahedral zinc-binding site in a large hydrophobic pocket that may represent the active site. The zinc ion, coordinated to four histidine side chains and two water molecules, could act as a Lewis acid in the aldol condensation reaction catalyzed by RemF, reminiscent of class II aldolases." 93 matched cddid_all.tbl CDD cd06980 cd06980 380385 cupin_bxe_c0505 "uncharacterized protein bxe_c0505, cupin domain. This family includes mostly bacterial proteins homologous to bxe_c0505, a Burkholderia xenovorans protein of unknown function. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 105 matched cddid_all.tbl CDD cd06981 cd06981 380386 cupin_reut_a1446 "Cupriavidus pinatubonensis reut_a1446 and related proteins, cupin domain. This family includes bacterial and some eukaryotic proteins homologous to reut_a1446, a Cupriavidus pinatubonensis protein of unknown function that may be related to mannose-6-phosphate isomerase. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 103 matched cddid_all.tbl CDD cd06982 cd06982 380387 cupin_BauB-like "Pseudomonas aeruginosa BauB and related proteins, cupin domain. This family includes bacterial proteins homologous to beta-alanine degradation protein BauB from Pseudomonas aeruginosa, which is involved in the degradation of beta-alanine. Also included are Rhodopseudomonas palustris Rpa4178 and Bordetella pertussis Bp2299, which are both proteins with unknown function. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 91 matched cddid_all.tbl CDD cd06983 cd06983 380388 cupin_dsy2733 "Desulfitobacterium hafniense dsy2733 and related proteins, cupin domain. This family includes bacterial proteins homologous to dsy2733, a Desulfitobacterium hafniense protein of unknown function. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 81 matched cddid_all.tbl CDD cd06984 cd06984 380389 cupin_Moth_1897 "uncharacterized Methanocaldococcus jannaschii Moth_1897 and related proteins, cupin domain. This family includes archaeal and bacterial proteins homologous to Moth_1897, a Methanocaldococcus jannaschii protein of unknown function. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 83 matched cddid_all.tbl CDD cd06985 cd06985 380390 cupin_BF4112 "Bacteroides fragilis BF4112 and related proteins, cupin domain. This family includes archaeal and bacterial proteins homologous to BF4112, a Bacteroides fragilis protein of unknown function. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 101 matched cddid_all.tbl CDD cd06986 cd06986 380391 cupin_MmsR-like_N AraC/XylS family transcriptional regulators similar to MmsR, N-terminal cupin domain. This family contains bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included is MmsR, a bacterial transcriptional regulator thought to positively regulate the expression of the mmsAB operon. The mmsAB operon contains two structural genes involved in valine metabolism: mmsA which encodes methylmalonate-semialdehyde dehydrogenase, and mmsB which encodes 3-hydroxyisobutyrate dehydrogenase. The cupin domain of members of this subfamily does not contain a metal binding site. 84 matched cddid_all.tbl CDD cd06987 cd06987 380392 cupin_MAE_RS03005 "Microcystis aeruginosa MAE_RS03005 and related proteins, cupin domain. This family includes bacterial and some eukaryotic proteins homologous to MAE_RS03005, a Microcystis aeruginosa protein of unknown function. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 122 matched cddid_all.tbl CDD cd06988 cd06988 380393 cupin_DddK "Dimethylsulfoniopropionate lyase DddK and related proteins, cupin domain. This family includes mostly bacterial proteins homologous to dimethylsulfoniopropionate lyase DddK from marine bacterium Pelagibacter. DddK cleaves dimethylsulfoniopropionate (DMSP), the organic osmolyte and antioxidant produced in marine environments, and yields acrylate and the climate-active gas dimethyl sulfide (DMS). DddK contains a double-stranded beta-helical motif which utilizes various divalent metal ions as cofactors for catalytic activity; however, nickel, an abundant metal ion in marine environments, confers the highest DMSP lyase activity. Also included in this family is Plu4264, a Photorhabdus luminescens manganese-containing cupin shown to have similar metal binding site to TM1287 decarboxylase, but two very different substrate binding pockets. The Plu4264 binding pocket shows a cavity and substrate entry point more than twice as large as and more hydrophobic than TM1287, suggesting that Plu4264 accepts a substrate that is significantly larger than that of TM1287, a putative oxalate decarboxylase. Thus, the function of Plu4264 could be similar to that of TM1287 but with a larger, less charged substrate. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 76 matched cddid_all.tbl CDD cd06989 cd06989 380394 cupin_DRT102 "Arabidopsis thaliana DRT102 and related proteins, cupin domain. This family includes bacterial and eukaryotic proteins homologous to DNA-damage-repair/toleration protein DRT102 found in Arabidopsis thaliana. DRT102 may be involved in DNA repair from UV damage. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 97 matched cddid_all.tbl CDD cd06990 cd06990 380395 cupin_DUF861 domain of unknown function DUF 861, cupin domain. This family contains proteins which seem to be specific to bacteria and some fungi. The function of this family is unknown but contains a cupin domain without a metal binding site. Cupins are a functionally diverse superfamily originally discovered based on the highly conserved motif found in germin and germin-like proteins. This conserved motif forms a beta-barrel fold found in all of the cupins, giving rise to the name cupin (cupa is the Latin term for small barrel). 101 matched cddid_all.tbl CDD cd06991 cd06991 380396 cupin_TcmJ-like "TcmJ monooxygenase and related proteins, cupin domain. This family includes TcmJ, a subunit of the tetracenomycin (TCM) polyketide synthase (PKS) type II complex in Streptomyces glaucescens. TcmJ is a quinone-forming monooxygenase involved in the modification of aromatic polyketides synthesized by polyketide synthases of types II and III. Orthologs of TcmJ include the Streptomyces BenD (benastatin biosynthetic pathway), the Streptomyces olivaceus ElmJ (polyketide antibiotic elloramycin biosynthetic pathway), the Actinomadura hibisca PdmL (pradimicin biosynthetic pathway), the Streptomyces cyaneus CurC (curamycin biosynthetic pathway), the Streptomyces rishiriensis Lct30 (lactonamycin biosynthetic pathway), and the Streptomyces WhiE II (spore pigment polyketide biosynthetic pathway). Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 105 matched cddid_all.tbl CDD cd06992 cd06992 380397 cupin_GDO-like_C gentisate 1,2-dioxygenase, 1-hydroxy-2-naphthoate dioxygenase, and salicylate 1,2-dioxygenase bicupin aromatic ring-cleaving dioxygenases, C-terminal cupin domain. This model represents the C-terminal cupin domains of three closely related bicupin aromatic ring-cleaving dioxygenases: gentisate 1,2-dioxygenase (GDO), salicylate 1,2-dioxygenase (SDO), and 1-hydroxy-2-naphthoate dioxygenase (NDO). GDO catalyzes the cleavage of the gentisate (2,5-dihydroxybenzoate) aromatic ring, a key step in the gentisate degradation pathway allowing soil bacteria to utilize 2,5-xylenol, 3,5-xylenol, and m-cresol as sole carbon and energy sources. NDO catalyzes the cleavage of 1-hydroxy-2-naphthoate as part of the bacterial phenanthrene degradation pathway. SDO is a ring cleavage dioxygenase from Pseudaminobacter salicylatoxidans that oxidizes salicylate to 2-oxohepta-3,5-dienedioic acid via a novel ring fission mechanism. SDO differs from other known GDO's and NDO's in its unique ability to oxidatively cleave many different salicylate, gentisate, and 1-hydroxy-2- naphthoate substrates with high catalytic efficiency. The active site of this enzyme is located in the N-terminal domain but could be influenced by changes in the C-terminal domain, which lacks the strictly conserved metal-binding residues found in other cupin domains and is thought to be an inactive vestigial remnant. 99 matched cddid_all.tbl CDD cd06993 cd06993 380398 cupin_CENP-C_C "centromere-binding protein CENP-C, C-terminal cupin domain. This family includes centromeric protein C (CENP-C; known as Mif2 in budding yeast and centromere protein 3 or cnp3 in fission yeast), which is an inner kinetochore centromere (CEN)-binding protein found in fungi and metazoans. CENP-C is a component of the CENP-A nucleosome-associated complex (NAC) that plays a central role in assembly of kinetochore proteins, mitotic progression and chromosome segregation. CENP-C localizes to the inner kinetochore plates adjacent to the centromeric DNA and is known to have DNA-binding ability. CENP-C, along with CENP-H, provides a platform onto which the mitotic kinetochore is assembled and thus plays a critical role in the structuring of kinethocore chromatin. The cupin domain at the C-terminus forms a homodimer which is part of an enhanceosome-like structure that nucleates kinetochore assembly in budding yeast. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 77 matched cddid_all.tbl CDD cd06995 cd06995 380399 cupin_YkgD-like_N "AraC/XylS family transcriptional regulators similar to Escherichia coli YkgD, N-terminal cupin domain. This family contains mostly bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included in this family is YkgD, an uncharacterized Escherichia coli protein thought to be a transcriptional regulator. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 114 matched cddid_all.tbl CDD cd06996 cd06996 380400 cupin_Lmo2851-like_N "AraC/XylS family transcriptional regulators similar to Listeria monocytogenes Lmo2851 protein, N-terminal cupin domain. This family contains bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators. Included is Listeria monocytogenes Lmo2851 protein, whose function is unknown. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 87 matched cddid_all.tbl CDD cd06997 cd06997 380401 cupin_MelR-like_N "AraC/XylS family transcriptional regulators similar to Escherichia coli MelR, N-terminal cupin domain. This family contains bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators, including Escherichia coli MelR, a transcription factor that controls melibiose utilization. MelR is encoded by the melR gene and is essential for melibiose-dependent triggering of the melAB operon that encodes products needed for melibiose catabolism and transport. Expression of melR is autoregulated by MelR, which represses the melR promoter by binding to a target that overlaps the transcript start. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 78 matched cddid_all.tbl CDD cd06998 cd06998 380402 cupin_D-LI-like "sugar isomerase such as lyxose isomerase, cupin domain. This family includes D-lyxose isomerase (D-LI; EC 5.3.1.15) homologous to YdaE from the sigma B regulon of Bacillus subtilis and to pathogenic Escherichia coli O157 z5688 D-lyxose isomerase (EcSI or Z5688), both having highly similar active sites. YdaE may have a synergistic role with ydaD, an NAD(P)-dependent alcohol dehydrogenase, in the adaptation to environment stresses, while EcSI has D-lyxose/D-mannose activity. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 100 matched cddid_all.tbl CDD cd06999 cd06999 380403 cupin_HpaA-like_N "AraC/XylS family transcriptional regulators similar to HpaA, N-terminal cupin domain. Members of this family contain an N-terminal cupin domain and a C-terminal AraC/XylS family helix-turn-helix (HTH) DNA-binding domain, similar to Escherichia coli 4-hydroxyphenylacetate catabolism regulatory protein HpaA (also known as 4HPA). HpaA is encoded by the hpaA gene which is located upstream of hpaBC. It is activated by 4-HPA, 3-HPA and phenylacetate, and represents a member of the AraC/XylS family of regulators that recognizes aromatic effectors. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 98 matched cddid_all.tbl CDD cd07000 cd07000 380404 cupin_HGO_N "homogentisate 1,2-dioxygenase and related proteins, N-terminal cupin domain. This family includes homogentisate 1,2-dioxygenase (also known as homogentisate oxygenase, homogentisic acid oxidase, homogentisicase, HGO, HGD, HGDO, or HmgA; EC 1.13.11.5), which is involved in the metabolic degradation of phenylalanine and tyrosine. It catalyzes the crucial aromatic ring opening reaction, utilizing nonheme Fe2+ to incorporate both atoms of molecular oxygen into homogentisate (2,5-dihydroxyphenylacetate) to yield 4-maleylacetoacetate as part of the homogentisate pathway. HGO deficiency caused by critical mutations and polymorphic sites, causes the metabolic disease alkaptonuria (AKU), a rare disorder of autosomal recessive inheritance. Homogentisate accumulation causes insoluble ochronotic pigments to deposit in connective tissues, resulting in degenerative arthritis. These enzymes are found in prokaryotes, eukaryotes, and archaea. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 109 matched cddid_all.tbl CDD cd07001 cd07001 380405 cupin_YbfI-like_N "AraC/XylS family transcriptional regulators similar to Bacillus subtilis YbfI, N-terminal cupin domain. This family contains bacterial proteins containing an AraC/XylS family helix-turn-helix (HTH) DNA-binding domain C-terminal to a cupin domain, and may be possible transcriptional regulators, including YbfI, an uncharacterized Bacillus subtilis. In Pseudomonas putida, this protein is thought to regulate the expression of phenylserine aldolase. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 76 matched cddid_all.tbl CDD cd07002 cd07002 380406 cupin_SznF-like_C "Streptomyces achromogenes SznF and related proteins, C-terminal cupin domain. This family includes bacterial proteins similar to Streptomyces achromogenes SznF, containing an N-terminal helical region that mediates dimerization, a central heme oxygenase domain, and a C-terminal cupin domain. SznF is a metalloenzyme that catalyzes an oxidative rearrangement of the guanidine group of N(omega)-methyl-L-arginine to generate an N-nitrosourea product, during the biosynthesis of streptozotocin, an N-nitrosourea natural product and an approved cancer chemotherapeutic. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold generally capable of homodimerization. However, in SznF, the cupin domain is not involved in dimerization." 96 matched cddid_all.tbl CDD cd07003 cd07003 380407 cupin_YobQ-like_N "Bacillus subtilis YobQ and related proteins, N-terminal cupin domain. This family includes bacterial proteins homologous to Bacillus subtilis YobQ and Photobacterium leiognathi LumQ, both uncharacterized proteins thought to be DNA-binding proteins that may function as AraC/XylS family transcriptional regulators. YobQ has an N-terminal cupin beta barrel domain (represented by this alignment model) and a C-terminal AraC/XylS family helix-turn-helix (HTH) DNA-binding domain. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 66 matched cddid_all.tbl CDD cd07005 cd07005 380408 cupin_WbuC-like "Escherichia coli WbuC and related proteins, cupin domain. This family includes bacterial proteins homologous to WbuC, an Escherichia coli protein of unknown function with a cupin beta barrel fold. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 114 matched cddid_all.tbl CDD cd07006 cd07006 380409 cupin_XcTcmJ-like "Xanthomonas campestris XcTcmJ and related proteins, cupin domain. This family includes bacterial and archaeal proteins homologous to plant pathogen Xanthomonas campestris tetracenomycin polyketide synthesis protein XcTcmJ, a protein encoded by the tcmJ gene. XcTcmJ is annotated as being involved in tetracenomycin polyketide biosynthesis. Also included is Xc5357 from a different strain of X. campestris. Structure studies show that binding of zinc induces conformational changes and serves a functional role in this cupin protein. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 89 matched cddid_all.tbl CDD cd07007 cd07007 380410 cupin_CapF-like_C "Staphylococcus aureus CapF and related proteins, C-terminal cupin domain. This family contains cupin domains of proteins homologous to Staphylococcus aureus CapF (also known as WbjC in Pseudomonas aeruginosa and FnlB in Escherichia coli). CapF is a bifunctional metalloenzyme produced by certain pathogenic bacteria and is essential in the biosynthetic path of capsular polysaccharide (CP), a mucous layer on the surface of bacterium that facilitates immune evasion and infection. Thus, CapF is an antibacterial/therapeutic target. In S. aureus, enzymes CapE, CapF and CapG catalyze the sequential transformation of UDP-D-GlcNAc in the CP precursor UDP-L-FucNAc via the intermediate compound UDP-N-acetyl-L-talosamine (UDP-L-TalNAc). CapF consists of two domains; the C-terminal cupin domain catalyzes the epimerization of the compound produced by the upstream enzyme CapE, and the N-terminal short-chain dehydrogenase/reductase (SDR) domain catalyzes the reduction of the compound afforded by the cupin domain, requiring one equivalent of NADPH. The cupin domain is crucial for catalyzing the first chemical reaction, and also important for the stability of the enzyme. Similarly, in P. aeruginosa, WbjC, WbjB and WbjD enzymes synthesize UDP-N-acetyl-L-fucosamine, a precursor of the lipopolysacharide component L-fucosamine. The cupin domains contain a conserved ""jelly roll-like"" beta-barrel fold." 109 matched cddid_all.tbl CDD cd07008 cd07008 380411 cupin_yp_001338853-like "Klebsiella pneumoniae yp_001338853.1 and related proteins, cupin domain. This family includes bacterial proteins homologous to Klebsiella pneumoniae yp_001338853.1, an uncharacterized conserved protein with double-stranded beta-helix domain. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 101 matched cddid_all.tbl CDD cd07009 cd07009 380412 cupin_BLL0285-like "Bradyrhizobium japonicum BLL0285 and related proteins, cupin domain. This family includes bacterial proteins homologous to BLL0285, a Bradyrhizobium japonicum protein of unknown function. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 81 matched cddid_all.tbl CDD cd07010 cd07010 380413 cupin_PMI_type_I_N_bac Phosphomannose isomerase in bacteria and archaea, N-terminal cupin domain. This subfamily contains type I phosphomannose isomerase (PMI; E.C. 5.3.1.8; also known as mannose-6-phosphate isomerase) found in many bacteria (e.g. Bacillus subtilis) and archaea. PMI catalyzes the reversible isomerization of fructose-6-phosphate (F6P) and mannose-6-phosphate (M6P), the first committed step in the synthesis of mannosylated glycoproteins. The active site, located within the N-terminal jelly roll-like beta-barrel cupin fold, contains a single essential zinc atom and forms a deep, open cavity large enough to contain M6P or F6P. PMI type I also has a C-terminal beta-barrel fold which has diverged considerably from the N-terminal domain and is not included here. This subfamily does not contain an alpha helical domain that exists in eukaryotic and some prokaryotic PMIs. F6P is a substrate for glycolysis and gluconeogenesis, while M6P is a substrate for production of activated mannose donor guanosine 5'-diphosphate D-mannose, an important precursor of mannosylated biomolecules such as glycoproteins, bacterial exopolysaccharides and fungal cell wall components. PMI is also essential for survival, virulence and possibly pathogenicity of some bacteria and protozoan parasites, as well as for cell wall integrity of certain yeasts. Thus, PMI is a potential target against fungal infections causing serious illness or death. 173 matched cddid_all.tbl CDD cd07011 cd07011 380414 cupin_PMI_type_I_N type I phosphomannose isomerase in eukaryotes and bacteria, N-terminal cupin domain. This subfamily contains type I phosphomannose isomerase (PMI; E.C. 5.3.1.8; also known as mannose-6-phosphate isomerase) found in eukaryotes and some bacteria such as Salmonella enterica. PMI catalyzes the reversible isomerization of fructose-6-phosphate (F6P) and mannose-6-phosphate (M6P), the first committed step in the synthesis of mannosylated glycoproteins. The active site, located within the N-terminal jelly roll-like beta-barrel cupin fold, contains a single essential zinc atom and forms a deep, open cavity large enough to contain M6P or F6P. PMI type I also has a C-terminal beta-barrel fold which has diverged considerably from the N-terminal domain and is not included here. This subfamily contains an alpha helical domain that is found in eukaryotic and some prokaryotic PMIs but is not present in their archaeal counterparts. F6P is a substrate for glycolysis and gluconeogenesis, while M6P is a substrate for production of activated mannose donor guanosine 5'-diphosphate D-mannose, an important precursor of mannosylated biomolecules such as glycoproteins, bacterial exopolysaccharides and fungal cell wall components. PMI is also essential for survival, virulence and possibly pathogenicity of some bacteria and protozoan parasites, as well as for cell wall integrity of certain yeasts. Thus, PMI is a potential target against fungal infections causing serious illness or death. 247 matched cddid_all.tbl CDD cd07012 cd07012 270234 PBP2_Bug_TTT Bug (Bordetella uptake gene) protein family of periplasmic solute-binding receptors; contains the type 2 periplasmic binding fold. The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) proteins present in a number of bacterial species, but mainly in proteobacteria. In eubacteria, at least three families of periplasmic binding-protein dependent transporters are known: the ATP-binding cassette (ABC) transporters, the tripartite ATP-independent periplasmic transporters, and the tripartite tricarboxylate transporters (TTT). Bug proteins are the PBP components of the TTT. Their expansive expansion in proteobacteria indicates a large functional diversity. The best studied examples are Bordetella pertussis BugD, which is an aspartic acid transporter, and BugE, which is glutamate transporter. 291 matched cddid_all.tbl CDD cd07013 cd07013 132924 S14_ClpP Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease. Clp protease (caseinolytic protease; ClpP; Peptidase S14) is a highly conserved serine protease present throughout in bacteria and eukaryota, but seems to be absent in archaea, mollicutes and some fungi. Clp proteases are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. Additionally, they are implicated in the control of cell growth, targeting DNA-binding protein from starved cells. ClpP has also been linked to the tight regulation of virulence genes in the pathogens Listeria monocytogenes and Salmonella typhimurium. This enzyme belong to the family of ATP-dependent proteases; the functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP, although the proteolytic subunit alone does possess some catalytic activity. Active site consists of the triad Ser, His and Asp; some members have lost all of these active site residues and are therefore inactive, while others may have one or two large insertions. ClpP seems to prefer hydrophobic or non-polar residues at P1 or P1' positions in its substrate. The protease exists as a tetradecamer made up of two heptameric rings stacked back-to-back such that the catalytic triad of each subunit is located at the interface between three monomers, thus making oligomerization essential for function. 162 matched cddid_all.tbl CDD cd07014 cd07014 132925 S49_SppA Signal peptide peptidase A. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppA is an intramembrane enzyme found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Unlike the eukaryotic functional homologs that are proposed to be aspartic proteases, site-directed mutagenesis and sequence analysis have shown these bacterial, archaeal and thylakoid SppAs to be ClpP-like serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain, cleaving peptide bonds in the plane of the lipid bilayer. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad (both residues absolutely conserved within bacteria, chloroplast and mitochondrial signal peptidase family members) and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. In addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members, the E. coli SppA contains an amino-terminal domain (sometimes referred to as 67K type). Others, including sohB peptidase, protein C, protein 1510-N and archaeal signal peptide peptidase, do not contain the amino-terminal domain (sometimes referred to as 36K type). Interestingly, the single membrane spanning E. coli SppA carries out catalysis using a Ser-Lys dyad with the serine located in the conserved carboxy-terminal protease domain and the lysine in the non-conserved amino-terminal domain. This family also contains homologs that either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases. 177 matched cddid_all.tbl CDD cd07015 cd07015 132926 Clp_protease_NfeD Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cleaving hydrophobic substrates. Difference in oligomeric form and catalytic residues between 1510-N (forming a dimer) and ClpP (forming a tetradecamer) shows a possible functional difference: 1510-N is likely to have a regulatory function while ClpP is involved in protein quality control. 172 matched cddid_all.tbl CDD cd07016 cd07016 132927 S14_ClpP_1 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease. Clp protease (caseinolytic protease; ClpP; Peptidase S14) is a highly conserved serine protease present throughout in bacteria and eukaryota, but seems to be absent in archaea, mollicutes and some fungi. This subfamily only contains bacterial sequences. Clp proteases are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. ClpP has also been linked to the tight regulation of virulence genes in the pathogens Listeria monocytogenes and Salmonella typhimurium. This enzyme belong to the family of ATP-dependent proteases; the functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP, although the proteolytic subunit alone does possess some catalytic activity. Active site consists of the triad Ser, His and Asp; some members have lost all of these active site residues and are therefore inactive, while others may have one or two large insertions. ClpP seems to prefer hydrophobic or non-polar residues at P1 or P1' positions in its substrate. The protease exists as a tetradecamer made up of two heptameric rings stacked back-to-back such that the catalytic triad of each subunit is located at the interface between three monomers, thus making oligomerization essential for function. 160 matched cddid_all.tbl CDD cd07017 cd07017 132928 S14_ClpP_2 Caseinolytic protease (ClpP) is an ATP-dependent, highly conserved serine protease. Clp protease (caseinolytic protease; ClpP; Peptidase S14) is a highly conserved serine protease present throughout in bacteria and eukaryota, but seems to be absent in archaea, mollicutes and some fungi. Clp proteases are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. ClpP has also been linked to the tight regulation of virulence genes in the pathogens Listeria monocytogenes and Salmonella typhimurium. This enzyme belong to the family of ATP-dependent proteases; the functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP, although the proteolytic subunit alone does possess some catalytic activity. Active site consists of the triad Ser, His and Asp; some members have lost all of these active site residues and are therefore inactive, while others may have one or two large insertions. ClpP seems to prefer hydrophobic or non-polar residues at P1 or P1' positions in its substrate. The protease exists as a tetradecamer made up of two heptameric rings stacked back-to-back such that the catalytic triad of each subunit is located at the interface between three monomers, thus making oligomerization essential for function. 171 matched cddid_all.tbl CDD cd07018 cd07018 132929 S49_SppA_67K_type Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 67K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily contain an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Unlike the eukaryotic functional homologs that are proposed to be aspartic proteases, site-directed mutagenesis and sequence analysis have shown that members in this subfamily, mostly bacterial, are serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad (both residues absolutely conserved within bacteria, chloroplast and mitochondrial signal peptidase family members) and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. Interestingly, the single membrane spanning E. coli SppA carries out catalysis using a Ser-Lys dyad with the serine located in the conserved carboxy-terminal protease domain and the lysine in the non-conserved amino-terminal domain. 222 matched cddid_all.tbl CDD cd07019 cd07019 132930 S49_SppA_1 Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppAs in this subfamily are found in all three domains of life and are involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Site-directed mutagenesis and sequence analysis have shown these bacterial, archaeal and thylakoid SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad (both residues absolutely conserved within bacteria, chloroplast and mitochondrial signal peptidase family members) and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. In addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members, the E. coli SppA contains an amino-terminal domain, similar to Arabidopsis thaliana SppA1 peptidase. Others, including sohB peptidase, protein C and archaeal signal peptide peptidase, do not contain the amino-terminal domain. Interestingly, the single membrane spanning E. coli SppA carries out catalysis using a Ser-Lys dyad with the serine located in the conserved carboxy-terminal protease domain and the lysine in the non-conserved amino-terminal domain. 211 matched cddid_all.tbl CDD cd07020 cd07020 132931 Clp_protease_NfeD_1 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cleaving hydrophobic substrates. Difference in oligomeric form and catalytic residues between 1510-N (forming a dimer) and ClpP (forming a tetradecamer) shows a possible functional difference: 1510-N is likely to have a regulatory function while ClpP is involved in protein quality control. 187 matched cddid_all.tbl CDD cd07021 cd07021 132932 Clp_protease_NfeD_like Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cleaving hydrophobic substrates. Difference in oligomeric form and catalytic residues between 1510-N (forming a dimer) and ClpP (forming a tetradecamer) shows a possible functional difference: 1510-N is likely to have a regulatory function while ClpP is involved in protein quality control. 178 matched cddid_all.tbl CDD cd07022 cd07022 132933 S49_Sppa_36K_type Signal peptide peptidase A (SppA) 36K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 36K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily are all bacterial and include sohB peptidase and protein C. These are sometimes referred to as 36K type since they contain only one domain, unlike E. coli SppA that also contains an amino-terminal domain. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. 214 matched cddid_all.tbl CDD cd07023 cd07023 132934 S49_Sppa_N_C Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. This subfamily contains members with either a single domain (sometimes referred to as 36K type), such as sohB peptidase, protein C and archaeal signal peptide peptidase, or an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad and not the usual Ser-His-Asp catalytic triad found in the majority of serine proteases. Interestingly, the single membrane spanning E. coli SppA carries out catalysis using a Ser-Lys dyad with the serine located in the conserved carboxy-terminal protease domain and the lysine in the non-conserved amino-terminal domain. 208 matched cddid_all.tbl CDD cd07025 cd07025 132882 Peptidase_S66 LD-Carboxypeptidase, a serine protease, includes microcin C7 self immunity protein. LD-carboxypeptidase (Muramoyltetrapeptide carboxypeptidase; EC 3.4.17.13; Merops family S66; initially described as Carboxypeptidase II) family also includes the microcin c7 self-immunity protein (MccF) as well as uncharacterized proteins including hypothetical proteins. LD-carboxypeptidase hydrolyzes the amide bond that links the dibasic amino acids to C-terminal D-amino acids. The physiological substrates of LD-carboxypeptidase are tetrapeptide fragments (such as UDP-MurNAc-tetrapeptides) that are produced when bacterial cell walls are degraded; they contain an L-configured residue (L-lysine or meso-diaminopimelic acid residue) as the penultimate residue and D-alanine as the ultimate residue. A possible role of LD-carboxypeptidase is in peptidoglycan recycling whereby the resulting tripeptide (precursor for murein synthesis) can be reconverted into peptidoglycan by attachment of preformed D-Ala-D-Ala dipeptides. Some enzymes possessing LD-carboxypeptidase activity also act as LD-transpeptidase by replacing the terminal D-Ala with another D-amino acid. MccF contributes to self-immunity towards microcin C7 (MccC7), a ribosomally encoded peptide antibiotic that contains a phosphoramidate linkage to adenosine monophosphate at its C-terminus. Its possible biological role is to defend producer cells against exogenous microcin from re-entering after having been exported. It is suggested that MccF is involved in microcin degradation or sequestration in the periplasm. 282 matched cddid_all.tbl CDD cd07026 cd07026 197305 Ribosomal_L20 Ribosomal protein L20. The ribosomal protein family L20 contains members from eubacteria, as well as their mitochondrial and plastid homologs. L20 is an assembly protein, required for the first in-vitro reconstitution step of the 50S ribosomal subunit, but does not seem to be essential for ribosome activity. L20 has been shown to partially unfold in the absence of RNA, in regions corresponding to the RNA-binding sites. L20 represses the translation of its own mRNA via specific binding to two distinct mRNA sites, in a manner similar to the L20 interaction with 23S ribosomal RNA. 106 matched cddid_all.tbl CDD cd07027 cd07027 132905 RNAP_RPB11_like RPB11 subunit of RNA polymerase. The eukaryotic RPB11 subunit of RNA polymerase (RNAP), as well as its archaeal (L subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts. 83 matched cddid_all.tbl CDD cd07028 cd07028 132906 RNAP_RPB3_like RPB3 subunit of RNA polymerase. The eukaryotic RPB3 subunit of RNA polymerase (RNAP), as well as its archaeal (D subunit) and bacterial (alpha subunit) counterparts, is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar to the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the archaeal (D/L subunits) and bacterial (alpha subunit) counterparts. 212 matched cddid_all.tbl CDD cd07029 cd07029 132907 RNAP_I_III_AC19 AC19 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC19 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC19 subunit is the equivalent of the RPB11 subunit of RNAP II. The RPB11 subunit heterodimerizes with the RPB3 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC19 to RPB11 suggests a similar function. The AC19 subunit is likely to associate with the RPB3 counterpart, AC40, to form a heterodimer, which stabilizes the association of the two largest subunits of RNAP I and RNAP III. 85 matched cddid_all.tbl CDD cd07030 cd07030 132908 RNAP_D "D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A"", B'/B"" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The assembly of the two largest archaeal RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of the archaeal D/L heterodimer." 259 matched cddid_all.tbl CDD cd07031 cd07031 132909 RNAP_II_RPB3 RPB3 subunit of Eukaryotic RNA polymerase II. The eukaryotic RPB3 subunit of RNA polymerase (RNAP) II is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP II is responsible for the synthesis of mRNA precursor. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization, and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. 265 matched cddid_all.tbl CDD cd07032 cd07032 132910 RNAP_I_II_AC40 AC40 subunit of Eukaryotic RNA polymerase (RNAP) I and RNAP III. The eukaryotic AC40 subunit of RNA polymerase (RNAP) I and RNAP III is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III. RNAP I is responsible for the synthesis of ribosomal RNA precursor, while RNAP III functions in the synthesis of 5S and tRNA. The AC40 subunit is the equivalent of the RPB3 subunit of RNAP II. The RPB3 subunit is similar to the bacterial RNAP alpha subunit in that it contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The RPB3 subunit heterodimerizes with the RPB11 subunit, and together with RPB10 and RPB12, anchors the two largest subunits, RPB1 and RPB2, and stabilizes their association. The homology of AC40 to RPB3 suggests a similar function. The AC40 subunit is likely to associate with the RPB11 counterpart, AC19, to form a heterodimer, which stabilizes the association of the two largest subunits of RNAP I and RNAP III. 291 matched cddid_all.tbl CDD cd07033 cd07033 132916 TPP_PYR_DXS_TK_like Pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and related proteins. Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain of 1-deoxy-D-xylulose-5-phosphate synthase (DXS), transketolase (TK), and the beta subunits of the E1 component of the human pyruvate dehydrogenase complex (E1- PDHc), subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this sub-family. Like many TPP-dependent enzymes DXS and TK are homodimers having a PYR and a PP domain on the same subunit. TK has two active sites per dimer which lie between PYR and PP domains of different subunits. For DXS each active site is located at the interface of a PYR and a PP domain from the same subunit. E1-PDHc is an alpha2beta2 dimer-of-heterodimers having two active sites but having the PYR and PP domains arranged on separate subunits, the PYR domains on the beta subunits, the PP domains on the alpha subunits. DXS is a regulatory enzyme of the mevalonate-independent pathway involved in terpenoid biosynthesis, it catalyzes a transketolase-type condensation of pyruvate with D-glyceraldehyde-3-phosphate to form 1-deoxy-D-xylulose-5-phosphate (DXP) and carbon dioxide. TK catalyzes the transfer of a two-carbon unit from ketose phosphates to aldose phosphates. In heterotrophic organisms, TK provides a link between glycolysis and the pentose phosphate pathway and provides precursors for nucleotide, aromatic amino acid and vitamin biosynthesis. TK also plays a central role in the Calvin cycle in plants. PDHc catalyzes the irreversible oxidative decarboxylation of pyruvate to produce acetyl-CoA in the bridging step between glycolysis and the citric acid cycle. This subfamily includes the beta subunits of the E1 component of the acetoin dehydrogenase complex (ADC) and the branched chain alpha-keto acid dehydrogenase/2-oxoisovalerate dehydrogenase complex (BCADC). ADC participates in the breakdown of acetoin. BCADC catalyzes the oxidative decarboxylation of 4-methyl-2-oxopentanoate, 3-methyl-2-oxopentanoate and 3-methyl-2-oxobutanoate during the breakdown of branched chain amino acids. 156 matched cddid_all.tbl CDD cd07034 cd07034 132917 TPP_PYR_PFOR_IOR-alpha_like Pyrimidine (PYR) binding domain of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase alpha subunit (IOR-alpha), and related proteins. Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain, of pyruvate ferredoxin oxidoreductase (PFOR), indolepyruvate ferredoxin oxidoreductase (IOR) alpha subunit (IOR-alpha), and related proteins, subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this sub-family. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. For many of these enzymes the active sites lie between PP and PYR domains on different subunits. However, for the homodimeric enzyme Desulfovibrio africanus pyruvate:ferredoxin oxidoreductase (PFOR), each active site lies at the interface of the PYR and PP domains from the same subunit. This subfamily includes proteins characterized as pyruvate NADP+ oxidoreductase (PNO). PFOR and PNO catalyze the oxidative decarboxylation of pyruvate to form acetyl-CoA, a crucial step in many metabolic pathways. The facultative anaerobic mitochondrion of the photosynthetic protist Euglena gracilis oxidizes pyruvate with PNO. IOR catalyzes the oxidative decarboxylation of arylpyruvates, such as indolepyruvate or phenylpyruvate. 160 matched cddid_all.tbl CDD cd07035 cd07035 132918 TPP_PYR_POX_like Pyrimidine (PYR) binding domain of POX and related proteins. Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of pyruvate oxidase (POX) and related protiens subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. For glyoxylate carboligase, which belongs to this subfamily, but lacks this conserved glutamate, the rate of the initial TPP activation step is reduced but the ensuing steps of the enzymic reaction proceed efficiently. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this sub-family. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites, for many the active sites lie between PP and PYR domains on different subunits. POX decarboxylates pyruvate, producing hydrogen peroxide and the energy-storage metabolite acetylphosphate. This subfamily includes pyruvate decarboxylase (PDC) and indolepyruvate decarboxylase (IPDC). PDC catalyzes the conversion of pyruvate to acetaldehyde and CO2 in alcoholic fermentation. IPDC plays a role in the indole-3-pyruvic acid (IPA) pathway in plants and various plant-associated bacteria, it catalyzes the decarboxylation of IPA to IAA. This subfamily also includes the large catalytic subunit of acetohydroxyacid synthase (AHAS). AHAS catalyzes the condensation of two molecules of pyruvate to give the acetohydroxyacid, 2-acetolactate, a precursor of the branched chain amino acids, valine and leucine. AHAS also catalyzes the condensation of pyruvate and 2-ketobutyrate to form 2-aceto-2-hydroxybutyrate in isoleucine biosynthesis. Methanococcus jannaschii sulfopyruvate decarboxylase (MjComDE) and phosphonopyruvate decarboxylase (PpyrDc) also belong to this subfamily. PpyrDc is a homotrimeric enzyme having the PP and PYR domains tandemly arranged on the same subunit. It functions in the biosynthesis of C-P compounds such as bialaphos tripeptide in Streptomyces hygroscopicus. MjComDE is a dodecamer having the PYR and PP domains on different subunits, it has six alpha (PYR/ComD) subunits and six beta (PP/ComE) subunits. MjComDE catalyzes the decarboxylation of sulfopyruvic acid to sulfoacetaldehyde in the coenzyme M pathway. 155 matched cddid_all.tbl CDD cd07036 cd07036 132919 TPP_PYR_E1-PDHc-beta_like Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins. Thiamine pyrophosphate (TPP) family, pyrimidine (PYR) binding domain of the beta subunits of the E1 components of: human pyruvate dehydrogenase complex (E1- PDHc), the acetoin dehydrogenase complex (ADC), and the branched chain alpha-keto acid dehydrogenase/2-oxoisovalerate dehydrogenase complex (BCADC), subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this sub-family. E1-PDHc is an alpha2beta2 dimer-of-heterodimers having two active sites lying between PYR and PP domains of separate subunits, the PYR domains are arranged on the beta subunit, the PP domains on the alpha subunits. PDHc catalyzes the irreversible oxidative decarboxylation of pyruvate to produce acetyl-CoA in the bridging step between glycolysis and the citric acid cycle. ADC participates in the breakdown of acetoin. BCADC catalyzes the oxidative decarboxylation of 4-methyl-2-oxopentanoate, 3-methyl-2-oxopentanoate and 3-methyl-2-oxobutanoate during the breakdown of branched chain amino acids. 167 matched cddid_all.tbl CDD cd07037 cd07037 132920 TPP_PYR_MenD Pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase (MenD) and related proteins. Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate (SEPHCHC) synthase (MenD) subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this sub-family. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. Escherichia coli MenD (EcMenD) is a homotetramer (dimer-of-homodimers), having two active sites per homodimer lying between PYR and PP domains of different subunits. EcMenD catalyzes a Stetter-like conjugate addition of alpha-ketoglutarate to isochorismate, leading to the formation of SEPHCHC and carbon dioxide, this addition is the first committed step in the biosynthesis of vitamin K2 (menaquinone). 162 matched cddid_all.tbl CDD cd07038 cd07038 132921 TPP_PYR_PDC_IPDC_like Pyrimidine (PYR) binding domain of pyruvate decarboxylase (PDC), indolepyruvate decarboxylase (IPDC) and related proteins. Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of pyruvate decarboxylase (PDC) and indolepyruvate decarboxylase (IPDC) subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this sub-family. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites, for many the active sites lie between PP and PYR domains on different subunits. PDC catalyzes the conversion of pyruvate to acetaldehyde and CO2 in alcoholic fermentation. IPDC plays a role in the indole-3-pyruvic acid (IPA) pathway in plants and various plant-associated bacteria, it catalyzes the decarboxylation of IPA to IAA. Also belonging to this group is Mycobacterium tuberculosis alpha-keto acid decarboxylase (MtKDC) which participates in amino acid degradation via the Ehrlich pathway, and Lactococcus lactis branched-chain keto acid decarboxylase (KdcA) an enzyme identified as being involved in cheese ripening, which exhibits a very broad substrate range in the decarboxylation and carboligation reactions. 162 matched cddid_all.tbl CDD cd07039 cd07039 132922 TPP_PYR_POX Pyrimidine (PYR) binding domain of POX. Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of pyruvate oxidase (POX) subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. The PYR and PP domains have a common fold, but do not share strong sequence conservation. The PP domain is not included in this sub-family. Most TPP-dependent enzymes have the PYR and PP domains on the same subunit although these domains can be alternatively arranged in the primary structure. TPP-dependent enzymes are multisubunit proteins, the smallest catalytic unit being a dimer-of-active sites. Lactobacillus plantarum POX is a homotetramer (dimer-of-homodimers), having two active sites per homodimer lying between PYR and PP domains of different subunits. POX decarboxylates pyruvate, producing hydrogen peroxide and the energy-storage metabolite acetylphosphate. 164 matched cddid_all.tbl CDD cd07040 cd07040 132716 HP Histidine phosphatase domain found in a functionally diverse set of proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction. Catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This set of proteins includes cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, histidine acid phosphatases, phytases, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system; phytases scavenge phosphate from extracellular sources. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. Clinical applications include the use of prostatic acid phosphatase (PAP) as a serum marker for prostate cancer. Agricultural applications include the addition of phytases to animal feed. 153 matched cddid_all.tbl CDD cd07041 cd07041 132912 STAS_RsbR_RsbS_like "Sulphate Transporter and Anti-Sigma factor antagonist domain of the ""stressosome"" complex proteins RsbS and RsbR, regulators of the bacterial stress activated alternative sigma factor sigma-B by phosphorylation. The STAS (Sulphate Transporter and Anti-Sigma factor antagonist) domain of proteins related to RsbS and RsbR which are part of the ""stressosome"" complex that plays an important role in the regulation of the bacterial stress activated alternative sigma factor sigma-B. During stress conditions RsbS and RsbR are phosphorylated which leads to the release of RsbT, an activator of of the RsbU phosphatase, which in turn activates RsbV which leads to the release and activation of sigma factor B. RsbS is a single domain protein (STAS domain), while RsbR-like proteins have a well-conserved C-terminal STATS domain and a variable N-terminal domain. The STAS domain is also found in the C- terminal region of sulphate transporters and anti-anti-sigma factors." 109 matched cddid_all.tbl CDD cd07042 cd07042 132913 STAS_SulP_like_sulfate_transporter Sulphate Transporter and Anti-Sigma factor antagonist domain of SulP-like sulfate transporters, plays a role in the function and regulation of the transport activity, proposed general NTP binding function. The SulP family is a large and diverse family of anion transporters, with members from eubacteria, plants, fungi, and mammals. They contain 10 to 14 transmembrane helices which form the catalytic core of the protein and a C-terminal extension, the STAS (Sulphate Transporter and AntiSigma factor antagonist) domain which plays a role in the function and regulation of the transport activity. The STAS domain is found in the C-terminal region of sulphate transporters and bacterial anti-sigma factor antagonists. It has been suggested that this domain may have a general NTP binding function. 107 matched cddid_all.tbl CDD cd07043 cd07043 132914 STAS_anti-anti-sigma_factors Sulphate Transporter and Anti-Sigma factor antagonist) domain of anti-anti-sigma factors, key regulators of anti-sigma factors by phosphorylation. Anti-anti-sigma factors play an important role in the regulation of several sigma factors and their corresponding anti-sigma factors. Upon dephosphorylation they bind the anti-sigma factor and induce the release of the sigma factor from the anti-sigma factor. In a feedback mechanism the anti-anti-sigma factor can be inactivated via phosphorylation by the anti-sigma factor. Well studied examples from Bacillus subtilis are SpoIIAA (regulating sigmaF and sigmaC which play an important role in sporulation) and RsbV (regulating sigmaB involved in the general stress response). The STAS domain is also found in the C- terminal region of sulphate transporters and stressosomes. 99 matched cddid_all.tbl CDD cd07044 cd07044 132871 CofD_YvcK Family of CofD-like proteins and proteins related to YvcK. CofD is a 2-phospho-L-lactate transferase that catalyzes the last step in the biosynthesis of coenzyme F(420)-0 (F(420) without polyglutamate) by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0). F420 is a hydride carrier, important for energy metabolism of methanogenic archaea, as well as for the biosynthesis of other natural products, like tetracycline in Streptomyces. F420 and some of its precursors are also utilized as cofactors for enzymes, like DNA photolyase in Mycobacterium tuberculosis. YvcK from Bacillus subtilis is a member of a family of mostly uncharacterized proteins and has been proposed to play a role in carbon metabolism, since its function is essential for growth on intermediates of the Krebs cycle and pentose phosphate pathway. Both families appear to have a conserved phosphate binding site, but have different substrate binding residues conserved within each family. 309 matched cddid_all.tbl CDD cd07045 cd07045 132885 BMC_CcmK_like Carbon dioxide concentrating mechanism K (CcmK)-like proteins, Bacterial Micro-Compartment (BMC) domain. Bacterial micro-compartments are primitive protein-based organelles that sequester specific metabolic pathways in bacterial cells. The prototypical bacterial microcompartment is the carboxysome shell, a bacterial polyhedral organelle which increase the efficiency of CO2 fixation by encapsulating RuBisCO and carbonic anhydrase. They can be divided into two types: alpha-type carboxysomes (alpha-cyanobacteria and proteobacteria) and beta-type carboxysomes (beta-cyanobacteria). Potential functional differences between the two types are not yet fully understood. In addition to these proteins there are several homologous shell proteins including those found in pdu organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol and eut organelles involved in the cobalamin-dependent degradation of ethanolamine. Structure evidence shows that several carboxysome shell proteins and their homologs (Csos1A, CcmK1,2,4, and PduU) exist as hexamers which might further assemble into extended, tightly packed layers hypothesized to represent the flat facets of the polyhedral organelles outer shell. Although it has been suggested that other homologous proteins in this family might also form hexamers and play similar functional roles in the construction of their corresponding organelle outer shells at present no experimental evidence directly supports this view. 84 matched cddid_all.tbl CDD cd07046 cd07046 132886 BMC_PduU-EutS 1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain. PduU encapsulates several related enzymes within a shell composed of a few thousand protein subunits. PduU exists as a hexamer which might further assemble into the flat facets of the polyhedral outer shell of the pdu organelle. This proteinaceous noncarboxysome microcompartment is involved in coenzyme B12-dependent degradation of 1,2-propanediol. The core of PduU is related to the typical BMC domain and its natural oligomeric state is a cyclic hexamer. Unlike other typical BMC domain proteins, the 3D topology of PduU reveals a circular permuted variation on the typical BMC fold which leads to several unique features. The exact functions related to those unique features are still not clear. Another difference is the presence of a deep cavity on one side of the hexamer as well as an intermolecular six-stranded beta barrel that seems to block the central pore that is present in other BMC domain proteins. EutS proteins included in this CD are sequence homologs of PduU. They are encoded within eut operon and may be required for the formation of the outer shell of bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutS might also form hexamers and play similar functional roles in the construction of the eut organelle outer shell at present no experimental evidence directly supports this view. 110 matched cddid_all.tbl CDD cd07047 cd07047 132887 BMC_PduB_repeat1 1,2-propanediol utilization protein B (PduB), Bacterial Micro-Compartment (BMC) domain repeat 1. PduB proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduB might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view. PduB proteins contain two tandem BMC domains repeats. This CD contains repeat 1 (the first BMC domain of PduB). 134 matched cddid_all.tbl CDD cd07048 cd07048 132888 BMC_PduB_repeat2 1,2-propanediol utilization protein B (PduB), Bacterial Micro-Compartment (BMC) domain repeat 2. PduB proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduB might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the pdu organelles at present no experimental evidence directly supports this view. PduB proteins contain two tandem BMC domains repeats. This CD contains repeat 2 (the second BMC domain of PduB). 70 matched cddid_all.tbl CDD cd07049 cd07049 132889 BMC_EutL_repeat1 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1. EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 1 (the first BMC domain of EutL). 103 matched cddid_all.tbl CDD cd07050 cd07050 132890 BMC_EutL_repeat2 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 2. EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 2 (the second BMC domain of EutL). 87 matched cddid_all.tbl CDD cd07051 cd07051 132891 BMC_like_1_repeat1 Bacterial Micro-Compartment (BMC)-like domain 1 repeat 1. BMC-like domains exist in cyanobacteria, proteobacteria, and actinobacteria and are homologs of the carboxysome shell proteins. They might be encoded from putative organelles involved in unknown metabolic process. Although it has been suggested that these carboxysome shell protein homologs form hexamers and further assemble into the flat facets of the polyhedral bacterial organelles shell at present no experimental evidence exists to directly support this view. Proteins in this CD contain two tandem BMC domains. This CD includes repeat 1 (the first BMC domain of BMC like 1 proteins). 111 matched cddid_all.tbl CDD cd07052 cd07052 132892 BMC_like_1_repeat2 Bacterial Micro-Compartment (BMC)-like domain 1 repeat 2. BMC-like domains exist in cyanobacteria, proteobacteria, and actinobacteria and are homologs of the carboxysome shell proteins. They might be encoded from putative organelles involved in unknown metabolic process. Although it has been suggested that these carboxysome shell protein homologs form hexamers and further assemble into the flat facets of the polyhedral bacterial organelles shell at present no experimental evidence exists to directly support this view. Proteins in this CD contain two tandem BMC domains. This CD includes repeat 2 (the second BMC domain of BMC like 1 proteins). 79 matched cddid_all.tbl CDD cd07053 cd07053 132893 BMC_PduT_repeat1 1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 1. PduT proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduT might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view. PduT proteins contain two tandem BMC domains repeats. This CD contains repeat 1 (the first BMC domain of PduT) as well as carboxysome shell protein sequence homolog, EutM protein, are also included in this CD. They too might exist as hexamers and might play similar functional roles in the construction of the eut organelle outer shell which still remains poorly understood. 76 matched cddid_all.tbl CDD cd07054 cd07054 132894 BMC_PduT_repeat2 1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 2. PduT proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduT might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles, at present no experimental evidence directly supports this view. PduT proteins contain two tandem BMC domains repeats. This CD contains repeat 2 (the second BMC domain of PduT) as well as carboxysome shell protein sequence homolog, EutM protein, are also included in this CD. They too might exist as hexamers and might play similar functional roles in the construction of the eut organelle outer shell which still remains poorly understood. 78 matched cddid_all.tbl CDD cd07055 cd07055 132895 BMC_like_2 Bacterial Micro-Compartment (BMC)-like domain 2. BMC like 2 domains exist in cyanobacteria, proteobacteria, and actinobacteria and are homologs of carboxysome shell proteins. They might be encoded from putative organelles involved in unknown metabolic process. Although it has been suggested that these carboxysome shell protein homologs form hexamers and further assemble into the flat facets of the polyhedral bacterial organelles shell at present no experimental evidence exists to directly support this view. 61 matched cddid_all.tbl CDD cd07056 cd07056 132896 BMC_PduK 1,2-propanediol utilization protein K (PduK), Bacterial Micro-Compartment (BMC) domain repeat 1l. PduK proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduK might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view. 77 matched cddid_all.tbl CDD cd07057 cd07057 132897 BMC_CcmK Carbon dioxide concentrating mechanism (CcmK); Bacterial Micro-Compartment (BMC) domain. CcmK1-4 and CcmL proteins found in Synechocystis sp. strain PCC 6803 make up the beta carboxysome shell. These CcmK proteins have been shown to form hexameric units, while the CcmL proteins have been shown to form pentameric units. Together these proteins further assemble into the flat facets of the polyhedral carboxysome shell. The structures suggest that the central pores and the gaps between hexamers limit the transport of metabolites into and out of the the carboxysome. 88 matched cddid_all.tbl CDD cd07058 cd07058 132898 BMC_CsoS1 Carboxysome Shell 1 (CsoS1); Bacterial Micro-Compartment (BMC) domain. The cso operon in Halothiobacillus neapolitanus contains the genes involved in alpha carboxysome function including those for the carboxysome shell proteins: CsoS1A, CsoS1B, and CsoS1C. CsoS1A has been shown to form hexameric units which further assemble into the flat facets of the polyhedral carboxysome shell. The structures suggest that the central pores and the gaps between hexamers limit the transport of metabolites into and out of the the carboxysome. Although it has been suggested that other homologous proteins, CsoS1B and CsoS1C, in this family might also form hexamers and play similar functional roles in the construction of carboxysome outer shell at present no experimental evidence directly supports this view. 88 matched cddid_all.tbl CDD cd07059 cd07059 132899 BMC_PduA 1,2-propanediol utilization protein A (PduA), Bacterial Micro-Compartment (BMC) domain. PduA is encoded within the 1,2-propanediol utilization (pdu) operon along with other homologous carboxysome shell proteins PduB, B', J, K, T, and U. PduA is thought to be required for the formation of the outer shell of bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduA might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles, like PduU does, at present no experimental evidence directly supports this view. 85 matched cddid_all.tbl CDD cd07060 cd07060 349952 SPOUT_MTase SPOUT superfamily of SAM-dependent RNA methyltransferases. The SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, also known as class IV methyltransferase family, is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. Members of the SPOUT superfamily that have been characterized functionally are involved in post-transcriptional RNA modification by catalyzing methylation of the 2-OH group of ribose, the N-1 atom of guanosine 37 in tRNA, or the N-3 atom of uridine 1498 in 16S rRNA. 99 matched cddid_all.tbl CDD cd07061 cd07061 132717 HP_HAP_like Histidine phosphatase domain found in histidine acid phosphatases and phytases; contains a His residue which is phosphorylated during the reaction. Catalytic domain of HAP (histidine acid phosphatases) and phytases (myo-inositol hexakisphosphate phosphohydrolases). The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. Functions in this subgroup include roles in metabolism, signaling, or regulation, for example Escherichia coli glucose-1-phosphatase functions to scavenge glucose from glucose-1-phosphate and the signaling molecules inositol 1,3,4,5,6-pentakisphosphate (InsP5) and inositol hexakisphosphate (InsP6) are in vivo substrates for eukaryotic multiple inositol polyphosphate phosphatase 1 (Minpp1). Phytases scavenge phosphate from extracellular sources and are added to animal feed while prostatic acid phosphatase (PAP) has been used for many years as a serum marker for prostate cancer. Recently PAP has been shown in mouse models to suppress pain by functioning as an ecto-5prime-nucleotidase. In vivo it dephosphorylates extracellular adenosine monophosphate (AMP) generating adenosine,and leading to the activation of A1-adenosine receptors in dorsal spinal cord. 242 matched cddid_all.tbl CDD cd07062 cd07062 132883 Peptidase_S66_mccF_like Microcin C7 self-immunity protein determines resistance to exogenous microcin C7. Microcin C7 self-immunity protein (mccF): MccF, a homolog of the LD-carboxypeptidase family, mediates resistance against exogenously added microcin C7 (MccC7), a ribosomally-encoded peptide antibiotic that contains a phosphoramidate linkage to adenosine monophosphate at its C-terminus. The plasmid-encoded mccF gene is transcribed in the opposite direction to the other five genes (mccA-E) and is required for the full expression of immunity but not for production. The catalytic triad residues (Ser, His, Glu) of LD-carboxypeptidase are also conserved in MccF, strongly suggesting that MccF shares the hydrolytic activity with LD-carboxypeptidases. Substrates of MccF have not been deduced, but could likely be microcin C7 precursors. The possible role of MccF is to defend producer cells against exogenous microcin from re-entering after having been exported. It is suggested that MccF is involved in microcin degradation or sequestration in the periplasm. 308 matched cddid_all.tbl CDD cd07064 cd07064 132881 AlkD_like_1 A new structural DNA glycosylase containing HEAT-like repeats. This domain represents a new and uncharacterized structural superfamily of DNA glycosylases that form an alpha-alpha superhelix fold that are not belong to the identified five structural DNA glycosylase superfamilies (UDG, AAG/MNPG, MutM/Fpg and helix-hairpin-helix). DNA glycosylases removing alkylated base residues have been identified in all organisms investigated and may be universally present in nature. DNA glycosylases catalyze the first step in Base Excision Repair (BER) pathway by cleaving damaged DNA bases within double strand DNA to produce an abasic site. The resulting abasic site is further processed by AP endonuclease, phosphodiesterase, DNA polymerases, and DNA ligase functions to restore the DNA to an undamaged state. All glycosylase examined to date utilize a similar strategy for binding DNA and base flipping despite their structural diversity. The known structures for members of this family, AlkC and AlkD from Bacillus cereus, are distant homologues and are composed of six variant HEAT (Huntington/Elongation/ A subunit/Target of rapamycin) repeats. HEAT motifs are ~45-amino acid sequences that form antiparallel alpha-helices, which are packed by a conserved hyrophobic interface and are tandemly repeated to form superhelical alpha-structures. AlkD and AlkC are specific for removal of 3-methyladenine (3mA) and 7-methylguanine (7mG) from the DNA by base excision repair. Homologues of AlkC and AlkD were also identified in other organisms. 208 matched cddid_all.tbl CDD cd07066 cd07066 143549 CRD_FZ CRD_domain cysteine-rich domain, also known as Fz (frizzled) domain. CRD_FZ is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines. 119 matched cddid_all.tbl CDD cd07067 cd07067 132718 HP_PGM_like Histidine phosphatase domain found in phosphoglycerate mutases and related proteins, mostly phosphatases; contains a His residue which is phosphorylated during the reaction. Subgroup of the catalytic domain of a functionally diverse set of proteins, most of which are phosphatases. The conserved catalytic core of this domain contains a His residue which is phosphorylated in the reaction. This subgroup contains cofactor-dependent and cofactor-independent phosphoglycerate mutases (dPGM, and BPGM respectively), fructose-2,6-bisphosphatase (F26BP)ase, Sts-1, SixA, and related proteins. Functions include roles in metabolism, signaling, or regulation, for example, F26BPase affects glycolysis and gluconeogenesis through controlling the concentration of F26BP; BPGM controls the concentration of 2,3-BPG (the main allosteric effector of hemoglobin in human blood cells); human Sts-1 is a T-cell regulator; Escherichia coli Six A participates in the ArcB-dependent His-to-Asp phosphorelay signaling system. Deficiency and mutation in many of the human members result in disease, for example erythrocyte BPGM deficiency is a disease associated with a decrease in the concentration of 2,3-BPG. 153 matched cddid_all.tbl CDD cd07068 cd07068 132753 NR_LBD_ER_like The ligand binding domain of estrogen receptor and estrogen receptor-related receptors. The ligand binding domain of estrogen receptor (ER) and estrogen receptor-related receptors (ERRs): Estrogen receptors are a group of receptors which are activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. ERRs are closely related to the estrogen receptor (ER) family. But, it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signaling pathway, positively or negatively. ERRs share target genes, co-regulators and promoters with the estrogen receptor (ER) family. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER and ERRs have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 221 matched cddid_all.tbl CDD cd07069 cd07069 132754 NR_LBD_Lrh-1 The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,. The ligand binding domain (LBD) of the liver receptor homolog-1 (LRH-1): LRH-1 belongs to nuclear hormone receptor superfamily, and is expressed mainly in the liver, intestine, exocrine pancreas, and ovary. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 binds DNA as a monomer, and is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. Recently, phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, LRH-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 241 matched cddid_all.tbl CDD cd07070 cd07070 132755 NR_LBD_SF-1 The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear receptor superfamily. The ligand binding domain of nuclear receptor steroidogenic factor 1 (SF-1): SF-1, a member of the nuclear hormone receptor superfamily, is an essential regulator of endocrine development and function and is considered a master regulator of reproduction. Most nuclear receptors function as homodimer or heterodimers, however SF-1 binds to its target genes as a monomer, recognizing the variations of the DNA sequence motif, T/CCA AGGTCA. SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been determined as potential ligands of SF-1. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, SF-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 237 matched cddid_all.tbl CDD cd07071 cd07071 132756 NR_LBD_Nurr1 The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of nuclear receptor Nurr1: Nurr1 belongs to the conserved family of nuclear receptors. It is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Nurr1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 238 matched cddid_all.tbl CDD cd07072 cd07072 132757 NR_LBD_DHR38_like Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily. The ligand binding domain of nuclear receptor DHR38_like proteins: DHR38 is a member of the steroid receptor superfamily in Drosophila. DHR38 interacts with the USP component of the ecdysone receptor complex, suggesting that DHR38 might modulate ecdysone-triggered signals in the fly, in addition to the ECR/USP pathway. At least four differentially expressed mRNA isoforms have been detected during development. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR38 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 239 matched cddid_all.tbl CDD cd07073 cd07073 132758 NR_LBD_AR Ligand binding domain of the nuclear receptor androgen receptor, ligand activated transcription regulator. The ligand binding domain of the androgen receptor (AR): AR is a member of the nuclear receptor family. It is activated by binding either of the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for male primary sexual characteristics and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of an androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR-regulated genes and modulates their expression. Another mode of action is independent of their interactions with DNA. The receptors interact directly with signal transduction proteins in the cytoplasm, causing rapid changes in cell function, such as ion transport. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, AR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD is not only involved in binding to androgen, but also involved in binding of coactivator proteins and dimerization. A ligand dependent nuclear export signal is also present at the ligand binding domain. 246 matched cddid_all.tbl CDD cd07074 cd07074 132759 NR_LBD_PR Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor. The ligand binding domain of the progesterone receptor (PR): PR is a member of the nuclear receptor superfamily of ligand dependent transcription factors, mediating the biological actions of progesterone. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, protein processing, and metabolism. When no binding hormone is present the carboxyl terminal inhibits transcription. Binding to a hormone induces a structural change that removes the inhibitory action. After progesterone binds to the receptor, PR forms a dimer and the complex enters the nucleus where it interacts with the hormone response element (HRE) in the promoters of progesterone responsive genes and alters their transcription. In addition, rapid actions of PR that occur independent of transcription, have also been observed in several tissues like brain, liver, mammary gland and spermatozoa. There are two natural PR isoforms called PR-A and PR-B. PR-B has an additional stretc h of 164 amino acids at the N terminus. The extra domain in PR-B performs activation functions by recruiting coactivators that could not be recruited by PR-A. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD is not only involved in binding to progesterone, but also involved in coactivator binding and dimerization. 248 matched cddid_all.tbl CDD cd07075 cd07075 132760 NR_LBD_MR Ligand binding domain of the mineralocorticoid receptor, a member of the nuclear receptor superfamily. The ligand binding domain of the mineralocorticoid receptor (MR): MR, also called aldosterone receptor, is a member of nuclear receptor superfamily involved in the regulation of electrolyte and fluid balance. The receptor is activated by mineralocorticoids such as aldosterone and deoxycorticosterone as well as glucocorticoids, like cortisol and cortisone. Binding of its ligand results in its translocation to the cell nucleus, homodimerization and binding to hormone response elements (HREs) present in the promoter of MR controlled genes. This results in the recruitment of the coactivators and the transcription of the activated genes. MR is expressed in many tissues and its activation results in the expression of proteins regulating electrolyte and fluid balance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, MR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD ). The LBD, in addition to binding ligand, contains a ligand-dependent activation function-2 (AF-2). 248 matched cddid_all.tbl CDD cd07076 cd07076 132761 NR_LBD_GR Ligand binding domain of the glucocorticoid receptor, a member of the nuclear receptor superfamily. The ligand binding domain of the glucocorticoid receptor (GR): GR is a ligand-activated transcription factor belonging to the nuclear receptor superfamily. It binds with high affinity to cortisol and other glucocorticoids. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. In the absence of hormone, the glucocorticoid receptor (GR) is complexes with a variety of heat shock proteins in the cytosol. The binding of the glucocorticoids results in release of the heat shock proteins and transforms it to its active state. One mechanism of action of GR is by direct activation of gene transcription. The activated form of GR forms dimers, translocates into the nucleus, and binds to specific hormone responsive elements, activating gene transcription. GR can also function as a repressor of other gene transcription activators, such as NF-kappaB and AF-1 by directly binding to them, and bloc king the expression of their activated genes. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD also functions for dimerization and chaperone protein association. 247 matched cddid_all.tbl CDD cd07077 cd07077 143396 ALDH-like NAD(P)+-dependent aldehyde dehydrogenase-like (ALDH-like) family. The aldehyde dehydrogenase-like (ALDH-like) group of the ALDH superfamily of NAD(P)+-dependent enzymes which, in general, oxidize a wide range of endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an important role in detoxification. This group includes families ALDH18, ALDH19, and ALDH20 and represents such proteins as gamma-glutamyl phosphate reductase, LuxC-like acyl-CoA reductase, and coenzyme A acylating aldehyde dehydrogenase. All of these proteins have a conserved cysteine that aligns with the catalytic cysteine of the ALDH group. 397 matched cddid_all.tbl CDD cd07078 cd07078 143397 ALDH NAD(P)+ dependent aldehyde dehydrogenase family. The aldehyde dehydrogenase family (ALDH) of NAD(P)+ dependent enzymes, in general, oxidize a wide range of endogenous and exogenous aliphatic and aromatic aldehydes to their corresponding carboxylic acids and play an important role in detoxification. Besides aldehyde detoxification, many ALDH isozymes possess multiple additional catalytic and non-catalytic functions such as participating in metabolic pathways, or as binding proteins, or as osmoregulants, to mention a few. The enzyme has three domains, a NAD(P)+ cofactor-binding domain, a catalytic domain, and a bridging domain; and the active enzyme is generally either homodimeric or homotetrameric. The catalytic mechanism is proposed to involve cofactor binding, resulting in a conformational change and activation of an invariant catalytic cysteine nucleophile. The cysteine and aldehyde substrate form an oxyanion thiohemiacetal intermediate resulting in hydride transfer to the cofactor and formation of a thioacylenzyme intermediate. Hydrolysis of the thioacylenzyme and release of the carboxylic acid product occurs, and in most cases, the reduced cofactor dissociates from the enzyme. The evolutionary phylogenetic tree of ALDHs appears to have an initial bifurcation between what has been characterized as the classical aldehyde dehydrogenases, the ALDH family (ALDH) and extended family members or aldehyde dehydrogenase-like (ALDH-like) proteins. The ALDH proteins are represented by enzymes which share a number of highly conserved residues necessary for catalysis and cofactor binding and they include such proteins as retinal dehydrogenase, 10-formyltetrahydrofolate dehydrogenase, non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase, delta(1)-pyrroline-5-carboxylate dehydrogenases, alpha-ketoglutaric semialdehyde dehydrogenase, alpha-aminoadipic semialdehyde dehydrogenase, coniferyl aldehyde dehydrogenase and succinate-semialdehyde dehydrogenase. Included in this larger group are all human, Arabidopsis, Tortula, fungal, protozoan, and Drosophila ALDHs identified in families ALDH1 through ALDH22 with the exception of families ALDH18, ALDH19, and ALDH20 which are present in the ALDH-like group. 432 matched cddid_all.tbl CDD cd07079 cd07079 143398 ALDH_F18-19_ProA-GPR Gamma-glutamyl phosphate reductase (GPR), aldehyde dehydrogenase families 18 and 19. Gamma-glutamyl phosphate reductase (GPR), a L-proline biosynthetic pathway (PBP) enzyme that catalyzes the NADPH dependent reduction of L-gamma-glutamyl 5-phosphate into L-glutamate 5-semialdehyde and phosphate. The glutamate route of the PBP involves two enzymatic steps catalyzed by gamma-glutamyl kinase (GK, EC 2.7.2.11) and GPR (EC 1.2.1.41). These enzymes are fused into the bifunctional enzyme, ProA or delta(1)-pyrroline-5-carboxylate synthetase (P5CS) in plants and animals, whereas they are separate enzymes in bacteria and yeast. In humans, the P5CS (ALDH18A1), an inner mitochondrial membrane enzyme, is essential to the de novo synthesis of the amino acids proline and arginine. Tomato (Lycopersicon esculentum) has both the prokaryotic-like polycistronic operons encoding GK and GPR (PRO1, ALDH19) and the full-length, bifunctional P5CS (PRO2, ALDH18B1). 406 matched cddid_all.tbl CDD cd07080 cd07080 143399 ALDH_Acyl-CoA-Red_LuxC Acyl-CoA reductase LuxC. Acyl-CoA reductase, LuxC, (EC=1.2.1.50) is the fatty acid reductase enzyme responsible for synthesis of the aldehyde substrate for the luminescent reaction catalyzed by luciferase. The fatty acid reductase, a luminescence-specific, multienzyme complex (LuxCDE), reduces myristic acid to generate the long chain fatty aldehyde required for the luciferase-catalyzed reaction resulting in the emission of blue-green light. Mutational studies of conserved cysteines of LuxC revealed that the cysteine which aligns with the catalytic cysteine conserved throughout the ALDH superfamily is the LuxC acylation site. This CD is composed of mainly bacterial sequences but also includes a few archaeal sequences similar to the Methanospirillum hungateiacyl acyl-CoA reductase RfbN. 422 matched cddid_all.tbl CDD cd07081 cd07081 143400 ALDH_F20_ACDH_EutE-like Coenzyme A acylating aldehyde dehydrogenase (ACDH), Ethanolamine utilization protein EutE, and related proteins. Coenzyme A acylating aldehyde dehydrogenase (ACDH), an NAD+ and CoA-dependent acetaldehyde dehydrogenase, acetylating (EC=1.2.1.10), functions as a single enzyme (such as the Ethanolamine utilization protein, EutE, in Salmonella typhimurium) or as part of a multifunctional enzyme to convert acetaldehyde into acetyl-CoA. The E. coli aldehyde-alcohol dehydrogenase includes the functional domains, alcohol dehydrogenase (ADH), ACDH, and pyruvate-formate-lyase deactivase; and the Entamoeba histolytica aldehyde-alcohol dehydrogenase 2 (ALDH20A1) includes the functional domains ADH and ACDH, and may be critical enzymes in the fermentative pathway. 439 matched cddid_all.tbl CDD cd07082 cd07082 143401 ALDH_F11_NP-GAPDH NADP+-dependent non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase and ALDH family 11. NADP+-dependent non-phosphorylating glyceraldehyde 3-phosphate dehydrogenase (NP-GAPDH, EC=1.2.1.9) catalyzes the irreversible oxidation of glyceraldehyde 3-phosphate to 3-phosphoglycerate generating NADPH for biosynthetic reactions. This CD also includes the Arabidopsis thaliana osmotic-stress-inducible ALDH family 11, ALDH11A3 and similar sequences. In autotrophic eukaryotes, NP-GAPDH generates NADPH for biosynthetic processes from photosynthetic glyceraldehyde-3-phosphate exported from the chloroplast and catalyzes one of the classic glycolytic bypass reactions unique to plants. 473 matched cddid_all.tbl CDD cd07083 cd07083 143402 ALDH_P5CDH ALDH subfamily NAD+-dependent delta(1)-pyrroline-5-carboxylate dehydrogenase-like. ALDH subfamily of the NAD+-dependent, delta(1)-pyrroline-5-carboxylate dehydrogenases (P5CDH, EC=1.5.1.12). The proline catabolic enzymes, proline dehydrogenase and P5CDH catalyze the two-step oxidation of proline to glutamate. P5CDH catalyzes the oxidation of glutamate semialdehyde, utilizing NAD+ as the electron acceptor. In some bacteria, the two enzymes are fused into the bifunctional flavoenzyme, proline utilization A (PutA). These enzymes play important roles in cellular redox control, superoxide generation, and apoptosis. In certain prokaryotes such as Escherichia coli, PutA is also a transcriptional repressor of the proline utilization genes. Monofunctional enzyme sequences such as those seen in the Bacillus RocA P5CDH are also present in this subfamily as well as the human ALDH4A1 P5CDH and the Drosophila Aldh17 P5CDH. 500 matched cddid_all.tbl CDD cd07084 cd07084 143403 ALDH_KGSADH-like ALDH subfamily: NAD(P)+-dependent alpha-ketoglutaric semialdehyde dehydrogenases and plant delta(1)-pyrroline-5-carboxylate dehydrogenase, ALDH family 12-like. ALDH subfamily which includes the NAD(P)+-dependent, alpha-ketoglutaric semialdehyde dehydrogenases (KGSADH, EC 1.2.1.26); plant delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH, EC=1.5.1.12 ), ALDH family 12; the N-terminal domain of the MaoC (monoamine oxidase C) dehydratase regulatory protein; and orthologs of MaoC, PaaZ and PaaN, which are putative ring-opening enzymes of the aerobic phenylacetic acid catabolic pathway. 442 matched cddid_all.tbl CDD cd07085 cd07085 143404 ALDH_F6_MMSDH Methylmalonate semialdehyde dehydrogenase and ALDH family members 6A1 and 6B2. Methylmalonate semialdehyde dehydrogenase (MMSDH, EC=1.2.1.27) [acylating] from Bacillus subtilis is involved in valine metabolism and catalyses the NAD+- and CoA-dependent oxidation of methylmalonate semialdehyde into propionyl-CoA. Mitochondrial human MMSDH ALDH6A1 and Arabidopsis MMSDH ALDH6B2 are also present in this CD. 478 matched cddid_all.tbl CDD cd07086 cd07086 143405 ALDH_F7_AASADH-like NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase and related proteins. ALDH subfamily which includes the NAD+-dependent, alpha-aminoadipic semialdehyde dehydrogenase (AASADH, EC=1.2.1.31), also known as Antiquitin-1, ALDH7A1, ALDH7B or delta-1-piperideine-6-carboxylate dehydrogenase (P6CDH), and other similar sequences, such as the uncharacterized aldehyde dehydrogenase of Candidatus kuenenia AldH (locus CAJ73105). 478 matched cddid_all.tbl CDD cd07087 cd07087 143406 ALDH_F3-13-14_CALDH-like ALDH subfamily: Coniferyl aldehyde dehydrogenase, ALDH families 3, 13, and 14, and other related proteins. ALDH subfamily which includes NAD(P)+-dependent, aldehyde dehydrogenase, family 3 member A1 and B1 (ALDH3A1, ALDH3B1, EC=1.2.1.5) and fatty aldehyde dehydrogenase, family 3 member A2 (ALDH3A2, EC=1.2.1.3), and also plant ALDH family members ALDH3F1, ALDH3H1, and ALDH3I1, fungal ALDH14 (YMR110C) and the protozoan family 13 member (ALDH13), as well as coniferyl aldehyde dehydrogenases (CALDH, EC=1.2.1.68), and other similar sequences, such as the Pseudomonas putida benzaldehyde dehydrogenase I that is involved in the metabolism of mandelate. 426 matched cddid_all.tbl CDD cd07088 cd07088 143407 ALDH_LactADH-AldA Escherichia coli lactaldehyde dehydrogenase AldA-like. Lactaldehyde dehydrogenase from Escherichia coli (AldA, LactADH, EC=1.2.1.22), an NAD(+)-dependent enzyme involved in the metabolism of L-fucose and L-rhamnose, and other similar sequences are present in this CD. 468 matched cddid_all.tbl CDD cd07089 cd07089 143408 ALDH_CddD-AldA-like Rhodococcus ruber 6-oxolauric acid dehydrogenase-like and related proteins. The 6-oxolauric acid dehydrogenase (CddD) from Rhodococcus ruber SC1 which converts 6-oxolauric acid to dodecanedioic acid; and the aldehyde dehydrogenase (locus SSP0762) from Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 and also, the Mycobacterium tuberculosis H37Rv ALDH AldA (locus Rv0768) sequence; and other similar sequences, are included in this CD. 459 matched cddid_all.tbl CDD cd07090 cd07090 143409 ALDH_F9_TMBADH NAD+-dependent 4-trimethylaminobutyraldehyde dehydrogenase, ALDH family 9A1. NAD+-dependent, 4-trimethylaminobutyraldehyde dehydrogenase (TMABADH, EC=1.2.1.47), also known as aldehyde dehydrogenase family 9 member A1 (ALDH9A1) in humans, is a cytosolic tetramer which catalyzes the oxidation of gamma-aminobutyraldehyde involved in 4-aminobutyric acid (GABA) biosynthesis and also oxidizes betaine aldehyde (gamma-trimethylaminobutyraldehyde) which is involved in carnitine biosynthesis. 457 matched cddid_all.tbl CDD cd07091 cd07091 143410 ALDH_F1-2_Ald2-like ALDH subfamily: ALDH families 1and 2, including 10-formyltetrahydrofolate dehydrogenase, NAD+-dependent retinal dehydrogenase 1 and related proteins. ALDH subfamily which includes the NAD+-dependent retinal dehydrogenase 1 (RALDH 1, ALDH1, EC=1.2.1.36), also known as aldehyde dehydrogenase family 1 member A1 (ALDH1A1), in humans, a homotetrameric, cytosolic enzyme that catalyzes the oxidation of retinaldehyde to retinoic acid. Human ALDH1B1 and ALDH2 are also in this cluster; both are mitochrondrial homotetramers which play important roles in acetaldehyde oxidation; ALDH1B1 in response to UV light exposure and ALDH2 during ethanol metabolism. 10-formyltetrahydrofolate dehydrogenase (FTHFDH, EC=1.5.1.6), also known as aldehyde dehydrogenase family 1 member L1 (ALDH1L1), in humans, a multi-domain homotetramer with an N-terminal formyl transferase domain and a C-terminal ALDH domain. FTHFDH catalyzes an NADP+-dependent dehydrogenase reaction resulting in the conversion of 10-formyltetrahydrofolate to tetrahydrofolate and CO2. Also included in this subfamily is the Arabidosis aldehyde dehydrogenase family 2 members B4 and B7 (EC=1.2.1.3), which are mitochondrial, homotetramers that oxidize acetaldehyde and glycolaldehyde, as well as, the Arabidosis cytosolic, homotetramer ALDH2C4 (EC=1.2.1.3), an enzyme involved in the oxidation of sinapalehyde and coniferaldehyde. Also included is the AldA aldehyde dehydrogenase of Aspergillus nidulans (locus AN0554), the aldehyde dehydrogenase 2 (YMR170c, ALD5, EC=1.2.1.5) of Saccharomyces cerevisiae, and other similar sequences. 476 matched cddid_all.tbl CDD cd07092 cd07092 143411 ALDH_ABALDH-YdcW Escherichia coli NAD+-dependent gamma-aminobutyraldehyde dehydrogenase YdcW-like. NAD+-dependent, tetrameric, gamma-aminobutyraldehyde dehydrogenase (ABALDH), YdcW of Escherichia coli K12, catalyzes the oxidation of gamma-aminobutyraldehyde to gamma-aminobutyric acid. ABALDH can also oxidize n-alkyl medium-chain aldehydes, but with a lower catalytic efficiency. 450 matched cddid_all.tbl CDD cd07093 cd07093 143412 ALDH_F8_HMSADH Human aldehyde dehydrogenase family 8 member A1-like. In humans, the aldehyde dehydrogenase family 8 member A1 (ALDH8A1) protein functions to convert 9-cis-retinal to 9-cis-retinoic acid and has a preference for NAD+. Also included in this CD is the 2-hydroxymuconic semialdehyde dehydrogenase (HMSADH) which catalyzes the conversion of 2-hydroxymuconic semialdehyde to 4-oxalocrotonate, a step in the meta cleavage pathway of aromatic hydrocarbons in bacteria. Such HMSADHs seen here are: XylG of the TOL plasmid pWW0 of Pseudomonas putida, TomC of Burkholderia cepacia G4, and AphC of Comamonas testosterone. 455 matched cddid_all.tbl CDD cd07094 cd07094 143413 ALDH_F21_LactADH-like ALDH subfamily: NAD+-dependent, lactaldehyde dehydrogenase, ALDH family 21 A1, and related proteins. ALDH subfamily which includes Tortula ruralis aldehyde dehydrogenase ALDH21A1 (RNP123), and NAD+-dependent, lactaldehyde dehydrogenase (EC=1.2.1.22) and like sequences. 453 matched cddid_all.tbl CDD cd07095 cd07095 143414 ALDH_SGSD_AstD N-succinylglutamate 5-semialdehyde dehydrogenase, AstD-like. N-succinylglutamate 5-semialdehyde dehydrogenase or succinylglutamic semialdehyde dehydrogenase (SGSD, E. coli AstD, EC=1.2.1.71) involved in L-arginine degradation via the arginine succinyltransferase (AST) pathway and catalyzes the NAD+-dependent reduction of succinylglutamate semialdehyde into succinylglutamate. 431 matched cddid_all.tbl CDD cd07097 cd07097 143415 ALDH_KGSADH-YcbD Bacillus subtilis NADP+-dependent alpha-ketoglutaric semialdehyde dehydrogenase ycbD-like. Kinetic studies of the Bacillus subtilis ALDH-like ycbD protein, which is involved in d-glucarate/d-galactarate utilization, reveal that it is a NADP+-dependent, alpha-ketoglutaric semialdehyde dehydrogenase (KGSADH). KGSADHs (EC 1.2.1.26) catalyze the NAD(P)+-dependent conversion of KGSA to alpha-ketoglutarate. Interestingly, the NADP+-dependent, tetrameric, 2,5-dioxopentanoate dehydrogenase (EC=1.2.1.26), an enzyme involved in the catabolic pathway for D-arabinose in Sulfolobus solfataricus, also clusters in this group. This CD shows a distant phylogenetic relationship to the Azospirillum brasilense KGSADH-II (-III) group. 473 matched cddid_all.tbl CDD cd07098 cd07098 143416 ALDH_F15-22 Aldehyde dehydrogenase family 15A1 and 22A1-like. Aldehyde dehydrogenase family members ALDH15A1 (Saccharomyces cerevisiae YHR039C) and ALDH22A1 (Arabidopsis thaliana, EC=1.2.1.3), and similar sequences, are in this CD. Significant improvement of stress tolerance in tobacco plants was observed by overexpressing the ALDH22A1 gene from maize (Zea mays) and was accompanied by a reduction of malondialdehyde derived from cellular lipid peroxidation. 465 matched cddid_all.tbl CDD cd07099 cd07099 143417 ALDH_DDALDH Methylomonas sp. 4,4'-diapolycopene-dialdehyde dehydrogenase-like. The 4,4'-diapolycopene-dialdehyde dehydrogenase (DDALDH) involved in C30 carotenoid synthesis in Methylomonas sp. strain 16a and other similar sequences are present in this CD. DDALDH converts 4,4'-diapolycopene-dialdehyde into 4,4'-diapolycopene-diacid. 453 matched cddid_all.tbl CDD cd07100 cd07100 143418 ALDH_SSADH1_GabD1 Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 1-like. Succinate-semialdehyde dehydrogenase 1 (SSADH1, GabD1, EC=1.2.1.16) catalyzes the NADP(+)-dependent oxidation of succinate semialdehyde (SSA) to succinate. SSADH activity in Mycobacterium tuberculosis (Mtb) is encoded by both gabD1 (Rv0234c) and gabD2 (Rv1731). The Mtb GabD1 SSADH1 reportedly is an enzyme of the gamma-aminobutyrate shunt, which forms a functional link between two TCA half-cycles by converting alpha-ketoglutarate to succinate. 429 matched cddid_all.tbl CDD cd07101 cd07101 143419 ALDH_SSADH2_GabD2 Mycobacterium tuberculosis succinate-semialdehyde dehydrogenase 2-like. Succinate-semialdehyde dehydrogenase 2 (SSADH2) and similar proteins are in this CD. SSADH1 (GabD1, EC=1.2.1.16) catalyzes the NADP(+)-dependent oxidation of succinate semialdehyde to succinate. SSADH activity in Mycobacterium tuberculosis is encoded by both gabD1 (Rv0234c) and gabD2 (Rv1731), however ,the Vmax of GabD1 was shown to be much higher than that of GabD2, and GabD2 (SSADH2) is likely to serve physiologically as a dehydrogenase for a different aldehyde(s). 454 matched cddid_all.tbl CDD cd07102 cd07102 143420 ALDH_EDX86601 Uncharacterized aldehyde dehydrogenase of Synechococcus sp. PCC 7335 (EDX86601). Uncharacterized aldehyde dehydrogenase of Synechococcus sp. PCC 7335 (locus EDX86601) and other similar sequences, are present in this CD. 452 matched cddid_all.tbl CDD cd07103 cd07103 143421 ALDH_F5_SSADH_GabD Mitochondrial succinate-semialdehyde dehydrogenase and ALDH family members 5A1 and 5F1-like. Succinate-semialdehyde dehydrogenase, mitochondrial (SSADH, GabD, EC=1.2.1.24) catalyzes the NAD+-dependent oxidation of succinate semialdehyde (SSA) to succinate. This group includes the human aldehyde dehydrogenase family 5 member A1 (ALDH5A1) which is a mitochondrial homotetramer that converts SSA to succinate in the last step of 4-aminobutyric acid (GABA) catabolism. This CD also includes the Arabidopsis SSADH gene product ALDH5F1. Mutations in this gene result in the accumulation of H2O2, suggesting a role in plant defense against the environmental stress of elevated reactive oxygen species. 451 matched cddid_all.tbl CDD cd07104 cd07104 143422 ALDH_BenzADH-like ALDH subfamily: NAD(P)+-dependent benzaldehyde dehydrogenase II, vanillin dehydrogenase, p-hydroxybenzaldehyde dehydrogenase and related proteins. ALDH subfamily which includes the NAD(P)+-dependent, benzaldehyde dehydrogenase II (XylC, BenzADH, EC=1.2.1.28) involved in the oxidation of benzyl alcohol to benzoate; p-hydroxybenzaldehyde dehydrogenase (PchA, HBenzADH) which catalyzes the oxidation of p-hydroxybenzaldehyde to p-hydroxybenzoic acid; vanillin dehydrogenase (Vdh, VaniDH) involved in the metabolism of ferulic acid as seen in Pseudomonas putida KT2440; and other related sequences. 431 matched cddid_all.tbl CDD cd07105 cd07105 143423 ALDH_SaliADH Salicylaldehyde dehydrogenase, DoxF-like. Salicylaldehyde dehydrogenase (DoxF, SaliADH, EC=1.2.1.65) involved in the upper naphthalene catabolic pathway of Pseudomonas strain C18 and other similar sequences are present in this CD. 432 matched cddid_all.tbl CDD cd07106 cd07106 143424 ALDH_AldA-AAD23400 Streptomyces aureofaciens putative aldehyde dehydrogenase AldA (AAD23400)-like. Putative aldehyde dehydrogenase, AldA, from Streptomyces aureofaciens (locus AAD23400) and other similar sequences are present in this CD. 446 matched cddid_all.tbl CDD cd07107 cd07107 143425 ALDH_PhdK-like Nocardioides 2-carboxybenzaldehyde dehydrogenase, PhdK-like. Nocardioides sp. strain KP72-carboxybenzaldehyde dehydrogenase (PhdK), an enzyme involved in phenanthrene degradation, and other similar sequences, are present in this CD. 456 matched cddid_all.tbl CDD cd07108 cd07108 143426 ALDH_MGR_2402 Magnetospirillum NAD(P)+-dependent aldehyde dehydrogenase MSR-1-like. NAD(P)+-dependent aldehyde dehydrogenase of Magnetospirillum gryphiswaldense MSR-1 (MGR_2402) , and other similar sequences, are present in this CD. 457 matched cddid_all.tbl CDD cd07109 cd07109 143427 ALDH_AAS00426 Uncharacterized Saccharopolyspora spinosa aldehyde dehydrogenase (AAS00426)-like. Uncharacterized aldehyde dehydrogenase of Saccharopolyspora spinosa (AAS00426) and other similar sequences, are present in this CD. 454 matched cddid_all.tbl CDD cd07110 cd07110 143428 ALDH_F10_BADH Arabidopsis betaine aldehyde dehydrogenase 1 and 2, ALDH family 10A8 and 10A9-like. Present in this CD are the Arabidopsis betaine aldehyde dehydrogenase (BADH) 1 (chloroplast) and 2 (mitochondria), also known as, aldehyde dehydrogenase family 10 member A8 and aldehyde dehydrogenase family 10 member A9, respectively, and are putative dehydration- and salt-inducible BADHs (EC 1.2.1.8) that catalyze the oxidation of betaine aldehyde to the compatible solute glycine betaine. 456 matched cddid_all.tbl CDD cd07111 cd07111 143429 ALDH_F16 Aldehyde dehydrogenase family 16A1-like. Uncharacterized aldehyde dehydrogenase family 16 member A1 (ALDH16A1) and other related sequences are present in this CD. The active site cysteine and glutamate residues are not conserved in the human ALDH16A1 protein sequence. 480 matched cddid_all.tbl CDD cd07112 cd07112 143430 ALDH_GABALDH-PuuC Escherichia coli NADP+-dependent gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase PuuC-like. NADP+-dependent, gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (GABALDH) PuuC of Escherichia coli which catalyzes the conversion of putrescine to 4-aminobutanoate and other similar sequences are present in this CD. 462 matched cddid_all.tbl CDD cd07113 cd07113 143431 ALDH_PADH_NahF Escherichia coli NAD+-dependent phenylacetaldehyde dehydrogenase PadA-like. NAD+-dependent, homodimeric, phenylacetaldehyde dehydrogenase (PADH, EC=1.2.1.39) PadA of Escherichia coli involved in the catabolism of 2-phenylethylamine, and other related sequences, are present in this CD. Also included is the Pseudomonas fluorescens ST StyD PADH involved in styrene catabolism, the Sphingomonas sp. LB126 FldD protein involved in fluorene degradation, and the Novosphingobium aromaticivorans NahF salicylaldehyde dehydrogenase involved in the NAD+-dependent conversion of salicylaldehyde to salicylate. 477 matched cddid_all.tbl CDD cd07114 cd07114 143432 ALDH_DhaS Uncharacterized Candidatus pelagibacter aldehyde dehydrogenase, DhaS-like. Uncharacterized aldehyde dehydrogenase from Candidatus pelagibacter (DhaS) and other related sequences are present in this CD. 457 matched cddid_all.tbl CDD cd07115 cd07115 143433 ALDH_HMSADH_HapE Pseudomonas fluorescens 4-hydroxymuconic semialdehyde dehydrogenase-like. 4-hydroxymuconic semialdehyde dehydrogenase (HapE, EC=1.2.1.61) of Pseudomonas fluorescens ACB involved in 4-hydroxyacetophenone degradation, and putative hydroxycaproate semialdehyde dehydrogenase (ChnE) of Brachymonas petroleovorans involved in cyclohexane metabolism, and other similar sequences, are present in this CD. 453 matched cddid_all.tbl CDD cd07116 cd07116 143434 ALDH_ACDHII-AcoD Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II-like. Included in this CD is the NAD+-dependent, acetaldehyde dehydrogenase II (AcDHII, AcoD, EC=1.2.1.3) from Ralstonia (Alcaligenes) eutrophus H16 involved in the catabolism of acetoin and ethanol, and similar proteins, such as, the dimeric dihydrolipoamide dehydrogenase of the acetoin dehydrogenase enzyme system of Klebsiella pneumonia. Also included are sequences similar to the NAD+-dependent chloroacetaldehyde dehydrogenases (AldA and AldB) of Xanthobacter autotrophicus GJ10 which are involved in the degradation of 1,2-dichloroethane. These proteins apparently require RpoN factors for expression. 479 matched cddid_all.tbl CDD cd07117 cd07117 143435 ALDH_StaphAldA1 Uncharacterized Staphylococcus aureus AldA1 (SACOL0154) aldehyde dehydrogenase-like. Uncharacterized aldehyde dehydrogenase from Staphylococcus aureus (AldA1, locus SACOL0154) and other similar sequences are present in this CD. 475 matched cddid_all.tbl CDD cd07118 cd07118 143436 ALDH_SNDH Gluconobacter oxydans L-sorbosone dehydrogenase-like. Included in this CD is the L-sorbosone dehydrogenase (SNDH) from Gluconobacter oxydans UV10. In G. oxydans, D-sorbitol is converted to 2-keto-L-gulonate (a precursor of L-ascorbic acid) in sequential oxidation steps catalyzed by a FAD-dependent, L-sorbose dehydrogenase and an NAD(P)+-dependent, L-sorbosone dehydrogenase. 454 matched cddid_all.tbl CDD cd07119 cd07119 143437 ALDH_BADH-GbsA Bacillus subtilis NAD+-dependent betaine aldehyde dehydrogenase-like. Included in this CD is the NAD+-dependent, betaine aldehyde dehydrogenase (BADH, GbsA, EC=1.2.1.8) of Bacillus subtilis involved in the synthesis of the osmoprotectant glycine betaine from choline or glycine betaine aldehyde. 482 matched cddid_all.tbl CDD cd07120 cd07120 143438 ALDH_PsfA-ACA09737 Pseudomonas putida aldehyde dehydrogenase PsfA (ACA09737)-like. Included in this CD is the aldehyde dehydrogenase (PsfA, locus ACA09737) of Pseudomonas putida involved in furoic acid metabolism. Transcription of psfA was induced in response to 2-furoic acid, furfuryl alcohol, and furfural. 455 matched cddid_all.tbl CDD cd07121 cd07121 143439 ALDH_EutE Ethanolamine utilization protein EutE-like. Coenzyme A acylating aldehyde dehydrogenase (ACDH), an NAD+ and CoA-dependent acetaldehyde dehydrogenase, acetylating (EC=1.2.1.10), converts acetaldehyde into acetyl-CoA. This CD is limited to such monofunctional enzymes as the Ethanolamine utilization protein, EutE, in Salmonella typhimurium. Mutations in eutE abolish the ability to utilize ethanolamine as a carbon source. 429 matched cddid_all.tbl CDD cd07122 cd07122 143440 ALDH_F20_ACDH Coenzyme A acylating aldehyde dehydrogenase (ACDH), ALDH family 20-like. Coenzyme A acylating aldehyde dehydrogenase (ACDH, EC=1.2.1.10), an NAD+ and CoA-dependent acetaldehyde dehydrogenase, functions as a single enzyme (such as the Ethanolamine utilization protein, EutE, in Salmonella typhimurium) or as part of a multifunctional enzyme to convert acetaldehyde into acetyl-CoA . The E. coli aldehyde-alcohol dehydrogenase includes the functional domains, alcohol dehydrogenase (ADH), ACDH, and pyruvate-formate-lyase deactivase; and the Entamoeba histolytica aldehyde-alcohol dehydrogenase 2 (ALDH20A1) includes the functional domains ADH and ACDH and may be critical enzymes in the fermentative pathway. 436 matched cddid_all.tbl CDD cd07123 cd07123 143441 ALDH_F4-17_P5CDH Delta(1)-pyrroline-5-carboxylate dehydrogenase, ALDH families 4 and 17. Delta(1)-pyrroline-5-carboxylate dehydrogenase (EC=1.5.1.12 ), families 4 and 17: a proline catabolic enzyme of the aldehyde dehydrogenase (ALDH) protein superfamily. Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH), also known as ALDH4A1 in humans, is a mitochondrial homodimer involved in proline degradation and catalyzes the NAD + -dependent conversion of P5C to glutamate. This is a necessary step in the pathway interconnecting the urea and tricarboxylic acid cycles. The preferred substrate is glutamic gamma-semialdehyde, other substrates include succinic, glutaric and adipic semialdehydes. Also included in this CD is the Aldh17 Drosophila melanogaster (Q9VUC0) P5CDH and similar sequences. 522 matched cddid_all.tbl CDD cd07124 cd07124 143442 ALDH_PutA-P5CDH-RocA Delta(1)-pyrroline-5-carboxylate dehydrogenase, RocA. Delta(1)-pyrroline-5-carboxylate dehydrogenase (EC=1.5.1.12 ), RocA: a proline catabolic enzyme of the aldehyde dehydrogenase (ALDH) protein superfamily. The proline catabolic enzymes, proline dehydrogenase and Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH), catalyze the two-step oxidation of proline to glutamate; P5CDH catalyzes the oxidation of glutamate semialdehyde, utilizing NAD+ as the electron acceptor. In some bacteria, the two enzymes are fused into the bifunctional flavoenzyme, proline utilization A (PutA). In this CD, monofunctional enzyme sequences such as seen in the Bacillus subtilis RocA P5CDH are also present. These enzymes play important roles in cellular redox control, superoxide generation, and apoptosis. 512 matched cddid_all.tbl CDD cd07125 cd07125 143443 ALDH_PutA-P5CDH Delta(1)-pyrroline-5-carboxylate dehydrogenase, PutA. The proline catabolic enzymes of the aldehyde dehydrogenase (ALDH) protein superfamily, proline dehydrogenase and Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH, (EC=1.5.1.12 )), catalyze the two-step oxidation of proline to glutamate; P5CDH catalyzes the oxidation of glutamate semialdehyde, utilizing NAD+ as the electron acceptor. In some bacteria, the two enzymes are fused into the bifunctional flavoenzyme, proline utilization A (PutA) These enzymes play important roles in cellular redox control, superoxide generation, and apoptosis. In certain prokaryotes such as Escherichia coli, PutA is also a transcriptional repressor of the proline utilization genes. 518 matched cddid_all.tbl CDD cd07126 cd07126 143444 ALDH_F12_P5CDH Delta(1)-pyrroline-5-carboxylate dehydrogenase, ALDH family 12. Delta(1)-pyrroline-5-carboxylate dehydrogenase (P5CDH, EC=1.5.1.12), family 12: a proline catabolic enzyme of the aldehyde dehydrogenase (ALDH) protein superfamily. P5CDH is a mitochondrial enzyme involved in proline degradation and catalyzes the NAD + -dependent conversion of P5C to glutamate. The P5CDH, ALDH12A1 gene, in Arabidopsis, has been identified as an osmotic-stress-inducible ALDH gene. This CD contains both Viridiplantae and Alveolata P5CDH sequences. 489 matched cddid_all.tbl CDD cd07127 cd07127 143445 ALDH_PAD-PaaZ Phenylacetic acid degradation proteins PaaZ (Escherichia coli) and PaaN (Pseudomonas putida)-like. Phenylacetic acid degradation (PAD) proteins PaaZ (Escherichia coli) and PaaN (Pseudomonas putida) are putative aromatic ring cleavage enzymes of the aerobic PA catabolic pathway. PaaZ mutants were defective for growth with PA as a sole carbon source due to interruption of the putative ring opening system. This CD is limited to bacterial monofunctional enzymes. 549 matched cddid_all.tbl CDD cd07128 cd07128 143446 ALDH_MaoC-N N-terminal domain of the monoamine oxidase C dehydratase. The N-terminal domain of the MaoC dehydratase, a monoamine oxidase regulatory protein. Orthologs of MaoC include PaaZ (Escherichia coli) and PaaN (Pseudomonas putida), which are putative ring-opening enzymes of the aerobic phenylacetic acid (PA) catabolic pathway. The C-terminal domain of MaoC has sequence similarity to enoyl-CoA hydratase. Also included in this CD is a novel Burkholderia xenovorans LB400 ALDH of the aerobic benzoate oxidation (box) pathway. This pathway involves first the synthesis of a CoA thio-esterified aromatic acid, with subsequent dihydroxylation and cleavage steps, yielding the CoA thio-esterified aliphatic aldehyde, 3,4-dehydroadipyl-CoA semialdehyde, which is further converted into its corresponding CoA acid by the Burkholderia LB400 ALDH. 513 matched cddid_all.tbl CDD cd07129 cd07129 143447 ALDH_KGSADH Alpha-Ketoglutaric Semialdehyde Dehydrogenase. Alpha-Ketoglutaric Semialdehyde (KGSA) Dehydrogenase (KGSADH, EC 1.2.1.26) catalyzes the NAD(P)+-dependent conversion of KGSA to alpha-ketoglutarate. This CD contains such sequences as those seen in Azospirillum brasilense, KGSADH-II (D-glucarate/D-galactarate-inducible) and KGSADH-III (hydroxy-L-proline-inducible). Both show similar high substrate specificity for KGSA and different coenzyme specificity; KGSADH-II is NAD+-dependent and KGSADH-III is NADP+-dependent. Also included in this CD is the NADP(+)-dependent aldehyde dehydrogenase from Vibrio harveyi which catalyzes the oxidation of long-chain aliphatic aldehydes to acids. 454 matched cddid_all.tbl CDD cd07130 cd07130 143448 ALDH_F7_AASADH NAD+-dependent alpha-aminoadipic semialdehyde dehydrogenase, ALDH family members 7A1 and 7B. Alpha-aminoadipic semialdehyde dehydrogenase (AASADH, EC=1.2.1.31), also known as ALDH7A1, Antiquitin-1, ALDH7B, or delta-1-piperideine-6-carboxylate dehydrogenase (P6CDH), is a NAD+-dependent ALDH. Human ALDH7A1 is involved in the pipecolic acid pathway of lysine catabolism, catalyzing the oxidation of alpha-aminoadipic semialdehyde to alpha-aminoadipate. Arabidopsis thaliana ALDH7B4 appears to be an osmotic-stress-inducible ALDH gene encoding a turgor-responsive or stress-inducible ALDH. The Streptomyces clavuligerus P6CDH appears to be involved in cephamycin biosynthesis, catalyzing the second stage of the two-step conversion of lysine to alpha-aminoadipic acid. The ALDH7A1 enzyme and others in this group have been observed as tetramers, yet the bacterial P6CDH enzyme has been reported as a monomer. 474 matched cddid_all.tbl CDD cd07131 cd07131 143449 ALDH_AldH-CAJ73105 Uncharacterized Candidatus kuenenia aldehyde dehydrogenase AldH (CAJ73105)-like. Uncharacterized aldehyde dehydrogenase of Candidatus kuenenia AldH (locus CAJ73105) and similar sequences with similarity to alpha-aminoadipic semialdehyde dehydrogenase (AASADH, human ALDH7A1, EC=1.2.1.31), Arabidopsis ALDH7B4, and Streptomyces clavuligerus delta-1-piperideine-6-carboxylate dehydrogenase (P6CDH) are included in this CD. 478 matched cddid_all.tbl CDD cd07132 cd07132 143450 ALDH_F3AB Aldehyde dehydrogenase family 3 members A1, A2, and B1 and related proteins. NAD(P)+-dependent, aldehyde dehydrogenase, family 3 members A1 and B1 (ALDH3A1, ALDH3B1, EC=1.2.1.5) and fatty aldehyde dehydrogenase, family 3 member A2 (ALDH3A2, EC=1.2.1.3), and similar sequences are included in this CD. Human ALDH3A1 is a homodimer with a critical role in cellular defense against oxidative stress; it catalyzes the oxidation of various cellular membrane lipid-derived aldehydes. Corneal crystalline ALDH3A1 protects the cornea and underlying lens against UV-induced oxidative stress. Human ALDH3A2, a microsomal homodimer, catalyzes the oxidation of long-chain aliphatic aldehydes to fatty acids. Human ALDH3B1 is highly expressed in the kidney and liver and catalyzes the oxidation of various medium- and long-chain saturated and unsaturated aliphatic aldehydes. 443 matched cddid_all.tbl CDD cd07133 cd07133 143451 ALDH_CALDH_CalB Coniferyl aldehyde dehydrogenase-like. Coniferyl aldehyde dehydrogenase (CALDH, EC=1.2.1.68) of Pseudomonas sp. strain HR199 (CalB) which catalyzes the NAD+-dependent oxidation of coniferyl aldehyde to ferulic acid, and similar sequences, are present in this CD. 434 matched cddid_all.tbl CDD cd07134 cd07134 143452 ALDH_AlkH-like Pseudomonas putida Aldehyde dehydrogenase AlkH-like. Aldehyde dehydrogenase AlkH (locus name P12693, EC=1.2.1.3) of the alkBFGHJKL operon that allows Pseudomonas putida to metabolize alkanes and the aldehyde dehydrogenase AldX of Bacillus subtilis (locus P46329, EC=1.2.1.3), and similar sequences, are present in this CD. 433 matched cddid_all.tbl CDD cd07135 cd07135 143453 ALDH_F14-YMR110C Saccharomyces cerevisiae aldehyde dehydrogenase family 14 and related proteins. Aldehyde dehydrogenase family 14 (ALDH14), isolated mainly from the mitochondrial outer membrane of Saccharomyces cerevisiae (YMR110C) and most closely related to the plant and animal ALDHs and fatty ALDHs family 3 members, and similar fungal sequences, are present in this CD. 436 matched cddid_all.tbl CDD cd07136 cd07136 143454 ALDH_YwdH-P39616 Bacillus subtilis aldehyde dehydrogenase ywdH-like. Uncharacterized Bacillus subtilis ywdH aldehyde dehydrogenase (locus P39616) most closely related to the ALDHs and fatty ALDHs of families 3 and 14, and similar sequences, are included in this CD. 449 matched cddid_all.tbl CDD cd07137 cd07137 143455 ALDH_F3FHI Plant aldehyde dehydrogenase family 3 members F1, H1, and I1 and related proteins. Aldehyde dehydrogenase family members 3F1, 3H1, and 3I1 (ALDH3F1, ALDH3H1, and ALDH3I1), and similar plant sequences, are in this CD. In Arabidopsis thaliana, stress-regulated expression of ALDH3I1 was observed in leaves and osmotic stress expression of ALDH3H1 was observed in root tissue, whereas, ALDH3F1 expression was not stress responsive. Functional analysis of ALDH3I1 suggest it may be involved in a detoxification pathway in plants that limits aldehyde accumulation and oxidative stress. 432 matched cddid_all.tbl CDD cd07138 cd07138 143456 ALDH_CddD_SSP0762 Rhodococcus ruber 6-oxolauric acid dehydrogenase-like. The 6-oxolauric acid dehydrogenase (CddD) from Rhodococcus ruber SC1 which converts 6-oxolauric acid to dodecanedioic acid, and the aldehyde dehydrogenase (locus SSP0762) from Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 and other similar sequences, are included in this CD. 466 matched cddid_all.tbl CDD cd07139 cd07139 143457 ALDH_AldA-Rv0768 Mycobacterium tuberculosis aldehyde dehydrogenase AldA-like. The Mycobacterium tuberculosis NAD+-dependent, aldehyde dehydrogenase PDB structure, 3B4W, and the Mycobacterium tuberculosis H37Rv aldehyde dehydrogenase AldA (locus Rv0768) sequence, as well as the Rhodococcus rhodochrous ALDH involved in haloalkane catabolism, and other similar sequences, are included in this CD. 471 matched cddid_all.tbl CDD cd07140 cd07140 143458 ALDH_F1L_FTFDH 10-formyltetrahydrofolate dehydrogenase, ALDH family 1L. 10-formyltetrahydrofolate dehydrogenase (FTHFDH, EC=1.5.1.6), also known as aldehyde dehydrogenase family 1 member L1 (ALDH1L1) in humans, is a multi-domain homotetramer with an N-terminal formyl transferase domain and a C-terminal ALDH domain. FTHFDH catalyzes an NADP+-dependent dehydrogenase reaction resulting in the conversion of 10-formyltetrahydrofolate to tetrahydrofolate and CO2. The ALDH domain is also capable of the oxidation of short chain aldehydes to their corresponding acids. 486 matched cddid_all.tbl CDD cd07141 cd07141 143459 ALDH_F1AB_F2_RALDH1 NAD+-dependent retinal dehydrogenase 1, ALDH families 1A, 1B, and 2-like. NAD+-dependent retinal dehydrogenase 1 (RALDH 1, ALDH1, EC=1.2.1.36) also known as aldehyde dehydrogenase family 1 member A1 (ALDH1A1) in humans, is a homotetrameric, cytosolic enzyme that catalyzes the oxidation of retinaldehyde to retinoic acid. Human ALDH1B1 and ALDH2 are also in this cluster; both are mitochrondrial homotetramers which play important roles in acetaldehyde oxidation; ALDH1B1 in response to UV light exposure and ALDH2 during ethanol metabolism. 481 matched cddid_all.tbl CDD cd07142 cd07142 143460 ALDH_F2BC Arabidosis aldehyde dehydrogenase family 2 B4, B7, C4-like. Included in this CD is the Arabidosis aldehyde dehydrogenase family 2 members B4 and B7 (EC=1.2.1.3), which are mitochondrial homotetramers that oxidize acetaldehyde and glycolaldehyde, but not L-lactaldehyde. Also in this group, is the Arabidosis cytosolic, homotetramer ALDH2C4 (EC=1.2.1.3), an enzyme involved in the oxidation of sinapalehyde and coniferaldehyde. 476 matched cddid_all.tbl CDD cd07143 cd07143 143461 ALDH_AldA_AN0554 Aspergillus nidulans aldehyde dehydrogenase, AldA (AN0554)-like. NAD(P)+-dependent aldehyde dehydrogenase (AldA) of Aspergillus nidulans (locus AN0554), and other similar sequences, are present in this CD. 481 matched cddid_all.tbl CDD cd07144 cd07144 143462 ALDH_ALD2-YMR170C Saccharomyces cerevisiae aldehyde dehydrogenase 2 (YMR170c)-like. NAD(P)+-dependent Saccharomyces cerevisiae aldehyde dehydrogenase 2 (YMR170c, ALD5, EC=1.2.1.5) and other similar sequences, are present in this CD. 484 matched cddid_all.tbl CDD cd07145 cd07145 143463 ALDH_LactADH_F420-Bios Methanocaldococcus jannaschii NAD+-dependent lactaldehyde dehydrogenase-like. NAD+-dependent, lactaldehyde dehydrogenase (EC=1.2.1.22) involved the biosynthesis of coenzyme F(420) in Methanocaldococcus jannaschii through the oxidation of lactaldehyde to lactate and generation of NAPH, and similar sequences are included in this CD. 456 matched cddid_all.tbl CDD cd07146 cd07146 143464 ALDH_PhpJ Streptomyces putative phosphonoformaldehyde dehydrogenase PhpJ-like. Putative phosphonoformaldehyde dehydrogenase (PhpJ), an aldehyde dehydrogenase homolog reportedly involved in the biosynthesis of phosphinothricin tripeptides in Streptomyces viridochromogenes DSM 40736, and similar sequences are included in this CD. 451 matched cddid_all.tbl CDD cd07147 cd07147 143465 ALDH_F21_RNP123 Aldehyde dehydrogenase family 21A1-like. Aldehyde dehydrogenase ALDH21A1 (gene name RNP123) was first described in the moss Tortula ruralis and is believed to play an important role in the detoxification of aldehydes generated in response to desiccation- and salinity-stress, and ALDH21A1 expression represents a unique stress tolerance mechanism. So far, of plants, only the bryophyte sequence has been observed, but similar protein sequences from bacteria and archaea are also present in this CD. 452 matched cddid_all.tbl CDD cd07148 cd07148 143466 ALDH_RL0313 Uncharacterized ALDH ( RL0313) with similarity to Tortula ruralis aldehyde dehydrogenase ALDH21A1. Uncharacterized aldehyde dehydrogenase (locus RL0313) with sequence similarity to the moss Tortula ruralis aldehyde dehydrogenase ALDH21A1 (RNP123) believed to play an important role in the detoxification of aldehydes generated in response to desiccation- and salinity-stress, and similar sequences are included in this CD. 455 matched cddid_all.tbl CDD cd07149 cd07149 143467 ALDH_y4uC Uncharacterized ALDH (y4uC) with similarity to Tortula ruralis aldehyde dehydrogenase ALDH21A1. Uncharacterized aldehyde dehydrogenase (ORF name y4uC) with sequence similarity to the moss Tortula ruralis aldehyde dehydrogenase ALDH21A1 (RNP123) believed to play an important role in the detoxification of aldehydes generated in response to desiccation- and salinity-stress, and similar sequences are included in this CD. 453 matched cddid_all.tbl CDD cd07150 cd07150 143468 ALDH_VaniDH_like Pseudomonas putida vanillin dehydrogenase-like. Vanillin dehydrogenase (Vdh, VaniDH) involved in the metabolism of ferulic acid and other related sequences are included in this CD. The E. coli vanillin dehydrogenase (LigV) preferred NAD+ to NADP+ and exhibited a broad substrate preference, including vanillin, benzaldehyde, protocatechualdehyde, m-anisaldehyde, and p-hydroxybenzaldehyde. 451 matched cddid_all.tbl CDD cd07151 cd07151 143469 ALDH_HBenzADH NADP+-dependent p-hydroxybenzaldehyde dehydrogenase-like. NADP+-dependent, p-hydroxybenzaldehyde dehydrogenase (PchA, HBenzADH) which catalyzes oxidation of p-hydroxybenzaldehyde to p-hydroxybenzoic acid and other related sequences are included in this CD. 465 matched cddid_all.tbl CDD cd07152 cd07152 143470 ALDH_BenzADH NAD-dependent benzaldehyde dehydrogenase II-like. NAD-dependent, benzaldehyde dehydrogenase II (XylC, BenzADH, EC=1.2.1.28) is involved in the oxidation of benzyl alcohol to benzoate. In Acinetobacter calcoaceticus, this process is carried out by the chromosomally encoded, benzyl alcohol dehydrogenase (xylB) and benzaldehyde dehydrogenase II (xylC) enzymes; whereas in Pseudomonas putida they are encoded by TOL plasmids. 443 matched cddid_all.tbl CDD cd07153 cd07153 133478 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions. For example, PerR, a metal-dependent sensor of hydrogen peroxide. PerR regulates DNA-binding activity through metal-based protein oxidation, and co-ordinates Mn2+ or Fe2+ at its regulatory site. Fur family proteins contain an N-terminal winged-helix DNA-binding domain followed by a dimerization domain; this CD spans both those domains. 116 matched cddid_all.tbl CDD cd07154 cd07154 143529 NR_DBD_PNR_like The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family. The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR-like receptors have a central well-conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 73 matched cddid_all.tbl CDD cd07155 cd07155 143530 NR_DBD_ER_like DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. ERRs and ERs exhibit the common modular structure with other nuclear receptors. They have a central highly conserved DNA binding domain (DBD), a non-conserved N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 75 matched cddid_all.tbl CDD cd07156 cd07156 143531 NR_DBD_VDR_like The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. Like other nuclear receptors, xenobiotic receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 72 matched cddid_all.tbl CDD cd07157 cd07157 143532 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers. The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown. 86 matched cddid_all.tbl CDD cd07158 cd07158 143533 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family. The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 73 matched cddid_all.tbl CDD cd07160 cd07160 143534 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE sequence is a direct repeat-4 (DR-4) DNA fragment consisting of two AGGTCA hexameric half-sites separated by a 4-nucleotide spacer. LXR has typical NR modular structure with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and the ligand binding domain (LBD) at the C-terminal. 101 matched cddid_all.tbl CDD cd07161 cd07161 143535 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers. DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 91 matched cddid_all.tbl CDD cd07162 cd07162 143536 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers. DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding domain, a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain. 87 matched cddid_all.tbl CDD cd07163 cd07163 143537 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 92 matched cddid_all.tbl CDD cd07164 cd07164 143538 NR_DBD_PNR_like_1 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 78 matched cddid_all.tbl CDD cd07165 cd07165 143539 NR_DBD_DmE78_like DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two C4-type zinc fingers. DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. The SmE78 may be involved in transduction of an ecdysone signal in S. mansoni, consistent with its function in Drosophila. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, E78-like receptors have a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 81 matched cddid_all.tbl CDD cd07166 cd07166 143540 NR_DBD_REV_ERB DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers. DNA-binding domain of REV-ERB receptor- like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. REV-ERB receptors are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. REV-ERB receptors bind as a monomer to a (A/G)GGTCA half-site with a 5' AT-rich extension or as a homodimer to a direct repeat 2 element (AGGTCA sequence with a 2-bp spacer), indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target genes. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB receptor. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, REV-ERB receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 89 matched cddid_all.tbl CDD cd07167 cd07167 143541 NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which is required at several stages of development. Particularly, FTZ-F1 regulated genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development; SF-1 is an essential regulator of endocrine development and function and is considered a master regulator of reproduction; SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). However, the ligand for FTZ-F1 has not yet been identified. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 and SF-1 bind to DNA as monomers. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, receptors in this family have a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 93 matched cddid_all.tbl CDD cd07168 cd07168 143542 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 90 matched cddid_all.tbl CDD cd07169 cd07169 143543 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 90 matched cddid_all.tbl CDD cd07170 cd07170 143544 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ERR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 97 matched cddid_all.tbl CDD cd07171 cd07171 143545 NR_DBD_ER DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ER interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Estrogen receptor is a transcription regulator that mediates the biological effects of hormone estrogen. The binding of estrogen to the receptor triggers the dimerization and the binding of the receptor dimer to estrogen response element, which is a palindromic inverted repeat: 5'GGTCAnnnTGACC-3', of target genes. Through ER, estrogen regulates development, reproduction and homeostasis. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well-conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 82 matched cddid_all.tbl CDD cd07172 cd07172 143546 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers. DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, protein processing, and metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GR and PR have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). 78 matched cddid_all.tbl CDD cd07173 cd07173 143547 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modulates their expression. Another mode of action of androgen receptor is independent of their interactions with DNA. The receptor interacts directly with signal transduction proteins in the cytoplasm, causing rapid changes in cell function, such as ion transport. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, AR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 82 matched cddid_all.tbl CDD cd07176 cd07176 143580 terB tellurite resistance protein terB. This family contains uncharacterized bacterial proteins involved in tellurium resistance. The prototype of this CD is the Kp-terB protein from Klebsiella pneumoniae, whose 3D structure was recently determined. The biological function of terB and the mechanism responsible for tellurium resistance are unknown. 111 matched cddid_all.tbl CDD cd07177 cd07177 143581 terB_like tellurium resistance terB-like protein. This family consists of tellurium resistance terB proteins, N-terminal domain of heat shock DnaJ-like proteins, N-terminal domain of Mo-dependent nitrogenase-like proteins, C-terminal domain of ABC transporter ATP-binding proteins, C-terminal domain of serine/threonine protein kinase, and many hypothetical bacterial proteins. The function of this family is unknown. 104 matched cddid_all.tbl CDD cd07178 cd07178 143582 terB_like_YebE tellurium resistance terB-like protein, subgroup 3. This family includes several uncharacterized bacterial proteins including an Escherichia coli protein called YebE. Protein sequence homology analysis shows they are similar to tellurium resistance protein terB, but the function of this family is unknown. 95 matched cddid_all.tbl CDD cd07179 cd07179 143548 2DBD_NR_DBD2 The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type zinc fingers. The second DNA-binding domain (DBD) of the 2DBD nuclear receptor (NR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. The proteins contain two DBDs in tandem, probably resulting from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown. 74 matched cddid_all.tbl CDD cd07180 cd07180 260001 RNase_HII_archaea_like Archaeal Ribonuclease HII. This family includes type 2 RNases H from archaea, some of which show broad divalent cation specificity. It is proposed that three of the four acidic residues at the active site are involved in metal binding and the fourth one is involved in the catalytic process in archaea. Most archaeal genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype in E. coli. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, archaeal RNase HII and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication or repair. 204 matched cddid_all.tbl CDD cd07181 cd07181 260002 RNase_HII_eukaryota_like Eukaryotic RNase HII. This family includes eukaryotic type 2 RNase H (RNase HII or H2) which is active during replication and is believed to play a role in the removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII (RNASEH2A) is functional when it forms a heterotrimeric complex with two other accessory proteins (RNASEH2B and RNASEH2C). It is speculated that these accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause the severe genetic neurological disorder Aicardi-Goutieres syndrome. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. 221 matched cddid_all.tbl CDD cd07182 cd07182 260003 RNase_HII_bacteria_HII_like Bacterial Ribonuclease HII-like. This family includes mostly bacterial type 2 RNases H, with some eukaryotic members. Bacterial RNase HII has a role in primer removal based on its involvement in ribonucleotide-specific catalytic activity in the presence of RNA/DNA hybrid substrates. Several bacteria, such as Bacillus subtilis, have two different type II RNases H, RNases HII and HIII; double deletion of these leads to cellular lethality. It appears that type I and type II RNases H also have overlapping functions in cells, as over-expression of Escherichia coli RNase HII can complement an RNase HI deletion phenotype. In Leishmania mitochondria, of the four distinct RNase H genes (H1, HIIA, HIIB, HIIC), HIIC is essential for the survival of the parasite and thus can be a potential target for anti-leishmanial chemotherapy. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. 177 matched cddid_all.tbl CDD cd07184 cd07184 199892 E_set_Isoamylase_like_N "N-terminal Early set domain associated with the catalytic domain of isoamylase-like (also called glycogen 6-glucanohydrolase) proteins. E or ""early"" set domains are associated with the catalytic domain of isoamylase-like proteins at the N-terminal end. Isoamylase is one of the starch-debranching enzymes that catalyze the hydrolysis of alpha-1,6-glucosidic linkages specific in alpha-glucans such as amylopectin or glycogen. Isoamylase contains a bound calcium ion, but this is not in the same position as the conserved calcium ion that has been reported in other alpha-amylase family enzymes. The N-terminal domain of isoamylase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase. This domain is also a member of the CBM48 (Carbohydrate Binding Module 48) family whose members include pullulanase, maltooligosyl trehalose synthase, starch branching enzyme, glycogen branching enzyme, glycogen debranching enzyme, and the beta subunit of AMP-activated protein kinase." 86 matched cddid_all.tbl CDD cd07185 cd07185 143586 OmpA_C-like Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA. OmpA-like domains (named after the C-terminal domain of Escherichia coli OmpA protein) have been shown to non-covalently associate with peptidoglycan, a network of glycan chains composed of disaccharides, which are crosslinked via short peptide bridges. Well-studied members of this family include the Escherichia coli outer membrane protein OmpA, the Escherichia coli lipoprotein PAL, Neisseria meningitdis RmpM, which interact with the outer membrane, as well as the Escherichia coli motor protein MotB, and the Vibrio flagellar motor proteins PomB and MotY, which interact with the inner membrane. 106 matched cddid_all.tbl CDD cd07186 cd07186 132872 CofD_like LPPG:FO 2-phospho-L-lactate transferase; important in F420 biosynthesis. CofD is a 2-phospho-L-lactate transferase that catalyzes the last step in the biosynthesis of coenzyme F(420)-0 (F(420) without polyglutamate) by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0). F420 is a hydride carrier, important for energy metabolism of methanogenic archaea, as well as for the biosynthesis of other natural products, like tetracycline in Streptomyces. F420 and some of its precursors are also utilized as cofactors for enzymes, like DNA photolyase in Mycobacterium tuberculosis. 303 matched cddid_all.tbl CDD cd07187 cd07187 132873 YvcK_like family of mostly uncharacterized proteins similar to B.subtilis YvcK. One member of this protein family, YvcK from Bacillus subtilis, has been proposed to play a role in carbon metabolism, since its function is essential for growth on intermediates of the Krebs cycle and the pentose phosphate pathway. In general, this family of mostly uncharacterized proteins is related to the CofD-like protein family. CofD has been characterized as a 2-phospho-L-lactate transferase involved in F420 biosynthesis. This family appears to have the same conserved phosphate binding site as the other family in this hierarchy, but a different substrate binding site. 308 matched cddid_all.tbl CDD cd07197 cd07197 143587 nitrilase Nitrilase superfamily, including nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes. This superfamily (also known as the C-N hydrolase superfamily) contains hydrolases that break carbon-nitrogen bonds; it includes nitrilases, cyanide dihydratases, aliphatic amidases, N-terminal amidases, beta-ureidopropionases, biotinidases, pantotheinase, N-carbamyl-D-amino acid amidohydrolases, the glutaminase domain of glutamine-dependent NAD+ synthetase, apolipoprotein N-acyltransferases, and N-carbamoylputrescine amidohydrolases, among others. These enzymes depend on a Glu-Lys-Cys catalytic triad, and work through a thiol acylenzyme intermediate. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. These oligomers include dimers, tetramers, hexamers, octamers, tetradecamers, octadecamers, as well as variable length helical arrangements and homo-oligomeric spirals. These proteins have roles in vitamin and co-enzyme metabolism, in detoxifying small molecules, in the synthesis of signaling molecules, and in the post-translational modification of proteins. They are used industrially, as biocatalysts in the fine chemical and pharmaceutical industry, in cyanide remediation, and in the treatment of toxic effluent. This superfamily has been classified previously in the literature, based on global and structure-based sequence analysis, into thirteen different enzyme classes (referred to as 1-13). This hierarchy includes those thirteen classes and a few additional subfamilies. A putative distant relative, the plasmid-borne TraB family, has not been included in the hierarchy. 253 matched cddid_all.tbl CDD cd07198 cd07198 132837 Patatin Patatin-like phospholipase. Patatin is a storage protein of the potato tuber that shows Phospholipase A2 activity (PLA2; EC 3.1.1.4). Patatin catalyzes the nonspecific hydrolysis of phospholipids, glycolipids, sulfolipids, and mono- and diacylglycerols, thereby showing lipid acyl hydrolase activity. The active site includes an oxyanion hole with a conserved GGxR motif; it is found in almost all the members of this family. The catalytic dyad is formed by a serine and an aspartate. Patatin belongs to the alpha-beta hydrolase family which is identified by a characteristic nucleophile elbow with a consensus sequence of Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu = nucleophile). Members of this family have been found also in vertebrates. This family includes PNPLA (1-9), TGL (3-5), ExoU-like, and SDP1-like subfamilies. There are some additional hypothetical proteins included in this family. 172 matched cddid_all.tbl CDD cd07199 cd07199 132838 Pat17_PNPLA8_PNPLA9_like Patatin-like phospholipase; includes PNPLA8, PNPLA9, and Pat17. Patatin is a storage protein of the potato tuber that shows Phospholipase A2 activity (PLA2; EC 3.1.1.4). Patatin catalyzes the nonspecific hydrolysis of phospholipids, glycolipids, sulfolipids, and mono- and diacylglycerols, thereby showing lipid acyl hydrolase activity. The active site includes an oxyanion hole with a conserved GGxR motif; it is found in almost all the members of this family. The catalytic dyad is formed by a serine and an aspartate. Patatin belongs to the alpha-beta hydrolase family which is identified by a characteristic nucleophile elbow with a consensus sequence of Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu = nucleophile). Members of this family have been found also in vertebrates. This family includes subfamily of PNPLA8 (iPLA2-gamma) and PNPLA9 (iPLA2-beta) like phospholipases from human as well as the Pat17 isozyme from Solanum cardiophyllum. 258 matched cddid_all.tbl CDD cd07200 cd07200 132839 cPLA2_Grp-IVA "Group IVA cytosolic phospholipase A2; catalytic domain; Ca-dependent. Group IVA cPLA2, an 85 kDa protein, consists of two domains: the regulatory C2 domain and the alpha/beta hydrolase PLA2 domain. Group IVA cPLA2 is also referred to as cPLA2-alpha. The catalytic domain of cytosolic phospholipase A2 (cPLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both ""closed lid"" and ""open lid"" forms. Movement of the cPLA2 lid possibly exposes a greater hydrophobic surface and the active site. cPLA2 belongs to the alpha-beta hydrolase family which is identified by a characteristic nucleophile elbow with a consensus sequence of Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu = nucleophile). Calcium is required for cPLA2 to bind with membranes or phospholipids. A calcium-dependent phospholipid binding domain resides in the N-terminal region of cPLA2; it is homologous to the C2 domain superfamily which is not included in this hierarchy. Includes PLA2G4A from chicken, human, and frog." 505 matched cddid_all.tbl CDD cd07201 cd07201 132840 cPLA2_Grp-IVB-IVD-IVE-IVF "Group IVB, IVD, IVE, and IVF cytosolic phospholipase A2; catalytic domain; Ca-dependent. Group IVB, IVD, IVE, and IVF cPLA2 consists of two domains: the regulatory C2 domain and alpha/beta hydrolase PLA2 domain. Group IVB, IVD, IVE, and IVF cPLA2 are also referred to as cPLA2-beta, -delta, -epsilon, and -zeta respectively. cPLA2-beta is approximately 30% identical to cPLA2-alpha and it shows low enzymatic activity compared to cPLA2alpha. cPLA2-beta hydrolyzes palmitic acid from 1-[14C]palmitoyl-2-arachidonoyl-PC and arachidonic acid from 1-palmitoyl-2[14C]arachidonoyl-PC, but not from 1-O-alkyl-2[3H]arachidonoyl-PC. cPLA2-delta, -epsilon, and -zeta are approximately 45-50% identical to cPLA2-beta and 31-37% identical to cPLA2-alpha. It's possible that cPLA2-beta, -delta, -epsilon, and -zeta may have arisen by gene duplication from an ancestral gene. The catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both ""closed lid"" and ""open lid"" forms. Movement of the cPLA2 lid possibly exposes a greater hydrophobic surface and the active site. cPLA2 belongs to the alpha-beta hydrolase family which is identified by a characteristic nucleophile elbow with a consensus sequence of Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu = nucleophile). Calcium is required for cPLA2 to bind with membranes or phospholipids. The calcium-dependent phospholipid binding domain resides in the N-terminal region of cPLA2; it is homologous to the C2 domain superfamily which is not included in this hierarchy. It includes PLA2G4B, PLA2G4D, PLA2G4E, and PLA2G4F from humans." 541 matched cddid_all.tbl CDD cd07202 cd07202 132841 cPLA2_Grp-IVC "Group IVC cytoplasmic phospholipase A2; catalytic domain; Ca-independent. Group IVC cPLA2, a small 61 kDa protein, is a single domain alpha/beta hydrolase. It lacks a C2 domain; therefore, it has no Ca-dependence. Group IVC cPLA2 is also referred to as cPLA2-gamma. The cPLA2-gamma enzyme is predominantly found in cardiac and skeletal muscles, and to a lesser extent in the brain. Human cPLA2-gamma is approximately 30% identical to cPLA2-alpha. The catalytic domain of cytosolic phospholipase A2 (PLA2; EC 3.1.1.4) hydrolyzes the sn-2-acyl ester bond of phospholipids to release arachidonic acid. At the active site, cPLA2 contains a serine nucleophile through which the catalytic mechanism is initiated. The active site is partially covered by a solvent-accessible flexible lid. cPLA2 displays interfacial activation as it exists in both ""closed lid"" and ""open lid"" forms. Movement of the cPLA2 lid possibly exposes a greater hydrophobic surface and the active site. cPLA2 belongs to the alpha-beta hydrolase family which is identified by a characteristic nucleophile elbow with a consensus sequence of Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu = nucleophile). Includes PLA2G4C protein from human and Pla2g4c protein from mouse." 430 matched cddid_all.tbl CDD cd07203 cd07203 132842 cPLA2_Fungal_PLB Fungal Phospholipase B-like; cPLA2 GrpIVA homologs; catalytic domain. Fungal phospholipase B are Group IV cPLA2 homologs. Aspergillus PLA2 is Ca-dependent, yet it does not contain a C2 domain. PLB deacylates both sn-1 and sn-2 chains of phospholipids and are abundantly expressed in fungi. It shows lysophospholipase (lysoPL) and transacylase activities. The active site residues from cPLA2 are also conserved in PLB. Like cPLA2, PLB also has a consensus sequence of Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu = nucleophile). It includes PLB1 from Schizosaccharomyces pombe, PLB2 from Candida glabrata, and PLB3 from Saccharomyces cerevisiae. PLB1, PLB2, and PLB3 show PLB and lysoPL activities; PLB3 is specific for phosphoinositides. 552 matched cddid_all.tbl CDD cd07204 cd07204 132843 Pat_PNPLA_like Patatin-like phospholipase domain containing protein family. Members of this family share a patain domain, initially discovered in potato tubers. PNPLA protein members show non-specific hydrolase activity with a variety of substrates such as triacylglycerol, phospholipids, and retinylesters. It contains the lipase consensus sequence (Gly-X-Ser-X-Gly). Nomenclature of PNPLA family could be misleading as some of the mammalian members of this family show hydrolase, but no phospholipase activity. 243 matched cddid_all.tbl CDD cd07205 cd07205 132844 Pat_PNPLA6_PNPLA7_NTE1_like Patatin-like phospholipase domain containing protein 6, protein 7, and fungal NTE1. Patatin-like phospholipase domain containing protein 6 (PNPLA6) and protein 7 (PNPLA7) are included in this family. PNPLA6 is commonly known as Neuropathy Target Esterase (NTE). NTE has at least two functional domains: the N-terminal domain putatively regulatory domain and the C-terminal catalytic domain which shows esterase activity. NTE shows phospholipase activity for lysophosphatidylcholine (LPC) and phosphatidylcholine (PC). Exposure of NTE to organophosphates leads to organophosphate-induced delayed neurotoxicity (OPIDN). OPIDN is a progressive neurological condition that is characterized by weakness, paralysis, pain, and paresthesia. PNPLA7 is an insulin-regulated phospholipase that is homologus to Neuropathy Target Esterase (NTE or PNPLA6) and is also known as NTE-related esterase (NRE). Human NRE is predominantly expressed in prostate, white adipose, and pancreatic tissue. NRE hydrolyzes sn-1 esters in lysophosphatidylcholine and lysophosphatidic acid, but shows no lipase activity with substrates like triacylglycerols (TG), cholesteryl esters, retinyl esters (RE), phosphatidylcholine (PC), or monoacylglycerol (MG). This family includes subfamily of PNPLA6 (NTE) and PNPLA7 (NRE)-like phospholipases. 175 matched cddid_all.tbl CDD cd07206 cd07206 132845 Pat_TGL3-4-5_SDP1 Triacylglycerol lipase 3, 4, and 5 and Sugar-Dependent 1 lipase. Triacylglycerol lipases are involved in triacylglycerol mobilization and degradation; they are found in lipid particles. TGL4 is 30% homologus to TGL3, whereas TGL5 is 26% homologus to TGL3. Sugar-Dependent 1 (SDP1) lipase has a patatin-like acyl-hydrolase domain that initiates the breakdown of storage oil in germinating Arabidopsis seeds. This family includes subfamilies of proteins: TGL3, TGL4, TGL5, and SDP1. 298 matched cddid_all.tbl CDD cd07207 cd07207 132846 Pat_ExoU_VipD_like ExoU and VipD-like proteins; homologus to patatin, cPLA2, and iPLA2. ExoU, a 74-kDa enzyme, is a potent virulence factor of Pseudomonas aeruginosa. One of the pathogenic mechanisms of P. aeruginosa is to induce cytotoxicity by the injection of effector proteins (e.g. ExoU) using the type III secretion (T3S) system. ExoU is homologus to patatin and also has the conserved catalytic residues of mammalian calcium-independent (iPLA2) and cytosolic (cPLA2) PLA2. In vitro, ExoU cytotoxity is blocked by the inhibitor of cytosolic and Ca2-independent phospholipase A2 (cPLA2 and iPLA2) enzymes, suggesting that phospholipase A2 inhibitors may represent a novel mode of treatment for acute P. aeruginosa infections. ExoU requires eukaryotic superoxide dismutase as a cofactor and cleaves phosphatidylcholine and phosphatidylethanolamine in vitro. VipD, a 69-kDa cytosolic protein, belongs to the members of Legionella pneumophila family and is homologus to ExoU from Pseudomonas. Even though VipD shows high sequence similarity with several functional regions of ExoU (e.g. oxyanion hole, active site serine, active site aspartate), it has been shown to have no phospholipase activity. This family includes ExoU from Pseudomonas aeruginosa and VipD of Legionella pneumophila. 194 matched cddid_all.tbl CDD cd07208 cd07208 132847 Pat_hypo_Ecoli_yjju_like Hypothetical patatin similar to yjju protein of Escherichia coli. Patatin-like phospholipase similar to yjju protein of Escherichia coli. This family predominantly consists of bacterial patatin glycoproteins, and some representatives from eukaryotes and archaea. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. 266 matched cddid_all.tbl CDD cd07209 cd07209 132848 Pat_hypo_Ecoli_Z1214_like Hypothetical patatin similar to Z1214 protein of Escherichia coli. Patatin-like phospholipase similar to Z1214 protein of Escherichia coli. This family predominantly consists of bacterial patatin glycoproteins and some representatives from eukaryotes and archaea. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. 215 matched cddid_all.tbl CDD cd07210 cd07210 132849 Pat_hypo_W_succinogenes_WS1459_like Hypothetical patatin similar to WS1459 of Wolinella succinogenes. Patatin-like phospholipase. This family predominantly consists of bacterial patatin glycoproteins. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have also been found in vertebrates. 221 matched cddid_all.tbl CDD cd07211 cd07211 132850 Pat_PNPLA8 Patatin-like phospholipase domain containing protein 8. PNPLA8 is a Ca-independent myocardial phospholipase which maintains mitochondrial integrity. PNPLA8 is also known as iPLA2-gamma. In humans, it is predominantly expressed in heart tissue. iPLA2-gamma can catalyze both phospholipase A1 and A2 reactions (PLA1 and PLA2 respectively). This family includes PNPLA8 (iPLA2-gamma) from Homo sapiens and iPLA2-2 from Mus musculus. 308 matched cddid_all.tbl CDD cd07212 cd07212 132851 Pat_PNPLA9 Patatin-like phospholipase domain containing protein 9. PNPLA9 is a Ca-independent phospholipase that catalyzes the hydrolysis of glycerophospholipids at the sn-2 position. PNPLA9 is also known as PLA2G6 (phospholipase A2 group VI) or iPLA2beta. PLA2G6 is stimulated by ATP and inhibited by bromoenol lactone (BEL). In humans, PNPLA9 in expressed ubiquitously and is involved in signal transduction, cell proliferation, and apoptotic cell death. Mutations in human PLA2G6 leads to infantile neuroaxonal dystrophy (INAD) and idiopathic neurodegeneration with brain iron accumulation (NBIA). This family includes PLA2G6 from Homo sapiens and Rattus norvegicus. 312 matched cddid_all.tbl CDD cd07213 cd07213 132852 Pat17_PNPLA8_PNPLA9_like1 Patatin-like phospholipase. Patatin is a storage protein of the potato tuber that shows Phospholipase A2 activity (PLA2; EC 3.1.1.4). Patatin catalyzes the nonspecific hydrolysis of phospholipids, glycolipids, sulfolipids, and mono- and diacylglycerols, thereby showing lipid acyl hydrolase activity. The active site includes an oxyanion hole with a conserved GGxR motif; it is found in almost all the members of this family. The catalytic dyad is formed by a serine and an aspartate. Patatin belongs to the alpha-beta hydrolase family which is identified by a characteristic nucleophile elbow with a consensus sequence of Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu = nucleophile). Members of this family have been found also in vertebrates. This family includes subfamily of PNPLA8 (iPLA2-gamma) and PNPLA9 (iPLA2-beta) like phospholipases from human as well as the Pat17 isozyme from Solanum cardiophyllum. 288 matched cddid_all.tbl CDD cd07214 cd07214 132853 Pat17_isozyme_like Patatin-like phospholipase of plants. Pat17 is an isozyme of patatin cloned from Solanum cardiophyllum. Patatin is a storage protein of the potato tuber that shows Phospholipase A2 activity (PLA2; EC 3.1.1.4). Patatin catalyzes the nonspecific hydrolysis of phospholipids, glycolipids, sulfolipids, and mono- and diacylglycerols, thereby showing lipid acyl hydrolase activity. The active site includes an oxyanion hole with a conserved GGxR motif; it is found in almost all the members of this family. The catalytic dyad is formed by a serine and an aspartate. Patatin belongs to the alpha-beta hydrolase family which is identified by a characteristic nucleophile elbow with a consensus sequence of Sm-X-Nu-Sm (Sm = small residue, X = any residue, and Nu = nucleophile). Patatin-like phospholipase are included in this group. Members of this family have also been found in vertebrates. 349 matched cddid_all.tbl CDD cd07215 cd07215 132854 Pat17_PNPLA8_PNPLA9_like2 Patatin-like phospholipase of bacteria. Patatin is a storage protein of the potato tuber that shows Phospholipase A2 activity (PLA2; EC 3.1.1.4). Patatin catalyzes the nonspecific hydrolysis of phospholipids, glycolipids, sulfolipids, and mono- and diacylglycerols, thereby showing lipid acyl hydrolase activity. The active site includes an oxyanion hole with a conserved GGxR motif; it is found in almost all the members of this family. The catalytic dyad is formed by a serine and an aspartate. Patatin belongs to the alpha-beta hydrolase family which is identified by a characteristic nucleophile elbow with a consensus sequence of Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu = nucleophile). Members of this family have been found also in vertebrates. This family includes subfamily of PNPLA8 (iPLA2-gamma) and PNPLA9 (iPLA2-beta) like phospholipases from human as well as the Pat17 isozyme from Solanum cardiophyllum. 329 matched cddid_all.tbl CDD cd07216 cd07216 132855 Pat17_PNPLA8_PNPLA9_like3 Patatin-like phospholipase. Patatin is a storage protein of the potato tuber that shows Phospholipase A2 activity (PLA2; EC 3.1.1.4). Patatin catalyzes the nonspecific hydrolysis of phospholipids, glycolipids, sulfolipids, and mono- and diacylglycerols, thereby showing lipid acyl hydrolase activity. The active site includes an oxyanion hole with a conserved GGxR motif; it is found in almost all the members of this family. The catalytic dyad is formed by a serine and an aspartate. Patatin belongs to the alpha-beta hydrolase family which is identified by a characteristic nucleophile elbow with a consensus sequence of Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu = nucleophile). Members of this family have been found also in vertebrates. This family includes subfamily of PNPLA8 (iPLA2-gamma) and PNPLA9 (iPLA2-beta) like phospholipases from human as well as the Pat17 isozyme from Solanum cardiophyllum. 309 matched cddid_all.tbl CDD cd07217 cd07217 132856 Pat17_PNPLA8_PNPLA9_like4 Patatin-like phospholipase. Patatin is a storage protein of the potato tuber that shows Phospholipase A2 activity (PLA2; EC 3.1.1.4). Patatin catalyzes the nonspecific hydrolysis of phospholipids, glycolipids, sulfolipids, and mono- and diacylglycerols, thereby showing lipid acyl hydrolase activity. The active site includes an oxyanion hole with a conserved GGxR motif; it is found in almost all the members of this family. The catalytic dyad is formed by a serine and an aspartate. Patatin belongs to the alpha-beta hydrolase family which is identified by a characteristic nucleophile elbow with a consensus sequence of Sm-X-Nu-Sm (Sm = small residue, X = any residue and Nu = nucleophile). Members of this family have been found also in vertebrates. This family includes subfamily of PNPLA8 (iPLA2-gamma) and PNPLA9 (iPLA2-beta) like phospholipases from human as well as the Pat17 isozyme from Solanum cardiophyllum. 344 matched cddid_all.tbl CDD cd07218 cd07218 132857 Pat_iPLA2 Calcium-independent phospholipase A2; Classified as Group IVA-1 PLA2. Calcium-independent phospholipase A2; otherwise known as Group IVA-1 PLA2. It contains the lipase consensus sequence (Gly-X-Ser-X-Gly);mutagenesis experiments confirm the role of this serine as a nucleophile. Some members of this group show triacylglycerol lipase activity (EC 3:1:1:3). Members include iPLA-1, iPLA-2, and iPLA-3 from Aedes aegypti and show acylglycerol transacylase/lipase activity. Also includes putative iPLA2-eta from Pediculus humanus corporis which shows patatin-like phospholipase activity. 245 matched cddid_all.tbl CDD cd07219 cd07219 132858 Pat_PNPLA1 Patatin-like phospholipase domain containing protein 1. Members of this family share a patatin domain, initially discovered in potato tubers. Some members of PNPLA1 subfamily do not have the lipase consensus sequence Gly-X-Ser-X-Gly which is essential for hydrolase activity. This family includes PNPLA1 from Homo sapiens and Gallus gallus. Currently, there is no literature available on the physiological role, structure, or enzymatic activity of PNPLA1. It is expressed in various human tissues in low mRNA levels. 382 matched cddid_all.tbl CDD cd07220 cd07220 132859 Pat_PNPLA2 Patatin-like phospholipase domain containing protein 2. PNPLA2 plays a key role in hydrolysis of stored triacylglecerols and is also known as adipose triglyceride lipase (ATGL). Members of this family share a patain domain, initially discovered in potato tubers. ATGL is expressed in white and brown adipose tissue in high mRNA levels. Mutations in PNPLA2 encoding adipose triglyceride lipase (ATGL) leads to neutral lipid storage disease (NLSD) which is characterized by the accumulation of triglycerides in multiple tissues. ATGL mutations are also commonly associated with severe forms of skeletal- and cardio-myopathy. This family includes patatin-like proteins: TTS-2.2 (transport-secretion protein 2.2), PNPLA2 (Patatin-like phospholipase domain-containing protein 2), and iPLA2-zeta (Calcium-independent phospholipase A2) from Homo sapiens. 249 matched cddid_all.tbl CDD cd07221 cd07221 132860 Pat_PNPLA3 Patatin-like phospholipase domain containing protein 3. PNPLA3 is a triacylglycerol lipase that mediates triacylglycerol hydrolysis in adipocytes and is an indicator of the nutritional state. PNPLA3 is also known as adiponutrin (ADPN) or iPLA2-epsilon. Human adiponutrins are bound to the cell membrane of adipocytes and show transacylase, TG hydrolase, and PLA2 activity. This family includes patatin-like proteins: ADPN (adiponutrin) from mammals, PNPLA3 (Patatin-like phospholipase domain-containing protein 3), and iPLA2-epsilon (Calcium-independent phospholipase A2) from Homo sapiens. 252 matched cddid_all.tbl CDD cd07222 cd07222 132861 Pat_PNPLA4 Patatin-like phospholipase domain containing protein 4. PNPLA4, also known as GS2 (gene sequence-2), shows both lipase and transacylation activities. GS2 lipase is expressed in various tissues, predominantly in muscle and adipocytes tissue. It is also expressed in keratinocytes and shows retinyl ester hydrolase, acylglycerol, TG hydrolase, and PLA2 activity. This family includes patatin-like proteins: GS2 from mammals, PNPLA4 (Patatin-like phospholipase domain-containing protein 4), and iPLA2-eta (Calcium-independent phospholipase A2) from Homo sapiens. 246 matched cddid_all.tbl CDD cd07223 cd07223 132862 Pat_PNPLA5-mammals Patatin-like phospholipase domain containing protein 5. PNPLA5, also known as GS2L (GS2-like), plays a role in regulation of adipocyte differentiation. PNPLA5 is expressed in brain tissue in high mRNA levels and low levels in liver tissue. There is no concrete evidence in support of the enzymatic activity of GS2L. This family includes patatin-like proteins: GS2L (GS2-like) and PNPLA5 (Patatin-like phospholipase domain-containing protein 5) reported exclusively in mammals. 405 matched cddid_all.tbl CDD cd07224 cd07224 132863 Pat_like Patatin-like phospholipase. Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of lipid acyl hydrolase, catalysing the cleavage of fatty acids from membrane lipids. Members of this family have been found also in vertebrates. 233 matched cddid_all.tbl CDD cd07225 cd07225 132864 Pat_PNPLA6_PNPLA7 Patatin-like phospholipase domain containing protein 6 and protein 7. Patatin-like phospholipase domain containing protein 6 (PNPLA6) and protein 7 (PNPLA7) are 60% identical to each other. PNPLA6 is commonly known as Neuropathy Target Esterase (NTE). NTE has at least two functional domains: the N-terminal domain putatively regulatory domain and the C-terminal catalytic domain which shows esterase activity. NTE shows phospholipase activity for lysophosphatidylcholine (LPC) and phosphatidylcholine (PC). Exposure of NTE to organophosphates leads to organophosphate-induced delayed neurotoxicity (OPIDN). OPIDN is a progressive neurological condition that is characterized by weakness, paralysis, pain, and paresthesia. PNPLA7 is an insulin-regulated phospholipase that is homologous to Neuropathy Target Esterase (NTE or PNPLA6) and is also known as NTE-related esterase (NRE). Human NRE is predominantly expressed in prostate, white adipose, and pancreatic tissue. NRE hydrolyzes sn-1 esters in lysophosphatidylcholine and lysophosphatidic acid, but shows no lipase activity with substrates like triacylglycerols (TG), cholesteryl esters, retinyl esters (RE), phosphatidylcholine (PC), or monoacylglycerol (MG). This family includes PNPLA6 and PNPLA7 from Homo sapiens, YMF9 from Yeast, and Swiss Cheese protein (sws) from Drosophila melanogaster. 306 matched cddid_all.tbl CDD cd07227 cd07227 132865 Pat_Fungal_NTE1 Fungal patatin-like phospholipase domain containing protein 6. These are fungal Neuropathy Target Esterase (NTE), commonly referred to as NTE1. Patatin-like phospholipase. NTE has at least two functional domains: the N-terminal domain putatively regulatory domain and the C-terminal catalytic domain which shows esterase activity. NTE shows phospholipase activity for lysophosphatidylcholine (LPC) and phosphatidylcholine (PC). Exposure of NTE to organophosphates leads to organophosphate-induced delayed neurotoxicity (OPIDN). OPIDN is a progressive neurological condition that is characterized by weakness, paralysis, pain, and paresthesia. This family includes NTE1 from fungi. 269 matched cddid_all.tbl CDD cd07228 cd07228 132866 Pat_NTE_like_bacteria Bacterial patatin-like phospholipase domain containing protein 6. Bacterial patatin-like phospholipase domain containing protein 6. PNPLA6 is commonly known as Neuropathy Target Esterase (NTE). NTE has at least two functional domains: the N-terminal domain putatively regulatory domain and the C-terminal catalytic domain which shows esterase activity. NTE shows phospholipase activity for lysophosphatidylcholine (LPC) and phosphatidylcholine (PC). Exposure of NTE to organophosphates leads to organophosphate-induced delayed neurotoxicity (OPIDN). OPIDN is a progressive neurological condition that is characterized by weakness, paralysis, pain, and paresthesia. This group includes YCHK and rssA from Escherichia coli as well as Ylbk from Bacillus amyloliquefaciens. 175 matched cddid_all.tbl CDD cd07229 cd07229 132867 Pat_TGL3_like Triacylglycerol lipase 3. Triacylglycerol lipase 3 (TGL3) are responsible for all the TAG lipase activity of the lipid particle. Triacylglycerol (TAG) lipases are also necessary for the mobilization of TAG stored in lipid particles. TGL3 contains the consensus sequence motif GXSXG, which is found in lipolytic enzymes. This family includes Tgl3p from Saccharomyces cerevisiae. 391 matched cddid_all.tbl CDD cd07230 cd07230 132868 Pat_TGL4-5_like Triacylglycerol lipase 4 and 5. TGL4 and TGL5 are triacylglycerol lipases that are involved in triacylglycerol mobilization and degradation; they are found in lipid particles. Tgl4 is a functional ortholog of mammalian adipose TG lipase (ATGL) and is phosphorylated and activated by cyclin-dependent kinase 1 (Cdk1/Cdc28). TGL4 is 30% homologus to TGL3, whereas TGL5 is 26% homologus to TGL3. This family includes TGL4 (STC1) and TGL5 (STC2) from Saccharomyces cerevisiae. 421 matched cddid_all.tbl CDD cd07231 cd07231 132869 Pat_SDP1-like Sugar-Dependent 1 like lipase. Sugar-Dependent 1 (SDP1) lipase has a patatin-like acyl-hydrolase domain that initiates the breakdown of storage oil in germinating Arabidopsis seeds. This acyl-hydrolase domain is homologus to yeast triacylglycerol lipase 3 and human adipose triglyceride lipase. This family includes SDP1 from Arabidopsis thaliana. 323 matched cddid_all.tbl CDD cd07232 cd07232 132870 Pat_PLPL Patain-like phospholipase. Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants and fungi. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein, but it also has the enzymatic activity of a lipid acyl hydrolase, catalyzing the cleavage of fatty acids from membrane lipids. Members of this family have been found also in vertebrates. 407 matched cddid_all.tbl CDD cd07233 cd07233 319900 GlxI_Zn Glyoxalase I that uses Zn(++) as cofactor. This family includes eukaryotic glyoxalase I that prefers the divalent cation zinc as cofactor. Glyoxalase I (also known as lactoylglutathione lyase; EC 4.4.1.5) is part of the glyoxalase system, a two-step system for detoxifying methylglyoxal, a side product of glycolysis. This system is responsible for the conversion of reactive, acyclic alpha-oxoaldehydes into the corresponding alpha-hydroxyacids and involves 2 enzymes, glyoxalase I and II. Glyoxalase I catalyses an intramolecular redox reaction of the hemithioacetal (formed from methylglyoxal and glutathione) to form the thioester, S-D-lactoylglutathione. This reaction involves the transfer of two hydrogen atoms from C1 to C2 of the methylglyoxal, and proceeds via an ene-diol intermediate. Glyoxalase I has a requirement for bound metal ions for catalysis. Eukaryotic glyoxalase I prefers the divalent cation zinc as cofactor, whereas Escherichia coil and other prokaryotic glyoxalase I uses nickel. However, eukaryotic Trypanosomatid parasites also use nickel as a cofactor, which could possibly be explained by acquiring their GLOI gene by horizontal gene transfer. Human glyoxalase I is a two-domain enzyme and it has the structure of a domain-swapped dimer with two active sites located at the dimer interface. In yeast, in various plants, insects and Plasmodia, glyoxalase I is four-domain, possibly the result of a further gene duplication and an additional gene fusing event. 142 matched cddid_all.tbl CDD cd07235 cd07235 319901 MRD Mitomycin C resistance protein (MRD). Mitomycin C (MC) is a naturally occurring antibiotic, and antitumor agent used in the treatment of cancer. Its antitumor activity is exerted primarily through monofunctional and bifunctional alkylation of DNA. MRD binds to MC and functions as a component of the MC exporting system. MC is bound to MRD by a stacking interaction between a His and a Trp. MRD adopts a structural fold similar to bleomycin resistance protein, glyoxalase I, and extradiol dioxygenases; and it has binding sites at an identical location to binding sites in these evolutionarily related enzymes. 123 matched cddid_all.tbl CDD cd07237 cd07237 319902 BphC1-RGP6_C_like C-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase. This subfamily contains the C-terminal, catalytic, domain of BphC1-RGP6 and similar proteins. BphC catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, the third step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). This subfamily of BphCs belongs to the type I extradiol dioxygenase family, which require a metal in the active site in its catalytic mechanism. Polychlorinated biphenyl degrading bacteria demonstrate a multiplicity of BphCs. For example, three types of BphC enzymes have been found in Rhodococcus globerulus (BphC1-RGP6 - BphC3-RGP6), all three enzymes are type I extradiol dioxygenases. BphC1-RGP6 has an internal duplication, it is a two-domain dioxygenase which forms octamers, and has Fe(II) at the catalytic site. Its C-terminal repeat is represented in this subfamily. BphC2-RGP6 and BphC3-RGP6 are one-domain dioxygenases, they belong to a different subfamily of the ED_TypeI_classII_C (C-terminal domain of type I, class II extradiol dioxygenases) family. 153 matched cddid_all.tbl CDD cd07238 cd07238 319903 VOC_like uncharacterized subfamily of vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 112 matched cddid_all.tbl CDD cd07239 cd07239 319904 BphC5-RK37_C_like C-terminal, catalytic domain of BphC5 (2,3-dihydroxybiphenyl 1,2-dioxygenase). 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, the third step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). The enzyme contains a N-terminal and a C-terminal domain of similar structure fold, resulting from an ancient gene duplication. BphC belongs to the type I extradiol dioxygenase family, which requires a metal in the active site for its catalytic activity. Polychlorinated biphenyl degrading bacteria demonstrate multiplicity of BphCs. Bacterium Rhodococcus rhodochrous K37 has eight genes encoding BphC enzymes. This family includes the C-terminal domain of BphC5-RrK37. The crystal structure of the protein from Novosphingobium aromaticivorans has a Mn(II)in the active site, although most proteins of type I extradiol dioxygenases are activated by Fe(II). 143 matched cddid_all.tbl CDD cd07241 cd07241 319905 VOC_BsYyaH vicinal oxygen chelate (VOC) family protein similar to Bacillus subtilis YyaH. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 125 matched cddid_all.tbl CDD cd07242 cd07242 319906 VOC_BsYqjT vicinal oxygen chelate (VOC) family protein similar to Bacillus subtilis YqjT. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 126 matched cddid_all.tbl CDD cd07243 cd07243 319907 2_3_CTD_C C-terminal domain of catechol 2,3-dioxygenase. This subfamily contains the C-terminal, catalytic, domain of catechol 2,3-dioxygenase. Catechol 2,3-dioxygenase (2,3-CTD, catechol:oxygen 2,3-oxidoreductase) catalyzes an extradiol cleavage of catechol to form 2-hydroxymuconate semialdehyde with the insertion of two atoms of oxygen. The enzyme is a homotetramer and contains catalytically essential Fe(II) . The reaction proceeds by an ordered bi-unit mechanism. First, catechol binds to the enzyme, this is then followed by the binding of dioxygen to form a tertiary complex, and then the aromatic ring is cleaved to produce 2-hydroxymuconate semialdehyde. Catechol 2,3-dioxygenase belongs to the type I extradiol dioxygenase family. The subunit comprises the N- and C-terminal domains of similar structure fold, resulting from an ancient gene duplication. The active site is located in a funnel-shaped space of the C-terminal domain. This subfamily represents the C-terminal domain. 144 matched cddid_all.tbl CDD cd07244 cd07244 319908 FosA fosfomycin resistant protein subfamily FosA. This subfamily family contains FosA, a fosfomycin resistant protein. FosA is a Mn(II) and K(+)-dependent glutathione transferase. Fosfomycin inhibits the enzyme UDP-N-acetylglucosamine-3-enolpyruvyltransferase (MurA), which catalyzes the first committed step in bacterial cell wall biosynthesis. FosA, catalyzes the addition of glutathione to the antibiotic fosfomycin, (1R,2S)-epoxypropylphosphonic acid, making it inactive. FosA is a Mn(II) dependent enzyme. It is evolutionarily related to glyoxalase I and type I extradiol dioxygenases. 121 matched cddid_all.tbl CDD cd07245 cd07245 319909 VOC_like uncharacterized subfamily of vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 117 matched cddid_all.tbl CDD cd07246 cd07246 319910 VOC_like uncharacterized subfamily of vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping 124 matched cddid_all.tbl CDD cd07247 cd07247 319911 SgaA_N_like N-terminal domain of Streptomyces griseus SgaA and similar domains. SgaA suppresses the growth disturbances caused by high osmolarity and a high concentration of A-factor, a microbial hormone, during the early growth phase in Streptomyces griseus. A-factor (2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone) controls morphological differentiation and secondary metabolism in Streptomyces griseus. It is a chemical signaling molecule that at a very low concentration acts as a switch for yellow pigment production, aerial mycelium formation, streptomycin production, and streptomycin resistance. The structure and amino acid sequence of SgaA are closely related to a group of antibiotics resistance proteins, including bleomycin resistance protein, mitomycin resistance protein, and fosfomycin resistance proteins. SgaA might also function as a streptomycin resistance protein. 114 matched cddid_all.tbl CDD cd07249 cd07249 319912 MMCE Methylmalonyl-CoA epimerase (MMCE). MMCE, also called methylmalonyl-CoA racemase (EC 5.1.99.1) interconverts (2R)-methylmalonyl-CoA and (2S)-methylmalonyl-CoA. MMCE has been found in bacteria, archaea, and in animals. In eukaryotes, MMCE is an essential enzyme in a pathway that converts propionyl-CoA to succinyl-CoA, and is important in the breakdown of odd-chain length fatty acids, branched-chain amino acids, and other metabolites. In bacteria, MMCE participates in the reverse pathway for propionate fermentation, glyoxylate regeneration, and the biosynthesis of polyketide antibiotics. MMCE is closely related to glyoxalase I and type I extradiol dioxygenases. 127 matched cddid_all.tbl CDD cd07250 cd07250 319913 HPPD_C_like C-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HppD) and hydroxymandelate synthase (HmaS). HppD and HmaS are non-heme iron-dependent dioxygenases, which modify a common substrate, 4-hydroxyphenylpyruvate (HPP), but yield different products. HPPD catalyzes the second reaction in tyrosine catabolism, the conversion of 4-hydroxyphenylpyruvate to homogentisate (2,5-dihydroxyphenylacetic acid, HG). HmaS converts HPP to 4-hydroxymandelate, a committed step in the formation of hydroxyphenylglycerine, a structural component of nonproteinogenic macrocyclic peptide antibiotics, such as vancomycin. If the emphasis is on catalytic chemistry, HPPD and HmaS are classified as members of a large family of alpha-keto acid dependent mononuclear non-heme iron oxygenases most of which require Fe(II), molecular oxygen, and an alpha-keto acid (typically alpha-ketoglutarate) to either oxygenate or oxidize a third substrate. Both enzymes are exceptions in that they require two, instead of three, substrates, do not use alpha-ketoglutarate, and incorporate both atoms of dioxygen into the aromatic product. Both HPPD and HmaS exhibit duplicate beta barrel topology in their N- and C-terminal domains which share sequence similarity, suggestive of a gene duplication. Each protein has only one catalytic site located in at the C-terminal domain. This HPPD_C_like domain represents the C-terminal domain. 194 matched cddid_all.tbl CDD cd07251 cd07251 319914 VOC_like uncharacterized subfamily of vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 120 matched cddid_all.tbl CDD cd07252 cd07252 319915 BphC1-RGP6_N_like N-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase. This subfamily contains the N-terminal, non-catalytic, domain of BphC1-RGP6 and similar proteins. BphC catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, the third step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). This subfamily of BphCs belongs to the type I extradiol dioxygenase family, which require a metal in the active site in its catalytic mechanism. Polychlorinated biphenyl degrading bacteria demonstrate a multiplicity of 2,3-dihydroxybiphenyl 1,2-dioxygenases. For example, three types of BphC enzymes have been found in Rhodococcus globerulus (BphC1-RGP6 - BphC3-RGP6), all three enzymes are type I extradiol dioxygenases. BphC1-RGP6 has an internal duplication, it is a two-domain dioxygenase which forms octamers, and has Fe(II) at the catalytic site. Its N-terminal repeat is represented in this subfamily. BphC2-RGP6 and BphC3-RGP6 are one-domain dioxygenases, they belong to a different family, the ED_TypeI_classII_C (C-terminal domain of type I, class II extradiol dioxygenases) family. 120 matched cddid_all.tbl CDD cd07253 cd07253 319916 GLOD5 Human glyoxalase domain-containing protein 5 and similar proteins. Uncharacterized subfamily of VOC family contains human glyoxalase domain-containing protein 5 and similar proteins. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 123 matched cddid_all.tbl CDD cd07254 cd07254 319917 VOC_like uncharacterized subfamily of vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 120 matched cddid_all.tbl CDD cd07255 cd07255 319918 VOC_BsCatE_like_N N-terminal of Bacillus subtilis CatE like protein. Uncharacterized subfamily of VOC superfamily contains Bacillus subtilis CatE and similar proteins. CatE is proposed to function as Catechol-2,3-dioxygenase. VOC is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 124 matched cddid_all.tbl CDD cd07256 cd07256 319919 HPCD_C_class_II C-terminal domain of 3,4-dihydroxyphenylacetate 2,3-dioxygenase (HPCD). This subfamily contains the C-terminal, catalytic, domain of HPCD. HPCD catalyses the second step in the degradation of 4-hydroxyphenylacetate to succinate and pyruvate. The aromatic ring of 4-hydroxyphenylacetate is opened by this dioxygenase to yield the 3,4-diol product, 2-hydroxy-5-carboxymethylmuconate semialdehyde. HPCD is a homotetramer and each monomer contains two structurally homologous barrel-shaped domains at the N- and C-terminus. The active-site metal is located in the C-terminal barrel and plays an essential role in the catalytic mechanism. Most extradiol dioxygenases contain Fe(II) in their active site, but HPCD can be activated by either Mn(II) or Fe(II). These enzymes belong to the type I class II family of extradiol dioxygenases. The class III 3,4-dihydroxyphenylacetate 2,3-dioxygenases belong to a different superfamily. 160 matched cddid_all.tbl CDD cd07257 cd07257 319920 THT_oxygenase_C The C-terminal domain of 2,4,5-trihydroxytoluene (THT) oxygenase. This subfamily contains the C-terminal, catalytic, domain of THT oxygenase. THT oxygenase is an extradiol dioxygenase in the 2,4-dinitrotoluene (DNT) degradation pathway. It catalyzes the conversion of 2,4,5-trihydroxytoluene to an unstable ring fission product, 2,4-dihydroxy-5-methyl-6-oxo-2,4-hexadienoic acid. The native protein was determined to be a dimer by gel filtration. The enzyme belongs to the type I family of extradiol dioxygenases which contains two structurally homologous barrel-shaped domains at the N- and C-terminus of each monomer. The active-site metal is located in the C-terminal barrel. Fe(II) is required for its catalytic activity. 152 matched cddid_all.tbl CDD cd07258 cd07258 319921 PpCmtC_C C-terminal domain of 2,3-dihydroxy-p-cumate-3,4-dioxygenase (PpCmtC). This subfamily contains the C-terminal, catalytic, domain of PpCmtC. 2,3-dihydroxy-p-cumate-3,4-dioxygenase (CmtC of Pseudomonas putida F1) is a dioxygenase involved in the eight-step catabolism pathway of p-cymene. CmtC acts upon the reaction intermediate 2,3-dihydroxy-p-cumate, yielding 2-hydroxy-3-carboxy-6-oxo-7-methylocta-2,4-dienoate. The CmtC belongs to the type I family of extradiol dioxygenases. Fe2+ was suggested as a cofactor, same as for other enzymes in the family. The type I family of extradiol dioxygenases contains two structurally homologous barrel-shaped domains at the N- and C-terminal. The active-site metal is located in the C-terminal barrel and plays an essential role in the catalytic mechanism. 138 matched cddid_all.tbl CDD cd07261 cd07261 319922 EhpR_like phenazine resistance protein, EhpR. Phenazine resistance protein (EhpR) in Enterobacter agglomerans confers resistance by binding D-alanyl-griseoluteic acid and acting as a chaperone involved in exporting the antibiotic rather than by altering it chemically. EhpR is evolutionarily related to glyoxalase I and type I extradiol dioxygenases. 114 matched cddid_all.tbl CDD cd07262 cd07262 319923 VOC_like uncharacterized subfamily of vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 121 matched cddid_all.tbl CDD cd07263 cd07263 319924 VOC_like uncharacterized subfamily of vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping 120 matched cddid_all.tbl CDD cd07264 cd07264 319925 VOC_like uncharacterized subfamily of vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 118 matched cddid_all.tbl CDD cd07265 cd07265 319926 2_3_CTD_N N-terminal domain of catechol 2,3-dioxygenase. This subfamily contains the N-terminal, non-catalytic, domain of catechol 2,3-dioxygenase. Catechol 2,3-dioxygenase (2,3-CTD, catechol:oxygen 2,3-oxidoreductase) catalyzes an extradiol cleavage of catechol to form 2-hydroxymuconate semialdehyde with the insertion of two atoms of oxygen. The enzyme is a homotetramer and contains catalytically essential Fe(II) . The reaction proceeds by an ordered bi-unit mechanism. First, catechol binds to the enzyme, this is then followed by the binding of dioxygen to form a tertiary complex, and then the aromatic ring is cleaved to produce 2-hydroxymuconate semialdehyde. Catechol 2,3-dioxygenase belongs to the type I extradiol dioxygenase family. The subunit comprises the N- and C-terminal domains of similar structure fold, resulting from an ancient gene duplication. The active site is located in a funnel-shaped space of the C-terminal domain. This subfamily represents the N-terminal domain. 122 matched cddid_all.tbl CDD cd07266 cd07266 319927 HPCD_N_class_II N-terminal domain of 3,4-dihydroxyphenylacetate 2,3-dioxygenase (HPCD). This subfamily contains the N-terminal, non-catalytic, domain of HPCD. HPCD catalyses the second step in the degradation of 4-hydroxyphenylacetate to succinate and pyruvate. The aromatic ring of 4-hydroxyphenylacetate is opened by this dioxygenase to yield the 3,4-diol product, 2-hydroxy-5-carboxymethylmuconate semialdehyde. HPCD is a homotetramer and each monomer contains two structurally homologous barrel-shaped domains at the N- and C-terminus. The active-site metal is located in the C-terminal barrel and plays an essential role in the catalytic mechanism. Most extradiol dioxygenases contain Fe(II) in their active site, but HPCD can be activated by either Mn(II) or Fe(II). These enzymes belong to the type I class II family of extradiol dioxygenases. The class III 3,4-dihydroxyphenylacetate 2,3-dioxygenases belong to a different superfamily. 118 matched cddid_all.tbl CDD cd07267 cd07267 319928 THT_Oxygenase_N N-terminal domain of 2,4,5-trihydroxytoluene (THT) oxygenase. This subfamily contains the N-terminal, non-catalytic, domain of THT oxygenase. THT oxygenase is an extradiol dioxygenase in the 2,4-dinitrotoluene (DNT) degradation pathway. It catalyzes the conversion of 2,4,5-trihydroxytoluene to an unstable ring fission product, 2,4-dihydroxy-5-methyl-6-oxo-2,4-hexadienoic acid. The native protein was determined to be a dimer by gel filtration. The enzyme belongs to the type I family of extradiol dioxygenases which contains two structurally homologous barrel-shaped domains at the N- and C-terminus of each monomer. The active-site metal is located in the C-terminal barrel. Fe(II) is required for its catalytic activity. 113 matched cddid_all.tbl CDD cd07268 cd07268 319929 VOC_EcYecM_like Escherichia coli YecM and similar proteins, a vicinal oxygen chelate subfamily. Uncharacterized subfamily of vicinal oxygen chelate (VOC) superfamily contains Escherichia coli YecM and similar proteins.The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 171 matched cddid_all.tbl CDD cd07276 cd07276 132809 PX_SNX16 The phosphoinositide binding Phox Homology domain of Sorting Nexin 16. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX16 contains a central PX domain followed by a coiled-coil region. SNX16 is localized in early and recycling endosomes through the binding of its PX domain to phosphatidylinositol-3-phosphate (PI3P). It plays a role in epidermal growth factor (EGF) signaling by regulating EGF receptor membrane trafficking. 110 matched cddid_all.tbl CDD cd07277 cd07277 132810 PX_RUN The phosphoinositide binding Phox Homology domain of uncharacterized proteins containing PX and RUN domains. The PX domain is a phosphoinositide (PI) binding module involved in targeting proteins to PI-enriched membranes. Members in this subfamily are uncharacterized proteins containing an N-terminal RUN domain and a C-terminal PX domain. PX domain harboring proteins have been implicated in highly diverse functions such as cell signaling, vesicular trafficking, protein sorting, lipid modification, cell polarity and division, activation of T and B cells, and cell survival. In addition to protein-lipid interaction, the PX domain may also be involved in protein-protein interaction. The RUN domain is found in GTPases in the Rap and Rab families and may play a role in Ras-like signaling pathways. 118 matched cddid_all.tbl CDD cd07278 cd07278 132811 PX_RICS_like The phosphoinositide binding Phox Homology domain of PX-RICS-like proteins. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Members of this family include PX-RICS, TCGAP (Tc10/Cdc42 GTPase-activating protein), and similar proteins. They contain N-terminal PX and Src Homology 3 (SH3) domains, a central Rho GAP domain, and C-terminal extensions. They act as Rho GTPase-activating proteins. PX-RICS is the main isoform expressed during neural development. It is involved in neural functions including axon and dendrite extension, postnatal remodeling, and fine-tuning of neural circuits during early brain development. The PX domain of PX-RICS specifically binds phosphatidylinositol 3-phosphate (PI3P), PI4P, and PI5P. TCGAP is widely expressed in the brain where it is involved in regulating the outgrowth of axons and dendrites and is regulated by the protein tyrosine kinase Fyn. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. 114 matched cddid_all.tbl CDD cd07279 cd07279 132812 PX_SNX20_21_like The phosphoinositide binding Phox Homology domain of Sorting Nexins 20 and 21. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. This subfamily consists of SNX20, SNX21, and similar proteins. SNX20 interacts with P-Selectin glycoprotein ligand-1 (PSGL-1), a surface-expressed mucin that acts as a ligand for the selectin family of adhesion proteins. It may function in the sorting and cycling of PSGL-1 into endosomes. SNX21, also called SNX-L, is distinctly and highly-expressed in fetal liver and may be involved in protein sorting and degradation during embryonic liver development. 112 matched cddid_all.tbl CDD cd07280 cd07280 132813 PX_YPT35 The phosphoinositide binding Phox Homology domain of the fungal protein YPT35. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. This subfamily is composed of YPT35 proteins from the fungal subkingdom Dikarya. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. The PX domain of YPT35 binds to phosphatidylinositol 3-phosphate (PI3P). It also serves as a protein interaction domain, binding to members of the Yip1p protein family, which localize to the ER and Golgi. YPT35 is mainly associated with endosomes and together with Yip1p proteins, may be involved in a specific function in the endocytic pathway. 120 matched cddid_all.tbl CDD cd07281 cd07281 132814 PX_SNX1 The phosphoinositide binding Phox Homology domain of Sorting Nexin 1. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX1 is both membrane associated and a cytosolic protein that exists as a tetramer in protein complexes. It can associate reversibly with membranes of the endosomal compartment, thereby coating these vesicles. SNX1 is a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi. The retromer consists of a cargo-recognition subcomplex and a subcomplex formed by a dimer of sorting nexins (SNX1 and/or SNX2), which ensures efficient cargo sorting by facilitating proper membrane localization of the cargo-recognition subcomplex. SNX1 contains a Bin/Amphiphysin/Rvs (BAR) domain C-terminal to the PX domain. The PX domain of SNX1 specifically binds phosphatidylinositol-3-phosphate (PI3P) and PI(3,5)P2, while the BAR domain detects membrane curvature. Both domains help determine the specific membrane-targeting of SNX1, which is localized to a microdomain in early endosomes where it regulates cation-independent mannose-6-phosphate receptor retrieval to the trans Golgi network. 124 matched cddid_all.tbl CDD cd07282 cd07282 132815 PX_SNX2 The phosphoinositide binding Phox Homology domain of Sorting Nexin 2. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX2 is a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi. The retromer consists of a cargo-recognition subcomplex and a subcomplex formed by a dimer of sorting nexins (SNX1 and/or SNX2), which ensures efficient cargo sorting by facilitating proper membrane localization of the cargo-recognition subcomplex. Similar to SNX1, SNX2 contains a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain. The PX domain of SNX2 preferentially binds phosphatidylinositol-3-phosphate (PI3P), but not PI(3,4,5)P3. Studies on mice deficient with SNX1 and/or SNX2 suggest that they provide an essential function in embryogenesis and are functionally redundant. 124 matched cddid_all.tbl CDD cd07283 cd07283 132816 PX_SNX30 The phosphoinositide binding Phox Homology domain of Sorting Nexin 30. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX30 harbors a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain, similar to the sorting nexins SNX1-2, SNX4-8, and SNX32. Both domains have been shown to determine the specific membrane-targeting of SNX1. The specific function of SNX30 has yet to be elucidated. 116 matched cddid_all.tbl CDD cd07284 cd07284 132817 PX_SNX7 The phosphoinositide binding Phox Homology domain of Sorting Nexin 7. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX7 harbors a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain, similar to the sorting nexins SNX1-2, SNX4-6, SNX8, SNX30, and SNX32. Both domains have been shown to determine the specific membrane-targeting of SNX1. The specific function of SNX7 has yet to be elucidated. 116 matched cddid_all.tbl CDD cd07285 cd07285 132818 PX_SNX9 The phosphoinositide binding Phox Homology domain of Sorting Nexin 9. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX9, also known as SH3PX1, is a cytosolic protein that interacts with proteins associated with clathrin-coated pits such as Cdc-42-associated tyrosine kinase 2 (ACK2). It contains an N-terminal Src Homology 3 (SH3) domain, a PX domain, and a C-terminal Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature. The PX-BAR structural unit helps determine specific membrane localization. Through its SH3 domain, SNX9 binds class I polyproline sequences found in dynamin 1/2 and the WASP/N-WASP actin regulators. SNX9 is localized to plasma membrane endocytic sites and acts primarily in clathrin-mediated endocytosis. Its array of interacting partners suggests that SNX9 functions at the interface between endocytosis and actin cytoskeletal organization. 126 matched cddid_all.tbl CDD cd07286 cd07286 132819 PX_SNX18 The phosphoinositide binding Phox Homology domain of Sorting Nexin 18. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX18, like SNX9, contains an N-terminal Src Homology 3 (SH3) domain, a PX domain, and a C-terminal Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature. The PX-BAR structural unit helps determine specific membrane localization. SNX18 is localized to peripheral endosomal structures, and acts in a trafficking pathway that is clathrin-independent but relies on AP-1 and PACS1. 127 matched cddid_all.tbl CDD cd07287 cd07287 132820 PX_RPK118_like The phosphoinositide binding Phox Homology domain of RPK118-like proteins. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Members of this subfamily bear similarity to human RPK118, which contains an N-terminal PX domain, a Microtubule Interacting and Trafficking (MIT) domain, and a kinase domain. RPK118 binds sphingosine kinase, a key enzyme in the synthesis of sphingosine 1-phosphate (SPP), a lipid messenger involved in many cellular events. RPK118 may be involved in transmitting SPP-mediated signaling. It also binds the antioxidant peroxiredoxin-3 (PRDX3) and may be involved in the transport of PRDX3 from the cytoplasm to its site of function in the mitochondria. Members of this subfamily also show similarity to sorting nexin 15 (SNX15), which contains PX and MIT domains but does not contain a kinase domain. SNXs make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNX15 plays a role in protein trafficking processes in the endocytic pathway and the trans-Golgi network. The PX domain of SNX15 interacts with the PDGF receptor and is responsible for the membrane association of the protein. 118 matched cddid_all.tbl CDD cd07288 cd07288 132821 PX_SNX15 The phosphoinositide binding Phox Homology domain of Sorting Nexin 15. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX15 contains an N-terminal PX domain and a C-terminal Microtubule Interacting and Trafficking (MIT) domain. It plays a role in protein trafficking processes in the endocytic pathway and the trans-Golgi network. The PX domain of SNX15 interacts with the PDGF receptor and is responsible for the membrane association of the protein. 118 matched cddid_all.tbl CDD cd07289 cd07289 132822 PX_PI3K_C2_alpha The phosphoinositide binding Phox Homology Domain of the Alpha Isoform of Class II Phosphoinositide 3-Kinases. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. The Phosphoinositide 3-Kinase (PI3K) family of enzymes catalyzes the phosphorylation of the 3-hydroxyl group of the inositol ring of phosphatidylinositol. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI3Ks are divided into three main classes (I, II, and III) based on their substrate specificity, regulation, and domain structure. Class II PI3Ks preferentially use PI as a substrate to produce PI3P, but can also phosphorylate PI4P to produce PI(3,4)P2. They function as monomers and do not associate with any regulatory subunits. Class II enzymes contain an N-terminal Ras binding domain, a lipid binding C2 domain, a PI3K homology domain of unknown function, an ATP-binding cataytic domain, a PX domain, and a second C2 domain at the C-terminus. The class II alpha isoform, PI3K-C2alpha, plays key roles in clathrin assembly and clathrin-mediated membrane trafficking, insulin signaling, vascular smooth muscle contraction, and the priming of neurosecretory granule exocytosis. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. 109 matched cddid_all.tbl CDD cd07290 cd07290 132823 PX_PI3K_C2_beta The phosphoinositide binding Phox Homology Domain of the Beta Isoform of Class II Phosphoinositide 3-Kinases. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. The Phosphoinositide 3-Kinase (PI3K) family of enzymes catalyzes the phosphorylation of the 3-hydroxyl group of the inositol ring of phosphatidylinositol. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. PI3Ks are divided into three main classes (I, II, and III) based on their substrate specificity, regulation, and domain structure. Class II PI3Ks preferentially use PI as a substrate to produce PI3P, but can also phosphorylate PI4P to produce PI(3,4)P2. They function as monomers and do not associate with any regulatory subunits. Class II enzymes contain an N-terminal Ras binding domain, a lipid binding C2 domain, a PI3K homology domain of unknown function, an ATP-binding cataytic domain, a PX domain, and a second C2 domain at the C-terminus. The class II beta isoform, PI3K-C2beta, contributes to the migration and survival of cancer cells. It regulates Rac activity and impacts membrane ruffling, cell motility, and cadherin-mediated cell-cell adhesion. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. 109 matched cddid_all.tbl CDD cd07291 cd07291 132824 PX_SNX5 The phosphoinositide binding Phox Homology domain of Sorting Nexin 5. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX5, abundantly expressed in macrophages, regulates macropinocytosis, a process that enables cells to internalize large amounts of external solutes. It may also be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. It also binds the Fanconi anaemia complementation group A protein (FANCA). SNX5 harbors a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain, similar to other sorting nexins including SNX1-2. The PX-BAR structural unit helps determine the specific membrane-targeting of some SNXs. The PX domain of SNX5 binds phosphatidylinositol-3-phosphate (PI3P) and PI(3,4)P2. SNX5 is localized to a subdomain of early endosome and is recruited to the plasma membrane following EGF stimulation and elevation of PI(3,4)P2 levels. 141 matched cddid_all.tbl CDD cd07292 cd07292 132825 PX_SNX6 The phosphoinositide binding Phox Homology domain of Sorting Nexin 6. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX6 forms a stable complex with SNX1 and may be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. It interacts with the receptor serine/threonine kinases from the transforming growth factor-beta family. It also plays roles in enhancing the degradation of EGFR and in regulating the activity of Na,K-ATPase through its interaction with Translationally Controlled Tumor Protein (TCTP). SNX6 harbors a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvature, C-terminal to the PX domain, similar to other sorting nexins including SNX1-2. The PX-BAR structural unit helps determine the specific membrane-targeting of some SNXs. 141 matched cddid_all.tbl CDD cd07293 cd07293 132826 PX_SNX3 The phosphoinositide binding Phox Homology domain of Sorting Nexin 3. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX3 associates with early endosomes through a PX domain-mediated interaction with phosphatidylinositol-3-phosphate (PI3P). It associates with the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, and functions as a cargo-specific adaptor for the retromer. SNX3 is required for the formation of multivesicular bodies, which function as transport intermediates to late endosomes. It also promotes cell surface expression of the amiloride-sensitive epithelial Na+ channel (ENaC), which is critical in sodium homeostasis and maintenance of extracellular fluid volume. 123 matched cddid_all.tbl CDD cd07294 cd07294 132827 PX_SNX12 The phosphoinositide binding Phox Homology domain of Sorting Nexin 12. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. The specific function of SNX12 has yet to be elucidated. 132 matched cddid_all.tbl CDD cd07295 cd07295 132828 PX_Grd19 The phosphoinositide binding Phox Homology domain of fungal Grd19. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Grd19 is involved in the localization of late Golgi membrane proteins in yeast. Grp19 associates with the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, and functions as a cargo-specific adaptor for the retromer. 116 matched cddid_all.tbl CDD cd07296 cd07296 132829 PX_PLD1 The phosphoinositide binding Phox Homology domain of Phospholipase D1. The PX domain is a phosphoinositide binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Phospholipase D (PLD) catalyzes the hydrolysis of the phosphodiester bond of phosphatidylcholine to generate membrane-bound phosphatidic acid and choline. PLDs are implicated in many cellular functions like signaling, cytoskeletal reorganization, vesicular transport, stress responses, and the control of differentiation, proliferation, and survival. PLD1 contains PX and Pleckstrin Homology (PH) domains in addition to the catalytic domain. It acts as an effector of Rheb in the signaling of the mammalian target of rapamycin (mTOR), a serine/threonine protein kinase that transduces nutrients and other stimuli to regulate many cellular processes. PLD1 also regulates the secretion of the procoagulant von Willebrand factor (VWF) in endothelial cells. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. The PX domain of PLD1 specifically binds to phosphatidylinositol-3,4,5-trisphosphate [PI(3,4,5)P3], which enables PLD1 to mediate signals via the ERK1/2 pathway. 135 matched cddid_all.tbl CDD cd07297 cd07297 132830 PX_PLD2 The phosphoinositide binding Phox Homology domain of Phospholipase D2. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. Phospholipase D (PLD) catalyzes the hydrolysis of the phosphodiester bond of phosphatidylcholine to generate membrane-bound phosphatidic acid and choline. PLD activity has been detected in viruses, bacteria, yeast, plants, and mammals, but the PX domain is not present in PLDs from viruses and bacteria. PLDs are implicated in many cellular functions like signaling, cytoskeletal reorganization, vesicular transport, stress responses, and the control of differentiation, proliferation, and survival. PLD2 contains PX and Pleckstrin Homology (PH) domains in addition to the catalytic domain. It mediates EGF-dependent insulin secretion and EGF-induced Ras activation by the guanine nucleotide-exchange factor Son of sevenless (Sos). It regulates mast cell activation by associating and promoting the activation of the protein tyrosine kinase Syk. PLD2 also participates in the sphingosine 1-phosphate-mediated pathway that stimulates the migration of endothelial cells, an important factor in angiogenesis. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. 130 matched cddid_all.tbl CDD cd07298 cd07298 132831 PX_RICS The phosphoinositide binding Phox Homology domain of PX-RICS. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. RICS is a Rho GTPase-activating protein for cdc42 and Rac1. It is implicated in the regulation of postsynaptic signaling and neurite outgrowth. An N-terminal splicing variant of RICS containing additional PX and Src Homology 3 (SH3) domains, also called PX-RICS, is the main isoform expressed during neural development. PX-RICS is involved in neural functions including axon and dendrite extension, postnatal remodeling, and fine-tuning of neural circuits during early brain development. The PX domain is involved in targeting of proteins to PI-enriched membranes, and may also be involved in protein-protein interaction. The PX domain of PX-RICS specifically binds phosphatidylinositol 3-phosphate (PI3P), PI4P, and PI5P. 115 matched cddid_all.tbl CDD cd07299 cd07299 132832 PX_TCGAP The phosphoinositide binding Phox Homology domain of Tc10/Cdc42 GTPase-activating protein. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions such as cell signaling, vesicular trafficking, protein sorting, and lipid modification, among others. TCGAP (Tc10/Cdc42 GTPase-activating protein) contains N-terminal PX and Src Homology 3 (SH3) domains, a central Rho GAP domain, and C-terminal proline-rich regions. It is widely expressed in the brain where it is involved in regulating the outgrowth of axons and dendrites and is regulated by the protein tyrosine kinase Fyn. It interacts with cdc42 and TC10beta through its GAP domain and with phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P2] through its PX domain. It is translocated to the plasma membrane in adipocytes in response to insulin and may be involved in the regulation of insulin-stimulated glucose transport. TCGAP has also been named sorting nexins 26 (SNX26). SNXs make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. It is unknown whether TCGAP also functions as a SNX. 113 matched cddid_all.tbl CDD cd07300 cd07300 132833 PX_SNX20 The phosphoinositide binding Phox Homology domain of Sorting Nexin 20. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX20 interacts with P-Selectin glycoprotein ligand-1 (PSGL-1), a surface-expressed mucin that acts as a ligand for the selectin family of adhesion proteins. The PX domain of SNX20 binds PIs and targets the SNX20/PSGL-1 complex to endosomes. SNX20 may function in the sorting and cycling of PSGL-1 into endosomes. 114 matched cddid_all.tbl CDD cd07301 cd07301 132834 PX_SNX21 The phosphoinositide binding Phox Homology domain of Sorting Nexin 21. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Some SNXs are localized in early endosome structures such as clathrin-coated pits, while others are located in late structures of the endocytic pathway. SNX21, also called SNX-L, is distinctly and highly-expressed in fetal liver and may be involved in protein sorting and degradation during embryonic liver development. 112 matched cddid_all.tbl CDD cd07302 cd07302 143636 CHD cyclase homology domain. Catalytic domains of the mononucleotidyl cyclases (MNC's), also called cyclase homology domains (CHDs), are part of the class III nucleotidyl cyclases. This class includes eukaryotic and prokaryotic adenylate cyclases (AC's) and guanylate cyclases (GC's). They seem to share a common catalytic mechanism in their requirement for two magnesium ions to bind the polyphosphate moiety of the nucleotide. 177 matched cddid_all.tbl CDD cd07303 cd07303 132765 Porin3 Eukaryotic porin family that forms channels in the mitochondrial outer membrane. The porin family 3 contains two sub-families that play vital roles in the mitochondrial outer membrane, a translocase for unfolded pre-proteins (Tom40) and the voltage-dependent anion channel (VDAC) that regulates the flux of mostly anionic metabolites through the outer mitochondrial membrane. 274 matched cddid_all.tbl CDD cd07304 cd07304 143612 Chorismate_synthase Chorismase synthase, the enzyme catalyzing the final step of the shikimate pathway. Chorismate synthase (CS; 5-enolpyruvylshikimate-3-phosphate phospholyase; 1-carboxyvinyl-3-phosphoshikimate phosphate-lyase; E.C. 4.2.3.5) catalyzes the seventh and final step in the shikimate pathway: the conversion of 5- enolpyruvylshikimate-3-phosphate (EPSP) to chorismate, a precursor for the biosynthesis of aromatic compounds. This process has an absolute requirement for reduced FMN as a co-factor which is thought to facilitate cleavage of C-O bonds by transiently donating an electron to the substrate, having no overall change its redox state. Depending on the capacity of these enzymes to regenerate the reduced form of FMN, chorismate synthases are divided into two classes: Enzymes, mostly from plants and eubacteria, that sequester CS from the cellular environment, are monofunctiona,l while those that can generate reduced FMN at the expense of NADPH, such as found in fungi and the ciliated protozoan Euglena gracilis, are bifunctional, having an additional NADPH:FMN oxidoreductase activity. Recently, bifunctionality of the Mycobacterium tuberculosis enzyme (MtCS) was determined by measurements of both chorismate synthase and NADH:FMN oxidoreductase activities. Since shikimate pathway enzymes are present in bacteria, fungi and apicomplexan parasites (such as Toxoplasma gondii, Plasmodium falciparum, and Cryptosporidium parvum) but absent in mammals, they are potentially attractive targets for the development of new therapy against infectious diseases such as tuberculosis (TB). 344 matched cddid_all.tbl CDD cd07305 cd07305 132766 Porin3_Tom40 Translocase of outer mitochondrial membrane 40 (Tom40). Tom40 forms a channel in the mitochondrial outer membrane with a pore about 1.5 to 2.5 nanometers wide. It functions as a transport channel for unfolded protein chains and forms a complex with Tom5, Tom6, Tom7, and Tom22. The primary receptors Tom20 and Tom70 recruit the unfolded precursor protein from the mitochondrial-import stimulating factor (MSF) or cytosolic Hsc70. The precursor passes through the Tom40 channel and through another channel in the inner membrane, formed by Tim23, to be finally translocated into the mitochondrial matrix. The process depends on a proton motive force across the inner membrane and requires a contact site where the outer and inner membranes come close. Tom40 is also involved in inserting outer membrane proteins into the membrane, most likely not via a lateral opening in the pore, but by transfering precursor proteins to an outer membrane sorting and assembly machinery. 279 matched cddid_all.tbl CDD cd07306 cd07306 132767 Porin3_VDAC Voltage-dependent anion channel of the outer mitochondrial membrane. The voltage-dependent anion channel (VDAC) regulates the flux of mostly anionic metabolites through the outer mitochondrial membrane, which is highly permeable to small molecules. VDAC is the most abundant protein in the outer membrane, and membrane potentials can toggle VDAC between open or high-conducting and closed or low-conducting forms. VDAC binds to and is regulated in part by hexokinase, an interaction that renders mitochondria less susceptible to pro-apoptotic signals, most likely by intefering with VDAC's capability to respond to Bcl-2 family proteins. While VDAC appears to play a key role in mitochondrially induced cell death, a proposed involvement in forming the mitochondrial permeability transition pore, which is characteristic for damaged mitochondria and apoptosis, has been challenged by more recent studies. 276 matched cddid_all.tbl CDD cd07307 cd07307 153271 BAR The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Mutations in BAR containing proteins have been linked to diseases and their inactivation in cells leads to altered membrane dynamics. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysins and endophilins, among others. BAR domains are also frequently found alongside domains that determine lipid specificity, such as the Pleckstrin Homology (PH) and Phox Homology (PX) domains which are present in beta centaurins (ACAPs and ASAPs) and sorting nexins, respectively. A FES-CIP4 Homology (FCH) domain together with a coiled coil region is called the F-BAR domain and is present in Pombe/Cdc15 homology (PCH) family proteins, which include Fes/Fes tyrosine kinases, PACSIN or syndapin, CIP4-like proteins, and srGAPs, among others. The Inverse (I)-BAR or IRSp53/MIM homology Domain (IMD) is found in multi-domain proteins, such as IRSp53 and MIM, that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The I-BAR domain induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. BAR domains that also serve as protein interaction domains include those of arfaptin and OPHN1-like proteins, among others, which bind to Rac and Rho GAP domains, respectively. 194 matched cddid_all.tbl CDD cd07308 cd07308 173892 lectin_leg-like "legume-like lectins: ERGIC-53, ERGL, VIP36, VIPL, EMP46, and EMP47. The legume-like (leg-like) lectins are eukaryotic intracellular sugar transport proteins with a carbohydrate recognition domain similar to that of the legume lectins. This domain binds high-mannose-type oligosaccharides for transport from the endoplasmic reticulum to the Golgi complex. These leg-like lectins include ERGIC-53, ERGL, VIP36, VIPL, EMP46, EMP47, and the UIP5 (ULP1-interacting protein 5) precursor protein. Leg-like lectins have different intracellular distributions and dynamics in the endoplasmic reticulum-Golgi system of the secretory pathway and interact with N-glycans of glycoproteins in a calcium-dependent manner, suggesting a role in glycoprotein sorting and trafficking. L-type lectins have a dome-shaped beta-barrel carbohydrate recognition domain with a curved seven-stranded beta-sheet referred to as the ""front face"" and a flat six-stranded beta-sheet referred to as the ""back face"". This domain homodimerizes so that adjacent back sheets form a contiguous 12-stranded sheet and homotetramers occur by a back-to-back association of these homodimers. Though L-type lectins exhibit both sequence and structural similarity to one another, their carbohydrate binding specificities differ widely." 218 matched cddid_all.tbl CDD cd07309 cd07309 213985 PHP Polymerase and Histidinol Phosphatase domain. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PHP in polymerases has trinuclear zinc/magnesium dependent proofreading activity. It has also been shown that the PHP domain functions in DNA repair. The PHP structures have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. 88 matched cddid_all.tbl CDD cd07311 cd07311 143583 terB_like_1 tellurium resistance terB-like protein, subgroup 1. This family includes several uncharacterized bacterial proteins. The prototype of this CD is tellurite resistance protein from Nostoc punctiforme that belongs to COG3793. Its precise biological function and its mechanism responsible for tellurium resistance still remains rather poorly understood. 150 matched cddid_all.tbl CDD cd07313 cd07313 143584 terB_like_2 tellurium resistance terB-like protein, subgroup 2. This family includes several uncharacterized bacterial proteins. Protein sequence homology analysis shows they are similar to tellurium resistance protein terB, but the function of this family is unknown. 104 matched cddid_all.tbl CDD cd07316 cd07316 143585 terB_like_DjlA N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins. Tellurium resistance terB-like domain of the DnaJ-like DjlA proteins. This family represents the terB-like domain of DjlA-like proteins, a subgroup of heat shock DnaJ-like proteins. Escherichia coli DjlA is a type III membrane protein with a small N-terminal transmembrane region and DnaJ-like domain on the extreme C-terminus. Overproduction has been shown to activate the RcsC pathway, which regulates the production of the capsular exopolysaccharide colanic acid. The specific function of this domain is unknown. 106 matched cddid_all.tbl CDD cd07320 cd07320 153371 Extradiol_Dioxygenase_3B_like Subunit B of Class III Extradiol ring-cleavage dioxygenases. Dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. Two major groups of dioxygenases have been identified according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be further divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two-domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B. This model represents the catalytic subunit B of extradiol dioxygenase class III enzymes. Enzymes belonging to this family include Protocatechuate 4,5-dioxygenase (LigAB), 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase (CarB), 4,5-DOPA Dioxygenase, 2,3-dihydroxyphenylpropionate 1,2-dioxygenase, and 3,4-dihydroxyphenylacetate (homoprotocatechuate) 2,3-dioxygenase (HPCD). There are also some family members that do not show the typical dioxygenase activity. 260 matched cddid_all.tbl CDD cd07321 cd07321 153390 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of class III extradiol dioxygenase enzymes. The A subunit is the smaller, non-catalytic subunit. Enzymes that belong to this family include Protocatechuate 4,5-dioxygenase (LigAB) A subunit, 2'-aminobiphenyl-2,3-diol 1,2-dioxygenase (CarB) A subunit, Gallate Dioxygenase and proteins of unknown function. 77 matched cddid_all.tbl CDD cd07322 cd07322 143474 PriL_PriS_Eukaryotic Eukaryotic core primase: Large subunit, PriL. Primases synthesize the RNA primers required for DNA replication. Primases are grouped into two classes, bacteria/bacteriophage and archaeal/eukaryotic. The proteins in the two classes differ in structure and the replication apparatus components. Archaeal/eukaryotic core primase is a heterodimeric enzyme consisting of a small catalytic subunit (PriS) and a large subunit (PriL). In eukaryotic organisms, a heterotetrameric enzyme formed by DNA polymerase alpha, the B subunit and two primase subunits has primase activity. Although the catalytic activity resides within PriS, the PriL subunit is essential for primase function as disruption of the PriL gene in yeast is lethal. PriL is composed of two structural domains. Several functions have been proposed for PriL such as stabilization of the PriS, involvement in synthesis initiation, improvement of primase processivity, determination of product size and transfer of the products to DNA polymerase alpha. 390 matched cddid_all.tbl CDD cd07323 cd07323 153396 LAM LA motif RNA-binding domain. This domain is found at the N-terminus of La RNA-binding proteins as well as in other related proteins. Typically, the domain co-occurs with an RNA-recognition motif (RRM), and together these domains function to bind primary transcripts of RNA polymerase III in the La autoantigen (Lupus La protein, LARP3, or Sjoegren syndrome type B antigen, SS-B). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. 75 matched cddid_all.tbl CDD cd07324 cd07324 320683 M48C_Oma1-like Oma1 peptidase-like, integral membrane metallopeptidase. This family contains peptidase M48 subfamily C (also known as Oma1 peptidase or mitochondrial metalloendopeptidase OMA1), including similar peptidases containing tetratricopeptide (TPR) repeats, as well as uncharacterized proteins such as E. coli bepA (formerly yfgC), ycaL and loiP (formerly yggG), considered to be putative metallopeptidases. Oma1 peptidase is part of the quality control system in the inner membrane of mitochondria, with its catalytic site facing the matrix space. It cleaves and thereby promotes the turnover of mistranslated or misfolded membrane proteins. Oma1 can cleave the misfolded multi-pass membrane protein Oxa1, thus exerting a function similar to the ATP-dependent m-AAA protease for quality control of inner membrane proteins. It has been proposed that in the absence of m-AAA protease, proteolysis of Oxa1 is mediated by Oma1 in an ATP-independent manner. Homologs of Oma1 are present in higher eukaryotes, eubacteria and archaebacteria, suggesting that Oma1 is the founding member of a conserved family of membrane-embedded metallopeptidases, all containing the zinc metalloprotease motif (HEXXH). M48 peptidases proteolytically remove the C-terminal three residues of farnesylated proteins. 142 matched cddid_all.tbl CDD cd07325 cd07325 320684 M48_Ste24p_like M48 Ste24 endopeptidase-like, integral membrane metallopeptidase. This family contains peptidase M48 family Ste24p-like proteins that are as yet uncharacterized, but probably function as intracellular, membrane-associated zinc metalloproteases; they all contain the HEXXH Zn-binding motif, which is critical for Ste24p activity. They likely remove the C-terminal three residues of farnesylated proteins proteolytically and are possibly associated with the endoplasmic reticulum and golgi. Some members also contain ankyrin domains which occur in very diverse families of proteins and mediate protein-protein interactions. 199 matched cddid_all.tbl CDD cd07326 cd07326 320685 M56_BlaR1_MecR1_like Peptidase M56-like including those in BlaR1 and MecR1, integral membrane metallopeptidase. This family contains peptidase M56, which includes zinc metalloprotease domain in MecR1 as well as BlaR1. MecR1 is a transmembrane beta-lactam sensor/signal transducer protein that regulates the expression of an altered penicillin-binding protein PBP2a, which resists inactivation by beta-lactam antibiotics, in methicillin-resistant Staphylococcus aureus (MRSA). BlaR1 regulates the inducible expression of a class A beta-lactamase that hydrolytically destroys certain ?-lactam antibiotics in MRSA. Both, MecR1 and BlaR1, are transmembrane proteins that consist of four transmembrane helices, a cytoplasmic zinc protease domain, and the soluble C-terminal extracellular sensor domain, and are highly similar in sequence and function. The signal for protein expression is transmitted by site-specific proteolytic cleavage of both the transducer, which auto-activates, and the repressor, which is inactivated, unblocking gene transcription. All members contain the zinc metalloprotease motif (HEXXH). Homologs of this peptidase domain are also found in a number of other bacterial genome sequences, most of which are as yet uncharacterized. 165 matched cddid_all.tbl CDD cd07327 cd07327 320686 M48B_HtpX_like HtpX-like membrane-bound metallopeptidase. This family contains peptidase M48 subfamily B, also known as HtpX, which consists of proteins smaller than Ste24p, with homology restricted to the C-terminal half of Ste24p. HtpX, an integral membrane (IM) metallopeptidase, is widespread in bacteria and archaea, and plays a central role in protein quality control by preventing the accumulation of misfolded proteins in the membrane. Its expression is controlled by the Cpx stress response system, which senses abnormal membrane proteins. HtpX participates in the proteolytic quality control of these misfolded proteins by undergoing self-degradation and eliminating them by collaborating with FtsH, a membrane-bound and ATP-dependent protease. HtpX contains the zinc binding motif (HEXXH), has an FtsH-like topology, and is capable of introducing endoproteolytic cleavages into SecY (also an FtsH substrate). However, HtpX does not have an ATPase activity and will only act against cytoplasmic regions of a target membrane protein. Thus, HtpX and FtsH have overlapping and/or complementary functions, which are especially important at high temperature; in E. coli and Xylella fastidiosa, HtpX is heat-inducible, while in Streptococcus gordonii it is not. Mutation studies of HtpX-like M48 metalloprotease from Leptospira interrogans (LA4131) has been shown to result in altered expression of a subset of metal toxicity and stress response genes. 183 matched cddid_all.tbl CDD cd07328 cd07328 320687 M48_Ste24p_like M48 Ste24 endopeptidase-like, integral membrane metallopeptidase. This family contains peptidase M48-like proteins that are as yet uncharacterized, but probably function as intracellular, membrane-associated zinc metalloproteases; they all contain the HEXXH Zn-binding motif, which is critical for Ste24p activity. They likely remove the C-terminal three residues of farnesylated proteins proteolytically and are possibly associated with the endoplasmic reticulum and golgi. 160 matched cddid_all.tbl CDD cd07329 cd07329 320688 M56_like Peptidase M56-like, integral membrane metallopeptidase in bacteria. This family contains peptidase M56, which includes zinc metalloprotease domain in MecR1 as well as BlaR1. MecR1 is a transmembrane beta-lactam sensor/signal transducer protein that regulates the expression of an altered penicillin-binding protein PBP2a, which resists inactivation by beta-lactam antibiotics, in methicillin-resistant Staphylococcus aureus (MRSA). BlaR1 regulates the inducible expression of a class A beta-lactamase that hydrolytically destroys certain beta-lactam antibiotics in MRSA. Both, MecR1 and BlaR1, are transmembrane proteins that consist of four transmembrane helices, a cytoplasmic zinc protease domain, and the soluble C-terminal extracellular sensor domain, and are highly similar in sequence and function. The signal for protein expression is transmitted by site-specific proteolytic cleavage of both the transducer, which auto-activates, and the repressor, which is inactivated, unblocking gene transcription. All members contain the zinc metalloprotease motif (HEXXH). Homologs of this peptidase domain are also found in a number of other bacterial genome sequences, most of which are as yet uncharacterized. 188 matched cddid_all.tbl CDD cd07330 cd07330 320689 M48A_Ste24p Peptidase M48 CaaX prenyl protease type 1, an integral membrane, Zn-dependent protein. This family of M48 CaaX prenyl protease 1-like family includes a number of well characterized genes such as those found in Taenia solium metacestode (TsSte24p), Arabidopsis (AtSte24), yeast Ste24p and human (Hs Ste24p) as well as several uncharacterized genes such as YhfN, some of which also containing tetratricopeptide (TPR) repeats. All members of this family contain the zinc metalloprotease motif (HEXXH), likely exposed on the cytoplasmic side. They are thought to be intimately associated with the endoplasmic reticulum (ER), regardless of whether their genes possess the conventional signal motif (KKXX) in the C-terminal. Proteins in this family proteolytically remove the C-terminal three residues of farnesylated proteins. The gene ZmpSte24, also known as FACE-1 in humans, a member of this family, is involved in the post-translational processing of prelamin A to mature lamin A, a major component of the nuclear envelope. ZmpSte24 deficiency causes an accumulation of prelamin A leading to lipodystrophy and other disease phenotypes while mutations in the protein lead to diseases of lamin processing (laminopathies), such as premature aging disease progeria and metabolic disorders. Some of these mutations map to the peptide-binding site. 285 matched cddid_all.tbl CDD cd07331 cd07331 320690 M48C_Oma1_like Peptidase M48C, integral membrane endopeptidase. This subfamily contains peptidase M48C Oma1 (also called mitochondrial metalloendopeptidase OMA1) protease homologs that are mostly uncharacterized. Oma1 is part of the quality control system in the inner membrane of mitochondria, with its catalytic site facing the matrix space. It cleaves and thereby promotes the turnover of mistranslated or misfolded membrane proteins. Oma1 can cleave the misfolded multi-pass membrane protein Oxa1, thus exerting a function similar to the ATP-dependent m-AAA protease for quality control of inner membrane proteins; it cleaves a misfolded polytopic membrane protein at multiple sites. It has been proposed that in the absence of m-AAA protease, proteolysis of Oxa1 is mediated by Oma1 in an ATP-independent manner. Oma1 is part of highly conserved mitochondrial metallopeptidases, with homologs present in higher eukaryotes, eubacteria and archaebacteria, all containing the zinc binding motif (HEXXH). It forms a high molecular mass complex in the inner membrane, possibly a homo-hexamer. 187 matched cddid_all.tbl CDD cd07332 cd07332 320691 M48C_Oma1_like Peptidase M48C Ste24p, integral membrane endopeptidase. This subfamily contains peptidase M48C Oma1 (also called mitochondrial metalloendopeptidase OMA1) protease homologs that are mostly uncharacterized. Oma1 is part of the quality control system in the inner membrane of mitochondria, with its catalytic site facing the matrix space. It cleaves and thereby promotes the turnover of mistranslated or misfolded membrane proteins. Oma1 can cleave the misfolded multi-pass membrane protein Oxa1, thus exerting a function similar to the ATP-dependent m-AAA protease for quality control of inner membrane proteins; it cleaves a misfolded polytopic membrane protein at multiple sites. It has been proposed that in the absence of m-AAA protease, proteolysis of Oxa1 is mediated by Oma1 in an ATP-independent manner. Oma1 is part of highly conserved mitochondrial metallopeptidases, with homologs present in higher eukaryotes, eubacteria and archaebacteria, all containing the zinc binding motif (HEXXH). It forms a high molecular mass complex in the inner membrane, possibly a homo-hexamer. 222 matched cddid_all.tbl CDD cd07333 cd07333 320692 M48C_bepA_like Peptidase M48C Ste24p bepA-like, integral membrane protein. This family contains peptidase M48C Ste24p protease bepA (formerly yfgC)-like proteins considered to be putative metallopeptidases, containing a zinc-binding motif, HEXXH, and a COOH-terminal ER retrieval signal (KKXX). They proteolytically remove the C-terminal three residues of farnesylated proteins. They are integral membrane proteins associated with the endoplasmic reticulum and golgi, binding one zinc ion per subunit. In eukaryotes, Ste24p is required for the first NH2-terminal proteolytic processing event within the a-factor precursor, which takes place after COOH-terminal CAAX modification (C is cysteine; A is usually aliphatic; X is one of several amino acids) is complete. Mutation studies have shown that the HEXXH protease motif, which is extracellular but adjacent to a transmembrane domain and therefore close to the membrane surface, is critical for Ste24p activity. Several members of this family also contain tetratricopeptide (TPR) repeat motifs, which are involved in a variety of functions including protein-protein interactions. BepA has been shown to possess protease activity and is responsible for the degradation of incorrectly folded LptD, an essential outer-membrane protein (OMP) involved in OM transport and assembly of lipopolysaccharide. Overexpression of the bepA protease causes abnormal biofilm architecture. 174 matched cddid_all.tbl CDD cd07334 cd07334 320693 M48C_loiP_like Peptidase M48C Ste24p loiP-like, integral membrane protein. This subfamily contains peptidase M48 Ste24p protease loiP (formerly yggG)-like family are mostly uncharacterized proteins that include E. coli loiP and ycaLG, considered to be putative metallopeptidases, containing a zinc-binding motif, HEXXH, and a COOH-terminal ER retrieval signal (KKXX). They proteolytically remove the C-terminal three residues of farnesylated proteins. They are integral membrane proteins associated with the endoplasmic reticulum and golgi, binding one zinc ion per subunit. In eukaryotes, Ste24p is required for the first NH2-terminal proteolytic processing event within the a-factor precursor, which takes place after COOH-terminal CAAX modification (C is cysteine; A is usually aliphatic; X is one of several amino acids) is complete. Mutation studies have shown that the HEXXH protease motif, which is extracellular but adjacent to a transmembrane domain and therefore close to the membrane surface, is critical for Ste24p activity. LoiP has been shown to be a metallopeptidase that cleaves its targets preferentially between Phe-Phe residues. It is upregulated when bacteria are subjected to media of low osmolarity, thus yggG was named LoiP (low osmolarity induced protease). Proper membrane localization of LoiP may depend on YfgC, another putative metalloprotease in this subfamily. 215 matched cddid_all.tbl CDD cd07335 cd07335 320694 M48B_HtpX_like Peptidase M48 subfamily B HtpX-like membrane-bound metallopeptidase. This family contains peptidase M48 subfamily B, also known as HtpX, which consists of proteins smaller than Ste24p, with homology restricted to the C-terminal half of Ste24p. HtpX, an integral membrane (IM) metallopeptidase, is widespread in bacteria and archaea, and plays a central role in protein quality control by preventing the accumulation of misfolded proteins in the membrane. Its expression is controlled by the Cpx stress response system, which senses abnormal membrane proteins. HtpX participates in the proteolytic quality control of these misfolded proteins by undergoing self-degradation and eliminating them by collaborating with FtsH, a membrane-bound and ATP-dependent protease. HtpX contains the zinc binding motif (HEXXH), has an FtsH-like topology, and is capable of introducing endoproteolytic cleavages into SecY (also an FtsH substrate). However, HtpX does not have an ATPase activity and will only act against cytoplasmic regions of a target membrane protein. Thus, HtpX and FtsH have overlapping and/or complementary functions, which are especially important at high temperature; in E. coli and Xylella fastidiosa, HtpX is heat-inducible, while in Streptococcus gordonii it is not. Mutation studies of HtpX-like M48 metalloprotease from Leptospira interrogans (LA4131) has been shown to result in altered expression of a subset of metal toxicity and stress response genes. 240 matched cddid_all.tbl CDD cd07336 cd07336 320695 M48B_HtpX_like Peptidase M48 subfamily B HtpX-like membrane-bound metallopeptidase. This HtpX family of peptidase M48 subfamily B includes uncharacterized HtpX homologs and consists of proteins smaller than Ste24p, with homology restricted to the C-terminal half of Ste24p. HtpX expression is controlled by the Cpx stress response system, which senses abnormal membrane proteins. HtpX participates in the proteolytic quality control of these misfolded proteins by undergoing self-degradation and collaborating with FtsH, a membrane-bound and ATP-dependent protease, to eliminate them. HtpX, a zinc metalloprotease with an active site motif HEXXH, has an FtsH-like topology, and is capable of introducing endoproteolytic cleavages into SecY (also an FtsH substrate). However, HtpX does not have an ATPase activity and will only act against cytoplasmic regions of a target membrane protein. Thus, HtpX and FtsH have overlapping and/or complementary functions, which are especially important at high temperature; in E. coli and Xylella fastidiosa, HtpX is heat-inducible, while in Streptococcus gordonii it is not. 266 matched cddid_all.tbl CDD cd07337 cd07337 320696 M48B_HtpX_like Peptidase M48 subfamily B HtpX-like membrane-bound metallopeptidase. This HtpX family of peptidase M48 subfamily B includes uncharacterized HtpX homologs and consists of proteins smaller than Ste24p, with homology restricted to the C-terminal half of Ste24p. HtpX expression is controlled by the Cpx stress response system, which senses abnormal membrane proteins. HtpX participates in the proteolytic quality control of these misfolded proteins by undergoing self-degradation and collaborating with FtsH, a membrane-bound and ATP-dependent protease, to eliminate them. HtpX, a zinc metalloprotease with an active site motif HEXXH, has an FtsH-like topology, and is capable of introducing endoproteolytic cleavages into SecY (also an FtsH substrate). However, HtpX does not have an ATPase activity and will only act against cytoplasmic regions of a target membrane protein. Thus, HtpX and FtsH have overlapping and/or complementary functions, which are especially important at high temperature; in E. coli and Xylella fastidiosa, HtpX is heat-inducible, while in Streptococcus gordonii it is not. 203 matched cddid_all.tbl CDD cd07338 cd07338 320697 M48B_HtpX_like Peptidase M48 subfamily B HtpX-like membrane-bound metallopeptidase. This HtpX family of peptidase M48 subfamily B includes uncharacterized HtpX homologs and consists of proteins smaller than Ste24p, with homology restricted to the C-terminal half of Ste24p. HtpX expression is controlled by the Cpx stress response system, which senses abnormal membrane proteins. HtpX participates in the proteolytic quality control of these misfolded proteins by undergoing self-degradation and collaborating with FtsH, a membrane-bound and ATP-dependent protease, to eliminate them. HtpX, a zinc metalloprotease with an active site motif HEXXH, has an FtsH-like topology, and is capable of introducing endoproteolytic cleavages into SecY (also an FtsH substrate). However, HtpX does not have an ATPase activity and will only act against cytoplasmic regions of a target membrane protein. Thus, HtpX and FtsH have overlapping and/or complementary functions, which are especially important at high temperature; in E. coli and Xylella fastidiosa, HtpX is heat-inducible, while in Streptococcus gordonii it is not. 216 matched cddid_all.tbl CDD cd07339 cd07339 320698 M48B_HtpX_like Peptidase M48 subfamily B HtpX-like membrane-bound metallopeptidase. This HtpX family of peptidase M48 subfamily B includes uncharacterized HtpX homologs and consists of proteins smaller than Ste24p, with homology restricted to the C-terminal half of Ste24p. HtpX expression is controlled by the Cpx stress response system, which senses abnormal membrane proteins. HtpX participates in the proteolytic quality control of these misfolded proteins by undergoing self-degradation and collaborating with FtsH, a membrane-bound and ATP-dependent protease, to eliminate them. HtpX, a zinc metalloprotease with an active site motif HEXXH, has an FtsH-like topology, and is capable of introducing endoproteolytic cleavages into SecY (also an FtsH substrate). However, HtpX does not have an ATPase activity and will only act against cytoplasmic regions of a target membrane protein. Thus, HtpX and FtsH have overlapping and/or complementary functions, which are especially important at high temperature; in E. coli and Xylella fastidiosa, HtpX is heat-inducible, while in Streptococcus gordonii it is not. 229 matched cddid_all.tbl CDD cd07340 cd07340 320699 M48B_Htpx_like Peptidase M48 subfamily B HtpX-like membrane-bound metallopeptidase. This HtpX family of peptidase M48 subfamily B includes uncharacterized HtpX homologs and consists of proteins smaller than Ste24p, with homology restricted to the C-terminal half of Ste24p. HtpX expression is controlled by the Cpx stress response system, which senses abnormal membrane proteins. HtpX participates in the proteolytic quality control of these misfolded proteins by undergoing self-degradation and collaborating with FtsH, a membrane-bound and ATP-dependent protease, to eliminate them. HtpX, a zinc metalloprotease with an active site motif HEXXH, has an FtsH-like topology, and is capable of introducing endoproteolytic cleavages into SecY (also an FtsH substrate). However, HtpX does not have an ATPase activity and will only act against cytoplasmic regions of a target membrane protein. Thus, HtpX and FtsH have overlapping and/or complementary functions, which are especially important at high temperature; in E. coli and Xylella fastidiosa, HtpX is heat-inducible, while in Streptococcus gordonii it is not. 246 matched cddid_all.tbl CDD cd07341 cd07341 320700 M56_BlaR1_MecR1_like Peptidase M56-like including those in BlaR1 and MecR1, integral membrane metallopeptidase. This family contains peptidase M56, which includes zinc metalloprotease domain in MecR1 as well as BlaR1. MecR1 is a transmembrane beta-lactam sensor/signal transducer protein that regulates the expression of an altered penicillin-binding protein PBP2a, which resists inactivation by beta-lactam antibiotics, in methicillin-resistant Staphylococcus aureus (MRSA). BlaR1 regulates the inducible expression of a class A beta-lactamase that hydrolytically destroys certain ?-lactam antibiotics in MRSA. Both, MecR1 and BlaR1, are transmembrane proteins that consist of four transmembrane helices, a cytoplasmic zinc protease domain, and the soluble C-terminal extracellular sensor domain, and are highly similar in sequence and function. The signal for protein expression is transmitted by site-specific proteolytic cleavage of both the transducer, which auto-activates, and the repressor, which is inactivated, unblocking gene transcription. All members contain the zinc metalloprotease motif (HEXXH). Homologs of this peptidase domain are also found in a number of other bacterial genome sequences, most of which are as yet uncharacterized. 187 matched cddid_all.tbl CDD cd07342 cd07342 320701 M48C_Oma1_like M48C peptidase, integral membrane endopeptidase. This subfamily contains peptidase M48C Oma1 (also called mitochondrial metalloendopeptidase OMA1) protease homologs that are mostly uncharacterized. Oma1 is part of the quality control system in the inner membrane of mitochondria, with its catalytic site facing the matrix space. It cleaves and thereby promotes the turnover of mistranslated or misfolded membrane proteins. Oma1 can cleave the misfolded multi-pass membrane protein Oxa1, thus exerting a function similar to the ATP-dependent m-AAA protease for quality control of inner membrane proteins; it cleaves a misfolded polytopic membrane protein at multiple sites. It has been proposed that in the absence of m-AAA protease, proteolysis of Oxa1 is mediated by Oma1 in an ATP-independent manner. Oma1 is part of highly conserved mitochondrial metallopeptidases, with homologs present in higher eukaryotes, eubacteria and archaebacteria, all containing the zinc binding motif (HEXXH). It forms a high molecular mass complex in the inner membrane, possibly a homo-hexamer. 158 matched cddid_all.tbl CDD cd07343 cd07343 320702 M48A_Zmpste24p_like Peptidase M48 subfamily A, a type 1 CaaX endopeptidase. This family contains peptidase family M48 subfamily A which includes a number of well-characterized genes such as those found in humans (ZMPSTE24, also known as farnesylated protein-converting enzyme 1 or FACE-1 or Hs Ste24), Taenia solium metacestode (TsSte24p), Arabidopsis (AtSte24) and yeast (Ste24p). Ste24p contains the zinc metalloprotease motif (HEXXH), likely exposed on the cytoplasmic side. It is thought to be intimately associated with the endoplasmic reticulum (ER), regardless of whether its genes possess the conventional signal motif (KKXX) in the C-terminal. Proteins in this family proteolytically remove the C-terminal three residues of farnesylated proteins. Ste24p is involved in the post-translational processing of prelamin A to mature lamin A, a major component of the nuclear envelope. ZmpSte24 deficiency causes an accumulation of prelamin A leading to lipodystrophy and other disease phenotypes, while mutations in this gene or in that encoding its substrate, prelamin A, result in a series of human inherited diseases known as laminopathies, the most severe of which are Hutchinson Gilford progeria syndrome (HGPS) and restrictive dermopathy (RD) which arise due to unsuccessful maturation of prelamin A. Two forms of mandibuloacral dysplasia, a condition that causes a variety of abnormalities involving bone development, skin pigmentation, and fat distribution, are caused by mutations in two different genes; mutations in the LMNA gene, which normally provides instructions for making lamin A and lamin C, cause mandibuloacral dysplasia with A-type lipodystrophy (MAD-A), and mutations in the ZMPSTE24 gene cause mandibuloacral dysplasia with B-type lipodystrophy (MAD-B). Within cells, these genes are involved in maintaining the structure of the nucleus and may play a role in many cellular processes. Certain HIV protease inhibitors have been shown to inhibit the enzymatic activity of ZMPSTE24, but not enzymes involved in prelamin A processing. 405 matched cddid_all.tbl CDD cd07344 cd07344 320703 M48_yhfN_like Peptidase M48 YhfN-like, a novel minigluzincin. M48 YhfN-like protease is considered as a CaaX prenyl protease 1 homolog, with most of the sequences in this family as yet uncharacterized. It contains the zinc metalloprotease motif (HEXXH), likely exposed on the cytoplasmic side. It is probably associated with the endoplasmic reticulum (ER), regardless of whether its genes possess the conventional signal motif (KKXX) in the C-terminal. Proteins in this family proteolytically remove the C-terminal three residues of farnesylated proteins. This novel family of related proteins consist of the soluble minimal scaffold similar to the catalytic domains of the integral-membrane metallopeptidase M48 and M56, thus called minigluzincins. 96 matched cddid_all.tbl CDD cd07345 cd07345 320704 M48A_Ste24p-like Peptidase M48 subfamily A-like, putative CaaX prenyl protease. This family contains peptidase family M48 subfamily A-like CaaX prenyl protease 1, most of which are uncharacterized. Some of these contain tetratricopeptide (TPR) repeats at the C-terminus. Proteins in this family contain the zinc metalloprotease motif (HEXXH), likely exposed on the cytoplasmic side. They are thought to be possibly associated with the endoplasmic reticulum (ER), regardless of whether their genes possess the conventional signal motif (KKXX) in the C-terminal. These proteins putatively remove the C-terminal three residues of farnesylated proteins proteolytically. 346 matched cddid_all.tbl CDD cd07346 cd07346 349983 ABC_6TM_exporters Six-transmembrane helical domain of the ATP-binding cassette transporters. This family represents a subunit of six transmembrane (TM) helices typically found in the ATP-binding cassette (ABC) transporters that function as exporters, which contain 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds and a various type of lipids. In addition to ABC exporters, ABC transporters include two classes of ABC importers, classified depending on details of their architecture and mechanism. Only the ABC exporters are included in this family. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting chemical diversity of the translocated substrates, whereas NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane. However, some ABC genes are organized as half-transporters, which must form either homodimers or heterodimers to form a functional unit. The ABC exporters play a role in multidrug resistance to antibiotics and anticancer agents, and mutations in these proteins have been shown to cause severe human diseases such as cystic fibrosis. 292 matched cddid_all.tbl CDD cd07347 cd07347 259818 harmonin_N_like N-terminal protein-binding module of harmonin and similar domains, also known as HHD (harmonin homology domain). This domain is found in harmonin, and similar proteins such as delphilin, and whirlin. These are postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold proteins. Harmonin and whirlin are organizers of the Usher protein network of the inner ear and the retina, delphilin is found at the cerebellar parallel fiber-Purkinje cell synapses. This domain is also found in CCM2 (also called malcavernin; C7orf22/chromosome 7 open reading frame 22; OSM). CCM2 along with CCM1 and CCM3 constitutes a set of proteins which when mutated are responsible for cerebral cavernous malformations, an autosomal dominant neurovascular disease characterized by cerebral hemorrhages and vascular malformations in the central nervous system. CCM2 plays many functional roles. CCM2 functions as a scaffold involved in small GTPase Rac-dependent p38 mitogen-activated protein kinase (MAPK) activation when the cell is under hyperosmotic stress. It associates with CCM1 in the signaling cascades that regulate vascular integrity and participates in HEG1 (the transmembrane receptor heart of glass 1) mediated endothelial cell junctions. CCM proteins also inhibit the activation of small GTPase RhoA and its downstream effector Rho kinase (ROCK) to limit vascular permeability. CCM2 mediates TrkA-dependent cell death via its N-terminal PTB domain in pediatric neuroblastic tumours; the C-terminal domain of malcavernin represented here has also been refered to as the Karet domain. Harmonin contains a single copy of this domain at its N-terminus which binds specifically to a short internal peptide fragment of the cadherin 23 cytoplasmic domain (a component of the Usher protein network). Whirlin contains two copies of this domain; the first of these has been assayed for interaction with the cytoplasmic domain of cadherin 23 and no interaction could be detected. 78 matched cddid_all.tbl CDD cd07348 cd07348 132762 NR_LBD_NGFI-B The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of Nerve growth factor-induced-B (NGFI-B): NGFI-B is a member of the nuclear#steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of the embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcriptional initiation. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, NGFI-B has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). 238 matched cddid_all.tbl CDD cd07349 cd07349 132763 NR_LBD_SHP The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of the Small Heterodimer Partner (SHP): SHP is a member of the nuclear receptor superfamily. SHP has a ligand binding domain, but lacks the DNA binding domain, typical to almost all of the nuclear receptors. It functions as a transcriptional coregulator by directly interacting with other nuclear receptors through its AF-2 motif. The closest relative of SHP is DAX1 and they can form heterodimer. SHP is an orphan receptor, lacking an identified ligand. 222 matched cddid_all.tbl CDD cd07350 cd07350 132764 NR_LBD_Dax1 The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of the DAX1 protein: DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) is a nuclear receptor with a typical ligand binding domain, but lacks the DNA binding domain. DAX1 plays an important role in the normal development of several hormone-producing tissues. Duplications of the region of the X chromosome containing DAX1 cause dosage sensitive sex reversal. DAX1 acts as a global repressor of many nuclear receptors, including SF-1, LRH-1, ERR, ER, AR and PR. DAX1 can form homodimer and heterodimerizes with its alternatively spliced isoform DAX1A and other nuclear receptors such as SHP, ERalpha and SF-1. 232 matched cddid_all.tbl CDD cd07353 cd07353 259819 harmonin_N N-terminal protein-binding module of harmonin. Harmonin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein, which organizes the Usher protein network of the inner ear and the retina. Harmonin contains a single copy of this domain, which is found at the N-terminus of all three harmonin isoform classes (a, b and c), and which preceeds the first PDZ protein-binding domain, PDZ1. This harmonin_N domain binds specifically to a short internal peptide fragment of the cadherin 23 cytoplasmic domain; cadherin 23 is a component of the Usher protein network. 79 matched cddid_all.tbl CDD cd07354 cd07354 259820 HN_L-delphilin-R1_like first harmonin_N_like domain (repeat 1) of L-delphilin, and related domains. This subgroup contains the first of two harmonin_N_like domains of an alternatively spliced longer variant of mouse delphilin (L-delphilin, isoform 1), and related domains. Delphilin is a scaffold protein which binds the glutamate receptor delta-2 (GRID2) subunit and the monocarboxylate transporter 2 at the cerebellar parallel fiber-Purkinje cell synapses. The N-terminus of L-delphilin contains this harmonin_N_like domain preceded by a postsynaptic density-95/discs-large/ZO-1 (PDZ) protein-binding domain, PDZ1. L-delphilin, in common with the shorter C-terminal isoforms (S-delphilin/delphilin alpha and delphilin beta) has a second harmonin_N_like domain (not belonging to this subgroup) and a second PDZ domain, PDZ2. This first harmonin_N_like domain is a putative protein-binding module based on its sequence similarity to the N-terminal domain of harmonin. 80 matched cddid_all.tbl CDD cd07355 cd07355 259821 HN_L-delphilin-R2_like second harmonin_N_like domain (repeat 2) of L-delphilin, and related domains. This subgroup contains the second of two harmonin_N_like domains of an alternatively spliced longer variant of mouse delphilin (L-delphilin), and related domains. Delphilin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein which binds the glutamate receptor delta-2 (GRID2) subunit and the monocarboxylate transporter 2 at the cerebellar parallel fiber-Purkinje cell synapses. This harmonin_N_like domain in L-delphilin follows the second PDZ protein-binding domain, PDZ2; it is also found in the shorter C-terminal isoforms (S-delphilin/delphilin alpha and delphilin beta). It is a putative protein-binding module based on its sequence similarity to the N-terminal domain of harmonin. The first harmonin_N_like domain of L-delphilin belongs to a different subgroup and is missing from S-delphilin. 80 matched cddid_all.tbl CDD cd07356 cd07356 259822 HN_L-whirlin_R1_like first harmonin_N_like domain (repeat 1) of the long isoform of whirlin, and related domains. This subgroup contains the first of two harmonin_N_like domains of the long isoform of whirlin, and related domains. Whirlin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein which binds various components of the Usher protein network of the inner ear and the retina: erythrocyte protein p55, usherin, VlGR1, and myosin XVa. The long isoform of whirlin contains two harmonin_N_like domains, and three PDZ protein-binding domains, PDZ1-3. This first harmonin_N_like domain precedes PDZ1, and is a putative protein-binding module based on its sequence similarity to the N-terminal domain of harmonin. This first harmonin_N_like domain has been assayed for interaction with the cytoplasmic domain of cadherin 23 (a component of the Usher network and an interacting partner of the harmonin N-domain), however no interaction could be detected. The short whirlin isoform, derived from an alternative start ATG, lacks this first harmonin_N_like domain. The short isoform has in common with the long isoform, the second harmonin_N_like domain (designated repeat 2, not present in this subgroup), and PDZ3. 78 matched cddid_all.tbl CDD cd07357 cd07357 259823 HN_L-whirlin_R2_like second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains. This subgroup contains the second of two harmonin_N_like domains found in the long isoform of whirlin, and related domains. Whirlin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein which binds various components of the Usher protein network of the inner ear and the retina: erythrocyte protein p55, usherin, VlGR1, and myosin XVa. The long isoform of whirlin contains two harmonin_N_like domains, and three PDZ protein-binding domains, PDZ1-3. The short whirlin isoform, derived from an alternative start ATG, lacks the first harmonin_N_like domain but has in common with the long isoform, this second harmonin_N_like domain (designated repeat 2, included in this subgroup) and PDZ3. This second harmonin_N_like domain is a putative protein-binding module based on its sequence similarity to the N-terminal domain of harmonin. 81 matched cddid_all.tbl CDD cd07358 cd07358 259824 HN_PDZD7_like harmonin_N_like domain, a protein-binding module of PDZ domain-containing protein 7 and related proteins. Human PDZD7 is a scaffolding protein which associates with the Usher Syndrome protein network, and localizes to the stereocilia Ankle-link. Usher syndrome is the leading cause of genetic deaf-blindness. PDZD7 has a role as in Usher syndrome type 2 (and not in USH1) in humans. Whirlin, Usherin and GRP98 are other USH2 proteins. The latter two form the ankle links and whirlin is thought to be a scaffold for protein interactions at these links. PDZD7, whirlin, and harmonin (an USH1 protein) have a similar domain composition. The domain represented here is a putative protein-binding module based on its sequence similarity to the N-terminal domain of harmonin. Cooperative effects of mutations in PDZD7 and Usherin, and in PDZD7 and GPR98, result in a digenic USH2 phenotype. 78 matched cddid_all.tbl CDD cd07359 cd07359 153372 PCA_45_Doxase_B_like Subunit B of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and simlar enzymes. This subfamily of class III extradiol dioxygenases consists of a number of proteins with known enzymatic activities: Protocatechuate (PCA) 4,5-dioxygenase (LigAB), 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB), 3-O-Methylgallate Dioxygenase, 2-aminophenol 1,6-dioxygenase, as well as proteins without any known enzymatic activity. These proteins play essential roles in the degradation of aromatic compounds by catalyzing the incorporation of both atoms of molecular oxygen into their preferred substrates. As members of the Class III extradiol dioxygenase family, the enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents the catalytic subunit, B. 271 matched cddid_all.tbl CDD cd07361 cd07361 153373 MEMO_like Memo (mediator of ErbB2-driven cell motility) is co-precipitated with the C terminus of ErbB2, a protein involved in cell motility. This subfamily is composed of Memo (mediator of ErbB2-driven cell motility) and similar proteins. Memo is a protein that is co-precipitated with the C terminus of ErbB2, a protein involved in cell motility. It is required for the ErbB2-driven cell mobility and is found in protein complexes with cofilin, ErbB2 and PLCgamma1. However, Memo is not homologous to any known signaling proteins, and its function in ErbB2 signaling is not known. Structural studies show that Memo binds directly to a specific ErbB2-derived phosphopeptide. Memo is homologous to class III nonheme iron-dependent extradiol dioxygenases, however, no metal binding or enzymatic activity can be detected for Memo. This subfamily also contains a few members containing a C-terminal AMMECR1-like domain. The AMMECR1 protein was proposed to be a regulatory factor that is potentially involved in the development of AMME contiguous gene deletion syndrome. 266 matched cddid_all.tbl CDD cd07362 cd07362 153374 HPCD_like Class III extradiol dioxygenases with similarity to homoprotocatechuate 2,3-dioxygenase, which catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate. This subfamily of class III extradiol dioxygenases consists of two types of proteins with known enzymatic activities; 3,4-dihydroxyphenylacetate (homoprotocatechuate) 2,3-dioxygenase (HPCD) and 2-amino-5-chlorophenol 1,6-dioxygenase. HPCD catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate (hpca), a central intermediate in the bacterial degradation of aromatic compounds. The enzyme incorporates both atoms of molecular oxygen into hpca, resulting in aromatic ring-opening to yield the product alpha-hydroxy-delta-carboxymethyl cis-muconic semialdehyde. 2-amino-5-chlorophenol 1,6-dioxygenase catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol, which is an intermediate during p-chloronitrobenzene degradation. The enzyme is probably a heterotetramer composed of two alpha and two beta subunits. Alpha and beta subunits share significant sequence similarity and both belong to this family. Like all Class III extradiol dioxygenases, these enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. 272 matched cddid_all.tbl CDD cd07363 cd07363 153375 45_DOPA_Dioxygenase The Class III extradiol dioxygenase, 4,5-DOPA Dioxygenase, catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine. This subfamily is composed of plant 4,5-DOPA Dioxygenase, the uncharacterized Escherichia coli protein Jw3007, and similar proteins. 4,5-DOPA Dioxygenase catalyzes the incorporation of both atoms of molecular oxygen into 4,5-dihydroxy-phenylalanine (4,5-DOPA). The reaction results in the opening of the cyclic ring between carbons 4 and 5 and producing an unstable seco-DOPA that rearranges to betalamic acid. 4,5-DOPA Dioxygenase is a key enzyme in the biosynthetic pathway of the plant pigment betalain. Homologs of DODA are present not only in betalain-producing plants but also in bacteria and archaea. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. 253 matched cddid_all.tbl CDD cd07364 cd07364 153376 PCA_45_Dioxygenase_B Subunit B of the Class III extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of protocatechuate. Protocatechuate 4,5-dioxygenase (LigAB) catalyzes the oxidization and subsequent ring-opening of protocatechuate (or 3,4-dihydroxybenzoic acid, PCA), an intermediate in the breakdown of lignin and other compounds. Protocatechuate 4,5-dioxygenase is an aromatic ring opening dioxygenase belonging to the class III extradiol enzyme family, a group of enyzmes that cleaves aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon using a non-heme Fe(II). LigAB is composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. The B subunit (LigB) is the catalytic subunit of LigAB. 277 matched cddid_all.tbl CDD cd07365 cd07365 153377 MhpB_like Subunit B of the Class III Extradiol ring-cleavage dioxygenase, 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB), which catalyzes the oxidization and subsequent ring-opening of 2,3-dihydroxyphenylpropionate. 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB) catalyzes the oxidization and subsequent ring-opening of 2,3-dihydroxyphenylpropionate, yielding the product 2-hydroxy-6-oxo-nona-2,4-diene 1,9-dicarboxylate. It is an essential enzyme in the beta-phenylpropionic degradation pathway, in which beta-phenylpropionic is first hydrolyzed to produce 2,3-dihydroxyphenylpropionate. The enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents the catalytic subunit, B. MhpB is likely to be a tetramer. 310 matched cddid_all.tbl CDD cd07366 cd07366 153378 3MGA_Dioxygenase Subunit B of the Class III Extradiol ring-cleavage dioxygenase, 3-O-Methylgallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 3-O-Methylgallate. 3-O-Methylgallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of 3-O-Methylgallate (3MGA) between carbons 2 and 3. 3-O-Methylgallate Dioxygenase is a key enzyme in the syringate degradation pathway, in which the syringate is first converted to 3-O-Methylgallate by O-demethylase. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which uses a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents the catalytic subunit, B. 328 matched cddid_all.tbl CDD cd07367 cd07367 153379 CarBb CarBb is the B subunit of the Class III Extradiol ring-cleavage dioxygenase, 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBb is the B subunit of 2-aminophenol 1,6-dioxygenase (CarB), which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. It is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, it has also shown high specificity for 2,3-dihydroxybiphenyl. 268 matched cddid_all.tbl CDD cd07368 cd07368 153380 PhnC_Bs_like PhnC is a Class III Extradiol ring-cleavage dioxygenase involved in the polycyclic aromatic hydrocarbon (PAH) catabolic pathway. This subfamily is composed of Burkholderia sp. PhnC and similar poteins. PhnC is one of nine protein products encoded by the phn locus. These proteins are involved in the polycyclic aromatic hydrocarbon (PAH) catabolic pathway. PhnC is a member of the class III extradiol dioxygenase family, a group os enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents the catalytic subunit, B. 277 matched cddid_all.tbl CDD cd07369 cd07369 153381 PydA_Rs_like PydA is a Class III Extradiol ring-cleavage dioxygenase required for the degradation of 3-hydroxy-4-pyridone (HP). This subfamily is composed of Rhizobium sp. PydA and similar proteins. PydA is required for the degradation of 3-hydroxy-4-pyridone (HP), an intermediate in the Leucaena toxin mimosine degradation pathway. It is a member of the class III extradiol dioxygenase family, a group of enzymes that use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents the catalytic subunit, B. 329 matched cddid_all.tbl CDD cd07370 cd07370 153382 HPCD The Class III extradiol dioxygenase, homoprotocatechuate 2,3-dioxygenase, catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate. 3,4-dihydroxyphenylacetate (homoprotocatechuate) 2,3-dioxygenase (HPCD) catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate (hpca), a central intermediate in the bacterial degradation of aromatic compounds. The enzyme incorporates both atoms of molecular oxygen into hpca, resulting in aromatic ring-opening to yield alpha-hydroxy-delta-carboxymethyl cis-muconic semialdehyde. HPCD is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. 280 matched cddid_all.tbl CDD cd07371 cd07371 153383 2A5CPDO_AB The alpha and beta subunits of the Class III extradiol dioxygenase, 2-amino-5-chlorophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol. This subfamily contains both alpha and beta subunits of 2-amino-5-chlorophenol 1,6-dioxygenase (2A5CPDO), which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol, an intermediate during p-chloronitrobenzene degradation. 2A5CPDO is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. The active enzyme is probably a heterotetramer, composed of two alpha and two beta subunits. Alpha and beta subunits share significant sequence similarity and may have evolved by gene duplication. 268 matched cddid_all.tbl CDD cd07372 cd07372 153384 2A5CPDO_B The beta subunit of the Class III extradiol dioxygenase, 2-amino-5-chlorophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol. 2-amino-5-chlorophenol 1,6-dioxygenase (2A5CPDO), catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol, which is an intermediate during p-chloronitrobenzene degradation. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. The active 2A5CPDO enzyme is probably a heterotetramer, composed of two alpha and two beta subunits. The alpha and beta subunits share significant sequence similarity and may have evolved by gene duplication. This model describes the beta subunit, which contains a putative metal binding site with two conserved histidines; these residues are equivalent to two out of three Fe(II) binding residues present in the catalytic subunit dioxygenase LigB. The alpha subunit does not contain these potential metal binding residues. The 2A5CPDO beta subunit may be the catalytic subunit of the enzyme. 294 matched cddid_all.tbl CDD cd07373 cd07373 153385 2A5CPDO_A The alpha subunit of the Class III extradiol dioxygenase, 2-amino-5-chlorophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol. 2-amino-5-chlorophenol 1,6-dioxygenase (2A5CPDO) catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol, which is an intermediate during p-chloronitrobenzene degradation. This enzyme is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. The active enzyme is probably a heterotetramer, composed of two alpha and two beta subunits. The alpha and beta subunits share significant sequence similarity and may have evolved by gene duplication. This model describes the alpha subunit, which does not contain a potential metal binding site and may not possess catalytic activity. 271 matched cddid_all.tbl CDD cd07374 cd07374 143620 CYTH-like_Pase CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) Phosphatases. CYTH-like superfamily enzymes hydrolyze triphosphate-containing substrates and require metal cations as cofactors. They have a unique active site located at the center of an eight-stranded antiparallel beta barrel tunnel (the triphosphate tunnel). The name CYTH originated from the gene designation for bacterial class IV adenylyl cyclases (CyaB), and from thiamine triphosphatase. Class IV adenylate cyclases catalyze the conversion of ATP to 3',5'-cyclic AMP (cAMP) and PPi. Thiamine triphosphatase is a soluble cytosolic enzyme which converts thiamine triphosphate to thiamine diphosphate. This domain superfamily also contains RNA triphosphatases, membrane-associated polyphosphate polymerases, tripolyphosphatases, nucleoside triphosphatases, nucleoside tetraphosphatases and other proteins with unknown functions. 174 matched cddid_all.tbl CDD cd07375 cd07375 153408 Anticodon_Ia_like Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains. This domain is found in a variety of class Ia aminoacyl tRNA synthetases, C-terminal to the catalytic core domain. It recognizes and specifically binds to the anticodon of the tRNA. Aminoacyl tRNA synthetases catalyze the transfer of cognate amino acids to the 3'-end of their tRNAs by specifically recognizing cognate from non-cognate amino acids. Members include valyl-, leucyl-, isoleucyl-, cysteinyl-, arginyl-, and methionyl-tRNA synthethases. This superfamily also includes a domain from MshC, an enzyme in the mycothiol biosynthetic pathway. 117 matched cddid_all.tbl CDD cd07376 cd07376 143511 PLPDE_III_DSD_D-TA_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase. This family includes eukaryotic D-serine dehydratases (DSD), cryptic DSDs from bacteria, D-threonine aldolases (D-TA), low specificity D-TAs, and similar uncharacterized proteins. DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. D-TA reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. Members of this family are fold type III PLP-dependent enzymes, similar to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on similarity to AR, it is possible members of this family also form dimers in solution. 345 matched cddid_all.tbl CDD cd07377 cd07377 153418 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences. 66 matched cddid_all.tbl CDD cd07378 cd07378 277324 MPP_ACP5 Homo sapiens acid phosphatase 5 and related proteins, metallophosphatase domain. Acid phosphatase 5 (ACP5) removes the mannose 6-phosphate recognition marker from lysosomal proteins. The exact site of dephosphorylation is not clear. Evidence suggests dephosphorylation may take place in a prelysosomal compartment as well as in the lysosome. ACP5 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 286 matched cddid_all.tbl CDD cd07379 cd07379 277325 MPP_239FB Homo sapiens 239FB and related proteins, metallophosphatase domain. 239FB (Fetal brain protein 239) is thought to play a role in central nervous system development, but its specific role in unknown. 239FB is expressed predominantly in human fetal brain from a gene located in the chromosome 11p13 region associated with the mental retardation component of the WAGR (Wilms tumor, Aniridia, Genitourinary anomalies, Mental retardation) syndrome. Orthologous brp-like (brain protein 239-like) proteins have been identified in the invertebrate amphioxus group and in vertebrates. 239FB belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 135 matched cddid_all.tbl CDD cd07380 cd07380 277326 MPP_CWF19_N Schizosaccharomyces pombe CWF19 and related proteins, N-terminal metallophosphatase domain. CWF19 cell cycle control protein (also known as CWF19-like 1 (CWF19L1) in Homo sapiens), N-terminal metallophosphatase domain. CWF19 contains C-terminal domains similar to that found in the CwfJ cell cycle control protein. The metallophosphatase domain belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 149 matched cddid_all.tbl CDD cd07381 cd07381 277327 MPP_CapA CapA and related proteins, metallophosphatase domain. CapA is one of three membrane-associated enzymes in Bacillus anthracis that is required for synthesis of gamma-polyglutamic acid (PGA), a major component of the bacterial capsule. The YwtB and PgsA proteins of Bacillus subtilis are closely related to CapA and are also included in this alignment model. CapA belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 239 matched cddid_all.tbl CDD cd07382 cd07382 277328 MPP_DR1281 Deinococcus radiodurans DR1281 and related proteins, metallophosphatase domain. DR1281 is an uncharacterized Deinococcus radiodurans protein with a domain that belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 255 matched cddid_all.tbl CDD cd07383 cd07383 277329 MPP_Dcr2 Saccharomyces cerevisiae DCR2 phosphatase and related proteins, metallophosphatase domain. DCR2 phosphatase (Dosage-dependent Cell Cycle Regulator 2) functions together with DCR1 (Gid8) in a common pathway to accelerate initiation of DNA replication in Saccharomyces cerevisiae. Genetic analysis suggests that DCR1 functions upstream of DCR2. DCR2 interacts with and dephosphorylates Sic1, an inhibitor of mitotic cyclin/cyclin-dependent kinase complexes, which may serve to trigger the initiation of cell division. DCR2 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 202 matched cddid_all.tbl CDD cd07384 cd07384 277330 MPP_Cdc1_like Saccharomyces cerevisiae CDC1 and related proteins, metallophosphatase domain. Cdc1 (also known as XlCdc1 in Xenopus laevis) is an endoplasmic reticulum-localized transmembrane lipid phosphatase with a metallophosphatase domain facing the ER lumen. In budding yeast, the gene encoding CDC1 is essential while nonlethal mutations cause defects in Golgi inheritance and actin polarization. Cdc1 mutant cells accumulate an unidentified phospholipid, suggesting that Cdc1 is a lipid phosphatase. Cdc1 mutant cells also have highly elevated intracellular calcium levels suggesting a possible role for Cdc1 in calcium regulation. The 5' flanking region of Cdc1 is a regulatory region with conserved binding site motifs for AP1, AP2, Sp1, NF-1 and CREB. DNA polymerase delta consists of at least four subunits - Pol3, Cdc1, Cdc27, and Cdm1. This group also contains Saccharomyces cerevisiae TED1 (Trafficking of Emp24p/Erv25p-dependent cargo disrupted 1), which acts together with Emp24p and Erv25p in cargo exit from the ER, and human MPPE1. The human MPPE1 gene is a candidate susceptibility gene for bipolar disorder. These proteins belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 172 matched cddid_all.tbl CDD cd07385 cd07385 277331 MPP_YkuE_C Bacillus subtilis YkuE and related proteins, C-terminal metallophosphatase domain. YkuE is an uncharacterized Bacillus subtilis protein with a C-terminal metallophosphatase domain and an N-terminal twin-arginine (RR) motif. An RR-signal peptide derived from the Bacillus subtilis YkuE protein can direct Tat-dependent secretion of agarase in Streptomyces lividans. This is an indication that YkuE is transported by the Bacillus subtilis Tat (Twin-arginine translocation) pathway machinery. YkuE belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 224 matched cddid_all.tbl CDD cd07386 cd07386 277332 MPP_DNA_pol_II_small_archeal_C archeal DNA polymerase II, small subunit, C-terminal metallophosphatase domain. The small subunit of the archeal DNA polymerase II contains a C-terminal metallophosphatase domain. This domain is thought to be functionally active because the active site residues required for phosphoesterase activity in other members of this superfamily are intact. The archeal replicative DNA polymerases are thought to possess intrinsic phosphatase activity that hydrolyzes the pyrophosphate released during nucleotide polymerization. This domain belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 243 matched cddid_all.tbl CDD cd07387 cd07387 277333 MPP_PolD2_C PolD2 (DNA polymerase delta, subunit 2), C-terminal domain. PolD2 (DNA polymerase delta, subunit 2) is an auxiliary subunit of the eukaryotic DNA polymerase delta (PolD) complex thought to play a regulatory role and to serve as a scaffold for PolD assembly by interacting simultaneously with all of the other three subunits. PolD2 is catalytically inactive and lacks the active site residues required for phosphoesterase activity in other members of this superfamily. PolD2 is also involved in the recruitment of several proteins regulating DNA metabolism, including p21, PDIP1, PDIP38, PDIP46, and WRN. Human PolD consists of four subunits: p125 (PolD1), p50 (PolD2), p66(PolD3), and p12(PolD4). PolD is one of three major replicases in eukaryotes. PolD also plays an essential role in translesion DNA synthesis, homologous recombination, and DNA repair. Within the PolD complex, PolD2 tightly associates with PolD3. PolD2 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 257 matched cddid_all.tbl CDD cd07388 cd07388 277334 MPP_Tt1561 Thermus thermophilus Tt1561 and related proteins, metallophosphatase domain. This family includes bacterial proteins related to Tt1561 (also known as Aq1956 in Aquifex aeolicus), an uncharacterized Thermus thermophilus protein. The conserved domain present in members of this family belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets, and is thought to allow for productive metal coordination. However, the active site residues required for phosphoesterase activity in other members of this superfamily are poorly conserved in this functionally uncharacterized family. 224 matched cddid_all.tbl CDD cd07389 cd07389 277335 MPP_PhoD Bacillus subtilis PhoD and related proteins, metallophosphatase domain. PhoD (also known as alkaline phosphatase D/APaseD in Bacillus subtilis) is a secreted phosphodiesterase encoded by phoD of the Pho regulon in Bacillus subtilis. PhoD homologs are found in prokaryotes, eukaryotes, and archaea. PhoD contains a twin arginine (RR) motif and is transported by the Tat (Twin-arginine translocation) translocation pathway machinery (TatAyCy). This family also includes the Fusarium oxysporum Fso1 protein. PhoD belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 242 matched cddid_all.tbl CDD cd07390 cd07390 277336 MPP_AQ1575 Aquifex aeolicus AQ1575 and related proteins, metallophosphatase domain. This family includes bacterial and archeal proteins homologous to AQ1575, an uncharacterized Aquifex aeolicus protein. AQ1575 may play an accessory role in DNA repair, based on the close proximity of its gene to Holliday junction resolvasome genes. The domain present in members of this family belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 170 matched cddid_all.tbl CDD cd07391 cd07391 277337 MPP_PF1019 Pyrococcus furiosus PF1019 and related proteins, metallophosphatase domain. This family includes bacterial and archeal proteins homologous to PF1019, an uncharacterized Pyrococcus furiosus protein. The domain present in members of this family belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 175 matched cddid_all.tbl CDD cd07392 cd07392 277338 MPP_PAE1087 Pyrobaculum aerophilum PAE1087 and related proteins, metallophosphatase domain. PAE1087 is an uncharacterized Pyrobaculum aerophilum protein with a metallophosphatase domain. The domain present in members of this family belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 190 matched cddid_all.tbl CDD cd07393 cd07393 277339 MPP_DR1119 Deinococcus radiodurans DR1119 and related proteins, metallophosphatase domain. DR1119 is an uncharacterized Deinococcus radiodurans protein with a metallophosphatase domain. The domain present in members of this family belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 238 matched cddid_all.tbl CDD cd07394 cd07394 163637 MPP_Vps29 Homo sapiens Vps29 and related proteins, metallophosphatase domain. Vps29 (vacuolar sorting protein 29), also known as vacuolar membrane protein Pep11, is a subunit of the retromer complex which is responsible for the retrieval of mannose-6-phosphate receptors (MPRs) from the endosomes for retrograde transport back to the Golgi. Vps29 has a phosphoesterase fold that acts as a protein interaction scaffold for retromer complex assembly as well as a phosphatase with specificity for the cytoplasmic tail of the MPR. The retromer includes the following 5 subunits: Vps35, Vps26, Vps29, and a dimer of the sorting nexins Vps5 (Snx1), and Vps17 (Snx2). Vps29 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 178 matched cddid_all.tbl CDD cd07395 cd07395 277340 MPP_CSTP1 Homo sapiens CSTP1 and related proteins, metallophosphatase domain. CSTP1 (complete S-transactivated protein 1) is an uncharacterized Homo sapiens protein with a metallophosphatase domain, that is transactivated by the complete S protein of hepatitis B virus. CSTP1 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 263 matched cddid_all.tbl CDD cd07396 cd07396 277341 MPP_Nbla03831 Homo sapiens Nbla03831 and related proteins, metallophosphatase domain. Nbla03831 (also known as LOC56985) is an uncharacterized Homo sapiens protein with a domain that belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 245 matched cddid_all.tbl CDD cd07397 cd07397 277342 MPP_NostocDevT-like Nostoc DevT and similar proteins, metallophosphatase domain. DevT (Alr4674) is a putative protein phosphatase from Nostoc PCC 7120 (Anabaena PCC 7120). DevT mutants form mature heterocysts, but they are unable to fix N(2) and must be supplied with a source of combined nitrogen in order to survive. Anabaena DevT shows homology to phosphatases of the PPP family and displays a Mn(2+)-dependent phosphatase activity. DevT is constitutively expressed in both vegetative cells and heterocysts, and is not regulated by NtcA. The heterocyst regulator HetR may exert a certain inhibition on the expression of devT. Under diazotrophic growth conditions, DevT protein accumulates specifically in mature heterocysts. The role that DevT plays in a late essential step of heterocyst differentiation is still unknown. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 245 matched cddid_all.tbl CDD cd07398 cd07398 277343 MPP_YbbF-LpxH Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain. YbbF/LpxH is an Escherichia coli UDP-2,3-diacylglucosamine hydrolase thought to catalyze the fourth step of lipid A biosynthesis, in which a precursor UDP-2,3-diacylglucosamine is hydrolyzed to yield 2,3-diacylglucosamine 1-phosphate and UMP. YbbF belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 217 matched cddid_all.tbl CDD cd07399 cd07399 277344 MPP_YvnB Bacillus subtilis YvnB and related proteins, metallophosphatase domain. YvnB (BSU35040) is an uncharacterized Bacillus subtilis protein with a metallophosphatase domain. This family includes bacterial and eukaryotic proteins similar to YvnB. YvnB belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 207 matched cddid_all.tbl CDD cd07400 cd07400 277345 MPP_1 Uncharacterized subfamily, metallophosphatase domain. Uncharacterized subfamily of the MPP superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 138 matched cddid_all.tbl CDD cd07401 cd07401 277346 MPP_TMEM62_N Homo sapiens TMEM62, N-terminal metallophosphatase domain. TMEM62 (transmembrane protein 62) is an uncharacterized Homo sapiens transmembrane protein with an N-terminal metallophosphatase domain. TMEM62 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 254 matched cddid_all.tbl CDD cd07402 cd07402 277347 MPP_GpdQ Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain. GpdQ (glycerophosphodiesterase Q, also known as Rv0805 in Mycobacterium tuberculosis) is a binuclear metallophosphoesterase from Enterobacter aerogenes that catalyzes the hydrolysis of mono-, di-, and triester substrates, including some organophosphate pesticides and products of the degradation of nerve agents. The GpdQ homolog, Rv0805, has 2',3'-cyclic nucleotide phosphodiesterase activity. GpdQ and Rv0805 belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 240 matched cddid_all.tbl CDD cd07403 cd07403 277348 MPP_TTHA0053 Thermus thermophilus TTHA0053 and related proteins, metallophosphatase domain. TTHA0053 is an uncharacterized Thermus thermophilus protein with a domain that belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 130 matched cddid_all.tbl CDD cd07404 cd07404 277349 MPP_MS158 Microscilla MS158 and related proteins, metallophosphatase domain. MS158 is an uncharacterized Microscilla protein with a metallophosphatase domain. Microscilla proteins MS152, and MS153 are also included in this family. The domain present in members of this family belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 201 matched cddid_all.tbl CDD cd07405 cd07405 277350 MPP_UshA_N Escherichia coli UshA and related proteins, N-terminal metallophosphatase domain. UshA is a bacterial periplasmic enzyme with UDP-sugar hydrolase and dinucleoside-polyphosphate hydrolase activities associated with its N-terminal metallophosphatase domain, and 5'-nucleotidase activity associated with its C-terminal domain. UshA has been studied in Escherichia coli where it is expressed from the ushA gene as an immature precursor and proteolytically cleaved to form a mature product upon export to the periplasm. UshA hydrolyzes many different nucleotides and nucleotide derivatives and has been shown to degrade external UDP-glucose to uridine, glucose 1-phosphate and phosphate for utilization by the cell. The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 287 matched cddid_all.tbl CDD cd07406 cd07406 277351 MPP_CG11883_N Drosophila melanogaster CG11883 and related proteins, N-terminal metallophosphatase domain. CG11883 is an uncharacterized Drosophila melanogaster UshA-like protein with two domains, an N-terminal metallophosphatase domain and a C-terminal nucleotidase domain. The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 257 matched cddid_all.tbl CDD cd07407 cd07407 277352 MPP_YHR202W_N Saccharomyces cerevisiae YHR202W and related proteins, N-terminal metallophosphatase domain. YHR202W is an uncharacterized Saccharomyces cerevisiae UshA-like protein with two domains, an N-terminal metallophosphatase domain and a C-terminal nucleotidase domain. The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 286 matched cddid_all.tbl CDD cd07408 cd07408 277353 MPP_SA0022_N Staphylococcus aureus SA0022 and related proteins, N-terminal metallophosphatase domain. SA0022 is an uncharacterized Staphylococcus aureus UshA-like protein with two putative domains, an N-terminal metallophosphatase domain and a C-terminal nucleotidase domain. SA0022 also contains a putative C-terminal cell wall anchor domain. The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 255 matched cddid_all.tbl CDD cd07409 cd07409 277354 MPP_CD73_N CD73 ecto-5'-nucleotidase and related proteins, N-terminal metallophosphatase domain. CD73 is a mammalian ecto-5'-nucleotidase expressed in endothelial cells and lymphocytes that catalyzes the conversion of 5'-AMP to adenosine in the final step of a pathway that generates adenosine from ATP. This pathway also includes a CD39 nucleoside triphosphate dephosphorylase that mediates the dephosphorylation of ATP to ADP and then to 5'-AMP. These enzymes all have an N-terminal metallophosphatase domain and a C-terminal 5'nucleotidase domain. The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 279 matched cddid_all.tbl CDD cd07410 cd07410 277355 MPP_CpdB_N Escherichia coli CpdB and related proteins, N-terminal metallophosphatase domain. CpdB is a bacterial periplasmic protein with an N-terminal metallophosphatase domain and a C-terminal 3'-nucleotidase domain. This alignment model represents the N-terminal metallophosphatase domain, which has 2',3'-cyclic phosphodiesterase activity, hydrolyzing the 2',3'-cyclic phosphates of adenosine, guanosine, cytosine and uridine to yield nucleoside and phosphate. CpdB also hydrolyzes the chromogenic substrates p-nitrophenyl phosphate (PNPP), bis(PNPP) and p-nitrophenyl phosphorylcholine (NPPC). CpdB is thought to play a scavenging role during RNA hydrolysis by converting the non-transportable nucleotides produced by RNaseI to nucleosides which can easily enter a cell for use as a carbon source. This family also includes YfkN, a Bacillus subtilis nucleotide phosphoesterase with two copies of each of the metallophosphatase and 3'-nucleotidase domains. The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 280 matched cddid_all.tbl CDD cd07411 cd07411 277356 MPP_SoxB_N Thermus thermophilus SoxB and related proteins, N-terminal metallophosphatase domain. SoxB (sulfur oxidation protein B) is a periplasmic thiosulfohydrolase and an essential component of the sulfur oxidation pathway in archaea and bacteria. SoxB has a dinuclear manganese cluster and is thought to catalyze the release of sulfate from a protein-bound cysteine S-thiosulfonate. SoxB is expressed from the sox (sulfur oxidation) gene cluster, which encodes 15 other sox genes, and has two domains, an N-terminal metallophosphatase domain and a C-terminal 5'-nucleotidase domain. SoxB binds the SoxYZ complex and is thought to function as a sulfate-thiohydrolase. SoxB is closely related to the UshA, YchR, and CpdB proteins, all of which have the same two-domain architecture. The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 273 matched cddid_all.tbl CDD cd07412 cd07412 277357 MPP_YhcR_N Bacillus subtilis YhcR endonuclease and related proteins, N-terminal metallophosphatase domain. YhcR is a Bacillus subtilis sugar-nonspecific endonuclease. It cleaves endonucleolytically to yield nucleotide 3'-monophosphate products, similar to Staphylococcus aureus micrococcal nuclease. YhcR appears to be located in the cell wall, and is thought to be a substrate for a Bacillus subtilis sortase. YhcR is the major calcium-activated nuclease of B. subtilis. The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 295 matched cddid_all.tbl CDD cd07413 cd07413 277358 MPP_PA3087 Pseudomonas aeruginosa PA3087 and related proteins, metallophosphatase domain. PA3087 is an uncharacterized protein from Pseudomonas aeruginosa with a metallophosphatase domain that belongs to the phosphoprotein phosphatase (PPP) family. The PPP family also includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all eukaryotes, and in most bacterial and archeal genomes. Dephosphorylation of phosphoserines and phosphothreonines on target proteins plays a central role in the regulation of many cellular processes. PPPs belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 222 matched cddid_all.tbl CDD cd07414 cd07414 277359 MPP_PP1_PPKL PP1, PPKL (PP1 and kelch-like) enzymes, and related proteins, metallophosphatase domain. PP1 (protein phosphatase type 1) is a serine/threonine phosphatase that regulates many cellular processes including: cell-cycle progression, protein synthesis, muscle contraction, carbohydrate metabolism, transcription and neuronal signaling, through its interaction with at least 180 known targeting proteins. PP1 occurs in all tissues and regulates many pathways, ranging from cell-cycle progression to carbohydrate metabolism. Also included here are the PPKL (PP1 and kelch-like) enzymes including the PPQ, PPZ1, and PPZ2 fungal phosphatases. These PPKLs have a large N-terminal kelch repeat in addition to a C-terminal phosphoesterase domain. The PPP (phosphoprotein phosphatase) family, to which PP1 belongs, is one of two known protein phosphatase families specific for serine and threonine. The PPP family also includes: PP2A, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all eukaryotes, and in most bacterial and archeal genomes. Dephosphorylation of phosphoserines and phosphothreonines on target proteins plays a central role in the regulation of many cellular processes. PPPs belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 291 matched cddid_all.tbl CDD cd07415 cd07415 277360 MPP_PP2A_PP4_PP6 PP2A, PP4, and PP6 phosphoprotein phosphatases, metallophosphatase domain. PP2A-like family of phosphoprotein phosphatases (PPP's) including PP4 and PP6. PP2A (Protein phosphatase 2A) is a critical regulator of many cellular activities. PP2A comprises about 1% of total cellular proteins. PP2A, together with protein phosphatase 1 (PP1), accounts for more than 90% of all serine/threonine phosphatase activities in most cells and tissues. The PP2A subunit in addition to having a catalytic domain homologous to PP1, has a unique C-terminal tail, containing a motif that is conserved in the catalytic subunits of all PP2A-like phosphatases including PP4 and PP6, and has an important role in PP2A regulation. The PP2A-like family of phosphatases all share a similar heterotrimeric architecture, that includes: a 65kDa scaffolding subunit (A), a 36kDa catalytic subunit (C), and one of 18 regulatory subunits (B). The PPP (phosphoprotein phosphatase) family, to which PP2A belongs, is one of two known protein phosphatase families specific for serine and threonine. The PPP family also includes: PP1, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all eukaryotes, and in most bacterial and archeal genomes. Dephosphorylation of phosphoserines and phosphothreonines on target proteins plays a central role in the regulation of many cellular processes. PPPs belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 285 matched cddid_all.tbl CDD cd07416 cd07416 277361 MPP_PP2B PP2B, metallophosphatase domain. PP2B (calcineurin) is a unique serine/threonine protein phosphatase in its regulation by a second messenger (calcium and calmodulin). PP2B is involved in many biological processes including immune responses, the second messenger cAMP pathway, sodium/potassium ion transport in the nephron, cell cycle progression in lower eukaryotes, cardiac hypertrophy, and memory formation. PP2B is highly conserved from yeast to humans, but is absent from plants. PP2B is a heterodimer consisting of a catalytic subunit (CnA) and a regulatory subunit (CnB); CnB contains four Ca2+ binding motifs referred to as EF hands. The PPP (phosphoprotein phosphatase) family, to which PP2B belongs, is one of two known protein phosphatase families specific for serine and threonine. The PPP family also includes: PP1, PP2A, PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all eukaryotes, and in most bacterial and archeal genomes. Dephosphorylation of phosphoserines and phosphothreonines on target proteins plays a central role in the regulation of many cellular processes. PPPs belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 305 matched cddid_all.tbl CDD cd07417 cd07417 277362 MPP_PP5_C PP5, C-terminal metallophosphatase domain. Serine/threonine protein phosphatase-5 (PP5) is a member of the PPP gene family of protein phosphatases that is highly conserved among eukaryotes and widely expressed in mammalian tissues. PP5 has a C-terminal phosphatase domain and an extended N-terminal TPR (tetratricopeptide repeat) domain containing three TPR motifs. The PPP (phosphoprotein phosphatase) family, to which PP5 belongs, is one of two known protein phosphatase families specific for serine and threonine. The PPP family also includes: PP1, PP2A, PP2B (calcineurin), PP4, PP6, PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all eukaryotes, and in most bacterial and archeal genomes. Dephosphorylation of phosphoserines and phosphothreonines on target proteins plays a central role in the regulation of many cellular processes. PPPs belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 316 matched cddid_all.tbl CDD cd07418 cd07418 163661 MPP_PP7 PP7, metallophosphatase domain. PP7 is a plant phosphoprotein phosphatase that is highly expressed in a subset of stomata and thought to play an important role in sensory signaling. PP7 acts as a positive regulator of signaling downstream of cryptochrome blue light photoreceptors. PP7 also controls amplification of phytochrome signaling, and interacts with nucleotidediphosphate kinase 2 (NDPK2), a positive regulator of phytochrome signalling. In addition, PP7 interacts with heat shock transcription factor HSF and up-regulates protective heat shock proteins. PP7 may also play a role in salicylic acid-dependent defense signaling. The PPP (phosphoprotein phosphatase) family, to which PP7 belongs, is one of two known protein phosphatase families specific for serine and threonine. The PPP family also includes: PP2A, PP2B (calcineurin), PP4, PP5, PP6, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all eukaryotes, and in most bacterial and archeal genomes. Dephosphorylation of phosphoserines and phosphothreonines on target proteins plays a central role in the regulation of many cellular processes. PPPs belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 377 matched cddid_all.tbl CDD cd07419 cd07419 277363 MPP_Bsu1_C Arabidopsis thaliana Bsu1 phosphatase and related proteins, C-terminal metallophosphatase domain. Bsu1 encodes a nuclear serine-threonine protein phosphatase found in plants and protozoans. Bsu1 has a C-terminal phosphatase domain and an N-terminal Kelch-repeat domain. Bsu1 is preferentially expressed in elongating plant cells. It modulates the phosphorylation state of Bes1, a transcriptional regulator phosphorylated by the glycogen synthase kinase Bin2, as part of a steroid hormone signal transduction pathway. The PPP (phosphoprotein phosphatase) family, to which Bsu1 belongs, is one of two known protein phosphatase families specific for serine and threonine. The PPP family also includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all eukaryotes, and in most bacterial and archeal genomes. Dephosphorylation of phosphoserines and phosphothreonines on target proteins plays a central role in the regulation of many cellular processes. PPPs belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 311 matched cddid_all.tbl CDD cd07420 cd07420 277364 MPP_RdgC Drosophila melanogaster RdgC and related proteins, metallophosphatase domain. RdgC (retinal degeneration C) is a vertebrate serine-threonine protein phosphatase that is required to prevent light-induced retinal degeneration. In addition to its catalytic domain, RdgC has two C-terminal EF hands. Homologs of RdgC include the human phosphatases protein phosphatase with EF hands 1 and -2 (PPEF-1 and -2). PPEF-1 transcripts are present at low levels in the retina, PPEF-2 transcripts and PPEF-2 protein are present at high levels in photoreceptors. The PPP (phosphoprotein phosphatase) family, to which RdgC belongs, is one of two known protein phosphatase families specific for serine and threonine. The PPP family also includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all eukaryotes, and in most bacterial and archeal genomes. Dephosphorylation of phosphoserines and phosphothreonines on target proteins plays a central role in the regulation of many cellular processes. PPPs belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 297 matched cddid_all.tbl CDD cd07421 cd07421 163664 MPP_Rhilphs Rhilph phosphatases, metallophosphatase domain. Rhilphs (Rhizobiales/ Rhodobacterales/ Rhodospirillaceae-like phosphatases) are a phylogenetically distinct group of PPP (phosphoprotein phosphatases), found only in land plants. They are named for their close relationship to to PPP phosphatases from alpha-Proteobacteria, including Rhizobiales, Rhodobacterales and Rhodospirillaceae. The PPP (phosphoprotein phosphatase) family, to which the Rhilphs belong, is one of two known protein phosphatase families specific for serine and threonine. The PPP family also includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all eukaryotes, and in most bacterial and archeal genomes. Dephosphorylation of phosphoserines and phosphothreonines on target proteins plays a central role in the regulation of many cellular processes. PPPs belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 304 matched cddid_all.tbl CDD cd07422 cd07422 277365 MPP_ApaH Escherichia coli ApaH and related proteins, metallophosphatase domain. ApaH (also known as symmetrically cleaving Ap4A hydrolase and bis(5'nucleosyl)-tetraphosphatase) is a bacterial member of the PPP (phosphoprotein phosphatase) family of serine/threonine phosphatases that hydrolyzes the nucleotide-signaling molecule diadenosine tetraphosphate (Ap(4)A) into two ADP and also hydrolyzes Ap(5)A, Gp(4)G, and other extending compounds. Null mutations in apaH result in high intracellular levels of Ap(4)A which correlate with multiple phenotypes, including a decreased expression of catabolite-repressible genes, a reduction in the expression of flagellar operons, and an increased sensitivity to UV and heat. Ap4A hydrolase is important in responding to heat shock and oxidative stress via regulating the concentration of Ap4A in bacteria. Ap4A hydrolase is also thought to play a role in siderophore production, but the mechanism by which ApaH interacts with siderophore pathways in unknown. The PPP (phosphoprotein phosphatase) family, to which ApaH belongs, is one of two known protein phosphatase families specific for serine and threonine. The PPP family also includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE, and PrpA/PrpB. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all eukaryotes, and in most bacterial and archeal genomes. Dephosphorylation of phosphoserines and phosphothreonines on target proteins plays a central role in the regulation of many cellular processes. PPPs belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 257 matched cddid_all.tbl CDD cd07423 cd07423 277366 MPP_Prp_like Bacillus subtilis PrpE and related proteins, metallophosphatase domain. PrpE (protein phosphatase E) is a bacterial member of the PPP (phosphoprotein phosphatase) family of serine/threonine phosphatases and a key signal transduction pathway component controlling the expression of spore germination receptors GerA and GerK in Bacillus subtilis. PrpE is closely related to ApaH (also known symmetrical Ap(4)A hydrolase and bis(5'nucleosyl)-tetraphosphatase). PrpE has specificity for phosphotyrosine only, unlike the serine/threonine phosphatases to which it is related. The Bacilli members of this family are single domain proteins while the other members have N- and C-terminal domains in addition to this phosphatase domain. Pnkp is the end-healing and end-sealing component of an RNA repair system present in bacteria. It is composed of three catalytic modules: an N-terminal polynucleotide 5' kinase, a central 2',3' phosphatase, and a C-terminal ligase. Pnkp is a Mn(2+)-dependent phosphodiesterase-monoesterase that dephosphorylates 2',3'-cyclic phosphate RNA ends. An RNA binding site is suggested by a continuous tract of positive surface potential flanking the active site. The PPP (phosphoprotein phosphatase) family, to which PrpE belongs, is one of two known protein phosphatase families specific for serine and threonine. The PPP family also includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all eukaryotes, and in most bacterial and archeal genomes. Dephosphorylation of phosphoserines and phosphothreonines on target proteins plays a central role in the regulation of many cellular processes. PPPs belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 235 matched cddid_all.tbl CDD cd07424 cd07424 277367 MPP_PrpA_PrpB PrpA and PrpB, metallophosphatase domain. PrpA and PrpB are bacterial type I serine/threonine and tyrosine phosphatases thought to modulate the expression of proteins that protect the cell upon accumulation of misfolded proteins in the periplasm. The PPP (phosphoprotein phosphatase) family, to which PrpA and PrpB belong, is one of two known protein phosphatase families specific for serine and threonine. This family also includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE, and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all eukaryotes, and in most bacterial and archeal genomes. Dephosphorylation of phosphoserines and phosphothreonines on target proteins plays a central role in the regulation of many cellular processes. PPPs belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 201 matched cddid_all.tbl CDD cd07425 cd07425 277368 MPP_Shelphs Shewanella-like phosphatases, metallophosphatase domain. This family includes bacterial, eukaryotic, and archeal proteins orthologous to the Shewanella cold-active protein-tyrosine phosphatase, CAPTPase. CAPTPase is an uncharacterized protein that belongs to the Shelph (Shewanella-like phosphatase) family of PPP (phosphoprotein phosphatases). The PPP family is one of two known protein phosphatase families specific for serine and threonine. In addition to Shelps, the PPP family also includes: PP1, PP2A, PP2B (calcineurin), PP4, PP5, PP6, PP7, Bsu1, RdgC, PrpE, PrpA/PrpB, and ApA4 hydrolase. The PPP catalytic domain is defined by three conserved motifs (-GDXHG-, -GDXVDRG- and -GNHE-). The PPP enzyme family is ancient with members found in all eukaryotes, and in most bacterial and archeal genomes. Dephosphorylation of phosphoserines and phosphothreonines on target proteins plays a central role in the regulation of many cellular processes. PPPs belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 209 matched cddid_all.tbl CDD cd07429 cd07429 143631 Cby_like Chibby, a nuclear inhibitor of Wnt/beta-catenin mediated transcription, and similar proteins. Chibby(Cby) is a well-conserved nuclear protein that functions as part of the Wnt/beta-catenin signaling pathway. Specifically, Cby binds directly to beta-catenin by interacting with its central region, which harbors armadillo repeats. Cby-beta-catenin interactions may also involve 14-3-3 proteins. By competing with other binding partners of beta-catenin, the Tcf/Lef transcription factors, Cby inhibits transcriptional activation. Cby has been shown to play a role in adipocyte differentiation. The C-terminal region of Cby appears to contain an alpha-helical coiled-coil motif. 108 matched cddid_all.tbl CDD cd07430 cd07430 143632 GH15_N Glycoside hydrolase family 15, N-terminal domain. Members of this family are N-terminal domains uniquely found in bacterial and archaeal glucoamylases and glucodextranases. Glucoamylase (glucan 1,4-alpha-glucosidase; 4-alpha-D-glucan glucohydrolase; amyloglucosidase; exo-1,4-alpha-glucosidase; gamma-amylase; lysosomal alpha-glucosidase; EC 3.2.1.3) hydrolyzes beta-1,4-glucosidic linkages of starch, glycogen and malto-oligosaccharides, releasing beta-D-glucose from the non-reducing end. Glucodextranase (glucan 1,6-alpha-glucosidase; exo-1,6-alpha-glucosidase; EC 3.2.1.70) uses an inverting reaction mechanism to hydrolyze alpha-1,6-glucosidic linkages of dextran and related oligosaccharides, releasing beta-D-glucose from the non-reducing end. These N-terminal domains adopt a structure consisting of antiparallel beta-strands, divided into two beta-sheets, with one sheet wrapped by an extended polypeptide, which appears to stabilize the domain. The function of these domains in the enzymes is as yet unknown. However, it is suggested that domain N of bacterial GA is involved in folding and/or the thermostability of the A domain that forms an (alpha/alpha)6-barrel structure. 260 matched cddid_all.tbl CDD cd07431 cd07431 213986 PHP_PolIIIA Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III. PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that is responsible for the replication of the DNA duplex. The alpha subunit of DNA polymerase III core enzyme catalyzes the reaction for polymerizing both DNA strands. The PolIIIA PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination, and like other PHP structures, exhibits a distorted (beta/alpha) 7 barrel and coordinates up to 3 metals. Initially, it was proposed that PHP region might be involved in pyrophosphate hydrolysis, but such activity has not been found. It has been shown that the PHP domain of PolIIIA has a trinuclear metal complex and is capable of proofreading activity. 179 matched cddid_all.tbl CDD cd07432 cd07432 213987 PHP_HisPPase Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase. HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to produce histidinol. HisPPase can be classified into two types: the bifunctional HisPPase found in proteobacteria that belongs to the DDDD superfamily and the monofunctional Bacillus subtilis type that is a member of the PHP family. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. The PHP domain of HisPPase is structurally homologous to other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. 129 matched cddid_all.tbl CDD cd07433 cd07433 213988 PHP_PolIIIA_DnaE1 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE1. PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that are responsible for the replication of the DNA duplex. PolIIIA core enzyme catalyzes the reaction for polymerizing both DNA strands. dnaE1 is the longest compared to dnaE2 and dnaE3. A unique motif was also identified in dnaE1 and dnaE3 genes. 277 matched cddid_all.tbl CDD cd07434 cd07434 213989 PHP_PolIIIA_DnaE2 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at DnaE2 gene. PolIIIA DnaE2 plays a role in SOS mutagenesis/translesion synthesis and has dominant effects in determining GC variability in the bacterial genome. PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that are responsible for the replication of the DNA duplex. PolIIIA core enzyme catalyzes the reaction for polymerizing both DNA strands. PolC PHP is located in a different location compared to dnaE1, 2, and 3. dnaE1 is the longest compared to dnaE2 and dnaE3. A unique motif was also identified in dnaE1 and dnaE3 genes. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PHP domains found in DnaEs of thermophilic origin exhibit 3'-5' exonuclease activity. 260 matched cddid_all.tbl CDD cd07435 cd07435 213990 PHP_PolIIIA_POLC Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III at PolC gene. DNA polymerase III alphas (PolIIIAs) that contain a PHP domain have been classified into four basic groups based on phylogenetic and domain structural analyses: polC, dnaE1, dnaE2, and dnaE3. The PolC group is distinct from the other three and is clustered together. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that are responsible for the replication of the DNA duplex. The alpha subunit of DNA polymerase III core enzyme catalyzes the reaction for polymerizing both DNA strands. PolC PHP is located in different location compare to dnaE1, 2, and 3. The PHP domain has four conserved sequence motifs and and contains an invariant histidine that is involved in metal ion coordination.The PHP domain of PolC is structurally homologous to other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. PHP domains found in dnaEs of thermophilic origin exhibit 3'-5' exonuclease activity. In contrast, PolC PHP lacks detectable nuclease activity. 268 matched cddid_all.tbl CDD cd07436 cd07436 213991 PHP_PolX Polymerase and Histidinol Phosphatase domain of bacterial polymerase X. The bacterial/archaeal X-family DNA polymerases (PolXs) have a PHP domain at their C-terminus. The bacterial/archaeal PolX core domain and PHP domain interact with each other and together are involved in metal dependent 3'-5' exonuclease activity. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. PolX is found in all kingdoms, however bacterial PolXs have a completely different domain structure from eukaryotic PolXs. Bacterial PolX has an extended conformation in contrast to the common closed 'right hand' conformation for DNA polymerases. This extended conformation is stabilized by the PHP domain. The PHP domain of PolX is structurally homologous to other members of the PHP family that has a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. 237 matched cddid_all.tbl CDD cd07437 cd07437 213992 PHP_HisPPase_Ycdx_like Polymerase and Histidinol Phosphatase domain of Ycdx like. PHP Ycdx-like is a stand alone PHP domain similar to Ycdx E. coli protein with an unknown physiological role. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. It has also been shown that the PHP domain functions in DNA repair. The PHP structures have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. YcdX may be involved in swarming. 233 matched cddid_all.tbl CDD cd07438 cd07438 213993 PHP_HisPPase_AMP Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase (HisPPase) AMP bound. The PHP domain of this HisPPase family has an unknown function. It has a second domain inserted in the middle that binds adenosine 5-monophosphate (AMP). The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to give histidinol. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. The PHP domain of HisPPase is structurally homologous to the other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. 155 matched cddid_all.tbl CDD cd07439 cd07439 143633 FANCE_c-term Fanconi anemia complementation group E protein, C-terminal domain. Fanconi Anemia (FA) is an autosomal recessive disorder associated with increased susceptibility to various cancers, bone marrow failure, cardiac, renal, and limb malformations, and other characteristics. Cells are highly sensitive to DNA damaging agents. A multi-subunit protein complex, the FA core complex, is responsible for ubiquitination of the protein FANCD2 in response to DNA damage. This monoubiquitination results in a downstream effect on homology-directed DNA repair. FANCE is part of the FA core complex and its C-terminal domain, which is modeled here, has been shown to directly interact with FANCD2. The domain contains a five-fold repeat of a structural unit similar to ARM and HEAT repeats. FANCE appears conserved in metazoa and in plants. 254 matched cddid_all.tbl CDD cd07440 cd07440 188659 RGS Regulator of G protein signaling (RGS) domain superfamily. The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. While inactive, G-alpha-subunits bind GDP, which is released and replaced by GTP upon agonist activation. GTP binding leads to dissociation of the alpha-subunit and the beta-gamma-dimer, allowing them to interact with effectors molecules and propagate signaling cascades associated with cellular growth, survival, migration, and invasion. Deactivation of the G-protein signaling controlled by the RGS domain accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in the reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins are also involved in apoptosis and cell proliferation, as well as modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play important roles in neuronal signals modulation. Some RGS proteins are principal elements needed for proper vision. 113 matched cddid_all.tbl CDD cd07441 cd07441 143550 CRD_SFRP3 Cysteine-rich domain of the secreted frizzled-related protein 3 (SFRP3, alias FRZB), a Wnt antagonist. The cysteine-rich domain (CRD) is an essential part of the secreted frizzled-related protein 3 (SFRP3, alias FRZB), which plays important roles in embryogenesis and postnatal development as an antagonist of Wnt proteins, key players in a number of fundamental cellular processes. SFRPs antagonize the activation of Wnt signaling by binding to the CRD domains of frizzled proteins (Fz), thereby preventing Wnt proteins from binding to these receptors. SFRPs are also known to have functions unrelated to Wnt, as enhancers of procollagen cleavage by the TLD proteinases. SFRPs and Fz proteins both contain CRD domains, but SFRPs lack the seven-pass transmembrane domain which is an integral part of Fzs. SFRP3 regulates Wnt signaling activity in bone development and homeostasis. It is also involved in the control of planar cell polarity. 126 matched cddid_all.tbl CDD cd07442 cd07442 143551 CRD_SFRP4 Cysteine-rich domain of the secreted frizzled-related protein 4 (SFRP4), a Wnt antagonist. The cysteine-rich domain (CRD) is an essential part of the secreted frizzled-related Protein 4 (SFRP4), which regulates the activity of Wnt proteins, key players in a number of fundamental cellular processes such as embryogenesis and postnatal development. SFRPs antagonize the activation of Wnt signaling by binding to the CRDs domains of frizzled (Fz) proteins, thereby preventing Wnt proteins from binding to these receptors. SFRPs are also known to have functions unrelated to Wnt, as enhancers of procollagen cleavage by the TLD proteinases. SFRPs and Fz proteins both contain CRD domains, but SFRPs lack the seven-pass transmembrane domain which is an integral part of Fzs. 127 matched cddid_all.tbl CDD cd07443 cd07443 143552 CRD_SFRP1 Cysteine-rich domain of the secreted frizzled-related protein 1 (SFRP1), a regulator of Wnt activity. The cysteine-rich domain (CRD) is an essential part of the secreted frizzled-related protein 1 (SFRP1), which regulates the activity of Wnt proteins, key players in a number of fundamental cellular processes such as embryogenesis and postnatal development. SFRPs antagonize the activation of Wnt signaling by binding to the CRDs domains of frizzled (Fz) proteins, thereby preventing Wnt proteins from binding to these receptors. SFRPs are also known to have functions unrelated to Wnt, as enhancers of procollagen cleavage by the TLD proteinases. SFRPs and Fz proteins both contain CRD domains, but SFRPs lack the seven-pass transmembrane domain which is an integral part of Fzs. SFRP1 is expressed in many tissues and is involved in the regulation of Wnt signaling in osteoblasts, leading to enhanced trabecular bone formation in adults; it has also been shown to control the growth of retinal ganglion cell axons and the elongation of the antero-posterior axis. 124 matched cddid_all.tbl CDD cd07444 cd07444 143553 CRD_SFRP5 Cysteine-rich domain of the secreted frizzled-related protein 5 (SFRP5), a regulator of Wnt activity. The cysteine-rich domain (CRD) is an essential part of the secreted frizzled-related Protein 5 (SFRP5), which regulates the activity of Wnt proteins, key players in a number of fundamental cellular processes such as embryogenesis and postnatal development. SFRPs antagonize the activation of Wnt signaling by binding to the CRD domains of frizzled (Fz) proteins, thereby preventing Wnt proteins from binding to these receptors. SFRPs are also known to have functions unrelated to Wnt, as enhancers of procollagen cleavage by the TLD proteinases. SFRPs and Fz proteins both contain CRD domains, but SFRPs lack the seven-pass transmembrane domain which is an integral part of Fzs. 127 matched cddid_all.tbl CDD cd07445 cd07445 143554 CRD_corin_1 One of two cysteine-rich domains of the corin protein, a type II transmembrane serine protease . The cysteine-rich domain (CRD) is an essential component of corin, a type II transmembrane serine protease which functions as the convertase of the pro-atrial natriuretic peptide (pro-ANP) in the heart. Corin contains two CRDs in its extracellular region, which play an important role in recognition of the physiological substrate, pro-ANP. This model characterizes the first (N-terminal) CRD. 130 matched cddid_all.tbl CDD cd07446 cd07446 143555 CRD_SFRP2 Cysteine-rich domain of the secreted frizzled-related protein 2 (SFRP2), a regulator of Wnt activity. The cysteine-rich-domain (CRD) is an essential part of the secreted frizzled related protein 2 (SFRP2), which regulates the activity of Wnt proteins, key players in a number of fundamental cellular processes such as embryogenesis and postnatal development. SFRPs antagonize the activation of Wnt signaling by binding to CRD domains of frizzled (Fz) proteins, thereby preventing Wnt proteins from binding to these receptors. SFRPs and Fz proteins both contain CRD domains, but SFRPs lack the seven-pass transmembrane domain which is an integral part of Fzs. As a Wnt antagonist, SFRP2 regulates Nkx2.2 expression in the ventral spinal cord and anteroposterior axis elongation. SFRP2 also has a Wnt-independent function as an enhancer of procollagen cleavage by the TLD proteinases. SFRP2 binds both procollagen and TLD, thus facilitating the enzymatic reaction by bringing together the proteinase and its substrate. 128 matched cddid_all.tbl CDD cd07447 cd07447 143556 CRD_Carboxypeptidase_Z Cysteine-rich domain of carboxypeptidase Z, a member of the carboxypeptidase E family. The cysteine-rich-domain (CRD) is an essential part of carboxypeptidase Z, a member of the carboxypeptidase E family of metallocarboxypeptidases. This is a group of Zn-dependent enzymes implicated in the intra- and extracellular processing of proteins. Carboxypeptidase Z removes C-terminal basic amino acid residues from its substrates, particularly arginine. The CRD acts as a ligand-binding domain for Wnts involved in developmental processes. CPZ binds and may process Wnt-4, CPZ has also been found to enhance the induction of the homeobox gene Cdx1. During vertebrate embryogenesis, the CRD of CPZ upregulates Pax3, a Wnt reporter gene essential for patterning of somites and limb development. 128 matched cddid_all.tbl CDD cd07448 cd07448 143557 CRD_FZ4 Cysteine-rich Wnt-binding domain of the frizzled 4 (Fz4) receptor. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 4 (Fz4) receptor, and is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and the Ca(2+) modulating signaling pathway. CRD containing Fzs have been found in diverse species from amoebas to mammals. 10 different frizzled proteins are found in vertebrata. Frizzled 4 (Fz4) activates the Ca(2+)/calmodulin-dependent protein kinase II and protein kinase C of the Wnt/Ca(2+) signaling pathway during retinal angiogenesis. Mutations in Fz4 lead to familial exudative vitreoretinopathy (FEVR), a hereditary ocular disorder characterized by failure of the peripheral retinal vascularization. In addition, the interplay between Fz4 and norrin as a receptor-ligand pair plays an important role in vascular development in the retina and inner ear in a Wnt-independent manner. 126 matched cddid_all.tbl CDD cd07449 cd07449 143558 CRD_FZ3 Cysteine-rich Wnt-binding domain (CRD) of the frizzled 3 (Fz3) receptor. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 3 (Fz3) receptor, and is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. CRD containing Fzs have been found in diverse species from amoebas to mammals. 10 different frizzled proteins are found in vertebrata. Fz3 plays a vital role in the anterior-posterior guidance of commissural axons. Knockout mice without Fz3 show defects in fiber tracts in the rostral CNS. 127 matched cddid_all.tbl CDD cd07450 cd07450 143559 CRD_FZ6 Cysteine-rich Wnt-binding domain (CRD) of the frizzled 6 (Fz6) receptor. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 6 (Fz6) receptor, and is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. CRD containing Fzs have been found in diverse species from amoebas to mammals. 10 different frizzled proteins are found in vertebrata. Frizzled 6 (Fz6) is expressed in the skin and hair follicles and controls hair patterning in mammals using a Fz-dependent tissue polarity system, which is similar to the one that patterns the Drosophila cuticle. 127 matched cddid_all.tbl CDD cd07451 cd07451 143560 CRD_SMO Cysteine-rich domain of the smoothened receptor (Smo) integral membrane protein. The cysteine-rich domain (CRD) is part of the smoothened receptor (Smo), an integral membrane protein and one of the key players in the Hedgehog (Hh) signaling pathway, critical for development, cell growth and migration, as well as stem cell maintenance. The CRD of Smo is conserved in vertebrates and can also be identified in invertebrates. The precise function of the CRD in Smo is unknown. Mutations in the Drosophila CRD disrupt Smo activity in vivo, while deletion of the CRD in mammalian cells does not seem to affect the activity of overexpressed Smo. 132 matched cddid_all.tbl CDD cd07452 cd07452 143561 CRD_sizzled Cysteine-rich domain of the sizzled protein. The cysteine-rich domain (CRD) is an essential part of the sizzled protein, which regulates bone morphogenetic protein (Bmp) signaling by stabilizing chordin, and plays a critical role in the patterning of vertebrate and invertebrate embryos. Sizzled also functions in the ventral region as a Wnt inhibitor and modulates canonical Wnt signaling. Sizzled proteins belong to the secreted frizzled-related protein family (SFRP), and have be identified in the genomes of birds, fishes and frogs, but not mammals. 141 matched cddid_all.tbl CDD cd07453 cd07453 143562 CRD_crescent Cysteine-rich domain of the crescent protein. The cysteine-rich domain (CRD) is an essential part of the crescent protein, a member of the secreted frizzled-related protein (SFRP) family, which regulates convergent extension movements (CEMs) during gastrulation and neurulation. Xenopus laevis crescent efficiently forms inhibitory complexes with Wnt5a and Wnt11, but this effect is cancelled in the presence of another member of the SFRP family, Frzb1. A potential role for Crescent in head formation is to regulate a non-canonical Wnt pathway positively in the adjacent posterior mesoderm, and negatively in the overlying anterior neuroectoderm. 135 matched cddid_all.tbl CDD cd07454 cd07454 143563 CRD_LIN_17 Cysteine-rich domain (CRD) of LIN_17. A cysteine-rich domain (CRD) is an essential component of a number of cell surface receptors, which are involved in multiple signal transduction pathways, particularly in modulating the activity of the Wnt proteins, which play a fundamental role in the early development of metazoans. CRD is also found in secreted frizzled related proteins (SFRPs), which lack the transmembrane segment found in the frizzled protein. The CRD domain is also present in the alpha-1 chain of mouse type XVIII collagen, in carboxypeptidase Z, several receptor tyrosine kinases, and the mosaic transmembrane serine protease corin. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. CRD domains have also been identified in multiple tandem copies in a Dictyostelium discoideum protein. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines. The protein lin-17 is involved in cell type specification during Caenorhabditis elegans vulval development. 124 matched cddid_all.tbl CDD cd07455 cd07455 143564 CRD_Collagen_XVIII Cysteine-rich domain of the variant 3 of collagen XVIII (V3C18 ). The cysteine-rich domain (CRD) is an essential part of the variant 3 of collagen XVIII (V3C18), which regulates major cellular functions such as the differential epithelial morphogenesis of early lung and kidney development. V3C18 is a 170 kD protein, which is proteolotically processed into the CRD-containing 50 kD glucoprotein precursor that binds Wnt3a through its CRD domain and suppresses the Wnt3a-induced stabilization of beta catenin. Full-length V3C18 is unable to inhibit Wnt signaling. 123 matched cddid_all.tbl CDD cd07456 cd07456 143565 CRD_FZ5_like Cysteine-rich Wnt-binding domain (CRD) of receptors similar to frizzled 5. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 5 (Fz5) and frizzled 8 (Fz8) receptors, and similar proteins. This domain is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines. 120 matched cddid_all.tbl CDD cd07457 cd07457 143566 CRD_FZ9_like Cysteine-rich Wnt-binding domain (CRD) of receptors similar to frizzled 9. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 9 (Fz9) and frizzled 10 (Fz10) receptors, and similar proteins. This domain is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines. 121 matched cddid_all.tbl CDD cd07458 cd07458 143567 CRD_FZ1_like Cysteine-rich Wnt-binding domain (CRD) of receptors similar to frizzled 1. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 1 (Fz1), frizzled 2 (Fz2), and frizzled 7 (Fz7) receptors, and similar proteins. This domain is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. The CRD domain is well conserved in metazoans - 10 frizzled proteins have been identified in mammals, 4 in Drosophila and 3 in Caenorhabditis elegans. Very little is known about the mechanism by which CRD domains interact with their ligands. The domain contains 10 conserved cysteines. 119 matched cddid_all.tbl CDD cd07459 cd07459 143568 CRD_TK_ROR_like Cysteine-rich domain of tyrosine kinase-like orphan receptors. The cysteine-rich domain (CRD) is an essential part of the tyrosine kinase-like orphan receptor (Ror) proteins, a conserved family of tyrosine kinases that function in various processes, including neuronal and skeletal development, cell polarity, and cell movement. Ror proteins are receptors of Wnt proteins, which are key players in a number of fundamental cellular processes in embryogenesis and postnatal development. In different cellular contexts, Ror proteins can either activate or repress transcription of Wnt target genes, and can modulate Wnt signaling by sequestering Wnt ligands. In addition, a number of Wnt-independent functions have been proposed for both Ror1 and Ror2. 135 matched cddid_all.tbl CDD cd07460 cd07460 143569 CRD_FZ5 Cysteine-rich Wnt-binding domain (CRD) of the frizzled 5 (Fz5) receptor.proteins. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 5 (Fz5) receptor, and is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. CRD containing Fzs have been found in diverse species from amoebas to mammals. 10 different frizzled proteins are found in vertebrata. Fz5 plays critical regulating roles in the yolk sac and placental angiogenesis, in the maturation of the Paneth cell phenotype, in governing the neural potential of progenitors in the developing retina, and in neuronal survival in the parafascicular nucleus. 127 matched cddid_all.tbl CDD cd07461 cd07461 143570 CRD_FZ8 Cysteine-rich Wnt-binding domain (CRD) of the frizzled 8 (Fz8) receptor. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 8 (Fz8) receptor, and is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. CRD containing Fzs have been found in diverse species from amoebas to mammals. 10 different frizzled proteins are found in vertebrata. Xenopus Fz8 is important in Wnt/beta-catenin signaling pathways controlling the transcriptional activation of target genes Siamois and Xnr3 in the animal caps of late blastula. 125 matched cddid_all.tbl CDD cd07462 cd07462 143571 CRD_FZ10 Cysteine-rich Wnt-binding domain (CRD) of the frizzled 10 (Fz10) receptor. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 10 (Fz10) receptor, and is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. CRD containing Fzs have been found in diverse species from amoebas to mammals. 10 different frizzled proteins are found in vertebrata. The cellular functon of Fz10 is unknown. 127 matched cddid_all.tbl CDD cd07463 cd07463 143572 CRD_FZ9 Cysteine-rich Wnt-binding domain (CRD) of the frizzled 9 (Fz9) receptor. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 9 (Fz9) receptor, and is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. CRD containing Fzs have been found in diverse species from amoebas to mammals. 10 different frizzled proteins are found in vertebrata. Fz9 may play a signaling role in lymphoid development and maturation, particularly at points where B cells undergo self-renewal prior to further differentiation. 127 matched cddid_all.tbl CDD cd07464 cd07464 143573 CRD_FZ2 Cysteine-rich Wnt-binding domain (CRD) of the frizzled 2 (Fz2) receptor. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 2 (Fz2) receptor, and is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. CRD containing Fzs have been found in diverse species from amoebas to mammals. 10 different frizzled proteins are found in vertebrata. Fz2 is involved in the Wnt/beta-catenin signaling pathway and in the activation of protein kinase C and calcium/calmodulin-dependent protein kinase (CaM kinase). 127 matched cddid_all.tbl CDD cd07465 cd07465 143574 CRD_FZ1 Cysteine-rich Wnt-binding domain (CRD) of the frizzled 1 (Fz1) receptor. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 1 (Fz1) receptor, and is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. CRD containing Fzs have been found in diverse species from amoebas to mammals. 10 different frizzled proteins are found in vertebrata. 127 matched cddid_all.tbl CDD cd07466 cd07466 143575 CRD_FZ7 Cysteine-rich Wnt-binding domain (CRD) of the frizzled 7 (Fz7) receptor. The cysteine-rich domain (CRD) is an essential extracellular portion of the frizzled 7 (Fz7) receptor, and is required for binding Wnt proteins, which play fundamental roles in many aspects of early development, such as cell and tissue polarity, neural synapse formation, and the regulation of proliferation. Fz proteins serve as Wnt receptors for multiple signal transduction pathways, including both beta-catenin dependent and -independent cellular signaling, as well as the planar cell polarity pathway and Ca(2+) modulating signaling pathway. CRD containing Fzs have been found in diverse species from amoebas to mammals. 10 different frizzled proteins are found in vertebrata. Xenopus Fz7 is important in Wnt/beta-catenin signaling pathways controlling the transcriptional activation of target genes Siamois and Xnr3 in the animal caps of late blastula. 125 matched cddid_all.tbl CDD cd07467 cd07467 143576 CRD_TK_ROR1 Cysteine-rich domain of tyrosine kinase-like orphan receptor 1. The cysteine-rich domain (CRD) is an essential part of the tyrosine kinase-like orphan receptor 1 (Ror1), a conserved family of tyrosine kinases that function in various processes, including neuronal and skeletal development, cell polarity, and cell movement. Ror proteins are receptors of Wnt proteins, which are key players in a number of fundamental cellular processes in embryogenesis and postnatal development. In different cellular contexts, Ror proteins can either activate or repress transcription of Wnt target genes, and can modulate Wnt signaling by sequestering Wnt ligands. In addition, a number of Wnt-independent functions have been proposed for both Ror1 and Ror2. 142 matched cddid_all.tbl CDD cd07468 cd07468 143577 CRD_TK_ROR2 Cysteine-rich domain of tyrosine kinase-like orphan receptor 2. The cysteine-rich domain (CRD) is an essential part of the tyrosine kinase-like orphan receptor (Ror2), a conserved family of tyrosine kinases that function in various processes, including neuronal and skeletal development, cell polarity, and cell movement. Ror proteins are receptors of Wnt proteins, which are key players in a number of fundamental cellular processes in embryogenesis and postnatal development. In different cellular contexts, Ror proteins can either activate or repress transcription of Wnt target genes, and can modulate Wnt signaling by sequestering Wnt ligands. In addition, a number of Wnt-independent functions have been proposed for both Ror1 and Ror2. 140 matched cddid_all.tbl CDD cd07469 cd07469 143578 CRD_TK_ROR_related Cysteine-rich domain of proteins similar to tyrosine kinase-like orphan receptors. The cysteine-rich domain (CRD) is an essential part of the tyrosine kinase-like orphan receptor (Ror) proteins, a conserved family of tyrosine kinases that function in various processes, including neuronal and skeletal development, cell polarity, and cell movement. Ror proteins are receptors of Wnt proteins, which are key players in a number of fundamental cellular processes in embryogenesis and postnatal development. In different cellular contexts, Ror proteins can either activate or repress transcription of Wnt target genes, and can modulate Wnt signaling by sequestering Wnt ligands. 147 matched cddid_all.tbl CDD cd07470 cd07470 143621 CYTH-like_mRNA_RTPase CYTH-like mRNA triphosphatase (RTPase) component of the mRNA capping apparatus. This subgroup includes fungal and protozoal RTPases. RTPase catalyzes the first step in the mRNA cap formation process, the removal of the gamma-phosphate of triphosphate terminated pre-mRNA. This activity is metal-dependent. The 5'-end of the resulting mRNA diphosphate is subsequently capped with GMP by RNA guanylytransferase, and then further modified by one or more methyltransferases. The mRNA cap-forming activity is an essential step in mRNA processing. The RTPases are not conserved among eukarya. The structure and mechanism of this fungal RTPase domain group is different from that of higher eukaryotes. This subgroup belongs to the CYTH/triphosphate tunnel metalloenzyme (TTM)-like superfamily, whose enzymes have a unique active site located within an eight-stranded beta barrel. The RTPase domain of the mimivirus RTPase-GTase fusion mRNA capping enzyme also belongs to this subgroup. 243 matched cddid_all.tbl CDD cd07472 cd07472 213030 HmuY_like Bacterial proteins similar to Porphyromonas gingivalis HmuY and the C-terminal domain of PARMER_03218. HmuY is a hemophore that scavenges heme from infected hosts and delivers it to the outer membrane receptor HmuR. Related but uncharacterized proteins do not appear to share the specific heme-binding site. The C-terminal domain of PARMER_03128, an uncharacterized protein from Parabacteroides merdae, plus related proteins from Bacteroidetes, appear to be a distantly related family and have been included in this model. 157 matched cddid_all.tbl CDD cd07473 cd07473 173799 Peptidases_S8_Subtilisin_like Peptidase S8 family domain in Subtilisin-like proteins. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 259 matched cddid_all.tbl CDD cd07474 cd07474 173800 Peptidases_S8_subtilisin_Vpr-like Peptidase S8 family domain in Vpr-like proteins. The maturation of the peptide antibiotic (lantibiotic) subtilin in Bacillus subtilis ATCC 6633 includes posttranslational modifications of the propeptide and proteolytic cleavage of the leader peptide. Vpr was identified as one of the proteases, along with WprA, that are capable of processing subtilin. Asp, Ser, His triadPeptidases S8 or Subtilases are a serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 295 matched cddid_all.tbl CDD cd07475 cd07475 173801 Peptidases_S8_C5a_Peptidase Peptidase S8 family domain in Streptococcal C5a peptidases. Streptococcal C5a peptidase (SCP), is a highly specific protease and adhesin/invasin. The subtilisin-like protease domain is located at the N-terminus and contains a protease-associated domain inserted into a loop. There are three fibronectin type III (Fn) domains at the C-terminus. SCP binds to integrins with the help of Arg-Gly-Asp motifs which are thought to stabilize conformational changes required for substrate binding. Peptidases S8 or Subtilases are a serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 346 matched cddid_all.tbl CDD cd07476 cd07476 173802 Peptidases_S8_thiazoline_oxidase_subtilisin-like_protease Peptidase S8 family domain in Thiazoline oxidase/subtilisin-like proteases. Thiazoline oxidase/subtilisin-like protease is produced by the symbiotic bacteria Prochloron spp. that inhabit didemnid family ascidians. The cyclic peptides of the patellamide class found in didemnid extracts are now known to be synthesized by the Prochloron spp. The prepatellamide is heterocyclized to form thiazole and oxazoline rings and the peptide is cleaved to form the two cyclic patellamides A and C. Subtilases, or subtilisin-like serine proteases, have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure (an example of convergent evolution). 267 matched cddid_all.tbl CDD cd07477 cd07477 173803 Peptidases_S8_Subtilisin_subset Peptidase S8 family domain in Subtilisin proteins. This group is composed of many different subtilisins: Pro-TK-subtilisin, subtilisin Carlsberg, serine protease Pb92 subtilisin, and BPN subtilisins just to name a few. Pro-TK-subtilisin is a serine protease from the hyperthermophilic archaeon Thermococcus kodakaraensis and consists of a signal peptide, a propeptide, and a mature domain. TK-subtilisin is matured from pro-TK-subtilisin upon autoprocessing and degradation of the propeptide. Unlike other subtilisins though, the folding of the unprocessed form of pro-TK-subtilisin is induced by Ca2+ binding which is almost completed prior to autoprocessing. Ca2+ is required for activity unlike the bacterial subtilisins. The propeptide is not required for folding of the mature domain unlike the bacterial subtilases because of the stability produced from Ca2+ binding. Subtilisin Carlsberg is extremely similar in structure to subtilisin BPN'/Novo thought it has a 30% difference in amino acid sequence. The substrate binding regions are also similar and 2 possible Ca2+ binding sites have been identified recently. Subtilisin Carlsberg possesses the highest commercial importance as a proteolytic additive for detergents. Serine protease Pb92, the serine protease from the alkalophilic Bacillus strain PB92, also contains two calcium ions and the overall folding of the polypeptide chain closely resembles that of the subtilisins. Members of the peptidases S8 and S35 clan include endopeptidases, exopeptidases and also a tripeptidyl-peptidase. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The S53 family contains a catalytic triad Glu/Asp/Ser. The stability of these enzymes may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 229 matched cddid_all.tbl CDD cd07478 cd07478 173804 Peptidases_S8_CspA-like Peptidase S8 family domain in CspA-like proteins. GSP (germination-specific protease) converts the spore peptidoglycan hydrolase (SleC) precursor to an active enzyme during germination of Clostridium perfringens S40 spores. Analysis of an enzyme fraction of GSP showed that it was composed of a gene cluster containing the processed forms of products of cspA, cspB, and cspC which are positioned in a tandem array just upstream of the 5' end of sleC. The amino acid sequences deduced from the nucleotide sequences of the csp genes showed significant similarity and showed a high degree of homology with those of the catalytic domain and the oxyanion binding region of subtilisin-like serine proteases. Members of the peptidases S8 and S35 clan include endopeptidases, exopeptidases and also a tripeptidyl-peptidase. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The S53 family contains a catalytic triad Glu/Asp/Ser. The stability of these enzymes may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 455 matched cddid_all.tbl CDD cd07479 cd07479 173805 Peptidases_S8_SKI-1_like Peptidase S8 family domain in SKI-1-like proteins. SKI-1 (type I membrane-bound subtilisin-kexin-isoenzyme) proteins are secretory Ca2+-dependent serine proteinases cleave at nonbasic residues: Thr, Leu, and Lys. SKI-1s play a critical role in the regulation of the synthesis and metabolism of cholesterol and fatty acid metabolism. Members of the peptidases S8 and S35 clan include endopeptidases, exopeptidases and also a tripeptidyl-peptidase. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The S53 family contains a catalytic triad Glu/Asp/Ser. The stability of these enzymes may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 255 matched cddid_all.tbl CDD cd07480 cd07480 173806 Peptidases_S8_12 Peptidase S8 family domain, uncharacterized subfamily 12. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 297 matched cddid_all.tbl CDD cd07481 cd07481 173807 Peptidases_S8_BacillopeptidaseF-like Peptidase S8 family domain in BacillopeptidaseF-like proteins. Bacillus subtilis produces and secretes proteases and other types of exoenzymes at the end of the exponential phase of growth. The ones that make up this group is known as bacillopeptidase F, encoded by bpr, a serine protease with high esterolytic activity which is inhibited by PMSF. Like other members of the peptidases S8 family these have a Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of these enzymes may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. 264 matched cddid_all.tbl CDD cd07482 cd07482 173808 Peptidases_S8_Lantibiotic_specific_protease Peptidase S8 family domain in Lantiobiotic (lanthionine-containing antibiotics) specific proteases. Lantiobiotic (lanthionine-containing antibiotics) specific proteases are very similar in structure to serine proteases. Lantibiotics are ribosomally synthesised antimicrobial agents derived from ribosomally synthesised peptides with antimicrobial activities against Gram-positive bacteria. The proteases that cleave the N-terminal leader peptides from lantiobiotics include: epiP, nsuP, mutP, and nisP. EpiP, from Staphylococcus, is thought to cleave matured epidermin. NsuP, a dehydratase from Streptococcus and NisP, a membrane-anchored subtilisin-like serine protease from Lactococcus cleave nisin. MutP is highly similar to epiP and nisP and is thought to process the prepeptide mutacin III of S. mutans. Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) clan include endopeptidases and exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin. The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base. However, the aspartic acid residue that acts as an electrophile is quite different. In S53 the it follows glutamic acid, while in S8 it precedes histidine. The stability of these enzymes may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. There is a great diversity in the characteristics of their members: some contain disulfide bonds, some are intracellular while others are extracellular, some function at extreme temperatures, and others at high or low pH values. 294 matched cddid_all.tbl CDD cd07483 cd07483 173809 Peptidases_S8_Subtilisin_Novo-like Peptidase S8 family domain in Subtilisin_Novo-like proteins. Subtilisins are a group of alkaline proteinases originating from different strains of Bacillus subtilis. Novo is one of the strains that produced enzymes belonging to this group. The enzymes obtained from the Novo and BPN' strains are identical. The Carlsburg and Novo subtilisins are thought to have arisen from a common ancestral protein. They have similar peptidase and esterase activities, pH profiles, catalyze transesterification reactions, and are both inhibited by diispropyl fluorophosphate, though they differ in 85 positions in the amino acid sequence. Members of the peptidases S8 and S35 clan include endopeptidases, exopeptidases and also a tripeptidyl-peptidase. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin.. The stability of these enzymes may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 291 matched cddid_all.tbl CDD cd07484 cd07484 173810 Peptidases_S8_Thermitase_like Peptidase S8 family domain in Thermitase-like proteins. Thermitase is a non-specific, trypsin-related serine protease with a very high specific activity. It contains a subtilisin like domain. The tertiary structure of thermitase is similar to that of subtilisin BPN'. It contains a Asp/His/Ser catalytic triad. Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) clan include endopeptidases and exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin. The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base. However, the aspartic acid residue that acts as an electrophile is quite different. In S53 the it follows glutamic acid, while in S8 it precedes histidine. The stability of these enzymes may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. There is a great diversity in the characteristics of their members: some contain disulfide bonds, some are intracellular while others are extracellular, some function at extreme temperatures, and others at high or low pH values. 260 matched cddid_all.tbl CDD cd07485 cd07485 173811 Peptidases_S8_Fervidolysin_like Peptidase S8 family domain in Fervidolysin. Fervidolysin found in Fervidobacterium pennivorans is an extracellular subtilisin-like keratinase. It is contains a signal peptide, a propeptide, and a catalytic region. The tertiary structure of fervidolysin is similar to that of subtilisin. It contains a Asp/His/Ser catalytic triad and is a member of the peptidase S8 (subtilisin and kexin) family. The catalytic triad is similar to that found in trypsin-like proteases, but it does not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin. The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid has the same role here as the histidine base. However, the aspartic acid residue that acts as an electrophile is quite different. In S53, it follows glutamic acid, while in S8 it precedes histidine. The stability of these enzymes may be enhanced by calcium; some members have been shown to bind up to 4 ions via binding sites with different affinity. There is a great diversity in the characteristics of their members: some contain disulfide bonds, some are intracellular while others are extracellular, some function at extreme temperatures, and others at high or low pH values. 273 matched cddid_all.tbl CDD cd07487 cd07487 173812 Peptidases_S8_1 Peptidase S8 family domain, uncharacterized subfamily 1. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 264 matched cddid_all.tbl CDD cd07488 cd07488 173813 Peptidases_S8_2 Peptidase S8 family domain, uncharacterized subfamily 2. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 247 matched cddid_all.tbl CDD cd07489 cd07489 173814 Peptidases_S8_5 Peptidase S8 family domain, uncharacterized subfamily 5. gap in seq This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 312 matched cddid_all.tbl CDD cd07490 cd07490 173815 Peptidases_S8_6 Peptidase S8 family domain, uncharacterized subfamily 6. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 254 matched cddid_all.tbl CDD cd07491 cd07491 173816 Peptidases_S8_7 Peptidase S8 family domain, uncharacterized subfamily 7. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 247 matched cddid_all.tbl CDD cd07492 cd07492 173817 Peptidases_S8_8 Peptidase S8 family domain, uncharacterized subfamily 8. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 222 matched cddid_all.tbl CDD cd07493 cd07493 173818 Peptidases_S8_9 Peptidase S8 family domain, uncharacterized subfamily 9. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 261 matched cddid_all.tbl CDD cd07494 cd07494 173819 Peptidases_S8_10 Peptidase S8 family domain, uncharacterized subfamily 10. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 298 matched cddid_all.tbl CDD cd07496 cd07496 173820 Peptidases_S8_13 Peptidase S8 family domain, uncharacterized subfamily 13. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 285 matched cddid_all.tbl CDD cd07497 cd07497 173821 Peptidases_S8_14 Peptidase S8 family domain, uncharacterized subfamily 14. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 311 matched cddid_all.tbl CDD cd07498 cd07498 173822 Peptidases_S8_15 Peptidase S8 family domain, uncharacterized subfamily 15. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. 242 matched cddid_all.tbl CDD cd07499 cd07499 319802 HAD_CBAP molecular class B acid phosphatases, similar to Escherichia coli AphA. class B acid phosphatases (CBAPs) have been detected in a minority of bacterial species which include a number of major pathogens such as Escherichia coli, Haemophilus influenzae, and Streptococcus pyogenes. This family includes the CBAP Escherichia coli AphA. The purified enzyme is a broad-spectrum nucleotidase highly active against both 3'- and 5'-mononucleotides and monodeoxynucleotides, which can also act as a phosphotransferase. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 185 matched cddid_all.tbl CDD cd07500 cd07500 319803 HAD_PSP phosphoserine phosphatase (PSP), similar to Methanococcus Jannaschii PSP and Saccharomyces cerevisiae SER2p. This family includes Methanococcus jannaschii PSP, and Saccharomyces cerevisiae phosphoserine phosphatase SER2p, EC 3.1.3.3, which participates in a pathway whereby serine and glycine are synthesized from the glycolytic intermediate 3-phosphoglycerate; phosphoserine phosphatase catalyzes the hydrolysis of phospho-L-serine to L-serine and inorganic phosphate, the third reaction in this pathway. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 180 matched cddid_all.tbl CDD cd07501 cd07501 319804 HAD_MDP-1_like eukaryotic hypothetical phosphotyrosine phosphatase MDP-1 and related phosphatases, similar to Bacillus cereus phosphonoacetaldehyde hydrolase and Streptomyces FkbH. This family includes eukaryotic magnesium-dependent phosphatase-1 (MDP-1) which is most likely a phosphotyrosine phosphatase catalyzing the dephosphorylation of tyrosine-phosphorylated proteins, Bacillus cereus phosphonoacetaldehyde hydrolase (phosphonatase)which catalyzes the hydrolysis of phosphonoacetaldehyde to acetaldehyde and phosphate using Mg(II) as cofactor, and sequences annotated as FkbH including BafAIV an FkbH-like protein from Streptomyces griseus encoded in ORF12 of the bafilomycin synthesis gene cluster. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 129 matched cddid_all.tbl CDD cd07502 cd07502 319805 HAD_PNKP-C C-terminal phosphatase domain of T4 polynucleotide kinase/phosphatase (PNKP) and related phosphatases. This family includes the C-terminal domain of the bifunctional enzyme T4 polynucleotide kinase/phosphatase, PNKP. The PNKP phosphatase domain can catalyze the hydrolytic removal of the 3'-phosphoryl of DNA, RNA and deoxynucleoside 3'-monophosphates. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 145 matched cddid_all.tbl CDD cd07503 cd07503 319806 HAD_HisB-N histidinol phosphate phosphatase and related phosphatases. This family includes the N-terminal domain of the Escherichia coli bifunctional enzyme histidinol-phosphate phosphatase/imidazole-glycerol-phosphate dehydratase, HisB. The N-terminal histidinol-phosphate phosphatase domain catalyzes the dephosphorylation of histidinol phosphate, the eight step of L-histidine biosynthesis. This family also includes Escherichia coli GmhB phosphatase which is highly specific for D-glycero-D-manno-heptose-1,7-bisphosphate, it removes the C(7)phosphate and not the C(1)phosphate, and this is the third essential step of lipopolysaccharide heptose biosynthesis. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 142 matched cddid_all.tbl CDD cd07504 cd07504 319807 HAD_5NT haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to human cytosolic IIIA and IIIB. 5'-nucleotidases dephosphorylate nucleoside 5prime-monophosphates. This family includes human 5'-nucleotidase, cytosolic IIIA (cN-IIIA, previously called cN-III; NT5C3A) the main pyrimidine 5'-nucleotidase in erythrocytes which dephosphorylates the pyrimidine nucleotides CMP, UMP, TMP, and the purine 7-methylguanosine monophosphate (m7GM), and possesses phosphotransferase activity. It also includes human 5'-nucleotidase, cytosolic IIIB (cN-IIIB; NT5C3B) which has a strong preference for m7GMP, dephosphorylates CMP and UMP and, with significantly lower efficiency, GMP and AMP, and can also act as a phosphotransferase. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 273 matched cddid_all.tbl CDD cd07505 cd07505 319808 HAD_BPGM-like beta-phosphoglucomutase-like family of the haloacid dehalogenase-like (HAD) hydrolase superfamily. This family represents the beta-phosphoglucomutase-like family of the haloacid dehalogenase-like (HAD) hydrolase superfamily. Family members include Lactococcus lactis beta-PGM, a mutase which catalyzes the interconversion of beta-D-glucose 1-phosphate (G1P) and D-glucose 6-phosphate (G6P), Saccharomyces cerevisiae phosphatases GPP1 and GPP2 that dephosphorylate DL-glycerol-3-phosphate and DOG1 and DOG2 that dephosphorylate 2-deoxyglucose-6-phosphate, and Escherichia coli 6-phosphogluconate phosphatase YieH. It belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 143 matched cddid_all.tbl CDD cd07506 cd07506 319809 HAD_like uncharacterized family of the haloacid dehalogenase-like (HAD) hydrolase superfamily. The haloacid dehalogenase-like (HAD) hydrolases are a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. Members are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 115 matched cddid_all.tbl CDD cd07507 cd07507 319810 HAD_Pase haloacid dehalogenase-like superfamily phosphatase similar to Pyrococcus horikoshii mannosyl-3-phosphoglycerate phosphatase and Persephonella marina glucosyl-3-phosphoglycerate phosphatase. This family includes Pyrococcus horikoshii and Thermus thermophilus HB27 mannosyl-3-phosphoglycerate phosphatases (MpgPs) which catalyze the dephosphorylation of alpha-mannosyl-3-phosphoglycerate (MPG) to produce alpha-mannosylglycerate (MG), and Persephonella marina glucosyl-3-phosphoglycerate phosphatase (GpgP) which catalyzes the dephosphorylation of glucosyl-3-phosphoglycerate (GPG) to produce glucosylglycerate (GG). It also includes Methanococcoides burtonii MpgP protein which is able to dephosphorylate GPG to GG, and MPG to MG. Similar flexibilities in substrate specificity have been confirmed in vitro for the MpgPs from Thermus thermophiles and Pyrococcus horikoshii. Screens with natural substrates have not yet detected activity for another member Escherichia Coli YedP. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 255 matched cddid_all.tbl CDD cd07508 cd07508 319811 HAD_Pase_UmpH-like haloacid dehalogenase-like superfamily phosphatases, UmpH/NagD family. Phosphatases in this UmpH/NagD family include Escherichia coli UmpH UMP phosphatase/NagD nucleotide phosphatase , Mycobacterium tuberculosis Rv1692 glycerol 3-phosphate phosphatase, human PGP phosphoglycolate phosphatase, Schizosaccharomyces pombe PHO2 p-nitrophenylphosphatase, Bacillus AraL a putative sugar phosphatase, and Plasmodium falciparum para nitrophenyl phosphate phosphatase PNPase. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 270 matched cddid_all.tbl CDD cd07509 cd07509 319812 HAD_PPase inorganic pyrophosphatase similar to a human phospholysine phosphohistidine inorganic pyrophosphate phosphatase (LHPP). LHPP hydrolyzes nitrogen-phosphorus bonds in phospholysine, phosphohistidine and imidodiphosphate as well as oxygen-phosphorus bonds in inorganic pyrophosphate in vitro. This family also includes human haloacid dehalogenase like hydrolase domain containing 2 protine (HDHD2) a phosphatase which may be involved in polygenic hypertension. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 248 matched cddid_all.tbl CDD cd07510 cd07510 319813 HAD_Pase_UmpH-like UmpH/NagD family phosphatase, similar to human PGP phosphoglycolate phosphatase and Schizosaccharomyces pombe PHO2 p-nitrophenylphosphatase. This subfamily includes the phosphoglycolate phosphatases (human PGP and Arabidopsis thaliana PGLP2) and p-nitrophenylphosphatases (Schizosaccharomyces pombe PHO2 and Saccharomyces PHO13p). It belongs to the UmpH/NagD phosphatase family, and to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 282 matched cddid_all.tbl CDD cd07511 cd07511 319814 HAD_like uncharacterized family of the haloacid dehalogenase-like (HAD) hydrolase superfamily, similar to the uncharacterized human CECR5 (cat eye syndrome critical region protein 5). This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 136 matched cddid_all.tbl CDD cd07512 cd07512 319815 HAD_PGPase haloacid dehalogenase-like superfamily phosphoglycolate phosphatase, similar to Rhodobacter sphaeroides CbbZ. Phosphoglycolate phosphatase catalyzes the dephosphorylation of phosphoglycolate; its activity requires divalent cations, especially Mg++. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 214 matched cddid_all.tbl CDD cd07514 cd07514 319816 HAD_Pase phosphatase, similar to Thermoplasma acidophilum TA0175 phosphoglycolate phosphatase (PCPase), and Pyrococcus horikoshii PH1421, a magnesium-dependent phosphatase; belongs to the haloacid dehalogenase-like superfamily. Thermoplasma acidophilum TA0175 phosphoglycolate phosphatase (PGPase) catalyzes the magnesium-dependent dephosphorylation of phosphoglycolate. This family also includes Pyrococcus horikoshii OT3 PH1421, a magnesium-dependent phosphatase. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 139 matched cddid_all.tbl CDD cd07515 cd07515 319817 HAD-like uncharacterized family of the haloacid dehalogenase-like (HAD) hydrolase superfamily. The haloacid dehalogenase-like (HAD) hydrolases are a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. Members are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 131 matched cddid_all.tbl CDD cd07516 cd07516 319818 HAD_Pase phosphatase, similar to Escherichia coli Cof and Thermotoga maritima TM0651; belongs to the haloacid dehalogenase-like superfamily. Escherichia coli Cof is involved in the hydrolysis of HMP-PP (4-amino-2-methyl-5-hydroxymethylpyrimidine pyrophosphate, an intermediate in thiamin biosynthesis), Cof also has phosphatase activity against the coenzymes pyridoxal phosphate (PLP) and FMN. Thermotoga maritima TM0651 acts as a phosphatase with a phosphorylated carbohydrate molecule as a possible substrate. Escherichia coli YbhA is also a member of this family and catalyzes the dephosphorylation of PLP, YbhA can also hydrolyze erythrose-4-phosphate and fructose-1,6-bis-phosphate. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 253 matched cddid_all.tbl CDD cd07517 cd07517 319819 HAD_HPP phosphatase, similar to Bacteroides thetaiotaomicron VPI-5482 BT4131 hexose phosphate phosphatase; belongs to the haloacid dehalogenase-like superfamily. Bacteroides thetaiotaomicron VPI-5482 BT4131 is a phosphatase with preference for hexose phosphates. In addition this family includes uncharacterized Bacillus subtilis YkrA, a putative phosphatase and uncharacterized Streptococcus pyogenes MGAS10394 a putative bifunctional phosphatase/peptidyl-prolyl cis-trans isomerase. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 213 matched cddid_all.tbl CDD cd07518 cd07518 319820 HAD_YbiV-Like Escherichia coli YbiV sugar phosphatase/phosphotransferase and related proteins; belongs to the haloacid dehalogenase-like superfamily. Escherichia coli YbiV can act as both a sugar phosphatase and as a phosphotransferase. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 184 matched cddid_all.tbl CDD cd07519 cd07519 319821 HAD_PTase hydrolase domain of the bifunctional HAD hydrolase/UbiA family prenyltransferase proteins and related domains; belongs to the haloacid dehalogenase-like superfamily. This family includes bifunctional enzymes that have both an N-terminal HAD hydrolase domain and a C-terminal UbiA family prenyltransferase domain. The haloacid dehalogenase-like (HAD) hydrolases are a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. Members are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. Many characterized members of the UbiA prenyltransferase family are aromatic prenyltransferases (PTases) and play an important role in the biosynthesis of heme, chlorophyll, vitamin E, and vitamin K. PTases catalyze the regioselective transfer of prenyl moieties onto a wide variety of substrates and play an important role in many biosynthetic pathways. 105 matched cddid_all.tbl CDD cd07520 cd07520 319822 HAD_like uncharacterized family of the haloacid dehalogenase-like (HAD) hydrolase superfamily. The haloacid dehalogenase-like (HAD) hydrolases are a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. Members are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 144 matched cddid_all.tbl CDD cd07521 cd07521 319823 HAD_FCP1-like human CTD phosphatase subunit 1 (CTDP1/FCP1) and related proteins; belongs to the haloacid dehalogenase-like superfamily. Human CTDP1/FCP1 is a protein phosphatase which dephosphorylates the phosphorylated C terminus (CTD) of RNA polymerase II. CTD phosphorylation is a key mechanism of regulation of gene expression in eukaryotes. CTDP1/FCP1 may have other roles in in transcription regulation independent of its phosphatase activity. This family also includes human translocase of inner mitochondrial membrane 50 (TIMM50), CTD small phosphatase like (CTDSPL) and CTD small phosphatase like 2 (CTDSPL2), Saccharomyces cerevisiae (nuclear envelope morphology protein 1) Nem1p, and Xenopus Dullard. Yeast Nem1p in complex with Spo7p dephosphorylates the nuclear membrane-associated phosphatidic acid phosphatase, Smp2p, which may be part of a signaling cascade playing a role in nuclear membrane biogenesis. Xenopus Dullard is a potential regulator of neural tube development. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 134 matched cddid_all.tbl CDD cd07522 cd07522 319824 HAD_cN-II cytosolic 5'-nucleotidase II (cN-II) similar to human NT5DC1 (5'-nucleotidase domain-containing protein 1) and NT5DC2. Cytosolic 5'-nucleotidase II (cN-II), also known as purine 5'-nucleotidase, IMP-GMP specific nucleotidase, or high Km 5prime-nucleotidase, catalyzes the dephosphorylation of 6-hydroxypurine nucleoside monophosphates. It is ubiquitously expressed and likely to play an important role in the regulation of purine nucleotide interconversions and in the regulation of IMP and GMP pools within the cell. It is also acts as a phosphotransferase, catalyzing the reverse reaction, the transfer of a phosphate from a monophosphate substrate to a nucleoside acceptor, to form a nucleoside monophosphate. The nucleoside acceptor is preferentially inosine and deoxyinosine, phosphate donors include any 6-hydroxypurine monophosphate substrate of the nucleotidase reaction. Both the dephosphorylation and phosphotransferase reactions are allosterically activated by adenine-based nucleotides and 2,3-bisphosphoglycerate. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 352 matched cddid_all.tbl CDD cd07523 cd07523 319825 HAD_YsbA-like uncharacterized family of the haloacid dehalogenase-like superfamily, similar to the uncharacterized Lactococcus lactis YsbA. The specific function of Lactococcus lactis YsbA is unknown. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases 173 matched cddid_all.tbl CDD cd07524 cd07524 319826 HAD_Pase phosphatase, similar to Bacillus subtilis MtnX; belongs to the haloacid dehalogenase-like superfamily. Bacillus subtilis recycles two toxic byproducts of polyamine metabolism, methylthioadenosine and methylthioribose, into methionine by a salvage pathway. The sixth reaction in this pathway is catalyzed by B. subtilis MtnX: the dephosphorylation of 2- hydroxy-3-keto-5-methylthiopentenyl-1-phosphate (HKMTP- 1-P) into 1,2-dihydroxy-3-keto-5-methylthiopentene. The hydrolysis of HK-MTP-1-P is a two-step mechanism involving the formation of a transiently phosphorylated aspartyl intermediate. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 211 matched cddid_all.tbl CDD cd07525 cd07525 319827 HAD_like uncharacterized family of the haloacid dehalogenase-like (HAD) hydrolase superfamily. The haloacid dehalogenase-like (HAD) hydrolases are a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. Members are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 253 matched cddid_all.tbl CDD cd07526 cd07526 319828 HAD_BPGM_like subfamily of beta-phosphoglucomutase-like family, similar to Escherichia coli 6-phosphogluconate phosphatase YieH. This subfamily includes Escherichia coli YieH/HAD3 an 6-phosphogluconate phosphatase, which can hydrolyzed purines and pyrimidines as secondary substrates. It belongs to the beta-phosphoglucomutase-like family whose other members include Lactococcus lactis beta-PGM, a mutase which catalyzes the interconversion of beta-D-glucose 1-phosphate (G1P) and D-glucose 6-phosphate (G6P), Saccharomyces cerevisiae phosphatases GPP1 and GPP2 that dephosphorylate DL-glycerol-3-phosphate, and DOG1 and DOG2 that dephosphorylate 2-deoxyglucose-6-phosphate. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 141 matched cddid_all.tbl CDD cd07527 cd07527 319829 HAD_ScGPP-like subfamily of beta-phosphoglucomutase-like family, similar to Saccharomyces cerevisiae DL-glycerol-3-phosphate phosphatase (GPP1p/ Rhr2p and GPP2p/HOR2p) and 2-deoxyglucose-6-phosphate phosphatase (DOG1p and DOG2p). This subfamily includes Saccharomyces cerevisiae DL-glycerol-3-phosphate phosphatase (GPP1p/ Rhr2p and GPP2p/HOR2p) and 2-deoxyglucose-6-phosphate phosphatase (DOG1p and DOG2p). GPP1p and GPP2p are involved in glycerol biosynthesis, GPP1 is induced in response to both anaerobic and hyperosmotic stress, GPP2 is induced in response to hyperosmotic or oxidative stress, and during diauxic shift; overexpression of DOG1 or DOG2 confers 2-deoxyglucose resistance. These belong to the beta-phosphoglucomutase-like family whose other members include Lactococcus lactis beta-PGM, a mutase which catalyzes the interconversion of beta-D-glucose 1-phosphate (G1P) and D-glucose 6-phosphate (G6P), and Escherichia coli 6-phosphogluconate phosphatase YieH. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 205 matched cddid_all.tbl CDD cd07528 cd07528 319830 HAD_CbbY-like subfamily of beta-phosphoglucomutase-like family, similar to Rhodobacter sphaeroides xylulose-1,5-bisphosphate phosphatase CbbY. This family includes Rhodobacter sphaeroides and Arabidopsis thaliana xylulose-1,5-bisphosphate phosphatase CbbY which convert xylulose-1,5-bisphosphate (a potent inhibitor of Ribulose-1,5-bisphosphate carboxylase/oxygenase, Rubisco), to the non-inhibitory compound xylulose-5-phosphate. It belongs to the beta-phosphoglucomutase-like family whose other members include Lactococcus lactis beta-PGM, a mutase which catalyzes the interconversion of beta-D-glucose 1-phosphate (G1P) and D-glucose 6-phosphate (G6P), Saccharomyces cerevisiae phosphatases GPP1 and GPP2 that dephosphorylate DL-glycerol-3-phosphate and DOG1 and DOG2 that dephosphorylate 2-deoxyglucose-6-phosphate, and Escherichia coli 6-phosphogluconate phosphatase YieH. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 199 matched cddid_all.tbl CDD cd07529 cd07529 319831 HAD_AtGPP-like subfamily of beta-phosphoglucomutase-like family, similar to Arabidopsis thaliana Gpp1 and Gpp2. This subfamily includes Arabidopsis thaliana AtGpp1 and AtGpp2, and Drosophila GS1-like protein (Dmel\Gs1l) of unknown function. AtGpp1 and AtGpp2 are constitutively expressed in all the Arabidopsis tissues and unaffected under abiotic stress. Overexpression of AtGpp2 in transgenic Arabidopsis plants increases the specific DL-glycerol-3-phosphatase activity and improves the plants tolerance to salt, osmotic and oxidative stress. It belongs to the beta-phosphoglucomutase-like family whose other members include Lactococcus lactis beta-PGM, a mutase which catalyzes the interconversion of beta-D-glucose 1-phosphate (G1P) and D-glucose 6-phosphate (G6P), Saccharomyces cerevisiae phosphatases GPP1 and GPP2 that dephosphorylate DL-glycerol-3-phosphate and DOG1 and DOG2 that dephosphorylate 2-deoxyglucose-6-phosphate, and Escherichia coli 6-phosphogluconate phosphatase YieH. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 192 matched cddid_all.tbl CDD cd07530 cd07530 319832 HAD_Pase_UmpH-like UmpH/NagD family phosphatase, similar to Escherichia coli UmpH UMP phosphatase/NagD nucleotide phosphatase and Mycobacterium tuberculosis Rv1692 glycerol 3-phosphate phosphatase. Escherichia coli UmpH/NagD is a ribonucleoside tri-, di-, and monophosphatase with a preference for purines, it shows peak activity with UMP and functions in UMP-degradation. It is also an effective phosphatase with AMP, GMP and CMP. Mycobacterium tuberculosis phosphatase, Rv1692 is a glycerol 3-phosphate phosphatase. Rv1692 is the final enzyme involved in glycerophospholipid recycling/catabolism. This subfamily belongs to the UmpH/NagD phosphatase family, and to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 247 matched cddid_all.tbl CDD cd07531 cd07531 319833 HAD_Pase_UmpH-like UmpH/NagD family phosphatase, similar to Bacillus AraL phosphatase, a putative sugar phosphatase. Bacillus subtilis AraL is a phosphatase displaying activity towards different sugar phosphate substrates; it is encoded by the arabinose metabolic operon araABDLMNPQ-abfA and may play a role in the dephosphorylation of substrates related to l-arabinose metabolism. This subfamily belongs to the UmpH/NagD phosphatase family, and to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 252 matched cddid_all.tbl CDD cd07532 cd07532 319834 HAD_PNPase_UmpH-like UmpH/NagD family phosphatase para nitrophenyl phosphate phosphatase, similar to Plasmodium falciparum PNPase. Plasmodium falciparum para nitrophenyl phosphate phosphatase (PNPase) catalyzes the dephosphorylation of thiamine monophosphate to thiamine, other substrates on which its active are nucleotides, phosphorylated sugars, pyridoxal-5-phosphate, and paranitrophenyl phosphate. This subfamily belongs to the UmpH/NagD phosphatase family, and to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 286 matched cddid_all.tbl CDD cd07533 cd07533 319835 HAD_like uncharacterized family of the haloacid dehalogenase-like (HAD) hydrolase superfamily, similar to Parvibaculum lavamentivorans HAD-superfamily hydrolase, subfamily IA, variant 1. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 207 matched cddid_all.tbl CDD cd07534 cd07534 319836 HAD_CAP molecular class C acid phosphatases, similar to Haemophilus influenzae e (P4) acid phosphatase; belongs to the haloacid dehalogenase-like hydrolase superfamily. Molecular class C acid phosphatases (CAPs) are nonspecific acid phosphatases with generally broad substrate specificity and optimum activity at neutral to acidic pH. Members include Haemophilus influenzae lipoprotein e (P4), Elizabethkingia meningosepticum OlpA, Helicobacter pylori HppA, Enterobacter sp. 4 acid phosphatase PhoI, and Streptococcus pyogenes M1 GAS LppC. Lipoprotein e (P4) exhibits phosphomonoesterase activity with aryl phosphate substrates including nicotinamide mononucleotide (NMN), tyrosine phosphate, phenyl phosphate, p-nitrophenyl phosphate, and 4-methylumbelliferyl phosphate. The role of P4 in NAD+ uptake appears to be the dephosphorylation of NMN to nicotinamide riboside, which is then taken up by the organism. Elizabethkingia meningosepticum OlpA is a broad-spectrum nucleotidase with preference for 5'-nucleotides, it efficiently hydrolyzes nucleotide monophosphates, with a strong preference for 5'-nucleotides and for 3'-AMP; OlpA can also hydrolyze sugar phosphates and beta-glycerol phosphate, although with a lower efficiency. Helicobacter pylori HppA is also a 5' nucleotidase. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 196 matched cddid_all.tbl CDD cd07535 cd07535 319837 HAD_VSP vegetative storage proteins similar to soybean VSPalpha and VSPbeta proteins; belongs to the haloacid dehalogenase-like superfamily. Soybean [Glycine max (L.) Merr.] vegetative storage protein VSPalpha and VSPbeta levels were identified as storage proteins due to their abundance and pattern of expression in plant tissues, they accumulate to almost one-half the amount of soluble leaf protein when soybean plants are continually depodded. They possess acid phosphatase activity which appears to be low compared to several other plant acid phosphatases, it increases in the leaves of depodded soybean plants, but to no more than 0.1% of the total acid phosphatase activity in these leaves. This acid phosphatase activity has maximal activity at pH 5.0 - 5.5, and can liberate Pi from different substrates such as napthyl acid phosphate, carboxyphenyl phosphate, sugar-phosphates, glyceraldehyde 3-phosphate, dihydroxyacetone phosphate, phosphoenolpyruvate, ATP, ADP, PPi, and short chain polyphosphates; they cleave phosphoenolpyruvate, ATP, ADP, PPI, and polyphosphates most efficiently. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Soybean VSPalpha and VSPbeta lack this active site aspartate, other members of this family have this aspartate and may be more active. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 186 matched cddid_all.tbl CDD cd07536 cd07536 319838 P-type_ATPase_APLT Aminophospholipid translocases (APLTs), similar to Saccharomyces cerevisiae Dnf1-3p, Drs2p, Neo1p, and human ATP8A2, -9B, -10D, -11B, and -11C. Aminophospholipid translocases (APLTs), also known as type 4 P-type ATPases, act as flippases, and translocate specific phospholipids from the exoplasmic leaflet to the cytoplasmic leaflet of biological membranes. Yeast Dnf1 and Dnf2 mediate the transport of phosphatidylethanolamine, phosphatidylserine, and phosphatidylcholine from the outer to the inner leaflet of the plasma membrane. Mammalian ATP11C may selectively transports PS and PE from the outer leaflet of the plasma membrane to the inner leaflet. The yeast Neo1p localizes to the endoplasmic reticulum and the Golgi complex and plays a role in membrane trafficking within the endomembrane system. Human putative ATPase phospholipid transporting 9B, ATP9B, localizes to the trans-golgi network in a CDC50 protein-independent manner. It also includes Arabidopsis phospholipid flippases including ALA1, and Caenorhabditis elegans flippases, including TAT-1, the latter has been shown to facilitate the inward transport of phosphatidylserine. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 805 matched cddid_all.tbl CDD cd07538 cd07538 319839 P-type_ATPase uncharacterized subfamily of P-type ATPase transporters. This subfamily contains P-type ATPase transporters of unknown function. The P-type ATPases, are a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids. They are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. A general characteristic of P-type ATPases is a bundle of transmembrane helices which make up the transport path, and three domains on the cytoplasmic side of the membrane. Members include pumps that transport various light metal ions, such as H(+), Na(+), K(+), Ca(2+), and Mg(2+), pumps that transport indispensable trace elements, such as Zn(2+) and Cu(2+), pumps that remove toxic heavy metal ions, such as Cd2+, and pumps such as aminophospholipid translocases which transport phosphatidylserine and phosphatidylethanolamine. 653 matched cddid_all.tbl CDD cd07539 cd07539 319840 P-type_ATPase uncharacterized subfamily of P-type ATPase transporters. This subfamily contains P-type ATPase transporters of unknown function. The P-type ATPases, are a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids. They are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. A general characteristic of P-type ATPases is a bundle of transmembrane helices which make up the transport path, and three domains on the cytoplasmic side of the membrane. Members include pumps that transport various light metal ions, such as H(+), Na(+), K(+), Ca(2+), and Mg(2+), pumps that transport indispensable trace elements, such as Zn(2+) and Cu(2+), pumps that remove toxic heavy metal ions, such as Cd2+, and pumps such as aminophospholipid translocases which transport phosphatidylserine and phosphatidylethanolamine. 634 matched cddid_all.tbl CDD cd07541 cd07541 319841 P-type_ATPase_APLT_Neo1-like Aminophospholipid translocases (APLTs), similar to Saccharomyces cerevisiae Neo1p and human putative APLT, ATP9B. Aminophospholipid translocases (APLTs), also known as type 4 P-type ATPases, act as a flippases, and translocate specific phospholipids from the exoplasmic leaflet to the cytoplasmic leaflet of biological membranes. The yeast Neo1 gene is an essential gene; Neo1p localizes to the endoplasmic reticulum and the Golgi complex and plays a role in membrane trafficking within the endomembrane system. Also included in this sub family is human putative ATPase phospholipid transporting 9B, ATP9B, which localizes to the trans-golgi network in a CDC50 protein-independent manner. Levels of ATP9B, along with levels of other ATPase genes, may contribute to expressivity of and atypical presentations of Hailey-Hailey disease (HHD), and the ATP9B gene has recently been identified as a putative Alzheimer's disease loci. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 792 matched cddid_all.tbl CDD cd07542 cd07542 319842 P-type_ATPase_cation P-type cation-transporting ATPases, similar to human ATPase type 13A2 (ATP13A2) protein and Saccharomyces cerevisiae Ypk9p. Saccharomyces cerevisiae Yph9p localizes to the yeast vacuole and may play a role in sequestering heavy metal ions, its deletion confers sensitivity for growth for cadmium, manganese, nickel or selenium. Human ATP13A2 (PARK9/CLN12) is a lysosomal transporter with zinc as the possible substrate. Mutation in the ATP13A2 gene has been linked to Parkinson's disease and Kufor-Rakeb syndrome, and to neuronal ceroid lipofuscinoses. ATP13A3/AFURS1 is a candidate gene for oculo auriculo vertebral spectrum (OAVS), being one of nine genes included in a 3q29 microduplication in a patient with OAVS. Mutation in the human ATP13A4 may be involved in a speech-language disorder. This subfamily also includes zebrafish ATP13A2 a lysosome-specific transmembrane ATPase protein of unknown function which plays a crucial role during embryonic development, its deletion is lethal. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 760 matched cddid_all.tbl CDD cd07543 cd07543 319843 P-type_ATPase_cation P-type cation-transporting ATPases, similar to human cation-transporting ATPase type 13A1 (ATP13A1) and Saccharomyces manganese-transporting ATPase 1 Spf1p. Saccharomyces Spf1p may mediate manganese transport into the endoplasmic reticulum (ER); one consequence of deletion of SPF1 is severe ER stress. This subfamily also includes Arabidopsis thaliana MIA (Male Gametogenesis Impaired Anthers) protein which is highly abundant in the endoplasmic reticulum and small vesicles of developing pollen grains and tapetum cells. The MIA gene functionally complements a mutant in the SPF1 from Saccharomyces cerevisiae. The expression of ATP13A1 has been followed during mouse development, ATP13A1 transcript expression showed an increase as development progressed, with the highest expression at the peak of neurogenesis. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 804 matched cddid_all.tbl CDD cd07544 cd07544 319844 P-type_ATPase_HM P-type heavy metal-transporting ATPase; uncharacterized subfamily. Uncharacterized subfamily of the heavy metal-transporting ATPases (Type IB ATPases) which transport heavy metal ions (Cu(+), Cu(2+), Zn(2+), Cd(2+), Co(2+), etc.) across biological membranes. The characteristic N-terminal heavy metal associated (HMA) domain of this group is essential for the binding of metal ions. This subclass of P-type ATPase is also referred to as CPx-type ATPases because their amino acid sequences contain a characteristic CPC or CPH motif associated with a stretch of hydrophobic amino acids and N-terminal ion-binding sequences. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 596 matched cddid_all.tbl CDD cd07545 cd07545 319845 P-type_ATPase_Cd-like P-type heavy metal-transporting ATPase, similar to Staphylococcus aureus plasmid pI258 CadA, a cadmium-efflux ATPase. CadA from gram-positive Staphylococcus aureus plasmid pI258 is required for full Cd(2+) and Zn(2+) resistance. This subfamily also includes CadA, from the gram-negative bacilli, Stenotrophomonas maltophilia D457R, which is a cadmium efflux pump acquired as part of a cluster of antibiotic and heavy metal resistance genes from gram-positive bacteria. This subclass of P-type ATPase is also referred to as CPx-type ATPases because their amino acid sequences contain a characteristic CPC or CPH motif associated with a stretch of hydrophobic amino acids and N-terminal ion-binding sequences. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 599 matched cddid_all.tbl CDD cd07546 cd07546 319846 P-type_ATPase_Pb_Zn_Cd2-like P-type heavy metal-transporting ATPase, similar to Escherichia coli ZntA which is selective for Pb(2+), Zn(2+), and Cd(2+). Escherichia coli ZntA mediates resistance to toxic levels of selected divalent metal ions. ZntA has the highest selectivity for Pb(2+), followed by Zn(2+) and Cd(2+); it also shows low levels of activity with Cu(2+), Ni(2+), and Co(2+). It is upregulated by the transcription factor ZntR at high zinc concentrations. This subclass of P-type ATPase is also referred to as CPx-type ATPases because their amino acid sequences contain a characteristic CPC or CPH motif associated with a stretch of hydrophobic amino acids and N-terminal ion-binding sequences. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 597 matched cddid_all.tbl CDD cd07548 cd07548 319847 P-type_ATPase-Cd_Zn_Co_like P-type heavy metal-transporting ATPase, similar to Bacillus subtilis CadA which appears to transport cadmium, zinc and cobalt but not copper out of the cell. Bacillus subtilis CadA/YvgW appears to transport cadmium, zinc and cobalt but not copper, out of the cell. Functions in metal ion resistance and cellular metal ion homeostasis. CadA/YvgW is also important for sporulation in B. subtilis, the significant specific expression of the cadA/yvgW gene during the late stage of sporulation, is controlled by forespore-specific sigma factor, sigma G, and mother cell-specific sigma factor, sigma E. This subfamily also includes Helicobacter pylori CadA an essential resistance pump with ion specificity towards Cd(2+), Zn(2+) and Co(2+), and Zn-transporting ATPase, ZiaA(N) in Synechocystis PCC 6803. Transcription of ziaA is induced by Zn under the control of the Zn responsive repressor ZiaR. This subclass of P-type ATPase is also referred to as CPx-type ATPases because their amino acid sequences contain a characteristic CPC or CPH motif associated with a stretch of hydrophobic amino acids and N-terminal ion-binding sequences. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 604 matched cddid_all.tbl CDD cd07550 cd07550 319848 P-type_ATPase_HM P-type heavy metal-transporting ATPase; uncharacterized subfamily. Uncharacterized subfamily of the heavy metal-transporting ATPases (Type IB ATPases) which transport heavy metal ions (Cu(+), Cu(2+), Zn(2+), Cd(2+), Co(2+), etc.) across biological membranes. The characteristic N-terminal heavy metal associated (HMA) domain of this group is essential for the binding of metal ions. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 592 matched cddid_all.tbl CDD cd07551 cd07551 319849 P-type_ATPase_HM_ZosA_PfeT-like P-type heavy metal-transporting ATPase, similar to Bacillus subtilis ZosA/PfeT which transports copper, and perhaps zinc under oxidative stress, and perhaps ferrous iron. Bacillus subtilis ZosA/PfeT (previously known as YkvW) transports copper, it may also transport zinc under oxidative stress and may also be involved in ferrous iron efflux. ZosA/PfeT is expressed under the regulation of the peroxide-sensing repressor PerR. It is involved in competence development. Disruption of the zosA/pfeT gene results in low transformability. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 611 matched cddid_all.tbl CDD cd07552 cd07552 319850 P-type_ATPase_Cu-like P-type heavy metal-transporting ATPase, similar to Archaeoglobus fulgidus CopB, a Cu(2+)-ATPase. Archaeoglobus fulgidus CopB transports Cu(2+) from the cytoplasm to the exterior of the cell using ATP as energy source, it transports preferentially Cu(2+) over Cu(+), it is activated by Cu(2+) with high affinity and partially by Cu(+) and Ag(+). This subclass of P-type ATPase is also referred to as CPx-type ATPases because their amino acid sequences contain a characteristic CPC or CPH motif associated with a stretch of hydrophobic amino acids and N-terminal ion-binding sequences. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 632 matched cddid_all.tbl CDD cd07553 cd07553 319851 P-type_ATPase_HM P-type heavy metal-transporting ATPase; uncharacterized subfamily. Uncharacterized subfamily of the heavy metal-transporting ATPases (Type IB ATPases) which transport heavy metal ions (Cu(+), Cu(2+), Zn(2+), Cd(2+), Co(2+), etc.) across biological membranes. The characteristic N-terminal heavy metal associated (HMA) domain of this group is essential for the binding of metal ions. This subclass of P-type ATPase is also referred to as CPx-type ATPases because their amino acid sequences contain a characteristic CPC or CPH motif associated with a stretch of hydrophobic amino acids and N-terminal ion-binding sequences. This subfamily belongs to the P-type ATPases, a large family of integral membrane transporters that are of critical importance in all kingdoms of life. They generate and maintain (electro-) chemical gradients across cellular membranes, by translocating cations, heavy metals and lipids, and are distinguished from other main classes of transport ATPases (F- , V- , and ABC- type) by the formation of a phosphorylated (P-) intermediate state in the catalytic cycle. 610 matched cddid_all.tbl CDD cd07556 cd07556 143637 Nucleotidyl_cyc_III Class III nucleotidyl cyclases. Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's). The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways. 133 matched cddid_all.tbl CDD cd07557 cd07557 143638 trimeric_dUTPase Trimeric dUTP diphosphatases. Trimeric dUTP diphosphatases, or dUTPases, are the most common family of dUTPase, found in bacteria, eukaryotes, and archaea. They catalyze the hydrolysis of the dUTP-Mg complex (dUTP-Mg) into dUMP and pyrophosphate. This reaction is crucial for the preservation of chromosomal integrity as it removes dUTP and therefore reduces the cellular dUTP/dTTP ratio, and prevents dUTP from being incorporated into DNA. It also provides dUMP as the precursor for dTTP synthesis via the thymidylate synthase pathway. dUTPases are homotrimeric, except some monomeric viral dUTPases, which have been shown to mimic a trimer. Active sites are located at the subunit interface. 92 matched cddid_all.tbl CDD cd07559 cd07559 143471 ALDH_ACDHII_AcoD-like Ralstonia eutrophus NAD+-dependent acetaldehyde dehydrogenase II and Staphylococcus aureus AldA1 (SACOL0154)-like. Included in this CD is the NAD+-dependent, acetaldehyde dehydrogenase II (AcDHII, AcoD, EC=1.2.1.3) from Ralstonia (Alcaligenes) eutrophus H16 involved in the catabolism of acetoin and ethanol, and similar proteins, such as, the dimeric dihydrolipoamide dehydrogenase of the acetoin dehydrogenase enzyme system of Klebsiella pneumonia. Also included are sequences similar to the NAD+-dependent chloroacetaldehyde dehydrogenases (AldA and AldB) of Xanthobacter autotrophicus GJ10 which are involved in the degradation of 1,2-dichloroethane, as well as, the uncharacterized aldehyde dehydrogenase from Staphylococcus aureus (AldA1, locus SACOL0154) and other similar sequences. 480 matched cddid_all.tbl CDD cd07560 cd07560 143476 Peptidase_S41_CPP C-terminal processing peptidase; serine protease family S41. The C-terminal processing peptidase (CPP, EC 3.4.21.102) also known as tail-specific protease (tsp), the photosystem II D1 C-terminal processing protease (D1P), and other related S41 protease family members are present in this CD. CPP is synthesized as a precursor form with a carboxyl-terminal extension. It specifically recognizes a C-terminal tripeptide, Xaa-Yaa-Zaa, in which Xaa is preferably Ala or Leu, Yaa is preferably Ala or Tyr and Zaa is preferably Ala, but then cleaves at a variable distance from the C-terminus. The C-terminal carboxylate group is essential, and proteins where this group is amidated are not substrates. This family of proteases contains the PDZ domain that promotes protein-protein interactions and is important for substrate recognition. The active site consists of a serine/lysine catalytic dyad. The bacterial CCP-1 is believed to be important for the degradation of incorrectly synthesized proteins as well as protection from thermal and osmotic stresses. In E. coli, it is involved in the cleavage of a C-terminal peptide of 11 residues from the precursor form of penicillin-binding protein 3 (PBP3). In the plant chloroplast, the enzyme removes the C-terminal extension of the D1 polypeptide of photosystem II, allowing the light-driven assembly of the tetranuclear manganese cluster, which is responsible for photosynthetic water oxidation. 211 matched cddid_all.tbl CDD cd07561 cd07561 143477 Peptidase_S41_CPP_like C-terminal processing peptidase-like; serine protease family S41. Bacterial protease homologs of the S41 family related to C-terminal processing peptidase (CPP). CPP-1 is believed to be important for the degradation of incorrectly synthesized proteins as well as protection from thermal and osmotic stresses. CPP is synthesized with an extension on its carboxyl-terminus and specifically recognizes a C-terminal tripeptide, but cleaves at variable distance from the C-terminus. The CPP active site consists of a serine/lysine catalytic dyad. Conservation of these residues is seen in the CPP-like proteins of this group. CPP proteins contain a PDZ domain that promotes protein-protein interactions and is important for substrate recognition however, most of CPP-like proteins only have an internal fragment or lack the PDZ domain. 256 matched cddid_all.tbl CDD cd07562 cd07562 143478 Peptidase_S41_TRI Tricorn protease; serine protease family S41. The tricorn protease (TRI), a member of the S41 peptidase family and named for its tricorn-like shape, exists only in some archaea and eubacteria. It has been shown to act as a carboxypeptidase, involved in the degradation of proteasomal products to preferentially yield di- and tripeptides, with subsequent and final degradations to free amino acid residues by tricorn interacting factors, F1, F2 and F3. Tricorn is a hexameric D3-symmetric protease of 720kD, and can self-associate further into a giant icosahedral capsid structure containing twenty copies of the complex. Each tricorn peptidase monomer consists of five structural domains: a six-bladed beta-propeller and a seven-bladed beta-propeller that limit access to the active site, the two domains (C1 and C2) that carry the active site residues, and a PDZ-like domain (proposed to be important for substrate recognition) between the C1 and C2 domains. The active site tetrad residues are distributed between the C1 and C2 domains, with serine and histidine on C1 and serine and glutamate on C2. 266 matched cddid_all.tbl CDD cd07563 cd07563 143479 Peptidase_S41_IRBP Interphotoreceptor retinoid-binding protein; serine protease family S41. Interphotoreceptor retinoid-binding protein (IRBP) is a homolog of the S41 protease, C-terminal processing peptidase (CTPase) family. It is thought to facilitate the compartmentalization of the visual cycle that requires poorly soluble and potentially toxic retinoids to cross the aqueous subretinal space between the photoreceptors and the retinal pigment epithelium (RPE). IRBP is secreted by photoreceptors into the interphotoreceptor matrix (IPM) where it is rapidly turned over by a combination of RPE and photoreceptor endocytosis. It is the most abundant soluble protein component of the IPM, consisting of homologous modules, each repeat structure arising through the duplication (as in teleost IRBP) or quadruplication (in tetrapods) of an ancient gene, arisen in the early evolution of the vertebrate eye. IRBP has been shown to promote the release of all-trans retinol from photoreceptors and facilitates its delivery to the RPE. Conversely, IRBP can promote the release of 11-cis-retinal from the RPE, prevent its isomerization in the subretinal space, and transfer it to photoreceptors. In vivo evidence implicates IRBP as a retinoid transporter in the visual cycle, suggesting a critical role for IRBP in cone function essential for human vision. IRBP is a dominant autoimmune antigen in the eye; IRBP proteolysis analysis has proven a useful biomarker for autoimmune uveitis (AU) disorders, a major cause of blindness. This family also includes a chlamydia-secreted protein, designated chlamydia protease-like activity factor (CPAF), known to degrade host proteins, enabling Chlamydia to evade host defenses and replicate. 250 matched cddid_all.tbl CDD cd07564 cd07564 143588 nitrilases_CHs Nitrilases, cyanide hydratase (CH)s, and similar proteins (class 1 nitrilases). Nitrilases (nitrile aminohydrolases, EC:3.5.5.1) hydrolyze nitriles (RCN) to ammonia and the corresponding carboxylic acid. Most nitrilases prefer aromatic nitriles, some prefer arylacetonitriles and others aliphatic nitriles. This group includes the nitrilase cyanide dihydratase (CDH), which hydrolyzes inorganic cyanide (HCN) to produce formate. It also includes cyanide hydratase (CH), which hydrolyzes HCN to formamide. This group includes four Arabidopsis thaliana nitrilases (Ath)NIT1-4. AthNIT1-3 have a strong substrate preference for phenylpropionitrile (PPN) and other nitriles which may originate from the breakdown of glucosinolates. The product of PPN hydrolysis, phenylacetic acid has auxin activity. AthNIT1-3 can also convert indoacetonitrile to indole-3-acetic acid (IAA, auxin), but with a lower affinity and velocity. From their expression patterns, it has been speculated that NIT3 may produce IAA during the early stages of germination, and that NIT3 may produce IAA during embryo development and maturation. AthNIT4 has a strong substrate specificity for the nitrile, beta-cyano-L-alanine (Ala(CN)), an intermediate of cyanide detoxification. AthNIT4 has both a nitrilase activity and a nitrile hydratase (NHase) activity, which generate aspartic acid and asparagine respectively from Ala(CN). NHase catalyzes the hydration of nitriles to their corresponding amides. This subgroup belongs to a larger nitrilase superfamily comprised of belong to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this subgroup corresponds to class 1. 297 matched cddid_all.tbl CDD cd07565 cd07565 143589 aliphatic_amidase aliphatic amidases (class 2 nitrilases). Aliphatic amidases catalyze the hydrolysis of short-chain aliphatic amides to form ammonia and the corresponding organic acid. This group includes Pseudomonas aeruginosa (Pa) AmiE, the amidase from Geobacillus pallidus RAPc8 (RAPc8 amidase), and Helicobacter pylori (Hp) AmiE and AmiF. PaAimE and HpAmiE hydrolyze various very short aliphatic amides, including propionamide, acetamide and acrylamide. HpAmiF is a formamidase which specifically hydrolyzes formamide. These proteins belong to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this subgroup corresponds to class 2. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. HpAmiE , HpAmiF, and RAPc8 amidase, and PaAimE appear to be homohexameric enzymes, trimer of dimers. 291 matched cddid_all.tbl CDD cd07566 cd07566 143590 ScNTA1_like Saccharomyces cerevisiae N-terminal amidase NTA1, and related proteins (class 3 nitrilases). Saccharomyces cerevisiae NTA1 functions in the N-end rule protein degradation pathway. It specifically deaminates the N-terminal asparagine and glutamine residues of substrates of this pathway, to aspartate and glutamate respectively, these latter are the destabilizing residues. This subgroup belongs to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this subgroup corresponds to class 3. 295 matched cddid_all.tbl CDD cd07567 cd07567 143591 biotinidase_like biotinidase and vanins (class 4 nitrilases). These secondary amidases participate in vitamin recycling. Biotinidase (EC 3.5.1.12) has both a hydrolase and a transferase activity. It hydrolyzes free biocytin or small biotinyl-peptides produced during the proteolytic degradation of biotin-dependent carboxylases, to release free biotin (vitamin H), and it can transfer biotin to acceptor molecules such as histones. Biotinidase deficiency in humans is an autosomal recessive disorder characterized by neurological and cutaneous symptoms. This subgroup includes the three human vanins, vanin1-3. Vanins are ectoenzymes, Vanin-1, and -2 are membrane associated, vanin-3 is secreted. They are pantotheinases (EC 3.5.1.92, pantetheine hydrolase), which convert pantetheine, to pantothenic acid (vitamin B5) and cysteamine (2-aminoethanethiol, a potent anti-oxidant). They are potential targets for therapeutic intervention in inflammatory disorders. Vanin-1 deficient mice lacking free cysteamine are less susceptible to intestinal inflammation, and expression of vanin-1 and -3 is induced as part of the inflammatory-regenerative differentiation program of human epidermis. This subgroup belongs to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this subgroup corresponds to class 4. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. 299 matched cddid_all.tbl CDD cd07568 cd07568 143592 ML_beta-AS_like mammalian-like beta-alanine synthase (beta-AS) and similar proteins (class 5 nitrilases). This family includes mammalian-like beta-AS (EC 3.5.1.6, also known as beta-ureidopropionase or N-carbamoyl-beta-alanine amidohydrolase). This enzyme catalyzes the third and final step in the catabolic pyrimidine catabolic pathway responsible for the degradation of uracil and thymine, the hydrolysis of N-carbamyl-beta-alanine and N-carbamyl-beta-aminoisobutyrate to the beta-amino acids, beta-alanine and beta-aminoisobutyrate respectively. This family belongs to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this subgroup corresponds to class 5. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. Beta-ASs from this subgroup are found in various oligomeric states, dimer (human), hexamer (calf liver), decamer (Arabidopsis and Zea mays), and in the case of Drosophila melanogaster beta-AS, as a homooctamer assembled as a left-handed helical turn, with the possibility of higher order oligomers formed by adding dimers at either end. Rat beta-AS changes its oligomeric state (hexamer, trimer, dodecamer) in response to allosteric effectors. Eukaryotic Saccharomyces kluyveri beta-AS belongs to a different superfamily. 287 matched cddid_all.tbl CDD cd07569 cd07569 143593 DCase N-carbamyl-D-amino acid amidohydrolase (DCase, class 6 nitrilases). DCase hydrolyses N-carbamyl-D-amino acids to produce D-amino acids. It is an important biocatalyst in the pharmaceutical industry, producing useful D-amino acids for example in the preparation of beta-lactam antibiotics. This subgroup belongs to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this subgroup corresponds to class 6. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. Agrobacterium radiobacter DCase forms a tetramer (dimer of dimers). Some DCases may form trimers. 302 matched cddid_all.tbl CDD cd07570 cd07570 143594 GAT_Gln-NAD-synth Glutamine aminotransferase (GAT, glutaminase) domain of glutamine-dependent NAD synthetases (class 7 and 8 nitrilases). Glutamine-dependent NAD synthetases are bifunctional enzymes, which have an N-terminal GAT domain and a C-terminal NAD+ synthetase domain. The GAT domain is a glutaminase (EC 3.5.1.2) which hydrolyses L-glutamine to L-glutamate and ammonia. The ammonia is used by the NAD+ synthetase domain in the ATP-dependent amidation of nicotinic acid adenine dinucleotide. Glutamine aminotransferases are categorized depending on their active site residues into different unrelated classes. This class of GAT domain belongs to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this subgroup corresponds to classes 7 and 8. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. Mycobacterium tuberculosis glutamine-dependent NAD+ synthetase forms a homooctamer. 261 matched cddid_all.tbl CDD cd07571 cd07571 143595 ALP_N-acyl_transferase Apolipoprotein N-acyl transferase (class 9 nitrilases). ALP N-acyl transferase (Lnt), is an essential membrane-bound enzyme in gram-negative bacteria, which catalyzes the N-acylation of apolipoproteins, the final step in lipoprotein maturation. This is a reverse amidase (i.e. condensation) reaction. This subgroup belongs to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this subgroup corresponds to class 9. 270 matched cddid_all.tbl CDD cd07572 cd07572 143596 nit Nit1, Nit 2, and related proteins, and the Nit1-like domain of NitFhit (class 10 nitrilases). This subgroup includes mammalian Nit1 and Nit2, the Nit1-like domain of the invertebrate NitFhit, and various uncharacterized bacterial and archaeal Nit-like proteins. Nit1 and Nit2 are candidate tumor suppressor proteins. In NitFhit, the Nit1-like domain is encoded as a fusion protein with the non-homologous tumor suppressor, fragile histidine triad (Fhit). Mammalian Nit1 and Fhit may affect distinct signal pathways, and both may participate in DNA damage-induced apoptosis. Nit1 is a negative regulator in T cells. Overexpression of Nit2 in HeLa cells leads to a suppression of cell growth through cell cycle arrest in G2. These Nit proteins and the Nit1-like domain of NitFhit belong to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this subgroup corresponds to class 10. 265 matched cddid_all.tbl CDD cd07573 cd07573 143597 CPA N-carbamoylputrescine amidohydrolase (CPA) (class 11 nitrilases). CPA (EC 3.5.1.53, also known as N-carbamoylputrescine amidase and carbamoylputrescine hydrolase) converts N-carbamoylputrescine to putrescine, a step in polyamine biosynthesis in plants and bacteria. This subgroup includes Arabidopsis thaliana CPA, also known as nitrilase-like 1 (NLP1), and Pseudomonas aeruginosa AguB. This subgroup belongs to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this subgroup corresponds to class 11. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer; P. aeruginosa AugB is a homohexamer, Arabidopsis thaliana NLP1 is a homooctomer. 284 matched cddid_all.tbl CDD cd07574 cd07574 143598 nitrilase_Rim1_like Uncharacterized subgroup of the nitrilase superfamily; some members of this subgroup have an N-terminal RimI domain (class 12 nitrilases). Some members of this subgroup are implicated in post-translational modification, as they contain an N-terminal GCN5-related N-acetyltransferase (GNAT) protein RimI family domain. The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this subgroup corresponds to class 12. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. 280 matched cddid_all.tbl CDD cd07575 cd07575 143599 Xc-1258_like Xanthomonas campestris XC1258 and related proteins, members of the nitrilase superfamily (putative class 13 nitrilases). Uncharacterized subgroup belonging to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), class 13 represents proteins that at the time were difficult to place in a distinct similarity group; this subgroup either represents a new class or one that was included previously in class 13. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. XC1258 is a homotetramer. 252 matched cddid_all.tbl CDD cd07576 cd07576 143600 R-amidase_like Pseudomonas sp. MCI3434 R-amidase and related proteins (putative class 13 nitrilases). Pseudomonas sp. MCI3434 R-amidase hydrolyzes (R,S)-piperazine-2-tert-butylcarboxamide to form (R)-piperazine-2-carboxylic acid. It does so with strict R-stereoselectively. Its preferred substrates are carboxamide compounds which have the amino or imino group connected to their beta- or gamma-carbon. This subgroup belongs to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), class 13 represents proteins that at the time were difficult to place in a distinct similarity group. It has been suggested that this subgroup represents a new class. Members of the nitrilase superfamily generally form homomeric complexes, the basic building block of which is a homodimer. Native R-amidase however appears to be a monomer. 254 matched cddid_all.tbl CDD cd07577 cd07577 143601 Ph0642_like Pyrococcus horikoshii Ph0642 and related proteins, members of the nitrilase superfamily (putative class 13 nitrilases). Uncharacterized subgroup of the nitrilase superfamily. This superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. Pyrococcus horikoshii Ph0642 is a hypothetical protein belonging to this subgroup. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). This subgroup was classified as belonging to class 13, which represents proteins that at the time were difficult to place in a distinct similarity group. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. 259 matched cddid_all.tbl CDD cd07578 cd07578 143602 nitrilase_1_R1 First nitrilase domain of an uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases). Members of this subgroup have two nitrilase domains. This is the first of those two domains. The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins that at the time were difficult to place in a distinct similarity group; this subgroup represents either a new class or one that was included previously in class 13. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. 258 matched cddid_all.tbl CDD cd07579 cd07579 143603 nitrilase_1_R2 Second nitrilase domain of an uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases). Members of this subgroup have two nitrilase domains. This is the second of those two domains. The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins that at the time were difficult to place in a distinct similarity group; this subgroup represents either a new class or one that was included previously in class 13. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. 279 matched cddid_all.tbl CDD cd07580 cd07580 143604 nitrilase_2 Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases). The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins that at the time were difficult to place in a distinct similarity group; this subgroup represents either a new class or one that was included previously in class 13. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. 268 matched cddid_all.tbl CDD cd07581 cd07581 143605 nitrilase_3 Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases). The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins that at the time were difficult to place in a distinct similarity group; this subgroup represents either a new class or one that was included previously in class 13. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. 255 matched cddid_all.tbl CDD cd07582 cd07582 143606 nitrilase_4 Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases). The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins that at the time were difficult to place in a distinct similarity group; this subgroup represents either a new class or one that was included previously in class 13. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. 294 matched cddid_all.tbl CDD cd07583 cd07583 143607 nitrilase_5 Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases). The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins that at the time were difficult to place in a distinct similarity group; this subgroup represents either a new class or one that was included previously in class 13. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. 253 matched cddid_all.tbl CDD cd07584 cd07584 143608 nitrilase_6 Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases). The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins that at the time were difficult to place in a distinct similarity group; this subgroup represents either a new class or one that was included previously in class 13. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. 258 matched cddid_all.tbl CDD cd07585 cd07585 143609 nitrilase_7 Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases). The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins that at the time were difficult to place in a distinct similarity group; this subgroup represents either a new class or one that was included previously in class 13. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. 261 matched cddid_all.tbl CDD cd07586 cd07586 143610 nitrilase_8 Uncharacterized subgroup of the nitrilase superfamily (putative class 13 nitrilases). The nitrilase superfamily is comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13). Class 13 represents proteins that at the time were difficult to place in a distinct similarity group; this subgroup represents either a new class or one that was included previously in class 13. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. 269 matched cddid_all.tbl CDD cd07587 cd07587 143611 ML_beta-AS mammalian-like beta-alanine synthase (beta-AS) and similar proteins (class 5 nitrilases). This subgroup includes mammalian-like beta-AS (EC 3.5.1.6, also known as beta-ureidopropionase or N-carbamoyl-beta-alanine amidohydrolase). This enzyme catalyzes the third and final step in the catabolic pyrimidine catabolic pathway responsible for the degradation of uracil and thymine, the hydrolysis of N-carbamyl-beta-alanine and N-carbamyl-beta-aminoisobutyrate to the beta-amino acids, beta-alanine and beta-aminoisobutyrate respectively. This subgroup belongs to a larger nitrilase superfamily comprised of nitrile- or amide-hydrolyzing enzymes and amide-condensing enzymes, which depend on a Glu-Lys-Cys catalytic triad. This superfamily has been classified in the literature based on global and structure based sequence analysis into thirteen different enzyme classes (referred to as 1-13), this subgroup corresponds to class 5. Members of this superfamily generally form homomeric complexes, the basic building block of which is a homodimer. Beta-ASs from this subgroup are found in various oligomeric states, dimer (human), hexamer (calf liver), decamer (Arabidopsis and Zea mays), and in the case of Drosophila melanogaster beta-AS, as a homooctamer assembled as a left-handed helical turn, with the possibility of higher order oligomers formed by adding dimers at either end. Rat beta-AS changes its oligomeric state (hexamer, trimer, dodecamer) in response to allosteric effectors. Eukaryotic Saccharomyces kluyveri beta-AS belongs to a different superfamily. 363 matched cddid_all.tbl CDD cd07588 cd07588 153272 BAR_Amphiphysin The Bin/Amphiphysin/Rvs (BAR) domain of Amphiphysins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Amphiphysins function primarily in endocytosis and other membrane remodeling events. They contain an N-terminal BAR domain with an additional N-terminal amphipathic helix (an N-BAR), a variable central domain, and a C-terminal SH3 domain. This subfamily is composed of different isoforms of amphiphysin and Bridging integrator 2 (Bin2). Amphiphysin I proteins, enriched in the brain and nervous system, contain domains that bind clathrin, Adaptor Protein complex 2 (AP2), dynamin and synaptojanin. They function in synaptic vesicle endocytosis. Some amphiphysin II isoforms, also called Bridging integrator 1 (Bin1), are localized in many different tissues and may function in intracellular vesicle trafficking. In skeletal muscle, Bin1 plays a role in the organization and maintenance of the T-tubule network. Bin2 is mainly expressed in hematopoietic cells and is upregulated during granulocyte differentiation. The N-BAR domains of amphiphysins form a curved dimer with a positively-charged concave face that can drive membrane bending and curvature. 211 matched cddid_all.tbl CDD cd07589 cd07589 153273 BAR_DNMBP The Bin/Amphiphysin/Rvs (BAR) domain of Dynamin Binding Protein. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. DyNamin Binding Protein (DNMBP), also called Tuba, is a Cdc42-specific Guanine nucleotide Exchange Factor (GEF) that binds dynamin and various actin regulatory proteins. It serves as a link between dynamin function, Rho GTPase signaling, and actin dynamics. It plays an important role in regulating cell junction configuration. DNMBP contains BAR and SH3 domains as well as a Dbl Homology domain (DH domain), which harbors GEF activity. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domain of DNMBP may be involved in binding to membranes. The gene encoding DNMBP is a candidate gene for late onset Alzheimer's disease. 195 matched cddid_all.tbl CDD cd07590 cd07590 153274 BAR_Bin3 The Bin/Amphiphysin/Rvs (BAR) domain of Bridging integrator 3. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Bridging integrator 3 (Bin3) is widely expressed in many tissues except in the brain. It plays roles in regulating filamentous actin localization and in cell division. In humans, the Bin3 gene is located in chromosome 8p21.3, a region that is implicated in cancer suppression. Homozygous inactivation of the Bin3 gene in mice led to the development of cataracts and an increased likelihood of lymphomas during aging, suggesting a role for Bin3 in lens development and cancer suppression. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 225 matched cddid_all.tbl CDD cd07591 cd07591 153275 BAR_Rvs161p The Bin/Amphiphysin/Rvs (BAR) domain of Saccharomyces cerevisiae Reduced viability upon starvation protein 161 and similar proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of fungal proteins with similarity to Saccharomyces cerevisiae Reduced viability upon starvation protein 161 (Rvs161p) and Schizosaccharomyces pombe Hob3 (homolog of Bin3). S. cerevisiae Rvs161p plays a role in regulating cell polarity, actin cytoskeleton polarization, vesicle trafficking, endocytosis, bud formation, and the mating response. It forms a heterodimer with another BAR domain protein Rvs167p. Rvs161p and Rvs167p share common functions but are not interchangeable. Their BAR domains cannot be replaced with each other and the overexpression of one cannot suppress the mutant phenotypes of the other. S. pombe Hob3 is important in regulating filamentous actin localization and may be required in activating Cdc42 and recruiting it to cell division sites. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 224 matched cddid_all.tbl CDD cd07592 cd07592 153276 BAR_Endophilin_A The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-A. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Endophilins are accessory proteins, localized at synapses, which interact with the endocytic proteins, dynamin and synaptojanin. They are essential for synaptic vesicle formation from the plasma membrane. They interact with voltage-gated calcium channels, thus linking vesicle endocytosis to calcium regulation. They also play roles in virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. Endophilins contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. They are classified into two types, A and B. Vertebrates contain three endophilin-A isoforms. Endophilin-A proteins are enriched in the brain and play multiple roles in receptor-mediated endocytosis. They tubulate membranes and regulate calcium influx into neurons to trigger the activation of the endocytic machinery. They are also involved in the sorting of plasma membrane proteins, actin filament assembly, and the uncoating of clathrin-coated vesicles for fusion with endosomes. The BAR domains of endophilin-A1 and A3 form crescent-shaped dimers that can detect membrane curvature and drive membrane bending. 223 matched cddid_all.tbl CDD cd07593 cd07593 153277 BAR_MUG137_fungi The Bin/Amphiphysin/Rvs (BAR) domain of Schizosaccharomyces pombe Meiotically Up-regulated Gene 137 protein and similar proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. This subfamily is composed predominantly of uncharacterized fungal proteins with similarity to Schizosaccharomyces pombe Meiotically Up-regulated Gene 137 protein (MUG137), which may play a role in meiosis and sporulation in fission yeast. MUG137 contains an N-terminal BAR domain and a C-terminal SH3 domain, similar to endophilins. Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 215 matched cddid_all.tbl CDD cd07594 cd07594 153278 BAR_Endophilin_B The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-B. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. Endophilins contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. They are classified into two types, A and B. Vertebrates contain two endophilin-B isoforms. Endophilin-B proteins are cytoplasmic proteins expressed mainly in the heart, placenta, and skeletal muscle. 229 matched cddid_all.tbl CDD cd07595 cd07595 153279 BAR_RhoGAP_Rich-like The Bin/Amphiphysin/Rvs (BAR) domain of Rich-like Rho GTPase Activating Proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of Rho and Rac GTPase activating proteins (GAPs) with similarity to GAP interacting with CIP4 homologs proteins (Rich). Members contain an N-terminal BAR domain, followed by a Rho GAP domain, and a C-terminal prolin-rich region. Vertebrates harbor at least three Rho GAPs in this subfamily including Rich1, Rich2, and SH3-domain binding protein 1 (SH3BP1). Rich1 and Rich2 play complementary roles in the establishment and maintenance of cell polarity. Rich1 is a Cdc42- and Rac-specific GAP that binds to polarity proteins through the scaffold protein angiomotin and plays a role in maintaining the integrity of tight junctions. Rich2 is a Rac GAP that interacts with CD317 and plays a role in actin cytoskeleton organization and the maintenance of microvilli in polarized epithelial cells. SH3BP1 is a Rac GAP that inhibits Rac-mediated platelet-derived growth factor (PDGF)-induced membrane ruffling. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domain of Rich1 has been shown to form oligomers, bind membranes and induce membrane tubulation. 244 matched cddid_all.tbl CDD cd07596 cd07596 153280 BAR_SNX The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 218 matched cddid_all.tbl CDD cd07597 cd07597 153281 BAR_SNX8 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 8. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX8 and the yeast counterpart Mvp1p are involved in sorting and delivery of late-Golgi proteins, such as carboxypeptidase Y, to vacuoles. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 246 matched cddid_all.tbl CDD cd07598 cd07598 153282 BAR_FAM92 The Bin/Amphiphysin/Rvs (BAR) domain of Family with sequence similarity 92 (FAM92). BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. This group is composed of proteins from the family with sequence similarity 92 (FAM92), which were originally identified by the presence of the unknown domain DUF1208. This domain shows similarity to the BAR domains of sorting nexins. Mammals contain at least two member types, FAM92A and FAM92B, which may exist in many variants. The Xenopus homolog of FAM92A1, xVAP019, is essential for embryo survival and cell differentiation. FAM92A1 may be involved in regulating cell proliferation and apoptosis. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 211 matched cddid_all.tbl CDD cd07599 cd07599 153283 BAR_Rvs167p The Bin/Amphiphysin/Rvs (BAR) domain of Saccharomyces cerevisiae Reduced viability upon starvation protein 167 and similar proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of fungal proteins with similarity to Saccharomyces cerevisiae Reduced viability upon starvation protein 167 (Rvs167p) and Schizosaccharomyces pombe Hob1 (homolog of Bin1). S. cerevisiae Rvs167p plays a role in regulation of the actin cytoskeleton, endocytosis, and sporulation. It forms a heterodimer with another BAR domain protein Rvs161p. Rvs161p and Rvs167p share common functions but are not interchangeable. Their BAR domains cannot be replaced with each other and the overexpression of one cannot suppress the mutant phenotypes of the other. Rvs167p also interacts with the GTPase activating protein (GAP) Gyp5p, which is involved in ER to Golgi vesicle trafficking. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 216 matched cddid_all.tbl CDD cd07600 cd07600 153284 BAR_Gvp36 The Bin/Amphiphysin/Rvs (BAR) domain of Saccharomyces cerevisiae Golgi vesicle protein of 36 kDa and similar proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. Proteomic analysis shows that Golgi vesicle protein of 36 kDa (Gvp36) may be involved in vesicular trafficking and nutritional adaptation. A Saccharomyces cerevisiae strain deficient in Gvp36 shows defects in growth, in actin cytoskeleton polarization, in endocytosis, in vacuolar biogenesis, and in the cell cycle. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 242 matched cddid_all.tbl CDD cd07601 cd07601 153285 BAR_APPL The Bin/Amphiphysin/Rvs (BAR) domain of Adaptor protein, Phosphotyrosine interaction, PH domain and Leucine zipper containing proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Adaptor protein, Phosphotyrosine interaction, PH domain and Leucine zipper containing (APPL) proteins are effectors of the small GTPase Rab5 that function in endosome-mediated signaling. They contain BAR, pleckstrin homology (PH) and phosphotyrosine binding (PTB) domains. They form homo- and hetero-oligomers that are mediated by their BAR domains, and are localized to cytoplasmic membranes. Vertebrates contain two APPL proteins, APPL1 and APPL2. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 215 matched cddid_all.tbl CDD cd07602 cd07602 153286 BAR_RhoGAP_OPHN1-like The Bin/Amphiphysin/Rvs (BAR) domain of Oligophrenin1-like Rho GTPase Activating Proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of Rho and Rac GTPase activating proteins (GAPs) with similarity to oligophrenin1 (OPHN1). Members contain an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, and a Rho GAP domain. Some members contain a C-terminal SH3 domain. Vertebrates harbor at least three Rho GAPs in this subfamily including OPHN1, GTPase Regulator Associated with Focal adhesion kinase (GRAF), GRAF2, and an uncharacterized protein called GAP10-like. OPHN1, GRAF and GRAF2 show GAP activity towards RhoA and Cdc42. In addition, OPHN1 is active towards Rac. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domains of OPHN1 and GRAF directly interact with their Rho GAP domains and inhibit their activity. The autoinhibited proteins are able to bind membranes and tubulate liposomes, showing that the membrane-tubulation and GAP-inhibitory functions of the BAR domains can occur simultaneously. 207 matched cddid_all.tbl CDD cd07603 cd07603 153287 BAR_ACAPs The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of ACAPs (ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins), which are Arf GTPase activating proteins (GAPs) containing an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. Vertebrates contain at least three members, ACAP1, ACAP2, and ACAP3. ACAP1 and ACAP2 are Arf6-specific GAPs, involved in the regulation of endocytosis, phagocytosis, cell adhesion and migration, by mediating Arf6 signaling. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 200 matched cddid_all.tbl CDD cd07604 cd07604 153288 BAR_ASAPs The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of ASAPs (ArfGAP with SH3 domain, ANK repeat and PH domain containing proteins), which are Arf GTPase activating proteins (GAPs) with similarity to ACAPs (ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins) in that they contain an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and ankyrin (ANK) repeats. However, ASAPs contain an additional C-terminal SH3 domain. ASAPs function in regulating cell growth, migration, and invasion. Vertebrates contain at least three members, ASAP1, ASAP2, and ASAP3. ASAP1 and ASAP2 shows GTPase activating protein (GAP) activity towards Arf1 and Arf5. They do not show GAP activity towards Arf6, but is able to mediate Arf6 signaling by binding stably to GTP-Arf6. ASAP3 is an Arf6-specific GAP. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domain of ASAP1 mediates membrane bending, is essential for function, and autoinhibits GAP activity by interacting with the PH and/or Arf GAP domains. 215 matched cddid_all.tbl CDD cd07605 cd07605 153289 I-BAR_IMD Inverse (I)-BAR, also known as the IRSp53/MIM homology Domain (IMD), a dimerization module that binds and bends membranes. Inverse (I)-BAR (or IMD) is a member of the Bin/Amphiphysin/Rvs (BAR) domain family. It is a dimerization and lipid-binding module that bends membranes and induces membrane protrusions in the opposite direction compared to classical BAR and F-BAR domains, which produce membrane invaginations. IMD domains are found in Insulin Receptor tyrosine kinase Substrate p53 (IRSp53), Missing in Metastasis (MIM), and Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2-like (BAIAP2L) proteins. These are multi-domain proteins that act as scaffolding proteins and transducers of a variety of signaling pathways that link membrane dynamics and the underlying actin cytoskeleton. Most members contain an N-terminal IMD, an SH3 domain, and a WASP homology 2 (WH2) actin-binding motif at the C-terminus, exccept for MIM which does not carry an SH3 domain. Some members contain additional domains and motifs. The IMD domain binds and bundles actin filaments, binds membranes and produces membrane protrusions, and interacts with the small GTPase Rac. 223 matched cddid_all.tbl CDD cd07606 cd07606 153290 BAR_SFC_plant The Bin/Amphiphysin/Rvs (BAR) domain of the plant protein SCARFACE (SFC). BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. The plant protein SCARFACE (SFC), also called VAscular Network 3 (VAN3), is a plant ACAP (ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein), an Arf GTPase Activating Protein (GAP) that plays a role in the trafficking of auxin efflux regulators from the plasma membrane to the endosome. It is required for the normal vein patterning in leaves. SCF contains an N-terminal BAR domain, followed by a Pleckstrin Homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 202 matched cddid_all.tbl CDD cd07607 cd07607 153291 BAR_SH3P_plant The Bin/Amphiphysin/Rvs (BAR) domain of the plant SH3 domain-containing proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. This group is composed of proteins with similarity to Arabidopsis thaliana SH3 domain-containing proteins 1 (SH3P1) and 2 (SH3P2). SH3P1 is involved in the trafficking of clathrin-coated vesicles. It is localized at the plasma membrane and is associated with vesicles of the trans-Golgi network. Yeast complementation studies reveal that SH3P1 has similar functions to the Saccharomyces cerevisiae Rvs167p, which is involved in endocytosis and actin cytoskeletal arrangement. Members of this group contain an N-terminal BAR domain and a C-terminal SH3 domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 209 matched cddid_all.tbl CDD cd07608 cd07608 153292 BAR_ArfGAP_fungi The Bin/Amphiphysin/Rvs (BAR) domain of uncharacterized fungal Arf GAP proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. This group is composed of uncharacterized fungal proteins containing an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, and an Arf GTPase Activating Protein (GAP) domain. These proteins may play roles in Arf-mediated functions involving membrane dynamics. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 192 matched cddid_all.tbl CDD cd07609 cd07609 153293 BAR_SIP3_fungi The Bin/Amphiphysin/Rvs (BAR) domain of fungal Snf1p-interacting protein 3. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions including organelle biogenesis, membrane trafficking or remodeling, and cell division and migration. This group is composed of mostly uncharacterized fungal proteins with similarity to Saccharomyces cerevisiae Snf1p-interacting protein 3 (SIP3). These proteins contain an N-terminal BAR domain followed by a Pleckstrin Homology (PH) domain. SIP3 interacts with SNF1 protein kinase and activates transcription when anchored to DNA. It may function in the SNF1 pathway. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 214 matched cddid_all.tbl CDD cd07610 cd07610 153294 FCH_F-BAR The Extended FES-CIP4 Homology (FCH) or F-BAR (FCH and Bin/Amphiphysin/Rvs) domain, a dimerization module that binds and bends membranes. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. F-BAR domain containing proteins, also known as Pombe Cdc15 homology (PCH) family proteins, include Fes and Fer tyrosine kinases, PACSINs/Syndapins, FCHO, PSTPIP, CIP4-like proteins and srGAPs. Many members also contain an SH3 domain and play roles in endocytosis. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. These tubules have diameters larger than those observed with N-BARs. The F-BAR domains of some members such as NOSTRIN and Rgd1 are important for the subcellular localization of the protein. 191 matched cddid_all.tbl CDD cd07611 cd07611 153295 BAR_Amphiphysin_I_II The Bin/Amphiphysin/Rvs (BAR) domain of Amphiphysin I and II. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Amphiphysins function primarily in endocytosis and other membrane remodeling events. They contain an N-terminal BAR domain with an additional N-terminal amphipathic helix (an N-BAR), a variable central domain, and a C-terminal SH3 domain. Amphiphysin I proteins, enriched in the brain and nervous system, contain domains that bind clathrin, Adaptor Protein complex 2 (AP2), dynamin and synaptojanin. They function in synaptic vesicle endocytosis. Some amphiphysin II isoforms, also called Bridging integrator 1 (Bin1), are localized in many different tissues and may function in intracellular vesicle trafficking. In skeletal muscle, Bin1 plays a role in the organization and maintenance of the T-tubule network. The N-BAR domain of amphiphysin forms a curved dimer with a positively-charged concave face that can drive membrane bending and curvature. Human autoantibodies to amphiphysin-1 hinder GABAergic signaling and contribute to the pathogenesis of paraneoplastic stiff-person syndrome. Mutations in amphiphysin-2 (BIN1) are associated with autosomal recessive centronuclear myopathy. 211 matched cddid_all.tbl CDD cd07612 cd07612 153296 BAR_Bin2 The Bin/Amphiphysin/Rvs (BAR) domain of Bridging integrator 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Bridging integrator 2 (Bin2) is a BAR domain containing protein that is mainly expressed in hematopoietic cells. It is upregulated during granulocyte differentiation and is thought to function primarily in this lineage. The BAR domain of Bin2 is closely related to the BAR domains of amphiphysins, which function primarily in endocytosis and other membrane remodeling events. Amphiphysins contain an N-terminal BAR domain with an additional N-terminal amphipathic helix (an N-BAR), a variable central domain, and a C-terminal SH3 domain. Unlike amphiphysins, Bin2 does not appear to contain a C-terminal SH3 domain. Amphiphysin I proteins, enriched in the brain and nervous system, function in synaptic vesicle endocytosis. Some amphiphysin II isoforms, also called Bridging integrator 1 (Bin1), function in intracellular vessicle trafficking. Bin2 can form a stable complex with Bin1 in cells but cannot replace the function of Bin1, and thus, appears to harbor a nonredundant function. The N-BAR domain of amphiphysin forms a curved dimer with a positively-charged concave face that can drive membrane bending and curvature. 211 matched cddid_all.tbl CDD cd07613 cd07613 153297 BAR_Endophilin_A1 The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-A1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. Endophilins contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. They are classified into two types, A and B. Vertebrates contain three endophilin-A isoforms. Endophilin-A proteins are enriched in the brain and play multiple roles in receptor-mediated endocytosis. Endophilin-A1 (or endophilin-1) is also referred to as SH3P4 (SH3 domain containing protein 4) or SH3GL2 (SH3 domain containing Grb2-like protein 2). It is localized in presynaptic nerve terminals. It plays many roles in clathrin-dependent endocytosis of synaptic vesicles including early vesicle formation, ubiquitin-dependent sorting of plasma membrane proteins, and regulation of calcium influx into neurons. The BAR domain of endophilin-A1 forms crescent-shaped dimers that can detect membrane curvature and drive membrane bending, while its SH3 domain binds the endocytic proteins, dynamin 1, synaptojanin 1, and amphiphysins. 223 matched cddid_all.tbl CDD cd07614 cd07614 153298 BAR_Endophilin_A2 The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-A2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Endophilins are accessory proteins, localized at synapses, which interact with the endocytic proteins, dynamin and synaptojanin. They are essential for synaptic vesicle formation from the plasma membrane. They interact with voltage-gated calcium channels, thus linking vesicle endocytosis to calcium regulation. They also play roles in virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. Endophilins contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. They are classified into two types, A and B. Endophilin-A proteins are enriched in the brain and play multiple roles in receptor-mediated endocytosis. Endophilin-A2 (or endophilin-2) is also referred to as SH3P8 (SH3 domain containing protein 8) or SH3GL1 (SH3 domain containing Grb2-like protein 1). It localizes to presynaptic nerve terminals and forms heterodimers with endophilin-A1 through their BAR domains. Endophilin-A2 binds dynamin 1, synaptojanin 1, and the beta1-adrenergic receptor cytoplasmic tail through its SH3 domain. 223 matched cddid_all.tbl CDD cd07615 cd07615 153299 BAR_Endophilin_A3 The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-A3. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Endophilins are accessory proteins localized at synapses that interacts with the endocytic proteins, dynamin and synaptojanin. They are essential for synaptic vesicle formation from the plasma membrane. They interact with voltage-gated calcium channels, thus linking vesicle endocytosis to calcium regulation. They also play roles in virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. Endophilins contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. They are classified into two types, A and B. Endophilin-A proteins are enriched in the brain and play multiple roles in receptor-mediated endocytosis. Endophilin-A3 (or endophilin-3) is also referred to as SH3P13 (SH3 domain containing protein 13) or SH3GL3 (SH3 domain containing Grb2-like protein 3). It regulates Arp2/3-dependent actin filament assembly during endocytosis. It binds N-WASP through its SH3 domain and enhances the ability of N-WASP to activate the Arp2/3 complex. Endophilin-A3 co-localizes with the vesicular glutamate transporter 1 (VGLUT1), and may play an important role in the synaptic release of glutamate. 223 matched cddid_all.tbl CDD cd07616 cd07616 153300 BAR_Endophilin_B1 The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-B1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. Endophilins contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. They are classified into two types, A and B. Endophilin-B proteins are cytoplasmic proteins expressed mainly in the heart, placenta, and skeletal muscle. Endophilin-B1, also called Bax-interacting factor 1 (Bif-1) or SH3GLB1 (SH3-domain GRB2-like endophilin B1), is localized mainly to the Golgi apparatus. It is involved in the regulation of many biological events including autophagy, tumorigenesis, nerve growth factor (NGF) trafficking, neurite outgrowth, mitochondrial outer membrane dynamics, and cell death. Endophilin-B1 forms homo- and heterodimers (with endophilin-B2) through its BAR domain, which can bind and bend membranes. It interacts with amphiphysin 1 and dynamin 1 through its SH3 domain. 229 matched cddid_all.tbl CDD cd07617 cd07617 153301 BAR_Endophilin_B2 The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-B2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. Endophilins contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. They are classified into two types, A and B. Vertebrates contain two endophilin-B isoforms. Endophilin-B proteins are cytoplasmic proteins expressed mainly in the heart, placenta, and skeletal muscle. Endophilin-B2, also called SH3GLB2 (SH3-domain GRB2-like endophilin B2), is a cytoplasmic protein that interacts with the apoptosis inducer Bax. It is overexpressed in prostate cancer metastasis and has been identified as a cancer antigen with potential utility in immunotherapy. Endophilin-B2 forms homo- and heterodimers (with endophilin-B1) through its BAR domain, which can bind and bend membranes. 220 matched cddid_all.tbl CDD cd07618 cd07618 153302 BAR_Rich1 The Bin/Amphiphysin/Rvs (BAR) domain of RhoGAP interacting with CIP4 homologs protein 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. RhoGAP interacting with CIP4 homologs protein 1 (Rich1) is also called Neuron-associated developmentally-regulated protein (Nadrin) or Rho GTPase activating protein 17 (ARHGAP17). It is a Cdc42- and Rac-specific GAP that binds to polarity proteins through the scaffold protein angiomotin and plays a role in maintaining the integrity of tight junctions. It may be a component of a sorting mechanism in the recycling of tight junction transmembrane proteins. Rich1 contains an N-terminal BAR domain followed by a Rho GAP domain and a C-terminal proline-rich domain. It interacts with the BAR domain proteins endophilin and amphiphysin through its proline-rich region. The BAR domain of Rich1 forms oligomers and can bind membranes and induce membrane tubulation. 246 matched cddid_all.tbl CDD cd07619 cd07619 153303 BAR_Rich2 The Bin/Amphiphysin/Rvs (BAR) domain of RhoGAP interacting with CIP4 homologs protein 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. RhoGAP interacting with CIP4 homologs protein 2 (Rich2) is a Rho GTPase activating protein that interacts with CD317, a lipid raft-associated integral membrane protein. It plays a role in actin cytoskeleton organization and the maintenance of microvilli in polarized epithelial cells. Rich2 contains an N-terminal BAR domain followed by a GAP domain for Rho and Rac GTPases and a C-terminal proline-rich domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 248 matched cddid_all.tbl CDD cd07620 cd07620 153304 BAR_SH3BP1 The Bin/Amphiphysin/Rvs (BAR) domain of SH3-domain Binding Protein 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. SH3-domain binding protein 1 (SH3BP1 or 3BP-1) is a Rac GTPase activating protein that inhibits Rac-mediated platelet-derived growth factor (PDGF)-induced membrane ruffling. SH3BP1 contains an N-terminal BAR domain followed by a GAP domain for Rho and Rac GTPases and a C-terminal proline-rich domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 257 matched cddid_all.tbl CDD cd07621 cd07621 153305 BAR_SNX5_6 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins 5 and 6. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. Members of this subfamily include SNX5, SNX6, the mammalian SNX32, and similar proteins. SNX5 and SNX6 may be components of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. The function of SNX32 is still unknown. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 219 matched cddid_all.tbl CDD cd07622 cd07622 153306 BAR_SNX4 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 4. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX4 is involved in recycling traffic from the sorting endosome (post-Golgi endosome) back to the late Golgi. It is also implicated in the regulation of plasma membrane receptor trafficking and interacts with receptors for EGF, insulin, platelet-derived growth factor and leptin. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 201 matched cddid_all.tbl CDD cd07623 cd07623 153307 BAR_SNX1_2 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins 1 and 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. This subfamily consists of SNX1, SNX2, and similar proteins. SNX1 and SNX2 are components of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi. The retromer consists of a cargo-recognition subcomplex and a subcomplex formed by a dimer of sorting nexins (SNX1 and/or SNX2), which ensures efficient cargo sorting by facilitating proper membrane localization of the cargo-recognition subcomplex. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 224 matched cddid_all.tbl CDD cd07624 cd07624 153308 BAR_SNX7_30 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins 7 and 30. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. This subfamily consists of SNX7, SNX30, and similar proteins. The specific functions of SNX7 and SNX30 have not been elucidated. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 200 matched cddid_all.tbl CDD cd07625 cd07625 153309 BAR_Vps17p The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Vps17p. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. Vsp17p forms a dimer with Vps5p, the yeast counterpart of human SNX1, and is part of the retromer complex that mediates the transport of the carboxypeptidase Y receptor Vps10p from endosomes to Golgi. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 230 matched cddid_all.tbl CDD cd07626 cd07626 153310 BAR_SNX9_like The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 9 and Similar Proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. This subfamily consists of SNX9, SNX18, SNX33, and similar proteins. SNX9 is localized to plasma membrane endocytic sites and acts primarily in clathrin-mediated endocytosis, while SNX18 is localized to peripheral endosomal structures, and acts in a trafficking pathway that is clathrin-independent but relies on AP-1 and PACS1. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 199 matched cddid_all.tbl CDD cd07627 cd07627 153311 BAR_Vps5p The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Vps5p. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. Vsp5p is the yeast counterpart of human SNX1 and is part of the retromer complex, which functions in the endosome-to-Golgi retrieval of vacuolar protein sorting receptor Vps10p, the Golgi-resident membrane protein A-ALP, and endopeptidase Kex2. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 216 matched cddid_all.tbl CDD cd07628 cd07628 153312 BAR_Atg24p The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Atg24p. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. Atg24p is involved in membrane fusion events at the vacuolar surface during pexophagy. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 185 matched cddid_all.tbl CDD cd07629 cd07629 153313 BAR_Atg20p The Bin/Amphiphysin/Rvs (BAR) domain of yeast Sorting Nexin Atg20p. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. The function of Atg20p is unknown but it has been shown to interact with Atg11p, which plays a role in linking cargo molecules with vesicle-forming components. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 187 matched cddid_all.tbl CDD cd07630 cd07630 153314 BAR_SNX_like The Bin/Amphiphysin/Rvs (BAR) domain of uncharacterized Sorting Nexins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of uncharacterized proteins with similarity to sorting nexins (SNXs), which are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 198 matched cddid_all.tbl CDD cd07631 cd07631 153315 BAR_APPL1 The Bin/Amphiphysin/Rvs (BAR) domain of Adaptor protein, Phosphotyrosine interaction, PH domain and Leucine zipper containing 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Adaptor protein, Phosphotyrosine interaction, PH domain and Leucine zipper containing (APPL) proteins are effectors of the small GTPase Rab5 that function in endosome-mediated signaling. They contain BAR, pleckstrin homology (PH) and phosphotyrosine binding (PTB) domains. They form homo- and hetero-oligomers that are mediated by their BAR domains. Vertebrates contain two APPL proteins, APPL1 and APPL2. APPL1 interacts with diverse receptors (e.g. NGF receptor TrkA, FSHR, adiponectin receptors) and signaling proteins (e.g. Akt, PI3K), and may function as an adaptor linked to many distinct signaling pathways. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 215 matched cddid_all.tbl CDD cd07632 cd07632 153316 BAR_APPL2 The Bin/Amphiphysin/Rvs (BAR) domain of Adaptor protein, Phosphotyrosine interaction, PH domain and Leucine zipper containing 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Adaptor protein, Phosphotyrosine interaction, PH domain and Leucine zipper containing (APPL) proteins are effectors of the small GTPase Rab5 that function in endosome-mediated signaling. They contain BAR, pleckstrin homology (PH) and phosphotyrosine binding (PTB) domains. They form homo- and hetero-oligomers that are mediated by their BAR domains. Vertebrates contain two APPL proteins, APPL1 and APPL2. Both APPL proteins interact with the transcriptional repressor Reptin, acting as activators of beta-catenin/TCF-mediated trancription. APPL2 is essential for cell proliferation. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 215 matched cddid_all.tbl CDD cd07633 cd07633 153317 BAR_OPHN1 The Bin/Amphiphysin/Rvs (BAR) domain of Oligophrenin-1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Oligophrenin-1 (OPHN1) is a GTPase activating protein (GAP) with activity towards RhoA, Rac, and Cdc42, that is expressed in developing spinal cord and in adult brain areas with high plasticity. It plays a role in regulating the actin cystoskeleton as well as morphology changes in axons and dendrites, and may also function in modulating neuronal connectivity. Mutations in the OPHN1 gene causes X-linked mental retardation associated with cerebellar hypoplasia, lateral ventricle enlargement and epilepsy. OPHN1 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, and a Rho GAP domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 207 matched cddid_all.tbl CDD cd07634 cd07634 153318 BAR_GAP10-like The Bin/Amphiphysin/Rvs (BAR) domain of Rho GTPase activating protein 10-like. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This group is composed of uncharacterized proteins called Rho GTPase activating protein (GAP) 10-like. GAP10-like may be a GAP with activity towards RhoA and Cdc42. Similar to GRAF and GRAF2, it contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domains of the related proteins GRAF and OPHN1, directly interact with their Rho GAP domains and inhibit theiractivity. The autoinhibited proteins are capable of binding membranes and tubulating liposomes, showing that the membrane-tubulation and GAP-inhibitory functions of the BAR domain can occur simultaneously. 207 matched cddid_all.tbl CDD cd07635 cd07635 153319 BAR_GRAF2 The Bin/Amphiphysin/Rvs (BAR) domain of GTPase Regulator Associated with Focal adhesion 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. GTPase Regulator Associated with Focal adhesion kinase 2 (GRAF2), also called Rho GTPase activating protein 10 (ARHGAP10) or PS-GAP, is a GAP with activity towards Cdc42 and RhoA which regulates caspase-activated p21-activated protein kinase-2 (PAK-2p34). GRAF2 interacts with PAK-2p34, leading to its stabilization and decrease of cell death. It is highly expressed in skeletal muscle and also interacts with PKNbeta, which is a target of Rho. GRAF2 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domain of the related protein GRAF directly interacts with its Rho GAP domain and inhibits its activity. Autoinhibited GRAF is capable of binding membranes and tubulating liposomes, showing that the membrane-tubulation and GAP-inhibitory functions of the BAR domain can occur simultaneously. 207 matched cddid_all.tbl CDD cd07636 cd07636 153320 BAR_GRAF The Bin/Amphiphysin/Rvs (BAR) domain of GTPase Regulator Associated with Focal adhesion kinase. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. GTPase Regulator Associated with Focal adhesion kinase (GRAF), also called Rho GTPase activating protein 26 (ARHGAP26), is a GAP with activity towards RhoA and Cdc42 and is only weakly active towards Rac1. It influences Rho-mediated cytoskeletal rearrangements and binds focal adhesion kinase (FAK), which is a critical component of integrin signaling. GRAF contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domain of GRAF directly interacts with its Rho GAP domain and inhibits its activity. Autoinhibited GRAF is capable of binding membranes and tubulating liposomes, showing that the membrane-tubulation and GAP-inhibitory functions of the BAR domain can occur simultaneously. 207 matched cddid_all.tbl CDD cd07637 cd07637 153321 BAR_ACAP3 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 3. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ACAP3 (ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 3), also called centaurin beta-5, is presumed to be an Arf GTPase activating protein (GAP) based on its similarity to the Arf6-specific GAPs ACAP1 and ACAP2. The specific function of ACAP3 is still unknown. ACAP3 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 200 matched cddid_all.tbl CDD cd07638 cd07638 153322 BAR_ACAP2 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ACAP2 (ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 2), also called centaurin beta-2, is an Arf6-specific GTPase activating protein (GAP) which mediates Arf6 signaling. Arf6 is involved in the regulation of endocytosis, phagocytosis, cell adhesion and migration. ACAP2 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 200 matched cddid_all.tbl CDD cd07639 cd07639 153323 BAR_ACAP1 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ACAP1 (ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 1), also called centaurin beta-1, is an Arf6-specific GTPase activating protein (GAP) which mediates Arf6 signaling. Arf6 is involved in the regulation of endocytosis, phagocytosis, cell adhesion and migration. ACAP1 also participates in the cargo sorting and recycling of the transferrin receptor and integrin beta1. It may also play a role in innate immune responses. ACAP1 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 200 matched cddid_all.tbl CDD cd07640 cd07640 153324 BAR_ASAP3 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 3. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ASAP3 (ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 3) is also known as ACAP4 (ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 4), DDEFL1 (Development and Differentiation Enhancing Factor-Like 1), or centaurin beta-6. It is an Arf6-specific GTPase activating protein (GAP) and is co-localized with Arf6 in ruffling membranes upon EGF stimulation. ASAP3 is implicated in the pathogenesis of hepatocellular carcinoma and plays a role in regulating cell migration and invasion. ASAP3 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, ankyrin (ANK) repeats, and a C-terminal SH3 domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domain of the related protein ASAP1 mediates membrane bending, is essential for function, and autoinhibits GAP activity by interacting with the PH and/or Arf GAP domains. 213 matched cddid_all.tbl CDD cd07641 cd07641 153325 BAR_ASAP1 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ASAP1 (ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 1) is also known as DDEF1 (Development and Differentiation Enhancing Factor 1), AMAP1, centaurin beta-4, or PAG2. ASAP1 is an Arf GTPase activating protein (GAP) with activity towards Arf1 and Arf5 but not Arf6 However, it has been shown to bind GTP-Arf6 stably without GAP activity. It has been implicated in cell growth, migration, and survival, as well as in tumor invasion and malignancy. It binds paxillin and cortactin, two components of invadopodia which are essential for tumor invasiveness. It also binds focal adhesion kinase (FAK) and the SH2/SH3 adaptor CrkL. ASAP1 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, ankyrin (ANK) repeats, and a C-terminal SH3 domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domain of ASAP1 mediates membrane bending, is essential for function, and autoinhibits GAP activity by interacting with the PH and/or Arf GAP domains. 215 matched cddid_all.tbl CDD cd07642 cd07642 153326 BAR_ASAP2 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ASAP2 (ArfGAP with SH3 domain, ANK repeat and PH domain containing protein 2) is also known as DDEF2 (Development and Differentiation Enhancing Factor 2), AMAP2, centaurin beta-3, or PAG3. ASAP2 mediates the functions of Arf GTPases vial dual mechanisms: it exhibits GTPase activating protein (GAP) activity towards class I (Arf1) and II (Arf5) Arfs; and binds class III Arfs (GTP-Arf6) stably without GAP activity. It binds paxillin and is implicated in Fcgamma receptor-mediated phagocytosis in macrophages and in cell migration. ASAP2 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, ankyrin (ANK) repeats, and a C-terminal SH3 domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domain of the related protein ASAP1 mediates membrane bending, is essential for function, and autoinhibits GAP activity by interacting with the PH and/or Arf GAP domains. 215 matched cddid_all.tbl CDD cd07643 cd07643 153327 I-BAR_IMD_MIM Inverse (I)-BAR, also known as the IRSp53/MIM homology Domain (IMD), of Missing In Metastasis. The IMD domain, also called Inverse-Bin/Amphiphysin/Rvs (I-BAR) domain, is a dimerization and lipid-binding module that bends membranes and induces membrane protrusions. Members of this subfamily include missing in metastasis (MIM) or metastasis suppressor 1 (MTSS1), metastasis suppressor 1-like (MTSSL) or ABBA (Actin-Bundling protein with BAIAP2 homology), and similar proteins. They contain an N-terminal IMD and a WASP homology 2 (WH2) actin-binding motif at the C-terminus. MIM was originally identified as a missing transcript from metastatic bladder and prostate cancer cells. It is a scaffold protein that functions in a signaling pathway between the PDGF receptor, Src kinases, and actin assembly. It may also function as a cofactor of the Sonic hedgehog (Shh) transcriptional pathway and may participate in tumor development and progression via this pathway. ABBA regulates actin and plasma membrane dynamics to promote the extension of radial glia, which is important in neuronal migration, axon guidance and neurogenesis. The IMD domain of MIM binds and bundles actin filaments, binds membranes, and interacts with the small GTPase Rac. 231 matched cddid_all.tbl CDD cd07644 cd07644 153328 I-BAR_IMD_BAIAP2L2 Inverse (I)-BAR, also known as the IRSp53/MIM homology Domain (IMD), of Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2-Like 2. The IMD domain, also called Inverse-Bin/Amphiphysin/Rvs (I-BAR) domain, is a dimerization and lipid-binding module that bends membranes and induces membrane protrusions. This group is composed of uncharacterized proteins known as BAIAP2L2 (Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2-Like 2). They contain an N-terminal IMD, an SH3 domain, and a WASP homology 2 (WH2) actin-binding motif at the C-terminus. The related proteins, BAIAP2L1 and IRSp53, function as regulators of membrane dynamics and the actin cytoskeleton. The IMD domain binds and bundles actin filaments, binds membranes and produces membrane protrusions, and interacts with the small GTPase Rac. 215 matched cddid_all.tbl CDD cd07645 cd07645 153329 I-BAR_IMD_BAIAP2L1 Inverse (I)-BAR, also known as the IRSp53/MIM homology Domain (IMD), of Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2-Like 1. The IMD domain, also called Inverse-Bin/Amphiphysin/Rvs (I-BAR) domain, is a dimerization and lipid-binding module that bends membranes and induces membrane protrusions. BAIAP2L1 (Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2-Like 1) is also known as IRTKS (Insulin Receptor Tyrosine Kinase Substrate). It is widely expressed, serves as a substrate for the insulin receptor, and binds the small GTPase Rac. It plays a role in regulating the actin cytoskeleton and colocalizes with F-actin, cortactin, VASP, and vinculin. BAIAP2L1 expression leads to the formation of short actin bundles, distinct from filopodia-like protrusions induced by the expression of the related protein IRSp53. It contains an N-terminal IMD, an SH3 domain, and a WASP homology 2 (WH2) actin-binding motif at the C-terminus. The IMD domain of BAIAP2L1 binds and bundles actin filaments, and binds the small GTPase Rac. 226 matched cddid_all.tbl CDD cd07646 cd07646 153330 I-BAR_IMD_IRSp53 Inverse (I)-BAR, also known as the IRSp53/MIM homology Domain (IMD), of Insulin Receptor tyrosine kinase Substrate p53. The IMD domain, also called Inverse-Bin/Amphiphysin/Rvs (I-BAR) domain, is a dimerization and lipid-binding module that bends membranes and induces membrane protrusions. IRSp53 (Insulin Receptor tyrosine kinase Substrate p53) is also known as BAIAP2 (Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2). It is a scaffolding protein that takes part in many signaling pathways including Cdc42-induced filopodia formation, Rac-mediated lamellipodia extension, and spine morphogenesis. IRSp53 exists as multiple splicing variants that differ mainly at the C-termini. One variant (T-form) is expressed exclusively in human breast cancer cells. The gene encoding IRSp53 is a putative susceptibility gene for Gilles de la Tourette syndrome. IRSp53 contains an N-terminal IMD, a CRIB (Cdc42 and Rac interactive binding motif), an SH3 domain, and a WASP homology 2 (WH2) actin-binding motif at the C-terminus. Its IMD domain binds and bundles actin filaments, binds membranes, and interacts with the small GTPase Rac. 232 matched cddid_all.tbl CDD cd07647 cd07647 153331 F-BAR_PSTPIP The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Proline-Serine-Threonine Phosphatase-Interacting Proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Vetebrates contain two Proline-Serine-Threonine Phosphatase-Interacting Proteins (PSTPIPs), PSTPIP1 and PSTPIP2. PSTPIPs are mainly expressed in hematopoietic cells and are involved in the regulation of cell adhesion and motility. Mutations in PSTPIPs have been shown to cause autoinflammatory disorders. PSTPIP1 contains an N-terminal F-BAR domain, PEST motifs, and a C-terminal SH3 domain, while PSTPIP2 contains only the N-terminal F-BAR domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 239 matched cddid_all.tbl CDD cd07648 cd07648 153332 F-BAR_FCHO The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH domain Only proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Proteins in this group have been named FCH domain Only (FCHO) proteins. Vertebrates have two members, FCHO1 and FCHO2. These proteins contain an F-BAR domain and a C-terminal domain of unknown function named SAFF which is also present in endophilin interacting protein 1. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 261 matched cddid_all.tbl CDD cd07649 cd07649 153333 F-BAR_GAS7 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Growth Arrest Specific protein 7. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Growth Arrest Specific protein 7 (GAS7) is mainly expressed in the brain and is required for neurite outgrowth. It may also play a role in the protection and migration of embryonic stem cells. Treatment-related acute myeloid leukemia (AML) has been reported resulting from mixed-lineage leukemia (MLL)-GAS7 translocations as a complication of primary cancer treatment. GAS7 contains an N-terminal SH3 domain, followed by a WW domain, and a central F-BAR domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 233 matched cddid_all.tbl CDD cd07650 cd07650 153334 F-BAR_Syp1p_like The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of yeast Syp1 protein. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Syp1p is associated with septins, a family of GTP-binding proteins that serve as elements of septin filaments, which are required for cell morphogenesis and division. Syp1p regulates cell-cycle dependent septin cytoskeletal dynamics in yeast. It contains an N-terminal F-BAR domain and a C-terminal domain of unknown function named SAFF which is also present in FCH domain Only (FCHO) proteins and endophilin interacting protein 1. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 228 matched cddid_all.tbl CDD cd07651 cd07651 153335 F-BAR_PombeCdc15_like The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Schizosaccharomyces pombe Cdc15, and similar proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. This subfamily is composed of Schizosaccharomyces pombe Cdc15 and Imp2, and similar proteins. These proteins contain an N-terminal F-BAR domain and a C-terminal SH3 domain. S. pombe Cdc15 and Imp2 play both distinct and overlapping roles in the maintenance and strengthening of the contractile ring at the division site, which is required in cell division. Cdc15 is a component of the actomyosin ring and is required in normal cytokinesis. Imp2 colocalizes with the medial ring during septation and is required for normal septation. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 236 matched cddid_all.tbl CDD cd07652 cd07652 153336 F-BAR_Rgd1 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Saccharomyces cerevisiae Rho GTPase activating protein Rgd1 and similar proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Saccharomyces cerevisiae Rgd1 is a GTPase activating protein (GAP) with activity towards Rho3p and Rho4p, which are involved in bud growth and cytokinesis, respectively. At low pH, S. cerevisiae Rgd1 is required for cell survival and the activation of the protein kinase C pathway, which is important in cell integrity and the maintenance of cell shape. It contains an N-terminal F-BAR domain and a C-terminal Rho GAP domain. The F-BAR domain of S. cerevisiae Rgd1 binds to phosphoinositides and plays an important role in the localization of the protein to the bud tip/neck during the cell cycle. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 234 matched cddid_all.tbl CDD cd07653 cd07653 153337 F-BAR_CIP4-like The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Cdc42-Interacting Protein 4 and similar proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. This subfamily is composed of Cdc42-Interacting Protein 4 (CIP4), Formin Binding Protein 17 (FBP17), FormiN Binding Protein 1-Like (FNBP1L), and similar proteins. CIP4 and FNBP1L are Cdc42 effectors that bind Wiskott-Aldrich syndrome protein (WASP) and function in endocytosis. CIP4 and FBP17 bind to the Fas ligand and may be implicated in the inflammatory response. CIP4 may also play a role in phagocytosis. Members of this subfamily typically contain an N-terminal F-BAR domain and a C-terminal SH3 domain. In addition, some members such as FNBP1L contain a central Cdc42-binding HR1 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 251 matched cddid_all.tbl CDD cd07654 cd07654 153338 F-BAR_FCHSD The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH and double SH3 domains proteins (FCHSD). F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. This subfamily is composed of FCH and double SH3 domain (FCHSD) proteins, so named as they contain an N-terminal F-BAR domain and two SH3 domains at the C-terminus. Vertebrates harbor two subfamily members, FCHSD1 and FCHSD2, which have been characterized only in silico. Their biological function is still unknown. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 264 matched cddid_all.tbl CDD cd07655 cd07655 153339 F-BAR_PACSIN The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Protein kinase C and Casein kinase Substrate in Neurons (PACSIN) proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Protein kinase C and Casein kinase Substrate in Neurons (PACSIN) proteins, also called Synaptic dynamin-associated proteins (Syndapins), act as regulators of cytoskeletal and membrane dynamics. They bind both dynamin and Wiskott-Aldrich syndrome protein (WASP), and may provide direct links between the actin cytoskeletal machinery through WASP and dynamin-dependent endocytosis. Vetebrates harbor three isoforms with distinct expression patterns and specific functions. PACSINs contain an N-terminal F-BAR domain and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 258 matched cddid_all.tbl CDD cd07656 cd07656 153340 F-BAR_srGAP The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Proteins. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Slit-Robo GTPase Activating Proteins (srGAPs) are Rho GAPs that interact with Robo1, the transmembrane receptor of Slit proteins. Slit proteins are secreted proteins that control axon guidance and the migration of neurons and leukocytes. Vertebrates contain three isoforms of srGAPs, all of which are expressed during embryonic and early development in the nervous system but with different localization and timing. srGAPs contain an N-terminal F-BAR domain, a Rho GAP domain, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 241 matched cddid_all.tbl CDD cd07657 cd07657 153341 F-BAR_Fes_Fer The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Fes (feline sarcoma) and Fer (Fes related) tyrosine kinases. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Fes (feline sarcoma), also called Fps (Fujinami poultry sarcoma), and Fer (Fes related) are cytoplasmic (or nonreceptor) tyrosine kinases that play roles in haematopoiesis, inflammation and immunity, growth factor signaling, cytoskeletal regulation, cell migration and adhesion, and the regulation of cell-cell interactions. Although Fes and Fer show redundancy in their biological functions, they show differences in their expression patterns. Fer is ubiquitously expressed while Fes is expressed predominantly in myeloid and endothelial cells. Fes and Fer contain an N-terminal F-BAR domain, an SH2 domain, and a C-terminal catalytic kinase domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. The F-BAR domain of Fes is critical in its role in microtubule nucleation and bundling. 237 matched cddid_all.tbl CDD cd07658 cd07658 153342 F-BAR_NOSTRIN The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Nitric Oxide Synthase TRaffic INducer (NOSTRIN). F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Nitric Oxide Synthase TRaffic INducer (NOSTRIN) is expressed in endothelial and epithelial cells and is involved in the regulation, trafficking and targeting of endothelial NOS (eNOS). NOSTRIN facilitates the endocytosis of eNOS by coordinating the functions of dynamin and the Wiskott-Aldrich syndrome protein (WASP). Increased expression of NOSTRIN may be correlated to preeclampsia. NOSTRIN contains an N-terminal F-BAR domain and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. The F-BAR domain of NOSTRIN is necessary and sufficient for its membrane association and is responsible for its subcellular localization. 239 matched cddid_all.tbl CDD cd07659 cd07659 153343 BAR_PICK1 The Bin/Amphiphysin/Rvs (BAR) domain of Protein Interacting with C Kinase 1. The BAR domain of Arfaptin-like proteins, also called the Arfaptin domain, is a dimerization and lipid binding module that can detect and drive membrane curvature. Protein Interacting with C Kinase 1 (PICK1), also called Protein kinase C-alpha-binding protein, is highly expressed in brain and testes. PICK1 plays a key role in the trafficking of AMPA receptors, which are critical for regulating synaptic strength and may be important in cellular processes involved in learning and memory. PICK1 is also critical in the early stages of spermiogenesis. Mice deficient in PICK1 are infertile and show characteristics of the human disease globozoospermia such as round-headed sperm, reduced sperm count, and severely impaired sperm motility. PICK1 may also be involved in the neuropathogenesis of schizophrenia. PICK1 contains an N-terminal PDZ domain and a C-terminal BAR domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. The BAR domain of PICK1 is necessary for its membrane localization and activation. 215 matched cddid_all.tbl CDD cd07660 cd07660 153344 BAR_Arfaptin The Bin/Amphiphysin/Rvs (BAR) domain of Arfaptin. The BAR domain of Arfaptin-like proteins, also called the Arfaptin domain, is a dimerization and lipid binding module that can detect and drive membrane curvature. Arfaptins are ubiquitously expressed proteins implicated in mediating cross-talk between Rac, a member of the Rho family GTPases, and Arf (ADP-ribosylation factor) small GTPases. Arfaptins bind to GTP-bound Arf1, Arf5, and Arf6, with strongest binding to GTP-Arf1. Arfaptins also bind to Rac-GTP and Rac-GDP with similar affinities. The Arfs are thought to bind to the same surface as Rac, and their binding is mutually exclusive. Mammals contain at least two isoforms of Arfaptin. Arfaptin 1 has been shown to inhibit the activation of Arf-dependent phospholipase D (PLD) and the secretion of matrix metalloproteinase-9 (MMP-9), an enzyme implicated in cancer invasiveness and metastasis. Arfaptin 2 regulates the aggregation of the protein huntingtin, which is implicated in Huntington disease. Arfaptins are single-domain proteins with a BAR-like structure. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 201 matched cddid_all.tbl CDD cd07661 cd07661 153345 BAR_ICA69 The Bin/Amphiphysin/Rvs (BAR) domain of Islet Cell Autoantigen 69-kDa. The BAR domain of Arfaptin-like proteins, also called the Arfaptin domain, is a dimerization and lipid binding module that can detect and drive membrane curvature. Islet cell autoantigen 69-kDa (ICA69) is a diabetes-associated autoantigen that is highly expressed in brain and beta cells. It is involved in membrane trafficking at the Golgi complex in neurosecretory cells. It is coexpressed with Protein Interacting with C Kinase 1 (PICK1), also a the BAR domain containing protein, in many tissues at different developmental stages. In neurons, ICA69 colocalizes with PICK1 in cell bodies and dendrites but is absent in synapses where PICK1 is enriched. ICA69 contains an N-terminal BAR domain and a conserved C-terminal domain of unknown function. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. ICA69 associates with PICK1 through their BAR domains to form a heterodimer which is involved in regulating the synaptic targeting and surface expression of AMPA receptors. Autoantibodies against ICA69 have been identified in patients with insulin-dependent diabetes mellitus, rheumatoid arthritis, and primary Sjogren's syndrome. ICA69 has also been shown to be released by pancreatic cancer cells. 204 matched cddid_all.tbl CDD cd07662 cd07662 153346 BAR_SNX6 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 6. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX6 forms a stable complex with SNX1 and may be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. It interacts with the receptor serine/threonine kinases from the transforming growth factor-beta family. It also plays roles in enhancing the degradation of EGFR and in regulating the activity of Na,K-ATPase through its interaction with Translationally Controlled Tumor Protein (TCTP). BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 218 matched cddid_all.tbl CDD cd07663 cd07663 153347 BAR_SNX5 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 5. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX5, abundantly expressed in macrophages, regulates macropinocytosis, a process that enables cells to internalize large amounts of external solutes. It may also be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. It also binds the Fanconi anaemia complementation group A protein (FANCA). SNX5 is localized to a subdomain of early endosome and is recruited to the plasma membrane following EGF stimulation and elevation of PI(3,4)P2 levels. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 218 matched cddid_all.tbl CDD cd07664 cd07664 153348 BAR_SNX2 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 2. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX2 is a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi. The retromer consists of a cargo-recognition subcomplex and a subcomplex formed by a dimer of sorting nexins (SNX1 and/or SNX2), which ensures effcient cargo sorting by facilitating proper membrane localization of the cargo-recognition subcomplex. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 234 matched cddid_all.tbl CDD cd07665 cd07665 153349 BAR_SNX1 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX1 is a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi. The retromer consists of a cargo-recognition subcomplex and a subcomplex formed by a dimer of sorting nexins (SNX1 and/or SNX2), which ensures effcient cargo sorting by facilitating proper membrane localization of the cargo-recognition subcomplex. SNX1 is localized to a microdomain in early endosomes where it regulates cation-independent mannose-6-phosphate receptor retrieval to the trans Golgi network. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 234 matched cddid_all.tbl CDD cd07666 cd07666 153350 BAR_SNX7 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 7. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. The specific function of SNX7 is still unknown. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 243 matched cddid_all.tbl CDD cd07667 cd07667 153351 BAR_SNX30 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 30. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. The specific function of SNX30 is still unknown. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 240 matched cddid_all.tbl CDD cd07668 cd07668 153352 BAR_SNX9 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 9. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX9, also known as SH3PX1, is a cytosolic protein that interacts with proteins associated with clathrin-coated pits such as Cdc-42-associated tyrosine kinase 2 (ACK2). It binds class I polyproline sequences found in dynamin 1/2 and the WASP/N-WASP actin regulators. SNX9 is localized to plasma membrane endocytic sites and acts primarily in clathrin-mediated endocytosis. Its array of interacting partners suggests that SNX9 functions at the interface between endocytosis and actin cytoskeletal organization. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 210 matched cddid_all.tbl CDD cd07669 cd07669 153353 BAR_SNX33 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 33. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX33 interacts with Wiskott-Aldrich syndrome protein (WASP) and plays a role in the maintenance of cell shape and cell cycle progression. It modulates the shedding and endocytosis of cellular prion protein (PrP(c)) and amyloid precursor protein (APP). BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 207 matched cddid_all.tbl CDD cd07670 cd07670 153354 BAR_SNX18 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 18. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX18 is localized to peripheral endosomal structures, and acts in a trafficking pathway that is clathrin-independent but relies on AP-1 and PACS1. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. 207 matched cddid_all.tbl CDD cd07671 cd07671 153355 F-BAR_PSTPIP1 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Proline-Serine-Threonine Phosphatase-Interacting Protein 1. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Proline-Serine-Threonine Phosphatase-Interacting Protein 1 (PSTPIP1), also known as CD2 Binding Protein 1 (CD2BP1), is mainly expressed in hematopoietic cells. It is a binding partner of the cell surface receptor CD2 and PTP-PEST, a tyrosine phosphatase which functions in cell motility and Rac1 regulation. It also plays a role in the activation of the Wiskott-Aldrich syndrome protein (WASP), which couples actin rearrangement and T cell activation. Mutations in the gene encoding PSTPIP1 cause the autoinflammatory disorder known as PAPA (pyogenic sterile arthritis, pyoderma gangrenosum, and acne) syndrome. PSTPIP1 contains an N-terminal F-BAR domain, PEST motifs, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 242 matched cddid_all.tbl CDD cd07672 cd07672 153356 F-BAR_PSTPIP2 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Proline-Serine-Threonine Phosphatase-Interacting Protein 2. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Proline-Serine-Threonine Phosphatase-Interacting Protein 2 (PSTPIP2), also known as Macrophage Actin-associated tYrosine Phosphorylated protein (MAYP), is mostly expressed in hematopoietic cells but is also expressed in the brain. It is involved in regulating cell adhesion and motility. Mutations in the gene encoding murine PSTPIP2 can cause autoinflammatory disorders such as chronic multifocal osteomyelitis and macrophage autoinflammatory disease. PSTPIP2 contains an N-terminal F-BAR domain and lacks the PEST motifs and SH3 domain that are found in PSTPIP1. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 240 matched cddid_all.tbl CDD cd07673 cd07673 153357 F-BAR_FCHO2 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH domain Only 2 protein. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. The specific function of FCH domain Only 2 (FCHO2) is still unknown. It contains an N-terminal F-BAR domain and a C-terminal domain of unknown function named SAFF which is also present in FCHO1 and endophilin interacting protein 1. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 269 matched cddid_all.tbl CDD cd07674 cd07674 153358 F-BAR_FCHO1 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH domain Only 1 protein. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. FCH domain Only 1 (FCHO1) may be involved in clathrin-coated vesicle formation. It contains an N-terminal F-BAR domain and a C-terminal domain of unknown function named SAFF which is also present in FCHO2 and endophilin interacting protein 1. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 261 matched cddid_all.tbl CDD cd07675 cd07675 153359 F-BAR_FNBP1L The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Formin Binding Protein 1-Like. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. FormiN Binding Protein 1-Like (FNBP1L), also known as Toca-1 (Transducer of Cdc42-dependent actin assembly), forms a complex with neural Wiskott-Aldrich syndrome protein (N-WASP). The FNBP1L/N-WASP complex induces the formation of filopodia and endocytic vesicles. FNBP1L is required for Cdc42-induced actin assembly and is essential for autophagy of intracellular pathogens. It contains an N-terminal F-BAR domain, a central Cdc42-binding HR1 domain, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 252 matched cddid_all.tbl CDD cd07676 cd07676 153360 F-BAR_FBP17 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Formin Binding Protein 17. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Formin Binding Protein 17 (FBP17), also called FormiN Binding Protein 1 (FNBP1), is involved in dynamin-mediated endocytosis. It is recruited to clathrin-coated pits late in the endocytosis process and may play a role in the invagination and scission steps. FBP17 binds in vivo to tankyrase, a protein involved in telomere maintenance and mitogen activated protein kinase (MAPK) signaling. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 253 matched cddid_all.tbl CDD cd07677 cd07677 153361 F-BAR_FCHSD2 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH and double SH3 domains 2 (FCHSD2). F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. FCH and double SH3 domains 2 (FCHSD2) contains an N-terminal F-BAR domain and two SH3 domains at the C-terminus. It has been characterized only in silico, and its biological function is still unknown. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 260 matched cddid_all.tbl CDD cd07678 cd07678 153362 F-BAR_FCHSD1 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of FCH and double SH3 domains 1 (FCHSD1). F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. FCH and double SH3 domains 1 (FCHSD1) contains an N-terminal F-BAR domain and two SH3 domains at the C-terminus. It has been characterized only in silico, and its biological function is still unknown. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 263 matched cddid_all.tbl CDD cd07679 cd07679 153363 F-BAR_PACSIN2 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Protein kinase C and Casein kinase Substrate in Neurons 2 (PACSIN2). F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Protein kinase C and Casein kinase Substrate in Neurons (PACSIN) proteins, also called Synaptic dynamin-associated proteins (Syndapins), act as regulators of cytoskeletal and membrane dynamics. Vetebrates harbor three isoforms with distinct expression patterns and specific functions. PACSIN 2 or Syndapin II is expressed ubiquitously and is involved in the regulation of tubulin polymerization. It associates with Golgi membranes and forms a complex with dynamin II which is crucial in promoting vesicle formation from the trans-Golgi network. PACSIN 2 contains an N-terminal F-BAR domain and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 258 matched cddid_all.tbl CDD cd07680 cd07680 153364 F-BAR_PACSIN1 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Protein kinase C and Casein kinase Substrate in Neurons 1 (PACSIN1). F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Protein kinase C and Casein kinase Substrate in Neurons (PACSIN) proteins, also called Synaptic dynamin-associated proteins (Syndapins), act as regulators of cytoskeletal and membrane dynamics. Vetebrates harbor three isoforms with distinct expression patterns and specific functions. PACSIN 1 or Syndapin I is expressed specifically in the brain and is localized in neurites and synaptic boutons. It binds the brain-specific proteins dynamin I, synaptojanin, synapsin I, and neural Wiskott-Aldrich syndrome protein (nWASP), and functions as a link between the cytoskeletal machinery and synaptic vesicle endocytosis. PACSIN 1 interacts with huntingtin and may be implicated in the neuropathology of Huntington's disease. It contains an N-terminal F-BAR domain and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 258 matched cddid_all.tbl CDD cd07681 cd07681 153365 F-BAR_PACSIN3 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Protein kinase C and Casein kinase Substrate in Neurons 3 (PACSIN3). F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Protein kinase C and Casein kinase Substrate in Neurons (PACSIN) proteins, also called Synaptic dynamin-associated proteins (Syndapins), act as regulators of cytoskeletal and membrane dynamics. Vetebrates harbor three isoforms with distinct expression patterns and specific functions. PACSIN 3 or Syndapin III is expressed ubiquitously and regulates glucose uptake in adipocytes through its role in GLUT1 trafficking. It also modulates the subcellular localization and stimulus-specific function of the cation channel TRPV4. PACSIN 3 contains an N-terminal F-BAR domain and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 258 matched cddid_all.tbl CDD cd07682 cd07682 153366 F-BAR_srGAP2 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Protein 2. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Slit-Robo GTPase Activating Proteins (srGAPs) are Rho GAPs that interact with Robo1, the transmembrane receptor of Slit proteins. Slit proteins are secreted proteins that control axon guidance and the migration of neurons and leukocytes. Vertebrates contain three isoforms of srGAPs. srGAP2 is expressed in zones of neuronal differentiation. It plays a role in the regeneration of neurons and axons. srGAP2 contains an N-terminal F-BAR domain, a Rho GAP domain, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 263 matched cddid_all.tbl CDD cd07683 cd07683 153367 F-BAR_srGAP1 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Protein 1. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Slit-Robo GTPase Activating Proteins (srGAPs) are Rho GAPs that interact with Robo1, the transmembrane receptor of Slit proteins. Slit proteins are secreted proteins that control axon guidance and the migration of neurons and leukocytes. Vertebrates contain three isoforms of srGAPs. srGAP1, also called Rho GTPase-Activating Protein 13 (ARHGAP13), is a Cdc42- and RhoA-specific GAP and is expressed later in the development of CNS (central nervous system) tissues. It is an important downstream signaling molecule of Robo1. srGAP1 contains an N-terminal F-BAR domain, a Rho GAP domain, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 253 matched cddid_all.tbl CDD cd07684 cd07684 153368 F-BAR_srGAP3 The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase Activating Protein 3. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Slit-Robo GTPase Activating Proteins (srGAPs) are Rho GAPs that interact with Robo1, the transmembrane receptor of Slit proteins. Slit proteins are secreted proteins that control axon guidance and the migration of neurons and leukocytes. Vertebrates contain three isoforms of srGAPs. srGAP3, also called MEGAP (MEntal disorder associated GTPase-Activating Protein), is a Rho GAP with activity towards Rac1 and Cdc42. It impacts cell migration by regulating actin and microtubule cytoskeletal dynamics. The association between srGAP3 haploinsufficiency and mental retardation is under debate. srGAP3 contains an N-terminal F-BAR domain, a Rho GAP domain, and a C-terminal SH3 domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 253 matched cddid_all.tbl CDD cd07685 cd07685 153369 F-BAR_Fes The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Fes (feline sarcoma) tyrosine kinase. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Fes (feline sarcoma), also called Fps (Fujinami poultry sarcoma), is a cytoplasmic (or nonreceptor) tyrosine kinase whose gene was first isolated from tumor-causing retroviruses. It is expressed in myeloid, vascular endothelial, epithelial, and neuronal cells, and plays important roles in cell growth and differentiation, angiogenesis, inflammation and immunity, and cytoskeletal regulation. Fes kinase has also been implicated as a tumor suppressor in colorectal cancer. It contains an N-terminal F-BAR domain, an SH2 domain, and a C-terminal catalytic kinase domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. The F-BAR domain of Fes is critical in its role in microtubule nucleation and bundling. 237 matched cddid_all.tbl CDD cd07686 cd07686 153370 F-BAR_Fer The F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain of Fer (Fes related) tyrosine kinase. F-BAR domains are dimerization modules that bind and bend membranes and are found in proteins involved in membrane dynamics and actin reorganization. Fer (Fes related) is a cytoplasmic (or nonreceptor) tyrosine kinase expressed in a wide variety of tissues, and is found to reside in both the cytoplasm and the nucleus. It plays important roles in neuronal polarization and neurite development, cytoskeletal reorganization, cell migration, growth factor signaling, and the regulation of cell-cell interactions mediated by adherens junctions and focal adhesions. Fer kinase also regulates cell cycle progression in malignant cells. It contains an N-terminal F-BAR domain, an SH2 domain, and a C-terminal catalytic kinase domain. F-BAR domains form banana-shaped dimers with a positively-charged concave surface that binds to negatively-charged lipid membranes. They can induce membrane deformation in the form of long tubules. 234 matched cddid_all.tbl CDD cd07687 cd07687 409484 IgC_TCR_delta Immunoglobulin (Ig) constant domain of the delta chain of delta/gamma T-cell antigen receptors (TCRs). The members here are composed of the constant domain of the delta chain of delta/gamma T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. The majority of T cells contain alpha-beta TCRs, but a small subset contain gamma-delta TCRs. Alpha-beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma-delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing and MHC independently of the bound peptide. Gamma-delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. 80 matched cddid_all.tbl CDD cd07688 cd07688 409485 IgC_TCR_alpha Immunoglobulin (Ig) constant domain the alpha chain of alpha/beta T-cell antigen receptors (TCRs). The members here are composed of the constant domain of the alpha chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes and are composed of alpha and beta, or gamma and delta polypeptide chains with variable (V) and constant (C) regions. This group includes the variable domain of the alpha chain. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The antigen binding site is formed by the variable domains of the alpha and beta chains, located at the N-terminus of each chain. Alpha/beta TCRs recognize antigens differently from gamma/delta TCRs. 83 matched cddid_all.tbl CDD cd07689 cd07689 409486 IgC2_VCAM-1 Immunoglobulin (Ig)-like domain of vascular endothelial cell adhesion molecule-1 (VCAM-1) and similar proteins; member of the C2-set of IgSF domains. The members here are composed of the immunoglobulin (Ig)-like domain of vascular endothelial cell adhesion molecule-1 (VCAM-1; also known as Cluster of Differentiation (CD) 106) and similar proteins. During the inflammation process, these molecules recruit leukocytes onto the vascular endothelium before extravasation to the injured tissues. The interaction of VCAM-1 binding to the beta1 integrin very late antigen 4 (VLA-4) expressed by lymphocytes and monocytes mediates the adhesion of leucocytes to blood vessel walls, and regulates migration across the endothelium. During metastasis, some circulating cancer cells extravasate to a secondary site by a similar process. VCAM-1 may be involved in organ targeted tumor metastasis and may also act as host receptors for viruses and parasites. VCAM-1 contains seven Ig domains. 101 matched cddid_all.tbl CDD cd07690 cd07690 409487 IgV_1_CD4 First immunoglobulin (Ig) domain of Cluster of Differentiation (CD) 4; member of the V-set of IgSF domains. The members here are composed of the first immunoglobulin (Ig) domain of Cluster of Differentiation (CD) 4. CD4 and CD8 are the two primary co-receptor proteins found on the surface of T cells, and the presence of either CD4 or CD8 determines the function of the T cell. CD4 is found on helper T cells, where it is required for the binding of MHC (major histocompatibility complex) class II molecules, while CD8 is found on cytotoxic T cells, where it is required for the binding of MHC class I molecules. CD4 contains four immunoglobulin domains, with the first three included in this hierarchy. The fourth domain has a general Ig architecture, but has slight topological changes in the arrangement of beta strands relative to the other structures in this family and is not specifically included in the hierarchy. 97 matched cddid_all.tbl CDD cd07691 cd07691 409488 IgC1_CD3_gamma_delta Immunoglobulin (Ig)-like domain of Cluster of Differentiation (CD) 3 gamma and delta chains; member of the C1-set of IgSF domains. The members here are composed of immunoglobulin (Ig)-like domain of Cluster of Differentiation (CD) 3 gamma and delta chains. CD3 is a T cell surface receptor that is associated with alpha/beta T cell receptors (TCRs). The CD3 complex consists of one gamma, one delta, two epsilon, and two zeta chains. The CD3 subunits form heterodimers as gamma/epsilon, delta/epsilon, and zeta/zeta. The gamma, delta, and epsilon chains each contain an extracellular Ig domain, whereas the extracellular domains of the zeta chains are very small and have unknown structure. The CD3 domain participates in intracellular signaling once the TCR has bound an MHC/antigen complex. 69 matched cddid_all.tbl CDD cd07692 cd07692 409489 IgC1_CD3_epsilon Immunoglobulin (Ig)-like domain of Cluster of Differentiation (CD) 3 epsilon chain; member of the C1-set of IgSF domains. The members here are composed of the immunoglobulin (Ig)-like domain of Cluster of Differentiation (CD) 3 epsilon chain. CD3 is a T cell surface receptor that is associated with alpha/beta T cell receptors (TCRs). The CD3 complex consists of one gamma, one delta, two epsilon, and two zeta chains. The CD3 subunits form heterodimers as gamma/epsilon, delta/epsilon, and zeta/zeta. The gamma, delta, and epsilon chains each contain an extracellular Ig domain, whereas the extracellular domains of the zeta chains are very small and have unknown structure. The CD3 domain participates in intracellular signaling once the TCR has bound an MHC/antigen complex. 75 matched cddid_all.tbl CDD cd07693 cd07693 409490 IgC_1_Robo First immunoglobulin (Ig)-like constant domain in Robo (roundabout) receptors, and similar domains. The members here are composed of the first immunoglobulin (Ig)-like domain in Roundabout (Robo) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (Robo1, Robo2, and Robo3), and three mammalian Slit homologs (Slit1, Slit2, Slit3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. Robo1, Robo2, and Robo3 are expressed by commissural neurons in the vertebrate spinal cord and Slit1, Slit2,and Slit3 are expressed at the ventral midline. Robo3 is a divergent member of the Robo family which instead of being a positive regulator of Slit responsiveness, antagonizes Slit responsiveness in precrossing axons. The Slit-Robo interaction is mediated by the second leucine-rich repeat (LRR) domain of Slit and the two N-terminal Ig domains of Robo, Ig1 and Ig2. The primary Robo binding site for Slit2 has been shown by surface plasmon resonance experiments and mutational analysis to be is the Ig1 domain, while the Ig2 domain has been proposed to harbor a weak secondary binding site. 99 matched cddid_all.tbl CDD cd07694 cd07694 409491 IgC2_2_CD4 Second immunoglobulin (Ig) domain of Cluster of Differentiation (CD) 4; member of the C2-set of IgSF domains. The members here are composed of the second immunoglobulin (Ig) Constant 2 (C2)-set domain of Cluster of Differentiation (CD) 4. CD4 and CD8 are the two primary co-receptor proteins found on the surface of T cells, and the presence of either CD4 or CD8 determines the function of the T cell. CD4 is found on helper T cells, where it is required for the binding of MHC (major histocompatibility complex) class II molecules, while CD8 is found on cytotoxic T cells, where it is required for the binding of MHC class I molecules. CD4 contains four immunoglobulin domains, with the first three included in this hierarchy. The fourth domain has a general Ig architecture, but has slight topological changes in the arrangement of beta strands relative to the other structures in this family and is not specifically included in the hierarchy. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. This group belongs to the C2-set of IgSF domains, having A, B, and E strands in one beta-sheet and A', G, F, C' in the other. Unlike other Ig domain sets, the C2-set lacks the D strand. 88 matched cddid_all.tbl CDD cd07695 cd07695 409492 IgV_3_CD4 Third immunoglobulin (Ig) Variable (V) domain of Cluster of Differentiation (CD) 4; member of the V-set of IgSF domains. The members here are composed of the third immunoglobulin variable (IgV) domain of Cluster of Differentiation (CD) 4. CD4 and CD8 are the two primary co-receptor proteins found on the surface of T cells, and the presence of either CD4 or CD8 determines the function of the T cell. CD4 is found on helper T cells, where it is required for the binding of MHC (major histocompatibility complex) class II molecules, while CD8 is found on cytotoxic T cells, where it is required for the binding of MHC class I molecules. CD4 contains four immunoglobulin domains, with the first three included in this hierarchy. The fourth domain has a general Ig architecture, but has slight topological changes in the arrangement of beta strands relative to the other structures in this family and is not specifically included in the hierarchy. 107 matched cddid_all.tbl CDD cd07696 cd07696 409493 IgC1_CH3_IgAEM_CH2_IgG CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, and mu chains, and CH2 domain (second constant Ig domain of the gheavy chain) in immunoglobulin heavy gamma chain; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the third immunoglobulin constant domain (IgC) of the gamma heavy chains and the second immunoglobulin constant domain (IgC) of alpha, epsilon, and mu heavy chains. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. 98 matched cddid_all.tbl CDD cd07697 cd07697 409494 IgC1_TCR_gamma T cell receptor (TCR) gamma chain constant immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin (Ig) constant (C) domain of the gamma chain of gamma-delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha-beta TCRs, but a small subset contain gamma-delta TCRs. Alpha-beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma-delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing and MHC independently of the bound peptide. Gamma-delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. 98 matched cddid_all.tbl CDD cd07698 cd07698 409495 IgC1_MHC_I_alpha3 Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. 92 matched cddid_all.tbl CDD cd07699 cd07699 409496 IgC1_L Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin (Ig) light chain constant (C) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains. 99 matched cddid_all.tbl CDD cd07700 cd07700 409497 IgV_CD8_beta "Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain. The members here are composed of the immunoglobulin (Ig)-like domain in Cluster of Differentiation (CD) 8 beta. The CD8 glycoprotein plays an essential role in the control of T-cell selection, maturation, and the T-cell receptor (TCR)-mediated response to peptide antigen. CD8 is comprised of alpha and beta subunits and is expressed as either an alpha/alpha or alpha/beta dimer. Both dimeric isoforms can serve as a coreceptor for T cell activation and differentiation, however they have distinct physiological roles, different cellular distributions, unique binding partners, etc. Each CD8 subunit is comprised of an extracellular domain containing a V-type Ig-like domain, a single pass transmembrane portion, and a short intracellular domain. Members of this group contain standard Ig superfamily V-set AGFCC'C""/DEB domain topology." 116 matched cddid_all.tbl CDD cd07701 cd07701 409498 IgV_1_Necl-3 First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule-3; member of the V-set of Ig superfamily (IgSF) domains. The members here are composed of the N-terminal immunoglobulin (Ig)-like domain of nectin-like molecule-3, Necl-3 (also known as cell adhesion molecule 2 (CADM2), SynCAM2, IGSF4D). Nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 - Necl-5). They all have an extracellular region containing three Ig-like domains, a transmembrane region, and a cytoplasmic region. The N-terminal Ig-like domain of the extracellular region, belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-3 accumulates in central and peripheral nervous system tissue, and has been shown to selectively interact with oligodendrocytes. 96 matched cddid_all.tbl CDD cd07702 cd07702 409499 IgI_VEGFR-1 "Immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor 1 (VEGFR-1); member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin (Ig)-like domain of vascular endothelial growth factor receptor 1 (VEGFR-1). VEGFRs have an extracellular component with seven Ig-like domains, a transmembrane segment, and an intracellular tyrosine kinase domain interrupted by a kinase-insert domain. VEGFRs bind VEGFs with high affinity at the Ig-like domains. VEGFR-1 binds VEGF-A strongly; VEGF-A is important to the growth and maintenance of vascular endothelial cells and to the development of new blood- and lymphatic-vessels in physiological and pathological states. VEGFR-1 may play an inhibitory role in the function of VEGFR-2 by binding VEGF-A and interfering with its interaction with VEGFR-2. VEGFR-1 has a signaling role in mediating monocyte chemotaxis and may mediate a chemotactic and a survival signal in hematopoietic stem cells or leukemia cells. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 92 matched cddid_all.tbl CDD cd07703 cd07703 409500 IgC1_2_Nectin-2_Necl-5_like Second immunoglobulin (Ig) domain of Nectin-2 and Nectin-like protein 5, and similar domains; member of the C1-set of the Ig superfamily (IgSF) domains. The members here are composed of the second immunoglobulin (Ig) domain of nectin-2 (also known as poliovirus receptor related protein 2 or Cluster of Differentiation 112 (CD112)), nectin-like protein 5 (CD155), and similar proteins. Nectins and Nectin-like molecules are a family of Ca(2+)-independent immunoglobulin-like transmembrane glycoproteins belonging to the class of adhesion receptors, consisting of nine members (nectins 1 through 4 and nectin-like proteins 1 through 5). Nectins are synaptic cell adhesion molecules (CAMs) which facilitate adhesion and signaling at various intracellular junctions. Nectins form homophilic cis-dimers, followed by homophilic and heterophilic trans-dimers involved in cell-cell adhesion. Nectin-2 and nectin-3 localize at Sertoli-spermatid junctions where they form heterophilic trans-interactions between the cells that are essential for the formation and maintenance of the junctions and for spermatid development. CD155 is the fifth member in the nectin-like molecule family, and functions as the receptor of poliovirus; therefore, CD155 is also referred to as Necl-5, or PVR. In contrast to all other family members, CD155 lacks self-adhesion capacity, yet it shares with nectins the feature to interact with other nectins. For instance, CD155 heterophilically trans-interacts with nectin-3, thereby contributing significantly to the establishment of adherens junctions between epithelial cells. This group belongs to the Constant 1 (C1)-set of IgSF domains, which has one beta-sheet that is formed by strands A-B-E-D and the other strands by G-F-C-C'. 97 matched cddid_all.tbl CDD cd07704 cd07704 409501 IgC1_2_Nectin-3-4_like Second immunoglobulin (Ig) domain of nectin-3 and nectin-4 (poliovirus receptor related protein 4), and similar domains; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the second immunoglobulin (Ig) domain of nectin-3 (also known as poliovirus receptor related protein 3 or cluster of differentiation (CD) 113) and nectin-4 (poliovirus receptor related protein 4). Nectin-3 and nectin-4 belong to the nectin family comprised of four transmembrane glycoproteins (nectin-1 through -4). Nectins are synaptic cell adhesion molecules (CAMs) which facilitate adhesion and signaling at various intracellular junctions. Nectins form homophilic cis-dimers, followed by homophilic and heterophilic trans-dimers involved in cell-cell adhesion. Nectin-2 and nectin-3 localize at Sertoli-spermatid junctions where they form heterophilic trans-interactions between the cells that are essential for the formation and maintenance of the junctions and for spermatid development. Nectin-3 has also been shown to form a heterophilic trans-interaction with nectin-1 in ciliary epithelia, establishing the apex-apex adhesion between the pigment and non-pigment cell layers. Nectin-4 has recently been identified in several types of breast carcinoma and can be used as a histological and serological marker for breast cancer. 96 matched cddid_all.tbl CDD cd07705 cd07705 409502 IgI_2_Necl-1 Second immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1); member of the I-set of Ig superfamily domains. The members here are composed of the second immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1; also known as cell adhesion molecule3 (CADM3)). These nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 through Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one cytoplasmic region. The N-terminal Ig-like domain of the extracellular region belongs to the V-type subfamily of Ig domains is essential to cell-cell adhesion and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-1 and Necl-2 have Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-1 is specifically expressed in neural tissue and is important to the formation of synapses, axon bundles, and myelinated axons. Necl-2 is expressed in a wide variety of tissues and is a putative tumour suppressor gene which is downregulated in aggressive neuroblastoma. Ig domains are likely to participate in ligand binding and recognition. 103 matched cddid_all.tbl CDD cd07706 cd07706 409503 IgV_TCR_delta "Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain. The members here are composed of the immunoglobulin (Ig) variable (V) domain of the delta chain of gamma/delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha/beta TCRs, but a small subset contain gamma/delta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma/delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing, and MHC independently of the bound peptide. Gamma/delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain standard Ig superfamily V-set AGFCC'C""/DEB domain topology." 112 matched cddid_all.tbl CDD cd07707 cd07707 293793 MBL-B1-B2-like metallo-beta-lactamases; subclasses B1 and B2 and related proteins; MBL-fold metallo-hydrolase domain. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. Subclass B1 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. B1 MBls include chromosomally-encoded MBLs such as Bacillus cereus BcII, Bacteroides fragilis CcrA, and Elizabethkingia meningoseptica (Chryseobacterium meningosepticum) BlaB and acquired MBLs including IMP-1, VIM-1, VIM-2, GIM-1, NDM-1 and FIM-1. B2 MBLs have a narrow substrate profile that includes carbapenems, and they are active with one zinc ion bound in the Asp-Cys-His site, binding of a second zinc ion in the modified 3H site (Asn-His-His) inhibits catalysis. B2 MBLs include Aeromonas hydrophyla CphA, Aeromonas veronii ImiS, and Serratia fonticola Sfh-I. 219 matched cddid_all.tbl CDD cd07708 cd07708 293794 MBL-B3-like metallo-beta-lactamases, subclass B3; MBL-fold metallo-hydrolase domain. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. Subclass B3 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. B3 MBLs include Fluoribacter gormanii FEZ-1, Elizabethkingia meningoseptica (Chryseobacterium meningosepticum) GOB-1, Stenotrophomonas Maltophilia L1, and Bradyrhizobium diazoefficiens BJP-1, Serratia marcescens SMB-1, and Pseudomonas Aeruginosa AIM-1. These B3 enzymes have a modified Zn2/DCH site (Asp-His-His). 248 matched cddid_all.tbl CDD cd07709 cd07709 293795 flavodiiron_proteins_MBL-fold catalytic domain of flavodiiron proteins (FDPs) and related proteins; MBL-fold metallo-hydrolase domain. FDPs catalyze the reduction of oxygen and/or nitric oxide to water or nitrous oxide respectively. In addition to this N-terminal catalytic domain they contain a C-terminal flavin mononucleotide-binding flavodoxin-like domain. Although some FDPs are able to reduce NO or O2 with similar catalytic efficiencies others are selective for either NO or O2, such as Escherichia coli flavorubredoxin which is selective toward NO and G. intestinalis FDP which is selective toward O2. These enzymes belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. Some members of this subgroup are single domain. 238 matched cddid_all.tbl CDD cd07710 cd07710 293796 arylsulfatase_Sdsa1-like_MBL-fold Pseudomonas aeruginosa arylsulfatase SdsA1, Pseudomonas sp. DSM6611 arylsulfatase Pisa1, and related proteins; MBL-fold metallo-hydrolase domain. Arylsulfatase (also known as aryl-sulfate sulfohydrolase, EC 3.1.6.1). Pseudomonas aeruginosa SdsA1 is a secreted SDS hydrolase that allows the bacterium to use primary sulfates such as the detergent SDS common in commercial personal hygiene products as a sole carbon or sulfur source. Pseudomonas inverting secondary alkylsulfatase 1 (Pisa1) is specific for secondary alkyl sulfates. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 239 matched cddid_all.tbl CDD cd07711 cd07711 293797 MBLAC1-like_MBL-fold uncharacterized human metallo-beta-lactamase domain-containing protein 1 and related proteins; MBL-fold metallo hydrolase domain. Includes the MBL-fold metallo hydrolase domain of uncharacterized human MBLAC1 and related proteins. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 190 matched cddid_all.tbl CDD cd07712 cd07712 293798 MBLAC2-like_MBL-fold uncharacterized human metallo-beta-lactamase domain-containing protein 2 and related proteins; MBL-fold metallo hydrolase domain. Includes the MBL-fold metallo hydrolase domain of uncharacterized human MBLAC2 and related proteins. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 182 matched cddid_all.tbl CDD cd07713 cd07713 293799 DHPS-like_MBL-fold Methanocaldococcus jannaschii dihydropteroate synthase, Thermoanaerobacter tengcongensis Tflp, and related proteins; MBL-fold metallo hydrolase domain. This subgroup includes Methanocaldococcus jannaschii 7,8-dihydropterin-6-methyl-4-(beta-D-ribofuranosyl)-aminobenzene-5'-phosphate synthase (EC 2.5.1.15), a folate biosynthetic enzyme also known as dihydropteroate synthase and 7,8 dihydropteroate synthase. Thermoanaerobacter tengcongensis Tflp is a ferredoxin-like member. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 269 matched cddid_all.tbl CDD cd07714 cd07714 293800 RNaseJ_MBL-fold RNAaseJ, MBL-fold metallo-hydrolase domain. RNase J, also called Ribonuclease J, is a prokaryotic ribonuclease which plays a key part in RNA processing and in RNA degradation. It can act as an endonuclease which is specific for single-stranded regions of RNA irrespective of their sequence or location, and as a processive 5' exonuclease which only acts on substrates having a single phosphate or a hydroxyl at the 5' end. Many bacterial species have only one RNase J, but some, such as Bacillus subtilis, have two. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 248 matched cddid_all.tbl CDD cd07715 cd07715 293801 TaR3-like_MBL-fold MBL-fold metallo-hydrolase domain of Myxococcus xanthus TaR3 and related proteins; MBL-fold metallo-hydrolase domain. Myxococcus xanthus Tar3 may function as an ammonium regulator/effector protein involved in biosynthesis of the antibiotic TA. Some are members of this subgroup are annotated as ribonucleases. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 212 matched cddid_all.tbl CDD cd07716 cd07716 293802 RNaseZ_short-form-like_MBL-fold uncharacterized bacterial subgroup of Ribonuclease Z, short form; MBL-fold metallo-hydrolase domain. The tRNA maturase RNase Z (also known as tRNase Z or 3' tRNase) catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors. Two forms of RNase Z exist in eukaryotes, one long (ELAC2) and one short form (ELAC1), the former may have resulted from a duplication of the shorter enzyme. Only the short form exists in bacteria. Members of this bacterial subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 175 matched cddid_all.tbl CDD cd07717 cd07717 293803 RNaseZ_ZiPD-like_MBL-fold Ribonuclease Z, E. coli 3' tRNA-processing endonuclease ZiPD and related proteins; MBL-fold metallo-hydrolase domain. The tRNA maturase RNase Z (also known as tRNase Z or 3' tRNase) catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors. Escherichia coli zinc phosphodiesterase (ZiPD, also known as ecoZ, tRNase Z, or RNase BN) is a 3' tRNA-processing endonuclease, encoded by the elaC gene. Two forms of RNase Z exist in eukaryotes, one long (ELAC2) and one short form (ELAC1), the former may have resulted from a duplication of the shorter enzyme; this subgroup includes the short form (ELAC1). Only the short form exists in bacteria. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 247 matched cddid_all.tbl CDD cd07718 cd07718 293804 RNaseZ_ELAC1_ELAC2-C-term-like_MBL-fold Ribonuclease Z ELAC1, C-terminus of ELAC2, and related proteins; MBL-fold metallo-hydrolase domain. The tRNA maturase RNase Z (also known as tRNase Z or 3' tRNase) catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors. Two forms of RNase Z exist in eukaryotes, one long (ELAC2) and one short form (ELAC1), the former may have resulted from a duplication of the shorter enzyme; this eukaryotic subgroup includes short forms (ELAC1) and the C-terminus of long forms including human ELAC2. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 204 matched cddid_all.tbl CDD cd07719 cd07719 293805 arylsulfatase_AtsA-like_MBL-fold Pseudoalteromonas carrageenovora arylsulfatase AtsA and related proteins; MBL-fold metallo-hydrolase domain. Arylsulfatase (also known as aryl-sulfate sulfohydrolase, EC 3.1.6.1). Pseudoalteromonas carrageenovora arylsulfatase AtsA may function as a glycosulfohydrolase involved with desulfation of sulfated polysaccharides, which catalyzes hydrolysis of the arylsulfate ester bond, producing the aryl compounds and inorganic sulfate. CD also includes some sequences annotated as ribonucleases. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily. 193 matched cddid_all.tbl CDD cd07720 cd07720 293806 OPHC2-like_MBL-fold Pseudomonas pseudoalcaligenes organophosphorus hydrolase C2, and related proteins; MBL-fold metallo hydrolase domain. Pseudomonas pseudoalcaligenes OPHC2 is a thermostable organophosphorus hydrolase which a broad substrate activity spectrum: it hydrolyzes various phosphotriesters, esters, and a lactone. This subgroup also includes Pseudomonas oleovorans PoOPH which exhibits high lactonase and esterase activities, and latent PTE activity. However, double mutations His250Ile/Ile263Trp switch PoOPH into an efficient and thermostable PTE. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 251 matched cddid_all.tbl CDD cd07721 cd07721 293807 yflN-like_MBL-fold uncharacterized subgroup which includes Bacillus subtilis yflN; MBL-fold metallo hydrolase domain. This subgroup includes the uncharacterized Bacillus subtilis yflN protein. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) from which this fold was named are only a small fraction of the activities which are included in this superfamily. Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. 202 matched cddid_all.tbl CDD cd07722 cd07722 293808 LACTB2-like_MBL-fold uncharacterized subgroup which includes human lactamase beta 2 and related proteins; MBL-fold metallo hydrolase domain. Includes functionally uncharacterized human lactamase beta 2. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) from which this fold was named are only a small fraction of the activities which are included in this superfamily. Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. 188 matched cddid_all.tbl CDD cd07723 cd07723 293809 hydroxyacylglutathione_hydrolase_MBL-fold hydroxyacylglutathione hydrolase, MBL-fold metallo-hydrolase domain. hydroxyacylglutathione hydrolase (EC 3.1.2.6, also known as, glyoxalase II; S-2-hydroxylacylglutathione hydrolase; hydroxyacylglutathione hydrolase; acetoacetylglutathione hydrolase). In the second step of the glycoxlase system this enzyme hydrolyzes S-d-lactoylglutathione to d-lactate and regenerates glutathione in the process. It has broad substrate specificity for glutathione thiol esters, hydrolyzing a number of these species to their corresponding carboxylic acids and reduced glutathione. It appears to hydrolyze 2-hydroxy thiol esters with greatest efficiency. It belongs to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 165 matched cddid_all.tbl CDD cd07724 cd07724 293810 POD-like_MBL-fold ETHE1 (PDO type I), persulfide dioxygenase A (PDOA, PDO type II) and related proteins; MBL-fold metallo-hydrolase domain. Persulfide dioxygenase (PDO, also known as sulfur dioxygenase, SDO, EC 1.13.11.18) is a non-heme iron-dependent oxygenase which catalyzes the oxidation of glutathione persulfide to glutathione and persulfite in the mitochondria. Mutations in ethe1 (the human PDO gene) are responsible for a rare autosomal recessive metabolic disorder called ethylmalonic encephalopathy. Arabidopsis thaliana ETHE1 is essential for embryo and endosperm development. Bacterial ETHE1-type PDOs are also called Type 1 PDOs. Type II PDOs (also called PDOAs), are mainly proteobacterial. These enzymes belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 177 matched cddid_all.tbl CDD cd07725 cd07725 293811 TTHA1429-like_MBL-fold uncharacterized Thermus thermophilus TTHA1429 and related proteins; MBL-fold metallo hydrolase domain. Includes the MBL-fold metallo hydrolase domain of uncharacterized Thermus thermophilus TTHA1429 and related proteins. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 184 matched cddid_all.tbl CDD cd07726 cd07726 293812 ST1585-like_MBL-fold uncharacterized subgroup which includes Sulfolobus tokodaii ST1585 protein; MBL-fold metallo hydrolase domain. This subgroup includes the uncharacterized Sulfolobus tokodaii ST1585 protein. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) from which this fold was named are only a small fraction of the activities which are included in this superfamily. Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. 215 matched cddid_all.tbl CDD cd07727 cd07727 293813 YmaE-like_MBL-fold uncharacterized subgroup which includes Bacillus subtilis YmaE and related proteins; MBL-fold metallo hydrolase domain. Includes the uncharacterized Bacillus subtilis YmaE and Nostoc all1228 proteins.Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) from which this fold was named are only a small fraction of the activities which are included in this superfamily. Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. 181 matched cddid_all.tbl CDD cd07728 cd07728 293814 YtnP-like_MBL-fold Bacillus subtilis YtnP and related proteins; MBL-fold metallo hydrolase domain. Bacillus subtilis YtnP inhibits the signaling pathway required for the streptomycin production and development of aerial mycelium in Streptomyces griseus. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 249 matched cddid_all.tbl CDD cd07729 cd07729 293815 AHL_lactonase_MBL-fold quorum-quenching N-acyl-homoserine lactonase, MBL-fold metallo-hydrolase domain. Acyl Homoserine Lactones (also known as AHLs) are signal molecules which coordinate gene expression in quorum sensing, in many Gram-negative bacteria. Quorum-quenching N-acyl-homoserine lactonase (also known as AHL lactonase, N-acyl-L-homoserine lactone hydrolase, EC 3.1.1.81) catalyzes the hydrolysis and opening of the homoserine lactone rings of AHLs, a reaction that can block quorum sensing. These enzymes belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 238 matched cddid_all.tbl CDD cd07730 cd07730 293816 metallo-hydrolase-like_MBL-fold uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain. Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily.Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. Some members of this subgroup are annotated as GumP protein. 250 matched cddid_all.tbl CDD cd07731 cd07731 293817 ComA-like_MBL-fold Competence protein ComA, ComEC and related proteins; MBL-fold metallo hydrolase domain. This subgroup includes proteins required for natural transformation competence including Neisseria gonorrhoeae ComA, Pseudomonas stutzeri ComA, Bacillus subtilis ComEC (also known as ComE operon protein 3) and Haemophilus influenza ORF2 encoded by the rec-2 gene, as well as Escherichia coli YcaI which does not mediate spontaneous plasmid transformation on nutrient-containing agar plates. It also includes the phosphorylcholine esterase (Pce) domain of choline-binding protein e from streptococcus pneumonia. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 179 matched cddid_all.tbl CDD cd07732 cd07732 293818 metallo-hydrolase-like_MBL-fold uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain. Includes functionally uncharacterized Enterococcus faecalis EF2904. Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily.Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. 202 matched cddid_all.tbl CDD cd07733 cd07733 293819 YycJ-like_MBL-fold uncharacterized subgroup which includes Bacillus subtilis YycJ and related proteins; MBL-fold metallo hydrolase domain. Includes the uncharacterized Bacillus subtilis YycJ protein. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) from which this fold was named are only a small fraction of the activities which are included in this superfamily. Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. 151 matched cddid_all.tbl CDD cd07734 cd07734 293820 Int9-11_CPSF2-3-like_MBL-fold Int9, Int11, CPSF2, CPSF3 and related cleavage and polyadenylation specificity factors; MBL-fold metallo-hydrolase domain. CPSF3 (cleavage and polyadenylation specificity factor subunit 3; also known as cleavage and polyadenylation specificity factor 73 kDa subunit, CPSF-73) and CPSF2 (also known as cleavage and polyadenylation specificity factor 100 kDa subunit /CPSF-100) are components of the CPSF complex, which plays a role in 3' end processing of pre-mRNAs during cleavage/polyadenylation, and during processing of metazoan histone pre-mRNAs. CPSF3 functions as a 3' endonuclease. Int11 (also known as cleavage and polyadenylation-specific factor (CPSF) 3-like protein, and protein related to CPSF subunits of 68 kDa (RC-68)), and Int9, also known as protein related to CPSF subunits of 74 kDa (RC-74) are subunits of Integrator, a metazoan-specific multifunctional protein complex composed of 14 subunits. Integrator has been implicated in a variety of Pol II transcription events including 3' end processing of snRNA, transcription initiation, promoter-proximal pausing, termination of protein-coding transcripts, and in HVS pre-miRNA 3' end processing. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 193 matched cddid_all.tbl CDD cd07735 cd07735 293821 class_II_PDE_MBL-fold class II cyclic nucleotide phosphodiesterases Saccharomyces cerevisiae PDE1, Dictyostelium discoideum PDE1 and PDE7, and related proteins; MBL-fold metallo-hydrolase domain. Cyclic nucleotide phosphodiesterases (PDEs) decompose the second messengers cyclic adenosine and guanosine 3',5'-monophosphate (cAMP and cGMP, respectively). Saccharomyces cerevisiae PDE1 and Dictyostelium discoideum PDE1 and PDE7, have dual cAMP/cGMP specificity. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 259 matched cddid_all.tbl CDD cd07736 cd07736 293822 PhnP-like_MBL-fold phosphodiesterase Escherichia coli PhnP and related proteins; MBL-fold metallo hydrolase domain. Escherichia coli PhnP catalyzes the hydrolysis of 5-phospho-D-ribose-1,2-cyclic phosphate to D-ribose-1,5-bisphosphate, a step in the C-P lyase pathway. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 186 matched cddid_all.tbl CDD cd07737 cd07737 293823 YcbL-like_MBL-fold Salmonella enterica serovar typhimurium YcbL and related proteins; MBL-fold metallo hydrolase domain. This subgroup includes Salmonella enterica serovar typhimurium YcbL which has type II hydroxyacylglutathione hydrolase (EC 3.1.2.6, also known as glyoxalase II) activity, and has a single metal ion binding site, and Thermus thermophilus TTHA1623 which does not have GLX2 activity and has two metal ion binding sites with a glyoxalase II-type metal coordination. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 190 matched cddid_all.tbl CDD cd07738 cd07738 293824 DdPDE5-like_MBL-fold Dictyostelium discoideum phosphodiesterase 5 and related proteins; MBL-fold metallo hydrolase domain. Includes Dictyostelium discoideum cAMP/cGMP-dependent 3',5'-cAMP/cGMP phosphodiesterase A (also known as cyclic GMP-binding protein A, phosphodiesterase 5, phosphodiesterase D, and PDE5) and cAMP/cGMP-dependent 3',5'-cAMP/cGMP phosphodiesterase B (also known as cyclic GMP-binding protein B, phosphodiesterase 6, phosphodiesterase E, and PDE6. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 189 matched cddid_all.tbl CDD cd07739 cd07739 293825 metallo-hydrolase-like_MBL-fold uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain. Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) from which this fold was named are only a small fraction of the activities which are included in this superfamily. Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. 201 matched cddid_all.tbl CDD cd07740 cd07740 293826 metallo-hydrolase-like_MBL-fold uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain. Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) from which this fold was named are only a small fraction of the activities which are included in this superfamily. Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. 194 matched cddid_all.tbl CDD cd07741 cd07741 293827 metallo-hydrolase-like_MBL-fold uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain. Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) from which this fold was named are only a small fraction of the activities which are included in this superfamily. Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. 212 matched cddid_all.tbl CDD cd07742 cd07742 293828 metallo-hydrolase-like_MBL-fold uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain. Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) from which this fold was named are only a small fraction of the activities which are included in this superfamily. Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. 249 matched cddid_all.tbl CDD cd07743 cd07743 293829 metallo-hydrolase-like_MBL-fold uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain. Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) from which this fold was named are only a small fraction of the activities which are included in this superfamily. Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. 197 matched cddid_all.tbl CDD cd07749 cd07749 143394 NT_Pol-beta-like_1 Nucleotidyltransferase (NT) domain of an uncharacterized subgroup of the Pol beta-like NT superfamily. The Pol beta-like NT superfamily includes DNA polymerase beta and other family X DNA Polymerases, as well as Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly(A) polymerases, terminal uridylyl transferases, Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. Proteins belonging to this subgroup are uncharacterized. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations essential for catalysis. These divalent metal ions are involved in a two-metal ion mechanism of nucleotide addition. These carboxylate residues are conserved in this subgroup. 156 matched cddid_all.tbl CDD cd07750 cd07750 143622 PolyPPase_VTC_like Polyphosphate(polyP) polymerase domain of yeast vacuolar transport chaperone (VTC) proteins VTC-2, -3 and- 4, and similar proteins. Saccharomyces cerevisiae VTC-1, -2, -3, and -4 comprise the membrane-integral VTC complex. VTC-2, -3, and -4 contain polyP polymerase domains. For S. cerevisiae VTC4 it has been shown that this domain generates polyP from ATP by a phosphotransfer reaction releasing ADP. This activity is metal ion-dependent. The ATP gamma phosphate may be cleaved and then transferred to an acceptor phosphate to form polyP. PolyP is ubiquitous. In prokaryotes, it is a store of phosphate and energy. In eukaryotes, polyPs have roles in bone calcification, and osmoregulation, and in phosphate transport in the symbiosis of mycorrhizal fungi and plants. This subgroup belongs to the CYTH/triphosphate tunnel metalloenzyme (TTM)-like superfamily, whose enzymes have a unique active site located within an eight-stranded beta barrel. 214 matched cddid_all.tbl CDD cd07751 cd07751 143623 PolyPPase_VTC4_like Polyphosphate(polyP) polymerase domain of yeast vacuolar transport chaperone (VTC) protein VTC4, and similar proteins. Saccharomyces cerevisiae VTC-1, -2, -3, and -4 comprise the membrane-integral VTC complex. VTC-2,-3, and -4 contain polyP polymerase domains. S. cerevisiae VTC4 belongs to this subgroup. For VTC4 it has been shown that this domain generates polyP from ATP by a phosphotransfer reaction releasing ADP. This activity is metal ion-dependent. The ATP gamma phosphate may be cleaved and then transferred to an acceptor phosphate to form polyP. PolyP is ubiquitous. In prokaryotes, it is a store of phosphate and energy. In eukaryotes, polyPs have roles in bone calcification, and osmoregulation, and in phosphate transport in the symbiosis of mycorrhizal fungi and plants. This subgroup belongs to the CYTH/triphosphate tunnel metalloenzyme (TTM)-like superfamily, whose enzymes have a unique active site located within an eight-stranded beta barrel. 290 matched cddid_all.tbl CDD cd07756 cd07756 143624 CYTH-like_Pase_CHAD Uncharacterized subgroup of the CYTH-like superfamily having an associated CHAD domain. This subgroup belongs to the CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) superfamily. Members of this superfamily hydrolyze triphosphate-containing substrates, require metal cations as cofactors, and have a unique active site located at the center of an eight-stranded antiparallel beta barrel tunnel (the triphosphate tunnel). A number of proteins in this subgroup also contain a C-terminal CHAD (Conserved Histidine Alpha-helical Domain) domain which may participate in metal chelation or act as a phosphor-acceptor. The name CYTH originated from the gene designation for bacterial class IV adenylyl cyclases (CyaB) and from thiamine triphosphatase. Class IV adenylate cyclases catalyze the conversion of ATP to 3',5'-cyclic AMP (cAMP) and PPi. Thiamine triphosphatase is a soluble cytosolic enzyme which converts thiamine triphosphate to thiamine diphosphate. This domain superfamily also contains RNA triphosphatases, membrane-associated polyphosphate polymerases, tripolyphosphatases, nucleoside triphosphatases, nucleoside tetraphosphatases and other proteins with unknown functions. Proteins of this subgroup have not been characterized. 197 matched cddid_all.tbl CDD cd07758 cd07758 143625 ThTPase Thiamine Triphosphatase. ThTPase is a soluble cytosolic enzyme which converts thiamine triphosphate (ThTP) to thiamine diphosphate. This catalytic activity depends on a divalent metal cofactor, for example Mg++. ThTPase regulates the intracellular concentration of ThTP, maintaining it at a low concentration in vivo. ThTP acts as a messenger in cell signaling in response to cellular stress, and in addition, can phosphorylate proteins in certain tissues. There is another class of membrane-associated enzymes in animal tissues which also convert ThTP to thiamine diphosphate, however they do not belong to this subgroup. This subgroup belongs to the CYTH/triphosphate tunnel metalloenzyme (TTM)-like superfamily, whose enzymes have a unique active site located within an eight-stranded beta barrel. 196 matched cddid_all.tbl CDD cd07761 cd07761 143626 CYTH-like_CthTTM-like Clostridium thermocellum (Cth)TTM and similar proteins, a subgroup of the CYTH-like superfamily. CthTTM is a metal dependent tripolyphosphatase, nucleoside triphosphatase, and nucleoside tetraphosphatase. It hydrolyzes the beta-gamma phosphoanhydride linkage of triphosphate-containing substrates including tripolyphosphate, nucleoside triphosphates and nucleoside tetraphosphates. These substrates are hydrolyzed, releasing Pi. Mg++ or Mn++ are required for the enzyme's activity. CthTTM appears to have no adenylate cyclase activity. This subgroup consists chiefly of bacterial sequences. Members of the CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) superfamily have a unique active site located within an eight-stranded beta barrel. 146 matched cddid_all.tbl CDD cd07762 cd07762 143627 CYTH-like_Pase_1 Uncharacterized subgroup 1 of the CYTH-like superfamily. Enzymes belonging to the CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) superfamily hydrolyze triphosphate-containing substrates, require metal cations as cofactors, and have a unique active site located at the center of an eight-stranded antiparallel beta barrel tunnel (the triphosphate tunnel). The name CYTH originated from the gene designation for bacterial class IV adenylyl cyclases (CyaB) and from thiamine triphosphatase. Class IV adenylate cyclases catalyze the conversion of ATP to 3',5'-cyclic AMP (cAMP) and PPi. Thiamine triphosphatase is a soluble cytosolic enzyme which converts thiamine triphosphate to thiamine diphosphate. This domain superfamily also contains RNA triphosphatases, membrane-associated polyphosphate polymerases, tripolyphosphatases, nucleoside triphosphatases, nucleoside tetraphosphatases and other proteins with unknown functions. Proteins of this subgroup are of bacterial origin and have not been characterized. 180 matched cddid_all.tbl CDD cd07765 cd07765 143639 KRAB_A-box KRAB (Kruppel-associated box) domain -A box. The KRAB domain is a transcription repression module, found in a subgroup of the zinc finger proteins (ZFPs) of the C2H2 family, KRAB-ZFPs. KRAB-ZFPs comprise the largest group of transcriptional regulators in mammals, and are only found in tetrapods. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through recruiting corepressors. A key mechanism appears to be the following: KRAB-AFPs tethered to DNA recruit, via their KRAB domain, the repressor KAP1 (KRAB-associated protein-1, also known as transcription intermediary factor 1 beta , KRAB-A interacting protein , and tripartite motif protein 28). The KAP1/ KRAB-AFP complex in turn recruits the heterochromatin protein 1 (HP1) family, and other chromatin modulating proteins, leading to transcriptional repression through heterochromatin formation. 40 matched cddid_all.tbl CDD cd07766 cd07766 341447 DHQ_Fe-ADH Dehydroquinate synthase-like (DHQ-like) and iron-containing alcohol dehydrogenases (Fe-ADH). This superfamily consists of two subgroups: the dehydroquinate synthase (DHQS)-like, and a large metal-containing alcohol dehydrogenases (ADH), known as iron-containing alcohol dehydrogenases. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds. Dehydroquinate synthase-like group includes dehydroquinate synthase, 2-deoxy-scyllo-inosose synthase, and 2-epi-5-epi-valiolone synthase. The alcohol dehydrogenases (ADHs) in this superfamily contain a dehydroquinate synthase-like protein structural fold and mostly contain iron. They are distinct from other alcohol dehydrogenases which contains different protein domains. There are several distinct families of alcohol dehydrogenases: Zinc-containing long-chain alcohol dehydrogenases; insect-type, or short-chain alcohol dehydrogenases; iron-containing alcohol dehydrogenases, and others. The iron-containing family has a Rossmann fold-like topology that resembles the fold of the zinc-dependent alcohol dehydrogenases, but lacks sequence homology, and differs in strand arrangement. ADH catalyzes the reversible oxidation of alcohol to acetaldehyde with the simultaneous reduction of NAD(P)+ to NAD(P)H. 271 matched cddid_all.tbl CDD cd07767 cd07767 163686 MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. JAB1 is a component of the COP9 signalosome (CSN), a regulatory particle of the ubiquitin (Ub)/26S proteasome system occurring in all eukaryotic cells; it cleaves the ubiquitin-like protein NEDD8 from the cullin subunit of the SCF (Skp1, Cullins, F-box proteins) family of E3 ubiquitin ligases. AMSH (associated molecule with the SH3 domain of STAM, also known as STAMBP), a member of JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves Lys 63-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. Similarly, BRCC36, part of the nuclear complex that includes BRCA1 protein and is targeted to DNA damage foci after irradiation, specifically disassembles K63-linked polyUb. BRCC36 is aberrantly expressed in sporadic breast tumors, indicative of a potential role in the pathogenesis of the disease. Some variants of the JAB1/MPN domains lack key residues in their JAMM motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the translation initiation factor 3 subunits f (p47) and h (p40) do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. 116 matched cddid_all.tbl CDD cd07768 cd07768 466788 ASKHA_NBD_FGGY_RBK-like nucleotide-binding domain (NBD) of ribulokinase-like carbohydrate kinases. The RBK family includes bacterial RBK, vertebrate D-ribulokinase FGGY (also known as FGGY carbohydrate kinase domain-containing protein), Saccharomyces cerevisiae D-ribulokinase YDR109C, and Yersinia Pseudotuberculosis uncharacterized carbohydrate kinase that has been named glyerol/xylulose kinase. RBK (EC 2.7.1.16; also known as L-ribulokinase) catalyzes the MgATP-dependent phosphorylation of L(or D)-ribulose to produce L(or D)-ribulose 5-phosphate and ADP, which is the second step in arabinose catabolism. It also phosphorylates a variety of other sugar substrates including ribitol and arabitol. D-ribulokinase (EC 2.7.1.47) catalyzes ATP-dependent phosphorylation of D-ribulose at C-5 to form D-ribulose 5-phosphate. It is postulated to function in a metabolite repair mechanism by preventing toxic accumulation of free D-ribulose formed by non-specific phosphatase activities. Alternatively, D-ribulokinase may play a role in regulating D-ribulose 5-phosphate recycling in the pentose phosphate pathway. Members of this subfamily belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 522 matched cddid_all.tbl CDD cd07769 cd07769 466789 ASKHA_NBD_FGGY_GK nucleotide-binding domain (NBD) of glycerol kinase (GK) and similar proteins. GK (EC 2.7.1.30), also called ATP:glycerol 3-phosphotransferase, or glycerokinase, is a key enzyme in the regulation of glycerol uptake and metabolism. It catalyzes the Mg-ATP-dependent phosphorylation of glycerol to yield sn-glycerol 3-phosphate. It also catalyzes the phosphorylation of dihydroxyacetone, L-glyceraldehyde and D-glyceraldehyde. The subfamily includes GKs and GK-like proteins from all three kingdoms of living organisms. Metazoan GKs, coded by X chromosome-linked GK genes, and GK-like proteins, coded by autosomal testis-specific GK-like genes GK2, GK3 and Gykl1 (in mouse) are closely related to the bacterial GKs. The metazoan GKs do have GK enzymatic activity. However, the GK-like metazoan proteins do not exhibit GK activity and their biological functions are not yet clear. Some of them lack important functional residues involved in the binding of ADP and Mg2+, which may result in the loss of GK catalytic function. Others that have conserved catalytic residues have lost their GK activity as well; the reason remains unclear. It has been suggested the conserved catalytic residues might facilitate them performing a distinct function. Under different conditions, GKs from different species may exist in different oligomeric states. Members of this subfamily belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 486 matched cddid_all.tbl CDD cd07770 cd07770 466790 ASKHA_NBD_FGGY_GntK nucleotide-binding domain (NBD) of gluconate kinase (GntK) and similar proteins. GntK (EC 2.7.1.12), also known as gluconokinase, catalyzes the ATP-dependent phosphorylation of D-gluconate and produce 6-phospho-D-gluconate and ADP. The presence of Mg2+ might be required for catalytic activity. The prototypical member of this subfamily is GntK from Lactobacillus acidophilus. Unlike Escherichia coli GntK, which belongs to the superfamily of P-loop containing nucleoside triphosphate hydrolases, Members of this subfamily are homologous to glycerol kinase, xylulose kinase, and rhamnulokinase from Escherichia coli. They have been classified as members of the FGGY family of carbohydrate kinases, which contain two large domains separated by a deep cleft that forms the active site. This model spans both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 478 matched cddid_all.tbl CDD cd07771 cd07771 466791 ASKHA_NBD_FGGY_RhaB-like nucleotide-binding domain (NBD) of rhamnulokinase (RhaB) and similar proteins. Rhamnulokinase (EC 2.7.1.5), also known as L-rhamnulose kinase, ATP:L-rhamnulose phosphotransferase, L-rhamnulose 1-kinase, or rhamnulose kinase, is an enzyme involved in the second step in rhamnose catabolism. It catalyzes the ATP-dependent phosphorylation of L-rhamnulose to produce L-rhamnulose-1-phosphate and ADP. Rhamnulokinase exists as a monomer composed of two large domains. The ATP binding site is located in the cleft between the two domains. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. The presence of divalent Mg2+ or Mn2+ is required for catalysis. The subfamily also includes Streptococcus pneumoniae L-fuculose k fuculose Kinase inase (FcsK) that uses ATP to phosphorylate fuculose creating fuculose-1-phosphate, and Alkalihalobacillus clausii bifunctional enzyme RhaA/RhaB. Members of this subfamily belong to the FGGY family of carbohydrate kinases. 460 matched cddid_all.tbl CDD cd07772 cd07772 466792 ASKHA_NBD_FGGY_NaCK-like nucleotide-binding domain (NBD) of Novosphingobium aromaticivorans carbohydrate kinase and similar proteins. This subfamily corresponds to a group of uncharacterized bacterial proteins with similarity to carbohydrate kinase from Novosphingobium aromaticivorans (NaCK). These proteins may catalyze the transfer of a phosphate group from ATP to their carbohydrate substrates. They belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 424 matched cddid_all.tbl CDD cd07773 cd07773 466793 ASKHA_NBD_FGGY_FK nucleotide-binding domain (NBD) of L-fuculokinase (FK) and similar proteins. FK (EC 2.7.1.51), also called L-fuculose kinase, catalyzes the ATP-dependent phosphorylation of L-fuculose to produce L-fuculose-1-phosphate and ADP. It can also phosphorylate, with lower efficiency, D-ribulose, D-xylulose and D-fructose. The presence of Mg2+ or Mn2+ is required for enzymatic activity. FKs belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 443 matched cddid_all.tbl CDD cd07775 cd07775 466794 ASKHA_NBD_FGGY_AI-2K nucleotide-binding domain (NBD) of autoinducer-2 kinase (AI-2 kinase) and similar proteins. AI-2 kinase (EC 2.7.1.189), also known as LsrK, catalyzes the phosphorylation of autoinducer-2 (AI-2) to phospho-AI-2, which subsequently inactivates the transcriptional regulator LsrR and leads to the transcription of the lsr operon. It phosphorylates the ring-open form of (S)-4,5-dihydroxypentane-2,3-dione (DPD), which is the precursor to all AI-2 signaling molecules, at the C5 position. It is required for the regulation of the lsr operon and many other genes. Members of this subfamily belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 492 matched cddid_all.tbl CDD cd07776 cd07776 466795 ASKHA_NBD_FGGY_SpXK-like nucleotide-binding domain (NBD) of Homo sapiens xylulose kinase (XK) and similar proteins. XK (EC 2.7.1.17), also called xylulokinase or D-xylulose kinase, catalyze the rate-limiting step in the ATP-dependent phosphorylation of D-xylulose to produce D-xylulose 5-phosphate (X5P), a molecule that may play an important role in the regulation of glucose metabolism and lipogenesis. The subfamily includes XKs mainly from eukaryote. They belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 514 matched cddid_all.tbl CDD cd07777 cd07777 466796 ASKHA_NBD_FGGY_SHK nucleotide-binding domain (NBD) of sedoheptulokinase (SHK) and similar proteins. SHK (EC 2.7.1.14), also called heptulokinase, or carbohydrate kinase-like protein (CARKL), is encoded by the carbohydrate kinase-like (CARKL/SHPK) gene. It acts as a modulator of macrophage activation through control of glucose metabolism. SHK catalyzes the ATP-dependent phosphorylation of sedoheptulose to produce sedoheptulose 7-phosphate and ADP. The presence of Mg2+ or Mn2+ might be required for catalytic activity. Members of this subfamily belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 436 matched cddid_all.tbl CDD cd07778 cd07778 466797 ASKHA_NBD_FGGY_MPA43-like nucleotide-binding domain (NBD) of Saccharomyces cerevisiae protein MPA43 and similar proteins. This subfamily contains a group of uncharacterized proteins with similarity to Saccharomyces cerevisiae protein MPA43. They belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 544 matched cddid_all.tbl CDD cd07779 cd07779 466798 ASKHA_NBD_FGGY_YgcE-like nucleotide-binding domain (NBD) of Escherichia coli sugar kinase YgcE and similar proteins. This subfamily contains a group of uncharacterized proteins with similarity to Escherichia coli sugar kinase YgcE. They belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 433 matched cddid_all.tbl CDD cd07781 cd07781 466799 ASKHA_NBD_FGGY_L-RBK nucleotide-binding domain (NBD) of ribulokinase (RBK) and similar proteins. RBK (EC 2.7.1.16; also known as L-ribulokinase) catalyzes the MgATP-dependent phosphorylation of L(or D)-ribulose to produce L(or D)-ribulose 5-phosphate and ADP, which is the second step in arabinose catabolism. It also phosphorylates a variety of other sugar substrates including ribitol and arabitol. Members of this subfamily belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 504 matched cddid_all.tbl CDD cd07782 cd07782 466800 ASKHA_NBD_FGGY_D-RBK nucleotide-binding domain (NBD) of D-ribulokinase FGGY and similar proteins. The subfamily includes vertebrate D-ribulokinase FGGY (also known as FGGY carbohydrate kinase domain-containing protein) and similar proteins, such as Saccharomyces cerevisiae D-ribulokinase YDR109C, Yersinia Pseudotuberculosis uncharacterized carbohydrate kinase that has been named glyerol/xylulose kinase. D-ribulokinase (EC 2.7.1.47) catalyzes ATP-dependent phosphorylation of D-ribulose at C-5 to form D-ribulose 5-phosphate. It is postulated to function in a metabolite repair mechanism by preventing toxic accumulation of free D-ribulose formed by non-specific phosphatase activities. Alternatively, D-ribulokinase may play a role in regulating D-ribulose 5-phosphate recycling in the pentose phosphate pathway. 540 matched cddid_all.tbl CDD cd07783 cd07783 466801 ASKHA_NBD_FGGY_SePSK_AtXK1-like nucleotide-binding domain (NBD) of Synechococcus elongatus putative sugar kinase (SePSK), Arabidopsis thaliana xylulose kinase-1 (AtXK-1) and similar proteins. This subfamily corresponds to a group of uncharacterized bacterial proteins with similarity to Synechococcus elongatus putative sugar kinase (also known as SePSK; D-ribulose kinase; D-ribulokinase) and Arabidopsis thaliana xylulose kinase-1 (also known as AtXK-1; D-ribulose kinase; D-ribulokinase; inactive xylulose kinase 1). Both kinases exhibit ATP hydrolysis without substrate and can phosphorylate D-ribulose. They belong to the ribulokinase-like carbohydrate kinases, a subfamily of FGGY family carbohydrate kinases. Ribulokinase-like carbohydrate kinases are responsible for the phosphorylation of sugars such as L-ribulose and D-ribulose. Their monomers contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 429 matched cddid_all.tbl CDD cd07786 cd07786 198361 FGGY_EcGK_like Escherichia coli glycerol kinase-like proteins; belongs to the FGGY family of carbohydrate kinases. This subgroup is composed of mostly bacterial and archaeal glycerol kinases (GK), including the well characterized proteins from Escherichia coli (EcGK), Thermococcus kodakaraensis (TkGK), and Enterococcus casseliflavus (EnGK). GKs contain two large domains separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. The high affinity ATP binding site of EcGK is created only by a substrate-induced conformational change, which is initiated by protein-protein interactions through complex formation with enzyme IIAGlc (also known as IIIGlc), the glucose-specific phosphocarrier protein of the phosphotransferase system (PTS). EcGK exists in a dimer-tetramer equilibrium. IIAGlc binds to both EcGK dimer and tetramer, and inhibits the uptake and subsequent metabolism of glycerol and maltose. Another well-known allosteric regulator of EcGK is fructose 1,6-bisphosphate (FBP), which binds to the EcGK tetramer and plays an essential role in the stabilization of the inactive tetrameric form. EcGK requires Mg2+ for its enzymatic activity. Members in this subgroup belong to the FGGY family of carbohydrate kinases 486 matched cddid_all.tbl CDD cd07792 cd07792 466802 ASKHA_NBD_FGGY_GK1-3-like nucleotide-binding domain (NBD) of metazoan glycerol kinase 1-3 (GK1-3) and similar proteins. This subfamily contains metazoan glycerol kinases (GKs), coded by X chromosome-linked GK genes, and glycerol kinase (GK)-like proteins, coded by autosomal testis-specific GK-like genes (GK-like genes, GK2 and GK3). Sequence comparison shows that metazoan GKs and GK-like proteins in this family are closely related to the bacterial GKs (EC 2.7.1.30), which catalyze the Mg-ATP dependent phosphorylation of glycerol to yield glycerol 3-phosphate (G3P). The metazoan GKs do have GK enzymatic activity. However, the GK-like metazoan proteins do not exhibit GK activity and their biological functions are not yet clear. Some of them lack important functional residues involved in the binding of ADP and Mg2+, which may result in the loss of GK catalytic function. Others that have conserved catalytic residues have lost their GK activity as well; the reason remains unclear. It has been suggested the conserved catalytic residues might facilitate them performing a distinct function. Members of this subfamily belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 499 matched cddid_all.tbl CDD cd07793 cd07793 466803 ASKHA_NBD_FGGY_GK5-like nucleotide-binding domain (NBD) of metazoan glycerol kinase 5 (GK5) and similar proteins. The subfamily corresponds to a group of metazoan putative glycerol kinases (GK), which may be coded by the GK-like gene, GK5. Sequence comparison shows members of this group are homologs of bacterial GKs, and they retain all functionally important residues. However, GK-like proteins in this family do not have detectable GK activity. The reason remains unclear. It has been suggested that the conserved catalytic residues might facilitate them performing a distinct function. GK5 is a skin-specific kinase expressed predominantly in sebaceous glands. It can form a complex with the sterol regulatory element-binding proteins (SREBPs) through their C-terminal regulatory domains, inhibiting SREBP processing and activation. GK5 also promotes gefitinib resistance by inhibiting apoptosis and cell cycle arrest. Members of this subfamily belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 501 matched cddid_all.tbl CDD cd07798 cd07798 466804 ASKHA_NBD_FGGY_YoaC-like nucleotide-binding domain (NBD) of Bacillus subtilis sugar kinase YoaC and similar proteins. The subfamily includes a group of uncharacterized proteins with similarity to Bacillus subtilis sugar kinase YoaC. It is part of the yoaDCB operon and induced by sulfate. Members of this subfamily belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 448 matched cddid_all.tbl CDD cd07802 cd07802 466805 ASKHA_NBD_FGGY_EcLyxK-like nucleotide-binding domain (NBD) of Escherichia coli L-xylulose/3-keto-L-gulonate kinase (EcLyxK) and similar proteins. The subfamily contains a group of uncharacterized proteins with similarity to Escherichia coli L-xylulose/3-keto-L-gulonate kinase (EcLyxK; EC 2.7.1.-/EC 2.7.1.53), Pasteurella multocida L-xylulose kinase (PmLyX, also known as L-xylulokinase; EC 2.7.1.53), and Brucella abortus erythritol kinase (BaEryA; EC 2.7.1.215). EcLyxK catalyzes the phosphorylation of L-xylulose and 3-keto-L-gulonate. It is involved in L-lyxose utilization via xylulose and may also be involved in the utilization of 2,3-diketo-L-gulonate. PmLyX catalyzes the phosphorylation of L-xylulose only. BaEryA catalyzes the phosphorylation of erythritol to D-erythritol-1-phosphate. Members of this subfamily belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 444 matched cddid_all.tbl CDD cd07804 cd07804 466806 ASKHA_NBD_FGGY_RrXK-like nucleotide-binding domain (NBD) of Rhodospirillum rubrum xylulose kinase (RrXK) and similar proteins. The subfamily contains a group of uncharacterized proteins with similarity to Rhodospirillum rubrum xylulose kinase (RrXK). Members of this subfamily belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 451 matched cddid_all.tbl CDD cd07805 cd07805 466807 ASKHA_NBD_FGGY_CvXK-like nucleotide-binding domain (NBD) of Chromobacterium violaceum xylulose kinase (CvXK) and similar proteins. The subfamily contains a group of uncharacterized proteins with similarity to Chromobacterium violaceum xylulose kinase (CvXK). Members of this subfamily belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 485 matched cddid_all.tbl CDD cd07808 cd07808 466808 ASKHA_NBD_FGGY_EcXK-like nucleotide-binding domain (NBD) of Escherichia coli xylulose kinase (EcXK) and similar proteins. The subfamily contains a group of uncharacterized proteins with similarity to Escherichia coli xylulose kinase (EcXK). XK (EC 2.7.1.17), also called xylulokinase or D-xylulose kinase, catalyze the rate-limiting step in the ATP-dependent phosphorylation of D-xylulose to produce D-xylulose 5-phosphate (X5P), a molecule that may play an important role in the regulation of glucose metabolism and lipogenesis. EcXK, also known as 1-deoxy-D-xylulokinase, can also catalyze the phosphorylation of 1-deoxy-D-xylulose to 1-deoxy-D-xylulose 5-phosphate, with lower efficiency. It can also use D-ribulose, xylitol and D-arabitol, but D-xylulose is preferred over the other substrates. EcXK has a weak substrate-independent Mg-ATP-hydrolyzing activity. Members of this subfamily belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 482 matched cddid_all.tbl CDD cd07809 cd07809 466809 ASKHA_NBD_FGGY_BaXK-like nucleotide-binding domain (NBD) of Bifidobacterium adolescentis xylulose kinase (XK) and similar proteins. The subfamily includes a group of uncharacterized proteins with similarity to xylulose kinases (XKs) from Bifidobacterium adolescentis, Streptomyces coelicolor, Actinoplanes missouriensis and Haemophilus influenzae. Members of this subfamily belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 443 matched cddid_all.tbl CDD cd07812 cd07812 176854 SRPBCC START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket; they bind diverse ligands. Included in this superfamily are the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), as well as the SRPBCC domains of phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of this superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins. 141 matched cddid_all.tbl CDD cd07813 cd07813 176855 COQ10p_like Coenzyme Q-binding protein COQ10p and similar proteins. Coenzyme Q-binding protein COQ10p and similar proteins. COQ10p is a hydrophobic protein located in the inner membrane of mitochondria that binds coenzyme Q (CoQ), also called ubiquinone, which is an essential electron carrier of the respiratory chain. Deletion of the gene encoding COQ10p (COQ10 or YOL008W) in Saccharomyces cerevisiae results in respiratory defect because of the inability to oxidize NADH and succinate. COQ10p may function in the delivery of CoQ (Q6 in budding yeast) to its proper location for electron transport. The human homolog, called Q-binding protein COQ10 homolog A (COQ10A), is able to fully complement for the absence of COQ10p in fission yeast. Human COQ10A also has a splice variant COQ10B. COQ10p belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. 138 matched cddid_all.tbl CDD cd07814 cd07814 176856 SRPBCC_CalC_Aha1-like Putative hydrophobic ligand-binding SRPBCC domain of Micromonospora echinospora CalC, human Aha1, and related proteins. This family includes the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of Micromonospora echinospora CalC, human Aha1, and related proteins. Proteins in this group belong to the SRPBCC domain superfamily of proteins, which bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. MeCalC confers resistance to the enediyne, calicheamicin gamma 1 (CLM), by a self sacrificing mechanism which results in inactivation of both CalC and the highly reactive diradical enediyne species. MeCalC can also inactivate two other enediynes, shishijimicin and namenamicin. A crucial Gly of the MeCalC CLM resistance mechanism is not conserved in this subgroup. This family also includes the C-terminal, Bet v1-like domain of Aha1, one of several co-chaperones, which regulate the dimeric chaperone Hsp90. Aha1 promotes dimerization of the N-terminal domains of Hsp90, and stimulates its low intrinsic ATPase activity, and may regulate the dwell time of Hsp90 with client proteins. Aha1 can act as either a positive or negative regulator of chaperone-dependent activation, depending on the client protein, but the mechanisms by which these opposing functions are achieved are unclear. Aha1 is upregulated in a number of tumor lines co-incident with the activation of several signaling kinases. 139 matched cddid_all.tbl CDD cd07815 cd07815 176857 SRPBCC_PITP Lipid-binding SRPBCC domain of Class I and Class II Phosphatidylinositol Transfer Proteins. This family includes the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of the phosphatidylinositol transfer protein (PITP) family of lipid transfer proteins. This family of proteins includes Class 1 PITPs (PITPNA/PITPalpha and PITPNB/PITPbeta, Drosophila vibrator and related proteins), Class IIA PITPs (PITPNM1/PITPalphaI/Nir2, PITPNM2/PITPalphaII/Nir3, Drosophila RdgB, and related proteins), and Class IIB PITPs (PITPNC1/RdgBbeta and related proteins). The PITP family belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. In vitro, PITPs bind phosphatidylinositol (PtdIns), as well as phosphatidylcholine (PtdCho) but with a lower affinity. They transfer these lipids from one membrane compartment to another. The cellular roles of PITPs include inositol lipid signaling, PtdIns metabolism, and membrane trafficking. Class III PITPs, exemplified by the Sec14p family, are found in yeast and plants but are unrelated in sequence and structure to Class I and II PITPs and belong to a different superfamily. 251 matched cddid_all.tbl CDD cd07816 cd07816 176858 Bet_v1-like Ligand-binding bet_v_1 domain of major pollen allergen of white birch (Betula verrucosa), Bet v 1, and related proteins. This family includes the ligand binding domain of Bet v 1 (the major pollen allergen of white birch, Betula verrucosa) and related proteins. In addition to birch Bet v 1, this family includes other plant intracellular pathogenesis-related class 10 (PR-10) proteins, norcoclaurine synthases (NCSs), cytokinin binding proteins (CSBPs), major latex proteins (MLPs), and ripening-related proteins. It belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. Members of this family binds a diverse range of ligands. Bet v 1 can bind brassinosteroids, cytokinins, flavonoids and fatty acids. Hyp-1, a PR-10 from Hypericum perforatum/St. John's wort, catalyzes the condensation of two molecules of emodin to the bioactive naphthodianthrone hypericin. NCSs catalyze the condensation of dopamine and 4-hydroxyphenylacetaldehyde to (S)-norcoclaurine, the first committed step in the biosynthesis of benzylisoquinoline alkaloids such as morphine. The role of MLPs is unclear; however, they are associated with fruit and flower development and in pathogen defense responses. A number of PR-10 proteins in this subgroup, including Bet v 1, have in vitro RNase activity, the biological significance of which is unclear. Bet v 1 family proteins have a conserved glycine-rich P (phosphate-binding)-loop proximal to the entrance of the ligand-binding pocket. However, its conformation differs from that of the canonical P-loop structure found in nucleotide-binding proteins. Several PR-10 members including Bet v1 are allergenic. Cross-reactivity of Bet v 1 with homologs from plant foods results in birch-fruit syndrome. 148 matched cddid_all.tbl CDD cd07817 cd07817 176859 SRPBCC_8 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins. Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), Class I and II phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of the superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins. 139 matched cddid_all.tbl CDD cd07818 cd07818 176860 SRPBCC_1 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins. Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), Class I and II phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of the superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins. 150 matched cddid_all.tbl CDD cd07819 cd07819 176861 SRPBCC_2 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins. Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), Class I and II phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of the superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins. 140 matched cddid_all.tbl CDD cd07820 cd07820 176862 SRPBCC_3 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins. Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), Class I and II phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of the superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins. 137 matched cddid_all.tbl CDD cd07821 cd07821 176863 PYR_PYL_RCAR_like Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins. The PYR/PYL/RCAR-like family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. PYR/PYL/RCAR plant proteins are receptors involved in signal transduction. They bind abscisic acid (ABA) and mediate its signaling. ABA is a vital plant hormone, which regulates plant growth, development, and response to environmental stresses. Upon binding ABA, these plant proteins interact with a type 2C protein phosphatase (PP2C), such as ABI1 and ABI2, and inhibit their activity. When ABA is bound, a loop (designated the gate/CL2 loop) closes over the ligand binding pocket, resulting in the weakening of the inactive PYL dimer and facilitating type 2C protein phosphatase binding. In the ABA:PYL1:ABI1 complex, the gate blocks substrate access to the phosphatase active site. A conserved Trp from PP2C inserts into PYL to lock the receptor in a closed formation. This group also contains Methylobacterium extorquens AM1 MxaD. The mxaD gene is located within the mxaFJGIR(S)ACKLDEHB cluster which encodes proteins involved in methanol oxidation. MxaD may participate in the periplasmic electron transport chain for oxidation of methanol. Mutants lacking MxaD exhibit a reduced growth on methanol, and a lower rate of respiration with methanol. 140 matched cddid_all.tbl CDD cd07822 cd07822 176864 SRPBCC_4 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins. Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), Class I and II phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of the superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins. 141 matched cddid_all.tbl CDD cd07823 cd07823 176865 SRPBCC_5 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins. Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), Class I and II phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of the superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins. 146 matched cddid_all.tbl CDD cd07824 cd07824 176866 SRPBCC_6 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins. Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), Class I and II phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of the superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins. 146 matched cddid_all.tbl CDD cd07825 cd07825 176867 SRPBCC_7 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins. Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), Class I and II phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of the superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins. 144 matched cddid_all.tbl CDD cd07826 cd07826 176868 SRPBCC_CalC_Aha1-like_9 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins. SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which regulate the dimeric chaperone Hsp90), and belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. 142 matched cddid_all.tbl CDD cd07827 cd07827 143640 RHD-n N-terminal sub-domain of the Rel homology domain (RHD). Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal sub-domain, which may be distantly related to the DNA-binding domain found in P53. The C-terminal sub-domain has an immunoglobulin-like fold and serves as a dimerization module that also binds DNA (see cd00102). The RHD is found in NF-kappa B, nuclear factor of activated T-cells (NFAT), the tonicity-responsive enhancer binding protein (TonEBP), and the arthropod proteins Dorsal and Relish (Rel). 174 matched cddid_all.tbl CDD cd07828 cd07828 381185 lipocalin_heme-bd-THAP4-like heme-binding beta-barrel domain of human THAP4, Arabidopsis thaliana nitrobindin, and similar proteins. Proteins in this subfamily use a beta-barrel domain to bind ferric heme. This group also includes the beta-barrel domain of human THAP domain containing 4 (THAP4). The THAP domain is found in proteins involved in transcriptional regulation, cell-cycle control, apoptosis and chromatin modification. Arabidopsis thaliana nitrobindin may reversibly bind nitric oxide (NO) and be involved in NO transport. It also includes the beta-barrel domain of Caenorhabditis elegans protein male abnormal 7 (Mab-7) which plays an important role in determining body shape and sensory ray morphology. This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 150 matched cddid_all.tbl CDD cd07829 cd07829 270823 STKc_CDK_like Catalytic domain of Cyclin-Dependent protein Kinase-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. CDKs are partly regulated by their subcellular localization, which defines substrate phosphorylation and the resulting specific function. CDK1, CDK2, CDK4, and CDK6 have well-defined functions in the cell cycle, such as the regulation of the early G1 phase by CDK4 or CDK6, the G1/S phase transition by CDK2, or the entry of mitosis by CDK1. They also exhibit overlapping cyclin specificity and functions in certain conditions. Knockout mice with a single CDK deleted remain viable with specific phenotypes, showing that some CDKs can compensate for each other. For example, CDK4 can compensate for the loss of CDK6, however, double knockout mice with both CDK4 and CDK6 deleted die in utero. CDK8 and CDK9 are mainly involved in transcription while CDK5 is implicated in neuronal function. CDK7 plays essential roles in both the cell cycle as a CDK-Activating Kinase (CAK) and in transcription as a component of the general transcription factor TFIIH. The CDK-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 282 matched cddid_all.tbl CDD cd07830 cd07830 270824 STKc_MAK_like Catalytic domain of Male germ cell-Associated Kinase-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of human MAK and MAK-related kinase (MRK), Saccharomyces cerevisiae Ime2p, Schizosaccharomyces pombe Mei4-dependent protein 3 (Mde3) and Pit1, Caenorhabditis elegans dyf-5, Arabidopsis thaliana MHK, and similar proteins. These proteins play important roles during meiosis. MAK is highly expressed in testicular cells specifically in the meiotic phase, but is not essential for spermatogenesis and fertility. It functions as a coactivator of the androgen receptor in prostate cells. MRK, also called Intestinal Cell Kinase (ICK), is expressed ubiquitously, with highest expression in the ovary and uterus. A missense mutation in MRK causes endocrine-cerebro-osteodysplasia, suggesting that this protein plays an important role in the development of many organs. MAK and MRK may be involved in regulating cell cycle and cell fate. Ime2p is a meiosis-specific kinase that is important during meiotic initiation and during the later stages of meiosis. Mde3 functions downstream of the transcription factor Mei-4 which is essential for meiotic prophase I. The MAK-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 283 matched cddid_all.tbl CDD cd07831 cd07831 270825 STKc_MOK Catalytic domain of the Serine/Threonine Kinase, MAPK/MAK/MRK Overlapping Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MOK, also called Renal tumor antigen 1 (RAGE-1), is widely expressed and is enriched in testis, kidney, lung, and brain. It is expressed in approximately 50% of renal cell carcinomas (RCC) and is a potential target for immunotherapy. MOK is stabilized by its association with the HSP90 molecular chaperone. It is induced by the transcription factor Cdx2 and may be involved in regulating intestinal epithelial development and differentiation. The MOK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 282 matched cddid_all.tbl CDD cd07832 cd07832 270826 STKc_CCRK Catalytic domain of the Serine/Threonine Kinase, Cell Cycle-Related Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CCRK was previously called p42. It is a Cyclin-Dependent Kinase (CDK)-Activating Kinase (CAK) which is essential for the activation of CDK2. It is indispensable for cell growth and has been implicated in the progression of glioblastoma multiforme. In the heart, a splice variant of CCRK with a different C-terminal half is expressed; this variant promotes cardiac cell growth and survival and is significantly down-regulated during the development of heart failure. The CCRK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 287 matched cddid_all.tbl CDD cd07833 cd07833 270827 STKc_CDKL Catalytic domain of Cyclin-Dependent protein Kinase Like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of CDKL1-5 and similar proteins. Some CDKLs, like CDKL1 and CDKL3, may be implicated in transformation and others, like CDKL3 and CDKL5, are associated with mental retardation when impaired. CDKL2 plays a role in learning and memory. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDKL subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 288 matched cddid_all.tbl CDD cd07834 cd07834 270828 STKc_MAPK Catalytic domain of the Serine/Threonine Kinase, Mitogen-Activated Protein Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MAPKs serve as important mediators of cellular responses to extracellular signals. They control critical cellular functions including differentiation, proliferation, migration, and apoptosis. They are also implicated in the pathogenesis of many diseases including multiple types of cancer, stroke, diabetes, and chronic inflammation. Typical MAPK pathways involve a triple kinase core cascade comprising of the MAPK, which is phosphorylated and activated by a MAPK kinase (MAP2K or MKK), which itself is phosphorylated and activated by a MAPK kinase kinase (MAP3K or MKKK). Each cascade is activated either by a small GTP-binding protein or by an adaptor protein, which transmits the signal either directly to a MAP3K to start the triple kinase core cascade or indirectly through a mediator kinase, a MAP4K. There are three typical MAPK subfamilies: Extracellular signal-Regulated Kinase (ERK), c-Jun N-terminal Kinase (JNK), and p38. Some MAPKs are atypical in that they are not regulated by MAP2Ks. These include MAPK4, MAPK6, NLK, and ERK7. The MAPK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 329 matched cddid_all.tbl CDD cd07835 cd07835 270829 STKc_CDK1_CdkB_like Catalytic domain of Cyclin-Dependent protein Kinase 1-like Serine/Threonine Kinases and of Plant B-type Cyclin-Dependent protein Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of CDK, CDK2, and CDK3. CDK1 is also called Cell division control protein 2 (Cdc2) or p34 protein kinase, and is regulated by cyclins A, B, and E. The CDK1/cyclin A complex controls G2 phase entry and progression while the CDK1/cyclin B complex is critical for G2 to M phase transition. CDK2 is regulated by cyclin E or cyclin A. Upon activation by cyclin E, it phosphorylates the retinoblastoma (pRb) protein which activates E2F mediated transcription and allows cells to move into S phase. The CDK2/cyclin A complex plays a role in regulating DNA replication. Studies in knockout mice revealed that CDK1 can compensate for the loss of the cdk2 gene as it can also bind cyclin E and drive G1 to S phase transition. CDK3 is regulated by cyclin C and it phosphorylates pRB specifically during the G0/G1 transition. This phosphorylation is required for cells to exit G0 efficiently and enter the G1 phase. The plant-specific B-type CDKs are expressed from the late S to the M phase of the cell cycle. They are characterized by the cyclin binding motif PPT[A/T]LRE. They play a role in controlling mitosis and integrating developmental pathways, such as stomata and leaf development. CdkB has been shown to associate with both cyclin B, which controls G2/M transition, and cyclin D, which acts as a mediator in linking extracellular signals to the cell cycle. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 283 matched cddid_all.tbl CDD cd07836 cd07836 143341 STKc_Pho85 Catalytic domain of the Serine/Threonine Kinase, Fungal Cyclin-Dependent protein Kinase Pho85. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Pho85 is a multifunctional CDK in yeast. It is regulated by 10 different cyclins (Pcls) and plays a role in G1 progression, cell polarity, phosphate and glycogen metabolism, gene expression, and in signaling changes in the environment. It is not essential for yeast viability and is the functional homolog of mammalian CDK5, which plays a role in central nervous system development. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The Pho85 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 284 matched cddid_all.tbl CDD cd07837 cd07837 270830 STKc_CdkB_plant Catalytic domain of the Serine/Threonine Kinase, Plant B-type Cyclin-Dependent protein Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The plant-specific B-type CDKs are expressed from the late S to the M phase of the cell cycle. They are characterized by the cyclin binding motif PPT[A/T]LRE. They play a role in controlling mitosis and integrating developmental pathways, such as stomata and leaf development. CdkB has been shown to associate with both cyclin B, which controls G2/M transition, and cyclin D, which acts as a mediator in linking extracellular signals to the cell cycle. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CdkB subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 294 matched cddid_all.tbl CDD cd07838 cd07838 270831 STKc_CDK4_6_like Catalytic domain of Cyclin-Dependent protein Kinase 4 and 6-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDK4 and CDK6 partner with D-type cyclins to regulate the early G1 phase of the cell cycle. They are the first kinases activated by mitogenic signals to release cells from the G0 arrested state. CDK4 and CDK6 are both expressed ubiquitously, associate with all three D cyclins (D1, D2 and D3), and phosphorylate the retinoblastoma (pRb) protein. They are also regulated by the INK4 family of inhibitors which associate with either the CDK alone or the CDK/cyclin complex. CDK4 and CDK6 show differences in subcellular localization, sensitivity to some inhibitors, timing in activation, tumor selectivity, and possibly substrate profiles. Although CDK4 and CDK6 seem to show some redundancy, they also have discrete, nonoverlapping functions. CDK6 plays an important role in cell differentiation. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDK4/6-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 287 matched cddid_all.tbl CDD cd07839 cd07839 143344 STKc_CDK5 Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 5. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDK5 is unusual in that it is regulated by non-cyclin proteins, p35 and p39. It is highly expressed in the nervous system and is critical in normal neural development and function. It plays a role in neuronal migration and differentiation, and is also important in synaptic plasticity and learning. CDK5 also participates in protecting against cell death and promoting angiogenesis. Impaired CDK5 activity is implicated in Alzheimer's disease, amyotrophic lateral sclerosis, Parkinson's disease, Huntington's disease and acute neuronal injury. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDK5 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 284 matched cddid_all.tbl CDD cd07840 cd07840 270832 STKc_CDK9_like Catalytic domain of Cyclin-Dependent protein Kinase 9-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of CDK9 and CDK12 from higher eukaryotes, yeast BUR1, C-type plant CDKs (CdkC), and similar proteins. CDK9, BUR1, and CdkC are functionally equivalent. They act as a kinase for the C-terminal domain of RNA polymerase II and participate in regulating mutliple steps of gene expression including transcription elongation and RNA processing. CDK9 and CdkC associate with T-type cyclins while BUR1 associates with the cyclin BUR2. CDK12 is a unique CDK that contains an arginine/serine-rich (RS) domain, which is predominantly found in splicing factors. CDK12 interacts with cyclins L1 and L2, and participates in regulating transcription and alternative splicing. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDK9-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 291 matched cddid_all.tbl CDD cd07841 cd07841 270833 STKc_CDK7 Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 7. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDK7 plays essential roles in the cell cycle and in transcription. It associates with cyclin H and MAT1 and acts as a CDK-Activating Kinase (CAK) by phosphorylating and activating cell cycle CDKs (CDK1/2/4/6). In the brain, it activates CDK5. CDK7 is also a component of the general transcription factor TFIIH, which phosphorylates the C-terminal domain (CTD) of RNA polymerase II when it is bound with unphosphorylated DNA, as present in the pre-initiation complex. Following phosphorylation, the CTD dissociates from the DNA which allows transcription initiation. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDK7 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 298 matched cddid_all.tbl CDD cd07842 cd07842 270834 STKc_CDK8_like Catalytic domain of Cyclin-Dependent protein Kinase 8-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of CDK8, CDC2L6, and similar proteins. CDK8 functions as a negative or positive regulator of transcription, depending on the scenario. Together with its regulator, cyclin C, it reversibly associates with the multi-subunit core Mediator complex, a cofactor that is involved in regulating RNA polymerase II-dependent transcription. CDC2L6 also associates with Mediator in complexes lacking CDK8. In VP16-dependent transcriptional activation, CDK8 and CDC2L6 exerts opposing effects by positive and negative regulation, respectively, in similar conditions. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDK8-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 316 matched cddid_all.tbl CDD cd07843 cd07843 173741 STKc_CDC2L1 Catalytic domain of the Serine/Threonine Kinase, Cell Division Cycle 2-like 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDC2L1, also called PITSLRE, exists in different isoforms which are named using the alias CDK11(p). The CDC2L1 gene produces two protein products, CDK11(p110) and CDK11(p58). CDC2L1 is also represented by the caspase-processed CDK11(p46). CDK11(p110), the major isoform, associates with cyclin L and is expressed throughout the cell cycle. It is involved in RNA processing and the regulation of transcription. CDK11(p58) associates with cyclin D3 and is expressed during the G2/M phase of the cell cycle. It plays roles in spindle morphogenesis, centrosome maturation, sister chromatid cohesion, and the completion of mitosis. CDK11(p46) is formed from the larger isoforms by caspases during TNFalpha- and Fas-induced apoptosis. It functions as a downstream effector kinase in apoptotic signaling pathways and interacts with eukaryotic initiation factor 3f (eIF3f), p21-activated kinase (PAK1), and Ran-binding protein (RanBPM). CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDC2L1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 293 matched cddid_all.tbl CDD cd07844 cd07844 270835 STKc_PCTAIRE_like Catalytic domain of PCTAIRE-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PCTAIRE-like proteins show unusual expression patterns with high levels in post-mitotic tissues, suggesting that they may be involved in regulating post-mitotic cellular events. They share sequence similarity with Cyclin-Dependent Kinases (CDKs), which belong to a large family of STKs that are regulated by their cognate cyclins. Together, CDKs and cyclins are involved in the control of cell-cycle progression, transcription, and neuronal function. The association of PCTAIRE-like proteins with cyclins has not been widely studied, although PFTAIRE-1 has been shown to function as a CDK which is regulated by cyclin D3 as well as the membrane-associated cyclin Y. The PCTAIRE-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 286 matched cddid_all.tbl CDD cd07845 cd07845 173742 STKc_CDK10 Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 10. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDK10, also called PISSLRE, is essential for cell growth and proliferation, and acts through the G2/M phase of the cell cycle. CDK10 has also been identified as an important factor in endocrine therapy resistance in breast cancer. CDK10 silencing increases the transcription of c-RAF and the activation of the p42/p44 MAPK pathway, which leads to antiestrogen resistance. Patients who express low levels of CDK10 relapse early on tamoxifen. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDK10 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 309 matched cddid_all.tbl CDD cd07846 cd07846 270836 STKc_CDKL2_3 Catalytic domain of the Serine/Threonine Kinases, Cyclin-Dependent protein Kinase Like 2 and 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDKL2, also called p56 KKIAMRE, is expressed in testis, kidney, lung, and brain. It functions mainly in mature neurons and plays an important role in learning and memory. Inactivation of CDKL3, also called NKIAMRE (NKIATRE in rat), by translocation is associated with mild mental retardation. It has been reported that CDKL3 is lost in leukemic cells having a chromosome arm 5q deletion, and may contribute to the transformed phenotype. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDKL2/3 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 286 matched cddid_all.tbl CDD cd07847 cd07847 270837 STKc_CDKL1_4 Catalytic domain of the Serine/Threonine Kinases, Cyclin-Dependent protein Kinase Like 1 and 4. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDKL1, also called p42 KKIALRE, is a glial protein that is upregulated in gliosis. It is present in neuroblastoma and A431 human carcinoma cells, and may be implicated in neoplastic transformation. The function of CDKL4 is unknown. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDKL1/4 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 286 matched cddid_all.tbl CDD cd07848 cd07848 270838 STKc_CDKL5 Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase Like 5. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Mutations in the gene encoding CDKL5, previously called STK9, are associated with early onset epilepsy and severe mental retardation [X-linked infantile spasm syndrome (ISSX) or West syndrome]. In addition, CDKL5 mutations also sometimes cause a phenotype similar to Rett syndrome (RTT), a progressive neurodevelopmental disorder. These pathogenic mutations are located in the N-terminal portion of the protein within the kinase domain. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDKL5 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 287 matched cddid_all.tbl CDD cd07849 cd07849 270839 STKc_ERK1_2_like Catalytic domain of Extracellular signal-Regulated Kinase 1 and 2-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of the mitogen-activated protein kinases (MAPKs) ERK1, ERK2, baker's yeast Fus3, and similar proteins. MAPK pathways are important mediators of cellular responses to extracellular signals. ERK1/2 activation is preferentially by mitogenic factors, differentiation stimuli, and cytokines, through a kinase cascade involving the MAPK kinases MEK1/2 and a MAPK kinase kinase from the Raf family. ERK1/2 have numerous substrates, many of which are nuclear and participate in transcriptional regulation of many cellular processes. They regulate cell growth, cell proliferation, and cell cycle progression from G1 to S phase. Although the distinct roles of ERK1 and ERK2 have not been fully determined, it is known that ERK2 can maintain most functions in the absence of ERK1, and that the deletion of ERK2 is embryonically lethal. The MAPK, Fus3, regulates yeast mating processes including mating-specific gene expression, G1 arrest, mating projection, and cell fusion. This ERK1/2-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 336 matched cddid_all.tbl CDD cd07850 cd07850 270840 STKc_JNK Catalytic domain of the Serine/Threonine Kinase, c-Jun N-terminal Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. JNKs are mitogen-activated protein kinases (MAPKs) that are involved in many stress-activated responses including those during inflammation, neurodegeneration, apoptosis, and persistent pain sensitization, among others. They are also essential regulators of physiological and pathological processes and are involved in the pathogenesis of several diseases such as diabetes, atherosclerosis, stroke, Parkinson's and Alzheimer's. Vetebrates harbor three different JNK genes (Jnk1, Jnk2, and Jnk3) that are alternatively spliced to produce at least 10 isoforms. JNKs are specifically activated by the MAPK kinases MKK4 and MKK7, which are in turn activated by upstream MAPK kinase kinases as a result of different stimuli including stresses such as ultraviolet (UV) irradiation, hyperosmolarity, heat shock, or cytokines. JNKs activate a large number of different substrates based on specific stimulus, cell type, and cellular condition, and may be implicated in seemingly contradictory functions. The JNK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 337 matched cddid_all.tbl CDD cd07851 cd07851 143356 STKc_p38 Catalytic domain of the Serine/Threonine Kinase, p38 Mitogen-Activated Protein Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. p38 kinases are mitogen-activated protein kinases (MAPKs), serving as important mediators of cellular responses to extracellular signals. They function in the regulation of the cell cycle, cell development, cell differentiation, senescence, tumorigenesis, apoptosis, pain development and pain progression, and immune responses. p38 kinases are activated by the MAPK kinases MKK3 and MKK6, which in turn are activated by upstream MAPK kinase kinases including TAK1, ASK1, and MLK3, in response to cellular stresses or inflammatory cytokines. p38 substrates include other protein kinases and factors that regulate transcription, nuclear export, mRNA stability and translation. p38 kinases are drug targets for the inflammatory diseases psoriasis, rheumatoid arthritis, and chronic pulmonary disease. Vertebrates contain four isoforms of p38, named alpha, beta, gamma, and delta, which show varying substrate specificity and expression patterns. p38alpha and p38beta are ubiquitously expressed, p38gamma is predominantly found in skeletal muscle, and p38delta is found in the heart, lung, testis, pancreas, and small intestine. The p38 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 343 matched cddid_all.tbl CDD cd07852 cd07852 270841 STKc_MAPK15-like Catalytic domain of the Serine/Threonine Kinase, Mitogen-Activated Protein Kinase 15 and similar MAPKs. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Human MAPK15 is also called Extracellular signal Regulated Kinase 8 (ERK8) while the rat protein is called ERK7. ERK7 and ERK8 display both similar and different biochemical properties. They autophosphorylate and activate themselves and do not require upstream activating kinases. ERK7 is constitutively active and is not affected by extracellular stimuli whereas ERK8 shows low basal activity and is activated by DNA-damaging agents. ERK7 and ERK8 also have different substrate profiles. Genome analysis shows that they are orthologs with similar gene structures. ERK7 and ERK 8 may be involved in the signaling of some nuclear receptor transcription factors. ERK7 regulates hormone-dependent degradation of estrogen receptor alpha while ERK8 down-regulates the transcriptional co-activation androgen and glucocorticoid receptors. MAPKs are important mediators of cellular responses to extracellular signals. The MAPK15 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 337 matched cddid_all.tbl CDD cd07853 cd07853 173748 STKc_NLK Catalytic domain of the Serine/Threonine Kinase, Nemo-Like Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. NLK is an atypical mitogen-activated protein kinase (MAPK) that is not regulated by a MAPK kinase. It functions downstream of the MAPK kinase kinase Tak1, which also plays a role in activating the JNK and p38 MAPKs. The Tak1/NLK pathways are regulated by Wnts, a family of secreted proteins that is critical in the control of asymmetric division and cell polarity. NLK can phosphorylate transcription factors from the TCF/LEF family, inhibiting their ability to activate the transcription of target genes. In prostate cancer cells, NLK is involved in regulating androgen receptor-mediated transcription and its expression is altered during cancer progression. MAPKs are important mediators of cellular responses to extracellular signals. The NLK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 372 matched cddid_all.tbl CDD cd07854 cd07854 143359 STKc_MAPK4_6 Catalytic domain of the Serine/Threonine Kinases, Mitogen-Activated Protein Kinases 4 (also called ERK4) and 6 (also called ERK3). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MAPK4 (also called ERK4 or p63MAPK) and MAPK6 (also called ERK3 or p97MAPK) are atypical MAPKs that are not regulated by MAPK kinases. MAPK6 is expressed ubiquitously with highest amounts in brain and skeletal muscle. It may be involved in the control of cell differentiation by negatively regulating cell cycle progression in certain conditions. It may also play a role in glucose-induced insulin secretion. MAPK6 and MAPK4 cooperate to regulate the activity of MAPK-activated protein kinase 5 (MK5), leading to its relocation to the cytoplasm and exclusion from the nucleus. The MAPK6/MK5 and MAPK4/MK5 pathways may play critical roles in embryonic and post-natal development. MAPKs are important mediators of cellular responses to extracellular signals. The MAPK4/6 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 342 matched cddid_all.tbl CDD cd07855 cd07855 270842 STKc_ERK5 Catalytic domain of the Serine/Threonine Kinase, Extracellular signal-Regulated Kinase 5. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. ERK5 (also called Big MAPK1 (BMK1) or MAPK7) has a unique C-terminal extension, making it approximately twice as big as other MAPKs. This extension contains transcriptional activation capability which is inhibited by the N-terminal half. ERK5 is activated in response to growth factors and stress by a cascade that leads to its phosphorylation by the MAP2K MEK5, which in turn is regulated by the MAP3Ks MEKK2 and MEKK3. Activated ERK5 phosphorylates its targets including myocyte enhancer factor 2 (MEF2), Sap1a, c-Myc, and RSK. It plays a role in EGF-induced cell proliferation during the G1/S phase transition. Studies on knockout mice revealed that ERK5 is essential for cardiovascular development and plays an important role in angiogenesis. It is also critical for neural differentiation and survival. The ERK5 pathway has been implicated in the pathogenesis of many diseases including cancer, cardiac hypertrophy, and atherosclerosis. MAPKs are important mediators of cellular responses to extracellular signals. The ERK5 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 336 matched cddid_all.tbl CDD cd07856 cd07856 270843 STKc_Sty1_Hog1 Catalytic domain of the Serine/Threonine Kinases, Fungal Mitogen-Activated Protein Kinases Sty1 and Hog1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of the MAPKs Sty1 from Schizosaccharomyces pombe, Hog1 from Saccharomyces cerevisiae, and similar proteins. Sty1 and Hog1 are stress-activated MAPKs that partipate in transcriptional regulation in response to stress. Sty1 is activated in response to oxidative stress, osmotic stress, and UV radiation. It is regulated by the MAP2K Wis1, which is activated by the MAP3Ks Wis4 and Win1, which receive signals of the stress condition from membrane-spanning histidine kinases Mak1-3. Activated Sty1 stabilizes the Atf1 transcription factor and induces transcription of Atf1-dependent genes of the core environmetal stress response. Hog1 is the key element in the high osmolarity glycerol (HOG) pathway and is activated upon hyperosmotic stress. Activated Hog1 accumulates in the nucleus and regulates stress-induced transcription. The HOG pathway is mediated by two transmembrane osmosensors, Sln1 and Sho1. MAPKs are important mediators of cellular responses to extracellular signals. The Sty1/Hog1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 328 matched cddid_all.tbl CDD cd07857 cd07857 173750 STKc_MPK1 Catalytic domain of the Serine/Threonine Kinase, Fungal Mitogen-Activated Protein Kinase MPK1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of the MAPKs MPK1 from Saccharomyces cerevisiae, Pmk1 from Schizosaccharomyces pombe, and similar proteins. MPK1 (also called Slt2) and Pmk1 (also called Spm1) are stress-activated MAPKs that regulate the cell wall integrity pathway, and are therefore important in the maintainance of cell shape, cell wall construction, morphogenesis, and ion homeostasis. MPK1 is activated in response to cell wall stress including heat stimulation, osmotic shock, UV irradiation, and any agents that interfere with cell wall biogenesis such as chitin antagonists, caffeine, or zymolase. MPK1 is regulated by the MAP2Ks Mkk1/2, which are regulated by the MAP3K Bck1. Pmk1 is also activated by multiple stresses including elevated temperatures, hyper- or hypotonic stress, glucose deprivation, exposure to cell-wall damaging compounds, and oxidative stress. It is regulated by the MAP2K Pek1, which is regulated by the MAP3K Mkh1. MAPKs are important mediators of cellular responses to extracellular signals. The MPK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 332 matched cddid_all.tbl CDD cd07858 cd07858 143363 STKc_TEY_MAPK Catalytic domain of the Serine/Threonine Kinases, Plant TEY Mitogen-Activated Protein Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Plant MAPKs are typed based on the conserved phosphorylation motif present in the activation loop, TEY and TDY. This subfamily represents the TEY subtype of plant MAPKs and is further subdivided into three groups (A, B, and C). Group A is represented by AtMPK3, AtMPK6, Nicotiana tabacum BTF4 (NtNTF4), among others. They are mostly involved in environmental and hormonal responses. AtMPK3 and AtMPK6 are also key regulators for stomatal development and patterning. Group B is represented by AtMPK4, AtMPK13, and NtNTF6, among others. They may be involved in both cell division and environmental stress response. AtMPK4 also participates in regulating innate immunity. Group C is represented by AtMPK1, AtMPK2, NtNTF3, Oryza sativa MAPK4 (OsMAPK4), among others. They may also be involved in stress responses. AtMPK1 and AtMPK2 are activated following mechanical injury and in the presence of stress chemicals such as jasmonic acid, hydrogen peroxide and abscisic acid. OsMAPK4 is also called OsMSRMK3 for Multiple Stress-Responsive MAPK3. In plants, MAPKs are associated with physiological, developmental, hormonal, and stress responses. Some plants show numerous gene duplications of MAPKs; Arabidopsis thaliana harbors at least 20 MAPKs, named AtMPK1-20. The TEY MAPK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 337 matched cddid_all.tbl CDD cd07859 cd07859 143364 STKc_TDY_MAPK Catalytic domain of the Serine/Threonine Kinases, Plant TDY Mitogen-Activated Protein Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Plant MAPKs are typed based on the conserved phosphorylation motif present in the activation loop, TEY and TDY. This subfamily represents the TDY subtype and is composed of Group D plant MAPKs including Arabidopsis thaliana MPK18 (AtMPK18), Oryza sativa Blast- and Wound-induced MAPK1 (OsBWMK1), OsWJUMK1 (Wound- and JA-Uninducible MAPK1), Zea mays MPK6, and the Medicago sativa TDY1 gene product. OsBWMK1 enhances resistance to pathogenic infections. It mediates stress-activated defense responses by activating a transcription factor that affects the expression of stress-related genes. AtMPK18 is involved in microtubule-related functions. In plants, MAPKs are associated with physiological, developmental, hormonal, and stress responses. Some plants show numerous gene duplications of MAPKs; Arabidopsis thaliana harbors at least 20 MAPKs, named AtMPK1-20 while Oryza sativa contains at least 17 MAPKs. Arabidopsis thaliana contains more TEY-type MAPKs than TDY-type, whereas the reverse is true for Oryza sativa. The TDY MAPK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 338 matched cddid_all.tbl CDD cd07860 cd07860 270844 STKc_CDK2_3 Catalytic domain of the Serine/Threonine Kinases, Cyclin-Dependent protein Kinase 2 and 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDK2 is regulated by cyclin E or cyclin A. Upon activation by cyclin E, it phosphorylates the retinoblastoma (pRb) protein which activates E2F mediated transcription and allows cells to move into S phase. The CDK2/cyclin A complex plays a role in regulating DNA replication. CDK2, together with CDK4, also regulates embryonic cell proliferation. Despite these important roles, mice deleted for the cdk2 gene are viable and normal except for being sterile. This may be due to compensation provided by CDK1 (also called Cdc2), which can also bind cyclin E and drive the G1 to S phase transition. CDK3 is regulated by cyclin C and it phosphorylates pRB specifically during the G0/G1 transition. This phosphorylation is required for cells to exit G0 efficiently and enter the G1 phase. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDK2/3 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 284 matched cddid_all.tbl CDD cd07861 cd07861 270845 STKc_CDK1_euk Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 1 from higher eukaryotes. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDK1 is also called Cell division control protein 2 (Cdc2) or p34 protein kinase, and is regulated by cyclins A, B, and E. The CDK1/cyclin A complex controls G2 phase entry and progression. CDK1/cyclin A2 has also been implicated as an important regulator of S phase events. The CDK1/cyclin B complex is critical for G2 to M phase transition. It induces mitosis by activating nuclear enzymes that regulate chromatin condensation, nuclear membrane degradation, mitosis-specific microtubule and cytoskeletal reorganization. CDK1 also associates with cyclin E and plays a role in the entry into S phase. CDK1 transcription is stable throughout the cell cycle but is modulated in some pathological conditions. It may play a role in regulating apoptosis under these conditions. In breast cancer cells, HER2 can mediate apoptosis by inactivating CDK1. Activation of CDK1 may contribute to HIV-1 induced apoptosis as well as neuronal apoptosis in neurodegenerative diseases. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 285 matched cddid_all.tbl CDD cd07862 cd07862 270846 STKc_CDK6 Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 6. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDK6 is regulated by D-type cyclins and INK4 inhibitors. It is active towards the retinoblastoma (pRb) protein, implicating it to function in regulating the early G1 phase of the cell cycle. It is expressed ubiquitously and is localized in the cytoplasm. It is also present in the ruffling edge of spreading fibroblasts and may play a role in cell spreading. It binds to the p21 inhibitor without any effect on its own activity and it is overexpressed in squamous cell carcinomas and neuroblastomas. CDK6 has also been shown to inhibit cell differentiation in many cell types. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDK6 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 290 matched cddid_all.tbl CDD cd07863 cd07863 143368 STKc_CDK4 Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 4. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDK4 partners with all three D-type cyclins (D1, D2, and D3) and is also regulated by INK4 inhibitors. It is active towards the retinoblastoma (pRb) protein and plays a role in regulating the early G1 phase of the cell cycle. It is expressed ubiquitously and is localized in the nucleus. CDK4 also shows kinase activity towards Smad3, a signal transducer of TGF-beta signaling which modulates transcription and plays a role in cell proliferation and apoptosis. CDK4 is inhibited by the p21 inhibitor and is specifically mutated in human melanoma. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDK4 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 288 matched cddid_all.tbl CDD cd07864 cd07864 270847 STKc_CDK12 Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 12. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDK12 is also called Cdc2-related protein kinase 7 (CRK7) or Cdc2-related kinase arginine/serine-rich (CrkRS). It is a unique CDK that contains an RS domain, which is predominantly found in splicing factors. CDK12 is widely expressed in tissues. It interacts with cyclins L1 and L2, and plays roles in regulating transcription and alternative splicing. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDK12 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 302 matched cddid_all.tbl CDD cd07865 cd07865 270848 STKc_CDK9 Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 9. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDK9, together with a cyclin partner (cyclin T1, T2a, T2b, or K), is the main component of distinct positive transcription elongation factors (P-TEFb), which function as Ser2 C-terminal domain kinases of RNA polymerase II. P-TEFb participates in multiple steps of gene expression including transcription elongation, mRNA synthesis, processing, export, and translation. It also plays a role in mediating cytokine induced transcription networks such as IL6-induced STAT3 signaling. In addition, the CDK9/cyclin T2a complex promotes muscle differentiation and enhances the function of some myogenic regulatory factors. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDK9 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 310 matched cddid_all.tbl CDD cd07866 cd07866 270849 STKc_BUR1 Catalytic domain of the Serine/Threonine Kinase, Fungal Cyclin-Dependent protein Kinase (CDK), Bypass UAS Requirement 1, and similar proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. BUR1, also called SGV1, is a yeast CDK that is functionally equivalent to mammalian CDK9. It associates with the cyclin BUR2. BUR genes were orginally identified in a genetic screen as factors involved in general transcription. The BUR1/BUR2 complex phosphorylates the C-terminal domain of RNA polymerase II. In addition, this complex regulates histone modification by phosporylating Rad6 and mediating the association of the Paf1 complex with chromatin. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The BUR1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 311 matched cddid_all.tbl CDD cd07867 cd07867 270850 STKc_CDC2L6 Catalytic domain of Serine/Threonine Kinase, Cell Division Cycle 2-like 6. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDC2L6 is also called CDK8-like and was previously referred to as CDK11. However, this is a confusing nomenclature as CDC2L6 is distinct from CDC2L1, which is represented by the two protein products from its gene, called CDK11(p110) and CDK11(p58), as well as the caspase-processed CDK11(p46). CDK11(p110), CDK11(p58), and CDK11(p46)do not belong to this subfamily. CDC2L6 is an associated protein of Mediator, a multiprotein complex that provides a platform to connect transcriptional and chromatin regulators and cofactors, in order to activate and mediate RNA polymerase II transcription. CDC2L6 is localized mainly in the nucleus amd exerts an opposing effect to CDK8 in VP16-dependent transcriptional activation by being a negative regulator. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDC2L6 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 318 matched cddid_all.tbl CDD cd07868 cd07868 270851 STKc_CDK8 Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 8. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CDK8 can act as a negative or positive regulator of transcription, depending on the scenario. Together with its regulator, cyclin C, it reversibly associates with the multi-subunit core Mediator complex, a cofactor that is involved in regulating RNA polymerase II (RNAP II)-dependent transcription. CDK8 phosphorylates cyclin H, a subunit of the general transcription factor TFIIH, which results in the inhibition of TFIIH-dependent phosphorylation of the C-terminal domain of RNAP II, facilitating the inhibition of transcription. It has also been shown to promote transcription by a mechanism that is likely to involve RNAP II phosphorylation. CDK8 also functions as a stimulus-specific positive coregulator of p53 transcriptional responses. CDKs belong to a large family of STKs that are regulated by their cognate cyclins. Together, they are involved in the control of cell-cycle progression, transcription, and neuronal function. The CDK8 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 333 matched cddid_all.tbl CDD cd07869 cd07869 143374 STKc_PFTAIRE1 Catalytic domain of the Serine/Threonine Kinase, PFTAIRE-1 kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PFTAIRE-1 is widely expressed except in the spleen and thymus. It is highly expressed in the brain, heart, pancreas, testis, and ovary, and is localized in the cytoplasm. It is regulated by cyclin D3 and is inhibited by the p21 cell cycle inhibitor. It has also been shown to interact with the membrane-associated cyclin Y, which recruits the protein to the plasma membrane. PFTAIRE-1 shares sequence similarity with Cyclin-Dependent Kinases (CDKs), which belong to a large family of STKs that are regulated by their cognate cyclins. Together, CDKs and cyclins are involved in the control of cell-cycle progression, transcription, and neuronal function. The PFTAIRE-1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 303 matched cddid_all.tbl CDD cd07870 cd07870 270852 STKc_PFTAIRE2 Catalytic domain of the Serine/Threonine Kinase, PFTAIRE-2 kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PFTAIRE-2 is also referred to as ALS2CR7 (amyotrophic lateral sclerosis 2 (juvenile) chromosome region candidate 7). It may be associated with amyotrophic lateral sclerosis 2 (ALS2), an autosomal recessive form of juvenile ALS. The function of PFTAIRE-2 is not yet known. It shares sequence similarity with Cyclin-Dependent Kinases (CDKs), which belong to a large family of STKs that are regulated by their cognate cyclins. Together, CDKs and cyclins are involved in the control of cell-cycle progression, transcription, and neuronal function. The PFTAIRE-2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 286 matched cddid_all.tbl CDD cd07871 cd07871 270853 STKc_PCTAIRE3 Catalytic domain of the Serine/Threonine Kinase, PCTAIRE-3 kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PCTAIRE-3 shows a restricted pattern of expression and is present in brain, kidney, and intestine. It is elevated in Alzheimer's disease (AD) and has been shown to associate with paired helical filaments (PHFs) and stimulate Tau phosphorylation. As AD progresses, phosphorylated Tau aggregates and forms PHFs, which leads to the formation of neurofibrillary tangles. In human glioma cells, PCTAIRE-3 induces cell cycle arrest and cell death. PCTAIRE-3 shares sequence similarity with Cyclin-Dependent Kinases (CDKs), which belong to a large family of STKs that are regulated by their cognate cyclins. Together, CDKs and cyclins are involved in the control of cell-cycle progression, transcription, and neuronal function. The PCTAIRE-3 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 288 matched cddid_all.tbl CDD cd07872 cd07872 143377 STKc_PCTAIRE2 Catalytic domain of the Serine/Threonine Kinase, PCTAIRE-2 kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PCTAIRE-2 is specifically expressed in neurons in the central nervous system, mainly in terminally differentiated neurons. It associates with Trap (Tudor repeat associator with PCTAIRE-2) and could play a role in regulating mitochondrial function in neurons. PCTAIRE-2 shares sequence similarity with Cyclin-Dependent Kinases (CDKs), which belong to a large family of STKs that are regulated by their cognate cyclins. Together, CDKs and cyclins are involved in the control of cell-cycle progression, transcription, and neuronal function. The PCTAIRE-2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 309 matched cddid_all.tbl CDD cd07873 cd07873 270854 STKc_PCTAIRE1 Catalytic domain of the Serine/Threonine Kinase, PCTAIRE-1 kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PCTAIRE-1 is expressed ubiquitously and is localized in the cytoplasm. Its kinase activity is cell cycle dependent and peaks at the S and G2 phases. PCTAIRE-1 is highly expressed in the brain and may play a role in regulating neurite outgrowth. It can also associate with Trap (Tudor repeat associator with PCTAIRE-2), a physiological partner of PCTAIRE-2; with p11, a small dimeric protein with similarity to S100; and with 14-3-3 proteins, mediators of phosphorylation-dependent interactions in many different proteins. PCTAIRE-1 shares sequence similarity with Cyclin-Dependent Kinases (CDKs), which belong to a large family of STKs that are regulated by their cognate cyclins. Together, CDKs and cyclins are involved in the control of cell-cycle progression, transcription, and neuronal function. The PCTAIRE-1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 297 matched cddid_all.tbl CDD cd07874 cd07874 143379 STKc_JNK3 Catalytic domain of the Serine/Threonine Kinase, c-Jun N-terminal Kinase 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. JNK3 is expressed primarily in the brain, and to a lesser extent in the heart and testis. Mice deficient in JNK3 are protected against kainic acid-induced seizures, stroke, sciatic axotomy neural death, and neuronal death due to NGF deprivation, oxidative stress, or exposure to beta-amyloid peptide. This suggests that JNK3 may play roles in the pathogenesis of these diseases. JNKs are mitogen-activated protein kinases (MAPKs) that are involved in many stress-activated responses including those during inflammation, neurodegeneration, apoptosis, and persistent pain sensitization, among others. The JNK3 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 355 matched cddid_all.tbl CDD cd07875 cd07875 143380 STKc_JNK1 Catalytic domain of the Serine/Threonine Kinase, c-Jun N-terminal Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. JNK1 is expressed in every cell and tissue type. It specifically binds with JAMP (JNK1-associated membrane protein), which regulates the duration of JNK1 activity in response to stimuli. Specific JNK1 substrates include Itch and SG10, which are implicated in Th2 responses and airway inflammation, and microtubule dynamics and axodendritic length, respectively. Mice deficient in JNK1 are protected against arthritis, obesity, type 2 diabetes, cardiac cell death, and non-alcoholic liver disease, suggesting that JNK1 may play roles in the pathogenesis of these diseases. Initially, it was thought that JNK1 and JNK2 were functionally redundant as mice deficient in either genes could survive but disruption of both genes resulted in lethality. However, recent studies have shown that JNK1 and JNK2 perform distinct functions through specific binding partners and substrates. JNKs are mitogen-activated protein kinases that are involved in many stress-activated responses including those during inflammation, neurodegeneration, apoptosis, and persistent pain sensitization, among others. The JNK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 364 matched cddid_all.tbl CDD cd07876 cd07876 143381 STKc_JNK2 Catalytic domain of the Serine/Threonine Kinase, c-Jun N-terminal Kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. JNK2 is expressed in every cell and tissue type. It is specifically translocated to the mitochondria during dopaminergic cell death. Specific substrates include the microtubule-associated proteins DCX and Tau, as well as TIF-IA which is involved in ribosomal RNA synthesis regulation. Mice deficient in Jnk2 show protection against arthritis, type 1 diabetes, atherosclerosis, abdominal aortic aneurysm, cardiac cell death, TNF-induced liver damage, and tumor growth, indicating that JNK2 may play roles in the pathogenesis of these diseases. Initially it was thought that JNK1 and JNK2 were functionally redundant as mice deficient in either genes could survive but disruption of both genes resulted in lethality. However, recent studies have shown that JNK1 and JNK2 perform distinct functions through specific binding partners and substrates. JNKs are mitogen-activated protein kinases (MAPKs) that are involved in many stress-activated responses including those during inflammation, neurodegeneration, apoptosis, and persistent pain sensitization, among others. The JNK2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 359 matched cddid_all.tbl CDD cd07877 cd07877 143382 STKc_p38alpha Catalytic domain of the Serine/Threonine Kinase, p38alpha Mitogen-Activated Protein Kinase (also called MAPK14). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. p38alpha/MAPK14 is expressed in most tissues and is the major isoform involved in the immune and inflammatory response. It is the central p38 MAPK involved in myogenesis. It plays a role in regulating cell cycle check-point transition and promoting cell differentiation. p38alpha also regulates cell proliferation and death through crosstalk with the JNK pathway. Its substrates include MAPK activated protein kinase 2 (MK2), MK5, and the transcription factors ATF2 and Mitf. p38 kinases MAPKs, serving as important mediators of cellular responses to extracellular signals. They are activated by the MAPK kinases MKK3 and MKK6, which in turn are activated by upstream MAPK kinase kinases including TAK1, ASK1, and MLK3, in response to cellular stresses or inflammatory cytokines. The p38alpha subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 345 matched cddid_all.tbl CDD cd07878 cd07878 143383 STKc_p38beta Catalytic domain of the Serine/Threonine Kinase, p38beta Mitogen-Activated Protein Kinase (also called MAPK11). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. p38beta/MAPK11 is widely expressed in tissues and shows more similarity with p38alpha than with the other isoforms. Both are sensitive to pyridinylimidazoles and share some common substrates such as MAPK activated protein kinase 2 (MK2) and the transcription factors ATF2, c-Fos and, ELK-1. p38beta is involved in regulating the activation of the cyclooxygenase-2 promoter and the expression of TGFbeta-induced alpha-smooth muscle cell actin. p38 kinases are mitogen-activated protein kinases (MAPKs), serving as important mediators of cellular responses to extracellular signals. They are activated by the MAPK kinases MKK3 and MKK6, which in turn are activated by upstream MAPK kinase kinases including TAK1, ASK1, and MLK3, in response to cellular stresses or inflammatory cytokines. The p38beta subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 343 matched cddid_all.tbl CDD cd07879 cd07879 143384 STKc_p38delta Catalytic domain of the Serine/Threonine Kinase, p38delta Mitogen-Activated Protein Kinase (also called MAPK13). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. p38delta/MAPK13 is found in skeletal muscle, heart, lung, testis, pancreas, and small intestine. It regulates microtubule function by phosphorylating Tau. It activates the c-jun promoter and plays a role in G2 cell cycle arrest. It also controls the degration of c-Myb, which is associated with myeloid leukemia and poor prognosis in colorectal cancer. p38delta is the main isoform involved in regulating the differentiation and apoptosis of keratinocytes. p38 kinases are MAPKs, serving as important mediators of cellular responses to extracellular signals. They are activated by the MAPK kinases MKK3 and MKK6, which in turn are activated by upstream MAPK kinase kinases including TAK1, ASK1, and MLK3, in response to cellular stresses or inflammatory cytokines. The p38delta subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 342 matched cddid_all.tbl CDD cd07880 cd07880 143385 STKc_p38gamma Catalytic domain of the Serine/Threonine Kinase, p38gamma Mitogen-Activated Protein Kinase (also called MAPK12). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. p38gamma/MAPK12 is predominantly expressed in skeletal muscle. Unlike p38alpha and p38beta, p38gamma is insensitive to pyridinylimidazoles. It displays an antagonizing function compared to p38alpha. p38gamma inhibits, while p38alpha stimulates, c-Jun phosphorylation and AP-1 mediated transcription. p38gamma also plays a role in the signaling between Ras and the estrogen receptor and has been implicated to increase cell invasion and breast cancer progression. In Xenopus, p38gamma is critical in the meiotic maturation of oocytes. p38 kinases are MAPKs, serving as important mediators of cellular responses to extracellular signals. They are activated by the MAPK kinases MKK3 and MKK6, which in turn are activated by upstream MAPK kinase kinases including TAK1, ASK1, and MLK3, in response to cellular stresses or inflammatory cytokines. The p38gamma subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 343 matched cddid_all.tbl CDD cd07881 cd07881 143641 RHD-n_NFAT N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor of activated T-cells (NFAT) proteins. Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the NFAT family of transcription factors. NFAT transcription complexes are a target of calcineurin, a calcium dependent phosphatase, and activate genes that are mainly involved in cell-cell interaction. Upon de-phosphorylation of the nuclear localization signal, NFAT enters the nucleus and acts as a transcription factor; its export from the nucleus is triggered by phosphorylation via export kinases. NFATs play important roles in mediating the immune response, and are found in T cells, B Cells, NK cells, mast cells, and monocytes. NFATs are also found in various non-hematopoietic cell types, where they play roles in development. 175 matched cddid_all.tbl CDD cd07882 cd07882 143642 RHD-n_TonEBP N-terminal sub-domain of the Rel homology domain (RHD) of tonicity-responsive enhancer binding protein (TonEBP). Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the tonicity-responsive enhancer binding protein (TonEBP), also called NFAT5. Mammalian TonEBP regulates the expression of genes in response to tonicity. It plays a pivotal role in urinary concentrating mechanisms in kidney medulla, by triggering the accumulation of osmolytes that enable renal medullary cells to tolerate high levels of urea and salt. 161 matched cddid_all.tbl CDD cd07883 cd07883 143643 RHD-n_NFkB N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor of kappa light polypeptide gene enhancer in B-cells (NF-kappa B). Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the NF-kappa B1 and B2 families of transcription factors, also referred to as class I members of the NF-kappa B family. In class I NF-kappa Bs, the RHD domain co-occurs with C-terminal ankyrin repeats. Family members include NF-kappa B1 and NF-kappa B2. NF-kappa B1 is commonly referred to as p105 or p50 (proteolytically processed form), while NF-kappa B2 is called p100 or p52 (proteolytically processed form). NF-kappa B proteins are part of a protein complex that acts as a transcription factor, which is responsible for regulating a host of cellular responses to a variety of stimuli. This complex tightly regulates the expression of a large number of genes, and is involved in processes such as adaptive and innate immunity, stress response, inflammation, cell adhesion, proliferation and apoptosis. The cytosolic NF-kappa B complex is activated via phosphorylation of the ankyrin-repeat containing inhibitory protein I-kappa B, which dissociates from the complex and exposes the nuclear localization signal of the heterodimer (NF-kappa B and REL). p105 and p100 may also act as I-kappa Bs due to their C-terminal ankyrin repeats. 197 matched cddid_all.tbl CDD cd07884 cd07884 143644 RHD-n_Relish N-terminal sub-domain of the Rel homology domain (RHD) of the arthropod protein Relish. Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the arthropod Relish protein, in which the RHD domain co-occurs with C-terminal ankyrin repeats. Family members are sometimes referred to as p110 or p68 (proteolytically processed form). Relish is an NF-kappa B-like transcription factor, which plays a role in mediating innate immunity in Drosophila. It is activated via the Imd (immune deficiency) pathway, which triggers phosphorylation of Relish. IKK-dependent proteolytic cleavage of Relish (which involves Dredd) results in a smaller active form (without the C-terminal ankyrin repeats), which is transported into the nucleus and functions as a transactivator. 159 matched cddid_all.tbl CDD cd07885 cd07885 143645 RHD-n_RelA N-terminal sub-domain of the Rel homology domain (RHD) of RelA. Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD domain of the RelA family of transcription factors, categorized as a class II member of the NF-kappa B family. In class II NF-kappa Bs, the RHD domain co-occurs with a C-terminal transactivation domain (TAD). NF-kappa B proteins are part of a protein complex that acts as a transcription factor, which is responsible for regulating a host of cellular responses to a variety of stimuli. This complex tightly regulates the expression of a large number of genes, and is involved in processes such as adaptive and innate immunity, stress response, inflammation, cell adhesion, proliferation and apoptosis. The cytosolic NF-kappa B complex is activated via phosphorylation of the ankyrin-repeat containing inhibitory protein I-kappa B, which dissociates from the complex and exposes the nuclear localization signal of the heterodimer (NF-kappa B and Rel). RelA (also called p65) forms heterodimers with NF-kappa B1 (p50) and B2 (p52). RelA also forms homodimers. 169 matched cddid_all.tbl CDD cd07886 cd07886 143646 RHD-n_RelB N-terminal sub-domain of the Rel homology domain (RHD) of the reticuloendotheliosis viral oncogene homolog B (RelB) protein. Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the RelB family of transcription factors, categorized as class II NF-kappa B family members. In class II NF-kappa Bs, the RHD domain co-occurs with a C-terminal transactivation domain (TAD). NF-kappa B proteins are part of a protein complex that acts as a transcription factor, which is responsible for regulating a host of cellular responses to a variety of stimuli. This complex tightly regulates the expression of a large number of genes, and is involved in processes such as adaptive and innate immunity, stress response, inflammation, cell adhesion, proliferation and apoptosis. The cytosolic NF-kappa B complex is activated via phosphorylation of the ankyrin-repeat containing inhibitory protein I-kappa B, which dissociates from the complex and exposes the nuclear localization signal of the heterodimer (NF-kappa B and Rel). RelB, is unable to homodimerize but is a potent transactivator in a heterodimer with NF-kappa B1 (p50) or B2 (p52). It is involved in the regulation of genes that play roles in inflammatory processes and the immune response. 172 matched cddid_all.tbl CDD cd07887 cd07887 143647 RHD-n_Dorsal_Dif N-terminal sub-domain of the Rel homology domain (RHD) of the arthropod protein Dorsal. Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the arthropod Dorsal and Dif (Dorsal-related immunity factor), and similar proteins. Dorsal and Dif are Rel-like transcription factors, which play roles in mediating innate immunity in Drosophila. They are activated via the Toll pathway. Cytoplasmic Dorsal/Dif are inactivated via forming a complex with Cactus, the Drosophila homologue of mammalian I-kappa B proteins. In response to signals, Cactus is degraded and Dorsal/Dif can be transported into the nucleus, where they act as transcription factors. Dorsal is also an essential gene in establishing the proper dorsal/ventral polarity in the developing embryo. 173 matched cddid_all.tbl CDD cd07888 cd07888 143579 CRD_corin_2 One of two cysteine-rich domains of the corin protein, a type II transmembrane serine protease . The cysteine-rich domain (CRD) is an essential component of corin, a type II transmembrane serine protease which functions as the convertase of the pro-atrial natriuretic peptide (pro-ANP) in the heart. Corin contains two CRDs in its extracellular region, which play an important role in recognition of the physiological substrate, pro-ANP. This model characterizes the second (C-terminal) CRD. 122 matched cddid_all.tbl CDD cd07890 cd07890 143628 CYTH-like_AC_IV-like Adenylyl cyclase (AC) class IV-like, a subgroup of the CYTH-like superfamily. This subgroup contains class IV ACs and similar proteins. AC catalyzes the conversion of ATP to 3',5'-cyclic AMP (cAMP) and PPi. cAMP is a key signaling molecule which conveys a variety of signals in different cell types. In prokaryotes, cAMP is a catabolite derepression signal which triggers the expression of metabolic pathways including the lactose operon. Six non-homologous classes of ACs have been identified (I-VI). Class IV ACs are found in this group. In bacteria, the gene encoding Class IV AC has been designated cyaB and the protein as AC2. AC-IV occurs in addition to AC-I in bacterial pathogens such as Yersinia pestis (plague disease). The role of AC-IV is unknown but it has been speculated that it may be a factor in pathogenesis, perhaps providing cAMP for a secondary internal signaling function, or for secretion and uptake into host cells, where it may disrupt normal cellular processes. This subgroup belongs to the CYTH/triphosphate tunnel metalloenzyme (TTM)-like superfamily, whose enzymes have a unique active site located within an eight-stranded beta barrel. 169 matched cddid_all.tbl CDD cd07891 cd07891 143629 CYTH-like_CthTTM-like_1 CYTH-like Clostridium thermocellum TTM-like subgroup 1. This subgroup contains the triphosphate tunnel metalloenzyme (TTM) from Clostridium thermocellum (CthTTM) and similar proteins. These are found primarily in bacteria. CthTTM is a metal dependent tripolyphosphatase, nucleoside triphosphatase, and nucleoside tetraphosphatase. It hydrolyzes the beta-gamma phosphoanhydride linkage of triphosphate-containing substrates including tripolyphosphate, nucleoside triphosphates and nucleoside tetraphosphates. These substrates are hydrolyzed, releasing Pi. Mg++ or Mn++ are required for the enzyme's activity. CthTTM appears to have no adenylate cyclase activity. This subgroup consists chiefly of bacterial sequences. These enzymes are members of the CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) superfamily, which have a unique active site located within an eight-stranded beta barrel. 148 matched cddid_all.tbl CDD cd07892 cd07892 143630 PolyPPase_VTC2-3_like Polyphosphate(polyP) polymerase domain of yeast vacuolar transport chaperone (VTC) proteins VTC-2, and -3 , and similar proteins. Saccharomyces cerevisiae VTC-1, -2, -3, and -4 comprise the membrane-integral VTC complex. VTC-2, -3, and -4 contain polyP polymerase domains. S. cerevisiae VTC-2,and -3 belong to this subgroup. For VTC4 it has been shown that this domain generates polyP from ATP by a phosphotransfer reaction releasing ADP. This activity is metal ion-dependent. The ATP gamma phosphate may be cleaved and then transferred to an acceptor phosphate to form polyP. PolyP is ubiquitous. In prokaryotes, it is a store of phosphate and energy. In eukaryotes, polyPs have roles in bone calcification, and osmoregulation, and in phosphate transport in the symbiosis of mycorrhizal fungi and plants. This subgroup belongs to the CYTH/triphosphate tunnel metalloenzyme (TTM)-like superfamily, whose enzymes have a unique active site located within an eight-stranded beta barrel. 303 matched cddid_all.tbl CDD cd07893 cd07893 153435 OBF_DNA_ligase The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain. 129 matched cddid_all.tbl CDD cd07894 cd07894 185705 Adenylation_RNA_ligase Adenylation domain of RNA circularization proteins. RNA circularization proteins are capable of circularizing RNA molecules in an ATP-dependent reaction. RNA circularization may protect RNA from exonuclease activity. This model comprises the adenylation domain, the minimal catalytic unit that is common to all members of the ATP-dependent DNA ligase family, and the carboxy-terminal extension of RNA circularization protein that serves as a dimerization module. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. The adenylation domain binds ATP and contains many active site residues. 342 matched cddid_all.tbl CDD cd07895 cd07895 185706 Adenylation_mRNA_capping Adenylation domain of GTP-dependent mRNA capping enzymes. RNA capping enzymes transfer GMP from GTP to the 5'-diphosphate end of nascent mRNAs to form a G(5')ppp(5')RNA cap structure. The RNA cap is found only in eukarya. RNA capping is chemically analogous to the first two steps of polynucleotide ligation. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. Structural studies reveal a shared structure for DNA ligases and capping enzymes, with a common catalytic core composed of an adenylation or nucleotidyltransferase domain and a C-terminal OB-fold domain containing conserved sequence motifs. The adenylation domain binds ATP and contains many active site residues. 215 matched cddid_all.tbl CDD cd07896 cd07896 185707 Adenylation_kDNA_ligase_like Adenylation domain of kDNA ligases and similar proteins. The mitochondrial DNA of parasitic protozoans is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-dependent ligases. They are involved in DNA replication or repair. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. They have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and the C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active-site residues. 174 matched cddid_all.tbl CDD cd07897 cd07897 185708 Adenylation_DNA_ligase_Bac1 Adenylation domain of putative bacterial ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of predicted bacterial ATP-dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active site residues. 207 matched cddid_all.tbl CDD cd07898 cd07898 185709 Adenylation_DNA_ligase Adenylation domain of ATP-dependent DNA Ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. ATP-dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site residues. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. 201 matched cddid_all.tbl CDD cd07900 cd07900 185710 Adenylation_DNA_ligase_I_Euk Adenylation domain of eukaryotic DNA Ligase I. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. DNA ligase I is the main replicative ligase in eukaryotes. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. 219 matched cddid_all.tbl CDD cd07901 cd07901 185711 Adenylation_DNA_ligase_Arch_LigB Adenylation domain of archaeal and bacterial LigB-like DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of archaeal DNA ligases and bacterial proteins similar to Mycobacterium tuberculosis LigB. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. 207 matched cddid_all.tbl CDD cd07902 cd07902 185712 Adenylation_DNA_ligase_III Adenylation domain of DNA Ligase III. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing factor 1 (XRCC1) and functions in single nucleotide Base Excision Repair (BER). The mitochondrial form of DNA ligase III originates from the nucleolus and is involved in the mitochondrial DNA repair pathway. This isoform is expressed by a second start site on the DNA ligase III gene. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many active site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. 213 matched cddid_all.tbl CDD cd07903 cd07903 185713 Adenylation_DNA_ligase_IV Adenylation domain of DNA Ligase IV. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligase in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent protein kinase. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. 225 matched cddid_all.tbl CDD cd07905 cd07905 185714 Adenylation_DNA_ligase_LigC Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. 194 matched cddid_all.tbl CDD cd07906 cd07906 185715 Adenylation_DNA_ligase_LigD_LigC Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is common to all members of the ATP-dependent DNA ligase family. The adenylation domain binds ATP and contains many of the active-site residues. The common catalytic core unit comprises six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. LigD consists of a central ATP-dependent DNA ligase catalytic core unit fused to a C-terminal polymerase domain and an N-terminal 3'-phosphoesterase (PE) module. LigD catalyzes the end-healing and end-sealing steps during non-homologous end joining. 190 matched cddid_all.tbl CDD cd07908 cd07908 153117 Mn_catalase_like Manganese catalase-like protein, ferritin-like diiron-binding domain. This uncharacterized bacterial protein family has a ferritin-like domain similar to that of the manganese catalase protein of Lactobacillus plantarum and the bll3758 protein of Bradyrhizobium japonicum. Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterioferritin, ferritin, rubrerythrin, aromatic and alkene monooxygenase hydroxylases (AAMH), ribonucleotide reductase R2 (RNRR2), acyl-ACP-desaturases (Acyl_ACP_Desat), manganese (Mn) catalases, demethoxyubiquinone hydroxylases (DMQH), DNA protecting proteins (DPS), and ubiquinol oxidases (AOX), and the aerobic cyclase system, Fe-containing subunit (ACSF). 154 matched cddid_all.tbl CDD cd07909 cd07909 153118 YciF YciF bacterial stress response protein, ferritin-like iron-binding domain. YciF is a bacterial protein of unknown function that is up-regulated when bacteria experience stress conditions, and is highly conserved in a broad range of bacterial species. YciF has a ferritin-like domain. Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterioferritin, ferritin, rubrerythrin, aromatic and alkene monooxygenase hydroxylases (AAMH), ribonucleotide reductase R2 (RNRR2), acyl-ACP-desaturases (Acyl_ACP_Desat), manganese (Mn) catalases, demethoxyubiquinone hydroxylases (DMQH), DNA protecting proteins (DPS), and ubiquinol oxidases (AOX), and the aerobic cyclase system, Fe-containing subunit (ACSF). 147 matched cddid_all.tbl CDD cd07910 cd07910 153119 MiaE MiaE tRNA-modifying nonheme diiron monooxygenase, ferritin-like diiron-binding domain. MiaE is a nonheme diiron monooxygenase that catalyzes the posttranscriptional allylic hydroxylation of a modified nucleoside in tRNA called 2-methylthio-N-6-isopentenyl adenosine (ms2i6A). ms2i6A is found at position 37, next to the anticodon at the 3' position in almost all eukaryotic and bacterial tRNA's that read codons beginning with uridine. The miaE gene is absent in Escherichia coli, a finding consistent with the absence of the hydroxylated derivative of ms2i6A in this species. 180 matched cddid_all.tbl CDD cd07911 cd07911 153120 RNRR2_Rv0233_like Ribonucleotide Reductase R2-like protein, Mn/Fe-binding domain. Rv0233 is a Mycobacterium tuberculosis ribonucleotide reductase R2 protein with a heterodinuclear manganese/iron-carboxylate cofactor located in its metal center. The Rv0233-like family may represent a structural/functional counterpart of the evolutionary ancestor of the RNRR2's (Ribonucleotide Reductase, R2/beta subunit) and the bacterial multicomponent monooxygenases. RNRR2s belong to a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in prokaryotes and archaea. The catalytically active form of RNR is a proposed alpha2-beta2 tetramer. The homodimeric alpha subunit (R1) contains the active site and redox active cysteines as well as the allosteric binding sites. 280 matched cddid_all.tbl CDD cd07912 cd07912 143653 Tweety_N N-terminal domain of the protein encoded by the Drosophila tweety gene and related proteins, a family of chloride ion channels. The protein product of the Drosophila tweety (tty) gene is thought to form a trans-membrane protein with five membrane-spanning regions and a cytoplasmic C-terminus. This N-terminal domain contains the putative transmembrane spanning regions. Tweety has been suggested as a candidate for a large conductance chloride channel, both in vertebrate and insect cells. Three human homologs have been identified and designated TTYH1-3. TTYH2 has been associated with the progression of cancer, and Drosophila melanogaster tweety has been assumed to play a role in development. TTYH2, and TTYH3 bind to and are ubiquinated by Nedd4-2, a HECT type E3 ubiquitin ligase, which most likely plays a role in controlling the cellular levels of tweety family proteins. 418 matched cddid_all.tbl CDD cd07914 cd07914 153419 IGPD Imidazoleglycerol-phosphate dehydratase. Imidazoleglycerol-phosphate dehydratase (IGPD; EC 4.2.1.19) catalyzes the dehydration of imidazole glycerol phosphate to imidazole acetol phosphate, the sixth step of histidine biosynthesis in plants and microorganisms where the histidine is synthesized de novo. There is an internal repeat in the protein domain that is related by pseudo-dyad symmetry, perhaps as a result of an ancient gene duplication. The apo-form of IGPD exists as a catalytically inactive trimer which, in the presence of specific divalent metal cations such as manganese (Mn2+), cobalt (Co2+), cadmium (Cd2+), nickel (Ni2+), iron (Fe2+) and zinc (Zn2+), assembles to form a biologically active high molecular weight metalloenzyme; a 24-mer with 4-3-2 symmetry. Each 24-mer has 24 active sites, and contains around 1.5 metal ions per monomer, each monomer contributing residues to three separate active sites. IGPD enzymes are monofunctional in fungi, plants, archaea and some eubacteria while they are encoded as bifunctional enzymes in other eubacteria, such that the enzyme is fused to histidinol-phosphate phosphatase, the penultimate enzyme of the histidine biosynthesis pathway. The histidine biosynthesis pathway is a potential target for development of herbicides, and IGPD is a target for the triazole phosphonate herbicides. 190 matched cddid_all.tbl CDD cd07920 cd07920 153420 Pumilio Pumilio-family RNA binding domain. Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canonical) repeats. 322 matched cddid_all.tbl CDD cd07921 cd07921 153391 PCA_45_Doxase_A_like Subunit A of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and similar enzymes. This subfamily includes the A subunit of protocatechuate (PCA) 4,5-dioxygenase (LigAB) and two subfamilies of unknown function. The A subunit is the smaller, non-catalytic subunit of LigAB. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As members of the Class III extradiol dioxygenase family, the enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. 106 matched cddid_all.tbl CDD cd07922 cd07922 153392 CarBa CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. 2-aminophenol 1,6-dioxygenase is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, the enzyme has also shown high specificity for 2,3-dihydroxybiphenyl. 81 matched cddid_all.tbl CDD cd07923 cd07923 153393 Gallate_dioxygenase_C The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of the PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. This model represents the C-terminal domain, which is similar to the A subunit of PCA 4,5-dioxygenase (or LigAB). The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. Since enzymes in this subfamily have fused A and B subunits, the dimer interface may resemble the tetramer interface of classical LigAB enzymes. This enzyme belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. 94 matched cddid_all.tbl CDD cd07924 cd07924 153394 PCA_45_Doxase_A The A subunit of Protocatechuate 4,5-dioxygenase (LigAB) is the smaller, non-catalytic subunit. The A subunit is the non-catalytic subunit of Protocatechuate (PCA) 4,5-dioxygenase (LigAB), which is composed of A and B subunits that form a tetramer. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As a member of the Class III extradiol dioxygenase family, LigAB uses a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. 121 matched cddid_all.tbl CDD cd07925 cd07925 153395 LigA_like_1 The A subunit of Uncharacterized proteins with similarity to Protocatechuate 4,5-dioxygenase (LigAB). The proteins of unknown function in this subfamily are similar to the A subunit of the Protocatechuate (PCA) 4,5-dioxygenase (LigAB). LigAB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Dioxygenases play key roles in the degradation of aromatic compounds. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. 106 matched cddid_all.tbl CDD cd07927 cd07927 143648 RHD-n_NFAT_like N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor of activated T-cells (NFAT) proteins and similar proteins. Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the NFAT family of transcription factors. NFAT transcription complexes are a target of calcineurin, a calcium dependent phosphatase, and activate genes that are mainly involved in cell-cell interaction. Upon de-phosphorylation of the nuclear localization signal, NFAT enters the nucleus and acts as a transcription factor; its export from the nucleus is triggered by phosphorylation via export kinases. NFATs play important roles in mediating the immune response, and are found in T cells, B Cells, NK cells, mast cells, and monocytes. NFATs are also found in various non-hematopoietic cell types, where they play roles in development. This group also contains the N-terminal RHD sub-domain of the non-calcium regulated tonicity-responsive enhancer binding protein (TonEBP), also called NFAT5. Mammalian TonEBP regulates the expression of genes in response to tonicity. It plays a pivotal role in urinary concentrating mechanisms in kidney medulla, by triggering the accumulation of osmolytes that enable renal medullary cells to tolerate high levels of urea and salt. 161 matched cddid_all.tbl CDD cd07930 cd07930 153077 bacterial_phosphagen_kinase Phosphagen (guanidino) kinases found in bacteria. Phosphagen (guanidino) kinases are enzymes that transphosphorylate a high energy phosphoguanidino compound, such as phosphocreatine (PCr) or phosphoarginine, which is used as an energy-storage and -transport metabolite, to ADP, thereby creating ATP. This subfamily is specific to bacteria and lacks an N-terminal domain, which otherwise forms part of the substrate binding site. Most of the catalytic residues are found in the larger C-terminal domain, however, which appears conserved in these bacterial proteins. Their functions have not been characterized. 232 matched cddid_all.tbl CDD cd07931 cd07931 153078 eukaryotic_phosphagen_kinases Phosphagen (guanidino) kinases mostly found in eukaryotes. Phosphagen (guanidino) kinases are enzymes that transphosphorylate a high energy phosphoguanidino compound, like phosphocreatine (PCr) in the case of creatine kinase (CK) or phosphoarginine in the case of arginine kinase, which is used as an energy-storage and -transport metabolite, to ADP, thereby creating ATP. The substrate binding site is located in the cleft between the N and C-terminal domains, but most of the catalytic residues are found in the larger C-terminal domain. In higher eukaryotes, CK exists in tissue-specific (muscle, brain), as well as compartment-specific (mitochondrial and cytosolic) isoforms. They are either coupled to glycolysis (cytosolic form) or oxidative phosphorylation (mitochondrial form). Besides CK and AK, the most studied members of this family are also other phosphagen kinases with different substrate specificities, like glycocyamine kinase (GK), lombricine kinase (LK), taurocyamine kinase (TK) and hypotaurocyamine kinase (HTK). 338 matched cddid_all.tbl CDD cd07932 cd07932 153079 arginine_kinase_like Phosphagen (guanidino) kinases such as arginine kinase and similar enzymes. Eukaryotic arginine kinase-like phosphagen (guanidino) kinases are enzymes that transphosphorylate a high energy phosphoguanidino compound, like phosphoarginine in the case of arginine kinase (AK), which is used as an energy-storage and -transport metabolite, to ADP, thereby creating ATP. The substrate binding site is located in the cleft between the N and C-terminal domains, but most of the catalytic residues are found in the larger C-terminal domain. Besides AK, one of the most studied members of this family, this model also represents a phosphagen kinase with different substrate specificity, hypotaurocyamine kinase (HTK). 350 matched cddid_all.tbl CDD cd07933 cd07933 143649 RHD-n_c-Rel N-terminal sub-domain of the Rel homology domain (RHD) of c-Rel. Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the c-Rel family of transcription factors, categorized as a class II member of the NF-kappa B family. In class II NF-kappa Bs, the RHD domain co-occurs with a C-terminal transactivation domain (TAD). NF-kappa B proteins are part of a protein complex that acts as a transcription factor, which is responsible for regulating a host of cellular responses to a variety of stimuli. This complex tightly regulates the expression of a large number of genes, and is involved in processes such as adaptive and innate immunity, stress response, inflammation, cell adhesion, proliferation and apoptosis. The cytosolic NF-kappa B complex is activated via phosphorylation of the ankyrin-repeat containing inhibitory protein I-kappa B, which dissociates from the complex and exposes the nuclear localization signal of the heterodimer (NF-kappa B and Rel). c-Rel plays an important role in B cell proliferation and survival. 172 matched cddid_all.tbl CDD cd07934 cd07934 143650 RHD-n_NFkB2 N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor kappa B2 (NF-kappa B2). Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the NF-kappa B2 family of transcription factors, a class I member of the NF-kappa B family. In class I NF-kappa Bs, the RHD domain co-occurs with C-terminal ankyrin repeats. NF-kappa B2 is commonly referred to as p100 or p52 (proteolytically processed form). NF-kappa B proteins are part of a protein complex that acts as a transcription factor, which is responsible for regulating a host of cellular responses to a variety of stimuli. This complex tightly regulates the expression of a large number of genes, and is involved in processes such as adaptive and innate immunity, stress response, inflammation, cell adhesion, proliferation and apoptosis. The cytosolic NF-kappa B complex is activated via phosphorylation of the ankyrin-repeat containing inhibitory protein I-kappa B, which dissociates from the complex and exposes the nuclear localization signal of the heterodimer (NF-kappa B and REL). NF-kappa B2 is involved in the alternative NF-kappa B signaling pathway which is activated by few agonists and plays an important role in secondary lymphoid organogenesis, maturation of B-cells, and adaptive humoral immunity. p100 may also act as an I-kappa B due to its C-terminal ankyrin repeats. 185 matched cddid_all.tbl CDD cd07935 cd07935 143651 RHD-n_NFkB1 N-terminal sub-domain of the Rel homology domain (RHD) of nuclear factor of kappa B1 (NF-kappa B1). Proteins containing the Rel homology domain (RHD) are metazoan transcription factors. The RHD is composed of two structural sub-domains; this model characterizes the N-terminal RHD sub-domain of the NF-kappa B1 family of transcription factors, a class I member of the NF-kappa B family. In class I NF-kappa Bs, the RHD domain co-occurs with C-terminal ankyrin repeats. NF-kappa B1 is commonly referred to as p105 or p50 (proteolytically processed form). NF-kappa B proteins are part of a protein complex that acts as a transcription factor, which is responsible for regulating a host of cellular responses to a variety of stimuli. This complex tightly regulates the expression of a large number of genes, and is involved in processes such as adaptive and innate immunity, stress response, inflammation, cell adhesion, proliferation and apoptosis. The cytosolic NF-kappa B complex is activated via phosphorylation of the ankyrin-repeat containing inhibitory protein I-kappa B, which dissociates from the complex and exposes the nuclear localization signal of the heterodimer (NF-kappa B and REL). NF-kappa B1 is involved in the canonical NF-kappa B signaling pathway which is activated by many agonists and is essential in immune and inflammatory responses, as well as cell survival. p105 is involved in its own specific NF-kappa B signaling pathway which is also implicated in immune and inflammatory responses. p105 may also act as an I-kappa B due to its C-terminal ankyrin repeats. It is also involved in mitogen-activated protein kinase (MAPK) signaling as its degradation leads to the activation of TPL-2, a MAPK kinase kinase which activates ERK pathways. 202 matched cddid_all.tbl CDD cd07936 cd07936 153421 SCAN SCAN oligomerization domain. The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several vertebrate proteins that contain C2H2 zinc finger motifs, many of which may be transcription factors playing roles in cell survival and differentiation. This protein-interaction domain is able to mediate homo- and hetero-oligomerization of SCAN-containing proteins. Some SCAN-containing proteins, including those of lower vertebrates, do not contain zinc finger motifs. It has been noted that the SCAN domain resembles a domain-swapped version of the C-terminal domain of the HIV capsid protein. This domain model features elements common to the three general groups of SCAN domains (SCAN-A1, SCAN-A2, and SCAN-B). The SCAND1 protein is truncated at the C-terminus with respect to this model, the SCAND2 protein appears to have a truncated central helix. 85 matched cddid_all.tbl CDD cd07937 cd07937 163675 DRE_TIM_PC_TC_5S "Pyruvate carboxylase and Transcarboxylase 5S, carboxyltransferase domain. This family includes the carboxyltransferase domains of pyruvate carboxylase (PC) and the transcarboxylase (TC) 5S subunit. Transcarboxylase 5S is a cobalt-dependent metalloenzyme subunit of the biotin-dependent transcarboxylase multienzyme complex. Transcarboxylase 5S transfers carbon dioxide from the 1.3S biotin to pyruvate in the second of two carboxylation reactions catalyzed by TC. The first reaction involves the transfer of carbon dioxide from methylmalonyl-CoA to the 1.3S biotin, and is catalyzed by the 12S subunit. These two steps allow a carboxylate group to be transferred from oxaloacetate to propionyl-CoA to yield pyruvate and methylmalonyl-CoA. The catalytic domain of transcarboxylase 5S has a canonical TIM-barrel fold with a large C-terminal extension that forms a funnel leading to the active site. Transcarboxylase 5S forms a homodimer and there are six dimers per complex. In addition to the catalytic domain, transcarboxylase 5S has several other domains including a carbamoyl-phosphate synthase domain, a biotin carboxylase domain, a carboxyltransferase domain, and an ATP-grasp domain. Pyruvate carboxylase, like TC, is a biotin-dependent enzyme that catalyzes the carboxylation of pyruvate to produce oxaloacetate. In mammals, PC has critical roles in gluconeogenesis, lipogenesis, glyceroneogenesis, and insulin secretion. Inherited PC deficiencies are linked to serious diseases in humans such as lactic acidemia, hypoglycemia, psychomotor retardation, and death. PC is a single-chain enzyme and is active only in its homotetrameric form. PC has three domains, an N-terminal biotin carboxylase domain, a carboxyltransferase domain (this alignment model), and a C-terminal biotin-carboxyl carrier protein domain. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name ""DRE-TIM""." 275 matched cddid_all.tbl CDD cd07938 cd07938 163676 DRE_TIM_HMGL "3-hydroxy-3-methylglutaryl-CoA lyase, catalytic TIM barrel domain. 3-hydroxy-3-methylglutaryl-CoA lyase (HMGL) catalyzes the cleavage of HMG-CoA to acetyl-CoA and acetoacetate, one of the terminal steps in ketone body generation and leucine degradation, and is a key enzyme in the pathway that supplies metabolic fuel to extrahepatic tissues. Mutations in HMGL cause a human autosomal recessive disorder called primary metabolic aciduria that affects ketogenesis and leucine catabolism and can be fatal due to an inability to tolerate hypoglycemia. HMGL has a TIM barrel domain with a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. The cleavage of HMG-CoA requires the presence of a divalent cation like Mg2+ or Mn2+, and the reaction is thought to involve general acid/base catalysis. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name ""DRE-TIM""." 274 matched cddid_all.tbl CDD cd07939 cd07939 163677 DRE_TIM_NifV "Streptomyces rubellomurinus FrbC and related proteins, catalytic TIM barrel domain. FrbC (NifV) of Streptomyces rubellomurinus catalyzes the condensation of acetyl-CoA and alpha-ketoglutarate to form homocitrate and CoA, a reaction similar to one catalyzed by homocitrate synthase. The gene encoding FrbC is one of several genes required for the biosynthesis of FR900098, a potent antimalarial antibiotic. This protein is also required for assembly of the nitrogenase MoFe complex but its exact role is unknown. This family also includes the NifV proteins of Heliobacterium chlorum and Gluconacetobacter diazotrophicus, which appear to be orthologous to FrbC. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name ""DRE-TIM""." 259 matched cddid_all.tbl CDD cd07940 cd07940 163678 DRE_TIM_IPMS "2-isopropylmalate synthase (IPMS), N-terminal catalytic TIM barrel domain. 2-isopropylmalate synthase (IPMS) catalyzes an aldol-type condensation of acetyl-CoA and 2-oxoisovalerate yielding 2-isopropylmalate and CoA, the first committed step in leucine biosynthesis. This family includes the Arabidopsis thaliana IPMS1 and IPMS2 proteins, the Glycine max GmN56 protein, and the Brassica insularis BatIMS protein. This family also includes a group of archeal IPMS-like proteins represented by the Methanocaldococcus jannaschii AksA protein. AksA catalyzes the condensation of alpha-ketoglutarate and acetyl-CoA to form trans-homoaconitate, one of 13 steps in the conversion of alpha-ketoglutarate and acetylCoA to alpha-ketosuberate, a precursor to coenzyme B and biotin. AksA also catalyzes the condensation of alpha-ketoadipate or alpha-ketopimelate with acetylCoA to form, respectively, the (R)-homocitrate homologs (R)-2-hydroxy-1,2,5-pentanetricarboxylic acid and (R)-2-hydroxy-1,2,6- hexanetricarboxylic acid. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name ""DRE-TIM""." 268 matched cddid_all.tbl CDD cd07941 cd07941 163679 DRE_TIM_LeuA3 "Desulfobacterium autotrophicum LeuA3 and related proteins, N-terminal catalytic TIM barrel domain. Desulfobacterium autotrophicum LeuA3 is sequence-similar to alpha-isopropylmalate synthase (LeuA) but its exact function is unknown. Members of this family have an N-terminal TIM barrel domain that belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name ""DRE-TIM""." 273 matched cddid_all.tbl CDD cd07942 cd07942 163680 DRE_TIM_LeuA "Mycobacterium tuberculosis LeuA3 and related proteins, N-terminal catalytic TIM barrel domain. Alpha-isopropylmalate synthase (LeuA), a key enzyme in leucine biosynthesis, catalyzes the first committed step in the pathway, converting acetyl-CoA and alpha-ketoisovalerate to alpha-isopropyl malate and CoA. Although the reaction catalyzed by LeuA is similar to that of the Arabidopsis thaliana IPMS1 protein, the two fall into phylogenetically distinct families within the same superfamily. LeuA has and N-terminal TIM barrel catalytic domain, a helical linker domain, and a C-terminal regulatory domain. LeuA forms a homodimer in which the linker domain of one monomer sits over the catalytic domain of the other, inserting residues into the active site that may be important for catalysis. Homologs of LeuA are found in bacteria as well as fungi. This family includes alpha-isopropylmalate synthases I (LEU4) and II (LEU9) from Saccharomyces cerevisiae. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name ""DRE-TIM""." 284 matched cddid_all.tbl CDD cd07943 cd07943 163681 DRE_TIM_HOA "4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain. 4-hydroxy 2-ketovalerate aldolase (Also known as 4-hydroxy-2-ketovalerate aldolase and 4-hydroxy-2-oxopentanoate aldolase (HOA)) converts 4-hydroxy-2-oxopentanoate to acetaldehyde and pyruvate, the penultimate step in the meta-cleavage pathway for the degradation of phenols, cresols and catechol. This family includes the Escherichia coli MhpE aldolase, the Pseudomonas DmpG aldolase, and the Burkholderia xenovorans BphI pyruvate aldolase. In Pseudomonas, the DmpG aldolase tightly associates with a dehydrogenase (DmpF ) and is inactive without it. HOA has a canonical TIM-barrel fold with a C-terminal extension that forms a funnel leading to the active site. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name ""DRE-TIM""." 263 matched cddid_all.tbl CDD cd07944 cd07944 163682 DRE_TIM_HOA_like "4-hydroxy-2-oxovalerate aldolase-like, N-terminal catalytic TIM barrel domain. This family of bacterial enzymes is sequence-similar to 4-hydroxy-2-oxovalerate aldolase (HOA) but its exact function is unknown. This family includes the Bacteroides vulgatus Bvu_2661 protein and belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name ""DRE-TIM""." 266 matched cddid_all.tbl CDD cd07945 cd07945 163683 DRE_TIM_CMS "Leptospira interrogans citramalate synthase (CMS) and related proteins, N-terminal catalytic TIM barrel domain. Citramalate synthase (CMS) catalyzes the conversion of pyruvate and acetyl-CoA to (R)-citramalate in the first dedicated step of the citramalate pathway. Citramalate is only found in Leptospira interrogans and a few other microorganisms. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name ""DRE-TIM""." 280 matched cddid_all.tbl CDD cd07947 cd07947 163684 DRE_TIM_Re_CS "Clostridium kluyveri Re-citrate synthase and related proteins, catalytic TIM barrel domain. Re-citrate synthase (Re-CS) is a Clostridium kluyveri enzyme that converts acetyl-CoA and oxaloacetate to citrate. In most organisms, this reaction is catalyzed by Si-citrate synthase which is Si-face stereospecific with respect to C-2 of oxaloacetate, and phylogenetically unrelated to Re-citrate synthase. Re-citrate synthase is also found in a few other strictly anaerobic organisms. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name ""DRE-TIM""." 279 matched cddid_all.tbl CDD cd07948 cd07948 163685 DRE_TIM_HCS "Saccharomyces cerevisiae homocitrate synthase and related proteins, catalytic TIM barrel domain. Homocitrate synthase (HCS) catalyzes the condensation of acetyl-CoA and alpha-ketoglutarate to form homocitrate, the first step in the lysine biosynthesis pathway. This family includes the Yarrowia lipolytica LYS1 protein as well as the Saccharomyces cerevisiae LYS20 and LYS21 proteins. This family belongs to the DRE-TIM metallolyase superfamily. DRE-TIM metallolyases include 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name ""DRE-TIM""." 262 matched cddid_all.tbl CDD cd07949 cd07949 153386 PCA_45_Doxase_B_like_1 The B subunit of unknown Class III extradiol dioxygenases with similarity to Protocatechuate 4,5-dioxygenase. This subfamily is composed of proteins of unknown function with similarity to the B subunit of Protocatechuate 4,5-dioxygenase (LigAB). LigAB belongs to the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Dioxygenases play key roles in the degradation of aromatic compounds. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents the catalytic subunit, B. 276 matched cddid_all.tbl CDD cd07950 cd07950 153387 Gallate_Doxase_N The N-terminal domain of the Class III extradiol dioxygenase, Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. LigAB-like enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. In this subfamily, the subunits A and B are fused to make a single polypeptide chain. The dimer interface for this subfamily may resemble the tetramer interface of classical LigAB enzymes. Gallate Dioxygenase belongs to the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. 277 matched cddid_all.tbl CDD cd07951 cd07951 153388 ED_3B_N_AMMECR1 The N-terminal domain, an extradiol dioxygenase class III subunit B-like domain, of unknown proteins containing a C-terminal AMMECR1 domain. This subfamily is composed of uncharacterized proteins containing an N-terminal domain with similarity to the catalytic B subunit of class III extradiol dioxygenases and a C-terminal AMMECR1-like domain. This model represents the N-terminal domain. Class III extradiol dioxygenases use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon, however, proteins in this subfamily do not contain a potential metal binding site and may not exhibit class III extradiol dioxygenase-like activity. The AMMECR1 protein was proposed to be a regulatory factor that is potentially involved in the development of AMME contiguous gene deletion syndrome. 256 matched cddid_all.tbl CDD cd07952 cd07952 153389 ED_3B_like Uncharacterized class III extradiol dioxygenases. This subfamily is composed of proteins of unknown function with similarity to the catalytic B subunit of class III extradiol dioxygenases. Class III extradiol dioxygenases use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. They play key roles in the degradation of aromatic compounds. 256 matched cddid_all.tbl CDD cd07953 cd07953 409289 PUA PUA RNA binding domain. The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, and a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was also found in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in regulating the expression of other genes. It has been shown that the PUA domain acts as an RNA binding domain in at least some of the proteins involved in RNA metabolism. 73 matched cddid_all.tbl CDD cd07954 cd07954 271157 AP_MHD_Cterm C-terminal domain of adaptor protein (AP) complexes medium mu subunits and its homologs (MHD). This family corresponds to the C-terminal domain of heterotetrameric AP complexes medium mu subunits and its homologs existing in monomeric stonins, delta-subunit of the heteroheptameric coat protein I (delta-COPI), a protein encoded by a pro-death gene referred as MuD (also known as MUDENG, mu-2 related death-inducing gene), an endocytic adaptor syp1, the mammalian FCH domain only proteins (FCHo1/2), SH3-containing GRB2-like protein 3-interacting protein 1 (SGIP1), and related proteins. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. Stonins have been characterized as clathrin-dependent AP-2 mu chain related factors and may act as cargo-specific sorting adaptors in endocytosis. Coat protein complex I (COPI)-coated vesicles function in the early secretory pathway. They mediate the retrograde transport from the Golgi to the ER, and intra-Golgi transport. MuD is distantly related to the C-terminal domain of mu2 subunit of AP-2. It is able to induce cell death by itself and plays an important role in cell death in various tissues. Syp1 represents a novel type of endocytic adaptor protein that participates in endocytosis, promotes vesicle tabulation, and contributes to cell polarity and stress responses. It shares the same domain architecture with its two ubiquitously expressed mammalian counterparts, FCHo1/2, which represent key initial proteins ultimately controlling cellular nutrient uptake, receptor regulation, and synaptic vesicle retrieval. They bind specifically to the plasma membrane and recruit the scaffold proteins eps15 and intersectin, which subsequently engage the adaptor complex AP2 and clathrin, leading to coated vesicle formation. Another mammalian neuronal-specific protein SGIP1 does have a C-terminal MHD and has been classified into this family as well. It is an endophilin-interacting protein that plays an obligatory role in the regulation of energy homeostasis. It is also involved in clathrin-mediated endocytosis by interacting with phospholipids and eps15. 245 matched cddid_all.tbl CDD cd07955 cd07955 153409 Anticodon_Ia_Cys_like Anticodon-binding domain of cysteinyl tRNA synthetases and domain found in MshC. This domain is found in cysteinyl tRNA synthetases (CysRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. CysRS catalyzes the transfer of cysteine to the 3'-end of its tRNA. The family also includes a domain of MshC, the rate-determining enzyme in the mycothiol biosynthetic pathway, which is specific to actinomycetes. The anticodon-binding site of CysRS lies C-terminal to this model's footprint and is not shared by MshC. 81 matched cddid_all.tbl CDD cd07956 cd07956 153410 Anticodon_Ia_Arg Anticodon-binding domain of arginyl tRNA synthetases. This domain is found in arginyl tRNA synthetases (ArgRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. ArgRS catalyzes the transfer of arginine to the 3'-end of its tRNA. 156 matched cddid_all.tbl CDD cd07957 cd07957 153411 Anticodon_Ia_Met Anticodon-binding domain of methionyl tRNA synthetases. This domain is found in methionyl tRNA synthetases (MetRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon (CAU). MetRS catalyzes the transfer of methionine to the 3'-end of its tRNA. 129 matched cddid_all.tbl CDD cd07958 cd07958 153412 Anticodon_Ia_Leu_BEm Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases. This domain is found in leucyl tRNA synthetases (LeuRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain. In contrast to other class Ia enzymes, the anticodon is not used as an identity element in LeuRS (with exceptions such as Saccharomyces cerevisiae and some other eukaryotes). No anticodon-binding site can be defined for this family, which includes bacterial and eukaryotic mitochondrial members, as well as LeuRS from the archaeal Halobacteria. LeuRS catalyzes the transfer of leucine to the 3'-end of its tRNA. 117 matched cddid_all.tbl CDD cd07959 cd07959 153413 Anticodon_Ia_Leu_AEc Anticodon-binding domain of archaeal and eukaryotic cytoplasmic leucyl tRNA synthetases. This domain is found in leucyl tRNA synthetases (LeuRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain. In contrast to other class Ia enzymes, the anticodon is not used as an identity element in LeuRS (with exceptions such as Saccharomyces cerevisiae and some other eukaryotes). No anticodon-binding site can be defined for this family, which includes archaeal and eukaryotic cytoplasmic members. LeuRS catalyzes the transfer of leucine to the 3'-end of its tRNA. 117 matched cddid_all.tbl CDD cd07960 cd07960 153414 Anticodon_Ia_Ile_BEm Anticodon-binding domain of bacterial and eukaryotic mitochondrial isoleucyl tRNA synthetases. This domain is found in isoleucyl tRNA synthetases (IleRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. This family includes bacterial and eukaryotic mitochondrial members. IleRS catalyzes the transfer of isoleucine to the 3'-end of its tRNA. 180 matched cddid_all.tbl CDD cd07961 cd07961 153415 Anticodon_Ia_Ile_ABEc Anticodon-binding domain of archaeal, bacterial, and eukaryotic cytoplasmic isoleucyl tRNA synthetases. This domain is found in isoleucyl tRNA synthetases (IleRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. This family includes bacterial, archaeal, and eukaryotic cytoplasmic members. IleRS catalyzes the transfer of isoleucine to the 3'-end of its tRNA. 183 matched cddid_all.tbl CDD cd07962 cd07962 153416 Anticodon_Ia_Val Anticodon-binding domain of valyl tRNA synthetases. This domain is found in valyl tRNA synthetases (ValRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. ValRS catalyzes the transfer of valine to the 3'-end of its tRNA. 135 matched cddid_all.tbl CDD cd07963 cd07963 153417 Anticodon_Ia_Cys Anticodon-binding domain of cysteinyl tRNA synthetases. This domain is found in cysteinyl tRNA synthetases (CysRS), which belong to the class Ia aminoacyl tRNA synthetases. It lies C-terminal to the catalytic core domain, and recognizes and specifically binds to the tRNA anticodon. CysRS catalyzes the transfer of cysteine to the 3'-end of its tRNA. 156 matched cddid_all.tbl CDD cd07964 cd07964 176481 RBP-H Head domain of virus receptor-binding proteins (RBP). Virus receptor-binding proteins (RBPs) are found in lactococcal bacteriophages, as well as in adenoviruses and reoviruses, which invade mammalian cells. Lactococcus lactis is widely used in dairy fermentations and infection of L. lactis by phages greatly impairs the fermentation process. Adenovirus typically infects respiratory tracts with symptoms ranging from the common cold to pneumonia. Onset of viral infections begin with the recognition of host cells through the receptor-binding protein complex located at the distal part of the virion. The RBP has three domains: the N- terminal shoulders domain, the interlaced neck domain, and the C-terminal head domain. Phages recognize their host through an interaction between the RBP head (RBP-H) domain and saccharidic receptors at the host cell surface. Adenovirus recognizes the membrane cofactor protein, CD46, as a cellular receptor. 103 matched cddid_all.tbl CDD cd07967 cd07967 153436 OBF_DNA_ligase_III The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing factor 1 (XRCC1) and functions in single nucleotide Base Excision Repair (BER). The mitochondrial form of DNA ligase III originates from the nucleolus and is involved in the mitochondrial DNA repair pathway. This isoform is expressed by a second start site on the DNA ligase III gene. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligouncleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain. 139 matched cddid_all.tbl CDD cd07968 cd07968 153437 OBF_DNA_ligase_IV The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent protein kinase. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligouncleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain. 140 matched cddid_all.tbl CDD cd07969 cd07969 153438 OBF_DNA_ligase_I The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). This group is composed of eukaryotic DNA ligase I, Sulfolobus solfataricus DNA ligase and similar proteins. DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain. 144 matched cddid_all.tbl CDD cd07970 cd07970 153439 OBF_DNA_ligase_LigC The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigC is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of Mycobacterium tuberculosis LigC and similar bacterial proteins. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain. 122 matched cddid_all.tbl CDD cd07971 cd07971 153440 OBF_DNA_ligase_LigD The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of Mycobacterium tuberculosis LigD and similar bacterial proteins. LigD, or DNA ligase D, catalyzes the end-healing and end-sealing steps during nonhomologous end joining. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain. 115 matched cddid_all.tbl CDD cd07972 cd07972 153441 OBF_DNA_ligase_Arch_LigB The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of Pyrococcus furiosus DNA ligase, Mycobacterium tuberculosis LigB, and similar archaeal and bacterial proteins. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain. 122 matched cddid_all.tbl CDD cd07973 cd07973 153422 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 complex. Spt4 homolog is not found in bacteria. 98 matched cddid_all.tbl CDD cd07976 cd07976 199899 TFIIA_alpha_beta_like Precursor of TFIIA alpha and beta subunits and similar proteins. Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of TATA-binding protein (TBP) for DNA in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from TATA-less promoters. TFIIA is composed of more than one subunit in various organisms. Mammalian TFIIA large subunits (TFIIA alpha and beta) and the smaller subunit (TFIIA gamma) form a heterotrimer. TFIIA alpha and beta are encoded by a single gene (TFIIA_alpha_beta), its protein product is post-translationally processed and cleaved. TOA1 and TOA2 are the two subunits of Yeast TFIIA which correspond to Mammalian TFIIA_alpha_beta and TFIIA gamma, respectively. TOA1 and TOA2 form a heterodimeric protein complex. TFIIA_alpha_beta alone is sufficient for transcription in early embryogenesis, but the cleaved forms, TFIIA alpha and TFIIA beta, represent the vast majority of TFIIA in most differentiated cells. The exact functional differences between cleaved and uncleaved forms are not yet clear. This model also contains paralogs of the canonical TFIIA_alpha_beta, such as the human ALF, which may be involved in gametogenesis and early embryogenesis (and is also subject to proteolytic cleavage). 102 matched cddid_all.tbl CDD cd07977 cd07977 153423 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional domains, an N-terminal serine-rich region, a central core domain exhibiting a winged-helix structure capable of binding double-stranded DNA, a leucine repeat, a sigma3 region, and a C-terminal domain containing two basic regions. The assembly of transcription preinitiation complex (PIC) includes the general transcription factors and RNA polymerase II (pol II) initiated by the binding of the TBP subunit of TFIID to the TATA box, followed by either the sequential assembly of other general transcription factors and pol II or a preassembled pol II holoenzyme pathway. TFIIE interacts directly with TFIIF, TFIIB, pol II, and promoter DNA. TFIIE recruits TFIIH and regulates its activities. TFIIE and TFIIH are also important for the transition from initiation to elongation. 75 matched cddid_all.tbl CDD cd07978 cd07978 467023 HFD_TAF13 histone-fold domain found in transcription initiation factor TFIID subunit 13 (TAF13) and similar proteins. TAF13, also called TATA Binding Protein (TBP) associated factor 13, transcription initiation factor TFIID 18 kDa subunit, TAF(II)18, TAFII-18, or TAFII18, is a component of the DNA-binding general RNA polymerase II transcription factor IID (TFIID) complex that is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). TFIID is one of the general transcription factors required for accurate and regulated initiation by RNA polymerase II. It plays a central role in mediating promoter responses to various activators and repressors. TAF13 interacts with TBP, and more strongly with TAF10 and TAF11. 77 matched cddid_all.tbl CDD cd07979 cd07979 467024 HFD_TAF9 histone-fold domain found in transcription initiation factor TFIID subunit 9 (TAF9) and similar proteins. The family includes TAF9 (also called TATA Binding Protein (TBP) associated factor 9, RNA polymerase II TBP-associated factor subunit G, STAF31/32, transcription initiation factor TFIID 31 kDa subunit, TAFII-31, TAFII31, transcription initiation factor TFIID 32 kDa subunit, TAFII-32, or TAFII32) and TAF9-like (also called transcription initiation factor TFIID subunit 9B, neuronal cell death-related protein 7, DN-7, or transcription-associated factor TAFII31L), which are essential for cell viability. They are involved in transcriptional activation as well as the repression of distinct but overlapping sets of genes. They may have roles in gene regulation associated with apoptosis. Both TAF9 and TAF9-like are TAFs that are components of the transcription factor IID (TFIID) complex, the TBP-free TAFII complex (TFTC), the PCAF histone acetylase complex and the STAGA transcription coactivator-HAT complex. TFIID or TFTC are essential for the regulation of RNA polymerase II-mediated transcription. TAF9 interacts directly with different transcription factors such as p53, herpes simplex virus activator vp16, and the basal transcription factor TFIIB. 95 matched cddid_all.tbl CDD cd07980 cd07980 259828 TFIIF_beta Transcription initiation factor IIF, beta subunit. The TFIIF-beta subunit, also called RNA Polymerase II-associating Protein 30 (RAP30), forms a heteromeric complex of RAP30/74 (TFIIF, beta/gamma) that is involved in both initiation and elongation of RNA chains by RNA polymerase II. Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. TFIIF-beta binds directly to RNA polymerase II and helps bring polymerase into a pre-initiation complex. 123 matched cddid_all.tbl CDD cd07981 cd07981 467025 HFD_TAF12 histone-fold domain found in transcription initiation factor TFIID subunit 12 (TAF12) and similar proteins. TAF12, also called TATA Binding Protein (TBP) associated factor 12, transcription initiation factor TFIID 20/15 kDa subunits, TAFII-20/TAFII-15, or TAFII20/TAFII15, is a TBP-associated factor (TAF). TAFs are components of the transcription factor IID (TFIID) complex, PCAF histone acetylase complex, and TBP-free TAFII complex (TFTC). TIIFD is multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. TFIID and PCAF are composed of TATA binding protein (TBP) and several TAFs. TBP is not part of TFTC. TAFs are essential for mediating regulation of RNA polymerase transcription. TAF12 interacts with TAF4 and makes a novel histone-like heterodimer that binds DNA and has a core promoter function of a subset of genes. It is important for RAS-induced transformation properties of human colorectal cancer cells; its levels are increased in the cells harboring the RAS mutation. Also, TAF12 interacts with activating transcription factor 7 (ATF7) and contributes to the hypersensitivity of osteoclast (OCL) precursors to 1,25-dihydroxyvitamin D2 (1,25-(OH)2D3; also known as calcitriol) in Paget's disease (PD), a disorder of the bone remodeling process, in which the body absorbs old bone and forms abnormal new bone. 74 matched cddid_all.tbl CDD cd07982 cd07982 467026 HFD_TAF10 histone-fold domain found in transcription initiation factor TFIID subunit 10 (TAF10) and similar proteins. TAF10, also called TATA Binding Protein (TBP) associated factor 10, STAF28, transcription initiation factor TFIID 30 kDa subunit, TAF(II)30, TAFII-30, or TAFII30, is a TBP-associated factor (TAF). TAFs are components of the transcription factor IID (TFIID) complex, PCAF histone acetylase complex, and TBP-free TAFII complex (TFTC). TIIFD is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. TFIID and PCAF are composed of TATA binding protein (TBP) and several TAFs. TBP is not part of TFTC. TAF10 regulates genes that are important for cell cycle progression and cell morphology. A lack of TAF10 leads to cell cycle arrest and cell death by apoptosis in mice. 98 matched cddid_all.tbl CDD cd07983 cd07983 153245 LPLAT_DUF374-like Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: DUF374. Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this subgroup are the uncharacterized DUF374 phospholipid/glycerol acyltransferases and similar proteins. 189 matched cddid_all.tbl CDD cd07984 cd07984 153246 LPLAT_LABLAT-like Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LABLAT-like. Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this subgroup are such LPLATs as lipid A biosynthesis lauroyl/myristoyl (LABLAT, HtrB) acyltransferases and similar proteins. 192 matched cddid_all.tbl CDD cd07985 cd07985 153247 LPLAT_GPAT Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT. Lysophospholipid acyltransferase (LPLAT) superfamily member: glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB). LPLATs are acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. This subgroup includes glycerol-3-phosphate 1-acyltransferase (GPAT, PlsB). 235 matched cddid_all.tbl CDD cd07986 cd07986 153248 LPLAT_ACT14924-like Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ACT14924. Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this subgroup are uncharacterized phospholipid/glycerol acyltransferases such as the Pectobacterium carotovorum subsp. carotovorum PC1 locus ACT14924 putative acyltransferase, and similar proteins. 210 matched cddid_all.tbl CDD cd07987 cd07987 153249 LPLAT_MGAT-like Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: MGAT-like. Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this suubgroup are such LPLATs as 2-acylglycerol O-acyltransferase (MGAT), and similar proteins. 212 matched cddid_all.tbl CDD cd07988 cd07988 153250 LPLAT_ABO13168-like Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown ABO13168. Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this subgroup are uncharacterized phospholipid/glycerol acyltransferases such as the Acinetobacter baumannii ATCC 17978 locus ABO13168 putative acyltransferase, and similar proteins. 163 matched cddid_all.tbl CDD cd07989 cd07989 153251 LPLAT_AGPAT-like Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: AGPAT-like. Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this subgroup are such LPLATs as 1-acyl-sn-glycerol-3-phosphate acyltransferase (AGPAT, PlsC), Tafazzin (product of Barth syndrome gene), and similar proteins. 184 matched cddid_all.tbl CDD cd07990 cd07990 153252 LPLAT_LCLAT1-like Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LCLAT1-like. Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this subgroup are such LPLATs as Lysocardiolipin acyltransferase 1 (LCLAT1) or 1-acyl-sn-glycerol-3-phosphate acyltransferase and similar proteins. 193 matched cddid_all.tbl CDD cd07991 cd07991 153253 LPLAT_LPCAT1-like Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: LPCAT1-like. Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this subgroup are such LPLATs as lysophosphatidylcholine acyltransferase 1 (LPCAT-1), glycerol-3-phosphate acyltransferase 3 (GPAT3), and similar sequences. 211 matched cddid_all.tbl CDD cd07992 cd07992 153254 LPLAT_AAK14816-like Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: Unknown AAK14816-like. Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this subgroup are uncharacterized glycerol-3-phosphate acyltransferases such as the Plasmodium falciparum locus AAK14816 putative acyltransferase, and similar proteins. 203 matched cddid_all.tbl CDD cd07993 cd07993 153255 LPLAT_DHAPAT-like Lysophospholipid Acyltransferases (LPLATs) of Glycerophospholipid Biosynthesis: GPAT-like. Lysophospholipid acyltransferase (LPLAT) superfamily member: acyltransferases of de novo and remodeling pathways of glycerophospholipid biosynthesis which catalyze the incorporation of an acyl group from either acylCoAs or acyl-acyl carrier proteins (acylACPs) into acceptors such as glycerol 3-phosphate, dihydroxyacetone phosphate or lyso-phosphatidic acid. Included in this subgroup are such LPLATs as dihydroxyacetone phosphate acyltransferase (DHAPAT, also known as 1 glycerol-3-phosphate O-acyltransferase 1) and similar proteins. 205 matched cddid_all.tbl CDD cd07994 cd07994 153424 WGR WGR domain. The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs) as well as the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, a small family of bacterial DNA ligases, and various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain occurs in single-domain proteins and in a variety of domain architectures, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain. 73 matched cddid_all.tbl CDD cd07995 cd07995 153431 TPK Thiamine pyrophosphokinase. Thiamine pyrophosphokinase (TPK, EC:2.7.6.2, also spelled thiamin pyrophosphokinase) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamine) to form the coenzyme thiamine pyrophosphate (TPP). TPP is required for central metabolic functions, and thiamine deficiency is associated with potentially fatal human diseases. The structure of thiamine pyrophosphokinase suggests that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis. 208 matched cddid_all.tbl CDD cd07996 cd07996 153425 WGR_MMR_like WGR domain of molybdate metabolism regulator and related proteins. The WGR domain is found in the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, as well as in various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain appears to occur in single-domain proteins and in a variety of domain architectures, together with ATP-dependent DNA ligase domains, WD40 repeats, leucine-rich repeats, and other domains. It has been proposed to function as a nucleic acid binding domain. 74 matched cddid_all.tbl CDD cd07997 cd07997 153426 WGR_PARP WGR domain of poly(ADP-ribose) polymerases. The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs). It has been called WGR after the most conserved central motif of the domain. The domain typically occurs together with a catalytic PARP domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain. PARPs catalyze the NAD(+)-dependent synthesis of ADP-ribose polymers and their addition to various nuclear proteins and histones. Higher eukaryotes contain several PARPs and there may be up to 17 human PARP-like proteins, with three of them (PARP-1, PARP-2, and PARP-3) containing a WGR domain. The synthesis of poly-ADP-ribose requires multiple enzymatic activities for initiation, trans-ADP-ribosylation, elongation, branching, and release of the polymer from the enzyme. Poly-ADP-ribosylation was thought to be a reversible post-translational covalent modification that serves as a regulatory mechanism for protein substrates. However, it is now known that it plays important roles in many cellular processes including maintenance of genomic stability, transcriptional regulation, energy metabolism, cell death and survival, among others. 102 matched cddid_all.tbl CDD cd07998 cd07998 153427 WGR_DNA_ligase WGR domain of bacterial DNA ligases. The WGR domain is found in a small family of predicted bacterial DNA ligases. It has been called WGR after the most conserved central motif of the domain. The domain typically occurs in together with an ATP-dependent DNA ligase domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain. 77 matched cddid_all.tbl CDD cd07999 cd07999 153432 GH7_CBH_EG Glycosyl hydrolase family 7. Glycosyl hydrolase family 7 contains eukaryotic endoglucanases (EGs) and cellobiohydrolases (CBHs) that hydrolyze glycosidic bonds using a double-displacement mechanism. This leads to a net retention of the conformation at the anomeric carbon. Both enzymes work synergistically in the degradation of cellulose,which is the main component of plant cell wall, and is composed of beta-1,4 linked glycosyl units. EG cleaves the beta-1,4 linkages of cellulose and CBH cleaves off cellobiose disaccharide units from the reducing end of the chain. In general, the O-glycosyl hydrolases are a widespread group of enzymes that hydrolyze the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A glycosyl hydrolase classification system based on sequence similarity has led to the definition of more than 95 different families inlcuding glycoside hydrolase family 7. 386 matched cddid_all.tbl CDD cd08000 cd08000 193574 NGN N-Utilization Substance G (NusG) N-terminal (NGN) domain Superfamily. The N-Utilization Substance G (NusG) and its eukaryotic homolog Spt5 are involved in transcription elongation and termination. NusG contains an NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus in bacteria and archaea. The eukaryotic ortholog, Spt5, is a large protein composed of an acidic N-terminus, an NGN domain, and multiple KOW motifs at its C-terminus. Spt5 forms a Spt4-Spt5 complex that is an essential RNA Polymerase II elongation factor. NusG was originally discovered as an N-dependent antitermination enhancing activity in Escherichia coli and has a variety of functions, such as being involved in RNA polymerase elongation and Rho-termination in bacteria. Orthologs of the NusG gene exist in all bacteria, but its functions and requirements are different. The diverse activities suggest that, after diverging from a common ancestor, NusG proteins became specialized in different bacteria. 99 matched cddid_all.tbl CDD cd08001 cd08001 153428 WGR_PARP1_like WGR domain of poly(ADP-ribose) polymerase 1 and similar proteins. The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs). It has been called WGR after the most conserved central motif of the domain. The domain typically occurs together with a catalytic PARP domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain. PARPs catalyze the NAD(+)-dependent synthesis of ADP-ribose polymers and their addition to various nuclear proteins. Higher eukaryotes contain several PARPs and and there may be up to 17 human PARP-like proteins, with three of them (PARP-1, PARP-2, and PARP-3) containing a WGR domain. The synthesis of poly-ADP-ribose requires multiple enzymatic activities for initiation, trans-ADP-ribosylation, elongation, branching, and release of the polymer from the enzyme. This subfamily is composed of vertebrate PARP-1 and similar proteins, including Arabidopsis thaliana PARP-1 and PARP-3. PARP-1 is the best-studied among the PARPs. It is a widely expressed nuclear chromatin-associated enzyme that possesses auto-mono-ADP-ribosylation (initiation), elongation, and branching activities. PARP-1 is implicated in DNA damage and cell death pathways and is important in maintaining genomic stability and regulating cell proliferation, differentiation, neuronal function, inflammation, and aging. 104 matched cddid_all.tbl CDD cd08002 cd08002 153429 WGR_PARP3_like WGR domain of poly(ADP-ribose) polymerase 3 and similar proteins. The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs). It has been called WGR after the most conserved central motif of the domain. The domain typically occurs together with a catalytic PARP domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain. PARPs catalyze the NAD(+)-dependent synthesis of ADP-ribose polymers and their addition to various nuclear proteins. Higher eukaryotes contain several PARPs and and there may be up to 17 human PARP-like proteins, with three of them (PARP-1, PARP-2, and PARP-3) containing a WGR domain. The synthesis of poly-ADP-ribose requires multiple enzymatic activities for initiation, trans-ADP-ribosylation, elongation, branching, and release of the polymer from the enzyme. This subfamily is composed of human PARP-3 and similar proteins, including Arabidopsis thaliana PARP-2. PARP-3 displays a tissue-specific expression, with highest amounts found in the nuclei of epithelial cells of prostate ducts, salivary glands, liver, pancreas, and in the neurons of terminal ganglia. Unlike PARP-1 and PARP-2, PARP-3 activity is not induced by DNA strand breaks. However, it co-localizes with Polycomb group bodies and is part of complexes making up DNA-PKcs, DNA ligases III and IV, Ku70, and Ku80. PARP-3 is a nuclear protein that may be involved in transcriptional control and responses to DNA damage. 100 matched cddid_all.tbl CDD cd08003 cd08003 153430 WGR_PARP2_like WGR domain of poly(ADP-ribose) polymerases. The WGR domain is found in a variety of eukaryotic poly(ADP-ribose) polymerases (PARPs). It has been called WGR after the most conserved central motif of the domain. The domain typically occurs together with a catalytic PARP domain, and is between 70 and 80 residues in length. It has been proposed to function as a nucleic acid binding domain. PARPs catalyze the NAD(+)-dependent synthesis of ADP-ribose polymers and their addition to various nuclear proteins. Higher eukaryotes contain several PARPs and and there may be up to 17 human PARP-like proteins, with three of them (PARP-1, PARP-2, and PARP-3) containing a WGR domain. The synthesis of poly-ADP-ribose requires multiple enzymatic activities for initiation, trans-ADP-ribosylation, elongation, branching, and release of the polymer from the enzyme. This subfamily is composed of human PARP-2 and similar proteins. Similar to PARP-1, PARP-2 is ubiquitously expressed and its activity is induced by DNA strand breaks. It also plays a role in cell differentiation, cell death, and maintaining genomic stability. Studies on mice deficient with PARP-2 shows that it is important in fat storage, T cell maturation, and spermatogenesis. 103 matched cddid_all.tbl CDD cd08010 cd08010 381750 MltG_like proteins similar to Escherichia coli YceG/mltG may function as endolytic murein transglycosylases. The gene product of Escherichia coli yceG/mltG has been erroneously annotated as an aminodeoxychorismate lyase. Its overexpression has been reported to cause abnormal biofilm architecture, and it has been reported to be part of a putative five-gene operon. More recently it has been proposed to function as a terminase for peptidoglycan polymerization. The family also includes Streptomyces caeruleus NovB, an uncharacterized member of the novobiocin biosynthetic gene cluster. 246 matched cddid_all.tbl CDD cd08011 cd08011 349933 M20_ArgE_DapE-like M20 Peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases. Peptidase M20 family, uncharacterized protein subfamily with similarity to acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE) subfamily. This group includes the hypothetical protein ygeY from Escherichia coli, a putative deacetylase, but many in this subfamily are classified as unassigned peptidases. ArgE/DapE enzymes catalyze analogous reactions and share a common activator, the metal ion (usually Co2+ or Zn2+). ArgE catalyzes a broad range of substrates, including N-acetylornithine, alpha-N-acetylmethionine and alpha-N-formylmethionine, while DapE catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelate (L,L-SDAP) to L,L-diaminopimelate and succinate. Proteins in this subfamily are mostly archaeal, and have been inferred by homology as being related to both ArgE and DapE. 355 matched cddid_all.tbl CDD cd08012 cd08012 349934 M20_ArgE-related M20 Peptidases with similarity to acetylornithine deacetylases. Peptidase M20 family, acetylornithine deacetylase (ArgE, Acetylornithinase, AO, N2-acetyl-L-ornithine amidohydrolase, EC 3.5.1.16)-related subfamily. Proteins in this subfamily have not yet been characterized, but have been predicted to have deacetylase activity. ArgE catalyzes the conversion of N-acetylornithine to ornithine, which can then be incorporated into the urea cycle for the final stage of arginine synthesis. The substrate specificity of ArgE is quite broad; several alpha-N-acyl-L-amino acids can be hydrolyzed, including alpha-N-acetylmethionine and alpha-N-formylmethionine. ArgE shares significant sequence homology and biochemical features, and possibly a common origin, with glutamate carboxypeptidase (CPG2) and succinyl-diaminopimelate desuccinylase (DapE), and aminoacylase I (ACY1), having all metal ligand binding residues conserved. 423 matched cddid_all.tbl CDD cd08013 cd08013 349935 M20_ArgE_DapE-like M20 peptidases with similarity to acetylornithine deacetylases and succinyl-diaminopimelate desuccinylases. Peptidase M20 family, uncharacterized protein subfamily with similarity to acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE) subfamily. This group includes the hypothetical protein ygeY from Escherichia coli, a putative deacetylase, but many in this subfamily are classified as unassigned peptidases. ArgE/DapE enzymes catalyze analogous reactions and share a common activator, the metal ion (usually Co2+ or Zn2+). ArgE catalyzes a broad range of substrates, including N-acetylornithine, alpha-N-acetylmethionine and alpha-N-formylmethionine, while DapE catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelate (L,L-SDAP) to L,L-diaminopimelate and succinate. Proteins in this subfamily are mostly fungal and bacterial, and have been inferred by homology as being related to both ArgE and DapE. 379 matched cddid_all.tbl CDD cd08014 cd08014 349936 M20_Acy1-like M20 Peptidase aminoacylase 1 subfamily. Peptidase M20 family, uncharacterized subfamily of uncharacterized bacterial proteins predicted as putative amidohydrolases. These are a class of zinc binding homodimeric enzymes involved in hydrolysis of N-acetylated proteins. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in protection and stability of proteins. Several types of aminoacylases can be distinguished on the basis of substrate specificity. Aminoacylase 1 (ACY1) breaks down cytosolic aliphatic N-acyl-alpha-amino acids (except L-aspartate), especially N-acetyl-methionine and acetyl-glutamate into L-amino acids and an acyl group. However, ACY1 can also catalyze the reverse reaction, the synthesis of acetylated amino acids. ACY1 may also play a role in xenobiotic bioactivation as well as the inter-organ processing of amino acid-conjugated xenobiotic derivatives (S-substituted-N-acetyl-L-cysteine). 371 matched cddid_all.tbl CDD cd08015 cd08015 349937 M28_like M28 Zn-peptidase-like; uncharacterized subfamily. Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. 218 matched cddid_all.tbl CDD cd08017 cd08017 349938 M20_IAA_Hyd M20 Peptidase Indole-3-acetic acid amino acid hydrolase. Peptidase M20 family, plant aminoacyclase-1 indole-3-acetic-L-aspartic acid hydrolase (IAA-Asp hydrolase; IAAspH; IAAH; IAA amidohydrolase; EC 3.5.1.-) subfamily. IAAspH hydrolyzes indole-3-acetyl-N-aspartic acid (IAA or auxin) to indole-3-acetic acid. Genes encoding IAA-amidohydrolases were first cloned from Arabidopsis; ILR1, IAR3, ILL1 and ILL2 encode active IAA- amino acid hydrolases, and three additional amidohydrolase-like genes (ILL3, ILL5, ILL6) have been isolated. In higher plants, the growth regulator indole-3-acetic acid (IAA or auxin) is found both free and conjugated via amide bonding to a variety of amino acids and peptides, and via an ester linkage to carbohydrates. IAA-Asp conjugates are involved in homeostatic control, protection, storing and subsequent use of free IAA. IAA-Asp is also found in some plants as a unique intermediate for entering into IAA non-decarboxylative oxidative pathway. IAA amidohydrolase cleaves the amide bond between the auxin and the conjugated amino acid. Enterobacter agglomerans IAAspH has very strong enzyme activity and substrate specificity towards IAA-Asp, although its substrate affinity is weaker compared to Arabidopsis enzymes of the ILR1 gene family. Enhanced IAA-hydrolase activity has been observed during clubroot disease in Chinese cabbage. 376 matched cddid_all.tbl CDD cd08018 cd08018 349939 M20_Acy1_amhX-like M20 Peptidase aminoacylase 1 amhX-like subfamily. Peptidase M20 family, uncharacterized subfamily of proteins predicted as putative amidohydrolases, including the amhX gene product from Bacillus subtilis. These are a class of zinc binding homodimeric enzymes involved in hydrolysis of N-acetylated proteins. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in protection and stability of proteins. Several types of aminoacylases can be distinguished on the basis of substrate specificity. Aminoacylase 1 (ACY1) breaks down cytosolic aliphatic N-acyl-alpha-amino acids (except L-aspartate), especially N-acetyl-methionine and acetyl-glutamate into L-amino acids and an acyl group. However, ACY1 can also catalyze the reverse reaction, the synthesis of acetylated amino acids. ACY1 may also play a role in xenobiotic bioactivation as well as the inter-organ processing of amino acid-conjugated xenobiotic derivatives (S-substituted-N-acetyl-L-cysteine). 365 matched cddid_all.tbl CDD cd08019 cd08019 349940 M20_Acy1-like M20 Peptidase aminoacylase 1 subfamily. Peptidase M20 family, uncharacterized subfamily of bacterial proteins predicted as putative amidohydrolases. These are a class of zinc binding homodimeric enzymes involved in hydrolysis of N-acetylated proteins. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in protection and stability of proteins. Several types of aminoacylases can be distinguished on the basis of substrate specificity. Aminoacylase 1 (ACY1) breaks down cytosolic aliphatic N-acyl-alpha-amino acids (except L-aspartate), especially N-acetyl-methionine and acetyl-glutamate into L-amino acids and an acyl group. However, ACY1 can also catalyze the reverse reaction, the synthesis of acetylated amino acids. ACY1 may also play a role in xenobiotic bioactivation as well as the inter-organ processing of amino acid-conjugated xenobiotic derivatives (S-substituted-N-acetyl-L-cysteine). 372 matched cddid_all.tbl CDD cd08021 cd08021 349941 M20_Acy1_YhaA-like M20 Peptidase aminoacylase 1 subfamily, includes Bacillus subtilis YhaA and Staphylococcus aureus amidohydrolase, SACOL0085. Peptidase M20 family, uncharacterized subfamily of bacterial proteins predicted as putative amidohydrolases or hippurate hydrolases. These are a class of zinc binding homodimeric enzymes involved in hydrolysis of N-acetylated proteins. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in protection and stability of proteins. Several types of aminoacylases can be distinguished on the basis of substrate specificity. Aminoacylase 1 (ACY1) breaks down cytosolic aliphatic N-acyl-alpha-amino acids (except L-aspartate), especially N-acetyl-methionine and acetyl-glutamate into L-amino acids and an acyl group. However, ACY1 can also catalyze the reverse reaction, the synthesis of acetylated amino acids. ACY1 may also play a role in xenobiotic bioactivation as well as the inter-organ processing of amino acid-conjugated xenobiotic derivatives (S-substituted-N-acetyl-L-cysteine). This family includes Staphylococcus aureus amidohydrolase, SACOL0085, which contains two manganese ions in the active site, and forms a homotetramer with variations in interdomain orientation which possibly plays a role in the regulation of catalytic activity. 384 matched cddid_all.tbl CDD cd08022 cd08022 349942 M28_PSMA_like M28 Zn-peptidase prostate-specific membrane antigen. Peptidase M28 family; prostate-specific membrane antigen (PSMA, also called glutamate carboxypeptidase II or GCP-II)-like subfamily. PSMA is a homodimeric type II transmembrane protein containing three distinct domains: protease-like, apical or protease-associated (PA) and helical domains. The protease-like domain is a large extracellular portion (ectodomain). PSMA is over-expressed predominantly in prostate cancer (PCa) as well as in the neovasculature of most solid tumors, but not in the vasculature of the normal tissues. PSMA is considered a biomarker for PCa and possibly for use as an imaging and therapeutic target. The extracellular domain of PSMA possesses two unique enzymatic functions: N-acetylated, alpha-linked acidic dipeptidase (NAALADase) which cleaves terminal glutamate from the neurodipeptide N-acetyl-aspartyl-glutamate (NAAG), and folate hydrolase (FOLH) which cleaves the terminal glutamates from gamma-linked polyglutamates (carboxypeptidase). A mutation in this gene may be associated with impaired intestinal absorption of dietary folates, resulting in low blood folate levels and consequent hyperhomocysteinemia. Expression of this protein in the brain may be involved in a number of pathological conditions associated with glutamate excitotoxicity. Inhibition of GCP-II has been shown to be effective in preclinical models of neurological disorders associated with excessive activation of glutamatergic systems. This gene likely arose from a duplication event of a nearby chromosomal region. Alternative splicing gives rise to multiple transcript variants. 287 matched cddid_all.tbl CDD cd08023 cd08023 185693 GH16_laminarinase_like Laminarinase, member of the glycosyl hydrolase family 16. Laminarinase, also known as glucan endo-1,3-beta-D-glucosidase, is a glycosyl hydrolase family 16 member that hydrolyzes 1,3-beta-D-glucosidic linkages in 1,3-beta-D-glucans such as laminarins, curdlans, paramylons, and pachymans, with very limited action on mixed-link (1,3-1,4-)-beta-D-glucans. 235 matched cddid_all.tbl CDD cd08024 cd08024 185694 GH16_CCF Coelomic cytolytic factor, member of glycosyl hydrolase family 16. Subgroup of glucanases of unknown function that are related to beta-GRP (beta-1,3-glucan recognition protein), but contain active site residues. Beta-GRPs are one group of pattern recognition receptors (PRRs), also referred to as biosensor proteins, that complexes with pathogen-associated beta-1,3-glucans and then transduces signals necessary for activation of an appropriate innate immune response. Beta-GRPs are present in insects and lack all catalytic residues. This subgroup contains related proteins that still contain the active site and are widely distributed in eukaryotes. Their structures adopt a jelly roll fold with a deep active site channel harboring the catalytic residues, like those of other glycosyl hydrolase family 16 members. 330 matched cddid_all.tbl CDD cd08025 cd08025 153090 RNR_PFL_like_DUF711 Uncharacterized proteins with similarity to Ribonucleotide reductase and Pyruvate formate lyase. This subfamily contains Streptococcus pneumoniae Sp0239 and similar uncharacterized proteins. Sp0239 is structurally similar to ribonucleotide reductase (RNR) and pyruvate formate lyase (PFL), which are believed to have diverged from a common ancestor. RNR and PFL possess a ten-stranded alpha-beta barrel domain that hosts the active site, and are radical enzymes. RNRs are found in all organisms and provide the only mechanism by which nucleotides are converted to deoxynucleotides. PFL is an essential enzyme in anaerobic bacteria that catalyzes the conversion of pyruvate and CoA to acteylCoA and formate. 400 matched cddid_all.tbl CDD cd08026 cd08026 153434 DUF326 Cysteine-rich 4 helical bundle widely conserved in bacteria. This functionally uncharacterized protein forms a 4-helical bundle with a bromodomain-like topology. It is present in major bacterial lineages and contains highly conserved cysteines in a repeated pattern, whose sidechains appear buried. Some family members have been (mis)annotated as putative ferredoxins. 102 matched cddid_all.tbl CDD cd08028 cd08028 153397 LARP_3 La RNA-binding domain of La-related protein 3. This domain is found at the N-terminus of the La autoantigen and similar proteins, and co-occurs with an RNA-recognition motif (RRM). Together these domains function to bind primary transcripts of RNA polymerase III at their 3' terminus and protect them from exonucleolytic degradation. Binding is specific for the 3'-terminal UUU-OH motif. The La autoantigen is also called Lupus La protein, LARP3, or Sjoegren syndrome type B antigen (SS-B). 82 matched cddid_all.tbl CDD cd08029 cd08029 153398 LA_like_fungal La-motif domain of fungal proteins similar to the La autoantigen. This domain is found in fungal proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. 76 matched cddid_all.tbl CDD cd08030 cd08030 153399 LA_like_plant La-motif domain of plant proteins similar to the La autoantigen. This domain is found in plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. 90 matched cddid_all.tbl CDD cd08031 cd08031 153400 LARP_4_5_like La RNA-binding domain of proteins similar to La-related proteins 4 and 5. This domain is found in proteins similar to La-related proteins 4 and 5 (LARP4, LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. 75 matched cddid_all.tbl CDD cd08032 cd08032 153401 LARP_7 La RNA-binding domain of La-related protein 7. LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation. 82 matched cddid_all.tbl CDD cd08033 cd08033 153402 LARP_6 La RNA-binding domain of La-related protein 6. This domain is found in animal and plant proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. 77 matched cddid_all.tbl CDD cd08034 cd08034 153403 LARP_1_2 La RNA-binding domain proteins similar to La-related proteins 1 and 2. This domain is found in proteins similar to vertebrate La-related proteins 1 and 2 (LARP1, LARP2). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. 73 matched cddid_all.tbl CDD cd08035 cd08035 153404 LARP_4 La RNA-binding domain of La-related protein 4. This domain is found in vertebrate La-related protein 4 (LARP4), also known as c-MPL binding protein. La-type domains often co-occur with RNA-recognition motifs (RRMs). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. 75 matched cddid_all.tbl CDD cd08036 cd08036 153405 LARP_5 La RNA-binding domain of La-related protein 5. This domain is found in vertebrate La-related protein 5 (LARP5). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. 75 matched cddid_all.tbl CDD cd08037 cd08037 153406 LARP_1 La RNA-binding domain of La-related protein 1. This domain is found in vertebrate La-related protein 1 (LARP1). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. 73 matched cddid_all.tbl CDD cd08038 cd08038 153407 LARP_2 La RNA-binding domain of La-related protein 2. This domain is found in vertebrate La-related protein 2 (LARP2). A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. 73 matched cddid_all.tbl CDD cd08039 cd08039 185716 Adenylation_DNA_ligase_Fungal Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. This group is composed of uncharacterized fungal proteins with similarity to ATP-dependent DNA ligases. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site residues. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. This model characterizes the adenylation domain of this group of uncharacterized fungal proteins. It is not known whether these proteins also contain an OB-fold domain. 235 matched cddid_all.tbl CDD cd08040 cd08040 153442 OBF_DNA_ligase_family The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain. 108 matched cddid_all.tbl CDD cd08041 cd08041 153443 OBF_kDNA_ligase_like The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. The mitochondrial DNA of parasitic protozoan is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-dependent ligases. They are involved in DNA replication or repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and VI) that define this family of related nucleotidyltransferases. The OB-fold domain contacts the nicked DNA substrate and is required for the ATP-dependent DNA ligase nucleotidylation step. The RxDK motif (motif VI), which is essential for ATP hydrolysis, is located in the OB-fold domain. 77 matched cddid_all.tbl CDD cd08044 cd08044 176269 TAF5_NTD2 TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated Factor 5 (TAF5), involved in forming Transcription Factor IID (TFIID). The TATA Binding Protein (TBP) Associated Factor 5 (TAF5) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TAF5 contains three domains, two conserved sequence motifs at the N-terminal and one at the C-terminal region. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the preinitiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. TAF5 may play a major role in forming TFIID and its related complexes. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. TAF5 has a paralog gene (TAF5L) which has a redundant function. Several hypotheses are proposed for TAFs functions such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. C-terminus of TAF5 contains six WD40 repeats that likely form a closed beta propeller structure and may be involved in protein-protein interaction. The first part of the TAF5 N-terminal (TAF5_NTD1) homodimerizes in the absence of other TAFs. The second conserved N-terminal part of TAF5 (TAF5_NTD2) has an alpha-helical domain. One study has shown that TAF5_NTD2 homodimerizes only at high concentration of calcium but not any other metals. No dimerization was observed in other structural studies of TAF_NTD2. Several TAFs interact via histone-fold (HFD) motifs; HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamer. However, TAF5 does not have a HFD motif. 133 matched cddid_all.tbl CDD cd08045 cd08045 467027 HFD_TAF4 histone-fold domain found in transcription initiation factor TFIID subunit 4 (TAF4) and similar proteins. TAF4, also called TATA Binding Protein (TBP) associated factor 4, RNA polymerase II TBP-associated factor subunit C, TBP-associated factor 4, transcription initiation factor TFIID 130 kDa subunit (TAF(II)130, TAFII-130, TAFII130), or transcription initiation factor TFIID 135 kDa subunit (TAF(II)135, TAFII-135, TAFII135), is a component of the TFIID complex that is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). TFIID is one of the general transcription factors required for accurate and regulated initiation by RNA polymerase II. It plays a central role in mediating promoter responses to various activators and repressors. TAF4 potentiates transcriptional activation by the AF-2S of retinoic acid, vitamin D3 and thyroid hormone. TAF4 also acts as a component of the TFTC-HAT complex and some MLL1/MLL complexes. TAF4 interacts with ATF7 and the interaction inhibits ATF7-mediated transactivation. 100 matched cddid_all.tbl CDD cd08047 cd08047 173966 TAF7 TATA Binding Protein (TBP) Associated Factor 7 (TAF7) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 7 (TAF7) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the preinitiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as activator-binding sites, core-promoter recognition or a role in essential catalytic activity. Each TAF, with the help of a specific activator, is required only for expression of subset of genes and is not universally involved for transcription as are GTFs. TAF7 is involved in the regulation of the transition from PIC assembly to initiation and elongation. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. Several TAFs interact via histone-fold (HFD) motifs; the HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. 162 matched cddid_all.tbl CDD cd08048 cd08048 467028 HFD_TAF11 histone-fold domain found in transcription initiation factor TFIID subunit 11 (TAF11) and similar proteins. TAF11, also called TATA Binding Protein (TBP) associated factor 11, TFIID subunit p30-beta, or transcription initiation factor TFIID 28 kDa subunit (TAF(II)28, TAFII-28, TAFII28), is a component of the TFIID complex that is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). TFIID is one of the general transcription factors required for accurate and regulated initiation by RNA polymerase II. It plays a central role in mediating promoter responses to various activators and repressors. TAF11 interacts with the ligand binding domains of the nuclear receptors for vitamin D3 and thyroid hormone. TAF11 also directly interacts with TFIIA, acting as a bridging factor that stabilizes the TFIIA-TBP-DNA complex. 87 matched cddid_all.tbl CDD cd08049 cd08049 176263 TAF8 TATA Binding Protein (TBP) Associated Factor 8. The TATA Binding Protein (TBP) Associated Factor 8 (TAF8) is one of several TAFs that bind TBP, and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and the assembly of the preinitiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs' functions, such as serving as activator-binding sites, involvement in the core-promoter recognition, or a role in the essential catalytic activity of the complex. The mouse ortholog of TAF8 is called taube nuss protein (TBN), and is required for early embryonic development. TBN mutant mice exhibit disturbances in the balance between cell death and cell survival in the early embryo. TAF8 plays a role in the differentiation of preadipocyte fibroblasts to adipocytes; it is also required for the integration of TAF10 into the TAF complex. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. TAF8 is also a component of a small TAF complex (SMAT), which contains TAF8, TAF10 and SUPT7L. Several TAFs interact via histone-fold motifs. The histone fold (HFD) is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamer. TAF8 contains an H4 related histone fold motif, and interacts with several subunits of TFIID, including TBP and the histone-fold protein TAF10. Currently, five HF-containing TAF pairs have been described or suggested to exist in TFIID: TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10. 54 matched cddid_all.tbl CDD cd08050 cd08050 381749 TAF6C C-terminal domain of TATA Binding Protein (TBP) Associated Factor 6 (TAF6). This model characterizes the carboxy (C)-terminal domain of TATA Binding Protein (TBP) Associated Factor 6 (TAF6), which is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. This C-terminal HEAT repeat domain of TAF6 (TAF6C) is proposed to form a homodimer that effectively bridges the downstream promoter-interacting TAFs (TAF1, -2, and -7) with lobe B of TFIID. This domain influences the TAF6-TAF9 complex, is thus important for TFIID assembly, and may trigger signals from transcriptional effectors. The HEAT domain motif is generally involved in protein/protein interactions, and in A. locustae, the conserved TAF6C domain is formed by five HEAT repeats, tightly packed against each other, defining a single structural domain. TFIID is one of several General Transcription Factors (GTFs), which also include TFIIA, TFIIB, TFIIE, TFIIF and TFIIH, that are involved in the accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays a key role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs' functions such as serving as activator-binding sites, core-promoter recognition, or a role in essential catalytic activity. These TAFs, with the help of specific activators, are required only for expression of a subset of genes and are not universally involved for transcription, as are GTFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. Several TAFs interact via histone-fold domain (HFD) motifs; the HFD is the interaction motif involved in heterodimerization of the core histones and their assembly into nucleosome octamers. The minimal HFD contains three alpha-helices linked by two loops and is found in core histones, TAFs and many other transcription factors. TFIID has a histone octamer-like substructure. TAF6 is a shared subunit of histone acetyltransferase complex SAGA and TFIID complexes. The N-terminal HFD of TAF6, interacts with the HFD of TAF9 and makes a novel histone-like heterodimer that is structurally related to histones H4 and H3. TAF6 may also interact with the downstream core promoter element (DPE). 216 matched cddid_all.tbl CDD cd08051 cd08051 153444 gp6_gp15_like Head-Tail Connector Proteins gp6 and gp15, and similar proteins. Members of this family include the proteins gp6 and gp15 from bacteriophage HK97 and SPP1, respectively. They are critical in the assembly of the connector, a specialized structure that serves as an interface for head and tail attachment, as well as a point at which DNA exits the head during infection by the bacteriophage. They form dodecameric ring structures that comprise the middle ring of the connector, located between the portal protein (attached to the head) and the gp7/gp16 ring (attached to the tail). They are components of the mature phage and the absence or mutation of HK97 gp6 or SPP1 gp15, respectively, result in defective head-tail joining and the absence of mature phage particles. The genome maps of HK97 and SPP1 show that genes encoding gp6 and gp15 are in the same relative position on the genome, located adjacent to the major capsid protein (MCP) gene and in between head and tail genes. Also included in this family is the uncharacterized Bacillus subtilis Yqbg protein, whose gene is part of the unusual genetic element called skin. The Yqbg gene is surrounded with genes similar to genes in the Bacillus subtilis prophage-like element PBSX, which encode for proteins comprising contractile-tailed phage-like particles that are produced upon mitomycin C treatment. Yqbg likely acts as a head-tail connector protein, similar to gp6 and gp15, of the PBSX-like prophage encoded in the skin element. 94 matched cddid_all.tbl CDD cd08053 cd08053 153445 Yqbg Putative Head-Tail Connector Protein Yqbg from Bacillus subtilis and similar proteins. The uncharacterized Bacillus subtilis Yqbg protein, whose gene is part of the unusual genetic element called skin, shows a similar structure to the connector proteins gp6 and gp15 from bacteriophage HK97 and SPP1, respectively. gp6 and gp15 are critical in the assembly of the connector, a specialized structure that serves as an interface for head and tail attachment, as well as a point at which DNA exits the head during infection by the bacteriophage. They form dodecameric ring structures that comprise the middle ring of the connector, located between the portal protein (attached to the head) and the gp7/gp16 ring (attached to the tail). The Yqbg gene is surrounded with genes similar to genes in the Bacillus subtilis prophage-like element PBSX, which encode for proteins comprising contractile-tailed phage-like particles that are produced upon mitomycin C treatment. Yqbg likely acts as a head-tail connector protein, similar to gp6 and gp15, of the PBSX-like prophage encoded in the skin element. 121 matched cddid_all.tbl CDD cd08054 cd08054 153446 gp6 Head-Tail Connector Protein gp6 of Bacteriophage HK97 and similar proteins. The bacteriophage HK97 gp6 protein is critical in the assembly of the connector, a specialized structure that serves as an interface for head and tail attachment, as well as a point at which DNA exits the head during infection by the bacteriophage. It forms a dodecameric ring structure that comprises the middle ring of the connector, located between the portal protein (attached to the head) and the gp7 ring (attached to the tail). It is a component of the mature phage and the absence of HK97 gp6 results in defective head-tail joining and the absence of mature phage particles. Although the crystal structure of HK97 gp6 shows an unexpected 13-mer ring, the biological form present in the mature phage is believed to be a dodecamer. 91 matched cddid_all.tbl CDD cd08055 cd08055 153447 gp15 Head-Tail Connector Protein gp15 of Bacteriophage SPP1 and similar proteins. The bacteriophage SPP1 gp15 protein is critical in the assembly of the connector, a specialized structure that serves as an interface for head and tail attachment, as well as a point at which DNA exits the head during infection by the bacteriophage. It forms a dodecameric ring structure that comprises the middle ring of the connector, located between the portal protein (attached to the head) and the gp16 ring (attached to the tail). Binding of the gp15 and gp16 rings to the portal protein is essential to prevent leakage of packaged DNA. gp15 is a component of the mature phage and its mutation results in defective head-tail joining. 95 matched cddid_all.tbl CDD cd08056 cd08056 163687 MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains without isopeptidase activity found in splicing factor Prp8. Members of this family are found in pre-mRNA-processing factor 8 (Prp8) which is a critical splicing factor, interacting with several other spliceosomal proteins, snRNAs, and the pre-mRNA, thus organizing and stabilizing the spliceosome catalytic core. Prp8 is one of the largest and most highly conserved of nuclear proteins, occupying a central position in the catalytic core of the spliceosome. Its C-terminal domain exhibits a JAB1/MPN-like core similar to deubiquitinating enzymes, but does not show catalytic isopeptidase activity, possibly because the putative isopeptidase center is covered by insertions and terminal appendices that are grafted onto this core, thus impairing the metal binding site. It is proposed that this domain is a protein interaction domain instead of a Zn(2+)-dependent metalloenzyme as proposed for some MPN proteins. The DEAD-box protein Brr2 and the GTPase Snu114 bind to the Prp8 C-terminus, a region where mutations in human Prp8 (hPrp8) cause a severe form of the genetic disorder retinitis pigmentosa, RP13, which leads to progressive photoreceptor degeneration in the retina and eventual blindness. At the N-terminus of Prp8, there are several domains, including a highly variable nuclear localization signal (NLS) motif rich in prolines, a conserved RNA recognition motif (RRM), and U5 and U6 snRNA binding sites. 252 matched cddid_all.tbl CDD cd08057 cd08057 163688 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic. This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. It cleaves ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. EIF3f s a potent inhibitor of HIV-1 replication as well as an important negative regulator of cell growth and proliferation. EIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. 157 matched cddid_all.tbl CDD cd08058 cd08058 163689 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic. This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor proteins, including p53, p27, and Smad4. Over-expression of CSN5 has been implicated in cancer initiation and progression. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. It is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity; it is targeted to DNA damage foci after irradiation. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. It is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene and serves as a marker in prostate tumors. 119 matched cddid_all.tbl CDD cd08059 cd08059 163690 MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic. This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site. 101 matched cddid_all.tbl CDD cd08060 cd08060 163691 MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family of unknown function includes neighbor of COX4 (Noc4p). This family includes Noc4p (neighbor of COX4; neighbor of Cytochrome c Oxidase 4; nucleolar complex associated 4 homolog) which belongs to the family of unknown function, UPF0172, with MPN/JAMM-like domains. Proteins in this family are homologs of the NOC4 gene which is conserved in eukaryotic members including human, dog, mouse, rat, chicken, zebrafish, fruit fly, mosquito, S.pombe, K.lactis, E.gossypii, M.grisea, N.crassa, A.thaliana, and rice. NOC4 highly expressed in the pancreas and moderately in liver, heart, lung, kidney, brain, skeletal muscle, and placenta. This nucleolar protein forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity. 182 matched cddid_all.tbl CDD cd08061 cd08061 163692 MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain. Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity. 274 matched cddid_all.tbl CDD cd08062 cd08062 163693 MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in 19S proteasomal subunits Rpn7 and Rpn8. This family includes lid subunits of the 26 S proteasome regulatory particles, Rpn7 (PSMD7; proteasome 26S non-ATPase subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be critical for the integrity of the 26 S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. Rpn7 and Rpn8 are ATP-independent components of the 19S regulator subunit, and contain the MPN structural motif on its N-terminal region. However, while they show a typical MPN metalloprotease fold, they lack the canonical JAMM motif, and therefore do not show catalytic isopeptidase activity. It is suggested that Rpn7 function is primarily structural. 280 matched cddid_all.tbl CDD cd08063 cd08063 163694 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6. CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleavage of Rbx1 and increased deneddylation of cullins inactivate CRLs and presumably stabilize pro-apoptotic factors for final apoptotic steps. While CSN6 shows a typical MPN metalloprotease fold, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity. 288 matched cddid_all.tbl CDD cd08064 cd08064 163695 MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF3f. Eukaryotic translation initiation factor 3 (eIF3) subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa; Mov34/MPN/PAD-1 family protein) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity. It has been shown that eIF3f mRNA expression is significantly decreased in many human tumors including pancreatic cancer and melanoma. EIF3f is a potent inhibitor of HIV-1 replication; it mediates restriction of HIV-1 expression through several factors including the serine/arginine-rich (SR) protein 9G8, and cyclin-dependent kinase 11 (CDK11). EIF3f phosphorylation by CDK11 is important in regulating its function in translation and apoptosis. It enhances its association with the core eIF3 subunits during apoptosis, suggesting that eIF3f may inhibit translation by increasing the binding to the eIF3 complex during apoptosis. Thus, eIF3f may be an important negative regulator of cell growth and proliferation. 265 matched cddid_all.tbl CDD cd08065 cd08065 163696 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h. Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.Together with eIF3e and eIF3f, eIF3h stabilizes the eIF3 complex. Results suggest that eIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. For example, EIF3h gene amplification is common in late-stage prostate cancer suggesting that it may be functionally involved in the progression of the disease. It has been shown that coamplification of MYC, a well characterized oncogene involved in cell growth, differentiation, and apoptosis, and EIF3h in patients with non-small cell lung cancer (NSCLC) improves survival if treated with the Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor (EGFR-TKI), Gefitinib. Plant eIF3h is implicated in translation of specific mRNAs. 266 matched cddid_all.tbl CDD cd08066 cd08066 163697 MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat. AMSH shares a common SH3-binding site with another endosomal DUB, UBPY (ubiquitin-specific protease Y; also known as USP8), the latter being a cysteine protease that does not discriminate between Lys48 and Lys63-linked ubiquitin. AMSH is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. AMSH also interacts with CHMP1, CHMP2, and CHMP3 proteins, all of which are components of ESCRT-III, suggested to be required for EGFR down-regulation. The function of AMSH-LP has not been elucidated; however, it exhibits two fundamentally distinct features from AMSH: first, there is a substitution in the critical amino acid residue in the SH3-binding motif (SBM) in the human AMSH-LP, but not in its mouse ortholog, and lacks STAM-binding ability; second, AMSH-LP lacks the ability to interact with CHMP proteins. It is therefore likely that AMSH and AMSH-LP play different roles on early endosomes. 173 matched cddid_all.tbl CDD cd08067 cd08067 163698 MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase. This family includes histone H2A deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases (DUBs), with possible Zn2+-dependent ubiquitin isopeptidase activity. It contains the SWIRM (Swi3p, Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR, TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain can bind directly to DNA. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF (p300/CBP-associated factor) in a co-regulatory protein complex, where the status of acetylation of nucleosomal histones modulates its deubiquitinase activity. 2A-DUB is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene; it participates in transcriptional regulation events in androgen receptor-dependent gene activation. In prostate tumors, the levels of uH2A are dramatically decreased, thus 2A-DUB serving as a cancer-related marker. 187 matched cddid_all.tbl CDD cd08068 cd08068 163699 MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex. BRCC36 (BRCA1-A complex subunit BRCC36; BRCA1/BRCA2-containing complex subunit 36; BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC complex subunit BRCC36; BRCC36 isopeptidase complex; Lys-63-specific deubiquitinase BRCC36) and BRCC36-like domains are members of JAMM/MPN+ deubiquitinases (DUBs), possibly with Zn2+-dependent ubiquitin isopeptidase activity. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity. It is targeted to DNA damage foci after irradiation; RAP80 recruits the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand breaks (DSBs) for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs. A new protein, MERIT40 (mediator of RAP80 interactions and targeting 40 kDa), also named NBA1 (new component of the BRCA1 A complex), exists in the same BRCA1-containing complex and is essential for the integrity of the complex. There are studies suggesting that MERIT40/NBA1 ties BRCA1 complex integrity, DSB recognition, and ubiquitin chain activities to the DNA damage response. It has also been shown that BRCA1-containing complex resembles the lid complex of the 26S proteasome. 244 matched cddid_all.tbl CDD cd08069 cd08069 163700 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5. This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; c-Jun activation domain-binding protein-1; CSN5/JAB1; JAB1). COP9 signalosome (CSN) and the proteasome lid are paralogous complexes and their respective subunits CSN5 and Rpn11 are most closely related between the two complexes, both containing the conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) motif involved in zinc ion coordination and providing the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology; mutations in Rpn11 cause cell cycle and mitochondrial defects, temperature sensitivity and sensitivity to DNA damaging reagents such as UV. It has been shown that the C-terminal region of Rpn11 is involved in the regulation of the mitochondrial fission and tubulation processes. CSN5, one of the eight subunits of CSN, is critical for nuclear export and the degradation of several tumor suppressor proteins, including p53, p27, and Smad4. Its MPN+ domain is critical for the physical interaction of RUNX3 and Jab1. It has been suggested that the direct interaction of CSN5/JAB1 with p27 provides p27 with a leucine-rich nuclear export signal (NES), which is required for binding to chromosomal region maintenance 1 (CRM1), and facilitates nuclear export. The over-expression of CSN5/JAB1 also has been implicated in cancer initiation and progression, including cancer of the lung, pancreas, mouth, thyroid, and breast, suggesting that the oncogenic activity of CSN5 is associated with the down-regulation of RUNX3. 268 matched cddid_all.tbl CDD cd08070 cd08070 163701 MPN_like Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding). This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site. 128 matched cddid_all.tbl CDD cd08071 cd08071 163702 MPN_DUF2466 Mov34/MPN/PAD-1 family. Mov34 DUF2466 (also known as DNA repair protein RadC) domain of unknown function contains the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. However, to date, the name RadC has been misleading and no function has been determined. 113 matched cddid_all.tbl CDD cd08072 cd08072 163703 MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1/MPN/Mov34 metalloenzyme. This family contains only archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site. 117 matched cddid_all.tbl CDD cd08073 cd08073 163704 MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains. This family contains bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains at the N-terminus of NlpC/P60 phage tail protein domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site. 108 matched cddid_all.tbl CDD cd08148 cd08148 173969 RuBisCO_large Ribulose bisphosphate carboxylase large chain. Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions. 366 matched cddid_all.tbl CDD cd08150 cd08150 163706 catalase_like Catalase-like heme-binding proteins and protein domains. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes involved in the protection of cells from the toxic effects of peroxides. It catalyses the conversion of hydrogen peroxide to water and molecular oxygen. Several other related protein families share the catalase fold and bind to heme, but do not necessarily have catalase activity. 283 matched cddid_all.tbl CDD cd08151 cd08151 163707 AOS Allene oxide synthase. Allene oxide synthase converts a fatty acid hydroperoxide to an allene oxide, which is an unstable epoxide. In corals, the enzyme is part of a eiconaosid synthesis pathway that is initiated by a lipoxygenase, which generates the fatty acid hydroperoxides in the first step. The structure of allene oxide synthase closely resembles that of catalase, but allene oxide synthase does not have catalase activity. 328 matched cddid_all.tbl CDD cd08152 cd08152 163708 y4iL_like Catalase-like heme-binding proteins similar to the uncharacterized y4iL. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes involved in the protection of cells from the toxic effects of peroxides. It catalyses the conversion of hydrogen peroxide to water and molecular oxygen. Several other related protein families share the catalase fold and bind to heme, but do not necessarily have catalase activity. This family contains uncharacterized proteins similar to Rhizobium sp. NGR234 y4iL, of mostly bacterial origin. 305 matched cddid_all.tbl CDD cd08153 cd08153 163709 srpA_like Catalase-like heme-binding proteins similar to the uncharacterized srpA. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes involved in the protection of cells from the toxic effects of peroxides. It catalyses the conversion of hydrogen peroxide to water and molecular oxygen. Several other related protein families share the catalase fold and bind to heme, but do not necessarily have catalase activity. This family contains uncharacterized proteins similar to the Synechococcus elongatus PCC 7942 periplasmic protein srpA, of mostly bacterial origin. The plasmid-encoded srpA is regulated by sulfate, but does not seem to function in its uptake or metabolism. 295 matched cddid_all.tbl CDD cd08154 cd08154 163710 catalase_clade_1 Clade 1 of the heme-binding enzyme catalase. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes, which is involved in the protection of cells from the toxic effects of peroxides. It catalyzes the conversion of hydrogen peroxide to water and molecular oxygen. Catalases also utilize hydrogen peroxide to oxidize various substrates such as alcohol or phenols. Clade 1 catalases are found in bacteria, algae, and plants; they have a relatively small subunit size of 55 to 69 kDa, and bind a protoheme IX (heme b) group buried deep inside the structure. They appear to form tetramers. In eukaryotic cells, catalases are located in peroxisomes. 469 matched cddid_all.tbl CDD cd08155 cd08155 163711 catalase_clade_2 Clade 2 of the heme-binding enzyme catalase. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes, which is involved in the protection of cells from the toxic effects of peroxides. It catalyzes the conversion of hydrogen peroxide to water and molecular oxygen. Catalases also utilize hydrogen peroxide to oxidize various substrates such as alcohol or phenols. Clade 2 catalases are mostly found in bacteria and fungi; they have a large subunit size of 75 to 84 kDa, and bind a heme d group buried deep inside the structure. They appear to form tetramers. In eukaryotic cells, catalases are located in peroxisomes. 443 matched cddid_all.tbl CDD cd08156 cd08156 163712 catalase_clade_3 Clade 3 of the heme-binding enzyme catalase. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes, which is involved in the protection of cells from the toxic effects of peroxides. It catalyzes the conversion of hydrogen peroxide to water and molecular oxygen. Catalases also utilize hydrogen peroxide to oxidize various substrates such as alcohol or phenols. Clade 3 catalases are the most abundant subfamily and are found in all three kingdoms of life; they have a relatively small subunit size of 43 to 75 kDa, and bind a protoheme IX (heme b) group buried deep inside the structure. Clade 3 catalases also bind NADPH as a second redox-active cofactor. They form tetramers, and in eukaryotic cells, catalases are located in peroxisomes. 429 matched cddid_all.tbl CDD cd08157 cd08157 163713 catalase_fungal Fungal catalases similar to yeast catalases A and T. Catalase is a ubiquitous enzyme found in both prokaryotes and eukaryotes, which is involved in the protection of cells from the toxic effects of peroxides. It catalyzes the conversion of hydrogen peroxide to water and molecular oxygen. Catalases also utilize hydrogen peroxide to oxidize various substrates such as alcohol or phenols. This family of fungal catalases has a relatively small subunit size, and binds a protoheme IX (heme b) group buried deep inside the structure. Fungal catalases also bind NADPH as a second redox-active cofactor. They form tetramers; in eukaryotic cells, catalases are typically located in peroxisomes. Saccharomyces cerevisiae catalase T is found in the cytoplasm, though. 451 matched cddid_all.tbl CDD cd08159 cd08159 176482 APC10-like APC10-like DOC1 domains in E3 ubiquitin ligases that mediate substrate ubiquitination. This family contains the single domain protein, APC10, a subunit of the anaphase-promoting complex (APC), as well as the DOC1 domain of multi-domain proteins present in E3 ubiquitin ligases. E3 ubiquitin ligases mediate substrate ubiquitination (or ubiquitylation), a component of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. The APC, a multi-protein complex (or cyclosome), is a cell cycle-regulated, E3 ubiquitin ligase that controls important transitions in mitosis and the G1 phase by ubiquitinating regulatory proteins, thereby targeting them for degradation. APC10-like DOC1 domains such as those present in HECT (Homologous to the E6-AP Carboxyl Terminus) and Cullin-RING (Really Interesting New Gene) E3 ubiquitin ligase proteins, HECTD3, and CUL7, respectively, are also included in this hierarchy. CUL7 is a member of the Cullin-RING ligase family and functions as a molecular scaffold assembling a SCF-ROC1-like E3 ubiquitin ligase complex consisting of Skp1, CUL7, Fbx29 F-box protein, and ROC1 (RING-box protein 1) and promotes ubiquitination. CUL7 is a multi-domain protein with a C-terminal cullin domain that binds ROC1 and a centrally positioned APC10/DOC1 domain. HECTD3 contains a C-terminal HECT domain which contains the active site for ubiquitin transfer onto substrates, and an N-terminal APC10 domain which is responsible for substrate recognition and binding. An APC10/DOC1 domain homolog is also present in HERC2 (HECT domain and RLD2), a large multi-domain protein with three RCC1-like domains (RLDs), additional internal domains including zinc finger ZZ-type and Cyt-b5 (Cytochrome b5-like Heme/Steroid binding) domains, and a C-terminal HECT domain. Recent studies have shown that the protein complex HERC2-RNF8 coordinates ubiquitin-dependent assembly of DNA repair factors on damaged chromosomes. Also included in this hierarchy is an uncharacterized APC10/DOC1-like domain found in a multi-domain protein, which also contains CUB, zinc finger ZZ-type, and EF-hand domains. The APC10/DOC1 domain forms a beta-sandwich structure that is related in architecture to the galactose-binding domain-like fold; their sequences are quite dissimilar, however, and are not included here. 129 matched cddid_all.tbl CDD cd08161 cd08161 380914 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain superfamily. The Su(var)3-9, Enhancer-of-zeste, Trithorax (SET) domain superfamily corresponds to SET domain-containing lysine methyltransferases, which catalyze site and state-specific methylation of lysine residues in histones that are fundamental in epigenetic regulation of gene activation and silencing in eukaryotic organisms. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains has been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as N-SET and C-SET. C-SET forms an unusual and conserved knot-like structure of probable functional importance. In addition to N-SET and C-SET, an insert region (I-SET) and flanking regions of high structural variability form part of the overall structure. Some family members contain a pre-SET domain, which is found in a number of histone methyltransferases (HMTase), and a post-SET domain, which harbors a zinc-binding site. 72 matched cddid_all.tbl CDD cd08162 cd08162 277369 MPP_PhoA_N Synechococcus sp. strain PCC 7942 PhoA and related proteins, N-terminal metallophosphatase domain. Synechococcus sp. strain PCC 7942 PhoA is a large atypical alkaline phosphatase. It is known to be transported across the inner cytoplasmic membrane and into the periplasmic space. In vivo inactivation of the gene encoding PhoA leads to a loss of extracellular, phosphate-regulated phosphatase activity, but does not appear to affect the cells capacity for phosphate uptake. PhoA may play a role in scavenging phosphate during growth of Synechococcus sp. strain PCC 7942 in its natural environment. PhoA belongs to a domain family which includes the bacterial enzyme UshA and several other related enzymes including SoxB, CpdB, YhcR, and CD73. All members have a similar domain architecture which includes an N-terminal metallophosphatase domain and a C-terminal nucleotidase domain. The N-terminal metallophosphatase domain belongs to a large superfamily of distantly related metallophosphatases (MPPs) that includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 325 matched cddid_all.tbl CDD cd08163 cd08163 277370 MPP_Cdc1 Saccharomyces cerevisiae CDC1 and related proteins, metallophosphatase domain. Cdc1 (also known as XlCdc1 in Xenopus laevis) is an endoplasmic reticulum-localized transmembrane lipid phosphatase with a metallophosphatase domain facing the ER lumen. In budding yeast, the gene encoding CDC1 is essential while nonlethal mutations cause defects in Golgi inheritance and actin polarization. Cdc1 mutant cells accumulate an unidentified phospholipid, suggesting that Cdc1 is a lipid phosphatase. Cdc1 mutant cells also have highly elevated intracellular calcium levels suggesting a possible role for Cdc1 in calcium regulation. The 5' flanking region of Cdc1 is a regulatory region with conserved binding site motifs for AP1, AP2, Sp1, NF-1 and CREB. DNA polymerase delta consists of at least four subunits - Pol3, Cdc1, Cdc27, and Cdm1. Cdc1 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 257 matched cddid_all.tbl CDD cd08164 cd08164 277371 MPP_Ted1 Saccharomyces cerevisiae Ted1 and related proteins, metallophosphatase domain. Saccharomyces cerevisiae Ted1 (trafficking of Emp24p/Erv25p-dependent cargo disrupted 1) is a metallophosphatase domain-containing protein which acts together with Emp24p and Erv25p in cargo exit from the ER. Ted1 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 193 matched cddid_all.tbl CDD cd08165 cd08165 277372 MPP_MPPE1 human MPPE1 and related proteins, metallophosphatase domain. MPPE1 is a functionally uncharacterized metallophosphatase domain-containing protein. The MPPE1 gene is located on chromosome 18 and is a candidate susceptibility gene for Bipolar disorder. MPPE1 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 156 matched cddid_all.tbl CDD cd08166 cd08166 277373 MPP_Cdc1_like_1 uncharacterized subgroup related to Saccharomyces cerevisiae CDC1, metallophosphatase domain. A functionally uncharacterized subgroup related to the metallophosphatase domain of Saccharomyces cerevisiae Cdc1, S. cerevisiae Ted1 and human MPPE1. Cdc1 is an endoplasmic reticulum-localized transmembrane lipid phosphatase and is a subunit of DNA polymerase delta. TED1 (trafficking of Emp24p/Erv25p-dependent cargo disrupted 1), acts together with Emp24p and Erv25p in cargo exit from the ER. The MPPE1 gene is a candidate susceptibility gene for Bipolar disorder. Proteins in this uncharacterized subgroup belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination. 195 matched cddid_all.tbl CDD cd08168 cd08168 173979 Cytochrom_C3 Heme-binding domain of the class III cytochrome C family and related proteins. This alignment models heme binding core motifs as encountered in the cytochrome C3 family and related proteins. Cytochrome C3 is a tetraheme protein found in sulfate-reducing bacteria which use either thiosulfate or sulfate as the ultimate electron acceptors. C3 is an integral part of a complex electron transfer chain. The model also contains triheme cytochromes C7 which function in electron transfer during Fe(III) respiration by Geobacter sulfurreducens (PpcA, PpcB, PpcC, PpcD, and PpcE) and four repeated core motifs as found in the 16-heme cytochrome C HmcA of Desulfovibrio vulgaris Hildenborough which plays a role in electron transfer through the membrane following periplasmic oxidation of hydrogen (resulting in sulfate reduction in the cytoplasm). 85 matched cddid_all.tbl CDD cd08169 cd08169 341448 DHQ-like Dehydroquinate synthase-like which includes dehydroquinate synthase, 2-deoxy-scyllo-inosose synthase, and 2-epi-5-epi-valiolone synthase. This group contains dehydroquinate synthase, 2-deoxy-scyllo-inosose synthase, and 2-epi-5-epi-valiolone synthase. These proteins exhibit the dehydroquinate synthase structural fold. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds. 2-deoxy-scyllo-inosose synthase (DOIS) catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multi-step reaction in the biosynthesis of aminoglycoside antibiotics. 2-deoxystreptamine (DOS)-containing aminoglycoside antibiotics includes neomycin, kanamycin, gentamicin, and ribostamycin. 2-epi-5-epi-valiolone synthases catalyze the cyclization of sedoheptulose 7-phosphate to 2-epi-5-epi-valiolone in the biosynthesis of C(7)N-aminocyclitol-containing products. The cyclization product, 2-epi-5-epi-valiolone ((2S,3S,4S,5R)-5-(hydroxymethyl)cyclohexanon-2,3,4,5-tetrol), is a precursor of the valienamine moiety. The valienamine unit is responsible for their biological activities as various glycosidic hydrolases inhibitors. Two important microbial secondary metabolites, validamycin and acarbose, are used in agricultural and biomedical applications. 328 matched cddid_all.tbl CDD cd08170 cd08170 341449 GlyDH Glycerol dehydrogenases (GlyDH) catalyzes oxidation of glycerol to dihydroxyacetone in glycerol dissmilation. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway. In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent; the zinc ion plays a role in stabilizing an alkoxide intermediate at the active site. 351 matched cddid_all.tbl CDD cd08171 cd08171 341450 GlyDH-like Glycerol dehydrogenase-like. This family contains glycerol dehydrogenase (GlyDH)-like proteins that have yet to be characterized, but show sequence homology with glycerol dehydrogenase. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway. In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent; the zinc ion plays a role in stabilizing an alkoxide intermediate at the active site. 345 matched cddid_all.tbl CDD cd08172 cd08172 341451 GlyDH-like Glycerol_dehydrogenase-like. This family contains glycerol dehydrogenase (GlyDH)-like proteins that have yet to be characterized, but show sequence homology with glycerol dehydrogenase. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway. In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent; the zinc ion plays a role in stabilizing an alkoxide intermediate at the active site. 346 matched cddid_all.tbl CDD cd08173 cd08173 341452 Gro1PDH Sn-glycerol-1-phosphate dehydrogenase (Gro1PDH) catalyzes the reversible conversion between dihydroxyacetone phosphate and glycerol-1-phosphate using either NADH or NADPH as a coenzyme. Sn-glycerol-1-phosphate dehydrogenase (Gro1PDH, EC 1.1.1.261) plays an important role in the formation of the enantiomeric configuration of the glycerophosphate backbone (sn-glycerol-1-phosphate) of archaeal ether lipids. It catalyzes the reversible conversion between dihydroxyacetone phosphate and glycerol-1-phosphate using either NADH or NADPH as a coenzyme. The activity is zinc-dependent. One characteristic feature of archaea is that their cellular membrane has an ether linkage between the glycerol backbone and the hydrocarbon residues. The polar lipids of the members of Archaea consist of di- and tetra-ethers of glycerol with isoprenoid alcohols bound at the sn-2 and sn-3 positions of the glycerol moiety. The archaeal polar lipids have the enantiomeric configuration of a glycerophosphate backbone [sn-glycerol-1-phosphate (G-1-P)] that is the mirror image structure of the bacterial or eukaryal counterpart [sn-glycerol- 3-phosphate (G-3-P)]. The absolute stereochemistry of the glycerol moiety in all archaeal polar lipids is opposite to that of glycerol ester lipids in bacteria and eukarya. 343 matched cddid_all.tbl CDD cd08174 cd08174 341453 G1PDH-like Glycerol-1-phosphate dehydrogenase-like. These glycerol-1-phosphate dehydrogenase-like proteins have not been characterized. The protein sequences have high similarity with that of glycerol-1-phosphate dehydrogenase (G1PDH) which plays a role in the synthesis of phosphoglycerolipids in Gram-positive bacterial species. It catalyzes the reversibly reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in a NADH-dependent manner. Its activity requires Ni++ ion. 332 matched cddid_all.tbl CDD cd08175 cd08175 341454 G1PDH Glycerol-1-phosphate dehydrogenase (G1PDH) catalyzes the reversible reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in an NADH-dependent manner. Glycerol-1-phosphate dehydrogenase (G1PDH) plays a role in the synthesis of phosphoglycerolipids in Gram-positive bacterial species. It catalyzes the reversibly reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in a NADH-dependent manner. Its activity requires a Ni++ ion. In Bacillus subtilis, it has been described as AraM gene in L-arabinose (ara) operon. AraM protein forms homodimer. 340 matched cddid_all.tbl CDD cd08176 cd08176 341455 LPO Lactadehyde:propanediol oxidoreductase (LPO) catalyzes the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria. Lactadehyde:propanediol oxidoreductase (LPO) is a member of the group III iron-activated dehydrogenases which catalyze the interconversion between L-lactaldehyde and L-1,2-propanediol in Escherichia coli and other enterobacteria. L-fucose and L-rhamnose are used by Escherichia coli through an inducible pathway mediated by the fucose regulon comprising four linked operons fucO, fucA, fucPIK, and fucR. The fucA-encoded aldolase catalyzes the formation of dihydroxyacetone phosphate and L-lactaldehyde. Under anaerobic conditions, with NADH as a cofactor, lactaldehyde is converted by a fucO-encoded lactadehyde:propanediol oxidoreductase (LPO) to L-1,2-propanediol, which is excreted as a fermentation product. In mutant strains, E. coli adapted to grow on L-1,2-propanediol, FucO catalyzes the oxidation of the polyol to L-lactaldehyde. FucO is induced regardless of the respiratory conditions of the culture, remains fully active in the absence of oxygen. In the presence of oxygen, this enzyme becomes oxidatively inactivated by a metal-catalyzed oxidation mechanism. FucO is an iron-dependent metalloenzyme that is inactivated by other metals, such as zinc, copper, or cadmium. This enzyme can also reduce glycol aldehyde with similar efficiency. Beside L-1,2-propanediol, the enzyme is also able to oxidize methanol as an alternative substrate. 378 matched cddid_all.tbl CDD cd08177 cd08177 341456 MAR Maleylacetate reductase is involved in many aromatic compounds degradation pathways of aerobic microbes. Maleylacetate reductase (MAR) plays an important role in the degradation of aromatic compounds in aerobic microbes. In fungi and yeasts, the enzyme is involved in the catabolism of compounds such as phenol, tyrosine, benzoate, 4-hydroxybenzoate and resorcinol. In bacteria, the enzyme contributes to the degradation of resorcinol, 2,4-dihydroxybenzoate ([beta]-resorcylate) and 2,6-dihydroxybenzoate ([gamma]-resorcylate) via hydroxyquinol and maleylacetate. Maleylacetate reductase catalyzes NADH- or NADPH-dependent reduction, at the carbon-carbon double bond, of maleylacetate or 2-chloromaleylacetate to 3-oxoadipate. In the case of 2-chloromaleylacetate, MAR initially catalyzes the NAD(P)H-dependent dechlorination to maleylacetate, which is then reduced to 3-oxoadipate. This enzyme is a homodimer and is inhibited by thiol-blocking reagents such as p-chloromercuribenzoate and Hg++, indicating that the cysteine residue is probably necessary for the catalytic activity of maleylacetate reductase. 337 matched cddid_all.tbl CDD cd08178 cd08178 341457 AAD_C C-terminal alcohol dehydrogenase domain of the acetaldehyde dehydrogenase-alcohol dehydrogenase bifunctional two-domain protein (AAD). This alcohol dehydrogenase domain is located on the C-terminal of a bifunctional two-domain protein. The N-terminal of the protein contains an acetaldehyde-CoA dehydrogenase domain. This protein is involved in pyruvate metabolism whereby pyruvate is converted to acetyl-CoA and formate by pyruvate formate-lysase (PFL). Under anaerobic condition, acetyl-CoA is reduced to acetaldehyde and ethanol by this two-domain protein. Acetyl-CoA is first converted into an enzyme-bound thiohemiacetal by the N-terminal acetaldehyde dehydrogenase domain. The enzyme-bound thiohemiacetal is subsequently reduced by the C-terminal NAD+-dependent alcohol dehydrogenase domain. In E. coli, this protein is called AdhE and has been shown to have pyruvate formate-lyase (PFL) deactivase activity, which leads to the inactivation of PFL, a key enzyme in anaerobic metabolism. In Escherichia coli and Entamoeba histolytica, this enzyme forms homopolymeric peptides composed of more than 20 protomers associated in a helical rod-like structure. 400 matched cddid_all.tbl CDD cd08179 cd08179 341458 NADPH_BDH NADPH-dependent butanol dehydrogenase involved in the butanol and ethanol formation pathway in bacteria. NADPH-dependent butanol dehydrogenase (BDH) is involved in the butanol and ethanol formation pathway of some bacteria. The fermentation process is characterized by an acid producing growth phase, followed by a solvent producing phase. The latter phase is associated with the induction of solventogenic enzymes such as butanol dehydrogenase. The activity of the enzyme requires NADPH as cofactor, as well as divalent ions zinc or iron. This family is a member of the iron-containing alcohol dehydrogenase superfamily. Protein structure has a dehydroquinate synthase-like fold. 379 matched cddid_all.tbl CDD cd08180 cd08180 341459 PDD 1,3-propanediol dehydrogenase (PPD) catalyzes the reduction of 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol in glycerol metabolism. 1,3-propanediol dehydrogenase (PPD) plays a role in glycerol metabolism of some bacteria in anaerobic conditions. In this degradation pathway, glycerol is converted in a two-step process to 1,3-propanediol (1,3-PD) which is then excreted into the extracellular medium. The first reaction involves the transformation of glycerol into 3-hydroxypropionaldehyde (3-HPA) by a coenzyme B-12-dependent dehydratase. The second reaction involves the dismutation of the 3-hydroxypropionaldehyde (3-HPA) to 1,3-propanediol by the NADH-linked 1,3-propanediol dehydrogenase (PPD). The enzyme requires iron ion for its function. Because many genes in this pathway are present in the propanediol utilization (pdu) operon, they are also named pdu genes. PPD is a member of the iron-containing alcohol dehydrogenase superfamily. The PPD structure has a dehydroquinate synthase-like fold. 333 matched cddid_all.tbl CDD cd08181 cd08181 341460 PPD-like 1,3-propanediol dehydrogenase-like (PPD). This family contains proteins similar to 1,3-propanediol dehydrogenase (PPD) which is a member of the iron-containing alcohol dehydrogenase superfamily, and exhibits a dehydroquinate synthase-like fold. Protein sequence similarity search and other biochemical evidences suggest that they are close to the iron-containing 1,3-propanediol dehydrogenase (EC 1.1.1.202). 1,3-propanediol dehydrogenase catalyzes the oxidation of propane-1,3-diol to 3-hydroxypropanal with the simultaneous reduction of NADP+ to NADPH. The protein structure of Thermotoga maritima TM0920 gene contains one NADP+ and one iron ion. 358 matched cddid_all.tbl CDD cd08182 cd08182 341461 HEPD Hydroxyethylphosphoate dehydrogenase (HEPD) catalyzes the reduction of phosphonoacetaldehyde (PnAA) to hydroxyethylphosphoate (HEP). Hydroxyethylphosphoate dehydrogenase (HEPD) catalyzes the reduction of phosphonoacetaldehyde (PnAA) to hydroxyethylphosphoate (HEP) with either NADH or NADPH as a cofactor, although NADH is the preferred cofactor. PnAA is a biosynthetic intermediate for several phosphonates such as the antibiotic fosfomycin, phosphinothricin tripeptide (PTT), and 2-aminoethylphosphonate (AEP). This enzyme is named PhpC in PTT biosynthesis pathway in Streptomyces hygroscopicus and S. viridochromogenes. 370 matched cddid_all.tbl CDD cd08183 cd08183 341462 Fe-ADH-like Iron-containing alcohol dehydrogenases-like. This family contains iron-containing alcohol dehydrogenase (Fe-ADH) which catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. It is distinct from other alcohol dehydrogenases which contain different protein domains. Proteins of this family have not been characterized. 377 matched cddid_all.tbl CDD cd08184 cd08184 341463 Fe-ADH_KdnB-like Iron-containing alcohol dehydrogenase similar to Shewanella oneidensis KdnB required for Kdo8N biosynthesis. This family contains iron-containing alcohol dehydrogenase-like proteins, many of which have not been characterized. Their specific function is unknown. The protein structure represents a dehydroquinate synthase-like fold and belongs to the iron-containing alcohol dehydrogenase-like superfamily. It is distinct from other alcohol dehydrogenases which contain different protein domains. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron or zinc ions. This family also includes Shewanella oneidensis KdnB which is required for biosynthesis of 8-Amino-3,8-dideoxy-D-manno-octulosonic acid (Kdo8N), a unique amino sugar that has thus far only been observed on the lipopolysaccharides of marine bacteria belonging to the genus Shewanella, and thought to be important for the integrity of the bacterial cell outer membrane. KdnB requires NAD(P) and zinc ion for activity. 348 matched cddid_all.tbl CDD cd08185 cd08185 341464 Fe-ADH-like Iron-containing alcohol dehydrogenases-like. This family contains iron-containing alcohol dehydrogenase-like (ADH) proteins. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase fold and is a member of the iron-containing alcohol dehydrogenase-like family. They are distinct from other alcohol dehydrogenases which contain different protein domains. Proteins of this family have not been characterized. 379 matched cddid_all.tbl CDD cd08186 cd08186 341465 Fe-ADH-like Iron-containing alcohol dehydrogenase. This family contains iron-containing alcohol dehydrogenase (ADH) which catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. The ADH of hyperthermophilic archaeon Thermococcus hydrothermalis oxidizes a series of primary aliphatic and aromatic alcohols, preferentially from C2 to C8, but is also active towards methanol and glycerol, and is stereospecific for monoterpenes. It has been suggested that the type III ADHs in microorganisms are involved in acetaldehyde detoxication rather than in alcohol turnover. 380 matched cddid_all.tbl CDD cd08187 cd08187 341466 BDH Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process. The butanol dehydrogenase (BDH) is involved in the final step of the butanol formation pathway in anaerobic micro-organism. Butanol dehydrogenase catalyzes the conversion of butyraldehyde to butanol with the cofactor NAD(P)H being oxidized in the process. Activity in the reverse direction is 50-fold lower than that in the forward direction. The NADH-BDH has higher activity with longer chained aldehydes and is inhibited by metabolites containing an adenine moiety. This protein family belongs to the so-called iron-containing alcohol dehydrogenase superfamily. Since members of this superfamily use different divalent ions, preferentially iron or zinc, it has been suggested to be renamed to family III metal-dependent polyol dehydrogenases. This family also includes E. coli YqhD enzyme, an NADP-dependent dehydrogenase whose activity measurements with several alcohols demonstrate preference for alcohols longer than C3. The active site of YqhD contains a Zn metal, and a modified NADPH cofactor bearing OH groups on the saturated C5 and C6 atoms, possibly due to oxygen stress on the enzyme, which would functionally work under anaerobic conditions. 382 matched cddid_all.tbl CDD cd08188 cd08188 341467 PDDH 1,3-Propanediol (1,3-PD) dehydrogenase. This family includes 1,3-propanediol (1,3-PD) dehydrogenase, a key enzyme in the microbial production of 1,3-PD that has been previously characterized as the product of dhaT gene in Klebsiella pneumoniae. 1,3-PD dehydrogenase is a member of the family III metal-dependent polyol dehydrogenases, which are shown to require a divalent metal ion for catalysis. However, some members of this family showed a dependence on Fe(2+) or Zn(2+) for activity. 377 matched cddid_all.tbl CDD cd08189 cd08189 341468 Fe-ADH-like Iron-containing alcohol dehydrogenases-like. This family contains iron-containing alcohol dehydrogenase (Fe-ADH) which catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and belongs to the alcohol dehydrogenase-like superfamily. It is distinct from other alcohol dehydrogenases which contain different protein domain. Proteins of this family have not been characterized. 378 matched cddid_all.tbl CDD cd08190 cd08190 341469 HOT Hydroxyacid-oxoacid transhydrogenase (HOT) involved in gamma-hydroxybutyrate metabolism. This family contains hydroxyacid-oxoacid transhydrogenase (HOT), also known as D-2-hydroxyglutarate transhydrogenase. It catalyzes the conversion of gamma-hydroxybutyrate (GHB) to succinic semialdehyde (SSA), coupled to the stoichiometric conversion of alpha-ketoglutarate to D-2-hydroxyglutarate in gamma-Hydroxybutyrate catabolism. Unlike many other alcohols, which are oxidized by NAD-linked dehydrogenases, gamma-hydroxybutyrate is metabolized to succinate semialdehyde by hydroxyacid-oxoacid transhydrogenase which does not require free NAD or NADP; instead, it uses alpha-ketoglutarate as an acceptor, converting it to d-2-hydroxyglutarate. Alpha-ketoglutarate serves as an intermediate acceptor to regenerate NAD(P) required for the oxidation of GHB. HOT also catalyzes the reversible oxidation of a hydroxyacid obligatorily coupled to the reduction of an oxoacid, and requires no cofactor. In mammals, the HOT enzyme is located in mitochondria, and is expressed with an N-terminal mitochondrial targeting sequence. HOT enzyme is member of the metal-containing alcohol dehydrogenase family. It typically contains an iron although other metal ions may be used. 412 matched cddid_all.tbl CDD cd08191 cd08191 341470 Fe-ADH-like Iron-containing alcohol dehydrogenases-like. This family contains iron-containing alcohol dehydrogenase (Fe-ADH) which catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. It is distinct from other alcohol dehydrogenases which contain different protein domain. Proteins of this family have not been characterized. 392 matched cddid_all.tbl CDD cd08192 cd08192 341471 MAR-like Maleylacetate reductase is involved in many aromatic compounds degradation pathways of aerobic microbes. Maleylacetate reductase (MAR) plays an important role in the degradation of aromatic compounds in aerobic microbes. In fungi and yeasts, the enzyme is involved in the catabolism of compounds such as phenol, tyrosine, benzoate, 4-hydroxybenzoate and resorcinol. In bacteria, the enzyme contributes to the degradation of resorcinol, 2,4-dihydroxybenzoate ([beta]-resorcylate) and 2,6-dihydroxybenzoate ([gamma]-resorcylate) via hydroxyquinol and maleylacetate. Maleylacetate reductase (MAR) catalyzes NADH- or NADPH-dependent reduction, at the carbon-carbon double bond, of maleylacetate or 2-chloromaleylacetate to 3-oxoadipate. In the case of 2-chloromaleylacetate, MAR initially catalyzes the NAD(P)H-dependent dechlorination to maleylacetate, which is then reduced to 3-oxoadipate. This enzyme is a homodimer. It is inhibited by thiol-blocking reagents such as p-chloromercuribenzoate and Hg++, indicating that the cysteine residue is probably necessary for the catalytic activity of maleylacetate reductase. 380 matched cddid_all.tbl CDD cd08193 cd08193 341472 HVD 5-hydroxyvalerate dehydrogenase (HVD) catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor. 5-hydroxyvalerate dehydrogenase (HVD) is an iron-containing (type III) NAD-dependent alcohol dehydrogenase. It plays a role in the cyclopentanol metabolism biochemical pathway. It catalyzes the oxidation of 5-hydroxyvalerate to 5-oxovalerate with NAD+ as cofactor. This cyclopentanol (cpn) degradation pathway is present in some bacteria which can use cyclopentanol as sole carbon source. In Comamonas sp. strain NCIMB 9872, this enzyme is encoded by the CpnD gene. 379 matched cddid_all.tbl CDD cd08194 cd08194 341473 Fe-ADH-like Iron-containing alcohol dehydrogenases-like. This family contains iron-containing alcohol dehydrogenase (Fe-ADH) most of which have not been characterized. Their specific function is unknown. The protein structure represents a dehydroquinate synthase-like fold and belongs to the alcohol dehydrogenase-like superfamily. It is distinct from other alcohol dehydrogenases which contain different protein domains. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. 378 matched cddid_all.tbl CDD cd08195 cd08195 341474 DHQS Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway, which involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds, is found in bacteria, microbial eukaryotes, and plants, but not in mammals. Therefore, enzymes of this pathway are attractive targets for the development of non-toxic antimicrobial compounds, herbicides and anti-parasitic agents. The activity of DHQS requires nicotinamide adenine dinucleotide (NAD) as cofactor. A single active site in DHQS catalyzes five sequential reactions involving alcohol oxidation, phosphate elimination, carbonyl reduction, ring opening, and intramolecular aldol condensation. The binding of substrates and ligands induces domain conformational changes. In some fungi and protozoa, this domain is fused with the other four domains in shikimate pathway and forms a penta-domain AROM protein, which catalyzes steps 2-6 in the shikimate pathway. 343 matched cddid_all.tbl CDD cd08196 cd08196 341475 Fe-ADH-like iron-containing alcohol dehydrogenases (Fe-ADH)-like. This family contains iron-containing alcohol dehydrogenase (Fe-ADH) which catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. It is distinct from other alcohol dehydrogenases which contains different protein domains. Proteins of this family have not been characterized. 367 matched cddid_all.tbl CDD cd08197 cd08197 341476 DOIS 2-deoxy-scyllo-inosose synthase (DOIS) catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose. 2-deoxy-scyllo-inosose synthase (DOIS) catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction in the biosynthesis of aminoglycoside antibiotics. 2-deoxystreptamine (DOS)-containing aminoglycoside antibiotics includes neomycin, kanamycin, gentamicin, and ribostamycin. They are important antibacterial agents. DOIS is a homolog of the dehydroquinate synthase which catalyzes the cyclization of 3-deoxy-D-arabino-heputulosonate-7-phosphate to dehydroquinate (DHQ) in the shikimate pathway. 355 matched cddid_all.tbl CDD cd08198 cd08198 341477 DHQS-like Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis. This family contains dehydroquinate synthase-like proteins. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds. The activity of DHQS requires NAD as cofactor. Proteins of this family share sequence similarity and functional motifs with that of dehydroquinate synthase, but the specific function has not been characterized. 366 matched cddid_all.tbl CDD cd08199 cd08199 341478 EEVS 2-epi-5-epi-valiolone synthase (EEVS). 2-epi-5-epi-valiolone synthase catalyzes the cyclization of sedoheptulose 7-phosphate to 2-epi-5-epi-valiolone in the biosynthesis of C(7)N-aminocyclitol-containing products. The cyclization product, 2-epi-5-epi-valiolone ((2S,3S,4S,5R)-5-(hydroxymethyl)cyclohexanon-2,3,4,5-tetrol), is a precursor of the valienamine moiety. The valienamine unit is responsible for their biological activities as various glycosidic hydrolases inhibitors. Two important microbial secondary metabolites, validamycin and acarbose, are used in agricultural and biomedical applications. Validamycin A is an antifungal antibiotic which has a strong trehalase inhibitory activity and has been used to control sheath blight disease in rice caused by Rhizoctonia solani. Acarbose is an alpha-glucosidase inhibitor used for the treatment of type II insulin-independent diabetes. Salbostatin produced by Streptomyces albus also belongs to this family. It exhibits strong trehalase inhibitory activity. 349 matched cddid_all.tbl CDD cd08200 cd08200 173828 catalase_peroxidase_2 C-terminal non-catalytic domain of catalase-peroxidases. This is a subgroup of heme-dependent peroxidases of the plant superfamily that share a heme prosthetic group and catalyze a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. Catalase-peroxidases can exhibit both catalase and broad-spectrum peroxidase activities depending on the steady-state concentration of hydrogen peroxide. These enzymes are found in many archaeal and bacterial organisms where they neutralize potentially lethal hydrogen peroxide molecules generated during photosynthesis or stationary phase. Along with related intracellular fungal and plant peroxidases, catalase-peroxidases belong to plant peroxidase superfamily. Unlike the eukaryotic enzymes, they are typically comprised of two homologous domains that probably arose via a single gene duplication event. The heme binding motif is present only in the N-terminal domain; the function of the C-terminal domain is not clear. 297 matched cddid_all.tbl CDD cd08201 cd08201 173829 plant_peroxidase_like_1 Uncharacterized family of plant peroxidase-like proteins. This is a subgroup of heme-dependent peroxidases similar to plant peroxidases. Along with animal peroxidases, these enzymes belong to a group of peroxidases containing a heme prosthetic group (ferriprotoporphyrin IX) which catalyzes a multistep oxidative reaction involving hydrogen peroxide as the electron acceptor. The plant peroxidase-like superfamily is found in all three kingdoms of life and carries out a variety of biosynthetic and degradative functions. 264 matched cddid_all.tbl CDD cd08203 cd08203 188876 SAM_PNT Sterile alpha motif (SAM)/Pointed domain. Sterile alpha motif (SAM)/Pointed domain is found in about 40% of transcriptional regulators of ETS family (initially named for Erythroblastosis virus, E26-E Twenty Six). SAM Pointed domain containing proteins of this family additionally have a C-terminal ETS DNA-binding domain. In a few cases, SAM Pointed domain appears as a single domain protein. Members of this group are mostly involved in regulation of embryonic development and growth control in eukaryotes. SAM Pointed domains mediate protein-protein interactions. Depending on the subgroup, they can interact with other SAM Pointed domains forming homo or hetero dimers/oligomers and/or they can recruit a protein kinase to its target which can be a SAM Pointed domain containing protein itself or another protein that has no kinase docking site. Thus, SAM Pointed domains participate in transcriptional regulation and signal transduction. Some genes coding ETS family transcriptional regulators are proto-oncogenes. They are prone to chromosomal translocations resulting in gene fusions. Chimeric proteins with SAM Pointed domains were found in a number of different human tumors including myeloid leukemia, lymphoblastic leukemia, Ewing's sarcoma and primitive neuroectodermal tumor. Members of this family are potential targets for cancer therapy. 67 matched cddid_all.tbl CDD cd08204 cd08204 350058 ArfGap GTPase-activating protein (GAP) for the ADP ribosylation factors (ARFs). ArfGAPs are a family of proteins containing an ArfGAP catalytic domain that induces the hydrolysis of GTP bound to the small guanine nucleotide-binding protein Arf, a member of the Ras superfamily of GTPases. Like all GTP-binding proteins, Arf proteins function as molecular switches, cycling between GTP (active-membrane bound) and GDP (inactive-cytosolic) form. Conversion to the GTP-bound form requires a guanine nucleotide exchange factor (GEF), whereas conversion to the GDP-bound form is catalyzed by a GTPase activating protein (GAP). In that sense, ArfGAPs were originally proposed to function as terminators of Arf signaling, which is mediated by regulating Arf family GTP-binding proteins. However, recent studies suggest that ArfGAPs can also function as Arf effectors, independently of their GAP enzymatic activity to transduce signals in cells. The ArfGAP domain contains a C4-type zinc finger motif and a conserved arginine that is required for activity, within a specific spacing (CX2CX16CX2CX4R). ArfGAPs, which have multiple functional domains, regulate the membrane trafficking and actin cytoskeleton remodeling via specific interactions with signaling lipids such as phosphoinositides and trafficking proteins, which consequently affect cellular events such as cell growth, migration, and cancer invasion. The ArfGAP family, which includes 31 human ArfGAP-domain containing proteins, is divided into 10 subfamilies based on domain structure and sequence similarity. The ArfGAP nomenclature is mainly based on the protein domain structure. For example, ASAP1 contains ArfGAP, SH3, ANK repeat and PH domains; ARAPs contain ArfGAP, Rho GAP, ANK repeat and PH domains; ACAPs contain ArfGAP, BAR (coiled coil), ANK repeat and PH domains; and AGAPs contain Arf GAP, GTP-binding protein-like, ANK repeat and PH domains. Furthermore, the ArfGAPs can be classified into two major types of subfamilies, according to the overall domain structure: the ArfGAP1 type includes 6 subfamilies (ArfGAP1, ArfGAP2/3, ADAP, SMAP, AGFG, and GIT), which contain the ArfGAP domain at the N-terminus of the protein; and the AZAP type includes 4 subfamilies (ASAP, ACAP, AGAP, and ARAP), which contain an ArfGAP domain between the PH and ANK repeat domains. 106 matched cddid_all.tbl CDD cd08205 cd08205 173970 RuBisCO_IV_RLP Ribulose bisphosphate carboxylase like proteins, Rubisco-Form IV. Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions, like for example 2,3-diketo-5-methylthiopentyl-1-phosphate enolase or 5-methylthio-d-ribulose 1-phosphate isomerase. 367 matched cddid_all.tbl CDD cd08206 cd08206 173971 RuBisCO_large_I_II_III Ribulose bisphosphate carboxylase large chain, Form I,II,III. Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubico-like proteins (RLP), are missing critical active site residues. 414 matched cddid_all.tbl CDD cd08207 cd08207 173972 RLP_NonPhot Ribulose bisphosphate carboxylase like proteins from nonphototrophic bacteria. Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions. The specific function of this subgroup is unknown. 406 matched cddid_all.tbl CDD cd08208 cd08208 173973 RLP_Photo Ribulose bisphosphate carboxylase like proteins from phototrophic bacteria. Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV, which differ in their taxonomic distribution and subunit composition. Form I-III have Rubisco activity, while Form IV, also called Rubisco-like proteins (RLP), are missing critical active site residues and therefore do not catalyze CO2 fixation. They are believed to utilize a related enzymatic mechanism, but have divergent functions. The specific function of this subgroup is unknown. 424 matched cddid_all.tbl CDD cd08209 cd08209 173974 RLP_DK-MTP-1-P-enolase 2,3-diketo-5-methylthiopentyl-1-phosphate enolase. Ribulose bisphosphate carboxylase like proteins (RLPs) similar to B. subtilis YkrW protein, have been identified as 2,3-diketo-5-methylthiopentyl-1-phosphate enolases. They catalyze the tautomerization of 2,3-diketo-5-methylthiopentane 1-phosphate (DK-MTP 1-P). This is an important step in the methionine salvage pathway in which 5-methylthio-D-ribose (MTR) derived from 5'-methylthioadenosine is converted to methionine. 391 matched cddid_all.tbl CDD cd08210 cd08210 173975 RLP_RrRLP Ribulose bisphosphate carboxylase like proteins (RLPs) similar to R.rubrum RLP. RLP from Rhodospirillum rubrum plays a role in an uncharacterized sulfur salvage pathway and has been shown to catalyze a novel isomerization reaction that converts 5-methylthio-d-ribulose 1-phosphate to a 3:1 mixture of 1-methylthioxylulose 5-phosphate and 1-methylthioribulose 5-phosphate. 364 matched cddid_all.tbl CDD cd08211 cd08211 173976 RuBisCO_large_II Ribulose bisphosphate carboxylase large chain, Form II. Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV , which differ in their taxonomic distribution and subunit composition. Form II is mainly found in bacteria, and forms large subunit oligomers (dimers, tetramers, etc.) that do not include small subunits. 439 matched cddid_all.tbl CDD cd08212 cd08212 173977 RuBisCO_large_I Ribulose bisphosphate carboxylase large chain, Form I. Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV , which differ in their taxonomic distribution and subunit composition. Form I is the most abundant class, present in plants, algae, and bacteria, and forms large complexes composed of 8 large and 8 small subunits. 450 matched cddid_all.tbl CDD cd08213 cd08213 173978 RuBisCO_large_III Ribulose bisphosphate carboxylase large chain, Form III. Ribulose bisphosphate carboxylase (Rubisco) plays an important role in the Calvin reductive pentose phosphate pathway. It catalyzes the primary CO2 fixation step. Rubisco is activated by carbamylation of an active site lysine, stabilized by a divalent cation, which then catalyzes the proton abstraction from the substrate ribulose 1,5 bisphosphate (RuBP) and leads to the formation of two molecules of 3-phosphoglycerate. Members of the Rubisco family can be divided into 4 subgroups, Form I-IV , which differ in their taxonomic distribution and subunit composition. Form III is only found in archaea and forms large subunit oligomers (dimers or decamers) that do not include small subunits. 412 matched cddid_all.tbl CDD cd08215 cd08215 270855 STKc_Nek Catalytic domain of the Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The Nek family is composed of 11 different mammalian members (Nek1-11) with similarity to the catalytic domain of Aspergillus nidulans NIMA kinase, the founding member of the Nek family, which was identified in a screen for cell cycle mutants that were prevented from entering mitosis. Neks contain a conserved N-terminal catalytic domain and a more divergent C-terminal regulatory region of various sizes and structures. They are involved in the regulation of downstream processes following the activation of Cdc2, and many of their functions are cell cycle-related. They play critical roles in microtubule dynamics during ciliogenesis and mitosis. The Nek family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 258 matched cddid_all.tbl CDD cd08216 cd08216 270856 PK_STRAD Pseudokinase domain of STE20-related kinase adapter protein. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. STRAD forms a complex with the scaffolding protein MO25, and the serine/threonine kinase (STK), LKB1, resulting in the activation of the kinase. In the complex, LKB1 phosphorylates and activates adenosine monophosphate-activated protein kinases (AMPKs), which regulate cell energy metabolism and cell polarity. LKB1 is a tumor suppressor linked to the rare inherited disease, Peutz-Jeghers syndrome, which is characterized by a predisposition to benign polyps and hyperpigmentation of the buccal mucosa. There are two forms of STRAD, alpha and beta, that complex with LKB1 and MO25. The structure of STRAD-alpha is available and shows that this protein binds ATP, has an ordered activation loop, and adopts a closed conformation typical of fully active protein kinases. It does not possess activity due to nonconservative substitutions of essential catalytic residues. ATP binding enhances the affinity of STRAD for MO25. The conformation of STRAD-alpha stabilized through ATP and MO25 may be needed to activate LKB1. The STRAD subfamily is part of a larger superfamily that includes the catalytic domains of STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 315 matched cddid_all.tbl CDD cd08217 cd08217 270857 STKc_Nek2 Catalytic domain of the Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The Nek2 subfamily includes Aspergillus nidulans NIMA kinase, the founding member of the Nek family, which was identified in a screen for cell cycle mutants prevented from entering mitosis. NIMA is essential for mitotic entry and progression through mitosis, and its degradation is essential for mitotic exit. NIMA is involved in nuclear membrane fission. Vertebrate Nek2 is a cell cycle-regulated STK, localized in centrosomes and kinetochores, that regulates centrosome splitting at the G2/M phase. It also interacts with other mitotic kinases such as Polo-like kinase 1 and may play a role in spindle checkpoint. An increase in the expression of the human NEK2 gene is strongly associated with the progression of non-Hodgkin lymphoma. Nek2 is one in a family of 11 different Neks (Nek1-11) that are involved in cell cycle control. It The Nek family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 265 matched cddid_all.tbl CDD cd08218 cd08218 270858 STKc_Nek1 Catalytic domain of the Protein Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Nek1 is associated with centrosomes throughout the cell cycle. It is involved in the formation of primary cilium and in the maintenance of centrosomes. It cycles through the nucleus and may be capable of relaying signals between the cilium and the nucleus. Nek1 is implicated in the development of polycystic kidney disease, which is characterized by benign polycystic tumors formed by abnormal overgrowth of renal epithelial cells. It appears also to be involved in DNA damage response, and may be important for both correct DNA damage checkpoint activation and DNA repair. Nek1 is one in a family of 11 different Neks (Nek1-11) that are involved in cell cycle control. The Nek family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd08219 cd08219 173759 STKc_Nek3 Catalytic domain of the Protein Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Nek3 is primarily localized in the cytoplasm and shows no cell cycle-dependent changes in its activity. It is present in the axons of neurons and affects morphogenesis and polarity through its regulation of microtubule acetylation. Nek3 modulates the signaling of the prolactin receptor through its activation of Vav2 and contributes to prolactin-mediated motility of breast cancer cells. It is one in a family of 11 different Neks (Nek1-11) that are involved in cell cycle control. The Nek family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 255 matched cddid_all.tbl CDD cd08220 cd08220 270859 STKc_Nek8 Catalytic domain of the Protein Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase 8. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Nek8 contains an N-terminal kinase catalytic domain and a C-terminal RCC1 (regulator of chromosome condensation) domain. A double point mutation in Nek8 causes cystic kidney disease in mice that genetically resembles human autosomal recessive polycystic kidney disease (ARPKD). Nek8 is also associated with a rare form of juvenile renal cystic disease, nephronophthisis type 9. It has been suggested that a defect in the ciliary localization of Nek8 contributes to the development of cysts manifested by these diseases. Nek8 is one in a family of 11 different Neks (Nek1-11) that are involved in cell cycle control. The Nek family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd08221 cd08221 270860 STKc_Nek9 Catalytic domain of the Protein Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase 9. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Nek9, also called Nercc1, is primarily a cytoplasmic protein but can also localize in the nucleus. It is involved in modulating chromosome alignment and splitting during mitosis. It interacts with the gamma-tubulin ring complex and the Ran GTPase, and is implicated in microtubule organization. Nek9 associates with FACT (FAcilitates Chromatin Transcription) and modulates interphase progression. It also interacts with Nek6, and Nek7, during mitosis, resulting in their activation. Nek9 is one in a family of 11 different Neks (Nek1-11) that are involved in cell cycle control. The Nek family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd08222 cd08222 270861 STKc_Nek11 Catalytic domain of the Protein Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase 11. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Nek11 is involved, through direct phosphorylation, in regulating the degradation of Cdc25A (Cell Division Cycle 25 homolog A), which plays a role in cell cycle progression and in activating cyclin dependent kinases. Nek11 is activated by CHK1 (CHeckpoint Kinase 1) and may be involved in the G2/M checkpoint. Nek11 may also play a role in the S-phase checkpoint as well as in DNA replication and genotoxic stress responses. It is one in a family of 11 different Neks (Nek1-11) that are involved in cell cycle control. The Nek family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 260 matched cddid_all.tbl CDD cd08223 cd08223 270862 STKc_Nek4 Catalytic domain of the Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase 4. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Nek4 is highly abundant in the testis. Its specific function is unknown. Neks are involved in the regulation of downstream processes following the activation of Cdc2, and many of their functions are cell cycle-related. They play critical roles in microtubule dynamics during ciliogenesis and mitosis. Nek4 is one in a family of 11 different Neks (Nek1-11). The Nek family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 257 matched cddid_all.tbl CDD cd08224 cd08224 270863 STKc_Nek6_7 Catalytic domain of the Serine/Threonine Kinases, Never In Mitosis gene A (NIMA)-related kinase 6 and 7. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Nek6 and Nek7 are the shortest Neks, consisting only of the catalytic domain and a very short N-terminal extension. They show distinct expression patterns and both appear to be downstream substrates of Nek9. They are required for mitotic spindle formation and cytokinesis. They may also be regulators of the p70 ribosomal S6 kinase. Nek6/7 is part of a family of 11 different Neks (Nek1-11) that are involved in cell cycle control. The Nek family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 262 matched cddid_all.tbl CDD cd08225 cd08225 173765 STKc_Nek5 Catalytic domain of the Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase 5. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Neks are involved in the regulation of downstream processes following the activation of Cdc2, and many of their functions are cell cycle-related. They play critical roles in microtubule dynamics during ciliogenesis and mitosis. The specific function of Nek5 is unknown. Nek5 is one in a family of 11 different Neks (Nek1-11). The Nek family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 257 matched cddid_all.tbl CDD cd08226 cd08226 270864 PK_STRAD_beta Pseudokinase domain of STE20-related kinase adapter protein beta. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity.STRAD-beta is also referred to as ALS2CR2 (Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 2 protein), since the human gene encoding it is located within the juvenile ALS2 critical region on chromosome 2q33-q34. It is not linked to the development of ALS2. STRAD forms a complex with the scaffolding protein MO25, and the serine/threonine kinase (STK), LKB1, resulting in the activation of the kinase. In the complex, LKB1 phosphorylates and activates adenosine monophosphate-activated protein kinases (AMPKs), which regulate cell energy metabolism and cell polarity. LKB1 is a tumor suppressor linked to the rare inherited disease, Peutz-Jeghers syndrome, which is characterized by a predisposition to benign polyps and hyperpigmentation of the buccal mucosa. The STRAD-beta subfamily is part of a larger superfamily that includes the catalytic domains of STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 328 matched cddid_all.tbl CDD cd08227 cd08227 173767 PK_STRAD_alpha Pseudokinase domain of STE20-related kinase adapter protein alpha. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. The structure of STRAD-alpha is available and shows that this protein binds ATP, has an ordered activation loop, and adopts a closed conformation typical of fully active protein kinases. It does not possess activity due to nonconservative substitutions of essential catalytic residues. ATP binding enhances the affinity of STRAD for MO25. The conformation of STRAD-alpha, stabilized through ATP and MO25, may be needed to activate LKB1. A mutation which results in a truncation of a C-terminal part of the human STRAD-alpha pseudokinase domain and disrupts its association with LKB1, leads to PMSE (polyhydramnios, megalencephaly, symptomatic epilepsy) syndrome. Several splice variants of STRAD-alpha exist which exhibit different effects on the localization and activation of LKB1. STRAD forms a complex with the scaffolding protein MO25, and the serine/threonine kinase (STK), LKB1, resulting in the activation of the kinase. In the complex, LKB1 phosphorylates and activates adenosine monophosphate-activated protein kinases (AMPKs), which regulate cell energy metabolism and cell polarity. The STRAD alpha subfamily is part of a larger superfamily that includes the catalytic domains of STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 327 matched cddid_all.tbl CDD cd08228 cd08228 270865 STKc_Nek6 Catalytic domain of the Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase 6. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Nek6 is required for the transition from metaphase to anaphase. It also plays important roles in mitotic spindle formation and cytokinesis. Activated by Nek9 during mitosis, Nek6 phosphorylates Eg5, a kinesin that is important for spindle bipolarity. Nek6 localizes to spindle microtubules during metaphase and anaphase, and to the midbody during cytokinesis. It is one in a family of 11 different Neks (Nek1-11) that are involved in cell cycle control. The Nek family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 268 matched cddid_all.tbl CDD cd08229 cd08229 270866 STKc_Nek7 Catalytic domain of the Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase 7. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Nek7 is required for mitotic spindle formation and cytokinesis. It is enriched in the centrosome and is critical for microtubule nucleation. Nek7 is activated by Nek9 during mitosis, and may regulate the p70 ribosomal S6 kinase. It is one in a family of 11 different Neks (Nek1-11) that are involved in cell cycle control. The Nek family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 292 matched cddid_all.tbl CDD cd08230 cd08230 176192 glucose_DH Glucose dehydrogenase. Glucose dehydrogenase (GlcDH), a member of the medium chain dehydrogenase/zinc-dependent alcohol dehydrogenase-like family, catalyzes the NADP(+)-dependent oxidation of glucose to gluconate, the first step in the Entner-Doudoroff pathway, an alternative to or substitute for glycolysis or the pentose phosphate pathway. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossman fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. 355 matched cddid_all.tbl CDD cd08231 cd08231 176193 MDR_TM0436_like Hypothetical enzyme TM0436 resembles the zinc-dependent alcohol dehydrogenases (ADH). This group contains the hypothetical TM0436 alcohol dehydrogenase from Thermotoga maritima, proteins annotated as 5-exo-alcohol dehydrogenase, and other members of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family. MDR, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. 361 matched cddid_all.tbl CDD cd08232 cd08232 176194 idonate-5-DH L-idonate 5-dehydrogenase. L-idonate 5-dehydrogenase (L-ido 5-DH ) catalyzes the conversion of L-lodonate to 5-ketogluconate in the metabolism of L-Idonate to 6-P-gluconate. In E. coli, this GntII pathway is a subsidiary pathway to the canonical GntI system, which also phosphorylates and transports gluconate. L-ido 5-DH is found in an operon with a regulator indR, transporter idnT, 5-keto-D-gluconate 5-reductase, and Gnt kinase. L-ido 5-DH is a zinc-dependent alcohol dehydrogenase-like protein. The alcohol dehydrogenase ADH-like family of proteins is a diverse group of proteins related to the first identified member, class I mammalian ADH. This group is also called the medium chain dehydrogenases/reductase family (MDR) which displays a broad range of activities and are distinguished from the smaller short chain dehydrogenases(~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal GroES-like catalytic domain. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 339 matched cddid_all.tbl CDD cd08233 cd08233 176195 butanediol_DH_like (2R,3R)-2,3-butanediol dehydrogenase. (2R,3R)-2,3-butanediol dehydrogenase, a zinc-dependent medium chain alcohol dehydrogenase, catalyzes the NAD(+)-dependent oxidation of (2R,3R)-2,3-butanediol and meso-butanediol to acetoin. BDH functions as a homodimer. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. The medium chain alcohol dehydrogenase family (MDR) have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. Sorbitol and aldose reductase are NAD(+) binding proteins of the polyol pathway, which interconverts glucose and fructose. Sorbitol dehydrogenase is tetrameric and has a single catalytic zinc per subunit. 351 matched cddid_all.tbl CDD cd08234 cd08234 176196 threonine_DH_like L-threonine dehydrogenase. L-threonine dehydrogenase (TDH) catalyzes the zinc-dependent formation of 2-amino-3-ketobutyrate from L-threonine, via NAD(H)-dependent oxidation. THD is a member of the zinc-requiring, medium chain NAD(H)-dependent alcohol dehydrogenase family (MDR). MDRs have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. Sorbitol and aldose reductase are NAD(+) binding proteins of the polyol pathway, which interconverts glucose and fructose. 334 matched cddid_all.tbl CDD cd08235 cd08235 176197 iditol_2_DH_like L-iditol 2-dehydrogenase. Putative L-iditol 2-dehydrogenase based on annotation of some members in this subgroup. L-iditol 2-dehydrogenase catalyzes the NAD+-dependent conversion of L-iditol to L-sorbose in fructose and mannose metabolism. This enzyme is related to sorbitol dehydrogenase, alcohol dehydrogenase, and other medium chain dehydrogenase/reductases. The zinc-dependent alcohol dehydrogenase (ADH-Zn)-like family of proteins is a diverse group of proteins related to the first identified member, class I mammalian ADH. This group is also called the medium chain dehydrogenases/reductase family (MDR) to highlight its broad range of activities and to distinguish from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal GroES-like catalytic domain. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 343 matched cddid_all.tbl CDD cd08236 cd08236 176198 sugar_DH NAD(P)-dependent sugar dehydrogenases. This group contains proteins identified as sorbitol dehydrogenases and other sugar dehydrogenases of the medium-chain dehydrogenase/reductase family (MDR), which includes zinc-dependent alcohol dehydrogenase and related proteins. Sorbitol and aldose reductase are NAD(+) binding proteins of the polyol pathway, which interconverts glucose and fructose. Sorbitol dehydrogenase is tetrameric and has a single catalytic zinc per subunit. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Related proteins include threonine dehydrogenase, formaldehyde dehydrogenase, and butanediol dehydrogenase. The medium chain alcohol dehydrogenase family (MDR) has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. Horse liver alcohol dehydrogenase is a dimeric enzyme and each subunit has two domains. The NAD binding domain is in a Rossmann fold and the catalytic domain contains a zinc ion to which substrates bind. There is a cleft between the domains that closes upon formation of the ternary complex. 343 matched cddid_all.tbl CDD cd08237 cd08237 176199 ribitol-5-phosphate_DH ribitol-5-phosphate dehydrogenase. NAD-linked ribitol-5-phosphate dehydrogenase, a member of the MDR/zinc-dependent alcohol dehydrogenase-like family, oxidizes the phosphate ester of ribitol-5-phosphate to xylulose-5-phosphate of the pentose phosphate pathway. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. 341 matched cddid_all.tbl CDD cd08238 cd08238 176200 sorbose_phosphate_red L-sorbose-1-phosphate reductase. L-sorbose-1-phosphate reductase, a member of the MDR family, catalyzes the NADPH-dependent conversion of l-sorbose 1-phosphate to d-glucitol 6-phosphate in the metabolism of L-sorbose to (also converts d-fructose 1-phosphate to d-mannitol 6-phosphate). The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of an beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. 410 matched cddid_all.tbl CDD cd08239 cd08239 176201 THR_DH_like L-threonine dehydrogenase (TDH)-like. MDR/AHD-like proteins, including a protein annotated as a threonine dehydrogenase. L-threonine dehydrogenase (TDH) catalyzes the zinc-dependent formation of 2-amino-3-ketobutyrate from L-threonine via NAD(H)-dependent oxidation. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Zinc-dependent ADHs are medium chain dehydrogenase/reductase type proteins (MDRs) and have a NAD(P)(H)-binding domain in a Rossmann fold of an beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. In addition to alcohol dehydrogenases, this group includes quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 339 matched cddid_all.tbl CDD cd08240 cd08240 176202 6_hydroxyhexanoate_dh_like 6-hydroxyhexanoate dehydrogenase. 6-hydroxyhexanoate dehydrogenase, an enzyme of the zinc-dependent alcohol dehydrogenase-like family of medium chain dehydrogenases/reductases catalyzes the conversion of 6-hydroxyhexanoate and NAD(+) to 6-oxohexanoate + NADH and H+. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H)-binding occurs in the cleft between the catalytic and coenzyme-binding domains, at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 350 matched cddid_all.tbl CDD cd08241 cd08241 176203 QOR1 Quinone oxidoreductase (QOR). QOR catalyzes the conversion of a quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR acts in the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens protein in some vertebrates (e.g. zeta-crystalin). QOR reduces quinones through a semi-quinone intermediate via a NAD(P)H-dependent single electron transfer. QOR is a member of the medium chain dehydrogenase/reductase family, but lacks the zinc-binding sites of the prototypical alcohol dehydrogenases of this group. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site, and a structural zinc in a lobe of the catalytic domain. NAD(H)-binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 323 matched cddid_all.tbl CDD cd08242 cd08242 176204 MDR_like Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family. This group contains members identified as related to zinc-dependent alcohol dehydrogenase and other members of the MDR family, including threonine dehydrogenase. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group includes various activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 319 matched cddid_all.tbl CDD cd08243 cd08243 176205 quinone_oxidoreductase_like_1 Quinone oxidoreductase (QOR). NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. The medium chain alcohol dehydrogenase family (MDR) have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. 320 matched cddid_all.tbl CDD cd08244 cd08244 176206 MDR_enoyl_red Possible enoyl reductase. Member identified as possible enoyl reductase of the MDR family. 2-enoyl thioester reductase (ETR) catalyzes the NADPH-dependent dependent conversion of trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl thioester reductase activity has been linked in Candida tropicalis as essential in maintaining mitiochondrial respiratory function. This ETR family is a part of the medium chain dehydrogenase/reductase family, but lack the zinc coordination sites characteristic of the alcohol dehydrogenases in this family. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site, and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. Candida tropicalis enoyl thioester reductase (Etr1p) catalyzes the NADPH-dependent reduction of trans-2-enoyl thioesters in mitochondrial fatty acid synthesis. Etr1p forms homodimers, with each subunit containing a nucleotide-binding Rossmann fold domain and a catalytic domain. 324 matched cddid_all.tbl CDD cd08245 cd08245 176207 CAD Cinnamyl alcohol dehydrogenases (CAD) and related proteins. Cinnamyl alcohol dehydrogenases (CAD), members of the medium chain dehydrogenase/reductase family, reduce cinnamaldehydes to cinnamyl alcohols in the last step of monolignal metabolism in plant cells walls. CAD binds 2 zinc ions and is NADPH- dependent. CAD family members are also found in non-plant species, e.g. in yeast where they have an aldehyde reductase activity. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes, or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 330 matched cddid_all.tbl CDD cd08246 cd08246 176208 crotonyl_coA_red crotonyl-CoA reductase. Crotonyl-CoA reductase, a member of the medium chain dehydrogenase/reductase family, catalyzes the NADPH-dependent conversion of crotonyl-CoA to butyryl-CoA, a step in (2S)-methylmalonyl-CoA production for straight-chain fatty acid biosynthesis. Like enoyl reductase, another enzyme in fatty acid synthesis, crotonyl-CoA reductase is a member of the zinc-dependent alcohol dehydrogenase-like medium chain dehydrogenase/reductase family. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. 393 matched cddid_all.tbl CDD cd08247 cd08247 176209 AST1_like AST1 is a cytoplasmic protein associated with the periplasmic membrane in yeast. This group contains members identified in targeting of yeast membrane proteins ATPase. AST1 is a cytoplasmic protein associated with the periplasmic membrane in yeast, identified as a multicopy suppressor of pma1 mutants which cause temperature sensitive growth arrest due to the inability of ATPase to target to the cell surface. This family is homologous to the medium chain family of dehydrogenases and reductases. Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of an beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. 352 matched cddid_all.tbl CDD cd08248 cd08248 176210 RTN4I1 Human Reticulon 4 Interacting Protein 1. Human Reticulon 4 Interacting Protein 1 is a member of the medium chain dehydrogenase/ reductase (MDR) family. Riticulons are endoplasmic reticulum associated proteins involved in membrane trafficking and neuroendocrine secretion. The MDR/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. 350 matched cddid_all.tbl CDD cd08249 cd08249 176211 enoyl_reductase_like enoyl_reductase_like. Member identified as possible enoyl reductase of the MDR family. 2-enoyl thioester reductase (ETR) catalyzes the NADPH-dependent dependent conversion of trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl thioester reductase activity has been linked in Candida tropicalis as essential in maintaining mitiochondrial respiratory function. This ETR family is a part of the medium chain dehydrogenase/reductase family, but lack the zinc coordination sites characteristic of the alcohol dehydrogenases in this family. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site, and a structural zinc in a lobe of the catalytic domain. NAD(H)-binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. Candida tropicalis enoyl thioester reductase (Etr1p) catalyzes the NADPH-dependent reduction of trans-2-enoyl thioesters in mitochondrial fatty acid synthesis. Etr1p forms homodimers with each subunit containing a nucleotide-binding Rossmann fold domain and a catalytic domain. 339 matched cddid_all.tbl CDD cd08250 cd08250 176212 Mgc45594_like Mgc45594 gene product and other MDR family members. Includes Human Mgc45594 gene product of undetermined function. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. 329 matched cddid_all.tbl CDD cd08251 cd08251 176213 polyketide_synthase polyketide synthase. Polyketide synthases produce polyketides in step by step mechanism that is similar to fatty acid synthesis. Enoyl reductase reduces a double to single bond. Erythromycin is one example of a polyketide generated by 3 complex enzymes (megasynthases). 2-enoyl thioester reductase (ETR) catalyzes the NADPH-dependent dependent conversion of trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl thioester reductase activity has been linked in Candida tropicalis as essential in maintaining mitiochondrial respiratory function. This ETR family is a part of the medium chain dehydrogenase/reductase family, but lack the zinc coordination sites characteristic of the alcohol dehydrogenases in this family. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site, and a structural zinc in a lobe of the catalytic domain. NAD(H)-binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. 303 matched cddid_all.tbl CDD cd08252 cd08252 176214 AL_MDR Arginate lyase and other MDR family members. This group contains a structure identified as an arginate lyase. Other members are identified quinone reductases, alginate lyases, and other proteins related to the zinc-dependent dehydrogenases/reductases. QOR catalyzes the conversion of a quinone and NAD(P)H to a hydroquinone and NAD(P+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR acts in the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens protein in some vertebrates (e.g. zeta-crystalin). QOR reduces quinones through a semi-quinone intermediate via a NAD(P)H-dependent single electron transfer. QOR is a member of the medium chain dehydrogenase/reductase family, but lacks the zinc-binding sites of the prototypical alcohol dehydrogenases of this group. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 336 matched cddid_all.tbl CDD cd08253 cd08253 176215 zeta_crystallin Zeta-crystallin with NADP-dependent quinone reductase activity (QOR). Zeta-crystallin is a eye lens protein with NADP-dependent quinone reductase activity (QOR). It has been cited as a structural component in mammalian eyes, but also has homology to quinone reductases in unrelated species. QOR catalyzes the conversion of a quinone and NAD(P)H to a hydroquinone and NAD(P+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR acts in the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens protein in some vertebrates (e.g. zeta-crystalin). QOR reduces quinones through a semi-quinone intermediate via a NAD(P)H-dependent single electron transfer. QOR is a member of the medium chain dehydrogenase/reductase family, but lacks the zinc-binding sites of the prototypical alcohol dehydrogenases of this group. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site, and a structural zinc in a lobe of the catalytic domain. NAD(H)-binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 325 matched cddid_all.tbl CDD cd08254 cd08254 176216 hydroxyacyl_CoA_DH 6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase, N-benzyl-3-pyrrolidinol dehydrogenase, and other MDR family members. This group contains enzymes of the zinc-dependent alcohol dehydrogenase family, including members (aka MDR) identified as 6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase and N-benzyl-3-pyrrolidinol dehydrogenase. 6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase catalyzes the conversion of 6-Hydroxycyclohex-1-enecarbonyl-CoA and NAD+ to 6-Ketoxycyclohex-1-ene-1-carboxyl-CoA,NADH, and H+. This group displays the characteristic catalytic and structural zinc sites of the zinc-dependent alcohol dehydrogenases. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H)-binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 338 matched cddid_all.tbl CDD cd08255 cd08255 176217 2-desacetyl-2-hydroxyethyl_bacteriochlorophyllide_like 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide and other MDR family members. This subgroup of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family has members identified as 2-desacetyl-2-hydroxyethyl bacteriochlorophyllide A dehydrogenase and alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. 277 matched cddid_all.tbl CDD cd08256 cd08256 176218 Zn_ADH2 Alcohol dehydrogenases of the MDR family. This group has the characteristic catalytic and structural zinc-binding sites of the zinc-dependent alcohol dehydrogenases of the MDR family. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. 350 matched cddid_all.tbl CDD cd08258 cd08258 176219 Zn_ADH4 Alcohol dehydrogenases of the MDR family. This group shares the zinc coordination sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of an beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 306 matched cddid_all.tbl CDD cd08259 cd08259 176220 Zn_ADH5 Alcohol dehydrogenases of the MDR family. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. This group contains proteins that share the characteristic catalytic and structural zinc-binding sites of the zinc-dependent alcohol dehydrogenase family. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H)-binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine (His-51), the ribose of NAD, a serine (Ser-48), then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 332 matched cddid_all.tbl CDD cd08260 cd08260 176221 Zn_ADH6 Alcohol dehydrogenases of the MDR family. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. This group has the characteristic catalytic and structural zinc sites of the zinc-dependent alcohol dehydrogenases. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H)-binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 345 matched cddid_all.tbl CDD cd08261 cd08261 176222 Zn_ADH7 Alcohol dehydrogenases of the MDR family. This group contains members identified as related to zinc-dependent alcohol dehydrogenase and other members of the MDR family. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group includes various activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 337 matched cddid_all.tbl CDD cd08262 cd08262 176223 Zn_ADH8 Alcohol dehydrogenases of the MDR family. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 341 matched cddid_all.tbl CDD cd08263 cd08263 176224 Zn_ADH10 Alcohol dehydrogenases of the MDR family. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H)-binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 367 matched cddid_all.tbl CDD cd08264 cd08264 176225 Zn_ADH_like2 Alcohol dehydrogenases of the MDR family. This group resembles the zinc-dependent alcohol dehydrogenases of the medium chain dehydrogenase family. However, this subgroup does not contain the characteristic catalytic zinc site. Also, it contains an atypical structural zinc-binding pattern: DxxCxxCxxxxxxxC. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H)-binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 325 matched cddid_all.tbl CDD cd08265 cd08265 176226 Zn_ADH3 Alcohol dehydrogenases of the MDR family. This group resembles the zinc-dependent alcohol dehydrogenase and has the catalytic and structural zinc-binding sites characteristic of this group. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc. 384 matched cddid_all.tbl CDD cd08266 cd08266 176227 Zn_ADH_like1 Alcohol dehydrogenases of the MDR family. This group contains proteins related to the zinc-dependent alcohol dehydrogenases. However, while the group has structural zinc site characteristic of these enzymes, it lacks the consensus site for a catalytic zinc. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site, and a structural zinc in a lobe of the catalytic domain. NAD(H)-binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 342 matched cddid_all.tbl CDD cd08267 cd08267 176228 MDR1 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family. This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 319 matched cddid_all.tbl CDD cd08268 cd08268 176229 MDR2 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family. This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 328 matched cddid_all.tbl CDD cd08269 cd08269 176230 Zn_ADH9 Alcohol dehydrogenases of the MDR family. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. 312 matched cddid_all.tbl CDD cd08270 cd08270 176231 MDR4 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family. This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 305 matched cddid_all.tbl CDD cd08271 cd08271 176232 MDR5 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family. This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 325 matched cddid_all.tbl CDD cd08272 cd08272 176233 MDR6 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family. This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 326 matched cddid_all.tbl CDD cd08273 cd08273 176234 MDR8 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family. This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 331 matched cddid_all.tbl CDD cd08274 cd08274 176235 MDR9 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family. This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 350 matched cddid_all.tbl CDD cd08275 cd08275 176236 MDR3 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family. This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 337 matched cddid_all.tbl CDD cd08276 cd08276 176237 MDR7 Medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family. This group is a member of the medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, but lacks the zinc-binding sites of the zinc-dependent alcohol dehydrogenases. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 336 matched cddid_all.tbl CDD cd08277 cd08277 176238 liver_alcohol_DH_like Liver alcohol dehydrogenase. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. There are 7 vertebrate ADH 7 classes, 6 of which have been identified in humans. Class III, glutathione-dependent formaldehyde dehydrogenase, has been identified as the primordial form and exists in diverse species, including plants, micro-organisms, vertebrates, and invertebrates. Class I, typified by liver dehydrogenase, is an evolving form. Gene duplication and functional specialization of ADH into ADH classes and subclasses created numerous forms in vertebrates. For example, the A, B and C (formerly alpha, beta, gamma) human class I subunits have high overall structural similarity, but differ in the substrate binding pocket and therefore in substrate specificity. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine (His-51), the ribose of NAD, a serine (Ser-48) , then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of an beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. 365 matched cddid_all.tbl CDD cd08278 cd08278 176239 benzyl_alcohol_DH Benzyl alcohol dehydrogenase. Benzyl alcohol dehydrogenase is similar to liver alcohol dehydrogenase, but has some amino acid substitutions near the active site, which may determine the enzyme's specificity of oxidizing aromatic substrates. Also known as aryl-alcohol dehydrogenases, they catalyze the conversion of an aromatic alcohol + NAD+ to an aromatic aldehyde + NADH + H+. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 365 matched cddid_all.tbl CDD cd08279 cd08279 176240 Zn_ADH_class_III Class III alcohol dehydrogenase. Glutathione-dependent formaldehyde dehydrogenases (FDHs, Class III ADH) are members of the zinc-dependent/medium chain alcohol dehydrogenase family. FDH converts formaldehyde and NAD(P) to formate and NAD(P)H. The initial step in this process the spontaneous formation of a S-(hydroxymethyl)glutathione adduct from formaldehyde and glutathione, followed by FDH-mediated oxidation (and detoxification) of the adduct to S-formylglutathione. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. Class III ADH are also known as glutathione-dependent formaldehyde dehydrogenase (FDH), which convert aldehydes to corresponding carboxylic acid and alcohol. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of an beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. 363 matched cddid_all.tbl CDD cd08281 cd08281 176241 liver_ADH_like1 Zinc-dependent alcohol dehydrogenases (ADH) and class III ADG (AKA formaldehyde dehydrogenase). NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes or ketones. This group contains members identified as zinc dependent alcohol dehydrogenases (ADH), and class III ADG (aka formaldehyde dehydrogenase, FDH). Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. Class III ADH are also know as glutathione-dependent formaldehyde dehydrogenase (FDH), which convert aldehydes to the corresponding carboxylic acid and alcohol. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 371 matched cddid_all.tbl CDD cd08282 cd08282 176242 PFDH_like Pseudomonas putida aldehyde-dismutating formaldehyde dehydrogenase (PFDH). Formaldehyde dehydrogenase (FDH) is a member of the zinc-dependent/medium chain alcohol dehydrogenase family. Unlike typical FDH, Pseudomonas putida aldehyde-dismutating FDH (PFDH) is glutathione-independent. PFDH converts 2 molecules of aldehydes to corresponding carboxylic acid and alcohol. MDH family uses NAD(H) as a cofactor in the interconversion of alcohols and aldehydes, or ketones. Like the zinc-dependent alcohol dehydrogenases (ADH) of the medium chain alcohol dehydrogenase/reductase family (MDR), these tetrameric FDHs have a catalytic zinc that resides between the catalytic and NAD(H)binding domains and a structural zinc in a lobe of the catalytic domain. Unlike ADH, where NAD(P)(H) acts as a cofactor, NADH in FDH is a tightly bound redox cofactor (similar to nicotinamide proteins). The medium chain alcohol dehydrogenase family (MDR) has a NAD(P)(H)-binding domain in a Rossmann fold of an beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. 375 matched cddid_all.tbl CDD cd08283 cd08283 176243 FDH_like_1 Glutathione-dependent formaldehyde dehydrogenase related proteins, child 1. Members identified as glutathione-dependent formaldehyde dehydrogenase(FDH), a member of the zinc-dependent/medium chain alcohol dehydrogenase family. FDH converts formaldehyde and NAD(P) to formate and NAD(P)H. The initial step in this process the spontaneous formation of a S-(hydroxymethyl)glutathione adduct from formaldehyde and glutathione, followed by FDH-mediated oxidation (and detoxification) of the adduct to S-formylglutathione. MDH family uses NAD(H) as a cofactor in the interconversion of alcohols and aldehydes, or ketones. Like many zinc-dependent alcohol dehydrogenases (ADH) of the medium chain alcohol dehydrogenase/reductase family (MDR), these FDHs form dimers, with 4 zinc ions per dimer. The medium chain alcohol dehydrogenase family (MDR) has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. 386 matched cddid_all.tbl CDD cd08284 cd08284 176244 FDH_like_2 Glutathione-dependent formaldehyde dehydrogenase related proteins, child 2. Glutathione-dependent formaldehyde dehydrogenases (FDHs) are members of the zinc-dependent/medium chain alcohol dehydrogenase family. Formaldehyde dehydrogenase (FDH) is a member of the zinc-dependent/medium chain alcohol dehydrogenase family. FDH converts formaldehyde and NAD to formate and NADH. The initial step in this process the spontaneous formation of a S-(hydroxymethyl)glutathione adduct from formaldehyde and glutathione, followed by FDH-mediated oxidation (and detoxification) of the adduct to S-formylglutathione. These tetrameric FDHs have a catalytic zinc that resides between the catalytic and NAD(H)binding domains and a structural zinc in a lobe of the catalytic domain. The medium chain alcohol dehydrogenase family (MDR) has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. 344 matched cddid_all.tbl CDD cd08285 cd08285 176245 NADP_ADH NADP(H)-dependent alcohol dehydrogenases. This group is predominated by atypical alcohol dehydrogenases; they exist as tetramers and exhibit specificity for NADP(H) as a cofactor in the interconversion of alcohols and aldehydes, or ketones. Like other zinc-dependent alcohol dehydrogenases (ADH) of the medium chain alcohol dehydrogenase/reductase family (MDR), tetrameric ADHs have a catalytic zinc that resides between the catalytic and NAD(H)binding domains; however, they do not have and a structural zinc in a lobe of the catalytic domain. The medium chain alcohol dehydrogenase family (MDR) has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. 351 matched cddid_all.tbl CDD cd08286 cd08286 176246 FDH_like_ADH2 formaldehyde dehydrogenase (FDH)-like. This group is related to formaldehyde dehydrogenase (FDH), which is a member of the zinc-dependent/medium chain alcohol dehydrogenase family. This family uses NAD(H) as a cofactor in the interconversion of alcohols and aldehydes, or ketones. Another member is identified as a dihydroxyacetone reductase. Like the zinc-dependent alcohol dehydrogenases (ADH) of the medium chain alcohol dehydrogenase/reductase family (MDR), tetrameric FDHs have a catalytic zinc that resides between the catalytic and NAD(H)binding domains and a structural zinc in a lobe of the catalytic domain. Unlike ADH, where NAD(P)(H) acts as a cofactor, NADH in FDH is a tightly bound redox cofactor (similar to nicotinamide proteins). The medium chain alcohol dehydrogenase family (MDR) has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. 345 matched cddid_all.tbl CDD cd08287 cd08287 176247 FDH_like_ADH3 formaldehyde dehydrogenase (FDH)-like. This group contains proteins identified as alcohol dehydrogenases and glutathione-dependant formaldehyde dehydrogenases (FDH) of the zinc-dependent/medium chain alcohol dehydrogenase family. The MDR family uses NAD(H) as a cofactor in the interconversion of alcohols and aldehydes, or ketones. FDH converts formaldehyde and NAD to formate and NADH. The initial step in this process the spontaneous formation of a S-(hydroxymethyl)glutathione adduct from formaldehyde and glutathione, followed by FDH-mediated oxidation (and detoxification) of the adduct to S-formylglutathione. The medium chain alcohol dehydrogenase family (MDR) has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. 345 matched cddid_all.tbl CDD cd08288 cd08288 176248 MDR_yhdh Yhdh putative quinone oxidoreductases. Yhdh putative quinone oxidoreductases (QOR). QOR catalyzes the conversion of a quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR actin the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens protein in some vertebrates (e.g. zeta-crystalin). QOR reduces quinones through a semi-quinone intermediate via a NAD(P)H-dependent single electron transfer. QOR is a member of the medium chain dehydrogenase/reductase family, but lacks the zinc-binding sites of the prototypical alcohol dehydrogenases of this group. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 324 matched cddid_all.tbl CDD cd08289 cd08289 176249 MDR_yhfp_like Yhfp putative quinone oxidoreductases. yhfp putative quinone oxidoreductases (QOR). QOR catalyzes the conversion of a quinone + NAD(P)H to a hydroquinone + NAD(P)+. Quinones are cyclic diones derived from aromatic compounds. Membrane bound QOR actin the respiratory chains of bacteria and mitochondria, while soluble QOR acts to protect from toxic quinones (e.g. DT-diaphorase) or as a soluble eye-lens protein in some vertebrates (e.g. zeta-crystalin). QOR reduces quinones through a semi-quinone intermediate via a NAD(P)H-dependent single electron transfer. QOR is a member of the medium chain dehydrogenase/reductase family, but lacks the zinc-binding sites of the prototypical alcohol dehydrogenases of this group. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site, and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 326 matched cddid_all.tbl CDD cd08290 cd08290 176250 ETR 2-enoyl thioester reductase (ETR). 2-enoyl thioester reductase (ETR) catalyzes the NADPH-dependent conversion of trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl thioester reductase activity has been linked in Candida tropicalis as essential in maintaining mitiochondrial respiratory function. This ETR family is a part of the medium chain dehydrogenase/reductase family, but lack the zinc coordination sites characteristic of the alcohol dehydrogenases in this family. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site, and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains, at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. Candida tropicalis enoyl thioester reductase (Etr1p) catalyzes the NADPH-dependent reduction of trans-2-enoyl thioesters in mitochondrial fatty acid synthesis. Etr1p forms homodimers, with each subunit containing a nucleotide-binding Rossmann fold domain and a catalytic domain. 341 matched cddid_all.tbl CDD cd08291 cd08291 176251 ETR_like_1 2-enoyl thioester reductase (ETR) like proteins, child 1. 2-enoyl thioester reductase (ETR) like proteins. ETR catalyzes the NADPH-dependent conversion of trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl thioester reductase activity has been linked in Candida tropicalis as essential in maintaining mitiochondrial respiratory function. This ETR family is a part of the medium chain dehydrogenase/reductase family, but lack the zinc coordination sites characteristic of the 2-enoyl thioester reductase (ETR) like proteins. ETR catalyzes the NADPH-dependent dependent conversion of trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl thioester reductase activity has been linked in Candida tropicalis as essential in maintaining mitiochondrial respiratory function. This ETR family is a part of the medium chain dehydrogenase/reductase family, but lack the zinc coordination sites characteristic of the alcohol dehydrogenases in this family. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. Candida tropicalis enoyl thioester reductase (Etr1p) catalyzes the NADPH-dependent reduction of trans-2-enoyl thioesters in mitochondrial fatty acid synthesis. Etr1p forms homodimers, with each subunit containing a nucleotide-binding Rossmann fold domain and a catalytic domain. 324 matched cddid_all.tbl CDD cd08292 cd08292 176252 ETR_like_2 2-enoyl thioester reductase (ETR) like proteins, child 2. 2-enoyl thioester reductase (ETR) like proteins. ETR catalyzes the NADPH-dependent conversion of trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl thioester reductase activity has been linked in Candida tropicalis as essential in maintaining mitiochondrial respiratory function. This ETR family is a part of the medium chain dehydrogenase/reductase family, but lack the zinc coordination sites characteristic of the 2-enoyl thioester reductase (ETR) like proteins. ETR catalyzes the NADPH-dependent dependent conversion of trans-2-enoyl acyl carrier protein/coenzyme A (ACP/CoA) to acyl-(ACP/CoA) in fatty acid synthesis. 2-enoyl thioester reductase activity has been linked in Candida tropicalis as essential in maintaining mitiochondrial respiratory function. This ETR family is a part of the medium chain dehydrogenase/reductase family, but lack the zinc coordination sites characteristic of the alcohol dehydrogenases in this family. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site, and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains, at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. Candida tropicalis enoyl thioester reductase (Etr1p) catalyzes the NADPH-dependent reduction of trans-2-enoyl thioesters in mitochondrial fatty acid synthesis. Etr1p forms homodimers, with each subunit containing a nucleotide-binding Rossmann fold domain and a catalytic domain. 324 matched cddid_all.tbl CDD cd08293 cd08293 176253 PTGR2 Prostaglandin reductase. Prostaglandins and related eicosanoids are metabolized by the oxidation of the 15(S)-hydroxyl group of the NAD+-dependent (type I 15-PGDH) 15-prostaglandin dehydrogenase (15-PGDH) followed by reduction by NADPH/NADH-dependent (type II 15-PGDH) delta-13 15-prostaglandin reductase (13-PGR) to 15-keto-13,14,-dihydroprostaglandins. 13-PGR is a bifunctional enzyme, since it also has leukotriene B(4) 12-hydroxydehydrogenase activity. These 15-PGDH and related enzymes are members of the medium chain dehydrogenase/reductase family. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. 345 matched cddid_all.tbl CDD cd08294 cd08294 176254 leukotriene_B4_DH_like 13-PGR is a bifunctional enzyme with delta-13 15-prostaglandin reductase and leukotriene B4 12 hydroxydehydrogenase activity. Prostaglandins and related eicosanoids are metabolized by the oxidation of the 15(S)-hydroxyl group of the NAD+-dependent (type I 15-PGDH) 15-prostaglandin dehydrogenase (15-PGDH) followed by reduction by NADPH/NADH-dependent (type II 15-PGDH) delta-13 15-prostaglandin reductase (13-PGR) to 15-keto- 13,14,-dihydroprostaglandins. 13-PGR is a bifunctional enzyme, since it also has leukotriene B(4) 12-hydroxydehydrogenase activity. These 15-PGDH and related enzymes are members of the medium chain dehydrogenase/reductase family. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. 329 matched cddid_all.tbl CDD cd08295 cd08295 176255 double_bond_reductase_like Arabidopsis alkenal double bond reductase and leukotriene B4 12-hydroxydehydrogenase. This group includes proteins identified as the Arabidopsis alkenal double bond reductase and leukotriene B4 12-hydroxydehydrogenase. The Arabidopsis enzyme, a member of the medium chain dehydrogenase/reductase family, catalyzes the reduction of 7-8-double bond of phenylpropanal substrates as a plant defense mechanism. Prostaglandins and related eicosanoids (lipid mediators involved in host defense and inflamation) are metabolized by the oxidation of the 15(S)-hydroxyl group of the NAD+-dependent (type I 15-PGDH) 15-prostaglandin dehydrogenase (15-PGDH) followed by reduction by NADPH/NADH-dependent (type II 15-PGDH) delta-13 15-prostaglandin reductase (13-PGR) to 15-keto-13,14,-dihydroprostaglandins. 13-PGR is a bifunctional enzyme, since it also has leukotriene B(4) 12-hydroxydehydrogenase activity. Leukotriene B4 (LTB4) can be metabolized by LTB4 20-hydroxylase in inflamatory cells, and in other cells by bifunctional LTB4 12-HD/PGR. These 15-PGDH and related enzymes are members of the medium chain dehydrogenase/reductase family. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of an beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. 338 matched cddid_all.tbl CDD cd08296 cd08296 176256 CAD_like Cinnamyl alcohol dehydrogenases (CAD). Cinnamyl alcohol dehydrogenases (CAD), members of the medium chain dehydrogenase/reductase family, reduce cinnamaldehydes to cinnamyl alcohols in the last step of monolignal metabolism in plant cells walls. CAD binds 2 zinc ions and is NADPH- dependent. CAD family members are also found in non-plant species, e.g. in yeast where they have an aldehyde reductase activity. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADHs), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 333 matched cddid_all.tbl CDD cd08297 cd08297 176257 CAD3 Cinnamyl alcohol dehydrogenases (CAD). These alcohol dehydrogenases are related to the cinnamyl alcohol dehydrogenases (CAD), members of the medium chain dehydrogenase/reductase family. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Cinnamyl alcohol dehydrogenases (CAD) reduce cinnamaldehydes to cinnamyl alcohols in the last step of monolignal metabolism in plant cells walls. CAD binds 2 zinc ions and is NADPH- dependent. CAD family members are also found in non-plant species, e.g. in yeast where they have an aldehyde reductase activity. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 341 matched cddid_all.tbl CDD cd08298 cd08298 176258 CAD2 Cinnamyl alcohol dehydrogenases (CAD). These alcohol dehydrogenases are related to the cinnamyl alcohol dehydrogenases (CAD), members of the medium chain dehydrogenase/reductase family. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Cinnamyl alcohol dehydrogenases (CAD) reduce cinnamaldehydes to cinnamyl alcohols in the last step of monolignal metabolism in plant cells walls. CAD binds 2 zinc ions and is NADPH- dependent. CAD family members are also found in non-plant species, e.g. in yeast where they have an aldehyde reductase activity. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. 329 matched cddid_all.tbl CDD cd08299 cd08299 176259 alcohol_DH_class_I_II_IV class I, II, IV alcohol dehydrogenases. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes or ketones. This group includes alcohol dehydrogenases corresponding to mammalian classes I, II, IV. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine (His-51), the ribose of NAD, a serine (Ser-48) , then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. 373 matched cddid_all.tbl CDD cd08300 cd08300 176260 alcohol_DH_class_III class III alcohol dehydrogenases. Members identified as glutathione-dependent formaldehyde dehydrogenase(FDH), a member of the zinc dependent/medium chain alcohol dehydrogenase family. FDH converts formaldehyde and NAD(P) to formate and NAD(P)H. The initial step in this process the spontaneous formation of a S-(hydroxymethyl)glutathione adduct from formaldehyde and glutathione, followed by FDH-mediated oxidation (and detoxification) of the adduct to S-formylglutathione. MDH family uses NAD(H) as a cofactor in the interconversion of alcohols and aldehydes or ketones. Like many zinc-dependent alcohol dehydrogenases (ADH) of the medium chain alcohol dehydrogenase/reductase family (MDR), these FDHs form dimers, with 4 zinc ions per dimer. The medium chain alcohol dehydrogenase family (MDR) have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The N-terminal region typically has an all-beta catalytic domain. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. 368 matched cddid_all.tbl CDD cd08301 cd08301 176261 alcohol_DH_plants Plant alcohol dehydrogenase. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. There are 7 vertebrate ADH 7 classes, 6 of which have been identified in humans. Class III, glutathione-dependent formaldehyde dehydrogenase, has been identified as the primordial form and exists in diverse species, including plants, micro-organisms, vertebrates, and invertebrates. Class I, typified by liver dehydrogenase, is an evolving form. Gene duplication and functional specialization of ADH into ADH classes and subclasses created numerous forms in vertebrates. For example, the A, B and C (formerly alpha, beta, gamma) human class I subunits have high overall structural similarity, but differ in the substrate binding pocket and therefore in substrate specificity. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine (His-51), the ribose of NAD, a serine (Ser-48) , then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which has a NAD(P)(H)-binding domain in a Rossmann fold of an beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H) binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. 369 matched cddid_all.tbl CDD cd08304 cd08304 176720 DD Death Domain Superfamily of protein-protein interaction domains. The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer. 69 matched cddid_all.tbl CDD cd08305 cd08305 260019 Pyrin Pyrin: a protein-protein interaction domain. The Pyrin domain (or PYD), also called DAPIN or PAAD, is a subfamily of the Death Domain (DD) superfamily and it functions in several signaling pathways. The Pyrin domain is found at the N-terminus of a variety of proteins and serves as a linker that recruits other domains into signaling complexes. Pyrin-containing proteins include NALPs, ASC (Apoptosis-associated speck-like protein containing a CARD), and the interferon-inducible p200 (IFI-200) family of proteins which includes the human IFI-16, myeloid cell nuclear differentiation antigen (MNDA) and absent in melanoma (AIM) 2. NALPs are members of the NBS-LRR family of proteins possessing a tripartite domain structure including a C-terminal LRR (leucine-rich repeats), a central nucleotide-binding site (NBS) domain or NACHT (for neuronal apoptosis inhibitor protein, CIITA, HET-E and TP1), and an N-terminal protein-protein interaction domain, which is a Pyrin domain in the case of NALPs. ASC and NALPs are involved in the regulation of inflammation. ASC, NALP1 and NALP3 are involved in the assembly of the 'inflammasome', a multiprotein platform which is formed in response to infection or injury and is responsible for caspase-1 activation and regulation of IL-1beta maturation. NALP12 functions as a negative regulator of inflammation. The p200 proteins are involved in the regulation of cell cycle and differentiation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including Caspase activation and recruitment domain (CARD) and Death Effector Domain (DED). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 73 matched cddid_all.tbl CDD cd08306 cd08306 260020 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. 85 matched cddid_all.tbl CDD cd08307 cd08307 260021 Death_Pelle Death domain of the protein kinase Pelle. Death domain (DD) of the protein kinase Pelle from Drosophila melanogaster and similar proteins. In Drosophila, interaction between the DDs of Tube and Pelle is an important component of the Toll pathway, which functions in establishing dorsoventral polarity in embryos and in mediating innate immune responses to pathogens. Tube and Pelle transmit the signal from the Toll receptor to the Dorsal/Cactus complex. Pelle also functions in photoreceptor axon targeting. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 97 matched cddid_all.tbl CDD cd08308 cd08308 260022 Death_Tube Death domain of Tube. Death domains (DDs) similar to the DD in the protein Tube from Drosophila melanogaster. In Drosophila, interaction between the DDs of Tube and Pelle is an important component of the Toll pathway, which functions in establishing dorsoventral polarity in embryos and also in mediating innate immune response to pathogens. Tube and Pelle transmit the signal from the Toll receptor to the Dorsal/Cactus complex. Some members of this subfamily contain a C-terminal kinase domain, like Pelle, in addition to the DD. Tube has no counterpart in vertebrates. It contains an N-terminal DD and a C-terminal region with five copies of the Tube repeat, an 8-amino acid motif. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 128 matched cddid_all.tbl CDD cd08309 cd08309 260023 Death_IRAK Death domain of Interleukin-1 Receptor-Associated Kinases. Death Domains (DDs) found in Interleukin-1 (IL-1) Receptor-Associated Kinases (IRAK1-4) and similar proteins. IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. All four types are involved in signal transduction involving IL-1 and IL-18 receptors, Toll-like receptors, nuclear factor-kappaB, and mitogen-activated protein kinase pathways. IRAK1 and IRAK4 are active kinases while IRAK2 and IRAK-M (also called IRAK3) are inactive. In general, IRAKs are expressed ubiquitously, except for IRAK-M which is detected only in macrophages. The insect homologs, Pelle and Tube, are important components of the Toll pathway, which functions in establishing dorsoventral polarity in embryos and also in the innate immune response. Most members have an N-terminal DD followed by a kinase domain. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 88 matched cddid_all.tbl CDD cd08310 cd08310 260024 Death_NFkB-like Death domain of Nuclear Factor-KappaB precursor proteins. Death Domain (DD) of Nuclear Factor-KappaB (NF-kB) precursor proteins. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). Two of these, NF-kB1 and NF-kB2 are produced from the processing of the precursor proteins p105 and p100, respectively. In addition to RHD, p105 and p100 contain ANK repeats and a C-terminal DD. NF-kBs are regulated by the Inhibitor of NF-kB (IkB) Kinase (IKK) complex through classical and non-canonical pathways, which differ in the IKK subunits involved and downstream targets. IKKs facilitate the release of NF-kB dimers from an inactive state, allowing them to migrate to the nucleus where they regulate gene transcription. The precursor proteins p105 and p100 function as IkBs and as NF-kB proteins after being processed by the proteasome. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 72 matched cddid_all.tbl CDD cd08311 cd08311 260025 Death_p75NR Death domain of p75 Neurotrophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 80 matched cddid_all.tbl CDD cd08312 cd08312 260026 Death_MyD88 Death domain of Myeloid Differentation primary response protein MyD88. Death Domain (DD) of Myeloid Differentiation primary response protein 88 (MyD88). MyD88 is an adaptor protein involved in interleukin-1 receptor (IL-1R)- and Toll-like receptor (TLR)-induced activation of nuclear factor-kappaB (NF-kB) and mitogen activated protein kinase pathways that lead to the induction of proinflammatory cytokines. It is a key component in the signaling pathway of pathogen recognition in the innate immune system. MyD88 contains an N-terminal DD and a C-terminal Toll/IL-1 Receptor (TIR) homology domain that mediates interaction with TLRs and IL-1R. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 79 matched cddid_all.tbl CDD cd08313 cd08313 176729 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 80 matched cddid_all.tbl CDD cd08315 cd08315 260027 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 88 matched cddid_all.tbl CDD cd08316 cd08316 260028 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 94 matched cddid_all.tbl CDD cd08317 cd08317 260029 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 84 matched cddid_all.tbl CDD cd08318 cd08318 260030 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 86 matched cddid_all.tbl CDD cd08319 cd08319 260031 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 83 matched cddid_all.tbl CDD cd08320 cd08320 260032 Pyrin_NALPs Pyrin death domain found in NALP proteins. Pyrin Death Domain found in NALP (NACHT, LRR and PYD domains) proteins including NALP1 (CARD7, NLRP1), NALP3 (NLRP3, Cryopyrin, CIAS1), and NALP12 (NLRP12, Monarch-1), among others. Mammals contains at least 14 NALP proteins, named NALP1-14 (or NLRP1-14). NALPs are members of the NBS-LRR family of proteins possessing a tripartite domain structure including a C-terminal LRR (leucine-rich repeats), a central nucleotide-binding site (NBS) domain or NACHT (for neuronal apoptosis inhibitor protein, CIITA, HET-E and TP1), and an N-terminal protein-protein interaction domain, which is a Pyrin domain in the case of NALPs. The NBS-LRR family is also referred to as the NLR (Nod-like Receptor) or CATERPILLAR (for CARD, transcription enhancer, R-(purine)-binding, pyrin, lots of LRRs) family. NALP1 contains an additional Caspase activation and recruitment domain (CARD) at the C-terminus. NALP1 and NALP3 are both involved in the assembly of the 'inflammasome', a multiprotein platform which is formed in response to infection or injury and is responsible for caspase-1 activation and regulation of IL-1beta maturation. NALP1-inflammasomes recognize specific substances while NALP3-inflammasomes responds to many diverse triggers. Mutations in the NALP3 gene are associated with a broad spectrum of autoinflammatory disorders including Muckle-Wells Syndrome (MWS), familial cold autoinflammatory syndrome (FCAS), and chronic neurologic cutaneous and articular syndrome (CINCA). NALP12 functions as a negative regulator of inflammation. In general, Pyrin is a subfamily of the Death Domain (DD) superfamily and functions in several signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 84 matched cddid_all.tbl CDD cd08321 cd08321 260033 Pyrin_ASC-like Pyrin Death Domain found in ASC. Pyrin Death Domain found in ASC (Apoptosis-associated speck-like protein containing a CARD) and similar proteins. ASC is an adaptor molecule that functions in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. ASC contains two domains from the Death Domain (DD) superfamily, an N-terminal pyrin-like domain and a C-terminal Caspase activation and recruitment domain (CARD). Through these 2 domains, ASC serves as an adaptor for inflammasome integrity and oligomerizes to form supramolecular assemblies. Included in this family is human PYNOD (also known as NLRP10 or NOD8) which via its Pyrin domain suppresses oligomerization of ASC, and ASC-mediated NF-kappaB activation. Other members of this subfamily are associated with ATPase domains and their function remains unknown. In general, Pyrin is a subfamily of the DD superfamily and functions in several signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD and Death Effector Domain (DED). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 82 matched cddid_all.tbl CDD cd08323 cd08323 260034 CARD_APAF1 Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1. Caspase activation and recruitment domain (CARD) similar to that found in apoptotic protease-activating factor 1 (APAF-1), which is an activator of caspase-9. APAF-1 contains WD-40 repeats, a CARD, and an ATPase domain. Upon stimulation, APAF-1, together with caspase-9, forms the heptameric 'apoptosome', which leads to the processing and activation of caspase-9, starting a caspase cascade which leads to apoptosis. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 86 matched cddid_all.tbl CDD cd08324 cd08324 260035 CARD_NOD1_CARD4 Caspase activation and recruitment domain similar to that found in NOD1. Caspase activation and recruitment domain (CARD) found in human NOD1 (CARD4) and similar proteins. NOD1 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD1, as well as NOD2, the N-terminal effector domain is a CARD. Nod1-CARD has been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 85 matched cddid_all.tbl CDD cd08325 cd08325 260036 CARD_CASP1-like Caspase activation and recruitment domain found in Caspase-1 and related proteins. Caspase activation and recruitment domain (CARD) similar to those found in Caspase-1 (CASP1, ICE) and related proteins, including CARD-only proteins such as ICEBERG or CARD18, INCA (CARD17), CARD16 (COP1, PSEUDO-ICE), CARD8 (DACAR, NDPP1, TUCAN), and CARD12 (NLRC4), as well as ICE-like caspases such as CASP12, CASP5 (ICH-3) and CASP4 (TX, ICH-2). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. CASP1 plays a central role in the cellular response to a wide variety of microbial and non-microbial stimuli, being activated by the inflammasome or the pyroptosome. CARD8 binds itself and the initiator caspase-9, interfering with the binding of APAF-1 and suppressing caspase-9 activation. CARD12 is a Nod-like receptor (NLR) that plays an important role in the innate immune response to Gram-negative bacteria. Caspase-4 (CASP4), -5 (CASP5), and -12 (CASP12) are inflammatory caspases implicated in inflammation and endoplasmic reticulum stress-induced apoptosis. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 83 matched cddid_all.tbl CDD cd08326 cd08326 176740 CARD_CASP9 Caspase activation and recruitment domain of Caspase-9. Caspase activation and recruitment domain (CARD) similar to that found in caspase-9 (CASP9, MCH6, APAF3), which interacts with the CARD of apoptotic protease-activating factor 1 (APAF-1). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-9 is the initiator caspase associated with the intrinsic or mitochondrial pathway of apoptosis, induced by many pro-apoptotic signals. Together with APAF-1, it forms the heptameric 'apoptosome' in response to the release of cytochrome c from mitochondria. Activated caspase-9 cleaves and activates downstream effector caspases, like caspase-3, caspase-6, and caspase-7, resulting in apoptosis. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 84 matched cddid_all.tbl CDD cd08327 cd08327 260037 CARD_RAIDD Caspase activation and recruitment domain of RIP-associated ICH-1 homologous protein with a death domain. Caspase activation and recruitment domain (CARD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal CARD, which interacts with the caspase-2 CARD, and a C-terminal Death domain (DD), which interacts with the DD of PIDD. In general, CARDs are DDs associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 94 matched cddid_all.tbl CDD cd08329 cd08329 260038 CARD_BIRC2_BIRC3 Caspase activation and recruitment domain found in Baculoviral IAP repeat-containing proteins, BIRC2 (c-IAP1) and BIRC3 (c-IAP2). Caspase activation and recruitment domain (CARD) similar to those found in Baculoviral IAP repeat (BIR)-containing protein 2 (BIRC2) or cellular Inhibitor of Apoptosis Protein 1 (c-IAP1), and BIRC3 (or c-IAP2). IAPs are anti-apoptotic proteins that contain at least one BIR domain. Most IAPs also contain a C-terminal RING domain. In addition, both BIRC2 and BIRC3 contain a CARD. BIRC2 and BIRC3, through their binding with TRAF (TNF receptor-associated factor) 2, are recruited to TNFR-1/2 signaling complexes, where they regulate caspase-8 activity. They also play important roles in pro-survival NF-kB signaling pathways. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 94 matched cddid_all.tbl CDD cd08330 cd08330 260039 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 81 matched cddid_all.tbl CDD cd08332 cd08332 260040 CARD_CASP2 Caspase activation and recruitment domain of Caspase-2. Caspase activation and recruitment domain (CARD) similar to that found in caspase-2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Caspase-2 (also known as ICH1, NEDD2, or CASP2) is one of the most evolutionarily conserved caspases, and plays a role in apoptosis, DNA damage response, cell cycle regulation, and tumor suppression. It is localized in the nucleus and exhibits properties of both an initiator and an effector caspase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 87 matched cddid_all.tbl CDD cd08333 cd08333 260041 DED_Caspase_8_r1 Death effector domain, repeat 1, of Caspase-8. Death effector domain (DED) found in caspase-8 (CASP8, FLICE), repeat 1. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-8 is an initiator of death receptor mediated apoptosis. Together with FADD, caspase-10, and the pseudo-caspase c-FLIP, it forms the death-inducing signaling complex (DISC), whose formation is triggered by the activation of type 1 tumor necrosis factor (TNF) receptors such as Fas, TNF receptor 1, and TRAIL receptor. Caspase-8 also plays many important non-apoptotic functions including roles in embryonic development, cell adhesion and motility, immune cell proliferation and differentiation, T-cell activation, and NFkappaB signaling. It contains two N-terminal DED domains and a C-terminal caspase domain. DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 82 matched cddid_all.tbl CDD cd08334 cd08334 260042 DED_Caspase_8_10_r2 Death effector domain, repeat 2, of initator caspases 8 and 10. Death Effector Domain (DED) found in caspase-8 and caspase-10, repeat 2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-8 and -10 are the initiators of death receptor mediated apoptosis, and they play partially redundant roles. Together with FADD and the pseudo-caspase c-FLIP, they form the death-inducing signaling complex (DISC), whose formation is triggered by the activation of type 1 tumor necrosis factor (TNF) receptors such as Fas, TNF receptor 1, and TRAIL receptor. Caspase-8 and -10 also play important functions in cell adhesion and motility. They contain two N-terminal DED domains and a C-terminal caspase domain. DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 83 matched cddid_all.tbl CDD cd08336 cd08336 260043 DED_FADD Death Effector Domain found in Fas-Associated via Death Domain. Death Effector Domain (DED) found in Fas-Associated via Death Domain (FADD). DEDs comprise a subfamily of the Death Domain (DD) superfamily. FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor and its DED recruits the initiator caspases 8 and 10 to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. 82 matched cddid_all.tbl CDD cd08337 cd08337 260044 DED_c-FLIP_r1 Death Effector Domain, repeat 1, of cellular FLICE-Inhibitory Protein. Death Effector Domain (DED), repeat 1, similar to that found in FLICE-inhibitory protein (c-FLIP/CASH, also known as Casper/iFLICE/FLAME-1/CLARP/MRIT/usurpin). c-FLIP is a catalytically inactive homolog of the initator procaspases-8 and -10. It negatively influences apoptotic signaling by interfering with the efficient formation of the Death Inducing Signalling Complex (DISC). At low levels, c-FLIP has been shown to enhance apoptotic signaling by allosterically activating caspase-8. As a modulator of the initiator caspases, c-FLIP regulates life and death in various types of cells and tissues. All members contain two N-terminal DEDs and a C-terminal pseudo-caspase domain. DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 80 matched cddid_all.tbl CDD cd08338 cd08338 260045 DED_PEA15 Death Effector Domain of Astrocyte phosphoprotein PEA-15. Death Effector Domain (DED) similar to that found in PEA-15 (Astrocyte phosphoprotein PEA-15). PEA-15 is a multifunctional phosphoprotein that modulates signaling pathways, like the ERK MAP kinase cascade by binding to ERK and changing its subcellular localization. It has been implicated in apoptosis, cell proliferation, and glucose metabolism. It does not possess enzymatic activity and mainly acts as an adaptor protein. PEA-15 contains an N-terminal DED domain and a C-terminal disordered region. DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. 84 matched cddid_all.tbl CDD cd08339 cd08339 176750 DED_DEDD-like Death Effector Domain of DEDD and DEDD2. Death Effector Domain (DED) found in DEDD and DEDD2. Both proteins have a single N-terminal DED and a long C-terminal portion with no known domains. DEDD has been shown to block mitotic progression by inhibiting Cdk1 and to be involved in regulating the insulin signaling cascade. DEDD and DEDD2 can bind to themselves, to each other, and to the two tandem DED-containing caspases, caspase-8 and -10. In general, DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. 97 matched cddid_all.tbl CDD cd08340 cd08340 260046 DED_c-FLIP_r2 Death Effector Domain, repeat 2, of cellular FLICE-Inhibitory Protein. Death Effector Domain (DED), repeat 2, similar to that found in cellular FLICE-inhibitory protein (c-FLIP/CASH, also known as Casper/iFLICE/FLAME-1/CLARP/MRIT/usurpin). c-FLIP is a catalytically inactive homolog of the initator procaspases-8 and -10. It negatively influences apoptotic signaling by interfering with the efficient formation of the Death Inducing Signalling Complex (DISC). At low levels, c-FLIP has been shown to enhance apoptotic signaling by allosterically activating caspase-8. As a modulator of the initiator caspases, c-FLIP regulates life and death in various types of cells and tissues. All members contain two N-terminal DEDs and a C-terminal pseudo-caspase domain. DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 81 matched cddid_all.tbl CDD cd08341 cd08341 260047 DED_Caspase_10_r1 Death effector domain, repeat 1, of Caspase-10. Death effector domain (DED) found in caspase-10, repeat 1. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-10 is an initiator of death receptor mediated apoptosis. Together with FADD, caspase-8 and the pseudo-caspase c-FLIP, it forms the death-inducing signaling complex (DISC), whose formation is triggered by the activation of type 1 tumor necrosis factor (TNF) receptors such as Fas, TNF receptor 1, and TRAIL receptor. It contains two N-terminal DED domains and a C-terminal caspase domain. DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 82 matched cddid_all.tbl CDD cd08342 cd08342 319930 HPPD_N_like N-terminal domain of 4-hydroxyphenylpyruvate dioxygenase (HPPD) and hydroxymandelate Synthase (HmaS). HppD and HmaS are non-heme iron-dependent dioxygenases, which modify a common substrate, 4-hydroxyphenylpyruvate (HPP), but yield different products. HPPD catalyzes the second reaction in tyrosine catabolism, the conversion of HPP to homogentisate (2,5-dihydroxyphenylacetic acid, HG). HmaS converts HPP to 4-hydroxymandelate, a committed step in the formation of hydroxyphenylglycerine, a structural component of nonproteinogenic macrocyclic peptide antibiotics, such as vancomycin. If the emphasis is on catalytic chemistry, HPPD and HmaS are classified as members of a large family of alpha-keto acid dependent mononuclear non-heme iron oxygenases most of which require Fe(II), molecular oxygen, and an alpha-keto acid (typically alpha-ketoglutarate) to either oxygenate or oxidize a third substrate. Both enzymes are exceptions in that they require two, instead of three, substrates, do not use alpha-ketoglutarate, and incorporate both atoms of dioxygen into the aromatic product. Both HPPD and HmaS exhibit duplicate beta barrel topology in their N- and C-terminal domains which share sequence similarity, suggestive of a gene duplication. Each protein has only one catalytic site located in at the C-terminal domain. This HPPD_N_like domain represents the N-terminal domain. 141 matched cddid_all.tbl CDD cd08343 cd08343 319931 ED_TypeI_classII_C C-terminal domain of type I, class II extradiol dioxygenases, catalytic domain. This family contains the C-terminal, catalytic domain of type I, class II extradiol dioxygenases. Dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. Two major groups of dioxygenases have been identified according to the cleavage site; extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon, whereas intradiol enzymes cleave the aromatic ring between two hydroxyl groups. Extradiol dioxygenases are classified into type I and type II enzymes. Type I extradiol dioxygenases include class I and class II enzymes. These two classes of enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. The extradiol dioxygenases represented in this family are type I, class II enzymes, and are composed of the N- and C-terminal domains of similar structure fold, resulting from an ancient gene duplication. The active site is located in a funnel-shaped space of the C-terminal domain. A catalytically essential metal, Fe(II) or Mn(II), presents in all the enzymes in this family. 132 matched cddid_all.tbl CDD cd08344 cd08344 319932 MhqB_like_N N-terminal domain of MhqB, a type I extradiol dioxygenase, and similar proteins. This subfamily contains the N-terminal, non-catalytic, domain of Burkholderia sp. NF100 MhqB and similar proteins. MhqB is a type I extradiol dioxygenase involved in the catabolism of methylhydroquinone, an intermediate in the degradation of fenitrothion. The purified enzyme has shown extradiol ring cleavage activity toward 3-methylcatechol. Fe2+ was suggested as a cofactor, the same as most other enzymes in the family. Burkholderia sp. NF100 MhqB is encoded on the plasmid pNF1. The type I family of extradiol dioxygenases contains two structurally homologous barrel-shaped domains at the N- and C-terminal. The active-site metal is located in the C-terminal barrel and plays an essential role in the catalytic mechanism. 112 matched cddid_all.tbl CDD cd08345 cd08345 319933 Fosfomycin_RP Fosfomycin resistant protein. This family contains three types of fosfomycin resistant protein. Fosfomycin inhibits the enzyme UDP-N-acetylglucosamine-3-enolpyruvyltransferase (MurA), which catalyzes the first committed step in bacterial cell wall biosynthesis. The three types of fosfomycin resistance proteins, employ different mechanisms to render fosfomycin [(1R,2S)-epoxypropylphosphonic acid] inactive. FosB catalyzes the addition of L-cysteine to the epoxide ring of fosfomycin. FosX catalyzes the addition of a water molecule to the C1 position of the antibiotic with inversion of configuration at C1. FosA catalyzes the addition of glutathione to the antibiotic fosfomycin, making it inactive. Catalytic activities of both FosX and FosA are Mn(II)-dependent, but FosB is activated by Mg(II). Fosfomycin resistant proteins are evolutionarily related to glyoxalase I and type I extradiol dioxygenases. 118 matched cddid_all.tbl CDD cd08346 cd08346 319934 PcpA_N_like N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins. The N-terminal domain of Sphingobium chlorophenolicum (formerly Sphingomonas chlorophenolica) 2,6-dichloro-p-hydroquinone1,2-dioxygenase (PcpA), and similar proteins. PcpA is a key enzyme in the pentachlorophenol (PCP) degradation pathway, catalyzing the conversion of 2,6-dichloro-p-hydroquinone to 2-chloromaleylacetate. This domain belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. 124 matched cddid_all.tbl CDD cd08347 cd08347 319935 PcpA_C_like C-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins. The C-terminal domain of Sphingobium chlorophenolicum (formerly Sphingomonas chlorophenolica) 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins. PcpA is a key enzyme in the pentachlorophenol (PCP) degradation pathway, catalyzing the conversion of 2,6-dichloro-p-hydroquinone to 2-chloromaleylacetate. This domain belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. 157 matched cddid_all.tbl CDD cd08348 cd08348 319936 BphC2-C3-RGP6_C_like The single-domain 2,3-dihydroxybiphenyl 1,2-dioxygenases. This subfamily contains Rhodococcus globerulus P6 BphC2-RGP6 and BphC3-RGP6, and similar proteins. BphC catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, yielding 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid. This is the third step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). This subfamily of BphCs belongs to the type I extradiol dioxygenase family, which require a metal in the active site in its catalytic mechanism. Most type I extradiol dioxygenases are activated by Fe(II). Polychlorinated biphenyl degrading bacteria demonstrate a multiplicity of BphCs. For example, three types of BphC enzymes have been found in Rhodococcus globerulus (BphC1-RGP6 - BphC3-RGP6), all three enzymes are type I extradiol dioxygenases. BphC2-RGP6 and BphC3-RGP6 are one-domain dioxygenases, which form hexamers. BphC1-RGP6 has an internal duplication, it is a two-domain dioxygenase which forms octamers, its two domains do not belong to this subfamily. 137 matched cddid_all.tbl CDD cd08349 cd08349 319937 BLMA_like Bleomycin binding protein (BLMA) and similar proteins. BLMA also called Bleomycin resistance protein, confers Bm resistance by directly binding to Bm. Bm is a glycopeptide antibiotic produced naturally by actinomycetes. It is a potent anti-cancer drug, which acts as a strong DNA-cutting agent, thereby causing cell death. BLMA is produced by actinomycetes to protect themselves against their own lethal compound. BLMA has two identically-folded subdomains, with the same alpha/beta fold; these two halves have no sequence similarity. BLMAs are dimers and each dimer binds to two Bm molecules at the Bm-binding pockets formed at the dimer interface; two Bm molecules are bound per dimer. BLMA belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. As for the larger superfamily, this family contains members with or without domain swapping. 114 matched cddid_all.tbl CDD cd08350 cd08350 319938 BLMT_like BLMT, a bleomycin resistance protein encoded on the transposon Tn5, and similar proteins. BLMT is a bleomycin (Bm) resistance protein, encoded by the ble gene on the transposon Tn5. This protein confers a survival advantage to Escherichia coli host cells. Bm is a glycopeptide antibiotic produced naturally by actinomycetes. It is a potent anti-cancer drug, which acts as a strong DNA-cutting agent, thereby causing cell death. BLMT has strong binding affinity to Bm and it protects against this lethal compound through drug sequestering. BLMT has two identically-folded subdomains, with the same alpha/beta fold; these two halves have no sequence similarity. BLMT is a dimer with two Bm-binding pockets formed at the dimer interface. 118 matched cddid_all.tbl CDD cd08351 cd08351 319939 ChaP_like ChaP, an enzyme involved in the biosynthesis of the antitumor agent chartreusin (cha), and similar proteins. ChaP is an enzyme involved in the biosynthesis of the potent antitumor agent chartreusin (cha). Cha is an aromatic polyketide glycoside produced by Streptomyces chartreusis. ChaP may play a role as a meta-cleavage dioxygenase in the oxidative rearrangement of the anthracyclic polyketide. ChaP belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. 118 matched cddid_all.tbl CDD cd08352 cd08352 319940 VOC_Bs_YwkD_like vicinal oxygen chelate (VOC) family protein Bacillus subtilis YwkD and similar proteins. uncharacterized subfamily of vicinal oxygen chelate (VOC) family contains Bacillus subtilis YwkD and similar proteins. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 123 matched cddid_all.tbl CDD cd08353 cd08353 319941 VOC_like uncharacterized subfamily of vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 142 matched cddid_all.tbl CDD cd08354 cd08354 319942 VOC_like uncharacterized subfamily of vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 122 matched cddid_all.tbl CDD cd08355 cd08355 319943 TioX_like Micromonospora sp. TioX and similar proteins. Micromonospora sp. TioX is encoded by a gene of the thiocoraline biosynthetic gene cluster. Thiocoraline is a thiodepsipeptide with potent antitumor activity. TioX may be involved in thiocoraline resistance or secretion. TioX belongs to vicinal oxygen chelate (VOC) superfamily that is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 123 matched cddid_all.tbl CDD cd08356 cd08356 319944 VOC_CChe_VCA0619_like uncharacterized subfamily of vicinal oxygen chelate (VOC) family. uncharacterized subfamily of vicinal oxygen chelate (VOC) family contains Vibrio cholerae VCA0619 and similar proteins. The VOC superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 113 matched cddid_all.tbl CDD cd08357 cd08357 319945 VOC_like uncharacterized subfamily of vicinal oxygen chelate (VOC) familyprotein, glyoxalase I, and type I ring-cleaving dioxygenases. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 124 matched cddid_all.tbl CDD cd08358 cd08358 319946 GLOD4_N N-terminal domain of human glyoxalase domain-containing protein 4 and similar proteins. Uncharacterized subfamily of the vicinal oxygen chelate (VOC) superfamily contains human glyoxalase domain-containing protein 4 and similar proteins. VOC is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 127 matched cddid_all.tbl CDD cd08359 cd08359 319947 VOC_like uncharacterized subfamily of vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 119 matched cddid_all.tbl CDD cd08360 cd08360 319948 MhqB_like_C C-terminal domain of Burkholderia sp. NF100 MhqB and similar proteins. This subfamily contains the C-terminal, catalytic, domain of Burkholderia sp. NF100 MhqB and similar proteins. MhqB is a type I extradiol dioxygenase involved in the catabolism of methylhydroquinone, an intermediate in the degradation of fenitrothion. The purified enzyme has shown extradiol ring cleavage activity toward 3-methylcatechol. Fe2+ was suggested as a cofactor, the same as most other enzymes in the family. Burkholderia sp. NF100 MhqB is encoded on the plasmid pNF1. The type I family of extradiol dioxygenases contains two structurally homologous barrel-shaped domains at the N- and C-terminal. The active-site metal is located in the C-terminal barrel and plays an essential role in the catalytic mechanism. 134 matched cddid_all.tbl CDD cd08361 cd08361 319949 PpCmtC_N N-terminal domain of 2,3-dihydroxy-p-cumate-3,4-dioxygenase (PpCmtC). This subfamily contains the N-terminal, non-catalytic, domain of PpCmtC. 2,3-dihydroxy-p-cumate-3,4-dioxygenase (CmtC of Pseudomonas putida F1) is a dioxygenase involved in the eight-step catabolism pathway of p-cymene. CmtC acts upon the reaction intermediate 2,3-dihydroxy-p-cumate, yielding 2-hydroxy-3-carboxy-6-oxo-7-methylocta-2,4-dienoate. The CmtC belongs to the type I family of extradiol dioxygenases. Fe2+ was suggested as a cofactor, same as other enzymes in the family. The type I family of extradiol dioxygenases contains two structurally homologous barrel-shaped domains at the N- and C-terminal. The active-site metal is located in the C-terminal barrel and plays an essential role in the catalytic mechanism. 124 matched cddid_all.tbl CDD cd08362 cd08362 319950 BphC5-RrK37_N_like N-terminal, non-catalytic, domain of BphC5 (2,3-dihydroxybiphenyl 1,2-dioxygenase) from Rhodococcus rhodochrous K37, and similar proteins. 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, the third step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). The enzyme contains a N-terminal and a C-terminal domain of similar structure fold, resulting from an ancient gene duplication. BphC belongs to the type I extradiol dioxygenase family, which requires a metal in the active site for its catalytic activity. Polychlorinated biphenyl degrading bacteria demonstrate multiplicity of BphCs. Bacterium Rhodococcus rhodochrous K37 has eight genes encoding BphC enzymes. This family includes the N-terminal domain of BphC5-RrK37. The crystal structure of the protein from Novosphingobium aromaticivorans has a Mn(II)in the active site, although most proteins of type I extradiol dioxygenases are activated by Fe(II). 120 matched cddid_all.tbl CDD cd08363 cd08363 319951 FosB fosfomycin resistant protein subfamily FosB. This subfamily family contains FosB, a fosfomycin resistant protein. FosB is a Mg(2+)-dependent L-cysteine thiol transferase. Fosfomycin inhibits the enzyme UDP-nacetylglucosamine-3-enolpyruvyltransferase (MurA), which catalyzes the first committed step in bacterial cell wall biosynthesis. FosB catalyzes the Mg(II) dependent addition of L-cysteine to the epoxide ring of fosfomycin, (1R,2S)-epoxypropylphosphonic acid, rendering it inactive. FosB is evolutionarily related to glyoxalase I and type I extradiol dioxygenases. 131 matched cddid_all.tbl CDD cd08364 cd08364 319952 FosX fosfomycin resistant protein subfamily FosX. This subfamily family contains FosX, a fosfomycin resistant protein. FosX is a Mn(II)-dependent fosfomycin-specific epoxide hydrolase. Fosfomycin inhibits the enzyme UDP-Nacetylglucosamine-3-enolpyruvyltransferase (MurA), which catalyzes the first committed step in bacterial cell wall biosynthesis. FosX catalyzes the addition of a water molecule to the C1 position of the antibiotic with inversion of the configuration at C1 in the presence of Mn(II). The hydrated fosfomycin loses the inhibition activity. FosX is evolutionarily related to glyoxalase I and type I extradiol dioxygenases. 130 matched cddid_all.tbl CDD cd08365 cd08365 176483 APC10-like1 APC10-like DOC1 domains of E3 ubiquitin ligases that mediate substrate ubiquitination. This model represens the APC10-like DOC1 domain of multi-domain proteins present in E3 ubiquitin ligases. E3 ubiquitin ligases mediate substrate ubiquitination (or ubiquitylation), a component of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. APC10/DOC1 domains such as those present in HECT (Homologous to the E6-AP Carboxyl Terminus) and Cullin-RING (Really Interesting New Gene) E3 ubiquitin ligase proteins, HECTD3, and CUL7, respectively, are also included here. CUL7 is a member of the Cullin-RING ligase family and functions as a molecular scaffold assembling a SCF-ROC1-like E3 ubiquitin ligase complex consisting of Skp1, CUL7, Fbx29 F-box protein, and ROC1 (RING-box protein 1) and promotes ubiquitination. CUL7 is a multi-domain protein with a C-terminal cullin domain that binds ROC1 and a centrally positioned APC10/DOC1 domain. HECTD3 contains a C-terminal HECT domain which contains the active site for ubiquitin transfer onto substrates, and an N-terminal APC10/DOC1 domain which is responsible for substrate recognition and binding. An APC10/DOC1 domain homolog is also present in HERC2 (HECT domain and RLD2), a large multi-domain protein with three RCC1-like domains (RLDs), additional internal domains including zinc finger ZZ-type and Cyt-b5 (Cytochrome b5-like Heme/Steroid binding) domains, and a C-terminal HECT domain. Recent studies have shown that the protein complex HERC2-RNF8 coordinates ubiquitin-dependent assembly of DNA repair factors on damaged chromosomes. Also included in this hierarchy is an uncharacterized APC10/DOC1-like domain found in a multi-domain protein, which also contains CUB, zinc finger ZZ-type, and EF-hand domains. The APC10/DOC1 domain forms a beta-sandwich structure that is related in architecture to the galactose-binding domain-like fold; their sequences are quite dissimilar, however, and are not included here. 131 matched cddid_all.tbl CDD cd08366 cd08366 176484 APC10 APC10 subunit of the anaphase-promoting complex (APC) that mediates substrate ubiquitination. This model represents the single domain protein APC10, a subunit of the anaphase-promoting complex (APC), which is a multi-subunit E3 ubiquitin ligase. E3 ubiquitin ligases mediate substrate ubiquitination (or ubiquitylation), a vital component of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. The APC (also known as the cyclosome), is a cell cycle-regulated E3 ubiquitin ligase that controls important transitions in mitosis and the G1 phase by ubiquitinating regulatory proteins, thereby targeting them for degradation. In mitosis, the APC initiates sister chromatid separation by ubiquitinating the anaphase inhibitor securin and triggers exit from mitosis by ubiquitinating cyclin B. The C-terminus of APC10 binds to CDC27/APC3, an APC subunit that contains multiple tetratrico peptide repeats. APC10 domains are homologous to the DOC1 domains present in the HECT (Homologous to the E6-AP Carboxyl Terminus) E3 ubiquitin ligase protein, and the Cullin-RING (Really Interesting New Gene) E3 ubiquitin ligase complex. The APC10/DOC1 domain forms a beta-sandwich structure that is related in architecture to the galactose-binding domain-like fold; their sequences are quite dissimilar, however, and are not included here. 139 matched cddid_all.tbl CDD cd08367 cd08367 176262 P53 P53 DNA-binding domain. P53 is a tumor suppressor gene product; mutations in p53 or lack of expression are found associated with a large fraction of all human cancers. P53 is activated by DNA damage and acts as a regulator of gene expression that ultimatively blocks progression through the cell cycle. P53 binds to DNA as a tetrameric transcription factor. In its inactive form, p53 is bound to the ring finger protein Mdm2, which promotes its ubiquitinylation and subsequent proteosomal degradation. Phosphorylation of p53 disrupts the Mdm2-p53 complex, while the stable and active p53 binds to regulatory regions of its target genes, such as the cyclin-kinase inhibitor p21, which complexes and inactivates cdk2 and other cyclin complexes. 179 matched cddid_all.tbl CDD cd08368 cd08368 259829 LIM LIM is a small protein-protein interaction domain, containing two zinc fingers. LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid). 53 matched cddid_all.tbl CDD cd08369 cd08369 187712 FMT_core Formyltransferase, catalytic core domain. Formyltransferase, catalytic core domain. The proteins of this superfamily contain a formyltransferase domain that hydrolyzes the removal of a formyl group from its substrate as part of a multistep transfer mechanism, and this alignment model represents the catalytic core of the formyltransferase domain. This family includes the following known members; Glycinamide Ribonucleotide Transformylase (GART), Formyl-FH4 Hydrolase, Methionyl-tRNA Formyltransferase, ArnA, and 10-Formyltetrahydrofolate Dehydrogenase (FDH). Glycinamide Ribonucleotide Transformylase (GART) catalyzes the third step in de novo purine biosynthesis, the transfer of a formyl group to 5'-phosphoribosylglycinamide. Formyl-FH4 Hydrolase catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate. Methionyl-tRNA Formyltransferase transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA, which plays important role in translation initiation. ArnA is required for the modification of lipid A with 4-amino-4-deoxy-l-arabinose (Ara4N) that leads to resistance to cationic antimicrobial peptides (CAMPs) and clinical antimicrobials such as polymyxin. 10-formyltetrahydrofolate dehydrogenase (FDH) catalyzes the conversion of 10-formyltetrahydrofolate, a precursor for nucleotide biosynthesis, to tetrahydrofolate. Members of this family are multidomain proteins. The formyltransferase domain is located at the N-terminus of FDH, Methionyl-tRNA Formyltransferase and ArnA, and at the C-terminus of Formyl-FH4 Hydrolase. Prokaryotic Glycinamide Ribonucleotide Transformylase (GART) is a single domain protein while eukaryotic GART is a trifunctional protein that catalyzes the second, third and fifth steps in de novo purine biosynthesis. 173 matched cddid_all.tbl CDD cd08370 cd08370 187727 FMT_C_like Carboxy-terminal domain of Formyltransferase and similar domains. This family represents the C-terminal domain of formyltransferase and similar proteins. This domain is found in a variety of enzymes with formyl transferase and alkyladenine DNA glycosylase activities. The proteins with formyltransferase function include methionyl-tRNA formyltransferase, ArnA, 10-formyltetrahydrofolate dehydrogenase and HypX proteins. Although most proteins with formyl transferase activity contain this C-terminal domain, prokaryotic glycinamide ribonucleotide transformylase (GART), a single domain protein, only contains the core catalytic domain. Thus, the C-terminal domain is not required for formyl transferase catalytic activity and may be involved in substrate binding. Some members of this family have shown nucleic acid binding capacity. The C-terminal domain of methionyl-tRNA formyltransferase is involved in tRNA binding. Alkyladenine DNA glycosylase is a distant member of this family with very low sequence similarity to other members. It catalyzes the first step in base excision repair (BER) by cleaving damaged DNA bases within double-stranded DNA to produce an abasic site and shows ability to bind to DNA. 73 matched cddid_all.tbl CDD cd08371 cd08371 187740 Lumazine_synthase-like lumazine synthase and riboflavin synthase; involved in the riboflavin (vitamin B2) biosynthetic pathway. This superfamily contains lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS) and riboflavin synthase (RS). Both enzymes play important roles in the riboflavin biosynthetic pathway. Riboflavin is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which are essential cofactors for the catalysis of a wide range of redox reactions. These cofactors are also involved in many other processes involving DNA repair, circadian time-keeping, light sensing, and bioluminescence. Riboflavin is biosynthesized in plants, fungi and certain microorganisms; as animals lack the necessary enzymes to produce this vitamin, they acquire it from dietary sources. In the final steps of the riboflavin biosynthetic pathway, LS catalyzes the condensation of the 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy- 2-butanone-4-phosphate to release water, inorganic phosphate and 6,7-dimethyl-8-ribityllumazine (DMRL), and RS catalyzes a dismutation of DMRL which yields riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. In the latter reaction, a four-carbon moiety is transferred between two DMRL molecules serving as donor and acceptor, respectively. Both the LS and RS catalyzed reactions are thermodynamically irreversible and can proceed in the absence of a catalyst. In bacteria and eukaryotes, there are two types of LS: type-I LS forms homo-pentamers or icosahedrally arranged dodecamers of pentamers, type-II LS forms decamers (dimers of pentamers). In archaea LSs and RSs appear to have diverged early in the evolution of archaea from a common ancestor. 129 matched cddid_all.tbl CDD cd08372 cd08372 197306 EEP Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily. This large superfamily includes the catalytic domain (exonuclease/endonuclease/phosphatase or EEP domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps proteins. 241 matched cddid_all.tbl CDD cd08373 cd08373 176019 C2A_Ferlin C2 domain first repeat in Ferlin. Ferlins are involved in vesicle fusion events. Ferlins and other proteins, such as Synaptotagmins, are implicated in facilitating the fusion process when cell membranes fuse together. There are six known human Ferlins: Dysferlin (Fer1L1), Otoferlin (Fer1L2), Myoferlin (Fer1L3), Fer1L4, Fer1L5, and Fer1L6. Defects in these genes can lead to a wide range of diseases including muscular dystrophy (dysferlin), deafness (otoferlin), and infertility (fer-1, fertilization factor-1). Structurally they have 6 tandem C2 domains, designated as (C2A-C2F) and a single C-terminal transmembrane domain, though there is a new study that disputes this and claims that there are actually 7 tandem C2 domains with another C2 domain inserted between C2D and C2E. In a subset of them (Dysferlin, Myoferlin, and Fer1) there is an additional conserved domain called DysF. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-II topology. 127 matched cddid_all.tbl CDD cd08374 cd08374 176020 C2F_Ferlin C2 domain sixth repeat in Ferlin. Ferlins are involved in vesicle fusion events. Ferlins and other proteins, such as Synaptotagmins, are implicated in facilitating the fusion process when cell membranes fuse together. There are six known human Ferlins: Dysferlin (Fer1L1), Otoferlin (Fer1L2), Myoferlin (Fer1L3), Fer1L4, Fer1L5, and Fer1L6. Defects in these genes can lead to a wide range of diseases including muscular dystrophy (dysferlin), deafness (otoferlin), and infertility (fer-1, fertilization factor-1). Structurally they have 6 tandem C2 domains, designated as (C2A-C2F) and a single C-terminal transmembrane domain, though there is a new study that disputes this and claims that there are actually 7 tandem C2 domains with another C2 domain inserted between C2D and C2E. In a subset of them (Dysferlin, Myoferlin, and Fer1) there is an additional conserved domain called DysF. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the sixth C2 repeat, C2E, and has a type-II topology. 133 matched cddid_all.tbl CDD cd08375 cd08375 176021 C2_Intersectin C2 domain present in Intersectin. A single instance of the C2 domain is located C terminally in the intersectin protein. Intersectin functions as a scaffolding protein, providing a link between the actin cytoskeleton and the components of endocytosis and plays a role in signal transduction. In addition to C2, intersectin contains several additional domains including: Eps15 homology domains, SH3 domains, a RhoGEF domain, and a PH domain. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. The members here have topology I. 136 matched cddid_all.tbl CDD cd08376 cd08376 176022 C2B_MCTP_PRT C2 domain second repeat found in Multiple C2 domain and Transmembrane region Proteins (MCTP). MCTPs are involved in Ca2+ signaling at the membrane. MCTP is composed of a variable N-terminal sequence, three C2 domains, two transmembrane regions (TMRs), and a short C-terminal sequence. It is one of four protein classes that are anchored to membranes via a transmembrane region; the others being synaptotagmins, extended synaptotagmins, and ferlins. MCTPs are the only membrane-bound C2 domain proteins that contain two functional TMRs. MCTPs are unique in that they bind Ca2+ but not phospholipids. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-II topology. 116 matched cddid_all.tbl CDD cd08377 cd08377 176023 C2C_MCTP_PRT C2 domain third repeat found in Multiple C2 domain and Transmembrane region Proteins (MCTP). MCTPs are involved in Ca2+ signaling at the membrane. The cds in this family contain multiple C2 domains as well as a C-terminal PRT domain. It is one of four protein classes that are anchored to membranes via a transmembrane region; the others being synaptotagmins, extended synaptotagmins, and ferlins. MCTPs are the only membrane-bound C2 domain proteins that contain two functional TMRs. MCTPs are unique in that they bind Ca2+ but not phospholipids. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the third C2 repeat, C2C, and has a type-II topology. 119 matched cddid_all.tbl CDD cd08378 cd08378 176024 C2B_MCTP_PRT_plant C2 domain second repeat found in Multiple C2 domain and Transmembrane region Proteins (MCTP); plant subset. MCTPs are involved in Ca2+ signaling at the membrane. Plant-MCTPs are composed of a variable N-terminal sequence, four C2 domains, two transmembrane regions (TMRs), and a short C-terminal sequence. It is one of four protein classes that are anchored to membranes via a transmembrane region; the others being synaptotagmins, extended synaptotagmins, and ferlins. MCTPs are the only membrane-bound C2 domain proteins that contain two functional TMRs. MCTPs are unique in that they bind Ca2+ but not phospholipids. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-II topology. 121 matched cddid_all.tbl CDD cd08379 cd08379 176025 C2D_MCTP_PRT_plant C2 domain fourth repeat found in Multiple C2 domain and Transmembrane region Proteins (MCTP); plant subset. MCTPs are involved in Ca2+ signaling at the membrane. Plant-MCTPs are composed of a variable N-terminal sequence, four C2 domains, two transmembrane regions (TMRs), and a short C-terminal sequence. It is one of four protein classes that are anchored to membranes via a transmembrane region; the others being synaptotagmins, extended synaptotagmins, and ferlins. MCTPs are the only membrane-bound C2 domain proteins that contain two functional TMRs. MCTPs are unique in that they bind Ca2+ but not phospholipids. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the fourth C2 repeat, C2D, and has a type-II topology. 126 matched cddid_all.tbl CDD cd08380 cd08380 176026 C2_PI3K_like C2 domain present in phosphatidylinositol 3-kinases (PI3Ks). C2 domain present in all classes of PI3Ks. PI3Ks (AKA phosphatidylinositol (PtdIns) 3-kinases) regulate cell processes such as cell growth, differentiation, proliferation, and motility. PI3Ks work on phosphorylation of phosphatidylinositol, phosphatidylinositide (4)P (PtdIns (4)P),2 or PtdIns(4,5)P2. Specifically they phosphorylate the D3 hydroxyl group of phosphoinositol lipids on the inositol ring. There are 3 classes of PI3Ks based on structure, regulation, and specificity. All classes contain a C2 domain, a PIK domain, and a kinase catalytic domain. In addition some PI3Ks contain a Ras-binding domain and/or a p85-binding domain. Class II PI3Ks contain both of these as well as a PX domain, and a C-terminal C2 domain containing a nuclear localization signal. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains members with the first C2 repeat, C2A, and a type-I topology, as well as some with a single C2 repeat. 156 matched cddid_all.tbl CDD cd08381 cd08381 176027 C2B_PI3K_class_II C2 domain second repeat present in class II phosphatidylinositol 3-kinases (PI3Ks). There are 3 classes of PI3Ks based on structure, regulation, and specificity. All classes contain a N-terminal C2 domain, a PIK domain, and a kinase catalytic domain. Unlike class I and class III, class II PI3Ks have additionally a PX domain and a C-terminal C2 domain containing a nuclear localization signal both of which bind phospholipids though in a slightly different fashion. PI3Ks (AKA phosphatidylinositol (PtdIns) 3-kinases) regulate cell processes such as cell growth, differentiation, proliferation, and motility. PI3Ks work on phosphorylation of phosphatidylinositol, phosphatidylinositide (4)P (PtdIns (4)P),2 or PtdIns(4,5)P2. Specifically they phosphorylate the D3 hydroxyl group of phosphoinositol lipids on the inositol ring. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-I topology. 122 matched cddid_all.tbl CDD cd08382 cd08382 176028 C2_Smurf-like C2 domain present in Smad ubiquitination-related factor (Smurf)-like proteins. A single C2 domain is found in Smurf proteins, C2-WW-HECT-domain E3s, which play an important role in the downregulation of the TGF-beta signaling pathway. Smurf proteins also regulate cell shape, motility, and polarity by degrading small guanosine triphosphatases (GTPases). C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. Members here have type-II topology. 123 matched cddid_all.tbl CDD cd08383 cd08383 176029 C2A_RasGAP C2 domain (first repeat) of Ras GTPase activating proteins (GAPs). RasGAPs suppress Ras function by enhancing the GTPase activity of Ras proteins resulting in the inactive GDP-bound form of Ras. In this way it can control cellular proliferation and differentiation. The proteins here all contain either a single C2 domain or two tandem C2 domains, a Ras-GAP domain, and a pleckstrin homology (PH)-like domain. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. Members here have a type-I topology. 117 matched cddid_all.tbl CDD cd08384 cd08384 176030 C2B_Rabphilin_Doc2 C2 domain second repeat present in Rabphilin and Double C2 domain. Rabphilin is found neurons and in neuroendrocrine cells, while Doc2 is found not only in the brain but in tissues, including mast cells, chromaffin cells, and osteoblasts. Rabphilin and Doc2s share highly homologous tandem C2 domains, although their N-terminal structures are completely different: rabphilin contains an N-terminal Rab-binding domain (RBD),7 whereas Doc2 contains an N-terminal Munc13-1-interacting domain (MID). C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-I topology. 133 matched cddid_all.tbl CDD cd08385 cd08385 176031 C2A_Synaptotagmin-1-5-6-9-10 C2A domain first repeat present in Synaptotagmins 1, 5, 6, 9, and 10. Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Synaptotagmin 1, a member of class 1 synaptotagmins, is located in the brain and endocranium and localized to the synaptic vesicles and secretory granules. It functions as a Ca2+ sensor for fast exocytosis as do synaptotagmins 5, 6, and 10. It is distinguished from the other synaptotagmins by having an N-glycosylated N-terminus. Synaptotagmins 5, 6, and 10, members of class 3 synaptotagmins, are located primarily in the brain and localized to the active zone and plasma membrane. They is distinguished from the other synaptotagmins by having disulfide bonds at its N-terminus. Synaptotagmin 6 also regulates the acrosome reaction, a unique Ca2+-regulated exocytosis, in sperm. Synaptotagmin 9, a class 5 synaptotagmins, is located in the brain and localized to the synaptic vesicles. It is thought to be a Ca2+-sensor for dense-core vesicle exocytosis. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-I topology. 124 matched cddid_all.tbl CDD cd08386 cd08386 176032 C2A_Synaptotagmin-7 C2A domain first repeat present in Synaptotagmin 7. Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Synaptotagmin 7, a member of class 2 synaptotagmins, is located in presynaptic plasma membranes in neurons, dense-core vesicles in endocrine cells, and lysosomes in fibroblasts. It has been shown to play a role in regulation of Ca2+-dependent lysosomal exocytosis in fibroblasts and may also function as a vesicular Ca2+-sensor. It is distinguished from the other synaptotagmins by having over 12 splice forms. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-I topology. 125 matched cddid_all.tbl CDD cd08387 cd08387 176033 C2A_Synaptotagmin-8 C2A domain first repeat present in Synaptotagmin 8. Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-I topology. 124 matched cddid_all.tbl CDD cd08388 cd08388 176034 C2A_Synaptotagmin-4-11 C2A domain first repeat present in Synaptotagmins 4 and 11. Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Synaptotagmins 4 and 11, class 4 synaptotagmins, are located in the brain. Their functions are unknown. They are distinguished from the other synaptotagmins by having and Asp to Ser substitution in their C2A domains. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-I topology. 128 matched cddid_all.tbl CDD cd08389 cd08389 176035 C2A_Synaptotagmin-14_16 C2A domain first repeat present in Synaptotagmins 14 and 16. Synaptotagmin 14 and 16 are membrane-trafficking proteins in specific tissues outside the brain. Both of these contain C-terminal tandem C2 repeats, but only Synaptotagmin 14 has an N-terminal transmembrane domain and a putative fatty-acylation site. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium and this is indeed the case here. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-I topology. 124 matched cddid_all.tbl CDD cd08390 cd08390 176036 C2A_Synaptotagmin-15-17 C2A domain first repeat present in Synaptotagmins 15 and 17. Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. It is thought to be involved in the trafficking and exocytosis of secretory vesicles in non-neuronal tissues and is Ca2+ independent. Human synaptotagmin 15 has 2 alternatively spliced forms that encode proteins with different C-termini. The larger, SYT15a, contains a N-terminal TM region, a putative fatty-acylation site, and 2 tandem C terminal C2 domains. The smaller, SYT15b, lacks the C-terminal portion of the second C2 domain. Unlike most other synaptotagmins it is nearly absent in the brain and rather is found in the heart, lungs, skeletal muscle, and testis. Synaptotagmin 17 is located in the brain, kidney, and prostate and is thought to be a peripheral membrane protein. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-I topology. 123 matched cddid_all.tbl CDD cd08391 cd08391 176037 C2A_C2C_Synaptotagmin_like C2 domain first and third repeat in Synaptotagmin-like proteins. Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains either the first or third repeat in Synaptotagmin-like proteins with a type-I topology. 121 matched cddid_all.tbl CDD cd08392 cd08392 176038 C2A_SLP-3 C2 domain first repeat present in Synaptotagmin-like protein 3. All Slp members basically share an N-terminal Slp homology domain (SHD) and C-terminal tandem C2 domains (named the C2A domain and the C2B domain) with the SHD and C2 domains being separated by a linker sequence of various length. SHD of Slp (except for the Slp4-SHD) function as a specific Rab27A/B-binding domain. In addition to Slp, rabphilin, Noc2, and Munc13-4 also function as Rab27-binding proteins. Little is known about the expression or localization of Slp3. The C2A domain of Slp3 is Ca2+ dependent. It has been demonstrated that Slp3 promotes dense-core vesicle exocytosis. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-I topology. 128 matched cddid_all.tbl CDD cd08393 cd08393 176039 C2A_SLP-1_2 C2 domain first repeat present in Synaptotagmin-like proteins 1 and 2. All Slp members basically share an N-terminal Slp homology domain (SHD) and C-terminal tandem C2 domains (named the C2A domain and the C2B domain) with the SHD and C2 domains being separated by a linker sequence of various length. Slp1/JFC1 and Slp2/exophilin 4 promote granule docking to the plasma membrane. Additionally, their C2A domains are both Ca2+ independent, unlike Slp3 and Slp4/granuphilin which are Ca2+ dependent. It is thought that SHD (except for the Slp4-SHD) functions as a specific Rab27A/B-binding domain. In addition to Slps, rabphilin, Noc2, and Munc13-4 also function as Rab27-binding proteins. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-I topology. 125 matched cddid_all.tbl CDD cd08394 cd08394 176040 C2A_Munc13 C2 domain first repeat in Munc13 (mammalian uncoordinated) proteins. C2-like domains are thought to be involved in phospholipid binding in a Ca2+ independent manner in both Unc13 and Munc13. Caenorabditis elegans Unc13 has a central domain with sequence similarity to PKC, which includes C1 and C2-related domains. Unc13 binds phorbol esters and DAG with high affinity in a phospholipid manner. Mutations in Unc13 results in abnormal neuronal connections and impairment in cholinergic neurotransmission in the nematode. Munc13 is the mammalian homolog which are expressed in the brain. There are 3 isoforms (Munc13-1, -2, -3) and are thought to play a role in neurotransmitter release and are hypothesized to be high-affinity receptors for phorbol esters. Unc13 and Munc13 contain both C1 and C2 domains. There are two C2 related domains present, one central and one at the carboxyl end. Munc13-1 contains a third C2-like domain. Munc13 interacts with syntaxin, synaptobrevin, and synaptotagmin suggesting a role for these as scaffolding proteins. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-II topology. 127 matched cddid_all.tbl CDD cd08395 cd08395 176041 C2C_Munc13 C2 domain third repeat in Munc13 (mammalian uncoordinated) proteins. C2-like domains are thought to be involved in phospholipid binding in a Ca2+ independent manner in both Unc13 and Munc13. Caenorabditis elegans Unc13 has a central domain with sequence similarity to PKC, which includes C1 and C2-related domains. Unc13 binds phorbol esters and DAG with high affinity in a phospholipid manner. Mutations in Unc13 results in abnormal neuronal connections and impairment in cholinergic neurotransmission in the nematode. Munc13 is the mammalian homolog which are expressed in the brain. There are 3 isoforms (Munc13-1, -2, -3) and are thought to play a role in neurotransmitter release and are hypothesized to be high-affinity receptors for phorbol esters. Unc13 and Munc13 contain both C1 and C2 domains. There are two C2 related domains present, one central and one at the carboxyl end. Munc13-1 contains a third C2-like domain. Munc13 interacts with syntaxin, synaptobrevin, and synaptotagmin suggesting a role for these as scaffolding proteins.C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the third C2 repeat, C2C, and has a type-II topology. 120 matched cddid_all.tbl CDD cd08397 cd08397 176042 C2_PI3K_class_III C2 domain present in class III phosphatidylinositol 3-kinases (PI3Ks). PI3Ks (AKA phosphatidylinositol (PtdIns) 3-kinases) regulate cell processes such as cell growth, differentiation, proliferation, and motility. PI3Ks work on phosphorylation of phosphatidylinositol, phosphatidylinositide (4)P (PtdIns (4)P),2 or PtdIns(4,5)P2. Specifically they phosphorylate the D3 hydroxyl group of phosphoinositol lipids on the inositol ring. There are 3 classes of PI3Ks based on structure, regulation, and specificity. All classes contain a C2 domain, a PIK domain, and a kinase catalytic domain. These are the only domains identified in the class III PI3Ks present in this cd. In addition some PI3Ks contain a Ras-binding domain and/or a p85-binding domain. Class II PI3Ks contain both of these as well as a PX domain, and a C-terminal C2 domain containing a nuclear localization signal. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-I topology. 159 matched cddid_all.tbl CDD cd08398 cd08398 176043 C2_PI3K_class_I_alpha C2 domain present in class I alpha phosphatidylinositol 3-kinases (PI3Ks). PI3Ks (AKA phosphatidylinositol (PtdIns) 3-kinases) regulate cell processes such as cell growth, differentiation, proliferation, and motility. PI3Ks work on phosphorylation of phosphatidylinositol, phosphatidylinositide (4)P (PtdIns (4)P),2 or PtdIns(4,5)P2. Specifically they phosphorylate the D3 hydroxyl group of phosphoinositol lipids on the inositol ring. There are 3 classes of PI3Ks based on structure, regulation, and specificity. All classes contain a C2 domain, a PIK domain, and a kinase catalytic domain. The members here are class I, alpha isoform PI3Ks and contain both a Ras-binding domain and a p85-binding domain. Class II PI3Ks contain both of these as well as a PX domain, and a C-terminal C2 domain containing a nuclear localization signal. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. Members have a type-I topology. 158 matched cddid_all.tbl CDD cd08399 cd08399 176044 C2_PI3K_class_I_gamma C2 domain present in class I gamma phosphatidylinositol 3-kinases (PI3Ks). PI3Ks (AKA phosphatidylinositol (PtdIns) 3-kinases) regulate cell processes such as cell growth, differentiation, proliferation, and motility. PI3Ks work on phosphorylation of phosphatidylinositol, phosphatidylinositide (4)P (PtdIns (4)P),2 or PtdIns(4,5)P2. Specifically they phosphorylate the D3 hydroxyl group of phosphoinositol lipids on the inositol ring. There are 3 classes of PI3Ks based on structure, regulation, and specificity. All classes contain a C2 domain, a PIK domain, and a kinase catalytic domain. The members here are class I, gamma isoform PI3Ks and contain both a Ras-binding domain and a p85-binding domain. Class II PI3Ks contain both of these as well as a PX domain, and a C-terminal C2 domain containing a nuclear localization signal. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. Members have a type-I topology. 178 matched cddid_all.tbl CDD cd08400 cd08400 176045 C2_Ras_p21A1 C2 domain present in RAS p21 protein activator 1 (RasA1). RasA1 is a GAP1 (GTPase activating protein 1), a Ras-specific GAP member, which suppresses Ras function by enhancing the GTPase activity of Ras proteins resulting in the inactive GDP-bound form of Ras. In this way it can control cellular proliferation and differentiation. RasA1 contains a C2 domain, a Ras-GAP domain, a pleckstrin homology (PH)-like domain, a SH3 domain, and 2 SH2 domains. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. Members here have a type-I topology. 126 matched cddid_all.tbl CDD cd08401 cd08401 176046 C2A_RasA2_RasA3 C2 domain first repeat present in RasA2 and RasA3. RasA2 and RasA3 are GAP1s (GTPase activating protein 1s ), Ras-specific GAP members, which suppresses Ras function by enhancing the GTPase activity of Ras proteins resulting in the inactive GDP-bound form of Ras. In this way it can control cellular proliferation and differentiation. RasA2 and RasA3 are both inositol 1,3,4,5-tetrakisphosphate-binding proteins and contain an N-terminal C2 domain, a Ras-GAP domain, a pleckstrin-homology (PH) domain which localizes it to the plasma membrane, and Bruton's Tyrosine Kinase (BTK) a zinc binding domain. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-I topology. 121 matched cddid_all.tbl CDD cd08402 cd08402 176047 C2B_Synaptotagmin-1 C2 domain second repeat present in Synaptotagmin 1. Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Synaptotagmin 1, a member of the class 1 synaptotagmins, is located in the brain and endocranium and localized to the synaptic vesicles and secretory granules. It functions as a Ca2+ sensor for fast exocytosis. It, like synaptotagmin-2, has an N-glycosylated N-terminus. Synaptotagmin 4, a member of class 4 synaptotagmins, is located in the brain. It functions are unknown. It, like synaptotagmin-11, has an Asp to Ser substitution in its C2A domain. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-I topology. 136 matched cddid_all.tbl CDD cd08403 cd08403 176048 C2B_Synaptotagmin-3-5-6-9-10 C2 domain second repeat present in Synaptotagmins 3, 5, 6, 9, and 10. Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Synaptotagmin 3, a member of class 3 synaptotagmins, is located in the brain and localized to the active zone and plasma membrane. It functions as a Ca2+ sensor for fast exocytosis. It, along with synaptotagmins 5,6, and 10, has disulfide bonds at its N-terminus. Synaptotagmin 9, a class 5 synaptotagmins, is located in the brain and localized to the synaptic vesicles. It is thought to be a Ca2+-sensor for dense-core vesicle exocytosis. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-I topology. 134 matched cddid_all.tbl CDD cd08404 cd08404 176049 C2B_Synaptotagmin-4 C2 domain second repeat present in Synaptotagmin 4. Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Synaptotagmin 4, a member of class 4 synaptotagmins, is located in the brain. It functions are unknown. It, like synaptotagmin-11, has an Asp to Ser substitution in its C2A domain. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-I topology. 136 matched cddid_all.tbl CDD cd08405 cd08405 176050 C2B_Synaptotagmin-7 C2 domain second repeat present in Synaptotagmin 7. Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Synaptotagmin 7, a member of class 2 synaptotagmins, is located in presynaptic plasma membranes in neurons, dense-core vesicles in endocrine cells, and lysosomes in fibroblasts. It has been shown to play a role in regulation of Ca2+-dependent lysosomal exocytosis in fibroblasts and may also function as a vesicular Ca2+-sensor. It is distinguished from the other synaptotagmins by having over 12 splice forms. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-I topology. 136 matched cddid_all.tbl CDD cd08406 cd08406 176051 C2B_Synaptotagmin-12 C2 domain second repeat present in Synaptotagmin 12. Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Synaptotagmin 12, a member of class 6 synaptotagmins, is located in the brain. It functions are unknown. It, like synaptotagmins 8 and 13, do not have any consensus Ca2+ binding sites. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-I topology. 136 matched cddid_all.tbl CDD cd08407 cd08407 176052 C2B_Synaptotagmin-13 C2 domain second repeat present in Synaptotagmin 13. Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Synaptotagmin 13, a member of class 6 synaptotagmins, is located in the brain. It functions are unknown. It, like synaptotagmins 8 and 12, does not have any consensus Ca2+ binding sites. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-I topology. 138 matched cddid_all.tbl CDD cd08408 cd08408 176053 C2B_Synaptotagmin-14_16 C2 domain second repeat present in Synaptotagmins 14 and 16. Synaptotagmin 14 and 16 are membrane-trafficking proteins in specific tissues outside the brain. Both of these contain C-terminal tandem C2 repeats, but only Synaptotagmin 14 has an N-terminal transmembrane domain and a putative fatty-acylation site. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium and this is indeed the case here. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-I topology. 138 matched cddid_all.tbl CDD cd08409 cd08409 176054 C2B_Synaptotagmin-15 C2 domain second repeat present in Synaptotagmin 15. Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. It is thought to be involved in the trafficking and exocytosis of secretory vesicles in non-neuronal tissues and is Ca2+ independent. Human synaptotagmin 15 has 2 alternatively spliced forms that encode proteins with different C-termini. The larger, SYT15a, contains a N-terminal TM region, a putative fatty-acylation site, and 2 tandem C terminal C2 domains. The smaller, SYT15b, lacks the C-terminal portion of the second C2 domain. Unlike most other synaptotagmins it is nearly absent in the brain and rather is found in the heart, lungs, skeletal muscle, and testis. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-I topology. 137 matched cddid_all.tbl CDD cd08410 cd08410 176055 C2B_Synaptotagmin-17 C2 domain second repeat present in Synaptotagmin 17. Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Synaptotagmin 17 is located in the brain, kidney, and prostate and is thought to be a peripheral membrane protein. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-I topology. 135 matched cddid_all.tbl CDD cd08411 cd08411 176103 PBP2_OxyR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily. OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The C-terminal domain also contains the redox-active cysteines that mediate the redox-dependent conformational switch. Thus, the interaction between the OxyR-tetramer and DNA is notably different between the oxidized and reduced forms. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 200 matched cddid_all.tbl CDD cd08412 cd08412 176104 PBP2_PAO1_like The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily. This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of N2 fixing bacteria, and synthesis of virulence factors, to a name a few. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 198 matched cddid_all.tbl CDD cd08413 cd08413 176105 PBP2_CysB_like The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 198 matched cddid_all.tbl CDD cd08414 cd08414 176106 PBP2_LTTR_aromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 197 matched cddid_all.tbl CDD cd08415 cd08415 176107 PBP2_LysR_opines_like The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. LysR is the transcriptional activator of lysA gene encoding diaminopimelate decarboxylase, an enzyme that catalyses the decarboxylation of diaminopimelate to produce lysine. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 196 matched cddid_all.tbl CDD cd08416 cd08416 176108 PBP2_MdcR The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold. This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate- binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 199 matched cddid_all.tbl CDD cd08417 cd08417 176109 PBP2_Nitroaromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 200 matched cddid_all.tbl CDD cd08418 cd08418 176110 PBP2_TdcA The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold. TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 201 matched cddid_all.tbl CDD cd08419 cd08419 176111 PBP2_CbbR_RubisCO_like The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold. CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 197 matched cddid_all.tbl CDD cd08420 cd08420 176112 PBP2_CysL_like C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold. CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 201 matched cddid_all.tbl CDD cd08421 cd08421 176113 PBP2_LTTR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 198 matched cddid_all.tbl CDD cd08422 cd08422 176114 PBP2_CrgA_like The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA and its related homologs, contains the type 2 periplasmic binding domain. This CD includes the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA and its related homologs. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 197 matched cddid_all.tbl CDD cd08423 cd08423 176115 PBP2_LTTR_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 200 matched cddid_all.tbl CDD cd08425 cd08425 176116 PBP2_CynR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold. CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 197 matched cddid_all.tbl CDD cd08426 cd08426 176117 PBP2_LTTR_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 199 matched cddid_all.tbl CDD cd08427 cd08427 176118 PBP2_LTTR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 195 matched cddid_all.tbl CDD cd08428 cd08428 176119 PBP2_IciA_ArgP The C-terminal substrate binding domain of LysR-type transcriptional regulator, ArgP (IciA), for arginine exporter (ArgO); contains the type 2 periplasmic binding fold. The inhibitor of chromosomal replication (iciA) protein encoded by Mycobacterium tuberculosis, which is implicated in chromosome replication initiation in vitro, has been identified as arginine permease (ArgP), a LysR-type transcriptional regulator for arginine outward transport, based on the same amino sequence and similar DNA binding targets. Arp has been shown to regulate various targets including DnaA (replication), ArgO (arginine export), dapB (lysine biosynthesis), and gdhA (glutamate biosynthesis). With abundant nutrition, ArgP activates the DnaA gene (to increase replication) and the ArgO (to export redundant molecules). However, when nutrition supply is limited, it is suggested that ArgP might function as an inhibitor of chromosome replication in order to slow replication. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 195 matched cddid_all.tbl CDD cd08429 cd08429 176120 PBP2_NhaR The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold. NhaR is a positive regulator of the LysR family and is known to be an activator of the nhaA gene encoding a Na(+)/H(+) antiporter. In Escherichia coli, NhaA is the vital antiporter that protects against high sodium stress, and it is essential for growth in high sodium levels, while NhaB becomes essential only if NhaA is not available. The nhaA gene of nhaAR operon is induced by monovalent cations. The nhaR of the operon activates nhaAR, as well as the osmC transcription which is induced at elevated osmolarity. OsmC is transcribed from the two overlapping promoters (osmCp1 and osmP2) and that NhaR is shown to activate only the expression of osmCp1. NhaR also activates the transcription of the pgaABCD operon which is required for production of the biofilm adhesion, poly-beta-1,6-N-acetyl-d-glucosamine (PGA) .Thus, it is suggested that NhaR has an extended role in promoting bacterial survival. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 204 matched cddid_all.tbl CDD cd08430 cd08430 176121 PBP2_IlvY The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic binding fold. In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-independent manner. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 199 matched cddid_all.tbl CDD cd08431 cd08431 176122 PBP2_HupR The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold. HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 195 matched cddid_all.tbl CDD cd08432 cd08432 176123 PBP2_GcdR_TrpI_HvrB_AmpR_like The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 194 matched cddid_all.tbl CDD cd08433 cd08433 176124 PBP2_Nac The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold. The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut. Hence, NAC allows the coupling of sigma70-RNAP dependent operons to the sigma54-RNAP dependent NTR system. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 198 matched cddid_all.tbl CDD cd08434 cd08434 176125 PBP2_GltC_like The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold. GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 195 matched cddid_all.tbl CDD cd08435 cd08435 176126 PBP2_GbpR The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold. Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 201 matched cddid_all.tbl CDD cd08436 cd08436 176127 PBP2_LTTR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 194 matched cddid_all.tbl CDD cd08437 cd08437 176128 PBP2_MleR The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold. MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 198 matched cddid_all.tbl CDD cd08438 cd08438 176129 PBP2_CidR The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 197 matched cddid_all.tbl CDD cd08439 cd08439 176130 PBP2_LrhA_like The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold. This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 185 matched cddid_all.tbl CDD cd08440 cd08440 176131 PBP2_LTTR_like_4 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 197 matched cddid_all.tbl CDD cd08441 cd08441 176132 PBP2_MetR The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold. MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mechanisms. In Escherichia coli and Salmonella enterica serovar Typhimurium, MetJ and MetR regulate the expression of methionine biosynthetic genes. The MetJ repressor negatively regulates the E. coli met genes, except for metH. Several of these genes are also under the positive control of MetR with homocysteine as a co-inducer. In Bacillus subtilis, the met genes are controlled by S-box termination-antitermination system. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 198 matched cddid_all.tbl CDD cd08442 cd08442 176133 PBP2_YofA_SoxR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold. YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 193 matched cddid_all.tbl CDD cd08443 cd08443 176134 PBP2_CysB The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 198 matched cddid_all.tbl CDD cd08444 cd08444 176135 PBP2_Cbl The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold. Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonation enzyme. Both Cbl and CysB require expression of the tau and ssu genes. Like many other members of the LTTR family, the Cbl is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 198 matched cddid_all.tbl CDD cd08445 cd08445 176136 PBP2_BenM_CatM_CatR The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold. This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes of the ortho-pathway required for benzoate catabolism: muconate lactonizing enzyme I, muconolactone isomerase, and catechol 1,2-dioxygenase. CatR normally responds to benzoate and cis,cis-muconate, an inducer molecule, to activate transcription of the catBCA operon, whose gene products convert benzoate to catechol. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the substrate-binding domains from ionotropic glutamate receptors, LysR-like transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 203 matched cddid_all.tbl CDD cd08446 cd08446 176137 PBP2_Chlorocatechol The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tfdA and tfdB gene expression. These genes encode enzymes for the conversion of 2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenol. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 198 matched cddid_all.tbl CDD cd08447 cd08447 176138 PBP2_LTTR_aromatics_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 198 matched cddid_all.tbl CDD cd08448 cd08448 176139 PBP2_LTTR_aromatics_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 197 matched cddid_all.tbl CDD cd08449 cd08449 176140 PBP2_XapR The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold. In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 197 matched cddid_all.tbl CDD cd08450 cd08450 176141 PBP2_HcaR The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold. HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 196 matched cddid_all.tbl CDD cd08451 cd08451 176142 PBP2_BudR The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 199 matched cddid_all.tbl CDD cd08452 cd08452 176143 PBP2_AlsR The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold. AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 197 matched cddid_all.tbl CDD cd08453 cd08453 176144 PBP2_IlvR The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold. The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 200 matched cddid_all.tbl CDD cd08456 cd08456 176145 PBP2_LysR The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold. LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functional roles including amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to a name a few. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 196 matched cddid_all.tbl CDD cd08457 cd08457 176146 PBP2_OccR The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 196 matched cddid_all.tbl CDD cd08458 cd08458 176147 PBP2_NocR The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 196 matched cddid_all.tbl CDD cd08459 cd08459 176148 PBP2_DntR_NahR_LinR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold. This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate of the oxidative degradation of the aromatic ring in soil bacteria. LinR positively regulates expression of the genes (linD and linE) encoding enzymes for gamma-hexachlorocyclohexane (a haloorganic insecticide) degradation. Expression of linD and linE are induced by their substrates, 2,5-dichlorohydroquinone (2,5-DCHQ) and chlorohydroquinone (CHQ). The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 201 matched cddid_all.tbl CDD cd08460 cd08460 176149 PBP2_DntR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 200 matched cddid_all.tbl CDD cd08461 cd08461 176150 PBP2_DntR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 198 matched cddid_all.tbl CDD cd08462 cd08462 176151 PBP2_NodD The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional regulators that regulates the expression of nodulation (nod) genes; contains the type 2 periplasmic binding fold. The nodulation (nod) genes in soil bacteria play important roles in the development of nodules. nod genes are involved in synthesis of Nod factors that are required for bacterial entry into root hairs. Thirteen nod genes have been identified and are classified into five transcription units: nodD, nodABCIJ, nodFEL, nodMNT, and nodO. NodD is negatively auto-regulates its own expression of nodD gene, while other nod genes are inducible and positively regulated by NodD in the presence of flavonoids released by plant roots. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 200 matched cddid_all.tbl CDD cd08463 cd08463 176152 PBP2_DntR_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 203 matched cddid_all.tbl CDD cd08464 cd08464 176153 PBP2_DntR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 200 matched cddid_all.tbl CDD cd08465 cd08465 176154 PBP2_ToxR The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold. In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 200 matched cddid_all.tbl CDD cd08466 cd08466 176155 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold. LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse model of Salmonella. In Vibrio cholerae, LeuO is involved in control of biofilm formation and in the stringent response. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 200 matched cddid_all.tbl CDD cd08467 cd08467 176156 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold. Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 200 matched cddid_all.tbl CDD cd08468 cd08468 176157 PBP2_Pa0477 The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold. LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 202 matched cddid_all.tbl CDD cd08469 cd08469 176158 PBP2_PnbR The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold. PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 221 matched cddid_all.tbl CDD cd08470 cd08470 176159 PBP2_CrgA_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 1. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 197 matched cddid_all.tbl CDD cd08471 cd08471 176160 PBP2_CrgA_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 2. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 201 matched cddid_all.tbl CDD cd08472 cd08472 176161 PBP2_CrgA_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 3. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 202 matched cddid_all.tbl CDD cd08473 cd08473 176162 PBP2_CrgA_like_4 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 4. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 202 matched cddid_all.tbl CDD cd08474 cd08474 176163 PBP2_CrgA_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 5. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 202 matched cddid_all.tbl CDD cd08475 cd08475 176164 PBP2_CrgA_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 6. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 199 matched cddid_all.tbl CDD cd08476 cd08476 176165 PBP2_CrgA_like_7 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 7. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 197 matched cddid_all.tbl CDD cd08477 cd08477 176166 PBP2_CrgA_like_8 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 8. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 197 matched cddid_all.tbl CDD cd08478 cd08478 176167 PBP2_CrgA The C-terminal substrate binding domain of LysR-type transcriptional regulator CrgA, contains the type 2 periplasmic binding domain. This CD represents the substrate binding domain of LysR-type transcriptional regulator (LTTR) CrgA. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis further showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 199 matched cddid_all.tbl CDD cd08479 cd08479 176168 PBP2_CrgA_like_9 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 9. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 198 matched cddid_all.tbl CDD cd08480 cd08480 176169 PBP2_CrgA_like_10 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator CrgA-like, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type transcriptional regulator (LTTR) CrgA-like 10. The LTTRs are acting as both auto-repressors and activators of target promoters, controlling operons involved in a wide variety of cellular processes such as amino acid biosynthesis, CO2 fixation, antibiotic resistance, degradation of aromatic compounds, nodule formation of nitrogen-fixing bacteria, and synthesis of virulence factors, to name a few. In contrast to the tetrameric form of other LTTRs, CrgA from Neisseria meningitides assembles into an octameric ring, which can bind up to four 63-bp DNA oligonucleotides. Phylogenetic cluster analysis showed that the CrgA-like regulators form a subclass of the LTTRs that function as octamers. The CrgA is an auto-repressor of its own gene and activates the expression of the mdaB gene which coding for an NADPH-quinone reductase and that its action is increased by MBL (alpha-methylene-gamma-butyrolactone), an inducer of NADPH-quinone oxidoreductase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 198 matched cddid_all.tbl CDD cd08481 cd08481 176170 PBP2_GcdR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold. GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 194 matched cddid_all.tbl CDD cd08482 cd08482 176171 PBP2_TrpI The C-terminal substrate binding domain of LysR-type transcriptional regulator TrpI, which is involved in control of tryptophan synthesis, contains type 2 periplasmic binding fold. TrpI and indoleglycerol phosphate (InGP), are required to activate transcription of the trpBA, the genes for tryptophan synthase. The trpBA is induced by the InGp substrate, rather than by tryptophan, but the exact mechanism of the activation event is not known. This substrate-binding domain of TrpI shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 195 matched cddid_all.tbl CDD cd08483 cd08483 176172 PBP2_HvrB The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold. The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 190 matched cddid_all.tbl CDD cd08484 cd08484 176173 PBP2_LTTR_beta_lactamase The C-terminal substrate-domain of LysR-type transcriptional regulators for beta-lactamase genes, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators, BlaA and AmpR, that are involved in control of the expression of beta-lactamase genes. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. BlaA (a constitutive class A penicillinase) belongs to the LysR family of transcriptional regulators, while BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin-binding protein, but it does not act as a beta-lactamase. AmpR regulates the expression of beta-lactamases in many enterobacterial strains and many other gram-negative bacilli. In contrast to BlaA, AmpR acts an activator only in the presence of the beta-lactam inducer. In the absence of the inducer, AmpR acts as a repressor. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 189 matched cddid_all.tbl CDD cd08485 cd08485 176174 PBP2_ClcR The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold. In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 198 matched cddid_all.tbl CDD cd08486 cd08486 176175 PBP2_CbnR The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of LysR-type regulator CbnR which is involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 198 matched cddid_all.tbl CDD cd08487 cd08487 176176 PBP2_BlaA The C-terminal substrate-binding domain of LysR-type trnascriptional regulator BlaA which involved in control of the beta-lactamase gene expression; contains the type 2 periplasmic binding fold. This CD represents the C-terminal substrate binding domain of LysR-type transcriptional regulator, BlaA, that involved in control of the expression of beta-lactamase genes, blaA and blaB. Beta-lactamases are responsible for bacterial resistance to beta-lactam antibiotics such as penicillins. The blaA gene is located just upstream of blaB in the opposite direction and regulates the expression of the blaB. BlaA also negatively auto-regulates the expression of its own gene, blaA. BlaA (a constitutive class A penicllinase) belongs to the LysR family of transcriptional regulators, whereas BlaB (an inducible class C cephalosporinase or AmpC) can be referred to as a penicillin binding protein but it does not act as a beta-lactamase. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 189 matched cddid_all.tbl CDD cd08488 cd08488 176177 PBP2_AmpR The C-terminal substrate domain of LysR-type transcriptional regulator AmpR that involved in control of the expression of beta-lactamase gene ampC, contains the type 2 periplasmic binding fold. AmpR acts as a transcriptional activator by binding to a DNA region immediately upstream of the ampC promoter. In the absence of a beta-lactam inducer, AmpR represses the synthesis of beta-lactamase, whereas expression is induced in the presence of a beta-lactam inducer. The AmpD, AmpG, and AmpR proteins are involved in the induction of AmpC-type beta-lactamase (class C) which produced by enterobacterial strains and many other gram-negative bacilli. The activation of ampC by AmpR requires ampG for induction or high-level expression of AmpC. It is probable that the AmpD and AmpG work together to modulate the ability of AmpR to activate ampC expression. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 191 matched cddid_all.tbl CDD cd08489 cd08489 173854 PBP2_NikA The substrate-binding component of an ABC-type nickel import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain of nickel transport system, which functions in the import of nickel and in the control of chemotactic response away from nickel. The ATP-binding cassette (ABC) type nickel transport system is comprised of five subunits NikABCDE: the two pore-forming integral inner membrane proteins NikB and NikC; the two inner membrane-associated proteins with ATPase activity NikD and NikE; and the periplasmic nickel binding NikA, the initial nickel receptor. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 488 matched cddid_all.tbl CDD cd08490 cd08490 173855 PBP2_NikA_DppA_OppA_like_3 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 470 matched cddid_all.tbl CDD cd08491 cd08491 173856 PBP2_NikA_DppA_OppA_like_12 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 473 matched cddid_all.tbl CDD cd08492 cd08492 173857 PBP2_NikA_DppA_OppA_like_15 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 484 matched cddid_all.tbl CDD cd08493 cd08493 173858 PBP2_DppA_like The substrate-binding component of an ABC-type dipeptide import system contains the type 2 periplasmic binding fold. This family represents the substrate-binding domain of an ATP-binding cassette (ABC)-type dipeptide import system. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 482 matched cddid_all.tbl CDD cd08494 cd08494 173859 PBP2_NikA_DppA_OppA_like_6 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 448 matched cddid_all.tbl CDD cd08495 cd08495 173860 PBP2_NikA_DppA_OppA_like_8 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 482 matched cddid_all.tbl CDD cd08496 cd08496 173861 PBP2_NikA_DppA_OppA_like_9 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA can bind peptides of a wide range of lengths (2-35 amino-acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 454 matched cddid_all.tbl CDD cd08497 cd08497 173862 MbnE-like Methanobactin MbnE, a periplasmic binding protein of the TonB-dependent transport system, and similar proteins. Methanobactin MbnE is a periplasmic binding protein that is involved in the TonB-dependent transport system in bacteria. The function of MbnE is to bind to methanobactin and transport it across the periplasmic space to the TonB receptor on the outer membrane of the cell. The binding of MbnE to methanobactin allows the bacteria to scavenge iron from the environment, which is essential for many biological processes. The evolutionary relationship between MbnE and the ABC transport system is not clear, as they are distinct systems that have evolved separately. However, it is possible that there have been some functional convergences between these systems in terms of nutrient uptake and transport. 491 matched cddid_all.tbl CDD cd08498 cd08498 173863 PBP2_NikA_DppA_OppA_like_2 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 481 matched cddid_all.tbl CDD cd08499 cd08499 173864 PBP2_Ylib_like The substrate-binding component of an uncharacterized ABC-type peptide import system Ylib contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding component of an uncharacterized ATP-binding cassette (ABC)-type peptide transport system YliB. Although the ligand specificity of Ylib protein is not known, it shares significant sequence similarity to the ABC-type dipeptide and oligopeptide binding proteins. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 474 matched cddid_all.tbl CDD cd08500 cd08500 173865 PBP2_NikA_DppA_OppA_like_4 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 499 matched cddid_all.tbl CDD cd08501 cd08501 173866 PBP2_Lpqw The substrate-binding domain of mycobacterial lipoprotein Lpqw contains type 2 periplasmic binding fold. LpqW is one of key players in synthesis and transport of the unique components of the mycobacterial cell wall which is a complex structure rich in two related lipoglycans, the phosphatidylinositol mannosides (PIMs) and lipoarabinomannans (LAMs). Lpqw is a highly conserved lipoprotein that transport intermediates from a pathway for mature PIMs production into a pathway for LAMs biosynthesis, thus controlling the relative abundance of these two essential components of cell wall. LpqW is thought to have been adapted by the cell-wall biosynthesis machinery of mycobacteria and other closely related pathogens, evolving to play an important role in PIMs/LAMs biosynthesis. Most of periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the LpqW protein. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 486 matched cddid_all.tbl CDD cd08502 cd08502 173867 PBP2_NikA_DppA_OppA_like_16 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 472 matched cddid_all.tbl CDD cd08503 cd08503 173868 PBP2_NikA_DppA_OppA_like_17 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 460 matched cddid_all.tbl CDD cd08504 cd08504 173869 PBP2_OppA The substrate-binding component of an ABC-type oligopetide import system contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding component of an ATP-binding cassette (ABC)-type oligopeptide transport system comprised of 5 subunits. The transport system OppABCDEF contains two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 498 matched cddid_all.tbl CDD cd08505 cd08505 173870 PBP2_NikA_DppA_OppA_like_18 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 528 matched cddid_all.tbl CDD cd08506 cd08506 173871 PBP2_clavulanate_OppA2 The substrate-binding domain of an oligopeptide binding protein (OppA2) from the biosynthesis pathway of the beta-lactamase inhibitor clavulanic acid contains the type 2 periplasmic binding fold. Clavulanic acid (CA), a clinically important beta-lactamase inhibitor, is one of a family of clavams produced as secondary metabolites by fermentation of Streptomyces clavuligeru. The biosynthesis of CA proceeds via multiple steps from the precursors, glyceraldehyde-3-phosphate and arginine. CA possesses a characteristic (3R,5R) stereochemistry essential for reaction with penicillin-binding proteins and beta-lactamases. Two genes (oppA1 and oppA2) in the clavulanic acid gene cluster encode oligopeptide-binding proteins that are required for CA biosynthesis. OppA1/2 is involved in the binding and transport of peptides across the cell membrane of Streptomyces clavuligerus. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 466 matched cddid_all.tbl CDD cd08507 cd08507 173872 PBP2_SgrR_like The C-terminal solute-binding domain of DNA-binding transcriptional regulator SgrR is related to the ABC-type oligopeptide-binding proteins and contains the type 2 periplasmic-binding fold. A novel family of SgrR transcriptional regulator contains a two-domain structure with an N terminal DNA-binding domain of the winged helix family and a C-terminal solute-binding domain. The C-terminal domain shows strong homology with the ABC-type oligopeptide-binding protein family, a member of the type 2 periplasmic-binding fold protein (PBP2) superfamily that also includes the C-terminal substrate-binding domain of LysR-type transcriptional regulators. SgrR (SugaR transport-related Regulator) is negatively autoregulated and activates transcription of divergent operon SgrS, which encodes a small RNA required for recovery from glucose-phosphate stress. Hence, the small RNA SgrS and SgrR, the transcription factor that controls sgrS expression, are both required for recovery from glucose-phosphate stress. Most of periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 448 matched cddid_all.tbl CDD cd08508 cd08508 173873 PBP2_NikA_DppA_OppA_like_1 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 470 matched cddid_all.tbl CDD cd08509 cd08509 173874 PBP2_TmCBP_oligosaccharides_like The substrate binding domain of a cellulose-binding protein from Thermotoga maritima contains the type 2 periplasmic binding fold. This family represents the substrate-binding domain of a cellulose-binding protein from the hyperthermophilic bacterium Thermotoga maritima (TmCBP) and its closest related proteins. TmCBP binds a variety of lengths of beta-1,4-linked glucose oligomers, ranging from two sugar rings (cellobiose) to five (cellopentose). TmCBP is structurally homologous to domains I and III of the ATP-binding cassette (ABC)-type oligopeptide-binding proteins and thus belongs to the type 2 periplasmic binding fold protein (PBP2) superfamily. The type 2 periplasmic binding proteins are soluble ligand-binding components of ABC or tripartite ATP-independent transporters and chemotaxis systems. Members of the PBP2 superfamily function in uptake of a variety of metabolites in bacteria such as amino acids, carbohydrate, ions, and polyamines. Ligands are then transported across the cytoplasmic membrane energized by ATP hydrolysis or electrochemical ion gradient. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 509 matched cddid_all.tbl CDD cd08510 cd08510 173875 PBP2_Lactococcal_OppA_like The substrate binding component of an ABC-type lactococcal OppA-like transport system contains. This family represents the substrate binding domain of an ATP-binding cassette (ABC)-type oligopeptide import system from Lactococcus lactis and other gram-positive bacteria, as well as its closet homologs from gram-negative bacteria. Oligopeptide-binding protein (OppA) from Lactococcus lactis can bind peptides of length from 4 to at least 35 residues without sequence preference. The oligopeptide import system OppABCDEF is consisting of five subunits: two homologous integral membrane proteins OppB and OppF that form the translocation pore; two homologous nucleotide-binding domains OppD and OppF that drive the transport process through binding and hydrolysis of ATP; and the substrate-binding protein or receptor OppA that determines the substrate specificity of the transport system. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and also is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 516 matched cddid_all.tbl CDD cd08511 cd08511 173876 PBP2_NikA_DppA_OppA_like_5 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This family represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 467 matched cddid_all.tbl CDD cd08512 cd08512 173877 PBP2_NikA_DppA_OppA_like_7 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 476 matched cddid_all.tbl CDD cd08513 cd08513 173878 PBP2_thermophilic_Hb8_like The substrate-binding component of ABC-type thermophilic oligopeptide-binding protein Hb8-like import systems, contains the type 2 periplasmic binding fold. This family includes the substrate-binding domain of an ABC-type oligopeptide-binding protein Hb8 from Thermus thermophilius and its closest homologs from other bacteria. The structural topology of this substrate-binding domain is similar to those of DppA from Escherichia coli and OppA from Salmonella typhimurium, and thus belongs to the type 2 periplasmic binding fold protein (PBP2) superfamily. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. The type 2 periplasmic binding proteins are soluble ligand-binding components of ABC or tripartite ATP-independent transporters and chemotaxis systems. Members of the PBP2 superfamily function in uptake of a variety of metabolites in bacteria such as amino acids, carbohydrate, ions, and polyamines. Ligands are then transported across the cytoplasmic membrane energized by ATP hydrolysis or electrochemical ion gradient. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 482 matched cddid_all.tbl CDD cd08514 cd08514 173879 PBP2_AppA_like The substrate-binding component of the oligopeptide-binding protein, AppA, from Bacillus subtilis contains the type 2 periplasmic-binding fold. This family represents the substrate-binding domain of the oligopeptide-binding protein, AppA, from Bacillus subtilis and its closest homologs from other bacteria and archaea. Bacillus subtilis has three ABC-type peptide transport systems, a dipeptide-binding protein (DppA) and two oligopeptide-binding proteins (OppA and AppA) with overlapping specificity. The dipeptide (DppA) and oligopeptide (OppA) binding proteins differ in several ways. The DppA binds dipeptides and some tripeptides and also is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 483 matched cddid_all.tbl CDD cd08515 cd08515 173880 PBP2_NikA_DppA_OppA_like_10 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 460 matched cddid_all.tbl CDD cd08516 cd08516 173881 PBP2_NikA_DppA_OppA_like_11 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 457 matched cddid_all.tbl CDD cd08517 cd08517 173882 PBP2_NikA_DppA_OppA_like_13 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 480 matched cddid_all.tbl CDD cd08518 cd08518 173883 PBP2_NikA_DppA_OppA_like_19 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 464 matched cddid_all.tbl CDD cd08519 cd08519 173884 PBP2_NikA_DppA_OppA_like_20 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 469 matched cddid_all.tbl CDD cd08520 cd08520 173885 PBP2_NikA_DppA_OppA_like_21 The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. 468 matched cddid_all.tbl CDD cd08521 cd08521 176056 C2A_SLP C2 domain first repeat present in Synaptotagmin-like proteins. All Slp members basically share an N-terminal Slp homology domain (SHD) and C-terminal tandem C2 domains (named the C2A domain and the C2B domain) with the SHD and C2 domains being separated by a linker sequence of various length. Slp1/JFC1 and Slp2/exophilin 4 promote granule docking to the plasma membrane. Additionally, their C2A domains are both Ca2+ independent, unlike the case in Slp3 and Slp4/granuphilin in which their C2A domains are Ca2+ dependent. It is thought that SHD (except for the Slp4-SHD) functions as a specific Rab27A/B-binding domain. In addition to Slps, rabphilin, Noc2, and Munc13-4 also function as Rab27-binding proteins. It has been demonstrated that Slp3 and Slp4/granuphilin promote dense-core vesicle exocytosis. Slp5 mRNA has been shown to be restricted to human placenta and liver suggesting a role in Rab27A-dependent membrane trafficking in specific tissues. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-I topology. 123 matched cddid_all.tbl CDD cd08523 cd08523 260080 Reeler_cohesin_like Domains similar to the eukaryotic reeler domain and bacterial cohesins. This diverse family summarizes a set of distantly related domains, as revealed by structural similarity 128 matched cddid_all.tbl CDD cd08524 cd08524 197341 Reelin_subrepeat_like Tandem repeat subunit of reelin and related proteins. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the subrepeats, which directly contact each other in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns. 144 matched cddid_all.tbl CDD cd08525 cd08525 197342 Reelin_subrepeat_1 N-terminal subrepeat in the tandem repeat unit of reelin and related proteins. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the N-terminal subrepeat, which directly contacts the C-terminal subrepeat and the EGF domain in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). 161 matched cddid_all.tbl CDD cd08526 cd08526 197343 Reelin_subrepeat_2 C-terminal subrepeat in the tandem repeat unit of reelin and related proteins. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the C-terminal subrepeat, which directly contacts the N-terminal subrepeat and the EGF domain in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). 152 matched cddid_all.tbl CDD cd08528 cd08528 270867 STKc_Nek10 Catalytic domain of the Serine/Threonine Kinase, Never In Mitosis gene A (NIMA)-related kinase 10. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. No function has yet been ascribed to Nek10. The gene encoding Nek10 is a putative causative gene for breast cancer; it is located within a breast cancer susceptibility loci on chromosome 3p24. Nek10 is one in a family of 11 different Neks (Nek1-11) that are involved in cell cycle control. The Nek family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 270 matched cddid_all.tbl CDD cd08529 cd08529 270868 STKc_FA2-like Catalytic domain of the Serine/Threonine Kinases, Chlamydomonas reinhardtii FA2 and similar proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Chlamydomonas reinhardtii FA2 was discovered in a genetic screen for deflagellation-defective mutants. It is essential for basal-body/centriole-associated microtubule severing, and plays a role in cell cycle progression. No cellular function has yet been ascribed to CNK4. The Chlamydomonas reinhardtii FA2-like subfamily belongs to the (NIMA)-related kinase (Nek) family, which includes seven different Chlamydomonas Neks (CNKs 1-6 and Fa2). This subfamily contains FA2 and CNK4. The Nek family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd08530 cd08530 270869 STKc_CNK2-like Catalytic domain of the Serine/Threonine Kinases, Chlamydomonas reinhardtii CNK2 and similar proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Chlamydomonas reinhardtii CNK2 has both cilliary and cell cycle functions. It influences flagellar length through promoting flagellar disassembly, and it regulates cell size, through influencing the size threshold at which cells commit to mitosis. This subfamily belongs to the (NIMA)-related kinase (Nek) family, which includes seven different Chlamydomonas Neks (CNKs 1-6 and Fa2). This subfamily includes CNK1, and -2. The Nek family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd08531 cd08531 188877 SAM_PNT-ERG_FLI-1 Sterile alpha motif (SAM)/Pointed domain of ERG (Ets related gene) and FLI-1 (Friend leukemia integration 1) transcription factors. SAM Pointed domain of ERG/FLI-1 subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. The ERG and FLI regulators are involved in endothelial cell differentiation, bone morphogenesis and neural crest development. They are proto-oncogenes implicated in cancer development such as myeloid leukemia, Ewing's sarcoma and erythroleukemia. Members of this subfamily are potential targets for cancer therapy. 75 matched cddid_all.tbl CDD cd08532 cd08532 188878 SAM_PNT-PDEF-like Sterile alpha motif (SAM)/Pointed domain of prostate-derived ETS factor. SAM Pointed domain of PDEF-like (Prostate-Derived ETS Factor) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. In human males this activator is highly expressed in the prostate gland and enhances androgen-mediated activation of the PSA promoter though interaction with the DNA binding domain of androgen receptor. PDEF may play a role in prostate cancer development as well as in goblet cell formation and mucus production in the epithelial lining of respiratory and intestinal tracts. 81 matched cddid_all.tbl CDD cd08533 cd08533 188879 SAM_PNT-ETS-1,2 Sterile alpha motif (SAM)/Pointed domain of ETS-1,2 family. SAM Pointed domain of ETS-1,2 family of transcriptional activators is a protein-protein interaction domain. It carries a kinase docking site and mediates interaction between ETS transcriptional activators and protein kinases. This group of transcriptional factors is involved in the Ras/MAP kinase signaling pathway. MAP kinases phosphorylate the transcription factors. Phosphorylated factors then recruit coactivators and enhance transactivation. Members of this group play a role in regulation of different embryonic developmental processes. ETS-1,2 transcriptional activators are proto-oncogenes involved in malignant transformation and tumor progression. They are potential molecular targets for selective cancer therapy. 71 matched cddid_all.tbl CDD cd08534 cd08534 176084 SAM_PNT-GABP-alpha Sterile alpha motif (SAM)/Pointed domain of GA-binding protein (GABP) alpha chain. SAM Pointed domain of GA-binding protein (GABP) alpha subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. This type of transcriptional regulators forms heterotetramers containing two alpha and two beta subunits. It interacts with GA repeats (purine rich repeats). GABP transcriptional factors control gene expression in cell cycle control, apoptosis, and cellular respiration. GABP participates in regulation of transmembrane receptors and key hormones especially in myeloid cells and at the neuromuscular junction. 89 matched cddid_all.tbl CDD cd08535 cd08535 176085 SAM_PNT-Tel_Yan Sterile alpha motif (SAM)/Pointed domain of Tel/Yan protein. SAM Pointed domain of Tel (Translocation, Ets, Leukemia)/Yan subfamily of ETS transcriptional repressors is a protein-protein interaction domain. SAM Pointed domains of this type of regulators can interact with each other, forming head-to-tail homodimers or homooligomers, and/or interact with SAM Pointed domains of another subfamily of ETS factors forming heterodimers. The oligomeric form is able to block transcription of target genes and is involved in MAPK signaling. They participate in regulation of different processes during embryoniv development including hematopoietic differentiation and eye development. Tel/Yan transcriptional factors are frequent targets of chromosomal translocations resulting in fusions of SAM domain with new neighboring genes. Such chimeric proteins were found in different tumors. Members of this subfamily are potential targets for cancer therapy. 68 matched cddid_all.tbl CDD cd08536 cd08536 176086 SAM_PNT-Mae Sterile alpha motif (SAM)/Pointed domain of Mae protein homolog. Mae (Modulator of the Activity of ETS) subfamily represents a group of SAM Pointed monodomain proteins. SAM Pointed domain is a protein-protein interaction domain. It can interact with other SAM pointed domains forming head-to-tail heterodimers and also provides a kinase docking site. For example, in Drosophila Mae is required for facilitating phosphorylation of the Yan factor and for blocking phosphorylation of the ETS-2 regulator. Mae interacts with the SAM Pointed domains of Yan and ETS-2. Binding enhances access of the kinase to the Yan phosphorylation site by providing a kinase docking site, or inhibits phosphorylation of ETS-2 by blocking its docking site. This type of factors participates in regulation of kinase signaling particularly during embryogenesis. 66 matched cddid_all.tbl CDD cd08537 cd08537 188880 SAM_PNT-ESE-1-like Sterile alpha motif (SAM)/Pointed domain of ESE-1 like ETS transcriptional regulators. SAM Pointed domain of ESE-1-like (Epithelium-Specific ETS) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. SAM Pointed domain of ESE-1 provides a potential docking site for signaling kinase Pak1 in humans. ESE-1 factors are involved in regulation of gene expression in different types of epithelial cells. ESE-1 is expressed in many different organs including intestine, stomach, pancreas, lungs, kidneys, and prostate. The DNA binding consensus motif for ESE-1 consists of a purine-rich GGA[AT] core sequence. The expression profile of these factors is altered in epithelial cancers if compared to normal tissues. Members of this subfamily are potential targets for cancer therapy. 81 matched cddid_all.tbl CDD cd08538 cd08538 188881 SAM_PNT-ESE-2-like Sterile alpha motif (SAM)/Pointed domain of ESE-2 like ETS transcriptional regulators. SAM Pointed domain of ESE-2-like (Epithelium-Specific ETS) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. It can act as a major transactivator by providing a potential docking site for co-activators. ESE-2 factors are involved in regulation of gene expression in a variety of epithelial (glandular and secretory) cells. ESE-2 mRNA was found in skin keratinocytes, salivary gland, mammary gland, stomach, prostate, and kidneys. The DNA binding consensus motif for ESE-2 consists of a GGA core and AT-rich flanks. The expression profiles of these factors are altered in epithelial cancers. Members of this subfamily are potential targets for cancer therapy. 84 matched cddid_all.tbl CDD cd08539 cd08539 188882 SAM_PNT-ESE-3-like Sterile alpha motif (SAM)/Pointed domain of ESE-3 like ETS transcriptional regulators. SAM Pointed domain of ESE-3-like (Epithelium-Specific ETS) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. It can act as a major transactivator by providing a potential docking site for co-activators. The ESE-3 transcriptional activator is involved in regulation of glandular epithelium differentiation through the MAP kinase signaling cascade. It is found to be expressed in glandular epithelium of prostate, pancreas, salivary gland, and trachea. Additionally, ESE-3 is differentially expressed during monocyte-derived dendritic cells development. DNA binding consensus motif for ESE-3 consists of purine-rich GGAA/T core sequence. The expression profiles of these factors are altered in epithelial cancers. Members of this subfamily are potential targets for cancer therapy. 78 matched cddid_all.tbl CDD cd08540 cd08540 176090 SAM_PNT-ERG Sterile alpha motif (SAM)/Pointed domain of ERG transcription factor. SAM Pointed domain of ERG subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. It may participate in formation of homodimers or heterodimers with ETS-2, Fli-1, ER81, and Pu-1. However, dimeric forms are inactive and SAM Pointed domain is not essential for dimerization, since ER81 and Pu-1 do not have it. In mouse, a regulator of this type binds the ESET histone H3-specific methyltransferase (human homolog is SETDB1), which leads to modification of the local chromatin structure through histone methylation. ERG regulators are involved in endothelial cell differentiation, bone morphogenesis and neural crest development. The Erg gene is a proto-oncogene. It is a target of chromosomal translocations resulting in fusions with other neighboring genes. Chimeric proteins were found in solid tumors such as myeloid leukemia or Ewing's sarcoma. Members of this subfamily are potential targets for cancer therapy. 75 matched cddid_all.tbl CDD cd08541 cd08541 188883 SAM_PNT-FLI-1 Sterile alpha motif (SAM)/Pointed domain of friend leukemia integration 1 transcription activator. SAM Pointed domain of FLI-1 (Friend Leukemia Integration) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. The FLI-1 protein participates in regulation of cellular differentiation, proliferation, and survival. The Fli-1 gene was initially described in Friend virus-induced erythroleukemias as a site for virus integration. It is highly expressed in hematopoietic tissues and at lower level in lungs, heart, and ovaries. Fli-1 is a proto-oncogene implicated in Ewing's sarcoma and erythroleukemia. Members of this subfamily are potential targets for cancer therapy. 91 matched cddid_all.tbl CDD cd08542 cd08542 176092 SAM_PNT-ETS-1 Sterile alpha motif (SAM)/Pointed domain of ETS-1. SAM Pointed domain of ETS-1 subfamily of ETS transcriptional activators is a protein-protein interaction domain. The ETS-1 activator is regulated by phosphorylation. It contains a docking site for the ERK2 MAP (Mitogen Activated Protein) kinase, while the ERK2 phosphorylation site is located in the N-terminal disordered region upstream of the SAM Pointed domain. Mutations of the kinase docking site residues inhibit phosphorylation. ETS-1 activators play a role in a number of different physiological processes, and they are expressed during embryonic development, including blood vessel formation, hematopoietic, lymphoid, neuronal and osteogenic differentiation. The Ets-1 gene is a proto-oncogene involved in progression of different tumors (including breast cancer, meningioma, and prostate cancer). Members of this subfamily are potential molecular targets for selective cancer therapy. 88 matched cddid_all.tbl CDD cd08543 cd08543 188884 SAM_PNT-ETS-2 Sterile alpha motif (SAM)/Pointed domain of ETS-2. SAM Pointed domain of ETS-2 subfamily of ETS transcriptional regulators is a protein-protein interaction domain. It contains a docking site for Cdk10 (cyclin-dependent kinase 10), a member of the Cdc2 kinase family. The interaction between ETS-2 and Cdk10 kinase inhibits ETS-2 transactivation activity in mammals. ETS-2 is also regulated by ERK2 MAP kinase. ETS-2, which is phosphorylated by ERK2, can interact with coactivators and enhance transactivation. ETS-2 transcriptional activators are involved in embryonic development and cell cycle control. The Ets-2 gene is a proto-oncogene. It is overexpressed in breast and prostate cancer cells and its overexpression is necessary for transformation of such cells. Members of ETS-2 subfamily are potential molecular targets for selective cancer therapy. 89 matched cddid_all.tbl CDD cd08544 cd08544 260081 Reeler Reeler, the N-terminal domain of reelin, F-spondin, and a variety of other proteins. This domain is found at the N-terminus of F-spondin, a protein attached to the extracellular matrix, which plays roles in neuronal development and vascular remodelling. The F-spondin reeler domain has been reported to bind heparin. The reeler domain is also found at the N-terminus of reelin, an extracellular glycoprotein involved in the development of the brain cortex, and in a variety of other eukaryotic proteins with different domain architectures, including the animal ferric-chelate reductase 1 or stromal cell-derived receptor 2, a member of the cytochrome B561 family, which reduces ferric iron before its transport from the endosome to the cytoplasm. Also included is the insect putative defense protein 1, which is expressed upon bacterial infection and appears to contain a single reeler domain. 135 matched cddid_all.tbl CDD cd08545 cd08545 260082 YcnI_like Reeler-like domain of YcnI and similar proteins. YcnI is a copper-responsive gene of Bacillus subtilis. It is homologous to an uncharacterized protein from Nocardia farcinica, which shares a conserved three-dimensional structure with cohesins and the reeler domain. Some members in this YcnI_like family have C-terminal domains (DUF461) that may bind copper. 152 matched cddid_all.tbl CDD cd08546 cd08546 260083 cohesin_like Cohesin domain, interaction parter of dockerin. Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. The cellulosome consists of scaffoldin, a noncatalytic scaffolding polypeptide, that comprises repeating cohesion modules and a single carbohydrate-binding module (CBM). Specific calcium-dependent interactions between cohesins and dockerins appear to be essential for cellulosome assembly. Cohesin modules are phylogenetically distributed into three groups: type I cohesin-dockerin interactions mediate assembly of a range of dockerin-borne enzymes to the complex, while type-II interactions mediate attachment of the cellulosome complex to the bacterial cell wall. Recently discovered type-III cohesins, such as found in the anchoring scaffoldin ScaE, appears to contribute to increased stability of the elaborate cellulosome complex. While the presence of cohesin and dockerin domains in a genome can be indicative of cellulolytic activity, cohesin domains may occur in a wider range of domain architectures, biological systems, and taxonomic lineages. 144 matched cddid_all.tbl CDD cd08547 cd08547 260084 Type_II_cohesin Type II cohesin domain, interaction partner of dockerin. Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. The cellulosome consists of scaffoldin, a noncatalytic scaffolding polypeptide, that comprises repeating cohesion modules and a single carbohydrate-binding module (CBM). Specific calcium-dependent interactions between cohesins and dockerins appear to be essential for cellulosome assembly. This subfamily represents type II cohesins; their interactions with dockerin mediate attachment of the cellulosome complex to the bacterial cell wall. 136 matched cddid_all.tbl CDD cd08548 cd08548 260085 Type_I_cohesin_like Type I cohesin domain, interaction partner of dockerin. Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. The cellulosome consists of scaffoldin, a noncatalytic scaffolding polypeptide, that comprises repeating cohesion modules and a single carbohydrate-binding module (CBM). Specific calcium-dependent interactions between cohesins and dockerins appear to be essential for cellulosome assembly. This subfamily represents type I cohesins; their interactions with dockerin mediate assembly of a range of dockerin-borne enzymes to the complex. 135 matched cddid_all.tbl CDD cd08549 cd08549 341479 G1PDH_related Glycerol-1-phosphate dehydrogenase and related proteins. This family contains bacterial and archeal glycerol-1-phosphate dehydrogenase-like oxidoreductases. These proteins have similarity with glycerol-1-phosphate dehydrogenase (G1PDH) which plays a role in the synthesis of phosphoglycerolipids in gram-positive bacterial species. It catalyzes the reversibly reduction of dihydroxyacetone phosphate (DHAP) to glycerol-1-phosphate (G1P) in a NADH-dependent manner. Its activity requires Ni++ ion. It also contains archaeal Sn-glycerol-1-phosphate dehydrogenase (Gro1PDH) that plays an important role in the formation of the enantiomeric configuration of the glycerophosphate backbone (sn-glycerol-1-phosphate) of archaeal ether lipids. 331 matched cddid_all.tbl CDD cd08550 cd08550 341480 GlyDH-like Glycerol_dehydrogenase-like. This family contains glycerol dehydrogenase (GlyDH)-like proteins. Glycerol dehydrogenases (GlyDH) is a key enzyme in the glycerol dissimilation pathway. In anaerobic conditions, many microorganisms utilize glycerol as a source of carbon through coupled oxidative and reductive pathways. One of the pathways involves the oxidation of glycerol to dihydroxyacetone with the reduction of NAD+ to NADH catalyzed by glycerol dehydrogenases. Dihydroxyacetone is then phosphorylated by dihydroxyacetone kinase and enters the glycolytic pathway for further degradation. The activity of GlyDH is zinc-dependent; the zinc ion plays a role in stabilizing an alkoxide intermediate at the active site. Some subfamilies have yet to be characterized. 347 matched cddid_all.tbl CDD cd08551 cd08551 341481 Fe-ADH iron-containing alcohol dehydrogenases (Fe-ADH)-like. This family contains large metal-containing alcohol dehydrogenases (ADH), known as iron-containing alcohol dehydrogenases. They contain a dehydroquinate synthase-like protein structural fold and mostly contain iron. They are distinct from other alcohol dehydrogenases which contains different protein domains. There are several distinct families of alcohol dehydrogenases: Zinc-containing long-chain alcohol dehydrogenases, insect-type, or short-chain alcohol dehydrogenases, iron-containing alcohol dehydrogenases, among others. The iron-containing family has a Rossmann fold-like topology that resembles the fold of the zinc-dependent alcohol dehydrogenases, but lacks sequence homology, and differs in strand arrangement. ADH catalyzes the reversible oxidation of alcohol to acetaldehyde with the simultaneous reduction of NAD(P)+ to NAD(P)H. 372 matched cddid_all.tbl CDD cd08553 cd08553 350202 PIN_Fcf1-like VapC-like PIN domain of rRNA-processing proteins, Fcf1 (Utp24, YDR339C), Utp23 (YOR004W), and other eukaryotic homologs. Fcf1 (FAF1-copurifying factor 1, also known as Utp24) and Utp23 (U three-associated protein 23) are essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly. Components of the small subunit (SSU) processome, Fcf1 and Utp23 are essential nucleolar proteins that are required for processing of the 18S pre-rRNA at sites A0-A2. The Fcf1 protein was reported to interact with Pmc1p (vacuolar Ca2+ ATPase) and Cor1p (core subunit of the ubiquinol-cytochrome c reductase complex). The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. The subfamily of Fcf1- and Utp23-like homologs have three of the four conserved residues found in S. cerevisiae Fcf1. Some members of the superfamily, including S. cerevisiae Utp23, lack several of these key catalytic residues. Mutation of the remaining conserved putative active site residues seen in Utp23 did not interfere with rRNA maturation and cell viability. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 123 matched cddid_all.tbl CDD cd08554 cd08554 176489 Cyt_b561 Eukaryotic cytochrome b(561). Cytochrome b(561) is a family of endosomal or secretory vesicle-specific electron transport proteins. They are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. This is an exclusively eukaryotic family. Members of the prokaryotic cytochrome b561 family are not deemed homologous. 131 matched cddid_all.tbl CDD cd08555 cd08555 176498 PI-PLCc_GDPD_SF Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily. The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria, as well as their uncharacterized homologs found in organisms ranging from bacteria and archaea to metazoans, plants, and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing the membrane lipid phosphoinositides to yield two important second messengers, inositol phosphates and diacylglycerol (DAG). GP-GDEs play essential roles in glycerol metabolism and catalyze the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols that are major sources of carbon and phosphate. Both, PI-PLCs and GP-GDEs, can hydrolyze the 3'-5' phosphodiester bonds in different substrates, and utilize a similar mechanism of general base and acid catalysis with conserved histidine residues, which consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This superfamily also includes Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81, glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs). The residues essential for enzyme activities and metal binding are not conserved in these sequence homologs, which might suggest that the function of catalytic domains in these proteins might be distinct from those in typical PLC-like phosphodiesterases. 179 matched cddid_all.tbl CDD cd08556 cd08556 176499 GDPD Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins. The typical glycerophosphodiester phosphodiesterase domain (GDPD) consists of a TIM barrel and a small insertion domain named the GDPD-insertion (GDPD-I) domain, which is specific for GDPD proteins. This family corresponds to both typical GDPD domain and GDPD-like domain which lacks the GDPD-I region. Members in this family mainly consist of a large family of prokaryotic and eukaryotic glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), and a number of uncharacterized homologs. Sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria are also included in this family. GDPD plays an essential role in glycerol metabolism and catalyzes the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols are major sources of carbon and phosphate. Its catalytic mechanism is based on the metal ion-dependent acid-base reaction, which is similar to that of phosphoinositide-specific phospholipases C (PI-PLCs, EC 3.1.4.11). Both, GDPD related proteins and PI-PLCs, belong to the superfamily of PI-PLC-like phosphodiesterases. 189 matched cddid_all.tbl CDD cd08557 cd08557 176500 PI-PLCc_bacteria_like Catalytic domain of bacterial phosphatidylinositol-specific phospholipase C and similar proteins. This subfamily corresponds to the catalytic domain present in bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) and their sequence homologs found in eukaryota. Bacterial PI-PLCs participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although their precise physiological function remains unclear, bacterial PI-PLCs may function as virulence factors in some pathogenic bacteria. Bacterial PI-PLCs contain a single TIM-barrel type catalytic domain. Its catalytic mechanism is based on general base and acid catalysis utilizing two well conserved histidines, and consists of two steps, a phosphotransfer and a phosphodiesterase reaction. Eukaryotic homologs in this family are named as phosphatidylinositol-specific phospholipase C X domain containing proteins (PI-PLCXD). They are distinct from the typical eukaryotic phosphoinositide-specific phospholipases C (PI-PLC, EC 3.1.4.11), which have a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, eukaryotic PI-PLCXDs contain a single TIM-barrel type catalytic domain, X domain, which is closely related to that of bacterial PI-PLCs. Although the biological function of eukaryotic PI-PLCXDs still remains unclear, it may be distinct from that of typical eukaryotic PI-PLCs. This family also includes a distinctly different type of eukaryotic PLC, glycosylphosphatidylinositol-specific phospholipase C (GPI-PLC), an integral membrane protein characterized in the protozoan parasite Trypanosoma brucei. T. brucei GPI-PLC hydrolyzes the GPI-anchor on the variant specific glycoprotein (VSG), releasing dimyristyl glycerol (DMG), which may facilitate the evasion of the protozoan to the host's immune system. It does not require Ca2+ for its activity and is more closely related to bacterial PI-PLCs, but not mammalian PI-PLCs. 271 matched cddid_all.tbl CDD cd08558 cd08558 176501 PI-PLCc_eukaryota Catalytic domain of eukaryotic phosphoinositide-specific phospholipase C and similar proteins. This family corresponds to the catalytic domain present in eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) and similar proteins. The higher eukaryotic PI-PLCs play a critical role in most signal transduction pathways, controlling numerous cellular events such as cell growth, proliferation, excitation and secretion. They strictly require Ca2+ for the catalytic activity. They display a clear preference towards the hydrolysis of the more highly phosphorylated membrane phospholipids PI-analogues, phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphatidylinositol-4-phosphate (PIP), to generate two important second messengers in eukaryotic signal transduction cascades, inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. The eukaryotic PI-PLCs have a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains, such as the pleckstrin homology (PH) domain, EF-hand motif, and C2 domain. The catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a linker region. The catalytic mechanism of eukaryotic PI-PLCs is based on general base and acid catalysis utilizing two well conserved histidines and consists of two steps, a phosphotransfer and a phosphodiesterase reaction. The mammalian PI-PLCs consist of 13 isozymes, which are classified into six-subfamilies, PI-PLC-delta (1,3 and 4), -beta(1-4), -gamma(1,2), -epsilon, -zeta, and -eta (1,2). Ca2+ is required for the activation of all forms of mammalian PI-PLCs, and the concentration of calcium influences substrate specificity. This family also includes metazoan phospholipase C related but catalytically inactive proteins (PRIP), which belong to a group of novel inositol trisphosphate binding proteins. Due to the replacement of critical catalytic residues, PRIP does not have PLC enzymatic activity. 226 matched cddid_all.tbl CDD cd08559 cd08559 176502 GDPD_periplasmic_GlpQ_like Periplasmic glycerophosphodiester phosphodiesterase domain (GlpQ) and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in bacterial and eukaryotic glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46) similar to Escherichia coli periplasmic phosphodiesterase GlpQ. GP-GDEs are involved in glycerol metabolism and catalyze the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols, which are major sources of carbon and phosphate. In E. coli, there are two major G3P uptake systems: Glp and Ugp, which contain genes coding for two different GP-GDEs. GlpQ gene from the glp operon codes for a periplasmic phosphodiesterase GlpQ. GlpQ is a dimeric enzyme that hydrolyzes periplasmic glycerophosphodiesters, such as glycerophosphocholine (GPC), glycerophosphoethanolanmine (GPE), glycerophosphoglycerol (GPG), glycerophosphoinositol (GPI), and glycerophosphoserine (GPS), to the corresponding alcohols and G3P, which is subsequently transported into the cell through the GlpT transport system. Ca2+ is required for GlpQ enzymatic activity. This subfamily also includes some GP-GDEs in higher plants and their eukaryotic homologs, which show very high sequence similarities with bacterial periplasmic GP-GDEs. 296 matched cddid_all.tbl CDD cd08560 cd08560 176503 GDPD_EcGlpQ_like_1 Glycerophosphodiester phosphodiesterase domain similar to Escherichia coli periplasmic phosphodiesterase (GlpQ) include uncharacterized proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46) and their hypothetical homologs. Members in this subfamily show high sequence similarity to Escherichia coli periplasmic phosphodiesterase GlpQ, which catalyzes the Ca2+-dependent degradation of periplasmic glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. 356 matched cddid_all.tbl CDD cd08561 cd08561 176504 GDPD_cytoplasmic_ScUgpQ2_like Glycerophosphodiester phosphodiesterase domain of Streptomyces coelicolor cytoplasmic phosphodiesterases UgpQ2 and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized cytoplasmic phosphodiesterases which predominantly exist in bacteria. The prototype of this family is a putative cytoplasmic phosphodiesterase encoded by gene ulpQ2 (SCO1419) in the Streptomyces coelicolor genome. It is distantly related to the Escherichia coli cytoplasmic phosphodiesterases UgpQ that catalyzes the hydrolysis of glycerophosphodiesters at the inner side of the cytoplasmic membrane to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. 249 matched cddid_all.tbl CDD cd08562 cd08562 176505 GDPD_EcUgpQ_like Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46), UgpQ, and similar proteins. GP-GDE plays an essential role in the metabolic pathway of E. coli. It catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols, which are major sources of carbon and phosphate. E. coli possesses two major G3P uptake systems: Glp and Ugp, which contain genes coding for two distinct GP-GDEs. UgpQ gene from the E. coli ugp operon codes for a cytosolic phosphodiesterase GlpQ, which is the prototype of this family. Various glycerophosphodiesters, such as glycerophosphocholine (GPC), glycerophosphoethanolanmine (GPE), glycerophosphoglycerol (GPG), glycerophosphoinositol (GPI), and glycerophosphoserine (GPS), can only be hydrolyzed by UgpQ during transport at the inner side of the cytoplasmic membrane to alcohols and G3P, which is a source of phosphate. In contrast to Ca2+-dependent periplasmic phosphodiesterase GlpQ, cytosolic phosphodiesterase UgpQ requires divalent cations, such as Mg2+, Co2+, or Mn2+, for its enzyme activity. 229 matched cddid_all.tbl CDD cd08563 cd08563 176506 GDPD_TtGDE_like Glycerophosphodiester phosphodiesterase domain of Thermoanaerobacter tengcongensis and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Thermoanaerobacter tengcongensis glycerophosphodiester phosphodiesterase (TtGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. Despite the fact that most of GDPD family members exist as the monomer, TtGDE can function as a dimeric unit. Its catalytic mechanism is based on the general base-acid catalysis, which is similar to that of phosphoinositide-specific phospholipases C (PI-PLCs, EC 3.1.4.11). A divalent metal cation is required for the enzyme activity of TtGDE. 230 matched cddid_all.tbl CDD cd08564 cd08564 176507 GDPD_GsGDE_like Glycerophosphodiester phosphodiesterase domain of putative Galdieria sulphuraria glycerophosphodiester phosphodiesterase and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in putative Galdieria sulphuraria glycerophosphodiester phosphodiesterase (GsGDE, EC 3.1.4.46) and its uncharacterized eukaryotic homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. 265 matched cddid_all.tbl CDD cd08565 cd08565 176508 GDPD_pAtGDE_like Glycerophosphodiester phosphodiesterase domain of putative Agrobacterium tumefaciens glycerophosphodiester phosphodiesterase and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in putative Agrobacterium tumefaciens glycerophosphodiester phosphodiesterase (pAtGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. 235 matched cddid_all.tbl CDD cd08566 cd08566 176509 GDPD_AtGDE_like Glycerophosphodiester phosphodiesterase domain of Agrobacterium tumefaciens and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Agrobacterium tumefaciens glycerophosphodiester phosphodiesterase (AtGDE, EC 3.1.4.46) and its uncharacterized eukaryotic homolgoues. Members in this family shows high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. AtGDE exists as a hexamer that is a trimer of dimers, which is unique among current known GDPD family members. However, it remains unclear if the hexamer plays a physiological role in AtGDE enzymatic function. 240 matched cddid_all.tbl CDD cd08567 cd08567 176510 GDPD_SpGDE_like Glycerophosphodiester phosphodiesterase domain of putative Silicibacter pomeroyi glycerophosphodiester phosphodiesterase and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46) and similar proteins. The prototype of this CD is a putative GP-GDE from Silicibacter pomeroyi (SpGDE). It shows high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. 263 matched cddid_all.tbl CDD cd08568 cd08568 176511 GDPD_TmGDE_like Glycerophosphodiester phosphodiesterase domain of Thermotoga maritime and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Thermotoga maritime glycerophosphodiester phosphodiesterase (TmGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. TmGDE exists as a monomer that might be the biologically relevant form. 226 matched cddid_all.tbl CDD cd08570 cd08570 176512 GDPD_YPL206cp_fungi Glycerophosphodiester phosphodiesterase domain of Saccharomyces cerevisiae YPL206cp and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Saccharomyces cerevisiae YPL206cp and uncharacterized hypothetical homologs existing in fungi. The product of S. cerevisiae ORF YPL206c (PGC1), YPL206cp (Pgc1p), displays homology to bacterial and mammalian glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. S. cerevisiae YPL206cp is an integral membrane protein with a single GDPD domain following by a short hydrophobic C-terminal tail that may function as a membrane anchor. This protein plays an essential role in the regulation of the cardiolipin (CL) biosynthetic pathway in yeast by removing the excess phosphatidylglycerol (PG) content of membranes via a phospholipase C-type degradation mechanism. YPL206cp has been characterized as a PG-specific phospholipase C that selectively catalyzes the cleavage of PG, not glycerophosphoinositol (GPI) or glycerophosphocholine (GPC), to diacylglycerol (DAG) and glycerophosphate. Members in this family are distantly related to S. cerevisiae YPL110cp, which selectively hydrolyzes glycerophosphocholine (GPC), not glycerophosphoinositol (GPI), to generate choline and glycerolphosphate, and has been characterized as a cytoplasmic GPC-specific phosphodiesterase. 234 matched cddid_all.tbl CDD cd08571 cd08571 176513 GDPD_SHV3_plant Glycerophosphodiester phosphodiesterase domain of glycerophosphodiester phosphodiesterase-like protein SHV3 and SHV3-like proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase (GDPD) domain present in glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs), which may play an important role in cell wall organization. The prototype of this family is a glycosylphosphatidylinositol (GPI) anchored protein SHV3 encoded by shaven3 (shv3) gene from Arabidopsis thaliana. Members in this family show sequence homology to bacterial GP-GDEs (EC 3.1.4.46) that catalyze the hydrolysis of various glycerophosphodiesters, and produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. Both, SHV3 and SVLs, have two tandemly repeated GDPD domains whose biochemical functions remain unclear. The residues essential for interactions with the substrates and calcium ions in bacterial GP-GDEs are not conserved in SHV3 and SVLs, which suggests that the function of GDPD domains in these proteins might be distinct from those in typical bacterial GP-GDEs. In addition, the two tandem repeats show low sequence similarity to each other, suggesting they have different biochemical function. Most members of this family are Arabidopsis-specific gene products. To date, SHV3 orthologues are only found in Physcomitrella patens. 302 matched cddid_all.tbl CDD cd08572 cd08572 176514 GDPD_GDE5_like Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE5-like proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian glycerophosphodiester phosphodiesterase GDE5-like proteins. GDE5 is widely expressed in mammalian tissues, with highest expression in spinal chord. Although its biological function remains unclear, mammalian GDE5 shows higher sequence homology to fungal and plant glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46) than to other bacterial and mammalian GP-GDEs. It may also hydrolyze glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. 293 matched cddid_all.tbl CDD cd08573 cd08573 176515 GDPD_GDE1 Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE1 and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian GDE1 (also known as MIR16, membrane interacting protein of RGS16) and their metazoan homologs. GDE1 is widely expressed in mammalian tissues, including the heart, brain, liver, and kidney. It shows sequence homology to bacterial glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), which catalyzes the hydrolysis of various glycerophosphodiesters, and produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. GDE1 has been characterized as GPI-GDE (EC 3.1.4.44) that selectively hydrolyzes extracellular glycerophosphoinositol (GPI) to generate glycerol phosphate and inositol. It functions as an integral membrane-bound glycoprotein interacting with regulator of G protein signaling protein RGS16, and is modulated by G protein-coupled receptor (GPCR) signaling. In addition, GDE1 may interact with PRA1 domain family, member 2 (PRAF2, also known as JM4), which is an interacting protein of the G protein-coupled chemokine receptor CCR5. The catalytic activity, which is dependent on the integrity of the GDPD domain, is required for GDE1 cellular function. 258 matched cddid_all.tbl CDD cd08574 cd08574 176516 GDPD_GDE_2_3_6 Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2, GDE3, GDE6-like proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian glycerophosphodiester phosphodiesterase domain-containing protein subtype 5 (GDE2), subtype 2 (GDE3), subtype 1 (GDE6), and their eukaryotic homologs. Mammalian GDE2, GDE3, and GDE6 show very high sequence similarity to each other and have been classified into the same family. Although they are all transmembrane proteins, based on different pattern of tissue distribution, these enzymes might display diverse cellular functions. Mammalian GDE2 is primarily expressed in mature neurons. It selectively hydrolyzes glycerophosphocholine (GPC) and mainly functions in a complex with an antioxidant scavenger peroxiredoxin1 (Prdx1) to control motor neuron differentiation in the spinal cord. Mammalian GDE3 is specifically expressed in bone tissues and spleen. It selectively hydrolyzes extracellular glycerophosphoinositol (GPI) to generate inositol 1-phosphate (Ins1P) and glycerol and functions as an inducer of osteoblast differentiation. Mammalian GDE6 is predominantly expressed in the spermatocytes of testis, and its specific physiological function has not been elucidated yet. 252 matched cddid_all.tbl CDD cd08575 cd08575 176517 GDPD_GDE4_like Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE4-like proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian GDE4 (also known as glycerophosphodiester phosphodiesterase domain-containing protein 1 (GDPD1)) and similar proteins. Mammalian GDE4 is a transmembrane protein whose cellular function is not elucidated. It is expressed widely, including in placenta, liver, kidney, pancreas, spleen, thymus, ovary, small intestine and peripheral blood leukocytes. It is also expressed in the growth cones in neuroblastoma Neuro2a cells, which suggests mammalian GDE4 may play some distinct role from other members of mammalian GDEs family. Also included in this subfamily are uncharacterized mammalian glycerophosphodiester phosphodiesterase domain-containing protein 3 (GDPD3) and similar proteins which display very high sequence homology to mammalian GDE4. 264 matched cddid_all.tbl CDD cd08576 cd08576 176518 GDPD_like_SMaseD_PLD Glycerophosphodiester phosphodiesterase-like domain of spider venom sphingomyelinases D, bacterial phospholipase D, and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase-like domain (GDPD-like) present in sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.4) from spider venom, the Corynebacterium pseudotuberculosis Phospholipase D (PLD)-like protein from pathogenic bacteria, and the Ajellomyces capsulatus H143 PLD-like protein from ascomycetes. Spider SMases D and bacterial PLD proteins catalyze the Mg2+-dependent hydrolysis of sphingomyelin producing choline and ceramide 1-phosphate (C1P), which possess a number of biological functions, such as regulating cell proliferation and apoptosis, participating in inflammatory responses, and playing a key role in phagocytosis. In the presence of Mg2+, SMases D can function as lysophospholipase D and hydrolyze lysophosphatidylcholine (LPC) to choline and lysophosphatidic acid (LPA), which is a multifunctional phospholipid involved in platelet aggregation, endothelial hyperpermeability, and pro-inflammatory responses. Loxosceles spider venoms' SMases D are the principal toxins responsible for dermonecrosis and complement dependent haemolysis induced by spider venom. Due to amino acid substitutions at the entrance to the active-site pocket, some members lack activity. The typical GDPD domain consists of a TIM barrel and a small insertion domain named as the GDPD-insertion (GDPD-I) domain, which is specific for GDPD proteins. Although proteins in this family contain a non-typical GDPD domain which lacks the GDPD-I, their catalytic mechanisms are based on Mg2+-dependent acid-base reactions similar to GDPD proteins. They might be divergent members of the GDPD family. Moreover, this family does not belong to phospholipase D (PLD) superfamily, since it lacks the conserved HKD sequence motif that characterizes the catalytic center of the PLD superfamily. It belongs to the superfamily of PLC-like phosphodiesterases. 265 matched cddid_all.tbl CDD cd08577 cd08577 176519 PI-PLCc_GDPD_SF_unchar3 Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases. This subfamily corresponds to a group of uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipase C (PI-PLC), and glycerophosphodiester phosphodiesterases (GP-GDE), and also sphingomyelinases D (SMases D) and similar proteins. They hydrolyze the 3'-5' phosphodiester bonds in different substrates, utilizing a similar mechanism of general base and acid catalysis involving two conserved histidine residues. 228 matched cddid_all.tbl CDD cd08578 cd08578 176520 GDPD_NUC-2_fungi Putative glycerophosphodiester phosphodiesterase domain of ankyrin repeat protein NUC-2 and similar proteins. This subfamily corresponds to a putative glycerophosphodiester phosphodiesterase domain (GDPD) present in Neurospora crassa ankyrin repeat protein NUC-2 and its Saccharomyces cerevisiae counterpart, Phosphate system positive regulatory protein PHO81. Some uncharacterized NUC-2 sequence homologs are also included in this family. NUC-2 plays an important role in the phosphate-regulated signal transduction pathway in Neurospora crassa. It shows high similarity to a cyclin-dependent kinase inhibitory protein PHO81, which is part of the phosphate regulatory cascade in S. cerevisiae. Both NUC-2 and PHO81 have multi-domain architecture, including an SPX N-terminal domain following by several ankyrin repeats and a putative C-terminal GDPD domain with unknown function. Although the putative GDPD domain displays sequence homology to that of bacterial glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), the residues essential for interactions with the substrates and calcium ions in bacterial GP-GDEs are not conserved in members of this family, which suggests the function of putative GDPD domains in these proteins might be distinct from those in typical bacterial GP-GDEs. 300 matched cddid_all.tbl CDD cd08579 cd08579 176521 GDPD_memb_like Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in uncharacterized bacterial glycerophosphodiester phosphodiesterases. In addition to a C-terminal GDPD domain, most members in this family have an N-terminus that functions as a membrane anchor. 220 matched cddid_all.tbl CDD cd08580 cd08580 176522 GDPD_Rv2277c_like Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial protein Rv2277c and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in uncharacterized bacterial protein Rv2277c and similar proteins. Members in this subfamily are bacterial homologous of mammalian GDE4, a transmembrane protein whose cellular function has not yet been elucidated. 263 matched cddid_all.tbl CDD cd08581 cd08581 176523 GDPD_like_1 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterase and similar proteins. They show high sequence similarity to Escherichia coli glycerophosphodiester phosphodiesterase, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. 229 matched cddid_all.tbl CDD cd08582 cd08582 176524 GDPD_like_2 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterase and similar proteins. They show high sequence similarity to Escherichia coli glycerophosphodiester phosphodiesterase, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. 233 matched cddid_all.tbl CDD cd08583 cd08583 176525 PI-PLCc_GDPD_SF_unchar1 Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases. This subfamily corresponds to a group of uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipase C (PI-PLC), and glycerophosphodiester phosphodiesterases (GP-GDE), and also sphingomyelinases D (SMases D) and similar proteins. They hydrolyze the 3'-5' phosphodiester bonds in different substrates, utilizing a similar mechanism of general base and acid catalysis involving two conserved histidine residues. 237 matched cddid_all.tbl CDD cd08584 cd08584 176526 PI-PLCc_GDPD_SF_unchar2 Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases. This subfamily corresponds to a group of uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipase C (PI-PLC), and glycerophosphodiester phosphodiesterases (GP-GDE), and also sphingomyelinases D (SMases D) and similar proteins. They hydrolyze the 3'-5' phosphodiester bonds in different substrates, utilizing a similar mechanism of general base and acid catalysis involving two conserved histidine residues. 192 matched cddid_all.tbl CDD cd08585 cd08585 176527 GDPD_like_3 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterase and similar proteins. They show high sequence similarity with Escherichia coli glycerophosphodiester phosphodiesterase, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. 237 matched cddid_all.tbl CDD cd08586 cd08586 176528 PI-PLCc_BcPLC_like Catalytic domain of Bacillus cereus phosphatidylinositol-specific phospholipases C and similar proteins. This subfamily corresponds to the catalytic domain present in Bacillus cereus phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) and its sequence homologs found in bacteria and eukaryota. Bacterial PI-PLCs participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although their precise physiological function remains unclear, bacterial PI-PLCs may function as virulence factors in some pathogenic bacteria. Bacterial PI-PLCs contain a single TIM-barrel type catalytic domain. Their catalytic mechanism is based on general base and acid catalysis utilizing two well conserved histidines, and consists of two steps, a phosphotransfer and a phosphodiesterase reaction. This family also includes some uncharacterized eukaryotic homologs, which contains a single TIM-barrel type catalytic domain, X domain. They are similar to bacterial PI-PLCs, and distinct from typical eukaryotic PI-PLCs, which have a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains, and strictly require Ca2+ for their catalytic activities. The prototype of this family is Bacillus cereus PI-PLC, which has a moderate thermal stability and is active as a monomer. 279 matched cddid_all.tbl CDD cd08587 cd08587 176529 PI-PLCXDc_like Catalytic domain of phosphatidylinositol-specific phospholipase C X domain containing and similar proteins. This family corresponds to the catalytic domain present in phosphatidylinositol-specific phospholipase C X domain containing proteins (PI-PLCXD) which are bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) sequence homologs mainly found in eukaryota. The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) have a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, eukaryotic PI-PLCXDs and their bacterial homologs contain a single TIM-barrel type catalytic domain, X domain, which is more closely related to that of bacterial PI-PLCs. Although the biological function of eukaryotic PI-PLCXDs still remains unclear, it may be distinct from that of typical eukaryotic PI-PLCs. 288 matched cddid_all.tbl CDD cd08588 cd08588 176530 PI-PLCc_At5g67130_like Catalytic domain of Arabidopsis thaliana PI-PLC X domain-containing protein At5g67130 and its uncharacterized homologs. This subfamily corresponds to the catalytic domain present in Arabidopsis thaliana PI-PLC X domain-containing protein At5g67130 and its uncharacterized homologs. Members in this family show high sequence similarity to bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), which participates in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). 270 matched cddid_all.tbl CDD cd08589 cd08589 176531 PI-PLCc_SaPLC1_like Catalytic domain of Streptomyces antibioticus phosphatidylinositol-specific phospholipase C1-like proteins. This subfamily corresponds to the catalytic domain present in Streptomyces antibioticus phosphatidylinositol-specific phospholipase C1 (SaPLC1) and similar proteins. The typical bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) catalyzes Ca2+-independent hydrolysis of the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). The catalytic mechanism is based on general base and acid catalysis utilizing two well conserved histidines, and consists of two steps, a phosphotransfer and a phosphodiesterase reaction. In contrast, SaPLC1 is the first known natural Ca2+-dependent bacterial PI-PLC. It is more closely related to the eukaryotic PI-PLCs rather than the typical bacterial PI-PLCs. It participates in PI metabolism to generate myo-inositol-1-phosphate and myo-inositol-1:2-cyclic phosphate simultaneously. SaPLC1 and other members in this subfamily have two Ca2+-chelating amino acid substitutions which convert them from metal-independent enzymes to metal-dependent bacterial PI-PLC. Additionally, SaPLC1 active site utilizes a mechanism of amino acid juxtaposition, swapping amino acid positions, to adapt a calcium binding pocket and maintain more ideal active site geometry to support efficient catalysis. 324 matched cddid_all.tbl CDD cd08590 cd08590 176532 PI-PLCc_Rv2075c_like Catalytic domain of uncharacterized Mycobacterium tuberculosis Rv2075c-like proteins. This subfamily corresponds to the catalytic domain present in uncharacterized Mycobacterium tuberculosis Rv2075c and its homologs. Members in this family are more closely related to the Streptomyces antibioticus phosphatidylinositol-specific phospholipase C1(SaPLC1)-like proteins rather than the typical bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), which participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). In contrast, SaPLC1-like proteins have two Ca2+-chelating amino acid substitutions which convert them to metal-dependent bacterial PI-PLC. Rv2075c and its homologs have the same amino acid substitutions as well, which might suggest they have metal-dependent PI-PLC activity. 267 matched cddid_all.tbl CDD cd08591 cd08591 176533 PI-PLCc_beta Catalytic domain of metazoan phosphoinositide-specific phospholipase C-beta. This subfamily corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-beta isozymes. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which goes on to phosphorylate other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PLC-beta represents a class of mammalian PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, a C2 domain, and a unique C-terminal coiled-coil (CT) domain necessary for homodimerization. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. There are four PLC-beta isozymes (1-4). They are activated by the heterotrimeric G protein alpha q subunits through their C2 domain and long C-terminal extension. The beta-gamma subunits of heterotrimeric G proteins are known to activate the PLC-beta2 and -beta3 isozymes only. Aside from four PLC-beta isozymes identified in mammals, some eukaryotic PLC-beta homologs have been classified into this subfamily, such as NorpA and PLC-21 from Drosophila and PLC-beta from turkey, Xenopus, sponge, and hydra. 257 matched cddid_all.tbl CDD cd08592 cd08592 176534 PI-PLCc_gamma Catalytic domain of metazoan phosphoinositide-specific phospholipase C-gamma. This family corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-gamma isozymes. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which goes on to phosphorylate other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PI-PLC-gamma represents a class of mammalian PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, and a C2 domain.The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. Unique to PI-PLC-gamma, a second PH domain, two SH2 (Src homology 2) regions, and one SH3 (Src homology 3) region is present within this linker region. There are two PI-PLC-gamma isozymes (1-2). They are activated by receptor and non-receptor tyrosine kinases due to the presence of two SH2 and a single SH3 domain within the linker region. Aside from the two PI-PLC-gamma isozymes identified in mammals, some eukaryotic PI-PLC-gamma homologs have been classified with this subfamily. 229 matched cddid_all.tbl CDD cd08593 cd08593 176535 PI-PLCc_delta Catalytic domain of metazoan phosphoinositide-specific phospholipase C-delta. This subfamily corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-delta isozymes. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PLC-delta represents a class of mammalian PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, and a C-terminal C2 domain. This CD corresponds to the catalytic domain which is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. There are three PI-PLC-delta isozymes (1,3 and 4). PI-PLC-delta1 is relatively well characterized. It is activated by high calcium levels generated by other PI-PLC family members, and therefore functions as a calcium amplifier within the cell. Different PI-PLC-delta isozymes have different tissue distribution and different subcellular locations. PI-PLC-delta1 is mostly a cytoplasmic protein, PI-PLC-delta3 is located in the membrane, and PI-PLC-delta4 is predominantly detected in the cell nucleus. Aside from three PI-PLC-delta isozymes identified in mammals, some eukaryotic PI-PLC-delta homologs have been classified to this CD. 257 matched cddid_all.tbl CDD cd08594 cd08594 176536 PI-PLCc_eta Catalytic domain of metazoan phosphoinositide-specific phospholipase C-eta. This family corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-eta isozymes. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PI-PLC-eta represents a class of neuron-speific PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, a C2 domain, and a unique C-terminal tail that terminates with a PDZ-binding motif, a potential interaction site for other signaling proteins. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. There are two PI-PLC-eta isozymes (1-2), both neuron-specific enzymes. They function as calcium sensors that are activated by small increases in intracellular calcium concentrations. The PI-PLC-eta isozymes are also activated through GPCR stimulation. Aside from the PI-PLC-eta isozymes identified in mammals, their eukaryotic homologs are also present in this family. 227 matched cddid_all.tbl CDD cd08595 cd08595 176537 PI-PLCc_zeta Catalytic domain of metazoan phosphoinositide-specific phospholipase C-zeta. This family corresponds to the catalytic domain presenting in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-zeta isozyme. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PI-PLC-zeta represents a class of sperm-specific PI-PLC that has an N-terminal EF-hand domain, a PLC catalytic core domain, and a C-terminal C2 domain. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. There is one PLC-zeta isozyme (1). PLC-zeta plays a fundamental role in vertebrate fertilization by initiating intracellular calcium oscillations that trigger the embryo development. However, the mechanism of its activation still remains unclear. Aside from PI-PLC-zeta identified in mammals, its eukaryotic homologs have been classified with this family. 257 matched cddid_all.tbl CDD cd08596 cd08596 176538 PI-PLCc_epsilon Catalytic domain of metazoan phosphoinositide-specific phospholipase C-epsilon. This family corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-epsilon isozymes. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PI-PLC-epsilon represents a class of mammalian PI-PLC that has an N-terminal CDC25 homology domain with a guanyl-nucleotide exchange factor (GFF) activity, a pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, a C2 domain, and two predicted RA (Ras association) domains that are implicated in the binding of small GTPases, such as Ras or Rap, from the Ras family. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. There is one PI-PLC-epsilon isozyme (1). PI-PLC-epsilon is activated by G alpha(12/13), G beta gamma, and activated members of Ras and Rho small GTPases. Aside from PI-PLC-epsilon identified in mammals, its eukaryotic homologs have been classified with this family. 254 matched cddid_all.tbl CDD cd08597 cd08597 176539 PI-PLCc_PRIP_metazoa Catalytic domain of metazoan phospholipase C related, but catalytically inactive protein. This family corresponds to the catalytic domain present in metazoan phospholipase C related, but catalytically inactive proteins (PRIP), which belong to a group of novel Inositol 1,4,5-trisphosphate (InsP3) binding protein. PRIP has a primary structure and domain architecture, incorporating a pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain with highly conserved X- and Y-regions split by a linker sequence, and a C-terminal C2 domain, similar to phosphoinositide-specific phospholipases C (PI-PLC, EC 3.1.4.11)-delta isoforms. Due to replacement of critical catalytic residues, PRIP do not have PLC enzymatic activity. PRIP consists of two subfamilies, PRIP-1(previously known as p130 or PLC-1), which is predominantly expressed in the brain, and PRIP-2 (previously known as PLC-2), which exhibits a relatively ubiquitous expression. Experiments show both, PRIP-1 and PRIP-2, are involved in InsP3-mediated calcium signaling pathway and GABA(A)receptor-mediated signaling pathway. In addition, PRIP-2 acts as a negative regulator of B-cell receptor signaling and immune responses. 260 matched cddid_all.tbl CDD cd08598 cd08598 176540 PI-PLC1c_yeast Catalytic domain of putative yeast phosphatidylinositide-specific phospholipases C. This family corresponds to the catalytic domain present in a group of putative phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) encoded by PLC1 genes from yeasts, which are homologs of the delta isoforms of mammalian PI-PLC in terms of overall sequence similarity and domain organization. Mammalian PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. Calcium is required for the catalysis. The prototype of this CD is protein Plc1p encoded by PLC1 genes from Saccharomyces cerevisiae. Plc1p contains both highly conserved X- and Y- regions of PLC catalytic core domain, as well as a presumptive EF-hand like calcium binding motif. Experiments show that Plc1p displays calcium dependent catalytic properties with high similarity to those of the mammalian PLCs, and plays multiple roles in modulating the membrane/protein interactions in filamentation control. CaPlc1p encoded by CAPLC1 from the closely related yeast Candida albicans, an orthologue of S. cerevisiae Plc1p, is also included in this group. Like Plc1p, CaPlc1p has conserved presumptive catalytic domain, shows PLC activity when expressed in E. coli, and is involved in multiple cellular processes. There are two other gene copies of CAPLC1 in C. albicans, CAPLC2 (also named as PIPLC) and CAPLC3. Experiments show CaPlc1p is the only enzyme in C. albicans which functions as PLC. The biological functions of CAPLC2 and CAPLC3 gene products must be clearly different from CaPlc1p, but their exact roles remain unclear. Moreover, CAPLC2 and CAPLC3 gene products are more similar to extracellular bacterial PI-PLC than to the eukaryotic PI-PLC, and they are not included in this subfamily. 231 matched cddid_all.tbl CDD cd08599 cd08599 176541 PI-PLCc_plant Catalytic domain of plant phosphatidylinositide-specific phospholipases C. This family corresponds to the catalytic domain present in a group of phosphoinositide-specific phospholipases C (PI-PLC, EC 3.1.4.11) encoded by PLC genes from higher plants, which are homologs of mammalian PI-PLC in terms of overall sequence similarity and domain organization. Mammalian PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. Calcium is required for the catalysis. The domain arrangement of plant PI-PLCs is structurally similar to the mammalian PLC-zeta isoform, which lacks the N-terminal pleckstrin homology (PH) domain, but contains EF-hand like motifs (which are absent in a few plant PLCs), a PLC catalytic core domain with X- and Y- highly conserved regions split by a linker sequence, and a C2 domain. However, at the sequence level, the plant PI-PLCs are closely related to the mammalian PLC-delta isoform. Experiments show that plant PLCs display calcium dependent PLC catalytic properties, although they lack some of the N-terminal motifs found in their mammalian counterparts. A putative calcium binding site may be located at the region spanning the X- and Y- domains. 228 matched cddid_all.tbl CDD cd08600 cd08600 176542 GDPD_EcGlpQ_like Glycerophosphodiester phosphodiesterase domain of Escherichia coli (GlpQ) and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Escherichia coli periplasmic glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46), GlpQ, and similar proteins. GP-GDE plays an essential role in the metabolic pathway of E. coli. It catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols, which are major sources of carbon and phosphate. E. coli possesses two major G3P uptake systems: Glp and Ugp, which contain genes coding for two different GP-GDEs. GlpQ gene from the E. coli glp operon codes for a periplasmic phosphodiesterase GlpQ, which is the prototype of this family. GlpQ is a dimeric enzyme that hydrolyzes periplasmic glycerophosphodiesters, such as glycerophosphocholine (GPC), glycerophosphoethanolanmine (GPE), glycerophosphoglycerol (GPG), glycerophosphoinositol (GPI), and glycerophosphoserine (GPS), to the corresponding alcohols and G3P, which is subsequently transported into the cell through the GlpT transport system. Ca2+ is required for the enzymatic activity of GlpQ. This family also includes a surface-exposed lipoprotein, protein D (HPD), from Haemophilus influenza Type b and nontypeable strains, which shows very high sequence similarity with E. coli GlpQ. HPD has been characterized as a human immunoglobulin D-binding protein with glycerophosphodiester phosphodiesterase activity. It can hydrolyze phosphatidylcholine from host membranes to produce free choline on the lipopolysaccharides on the surface of pathogenic bacteria. 318 matched cddid_all.tbl CDD cd08601 cd08601 176543 GDPD_SaGlpQ_like Glycerophosphodiester phosphodiesterase domain of Staphylococcus aureus and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in uncharacterized glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46) from Staphylococcus aureus, Bacillus subtilis and similar proteins. Members in this family show very high sequence similarity to Escherichia coli periplasmic phosphodiesterase GlpQ, which catalyzes the Ca2+-dependent degradation of periplasmic glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. 256 matched cddid_all.tbl CDD cd08602 cd08602 176544 GDPD_ScGlpQ1_like Glycerophosphodiester phosphodiesterase domain of Streptomycin coelicolor (GlpQ1) and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of putative bacterial and eukaryotic glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46) similar to Escherichia coli periplasmic phosphodiesterase GlpQ, as well as plant glycerophosphodiester phosphodiesterases (GP-PDEs), all of which catalyzes the Ca2+-dependent degradation of periplasmic glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. The prototypes of this family include putative secreted phosphodiesterase encoded by gene glpQ1 (SCO1565) from the pho regulon in Streptomyces coelicolor genome, and in plants, two distinct Arabidopsis thaliana genes, AT5G08030 and AT1G74210, coding putative GP-PDEs from the cell walls and vacuoles, respectively. 309 matched cddid_all.tbl CDD cd08603 cd08603 176545 GDPD_SHV3_repeat_1 Glycerophosphodiester phosphodiesterase domain repeat 1 of glycerophosphodiester phosphodiesterase-like protein SHV3 and SHV3-like proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) repeat 1 present in glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs), which may play an important role in cell wall organization. The prototype of this family is a glycosylphosphatidylinositol (GPI) anchored protein SHV3 encoded by shaven3 (shv3) gene from Arabidopsis thaliana. Members in this family show sequence homology to bacterial GP-GDEs (EC 3.1.4.46) that catalyze the hydrolysis of various glycerophosphodiesters, and produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. Both, SHV3 and SVLs, have two tandemly repeated GDPD domains whose biochemical functions remain unclear. The residues essential for interactions with the substrates and calcium ions in bacterial GP-GDEs are not conserved in SHV3 and SVLs, which suggests that the function of GDPD domains in these proteins might be distinct from those in typical bacterial GP-GDEs. In addition, the two tandem repeats show low sequence similarity to each other, suggesting they have different biochemical function. Most of the members of this family are Arabidopsis-specific gene products. To date, SHV3 orthologues are only found in Physcomitrella patens. This family includes domain I, the first GDPD domain of SHV3 and SVLs. 299 matched cddid_all.tbl CDD cd08604 cd08604 176546 GDPD_SHV3_repeat_2 Glycerophosphodiester phosphodiesterase domain repeat 2 of glycerophosphodiester phosphodiesterase-like protein SHV3 and SHV3-like proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) repeat 2 present in glycerophosphodiester phosphodiesterase (GP-GDE)-like protein SHV3 and SHV3-like proteins (SVLs), which may play important an role in cell wall organization. The prototype of this family is a glycosylphosphatidylinositol (GPI) anchored protein SHV3 encoded by shaven3 (shv3) gene from Arabidopsis thaliana. Members in this family show sequence homology to bacterial GP-GDEs (EC 3.1.4.46) that catalyze the hydrolysis of various glycerophosphodiesters, and produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. Both, SHV3 and SVLs, have two tandemly repeated GDPD domains whose biochemical functions remain unclear. The residues essential for interactions with the substrates and calcium ions in bacterial GP-GDEs are not conserved in SHV3 and SVLs, which suggests that the function of GDPD domains in these proteins might be distinct from those in typical bacterial GP-GDEs. In addition, the two tandem repeats show low sequence similarity to each other, suggesting they have different biochemical function. Most of the members of this family are Arabidopsis-specific gene products. To date, SHV3 orthologues are only found in Physcomitrella patens. This CD includes domain II (the second GDPD domain of SHV3 and SVLs), which is necessary for SHV3 function. 300 matched cddid_all.tbl CDD cd08605 cd08605 176547 GDPD_GDE5_like_1_plant Glycerophosphodiester phosphodiesterase domain of uncharacterized plant glycerophosphodiester phosphodiesterase-like proteins similar to mammalian GDE5. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized plant glycerophosphodiester phosphodiesterase (GP-PDE)-like proteins. Members in this family show very high sequence homology to mammalian glycerophosphodiester phosphodiesterase GDE5 and are distantly related to plant GP-PDEs. 282 matched cddid_all.tbl CDD cd08606 cd08606 176548 GDPD_YPL110cp_fungi Glycerophosphodiester phosphodiesterase domain of Saccharomyces cerevisiae YPL110cp and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Saccharomyces cerevisiae YPL110cp and other uncharacterized fungal homologs. The product of S. cerevisiae ORF YPL110c (GDE1), YPL110cp (Gde1p), displays homology to bacterial and mammalian glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. S. cerevisiae YPL110cp has been characterized as a cytoplasmic glycerophosphocholine (GPC)-specific phosphodiesterase that selectively hydrolyzes GPC, not glycerophosphoinositol (GPI), to generate choline and glycerolphosphate. YPL110cp has multi-domain architecture, including not only C-terminal GDPD, but also an SPX N-terminal domain along with several ankyrin repeats, which implies that YPL110cp may mediate protein-protein interactions in a variety of proteins and play a role in maintaining cellular phosphate levels. Members in this family are distantly related to S. cerevisiae YPL206cp, which selectively catalyzes the cleavage of phosphatidylglycerol (PG), not glycerophosphoinositol (GPI) or glycerophosphocholine (GPC), to diacylglycerol (DAG) and glycerophosphate, and has been characterized as a PG-specific phospholipase C. 286 matched cddid_all.tbl CDD cd08607 cd08607 176549 GDPD_GDE5 Glycerophosphodiester phosphodiesterase domain of putative mammalian glycerophosphodiester phosphodiesterase GDE5 and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in putative mammalian GDE5 and similar proteins. Mammalian GDE5 is widely expressed in mammalian tissues, with highest expression in the spinal chord. Although its biological function remains unclear, mammalian GDE5 shows higher sequence homology to fungal and plant glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46) than to other bacterial and mammalian GP-GDEs. It may also hydrolyze glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. In addition to C-terminal GDPD domain, all members in this subfamily have a starch binding domain (CBM20) in the N-terminus, which suggests these proteins may play a distinct role in glycerol metabolism. 290 matched cddid_all.tbl CDD cd08608 cd08608 176550 GDPD_GDE2 Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2 and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian GDE2 (also known as glycerophosphodiester phosphodiesterase domain-containing protein 5 (GDPD5)) and their metazoan homologs. Mammalian GDE2 is transmembrane protein primarily expressed in mature neurons. It is a mammalian homolog of bacterial glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), which catalyze the hydrolysis of various glycerophosphodiesters, and produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. Mammalian GDE2 selectively hydrolyzes glycerophosphocholine (GPC) and has been characterized as GPC-GDE (EC 3.1.4.2) that contributes to osmotic regulation of cellular GPC. Mammalian GDE2 functions in a complex with an antioxidant scavenger peroxiredoxin1 (Prdx1) to control motor neuron differentiation in the spinal cord. Mammalian GDE2 also plays a critical role for retinoid-induced neuronal outgrowth. The catalytic activity of GDPD domain is essential for mammalian GDE2 cellular function. 351 matched cddid_all.tbl CDD cd08609 cd08609 176551 GDPD_GDE3 Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE3 and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian GDE3 (also known as glycerophosphodiester phosphodiesterase domain-containing protein 2 (GDPD2), Osteoblast differentiation promoting factor) and their metazoan homologs. Mammalian GDE3 is a transmembrane protein specifically expressed in bone tissues and spleen. It is a mammalian homolog of bacterial glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), which catalyzes the hydrolysis of various glycerophosphodiesters, and produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. Mammalian GDE3 has been characterized as glycerophosphoinositol inositolphosphodiesterase (EC 3.1.4.43) that selectively hydrolyzes extracellular glycerophosphoinositol (GPI) to generate inositol 1-phosphate (Ins1P) and glycerol. Mammalian GDE3 functions as an inducer of osteoblast differentiation. It also plays a critical role for actin cytoskeletal modulation. The catalytic activity of GDPD domain is essential for mammalian GDE3 cellular function. 315 matched cddid_all.tbl CDD cd08610 cd08610 176552 GDPD_GDE6 Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE6 and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian GDE6 (also known as glycerophosphodiester phosphodiesterase domain-containing protein 4 (GDPD4)) and their metazoan homologs. Mammalian GDE6 is a transmembrane protein predominantly expressed in the spermatocytes of testis. Although the specific physiological function of mammalian GDE6 has not been elucidated, its different pattern of tissue distribution suggests it might play a critical role in the completion of meiosis during male germ cell differentiation. 316 matched cddid_all.tbl CDD cd08612 cd08612 176553 GDPD_GDE4 Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE4 and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian GDE4 (also known as glycerophosphodiester phosphodiesterase domain-containing protein 1 (GDPD1)) and similar proteins. Mammalian GDE4 is a transmembrane protein whose cellular function has not yet been elucidated. It is expressed widely, including in placenta, liver, kidney, pancreas, spleen, thymus, ovary, small intestine and peripheral blood leukocytes. It is also expressed in the growth cones in neuroblastoma Neuro2a cells, which suggests GDE4 may play some distinct role from other members of the GDE family. 300 matched cddid_all.tbl CDD cd08613 cd08613 176554 GDPD_GDE4_like_1 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial homologs of mammalian glycerophosphodiester phosphodiesterase GDE4. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in uncharacterized bacterial homologs of mammalian GDE4, a transmembrane protein whose cellular function has not been elucidated yet. 309 matched cddid_all.tbl CDD cd08616 cd08616 176555 PI-PLCXD1c Catalytic domain of phosphatidylinositol-specific phospholipase C, X domain containing 1. This subfamily corresponds to the catalytic domain present in a group of phosphatidylinositol-specific phospholipase C X domain containing 1 (PI-PLCXD1), 2 (PI-PLCXD2) and 3 (PI-PLCXD3), which are bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13) sequence homologs found in vertebrates. The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) has a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, members in this group contain a single TIM-barrel type catalytic domain, X domain, and are more closely related to bacterial PI-PLCs, which participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although the biological function of eukaryotic PI-PLCXDs still remains unclear, it may distinct from that of typical eukaryotic PI-PLCs. 290 matched cddid_all.tbl CDD cd08619 cd08619 176556 PI-PLCXDc_plant Catalytic domain of phosphatidylinositol-specific phospholipase C, X domain containing proteins found in plants. The CD corresponds to the catalytic domain present in uncharacterized plant phosphatidylinositol-specific phospholipase C, X domain containing proteins (PI-PLCXD). The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) has a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, plant PI-PLCXDs contain a single TIM-barrel type catalytic domain, X domain, and are more closely related to bacterial PI-PLCs, which participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although the biological function of plant PI-PLCXDs still remains unclear, it may distinct from that of typical eukaryotic PI-PLCs. 285 matched cddid_all.tbl CDD cd08620 cd08620 176557 PI-PLCXDc_like_1 Catalytic domain of uncharacterized hypothetical proteins similar to eukaryotic phosphatidylinositol-specific phospholipase C, X domain containing proteins. This subfamily corresponds to the catalytic domain present in a group of uncharacterized hypothetical proteins found in bacteria and fungi, which are similar to eukaryotic phosphatidylinositol-specific phospholipase C, X domain containing proteins (PI-PLCXD). The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) has a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, eukaryotic PI-PLCXDs contain a single TIM-barrel type catalytic domain, X domain, and are more closely related to bacterial PI-PLCs, which participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although the biological function of eukaryotic PI-PLCXDs still remains unclear, it may distinct from that of typical eukaryotic PI-PLCs. 281 matched cddid_all.tbl CDD cd08621 cd08621 176558 PI-PLCXDc_like_2 Catalytic domain of uncharacterized hypothetical proteins similar to eukaryotic phosphatidylinositol-specific phospholipase C, X domain containing proteins. This subfamily corresponds to the catalytic domain present in a group of uncharacterized hypothetical proteins found in bacteria and fungi, which are similar to eukaryotic phosphatidylinositol-specific phospholipase C, X domain containing proteins (PI-PLCXD). The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) has a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, eukaryotic PI-PLCXDs contain a single TIM-barrel type catalytic domain, X domain, and are more closely related to bacterial PI-PLCs, which participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although the biological function of eukaryotic PI-PLCXDs still remains unclear, it may distinct from that of typical eukaryotic PI-PLCs. 300 matched cddid_all.tbl CDD cd08622 cd08622 176559 PI-PLCXDc_CG14945_like Catalytic domain of Drosophila melanogaster CG14945-like proteins similar to phosphatidylinositol-specific phospholipase C, X domain containing. This subfamily corresponds to the catalytic domain present in uncharacterized metazoan Drosophila melanogaster CG14945-like proteins, which are similar to eukaryotic phosphatidylinositol-specific phospholipase C, X domain containing proteins (PI-PLCXD). The typical eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) has a multidomain organization that consists of a PLC catalytic core domain, and various regulatory domains. The catalytic core domain is assembled from two highly conserved X- and Y-regions split by a divergent linker sequence. In contrast, eukaryotic PI-PLCXDs contain a single TIM-barrel type catalytic domain, X domain, and are more closely related to bacterial PI-PLCs, which participate in Ca2+-independent PI metabolism, hydrolyzing the membrane lipid phosphatidylinositol (PI) to produce phosphorylated myo-inositol and diacylglycerol (DAG). Although the biological function of eukaryotic PI-PLCXDs still remains unclear, it may distinct from that of typical eukaryotic PI-PLCs. 276 matched cddid_all.tbl CDD cd08623 cd08623 176560 PI-PLCc_beta1 Catalytic domain of metazoan phosphoinositide-specific phospholipase C-beta1. This subfamily corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-beta isozyme 1. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which goes on to phosphorylate other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PLC-beta represents a class of mammalian PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, a C2 domain, and a unique C-terminal coiled-coil (CT) domain necessary for homodimerization. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. PI-PLC-beta1 is expressed at highest levels in specific regions of the brain. It is activated by the heterotrimeric G protein alpha q subunits through their C2 domain and long C-terminal extension. 258 matched cddid_all.tbl CDD cd08624 cd08624 176561 PI-PLCc_beta2 Catalytic domain of metazoan phosphoinositide-specific phospholipase C-beta2. This subfamily corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-beta isozyme 2. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which goes on to phosphorylate other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PLC-beta represents a class of mammalian PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, a C2 domain, and a unique C-terminal coiled-coil (CT) domain necessary for homodimerization. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. PI-PLC-beta2 is expressed at highest levels in cells of hematopoietic origin. It is activated by the heterotrimeric G protein alpha q subunits through their C2 domain and long C-terminal extension. It is also activated by the beta-gamma subunits of heterotrimeric G proteins. 261 matched cddid_all.tbl CDD cd08625 cd08625 176562 PI-PLCc_beta3 Catalytic domain of metazoan phosphoinositide-specific phospholipase C-beta3. This subfamily corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-beta isozyme 3. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which goes on to phosphorylate other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PLC-beta represents a class of mammalian PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, a C2 domain, and a unique C-terminal coiled-coil (CT) domain necessary for homodimerization. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. PI-PLC-beta3 is widely expressed at highest levels in brain, liver, and parotid gland. It is activated by the heterotrimeric G protein alpha q subunits through their C2 domain and long C-terminal extension. It is also activated by the beta-gamma subunits of heterotrimeric G proteins. 258 matched cddid_all.tbl CDD cd08626 cd08626 176563 PI-PLCc_beta4 Catalytic domain of metazoan phosphoinositide-specific phospholipase C-beta4. This subfamily corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-beta isozyme 4. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which goes on to phosphorylate other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PLC-beta represents a class of mammalian PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, a C2 domain, and a unique C-terminal coiled-coil (CT) domain necessary for homodimerization. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. PI-PLC-beta4 is expressed in high concentrations in cerebellar Purkinje and granule cells, the median geniculate body, and the lateral geniculate nucleus. It is activated by the heterotrimeric G protein alpha q subunits through their C2 domain and long C-terminal extension. 257 matched cddid_all.tbl CDD cd08627 cd08627 176564 PI-PLCc_gamma1 Catalytic domain of metazoan phosphoinositide-specific phospholipase C-gamma1. This subfamily corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-gamma isozyme 1. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which goes on to phosphorylate other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PI-PLC-gamma represents a class of mammalian PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, and a C2 domain. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. Unique to PI-PLC-gamma1, a second PH domain, two SH2 (Src homology 2) regions, and one SH3 (Src homology 3) region is present within this linker region. PI-PLC-gamma1 is ubiquitously expressed. It is activated by receptor and non-receptor tyrosine kinases due to the presence of two SH2 and a single SH3 domain within the linker region. 229 matched cddid_all.tbl CDD cd08628 cd08628 176565 PI-PLCc_gamma2 Catalytic domain of metazoan phosphoinositide-specific phospholipase C-gamma2. This subfamily corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-gamma isozyme 2. PI-PLC is a signaling enzyme that hydrolyze the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which goes on to phosphorylate other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PI-PLC-gamma represents a class of mammalian PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, and a C2 domain. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. Unique to PI-PLC-gamma2, a second PH domain, two SH2 (Src homology 2) regions, and one SH3 (Src homology 3) region is present within this linker region. PI-PLC-gamma2 is highly expressed in cells of hematopoietic origin. It is activated by receptor and non-receptor tyrosine kinases due to the presence of two SH2 and a single SH3 domain within the linker region. Unlike PI-PLC-gamma1, the activation of PI-PLC-gamma2 may require concurrent stimulation of PI 3-kinase. 254 matched cddid_all.tbl CDD cd08629 cd08629 176566 PI-PLCc_delta1 Catalytic domain of metazoan phosphoinositide-specific phospholipase C-delta1. This subfamily corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-delta1 isozymes. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PLC-delta represents a class of mammalian PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, and a C-terminal C2 domain. This subfamily corresponds to the catalytic domain which is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. There are three PI-PLC-delta isozymes (1,3 and 4). PI-PLC-delta1 is relatively well characterized. It is activated by high calcium levels generated by other PI-PLC family members, and therefore functions as a calcium amplifier within the cell. Unlike PI-PLC-delta 4, PI-PLC-delta1 and 3 possess a putative nuclear export sequence (NES) located in the EF-hand domain, which may be responsible transporting PI-PLC-delta1and 3 from the cell nucleus. Experiments show PI-PLC-delta1 is essential for normal hair formation. 258 matched cddid_all.tbl CDD cd08630 cd08630 176567 PI-PLCc_delta3 Catalytic domain of metazoan phosphoinositide-specific phospholipase C-delta3. This subfamily corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-delta3 isozymes. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PLC-delta represents a class of mammalian PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, and a C-terminal C2 domain. This family corresponds to the catalytic domain which is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. There are three PI-PLC-delta isozymes (1,3 and 4). Unlike PI-PLC-delta 4, PI-PLC-delta1 and 3 possess a putative nuclear export sequence (NES) located in the EF-hand domain, which may be responsible transporting PI-PLC-delta1 and 3 from the cell nucleus. 258 matched cddid_all.tbl CDD cd08631 cd08631 176568 PI-PLCc_delta4 Catalytic domain of metazoan phosphoinositide-specific phospholipase C-delta4. This subfamily corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-delta4 isozymes. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PLC-delta represents a class of mammalian PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, and a C-terminal C2 domain. This CD corresponds to the catalytic domain which is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. There are three PI-PLC-delta isozymes (1,3 and 4). Unlike PI-PLC-delta 1 and 3, a putative nuclear export sequence (NES) located in the EF-hand domain, which may be responsible transporting PI-PLC-delta1 and 3 from the cell nucleus, is not present in PI-PLC-delta4. Experiments show PI-PLC-delta4 is required for the acrosome reaction in fertilization. 258 matched cddid_all.tbl CDD cd08632 cd08632 176569 PI-PLCc_eta1 Catalytic domain of metazoan phosphoinositide-specific phospholipase C-eta1. This subfamily corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-eta isozyme 1. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PI-PLC-eta represents a class of neuron-speific PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, a C2 domain, and a unique C-terminal tail that terminates with a PDZ-binding motif, a potential interaction site for other signaling proteins. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. PI-PLC-eta1 is a neuron-specific enzyme and expressed in only nerve tissues such as the brain and spinal cord. It may perform a fundamental role in the brain. 253 matched cddid_all.tbl CDD cd08633 cd08633 176570 PI-PLCc_eta2 Catalytic domain of metazoan phosphoinositide-specific phospholipase C-eta2. This subfamily corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-eta isozyme 2. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PI-PLC-eta represents a class of neuron-speific PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, a C2 domain, and a unique C-terminal tail that terminates with a PDZ-binding motif, a potential interaction site for other signaling proteins. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. PI-PLC-eta2 is a neuron-specific enzyme and expressed in the brain. It may in part function downstream of G-protein-coupled receptors and play an important role in the formation and maintenance of the neuronal network in the postnatal brain. 254 matched cddid_all.tbl CDD cd08637 cd08637 176474 DNA_pol_A_pol_I_C Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and DNA polymerase activity to fill in the resulting gap. A combination of phylogenomic and signature sequence-based (or phonetic) approaches is used to understand the evolutionary relationships among bacteria. DNA polymerase I is one of the conserved proteins that is used to search for protein signatures. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains. 377 matched cddid_all.tbl CDD cd08638 cd08638 176475 DNA_pol_A_theta DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis and in somatic hypermutation. DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis (TLS) and in somatic hypermutation (SHM). DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Pol theta is an exception among family A polymerases and generates processive single base substitutions. Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and DNA polymerase activity to fill in the resulting gap. Polymerase theta mostly has amino-terminal helicase domain, a carboxy-terminal polymerase domain and an intervening space region. 373 matched cddid_all.tbl CDD cd08639 cd08639 176476 DNA_pol_A_Aquificae_like Phylum Aquificae Pol A is different from Escherichia coli Pol A by three signature sequences. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and DNA polymerase activity to fill in the resulting gap. A combination of phylogenomic and signature sequence-based (or phonetic) approaches is used to understand the evolutionary relationships among bacteria. DNA polymerase I is one of the conserved proteins that is used for phylogenetic anaylsis of bacteria. Species of the phylum Aquificae grow in extreme thermophilic environments. The Aquificae are non-spore-forming, Gram-negative rods and strictly thermophilic. Phylum Aquificae Pol A is different from E. coli Pol I by three signature sequences consisting of a 2 amino acids (aa) insert, a 5-6 aa insert and a 6 aa deletion. These signature sequences may provide a molecular marker for the family Aquificaceae and related species. 324 matched cddid_all.tbl CDD cd08640 cd08640 176477 DNA_pol_A_plastid_like DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication. DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). The three-dimensional structure of plastid DNA polymerase has substantial similarity to Pol I. The structure of Pol I resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains. 371 matched cddid_all.tbl CDD cd08641 cd08641 176478 DNA_pol_gammaA Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. DNA polymerase gamma (Pol gamma), 5'-3' polymerase domain (Pol gammaA). Pol gammaA is a family A polymerase that is responsible for DNA replication and repair in mitochondria. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified into six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class X), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerases are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I, mitochondrial polymerase gammaA, and several bacteriophage polymerases including those from odd-numbered phage (T3, T5, and T7). The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains. Pol gammaA has also the right hand configuration. Pol gammaA has both polymerase and proofreading exonuclease activities separated by a spacer. Pol gamma holoenzyme is a heterotrimer containing one Pol gammaA subunit and a dimeric Pol gammaB subunit. Pol gamma is important for mitochondria DNA maintenance and mutation of the catalytic subunit of Pol gamma is implicated in more than 30 human diseases. 425 matched cddid_all.tbl CDD cd08642 cd08642 176479 DNA_pol_A_pol_I_A Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and DNA polymerase activity to fill in the resulting gap. A combination of phylogenomic and signature sequence-based (or phonetic) approaches is used to understand the evolutionary relationships among bacteria. DNA polymerase I is one of the conserved proteins that is used to search for protein signatures. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains. 378 matched cddid_all.tbl CDD cd08643 cd08643 176480 DNA_pol_A_pol_I_B Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5' nuclease activity to remove the ribonucleotide portion of newly synthesized Okazaki fragments and DNA polymerase activity to fill in the resulting gap. A combination of phylogenomic and signature sequence-based (or phonetic) approaches is used to understand the evolutionary relationships among bacteria. DNA polymerase I is one of the conserved proteins that is used to search for protein signatures. The structure of these polymerases resembles in overall morphology a cupped human right hand, with fingers (which bind an incoming nucleotide and interact with the single-stranded template), palm (which harbors the catalytic amino acid residues and also binds an incoming dNTP) and thumb (which binds double-stranded DNA) subdomains. 429 matched cddid_all.tbl CDD cd08644 cd08644 187713 FMT_core_ArnA_N ArnA, N-terminal formyltransferase domain. ArnA_N: ArnA is a bifunctional enzyme required for the modification of lipid A with 4-amino-4-deoxy-L-arabinose (Ara4N) that leads to resistance to cationic antimicrobial peptides (CAMPs) and clinical antimicrobials such as polymyxin. The C-terminal dehydrogenase domain of ArnA catalyzes the oxidative decarboxylation of UDP-glucuronic acid (UDP-GlcUA) to UDP-4-keto-arabinose (UDP-Ara4O), while the N-terminal formyltransferase domain of ArnA catalyzes the addition of a formyl group to UDP-4-amino-4-deoxy-L-arabinose (UDP-L-Ara4N) to form UDP-L-4-formamido-arabinose (UDP-L-Ara4FN). This domain family represents the catalytic core of the N-terminal formyltransferase domain. The formyltransferase also contains a smaller C-terminal domain the may be involved in substrate binding. ArnA forms a hexameric structure, in which the dehydrogenase domains are arranged at the center of the particle with the transformylase domains on the outside of the particle. 203 matched cddid_all.tbl CDD cd08645 cd08645 187714 FMT_core_GART Phosphoribosylglycinamide formyltransferase (GAR transformylase, GART). Phosphoribosylglycinamide formyltransferase, also known as GAR transformylase or GART, is an essential enzyme that catalyzes the third step in de novo purine biosynthesis. This enzyme uses formyl tetrahydrofolate as a formyl group donor to produce 5'-phosphoribosyl-N-formylglycinamide. In prokaryotes, GART is a single domain protein but in most eukaryotes it is the C-terminal portion of a large multifunctional protein which also contains GAR synthetase and aminoimidazole ribonucleotide synthetase activities. 183 matched cddid_all.tbl CDD cd08646 cd08646 187715 FMT_core_Met-tRNA-FMT_N Methionyl-tRNA formyltransferase, N-terminal hydrolase domain. Methionyl-tRNA formyltransferase (Met-tRNA-FMT), N-terminal formyltransferase domain. Met-tRNA-FMT transfers a formyl group from N-10 formyltetrahydrofolate to the amino terminal end of a methionyl-aminoacyl-tRNA acyl moiety, yielding formyl-Met-tRNA. Formyl-Met-tRNA plays essential role in protein translation initiation by forming complex with IF2. The formyl group plays a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and by impairing its binding to EFTU-GTP. The N-terminal domain contains a Rossmann fold and it is the catalytic domain of the enzyme. 204 matched cddid_all.tbl CDD cd08647 cd08647 187716 FMT_core_FDH_N 10-formyltetrahydrofolate dehydrogenase (FDH), N-terminal hydrolase domain. This family represents the N-terminal hydrolase domain of the bifunctional protein 10-formyltetrahydrofolate dehydrogenase (FDH). This domain contains a 10-formyl-tetrahydrofolate (10-formyl-THF) binding site and shares sequence homology and structural topology with other enzymes utilizing this substrate. This domain functions as a hydrolase, catalyzing the conversion of 10-formyl-THF, a precursor for nucleotide biosynthesis, to tetrahydrofolate (THF). The overall FDH reaction mechanism is a coupling of two sequential reactions, a hydrolase and a formyl dehydrogenase, bridged by a substrate transfer step. The N-terminal hydrolase domain removes the formyl group from 10-formyl-THF and the C-terminal NADP-dependent dehydrogenase domain then reduces the formyl group to carbon dioxide. The two catalytic domains are connected by a third intermediate linker domain that transfers the formyl group, covalently attached to the sulfhydryl group of the phosphopantetheine arm, from the N-terminal domain to the C-terminal domain. 203 matched cddid_all.tbl CDD cd08648 cd08648 187717 FMT_core_Formyl-FH4-Hydrolase_C Formyltetrahydrofolate deformylase (Formyl-FH4 hydrolase), C-terminal hydrolase domain. Formyl-FH4 Hydrolase catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate. Formate is the substrate of phosphoribosylglycinamide transformylase for step three of de novo purine nucleotide synthesis. Formyl-FH4 hydrolase has been proposed to regulate the balance of FH4 and C1-FH4 in the cell. The enzyme uses methionine and glycine to sense the pools of C1-FH4 and FH4, respectively. This domain belongs to the formyltransferase (FMT) domain superfamily. Members of this family have an N-terminal ACT domain, which is commonly involved in specifically bind an amino acid or other small ligand leading to regulation of the enzyme. The N-terminal of this protein family may be responsible for the binding of the regulators methionine and glycine. 196 matched cddid_all.tbl CDD cd08649 cd08649 187718 FMT_core_NRPS_like N-terminal formyl transferase catalytic core domain of NRPS_like proteins, one of the proteins involved in the synthesis of Oxazolomycin. This family represents the N-terminal formyl transferase catalytic core domain present in a subgroup of non-ribosomal peptide synthetases. In Streptomyces albus a member of this family has been shown to be involved in the synthesis of oxazolomycin (OZM). OZM is a hybrid peptide-polyketide antibiotic and exhibits potent antitumor and antiviral activities. It is a multi-domain protein consisting of a formyl transferase domain, a Flavin-utilizing monoxygenase domain, a LuxE domain functioning as an acyl protein synthetase and a pp-binding domain, which may function as an acyl carrier. It shows sequence similarity with other peptide-polyketide biosynthesis proteins. 166 matched cddid_all.tbl CDD cd08650 cd08650 187719 FMT_core_HypX_N HypX protein, N-terminal hydrolase domain. The family represents the N-terminal hydrolase domain of HypX protein. HypX is involved in the maturation process of active [NiFe] hydrogenase. [NiFe] hydrogenases function in H2 metabolism in a variety of microorganisms, enabling them to use H2 as a source of reducing equivalent under aerobic and anaerobic conditions. [NiFe] hydrogenases consist of a large and a small subunit. The large subunit contains [NiFe] active site, which is synthesized as a precursor without the [NiFe] active site. This precursor then undergoes a complex post-translational maturation process that requires the presence of a number of accessory proteins. HypX has been shown to be involved in this maturation process and have been proposed to participate in the generation and transport of the CO and CN ligands. However, HypX is not present in all hydrogen-metabolizing bacteria. Furthermore, hypX deletion mutants have a reduced but detectable level of hydrogenase activity. Thus, HypX might not be a determining factor in the matur ation process. Members of this group have an N-terminal formyl transferase domain and a C-terminal enoyl-CoA hydratase/isomerase domain. 151 matched cddid_all.tbl CDD cd08651 cd08651 187720 FMT_core_like_4 Formyl transferase catalytic core domain found in a group of proteins with unknown functions. Formyl transferase catalytic core domain found in a group of proteins with unknown functions. Formyl transferase catalyzes the transfer of one-carbon groups, specifically the formyl- or hydroxymethyl- group. This domain contains a Rossmann fold and it is the catalytic domain of the enzyme. 180 matched cddid_all.tbl CDD cd08653 cd08653 187721 FMT_core_like_3 Formyl transferase catalytic core domain found in a group of proteins with unknown functions. Formyl transferase catalytic core domain found in a group of proteins with unknown functions. Formyl transferase catalyzes the transfer of one-carbon groups, specifically the formyl- or hydroxymethyl- group. This domain contains a Rossmann fold and it is the catalytic domain of the enzyme. 152 matched cddid_all.tbl CDD cd08656 cd08656 349943 M28_like M28 Zn-peptidase; uncharacterized subfamily. Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. 287 matched cddid_all.tbl CDD cd08659 cd08659 349944 M20_ArgE_DapE-like Peptidase M20 acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE)-like. Peptidase M20 acetylornithine deacetylase/succinyl-diaminopimelate desuccinylase (ArgE/DapE) like family of enzymes catalyze analogous reactions and share a common activator, the metal ion (usually Co2+ or Zn2+). ArgE catalyzes a broad range of substrates, including N-acetylornithine, alpha-N-acetylmethionine and alpha-N-formylmethionine, while DapE catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelate (L,L-SDAP) to L,L-diaminopimelate and succinate. Proteins in this family are mostly bacterial and have been inferred by homology as being related to both ArgE and DapE. This family also includes N-acetyl-L-citrulline deacetylase (ACDase; acetylcitrulline deacetylase), a unique, novel enzyme found in Xanthomonas campestris, a plant pathogen, in which N-acetyl-L-ornithine is the substrate for transcarbamoylation reaction, and the product is N-acetyl-L-citrulline. Thus, in the arginine biosynthesis pathway, ACDase subsequently catalyzes the hydrolysis of N-acetyl-L-citrulline to acetate and L-citrulline. 361 matched cddid_all.tbl CDD cd08660 cd08660 349945 M20_Acy1-like M20 Peptidase Aminoacylase 1-like family. This family includes aminoacylase 1 (ACY1) and Aminoacylase 1-like protein 2 (ACY1L2). Aminoacylase 1 proteins are a class of zinc binding homodimeric enzymes involved in hydrolysis of N-acetylated proteins. ACY1 (acyl-L-amino-acid amidohydrolase; EC 3.5.1.14) is the most abundant of the aminoacylases, a class of zinc binding homodimeric enzymes involved in hydrolysis of N-acetylated proteins. It is encoded by the aminoacylase 1 gene (Acy1) on chromosome 3p21 that comprises 15 exons. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in protection and stability of proteins. Several types of aminoacylases can be distinguished on the basis of substrate specificity; substrates include indoleacetic acid (IAA) N-conjugates of amino acids, N-acetyl-L-amino acids and aminobenzoylglutamate. ACY1 breaks down cytosolic aliphatic N-acyl-alpha-amino acids (except L-aspartate), especially N-acetyl-methionine and acetyl-glutamate into L-amino acids and an acyl group. However, ACY1 can also catalyze the reverse reaction, the synthesis of acetylated amino acids. ACY1L2 family contains many uncharacterized proteins predicted as amidohydrolases, including gene products of abgA and abgB that catalyze the cleavage of p-aminobenzoyl-glutamate, a folate catabolite in E. coli, to p-aminobenzoate and glutamate. p-Aminobenzoyl-glutamate utilization is catalyzed by the abg region gene product, AbgT. Defects in ACY1 are the cause of aminoacylase-1 deficiency (ACY1D) resulting in a metabolic disorder manifesting with encephalopathy and psychomotor delay. 366 matched cddid_all.tbl CDD cd08662 cd08662 341056 M13 Peptidase family M13 includes neprilysin and endothelin-converting enzyme I. The M13 family of metallopeptidases includes neprilysin (neutral endopeptidase, NEP, enkephalinase, CD10, CALLA, EC 3.4.24.11), endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), erythrocyte surface antigen KELL (ECE-3), phosphate-regulating gene on the X chromosome (PHEX), soluble secreted endopeptidase (SEP), and damage-induced neuronal endopeptidase (DINE)/X-converting enzyme (XCE). Proteins in this family fulfill a broad range of physiological roles due to the greater variation in the active site's S2' subsite allowing substrate specificity. NEP is expressed in a variety of tissues including kidney and brain, and is involved in many physiological and pathological processes, including blood pressure and inflammatory response. It degrades a wide array of substrates such as substance P, enkephalins, cholecystokinin, neurotensin and somatostatin. It is an important enzyme in the regulation of amyloid-beta (Abeta) protein that forms amyloid plaques that are associated with Alzeimers disease (AD). ECE-1 catalyzes the final rate-limiting step in the biosynthesis of endothelins via post-translational conversion of the biologically inactive big endothelins. Like NEP, it also hydrolyzes bradykinin, substance P, neurotensin, and Abeta. Endothelin-1 overproduction has been implicated in various diseases including stroke, asthma, hypertension, and cardiac and renal failure. Kell is a homolog of NEP and constitutes a major antigen on human erythrocytes; it preferentially cleaves big endothelin-3 to produce bioactive endothelin-3, but is also known to cleave substance P and neurokinin A. PHEX forms a complex interaction with fibroblast growth factor 23 (FGF23) and matrix extracellular phosphoglycoprotein, causing bone mineralization. A loss-of-function mutation in PHEX disrupts this interaction leading to hypophosphatemic rickets; X-linked hypophosphatemic (XLH) rickets is the most common form of metabolic rickets. ECEL1 is a brain metalloprotease which plays a critical role in the nervous regulation of the respiratory system, while DINE is abundantly expressed in the hypothalamus and its expression responds to nerve injury. A majority of these M13 proteases are prime therapeutic targets for selective inhibition. 642 matched cddid_all.tbl CDD cd08663 cd08663 176450 DAP_dppA_1 Peptidase M55, D-aminopeptidase dipeptide-binding protein family. M55 Peptidase, D-Aminopeptidase dipeptide-binding protein (dppA; DAP dppA; EC 3.4.11.-) domain: Peptide transport systems are found in many bacterial species and generally function to accumulate intact peptides in the cell, where they are hydrolyzed. The dipeptide-binding protein (dppA) of Bacillus subtilis belongs to the dipeptide ABC transport (dpp) operon expressed early during sporulation. It is a binuclear zinc-dependent, D-specific aminopeptidase. The biologically active enzyme is a homodecamer with active sites buried in its channel. These self-compartmentalizing proteases are characterized by a SXDXEG motif. D-Ala-D-Ala and D-Ala-Gly-Gly are the preferred substrates. Bacillus subtilis dppA is thought to function as an adaptation to nutrient deficiency; hydrolysis of its substrate releases D-Ala which can be used subsequently as metabolic fuel. This family also contains a number of uncharacterized putative peptidases. 266 matched cddid_all.tbl CDD cd08664 cd08664 176485 APC10-HERC2 APC10-like DOC1 domain present in HERC2 (HECT domain and RLD2). This model represents the APC10/DOC1 domain present in HERC2 (HECT domain and RLD2), a large multi-domain protein with three RCC1-like domains (RLDs), additional internal domains including a zinc finger ZZ-type and Cyt-b5 (Cytochrome b5-like Heme/Steroid binding) domains, and a C-terminal HECT (Homologous to the E6-AP Carboxyl Terminus) domain. The APC10/DOC1 domain of HERC2 is a homolog of the APC10 subunit and the DOC1 domain present in E3 ubiquitin ligases which mediate substrate ubiquitination (or ubiquitylation), a component of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. As suggested by structural relationships between HERC2 and other proteins such as HERC1, the proposed role for HERC2 in protein trafficking and degradation pathways is consistent with observations that mutations in HERC2 lead to neuromuscular secretory vesicle and sperm acrosome defects, other developmental abnormalities, and juvenile lethality of jdf2 mice. Recent studies have shown that the protein complex, HERC2-RNF8, coordinates ubiquitin-dependent assembly of DNA repair factors on damaged chromosomes. 152 matched cddid_all.tbl CDD cd08665 cd08665 176486 APC10-CUL7 APC10-like DOC1 domain of CUL7, subunit of the SCF-ROC1-like E3 ubiquitin ligase complex that mediates substrate ubiquitination. This model represents the APC10/DOC1 domain present in CUL7, a subunit of the SCF-ROC1-like E3 Ubiquitin (Ub) ligase complex, which mediates substrate ubiquitination (or ubiquitylation), and is a component of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. CUL7 is a member of the Cullin-RING ligase family and functions as a molecular scaffold assembling the SCF-ROC1-like E3 Ub ligase complex consisting of the adapter protein Skp1, CUL7, the WD40 repeat-containing F-box Fbw8 (also known as Fbx29), and ROC1 (RING-box protein 1). CUL7 is a large protein with a C-terminal cullin domain that binds ROC1 and additional domains, including an APC10/DOC1 domain. While the Fbw8 protein is responsible for substrate protein recognition, the ROC1 RING domain recruits an Ub-charged E2 Ub-conjugating enzyme for substrate ubiquitination. It remains to be determined how CUL7 binds to the Skp1-Fbw8 heterodimer. The CUL7 E3 Ub ligase has been implicated in the proteasomal degradation of the cellular proteins, cyclin D1, an important regulator of the G1 to S-phase cell cycle progression, and insulin receptor substrate 1, a critical component of the signaling pathways downstream of the insulin and insulin-like growth factor 1 receptor. CUL7 appears to be an important regulator of placental development. Germ line mutations of CUL7 are linked to 3-M syndrome and Yakuts short stature syndrome. 131 matched cddid_all.tbl CDD cd08666 cd08666 176487 APC10-HECTD3 APC10-like DOC1 domain of HECTD3, a HECT E3 ubiquitin ligase protein that mediates substrate ubiquitination. This model represents the APC10/DOC1 domain present in HECTD3, a HECT (Homologous to the E6-AP Carboxyl Terminus) E3 ubiquitin ligase protein. HECT E3 ubiquitin ligases mediate substrate ubiquitination (or ubiquitylation), and are a component of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. They also regulate the trafficking of many receptors, channels, transporters and viral proteins. HECTD3 (HECT domain-containing protein3) contains a C-terminal HECT domain with the active site for ubiquitin transfer onto substrates, and an N-terminal APC10/DOC1 domain, which is responsible for substrate recognition and binding. HECTD3 specifically recognizes the Trio-binding protein, Tara (Trio-associated repeat on actin), implicated in regulating actin cytoskeletal, cell motility and cell growth. Tara also binds to TRF1 and may participate in telomere maintenance and/or mitotic regulation through interacting with TRF1. HECTD3 interacts with and promotes the ubiquitination of Syntaxin 8, an endosomal syntaxin proposed to mediate distinct steps of endosomal protein trafficking. HECTD3-mediated Syntaxin 8 degradation has been suggested to contribute to the pathophysiology of neurodegenerative diseases. 134 matched cddid_all.tbl CDD cd08667 cd08667 176488 APC10-ZZEF1 APC10/DOC1-like domain of uncharacterized Zinc finger ZZ-type and EF-hand domain-containing protein 1 (ZZEF1) and homologs. This model represents the APC10/DOC1-like domain present in the uncharacterized Zinc finger ZZ-type and EF-hand domain-containing protein 1 (ZZEF1) of Mus musculus. Members of this family contain EF-hand, APC10, CUB, and zinc finger ZZ-type domains. ZZEF1-like APC10 domains are homologous to the APC10 subunit/DOC1 domains present in E3 ubiquitin ligases, which mediate substrate ubiquitination (or ubiquitylation), and are components of the ubiquitin-26S proteasome pathway for selective proteolytic degradation. 131 matched cddid_all.tbl CDD cd08674 cd08674 176571 Cdt1_m The middle winged helix fold of replication licensing factor Cdt1 binds geminin to inhibit binding of the MCM complex to origins of replication and DNA. Cdt1 is a replication licensing factor in eukaryotes that recruits the Minichromosome Maintenance Complex (MCM2-7) to the origin recognition complex (ORC). The Cdt1 protein is divided into three regions based on sequence comparison and biochemical analyses: the N-terminal region (Cdt1_n) binds DNA in a sequence-, strand-, and conformation-independent manner; the middle winged helix fold (Cdt1_m) binds geminin to inhibit both binding of the MCM complex to origins of replication and DNA; and the C-terminal region (Cdt1_c) is essential for Cdt1 activity and directly interacts with the MCM2-7 helicase. Precise duplication of chromosomal DNA is required for genomic stability during replication. Assembly of replication factors to start DNA replication in eukaryotes must occur only once per cell cycle. To form a pre-replicative complex on replication origins in the G phase, ORC first binds origin DNA and triggers the binding of Cdc6 and Cdt1. These two factors recruit a putative replicative helicase and the MCM2-7. The MCM2-7 complex promotes the unwinding of DNA origins, and the binding of additional factors to initiate the DNA replication in S-phase. Cdt1 is present during G1 and early S phase of the cell cycle and degraded during the late S, G2, and M phases. The winged helix fold structure of Cdt1_m is similar to the structures of Cdt1_c and other archaeal homologues of the eukaryotic replication initiator, without apparent sequence similarity. 185 matched cddid_all.tbl CDD cd08675 cd08675 176057 C2B_RasGAP C2 domain second repeat of Ras GTPase activating proteins (GAPs). RasGAPs suppress Ras function by enhancing the GTPase activity of Ras proteins resulting in the inactive GDP-bound form of Ras. In this way it can control cellular proliferation and differentiation. The proteins here all contain two tandem C2 domains, a Ras-GAP domain, and a pleckstrin homology (PH)-like domain. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. Members here have a type-I topology. 137 matched cddid_all.tbl CDD cd08676 cd08676 176058 C2A_Munc13-like C2 domain first repeat in Munc13 (mammalian uncoordinated)-like proteins. C2-like domains are thought to be involved in phospholipid binding in a Ca2+ independent manner in both Unc13 and Munc13. Caenorabditis elegans Unc13 has a central domain with sequence similarity to PKC, which includes C1 and C2-related domains. Unc13 binds phorbol esters and DAG with high affinity in a phospholipid manner. Mutations in Unc13 results in abnormal neuronal connections and impairment in cholinergic neurotransmission in the nematode. Munc13 is the mammalian homolog which are expressed in the brain. There are 3 isoforms (Munc13-1, -2, -3) and are thought to play a role in neurotransmitter release and are hypothesized to be high-affinity receptors for phorbol esters. Unc13 and Munc13 contain both C1 and C2 domains. There are two C2 related domains present, one central and one at the carboxyl end. Munc13-1 contains a third C2-like domain. Munc13 interacts with syntaxin, synaptobrevin, and synaptotagmin suggesting a role for these as scaffolding proteins. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the second C2 repeat, C2B, and has a type-II topology. 153 matched cddid_all.tbl CDD cd08677 cd08677 176059 C2A_Synaptotagmin-13 C2 domain. Synaptotagmin is a membrane-trafficking protein characterized by a N-terminal transmembrane region, a linker, and 2 C-terminal C2 domains. Synaptotagmin 13, a member of class 6 synaptotagmins, is located in the brain. It functions are unknown. It, like synaptotagmins 8 and 12, does not have any consensus Ca2+ binding sites. Previously all synaptotagmins were thought to be calcium sensors in the regulation of neurotransmitter release and hormone secretion, but it has been shown that not all of them bind calcium. Of the 17 identified synaptotagmins only 8 bind calcium (1-3, 5-7, 9, 10). The function of the two C2 domains that bind calcium are: regulating the fusion step of synaptic vesicle exocytosis (C2A) and binding to phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the absence of calcium ions and to phosphatidylinositol bisphosphate (PIP2) in their presence (C2B). C2B also regulates also the recycling step of synaptic vesicles. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This CD contains the first C2 repeat, C2A, and has a type-I topology. 118 matched cddid_all.tbl CDD cd08678 cd08678 176060 C2_C21orf25-like C2 domain found in the Human chromosome 21 open reading frame 25 (C21orf25) protein. The members in this cd are named after the Human C21orf25 which contains a single C2 domain. Several other members contain a C1 domain downstream of the C2 domain. No other information on this protein is currently known. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 126 matched cddid_all.tbl CDD cd08679 cd08679 176061 C2_DOCK180_related C2 domains found in Dedicator Of CytoKinesis 1 (DOCK 180) and related proteins. Dock180 was first identified as an 180kd proto-oncogene product c-Crk-interacting protein involved in actin cytoskeletal changes. It is now known that it has Rac-specific GEF activity, but lacks the conventional Dbl homology (DH) domain. There are 10 additional related proteins that can be divided into four classes based on sequence similarity and domain organization: Dock-A which includes Dock180/Dock1, Dock2, and Dock5; Dock-B which includes Dock3/MOCA (modifier of cell adhesion) and Dock4; Dock-C which includes Dock6/Zir1, Dock7/Zir2, and Dock8/Zir3; and Dock-D, which includes Dock9/Zizimin1, Dock10/Zizimin3, and Dock11/Zizimin2/ACG (activated Cdc42-associated GEF). Most of members of classes Dock-A and Dock-B are the GEFs specific for Rac. Those of Dock-D are Cdc42-specific GEFs while those of Dock-C are the GEFs for both. All Dock180-related proteins have two common homology domains: the C2 domain (AKA Dock homology region (DHR)-1, CED-5, Dock180, MBC-zizimin homology (CZH) 1) and the DHR-2 (AKA CZH2, or Docker). DHR-2 has the catalytic activity for Rac and/or Cdc42, but is structurally unrelated to the DH domain. The C2/DHR-1 domains of Dock180 and Dock4 have been shown to bind phosphatidylinositol-3, 4, 5-triphosphate (PtdIns(3,4,5)P3). The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 178 matched cddid_all.tbl CDD cd08680 cd08680 176062 C2_Kibra C2 domain found in Human protein Kibra. Kibra is thought to be a regulator of the Salvador (Sav)/Warts (Wts)/Hippo (Hpo) (SWH) signaling network, which limits tissue growth by inhibiting cell proliferation and promoting apoptosis. The core of the pathway consists of a MST and LATS family kinase cascade that ultimately phosphorylates and inactivates the YAP/Yorkie (Yki) transcription coactivator. The FERM domain proteins Merlin (Mer) and Expanded (Ex) are part of the upstream regulation controlling pathway mechanism. Kibra colocalizes and associates with Mer and Ex and is thought to transduce an extracellular signal via the SWH network. The apical scaffold machinery that contains Hpo, Wts, and Ex recruits Yki to the apical membrane facilitating its inhibitory phosphorlyation by Wts. Since Kibra associates with Ex and is apically located it is hypothesized that KIBRA is part of the scaffold, helps in the Hpo/Wts complex, and helps recruit Yki for inactivation that promotes SWH pathway activity. Kibra contains two amino-terminal WW domains, an internal C2-like domain, and a carboxy-terminal glutamic acid-rich stretch. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 124 matched cddid_all.tbl CDD cd08681 cd08681 176063 C2_fungal_Inn1p-like C2 domain found in fungal Ingression 1 (Inn1) proteins. Saccharomyces cerevisiae Inn1 associates with the contractile actomyosin ring at the end of mitosis and is needed for cytokinesis. The C2 domain of Inn1, located at the N-terminus, is required for ingression of the plasma membrane. The C-terminus is relatively unstructured and contains eight PXXP motifs that are thought to mediate interaction of Inn1 with other proteins with SH3 domains in the cytokinesis proteins Hof1 (an F-BAR protein) and Cyk3 (whose overexpression can restore primary septum formation in Inn1Delta cells) as well as recruiting Inn1 to the bud-neck by binding to Cyk3. Inn1 and Cyk3 appear to cooperate in activating chitin synthase Chs2 for primary septum formation, which allows coordination of actomyosin ring contraction with ingression of the cleavage furrow. It is thought that the C2 domain of Inn1 helps to preserve the link between the actomyosin ring and the plasma membrane, contributing both to membrane ingression, as well as to stability of the contracting ring. Additionally, Inn1 might induce curvature of the plasma membrane adjacent to the contracting ring, thereby promoting ingression of the membrane. It has been shown that the C2 domain of human synaptotagmin induces curvature in target membranes and thereby contributes to fusion of these membranes with synaptic vesicles. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 118 matched cddid_all.tbl CDD cd08682 cd08682 176064 C2_Rab11-FIP_classI C2 domain found in Rab11-family interacting proteins (FIP) class I. Rab GTPases recruit various effector proteins to organelles and vesicles. Rab11-family interacting proteins (FIPs) are involved in mediating the role of Rab11. FIPs can be divided into three classes: class I FIPs (Rip11a, Rip11b, RCP, and FIP2) which contain a C2 domain after N-terminus of the protein, class II FIPs (FIP3 and FIP4) which contain two EF-hands and a proline rich region, and class III FIPs (FIP1) which exhibits no homology to known protein domains. All FIP proteins contain a highly conserved, 20-amino acid motif at the C-terminus of the protein, known as Rab11/25 binding domain (RBD). Class I FIPs are thought to bind to endocytic membranes via their C2 domain, which interacts directly with phospholipids. Class II FIPs do not have any membrane binding domains leaving much to speculate about the mechanism involving FIP3 and FIP4 interactions with endocytic membranes. The members in this CD are class I FIPs. The exact function of the Rab11 and FIP interaction is unknown, but there is speculation that it involves the role of forming a targeting complex that recruits a group of proteins involved in membrane transport to organelles. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 126 matched cddid_all.tbl CDD cd08683 cd08683 176065 C2_C2cd3 C2 domain found in C2 calcium-dependent domain containing 3 (C2cd3) proteins. C2cd3 is a novel C2 domain-containing protein specific to vertebrates. C2cd3 functions in regulator of cilia formation, Hedgehog signaling, and mouse embryonic development. Mutations in C2cd3 mice resulted in lethality in some cases and exencephaly, a twisted body axis, and pericardial edema in others. The presence of calcium-dependent lipid-binding domains in C2cd3 suggests a potential role in vesicular transport. C2cd3 is also an interesting candidate for ciliopathy because of its orthology to certain cilia-related genetic disease loci on chromosome. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 143 matched cddid_all.tbl CDD cd08684 cd08684 176066 C2A_Tac2-N C2 domain first repeat found in Tac2-N (Tandem C2 protein in Nucleus). Tac2-N contains two C2 domains and a short C-terminus including a WHXL motif, which are key in stabilizing transport vesicles to the plasma membrane by binding to a plasma membrane. However unlike the usual carboxyl-terminal-type (C-type) tandem C2 proteins, it lacks a transmembrane domain, a Slp-homology domain, and a Munc13-1-interacting domain. Homology search analysis indicate that no known protein motifs are located in its N-terminus, making Tac2-N a novel class of Ca2+-independent, C-type tandem C2 proteins. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 103 matched cddid_all.tbl CDD cd08685 cd08685 176067 C2_RGS-like C2 domain of the Regulator Of G-Protein Signaling (RGS) family. This CD contains members of the regulator of G-protein signaling (RGS) family. RGS is a GTPase activating protein which inhibits G-protein mediated signal transduction. The protein is largely cytosolic, but G-protein activation leads to translocation of this protein to the plasma membrane. A nuclear form of this protein has also been described, but its sequence has not been identified. There are multiple alternatively spliced transcript variants in this family with some members having additional domains (ex. PDZ and RGS) downstream of the C2 domain. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 119 matched cddid_all.tbl CDD cd08686 cd08686 176068 C2_ABR C2 domain in the Active BCR (Breakpoint cluster region) Related protein. The ABR protein is similar to the breakpoint cluster region protein. It has homology to guanine nucleotide exchange proteins and GTPase-activating proteins (GAPs). ABR is expressed primarily in the brain, but also includes non-neuronal tissues such as the heart. It has been associated with human diseases such as Miller-Dieker syndrome in which mental retardation and malformations of the heart are present. ABR contains a RhoGEF domain and a PH-like domain upstream of its C2 domain and a RhoGAP domain downstream of this domain. A few members also contain a Bcr-Abl oncoprotein oligomerization domain at the very N-terminal end. Splice variants of ABR have been identified. ABR is found in a wide variety of organisms including chimpanzee, dog, mouse, rat, fruit fly, and mosquito. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 118 matched cddid_all.tbl CDD cd08687 cd08687 176069 C2_PKN-like C2 domain in Protein kinase C-like (PKN) proteins. PKN is a lipid-activated serine/threonine kinase. It is a member of the protein kinase C (PKC) superfamily, but lacks a C1 domain. There are at least 3 different isoforms of PKN (PRK1/PKNalpha/PAK1; PKNbeta, and PRK2/PAK2/PKNgamma). The C-terminal region contains the Ser/Thr type protein kinase domain, while the N-terminal region of PKN contains three antiparallel coiled-coil (ACC) finger domains which are relatively rich in charged residues and contain a leucine zipper-like sequence. These domains binds to the small GTPase RhoA. Following these domains is a C2-like domain. Its C-terminal part functions as an auto-inhibitory region. PKNs are not activated by classical PKC activators such as diacylglycerol, phorbol ester or Ca2+, but instead are activated by phospholipids and unsaturated fatty acids. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 98 matched cddid_all.tbl CDD cd08688 cd08688 176070 C2_KIAA0528-like C2 domain found in the Human KIAA0528 cDNA clone. The members of this CD are named after the Human KIAA0528 cDNA clone. All members here contain a single C2 repeat. No other information on this protein is currently known. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 110 matched cddid_all.tbl CDD cd08689 cd08689 176071 C2_fungal_Pkc1p C2 domain found in protein kinase C (Pkc1p) in Saccharomyces cerevisiae. This family is named after the protein kinase C in Saccharomyces cerevisiae, Pkc1p. Protein kinase C is a member of a family of Ser/Thr phosphotransferases that are involved in many cellular signaling pathways. PKC has two antiparallel coiled-coiled regions (ACC finger domain) (AKA PKC homology region 1 (HR1)/ Rho binding domain) upstream of the C2 domain and two C1 domains downstream. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains, like those of PKC, are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 109 matched cddid_all.tbl CDD cd08690 cd08690 176072 C2_Freud-1 C2 domain found in 5' repressor element under dual repression binding protein-1 (Freud-1). Freud-1 is a novel calcium-regulated repressor that negatively regulates basal 5-HT1A receptor expression in neurons. It may also play a role in the altered regulation of 5-HT1A receptors associated with anxiety or major depression. Freud-1 contains two DM-14 basic repeats, a helix-loop-helix DNA binding domain, and a C2 domain. The Freud-1 C2 domain is thought to be calcium insensitive and it lacks several acidic residues that mediate calcium binding of the PKC C2 domain. In addition, it contains a poly-basic insert that is not present in calcium-dependent C2 domains and may function as a nuclear localization signal. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. This cd contains the first C2 repeat, C2A, and has a type-II topology. 155 matched cddid_all.tbl CDD cd08691 cd08691 176073 C2_NEDL1-like C2 domain present in NEDL1 (NEDD4-like ubiquitin protein ligase-1). NEDL1 (AKA HECW1(HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1)) is a newly identified HECT-type E3 ubiquitin protein ligase highly expressed in favorable neuroblastomas. In vertebrates it is found primarily in neuronal tissues, including the spinal cord. NEDL1 is thought to normally function in the quality control of cellular proteins by eliminating misfolded proteins. This is thought to be accomplished via a mechanism analogous to that of ER-associated degradation by forming tight complexes and aggregating misfolded proteins that have escaped ubiquitin-mediated degradation. NEDL1, is composed of a C2 domain, two WW domains, and a ubiquitin ligase Hect domain. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 137 matched cddid_all.tbl CDD cd08692 cd08692 176074 C2B_Tac2-N C2 domain second repeat found in Tac2-N (Tandem C2 protein in Nucleus). Tac2-N contains two C2 domains and a short C-terminus including a WHXL motif, which are key in stabilizing transport vesicles to the plasma membrane by binding to a plasma membrane. However unlike the usual carboxyl-terminal-type (C-type) tandem C2 proteins, it lacks a transmembrane domain, a Slp-homology domain, and a Munc13-1-interacting domain. Homology search analysis indicate that no known protein motifs are located in its N-terminus, making Tac2-N a novel class of Ca2+-independent, C-type tandem C2 proteins. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 135 matched cddid_all.tbl CDD cd08693 cd08693 176075 C2_PI3K_class_I_beta_delta C2 domain present in class I beta and delta phosphatidylinositol 3-kinases (PI3Ks). PI3Ks (AKA phosphatidylinositol (PtdIns) 3-kinases) regulate cell processes such as cell growth, differentiation, proliferation, and motility. PI3Ks work on phosphorylation of phosphatidylinositol, phosphatidylinositide (4)P (PtdIns (4)P),2 or PtdIns(4,5)P2. Specifically they phosphorylate the D3 hydroxyl group of phosphoinositol lipids on the inositol ring. There are 3 classes of PI3Ks based on structure, regulation, and specificity. All classes contain a C2 domain, a PIK domain, and a kinase catalytic domain. The members here are class I, beta and delta isoforms of PI3Ks and contain both a Ras-binding domain and a p85-binding domain. Class II PI3Ks contain both of these as well as a PX domain, and a C-terminal C2 domain containing a nuclear localization signal. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. Members have a type-I topology. 173 matched cddid_all.tbl CDD cd08694 cd08694 176076 C2_Dock-A C2 domains found in Dedicator Of CytoKinesis (Dock) class A proteins. Dock-A is one of 4 classes of Dock family proteins. The members here include: Dock180/Dock1, Dock2, and Dock5. Most of these members have been shown to be GEFs specific for Rac. Dock5 has not been well characterized to date, but most likely also is a GEF specific for Rac. In addition to the C2 domain (AKA Dock homology region (DHR)-1, CED-5, Dock180, MBC-zizimin homology (CZH) 1) and the DHR-2 (AKA CZH2, or Docker), which all Dock180-related proteins have, Dock-A members contain a proline-rich region and a SH3 domain upstream of the C2 domain. DHR-2 has the catalytic activity for Rac and/or Cdc42, but is structurally unrelated to the DH domain. The C2/DHR-1 domains of Dock180 and Dock4 have been shown to bind phosphatidylinositol-3, 4, 5-triphosphate (PtdIns(3,4,5)P3). The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 196 matched cddid_all.tbl CDD cd08695 cd08695 176077 C2_Dock-B C2 domains found in Dedicator Of CytoKinesis (Dock) class B proteins. Dock-B is one of 4 classes of Dock family proteins. The members here include: Dock3/MOCA (modifier of cell adhesion) and Dock4. Most of these members have been shown to be GEFs specific for Rac, although Dock4 has also been shown to interact indirectly with the Ras family GTPase Rap1, probably through Rap regulatory proteins. In addition to the C2 domain (AKA Dock homology region (DHR)-1, CED-5, Dock180, MBC-zizimin homology (CZH) 1) and the DHR-2 (AKA CZH2, or Docker), which all Dock180-related proteins have, Dock-B members contain a SH3 domain upstream of the C2 domain and a proline-rich region downstream. DHR-2 has the catalytic activity for Rac and/or Cdc42, but is structurally unrelated to the DH domain. The C2/DHR-1 domains of Dock180 and Dock4 have been shown to bind phosphatidylinositol-3, 4, 5-triphosphate (PtdIns(3,4,5)P3). The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 189 matched cddid_all.tbl CDD cd08696 cd08696 176078 C2_Dock-C C2 domains found in Dedicator Of CytoKinesis (Dock) class C proteins. Dock-C is one of 4 classes of Dock family proteins. The members here include: Dock6/Zir1, Dock7/Zir2, and Dock8/Zir3. Dock-C members are GEFs for both Rac and Cdc42. In addition to the C2 domain (AKA Dock homology region (DHR)-1, CED-5, Dock180, MBC-zizimin homology (CZH) 1) and the DHR-2 (AKA CZH2, or Docker), which all Dock180-related proteins have, Dock-C members contain a functionally uncharacterized domain upstream of the C2 domain. DHR-2 has the catalytic activity for Rac and/or Cdc42, but is structurally unrelated to the DH domain. The C2/DHR-1 domains of Dock180 and Dock4 have been shown to bind phosphatidylinositol-3, 4, 5-triphosphate (PtdIns(3,4,5)P3). The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 179 matched cddid_all.tbl CDD cd08697 cd08697 176079 C2_Dock-D C2 domains found in Dedicator Of CytoKinesis (Dock) class C proteins. Dock-D is one of 4 classes of Dock family proteins. The members here include: Dock9/Zizimin1, Dock10/Zizimin3, and Dock11/Zizimin2/ACG (activated Cdc42-associated GEF). Dock-D are Cdc42-specific GEFs. In addition to the C2 domain (AKA Dock homology region (DHR)-1, CED-5, Dock180, MBC-zizimin homology (CZH) 1) and the DHR-2 (AKA CZH2, or Docker), which all Dock180-related proteins have, Dock-D members contain a functionally uncharacterized domain and a PH domain upstream of the C2 domain. DHR-2 has the catalytic activity for Rac and/or Cdc42, but is structurally unrelated to the DH domain. The C2/DHR-1 domains of Dock180 and Dock4 have been shown to bind phosphatidylinositol-3, 4, 5-triphosphate (PtdIns(3,4,5)P3). The PH domain broadly binds to phospholipids and is thought to be involved in targeting the plasma membrane. The C2 domain was first identified in PKC. C2 domains fold into an 8-standed beta-sandwich that can adopt 2 structural arrangements: Type I and Type II, distinguished by a circular permutation involving their N- and C-terminal beta strands. Many C2 domains are Ca2+-dependent membrane-targeting modules that bind a wide variety of substances including bind phospholipids, inositol polyphosphates, and intracellular proteins. Most C2 domain proteins are either signal transduction enzymes that contain a single C2 domain, such as protein kinase C, or membrane trafficking proteins which contain at least two C2 domains, such as synaptotagmin 1. However, there are a few exceptions to this including RIM isoforms and some splice variants of piccolo/aczonin and intersectin which only have a single C2 domain. C2 domains with a calcium binding region have negatively charged residues, primarily aspartates, that serve as ligands for calcium ions. 185 matched cddid_all.tbl CDD cd08698 cd08698 381627 TGF_beta_SF transforming growth factor beta (TGF-beta) like domain found in TGF-beta superfamily. TGF-beta superfamily consists of a large group of cell regulatory proteins, such as TFG-betas, Nodal, Activins/Inhibins, glial cell-line-derived neurotrophic factor (GDNF) family of ligands, bone morphogenetic proteins (BMPs), and growth and differentiation factors (GDFs). They play important roles in developmental and physiological processes in a variety of species, including invertebrates as well as vertebrates, through specific receptor complexes that are composed of type I and type II serine/threonine receptor kinases. The receptor kinases subsequently activate Smad proteins, which then propagate the signals into the nucleus to regulate target gene expression. Proteins from the TGF-beta superfamily are only active as homo- or heterodimer. 100 matched cddid_all.tbl CDD cd08700 cd08700 187728 FMT_C_OzmH_like C-terminal subdomain of the Formyltransferase-like domain found in OzmH-like proteins. Domain found in OzmH-like proteins with similarity to the C-terminal domain of Formyltransferase. OzmH is one of the proteins involved in the synthesis of Oxazolomycin (OZM), which is a hybrid peptide-polyketide antibiotic that exhibits potent antitumor and antiviral activities. OzmH is a multi-domain protein consisting of a formyl transferase domain, a flavin-utilizing monoxygenase domain, a LuxE domain functioning as an acyl protein synthetase and a phosphopantetheine (PP)-binding domain, which may function as an acyl carrier. It shows sequence similarity with other peptide-polyketide biosynthesis proteins. 100 matched cddid_all.tbl CDD cd08701 cd08701 187729 FMT_C_HypX C-terminal subdomain of the Formyltransferase-like domain found in HypX-like proteins. Domain found in HypX-like proteins with similarity to the C-terminal domain of Formyltransferase. HypX is involved in the maturation process of active [NiFe] hydrogenase. [NiFe] hydrogenases function in H2 metabolism in a variety of microorganisms, enabling them to use H2 as a source of reducing equivalents under aerobic and anaerobic conditions. [NiFe] hydrogenases consist of a large and a small subunit. The large subunit contains the [NiFe] active site but is synthesized as a precursor without the [NiFe] active site. This precursor undergoes a complex post-translational maturation process that requires the presence of a number of accessory proteins. HypX has been shown to be involved in this maturation process and have been proposed to participate in the generation and transport of the CO and CN ligands. However, HypX is not present in all hydrogen-metabolizing bacteria. Furthermore, hypX deletion mutants have a reduced but detectable level of hydrogenase activity. Thus, HypX might not be the determining factor in the maturation process. Members of this group have an N-terminal formyl transferase domain and a C-terminal enoyl-CoA hydratase/isomerase domain. 96 matched cddid_all.tbl CDD cd08702 cd08702 187730 Arna_FMT_C C-terminal subdomain of the formyltransferase domain on ArnA, which modifies lipid A with 4-amino-4-deoxy-l-arabinose. Domain found in ArnA with similarity to the C-terminal domain of Formyltransferase. ArnA is a bifunctional enzyme required for the modification of lipid A with 4-amino-4-deoxy-l-arabinose (Ara4N) that leads to resistance to cationic antimicrobial peptides (CAMPs) and clinical antimicrobials such as polymyxin. The C-terminal domain of ArnA is a dehydrogenase domain that catalyzes the oxidative decarboxylation of UDP-glucuronic acid (UDP-GlcUA) to UDP-4-keto-arabinose (UDP-Ara4O) and the N-terminal domain is a formyltransferase domain that catalyzes the addition of a formyl group to UDP-4-amino-4-deoxy-L-arabinose (UDP-L-Ara4N) to form UDP-L-4-formamido-arabinose (UDP-L-Ara4FN). This domain family represents the C-terminal subdomain of the formyltransferase domain, downstream of the N-terminal subdomain containing the catalytic center. ArnA forms a hexameric structure (a dimer of trimers), in which the dehydrogenase domains are arranged at the center with the transformylase domains on the outside of the complex. 92 matched cddid_all.tbl CDD cd08703 cd08703 187731 FDH_Hydrolase_C The C-terminal subdomain of the hydrolase domain on the bi-functional protein 10-formyltetrahydrofolate dehydrogenase. The family represents the C-terminal subdomain of the hydrolase domain on the bi-functional protein, 10-formyltetrahydrofolate dehydrogenase (FDH). FDH catalyzes the conversion of 10-formyltetrahydrofolate, a precursor for nucleotide biosynthesis, to tetrahydrofolate. The protein comprises two functional domains: the N-terminal hydrolase domain that removes a formyl group from 10-formyltetrahydrofolate and the C-terminal NADP-dependent dehydrogenase domain that reduces the formyl group to carbon dioxide. The hydrolase domain contains an N-terminal formyl transferase catalytic core subdomain and this C-terminal subdomain, which may be involved in substrate binding. 100 matched cddid_all.tbl CDD cd08704 cd08704 187732 Met_tRNA_FMT_C C-terminal domain of Formyltransferase and other enzymes. C-terminal domain of formyl transferase and other proteins with diverse enzymatic activities. Proteins found in this family include methionyl-tRNA formyltransferase, ArnA, and 10-formyltetrahydrofolate dehydrogenase. Methionyl-tRNA formyltransferases constitute the majority of the family and also demonstrate greater sequence diversity. Although most proteins with formyltransferase activity contain the C-terminal domain, some formyltransferases ( for example, prokaryotic glycinamide ribonucleotide transformylase (GART)) only have the core catalytic domain, indicating that the C-terminal domain is not a requirement for catalytic activity and may be involved in substrate binding. For example, the C-terminal domain of methionyl-tRNA formyltransferase is involved in the tRNA binding. 87 matched cddid_all.tbl CDD cd08705 cd08705 188660 RGS_R7-like Regulator of G protein signaling (RGS) domain found in the R7 subfamily of proteins. The RGS (Regulator of G-protein Signaling) domain is an essential part of the R7 (Neuronal RGS) protein subfamily of the RGS protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. The R7 subfamily includes RGS6, RGS7, RGS9, and RGS11, all of which, in humans, are expressed predominantly in the nervous system, form an obligatory complex with G-beta-5, and play important roles in the regulation of crucial neuronal processes. In addition, R7 proteins were found to bind many other proteins outside of the G protein signaling pathways including: m-opioid receptor, beta-arrestin, alpha-actinin-2, NMDAR, polycystin, spinophilin, guanylyl cyclase, among others. 121 matched cddid_all.tbl CDD cd08706 cd08706 188661 RGS_R12-like Regulator of G protein signaling (RGS) domain found in the R12 subfamily of proteins. The RGS (Regulator of G-protein Signaling) domain is an essential part of the R12 (Neuronal RGS) protein subfamily of the RGS protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play a critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. Deactivation of G-protein signaling, controlled by RGS domain, accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP that results in reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. The R12 RGS subfamily includes RGS10, RGS12 and RGS14 all of which are highly selective for G-alpha-i1 over G-alpha-q. 113 matched cddid_all.tbl CDD cd08707 cd08707 188662 RGS_Axin Regulator of G protein signaling (RGS) domain found in the Axin protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the Axin protein. Axin is a member of the RA/RGS subfamily of the RGS protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, and skeletal and muscle development. The RGS domain of Axin is specifically interacts with the heterotrimeric G-alpha12 protein, but not with closely related G-alpha13, and provides a unique tool to regulate G-alpha12-mediated signaling processes. The RGS domain of Axin also interacts with the tumor suppressor protein APC (Adenomatous Polyposis Coli) in order to control the cytoplasmic level of the proto-oncogene, beta-catenin. 117 matched cddid_all.tbl CDD cd08708 cd08708 188663 RGS_FLBA Regulator of G protein signaling (RGS) domain found in the FLBA (Fluffy Low BrlA) protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the FLBA (Fluffy Low BrlA) protein. FLBA is a member of the RGS protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins play a critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. Deactivation of the G-protein signaling controlled by the RGS domain accelerates the GTPase activity of the alpha subunit by hydrolysis of GTP to GDP which results in reassociation of the alpha-subunit with the beta-gamma-dimer and thereby inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes. The RGS domain of the FLBA protein antagonizes G protein signaling to block proliferation and allow development. It is required for control of mycelial proliferation and activation of asexual sporulation in yeast. 148 matched cddid_all.tbl CDD cd08709 cd08709 188664 RGS_RGS2 Regulator of G protein signaling (RGS) domain found in the RGS2 protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the RGS2 protein. RGS2 is a member of R4/RGS subfamily of RGS family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. The RGS domain controls G-protein signaling by accelerating the GTPase activity of the G- alpha subunit which leads to G protein deactivation and promotes desensitization. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS2 plays important roles in the regulation of blood pressure and the pathogenesis of human hypertension, as well as in bone formation in osteoblasts. Outside of the GPCR pathway RGS2 interacts with calmodulin, beta- COP, tubulin, PKG1-alpha, and TRPV6. 114 matched cddid_all.tbl CDD cd08710 cd08710 188665 RGS_RGS16 Regulator of G protein signaling (RGS) domain found in the RGS16 protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the RGS16 protein. RGS16 is a member of the RGS protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha subunits. The RGS domain controls G-protein signaling by accelerating the GTPase activity of the G-alpha subunit which leads to G protein deactivation and promotes desensitization. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS16 is a member of the R4/RGS subfamily and interacts with neuronal G-alpha0. RGS16 expression is upregulated by IL-17 of the NF-kappaB signaling pathway in autoimmune B cells. 114 matched cddid_all.tbl CDD cd08711 cd08711 188666 RGS_RGS8 Regulator of G protein signaling (RGS) domain found in the RGS8 protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the RGS8 protein. RGS8 is a member of R4/RGS subfamily of RGS family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha subunits. The RGS domain controls G-protein signaling by accelerating the GTPase activity of the G-alpha subunit which leads to G protein deactivation and promotes desensitization. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS8 is involved in G-protein-gated potassium channels regulation and predominantly expressed in the brain. RGS8 also is selectively expressed in the hematopoietic system (NK cells). 125 matched cddid_all.tbl CDD cd08712 cd08712 188667 RGS_RGS18 Regulator of G protein signaling (RGS) domain found in the RGS18 protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the RGS18 protein. RGS18 is a member of the RGS protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha subunits. The RGS domain controls G-protein signaling by accelerating the GTPase activity of the G-alpha subunit which leads to G protein deactivation and promotes desensitization. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS18 is a member of the R4/RGS subfamily and is expressed predominantly in osteoclasts where it acts as a negative regulator of the acidosis-induced osteoclastogenic OGR1/NFAT signaling pathway. RANKL (receptor activator of nuclear factor B ligand) stimulates osteoclastogenesis by inhibiting expression of RGS18. 114 matched cddid_all.tbl CDD cd08713 cd08713 188668 RGS_RGS3 Regulator of G protein signaling (RGS) domain found in the RGS3 protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the RGS3 protein. RGS3 is a member of the R4/RGS subfamily of the RGS family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha subunits. The RGS domain controls G-protein signaling by accelerating the GTPase activity of the G-alpha subunit which leads to G protein deactivation and promotes desensitization. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes. RGS3 induces apoptosis when overexpressed and is involved in cell migration through interaction with the Ephrin receptor. RGS3 exits as several splice isoforms and interacts with neuroligin, estrogen receptor-alpha, and 14-3-3 outside of the GPCR pathways. 114 matched cddid_all.tbl CDD cd08714 cd08714 188669 RGS_RGS4 Regulator of G protein signaling (RGS) domain found in the RGS4 protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the RGS4 protein. RGS4 is a member of the R4/RGS subfamily of the RGS family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha subunits. The RGS domain controls G-protein signaling by accelerating the GTPase activity of the G-alpha subunit which leads to G protein deactivation and promotes desensitization. RGS4 is expressed widely in brain including prefrontal cortex, striatum, locus coeruleus (LC), and hippocampus and has been implicated in regulation of opioid, cholinergic, and serotonergic signaling. Dysfunctions in RGS4 proteins are involved in etiology of Parkinson's disease, addiction, and schizophrenia. RGS4 also is up-regulated in the failing human heart. RGS4 interacts with many binding partners outside of GPCR pathways, including calmodulin, COP, Kir3, PIP, calcium/CaM, PA, ErbB3, and 14-3-3. 114 matched cddid_all.tbl CDD cd08715 cd08715 188670 RGS_RGS1 Regulator of G protein signaling (RGS) domain found in the RGS1 protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the RGS1 protein. RGS1 is a member of the R4/RGS subfamily of the RGS family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha subunits. The RGS domain controls G-protein signaling by accelerating the GTPase activity of the G-alpha subunit which leads to G protein deactivation and promotes desensitization. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS 1 is expressed predominantly in hematopoietic compartments, including T and B lymphocytes, and may play a major role in chemokine-mediated homing of lymphocytes to secondary lymphoid organs. In addition, RGS1 interacts with calmodulin and 14-3-3 protein outside of the GPCR pathway. 114 matched cddid_all.tbl CDD cd08716 cd08716 188671 RGS_RGS13 Regulator of G protein signaling (RGS) domain found in the RGS13 protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the RGS13 protein. RGS13 is member of the R4/RGS subfamily of the RGS family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha subunits. The RGS domain controls G-protein signaling by accelerating the GTPase activity of the G-alpha subunit which leads to G protein deactivation and promotes desensitization. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS13 is predominantly expressed in T and B lymphocytes and in mast cells, and plays a role in adaptive immune responses. RGS13 also found in Rgs13, which is also expressed in dendritic cells and in neuroendocrine cells of the thymus, gastrointestinal, and respiratory tracts. Outside of the GPCR pathway, RGS5 interacts with the PIP3 protein. 114 matched cddid_all.tbl CDD cd08717 cd08717 188672 RGS_RGS5 Regulator of G protein signaling (RGS) domain found in the RGS5 protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the RGS5 protein. RGS5 is member of the R4/RGS subfamily of the RGS family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha subunits. The RGS domain controls G-protein signaling by accelerating the GTPase activity of the G-alpha subunit which leads to G protein deactivation and promotes desensitization. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. Two splice isoforms of RGS5 has been found: RGS5L (long) which is expressed in smooth muscle cells (pericytes) and heart and RGS5S (short) which is highly expressed in the ciliary body of the eye, kidney, brain, spleen, skeletal muscle, and small intestine. Outside of the GPCR pathway, RGS5 interacts with the 14-3-3 protein. 114 matched cddid_all.tbl CDD cd08718 cd08718 188673 RGS_RZ-like Regulator of G protein signaling (RGS) domain found in the RZ protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the RZ subfamily of the RGS protein family. They are a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. Deactivation of G-protein signaling is controlled by RGS domains, which accelerate GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, which results in reassociation of the alpha-subunit with the beta-gamma-dimer and inhibition of downstream activity. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. The RZ subfamily of RGS proteins includes RGS17, RGS19 (former GAIP), RGS20, and its splice variant Ret-RGS. 118 matched cddid_all.tbl CDD cd08719 cd08719 188674 RGS_SNX13 Regulator of G protein signaling (RGS) domain found in the Sorting Nexin 13 (SNX13) protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the SNX13 (Sorting Nexin 13) protein, a member of the RGS protein family. They are a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. The RGS-domain of SNX13 plays a major role through attenuation of Galphas-mediated signaling and regulates endocytic trafficking and degradation of the epidermal growth factor receptor. Snx13-null mice were embryonic lethal around midgestation which supports an essential role for SNX13 in mouse development and regulation of endocytosis dynamics. 135 matched cddid_all.tbl CDD cd08720 cd08720 188675 RGS_SNX25 Regulator of G protein signaling (RGS) domain found in the Sorting Nexin 25 (SNX25) protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the SNX25 (Sorting Nexin 25) protein, a member of the RGS protein family. They are a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. SNX25 is a member of the Dopamine receptors (DAR) signalplex and regulates the trafficking of D1 and D2 DARs. 110 matched cddid_all.tbl CDD cd08721 cd08721 188676 RGS_AKAP2_2 Regulator of G protein signaling (RGS) domain 2 found in the A-kinase anchoring protein, D-AKAP2. The RGS (Regulator of G-protein Signaling) domain is an essential part of the D-AKAP2 (A-kinase anchoring protein), a member of the RGS protein family. They are a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. D-AKAP2 contains two RGS domains which play an important role in spatiotemporal localization of cAMP-dependent PKA (cyclic AMP-dependent protein kinase) that regulates many different signaling pathways by phosphorylation of target proteins. This cd contains the second RGS domain. 121 matched cddid_all.tbl CDD cd08722 cd08722 188677 RGS_SNX14 Regulator of G protein signaling (RGS) domain found in the Sorting Nexin14 (SNX14) protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the SNX14 (Sorting Nexin14) protein, a member of the RGS protein family. They are a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. SNX14 is believed to regulates membrane trafficking in motor neurons. 127 matched cddid_all.tbl CDD cd08723 cd08723 188678 RGS_RGS21 Regulator of G protein signaling (RGS) domain found in the RGS21 protein. The RGS (Regulator of G-protein Signaling) domain is an essential part RGS21 protein, a member of RGS protein family. They are a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes. RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, apoptosis, and cell proliferation, as well as modulation of cardiac development. RGS21 is a member of the R4/RGS subfamily and its mRNA was detected only in sensory taste cells that express sweet taste receptors and the taste G-alpha subunit, gustducin, suggesting a potential role in regulating taste transduction. 111 matched cddid_all.tbl CDD cd08724 cd08724 188679 RGS_GRK-like Regulator of G protein signaling domain (RGS) found in G protein-coupled receptor kinase (GRK). The RGS domain is found in G protein-coupled receptor kinases (GRKs). These proteins play a key role in phosphorylation-dependent desensitization/resensitization of GPCRs (G protein-coupled receptors), intracellular trafficking, endocytosis, as well as in the modulation of important intracellular signaling cascades by GPCR. GRKs also modulate cellular response in phosphorylation-independent manner using their ability to interact with multiple signaling proteins involved in many essential cellular pathways. The RGS domain of the GRKs has very little sequence similarity with the canonical RGS domain of the RGS proteins and therefore is often refered to as the RH (RGS Homology) domain. Based on sequence homology the GRK family consists of three major subfamilies: the GRK4 subfamily (GRK4, GRK5 and GRK6), the rhodopsin kinase or visual GRK subfamily (GRK1 and GRK7), and the beta-adrenergic receptor kinases subfamily (GRK2/GRK3). RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. 114 matched cddid_all.tbl CDD cd08725 cd08725 188680 RGS_RGS22_4 Regulator of G protein signaling domain RGS_RGS22_4. The RGS (Regulator of G-protein Signaling) domain found in the RGS22 protein, a member of the RA/RGS subfamily of the RGS protein family. They are a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. RGS22 contains at least 3 copies of the RGS domain in vertebrata and exists in multiple splicing variants. RGS22 is predominantly expressed in testis and believed to play an important role in spermatogenesis. 123 matched cddid_all.tbl CDD cd08726 cd08726 188681 RGS_RGS22_3 Regulator of G protein signaling domain RGS_RGS22_3. The RGS (Regulator of G-protein Signaling) domain found in the RGS22 protein, a member of the RA/RGS subfamily of the RGS protein family. They are a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. RGS22 contains at least 3 copies of the RGS domain in vertebrata and exists in multiple splicing variants. RGS22 is predominantly expressed in testis and believed to play an important role in spermatogenesis. 130 matched cddid_all.tbl CDD cd08727 cd08727 188682 RGS_RGS22_2 Regulator of G protein signaling domain RGS_RGS22_2. The RGS (Regulator of G-protein Signaling) domain found in the RGS22 protein, a member of the RA/RGS subfamily of the RGS protein family. They are a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. RGS22 contains at least 3 copies of the RGS domain in vertebrata and exists in multiple splicing variants. RGS22 is predominantly expressed in testis and believed to play an important role in spermatogenesis. 116 matched cddid_all.tbl CDD cd08728 cd08728 188683 RGS-like_2 Uncharacterized Regulator of G protein Signaling (RGS) domain subfamily, child 2. These uncharacterized RGS-like domains consists largely of hypothetical proteins. The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play an important role in neuronal signal modulation. Some RGS proteins are the principal elements needed for proper vision. 179 matched cddid_all.tbl CDD cd08729 cd08729 188684 RGS_PX Regulator of G protein signaling domain. These uncharacterized RGS-like domains are found in proteins that also contain one or more PX domains. The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. As a major G-protein regulator, the RGS domain containing proteins that are involves in many crucial cellular processes. RGS proteins regulate intracellular trafficking and provide vital support for signal transduction. RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. Several RGS proteins can fine-tune immune responses, others RGS proteins play important role in neuronal signals modulation. Some RGS proteins are the principal elements needed for proper vision. 136 matched cddid_all.tbl CDD cd08730 cd08730 188685 RGS-like_3 Uncharacterized Regulator of G protein Signaling (RGS) domain subfamily, child 3. These uncharacterized RGS-like domains consists largely of hypothetical proteins. The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. As a major G-protein regulator, the RGS domain containing proteins that are involved in many crucial cellular processes. RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play an important role in neuronal signal modulation. Some RGS proteins are the principal elements needed for proper vision. 165 matched cddid_all.tbl CDD cd08731 cd08731 188686 RGS_RGS22_1 Regulator of G protein signaling domain RGS_RGS22_1. The RGS (Regulator of G-protein Signaling) domain found in the RGS22 protein, a member of the RA/RGS subfamily of the RGS protein family, which is a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. RGS22 contains at least 3 copies of the RGS domain in vertebrata and exists in multiple splicing variants. RGS22 is predominantly expressed in testis and believed to play an important role in spermatogenesis. 125 matched cddid_all.tbl CDD cd08732 cd08732 188687 RGS-like_4 Uncharacterized Regulator of G protein Signaling (RGS) domain subfamily, child 4. These uncharacterized RGS-like domains consists largely of hypothetical proteins. The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play an important role in neuronal signal modulation. Some RGS proteins are the principal elements needed for proper vision. 139 matched cddid_all.tbl CDD cd08734 cd08734 188688 RGS-like_1 Uncharacterized Regulator of G protein Signaling (RGS) domain subfamily, child 1. These uncharacterized RGS-like domains consists largely of hypothetical proteins. The RGS domain is an essential part of the Regulator of G-protein Signaling (RGS) protein family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. As a major G-protein regulator, the RGS domain containing proteins that are involved in many crucial cellular processes. RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. Several RGS proteins can fine-tune immune responses, while others play an important role in neuronal signal modulation. Some RGS proteins are the principal elements needed for proper vision. 109 matched cddid_all.tbl CDD cd08735 cd08735 188689 RGS_AKAP2_1 Regulator of G protein signaling (RGS) domain 1 found in the A-kinase anchoring protein, D-AKAP2. The RGS (Regulator of G-protein Signaling) domain is an essential part of the D-AKAP2 (A-kinase anchoring protein), a member of the RGS protein family. They are a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. D-AKAP2 contains two RGS domains which play an important role in spatiotemporal localization of cAMP-dependent PKA (cyclic AMP-dependent protein kinase) that regulates many different signaling pathways by phosphorylation of target proteins. This cd contains the first RGS domain. 171 matched cddid_all.tbl CDD cd08736 cd08736 188690 RGS_RhoGEF-like Regulator of G protein signaling (RGS) domain found in the Rho guanine nucleotide exchange factor (RhoGEF) protein. The RGS domain found in the Rho guanine nucleotide exchange factor (RhoGEF) protein subfamily of the RGS domain containing protein family, which is a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RhoGEFs link signals from heterotrimeric G-alpha12/13 protein-coupled receptors to Rho GTPase activation, leading to various cellular responses, such as actin reorganization and gene expression. The RGS domain of the RhoGEFs has very little sequence similarity with the canonical RGS domain of the RGS proteins and therefore is often refered to as the RH (RGS Homology) domain. The RGS-GEFs subfamily includes the leukemia-associated RhoGEF (LARG), p115RhoGEF, and PDZ-RhoGEF. RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. 120 matched cddid_all.tbl CDD cd08737 cd08737 188691 RGS_RGS6 Regulator of G protein signaling (RGS) domain found in the RGS6 protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the RGS6 protein, a member of R7 subfamily of the RGS protein family. RGS is a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). Other members of the R7 subfamily (Neuronal RGS) include: RGS7, RGS9, and RGS11, all of which are expressed predominantly in the nervous system, form an obligatory complex with G-beta-5, and play important roles in the regulation of crucial neuronal processes such as vision and motor control. Additionally they have been implicated in many neurological conditions such as anxiety, schizophrenia, and drug dependence. RGS6 exists in multiple splice isoforms with identical RGS domains, but possess complete or incomplete GGL domains and distinct N- and C-terminal domains. RGS6 interacts with SCG10, a neuronal growth-associated protein and therefore regulates neuronal differentiation. Another RGS6-binding protein is DMAP1, a component of the Dnmt1 complex involved in repression of newly replicated genes. Mutations of a critical residue required for interaction of RGS6 protein with G proteins did not affect the ability of RGS6 to interact with both SCG10 and DMAP1. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. 125 matched cddid_all.tbl CDD cd08738 cd08738 188692 RGS_RGS7 Regulator of G protein signaling (RGS) domain found in the RGS7 protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the RGS7 protein, a member of R7 subfamily of the RGS protein family. RGS is a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. Other members of the R7 subfamily (Neuronal RGS) include: RGS6, RGS9, and RGS11, all of which are expressed predominantly in the nervous system, form an obligatory complex with G-beta-5, and play important roles in the regulation of crucial neuronal processes such as vision and motor control. Additionally they have been implicated in many neurological conditions such as anxiety, schizophrenia, and drug dependence. R7 RGS proteins are key modulators of the pharmacological effects of drugs involved in the development of tolerance and addiction. In addition, RGS7 was found to bind a component of the synaptic fusion complex, snapin, and some other proteins outside of G protein signaling pathways. 121 matched cddid_all.tbl CDD cd08739 cd08739 188693 RGS_RGS9 Regulator of G protein signaling (RGS) domain found in the RGS9 protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the RGS9 protein, a member of R7 subfamily of the RGS protein family. RGS is a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. Other members of the R7 subfamily (Neuronal RGS) include: RGS6, RGS7, and RGS11, all of which are expressed predominantly in the nervous system, form an obligatory complex with G-beta-5, and play important roles in the regulation of crucial neuronal processes such as vision and motor control. Additionally they have been implicated in many neurological conditions such as anxiety, schizophrenia, and drug dependence. RGS9 forms constitutive complexes with G-beta-5 subunit and controls such fundamental functions as vision and behavior. RGS9 exists in two splice isoforms: RGS9-1 which regulates phototransduction in rods and cones and RGS9-2 which regulates dopamine and opioid signaling in the basal ganglia. In addition, RGS9 was found to bind many other proteins outside of G protein signaling pathways including: mu-opioid receptor, beta-arrestin, alpha-actinin-2, NMDAR, polycystin, spinophilin, and guanylyl cyclase, among others. 121 matched cddid_all.tbl CDD cd08740 cd08740 188694 RGS_RGS11 Regulator of G protein signaling (RGS) domain found in the RGS11 protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the RGS11 protein, a member of R7 subfamily of the RGS protein family. RGS is a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. Other members of the R7 subfamily (Neuronal RGS) include: RGS6, RGS7, and RGS9, all of which are expressed predominantly in the nervous system, form an obligatory complex with G-beta-5, and play important roles in the regulation of crucial neuronal processes such as vision and motor control. Additionally they have been implicated in many neurological conditions such as anxiety, schizophrenia, and drug dependence. RGS11 is expressed exclusively in retinal ON-bipolar neurons in which it forms complexes with G-beta-5 and R7AP (RGS7 anchor protein ) and plays crucial roles in processing the light responses of retinal neurons. 126 matched cddid_all.tbl CDD cd08741 cd08741 188695 RGS_RGS10 Regulator of G protein signaling (RGS) domain found in the RGS10 protein. RGS (Regulator of G-protein Signaling) domain is an essential part of the RGS10 protein. RGS10 is a member of the RA/RGS subfamily of RGS proteins family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS10 belong to the R12 RGS subfamily, which includes RGS12 and RGS14, all of which are highly selective for G-alpha-i1 over G-alpha-q. RGS10 exists in 2 splice isoforms. RGS10A is specifically expressed in osteoclasts and is a key component in the RANKL signaling mechanism for osteoclast differentiation, whereas RGS10B expressed in brain and in immune tissues and has been implicated in diverse processes including: promoting of dopaminergic neuron survival via regulation of the microglial inflammatory response, modulation of presynaptic and postsynaptic G-protein signalling, as well as a possible role in regulation of gene expression. 113 matched cddid_all.tbl CDD cd08742 cd08742 188696 RGS_RGS12 Regulator of G protein signaling (RGS) domain found in the RGS12 protein. RGS (Regulator of G-protein Signaling) domain is an essential part of the RGS12 protein. RGS12 is a member of the RA/RGS subfamily of RGS proteins family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS12 belong to the R12 RGS subfamily, which includes RGS10 and RGS14, all of which are highly selective for G-alpha-i1 over G-alpha-q. RGS12 exist in multiple splice variants: RGS12s (short) contains the core RGS/RBD/GoLoco domains, while RGS12L (long) has additional N-terminal PDZ and PTB domains. RGS12 splice variants show distinct expression patterns, suggesting that they have discrete functions during mouse embryogenesis. RGS12 also may play a critical role in coordinating Ras-dependent signals that are required for promoting and maintaining neuronal differentiation. 115 matched cddid_all.tbl CDD cd08743 cd08743 188697 RGS_RGS14 Regulator of G protein signaling (RGS) domain found in the RGS14 protein. RGS (Regulator of G-protein Signaling) domain is an essential part of the RGS14 protein. RGS14 is a member of the RA/RGS subfamily of RGS proteins family, a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). As a major G-protein regulator, RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS14 belong to the R12 RGS subfamily, which includes RGS10 and RGS12, all of which are highly selective for G-alpha-i1 over G-alpha-q. RGS14 binds and regulates the subcellular localization and activities of H-Ras and Raf kinases in cells and thereby integrates G protein and Ras/Raf signaling pathways. 129 matched cddid_all.tbl CDD cd08744 cd08744 188698 RGS_RGS17 Regulator of G protein signaling (RGS) domain found in the RGS17 protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the RGS17 protein, a member of the RZ subfamily of the RGS protein family. They are a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). As a major G-protein regulator, the RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. Deactivation of the G-protein signaling controlled by the RGS domain, which accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, results in reassociation of the alpha-subunit with the beta-gamma-dimer and inhibition of downstream activity. The RZ subfamily of RGS proteins includes RGS19 (former GAIP), RGS20, and its splice variant Ret-RGS. RGS17 is a relatively non-selective GAP for G-alpha-z and other G-alpha-i/o proteins. RGS17 blocks dopamine receptor-mediated inhibition of cAMP accumulation; it also blocks thyrotropin releasing hormone-stimulated Ca++ mobilization. RGS17, like other members of RZ subfamily, can act either as a GAP or as G-protein effector antogonist. 118 matched cddid_all.tbl CDD cd08745 cd08745 188699 RGS_RGS19 Regulator of G protein signaling (RGS) domain found in the RGS19 protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the RGS19 protein (also known as GAIP), a member of the RZ subfamily of the RGS protein family. They are a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. Deactivation of G-protein signaling is controlled by RGS domains, which accelerate GTPase activity of the alpha subunit by hydrolysis of GTP to GDP, resulting in a reassociation of the alpha-subunit with the beta-gamma-dimer and an inhibition of downstream activity. As a major G-protein regulator, the RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. The RZ subfamily of RGS proteins includes RGS17, RGS20, and its splice variant Ret-RGS. RGS19 participates in regulation of dopamine receptor D2R and D3R, as well as beta-adrenergic receptors . 118 matched cddid_all.tbl CDD cd08746 cd08746 188700 RGS_RGS20 Regulator of G protein signaling (RGS) domain found in the RGS20 protein. The RGS (Regulator of G-protein Signaling) domain is an essential part of the RGS20 protein (also known as RGSZ1), a member of the RZ subfamily of the RGS protein family. They are a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). RGS proteins play critical regulatory roles as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. Deactivation of G-protein signaling is controlled by the RGS domain, which accelerates GTPase activity of the alpha subunit by hydrolysis of GTP to GDP resulting in reassociation of the alpha-subunit with the beta-gamma-dimer and inhibition of downstream activity. As a major G-protein regulator, the RGS domain containing proteins are involved in many crucial cellular processes such as regulation of intracellular trafficking, glial differentiation, embryonic axis formation, skeletal and muscle development, and cell migration during early embryogenesis. The RZ subfamily of RGS proteins include RGS17, RGS19 (former GAIP), and the splice variant of RGS20, Ret-RGS. RGS20 is expressed exclusively in brain, with the highest concentrations in the temporal lobe and the caudate nucleus and may play a role in signaling regulation in these brain regions. RGS20 acts as a GAP of both G-alpha-z and G-alpha-I and controls signaling in the mu opioid receptor pathway. 167 matched cddid_all.tbl CDD cd08747 cd08747 188701 RGS_GRK2_GRK3 Regulator of G protein signaling domain (RGS) found in G protein-coupled receptor kinase 2 (GRK2) and G protein-coupled receptor kinase 3 (GRK3). The RGS domain is an essential part of the GRK2 (G protein-coupled receptor kinases 2) and the GRK3 proteins, which are members of the beta-adrenergic receptor kinases subfamily. GRK2 and GRK3 are ubiquitously expressed and can phosphorylate many different GPCR. The C-terminus of GRK2 and 3 contains a plekstrin homology domain (PH) with binding sites for the membrane phospholipid PIP2 and free G#? subunits. These specific interactions could help to maintain a membrane-bound population of GRK2 prior to the agonist-dependent overt GRK2 translocation. GRK2 and GRK3 are members of the GRK kinase family which includes three major subfamilies: the GRK4 subfamily (GRK4, GRK5 and GRK6), the rhodopsin kinase or visual GRK subfamily (GRK1 and GRK7), and the beta-adrenergic receptor kinases subfamily (GRK2/GRK3). The RGS domain of the GRKs has very little sequence similarity with the canonical RGS domain of the RGS proteins and therefore is often refered to as the RH (RGS Homology) domain. RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. 157 matched cddid_all.tbl CDD cd08748 cd08748 188702 RGS_GRK1 Regulator of G protein signaling domain (RGS) found in G protein-coupled receptor kinase 1 (GRK1). The RGS domain is found in G protein-coupled receptor kinases 1 (GRK1, also refered to as Rhodopsin kinase) which play a key role in phosphorylation of rhodopsin (Rho), a G protein-coupled receptor responsible for visual signal transduction in rod cell. GRK1 is a member of the GRK kinase family which includes three major subfamilies: the GRK4 subfamily (GRK4, GRK5 and GRK6), the rhodopsin kinase or visual GRK subfamily (GRK1 and GRK7), and the beta-adrenergic receptor kinases subfamily (GRK2/GRK3). The RGS domain of the GRKs has very little sequence similarity with the canonical RGS domain of the RGS proteins and therefore is often refered to as the RH (RGS Homology) domain. A few inactivation mutations in GRK1 have been found in patients with Oguchi disease, a stationary form of night blindness. RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. 138 matched cddid_all.tbl CDD cd08749 cd08749 188703 RGS_GRK7 Regulator of G protein signaling domain (RGS) found in G protein-coupled receptor kinase 7 (GRK7). The RGS domain is an essential part of the GRK7 (G protein-coupled receptor kinases 7) proteins which together with GRK1 (Rhodopsin kinase) have been implicated in the shutoff of the photoresponse and adaptation to changing light conditions via rod and cone opsin phosphorylation. GRK7 is a member of the GRK kinase family which includes three major subfamilies: the GRK4 subfamily (GRK4, GRK5 and GRK6), the rhodopsin kinase or visual GRK subfamily (GRK1 and GRK7), and the beta-adrenergic receptor kinases subfamily (GRK2/GRK3). The RGS domain of the GRKs has very little sequence similarity with the canonical RGS domain of the RGS proteins and therefore is often refered to as the RH (RGS Homology) domain. GRK7 is expressed in all vertebrate cones except that of mice and rats, which do not have the gene for GRK7. Lack of either GRK7 or both GRK1 and GRK7 in human leads to a vision defect called Enhanced S Cone syndrome. RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. 139 matched cddid_all.tbl CDD cd08750 cd08750 188704 RGS_GRK4 Regulator of G protein signaling domain (RGS) found in G protein-coupled receptor kinase 4 (GRK4). The RGS domain is an essential part of the GRK4 (G protein-coupled receptor kinase4) proteins, which are membrane-associated serine/threonine protein kinases that phosphorylate G protein-coupled receptors (GPCRs) upon agonist stimulation. This phosphorylation initiates beta-arrestin-mediated receptor desensitization, internalization, and signaling events. GRK4 is a member of the GRK kinase family which includes three major subfamilies: the GRK4 subfamily (GRK4, GRK5 and GRK6), the rhodopsin kinase or visual GRK subfamily (GRK1 and GRK7), and the beta-adrenergic receptor kinases subfamily (GRK2/GRK3). The RGS domain of the GRKs has very little sequence similarity with the canonical RGS domain of the RGS proteins and therefore is often refered to as the RH (RGS Homology) domain. GRK4 plays a key role in regulating dopaminergic-mediated natriuresis and is associated with essential hypertension and/or salt-sensitive hypertension. GRK4 exists in four splice variants involved in hyperphosphorylation, desensitization, and internalization of two dopamine receptors (D1R and D3R). GRK4 also increases the expression of a key receptor of the renin-angiotensin system, the AT1R (angiotensin type 1 receptor). RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. 132 matched cddid_all.tbl CDD cd08751 cd08751 188705 RGS_GRK6 Regulator of G protein signaling domain (RGS) found in G protein-coupled receptor kinase 6 (GRK6). The RGS domain is an essential part of the GRK6 (G protein-coupled receptor kinase 6) protein which plays an important role in the regulating of dopamine, opioids, M3 muscarinic, and chemokine receptor signaling. GRK6 is a member of the GRK kinase family which includes three major subfamilies: the GRK4 subfamily (GRK4, GRK5 and GRK6), the rhodopsin kinase or visual GRK subfamily (GRK1 and GRK7), and the beta-adrenergic receptor kinases subfamily (GRK2/GRK3). The RGS domain of the GRKs has very little sequence similarity with the canonical RGS domain of the RGS proteins and therefore is often refered to as the RH (RGS Homology) domain. The RH domain of GRK6 does not have structural determinants that are required for binding G-alpha subunit, in contrast to GRK2 and many other RGS proteins. GRK6 is an important target for treatment of addiction and Parkinson disease. RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. 145 matched cddid_all.tbl CDD cd08752 cd08752 188706 RGS_GRK5 Regulator of G protein signaling domain (RGS) found in G protein-coupled receptor kinase 5 (GRK5). The RGS domain is an essential part of the GRK5 (G protein-coupled receptor kinase 5) protein, a membrane-associated serine/threonine protein kinases which phosphorylates G protein-coupled receptors (GPCRs) upon agonist stimulation. This phosphorylation initiates beta-arrestin-mediated receptor desensitization, internalization, and signaling events. GRK5 is a member of the GRK kinase family which include three major subfamilies: the GRK4 subfamily (GRK4, GRK5 and GRK6), the rhodopsin kinase or visual GRK subfamily (GRK1 and GRK7), and the beta-adrenergic receptor kinases subfamily (GRK2/GRK3). The RGS domain of the GRKs has very little sequence similarity with the canonical RGS domain of the RGS proteins and therefore is often refered to as the RH (RGS Homology) domain. RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. 123 matched cddid_all.tbl CDD cd08753 cd08753 188707 RGS_PDZRhoGEF Regulator of G protein signaling (RGS) domain found in the PDZ-Rho guanine nucleotide exchange factor (RhoGEF) protein. The RGS domain is an essential part of the PDZ-RhoGEF (PDZ:Postsynaptic density 95, Disk large, Zona occludens-1; RhoGEF: Rho guanine nucleotide exchange factor; alias PRG) protein, a member of RhoGEFs subfamily of the RGS protein family. The RhoGEFs are peripheral membrane proteins that regulate essential cellular processes, including cell shape, cell migration, and cell cycle progression, as well as gene transcription by linking signals from heterotrimeric G-alpha12/13 protein-coupled receptors to Rho GTPase activation, leading to various cellular responses, such as actin reorganization and gene expression. RhoGEFs subfamily includes leukemia-associated RhoGEF protein (LARG), p115RhoGEF, PDZ-RhoGEF and its rat specific splice variant GTRAP48. The RGS domain of RhoGEFs has very little sequence similarity with the canonical RGS domain of the RGS proteins and is often refered to as RH (RGS Homology) domain. In contrast to p115RhoGEF and LARG, PDZ-RhoGEF cannot serve as a GTPase-activating protein (GAP), due to the mutation of sites in the RGS domain region that are crucial for GAP activity. RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. 145 matched cddid_all.tbl CDD cd08754 cd08754 188708 RGS_LARG Regulator of G protein signaling (RGS) domain found in the leukemia-associated Rho guanine nucleotide exchange factor (RhoGEF) protein (LARG). The RGS domain is an essential part of the leukemia-associated RhoGEF protein (LARG), a member of the RhoGEF (Rho guanine nucleotide exchange factor) subfamily of the RGS protein family. The RhoGEFs are peripheral membrane proteins that regulate essential cellular processes, including cell shape, cell migration, cell cycle progression of cells, and gene transcription by linking signals from heterotrimeric G-alpha12/13 protein-coupled receptors to Rho GTPase activation, leading to various cellular responses, such as actin reorganization and gene expression. The RhoGEF subfamily includes p115RhoGEF, LARG, PDZ-RhoGEF, and its rat specific splice variant GTRAP48. The RGS domain of RhoGEFs has very little sequence similarity with the canonical RGS domain of the RGS proteins and is often refered to as RH (RGS Homology) domain. In addition to being a G-alpha13 effector, the LARG protein also functions as a GTPase-activating protein (GAP) for G-alpha13. RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. 222 matched cddid_all.tbl CDD cd08755 cd08755 188709 RGS_p115RhoGEF Regulator of G protein signaling (RGS) domain found in the Rho guanine nucleotide exchange factor (GEF), p115 RhoGEF. The RGS (Regulator of G-protein Signaling) domain is an essential part of the p115RhoGEF protein, a member of the RhoGEF (Rho guanine nucleotide exchange factor) subfamily of the RGS protein family. The RhoGEFs are peripheral membrane proteins that regulate essential cellular processes, including cell shape, cell migration, cell cycle progression of cells, and gene transcription by linking signals from heterotrimeric G-alpha12/13 protein-coupled receptors to Rho GTPase activation, leading to various cellular responses, such as actin reorganization and gene expression. The RhoGEF subfamily includes p115RhoGEF, LARG, PDZ-RhoGEF and its rat specific splice variant GTRAP48. The RGS domain of RhoGEFs has very little sequence similarity with the canonical RGS domain of the RGS proteins and is often refered to as RH (RGS Homology) domain. In addition to being a G-alpha13/12 effector, the p115RhoGEF protein also functions as a GTPase-activating protein (GAP) for G-alpha13. RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. 193 matched cddid_all.tbl CDD cd08756 cd08756 188710 RGS_GEF_like Regulator of G protein signaling (RGS) domain found in the Rho guanine nucleotide exchange factor (RhoGEF) protein. The RGS domain found in the Rho guanine nucleotide exchange factor (RhoGEF) protein subfamily of the RGS domain containing protein family, which is a diverse group of multifunctional proteins that regulate cellular signaling events downstream of G-protein coupled receptors (GPCRs). The RhoGEFs are peripheral membrane proteins that regulate essential cellular processes, including cell shape, cell migration and cell cycle progression as well as gene transcription by linking signals from heterotrimeric G-alpha12/13 protein-coupled receptors to Rho GTPase activation, leading to various cellular responses, such as actin reorganization and gene expression. The RhoGEF subfamily includes the leukemia-associated RhoGEF protein (LARG), p115RhoGEF, PDZ-RhoGEF, and its rat specific splice variant GTRAP48. The RGS domain of RhoGEFs has very little sequence similarity with the canonical RGS domain of the RGS proteins and is often refered to as RH (RGS Homology) domain. RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. RGS proteins play critical regulatory role as GTPase activating proteins (GAPs) of the heterotrimeric G-protein G-alpha-subunits. RGS proteins regulate many aspects of embryonic development such as glial differentiation, embryonic axis formation, skeletal and muscle development, cell migration during early embryogenesis, as well as apoptosis, cell proliferation, and modulation of cardiac development. 122 matched cddid_all.tbl CDD cd08757 cd08757 188885 SAM_PNT_ESE Sterile alpha motif (SAM)/Pointed domain of ESE-like ETS transcriptional regulators. SAM Pointed domain of ESE-like (Epithelium-Specific ETS) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. It can act as a major transactivator by providing a potential docking site for co-activators. ETS factors are important for cell differentiation. They can be involved in regulation of gene expression in different types of epithelial cells. They are expressed in salivary gland, intestine, stomach, pancreas, lungs, kidneys, colon, mammary gland, and prostate. Members of this group are proto-oncogenes. Expression profiles of these factors are altered in epithelial cancers, which makes them potential targets for cancer therapy. 69 matched cddid_all.tbl CDD cd08759 cd08759 260086 Type_III_cohesin_like Cohesin domain, interaction partner of dockerin. Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. Two specific calcium-dependent interactions between cohesin and dockerin appear to be essential for cellulosome assembly, type I and type II. This subfamily represents type III cohesins and closely related domains. 167 matched cddid_all.tbl CDD cd08760 cd08760 176490 Cyt_b561_FRRS1_like Eukaryotic cytochrome b(561), including the FRRS1 gene product. Cytochrome b(561), as found in eukaryotes, similar to and including the human FRRS1 gene product (ferric-chelate reductase 1), also called SDR-2 (stromal cell-derived receptor 2). This family comprises a variety of domain architectures, many of which contain dopamine beta-monooxygenase (DOMON) domains. The protein might act as a ferric-chelate reductase, catalyzing the reduction of Fe(3+) to Fe(2+), such as associated with the transport of iron from the endosome to the cytoplasm. It is assumed that this protein uses ascorbate as the electron donor. Belongs to the cytochrome b(561) family, which are secretory vesicle-specific electron transport proteins. Cytochromes b(561) are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. 191 matched cddid_all.tbl CDD cd08761 cd08761 176491 Cyt_b561_CYB561D2_like Eukaryotic cytochrome b(561), including the CYB561D2 gene product. Cytochrome b(561), as found in eukaryotes, similar to and including the human CYB561D2 gene product. CYB561D2 is a candidate tumor suppressor. The protein might act as a ferric-chelate reductase, catalyzing the reduction of Fe(3+) to Fe(2+), such as associated with the transport of iron from the endosome to the cytoplasm. It is assumed that this protein uses ascorbate as the electron donor. Belongs to the cytochrome b(561) family, which are secretory vesicle-specific electron transport proteins. Cytochromes b(561) are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. 183 matched cddid_all.tbl CDD cd08762 cd08762 176492 Cyt_b561_CYBASC3 Vertebrate cytochrome b(561), CYBASC3 gene product. Cytochrome b ascorbate-dependent 3, as found in vertebrates, which might act as a ferric-chelate reductase, catalyzing the reduction of Fe(3+) to Fe(2+), such as associated with the transport of iron from the endosome to the cytoplasm. It is assumed that this protein uses ascorbate as the electron donor. Belongs to the cytochrome b(561) family, which are secretory vesicle-specific electron transport proteins. Cytochromes b(561) are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. 179 matched cddid_all.tbl CDD cd08763 cd08763 176493 Cyt_b561_CYB561 Vertebrate cytochrome b(561), CYB561 gene product. Cytochrome b(561), as found in vertebrates, which might act as a ferric-chelate reductase, catalyzing the reduction of Fe(3+) to Fe(2+), such as associated with the transport of iron from the endosome to the cytoplasm. It is assumed that this protein uses ascorbate as the electron donor. Belongs to the cytochrome b(561) family, which are secretory vesicle-specific electron transport proteins. Cytochromes b(561) are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. 143 matched cddid_all.tbl CDD cd08764 cd08764 176494 Cyt_b561_CG1275_like Non-vertebrate eumetazoan cytochrome b(561). Cytochrome b(561), as found in non-vertebrate eumetazoans, similar to the Drosophila melanogaster CG1275 gene product. This protein might act as a ferric-chelate reductase, catalyzing the reduction of Fe(3+) to Fe(2+), such as associated with the transport of iron from the endosome to the cytoplasm. It is assumed that this protein uses ascorbate as the electron donor. Belongs to the cytochrome b(561) family, which are secretory vesicle-specific electron transport proteins. Cytochromes b(561) are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. 214 matched cddid_all.tbl CDD cd08765 cd08765 176495 Cyt_b561_CYBRD1 Vertebrate cytochrome b(561), CYBRD1 gene product. Duodenal cytochrome b or ferric-chelate reductase 3, a cytochrome b(561), as found in vertebrates, which might act as a ferric-chelate reductase, catalyzing the reduction of Fe(3+) to Fe(2+), such as associated with the transport of iron from the endosome to the cytoplasm. It is assumed that this protein uses ascorbate as the electron donor. This protein is expressed at the brush border of duodenal enterocytes and may play a role in the uptake of dietary Fe(3+), facilitating its transport into the mucosal cells. It may also be involved in the recycling of extracellular ascorbate in erythrocyte membranes, and act as a ferrireductase in epithelial cells of the respiratory system. Belongs to the cytochrome b(561) family, which are secretory vesicle-specific electron transport proteins. Cytochromes b(561) are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. 153 matched cddid_all.tbl CDD cd08766 cd08766 176496 Cyt_b561_ACYB-1_like Plant cytochrome b(561), including the carbon monoxide oxygenase ACYB-1. Cytochrome b(561), as found in plants, similar to the Arabidopsis thaliana ACYB-1 gene product, a cytochrome b561 isoform localized to the tonoplast. This protein might act as a ferric-chelate reductase, catalyzing the reduction of Fe(3+) to Fe(2+), and might be capable of trans-membrane electron transport from intracellular ascorbate to extracellular ferric chelates. It is assumed that this protein uses ascorbate as the electron donor. Belongs to the cytochrome b(561) family, which are secretory vesicle-specific electron transport proteins. Cytochromes b(561) are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. 144 matched cddid_all.tbl CDD cd08767 cd08767 176572 Cdt1_c The C-terminal fold of replication licensing factor Cdt1 is essential for Cdt1 activity and directly interacts with MCM2-7 helicase. Cdt1 is a replication licensing factor in eukaryotes that recruits the Minichromosome Maintenance Complex (MCM2-7) to the Origin Recognition Complex (ORC). The Cdt1 protein is divided into three regions based on sequence comparison and biochemical analyses: the N-terminal region (Cdt1_n) binds DNA in a sequence-, strand-, and conformation-independent manner; the middle winged helix fold (Cdt1_m) binds geminin to inhibit both binding of the MCM complex to origins of replication and DNA; and the C-terminal region (Cdt1_c) is essential for Cdt1 activity and directly interacts with the MCM2-7 helicase. Precise duplication of chromosomal DNA is required for genomic stability during replication. Assembly of replication factors to start DNA replication in eukaryotes must occur only once per cell cycle. To form a pre-replicative complex on replication origins in the G phase, ORC first binds origin DNA and triggers the binding of Cdc6 and Cdt1. These two factors recruit a putative replicative helicase and the MCM2-7. The MCM2-7 complex promotes the unwinding of DNA origins, and the binding of additional factors to initiate the DNA replication in S-phase. Cdt1 is present during G1 and early S phase of the cell cycle and is degraded during the late S, G2, and M phases. The winged helix fold structure of Cdt1_m is similar to the structures of Cdt1_c and archaeal homologues of the eukaryotic replication initiator, without apparent sequence similarity. 126 matched cddid_all.tbl CDD cd08768 cd08768 176573 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases the specificity of the ORC-origins interaction. Further studies suggest that hydrolysis of Cdc6-bound ATP promotes the association of the replication licensing factor Cdt1 with origins through an interaction with Orc6 and this in turn promotes the loading of MCM2-7 helicase onto chromatin. The MCM2-7 complex promotes the unwinding of DNA origins, and the binding of additional factors to initiate the DNA replication. S-Cdk (S-phase cyclin and cyclin-dependent kinase complex) prevents rereplication by causing the Cdc6 protein to dissociate from ORC and prevents the Cdc6 and MCM proteins from reassembling at any origin. By phosphorylating Cdc6, S-Cdk also triggers Cdc6's ubiquitination. The Cdc6 protein is composed of three domains, an N-terminal AAA+ domain with Walker A and B, and Sensor-1 and -2 motifs. The central region contains a conserved nucleotide binding/ATPase domain and is a member of the ATPase superfamily. The C-terminal domain (Cdc6_C) is a conserved winged-helix domain that possibly mediates protein-protein interactions or direct DNA interactions. Cdc6 is conserved in eukaryotes, and related genes are found in Archaea. The winged helix fold structure of Cdc6_C is similar to the structures of other eukaryotic replication initiators without apparent sequence similarity. 87 matched cddid_all.tbl CDD cd08769 cd08769 176451 DAP_dppA_2 Peptidase M55, D-aminopeptidase dipeptide-binding protein family. M55 Peptidase, D-Aminopeptidase dipeptide-binding protein (dppA; DAP dppA; EC 3.4.11.-) domain: Peptide transport systems are found in many bacterial species and generally function to accumulate intact peptides in the cell, where they are hydrolyzed. The dipeptide-binding protein (dppA) of Bacillus subtilis belongs to the dipeptide ABC transport (dpp) operon expressed early during sporulation. It is a binuclear zinc-dependent, D-specific aminopeptidase. The biologically active enzyme is a homodecamer with active sites buried in its channel. These self-compartmentalizing proteases are characterized by a SXDXEG motif. D-Ala-D-Ala and D-Ala-Gly-Gly are the preferred substrates. Bacillus subtilis dppA is thought to function as an adaptation to nutrient deficiency; hydrolysis of its substrate releases D-Ala which can be used subsequently as metabolic fuel. This family also contains a number of uncharacterized putative peptidases. 270 matched cddid_all.tbl CDD cd08770 cd08770 176452 DAP_dppA_3 Peptidase M55, D-aminopeptidase dipeptide-binding protein family. M55 Peptidase, D-Aminopeptidase dipeptide-binding protein (dppA; DAP dppA; EC 3.4.11.-) domain: Peptide transport systems are found in many bacterial species and generally function to accumulate intact peptides in the cell, where they are hydrolyzed. The dipeptide-binding protein (dppA) of Bacillus subtilis belongs to the dipeptide ABC transport (dpp) operon expressed early during sporulation. It is a binuclear zinc-dependent, D-specific aminopeptidase. The biologically active enzyme is a homodecamer with active sites buried in its channel. These self-compartmentalizing proteases are characterized by a SXDXEG motif. D-Ala-D-Ala and D-Ala-Gly-Gly are the preferred substrates. Bacillus subtilis dppA is thought to function as an adaptation to nutrient deficiency; hydrolysis of its substrate releases D-Ala which can be used subsequently as metabolic fuel. This family also contains a number of uncharacterized putative peptidases. 263 matched cddid_all.tbl CDD cd08771 cd08771 206738 DLP_1 Dynamin_like protein family includes dynamins and Mx proteins. The dynamin family of large mechanochemical GTPases includes the classical dynamins and dynamin-like proteins (DLPs) that are found throughout the Eukarya. These proteins catalyze membrane fission during clathrin-mediated endocytosis. Dynamin consists of five domains; an N-terminal G domain that binds and hydrolyzes GTP, a middle domain (MD) involved in self-assembly and oligomerization, a pleckstrin homology (PH) domain responsible for interactions with the plasma membrane, GED, which is also involved in self-assembly, and a proline arginine rich domain (PRD) that interacts with SH3 domains on accessory proteins. To date, three vertebrate dynamin genes have been identified; dynamin 1, which is brain specific, mediates uptake of synaptic vesicles in presynaptic terminals; dynamin-2 is expressed ubiquitously and similarly participates in membrane fission; mutations in the MD, PH and GED domains of dynamin 2 have been linked to human diseases such as Charcot-Marie-Tooth peripheral neuropathy and rare forms of centronuclear myopathy. Dynamin 3 participates in megakaryocyte progenitor amplification, and is also involved in cytoplasmic enlargement and the formation of the demarcation membrane system. This family also includes interferon-induced Mx proteins that inhibit a wide range of viruses by blocking an early stage of the replication cycle. Dynamin oligomerizes into helical structures around the neck of budding vesicles in a GTP hydrolysis-dependent manner. 278 matched cddid_all.tbl CDD cd08772 cd08772 350091 GH43_62_32_68_117_130 Glycosyl hydrolase families: GH43, GH62, GH32, GH68, GH117, CH130. Members of the glycosyl hydrolase families 32, 43, 62, 68, 117 and 130 (GH32, GH43, GH62, GH68, GH117, GH130) all possess 5-bladed beta-propeller domains and comprise clans F and J, as classified by the carbohydrate-active enzymes database (CAZY). Clan F consists of families GH43 and GH62. GH43 includes beta-xylosidases (EC 3.2.1.37), beta-xylanases (EC 3.2.1.8), alpha-L-arabinases (EC 3.2.1.99), and alpha-L-arabinofuranosidases (EC 3.2.1.55), using aryl-glycosides as substrates, while family GH62 contains alpha-L-arabinofuranosidases (EC 3.2.1.55) that specifically cleave either alpha-1,2 or alpha-1,3-L-arabinofuranose sidechains from xylans. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Clan J consists of families GH32 and GH68. GH32 comprises sucrose-6-phosphate hydrolases, invertases (EC 3.2.1.26), inulinases (EC 3.2.1.7), levanases (EC 3.2.1.65), eukaryotic fructosyltransferases, and bacterial fructanotransferases while GH68 consists of frucosyltransferases (FTFs) that include levansucrase (EC 2.4.1.10); beta-fructofuranosidase (EC 3.2.1.26); inulosucrase (EC 2.4.1.9), while GH68 consists of frucosyltransferases (FTFs) that include levansucrase (EC 2.4.1.10); beta-fructofuranosidase (EC 3.2.1.26); inulosucrase (EC 2.4.1.9), all of which use sucrose as their preferential donor substrate. Members of this clan are retaining enzymes (i.e. they retain the configuration at anomeric carbon atom of the substrate) that catalyze hydrolysis in two steps involving a covalent glycosyl enzyme intermediate: an aspartate located close to the N-terminus acts as the catalytic nucleophile and a glutamate acts as the general acid/base; a conserved aspartate residue in the Arg-Asp-Pro (RDP) motif stabilizes the transition state. Structures of all families in the two clans manifest a funnel-shaped active site that comprises two subsites with a single route for access by ligands. Also included in this superfamily are GH117 enzymes that have exo-alpha-1,3-(3,6-anhydro)-l-galactosidase activity, removing terminal non-reducing alpha-1,3-linked 3,6-anhydro-l-galactose residues from their neoagarose substrate, and GH130 that are phosphorylases and hydrolases for beta-mannosides, involved in the bacterial utilization of mannans or N-linked glycans. 257 matched cddid_all.tbl CDD cd08773 cd08773 176798 FpgNei_N N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. These enzymes initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycolsylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. The FpgNei DNA glycosylases represent one of the two structural superfamilies of DNA glycosylases that recognize oxidized bases (the other is the HTH-GPD superfamily exemplified by Escherichia coli Nth). Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. One exception is mouse Nei-like glycosylase 3 (Neil3) which forms a Schiff base intermediate via its N-terminal valine. In addition to this FpgNei_N domain, FpgNei proteins have a helix-two-turn-helix (H2TH) domain and a zinc (or zincless)-finger motif which also contribute residues to the active site. FpgNei DNA glycosylases have a broad substrate specificity. They are bifunctional, in addition to the glycosylase (recognition) activity, they have a lyase (cleaving) activity on the phosphodiester backbone of the DNA at the AP site. This superfamily includes eukaryotic, bacterial, and viral proteins. 117 matched cddid_all.tbl CDD cd08774 cd08774 206755 14-3-3 14-3-3 domain. 14-3-3 domain is an essential part of 14-3-3 proteins, a ubiquitous class of regulatory, phosphoserine/threonine-binding proteins found in all eukaryotic cells, including yeast, protozoa and mammalian cells. 14-3-3 proteins play important roles in many biological processes that are regulated by phosphorylation, including cell cycle regulation, cell proliferation, protein trafficking, metabolic regulation and apoptosis. More than 300 binding partners of the 14-3-3 domain have been identified in all subcellular compartments and include transcription factors, signaling molecules, tumor suppressors, biosynthetic enzymes, cytoskeletal proteins and apoptosis factors. 14-3-3 binding can alter the conformation, localization, stability, phosphorylation state, activity as well as molecular interactions of a target protein. They function only as dimers, some preferring strictly homodimeric interaction, while others form heterodimers. Binding of the 14-3-3 domain to its target occurs in a phosphospecific manner where it binds to one of two consensus sequences of their target proteins; RSXpSXP (mode-1) and RXXXpSXP (mode-2). In some instances, 14-3-3 domain containing proteins are involved in regulation and signaling of a number of cellular processes in phosphorylation-independent manner. Many organisms express multiple isoforms: there are seven mammalian 14-3-3 family members (beta, gamma, eta, theta, epsilon, sigma, zeta), each encoded by a distinct gene, while plants contain up to 13 isoforms. The flexible C-terminal segment of 14-3-3 isoforms shows the highest sequence variability and may significantly contribute to individual isoform uniqueness by playing an important regulatory role by occupying the ligand binding groove and blocking the binding of inappropriate ligands in a distinct manner. Elevated amounts of 14-3-3 proteins are found in the cerebrospinal fluid of patients with Creutzfeldt-Jakob disease. In protozoa, like Plasmodium or Cryptosporidium parvum 14-3-3 proteins play an important role in key steps of parasite development. 225 matched cddid_all.tbl CDD cd08775 cd08775 176753 DED_Caspase-like_r2 Death effector domain, repeat 2, of initator caspase-like proteins. Death Effector Domain (DED), second repeat, found in initator caspase-like proteins like caspase-8, -10 and c-FLIP. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-8 and -10 are the initiators of death receptor mediated apoptosis. Together with FADD and the pseudo-caspase c-FLIP, they form the death-inducing signaling complex (DISC), whose formation is triggered by the activation of type 1 tumor necrosis factor (TNF) receptors such as Fas, TNF receptor 1, and TRAIL receptor. Caspase-8 and -10 also play important functions in cell adhesion and motility. c-FLIP is a catalytically inactive homolog of the initator procaspases-8 and -10. It negatively influences apoptotic signaling by interfering with the efficient formation of DISC. All members contain two N-terminal DED domains and a C-terminal caspase domain. DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 81 matched cddid_all.tbl CDD cd08776 cd08776 176754 DED_Caspase-like_r1 Death effector domain, repeat 1, of initator caspase-like proteins. Death Effector Domain (DED), first repeat, found in initator caspase-like proteins, like caspase-8 and -10 and c-FLIP. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-8 and -10 are the initiators of death receptor mediated apoptosis. Together with FADD and the pseudo-caspase c-FLIP, they form the death-inducing signaling complex (DISC), whose formation is triggered by the activation of type 1 tumor necrosis factor (TNF) receptors such as Fas, TNF receptor 1, and TRAIL receptor. Caspase-8 and -10 also play important functions in cell adhesion and motility. c-FLIP is a catalytically inactive homolog of the initator procaspases-8 and -10. It negatively influences apoptotic signaling by interfering with the efficient formation of DISC. All members contain two N-terminal DED domains and a C-terminal caspase domain. DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 71 matched cddid_all.tbl CDD cd08777 cd08777 260048 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 86 matched cddid_all.tbl CDD cd08778 cd08778 176756 Death_TNFRSF21 Death domain of tumor necrosis factor receptor superfamily member 21. Death domain (DD) found in tumor necrosis factor receptor superfamily member 21 (TNFRSF21), also called death receptor-6, DR6. DR6 is an orphan receptor that is expressed ubiquitously, but shows high expression in lymphoid organs, heart, brain and pancreas. Results from DR6(-/-) mice indicate that DR6 plays an important regulatory role for the generation of adaptive immunity. It may also be involved in tumor cell survival and immune evasion. In neuronal cells, it binds beta-amyloid precursor protein (APP) and activates caspase-dependent cell death. It may contribute to the pathogenesis of Alzheimer's disease. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 84 matched cddid_all.tbl CDD cd08779 cd08779 260049 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 86 matched cddid_all.tbl CDD cd08780 cd08780 260050 Death_TRADD Death Domain of Tumor Necrosis Factor Receptor 1-Associated Death Domain protein. Death domain (DD) of TRADD (TNF Receptor 1-Associated Death Domain or TNFRSF1A-associated via death domain) protein. TRADD is a central signaling adaptor for TNF-receptor 1 (TNFR1), mediating activation of Nuclear Factor -kappaB (NF-kB) and c-Jun N-terminal kinase (JNK), as well as caspase-dependent apoptosis. It also carries important immunological roles including germinal center formation, DR3-mediated T-cell stimulation, and TNFalpha-mediated inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 90 matched cddid_all.tbl CDD cd08781 cd08781 260051 Death_UNC5-like Death domain found in Uncoordinated-5 homolog family. Death Domain (DD) found in Uncoordinated-5 (UNC-5) homolog family, which includes Unc5A, B, C and D in vertebrates. UNC5 proteins are receptors for secreted netrins (netrin-1, -3 and -4) that are involved in diverse processes like axonal guidance, neuronal migration, blood vessel patterning, and apoptosis. They are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 83 matched cddid_all.tbl CDD cd08782 cd08782 260052 Death_DAPK1 Death domain found in death-associated protein kinase 1. Death domain (DD) found in death-associated protein kinase 1 (DAPK1). DAPK1 is composed of several functional domains, including a kinase domain, a CaM regulatory domain, ankyrin repeats, a cytoskeletal-binding domain and a C-terminal DD. It plays important roles in a diverse range of signal transduction pathways including apoptosis, growth factor signalling, and autophagy. Loss of DAPK1 expression, usually because of DNA methylation, is implicated in many tumor types. DAPK1 is highly abundant in the brain and has also been associated with neurodegeneration. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 82 matched cddid_all.tbl CDD cd08783 cd08783 260053 Death_MALT1 Death domain similar to that found in Mucosa-associated lymphoid tissue-lymphoma-translocation gene 1. Death domain (DD) similar to that found in Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1). Malt1, together with Bcl10 (B-cell lymphoma 10), are the integral components of the CBM signalosome. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells) and with CARMA1 to form L-CBM (CBM complex in lymphoid immune cells), to mediate activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 96 matched cddid_all.tbl CDD cd08784 cd08784 260054 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 80 matched cddid_all.tbl CDD cd08785 cd08785 260055 CARD_CARD9-like Caspase activation and recruitment domain of CARD9 and related proteins. Caspase activation and recruitment domain (CARD) found in CARD9, CARD14 (CARMA2), CARD10 (CARMA3), CARD11 (CARMA1) and BCL10. BCL10 (B-cell lymphoma 10), together with Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1), are integral components of the CBM signalosome. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells), and with CARD11 to form L-CBM (CBM complex in lymphoid immune cells), which mediates activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. BCL10/Malt1 also associates with CARD10, which is more widely expressed and is not restricted to hematopoietic cells, to play a role in GPCR-induced NF-kB activation. CARD14 has also been shown to associate with BCL10. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 84 matched cddid_all.tbl CDD cd08786 cd08786 176764 CARD_RIP2_CARD3 Caspase activation and recruitment domain of Receptor Interacting Protein 2. Caspase activation and recruitment domain (CARD) of Receptor Interacting Protein 2 (RIP2/RIPK2/RICK/CARDIAK/CARD3). RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP2 harbors a C-terminal CARD domain and functions as an effector kinase downstream of the pattern recognition receptors from the Nod-like (NLR)-family, NOD1 and NOD2, which recognizes bacterial peptidoglycans released upon infection. This cascade is implicated in inflammatory immune responses and the clearance of intracellular pathogens. RIP2 associates with NOD1 and NOD2 via CARD-CARD interactions. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 87 matched cddid_all.tbl CDD cd08787 cd08787 176765 CARD_NOD2_1_CARD15 Caspase activation and recruitment domain of NOD2, repeat 1. Caspase activation and recruitment domain (CARD) similar to that found in human NOD2 (CARD15), repeat 1. NOD2 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD2, as well as NOD1, the N-terminal effector domain is a CARD. NOD2 contains two N-terminal CARD repeats. Mutations in NOD2 have been associated with Crohns disease and Blau syndrome. Nod2-CARDs have been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 87 matched cddid_all.tbl CDD cd08788 cd08788 260056 CARD_NOD2_2_CARD15 Caspase activation and recruitment domain of NOD2, repeat 2. Caspase activation and recruitment domain (CARD) similar to that found in human NOD2 (CARD15), repeat 2. NOD2 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD2, as well as NOD1, the N-terminal effector domain is a CARD. NOD2 contains two N-terminal CARD repeats. Mutations in NOD2 have been associated with Crohns disease and Blau syndrome. Nod2-CARDs have been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 81 matched cddid_all.tbl CDD cd08789 cd08789 260057 CARD_IPS-1_RIG-I Caspase activation and recruitment domains (CARDs) found in IPS-1 and RIG-I-like RNA helicases. Caspase activation and recruitment domains (CARDs) found in IPS-1 (Interferon beta promoter stimulator protein 1) and Retinoic acid Inducible Gene I (RIG-I)-like DEAD box helicases. RIG-I-like helicases and IPS-1 play important roles in the induction of interferons in response to viral infection. They are crucial in triggering innate immunity and in developing adaptive immunity against viral pathogens. RIG-I-like helicases, including MDA5 and RIG-I, contain two N-terminal CARD domains and a C-terminal DEAD box RNA helicase domain. They are cytoplasmic RNA helicases that play an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. MDA5 and RIG-I associate with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 91 matched cddid_all.tbl CDD cd08790 cd08790 260058 DED_DEDD Death Effector Domain of DEDD. Death Effector Domain (DED) found in DEDD. DEDD has been shown to block mitotic progression by inhibiting Cdk1 and to be involved in regulating the insulin signaling cascade. DEDD can bind to itself, to DEDD2, and to the two tandem DED-containing caspases, caspase-8 and -10. In general, DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 97 matched cddid_all.tbl CDD cd08791 cd08791 176769 DED_DEDD2 Death Effector Domain of DEDD2. Death Effector Domain (DED) found in DEDD2. DEDD2 has been shown to bind to itself, DEDD, and to the two tandem DED-containing caspases, caspase-8 and -10. It may play a role in apoptosis. In general, DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. 106 matched cddid_all.tbl CDD cd08792 cd08792 260059 DED_Caspase_8_10_r1 Death effector domain, repeat 1, of initator caspases 8 and 10. Death Effector Domain (DED) found in caspase-8 and caspase-10, repeat 1. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-8 and -10 are the initiators of death receptor mediated apoptosis, and they play partially redundant roles. Together with FADD and the pseudo-caspase c-FLIP, they form the death-inducing signaling complex (DISC), whose formation is triggered by the activation of type 1 tumor necrosis factor (TNF) receptors such as Fas, TNF receptor 1, and TRAIL receptor. Caspase-8 and -10 also play important functions in cell adhesion and motility. They contain two N-terminal DED domains and a C-terminal caspase domain. DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 77 matched cddid_all.tbl CDD cd08793 cd08793 260060 Death_IRAK4 Death domain of Interleukin-1 Receptor-Associated Kinase 4. Death Domain (DD) of Interleukin-1 Receptor-Associated Kinase 4 (IRAK4). IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. They are involved in signal transduction pathways involving IL-1 and IL-18 receptors, Toll-like receptors, nuclear factor-kappaB, and mitogen-activated protein kinases. IRAKs contain an N-terminal DD domain and a C-terminal kinase domain. IRAK4 is an active kinase that is also involved in T-cell receptor signaling pathways, implying that it may function in acquired immunity and not just in innate immunity. It is known as the master IRAK member because its absence strongly impairs TLR- and IL-1-mediated signaling and innate immune defenses, while the absence of other IRAK proteins only shows slight effects. IRAK4-deficient patients have impaired inflammatory responses and recurrent life-threatening infections. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 100 matched cddid_all.tbl CDD cd08794 cd08794 260061 Death_IRAK1 Death domain of Interleukin 1 Receptor Associated Kinase-1. Death Domain (DD) of Interleukin-1 Receptor-Associated Kinase 1 (IRAK1). IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. They are involved in signal transduction pathways involving IL-1 and IL-18 receptors, Toll-like receptors, nuclear factor-kappaB (NF-kB), and mitogen-activated protein kinases (MAPKs). IRAKs contain an N-terminal DD domain and a C-terminal kinase domain. IRAK1 is an active kinase and also plays adaptor functions. It binds to the MyD88-IRAK4 complex via its DD, which facilitates its phosphorylation by IRAK4, activating it for further auto-phosphorylation. Hyper-phosphorylated IRAK1 forms a cytosolic complex with TRAF6, leading to the activation of NF-kB and MAPK pathways. IRAK1 is involved in autoimmunity and may be associated with lupus pathogenesis. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 84 matched cddid_all.tbl CDD cd08795 cd08795 176773 Death_IRAK2 Death domain of Interleukin 1 Receptor Associated Kinase-2. Death Domain (DD) of Interleukin-1 Receptor-Associated Kinase 1 (IRAK1). IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. They are involved in signal transduction pathways involving IL-1 and IL-18 receptors, Toll-like receptors (TLRs), nuclear factor-kappaB (NF-kB), and mitogen-activated protein kinases (MAPKs). IRAKs contain an N-terminal DD domain and a C-terminal kinase domain. IRAK2 is an essential component of several signaling pathways, including NF-kappaB and the IL-1 signaling pathways. It is an inactive kinase that participates in septic shock mediated by TLR4 and TLR9. It plays a redundant role with IRAK1 in early NF-kB and MAPK responses, and remains present at later stages whereas IRAK1 disappears. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 88 matched cddid_all.tbl CDD cd08796 cd08796 260062 Death_IRAK-M Death domain of Interleukin 1 Receptor Associated Kinase-M. Death Domain (DD) of Interleukin-1 Receptor-Associated Kinase M (IRAK-M). IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. They are involved in signal transduction pathways involving IL-1 and IL-18 receptors, Toll-like receptors(TLRs), nuclear factor-kappaB (NF-kB), and mitogen-activated protein kinases (MAPKs). IRAKs contain an N-terminal DD domain and a C-terminal kinase domain. IRAK-M, also called IRAK-3, is an inactive kinase present only in macrophages in an inducible manner. It is a negative regulator of TLR signaling and it contributes to the attenuation of NF-kB activation. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 89 matched cddid_all.tbl CDD cd08797 cd08797 260063 Death_NFkB1_p105 Death domain of the Nuclear Factor-KappaB1 precursor protein p105. Death Domain (DD) of the Nuclear Factor-KappaB1 (NF-kB1) precursor protein p105. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). NF-kB1 (or p50) is produced from the processing of the precursor protein p105, which contains ANK repeats and a C-terminal DD in addition to the RHD. It is regulated by the classical (or canonical) NF-kB pathway. In the cytosol, p50 forms an inactive complex with RelA (or p65) and the Inhibitor of NF-kB (IkB). Activation is triggered by the phosphorylation and degradation of IkB, resulting in the active DNA-binding p50-RelA dimer to migrate to the nucleus. The classical pathway regulates the majority of genes activated by NF-kB including those encoding cytokines, chemokines, leukocyte adhesion molecules, and anti-apoptotic factors. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 76 matched cddid_all.tbl CDD cd08798 cd08798 176776 Death_NFkB2_p100 Death domain of the Nuclear Factor-KappaB2 precursor protein p100. Death Domain (DD) of the Nuclear Factor-KappaB2 (NF-kB2) precursor protein p100. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). NF-kB2 (or p52) is produced from the processing of the precursor protein p100, which contains ANK repeats and a C-terminal DD in addition to the RHD. It is regulated by the non-canonical NF-kB pathway. The p100 precursor is cytosolic and interacts with RelB. Upon phosphorylation by IKKalpha, p100 is processed to its 52kDa active, DNA-binding form and the p52/RelB complex is translocated into the nucleus. The non-canonical pathway plays a role in adaptive immunity and lymphorganogenesis. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 76 matched cddid_all.tbl CDD cd08799 cd08799 260064 Death_UNC5C Death domain found in Uncoordinated-5C. Death Domain (DD) found in Uncoordinated-5C (UNC5C). UNC5C is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5C plays a critical role in the development of spinal accessory motor neurons. Methylation of the UNC5C gene is associated with early stages of colorectal carcinogenesis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 83 matched cddid_all.tbl CDD cd08800 cd08800 260065 Death_UNC5A Death domain found in Uncoordinated-5A. Death Domain (DD) found in Uncoordinated-5A (UNC5A). UNC5A is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a critical role in neuronal development and differentiation, as well as axon-guidance. It also plays a role in regulating apoptosis in non-neuronal cells as a downstream target of p53. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 84 matched cddid_all.tbl CDD cd08801 cd08801 176779 Death_UNC5D Death domain found in Uncoordinated-5D. Death Domain (DD) found in Uncoordinated-5D (UNC5D). UNC5D is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 98 matched cddid_all.tbl CDD cd08802 cd08802 176780 Death_UNC5B Death domain found in Uncoordinated-5B. Death Domain (DD) found in Uncoordinated-5B (UNC5B). UNC5B is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5B signaling is involved in the netrin-1-induced proliferation and migration of renal proximal tubular cells. It is also required for vascular patterning during embryonic development, and its activation inhibits sprouting angiogenesis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 84 matched cddid_all.tbl CDD cd08803 cd08803 176781 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fatal arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 84 matched cddid_all.tbl CDD cd08804 cd08804 260066 Death_ank2 "Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with ""Ankyrin-B syndrome"", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes." 84 matched cddid_all.tbl CDD cd08805 cd08805 260067 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 84 matched cddid_all.tbl CDD cd08806 cd08806 260068 CARD_CARD14_CARMA2 Caspase activation and recruitment domain of CARD14-like proteins. Caspase activation and recruitment domain (CARD) similar to that found in CARD14, also known as BIMP2 or CARMA2 (caspase recruitment domain-containing membrane-associated guanylate kinase protein 2). CARD14 has been identified as a novel member of the MAGUK (membrane-associated guanylate kinase) family that functions as upstream activators of BCL10 (B-cell lymphoma 10) and NF-kB signaling. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 86 matched cddid_all.tbl CDD cd08807 cd08807 260069 CARD_CARD10_CARMA3 Caspase activation and recruitment domain of CARD10-like proteins. Caspase activation and recruitment domain (CARD) similar to that found in CARD10, also known as CARMA3 (caspase recruitment domain-containing membrane-associated guanylate kinase protein 3) or BIMP1. The CARMA3-BCL10-MALT1 signalosome plays a role in the GPCR-induced NF-kB activation. CARMA3 is more widely expressed than CARMA1, which is found only in hematopoietic cells. In endothelial and smooth muscle cells, CARMA3-mediated NF-kB activation induces pro-inflammatory signals within the vasculature and is a key factor in atherogenesis. In bronchial epithelial cells, CARMA3-mediated NF-kB signaling is important for the development of allergic airway inflammation. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 86 matched cddid_all.tbl CDD cd08808 cd08808 260070 CARD_CARD11_CARMA1 Caspase activation and recruitment domain of CARD11-like proteins. Caspase activation and recruitment domain (CARD) similar to that found in CARD11, also known as caspase recruitment domain-containing membrane-associated guanylate kinase protein 1 (CARMA1). CARMA1, together with BCL10 (B-cell lymphoma 10) and Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1), form the L-CBM signalosome (CBM complex in lymphoid immune cells) which mediates activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. CARMA1 associates with BCL10 via a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 86 matched cddid_all.tbl CDD cd08809 cd08809 260071 CARD_CARD9 Caspase activation and recruitment domain of CARD9-like proteins. Caspase activation and recruitment domain (CARD) similar to that found in CARD9. CARD9 is a central regulator of innate immunity and is highly expressed in dendritic cells and macrophages. Together with BCL10 (B-cell lymphoma 10) and Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1), it forms the M-CBM signalosome (the CBM complex in myeloid immune cells), which mediates activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. CARD9 associates with BCL10 via a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 86 matched cddid_all.tbl CDD cd08810 cd08810 260072 CARD_BCL10 Caspase activation and recruitment domain of B-cell lymphoma 10. Caspase activation and recruitment domain (CARD) similar to that found in BCL10 (B-cell lymphoma 10). BCL10 and Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1) are the integral components of CBM signalosomes. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells) and with CARMA1 to form L-CBM (CBM complex in lymphoid immune cells), to mediate activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. Both CARMA1 and CARD9 associate with BCL10 via a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 85 matched cddid_all.tbl CDD cd08811 cd08811 260073 CARD_IPS1 Caspase activation and recruitment domain (CARD) found in IPS-1. Caspase activation and recruitment domain (CARD) found in IPS-1 (Interferon beta promoter stimulator protein 1), also known as CARDIF, VISA or MAVS. IPS-1 is an adaptor protein that plays an important role in interferon induction in response to viral infection. It is crucial in triggering innate immunity and in developing adaptive immunity against viral pathogens. The CARD of IPS-1 associates with the CARDs of two RNA helicases, RIG-I and MDA5, which bind viral DNA in the cytoplasm during the initial stage of intracellular antiviral response, leading to the induction of type I interferons. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 92 matched cddid_all.tbl CDD cd08813 cd08813 176791 DED_Caspase_8_r2 Death Effector Domain, repeat 2, of Caspase-8. Death effector domain (DED) found in caspase-8 (CASP8, FLICE), repeat 2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-8 is an initiator of death receptor mediated apoptosis. Together with FADD, caspase-10, and the pseudo-caspase c-FLIP, it forms the death-inducing signaling complex (DISC), whose formation is triggered by the activation of type 1 tumor necrosis factor (TNF) receptors such as Fas, TNF receptor 1, and TRAIL receptor. Caspase-8 also plays many important non-apoptotic functions including roles in embryonic development, cell adhesion and motility, immune cell proliferation and differentiation, T-cell activation, and NFkappaB signaling. It contains two N-terminal DED domains and a C-terminal caspase domain. DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 83 matched cddid_all.tbl CDD cd08814 cd08814 260074 DED_Caspase_10_r2 Death Effector Domain, repeat 2, of Caspase-10. Death effector domain (DED) found in Caspase-10, repeat 2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-10 is an initiator of death receptor mediated apoptosis. Together with FADD, caspase-8 and the pseudo-caspase c-FLIP, it forms the death-inducing signaling complex (DISC), whose formation is triggered by the activation of type 1 tumor necrosis factor (TNF) receptors such as Fas, TNF receptor 1, and TRAIL receptor. It contains two N-terminal DED domains and a C-terminal caspase domain. DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 79 matched cddid_all.tbl CDD cd08815 cd08815 176793 Death_TNFRSF25_DR3 Death domain of Tumor Necrosis Factor Receptor superfamily 25. Death Domain (DD) found in Tumor Necrosis Factor (TNF) receptor superfamily 25 (TNFRSF25), also known as TRAMP (TNF receptor-related apoptosis-mediating protein), LARD, APO-3, WSL-1, or DR3 (Death Receptor-3). TNFRSF25 is primarily expressed in T cells, is activated by binding to its ligand TL1A, and plays an important role in T-cell function. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 77 matched cddid_all.tbl CDD cd08816 cd08816 260075 CARD_RIG-I_r1 Caspase activation and recruitment domain found in RIG-I, first repeat. Caspase activation and recruitment domain (CARD) found in RIG-I (Retinoic acid Inducible Gene I, also known as Ddx58), first repeat. RIG-I is a cytoplasmic RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. RIG-I contains two N-terminal CARD domains and a C-terminal RNA helicase. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, RIG-I recognizes different sets of viruses compared to MDA5, a related RNA helicase. RIG-I associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 90 matched cddid_all.tbl CDD cd08817 cd08817 260076 CARD_RIG-I_r2 Caspase activation and recruitment domain found in RIG-I, second repeat. Caspase activation and recruitment domain (CARD) found in RIG-I (Retinoic acid Inducible Gene I, also known as Ddx58), second repeat. RIG-I is a cytoplasmic RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. RIG-I contains two N-terminal CARD domains and a C-terminal RNA helicase. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, RIG-I recognizes different sets of viruses compared to MDA5, a related RNA helicase. RIG-I associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 91 matched cddid_all.tbl CDD cd08818 cd08818 260077 CARD_MDA5_r1 Caspase activation and recruitment domain found in MDA5, first repeat. Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), first repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 92 matched cddid_all.tbl CDD cd08819 cd08819 260078 CARD_MDA5_r2 Caspase activation and recruitment domain found in MDA5, second repeat. Caspase activation and recruitment domain (CARD) found in MDA5 (melanoma-differentiation-associated gene 5), second repeat. MDA5, also known as IFIH1, contains two N-terminal CARD domains and a C-terminal RNA helicase domain. MDA5 is a cytoplasmic DEAD box RNA helicase that plays an important role in host antiviral response by sensing incoming viral RNA. Upon activation, the signal is transferred to downstream pathways via the adaptor molecule IPS-1 (MAVS, VISA, CARDIF), leading to the induction of type I interferons. Although very similar in sequence, MDA5 recognizes different sets of viruses compared to RIG-I, a related RNA helicase. MDA5 associates with IPS-1 through a CARD-CARD interaction. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 92 matched cddid_all.tbl CDD cd08820 cd08820 187722 FMT_core_like_6 Formyl transferase catalytic core domain found in a group of proteins with unknown functions. Formyl transferase catalytic core domain found in a group of proteins with unknown functions. Formyl transferase catalyzes the transfer of one-carbon groups, specifically the formyl- or hydroxymethyl- group. This domain contains a Rossmann fold and it is the catalytic domain of the enzyme. 173 matched cddid_all.tbl CDD cd08821 cd08821 187723 FMT_core_like_1 Formyl transferase catalytic core domain found in a group of proteins with unknown functions. Formyl transferase catalytic core domain found in a group of proteins with unknown functions. Formyl transferase catalyzes the transfer of one-carbon groups, specifically the formyl- or hydroxymethyl- group. This domain contains a Rossmann fold and it is the catalytic domain of the enzyme. 211 matched cddid_all.tbl CDD cd08822 cd08822 187724 FMT_core_like_2 Formyl transferase catalytic core domain found in a group of proteins with unknown functions. Formyl transferase catalytic core domain found in a group of proteins with unknown functions. Formyl transferase catalyzes the transfer of one-carbon groups, specifically the formyl- or hydroxymethyl- group. This domain contains a Rossmann fold and it is the catalytic domain of the enzyme. 192 matched cddid_all.tbl CDD cd08823 cd08823 187725 FMT_core_like_5 Formyl transferase catalytic core domain found in a group of proteins with unknown functions. Formyl transferase catalytic core domain found in a group of proteins with unknown functions. Formyl transferase catalyzes the transfer of one-carbon groups, specifically the formyl- or hydroxymethyl- group. This domain contains a Rossmann fold and it is the catalytic domain of the enzyme. 177 matched cddid_all.tbl CDD cd08824 cd08824 193585 LOTUS LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7. LOTUS is an uncharacterized small globular domain found in Limkain b1, Oskar and Tudor-containing proteins 5 and 7. The LOTUS containing proteins are germline-specific and are found in the nuage/polar granules of germ cells. Tudor-containing protein 5 and 7 belong to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD5 and TDRD7 are components of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. Oskar protein is a critical component of the pole plasm in the Drosophila oocyte, which is required for germ cell formation. Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be characterized. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. 70 matched cddid_all.tbl CDD cd08825 cd08825 259807 MVP_shoulder Shoulder domain of the major vault protein. The major vault protein is the major polypeptide component of a large cellular ribonuclear protein complex found in the cytoplasm of eukaryotic cells. Its shoulder domain appears to be a homolog of the SPFH core domain. Vault proteins may be involved in detoxification processes, and have been associated with the multi-drug resistance (MDR) phenotype in malignancies. Presumably they play a role in transport processes. 151 matched cddid_all.tbl CDD cd08826 cd08826 259808 SPFH_eoslipins_u1 Uncharacterized prokaryotic subgroup of the stomatin-like proteins (slipins) family; belonging to the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model summarizes a subgroup of the stomatin-like protein family (SLPs or slipins) that is found in bacteria and archaebacteria. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Individual proteins of the SPFH superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Bacterial and archaebacterial SLPs remain uncharacterized. This subgroup contains PH1511 from the hyperthermophilic archaeon Pyrococcus horikoshi. 178 matched cddid_all.tbl CDD cd08827 cd08827 259809 SPFH_podocin Podocin, a subgroup of the stomatin-like proteins (slipins) family; belonging to the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model summarizes a subgroup of the stomatin-like protein family (SLPs or slipins) that is found in vertebrates. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Individual proteins of the SPFH superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Podocin is expressed in the kidney and mutations in the gene have been linked to familial idiopathic nephrotic syndrome. Podocin interacts with the TRP ion channel TRPV-6 and may function as a scaffolding protein in the organization of lipid-protein domains. 223 matched cddid_all.tbl CDD cd08828 cd08828 259810 SPFH_SLP-3 Slipin-3 (SLP-3), an uncharacterized subgroup of the stomatin-like proteins (slipins) family; belonging to the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model summarizes a subgroup of the stomatin-like protein family (SLPs or slipins) that is found in vertebrates. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Individual proteins of the SPFH superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Members of this slipin subgroup remain uncharacterized, except for Caenorhabditis elegans UNC-1. Mutations in the unc-1 gene result in abnormal motion and altered patterns of sensitivity to volatile anesthetics. 154 matched cddid_all.tbl CDD cd08829 cd08829 259811 SPFH_paraslipin Paraslipin or slipin-2 (SLP-2, a subgroup of the stomatin-like proteins (slipins) family; belonging to the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model summarizes a subgroup of the stomatin-like protein family (SLPs or slipins) that is found in all three kingdoms of life. The conserved domain common to these families has also been referred to as the Band 7 domain. Individual proteins of the SPFH family may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. This subgroup of the SLPs remains largely uncharacterized. It includes human SLP-2 which is upregulated and involved in the progression and development in several types of cancer, including esophageal squamous cell carcinoma, endometrial adenocarcinoma, breast cancer, and glioma. 111 matched cddid_all.tbl CDD cd08830 cd08830 350059 ArfGap_ArfGap1 Arf1 GTPase-activating protein 1. ArfGAP (ADP Ribosylation Factor GTPase Activating Protein) domain is a part of ArfGap1-like proteins that play a crucial role in controlling of membrane trafficking, particularly in the formation of COPI (coat protein complex I)-coated vesicles on Golgi membranes. The ArfGAP1 protein subfamily consists of three members: ArfGAP1 (Gcs1p in yeast), ArfGAP2 and ArfGAP3 (both are homologs of yeast Glo3p). ArfGAP2/3 are closely related, but with little similarity to ArfGAP1, except the catalytic ArfGAP domain. They promote hydrolysis of GTP bound to the small G protein ADP-ribosylation factor 1 (Arf1), which leads to the dissociation of coat proteins from Golgi-derived membranes and vesicles. Dissociation of the coat proteins is required for the fusion of these vesicles with target compartments. Thus, the GAP catalytic activity plays a key role in the formation of COPI vesicles from Golgi membrane. In contrast to ArfGAP1, which displays membrane curvature-dependent ArfGAP activity, ArfGAP2 and ArfGAP3 activities are dependent on coatomer (the core COPI complex) which required for efficient recruitment of ArfGAP2 and ArfGAP3 to the Golgi membrane. Accordingly, ArfGAP2/3 has been implicated in coatomer-mediated protein transport between the Golgi complex and the endoplasmic reticulum. Unlike ArfGAP1, which is controlled by membrane curvature through its amphipathic lipid packing sensor (ALPS) motifs, ArfGAP2/3 do not possess ALPS motif. 115 matched cddid_all.tbl CDD cd08831 cd08831 350060 ArfGap_ArfGap2_3_like Arf1 GTPase-activating protein 2/3-like. ArfGAP (ADP Ribosylation Factor GTPase Activating Protein) domain is a part of ArfGap1-like proteins that play a crucial role in controlling of membrane trafficking, particularly in the formation of COPI (coat protein complex I)-coated vesicles on Golgi membranes. The ArfGAP1 protein subfamily consists of three members: ArfGAP1 (Gcs1p in yeast), ArfGAP2 and ArfGAP3 (both are homologs of yeast Glo3p). ArfGAP2/3 are closely related, but with little similarity to ArfGAP1, except the catalytic ArfGAP domain. They promote hydrolysis of GTP bound to the small G protein ADP-ribosylation factor 1 (Arf1), which leads to the dissociation of coat proteins from Golgi-derived membranes and vesicles. Dissociation of the coat proteins is required for the fusion of these vesicles with target compartments. Thus, the GAP catalytic activity plays a key role in the formation of COPI vesicles from Golgi membrane. In contrast to ArfGAP1, which displays membrane curvature-dependent ArfGAP activity, ArfGAP2 and ArfGAP3 activities are dependent on coatomer (the core COPI complex) which required for efficient recruitment of ArfGAP2 and ArfGAP3 to the Golgi membrane. Accordingly, ArfGAP2/3 has been implicated in coatomer-mediated protein transport between the Golgi complex and the endoplasmic reticulum. Unlike ArfGAP1, which is controlled by membrane curvature through its amphipathic lipid packing sensor (ALPS) motifs, ArfGAP2/3 do not possess ALPS motif. 116 matched cddid_all.tbl CDD cd08832 cd08832 350061 ArfGap_ADAP ArfGap with dual PH domains. The ADAP subfamily, ArfGAPs with dual pleckstrin homology (PH) domains, includes two members: ADAP1 and ADAP2. Both ADAP1 (also known as centaurin-alpha1, p42(IP4), or PIP3BP) and ADAP2 (centaurin-alpha2) display a GTPase-activating protein (GAP) activity toward Arf6 (ADP-ribosylation factor 6), which is involved in protein trafficking that regulates endocytic recycling, cytoskeleton remodeling, and neuronal differentiation. ADAP2 has high sequence similarity to the ADAP1 and they both contain a ArfGAP domain at the N-terminus, followed by two PH domains. However, ADAP1, unlike ADAP2, contains a putative N-terminal nuclear localization signal. The PH domains of ADAP1bind to the two second messenger molecules phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3) and inositol 1,3,4,5-tetrakisphosphate (I(1,3,4,5)P4) with identical high affinity, whereas those of ADAP2 specifically binds phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2) and PI(3,4,5)P3, which are produced by activated phosphatidylinositol 3-kinase. ADAP1 is predominantly expressed in the brain neurons, while ADAP2 is broadly expressed, including the adipocytes, heart, and skeletal muscle but not in the brain. The limited distribution and high expression of ADAP1 in the brain indicates that ADAP1 is important for neuronal functions. ADAP1 has been shown to highly expressed in the neurons and plagues of Alzheimer's disease patients. In other hand, ADAP2 gene deletion has been shown to cause circulatory deficiencies and heart shape defects in zebrafish, indicating that ADAP2 has a vital role in heart development. Taken together, the hemizygous deletion of ADAP2 gene may be contributing to the cardiovascular malformation in patients with neurofibromatosis type 1 (NF1) microdeletions. 113 matched cddid_all.tbl CDD cd08833 cd08833 350062 ArfGap_GIT The GIT subfamily of ADP-ribosylation factor GTPase-activating proteins. The GIT (G-protein coupled receptor kinase-interacting protein) subfamily includes GIT1 and GIT2, which have three ANK repeats, a Spa-homology domain (SHD), a coiled-coil domain and a C-terminal paxillin-binding site (PBS). The GIT1/2 proteins are GTPase-activating proteins that function as an inactivator of Arf signaling, and interact with the PIX/Cool family of Rac/Cdc42 guanine nucleotide exchange factors (GEFs). Unlike other ArfGAPs, GIT and PIX (Pak-interacting exchange factor) proteins are tightly associated to form an oligomeric complex that acts as a scaffold and signal integrator that can be recruited for multiple signaling pathways. The GIT/PIX complex functions as a signaling scaffold by binding to specific protein partners. As a result, the complex is transported to specific cellular locations. For instance, the GIT partners paxillin or integrin-alpha4 (to focal adhesions), piccolo and liprin-alpha (to synapses), and the beta-PIX partner Scribble (to epithelial cell-cell contacts and synapses). Moreover, the GIT/PIT complex functions to integrate signals from multiple GTP-binding protein and protein kinase pathways to regulate the actin cytoskeleton and thus cell polarity, adhesion and migration. 109 matched cddid_all.tbl CDD cd08834 cd08834 350063 ArfGap_ASAP ArfGAP domain of ASAP (Arf GAP, SH3, ANK repeat and PH domains) subfamily of ADP-ribosylation factor GTPase-activating proteins. The ArfGAPs are a family of multidomain proteins with a common catalytic domain that promotes the hydrolysis of GTP bound to Arf, thereby inactivating Arf signaling. ASAP-subfamily GAPs include three members: ASAP1, ASAP2, ASAP3. The ASAP subfamily comprises Arf GAP, SH3, ANK repeat and PH domains. From the N-terminus, each member has a BAR, PH, Arf GAP, ANK repeat, and proline rich domains. Unlike ASAP3, ASAP1 and ASAP2 also have an SH3 domain at the C-terminus. ASAP1 and ASAP2 show strong GTPase-activating protein (GAP) activity toward Arf1 and Arf5 and weak activity toward Arf6. ASAP1 is a target of Src and FAK signaling that regulates focal adhesions, circular dorsal ruffles (CDR), invadopodia, and podosomes. ASAP1 GAP activity is synergistically stimulated by phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphatidic acid. ASAP2 is believed to function as an ArfGAP that controls ARF-mediated vesicle budding when recruited to Golgi membranes. It also functions as a substrate and downstream target for protein tyrosine kinases Pyk2 and Src, a pathway that may be involved in the regulation of vesicular transport. ASAP3 is a focal adhesion-associated ArfGAP that functions in cell migration and invasion. Similar to ASAP1, the GAP activity of ASAP3 is strongly enhanced by PIP2 via PH domain. Like ASAP1, ASAP3 associates with focal adhesions and circular dorsal ruffles. However, unlike ASAP1, ASAP3 does not localize to invadopodia or podosomes. Both ASAP 1 and 3 have been implicated in oncogenesis, as ASAP1 is highly expressed in metastatic breast cancer and ASAP3 in hepatocellular carcinoma. 117 matched cddid_all.tbl CDD cd08835 cd08835 350064 ArfGap_ACAP ArfGAP domain of ACAP (ArfGAP with Coiled-coil, ANK repeat and PH domains) proteins. ArfGAP domain is an essential part of ACAP proteins that play important role in endocytosis, actin remodeling and receptor tyrosine kinase-dependent cell movement. ACAP subfamily of ArfGAPs are composed of coiled coils (BAR, Bin-Amphiphysin-Rvs), PH, ArfGAP and ANK repeats domains. ACAP1 (centaurin beta1) and ACAP2 centaurin beta2) have a GAP (GTPase-activating protein) activity preferentially toward Arf6, which regulates endocytic recycling. Both ACAP1/2 are activated by are activated by the phosphoinositides, PI(4,5)P2 and PI(3,5)P2. ACAP1 binds specifically with recycling cargo proteins such as transferrin receptor (TfR) and cellubrevin. Thus, ACAP1 promotes cargo sorting to enhance TfR recycling from the recycling endosome. In addition, phosphorylation of ACAP by Akt, a serine/threonine protein kinase, regulates the recycling of integrin beta1 to control cell migration. In contrast, ACAP2 does not exhibit a similar interaction with the recycling cargo proteins. It has been shown that ACAP2 functions both as an effector of Ras-related protein Rab35 and as an Arf6-GTPase-activating protein (GAP) during neurite outgrowth of PC12 cells. In addition, ACAP2, together with Rab35, regulates phagocytosis in mammalian macrophages. ACAP3 also positively regulates neurite outgrowth through its GAP activity specific to Arf6 in mouse hippocampal neurons. 116 matched cddid_all.tbl CDD cd08836 cd08836 350065 ArfGap_AGAP ArfGAP with GTPase domain, ANK repeat and PH domains. The AGAP subfamily of ADP-ribosylation factor GTPase-activating proteins (Arf GAPs) includes three members: AGAP1-3. In addition to the Arf GAP domain, AGAP proteins contain GTP-binding protein-like, ANK repeat and pleckstrin homology (PH) domains. AGAP1 and AGAP2 have phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2)-mediated GTPase-activating protein (GAP) activity preferentially toward Arf1, and function in the endocytic system. AGAP1 and AGAP2 independently regulate AP-3 endosomes and AP-1/Rab4 fast recycling endosomes, respectively. AGAP1, via its PH domain, directly interacts with the adapter protein 3 (AP-3), which is a coat protein involved in trafficking in the endosomal-lysosomal system, and regulates AP-3-dependent trafficking. In other hand, AGAP2 specifically binds the clathrin adaptor protein AP-1 and regulates the AP-1/Rab-4 dependent endosomal trafficking. AGAP2 is overexpressed in different human cancers including prostate carcinoma and glioblastoma, and promotes cancer cell invasion. AGAP3 exists as a component of the NMDA receptor complex that regulates Arf6 and Ras/ERK signaling pathways. Moreover, AGAP3 regulates AMPA receptor trafficking through the ArfGAP domain. Together, AGAP3 is believed to involve in linking NMDA receptor activation to AMPA receptor trafficking. 108 matched cddid_all.tbl CDD cd08837 cd08837 350066 ArfGap_ARAP ArfGap with Rho-Gap domain, ANK repeat and PH domain-containing proteins. The ARAP subfamily includes three members, ARAP1-3, and belongs to the ADP-ribosylation factor GTPase-activating proteins (Arf GAPs) family of proteins that promotes the hydrolysis of GTP bound to Arf, thereby inactivating Arf signaling. The function of Arfs is dependent on GAPs and guanine nucleotide exchange factors (GEFs), which allow Arfs to cycle between the GDP-bound and GTP-bound forms. In addition to the Arf GAP domain, ARAPs contain the SAM (sterile-alpha motif) domain, 5 pleckstrin homology (PH) domains, the Rho-GAP domain, the Ras-association domain, and ANK repeats. ARAPs show phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3)-dependent GAP activity toward Arf6. ARAPs play important roles in endocytic trafficking, cytoskeleton reorganization in response to growth factors stimulation, and focal adhesion dynamics. 116 matched cddid_all.tbl CDD cd08838 cd08838 350067 ArfGap_AGFG ArfGAP domain of the AGFG subfamily (ArfGAP domain and FG repeat-containing proteins). The ArfGAP domain and FG repeat-containing proteins (AFGF) subfamily of Arf GTPase-activating proteins consists of the two structurally-related members: AGFG1 and AGFG2. AGFG1 (alias: HIV-1 Rev binding protein, HRB; Rev interacting protein, RIP; Rev/Rex activating domain-binding protein, RAB) and AGFG2 are involved in the maintenance and spread of immunodeficiency virus type 1 (HIV-1) infection. The ArfGAP domain of AGFG is related to nucleoporins, which is a class of proteins that mediate nucleocytoplasmic transport. AGFG plays a role in the Rev export pathway, which mediates the nucleocytoplasmic transfer of proteins and RNAs, possibly together by the nuclear export receptor CRM1. In humans, the presence of the FG repeat motifs (11 in AGFG1 and 7 in AGFG2) are thought to be required for these proteins to act as HIV-1 Rev cofactors. Hence, AGFG promotes movement of Rev-responsive element-containing RNAs from the nuclear periphery to the cytoplasm, which is an essential step for HIV-1 replication. 113 matched cddid_all.tbl CDD cd08839 cd08839 350068 ArfGap_SMAP Stromal membrane-associated proteins; a subfamily of the ArfGAP family. The SMAP subfamily of Arf GTPase-activating proteins consists of the two structurally-related members, SMAP1 and SMAP2. Each SMAP member exhibits common and distinct functions in vesicle trafficking. They both bind to clathrin heavy chain molecules and are involved in the trafficking of clathrin-coated vesicles. SMAP1 preferentially exhibits GAP toward Arf6, while SMAP2 prefers Arf1 as a substrate. SMAP1 is involved in Arf6-dependent vesicle trafficking, but not Arf6-mediated actin cytoskeleton reorganization, and regulates clathrin-dependent endocytosis of the transferrin receptors and E-cadherin. SMAP2 regulates Arf1-dependent retrograde transport of TGN38/46 from the early endosome to the trans-Golgi network (TGN). SMAP2 has the Clathrin Assembly Lymphoid Myeloid (CALM)-binding domain, but SMAP1 does not. 103 matched cddid_all.tbl CDD cd08843 cd08843 350069 ArfGap_ADAP1 ADAP1 GTPase activating protein for Arf, with dual PH domains. The ADAP subfamily, ArfGAPs with dual pleckstrin homology (PH) domains, includes two members: ADAP1 and ADAP2. Both ADAP1 (also known as centaurin-alpha1, p42(IP4), or PIP3BP) and ADAP2 (centaurin-alpha2) display a GTPase-activating protein (GAP) activity toward Arf6 (ADP-ribosylation factor 6), which is involved in protein trafficking that regulates endocytic recycling, cytoskeleton remodeling, and neuronal differentiation. ADAP2 has high sequence similarity to the ADAP1 and they both contain a ArfGAP domain at the N-terminus, followed by two PH domains. However, ADAP1, unlike ADAP2, contains a putative N-terminal nuclear localization signal. The PH domains of ADAP1bind to the two second messenger molecules phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3) and inositol 1,3,4,5-tetrakisphosphate (I(1,3,4,5)P4) with identical high affinity, whereas those of ADAP2 specifically binds phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2) and PI(3,4,5)P3, which are produced by activated phosphatidylinositol 3-kinase. ADAP1 is predominantly expressed in the brain neurons, while ADAP2 is broadly expressed, including the adipocytes, heart, and skeletal muscle but not in the brain. The limited distribution and high expression of ADAP1 in the brain indicates that ADAP1 is important for neuronal functions. ADAP1 has been shown to highly expressed in the neurons and plagues of Alzheimer's disease patients. In other hand, ADAP2 gene deletion has been shown to cause circulatory deficiencies and heart shape defects in zebrafish, indicating that ADAP2 has a vital role in heart development. Taken together, the hemizygous deletion of ADAP2 gene may be contributing to the cardiovascular malformation in patients with neurofibromatosis type 1 (NF1) microdeletions. 112 matched cddid_all.tbl CDD cd08844 cd08844 350070 ArfGap_ADAP2 ADAP2 GTPase activating protein for Arf, with dual PH domains. The ADAP subfamily, ArfGAPs with dual pleckstrin homology (PH) domains, includes two members: ADAP1 and ADAP2. Both ADAP1 (also known as centaurin-alpha1, p42(IP4), or PIP3BP) and ADAP2 (centaurin-alpha2) display a GTPase-activating protein (GAP) activity toward Arf6 (ADP-ribosylation factor 6), which is involved in protein trafficking that regulates endocytic recycling, cytoskeleton remodeling, and neuronal differentiation. ADAP2 has high sequence similarity to the ADAP1 and they both contain a ArfGAP domain at the N-terminus, followed by two PH domains. However, ADAP1, unlike ADAP2, contains a putative N-terminal nuclear localization signal. The PH domains of ADAP1bind to the two second messenger molecules phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3) and inositol 1,3,4,5-tetrakisphosphate (I(1,3,4,5)P4) with identical high affinity, whereas those of ADAP2 specifically binds phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2) and PI(3,4,5)P3, which are produced by activated phosphatidylinositol 3-kinase. ADAP1 is predominantly expressed in the brain neurons, while ADAP2 is broadly expressed, including the adipocytes, heart, and skeletal muscle but not in the brain. The limited distribution and high expression of ADAP1 in the brain indicates that ADAP1 is important for neuronal functions. ADAP1 has been shown to highly expressed in the neurons and plagues of Alzheimer's disease patients. In other hand, ADAP2 gene deletion has been shown to cause circulatory deficiencies and heart shape defects in zebrafish, indicating that ADAP2 has a vital role in heart development. Taken together, the hemizygous deletion of ADAP2 gene may be contributing to the cardiovascular malformation in patients with neurofibromatosis type 1 (NF1) microdeletions. 112 matched cddid_all.tbl CDD cd08846 cd08846 350071 ArfGap_GIT1 GIT1 GTPase activating protein for Arf. The GIT (G-protein coupled receptor kinase-interacting protein) subfamily includes GIT1 and GIT2, which have three ANK repeats, a Spa-homology domain (SHD), a coiled-coil domain and a C-terminal paxillin-binding site (PBS). The GIT1/2 proteins are GTPase-activating proteins that function as an inactivator of Arf signaling, and interact with the PIX/Cool family of Rac/Cdc42 guanine nucleotide exchange factors (GEFs). Unlike other ArfGAPs, GIT and PIX (Pak-interacting exchange factor) proteins are tightly associated to form an oligomeric complex that acts as a scaffold and signal integrator that can be recruited for multiple signaling pathways. The GIT/PIX complex functions as a signaling scaffold by binding to specific protein partners. As a result, the complex is transported to specific cellular locations. For instance, the GIT partners paxillin or integrin-alpha4 (to focal adhesions), piccolo and liprin-alpha (to synapses), and the beta-PIX partner Scribble (to epithelial cell-cell contacts and synapses). Moreover, the GIT/PIT complex functions to integrate signals from multiple GTP-binding protein and protein kinase pathways to regulate the actin cytoskeleton and thus cell polarity, adhesion and migration. 111 matched cddid_all.tbl CDD cd08847 cd08847 350072 ArfGap_GIT2 GIT2 GTPase activating protein for Arf. The GIT (G-protein coupled receptor kinase-interacting protein) subfamily includes GIT1 and GIT2, which have three ANK repeats, a Spa-homology domain (SHD), a coiled-coil domain and a C-terminal paxillin-binding site (PBS). The GIT1/2 proteins are GTPase-activating proteins that function as an inactivator of Arf signaling, and interact with the PIX/Cool family of Rac/Cdc42 guanine nucleotide exchange factors (GEFs). Unlike other ArfGAPs, GIT and PIX (Pak-interacting exchange factor) proteins are tightly associated to form an oligomeric complex that acts as a scaffold and signal integrator that can be recruited for multiple signaling pathways. The GIT/PIX complex functions as a signaling scaffold by binding to specific protein partners. As a result, the complex is transported to specific cellular locations. For instance, the GIT partners paxillin or integrin-alpha4 (to focal adhesions), piccolo and liprin-alpha (to synapses), and the beta-PIX partner Scribble (to epithelial cell-cell contacts and synapses). Moreover, the GIT/PIT complex functions to integrate signals from multiple GTP-binding protein and protein kinase pathways to regulate the actin cytoskeleton and thus cell polarity, adhesion and migration. 111 matched cddid_all.tbl CDD cd08848 cd08848 350073 ArfGap_ASAP1 ArfGAP domain of ASAP1 (ArfGAP with SH3 domain, ANK repeat and PH domain-containing protein 1). The ArfGAPs are a family of multidomain proteins with a common catalytic domain that promotes the hydrolysis of GTP bound to Arf, thereby inactivating Arf signaling. ASAP-subfamily GAPs include three members: ASAP1, ASAP2, ASAP3. The ASAP subfamily comprises Arf GAP, SH3, ANK repeat and PH domains. From the N-terminus, each member has a BAR, PH, Arf GAP, ANK repeat, and proline rich domains. Unlike ASAP3, ASAP1 and ASAP2 also have an SH3 domain at the C-terminus. ASAP1 and ASAP2 show strong GTPase-activating protein (GAP) activity toward Arf1 and Arf5 and weak activity toward Arf6. ASAP1 is a target of Src and FAK signaling that regulates focal adhesions, circular dorsal ruffles (CDR), invadopodia, and podosomes. ASAP1 GAP activity is synergistically stimulated by phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphatidic acid. ASAP2 is believed to function as an ArfGAP that controls ARF-mediated vesicle budding when recruited to Golgi membranes. It also functions as a substrate and downstream target for protein tyrosine kinases Pyk2 and Src, a pathway that may be involved in the regulation of vesicular transport. ASAP3 is a focal adhesion-associated ArfGAP that functions in cell migration and invasion. Similar to ASAP1, the GAP activity of ASAP3 is strongly enhanced by PIP2 via PH domain. Like ASAP1, ASAP3 associates with focal adhesions and circular dorsal ruffles. However, unlike ASAP1, ASAP3 does not localize to invadopodia or podosomes. ASAP 1 and 3 have been implicated in oncogenesis, as ASAP1 is highly expressed in metastatic breast cancer and ASAP3 in hepatocellular carcinoma. 122 matched cddid_all.tbl CDD cd08849 cd08849 350074 ArfGap_ASAP2 ArfGAP domain of ASAP2 (ArfGAP2 with SH3 domain, ANK repeat and PH domain-containing protein 2). The Arf GAPs are a family of multidomain proteins with a common catalytic domain that promotes the hydrolysis of GTP bound to Arf , thereby inactivating Arf signaling. ASAP-subfamily GAPs include three members: ASAP1, ASAP2, ASAP3. The ASAP subfamily comprises Arf GAP, SH3, ANK repeat and PH domains. From the N-terminus, each member has a BAR, PH, Arf GAP, ANK repeat, and proline rich domains. Unlike ASAP3, ASAP1 and ASAP2 also have an SH3 domain at the C-terminus. ASAP1 and ASAP2 show strong GTPase-activating protein (GAP) activity toward Arf1 and Arf5 and weak activity toward Arf6. ASAP1 is a target of Src and FAK signaling that regulates focal adhesions, circular dorsal ruffles (CDR), invadopodia, and podosomes. ASAP1 GAP activity is synergistically stimulated by phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphatidic acid. ASAP2 is believed to function as an ArfGAP that controls ARF-mediated vesicle budding when recruited to Golgi membranes. It also functions as a substrate and downstream target for protein tyrosine kinases Pyk2 and Src, a pathway that may be involved in the regulation of vesicular transport. 123 matched cddid_all.tbl CDD cd08850 cd08850 350075 ArfGap_ACAP3 ArfGAP domain of ACAP3 (ArfGAP with Coiled-coil, ANK repeat and PH domains 3). ACAP3 belongs to the ACAP subfamily of GAPs (GTPase-activating proteins) for the small GTPase Arf (ADP-ribosylation factor). ACAP subfamily of ArfGAPs are composed of Coiled coli (BAR, Bin-Amphiphysin-Rvs), PH, ArfGAP and ANK repeats domains. It has been shown that ACAP3 positively regulates neurite outgrowth through its GAP activity specific to Arf6 in mouse hippocampal neurons. ACAP1 (centaurin beta1) and ACAP2 centaurin beta2) also have a GAP (GTPase-activating protein) activity preferentially toward Arf6, which regulates endocytic recycling. Both ACAP1/2 are activated by are activated by the phosphoinositides, PI(4,5)P2 and PI(3,5)P2. ACAP1 binds specifically with recycling cargo proteins such as transferrin receptor (TfR) and cellubrevin. Thus, ACAP1 promotes cargo sorting to enhance TfR recycling from the recycling endosome. In addition, phosphorylation of ACAP by Akt, a serine/threonine protein kinase, regulates the recycling of integrin beta1 to control cell migration. In contrast, ACAP2 does not exhibit a similar interaction with the recycling cargo proteins. It has been shown that ACAP2 functions both as an effector of Ras-related protein Rab35 and as an Arf6-GTPase-activating protein (GAP) during neurite outgrowth of PC12 cells. Moreover, ACAP2, together with Rab35, regulates phagocytosis in mammalian macrophages. 116 matched cddid_all.tbl CDD cd08851 cd08851 350076 ArfGap_ACAP2 ArfGAP domain of ACAP2 (ArfGAP with Coiled-coil, ANK repeat and PH domains 2). ACAP2 belongs to the ACAP subfamily of GAPs (GTPase-activating proteins) for the small GTPase Arf (ADP-ribosylation factor). ACAP subfamily of ArfGAPs are composed of Coiled coli (BAR, Bin-Amphiphysin-Rvs), PH, ArfGAP and ANK repeats domains. ACAP1 (centaurin beta1) and ACAP2 centaurin beta2) have a GAP (GTPase-activating protein) activity preferentially toward Arf6, which regulates endocytic recycling. Both ACAP1/2 are activated by are activated by the phosphoinositides, PI(4,5)P2 and PI(3,5)P2. ACAP1 binds specifically with recycling cargo proteins such as transferrin receptor (TfR) and cellubrevin. Thus, ACAP1 promotes cargo sorting to enhance TfR recycling from the recycling endosome. In addition, phosphorylation of ACAP by Akt, a serine/threonine protein kinase, regulates the recycling of integrin beta1 to control cell migration. In contrast, ACAP2 does not exhibit a similar interaction with the recycling cargo proteins. It has been shown that ACAP2 functions both as an effector of Ras-related protein Rab35 and as an Arf6-GTPase-activating protein (GAP) during neurite outgrowth of PC12 cells. Moreover, ACAP2, together with Rab35, regulates phagocytosis in mammalian macrophages. ACAP3 also positively regulates neurite outgrowth through its GAP activity specific to Arf6 in mouse hippocampal neurons. 116 matched cddid_all.tbl CDD cd08852 cd08852 350077 ArfGap_ACAP1 ArfGAP domain of ACAP1 (ArfGAP with Coiled-coil, ANK repeat and PH domains 1). ACAP1 belongs to the ACAP subfamily of GAPs (GTPase-activating proteins) for the small GTPase Arf (ADP-ribosylation factor). ACAP subfamily of ArfGAPs are composed of Coiled coli (BAR, Bin-Amphiphysin-Rvs), PH, ArfGAP and ANK repeats domains. ACAP1 (centaurin beta1) and ACAP2 centaurin beta2) have a GAP (GTPase-activating protein) activity preferentially toward Arf6, which regulates endocytic recycling. Both ACAP1/2 are activated by are activated by the phosphoinositides, PI(4,5)P2 and PI(3,5)P2. ACAP1 binds specifically with recycling cargo proteins such as transferrin receptor (TfR) and cellubrevin. Thus, ACAP1 promotes cargo sorting to enhance TfR recycling from the recycling endosome. In addition, phosphorylation of ACAP by Akt, a serine/threonine protein kinase, regulates the recycling of integrin beta1 to control cell migration. In contrast, ACAP2 does not exhibit a similar interaction with the recycling cargo proteins. It has been shown that ACAP2 functions both as an effector of Ras-related protein Rab35 and as an Arf6-GTPase-activating protein (GAP) during neurite outgrowth of PC12 cells. Moreover, ACAP2, together with Rab35, regulates phagocytosis in mammalian macrophages. ACAP3 also positively regulates neurite outgrowth through its GAP activity specific to Arf6 in mouse hippocampal neurons. 120 matched cddid_all.tbl CDD cd08853 cd08853 350078 ArfGap_AGAP2 ArfGAP with GTPase domain, ANK repeat and PH domain 2. The AGAP subfamily of ADP-ribosylation factor GTPase-activating proteins (Arf GAPs) includes three members: AGAP1-3. In addition to the Arf GAP domain, AGAP proteins contain GTP-binding protein-like, ANK repeat and pleckstrin homology (PH) domains. AGAP1 and AGAP2 have phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2)-mediated GTPase-activating protein (GAP) activity preferentially toward Arf1, and function in the endocytic system. AGAP1 and AGAP2 independently regulate AP-3 endosomes and AP-1/Rab4 fast recycling endosomes, respectively. AGAP1, via its PH domain, directly interacts with the adapter protein 3 (AP-3), which is a coat protein involved in trafficking in the endosomal-lysosomal system, and regulates AP-3-dependent trafficking. In other hand, AGAP2 specifically binds the clathrin adaptor protein AP-1 and regulates the AP-1/Rab-4 dependent endosomal trafficking. AGAP2 is overexpressed in different human cancers including prostate carcinoma and glioblastoma, and promotes cancer cell invasion. AGAP3 exists as a component of the NMDA receptor complex that regulates Arf6 and Ras/ERK signaling pathways. Moreover, AGAP3 regulates AMPA receptor trafficking through the ArfGAP domain. Together, AGAP3 is believed to involve in linking NMDA receptor activation to AMPA receptor trafficking. 109 matched cddid_all.tbl CDD cd08854 cd08854 350079 ArfGap_AGAP1 ArfGAP with GTPase domain, ANK repeat and PH domain 1. The AGAP subfamily of ADP-ribosylation factor GTPase-activating proteins (Arf GAPs) includes three members: AGAP1-3. In addition to the Arf GAP domain, AGAP proteins contain GTP-binding protein-like, ANK repeat and pleckstrin homology (PH) domains. AGAP1 and AGAP2 have phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2)-mediated GTPase-activating protein (GAP) activity preferentially toward Arf1, and function in the endocytic system. AGAP1 and AGAP2 independently regulate AP-3 endosomes and AP-1/Rab4 fast recycling endosomes, respectively. AGAP1, via its PH domain, directly interacts with the adapter protein 3 (AP-3), which is a coat protein involved in trafficking in the endosomal-lysosomal system, and regulates AP-3-dependent trafficking. In other hand, AGAP2 specifically binds the clathrin adaptor protein AP-1 and regulates the AP-1/Rab-4 dependent endosomal trafficking. AGAP2 is overexpressed in different human cancers including prostate carcinoma and glioblastoma, and promotes cancer cell invasion. AGAP3 exists as a component of the NMDA receptor complex that regulates Arf6 and Ras/ERK signaling pathways. Moreover, AGAP3 regulates AMPA receptor trafficking through the ArfGAP domain. Together, AGAP3 is believed to involve in linking NMDA receptor activation to AMPA receptor trafficking. 109 matched cddid_all.tbl CDD cd08855 cd08855 350080 ArfGap_AGAP3 ArfGAP with GTPase domain, ANK repeat and PH domain 3. The AGAP subfamily of ADP-ribosylation factor GTPase-activating proteins (Arf GAPs) includes three members: AGAP1-3. In addition to the Arf GAP domain, AGAP proteins contain GTP-binding protein-like, ANK repeat and pleckstrin homology (PH) domains. AGAP3 exists as a component of the NMDA receptor complex that regulates Arf6 and Ras/ERK signaling pathways. Moreover, AGAP3 regulates AMPA receptor trafficking through the ArfGAP domain. Together, AGAP3 is believed to involve in linking NMDA receptor activation to AMPA receptor trafficking. AGAP1 and AGAP2 have phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2)-mediated GTPase-activating protein (GAP) activity preferentially toward Arf1, and function in the endocytic system. AGAP1 and AGAP2 independently regulate AP-3 endosomes and AP-1/Rab4 fast recycling endosomes, respectively. AGAP1, via its PH domain, directly interacts with the adapter protein 3 (AP-3), which is a coat protein involved in trafficking in the endosomal-lysosomal system, and regulates AP-3-dependent trafficking. In other hand, AGAP2 specifically binds the clathrin adaptor protein AP-1 and regulates the AP-1/Rab-4 dependent endosomal trafficking. AGAP2 is overexpressed in different human cancers including prostate carcinoma and glioblastoma, and promotes cancer cell invasion. 110 matched cddid_all.tbl CDD cd08856 cd08856 350081 ArfGap_ARAP2 ArfGap with Rho-Gap domain, ANK repeat and PH domain-containing protein 2. The ARAP subfamily includes three members, ARAP1-3, and belongs to the ADP-ribosylation factor GTPase-activating proteins (Arf GAPs) family of proteins that promotes the hydrolysis of GTP bound to Arf, thereby inactivating Arf signaling. The function of Arfs is dependent on GAPs and guanine nucleotide exchange factors (GEFs), which allow Arfs to cycle between the GDP-bound and GTP-bound forms. In addition to the Arf GAP domain, ARAPs contain the SAM (sterile-alpha motif) domain, 5 pleckstrin homology (PH) domains, the Rho-GAP domain, the Ras-association domain, and ANK repeats. ARAPs show phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3)-dependent GAP activity toward Arf6. ARAPs play important roles in endocytic trafficking, cytoskeleton reorganization in response to growth factors stimulation, and focal adhesion dynamics. ARAP2 localizes to the cell periphery and on focal adhesions composed of paxillin and vinculin, and functions downstream of RhoA to regulate focal adhesion dynamics. ARAP2 is a PI(3,4,5)P3-dependent Arf6 GAP that binds RhoA-GTP, but it lacks the predicted catalytic arginine in the RhoGAP domain and does not have RhoGAP activity. ARAP2 reduces Rac1oGTP levels by reducing Arf6oGTP levels through GAP activity. AGAP2 also binds to and regulates focal adhesion kinase (FAK). Thus, ARAP2 signals through Arf6 and Rac1 to control focal adhesion morphology. 121 matched cddid_all.tbl CDD cd08857 cd08857 350082 ArfGap_AGFG1 ArfGAP domain of AGFG1 (ArfGAP domain and FG repeat-containing protein 1). The ArfGAP domain and FG repeat-containing proteins (AFGF) subfamily of Arf GTPase-activating proteins consists of the two structurally-related members: AGFG1 and AGFG2. AGFG1 (alias: HIV-1 Rev binding protein, HRB; Rev interacting protein, RIP; Rev/Rex activating domain-binding protein, RAB) and AGFG2 are involved in the maintenance and spread of immunodeficiency virus type 1 (HIV-1) infection. The ArfGAP domain of AGFG1 is related to nucleoporins, which is a class of proteins that mediate nucleocytoplasmic transport. AGFG1 plays a role in the Rev export pathway, which mediates the nucleocytoplasmic transfer of proteins and RNAs, possibly together by the nuclear export receptor CRM1. In humans, the presence of the FG repeat motifs (11 in AGFG1 and 7 in AGFG2) are thought to be required for these proteins to act as HIV-1 Rev cofactors. Hence, AGFG1 promotes movement of Rev-responsive element-containing RNAs from the nuclear periphery to the cytoplasm, which is an essential step for HIV-1 replication. 116 matched cddid_all.tbl CDD cd08859 cd08859 350083 ArfGap_SMAP2 Stromal membrane-associated protein 2; a subfamily of the ArfGAP family. The SMAP subfamily of Arf GTPase-activating proteins consists of the two structurally-related members, SMAP1 and SMAP2. Each SMAP member exhibits common and distinct functions in vesicle trafficking. They both bind to clathrin heavy chain molecules and are involved in the trafficking of clathrin-coated vesicles. SMAP1 preferentially exhibits GAP toward Arf6, while SMAP2 prefers Arf1 as a substrate. SMAP1 is involved in Arf6-dependent vesicle trafficking, but not Arf6-mediated actin cytoskeleton reorganization, and regulates clathrin-dependent endocytosis of the transferrin receptors and E-cadherin. SMAP2 regulates Arf1-dependent retrograde transport of TGN38/46 from the early endosome to the trans-Golgi network (TGN). SMAP2 has the Clathrin Assembly Lymphoid Myeloid (CALM)-binding domain, but SMAP1 does not. 107 matched cddid_all.tbl CDD cd08860 cd08860 176869 TcmN_ARO-CYC_like N-terminal aromatase/cyclase domain of the multifunctional protein tetracenomycin (TcmN) and related domains. This family includes the N-terminal aromatase/cyclase (ARO/CYC) domain of Streptomyces glaucescens TcmN, and related domains. It belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. ARO/CYC domains participate in the diversification of aromatic polyketides by promoting polyketide cyclization. They occur in two architectural forms, monodomain and didomain. Monodomain aromatase/cyclases have a single ARO/CYC domain. For some, such as TcmN, this single domain is linked to a second domain of unrelated function. TcmN is a multifunctional cyclase-dehydratase-O-methyl transferase. Its N-terminal ARO/CYC domain participates in polyketide binding and catalysis; it promotes C9-C14 first-ring (and C7-C16 second-ring) cyclizations. Its C-terminal domain has O-methyltransferase activity. Didomain aromatase/cyclases contain two ARO/CYC domains, and they biosynthesize C7-C12 first ring cyclized polyketides. These latter domains belong to a different subfamily in the SRPBCC superfamily. 146 matched cddid_all.tbl CDD cd08861 cd08861 176870 OtcD1_ARO-CYC_like N-terminal and C-terminal aromatase/cyclase domains of Streptomyces rimosus OtcD1 and related domains. This family includes the N- and C- terminal aromatase/cyclase (ARO/CYC) domains of Streptomyces rimosus OtcD1 and related domains. It belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. ARO/CYC domains participate in the diversification of aromatic polyketides by promoting polyketide cyclization. They occur in two architectural forms, didomain and monodomain. Didomain aromatase/cyclases (ARO/CYCs), contain two ARO/CYC domains, and are associated with C7-C12 first ring cyclized polyketides. Streptomyces rimosus OtcD1 is a didomain ARO/CYC. The polyketide Oxytetracycline (OTC) is a broad spectrum antibiotic made by Streptomyces rimosus. The gene encoding OtcD1 is part of oxytetracycline (OTC) gene cluster. Disruption of this gene results in the production of novel polyketides having shorter chain lengths (by up to 10 carbons) than OTC. Monodomain ARO/CYCs have a single ARO/CYC domain, and are often associated with C9-C14 first ring cyclizations, these latter domains belong to a different subfamily in the SRPBCC superfamily. 142 matched cddid_all.tbl CDD cd08862 cd08862 176871 SRPBCC_Smu440-like Ligand-binding SRPBCC domain of Streptococcus mutans Smu.440 and related proteins. This family includes the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of Streptococcus mutans Smu.440 and related proteins. This domain belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. Streptococcus mutans is a dental pathogen, and the leading cause of dental caries. In this pathogen, the gene encoding Smu.440 is in the same operon as the gene encoding SMU.441, a member of the MarR protein family of transcriptional regulators involved in multiple antibiotic resistance. It has been suggested that SMU.440 is involved in polyketide-like antibiotic resistance. 138 matched cddid_all.tbl CDD cd08863 cd08863 176872 SRPBCC_DUF1857 DUF1857, an uncharacterized ligand-binding domain of the SRPBCC domain superfamily. Uncharacterized family of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), Class I and II phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of the superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins. 141 matched cddid_all.tbl CDD cd08864 cd08864 176873 SRPBCC_DUF3074 DUF3074, an uncharacterized ligand-binding domain of the SRPBCC domain superfamily. Uncharacterized family of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), Class I and II phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of the superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins. 208 matched cddid_all.tbl CDD cd08865 cd08865 176874 SRPBCC_10 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins. Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), Class I and II phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of the superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins. 140 matched cddid_all.tbl CDD cd08866 cd08866 176875 SRPBCC_11 Ligand-binding SRPBCC domain of an uncharacterized subfamily of proteins. Uncharacterized group of the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. SRPBCC domains include the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), Class I and II phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of the superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins. 144 matched cddid_all.tbl CDD cd08867 cd08867 176876 START_STARD4_5_6-like Lipid-binding START domain of mammalian STARD4, -5, -6, and related proteins. This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD4, -5, and -6. The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD4 plays an important role in steroidogenesis, trafficking cholesterol into mitochondria. It specifically binds cholesterol, and demonstrates limited binding to another sterol, 7a-hydroxycholesterol. STARD4 and STARD5 are ubiquitously expressed, with highest levels in liver and kidney. STRAD5 functions in the kidney within the proximal tubule cells where it is associated with the Endoplasmic Reticulum (ER), and may participate in ER-associated cholesterol transport. It binds cholesterol and 25-hydroxycholesterol. Expression of the gene encoding STARD5 is increased by ER stress, and its mRNA and protein levels are elevated in a type I diabetic mouse model of human diabetic nephropathy. STARD6 is expressed in male germ cells of normal rats, and in the steroidogenic Leydig cells of perinatal hypothyroid testes. It may play a pivotal role in the steroidogenesis as well as in the spermatogenesis of normal rats. STARD6 has also been detected in the rat nervous system, and may participate in neurosteroid synthesis. 206 matched cddid_all.tbl CDD cd08868 cd08868 176877 START_STARD1_3_like Cholesterol-binding START domain of mammalian STARD1, -3 and related proteins. This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of STARD1 (also known as StAR) and STARD3 (also known as metastatic lymph node 64/MLN64). The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. This STARD1-like subfamily has a high affinity for cholesterol. STARD1/StAR can reduce macrophage lipid content and inflammatory status. It plays an essential role in steroidogenic tissues: transferring the steroid precursor, cholesterol, from the outer to the inner mitochondrial membrane, across the aqueous space. Mutations in the gene encoding STARD1/StAR can cause lipid congenital adrenal hyperplasia (CAH), an autosomal recessive disorder characterized by a steroid synthesis deficiency and an accumulation of cholesterol in the adrenal glands and the gonads. STARD3 may function in trafficking endosomal cholesterol to a cytosolic acceptor or membrane. In addition to having a cytoplasmic START cholesterol-binding domain, STARD3 also contains an N-terminal MENTAL cholesterol-binding and protein-protein interaction domain. The MENTAL domain contains transmembrane helices and anchors MLN64 to endosome membranes. The gene encoding STARD3 is overexpressed in about 25% of breast cancers. 208 matched cddid_all.tbl CDD cd08869 cd08869 176878 START_RhoGAP C-terminal lipid-binding START domain of mammalian STARD8, -12, -13 and related proteins, which also have an N-terminal Rho GTPase-activating protein (RhoGAP) domain. This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of STARD8 (also known as deleted in liver cancer 3/DLC3, and Arhgap38), STARD12 (also known as DLC-1, Arhgap7, and p122-RhoGAP), and STARD13 (also known as DLC-2, Arhgap37, and SDCCAG13). The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. Proteins belonging to this subfamily also have a RhoGAP domain. Some, including STARD12, -and -13, also have an N-terminal SAM (sterile alpha motif) domain; these have a SAM-RhoGAP-START domain organization. This subfamily is involved in cancer development. A large spectrum of cancers have dysregulated genes encoding these proteins. The precise function of the START domain in this subfamily is unclear. 197 matched cddid_all.tbl CDD cd08870 cd08870 176879 START_STARD2_7-like Lipid-binding START domain of mammalian STARD2, -7, and related proteins. This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of STARD2 (also known as phosphatidylcholine transfer protein/PC-TP), and STARD7 (also known as gestational trophoblastic tumor 1/GTT1). The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD2 is a cytosolic phosphatidycholine (PtdCho) transfer protein, which traffics PtdCho, the most common class of phospholipids in eukaryotes, between membranes. It represents a minimal START domain structure. STARD2 plays roles in hepatic cholesterol metabolism, in the development of atherosclerosis, and may also have a mitochondrial function. The gene encoding STARD7 is overexpressed in choriocarcinoma. STARD7 appears to be involved in the intracellular trafficking of PtdCho to mitochondria. STARD7 was shown to be surface active and to interact differentially with phospholipid monolayers. It showed a preference for phosphatidylserine, cholesterol, and phosphatidylglycerol. 209 matched cddid_all.tbl CDD cd08871 cd08871 176880 START_STARD10-like Lipid-binding START domain of mammalian STARD10 and related proteins. This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD10 (also known as CGI-52, PTCP-like, and SDCCAG28). The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD10 binds phophatidylcholine and phosphatidylethanolamine. This protein is widely expressed and is synthesized constitutively in many organs. It may function in the liver in the export of phospholipids into bile. It is concentrated in the sperm flagellum, and may play a role in energy metabolism. In the mammary gland it may participate in the enrichment of lipids in milk, and be a potential marker of differentiation. Its expression is induced in this gland during gestation and lactation. It is overexpressed in mammary tumors from Neu/ErbB2 transgenic mice, in several breast carcinoma cell lines, and in 35% of primary human breast cancers, and may cooperate with c-erbB receptor signaling in breast oncogenesis. It is a potential marker of disease outcome in breast cancer; loss of STARD10 expression in breast cancer strongly predicts an aggressive disease course. The lipid transfer activity of STRAD10 is downregulated by phosphorylation of its Ser284 by CK2 (casein kinase 2). 222 matched cddid_all.tbl CDD cd08872 cd08872 176881 START_STARD11-like Ceramide-binding START domain of mammalian STARD11 and related domains. This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD11 and related domains. The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD11 can mediate transfer of the natural ceramide isomers, dihydroceramide and phytoceramide, as well as ceramides having C14, C16, C18, and C20 chains. They can also transfer diacylglycerol, but with a lower efficiency. STARD11 is synthesized from two major transcripts: a larger one encoding Goodpasture antigen-binding protein (GPBP)/ceramide transporter long form (CERTL); and a smaller one encoding GPBPdelta26/CERT, which is deleted for 26 amino acids. Both splicing variants mediate ceramide transfer from the ER to the Golgi, in a non-vesicular manner. It is likely that these two carry out different functions in specific sub-cellular locations. These proteins have roles in brain homeostasis and disease processes. GPBP/CERTL exists in multiple isoforms originating from alternative translation initiation sites and post-translational modifications. Goodpasture syndrome is a human disorder caused by antibodies directed against the a3-chain of collagen type IV. GPBP/CERTL binds and phosphorylates this antigen. The human gene encoding STARD11 is referred to as COL4A3BP referring to its collagen binding function. It is unknown whether the ceramide-transfer function of GPBP/CERTL is related to this collagen interaction. The expression of GPBP/CERTL is elevated in these and other spontaneous autoimmune disorders including cutaneous lupus erythematosus, pemphigoid, and lichen planus. GPBL/CERTL contains an N-terminal pleckstrin homology domain (PH), which targets the protein to the Golgi, a middle region containing two serine-rich domains (SR1, SR2), a FFAT (two phenylalanine amino acids in an acidic tract) motif which is involved in endoplasmic reticulum targeting, and this C-terminal SMART domain. The shorter splicing variant, CERT, lacks the SR2 domain. 235 matched cddid_all.tbl CDD cd08873 cd08873 176882 START_STARD14_15-like Lipid-binding START domain of mammalian STARDT14, -15, and related proteins. This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian brown fat-inducible STARD14 (also known as Acyl-Coenzyme A Thioesterase 11 or ACOT11, BFIT, THEA, THEM1, KIAA0707, and MGC25974), STARD15/ACOT12 (also known as cytoplasmic acetyl-CoA hydrolase/CACH, THEAL, and MGC105114), and related domains. The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD14/ACOT11 and STARD15/ACOT12 are type II acetyl-CoA thioesterases; they catalyze the hydrolysis of acyl-CoAs to free fatty acid and CoASH. Human STARD14 displays acetyl-CoA thioesterase activity towards medium(C12)- and long(C16)-chain fatty acyl-CoA substrates. Rat CACH hydrolyzes acetyl-CoA to acetate and CoA. In addition to having a START domain, STARD14 and STARD15 each have two tandem copies of the hotdog domain. There are two splice variants of human STARD14, named BFIT1 and BFIT2, which differ in their C-termini. Human BFIT2 is equivalent to mouse mBFIT/Acot11, whose transcription is increased two fold in obesity-resistant mice compared with obesity-prone mice. Human STARD15 may have roles in cholesterol metabolism and in beta-oxidation. 235 matched cddid_all.tbl CDD cd08874 cd08874 176883 START_STARD9-like C-terminal START domain of mammalian STARD9, and related domains; lipid binding. This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD9 (also known as KIAA1300), and related domains. The START domain family belongs to the SRPBCC (START/RHO_alpha_C /PITP /Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. Some members of this subfamily have N-terminal kinesin motor domains. STARD9 interacts with supervillin, a protein important for efficient cytokinesis, perhaps playing a role in coordinating microtubule motors with actin and myosin II functions at membranes. The human gene encoding STARD9 lies within a target region for LGMD2A, an autosomal recessive form of limb-girdle muscular dystrophy. 205 matched cddid_all.tbl CDD cd08875 cd08875 176884 START_ArGLABRA2_like C-terminal lipid-binding START domain of the Arabidopsis homeobox protein GLABRA 2 and related proteins. This subfamily includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of the Arabidopsis homeobox protein GLABRA 2 and related proteins. The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. Most proteins in this subgroup contain an N-terminal homeobox DNA-binding domain, some contain a leucine zipper. ArGLABRA2 plays a role in the differentiation of hairless epidermal cells of the Arabidopsis root. It acts in a cell-position-dependent manner to suppress root hair formation in those cells. 229 matched cddid_all.tbl CDD cd08876 cd08876 176885 START_1 Uncharacterized subgroup of the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain family. Functionally uncharacterized subgroup of the START domain family. The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. For some mammalian members of the START family (STARDs), it is known which lipids bind in this pocket; these include cholesterol (STARD1, -3, -4, and -5), 25-hydroxycholesterol (STARD5), phosphatidylcholine (STARD2, -7, and -10), phosphatidylethanolamine (STARD10) and ceramides (STARD11). Mammalian STARDs participate in the control of various cellular processes, including lipid trafficking between intracellular compartments, lipid metabolism, and modulation of signaling events. Mutation or altered expression of STARDs is linked to diseases such as cancer, genetic disorders, and autoimmune disease. 195 matched cddid_all.tbl CDD cd08877 cd08877 176886 START_2 Uncharacterized subgroup of the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain family. Functionally uncharacterized subgroup of the START domain family. The START domain family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. For some mammalian members of the START family (STARDs), it is known which lipids bind in this pocket; these include cholesterol (STARD1, -3, -4, and -5), 25-hydroxycholesterol (STARD5), phosphatidylcholine (STARD2, -7, and -10), phosphatidylethanolamine (STARD10) and ceramides (STARD11). Mammalian STARDs participate in the control of various cellular processes, including lipid trafficking between intracellular compartments, lipid metabolism, and modulation of signaling events. Mutation or altered expression of STARDs is linked to diseases such as cancer, genetic disorders, and autoimmune disease. 215 matched cddid_all.tbl CDD cd08878 cd08878 176887 RHO_alpha_C_DMO-like C-terminal catalytic domain of the oxygenase alpha subunit of dicamba O-demethylase and related aromatic ring hydroxylating dioxygenases. C-terminal catalytic domain of the oxygenase alpha subunit of Stenotrophomonas maltophilia dicamba O-demethylase (DMO) and related Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs, also known as aromatic ring hydroxylating dioxygenases). RHOs utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ring, an initial step in the oxidative degradation of aromatic compounds. RHOs are composed of either two or three protein components, and are comprised of an electron transport chain (ETC) and an oxygenase. The ETC transfers reducing equivalents from the electron donor to the oxygenase component, which in turn transfers electrons to the oxygen molecules. The oxygenase components are oligomers, either (alpha)n or (alpha)n(beta)n. The alpha subunits are the catalytic components and have an N-terminal domain, which binds a Rieske-like 2Fe-2S cluster, and the C-terminal catalytic domain which binds the non-heme Fe(II). The Fe(II) is co-ordinated by conserved His and Asp residues. Oxygenases belonging to this subgroup include the alpha subunits of carbazole 1,9a-dioxygenase, phthalate dioxygenase, vanillate O-demethylase, Pseudomonas putida 2-oxoquinoline 8-monooxygenase, and Comamonas testosteroni T-2 p-toluenesulfonate dioxygenase. It also includes the C-terminal domain of the lignin biphenyl-specific O-demethylase (LigX) of the 5,5'-dehydrodivanillic acid O- demethylation system of Sphingomonas paucimobilis SYK-6. This subfamily belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. 196 matched cddid_all.tbl CDD cd08879 cd08879 176888 RHO_alpha_C_AntDO-like C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases. C-terminal catalytic domain of the oxygenase alpha subunit of anthranilate 1,2-dioxygenase (AntDO) and related Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs, also known as aromatic ring hydroxylating dioxygenases). RHOs utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ring, an initial step in the oxidative degradation of aromatic compounds. RHOs are composed of either two or three protein components, and are comprised of an electron transport chain (ETC) and an oxygenase. The ETC transfers reducing equivalents from the electron donor to the oxygenase component, which in turn transfers electrons to the oxygen molecules. The oxygenase components are oligomers, either (alpha)n or (alpha)n(beta)n. The alpha subunits are the catalytic components and have an N-terminal domain, which binds a Rieske-like 2Fe-2S cluster, and the C-terminal catalytic domain which binds the non-heme Fe(II). The Fe(II) is co-ordinated by conserved His and Asp residues. Oxygenases belonging to this subgroup include the alpha subunits of AntDO, aniline dioxygenase, Acinetobacter calcoaceticus benzoate 1,2-dioxygenase, 2-halobenzoate 1,2-dioxygenase from Pseudomonas cepacia 2CBS, 2,4,5-trichlorophenoxyacetic acid oxygenase from Pseudomonas cepacia AC1100, 2,4-dichlorophenoxyacetic acid oxygenase from Bradyrhizobium sp. strain HW13, p-cumate 2,3-dioxygenase, 2-halobenzoate 1,2-dioxygenase form Pseudomonas cepacia 2CBS, and Pseudomonas putida IacC, which may be involved in the catabolism of the plant hormone indole 3-acetic acid. This subfamily belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. 237 matched cddid_all.tbl CDD cd08880 cd08880 176889 RHO_alpha_C_ahdA1c-like C-terminal catalytic domain of the large/alpha subunit (ahdA1c) of a ring-hydroxylating dioxygenase from Sphingomonas sp. strain P2 and related proteins. C-terminal catalytic domain of the large subunit (ahdA1c) of the AhdA3A4A2cA1c salicylate 1-hydroxylase complex from Sphingomonas sp. strain P2, and related Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs, also known as aromatic ring hydroxylating dioxygenases). AhdA3A4A2cA1c is one of three known isofunctional salicylate 1-hydroxylase complexes in strain P2, involved in phenanthrene degradation, which catalyze the monooxygenation of salicylate, the metabolite of phenanthene degradation, to produce catechol. This complex prefers salicylate over other substituted salicylates; the other two salicylate 1-hydroxylases have different substrate preferences. RHOs utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ring, an initial step in the oxidative degradation of aromatic compounds. RHOs are composed of either two or three protein components, and are comprised of an electron transport chain (ETC) and an oxygenase. The ETC transfers reducing equivalents from the electron donor to the oxygenase component, which in turn transfers electrons to the oxygen molecules. The oxygenase components are oligomers, either (alpha)n or (alpha)n(beta)n. The alpha subunits are the catalytic components and have an N-terminal domain, which binds a Rieske-like 2Fe-2S cluster, and a C-terminal domain which binds the non-heme Fe(II). The Fe(II) is co-ordinated by conserved His and Asp residues. Other oxygenases belonging to this subgroup include the alpha subunits of anthranilate 1,2-dioxygenase from Burkholderia cepacia DBO1, a polycyclic aromatic hydrocarbon dioxygenase from Cycloclasticus sp. strain A5 (PhnA dioxygenase), salicylate-5-hydroxylase from Ralstonia sp. U2, ortho-halobenzoate 1,2-dioxygenase from Pseudomonas aeruginosa strain JB2, and the terephthalate 1,2-dioxygenase system from Delftia tsuruhatensis strain T7. This subfamily belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. 222 matched cddid_all.tbl CDD cd08881 cd08881 176890 RHO_alpha_C_NDO-like C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related aromatic ring hydroxylating dioxygenases. C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs, also known as aromatic ring hydroxylating dioxygenases). This domain binds non-heme Fe(II). RHOs utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ring, an initial step in the oxidative degradation of aromatic compounds. RHOs are composed of either two or three protein components, and are comprised of an electron transport chain (ETC) and an oxygenase. The ETC transfers reducing equivalents form the electron donor to the oxygenase component, which in turn transfers electrons to the oxygen molecules. The oxygenase components are oligomers, either (alpha)n or (alpha)n(beta)n. The alpha subunits are the catalytic components and have an N-terminal domain, which binds a Rieske-like 2Fe-2S cluster, and a C-terminal domain which binds the non-heme Fe(II). The Fe(II) is co-ordinated by conserved His and Asp residues. Proteins belonging to this subgroup include the terminal oxygenase alpha subunits of biphenyl dioxygenase, cumene dioxygenase from Pseudomonas fluorescens IP01, ethylbenzene dioxygenase, naphthalene 1,2-dioxygenase, nitrobenzene dioxygenase from Comamonas sp. strain JS765, toluene 2,3-dioxygenase from Pseudomonas putida F1, dioxin dioxygenase of Sphingomonas sp. Strain RW1, and the polycyclic aromatic hydrocarbons (PAHs)degrading ring-hydroxylating dioxygenase from Sphingomonas CHY-1. This subfamily belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. 206 matched cddid_all.tbl CDD cd08882 cd08882 176891 RHO_alpha_C_MupW-like C-terminal catalytic domain of Pseudomonas fluorescens MupW and related aromatic ring hydroxylating dioxygenases. C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas fluorescens MupW and related Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs, also known as aromatic ring hydroxylating dioxygenases). RHOs utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ring, an initial step in the oxidative degradation of aromatic compounds. RHOs are composed of either two or three protein components, and are comprised of an electron transport chain (ETC) and an oxygenase. The ETC transfers reducing equivalents from the electron donor to the oxygenase component, which in turn transfers electrons to the oxygen molecules. The oxygenase components are oligomers, either (alpha)n or (alpha)n(beta)n. The alpha subunits are the catalytic components and have an N-terminal domain, which binds a Rieske-like 2Fe-2S cluster, and a C-terminal domain which binds the non-heme Fe(II). The Fe(II) is co-ordinated by conserved His and Asp residues. MupW is part of the mupirocin biosynthetic gene cluster in Pseudomonas fluorescens, and may catalyze the oxidation of the 16-methyl group during biosynthesis of this polyketide antibiotic. Mupirocin is a mixture of pseudomonic acids which targets isoleucyl-tRNA synthase and is a strong inhibitor of Gram positive bacterial and mycoplasmal pathogens. This subfamily belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. 243 matched cddid_all.tbl CDD cd08883 cd08883 176892 RHO_alpha_C_CMO-like C-terminal catalytic domain of plant choline monooxygenase (CMO) and related aromatic ring hydroxylating dioxygenases. C-terminal catalytic domain of plant choline monooxygenase and related Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs, also known as aromatic ring hydroxylating dioxygenases). RHOs utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ring, an initial step in the oxidative degradation of aromatic compounds. RHOs are composed of either two or three protein components, and are comprised of an electron transport chain (ETC) and an oxygenase. The ETC transfers reducing equivalents from the electron donor to the oxygenase component, which in turn transfers electrons to the oxygen molecules. The oxygenase components are oligomers, either (alpha)n or (alpha)n(beta)n. The alpha subunits are the catalytic components and have an N-terminal domain, which binds a Rieske-like 2Fe-2S cluster, and a C-terminal domain which binds the non-heme Fe(II). The Fe(II) is co-ordinated by conserved His and Asp residues. Plant choline monooxygenase catalyzes the first step in a two-step oxidation of choline to the osmoprotectant glycine betaine. This subfamily belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. 175 matched cddid_all.tbl CDD cd08884 cd08884 176893 RHO_alpha_C_GbcA-like C-terminal catalytic domain of GbcA (glycine betaine catabolism A) from Pseudomonas aeruginosa PAO1 and related aromatic ring hydroxylating dioxygenases. C-terminal catalytic domain of GbcA (glycine betaine catabolism A) from Pseudomonas aeruginosa PAO1 and related Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs, also known as aromatic ring hydroxylating dioxygenases). RHOs utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ring, an initial step in the oxidative degradation of aromatic compounds. RHOs are composed of either two or three protein components, and are comprised of an electron transport chain (ETC) and an oxygenase. The ETC transfers reducing equivalents from the electron donor to the oxygenase component, which in turn transfers electrons to the oxygen molecules. The oxygenase components are oligomers, either (alpha)n or (alpha)n(beta)n. The alpha subunits are the catalytic components and have an N-terminal domain, which binds a Rieske-like 2Fe-2S cluster, and a C-terminal domain which binds the non-heme Fe(II). The Fe(II) is co-ordinated by conserved His and Asp residues. GbcA is involved in glycine betaine (GB) catabolism in Pseudomonas aeruginosa; it may remove a methyl group from GB via a dioxygenase mechanism, producing dimethylglycine and formaldehyde. This subfamily belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. 205 matched cddid_all.tbl CDD cd08885 cd08885 176894 RHO_alpha_C_1 C-terminal catalytic domain of the oxygenase alpha subunit of an uncharacterized subgroup of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases. C-terminal catalytic domain of the oxygenase alpha subunit of a functionally uncharacterized subgroup of the Rieske-type non-heme iron aromatic ring-hydroxylating oxygenase (RHO) family. RHOs, also known as aromatic ring hydroxylating dioxygenases, utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ring, an initial step in the oxidative degradation of aromatic compounds. RHOs are composed of either two or three protein components, and are comprised of an electron transport chain (ETC) and an oxygenase. The ETC transfers reducing equivalents from the electron donor to the oxygenase component, which in turn transfers electrons to the oxygen molecules. The oxygenase components are oligomers, either (alpha)n or (alpha)n(beta)n. The alpha subunits are the catalytic components and have an N-terminal domain, which binds a Rieske-like 2Fe-2S cluster, and a C-terminal domain which binds the non-heme Fe(II). The Fe(II) is co-ordinated by conserved His and Asp residues. This group contains two putative Parvibaculum lavamentivorans (T) DS-1 oxygenases; this organism catabolizes commercial linear alkylbenzenesulfonate surfactant (LAS) and other surfactants, by a pathway involving an undefined 'omega-oxygenation' and beta-oxidation of the LAS side chain. The nature of the LAS-oxygenase is unknown but is likely a multicomponent system. This subfamily belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. 190 matched cddid_all.tbl CDD cd08886 cd08886 176895 RHO_alpha_C_2 C-terminal catalytic domain of the oxygenase alpha subunit of an uncharacterized subgroup of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases. C-terminal catalytic domain of the oxygenase alpha subunit of a functionally uncharacterized subgroup of the Rieske-type non-heme iron aromatic ring-hydroxylating oxygenase (RHO) family. RHOs, also known as aromatic ring hydroxylating dioxygenases, utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ring, an initial step in the oxidative degradation of aromatic compounds. RHOs are composed of either two or three protein components, and are comprised of an electron transport chain (ETC) and an oxygenase. The ETC transfers reducing equivalents from the electron donor to the oxygenase component, which in turn transfers electrons to the oxygen molecules. The oxygenase components are oligomers, either (alpha)n or (alpha)n(beta)n. The alpha subunits are the catalytic components and have an N-terminal domain, which binds a Rieske-like 2Fe-2S cluster, and a C-terminal domain which binds the non-heme Fe(II). The Fe(II) is co-ordinated by conserved His and Asp residues. This subfamily belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. 182 matched cddid_all.tbl CDD cd08887 cd08887 176896 RHO_alpha_C_3 C-terminal catalytic domain of the oxygenase alpha subunit of an uncharacterized subgroup of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases. C-terminal catalytic domain of the oxygenase alpha subunit of a functionally uncharacterized subgroup of the Rieske-type non-heme iron aromatic ring-hydroxylating oxygenase (RHO) family. RHOs, also known as aromatic ring hydroxylating dioxygenases, utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ring, an initial step in the oxidative degradation of aromatic compounds. RHOs are composed of either two or three protein components, and are comprised of an electron transport chain (ETC) and an oxygenase. The ETC transfers reducing equivalents from the electron donor to the oxygenase component, which in turn transfers electrons to the oxygen molecules. The oxygenase components are oligomers, either (alpha)n or (alpha)n(beta)n. The alpha subunits are the catalytic components and have an N-terminal domain, which binds a Rieske-like 2Fe-2S cluster, and a C-terminal domain which binds the non-heme Fe(II). The Fe(II) is co-ordinated by conserved His and Asp residues. This group contains a putative Parvibaculum lavamentivorans (T) DS-1 oxygenase; this organism catabolizes commercial linear alkylbenzenesulfonate surfactant (LAS) and other surfactants, by a pathway involving an undefined 'omega-oxygenation' and beta-oxidation of the LAS side chain. The nature of the LAS-oxygenase is unknown but is likely a multicomponent system. This subfamily belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. 185 matched cddid_all.tbl CDD cd08888 cd08888 176897 SRPBCC_PITPNA-B_like Lipid-binding SRPBCC domain of mammalian PITPNA, -B, and related proteins (Class I PITPs). This subgroup includes the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of mammalian Class 1 phosphatidylinositol transfer proteins (PITPs), PITPNA/PITPalpha and PITPNB/PITPbeta, Drosophila vibrator, and related proteins. These are single domain proteins belonging to the PITP family of lipid transfer proteins, and to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. In vitro, PITPs bind phosphatidylinositol (PtdIns), as well as phosphatidylcholine (PtdCho) but with a lower affinity. They transfer these lipids from one membrane compartment to another. The cellular roles of PITPs include inositol lipid signaling, PtdIns metabolism, and membrane trafficking. In addition, PITPNB transfers sphingomyelin in vitro, with a low affinity. PITPNA is found chiefly in the nucleus and cytoplasm; it is enriched in the brain and predominantly localized in the axons. A reduced expression of PITPNA contributes to the neurodegenerative phenotype of the mouse vibrator mutation. The role of PITPNA in vivo may be to provide PtdIns for localized PI3K-dependent signaling, thereby controlling the polarized extension of axonal processes. PITPNA homozygous null mice die soon after birth from complicated organ failure, including intestinal and hepatic steatosis, hypoglycemia, and spinocerebellar disease. PITPNB is associated with the Golgi and ER, and is highly expressed in the liver. Deletion of the PITPNB gene results in embryonic lethality. The PtdIns and PtdCho exchange activity of PITPNB is required for COPI-mediated retrograde transport from the Golgi to the ER. Drosophila vibrator localizes to the ER, and has an essential role in cytokinesis during mitosis and meiosis. 258 matched cddid_all.tbl CDD cd08889 cd08889 176898 SRPBCC_PITPNM1-2_like Lipid-binding SRPBCC domain of mammalian PITPNM1-2 and related proteins (Class IIA PITPs). This subgroup includes an N-terminal SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of mammalian Class II phosphatidylinositol transfer protein (PITPs), PITPNM1/PITPalphaI/Nir2 (PYK2 N-terminal domain-interacting receptor2) and PITPNM2/PITPalphaII/Nir3), Drosophila RdgB, and related proteins. These are membrane associated multidomain proteins belonging to the PITP family of lipid transfer proteins, and to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. In vitro, PITPs bind phosphatidylinositol (PtdIns), as well as phosphatidylcholine (PtdCho) but with a lower affinity. They transfer these lipids from one membrane compartment to another. The cellular roles of PITPs include inositol lipid signaling, PtdIns metabolism, and membrane trafficking. Ablation of the mouse gene encoding PITPNM1 results in early embryonic death. PITPNM1 is localized chiefly to the Golgi apparatus, and under certain conditions translocates to the lipid droplets. Targeting to the latter is dependent on a specific threonine residue within the SRPBCC domain. PITPNM1 plays a part in Golgi-mediated transport. It regulates diacylglycerol (DAG) production at the trans-Golgi network (TGN) via the CDP-choline pathway. Drosophila RdgB, the founding member of the PITP family, is implicated in the visual and olfactory transduction. RdgB is required for maintenance of ultra structure in photoreceptors and for sensory transduction. The mouse PITPNM1 gene rescues the phenotype of Drosophila rdgB mutant flies. In addition to the SRPBCC domain, PITPNM1 and -2 contain a Rho-inhibitory domain (Rid), six hydrophobic stretches, a DDHD calcium binding region, and a C-terminal tyrosine kinase Pyk2-binding / HAD-like phosphohydrolase domain. PITPNM1 has a role in regulating cell morphogenesis through its Rho inhibitory domain (Rid). This SRPBCC_PITPNM1-2_like domain model includes the first 52 residues of the 224 residues Rid (Rho-inhibitory domain). 260 matched cddid_all.tbl CDD cd08890 cd08890 176899 SRPBCC_PITPNC1_like Lipid-binding SRPBCC domain of mammalian PITPNC1,and related proteins (Class IIB PITPs). This subgroup includes the N-terminal SRPBCC (START/RHO_alpha_C /PITP /Bet_v1/CoxG/CalC) domain of mammalian Class IIB phosphatidylinositol transfer protein (PITP), PITPNC1/RdgBbeta, and related proteins. These are metazoan proteins belonging to the PITP family of lipid transfer proteins, and to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. In vitro, PITPs bind phosphatidylinositol (PtdIns), as well as phosphatidylcholine (PtdCho) but with a lower affinity. They transfer these lipids from one membrane compartment to another. The cellular roles of PITPs include inositol lipid signaling, PtdIns metabolism, and membrane trafficking. Mammalian PITPNC1 contains an amino-terminal SRPBCC PITP-like domain and a short carboxyl-terminal domain. It is a cytoplasmic protein, and is ubiquitously expressed. It can transfer phosphatidylinositol (PtdIns) in vitro with a similar ability to other PITPs. 250 matched cddid_all.tbl CDD cd08891 cd08891 176900 SRPBCC_CalC Ligand-binding SRPBCC domain of Micromonospora echinospora CalC and related proteins. This subfamily includes Micromonospora echinospora CalC (MeCalC) and related proteins. These proteins belong to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins which bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. MeCalC confers resistance to the enediyne, calicheamicin gamma 1 (CLM). Enediyne antibiotics are antitumor agents. Enediynes have an in vitro and in vivo role as DNA damaging agents; they consist of a DNA recognition unit (e.g., aryltetrasaccharide of CLM), an activating component (e.g., methyl trisulfide of CLM), which promotes cycloaromatization, and the enediyne warhead which cycloaromatizes to a reactive diradical species, resulting in oxidative strand cleavage of the targeted DNA sequence. MeCalC confers resistance to CLM by a self sacrificing mechanism: the transient enediyne diradical species abstracts a CalC Gly Calpha-hydrogen, thereby quenching the reactive enediyne moiety, and generating a CalC Gly Calpha radical. This radical then reacts with oxygen, leading to oxidative site-specific proteolysis of CalC. This antibiotic-induced proteolysis of CalC results in inactivation of both CalC and the highly reactive diradical species. CalC has also been shown to inactivate two other enediynes, shishijimicin and namenamicin. The crucial Gly of the MeCalC CLM resistance mechanism is contained in a loop (L1) which is displaced when CLM is bound, this Gly is not conserved in this subgroup. 149 matched cddid_all.tbl CDD cd08892 cd08892 176901 SRPBCC_Aha1 Putative hydrophobic ligand-binding SRPBCC domain of the Hsp90 co-chaperone Aha1 and related proteins. This subfamily includes the C-terminal SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of Aha1, and related domains. Proteins in this group belong to the SRPBCC domain superfamily of proteins which bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. Aha1 is one of several co-chaperones, which regulate the dimeric chaperone Hsp90. Hsp90, Aha1, and other accessory proteins interact in a chaperone cycle driven by ATP binding and hydrolysis. Aha1 promotes dimerization of the N-terminal domains of Hsp90, and stimulates its low intrinsic ATPase activity. One Aha1 molecule binds per Hsp90 dimer. The N- and C- terminal domains of Aha1 cooperatively bind across the dimer interface of Hsp90. The C-terminal domain of Aha1 binds the N-terminal Hsp90 ATPase domain. Aha1 may regulate the dwell time of Hsp90 with client proteins. Aha1 may act as either a negative or positive regulator of chaperone-dependent activation, depending on the client protein; for example, it acts as a negative regulator in the case of Saccharomyces cerevisiae MAL63 MAL-activator, and acts as a positive regulator in the case of glucocorticoid receptor and v-Src kinase. The mechanisms by which these opposing functions are achieved are unclear. Aha1 is upregulated in a number of tumor lines co-incident with the activation of several signaling kinases. 126 matched cddid_all.tbl CDD cd08893 cd08893 176902 SRPBCC_CalC_Aha1-like_GntR-HTH Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins; some contain an N-terminal GntR family winged HTH DNA-binding domain. SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which regulate the dimeric chaperone Hsp90), and belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. Some proteins in this subgroup contain an N-terminal winged helix-turn-helix DNA-binding domain found in the GntR family of proteins which include bacterial transcriptional regulators and their putative homologs from eukaryota and archaea. 136 matched cddid_all.tbl CDD cd08894 cd08894 176903 SRPBCC_CalC_Aha1-like_1 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins. SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which regulate the dimeric chaperone Hsp90), and belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. 139 matched cddid_all.tbl CDD cd08895 cd08895 176904 SRPBCC_CalC_Aha1-like_2 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins. SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which regulate the dimeric chaperone Hsp90), and belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. 146 matched cddid_all.tbl CDD cd08896 cd08896 176905 SRPBCC_CalC_Aha1-like_3 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins. SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which regulate the dimeric chaperone Hsp90), and belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. 146 matched cddid_all.tbl CDD cd08897 cd08897 176906 SRPBCC_CalC_Aha1-like_4 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins. SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which regulate the dimeric chaperone Hsp90), and belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. 133 matched cddid_all.tbl CDD cd08898 cd08898 176907 SRPBCC_CalC_Aha1-like_5 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins. SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which regulate the dimeric chaperone Hsp90), and belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. 145 matched cddid_all.tbl CDD cd08899 cd08899 176908 SRPBCC_CalC_Aha1-like_6 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins. SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which regulate the dimeric chaperone Hsp90), and belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. 157 matched cddid_all.tbl CDD cd08900 cd08900 176909 SRPBCC_CalC_Aha1-like_7 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins. SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which regulate the dimeric chaperone Hsp90), and belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. 143 matched cddid_all.tbl CDD cd08901 cd08901 176910 SRPBCC_CalC_Aha1-like_8 Putative hydrophobic ligand-binding SRPBCC domain of an uncharacterized subgroup of CalC- and Aha1-like proteins. SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of a functionally uncharacterized subgroup of CalC- and Aha1-like proteins. This group shows similarity to the SRPBCC domains of Micromonospora echinospora CalC (a protein which confers resistance to enediynes) and human Aha1 (one of several co-chaperones which regulate the dimeric chaperone Hsp90), and belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket and they bind diverse ligands. 136 matched cddid_all.tbl CDD cd08902 cd08902 176911 START_STARD4-like Lipid-binding START domain of mammalian STARD4 and related proteins. This subgroup includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD4 and related domains. It belongs to the START domain family, and in turn to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD4 plays an important role in steroidogenesis, trafficking cholesterol into mitochondria. It specifically binds cholesterol, and demonstrates limited binding to another sterol, 7alpha-hydroxycholesterol. STARD4 is ubiquitously expressed, with highest levels in liver and kidney. 202 matched cddid_all.tbl CDD cd08903 cd08903 176912 START_STARD5-like Lipid-binding START domain of mammalian STARD5 and related proteins. This subgroup includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD5, and related domains. It belongs to the START domain family, and in turn to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD5 is ubiquitously expressed, with highest levels in liver and kidney. STARD5 functions in the kidney within the proximal tubule cells where it is associated with the Endoplasmic Reticulum (ER), and may participate in ER-associated cholesterol transport. It binds cholesterol and 25-hydroxycholesterol. Expression of the gene encoding STARD5 is increased by ER stress, and its mRNA and protein levels are elevated in a type I diabetic mouse model of human diabetic nephropathy. 208 matched cddid_all.tbl CDD cd08904 cd08904 176913 START_STARD6-like Lipid-binding START domain of mammalian STARD6 and related proteins. This subgroup includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD6 and related domains. It belongs to the START domain family, and in turn to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD6 is expressed in male germ cells of normal rats, and in the steroidogenic Leydig cells of perinatal hypothyroid testes. It may play a pivotal role in the steroidogenesis as well as in the spermatogenesis of normal rats. STARD6 has also been detected in the rat nervous system, and may participate in neurosteroid synthesis. 204 matched cddid_all.tbl CDD cd08905 cd08905 176914 START_STARD1-like Cholesterol-binding START domain of mammalian STARD1 and related proteins. This subgroup includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of STARD1 (also known as StAR) and related proteins. It belongs to the START domain family, and in turn to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD1 has a high affinity for cholesterol. It can reduce macrophage lipid content and inflammatory status. It plays an essential role in steroidogenic tissues: transferring the steroid precursor, cholesterol, from the outer to the inner mitochondrial membrane, across the aqueous space. Mutations in the gene encoding STARD1/StAR can cause lipid congenital adrenal hyperplasia (CAH), an autosomal recessive disorder characterized by a steroid synthesis deficiency and an accumulation of cholesterol in the adrenal glands and the gonads. 209 matched cddid_all.tbl CDD cd08906 cd08906 176915 START_STARD3-like Cholesterol-binding START domain of mammalian STARD3 and related proteins. This subgroup includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of STARD3 (also known as metastatic lymph node 64/MLN64) and related proteins. It belongs to the START domain family, and in turn to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD3 has a high affinity for cholesterol. It may function in trafficking endosomal cholesterol to a cytosolic acceptor or membrane. In addition to having a cytoplasmic START cholesterol-binding domain, STARD3 also contains an N-terminal MENTAL cholesterol-binding and protein-protein interaction domain. The MENTAL domain contains transmembrane helices and anchors MLN64 to endosome membranes. The gene encoding STARD3 is overexpressed in about 25% of breast cancers. 209 matched cddid_all.tbl CDD cd08907 cd08907 176916 START_STARD8-like C-terminal lipid-binding START domain of mammalian STARD8 and related proteins, which also have an N-terminal Rho GTPase-activating protein (RhoGAP) domain. This subgroup includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of STARD8 (also known as deleted in liver cancer 3/DLC3, and Arhgap38) and related proteins. It belongs to the START domain family, and in turn to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. Proteins belonging to this subfamily also have a RhoGAP domain. The precise function of the START domain in this subgroup is unclear. 205 matched cddid_all.tbl CDD cd08908 cd08908 176917 START_STARD12-like C-terminal lipid-binding START domain of mammalian STARD12 and related proteins, which also have an N-terminal Rho GTPase-activating protein (RhoGAP) domain. This subgroup includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of STARD12 (also known as DLC-1, Arhgap7, and p122-RhoGAP) and related proteins. It belongs to the START domain family, and in turn to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. Proteins belonging to this subgroup also have an N-terminal SAM (sterile alpha motif) domain and a RhoGAP domain, and have a SAM-RhoGAP-START domain organization. The precise function of the START domain in this subgroup is unclear. 204 matched cddid_all.tbl CDD cd08909 cd08909 176918 START_STARD13-like C-terminal lipid-binding START domain of mammalian STARD13 and related proteins, which also have an N-terminal Rho GTPase-activating protein (RhoGAP) domain. This subgroup includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of STARD13 (also known as DLC-2, Arhgap37, and SDCCAG13) and related proteins. It belongs to the START domain family, and in turn to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. Proteins belonging to this subfamily also have a RhoGAP domain. The precise function of the START domain in this subgroup is unclear. 205 matched cddid_all.tbl CDD cd08910 cd08910 176919 START_STARD2-like Lipid-binding START domain of mammalian STARD2 and related proteins. This subgroup includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of STARD2 (also known as phosphatidylcholine transfer protein/PC-TP) and related proteins. It belongs to the START domain family, and in turn to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD2 is a cytosolic phosphatidycholine (PtdCho) transfer protein, which traffics PtdCho, the most common class of phospholipids in eukaryotes, between membranes. It represents a minimal START domain structure. STARD2 plays roles in hepatic cholesterol metabolism, in the development of atherosclerosis, and may have a mitochondrial function. 207 matched cddid_all.tbl CDD cd08911 cd08911 176920 START_STARD7-like Lipid-binding START domain of mammalian STARD7 and related proteins. This subgroup includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of STARD7 (also known as gestational trophoblastic tumor 1/GTT1). It belongs to the START domain family, and in turn to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. The gene encoding STARD7 is overexpressed in choriocarcinoma. STARD7 appears to be involved in the intracellular trafficking of phosphatidycholine (PtdCho) to mitochondria. STARD7 was shown to be surface active and to interact differentially with phospholipid monolayers, it showed a preference for phosphatidylserine, cholesterol, and phosphatidylglycerol. 207 matched cddid_all.tbl CDD cd08913 cd08913 176921 START_STARD14-like Lipid-binding START domain of mammalian STARDT14 and related proteins. This subgroup includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian brown fat-inducible STARD14 (also known as Acyl-Coenzyme A Thioesterase 11 or ACOT11, BFIT, THEA, THEM1, KIAA0707, and MGC25974) and related proteins. It belongs to the START domain family, and in turn to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD14/ACOT11 is a type II acetyl-CoA thioesterase; it catalyzes the hydrolysis of acyl-CoAs to free fatty acid and CoASH. Human STARD14 displays acetyl-CoA thioesterase activity towards medium(C12)- and long(C16)-chain fatty acyl-CoA substrates. In addition to having a START domain, most proteins in this subgroup have two tandem copies of the hotdog domain. There are two splice variants of human STARD14, named BFIT1 and BFIT2, which differ in their C-termini. Human BFIT2 is equivalent to mouse mBFIT/Acot11, whose transcription is increased two fold in obesity-resistant mice compared with obesity-prone mice. 240 matched cddid_all.tbl CDD cd08914 cd08914 176922 START_STARD15-like Lipid-binding START domain of mammalian STARD15 and related proteins. This subgroup includes the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of STARD15/ACOT12 (also known as cytoplasmic acetyl-CoA hydrolase/CACH, THEAL, and MGC105114) and related domains. It belongs to the START domain family, and in turn to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. STARD15/ACOT12 is a type II acetyl-CoA thioesterase; it catalyzes the hydrolysis of acyl-CoAs to free fatty acid and CoASH. Rat CACH hydrolyzes acetyl-CoA to acetate and CoA. In addition to having a START domain, most proteins in this subgroup have two tandem copies of the hotdog domain. Human STARD15/ACOT12 may have roles in cholesterol metabolism and in beta-oxidation. 236 matched cddid_all.tbl CDD cd08915 cd08915 185746 V_Alix_like Protein-interacting V-domain of mammalian Alix and related domains. This superfamily contains the V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. The Alix V-domain contains a binding site, partially conserved in this superfamily, for the retroviral late assembly (L) domain YPXnL motif. The Alix V-domain is also a dimerization domain. Members of this superfamily have an N-terminal Bro1-like domain, which binds components of the ESCRT-III complex. The Bro1-like domains of Alix and HD-PTP can also bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Many members, including Alix, HD-PTP, and Bro1, also have a proline-rich region (PRR), which binds multiple partners in Alix, including Tsg101 (tumor susceptibility gene 101, a component of ESCRT-1) and the apoptotic protein ALG-2. The C-terminal portion (V-domain and PRR) of Bro1 interacts with Doa4, a ubiquitin thiolesterase needed to remove ubiquitin from MVB cargoes; it interacts with a YPxL motif in Doa4s catalytic domain to stimulate its deubiquitination activity. Rim20 may bind the ESCRT-III subunit Snf7, bringing the protease Rim13 (a YPxL-containing transcription factor) into proximity with Rim101, and promoting the proteolytic activation of Rim101. HD-PTP is encoded by the PTPN23 gene, a tumor suppressor gene candidate often absent in human kidney, breast, lung, and cervical tumors. HD-PTP has a C-terminal catalytically inactive tyrosine phosphatase domain. 342 matched cddid_all.tbl CDD cd08916 cd08916 381257 TrHb3_P Truncated hemoglobins (TrHbs, 2/2Hb, 2/2 globins); group 3 (P). The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. They are classified into three main groups based on their structural properties and named after Mycobacterium sp. genes glbN, glbO, and glbP: TrHb1s (N), TrHb2s (O) and TrHb3s (P). TrHb3s include Campylobacter jejuni Ctb, encoded by Cj0465c, which may play a role in moderating O2 flux within C. jejuni. 116 matched cddid_all.tbl CDD cd08917 cd08917 381258 TrHb2_O Truncated hemoglobins (TrHbs, 2/2Hb, 2/2 globins); group 2 (O). The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. TrHbs are classified into three main groups based on their structural properties and named after Mycobacterium sp. genes glbN, glbO, and glbP: TrHb1s (N), TrHb2s (O) and TrHb3s (P). TrHb2s include the dimeric Arabidopsis thaliana TrHb2 AtGLB3. GLB3 is likely to have a function distinct from other plant globins: it exhibits a low O2 affinity, an unusual concentration-independent binding of O2 and CO, and does not respond to any of the treatments that induce plant 3-on-3 globins. Other TrHb2's include Bacillus subtilis trHb (Bs-trHb) which exhibits an extremely high oxygen affinity, and Pseudoalteromonas haloplanktis PhHbO (encoded by the PSHAa0030 gene) which appears to be involved in oxidative and nitrosative stress resistance. 116 matched cddid_all.tbl CDD cd08919 cd08919 381259 PBP-like Phycobiliproteins (PBPs) and related proteins. phycobilisomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker polypeptides. PBPs have different numbers of chromophores, and the basic monomer component (alpha/beta heterodimers) can further oligomerize to ring-shaped trimers (heterohexamers) and hexamers (heterododecamers). Stacked PBP hexamers form both the core and the rods of the PBS; the core is mainly made up by allophycocyanin (APC) while the rods can be composed of the PBPs phycoerythrin (PE), phycocyanin (PC) and phycoerythrocyanin (PEC). This family also contains allophycocyanin-like (Apl) proteins, which conserve the residues critical for chromophore interactions, but may not maintain the proper alpha-beta subunit interactions and tertiary structure of PBPs. The genes encoding the Apl proteins cluster with light-responsive regulatory components, so these may have photoresponsive regulatory role(s). Included in this family is the PBP-like domain of the core-membrane linker polypeptide (LCM). The LCM serves both as a terminal energy acceptor and as a linker polypeptide. Its single phycocyanobilin (PCB) chromophore is one of two terminal energy transmitters, and transfers excitations from the hundreds of chromophores of the PBS to the RCs. This family also includes some proteins which have glutathione-S-transferases (GST) domains N-terminal to this PBP-like domain. 153 matched cddid_all.tbl CDD cd08920 cd08920 271272 Ngb Neuroglobins. The Ngb described in this subfamily is a hexacoordinated heme globin chiefly expressed in neurons of the brain and retina. In the human brain, it is highly expressed in the hypothalamus, amygdala, and in the pontine tegmental nuclei. It affords protection of brain neurons from ischemia and hypoxia. In rats, it plays a role in the neuroprotection of limb ischemic preconditioning (LIP). It plays roles as: a sensor of oxygen levels; a store or reservoir for oxygen; a facilitator for oxygen transport; a regulator of ROS; and a scavenger of nitric oxide. It also functions in the protection against apoptosis and in sleep regulation. This subgroup contains Ngb from mammalian and non-mammalian vertebrates, including fish, amphibians and reptiles; the functionally pentacoordinated acoelomorph Symsagittifera roscoffensis Ngb does not belong to this subgroup. 148 matched cddid_all.tbl CDD cd08922 cd08922 381260 FHb-globin Globin domain of flavohemoglobins (flavoHbs). FlavoHbs function primarily as nitric oxide dioxygenases (NODs, EC 1.14.12.17), converting NO and O2 to inert NO3- (nitrate). They have an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD- and FAD-binding domain, and use the reducing power of cellular NAD(P)H to drive regeneration of the ferrous heme. They protect from nitrosative stress (the broad range of cellular toxicities caused by NO), and modulate NO signaling pathways. NO scavenging by flavoHb attenuates the expression of the nitrosative stress response, affects the swarming behavior of Escherichia coli, and maintains squid-Vibrio fischeri and Medicago truncatula-Sinorhizobium meliloti symbioses. FlavoHb expression affects Aspergillus nidulans sexual development and mycotoxin production, and Dictyostelium discoideum development. This family also includes some single-domain goblins (SDgbs). 140 matched cddid_all.tbl CDD cd08923 cd08923 381261 class1-2_nsHbs_Lbs Class1 nonsymbiotic hemoglobins (nsHbs), class II nsHbs, leghemoglobins (Lbs,) and related proteins. Class1 nsHbs include the dimeric hexacoordinate Trema tomentosa nsHb and the dimeric hexacoordinate nsHb from monocot barley. Also belonging to this family is ParaHb, a dimeric pentacoordinate Hb from the root nodules of Parasponia andersonii, a non-legume capable of symbiotic nitrogen fixation. ParaHb is unusual in that it has different heme redox potentials for each subunit; it may have evolved from class1 nsHbs. Lbs are pentacoordinate, and facilitate the diffusion of O2 to the respiring Rhizobium bacteroids within root nodules. They may have evolved from class 2 nonsymbiotic hemoglobins (class2 nsHb). 147 matched cddid_all.tbl CDD cd08924 cd08924 271275 Cygb Cytoglobin and related globins. Cygb is a hexacoordinated heme-containing protein, able to bind O2, NO and carbon monoxide. It has both nitric oxide dioxygenase and lipid peroxidase activities, and potentially participates in the maintenance of normal phenotype by implementing a homeostatic effect, to counteract stress conditions imposed on a cell. Cygb is implicated in multiple human pathologies: it is up-regulated in fibrosis and neurodegenerative disorders, and down-regulated in multiple cancer types, and may have a tumor suppressor role. It is expressed ubiquitously across a broad range of vertebrate organs including liver, heart, brain, lung, retina, and gut. In the human brain, it was detected at high levels in the habenula, hypothalamus, thalamus, hippocampus and pontine tegmental nuclei, detected at a low level in the cerebral cortex, and undetected in the cerebellar cortex. 153 matched cddid_all.tbl CDD cd08925 cd08925 381262 Hb-beta-like Hemoglobin beta, gamma, delta, epsilon, and related Hb subunits. Hb is the oxygen transport protein of erythrocytes. It is an allosterically modulated heterotetramer. Hemoglobin A (HbA) is the most common Hb in adult humans, and is formed from two alpha-chains and two beta-chains (alpha2beta2). An equilibrium exists between deoxygenated/unliganded/T(tense state) Hb having low oxygen affinity, and oxygenated /liganded/R(relaxed state) Hb having a high oxygen affinity. Various endogenous heterotropic effectors bind Hb to modulate its oxygen affinity and cooperative behavior, e.g. hydrogen ions, chloride ions, carbon dioxide and 2,3-bisphosphoglycerate. Hb is also an allosterically regulated nitrite reductase; the plasma nitrite anion may be activated by hemoglobin in areas of hypoxia to bring about vasodilation. Other Hb types are: HbA2 (alpha2delta2) which in normal individuals, is naturally expressed at a low level; Hb Portland-1 (zeta2gamma2), Hb Gower-1 (zeta2epsilon2), and Hb Gower-2 (alpha2epsilon2), which are Hbs present during the embryonic period; and fetal hemoglobin (HbF, alpha2gamma2), the primary hemoglobin throughout most of gestation. These Hbs types have differences in O2 affinity and in their interactions with allosteric effectors. 139 matched cddid_all.tbl CDD cd08926 cd08926 271277 Mb Animal Myoglobins. Myoglobin (Mb) is a monomeric pentacoordinate heme-bound globin protein whose expression has long been considered limited to cardiomyocytes and striated skeletal muscle cell, however it has recently been found localized in a wide variety of tissues including smooth muscle cells. As a physiological catalyst, it can modulate reactive oxygen species levels, facilitate oxygen diffusion within the cell, and scavenge or generate NO depending on oxygen tensions within the cell. Through its NO dioxygenase and nitrite reductase activities, Mb regulates mitochondrial function in energy-demanding tissues. 148 matched cddid_all.tbl CDD cd08927 cd08927 381263 Hb-alpha-like Hemoglobin alpha, zeta, mu, theta, and related Hb subunits. Hb is the oxygen transport protein of erythrocytes. It is an allosterically modulated heterotetramer. Hemoglobin A (HbA) is the most common Hb in adult humans, and is formed from two alpha-chains and two beta-chains (alpha2beta2). An equilibrium exists between deoxygenated/unliganded/T(tense state) Hb having low oxygen affinity, and oxygenated /liganded/R(relaxed state) Hb having a high oxygen affinity. Various endogenous heterotropic effectors bind Hb to modulate its oxygen affinity and cooperative behavior, e.g. hydrogen ions, chloride ions, carbon dioxide and 2,3-bisphosphoglycerate. Hb is also an allosterically regulated nitrite reductase; the plasma nitrite anion may be activated by hemoglobin in areas of hypoxia to bring about vasodilation. Other Hb types are: HbA2 (alpha2delta2) which in normal individuals, is naturally expressed at a low level; Hb Portland-1 (zeta2gamma2), Hb Gower-1 (zeta2epsilon2), and Hb Gower-2 (alpha2epsilon2), which are Hbs present during the embryonic period; and fetal hemoglobin (HbF, alpha2gamma2), the primary hemoglobin throughout most of gestation. These Hbs types have differences in O2 affinity and in their interactions with allosteric effectors. 140 matched cddid_all.tbl CDD cd08928 cd08928 187633 KR_fFAS_like_SDR_c_like ketoacyl reductase (KR) domain of fungal-type fatty acid synthase (fFAS)-like, classical (c)-like SDRs. KR domain of FAS, including the fungal-type multidomain FAS alpha chain, and the single domain daunorubicin C-13 ketoreductase. Fungal-type FAS is a heterododecameric FAS composed of alpha and beta multifunctional polypeptide chains. The KR, an SDR family member is located centrally in the alpha chain. KR catalyzes the NADP-dependent reduction of ketoacyl-ACP to hydroxyacyl-ACP. KR shares the critical active site Tyr of the classical SDR and has partial identity of the active site tetrad, but the upstream Asn is replaced in KR by Met. As in other SDRs, there is a glycine rich NAD(P)-binding motif, but the pattern found in KR does not match the classical SDRs, and is not strictly conserved within this group. Daunorubicin is a clinically important therapeutic compound used in some cancer treatments. Single domain daunorubicin C-13 ketoreductase is member of the classical SDR family with a canonical glycine-rich NAD(P)-binding motif, but lacking a complete match to the active site tetrad characteristic of this group. The critical Tyr, plus the Lys and upstream Asn are present, but the catalytic Ser is replaced, generally by Gln. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human prostaglandin dehydrogenase (PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107, PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type KRs have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 248 matched cddid_all.tbl CDD cd08929 cd08929 187634 SDR_c4 classical (c) SDR, subgroup 4. This subgroup has a canonical active site tetrad and a typical Gly-rich NAD-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 226 matched cddid_all.tbl CDD cd08930 cd08930 187635 SDR_c8 classical (c) SDR, subgroup 8. This subgroup has a fairly well conserved active site tetrad and domain size of the classical SDRs, but has an atypical NAD-binding motif ([ST]G[GA]XGXXG). SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 250 matched cddid_all.tbl CDD cd08931 cd08931 187636 SDR_c9 classical (c) SDR, subgroup 9. This subgroup has the canonical active site tetrad and NAD-binding motif of the classical SDRs. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 227 matched cddid_all.tbl CDD cd08932 cd08932 212493 HetN_like_SDR_c HetN oxidoreductase-like, classical (c) SDR. This subgroup includes Anabaena sp. strain PCC 7120 HetN, a putative oxidoreductase involved in heterocyst differentiation, and related proteins. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 223 matched cddid_all.tbl CDD cd08933 cd08933 187638 RDH_SDR_c retinal dehydrogenase-like, classical (c) SDR. These classical SDRs includes members identified as retinol dehydrogenases, which convert retinol to retinal, a property that overlaps with 17betaHSD activity. 17beta-dehydrogenases are a group of isozymes that catalyze activation and inactivation of estrogen and androgens, and include members of the short-chain dehydrogenases/reductase family. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 261 matched cddid_all.tbl CDD cd08934 cd08934 187639 CAD_SDR_c clavulanic acid dehydrogenase (CAD), classical (c) SDR. CAD catalyzes the NADP-dependent reduction of clavulanate-9-aldehyde to clavulanic acid, a beta-lactamase inhibitor. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 243 matched cddid_all.tbl CDD cd08935 cd08935 187640 mannonate_red_SDR_c putative D-mannonate oxidoreductase, classical (c) SDR. D-mannonate oxidoreductase catalyzes the NAD-dependent interconversion of D-mannonate and D-fructuronate. This subgroup includes Bacillus subtitils UxuB/YjmF, a putative D-mannonate oxidoreductase; the B. subtilis UxuB gene is part of a putative ten-gene operon (the Yjm operon) involved in hexuronate catabolism. Escherichia coli UxuB does not belong to this subgroup. This subgroup has a canonical active site tetrad and a typical Gly-rich NAD-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 271 matched cddid_all.tbl CDD cd08936 cd08936 187641 CR_SDR_c Porcine peroxisomal carbonyl reductase like, classical (c) SDR. This subgroup contains porcine peroxisomal carbonyl reductase and similar proteins. The porcine enzyme efficiently reduces retinals. This subgroup also includes human dehydrogenase/reductase (SDR family) member 4 (DHRS4), and human DHRS4L1. DHRS4 is a peroxisomal enzyme with 3beta-hydroxysteroid dehydrogenase activity; it catalyzes the reduction of 3-keto-C19/C21-steroids into 3beta-hydroxysteroids more efficiently than it does the retinal reduction. The human DHRS4 gene cluster contains DHRS4, DHRS4L2 and DHRS4L1. DHRS4L2 and DHRS4L1 are paralogs of DHRS4, DHRS4L2 being the most recent member. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 256 matched cddid_all.tbl CDD cd08937 cd08937 187642 DHB_DH-like_SDR_c 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase (DHB DH)-like, classical (c) SDR. DHB DH (aka 1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate dehydrogenase) catalyzes the NAD-dependent conversion of 1,2-dihydroxycyclohexa-3,4-diene carboxylate to a catechol. This subgroup also contains Pseudomonas putida F1 CmtB, 2,3-dihydroxy-2,3-dihydro-p-cumate dehydrogenase, the second enzyme in the pathway for catabolism of p-cumate catabolism. This subgroup shares the glycine-rich NAD-binding motif of the classical SDRs and shares the same catalytic triad; however, the upstream Asn implicated in cofactor binding or catalysis in other SDRs is generally substituted by a Ser. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 256 matched cddid_all.tbl CDD cd08939 cd08939 187643 KDSR-like_SDR_c 3-ketodihydrosphingosine reductase (KDSR) and related proteins, classical (c) SDR. These proteins include members identified as KDSR, ribitol type dehydrogenase, and others. The group shows strong conservation of the active site tetrad and glycine rich NAD-binding motif of the classical SDRs. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 239 matched cddid_all.tbl CDD cd08940 cd08940 187644 HBDH_SDR_c d-3-hydroxybutyrate dehydrogenase (HBDH), classical (c) SDRs. DHBDH, an NAD+ -dependent enzyme, catalyzes the interconversion of D-3-hydroxybutyrate and acetoacetate. It is a classical SDR, with the canonical NAD-binding motif and active site tetrad. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 258 matched cddid_all.tbl CDD cd08941 cd08941 187645 3KS_SDR_c 3-keto steroid reductase, classical (c) SDRs. 3-keto steroid reductase (in concert with other enzymes) catalyzes NADP-dependent sterol C-4 demethylation, as part of steroid biosynthesis. 3-keto reductase is a classical SDR, with a well conserved canonical active site tetrad and fairly well conserved characteristic NAD-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 290 matched cddid_all.tbl CDD cd08942 cd08942 187646 RhlG_SDR_c RhlG and related beta-ketoacyl reductases, classical (c) SDRs. Pseudomonas aeruginosa RhlG is an SDR-family beta-ketoacyl reductase involved in Rhamnolipid biosynthesis. RhlG is similar to but distinct from the FabG family of beta-ketoacyl-acyl carrier protein (ACP) of type II fatty acid synthesis. RhlG and related proteins are classical SDRs, with a canonical active site tetrad and glycine-rich NAD(P)-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 250 matched cddid_all.tbl CDD cd08943 cd08943 187647 R1PA_ADH_SDR_c rhamnulose-1-phosphate aldolase/alcohol dehydrogenase, classical (c) SDRs. This family has bifunctional proteins with an N-terminal aldolase and a C-terminal classical SDR domain. One member is identified as a rhamnulose-1-phosphate aldolase/alcohol dehydrogenase. The SDR domain has a canonical SDR glycine-rich NAD(P) binding motif and a match to the characteristic active site triad. However, it lacks an upstream active site Asn typical of SDRs. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 250 matched cddid_all.tbl CDD cd08944 cd08944 187648 SDR_c12 classical (c) SDR, subgroup 12. These are classical SDRs, with the canonical active site tetrad and glycine-rich NAD-binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 246 matched cddid_all.tbl CDD cd08945 cd08945 187649 PKR_SDR_c Polyketide ketoreductase, classical (c) SDR. Polyketide ketoreductase (KR) is a classical SDR with a characteristic NAD-binding pattern and active site tetrad. Aromatic polyketides include various aromatic compounds of pharmaceutical interest. Polyketide KR, part of the type II polyketide synthase (PKS) complex, is comprised of stand-alone domains that resemble the domains found in fatty acid synthase and multidomain type I PKS. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 258 matched cddid_all.tbl CDD cd08946 cd08946 212494 SDR_e extended (e) SDRs. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 200 matched cddid_all.tbl CDD cd08947 cd08947 187651 NmrA_TMR_like_SDR_a NmrA (a transcriptional regulator), HSCARG (an NADPH sensor), and triphenylmethane reductase (TMR) like proteins, atypical (a) SDRs. Atypical SDRs belonging to this subgroup include NmrA, HSCARG, and TMR, these proteins bind NAD(P) but they lack the usual catalytic residues of the SDRs. Atypical SDRs are distinct from classical SDRs. NmrA is a negative transcriptional regulator of various fungi, involved in the post-translational modulation of the GATA-type transcription factor AreA. NmrA lacks the canonical GXXGXXG NAD-binding motif and has altered residues at the catalytic triad, including a Met instead of the critical Tyr residue. NmrA may bind nucleotides but appears to lack any dehydrogenase activity. HSCARG has been identified as a putative NADP-sensing molecule, and redistributes and restructures in response to NADPH/NADP ratios. Like NmrA, it lacks most of the active site residues of the SDR family, but has an NAD(P)-binding motif similar to the extended SDR family, GXXGXXG. TMR, an NADP-binding protein, lacks the active site residues of the SDRs but has a glycine rich NAD(P)-binding motif that matches the extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 224 matched cddid_all.tbl CDD cd08948 cd08948 187652 5beta-POR_like_SDR_a progesterone 5-beta-reductase-like proteins (5beta-POR), atypical (a) SDRs. 5beta-POR catalyzes the reduction of progesterone to 5beta-pregnane-3,20-dione in Digitalis plants. This subgroup of atypical-extended SDRs, shares the structure of an extended SDR, but has a different glycine-rich nucleotide binding motif (GXXGXXG) and lacks the YXXXK active site motif of classical and extended SDRs. Tyr-179 and Lys 147 are present in the active site, but not in the usual SDR configuration. Given these differences, it has been proposed that this subfamily represents a new SDR class. Other atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 308 matched cddid_all.tbl CDD cd08950 cd08950 187653 KR_fFAS_SDR_c_like ketoacyl reductase (KR) domain of fungal-type fatty acid synthase (fFAS), classical (c)-like SDRs. KR domain of fungal-type fatty acid synthase (FAS), type I. Fungal-type FAS is a heterododecameric FAS composed of alpha and beta multifunctional polypeptide chains. The KR, an SDR family member, is located centrally in the alpha chain. KR catalyzes the NADP-dependent reduction of ketoacyl-ACP to hydroxyacyl-ACP. KR shares the critical active site Tyr of the Classical SDR and has partial identity of the active site tetrad, but the upstream Asn is replaced in KR by Met. As in other SDRs, there is a glycine rich NAD-binding motif, but the pattern found in KR does not match the classical SDRs, and is not strictly conserved within this group. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human prostaglandin dehydrogenase (PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107, PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type KRs have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 259 matched cddid_all.tbl CDD cd08951 cd08951 187654 DR_C-13_KR_SDR_c_like daunorubicin C-13 ketoreductase (KR), classical (c)-like SDRs. Daunorubicin is a clinically important therapeutic compound used in some cancer treatments. Daunorubicin C-13 ketoreductase is member of the classical SDR family with a canonical glycine-rich NAD(P)-binding motif, but lacking a complete match to the active site tetrad characteristic of this group. The critical Tyr, plus the Lys and upstream Asn are present, but the catalytic Ser is replaced, generally by Gln. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human prostaglandin dehydrogenase (PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107, PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type KRs have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 260 matched cddid_all.tbl CDD cd08952 cd08952 187655 KR_1_SDR_x ketoreductase (KR), subgroup 1, complex (x) SDRs. Ketoreductase, a module of the multidomain polyketide synthase (PKS), has 2 subdomains, each corresponding to a SDR family monomer. The C-terminal subdomain catalyzes the NADPH-dependent reduction of the beta-carbonyl of a polyketide to a hydroxyl group, a step in the biosynthesis of polyketides, such as erythromycin. The N-terminal subdomain, an interdomain linker, is a truncated Rossmann fold which acts to stabilizes the catalytic subdomain. Unlike typical SDRs, the isolated domain does not oligomerize but is composed of 2 subdomains, each resembling an SDR monomer. The active site resembles that of typical SDRs, except that the usual positions of the catalytic Asn and Tyr are swapped, so that the canonical YXXXK motif changes to YXXXN. Modular PKSs are multifunctional structures in which the makeup recapitulates that found in (and may have evolved from) FAS. Polyketide synthesis also proceeds via the addition of 2-carbon units as in fatty acid synthesis. The complex SDR NADP-binding motif, GGXGXXG, is often present, but is not strictly conserved in each instance of the module. This subfamily includes KR domains found in many multidomain PKSs, including six of seven Sorangium cellulosum PKSs (encoded by spiDEFGHIJ) which participate in the synthesis of the polyketide scaffold of the cytotoxic spiroketal polyketide spirangien. These seven PKSs have either a single PKS module (SpiF), two PKR modules (SpiD,-E,-I,-J), or three PKS modules (SpiG,-H). This subfamily includes the single KR domain of SpiF, the first KR domains of SpiE,-G,H,-I,and #J, the third KR domain of SpiG, and the second KR domain of SpiH. The second KR domains of SpiE,-G, I, and #J, and the KR domains of SpiD, belong to a different KR_FAS_SDR subfamily. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human prostaglandin dehydrogenase (PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107, PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type KRs have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 480 matched cddid_all.tbl CDD cd08953 cd08953 187656 KR_2_SDR_x ketoreductase (KR), subgroup 2, complex (x) SDRs. Ketoreductase, a module of the multidomain polyketide synthase (PKS), has 2 subdomains, each corresponding to a SDR family monomer. The C-terminal subdomain catalyzes the NADPH-dependent reduction of the beta-carbonyl of a polyketide to a hydroxyl group, a step in the biosynthesis of polyketides, such as erythromycin. The N-terminal subdomain, an interdomain linker, is a truncated Rossmann fold which acts to stabilizes the catalytic subdomain. Unlike typical SDRs, the isolated domain does not oligomerize but is composed of 2 subdomains, each resembling an SDR monomer. The active site resembles that of typical SDRs, except that the usual positions of the catalytic Asn and Tyr are swapped, so that the canonical YXXXK motif changes to YXXXN. Modular PKSs are multifunctional structures in which the makeup recapitulates that found in (and may have evolved from) FAS. Polyketide synthesis also proceeds via the addition of 2-carbon units as in fatty acid synthesis. The complex SDR NADP-binding motif, GGXGXXG, is often present, but is not strictly conserved in each instance of the module. This subfamily includes both KR domains of the Bacillus subtilis Pks J,-L, and PksM, and all three KR domains of PksN, components of the megacomplex bacillaene synthase, which synthesizes the antibiotic bacillaene. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human prostaglandin dehydrogenase (PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107, PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type KRs have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 436 matched cddid_all.tbl CDD cd08954 cd08954 187657 KR_1_FAS_SDR_x beta-ketoacyl reductase (KR) domain of fatty acid synthase (FAS), subgroup 1, complex (x) SDRs. NADP-dependent KR domain of the multidomain type I FAS, a complex SDR family. This subfamily also includes proteins identified as polyketide synthase (PKS), a protein with related modular protein architecture and similar function. It includes the KR domains of mammalian and chicken FAS, and Dictyostelium discoideum putative polyketide synthases (PKSs). These KR domains contain two subdomains, each of which is related to SDR Rossmann fold domains. However, while the C-terminal subdomain has an active site similar to the other SDRs and a NADP-binding capability, the N-terminal SDR-like subdomain is truncated and lacks these functions, serving a supportive structural role. In some instances, such as porcine FAS, an enoyl reductase (a Rossman fold NAD-binding domain of the medium-chain dehydrogenase/reductase, MDR family) module is inserted between the sub-domains. Fatty acid synthesis occurs via the stepwise elongation of a chain (which is attached to acyl carrier protein, ACP) with 2-carbon units. Eukaryotic systems consists of large, multifunctional synthases (type I) while bacterial, type II systems, use single function proteins. Fungal fatty acid synthesis uses a dodecamer of 6 alpha and 6 beta subunits. In mammalian type FAS cycles, ketoacyl synthase forms acetoacetyl-ACP which is reduced by the NADP-dependent beta-ketoacyl reductase (KR), forming beta-hydroxyacyl-ACP, which is in turn dehydrated by dehydratase to a beta-enoyl intermediate, which is reduced by NADP-dependent beta-enoyl reductase (ER); this KR and ER are members of the SDR family. This KR subfamily has an active site tetrad with a similar 3D orientation compared to archetypical SDRs, but the active site Lys and Asn residue positions are swapped. The characteristic NADP-binding is typical of the multidomain complex SDRs, with a GGXGXXG NADP binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human prostaglandin dehydrogenase (PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107, PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type KRs have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 452 matched cddid_all.tbl CDD cd08955 cd08955 187658 KR_2_FAS_SDR_x beta-ketoacyl reductase (KR) domain of fatty acid synthase (FAS), subgroup 2, complex (x). Ketoreductase, a module of the multidomain polyketide synthase, has 2 subdomains, each corresponding to a short-chain dehydrogenases/reductase (SDR) family monomer. The C-terminal subdomain catalyzes the NADPH-dependent reduction of the beta-carbonyl of a polyketide to a hydroxyl group, a step in the biosynthesis of polyketides, such as erythromycin. The N-terminal subdomain, an interdomain linker, is a truncated Rossmann fold which acts to stabilizes the catalytic subdomain. Unlike typical SDRs, the isolated domain does not oligomerizes but is composed of 2 subdomains, each resembling an SDR monomer. In some instances, as in porcine FAS, an enoyl reductase (a Rossman fold NAD binding domain of the MDR family) module is inserted between the sub-domains. The active site resembles that of typical SDRs, except that the usual positions of the catalytic asparagine and tyrosine are swapped, so that the canonical YXXXK motif changes to YXXXN. Modular polyketide synthases are multifunctional structures in which the makeup recapitulates that found in (and may have evolved from) fatty acid synthase. In some instances, such as porcine FAS , an enoyl reductase module is inserted between the sub-domains. Fatty acid synthesis occurs via the stepwise elongation of a chain (which is attached to acyl carrier protein, ACP) with 2-carbon units. Eukaryotic systems consists of large, multifunctional synthases (type I) while bacterial, type II systems, use single function proteins. Fungal fatty acid synthesis uses dodecamer of 6 alpha and 6 beta subunits. In mammalian type FAS cycles, ketoacyl synthase forms acetoacetyl-ACP which is reduced by the NADP-dependent beta-ketoacyl reductase (KR), forming beta-hydroxyacyl-ACP, which is in turn dehydrated by dehydratase to a beta-enoyl intermediate, which is reduced by NADP-dependent beta-enoyl reductase (ER). Polyketide syntheses also proceeds via the addition of 2-carbon units as in fatty acid synthesis. The complex SDR NADP binding motif, GGXGXXG, is often present, but is not strictly conserved in each instance of the module. This subfamily includes the KR domain of the Lyngbya majuscule Jam J, -K, and #L which are encoded on the jam gene cluster and are involved in the synthesis of the Jamaicamides (neurotoxins); Lyngbya majuscule Jam P belongs to a different KR_FAS_SDR_x subfamily. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human prostaglandin dehydrogenase (PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107, PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type KRs have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 376 matched cddid_all.tbl CDD cd08956 cd08956 187659 KR_3_FAS_SDR_x beta-ketoacyl reductase (KR) domain of fatty acid synthase (FAS), subgroup 3, complex (x). Ketoreductase, a module of the multidomain polyketide synthase (PKS), has 2 subdomains, each corresponding to a SDR family monomer. The C-terminal subdomain catalyzes the NADPH-dependent reduction of the beta-carbonyl of a polyketide to a hydroxyl group, a step in the biosynthesis of polyketides, such as erythromycin. The N-terminal subdomain, an interdomain linker, is a truncated Rossmann fold which acts to stabilizes the catalytic subdomain. Unlike typical SDRs, the isolated domain does not oligomerize but is composed of 2 subdomains, each resembling an SDR monomer. The active site resembles that of typical SDRs, except that the usual positions of the catalytic Asn and Tyr are swapped, so that the canonical YXXXK motif changes to YXXXN. Modular PKSs are multifunctional structures in which the makeup recapitulates that found in (and may have evolved from) FAS. In some instances, such as porcine FAS, an enoyl reductase (ER) module is inserted between the sub-domains. Fatty acid synthesis occurs via the stepwise elongation of a chain (which is attached to acyl carrier protein, ACP) with 2-carbon units. Eukaryotic systems consists of large, multifunctional synthases (type I) while bacterial, type II systems, use single function proteins. Fungal fatty acid synthesis uses a dodecamer of 6 alpha and 6 beta subunits. In mammalian type FAS cycles, ketoacyl synthase forms acetoacetyl-ACP which is reduced by the NADP-dependent beta-KR, forming beta-hydroxyacyl-ACP, which is in turn dehydrated by dehydratase to a beta-enoyl intermediate, which is reduced by NADP-dependent beta- ER. Polyketide synthesis also proceeds via the addition of 2-carbon units as in fatty acid synthesis. The complex SDR NADP-binding motif, GGXGXXG, is often present, but is not strictly conserved in each instance of the module. This subfamily includes KR domains found in many multidomain PKSs, including six of seven Sorangium cellulosum PKSs (encoded by spiDEFGHIJ) which participate in the synthesis of the polyketide scaffold of the cytotoxic spiroketal polyketide spirangien. These seven PKSs have either a single PKS module (SpiF), two PKR modules (SpiD,-E,-I,-J), or three PKS modules (SpiG,-H). This subfamily includes the second KR domains of SpiE,-G, I, and -J, both KR domains of SpiD, and the third KR domain of SpiH. The single KR domain of SpiF, the first and second KR domains of SpiH, the first KR domains of SpiE,-G,- I, and -J, and the third KR domain of SpiG, belong to a different KR_FAS_SDR subfamily. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human prostaglandin dehydrogenase (PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107, PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type KRs have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 448 matched cddid_all.tbl CDD cd08957 cd08957 187660 WbmH_like_SDR_e Bordetella bronchiseptica enzymes WbmH and WbmG-like, extended (e) SDRs. Bordetella bronchiseptica enzymes WbmH and WbmG, and related proteins. This subgroup exhibits the active site tetrad and NAD-binding motif of the extended SDR family. It has been proposed that the active site in Bordetella WbmG and WbmH cannot function as an epimerase, and that it plays a role in O-antigen synthesis pathway from UDP-2,3-diacetamido-2,3-dideoxy-l-galacturonic acid. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 307 matched cddid_all.tbl CDD cd08958 cd08958 187661 FR_SDR_e flavonoid reductase (FR), extended (e) SDRs. This subgroup contains FRs of the extended SDR-type and related proteins. These FRs act in the NADP-dependent reduction of flavonoids, ketone-containing plant secondary metabolites; they have the characteristic active site triad of the SDRs (though not the upstream active site Asn) and a NADP-binding motif that is very similar to the typical extended SDR motif. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 293 matched cddid_all.tbl CDD cd08959 cd08959 350084 ArfGap_ArfGap1_like ARF1 GTPase-activating protein 1-like. ArfGAP (ADP Ribosylation Factor GTPase Activating Protein) domain is a part of ArfGap1-like proteins that play a crucial role in controlling of membrane trafficking, particularly in the formation of COPI (coat protein complex I)-coated vesicles on Golgi membranes. The ArfGAP1 protein subfamily consists of three members: ArfGAP1 (Gcs1p in yeast), ArfGAP2 and ArfGAP3 (both are homologs of yeast Glo3p). ArfGAP2/3 are closely related, but with little similarity to ArfGAP1, except the catalytic ArfGAP domain. They promote hydrolysis of GTP bound to the small G protein ADP-ribosylation factor 1 (Arf1), which leads to the dissociation of coat proteins from Golgi-derived membranes and vesicles. Dissociation of the coat proteins is required for the fusion of these vesicles with target compartments. Thus, the GAP catalytic activity plays a key role in the formation of COPI vesicles from Golgi membrane. In contrast to ArfGAP1, which displays membrane curvature-dependent ArfGAP activity, ArfGAP2 and ArfGAP3 activities are dependent on coatomer (the core COPI complex) which required for efficient recruitment of ArfGAP2 and ArfGAP3 to the Golgi membrane. Accordingly, ArfGAP2/3 has been implicated in coatomer-mediated protein transport between the Golgi complex and the endoplasmic reticulum. Unlike ArfGAP1, which is controlled by membrane curvature through its amphipathic lipid packing sensor (ALPS) motifs, ArfGAP2/3 do not possess ALPS motif. 115 matched cddid_all.tbl CDD cd08961 cd08961 185752 GH64-TLP-SF glycoside hydrolase family 64 (beta-1,3-glucanases which produce specific pentasaccharide oligomers) and thaumatin-like proteins. This superfamily includes glycoside hydrolases of family 64 (GH64), these are mostly bacterial beta-1,3-glucanases which cleave long-chain polysaccharide beta-1,3-glucans, into specific pentasaccharide oligomers and are implicated in fungal cell wall degradation. Also included in this superfamily are thaumatin, the sweet-tasting protein from the African berry Thaumatococcus daniellii, and thaumatin-like proteins (TLPs) which are involved in host defense and a wide range of developmental processes in fungi, plants, and animals. Like GH64s, some TLPs also hydrolyze the beta-1,3-glucans of the type commonly found in fungal walls. Plant TLPs are classified as pathogenesis-related (PR) protein family 5 (PR5), their expression is induced by environmental stresses such as pathogen/pest attack, drought and cold. Several members of the plant TLP family have been reported as food allergens from fruits, and pollen allergens from conifers. Streptomyces matensis laminaripentaose-producing, beta-1,3-glucanase (GH64-LPHase), and TLPs have in common, a core N-terminal barrel domain (domain I) composed of 10 beta-strands, two coming from the C-terminal region of the protein. In TLPs, this core domain is flanked by two shorter domains (domains II and III). Small TLPs, such as Triticum aestivum thaumatin-like xylanase inhibitor, have a deletion in the third domain (domain II). GH64-LPHase has a second C-terminal domain which corresponds positional to, but is much larger than, domain III of TLP. GH64-LPHase and TLPs are described as crescent-fold structures. Critical functional residues, common to GH64-LPHase and TLPs are a Glu and an Asp residue. LPHase has an electronegative, substrate-binding cleft and the afore mentioned conserved Glu and Asp residues are the catalytic residues essential for beta-1,3-glucan cleavage. In TLPs, these residues are two of the four conserved residues which contribute to the strong electronegative character of the cleft which is associated with the antifungal activity of TLPs. 153 matched cddid_all.tbl CDD cd08962 cd08962 199206 GatD GatD subunit of archaeal Glu-tRNA amidotransferase. GatD is involved in the alternative synthesis of Gln-tRNA(Gln) in archaea via the transamidation of incorrectly charged Glu-tRNA(Gln). GatD is active as a dimer, and it provides the amino group required for this reaction. GatD is related to bacterial L-asparaginases (amidohydrolases), which catalyze the hydrolysis of asparagine to aspartic acid and ammonia. This CD spans both the L-asparaginase_like domain and an N-terminal supplementary domain. 402 matched cddid_all.tbl CDD cd08963 cd08963 199207 L-asparaginase_I Type I (cytosolic) bacterial L-asparaginase. Asparaginases (amidohydrolases, E.C. 3.5.1.1) are enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases. This model represents type I L-asparaginases, which are highly specific for asparagine and localized in the cytosol. Type I L-asparaginase acts as a dimer. A conserved threonine residue is thought to supply the nucleophile hydroxy-group that attacks the amide bond. Many bacterial L-asparaginases have both L-asparagine and L-glutamine hydrolysis activities, to a different degree, and some of them are annotated as asparaginase/glutaminase. One example of an enzyme with no L-glutaminase activity is the type I L-asparaginase from Wolinella succinogenes. 316 matched cddid_all.tbl CDD cd08964 cd08964 199208 L-asparaginase_II Type II (periplasmic) bacterial L-asparaginase. Asparaginases (amidohydrolases, E.C. 3.5.1.1) are enzymes that catalyze the hydrolysis of asparagine to aspartic acid and ammonia. In bacteria, there are two classes of amidohydrolases. This model represents type II L-asparaginases, which tend to be highly specific for asparagine and localized to the periplasm. They are potent antileukemic agents and have been used in the treatment of acute lymphoblastic leukemia (ALL), but not without severe side effects. Tumor cells appear to have a heightened dependence on exogenous L-aspartate, and depleting their surroundings of L-aspartate may starve cancerous ALL cells. Type II L-asparaginase acts as a tetramer, which is actually a dimer of two tightly bound dimers. A conserved threonine residue is thought to supply the nucleophile hydroxy-group that attacks the amide bond. Many bacterial L-asparaginases have both L-asparagine and L-glutamine hydrolysis activities, to a different degree, and some of them are annotated as asparaginase/glutaminase. 319 matched cddid_all.tbl CDD cd08965 cd08965 176799 EcNei-like_N N-terminal domain of Escherichia coli Nei/endonuclease VIII and related DNA glycosylases. This family contains the N-terminal domain of proteobacteria Nei and related DNA glycosylases. It includes Escherichia coli Nei, and belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. Escherichia coli Nei has been well studied, it is a DNA glycosylase/AP lyase that excises damaged pyrimidines, including 5-hydroxycytosine, 5-hydroxyuracil, and uracil glycol. In addition to this EcNei-like_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a canonical zinc-finger motif. 115 matched cddid_all.tbl CDD cd08966 cd08966 176800 EcFpg-like_N N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases. This family contains the N-terminal domain of Escherichia coli Fpg1/MutM and related bacterial DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. Escherichia coli Fpg mainly recognizes and excises damaged purines such as 8-oxo-7,8-dihydroguanine (8-oxoG) and 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG). It is bifunctional, having both a DNA glycosylase (recognition activity) and a AP lyase activity. In addition to this EcFpg-like_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif, which also contribute residues to the active site. 120 matched cddid_all.tbl CDD cd08967 cd08967 176801 MeNeil1_N "N-terminal domain of metazoan Nei-like glycosylase 1 (NEIL1). This family contains the N-terminal domain of metazoan NEIL1. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. NEIL1 recognizes the oxidized pyrimidines 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) and 4,6-diamino- 5-formamidopyrimidine (FapyA), thymine glycol (Tg) and 5-hydroxyuracil (5-OHU). However, even though it has weak activity on 8-oxo-7,8-dihydroguanine (8-oxoG), it does show strong preference for the products of its further oxidation: spiroiminodihydantoin and guanidinohydantoin. In addition to this MeNeil1_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zincless finger motif. This characteristic ""zincless finger"" motif, is a structural equivalent of the zinc finger common to other members of the Fpg/Nei family. Neil1 is one of three homologs found in eukaryotes and its lineage extends back as far as early metazoans." 131 matched cddid_all.tbl CDD cd08968 cd08968 176802 MeNeil2_N N-terminal domain of metazoan Nei-like glycosylase 2 (NEIL2). This family contains the N-terminal domain of the metazoan protein Neil2. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. NEIL2 repairs 5-hydroxyuracil (5-OHU) and other oxidized derivatives of cytosine, but it shows preference for DNA bubble structures. In addition to this MeNeil2_N domain, NEIL2 contains a helix-two turn-helix (H2TH) domain and a characteristic CHCC zinc finger motif. Neil2 is one of three homologs found in eukaryotes. 126 matched cddid_all.tbl CDD cd08969 cd08969 176803 MeNeil3_N N-terminal domain of metazoan Nei-like glycosylase 3 (NEIL3). This family contains the N-terminal domain of the Metazoan Neil3. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. In contrast, mouse NEIL3 (MmuNEIL3) forms a Schiff base intermediate via its N-terminal valine. The latter is a functional DNA glycosylase in vitro and in vivo. MmuNEIL3 prefers lesions in single-stranded DNA and in bubble structures. In duplex DNA, it recognizes the oxidized purines spiroiminodihydantoin (Sp), guanidinohydantoin (Gh), 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) and 4,6-diamino-5-formamidopyrimidine (FapyA), but not 8-oxo-7,8-dihydroguanine (8-oxoG). Since the expression of the MmuNeil3 glycosylase domain (MmuNeil3delta324) reduces both the high spontaneous mutation frequency and the FapyG level in a Escherichia coli mutant lacking Fpg, Nei and MutY glycosylase activites, NEIL3 may play a role in repairing FapyG in vivo. In addition to this MeNeil3_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc finger motif, plus a characteristic C-terminal extension that contains additional zinc fingers. Neil3 is one of three homologs found in eukaryotes. 140 matched cddid_all.tbl CDD cd08970 cd08970 176804 AcNei1_N N-terminal domain of the actinomycetal Nei1 and related DNA glycosylases. This family contains the N-terminal domain of the actinomycetal Nei1 and related DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This family contains mostly actinomycetes and includes Mycobacterium tuberculosis Nei1 (MtuNei1). MtuNei1 recognizes oxidized pyrimidines such as thymine glycol (Tg) and 5,6-dihydrouracil on both double stranded and single stranded DNA, it has a strong preference for the 5R isomer of Tg. In addition to this domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif. 110 matched cddid_all.tbl CDD cd08971 cd08971 176805 AcNei2_N N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases. This family contains the N-terminal domain of the actinomycetal Nei2 and related DNA glycosylases. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This family contains mostly actinomycetes and includes Mycobacterium tuberculosis Nei2 (MtuNei2). Complementation experiments in repair-deficient Escherichia coli (fpg mutY nei triple and nei nth double mutants), support that MtuNei2 is functionally active in vivo and recognizes both guanine and cytosine oxidation products. In addition to this AcNei2_N domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif. 114 matched cddid_all.tbl CDD cd08972 cd08972 176806 PF_Nei_N N-terminal domain of the plant and fungal Nei and related proteins. This family contains the N-terminal domain of plant and Fungi Nei and related proteins. It belongs to the FpgNei_N, [N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII)] domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. The plant and fungal FpgNei glycosylases prefer the oxidized pyrimidines spiroiminodihydantoin (Sp), guanidinohydantoin (Gh) over 8-oxoguanine in double stranded oligonucleotides and also show weak activity on single stranded DNA. In addition to this domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a characteristic zincless finger motif. They share a common ancestor not shared with other eukaryotic members of the FpgNei family. 137 matched cddid_all.tbl CDD cd08973 cd08973 176807 BaFpgNei_N_1 Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8-oxo-7,8-dihydroguanine (8-oxoG) and oxidized purines and Escherichia coli Nei recognizes oxidized pyrimidines. However, neither Escherichia coli Fpg or Nei belong to this family. In addition to this BaFpgNei_N_1 domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif. 122 matched cddid_all.tbl CDD cd08974 cd08974 176808 BaFpgNei_N_2 Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8-oxo-7,8-dihydroguanine (8-oxoG) and oxidized purines, and Escherichia coli Nei recognizes oxidized pyrimidines. However, neither Escherichia coli Fpg or Nei belong to this family. In addition to this BaFpgNei_N_2 domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain. Most also contain a zinc-finger motif. 98 matched cddid_all.tbl CDD cd08975 cd08975 176809 BaFpgNei_N_3 Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. One exception is mouse Nei-like glycosylase 3 (Neil3) which forms a Schiff base intermediate via its N-terminal valine. In this family the N-terminal proline is replaced by an isoleucine or valine. Escherichia coli Fpg prefers 8-oxo-7,8-dihydroguanine (8-oxoG) and oxidized purines and Escherichia coli Nei recognizes oxidized pyrimidines. However, neither Escherichia coli Fpg or Nei belong to this family. In addition to this BaFpgNei_N_3 domain, enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif. 117 matched cddid_all.tbl CDD cd08976 cd08976 176810 BaFpgNei_N_4 Uncharacterized bacterial subgroup of the N-terminal domain of Fpg (formamidopyrimidine-DNA glycosylase, MutM)_Nei (endonuclease VIII) base-excision repair DNA glycosylases. This family is an uncharacterized bacterial subgroup of the FpgNei_N domain superfamily. DNA glycosylases maintain genome integrity by recognizing base lesions created by ionizing radiation, alkylating or oxidizing agents, and endogenous reactive oxygen species. They initiate the base-excision repair process, which is completed with the help of enzymes such as phosphodiesterases, AP endonucleases, DNA polymerases and DNA ligases. DNA glycosylases cleave the N-glycosyl bond between the sugar and the damaged base, creating an AP (apurinic/apyrimidinic) site. Most FpgNei DNA glycosylases use their N-terminal proline residue as the key catalytic nucleophile, and the reaction proceeds via a Schiff base intermediate. This N-terminal proline is conserved in this family. Escherichia coli Fpg prefers 8-oxo-7,8-dihydroguanine (8-oxoG) and oxidized purines and Escherichia coli Nei recognizes oxidized pyrimidines. However, neither Escherichia coli Fpg or Nei belong to this family. In addition to this BaFpgNei_N_4 domain, most enzymes belonging to this family contain a helix-two turn-helix (H2TH) domain and a zinc-finger motif. 117 matched cddid_all.tbl CDD cd08977 cd08977 185760 SusD starch binding outer membrane protein SusD. SusD-like proteins from Bacteroidetes, members of the human distal gut microbiota, are part of the starch utilization system (Sus). Sus is one of the large clusters of glycosyl hydrolases, called polysaccharide utilization loci (PULs), which play an important role in polysaccharide recognition and uptake, and it is needed for growth on amylose, amylopectin, pullulan, and maltooligosaccharides. SusD, together with SusC, a predicted beta-barrel porin, forms the minimum outer-membrane starch-binding complex. The adult human distal gut microbiota is essential for digestion of a large variety of dietary polysaccharides, for which humans lack the necessary glycosyl hydrolases. 359 matched cddid_all.tbl CDD cd08978 cd08978 350092 GH_F Glycosyl hydrolase families 43 and 62 form CAZY clan GH-F. This glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) includes family 43 (GH43) and 62 (GH62). GH43 includes enzymes with beta-xylosidase (EC 3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-), alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase (EC 3.2.1.99), xylanase (EC 3.2.1.8), endo-alpha-L-arabinanases (beta-xylanases) and galactan 1,3-beta-galactosidase (EC 3.2.1.145) activities. GH62 includes enzymes characterized as arabinofuranosidases (alpha-L-arabinofuranosidases; EC 3.2.1.55) that specifically cleave either alpha-1,2 or alpha-1,3-L-arabinofuranose side chains from xylans. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many of the enzymes in this family display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. GH62 are also predicted to be inverting enzymes. A common structural feature of both, GH43 and GH62 enzymes, is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 251 matched cddid_all.tbl CDD cd08979 cd08979 350093 GH_J Glycosyl hydrolase families 32 and 68, which form the clan GH-J. This glycosyl hydrolase family clan J (according to carbohydrate-active enzymes database (CAZY)) includes family 32 (GH32) and 68 (GH68). GH32 enzymes include invertase (EC 3.2.1.26) and other other fructofuranosidases such as inulinase (EC 3.2.1.7), exo-inulinase (EC 3.2.1.80), levanase (EC 3.2.1.65), and transfructosidases such sucrose:sucrose 1-fructosyltransferase (EC 2.4.1.99), fructan:fructan 1-fructosyltransferase (EC 2.4.1.100), sucrose:fructan 6-fructosyltransferase (EC 2.4.1.10), fructan:fructan 6G-fructosyltransferase (EC 2.4.1.243) and levan fructosyltransferases (EC 2.4.1.-). The GH68 family consists of frucosyltransferases (FTFs) that include levansucrase (EC 2.4.1.10, also known as beta-D-fructofuranosyl transferase), beta-fructofuranosidase (EC 3.2.1.26) and inulosucrase (EC 2.4.1.9). GH32 and GH68 family enzymes are retaining enzymes (i.e. they retain the configuration at anomeric carbon atom of the substrate) and catalyze hydrolysis in two steps involving a covalent glycosyl enzyme intermediate: an aspartate located close to the N-terminus acts as the catalytic nucleophile and a glutamate acts as the general acid/base; a conserved aspartate residue in the Arg-Asp-Pro (RDP) motif stabilizes the transition state. A common structural feature of all these enzymes is a 5-bladed beta-propeller domain, similar to GH43, that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 292 matched cddid_all.tbl CDD cd08980 cd08980 350094 GH43_LbAraf43-like Glycosyl hydrolase family 43 proteins such as Lactobacillus brevis alpha-L-arabinofuranosidase LbAraf43 and Geobacillus thermoleovorans GbtXyl43B. This glycosyl hydrolase family 43 (GH43) subgroup includes enzymes with beta-xylosidase (EC 3.2.1.37), alpha-L-arabinofuranosidase (EC 3.2.1.55) and possibly bifunctional xylosidase/arabinofuranosidase activities. In addition to Lactobacillus brevis alpha-L-arabinofuranosidase LbAraf43 and Geobacillus thermoleovorans IT-08 beta-xylosidase / exo-xylanase (GbtXyl43B). It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) familiesGH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 276 matched cddid_all.tbl CDD cd08981 cd08981 350095 GH43_Bt1873-like Glycosyl hydrolase family 43 protein such as Bacteroides thetaiotaomicron BT_1873. This glycosyl hydrolase family 43 (GH43) subfamily includes Bacteroides thetaiotaomicron VPI-5482 endo-arabinase (Bt1873;BT_1873), as well as uncharacterized enzymes similar to those with beta-1,4-xylosidase (xylan 1,4-beta-xylosidase; EC 3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-), alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase (EC 3.2.1.99), xylanase (EC 3.2.1.8), endo-alpha-L-arabinanase and galactan 1,3-beta-galactosidase (EC 3.2.1.145) activities. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many of the GH43 enzymes in this family may display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 289 matched cddid_all.tbl CDD cd08982 cd08982 350096 GH43-like Glycosyl hydrolase family 43 protein; uncharacterized. This glycosyl hydrolase family 43 (GH43)-like subfamily includes uncharacterized enzymes similar to those with beta-1,4-xylosidase (xylan 1,4-beta-xylosidase; EC 3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-), alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase (EC 3.2.1.99), xylanase (EC 3.2.1.8), endo-alpha-L-arabinanase and galactan 1,3-beta-galactosidase (EC 3.2.1.145) activities. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many of the enzymes in this family display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 308 matched cddid_all.tbl CDD cd08983 cd08983 350097 GH43_Bt3655-like Glycosyl hydrolase family 43 protein such as Bacteroides thetaiotaomicron VPI-5482 arabinofuranosidase Bt3655. This glycosyl hydrolase family 43 (GH43)-like family includes the characterized arabinofuranosidases (EC 3.2.1.55): Bacteroides thetaiotaomicron VPI-5482 (Bt3655;BT_3655) and Penicillium chrysogenum 31B Abf43B, as well as Bifidobacterium adolescentis ATCC 15703 beta-xylosidase (EC 3.2.1.37) BAD_1527. It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. GH43 includes enzymes with beta-xylosidase (EC 3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-), alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase (EC 3.2.1.99), xylanase (EC 3.2.1.8), endo-alpha-L-arabinanases (beta-xylanases) and galactan 1,3-beta-galactosidase (EC 3.2.1.145) activities. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 262 matched cddid_all.tbl CDD cd08984 cd08984 350098 GH43-like Glycosyl hydrolase family 43. This glycosyl hydrolase family 43 (GH43)-like subfamily includes uncharacterized enzymes similar to those with beta-1,4-xylosidase (xylan 1,4-beta-xylosidase; EC 3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-), alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase (EC 3.2.1.99), xylanase (EC 3.2.1.8), endo-alpha-L-arabinanase and galactan 1,3-beta-galactosidase (EC 3.2.1.145) activities. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many of the enzymes in this family display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 291 matched cddid_all.tbl CDD cd08985 cd08985 350099 GH43_CtGH43-like Glycosyl hydrolase family 43 protein such as Clostridium thermocellum exo-beta-1,3-galactanase CtGH43 and Ruminococcus champanellensis arabinanase Ara43A. This glycosyl hydrolase family 43 (GH43) subgroup includes characterized enzymes with exo-beta-1,3-galactanase (EC 3.2.1.145, also known as galactan 1,3-beta-galactosidase) activity such as Clostridium thermocellum (Ct1,3Gal43A or CtGH43) and Phanerochaete chrysosporium 1,3Gal43A (Pc1, 3Gal43A), and arabinanase (EC 3.2.1.99) activity such as Ruminococcus champanellensis Ara43A. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 273 matched cddid_all.tbl CDD cd08986 cd08986 350100 GH43-like Glycosyl hydrolase family 43 protein; uncharacterized. This glycosyl hydrolase family 43 (GH43)-like subfamily includes uncharacterized enzymes similar to those with beta-1,4-xylosidase (xylan 1,4-beta-xylosidase; EC 3.2.1.37), beta-1,3-xylosidase (EC 3.2.1.-), alpha-L-arabinofuranosidase (EC 3.2.1.55), arabinanase (EC 3.2.1.99), xylanase (EC 3.2.1.8), endo-alpha-L-arabinanase and galactan 1,3-beta-galactosidase (EC 3.2.1.145) activities. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many of the enzymes in this family display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 257 matched cddid_all.tbl CDD cd08987 cd08987 350101 GH62 Glycosyl hydrolase family 62, characterized arabinofuranosidases. The glycosyl hydrolase family 62 (GH62) includes eukaryotic (mostly fungal) and prokaryotic enzymes which are characterized arabinofuranosidases (alpha-L-arabinofuranosidases; EC 3.2.1.55) that specifically cleave either alpha-1,2 or alpha-1,3-L-arabinofuranose side chains from xylans. These enzymes show significantly different substrate preference with rather low specific activity towards natural substrates and differ in catalytic efficiency. They do not act on xylose moieties in xylan that are adorned with an arabinose side chain at both O2 and O3 positions, nor do they display any non-specific arabinofuranosidase activity. The synergistic action in biomass degradation makes GH62 promising candidates for biotechnological improvements of biofuel production and in various biorefinery applications. These enzymes also contain carbohydrate binding modules (CBMs) that bind cellulose or xylan. 304 matched cddid_all.tbl CDD cd08988 cd08988 350102 GH43_ABN Glycosyl hydrolase family 43. This glycosyl hydrolase family 43 (GH43) subgroup includes mostly enzymes with alpha-L-arabinofuranosidase (ABF; EC 3.2.1.55) and endo-alpha-L-arabinanase (ABN; EC 3.2.1.99) activities. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. The GH43 ABN enzymes hydrolyze alpha-1,5-L-arabinofuranoside linkages while the ABF enzymes cleave arabinose side chains so that the combined actions of these two enzymes reduce arabinan to L-arabinose and/or arabinooligosaccharides. These arabinan-degrading enzymes are important in the food industry for efficient production of L-arabinose from agricultural waste; L-arabinose is often used as a bioactive sweetener. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 277 matched cddid_all.tbl CDD cd08989 cd08989 350103 GH43_XYL-like Glycosyl hydrolase family 43, beta-D-xylosidases and arabinofuranosidases. This glycosyl hydrolase family 43 (GH43) subgroup includes mostly enzymes that have been annotated as having beta-1,4-xylosidase (beta-D-xylosidase;xylan 1,4-beta-xylosidase; EC 3.2.1.37) activity, including Selenomonas ruminantium beta-D-xylosidase SXA. These are part of an array of hemicellulases that are involved in the final breakdown of plant cell-wall whereby they degrade xylan. They hydrolyze beta-1,4 glycosidic bonds between two xylose units in short xylooligosaccharides. It also includes various GH43 family GH43 arabinofuranosidases (EC 3.2.1.55) including Humicola insolens alpha-L-arabinofuranosidase AXHd3, Bacteroides ovatus alpha-L-arabinofuranosidase (BoGH43, XynB), and the bifunctional Phanerochaete chrysosporium xylosidase/arabinofuranosidase (Xyl;PcXyl). GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 272 matched cddid_all.tbl CDD cd08990 cd08990 350104 GH43_AXH_like Glycosyl hydrolase family 43 protein, includes arabinoxylan arabinofuranohydrolase, beta-xylosidase, endo-1,4-beta-xylanase, and alpha-L-arabinofuranosidase. This subgroup includes Bacillus subtilis arabinoxylan arabinofuranohydrolase (XynD;BsAXH-m23;BSU18160), Butyrivibrio proteoclasticus alpha-L-arabinofuranosidase (Xsa43E;bpr_I2319), Clostridium stercorarium alpha-L-arabinofuranosidase XylA, and metagenomic beta-xylosidase (EC 3.2.1.37) / alpha-L-arabinofuranosidase (EC 3.2.1.55) CoXyl43. It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. The GH43_AXH-like subgroup includes enzymes that have been characterized with beta-xylosidase, alpha-L-arabinofuranosidase, endo-alpha-L-arabinanase as well as arabinoxylan arabinofuranohydrolase (AXH) activities. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. AXHs specifically hydrolyze the glycosidic bond between arabinofuranosyl substituents and xylopyranosyl backbone residues of arabinoxylan. Metagenomic beta-xylosidase/alpha-L-arabinofuranosidase CoXyl43 shows synergy with Trichoderma reesei cellulases and promotes plant biomass saccharification by degrading xylo-oligosaccharides, such as xylobiose and xylotriose, into the monosaccharide xylose. Studies show that the hydrolytic activity of CoXyl43 is stimulated in the presence of calcium. Several of these enzymes also contain carbohydrate binding modules (CBMs) that bind cellulose or xylan. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 269 matched cddid_all.tbl CDD cd08991 cd08991 350105 GH43_HoAraf43-like Glycosyl hydrolase family 43 protein such as Halothermothrix orenii H 168 alpha-L-arabinofuranosidase (HoAraf43;Hore_20580). This glycosyl hydrolase family 43 (GH43) subgroup includes Halothermothrix orenii H 168 alpha-L-arabinofuranosidase (EC 3.2.1.55) (HoAraf43;Hore_20580). It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. This GH43_ HoAraf43-like subgroup includes enzymes that have been annotated as having xylan-digesting beta-xylosidase (EC 3.2.1.37) and xylanase (endo-alpha-L-arabinanase, EC 3.2.1.8) activities. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 283 matched cddid_all.tbl CDD cd08992 cd08992 350106 GH117 Glycosyl hydrolase family 117 (GH117). This glycoside hydrolase 117 (GH117) family includes alpha-1,3-L-neoagarooligosaccharide hydrolase (EC 3.2.1.-); alpha-1,3-L-neoagarobiase/neoagarobiose hydrolase (NABH, EC 3.2.1.-). In the agarolytic pathway, in order to metabolize agar, NABH is an essential enzyme because it converts alpha-neoagarobiose (O-3,6-anhydro-alpha-l-galactopyranosyl-(1,3)-d-galactose) into fermentable monosaccharides (d-galactose and 3,6-anhydro-l-galactose). Thus, these enzymes have exo-alpha-1,3-(3,6-anhydro)-l-galactosidase activity, removing terminal non-reducing alpha-1,3-linked 3,6-anhydro-l-galactose residues from their neoagarose substrate. This family includes Zobellia galactanivorans enzymes, Zg4663 and Zg3615 (also known as ZgAhgA and ZgAhgB, respectively) that have been shown to have similar activity on unsubstituted agarose oligosaccharides while Zg3597 has been shown to be inactive, possibly due to differences in dimerization conformation, active-site structure and function. GH117 shares distant sequence similarity with families GH43 and GH32. A common structural feature of all these enzymes is a 5-bladed beta-propeller domain, similar to GH43, that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 314 matched cddid_all.tbl CDD cd08993 cd08993 350107 GH130 Glycosyl hydrolase family 130. This subfamily contains glycosyl hydrolase family 130 (GH130) proteins, as classified by the carbohydrate-active enzymes database (CAZY), are phosphorylases and hydrolases for beta-mannosides, and include beta-1,4-mannosylglucose phosphorylase (EC 2.4.1.281), beta-1,4-mannooligosaccharide phosphorylase (EC 2.4.1.319), among others that have yet to be characterized. They possess 5-bladed beta-propeller domains similar to families 32, 43, 62, 68, 117 (GH32, GH43, GH62, GH68, GH117). GH130 enzymes are involved in the bacterial utilization of mannans or N-linked glycans. Beta-1,4-mannosylglucose phosphorylase is involved in degradation of beta-1,4-D-mannosyl-N-acetyl-D-glucosamine linkages in the core of N-glycans; it produces alpha-mannose 1-phosphate and glucose from 4-O-beta-D-mannosyl-D-glucose and inorganic phosphate, using a critical catalytic Asp as a proton donor. This family includes Ruminococcus albus 4-O-beta-D-mannosyl-D-glucose phosphorylase (RaMP1) and beta-(1,4)-mannooligosaccharide phosphorylase (RaMP2), enzymes that phosphorolyze beta-mannosidic linkages at the non-reducing ends of their substrates, and have substantially diverse substrate specificity that are determined by three loop regions. 279 matched cddid_all.tbl CDD cd08994 cd08994 350108 GH43_62_32_68_117_130-like Glycosyl hydrolase families: GH43, GH62, GH32, GH68, GH117, CH130. Members of the glycosyl hydrolase families 32, 43, 62, 68, 117 and 130 (GH32, GH43, GH62, GH68, GH117, GH130) all possess 5-bladed beta-propeller domains and comprise clans F and J, as classified by the carbohydrate-active enzymes database (CAZY). Clan F consists of families GH43 and GH62. GH43 includes beta-xylosidases (EC 3.2.1.37), beta-xylanases (EC 3.2.1.8), alpha-L-arabinases (EC 3.2.1.99), and alpha-L-arabinofuranosidases (EC 3.2.1.55), using aryl-glycosides as substrates, while family GH62 contains alpha-L-arabinofuranosidases (EC 3.2.1.55) that specifically cleave either alpha-1,2 or alpha-1,3-L-arabinofuranose sidechains from xylans. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Clan J consists of families GH32 and GH68. GH32 comprises sucrose-6-phosphate hydrolases, invertases (EC 3.2.1.26), inulinases (EC 3.2.1.7), levanases (EC 3.2.1.65), eukaryotic fructosyltransferases, and bacterial fructanotransferases while GH68 consists of frucosyltransferases (FTFs) that include levansucrase (EC 2.4.1.10); beta-fructofuranosidase (EC 3.2.1.26); inulosucrase (EC 2.4.1.9), while GH68 consists of frucosyltransferases (FTFs) that include levansucrase (EC 2.4.1.10); beta-fructofuranosidase (EC 3.2.1.26); inulosucrase (EC 2.4.1.9), all of which use sucrose as their preferential donor substrate. Members of this clan are retaining enzymes (i.e. they retain the configuration at anomeric carbon atom of the substrate) that catalyze hydrolysis in two steps involving a covalent glycosyl enzyme intermediate: an aspartate located close to the N-terminus acts as the catalytic nucleophile and a glutamate acts as the general acid/base; a conserved aspartate residue in the Arg-Asp-Pro (RDP) motif stabilizes the transition state. Structures of all families in the two clans manifest a funnel-shaped active site that comprises two subsites with a single route for access by ligands. Also included in this superfamily are GH117 enzymes that have exo-alpha-1,3-(3,6-anhydro)-l-galactosidase activity, removing terminal non-reducing alpha-1,3-linked 3,6-anhydro-l-galactose residues from their neoagarose substrate, and GH130 that are phosphorylases and hydrolases for beta-mannosides, involved in the bacterial utilization of mannans or N-linked glycans. 294 matched cddid_all.tbl CDD cd08995 cd08995 350109 GH32_EcAec43-like Glycosyl hydrolase family 32, such as the putative glycoside hydrolase Escherichia coli Aec43 (FosGH2). This glycosyl hydrolase family 32 (GH32) subgroup includes Escherichia coli strain BEN2908 putative glycoside hydrolase Aec43 (FosGH2). GH32 enzymes cleave sucrose into fructose and glucose via beta-fructofuranosidase activity, producing invert sugar that is a mixture of dextrorotatory D-glucose and levorotatory D-fructose, thus named invertase (EC 3.2.1.26). GH32 family also contains other fructofuranosidases such as inulinase (EC 3.2.1.7), exo-inulinase (EC 3.2.1.80), levanase (EC 3.2.1.65), and transfructosidases such sucrose:sucrose 1-fructosyltransferase (EC 2.4.1.99), fructan:fructan 1-fructosyltransferase (EC 2.4.1.100), sucrose:fructan 6-fructosyltransferase (EC 2.4.1.10), fructan:fructan 6G-fructosyltransferase (EC 2.4.1.243) and levan fructosyltransferases (EC 2.4.1.-). These retaining enzymes (i.e. they retain the configuration at anomeric carbon atom of the substrate) catalyze hydrolysis in two steps involving a covalent glycosyl enzyme intermediate: an aspartate located close to the N-terminus acts as the catalytic nucleophile and a glutamate acts as the general acid/base; a conserved aspartate residue in the Arg-Asp-Pro (RDP) motif stabilizes the transition state. These enzymes are predicted to display a 5-fold beta-propeller fold as found for GH43 and CH68. The breakdown of sucrose is widely used as a carbon or energy source by bacteria, fungi, and plants. Invertase is used commercially in the confectionery industry, since fructose has a sweeter taste than sucrose and a lower tendency to crystallize. 281 matched cddid_all.tbl CDD cd08996 cd08996 350110 GH32_FFase Glycosyl hydrolase family 32, beta-fructosidases. Glycosyl hydrolase family GH32 cleaves sucrose into fructose and glucose via beta-fructofuranosidase activity, producing invert sugar that is a mixture of dextrorotatory D-glucose and levorotatory D-fructose, thus named invertase (EC 3.2.1.26). This family also contains other fructofuranosidases such as inulinase (EC 3.2.1.7), exo-inulinase (EC 3.2.1.80), levanase (EC 3.2.1.65), and transfructosidases such sucrose:sucrose 1-fructosyltransferase (EC 2.4.1.99), fructan:fructan 1-fructosyltransferase (EC 2.4.1.100), sucrose:fructan 6-fructosyltransferase (EC 2.4.1.10), fructan:fructan 6G-fructosyltransferase (EC 2.4.1.243) and levan fructosyltransferases (EC 2.4.1.-). These retaining enzymes (i.e. they retain the configuration at anomeric carbon atom of the substrate) catalyze hydrolysis in two steps involving a covalent glycosyl enzyme intermediate: an aspartate located close to the N-terminus acts as the catalytic nucleophile and a glutamate acts as the general acid/base; a conserved aspartate residue in the Arg-Asp-Pro (RDP) motif stabilizes the transition state. These enzymes are predicted to display a 5-fold beta-propeller fold as found for GH43 and CH68. The breakdown of sucrose is widely used as a carbon or energy source by bacteria, fungi, and plants. Invertase is used commercially in the confectionery industry, since fructose has a sweeter taste than sucrose and a lower tendency to crystallize. A common structural feature of all these enzymes is a 5-bladed beta-propeller domain, similar to GH43, that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 281 matched cddid_all.tbl CDD cd08997 cd08997 350111 GH68 Glycosyl hydrolase family 68, includes levansucrase, beta-fructofuranosidase and inulosucrase. Glycosyl hydrolase family 68 (GH68) consists of frucosyltransferases (FTFs) that include levansucrase (EC 2.4.1.10), beta-fructofuranosidase (EC 3.2.1.26) and inulosucrase (EC 2.4.1.9), all of which use sucrose as their preferential donor substrate. Levansucrase, also known as beta-D-fructofuranosyl transferase, catalyzes the transfer of the sucrose fructosyl moiety to a growing levan chain. Similarly, inulosucrase catalyzes long inulin-type of fructans, and beta-fructofuranosidases create fructooligosaccharides (FOS). However, in the absence of high fructan/sucrose ratio, some GH68 enzymes can also use fructan as donor substrate. GH68 retaining enzymes (i.e. they retain the configuration at anomeric carbon atom of the substrate) catalyze hydrolysis in two steps involving a covalent glycosyl enzyme intermediate: an aspartate located close to the N-terminus acts as the catalytic nucleophile and a glutamate acts as the general acid/base; a conserved aspartate residue in the Arg-Asp-Pro (RDP) motif stabilizes the transition state. A common structural feature of all these enzymes is a 5-bladed beta-propeller domain, similar to GH43, that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. Biotechnological applications of these enzymes include use of inulin in inexpensive production of rich fructose syrups as well as use of FOS as health-promoting pre-biotics. 354 matched cddid_all.tbl CDD cd08998 cd08998 350112 GH43_Arb43a-like Glycosyl hydrolase family 43 protein such as Bacillus subtilis subsp. subtilis str. 168 endo-alpha-1,5-L-arabinanase Arb43A. This glycosyl hydrolase family 43 (GH43) subgroup belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. The GH43 ABN enzymes hydrolyze alpha-1,5-L-arabinofuranoside linkages while the ABF enzymes cleave arabinose side chains so that the combined actions of these two enzymes reduce arabinan to L-arabinose and/or arabinooligosaccharides. Many of these enzymes such as the Bacillus subtilis arabinanase Abn2, that hydrolyzes sugar beet arabinan (branched), linear alpha-1,5-L-arabinan and pectin, are different from other arabinases; they are organized into two different domains with a divalent metal cluster close to the catalytic residues to guarantee the correct protonation state of the catalytic residues and consequently the enzyme activity. These arabinan-degrading enzymes are important in the food industry for efficient production of L-arabinose from agricultural waste; L-arabinose is often used as a bioactive sweetener. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 278 matched cddid_all.tbl CDD cd08999 cd08999 350113 GH43_ABN-like Glycosyl hydrolase family 43 protein such as endo-alpha-L-arabinanase. This glycosyl hydrolase family 43 (GH43) subgroup includes mostly enzymes with alpha-L-arabinofuranosidase (ABF; EC 3.2.1.55) and endo-alpha-L-arabinanase (ABN; EC 3.2.1.99) activities. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. The GH43 ABN enzymes hydrolyze alpha-1,5-L-arabinofuranoside linkages while the ABF enzymes cleave arabinose side chains so that the combined actions of these two enzymes reduce arabinan to L-arabinose and/or arabinooligosaccharides. These arabinan-degrading enzymes are important in the food industry for efficient production of L-arabinose from agricultural waste; L-arabinose is often used as a bioactive sweetener. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 284 matched cddid_all.tbl CDD cd09000 cd09000 350114 GH43_SXA-like Glycosyl hydrolase family 43, such as Selenomonas ruminantium beta-D-xylosidase SXA. This glycosyl hydrolase family 43 (GH43) includes enzymes that have been characterized to mainly have beta-1,4-xylosidase (beta-D-xylosidase;xylan 1,4-beta-xylosidase; EC 3.2.1.37) activity, including Selenomonas ruminantium (Xsa;Sxa;SXA), Bifidobacterium adolescentis ATCC 15703 (XylC;XynB;BAD_0428) and Bacillus sp. KK-1 XylB. They are part of an array of hemicellulases that are involved in the final breakdown of plant cell-wall whereby they degrade xylan. They hydrolyze beta-1,4 glycosidic bonds between two xylose units in short xylooligosaccharides. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. These enzymes possess an additional C-terminal beta-sandwich domain that restricts access for substrates to a portion of the active site to form a pocket. The active-site pockets comprise of two subsites, with binding capacity for two monosaccharide moieties and a single route of access for small molecules such as substrate. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 292 matched cddid_all.tbl CDD cd09001 cd09001 350115 GH43_FsAxh1-like Glycosyl hydrolase family 43 such as Fibrobacter succinogenes subsp. succinogenes S85 arabinoxylan alpha-L-arabinofuranosidase. This glycosyl hydrolase family 43 (GH43) includes mostly enzymes that have been annotated as having beta-1,4-xylosidase (beta-D-xylosidase; xylan 1,4-beta-xylosidase; EC 3.2.1.37) activity. They are part of an array of hemicellulases that are involved in the final breakdown of plant cell-wall whereby they degrade xylan. They hydrolyze beta-1,4 glycosidic bonds between two xylose units in short xylooligosaccharides. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. This subfamily includes the characterized Clostridium stercorarium F-9 beta-xylosidase Xyl43B. It also includes Humicola insolens AXHd3 (HiAXHd3), a GH43 arabinofuranosidase (EC 3.2.1.55) that hydrolyzes O3-linked arabinose of doubly substituted xylans, a feature of the polysaccharide that is recalcitrant to degradation. It possesses an additional C-terminal beta-sandwich domain such that the interface between the domains comprises a xylan binding cleft that houses the active site pocket. The HiAXHd3 active site is tuned to hydrolyze arabinofuranosyl or xylosyl linkages, and the topology of the distal regions of the substrate binding surface confers specificity. It also includes Fibrobacter succinogenes subsp. succinogenes S85 arabinoxylan alpha-L-arabinofuranosidase (Axh1;Fisuc_1769;FSU_2269), Paenibacillus sp. E18 alpha-L-arabinofuranosidase (Abf43A), Bifidobacterium adolescentis ATCC 15703 double substituted xylan alpha-1,3-L-specific arabinofuranosidase d3 (AXHd3;AXH-d3;BaAXH-d3;BAD_0301;E-AFAM2), and Chrysosporium lucknowense C1 arabinoxylan hydrolase / double substituted xylan alpha-1,3-L-arabinofuranosidase (Abn7;AXHd). A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 270 matched cddid_all.tbl CDD cd09002 cd09002 350116 GH43_XYL-like Glycosyl hydrolase family 43, beta-D-xylosidase (uncharacterized). This glycosyl hydrolase family 43 (GH43) subgroup includes enzymes that have been annotated as having beta-1,4-xylosidase (beta-D-xylosidase;xylan 1,4-beta-xylosidase; EC 3.2.1.37) activity. They are part of an array of hemicellulases that are involved in the final breakdown of plant cell-wall whereby they degrade xylan. They hydrolyze beta-1,4 glycosidic bonds between two xylose units in short xylooligosaccharides. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 271 matched cddid_all.tbl CDD cd09003 cd09003 350117 GH43_XynD-like Glycosyl hydrolase family 43 protein such as Bacillus subtilis arabinoxylan arabinofuranohydrolase (XynD;BsAXH-m23;BSU18160). This glycosyl hydrolase family 43 (GH43) subgroup includes characterized Bacillus subtilis arabinoxylan arabinofuranohydrolase (AXH), Caldicellulosiruptor sp. Tok7B.1 beta-1,4-xylanase (EC 3.2.1.8) / alpha-L-arabinosidase (EC 3.2.1.55) XynA, Caldicellulosiruptor sp. Rt69B.1 xylanase C (EC 3.2.1.8) XynC, and Caldicellulosiruptor saccharolyticus beta-xylosidase (EC 3.2.1.37)/ alpha-L-arabinofuranosidase (EC 3.2.1.55) XynF. It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. It belongs to the GH43_AXH-like subgroup which includes enzymes that have been annotated as having beta-xylosidase, alpha-L-arabinofuranosidase and arabinoxylan alpha-L-1,3-arabinofuranohydrolase, xylanase (endo-alpha-L-arabinanase) as well as AXH activities. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. AXHs specifically hydrolyze the glycosidic bond between arabinofuranosyl substituents and xylopyranosyl backbone residues of arabinoxylan. Bacillus subtilis AXH (BsAXH-m2,3) has been shown to cleave arabinose units from O-2- or O-3-mono-substituted xylose residues and superposition of its structure with known structures of the GH43 exo-acting enzymes, beta-xylosidase and alpha-L-arabinanase, each in complex with their substrate, reveals a different orientation of the sugar backbone. Several of these enzymes also contain carbohydrate binding modules (CBMs) that bind cellulose or xylan. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 315 matched cddid_all.tbl CDD cd09004 cd09004 350118 GH43_bXyl-like Glycosyl hydrolase family 43 protein such as Bacteroides thetaiotaomicron VPI-5482 alpha-L-arabinofuranosidases (BT3675;BT_3675) and (BT3662;BT_3662); includes mostly xylanases. This glycosyl hydrolase family 43 (GH43) subgroup includes enzymes that have been annotated as xylan-digesting beta-xylosidase (EC 3.2.1.37) and xylanase (endo-alpha-L-arabinanase, EC 3.2.1.8) activities, as well the Bacteroides thetaiotaomicron VPI-5482 alpha-L-arabinofuranosidases (EC 3.2.1.55) (BT3675;BT_3675) and (BT3662;BT_3662). It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 266 matched cddid_all.tbl CDD cd09005 cd09005 350156 NP-I nucleoside phosphorylase-I family. The nucleoside phosphorylase-I family members accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. The NP-1 family includes phosphorolytic nucleosidases such as purine nucleoside phosphorylase (PNP, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases such as AMP nucleosidase (AMN, EC 3.2.2.4) and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). Members of this family display different physiologically relevant quaternary structures: hexameric (trimer-of-dimers arrangement of Shewanella oneidensis MR-1 UP); homotrimeric (human PNP and Escherichia coli PNPII or XapA); hexameric (with some evidence for co-existence of a trimeric form) such as E. coli PNPI (DeoD); or homodimeric such as human and Trypanosoma brucei UP. The NP-I family is distinct from nucleoside phosphorylase-II, which belongs to a different structural family. 216 matched cddid_all.tbl CDD cd09006 cd09006 350157 PNP_EcPNPI-like purine nucleoside phosphorylases similar to Escherichia coli PNP-I (DeoD) and Trichomonas vaginalis PNP. Escherichia coli purine nucleoside phosphorylase (PNP)-I (or DeoD) accepts both 6-oxo and 6-amino purine nucleosides as substrates. Trichomonas vaginalis PNP has broad substrate specificity, having phosphorolytic catalytic activity with adenosine, inosine, and guanosine (with adenosine as the preferred substrate). This subfamily belongs to the nucleoside phosphorylase-I (NP-I) family, whose members accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. The NP-1 family includes phosphorolytic nucleosidases, such as purine nucleoside phosphorylase (PNPs, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases, such as AMP nucleosidase (AMN, EC 3.2.2.4), and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). The NP-I family is distinct from nucleoside phosphorylase-II, which belongs to a different structural family. 228 matched cddid_all.tbl CDD cd09007 cd09007 350158 NP-I_spr0068 uncharacterized subfamily of the nucleoside phosphorylase-I family. This subfamily is composed of uncharacterized members including Streptococcus pneumoniae hypothetical protein spr0068. The nucleoside phosphorylase-I (NP-I) family members accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. The NP-1 family includes phosphorolytic nucleosidases such as purine nucleoside phosphorylase (PNP, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases such as AMP nucleosidase (AMN, EC 3.2.2.4) and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). Members of the NP-I family display different physiologically relevant quaternary structures: hexameric (trimer-of-dimers arrangement of Shewanella oneidensis MR-1 UP); homotrimeric (human PNP and Escherichia coli PNPII or XapA); hexameric (with some evidence for co-existence of a trimeric form) such as E. coli PNPI (DeoD); or homodimeric such as human and Trypanosoma brucei UP. The NP-I family is distinct from nucleoside phosphorylase-II, which belongs to a different structural family. 221 matched cddid_all.tbl CDD cd09008 cd09008 350159 MTAN 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidases. This subfamily includes both bacterial and plant 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidases (MTANs): bacterial MTANs show comparable efficiency in hydrolyzing MTA and SAH, while plant enzymes are highly specific for MTA and are unable to metabolize SAH or show significantly reduced activity towards SAH. MTAN is involved in methionine and S-adenosyl-methionine recycling, polyamine biosynthesis, and bacterial quorum sensing. This subfamily belongs to the nucleoside phosphorylase-I (NP-I) family, whose members accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. The NP-1 family includes phosphorolytic nucleosidases, such as purine nucleoside phosphorylase (PNPs, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases, such as AMP nucleosidase (AMN, EC 3.2.2.4), and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). The NP-I family is distinct from nucleoside phosphorylase-II, which belongs to a different structural family. 222 matched cddid_all.tbl CDD cd09009 cd09009 350160 PNP-EcPNPII_like purine nucleoside phosphorylases similar to human PNP and Escherichia coli PNP-II (XapA). Human PNP catalyzes the reversible phosphorolysis of the purine nucleosides and deoxynucleosides inosine, guanosine, deoxyinosine, and deoxyguanosine. Patients with PNP deficiency typically present with severe immunodeficiency, neurological dysfunction, and autoimmunity. Escherichia coli PNPII, product of the xapA/pndA gene, catalyzes the phosphorolysis of xanthosine, inosine and guanosine with equal efficiency and has been referred to as xanthosine phosphorylase and inosine-guanosine phosphorylase. E. coli PNPII is also capable of converting nicotinamide to nicotinamide riboside, and may be involved in the NAD+ salvage pathway. It is one of two purine nucleoside phosphorylases found in E. coli, which also contains PNPI, which displays a different substrate specificity and belongs to a different subgroup of the nucleoside phosphorylase-I (NP-I) family than PNPII. NP-I family members accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. The NP-1 family includes phosphorolytic nucleosidases, such as purine nucleoside phosphorylase (PNPs, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases, such as AMP nucleosidase (AMN, EC 3.2.2.4), and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). The NP-I family is distinct from nucleoside phosphorylase-II, which belongs to a different structural family. 265 matched cddid_all.tbl CDD cd09010 cd09010 350161 MTAP_SsMTAPII_like_MTIP 5'-deoxy-5'-methylthioadenosine phosphorylases (MTAP) similar to Sulfolobus solfataricus MTAPII and Pseudomonas aeruginosa PAO1 5'-methylthioinosine phosphorylase (MTIP). MTAP catalyzes the reversible phosphorolysis of 5'-deoxy-5'-methylthioadenosine (MTA) to adenine and 5-methylthio-D-ribose-1-phosphate. This subfamily includes human MTAP which is highly specific for MTA, and Sulfolobus solfataricus MTAPII which accepts adenosine in addition to MTA. Two MTAPs have been isolated from S. solfataricus: SsMTAP1 and SsMTAPII, SsMTAP1 belongs to a different subfamily of the nucleoside phosphorylase-I (NP-I) family. This group also includes Pseudomonas aeruginosa PAO1 MTI phosphorylase (MTIP) which uses 5'-methylthioinosine (MTI) as a preferred substrate, and does not use MTA. NP-I family members accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. The NP-1 family includes phosphorolytic nucleosidases, such as purine nucleoside phosphorylase (PNPs, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases, such as AMP nucleosidase (AMN, EC 3.2.2.4), and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). The NP-I family is distinct from nucleoside phosphorylase-II, which belongs to a different structural family. 238 matched cddid_all.tbl CDD cd09011 cd09011 319953 VOC_like uncharacterized subfamily of vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 122 matched cddid_all.tbl CDD cd09012 cd09012 319954 VOC_like uncharacterized subfamily of vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 127 matched cddid_all.tbl CDD cd09013 cd09013 319955 BphC-JF8_N_like N-terminal, non-catalytic, domain of BphC_JF8, (2,3-dihydroxybiphenyl 1,2-dioxygenase) from Bacillus sp. JF8, and similar proteins. 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, a key step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). BphC belongs to the type I extradiol dioxygenase family, which requires a metal ion in the active site in its catalytic mechanism. Polychlorinated biphenyl degrading bacteria demonstrate a multiplicity of BphCs. This subfamily of BphC is represented by the enzyme purified from the thermophilic biphenyl and naphthalene degrader, Bacillus sp. JF8. The members in this family of BphC enzymes may use either Mn(II) or Fe(II) as cofactors. The enzyme purified from Bacillus sp. JF8 is Mn(II)-dependent, however, the enzyme from Rhodococcus jostii RHAI has Fe(II) bound to it. BphC_JF8 is thermostable and its optimum activity is at 85 degrees C. The enzymes in this family have an internal duplication. This family represents the N-terminal repeat. 121 matched cddid_all.tbl CDD cd09014 cd09014 319956 BphC-JF8_C_like C-terminal, catalytic domain of BphC_JF8, (2,3-dihydroxybiphenyl 1,2-dioxygenase). 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, a key step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). BphC belongs to the type I extradiol dioxygenase family, which requires a metal ion in the active site in its catalytic mechanism. Polychlorinated biphenyl degrading bacteria demonstrate a multiplicity of BphCs. This subfamily of BphC is represented by the enzyme purified from the thermophilic biphenyl and naphthalene degrader, Bacillus sp. JF8. The members in this family of BphC enzymes may use either Mn(II) or Fe(II) as cofactors. The enzyme purified from Bacillus sp. JF8 is Mn(II)-dependent, however, the enzyme from Rhodococcus jostii RHAI has Fe(II) bound to it. BphC_JF8 is thermostable and its optimum activity is at 85 degrees C. The enzymes in this family have an internal duplication. This family represents the C-terminal repeat. 167 matched cddid_all.tbl CDD cd09015 cd09015 212511 Ureohydrolase Ureohydrolase superfamily includes arginase, formiminoglutamase, agmatinase and proclavaminate amidinohydrolase (PAH). This family, also known as arginase-like amidino hydrolase family, includes Mn-dependent enzymes: arginase (Arg, EC 3.5.3.1), formimidoylglutamase (HutG, EC 3.5.3.8 ), agmatinase (SpeB, EC 3.5.3.11), guanidinobutyrase (Gbh, EC=3.5.3.7), proclavaminate amidinohydrolase (PAH, EC 3.5.3.22) and related proteins. These enzymes catalyze hydrolysis of amide bond. They are involved in control of cellular levels of arginine and ornithine (both involved in protein biosynthesis, and production of creatine, polyamines, proline and nitric acid), in histidine and arginine degradation, and in clavulanic acid biosynthesis. 270 matched cddid_all.tbl CDD cd09018 cd09018 176656 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonuclease domains which do not possess the metal-binding residues necessary for activity. 150 matched cddid_all.tbl CDD cd09019 cd09019 185696 galactose_mutarotase_like galactose mutarotase_like. Galactose mutarotase catalyzes the conversion of beta-D-galactose to alpha-D-galactose. Beta-D-galactose is produced by the degradation of lactose, a disaccharide composed of beta-D-glucose and beta-D-galactose. This epimerization reaction is the first step in the four-step Leloir pathway, which converts galactose into metabolically important glucose. This epimerization step is followed by the phosophorylation of alpha-D-galactose by galactokinase, an enzyme which can only act on the alpha anomer. A glutamate and a histidine residue of the galactose mutarotase have been shown to be critical for catalysis, the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate, and the histidine as the active site acid to protonate the C-5 ring oxygen. Galactose mutarotase is a member of the aldose-1-epimerase superfamily. 326 matched cddid_all.tbl CDD cd09020 cd09020 185697 D-hex-6-P-epi_like D-hexose-6-phosphate epimerase-like. D-Hexose-6-phosphate epimerase Ymr099c from Saccharomyces cerevisiae belongs to the large superfamily of aldose-1-epimerases. Its active site is very similar to the catalytic site of galactose mutarotase, the best studied member of the superfamily. It also contains the conserved glutamate and histidine residues that have been shown in galactose mutarotase to be critical for catalysis, the glutamate serving as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate, and the histidine as the active site acid to protonate the C-5 ring oxygen. In addition Ymr099c contains 2 conserved arginine residues which are involved in phosphate binding, and exhibits hexose-6-phosphate mutarotase activity on glucose-6-P, galactose-6-P and mannose-6-P. 269 matched cddid_all.tbl CDD cd09021 cd09021 185698 Aldose_epim_Ec_YphB aldose 1-epimerase, similar to Escherichia coli YphB. Proteins similar to Escherichia coli YphB are uncharacterized members of the aldose-1-epimerase superfamily. Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism, catalyzing the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate, and the histidine as the active site acid to protonate the C-5 ring oxygen. 273 matched cddid_all.tbl CDD cd09022 cd09022 185699 Aldose_epim_Ec_YihR Aldose 1-epimerase, similar to Escherichia coli YihR. Proteins similar to Escherichia coli YihR are uncharacterized members of aldose-1-epimerase superfamily. Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism, catalyzing the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate, and the histidine as the active site acid to protonate the C-5 ring oxygen. 284 matched cddid_all.tbl CDD cd09023 cd09023 185700 Aldose_epim_Ec_c4013 Aldose 1-epimerase, similar to Escherichia coli c4013. Proteins, similar to Escherichia coli c4013, are uncharacterized members of aldose-1-epimerase superfamily. Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism, catalyzing the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate, and the histidine as the active site acid to protonate the C-5 ring oxygen. 284 matched cddid_all.tbl CDD cd09024 cd09024 185701 Aldose_epim_lacX Aldose 1-epimerase, similar to Lactococcus lactis lacX. Proteins similar to Lactococcus lactis lacX are uncharacterized members of aldose-1-epimerase superfamily. Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism, catalyzing the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate, and the histidine as the active site acid to protonate the C-5 ring oxygen. 288 matched cddid_all.tbl CDD cd09025 cd09025 185702 Aldose_epim_Slr1438 Aldose 1-epimerase, similar to Synechocystis Slr1438. Proteins similar to Synechocystis Slr1438 are uncharacterized members of aldose-1-epimerase superfamily. Aldose 1-epimerases or mutarotases are key enzymes of carbohydrate metabolism, catalyzing the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate, and the histidine as the active site acid to protonate the C-5 ring oxygen. 271 matched cddid_all.tbl CDD cd09027 cd09027 193601 PET PET ((Prickle Espinas Testin) domain is involved in protein-protein interactions. PET domain is involved in protein-protein interactions and is usually found in conjunction with LIM domain, which is also a protein-protein interaction domain. The PET containing proteins serve as adaptors or scaffolds to support the assembly of multimeric protein complexes. The PET domain has been found at the N-terminal of four known groups of proteins: prickle, testin, LIMPETin/LIM-9 and overexpressed breast tumor protein (OEBT). Prickle has been implicated in regulation of cell movement through its association with the Dishevelled (Dsh) protein in the planar cell polarity (PCP) pathway. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell contact areas, and at focal adhesion plaques. It interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin, and is involved in cell motility and adhesion events. Knockout mice experiments reveal tumor repressor function of Testin. LIMPETin/LIM-9 contains an N-terminal PET domain and 6 LIM domains at the C-terminal. In Schistosoma mansoni, where LIMPETin was first identified, it is down regulated in sexually mature adult females compared to sexually immature adult females and adult males. Its differential expression indicates that it is a transcription regulator. In C. elegans, LIM-9 may play a role in regulating the assembly and maintenance of the muscle A-band by forming a protein complex with SCPL-1 and UNC-89 and other proteins. OEBT displays a PET domain with two LIM domains, and is predicted to be localized in the nucleus with a possible role in cancer differentiation. 82 matched cddid_all.tbl CDD cd09028 cd09028 350085 ArfGap_ArfGap3 Arf1 GTPase-activating protein 3. ArfGAP (ADP Ribosylation Factor GTPase Activating Protein) domain is a part of ArfGap1-like proteins that play a crucial role in controlling of membrane trafficking, particularly in the formation of COPI (coat protein complex I)-coated vesicles on Golgi membranes. The ArfGAP1 protein subfamily consists of three members: ArfGAP1 (Gcs1p in yeast), ArfGAP2 and ArfGAP3 (both are homologs of yeast Glo3p). ArfGAP2/3 are closely related, but with little similarity to ArfGAP1, except the catalytic ArfGAP domain. They promote hydrolysis of GTP bound to the small G protein ADP-ribosylation factor 1 (Arf1), which leads to the dissociation of coat proteins from Golgi-derived membranes and vesicles. Dissociation of the coat proteins is required for the fusion of these vesicles with target compartments. Thus, the GAP catalytic activity plays a key role in the formation of COPI vesicles from Golgi membrane. In contrast to ArfGAP1, which displays membrane curvature-dependent ArfGAP activity, ArfGAP2 and ArfGAP3 activities are dependent on coatomer (the core COPI complex) which required for efficient recruitment of ArfGAP2 and ArfGAP3 to the Golgi membrane. Accordingly, ArfGAP2/3 has been implicated in coatomer-mediated protein transport between the Golgi complex and the endoplasmic reticulum. Unlike ArfGAP1, which is controlled by membrane curvature through its amphipathic lipid packing sensor (ALPS) motifs, ArfGAP2/3 do not possess ALPS motif. 120 matched cddid_all.tbl CDD cd09029 cd09029 350086 ArfGap_ArfGap2 Arf1 GTPase-activating protein 2. ArfGAP (ADP Ribosylation Factor GTPase Activating Protein) domain is a part of ArfGap1-like proteins that play a crucial role in controlling of membrane trafficking, particularly in the formation of COPI (coat protein complex I)-coated vesicles on Golgi membranes. The ArfGAP1 protein subfamily consists of three members: ArfGAP1 (Gcs1p in yeast), ArfGAP2 and ArfGAP3 (both are homologs of yeast Glo3p). ArfGAP2/3 are closely related, but with little similarity to ArfGAP1, except the catalytic ArfGAP domain. They promote hydrolysis of GTP bound to the small G protein ADP-ribosylation factor 1 (Arf1), which leads to the dissociation of coat proteins from Golgi-derived membranes and vesicles. Dissociation of the coat proteins is required for the fusion of these vesicles with target compartments. Thus, the GAP catalytic activity plays a key role in the formation of COPI vesicles from Golgi membrane. In contrast to ArfGAP1, which displays membrane curvature-dependent ArfGAP activity, ArfGAP2 and ArfGAP3 activities are dependent on coatomer (the core COPI complex) which required for efficient recruitment of ArfGAP2 and ArfGAP3 to the Golgi membrane. Accordingly, ArfGAP2/3 has been implicated in coatomer-mediated protein transport between the Golgi complex and the endoplasmic reticulum. Unlike ArfGAP1, which is controlled by membrane curvature through its amphipathic lipid packing sensor (ALPS) motifs, ArfGAP2/3 do not possess ALPS motif. 120 matched cddid_all.tbl CDD cd09030 cd09030 176923 DUF1425 Putative periplasmic lipoprotein. This bacterial family of proteins contains members described as putative lipoproteins, some are also known as YcfL. The function of this family is unknown. Family members have also been annotated as predicted periplasmic lipoproteins (COG5633), and appear to contain an N-terminal membrane lipoprotein lipid attachment side (pfam08139), which is not included in this alignment model. 101 matched cddid_all.tbl CDD cd09031 cd09031 411807 KH-I_NOVA_rpt3 third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova). The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one. 71 matched cddid_all.tbl CDD cd09032 cd09032 411808 KH-I_N4BP1_like_rpt1 first type I K homology (KH) RNA-binding domain found in the family of NEDD4-binding protein 1 (N4BP1). The N4BP1 family includes N4BP1, NYN domain and retroviral integrase catalytic domain-containing protein (NYNRIN) and KH and NYN domain-containing protein (KHNYN). These proteins are probably of retroviral origin. N4BP1 interacts with and is a substrate of NEDD4 ubiquitin ligase (neural precursor cell expressed, developmentally downregulated 4, E3 ubiquitin protein ligase). It is also an inhibitor of the E3 ubiquitin-protein ligase ITCH, a NEDD4 structurally related E3. N4BP1 acts by interacting with the second WW domain of ITCH, leading to compete with ITCH's substrates and impairing ubiquitination of substrates. NYNRIN, also known as CGIN1/Cousin of GIN1, may contribute to retroviral resistance in mammals by regulating the ubiquitination of viral proteins. KHNYN acts as a novel cofactor for zinc finger antiviral protein (ZAP) to target CpG-containing retroviral RNA for degradation. Members of this family contains two type I K homology (KH) RNA-binding domain. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif. 65 matched cddid_all.tbl CDD cd09033 cd09033 411809 KH-I_PNPT1 type I K homology (KH) RNA-binding domain found in mitochondrial polyribonucleotide nucleotidyltransferase 1 (PNPT1) and similar proteins. PNPT1, also called 3'-5' RNA exonuclease OLD35, or PNPase old-35, or polynucleotide phosphorylase 1, or PNPase 1, or polynucleotide phosphorylase-like protein, is an RNA-binding protein implicated in numerous RNA metabolic processes. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'-to-5' direction. It acts as a mitochondrial intermembrane factor with RNA-processing exoribonulease activity. PNPT1 is a component of the mitochondrial degradosome (mtEXO) complex, that degrades 3' overhang double-stranded RNA with a 3'-to-5' directionality in an ATP-dependent manner. It is involved in the degradation of non-coding mitochondrial transcripts (MT-ncRNA) and tRNA-like molecules and required for correct processing and polyadenylation of mitochondrial mRNAs. PNPT1 also plays a role as a cytoplasmic RNA import factor that mediates the translocation of small RNA components, like the 5S RNA, the RNA subunit of ribonuclease P and the mitochondrial RNA-processing (MRP) RNA, into the mitochondrial matrix. 67 matched cddid_all.tbl CDD cd09034 cd09034 185761 BRO1_Alix_like Protein-interacting Bro1-like domain of mammalian Alix and related domains. This superfamily includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and Rhophilin-2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Brox, Bro1 and Rim20 interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. Bro1-like domains bind components of the ESCRT-III complex: CHMP4 (in the case of Alix, HD-PTP, and Brox) and Snf7 (in the case of yeast Bro1, and Rim20). The single domain protein human Brox, and the isolated Bro1-like domains of Alix, HD-PTP and Rhophilin can bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Alix, HD-PTP, Bro1, and Rim20 also have a V-shaped (V) domain, which in the case of Alix, has been shown to be a dimerization domain and to contain a binding site for the retroviral late assembly (L) domain YPXnL motif, which is partially conserved in this superfamily. Alix, HD-PTP and Bro1 also have a proline-rich region (PRR); the Alix PRR binds multiple partners. Rhophilin-1, and -2, in addition to this Bro1-like domain, have an N-terminal Rho-binding domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1) domain. HD-PTP is encoded by the PTPN23 gene, a tumor suppressor gene candidate frequently absent in human kidney, breast, lung, and cervical tumors. This protein has a C-terminal, catalytically inactive tyrosine phosphatase domain. 345 matched cddid_all.tbl CDD cd09071 cd09071 176924 FAR_C C-terminal domain of fatty acyl CoA reductases. C-terminal domain of fatty acyl CoA reductases, a family of SDR-like proteins. SDRs or short-chain dehydrogenases/reductases are Rossmann-fold NAD(P)H-binding proteins. Many proteins in this FAR_C family may function as fatty acyl-CoA reductases (FARs), acting on medium and long chain fatty acids, and have been reported to be involved in diverse processes such as the biosynthesis of insect pheromones, plant cuticular wax production, and mammalian wax biosynthesis. In Arabidopsis thaliana, proteins with this particular architecture have also been identified as the MALE STERILITY 2 (MS2) gene product, which is implicated in male gametogenesis. Mutations in MS2 inhibit the synthesis of exine (sporopollenin), rendering plants unable to reduce pollen wall fatty acids to corresponding alcohols. The function of this C-terminal domain is unclear. 92 matched cddid_all.tbl CDD cd09073 cd09073 197307 ExoIII_AP-endo Escherichia coli exonuclease III (ExoIII)-like apurinic/apyrimidinic (AP) endonucleases. The ExoIII family AP endonucleases belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, which is then followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, which have both mutagenic and cytotoxic effects. AP endonucleases can carry out a wide range of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two functional AP endonucleases, for example, APE1/Ref-1 and Ape2 in humans, Apn1 and Apn2 in bakers yeast, Nape and NExo in Neisseria meningitides, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. Usually, one of the two is the dominant AP endonuclease, the other has weak AP endonuclease activity, but exhibits strong 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, and 3'-phosphatase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes. This family contains the ExoIII family; the EndoIV family belongs to a different superfamily. 251 matched cddid_all.tbl CDD cd09074 cd09074 197308 INPP5c Catalytic domain of inositol polyphosphate 5-phosphatases. Inositol polyphosphate 5-phosphatases (5-phosphatases) are signal-modifying enzymes, which hydrolyze the 5-phosphate from the inositol ring of specific 5-position phosphorylated phosphoinositides (PIs) and inositol phosphates (IPs), such as PI(4,5)P2, PI(3,4,5)P3, PI(3,5)P2, I(1,4,5)P3, and I(1,3,4,5)P4. These enzymes are Mg2+-dependent, and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. In addition to this INPP5c domain, 5-phosphatases often contain additional domains and motifs, such as the SH2 domain, the Sac-1 domain, the proline-rich domain (PRD), CAAX, RhoGAP (RhoGTPase-activating protein), and SKICH [SKIP (skeletal muscle- and kidney-enriched inositol phosphatase) carboxyl homology] domains, that are important for protein-protein interactions and/or for the subcellular localization of these enzymes. 5-phosphatases incorporate into large signaling complexes, and regulate diverse cellular processes including postsynaptic vesicular trafficking, insulin signaling, cell growth and survival, and endocytosis. Loss or gain of function of 5-phosphatases is implicated in certain human diseases. This family also contains a functionally unrelated nitric oxide transport protein, Cimex lectularius (bedbug) nitrophorin, which catalyzes a heme-assisted S-nitrosation of a proximal thiolate; the heme however binds at a site distinct from the active site of the 5-phosphatases. 299 matched cddid_all.tbl CDD cd09075 cd09075 197309 DNase1-like Deoxyribonuclease 1 and related proteins. This family includes Deoxyribonuclease 1 (DNase1, EC 3.1.21.1) and related proteins. DNase1, also known as DNase I, is a Ca2+, Mg2+/Mn2+-dependent secretory endonuclease, first isolated from bovine pancreas extracts. It cleaves DNA preferentially at phosphodiester linkages next to a pyrimidine nucleotide, producing 5'-phosphate terminated polynucleotides with a free hydroxyl group on position 3'. It generally produces tetranucleotides. DNase1 substrates include single-stranded DNA, double-stranded DNA, and chromatin. This enzyme may be responsible for apoptotic DNA fragmentation. Other deoxyribonucleases in this subfamily include human DNL1L (human DNase I lysosomal-like, also known as DNASE1L1, Xib and DNase X ), human DNASE1L2 (also known as DNAS1L2), and DNASE1L3 (also known as DNAS1L3, nhDNase, LS-DNase, DNase Y, and DNase gamma). DNASE1L3 is also implicated in apoptotic DNA fragmentation. DNase1 is also a cytoskeletal protein which binds actin. A recombinant form of human DNase1 is used as a mucoactive therapy in patients with cystic fibrosis; it hydrolyzes the extracellular DNA in sputum and reduces its viscosity. Mutations in the gene encoding DNase1 have been associated with Systemic Lupus Erythematosus, a multifactorial autoimmune disease. This family also includes a subfamily of mostly uncharacterized proteins, which includes Mycoplasma pulmonis MnuA, a membrane-associated nuclease. The in vivo role of MnuA is as yet undetermined. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. 258 matched cddid_all.tbl CDD cd09076 cd09076 197310 L1-EN Endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains. This family contains the endonuclease domain (L1-EN) of the non-LTR retrotransposon LINE-1 (L1), and related domains, including the endonuclease of Xenopus laevis Tx1. These retrotranspons belong to the subtype 2, L1-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. LINE-1/L1 elements (full length and truncated) comprise about 17% of the human genome. This endonuclease nicks the genomic DNA at the consensus target sequence 5'TTTT-AA3' producing a ribose 3'-hydroxyl end as a primer for reverse transcription of associated template RNA. This subgroup also includes the endonuclease of Xenopus laevis Tx1, another member of the L1-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. 236 matched cddid_all.tbl CDD cd09077 cd09077 197311 R1-I-EN Endonuclease domain encoded by various R1- and I-clade non-long terminal repeat retrotransposons. This family contains the endonuclease (EN) domain of various non-long terminal repeat (non-LTR) retrotransposons, long interspersed nuclear elements (LINEs) which belong to the subtype 2, R1- and I-clade. LINES can be classified into two subtypes. Subtype 2 has two ORFs: the second (ORF2) encodes a modular protein consisting of an N-terminal apurine/apyrimidine endonuclease domain (EN), a central reverse transcriptase, and a zinc-finger-like domain at the C-terminus. Most non-LTR retrotransposons are inserted throughout the host genome; however, many retrotransposons of the R1 clade exhibit target-specific retrotransposition. This family includes the endonucleases of SART1 and R1bm, from the silkworm Bombyx mori, which belong to the R1-clade. It also includes the endonuclease of snail (Biomphalaria glabrata) Nimbus/Bgl and mosquito Aedes aegypti (MosquI), both which belong to the I-clade. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. 205 matched cddid_all.tbl CDD cd09078 cd09078 197312 nSMase "Neutral sphingomyelinases (nSMase) catalyze the hydrolysis of sphingomyelin in biological membranes to ceramide and phosphorylcholine. Sphingomyelinases (SMase) are phosphodiesterases that catalyze the hydrolysis of sphingomyelin to ceramide and phosphorylcholine. Eukaryotic SMases have been classified according to their pH optima and are known as acid SMase, alkaline SMase, and neutral SMase (nSMase). Eukaryotic proteins in this family are nSMases, and are activated by a variety of stress-inducing agents such as cytokines or UV radiation. Ceramides and other metabolic derivatives, including sphingosine, are lipid ""second messenger"" molecules that participate in the regulation of stress-induced cellular responses, including cell death, adhesion, differentiation, and proliferation. Bacterial neutral SMases, which also belong to this domain family, are secreted proteins that act as membrane-damaging virulence factors. They promote colonization of the host tissue. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds." 280 matched cddid_all.tbl CDD cd09079 cd09079 197313 RgfB-like Streptococcus agalactiae RgfB, part of a putative two component signal transduction system, and related proteins. This family includes Streptococcus agalactiae RgfB (for regulator of fibrinogen binding) and related proteins. The function of RgfB is unknown. It is part of a putative two component signal transduction system designated rgfBDAC (the rgf locus was identified in a screen for mutants of Streptococcus agalactiae with altered binding to fibrinogen). RgfA,-C,and -D do not belong to this superfamily: rgfA encodes a putative response regulator, and rgfC, a putative histidine kinase. All four genes are co-transcribed, and may be involved in regulating expression of bacterial cell surface components. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. 259 matched cddid_all.tbl CDD cd09080 cd09080 197314 TDP2 Phosphodiesterase domain of human TDP2, a 5'-tyrosyl DNA phosphodiesterase, and related domains. Human TDP2, also known as TTRAP (TRAF/TNFR-associated factors, and tumor necrosis factor receptor/TNFR-associated protein), is a 5'-tyrosyl DNA phosphodiesterase. It is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini, needed for subsequent DNA ligation, and hence repair of the break. TDP2 and 3'-tyrosyl DNA phosphodiesterase (TDP1) are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TTRAP has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation, and it may inhibit the activation of nuclear factor-kB. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. 248 matched cddid_all.tbl CDD cd09081 cd09081 197315 CdtB CdtB, the catalytic DNase I-like subunit of cytolethal distending toxin (CDT) protein. CDT is a secreted protein toxin produced by a number of Gram-negative disease-causing bacteria. CDT causes cell cycle arrest and eventual cell death in eukaryotic cells, as a result of chromosomal DNA damage caused by the catalytic, DNase I-like, CdtB subunit. Bacterial CDTs are generally comprised of three subunits, CdtA, -B and -C. CdtB is translocated into the host cell, where it acts as a genotoxin. CdtA and CdtC are needed for cell surface binding and cellular entry, and it is likely that they remain associated with the membrane, when CdtB is internalized. CdtB enters the target nucleus via nuclear translocation signal domain(s). This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. 247 matched cddid_all.tbl CDD cd09082 cd09082 197316 Deadenylase C-terminal deadenylase domain of CCR4, nocturnin, and related domains. This family contains the C-terminal catalytic domains of the deadenylases, CCR4 and nocturnin, and related domains. Nocturnin is a poly(A)-specific 3' exonuclease that specifically degrades the 3' poly(A) tail of RNA in a process known as deadenylation. This nuclease activity is manganese dependent. Nocturnin is expressed in the cytoplasm of the Xenopus laevis retinal photoreceptor cells in a rhythmic fashion, and it has been proposed that it participates in posttranscriptional regulation of the circadian clock or its outputs, and that the mRNA target(s) of this deadenylase are circadian clock-related. Saccharomyces cerevisiae CCR4p is a 3'-5' poly(A) RNA and ssDNA exonuclease. It is the catalytic subunit of the yeast mRNA deadenylase (Ccr4p/Pop2p/Not complex). This complex participates in various ways in mRNA metabolism, including transcription initiation and elongation, and mRNA degradation. The deadenylase activities of Ccr4p and nocturnin differ: nocturnin degrades poly(A), Ccr4p degrades both poly(A) and single-stranded DNA, and in contrast to Ccr4p, nocturnin appears to function in a highly processive manner. This family belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. 348 matched cddid_all.tbl CDD cd09083 cd09083 197317 EEP-1 Exonuclease-Endonuclease-Phosphatase domain; uncharacterized family 1. This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds. Their substrates range from nucleic acids to phospholipids and perhaps, proteins. 252 matched cddid_all.tbl CDD cd09084 cd09084 197318 EEP-2 Exonuclease-Endonuclease-Phosphatase (EEP) domain superfamily; uncharacterized family 2. This family of uncharacterized proteins belongs to a superfamily that includes the catalytic domain (exonuclease/endonuclease/phosphatase, EEP, domain) of a diverse set of proteins including the ExoIII family of apurinic/apyrimidinic (AP) endonucleases, inositol polyphosphate 5-phosphatases (INPP5), neutral sphingomyelinases (nSMases), deadenylases (such as the vertebrate circadian-clock regulated nocturnin), bacterial cytolethal distending toxin B (CdtB), deoxyribonuclease 1 (DNase1), the endonuclease domain of the non-LTR retrotransposon LINE-1, and related domains. These diverse enzymes share a common catalytic mechanism of cleaving phosphodiester bonds; their substrates range from nucleic acids to phospholipids and perhaps, proteins. 246 matched cddid_all.tbl CDD cd09085 cd09085 197319 Mth212-like_AP-endo Methanothermobacter thermautotrophicus Mth212-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases. This subfamily includes the thermophilic archaeon Methanothermobacter thermautotrophicus Mth212and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Mth212 is an AP endonuclease, and a DNA uridine endonuclease (U-endo) that nicks double-stranded DNA at the 5'-side of a 2'-d-uridine residue. After incision at the 5'-side of a 2'-d-uridine residue by Mth212, DNA polymerase B takes over the 3'-OH terminus and carries out repair synthesis, generating a 5'-flap structure that is resolved by a 5'-flap endonuclease. Finally, DNA ligase seals the resulting nick. This U-endo activity shares the same catalytic center as its AP-endo activity, and is absent from other AP endonuclease homologues. 252 matched cddid_all.tbl CDD cd09086 cd09086 197320 ExoIII-like_AP-endo Escherichia coli exonuclease III (ExoIII) and Neisseria meningitides NExo-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases. This subfamily includes Escherichia coli ExoIII, Neisseria meningitides NExo,and related proteins. These are ExoIII family AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiencies. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For example, Neisseria meningitides Nape and NExo, and exonuclease III (ExoIII) and endonuclease IV (EndoIV) in Escherichia coli. NExo and ExoIII are found in this subfamily. NExo is the non-dominant AP endonuclease. It exhibits strong 3'-5' exonuclease and 3'-deoxyribose phosphodiesterase activities. Escherichia coli ExoIII is an active AP endonuclease, and in addition, it exhibits double strand (ds)-specific 3'-5' exonuclease, exonucleolytic RNase H, 3'-phosphomonoesterase and 3'-phosphodiesterase activities, all catalyzed by a single active site. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes ExoIII and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily. 254 matched cddid_all.tbl CDD cd09087 cd09087 197321 Ape1-like_AP-endo Human Ape1-like subfamily of the ExoIII family apurinic/apyrimidinic (AP) endonucleases. This subfamily includes human Ape1 (also known as Apex, Hap1, or Ref-1) and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Ape1 and Ape2 in humans. Ape1 is found in this subfamily, it exhibits strong AP-endonuclease activity but shows weak 3'-5' exonuclease and 3'-phosphodiesterase activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily. 253 matched cddid_all.tbl CDD cd09088 cd09088 197322 Ape2-like_AP-endo Human Ape2-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases. This subfamily includes human APE2, Saccharomyces cerevisiae Apn2/Eth1, and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and they belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER, the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity. For examples, Ape1 and Ape2 in humans, and Apn1 and Apn2 in bakers yeast. Ape2 and Apn2/Eth1 are both found in this subfamily, and have the weaker AP endonuclease activity. Ape2 shows strong 3'-5' exonuclease and 3'-phosphodiesterase activities; it can reduce the mutagenic consequences of attack by reactive oxygen species by removing 3'-end adenine opposite from 8-oxoG, in addition to repairing 3'-damaged termini. Apn2/Eth1 exhibits AP endonuclease activity, but has 30-40 fold more active 3'-phosphodiesterase and 3'-5' exonuclease activities. Class II AP endonucleases have been classified into two families, designated ExoIII and EndoIV, based on their homology to the Escherichia coli enzymes exonuclease III (ExoIII) and endonuclease IV (EndoIV). This subfamily belongs to the ExoIII family; the EndoIV family belongs to a different superfamily. 309 matched cddid_all.tbl CDD cd09089 cd09089 197323 INPP5c_Synj Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanins. This subfamily contains the INPP5c domains of two human synaptojanins, synaptojanin 1 (Synj1) and synaptojanin 2 (Synj2), and related proteins. It belongs to a family of Mg2+-dependent inositol polyphosphate 5-phosphatases, which hydrolyze the 5-phosphate from the inositol ring of various 5-position phosphorylated phosphoinositides (PIs) and inositol phosphates (IPs). They belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. Synj1 occurs as two main isoforms: a brain enriched 145 KDa protein (Synj1-145) and a ubiquitously expressed 170KDa protein (Synj1-170). Synj1-145 participates in clathrin-mediated endocytosis. The primary substrate of the Synj1-145 INPP5c domain is PI(4,5)P2, which it converts to PI4P. Synj1-145 may work with membrane curvature sensors/generators (such as endophilin) to remove PI(4,5)P2 from curved membranes. The recruitment of the INPP5c domain of Synj1-145 to endophilin-induced membranes leads to a fragmentation and condensation of these structures. The PI(4,5)P2 to PI4P conversion may cooperate with dynamin to produce membrane fission. In addition to this INPP5c domain, Synjs contain an N-terminal Sac1-like domain; the Sac1 domain can dephosphorylate a variety of phosphoinositides in vitro. Synj2 can hydrolyze phosphatidylinositol diphosphate (PIP2) to phosphatidylinositol phosphate (PIP). Synj2 occurs as multiple alternative splice variants in various tissues. These variants share the INPP5c domain and the Sac1 domain. Synj2A is recruited to the mitochondria via its interaction with OMP25 (a mitochondrial outer membrane protein). Synj2B is found at nerve terminals in the brain and at the spermatid manchette in testis. Synj2B undergoes further alternative splicing to give 2B1 and 2B2. In clathrin-mediated endocytosis, Synj2 participates in the formation of clathrin-coated pits, and perhaps also in vesicle decoating. Rac1 GTPase regulates the intracellular localization of Synj2 forms, but not Synj1. Synj2 may contribute to the role of Rac1 in cell migration and invasion, and is a potential target for therapeutic intervention in malignant tumors. 328 matched cddid_all.tbl CDD cd09090 cd09090 197324 INPP5c_ScInp51p-like Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of Saccharomyces cerevisiae Inp51p, Inp52p, and Inp53p, and related proteins. This subfamily contains the INPP5c domain of three Saccharomyces cerevisiae synaptojanin-like inositol polyphosphate 5-phosphatases (INP51, INP52, and INP53), Schizosaccharomyces pombe synaptojanin (SPsynaptojanin), and related proteins. It belongs to a family of Mg2+-dependent inositol polyphosphate 5-phosphatases, which hydrolyze the 5-phosphate from the inositol ring of various 5-position phosphorylated phosphoinositides (PIs) and inositol phosphates (IPs), and to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. In addition to this INPP5c domain, these proteins have an N-terminal catalytic Sac1-like domain (found in other proteins including the phophoinositide phosphatase Sac1p), and a C-terminal proline-rich domain (PRD). The Sac1 domain allows Inp52p and Inp53p to recognize and dephosphorylate a wider range of substrates including PI3P, PI4P, and PI(3,5)P2. The Sac1 domain of Inp51p is non-functional. Disruption of any two of INP51, INP52, and INP53, in S. cerevisiae leads to abnormal vacuolar and plasma membrane morphology. During hyperosmotic stress, Inp52p and Inp53p localize at actin patches, where they may facilitate the hydrolysis of PI(4,5)P2, and consequently promote actin rearrangement to regulate cell growth. SPsynaptojanin is also active against a range of soluble and lipid inositol phosphates, including I(1,4,5)P3, I(1,3,4,5)P4, I(1,4,5,6)P4, PI(4,5)P2, and PIP3. Transformation of S. cerevisiae with a plasmid expressing the SPsynaptojanin 5-phosphatase domain rescues inp51/inp52/inp53 triple-mutant strains. 291 matched cddid_all.tbl CDD cd09091 cd09091 197325 INPP5c_SHIP Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of SH2 domain containing inositol polyphosphate 5-phosphatase-1 and -2, and related proteins. This subfamily contains the INPP5c domain of SHIP1 (SH2 domain containing inositol polyphosphate 5-phosphatase-1, also known as SHIP/INPP5D), and SHIP2 (also known as INPPL1). It belongs to a family of Mg2+-dependent inositol polyphosphate 5-phosphatases, which hydrolyze the 5-phosphate from the inositol ring of various 5-position phosphorylated phosphoinositides (PIs) and inositol phosphates (IPs), and to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. Both SHIP1 and -2 catalyze the dephosphorylation of the PI, phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P3], to phosphatidylinositol 3,4-bisphosphate [PI(3,4)P2]. SHIP1 also converts inositol-1,3,4,5- polyphosphate [I(1,3,4,5)P4] to inositol-1,3,4-polyphosphate [I(1,3,4)P3]. SHIP1 and SHIP2 have little overlap in their in vivo functions. SHIP1 is a negative regulator of cell growth and plays a major part in mediating the inhibitory signaling in B cells; it is predominantly expressed in hematopoietic cells. SHIP2 is as an inhibitor of the insulin signaling pathway, and is implicated in actin structure remodeling, cell adhesion and cell spreading, receptor endocytosis and degradation, and in the JIP1-mediated JNK pathway. SHIP2 is widely expressed, most prominently in brain, heart and in skeletal muscle. In addition to this INPP5c domain, SHIP1 has an N-terminal SH2 domain, two NPXY motifs, and a C-terminal proline-rich region (PRD), while SHIP2 has an N-terminal SH2 domain, a C-terminal proline-rich domain (PRD), which includes a WW-domain binding motif (PPLP), an NPXY motif, and a sterile alpha motif (SAM) domain. The gene encoding SHIP2 is a candidate gene for conferring a predisposition for type 2 diabetes. 307 matched cddid_all.tbl CDD cd09092 cd09092 197326 INPP5A Type I inositol polyphosphate 5-phosphatase I. Type I inositol polyphosphate 5-phosphatase I (INPP5A) hydrolyzes the 5-phosphate from inositol 1,3,4,5-tetrakisphosphate [I(1,3,4,5)P4] and inositol 1,4,5-trisphosphate [I(1,4,5)P3]. It belongs to a family of Mg2+-dependent inositol polyphosphate 5-phosphatases, which hydrolyze the 5-phosphate from the inositol ring of various 5-position phosphorylated phosphoinositides (PIs) and inositol phosphates (IPs), and to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. As the substrates of INPP5A mobilize intracellular calcium ions, INPP5A is a calcium signal-terminating enzyme. In platelets, phosphorylated pleckstrin binds and activates INPP5A in a 1:1 complex, and accelerates the degradation of the calcium ion-mobilizing I(1,4,5)P3. 383 matched cddid_all.tbl CDD cd09093 cd09093 197327 INPP5c_INPP5B Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of Type II inositol polyphosphate 5-phosphatase I, Oculocerebrorenal syndrome of Lowe 1, and related proteins. This subfamily contains the INPP5c domain of type II inositol polyphosphate 5-phosphatase I (INPP5B), Oculocerebrorenal syndrome of Lowe 1 (OCRL-1), and related proteins. It belongs to a family of Mg2+-dependent inositol polyphosphate 5-phosphatases, which hydrolyze the 5-phosphate from the inositol ring of various 5-position phosphorylated phosphoinositides (PIs) and inositol phosphates (IPs), and to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. INPP5B and OCRL1 preferentially hydrolyze the 5-phosphate of phosphatidylinositol (4,5)- bisphosphate [PI(4,5)P2] and phosphatidylinositol (3,4,5)- trisphosphate [PI(3,4,5)P3]. INPP5B can also hydrolyze soluble inositol (1,4,5)-trisphosphate [I(1,4,5)P3] and inositol (1,3,4,5)-tetrakisphosphate [I(1,3,4,5)P4]. INPP5B participates in the endocytic pathway and in the early secretory pathway. In the latter, it may function in retrograde ERGIC (ER-to-Golgi intermediate compartment)-to-ER transport; it binds specific RAB proteins within the secretory pathway. In the endocytic pathway, it binds RAB5 and during endocytosis, may function in a RAB5-controlled cascade for converting PI(3,4,5)P3 to phosphatidylinositol 3-phosphate (PI3P). This cascade may link growth factor signaling and membrane dynamics. Mutation in OCRL1 is implicated in Lowe syndrome, an X-linked recessive multisystem disorder, which includes defects in eye, brain, and kidney function, and in Type 2 Dent's disease, a disorder with only the renal symptoms. OCRL-1 may have a role in membrane trafficking within the endocytic pathway and at the trans-Golgi network, and may participate in actin dynamics or signaling from endomembranes. OCRL1 and INPP5B have overlapping functions: deletion of both 5-phosphatases in mice is embryonic lethal, deletion of OCRL1 alone has no phenotype, and deletion of Inpp5b alone has only a mild phenotype (male sterility). Several of the proteins that interact with OCRL1 also bind INPP5B, for examples, inositol polyphosphate phosphatase interacting protein of 27kDa (IPIP27)A and B (also known as Ses1 and 2), and endocytic signaling adaptor APPL1. OCRL1, but not INPP5B, binds clathrin heavy chain, the plasma membrane AP2 adaptor subunit alpha-adaptin. In addition to this INPP5c domain, most proteins in this subfamily have a C-terminal RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain. 292 matched cddid_all.tbl CDD cd09094 cd09094 197328 INPP5c_INPP5J-like Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of inositol polyphosphate 5-phosphatase J and related proteins. INPP5c domain of Inositol polyphosphate-5-phosphatase J (INPP5J), also known as PIB5PA or PIPP, and related proteins. This subfamily belongs to a family of Mg2+-dependent inositol polyphosphate 5-phosphatases, which hydrolyze the 5-phosphate from the inositol ring of various 5-position phosphorylated phosphoinositides (PIs) and inositol phosphates (IPs), and to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. INPP5J hydrolyzes PI(4,5)P2, I(1,4,5)P3, and I(1,3,4,5)P4 at ruffling membranes. These proteins contain a C-terminal, SKIP carboxyl homology domain (SKICH), which may direct plasma membrane ruffle localization. 300 matched cddid_all.tbl CDD cd09095 cd09095 197329 INPP5c_INPP5E-like Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of Inositol polyphosphate-5-phosphatase E and related proteins. INPP5c domain of Inositol polyphosphate-5-phosphatase E (also called type IV or 72 kDa 5-phosphatase), rat pharbin, and related proteins. This subfamily belongs to a family of Mg2+-dependent inositol polyphosphate 5-phosphatases, which hydrolyze the 5-phosphate from the inositol ring of various 5-position phosphorylated phosphoinositides (PIs) and inositol phosphates (IPs), and to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. INPP5E hydrolyzes the 5-phosphate from PI(3,5)P2, PI(4,5)P2 and PI(3,4,5)P3, forming PI3P, PI4P, and PI(3,4)P2, respectively. It is a very potent PI(3,4,5)P3 5-phosphatase. Its intracellular localization is chiefly cytosolic, with pronounced perinuclear/Golgi localization. INPP5E also has an N-terminal proline rich domain (PRD) and a C-terminal CAAX motif. This protein is expressed in a variety of tissues, including the breast, brain, testis, and haemopoietic cells. It is differentially expressed in several cancers, for example, it is up-regulated in cervical cancer and down-regulated in stomach cancer. It is a candidate target for therapeutics of obesity and related disorders, as it is expressed in the hypothalamus, and following insulin stimulation, it undergoes tyrosine phosphorylation, associates with insulin receptor substrate-1, -2, and PI3-kinase, and become active as a 5-phosphatase. INPP5E may play a role, along with other 5-phosphatases SHIP2 and SKIP, in regulating glucose homoeostasis and energy metabolism. Mice deficient in INPPE5 develop a multi-organ disorder associated with structural defects of the primary cilium. 298 matched cddid_all.tbl CDD cd09096 cd09096 197330 Deadenylase_nocturnin C-terminal deadenylase domain of nocturnin and related domains. This subfamily contains the C-terminal catalytic domain of the deadenylase, nocturnin, and related domains. Nocturnin is a poly(A)-specific 3' exonuclease that specifically degrades the 3' poly(A) tail of RNA in a process known as deadenylation. This nuclease activity is manganese dependent. Nocturnin is expressed in the cytoplasm of Xenopus laevis retinal photoreceptor cells in a rhythmic fashion, and it has been proposed that it participates in posttranscriptional regulation of the circadian clock or its outputs, and that the mRNA target(s) of this deadenylase are circadian clock-related. In mouse, the nocturnin gene, mNoc, is expressed in a circadian pattern in a range of tissues including retina, spleen, heart, kidney, and liver. It is highly expressed in bone-marrow stromal cells, adipocytes and hepatocytes. In mammals, nocturnin plays a role in regulating mesenchymal stem-cell lineage allocation, perhaps through regulating PPAR-gamma (peroxisome proliferator-activated receptor-gamma) nuclear translocation. This subfamily belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. 280 matched cddid_all.tbl CDD cd09097 cd09097 197331 Deadenylase_CCR4 C-terminal deadenylase domain of CCR4 and related domains. This subfamily contains the C-terminal catalytic domain of the deadenylases, Saccharomyces cerevisiae Ccr4p and two vertebrate homologs (CCR4a and CCR4b), and related domains. CCR4 belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. CCR4 is the major deadenylase subunit of the CCR4-NOT transcription complex, which contains two deadenylase subunits and several noncatalytic subunits. The other deadenylase subunit, Caf1 (called Pop2 in yeast), is a DEDD-type protein and does not belong in this superfamily. Saccharomyces cerevisiae CCR4 (or Ccr4p) is a 3'-5' poly(A) RNA and ssDNA exonuclease. It is the catalytic subunit of the yeast mRNA deadenylase (Ccr4p/Pop2p/Not complex). This complex participates in various ways in mRNA metabolism, including transcription initiation and elongation, and mRNA degradation. Ccr4p degrades both poly(A) and single-stranded DNA. There are two vertebrate homologs of Ccr4p, CCR4a (also called CCR4-NOT transcription complex subunit 6 or CNOT6) and CCR4b (also called CNOT6-like or CNOT6L), which independently associate with other components to form distinct CCR4-NOT multisubunit complexes. The nuclease domain of CNOT6 and CNOT6L exhibits Mg2+-dependent deadenylase activity, with specificity for poly (A) RNA as substrate. CCR4a is a component of P-bodies and is necessary for foci formation. CCR4b regulates p27/Kip1 mRNA levels, thereby influencing cell cycle progression. They both contribute to the prevention of cell death by regulating insulin-like growth factor-binding protein 5. 329 matched cddid_all.tbl CDD cd09098 cd09098 197332 INPP5c_Synj1 Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 1. This subfamily contains the INPP5c domains of human synaptojanin 1 (Synj1) and related proteins. It belongs to a family of Mg2+-dependent inositol polyphosphate 5-phosphatases, which hydrolyze the 5-phosphate from the inositol ring of various 5-position phosphorylated phosphoinositides (PIs) and inositol phosphates (IPs), and to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. Synj1 occurs as two main isoforms: a brain enriched 145 KDa protein (Synj1-145) and a ubiquitously expressed 170KDa protein (Synj1-170). Synj1-145 participates in clathrin-mediated endocytosis. The primary substrate of the Synj1-145 INPP5c domain is PI(4,5)P2, which it converts to PI4P. Synj1-145 may work with membrane curvature sensors/generators (such as endophilin) to remove PI(4,5)P2 from curved membranes. The recruitment of the INPP5c domain of Synj1-145 to endophilin-induced membranes leads to a fragmentation and condensation of these structures. The PI(4,5)P2 to PI4P conversion may cooperate with dynamin to produce membrane fission. In addition to this INPP5c domain, these proteins contain an N-terminal Sac1-like domain; the Sac1 domain can dephosphorylate a variety of phosphoinositides in vitro. 336 matched cddid_all.tbl CDD cd09099 cd09099 197333 INPP5c_Synj2 Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of synaptojanin 2. This subfamily contains the INPP5c domains of human synaptojanin 2 (Synj2) and related proteins. It belongs to a family of Mg2+-dependent inositol polyphosphate 5-phosphatases, which hydrolyze the 5-phosphate from the inositol ring of various 5-position phosphorylated phosphoinositides (PIs) and inositol phosphates (IPs), and to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. Synj2 can hydrolyze phosphatidylinositol diphosphate (PIP2) to phosphatidylinositol phosphate (PIP). In addition to this INPP5c domain, these proteins contain an N-terminal Sac1-like domain; the Sac1 domain can dephosphorylate a variety of phosphoinositides in vitro. Synj2 occurs as multiple alternative splice variants in various tissues. These variants share the INPP5c domain and the Sac1 domain. Synj2A is recruited to the mitochondria via its interaction with OMP25, a mitochondrial outer membrane protein. Synj2B is found at nerve terminals in the brain and at the spermatid manchette in testis. Synj2B undergoes further alternative splicing to give 2B1 and 2B2. In clathrin-mediated endocytosis, Synj2 participates in the formation of clathrin-coated pits, and perhaps also in vesicle decoating. Rac1 GTPase regulates the intracellular localization of Synj2 forms, but not Synj1. Synj2 may contribute to the role of Rac1 in cell migration and invasion, and is a potential target for therapeutic intervention in malignant tumors. 336 matched cddid_all.tbl CDD cd09100 cd09100 197334 INPP5c_SHIP1-INPP5D Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of SH2 domain containing inositol polyphosphate 5-phosphatase-1 and related proteins. This subfamily contains the INPP5c domain of SHIP1 (SH2 domain containing inositol polyphosphate 5-phosphatase-1, also known as SHIP/INPP5D) and related proteins. It belongs to a family of Mg2+-dependent inositol polyphosphate 5-phosphatases, which hydrolyze the 5-phosphate from the inositol ring of various 5-position phosphorylated phosphoinositides (PIs) and inositol phosphates (IPs), and to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. SHIP1's enzymic activity is restricted to phosphatidylinositol 3,4,5-trisphosphate [PI (3,4,5)P3] and inositol-1,3,4,5- polyphosphate [I(1,3,4,5)P4]. It converts these two phosphoinositides to phosphatidylinositol 3,4-bisphosphate [PI (3,4)P2] and inositol-1,3,4-polyphosphate [I(1,3,4)P3], respectively. SHIP1 is a negative regulator of cell growth and plays a major part in mediating the inhibitory signaling in B cells; it is predominantly expressed in hematopoietic cells. In addition to this INPP5c domain, SHIP1 has an N-terminal SH2 domain, two NPXY motifs, and a C-terminal proline-rich region (PRD). SHIP1's phosphorylated NPXY motifs interact with proteins with phosphotyrosine binding (PTB) domains, and facilitate the translocation of SHIP1 to the plasma membrane to hydrolyze PI(3,4,5)P3. SHIP1 generally acts to oppose the activity of phosphatidylinositol 3-kinase (PI3K). It acts as a negative signaling molecule, reducing the levels of PI(3,4,5)P3, thereby removing the latter as a membrane-targeting signal for PH domain-containing effector molecules. SHIP1 may also, in certain contexts, amplify PI3K signals. SHIP1 and SHIP2 have little overlap in their in vivo functions. 307 matched cddid_all.tbl CDD cd09101 cd09101 197335 INPP5c_SHIP2-INPPL1 Catalytic inositol polyphosphate 5-phosphatase (INPP5c) domain of SH2 domain containing inositol 5-phosphatase-2 and related proteins. This subfamily contains the INPP5c domain of SHIP2 (SH2 domain containing inositol 5-phosphatase-2, also called INPPL1) and related proteins. It belongs to a family of Mg2+-dependent inositol polyphosphate 5-phosphatases, which hydrolyze the 5-phosphate from the inositol ring of various 5-position phosphorylated phosphoinositides (PIs) and inositol phosphates (IPs), and to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. SHIP2 catalyzes the dephosphorylation of the PI, phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P3], to phosphatidylinositol 3,4-bisphosphate [PI(3,4)P2]. SHIP2 is widely expressed, most prominently in brain, heart and in skeletal muscle. SHIP2 is an inhibitor of the insulin signaling pathway. It is implicated in actin structure remodeling, cell adhesion and cell spreading, receptor endocytosis and degradation, and in the JIP1-mediated JNK pathway. Its interacting partners include filamin/actin, p130Cas, Shc, Vinexin, Interesectin 1, and c-Jun NH2-terminal kinase (JNK)-interacting protein 1 (JIP1). A large variety of extracellular stimuli appear to lead to the tyrosine phosphorylation of SHIP2, including epidermal growth factor (EGF), platelet-derived growth factor (PDGF), insulin, macrophage colony-stimulating factor (M-CSF) and hepatocyte growth factor (HGF). SHIP2 is localized to the cytosol in quiescent cells; following growth factor stimulation and /or cell adhesion, it relocalizes to membrane ruffles. In addition to this INPP5c domain, SHIP2 has an N-terminal SH2 domain, a C-terminal proline-rich domain (PRD), which includes a WW-domain binding motif (PPLP), an NPXY motif and a sterile alpha motif (SAM) domain. The gene encoding SHIP2 is a candidate for conferring a predisposition for type 2 diabetes; it has been suggested that suppression of SHIP2 may be of benefit in the treatment of obesity and thereby prevent type 2 diabetes. SHIP2 and SHIP1 have little overlap in their in vivo functions. 304 matched cddid_all.tbl CDD cd09102 cd09102 197201 PLDc_CDP-OH_P_transf_II_1 Catalytic domain, repeat 1, of CDP-alcohol phosphatidyltransferase class-II family members. Catalytic domain, repeat 1, of CDP-alcohol phosphatidyltransferase class-II family members, which mainly include gram-negative bacterial phosphatidylserine synthases (PSS; CDP-diacylglycerol--serine O-phosphatidyltransferase, EC 2.7.8.8), yeast phosphatidylglycerophosphate synthase (PGP synthase; CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, EC 2.7.8.5), and metazoan PGP synthase 1. All members in this subfamily have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterize the phospholipase D (PLD) superfamily. They may utilize a common two-step ping-pong catalytic mechanism, involving a substrate-enzyme intermediate, to cleave phosphodiester bonds. The two motifs are suggested to constitute the active site involving phosphatidyl group transfer. Phosphatidylserine synthases from gram-positive bacteria and eukaryotes, and prokaryotic phosphatidylglycerophosphate synthases are not members of this subfamily. 168 matched cddid_all.tbl CDD cd09103 cd09103 197202 PLDc_CDP-OH_P_transf_II_2 Catalytic domain, repeat 2, of CDP-alcohol phosphatidyltransferase class-II family members. Catalytic domain, repeat 2, of CDP-alcohol phosphatidyltransferase class-II family members, which mainly include gram-negative bacterial phosphatidylserine synthases (PSS; CDP-diacylglycerol--serine O-phosphatidyltransferase, EC 2.7.8.8), yeast phosphatidylglycerophosphate synthase (PGP synthase; CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase, EC 2.7.8.5), and metazoan PGP synthase 1. All members in this subfamily have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterize the phospholipase D (PLD) superfamily. They may utilize a common two-step ping-pong catalytic mechanism, involving a substrate-enzyme intermediate, to cleave phosphodiester bonds. The two motifs are suggested to constitute the active site involving phosphatidyl group transfer. Phosphatidylserine synthases from gram-positive bacteria and eukaryotes, and prokaryotic phosphatidylglycerophosphate synthases are not members of this subfamily. 184 matched cddid_all.tbl CDD cd09104 cd09104 197203 PLDc_vPLD1_2_like_1 Catalytic domain, repeat 1, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins. Catalytic domain, repeat 1, of phospholipase D (PLD, EC 3.1.4.4) found in yeast, plants, and vertebrates, and their bacterial homologs. PLDs are involved in signal transduction, vesicle formation, protein transport, and mitosis by participating in phospholipid metabolism. They hydrolyze the terminal phosphodiester bond of phospholipids resulting in the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. PLDs also catalyze the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. Both prokaryotic and eukaryotic PLDs have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. PLDs are active as bi-lobed monomers. Each monomer contains two domains, each of which carries one copy of the HKD motif. Two HKD motifs from two domains form a single active site. PLDs utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. 147 matched cddid_all.tbl CDD cd09105 cd09105 197204 PLDc_vPLD1_2_like_2 Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, and similar proteins. Catalytic domain, repeat 2, of phospholipase D (PLD, EC 3.1.4.4) found in yeast, plants, and vertebrates, and their bacterial homologs. PLDs are involved in signal transduction, vesicle formation, protein transport, and mitosis by participating in phospholipid metabolism. They hydrolyze the terminal phosphodiester bond of phospholipids resulting in the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. PLDs also catalyze the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. Both prokaryotic and eukaryotic PLDs have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. PLDs are active as bi-lobed monomers. Each monomer contains two domains, each of which carries one copy of the HKD motif. Two HKD motifs from two domains form a single active site. PLDs utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. 146 matched cddid_all.tbl CDD cd09106 cd09106 197205 PLDc_vPLD3_4_5_like_1 Putative catalytic domain, repeat 1, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral envelope proteins K4 and p37, and similar proteins. Putative catalytic domain, repeat 1, of vertebrate phospholipases D, PLD3, PLD4, and PLD5 (EC 3.1.4.4), viral envelope proteins (vaccinia virus proteins K4 and p37), and similar proteins. Most family members contain two copies of the HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue), and have been classified into the phospholipase D (PLD) superfamily. Proteins in this subfamily are associated with Golgi membranes, altering their lipid content by the conversion of phospholipids into phosphatidic acid, which is thought to be involved in the regulation of lipid movement. ADP ribosylation factor (ARF), a small guanosine triphosphate binding protein, might be required activity. The vaccinia virus p37 protein, encoded by the F13L gene, is also associated with Golgi membranes and is required for the envelopment and spread of the extracellular enveloped virus (EEV). The vaccinia virus protein K4, encoded by the HindIII K4L gene, remains to be characterized. Sequence analysis indicates that the vaccinia virus proteins K4 and p37 might have evolved from one or more captured eukaryotic genes involved in cellular lipid metabolism. Up to date, no catalytic activity of PLD3 has been shown. Furthermore, due to the lack of functional important histidine and lysine residues in the HKD motif, mammalian PLD5 has been characterized as an inactive PLD. The poxvirus p37 proteins may also lack PLD enzymatic activity, since they contain only one partially conserved HKD motif (N-x-K-x(4)-D). 153 matched cddid_all.tbl CDD cd09107 cd09107 197206 PLDc_vPLD3_4_5_like_2 Putative catalytic domain, repeat 2, of vertebrate phospholipases, PLD3, PLD4 and PLD5, viral envelope proteins K4 and p37, and similar proteins. Putative catalytic domain, repeat 2, of vertebrate phospholipases D, PLD3, PLD4, and PLD5 (EC 3.1.4.4), viral envelope proteins (vaccinia virus proteins K4 and p37), and similar proteins. Most family members contain two copies of the HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue), and have been classified into the phospholipase D (PLD) superfamily. Proteins in this subfamily are associated with Golgi membranes, altering their lipid content by the conversion of phospholipids into phosphatidic acid, which is thought to be involved in the regulation of lipid movement. ADP ribosylation factor (ARF), a small guanosine triphosphate binding protein, might be required activity. The vaccinia virus p37 protein, encoded by the F13L gene, is also associated with Golgi membranes and is required for the envelopment and spread of the extracellular enveloped virus (EEV). The vaccinia virus protein K4, encoded by the HindIII K4L gene, remains to be characterized. Sequence analysis indicates that the vaccinia virus proteins K4 and p37 might have evolved from one or more captured eukaryotic genes involved in cellular lipid metabolism. Up to date, no catalytic activity of PLD3 has been shown. Furthermore, due to the lack of functional important histidine and lysine residues in the HKD motif, mammalian PLD5 has been characterized as an inactive PLD. The poxvirus p37 proteins may also lack PLD enzymatic activity, since they contain only one partially conserved HKD motif (N-x-K-x(4)-D). 175 matched cddid_all.tbl CDD cd09108 cd09108 197207 PLDc_PMFPLD_like_1 Catalytic domain, repeat 1, of phospholipase D from Streptomyces Sp. Strain PMF and similar proteins. Catalytic domain, repeat 1, of phospholipases D (PLD, EC 3.1.4.4) from Streptomyces Sp. Strain PMF (PMFPLD) and similar proteins, which are generally extracellular and bear N-terminal signal sequences. PMFPLD hydrolyzes the terminal phosphodiester bond of phospholipids with the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. It also catalyzes a transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. In contrast to eukaryotic PLDs, PMFPLD has a compact structure, which consists of two catalytic domains, but lacks the regulatory domains. Each catalytic domain contains one copy of the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. Two HKD motifs from two domains form a single active site. Like other PLD enzymes, PMFPLD may utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. A calcium-dependent PLD from Streptomyce chromofuscus is excluded from this family, since it displays very little sequence homology with other Streptomyces PLDs. Moreover, it does not contain the conserved HKD motif and hydrolyzes the phospholipids via a different mechanism. 210 matched cddid_all.tbl CDD cd09109 cd09109 197208 PLDc_PMFPLD_like_2 Catalytic domain, repeat 2, of phospholipase D from Streptomyces Sp. Strain PMF and similar proteins. Catalytic domain, repeat 2, of phospholipases D (PLD, EC 3.1.4.4) from Streptomyces Sp. Strain PMF (PMFPLD) and similar proteins, which are generally extracellular and bear N-terminal signal sequences. PMFPLD hydrolyzes the terminal phosphodiester bond of phospholipids with the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. It also catalyzes a transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. In contrast to eukaryotic PLDs, PMFPLD has a compact structure, which consists of two catalytic domains, but lacks the regulatory domains. Each catalytic domain contains one copy of the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. Two HKD motifs from two domains form a single active site. Like other PLD enzymes, PMFPLD may utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. A calcium-dependent PLD from Streptomyce chromofuscus is excluded from this family, since it displays very little sequence homology with other Streptomyces PLDs. Moreover, it does not contain the conserved HKD motif and hydrolyzes the phospholipids via a different mechanism. 212 matched cddid_all.tbl CDD cd09110 cd09110 197209 PLDc_CLS_1 Catalytic domain, repeat 1, of bacterial cardiolipin synthase and similar proteins. Catalytic domain, repeat 1, of bacterial cardiolipin (CL) synthase and a few homologs found in eukaryotes and archaea. Bacterial CL synthases catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. The monomer of bacterial CL synthase consists of two catalytic domains. Each catalytic domain contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. Two HKD motifs from two domains form a single active site involved in phosphatidyl group transfer. Bacterial CL synthases can be stimulated by phosphate and inhibited by CL, the product of the reaction, and by phosphatidate. Phosphate stimulation may be unique to enzymes with CL synthase activity belonging to the PLD superfamily. Like other PLD enzymes, bacterial CL synthases utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. 154 matched cddid_all.tbl CDD cd09111 cd09111 197210 PLDc_ymdC_like_1 Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins. Putative catalytic domain, repeat 1, of Escherichia coli uncharacterized protein ymdC and similar proteins. In Escherichia coli, there are two genes, f413 (ybhO) and o493 (ymdC), which are homologous to gene cls that encodes the Escherichia coli cardiolipin (CL) synthase. The prototype of this subfamily is an uncharacterized protein ymdC specified by the o493 (ymdC) gene. Although the functional characterization of ymdC and similar proteins remains unknown, members of this subfamily show high sequence homology to bacterial CL synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Moreover, ymdC and its similar proteins contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characteriszes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer. 162 matched cddid_all.tbl CDD cd09112 cd09112 197211 PLDc_CLS_2 catalytic domain repeat 2 of bacterial cardiolipin synthase and similar proteins. This CD corresponds to the catalytic domain repeat 2 of bacterial cardiolipin synthase (CL synthase, EC 2.7.8.-) and a few homologs found in eukaryotes and archea. Bacterial CL synthases catalyze reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form cardiolipin (CL) and glycerol. The monomer of bacterial CL synthase consists of two catalytic domains. Each catalytic domain contains one copy of conserved HKD motifs (H-X-K-X(4)-D, X represents any amino acid residue) that are the characteristic of the phospholipase D (PLD) superfamily. Two HKD motifs from two domains together form a single active site involving in phosphatidyl group transfer. Bacterial CL synthases can be stimulated by phosphate and inhibited by CL, the product of the reaction, and by phosphatidate. Phosphate stimulation may be unique to enzymes with CL synthase activity in PLD superfamily. Like other PLD enzymes, bacterial CL synthase utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid stabilizing the leaving group. 174 matched cddid_all.tbl CDD cd09113 cd09113 197212 PLDc_ymdC_like_2 Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins. Putative catalytic domain, repeat 2, of Escherichia coli uncharacterized protein ymdC and similar proteins. In Escherichia coli, there are two genes, f413 (ybhO) and o493 (ymdC), which are homologous to gene cls that encodes the Escherichia coli cardiolipin (CL) synthase. The prototype of this subfamily is an uncharacterized protein ymdC specified by the o493 (ymdC) gene. Although the functional characterization of ymdC and similar proteins remains unknown, members of this subfamily show high sequence homology to bacterial CL synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Moreover, ymdC and its similar proteins contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characteriszes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer. 218 matched cddid_all.tbl CDD cd09114 cd09114 197213 PLDc_PPK1_C1 Catalytic C-terminal domain, first repeat, of prokaryotic polyphosphate kinase 1 and similar proteins. Catalytic C-terminal domain, first repeat (C1 domain), of bacterial polyphosphate kinases 1 (Poly P kinase 1 or PPK1, EC 2.7.4.1) and similar proteins. Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PPK1 is the key enzyme responsible for the synthesis of Poly P in bacteria. It can catalyze the reversible conversion of the terminal-phosphate of ATP to Poly P. Therefore, PPK1 is essential for bacterial motility, quorum sensing, biofilm formation, and the production of virulence factors and may serve as an attractive antimicrobial drug target. Dimerization is crucial for the enzymatic activity of PPK1. Each PPK1 monomer includes four structural domains, the N-terminal (N) domain, the head (H) domain, and two closely related C-terminal (C1 and C2) domains. The N domain provides the upper binding interface for the adenine ring of the ATP. The H domain is involved in dimerization, while both the C1 and C2 domains contain residues crucial for catalytic activity. The intersection of the N, C1, and C2 domains forms a structural tunnel in which the PPK catalytic reactions are carried out. In spite of the lack of sequence homology, the C1 and C2 domains of PPK1 are structurally similar to the two repetitive catalytic domains of phospholipase D (PLD). Moreover, some residues in the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) of the PLD superfamily are spatially conserved in the active site of PPK1. It is possible that the bacterial PPK1 family and the PLD family have a common ancestor and diverged early in evolution. There is a second bacterial-type enzyme, PPK2, which is involved in the synthesis of poly P from GTP or ATP. PPK2 shows no sequence similarity to PPK1 and belongs to different superfamily. 162 matched cddid_all.tbl CDD cd09115 cd09115 197214 PLDc_PPK1_C2 Catalytic C-terminal domain, second repeat, of prokaryotic polyphosphate kinase 1 and similar proteins. Catalytic C-terminal domain, second repeat (C2 domain), of bacterial polyphosphate kinases 1 (Poly P kinase 1 or PPK1, EC 2.7.4.1) and similar proteins. Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PPK1 is the key enzyme responsible for the synthesis of Poly P in bacteria. It can catalyze the reversible conversion of the terminal-phosphate of ATP to Poly P. Therefore, PPK1 is essential for bacterial motility, quorum sensing, biofilm formation, and the production of virulence factors and may serve as an attractive antimicrobial drug target. Dimerization is crucial for the enzymatic activity of PPK1. Each PPK1 monomer includes four structural domains, the N-terminal (N) domain, the head (H) domain, and two closely related C-terminal (C1 and C2) domains. The N domain provides the upper binding interface for the adenine ring of the ATP. The H domain is involved in dimerization, while both the C1 and C2 domains contain residues crucial for catalytic activity. The intersection of the N, C1, and C2 domains forms a structural tunnel in which the PPK catalytic reactions are carried out. In spite of the lack of sequence homology, the C1 and C2 domains of PPK1 are structurally similar to the two repetitive catalytic domains of phospholipase D (PLD). Moreover, some residues in the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) of the PLD superfamily are spatially conserved in the active site of PPK1. It is possible that the bacterial PPK1 family and the PLD family have a common ancestor and diverged early in evolution. There is a second bacterial-type enzyme, PPK2, which is involved in the synthesis of poly P from GTP or ATP. PPK2 shows no sequence similarity to PPK1 and belongs to different superfamily. 162 matched cddid_all.tbl CDD cd09116 cd09116 197215 PLDc_Nuc_like Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6, and similar proteins. Catalytic domain of EDTA-resistant nuclease Nuc, vertebrate phospholipase D6 (PLD6, EC 3.1.4.4), and similar proteins. Nuc is an endonuclease from Salmonella typhimurium and the smallest known member of the PLD superfamily. It cleaves both single- and double-stranded DNA. PLD6 selectively hydrolyzes the terminal phosphodiester bond of phosphatidylcholine (PC), with the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. PLD6 also catalyzes the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. Both Nuc and PLD6 belong to the phospholipase D (PLD) superfamily. They contain a short conserved sequence motif, the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), which is essential for catalysis. PLDs utilize a two-step mechanism to cleave phosphodiester bonds: Upon substrate binding, the bond is first attacked by a histidine residue from one HKD motif to form a covalent phosphohistidine intermediate, which is then hydrolyzed by water with the aid of a second histidine residue from the other HKD motif in the opposite subunit. This subfamily also includes some uncharacterized hypothetical proteins, which have two HKD motifs in a single polypeptide chain. 138 matched cddid_all.tbl CDD cd09117 cd09117 197216 PLDc_Bfil_DEXD_like Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, and uncharacterized proteins with a DEAD domain. Catalytic domain of type II restriction endonucleases BfiI and NgoFVII, uncharacterized type III restriction endonuclease Res subunit, and uncharacterized DNA/RNA helicase superfamily II members. Proteins in this family are found mainly in prokaryotes. They contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in a single polypeptide chain, and have been classified as members of the phospholipase D (PLD, EC 3.1.4.4) superfamily. BfiI consists of two discrete domains with distinct functions: an N-terminal catalytic domain with non-specific nuclease activity and dimerization function that is more closely related to Nuc, an EDTA-resistant nuclease from the phospholipase D (PLD) superfamily; and a C-terminal domain that specifically recognizes its target sequences, 5'-ACTGGG-3'. BfiI forms a functionally active homodimer which has two DNA-binding surfaces located at the C-terminal domains but only one active site, located at the dimer interface between the two N-terminal catalytic domains that contain the two HKD motifs from both subunits. BfiI utilizes a single active site to cut both DNA strands, which represents a novel mechanism for the scission of double-stranded DNA. It uses a histidine residue from the HKD motif in one subunit as the nucleophile for the cleavage of the target phosphodiester bond in both of the anti-parallel DNA strands, while the symmetrically-related histidine residue from the HKD motif of the opposite subunit acts as the proton donor/acceptor during both strand-scission events. 117 matched cddid_all.tbl CDD cd09118 cd09118 197217 PLDc_yjhR_C_like C-terminal domain of Escherichia coli uncharacterized protein yjhR and similar proteins. C-terminal domain of Escherichia coli uncharacterized protein yjhR, encoded by the o338 gene, and similar proteins. Although the biological function of yjhR remains unknown, it shows sequence similarity to the C-terminal portions of superfamily I DNA and RNA helicases, which are ubiquitous enzymes mediating ATP-dependent unwinding of DNA and RNA duplexes, and play essential roles in gene replication and expression. Moreover, The C-termini of yjhR and similar proteins contain one HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The PLDc-like domain of yjhR is similar to bacterial endonucleases, Nuc and BfiI, both of which have only one copy of the HKD motif per chain. They function as homodimers, with a single active site at the dimer interface containing the HKD motifs from both subunits. They utilize a two-step mechanism to cleave phosphodiester bonds. Upon substrate binding, the bond is first attacked by a histidine residue from one HKD motif to form a covalent phosphohistidine intermediate, which is then hydrolyzed by water with the aid of a second histidine residue from the other HKD motif in the opposite subunit. 144 matched cddid_all.tbl CDD cd09119 cd09119 197218 PLDc_FAM83_N N-terminal phospholipase D-like domain of proteins from the Family with sequence similarity 83. N-terminal phospholipase D (PLD)-like domain of vetebrate proteins from the Family with sequence similarity 83 (FAM83), which is comprised of 8 members, designated FAM83A through FAM83H. Since the N-terminal PLD-like domain of FAM83 proteins shows only trace similarity to the PLD catalytic domain and lacks the functionally important histidine residue, the FAM83 proteins may share a similar three-dimensional fold with PLD enzymes, but are unlikely to carry PLD activity. Members of the FAM83 are mostly uncharacterized proteins. FAM83A, also known as tumor antigen BJ-TSA-9, is a novel tumor-specific gene highly expressed in human lung adenocarcinoma. FAM83D, also known as spindle protein CHICA, is a cell-cycle-regulated spindle component which localizes to the mitotic spindle and is both upregulated and phosphorylated during mitosis. The gene encoding protein FAM83H is the first gene involved in the etiology of amelogenesis imperfecta (AI), that encodes a non-secreted protein due to the absence of a signal peptide. Defects in gene FAM83H cause autosomal dominant hypocalcified amelogenesis imperfecta (ADHCAI). FAM83B, FAM83C, FAM83F, and FAM83G are uncharacterized proteins present across vertebrates while FAM83E is an uncharacterized protein found only in mammals. 269 matched cddid_all.tbl CDD cd09120 cd09120 197219 PLDc_DNaseII_1 Catalytic domain, repeat 1, of Deoxyribonuclease II and similar proteins. Catalytic domain, repeat 1, of Deoxyribonuclease II (DNase II, EC 3.1.22.1), an endodeoxyribonuclease with ubiquitous tissue distribution. It is essential for accessory apoptotic DNA fragmentation and DNA clearance during development, as well as in tissue regeneration in higher eukaryotes. Unlike the majority of nucleases, DNase II functions optimally at acidic pH in the absence of divalent metal ion cofactors. It hydrolyzes the phosphodiester backbone of DNA by a single strand cleavage mechanism to generate 3'-phosphate termini. The majority of family members contain an N-terminal signal-peptide leader sequence, which is critical for N-glycosylation and DNase II activity. DNase II is a monomeric nuclease that contains two copies of a variant HKD motif, where the aspartic acid residue is not conserved. The HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. The catalytic center of DNase II is formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way. Members of this family are mainly found in metazoans, and vertebrate proteins have been further classified into DNase II alpha and beta (also known as DNase II-like acid DNase, DLAD) subtypes. A few homologs are found in non-metazoan species, but none are found in fungi, plants or prokaryotes, with the sole exception of Burkholderia pseudomallei. Among those homologs, the Caenorhabditis elegans C07B5.5 ORF encoding NUC-1 apoptotic nuclease, the uncharacterized C. elegans crn-6 (cell death related nuclease) gene encoding protein, and the putative gene CG7780 encoding Drosophila DNase II (dDNase II) have similar cleavage activity and specificity to mammalian DNase II enzymes. They may function like an acid DNase implicated in degrading DNA from apoptotic cells engulfed by macrophages. Plancitoxin I, the major lethal factor from the Acanthaster planci venom, is a unique homolog of mammalian DNase II. It has potent hepatotoxicity and the optimum pH for its activity is 7.2, unlike the optimum acidic PH for mammalian DNase II. Some members of this family contain substitutions of conserved residues found in the putative active site, which suggest that these proteins may have diverged from a canonical DNase II activity and may perform other functions. 141 matched cddid_all.tbl CDD cd09121 cd09121 197220 PLDc_DNaseII_2 Catalytic domain, repeat 2, of Deoxyribonuclease II and similar proteins. Catalytic domain, repeat 2, of Deoxyribonuclease II (DNase II, EC 3.1.22.1), an endodeoxyribonuclease with ubiquitous tissue distribution. It is essential for accessory apoptotic DNA fragmentation and DNA clearance during development, as well as in tissue regeneration in higher eukaryotes. Unlike the majority of nucleases, DNase II functions optimally at acidic pH in the absence of divalent metal ion cofactors. It hydrolyzes the phosphodiester backbone of DNA by a single strand cleavage mechanism to generate 3'-phosphate termini. The majority of family members contain an N-terminal signal-peptide leader sequence, which is critical for N-glycosylation and DNase II activity. DNase II is a monomeric nuclease that contains two copies of a variant HKD motif, where the aspartic acid residue is not conserved. The HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. The catalytic center of DNase II is formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way. Members of this family are mainly found in metazoans, and vertebrate proteins have been further classified into DNase II alpha and beta (also known as DNase II-like acid DNase, DLAD) subtypes. A few homologs are found in non-metazoan species, but none are found in fungi, plants or prokaryotes, with the sole exception of Burkholderia pseudomallei. Among those homologs, the Caenorhabditis elegans C07B5.5 ORF encoding NUC-1 apoptotic nuclease, the uncharacterized C. elegans crn-6 (cell death related nuclease) gene encoding protein, and the putative gene CG7780 encoding Drosophila DNase II (dDNase II) have similar cleavage activity and specificity to mammalian DNase II enzymes. They may function like an acid DNase implicated in degrading DNA from apoptotic cells engulfed by macrophages. Plancitoxin I, the major lethal factor from the Acanthaster planci venom, is a unique homolog of mammalian DNase II. It has potent hepatotoxicity and the optimum pH for its activity is 7.2, unlike the optimum acidic PH for mammalian DNase II. Some members of this family contain substitutions of conserved residues found in the putative active site, which suggest that these proteins may have diverged from the canonical DNase II activity and may perform other functions. 139 matched cddid_all.tbl CDD cd09122 cd09122 197221 PLDc_Tdp1_1 Catalytic domain, repeat 1, of Tyrosyl-DNA phosphodiesterase. Catalytic domain, repeat 1, of Tyrosyl-DNA phosphodiesterase (Tdp1, EC 3.1.4.-), which exists in eukaryotes but not in prokaryotes. Tdp1 acts as an important DNA repair enzyme that removes stalled topoisomerase I-DNA complexes by catalyzing the hydrolysis of a phosphodiester bond between a tyrosine side chain and a DNA 3'-phosphate. It is a monomeric protein that contains two copies of a variant HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), which consists of the highly conserved histidine and lysine residues, but lacks the aspartate residue that is well conserved in other phospholipase D (PLD, EC 3.1.4.4) enzymes. Thus, this family represents a distinct class within the PLD superfamily. Like other PLD enzymes, Tdp1 may utilize a common two-step general acid/base catalytic mechanism, involving a DNA-enzyme intermediate to cleave phosphodiester bonds. A single active site involved in phosphatidyl group transfer would be formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way. 145 matched cddid_all.tbl CDD cd09123 cd09123 197222 PLDc_Tdp1_2 Catalytic domain, repeat 2, of tyrosyl-DNA phosphodiesterase. Catalytic domain, repeat 2, of Tyrosyl-DNA phosphodiesterase (Tdp1, EC 3.1.4.-), which exists in eukaryotes but not in prokaryotes. Tdp1 acts as an important DNA repair enzyme that removes stalled topoisomerase I-DNA complexes by catalyzing the hydrolysis of a phosphodiester bond between a tyrosine side chain and a DNA 3'-phosphate. It is a monomeric protein that contains two copies of a variant HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), which consists of the highly conserved histidine and lysine residues, but lacks the aspartate residue that is well conserved in other phospholipase D (PLD, EC 3.1.4.4) enzymes. Thus, this family represents a distinct class within the PLD superfamily. Like other PLD enzymes, Tdp1 may utilize a common two-step general acid/base catalytic mechanism, involving a DNA-enzyme intermediate to cleave phosphodiester bonds. A single active site involved in phosphatidyl group transfer would be formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way. 182 matched cddid_all.tbl CDD cd09124 cd09124 197223 PLDc_like_TrmB_middle Middle phospholipase D-like domain of the transcriptional regulator TrmB and similar proteins. Middle phospholipase D (PLD)-like domain of the transcriptional regulator TrmB and similar proteins. TrmB acts as a bifunctional sugar-sensing transcriptional regulator which controls two operons encoding maltose/trehalose and maltodextrin ABC transporters of Pyrococcus fruiosus. It functions as a dimer. Full length TrmB includes an N-terminal DNA-binding domain, a C-terminal sugar-binding domain and middle region that has been named as a PLD-like domain. The middle domain displays homology to PLD enzymes, which contain one or two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) per chain. The HKD motif characterizes the PLD superfamily. Due to the lack of key residues related to PLD activity in the PLD-like domain, members of this subfamily are unlikely to carry PLD activity. 126 matched cddid_all.tbl CDD cd09126 cd09126 197224 PLDc_C_DEXD_like C-terminal putative phospholipase D-like domain of uncharacterized prokaryotic HKD family nucleases fused to DEAD/DEAH box helicases. C-terminal putative phospholipase D (PLD)-like domain of uncharacterized prokaryotic HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. In addition to the helicase-like region, members of this family also contain a PLD-like domain in the C-terminal region, which is characterized by a variant HKD (H-x-K-x(4)-D motif, where x represents any amino acid residue) motif. Due to the lack of key residues related to PLD activity in the variant HKD motif, members of this subfamily are most unlikely to carry PLD activity. 126 matched cddid_all.tbl CDD cd09127 cd09127 197225 PLDc_unchar1_1 Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins. Putative catalytic domain, repeat 1, of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer. 141 matched cddid_all.tbl CDD cd09128 cd09128 197226 PLDc_unchar1_2 Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins. Putative catalytic domain, repeat 2, of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer. 142 matched cddid_all.tbl CDD cd09129 cd09129 197227 PLDc_unchar2_1 Putative catalytic domain, repeat 1, of uncharacterized phospholipase D-like proteins. Putative catalytic domain, repeat 1, of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer. 196 matched cddid_all.tbl CDD cd09130 cd09130 197228 PLDc_unchar2_2 Putative catalytic domain, repeat 2, of uncharacterized phospholipase D-like proteins. Putative catalytic domain, repeat 2, of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer. 157 matched cddid_all.tbl CDD cd09131 cd09131 197229 PLDc_unchar3 Putative catalytic domain of uncharacterized phospholipase D-like proteins. Putative catalytic domain of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. Members of this subfamily contain one copy of HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. 143 matched cddid_all.tbl CDD cd09132 cd09132 197230 PLDc_unchar4 Putative catalytic domain of uncharacterized phospholipase D-like proteins. Putative catalytic domain of uncharacterized phospholipase D (PLD, EC 3.1.4.4)-like proteins. Members of this subfamily contain one copy of HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. 122 matched cddid_all.tbl CDD cd09133 cd09133 197231 PLDc_unchar5 Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of the HKD motif. Putative catalytic domain of uncharacterized hypothetical proteins with similarity to phospholipase D (PLD, EC 3.1.4.4). PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain one or two copies of the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. 127 matched cddid_all.tbl CDD cd09134 cd09134 197232 PLDc_PSS_G_neg_1 Catalytic domain, repeat 1, of phosphatidylserine synthases from gram-negative bacteria. Catalytic domain, repeat 1, of phosphatidylserine synthases (PSSs) from gram-negative bacteria. There are two subclasses of PSS enzymes in bacteria: subclass I of gram-negative bacteria and subclass II of gram-positive bacteria. It is common that PSSs in gram-positive bacteria and yeast are tight membrane-associated enzymes. By contrast, the gram-negative bacterial PSSs, such as Escherichia coli PSS, are commonly bound to the ribosomes. They are peripheral membrane proteins that can interact with the surface of the inner membrane by binding to the lipid substrate (CDP-diacylglycerol) and the lipid product (phosphatidylserine). The prototypical member of this subfamily is Escherichia coli PSS (also called CDP-diacylglycerol-L-serine O-phosphatidyltransferase, EC 2.7.8.8), which catalyzes the exchange reactions between CMP and CDP-diacylglycerol, and between serine and phosphatidylserine. The phosphatidylserine is then decarboxylated by phosphatidylserine decarboxylase to yield phosphatidylethanolamine, the major phospholipid in Escherichia coli. It also catalyzes the hydrolysis of CDP-diacylglycerol to form phosphatidic acid with the release of CMP. PSS may utilize a ping-pong mechanism involving a phosphatidyl-enzyme intermediate, which is distinct from those of gram-positive bacterial phosphatidylserine synthases. Moreover, all members in this subfamily have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs constitute an active site for the formation of a covalent substrate-enzyme intermediate. 173 matched cddid_all.tbl CDD cd09135 cd09135 197233 PLDc_PGS1_euk_1 Catalytic domain, repeat 1, of eukaryotic PhosphatidylGlycerophosphate Synthases. Catalytic domain, repeat 1, of eukaryotic phosphatidylglycerophosphate (PGP) synthases, also called CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (EC 2.7.8.5). Eukaryotic PGP synthases are different and unrelated to prokaryotic PGP synthases and yeast phosphatidylserine synthase. They catalyze the synthesis of PGP from CDP-diacylglycerol and sn-glycerol 3-phosphate, the committed and rate-limiting step in the biosynthesis of cardiolipin (CL), which is an essential component of many mitochondrial functions in eukaryotes. Members in this subfamily all have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. They may utilize a common two-step ping-pong catalytic mechanism involving a substrate-enzyme intermediate to cleave phosphodiester bonds. The two motifs are suggested to constitute the active site involved in the phosphatidyl group transfer. 170 matched cddid_all.tbl CDD cd09136 cd09136 197234 PLDc_PSS_G_neg_2 Catalytic domain, repeat 2, of phosphatidylserine synthases from gram-negative bacteria. Catalytic domain, repeat 2, of phosphatidylserine synthases (PSSs) from gram-negative bacteria. There are two subclasses of PSS enzymes in bacteria: subclass I of gram-negative bacteria and subclass II of gram-positive bacteria. It is common that PSSs in gram-positive bacteria and yeast are tight membrane-associated enzymes. By contrast, the gram-negative bacterial PSSs, such as Escherichia coli PSS, are commonly bound to the ribosomes. They are peripheral membrane proteins that can interact with the surface of the inner membrane by binding to the lipid substrate (CDP-diacylglycerol) and the lipid product (phosphatidylserine). The prototypical member of this subfamily is Escherichia coli PSS (also called CDP-diacylglycerol-L-serine O-phosphatidyltransferase, EC 2.7.8.8), which catalyzes the exchange reactions between CMP and CDP-diacylglycerol, and between serine and phosphatidylserine. The phosphatidylserine is then decarboxylated by phosphatidylserine decarboxylase to yield phosphatidylethanolamine, the major phospholipid in Escherichia coli. It also catalyzes the hydrolysis of CDP-diacylglycerol to form phosphatidic acid with the release of CMP. PSS may utilize a ping-pong mechanism involving a phosphatidyl-enzyme intermediate, which is distinct from those of gram-positive bacterial phosphatidylserine synthases. Moreover, all members in this subfamily have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs constitute an active site for the formation of a covalent substrate-enzyme intermediate. 215 matched cddid_all.tbl CDD cd09137 cd09137 197235 PLDc_PGS1_euk_2 Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate synthases. Catalytic domain, repeat 2, of eukaryotic phosphatidylglycerophosphate (PGP) synthases, also called CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (EC 2.7.8.5). Eukaryotic PGP synthases are different and unrelated to prokaryotic PGP synthases and yeast phosphatidylserine synthase. They catalyze the synthesis of PGP from CDP-diacylglycerol and sn-glycerol 3-phosphate, the committed and rate-limiting step in the biosynthesis of cardiolipin (CL), which is an essential component of many mitochondrial functions in eukaryotes. Members in this subfamily all have two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. They may utilize a common two-step ping-pong catalytic mechanism involving a substrate-enzyme intermediate to cleave phosphodiester bonds. The two motifs are suggested to constitute the active site involved in the phosphatidyl group transfer. 186 matched cddid_all.tbl CDD cd09138 cd09138 197236 PLDc_vPLD1_2_yPLD_like_1 Catalytic domain, repeat 1, of vertebrate phospholipases, PLD1 and PLD2, yeast PLDs, and similar proteins. Catalytic domain, repeat 1, of vertebrate phospholipases D (PLD1 and PLD2), yeast phospholipase D (PLD SPO14/PLD1), and other similar eukaryotic proteins. These PLD enzymes play a pivotal role in transmembrane signaling and cellular regulation. They hydrolyze the terminal phosphodiester bond of phospholipids resulting in the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. PLDs also catalyze the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. The vertebrate PLD1 and PLD2 are membrane associated phosphatidylinositol 4,5-bisphosphate (PIP2)-dependent enzymes that selectively hydrolyze phosphatidylcholine (PC). Protein cofactors and calcium may be required for their activation. Yeast SPO14/PLD1 is a calcium-independent PLD, which needs PIP2 for its activity. Instead of the regulatory calcium-dependent phospholipid-binding C2 domain in plants, most mammalian and yeast PLDs have adjacent Phox (PX) and the Pleckstrin homology (PH) domains at the N-terminus, which have been shown to mediate membrane targeting of the protein and are closely linked to polyphosphoinositide signaling. The PX and PH domains are also present in zeta-type PLD from Arabidopsis, which is more closely related to vertebrate PLDs than to other plant PLD types. In addition, this subfamily also includes some related proteins which have either PX-like or PH domains in their N-termini. Like other members of the PLD superfamily, the monomer of mammalian and yeast PLDs consists of two catalytic domains, each containing one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from the two domains form a single active site. These PLDs utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. 146 matched cddid_all.tbl CDD cd09139 cd09139 197237 PLDc_pPLD_like_1 Catalytic domain, repeat 1, of plant phospholipase D and similar proteins. Catalytic domain, repeat 1, of plant phospholipase D (PLD, EC 3.1.4.4) and similar proteins. Plant PLDs have broad substrate specificity and can hydrolyze the terminal phosphodiester bond of several common membrane phospholipids such as phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and phosphatidylserine (PS), with the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. PLDs also catalyze the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. Most plant PLDs possess a regulatory calcium-dependent phospholipid-binding C2 domain in the N-terminus and require calcium for activity, which is unique to plant PLDs and is not present in animal or fungal PLDs. Like other PLD enzymes, the monomer of plant PLDs consists of two catalytic domains, each of which contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from two domains form a single active site. Plant PLDs may utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. This subfamily includes two types of plant PLDs, alpha-type and beta-type PLDs, which are derived from different gene products and distinctly regulated. The zeta-type PLD from Arabidopsis is not included in this subfamily. 176 matched cddid_all.tbl CDD cd09140 cd09140 197238 PLDc_vPLD1_2_like_bac_1 Catalytic domain, repeat 1, of uncharacterized bacterial proteins with similarity to vertebrate phospholipases, PLD1 and PLD2. Catalytic domain, repeat 1, of uncharacterized bacterial counterparts of vertebrate, yeast and plant phospholipase D (PLD, EC 3.1.4.4). PLDs hydrolyze the terminal phosphodiester bond of phospholipids with the formation of phosphatidic acid and alcohols. They also catalyze the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. Instead of the regulatory C2 (calcium-activated lipid binding) domain in plants and the adjacent Phox (PX) and the Pleckstrin homology (PH) N-terminal domains in most mammalian and yeast PLDs, many members in this subfamily contain a SNARE associated C-terminal domain, whose functional role is unclear. Like other PLD enzymes, members in this subfamily contain two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), that may play an important role in the catalysis. 146 matched cddid_all.tbl CDD cd09141 cd09141 197239 PLDc_vPLD1_2_yPLD_like_2 Catalytic domain, repeat 2, of vertebrate phospholipases, PLD1 and PLD2, yeast PLDs, and similar proteins. Catalytic domain, repeat 2, of vertebrate phospholipases D (PLD1 and PLD2), yeast phospholipase D (PLD SPO14/PLD1), and other similar eukaryotic proteins. These PLD enzymes play a pivotal role in transmembrane signaling and cellular regulation. They hydrolyze the terminal phosphodiester bond of phospholipids resulting in the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. PLDs also catalyze the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. The vertebrate PLD1 and PLD2 are membrane associated phosphatidylinositol 4,5-bisphosphate (PIP2)-dependent enzymes that selectively hydrolyze phosphatidylcholine (PC). Protein cofactors and calcium may be required for their activation. Yeast SPO14/PLD1 is a calcium-independent PLD, which needs PIP2 for its activity. Instead of the regulatory calcium-dependent phospholipid-binding C2 domain in plants, most mammalian and yeast PLDs have adjacent Phox (PX) and the Pleckstrin homology (PH) domains at the N-terminus, which have been shown to mediate membrane targeting of the protein and are closely linked to polyphosphoinositide signaling. The PX and PH domains are also present in zeta-type PLD from Arabidopsis, which is more closely related to vertebrate PLDs than to other plant PLD types. In addition, this subfamily also includes some related proteins which have either PX-like or PH domains in their N-termini. Like other members of the PLD superfamily, the monomer of mammalian and yeast PLDs consists of two catalytic domains, each containing one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from the two domains form a single active site. These PLDs utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. 183 matched cddid_all.tbl CDD cd09142 cd09142 197240 PLDc_pPLD_like_2 Catalytic domain, repeat 2, of plant phospholipase D and similar proteins. Catalytic domain, repeat 2, of plant phospholipase D (PLD, EC 3.1.4.4) and similar proteins. Plant PLDs have broad substrate specificity and can hydrolyze the terminal phosphodiester bond of several common membrane phospholipids such as phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), and phosphatidylserine (PS), with the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. PLDs also catalyze the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. Most plant PLDs possess a regulatory calcium-dependent phospholipid-binding C2 domain in the N-terminus and require calcium for activity, which is unique to plant PLDs and is not present in animal or fungal PLDs. Like other PLD enzymes, the monomer of plant PLDs consists of two catalytic domains, each of which contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from two domains form a single active site. Plant PLDs may utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. This subfamily includes two types of plant PLDs, alpha-type and beta-type PLDs, which are derived from different gene products and distinctly regulated. The zeta-type PLD from Arabidopsis is not included in this subfamily. 208 matched cddid_all.tbl CDD cd09143 cd09143 197241 PLDc_vPLD1_2_like_bac_2 Catalytic domain, repeat 2, of uncharacterized bacterial proteins with similarity to vertebrate phospholipases, PLD1 and PLD2. Catalytic domain, repeat 2, of uncharacterized bacterial counterparts of vertebrate, yeast and plant phospholipase D (PLD, EC 3.1.4.4). PLDs hydrolyze the terminal phosphodiester bond of phospholipids with the formation of phosphatidic acid and alcohols. They also catalyze the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. Instead of the regulatory C2 (calcium-activated lipid binding) domain in plants and the adjacent Phox (PX) and the Pleckstrin homology (PH) N-terminal domains in most mammalian and yeast PLDs, many members in this subfamily contain a SNARE associated C-terminal domain, whose functional role is unclear. Like other PLD enzymes, members in this subfamily contain two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), that may play an important role in the catalysis. 142 matched cddid_all.tbl CDD cd09144 cd09144 197242 PLDc_vPLD3_1 Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD3. Putative catalytic domain, repeat 1, of phospholipase D3 (PLD3, EC 3.1.4.4). The human protein is also known as Hu-K4 or HUK4 and it was identified as a human homolog of the vaccinia virus protein K4, which is encoded by the HindIII K4L gene. PLD3 is found in many human organs with highest expression levels found in the central nervous system. Due to the presence of two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), PLD3 has been assigned to the PLD superfamily although no catalytic activity has been detected experimentally. PLD3 is a membrane-bound protein that colocalizes with protein disulfide isomerase, an endoplasmic reticulum (ER) protein. Like other homologs of protein K4, PLD3 might alter the lipid content of associated membranes by selectively hydrolyzing phosphatidylcholine (PC) into the corresponding phosphatidic acid, which is thought to be involved in the regulation of lipid movement. 172 matched cddid_all.tbl CDD cd09145 cd09145 197243 PLDc_vPLD4_1 Putative catalytic domain, repeat 1, of vertebrate phospholipase PLD4. Putative catalytic domain, repeat 1, of vertebrate phospholipases D4 (PLD4, EC 3.1.4.4), homologs of the vaccinia virus protein K4 which is encoded by the HindIII K4L gene. Due to the presence of two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), PLD4 has been assigned to PLD superfamily although no catalytic activity has been detected to date. Unlike PLD1 and PLD2, PLD4 does not contain Phox (PX) and Pleckstrin homology (PH) domains but has a putative transmembrane domain. Like other vertebrate homologs of protein K4, PLD4 might be associated with Golgi membranes and alter their lipid content by selectively hydrolyze phosphatidylcholine (PC) into corresponding phosphatidic acid, which is thought to be involved in the regulation of lipid movement. 170 matched cddid_all.tbl CDD cd09146 cd09146 197244 PLDc_vPLD5_1 Putative catalytic domain, repeat 1, of inactive veterbrate phospholipase PLD5. Putative catalytic domain, repeat 1, of inactive veterbrate phospholipases D5 (PLD5, EC 3.1.4.4), homologs of the vaccinia virus protein K4 encoded by the HindIII K4L gene. Vertebrate PLD5 has been assigned to the PLD superfamily, since it shows high sequence similarity to other human homologs of protein K4, which contain two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). However, due to the lack of functionally important histidine and lysine residues in the HKD motif, vetebrate PLD5 has been characterized as an inactive PLD. 163 matched cddid_all.tbl CDD cd09147 cd09147 197245 PLDc_vPLD3_2 Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD3. Putative catalytic domain, repeat 2, of phospholipase D3 (PLD3, EC 3.1.4.4). The human protein is also known as Hu-K4 or HUK4 and it was identified as a human homolog of the vaccinia virus protein K4, which is encoded by the HindIII K4L gene. PLD3 is found in many human organs with highest expression levels found in the central nervous system. Due to the presence of two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), PLD3 has been assigned to the PLD superfamily although no catalytic activity has been detected experimentally. PLD3 is a membrane-bound protein that colocalizes with protein disulfide isomerase, an endoplasmic reticulum (ER) protein. Like other homologs of protein K4, PLD3 might alter the lipid content of associated membranes by selectively hydrolyzing phosphatidylcholine (PC) into the corresponding phosphatidic acid, which is thought to be involved in the regulation of lipid movement. 186 matched cddid_all.tbl CDD cd09148 cd09148 197246 PLDc_vPLD4_2 Putative catalytic domain, repeat 2, of vertebrate phospholipase PLD4. Putative catalytic domain, repeat 2, of vertebrate phospholipases D4 (PLD4, EC 3.1.4.4), homologs of the vaccinia virus protein K4 which is encoded by the HindIII K4L gene. Due to the presence of two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), PLD4 has been assigned to PLD superfamily although no catalytic activity has been detected to date. Unlike PLD1 and PLD2, PLD4 does not contain Phox (PX) and Pleckstrin homology (PH) domains but has a putative transmembrane domain. Like other vertebrate homologs of protein K4, PLD4 might be associated with Golgi membranes and alter their lipid content by selectively hydrolyze phosphatidylcholine (PC) into corresponding phosphatidic acid, which is thought to be involved in the regulation of lipid movement. 187 matched cddid_all.tbl CDD cd09149 cd09149 197247 PLDc_vPLD5_2 Putative catalytic domain, repeat 2, of inactive veterbrate phospholipase PLD5. Putative catalytic domain, repeat 2, of inactive veterbrate phospholipases D5 (PLD5, EC 3.1.4.4), homologs of the vaccinia virus protein K4 encoded by the HindIII K4L gene. Vertebrate PLD5 has been assigned to the PLD superfamily, since it shows high sequence similarity to other human homologs of protein K4, which contain two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). However, due to the lack of functionally important histidine and lysine residues in the HKD motif, vetebrate PLD5 has been characterized as an inactive PLD. 188 matched cddid_all.tbl CDD cd09150 cd09150 197248 PLDc_Ymt_1 Putative catalytic domain, repeat 1, of Yersinia pestis murine toxin-like proteins. Putative catalytic domain, repeat 1, of Yersinia pestis murine toxin (Ymt), a plasmid-encoded phospholipase D (PLD, EC 3.1.4.4), and similar proteins. Ymt is important in order for Yersinia pestis to survive and spread. It is toxic to mice and rats but not to other animals. It is not a conventional secreted exotoxin, but a cytoplasmic protein that is released upon bacterial lysis. Ymt may be active as a dimer. The monomeric Ymt consists of two catalytic domains, each of which contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from two domains form a single active site. Ymt has PLD-like activity and has been classified into the PLD superfamily. It hydrolyzes the terminal phosphodiester bond in several phospholipids, with preference for phosphatidylethanolamine (PE) over phosphatidylcholine (PC) and phosphatidylserine (PS). Like other PLD enzymes, Ymt may utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. In terms of sequence similarity, Ymt is closely related to Streptomyces PLDs. 215 matched cddid_all.tbl CDD cd09151 cd09151 197249 PLDc_Ymt_2 Putative catalytic domain, repeat 2, of Yersinia pestis murine toxin-like proteins. Putative catalytic domain, repeat 2, of Yersinia pestis murine toxin (Ymt), a plasmid-encoded phospholipase D (PLD, EC 3.1.4.4), and similar proteins. Ymt is important in order for Yersinia pestis to survive and spread. It is toxic to mice and rats but not to other animals. It is not a conventional secreted exotoxin, but a cytoplasmic protein that is released upon bacterial lysis. Ymt may be active as a dimer. The monomeric Ymt consists of two catalytic domains, each of which contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from two domains form a single active site. Ymt has PLD-like activity and has been classified into the PLD superfamily. It hydrolyzes the terminal phosphodiester bond in several phospholipids, with preference for phosphatidylethanolamine (PE) over phosphatidylcholine (PC) and phosphatidylserine (PS). Like other PLD enzymes, Ymt may utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. In terms of sequence similarity, Ymt is closely related to Streptomyces PLDs. 264 matched cddid_all.tbl CDD cd09152 cd09152 197250 PLDc_EcCLS_like_1 Catalytic domain, repeat 1, of Escherichia coli cardiolipin synthase and similar proteins. Catalytic domain, repeat 1, of Escherichia coli cardiolipin (CL) synthase and similar proteins. Escherichia coli CL synthase (EcCLS), specified by the cls gene, is the prototype of this family. EcCLS is a multi-pass membrane protein that catalyzes reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form cardiolipin (CL) and glycerol. The monomer of EcCLS consists of two catalytic domains. Each catalytic domain contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. Two HKD motifs from two domains form a single active site involved in phosphatidyl group transfer. EcCLS can be stimulated by phosphate and inhibited by CL, the product of the reaction, and by phosphatidate. Phosphate stimulation may be unique to enzymes with CL synthase activity belonging to the PLD superfamily. Like other PLD enzymes, EcCLS utilizes a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. 163 matched cddid_all.tbl CDD cd09154 cd09154 197251 PLDc_SMU_988_like_1 Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins. Putative catalytic domain, repeat 1, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins. Although SMU_988 and similar proteins have not been functionally characterized, members in this subfamily show high sequence homology to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer. 155 matched cddid_all.tbl CDD cd09155 cd09155 197252 PLDc_PaCLS_like_1 Putative catalytic domain, repeat 1, of Pseudomonas aeruginosa cardiolipin synthase and similar proteins. Putative catalytic domain, repeat 1, of Pseudomonas aeruginosa cardiolipin (CL) synthase (PaCLS) and similar proteins. Although PaCLS and similar proteins have not been functionally characterized, members in this subfamily show high sequence homology to bacterial CL synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Moreover, PaCLS and other members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer. 156 matched cddid_all.tbl CDD cd09156 cd09156 197253 PLDc_CLS_unchar1_1 Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin synthase. Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer. 154 matched cddid_all.tbl CDD cd09157 cd09157 197254 PLDc_CLS_unchar2_1 Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin synthase. Putative catalytic domain, repeat 1, of uncharacterized proteins similar to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer. 155 matched cddid_all.tbl CDD cd09158 cd09158 197255 PLDc_EcCLS_like_2 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase and similar proteins. Catalytic domain, repeat 2, of Escherichia coli cardiolipin (CL) synthase and similar proteins. Escherichia coli CL synthase (EcCLS), specified by the cls gene, is the prototype of this family. EcCLS is a multi-pass membrane protein that catalyzes reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form cardiolipin (CL) and glycerol. The monomer of EcCLS consists of two catalytic domains. Each catalytic domain contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. Two HKD motifs from two domains form a single active site involved in phosphatidyl group transfer. EcCLS can be stimulated by phosphate and inhibited by CL, the product of the reaction, and by phosphatidate. Phosphate stimulation may be unique to enzymes with CL synthase activity belonging to the PLD superfamily. Like other PLD enzymes, EcCLS utilizes a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. 174 matched cddid_all.tbl CDD cd09159 cd09159 197256 PLDc_ybhO_like_2 Catalytic domain, repeat 2, of Escherichia coli cardiolipin synthase ybhO and similar proteins. Catalytic domain, repeat 2, of Escherichia coli cardiolipin (CL) synthase ybhO and similar proteins. In Escherichia coli, there are two genes, f413 (ybhO) and o493 (ymdC), which are homologous to gene cls that encodes the Escherichia coli CL synthase. The prototype of this subfamily is Escherichia coli CL synthase ybhO specified by the f413 (ybhO) gene. ybhO is a membrane-bound protein that catalyzes the formation of cardiolipin (CL) by transferring phosphatidyl group between two phosphatidylglycerol molecules. It can also catalyze phosphatidyl group transfer to water to form phosphatidate. In contrast to the Escherichia coli CL synthase encoded by the cls gene (EcCLS), ybhO does not hydrolyze CL. Moreover, ybhO lacks an N-terminal segment encoded by Escherichia coli cls, which makes ybhO easy to denature. The monomer of ybhO consists of two catalytic domains. Each catalytic domain contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. Two HKD motifs from two domains form a single active site involved in phosphatidyl group transfer. ybhO can be stimulated by phosphate and inhibited by CL, the product of the reaction, and by phosphatidate. Phosphate stimulation may be unique to enzymes with CL synthase activity belonging to the PLD superfamily. 170 matched cddid_all.tbl CDD cd09160 cd09160 197257 PLDc_SMU_988_like_2 Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins. Putative catalytic domain, repeat 2, of Streptococcus mutans uncharacterized protein SMU_988 and similar proteins. Although SMU_988 and similar proteins have not been functionally characterized, members in this subfamily show high sequence homology to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer. 176 matched cddid_all.tbl CDD cd09161 cd09161 197258 PLDc_PaCLS_like_2 Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin synthase and similar proteins. Putative catalytic domain, repeat 2, of Pseudomonas aeruginosa cardiolipin (CL) synthase (PaCLS) and similar proteins. Although PaCLS and similar proteins have not been functionally characterized, members in this subfamily show high sequence homology to bacterial CL synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Moreover, PaCLS and other members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer. 176 matched cddid_all.tbl CDD cd09162 cd09162 197259 PLDc_CLS_unchar1_2 Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin synthase. Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer. 172 matched cddid_all.tbl CDD cd09163 cd09163 197260 PLDc_CLS_unchar2_2 Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin synthase. Putative catalytic domain, repeat 2, of uncharacterized proteins similar to bacterial cardiolipin (CL) synthases, which catalyze the reversible phosphatidyl group transfer between two phosphatidylglycerol molecules to form CL and glycerol. Members of this subfamily contain two HKD motifs (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the phospholipase D (PLD) superfamily. The two motifs may be part of the active site and may be involved in phosphatidyl group transfer. 176 matched cddid_all.tbl CDD cd09164 cd09164 197261 PLDc_EcPPK1_C1_like Catalytic C-terminal domain, first repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins. Catalytic C-terminal domain, first repeat (C1 domain), of Escherichia coli polyphosphate kinase 1 (Poly P kinase 1 or PPK1, EC 2.7.4.1) and similar proteins. Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PPK1 is the key enzyme responsible for the synthesis of Poly P in bacteria. It can catalyze the reversible conversion of the terminal-phosphate of ATP to Poly P. Therefore, PPK1 is essential for bacterial motility, quorum sensing, biofilm formation, and the production of virulence factors and may serve as an attractive antimicrobial drug target. Dimerization is crucial for the enzymatic activity of PPK1. The prototype of this subfamily is Escherichia coli polyphosphate kinase (EcPPK), which forms a homotetramer in solution, and becomes a homodimer upon the binding of AMPPNP, a non-hydrolysable ATP analogue. Each EcPPK monomer includes four structural domains, the N-terminal (N) domain, the head (H) domain, and two closely related C-terminal (C1 and C2)domains. The N domain provides the upper binding interface for the adenine ring of the ATP. The H domain is involved in dimerization, while both the C1 and C2 domains contain residues crucial for catalytic activity. The intersection of the N, C1, and C2 domains forms a structural tunnel in which the PPK catalytic reactions are carried out. In spite of the lack of sequence homology, the C1 and C2 domains of EcPPK are structurally similar to the two repetitive catalytic domains of phospholipase D (PLD). Moreover, some residues in the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) of the PLD superfamily are spatially conserved in the active site of EcPPK. It is possible that the bacterial PPK1 family and the PLD family have a common ancestor and diverged early in evolution. 162 matched cddid_all.tbl CDD cd09165 cd09165 197262 PLDc_PaPPK1_C1_like Catalytic C-terminal domain, first repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins. Catalytic C-terminal domain, first repeat (C1 domain), of polyphosphate kinase (Poly P kinase 1 or PPK1, EC 2.7.4.1) from Pseudomonas aeruginosa (PaPPK1), Dictyostelium discoideum (DdPPK1), and other similar proteins. Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PaPPK1 is the key enzyme responsible for the synthesis of Poly P in Pseudomonas aeruginosa. It can catalyze the reversible conversion of the terminal-phosphate of ATP to Poly P. PaPPK1 shows high sequence homolog to Escherichia coli polyphosphate kinase (EcPPK), which contains four structural domains per chain: the N-terminal (N) domain, the head (H) domain, and two closely related C-terminal (C1 and C2) domains. The N domain provides the upper binding interface for the adenine ring of the ATP. The H domain is involved in dimerization, while both the C1 and C2 domains contain residues crucial for catalytic activity. The intersection of the N, C1, and C2 domains forms a structural tunnel in which the PPK catalytic reactions are carried out. The polyphosphate kinase from Dictyostelium discoideum (DdPPK1) shares similar structural features with EcPPK1 in the ATP-binding pocket and poly P tunnel, but has a unique N-terminal extension that may be responsible for its enzymatic activity, cellular localization, and physiological functions. In spite of the lack of sequence homology, the C1 and C2 domains of the family members are structurally similar to the two repetitive catalytic domains of phospholipase D (PLD). Moreover, some residues in the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) of the PLD superfamily are spatially conserved in the active site of PPK1. It is possible that the bacterial PPK1 family and the PLD family have a common ancestor and diverged early in evolution. In some bacteria, such as Pseudomonas aeruginosa, a second enzyme, PPK2, which is involved in the alternative pathway of polyphosphate synthesis, has been found. It can catalyze the synthesis of poly P from GTP or ATP, with a preference for Mn2+ over Mg2+. PPK2 shows no sequence similarity to PPK1 and belongs to a different superfamily. 164 matched cddid_all.tbl CDD cd09166 cd09166 197263 PLDc_PPK1_C1_unchar Catalytic C-terminal domain, first repeat, of uncharacterized prokaryotic polyphosphate kinases. Catalytic C-terminal domain, first repeat (C1 domain), of a group of uncharacterized prokaryotic polyphosphate kinases (Poly P kinase 1 or PPK1, EC 2.7.4.1). Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PPK1 is the key enzyme responsible for the synthesis of Poly P in bacteria. It can catalyze the reversible conversion of the terminal-phosphate of ATP to Poly P. Therefore, PPK1 is essential for bacterial motility, quorum sensing, biofilm formation, and the production of virulence factors and may serve as an attractive antimicrobial drug target. Dimerization is crucial for the enzymatic activity of PPK1. Each PPK1 monomer includes four structural domains, the N-terminal (N) domain, the head (H) domain, and two closely related C-terminal (C1 and C2) domains. The N domain provides the upper binding interface for the adenine ring of the ATP. The H domain is involved in dimerization, while both the C1 and C2 domains contain residues crucial for catalytic activity. The intersection of the N, C1, and C2 domains forms a structural tunnel in which the PPK catalytic reactions are carried out. In spite of the lack of sequence homology, the C1 and C2 domains of PPK1 are structurally similar to the two repetitive catalytic domains of phospholipase D (PLD). Moreover, some residues in the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) of the PLD superfamily are spatially conserved in the active site of PPK1. It is possible that the bacterial PPK1 family and the PLD family have a common ancestor and diverged early in evolution. 162 matched cddid_all.tbl CDD cd09167 cd09167 197264 PLDc_EcPPK1_C2_like Catalytic C-terminal domain, second repeat, of Escherichia coli polyphosphate kinase 1 and similar proteins. Catalytic C-terminal domain, second repeat (C2 domain), of Escherichia coli polyphosphate kinase 1 (Poly P kinase 1 or PPK1, EC 2.7.4.1) and similar proteins. Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PPK1 is the key enzyme responsible for the synthesis of Poly P in bacteria. It can catalyze the reversible conversion of the terminal-phosphate of ATP to Poly P. Therefore, PPK1 is essential for bacterial motility, quorum sensing, biofilm formation, and the production of virulence factors and may serve as an attractive antimicrobial drug target. Dimerization is crucial for the enzymatic activity of PPK1. The prototype of this subfamily is Escherichia coli polyphosphate kinase (EcPPK), which forms a homotetramer in solution, and becomes a homodimer upon the binding of AMPPNP, a non-hydrolysable ATP analogue. Each EcPPK monomer includes four structural domains, the N-terminal (N) domain, the head (H) domain, and two closely related C-terminal (C1 and C2)domains. The N domain provides the upper binding interface for the adenine ring of the ATP. The H domain is involved in dimerization, while both the C1 and C2 domains contain residues crucial for catalytic activity. The intersection of the N, C1, and C2 domains forms a structural tunnel in which the PPK catalytic reactions are carried out. In spite of the lack of sequence homology, the C1 and C2 domains of EcPPK are structurally similar to the two repetitive catalytic domains of phospholipase D (PLD). Moreover, some residues in the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) of the PLD superfamily are spatially conserved in the active site of EcPPK. It is possible that the bacterial PPK1 family and the PLD family have a common ancestor and diverged early in evolution. 165 matched cddid_all.tbl CDD cd09168 cd09168 197265 PLDc_PaPPK1_C2_like Catalytic C-terminal domain, second repeat, of Pseudomonas aeruginosa polyphosphate kinase 1 and similar proteins. Catalytic C-terminal domain, second repeat (C2 domain), of polyphosphate kinase (Poly P kinase 1 or PPK1, EC 2.7.4.1) from Pseudomonas aeruginosa (PaPPK1), Dictyostelium discoideum (DdPPK1), and other similar proteins. Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PaPPK1 is the key enzyme responsible for the synthesis of Poly P in Pseudomonas aeruginosa. It can catalyze the reversible conversion of the terminal-phosphate of ATP to Poly P. PaPPK1 shows high sequence homolog to Escherichia coli polyphosphate kinase (EcPPK), which contains four structural domains per chain: the N-terminal (N) domain, the head (H) domain, and two closely related C-terminal (C1 and C2) domains. The N domain provides the upper binding interface for the adenine ring of the ATP. The H domain is involved in dimerization, while both the C1 and C2 domains contain residues crucial for catalytic activity. The intersection of the N, C1, and C2 domains forms a structural tunnel in which the PPK catalytic reactions are carried out. The polyphosphate kinase from Dictyostelium discoideum (DdPPK1) shares similar structural features with EcPPK1 in the ATP-binding pocket and poly P tunnel, but has a unique N-terminal extension that may be responsible for its enzymatic activity, cellular localization, and physiological functions. In spite of the lack of sequence homology, the C1 and C2 domains of the family members are structurally similar to the two repetitive catalytic domains of phospholipase D (PLD). Moreover, some residues in the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) of the PLD superfamily are spatially conserved in the active site of PPK1. It is possible that the bacterial PPK1 family and the PLD family have a common ancestor and diverged early in evolution. In some bacteria, such as Pseudomonas aeruginosa, a second enzyme, PPK2, which is involved in the alternative pathway of polyphosphate synthesis, has been found. It can catalyze the synthesis of poly P from GTP or ATP, with a preference for Mn2+ over Mg2+. PPK2 shows no sequence similarity to PPK1 and belongs to a different superfamily. 163 matched cddid_all.tbl CDD cd09169 cd09169 197266 PLDc_PPK1_C2_unchar Catalytic C-terminal domain, second repeat, of uncharacterized prokaryotic polyphosphate kinases. Catalytic C-terminal domain, second repeat (C2 domain), of a group of uncharacterized prokaryotic polyphosphate kinases (Poly P kinase 1 or PPK1, EC 2.7.4.1). Inorganic polyphosphate (Poly P) plays an important role in bacterial stress responses and stationary-phase survival. PPK1 is the key enzyme responsible for the synthesis of Poly P in bacteria. It can catalyze the reversible conversion of the terminal-phosphate of ATP to Poly P. Therefore, PPK1 is essential for bacterial motility, quorum sensing, biofilm formation, and the production of virulence factors and may serve as an attractive antimicrobial drug target. Dimerization is crucial for the enzymatic activity of PPK1. Each PPK1 monomer includes four structural domains, the N-terminal (N) domain, the head (H) domain, and two closely related C-terminal (C1 and C2) domains. The N domain provides the upper binding interface for the adenine ring of the ATP. The H domain is involved in dimerization, while both the C1 and C2 domains contain residues crucial for catalytic activity. The intersection of the N, C1, and C2 domains forms a structural tunnel in which the PPK catalytic reactions are carried out. In spite of the lack of sequence homology, the C1 and C2 domains of PPK1 are structurally similar to the two repetitive catalytic domains of phospholipase D (PLD). Moreover, some residues in the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) of the PLD superfamily are spatially conserved in the active site of PPK1. It is possible that the bacterial PPK1 family and the PLD family have a common ancestor and diverged early in evolution. 162 matched cddid_all.tbl CDD cd09170 cd09170 197267 PLDc_Nuc Catalytic domain of EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins. Catalytic domain of an EDTA-resistant nuclease Nuc from Salmonella typhimurium and similar proteins. Nuc is an endonuclease cleaving both single- and double-stranded DNA. It is the smallest known member of the phospholipase D (PLD, EC 3.1.4.4) superfamily that includes a diverse group of proteins with various catalytic functions. Most members of this superfamily have two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in a single polypeptide chain and both are required for catalytic activity. However, Nuc only has one copy of the HKD motif per subunit but form a functionally active homodimer (it is most likely also active in solution as a multimeric protein), which has a single active site at the dimer interface containing the HKD motifs from both subunits. Due to the lack of a distinct domain for DNA binding, Nuc cuts DNA non-specifically. It utilizes a two-step mechanism to cleave phosphodiester bonds: Upon substrate binding, the bond is first attacked by a histidine residue from one HKD motif to form a covalent phosphohistidine intermediate, which is then hydrolyzed by water with the aid of a second histidine residue from the other HKD motif in the opposite subunit. 142 matched cddid_all.tbl CDD cd09171 cd09171 197268 PLDc_vPLD6_like Catalytic domain of vertebrate phospholipase D6 and similar proteins. Catalytic domain of vertebrate phospholipase D6 (PLD6, EC 3.1.4.4), a homolog of the EDTA-resistant nuclease Nuc from Salmonella typhimurium, and similar proteins. PLD6 can selectively hydrolyze the terminal phosphodiester bond of phosphatidylcholine (PC) with the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. It also catalyzes the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. PLD6 belongs to the phospholipase D (PLD) superfamily. Its monomer contains a short conserved sequence motif, H-x-K-x(4)-D (where x represents any amino acid residue), termed the HKD motif, which is essential in catalysis. PLD6 is more closely related to the nuclease Nuc than to other vertebrate phospholipases, which have two copies of the HKD motif in a single polypeptide chain. Like Nuc, PLD6 may utilize a two-step mechanism to cleave phosphodiester bonds: Upon substrate binding, the bond is first attacked by a histidine residue from the HKD motif of one subunit to form a covalent phosphohistidine intermediate, which is then hydrolyzed by water with the aid of a second histidine residue from the other HKD motif in the opposite subunit. 136 matched cddid_all.tbl CDD cd09172 cd09172 197269 PLDc_Nuc_like_unchar1_1 Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins similar to Nuc, an endonuclease from Salmonella typhimurium. Putative catalytic domain, repeat 1, of uncharacterized hypothetical proteins, which show high sequence homology to the endonuclease from Salmonella typhimurium and vertebrate phospholipase D6. Nuc and PLD6 belong to the phospholipase D (PLD) superfamily. They contain a short conserved sequence motif, the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), which characterizes the PLD superfamily and is essential for catalysis. Nuc and PLD6 utilize a two-step mechanism to cleave phosphodiester bonds: Upon substrate binding, the bond is first attacked by a histidine residue from one HKD motif to form a covalent phosphohistidine intermediate, which is then hydrolyzed by water with the aid of a second histidine residue from the other HKD motif in the opposite subunit. However, proteins in this subfamily have two HKD motifs in a single polypeptide chain. 144 matched cddid_all.tbl CDD cd09173 cd09173 197270 PLDc_Nuc_like_unchar1_2 Putative catalytic domain, repeat 2, of uncharacterized hypothetical proteins similar to Nuc, an endonuclease from Salmonella typhimurium. Putative catalytic domain, repeat 2, of uncharacterized hypothetical proteins, which show high sequence homology to the endonuclease from Salmonella typhimurium and vertebrate phospholipase D6. Nuc and PLD6 belong to the phospholipase D (PLD) superfamily. They contain a short conserved sequence motif, the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), which characterizes the PLD superfamily and is essential for catalysis. Nuc and PLD6 utilize a two-step mechanism to cleave phosphodiester bonds: Upon substrate binding, the bond is first attacked by a histidine residue from one HKD motif to form a covalent phosphohistidine intermediate, which is then hydrolyzed by water with the aid of a second histidine residue from the other HKD motif in the opposite subunit. However, proteins in this subfamily have two HKD motifs in a single polypeptide chain. 159 matched cddid_all.tbl CDD cd09174 cd09174 197271 PLDc_Nuc_like_unchar2 Putative catalytic domain of uncharacterized hypothetical proteins closely related to Nuc, , an endonuclease from Salmonella typhimurium. Putative catalytic domain of uncharacterized hypothetical proteins, which show high sequence homology to the endonuclease from Salmonella typhimurium and vertebrate phospholipase D6. Nuc and PLD6 belong to the phospholipase D (PLD) superfamily. They contain a short conserved sequence motif, the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), which characterizes the PLD superfamily and is essential for catalysis. Nuc and PLD6 utilize a two-step mechanism to cleave phosphodiester bonds: Upon substrate binding, the bond is first attacked by a histidine residue from one HKD motif to form a covalent phosphohistidine intermediate, which is then hydrolyzed by water with the aid of a second histidine residue from the other HKD motif in the opposite subunit. However, proteins in this subfamily have two HKD motifs in a single polypeptide chain. 136 matched cddid_all.tbl CDD cd09175 cd09175 197272 PLDc_Bfil Catalytic domain of type IIs restriction endonuclease BfiI and similar proteins. Catalytic domain of a novel type IIs restriction endonuclease BfiI and similar proteins. Type II restriction endonucleases are components of restriction modification (RM) systems that protect bacteria and archaea against invading foreign DNA. They usually function as homodimers or homotetramers that cleave DNA at defined sites of 4 to 8 bp in length, and they require Mg2+, not ATP or GTP, for catalysis. Unlike all other restriction enzymes known to date, BfiI is unique in cleaving DNA at fixed positions downstream of an asymmetric sequence in the absence of Mg2+. BfiI consists of two discrete domains with distinct functions: an N-terminal catalytic domain with non-specific nuclease activity and dimerization function that is more closely related to Nuc, an EDTA-resistant nuclease from the phospholipase D (PLD) superfamily; and a C-terminal domain that specifically recognizes its target sequences, 5'-ACTGGG-3'. BfiI presumably evolved through domain fusion of a DNA recognition domain to the catalytic Nuc-like domain from the PLD superfamily. Most PLD enzymes have two copies of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in a single polypeptide chain and both are required for catalytic activity. However, BfiI contains only one HKD motif per protein chain and forms a functionally active homodimer which has two DNA-binding surfaces located at the C-terminal domains but only one active site, located at the dimer interface between the two N-terminal catalytic domains that contain the two HKD motifs from both subunits. BfiI utilizes a single active site to cut both DNA strands, which represents a novel mechanism for the scission of double-stranded DNA. It uses a histidine residue from the HKD motif in one subunit as the nucleophile for the cleavage of the target phosphodiester bond in both of the anti-parallel DNA strands, while the symmetrically-related histidine residue from the HKD motif of the opposite subunit acts as the proton donor/acceptor during both strand-scission events. 161 matched cddid_all.tbl CDD cd09176 cd09176 197273 PLDc_unchar6 Putative catalytic domain of uncharacterized hypothetical proteins with one or two copies of the HKD motif. Putative catalytic domain of uncharacterized hypothetical proteins with similarity to phospholipase D (PLD, EC 3.1.4.4). PLD enzymes hydrolyze phospholipid phosphodiester bonds to yield phosphatidic acid and a free polar head group. They can also catalyze transphosphatidylation of phospholipids to acceptor alcohols. Members of this subfamily contain one or two copies of the HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) that characterizes the PLD superfamily. 114 matched cddid_all.tbl CDD cd09177 cd09177 197274 PLDc_RE_NgoFVII Putative catalytic domain of type II restriction enzyme NgoFVII and similar proteins. Putative catalytic domain of type II restriction enzyme NgoFVII (EC 3.1.21.4), which shows high sequence similarity to type IIs restriction endonuclease BfiI. Type II restriction endonucleases are components of restriction modification (RM) systems that protect bacteria and archaea against invading foreign DNA. They usually function as homodimers or homotetramers that cleave DNA at defined sites of 4 to 8 bp in length, and they require Mg2+, not ATP or GTP, for catalysis. The prototype of this subfamily is the NgoFVII restriction endonuclease from Neisseria gonorrhoeae. It plays an essential role in the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. It recognizes the double-stranded sequence GCSGC and cleaves after G-4. Members of this subfamily contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) per protein chain and have been classified into the phospholipase D (PLD, EC 3.1.4.4) superfamily. 143 matched cddid_all.tbl CDD cd09178 cd09178 197275 PLDc_N_Snf2_like N-terminal putative catalytic domain of uncharacterized HKD family nucleases fused to putative helicases from the Snf2-like family. N-terminal putative catalytic domain of uncharacterized archaeal and prokaryotic HKD family nucleases fused to putative helicases from the Snf2-like family, which belong to the DNA/RNA helicase superfamily II (SF2). Although Snf2-like family enzymes do not possess helicase activity, they contain a helicase-like region, where seven helicase-related sequence motifs are found, similar to those in DEAD/DEAH box helicases, which represent the biggest family within the SF2 superfamily. In addition to the helicase-like region, members of this family also contain an N-terminal putative catalytic domain with one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), and have been classified as members of the phospholipase D (PLD, EC 3.1.4.4) superfamily. 134 matched cddid_all.tbl CDD cd09179 cd09179 197276 PLDc_N_DEXD_a N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a DEAD/DEAH box helicase domain), include the DNA/RNA helicase superfamily II (SF2) and Res-subunit of type III restriction endonucleases. In addition to the helicase-like region, members of this subfamily also contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in the N-terminal putative catalytic domain. The HKD motif characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. 190 matched cddid_all.tbl CDD cd09180 cd09180 197277 PLDc_N_DEXD_b N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a DEAD/DEAH box helicase domain), include the DNA/RNA helicase superfamily II (SF2) and Res-subunit of type III restriction endonucleases. In addition to the helicase-like region, members of this subfamily also contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in the N-terminal putative catalytic domain. The HKD motif characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. A few family members contain additional domains, like a C-terminal peptidase S24-like domain. 142 matched cddid_all.tbl CDD cd09181 cd09181 197278 PLDc_FAM83A_N N-terminal phospholipase D-like domain of the uncharacterized protein, Family with sequence similarity 83A. N-terminal phospholipase D (PLD)-like domain of the uncharacterized protein, Family with sequence similarity 83A (FAM83A), also known as tumor antigen BJ-TSA-9. FAM83A or BJ-TSA-9 is a novel tumor-specific gene highly expressed in human lung adenocarcinoma. Due to this specific expression pattern, it may serve as a biomarker for lung cancer, especially in the early detection of micrometastasis for lung adenocarcinoma patients. Since the N-terminal PLD-like domain of FAM83 proteins shows only trace similarity to the PLD catalytic domain and lacks the functionally important histidine residue, FAM83 proteins may share a similar three-dimensional fold with PLD enzymes, but are most unlikely to carry PLD activity. 276 matched cddid_all.tbl CDD cd09182 cd09182 197279 PLDc_FAM83B_N N-terminal phospholipase D-like domain of the uncharacterized protein, Family with sequence similarity 83B. N-terminal phospholipase D (PLD)-like domain of the uncharacterized protein, Family with sequence similarity 83B (FAM83B). Since the N-terminal PLD-like domain of FAM83 proteins shows only trace similarity to the PLD catalytic domain and lacks the functionally important histidine residue, FAM83 proteins may share a similar three-dimensional fold with PLD enzymes, but are most unlikely to carry PLD activity. The N-terminus of FAM83B shows high homology to other FAM83 family members, indicating that FAM83B might have arisen early in vertebrate evolution by duplication of a gene in the FAM83 family. 266 matched cddid_all.tbl CDD cd09183 cd09183 197280 PLDc_FAM83C_N N-terminal phospholipase D-like domain of the uncharacterized protein, Family with sequence similarity 83C. N-terminal phospholipase D (PLD)-like domain of the uncharacterized protein, Family with sequence similarity 83C (FAM83C). Since the N-terminal PLD-like domain of FAM83 proteins shows only trace similarity to the PLD catalytic domain and lacks the functionally important histidine residue, FAM83 proteins may share a similar three-dimensional fold with PLD enzymes, but are most unlikely to carry PLD activity. The N-terminus of FAM83C shows high homology to other FAM83 family members, indicating that FAM83C might have arisen early in vertebrate evolution by duplication of a gene in the FAM83 family. 274 matched cddid_all.tbl CDD cd09184 cd09184 197281 PLDc_FAM83D_N N-terminal phospholipase D-like domain of the protein, Family with sequence similarity 83D. N-terminal phospholipase D (PLD)-like domain of the protein Family with sequence similarity 83D (FAM83D), also known as spindle protein CHICA. CHICA is a cell-cycle-regulated spindle component, which localizes to the mitotic spindle and is both upregulated and phosphorylated during mitosis. CHICA is required to localize the chromokinesin Kid to the mitotic spindle and serves as a novel interaction partner of Kid, which is required for the generation of polar ejection forces and chromosome congression. Since the N-terminal PLD-like domain of FAM83D shows only trace similarity to the PLD catalytic domain and lacks the functionally important histidine residue, FAM83D may share a similar three-dimensional fold with PLD enzymes, but is unlikely to carry PLD activity. 271 matched cddid_all.tbl CDD cd09186 cd09186 197282 PLDc_FAM83F_N N-terminal phospholipase D-like domain of the uncharacterized protein, Family with sequence similarity 83F. N-terminal phospholipase D (PLD)-like domain of the uncharacterized protein, Family with sequence similarity 83F (FAM83F). Since the N-terminal PLD-like domain of FAM83 proteins shows only trace similarity to the PLD catalytic domain and lacks the functionally important histidine residue, FAM83 proteins may share a similar three-dimensional fold with PLD enzymes, but are most unlikely to carry PLD activity. The N-terminus of FAM83F shows high homology to other FAM83 family members, indicating that FAM83F might have arisen early in vertebrate evolution by duplication of a gene in the FAM83 family. 268 matched cddid_all.tbl CDD cd09187 cd09187 197283 PLDc_FAM83G_N N-terminal phospholipase D-like domain of the uncharacterized protein Family with sequence similarity 83G. N-terminal phospholipase D (PLD)-like domain of the uncharacterized protein, Family with sequence similarity 83G (FAM83G). Since the N-terminal PLD-like domain of FAM83 proteins shows only trace similarity to the PLD catalytic domain and lacks the functionally important histidine residue, FAM83 proteins may share a similar three-dimensional fold with PLD enzymes, but are most unlikely to carry PLD activity. The N-terminus of FAM83G shows high homology to other FAM83 family members, indicating that FAM83G might have arisen early in vertebrate evolution by duplication of a gene in the FAM83 family. 275 matched cddid_all.tbl CDD cd09188 cd09188 197284 PLDc_FAM83H_N N-terminal phospholipase D-like domain of the uncharacterized protein, Family with sequence similarity 83H. N-terminal phospholipase D (PLD)-like domain of the protein, Family with sequence similarity 83H (FAM83H) on chromosome 8q24.3, which localizes in the intracellular environment and is associated with vesicles, can be regulated by kinases, and plays important roles during ameloblast differentiation and enamel matrix calcification. The gene encoding protein FAM83H is the first gene involved in the etiology of amelogenesis imperfecta (AI), that encodes a non-secreted protein due to the absence of a signal peptide. Defects in gene FAM83H cause autosomal dominant hypocalcified amelogenesis imperfecta (ADHCAI). Since the N-terminal PLD-like domain of FAM83H shows only trace similarity to the PLD catalytic domain and lacks the functionally important histidine residue, FAM83H may share a similar three-dimensional fold with PLD enzymes, but is most unlikely to carry PLD activity. 265 matched cddid_all.tbl CDD cd09189 cd09189 197285 PLDc_DNaseII_alpha_1 Catalytic domain, repeat 1, of Deoxyribonuclease II alpha and similar proteins. Catalytic domain, repeat 1, of Deoxyribonuclease II alpha (DNase II alpha, EC 3.1.22.1) and similar proteins. DNase II is a monomeric nuclease that contains two copies of a variant HKD motif, where the aspartic acid residue is not conserved. The HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. The catalytic center of DNase II is formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way. Members of this family are mainly found in metazoans, and vertebrate proteins have been further classified into DNase II alpha and beta. DNase II alpha is an acidic endonuclease found in lysosomes, nuclei, and various secretions. It plays a critical role in the degradation of nuclear DNA expelled from erythroid precursor cells, as well as in the degradation of the apoptotic DNA after macrophages engulf them. It cleaves double-stranded DNA to short 3'-phosphoryl oligonucleotides, rather than 3'-hydroxyl groups, and functions optimally at acidic pH in the absence of divalent metal ion cofactors. 162 matched cddid_all.tbl CDD cd09190 cd09190 197286 PLDc_DNaseII_beta_1 Catalytic domain, repeat 1, of Deoxyribonuclease II beta and similar proteins. Catalytic domain, repeat 1, of Deoxyribonuclease II beta (DNase II beta, EC 3.1.22.1), also known as DNase II-like acid DNase (DLAD), and similar proteins. DNase II is a monomeric nuclease that contains two copies of a variant HKD motif, where the aspartic acid residue is not conserved. The HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. The catalytic center of DNase II is formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way. Members of this family are mainly found in metazoans, and vertebrate proteins have been further classified into DNase II alpha and beta. DNase II beta, or DLAD, is a novel mammalian divalent cation-independent endonuclease with homology to DNase II alpha. It is highly expressed in the eye lens and in salivary glands and is responsible for the degradation of nuclear DNA during lens cell differentiation. DLAD mainly exists as a cytoplasmic protein and cleaves DNA to produce 3'-phosphoryl/5'-hydroxyl ends. Like DNase II alpha, DLAD is active under acidic conditions with maximum activity at pH 5.2. Aurintricarboxylic acid and Zn2+ are effective inhibitors of DLAD activity. Mice deficient in DLAD develop cataracts as they are unable to degrade DNA during differentiation of the lens cells. 165 matched cddid_all.tbl CDD cd09191 cd09191 197287 PLDc_DNaseII_alpha_2 Catalytic domain, repeat 2, of Deoxyribonuclease II alpha and similar proteins. Catalytic domain, repeat 2, of Deoxyribonuclease II alpha (DNase II alpha, EC 3.1.22.1) and similar proteins. DNase II is a monomeric nuclease that contains two copies of a variant HKD motif, where the aspartic acid residue is not conserved. The HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. The catalytic center of DNase II is formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way. Members of this family are mainly found in metazoans, and vertebrate proteins have been further classified into DNase II alpha and beta. DNase II alpha is an acidic endonuclease found in lysosomes, nuclei, and various secretions. It plays a critical role in the degradation of nuclear DNA expelled from erythroid precursor cells, as well as in the degradation of the apoptotic DNA after macrophages engulf them. It cleaves double-stranded DNA to short 3'-phosphoryl oligonucleotides, rather than 3'-hydroxyl groups, and functions optimally at acidic pH in the absence of divalent metal ion cofactors. 137 matched cddid_all.tbl CDD cd09192 cd09192 197288 PLDc_DNaseII_beta_2 Catalytic domain, repeat 2, of Deoxyribonuclease II beta and similar proteins. Catalytic domain, repeat 2, of Deoxyribonuclease II beta (DNase II beta, EC 3.1.22.1), also known as DNase II-like acid DNase (DLAD), and similar proteins. DNase II is a monomeric nuclease that contains two copies of a variant HKD motif, where the aspartic acid residue is not conserved. The HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. The catalytic center of DNase II is formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way. Members of this family are mainly found in metazoans, and vertebrate proteins have been further classified into DNase II alpha and beta. DNase II beta, or DLAD, is a novel mammalian divalent cation-independent endonuclease with homology to DNase II alpha. It is highly expressed in the eye lens and in salivary glands and is responsible for the degradation of nuclear DNA during lens cell differentiation. DLAD mainly exists as a cytoplasmic protein and cleaves DNA to produce 3'-phosphoryl/5'-hydroxyl ends. Like DNase II alpha, DLAD is active under acidic conditions with maximum activity at pH 5.2. Aurintricarboxylic acid and Zn2+ are effective inhibitors of DLAD activity. Mice deficient in DLAD develop cataracts as they are unable to degrade DNA during differentiation of the lens cells. 139 matched cddid_all.tbl CDD cd09193 cd09193 197289 PLDc_mTdp1_1 Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase. Catalytic domain, repeat 1, of metazoan tyrosyl-DNA phosphodiesterase (Tdp1, EC 3.1.4.-). Human Tdp1 (hTdp1) acts as an important DNA repair enzyme with a preference for single-stranded or blunt-ended duplex oligonucleotides. It can remove stalled topoisomerase I-DNA complexes by catalyzing the hydrolysis of a phosphodiester bond between a tyrosine side chain and a DNA 3'-phosphate. It is therefore a potential molecular target for new anti-cancer drugs. hTdp1 has been shown to associate with additional proteins, such as XRCC1, to form a multi-enzyme complex. These additional proteins may be involved in recognizing 3'-phoshotyrosyl DNA in vivo. hTdp1 is a monomeric protein containing two copies of a variant HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), which consists of the highly conserved histidine and lysine residues, but lacks the aspartate residue that is well conserved in other phospholipase D (PLD, EC 3.1.4.4) enzymes. Like other PLD enzymes, hTdp1 may utilize a common two-step general acid/base catalytic mechanism, involving a DNA-enzyme intermediate to cleave phosphodiester bonds. A single active site involved in phosphatidyl group transfer would be formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way. 169 matched cddid_all.tbl CDD cd09194 cd09194 197290 PLDc_yTdp1_1 Catalytic domain, repeat 1, of yeast tyrosyl-DNA phosphodiesterase. Catalytic domain, repeat 1, of yeast tyrosyl-DNA phosphodiesterase (yTdp1, EC 3.1.4.-). yTdp1 is involved in the repair of topoisomerase I DNA lesions by hydrolyzing the topoisomerase from the 3'-end of the DNA during double-strand break repair. Unlike human Tdp1 whose substrate-binding pocket can accommodate a fairly large topoisomerase I peptide fragment, yTdp1 has a preference for substrates containing one to four amino acid residues. The monomeric yTdp1 contains two copies of a variant HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), which consists of the highly conserved histidine and lysine residues, but lacks the aspartate residue that is well conserved in other phospholipase D (PLD, EC 3.1.4.4) enzymes. Like other PLD enzymes, yTdp1 may utilize a common two-step general acid/base catalytic mechanism, involving a DNA-enzyme intermediate to cleave phosphodiester bonds. A single active site involved in phosphatidyl group transfer would be formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way. 166 matched cddid_all.tbl CDD cd09195 cd09195 197291 PLDc_mTdp1_2 Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase. Catalytic domain, repeat 2, of metazoan tyrosyl-DNA phosphodiesterase (Tdp1, EC 3.1.4.-). Human Tdp1 (hTdp1) acts as an important DNA repair enzyme with a preference for single-stranded or blunt-ended duplex oligonucleotides. It can remove stalled topoisomerase I-DNA complexes by catalyzing the hydrolysis of a phosphodiester bond between a tyrosine side chain and a DNA 3'-phosphate. It is therefore a potential molecular target for new anti-cancer drugs. hTdp1 has been shown to associate with additional proteins, such as XRCC1, to form a multi-enzyme complex. These additional proteins may be involved in recognizing 3'-phoshotyrosyl DNA in vivo. hTdp1 is a monomeric protein containing two copies of a variant HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), which consists of the highly conserved histidine and lysine residues, but lacks the aspartate residue that is well conserved in other phospholipase D (PLD, EC 3.1.4.4) enzymes. Like other PLD enzymes, hTdp1 may utilize a common two-step general acid/base catalytic mechanism, involving a DNA-enzyme intermediate to cleave phosphodiester bonds. A single active site involved in phosphatidyl group transfer would be formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way. 191 matched cddid_all.tbl CDD cd09196 cd09196 197292 PLDc_yTdp1_2 Catalytic domain, repeat 2, of yeast tyrosyl-DNA phosphodiesterase. Catalytic domain, repeat 2, of yeast tyrosyl-DNA phosphodiesterase (yTdp1, EC 3.1.4.-). yTdp1 is involved in the repair of topoisomerase I DNA lesions by hydrolyzing the topoisomerase from the 3'-end of the DNA during double-strand break repair. Unlike human Tdp1 whose substrate-binding pocket can accommodate a fairly large topoisomerase I peptide fragment, yTdp1 has a preference for substrates containing one to four amino acid residues. The monomeric yTdp1 contains two copies of a variant HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue), which consists of the highly conserved histidine and lysine residues, but lacks the aspartate residue that is well conserved in other phospholipase D (PLD, EC 3.1.4.4) enzymes. Like other PLD enzymes, yTdp1 may utilize a common two-step general acid/base catalytic mechanism, involving a DNA-enzyme intermediate to cleave phosphodiester bonds. A single active site involved in phosphatidyl group transfer would be formed by the two variant HKD motifs from the N- and C-terminal domains in a pseudodimeric way. 200 matched cddid_all.tbl CDD cd09197 cd09197 197293 PLDc_pPLDalpha_1 Catalytic domain, repeat 1, of plant alpha-type phospholipase D. Catalytic domain, repeat 1, of plant alpha-type phospholipase D (PLDalpha, EC 3.1.4.4). Plant PLDalpha is a phosphatidylinositol 4,5-bisphosphate (PIP2)-independent PLD that possesses a regulatory calcium-dependent phospholipid-binding C2 domain in the N-terminus and require millimolar calcium for optimal activity. The C2 domain is unique to plant PLDs and is not present in animal or fungal PLDs. Like other PLD enzymes, the monomer of plant PLDalpha consists of two catalytic domains, each of which contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from two domains form a single active site. Plant PLDalpha may utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. 178 matched cddid_all.tbl CDD cd09198 cd09198 197294 PLDc_pPLDbeta_1 Catalytic domain, repeat 1, of plant beta-type phospholipase D. Catalytic domain, repeat 1, of plant beta-type phospholipase D (PLDbeta, EC 3.1.4.4). Plant PLDbeta is a phosphatidylinositol 4,5-bisphosphate (PIP2)-dependent PLD that possesses a regulatory calcium-dependent phospholipid-binding C2 domain in the N-terminus and requires nanomolar calcium and cytosolic factors for optimal activity. The C2 domain is unique to plant PLDs and is not present in animal or fungal PLDs. Sequence analysis shows that plant PLDbeta is evolutionarily divergent from alpha-type plant PLD, and plant PLDbeta is more closely related to mammalian and yeast PLDs than to plant PLDalpha. Like other PLD enzymes, the monomer of plant PLDbeta consists of two catalytic domains, each of which contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from two domains form a single active site. Plant PLDbeta may utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. 180 matched cddid_all.tbl CDD cd09199 cd09199 197295 PLDc_pPLDalpha_2 Catalytic domain, repeat 2, of plant alpha-type phospholipase D. Catalytic domain, repeat 2, of plant alpha-type phospholipase D (PLDalpha, EC 3.1.4.4). Plant PLDalpha is a phosphatidylinositol 4,5-bisphosphate (PIP2)-independent PLD that possesses a regulatory calcium-dependent phospholipid-binding C2 domain in the N-terminus and require millimolar calcium for optimal activity. The C2 domain is unique to plant PLDs and is not present in animal or fungal PLDs. Like other PLD enzymes, the monomer of plant PLDalpha consists of two catalytic domains, each of which contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from two domains form a single active site. Plant PLDalpha may utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. 211 matched cddid_all.tbl CDD cd09200 cd09200 197296 PLDc_pPLDbeta_2 Catalytic domain, repeat 2, of plant beta-type phospholipase D. Catalytic domain, repeat 2, of plant beta-type phospholipase D (PLDbeta, EC 3.1.4.4). Plant PLDbeta is a phosphatidylinositol 4,5-bisphosphate (PIP2)-dependent PLD that possesses a regulatory calcium-dependent phospholipid-binding C2 domain in the N-terminus and requires nanomolar calcium and cytosolic factors for optimal activity. The C2 domain is unique to plant PLDs and is not present in animal or fungal PLDs. Sequence analysis shows that plant PLDbeta is evolutionarily divergent from alpha-type plant PLD, and plant PLDbeta is more closely related to mammalian and yeast PLDs than to plant PLDalpha. Like other PLD enzymes, the monomer of plant PLDbeta consists of two catalytic domains, each of which contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from two domains form a single active site. Plant PLDbeta may utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. 211 matched cddid_all.tbl CDD cd09203 cd09203 197297 PLDc_N_DEXD_b1 N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a DEAD/DEAH box helicase domain), include the DNA/RNA helicase superfamily II (SF2) and Res-subunit of type III restriction endonucleases. In addition to the helicase-like region, members of this subfamily also contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in the N-terminal putative catalytic domain. The HKD motif characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. 143 matched cddid_all.tbl CDD cd09204 cd09204 197298 PLDc_N_DEXD_b2 N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a DEAD/DEAH box helicase domain), include the DNA/RNA helicase superfamily II (SF2) and Res-subunit of type III restriction endonucleases. In addition to the helicase-like region, members of this subfamily also contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in the N-terminal putative catalytic domain. The HKD motif characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. 139 matched cddid_all.tbl CDD cd09205 cd09205 197299 PLDc_N_DEXD_b3 N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a DEAD/DEAH box helicase domain), include the DNA/RNA helicase superfamily II (SF2) and Res-subunit of type III restriction endonucleases. In addition to the helicase-like region, members of this subfamily also contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in the N-terminal putative catalytic domain. The HKD motif characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. A few family members contain additional domains, like a C-terminal peptidase S24-like domain. 143 matched cddid_all.tbl CDD cd09208 cd09208 187741 Lumazine_synthase-II lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-II. Type-II LS also known as RibH2, catalyzes the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. LS catalyses the formation of 6,7-dimethyl-8-ribityllumazine by the condensation of 5-amino-6-ribitylamino- 2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy- 2-butanone-4-phosphate. Subsequently, the lumazine intermediate dismutates yielding riboflavin and 5-amino-6-ribitylamino- 2,4(1H,3H)-pyrimidinedione, in a reaction catalyzed by riboflavin synthase (RS); RS belongs to a different family of the Lumazine-synthase-like superfamily. Riboflavin is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which are essential cofactors for the catalysis of a wide range of redox reactions. These cofactors are also involved in many other processes involving DNA repair, circadian time-keeping, light sensing, and bioluminescence. Riboflavin is biosynthesized in plants, fungi and certain microorganisms; as animals lack the necessary enzymes to produce this vitamin, they acquire it from dietary sources. Type II LSs are distinct from type-I LS not only in protein sequence, but in that they exhibit different quaternary assemblies; type-II LSs form decamers (dimers of pentamers). The pathogen Brucella spp. have both a type-I LS and a type-II LS called RibH1 and RibH2, respectively. RibH1/type-I LS appears to be a functional LS in Brucella spp., whereas RibH2/type-II LS has much lower catalytic activity as LS and may be regulated by a riboswitch that senses FMN, suggesting that the type-II LSs may have evolved into very poor catalysts or, that they may harbor a new, as-yet-unknown function. 137 matched cddid_all.tbl CDD cd09209 cd09209 187742 Lumazine_synthase-I lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS), catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2); type-I. Type-I LS, also known as RibH1, catalyzes the penultimate step in the biosynthesis of riboflavin in plants and microorganisms. LS catalyse the formation of 6,7-dimethyl-8-ribityllumazine by the condensation of 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy- 2-butanone-4-phosphate. Subsequently, the lumazine intermediate dismutates to yield riboflavin and 5-amino-6-ribitylamino- 2,4(1H,3H)-pyrimidinedione, in a reaction catalyzed by riboflavin synthase synthase (RS); RS belongs to a different family of the Lumazine-synthase-like superfamily. Riboflavin is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which are essential cofactors for the catalysis of a wide range of redox reactions. These cofactors are also involved in many other processes involving DNA repair, circadian time-keeping, light sensing, and bioluminescence. Riboflavin is biosynthesized in plants, fungi and certain microorganisms; as animals lack the necessary enzymes to produce this vitamin, they acquire it from dietary sources. Type II LSs are distinct from type-I LS not only in protein sequence, but in that they exhibit different quaternary assemblies; type-I LSs form pentamers. The pathogen Brucella spp. encode both a Type-I LS and a Type-II LS called RibH1 and RibH2, respectively. RibH1/type-I LS appears to be the functional LS in Brucella spp., whereas RibH2/type-II LS has much lower catalytic activity as LS. The pathogen Brucella spp. have both a type-I LS and a type-II LS called RibH1 and RibH2, respectively. RibH1/type-I LS appears to be a functional LS in Brucella spp., whereas RibH2/type-II LS has much lower catalytic activity as LS. 133 matched cddid_all.tbl CDD cd09210 cd09210 187743 Riboflavin_synthase_archaeal archaeal riboflavin synthase (RS); involved in the biosynthesis pathway of riboflavin (vitamin B2). Archaeal RSs are homopentamers catalyzing the formation of riboflavin from 6,7-dimethyl-8-ribityllumazine in riboflavin biosynthesis. Divalent metal ions, preferably manganese or magnesium, are needed for maximum activity. Riboflavin serves as the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), essential cofactors for several oxidoreductases that are indispensable in most living cells. In the final steps of the riboflavin biosynthetic pathway, lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS) catalyzes the condensation of the 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy- 2-butanone-4-phosphate to release water, inorganic phosphate and 6,7-dimethyl-8-ribityllumazine (DMRL), followed by RS which catalyzes a dismutation of DMRL yielding riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. In the latter reaction, a four-carbon moiety is transferred between two DMRL molecules serving as donor and acceptor, respectively. Both the LS and RS catalyzed reactions are thermodynamically irreversible and can proceed in the absence of a catalyst. Archaeal RSs share sequence similarity with LSs, both appear to have diverged early in the evolution of archaea from a common ancestor. 143 matched cddid_all.tbl CDD cd09211 cd09211 187744 Lumazine_synthase_archaeal lumazine synthase (6,7-dimethyl-8-ribityllumazine synthase, LS); catalyzes the penultimate step in the biosynthesis of riboflavin (vitamin B2). Archaeal LS is an important enzyme in the riboflavin biosynthetic pathway. Riboflavin is the precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) which are essential cofactors for the catalysis of a wide range of redox reactions. These cofactors are also involved in many other processes involving DNA repair, circadian time-keeping, light sensing, and bioluminescence. In the final steps of the riboflavin biosynthetic pathway LS catalyzes the condensation of the 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione with 3,4-dihydroxy- 2-butanone-4-phosphate to release water, inorganic phosphate and 6,7-dimethyl-8-ribityllumazine (DMRL), and riboflavin synthase (RS) catalyzes a dismutation of DMRL which yields riboflavin and 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione. In the latter reaction, a four-carbon moiety is transferred between two DMRL molecules serving as donor and acceptor, respectively. Both the LS and RS catalyzed reactions are thermodynamically irreversible and can proceed in the absence of a catalyst. LS from Methanococcus jannaschii forms capsids with icosahedral 532 symmetry consisting of 60 subunits. Archaeal LSs share sequence similarity with archaeal RSs, both appear to have diverged early in the evolution of archaea from a common ancestor. 131 matched cddid_all.tbl CDD cd09212 cd09212 198416 PUB PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins. The PUB domain is found in p97 adaptor proteins such as PNGase, UBXD1 (UBX domain-containing protein 1), and RNF31 (RING finger protein 31). It functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The p97, a type II AAA+ ATPase, is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The PUB domain in UBX-domain protein 1 (UBXD1), which is widely expressed in higher eukaryotes (except for fungi) and which is involved in substrate recruitment to p97, interacts strongly with the C-terminus of p97. Peptide:N-glycanase (PNGase), a deglycosylating enzyme that functions in proteasome-dependent degradation of misfolded glycoproteins which are translocated from the endoplasmic reticulum (ER) to the cytosol during ERAD, associates with the ubiquitin-proteasome system proteins mediated by the N-terminal PUB domain. PNGase is present in all eukaryotic organisms; however, the yeast PNGase ortholog does not contain the PUB domain. The RNF31 protein, also known as HOIP or Zibra, contains an N-terminal PUB domain similar to those in PNGase and UBXD1, suggesting its association with p97. 96 matched cddid_all.tbl CDD cd09213 cd09213 188873 Luminal_IRE1_like The Luminal domain, a dimerization domain, of Inositol-requiring protein 1-like proteins. The Luminal domain is a dimerization domain present in Inositol-requiring protein 1 (IRE1), eukaryotic translation Initiation Factor 2-Alpha Kinase 3 (EIF2AK3), and similar proteins. IRE1 and EIF2AK3 are serine/threonine protein kinases (STKs) and are type I transmembrane proteins that are localized in the endoplasmic reticulum (ER). They are kinase receptors that are activated through the release of BiP, a chaperone bound to their luminal domains under unstressed conditions. This results in dimerization through their luminal domains, allowing trans-autophosphorylation of their kinase domains and activation. They play roles in the signaling of the unfolded protein response (UPR), which is activated when protein misfolding is detected in the ER in order to decrease the synthesis of new proteins and increase the capacity of the ER to cope with the stress. IRE1, also called Endoplasmic reticulum (ER)-to-nucleus signaling protein (or ERN), contains an endoribonuclease domain in its cytoplasmic side and acts as an ER stress sensor. It is the oldest and most conserved component of the UPR in eukaryotes. Its activation results in the cleavage of its mRNA substrate, HAC1 in yeast and Xbp1 in metazoans, promoting a splicing event that enables translation into a transcription factor which activates the UPR. EIF2AK3, also called PKR-like Endoplasmic Reticulum Kinase (PERK), phosphorylates the alpha subunit of eIF-2, resulting in the downregulation of protein synthesis. It functions as the central regulator of translational control during the UPR pathway. In addition to the eIF-2 alpha subunit, EIF2AK3 also phosphorylates Nrf2, a leucine zipper transcription factor which regulates cellular redox status and promotes cell survival during the UPR. 312 matched cddid_all.tbl CDD cd09214 cd09214 185753 GH64-like glycosyl hydrolase 64 family. This family is represented by the laminaripentaose-producing, beta-1,3-glucanase (LPHase) of Streptomyces matensis and related bacterial and ascomycete proteins. LPHase is a member of glycoside hydrolase family 64 (GH64), it is an inverting enzyme involved in the cleavage of long-chain polysaccharide beta-1,3-glucans, into specific pentasaccharide oligomers. LPHase is a two-domain crescent fold structure: one domain is composed of 10 beta-strands, eight coming from the N-terminus of the protein and two from the C-terminal region, and the protein has a second inserted domain; this cd includes both domains. This protein has an electronegative, substrate-binding cleft, and conserved Glu and Asp residues involved in the cleavage of the beta-1,3-glucan, laminarin, a plant and fungal cell wall component. Among bacteria, many beta-1,3-glucanases are implicated in fungal cell wall degradation. Also included in this family is GluB , the beta-1,3-glucanase B from Lysobacter enzymogenes Strain N4-7. Recombinant GluB demonstrated higher relative activity toward the branched-chain beta-1,3 glucan substrate zymosan A than toward linear beta-1,3 glucan substrates. Sometimes these two domains are found associated with other domains such as in the Catenulispora acidiphila DSM 44928 carbohydrate binding family 6 protein in which they are positioned N-terminal of a carbohydrate binding module, family 6 (CBM_6) domain. In the Cellulosimicrobium cellulans, glucan endo-1,3-beta-glucosidase, they are positioned N-terminal of a RICIN, carbohydrate-binding domain, and in the Salinispora tropica CNB-440, coagulation factor 5/8 C-terminal domain (FA58C) protein, they are positioned C-terminal of two FA58C domains which are proposed to function as cell surface-attached, carbohydrate-binding domain. This FA58C-containing protein has an internal peptide deletion (of approx. 44 residues) in the LPHase domain II. 319 matched cddid_all.tbl CDD cd09215 cd09215 185754 Thaumatin-like the sweet-tasting protein, thaumatin, and thaumatin-like proteins involved in host defense. This family is represented by the sweet-tasting protein thaumatin from the African berry Thaumatococcus daniellii and thaumatin-like proteins (TLPs) involved in host defense and a wide range of developmental processes in fungi, plants, and animals. Plant TLPs are classified as pathogenesis-related (PR) protein family 5 (PR5), their expression is induced by environmental stresses such as pathogen/pest attack, drought and cold. TLPs included in this family are such proteins as zeamatin, found in high concentrations in cereal seeds; osmotin, a salt-induced protein in osmotically stressed plants; and PpAZ44, a propylene-induced TLP in abscission of young fruit. Several members of the plant TLP family have been reported as food allergens from fruits (i.e., cherry, Pru av 2; bell pepper, Cap a1; tomatoes, Lyc e NP24) and pollen allergens from conifers (i.e., mountain cedar, Jun a 3; Arizona cypress, Cup a3; Japanese cedar, Cry j3). Thaumatin and TLPs are three-domain, crescent-fold structures with either an electronegative, electropositive, or neutral cleft occurring between domains I and II. It has been proposed that the antifungal activity of plant PR5 proteins relies on the strong electronegative character of this cleft. Some TLPs hydrolyze the beta-1,3-glucans of the type commonly found in fungal walls. Most TLPs contain 16 conserved Cys residues. A deletion within the third domain (domain II) of the Triticum aestivum thaumatin-like xylanase inhibitor is observed, thus, only 10 conserved Cys residues are present within this smaller TLP and similar homologs. 157 matched cddid_all.tbl CDD cd09216 cd09216 185755 GH64-LPHase-like glycoside hydrolase family 64: laminaripentaose-producing, beta-1,3-glucanase (LPHase)-like. This subfamily is represented by the laminaripentaose-producing, beta-1,3-glucanase (LPHase) of Streptomyces matensis and related bacterial and ascomycete proteins. LPHase is a member of glycoside hydrolase family 64 (GH64), it is an inverting enzyme involved in the cleavage of long-chain polysaccharide beta-1,3-glucans, into specific pentasaccharide oligomers. LPHase is a two-domain crescent fold structure: one domain is composed of 10 beta-strands, eight coming from the N-terminus of the protein and two from the C-terminal region, and the protein has a second inserted domain; this cd includes both domains. This protein has an electronegative, substrate-binding cleft, and conserved Glu and Asp residues involved in the cleavage of the beta-1,3-glucan, laminarin, a plant and fungal cell wall component. Among bacteria, many beta-1,3-glucanases are implicated in fungal cell wall degradation. Also included in this family is GluB , the beta-1,3-glucanase B from Lysobacter enzymogenes Strain N4-7. Recombinant GluB demonstrated higher relative activity toward the branched-chain beta-1,3 glucan substrate zymosan A than toward linear beta-1,3 glucan substrates. Sometimes these two domains are found associated with other domains such as in the Catenulispora acidiphila DSM 44928 carbohydrate binding family 6 protein in which they are positioned N-terminal of a carbohydrate binding module, family 6 (CBM_6) domain. In the Cellulosimicrobium cellulans, glucan endo-1,3-beta-glucosidase, they are positioned N-terminal of a RICIN, carbohydrate-binding domain. 353 matched cddid_all.tbl CDD cd09217 cd09217 185756 TLP-P thaumatin and allergenic/antifungal thaumatin-like proteins: plant homologs. This subfamily is represented by the sweet-tasting protein thaumatin from the African berry Thaumatococcus daniellii, allergenic/antifungal Thaumatin-like proteins (TLPs), and related plant proteins. TLPs are involved in host defense and a wide range of developmental processes in fungi, plants, and animals. Plant TLPs are classified as pathogenesis-related (PR) protein family 5 (PR5), their expression is induced by environmental stresses such as pathogen/pest attack, drought and cold. TLPs in this subfamily include such proteins as zeamatin, found in high concentrations in cereal seeds, and osmotin, a salt-induced protein in osmotically stressed plants. Several members of the plant TLP family have been reported as food allergens from fruits (i.e., cherry, Pru av 2; bell pepper, Cap a1; tomatoes, Lyc e NP24) and pollen allergens from conifers (i.e., mountain cedar, Jun a 3; Arizona cypress, Cup a3; Japanese cedar, Cry j3). Thaumatin and TLPs are three-domain, crescent-fold structures with either an electronegative, electropositive, or neutral cleft occurring between domains I and II. It has been proposed that the antifungal activity of plant PR5 proteins relies on the strong electronegative character of this cleft. IgE-binding epitopes of mountain Cedar (Juniperus ashei) allergen Jun a 3, which interact with pooled IgE from patients suffering allergenic response to this allergen, were mainly located on the helical domain II; the best-conserved IgE-binding epitope predicted for TLPs corresponds to this region. Some TLPs hydrolyze the beta-1,3-glucans of the type commonly found in fungal walls. Most TLPs contain 16 conserved Cys residues. A deletion within the third domain (domain II) of the Triticum aestivum thaumatin-like xylanase inhibitor is observed, thus, only 10 conserved Cys residues are present within this smaller TLP and similar homologs. 151 matched cddid_all.tbl CDD cd09218 cd09218 185757 TLP-PA allergenic/antifungal thaumatin-like proteins: plant and animal homologs. This subfamily is represented by the thaumatin-like proteins (TLPs), Cherry Allergen Pru Av 2 TLP, Peach PpAZ44 TLP (a propylene-induced TLP in abscission), the Caenorhabditis elegans thaumatin family member (thn-6), and other plant and animal homologs. TLPs are involved in host defense and a wide range of developmental processes in fungi, plants, and animals. Due to their inducible expression by environmental stresses such as pathogen/pest attack, drought and cold, plant TLPs are classified as the pathogenesis-related (PR) protein family 5 (PR5). Several members of the plant TLP family have been reported as food allergens from fruits (i.e., cherry, Pru av 2; bell pepper, Cap a1; tomatoes, Lyc e NP24) and pollen allergens from conifers (i.e., mountain cedar, Jun a 3; Arizona cypress, Cup a3; Japanese cedar, Cry j3). TLPs are three-domain, crescent-fold structures with either an electronegative, electropositive, or neutral cleft occurring between domains I and II. It has been proposed that the antifungal activity of plant PR5 proteins relies on the strong electronegative character of this cleft. Some TLPs hydrolyze the beta-1,3-glucans of the type commonly found in fungal walls. TLPs within this subfamily contain 16 conserved Cys residues. 219 matched cddid_all.tbl CDD cd09219 cd09219 185758 TLP-F thaumatin-like proteins: basidiomycete homologs. This subfamily is represented by Lentinula edodes TLG1, a thaumatin-like protein (TLP), as well as, other basidiomycete homologs. In general, TLPs are involved in host defense and a wide range of developmental processes in fungi, plants, and animals. TLG1 TLP is involved in lentinan degradation and fruiting body senescence. TLG1 expressed in Escherichia coli and Aspergillus oryzae exhibited beta-1,3-glucanase activity and demonstrated lentinan degrading activity. TLG1 is proposed to be involved in lentinan and cell wall degradation during senescence following harvest and spore diffusion. TLPs are three-domain, crescent-fold structures with either an electronegative, electropositive, or neutral cleft occurring between domains I and II. TLG1 from Lentinula edodes contains the required acidic amino acids conserved in the appropriate positions to possess an electronegative cleft. TLPs within this subfamily contain 13 conserved Cys residues; the number of total Cys residues in these TLPs varies from 16 in L. edodes TLG1 to 18 in other basidiomycete homologs. 229 matched cddid_all.tbl CDD cd09220 cd09220 185759 GH64-GluB-like glycoside hydrolase family 64: beta-1,3-glucanase B (GluB)-like. This subfamily is represented by GluB, beta-1,3-glucanase B , from Lysobacter enzymogenes Strain N4-7 and related bacterial and ascomycete proteins. GluB is a member of the glycoside hydrolase family 64 (GH64) involved in the cleavage of long-chain polysaccharide beta-1,3-glucans, into specific pentasaccharide oligomers. Among bacteria, many beta-1,3-glucanases are implicated in fungal cell wall degradation. GluB possesses the conserved Glu and Asp residues required to cleave substrate beta-1,3-glucans. Recombinant GluB demonstrated higher relative activity toward the branched-chain beta-1,3 glucan substrate zymosan A than toward linear beta-1,3 glucan substrates. Based on the structure of laminaripentaose-producing, beta-1,3-glucanase (LPHase) of Streptomyces matensis, which belongs to the same family as GluB but to a different subfamily, this cd is a two-domain model. Sometimes these two domains are found associated with other domains such as in the Catenulispora acidiphila DSM 44928 carbohydrate binding family 6 protein in which they are positioned N-terminal of a carbohydrate binding module, family 6 (CBM_6) domain. 369 matched cddid_all.tbl CDD cd09223 cd09223 187745 Photo_RC D1, D2 subunits of photosystem II (PSII); M, L subunits of bacterial photosynthetic reaction center. This protein superfamily contains the D1, D2 subunits of the photosystem II (PS II) and the M, L subunits of the bacterial photosynthetic reaction center (RC). These four proteins are highly homologous and share a common fold. PS II is a multi-subunit protein found in the photosynthetic membranes of plants, algae, and cyanobacteria. It utilizes light-induced electron transfer and water-splitting reactions to produce protons, electrons, and molecular oxygen. The protons generated are instrumental in ATP formation. Bacterial photosynthetic reaction center (RC) complex is found in photosynthetic bacteria, such as purple bacteria and other proteobacteria species. It couples light-induced electron transfer to proton pumping across the membrane by reactions of a quinone molecule (QB) that binds two electrons and two protons at the active site. Protons are translocated from the bacterial cytoplasm to the periplasmic space, generating an electrochemical gradient of protons (the protonmotive force) that can be used to power reactions such as the synthesis of ATP. 199 matched cddid_all.tbl CDD cd09224 cd09224 198423 CytoC_RC Cytochrome C subunit of the bacterial photosynthetic reaction center. Photosynthesis in purple bacteria is dependent on light-induced electron transfer in the reaction center (RC), coupled to the uptake of protons from the cytoplasm. The RC contains a cytochrome molecule which re-reduces the oxidized electron donor. The electron transfer reactions of photosynthesis are performed by the following three components: the photosynthetic reaction center (RC), the cytochrome, and the soluble electron carrier protein. Firstly, the RC promotes the light-induced charge separation across the plasma membrane, which results in the oxidation of a pair of light-harvesting complexes, LH1 and LH2, and the reduction of quinone to quinol. The quinol then leaves the RC and moves to the cytochrome complex through the quinone pool of the plasma membrane. Secondly, the cytochrome complex reoxidizes the quinol to quinone, and the released electrons are transferred to soluble electron carriers. Third, the soluble electron carriers transport the electrons to the RC through the periplasmic space. Finally, the photo-oxidized light-harvesting complex is reduced by the soluble electron carriers, and the RC comes back to the initial state. In the course of the oxidation and reduction of the quinones, a transmembrane electrochemical gradient of protons is formed, and its energy is used to produce ATP by the ATP synthase complex. 300 matched cddid_all.tbl CDD cd09232 cd09232 185717 Snurportin-1_C C-terminal m3G cap-binding domain of nuclear import adaptor snurportin-1. Snurportin-1 (SPN1 or SNUPN) is a nuclear import adaptor for m3G-capped spliceosomal U small nucleoproteins (snRNPs), which are assembled in the cytoplasm. After capping and assembly, the U snRNPs are transported into the nucleus by SPN1 and importin beta; SPN1 is then returned to the cytoplasm by exportin 1 (CRM1), which also transports the non-capped U snRNPs. The U snRNPs are essential elements of the spliceosome, which catalyzes the excision of introns and the ligation of exons to form a mature mRNA. SPN1 contains two domains, an N-terminal importin beta-binding (IBB) domain and a C-terminal m3G cap-binding domain. 186 matched cddid_all.tbl CDD cd09233 cd09233 187750 ACE1-Sec16-like Ancestral coatomer element 1 (ACE1) of COPII coat complex assembly protein Sec16. COPII coat complex plays an important role in vesicular traffic of newly synthezised proteins from the endoplasmatic reticulum (ER) to the Golgi apparatus by mediating the formation of transport vesicles. COPII consists of an outer coat, made up of the scaffold proteins Sec31 and Sec13, and the cargo adaptor complex, Sec23 and Sec24, which are recruited by the small GTPase Sar1. Sec16 is involved in the early steps of the assembly process. Sec16 forms elongated heterotetramers with Sec13, Sec13-(Sec16)2-Sec13. It interacts with Sec13 by insertion of a single beta-blade to close the six-bladded beta propeller of Sec13. In the same way Sec13 interacts with Sec31 and Nup145C, a nuclear pore protein, all of these contain a structurally related ancestral coatomer element 1 (ACE1). Sec16 is believed to be a key component in maintaining the integrity of the ER exit site. 314 matched cddid_all.tbl CDD cd09234 cd09234 185747 V_HD-PTP_like Protein-interacting V-domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains. This family contains the V-shaped (V) domain of mammalian His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23) and related domains. It belongs to the V_Alix_like superfamily which includes the V domains of Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X/ also known as apoptosis-linked gene-2 interacting protein 1, AIP1), and related domains. HD_PTP interacts with the ESCRT (Endosomal Sorting Complexes Required for Transport) system, and participates in cell migration and endosomal trafficking. The related Alix V-domain (belonging to a different family in this superfamily) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. The Alix V-domain is also a dimerization domain. In addition to the V-domain, HD_PTP also has an N-terminal Bro1-like domain, a proline-rich region (PRR), a catalytically inactive tyrosine phosphatase domain, and a region containing a PEST motif. Bro1-like domains bind components of the ESCRT-III complex, specifically to CHMP4 in the case of HD-PTP. The Bro1-like domain of HD-PTP can also bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. HD-PTP is encoded by the PTPN23 gene, a tumor suppressor gene candidate frequently absent in human kidney, breast, lung, and cervical tumors. This family also contains Drosophila Myopic, which promotes epidermal growth factor receptor (EGFR) signaling, and Caenorhabditis elegans (enhancer of glp-1) EGO-2 which promotes Notch signaling. 337 matched cddid_all.tbl CDD cd09235 cd09235 185748 V_Alix Middle V-domain of mammalian Alix and related domains are dimerization and protein interaction modules. This family contains the middle V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X) and related domains. It belongs to the V_Alix_like superfamily which includes the V-domains of Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, mammalian His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), is part of the ESCRT (Endosomal Sorting Complexes Required for Transport) system, and participates in membrane remodeling processes, including the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), the abscission reactions of mammalian cell division, and in apoptosis. The Alix V-domain is a dimerization domain, and contains a binding site, partially conserved in the V_Alix_like superfamily, for the retroviral late assembly (L) domain YPXnL motif. In addition to the V-domain, Alix also has an N-terminal Bro1-like domain, which binds components of the ESCRT-III complex, in particular CHMP4. The Bro1-like domain of Alix can also bind to human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Alix also has a C-terminal proline-rich region (PRR) that binds multiple partners including Tsg101 (tumor susceptibility gene 101, a component of ESCRT-1), and the apoptotic protein ALG-2. 339 matched cddid_all.tbl CDD cd09236 cd09236 185749 V_AnPalA_UmRIM20_like Protein-interacting V-domains of Aspergillus nidulans PalA/RIM20, Ustilago maydis RIM20, and related proteins. This family belongs to the V_Alix_like superfamily which includes the V-shaped (V) domains of Bro1 and Rim20 from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Aspergillus nidulas PalA/RIM20 and Ustilago maydis RIM20, like Saccharomyces cerevisiae Rim20, participate in the response to the external pH via the Pal/Rim101 pathway; however, Saccharomyces cerevisiae Rim20 does not belong to this family. This pathway is a signaling cascade resulting in the activation of the transcription factor PacC/Rim101. The mammalian Alix V-domain (belonging to a different family) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. Aspergillus nidulas PalA binds a nonviral YPXnL motif (tandem YPXL/I motifs within PacC). The Alix V-domain is also a dimerization domain. In addition to this V-domain, members of the V_Alix_like superfamily also have an N-terminal Bro1-like domain, which has been shown to bind CHMP4/Snf7, a component of the ESCRT-III complex. 353 matched cddid_all.tbl CDD cd09237 cd09237 185750 V_ScBro1_like Protein-interacting V-domain of Saccharomyces cerevisiae Bro1 and related domains. This family contains the V-shaped (V) domain of Saccharomyces cerevisiae Bro1, and related domains. It belongs to the V_Alix_like superfamily which also includes the V-domain of Saccharomyces cerevisiae Rim20 (also known as PalA), mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Bro1 interacts with the ESCRT (Endosomal Sorting Complexes Required for Transport) system, and participates in endosomal trafficking. The mammalian Alix V-domain (belonging to a different family) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. The Alix V-domain is also a dimerization domain. Bro1 also has an N-terminal Bro1-like domain, which binds Snf7, a component of the ESCRT-III complex, and a C-terminal proline-rich region (PRR). The C-terminal portion (V-domain and PRR) of S. cerevisiae Bro1 interacts with Doa4, a ubiquitin thiolesterase needed to remove ubiquitin from MVB cargoes. It interacts with a YPxL motif in the Doa4s catalytic domain to stimulate its deubiquitination activity. 356 matched cddid_all.tbl CDD cd09238 cd09238 185751 V_Alix_like_1 Protein-interacting V-domain of an uncharacterized family of the V_Alix_like superfamily. This domain family is comprised of uncharacterized plant proteins. It belongs to the V_Alix_like superfamily which includes the V-shaped (V) domains of Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, mammalian Alix (apoptosis-linked gene-2 interacting protein X), (His-Domain) type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP functions in cell migration and endosomal trafficking, Bro1 in endosomal trafficking, and Rim20 in the response to the external pH via the Rim101 pathway. Alix, HD-PTP, Bro1, and Rim20 all interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. The mammalian Alix V-domain (belonging to a different family) contains a binding site, partially conserved in the superfamily, for the retroviral late assembly (L) domain YPXnL motif. The Alix V-domain is also a dimerization domain. In addition to this V-domain, members of the V_Alix_Rim20_Bro1_like superfamily also have an N-terminal Bro1-like domain, which binds components of the ESCRT-III complex. The Bro1-like domains of Alix and HD-PTP can also bind to human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Many members of the V_Alix_like superfamily also have a proline-rich region (PRR). 339 matched cddid_all.tbl CDD cd09239 cd09239 185762 BRO1_HD-PTP_like Protein-interacting, N-terminal, Bro1-like domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains. This family contains the N-terminal, Bro1-like domain of mammalian His-Domain type N23 protein tyrosine phosphatase (HD-PTP) and related domains. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), HD-PTP, Brox, Bro1, Rim20, and Rim23, interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. HD-PTP participates in cell migration and endosomal trafficking. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. Bro1-like domains bind components of the ESCRT-III complex: CHMP4 in the case of HD-PTP. The Bro1-like domain of HD-PTP can also bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. HD-PTP, and some other members of the BRO1_Alix_like superfamily including Alix, also have a V-shaped (V) domain. In the case of Alix, the V-domain contains a binding site for the retroviral late assembly (L) domain YPXnL motif, which is partially conserved in the V-domain superfamily. HD-PTP is encoded by the PTPN23 gene, a tumor suppressor gene candidate frequently absent in human kidney, breast, lung, and cervical tumors. This family also contains Drosophila Myopic which promotes epidermal growth factor receptor (EGFR) signaling, and Caenorhabditis elegans (enhancer of glp-1) EGO-2 which promotes Notch signaling. 361 matched cddid_all.tbl CDD cd09240 cd09240 185763 BRO1_Alix Protein-interacting, N-terminal, Bro1-like domain of mammalian Alix and related domains. This family contains the N-terminal, Bro1-like domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), also called apoptosis-linked gene-2 interacting protein 1 (AIP1). It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Alix, HD-PTP, Brox, Bro1, Rim20, and Rim23, interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. Bro1-like domains bind components of the ESCRT-III complex: CHMP4, in the case of Alix. The Alix Bro1-like domain can also bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid and Rab5-specfic GAP (RabGAP5, also known as Rab-GAPLP). In addition to this Bro1-like domain, Alix has a middle V-shaped (V) domain. The Alix V-domain is a dimerization domain, and carries a binding site for the retroviral late assembly (L) domain YPXnL motif, which is partially conserved in the superfamily. Alix also has a C-terminal proline-rich region (PRR) that binds multiple partners including Tsg101 (tumor susceptibility gene 101, a component of ESCRT-1) and the apoptotic protein ALG-2. 346 matched cddid_all.tbl CDD cd09241 cd09241 185764 BRO1_ScRim20-like Protein-interacting, N-terminal, Bro1-like domain of Saccharomyces cerevisiae Rim20 and related proteins. This family contains the N-terminal, Bro1-like domain of Saccharomyces cerevisiae Rim20 (also known as PalA) and related proteins. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Brox, Saccharomyces cerevisiae Bro1, Ustilago maydis Rim23 (also known as PalC), and related domains. Alix, HD-PTP, Brox, Bro1, Rim20, and Rim23, interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Rim20 and Rim23 participate in the response to the external pH via the Rim101 pathway. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. Bro1-like domains bind components of the ESCRT-III complex: Snf7 in the case of Rim20. RIM20, and some other members of the BRO1_Alix_like superfamily including Alix, also have a V-shaped (V) domain. In the case of Alix, the V-domain is a dimerization domain that also contains a binding site for the retroviral late assembly (L) domain YPXnL motif, which is partially conserved in the V-domain superfamily. Rim20 localizes to endosomes under alkaline pH conditions. By binding Snf7, it may bring the protease Rim13 (a YPxL-containing transcription factor) into proximity with Rim101, and thus aid in the proteolytic activation of the latter. Rim20 and other intermediates in the Rim101 pathway play roles in the pathogenesis of fungal corneal infection during Candida albicans keratitis. 355 matched cddid_all.tbl CDD cd09242 cd09242 185765 BRO1_ScBro1_like Protein-interacting, N-terminal, Bro1-like domain of Saccharomyces cerevisiae Bro1 and related proteins. This family contains the N-terminal, Bro1-like domain of Saccharomyces cerevisiae Bro1 and related proteins. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Brox, Saccharomyces cerevisiae Rim20 (also known as PalA), Ustilago maydis Rim23 (also known as PalC), and related domains. Alix, HD-PTP, Brox, Bro1, Rim20, and Rim23, interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Bro1 participates in endosomal trafficking. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. Bro1-like domains bind components of the ESCRT-III complex: Snf7 in the case of Bro1. Snf7 binds to a conserved hydrophobic patch on the middle of the concave side of the Bro1 domain. RIM20, and some other members of the BRO1_Alix_like superfamily including Alix, also have a V-shaped (V) domain. In the case of Alix, the V-domain contains a binding site for the retroviral late assembly (L) domain YPXnL motif, which is partially conserved in the superfamily. The Alix V-domain is also a dimerization domain. The C-terminal portion (V-domain and proline rich-region) of Bro1 interacts with Doa4, a protease that deubiquitinates integral membrane proteins sorted into the lumenal vesicles of late-endosomal multivesicular bodies. It interacts with a YPxL motif in the Doa4 catalytic domain to stimulate its deubiquitination activity. 348 matched cddid_all.tbl CDD cd09243 cd09243 185766 BRO1_Brox_like Protein-interacting Bro1-like domain of human Brox1 and related proteins. This family contains the Bro1-like domain of a single-domain protein, human Brox, and related domains. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Alix, HD-PTP, Brox, Bro1, Rim20, and Rim23, interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. Bro1-like domains bind components of the ESCRT-III complex: CHMP4 in the case of Brox. Human Brox can bind to human immunodeficiency virus type 1 (HIV-1) nucleocapsid. In addition to a Bro1-like domain, Brox also has a C-terminal thioester-linkage site for isoprenoid lipids (CaaX motif). This family lacks the V-shaped (V) domain found in many members of the BRO1_Alix_like superfamily. 353 matched cddid_all.tbl CDD cd09244 cd09244 185767 BRO1_Rhophilin Protein-interacting Bro1-like domain of RhoA-binding protein Rhophilin and related domains. This family contains the Bro1-like domain of RhoA-binding proteins, Rhophilin-1 and -2, and related domains. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Rhophilin-1 and -2 bind both GDP- and GTP-bound RhoA. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. In addition to this Bro1-like domain, Rhophilin-1 and -2, contain an N-terminal Rho-binding domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1) domain. Their PDZ domains have limited homology. Rhophilin-1 and -2 have different activities. The Drosophila knockout of Rhophilin-1 is embryonic lethal, suggesting an essential role in embryonic development. Roles of Rhophilin-2 may include limiting stress fiber formation or increasing the turnover of F-actin in the absence of high levels of RhoA signaling activity. The isolated Bro1-like domain of Rhophilin-1 binds human immunodeficiency virus type 1 (HIV-1) nucleocapsid. This family lacks the V-shaped (V) domain found in many members of the BRO1_Alix _like superfamily. 350 matched cddid_all.tbl CDD cd09245 cd09245 185768 BRO1_UmRIM23-like Protein-interacting, Bro1-like domain of Ustilago maydis Rim23 (PalC), and related domains. This family contains the Bro1-like domain of Ustilago maydis Rim23 (also known as PalC), and related proteins. It belongs to the BRO1_Alix_like superfamily which includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, and related domains. Alix, HD-PTP, Brox, Bro1, Rim20, and Rim23 interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Rim20 and Rim23 participate in the response to the external pH via the Rim101 pathway. Through its Bro1-like domain, Rim23 allows the interaction between the endosomal and plasma membrane complexes. Bro1-like domains are boomerang-shape, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. Intermediates in the Rim101 pathway may play roles in the pathogenesis of fungal corneal infection during Candida albicans keratitis. This family lacks the V-shaped (V) domain found in many members of the BRO1_Alix_like superfamily. 413 matched cddid_all.tbl CDD cd09246 cd09246 185769 BRO1_Alix_like_1 Protein-interacting, N-terminal, Bro1-like domain of an Uncharacterized family of the BRO1_Alix_like superfamily. This domain family is comprised of uncharacterized proteins. It belongs to the BRO1_Alix_like superfamily which includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Alix, HD-PTP, Brox, Bro1, Rim20 and Rim23 interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP and Bro1 function in endosomal trafficking, with HD-PTP having additional functions in cell migration. Rim20 and Rim23 play roles in the response to the external pH via the Rim101 pathway. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. Bro1-like domains bind components of the ESCRT-III complex: CHMP4 (in the case of Alix, Brox and HD-PTP) and Snf7 (in the case of yeast Bro1 and Rim20). The Bro1-like domains of Alix, HD-PTP, Brox, and Rhophilin can bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. In addition to this Bro1-like domain, Alix, Bro1, Rim20, HD_PTP, and proteins belonging to this uncharacterized family, also have a V-shaped (V) domain. The Alix V-domain is a dimerization domain, and contains a binding site for the retroviral late assembly (L) domain YPXnL motif, which is partially conserved in the BRO1_Alix_like superfamily. Many members of this superfamily also have a proline-rich region (PRR), a protein interaction domain. 353 matched cddid_all.tbl CDD cd09247 cd09247 185770 BRO1_Alix_like_2 Protein-interacting Bro1-like domain of an Uncharacterized family of the BRO1_Alix_like superfamily. This domain family is comprised of uncharacterized proteins. It belongs to the BRO1_Alix_like superfamily which includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Alix, HD-PTP, Brox, Bro1, Rim20 and Rim23 interact with the ESCRT (Endosomal Sorting Complexes Required for Transport) system. Alix participates in membrane remodeling processes during the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), and the abscission reactions of mammalian cell division. It also functions in apoptosis. HD-PTP and Bro1 function in endosomal trafficking, with HD-PTP having additional functions in cell migration. Rim20 and Rim23 play roles in the response to the external pH via the Rim101 pathway. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. These domains bind components of the ESCRT-III complex: CHMP4 (in the case of Alix, Brox and HD-PTP) and Snf7 (in the case of yeast Bro1 and Rim20). The Bro1-like domains of Alix, HD-PTP, Brox, and Rhophilin can bind human immunodeficiency virus type 1 (HIV-1) nucleocapsid. This family lacks the V-shaped (V) domain found in many members of the BRO1_Alix_like superfamily. 346 matched cddid_all.tbl CDD cd09248 cd09248 185771 BRO1_Rhophilin_1 Protein-interacting Bro1-like domain of RhoA-binding protein Rhophilin-1. This subfamily contains the Bro1-like domain of the RhoA-binding protein, Rhophilin-1. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domains of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding protein Rhophilin-2, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Rhophilin-1 binds both GDP- and GTP-bound RhoA. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. In addition to this Bro1-like domain, Rhophilin-1 contains an N-terminal Rho-binding domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1) domain. The Drosophila knockout of the Rhophilin-1 is embryonic lethal, suggesting an essential role in embryonic development. The isolated Bro1-like domain of Rhophilin-1 binds human immunodeficiency virus type 1 (HIV-1) nucleocapsid. Rhophilin-1 lacks the V-shaped (V) domain found in many members of the BRO1_Alix_ like superfamily. 384 matched cddid_all.tbl CDD cd09249 cd09249 185772 BRO1_Rhophilin_2 Protein-interacting Bro1-like domain of RhoA-binding protein Rhophilin-2. This subfamily contains the Bro1-like domain of RhoA-binding protein, Rhophilin-2. It belongs to the BRO1_Alix_like superfamily which also includes the Bro1-like domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X), His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), RhoA-binding protein Rhophilin-1, Brox, Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, Ustilago maydis Rim23 (also known as PalC), and related domains. Rhophilin-2, binds both GDP- and GTP-bound RhoA. Bro1-like domains are boomerang-shaped, and part of the domain is a tetratricopeptide repeat (TPR)-like structure. In addition to this Bro1-like domain, Rhophilin-2 contains an N-terminal Rho-binding domain and a C-terminal PDZ (PS.D.-95, Disc-large, ZO-1) domain. Roles for Rhophilin-2 may include limiting stress fiber formation or increasing the turnover of F-actin in the absence of high levels of RhoA signaling activity. Rhophilin-2 lacks the V-shaped (V) domain found in many members of the BRO1_Alix_like superfamily. 385 matched cddid_all.tbl CDD cd09250 cd09250 271158 AP-1_Mu1_Cterm C-terminal domain of medium Mu1 subunit in clathrin-associated adaptor protein (AP) complex AP-1. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This family corresponds to the C-terminal domain of heterotetrameric clathrin-associated adaptor protein complex 1 (AP-1) medium mu1 subunit, which includes two closely related homologs, mu1A (encoded by ap1m1) and mu1B (encoded by ap1m2). Mu1A is ubiquitously expressed, but mu1B is expressed exclusively in polarized epithelial cells. AP-1 has been implicated in bi-directional transport between the trans-Golgi network (TGN) and endosomes. It plays an essential role in the formation of clathrin-coated vesicles (CCVs) from the trans-Golgi network (TGN). Epithelial cell-specific AP-1 is also involved in sorting to the basolateral surface of polarized epithelial cells. Recruitment of AP-1 to the TGN membrane is regulated by a small GTPase, ADP-ribosylation factor 1 (ARF1). Phosphorylation/dephosphorylation events can also regulate the function of AP-1. The membrane-anchored cargo molecules can be linked to the outer lattice of CCVs by AP-1. Those cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-1 mu1 subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. 272 matched cddid_all.tbl CDD cd09251 cd09251 271159 AP-2_Mu2_Cterm C-terminal domain of medium Mu2 subunit in ubiquitously expressed clathrin-associated adaptor protein (AP) complex AP-2. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, -2, -3, and -4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This family corresponds to the C-terminal domain of heterotetrameric clathrin-associated adaptor protein complex 2 (AP-2) medium mu2 subunit. Mu2 is ubiquitously expressed in mammals. In higher eukaryotes, AP-2 plays a critical role in clathrin-mediated endocytosis from the plasma membrane in different cells. The membrane-anchored cargo molecules can be linked to the outer lattice of CCVs by AP-2. Those cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-2 mu2 subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. Since the Y-X-X-Phi binding site is buried in the core structure of AP-2, a phosphorylation induced conformational change is required when the cargo molecules binds to AP-2. In addition, the C-terminal domain of mu2 subunit has been shown to bind other molecules. For instance, it can bind phosphoinositides, in particular PI[4,5]P2, which might be involved in the recognition process of the tyrosine-based signals. It can also interact with synaptotagmins, a family of important modulators of calcium-dependent neurosecretion within the synaptic vesicle (SV) membrane. Since many of the other endocytic adaptors responsible for biogenesis of synaptic vesicles exist, in the absence of AP-2, clathrin-mediated endocytosis can still occur. However, the cells may not survive in the complete absence of clathrin as well as AP-2. 263 matched cddid_all.tbl CDD cd09252 cd09252 271160 AP-3_Mu3_Cterm C-terminal domain of medium Mu3 subunit in adaptor protein (AP) complex AP-3. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This family corresponds to the C-terminal domain of heterotetrameric adaptor protein complex 3 (AP-3) medium mu3 subunit, which includes two closely related homologs, mu3A (P47A, encoded by ap3m1) and mu1B (P47B, encoded by ap3m2). Mu3A is ubiquitously expressed, but mu3B is specifically expressed in neurons and neuroendocrine cells. AP-3 is particularly important for targeting integral membrane proteins to lysosomes and lysome-related organelles at trans-Golgi network (TGN) and/or endosomes, such as the yeast vacuole, fly pigment granules and mammalian melanosomes, platelet dense bodies and the secretory lysosomes of cytotoxic T lymphocytes. Unlike AP-1 and AP-2, which function in conjunction with clathrin which is a scaffolding protein participating in the formation of coated vesicles, the nature of the outer shell of AP-3 containing coats remains to be elucidated. Membrane-anchored cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-3 mu3 subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. 251 matched cddid_all.tbl CDD cd09253 cd09253 271161 AP-4_Mu4_Cterm C-terminal domain of medium Mu4 subunit in adaptor protein (AP) complex AP-4. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This family corresponds to the C-terminal domain of heterotetrameric adaptor protein complex 4 (AP-4) medium mu4 subunit. AP-4 plays a role in signal-mediated trafficking of integral membrane proteins in mammalian cells. Unlike other AP complexes, AP-4 is found only in mammals and plants. It is believed to be part of a nonclathrin coat, since it might function independently of clathrin, a scaffolding protein participating in the formation of coated vesicles. Recruitment of AP-4 to the trans-Golgi network (TGN) membrane is regulated by a small GTPase, ADP-ribosylation factor 1 (ARF1) or a related protein. Membrane-anchored cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. One of the most important sorting signals binding to mu subunits of AP complexes are tyrosine-based endocytotic signals, which are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. However, AP-4 does not bind most canonical tyrosine-based signals except for two naturally occurring ones from the lysosomal membrane proteins CD63 and LAMP-2a. It binds YX [FYL][FL]E motif, where X can be any residue, from the cytosolic tails of amyloid precursor protein (APP) family members in a distinct way. 271 matched cddid_all.tbl CDD cd09254 cd09254 271162 AP_delta-COPI_MHD Mu homology domain (MHD) of adaptor protein (AP) coat protein I (COPI) delta subunit. COPI complex-coated vesicles function in the early secretory pathway. They mediate the retrograde transport from the Golgi to the ER, and intra-Golgi transport. COPI complex-coated vesicles consist of a small GTPase, ADP-ribosylation factor 1 (ARF1) and a heteroheptameric coatomer composed of two subcomplexes, F-COPI and B-COPI. ARF1 regulates COPI vesicle formation by recruiting the coatomer onto Golgi membranes to initiate its coat function. Coatomer complexes then bind cargo molecules and self-assemble to form spherical cages that yield COPI-coated vesicles. The heterotetrameric F-COPI subcomplex contains beta-, gamma-, delta-, and zeta-COP subunits, where beta- and gamma-COP subunits are related to the large AP subunits, and delta- and zeta-COP subunits are related to the medium and small AP subunits, respectively. Due to the sequence similarity to the AP complexes, the F-COPI subcomplex might play a role in the cargo-binding. The heterotrimeric B-COPI contains alpha-, beta-, and epsilon-COP subunits, which are not related to the adaptins. This subcomplex is thought to participate in the cage-forming and might serve a function similar to that of clathrin. This family corresponds to the mu homology domain of delta-subunit of COPI complex (delta-COP), which is distantly related to the C-terminal domain of mu chains among AP complexes. The delta-COP subunit appears tightly associated with the beta-COP subunit to confer its interaction with ARF1. In addition, both delta- and beta-COP subunits contribute to a common binding site for arginine (R)-based signals, which are sorting motifs conferring transient endoplasmic reticulum (ER) localization to unassembled subunits of multimeric membrane proteins. 237 matched cddid_all.tbl CDD cd09255 cd09255 271163 AP-like_stonins_MHD Mu homology domain (MHD) of adaptor-like proteins (AP-like), stonins. A small family of proteins named stonins has been characterized as clathrin-dependent AP-2 mu2 chain related factors, which may act as cargo-specific sorting adaptors in endocytosis. Stonins include stonin 1 and stonin 2, which are only mammalian homologs of Drosophila stoned B, a presynaptic protein implicated in neurotransmission and synaptic vesicle (SV) recycling. They are conserved from C. elegans to humans, but are not found in prokaryotes or yeasts. This family corresponds to the mu homology domain of stonins, which is distantly related to the C-terminal domain of mu chains among AP complexes. Due to the low degree of sequence conservation of the corresponding binding site, the mu homology domain of stonins is unable to recognize tyrosine-based endocytic sorting signals. To data, little is known about the localization and function of stonin 1. Stonin 2, also known as stoned B, acts as an AP-2-dependent synaptotagmin-specific sorting adaptors for SV endocytosis. Stoned A is not a stonin. It is structurally unrelated to the adaptins and does not appear to have mammalian homologs. It is not included in this family. 315 matched cddid_all.tbl CDD cd09256 cd09256 271164 AP_MuD_MHD Mu-homology domain (MHD) of a adaptor protein (AP) encoded by mu-2 related death-inducing gene, MuD (also known as MUDENG). This family corresponds to the MHD found in a protein encoded by MuD (also known as Adapter-related protein complex 5 subunit mu-1), which is distantly related to the C-terminal domain of the mu2 subunit of AP complexes that participates in clathrin-mediated endocytosis. MuD is evolutionary conserved from mammals to amphibians. It is able to induce cell death by itself and plays an important role in cell death in various tissues. 276 matched cddid_all.tbl CDD cd09257 cd09257 271165 AP_muniscins_like_MHD Mu-homology domain (MHD) of muniscins adaptor proteins (AP) and similar proteins. This family corresponds to the MHD found in muniscins, a novel family of endocytic adaptor proteins. The term, muniscins, has been assigned to name the MHD of proteins with both EFC/F-BAR domain and MHD. These two domains are responsible for the membrane-tubulation activity associated with transmembrane cargo proteins. Members in this family include an endocytic adaptor Syp1, the mammalian FCH domain only proteins (FCHo1/2), SH3-containing GRB2-like protein 3-interacting protein 1 (SGIP1), and related uncharacterized proteins. Syp1 is a poorly characterized yeast protein with multiple biological functions. Syp1 contains an N-terminal EFC/F-BAR domain that induces membrane tabulation, a proline-rich domain (PRD) in the middle region, and a C-terminal MHD that can directly binds to the endocytic adaptor/scaffold protein Ede1 or a transmembrane stress sensor cargo protein Mid2. Thus, Syp1 represents a novel type of endocytic adaptor protein that participates in endocytosis, promotes vesicle tabulation, and contributes to cell polarity and stress response. Syp1 shares the same domain architecture with its two ubiquitously expressed mammalian counterparts, the membrane-sculpting F-BAR domain-containing Fer/Cip4 homology domain-only proteins 1 and 2 (FCHo1/2). FCHo1/2 represent key initial proteins ultimately controlling cellular nutrient uptake, receptor regulation, and synaptic vesicle retrieval. They are required for plasma membrane clathrin-coated vesicle (CCV) budding and marked sites of CCV formation. They bind specifically to the plasma membrane and recruit the scaffold proteins eps15 and intersectin, which subsequently engage the adaptor complex AP2 and clathrin, leading to coated vesicle formation. Another mammalian neuronal-specific protein, neuronal-specific transcript Scr homology 3 (SH3)-domain growth factor receptor-bound 2 (GRB2)-like (endophilin) interacting protein 1 [SGIP1] does not contain EFC/F-BAR domain, but does have a PRD and a C-terminal MHD and has been classified into this family as well. SGIP1 is an endophilin-interacting protein that plays an obligatory role in the regulation of energy homeostasis. It is also involved in clathrin-mediated endocytosis by interacting with phospholipids and eps15. 244 matched cddid_all.tbl CDD cd09258 cd09258 271166 AP-1_Mu1A_Cterm C-terminal domain of medium Mu1A subunit in ubiquitously expressed clathrin-associated adaptor protein (AP) complex AP-1. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This subfamily corresponds to the C-terminal domain of heterotetrameric clathrin-associated adaptor protein complex 1 (AP-1) medium mu1A subunit encoded by ap1m1 gene, which is ubiquitously expressed in all mammalian tissues and cells. AP-1 has been implicated in bidirectional transport between the trans-Golgi network (TGN) and endosomes. It is involved in the formation of clathrin-coated vesicles (CCVs) from the trans-Golgi network (TGN). The ubiquitous AP-1 is recruited to the TGN membrane, as well as to immature secretory granules. Recruitment of AP-1 to the TGN membrane is regulated by a small GTPase, ADP-ribosylation factor 1 (ARF1). Phosphorylation/dephosphorylation events can also regulate the function of AP-1. The membrane-anchored cargo molecules can be linked to the outer lattice of CCVs by AP-1. Those cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-1 mu1A subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. 270 matched cddid_all.tbl CDD cd09259 cd09259 271167 AP-1_Mu1B_Cterm C-terminal domain of medium Mu1B subunit in epithelial cell-specific clathrin-associated adaptor protein (AP) complex AP-1. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from different AP complexes exhibits similarity with each other. This subfamily corresponds to the C-terminal domain of heterotetrameric clathrin-associated adaptor protein complex 1 (AP-1) medium mu1B subunit encoded by ap1m2 gene exclusively expressed in polarized epithelial cells. Epithelial cell-specific AP-1 is used to sort proteins to the basolateral plasma membrane, which involves the formation of clathrin-coated vesicles (CCVs) from the trans-Golgi network (TGN). Recruitment of AP-1 to the TGN membrane is regulated by a small GTPase, ADP-ribosylation factor 1 (ARF1). The phosphorylation/dephosphorylation events can also regulate the function of AP-1. The membrane-anchored cargo molecules can be linked to the outer lattice of CCVs by AP-1. Those cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-1 mu1B subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic reside-binding. Besides, AP-1 mu1B subunit mediates the basolateral recycling of low-density lipoprotein receptor (LDLR) and transferrin receptor (TfR) from the sorting endosomes, where the basolateral sorting signal does not belong to the tyrosine-based signals. Thus, the binding site in mu1B subunit of AP-1 for the signals of LDLR and TfR might be distinct from that for YXXPhi signals. 268 matched cddid_all.tbl CDD cd09260 cd09260 211371 AP-3_Mu3A_Cterm C-terminal domain of medium Mu3A subunit in ubiquitously expressed adaptor protein (AP) complex AP-3. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This subfamily corresponds to the C-terminal domain of heterotetrameric adaptor protein complex 3 (AP-3) medium mu3A subunit encoded by ap3m1gene. Mu3A is ubiquitously expressed in all mammalian tissues and cells. It appears to be localized to the trans-Golgi network (TGN) and/or endosomes and participates in trafficking to the vacuole/lysosome in yeast, flies, and mammals. Unlike AP-1 and AP-2, which function in conjunction with clathrin which is a scaffolding protein participating in the formation of coated vesicles, the nature of the outer shell of ubiquitous AP-3 containing coats remains to be elucidated. Membrane-anchored cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-3 mu3A subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. 254 matched cddid_all.tbl CDD cd09261 cd09261 211372 AP-3_Mu3B_Cterm C-terminal domain of medium Mu3B subunit in neuron-specific adaptor protein (AP) complex AP-3. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This subfamily corresponds to the C-terminal domain of heterotetrameric adaptor protein complex 3 (AP-3) medium mu3B subunit encoded by ap3m2 gene. Mu3B is specifically expressed in neurons and neuroendocrine cells. Neuron-specific AP-3 appears to be involved in synaptic vesicle biogenesis from endosomes in neurons and plays an important role in synaptic transmission in the central nervous system. Unlike AP-1 and AP-2, which function in conjunction with clathrin which is a scaffolding protein participating in the formation of coated vesicles, the nature of the outer shell of neuron-specific AP-3 containing coats remains to be elucidated. Membrane-anchored cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-3 mu3B subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. 254 matched cddid_all.tbl CDD cd09262 cd09262 271168 AP_stonin-1_MHD Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-1 (also called Stoned B-like factor). A small family of proteins named stonins has been characterized as clathrin-dependent AP-2 mu2 chain related factors, which may act as cargo-specific sorting adaptors in endocytosis. Stonins include stonin 1 and stonin 2, which are the only mammalian homologs of Drosophila stoned B, a presynaptic protein implicated in neurotransmission and synaptic vesicle (SV) recycling. They are conserved from C. elegans to humans, but are not found in prokaryotes or yeasts. This family corresponds to the mu homology domain of stonin 1, which is distantly related to the C-terminal domain of mu chains among AP complexes. Due to the low degree of sequence conservation of the corresponding binding site, the mu homology domain of stonin-1 is unable to recognize tyrosine-based endocytic sorting signals. To data, little is known about the localization and function of stonin-1. 314 matched cddid_all.tbl CDD cd09263 cd09263 271169 AP_stonin-2_MHD Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-2. A small family of proteins named stonins has been characterized as clathrin-dependent AP-2 mu2 chain related factors, which may act as cargo-specific sorting adaptors in endocytosis. Stonins include stonin 1 and stonin 2, which are the only mammalian homologs of Drosophila stoned B, a presynaptic protein implicated in neurotransmission and synaptic vesicle (SV) recycling. They are conserved from C. elegans to humans, but are not found in prokaryotes or yeasts. This family corresponds to the mu homology domain of stonin 2, which is distantly related to the C-terminal domain of mu chains among AP complexes. Due to the low degree of sequence conservation of the corresponding binding site, the mu homology domain of stonin-2 is unable to recognize tyrosine-based endocytic sorting signals. It acts as an AP-2-dependent synaptotagmin-specific sorting adaptor for SV endocytosis. 318 matched cddid_all.tbl CDD cd09264 cd09264 271170 AP_Syp1_MHD mu-homology domain (MHD) of adaptor protein (AP), Syp1, and related proteins. This family corresponds to the MHD found in a novel endocytic adaptor Syp1 and related proteins. Syp1 is a poorly characterized yeast protein with multiple biological functions. It was originally identified as a suppressor of a yeast profiling deletion and later as a suppressor of arf3delta (Arf3 is the yeast homologue of Arf6, a mammalian regulator of endocytosis). Syp1 can bind to septins and physically link with cell polarity factors. It also directly binds to the endocytic adaptor/scaffold protein Ede1, and plays a role in endocytosis. Further studies show that Syp1 is itself an endocytic adaptor protein contributing to stress responses. Its mu-homology domain at the C-terminus binds to the cargo protein Mid2, a transmembrane stress sensor protein, and mediates Mid2 internalization. In addition, Syp1 contains an EFC/F-BAR domain which can induce membrane tabulation. 257 matched cddid_all.tbl CDD cd09265 cd09265 271171 AP_Syp1_like_MHD Mu-homology domain (MHD) of endocytic adaptor protein (AP), Syp1. This family corresponds to the MHD found in the metazoan counterparts of yeast Syp1, which includes two ubiquitously expressed membrane-sculpting F-BAR domain-containing Fer/Cip4 homology domain-only proteins 1 and 2 (FCH domain only 1 and 2, or FCHo1/FCHo2), neuronal-specific SH3-containing GRB2-like protein 3-interacting protein 1 (SGIP1), and related uncharacterized proteins. FCHo1/FCHo2 represent key initial proteins ultimately controlling cellular nutrient uptake, receptor regulation, and synaptic vesicle retrieval. They are required for plasma membrane clathrin-coated vesicle (CCV) budding and marked sites of CCV formation. They bind specifically to the plasma membrane and recruit the scaffold proteins eps15 and intersectin, which subsequently engage the adaptor complex AP2 and clathrin, leading to coated vesicle formation. Both FCHo1/FCHo2 contain an N-terminal EFC/F-BAR domain that induces membrane tabulation, a proline-rich domain (PRD) in the middle region, and a C-terminal MHD responsible for the binding of eps15 and intersectin. Another mammalian neuronal-specific protein, neuronal-specific transcript Scr homology 3 (SH3)-domain growth factor receptor-bound 2 (GRB2)-like (endophilin) interacting protein 1 [SGIP1] does not contain EFC/F-BAR domain, but does have a PRD and a C-terminal MHD and has been classified into this family as well. SGIP1 is an endophilin-interacting protein that plays an obligatory role in the regulation of energy homeostasis. It is also involved in clathrin-mediated endocytosis by interacting with phospholipids and eps15. 266 matched cddid_all.tbl CDD cd09266 cd09266 271172 SGIP1_MHD mu-homology domain (MHD) of Scr homology 3 (SH3)-domain growth factor receptor-bound 2 (GRB2)-like (endophilin) interacting protein 1 (also known as endophilin-3-interacting protein, SGIP1) and similar proteins. This family corresponds to the MHD found in mammalian neuronal-specific transcript SGIP1 and similar proteins. Unlike other members in this family, SGIP1 does not contain EFC/F-BAR domain, but does have a proline-rich domain (PRD) and a C-terminal MHD. It is an endophilin-interacting protein that plays an obligatory role in the regulation of energy homeostasis, and is also involved in clathrin-mediated endocytosis by interacting with phospholipids and eps15. 267 matched cddid_all.tbl CDD cd09267 cd09267 211378 FCHo2_MHD mu-homology domain (MHD) of F-BAR domain-containing Fer/Cip4 homology domain-only protein 2 (FCH domain only 2 or FCHo2) and similar proteins. This family corresponds to the MHD found in the ubiquitously expressed mammalian membrane-sculpting FCHo2 and similar proteins. FCHo2 represents a key initial protein that ultimately controls cellular nutrient uptake, receptor regulation, and synaptic vesicle retrieval. It is required for plasma membrane clathrin-coated vesicle (CCV) budding and marks sites of CCV formation. It binds specifically to the plasma membrane and recruits the scaffold proteins eps15 and intersectin, which subsequently engages the adaptor complex AP2 and clathrin, leading to coated vesicle formation. FCHo2 contains an N-terminal EFC/F-BAR domain, a proline-rich domain (PRD) in the middle region, and a C-terminal MHD. The crescent-shaped EFC/F-BAR domain can form an antiparallel dimer structure that binds PtdIns(4,5)P2-enriched membranes and can polymerize into rings to generate membrane tubules. The MHD is structurally related to the cargo-binding mu2 subunit of adaptor complex 2 (AP-2) and is responsible for the binding of eps15 and intersectin. 267 matched cddid_all.tbl CDD cd09268 cd09268 271173 FCHo1_MHD mu-homology domain (MHD) of F-BAR domain-containing Fer/Cip4 homology domain-only protein 1 (FCH domain only 1 or FCHo1, also known as KIAA0290) and similar proteins. This family corresponds to the MHD found in ubiquitously expressed mammalian membrane-sculpting FCHo1 and similar proteins. FCHo1 represents a key initial protein that ultimately controls cellular nutrient uptake, receptor regulation, and synaptic vesicle retrieval. It is required for plasma membrane clathrin-coated vesicle (CCV) budding and marks sites of CCV formation. It binds specifically to the plasma membrane and recruits the scaffold proteins eps15 and intersectin, which subsequently engage the adaptor complex AP2 and clathrin, leading to coated vesicle formation. FCHo1 contains an N-terminal EFC/F-BAR domain, a proline-rich domain (PRD) in the middle region, and a C-terminal MHD. The crescent-shaped EFC/F-BAR domain can form an antiparallel dimer structure that binds PtdIns(4,5)P2-enriched membranes and can polymerize into rings to generate membrane tubules. The MHD is structurally related to the cargo-binding mu2 subunit of adaptor complex 2 (AP-2) and is responsible for the binding of eps15 and intersectin. Unlike other F-BAR domain containing proteins, FCHo1 has neither the Src homology 3 (SH3) domain nor any other known domain for interaction with dynamin and actin cytoskeleton. However, it can periodically accumulate at the budding site of clathrin. FCHo1 may utilize a unique action mode for vesicle formation as compared with other F-BAR proteins. 265 matched cddid_all.tbl CDD cd09269 cd09269 185703 deoxyribose_mutarotase deoxyribose mutarotase_like. Salmonella enterica serovar Typhi DeoM (earlier named as DeoX) is a mutarotase with high specificity for deoxyribose. It is encoded by one of four genes beonging to the deoK operon. This operon has also been found in Escherichia coli where it is more common in pathogenic than in commensal strains and is associated with pathogenicity. It has been found on a pathogenicity island from a human blood isolate AL863 and confers the ability to use deoxyribose as a carbon source; deoxyribose is not fermented by non-pathogenic E.coli K-12. Proteins in this family are members of the aldose-1-epimerase superfamily. Aldose 1-epimerases, or mutarotases, are key enzymes of carbohydrate metabolism, catalyzing the interconversion of the alpha- and beta-anomers of hexose sugars such as glucose and galactose. This interconversion is an important step that allows anomer specific metabolic conversion of sugars. Studies of the catalytic mechanism of the best known member of the family, galactose mutarotase, have shown a glutamate and a histidine residue to be critical for catalysis; the glutamate serves as the active site base to initiate the reaction by removing the proton from the C-1 hydroxyl group of the sugar substrate, and the histidine as the active site acid to protonate the C-5 ring oxygen. Site directed mutagenesis of this latter histidine residue renders Salmonella enterica DeoM inactive. 293 matched cddid_all.tbl CDD cd09270 cd09270 187751 RNase_H2-B Ribonuclease H2-B is a subunit of the eukaryotic RNase H complex which cleaves RNA-DNA hybrids. Ribonuclease H2B is one of the three proteins of eukaryotic RNase H2 complex that is required for nucleic acid binding and hydrolysis. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. Eukaryotic RNase HII is active during replication and is believed to play a role in removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII is functional when it forms a complex with RNase H2B and RNase H2C proteins. It is speculated that the two accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause neurological disorder. 211 matched cddid_all.tbl CDD cd09271 cd09271 187752 RNase_H2-C Ribonuclease H2-C is a subunit of the eukaryotic RNase H complex which cleaves RNA-DNA hybrids. Ribonuclease H2C is one of the three protein of eukaryotic RNase H2 complex that is required for nucleic acid binding and hydrolysis. RNase H is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2/HII). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. The enzyme can be found in bacteria, archaea, and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite a lack of evidence for homology from sequence comparisons, type I and type II RNase H share a common fold and similar steric configurations of the four acidic active-site residues, suggesting identical or very similar catalytic mechanisms. Eukaryotic RNase HII is active during replication and is believed to play a role in removal of Okazaki fragment primers and single ribonucleotides in DNA-DNA duplexes. Eukaryotic RNase HII is functional when it forms a complex with RNase H2B and RNase H2C proteins. It is speculated that the two accessory subunits are required for correct folding of the catalytic subunit of RNase HII. Mutations in the three subunits of human RNase HII cause neurological disorder. 93 matched cddid_all.tbl CDD cd09272 cd09272 260004 RNase_HI_RT_Ty1 Ty1/Copia family of RNase HI in long-term repeat retroelements. Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms including bacteria, archaea, and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD) are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1, and the vertebrate retroviruses. The Ty1/Copia family is widely distributed among the genomes of plants, fungi, and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. 140 matched cddid_all.tbl CDD cd09273 cd09273 260005 RNase_HI_RT_Bel Bel/Pao family of RNase HI in long-term repeat retroelements. Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Bel/Pao family has been described only in metazoan genomes. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. 131 matched cddid_all.tbl CDD cd09274 cd09274 260006 RNase_HI_RT_Ty3 Ty3/Gypsy family of RNase HI in long-term repeat retroelements. Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. Ty3/Gypsy family widely distributed among the genomes of plants, fungi and animals. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. 121 matched cddid_all.tbl CDD cd09275 cd09275 260007 RNase_HI_RT_DIRS1 DIRS1 family of RNase HI in long-term repeat retroelements. Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as adjunct domains to the reverse transcriptase gene in retroviruses, in long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. Phylogenetic patterns of RNase HI of LTR retroelements is classified into five major families, Ty3/Gypsy, Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate retroviruses. The structural features of DIRS1-group elements are different from typical LTR elements. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. 120 matched cddid_all.tbl CDD cd09276 cd09276 260008 Rnase_HI_RT_non_LTR non-LTR RNase HI domain of reverse transcriptases. Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). Ribonuclease HI (RNase HI) is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. RNase HI has also been observed as an adjunct domain to the reverse transcriptase gene in retroviruses, long-term repeat (LTR)-bearing retrotransposons and non-LTR retrotransposons. RNase HI in LTR retrotransposons perform degradation of the original RNA template, generation of a polypurine tract (the primer for plus-strand DNA synthesis), and final removal of RNA primers from newly synthesized minus and plus strands. The catalytic residues for RNase H enzymatic activity, three aspartatic acids and one glutamic acid residue (DEDD), are unvaried across all RNase H domains. The position of the RNase domain of non-LTR and LTR transposons is at the carboxyl terminal of the reverse transcriptase (RT) domain and their RNase domains group together, indicating a common evolutionary origin. Many non-LTR transposons have lost the RNase domain because their activity is at the nucleus and cellular RNase may suffice; however LTR retrotransposons always encode their own RNase domain because it requires RNase activity in RNA-protein particles in the cytoplasm. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. 131 matched cddid_all.tbl CDD cd09277 cd09277 260009 RNase_HI_bacteria_like Bacterial RNase HI containing a hybrid binding domain (HBD) at the N-terminus. Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, Type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability. Some bacteria distinguished from other bacterial RNase HI in the presence of a hybrid binding domain (HBD) at the N-terminus which is commonly present at the N-termini of eukaryotic RNase HI. It has been reported that this domain is required for dimerization and processivity of RNase HI upon binding to RNA-DNA hybrids. 133 matched cddid_all.tbl CDD cd09278 cd09278 260010 RNase_HI_prokaryote_like RNase HI family found mainly in prokaryotes. Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD), residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Prokaryotic RNase H varies greatly in domain structures and substrate specificities. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability. 139 matched cddid_all.tbl CDD cd09279 cd09279 260011 RNase_HI_like RNAse HI family that includes archaeal, some bacterial as well as plant RNase HI. Ribonuclease H (RNase H) is classified into two evolutionarily unrelated families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. Most archaeal genomes contain only type 2 RNase H (RNase HII); however, a few contain RNase HI as well. Although archaeal RNase HI sequences conserve the DEDD active-site motif, they lack other common features important for catalytic function, such as the basic protrusion region. Archaeal RNase HI homologs are more closely related to retroviral RNase HI than bacterial and eukaryotic type I RNase H in enzymatic properties. 128 matched cddid_all.tbl CDD cd09280 cd09280 260012 RNase_HI_eukaryote_like Eukaryotic RNase H is essential and is longer and more complex than their prokaryotic counterparts. Ribonuclease H (RNase H) is classified into two families, type 1 (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type 2 (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H is widely present in various organisms, including bacteria, archaea and eukaryote and most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site (DEDD) residues and have the same catalytic mechanism and functions in cells. Eukaryotic RNase H is longer and more complex than in prokaryotes. Almost all eukaryotic RNase HI have highly conserved regions at their N-termini called hybrid binding domain (HBD). It is speculated that the HBD contributes to binding the RNA/DNA hybrid. Prokaryotes and some single-cell eukaryotes do not require RNase H for viability, but RNase H is essential in higher eukaryotes. RNase H knockout mice lack mitochondrial DNA replication and die as embryos. 145 matched cddid_all.tbl CDD cd09281 cd09281 187753 UPF0066 Escherichia coli YaeB and related proteins. Uncharacterized protein family UPF0066. This domain includes Escherichia coli YeaB, Archeoglobus fulgidus AF0241, and Agrobacterium tumefaciens VirR. Proteins with this domain are probable S-adenosylmethionine-dependent methyltransferases but they have not been functionally characterized and the substrate is unknown. 124 matched cddid_all.tbl CDD cd09286 cd09286 185681 NMNAT_Eukarya Nicotinamide/nicotinate mononucleotide adenylyltransferase, Eukaryotic. Nicotinamide/nicotinate mononucleotide (NMN/ NaMN)adenylyltransferase (NMNAT). NMNAT represents the primary bacterial and eukaryotic adenylyltransferases for nicotinamide-nucleotide and for the deamido form, nicotinate nucleotide. It is an indispensable enzyme in the biosynthesis of NAD(+) and NADP(+). Nicotinamide-nucleotide adenylyltransferase synthesizes NAD via the salvage pathway, while nicotinate-nucleotide adenylyltransferase synthesizes the immediate precursor of NAD via the de novo pathway. Human NMNAT displays unique dual substrate specificity toward both NMN and NaMN, and can participate in both de novo and salvage pathways of NAD synthesis. This subfamily consists strictly of eukaryotic members and includes secondary structural elements not found in all NMNATs. 225 matched cddid_all.tbl CDD cd09287 cd09287 185682 GluRS_non_core "catalytic core domain of non-discriminating glutamyl-tRNA synthetase. Non-discriminating Glutamyl-tRNA synthetase (GluRS) cataytic core domain. These enzymes attach Glu to the appropriate tRNA. Like other class I tRNA synthetases, they aminoacylate the 2'-OH of the nucleotide at the 3' end of the tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. These enzymes function as monomers. Archaea and most bacteria lack GlnRS. In these organisms, the ""non-discriminating"" form of GluRS aminoacylates both tRNA(Glu) and tRNA(Gln) with Glu, which is converted to Gln when appropriate by a transamidation enzyme." 240 matched cddid_all.tbl CDD cd09288 cd09288 187746 Photosystem-II_D2 D2 subunit of photosystem II (PS II). Photosystem II (PS II), D2 subunit. PS II is a multi-subunit protein found in the photosynthetic membranes of plants, algae, and cyanobacteria. It utilizes light-induced electron transfer and water-splitting reactions to produce protons, electrons, and molecular oxygen. The protons generated are instrumental in ATP formation. Molecular dioxygen is released as a by-product. PS II can be described as containing two parts: the photochemical part and the catalytic part. The photochemical portion promotes the fast, efficient light-induced charge separation and stabilization that occur when light is absorbed by chlorophyll. The catalytic portion, where water is oxidized, involves a cluster of Mn ions close to a redox-active tyrosine residue. The Mn cluster and its ligands form a functional unit called the oxygen-evolving complex (OEC) or the water-oxidizing complex (WOC). The D1 and D2 subunits are a pair of intertwined polypeptides. They contain all the cofactors involved directly in water oxidation and plastoquinone reduction. D1 and D2 are highly homologous and are also similar to the L and M proteins in bacterial photosynthetic reaction centers. 339 matched cddid_all.tbl CDD cd09289 cd09289 187747 Photosystem-II_D1 D1 subunit of photosystem II (PS II). Photosystem II (PS II), D2 subunit. PS II is a multi-subunit protein found in the photosynthetic membranes of plants, algae, and cyanobacteria. It utilizes light-induced electron transfer and water-splitting reactions to produce protons, electrons, and molecular oxygen. The protons generated are instrumental in ATP formation. Molecular dioxygen is released as a by-product. PS II can be described as containing two parts: the photochemical part and the catalytic part. The photochemical portion promotes the fast, efficient light-induced charge separation and stabilization that occur when light is absorbed by chlorophyll. The catalytic portion, where water is oxidized, involves a cluster of Mn ions close to a redox-active tyrosine residue. The Mn cluster and its ligands form a functional unit called the oxygen-evolving complex (OEC) or the water-oxidizing complex (WOC). The D1 and D2 subunits are a pair of interwined polypeptides. They contain all the cofactors involved directly in water oxidation and plastoquinone reduction. The D1 subunit contains the Mn cluster that constitutes the site of water oxidation. D1 and D2 are highly homologous and are also similar to the L and M proteins in bacterial photosynthetic reaction centers. 338 matched cddid_all.tbl CDD cd09290 cd09290 187748 Photo-RC_L Subunit L of bacterial photosynthetic reaction center. Bacterial photosynthetic reaction center (RC) complex, subunit L. The bacterial photosynthetic reaction center couples light-induced electron transfer with pumping protons across the membrane using reactions involving a quinone molecule (QB) that binds two electrons and two protons at the active site. The reaction center consists of three membrane-bound subunits, designated L, M, and H, plus an additional extracellular cytochrome subunit. The L and M subunits are arranged around an axis of 2-fold rotational symmetry perpendicular to the membrane, forming a scaffold that maintains the cofactors in a precise configuration. The L and M subunits have both sequence and structural similarity, suggesting a common evolutionary origin. The L and M subunits bind noncovalently to the nine cofactors in 2-fold symmetric branches: four bacteriochlorophylls (Bchl), two bacteriopheophytins (Bphe), two ubiquinone molecules (QA and QB), and a non-heme iron. Two Bchls on the periplasmic side of the membrane form the 'special pair' or dimer which is the primary electron donor for the photosynthetic reactions. The electron transfer reaction proceeds from the dimer to an intermediate acceptor (PA), a primary quinone (QA), and a secondary quinone (QB). Protons are translocated from the bacterial cytoplasm to the periplasmic space, generating an electrochemical gradient of protons (the protonmotive force) that can be used to power reactions such as ATP synthesis. The RC complex is found in photosynthetic bacteria, such as purple bacteria and other proteobacteria species. 273 matched cddid_all.tbl CDD cd09291 cd09291 187749 Photo-RC_M Subunit M of bacterial photosynthetic reaction center. Bacterial photosynthetic reaction center (RC) complex, subunit M. The bacterial photosynthetic reaction center couples light-induced electron transfer with pumping protons across the membrane using reactions involving a quinone molecule (QB) that binds two electrons and two protons at the active site. The reaction center consists of three membrane-bound subunits, designated L, M, and H, plus an additional extracellular cytochrome subunit. The L and M subunits are arranged around an axis of 2-fold rotational symmetry perpendicular to the membrane, forming a scaffold that maintains the cofactors in a precise configuration. The L and M subunits have both sequence and structural similarity, suggesting a common evolutionary origin. The L and M subunits bind noncovalently to the nine cofactors in 2-fold symmetric branches: four bacteriochlorophylls (Bchl), two bacteriopheophytins (Bphe), two ubiquinone molecules (QA and QB), and a non-heme iron. Two Bchls on the periplasmic side of the membrane form the 'special pair' or dimer which is the primary electron donor for the photosynthetic reactions. The electron transfer reaction proceeds from the dimer to an intermediate acceptor (PA), a primary quinone (QA), and a secondary quinone (QB). Protons are translocated from the bacterial cytoplasm to the periplasmic space, generating an electrochemical gradient of protons (the protonmotive force) that can be used to power reactions such as ATP synthesis. The RC complex is found in photosynthetic bacteria, such as purple bacteria and other proteobacteria species. 297 matched cddid_all.tbl CDD cd09293 cd09293 187754 AMN1 Antagonist of mitotic exit network protein 1. Amn1 has been functionally characterized in Saccharomyces cerevisiae as a component of the Antagonist of MEN pathway (AMEN). The AMEN network is activated by MEN (mitotic exit network) via an active Cdc14, and in turn switches off MEN. Amn1 constitutes one of the alternative mechanisms by which MEN may be disrupted. Specifically, Amn1 binds Tem1 (Termination of M-phase, a GTPase that belongs to the RAS superfamily), and disrupts its association with Cdc15, the primary downstream target. Amn1 is a leucine-rich repeat (LRR) protein, with 12 repeats in the S. cerevisiae ortholog. As a negative regulator of the signal transduction pathway MEN, overexpression of AMN1 slows the growth of wild type cells. The function of the vertebrate members of this family has not been determined experimentally, they have fewer LRRs that determine the extent of this model. 226 matched cddid_all.tbl CDD cd09294 cd09294 187755 SmpB Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for releasing stalled ribosome from damaged messenger RNAs. Small protein B (SmpB) is a component of the trans-translation system in prokaryotes for releasing stalled ribosome from damaged messenger RNAs and targeting incompletely synthesized protein fragments for degradation. Trans-translation system is composed of a ribonucleoprotein complex of tmRNA, a specialized RNA with properties of both tRNA and mRNA, and SmpB. SmpB is highly conserved and present in all bacterial kingdoms and is also found in some chloroplasts and mitochondria. This is suggesting Trans-translation arose early in bacterial evolution and its mechanism is a quality control for protein synthesis in spite of challenges such as transcription errors, mRNA damage, and translation frame shifting. SmpB deletion results in phage development defects phenotype and absence of tagged proteins translated from defective mRNAs. 116 matched cddid_all.tbl CDD cd09295 cd09295 200495 Sema The Sema domain, a protein interacting module, of semaphorins and plexins. Both semaphorins and plexins have a Sema domain on their N-termini. Plexins function as receptors for the semaphorins. Evolutionarily, plexins may be the ancestor of semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems, and cancer. Semaphorins can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in invertebrates. Class 2 and 3 semaphorins are secreted; classes 1 and 4 through 6 are transmembrane proteins; and class 7 is membrane associated via glycosylphosphatidylinositol (GPI) linkage. Plexins are a large family of transmembrane proteins, which are divided into four types (A-D) according to sequence similarity. In vertebrates, type A plexins serve as co-receptors for neuropilins to mediate the signalling of class 3 semaphorins. Plexins serve as direct receptors for several other members of the semaphorin family: class 6 semaphorins signal through type A plexins and class 4 semaphorins through type B plexins. This family also includes the MET and RON receptor tyrosine kinases. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves to recognize and bind receptors. 392 matched cddid_all.tbl CDD cd09299 cd09299 187756 TDT The Tellurite-resistance/Dicarboxylate Transporter (TDT) family. The Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes members from all three kingdoms, but only three members of the family have been functionally characterized: the TehA protein of E. coli functioning as a tellurite-resistance uptake permease, the Mae1 protein of S. pombe functioning in the uptake of malate and other dicarboxylates, and the sulfite efflux pump (SSU1) of Saccharomyces cerevisiae. In plants, the plasma membrane protein SLAC1 (Slow Anion Channel-Associated 1), which is preferentially expressed in guard cells, encodes a distant homolog of fungal and bacterial dicarboxylate/malic acid transport proteins. SLAC1 is essential in mediating stomatal responses to physiological and stress stimuli. Members of the TDT family exhibit 10 putative transmembrane alpha-helical spanners (TMSs). 326 matched cddid_all.tbl CDD cd09300 cd09300 350171 DEAD-like_helicase_C C-terminal helicase domain of the DEAD-like helicases. This hierarchy of DEAD-like helicases is composed of two superfamilies, SF1 and SF2, that share almost identical folds and extensive structural similarity in their catalytic core. Helicases are involved in ATP-dependent RNA or DNA unwinding. Two distinct types of helicases exist, those forming toroidal, predominantly hexameric structures, and those that do not. SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Their conserved helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 59 matched cddid_all.tbl CDD cd09301 cd09301 212512 HDAC Histone deacetylase (HDAC) classes I, II, IV and related proteins. The HDAC/HDAC-like family includes Zn-dependent histone deacetylase classes I, II and IV (class III HDACs, also called sirtuins, are NAD-dependent and structurally unrelated, and therefore not part of this family). Histone deacetylases catalyze hydrolysis of N(6)-acetyl-lysine residues in histone amino termini to yield a deacetylated histone (EC 3.5.1.98), as opposed to the acetylation reaction by some histone acetyltransferases (EC 2.3.1.48). Deacetylases of this family are involved in signal transduction through histone and other protein modification, and can repress/activate transcription of a number of different genes. They usually act via the formation of large multiprotein complexes. They are involved in various cellular processes, including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. In mammals, they are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs. 279 matched cddid_all.tbl CDD cd09302 cd09302 187706 Jacalin_like Jacalin-like lectin domain. Jacalin-like lectins are sugar-binding protein domains mostly found in plants. They adopt a beta-prism topology consistent with a circularly permuted three-fold repeat of a structural motif. Proteins containing this domain may bind mono- or oligosaccharides with high specificity. The domain can occur in tandem-repeat arrangements with up to six copies, and in architectures combined with a variety of other functional domains. Taxonomic distribution is not restricted to plants, the domain is also found in various mammalian proteins, for example. 128 matched cddid_all.tbl CDD cd09317 cd09317 187757 TDT_Mae1_like C4-dicarboxylate transporter/malic acid transport protein family includes Mae1. This family contains eukaryotic homologs of C4-dicarboxylate transporter/malic acid transport proteins which are part of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family. This includes the MAE1 gene in Schizosaccharomyces pombe gene that encodes malate permease, Mae1, which functions by proton symport and transports C4-dicarboxylates (malate, fumarate, succinate, oxaloacetate, etc.), but not K-ketoglutarate. 330 matched cddid_all.tbl CDD cd09318 cd09318 187758 TDT_SSU1 Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes sulfite sensitivity protein (sulfite efflux pump; SSU1). This family contains the sulfite sensitivity protein (sulfite efflux pump; SSU1) and belongs to the tellurite-resistance/dicarboxylate transporter (TDT) family. The SSU1 gene encodes the sulfite pump required for efficient sulfite efflux. Mutations in the SSU1 gene cause sensitivity to sulfite while overexpression confers heightened resistance to sulfite toxicity. In dematophytes and other filamentous fungi, sulfite is excreted as a reducing agent during keratin degradation; thus sulfite transporters in keratinolytic fungi could be a new target for antifungal drugs in dermatology. The number of genes encoding sulfite efflux pumps in fungal genomes varies from species to species. 341 matched cddid_all.tbl CDD cd09319 cd09319 187759 TDT_like_1 The Tellurite-resistance/Dicarboxylate Transporter (TDT) family. The Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes members from all three kingdoms, but only three members of the family have been functionally characterized: the TehA protein of E. coli functioning as a tellurite-resistance uptake permease, the Mae1 protein of S. pombe functioning in the uptake of malate and other dicarboxylates, and the sulfite efflux pump (SSU1) of Saccharomyces cerevisiae. In plants, the plasma membrane protein SLAC1 (Slow Anion Channel-Associated 1), which is preferentially expressed in guard cells, encodes a distant homolog of fungal and bacterial dicarboxylate/malic acid transport proteins. SLAC1 is essential in mediating stomatal responses to physiological and stress stimuli. Members of the TDT family exhibit 10 putative transmembrane alpha-helical spanners (TMSs). 317 matched cddid_all.tbl CDD cd09320 cd09320 187760 TDT_like_2 The Tellurite-resistance/Dicarboxylate Transporter (TDT) family. The Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes members from all three kingdoms, but only three members of the family have been functionally characterized: the TehA protein of E. coli functioning as a tellurite-resistance uptake permease, the Mae1 protein of S. pombe functioning in the uptake of malate and other dicarboxylates, and the sulfite efflux pump (SSU1) of Saccharomyces cerevisiae. In plants, the plasma membrane protein SLAC1 (Slow Anion Channel-Associated 1), which is preferentially expressed in guard cells, encodes a distant homolog of fungal and bacterial dicarboxylate/malic acid transport proteins. SLAC1 is essential in mediating stomatal responses to physiological and stress stimuli. Members of the TDT family exhibit 10 putative transmembrane alpha-helical spanners (TMSs). 327 matched cddid_all.tbl CDD cd09321 cd09321 187761 TDT_like_3 The Tellurite-resistance/Dicarboxylate Transporter (TDT) family. The Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes members from all three kingdoms, but only three members of the family have been functionally characterized: the TehA protein of E. coli functioning as a tellurite-resistance uptake permease, the Mae1 protein of S. pombe functioning in the uptake of malate and other dicarboxylates, and the sulfite efflux pump (SSU1) of Saccharomyces cerevisiae. In plants, the plasma membrane protein SLAC1 (Slow Anion Channel-Associated 1), which is preferentially expressed in guard cells, encodes a distant homolog of fungal and bacterial dicarboxylate/malic acid transport proteins. SLAC1 is essential in mediating stomatal responses to physiological and stress stimuli. Members of the TDT family exhibit 10 putative transmembrane a-helical spanners (TMSs). 327 matched cddid_all.tbl CDD cd09322 cd09322 187762 TDT_TehA_like The Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes TehA proteins. The Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes members from all three kingdoms, but only three members of the family have been functionally characterized: the TehA protein of E. coli functioning as a tellurite-resistance uptake permease, the Mae1 protein of S. pombe functioning in the uptake of malate and other dicarboxylates, and the sulfite efflux pump (SSU1) of Saccharomyces cerevisiae. In plants, the plasma membrane protein SLAC1 (Slow Anion Channel-Associated 1), which is preferentially expressed in guard cells, encodes a distant homolog of fungal and bacterial dicarboxylate/malic acid transport proteins. SLAC1 is essential in mediating stomatal responses to physiological and stress stimuli. Members of the TDT family exhibit 10 putative transmembrane a-helical spanners (TMSs). 289 matched cddid_all.tbl CDD cd09323 cd09323 187763 TDT_SLAC1_like Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes SLAC1 (Slow Anion Channel-Associated 1). SLAC1 (Slow Anion Channel-Associated 1) is a plasma membrane protein, preferentially expressed in guard cells, which encodes a distant homolog of fungal and bacterial dicarboxylate/malic acid transport proteins. It is essential for stomatal closure in response to carbon dioxide, abscisic acid, ozone, light/dark transitions, humidity change, calcium ions, hydrogen peroxide and nitric oxide. In the Arabidopsis genome, SLAC1 is part of a gene family with five members and encodes a membrane protein that has ten putative transmembrane domains flanked by large N- and C-terminal domains. Mutations in SLAC1 impair slow (S-type) anion channel currents that are activated by cytosolic calcium ions and abscisic acid, but do not affect rapid (R-type) anion channel currents or calcium ion channel function. 297 matched cddid_all.tbl CDD cd09324 cd09324 187764 TDT_TehA Tellurite-resistance/Dicarboxylate Transporter (TDT) family includes TehA protein. This subfamily includes Tellurite resistance protein TehA that belongs to the C4-dicarboxylate transporter/malic acid transport (TDT) protein family and is a homolog of plant Slow Anion Channel-Associated 1 (SLAC1). The tehA gene encodes an integral membrane protein that has been shown to have efflux activity of quaternary ammonium compounds. TehA protein of Escherichia coli functions as a tellurite-resistance uptake permease. 301 matched cddid_all.tbl CDD cd09325 cd09325 187765 TDT_C4-dicarb_trans C4-dicarboxylate transporters of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family. This subfamily contains bacterial C4-dicarboxylate transporters, which is part of the Tellurite-resistance/Dicarboxylate Transporter (TDT) family. It includes Tellurite resistance protein tehA; the tehA gene encodes an integral membrane protein that has been shown to have efflux activity of quaternary ammonium compounds. TehA protein of Escherichia coli functions as a tellurite-resistance uptake permease. 293 matched cddid_all.tbl CDD cd09326 cd09326 188712 LIM_CRP_like The LIM domains of Cysteine Rich Protein (CRP) family. The LIM domains of Cysteine Rich Protein (CRP) family: Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The known CRP family members include CRP1, CRP2, and CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 53 matched cddid_all.tbl CDD cd09327 cd09327 188713 LIM1_abLIM The first LIM domain of actin binding LIM (abLIM) proteins. The first LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09328 cd09328 188714 LIM2_abLIM The second LIM domain on actin binding LIM (abLIM) proteins. The second LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 56 matched cddid_all.tbl CDD cd09329 cd09329 188715 LIM3_abLIM The third LIM domain of actin binding LIM (abLIM) proteins. The third LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09330 cd09330 188716 LIM4_abLIM The fourth LIM domain of actin binding LIM (abLIM) proteins. The fourth LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 56 matched cddid_all.tbl CDD cd09331 cd09331 188717 LIM1_PINCH The first LIM domain of protein PINCH. The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 59 matched cddid_all.tbl CDD cd09332 cd09332 188718 LIM2_PINCH The second LIM domain of protein PINCH. The second LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09333 cd09333 188719 LIM3_PINCH The third LIM domain of protein PINCH. The third LIM domain of protein PINCH: PINCH plays pivotal roles in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 51 matched cddid_all.tbl CDD cd09334 cd09334 188720 LIM4_PINCH The fourth LIM domain of protein PINCH. The fourth LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. The PINCH LIM4 domain recognizes the third SH3 domain of another adaptor protein, Nck2. This step is an important component of integrin signaling event. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assem bly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09335 cd09335 188721 LIM5_PINCH The fifth LIM domain of protein PINCH. The fifth LIM domain of protein PINCH: PINCH plays pivotal roles in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09336 cd09336 259830 LIM1_Paxillin_like The first LIM domain of the paxillin like protein family. The first LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 53 matched cddid_all.tbl CDD cd09337 cd09337 188723 LIM2_Paxillin_like The second LIM domain of the paxillin like protein family. The second LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09338 cd09338 188724 LIM3_Paxillin_like The third LIM domain of the paxillin like protein family. The third LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 53 matched cddid_all.tbl CDD cd09339 cd09339 188725 LIM4_Paxillin_like The fourth LIM domain of the Paxillin-like protein family. The fourth LIM domain of the Paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09340 cd09340 188726 LIM1_Testin_like The first LIM domain of Testin-like family. The first LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 58 matched cddid_all.tbl CDD cd09341 cd09341 188727 LIM2_Testin_like The second LIM domain of Testin-like family. The second LIM domain of Testin-like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 56 matched cddid_all.tbl CDD cd09342 cd09342 188728 LIM3_Testin_like The third LIM domain of Testin-like family. The third LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 57 matched cddid_all.tbl CDD cd09343 cd09343 188729 LIM1_FHL The first LIM domain of Four and a half LIM domains protein (FHL). The first LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 59 matched cddid_all.tbl CDD cd09344 cd09344 188730 LIM1_FHL1 The first LIM domain of Four and a half LIM domains protein 1. The first LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09345 cd09345 188731 LIM2_FHL The second LIM domain of Four and a half LIM domains protein (FHL). The second LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09346 cd09346 188732 LIM3_FHL The third LIM domain of Four and a half LIM domains protein (FHL). The third LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09347 cd09347 188733 LIM4_FHL The fourth LIM domain of Four and a half LIM domains protein (FHL). The fourth LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 56 matched cddid_all.tbl CDD cd09348 cd09348 188734 LIM4_FHL1 The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1). The fourth LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 64 matched cddid_all.tbl CDD cd09349 cd09349 188735 LIM1_Zyxin The first LIM domain of Zyxin. The first LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cell substratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 87 matched cddid_all.tbl CDD cd09350 cd09350 188736 LIM1_TRIP6 The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6). The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 54 matched cddid_all.tbl CDD cd09351 cd09351 188737 LIM1_LPP The first LIM domain of lipoma preferred partner (LPP). The first LIM domain of lipoma preferred partner (LPP): LPP is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal and proline-rich region at the N-terminal. LPP initially identified as the most frequent translocation partner of HMGA2 (High Mobility Group A2) in a subgroup of benign tumors of adipose tissue (lipomas). It was also shown to be rearranged in a number of other soft tissues, as well as in a case of acute monoblastic leukemia. In addition to its involvement in tumors, LPP was inedited as a smooth muscle restricted LIM protein that plays an important role in SMC migration. LPP is localized at sites of cell adhesion, cell-cell contacts and transiently in the nucleus. In nucleus, it acts as a coactivator for the ETS domain transcription factor PEA3. In addition to PEA3, it interacts with alpha-actinin,vasodilator stimulated phosphoprotein (VASP),Palladin, and Scrib. The LIM domains are the main focal adhesion targeting elements and that the proline- rich region, which harbors binding sites for alpha-actinin and vasodilator- stimulated phosphoprotein (VASP), has a weak targeting capacity. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 54 matched cddid_all.tbl CDD cd09352 cd09352 188738 LIM1_Ajuba_like The first LIM domain of Ajuba-like proteins. The first LIM domain of Ajuba-like proteins: Ajuba like LIM protein family includes three highly homologous proteins Ajuba, Limd1, and WTIP. Members of the family contain three tandem C-terminal LIM domains and a proline-rich N-terminal region. This family of proteins functions as scaffolds, participating in the assembly of numerous protein complexes. In the cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated ERK activation. Ajuba also recruits the TNF receptor-associated factor 6 (TRAF6) to p62 and activates PKCKappa activity. Ajuba interacts with alpha-catenin and F-actin to contribute to the formation or stabilization of adheren junctions by linking adhesive receptors to the actin cytoskeleton. Although Ajuba is a cytoplasmic protein, it can shuttle into the nucleus. In nucleus, Ajuba functions as a corepressor for the zinc finger-protein Snail. It binds to the SNAG repression domain of Snail through its LIM region. Arginine methyltransferase-5 (Prmt5), a protein in the complex, is recruited to Snai l through an interaction with Ajuba. This ternary complex functions to repress E-cadherin, a Snail target gene. In addition, Ajuba contains functional nuclear-receptor interacting motifs and selectively interacts with retinoic acid receptors (RARs) and rexinoid receptor (RXRs) to negatively regulate retinoic acid signaling. Wtip, the Wt1-interacting protein, was originally identified as an interaction partner of the Wilms tumour protein 1 (WT1). Wtip is involved in kidney and neural crest development. Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signaling. LIMD1 was reported to inhibit cell growth and metastases. The inhibition may be mediated through an interaction with the protein barrier-to-autointegration (BAF), a component of SWI/SNF chromatin-remodeling protein; or through the interaction with retinoblastoma protein (pRB), resulting in inhibition of E2F-mediated transcription, and expression of the majority of genes with E2F1- responsive elements. Recently, Limd1 was shown to interact with the p62/sequestosome protein and influence IL-1 and RANKL signaling by facilitating the assembly of a p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62 interaction affects both NF-kappaB and AP-1 activity in epithelial cells and osteoclasts. Moreover, LIMD1 functions as tumor repressor to block lung tumor cell line in vitro and in vivo. Recent studies revealed that LIM proteins Wtip, LIMD1 and Ajuba interact with components of RNA induced silencing complexes (RISC) as well as eIF4E and the mRNA m7GTP cap-protein complex and are required for microRNA-mediated gene silencing. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 54 matched cddid_all.tbl CDD cd09353 cd09353 188739 LIM2_Zyxin The second LIM domain of Zyxin. The second LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cellsubstratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors o r scaffolds to support the assembly of multimeric protein. 60 matched cddid_all.tbl CDD cd09354 cd09354 188740 LIM2_LPP The second LIM domain of lipoma preferred partner (LPP). The second LIM domain of lipoma preferred partner (LPP): LPP is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal and proline-rich region at the N-terminal. LPP initially identified as the most frequent translocation partner of HMGA2 (High Mobility Group A2) in a subgroup of benign tumors of adipose tissue (lipomas). It was also shown to be rearranged in a number of other soft tissues, as well as in a case of acute monoblastic leukemia. In addition to its involvement in tumors, LPP was inedited as a smooth muscle restricted LIM protein that plays an important role in SMC migration. LPP is localized at sites of cell adhesion, cell-cell contacts and transiently in the nucleus. In nucleus, it acts as a coactivator for the ETS domain transcription factor PEA3. In addition to PEA3, it interacts with alpha-actinin,vasodilator stimulated phosphoprotein (VASP),Palladin, and Scrib. The LIM domains are the main focal adhesion targeting elements and that the proline- rich region, which harbors binding sites for alpha-actinin and vasodilator- stimulated phosphoprotein (VASP), has a weak targeting capacity. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 60 matched cddid_all.tbl CDD cd09355 cd09355 188741 LIM2_Ajuba_like The second LIM domain of Ajuba-like proteins. The second LIM domain of Ajuba-like proteins: Ajuba like LIM protein family includes three highly homologous proteins Ajuba, Limd1, and WTIP. Members of the family contain three tandem C-terminal LIM domains and a proline-rich N-terminal region. This family of proteins functions as scaffolds, participating in the assembly of numerous protein complexes. In the cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated ERK activation. Ajuba also recruits the TNF receptor-associated factor 6 (TRAF6) to p62 and activates PKCKappa activity. Ajuba interacts with alpha-catenin and F-actin to contribute to the formation or stabilization of adheren junctions by linking adhesive receptors to the actin cytoskeleton. Although Ajuba is a cytoplasmic protein, it can shuttle into the nucleus. In nucleus, Ajuba functions as a corepressor for the zinc finger-protein Snail. It binds to the SNAG repression domain of Snail through its LIM region. Arginine methyltransferase-5 (Prmt5), a protein in the complex, is recruited to Snai l through an interaction with Ajuba. This ternary complex functions to repress E-cadherin, a Snail target gene. In addition, Ajuba contains functional nuclear-receptor interacting motifs and selectively interacts with retinoic acid receptors (RARs) and rexinoid receptor (RXRs) to negatively regulate retinoic acid signaling. Wtip, the Wt1-interacting protein, was originally identified as an interaction partner of the Wilms tumour protein 1 (WT1). Wtip is involved in kidney and neural crest development. Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signaling. LIMD1 was reported to inhibit cell growth and metastases. The inhibition may be mediated through an interaction with the protein barrier-to-autointegration (BAF), a component of SWI/SNF chromatin-remodeling protein; or through the interaction with retinoblastoma protein (pRB), resulting in inhibition of E2F-mediated transcription, and expression of the majority of genes with E2F1- responsive elements. Recently, Limd1 was shown to interact with the p62/sequestosome protein and influence IL-1 and RANKL signaling by facilitating the assembly of a p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62 interaction affects both NF-kappaB and AP-1 activity in epithelial cells and osteoclasts. Moreover, LIMD1 functions as tumor repressor to block lung tumor cell line in vitro and in vivo. Recent studies revealed that LIM proteins Wtip, LIMD1 and Ajuba interact with components of RNA induced silencing complexes (RISC) as well as eIF4E and the mRNA m7GTP cap-protein complex and are required for microRNA-mediated gene silencing. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 53 matched cddid_all.tbl CDD cd09356 cd09356 188742 LIM2_TRIP6 The second LIM domain of Thyroid receptor-interacting protein 6 (TRIP6). The second LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 53 matched cddid_all.tbl CDD cd09357 cd09357 188743 LIM3_Zyxin_like The third LIM domain of Zyxin-like family. The third LIM domain of Zyxin like family: This family includes Ajuba, Limd1, WTIP, Zyxin, LPP, and Trip6 LIM proteins. Members of Zyxin family contain three tandem C-terminal LIM domains, and a proline-rich N-terminal region. Zyxin proteins are detected primarily in focal adhesion plaques. They function as scaffolds, participating in the assembly of multiple interactions and signal transduction networks, which regulate cell adhesion, spreading, and motility. They can also shuffle into nucleus. In nucleus, zyxin proteins affect gene transcription by interaction with a variety of nuclear proteins, including several transcription factors, playing regulating roles in cell proliferation, differentiation and apoptosis. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 63 matched cddid_all.tbl CDD cd09358 cd09358 188744 LIM_Mical_like The LIM domain of Mical (molecule interacting with CasL) like family. The LIM domain of Mical (molecule interacting with CasL) like family: Known members of this family includes LIM domain containing proteins; Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2) and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth and mobility. Eplin has also found to be tumor suppressor. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs.. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 53 matched cddid_all.tbl CDD cd09359 cd09359 188745 LIM_LASP_like The LIM domain of LIM and SH3 Protein (LASP)-like proteins. The LIM domain of LIM and SH3 Protein (LASP) like proteins: This family contains two types of LIM containing proteins; LASP and N-RAP. LASP family contains two highly homologous members, LASP-1 and LASP-2. LASP contains a LIM motif at its amino terminus, a src homology 3 (SH3) domains at its C-terminal part, and a nebulin-like region in the middle. LASP-1 and -2 are highly conserved in their LIM, nebulin-like, and SH3 domains, but differ significantly at their linker regions. Both proteins are ubiquitously expressed and involved in cytoskeletal architecture, especially in the organization of focal adhesions. LASP-1 and LASP-2, are important during early embryo- and fetogenesis and are highly expressed in the central nervous system of the adult. However, only LASP-1 seems to participate significantly in neuronal differentiation and plays an important functional role in migration and proliferation of certain cancer cells while the role of LASP-2 is more structural. The expression of LASP-1 in breast tumors is increased significantly. N-RAP is a muscle-specific protein concentrated at myotendinous junctions in skeletal muscle and intercalated disks in cardiac muscle. LIM domain is found at the N-terminus of N-RAP and the C-terminal of N-RAP contains a region with multiple of nebulin repeats. N-RAP functions as a scaffolding protein that organizes alpha-actinin and actin into symmetrical I-Z-I structures in developing myofibrils. Nebulin repeat is known as actin binding domain. The N-RAP is hypothesized to form antiparallel dimerization via its LIM domain. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 53 matched cddid_all.tbl CDD cd09360 cd09360 188746 LIM_ALP_like The LIM domain of ALP (actinin-associated LIM protein) family. This family represents the LIM domain of ALP (actinin-associated LIM protein) family. Four proteins: ALP, CLP36, RIL, and Mystique have been classified into the ALP subfamily of LIM domain proteins. Each member of the subfamily contains an N-terminal PDZ domain and a C-terminal LIM domain. Functionally, these proteins bind to alpha-actinin through their PDZ domains and bind or other signaling molecules through their LIM domains. ALP proteins have been implicated in cardiac and skeletal muscle structure, function and disease, platelet, and epithelial cell motility. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09361 cd09361 188747 LIM1_Enigma_like The first LIM domain of Enigma-like family. The first LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09362 cd09362 188748 LIM2_Enigma_like The second LIM domain of Enigma-like family. The second LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09363 cd09363 188749 LIM3_Enigma_like The third LIM domain of Enigma-like family. The third LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09364 cd09364 188750 LIM1_LIMK The first LIM domain of LIMK (LIM domain Kinase ). The first LIM domain of LIMK (LIM domain Kinase ): LIMK protein family is comprised of two members LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerisation. LIMKs can function in both cytoplasm and nucleus and are expressed in all tissues. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. However, LIMK1 and LIMk2 have different cellular locations. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The LIM domains of LIMK have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 53 matched cddid_all.tbl CDD cd09365 cd09365 188751 LIM2_LIMK The second LIM domain of LIMK (LIM domain Kinase ). The second LIM domain of LIMK (LIM domain Kinase ): LIMK protein family is comprised of two members LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus and are expressed in all tissues. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. However, LIMK1 and LIMk2 have different cellular locations. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The LIM domains of LIMK have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09366 cd09366 188752 LIM1_Isl The first LIM domain of Isl, a member of LHX protein family. The first LIM domain of Isl: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Isl1 and Isl2 are the two conserved members of this family. Proteins in this group are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Isl-1 is one of the LHX proteins isolated originally by virtue of its ability to bind DNA sequences from the 5'-flanking region of the rat insulin gene in pancreatic insulin-producing cells. Mice deficient in Isl-1 fail to form the dorsal exocrine pancreas and islet cells fail to differentiate. On the other hand, Isl-1 takes part in the pituitary development by activating the gonadotropin-releasing hormone receptor gene together with LHX3 and steroidogenic factor 1. Mouse Is l2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Same as Isl1, Isl2 may also be able to bind to the insulin gene enhancer to promote gene activation. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 55 matched cddid_all.tbl CDD cd09367 cd09367 188753 LIM1_Lhx1_Lhx5 The first LIM domain of Lhx1 (also known as Lim1) and Lhx5. The first LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09368 cd09368 188754 LIM1_Lhx3_Lhx4 The first LIM domain of Lhx3 and Lhx4 family. The first LIM domain of Lhx3-Lhx4 family: Lhx3 and Lhx4 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. The LHX3 and LHX4 LIM-homeodomain transcription factors play essential roles in pituitary gland and nervous system development. Although LHX3 and LHX4 share marked sequence homology, the genes have different expression patterns. They play overlapping, but distinct functions during the establishment of the specialized cells of the mammalian pituitary gland and the nervous system. Lhx3 proteins have been demonstrated the ability to directly bind to the promoters/enhancers of several pituitary hormone gene promoters to cause increased transcription. Lhx3a and Lhx3b, whose mRNAs have distinct temporal expression profiles during development, are two isoforms of Lhx3. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 52 matched cddid_all.tbl CDD cd09369 cd09369 188755 LIM1_Lhx2_Lhx9 The first LIM domain of Lhx2 and Lhx9 family. The first LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Although Lhx2 and Lhx9 are highly homologous, they seems to play regulatory roles in different organs. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. Lhx9 is expressed in several regions of the developing mouse brain , the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 54 matched cddid_all.tbl CDD cd09370 cd09370 188756 LIM1_Lmx1a The first LIM domain of Lmx1a. The first LIM domain of Lmx1a: Lmx1a belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Mouse Lmx1a is expressed in multiple tissues, including the roof plate of the neural tube, the developing brain, the otic vesicles, the notochord, and the pancreas. Human Lmx1a can be found in pancreas, skeletal muscle, adipose tissue, developing brain, mammary glands, and pituitary. The functions of Lmx1a in the developing nervous system were revealed by studies of mutant mouse. In mouse, mutations in Lmx1a result in failure of the roof plate to develop. Lmx1a may act upstream of other roof plate markers such as MafB, Gdf7, Bmp 6, and Bmp7. Further characterization of these mice reveals numerous defects including disorganized cerebellum, hippocampus, and cortex; altered pigmentation; female sterility; skeletal defects; and behavioral abnormalities. Within pancreatic cells, the Lmx1a protein interacts synergistically with the bHLH transcription factor E47 to activate the insulin gene enhancer/promoter. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 52 matched cddid_all.tbl CDD cd09371 cd09371 188757 LIM1_Lmx1b The first LIM domain of Lmx1b. The first LIM domain of Lmx1b: Lmx1b belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. In mouse, Lmx1b functions in the developing limbs and eyes, the kidneys, the brain, and in cranial mesenchyme. The disruption of Lmx1b gene results kidney and limb defects. In the brain, Lmx1b is important for generation of mesencephalic dopamine neurons and the differentiation of serotonergic neurons. In the mouse eye, Lmx1b regulates anterior segment (cornea, iris, ciliary body, trabecular meshwork, and lens) development. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 53 matched cddid_all.tbl CDD cd09372 cd09372 188758 LIM2_FBLP-1 The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1). The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1): Fblp-1 contains a proline-rich domain near its N terminus and two LIM domains at its C terminus. FBLP-1 mRNA was detected in a variety of tissues and cells including platelets and endothelial cells. FBLP-1 binds to Filamins. The association between filamin B and FBLP-1 may play an unknown role in cytoskeletal function, cell adhesion, and cell motility. As in other LIM domains, this domain family is 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 53 matched cddid_all.tbl CDD cd09373 cd09373 188759 LIM1_AWH The first LIM domain of Arrowhead (AWH). The first LIM domain of Arrowhead (AWH): Arrowhead belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. During embryogenesis of Drosophila, Arrowhead is expressed in each abdominal segment and in the labial segment. Late in embryonic development, expression of arrowhead is refined to the abdominal histoblasts and salivary gland imaginal ring cells themselves. The Arrowhead gene required for establishment of a subset of imaginal tissues: the abdominal histoblasts and the salivary gland imaginal rings. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 54 matched cddid_all.tbl CDD cd09374 cd09374 188760 LIM2_Isl The second LIM domain of Isl, a member of LHX protein family. The second LIM domain of Isl: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Isl1 and Isl2 are the two conserved members of this family. Proteins in this group are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Isl-1 is one of the LHX proteins isolated originally by virtue of its ability to bind DNA sequences from the 5'-flanking region of the rat insulin gene in pancreatic insulin-producing cells. Mice deficient in Isl-1 fail to form the dorsal exocrine pancreas and islet cells fail to differentiate. On the other hand, Isl-1 takes part in the pituitary development by activating the gonadotropin-releasing hormone receptor gene together with LHX3 and steroidogenic factor 1. Mouse Isl2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Same as Isl1, Isl2 may also be able to bind to the insulin gene enhancer to promote gene activation. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 55 matched cddid_all.tbl CDD cd09375 cd09375 188761 LIM2_Lhx1_Lhx5 The second LIM domain of Lhx1 (also known as Lim1) and Lhx5. The second LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 56 matched cddid_all.tbl CDD cd09376 cd09376 188762 LIM2_Lhx3_Lhx4 The second LIM domain of Lhx3-Lhx4 family. The second LIM domain of Lhx3-Lhx4 family: Lhx3 and Lhx4 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. The LHX3 and LHX4 LIM-homeodomain transcription factors play essential roles in pituitary gland and nervous system development. Although LHX3 and LHX4 share marked sequence homology, the genes have different expression patterns. They play overlapping, but distinct functions during the establishment of the specialized cells of the mammalian pituitary gland and the nervous system. Lhx3 proteins have been demonstrated the ability to directly bind to the promoters/enhancers of several pituitary hormone gene promoters to cause increased transcription.Lhx3a and Lhx3b, whose mRNAs have distinct temporal expression profiles during development, are two isoforms of Lhx3. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 56 matched cddid_all.tbl CDD cd09377 cd09377 188763 LIM2_Lhx2_Lhx9 The second LIM domain of Lhx2 and Lhx9 family. The second LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Although Lhx2 and Lhx9 are highly homologous, they seems to play regulatory roles in different organs. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. Lhx9 is expressed in several regions of the developing mouse brain, the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 59 matched cddid_all.tbl CDD cd09378 cd09378 188764 LIM2_Lmx1a_Lmx1b The second LIM domain of Lmx1a and Lmx1b. The second LIM domain of Lmx1a and Lmx1b: Lmx1a and Lmx1b belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Mouse Lmx1a is expressed in multiple tissues, including the roof plate of the neural tube, the developing brain, the otic vesicles, the notochord, and the pancreas. In mouse, mutations in Lmx1a result in failure of the roof plate to develop. Lmx1a may act upstream of other roof plate markers such as MafB, Gdf7, Bmp6, and Bmp7. Further characterization of these mice reveals numerous defects including disorganized cerebellum, hippocampus, and cortex; altered pigmentation; female sterility, skeletal defects, and behavioral abnormalities. In the mouse, Lmx1b functions in the developing limbs and eyes, the kidneys, the brain, and in cranial mesenchyme. The disruption of Lmx1b gene results kidney and limb defects. In the brain, Lmx1b is important for generation of mesencephalic dopamine neurons and the differentiation of serotonergic neurons. In the mouse eye, Lmx1b regulates anterior segment (cornea, iris, ciliary body, trabecular meshwork, and lens) development. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 55 matched cddid_all.tbl CDD cd09379 cd09379 188765 LIM2_AWH The second LIM domain of Arrowhead (AWH). The second LIM domain of Arrowhead (AWH): Arrowhead belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. During embryogenesis of Drosophila, Arrowhead is expressed in each abdominal segment and in the labial segment. Late in embryonic development, expression of arrowhead is refined to the abdominal histoblasts and salivary gland imaginal ring cells themselves. The Arrowhead gene required for establishment of a subset of imaginal tissues: the abdominal histoblasts and the salivary gland imaginal rings. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 55 matched cddid_all.tbl CDD cd09380 cd09380 188766 LIM1_Lhx6 The first LIM domain of Lhx6. The first LIM domain of Lhx6. Lhx6 is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Lhx6 functions in the brain and nervous system. It is expressed at high levels in several regions of the embryonic mouse CNS, including the telencephalon and hypothalamus, and the first branchial arch. Lhx6 is proposed to have a role in patterning of the mandible and maxilla, and in signaling during odontogenesis. In brain sections, knockdown of Lhx6 gene blocks the normal migration of neurons to the cortex. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09381 cd09381 188767 LIM1_Lhx7_Lhx8 The first LIM domain of Lhx7 and Lhx8. The first LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Studies using mutant mice have revealed roles for Lhx7 and Lhx8 in the development of cholinergic neurons in the telencephalon and in basal forebrain development. Mice lacking alleles of the LIM-homeobox gene Lhx7 or Lhx8 display dramatically reduced number of forebrain cholinergic neurons. In addition, Lhx7 mutation affects male and female mice differently, with females appearing more affected than males. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 56 matched cddid_all.tbl CDD cd09382 cd09382 188768 LIM2_Lhx6 The second LIM domain of Lhx6. The second LIM domain of Lhx6. Lhx6 is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Lhx6 functions in brain and nervous system. It is expressed at high levels in several regions of the embryonic mouse CNS, including the telencephalon and hypothalamus, and the first branchial arch. Lhx6 is proposed to have a role in patterning of the mandible and maxilla, and in signaling during odontogenesis. In brain sections, knockdown of Lhx6 gene blocks the normal migration of neurons to the cortex. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 55 matched cddid_all.tbl CDD cd09383 cd09383 188769 LIM2_Lhx7_Lhx8 The second LIM domain of Lhx7 and Lhx8. The second LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Studies using mutant mice have revealed roles for Lhx7 and Lhx8 in the development of cholinergic neurons in the telencephalon and in basal forebrain development. Mice lacking alleles of the LIM-homeobox gene Lhx7 or Lhx8 display dramatically reduced number of forebrain cholinergic neurons. In addition, Lhx7 mutation affects male and female mice differently, with females appearing more affected than males. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 55 matched cddid_all.tbl CDD cd09384 cd09384 188770 LIM1_LMO2 The first LIM domain of LMO2 (LIM domain only protein 2). The first LIM domain of LMO2 (LIM domain only protein 2): LMO2 is a nuclear protein that plays important roles in transcriptional regulation and development. The two tandem LIM domains of LMO2 support the assembly of a crucial cell-regulatory complex by interacting with both the TAL1-E47 and GATA1 transcription factors to form a DNA-binding complex that is capable of transcriptional activation. LMOs have also been shown to be involved in oncogenesis. LMO1 and LMO2 are activated in T-cell acute lymphoblastic leukemia by distinct chromosomal translocations. LMO2 was also shown to be involved in erythropoiesis and is required for the hematopoiesis in the adult animals. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 56 matched cddid_all.tbl CDD cd09385 cd09385 188771 LIM2_LMO2 The second LIM domain of LMO2 (LIM domain only protein 2). The second LIM domain of LMO2 (LIM domain only protein 2): LMO2 is a nuclear protein that plays important roles in transcriptional regulation and development. The two tandem LIM domains of LMO2 support the assembly of a crucial cell-regulatory complex by interacting with both the TAL1-E47 and GATA1 transcription factors to form a DNA-binding complex that is capable of transcriptional activation. LMOs have also been shown to be involved in oncogenesis. LMO1 and LMO2 are activated in T-cell acute lymphoblastic leukemia by distinct chromosomal translocations. LMO2 was also shown to be involved in erythropoiesis and is required for the hematopoiesis in the adult animals. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 56 matched cddid_all.tbl CDD cd09386 cd09386 188772 LIM1_LMO4 The first LIM domain of LMO4 (LIM domain only protein 4). The first LIM domain of LMO4 (LIM domain only protein 4): LMO4 is a nuclear protein that plays important roles in transcriptional regulation and development. LMO4 is involved in various functions in tumorigenesis and cellular differentiation. LMO4 proteins regulate gene expression by interacting with a wide variety of transcription factors and cofactors to form large transcription complexes. It can interact with Smad proteins, and associate with the promoter of the PAI-1 (plasminogen activator inhibitor-1) gene in a TGFbeta (transforming growth factor beta)-dependent manner. LMO4 can also form a complex with transcription regulator CREB (cAMP response element-binding protein) and interact with CLIM1 and CLIM2. In breast tissue, LMO4 interacts with multiple proteins, including the cofactor CtIP [CtBP (C-terminal binding protein)-interacting protein], the breast and ovarian tumor suppressor BRCA1 (breast-cancer susceptibility gene 1) and the LIM-domain-binding protein LDB1. Functionally, LMO4 is shown to repress BRCA1-mediated transcription activation, thus invoking a potential role for LMO4 as a negative regulator of BRCA1 in sporadic breast cancer. LMO4 also forms complex to both ERa (oestrogen receptor alpha), MTA1 (metastasis tumor antigen 1), and HDACs (histone deacetylases), implying that LMO4 is also a component of the MTA1 corepressor complex. Over-expressed LMO4 represses ERa transactivation functions in an HDAC-dependent manner, and contributes to the process of breast cancer progression by allowing the development of Era-negative phenotypes. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 55 matched cddid_all.tbl CDD cd09387 cd09387 188773 LIM2_LMO4 The second LIM domain of LMO4 (LIM domain only protein 4). The second LIM domain of LMO4 (LIM domain only protein 4): LMO4 is a nuclear protein that plays important roles in transcriptional regulation and development. LMO4 is involved in various functions in tumorigenesis and cellular differentiation. LMO4 proteins regulate gene expression by interacting with a wide variety of transcription factors and cofactors to form large transcription complexes. It can interact with Smad proteins, and associate with the promoter of the PAI-1 (plasminogen activator inhibitor-1) gene in a TGFbeta (transforming growth factor beta)-dependent manner. LMO4 can also form a complex with transcription regulator CREB (cAMP response element-binding protein) and interact with CLIM1 and CLIM2. In breast tissue, LMO4 interacts with multiple proteins, including the cofactor CtIP [CtBP (C-terminal binding protein)-interacting protein], the breast and ovarian tumor suppressor BRCA1 (breast-cancer susceptibility gene 1) and the LIM-domain-binding protein LDB1. Functionally, LMO4 is shown to repress BRCA1-mediated transcription activation, thus invoking a potential role for LMO4 as a negative regulator of BRCA1 in sporadic breast cancer. LMO4 also forms complex to both ERa (oestrogen receptor alpha), MTA1 (metastasis tumor antigen 1), and HDACs (histone deacetylases), implying that LMO4 is also a component of the MTA1 corepressor complex. Over-expressed LMO4 represses ERa transactivation functions in an HDAC-dependent manner, and contributes to the process of breast cancer progression by allowing the development of Era-negative phenotypes. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 55 matched cddid_all.tbl CDD cd09388 cd09388 188774 LIM1_LMO1_LMO3 The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3). The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3): LMO1 and LMO3 are highly homologous and belong to the LMO protein family. LMO1 and LMO3 are nuclear protein that plays important roles in transcriptional regulation and development. As LIM domains lack intrinsic DNA-binding activity, nuclear LMOs are involved in transcriptional regulation by forming complexes with other transcription factors or cofactors. For example, LMO1 interacts with the the bHLH domain of bHLH transcription factor, TAL1 (T-cell acute leukemia1)/SCL (stem cell leukemia) . LMO1 inhibits the expression of TAL1/SCL target genes. LMO3 facilitates p53 binding to its response elements, which suggests that LMO3 acts as a co-repressor of p53, suppressing p53-dependent transcriptional regulation. In addition, LMO3 interacts with neuronal transcription factor, HEN2, and acts as an oncogene in neuroblastoma. Another binding partner of LMO3 is calcium- and integrin-binding protein CIB, which binds via the second LIM domain (LIM2) of LMO3. One role of the CIB/LMO3 complex is to inhibit cell proliferation. Although LMO1 and LMO3 are highly homologous proteins, they play different roles in the regulation of the pituitary glycoprotein hormone alpha-subunit (alpha GSU) gene. Alpha GSU promoter activity was markedly repressed by LMO1 but activated by LMO3. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 55 matched cddid_all.tbl CDD cd09389 cd09389 188775 LIM2_LMO1_LMO3 The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3). The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3): LMO1 and LMO3 are highly homologous and belong to the LMO protein family. LMO1 and LMO3 are nuclear protein that plays important roles in transcriptional regulation and development. As LIM domains lack intrinsic DNA-binding activity, nuclear LMOs are involved in transcriptional regulation by forming complexes with other transcription factors or cofactors. For example, LMO1 interacts with the the bHLH domain of bHLH transcription factor, TAL1 (T-cell acute leukemia1)/SCL (stem cell leukemia) . LMO1 inhibits the expression of TAL1/SCL target genes. LMO3 facilitates p53 binding to its response elements, which suggests that LMO3 acts as a co-repressor of p53, suppressing p53-dependent transcriptional regulation. In addition, LMO3 interacts with neuronal transcription factor, HEN2, and acts as an oncogene in neuroblastoma. Another binding partner of LMO3 is calcium- and integrin-binding protein CIB, which binds via the second LIM domain (LIM2) of LMO3. One role of the CIB/LMO3 complex is to inhibit cell proliferation. Although LMO1 and LMO3 are highly homologous proteins, they play different roles in the regulation of the pituitary glycoprotein hormone alpha-subunit (alpha GSU) gene. Alpha GSU promoter activity was markedly repressed by LMO1 but activated by LMO3. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 55 matched cddid_all.tbl CDD cd09390 cd09390 188776 LIM2_dLMO The second LIM domain of dLMO (Beaderx). The second LIM domain of dLMO (Beaderx): dLMO is a nuclear protein that plays important roles in transcriptional regulation and development. In Drosophila dLMO modulates the activity of LIM-homeodomain protein Apterous (Ap), which regulates the formation of the dorsal-ventral axis of the Drosophila wing. Biochemical analysis shows that dLMO protein influences the activity of Apterous by binding of its cofactor Chip. Further studies shown that dLMO proteins might function in an evolutionarily conserved mechanism involved in patterning the appendages. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 55 matched cddid_all.tbl CDD cd09391 cd09391 188777 LIM1_Lrg1p_like The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein. The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 57 matched cddid_all.tbl CDD cd09392 cd09392 188778 LIM2_Lrg1p_like The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein. The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 53 matched cddid_all.tbl CDD cd09393 cd09393 188779 LIM3_Lrg1p_like The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein. The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 56 matched cddid_all.tbl CDD cd09394 cd09394 188780 LIM1_Rga The first LIM domain of Rga GTPase-Activating Proteins. The first LIM domain of Rga GTPase-Activating Proteins: The members of this family contain two tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Rga activates GTPases during polarized morphogenesis. In yeast, a known regulating target of Rga is CDC42p, a small GTPase. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 55 matched cddid_all.tbl CDD cd09395 cd09395 188781 LIM2_Rga The second LIM domain of Rga GTPase-Activating Proteins. The second LIM domain of Rga GTPase-Activating Proteins: The members of this family contain two tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Rga activates GTPases during polarized morphogenesis. In yeast, a known regulating target of Rga is CDC42p, a small GTPase. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 53 matched cddid_all.tbl CDD cd09396 cd09396 188782 LIM_DA1 The Lim domain of DA1. The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain of unknown function. DA1 is predicted as an ubiquitin receptor, which sets final seed and organ size by restricting the period of cell proliferation. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 53 matched cddid_all.tbl CDD cd09397 cd09397 188783 LIM1_UF1 LIM domain in proteins of unknown function. The first Lim domain of a LIM domain containing protein: The functions of the proteins are unknown. The members of this family contain two copies of LIM domain. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 58 matched cddid_all.tbl CDD cd09400 cd09400 188784 LIM_like_1 LIM domain in proteins of unknown function. LIM domain in proteins of unknown function: LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation, and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. The LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid). 61 matched cddid_all.tbl CDD cd09401 cd09401 188785 LIM_TLP_like The LIM domains of thymus LIM protein (TLP). The LIM domain of thymus LIM protein (TLP) like proteins: This family includes the LIM domains of TLP and CRIP (Cysteine-Rich Intestinal Protein). TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. CRIP is a short LIM protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 53 matched cddid_all.tbl CDD cd09402 cd09402 188786 LIM1_CRP The first LIM domain of Cysteine Rich Protein (CRP). The first LIM domain of Cysteine Rich Protein (CRP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. It is evident that CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. Although members of the CRP family share common binding partners, they are also capable of recognizing different and specific targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 53 matched cddid_all.tbl CDD cd09403 cd09403 188787 LIM2_CRP The second LIM domain of Cysteine Rich Protein (CRP). The second LIM domain of Cysteine Rich Protein (CRP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. It is evident that CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. Although members of the CRP family share common binding partners, they are also capable of recognizing different and specific targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residu es, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09404 cd09404 188788 LIM1_MLP84B_like The LIM domain of Mlp84B and Mlp60A. The LIM domain of Mlp84B and Mlp60A: Mlp84B and Mlp60A belong to the CRP LIM domain protein family. The Mlp84B protein contains five copies of the LIM domains, each followed by a Glycin Rich Region (GRR). However, only the first LIM domain of Mlp84B is in this family. Mlp60A exhibits only one LIM domain linked to a glycin-rich region. Mlp84B and Mlp60A are muscle specific proteins and have been implicated in muscle differentiation. While Mlp84B transcripts are enriched at the terminal ends of muscle fibers, Mlp60A transcripts are found throughout the muscle fibers. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09405 cd09405 188789 LIM1_Paxillin The first LIM domain of paxillin. The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight cons erved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09406 cd09406 188790 LIM1_Leupaxin The first LIM domain of Leupaxin. The first LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 55 matched cddid_all.tbl CDD cd09407 cd09407 188791 LIM2_Paxillin The second LIM domain of paxillin. The second LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09408 cd09408 188792 LIM2_Leupaxin The second LIM domain of Leupaxin. The second LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09409 cd09409 188793 LIM3_Paxillin The third LIM domain of paxillin. The third LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 53 matched cddid_all.tbl CDD cd09410 cd09410 188794 LIM3_Leupaxin The third LIM domain of Leupaxin. The third LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 53 matched cddid_all.tbl CDD cd09411 cd09411 188795 LIM4_Paxillin The fourth LIM domain of Paxillin. The fourth LIM domain of Paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09412 cd09412 188796 LIM4_Leupaxin The fourth LIM domain of Leupaxin. The fourth LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09413 cd09413 188797 LIM1_Testin The first LIM domain of Testin. The first LIM domain of Testin: Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N-terminal. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Knockout mice experiments reveal that tumor repressor function of Testin. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 58 matched cddid_all.tbl CDD cd09414 cd09414 188798 LIM1_LIMPETin The first LIM domain of protein LIMPETin. The first LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 58 matched cddid_all.tbl CDD cd09415 cd09415 188799 LIM1_Prickle The first LIM domain of Prickle. The first LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 59 matched cddid_all.tbl CDD cd09416 cd09416 188800 LIM2_Testin The second LIM domain of Testin. The second LIM domain of Testin: Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N-terminal. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Knockout mice experiments reveal that tumor repressor function of testin. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 56 matched cddid_all.tbl CDD cd09417 cd09417 188801 LIM2_LIMPETin_like The second LIM domain of protein LIMPETin and related proteins. The second LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 56 matched cddid_all.tbl CDD cd09418 cd09418 188802 LIM2_Prickle The second LIM domain of Prickle. The second LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 56 matched cddid_all.tbl CDD cd09419 cd09419 188803 LIM3_Testin The third LIM domain of Testin. The third LIM domain of Testin: Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N-terminal. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers at cell-cell-contact areas and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Knockout mice experiments reveal that tumor repressor function of Testin. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 59 matched cddid_all.tbl CDD cd09420 cd09420 188804 LIM3_Prickle The third LIM domain of Prickle. The third LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 59 matched cddid_all.tbl CDD cd09421 cd09421 188805 LIM3_LIMPETin The third LIM domain of protein LIMPETin. The third LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 59 matched cddid_all.tbl CDD cd09422 cd09422 188806 LIM1_FHL2 The first LIM domain of Four and a half LIM domains protein 2 (FHL2). The first LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung at lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 62 matched cddid_all.tbl CDD cd09423 cd09423 188807 LIM1_FHL3 The first LIM domain of Four and a half LIM domains protein 3 (FHL3). The first LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 59 matched cddid_all.tbl CDD cd09424 cd09424 188808 LIM2_FHL1 The second LIM domain of Four and a half LIM domains protein 1 (FHL1). The second LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 58 matched cddid_all.tbl CDD cd09425 cd09425 188809 LIM4_LIMPETin The fourth LIM domain of protein LIMPETin. The fourth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09426 cd09426 188810 LIM2_FHL2 The second LIM domain of Four and a half LIM domains protein 2 (FHL2). The second LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes. 57 matched cddid_all.tbl CDD cd09427 cd09427 188811 LIM2_FHL3 The second LIM domain of Four and a half LIM domains protein 3 (FHL3). The second LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 58 matched cddid_all.tbl CDD cd09428 cd09428 188812 LIM2_FHL5 The second LIM domain of Four and a half LIM domains protein 5 (FHL5). The second LIM domain of Four and a half LIM domains protein 5 (FHL5): FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors , which are highly expressed in male germ cells and is required for post-meiotic gene expression. FHL5 associates with CREM and confers a powerful transcriptional activation function. Activation by CREB has known to occur upon phosphorylation at an essential regulatory site and the subsequent interaction with the ubiquitous coactivator CREB-binding protein (CBP). However, the activation by FHL5 is independent of phosphorylation and CBP association. It represents a new route for transcriptional activation by CREM and CREB. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09429 cd09429 188813 LIM3_FHL1 The third LIM domain of Four and a half LIM domains protein 1 (FHL1). The third LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 53 matched cddid_all.tbl CDD cd09430 cd09430 188814 LIM5_LIMPETin The fifth LIM domain of protein LIMPETin. The fifth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09431 cd09431 188815 LIM3_Fhl2 The third LIM domain of Four and a half LIM domains protein 2 (FHL2). The third LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes. 57 matched cddid_all.tbl CDD cd09432 cd09432 188816 LIM6_LIMPETin The sixth LIM domain of protein LIMPETin. The sixth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 56 matched cddid_all.tbl CDD cd09433 cd09433 188817 LIM4_FHL2 The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2). The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes. 58 matched cddid_all.tbl CDD cd09434 cd09434 188818 LIM4_FHL3 The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3). The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 56 matched cddid_all.tbl CDD cd09435 cd09435 188819 LIM3_Zyxin The third LIM domain of Zyxin. The third LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cellsubstratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 67 matched cddid_all.tbl CDD cd09436 cd09436 188820 LIM3_TRIP6 The third LIM domain of Thyroid receptor-interacting protein 6 (TRIP6). The third LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 66 matched cddid_all.tbl CDD cd09437 cd09437 188821 LIM3_LPP The third LIM domain of lipoma preferred partner (LPP). The third LIM domain of lipoma preferred partner (LPP): LPP is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal and proline-rich region at the N-terminal. LPP initially identified as the most frequent translocation partner of HMGA2 (High Mobility Group A2) in a subgroup of benign tumors of adipose tissue (lipomas). It was also shown to be rearranged in a number of other soft tissues, as well as in a case of acute monoblastic leukemia. In addition to its involvement in tumors, LPP was inedited as a smooth muscle restricted LIM protein that plays an important role in SMC migration. LPP is localized at sites of cell adhesion, cell-cell contacts and transiently in the nucleus. In nucleus, it acts as a coactivator for the ETS domain transcription factor PEA3. In addition to PEA3, it interacts with alpha-actinin,vasodilator stimulated phosphoprotein (VASP), Palladin, and Scrib. The LIM domains are the main focal adhesion targeting elements and that the proline- rich region, which harbors binding sites for alpha-actinin and vasodilator- stimulated phosphoprotein (VASP), has a weak targeting capacity. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 68 matched cddid_all.tbl CDD cd09438 cd09438 188822 LIM3_Ajuba_like The third LIM domain of Ajuba-like proteins. The third LIM domain of Ajuba-like proteins: Ajuba like LIM protein family includes three highly homologous proteins Ajuba, Limd1, and WTIP. Members of the family contain three tandem C-terminal LIM domains and a proline-rich N-terminal region. This family of proteins functions as scaffolds, participating in the assembly of numerous protein complexes. In the cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated ERK activation. Ajuba also recruits the TNF receptor-associated factor 6 (TRAF6) to p62 and activates PKCKappa activity. Ajuba interacts with alpha-catenin and F-actin to contribute to the formation or stabilization of adheren junctions by linking adhesive receptors to the actin cytoskeleton. Although Ajuba is a cytoplasmic protein, it can shuttle into the nucleus. In nucleus, Ajuba functions as a corepressor for the zinc finger-protein Snail. It binds to the SNAG repression domain of Snail through its LIM region. Arginine methyltransferase-5 (Prmt5), a protein in the complex, is recruited to Snai l through an interaction with Ajuba. This ternary complex functions to repress E-cadherin, a Snail target gene. In addition, Ajuba contains functional nuclear-receptor interacting motifs and selectively interacts with retinoic acid receptors (RARs) and rexinoid receptor (RXRs) to negatively regulate retinoic acid signaling. Wtip, the Wt1-interacting protein, was originally identified as an interaction partner of the Wilms tumour protein 1 (WT1). Wtip is involved in kidney and neural crest development. Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signaling. LIMD1 was reported to inhibit cell growth and metastases. The inhibition may be mediated through an interaction with the protein barrier-to-autointegration (BAF), a component of SWI/SNF chromatin-remodeling protein; or through the interaction with retinoblastoma protein (pRB), resulting in inhibition of E2F-mediated transcription, and expression of the majority of genes with E2F1- responsive elements. Recently, Limd1 was shown to interact with the p62/sequestosome protein and influence IL-1 and RANKL signaling by facilitating the assembly of a p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62 interaction affects both NF-kappaB and AP-1 activity in epithelial cells and osteoclasts. Moreover, LIMD1 functions as tumor repressor to block lung tumor cell line in vitro and in vivo. Recent studies revealed that LIM proteins Wtip, LIMD1 and Ajuba interact with components of RNA induced silencing complexes (RISC) as well as eIF4E and the mRNA m7GTP cap-protein complex and are required for microRNA-mediated gene silencing. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 62 matched cddid_all.tbl CDD cd09439 cd09439 188823 LIM_Mical The LIM domain of Mical (molecule interacting with CasL). The LIM domain of Mical (molecule interacting with CasL): MICAL is a large, multidomain, cytosolic protein with a single LIM domain, a calponin homology (CH) domain and a flavoprotein monooxygenase domain. In Drosophila, MICAL is expressed in axons, interacts with the neuronal A (PlexA) receptor and is required for Semapho-rin 1a (Sema-1a)-PlexA-mediated repulsive axon guidance. The LIM domain and calporin homology domain are known for interactions with the cytoskeleton, cytoskeletal adaptor proteins, and other signaling proteins. The flavoprotein monooxygenase (MO) is required for semaphorin-plexin repulsive axon guidance during axonal pathfinding in the Drosophila neuromuscular system. In addition, MICAL was characterized to interact with Rab13 and Rab8 to coordinate the assembly of tight junctions and adherens junctions in epithelial cells. Thus, MICAL was also named junctional Rab13-binding protein (JRAB). As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 55 matched cddid_all.tbl CDD cd09440 cd09440 188824 LIM1_SF3 The first Lim domain of pollen specific protein SF3. The first Lim domain of pollen specific protein SF3: SF3 is a Lim protein that is found exclusively in mature plant pollen grains. It contains two LIM domains. The exact function of SF3 is unknown. It may be a transcription factor required for the expression of late pollen genes. It is possible that SF3 protein is involved in controlling pollen-specific processes such as male gamete maturation, pollen tube formation, or even fertilization. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 63 matched cddid_all.tbl CDD cd09441 cd09441 188825 LIM2_SF3 The second Lim domain of pollen specific protein SF3. The second Lim domain of pollen specific protein SF3: SF3 is a Lim protein that is found exclusively in mature plant pollen grains. It contains two LIM domains. The exact function of SF3 is unknown. It may be a transcription factor required for the expression of late pollen genes. It is possible that SF3 protein is involved in controlling pollen-specific processes such as male gamete maturation, pollen tube formation, or even fertilization. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 61 matched cddid_all.tbl CDD cd09442 cd09442 188826 LIM_Eplin_like The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins. The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins: This family contains Epithelial Protein Lost in Neoplasm in Neoplasm (Eplin), xin actin-binding repeat-containing protein 2 (XIRP2) and a group of protein with unknown function. The members of this family all contain a single LIM domain. Epithelial Protein Lost in Neoplasm is a cytoskeleton-associated tumor suppressor whose expression inversely correlates with cell growth, motility, invasion and cancer mortality. Eplin interacts and stabilizes F-actin filaments and stress fibers, which correlates with its ability to suppress anchorage independent growth. In epithelial cells, Eplin is required for formation of the F-actin adhesion belt by binding to the E-cadherin-catenin complex through alpha-catenin. Eplin is expressed in two isoforms, a longer Eplin-beta and a shorter Eplin-alpha. Eplin-alpha mRNA is detected in various tissues and cell lines, but is absent or down regulated in cancer cells. Xirp2 contains a LIM domain and Xin re peats for binding to and stabilising F-actin. Xirp2 is expressed in muscles and is significantly induced in the heart in response to systemic administration of angiotensin II. Xirp2 is an important effector of the Ang II signaling pathway in the heart. The expression of Xirp2 is activated by myocyte enhancer factor (MEF)2A, whose transcriptional activity is stimulated by angiotersin II. Thus, Xirp2 plays important pathological roles in the angiotensin II induced hypertension. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 53 matched cddid_all.tbl CDD cd09443 cd09443 188827 LIM_Ltd-1 The LIM domain of LIM and transglutaminase domains protein (Ltd-1). The LIM domain of LIM and transglutaminase domains protein (Ltd-1): This family includes mouse Ky protein and Caenorhabditis elegans Ltd-1 protein. The members of this family consists a N-terminal Lim domain and a C-terminal transglutaminase domain. The mouse Ky protein has putative function in muscle development. The mouse with ky mutant exhibits combined posterior and lateral curvature of the spine. The Ltd-1 gene in C. elegans is expressed in developing hypodermal cells from the twofold stage embryo through adulthood. These data define the ltd-1 gene as a novel marker for C. elegans epithelial cell development. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 55 matched cddid_all.tbl CDD cd09444 cd09444 188828 LIM_Mical_like_1 This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL) like proteins. The LIM domain on proteins of unknown function: This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL) like proteins. Known members of the Mical-like family includes single LIM domain containing proteins, Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2), and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth, and mobility. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 55 matched cddid_all.tbl CDD cd09445 cd09445 188829 LIM_Mical_like_2 This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL) like proteins. The LIM domain on proteins of unknown function: This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL)-like proteins. Known members of the Mical-like family includes single LIM domain containing proteins, Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2), and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth, and mobility. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 53 matched cddid_all.tbl CDD cd09446 cd09446 188830 LIM_N_RAP The LIM domain of N-RAP. The LIM domain of N-RAP: N-RAP is a muscle-specific protein concentrated at myotendinous junctions in skeletal muscle and intercalated disks in cardiac muscle. LIM domain is found at the N-terminus of N-RAP and the C-terminal of N-RAP contains a region with multiple of nebulin repeats. N-RAP functions as a scaffolding protein that organizes alpha-actinin and actin into symmetrical I-Z-I structures in developing myofibrils. Nebulin repeat is known as actin binding domain. The N-RAP is hypothesized to form antiparallel dimerization via its LIM domain. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 53 matched cddid_all.tbl CDD cd09447 cd09447 188831 LIM_LASP The LIM domain of LIM and SH3 Protein (LASP). The LIM domain of LIM and SH3 Protein (LASP): LASP family contains two highly homologous members, LASP-1 and LASP-2. LASP contains a LIM motif at its amino terminus, a src homology 3 (SH3) domains at its C-terminal part, and a nebulin-like region in the middle. LASP-1 and -2 are highly conserved in their LIM, nebulin-like, and SH3 domains ,but differ significantly at their linker regions. Both proteins are ubiquitously expressed and involved in cytoskeletal architecture, especially in the organization of focal adhesions. LASP-1 and LASP-2, are important during early embryo- and fetogenesis and are highly expressed in the central nervous system of the adult. However, only LASP-1 seems to participate significantly in neuronal differentiation and plays an important functional role in migration and proliferation of certain cancer cells while the role of LASP-2 is more structural. The expression of LASP-1 in breast tumors is increased significantly. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 53 matched cddid_all.tbl CDD cd09448 cd09448 188832 LIM_CLP36 This family represents the LIM domain of CLP36. This family represents the LIM domain of CLP36. CLP36 has also been named as CLIM1, Elfin, or PDLIM1. CLP36 contains a C-terminal LIM domain and an N-terminal PDZ domain. CLP36 is highly expressed in heart and is present in many other tissues including lung, liver, spleen, and blood. CLP36 has been implicated in many processes including hypoxia and regulation of actin stress fibers. CLP36 co-localizes with alpha-actinin-2 at the Z-lines in myocardium. In addition, CLP36 binds to alpha-actinin-1 and alpha-actinin-4, and associates with F-actin filaments and stress fibers. CLP36 might be involved in not only the function of sarcomeres in muscle cells, but also in actin stress fiber-mediated cellular processes, such as cell shape, migration, polarit, and cytokinesis in non-muscle cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09449 cd09449 188833 LIM_Mystique The LIM domain of Mystique, a subfamily of ALP LIM domain proteins. The LIM domain of Mystique, a subfamily of ALP LIM domain proteins: Mystique is the most recently identified member of the ALP protein family. It also interacts with alpha-actinin, as other ALP proteins do. Mystique promotes cell attachment and migration and suppresses anchorage-independent growth. The LIM domain of Mystique is required for the suppression function. Moreover, Mystique functions as an ubiquitin E3 ligase acting on STAT proteins to cause their proteosome mediated degradation. As in all LIM domains, this domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 53 matched cddid_all.tbl CDD cd09450 cd09450 188834 LIM_ALP This family represents the LIM domain of ALP, actinin-associated LIM protein. This family represents the LIM domain of ALP, actinin-associated LIM protein. ALP contains an N-terminal PDZ domain, a C-terminal LIM domain and an ALP-subfamily-specific 34-amino-acid motif termed ALP-like motif (AM), which contains a putative consensus protein kinase C (PKC) phosphorylation site and two alpha-helices. ALP proteins are found in heart and in skeletal muscle. ALP may act as a signaling molecule which is regulated by PKC-dependent signaling. ALP plays an essential role in the development of RV (right ventricle) chamber. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 53 matched cddid_all.tbl CDD cd09451 cd09451 188835 LIM_RIL The LIM domain of RIL. The LIM domain of RIL: RIL contains an N-terminal PDZ domain, a LIM domain, and a short consensus C-terminal region. It is the smallest molecule in the ALP LIM domain containing protein family. RIL was identified in rat fibroblasts and in human lymphocytes. The LIM domain interacts with the AMPA glutamate receptor in dendritic spines. The consensus C-terminus interacts with PTP-BL, a submembranous protein tyrosine phosphatase and the PDZ domain is responsible to interact with alpha-actinin molecules. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 53 matched cddid_all.tbl CDD cd09452 cd09452 188836 LIM1_Enigma The first LIM domain of Enigma. The first LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09453 cd09453 188837 LIM1_ENH The first LIM domain of the Enigma Homolog (ENH) family. The first LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09454 cd09454 188838 LIM1_ZASP_Cypher The first LIM domain of ZASP/Cypher family. The first LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09455 cd09455 188839 LIM1_Enigma_like_1 The first LIM domain of an Enigma subfamily with unknown function. The first LIM domain of an Enigma subfamily with unknown function: The Enigma LIM domain family is comprised of three characterized members: Enigma, ENH and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. They serve as adaptor proteins, where the PDZ domain tethers the protein to the cytoskeleton and the LIM domains, recruit signaling proteins to implement corresponding functions. The members of the Enigma family have been implicated in regulating or organizing cytoskeletal structure, as well as involving multiple signaling pathways. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09456 cd09456 188840 LIM2_Enigma The second LIM domain of Enigma. The second LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09457 cd09457 188841 LIM2_ENH The second LIM domain of the Enigma Homolog (ENH) family. The second LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 52 matched cddid_all.tbl CDD cd09458 cd09458 188842 LIM3_Enigma The third LIM domain of Enigma. The third LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 55 matched cddid_all.tbl CDD cd09459 cd09459 188843 LIM3_ENH The third LIM domain of the Enigma Homolog (ENH) family. The third LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 55 matched cddid_all.tbl CDD cd09460 cd09460 188844 LIM3_ZASP_Cypher The third LIM domain of ZASP/Cypher family. The third LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 55 matched cddid_all.tbl CDD cd09461 cd09461 188845 LIM3_Enigma_like_1 The third LIM domain of an Enigma subfamily with unknown function. The third LIM domain of an Enigma subfamily with unknown function: The Enigma LIM domain family is comprised of three characterized members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. They serve as adaptor proteins, where the PDZ domain tethers the protein to the cytoskeleton and the LIM domains, recruit signaling proteins to implement corresponding functions. The members of the enigma family have been implicated in regulating or organizing cytoskeletal structure, as well as involving multiple signaling pathways. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09462 cd09462 188846 LIM1_LIMK1 The first LIM domain of LIMK1 (LIM domain Kinase 1). The first LIM domain of LIMK1 (LIM domain Kinase 1): LIMK1 belongs to the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK1 is expressed in all tissues and is localized to focal adhesions in the cell. LIMK1 can form homodimers upon binding of HSP90 and is activated by Rho effector Rho kinase and MAPKAPK2. LIMK1 is important for normal central nervous system development, and its deletion has been implicated in the development of the human genetic disorder Williams syndrome. Moreover, LIMK1 up-regulates the promoter activity of urokinase type plasminogen activator and induces its mRNA and protein expression in breast cancer cells. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 74 matched cddid_all.tbl CDD cd09463 cd09463 188847 LIM1_LIMK2 The first LIM domain of LIMK2 (LIM domain Kinase 2). The first LIM domain of LIMK2 (LIM domain Kinase 2): LIMK2 is a member of the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, altering the rate of actin depolymerization. LIMK activity is activated by phosphorylation of a threonine residue within the activation loop of the kinase by p21-activated kinases 1 and 4 and by Rho kinase. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK2 is expressed in all tissues. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The activity of LIM kinase 2 to regulate cofilin phosphorylation is inhibited by the direct binding of Par-3. LIMK2 activation promotes cell cycle progression. The phenotype of Limk2 knockout mice shows a defect in spermatogenesis. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 53 matched cddid_all.tbl CDD cd09464 cd09464 188848 LIM2_LIMK1 The second LIM domain of LIMK1 (LIM domain Kinase 1). The second LIM domain of LIMK1 (LIM domain Kinase 1): LIMK1 belongs to the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK1 is expressed in all tissues and is localized to focal adhesions in the cell. LIMK1 can form homodimers upon binding of HSP90 and is activated by Rho effector Rho kinase and MAPKAPK2. LIMK1 is important for normal central nervous system development, and its deletion has been implicated in the development of the human genetic disorder Williams syndrome. Moreover, LIMK1 up-regulates the promoter activity of urokinase type plasminogen activator and induces its mRNA and protein expression in breast cancer cells. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 55 matched cddid_all.tbl CDD cd09465 cd09465 188849 LIM2_LIMK2 The second LIM domain of LIMK2 (LIM domain Kinase 2). The second LIM domain of LIMK2 (LIM domain Kinase 2): LIMK2 is a member of the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, altering the rate of actin depolymerisation. LIMK activity is activated by phosphorylation of a threonine residue within the activation loop of the kinase by p21-activated kinases 1 and 4 and by Rho kinase. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK2 is expressed in all tissues. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The activity of LIM kinase 2 to regulate cofilin phosphorylation is inhibited by the direct binding of Par-3. LIMK2 activation promotes cell cycle progression. The phenotype of Limk2 knockout mice shows a defect in spermatogenesis. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 59 matched cddid_all.tbl CDD cd09466 cd09466 188850 LIM1_Lhx3a The first LIM domain of Lhx3a. The first LIM domain of Lhx3a: Lhx3a is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3a is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 56 matched cddid_all.tbl CDD cd09467 cd09467 188851 LIM1_Lhx3b The first LIM domain of Lhx3b. The first LIM domain of Lhx3b. Lhx3b is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 55 matched cddid_all.tbl CDD cd09468 cd09468 188852 LIM1_Lhx4 The first LIM domain of Lhx4. The first LIM domain of Lhx4. Lhx4 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 52 matched cddid_all.tbl CDD cd09469 cd09469 188853 LIM1_Lhx2 The first LIM domain of Lhx2. The first LIM domain of Lhx2: Lhx2 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. The Lhx2 protein has been shown to bind to the mouse M71 olfactory receptor promoter. Similar to other LIM domains, this domain family is 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 64 matched cddid_all.tbl CDD cd09470 cd09470 188854 LIM1_Lhx9 The first LIM domain of Lhx9. The first LIM domain of Lhx9: Lhx9 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx9 is highly homologous to Lhx2. It is expressed in several regions of the developing mouse brain, the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice have reduced levels of the Sf1 nuclear receptor that is required for gonadogenesis, and recent studies have shown that Lhx9 is able to activate the Sf1/FtzF1 gene. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 54 matched cddid_all.tbl CDD cd09471 cd09471 188855 LIM2_Isl2 The second LIM domain of Isl2. The second LIM domain of Isl2: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Isl proteins are found in the nucleus and act as transcription factors or cofactors. Isl1 and Isl2 are the two conserved members of this family. Mouse Isl2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Isl2 may be able to bind to the insulin gene enhancer to promote gene activation. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 55 matched cddid_all.tbl CDD cd09472 cd09472 188856 LIM2_Lhx3b The second LIM domain of Lhx3b. The second LIM domain of Lhx3b. Lhx3b is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein 57 matched cddid_all.tbl CDD cd09473 cd09473 188857 LIM2_Lhx4 The second LIM domain of Lhx4. The second LIM domain of Lhx4. Lhx4 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 56 matched cddid_all.tbl CDD cd09474 cd09474 188858 LIM2_Lhx2 The second LIM domain of Lhx2. The second LIM domain of Lhx2: Lhx2 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. The Lhx2 protein has been shown to bind to the mouse M71 olfactory receptor promoter. Similar to other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 59 matched cddid_all.tbl CDD cd09475 cd09475 188859 LIM2_Lhx9 The second LIM domain of Lhx9. The second LIM domain of Lhx9: Lhx9 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx9 is highly homologous to Lhx2. It is expressed in several regions of the developing mouse brain, the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice have reduced levels of the Sf1 nuclear receptor that is required for gonadogenesis, and recent studies have shown that Lhx9 is able to activate the Sf1/FtzF1 gene. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 59 matched cddid_all.tbl CDD cd09476 cd09476 188860 LIM1_TLP The first LIM domain of thymus LIM protein (TLP). The first LIM domain of thymus LIM protein (TLP): TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09477 cd09477 188861 LIM2_TLP The second LIM domain of thymus LIM protein (TLP). The second LIM domain of thymus LIM protein (TLP): TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09478 cd09478 188862 LIM_CRIP The LIM domain of Cysteine-Rich Intestinal Protein (CRIP). The LIM domain of Cysteine-Rich Intestinal Protein (CRIP): CRIP is a short protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09479 cd09479 188863 LIM1_CRP1 The first LIM domain of Cysteine Rich Protein 1 (CRP1). The first LIM domain of Cysteine Rich Protein 1 (CRP1): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1 can associate with the actin cytoskeleton and are capable of interacting with alpha-actinin and zyxin. CRP1 was shown to regulate actin filament bundling by interaction with alpha-actinin and direct binding to actin filaments. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 56 matched cddid_all.tbl CDD cd09480 cd09480 188864 LIM1_CRP2 The first LIM domain of Cysteine Rich Protein 2 (CRP2). The first LIM domain of Cysteine Rich Protein 2 (CRP2): The CRP family members include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP2 specifically binds to protein inhibitor of activated STAT-1 (PIAS1) and a novel human protein designed CRP2BP (for CRP2 binding partner). PIAS1 specifically inhibits the STAT-1 pathway and CRP2BP is homologous to members of the histone acetyltransferase family raising the possibility that CRP2 is a modulator of cytokine-controlled pathways or is functionally active in the transcriptional regulatory network. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 55 matched cddid_all.tbl CDD cd09481 cd09481 188865 LIM1_CRP3 The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP). The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcriptio n factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09482 cd09482 188866 LIM2_CRP3 The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP). The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09483 cd09483 188867 LIM1_Prickle_1 The first LIM domain of Prickle 1. The first LIM domain of Prickle 1. Prickle contains three C-terminal LIM domains and a N-terminal PET domain Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in mainly expressed in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. In addition, Prickle 1 regulates cell movements during gastrulation and neuronal migration through interaction with the noncanonical Wnt11/Wnt5 pathway in zebrafish. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 59 matched cddid_all.tbl CDD cd09484 cd09484 188868 LIM1_Prickle_2 The first LIM domain of Prickle 2. The first LIM domain of Prickle 2: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 59 matched cddid_all.tbl CDD cd09485 cd09485 188869 LIM_Eplin_alpha_beta The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin). The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin): Epithelial Protein Lost in Neoplasm is a cytoskeleton-associated tumor suppressor whose expression inversely correlates with cell growth, motility, invasion and cancer mortality. Eplin interacts and stabilizes F-actin filaments and stress fibers, which correlates with its ability to suppress anchorage independent growth. In epithelial cells, Eplin is required for formation of the F-actin adhesion belt by binding to the E-cadherin-catenin complex through alpha-catenin. Eplin is expressed in two isoforms, a longer Eplin-beta and a shorter Eplin-alpha. Eplin-alpha mRNA is detected in various tissues and cell lines, but is absent or down regulated in cancer cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 53 matched cddid_all.tbl CDD cd09486 cd09486 188870 LIM_Eplin_like_1 a LIM domain subfamily on a group of proteins with unknown function. This model represents a LIM domain subfamily of Eplin-like family. This family shows highest homology to the LIM domains on Eplin and XIRP2 protein families. Epithelial Protein Lost in Neoplasm is a cytoskeleton-associated tumor suppressor whose expression inversely correlates with cell growth, motility, invasion and cancer mortality. Xirp2 is expressed in muscles and is an important effector of the Ang II signaling pathway in the heart. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. 53 matched cddid_all.tbl CDD cd09487 cd09487 188886 SAM_superfamily SAM (Sterile alpha motif ). SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases. 56 matched cddid_all.tbl CDD cd09488 cd09488 188887 SAM_EPH-R SAM domain of EPH family of tyrosine kinase receptors. SAM (sterile alpha motif) domain of EPH (erythropoietin-producing hepatocyte) family of receptor tyrosine kinases is a C-terminal signal transduction module located in the cytoplasmic region of these receptors. SAM appears to mediate cell-cell initiated signal transduction via binding proteins to a conserved tyrosine that is phosphorylated. In some cases the SAM domain mediates homodimerization/oligomerization and plays a role in the clustering process necessary for signaling. EPH kinases are the largest family of receptor tyrosine kinases. They are classified into two groups based on their abilities to bind ephrin-A and ephrin-B ligands. The EPH receptors are involved in regulation of cell movement, shape, and attachment during embryonic development; they control cell-cell interactions in the vascular, nervous, epithelial, and immune systems, and in many tumors. They are potential molecular markers for cancer diagnostics and potential targets for cancer therapy. 61 matched cddid_all.tbl CDD cd09489 cd09489 188888 SAM_Smaug-like SAM (Sterile alpha motif ). SAM (sterile alpha motif) domain of Smaug-like subfamily proteins is an RNA binding domain. SAM interacts with stem-loop structures in target mRNAs. Proteins of this subfamily are post-transcriptional regulators involved in mRNA silencing and deadenylation; they can be implicated in transcript stability regulation and vacuolar protein transport as well. SAM_Smaug-like domain-containing proteins are found in metazoa from yeast to human. In animals they are active during early embryogenesis. 57 matched cddid_all.tbl CDD cd09490 cd09490 188889 SAM_Arap1,2,3 SAM domain of Arap1,2,3 (angiotensin receptor-associated protein). SAM (sterile alpha motif) domain of Arap1,2,3 subfamily proteins (angiotensin receptor-associated) is a protein-protein interaction domain. Arap1,2,3 proteins are phosphatidylinositol-3,4,5-trisphosphate-dependent GTPase-activating proteins. They are involved in phosphatidylinositol-3 kinase (PI3K) signaling pathways. In addition to SAM domain, Arap1,2,3 proteins contain ArfGap, PH-like, RhoGAP and UBQ domains. SAM domain of Arap3 protein was shown to interact with SAM domain of Ship2 phosphatidylinositol-trisphosphate phosphatase proteins. Such interaction apparently plays a role in inhibition of PI3K regulated pathways since Ship2 converts PI(3,4,5)P3 into PI(3,4)P2. Proteins of this subfamily participate in regulation of signaling and trafficking associated with a number of different receptors (including EGFR, TRAIL-R1/DR4, TRAIL-R2/DR5) in normal and cancer cells; they are involved in regulation of actin cytoskeleton remodeling, cell spreading and formation of lamellipodia. 63 matched cddid_all.tbl CDD cd09491 cd09491 188890 SAM_Ship2 SAM domain of Ship2 lipid phosphatase proteins. SAM (sterile alpha motif) domain of Ship2 subfamily is a protein-protein interaction domain. Ship2 proteins are lipid phosphatases (Phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2) containing an N-terminal SH2 domain, a central phosphatase domain and a C-terminal SAM domain. Ship2 is involved in a number of PI3K signaling pathways. For example, it plays a role in regulation of the actin cytoskeleton remodeling, in insulin signaling pathways, and in EphA2 receptor endocytosis. SAM domain of Ship2 can interact with SAM domain of other proteins in these pathways, thus participating in signal transduction. In particular, SAM of Ship2 is known to form heterodimers with SAM domain of Eph-A2 receptor tyrosine kinase during receptor endocytosis as well as with SAM domain of PI3K effector protein Arap3 in the actin cytoskeleton signaling network. Since Ship2 plays a role in negatively regulating insulin signaling, it has been suggested that inhibition of its expression or function may contribute in treating type 2 diabetes and obesity-induced insulin resistance. 63 matched cddid_all.tbl CDD cd09492 cd09492 188891 SAM_SASH1_repeat2 SAM domain of SASH1 proteins, repeat 2. SAM (sterile alpha motif) repeat 2 of SASH1 proteins is a protein-protein interaction domain. Members of this subfamily are putative adaptor proteins. They appear to mediate signal transduction. SASH1 can bind 14-3-3 proteins in response to IGF1/phosphatidylinositol 3-kinase signaling. SASH1 was found upregulated in different tissues including thymus, placenta, lungs and downregulated in some breast tumors, liver metastases and colon cancers if compare to corresponding normal tissues. SASH1 is a potential candidate for a tumor suppressor gene in breast cancers. At the same time, downregulation of SASH1 in colon cancer is associated with metastasis and a poor prognosis. 70 matched cddid_all.tbl CDD cd09493 cd09493 188892 SAM_SASH-like SAM (Sterile alpha motif ), SASH1-like. SAM (sterile alpha motif) domain of SASH1-like proteins is a protein-protein interaction domain. Members of this subfamily are putative adaptor proteins. They appear to mediate signal transduction. Proteins of this subfamily are known to be involved in preventing DN thymocytes from premature initiation of programmed cell death and in B cells activation and differentiation. They have been found downregulated in some breast tumors, liver metastases and colon cancers if compare to corresponding normal tissues. 60 matched cddid_all.tbl CDD cd09494 cd09494 188893 SAM_liprin-kazrin_repeat1 SAM domain of liprin/kazrin proteins repeat 1. SAM (sterile alpha motif) domain repeat 1 of liprin/kazrin proteins is a protein-protein interaction domain. The long form of liprin/kazrin proteins contains three copies (repeats) of the SAM domain. Liprin-alpha may form heterodimers with liprin-beta through their SAM domains. Liprins were originally identified as LAR (leukocyte common antigen-related) transmembrane protein-tyrosine phosphatase-interacting proteins. They participate in mammary gland development and in axon guidance. In particular, liprin-alpha is involved in formation of the presynaptic active zone; liprin-beta is involved in the maintenance of lymphatic vessel integrity. Kazrins are involved in interplay between desmosomes and adherens junctions; additionally they play a role in regulation of intercellular differentiation, junction assembly, and cytoskeletal organization. 58 matched cddid_all.tbl CDD cd09495 cd09495 188894 SAM_liprin-kazrin_repeat2 SAM domain of liprin/kazrin proteins repeat 2. SAM (sterile alpha motif) domain repeat 2 of liprin/kazrin proteins is a protein-protein interaction domain. The long form of liprin/kazrin proteins contains three copies (repeats) of SAM domain. Liprin-alpha may form heterodimers with liprin-beta through their SAM domains. Liprins were originally identified as LAR (leukocyte common antigen-related) transmembrane protein-tyrosine phosphatase-interacting proteins. They participate in mammary gland development and in axon guidance. In particular, liprin-alpha is involved in formation of the presynaptic active zone; liprin-beta is involved in the maintenance of lymphatic vessel integrity. Kazrins are involved in interplay between desmosomes and in adheren junctions; additionally they play a role in regulation of intercellular differentiation, junction assembly, and cytoskeletal organization. 60 matched cddid_all.tbl CDD cd09496 cd09496 188895 SAM_liprin-kazrin_repeat3 SAM domain of liprin/kazrin proteins repeat 3. SAM (sterile alpha motif) domain repeat 3 of liprin/kazrin proteins is a protein-protein interaction domain. The long form of liprin/kazrin proteins contains three copies (repeats) of SAM domain. Liprin-alpha may form heterodimers with liprin-beta through their SAM domains. Liprins were originally identified as LAR (leukocyte common antigen-related) transmembrane protein-tyrosine phosphatase-interacting proteins. They participate in mammary gland development and in axon guidance. In particular, liprin-alpha is involved in formation of the presynaptic active zone; liprin-beta is involved in the maintenance of lymphatic vessel integrity. Kazrins are involved in interplay between desmosomes and in adherens junctions; additionally they play a role in regulation of intercellular differentiation, junction assembly, and cytoskeletal organization. 62 matched cddid_all.tbl CDD cd09497 cd09497 188896 SAM_caskin1,2_repeat1 SAM domain of caskin protein repeat 1. SAM (sterile alpha motif) domain repeat 1 of caskin1,2 proteins is a protein-protein interaction domain. Caskin has two tandem SAM domains. Caskin protein is known to interact with membrane-associated guanylate kinase CASK, and apparently may play a role in neural development, synaptic protein targeting, and regulation of gene expression. 66 matched cddid_all.tbl CDD cd09498 cd09498 188897 SAM_caskin1,2_repeat2 SAM domain of caskin protein repeat 2. SAM (sterile alpha motif) domain repeat 2 of caskin1,2 proteins is a protein-protein interaction domain. Caskin has two tandem SAM domains. Caskin protein is known to interact with membrane-associated guanylate kinase CASK, and may play a role in neural development, synaptic protein targeting, and regulation of gene expression. 71 matched cddid_all.tbl CDD cd09499 cd09499 188898 SAM_AIDA1AB-like_repeat1 SAM domain of AIDA1AB-like proteins, repeat 1. SAM (sterile alpha motif) domain repeat 1 of AIDA1AB-like proteins is a protein-protein interaction domain. AIDA1AB-like proteins have two tandem SAM domains. They may form an intramolecular head-to-tail homodimer. One of two basic motifs of the nuclear localization signal (NLS) is located within helix 5 of SAM2 (motif HKRK). This signal plays a role in decoupling of SAM2 from SAM1, thus facilitating translocation of this type proteins into the nucleus. SAM1 domain has a potential phosphorylation site for CMGC group of serine/threonine kinases. SAM domains of the AIDA1-like subfamily can directly bind ubiquitin and participate in regulating the degradation of ubiquitinated EphA receptors, particularly EPH-A8 receptor. Additionally AIDA1AB-like proteins may participate in the regulation of nucleoplasmic coilin protein interactions. 67 matched cddid_all.tbl CDD cd09500 cd09500 188899 SAM_AIDA1AB-like_repeat2 SAM domain of AIDA1AB-like proteins, repeat 2. SAM (sterile alpha motif) domain repeat 2 of AIDA1AB-like proteins is a protein-protein interaction domain. AIDA1AB-like proteins have two tandem SAM domains. They may form an intramolecular head-to-tail homodimer. One of two basic motifs of the nuclear localization signal (NLS) is located within helix 5 of the SAM2 (motif HKRK). This signal plays a role in decoupling of SAM2 from SAM1, thus facilitating translocation of this type proteins into the nucleus. SAM domains of the AIDA1AB-like subfamily can directly bind ubiquitin and participate in regulating the degradation of ubiquitinated EphA receptors, particularly EPH-A8 receptor. Additionally AIDA1AB-like proteins may participate in the regulation of nucleoplasmic coilin protein interactions. 65 matched cddid_all.tbl CDD cd09501 cd09501 188900 SAM_SARM1-like_repeat1 SAM domain ot SARM1-like proteins, repeat 1. SAM (sterile alpha motif) domain repeat 1 of SARM1-like adaptor proteins is a protein-protein interaction domain. SARM1-like proteins contain two tandem SAM domains. SARM1-like proteins are involved in TLR (Toll-like receptor) signaling. They are responsible for targeted localization of the whole protein to post-synaptic regions of axons. In humans SARM1 expression is detected in kidney and liver. 69 matched cddid_all.tbl CDD cd09502 cd09502 188901 SAM_SARM1-like_repeat2 SAM domain of SARM1-like, repeat 2. SAM (sterile alpha motif) domain repeat 2 of SARM1-like adaptor proteins is a protein-protein interaction domain. SARM1-like proteins contain two tandem SAM domains. SARM1-like proteins are involved in TLR (Toll-like receptor) signaling. They are responsible for targeted localization of the whole protein to post-synaptic regions of axons. In humans SARM1 expression is detected in kidney and liver. 70 matched cddid_all.tbl CDD cd09503 cd09503 188902 SAM_tumor-p63,p73 SAM domain of tumor-p63,p73 proteins. SAM (sterile alpha motif) domain of p63, p73 transcriptional factors is a putative protein-protein interaction domain and lipid-binding domain. p63 and p73 are homologs to the tumor suppressor p53. They have a C-terminal SAM domain in their longest spliced alpha forms, while p53 doesn't have it. p63 or p73 knockout mice show significant developmental abnormalities but no increased cancer susceptibility, suggesting that p63 and p73 play a role in regulation of normal development. It was shown that SAM domain of p73 is able to bind some membrane lipids. The structural rearrangements in SAM are necessary to accomplish the binding. No evidence for homooligomerization through SAM domains was found for p63/p73 subfamily. It was suggested that the partner proteins should be either more distantly related SAM-containing domain proteins or proteins without the SAM domain. 65 matched cddid_all.tbl CDD cd09504 cd09504 188903 SAM_STIM-1,2-like "SAM domain of STIM-1,2-like proteins. SAM (sterile alpha motif) domain of STIM-1,2-like (Stromal interaction molecule) proteins is a putative protein-protein interaction domain. STIM1 and STIM2 human proteins are type I transmembrane proteins. The N-terminal part of them includes ""hidden"" EF-hand and SAM domains. This region is responsible for sensing changes in store-operated and basal cytoplasmic Ca2+ levels and initiates oligomerization. ""Hidden"" EF hand and SAM domains have a stable intramolecular association, and the SAM domain is a component that regulates stability within STIM proteins. Destabilization of the EF-SAM association during Ca2+ depletion leads to partial unfolding and aggregation (homooligomerization), thus activating the store-operated Ca2+ entry. Immunoprecipitation analysis indicates that STIM1 and STIM2 can form co-precipitable oligomeric associations in vivo. It was suggested that STIM1 and STIM2 are involved in opposite regulation of store operated channels in plasma membrane." 74 matched cddid_all.tbl CDD cd09505 cd09505 188904 SAM_WDSUB1 SAM domain of WDSUB1 proteins. SAM (sterile alpha motif) domain of WDSUB1 subfamily proteins is a putative protein-protein interaction domain. Proteins of this group contain multiple domains: SAM, one or more WD40 repeats and U-box (derived version of the RING-finger domain). Apparently the WDSUB1 subfamily proteins participate in protein degradation through ubiquitination, since U-box domain are known as a member of E3 ubiquitin ligase family, while SAM and WD40 domains most probably are responsible for an E2 ubiquitin-conjugating enzyme binding and a target protein binding. 72 matched cddid_all.tbl CDD cd09506 cd09506 188905 SAM_Shank1,2,3 SAM domain of Shank1,2,3 family proteins. SAM (sterile alpha motif) domain of Shank1,2,3 family proteins is a protein-protein interaction domain. Shank1,2,3 proteins are scaffold proteins that are known to interact with a variety of cytoplasmic and membrane proteins. SAM domains of the Shank1,2,3 family are prone to homooligomerization. They are highly enriched in the postsynaptic density, acting as scaffolds to organize assembly of postsynaptic proteins. SAM domains of Shank3 proteins can form large sheets of helical fibers. Shank genes show distinct patterns of expression, in rat Shank1 mRNA is found almost exclusively in brain, Shank2 in brain, kidney and liver, and Shank3 in heart, brain and spleen. 66 matched cddid_all.tbl CDD cd09507 cd09507 188906 SAM_DGK-delta-eta SAM domain of diacylglycerol kinase delta and eta subunits. SAM (sterile alpha motif) domain of DGK-eta-delta subfamily proteins is a protein-protein interaction domain. Proteins of this subfamily are multidomain diacylglycerol kinases with a SAM domain located at the C-terminus. DGK proteins participate in signal transduction. They regulate the level of second messengers such as diacylglycerol and phosphatidic acid. The SAM domain of DGK proteins can form high molecular weight homooligomers through head-to-tail interactions as well as heterooligomers between the SAM domains of DGK delta and eta proteins. The oligomerization plays a role in the regulation of DGK intracellular localization. 65 matched cddid_all.tbl CDD cd09508 cd09508 188907 SAM_HD SAM domain of HD-phosphohydrolase. SAM (sterile alpha motif) domain of SAM_HD subfamily proteins is a putative protein-protein interaction domain. Proteins of this group, additionally to the SAM domain, contain a HD hydrolase domain. Human SAM-HD1 is a nuclear protein involved in innate immune response and may act as a negative regulator of the cell-intrinsic antiviral response. Mutations in this gene lead to Aicardi-Goutieres syndrome (symptoms include cerebral atrophy, leukoencephalopathy, hepatosplenomegaly, and increased production of alpha-interferon). 70 matched cddid_all.tbl CDD cd09509 cd09509 188908 SAM_Polycomb SAM domain of Polycomb group. SAM (sterile alpha motif) domain of Polycomb group is a protein-protein interaction domain. The Polycomb group includes transcriptional repressors which are involved in the regulation of some key regulatory genes during development in many organisms. They are best known for silencing Hox (Homeobox) genes. Polycomb proteins work together in large multimeric and chromatin-associated complexes. They organize chromatin of the target genes and maintain repressed states during many cell divisions. Polycomb proteins are classified based on their common function, but not on conserved domains and/or motifs; however many Polycomb proteins (members of PRC1 class complex) contain SAM domains which are more similar to each other inside of the Polycomb group than to SAM domains outside of it. Most information about structure and function of Polycomb SAM domains comes from studies of Ph (Polyhomeotic) and Scm (Sex comb on midleg) proteins. Polycomb SAM domains usually can be found at the C-terminus of the proteins. Some members of this group contain, in addition to the SAM domain, MTB repeats, Zn finger, and/or DUF3588 domains. Polycomb SAM domains can form homo- and/or heterooligomers through ML and EH surfaces. SAM/SAM oligomers apparently play a role in transcriptional repression through polymerization along the chromosome. Polycomb proteins are known to be highly expressed in some cells years before their cancer pathology; thus they are attractive markers for early cancer therapy. 64 matched cddid_all.tbl CDD cd09510 cd09510 188909 SAM_aveugle-like SAM domain of aveugle-like subfamily. SAM (sterile alpha motif) domain of SAM_aveugle-like subfamily is a protein-protein interaction domain. In Drosophila, the aveugle (AVE) protein (also known as HYP (Hyphen)) is involved in normal photoreceptor differentiation, and required for epidermal growth factor receptor (EGFR) signaling between ras and raf genes during eye development and wing vein formation. SAM domain of the HYP(AVE) protein interacts with SAM domain of CNK, the multidomain scaffold protein connector enhancer of kinase suppressor of ras. CNK/HYP(AVE) complex interacts with KSR (kinase suppressor of Ras) protein. This interaction leads to stimulation of Ras-dependent Raf activation. This subfamily also includes vertebrate AVE homologs - Samd10 and Samd12 proteins. Their exact function is unknown, but they may play a role in signal transduction during embryogenesis. 75 matched cddid_all.tbl CDD cd09511 cd09511 188910 SAM_CNK1,2,3-suppressor SAM domain of CNK1,2,3-suppressor subfamily. SAM (sterile alpha motif) domain of CNK (connector enhancer of kinase suppressor of ras (Ksr)) subfamily is a protein-protein interaction domain. CNK proteins are multidomain scaffold proteins containing a few protein-protein interaction domains and are required for connecting Rho and Ras signaling pathways. In Drosophila, the SAM domain of CNK is known to interact with the SAM domain of the aveugle protein, forming a heterodimer. Mutation of the SAM domain in human CNK1 abolishes the ability to cooperate with the Ras effector, supporting the idea that this interaction is necessary for proper Ras signal transduction. 69 matched cddid_all.tbl CDD cd09512 cd09512 188911 SAM_Neurabin-like SAM domain of SAM_Neurabin-like subfamily. SAM (sterile alpha motif) domain of Neurabin-like (Neural actin-binding) subfamily is a putative protein-protein interaction domain. This group currently includes the SAM domains of neurobin-I, SAMD14 and neurobin-I/SAMD14-like proteins. Most are multidomain proteins and in addition to SAM domain they contain other protein-binding domains such as PDZ and actin-binding domains. Members of this subfamily participate in signal transduction. Neurabin-I is involved in the regulation of Ca signaling intensity in alpha-adrenergic receptors; it forms a functional pair of opposing regulators with neurabin-II. Neurabins are expressed almost exclusively in neuronal cells. They are known to interact with protein phosphatase 1 and inhibit its activity; they also can bind actin filaments; however, the exact role of the SAM domain is unclear, since SAM doesn't participate in these interactions. 70 matched cddid_all.tbl CDD cd09513 cd09513 188912 SAM_BAR SAM domain of BAR subfamily. SAM (sterile alpha motif) domain of BAR (Bifunctional Apoptosis Regulator) subfamily is a protein-protein interaction domain. In addition to the SAM domain, this type of regulator has a RING finger domain. Proteins of this subfamily are involved in the apoptosis signal network. Their overexpression in human neuronal cells significantly protects cells from a broad range of cell death stimuli. SAM domain can interact with Caspase8, Bcl-2 and Bcl-X resulting in suppression of Bax-induced cell death. 71 matched cddid_all.tbl CDD cd09514 cd09514 188913 SAM_SGMS1 SAM domain of sphingomyelin synthase. SAM (sterile alpha motif) domain of SGMS-1 (sphingomyelin synthase) subfamily is a potential protein-protein interaction domain. Sphingomyelin synthase 1 is a transmembrane protein with a SAM domain at the N-terminus and a catalytic domain at the C-terminus. Sphingomyelin synthase 1 is a Golgi-associated enzyme, and depending on the concentration of diacylglycerol and ceramide, can catalyze synthesis phosphocholine or sphingomyelin, respectively. It plays a central role in sphingolipid and glycerophospholipid metabolism. 72 matched cddid_all.tbl CDD cd09515 cd09515 188914 SAM_SGMS1-like SAM domain of sphingomyelin synthase related subfamily. SAM (sterile alpha motif) domain of SGMS-like (sphingomyelin synthase) subfamily is a potential protein-protein interaction domain. This group of proteins is related to sphingomyelin synthase 1, and contains an N-terminal SAM domain. The function of SGMS1-like proteins is unknown; they may play a role in sphingolipid metabolism. 70 matched cddid_all.tbl CDD cd09516 cd09516 188915 SAM_sec23ip-like SAM domain of sec23ip-like subfamily. SAM (sterile alpha motif) domain of Sec23ip-like (Sec23 interacting protein) subfamily is a potential protein-protein interaction domain. This group of proteins includes Sec23ip and DDHD2 proteins. All of them contain at least two domains: a SAM domain and a predicted metal-binding domain. For mammalian DDHD2 members of this group, phospholipase activity has been demonstrated. Sec23ip proteins of this group interact with Sec23 proteins via an N-terminal proline-rich region. Members of this subfamily are involved in organization of ER/Golgi intermediate compartment. 69 matched cddid_all.tbl CDD cd09517 cd09517 188916 SAM_USH1G_HARP SAM domain of USH1G_HARP family. SAM (sterile alpha motif) domain of USH1G/HARP (Usher syndrome type-1G/ Harmonin-interacting Ankyrin Repeat-containing protein) family is a protein-protein interaction domain. Members of this family have an N-terminal ankyrin repeat region and a C-terminal SAM domain. In mammals these proteins can interact via the SAM domain with the PDZ domain of harmonin to form a scaffolding complex that facilitates signal transduction in epithelial and inner ear sensory cells. It was suggested that USH1G and HARP can be tissue specific partners of harmonin. Mutations in ush1g genes lead to Usher syndrome type 1G. This syndrome is the cause of deaf-blindness in humans. 66 matched cddid_all.tbl CDD cd09518 cd09518 188917 SAM_ANKS6 SAM domain of ANKS6 (or SamCystin) subfamily. SAM (sterile alpha motif) domain of ANKS6 (or SamCystin) subfamily is a potential protein-protein interaction domain. Proteins of this subfamily have N-terminal ankyrin repeats and a C-terminal SAM domain. They are able to form self-associated complexes and both (SAM and ANK) domains play a role in such interactions. Mutations in Anks6 gene are associated with polycystic kidney disease. They cause formation of renal cysts in rodent models. It was suggested that the ANKS6 protein can interact indirectly (through RNA and protein intermediates) with BICC1, another polycystic kidney disease-associated protein. 65 matched cddid_all.tbl CDD cd09519 cd09519 188918 SAM_ANKS3 SAM domain of ANKS3 subfamily. SAM (sterile alpha motif) domain of ANKS3 subfamily is a potential protein-protein interaction domain. Proteins of this subfamily have N-terminal ankyrin repeats and a C-terminal SAM domain. SAM is a widespread domain in signaling proteins. In many cases it mediates homo-dimerization/oligomerization. 64 matched cddid_all.tbl CDD cd09520 cd09520 188919 SAM_BICC1 SAM domain of BICC1 (bicaudal) subfamily. SAM (sterile alpha motif) domain of BICC1 (bicaudal) subfamily is a protein-protein interaction domain. Proteins of this group have N-terminal K homology RNA-binding vigilin-like repeats and a C-terminal SAM domain. BICC1 is involved in the regulation of embryonic differentiation. It plays a role in the regulation of Dvl (Dishevelled) signaling, particularly in the correct cilia orientation and nodal flow generation. In Drosophila, disruption of BICC1 can disturb the normal migration direction of the anterior follicle cell of oocytes; the specific function of SAM is to recruit whole protein to the periphery of P-bodies. In mammals, mutations in this gene are associated with polycystic kidney disease and it was suggested that the BICC1 protein can indirectly interact with ANKS6 protein (ANKS6 is also associated with polycystic kidney disease) through some protein and RNA intermediates. 65 matched cddid_all.tbl CDD cd09521 cd09521 188920 SAM_ASZ1 SAM domain of ASZ1 subfamily. SAM (sterile alpha motif) domain of ASZ1 (Ankyrin, SAM, leucine Zipper) also known as GASZ (Germ cell-specific Ankyrin, SAM, leucine Zipper) subfamily is a potential protein-protein interaction domain. Proteins of this group are involved in the repression of transposable elements during spermatogenesis, oogenesis, and preimplantation embryogenesis. They support synthesis of PIWI-interacting RNA via association with some PIWI proteins, such as MILI and MIWI. This association is required for initiation and maintenance of retrotransposon repression during the meiosis. In mice lacking ASZ1, DNA damage and delayed germ cell maturation was observed due to retrotransposons releasing from their repressed state. 64 matched cddid_all.tbl CDD cd09522 cd09522 188921 SAM_SLP76 SAM domain of SLP76 subfamily. SAM (sterile alpha motif) domain of SLP76 (SH2 domain-containing leukocyte protein 76), also known as LCP2 (Lymphocyte cytosolic protein), subfamily is a protein-protein interaction domain. Proteins of this group have an N-terminal SAM domain, 3 phosphotyrosine motifs, a proline-rich region and a C-terminal SH2 domain. They are scaffold proteins involved in protein complex formation. The complexes play a role in T-cell receptor mediated signaling pathways such as integrin activation, cytoskeletal organization, MARK activation, and calcium flux. SAM domain deleted SLP76 knockin mice show a number of defects, including partially blocked thymocyte development, impaired positive and negative thymic selection and changes in T-cell receptor mediated signaling. 69 matched cddid_all.tbl CDD cd09523 cd09523 188922 SAM_TAL SAM domain of TAL subfamily. SAM (sterile alpha motif) domain of TAL (Tsg101-associated ligase) proteins, also known as LRSAM1 (Leucine-rich repeat and sterile alpha motif-containing) proteins, is a putative protein-protein interaction domain. Proteins of this subfamily participate in the regulation of retrovirus budding and receptor endocytosis. They show E3 ubiquitin ligase activity. Human TAL protein interacts with Tsg101 and TAL's C-terminal ring finger domain is essential for the multiple monoubiquitylation of Tsg101. 65 matched cddid_all.tbl CDD cd09524 cd09524 188923 SAM_tankyrase1,2 SAM domain of tankyrase1,2 subfamily. SAM (sterile alpha motif) domain of Tankyrase1,2 subfamily is a protein-protein interaction domain. In addition to the SAM domain, proteins of this group have ankyrin repeats and a ADP- ribosyltransferase (poly-(ADP-ribose) synthase) domain. Tankyrases can polymerize through their SAM domains forming homoligomers and these complexes are disrupted by autoribosylation. Tankyrases apparently act as master scaffolding proteins and thus may interact simultaneously with multiple proteins, in particular with TRF1, NuMA, IRAP and Grb14 (ankyrin repeats are involved in these interactions). Tankyrases participate in a variety of cell signaling pathways as effector molecules. Their functions are different depending on the intracellular location: at telomeres they play a role in the regulation of telomere length via control of telomerase access to telomeres, at centrosomes they promote spindle assembly/disassembly, in Golgi vesicles they participate in the regulation of vesicle trafficking and Golgi dynamics. Tankyrase 1 may be of interest as new potential target for telomerase-directed cancer therapy. 66 matched cddid_all.tbl CDD cd09525 cd09525 188924 SAM_GAREM SAM domain of GAREM subfamily. SAM (sterile alpha motif) domain of GAREM (Grb2-associated and regulator of Erk/MARK) protein subfamily (also known as FAM59A) is a putative protein-protein interaction domain. SAM domain is a widespread domain in signaling proteins. Proteins of this group have SAM at the C-terminus. Human GAREM protein is known to play a role in regulation of the EGF (Epidermal Growth Factor) receptor and of Gab or insulin preceptor substrate-1 family proteins. Grb2 (Growth factor receptor-bound) protein was identified as a binding partner of human GAREM. Proline-rich motifs and phosphorylation of two conserved tyrosines in GAREM are important for the interaction with the SH3 domains of Grb2 protein; however these motifs and residues do not belong to the SAM domain. 67 matched cddid_all.tbl CDD cd09526 cd09526 188925 SAM_Samd3 SAM domain of Samd3 subfamily. SAM (sterile alpha motif) domain of the Samd3 subfamily is a putative protein-protein interaction domain. Proteins of this subfamily have a SAM domain at the N-terminus. SAM is a widespread domain in signaling and regulatory proteins. In many cases SAM mediates dimerization/oligomerization. Exact function of proteins belonging to this subfamily is unknown. 66 matched cddid_all.tbl CDD cd09527 cd09527 188926 SAM_Samd5 SAM domain of Samd5 subfamily. SAM (sterile alpha motif) domain of Samd5 subfamily is a putative protein-protein interaction domain. Proteins of this subfamily have a SAM domain at the N-terminus. SAM is a widespread domain in signaling and regulatory proteins. In many cases SAM mediates dimerization/oligomerization. The exact function of proteins belonging to this subfamily is unknown. 63 matched cddid_all.tbl CDD cd09528 cd09528 188927 SAM_Samd9_Samd9L SAM domain of Samd9/Samd9L subfamily. SAM (sterile alpha motif) domain of Samd9/Samd9L subfamily is a putative protein-protein interaction domain. SAM is a widespread domain in signaling proteins. Samd9 is a tumor suppressor gene. It is involved in death signaling of malignant glioblastoma. Samd9 suppression blocks cancer cell death induced by HVJ-E or IFN-beta treatment. Deleterious mutations in Samd9 lead to normophosphatemic familial tumoral calcinosis, a cutaneous disorder characterized by cutaneous calcification or ossification. 64 matched cddid_all.tbl CDD cd09529 cd09529 188928 SAM_MLTK SAM domain of MLTK subfamily. SAM (sterile alpha motif) domain of MLTK subfamily is a protein-protein interaction domain. Besides SAM domain, these proteins have N-terminal protein tyrosine kinase domain and leucine-zipper motif. Proteins of this group act as mitogen-activated protein triple kinase in a number of MAPK cascades. They can be activated by autophosphorylation in response to stress signals. MLTK-alpha is known to phosphorylate histone H3. In mammals, MLTKs participate in the activation of the JNK/SAPK, p38, ERK5 pathways, the transcriptional factor NF-kB, in the regulation of the cell cycle checkpoint, and in the induction of apoptosis in a hepatoma cell line. Some members of this subfamily are proto-oncogenes, thus MLTK-alpha is involved in neoplasmic cell transformation and/or skin cancer development in athymic nude mice. Based on in vivo coprecipitation experiments in mammalian cells, it has been demonstrated that MLTK proteins might form homodimers/oligomers via their SAM domains. 71 matched cddid_all.tbl CDD cd09530 cd09530 188929 SAM_Samd14 SAM domain of Samd14 subfamily. SAM (sterile alpha motif) domain of SamD14 (or FAM15A) subfamily is a putative protein-protein interaction domain. SAM is widespread domain in proteins involved in signal transduction and regulation. In many cases SAM mediates homodimerization/oligomerization. The exact function of proteins belonging to this subfamily is unknown. 67 matched cddid_all.tbl CDD cd09531 cd09531 188930 SAM_CS047 SAM domain of CS047 subfamily. SAM (sterile alpha motif) domain of CS047 subfamily is a putative protein-protein interaction domain. Proteins of this subfamily have a SAM domain at the N-terminus. SAM is a widespread domain in signaling and regulatory proteins. In many cases SAM mediates homodimerization/oligomerization. The exact function of proteins belonging to this group is unknown. 65 matched cddid_all.tbl CDD cd09532 cd09532 188931 SAM_SLA1_fungal SAM domain of SLA1 subfamily. SAM (sterile alpha motif) domain of fungal SLA1 proteins is a protein-protein interaction domain. Proteins of this group consist of a few N-terminal SH3 domains followed by SHD1 domain, SAM domain (also known as SHD2) and multiple C-terminal repeats. The yeast SLA1 protein is an endocytic clathrin adaptor. It is associated with a variety of endocytic accessory factors and required for endocytic vesicle formation and for clathrin and actin-dependent cargo recognition. SLA1 binds clathrin through a variant clathrin-binding motif (vCB). The SAM domain negatively regulates this binding by blocking the vCB site. The SAM domains of SLA1 proteins can form oligomers via their mid-loop (ML) and end-helix (EH) regions. Such self-associations apparently are important for SLA1 function. A proposed regulatory model suggests that SAM can be considered a mediator of two aspects of clathrin adaptor function. It plays a role in negative regulation of clathrin binding via an intramolecular interaction with the vCB, and a role in positive regulation of vesicle coat assembly via self-oligomerization. 62 matched cddid_all.tbl CDD cd09533 cd09533 188932 SAM_Ste50-like_fungal SAM domain of Ste50_like (ubc2) subfamily. SAM (sterile alpha motif) domain of Ste50-like (or Ubc2 for Ustilago bypass of cyclase) subfamily is a putative protein-protein interaction domain. This group includes only fungal proteins. Basidiomycetes have an N-terminal SAM domain, central UBQ domain, and C-terminal SH3 domain, while Ascomycetes lack the SH3 domain. Ubc2 of Ustilago maydis is a major virulence and maize pathogenicity factor. It is required for filamentous growth (the budding haploid form of Ustilago maydis is a saprophyte, while filamentous dikaryotic form is a pathogen). Also the Ubc2 protein is involved in the pheromone-responsive morphogenesis via the MAP kinase cascade. The SAM domain is necessary for ubc2 function; deletion of SAM eliminates this function. A Lys-to-Glu mutation in the SAM domain of ubc2 gene induces temperature sensitivity. 58 matched cddid_all.tbl CDD cd09534 cd09534 188933 SAM_Ste11_fungal SAM domain of Ste11_fungal subfamily. SAM (sterile alpha motif) domain of Ste11 subfamily is a protein-protein interaction domain. Proteins of this subfamily have SAM domain at the N-terminus and protein kinase domain at the C-terminus. They participate in regulation of mating pheromone response, invasive growth and high osmolarity growth response. MAP triple kinase Ste11 from S.cerevisia is known to interact with Ste20 kinase and Ste50 regulator. These kinases are able to form homodimers interacting through their SAM domains as well as heterodimers or heterogenous complexes when either SAM domain of monomeric or homodimeric form of Ste11 interacts with Ste50 regulator. 62 matched cddid_all.tbl CDD cd09535 cd09535 188934 SAM_BOI-like_fungal SAM domain of BOI-like fungal subfamily. SAM (sterile alpha motif) domain of BOI-like fungal subfamily is a potential protein-protein interaction domain. Proteins of this subfamily are apparently scaffold proteins, since most contain SH3 and PH domains, which are also protein-protein interaction domains, in addition to SAM domain. BOI-like proteins participate in cell cycle regulation. In particular BOI1 and BOI2 proteins of budding yeast S.cerevisiae are involved in bud formation, and POB1 protein of fission yeast S.pombe plays a role in cell elongation and separation. Among binding partners of BOI-like fungal subfamily members are such proteins as Bem1 and Cdc42 (they are known to be involved in cell polarization and bud formation). 65 matched cddid_all.tbl CDD cd09536 cd09536 188935 SAM_Ste50_fungal SAM domain of Ste50 fungal subfamily. SAM (sterile alpha motif) domain of Ste50 fungal subfamily is a protein-protein interaction domain. Proteins of this subfamily have SAM domain at the N-terminus and Ras-associated UBQ superfamily domain at the C-terminus. They participate in regulation of mating pheromone response, invasive growth and high osmolarity growth response, and contribute to cell wall integrity in vegetative cells. Ste50 of S.cerevisiae acts as an adaptor protein between G protein and MAP triple kinase Ste11. Ste50 proteins are able to form homooligomers, binding each other via their SAM domains, as well as heterodimers and heterogeneous complexes with SAM domain or SAM homodimers of MAPKKK Ste11 protein kinase. 74 matched cddid_all.tbl CDD cd09537 cd09537 188936 SAM_CP2-like SAM domain of CP2-like transcription factors. SAM (sterile alpha motif) domain of CP2-like transcription factor is a putative protein-protein interaction domain. Proteins of this group have an N-terminal DNA-binding CP2 domain, a central predicted SAM domain and some also have a C-terminal dimerization domain. CP2-like family of transcriptional factors includes three subgroups: LBP1, TFCP2, and LBP9. Members of this family are involved in transcriptional regulation from early development to terminal differentiation. They play a role in regulation of expression of P450scc (the cholesterol side-chain cleavage enzyme, cytochrome) in placenta, and alpha-globin in erythroid cells. They are required for proper maturation of the dust (epithelial component of tubular organs) of kidney and salivary gland. Human LBP1 is known to be induced by HIV type I infection in lymphocytes; it represses HIV transcription by preventing the binding of TFIID to the virus promoter. Additionally, it has been suggested that UBP1 (LBP1) regulator might be a member of a blood pressure controlling network. LBP1 protein isoforms are able to form dimers apparently via SAM domain since SAM deletion or mutation resulted in a loss of this ability. 67 matched cddid_all.tbl CDD cd09538 cd09538 188937 SAM_DLC1,2-like SAM domain of DLC1,2-like subfamily. SAM (sterile alpha motif) domain of DLC-1,2-like (Deleted in liver cancer) subfamily is a protein-protein interaction domain located at the N-terminus of the protein. Members of this subfamily do not form dimers/oligomers through their SAM domains. They participate in regulation of cell migration and lipid transfer. SAM domain of human DLC1 protein contains the EF1A1 (eukaryotic elongation factor) binding motif, thus SAM facilitates recruitment of EF1A1 to the membrane periphery and suppresses cell migration. Human Dlc2 gene is known as a tumor suppressor gene. It was found underexpressed in hepatocellular carcinoma. 60 matched cddid_all.tbl CDD cd09539 cd09539 188938 SAM_TNK-like SAM domain of TNK(ACK)-like non-receptor tyrosine-protein kinases. SAM (sterile alpha motif) domain of TNK-like subfamily is a putative protein-protein interaction domain. This subfamily includes TNK1 and TNK2 (also known as ACK1) non-receptor tyrosine-protein kinases. They contain a SAM domain at the N-terminus followed by a catalytic domain and a few other domains. Members of this group are involved in the regulation of cell adhesion and growth, receptor degradation, and axonal guidance. Deletion of the SAM domain resulted in reduction of Ack1 ability to undergo autophosphorylation and dramatically reduces ubiquitination of Ack1 catalyzed by HECT E3 ubiquitin ligase (Nedd4-1) during EGF-induced Ack1 degradation. It has been suggested that the lysine-rich region in SAM domain might be a major ubiquitination site. Members of this group are also associated with some cancers. Amplification of the Ack1 gene correlates with prostate and lung cancer progression, and Ack1 overexpression increases invasiveness. Oncogenecity of Tnk1 gene apparently depends on cell context; it may play a role in tumor suppression since Tnk1 knockout mice can develop spontaneous tumors. 62 matched cddid_all.tbl CDD cd09540 cd09540 188939 SAM_EPS8-like SAM domain of EPS8-like subfamily. SAM (sterile alpha motif) domain of EPS8-like subfamily is a putative protein-protein interaction domain. This subfamily includes epidermal growth factor receptor kinase substrate 8 proteins (EPS8) and epidermal growth factor receptor kinase substrate 8-like (EPSL8) 1, 2, 3 proteins with the SAM domain located in the C-terminal effector region. This region is responsible for intracellular protein localization and is involved in small GTPases (such as Rac and Rab5) activation/inhibition. Proteins belonging to this group participate in coordination and integration of multiple signaling pathways; in particular, they play a role in the control of actin dynamics and in receptor endocytosis. They can form complexes with other proteins; for example, in the actin signaling network they interact with SOS1 and E3b1 (Abl1) proteins as well as with CRIB (via SH3 domains) during the actin filament formation, and in the receptor endocytosis their partner is RN-tre protein. 66 matched cddid_all.tbl CDD cd09541 cd09541 188940 SAM_KIF24-like SAM domain of KIF24-like subfamily. SAM (sterile alpha motif) domain of KIF24 subfamily is a putative protein-protein interaction domain. This subfamily includes proteins related to human kinesin-like protein KIF24. SAM domain is located at the N-terminus followed by kinesin motor domain. Kinesins are proteins involved in a number of different cell processes including microtubule dynamics and axonal transport. Kinesins of this group belong to N-type; they drive microtubule plus end-directed transport. SAM apparently plays the role of adaptor or scaffold domain. In many cases SAM is known as a mediator of dimerization/oligomerization. 60 matched cddid_all.tbl CDD cd09542 cd09542 188941 SAM_EPH-A1 SAM domain of EPH-A1 subfamily of tyrosine kinase receptors. SAM (sterile alpha motif) domain of EPH-A1 subfamily of the receptor tyrosine kinases is a C-terminal protein-protein interaction domain. This domain is located in the cytoplasmic region of EPH-A1 receptors and appears to mediate cell-cell initiated signal transduction. Activation of these receptors leads to inhibition of cell spreading and migration in a RhoA-ROCK-dependent manner. EPH-A1 receptors are known to bind ILK (integrin-linked kinase) which is the mediator of interactions between integrin and the actin cytoskeleton. However SAM is not sufficient for this interaction; it rather plays an ancillary role. SAM domains of Eph-A1 receptors do not form homo/hetero dimers/oligomers. EphA1 gene was found expressed widely in differentiated epithelial cells. In a number of different malignant tumors EphA1 genes are downregulated. In breast carcinoma the downregulation is associated with invasive behavior of the cell. 63 matched cddid_all.tbl CDD cd09543 cd09543 188942 SAM_EPH-A2 SAM domain of EPH-A2 family of tyrosine kinase receptors. SAM (sterile alpha motif) domain of EPH-A2 subfamily of receptor tyrosine kinases is a C-terminal protein-protein interaction domain. This domain is located in the cytoplasmic region of EPH-A2 receptors and appears to mediate cell-cell initiated signal transduction. For example, SAM domain of EPH-A2 receptors interacts with SAM domain of Ship2 proteins (SH2 containing phosphoinositide 5-phosphotase-2) forming heterodimers; such recruitment of Ship2 by EPH-A2 attenuates the positive signal for receptor endocytosis. Eph-A2 is found overexpressed in many types of human cancer, including breast, prostate, lung and colon cancer. High level of expression could induce cancer progression by a variety of mechanisms and could be used as a novel tag for cancer immunotherapy. EPH-A2 receptors are attractive targets for drag design. 70 matched cddid_all.tbl CDD cd09544 cd09544 188943 SAM_EPH-A3 SAM domain of EPH-A3 subfamily of tyrosine kinase receptors. SAM (sterile alpha motif) domain of EPH-A3 subfamily of receptor tyrosine kinases is a C-terminal putative protein-protein interaction domain. This domain is located in the cytoplasmic region of EPH-A3 receptors and appears to mediate cell-cell initiated signal transduction. EPH-A3 receptors bind SH2/SH3 containing adaptor protein Nck1 and this adaptor is a key factor in EPH-A3 mediated signaling. However SAM domain is not implemented in this interaction. Activation of EPH-A3 receptors inhibits outgrowth and cell migration. Mutations in SAM domain may play a role in development of hepatocellular carcinoma. Expression of EPH-A3 is associated with lymphocytic leukemia and defines the subset of rhabdomyosarcoma tumors. EPH-A3 receptors are attractive targets for drug design. 63 matched cddid_all.tbl CDD cd09545 cd09545 188944 SAM_EPH-A4 SAM domain of EPH-A4 subfamily of tyrosine kinase receptors. SAM (sterile alpha motif) domain of EPH-A4 subfamily of receptor tyrosine kinases is a C-terminal potential protein-protein interaction domain. This domain is located in the cytoplasmic region of EPH-A4 receptors and appears to mediate cell-cell initiated signal transduction. SAM domains of EPH-A4 receptors can form homodimers. EPH-A4 receptors bind ligands such as erphirin A1, A4, A5. They are known to interact with a number of different proteins, including meltrin beta metalloprotease, Cdk5, and EFS2alpha, however SAM domain doesn't participate in these interactions. EPH-A4 receptors are involved in regulation of corticospinal tract formation, in pathway controlling voluntary movements, in formation of motor neurons, and in axon guidance (SAM domain is not required for axon guidance or for EPH-A4 kinase signaling). In Xenopus embryos EPH-A4 induces loss of cell adhesion, ventro-lateral protrusions, and severely expanded posterior structures. Mutations in SAM domain conserved tyrosine (Y928F) enhance the ability of EPH-A4 to induce these phenotypes, thus supporting the idea that the SAM domain may negatively regulate some aspects of EPH-A4 activity. EphA4 gene was found overexpressed in a number of different cancers including human gastric cancer, colorectal cancer, and pancreatic ductal adenocarcinoma. It is likely to be a promising molecular target for the cancer therapy. 71 matched cddid_all.tbl CDD cd09546 cd09546 188945 SAM_EPH-A5 SAM domain of EPH-A5 subfamily of tyrosine kinase receptors. SAM (sterile alpha motif) domain of EPH-A5 subfamily of receptor tyrosine kinases is a C-terminal potential protein-protein interaction domain. This domain is located in the cytoplasmic region of EPH-A5 receptors and appears to mediate cell-cell initiated signal transduction. Eph-A5 gene is almost exclusively expressed in the nervous system. Murine EPH-A5 receptors participate in axon guidance during embryogenesis and play a role in the adult synaptic plasticity, particularly in neuron-target interactions in multiple neural circuits. Additionally EPH-A5 receptors and its ligand ephrin A5 regulate dopaminergic axon outgrowth and influence the formation of the midbrain dopaminergic pathways. EphA5 gene expression was found decreased in a few different breast cancer cell lines, thus it might be a potential molecular marker for breast cancer carcinogenesis and progression. 66 matched cddid_all.tbl CDD cd09547 cd09547 188946 SAM_EPH-A6 SAM domain of EPH-A6 subfamily of tyrosine kinase receptors. SAM (sterile alpha motif) domain of EPH-A6 subfamily of receptor tyrosine kinases is a C-terminal potential protein-protein interaction domain. This domain is located in the cytoplasmic region of EPH-A6 receptors and appears to mediate cell-cell initiated signal transduction. Eph-A6 gene is preferentially expressed in the nervous system. EPH-A6 receptors are involved in primate retina vascular and axon guidance, and in neural circuits responsible for learning and memory. EphA6 gene was significantly down regulated in colorectal cancer and in malignant melanomas. It is a potential molecular marker for these cancers. 64 matched cddid_all.tbl CDD cd09548 cd09548 188947 SAM_EPH-A7 SAM domain of EPH-A7 subfamily of tyrosine kinase receptors. SAM (sterile alpha motif) domain of EPH-A7 subfamily of receptor tyrosine kinases is a C-terminal potential protein-protein interaction domain. This domain is located in the cytoplasmic region of EPH-A7 receptors and appears to mediate cell-cell initiated signal transduction. EphA7 was found expressed in human embryonic stem (ES) cells, neural tissues, kidney vasculature. EphA7 knockout mice show decrease in cortical progenitor cell death at mid-neurogenesis and significant increase in cortical size. EphA7 may be involved in the pathogenesis and development of different cancers; in particular, EphA7 was found upregulated in glioblastoma and downregulated in colorectal cancer and gastric cancer. Thus, it is a potential molecular marker and/or therapy target for these types of cancers. 70 matched cddid_all.tbl CDD cd09549 cd09549 188948 SAM_EPH-A10 SAM domain of EPH-A10 subfamily of tyrosine kinase receptors. SAM (sterile alpha motif) domain of EPH-A10 subfamily of receptor tyrosine kinases is a C-terminal potential protein-protein interaction domain. This domain is located in the cytoplasmic region of EPH-A10 receptors and appears to mediate cell-cell initiated signal transduction. It was found preferentially expressed in the testis. EphA10 may be involved in the pathogenesis and development of prostate carcinoma and lymphocytic leukemia. It is a potential molecular marker and/or therapy target for these types of cancers. 70 matched cddid_all.tbl CDD cd09550 cd09550 188949 SAM_EPH-A8 SAM domain of EPH-A8 subfamily of tyrosine kinase receptors. SAM (sterile alpha motif) domain of EPH-A8 subfamily of receptor tyrosine kinases is a C-terminal potential protein-protein interaction domain. This domain is located in the cytoplasmic region of EPH-A8 receptors and appears to mediate cell-cell initiated signal transduction. EPH-A8 receptors are involved in ligand dependent (ephirin A2, A3, A5) regulation of cell adhesion and migration, and in ligand independent regulation of neurite outgrowth in neuronal cells. They perform signaling in kinase dependent and kinase independent manner. EPH-A8 receptors are known to interact with a number of different proteins including PI 3-kinase and AIDA1-like subfamily SAM repeat domain containing proteins. However other domains (not SAM) of EPH-A8 receptors are involved in these interactions. 65 matched cddid_all.tbl CDD cd09551 cd09551 188950 SAM_EPH-B1 SAM domain of EPH-B1 subfamily of tyrosine kinase receptors. SAM (sterile alpha motif) domain of EPH-B1 subfamily of receptor tyrosine kinases is a C-terminal potential protein-protein interaction domain. This domain is located in the cytoplasmic region of EPH- B1 receptors. In human vascular endothelial cells it appears to mediate cell-cell initiated signal transduction via the binding of the adaptor protein GRB10 (growth factor) through its SH2 domain to a conserved tyrosine that is phosphorylated. EPH-B1 receptors play a role in neurogenesis, in particular in regulation of proliferation and migration of neural progenitors in the hippocampus and in corneal neovascularization; they are involved in converting the crossed retinal projection to ipsilateral retinal projection. They may be potential targets in angiogenesis-related disorders. 68 matched cddid_all.tbl CDD cd09552 cd09552 188951 SAM_EPH-B2 SAM domain of EPH-B2 subfamily of tyrosine kinase receptors. SAM (sterile alpha motif) domain of EPH-B2 subfamily of receptor tyrosine kinases is a C-terminal potential protein-protein interaction domain. This domain is located in the cytoplasmic region of EPH-B2 receptors and appears to mediate cell-cell initiated signal transduction. SAM domains of this subfamily form homodimers/oligomers (in head-to-head/tail-to-tail orientation); apparently such clustering is necessary for signaling. EPH-B2 receptor is involved in regulation of synaptic function; it is needed for normal vestibular function, proper formation of anterior commissure, control of cell positioning, and ordered migration in the intestinal epithelium. EPH-B2 plays a tumor suppressor role in colorectal cancer. It was found to be downregulated in gastric cancer and thus may be a negative biomarker for it. 71 matched cddid_all.tbl CDD cd09553 cd09553 188952 SAM_EPH-B3 SAM domain of EPH-B3 subfamily of tyrosine kinase receptors. SAM (sterile alpha motif) domain of EPH-B3 subfamily of receptor tyrosine kinases is a C-terminal potential protein-protein interaction domain. This domain is located in the cytoplasmic region of EPH-B3 receptors and appears to mediate cell-cell initiated signal transduction. EPH-B3 receptor protein kinase performs kinase-dependent and kinase-independent functions. It is known to be involved in thymus morphogenesis, in regulation of cell adhesion and migration. Also EphB3 controls cell positioning and ordered migration in the intestinal epithelium and plays a role in the regulation of adult retinal ganglion cell axon plasticity after optic nerve injury. In some experimental models overexpression of EphB3 enhances cell/cell contacts and suppresses colon tumor growth. 69 matched cddid_all.tbl CDD cd09554 cd09554 188953 SAM_EPH-B4 SAM domain of EPH-B4 subfamily of tyrosine kinase receptors. SAM (sterile alpha motif) domain of EPH-B4 subfamily of receptor tyrosine kinases is a C-terminal potential protein-protein interaction domain. This domain is located in the cytoplasmic region of EPH-B4 receptors and appears to mediate cell-cell initiated signal transduction. EPH-B4 protein kinase performs kinase-dependent and kinase-independent functions. These receptors play a role in the regular vascular system development during embryogenesis. They were found overexpressed in a variety of cancers, including carcinoma of the head and neck, ovarian cancer, bladder cancer, and downregulated in bone myeloma. Thus, EphB4 is a potential biomarker and a target for drug design. 67 matched cddid_all.tbl CDD cd09555 cd09555 188954 SAM_EPH-B6 SAM domain of EPH-B6 subfamily of tyrosine kinase receptors. SAM (sterile alpha motif) domain of EPH-B6 subfamily of receptor tyrosine kinases is a C-terminal potential protein-protein interaction domain. This domain is located in the cytoplasmic region of EPH-B6 receptors and appears to mediate cell-cell initiated signal transduction. Receptors of this type are highly expressed in embryo and adult nervous system, in thymus and also in T-cells. They are involved in regulation of cell adhesion and migration. (EPH-B6 receptor is unusual; it fails to show catalytic activity due to alteration in kinase domain). EPH-B6 may be considered as a biomarker in some types of tumors; EPH-B6 activates MAP kinase signaling in lung adenocarcinoma, suppresses metastasis formation in non-small cell lung cancer, and slows invasiveness in some breast cancer cell lines. 69 matched cddid_all.tbl CDD cd09556 cd09556 188955 SAM_VTS1_fungal SAM domain of VTS1 RNA-binding proteins. SAM (sterile alpha motif) domain of VTS1 subfamily proteins is RNA binding domain located in the C-terminal region. SAM interacts with stem-loop structures of mRNA. Proteins of this subfamily participate in regulation of transcript stability and degradation, and also may be involved in vacuolar protein transport regulation. VTS1 protein of S.cerevisiae induces mRNA degradation via the major deadenylation-dependent mRNA decay pathway; VTS1 recruits CCR4/POP2/NOT deadenylase complex to target mRNA. The recruitment is the initial step resulting in poly(A) tail removal transcripts. Potentially SAM domain may be responsible not only for RNA binding but also for deadenylase binding. 69 matched cddid_all.tbl CDD cd09557 cd09557 188956 SAM_Smaug SAM domain of Smaug subfamily. SAM (sterile alpha motif) domain of Smaug proteins is an RNA recognition domain. It binds a specific RNA motif known as Smaug recognition element (SRE). Among members of this group are invertebrate Smaug (Smg) proteins and vertebrate Smaug1 and Smaug2 proteins. They are involved in post-transcriptional control during early embryogenesis in animals. In Drosophila, Smaug protein is a translational repressor of mRNA of Nanos (Nos) protein. Gradient of Nanos is required for proper abdominal segmentation. SAM domain interacts specifically with the Nanos mRNA regulatory regions. Moreover, Smaug protein is involved in regulation of specific maternal transcripts degradation in Drosophila early embryo via recruitment of the CCR4/POP2/NOT deadenylase. 63 matched cddid_all.tbl CDD cd09558 cd09558 188957 SAM_ZCCH14 SAM domain of ZCCH14 subfamily. SAM (sterile alpha motif) domain of ZCCH14 (Zinc finger CCHC domain 14) protein subfamily (also known as BDG-29 or KIAA0579) is a putative RNA binding domain. Members of this group are believed to be involved in post-translational regulation during early embryogenesis. 65 matched cddid_all.tbl CDD cd09559 cd09559 188958 SAM_SASH1_repeat1 SAM domain of SASH1 proteins, repeat 1. SAM (sterile alpha motif) repeat 1 of SASH1 proteins is a predicted protein-protein interaction domain. Members of this subfamily are putative adaptor proteins. They appear to mediate signal transduction. SASH1 can bind 14-3-3 proteins in response to IGF1/phosphatidylinositol 3-kinase signaling. SASH1 was found upregulated in different tissues including thymus, placenta, lungs and downregulated in some breast tumors, liver metastases and colon cancers, relative to corresponding normal tissues. SASH1 is a potential candidate for a tumor suppressor gene in breast cancers. At the same time, downregulation of SASH1 in colon cancer is associated with metastasis and a poor prognosis. 66 matched cddid_all.tbl CDD cd09560 cd09560 188959 SAM_SASH3 SAM domain of SASH3 subfamily. SAM (sterile alpha motif) domain of SAHS3 (also known as SLY) proteins is a predicted protein-protein interaction domain. Members of this subfamily are putative signaling/adaptor proteins. In addition to SAM, they contain SLY and SH3 domains. They appear to mediate signal transduction in lymphoid tissues. Murine SASH3 is involved in preventing DN thymocytes from premature initiation of programmed cell death and in mTOR (mammalian target of rapamycin) activation via signal integration of the Notch receptor and preTCR (T cell receptor) pathways. 68 matched cddid_all.tbl CDD cd09561 cd09561 188960 SAM_SAMSN1 SAM domain of SAMSN1 subfamily. SAM (sterile alpha motif) domain of SAMSN1 (also known as HACS1 or NASH1) proteins is a predicted protein-protein interaction domain. Members of this group are putative signaling/adaptor proteins. They appear to mediate signal transduction in lymphoid tissues. Murine HACS1 protein likely plays a role in B cell activation and differentiation. Potential binding partners of HACS1 are SLAM, DEC205 and PIR-B receptors and also some unidentified tyrosine-phosphorylated proteins. Proteins of this group were found preferentially expressed in normal hematopietic tissues and in some malignancies including lymphoma, myeloid leukemia and myeloma. 66 matched cddid_all.tbl CDD cd09562 cd09562 188961 SAM_liprin-alpha1,2,3,4_repeat1 SAM domain of liprin-alpha1,2,3,4 proteins repeat 1. SAM (sterile alpha motif) domain repeat 1 of liprin-alpha1,2,3,4 proteins is a protein-protein interaction domain. Liprin-alpha proteins contain three copies (repeats) of SAM domain. They may form heterodimers with liprin-beta proteins through their SAM domains. Liprins were originally identified as LAR (leukocyte common antigen-related) transmembrane protein-tyrosine phosphatase-interacting proteins. They participate in mammary gland development and in axon guidance; in particular, liprin-alpha is involved in formation of the presynaptic active zone. 71 matched cddid_all.tbl CDD cd09563 cd09563 188962 SAM_liprin-beta1,2_repeat1 SAM domain of liprin-beta1,2 proteins repeat 1. SAM (sterile alpha motif) domain repeat 1 of liprin-beta1,2 proteins is a protein-protein interaction domain. Liprin-beta protein contain three copies (repeats) of SAM domain. They may form heterodimers with liprins-alpha through their SAM domains. It was suggested based on bioinformatic approaches that the second SAM domain of liprin-beta is potentially able to form polymers. Liprins were originally identified as LAR (leukocyte common antigen-related) transmembrane protein-tyrosine phosphatase-interacting proteins. They participate in mammary gland development, in axon guidance, and in the maintenance of lymphatic vessel integrity. 64 matched cddid_all.tbl CDD cd09564 cd09564 188963 SAM_kazrin_repeat1 SAM domain of kazrin proteins repeat 1. SAM (sterile alpha motif) domain repeat 1 of kazrin proteins is a protein-protein interaction domain. The long isoform of kazrin contains three copies (repeats) of SAM domain. Kazrin can interact with periplakin. It is involved into interplay between desmosomes and in adheren junctions. Additionally kazrins play a role in regulation of intercellular differentiation, junction assembly, and cytoskeletal organization. 70 matched cddid_all.tbl CDD cd09565 cd09565 188964 SAM_liprin-alpha1,2,3,4_repeat2 SAM domain of liprin-alpha1,2,3,4 proteins repeat 2. SAM (sterile alpha motif) domain repeat 2 of liprin-alpha1,2,3,4 proteins is a protein-protein interaction domain. Liprin-alpha proteins contain three copies (repeats) of SAM domain. They may form heterodimers with liprin-beta proteins through their SAM domains. Liprins were originally identified as LAR (leukocyte common antigen-related) transmembrane protein-tyrosine phosphatase-interacting proteins. They participate in mammary gland development, and in axon guidance; in particular, liprin-alpha is involved in formation of the presynaptic active zone. 66 matched cddid_all.tbl CDD cd09566 cd09566 188965 SAM_liprin-beta1,2_repeat2 SAM domain of liprin-beta1,2 proteins repeat 2. SAM (sterile alpha motif) domain repeat 2 of liprin-beta1,2 proteins is a protein-protein interaction domain. Liprin-beta proteins contain three copies (repeats) of SAM domain. They may form heterodimers with liprin-alpha proteins through their SAM domains. It was suggested based on bioinformatic approaches that the second SAM domain of liprin-beta potentially is able to form polymers. Liprins were originally identified as LAR (leukocyte common antigen-related) transmembrane protein-tyrosine phosphatase-interacting proteins. They participate in mammary gland development, in axon guidance, and in the maintenance of lymphatic vessel integrity. 63 matched cddid_all.tbl CDD cd09567 cd09567 188966 SAM_kazrin_repeat2 SAM domain of kazrin proteins repeat 2. SAM (sterile alpha motif) domain repeat 2 of kazrin proteins is a protein-protein interaction domain. The long isoform of kazrins contains three copies (repeats) of SAM domain. Kazrin can interact with periplakin. It is involved in interplay between desmosomes and in adheren junctions. Additionally kazrins play a role in regulation of intercellular differentiation, junction assembly, and cytoskeletal organization. 65 matched cddid_all.tbl CDD cd09568 cd09568 188967 SAM_liprin-alpha1,2,3,4_repeat3 SAM domain of liprin-alpha1,2,3,4 proteins repeat 3. SAM (sterile alpha motif) domain repeat 3 of liprin-alpha1,2,3,4 proteins is a protein-protein interaction domain. Liprin-alpha proteins contain three copies (repeats) of SAM domain. They may form heterodimers with liprin-beta proteins through their SAM domains. Liprins were originally identified as LAR (leukocyte common antigen-related) transmembrane protein-tyrosine phosphatase-interacting proteins. They participate in mammary gland development and in axon guidance; in particular, liprin-alpha is involved in formation of the presynaptic active zone. 72 matched cddid_all.tbl CDD cd09569 cd09569 188968 SAM_liprin-beta1,2_repeat3 SAM domain of liprin-beta proteins repeat 3. SAM (sterile alpha motif) domain repea t3 of liprin-beta1,2 proteins is a protein-protein interaction domain. Liprin-beta proteins contain three copies (repeats) of SAM domain. They may form heterodimers with liprin-alpha proteins through their SAM domains. Liprins were originally identified as LAR (leukocyte common antigen-related) transmembrane protein-tyrosine phosphatase-interacting proteins. They participate in mammary gland development, in axon guidance, and in the maintenance of lymphatic vessel integrity. 72 matched cddid_all.tbl CDD cd09570 cd09570 188969 SAM_kazrin_repeat3 SAM domain of kazrin proteins repeat 3. SAM (sterile alpha motif) domain repeat 3 of kazrin proteins is a protein-protein interaction domain. The long isoform of kazrins contains three copies (repeats) of SAM domain. Kazrin can interact with periplakin. It is involved in interplay between desmosomes and in adheren junctions. Additionally kazrins play a role in regulation of intercellular differentiation, junction assembly, and cytoskeletal organization. 72 matched cddid_all.tbl CDD cd09571 cd09571 188970 SAM_tumor-p73 SAM domain of tumor-p73 proteins. SAM (sterile alpha motif) domain of p73 proteins is a putative protein-protein interaction and lipid-binding domain. p73 is a homolog to the tumor suppressor p53. p73 has a C-terminal SAM domain in the longest spliced alpha form, while p53 doesn't have it. p73 knockout mouse shows significant developmental abnormalities but no increased cancer susceptibility, suggesting that p73 plays a role in regulation of normal development. It was shown that SAM domain of p73 is able to bind some membrane lipids. The structural rearrangements in SAM are necessary to accomplish the binding. No evidence for homooligomerization through SAM domains was found for the p73 subfamily. It was suggested that the partner proteins should be either more distantly related SAM-containing domain proteins or proteins without the SAM domain. 65 matched cddid_all.tbl CDD cd09572 cd09572 188971 SAM_tumor-p63 SAM domain of tumor-p63 proteins. SAM (sterile alpha motif) domain of p63 proteins is a putative protein-protein interaction domain. p63 is homolog to the tumor suppressor p53. p63 has a C-terminal SAM domain in the longest spliced alpha form, while p53 doesn't have it. p63 knockout mice show significant developmental abnormalities but no increased cancer susceptibility, suggesting that p63 plays a role in regulation of normal development. No evidence for homooligomerization through SAM domains was found for the p63 subfamily. It was suggested that the partner proteins should be either more distantly related SAM-containing domain proteins or proteins without the SAM domain. Mutations in the SAM domain of p63 are found in AEC syndrome patients. 65 matched cddid_all.tbl CDD cd09573 cd09573 188972 SAM_STIM1 "SAM domain of STIM1 subfamily proteins. SAM (sterile alpha motif) domain of STIM1 (Stromal interaction molecule) subfamily proteins is a putative protein-protein interaction domain. STIM1 and STIM2 human proteins are type I transmembrane proteins. The N-terminal part of them includes ""hidden"" EF-hand and SAM domains. This region is responsible for sensing changes in store-operated and basal cytoplasmic Ca2+ levels and initiates oligomerization. ""Hidden"" EF hand and SAM domains have a stable intramolecular association, and the SAM domain is a component that regulates stability within STIM proteins. Destabilization of the EF-SAM association during Ca2+ depletion leads to partial unfolding and aggregation (homooligomerization), thus activating the store-operated Ca2+ entry. Immunoprecipitation analysis indicates that STIM1 and STIM2 can form co-precipitable oligomeric associations in vivo. It was suggested that STIM1 protein is an activator of store operated channels in plasma membrane." 74 matched cddid_all.tbl CDD cd09574 cd09574 188973 SAM_STIM2 "SAM domain of STIM2 subfamily proteins. SAM (sterile alpha motif) domain of STIM2 (Stromal interaction molecule) subfamily proteins is a putative protein-protein interaction domain. STIM1 and STIM2 human proteins are type I transmembrane proteins. The N-terminal part of them includes ""hidden"" EF-hand and SAM domains. This region is responsible for sensing changes in store-operated and basal cytoplasmic Ca2+ levels and initiates oligomerization. ""Hidden"" EF hand and SAM domains have a stable intramolecular association, and the SAM domain is a component that regulates stability within STIM proteins. Destabilization of the EF-SAM association during Ca2+ depletion leads to partial unfolding and aggregation (homooligomerization), thus activating the store-operated Ca2+ entry. Immunoprecipitation analysis indicates that STIM1 and STIM2 can form co-precipitable oligomeric associations in vivo. It was suggested that STIM2 protein is an inhibitor of store operated channels in plasma membrane." 74 matched cddid_all.tbl CDD cd09575 cd09575 188974 SAM_DGK-delta SAM domain of diacylglycerol kinase delta. SAM (sterile alpha motif) domain of DGK-delta subfamily proteins is a protein-protein interaction domain. Proteins of this subfamily are multidomain diacylglycerol kinases with a SAM domain located at the C-terminus. DGK-delta proteins participate in signal transduction. They regulate the level of second messengers such as diacylglycerol and phosphatidic acid. In particular DGK-delta is involved in the regulation of clathrin-dependent endocytosis. The SAM domain of DGK-delta proteins can form high molecular weight homooligomers through head-to-tail interactions as well as heterooligomers with the SAM domain of DGK-eta proteins. The oligomerization plays a role in the regulation of the DGK-delta intracellular localization: it inhibits the translocation of the protein to the plasma membrane from the cytoplasm. The SAM domain also can bind Zn at multiple (not conserved) sites driving the formation of highly ordered large sheets of polymers, thus suggesting that Zn may play important role in the function of DCK-delta. 65 matched cddid_all.tbl CDD cd09576 cd09576 188975 SAM_DGK-eta SAM domain of diacylglycerol kinase eta. SAM (sterile alpha motif) domain of DGK-eta subfamily proteins is a protein-protein interaction domain. Proteins of this subfamily are multidomain diacylglycerol kinases. The SAM domain is located at the C-terminus of two out of three isoforms of DGK-eta protein. DGK-eta proteins participate in signal transduction. They regulate the level of second messengers such as diacylglycerol and phosphatidic acid. The SAM domain of DCK-eta proteins can form high molecular weight homooligomers through head-to-tail interactions as well as heterooligomers with the SAM domain of DGK-delta proteins. The oligomerization plays a role in the regulation of the DGK-delta intracellular localization: it is responsible for sustained endosomal localization of the protein and resulted in negative regulation of DCK-eta catalytic activity. 65 matched cddid_all.tbl CDD cd09577 cd09577 188976 SAM_Ph1,2,3 SAM domain of Ph (polyhomeotic) proteins of Polycomb group. SAM (sterile alpha motif) domain of Ph (polyhomeotic) proteins of Polycomb group is a protein-protein interaction domain. Ph1,2,3 proteins are members of PRC1 complex. This complex is involved in transcriptional repression of Hox (Homeobox) cluster genes. It is recruited through methylated H3Lys27 and supports the repression state by mediating monoubiquitination of histone H2A. Proteins of the Ph1,2,3 subfamily contribute to anterior-posterior neural tissue specification during embryogenesis. Additionally, the P2 protein of zebrafish is known to be involved in epiboly and tailbud formation. SAM domains of Ph proteins may interact with each other, forming homooligomers, as well as with SAM domains of other proteins, in particular with the SAM domain of Scm (sex comb on midleg) proteins, forming heterooligomers. Homooligomers are similar to the ones formed by SAM Pointed domains of the TEL proteins. Such SAM/SAM oligomers apparently play a role in transcriptional repression through polymerization along the chromosome. 69 matched cddid_all.tbl CDD cd09578 cd09578 188977 SAM_Scm SAM domain of Scm proteins of Polycomb group. SAM (sterile alpha motif) domain of Scm (Sex comb on midleg) subfamily of Polycomb group is a protein-protein interaction domain. Proteins of this subfamily are transcriptional repressors associated with PRC1 complex. This group includes invertebrate Scm protein and chordate Scm homolog 1 and Scm-like 1, 2, 3 proteins. Most have a SAM domain, two MBT repeats, and a DUF3588 domain, except Scm-like 4 proteins which do not have MBT repeats. Originally the Scm protein was described in Drosophila as a regulator required for proper spatial expression of homeotic genes. It plays a major role during early embryogenesis. SAM domains of Scm proteins can interact with each other, forming homooligomers, as well as with SAM domains of other proteins, in particular with SAM domains of Ph (polyhomeotic) proteins, forming heterooligomers. Homooligomers are similar to the ones formed by SAM Pointed domains of the TEL proteins. Such SAM/SAM oligomers apparently play a role in transcriptional repression through polymerization along the chromosome. Mammalian Scmh1 protein is known be indispensible member of PRC1 complex; it plays a regulatory role for the complex during meiotic prophase of male sperm cells, and is particularly involved in regulation of chromatin modification at the XY chromatin domain of the pachytene spermatocytes. 72 matched cddid_all.tbl CDD cd09579 cd09579 188978 SAM_Samd7,11 SAM domain of Samd7,11 subfamily of Polycomb group. SAM (sterile alpha motif) domain is a protein-protein interaction domain. Phylogenetic analysis suggests that proteins of this subfamily are most closely related to SAM-Ph1,2,3 subfamily of Polycomb group. They are predicted transcriptional repressors in photoreceptor cells and pinealocytes of vertebrates. SAM domain containing protein 11 is also known as Mr-s (major retinal SAM) protein. In mouse, it is predominantly expressed in developing retinal photoreceptors and in adult pineal gland. The SAM domain is involved in homooligomerization of whole proteins (it was shown based on immunoprecipitation assay and mutagenesis), however its repression activity is not due to SAM/SAM interactions but to the C-terminal region. 68 matched cddid_all.tbl CDD cd09580 cd09580 188979 SAM_Scm-like-4MBT SAM domain of Scm-like-4MBT proteins of Polycomb group. SAM (sterile alpha motif) domain of Scm-like-4MBT (Sex comb on midleg like, Malignant Brain Tumor) subfamily proteins of the polycomb group is a putative protein-protein interaction domain. Additionally to the SAM domain, most of the proteins of this subfamily have 4 MBT repeats. In Drosophila SAM-Scm-like-4MBT protein (known as dSfmbt) is a member of Pho repressive complex (PhoRC). Additionally to dSfmbt, the PhoRC complex includes Pho or Pho-like proteins. This complex is responsible for HOX (Homeobox) gene silencing: Pho or Pho-like proteins bind DNA and dSmbt binds methylated histones. dSmbt can interact with mono- and di-methylated histones H3 and H4 (however this activity has been shown for the MBT repeats, while exact function of the SAM domain is unclear). Besides interaction with histones, dSmbt can interact with Scm (a member of PRC complex), but this interaction also seems to be SAM domain independent. 67 matched cddid_all.tbl CDD cd09581 cd09581 188980 SAM_Scm-like-4MBT1,2 SAM domain of Scm-like-4MBT1,2 proteins of Polycomb group. SAM (sterile alpha motif) domain of Scm-like-4MBT1,2 (Sex comb on midleg, Malignant Brain Tumor) subfamily proteins (also known as Sfmbt1,2 proteins) is a putative protein-protein interaction domain. Proteins of this subfamily are transcriptional regulators belonging to Polycomb group. The majority of them are multidomain proteins: in addition to the C-terminal SAM domain, they contain four MBT repeats and DUF5388 domain. The MBT repeats of the human sfmbt1 protein are responsible for association with the nuclear matrix and for selective binding of H3 histone N-terminal tails, while the exact function of the SAM domain is unclear. 85 matched cddid_all.tbl CDD cd09582 cd09582 188981 SAM_Scm-like-3MBT3,4 SAM domain of Scm-like-3MBT3,4 proteins of Polycomb group. SAM (sterile alpha motif) domain of Scm-like-3MBT3,4 (Sex comb on midleg, Malignant brain tumor) subfamily proteins (also known as L3mbtl3,4 proteins) is a putative protein-protein interaction domain. Proteins of this subfamily are predicted transcriptional regulators belonging to Polycomb group. The majority of them are multidomain proteins: in addition to the C-terminal SAM domain, they contain three MBT repeats and Zn finger domain. Murine L3mbtl3 protein of this subfamily is essential for maturation of myeloid progenitor cells during differentiation. Human L3mbtl4 is a potential tumor suppressor gene in breast cancer, while deregulation of L3MBTL3 is associated with neuroblastoma. 66 matched cddid_all.tbl CDD cd09583 cd09583 188982 SAM_Atherin-like SAM domain of Atherin/Atherin-like subfamily. SAM (sterile alpha motif) domain of SAM_Atherin and Atherin-like subfamily proteins is a putative protein-protein and/or protein-lipid interaction domain. In addition to the C-terminal SAM domain, the majority of proteins belonging to this group also have PHD (or Zn finger) domain. As potential members of the polycomb group, these proteins may be involved in regulation of some key regulatory genes during development. Atherin can be recruited by Ruk/CIN85 kinase-binding proteins via its SH3 domains thus participating in the signal transferring kinase cascades. Also, atherin was found associated with low density lipids (LDL) in atherosclerotic lesions in human. It was suggested that atherin plays an essential role in atherogenesis via immobilization of LDL in the arterial wall. SAM domains of atherins are predicted to form polymers. Inhibition of polymer formation could be a potential antiatherosclerotic therapy. 69 matched cddid_all.tbl CDD cd09584 cd09584 188983 SAM_sec23ip SAM domain of sec23ip. SAM (sterile alpha motif) domain of Sec23ip (Sec23 interacting protein) group is a potential protein-protein interaction domain. Sec23ip proteins (also known as p125) contain an N-terminal proline-rich region, a central region containing a SAM domain and a C-terminal region with a predicted metal-binding domain. Sec23ip interacts with Sec23p/Sec24p part of COPII-coated vesicles complex involved in protein transport from the ER to the Golgi apparatus. The proline-rich region plays an essential role in this interaction. Overexpression of Sec23ip leads to disorganization of ER/Golgi intermediate compartment. 69 matched cddid_all.tbl CDD cd09585 cd09585 188984 SAM_DDHD2 SAM domain of DDHD2. SAM (sterile alpha motif) domain of DDHD2 group is a potential protein-protein interaction domain. DDHD2 proteins contain at least two domains:a SAM domain and a predicted metal-binding domain. Phospholipase A1 activity was demonstrated for the mammalian DDHD2 protein. Mutation of the putative catalytic serine resulted in elimination of activity. Unlike SEC23IP, DDHD2 proteins do not have an N-terminal proline-rich region and correspondingly they are not able to interact with Sec23p/Sec24p complex. Overexpression of DDHD2 is the cause of dispersion of ER/Golgi intermediate compartment and dispersion of tethering proteins located in the Golgi region, leading to aggregation in the endoplasmic reticulum. 69 matched cddid_all.tbl CDD cd09586 cd09586 188985 SAM_USH1G SAM domain of USH1G. SAM (sterile alpha motif) domain of USH1G (Usher syndrome type-1G protein) proteins (also known as SANS) is a putative protein-protein interaction domain. Members of this group have an N-terminal ankyrin repeat region and C-terminal SAM domain. USH1G is expressed in the hair bundles of the inner ear sensory cells. It can form a functional network with USH1B (myosin VIIa), USH1C (harmonin b), USH1F (protocadherin-related 15), and USH1D (cadherin 23). The SAM domain of the USH1G protein is involved in synergetic interactions with the PDZ domain of harmonin. Such interactions contribute to the stability of harmonin. The network is required for the correct cohesion of the hair bundle. Mutations in the ush1g gene lead to Usher syndrome type 1G. This syndrome is the cause of deaf-blindness in humans. 66 matched cddid_all.tbl CDD cd09587 cd09587 188986 SAM_HARP SAM domain of HARP subfamily. SAM (sterile alpha motif) domain of HARP (Harmonin-interacting Ankyrin Repeat-containing) proteins, also known as ANKS4B, is a protein-protein interaction domain. Proteins of this subfamily have an N-terminal ankyrin repeat region and C-terminal SAM. In mouse epithelial tissues, HARP protein interacts with the PDZ domain of harmonin. This scaffolding complex facilitates signal transduction in epithelia. HARP was found co-expressed with harmonin in a number of epithelial cells including pancreatic ductal epithelium, embryonic epithelia of the lung, kidney, salivary glands, and cochlea. 67 matched cddid_all.tbl CDD cd09588 cd09588 188987 SAM_LBP1 SAM domain of LBP1 (UBP1) transcription factors. SAM (sterile alpha motif) domain of LBP1 (also known as UBP1) transcription factor is a putative protein-protein interaction domain. Proteins of this group have an N-terminal DNA-binding CP2 domain, a central predicted SAM domain and some also have a C-terminal dimerization domain. They are involved in transcriptional regulation from early development to terminal differentiation. In particular, they regulate alpha-globin in erythroid cells and P450scc (the cholesterol side-chain cleavage enzyme, cytochrome) in human placenta. Human LBP1 is known to be induced by HIV type I infection in lymphocytes; it represses HIV transcription by preventing the binding of TFIID to the virus promoter. Additionally, it has been suggested that UBP1 (LPB1) regulator might be a member of a blood pressure controlling network. LBP1 protein isoforms are able to form dimers, apparently via SAM domain since SAM deletion or mutation resulted in a loss of this ability. 67 matched cddid_all.tbl CDD cd09589 cd09589 188988 SAM_TFCP2 SAM domain of TFCP2 transcription factors. SAM (sterile alpha motif) domain of TFCP2 transcription factors is a putative protein-protein interaction domain. Proteins of this group have an N-terminal DNA-binding CP2 domain, a central predicted SAM domain and a C-terminal dimerization domain. They are involved in transcriptional regulation from early development to terminal differentiation. In particular, they regulate expression of erythroid cell-specific alpha-globin, fibrinogen, and sex-determining gene SRY as well as lens alpha-crystallin. TFCP2 regulators can interact with NF-E4 proteins forming heteromeric stage selector protein complex (SSP). This complex is able to bind stage selector element (SSE) and regulate embryonic globin expression in fetal-erythroid cells. 67 matched cddid_all.tbl CDD cd09590 cd09590 188989 SAM_LBP9 SAM domain of LBP9 transcriptional factors. SAM (sterile alpha motif) domain of LBP9 (also known as TFCP2L1 or CRTR-1 (CP2-Related Transcriptional Repressor-1)) transcription factor is a putative protein-protein interaction domain. Proteins of this group have an N-terminal DNA-binding CP2 domain, a central predicted SAM domain and a C-terminal dimerization domain. They are involved in transcriptional regulation from early development to terminal differentiation. In particular, they are required for proper maturation of the dust (epithelial component of tubular organs) of kidney and salivary gland as well as for regulation of P450scc (the cholesterol side-chain cleavage enzyme, cytochrome) in human placenta. 67 matched cddid_all.tbl CDD cd09591 cd09591 188990 SAM_DLC1 SAM domain of DLC1 subfamily. SAM (sterile alpha motif) domain of DLC1 (Deleted in liver cancer) protein is a protein-protein interaction domain located at the N-terminus. Proteins of this subfamily do not form dimers/oligomers through their SAM domains. They participate in regulation of cell migration. SAM domain of human DLC1 protein contains the EF1A1 (eukaryotic elongation factor) binding motif, thus SAM facilitates recruitment of EF1A1 to the membrane periphery and suppresses cell migration. 60 matched cddid_all.tbl CDD cd09592 cd09592 188991 SAM_DLC2 SAM domain of STARD13-like subfamily. SAM (sterile alpha motif) domain of DLC2 (Deleted in liver cancer) protein is a lipid-binding and putative protein-protein interaction domain located at the N-terminus of the protein. Members of this subfamily do not form dimers/oligomers through their SAM domains. They participate in lipid transfer. Human Dlc2 gene is known as a tumor suppressor gene. It was found underexpressed in hepatocellular carcinoma. 64 matched cddid_all.tbl CDD cd09593 cd09593 381677 UDG-like uracil-DNA glycosylases (UDG) and related enzymes. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil may arise from misincorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations; thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. UDG family 1 is the most efficient uracil-DNA glycosylase (UDG, also known as UNG) and shows a specificity for uracil in DNA. UDG family 2 includes thymine DNA glycosylase which removes uracil and thymine from G:U and G:T mismatches, and mismatch-specific uracil DNA glycosylase (MUG) which in Escherichia coli is highly specific to G:U mismatches, but also repairs G:T mismatches at high enzyme concentration. UDG family 3 includes Human SMUG1 which can remove uracil and its oxidized pyrimidine derivatives from, single-stranded DNA and double-stranded DNA with a preference for single-stranded DNA. Pedobacter heparinus SMUG2, which is UDG family 3 SMUG1-like, displays catalytic activities towards DNA containing uracil or hypoxanthine/xanthine. UDG family 4 includes Thermotoga maritima TTUDGA, a robust UDG which like family 1, acts on double-stranded and single-stranded uracil-containing DNA. UDG family 5 (UDGb) includes Thermus thermophilus HB8 TTUDGB which acts on double-stranded uracil-containing DNA; it is a hypoxanthine DNA glycosylase acting on double-stranded hypoxanthine-containing DNA except for the C/I base pair, as well as a xanthine DNA glycosylase which acts on both double-stranded and single-stranded xanthine-containing DNA. UDG family 6 hypoxanthine-DNA glycosylase lacks any detectable UDG activity; it excises hypoxanthine. Other UDG families include one represented by Bradyrhizobium diazoefficiens Blr0248 which prefers single-stranded DNA and removes uracil, 5-hydroxymethyl-uracil or xanthine from it. 125 matched cddid_all.tbl CDD cd09594 cd09594 341057 GluZincin Gluzincin Peptidase family (thermolysin-like proteinases, TLPs) which includes peptidases M1, M2, M3, M4, M13, M32 and M36 (fungalysins). The Gluzincin family (thermolysin-like peptidases or TLPs) includes several zinc-dependent metallopeptidases such as M1, M2, M3, M4, M13, M32, M36 peptidases (MEROPS classification), which contain the HEXXH motif as part of their active site. Peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. The M1 family includes aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H). APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity such that the two activities occupy different, but overlapping sites. The M3_like peptidases include the M2_ACE, M3 or neurolysin-like family (subfamilies M3B_PepF and M3A) and M32_Taq peptidases. The M2 peptidase angiotensin converting enzyme (ACE, EC 3.4.15.1) catalyzes the conversion of decapeptide angiotensin I to the potent vasopressor octapeptide angiotensin II. ACE is a key component of the renin-angiotensin system that regulates blood pressure, thus ACE inhibitors are important for the treatment of hypertension. M3A includes thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (3.4.24.16), and the mitochondrial intermediate peptidase; and M3B includes oligopeptidase F. The M32 family includes eukaryotic enzymes from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and from Leishmania major, a parasite that causes leishmaniasis, making these enzymes attractive targets for drug development. The M4 family includes secreted protease thermolysin (EC 3.4.24.27), pseudolysin, aureolysin, and neutral protease as well as bacillolysin (EC 3.4.24.28) that degrade extracellular proteins and peptides for bacterial nutrition, especially prior to sporulation. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing as well as in production of the artificial sweetener aspartame. The M13 family includes neprilysin (EC 3.4.24.11) and endothelin-converting enzyme I (ECE-1, EC 3.4.24.71), which fulfill a broad range of physiological roles due to the greater variation in the S2' subsite allowing substrate specificity and are prime therapeutic targets for selective inhibition. The peptidase M36 fungalysin family includes endopeptidases from pathogenic fungi. Fungalysin hydrolyzes extracellular matrix proteins such as elastin and keratin. Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals and secreting fungalysin that possibly breaks down proteinaceous structural barriers. 105 matched cddid_all.tbl CDD cd09595 cd09595 341058 M1 Peptidase M1 family includes the catalytic domains of aminopeptidase N and leukotriene A4 hydrolase. The model represents the catalytic domains of M1 peptidase family members including aminopeptidase N (APN) and leukotriene A4 hydrolase (LTA4H). All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile upon activation during catalysis. APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types. APN expression is dysregulated in many inflammatory diseases and is enhanced in numerous tumor cells, making it a lead target in the development of anti-cancer and anti-inflammatory drugs. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity. The two activities occupy different, but overlapping sites. The activity and physiological relevance of the aminopeptidase in LTA4H is as yet unknown, while the epoxide hydrolase converts leukotriene A4 (LTA4) into leukotriene B4 (LTB4), a potent chemotaxin that is fundamental to the inflammatory response of mammals. 413 matched cddid_all.tbl CDD cd09596 cd09596 341059 M36 Peptidase M36 family, also known as fungalysin family. The M36 peptidase family, also known as fungalysin (elastinolytic metalloproteinase) family, includes endopeptidases from pathogenic fungi. Fungalysin can hydrolyze extracellular matrix proteins such as elastin and keratin, with a preference for cleavage on the amino side of hydrophobic residues with bulky side-chains. This family is similar to the M4 (thermolysin) family due to the presence of the HEXXH motif in the active site residues, as well as its fold prediction. Some of these enzymes also contain a protease-associated (PA) domain insert. The eukaryotic M36 and bacterial M4 families of metalloproteases also share a conserved domain in their propeptides called FTP (fungalysin/thermolysin propeptide). Aspergillus fumigatus causes the pulmonary disease aspergillosis by invading the lungs of immuno-compromised animals; it secretes fungalysin that possibly breaks down proteinaceous structural barriers. A solid lesion known as an aspergilloma can grow in a lung cavity, particularly following recovery from tuberculosis. Fungalysins are also found as multiple copies in the human and animal pathogenic fungi such as Microsporum canis, Trichophyton rubrum and T. mentagrophytes, which cause cutaneous infections. 317 matched cddid_all.tbl CDD cd09597 cd09597 341060 M4_TLP Peptidase M4 family including thermolysin, protealysin, aureolysin, and neutral protease. This peptidase M4 family includes several endopeptidases such as thermolysin (EC 3.4.24.27), aureolysin (the extracellular metalloproteinase from Staphylococcus aureus), neutral protease from Bacillus cereus, protealysin, and bacillolysin (EC 3.4.24.28). Typically, the M4 peptidases consist of a presequence (signal sequence), a propeptide sequence, and a peptidase unit. The presequence is cleaved off during export while the propeptide has inhibitory and chaperone functions and facilitates folding. The propeptide remains attached until the peptidase is secreted and can be safely activated. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. The active site is found between two sub-domains; the N-terminal domain contains the HEXXH zinc-binding motif while the helical C-terminal domain, which is unique for the family, carries the third zinc ligand. These peptidases are secreted eubacterial endopeptidases from Gram-positive or Gram-negative sources that degrade extracellular proteins and peptides for bacterial nutrition. They are selectively inhibited by Steptomyces metalloproteinase inhibitor (SMPI) as well as by phosphoramidon from Streptomyces tanashiensis. A large number of these enzymes are implicated as key factors in the pathogenesis of various diseases, including gastritis, peptic ulcer, gastric carcinoma, cholera and several types of bacterial infections, and are therefore important drug targets. Some enzymes of the family can function at extremes of temperatures, while some function in organic solvents, thus rendering them novel targets for biotechnological applications. Thermolysin is widely used as a nonspecific protease to obtain fragments for peptide sequencing. It has also been used in production of the artificial sweetener aspartame. 278 matched cddid_all.tbl CDD cd09598 cd09598 341061 M4_like Peptidase M4 family containing mostly uncharacterized proteins. This family of uncharacterized bacterial proteins are homologs of the M4 peptidase family that is also known as the thermolysin-like peptidase (TLP) family. Typically, the M4 peptidases consist of a presequence (signal sequence), a propeptide sequence and a peptidase unit. The presequence is cleaved off during export while the propeptide has inhibitory and chaperone functions and facilitates folding. The propeptide remains attached until the peptidase is secreted and can be safely activated. All peptidases in this family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. TLPs are secreted eubacterial endopeptidases from Gram-positive or Gram-negative sources that degrade extracellular proteins and peptides for bacterial nutrition. They contain the HEXXH motif as part of their active site and belong to the Gluzincins family and are selectively inhibited by Steptomyces metalloproteinase inhibitor (SMPI) as well as by phosphoramidon from Streptomyces tanashiensis. A large number of these enzymes are implicated as key factors in the pathogenesis of various diseases, including gastritis, peptic ulcer, gastric carcinoma, cholera and several types of bacterial infections, and are therefore important drug targets. Some enzymes of the family can function at extremes of temperatures, while some function in organic solvents, thus rendering them novel targets for biotechnological applications. 263 matched cddid_all.tbl CDD cd09599 cd09599 341062 M1_LTA4H Peptidase M1 family including Leukotriene A4 hydrolase catalytic domain. This model represents the N-terminal catalytic domain of leukotriene A4 hydrolase (LTA4H; E.C. 3.3.2.6) and the close homolog cold-active aminopeptidase (Colwellia psychrerythraea-type peptidase; ColAP), both members of the aminopeptidase M1 family. LTA4H is a bifunctional enzyme, possessing an aminopeptidase as well as an epoxide hydrolase activity. The two activities occupy different, but overlapping sites. The activity and physiological relevance of the aminopeptidase is poorly understood while the epoxide hydrolase converts leukotriene A4 (LTA4) into leukotriene B4 (LTB4), a potent chemotaxin that is fundamental to the inflammatory response of mammals. It accepts a variety of substrates, including some opioid, di- and tripeptides, as well as chromogenic aminoacyl-p-nitroanilide derivatives. The aminopeptidase activity of LTA4H is possibly involved in the processing of peptides related to inflammation and host defense. Kinetic analysis shows that LTA4H hydrolyzes arginyl tripeptides with high efficiency and specificity, indicating its function as an arginyl aminopeptidase. Thermodynamic characterization using different biophysical methods shows that structurally distinct inhibitors of the LTA4H occupy different regions of the binding site; while some (RB202, ARM1 and SC57461A) bind to the hydrophobic hydrolase side, both bestatin and captopril are located at the hydrophilic peptidase side. LTB4H overexpression is associated with different pathological conditions and diseases such as cystic fibrosis, coronary heart disease, sepsis, shock, connective tissue disease, and chronic obstructive pulmonary disease. It is also overexpressed in certain human cancers, and has been identified as a functionally important target for mediating anticancer properties of resveratrol, a well-known red wine polyphenolic compound with cancer chemopreventive activity. 442 matched cddid_all.tbl CDD cd09600 cd09600 341063 M1_APN Peptidase M1 family, including aminopeptidase N catalytic domain. This model represents the catalytic domain of aminopeptidase N (APN; CD13; alanyl aminopeptidase; EC 3.4.11.2), a type II integral membrane protease belonging to the M1 gluzincin family. It includes bacterial-type alanyl aminopeptidases as well as PfA-M1 aminopeptidase (Plasmodium falciparum-type). APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and, in higher eukaryotes, is present in a variety of human tissues and cell types (leukocyte, fibroblast, endothelial and epithelial cells). APN expression is dysregulated in inflammatory diseases such as chronic pain, rheumatoid arthritis, multiple sclerosis, systemic sclerosis, systemic lupus erythematosus, polymyositis/dermatomyosytis and pulmonary sarcoidosis, and is enhanced in tumor cells such as melanoma, renal, prostate, pancreas, colon, gastric and thyroid cancers. It is predominantly expressed on stem cells and on cells of the granulocytic and monocytic lineages at distinct stages of differentiation, thus considered a marker of differentiation. Thus, APN inhibition may lead to the development of anti-cancer and anti-inflammatory drugs. APNs are also present in many pathogenic bacteria and represent potential drug targets. Some APNs have been used commercially, such as one from Lactococcus lactis used in the food industry. APN also serves as a receptor for coronaviruses, although the virus receptor interaction site seems to be distinct from the enzymatic site and aminopeptidase activity is not necessary for viral infection. APNs have also been extensively studied as putative Cry toxin receptors. Cry1 proteins are pore-forming toxins that bind to the midgut epithelial cell membrane of susceptible insect larvae, causing extensive damage. Several different toxins, including Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have been shown to bind to APNs; however, a direct role of APN in cytotoxicity has been yet to be firmly established. 434 matched cddid_all.tbl CDD cd09601 cd09601 341064 M1_APN-Q_like Peptidase M1 aminopeptidase N catalytic domain family which includes aminopeptidase N (APN), aminopeptidase Q (APQ), tricorn interacting factor F3, and endoplasmic reticulum aminopeptidase 1 (ERAP1). This M1 peptidase family includes eukaryotic and bacterial members: the catalytic domains of aminopeptidase N (APN), aminopeptidase Q (APQ, laeverin), endoplasmic reticulum aminopeptidase 1 (ERAP1) as well as tricorn interacting factor F3. Aminopeptidase N (APN; CD13; alanyl aminopeptidase; EC 3.4.11.2), a type II integral membrane protease, preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and is present in a variety of human tissues and cell types (leukocyte, fibroblast, endothelial and epithelial cells). APN expression is dysregulated in inflammatory diseases such as chronic pain, rheumatoid arthritis, multiple sclerosis, systemic sclerosis, systemic lupus erythematosus, polymyositis/dermatomyosytis and pulmonary sarcoidosis, and is enhanced in tumor cells such as melanoma, renal, prostate, pancreas, colon, gastric and thyroid cancers. It is considered a marker of differentiation since it is predominantly expressed on stem cells and on cells of the granulocytic and monocytic lineages at distinct stages of differentiation. Thus, APN inhibition may lead to the development of anti-cancer and anti-inflammatory drugs. ERAP1, also known as endoplasmic reticulum aminopeptidase associated with antigen processing (ERAAP), adipocyte derived leucine aminopeptidase (A-LAP), or aminopeptidase regulating tumor necrosis factor receptor I (THFRI) shedding (ARTS-1), associates with the closely related ER aminopeptidase ERAP2, for the final trimming of peptides within the ER for presentation by MHC class I molecules. ERAP1 is associated with ankylosing spondylitis (AS), an inflammatory arthritis that predominantly affects the spine. ERAP1 also aids in the shedding of membrane-bound cytokine receptors. The tricorn interacting factor F3, together with factors F1 and F2, degrades the tricorn protease products, producing free amino acids, thus completing the proteasomal degradation pathway. F3 is homologous to F2, but not F1, and shows a strong preference for glutamate in the P1' position. APQ, also known as laeverin, is specifically expressed in human embryo-derived extravillous trophoblasts (EVTs) that invade the uterus during early placentation. It cleaves the N-terminal amino acid of various peptides such as angiotensin III, endokinin C, and kisspeptin-10, all expressed in the placenta in large quantities. APN is a receptor for coronaviruses, although the virus receptor interaction site seems to be distinct from the enzymatic site and aminopeptidase activity is not necessary for viral infection. APNs are also putative Cry toxin receptors. Cry1 proteins are pore-forming toxins that bind to the midgut epithelial cell membrane of susceptible insect larvae, causing extensive damage. Several different toxins, including Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have been shown to bind to APNs; however, a direct role of APN in cytotoxicity has been yet to be firmly established. 442 matched cddid_all.tbl CDD cd09602 cd09602 341065 M1_APN Peptidase M1 family including aminopeptidase N catalytic domain. This model represents the catalytic domain of bacterial and eukaryotic aminopeptidase N (APN; CD13; alanyl aminopeptidase; EC 3.4.11.2), a type II integral membrane protease belonging to the M1 gluzincin family. APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and, in higher eukaryotes, is present in a variety of human tissues and cell types (leukocyte, fibroblast, endothelial and epithelial cells). APN expression is dysregulated in inflammatory diseases such as chronic pain, rheumatoid arthritis, multiple sclerosis, systemic sclerosis, systemic lupus erythematosus, polymyositis/dermatomyosytis and pulmonary sarcoidosis, and is enhanced in tumor cells such as melanoma, renal, prostate, pancreas, colon, gastric and thyroid cancers. It is predominantly expressed on stem cells and on cells of the granulocytic and monocytic lineages at distinct stages of differentiation, thus considered a marker of differentiation. Thus, APN inhibition may lead to the development of anti-cancer and anti-inflammatory drugs. APNs are also present in many pathogenic bacteria and represent potential drug targets. Some APNs have been used commercially, such as one from Lactococcus lactis used in the food industry. APN also serves as a receptor for coronaviruses, although the virus receptor interaction site seems to be distinct from the enzymatic site and aminopeptidase activity is not necessary for viral infection. APNs have also been extensively studied as putative Cry toxin receptors. Cry1 proteins are pore-forming toxins that bind to the midgut epithelial cell membrane of susceptible insect larvae, causing extensive damage. Several different toxins, including Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have been shown to bind to APNs; however, a direct role of APN in cytotoxicity has been yet to be firmly established. 440 matched cddid_all.tbl CDD cd09603 cd09603 341066 M1_APN_like Peptidase M1 family similar to aminopeptidase N catalytic domain. This family contains mostly bacterial and some archaeal M1 peptidases with smilarity to the catalytic domain of aminopeptidase N (APN; CD13; alanyl aminopeptidase; EC 3.4.11.2), a type II integral membrane protease belonging to the M1 gluzincin family. APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and, in higher eukaryotes, is present in a variety of human tissues and cell types (leukocyte, fibroblast, endothelial and epithelial cells). APN expression is dysregulated in inflammatory diseases such as chronic pain, rheumatoid arthritis, multiple sclerosis, systemic sclerosis, systemic lupus erythematosus, polymyositis/dermatomyosytis and pulmonary sarcoidosis, and is enhanced in tumor cells such as melanoma, renal, prostate, pancreas, colon, gastric and thyroid cancers. It is predominantly expressed on stem cells and on cells of the granulocytic and monocytic lineages at distinct stages of differentiation, thus considered a marker of differentiation. Thus, APN inhibition may lead to the development of anti-cancer and anti-inflammatory drugs. APNs are also present in many pathogenic bacteria and represent potential drug targets. Some APNs have been used commercially, such as one from Lactococcus lactis used in the food industry. APN also serves as a receptor for coronaviruses, although the virus receptor interaction site seems to be distinct from the enzymatic site and aminopeptidase activity is not necessary for viral infection. APNs have also been extensively studied as putative Cry toxin receptors. Cry1 proteins are pore-forming toxins that bind to the midgut epithelial cell membrane of susceptible insect larvae, causing extensive damage. Several different toxins, including Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have been shown to bind to APNs; however, a direct role of APN in cytotoxicity has been yet to be firmly established. 410 matched cddid_all.tbl CDD cd09604 cd09604 341067 M1_APN_like Peptidase M1 family similar to aminopeptidase N catalytic domain. This family contains bacterial M1 peptidases with smilarity to the catalytic domain of aminopeptidase N (APN; CD13; alanyl aminopeptidase; EC 3.4.11.2), a type II integral membrane protease belonging to the M1 gluzincin family. APN preferentially cleaves neutral amino acids from the N-terminus of oligopeptides and, in higher eukaryotes, is present in a variety of human tissues and cell types (leukocyte, fibroblast, endothelial and epithelial cells). APN expression is dysregulated in inflammatory diseases such as chronic pain, rheumatoid arthritis, multiple sclerosis, systemic sclerosis, systemic lupus erythematosus, polymyositis/dermatomyosytis and pulmonary sarcoidosis, and is enhanced in tumor cells such as melanoma, renal, prostate, pancreas, colon, gastric and thyroid cancers. It is predominantly expressed on stem cells and on cells of the granulocytic and monocytic lineages at distinct stages of differentiation, thus considered a marker of differentiation. Thus, APN inhibition may lead to the development of anti-cancer and anti-inflammatory drugs. APNs are also present in many pathogenic bacteria and represent potential drug targets. Some APNs have been used commercially, such as one from Lactococcus lactis used in the food industry. APN also serves as a receptor for coronaviruses, although the virus receptor interaction site seems to be distinct from the enzymatic site and aminopeptidase activity is not necessary for viral infection. APNs have also been extensively studied as putative Cry toxin receptors. Cry1 proteins are pore-forming toxins that bind to the midgut epithelial cell membrane of susceptible insect larvae, causing extensive damage. Several different toxins, including Cry1Aa, Cry1Ab, Cry1Ac, Cry1Ba, Cry1Ca and Cry1Fa, have been shown to bind to APNs; however, a direct role of APN in cytotoxicity has been yet to be firmly established. 440 matched cddid_all.tbl CDD cd09605 cd09605 341068 M3A "Peptidase M3A family includes thimet oligopeptidase, dipeptidyl carboxypeptidase and mitochondrial intermediate peptidase. The M3-like family also called neurolysin-like family, is part of the ""zincins"" metallopeptidases, and includes M3, M2 and M32 families of metallopeptidases. The M3 family is subdivided into two subfamilies: the widespread M3A, represented by this CD, which comprises a number of high-molecular mass endo- and exopeptidases from bacteria, archaea, protozoa, fungi, plants and animals, and the small M3B, whose members are enzymes primarily from bacteria. Well-known mammalian/eukaryotic M3A endopeptidases are the thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (alias endopeptidase 3.4.24.16), and the mitochondrial intermediate peptidase. The first two are intracellular oligopeptidases, which act only on relatively short substrates of less than 20 amino acid residues, while the latter cleaves N-terminal octapeptides from proteins during their import into the mitochondria. The M3A subfamily also contains several bacterial endopeptidases, called oligopeptidases A, as well as a large number of bacterial carboxypeptidases, called dipeptidyl peptidases (Dcp; Dcp II; peptidyl dipeptidase; EC 3.4.15.5). The peptidases in the M3 family contain the HEXXH motif that forms part of the active site in conjunction with a C-terminally-located Glutamic acid (Glu) residue. A single zinc ion is ligated by the side-chains of the two Histidine (His) residues, and the more C-terminal Glu. Most of the peptidases are synthesized without signal peptides or propeptides, and function intracellularly." 587 matched cddid_all.tbl CDD cd09606 cd09606 341069 M3B_PepF Peptidase family M3B, oligopeptidase F (PepF). Peptidase family M3 oligopeptidase F (oligendopeptidase) is mostly bacterial and includes oligoendopeptidase F from Geobacillus stearothermophilus. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids and may cleave proteins at Leu-Gly. The PepF gene is duplicated in Lactococcus lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most bacterial PepFs are cytoplasmic endopeptidases; however, the Bacillus amyloliquefaciens PepF oligopeptidase is a secreted protein and may facilitate the process of sporulation. Specifically, the yjbG gene encoding the homolog of the PepF1 and PepF2 oligoendopeptidases of Lactococcus lactis has been identified in Bacillus subtilis as an inhibitor of sporulation initiation when over-expressed from a multicopy plasmid. 543 matched cddid_all.tbl CDD cd09607 cd09607 341070 M3B_PepF Peptidase family M3B, oligopeptidase F (PepF). Peptidase family M3B Oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and is similar to oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most bacterial PepFs are cytoplasmic endopeptidases; however, the Bacillus amyloliquefaciens PepF oligopeptidase is a secreted protein and may facilitate the process of sporulation. Specifically, the yjbG gene encoding the homolog of the PepF1 and PepF2 oligoendopeptidases of Lactococcus lactis has been identified in Bacillus subtilis as an inhibitor of sporulation initiation when over-expressed from a multicopy plasmid. 580 matched cddid_all.tbl CDD cd09608 cd09608 341071 M3B_PepF Peptidase family M3B, oligopeptidase F (PepF). Peptidase family M3B oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and includes oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most bacterial PepFs are cytoplasmic endopeptidases; however, the Bacillus amyloliquefaciens PepF oligopeptidase is a secreted protein and may facilitate the process of sporulation. Specifically, the yjbG gene encoding the homolog of the PepF1 and PepF2 oligoendopeptidases of Lactococcus lactis has been identified in Bacillus subtilis as an inhibitor of sporulation initiation when over-expressed from a multicopy plasmid. This PepF family includes Streptococcus agalactiae PepB, a group B streptococcal oligopeptidase which has been shown to degrade a variety of bioactive peptides as well as the synthetic collagen-like substrate N-(3-[2-furyl]acryloyl)-Leu-Gly- Pro-Ala in vitro. 560 matched cddid_all.tbl CDD cd09609 cd09609 341072 M3B_PepF Peptidase family M3B, oligopeptidase F (PepF). Peptidase family M3B oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and is similar to oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most bacterial PepFs are cytoplasmic endopeptidases; however, the Bacillus amyloliquefaciens PepF oligopeptidase is a secreted protein and may facilitate the process of sporulation. Specifically, the yjbG gene encoding the homolog of the PepF1 and PepF2 oligoendopeptidases of Lactococcus lactis has been identified in Bacillus subtilis as an inhibitor of sporulation initiation when over-expressed from a multicopy plasmid. 586 matched cddid_all.tbl CDD cd09610 cd09610 341073 M3B_PepF Peptidase family M3B, oligopeptidase F (PepF). Peptidase family M3B oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and is similar to oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most bacterial PepFs are cytoplasmic endopeptidases; however, the Bacillus amyloliquefaciens PepF oligopeptidase is a secreted protein and may facilitate the process of sporulation. Specifically, the yjbG gene encoding the homolog of the PepF1 and PepF2 oligoendopeptidases of Lactococcus lactis has been identified in Bacillus subtilis as an inhibitor of sporulation initiation when over-expressed from a multicopy plasmid. 532 matched cddid_all.tbl CDD cd09611 cd09611 187707 Jacalin_ZG16_like Jacalin-like lectin domain of the zymogen granule protein 16 and related proteins. ZG16p is a conserved secreted vertebrate protein with tissue-specific expression profiles, which might play a role in glycoprotein secretion, perhaps as a linker protein that participates in the formation and/or transport of the zymogen granule. Its paralog ZG16b (PAUF) has been associated with roles in gene regulation and cancer. This domain family also contains mammalian proteins labelled as prostatic spermine-binding protein (SBP) and salivary-gland specific secreted proteins. 128 matched cddid_all.tbl CDD cd09612 cd09612 187708 Jacalin Jacalin-like plant lectin domain. Jacalin-like lectins are sugar-binding protein domains mostly found in plants. They adopt a beta-prism topology consistent with a circularly permuted three-fold repeat of a structural motif. Proteins containing this domain may bind mono- or oligosaccharides with high specificity. The domain can occur in tandem-repeat arrangements with up to six copies, and in architectures combined with a variety of other functional domains. The family was initially named after an abundant protein found in the jackfruit seed. Jacalin specifically binds to the alpha-O-glycoside of the disaccharide Gal-beta1-3-GalNAc, and has proven useful in the study of O-linked glycoproteins. Jacalin-like lectins in this family may occur in various oligomerization states. 130 matched cddid_all.tbl CDD cd09613 cd09613 187709 Jacalin_metallopeptidase_like Jacalin-like lectin domain of putative metalloproteases and similar proteins. Members of this family, which appears restricted to fungi, co-occur with protein domains that contain an HExxH motif characteristic of metallopeptidases. They have not been functionally characterized. 124 matched cddid_all.tbl CDD cd09614 cd09614 187710 griffithsin_like Jacalin-like lectin domain of griffithsin and related proteins. Griffithsin is a lectin isolated from a red alga, which has shown potential as an inhibitor of viral entry, exhibiting antiviral activity against HIV and SARS. The biological functions of griffithsin and griffithsin-like proteins with respect to their source organisms are not known. 128 matched cddid_all.tbl CDD cd09615 cd09615 187711 Jacalin_EEP Jacalin-like lectin domains of putative endonucleases/exonucleases/phosphatases and related proteins. Members of this taxonomically diverse family co-occur with metal-dependent endonucleases/exonucleases/phosphatases. They have not been functionally characterized. 134 matched cddid_all.tbl CDD cd09616 cd09616 187737 Peptidase_C12_UCH_L1_L3 Cysteine peptidase C12 containing ubiquitin carboxyl-terminal hydrolase (UCH) families L1 and L3. This ubiquitin C-terminal hydrolase (UCH) family includes UCH-L1 and UCH-L3, the two members sharing around 53% sequence identity as well as conserved catalytic residues. Both enzymes hydrolyze carboxyl terminal esters and amides of ubiquitin (Ub). UCH-L1, in dimeric form, has additional enzymatic activity as a ubiquitin ligase. It is highly abundant in the brain, constituting up to 2% of total protein, and is expressed exclusively in neurons and testes. Abnormal expression of UCH-L1 has been shown to correlate with several forms of cancer, including several primary lung tumors, lung tumor cell lines, and colorectal cancers. Mutations in the UCH-L1 gene have been linked to susceptibility to and protection from Parkinson's disease (PD); dysfunction of the hydrolase activity can lead to an accumulation of alpha-synuclein, which is linked to Parkinson's disease (PD), while accumulation of neurofibrillary tangles is linked to Alzheimer's disease (AD). UCH-L3 hydrolyzes isopeptide bonds at the C-terminal glycine of either Ub or Nedd8, a ubiquitin-like protein. It can also interact with Lys48-linked Ub dimers to protect them from degradation while inhibiting its hydrolase activity at the same time. Unlike UCH-L1, neither dimerization nor ligase activity have been observed for UCH-L3. It has been shown that levels of Nedd8 and the apoptotic protein p53 and Bax are elevated in UCH-L3 knockout mice upon cryptorchid injury, possibly contributing to profound germ cell loss via apoptosis. 222 matched cddid_all.tbl CDD cd09617 cd09617 187738 Peptidase_C12_UCH37_BAP1 Cysteine peptidase C12 containing ubiquitin carboxyl-terminal hydrolase (UCH) families UCH37 (UCH-L5) and BAP1. This ubiquitin C-terminal hydrolase (UCH) family includes UCH37 (also known as UCH-L5) and BRCA1-associated protein-1 (BAP1). They contain a UCH catalytic domain as well as an additional C-terminal extension which plays a role in protein-protein interactions. UCH37 is responsible for ubiquitin (Ub) isopeptidase activity in the 19S proteasome regulatory complex; it disassembles Lys48-linked poly-ubiquitin from the distal end of the chain. It is also associated with the human Ino80 chromatin-remodeling complex (hINO80) in the nucleus and can be activated through transient association of hINO80 with hRpn13 that is bound to the 19S regulatory particle or the proteasome. UCH37 possibly plays a role in oncogenesis; it competes with Smad ubiquitination regulatory factor 2 (Smurf2, ubiquitin ligase) in binding concurrently to Smad7 in order to deubiquitinate the activated type I transforming growth factor beta (TGF-beta) receptor, thus rescuing it from proteasomal degradation. BAP1 binds to the wild-type BRCA1 RING finger domain, localized in the nucleus. In addition to the UCH catalytic domain, BAP1 contains a UCH37-like domain (ULD), binding domains for BRCA1 and BARD1, which form a tumor suppressor heterodimeric complex, and a binding domain for HCFC1, which interacts with histone-modifying complexes during cell division. The full-length human BRCA1 is a ubiquitin ligase. However, BAP1 does not appear to function in the deubiquitination of autoubiquitinated BRCA1. BAP1 exhibits tumor suppressor activity in cancer cells, and gene mutations have been reported in a small number of breast and lung cancer samples. In metastasis of uveal melanoma, the most common primary cancer of the eye, inactivating somatic mutations have been identified in the gene encoding BAP1 on chromosome 3p21.1. These mutations include several that cause premature protein termination as well as affect its UCH domain, thus implicating loss of BAP1 and suggesting that the BAP1 pathway may be a valuable therapeutic target. 219 matched cddid_all.tbl CDD cd09618 cd09618 187676 CBM9_like_2 DOMON-like type 9 carbohydrate binding module. Family 9 carbohydrate-binding modules (CBM9) play a role in the microbial degradation of cellulose and hemicellulose (materials found in plants). The domain has previously been called cellulose-binding domain. The polysaccharide binding sites of CBMs with available 3D structure have been found to be either flat surfaces with interactions formed by predominantly aromatic residues (tryptophan and tyrosine), or extended shallow grooves. CBM9 domains found in this uncharacterized subfamily are typically found at the N-terminus of longer proteins that lack additional annotation with domain footprints. 186 matched cddid_all.tbl CDD cd09619 cd09619 187677 CBM9_like_4 DOMON-like type 9 carbohydrate binding module. Family 9 carbohydrate-binding modules (CBM9) play a role in the microbial degradation of cellulose and hemicellulose (materials found in plants). The domain has previously been called cellulose-binding domain. The polysaccharide binding sites of CBMs with available 3D structure have been found to be either flat surfaces with interactions formed by predominantly aromatic residues (tryptophan and tyrosine), or extended shallow grooves. CBM9 domains found in this uncharacterized heterogeneous subfamily are often located at the C-terminus of longer proteins and may co-occur with various other domains. 187 matched cddid_all.tbl CDD cd09620 cd09620 187678 CBM9_like_3 DOMON-like type 9 carbohydrate binding module. Family 9 carbohydrate-binding modules (CBM9) play a role in the microbial degradation of cellulose and hemicellulose (materials found in plants). The domain has previously been called cellulose-binding domain. The polysaccharide binding sites of CBMs with available 3D structure have been found to be either flat surfaces with interactions formed by predominantly aromatic residues (tryptophan and tyrosine), or extended shallow grooves. CBM9 domains found in this uncharacterized heterogeneous subfamily may co-occur with various other domains. 200 matched cddid_all.tbl CDD cd09621 cd09621 187679 CBM9_like_5 DOMON-like type 9 carbohydrate binding module. Family 9 carbohydrate-binding modules (CBM9) play a role in the microbial degradation of cellulose and hemicellulose (materials found in plants). The domain has previously been called cellulose-binding domain. The polysaccharide binding sites of CBMs with available 3D structure have been found to be either flat surfaces with interactions formed by predominantly aromatic residues (tryptophan and tyrosine), or extended shallow grooves. CBM9 domains found in this uncharacterized heterogeneous subfamily are often located at the C-terminus of longer proteins and may co-occur with various other functional domains such as glycosyl hydrolases. The CBM9 module in these architectures may be involved in binding to carbohydrates. 188 matched cddid_all.tbl CDD cd09622 cd09622 187680 CBM9_like_HisKa DOMON-like type 9 carbohydrate binding module at the N-terminus of bacterial sensor histidine kinases. Family 9 carbohydrate-binding modules (CBM9) play a role in the microbial degradation of cellulose and hemicellulose (materials found in plants). The domain has previously been called cellulose-binding domain. The polysaccharide binding sites of CBMs with available 3D structure have been found to be either flat surfaces with interactions formed by predominantly aromatic residues (tryptophan and tyrosine), or extended shallow grooves. CBM9 domains found in this family are located at the N-terminus of bacterial sensor histidine kinases and may constitute or contribute to the ligand-binding moiety. 265 matched cddid_all.tbl CDD cd09623 cd09623 187681 DOMON_EBDH Heme-binding domain of bacterial ethylbenzene dehydrogenase. Ethylbenzene dehydrogenase (EBDH) is a bacterial molybdopterin enzyme. It catalyzes anaerobic hydroxylation of alkylaromatic compounds to secondary alcohols. The DOMON domain in EBDH and related proteins, typically called the gamma subunit, binds a heme; its function in the catalytic mechanism is unclear. It co-occurs with a molybdopterin-binding subunit and an iron-sulfur protein. This family also contains heme-binding domains of dimethylsulfide dehydrogenase, selenate reductases, and chlorate reductase. 224 matched cddid_all.tbl CDD cd09624 cd09624 187682 DOMON_b558_566 DOMON-like heme-binding domain of CbsA. This family, conserved in some lineages of the Crenarchaeota, represents a mono-heme cytochrome b558/566. CbsA is reported to be a subunit in a heterodimeric complex (CbsA-CbsB in Sulfolobus species), and appears to be glycosylated. 279 matched cddid_all.tbl CDD cd09625 cd09625 187683 DOMON_like_cytochrome DOMON-like domain of an uncharacterized protein family. This family of uncharacterized bacterial proteins contains a DOMON-like domain and an N-terminal B- or C-type cytochrome domain. DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases. 348 matched cddid_all.tbl CDD cd09626 cd09626 187684 DOMON_glucodextranase_like DOMON-like domain of various glycoside hydrolases. This DOMON-like domain is found at the C-terminus of various bacterial proteins that play roles in metabolizing carbohydrates, such as glucodextranase (hydrolyzes alpha-1,6-glucosidic linkages of dextran from the non-reducing end), glucan alpha-1,4-glucosidase, pullulanase (degrades pullulan, a polysaccharide built from maltotriose units), arabinogalactan endo-1,4-beta-galactosidase, and others. Consequently, the DOMON-like domains in this family co-occur with catalytic domains from various glycosyl hydrolase families. The precise function of the DOMON domains in these proteins is not clear, they may be involved in interactions with carbohydrates. 220 matched cddid_all.tbl CDD cd09627 cd09627 187685 DOMON_murB_like Domon-like domain of UDP-N-acetylenolpyruvoylglucosamine reductase. UDP-N-acetylenolpyruvoylglucosamine reductase (murB) catalyzes an essential step in peptidoglycan biosynthesis, the reduction of UDP-N-acetylglucosamine-enolpyruvate to UDP-N-acetylmuramate. A subset of these FAD-dependent enzymes contains a C-terminal DOMON-like domain. DOMON domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes; initially DOMON domains were suspected to confer protein-protein interactions. The DOMON-like domain in murB may bind a heme. 179 matched cddid_all.tbl CDD cd09628 cd09628 187686 DOMON_SDR_2_like DOMON domain of stromal cell-derived receptor 2 (ferric chelate reductase 1) and related proteins. Stromal cell-derived receptor 2 (or ferric chelate reductase 1) reduces Fe(3+) to Fe(2+) ahead of iron transport from the endosome to the cytoplasm. This transmembrane protein is a member of the cytochrome b561 family and contains a DOMON domain which may bind to heme or another ligand. DOMON-like domains can be found in all three kindgoms of life and are a diverse group of ligand binding domains that have been shown to interact with sugars and hemes. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases. 169 matched cddid_all.tbl CDD cd09629 cd09629 187687 DOMON_CIL1_like DOMON-like domain of Brassica carinata CIL1 and similar proteins. Brassica carinata CIL1 has been described as involved in suppression of axillary meristem development. It contains a single DOMON domain, the function of which is unclear. Members in this diverse family of plant proteins may have a cytochrome b561 domain C-terminal to the DOMON domain, some members from Arabidopsis have been characterized as auxin-responsive or auxin-induced proteins. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases. 152 matched cddid_all.tbl CDD cd09630 cd09630 187688 CDH_like_cytochrome Heme-binding cytochrome domain of fungal cellobiose dehydrogenases. Cellobiose dehydrogenase (CellobioseDH or CDH) is an extracellular fungal oxidoreductase that degrades both lignin and cellulose. Specifically, CDHs oxidize cellobiose, cellodextrins, and lactose to corresponding lactones, utilizing a variety of electron acceptors. Class-II CDHs are monomeric hemoflavoenzymes that are comprised of a b-type cytochrome domain linked to a large flavodehydrogenase domain. The cytochrome domain of CDH and related enzymes, which this model describes, folds as a beta sandwich and complexes a heme molecule. It is found at the N-terminus of this family of enzymes, and belongs to the DOMON domain superfamily, a ligand-interacting motif found in all three kingdoms of life. 168 matched cddid_all.tbl CDD cd09631 cd09631 187689 DOMON_DOH DOMON-like domain of copper-dependent monooxygenases and related proteins. This diverse family characterizes DOMON domains found in dopamine beta-hydroxylase (DBH), monooxygenase X (MOX), and various other proteins, some of which contain DOMON domains exclusively; the family is not restricted to eukaryotes. DBH is a membrane-bound enzyme that converts dopamine to L-norepinephrine, and plays a central role in the metabolism of catecholamine neurotransmitters. DOMON domains were initially thought to confer protein-protein interactions. They were subsequently found as a heme-binding motif in cellobiose dehydrogenase, an extracellular fungal oxidoreductase that degrades both lignin and cellulose, and in ethylbenzene dehydrogenase, an enzyme that aids in the anaerobic degradation of hydrocarbons. The domain interacts with sugars in the type 9 carbohydrate binding modules (CBM9), which are present in a variety of glycosyl hydrolases, and it can also be found at the N-terminus of sensor histidine kinases. 138 matched cddid_all.tbl CDD cd09632 cd09632 193606 PliI_like Periplasmic lysozyme inhibitor, I-type (PliI) and similar proteins. Aeromonas hydrophila PliI is a dimeric periplasmic protein that enables bacteria to resist permeabilization of the outer membrane by the bactericidal action of lysozyme. PliI may be a direct inhibitor of lysozyme that inserts a conserved loop into the active site of type I (invertebrate) lysozymes. 109 matched cddid_all.tbl CDD cd09633 cd09633 193607 Deltex_C Domain found at the C-terminus of deltex-like. The deltex family of proteins is involved in the regulation of Notch signaling, and therefore may play roles in cell-to-cell communications that regulate mechanisms determining cell fate. They have a central RING-type zinc finger domain and contain a C-terminal domain, described here, that is also found in other domain architectures. Deltex-1 (DTX1) contains a RING finger and two WWE domains, indicating that it may be an E3 ubiquitin ligase. Human deltex 3-like, which contains an additional N-terminal domain (presumably with ubiquitin ligase activity) is also described as E3 ubiquitin-protein ligase DTX3L, B-lymphoma- and BAL-associated protein (BBAP), or rhysin-2. DTX3L mediates monoubiquitination of K91 of histone H4 in response to DNA damage. 131 matched cddid_all.tbl CDD cd09634 cd09634 187766 Cas1_I-II-III CRISPR/Cas system-associated protein Cas1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer integration; Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a N-terminal beta-strand domain and a C-terminal alpha-helical domain 317 matched cddid_all.tbl CDD cd09636 cd09636 187767 Cas1_I-II-III CRISPR/Cas system-associated protein Cas1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer integration; Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a N-terminal beta-strand domain and a C-terminal alpha-helical domain 260 matched cddid_all.tbl CDD cd09637 cd09637 187768 Cas4_I-A_I-B_I-C_I-D_II-B CRISPR/Cas system-associated protein Cas4. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas4 is RecB-like nuclease with three-cysteine C-terminal cluster 178 matched cddid_all.tbl CDD cd09638 cd09638 187769 Cas2_I_II_III CRISPR/Cas system-associated protein Cas2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas2 is present in majority of CRISPR/Cas systems along with Cas1; RNAse specific to U-rich regions; Possesses an RRM/ferredoxin fold 90 matched cddid_all.tbl CDD cd09639 cd09639 187770 Cas3_I CRISPR/Cas system-associated protein Cas3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DEAD/DEAH box helicase DNA helicase cas3'; Often but not always is fused to HD nuclease domain; signature gene for Type I 353 matched cddid_all.tbl CDD cd09640 cd09640 187771 Cas7_I-C CRISPR/Cas system-associated RAMP superfamily protein Cas7. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas7 is a RAMP superfamily protein; Subunit of the Cascade complex; also known as CT1132 family 258 matched cddid_all.tbl CDD cd09641 cd09641 193608 Cas3''_I CRISPR/Cas system-associated protein Cas3''. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; HD-like nuclease, specifically digesting double-stranded oligonucleotides and preferably cleaving at G:C pairs; signature gene for Type I 200 matched cddid_all.tbl CDD cd09642 cd09642 187773 Cas8c_I-C CRISPR/Cas system-associated protein Cas8c. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; signature gene for I-C subtype; also known as Csd1 family 574 matched cddid_all.tbl CDD cd09643 cd09643 187774 Csn1 CRISPR/Cas system-associated protein Cas9. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Very large protein containing McrA/HNH-nuclease related domain and a RuvC-like nuclease domain; signature gene for type II 799 matched cddid_all.tbl CDD cd09644 cd09644 213407 Csn2 CRISPR/Cas system-associated protein Csn2. Csn2 is a Nmeni subtype-specific Cas protein, which may function in the adaptation process which mediates the incorporation of foreign nucleic acids into the microbial host genome. Csn 2 may interact directly with double-stranded DNA. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Csn2 has been predicted to be a functional analog of Cas4 based on anti-correlated phyletic patterns; also known as SPy1049 family. 223 matched cddid_all.tbl CDD cd09645 cd09645 187776 Cas5_I-E CRISPR/Cas system-associated RAMP superfamily protein Cas5. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex 137 matched cddid_all.tbl CDD cd09646 cd09646 187777 Cas7_I-E CRISPR/Cas system-associated RAMP superfamily protein Cas7. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas7 is a RAMP superfamily protein; Subunit of the Cascade complex; also known as Cse4/CasC family 325 matched cddid_all.tbl CDD cd09647 cd09647 187778 Csm2_III-A CRISPR/Cas system-associated protein Csm2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small alpha-helical protein; signature gene for subtype III-A 95 matched cddid_all.tbl CDD cd09648 cd09648 187779 Cas2_I-E CRISPR/Cas system-associated protein Cas2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas2 is present in majority of CRISPR/Cas systems along with Cas1; RNAse specific to U-rich regions; Possesses an RRM/ferredoxin fold 93 matched cddid_all.tbl CDD cd09649 cd09649 187780 Cas5_I-A CRISPR/Cas system-associated RAMP superfamily protein Cas5. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex 143 matched cddid_all.tbl CDD cd09650 cd09650 187781 Cas7_I CRISPR/Cas system-associated RAMP superfamily protein Cas7. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas7 is a RAMP superfamily protein; Subunit of the Cascade complex; also known as MJ0381 family 189 matched cddid_all.tbl CDD cd09651 cd09651 187782 Cas5_I-C CRISPR/Cas system-associated RAMP superfamily protein Cas5. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex; in subtype I-C this protein might be the endoribonuclease that generates crRNAs; also known as DevS family 198 matched cddid_all.tbl CDD cd09652 cd09652 410980 Cas6 Class 1 CRISPR-associated endoribonuclease Cas6. CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins) adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. These systems are divided into two classes: class 1 systems utilize multiple Cas proteins and CRISPR RNA (crRNA) to form an effector complex while class 2 systems employ a large, single effector with crRNA to mediate interference. Cas6 family endoribonucleases are typically found within types I and III CRISPR-Cas systems and are metal-independent nucleases that catalyze RNA cleavage via a mechanism involving a 2'-3' cyclic intermediate. They share a common ferredoxin or RNA recognition motif (RRM) fold, and they recognize and excise CRISPR repeat RNAs that vary widely in primary and secondary structures. Cas6 is also found in the rare type IV system that includes rudimentary CRISPR-cas loci lacking the adaptation module. 258 matched cddid_all.tbl CDD cd09653 cd09653 187784 Csa5_I-A CRISPR/Cas system-associated protein Csa5. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Predicted transcriptional regulator of CRISPR/Cas system; contains DNA binding HTH domain; also known as Csa5 family 97 matched cddid_all.tbl CDD cd09654 cd09654 187785 Cmr5_III-B CRISPR/Cas system-associated protein Cmr5. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small alpha-helical protein; signature gene for subtype III-B 127 matched cddid_all.tbl CDD cd09655 cd09655 187786 CasRa_I-A CRISPR/Cas system-associated transcriptional regulator CasRa. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Predicted transcriptional regulator of CRISPR/Cas system 198 matched cddid_all.tbl CDD cd09656 cd09656 187787 Cmr3_III-B CRISPR/Cas system-associated RAMP superfamily protein Cmr3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; This protein is a subunit of Cmr complex 318 matched cddid_all.tbl CDD cd09657 cd09657 187788 Cmr1_III-B CRISPR/Cas system-associated RAMP superfamily protein Cmr1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; This protein is a subunit of Cmr complex 132 matched cddid_all.tbl CDD cd09658 cd09658 187789 Cas5_I-B CRISPR/Cas system-associated RAMP superfamily protein Cas5. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex 181 matched cddid_all.tbl CDD cd09659 cd09659 187790 Cas4_I-A CRISPR/Cas system-associated protein Cas4. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas4 is RecB-like nuclease with three-cysteine C-terminal cluster 270 matched cddid_all.tbl CDD cd09660 cd09660 187791 Csx1_III-U CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as MJ1666 family 394 matched cddid_all.tbl CDD cd09661 cd09661 187792 Cmr6_III-B CRISPR/Cas system-associated RAMP superfamily protein Cmr6. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; This protein is a subunit of Cmr complex 210 matched cddid_all.tbl CDD cd09662 cd09662 187793 Csm5_III-A CRISPR/Cas system-associated RAMP superfamily protein Csm5. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein 365 matched cddid_all.tbl CDD cd09663 cd09663 187794 Csm4_III-A CRISPR/Cas system-associated RAMP superfamily protein Csm4. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein 301 matched cddid_all.tbl CDD cd09664 cd09664 187795 Cas6_I-E CRISPR/Cas system-associated RAMP superfamily protein Cas6e. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas6e is an endoribonuclease that generates crRNA; This family is specific for CRISPR/Cas system I-E subtype; Homologous to Cas6 (RAMP superfamily protein); Possesses double RRM/ferredoxin fold; also known as Cse3 family 210 matched cddid_all.tbl CDD cd09665 cd09665 187796 Cas8a1_I-A CRISPR/Cas system-associated protein Cas8a1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; signature gene for I-A subtype; also known as CXXC_CXXC family 334 matched cddid_all.tbl CDD cd09666 cd09666 187797 Cas8a2_I-A CRISPR/Cas system-associated protein Csa8a2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Zn-finger domain containing protein, distant homologs of Cas8 proteins; signature gene for I-A subtype; also known as Csa4 family 352 matched cddid_all.tbl CDD cd09667 cd09667 187798 Csb2_I-U CRISPR/Cas system-associated protein Csb2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Duplicated RAMP domains; also known as GSU0054 family 418 matched cddid_all.tbl CDD cd09668 cd09668 187799 Csx1_III-U CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as TM1812 family 214 matched cddid_all.tbl CDD cd09669 cd09669 187800 Cse1_I-E CRISPR/Cas system-associated protein Cse1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; subunit of the Cascade complex; signature gene for I-E subtype; also known as Cse1/CasA/YgcL family 477 matched cddid_all.tbl CDD cd09670 cd09670 187801 Cse2_I-E CRISPR/Cas system-associated protein Cse2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small alpha-helical protein; also known as Cse2/CasB/YgcK family; specific gene for I-E subtype; 152 matched cddid_all.tbl CDD cd09671 cd09671 187802 Csx1_III-U CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as DxTHG family 346 matched cddid_all.tbl CDD cd09672 cd09672 187803 Cas8a1_I-A CRISPR/Cas system-associated protein Cas8a1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; signature gene for I-A subtype; also known as TM1802 family 545 matched cddid_all.tbl CDD cd09673 cd09673 187804 Cas3_Cas2_I-F CRISPR/Cas system-associated protein Cas3/Cas2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas3/Cas2 fusion; This protein includes both DEAH and HD motifs for helicase and N-terminal domain corresponding to Cas2 RNAse; signature gene for Type I and subtype I-F 1106 matched cddid_all.tbl CDD cd09674 cd09674 187805 Cas6_I-F CRISPR/Cas system-associated RAMP superfamily protein Cas6f. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas6f is an endoribonuclease that generates crRNA; This family is specific for CRISPR/Cas system I-F subtype; Possesses RRM fold; also known as Csy4 family 186 matched cddid_all.tbl CDD cd09675 cd09675 187806 Csy1_I-F CRISPR/Cas system-associated protein Csy1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins; Predicted subunit of the Cascade complex; signature gene for I-F subtype; also known as Csy1 family 384 matched cddid_all.tbl CDD cd09676 cd09676 187807 Csy2_I-F CRISPR/Cas system-associated RAMP superfamily protein Csy2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; predicted Cas5 ortholog 292 matched cddid_all.tbl CDD cd09677 cd09677 187808 Csy3_I-F CRISPR/Cas system-associated RAMP superfamily protein Csy3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; predicted Cas7 ortholog 339 matched cddid_all.tbl CDD cd09678 cd09678 187809 Csb1_I-U CRISPR/Cas system-associated protein Csb1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; Contains several motifs similar to Cas7 family; also known as GSU0053 family 174 matched cddid_all.tbl CDD cd09679 cd09679 187810 Cas10_III CRISPR/Cas system-associated protein Cas10. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Multidomain protein with permuted HD nuclease domain, palm domain and Zn-ribbon; MTH326-like has inactivated polymerase catalytic domain; alr1562 and slr7011 - predicted only on the basis of size, presence of HD domain, and location with RAMPs in one operon; signature gene for type III; also known as Crm2 family 475 matched cddid_all.tbl CDD cd09680 cd09680 187811 Cas10_III CRISPR/Cas system-associated protein Cas10. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Multidomain protein with permuted HD nuclease domain, palm domain and Zn-ribbon; signature gene for type III; also known as Csm1 family 650 matched cddid_all.tbl CDD cd09681 cd09681 187812 Csx3_III-U CRISPR/Cas system-associated protein Csx3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small protein in some cases fused to Csx1 (COG1517) family domains 83 matched cddid_all.tbl CDD cd09682 cd09682 187813 Cmr4_III-B CRISPR/Cas system-associated RAMP superfamily protein Cmr4. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; This protein is a subunit of Cmr complex 242 matched cddid_all.tbl CDD cd09683 cd09683 187814 Csm3_III-A CRISPR/Cas system-associated RAMP superfamily protein Csm3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein 216 matched cddid_all.tbl CDD cd09684 cd09684 187815 Csm3_III-A CRISPR/Cas system-associated RAMP superfamily protein Csm3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein 215 matched cddid_all.tbl CDD cd09685 cd09685 187816 Cas7_I-A CRISPR/Cas system-associated RAMP superfamily protein Cas7. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas7 is a RAMP superfamily protein; Subunit of the Cascade complex; also known as DevR family 274 matched cddid_all.tbl CDD cd09686 cd09686 187817 Csx1_III-U CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as NE0113 family 209 matched cddid_all.tbl CDD cd09687 cd09687 187818 Cas7_I-C CRISPR/Cas system-associated RAMP superfamily protein Cas7. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas7 is a RAMP superfamily protein; Subunit of the Cascade complex; also known as Cst2/DevR family 302 matched cddid_all.tbl CDD cd09688 cd09688 187819 Cas5_I-C CRISPR/Cas system-associated RAMP superfamily protein Cas5. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex; in subtype I-C this protein might be the endoribonuclease that generates crRNAs; also known as DevS family 174 matched cddid_all.tbl CDD cd09689 cd09689 187820 Cas7_I-C CRISPR/Cas system-associated RAMP superfamily protein Cas7. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas7 is a RAMP superfamily protein; Subunit of the Cascade complex; also known as Csd2 family 278 matched cddid_all.tbl CDD cd09690 cd09690 187821 Cas7_I-B CRISPR/Cas system-associated RAMP superfamily protein Cas7. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas7 is a RAMP superfamily protein; Subunit of the Cascade complex; also known as Csh2 family 286 matched cddid_all.tbl CDD cd09691 cd09691 187822 Cas8b_I-B CRISPR/Cas system-associated protein Cas8b. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Zn-finger domain containing protein, distant homologs of Cas8 proteins; signature gene for I-B subtype; also known as Csh1 family 381 matched cddid_all.tbl CDD cd09692 cd09692 187823 Cas5_I-B CRISPR/Cas system-associated RAMP superfamily protein Cas5. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex 189 matched cddid_all.tbl CDD cd09693 cd09693 187824 Cas5_I CRISPR/Cas system-associated RAMP superfamily protein Cas5. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex 202 matched cddid_all.tbl CDD cd09694 cd09694 187825 Csm6_III-A CRISPR/Cas system-associated protein Csm6. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; loosely associated with CRISPR/Cas systems 181 matched cddid_all.tbl CDD cd09695 cd09695 187826 Csx16_III-U CRISPR/Cas system-associated protein Csx16. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small protein often seen in proximity to Csx1 (COG1517) family; also known as VVA1548 family 76 matched cddid_all.tbl CDD cd09696 cd09696 187827 Cas3_I CRISPR/Cas system-associated protein Cas3; Distinct Cas3 family with HD domain fused to C-termus of Helicase domain. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DNA helicase Cas3; This protein includes both DEAH and HD motifs; signature gene for Type I 843 matched cddid_all.tbl CDD cd09697 cd09697 187828 Cas8a1_I-A CRISPR/Cas system-associated protein Cas8a1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; signature gene for I-A subtype; also known as Csx8 family 441 matched cddid_all.tbl CDD cd09698 cd09698 187829 Cas8a2_I-A CRISPR/Cas system-associated protein Csa8a2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; signature gene for I-A subtype; also known as Csx9 family 377 matched cddid_all.tbl CDD cd09699 cd09699 187830 Csm6_III-A CRISPR/Cas system-associated protein Csm6. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; loosely associated with CRISPR/Cas systems 360 matched cddid_all.tbl CDD cd09700 cd09700 187831 Csx10 CRISPR/Cas system-associated RAMP superfamily protein Csx10. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Duplicated RAMP domains 386 matched cddid_all.tbl CDD cd09701 cd09701 187832 Cas10_III CRISPR/Cas system-associated protein Cas10. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Multidomain protein with permuted HD nuclease domain, inactivated palm domain and Zn-ribbon; signature gene for type III 909 matched cddid_all.tbl CDD cd09702 cd09702 187833 Csx1_III-U CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as TIGR02710 family 378 matched cddid_all.tbl CDD cd09703 cd09703 187834 Cas6-I-III CRISPR/Cas system-associated RAMP superfamily protein Cas6. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas6 is an endoribonuclease that generates crRNAs, predicted subunit of Cascade complex; RAMP superfamily protein; Possesses double RRM/ferredoxin fold; also known as Cse3 family 188 matched cddid_all.tbl CDD cd09704 cd09704 187835 Csx12 CRISPR/Cas system-associated protein Cas9. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Very large protein containing McrA/HNH-nuclease related domain and a RuvC-like nuclease domain; signature gene for type II 804 matched cddid_all.tbl CDD cd09705 cd09705 187836 Csf1_U CRISPR/Cas system-associated protein Csf1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Zn-finger domain containing protein; also known as Csf1 family 202 matched cddid_all.tbl CDD cd09706 cd09706 187837 Csf2_U CRISPR/Cas system-associated RAMP superfamily protein Csf2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; Contains several motifs similar to Cas7 family 328 matched cddid_all.tbl CDD cd09707 cd09707 187838 Csf3_U CRISPR/Cas system-associated RAMP superfamily protein Csf3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein 214 matched cddid_all.tbl CDD cd09708 cd09708 187839 Csf4_U CRISPR/Cas system-associated DinG family helicase Csf4. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; DinG family DNA helicase 632 matched cddid_all.tbl CDD cd09709 cd09709 187840 Csc2_I-D CRISPR/Cas system-associated protein Csc2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; predicted Cas7 ortholog; also known as Cse1 family 274 matched cddid_all.tbl CDD cd09710 cd09710 187841 Cas3_I-D CRISPR/Cas system-associated protein Cas3; Distinct diverged subfamily of Cas3 helicase domain. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Diverged DNA helicase Cas3'; signature gene for Type I and subtype I-D 353 matched cddid_all.tbl CDD cd09711 cd09711 187842 Csc1_I-D CRISPR/Cas system-associated protein Csc1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; predicted Cas5 ortholog; also known as CasA/Cse1 family 210 matched cddid_all.tbl CDD cd09712 cd09712 187843 Cas10d_I-D CRISPR/Cas system-associated protein Cas10d. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain. Fused to N-terminal HD domain; signature gene for I-D subtype; also known as Csc3 family 900 matched cddid_all.tbl CDD cd09713 cd09713 187844 Cas8c_I-C CRISPR/Cas system-associated protein Cas8c. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; signature gene for I-C subtype; also known as Csx13_N family 316 matched cddid_all.tbl CDD cd09714 cd09714 187845 Cas8c'_I-D CRISPR/Cas system-associated protein Cas8c'. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; signature gene for I-C subtype; also known as Csx13_C family 152 matched cddid_all.tbl CDD cd09715 cd09715 187846 Csp2_I-U CRISPR/Cas system-associated protein Cas8c. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Predicted Cas8 ortholog 474 matched cddid_all.tbl CDD cd09716 cd09716 187847 Cas5_I CRISPR/Cas system-associated RAMP superfamily protein Cas5. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex 220 matched cddid_all.tbl CDD cd09717 cd09717 187848 Cas7_I CRISPR/Cas system-associated RAMP superfamily protein Cas7. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas7 is a RAMP superfamily protein; Subunit of the Cascade complex; also known as Csp1 family 292 matched cddid_all.tbl CDD cd09718 cd09718 187849 Cas1_I-F CRISPR/Cas system-associated protein Cas1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer integration; Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a N-terminal beta-strand domain and a C-terminal alpha-helical domain 306 matched cddid_all.tbl CDD cd09719 cd09719 187850 Cas1_I-E CRISPR/Cas system-associated protein Cas1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer integration; Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a N-terminal beta-strand domain and a C-terminal alpha-helical domain 262 matched cddid_all.tbl CDD cd09720 cd09720 187851 Cas1_II CRISPR/Cas system-associated protein Cas1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer intergration. Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a N-terminal beta-strand domain and a C-terminal alpha-helical domain. 275 matched cddid_all.tbl CDD cd09721 cd09721 187852 Cas1_I-C CRISPR/Cas system-associated protein Cas1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer integration; Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a N-terminal beta-strand domain and a C-terminal alpha-helical domain 338 matched cddid_all.tbl CDD cd09722 cd09722 187853 Cas1_I-B CRISPR/Cas system-associated protein Cas1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas1 is the most universal CRISPR system protein thought to be involved in spacer integration; Cas1 is metal-dependent deoxyribonuclease, also binds RNA; Shown to possess a unique fold consisting of a N-terminal beta-strand domain and a C-terminal alpha-helical domain 320 matched cddid_all.tbl CDD cd09723 cd09723 187854 Csx1_III-U CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as csx13 family 132 matched cddid_all.tbl CDD cd09724 cd09724 187855 CsaX_III-U CRISPR/Cas system-associated protein CsaX. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; No prediction 296 matched cddid_all.tbl CDD cd09725 cd09725 187856 Cas2_I_II_III CRISPR/Cas system-associated protein Cas2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas2 is present in majority of CRISPR/Cas systems along with Cas1; RNAse specific to U-rich regions; Possesses an RRM/ferredoxin fold 79 matched cddid_all.tbl CDD cd09726 cd09726 187857 RAMP_I_III CRISPR/Cas system-associated RAMP superfamily protein. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily proteins 177 matched cddid_all.tbl CDD cd09727 cd09727 187858 Cas6_I-E CRISPR/Cas system-associated RAMP superfamily protein Cas6e. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas6e is an endoribonuclease that generates crRNA; This family is specific for CRISPR/Cas system I-E subtype; Homologous to Cas6 (RAMP superfamily protein); Possesses double RRM/ferredoxin fold; also known as Cse3 family 210 matched cddid_all.tbl CDD cd09728 cd09728 187859 Csx1_III-U CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as DxTHG family 400 matched cddid_all.tbl CDD cd09729 cd09729 187860 Cse1_I-E CRISPR/Cas system-associated protein Cse1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; subunit of the Cascade complex; signature gene for I-E subtype; also known as Cse1/CasA/YgcL family 465 matched cddid_all.tbl CDD cd09730 cd09730 187861 Cas8a1_I-A CRISPR/Cas system-associated protein Cas8a1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; signature gene for I-A subtype; also known as TM1802 family 579 matched cddid_all.tbl CDD cd09731 cd09731 187862 Cse2_I-E CRISPR/Cas system-associated protein Cse2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small alpha-helical protein; also known as Cse2/CasB/YgcK family; specific gene for I-E subtype; 141 matched cddid_all.tbl CDD cd09732 cd09732 187863 Csx1_III-U CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as TM1812 family 221 matched cddid_all.tbl CDD cd09733 cd09733 187864 Cas6-I-III CRISPR/Cas system-associated RAMP superfamily protein Cas6. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas6 is an endoribonuclease that generates crRNAs, predicted subunit of Cascade complex; RAMP superfamily protein; Possesses double RRM/ferredoxin fold; also known as AF0072 family 193 matched cddid_all.tbl CDD cd09734 cd09734 320705 Csb2_I-U CRISPR/Cas system-associated protein Csb2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Duplicated RAMP domains; also known as GSU0054 family 496 matched cddid_all.tbl CDD cd09735 cd09735 187866 Csy1_I-F CRISPR/Cas system-associated protein Csy1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins; Predicted subunit of the Cascade complex; signature gene for I-F subtype; also known as Csy1 family 377 matched cddid_all.tbl CDD cd09736 cd09736 187867 Csy2_I-F CRISPR/Cas system-associated RAMP superfamily protein Csy2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; predicted Cas5 ortholog 289 matched cddid_all.tbl CDD cd09737 cd09737 187868 Csy3_I-F CRISPR/Cas system-associated RAMP superfamily protein Csy3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; predicted Cas7 ortholog 329 matched cddid_all.tbl CDD cd09738 cd09738 187869 Csb1_I-U CRISPR/Cas system-associated protein Csb1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; Contains several motifs similar to Cas7 family; also known as GSU0053 family 168 matched cddid_all.tbl CDD cd09739 cd09739 187870 Cas6_I-F CRISPR/Cas system-associated RAMP superfamily protein Cas6f. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas6f is an endoribonuclease that generates crRNA; This family is specific for CRISPR/Cas system I-F subtype; Possesses RRM fold; also known as Csy4 family 185 matched cddid_all.tbl CDD cd09740 cd09740 187871 Csx3_III-U CRISPR/Cas system-associated protein Csx3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small protein in some cases fused to Csx1 (COG1517) family domains 84 matched cddid_all.tbl CDD cd09741 cd09741 187872 Csx1_III-U CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as NE0113 family 219 matched cddid_all.tbl CDD cd09742 cd09742 187873 Csm6_III-A CRISPR/Cas system-associated protein Csm6. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; loosely associated with CRISPR/Cas systems; also known as APE2256 family 183 matched cddid_all.tbl CDD cd09743 cd09743 187874 Csx16_III-U CRISPR/Cas system-associated protein Csx16. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small protein often seen in proximity to Csx1 (COG1517) family; also known as VVA1548 family 90 matched cddid_all.tbl CDD cd09744 cd09744 187875 Cas8a1_I-A CRISPR/Cas system-associated protein Cas8a1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; signature gene for I-A subtype; also known as Csx8 family 441 matched cddid_all.tbl CDD cd09745 cd09745 187876 Cas8a2_I-A CRISPR/Cas system-associated protein Csa8a2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; signature gene for I-A subtype; also known as Csx9 family 377 matched cddid_all.tbl CDD cd09746 cd09746 187877 Csm6_III-A CRISPR/Cas system-associated protein Csm6. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; loosely associated with CRISPR/Cas systems 382 matched cddid_all.tbl CDD cd09747 cd09747 187878 Csx1_III-U CRISPR/Cas system-associated protein Csx1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein of this family often fused to HTH domain; Some proteins could have an additional fusion with RecB-family nuclease domain; Core domain appears to have a Rossmann-like fold; loosely associated with CRISPR/Cas systems; also known as Cas02710 family 378 matched cddid_all.tbl CDD cd09748 cd09748 187879 Cmr3_III-B CRISPR/Cas system-associated RAMP superfamily protein Cmr3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; This protein is a subunit of Cmr complex 356 matched cddid_all.tbl CDD cd09749 cd09749 187880 Cmr5_III-B CRISPR/Cas system-associated protein Cmr5. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small alpha-helical protein; signature gene for subtype III-B 119 matched cddid_all.tbl CDD cd09750 cd09750 187881 Csa5_I-A CRISPR/Cas system-associated protein Csa5. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Predicted transcriptional regulator of CRISPR/Cas system; contains DNA binding HTH domain; also known as Csa5 family 101 matched cddid_all.tbl CDD cd09751 cd09751 187882 Cas8a2_I-A CRISPR/Cas system-associated protein Csa8a2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Zn-finger domain containing protein, distant homologs of Cas8 proteins; signature gene for I-A subtype; also known as Csa4 family 355 matched cddid_all.tbl CDD cd09752 cd09752 187534 Cas5_I-C CRISPR/Cas system-associated RAMP superfamily protein Cas5. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex; in subtype I-C this protein might be the endoribonuclease that generates crRNAs; also known as DevS family 198 matched cddid_all.tbl CDD cd09753 cd09753 187883 Cas5_I-A CRISPR/Cas system-associated RAMP superfamily protein Cas5. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex 147 matched cddid_all.tbl CDD cd09754 cd09754 187884 Cas8a1_I-A CRISPR/Cas system-associated protein Cas8a1. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins, some contain Zn-finger domain; signature gene for I-A subtype; also known as CXXC_CXXC family 65 matched cddid_all.tbl CDD cd09755 cd09755 187885 Cas2_I-E CRISPR/Cas system-associated protein Cas2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas2 is present in majority of CRISPR/Cas systems along with Cas1; RNAse specific to U-rich regions; Possesses an RRM/ferredoxin fold 62 matched cddid_all.tbl CDD cd09756 cd09756 187886 Cas5_I-E CRISPR/Cas system-associated RAMP superfamily protein Cas5. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas5 is a RAMP superfamily protein; Subunit of the Cascade complex 135 matched cddid_all.tbl CDD cd09757 cd09757 187887 Cas8c_I-C CRISPR/Cas system-associated protein Cas8c. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Zn-finger domain containing protein, distant homologs of Cas8 proteins; signature gene for I-C subtype; also known as Csd1 family 569 matched cddid_all.tbl CDD cd09758 cd09758 213408 Csn2 CRISPR/Cas system-associated protein Csn2. Csn2 is a Nmeni subtype-specific Cas protein, which may function in the adaptation process which mediates the incorporation of foreign nucleic acids into the microbial host genome. Csn 2 may interact directly with double-stranded DNA. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA. Csn2 has been predicted to be a functional analog of Cas4 based on anti-correlated phyletic patterns; also known as SPy1049 family. 218 matched cddid_all.tbl CDD cd09759 cd09759 187889 Cas6_I-A CRISPR/Cas system-associated RAMP superfamily protein Cas6. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas6 is an endoribonuclease that generates crRNAs, predicted subunit of Cascade complex; RAMP superfamily protein; Possesses double RRM/ferredoxin fold 240 matched cddid_all.tbl CDD cd09760 cd09760 187890 Cas6_III CRISPR/Cas system-associated RAMP superfamily protein Cas6. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Cas6 is an endoribonuclease that generates crRNAs, predicted subunit of Cascade complex 289 matched cddid_all.tbl CDD cd09761 cd09761 187662 A3DFK9-like_SDR_c Clostridium thermocellum A3DFK9-like, a putative carbohydrate or polyalcohol metabolizing SDR, classical (c) SDRs. This subgroup includes a putative carbohydrate or polyalcohol metabolizing SDR (A3DFK9) from Clostridium thermocellum. Its members have a TGXXXGXG classical-SDR glycine-rich NAD-binding motif, and some have a canonical SDR active site tetrad (A3DFK9 lacks the upstream Asn). SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 242 matched cddid_all.tbl CDD cd09762 cd09762 187663 HSDL2_SDR_c human hydroxysteroid dehydrogenase-like protein 2 (HSDL2), classical (c) SDRs. This subgroup includes human HSDL2 and related protens. These are members of the classical SDR family, with a canonical Gly-rich NAD-binding motif and the typical YXXXK active site motif. However, the rest of the catalytic tetrad is not strongly conserved. HSDL2 may play a part in fatty acid metabolism, as it is found in peroxisomes. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 243 matched cddid_all.tbl CDD cd09763 cd09763 187664 DHRS1-like_SDR_c human dehydrogenase/reductase (SDR family) member 1 (DHRS1) -like, classical (c) SDRs. This subgroup includes human DHRS1 and related proteins. These are members of the classical SDR family, with a canonical Gly-rich NAD-binding motif and the typical YXXXK active site motif. However, the rest of the catalytic tetrad is not strongly conserved. DHRS1 mRNA has been detected in many tissues, liver, heart, skeletal muscle, kidney and pancreas; a longer transcript is predominantly expressed in the liver , a shorter one in the heart. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRS are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes have a 3-glycine N-terminal NAD(P)(H)-binding pattern (typically, TGxxxGxG in classical SDRs and TGxxGxxG in extended SDRs), while substrate binding is in the C-terminal region. A critical catalytic Tyr residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering), is often found in a conserved YXXXK pattern. In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) or additional Ser, contributing to the active site. Substrates for these enzymes include sugars, steroids, alcohols, and aromatic compounds. The standard reaction mechanism is a proton relay involving the conserved Tyr and Lys, as well as Asn (or Ser). Some SDR family members, including 17 beta-hydroxysteroid dehydrogenase contain an additional helix-turn-helix motif that is not generally found among SDRs. 265 matched cddid_all.tbl CDD cd09764 cd09764 187733 Csb3_I-U CRISPR/Cas system-associated RAMP superfamily protein Csb3. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; RAMP superfamily protein; Might be a catalytically active RNA endoribonuclease 341 matched cddid_all.tbl CDD cd09765 cd09765 187734 Csx14_I-U CRISPR/Cas system-associated protein Csx14. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Protein containing C-terminal alpha-helical domain resembling Cas8a2, also known as GSU0052 272 matched cddid_all.tbl CDD cd09766 cd09766 187735 Csx15_I-U CRISPR/Cas system-associated protein Csx15. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Small protein loosely associated with CRISPR/Cas systems; some are fused to AAA ATPase domain, also known as TTE2665 family 101 matched cddid_all.tbl CDD cd09767 cd09767 187705 Csx17_I-U CRISPR/Cas system-associated protein Csx17. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; Large proteins; Predicted subunit of the Cascade complex; 652 matched cddid_all.tbl CDD cd09768 cd09768 188874 Luminal_EIF2AK3 The Luminal domain, a dimerization domain, of the Serine/Threonine protein kinase, eukaryotic translation Initiation Factor 2-Alpha Kinase 3. The Luminal domain is a dimerization domain present in eukaryotic translation Initiation Factor 2-Alpha Kinase 3 (EIF2AK3), also called PKR-like Endoplasmic Reticulum Kinase (PERK). EIF2AK3 is a serine/threonine protein kinase (STK) and a type I transmembrane protein that is localized in the endoplasmic reticulum (ER). As a EIF2AK, it phosphorylates the alpha subunit of eIF-2, resulting in the downregulation of protein synthesis. eIF-2 phosphorylation is induced in response to cellular stresses including virus infection, heat shock, nutrient deficiency, and the accummulation of unfolded proteins, among others. There are four distinct kinases that phosphorylate eIF-2 and control protein synthesis: General Control Non-derepressible-2 (GCN2), protein kinase regulated by RNA (PKR), heme-regulated inhibitor kinase (HRI), and PERK. PERK contains a luminal domain bound with the chaperone BiP under unstressed conditions and a cytoplasmic catalytic kinase domain. In response to the accumulation of misfolded or unfolded proteins in the ER, PERK is activated through the release of BiP, allowing it to dimerize through its luminal domain and autophosphorylate. It functions as the central regulator of translational control during the Unfolded Protein Response (UPR) pathway. In addition to the eIF-2 alpha subunit, PERK also phosphorylates Nrf2, a leucine zipper transcription factor which regulates cellular redox status and promotes cell survival during the UPR. 301 matched cddid_all.tbl CDD cd09769 cd09769 188875 Luminal_IRE1 The Luminal domain, a dimerization domain, of the Serine/Threonine protein kinase, Inositol-requiring protein 1. The Luminal domain is a dimerization domain present in Inositol-requiring protein 1 (IRE1), a serine/threonine protein kinase (STK) and a type I transmembrane protein that is localized in the endoplasmic reticulum (ER). IRE1, also called Endoplasmic reticulum (ER)-to-nucleus signaling protein (or ERN), is a kinase receptor that also contains an endoribonuclease domain in the cytoplasmic side. It plays roles in the signaling of the unfolded protein response (UPR), which is activated when protein misfolding is detected in the ER in order to decrease the synthesis of new proteins and increase the capacity of the ER to cope with the stress. IRE1 acts as an ER stress sensor and is the oldest and most conserved component of the UPR in eukaryotes. During ER stress, IRE1 dimerizes through its luminal domain and forms oligomers, allowing the kinase domain to undergo trans-autophosphorylation. This leads to a conformational change that stimulates its endoribonuclease activity and results in the cleavage of its mRNA substrate, HAC1 in yeast and Xbp1 in metazoans, promoting a splicing event that enables translation into a transcription factor which activates the UPR. Mammals contain two IRE1 proteins, IRE1alpha (or ERN1) and IRE1beta (or ERN2). IRE1alpha is expressed in all cells and tissues while IRE1beta is found only in intestinal epithelial cells. 295 matched cddid_all.tbl CDD cd09803 cd09803 197361 UBAN polyubiquitin binding domain of NEMO and related proteins. NEMO (NF-kappaB essential modulator) is a regulatory subunit of the kinase complex IKK, which is involved in the activation of NF-kappaB via phosporylation of inhibitory IkappaBs. This mechanism requires the binding of NEMO to ubiquinated substrates. Binding is achieved via the UBAN motif (ubiquitin binding in ABIN and NEMO), which is described in this model. This region of NEMO has also been named CoZi (for coiled-coil 2 and leucine zipper). ABINs (A20-binding inhibitors of NF-kappaB) are sensors for ubiquitin that are involved in regulation of apoptosis, ABIN-1 is presumed to inhibit signalling via the NF-kappaB route. The UBAN motif is also found in optineurin, the product of a gene associated with glaucoma, which has been characterized as a negative regulator of NF-kappaB as well. 87 matched cddid_all.tbl CDD cd09804 cd09804 197362 Dcp1 mRNA decapping enzyme 1 (Dcp1). mRNA decapping enzyme 1 (Dcp1), together with Dcp2, is part of the decapping complex which catalyzes the removal of the 5' cap structure of mRNA. This decapping reaction is an essential step in mRNA degradation, by exposing the 5' end for exonucleolytic digestion. Dcp1 binds to the N-terminal helical domain of catalytic subunit Dcp2 and enhances its function by promoting Dsp2's closed conformation which is catalytically more active. 121 matched cddid_all.tbl CDD cd09805 cd09805 187665 type2_17beta_HSD-like_SDR_c human 17beta-hydroxysteroid dehydrogenase type 2 (type 2 17beta-HSD)-like, classical (c) SDRs. 17beta-hydroxysteroid dehydrogenases are a group of isozymes that catalyze activation and inactivation of estrogen and androgens. This classical-SDR subgroup includes the human proteins: type 2 17beta-HSD, type 6 17beta-HSD, type 2 11beta-HSD, dehydrogenase/reductase SDR family member 9, short-chain dehydrogenase/reductase family 9C member 7, 3-hydroxybutyrate dehydrogenase type 1, and retinol dehydrogenase 5. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 281 matched cddid_all.tbl CDD cd09806 cd09806 187666 type1_17beta-HSD-like_SDR_c human estrogenic 17beta-hydroxysteroid dehydrogenase type 1 (type 1 17beta-HSD)-like, classical (c) SDRs. 17beta-hydroxysteroid dehydrogenases are a group of isozymes that catalyze activation and inactivation of estrogen and androgens. This classical SDR subgroup includes human type 1 17beta-HSD, human retinol dehydrogenase 8, zebrafish photoreceptor associated retinol dehydrogenase type 2, and a chicken ovary-specific 17beta-hydroxysteroid dehydrogenase. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 258 matched cddid_all.tbl CDD cd09807 cd09807 212495 retinol-DH_like_SDR_c retinol dehydrogenases (retinol-DHs), classical (c) SDRs. Classical SDR-like subgroup containing retinol-DHs and related proteins. Retinol is processed by a medium chain alcohol dehydrogenase followed by retinol-DHs. Proteins in this subfamily share the glycine-rich NAD-binding motif of the classical SDRs, have a partial match to the canonical active site tetrad, but lack the typical active site Ser. This subgroup includes the human proteins: retinol dehydrogenase -12, -13 ,and -14. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 274 matched cddid_all.tbl CDD cd09808 cd09808 187668 DHRS-12_like_SDR_c-like human dehydrogenase/reductase SDR family member (DHRS)-12/FLJ13639-like, classical (c)-like SDRs. Classical SDR-like subgroup containing human DHRS-12/FLJ13639, the 36K protein of zebrafish CNS myelin, and related proteins. DHRS-12/FLJ13639 is expressed in neurons and oligodendrocytes in the human cerebral cortex. Proteins in this subgroup share the glycine-rich NAD-binding motif of the classical SDRs, have a partial match to the canonical active site tetrad, but lack the typical active site Ser. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 255 matched cddid_all.tbl CDD cd09809 cd09809 187669 human_WWOX_like_SDR_c-like human WWOX (WW domain-containing oxidoreductase)-like, classical (c)-like SDRs. Classical-like SDR domain of human WWOX and related proteins. Proteins in this subfamily share the glycine-rich NAD-binding motif of the classical SDRs, have a partial match to the canonical active site tetrad, but lack the typical active site Ser. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 284 matched cddid_all.tbl CDD cd09810 cd09810 187670 LPOR_like_SDR_c_like light-dependent protochlorophyllide reductase (LPOR)-like, classical (c)-like SDRs. Classical SDR-like subgroup containing LPOR and related proteins. Protochlorophyllide (Pchlide) reductases act in chlorophyll biosynthesis. There are distinct enzymes that catalyze Pchlide reduction in light or dark conditions. Light-dependent reduction is via an NADP-dependent SDR, LPOR. Proteins in this subfamily share the glycine-rich NAD-binding motif of the classical SDRs, have a partial match to the canonical active site tetrad, but lack the typical active site Ser. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase (15-PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, 15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 311 matched cddid_all.tbl CDD cd09811 cd09811 187671 3b-HSD_HSDB1_like_SDR_e human 3beta-HSD (hydroxysteroid dehydrogenase) and HSD3B1(delta 5-delta 4-isomerase)-like, extended (e) SDRs. This extended-SDR subgroup includes human 3 beta-HSD/HSD3B1 and C(27) 3beta-HSD/ [3beta-hydroxy-delta(5)-C(27)-steroid oxidoreductase; HSD3B7], and related proteins. These proteins have the characteristic active site tetrad and NAD(P)-binding motif of extended SDRs. 3 beta-HSD catalyzes the oxidative conversion of delta 5-3 beta-hydroxysteroids to the delta 4-3-keto configuration; this activity is essential for the biosynthesis of all classes of hormonal steroids. C(27) 3beta-HSD is a membrane-bound enzyme of the endoplasmic reticulum, it catalyzes the isomerization and oxidation of 7alpha-hydroxylated sterol intermediates, an early step in bile acid biosynthesis. Mutations in the human gene encoding C(27) 3beta-HSD underlie a rare autosomal recessive form of neonatal cholestasis. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid sythase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 354 matched cddid_all.tbl CDD cd09812 cd09812 187672 3b-HSD_like_1_SDR_e 3beta-hydroxysteroid dehydrogenase (3b-HSD)-like, subgroup1, extended (e) SDRs. An uncharacterized subgroup of the 3b-HSD-like extended-SDR family. Proteins in this subgroup have the characteristic active site tetrad and NAD(P)-binding motif of extended-SDRs. 3 beta-HSD catalyzes the oxidative conversion of delta 5-3 beta-hydroxysteroids to the delta 4-3-keto configuration; this activity is essential for the biosynthesis of all classes of hormonal steroids. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid sythase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 339 matched cddid_all.tbl CDD cd09813 cd09813 187673 3b-HSD-NSDHL-like_SDR_e human NSDHL (NAD(P)H steroid dehydrogenase-like protein)-like, extended (e) SDRs. This subgroup includes human NSDHL and related proteins. These proteins have the characteristic active site tetrad of extended SDRs, and also have a close match to their NAD(P)-binding motif. Human NSDHL is a 3beta-hydroxysteroid dehydrogenase (3 beta-HSD) which functions in the cholesterol biosynthetic pathway. 3 beta-HSD catalyzes the oxidative conversion of delta 5-3 beta-hydroxysteroids to the delta 4-3-keto configuration; this activity is essential for the biosynthesis of all classes of hormonal steroids. Mutations in the gene encoding NSDHL cause CHILD syndrome (congenital hemidysplasia with ichthyosiform nevus and limb defects), an X-linked dominant, male-lethal trait. This subgroup also includes an unusual bifunctional [3beta-hydroxysteroid dehydrogenase (3b-HSD)/C-4 decarboxylase from Arabidopsis thaliana, and Saccharomyces cerevisiae ERG26, a 3b-HSD/C-4 decarboxylase, involved in the synthesis of ergosterol, the major sterol of yeast. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid sythase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. 335 matched cddid_all.tbl CDD cd09815 cd09815 381167 TP_methylase S-AdoMet-dependent tetrapyrrole methylases. This superfamily uses S-AdoMet (S-adenosyl-L-methionine or SAM) in the methylation of diverse substrates. Most members catalyze various methylation steps in cobalamin (vitamin B12) biosynthesis. There are two distinct cobalamin biosynthetic pathways in bacteria. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt insertion is the first committed step towards cobalamin synthesis. The enzymes involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Most of the enzymes are shared by both pathways and a few enzymes are pathway-specific. Diphthine synthase and ribosomal RNA small subunit methyltransferase I (RsmI) are two superfamily members that are not involved in cobalamin biosynthesis. Diphthine synthase participates in the posttranslational modification of a specific histidine residue in elongation factor 2 (EF-2) of eukaryotes and archaea to diphthamide. RsmI catalyzes the 2-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA. Other superfamily members not involved in cobalamin biosynthesis include the N-terminal tetrapyrrole methylase domain of Bacillus subtilis YabN whose specific function is unknown, and Omphalotus olearius omphalotin methyltransferase which catalyzes the automethylation of its own C-terminus; this C terminus is subsequently released and macrocyclized to give Omphalotin A, a potent nematicide. 219 matched cddid_all.tbl CDD cd09816 cd09816 188648 prostaglandin_endoperoxide_synthase Animal prostaglandin endoperoxide synthase and related bacterial proteins. Animal prostaglandin endoperoxide synthases, including prostaglandin H2 synthase and a set of similar bacterial proteins which may function as cyclooxygenases. Prostaglandin H2 synthase catalyzes the synthesis of prostaglandin H2 from arachidonic acid. In two reaction steps, arachidonic acid is converted to Prostaglandin G2, a peroxide (cyclooxygenase activity) and subsequently converted to the end product via the enzyme's peroxidase activity. Prostaglandin H2 synthase is the target of aspirin and other non-steroid anti-inflammatory drugs such as ibuprofen, which block the substrate's access to the active site and may acetylate a conserved serine residue. In humans and other mammals, prostaglandin H2 synthase (PGHS), also called cyclooxygenase (COX) is present as at least two isozymes, PGHS-1 (or COX-1) and PGHS-2 (or COX-2), respectively. PGHS-1 is expressed constitutively in most mammalian cells, while the expression of PGHS-2 is induced via inflammation response in endothelial cells, activated macrophages, and others. COX-3 is a splice variant of COX-1. 490 matched cddid_all.tbl CDD cd09817 cd09817 188649 linoleate_diol_synthase_like Linoleate (8R)-dioxygenase and related enzymes. These fungal enzymes, related to animal heme peroxidases, catalyze the oxygenation of linoleate and similar targets. Linoleate (8R)-dioxygenase, also called linoleate:oxygen 7S,8S-oxidoreductase, generates (9Z,12Z)-(7S,8S)-dihydroxyoctadeca-9,12-dienoate as a product. Other members are 5,8-linoleate dioxygenase (LDS, ppoA) and linoleate 10R-dioxygenase (ppoC), involved in the biosynthesis of oxylipins. 550 matched cddid_all.tbl CDD cd09818 cd09818 188650 PIOX_like Animal heme oxidases similar to plant pathogen-inducible oxygenases. This is a diverse family of oxygenases related to the animal heme peroxidases, with members from plants, animals, and bacteria. The plant pathogen-inducible oxygenases (PIOX) oxygenate fatty acids into 2R-hydroperoxides. They may be involved in the hypersensitive reaction, rapid and localized cell death induced by infection with pathogens, and the rapidly induced expression of PIOX may be caused by the oxidative burst that occurs in the process of cell death. 484 matched cddid_all.tbl CDD cd09819 cd09819 188651 An_peroxidase_bacterial_1 Uncharacterized bacterial family of heme peroxidases. Animal heme peroxidases are diverse family of enzymes which are not restricted to metazoans; members are also found in fungi, and plants, and in bacteria - like this family of uncharacterized proteins. 465 matched cddid_all.tbl CDD cd09820 cd09820 188652 dual_peroxidase_like Dual oxidase and related animal heme peroxidases. Animal heme peroxidases of the dual-oxidase like subfamily play vital roles in the innate mucosal immunity of gut epithelia. They provide reactive oxygen species which help control infection. 558 matched cddid_all.tbl CDD cd09821 cd09821 188653 An_peroxidase_bacterial_2 Uncharacterized bacterial family of heme peroxidases. Animal heme peroxidases are diverse family of enzymes which are not restricted to metazoans; members are also found in fungi, and plants, and in bacteria - like this family of uncharacterized proteins. 570 matched cddid_all.tbl CDD cd09822 cd09822 188654 peroxinectin_like_bacterial Uncharacterized family of heme peroxidases, mostly bacterial. Animal heme peroxidases are diverse family of enzymes which are not restricted to animals. Members are also found in metazoans, fungi, and plants, and also in bacteria - like most members of this family of uncharacterized proteins. 420 matched cddid_all.tbl CDD cd09823 cd09823 188655 peroxinectin_like peroxinectin_like animal heme peroxidases. Peroxinectin is an arthropod protein that plays a role in invertebrate immunity mechanisms. Specifically, peroxinectins are secreted as cell-adhesive and opsonic peroxidases. The immunity mechanism appears to involve an interaction between peroxinectin and a transmembrane receptor of the integrin family. Human myeloperoxidase, which is included in this wider family, has also been reported to interact with integrins. 378 matched cddid_all.tbl CDD cd09824 cd09824 188656 myeloperoxidase_like Myeloperoxidases, eosinophil peroxidases, and lactoperoxidases. This well conserved family of animal heme peroxidases contains members with somewhat diverse functions. Myeloperoxidases are lysosomal proteins found in azurophilic granules of neutrophils and the lysosomes of monocytes. They are involved in the formation of microbicidal agents upon activation of activated neutrophils (neutrophils undergoing respiratory bursts as a result of phagocytosis), by catalyzing the conversion of hydrogen peroxide to hypochlorous acid. As a heme protein, myeloperoxidase is responsible for the greenish tint of pus, which is rich in neutrophils. Eosinophil peroxidases are haloperoxidases as well, preferring bromide over chloride. Expressed by eosinophil granulocytes, they are involved in attacking multicellular parasites and play roles in various inflammatory diseases such as asthma. The haloperoxidase lactoperoxidase is secreted from mucosal glands and provides antibacterial activity by oxidizing a variety of substrates such as bromide or chloride in the presence of hydrogen peroxide. 411 matched cddid_all.tbl CDD cd09825 cd09825 188657 thyroid_peroxidase Thyroid peroxidase (TPO). TPO is a member of the animal heme peroxidase family, which is expressed in the thyroid and involved in the processing of iodine and iodine compounds. Specifically, TPO oxidizes iodide via hydrogen peroxide to form active iodine, which is then, for example, incorporated into the tyrosine residues of thyroglobulin to yield mono- and di-iodotyrosines. 565 matched cddid_all.tbl CDD cd09826 cd09826 188658 peroxidasin_like Animal heme peroxidase domain of peroxidasin and related proteins. Peroxidasin is a secreted heme peroxidase which is involved in hydrogen peroxide metabolism and peroxidative reactions in the cardiovascular system. The domain co-occurs with extracellular matrix domains and may play a role in the formation of the extracellular matrix. 440 matched cddid_all.tbl CDD cd09827 cd09827 193602 PET_Prickle The PET domain of Prickle. The PET domain of Prickle: Prickle contains an N-terminal PET domain and three C-terminal LIM domains. Prickle has been implicated in regulation of cell movement in the planar cell polarity (PCP) pathway which requires the conserved Frizzled/Dishevelled (Dsh); Prickle interacts with Dishevelled, thereby modulating the activity of Frizzled/Dishevelled and the PCP signaling. Two forms of Prickle have been identified, namely Prickle 1 and Prickle 2. These are differentially expressed; Prickle 1 is found in fetal heart and hematological malignancies, while Prickle 2 is expressed in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. The PET domain is a protein-protein interaction domain, usually found in conjunction with the LIM domain, which is also involved in protein-protein interactions. The PET containing proteins serve as adaptors or scaffolds to support the assembly of multimeric protein complexes. 97 matched cddid_all.tbl CDD cd09828 cd09828 193603 PET_OEBT The PET domain of overexpressed breast tumor protein (OEBT). The PET domain of overexpressed breast tumor protein (OEBT): OEBT contains an N-terminal PET domain and two C-terminal LIM domains, and is predicted to be localized in the nucleus. The expression pattern of OEBT in malignant tissues indicates a possible role of OEBT in cancer differentiation. The PET domain is a protein-protein interaction domain and is usually found in conjunction with LIM domain, which is also involved in protein-protein interactions. PET containing proteins serve as adaptors or scaffolds to support the assembly of multimeric protein complexes. 116 matched cddid_all.tbl CDD cd09829 cd09829 193604 PET_testin The PET domain of Testin. The PET domain of Testin: Testin contains a PET domain at the N-terminus and three C-terminal LIM domains. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and is involved in cell motility and adhesion events. Knockout mice experiments reveal a tumor repressor function of Testin. The PET domain is a protein-protein interaction domain and is usually found in conjunction with LIM domain, which is also involved in protein-protein interactions. The PET containing proteins serve as adaptors or scaffolds to support the assembly of multimeric protein complexes. 88 matched cddid_all.tbl CDD cd09830 cd09830 193605 PET_LIMPETin_LIM-9 The PET domain of protein LIMPETin and LIM-9. The PET domain of protein LIMPETin and LIM-9: Members of this family contain an N-terminal PETdomain and five to six LIM domains at the C-terminus. Four of the six LIM domains are highly homologous to the four-and-half LIM (FHL) domain family while the other two show sequence similarity to LIM domains of the Testin family. Thus, proteins of this family may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Thus, proteins of this family may be the recombinant product of genes coding Testin and FHL proteins. SmLIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult males. Its differential expression indicates that it is a transcription regulator. In C. elegans, LIM-9 binds to UNC-97 and UNC-96, components of sarcomeric muscle M-lines. LIM-9 also forms a complex with SCPL-1 and UNC-89, whose function is to organize sarcomeric A-bands, especially the M-line of muscle. Thus, it might play a role in regulating the assembly and maintenance of muscle A-band. The PET domain is a protein-protein interaction domain and is usually found in conjunction with LIM domain, which is also involved in protein-protein interactions. The PET containing proteins serve as adaptors or scaffolds to support the assembly of multimeric protein complexes. 83 matched cddid_all.tbl CDD cd09831 cd09831 341402 CBS_pair_ABC_Gly_Pro_assoc Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains found associated with the glycine betaine/L-proline ABC transporter. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains found in association with the ABC transporter OpuCA. OpuCA is the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment but the function of the CBS domains in OpuCA remains unknown. In the related ABC transporter, OpuA, the tandem CBS domains have been shown to function as sensors for ionic strength, whereby they control the transport activity through an electronic switching mechanism. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. They are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 116 matched cddid_all.tbl CDD cd09833 cd09833 341403 CBS_pair_GGDEF_PAS_repeat1 Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains found in diguanylate cyclase/phosphodiesterase proteins with PAS sensors, repeat 1. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains found in diguanylate cyclase/phosphodiesterase proteins with PAS sensors. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and is thought to be involved in regulating cell surface adhesiveness in bacteria. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 116 matched cddid_all.tbl CDD cd09834 cd09834 341404 CBS_pair_bac Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in bacteria. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 118 matched cddid_all.tbl CDD cd09836 cd09836 341405 CBS_pair_arch Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 116 matched cddid_all.tbl CDD cd09837 cd09837 341406 CBS_pair_chlorobiales Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in chlorobiales. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 111 matched cddid_all.tbl CDD cd09839 cd09839 341074 M1_like_TAF2 TATA binding protein (TBP) associated factor 2. This family includes TATA binding protein (TBP) associated factor 2 (TAF2, TBP-associated factor TAFII150, transcription initiation factor TFIID subunit 2, RNA polymerase II TBP-associated factor subunit B), and has homology to the M1 gluzincin family. TAF2 is part of the TFIID multidomain subunit complex essential for transcription of most protein-encoded genes by RNA polymerase II. TAF2 is known to interact with the initiator element (Inr) found at the transcription start site of many genes, thus possibly playing a key role in promoter binding as well as start-site selection. Image analysis has shown TAF2 to form a complex with TAF1 and TBP, inferring its role in promoter recognition. Peptidases in the M1 family bind a single catalytic zinc ion which is tetrahedrally co-ordinated by three amino acid ligands and a water molecule that forms the nucleophile on activation during catalysis. TAF2, however, lacks these active site residues. 531 matched cddid_all.tbl CDD cd09840 cd09840 188871 LIM2_CRP2 The second LIM domain of Cysteine Rich Protein 2 (CRP2). The second LIM domain of Cysteine Rich Protein 2 (CRP2): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 54 matched cddid_all.tbl CDD cd09841 cd09841 188872 LIM1_Prickle_3 The first LIM domain of Prickle 3. The first LIM domain of Prickle 3/LIM domain only 6 (LM06): Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. 59 matched cddid_all.tbl CDD cd09842 cd09842 197300 PLDc_vPLD1_1 Catalytic domain, repeat 1, of vertebrate phospholipase D1. Catalytic domain, repeat 1, of vertebrate phospholipase D1 (PLD1). PLDs play a pivotal role in transmembrane signaling and cellular regulation. They hydrolyze the terminal phosphodiester bond of phospholipids resulting in the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. PLDs also catalyze the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. Vertebrate PLD1 is a membrane associated phosphatidylinositol 4,5-bisphosphate (PIP2)-dependent enzyme that selectively hydrolyzes phosphatidylcholine (PC). Protein cofactors and calcium might be required for its activation. Most vertebrate PLDs have adjacent Phox (PX) and the Pleckstrin homology (PH) domains at their N-terminus, which have been shown to mediate membrane targeting of the protein and are closely linked to polyphosphoinositide signaling. Like other members of the PLD superfamily, the monomer of vertebrate PLDs consists of two catalytic domains, each of which contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from two domains form a single active site. These PLDs utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. 151 matched cddid_all.tbl CDD cd09843 cd09843 197301 PLDc_vPLD2_1 Catalytic domain, repeat 1, of vertebrate phospholipase D2. Catalytic domain, repeat 1, of vertebrate phospholipase D2 (PLD2). PLDs play a pivotal role in transmembrane signaling and cellular regulation. They hydrolyze the terminal phosphodiester bond of phospholipids with the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. They also catalyze a transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. Vertebrate PLD2 is a membrane associated phosphatidylinositol 4,5-bisphosphate (PIP2)-dependent enzyme that selectively hydrolyzes phosphatidylcholine (PC). Protein cofactors and calcium might be required for its activation. Most vertebrate PLDs have adjacent Phox (PX) and the Pleckstrin homology (PH) domains at their N-terminus, which have been shown to mediate membrane targeting of the protein and are closely linked to polyphosphoinositide signaling. Like other members of the PLD superfamily, the monomer of vertebrate PLDs consists of two catalytic domains, each of which contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from two domains form a single active site. These PLDs utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. 145 matched cddid_all.tbl CDD cd09844 cd09844 197302 PLDc_vPLD1_2 Catalytic domain, repeat 2, of vertebrate phospholipase D1. Catalytic domain, repeat 2, of vertebrate phospholipase D1 (PLD1). PLDs play a pivotal role in transmembrane signaling and cellular regulation. They hydrolyze the terminal phosphodiester bond of phospholipids resulting in the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. PLDs also catalyze the transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. Vertebrate PLD1 is a membrane associated phosphatidylinositol 4,5-bisphosphate (PIP2)-dependent enzyme that selectively hydrolyzes phosphatidylcholine (PC). Protein cofactors and calcium might be required for its activation. Most vertebrate PLDs have adjacent Phox (PX) and the Pleckstrin homology (PH) domains at their N-terminus, which have been shown to mediate membrane targeting of the protein and are closely linked to polyphosphoinositide signaling. Like other members of the PLD superfamily, the monomer of vertebrate PLDs consists of two catalytic domains, each of which contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from two domains form a single active site. These PLDs utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. 182 matched cddid_all.tbl CDD cd09845 cd09845 197303 PLDc_vPLD2_2 Catalytic domain, repeat 2, of vertebrate phospholipase D2. Catalytic domain, repeat 2, of vertebrate phospholipase D2 (PLD2). PLDs play a pivotal role in transmembrane signaling and cellular regulation. They hydrolyze the terminal phosphodiester bond of phospholipids with the formation of phosphatidic acid and alcohols. Phosphatidic acid is an essential compound involved in signal transduction. They also catalyze a transphosphatidylation of phospholipids to acceptor alcohols, by which various phospholipids can be synthesized. Vertebrate PLD2 is a membrane associated phosphatidylinositol 4,5-bisphosphate (PIP2)-dependent enzyme that selectively hydrolyzes phosphatidylcholine (PC). Protein cofactors and calcium might be required for its activation. Most vertebrate PLDs have adjacent Phox (PX) and the Pleckstrin homology (PH) domains at their N-terminus, which have been shown to mediate membrane targeting of the protein and are closely linked to polyphosphoinositide signaling. Like other members of the PLD superfamily, the monomer of vertebrate PLDs consists of two catalytic domains, each of which contains one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue). Two HKD motifs from two domains form a single active site. These PLDs utilize a common two-step ping-pong catalytic mechanism involving an enzyme-substrate intermediate to cleave phosphodiester bonds. The two histidine residues from the two HKD motifs play key roles in the catalysis. Upon substrate binding, a histidine residue from one HKD motif could function as the nucleophile, attacking the phosphodiester bond to create a covalent phosphohistidine intermediate, while the other histidine residue from the second HKD motif could serve as a general acid, stabilizing the leaving group. 182 matched cddid_all.tbl CDD cd09846 cd09846 197363 DUF1312 N-Utilization Substance G (NusG) N terminal (NGN) insert and Lin0431 are part of DUF1312. Domains of Unknown Function 1312 (DUF1312) are represented in at least 71 bacterial species with no functional annotation. Included in this family are N-Utilization Substance G (NusG) N terminal (NGN) insert and Lin0431, having similar structure and surface features that appear to be conserved across these domain families, suggesting similar function. NusG contains NGN at the N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at the C-terminus in bacteria and archaea, and this insert (often known as Domain II) is found in several bacteria. Lin0431 is similar to NGN-insert but does ot contain the disulphite bridge 81 matched cddid_all.tbl CDD cd09848 cd09848 349946 M28_TfR M28 Zn-peptidase Transferrin Receptor family. Peptidase M28 family; Transferrin Receptor (TfR) subfamily. TfRs are homodimeric type II transmembrane proteins containing three distinct domains: protease-like, apical or protease-associated (PA), and helical domains. The protease-like domain is a large extracellular portion (ectodomain). In TfR, it contains a binding site for the transferrin molecule and has 28% identity to membrane glutamate carboxypeptidase II (mGCP-II or PSMA). The PA domain is inserted between the first and second strands of the central beta sheet in the protease-like domain. TfR1 is widely expressed, and is a key player in the uptake of iron-loaded transferrin (Tf) into cells. The TfR1 homodimer binds two molecules of Tf and the complex is then internalized. TfR1 may also participate in cell growth and proliferation. TfR2 binds Tf but with a significantly lower affinity than TfR1. It is expressed chiefly in hepatocytes, hematopoietic cells, and duodenal crypt cells; its expression overlaps with that of hereditary hemochromatosis protein (HFE). TfR2 is involved in iron homeostasis; in humans, mutations in TfR2 are associated with a form of hemochromatosis (HFE3). While related in sequence to peptidase M28 glutamate carboxypeptidase II (also called prostate-specific membrane antigen or PSMA), TfR lacks the metal ion coordination centers and protease activity of that group. 285 matched cddid_all.tbl CDD cd09849 cd09849 349947 M20_Acy1L2-like M20 Peptidase aminoacylase 1-like protein 2, amidohydrolase family. Peptidase M20 family, aminoacylase 1-like protein 2 (ACY1L2; amidohydrolase)-like subfamily. This group contains many uncharacterized proteins predicted as amidohydrolases, including gene products of abgA and abgB that catalyze the cleavage of p-aminobenzoyl-glutamate, a folate catabolite in Escherichia coli , to p-aminobenzoate and glutamate. p-Aminobenzoyl-glutamate utilization is catalyzed by the abg region gene product, AbgT. Aminoacylase 1 (ACY1) proteins are a class of zinc binding homodimeric enzymes involved in hydrolysis of N-acetylated proteins. N-terminal acetylation of proteins is a widespread and highly conserved process that is involved in the protection and stability of proteins. Several types of aminoacylases can be distinguished on the basis of substrate specificity. ACY1 breaks down cytosolic aliphatic N-acyl-alpha-amino acids (except L-aspartate), especially N-acetyl-methionine and acetyl-glutamate into L-amino acids and an acyl group. However, ACY1 can also catalyze the reverse reaction, the synthesis of acetylated amino acids. ACY1 may also play a role in xenobiotic bioactivation as well as the inter-organ processing of amino acid-conjugated xenobiotic derivatives (S-substituted-N-acetyl-L-cysteine). 389 matched cddid_all.tbl CDD cd09850 cd09850 197367 Ebola-like_HR1-HR2 heptad repeat 1-heptad repeat 2 region of the transmembrane subunit of Filoviridae viruses, Ebola virus and Marburg virus, and related domains. This domain subfamily spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including Ebola virus gp2, Marburg virus gp, and the envelope proteins of various ERVs, including human HERV-R_c7q21.2 (ERV-3). This domain includes an N-terminal heptad repeat, a CKS17-like immunosuppressive region, a CX6C motif that forms an intrasubunit disulfide bond, and a C-terminal heptad repeat. N-terminal to HR1-HR2 region is a fusion peptide (FP), and C-terminal, is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1s helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some ERVs play specific roles in the host. However, it is unclear whether ERV-3 has a critical biological role: it is expressed in the placenta, but is not fusogenic, has an immunosuppressive domain, but lacks a fusion peptide. Filoviridae, the family of viruses including Ebola and Marburg, may have acquired this domain via horizontal transfer from retroviruses. 77 matched cddid_all.tbl CDD cd09851 cd09851 197368 HTLV-1-like_HR1-HR2 heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of human T-cell leukemia virus type 1 (HTLV-1), and related domains. This domain subfamily spans both heptad repeats of the glycoprotein (gp)/transmembrane(TM) subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including HTLV-1, HTLV -2, primate Mason-Pfizer monkey virus, Moloney murine leukemia virus, simian T-cell lymphotropic virus, feline leukemia virus (FeLV), bovine leukemia virus, and various human endogenous retroviruses (HERVs), including, HERV-H1_c2q24.3, HERV-H2_3q26, HERV-F(c)1_cXq21.33, HERV-T_19q13.11, Syncytin-1 (HERV-W_c7q21.2/ ERVWE1), Syncytin-2 (HERV-FRD_6p24.1), and related domains. This domain includes an N-terminal heptad repeat, a CKS17-like immunosuppressive region, a CX6C motif that forms an intrasubunit disulfide bond, and a C-terminal heptad repeat. N-terminal to HR1-HR2 region is a fusion peptide (FP), and C-terminal, is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1s helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some modern ERVs, those that integrated into the host genome post-speciation, have a currently active exogenous counterpart, such as FeLV. Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Syncytin-1 and Syncytin-2 are expressed in the placenta, and are fusogenic, although they have a different cell specificity for fusion. Syncytin-2, but not Syncytin-1, is immunosuppressive; its immunosuppressive domain may protect the fetus from the mother's immune system. Syncytin-1 may participate in the formation of the placental trophoblast; it is also implicated in cell fusions between cancer and host cells and between cancer cell, and in human osteclast fusion. This subfamily also contains a mouse envelope protein encoded by the Fv-4 env gene, that blocks infection by exogenous MuLV. 78 matched cddid_all.tbl CDD cd09852 cd09852 350203 PIN_SF PIN (PilT N terminus) domain: Superfamily. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily, and were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. The PIN domain superfamily includes: the FEN-like PIN domain family such as the PIN domains of Flap endonuclease-1 (FEN1), exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease, 5'-3' exonucleases of DNA polymerase I and bacteriophage T4- and T5-5' nucleases; the VapC-like PIN domain family which includes toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1; the LabA-like PIN domain family which includes the PIN domains of Synechococcus elongatus LabA (low-amplitude and bright); the PRORP-Zc3h12a-like PIN domain family which includes the PIN domains of RNase P (PRORP), ribonuclease Zc3h12a; and Bacillus subtilis YacP/Rae1-like PIN domains. It also includes the Mut7-C PIN domain family, which is not represented here as it is a shortened version of the PIN fold and lacks a core strand and helix (H3 and S3). The Mut7-C PIN domain family includes the C-terminus of Caenorhabditis elegans exonuclease Mut-7. 114 matched cddid_all.tbl CDD cd09853 cd09853 350204 PIN_FEN-like FEN-like PIN domains of structure-specific 5' nucleases (or Flap endonuclease-1-like) involved in DNA replication, repair, and recombination. Structure-specific 5' nucleases are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner. The family includes the PIN (PilT N terminus) domains of Flap endonuclease-1 (FEN1), exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease. Also included are the PIN domains of the 5'-3' exonucleases of DNA polymerase I and single domain protein homologs, as well as, the bacteriophage T4- and T5-5' nucleases, and other homologs. Canonical members of this FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 174 matched cddid_all.tbl CDD cd09854 cd09854 350205 PIN_VapC-like VapC-like PIN domains of VapC and Smg6 ribonucleases, ribosome assembly factor NOB1, rRNA-processing protein Fcf1, Archaeoglobus fulgidus AF0591 protein, and homologs. PIN (PilT N terminus) domains of such ribonucleases as the toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1, are included in VapC-like this family. Also included are the PIN domains of the Pyrobaculum aerophilum Pea0151 and Archaeoglobus fulgidus AF0591 proteins and other similar archaeal homologs. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 129 matched cddid_all.tbl CDD cd09856 cd09856 350206 PIN_FEN1-like FEN-like PIN domains of Flap endonuclease-1 (FEN1)-like, structure-specific, divalent-metal-ion dependent, 5' nucleases. PIN (PilT N terminus) domain of Flap endonuclease-1 (FEN1)-like nucleases: FEN1, Gap endonuclease 1 (GEN1) and Xeroderma pigmentosum complementation group G (XPG) nuclease. Nucleases in this subfamily are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 235 matched cddid_all.tbl CDD cd09857 cd09857 350207 PIN_EXO1 FEN-like PIN domains of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs. exonuclease-1 (EXO1) is involved in multiple, eukaryotic DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity), DNA repair processes (DNA mismatch repair (MMR) and post-replication repair (PRR)), recombination, and telomere integrity. EXO1 functions in the MMS2 error-free branch of the PRR pathway in the maintenance and repair of stalled replication forks. Studies also suggest that EXO1 plays both structural and catalytic roles during MMR-mediated mutation avoidance. These nucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. EXO1 nucleases also have C-terminal Mlh1- and Msh2-binding domains which allow interaction with MMR and PRR proteins, respectively. 202 matched cddid_all.tbl CDD cd09858 cd09858 350208 PIN_MKT1 FEN-like PIN domains of Mkt1, a global regulator of mRNAs encoding mitochondrial proteins and eukaryotic homologs. The Mkt1 gene product interacts with the Poly(A)-binding protein associated factor, Pbp1, and is present at the 3' end of RNA transcripts during translation. The Mkt1-Pbp1 complex is involved in the post-transcriptional regulation of HO endonuclease expression. Mkt1 and eukaryotic homologs are atypical members of the structure-specific, 5' nuclease family (FEN-like). Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. Although Mkt1 appears to possess both a PIN and H3TH domain, the Mkt1 PIN domain lacks several of the active site residues necessary to bind essential divalent metal ion cofactors (Mg2+/Mn2+) required for nuclease activity in this family. Also, Mkt1 lacks the glycine-rich loop in the H3TH domain which is proposed to facilitate duplex DNA binding. 206 matched cddid_all.tbl CDD cd09859 cd09859 350209 PIN_53EXO FEN-like PIN domains of PIN domain of the 5'-3' exonuclease of Thermus aquaticus DNA polymerase I (Taq) and homologs. The 5'-3' exonuclease (53EXO) PIN (PilT N terminus) domain of multi-domain DNA polymerase I and single domain protein homologs are included in this family. Taq contains a polymerase domain for synthesizing a new DNA strand and a 53EXO PIN domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO PIN domain recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The 53EXO PIN domain cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 160 matched cddid_all.tbl CDD cd09860 cd09860 350210 PIN_T4-like FEN-like PIN domains of bacteriophage T3, T4 RNase H, T5-5'nuclease, and homologs. PIN (PilT N terminus) domain of bacteriophage T5-5'nuclease (5'-3' exonuclease or T5FEN), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar 5' nucleases are included in this family. T5-5'nuclease is a 5'-3'exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3'exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. Bacteriophage T3 is believed to function in the removal of DNA-linked RNA primers and is essential for phage DNA replication and also necessary for host DNA degradation and phage genetic recombination. These nucleases are members of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. In the T5-5'nuclease, structure-specific endonuclease activity requires binding of a single metal ion in the high-affinity, metal binding site 1, whereas exonuclease activity requires both, the high-affinity, metal binding site 1 and the low-affinity, metal binding site 2 to be occupied by a divalent cofactor. The T5-5'nuclease is reported to be able to bind several metal ions including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors. 158 matched cddid_all.tbl CDD cd09862 cd09862 350211 PIN_Rrp44-like VapC-like PIN domain of yeast exosome subunit Rrp44 endoribonuclease and other eukaryotic homologs. PIN (PilT N terminus) domain of the Saccharomyces cerevisiae exosome subunit Rrp44 (Ribosomal RNA-processing protein 44 or Protein Dis3 homolog) and other similar eukaryotic homologs are included in this family. The eukaryotic exosome is a conserved macromolecular complex responsible for many RNA-processing and RNA-degradation reactions. It is composed of nine core subunits that directly binds Rrp44. The Rrp44 nuclease is the catalytic subunit of the exosome and has endonuclease activity in the PIN domain and an exoribonuclease activity in its RNase II-like region. Rrp44 binding to the exosome is mediated mainly by the PIN domain and by subunits Rrp41-Rrp45, and binding predictions indicate that the PIN domain active site is positioned on the outer surface of the exosome. This subgroup belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. PIN domains within this subgroup contain four of these residues which cluster at the C-terminal end of the beta-sheet and form a negatively charged pocket near the center of the molecule. Recombinant Rrp44 was shown to possess manganese-dependent endonuclease activity in vitro that was abolished by point mutations in these putative metal binding residues of its PIN domain. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 178 matched cddid_all.tbl CDD cd09864 cd09864 350212 PIN_Fcf1-like VapC-like PIN domain of rRNA-processing protein, Fcf1 (Utp24, YDR339C), and other eukaryotic homologs. Fcf1/Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) is an essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly. Component of the small subunit (SSU) processome, Fcf1 is an essential nucleolar protein that is required for processing of the 18S pre-rRNA at sites A0-A2. The Fcf1 protein was reported to interact with Pmc1p (vacuolar Ca2+ ATPase) and Cor1p (core subunit of the ubiquinol-cytochrome c reductase complex). The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. Most members of the Fcf1 PIN domain subfamily have four of these conserved residues and the Fcf1-Utp23 homolog PIN domain subfamily has three. Point mutation studies of the conserved acidic residues in the putative active site of Saccharomyces cerevisiae Fcf1 determined they were essential for pre-rRNA processing at sites A1 and A2, whereas the presence of the Fcf1 protein itself is also required for cleavage at site A0. 131 matched cddid_all.tbl CDD cd09865 cd09865 350213 PIN_ScUtp23p-like VapC-like PIN domain of rRNA-processing protein, Utp23 (YOR004W), and other fungal homologs. Saccharomyces cerevisiae Utp23 (U three-associated protein 23), component of the small subunit (SSU) processome, is an essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily, including S. cerevisiae Utp23, lack several of these key catalytic residues. Mutation of the remaining conserved putative active site residues seen in Utp23 did not interfere with rRNA maturation and cell viability. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 149 matched cddid_all.tbl CDD cd09866 cd09866 350214 PIN_Fcf1-Utp23-H VapC-like PIN domain of rRNA-processing protein Fcf1- and Utp23-like homologs found in eukaryotes except fungi; similar to human rRNA-processing protein UTP23. PIN domain homologs of Fcf1/Utp24 (FAF1-copurifying factor 1/U three-associated protein 24) and Utp23, essential proteins involved in pre-rRNA processing and 40S ribosomal subunit assembly, are included in this subfamily. It includes human UTP24 which hUTP24 plays a crucial role in human rRNA processing and is essential for accurate endonucleolytic cleavage at the 5'-end of 18S rRNA. Fcf1 is a component of the small subunit (SSU) processome and an essential nucleolar protein required for processing of the 18S pre-rRNA at sites A0-A2. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The Fcf1-Utp23 homolog PIN domain subfamily has three of these conserved acidic residues rather than the four seen in the Fcf1 PIN domain subfamily. 130 matched cddid_all.tbl CDD cd09867 cd09867 350215 PIN_FEN1 FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs. Flap endonuclease-1 (FEN1) is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes (long-patch base excision repair) in eukaryotes and archaea. Interaction between FEN1 and PCNA (Proliferating cell nuclear antigen) is an essential prerequisite to FEN1's DNA replication functionality and stimulates FEN1 nuclease activity by 10-50 fold. FEN1 belongs to the FEN1-EXO1-like subfamily of structure-specific, 5' nucleases (FEN-like family). Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. FEN1 has a C-terminal extension containing residues forming the consensus PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA. 251 matched cddid_all.tbl CDD cd09868 cd09868 350216 PIN_XPG_RAD2 FEN-like PIN domains of Xeroderma pigmentosum complementation group G (XPG) nuclease, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs. The Xeroderma pigmentosum complementation group G (XPG) nuclease plays a central role in nucleotide excision repair (NER) in cleaving DNA bubble structures or loops. XPG is a member of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 209 matched cddid_all.tbl CDD cd09869 cd09869 350217 PIN_GEN1 FEN-like PIN domains of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs. Gap Endonuclease 1 (GEN1) is a Holliday junction resolvase reported to symmetrically cleave Holliday junctions and allow religation without additional processing. GEN1 is a member of the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 227 matched cddid_all.tbl CDD cd09870 cd09870 350218 PIN_YEN1 FEN-like PIN domains of Saccharomyces cerevisiae endonuclease 1 (YEN1), Chaetomium thermophilum junction-resolving enzyme GEN1, and fungal homologs. Fungal Endonuclease 1 (YEN1 and GEN1, GEN1 is known as YEN1 in Saccharomyces cerevisiae) is a four-way (Holliday) junction resolvase. Members of this subgroup belong to the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 229 matched cddid_all.tbl CDD cd09871 cd09871 350219 PIN_MtVapC28-VapC30-like VapC-like PIN domain of Mycobacterium tuberculosis VapC28 and 30 and related proteins. This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC28 and VapC30 toxins. M. tuberculosis VapC28 and VapC30 both cleave tRNA25Ser-TGA and tRNA28Ser-CGA. It belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is a PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 128 matched cddid_all.tbl CDD cd09872 cd09872 350220 PIN_Sll0205-like VapC-like PIN domain of Sll0205 protein and homologs. Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of the Synechocystis sp. (strain PCC 6803) Sll0205 protein and other uncharacterized homologs are included in this subfamily. They are similar to the PIN domains of the Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB toxins of the prokaryotic toxin/antitoxin operons, VapBC and FitAB, respectively, which are believed to be involved in growth inhibition by regulating translation. These toxins are nearly always co-expressed with an antitoxin, a cognate protein inhibitor, forming an inert protein complex. Disassociation of the protein complex activates the ribonuclease activity of the toxin by an, as yet undefined mechanism. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 125 matched cddid_all.tbl CDD cd09873 cd09873 350221 PIN_Pae0151-like VapC-like PIN domain of the Pyrobaculum aerophilum Pae0151 and Pae2754 proteins and homologs. Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of the Pyrobaculum aerophilum proteins, Pae0151 and Pae2754, and homologs are included in this subfamily. They are similar to the PIN domains of the Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB toxins of the prokaryotic toxin/antitoxin operons, VapBC and FitAB, respectively, which are believed to be involved in growth inhibition by regulating translation. These toxins are nearly always co-expressed with an antitoxin, a cognate protein inhibitor, forming an inert protein complex. Disassociation of the protein complex activates the ribonuclease activity of the toxin by an, as yet undefined mechanism. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 128 matched cddid_all.tbl CDD cd09874 cd09874 350222 PIN_MT3492-like VapC-like PIN domain of the hypothetical protein MT3492 of Mycobacterium tuberculosis CDC1551 and other uncharacterized, annotated PilT protein domain proteins. Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis CDC1551, hypothetical protein MT3492, and similar bacterial and archaeal proteins are included in this subfamily. They are PIN domain homologs of the Mycobacterium tuberculosis VapC and Neisseria gonorrhoeae FitB toxins of the prokaryotic toxin/antitoxin operons, VapBC and FitAB, respectively, which are believed to be involved in growth inhibition by regulating translation. These toxins are nearly always co-expressed with an antitoxin, a cognate protein inhibitor, forming an inert protein complex. Disassociation of the protein complex activates the ribonuclease activity of the toxin by an, as yet undefined mechanism. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 134 matched cddid_all.tbl CDD cd09875 cd09875 350223 PIN_VapC-FitB-like VapC-like PIN domain of ribonucleases (toxins), VapC and FitB, of prokaryotic toxin/antitoxin operons, Pyrococcus horikoshii protein PH0500, and other similar bacterial and archaeal homologs. PIN (PilT N terminus) domain-containing proteins of prokaryotic toxin/antitoxin (TA) operons, such as, Mycobacterium tuberculosis VapC of the VapBC (virulence associated proteins) TA operon, and Neisseria gonorrhoeae FitB of the FitAB (fast intracellular trafficking) TA operon, as well as, the archaeal Pyrococcus horikoshii protein PH0500 are included in this family. Toxins of TA operons are believed to be involved in growth inhibition by regulating translation and are nearly always co-expressed with an antitoxin, a cognate protein inhibitor, forming an inert protein complex. Disassociation of the complex activates the ribonuclease activity of the toxin. In N. gonorrhoeae, FitA and FitB form a heterodimer: FitA is the DNA binding subunit and FitB contains a ribonuclease activity that is blocked by the presence of FitA. A tetramer of FitAB heterodimers binds DNA from the fitAB upstream promoter region with high affinity. This results in both sequestration of FitAB and repression of fitAB transcription. It is thought that FitAB release from the DNA and subsequent dissociation both slows N. gonorrhoeae replication and transcytosis by an as yet undefined mechanism. The toxin M. tuberculosis VapC is a structural homolog of N. gonorrhoeae FitB, but their antitoxin partners, VapB and FitA, respectively, differ structurally. The M. tuberculosis VapC-5 is proposed to be both an endoribonuclease and an exoribonuclease that can act on free RNA in a similar manner to the endo and exonuclease Flap endonuclease-1 (FEN1). VapC-like toxins are structural homologs of FEN1-like PIN domains, but lack the extensive arch/clamp region and the H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region, seen in FEN1-like PIN domains. PIN domains within this group typically contain three or four conserved acidic residues that cluster at the C-terminal end of the beta-sheet and form a negatively charged pocket near the center of the molecule. These putative active site residues are thought to bind Mg2+ and/or Mn2+ ions and be essential for single-stranded ribonuclease activity. VapC-like PIN domains are single domain proteins that form dimers and dimerization configures the active sites in a groove along the long-axis of the structure. 130 matched cddid_all.tbl CDD cd09876 cd09876 350224 PIN_Nob1-like VapC-like PIN domain of eukaryotic ribosome assembly factor Nob1 and archaeal UPF0129 protein Ta0041-like homologs. PIN (PilT N terminus) domain of the Saccharomyces cerevisiae ribosome assembly factor, Nob1 (Nin one binding) protein, the Thermoplasma acidophilum DSM 1728, UPF0129 protein Ta0041, and similar eukaryotic and archaeal homologs are included in this family. The Nob1 PIN domain binds the single-stranded cleavage site D at the 3-prime end of 18S rRNA. Recombinant Nob1 binds as a tetramer to pre-18S rRNA fragments containing cleavage site D and believed to cleave at this site. This subgroup belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_6. 112 matched cddid_all.tbl CDD cd09877 cd09877 350225 PIN_YacL-like VapC-like PIN domain of Thermus Thermophilus Hb8, uncharacterized Bacillus subtilis YacL, and other bacterial homologs. PIN (PilT N terminus) domain of the conserved membrane protein of unknown function of Thermus Thermophilus Hb8, Bacillus subtilis YacL and other similar homologs are included in this family. This subgroup belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Proteins in this group have a C-terminal TRAM domain whose function is unknown but predicted to be a RNA-binding domain common to tRNA uracil methylation and adenine thiolation enzymes. 127 matched cddid_all.tbl CDD cd09878 cd09878 350226 PIN_VapC_VirB11L-ATPase-like VapC-like PIN domain of an uncharacterized AAA+, VirB11-like ATPase-, KH- and PIN-domain containing protein MJ1533 from Methanocaldococcus jannaschii DSM 2661, and other similar archaeal homologs. PIN (PilT N terminus) domain present N-terminal of AAA+, VirB11-like ATPases. Several members of this subfamily possess an AAA+, VirB11-like ATPase domain, flanked by PIN and KH nucleic acid-binding domains. VirB11-ATPase is a type IV secretory pathway component required for T-pilus biogenesis and virulence. This subgroup belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. PIN domains within this subgroup contain four of these highly conserved residues which cluster at the C-terminal end of the beta-sheet and form a negatively charged pocket near the center of the molecule. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 125 matched cddid_all.tbl CDD cd09879 cd09879 350227 PIN_VapC_AF0591-like VapC-like PIN domain of Archaeoglobus fulgidus AF0591 protein and other similar archaeal homologs. PIN (PilT N terminus) domain of Archaeoglobus fulgidus AF0591 protein and other similar uncharacterized archaeal homologs are included in this family. This subgroup belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. PIN domains within this subgroup contain four of these highly conserved putative metal-binding, active site residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains and included distant subgroups, this subgroup includes some sequences belonging to one of these, PIN_14. 118 matched cddid_all.tbl CDD cd09880 cd09880 350228 PIN_Smg5-6-like VapC-like PIN domain of nonsense-mediated decay (NMD) factors, Smg5 and Smg6, and related proteins. PIN (PilT N terminus) domain of nonsense-mediated decay (NMD) factors, Smg5 and Smg6, and homologs are included in this family. Smg5 and Smg6 are essential factors in NMD, a post-transcriptional regulatory pathway that recognizes and rapidly degrades mRNAs containing premature translation termination codons. In vivo, the Smg6 PIN domain elicits degradation of bound mRNAs, as well as, metal-ion dependent, degradation of single-stranded RNA, in vitro. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Point mutation studies of the conserved aspartate residues in the catalytic center of the Smg6 PIN domain revealed that Smg6 is the endonuclease involved in human NMD. However, Smg5 lacks several of these key catalytic residues and does not degrade single-stranded RNA, in vivo. Many of the bacterial homologs in this group have an N-terminal PIN domain and a C-terminal PhoH-like ATPase domain. 152 matched cddid_all.tbl CDD cd09881 cd09881 350229 PIN_VapC4-5_FitB-like VapC-like PIN domain of Mycobacterium tuberculosis VapC4 and VapC5, and Neisseria gonorrhoeae FitB and related proteins. This family includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This family belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 127 matched cddid_all.tbl CDD cd09882 cd09882 350230 PIN_MtVapC3-like_start VapC-like PIN domain of Mycobacterium tuberculosis VapC3 toxin and related proteins. The VapC3-like nuclease subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of various Mycobacterium tuberculosis VapC toxins including VapC3, VapC11, VapC15, and VapC21. It belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is a PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 128 matched cddid_all.tbl CDD cd09883 cd09883 350231 PIN_VapC_PhoHL-ATPase VapC-like PIN domain of bacterial Smg6-like proteins with C-terminal PhoH-like ATPase domains. PIN (PilT N terminus) domain of Smg6-like bacterial proteins with C-terminal PhoH-like ATPase domains and other similar homologs are included in this family. Eukaryotic Smg5 and Smg6 nucleases are essential factors in nonsense-mediated mRNA decay (NMD), a post-transcriptional regulatory pathway that recognizes and rapidly degrades mRNAs containing premature translation termination codons. In vivo, the Smg6 PIN domain elicits degradation of bound mRNAs, as well as, metal ion dependent, degradation of single-stranded RNA, in vitro. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. PIN domains within this subgroup contain four highly conserved acidic residues (putative metal-binding, active site residues). Many of the bacterial homologs in this group have an N-terminal PIN domain and a C-terminal PhoH-like ATPase domain and are predicted to be ATPases which are induced by phosphate starvation. 146 matched cddid_all.tbl CDD cd09884 cd09884 350232 PIN_Smg5-like VapC-like PIN domain of human nonsense-mediated decay factor Smg5, and other similar eukaryotic homologs. Nonsense-mediated decay (NMD) factors, Smg5 and Smg6 are essential to the post-transcriptional regulatory pathway, NMD, which recognizes and rapidly degrades mRNAs containing premature translation termination codons. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Point mutation studies of the conserved aspartate residues in the catalytic center of the Smg6 PIN domain revealed that Smg6 is the endonuclease involved in human NMD. However, Smg5 lacks several of these key catalytic residues and does not degrade single-stranded RNA, in vivo. 160 matched cddid_all.tbl CDD cd09885 cd09885 350233 PIN_Smg6-like VapC-like PIN domain of human telomerase-binding protein EST1, Smg6, and other similar eukaryotic homologs. Nonsense-mediated decay (NMD) factors, Smg5 and Smg6 are essential to the post-transcriptional regulatory pathway, NMD, which recognizes and rapidly degrades mRNAs containing premature translation termination codons. In vivo, the Smg6 PIN (PilT N terminus) domain elicits degradation of bound mRNAs, as well as, metal ion dependent, degradation of single-stranded RNA, in vitro. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. PIN domains within this subgroup contain four highly conserved acidic residues (putative metal-binding, active site residues) which cluster at the C-terminal end of the beta-sheet and form a negatively charged pocket near the center of the molecule. Point mutation studies of the conserved aspartate residues in the catalytic center of the Smg6 PIN domain revealed that Smg6 is the endonuclease involved in human NMD. However, Smg5 lacks several of these key catalytic residues and does not degrade single-stranded RNA, in vivo. Eukaryotic Smg6 PIN domains are present at the C-terminal end of the telomerase activating proteins, EST1. 178 matched cddid_all.tbl CDD cd09886 cd09886 193575 NGN_SP N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP). The N-Utilization Substance G (NusG) protein is involved in transcription elongation and termination. NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination in bacteria. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS biosynthesis genes. NusG SP family members are operon-specific transcriptional antitermination factors. The NusG N-terminal (NGN) domain is quite similar in all NusG orthologs, but its C-terminal domains and the linker that separate these two domains are different. The domain organization of NusG and its orthologs suggest that the common properties of NusG and its orthologs and paralogs are due to their similar NGN domains. 97 matched cddid_all.tbl CDD cd09887 cd09887 193576 NGN_Arch Archaeal N-Utilization Substance G (NusG) N-terminal (NGN) domain. The N-Utilization Substance G (NusG) protein and its eukaryotic homolog, Spt5, are involved in transcription elongation and termination. Transcription in archaea has a eukaryotic-type transcription apparatus, but contains bacterial-type transcription factors. NusG is one of the few archaeal transcription factors that has orthologs in both bacteria and eukaryotes. Archaeal NusG is similar to bacterial NusG, composed of an NGN domain and a Kyrpides Ouzounis and Woese (KOW) repeat. The eukaryotic ortholog, Spt5, is a large protein composed of an acidic N-terminus, an NGN domain, and multiple KOW motifs at its C-terminus. NusG was originally discovered as a N-dependent antitermination enhancing activity in Escherichia coli and has a variety of functions, such as being involved in RNA polymerase elongation and Rho-termination in bacteria. Archaeal NusG forms a complex with DNA-directed RNA polymerase subunit E (rpoE) that is similar to the Spt5-Spt4 complex in eukaryotes. 82 matched cddid_all.tbl CDD cd09888 cd09888 193577 NGN_Euk Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1). The N-Utilization Substance G (NusG) protein and its eukaryotic homolog, Spt5, are involved in transcription elongation and termination. NusG contains an NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus. Spt5 forms an Spt4-Spt5 complex that is an essential RNA polymerase II elongation factor. NusG was originally discovered as an N-dependent antitermination enhancing activity in Escherichia coli, and has a variety of functions such as its involvement in RNA polymerase elongation and Rho-termination in bacteria. Orthologs of the NusG gene exist in all bacteria, but their functions and requirements are different. Spt5-like is homologous to the Spt5 proteins present in all eukaryotes, which is unique as it encodes a protein with an additional long carboxy-terminal extension that contains WG/GW motifs. Spt5-like, or KTF1 (KOW domain-containing Transcription Factor 1), is a RNA-directed DNA methylation (RdDM) pathway effector in plants. 86 matched cddid_all.tbl CDD cd09889 cd09889 193578 NGN_Bact_2 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 2. The N-Utilization Substance G (NusG) protein is involved in transcription elongation and termination. NusG is essential in Escherichia coli and associates with RNA polymerase elongation and Rho-termination. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS biosynthesis genes. NusG SP family members are operon-specific transcriptional antitermination factors. The NusG N-terminal domain (NGN) is quite similar in all NusG orthologs, but its C-terminal domain and the linker that separates these two domains are different. The domain organization of NusG and its orthologs suggests that the common properties of NusG and its orthologs and paralogs are due to their similar NGN domains. 100 matched cddid_all.tbl CDD cd09890 cd09890 193579 NGN_plant Plant N-Utilization Substance G (NusG) N-terminal (NGN) domain. The N-Utilization Substance G (NusG) protein and its eukaryotic homolog, Spt5, are involved in transcription elongation and termination. NusG contains a NGN domain at its N-terminus and Kyrpides Ouzounis and Woese (KOW) repeats at its C-terminus in bacteria and archaea. The eukaryotic ortholog, Spt5, is a large protein comprising an acidic N-terminus, an NGN domain, and multiple KOW motifs at its C-terminus. Spt5 forms an Spt4-Spt5 complex that is an essential RNA polymerase II elongation factor. The bacterial infected plants contain bacterial DNA, such as NGN sequences, that can be used to clone the DNA of uncultured organisms. 113 matched cddid_all.tbl CDD cd09891 cd09891 193580 NGN_Bact_1 Bacterial N-Utilization Substance G (NusG) N-terminal (NGN) domain, subgroup 1. The N-Utilization Substance G (NusG) protein is involved in transcription elongation and termination in bacteria. NusG is essential in Escherichia coli and associates with RNA polymerase elongation and Rho-termination. Homologs of the NusG gene exist in all bacteria. The NusG N-terminal domain (NGN) is similar in all NusG homologs, but its C-terminal domain and the linker that separates these two domains are different. The domain organization of NusG suggests that the common properties of NusG and its homologs are due to their similar NGN domains. 107 matched cddid_all.tbl CDD cd09892 cd09892 193581 NGN_SP_RfaH N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), RfaH. RfaH is an operon-specific virulence regulator, thought to have arisen from an early duplication of N-Utilization Substance G (NusG). Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS biosynthesis genes. NusG SP family members are operon-specific transcriptional antitermination factors. NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination in bacteria. In contrast, RfaH is a non-essential protein that controls expression of operons containing an ops (operon polarity suppressor) element in their transcribed DNA. RfaH and NusG are different in their response to Rho-dependent terminators and regulatory targets. The NusG N-terminal (NGN) domain is quite similar in all NusG orthologs, but its C-terminal domains and the linker that separate these two domains are different. The domain organization of NusG and its homologs suggest that the common properties of NusG and RfaH are due to their similar NGN domains. 96 matched cddid_all.tbl CDD cd09893 cd09893 193582 NGN_SP_TaA N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), TaA. The N-Utilization Substance G (NusG) protein is involved in transcription elongation and termination. NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination in bacteria. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS biosynthesis genes. NusG SP family members are operon-specific transcriptional antiterminationn factors. TaA is a NusG SP factor that is required for synthesis of a polyketide antibiotic TA in Myxococcus xanthus. Orthologs of the NusG gene exist in all bacteria, but its functions and requirements are different. The NusG N-terminal (NGN) domain is quite similar in all NusG orthologs, but its C-terminal domains and the linker that separate these two domains are different. The domain organization of NusG and its orthologs suggest that the common properties of NusG and its orthologs and paralogs are due to their similar NGN domains. 95 matched cddid_all.tbl CDD cd09894 cd09894 193583 NGN_SP_AnfA1 N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), AnFA1. Regulation of the afp, antifeeding prophage, gene cluster is mediated by AnFA1, a RfaH-like transcriptional antiterminator. RfaH is an operon-specific virulence regulator, thought to arisen from an early duplication of N-Utilization Substance G (NusG). NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination in bacteria. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS biosynthesis genes. NusG SP family members are operon-specific transcriptional antitermination factors. Orthologs of the NusG gene exist in all bacteria, but their functions and requirements are different. The NusG N-terminal domain (NGN) is similar in all NusG orthologs, but its C-terminal domain and the linker that separate these two domains are different. The domain organization of NusG and its orthologs suggests that the common properties of NusG and its orthologs and paralogs are due to their similar NGN domains. 99 matched cddid_all.tbl CDD cd09895 cd09895 193584 NGN_SP_UpxY N-Utilization Substance G (NusG) N-terminal domain in the NusG Specialized Paralog (SP), UpxY. The N-Utilization Substance G (NusG) proteins are involved in transcription elongation and termination. NusG is essential in Escherichia coli and is associated with RNA polymerase elongation and Rho-termination. Paralogs of eubacterial NusG, NusG SP (Specialized Paralog of NusG), are more diverse and often found as the first ORF in operons encoding secreted proteins and LPS (lipopolysaccharide) biosynthesis genes. NusG SP family members are operon-specific transcriptional antitermination factors. UpxY proteins, UpxY proteins, where the x is replaced by the letter designation of the specific polysaccharide (UpaY to UphY), are a family of NusG SP factors that act specifically in transcriptional antitermination of operons from which they are encoded. UpxYs are necessary and specific for transcription regulation of the polysaccharide biosynthesis operon. Orthologs of the NusG gene exist in all bacteria, but their functions and requirements are different. The NusG N-terminal (NGN) domain is similar in all NusG orthologs, but its C-terminal domain and the linker that separate these two domains are different. The domain organization of NusG and its orthologs suggests that the common properties of NusG and its orthologs and paralogs are due to their similar NGN domains. 95 matched cddid_all.tbl CDD cd09897 cd09897 188617 H3TH_FEN1-XPG-like H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases. The 5' nucleases within this family are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. This family includes the H3TH (helix-3-turn-helix) domains of Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), Xeroderma pigmentosum complementation group G (XPG) nuclease, and other eukaryotic and archaeal homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. With the except of the Mkt1-like proteins, the nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. 68 matched cddid_all.tbl CDD cd09898 cd09898 188618 H3TH_53EXO H3TH domain of the 5'-3' exonuclease of Taq DNA polymerase I and homologs. H3TH (helix-3-turn-helix) domains of the 5'-3' exonuclease (53EXO) of mutli-domain DNA polymerase I and single domain protein homologs are included in this family. Taq DNA polymerase I contains a polymerase domain for synthesizing a new DNA strand and a 53EXO domain for cleaving RNA primers or damaged DNA strands. Taq's 53EXO recognizes and endonucleolytically cleaves a structure-specific DNA substrate that has a bifurcated downstream duplex and an upstream template-primer duplex that overlaps the downstream duplex by 1 bp. The 53EXO cleaves the unpaired 5'-arm of the overlap flap DNA substrate. 5'-3' exonucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+ or Mn2+ or Zn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and two Asp residues from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. 73 matched cddid_all.tbl CDD cd09899 cd09899 188619 H3TH_T4-like H3TH domain of bacteriophage T3, T4 RNase H, T5-5' nucleases, and homologs. H3TH (helix-3-turn-helix) domains of bacteriophage T5-5'nuclease (5'-3' exonuclease or T5FEN), bacteriophage T4 RNase H (T4FEN), bacteriophage T3 (T3 phage exodeoxyribonuclease) and other similar 5' nucleases are included in this family. The T5-5'nuclease is a 5'-3' exodeoxyribonuclease that also exhibits endonucleolytic activity on flap structures (branched duplex DNA containing a free single-stranded 5'end). T4 RNase H, which removes the RNA primers that initiate lagging strand fragments, has 5'- 3' exonuclease activity on DNA/DNA and RNA/DNA duplexes and has endonuclease activity on flap or forked DNA structures. Bacteriophage T3 is believed to function in the removal of DNA-linked RNA primers and is essential for phage DNA replication and also necessary for host DNA degradation and phage genetic recombination. These nucleases are members of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. They contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors required for nuclease activity. The first metal binding site (MBS-1) is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site (MBS-2) is composed generally of two Asp residues from the PIN domain and two Asp residues from the H3TH domain. In the T5-5'nuclease, structure-specific endonuclease activity requires binding of a single metal ion in the high-affinity, MBS-1, whereas exonuclease activity requires both, the high-affinity, MBS-1 and the low-affinity, MBS-2 to be occupied by a divalent cofactor. The T5-5'nuclease is reported to be able to bind several metal ions including, Mg2+, Mn2+, Zn2+ and Co2+, as co-factors. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. 74 matched cddid_all.tbl CDD cd09900 cd09900 188620 H3TH_XPG-like H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 (archaeal), GEN1, YEN1, and XPG. The 5' nucleases within this family are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. This family includes the H3TH (helix-3-turn-helix) domains of archaeal Flap Endonuclease-1 (FEN1), Gap Endonuclease 1 (GEN1), Yeast Endonuclease 1 (YEN1), Xeroderma pigmentosum complementation group G (XPG) nuclease, and other eukaryotic and archaeal homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. With the except of the Mkt1-like proteins, the nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. 52 matched cddid_all.tbl CDD cd09901 cd09901 188621 H3TH_FEN1-like H3TH domains of Flap endonuclease-1 (FEN1)-like structure specific 5' nucleases: FEN1 (eukaryotic) and EXO1. The 5' nucleases within this family are capable of both 5'-3' exonucleolytic activity and cleaving bifurcated or branched DNA, in an endonucleolytic, structure-specific manner, and are involved in DNA replication, repair, and recombination. This family includes the H3TH (helix-3-turn-helix) domains of eukaryotic Flap Endonuclease-1 (FEN1), Exonuclease-1 (EXO1), and other eukaryotic homologs. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this family have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (i. e., Mg2+, Mn2+, Zn2+, or Co2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. 73 matched cddid_all.tbl CDD cd09902 cd09902 188622 H3TH_MKT1 H3TH domain of Mkt1: A global regulator of mRNAs encoding mitochondrial proteins and eukaryotic homologs. The Mkt1 gene product interacts with the Poly(A)-binding protein associated factor, Pbp1, and is present at the 3' end of RNA transcripts during translation. The Mkt1-Pbp1 complex is involved in the post-transcriptional regulation of HO endonuclease expression. Mkt1 and eukaryotic homologs are atypical members of the structure-specific, 5' nuclease family. Conical members of this family possess a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH (helix-3-turn-helix) domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Although Mkt1 appears to possess both a PIN and H3TH domain, the Mkt1 PIN domain lacks several of the active site residues necessary to bind essential divalent metal ion cofactors (Mg2+/Mn2+) required for nuclease activity in this family. Also, Mkt1 lacks the glycine-rich loop in the H3TH domain which is proposed to facilitate duplex DNA binding. 81 matched cddid_all.tbl CDD cd09903 cd09903 188623 H3TH_FEN1-Arc H3TH domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease: Archaeal homologs. Members of this subgroup include the H3TH (helix-3-turn-helix) domains of archaeal Flap endonuclease-1 (FEN1), 5' nucleases. FEN1 is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes (long-patch base excision repair) in eukaryotes and archaea. Interaction between FEN1 and PCNA (Proliferating cell nuclear antigen) is an essential prerequisite to FEN1's DNA replication functionality and stimulates FEN1 nuclease activity by 10-50 fold. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this subfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Also, FEN1 has a C-terminal extension containing residues forming the consensus PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA. 65 matched cddid_all.tbl CDD cd09904 cd09904 188624 H3TH_XPG H3TH domain of Xeroderma pigmentosum complementation group G (XPG) nuclease, a structure-specific, divalent-metal-ion dependent, 5' nuclease. The Xeroderma pigmentosum complementation group G (XPG) nuclease plays a central role in nucleotide excision repair (NER) in cleaving DNA bubble structures or loops. XPG is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Members of this subgroup include the H3TH (helix-3-turn-helix) domains of XPG and other similar eukaryotic 5' nucleases. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. These nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. 97 matched cddid_all.tbl CDD cd09905 cd09905 188625 H3TH_GEN1 H3TH domain of Gap Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease. Gap Endonuclease 1 (GEN1): Holliday junction resolvase reported to symmetrically cleave Holliday junctions and allow religation without additional processing. GEN1 is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Members of this subgroup include the H3TH (helix-3-turn-helix) domains of GEN1 and other similar eukaryotic 5' nucleases. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. These nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. 108 matched cddid_all.tbl CDD cd09906 cd09906 188626 H3TH_YEN1 H3TH domain of Yeast Endonuclease 1, a structure-specific, divalent-metal-ion dependent, 5' nuclease. Yeast Endonuclease 1 (YEN1): Holliday junction resolvase which promotes reciprocal exchange during mitotic recombination to maintain genome integrity in budding yeast. YEN1 is a member of the structure-specific, 5' nuclease family that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Members of this subgroup include the H3TH (helix-3-turn-helix) domains of YEN1 and other similar fungal 5' nucleases. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. These nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. 105 matched cddid_all.tbl CDD cd09907 cd09907 188627 H3TH_FEN1-Euk H3TH domain of Flap Endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease: Eukaryotic homologs. Members of this subgroup include the H3TH (helix-3-turn-helix) domains of eukaryotic Flap endonuclease-1 (FEN1), 5' nucleases. FEN1 is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes (long-patch base excision repair) in eukaryotes and archaea. Interaction between FEN1 and PCNA (Proliferating cell nuclear antigen) is an essential prerequisite to FEN1's DNA replication functionality and stimulates FEN1 nuclease activity by 10-50 fold. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. The nucleases within this subfamily have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. Also, FEN1 has a C-terminal extension containing residues forming the consensus PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA. 70 matched cddid_all.tbl CDD cd09908 cd09908 188628 H3TH_EXO1 H3TH domain of Exonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease. Exonuclease-1 (EXO1) is involved in multiple, eukaryotic DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity), DNA repair processes (DNA mismatch repair (MMR) and post-replication repair (PRR), recombination, and telomere integrity. EXO1 functions in the MMS2 error-free branch of the PRR pathway in the maintenance and repair of stalled replication forks. Studies also suggest that EXO1 plays both structural and catalytic roles during MMR-mediated mutation avoidance. Members of this subgroup include the H3TH (helix-3-turn-helix) domains of EXO1 and other similar eukaryotic 5' nucleases. These nucleases contain a PIN (PilT N terminus) domain with a helical arch/clamp region/I domain (not included here) and inserted within the PIN domain is an atypical helix-hairpin-helix-2 (HhH2)-like region. This atypical HhH2 region, the H3TH domain, has an extended loop with at least three turns between the first two helices, and only three of the four helices appear to be conserved. Both the H3TH domain and the helical arch/clamp region are involved in DNA binding. Studies suggest that a glycine-rich loop in the H3TH domain contacts the phosphate backbone of the template strand in the downstream DNA duplex. These nucleases have a carboxylate rich active site that is involved in binding essential divalent metal ion cofactors (Mg2+ or Mn2+) required for nuclease activity. The first metal binding site is composed entirely of Asp/Glu residues from the PIN domain, whereas, the second metal binding site is composed generally of two Asp residues from the PIN domain and one Asp residue from the H3TH domain. Together with the helical arch and network of amino acids interacting with metal binding ions, the H3TH region defines a positively charged active-site DNA-binding groove in structure-specific 5' nucleases. EXO1 nucleases also have C-terminal Mlh1- and Msh2-binding domains which allow interaction with MMR and PRR proteins, respectively. 73 matched cddid_all.tbl CDD cd09909 cd09909 197369 HIV-1-like_HR1-HR2 heptad repeat 1-heptad repeat 2 region (ectodomain) of the gp41 subunit of human immunodeficiency virus (HIV-1), and related domains. This domain family spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including human, simian, and feline immunodeficiency viruses (HIV, SIV, and FIV), bovine immunodeficiency-like virus (BIV), equine infectious anaemia virus (EIAV), and Jaagsiekte sheep retrovirus (JSRV), mouse mammary tumour virus (MMTV) and various ERVs including sheep enJSRV-26, and human ERVs (HERVs): HERV-K_c1q23.3 and HERV-K_c12q14.1. This domain belongs to a larger superfamily containing the HR1-HR2 domain of ERVs and infectious retroviruses, including Ebola virus, and Rous sarcoma virus. Proteins in this family lack the canonical CSK17-like immunosuppressive sequence, and the intrasubunit disulfide bond-forming CX6C motif found in linker region between HR1 and HR2 in the Ebola_RSV-like_HR1-HR2 family. N-terminal to the HR1-HR2 region is a fusion peptide (FP), and C-terminal is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1 helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some modern ERVs, those that integrated into the host genome post-speciation, have a currently active exogenous counterpart, such as JSRV. Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Included in this subgroup are ERVs from domestic sheep that are related to JSRV, the agent of transmissible lung cancer in sheep, for example enJSRV-26 that retains an intact genome. These endogenous JSRVs protect the sheep against JSRV infection and are required for sheep placental development. HERV-K_c12q14.1 is potentially a complete envelope protein; however, it does not appear to be fusogenic. 128 matched cddid_all.tbl CDD cd09910 cd09910 197364 NGN-insert_like NGN-insert domain found between N-terminal domain (D1) and C-terminal KOW domain (DIII) repeats of some N-Utilization Substance G (NusG) N-terminal (NGN). This family contains a unique insert (domain II, DII) found between the highly conserved N-terminal domain (NGN, domain I, D1) and C-terminal Kyrpides Ouzounis and Woese domain (KOW, domain III, DIII) repeats of some N-Utilization Substance G (NusG) N-terminal (NGN) proteins in bacteria such as Aquifex aeolicus NusG (AaeNusG). NusG was originally discovered as having an N-dependent antitermination enhancing activity in Escherichia coli, and has since been shown to have a variety of functions such as being involved in RNA polymerase elongation and Rho-termination. Orthologs of NusG gene exist in bacteria, but their functions and requirements are diverse. The function of DII is as yet unknown, and belongs to Domains of Unknown Function 1312 (DUF1312). 80 matched cddid_all.tbl CDD cd09911 cd09911 197365 Lin0431_like Listerrria innocua Lin0431 is similar to the N-Utilization Substance G (NusG) N terminal (NGN) insert (DII). This family contains domains homologous to Listeria innocua Lin0431, a protein that is similar to the N-Utilization Substance G (NusG) N terminal (NGN) insert (domain II, DII). Lin0431 and Aquifex aeolicus NusG DII (AaeNusG DII ) have similar structure and similar basic charged surface distributions that may bind negatively charged nucleic acids and/or another anionic binding partner, suggesting a possible role in transcription/translation regulating functions. Despite these two domains having low sequence similarity, the NusG DII and DUF1312 domain families may have diverged from common evolutionary ancestral proteins, and may have similar biochemical functions. 82 matched cddid_all.tbl CDD cd09912 cd09912 206739 DLP_2 Dynamin-like protein including dynamins, mitofusins, and guanylate-binding proteins. The dynamin family of large mechanochemical GTPases includes the classical dynamins and dynamin-like proteins (DLPs) that are found throughout the Eukarya. This family also includes bacterial DLPs. These proteins catalyze membrane fission during clathrin-mediated endocytosis. Dynamin consists of five domains; an N-terminal G domain that binds and hydrolyzes GTP, a middle domain (MD) involved in self-assembly and oligomerization, a pleckstrin homology (PH) domain responsible for interactions with the plasma membrane, GED, which is also involved in self-assembly, and a proline arginine rich domain (PRD) that interacts with SH3 domains on accessory proteins. To date, three vertebrate dynamin genes have been identified; dynamin 1, which is brain specific, mediates uptake of synaptic vesicles in presynaptic terminals; dynamin-2 is expressed ubiquitously and similarly participates in membrane fission; mutations in the MD, PH and GED domains of dynamin 2 have been linked to human diseases such as Charcot-Marie-Tooth peripheral neuropathy and rare forms of centronuclear myopathy. Dynamin 3 participates in megakaryocyte progenitor amplification, and is also involved in cytoplasmic enlargement and the formation of the demarcation membrane system. This family also includes mitofusins (MFN1 and MFN2 in mammals) that are involved in mitochondrial fusion. Dynamin oligomerizes into helical structures around the neck of budding vesicles in a GTP hydrolysis-dependent manner. 180 matched cddid_all.tbl CDD cd09913 cd09913 206740 EHD Eps15 homology domain (EHD), C-terminal domain. Dynamin-like C-terminal Eps15 homology domain (EHD) proteins regulate endocytic events; they have been linked to a number of Rab proteins through their association with mutual effectors, suggesting a coordinate role in endocytic regulation. Eukaryotic EHDs comprise four members (EHD1-4) in mammals and single members in Caenorhabditis elegans (Rme-1), Drosophila melanogaster (Past1) as well as several eukaryotic parasites. EHD1 regulates trafficking of multiple receptors from the endocytic recycling compartment (ERC) to the plasma membrane; EHD2 regulates trafficking from the plasma membrane by controlling Rac1 activity; EHD3 regulates endosome-to-Golgi transport, and preserves Golgi morphology; EHD4 is involved in the control of trafficking at the early endosome and regulates exit of cargo toward the recycling compartment as well as late endocytic pathway. Rme-1, an ortholog of human EHD1, controls the recycling of internalized receptors from the endocytic recycling compartment to the plasma membrane. In D. melanogaster, deletion of the Past1 gene leads to infertility as well as premature death of adult flies. Arabidopsis thaliana also has homologs of EHD proteins (AtEHD1 and AtEHD2), possibly involved in regulating endocytosis and signaling. 241 matched cddid_all.tbl CDD cd09914 cd09914 206741 RocCOR Ras of complex proteins (Roc) C-terminal of Roc (COR) domain family. RocCOR (or Roco) protein family is characterized by a superdomain containing a Ras-like GTPase domain, called Roc (Ras of complex proteins), and a characteristic second domain called COR (C-terminal of Roc). A kinase domain and diverse regulatory domains are also often found in Roco proteins. Their functions are diverse; in Dictyostelium discoideum, which encodes 11 Roco proteins, they are involved in cell division, chemotaxis and development, while in human, where 4 Roco proteins (LRRK1, LRRK2, DAPK1, and MFHAS1) are encoded, these proteins are involved in epilepsy and cancer. Mutations in LRRK2 (leucine-rich repeat kinase 2) are known to cause familial Parkinson's disease. 161 matched cddid_all.tbl CDD cd09915 cd09915 206742 Rag Rag GTPase subfamily of Ras-related GTPases. Rag GTPases (ras-related GTP-binding proteins) constitute a unique subgroup of the Ras superfamily, playing an essential role in regulating amino acid-induced target of rapamycin complex 1 (TORC1) kinase signaling, exocytic cargo sorting at endosomes, and epigenetic control of gene expression. This subfamily consists of RagA and RagB as well as RagC and RagD that are closely related. Saccharomyces cerevisiae encodes single orthologs of metazoan RagA/B and RagC/D, Gtr1 and Gtr2, respectively. Dimer formation is important for their cellular function; these domains form heterodimers, as RagA or RagB dimerizes with RagC or RagD, and similarly, Gtr1 dimerizes with Gtr2. In response to amino acids, the Rag GTPases guide the TORC1 complex to activate the platform containing Rheb proto-oncogene by driving the relocalization of mTORC1 from discrete locations in the cytoplasm to a late endosomal and/or lysosomal compartment that is Rheb-enriched and contains Rab-7. 175 matched cddid_all.tbl CDD cd09916 cd09916 197366 CpxP_like CpxP component of the bacterial Cpx-two-component system and related proteins. This family summarizes bacterial proteins related to CpxP, a periplasmic protein that forms part of a two-component system which acts as a global modulator of cell-envelope stress in gram-negative bacteria. CpxP aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH. Functioning as a dimer, it inhibits activation of the kinase CpxA, but also plays a vital role in the quality control system of P pili. It has been suggested that CpxP directly interacts with CpxA via its concave polar surface. Another member of this family, Spy, is also a periplasmic protein that may be involved in the response to stress. The homology between CpxP and Spy suggests similar functions. A characteristic 5-residue sequence motif LTXXQ is found repeated twice in many members of this family. 96 matched cddid_all.tbl CDD cd09917 cd09917 438852 F-box_SF F-box domain superfamily. This short domain is commonly found at the N-terminus of various proteins, and typically co-occurs with one or more other conserved domains or motifs, such as leucine rich repeats, WD40 repeats, kelch, tub, spry, and others. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. One of the best researched roles of F-box proteins is their participation in SCF (Skp1-Cul1-F-box protein), a multi-protein complex that functions as a ubiquitin E3 ligase, where the role of the F-box protein is to recruit target substrates. Gene families containing the F-box are found greatly expanded in narrow taxonomic lineages, such as flowering plants and nematodes. In this hierarchical classification, many of the subfamilies are named according to their domain architectures. 35 matched cddid_all.tbl CDD cd09918 cd09918 198174 SH2_Nterm_SPT6_like N-terminal Src homology 2 (SH2) domain found in Spt6. N-terminal SH2 domain in Spt6. Spt6 is an essential transcription elongation factor and histone chaperone that binds the C-terminal repeat domain (CTD) of RNA polymerase II. Spt6 contains a tandem SH2 domain with a novel structure and CTD-binding mode. The tandem SH2 domain binds to a serine 2-phosphorylated CTD peptide in vitro, whereas its N-terminal SH2 subdomain does not. CTD binding requires a positively charged crevice in the C-terminal SH2 subdomain, which lacks the canonical phospho-binding pocket of SH2 domains. The tandem SH2 domain is apparently required for transcription elongation in vivo as its deletion in cells is lethal in the presence of 6-azauracil. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 85 matched cddid_all.tbl CDD cd09919 cd09919 198175 SH2_STAT_family Src homology 2 (SH2) domain found in signal transducer and activator of transcription (STAT) family. STAT proteins mediate the signaling of cytokines and a number of growth factors from the receptors of these extracellular signaling molecules to the cell nucleus. STATs are specifically phosphorylated by receptor-associated Janus kinases, receptor tyrosine kinases, or cytoplasmic tyrosine kinases. The phosphorylated STAT molecules dimerize by reciprocal binding of their SH2 domains to the phosphotyrosine residues. These dimeric STATs translocate into the nucleus, bind to specific DNA sequences, and regulate the transcription of their target genes. However there are a number of unphosphorylated STATs that travel between the cytoplasm and nucleus and some STATs that exist as dimers in unstimulated cells that can exert biological functions independent of being activated by a receptor. There are seven mammalian STAT family members which have been identified: STAT1, STAT2, STAT3, STAT4, STAT5 (STAT5A and STAT5B), and STAT6. There are 6 conserved domains in STAT: N-terminal domain (NTD), coiled-coil domain (CCD), DNA-binding domain (DBD), alpha-helical linker domain (LD), SH2 domain, and transactivation domain (TAD). NTD is involved in dimerization of unphosphorylated STATs monomers and for the tetramerization between STAT1, STAT3, STAT4 and STAT5 on promoters with two or more tandem STAT binding sites. It also plays a role in promoting interactions with transcriptional co-activators such as CREB binding protein (CBP)/p300, as well as being important for nuclear import and deactivation of STATs involving tyrosine de-phosphorylation. The CCD interacts with other proteins, such as IFN regulatory protein 9 (IRF-9/p48) with STAT1 and c-JUN with STAT3 and is also thought to participate in the negative regulation of these proteins. Distinct genes are bound to STATs via their DBD domain. This domain is also involved in nuclear translocation of activated STAT1 and STAT3 phosphorylated dimers upon cytokine stimulation. LD links the DNA-binding and SH2 domains and is important for the transcriptional activation of STAT1 in response to IFN-gamma. It also plays a role in protein-protein interactions and has also been implicated in the constitutive nucleocytoplasmic shuttling of unphosphorylated STATs in resting cells. The SH2 domain is necessary for receptor association and tyrosine phosphodimer formation. Residues within this domain may be particularly important for some cellular functions mediated by the STATs as well as residues adjacent to this domain. The TAD interacts with several proteins, namely minichromosome maintenance complex component 5 (MCM5), breast cancer 1 (BRCA1) and CBP/p300. TAD also contains a modulatory phosphorylation site that regulates STAT activity and is necessary for maximal transcription of a number of target genes. The conserved tyrosine residue present in the C-terminus is crucial for dimerization via interaction with the SH2 domain upon the interaction of the ligand with the receptor. STAT activation by tyrosine phosphorylation also determines nuclear import and retention, DNA binding to specific DNA elements in the promoters of responsive genes, and transcriptional activation of STAT dimers. In addition to the SH2 domain there is a coiled-coil domain, a DNA binding domain, and a transactivation domain in the STAT proteins. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 115 matched cddid_all.tbl CDD cd09920 cd09920 198176 SH2_Cbl-b_TKB Src homology 2 (SH2) domain found in the Cbl-b TKB domain. SH2 found in the Cbl-b TKB domain. The Cbl (for Casitas B-lineage lymphoma) family of E3 ubiquitin ligases contains three members Cbl, Cbl-b and Cbl-c. The founding member Cbl was discovered first as the oncogenic protein v-Cbl, a Gag-fusion transforming protein of Cas NS-1 retrovirus, which causes pre- and pro-B lymphomas in mice. The N-terminus of the Cbl proteins is composed of a tyrosine kinase-binding (TKB) domain, also called phosphotyrosine binding (PTB) domain, a short linker region and the RING-type zinc finger. In addition, Cbl and Cbl-b contain a leucine zipper motif and a proline-rich domain in the C-terminus. The TKB domain consists of a four-helix bundle (4H), a calcium-binding EF hand and a divergent SH2 domain. Cbl-b plays a role in early hematopoietic development and is a negative regulator of T-cell receptor, B-cell receptor and high affinity immunoglobulin epsilon receptor signal transduction pathways. It also negatively regulates insulin-like growth factor 1 signaling during muscle atrophy caused by unloading and is involved in EGFR ubiquitination and internalization. Diseases associated with defects in Cbl-b include: multiple sclerosis, autoimmune diseases, including type 1 diabetes, and a craniofacial phenotype. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 97 matched cddid_all.tbl CDD cd09921 cd09921 198177 SH2_Jak_family Src homology 2 (SH2) domain in the Janus kinase (Jak) family. The Janus kinases (Jak) are a family of 4 non-receptor tyrosine kinases (Jak1, Jak2, Jak3, Tyk2) which respond to cytokine or growth factor receptor activation. To transduce cytokine signaling, a series of conformational changes occur in the receptor-Jak complex upon extracellular ligand binding. This results in trans-activation of the receptor-associated Jaks followed by phosphorylation of receptor tail tyrosine sites. The Signal Transducers and Activators of Transcription (STAT) are then recruited to the receptor tail, become phosphorylated and translocate to the nucleus to regulate transcription. Jaks have four domains: the pseudokinase domain, the catalytic tyrosine kinase domain, the FERM (band four-point-one, ezrin, radixin, and moesin) domain, and the SH2 (Src Homology-2) domain. The Jak kinases are regulated by several enzymatic and non-enzymatic mechanisms. First, the Jak kinase domain is regulated by phosphorylation of the activation loop which is associated with the catalytically competent kinase conformation and is distinct from the inactive kinase conformation. Second, the pseudokinase domain directly modulates Jak catalytic activity with the FERM domain maintaining an active state. Third, the suppressor of cytokine signaling (SOCS) family and tyrosine phosphatases directly regulate Jak activity. Dysregulation of Jak activity can manifest as either a reduction or an increase in kinase activity resulting in immunodeficiency, inflammatory diseases, hematological defects, autoimmune and myeloproliferative disorders, and susceptibility to infection. Altered Jak regulation occurs by many mechanisms, including: gene translocations, somatic or inherited point mutations, receptor mutations, and alterations in the activity of Jak regulators such as SOCS or phosphatases. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 97 matched cddid_all.tbl CDD cd09923 cd09923 198178 SH2_SOCS_family Src homology 2 (SH2) domain found in suppressor of cytokine signaling (SOCS) family. SH2 domain found in SOCS proteins. SOCS was first recognized as a group of cytokine-inducible SH2 (CIS) domain proteins comprising eight family members in human (CIS and SOCS1-SOCS7). In addition to the SH2 domain, SOCS proteins have a variable N-terminal domain and a conserved SOCS box in the C-terminal domain. SOCS proteins bind to a substrate via their SH2 domain. The prototypical members, CIS and SOCS1-SOCS3, have been shown to regulate growth hormone signaling in vitro and in a classic negative feedback response compete for binding at phosphotyrosine sites in JAK kinase and receptor pathways to displace effector proteins and target bound receptors for proteasomal degradation. Loss of SOCS activity results in excessive cytokine signaling associated with a variety of hematopoietic, autoimmune, and inflammatory diseases and certain cancers. Members (SOCS4-SOCS7) were identified by their conserved SOCS box, an adapter motif of 3 helices that associates substrate binding domains, such as the SOCS SH2 domain, ankryin, and WD40 with ubiquitin ligase components. These show limited cytokine induction. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 81 matched cddid_all.tbl CDD cd09925 cd09925 198179 SH2_SHC Src homology 2 (SH2) domain found in SH2 adaptor protein C (SHC). SHC is involved in a wide variety of pathways including regulating proliferation, angiogenesis, invasion and metastasis, and bone metabolism. An adapter protein, SHC has been implicated in Ras activation following the stimulation of a number of different receptors, including growth factors [insulin, epidermal growth factor (EGF), nerve growth factor, and platelet derived growth factor (PDGF)], cytokines [interleukins 2, 3, and 5], erythropoietin, and granulocyte/macrophage colony-stimulating factor, and antigens [T-cell and B-cell receptors]. SHC has been shown to bind to tyrosine-phosphorylated receptors, and receptor stimulation leads to tyrosine phosphorylation of SHC. Upon phosphorylation, SHC interacts with another adapter protein, Grb2, which binds to the Ras GTP/GDP exchange factor mSOS which leads to Ras activation. SHC is composed of an N-terminal domain that interacts with proteins containing phosphorylated tyrosines, a (glycine/proline)-rich collagen-homology domain that contains the phosphorylated binding site, and a C-terminal SH2 domain. SH2 has been shown to interact with the tyrosine-phosphorylated receptors of EGF and PDGF and with the tyrosine-phosphorylated C chain of the T-cell receptor, providing one of the mechanisms of T-cell-mediated Ras activation. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 104 matched cddid_all.tbl CDD cd09926 cd09926 198180 SH2_CRK_like Src homology 2 domain found in cancer-related signaling adaptor protein CRK. SH2 domain in the CRK proteins. CRKI (SH2-SH3) and CRKII (SH2-SH3-SH3) are splicing isoforms of the oncoprotein CRK. CRKs regulate transcription and cytoskeletal reorganization for cell growth and motility by linking tyrosine kinases to small G proteins. The SH2 domain of CRK associates with tyrosine-phosphorylated receptors or components of focal adhesions, such as p130Cas and paxillin. CRK transmits signals to small G proteins through effectors that bind its SH3 domain, such as C3G, the guanine-nucleotide exchange factor (GEF) for Rap1 and R-Ras, and DOCK180, the GEF for Rac6. The binding of p130Cas to the CRK-C3G complex activates Rap1, leading to regulation of cell adhesion, and activates R-Ras, leading to JNK-mediated activation of cell proliferation, whereas the binding of CRK DOCK180 induces Rac1-mediated activation of cellular migration. The activity of the different splicing isoforms varies greatly with CRKI displaying substantial transforming activity, CRKII less so, and phosphorylated CRKII with no biological activity whatsoever. CRKII has a linker region with a phosphorylated Tyr and an additional C-terminal SH3 domain. The phosphorylated Tyr creates a binding site for its SH2 domain which disrupts the association between CRK and its SH2 target proteins. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 106 matched cddid_all.tbl CDD cd09927 cd09927 198181 SH2_Tensin_like Src homology 2 domain found in Tensin-like proteins. SH2 domain found in Tensin-like proteins. The Tensins are a family of intracellular proteins that interact with receptor tyrosine kinases (RTKs), integrins, and actin. They are thought act as signaling bridges between the extracellular space and the cytoskeleton. There are four homologues: Tensin1, Tensin2 (TENC1, C1-TEN), Tensin3 and Tensin4 (cten), all of which contain a C-terminal tandem SH2-PTB domain pairing, as well as actin-binding regions that may localize them to focal adhesions. The isoforms of Tensin2 and Tensin3 contain N-terminal C1 domains, which are atypical and not expected to bind to phorbol esters. Tensins 1-3 contain a phosphatase (PTPase) and C2 domain pairing which resembles PTEN (phosphatase and tensin homologue deleted on chromosome 10) protein. PTEN is a lipid phosphatase that dephosphorylates phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) to yield phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2). As PtdIns(3,4,5)P3 is the product of phosphatidylinositol 3-kinase (PI3K) activity, PTEN is therefore a key negative regulator of the PI3K pathway. Because of their PTEN-like domains, the Tensins may also possess phosphoinositide-binding or phosphatase capabilities. However, only Tensin2 and Tensin3 have the potential to be phosphatases since only their PTPase domains contain a cysteine residue that is essential for catalytic activity. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 116 matched cddid_all.tbl CDD cd09928 cd09928 198182 SH2_Cterm_SPT6_like C-terminal Src homology 2 (SH2) domain found in Spt6. Spt6 is an essential transcription elongation factor and histone chaperone that binds the C-terminal repeat domain (CTD) of RNA polymerase II. Spt6 contains a tandem SH2 domain with a novel structure and CTD-binding mode. The tandem SH2 domain binds to a serine 2-phosphorylated CTD peptide in vitro, whereas its N-terminal SH2 subdomain does not. CTD binding requires a positively charged crevice in the C-terminal SH2 subdomain, which lacks the canonical phospho-binding pocket of SH2 domains. The tandem SH2 domain is apparently required for transcription elongation in vivo as its deletion in cells is lethal in the presence of 6-azauracil. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 89 matched cddid_all.tbl CDD cd09929 cd09929 198183 SH2_BLNK_SLP-76 Src homology 2 (SH2) domain found in B-cell linker (BLNK) protein and SH2 domain-containing leukocyte protein of 76 kDa (SLP-76). BLNK (also known as SLP-65 or BASH) is an important adaptor protein expressed in B-lineage cells. BLNK consists of a N-terminal sterile alpha motif (SAM) domain and a C-terminal SH2 domain. BLNK is a cytoplasmic protein, but a part of it is bound to the plasma membrane through an N-terminal leucine zipper motif and transiently bound to a cytoplasmic domain of Iga through its C-terminal SH2 domain upon B cell antigen receptor (BCR)-stimulation. A non-ITAM phosphotyrosine in Iga is necessary for the binding with the BLNK SH2 domain and/or for normal BLNK function in signaling and B cell activation. Upon phosphorylation BLNK binds Btk and PLCgamma2 through their SH2 domains and mediates PLCgamma2 activation by Btk. BLNK also binds other signaling molecules such as Vav, Grb2, Syk, and HPK1. BLNK has been shown to be necessary for BCR-mediated Ca2+ mobilization, for the activation of mitogen-activated protein kinases such as ERK, JNK, and p38 in a chicken B cell line DT40, and for activation of transcription factors such as NF-AT and NF-kappaB in human or mouse B cells. BLNK is involved in B cell development, B cell survival, activation, proliferation, and T-independent immune responses. BLNK is structurally homologous to SLP-76. SLP-76 and (linker for activation of T cells) LAT are adaptor/linker proteins in T cell antigen receptor activation and T cell development. BLNK interacts with many downstream signaling proteins that interact directly with both SLP-76 and LAT. New data suggest functional complementation of SLP-76 and LAT in T cell antigen receptor function with BLNK in BCR function. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 121 matched cddid_all.tbl CDD cd09930 cd09930 198184 SH2_cSH2_p85_like C-terminal Src homology 2 (cSH2) domain found in p85. Phosphoinositide 3-kinases (PI3Ks) are essential for cell growth, migration, and survival. p110, the catalytic subunit, is composed of an adaptor-binding domain, a Ras-binding domain, a C2 domain, a helical domain, and a kinase domain. The regulatory unit is called p85 and is composed of an SH3 domain, a RhoGap domain, a N-terminal SH2 (nSH2) domain, a inter SH2 (iSH2) domain, and C-terminal (cSH2) domain. There are 2 inhibitory interactions between p110alpha and p85 of P13K: 1) p85 nSH2 domain with the C2, helical, and kinase domains of p110alpha and 2) p85 iSH2 domain with C2 domain of p110alpha. There are 3 inhibitory interactions between p110beta and p85 of P13K: 1) p85 nSH2 domain with the C2, helical, and kinase domains of p110beta, 2) p85 iSH2 domain with C2 domain of p110alpha, and 3) p85 cSH2 domain with the kinase domain of p110alpha. It is interesting to note that p110beta is oncogenic as a wild type protein while p110alpha lacks this ability. One explanation is the idea that the regulation of p110beta by p85 is unique because of the addition of inhibitory contacts from the cSH2 domain and the loss of contacts in the iSH2 domain. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 104 matched cddid_all.tbl CDD cd09931 cd09931 198185 SH2_C-SH2_SHP_like C-terminal Src homology 2 (C-SH2) domain found in SH2 domain Phosphatases (SHP) proteins. The SH2 domain phosphatases (SHP-1, SHP-2/Syp, Drosophila corkscrew (csw), and Caenorhabditis elegans Protein Tyrosine Phosphatase (Ptp-2)) are cytoplasmic signaling enzymes. They are both targeted and regulated by interactions of their SH2 domains with phosphotyrosine docking sites. These proteins contain two SH2 domains (N-SH2, C-SH2) followed by a tyrosine phosphatase (PTP) domain, and a C-terminal extension. Shp1 and Shp2 have two tyrosyl phosphorylation sites in their C-tails, which are phosphorylated differentially by receptor and nonreceptor PTKs. Csw retains the proximal tyrosine and Ptp-2 lacks both sites. Shp-binding proteins include receptors, scaffolding adapters, and inhibitory receptors. Some of these bind both Shp1 and Shp2 while others bind only one. Most proteins that bind a Shp SH2 domain contain one or more immuno-receptor tyrosine-based inhibitory motifs (ITIMs): [SIVL]xpYxx[IVL]. Shp1 N-SH2 domain blocks the catalytic domain and keeps the enzyme in the inactive conformation, and is thus believed to regulate the phosphatase activity of SHP-1. Its C-SH2 domain is thought to be involved in searching for phosphotyrosine activators. The SHP2 N-SH2 domain is a conformational switch; it either binds and inhibits the phosphatase, or it binds phosphoproteins and activates the enzyme. The C-SH2 domain contributes binding energy and specificity, but it does not have a direct role in activation. Csw SH2 domain function is essential, but either SH2 domain can fulfill this requirement. The role of the csw SH2 domains during Sevenless receptor tyrosine kinase (SEV) signaling is to bind Daughter of Sevenless rather than activated SEV. Ptp-2 acts in oocytes downstream of sheath/oocyte gap junctions to promote major sperm protein (MSP)-induced MAP Kinase (MPK-1) phosphorylation. Ptp-2 functions in the oocyte cytoplasm, not at the cell surface to inhibit multiple RasGAPs, resulting in sustained Ras activation. It is thought that MSP triggers PTP-2/Ras activation and ROS production to stimulate MPK-1 activity essential for oocyte maturation and that secreted MSP domains and Cu/Zn superoxide dismutases function antagonistically to control ROS and MAPK signaling. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 99 matched cddid_all.tbl CDD cd09932 cd09932 198186 SH2_C-SH2_PLC_gamma_like C-terminal Src homology 2 (C-SH2) domain in Phospholipase C gamma. Phospholipase C gamma is a signaling molecule that is recruited to the C-terminal tail of the receptor upon autophosphorylation of a highly conserved tyrosine. PLCgamma is composed of a Pleckstrin homology (PH) domain followed by an elongation factor (EF) domain, 2 catalytic regions of PLC domains that flank 2 tandem SH2 domains (N-SH2, C-SH2), and ending with a SH3 domain and C2 domain. N-SH2 SH2 domain-mediated interactions represent a crucial step in transmembrane signaling by receptor tyrosine kinases. SH2 domains recognize phosphotyrosine (pY) in the context of particular sequence motifs in receptor phosphorylation sites. Both N-SH2 and C-SH2 have a very similar binding affinity to pY. But in growth factor stimulated cells these domains bind to different target proteins. N-SH2 binds to pY containing sites in the C-terminal tails of tyrosine kinases and other receptors. Recently it has been shown that this interaction is mediated by phosphorylation-independent interactions between a secondary binding site found exclusively on the N-SH2 domain and a region of the FGFR1 tyrosine kinase domain. This secondary site on the SH2 cooperates with the canonical pY site to regulate selectivity in mediating a specific cellular process. C-SH2 binds to an intramolecular site on PLCgamma itself which allows it to hydrolyze phosphatidylinositol-4,5-bisphosphate into diacylglycerol and inositol triphosphate. These then activate protein kinase C and release calcium. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 104 matched cddid_all.tbl CDD cd09933 cd09933 199827 SH2_Src_family Src homology 2 (SH2) domain found in the Src family of non-receptor tyrosine kinases. The Src family kinases are nonreceptor tyrosine kinases that have been implicated in pathways regulating proliferation, angiogenesis, invasion and metastasis, and bone metabolism. It is thought that transforming ability of Src is linked to its ability to activate key signaling molecules in these pathways, rather than through direct activity. As such blocking Src activation has been a target for drug companies. Src family members can be divided into 3 groups based on their expression pattern: 1) Src, Fyn, and Yes; 2) Blk, Fgr, Hck, Lck, and Lyn; and 3) Frk-related kinases Frk/Rak and Iyk/Bsk Of these, cellular c-Src is the best studied and most frequently implicated in oncogenesis. The c-Src contains five distinct regions: a unique N-terminal domain, an SH3 domain, an SH2 domain, a kinase domain and a regulatory tail, as do the other members of the family. Src exists in both active and inactive conformations. Negative regulation occurs through phosphorylation of Tyr, resulting in an intramolecular association between phosphorylated Tyr and the SH2 domain of SRC, which locks the protein in a closed conformation. Further stabilization of the inactive state occurs through interactions between the SH3 domain and a proline-rich stretch of residues within the kinase domain. Conversely, dephosphorylation of Tyr allows SRC to assume an open conformation. Full activity requires additional autophosphorylation of a Tyr residue within the catalytic domain. Loss of the negative-regulatory C-terminal segment has been shown to result in increased activity and transforming potential. Phosphorylation of the C-terminal Tyr residue by C-terminal Src kinase (Csk) and Csk homology kinase results in increased intramolecular interactions and consequent Src inactivation. Specific phosphatases, protein tyrosine phosphatase a (PTPa) and the SH-containing phosphatases SHP1/SHP2, have also been shown to take a part in Src activation. Src is also activated by direct binding of focal adhesion kinase (Fak) and Crk-associated substrate (Cas) to the SH2 domain. SRC activity can also be regulated by numerous receptor tyrosine kinases (RTKs), such as Her2, epidermal growth factor receptor (EGFR), fibroblast growth factor receptor, platelet-derived growth factor receptor (PDGFR), and vascular endothelial growth factor receptor (VEGFR). In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 101 matched cddid_all.tbl CDD cd09934 cd09934 198188 SH2_Tec_family Src homology 2 (SH2) domain found in Tec-like proteins. The Tec protein tyrosine kinase is the founding member of a family that includes Btk, Itk, Bmx, and Txk. The members have a PH domain, a zinc-binding motif, a SH3 domain, a SH2 domain, and a protein kinase catalytic domain. Btk is involved in B-cell receptor signaling with mutations in Btk responsible for X-linked agammaglobulinemia (XLA) in humans and X-linked immunodeficiency (xid) in mice. Itk is involved in T-cell receptor signaling. Tec is expressed in both T and B cells, and is thought to function in activated and effector T lymphocytes to induce the expression of genes regulated by NFAT transcription factors. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 104 matched cddid_all.tbl CDD cd09935 cd09935 198189 SH2_ABL Src homology 2 (SH2) domain found in Abelson murine lymphosarcoma virus (ABL) proteins. ABL-family proteins are highly conserved tyrosine kinases. Each ABL protein contains an SH3-SH2-TK (Src homology 3-Src homology 2-tyrosine kinase) domain cassette, which confers autoregulated kinase activity and is common among nonreceptor tyrosine kinases. Several types of posttranslational modifications control ABL catalytic activity, subcellular localization, and stability, with consequences for both cytoplasmic and nuclear ABL functions. Binding partners provide additional regulation of ABL catalytic activity, substrate specificity, and downstream signaling. By combining this cassette with actin-binding and -bundling domain, ABL proteins are capable of connecting phosphoregulation with actin-filament reorganization. Vertebrate paralogs, ABL1 and ABL2, have evolved to perform specialized functions. ABL1 includes nuclear localization signals and a DNA binding domain which is used to mediate DNA damage-repair functions, while ABL2 has additional binding capacity for actin and for microtubules to enhance its cytoskeletal remodeling functions. SH2 is involved in several autoinhibitory mechanism that constrain the enzymatic activity of the ABL-family kinases. In one mechanism SH2 and SH3 cradle the kinase domain while a cap sequence stabilizes the inactive conformation resulting in a locked inactive state. Another involves phosphatidylinositol 4,5-bisphosphate (PIP2) which binds the SH2 domain through residues normally required for phosphotyrosine binding in the linker segment between the SH2 and kinase domains. The SH2 domain contributes to ABL catalytic activity and target site specificity. It is thought that the ABL catalytic site and SH2 pocket have coevolved to recognize the same sequences. Recent work now supports a hierarchical processivity model in which the substrate target site most compatible with ABL kinase domain preferences is phosphorylated with greatest efficiency. If this site is compatible with the ABL SH2 domain specificity, it will then reposition and dock in the SH2 pocket. This mechanism also explains how ABL kinases phosphorylates poor targets on the same substrate if they are properly positioned and how relatively poor substrate proteins might be recruited to ABL through a complex with strong substrates that can also dock with the SH2 pocket. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 94 matched cddid_all.tbl CDD cd09937 cd09937 198190 SH2_csk_like Src homology 2 (SH2) domain found in Carboxyl-Terminal Src Kinase (Csk). Both the C-terminal Src kinase (CSK) and CSK-homologous kinase (CHK) are members of the CSK-family of protein tyrosine kinases. These proteins suppress activity of Src-family kinases (SFK) by selectively phosphorylating the conserved C-terminal tail regulatory tyrosine by a similar mechanism. CHK is also capable of inhibiting SFKs by a non-catalytic mechanism that involves binding of CHK to SFKs to form stable protein complexes. The unphosphorylated form of SFKs is inhibited by CSK and CHK by a two-step mechanism. The first step involves the formation of a complex of SFKs with CSK/CHK with the SFKs in the complex are inactive. The second step, involves the phosphorylation of the C-terminal tail tyrosine of SFKs, which then dissociates and adopt an inactive conformation. The structural basis of how the phosphorylated SFKs dissociate from CSK/CHK to adopt the inactive conformation is not known. The inactive conformation of SFKs is stabilized by two intramolecular inhibitory interactions: (a) the pYT:SH2 interaction in which the phosphorylated C-terminal tail tyrosine (YT) binds to the SH2 domain, and (b) the linker:SH3 interaction of which the SH2-kinase domain linker binds to the SH3 domain. SFKs are activated by multiple mechanisms including binding of the ligands to the SH2 and SH3 domains to displace the two inhibitory intramolecular interactions, autophosphorylation, and dephosphorylation of YT. By selective phosphorylation and the non-catalytic inhibitory mechanism CSK and CHK are able to inhibit the active forms of SFKs. CSK and CHK are regulated by phosphorylation and inter-domain interactions. They both contain SH3, SH2, and kinase domains separated by the SH3-SH2 connector and SH2 kinase linker, intervening segments separating the three domains. They lack a conserved tyrosine phosphorylation site in the kinase domain and the C-terminal tail regulatory tyrosine phosphorylation site. The CSK SH2 domain is crucial for stabilizing the kinase domain in the active conformation. A disulfide bond here regulates CSK kinase activity. The subcellular localization and activity of CSK are regulated by its SH2 domain. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 98 matched cddid_all.tbl CDD cd09938 cd09938 198191 SH2_N-SH2_Zap70_Syk_like N-terminal Src homology 2 (SH2) domain found in Zeta-chain-associated protein kinase 70 (ZAP-70) and Spleen tyrosine kinase (Syk) proteins. ZAP-70 and Syk comprise a family of hematopoietic cell specific protein tyrosine kinases (PTKs) that are required for antigen and antibody receptor function. ZAP-70 is expressed in T and natural killer (NK) cells and Syk is expressed in B cells, mast cells, polymorphonuclear leukocytes, platelets, macrophages, and immature T cells. They are required for the proper development of T and B cells, immune receptors, and activating NK cells. They consist of two N-terminal Src homology 2 (SH2) domains and a C-terminal kinase domain separated from the SH2 domains by a linker or hinge region. Phosphorylation of both tyrosine residues within the Immunoreceptor Tyrosine-based Activation Motifs (ITAM; consensus sequence Yxx[LI]x(7,8)Yxx[LI]) by the Src-family PTKs is required for efficient interaction of ZAP-70 and Syk with the receptor subunits and for receptor function. ZAP-70 forms two phosphotyrosine binding pockets, one of which is shared by both SH2 domains. In Syk the two SH2 domains do not form such a phosphotyrosine-binding site. The SH2 domains here are believed to function independently. In addition, the two SH2 domains of Syk display flexibility in their relative orientation, allowing Syk to accommodate a greater variety of spacing sequences between the ITAM phosphotyrosines and singly phosphorylated non-classical ITAM ligands. This model contains the N-terminus SH2 domains of both Syk and Zap70. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 104 matched cddid_all.tbl CDD cd09939 cd09939 198192 SH2_STAP_family Src homology 2 domain found in Signal-transducing adaptor protein (STAP) family. STAP1 and STAP2 are signal-transducing adaptor proteins. They are composed of a Pleckstrin homology (PH) and SH2 domains along with several tyrosine phosphorylation sites. STAP-1 is an ortholog of BRDG1 (BCR downstream signaling 1). STAP1 protein functions as a docking protein acting downstream of Tec tyrosine kinase in B cell antigen receptor signaling. The protein is phosphorylated by Tec and participates in a positive feedback loop, increasing Tec activity. STAP1 has been shown to interact with C19orf2, an unconventional prefoldin RPB5 interactor. The STAP2 protein is the substrate of breast tumor kinase, an Src-type non-receptor tyrosine kinase that mediates the interactions linking proteins involved in signal transduction pathways. STAP2 has alternative splicing variants. STAP2 has been shown to interact with tyrosine-protein kinase 6 (PTK6). In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 94 matched cddid_all.tbl CDD cd09940 cd09940 198193 SH2_Vav_family Src homology 2 (SH2) domain found in the Vav family. Vav proteins are involved in several processes that require cytoskeletal reorganization, such as the formation of the immunological synapse (IS), phagocytosis, platelet aggregation, spreading, and transformation. Vavs function as guanine nucleotide exchange factors (GEFs) for the Rho/Rac family of GTPases. Vav family members have several conserved motifs/domains including: a leucine-rich region, a leucine-zipper, a calponin homology (CH) domain, an acidic domain, a Dbl-homology (DH) domain, a pleckstrin homology (PH) domain, a cysteine-rich domain, 2 SH3 domains, a proline-rich region, and a SH2 domain. Vavs are the only known Rho GEFs that have both the DH/PH motifs and SH2/SH3 domains in the same protein. The leucine-rich helix-loop-helix (HLH) domain is thought to be involved in protein heterodimerization with other HLH proteins and it may function as a negative regulator by forming inactive heterodimers. The CH domain is usually involved in the association with filamentous actin, but in Vav it controls NFAT stimulation, Ca2+ mobilization, and its transforming activity. Acidic domains are involved in protein-protein interactions and contain regulatory tyrosines. The DH domain is a GDP-GTP exchange factor on Rho/Rac GTPases. The PH domain in involved in interactions with GTP-binding proteins, lipids and/or phosphorylated serine/threonine residues. The SH3 domain is involved in localization of proteins to specific sites within the cell interacting with protein with proline-rich sequences. The SH2 domain mediates a high affinity interaction with tyrosine phosphorylated proteins. There are three Vav mammalian family members: Vav1 which is expressed in the hematopoietic system, Vav2 and Vav3 are more ubiquitously expressed. The members here include insect and amphibian Vavs. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 102 matched cddid_all.tbl CDD cd09941 cd09941 199828 SH2_Grb2_like Src homology 2 domain found in Growth factor receptor-bound protein 2 (Grb2) and similar proteins. The adaptor proteins here include homologs Grb2 in humans, Sex muscle abnormal protein 5 (Sem-5) in Caenorhabditis elegans, and Downstream of receptor kinase (drk) in Drosophila melanogaster. They are composed of one SH2 and two SH3 domains. Grb2/Sem-5/drk regulates the Ras pathway by linking the tyrosine kinases to the Ras guanine nucleotide releasing protein Sos, which converts Ras to the active GTP-bound state. The SH2 domain of Grb2/Sem-5/drk binds class II phosphotyrosyl peptides while its SH3 domain binds to Sos and Sos-derived, proline-rich peptides. Besides it function in Ras signaling, Grb2 is also thought to play a role in apoptosis. Unlike most SH2 structures in which the peptide binds in an extended conformation (such that the +3 peptide residue occupies a hydrophobic pocket in the protein, conferring a modest degree of selectivity), Grb2 forms several hydrogen bonds via main chain atoms with the side chain of +2 Asn. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 95 matched cddid_all.tbl CDD cd09942 cd09942 198195 SH2_nSH2_p85_like N-terminal Src homology 2 (nSH2) domain found in p85. Phosphoinositide 3-kinases (PI3Ks) are essential for cell growth, migration, and survival. p110, the catalytic subunit, is composed of an adaptor-binding domain, a Ras-binding domain, a C2 domain, a helical domain, and a kinase domain. The regulatory unit is called p85 and is composed of an SH3 domain, a RhoGap domain, a N-terminal SH2 (nSH2) domain, an internal SH2 (iSH2) domain, and C-terminal (cSH2) domain. There are 2 inhibitory interactions between p110alpha and p85 of P13K: (1) p85 nSH2 domain with the C2, helical, and kinase domains of p110alpha and (2) p85 iSH2 domain with C2 domain of p110alpha. There are 3 inhibitory interactions between p110beta and p85 of P13K: (1) p85 nSH2 domain with the C2, helical, and kinase domains of p110beta, (2) p85 iSH2 domain with C2 domain of p110alpha, and (3) p85 cSH2 domain with the kinase domain of p110alpha. It is interesting to note that p110beta is oncogenic as a wild type protein while p110alpha lacks this ability. One explanation is the idea that the regulation of p110beta by p85 is unique because of the addition of inhibitory contacts from the cSH2 domain and the loss of contacts in the iSH2 domain. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 110 matched cddid_all.tbl CDD cd09943 cd09943 198196 SH2_Nck_family Src homology 2 (SH2) domain found in the Nck family. Nck proteins are adaptors that modulate actin cytoskeleton dynamics by linking proline-rich effector molecules to tyrosine kinases or phosphorylated signaling intermediates. There are two members known in this family: Nck1 (Nckalpha) and Nck2 (Nckbeta and Growth factor receptor-bound protein 4 (Grb4)). They are characterized by having 3 SH3 domains and a C-terminal SH2 domain. Nck1 and Nck2 have overlapping functions as determined by gene knockouts. Both bind receptor tyrosine kinases and other tyrosine-phosphorylated proteins through their SH2 domains. In addition they also bind distinct targets. Neuronal signaling proteins: EphrinB1, EphrinB2, and Disabled-1 (Dab-1) all bind to Nck-2 exclusively. And in the case of PDGFR, Tyr(P)751 binds to Nck1 while Tyr(P)1009 binds to Nck2. Nck1 and Nck2 have a role in the infection process of enteropathogenic Escherichia coli (EPEC). Their SH3 domains are involved in recruiting and activating the N-WASP/Arp2/3 complex inducing actin polymerization resulting in the production of pedestals, dynamic bacteria-presenting protrusions of the plasma membrane. A similar thing occurs in the vaccinia virus where motile plasma membrane projections are formed beneath the virus. Recently it has been shown that the SH2 domains of both Nck1 and Nck2 bind the G-protein coupled receptor kinase-interacting protein 1 (GIT1) in a phosphorylation-dependent manner. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 93 matched cddid_all.tbl CDD cd09944 cd09944 198197 SH2_Grb7_family Src homology 2 (SH2) domain found in the growth factor receptor bound, subclass 7 (Grb7) proteins. The Grb family binds to the epidermal growth factor receptor (EGFR, erbB1) via their SH2 domains. There are 3 members of the Grb7 family of proteins: Grb7, Grb10, and Grb14. They are composed of an N-terminal Proline-rich domain, a Ras Associating-like (RA) domain, a Pleckstrin Homology (PH) domain, a phosphotyrosine interaction region (PIR, BPS) and a C-terminal SH2 domain. The SH2 domains of Grb7, Grb10 and Grb14 preferentially bind to a different RTK. Grb7 binds strongly to the erbB2 receptor, unlike Grb10 and Grb14 which bind weakly to it. Grb14 binds to Fibroblast Growth Factor Receptor (FGFR). Grb10 has been shown to interact with many different proteins, including the insulin and IGF1 receptors, platelet-derived growth factor (PDGF) receptor-beta, Ret, Kit, Raf1 and MEK1, and Nedd4. Grb7 family proteins are phosphorylated on serine/threonine as well as tyrosine residues. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 108 matched cddid_all.tbl CDD cd09945 cd09945 198198 SH2_SHB_SHD_SHE_SHF_like Src homology 2 domain found in SH2 domain-containing adapter proteins B, D, E, and F (SHB, SHD, SHE, SHF). SHB, SHD, SHE, and SHF are SH2 domain-containing proteins that play various roles throughout the cell. SHB functions in generating signaling compounds in response to tyrosine kinase activation. SHB contains proline-rich motifs, a phosphotyrosine binding (PTB) domain, tyrosine phosphorylation sites, and a SH2 domain. SHB mediates certain aspects of platelet-derived growth factor (PDGF) receptor-, fibroblast growth factor (FGF) receptor-, neural growth factor (NGF) receptor TRKA-, T cell receptor-, interleukin-2 (IL-2) receptor- and focal adhesion kinase- (FAK) signaling. SRC-like FYN-Related Kinase FRK/RAK (also named BSK/IYK or GTK) and SHB regulate apoptosis, proliferation and differentiation. SHB promotes apoptosis and is also required for proper mitogenicity, spreading and tubular morphogenesis in endothelial cells. SHB also plays a role in preventing early cavitation of embryoid bodies and reduces differentiation to cells expressing albumin, amylase, insulin and glucagon. SHB is a multifunctional protein that has difference responses in different cells under various conditions. SHE is expressed in heart, lung, brain, and skeletal muscle, while expression of SHD is restricted to the brain. SHF is mainly expressed in skeletal muscle, brain, liver, prostate, testis, ovary, small intestine, and colon. SHD may be a physiological substrate of c-Abl and may function as an adapter protein in the central nervous system. It is also thought to be involved in apoptotic regulation. SHD contains five YXXP motifs, a substrate sequence preferred by Abl tyrosine kinases, in addition to a poly-proline rich region and a C-terminal SH2 domain. SHE contains two pTry protein binding domains, protein interaction domain (PID) and a SH2 domain, followed by a glycine-proline rich region, all of which are N-terminal to the phosphotyrosine binding (PTB) domain. SHF contains four putative tyrosine phosphorylation sites and an SH2 domain. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 98 matched cddid_all.tbl CDD cd09946 cd09946 198199 SH2_HSH2_like Src homology 2 domain found in hematopoietic SH2 (HSH2) protein. HSH2 is thought to function as an adapter protein involved in tyrosine kinase signaling. It may also be involved in regulating cytokine signaling and cytoskeletal reorganization in hematopoietic cells. HSH2 contains several putative protein-binding motifs, SH3-binding proline-rich regions, and phosphotyrosine sites, but lacks enzymatic motifs. HSH2 was found to interact with cytokine-regulated tyrosine kinase c-FES and an activated Cdc42-associated tyrosine kinase ACK1. HSH2 binds c-FES through both its C-terminal region and its N-terminal region including the SH2 domain and binds ACK1 via its N-terminal proline-rich region. Both kinases bound and tyrosine-phosphorylated HSH2 in mammalian cells. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 102 matched cddid_all.tbl CDD cd09947 cd09947 197370 Ebola_HIV-1-like_HR1-HR2 heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including Ebola virus and human immunodeficiency virus type 1 (HIV-1). This domain superfamily spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including Ebola virus gp2, Rous sarcoma virus gp37, human immunodeficiency virus type 1 (HIV-1) gp41, and the envelope proteins of various ERVs. In the HR1-HR2 region of Ebola virus and RSV, the linker region between the two repeats includes a CKS17-like immunosuppressive region and a CX6C motif that forms an intra-subunit disulfide bond; MMTV, HIV-1, HERV-K endogenous retroviruses and related sequences lack a canonical CSK17-like sequence, and CX6C motif. N-terminal to the HR1-HR2 region is a fusion peptide (FP), and C-terminal, is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1 helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some modern ERVs, those that integrated into the host genome post-speciation, have a currently active exogenous counterpart, such as Jaagsiekte sheep retrovirus (JSRV), feline leukemia virus (FeLV), and avian leukemia virus (ALV). Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Human ERVs (HERVs) belonging to this superfamily include Syncytin-1 (HERV-W_c7q21.2/ ERVWE1), and Syncytin-2 (HERV-FRD_6p24.1) which are expressed in the placenta, and are fusogenic, although they have a different cell specificity for fusion. Syncytin-2, but not Syncytin-1, is immunosuppressive; its immunosuppressive domain may protect the fetus from the mother's immune system. Syncytin-1 may participate in the formation of the placental trophoblast; it is also implicated in cell fusions between cancer and host cells and between cancer cell, and in human osteclast fusion. This superfamily also contains human HERV-R_c7q21.2 (ERV-3), which is also expressed in the placenta, but is not fusogenic, and has an immunosuppressive domain, but lacks a fusion peptide. It is unclear whether ERV-3 has a critical biological role. Included in this superfamily are ERVs from domestic sheep that are related to JSRV, the agent of transmissible lung cancer in sheep; for example, enJSRV-26 that retains an intact genome. These endogenous JSRVs protect the sheep against JSRV infection and are required for sheep placental development. 73 matched cddid_all.tbl CDD cd09948 cd09948 197371 Ebola_RSV-like_HR1-HR2 heptad repeat 1-heptad repeat 2 region of the transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including Ebola virus and Rous sarcoma virus. This domain family spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of endogenous retroviruses (ERVs) and infectious retroviruses, including Ebola virus gp2, Rous sarcoma virus gp37, and the envelope proteins of various ERVs. This domain includes an N-terminal heptad repeat, a CKS17-like immunosuppressive region, a CX6C motif that forms an intra-subunit disulfide bond, and a C-terminal heptad repeat. N-terminal to HR1-HR2 region is a fusion peptide (FP), while C-terminal, is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1s helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some modern ERVs, those that integrated into the host genome post-speciation, have a currently active exogenous counterpart, such as Jaagsiekte sheep retrovirus (JSRV), feline leukemia virus (FeLV), and avian leukemia virus (ALV). Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Human ERVs (HERVs) belonging to this family include Syncytin-1 (HERV-W_c7q21.2/ ERVWE1), and Syncytin-2 (HERV-FRD_6p24.1) which are expressed in the placenta, and are fusogenic, although they have a different cell specificity for fusion. Syncytin-2, but not Syncytin-1, is immunosuppressive. Its immunosuppressive domain may protect the fetus from the mother's immune system. Syncytin-1 may participate in the formation of the placental trophoblast. It is also implicated in cell fusions between cancer and host cells and between cancer cells, and in human osteclast fusion. This family also contains human HERV-R_c7q21.2 (ERV-3), which is also expressed in the placenta, but is not fusogenic, has an immunosuppressive domain, but lacks a fusion peptide. It is unclear whether ERV-3 has a critical biological role. 72 matched cddid_all.tbl CDD cd09949 cd09949 197372 RSV-like_HR1-HR2 heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of Rous sarcoma virus (RSV), and related domains. This domain subfamily spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including Rous sarcoma virus gp37, Avian leukosis virus subgroup J (ALV-J) envelope protein, and the envelope proteins of various ERVs, including those belonging to the ev/J (or EAV-HP) family of chicken ERVs, such as ev/J 4.1 Rb. ALV-J is a recently emerged avian pathogen, the causative agent of myeloid leukosis in meat-type chicken. ERVs are likely to originate from ancient germ-line infections by active retroviruses. ALV-J may have emerged from a recombination event between an unknown ALV and an EAV-HP ERV. This domain includes an N-terminal heptad repeat, a CKS17-like immunosuppressive region, a CX6C motif that forms an intrasubunit disulfide bond, and a C-terminal heptad repeat. N-terminal to HR1-HR2 region is a fusion peptide (FP), and C-terminal, is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1s helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. 72 matched cddid_all.tbl CDD cd09950 cd09950 197373 ENVV1-like_HR1-HR2 heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of the human endogenous retrovirus ENVV1, and related domains. This domain subfamily spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs), including chicken FET-1 (Female Expressed Transcript 1) protein, and the envelope proteins of the human ERVs (HERVs): ENVV1 (also known as HERV-V2_c19q13.41) and ENVV2 (also known as HERV-V1_c19q13.41 ). This domain belongs to a larger superfamily containing the HR1-HR2 domain of endogenous retroviruses (ERVs) and infectious retroviruses, such as Ebola virus, Rous sarcoma virus and human immunodeficiency virus type 1. This domain includes an N-terminal heptad repeat, a CKS17-like immunosuppressive region, a CX6C motif that forms an intra-subunit disulfide bond, and a C-terminal heptad repeat. N-terminal to HR1-HR2 region is a fusion peptide (FP), and C-terminal, is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1 helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. FET-1 may have an ovary-determining role. The FET-1 gene is located on the female specific W chromosome in chickens. During the sex-determining period, the FET-1 transcript is up-regulated in the cortex of the left gonad (the only gonad which develops in female chickens); it is also expressed at a lower level, in neural tissue and waste collection ducts. The genes encoding ENVV1 and ENVV2 proteins are located in tandem on chromosome 19q13.41, and show placenta-specific expression in human and baboon. 72 matched cddid_all.tbl CDD cd09951 cd09951 197374 HERV-Rb-like_HR1-HR2 heptad repeat 1- heptad repeat 2 region (ectodomain) of the transmembrane subunit of the human endogenous retrovirus HERV-R(b)_c3p24.3 and related domains. This domain subfamily spans both heptad repeats of the glycoprotein (gp)/transmembrane subunit of various endogenous retroviruses (ERVs) including the human ERVs (HERVs): HERV-R(b)_c3p24.3 and Syncytin-3 (also known as HERV-P(b)_c14q32.12). This domain belongs to a larger superfamily containing the HR1-HR2 domain of endogenous retroviruses (ERVs) and infectious retroviruses, such as Ebola virus, Rous sarcoma virus (RSV) and human immunodeficiency virus type 1 (HIV-1). This domain includes an N-terminal heptad repeat, a CKS17-like immunosuppressive region, a CX6C motif that forms an intrasubunit disulfide bond, and a C-terminal, is a heptad repeat. In intact retroviruses, N-terminal to HR1-HR2 region is a fusion peptide (FP), and C-terminal, is a membrane-spanning region (MSR). Viral infection involves the formation of a trimer-of-hairpins structure (three HR1s helices, buttressed by three HR2 helices lying in antiparallel orientation). In this structure, the FP (inserted in the host cell membrane) and MSR (inserted in the viral membrane) are in close proximity. ERVs are likely to originate from ancient germ-line infections by active retroviruses. Some ERVs play specific roles in the host, including placental development, protection of the host from infection by related pathogenic and exogenous retroviruses, and genome plasticity. Syncytin-3 is fusogenic, HERV-R(b)_c3p24.3 appears not to have fusogenic activity. 81 matched cddid_all.tbl CDD cd09966 cd09966 197375 UP_III_II Uroplakin IIIb, IIIa and II. Uroplakins (UPs) are a family of proteins that associate with each other to form plaques on the apical surface of the urothelium, the pseudo-stratified epithelium lining the urinary tract from renal pelvis to the bladder outlet. UPs are classified into 3 types: UPIa and UPIb, UPII, and UPIIIa and IIIb. UPIs are tetraspanins that have four transmembrane domains separating one large and one small extracellular domain while UPII and UPIIIs are single-pass transmembrane proteins. UPIa and UPIb form specific heterodimers with UPII and UPIII, respectively, which allows them to exit the endoplasmatic rediculum. UPII/UPIa and UPIIIs/UPIb form heterotetramers; six of these tetramers form the 16nm particle, seen in the hexagonal array of the asymmetric unit membrane, which is believed to form a urinary tract barrier. Uroplakins are also believed to play a role during urinary tract morphogenesis. 181 matched cddid_all.tbl CDD cd09967 cd09967 197376 UP_II Uroplakin II. Uroplakin II, the dimerization partner of uroplakin Ia, is a member of the uroplakin family. Uroplakins (UPs) are a family of proteins that associate with each other to form plaques on the apical surface of the urothelium, the pseudo-stratified epithelium lining the urinary tract from renal pelvis to the bladder outlet. UPs are classified into 3 types: UPIa and UPIb, UPII, and UPIIIa and IIIb. UPIs are tetraspanins that have four transmembrane domains seperating one large and one small extracellular domain while UPII and UPIIIs are single-pass transmembrane proteins. UPIa and UPIb form specific heterodimers with UPII and UPIII, respectively, which allows them to exit the endoplasmatic rediculum. UPII/UPIa and UPIIIs/UPIb form heterotetramers and six of these tetramers form the 16nm particle, seen in the hexagonal array of the asymmetric unit membrane, which is believed to form a urinary tract barrier. Uroplakins are also believed to play a role during urinary tract morphogenesis. 165 matched cddid_all.tbl CDD cd09968 cd09968 197377 UP_III Uroplakin III. Uroplakin IIIa and IIIb, the dimerization partners of uroplakin Ib, are a members of the uroplakin family. Uroplakins (UPs) are a family of proteins that associate with each other to form plaques on the apical surface of the urothelium, the pseudo-stratified epithelium lining the urinary tract from renal pelvis to the bladder outlet. UPs are classified into 3 types: UPIa and UPIb, UPII, and UPIIIa and IIIb. UPIs are tetraspanins that have four transmembrane domains seperating one large and one small extracellular domain while UPII and UPIIIs are single-pass transmembrane proteins. UPIa and UPIb form specific heterodimers with UPII and UPIII, respectively, which allows them to exit the endoplasmatic rediculum. UPII/UPIa and UPIIIs/UPIb form heterotetramers and six of these tetramers form the 16nm particle, seen in the hexagonal array of the asymmetric unit membrane, which is believed to form a urinary tract barrier. Uroplakins are also believed to play a role during urinary tract morphogenesis. 187 matched cddid_all.tbl CDD cd09969 cd09969 197378 UP_IIIb Uroplakin IIIb. Uroplakin IIIb, minor isoform of the dimerization partner of uroplakin Ib, is a members of the uroplakin family. Uroplakins (UPs) are a family of proteins that associate with each other to form plaques on the apical surface of the urothelium, the pseudo-stratified epithelium lining the urinary tract from renal pelvis to the bladder outlet. UPs are classified into 3 types: UPIa and UPIb, UPII, and UPIIIa and IIIb. UPIs are tetraspanins that have four transmembrane domains seperating one large and one small extracellular domain while UPII and UPIIIs are single-pass transmembrane proteins. UPIa and UPIb form specific heterodimers with UPII and UPIII, respectively, which allows them to exit the endoplasmatic rediculum. UPII/UPIa and UPIIIs/UPIb form heterotetramers and six of these tetramers form the 16nm particle, seen in the hexagonal array of the asymmetric unit membrane, which is believed to form a urinary tract barrier. Uroplakins are also believed to play a role during urinary tract morphogenesis. 184 matched cddid_all.tbl CDD cd09970 cd09970 197379 UP_IIIa Uroplakin IIIa. Uroplakin IIIa, mayor isoform of the dimerization partner of uroplakin Ib, is a members of the uroplakin family. Uroplakins (UPs) are a family of proteins that associate with each other to form plaques on the apical surface of the urothelium, the pseudo-stratified epithelium lining the urinary tract from renal pelvis to the bladder outlet. UPs are classified into 3 types: UPIa and UPIb, UPII, and UPIIIa and IIIb. UPIs are tetraspanins that have four transmembrane domains seperating one large and one small extracellular domain while UPII and UPIIIs are single-pass transmembrane proteins. UPIa and UPIb form specific heterodimers with UPII and UPIII, respectively, which allows them to exit the endoplasmatic rediculum. UPII/UPIa and UPIIIs/UPIb form heterotetramers and six of these tetramers form the 16nm particle, seen in the hexagonal array of the asymmetric unit membrane, which is believed to form a urinary tract barrier. Uroplakins are also believed to play a role during urinary tract morphogenesis. 212 matched cddid_all.tbl CDD cd09971 cd09971 197380 SdiA-regulated SdiA-regulated. This model represents a bacterial family of proteins that may be regulated by SdiA, a member of the LuxR family of transcriptional regulators. The C-terminal domain included in the alignment forms a five-bladed beta-propeller structure. The X-ray structure of Escherichia coli yjiK (C-terminal domain) exhibits binding of calcium ions (Ca++) in what appears to be an evolutionarily conserved site. Sequence analysis suggests a distant relationship to proteins that are characterized as containing NHL-repeats. The latter also form beta-propeller structures, with several examples known to form six-bladed beta-propellers. Several of the six-bladed beta-propellers containing NHL repeats have been characterized functionally, including members with enzymatic functions that are dependent on metal ions. No functional characterization is available for this family of five-bladed propellers, though. 242 matched cddid_all.tbl CDD cd09972 cd09972 193586 LOTUS_TDRD_OSKAR The first LOTUS domain in Oskar and Tudor-containing proteins 5 and 7. The first LOTUS domain in Oskar and Tudor-containing proteins 5 and 7: The LOTUS containing proteins are germline-specific and are found in the nuage/polar granules of germ cells. Tudor-containing protein 5 and 7 belong to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD5 and TDRD7 are components of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. Oskar protein is a critical component of the pole plasm in the Drosophila oocyte, which is required for germ cell formation.The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. 87 matched cddid_all.tbl CDD cd09973 cd09973 193587 LOTUS_2_TDRD7 The second LOTUS domain on Tudor-containing protein 7 (TDRD7). The second LOTUS domain on Tudor-containing protein 7 (TDRD7): TDRD7 contains three N-terminal LOTUS domains and three Tudor domain repeats at the C-terminus. It belongs to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD7 together with TDRD1/MTR-1, TDRD5 and TDRD6 forms a ribonucleoprotein complex in the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs) involving in RNA processing for spermatogenesis. TDRD7 is functionally essential for the differentiation of germ cells. The exact molecular function of LOTUS domain on TDRD7 remains to be characterized. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. 68 matched cddid_all.tbl CDD cd09974 cd09974 193588 LOTUS_3_TDRD7 The third LOTUS domain on Tudor-containing protein 7 (TDRD7). The third LOTUS domain on Tudor-containing protein 7 (TDRD7): TDRD7 contains three N-terminal LOTUS domains and three Tudor domain repeats at the C-terminus. It belongs to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD7 together with TDRD1/MTR-1, TDRD5 and TDRD6 forms a ribonucleoprotein complex in the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs) involving in RNA processing for spermatogenesis. TDRD7 is functionally essential for the differentiation of germ cells. The exact molecular function of LOTUS domain on TDRD7 remains to be characterized. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. 67 matched cddid_all.tbl CDD cd09975 cd09975 193589 LOTUS_2_TDRD5 The second LOTUS domain on Tudor-containing protein 5 (TDRD5). The second LOTUS domain on Tudor-containing protein 5 (TDRD5): TDRD5 contains three N-terminal LOTUS domains and a C-terminal Tudor domain. It belongs to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice TDRD5 is a component of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. The exact molecular function of LOTUS domain on TDRD5 remains to be discovered. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. 70 matched cddid_all.tbl CDD cd09976 cd09976 193590 LOTUS_3_TDRD5 The third LOTUS domain on Tudor-containing protein 5 (TDRD5). The third LOTUS domain on Tudor-containing protein 5 (TDRD5): TDRD5 contains three N-terminal LOTUS domains and a C-terminal Tudor domain. It belongs to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice TDRD5 is a component of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. The exact molecular function of LOTUS domain on TDRD5 remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. 74 matched cddid_all.tbl CDD cd09977 cd09977 193591 LOTUS_1_Limkain_b1 The first LOTUS domain on Limkain b1(LKAP). The first LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. 62 matched cddid_all.tbl CDD cd09978 cd09978 193592 LOTUS_2_Limkain_b1 The second LOTUS domain on Limkain b1(LKAP). The second LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization 71 matched cddid_all.tbl CDD cd09979 cd09979 193593 LOTUS_3_Limkain_b1 The third LOTUS domain on Limkain b1(LKAP). The third LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. 72 matched cddid_all.tbl CDD cd09980 cd09980 193594 LOTUS_4_Limkain_b1 The fourth LOTUS domain on Limkain b1(LKAP). The fourth LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. 72 matched cddid_all.tbl CDD cd09981 cd09981 193595 LOTUS_5_Limkain_b1 The fifth LOTUS domain on Limkain b1(LKAP). The fifth LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. 71 matched cddid_all.tbl CDD cd09982 cd09982 193596 LOTUS_6_Limkain_b1 The sixth LOTUS domain on Limkain b1(LKAP). The sixth LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. 71 matched cddid_all.tbl CDD cd09983 cd09983 193597 LOTUS_7_Limkain_b1 The seventh LOTUS domain on Limkain b1(LKAP). The seventh LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. 73 matched cddid_all.tbl CDD cd09984 cd09984 193598 LOTUS_8_Limkain_b1 The eighth LOTUS domain on Limkain b1(LKAP). The eighth LOTUS domain on Limkain b1(LKAP): Limkain b1 is a novel human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. The protein contains multiple copies of LOTUS domains and a conserved RNA recognition motif. The exact molecular function of LOTUS domain remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. 76 matched cddid_all.tbl CDD cd09985 cd09985 193599 LOTUS_1_TDRD5 The first LOTUS domain on Tudor-containing protein 5 (TDRD5). The first LOTUS domain on Tudor-containing protein 5 (TDRD5): TDRD5 contains three N-terminal LOTUS domains and a C-terminal Tudor domain. It belongs to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD5 is a component of the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs), which are cytoplasmic ribonucleoprotein granules involved in RNA processing for spermatogenesis. The exact molecular function of LOTUS domain on TDRD5 remains to be identified. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. 95 matched cddid_all.tbl CDD cd09986 cd09986 193600 LOTUS_1_TDRD7 The first LOTUS domain on Tudor-containing protein 7 (TDRD7). The first LOTUS domain on Tudor-containing protein 7 (TDRD7): TDRD7 contains three N-terminal LOTUS domains and three Tudor domain repeats at the C-terminus. It belongs to the evolutionary conserved Tudor domain-containing protein (TDRD) family involved in germ cell development. In mice, TDRD7 together with TDRD1/MTR-1, TDRD5 and TDRD6 forms a ribonucleoprotein complex in the intermitochondrial cements (IMCs) and the chromatoid bodies (CBs) involving in RNA processing for spermatogenesis. TDRD7 is functionally essential for the differentiation of germ cells. The exact molecular function of LOTUS domain on TDRD7 remains to be characterized. Its occurrence in proteins associated with RNA metabolism suggests that it might be involved in RNA binding function. The presence of several basic residues and RNA fold recognition motifs support this hypothesis. The RNA binding function might be the first step of regulating mRNA translation or localization. 88 matched cddid_all.tbl CDD cd09987 cd09987 212513 Arginase_HDAC Arginase-like and histone-like hydrolases. Arginase-like/histone-like hydrolase superfamily includes metal-dependent enzymes that belong to Arginase-like amidino hydrolase family and histone/histone-like deacetylase class I, II, IV family, respectively. These enzymes catalyze hydrolysis of amide bond. Arginases are known to be involved in control of cellular levels of arginine and ornithine, in histidine and arginine degradation and in clavulanic acid biosynthesis. Deacetylases play a role in signal transduction through histone and/or other protein modification and can repress/activate transcription of a number of different genes. They participate in different cellular processes including cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and post-translational control of the acetyl coenzyme A synthetase. Mammalian histone deacetyases are known to be involved in progression of different tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs. 217 matched cddid_all.tbl CDD cd09988 cd09988 212514 Formimidoylglutamase Formimidoylglutamase or HutE. Formimidoylglutamase (N-formimidoyl-L-glutamate formimidoylhydrolase; formiminoglutamase; N-formiminoglutamate hydrolase; N-formimino-L-glutamate formiminohydrolase; HutE; EC 3.5.3.8) is a metalloenzyme that catalyzes hydrolysis of N-formimidoyl-L-glutamate to L-glutamate and formamide. This enzyme is involved in histidine degradation, requiring Mn as a cofactor while glutathione may be required for maximal activity. In Pseudomonas PAO1, mutation studies show that histidine degradation proceeds via a 'four-step' pathway if the 'five-step' route is absent and vice versa; in the four-step pathway, formiminoglutaminase (HutE, EC 3.5.3.8) directly converts formiminoglutamate (FIGLU) to L-glutamate and formamide in a single step. Formiminoglutamase has traditionally also been referred to as HutG; however, formiminoglutamase is structurally and mechanistically unrelated to N-formyl-glutamate deformylase (also called HutG). Phylogenetic analysis has suggested that HutE was acquired by horizontal gene transfer from a Ralstonia-like ancestor. 262 matched cddid_all.tbl CDD cd09989 cd09989 212515 Arginase Arginase family. This family includes arginase, also known as arginase-like amidino hydrolase family, and related proteins. Arginase is a binuclear Mn-dependent metalloenzyme and catalyzes hydrolysis of L-arginine to L-ornithine and urea (Arg, EC 3.5.3.1), the reaction being the fifth and final step in the urea cycle, providing the path for the disposal of nitrogenous compounds. Arginase controls cellular levels of arginine and ornithine which are involved in protein biosynthesis, and in production of creatine, polyamines, proline and nitric acid. In vertebrates, at least two isozymes have been identified: type I (ARG1) cytoplasmic or hepatic liver-type arginase and type II (ARG2) mitochondrial or non-hepatic arginase. Point mutations in human arginase ARG1 gene lead to hyperargininemia with consequent mental disorders, retarded development and early death. Hyperargininemia is associated with a several-fold increase in the activity of the mitochondrial arginase (ARG2), causing persistent ureagenesis in patients. ARG2 overexpression plays a critical role in the pathophysiology of cholesterol mediated endothelial dysfunction. Thus, arginase is a therapeutic target to treat asthma, erectile dysfunction, atherosclerosis and cancer. 290 matched cddid_all.tbl CDD cd09990 cd09990 212516 Agmatinase-like Agmatinase-like family. Agmatinase subfamily currently includes metalloenzymes such as agmatinase, guanidinobutyrase, guanidopropionase, formimidoylglutamase and proclavaminate amidinohydrolase. Agmatinase (agmatine ureohydrolase; SpeB; EC=3.5.3.11) is the key enzyme in the synthesis of polyamine putrescine; it catalyzes hydrolysis of agmatine to yield putrescine and urea. This enzyme has been found in bacteria, archaea and eukaryotes, requiring divalent Mn and sometimes Zn, Co or Ca for activity. In mammals, the highest level of agmatinase mRNA was found in liver and kidney. However, catabolism of agmatine via agmatinase apparently is a not major path; it is mostly catabolized via diamine oxidase. Agmatinase has been shown to be down-regulated in tumor renal cells. Guanidinobutyrase (Gbh, EC=3.5.3.7) catalyzes hydrolysis of 4-guanidinobutanoate to yield 4-aminobutanoate and urea in arginine degradation pathway. Activity has been shown for purified enzyme from Arthrobacter sp. KUJ 8602. Additionally, guanidinobutyrase is able to hydrolyze D-arginine, 3-guanidinopropionate, 5-guanidinovaleriate and L-arginine with much less affinity, having divalent Zn ions for catalysis. Proclavaminate amidinohydrolase (Pah, EC 3.5.3.22) hydrolyzes amidinoproclavaminate to yield proclavaminate and urea in clavulanic acid biosynthesis. Activity has been shown for purified enzyme from Streptomyces clavuligerus. Clavulanic acid is the effective inhibitor of beta-lactamases. This acid is used in combination with the penicillin amoxicillin to prevent antibiotic's beta-lactam rings from hydrolysis, thus keeping the antibiotics biologically active. 275 matched cddid_all.tbl CDD cd09991 cd09991 212517 HDAC_classI Class I histone deacetylases. Class I histone deacetylases (HDACs) are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues in histone amino termini to yield a deacetylated histone (EC 3.5.1.98). Enzymes belonging to this group participate in regulation of a number of processes through protein (mostly different histones) modification (deacetylation). Class I histone deacetylases in general act via the formation of large multiprotein complexes. This group includes animal HDAC1, HDAC2, HDAC3, HDAC8, fungal RPD3, HOS1 and HOS2, plant HDA9, protist, archaeal and bacterial (AcuC) deacetylases. Members of this class are involved in cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and in posttranslational control of the acetyl coenzyme A synthetase. In mammals, they are known to be involved in progression of various tumors. Specific inhibitors of mammalian histone deacetylases are an emerging class of promising novel anticancer drugs. 306 matched cddid_all.tbl CDD cd09992 cd09992 212518 HDAC_classII Histone deacetylases and histone-like deacetylases, classII. Class II histone deacetylases are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) and possibly other proteins to yield deacetylated histones/other proteins. This group includes animal HDAC4,5,6,7,8,9,10, fungal HOS3 and HDA1, plant HDA5 and HDA15 as well as other eukaryotes, archaeal and bacterial histone-like deacetylases. Eukaryotic deacetylases mostly use histones (H2, H3, H4) as substrates for deacetylation; however, non-histone substrates are known (for example, tubulin). Substrates for prokaryotic histone-like deacetylases are not known. Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Interaction partners of class II deacetylases include 14-3-3 proteins, MEF2 family of transcriptional factors, CtBP, calmodulin (CaM), SMRT, N-CoR, BCL6, HP1alpha and SUMO. Histone deacetylases play a role in the regulation of cell cycle, cell differentiation and survival. Class II mammalian HDACs are differentially inhibited by structurally diverse compounds with known antitumor activities, thus presenting them as potential drug targets for human diseases resulting from aberrant acetylation. 291 matched cddid_all.tbl CDD cd09993 cd09993 212519 HDAC_classIV Histone deacetylase class IV also known as histone deacetylase 11. Class IV histone deacetylases (HDAC11; EC 3.5.1.98) are predicted Zn-dependent enzymes. This class includes animal HDAC11, plant HDA2 and related bacterial deacetylases. Enzymes in this subfamily participate in regulation of a number of different processes through protein modification (deacetylation). They catalyze hydrolysis of N(6)-acetyl-lysine of histones (or other proteins) to yield a deacetylated proteins. Histone deacetylases often act as members of large multi-protein complexes such as mSin3A or SMRT/N-CoR. Human HDAC11 does not associate with them but can interact with HDAC6 in vivo. It has been suggested that HDAC11 and HDAC6 may use non-histone proteins as their substrates and play a role other than to directly modulate chromatin structure. In normal tissues, expression of HDAC11 is limited to kidney, heart, brain, skeletal muscle and testis, suggesting that its function might be tissue-specific. In mammals, HDAC11 proteins are known to be involved in progression of various tumors. HDAC11 plays an essential role in regulating OX40 ligand (OX40L) expression in Hodgkin lymphoma (HL); selective inhibition of HDAC11 expression significantly up-regulates OX40L and induces apoptosis in HL cell lines. Thus, inhibition of HDAC11 could be a therapeutic drug option for antitumor immune response in HL patients. 275 matched cddid_all.tbl CDD cd09994 cd09994 212520 HDAC_AcuC_like Class I histone deacetylase AcuC (Acetoin utilization protein)-like enzymes. AcuC (Acetoin utilization protein) is a class I deacetylase found only in bacteria and is involved in post-translational control of the acetyl-coenzyme A synthetase (AcsA). Deacetylase AcuC works in coordination with deacetylase SrtN (class III), possibly to maintain AcsA in active (deacetylated) form and let the cell grow under low concentration of acetate. B. subtilis AcuC is a member of operon acuABC; this operon is repressed by the presence of glucose and does not show induction by acetoin; acetoin is a bacterial fermentation product that can be converted to acetate via the butanediol cycle in absence of other carbon sources. Inactivation of AcuC leads to slower growth and lower cell yield under low-acetate conditions in Bacillus subtilis. In general, Class I histone deacetylases (HDACs) are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues in histone amino termini to yield a deacetylated histone (EC 3.5.1.98). Enzymes belonging to this group participate in regulation of a number of processes through protein (mostly different histones) modification (deacetylation). Class I histone deacetylases in general act via the formation of large multiprotein complexes. Members of this class are involved in cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and in posttranslational control of the acetyl coenzyme A synthetase. 313 matched cddid_all.tbl CDD cd09996 cd09996 212521 HDAC_classII_1 Histone deacetylases and histone-like deacetylases, classII. This subfamily includes bacterial as well as eukaryotic Class II histone deacetylase (HDAC) and related proteins. Deacetylases of class II are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) and possibly other proteins to yield deacetylated histones/other proteins. Included in this family is a bacterial HDAC-like amidohydrolase (Bordetella/Alcaligenes species FB18817, denoted as FB188 HDAH) shown to be most similar in sequence and function to class II HDAC6 domain 3 or b (HDAC6b). FB188 HDAH is able to remove the acetyl moiety from acetylated histones, and can be inhibited by common HDAC inhibitors such as SAHA (suberoylanilide hydroxamic acid) as well as class II-specific but not class I specific inhibitors. 359 matched cddid_all.tbl CDD cd09998 cd09998 212522 HDAC_Hos3 Class II histone deacetylases Hos3 and related proteins. Fungal histone deacetylase Hos3 from Saccharomyces cerevisiae is a Zn-dependent enzyme belonging to HDAC class II. It catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Hos3 deacetylase is homodimer, in vitro it shows specificity to H4, H3 and H2A. 353 matched cddid_all.tbl CDD cd09999 cd09999 212523 Arginase-like_1 Arginase-like amidino hydrolase family. This family includes arginase, also known as arginase-like amidino hydrolase family, as well as arginase-like proteins and are found in bacteria, archaea and eykaryotes, but does not include metazoan arginases. Arginase is a binuclear Mn-dependent metalloenzyme and catalyzes hydrolysis of L-arginine to L-ornithine and urea (Arg, EC 3.5.3.1), the reaction being the fifth and final step in the urea cycle, providing the path for the disposal of nitrogenous compounds. Arginase controls cellular levels of arginine and ornithine which are involved in protein biosynthesis, and in production of creatine, polyamines, proline and nitric acid. 272 matched cddid_all.tbl CDD cd10000 cd10000 212524 HDAC8 Histone deacetylase 8 (HDAC8). HDAC8 is a Zn-dependent class I histone deacetylase that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. HDAC8 is found in human cytoskeleton-bound protein fraction and insoluble cell pellets. It plays a crucial role in intramembraneous bone formation; germline deletion of HDAC8 is detrimental to skull bone formation. HDAC8 is possibly associated with the smooth muscle actin cytockeleton and may regulate the contractive capacity of smooth muscle cells. HDAC8 is also involved in the metabolic control of the estrogen receptor related receptor (ERR)-alpha/peroxisome proliferator activated receptor (PPAR) gamma coactivator 1 alpha (PGC1-alpha) transcriptional complex as well as in the development of neuroblastoma and T-cell lymphoma. HDAC8-selective small-molecule inhibitors could be a therapeutic drug option for these diseases. 364 matched cddid_all.tbl CDD cd10001 cd10001 212525 HDAC_classII_APAH Histone deacetylase class IIa. This subfamily includes bacterial acetylpolyamine amidohydrolase (APAH) as well as other Class II histone deacetylase (HDAC) and related proteins. Deacetylases of class II are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) and possibly other proteins to yield deacetylated histones/other proteins. Mycoplana ramosa APAH exhibits broad substrate specificity and catalyzes the deacetylation of polyamines such as putrescine, spermidine, and spermine by cleavage of a non-peptide amide bond. 298 matched cddid_all.tbl CDD cd10002 cd10002 212526 HDAC10_HDAC6-dom1 Histone deacetylase 6, domain 1 and histone deacetylase 10. Histone deacetylases 6 and 10 are class IIb Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDACs usually act via association with DNA binding proteins to target specific chromatin regions. HDAC6 is the only histone deacetylase with internal duplication of two catalytic domains which appear to function independently of each other, and also has a C-terminal ubiquitin-binding domain. It is located in the cytoplasm and associates with microtubule motor complex, functioning as the tubulin deacetylase and regulating microtubule-dependent cell motility. HDAC10 has an N-terminal deacetylase domain and a C-terminal pseudo-repeat that shares significant similarity with its catalytic domain. It is located in the nucleus and cytoplasm, and is involved in regulation of melanogenesis. It transcriptionally down-regulates thioredoxin-interacting protein (TXNIP), leading to altered reactive oxygen species (ROS) signaling in human gastric cancer cells. Known interaction partners of HDAC6 are alpha tubulin (substrate) and ubiquitin-like modifier FAT10 (also known as Ubiquitin D or UBD) while interaction partners of HDAC10 are Pax3, KAP1, hsc70 and HDAC3 proteins. 336 matched cddid_all.tbl CDD cd10003 cd10003 212527 HDAC6-dom2 Histone deacetylase 6, domain 2. Histone deacetylase 6 is a class IIb Zn-dependent enzyme that catalyzes hydrolysis of N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDACs usually act via association with DNA binding proteins to target specific chromatin regions. HDAC6 is the only histone deacetylase with internal duplication of two catalytic domains which appear to function independently of each other, and also has a C-terminal ubiquitin-binding domain. It is located in the cytoplasm and associates with microtubule motor complex, functioning as the tubulin deacetylase and regulating microtubule-dependent cell motility. Known interaction partners of HDAC6 are alpha tubulin and ubiquitin-like modifier FAT10 (also known as Ubiquitin D or UBD). 350 matched cddid_all.tbl CDD cd10004 cd10004 212528 RPD3-like reduced potassium dependency-3 (RPD3)-like. Proteins of the Rpd3-like family are class I Zn-dependent Histone deacetylases that catalyze hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). RPD3 is the yeast homolog of class I HDACs. The main function of RPD3-like group members is regulation of a number of different processes through protein (mostly different histones) modification (deacetylation). This group includes fungal RPD3 and acts via the formation of large multiprotein complexes. Members of this group are involved in cell cycle regulation, DNA damage response, embryonic development and cytokine signaling important for immune response. Histone deacetylation by yeast RPD3 represses genes regulated by the Ash1 and Ume6 DNA-binding proteins. In mammals, they are known to be involved in progression of various tumors. Specific inhibitors of mammalian histone deacetylases could be a therapeutic drug option. 375 matched cddid_all.tbl CDD cd10005 cd10005 212529 HDAC3 Histone deacetylase 3 (HDAC3). HDAC3 is a Zn-dependent class I histone deacetylase that catalyzes hydrolysis of N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. In order to target specific chromatin regions, HDAC3 can interact with DNA-binding proteins (transcriptional factors) either directly or after forming complexes with a number of other proteins, as observed for the SMPT/N-CoR complex which recruits human HDAC3 to specific chromatin loci and activates deacetylation. Human HDAC3 is also involved in deacetylation of non-histone substrates such as RelA, SPY and p53 factors. This protein can also down-regulate p53 function and subsequently modulate cell growth and apoptosis. This gene is therefore regarded as a potential tumor suppressor gene. HDAC3 plays a role in various physiological processes, including subcellular protein localization, cell cycle progression, cell differentiation, apoptosis and survival. HDAC3 has been found to be overexpressed in some tumors including leukemia, lung carcinoma, colon cancer and maxillary carcinoma. Thus, inhibitors precisely targeting HDAC3 (in some cases together with retinoic acid or hyperthermia) could be a therapeutic drug option. 381 matched cddid_all.tbl CDD cd10006 cd10006 212530 HDAC4 Histone deacetylase 4. Histone deacetylase 4 is a class IIa Zn-dependent enzyme that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Class IIa histone deacetylases are signal-dependent co-repressors, having N-terminal regulatory domain with two or three conserved serine residues; phosphorylation of these residues is important for ability to shuttle between the nucleus and cytoplasm and act as transcriptional co-repressors. HDAC4 participates in regulation of chondrocyte hypertrophy and skeletogenesis. However, biological substrates for HDAC4 have not been identified; only low lysine deacetylation activity has been demonstrated and active site mutant has enhanced activity toward acetylated lysines. HDAC4 does not bind DNA directly, but through transcription factors MEF2C (myocyte enhancer factor-2C) and MEF2D. Other known interaction partners of the protein are 14-3-3 proteins, SMRT and N-CoR co-repressors, BCL6, HP1, SUMO-1 ubiquitin-like protein, and ANKRA2. It appears to interact in a multiprotein complex with RbAp48 and HDAC3. Furthermore, HDAC4 is required for TGFbeta1-induced myofibroblastic differentiation. 409 matched cddid_all.tbl CDD cd10007 cd10007 212531 HDAC5 Histone deacetylase 5. Histone deacetylase 5 is a class IIa Zn-dependent enzyme that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Class IIa histone deacetylases are signal-dependent co-repressors, having N-terminal regulatory domain with two or three conserved serine residues; phosphorylation of these residues is important for ability to shuttle between the nucleus and cytoplasm and act as transcriptional co-repressors. HDAC5 is involved in integration of chronic drug (cocaine) addiction and depression with changes in chromatin structure and gene expression; cocaine regulates HDAC5 function to antagonize the rewarding impact of cocaine, possibly by blocking drug-stimulated gene expression that supports drug-induced behavioral change. It is also involved in regulation of angiogenesis and cell cycle as well as immune system development. HDAC5 and HDAC9 have been found to be significantly up-regulated in high-risk medulloblastoma compared with low-risk and may potentially be novel drug targets. 420 matched cddid_all.tbl CDD cd10008 cd10008 212532 HDAC7 Histone deacetylase 7. Histone deacetylase 7 is a class IIa Zn-dependent enzyme that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Class IIa histone deacetylases are signal-dependent co-repressors, having N-terminal regulatory domain with two or three conserved serine residues; phosphorylation of these residues is important for ability to shuttle between the nucleus and cytoplasm and act as transcriptional co-repressors. HDAC7 is involved in regulation of myocyte migration and differentiation. Known interaction partners of class IIa HDAC7 are myocyte enhancer factors - MEF2A, -2C, and -2D, 14-3-3 proteins, SMRT and N-CoR co-repressors, HDAC3, ETA (endothelin receptor). This enzyme is also involved in the development of the immune system as well as brain and heart development. Multiple alternatively spliced transcript variants encoding several isoforms have been found for this gene. 378 matched cddid_all.tbl CDD cd10009 cd10009 212533 HDAC9 Histone deacetylase 9. Histone deacetylase 9 is a class IIa Zn-dependent enzyme that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Class IIa histone deacetylases are signal-dependent co-repressors, they have N-terminal regulatory domain with two or three conserved serine residues, phosphorylation of these residues is important for ability to shuttle between the nucleus and cytoplasm and act as transcriptional co-repressors. HDAC9 is involved in regulation of gene expression and dendritic growth in developing cortical neurons. It also plays a role in hematopoiesis. Its deregulated expression may be associated with some human cancers. HDAC5 and HDAC9 have been found to be significantly up-regulated in high-risk medulloblastoma compared with low-risk and may potentially be novel drug targets. 379 matched cddid_all.tbl CDD cd10010 cd10010 212534 HDAC1 Histone deacetylase 1 (HDAC1). Histone deacetylase 1 (HDAC1) is a Zn-dependent class I enzyme that catalyzes hydrolysis of N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDAC1 is involved in regulation through association with DNA binding proteins to target specific chromatin regions. In particular, HDAC1 appears to play a major role in pre-implantation embryogenesis in establishing a repressive chromatin state. Its interaction with retinoblastoma tumor-suppressor protein is essential in the control of cell proliferation and differentiation. Together with metastasis-associated protein-2 (MTA2), it deacetylates p53, thereby modulating its effect on cell growth and apoptosis. It participates in DNA-damage response, along with HDAC2; together, they promote DNA non-homologous end-joining. HDAC1 is also involved in tumorogenesis; its overexpression modulates cancer progression. Specific inhibitors of HDAC1 are currently used in cancer therapy. 371 matched cddid_all.tbl CDD cd10011 cd10011 212535 HDAC2 Histone deacetylase 2 (HDAC2). Histone deacetylase 2 (HDAC2) is a Zn-dependent class I enzyme that catalyzes hydrolysis of N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDAC2 is involved in regulation through association with DNA binding proteins to target specific chromatin regions. It forms transcriptional repressor complexes by associating with several proteins, including the mammalian zinc-finger transcription factor YY1, thus playing an important role in transcriptional regulation, cell cycle progression and developmental events. Additionally, a few non-histone HDAC2 substrates have been found. HDAC2 plays a role in embryonic development and cytokine signaling important for immune response, and is over-expressed in several solid tumors including oral, prostate, ovarian, endometrial and gastric cancer. It participates in DNA-damage response, along with HDAC1; together, they can promote DNA non-homologous end-joining. HDAC2 is considered an important cancer prognostic marker. Inhibitors specifically targeting HDAC2 could be a therapeutic drug option. 366 matched cddid_all.tbl CDD cd10013 cd10013 193609 Cas3''_I CRISPR/Cas system-associated protein Cas3''. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA; HD-like nuclease, specifically digesting double-stranded oligonucleotides and preferably cleaving at G:C pairs; signature gene for Type I 188 matched cddid_all.tbl CDD cd10014 cd10014 199900 TFIIA_gamma_C Gamma subunit of transcription initiation factor IIA, C-terminal domain. Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of the TATA-binding protein (TBP) for DNA, in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from TATA-less promoters. TFIIA is composed of more than one subunit in various organisms. Mammalian TFIIA large subunits (TFIIA alpha and beta), and the smaller subunit (TFIIA gamma) form a heterotrimer. TFIIA alpha and beta are encoded by a single TFIIA_alpha_beta gene and post-translationally processed and cleaved. TOA1 and TOA2 are the two subunits of Yeast TFIIA which correspond to Mammalian TFIIA_alpha_beta and TFIIA gamma, respectively. TOA1 and TOA2 form a heterodimeric protein complex. The TFIIA gamma subunit is highly conserved between humans, Drosophila and yeast and it is required for TFIIA function. The C-terminal domain of the gamma (TFIIA_gamma_C) subunit forms a beta-barrel structure together with TFIIA beta. 47 matched cddid_all.tbl CDD cd10015 cd10015 197381 BfiI_C_EcoRII_N_B3 DNA binding domains of BfiI, EcoRII and plant B3 proteins. This family contains the N-terminal DNA binding domain of type IIE restriction endonuclease EcoRII-like proteins, the C-terminal DNA binding domain of type IIS restriction endonuclease BfiI-like proteins and plant-specific B3 proteins. Type II restriction endonucleases are components of restriction modification (RM) systems that protect bacteria and archaea against invading foreign DNA. They usually function as homodimers or homotetramers that cleave DNA at defined sites of 4 to 8 bp in length, and they require Mg2+, not ATP or GTP, for catalysis. EcoRII is specific for the 5'-CCWGG sequence (W stands for A or T). EcoRII consists of 2 domains, the C-terminal catalytic/dimerization domain (EcoRII-C), and the N-terminal effector DNA binding domain (EcoRII-N). BfiI is unique in cleaving DNA at fixed positions downstream of an asymmetric sequence in the absence of Mg2+. BfiI consists of two discrete domains with distinct functions: an N-terminal catalytic domain with non-specific nuclease activity and dimerization function that is more closely related to Nuc, an EDTA-resistant nuclease from the phospholipase D (PLD) superfamily; and a C-terminal domain that specifically recognizes its target sequences, 5'-ACTGGG-3'. B3 proteins are a family of plant-specific transcription factors, involved in a great variety of processes, including seed development and auxin response. 109 matched cddid_all.tbl CDD cd10016 cd10016 197382 EcoRII_N N-terminal domain of type IIE restriction endonuclease EcoRII and similar proteins. N-terminal domain of type IIE restriction endonuclease EcoRII and similar proteins. Type II restriction endonucleases are components of restriction modification (RM) systems that protect bacteria and archaea against invading foreign DNA. They usually function as homodimers or homotetramers that cleave DNA at defined sites of 4 to 8 bp in length, and they require Mg2+, not ATP or GTP, for catalysis. EcoRII is specific for the 5'-CCWGG sequence (W stands for A or T). EcoRII consists of 2 domains, the C-terminal catalytic/dimerization domain (EcoRII-C), and the N-terminal effector DNA binding domain (EcoRII-N). To be catalytically active, EcoRII has to form a dimer. 142 matched cddid_all.tbl CDD cd10017 cd10017 197383 B3_DNA Plant-specific B3-DNA binding domain. The plant-specific B3 DNA binding domain superfamily includes the well-characterized auxin response factor (ARF) and the LAV (Leafy cotyledon2 [LEC2]-Abscisic acid insensitive3 [ABI3]-VAL) families, as well as the RAV (Related to ABI3 and VP1) and REM (REproductive Meristem) families. LEC2 and ABI3 have been shown to be involved in seed development, while other members of the LAV family seem to have a more general role, being expressed in many organs during plant development. Members of the ARF family bind to the auxin response element and depending on presence of an activation or repression domain, they activate or repress transcription. RAV and REM families are less studied B3 protein famillies. 98 matched cddid_all.tbl CDD cd10018 cd10018 197384 BfiI_C C-terminal domain of type IIs restriction endonuclease BfiI and similar proteins. C-terminal domain of a novel type IIs restriction endonuclease BfiI and similar proteins. Type II restriction endonucleases are components of restriction modification (RM) systems that protect bacteria and archaea against invading foreign DNA. They usually function as homodimers or homotetramers that cleave DNA at defined sites of 4 to 8 bp in length, and they require Mg2+, not ATP or GTP, for catalysis. Unlike all other restriction enzymes known to date, BfiI is unique in cleaving DNA at fixed positions downstream of an asymmetric sequence in the absence of Mg2+. BfiI consists of two discrete domains with distinct functions: an N-terminal catalytic domain with non-specific nuclease activity and dimerization function that is more closely related to Nuc, an EDTA-resistant nuclease from the phospholipase D (PLD) superfamily; and a C-terminal domain that specifically recognizes its target sequences, 5'-ACTGGG-3'. BfiI presumably evolved through domain fusion of a DNA recognition domain to the catalytic Nuc-like domain from the PLD superfamily. BfiI forms a functionally active homodimer which has two DNA-binding surfaces located at the C-terminal domains but only one active site, located at the dimer interface between the two N-terminal catalytic domains. 157 matched cddid_all.tbl CDD cd10019 cd10019 206756 14-3-3_sigma 14-3-3 sigma, an isoform of 14-3-3 protein. 14-3-3 protein sigma isoform, also known as stratifin or human mammary epithelial marker (HME) 1, has been most directly linked to tumor development. In humans, it is expressed by the SFN gene, strictly in stratified squamous epithelial cells in response to DNA damage where it is transcriptionally induced in a p53-dependent manner, subsequently causing cell-cycle arrest at the G2/M checkpoint. Up-regulation and down-regulation of 14-3-3 sigma expression have both been described in tumors. For example, in human breast cancer, 14-3-3 sigma is predominantly down-regulated by CpG methylation, acting as both a tumor suppressor and a prognostic indicator, while in human scirrhous-type gastric carcinoma (SGC), it is up-regulated and may play an important role in SGC carcinogenesis and progression. Loss of 14-3-3 sigma expression sensitizes tumor cells to treatment with conventional cytostatic drugs, making this protein an attractive therapeutic target. 14-3-3 domains are an essential part of 14-3-3 proteins, a ubiquitous class of regulatory, phosphoserine/threonine-binding proteins found in all eukaryotic cells, including yeast, protozoa and mammalian cells. 242 matched cddid_all.tbl CDD cd10020 cd10020 206757 14-3-3_epsilon 14-3-3 epsilon, an isoform of 14-3-3 protein. 14-3-3 protein epsilon isoform (isoform (also known as tyrosine 3-monooxygenase/ tryptophan 5-monooxygenase activation protein, epsilon polypeptide) is encoded by the YWHAE gene in humans and is involved in cancer cell survival and growth. It interacts with CDC25 phosphatases, RAF1 and IRS1 proteins, suggesting its role in diverse biochemical activities related to signal transduction, such as cell division and regulation of insulin sensitivity. Overexpression of 14-3-3 epsilon in primary hepatocellular carcinoma (HCC) tissues predicts a high risk of extrahepatic metastasis and worse survival, and is a potential therapeutic target. It has also been implicated in the pathogenesis of small cell lung cancer. 14-3-3 epsilon overexpression protects colorectal cancer and endothelial cells from oxidative stress-induced apoptosis, while its suppression by non-steroidal anti-inflammatory drugs induces cancer and endothelial cell death. Cellular levels of 14-3-3 epsilon could possibly serve as an important regulator of cell survival in response to oxidative stress and other death signals. 14-3-3 domains are an essential part of 14-3-3 proteins, a ubiquitous class of regulatory, phosphoserine/threonine-binding proteins found in all eukaryotic cells, including yeast, protozoa and mammalian cells. 230 matched cddid_all.tbl CDD cd10022 cd10022 206758 14-3-3_beta_zeta 14-3-3 beta and zeta isoforms of 14-3-3 protein. 14-3-3 protein beta and zeta isoform (also known as tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta and zeta polypeptide) are encoded by the YWHAB gene and YWHAZ gene in humans. They have been linked to mitogenic signaling and the cell cycle machinery, and to cancer initiation and progression, respectively. The beta isoform has been shown to interact with RAF1 and CDC25 phosphatases and its overexpression is associated with invasion, migration, metastasis and proliferation of tumor cells and its elevated levels are correlated with tumor size, the number of lymph node metastases and a reduced survival rate. It is significantly overexpressed in lung cancer tissues, mutated chronic lymphocytic leukemia (M-CLL), gastric cancer tissues, aflatoxin B1-induced rat hepatocellular carcinoma K1 and K2 cells, as well as renal cell carcinoma cysts, and can potentially be used as a diagnostic and prognostic biomarker in the cancer. Numerous proteins involved in anti-apoptosis and tumor progression were also found to be differentially expressed in gastric cancer cells where 14-3-3 beta is overexpressed. 14-3-3 beta also interacts with human Dapper1 (hDpr1), a key negative regulator of Wnt signaling, via hDpr1 phosphorylation by protein kinase A, thus attenuating the ability of hDpr1 to promote Dishevelled (Dvl) degradation, and subsequently enhancing Wnt signaling. The zeta isoform is ubiquitously expressed and localized to most subcellular regions, including the cytoplasm, plasma membrane, mitochondria, and nucleus. Its overexpression and gene amplification in multiple cancers are correlated with poor prognosis and chemoresistance in cancer patients. 14-3-3 zeta has been identified as a biomarker with high sensitivity and specificity for diagnosis and prognosis in multiple tumor types, including hepatocellular carcinoma, head and neck cancer, indicating a potential clinical application for using 14-3-3 zeta in selecting treatment options and predicting cancer outcome. It also interacts with IRS1 protein, suggesting a role in regulating insulin sensitivity. 14-3-3 domains are an essential part of 14-3-3 proteins, a ubiquitous class of regulatory, phosphoserine/threonine-binding proteins found in all eukaryotic cells, including yeast, protozoa and mammalian cells. 229 matched cddid_all.tbl CDD cd10023 cd10023 206759 14-3-3_theta 14-3-3 theta/tau (theta in mice, tau in human), an isoform of 14-3-3 protein. 14-3-3 tau/theta (tau in humans, theta in mice) isoform (also known as tyrosine 3-monooxygenase/ tryptophan 5-monooxygenase activation protein, theta polypeptide) is encoded by the YWHAQ gene in humans and plays an important role in controlling apoptosis through interactions with ASK1, c-jun NH-terminal kinase, and p38 mitogen-activated protein kinase (MAPK). Its interaction with CDC25c regulates entry into the cell cycle and subsequent interaction with Bad prevents apoptosis. 14-3-3 theta protein expression is induced in patients with amyotrophic lateral sclerosis. 14-3-3 tau is often overexpressed in breast cancer, which is associated with the downregulation of p21, a p53 target gene, and thus leads to tamoxifen resistance in MCF7 breast cancer cells and shorter patient survival. Therefore, 14-3-3 tau may be a potential therapeutic target in breast cancer. Additionally, 14-3-3 theta mediates nucleocytoplasmic shuttling of the coronavirus nucleocapsid protein which causes severe acute respiratory syndrome. 14-3-3 domain is an essential part of 14-3-3 proteins, a ubiquitous class of regulatory, phosphoserine/threonine-binding proteins found in all eukaryotic cells, including yeast, protozoa and mammalian cells. 234 matched cddid_all.tbl CDD cd10024 cd10024 206760 14-3-3_gamma 14-3-3 gamma, an isoform of 14-3-3 protein. 14-3-3 gamma isoform (also known as tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, gamma polypeptide) is encoded by the YWHAG gene in humans and is induced by growth factors in human vascular smooth muscle cells. It is also highly expressed in skeletal and heart muscles, suggesting an important role in muscle tissue. It has been shown to interact with RAF1 and protein kinase C, proteins involved in various signal transduction pathways. 14-3-3 gamma mediates Cdc25A proteolysis to block premature mitotic entry after DNA damage. 14-3-3 gamma mediates the interaction between Chk1 and Cdc25A; this complex has an essential function in Cdc25A phosphorylation and degradation to block premature mitotic entry after DNA damage. Increased expression of 14-3-3 gamma in lung cancer coincides with loss of functional p53, possibly in a cooperative manner promoting genomic instability. Also, during cell cycle, 14-3-3 gamma protects p21, a cyclin-dependent kinase inhibitor, from degradation mediated by the p53 suppressor MDMX, which may account for elevation of p21 levels independent of p53 and in response to DNA damage. Elevated expression of 14-3-3 gamma in human hepatocellular carcinoma predicts extrahepatic metastasis and worse survival, thus making this protein a candidate biomarker and a potential target for novel therapies against the disease. 246 matched cddid_all.tbl CDD cd10025 cd10025 206761 14-3-3_eta 14-3-3 eta, an isoform of 14-3-3 protein. 14-3-3 eta isoform (also known as tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide) is expressed mainly in brain, and is involved in hypothalamic-pituitary-adrenocortical (HPA) axis regulation. In humans, it is encoded by the YWHAH gene, and is a positional and functional candidate for schizophrenia as well as bipolar disorder (BP). This gene contains a 7 bp repeat sequence in its 5' Untranslated Region (UTR), and early-onset schizophrenia has been associated with changes in the number of this repeat. 14-3-3 eta and gamma are found in the serum and synovial fluid of patients with joint inflammation. Specifically, 14-3-3 eta, which plays a regulatory role in chondrogenic differentiation, is significantly overexpressed in juvenile rheumatoid arthritis (JRA), a chronic inflammatory disease often associated with growth impairment. Overexpression of Gremlin 1, the bone morphogenetic protein antagonist, may play an oncogenic role in carcinomas of the uterine cervix, lung, ovary, kidney, breast, colon, pancreas, and sarcoma, since it functions by interaction with the 14-3-3 eta domain. Therefore, Gremlin 1 and its binding protein 14-3-3 eta could be appropriate targets for developing diagnostic and therapeutic strategies against human cancers. 14-3-3 domain is an essential part of 14-3-3 proteins, a ubiquitous class of regulatory, phosphoserine/threonine-binding proteins found in all eukaryotic cells, including yeast, protozoa and mammalian cells. 239 matched cddid_all.tbl CDD cd10026 cd10026 206762 14-3-3_plant Plant 14-3-3 protein domain. Plant 14-3-3 isoforms, similar to their highly conserved homologs in mammals, bind to phosphorylated target proteins to modulate their function. They have been implicated in a variety of physiological functions; in particular, abiotic and biotic stress responses, primary metabolism, as well as various aspects of plant growth and development. They function through the regulation of a diverse range of proteins including transcription factors, kinases, structural proteins, ion channels as well as pathogen defense-related proteins. The 14-3-3 proteins are affected transcriptionally as well as functionally by the environment of the plant, both intracellular and extracellular, thus playing a key role in the response to environmental stress, pathogens and light conditions. Plant 14-3-3 proteins have been divided into epsilon-like groups and non-epsilon groups based on phylogenetic clustering. They have a varying number of isoforms (for example, Arabidopsis has thirteen known protein isoforms, cotton has six) with variation in their affinity for specific binding partners, suggesting specific roles in specific processes. 237 matched cddid_all.tbl CDD cd10027 cd10027 381678 UDG-F1-like Uracil DNA glycosylase family 1 subfamily, includes Human uracil DNA glycosylase and similar proteins. Uracil DNA glycosylase family 1 is the most efficient of all uracil-DNA glycosylases (UDGs, also known as UNGs) and shows a specificity for uracil in DNA. UDG catalyzes the removal of uracil from DNA to initiate the DNA base excision repair pathway. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or deamination of cytosine. Uracil mispaired with guanine in DNA is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. 200 matched cddid_all.tbl CDD cd10028 cd10028 381679 UDG-F2_TDG_MUG Uracil DNA glycosylase family 2, includes thymine DNA glycosylase, mismatch-specific uracil DNA glycosylase and similar proteins. Uracil DNA glycosylase family 2 consists of thymine DNA glycosylase (TDG), which removes uracil and thymine from G:U and G:T mismatches in double-stranded DNA. It includes mismatch-specific uracil DNA glycosylase (MUG), the prokaryotic homolog of TDG. Escherichia coli MUG is highly specific to G:U mismatches but also repairs G:T mismatches at high enzyme concentration. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil in DNA can arise as a result of misincorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other.. 163 matched cddid_all.tbl CDD cd10030 cd10030 381680 UDG-F4_TTUDGA_SPO1dp_like Uracil DNA glycosylase family 4, includes Thermotoga maritima TTUDGA, Bacillus phage SPO1 DNA polymerase, and similar proteins. Uracil DNA glycosylase family 4 includes Thermotoga maritima TTUDGA, a robust uracil DNA glycosylase that shares narrow substrate specificity and high catalytic efficiency with family 1, acting on double-stranded and single-stranded uracil-containing DNA. Members of this family possess four conserved cysteine residues required to coordinate the [4Fe-4S] iron-sulfur cluster. This family also includes the N-terminal domain of Bacillus phage SPO1 DNA polymerase. Bacteriophage SPO1 is one of a group of large, lytic, tailed bacteriophages of Bacillus subtilis, and contains hydroxymethyluracil (hmUra) in place of thymine in their DNA. It has been speculated that this UDG domain may help discriminate between hmUra containing SPO1 DNA and thymine-containing host DNA. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. 165 matched cddid_all.tbl CDD cd10031 cd10031 381681 UDG-F5_TTUDGB_like Uracil DNA glycosylase family 5, includes Thermotoga maritima TTUDGB and similar proteins. Uracil DNA glycosylase family 5 includes Thermus thermophilus HB8 TTUDGB (also called UDGb) which is not only a UDG acting on double-stranded uracil-containing DNA, but also a hypoxanthine DNA glycosylase acting on double-stranded hypoxanthine-containing DNA (except for the C/I base pair), as well as a xanthine DNA glycosylase acting on both, double-stranded and single-stranded xanthine-containing DNA. TTUDGB also excises thymine from G:T mismatched DNA, and removes analogs of uracil from DNA, including 5-hydroxymethyluracil (hmU) and 5-fluorouracil (fU). This subfamily also contains Bradyrhizobium diazoefficiens family 5 homolog Blr5068 (UdgB) which has been found to efficiently excise uracil from ssDNA and dsDNA. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Similar to family 4 UDGs, members of this family possess four conserved cysteine residues required to coordinate the [4Fe-4S] iron-sulfur cluster. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. 204 matched cddid_all.tbl CDD cd10032 cd10032 381682 UDG-F6_HDG Uracil DNA glycosylase family 6, includes hypoxanthine-DNA glycosylase and similar proteins. Uracil DNA glycosylase family 6 hypoxanthine-DNA glycosylase (HDG) lacks any detectable UDG activity; it excises hypoxanthine, a deamination product of adenine, from double-stranded DNA. Uracil-DNA glycosylase (UDGs) initiates repair of uracils in DNA. Uracil in DNA can arise as a result of misincorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. 141 matched cddid_all.tbl CDD cd10033 cd10033 381683 UDG_like uncharacterized family of the uracil-DNA glycosylase superfamily. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil may arise from mis-incorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations; thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. UDG family 1 is the most efficient uracil-DNA glycosylase (UDG, also known as UNG) and shows a specificity for uracil in DNA. UDG family 2 includes thymine DNA glycosylase which removes uracil and thymine from G:U and G:T mismatches, and mismatch-specific uracil DNA glycosylase (MUG) which in Escherichia coli is highly specific to G:U mismatches but also repairs G:T mismatches at high enzyme concentration. UDG family 3 includes Human SMUG1 which can remove uracil and its oxidized pyrimidine derivatives from, single-stranded DNA and double-stranded DNA with a preference for single-stranded DNA. Pedobacter heparinus SMUG2, which is UDG family 3 SMUG1-like, displays catalytic activities towards DNA containing uracil or hypoxanthine/xanthine. UDG family 4 includes Thermotoga maritima TTUDGA, a robust UDG which like family 1, acts on double-stranded and single-stranded uracil-containing DNA. UDG family 5 (UDGb) includes Thermus thermophilus HB8 TTUDGB which acts on double-stranded uracil-containing DNA; it is a hypoxanthine DNA glycosylase acting on double-stranded hypoxanthine-containing DNA except for the C/I base pair, as well as a xanthine DNA glycosylase which acts on both double-stranded and single-stranded xanthine-containing DNA. UDG family 6 hypoxanthine-DNA glycosylase lacks any detectable UDG activity; it excises hypoxanthine. Other UDG families include one represented by Bradyrhizobium diazoefficiens Blr0248 which prefers single-stranded DNA and removes uracil, 5-hydroxymethyl-uracil or xanthine from it. 171 matched cddid_all.tbl CDD cd10034 cd10034 381684 UDG_BdiUng_like Uracil DNA glycosylase family which includes Bradyrhizobium diazoefficiens Blr0248 (BdiUng) and similar proteins. Bradyrhizobium diazoefficiens (previously B. japonicum) Blr0248 uracil-DNA glycosylase (BdiUng) has broad substrate specificity, preferring single-stranded DNA and removing uracil, 5-hydroxymethyl-uracil or xanthine from it. BdiUng is impervious to inhibition by AP DNA, and Ugi protein that specifically inhibits conventional family 1 UDGs. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. 181 matched cddid_all.tbl CDD cd10035 cd10035 381685 UDG_like uncharacterized family of the uracil-DNA glycosylase superfamily. Uracil-DNA glycosylases (UDGs) initiate repair of uracils in DNA. Uracil may arise from misincorporation of dUMP residues by DNA polymerase or via deamination of cytosine. Uracil in DNA mispaired with guanine is one of the major pro-mutagenic events, causing G:C->A:T mutations; thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. UDG family 1 is the most efficient uracil-DNA glycosylase (UDG, also known as UNG) and shows a specificity for uracil in DNA. UDG family 2 includes thymine DNA glycosylase which removes uracil and thymine from G:U and G:T mismatches, and mismatch-specific uracil DNA glycosylase (MUG) which in Escherichia coli is highly specific to G:U mismatches, but also repairs G:T mismatches at high enzyme concentration. UDG family 3 includes Human SMUG1 which can remove uracil and its oxidized pyrimidine derivatives from, single-stranded DNA and double-stranded DNA with a preference for single-stranded DNA. Pedobacter heparinus SMUG2, which is UDG family 3 SMUG1-like, displays catalytic activities towards DNA containing uracil or hypoxanthine/xanthine. UDG family 4 includes Thermotoga maritima TTUDGA, a robust UDG which like family 1, acts on double-stranded and single-stranded uracil-containing DNA. UDG family 5 (UDGb) includes Thermus thermophilus HB8 TTUDGB which acts on double-stranded uracil-containing DNA; it is a hypoxanthine DNA glycosylase acting on double-stranded hypoxanthine-containing DNA except for the C/I base pair, as well as a xanthine DNA glycosylase which acts on both double-stranded and single-stranded xanthine-containing DNA. UDG family 6 hypoxanthine-DNA glycosylase lacks any detectable UDG activity; it excises hypoxanthine. Other UDG families include one represented by Bradyrhizobium diazoefficiens Blr0248 which prefers single-stranded DNA and removes uracil, 5-hydroxymethyl-uracil or xanthine from it. 143 matched cddid_all.tbl CDD cd10036 cd10036 197344 Reelin_subrepeat_Nt Additional N-terminal subrepeat of reelin. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. Some family members appear to have an additional subrepeat at the N-terminus as characterized in this model. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). Genetic deficiency of reelin, or ApoER2 and VLDLR, or Dab1, all exhibit the same phenotypes, including ataxia, cortical layer inversion and abnormal positioning patterns. 151 matched cddid_all.tbl CDD cd10037 cd10037 197345 Reelin_repeat_1_subrepeat_1 N-terminal subrepeat of tandem repeat unit 1 of reelin and related proteins. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the N-terminal subrepeat, which directly contacts the C-terminal subrepeat and the EGF domain in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). 146 matched cddid_all.tbl CDD cd10038 cd10038 197346 Reelin_repeat_2_subrepeat_1 N-terminal subrepeat of tandem repeat unit 2 of reelin and related proteins. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the N-terminal subrepeat, which directly contacts the C-terminal subrepeat and the EGF domain in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). 168 matched cddid_all.tbl CDD cd10039 cd10039 197347 Reelin_repeat_3_subrepeat_1 N-terminal subrepeat of tandem repeat unit 3 of reelin and related proteins. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the N-terminal subrepeat, which directly contacts the C-terminal subrepeat and the EGF domain in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). 170 matched cddid_all.tbl CDD cd10040 cd10040 197348 Reelin_repeat_4_subrepeat_1 N-terminal subrepeat of tandem repeat unit 4 of reelin and related proteins. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the N-terminal subrepeat, which directly contacts the C-terminal subrepeat and the EGF domain in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). 170 matched cddid_all.tbl CDD cd10041 cd10041 197349 Reelin_repeat_5_subrepeat_1 N-terminal subrepeat of tandem repeat unit 5 of reelin and related proteins. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the N-terminal subrepeat, which directly contacts the C-terminal subrepeat and the EGF domain in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). 174 matched cddid_all.tbl CDD cd10042 cd10042 197350 Reelin_repeat_6_subrepeat_1 N-terminal subrepeat of tandem repeat unit 6 of reelin and related proteins. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the N-terminal subrepeat, which directly contacts the C-terminal subrepeat and the EGF domain in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). 157 matched cddid_all.tbl CDD cd10043 cd10043 197351 Reelin_repeat_7_subrepeat_1 N-terminal subrepeat of tandem repeat unit 7 of reelin and related proteins. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the N-terminal subrepeat, which directly contacts the C-terminal subrepeat and the EGF domain in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). 171 matched cddid_all.tbl CDD cd10044 cd10044 197352 Reelin_repeat_8_subrepeat_1 N-terminal subrepeat of tandem repeat unit 8 of reelin and related proteins. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the N-terminal subrepeat, which directly contacts the C-terminal subrepeat and the EGF domain in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). 176 matched cddid_all.tbl CDD cd10045 cd10045 197353 Reelin_repeat_1_subrepeat_2 C-terminal subrepeat of tandem repeat unit 1 of reelin and related proteins. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the C-terminal subrepeat, which directly contacts the N-terminal subrepeat and the EGF domain in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). 155 matched cddid_all.tbl CDD cd10046 cd10046 197354 Reelin_repeat_2_subrepeat_2 C-terminal subrepeat of tandem repeat unit 2 of reelin and related proteins. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the C-terminal subrepeat, which directly contacts the N-terminal subrepeat and the EGF domain in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). 156 matched cddid_all.tbl CDD cd10047 cd10047 197355 Reelin_repeat_3_subrepeat_2 C-terminal subrepeat of tandem repeat unit 3 of reelin and related proteins. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the C-terminal subrepeat, which directly contacts the N-terminal subrepeat and the EGF domain in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). 151 matched cddid_all.tbl CDD cd10048 cd10048 197356 Reelin_repeat_4_subrepeat_2 C-terminal subrepeat of tandem repeat unit 4 of reelin and related proteins. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the C-terminal subrepeat, which directly contacts the N-terminal subrepeat and the EGF domain in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). 150 matched cddid_all.tbl CDD cd10049 cd10049 197357 Reelin_repeat_5_subrepeat_2 C-terminal subrepeat of tandem repeat unit 5 of reelin and related proteins. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the C-terminal subrepeat, which directly contacts the N-terminal subrepeat and the EGF domain in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). 150 matched cddid_all.tbl CDD cd10050 cd10050 197358 Reelin_repeat_6_subrepeat_2 C-terminal subrepeat of tandem repeat unit 6 of reelin and related proteins. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the C-terminal subrepeat, which directly contacts the N-terminal subrepeat and the EGF domain in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). 148 matched cddid_all.tbl CDD cd10051 cd10051 197359 Reelin_repeat_7_subrepeat_2 C-terminal subrepeat of tandem repeat unit 7 of reelin and related proteins. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the C-terminal subrepeat, which directly contacts the N-terminal subrepeat and the EGF domain in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). 162 matched cddid_all.tbl CDD cd10052 cd10052 197360 Reelin_repeat_8_subrepeat_2 C-terminal subrepeat of tandem repeat unit 8 of reelin and related proteins. Reelin is an extracellular glycoprotein involved in neuronal development, specifically in the brain cortex. It contains 8 tandemly repeated units, each of which is composed of two highly similar subrepeats and a central EGF domain. This model characterizes the C-terminal subrepeat, which directly contacts the N-terminal subrepeat and the EGF domain in a compact arrangement. Consecutive reelin repeat units are packed together to form an overall rod-like molecular structure. Reelin repeats 5 and 6 are reported to interact with neuronal receptors, the apolipoprotein E receptor 2 (ApoER2) and the very-low-density lipoprotein receptor (VLDLR), triggering a signaling cascade upon binding and subsequent tyrosine phosphorylation of the cytoplasmic disabled-1 (Dab1). 161 matched cddid_all.tbl CDD cd10140 cd10140 380782 PFM_aerolysin_family pore-forming module of aerolysin-type beta-barrel pore-forming proteins. Pore-forming proteins (PFPs) are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta pore-forming proteins (beta-PFPs) form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). Members of this family includes enterolobin, a cytolytic, inflammatory and insecticidal protein from the Brazilian tree Enterolobium contortisiliquum. 92 matched cddid_all.tbl CDD cd10141 cd10141 381074 CopZ-like_Fer2_BFD-like bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain of Archaeoglobus fulgidus CopZ, and similar proteins. Archaeoglobus fulgidus CopZ is a fusion of a redox-active domain (containing a mononuclear metal center and an [2Fe-2S] cluster) with a CXXC-containing copper-binding domain. It is a soluble Cu+ chaperone which delivers cytoplasmic Cu+ to the transmembrane metal-binding sites in the Cu+-ATPase CopA; CopA couples the hydrolysis of ATP to the efflux of cytoplasmic Cu+. In addition to CopZ, the BFD-like [2Fe-2S]-binding domain is found in a variety of other proteins including bacterioferritin-associated ferredoxin (BFD), and the large subunit of NADH-dependent nitrite reductase. It comprises a helix-turn-helix fold, and binds an [2Fe-2S] cluster via 4 highly-conserved Cys residues, found in loops between the alpha-helices. For the class of proteins having a BFD-like [2Fe-2S]-binding domain, the Cys residues are organized in a unique C-X2-C-X31-35-C-X2-9-C-arrangement. [2Fe-2S] clusters are sulfide-linked diiron centers, a primary role for which is electron transport. 58 matched cddid_all.tbl CDD cd10142 cd10142 408998 HD_SAS6_N N-terminal head domain found in spindle assembly abnormal protein 6 and similar proteins. Spindle assembly abnormal protein 6 (SAS6) is a central scaffolding component of the centrioles that ensures their 9-fold symmetry. It is required for centrosome biogenesis and duplication, and is required for both mother-centriole-dependent centriole duplication and deuterosome-dependent centriole amplification in multiciliated cells. It is also required for the recruitment of microcephaly protein STIL to the procentriole and for STIL-mediated centriole amplification. SAS6 is comprised of an N-terminal globular head domain, a centrally located coiled-coil domain, and a disordered C-terminus. These monomers homodimerize symmetrically, through two dimerization domains, the N-terminal globular head domains and long extended alpha-helical coiled-coil regions. These homodimers can self-assemble into a 9-fold symmetric cartwheel structure comprised of nine SAS6 homodimers associated via their head domains; the dimerized coiled-coil domains being the spokes, the central hub being the head domains. This model corresponds to the N-terminal head domain of SAS6, which is structurally related to other XRCC4-superfamily members, XRCC4, PAXX, XLF and CCDC61. 137 matched cddid_all.tbl CDD cd10144 cd10144 381748 Peptidase_S74_CIMCD Peptidase S74 family, C-terminal intramolecular chaperone domain of Escherichia coli phage K1F endosialidase and related proteins. This peptidase S74 family includes C-terminal intramolecular chaperone domain (CIMCD) of Escherichia coli phage K1F endosialidase, Bacillus phage GA-1 neck appendage protein, and Bacteriophage T5 L-shaped tail fibre. This domain acts as a molecular chaperone; during virus particle assembly, the CIMCD of phage tailspike proteins induces the homo-trimerization of phage tailspike proteins by chaperoning the formation of a triple beta-helix. Homo-trimeric phage tailspike proteins are then auto-cleaved by the CIMCD domain. This family also includes the peptidase S74 Intramolecular Chaperone Auto-processing (ICA) domain of mammalian Myrf. The ICA domain drives the homo-oligomerization of Myrf in the endoplasmic reticulum (ER) membrane. The homo-oligomeric Myrf is proteolyzed by the ICA domain, releasing its N-terminal fragments from the ER membrane. 113 matched cddid_all.tbl CDD cd10145 cd10145 199901 TFIIA_gamma_N Gamma subunit of transcription initiation factor IIA, N-terminal helical domain. Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of the TATA-binding protein (TBP) for DNA, in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from TATA-less promoters. TFIIA is composed of more than one subunit in various organisms. Mammalian TFIIA large subunits (TFIIA alpha and beta), and the smaller subunit (TFIIA gamma) form a heterotrimer. TFIIA alpha and beta are encoded by a single TFIIA_alpha_beta gene and post-translationally processed and cleaved. TOA1 and TOA2 are the two subunits of Yeast TFIIA which correspond to Mammalian TFIIA_alpha_beta and TFIIA gamma, respectively. TOA1 and TOA2 form a heterodimeric protein complex. The TFIIA gamma subunit is highly conserved between humans, Drosophila and yeast and it is required for TFIIA function. The N-terminal domain of the gamma subunit forms a 4-helix bundle together with the alpha subunit. 49 matched cddid_all.tbl CDD cd10146 cd10146 199214 LabA_like_C C-terminal domain of LabA_like proteins. This C-terminal domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain an N-terminal LabA-like domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain) has been shown to play a role in cyanobacterial circadian timing. LabA-like C-terminal domains described here may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains). 69 matched cddid_all.tbl CDD cd10147 cd10147 199902 Wzt_C-like C-Terminal domain of O-antigenic polysaccharide transporter protein Wzt and related proteins. The Escherichia coli ABC protein Wzt consists of 2 domains, a conventional ABC domain that binds ATP and utilizes its energy to transport molecules across membranes, and a C terminal domain which is responsible for its target molecule specificity. Wzt is part of the ATP-binding-cassette (ABC) transporter complex, responsible for the transport of the O-antigenic polysaccharide (O-PS) portion of lipopolysaccharide (LPS), a major component of the outer membrane of Gram-negative bacteria. This CD includes Wzt proteins from two Escherichia coli serotypes O8 and O9a, WztO8 and WztO9a; these proteins are specific for their cognate polysaccharides (O8 or O9a O-PS). 144 matched cddid_all.tbl CDD cd10148 cd10148 197385 CsoR-like_DUF156 Transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this domain superfamily was previously known as DUF156. This superfamily includes various transcriptional regulators that respond to stressors including Cu(I), Ni(I), sulfite, and formaldehyde. It includes CsoR (copper-sensitive operon repressor) from Mycobacterium tuberculosis (MtCsoR), Bacillus subtilis (BsCsoR), Thermus thermophilus (TthCsoR), and Staphylococcus aureus (SaCsoR), Mycobacterium tuberculosis RicR (regulated in copper repressor, MtRicR), Escherichia coli RncR (formally known as YohL, nickel and cobalt-sensitive), Alcaligenes xylosoxidans NreA (nickel-sensitive), E. coli FrmR (formally known as YaiN, formaldehyde sensitive), and Staphylococcus aureus CstR (CsoR-like sulfur transferase repressor, NWMN_0026.5, SaCstR). CsoR is Cu(I)-inducible, and regulates the expression of genes involved in copper homeostasis. For example, TthCsoR binds the promoter region of the copZ-csoR-copA operon, and represses expression of these genes, which encode the copper chaperone CopZ, CsoR, and the copper efflux P-type ATPase CopA, respectively. In the presence of excess Cu(I), TthCsoR binds this ion, and is released from the DNA, allowing expression of the downstream genes. TthCsoR also senses other metal ions such as Cu(II), Zn(II), Ag(I), Cd(II) and Ni(II). CsoRs form a homotetramer (dimer of dimers). In the case of MtCsoR, two Cys residues on opposite subunits within each dimer, along with a His residue, bind the Cu(I) ion. These residues are conserved in the majority of members of this superfamily. Exceptions include the functionally uncharacterized Bacillus subtilis YrkD where there is an Asn instead of His (C-N-C), E.coli RcnR where there is a Thr instead of the second Cys (C-H-T), or TthCsoR and E.coli FrmR where there is a His instead of the second Cys and which have an additional N-terminal His (not found in those family members having C-H-C) that may also be involved in metal binding (H-C-H-H). A conserved Tyr and a Glu residue facilitate allosteric regulation of DNA binding. SaCstR regulates genes predicted to function in sulfur metabolism; it is thought that oxidation of the intersubunit Cys pair to a mixture of disulphide and trisulphide linkages by sulfite, results in a reduced affinity of SaCstR for the operator DNA. SaCstR exists as a mixture of oligomeric states, including dimers, tetramers and octamers. The sequence of SaCstR was not available at the time this hierarchy was curated and therefore was not included. Escherichia coli RncR represses expression of the gene encoding the nickel and cobalt-efflux protein RcnA. The gene encoding Alcaligenes xylosoxidans NreA is part of the nre nickel resistance locus located on the pTOM9 plasmid from thisbacteria. Escherichia coli FrmR regulates the formaldehyde degradation frmRAB operon. 80 matched cddid_all.tbl CDD cd10149 cd10149 197397 ClassIIa_HDAC_Gln-rich-N Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9). This superfamily consists of a glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDAC9; it is missing in HDAC7. It is referred to as the glutamine-rich domain, and confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors. This domain is able to repress transcription independently of the HDAC's C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues. 90 matched cddid_all.tbl CDD cd10150 cd10150 199903 CobN_like CobN subunit of cobaltochelatase, bchH and chlH subunits of magnesium chelatases, and similar proteins. Cobaltochelatase is a complex enzyme that catalyzes the insertion of cobalt into hydrogenobyrinic acid a,c-diamide, resulting in cobyrinic acid, as demonstrated for Pseudomonas denitrificans. This is an essential step in the bacterial synthesis of cobalamine (B12). The insertion of cobalt requires a complex composed of three polypeptides, cobN, cobS, and cobT. Also included in this family are protoporphyrin IX magnesium chelatases involved in the synthesis of chlorophyll and bacteriochlorophyll, specifically the large (chlH or bchH) subunits.They are thought to bind both the protoporphyrin and the magnesium ion. Hydrolysis of ATP by the smaller subunits in the complex may trigger a conformational change that results in the insertion of the ion into the protoporphyrin scaffold. Cryo electron microscopy studies have suggested that a distinct bchH C-terminal domain may bind tightly to the N-terminal domain upon substrate binding, requiring a substantial conformational change of the bchH subunit. It has also been suggested that chlH of higher plants binds abscisic acid via a C-terminal domain and plays a role in abscisic acid signaling, and that the protein spans the chloroplast envelope, with the C-terminus exposed to the cytosol. 910 matched cddid_all.tbl CDD cd10151 cd10151 197386 TthCsoR-like_DUF156 Thermus thermophilus CsoR, a Cu(I)-sensing transcriptional regulator, and related domains; this domain family was previously known as part of DUF156. This domain family contains various Cu(I)-inducible transcriptional regulators including CsoR (copper-sensitive operon repressor) from Mycobacterium tuberculosis (MtCsoR), and Thermus thermophilus (TthCsoR). CsoR regulates the expression of genes involved in copper homeostasis. For example, TthCsoR binds the promoter region of the copZ-csoR-copA operon, and represses expression of these genes, which encode the copper chaperone CopZ, CsoR, and the copper efflux P-type ATPase CopA, respectively. In the presence of excess Cu(I), TthCsoR binds this ion, and is released from the DNA, allowing expression of the downstream genes. TthCsoR also senses other metal ions such as Cu(II), Zn(II), Ag(I), Cd(II) and Ni(II). MtCsoR regulates an operon that includes CsoR and a putative copper transporter gene, ctpV (cation transporter P-type ATPase). CsoRs form a homotetramer (dimer of dimers). In MtCsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in some but not all members of this family; for example, for TthCsoR, there is a His instead of the second Cys as well as an N-terminal His (not found in those family members having C-H-C) which may also be involved in metal binding (H-C-H-H). A conserved Tyr and a Glu residue facilitate allosteric regulation of DNA binding. 82 matched cddid_all.tbl CDD cd10152 cd10152 197387 SaCsoR-like_DUF156 Staphylococcus aureus copper-sensitive operon repressor (CsoR), and related domains; this family was previously known as part of DUF156. This domain family includes Staphylococcus aureus CsoR (SaCsoR). SaCsoR is Cu(I)-inducible, and regulates the expression of genes involved in copper homeostasis; it represses a genetically unlinked copA-copZ operon. copA encodes a copper efflux P-type ATPase, and copZ, a copper chaperone. This family belongs to a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes Mycobacterium tuberculosis CsoR (MtCsoR), Bacillus subtilis CsoR, and Thermus thermophilus CsoR. The latter three proteins do not belong to this family. CsoRs form homotetramers (dimer of dimers). In MtCsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily, including this family, and a conserved Tyr and a Glu residue that facilitate allosteric regulation of DNA binding for CsoRs are also well conserved. 82 matched cddid_all.tbl CDD cd10153 cd10153 197388 RcnR-FrmR-like_DUF156 Transcriptional regulators RcnR and FrmR, and related domains; this domain family was previously known as part of DUF156. This domain family includes various transcriptional regulators that respond to different stressors. It includes Escherichia coli RncR (formally known as YohL, nickel and cobalt-sensitive), and E. coli FrmR (formally known as YaiN, formaldehyde sensitive). Escherichia coli RncR represses expression of the gene encoding the nickel and cobalt-efflux protein RcnA; RcnA may act through modulating NikR, to repress the NIkABCDE nickel transporter. In vitro, purified RncR binds to the rncA promoter DNA fragment in the absence of Ni2+ or Co2+, and the affinity of RncR for this promoter is reduced in the presence of excess nickel. Escherichia coli FrmR regulates the formaldehyde degradation frmRAB operon. This family belongs to a larger superfamily that includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily. In this family, however, not all these residues are conserved; in E.coli RcnR and FrmR there is a His or a Thr instead of the second Cys (C-H-H or C-H-T) respectively. For E. coli FrmR, an N-terminal His residue, not conserved in all members of this family, is also involved in metal binding (H-C-H-H). A conserved Tyr and a Glu residue that facilitate allosteric regulation of DNA binding for CsoRs are poorly conserved in this family. 88 matched cddid_all.tbl CDD cd10154 cd10154 197389 NreA-like_DUF156 Alcaligenes xylosoxidans NreA and related domains; this domain family was previously known as part of DUF156. This domain family includes Alcaligenes xylosoxidans NreA, Psudomonas putida MreA, and related domains. The gene encoding Alcaligenes xylosoxidans NreA is part of the nre nickel resistance locus located on the pTOM9 plasmid from this bacteria; it confers low-level nickel resistance on both Ralstonia and Escherichia coli strains. The Pseudomonas putida MreA gene is found in association with a gene encoding mrdH, a heavy metal efflux transporter of broad specificity. MreA may have a role in cadmium and nickel resistance. This family is part of a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily, including members of this family; however, a conserved Tyr and a Glu residue that facilitates allosteric regulation of DNA binding for CsoRs are poorly conserved. 86 matched cddid_all.tbl CDD cd10155 cd10155 197390 BsYrkD-like_DUF156 Uncharacterized protein YrkD from Bacillus subtilis and related domains; this domain superfamily was previously known as part of DUF156. This domain family contains an uncharacterized protein YrkD from Bacillus subtilis and related proteins. This family is part of a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily. In this family, however, not all these residues are conserved, there is an Asn instead of the His (C-N-C); also a conserved Tyr and a Glu residue that facilitates allosteric regulation of DNA binding for CsoRs are very poorly conserved. 82 matched cddid_all.tbl CDD cd10156 cd10156 197391 FpFrmR-Cterm-like_DUF156 C-terminal domain of Faecalibacterium prausnitzii A2-165 FrmR , and related domains; this domain family was previously known as part of DUF156. This domain family contains the C-terminal domain of the functionally uncharacterized protein Faecalibacterium prausnitzii A2-165 FrmR, and related domains. This family is part of a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily, including this family, and a conserved Tyr and a Glu residue that facilitate allosteric regulation of DNA binding for CsoRs are also conserved. 86 matched cddid_all.tbl CDD cd10157 cd10157 197392 BsCsoR-like_DUF156 Bacillus subtilis copper-sensitive operon repressor (BsCsoR), and related domains; this family was previously known as part of DUF156. This domain family includes Bacillus subtilis CsoR (BsCsoR). CsoRs are Cu(I)-inducible, and regulate the expression of genes involved in copper homeostasis. BsCsoR regulates the copZA operon which encodes the copper chaperone CopZ, and the copper efflux P-type ATPase CopA. This family belongs to a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes Mycobacterium tuberculosis CsoR (MtCsoR), Thermus thermophilus CsoR, and Staphylococcus aureus CsoR. The latter three proteins do not belong to this family. CsoRs regulate the expression of genes involved in copper homeostasis. CsoRs form homotetramers (dimer of dimers). In MtCsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily, including this family, and the conserved Tyr and a Glu residue that facilitate allosteric regulation of DNA binding for CsoRs are also well conserved. 85 matched cddid_all.tbl CDD cd10158 cd10158 197393 CsoR-like_DUF156_1 Uncharacterized family 1; belongs to a superfamily containing the transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this family was previously known as part of DUF156. Uncharacterized family 1, belonging to a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily, including this family; however, a conserved Tyr and a Glu residue that facilitates allosteric regulation of DNA binding for CsoRs are poorly conserved. 81 matched cddid_all.tbl CDD cd10159 cd10159 197394 CsoR-like_DUF156_2 Uncharacterized family 2; belongs to a superfamily containing transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this family was previously known as part of DUF156. Uncharacterized family 2, belonging to a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily, including this family, and a conserved Tyr and a Glu residue that facilitate allosteric regulation of DNA binding for CsoRs are also conserved. 82 matched cddid_all.tbl CDD cd10160 cd10160 197395 CsoR-like_DUF156_3 Uncharacterized family 3; belongs to a superfamily containing the transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this family was previously known as part of DUF156. Uncharacterized family 3, belonging to a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily, including this family; however, a conserved Tyr and a Glu residue that facilitate allosteric regulation of DNA binding for CsoRs are not conserved. 85 matched cddid_all.tbl CDD cd10161 cd10161 197396 CsoR-like_DUF156_4 Uncharacterized family 4; belongs to a superfamily containing the transcriptional regulators CsoR (copper-sensitive operon repressor), RcnR, and FrmR, and related domains; this family was previously known as part of DUF156. Uncharacterized family 4, belonging to a larger superfamily that contains various transcriptional regulators that respond to different stressors such as Cu(I), Ni(I), sulfite, and formaldehyde, and includes CsoRs (copper-sensitive operon repressors). CsoRs form homotetramers (dimer of dimers). In Mycobacterium tuberculosis CsoR, within each dimer, two Cys residues on opposite subunits, along with a His residue, bind the Cu(I) ion (forming a triagonal S2N coordination complex, C-H-C). These residues are conserved in the majority of members of this superfamily. In this family, however, only one of these residues is conserved (the first Cys); and a conserved Tyr and a Glu residue that facilitate allosteric regulation of DNA binding for CsoRs are also not conserved. 82 matched cddid_all.tbl CDD cd10162 cd10162 197398 ClassIIa_HDAC4_Gln-rich-N Glutamine-rich N-terminal helical domain of HDAC4, a Class IIa histone deacetylase. This family consists of the glutamine-rich domain of histone deacetylase 4 (HDAC4). It belongs to a superfamily that consists of the glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDCA9; it is missing from HDAC7. This domain confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors, and it is able to repress transcription independently of the HDAC C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues. 90 matched cddid_all.tbl CDD cd10163 cd10163 197399 ClassIIa_HDAC9_Gln-rich-N Glutamine-rich N-terminal helical domain of HDAC9, a Class IIa histone deacetylase. This family consists of the glutamine-rich domain of histone deacetylase 9 (HDAC9). It belongs to a superfamily that consists of the glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDCA9; it is missing from HDAC7. This domain confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors, and it is able to repress transcription independently of the HDAC C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues. 90 matched cddid_all.tbl CDD cd10164 cd10164 197400 ClassIIa_HDAC5_Gln-rich-N Glutamine-rich N-terminal helical domain of HDAC5, a Class IIa histone deacetylase. This family consists of the glutamine-rich domain of histone deacetylase 5 (HDAC5). It belongs to a superfamily that consists of the glutamine-rich N-terminal helical extension to certain Class IIa histone deacetylases (HDACs), including HDAC4, HDAC5 and HDCA9; it is missing from HDAC7. This domain confers responsiveness to calcium signals and mediates interactions with transcription factors and cofactors, and it is able to repress transcription independently of the HDAC C-terminal, zinc-dependent catalytic domain. It has many intra- and inter-helical interactions which are possibly involved in reversible assembly and disassembly of proteins. HDACs regulate diverse cellular processes through enzymatic deacetylation of histone as well as non-histone proteins, in particular deacetylating N(6)-acetyl-lysine residues. 97 matched cddid_all.tbl CDD cd10169 cd10169 466810 ASKHA_NBD_actin-like nucleotide-binding domain (NBD) of actin and actin-related proteins (ARPs). Actin is ubiquitous in eukaryotes, and the major component of the actin cytoskeleton; monomeric globular protein (G-actin) reversibly polymerizes to form filaments (F-actin). Each actin protomer binds one molecule of ATP and either calcium or magnesium ions. F-actin filaments form with the consequent hydrolysis of ATP. Some actin-related proteins (Arps) have roles in cytoskeletal functions, such as actin polymerization (Arp2/3) and dynein motor activity (Arp1). Both conventional actin and specific Arps have been implicated in chromatin remodeling and/or transcription regulation. The actin/ARP family belongs to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 258 matched cddid_all.tbl CDD cd10170 cd10170 466811 ASKHA_NBD_HSP70 "nucleotide-binding domain (NBD) of the HSP70 family. HSP70 (70-kDa heat shock protein) family chaperones assist in protein folding and assembly and can direct incompetent ""client"" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. HSP70 chaperone activity is regulated by various co-chaperones: J-domain proteins and nucleotide exchange factors (NEFs). Some HSP70 family members are not chaperones but instead, function as NEFs to remove ADP from their HSP70 chaperone partners during the ATP hydrolysis cycle, some may function as both chaperones and NEFs. The HSP70 family belongs to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains." 329 matched cddid_all.tbl CDD cd10206 cd10206 466812 ASKHA_NBD_Arp8-like nucleotide-binding domain (NBD) of the actin-related protein 8 (Arp8)-like subfamily. The Arp8-like family includes Arp8, also called actin-like protein 8, from vertebrates and fungi. Human Arp8 is encoded by the ACTR8 gene and is also known as INO80 complex subunit N. It plays an important role in the functional organization of mitotic chromosomes. Arp8 exhibits low basal ATPase activity, and is unable to polymerize. It is probably a core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication, and probably DNA repair. it is required for the recruitment of INO80 (and probably the INO80 complex) to sites of DNA damage. Arp8 strongly prefers nucleosomes and H3-H4 tetramers over H2A-H2B dimers, suggesting it may act as a nucleosome recognition module within the complex. This subfamily also contains Arabidopsis thaliana Arp9. 447 matched cddid_all.tbl CDD cd10207 cd10207 466813 ASKHA_NBD_Arp10 nucleotide-binding domain (NBD) of actin-related protein 10 (Arp10) and similar proteins. Arp10, also known as actin-related protein 11 (Arp11), is a subunit of the cargo-binding portion of the dynein activator, dynactin. It, together with dynactin4 (p62), -5(p25), and -6(p27), forms a heterotetrameric complex located at the pointed end of Arp1. Arp1 forms a mini-filament of uniform size, with proteins bound along its length and at both ends. Human Arp10 is encoded by the ACTR10 gene. 375 matched cddid_all.tbl CDD cd10208 cd10208 466814 ASKHA_NBD_ScArp9-like nucleotide-binding domain (NBD) of Saccharomyces cerevisiae actin-related protein 9 (Arp9) and similar proteins. Saccharomyces cerevisiae Arp9, also called actin-like protein 9, chromatin structure-remodeling complex protein ARP9, or SWI/SNF complex component ARP9, is a component of the chromatin structure remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning. It is also part of the SWI/SNF complex, an ATP-dependent chromatin remodeling complex, which is required for the positive and negative regulation of gene expression of many genes. Arp9 forms a stable heterodimer with Arp7 protein in both the RSC and SWI/SNF chromatin-remodeling complexes. It has been suggested that this dimer functions as a module with DNA bending proteins, to achieve correct architecture and facilitate complex-complex interactions. Fission yeast SWI/SNF and RSC complexes do not contain Arp7 and Arp8, but instead contain Arp9 and Arp42. 356 matched cddid_all.tbl CDD cd10209 cd10209 466815 ASKHA_NBD_AtARP7-like nucleotide-binding domain (NBD) of Arabidopsis thaliana actin-related protein 7 and similar proteins. Arabidopsis thaliana ARP7 is an essential nuclear protein, ubiquitously expressed in all cell types. It is needed for normal embryogenesis, plant architecture, and floral organ abscission. It may play a role in regulating various phases of plant development through chromatin-mediated gene regulation. 354 matched cddid_all.tbl CDD cd10210 cd10210 466816 ASKHA_NBD_Arp6 nucleotide-binding domain (NBD) of actin-related protein6 (Arp6) and similar proteins. Arp6, also called actin-like protein 6, is required for formation and/or maintenance of proper nucleolar structure and function, plays a dual role in the regulation of ribosomal DNA (rDNA) transcription. In the presence of high glucose, Arp6 maintains active rDNA transcription through H2A.Z deposition and under glucose starvation, it is required for the repression of rDNA transcription, and this function may be independent of H2A.Z. Arp6 is also required for telomere silencing in both fission and budding yeast. It is a component of the budding yeast and Arabidopsis SWR1 complex (SWR1C) and the human SWI2/SNF2-related CBP activator protein (SRCAP) chromatin remodeling complexes which catalyze the exchange of the histone H2A with the H2AZ. Drosophila Arp6 colocalizes with HP1 (heterochromatin protein 1) in the pericentric heterochromatin, and vertebrate Arp6 also interacts with HP1. Human Arp6 is encoded by the ACTR6 gene. Arabidopsis thaliana ACTIN RELATED PROTEIN 6/EARLY IN SHORT DAYS 1/SUPPRESSOR OF FRIGIDA 3 (encoded by ARP6/ESD1/SUF3) participates in regulating several leaf and flower development stages. It is needed for Flowering locus C (FLC, the master repressor of flowering) and FLC-like gene expression in the shoot and root apex, and for the activity of the floral repressor pathway. 389 matched cddid_all.tbl CDD cd10211 cd10211 466817 ASKHA_NBD_Arp5 nucleotide-binding domain (NBD) of actin-related protein5 (Arp5) and similar proteins. Arp5, also called actin-like protein 5, may act as a core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair. It is involved in DNA double-strand break repair and UV-damage excision repair. Human Arp5 is encoded by the ACTR5 gene. Arabidopsis thaliana ARP5 (AtARp5) is a ubiquitously expressed nuclear protein involved in DNA repair and required for multicellular development of all organs. AtARp5 may be part of other chromatin remodeling machines in addition to INO80. 345 matched cddid_all.tbl CDD cd10212 cd10212 466818 ASKHA_NBD_ScArp7-like nucleotide-binding domain (NBD) of Saccharomyces cerevisiae actin-related protein7 (Arp7) and similar proteins. Saccharomyces cerevisiae Arp7, also called actin-like protein 7, is a component of the chromatin structure remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning. It is also part of the SWI/SNF complex, an ATP-dependent chromatin remodeling complex, which is required for the positive and negative regulation of gene expression of many genes. Arp7 forms a stable heterodimer with Arp9 protein in both the RSC and SWI/SNF chromatin-remodeling complexes. It has been suggested that this dimer functions as a module with DNA bending proteins, to achieve correct architecture and facilitate complex-complex interactions. Fission yeast SWI/SNF and RSC complexes do not contain Arp7 and Arp8, but instead contain Arp9 and Arp42. 424 matched cddid_all.tbl CDD cd10214 cd10214 466819 ASKHA_NBD_ACTL7 nucleotide-binding domain (NBD) of the actin-like protein 7 (ACTL7)-like family. The ACTL7-like family includes ACTL7A, ACTL7B and ACTL9 (also known as ACTL7C). In mammalian, ACTL7A is expressed in a wide variety of adult tissues, while the ACTL7B is expressed in spermatids through the elongation phase of spermatid development. ACTL7A, also called actin-like-7-alpha, or T-ACTIN-2 in mouse, may play an important role in formation and fusion of Golgi-derived vesicles during acrosome biogenesis. ACTL7B, also called actin-like-7-beta, acts as a key regulator of spermiogenesis that is required for male fertility. ACTL9 is a testis-specific protein that plays an important role in fusion of proacrosomal vesicles and perinuclear theca formation. 368 matched cddid_all.tbl CDD cd10216 cd10216 466820 ASKHA_NBD_Arp1 nucleotide-binding domain (NBD) of actin-related protein 1 (Arp1) and similar proteins. Arp1, also called centractin, actin-like protein, alpha-centractin, actin-RPV, or centrosome-associated actin homolog, may be a component of a multi-subunit centrosomal complex involved in microtubule-based vesicle motility. In yeast, actin-related protein is essential for viability and is associated with the centrosome. In vertebrates, Arp1 is a core component of the dynactin complex which assists cytoplasmic dynein by increasing its processivity and by regulation of its cargo binding. The dynactin complex is required for the spindle translocation late in anaphase and is involved in a cell wall synthesis checkpoint. ARP1 forms the backbone filament of the dynactin rod structure and serves as the scaffold for the remaining subunits. It is required for proper orientation of the mitotic spindle. Arp1 is the only actin-related protein known to form actin-like filaments. Human Arp1/centractin is encoded by the ACTR1A gene. 370 matched cddid_all.tbl CDD cd10220 cd10220 466821 ASKHA_NBD_Arp2 nucleotide-binding domain (NBD) of actin-related protein2 (Arp2) and similar proteins. Arp2, also called actin-like protein 2, is the ATP-binding component of the Arp2/3 complex, a multiprotein complex that mediates actin polymerization upon stimulation by nucleation-promoting factor (NPF). The Arp2/3 complex is comprised of 7 proteins (Arp2, Arp3, and five conserved proteins, ARPC1-5). It generates cytoplasmic branched filaments networks, by promoting nucleation of actin filaments as 70 degrees branches on the side of older filaments. It is activated, by simultaneously binding to a pre-existing filament and a nucleation promoting factor plus an actin monomer. Daughter branches subsequently detach/debranch from the mother filament. Its Arp2 and Arp3 subunits must be loaded with ATP for it to initiate the assembly of branched actin filaments. ATP hydrolysis may be required for branch initiation or debranching. The Arp2/3 complex is also found in the nucleus where it plays a role in promoting de novo actin polymerization and in RNA polymerase II-dependent transcription. This may in part be through regulating nuclear actin polymerization in a way like its function in the cytoplasm. Human Arp2 is encoded by the ACTR2 gene. 381 matched cddid_all.tbl CDD cd10221 cd10221 466822 ASKHA_NBD_Arp3-like nucleotide-binding domain (NBD) of actin-related protein3 (Arp3) and similar proteins. Arp3, also called actin-like protein 3, is the ATP-binding component of the Arp2/3 complex, a multiprotein complex that mediates actin polymerization upon stimulation by nucleation-promoting factor (NPF). The Arp2/3 complex is comprised of 7 proteins (Arp2, Arp3, and five conserved proteins, ARPC1-5). It generates cytoplasmic branched filaments networks, by promoting nucleation of actin filaments as 70 degrees branches on the side of older filaments. It is activated, by simultaneously binding to a pre-existing filament and a nucleation promoting factor plus an actin monomer. Daughter branches subsequently detach/debranch from the mother filament. Its Arp2 and Arp3 subunits must be loaded with ATP for it to initiate the assembly of branched actin filaments. ATP hydrolysis may be required for branch initiation or debranching. The Arp2/3 complex is also found in the nucleus where it plays a role in promoting de novo actin polymerization and in RNA polymerase II-dependent transcription. This may in part be through regulating nuclear actin polymerization in a way like its function in the cytoplasm. Human Arp3 and Arp3B are encoded by the ACTR3 and ACTR3B genes respectively. Arp3B is also known as actin-related protein Arp4. 404 matched cddid_all.tbl CDD cd10224 cd10224 466823 ASKHA_NBD_actin nucleotide-binding domain (NBD) of actin and similar proteins. Actin is a ubiquitous protein involved in the formation of filaments that are major components of the cytoskeleton. It is a highly dynamic structural protein network involved in processes such as cell contraction, cell motility, vesicle trafficking, intracellular organization, cytokinesis, endocytosis and apoptosis. Actin is a monomeric globular protein (G-actin) that reversibly polymerizes to form filaments (F-actin). Each actin protomer binds one molecule of ATP and either calcium or magnesium ions. At low salt concentrations, actin exists as a monomer, and as the salt concentration rises F-actin forms, with the consequent hydrolysis of ATP. F-actin assembly is in constant flux with G-actin association occurring at the barbed end (+) and its disassociation at the pointed end (-). Actin monomers that have been released from the pointed end can be reused, if the ADP is exchanged for ATP. F-actin filaments can assemble into higher order structures, for example branched F-actin, and stress fibers. Actin binding proteins regulate actin filament dynamics by a range of functions including actin severing, depolymerizing, capping, stabilizing and de novo actin polymerization. Actins interaction with myosin is the basis of muscular contraction and many aspects of cell motility. In vertebrates there are three main groups of actin isoforms, alpha, beta and gamma. The alpha actins found in muscle tissues are a major constituent of the contractile apparatus. The beta and gamma actins co-exist in most cell types as components of the cytoskeleton and as mediators of internal cell motility. In plants there are many isoforms which are probably involved in a variety of functions such as cytoplasmic streaming, cell shape determination, tip growth, graviperception, cell wall deposition, etc. 365 matched cddid_all.tbl CDD cd10225 cd10225 466824 ASKHA_NBD_MreB-like nucleotide-binding domain (NBD) of the cell shape-determining proteins MreB, Mbl, MreBH and similar proteins. MreB proteins are bacterial actin homologs that may play a role in cell shape determination by positioning the cell wall synthetic machinery. MreB has also been implicated in chromosome segregation; specifically, MreB is thought to bind to and segregate the replication origin of bacterial chromosomes. The family includes three MreB isoforms, MreB (also called actin-like MreB protein or rod shape-determining protein MreB), Mbl (also called actin-like Mbl protein or rod shape-determining protein Mbl) and MreBH (also called actin-like MreBH protein or rod shape-determining protein MreBH), in cell morphogenesis of Bacillus subtilis. All isoforms can support rod-shaped cell growth normal conditions. They form membrane-associated dynamic filaments that are essential for cell shape determination. They act by regulating cell wall synthesis and cell elongation, and thus cell shape. The feedback loops between cell geometry and their localizations may maintain elongated cell shape by targeting cell wall growth to regions of negative cell wall curvature. Filaments rotate around the cell circumference in concert with the cell wall synthesis enzymes. The process is driven by the cell wall synthesis machinery and does not depend on their polymerization. They organize peptidoglycan synthesis in the lateral cell wall. MreB, Mbl and MreBH can form a complex. The MreB-like family belongs to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 317 matched cddid_all.tbl CDD cd10227 cd10227 466825 ASKHA_NBD_ParM-like nucleotide-binding domain (NBD) of the plasmid segregation protein ParM-like domain family. ParM is a plasmid-encoded bacterial homolog of actin, which polymerizes into filaments similar to F-actin, and plays a vital role in plasmid segregation. ParM filaments segregate plasmids paired at midcell into the individual daughter cells. This subfamily also contains Thermoplasma acidophilum Ta0583, an active ATPase at physiological temperatures, which has a propensity to form filaments. ParM-like proteins belong to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily of phosphotransferases, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 263 matched cddid_all.tbl CDD cd10228 cd10228 466826 ASKHA_NBD_HSP70_HSPA4_like "nucleotide-binding domain (NBD) of the heat shock 70 kDa protein 4 (HSPA4)-like subfamily. This subgroup includes the human proteins, HSPA4 (also known as 70-kDa heat shock protein 4; APG-2; HS24/P52; hsp70 RY; HSPH2), HSPA4L (also known as 70-kDa heat shock protein 4-like; APG-1; HSPH3; OSP94), and HSPH1 (also known as heat shock 105kDa/110kDa protein 1; HSP105; HSP105A; HSP105B; NY-CO-25). They belong to the 105/110 kDa heat shock protein (HSP105/110) subfamily of the HSP70-like family, and includes proteins believed to function generally as co-chaperones of HSP70 chaperones, acting as nucleotide exchange factors (NEFs), to remove ADP from their HSP70 chaperone partners during the ATP hydrolysis cycle. HSP70 chaperones assist in protein folding and assembly, and can direct incompetent ""client"" proteins towards degradation. Like HSP70 chaperones, HSP105/110s have an N-terminal nucleotide-binding domain (NBD) and a C-terminal substrate-binding domain (SBD). For HSP70 chaperones, the nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. Hsp70 chaperone activity is also regulated by J-domain proteins." 378 matched cddid_all.tbl CDD cd10229 cd10229 466827 ASKHA_NBD_HSP70_HSPA12 "nucleotide-binding domain (NBD) of heat shock 70 kDa proteins HSPA12A, HSPA12B and similar proteins. The family includes heat shock 70 kDa proteins HSPA12A and HSPA12B. HSPA12A is an adapter protein for SORL1, but not SORT1. It delays SORL1 internalization and affects SORL1 subcellular localization. HSPA12B, predominantly expressed in endothelial cells, is required for angiogenesis, and may interact with known angiogenesis mediators. It may be important for host defense in microglia-mediated immune response. Both HSPA12A and HSPA12B belong to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly, and can direct incompetent ""client"" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. HSP70 chaperone activity is regulated by various co-chaperones: J-domain proteins and nucleotide exchange factors (NEFs). No co-chaperones have yet been identified for HSPA12A and HSPA12B." 372 matched cddid_all.tbl CDD cd10230 cd10230 466828 ASKHA_NBD_HSP70_HYOU1 "nucleotide-binding domain (NBD) of hypoxia up-regulated protein 1 (HYOU1) and similar proteins. This subgroup includes human HYOU1 (also known as human hypoxia up-regulated 1, 170 kDa glucose-regulated protein/GRP170; HSP12A; 150 kDa oxygen-regulated protein/ORP150; GRP-170; ORP-150) and Saccharomyces cerevisiae Lhs1p (also known as Cer1p, SsI1). Mammalian HYOU1 has a pivotal role in cytoprotective cellular mechanisms triggered by oxygen deprivation. It may play a role as a molecular chaperone and participate in protein folding. HYOU1 functions as a nucleotide exchange factor (NEF) for HSPA5 (also known as BiP, Grp78 or HspA5) and may also act as a HSPA5-independent chaperone. S. cerevisiae Lhs1p, does not have a detectable endogenous ATPase activity like canonical HSP70s, but functions as a NEF for Kar2p; it's interaction with Kar2p is stimulated by nucleotide-binding. In addition, Lhs1p has a nucleotide-independent holdase activity that prevents heat-induced aggregation of proteins in vitro. Members in this subgroup belong to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly and can direct incompetent ""client"" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. HSP70 chaperone activity is regulated by various co-chaperones: J-domain proteins and nucleotide exchange factors (NEFs)." 353 matched cddid_all.tbl CDD cd10231 cd10231 466829 ASKHA_NBD_HSP70_YegD-like "nucleotide-binding domain (NBD) of Escherichia coli chaperone protein YegD and similar proteins. The family includes a group of uncharacterized proteins similar to Escherichia coli chaperone protein YegD that belongs to the heat shock protein 70 family of chaperones that assist in protein folding and assembly and can direct incompetent ""client"" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. YegD lacks the SBD. HSP70 chaperone activity is regulated by various co-chaperones: J-domain proteins and nucleotide exchange factors (NEFs). Some family members are not chaperones but instead, function as NEFs for their Hsp70 partners, other family members function as both chaperones and NEFs." 409 matched cddid_all.tbl CDD cd10232 cd10232 466830 ASKHA_NBD_HSP70_ScSsz1p-like "nucleotide-binding domain (NBD) of Saccharomyces cerevisiae ribosome-associated complex subunit Ssz1 and similar proteins. Ssz1, also called DnaK-related protein Ssz1, heat shock protein 70 homolog Ssz1, or pleiotropic drug resistance protein 13 (PDR13), is a component of the ribosome-associated complex (RAC), a heterodimeric chaperone complex involved in regulation of accurate translation termination and in folding or maintaining nascent polypeptides in a folding-competent state. RAC stimulates the ATPase activity of the ribosome-associated pool of Hsp70-type chaperones Ssb1/Ssb2 that bind to the nascent polypeptide chain. Ssz1 is required for Zuo1 to function efficiently as a J-protein for Ssb1/Ssb2. It is also involved in pleiotropic drug resistance by post-translational activation of transcription factor PDR1. Members in this subfamily belong to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly and can direct incompetent ""client"" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis." 349 matched cddid_all.tbl CDD cd10233 cd10233 466831 ASKHA_NBD_HSP70_HSPA1 "nucleotide-binding domain (NBD) of 70-kDa heat shock protein 1 (HSPA1) and similar proteins. This subfamily includes human HSPA1A (70-kDa heat shock protein 1A, also known as HSP72; HSPA1; HSP70I; HSPA1B; HSP70-1; HSP70-1A), HSPA1B (70-kDa heat shock protein 1B, also known as HSPA1A; HSP70-2; HSP70-1B), and HSPA1L (70-kDa heat shock protein 1-like, also known as HSP70T; hum70t; HSP70-1L; HSP70-HOM), HSPA2 (70-kDa heat shock protein 2, also known as HSP70-2; HSP70-3), HSPA6 (also known as heat shock 70kDa protein 6; HSP70B'), HSPA7 (heat shock 70kDa protein 7 , also known as HSP70B), and HSPA8 (heat shock 70kDa protein 8, also known as Lipopolysaccharide-associated protein 1/LAP1; HSC70; HSP73; HSPA10). They are molecular chaperones implicated in a wide variety of cellular processes, including protection of the proteome from stress, folding and transport of newly synthesized polypeptides, activation of proteolysis of misfolded proteins and the formation and dissociation of protein complexes. They play pivotal roles in the protein quality control system, ensuring the correct folding of proteins, the re-folding of misfolded proteins and controlling the targeting of proteins for subsequent degradation. This is achieved through cycles of ATP binding, ATP hydrolysis and ADP release, mediated by co-chaperones. The subfamily also includes Saccharomyces cerevisiae heat shock protein Ssa1-4, which may play a role in the transport of polypeptides both across the mitochondrial membranes and into the endoplasmic reticulum. This subfamily belongs to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly and can direct incompetent ""client"" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. HSP70 chaperone activity is regulated by various co-chaperones: J-domain proteins and nucleotide exchange factors (NEFs)." 375 matched cddid_all.tbl CDD cd10234 cd10234 466832 ASKHA_NBD_HSP70_DnaK-like "nucleotide-binding domain (NBD) of Escherichia coli chaperone protein DnaK and similar proteins. This subfamily includes Escherichia coli chaperone protein DnaK (also known as heat shock 70 kDa protein/HSP70), human mitochondrial heat shock 70 kDa protein HSPA9 (also known as mitochondrial stress-70 protein; mortalin; 75 kDa glucose-regulated protein/GRP-75; HSPA9B; MOT; peptide-binding protein 74/PBP74), Saccharomyces cerevisiae stress-seventy subfamily C proteins, Ssc1p (also called import motor subunit, mitochondrial; endonuclease SceI 75 kDa subunit; mtHSP70; ENS1; endonuclease SceI 75 kDa subunit) and Ssc3p (also called extracellular mutant protein 10/Ecm10), and Saccharomyces cerevisiae Stress-seventy subfamily Q protein 1/Ssq1p (also called Ssc2p; Ssh1p; mtHSP70 homolog). They all belong to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly, and can direct incompetent ""client"" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. Hsp70 chaperone activity is regulated by various co-chaperones: J-domain proteins and nucleotide exchange factors (NEFs); for Escherichia coli DnaK, these are the DnaJ and GrpE, respectively." 373 matched cddid_all.tbl CDD cd10235 cd10235 466833 ASKHA_NBD_HSP70_HscC "nucleotide-binding domain (NBD) of Escherichia coli chaperone protein HscC and similar proteins. Escherichia coli HscC, also called Hsc62, or YbeW, may act as the chaperone. It has ATPase activity. It cannot be stimulated by DnaJ. Members in this subfamily belong to the heat shock protein 70 (Hsp70) family of chaperones that assist in protein folding and assembly and can direct incompetent ""client"" proteins towards degradation. Typically, Hsp70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. Hsp70 chaperone activity is regulated by various co-chaperones: J-domain proteins and nucleotide exchange factors (NEFs). Two genes in the vicinity of the HscC gene code for potential cochaperones: J-domain containing proteins, DjlB/YbeS and DjlC/YbeV. HscC and its co-chaperone partners may play a role in the SOS DNA damage response. HscC does not appear to require a NEF." 343 matched cddid_all.tbl CDD cd10236 cd10236 466834 ASKHA_NBD_HSP70_HscA "nucleotide-binding domain (NBD) of Escherichia coli chaperone protein HscA and similar proteins. Escherichia coli HscA, also called Hsc66, acts as a chaperone involved in the maturation of iron-sulfur cluster-containing proteins. It has a low intrinsic ATPase activity which is markedly stimulated by HscB. It is involved in the maturation of IscU. Members in this subfamily belong to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly and can direct incompetent ""client"" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. HSP70 chaperone activity is regulated by various co-chaperones: J-domain proteins and nucleotide exchange factors (NEFs). HscA's partner J-domain protein is HscB; it does not appear to require a NEF and has been shown to be induced by cold-shock. The HscA-HscB chaperone/co-chaperone pair is involved in [Fe-S] cluster assembly." 367 matched cddid_all.tbl CDD cd10237 cd10237 466835 ASKHA_NBD_HSP70_HSPA13 "nucleotide-binding domain (NBD) of heat shock 70 kDa protein 13 (HSPA13) and similar proteins. HSPA13, also called 70-kDa heat shock protein 13, STCH, microsomal stress-70 protein ATPase core, or stress-70 protein chaperone microsome-associated 60 kDa protein, has peptide-independent ATPase activity. It belongs to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly and can direct incompetent ""client"" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. HSP70 chaperone activity is regulated by various co-chaperones: J-domain proteins and nucleotide exchange factors (NEFs). HSPA13 contains an NBD but lacks an SBD. It may function to regulate cell proliferation and survival and modulate the TRAIL-mediated cell death pathway. The HSPA13 gene is a candidate stomach cancer susceptibility gene; a mutation in the NBD coding region of HSPA13 has been identified in stomach cancer cells. The NBD of HSPA13 interacts with the ubiquitin-like proteins Chap1 and Chap2, implicating HSPA13 in regulating cell cycle and cell death events. HSPA13 is induced by the Ca2+ ionophore A23187." 409 matched cddid_all.tbl CDD cd10238 cd10238 466836 ASKHA_NBD_HSP70_HSPA14 "nucleotide-binding domain (NBD) of heat shock 70 kDa protein 14 (HSPA14) and similar proteins. HSPA14, also called HSP70-like protein 1 (Hsp70L1), or heat shock protein HSP60, is a component of the ribosome-associated complex (RAC), a complex involved in folding or maintaining nascent polypeptides in a folding-competent state. In the RAC complex, HSPA14 binds to the nascent polypeptide chain, while DNAJC2 stimulates its ATPase activity. It belongs to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly and can direct incompetent ""client"" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis." 377 matched cddid_all.tbl CDD cd10241 cd10241 466837 ASKHA_NBD_HSP70_BiP "nucleotide-binding domain (NBD) of binding-immunoglobulin protein (BiP) and similar proteins. This subfamily includes human BiP (also known as HSP70 family protein 5 /HSPA5; 70-kDa heat shock protein 5; glucose-regulated protein 78/GRP78; immunoglobulin heavy chain-binding protein), Sacchaormyces cerevisiae BiP (also known as Grp78p), Arabidopsis thaliana BiP1-3 (also known as luminal-binding protein 1-3) and related proteins. BiP plays a key role in protein folding and quality control in the endoplasmic reticulum lumen. It plays an auxiliary role in post-translational transport of small presecretory proteins across endoplasmic reticulum (ER). BiP may function as an allosteric modulator for SEC61 channel-forming translocon complex, likely cooperating with SEC62 to enable the productive insertion of these precursors into SEC61 channel. It appears to specifically regulate translocation of precursors having inhibitory residues in their mature region that weaken channel gating. BiP may also play a role in apoptosis and cell proliferation. Plant BiP may be required for pollen development and pollen tube growth. This subfamily belongs to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly and can direct incompetent ""client"" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. HSP70 chaperone activity is regulated by various co-chaperones: J-domain proteins and nucleotide exchange factors (NEFs)." 376 matched cddid_all.tbl CDD cd10276 cd10276 199834 BamB_YfgL Beta-barrel assembly machinery (Bam) complex component B and related proteins. BamB (YflG) is a non-essential component of the beta-barrel assembly machinery (Bam), a multi-subunit complex that inserts proteins with beta-barrel topology into the outer membrane. BamB has been found to interact with BamA, which in turn binds and stabilizes pre-folded beta-barrel proteins; it has been suggested that BamB participates in the stabilization. 358 matched cddid_all.tbl CDD cd10277 cd10277 199835 PQQ_ADH_I Ethanol dehydrogenase, a bacterial quinoprotein (PQQ-dependent type I alcohol dehydrogenase). This bacterial family of homodimeric ethanol dehydrogenases utilize pyrroloquinoline quinone (PQQ) as a cofactor. It represents proteins whose expression may be induced by ethanol, and which are similar to quinoprotein methanol dehydrogenases, but have higher specificities for ethanol and other primary and secondary alcohols. Dehydrogenases with PQQ cofactors, such as ethanol, methanol, and membrane-bound glucose dehydrogenases, form an 8-bladed beta-propeller. 529 matched cddid_all.tbl CDD cd10278 cd10278 199836 PQQ_MDH Large subunit of methanol dehydrogenase (moxF). Methanol dehydrogenase is a key enzyme in the utilization of C1 compounds as a source of energy and carbon by bacteria. It catalyzes the oxidation of methanol to formaldehyde, transfering two electrons per methanol to cytochrome c(L) as the acceptor. Methanol dehydrogenase belongs to a family of dehydrogenases with pyrroloquinoline quinone (PQQ) as cofactor, which also includes dehydrogenases specific to other alcohols and membrane-bound glucose dehydrogenases. This alignment model for the large subunit contains an 8-bladed beta-propeller; the functional enzyme forms a heterotetramer composed of two large and two small subunits. 553 matched cddid_all.tbl CDD cd10279 cd10279 199837 PQQ_ADH_II PQQ_like domain of the quinohemoprotein alcohol dehydrogenase (type II). This family of monomeric and soluble type II alcohol dehydrogenases utilizes pyrroloquinoline quinone (PQQ) as a cofactor and is related to ethanol, methanol, and membrane-bound glucose dehydrogenases. The alignment model contains an 8-bladed beta-propeller. 549 matched cddid_all.tbl CDD cd10280 cd10280 199838 PQQ_mGDH Membrane-bound PQQ-dependent glucose dehydrogenase. This bacterial subfamily of enzymes belongs to the dehydrogenase family with pyrroloquinoline quinone (PQQ) as cofactor, and is the only subfamily that is bound to the membrane. Glucose dehydrogenase converts D-glucose to D-glucono-1,5-lactone in a reaction that is coupled with the respiratory chain in the periplasmic oxidation of sugars and alcohols in gram-negative bacteria. Ubiquinone functions as the electron acceptor. The alignment model contains an 8-bladed beta-propeller. 616 matched cddid_all.tbl CDD cd10281 cd10281 197336 Nape_like_AP-endo Neisseria meningitides Nape-like subfamily of the ExoIII family purinic/apyrimidinic (AP) endonucleases. This subfamily includes Neisseria meningitides Nape and related proteins. These are Escherichia coli exonuclease III (ExoIII)-like AP endonucleases and belong to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. AP endonucleases participate in the DNA base excision repair (BER) pathway. AP sites are one of the most common lesions in cellular DNA. During BER the damaged DNA is first recognized by DNA glycosylase. AP endonucleases then catalyze the hydrolytic cleavage of the phosphodiester bond 5' to the AP site, and this is followed by the coordinated actions of DNA polymerase, deoxyribose phosphatase, and DNA ligase. If left unrepaired, AP sites block DNA replication, and have both mutagenic and cytotoxic effects. AP endonucleases can carry out a variety of excision and incision reactions on DNA, including 3'-5' exonuclease, 3'-deoxyribose phosphodiesterase, 3'-phosphatase, and occasionally, nonspecific DNase activities. Different AP endonuclease enzymes catalyze the different reactions with different efficiences. Many organisms have two AP endonucleases, usually one is the dominant AP endonuclease, the other has weak AP endonuclease activity; for example, Neisseria meningitides Nape and NExo. Nape, found in this subfamily, is the dominant AP endonuclease. It exhibits strong AP endonuclease activity, and also exhibits 3'-5'exonuclease and 3'-deoxyribose phosphodiesterase activities. 253 matched cddid_all.tbl CDD cd10282 cd10282 197337 DNase1 Deoxyribonuclease 1. Deoxyribonuclease 1 (DNase1, EC 3.1.21.1), also known as DNase I, is a Ca2+, Mg2+/Mn2+-dependent secretory endonuclease, first isolated from bovine pancreas extracts. It cleaves DNA preferentially at phosphodiester linkages next to a pyrimidine nucleotide, producing 5'-phosphate terminated polynucleotides with a free hydroxyl group on position 3'. It generally produces tetranucleotides. DNase1 substrates include single-stranded DNA, double-stranded DNA, and chromatin. This enzyme may be responsible for apoptotic DNA fragmentation. Other deoxyribonucleases in this subfamily include human DNL1L (human DNase I lysosomal-like, also known as DNASE1L1, Xib, and DNase X ), human DNASE1L2 (also known as DNAS1L2), and DNASE1L3 (also known as DNAS1L3, nhDNase, LS-DNase, DNase Y, and DNase gamma) . DNASE1L3 is implicated in apoptotic DNA fragmentation. DNase I is also a cytoskeletal protein which binds actin. A recombinant form of human DNase1 is used as a mucoactive therapy in patients with cystic fibrosis; it hydrolyzes the extracellular DNA in sputum and reduces its viscosity. Mutations in the gene encoding DNase1 have been associated with Systemic Lupus Erythematosus, a multifactorial autoimmune disease. This subfamily belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. 256 matched cddid_all.tbl CDD cd10283 cd10283 197338 MnuA_DNase1-like Mycoplasma pulmonis MnuA nuclease-like. This subfamily includes Mycoplasma pulmonis MnuA, a membrane-associated nuclease related to Deoxyribonuclease 1 (DNase1 or DNase I, EC 3.1.21.1). The in vivo role of MnuA is as yet undetermined. This subfamily belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. 266 matched cddid_all.tbl CDD cd10284 cd10284 198434 growth_hormone_like Somatotropin/prolactin hormone family. The somatotropin/prolactin hormone family includes growth hormones 1 and 2, prolactin, prolactin 2, and other members that play vital roles in a variety of processes, including growth control. They are long-chain class-I helical cytokines, most of which are secreted by the pituitary gland, and are active as monomers, binding to cellular receptors with EpoR-like ligand binding domains. 178 matched cddid_all.tbl CDD cd10285 cd10285 198435 somatotropin_like Somatotropin or growth hormone (GH), placental lactogen, and related pituitary gland hormones. Growth hormone (GH) or somatotropin is a peptide hormone synthesized by the pituitary gland, which mediates anabolic effects in development. GH is known to activate, via binding to specific cellular receptors, the MAPK/ERK and JAK-STAT signaling pathways. Via the latter, it triggers the secretion of insulin-like growth factor 1 (mostly in the liver). Besides increasing body height, GH has been shown to have a host of other effects. 180 matched cddid_all.tbl CDD cd10286 cd10286 198436 somatolactin Somatolactin (SL) and somatolactin-like proteins. This family of hormones specific to Actinopterygii is expressed in the pars intermedia bordering the neurohypophysis (posterior pituitary). Somatolactin appears to be involved in acid-base regulation, but much of its physiological role remains to be understood. 207 matched cddid_all.tbl CDD cd10287 cd10287 198437 prolactin_2 Vertebrate, non-mammalian prolactin 2 (PRL2). A functionally uncharacterized subfamily of the growth-hormone-like helical cytokines, which is found in vertebrata (except for mammals). The protein has been shown to be expressed in the zebrafish eye and brain, but not the pituitary gland, and might play a role in retina development. 184 matched cddid_all.tbl CDD cd10288 cd10288 198438 prolactin_like Prolactin (PRL or PRL1), chorionic somatomammotropin, and related pituitary gland hormones. Prolactin is primarily responsible for stimulating milk production and breast development in mammals. Aside from roles in reproduction, various functions have been attributed to prolactin, more than for other pituitary gland hormones combined. These are roles in growth and development, metamorphosis, metabolism of lipids, carbohydrates, and steroids, brain biochemistry and even immunoregulation, among others. Most of these roles are poorly understood, but it has become clear that many prolactin-like hormones are actually produced in the placenta and not the pituitary. 199 matched cddid_all.tbl CDD cd10289 cd10289 198322 GST_C_AaRS_like Glutathione S-transferase C-terminal-like, alpha helical domain of various Aminoacyl-tRNA synthetases and similar domains. Glutathione S-transferase (GST) C-terminal domain family, Aminoacyl-tRNA synthetase (AaRS)-like subfamily; This model characterizes the GST_C-like domain found in the N-terminal region of some eukaryotic AaRSs, as well as similar domains found in proteins involved in protein synthesis including Aminoacyl tRNA synthetase complex-Interacting Multifunctional Protein 2 (AIMP2), AIMP3, and eukaryotic translation Elongation Factor 1 beta (eEF1b). AaRSs comprise a family of enzymes that catalyze the coupling of amino acids with their matching tRNAs. This involves the formation of an aminoacyl adenylate using ATP, followed by the transfer of the activated amino acid to the 3'-adenosine moiety of the tRNA. AaRSs may also be involved in translational and transcriptional regulation, as well as in tRNA processing. AaRSs in this subfamily include GluRS from lower eukaryotes, as well as GluProRS, MetRS, and CysRS from higher eukaryotes. AIMPs are non-enzymatic cofactors that play critical roles in the assembly and formation of a macromolecular multi-tRNA synthetase protein complex found in higher eukaryotes. The GST_C-like domain is involved in protein-protein interactions, mediating the formation of aaRS complexes such as the MetRS-Arc1p-GluRS ternary complex in lower eukaryotes and the multi-aaRS complex in higher eukaryotes, that act as molecular hubs for protein synthesis. AaRSs from prokaryotes, which are active as dimers, do not contain this GST_C-like domain. 82 matched cddid_all.tbl CDD cd10290 cd10290 198323 GST_C_MetRS_N_fungi Glutathione S-transferase C-terminal-like, alpha helical domain of Saccharomycetales Methionyl-tRNA synthetase. Glutathione S-transferase (GST) C-terminal domain family, Saccharomycetales Methionyl-tRNA synthetase (MetRS) subfamily; This model characterizes the GST_C-like domain found in the N-terminal region of Saccharomycetales MetRS. Aminoacyl-tRNA synthetases (aaRSs) comprise a family of enzymes that catalyze the coupling of amino acids with their matching tRNAs. This involves the formation of an aminoacyl adenylate using ATP, followed by the transfer of the activated amino acid to the 3'-adenosine moiety of the tRNA. AaRSs may also be involved in translational and transcriptional regulation, as well as in tRNA processing. MetRS is a class I aaRS, containing a Rossman fold catalytic core. It recognizes the initiator tRNA as well as the Met-tRNA for protein chain elongation. The GST_C-like domain of MetRS from Saccharomycetales is involved in protein-protein interactions, to mediate the formation of the the MetRS-Arc1p-GluRS ternary complex which is considered an evolutionary intermediate between prokaryotic aaRS and the multi-aaRS complex found in higher eukaryotes. AaRSs from prokaryotes, which are active as dimers, do not contain this GST_C-like domain. 95 matched cddid_all.tbl CDD cd10291 cd10291 198324 GST_C_YfcG_like C-terminal, alpha helical domain of Escherichia coli YfcG Glutathione S-transferases and related uncharacterized proteins. Glutathione S-transferase (GST) C-terminal domain family, YfcG-like subfamily; composed of the Escherichia coli YfcG and related proteins. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST active site is located in a cleft between the N- and C-terminal domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. YfcG is one of nine GST homologs in Escherichia coli. It is expressed predominantly during the late stationary phase where the predominant form of GSH is glutathionylspermidine (GspSH), suggesting that YfcG might interact with GspSH. It has very low or no GSH transferase or peroxidase activity, but displays a unique disulfide bond reductase activity that is comparable to thioredoxins (TRXs) and glutaredoxins (GRXs). However, unlike TRXs and GRXs, YfcG does not contain a redox active cysteine residue and may use a bound thiol disulfide couple such as 2GSH/GSSG for activity. The crystal structure of YcfG reveals a bound GSSG molecule in its active site. The actual physiological substrates for YfcG are yet to be identified. 110 matched cddid_all.tbl CDD cd10292 cd10292 198325 GST_C_YghU_like C-terminal, alpha helical domain of Escherichia coli Yghu Glutathione S-transferases and related uncharacterized proteins. Glutathione S-transferase (GST) C-terminal domain family, YghU-like subfamily; composed of the Escherichia coli YghU and related proteins. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST active site is located in a cleft between the N- and C-terminal domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. YghU is one of nine GST homologs in the genome of Escherichia coli. It is similar to Escherichia coli YfcG in that it has poor GSH transferase activity towards typical substrates. It shows modest reductase activity towards some organic hydroperoxides. Like YfcG, YghU also shows good disulfide bond oxidoreductase activity comparable to the activities of glutaredoxins and thioredoxins. YghU does not contain a redox active cysteine residue, and may use a bound thiol disulfide couple such as 2GSH/GSSG for activity. The crystal structure of YghU reveals two GSH molecules bound in its active site. 118 matched cddid_all.tbl CDD cd10293 cd10293 198326 GST_C_Ure2p C-terminal, alpha helical domain of fungal Ure2p Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, Ure2p subfamily; composed of the Saccharomyces cerevisiae Ure2p and related fungal proteins. Ure2p is a regulator for nitrogen catabolism in yeast. It represses the expression of several gene products involved in the use of poor nitrogen sources when rich sources are available. A transmissible conformational change of Ure2p results in a prion called [Ure3], an inactive, self-propagating and infectious amyloid. Ure2p displays a GST fold containing an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain. The N-terminal thioredoxin-fold domain is sufficient to induce the [Ure3] phenotype and is also called the prion domain of Ure2p. In addition to its role in nitrogen regulation, Ure2p confers protection to cells against heavy metal ion and oxidant toxicity, and shows glutathione (GSH) peroxidase activity. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of GSH with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST active site is located in a cleft between the N- and C-terminal domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. 117 matched cddid_all.tbl CDD cd10294 cd10294 198327 GST_C_ValRS_N Glutathione S-transferase C-terminal-like, alpha helical domain of vertebrate Valyl-tRNA synthetase. Glutathione S-transferase (GST) C-terminal domain family, Valyl-tRNA synthetase (ValRS) subfamily; This model characterizes the GST_C-like domain found in the N-terminal region of human ValRS and its homologs from other vertebrates such as frog and zebrafish. Aminoacyl-tRNA synthetases (aaRSs) comprise a family of enzymes that catalyze the coupling of amino acids with their matching tRNAs. This involves the formation of an aminoacyl adenylate using ATP, followed by the transfer of the activated amino acid to the 3'-adenosine moiety of the tRNA. AaRSs may also be involved in translational and transcriptional regulation, as well as in tRNA processing. They typically form large stable complexes with other proteins. ValRS forms a stable complex with Elongation Factor-1H (EF-1H), and together, they catalyze consecutive steps in protein biosynthesis, tRNA aminoacylation and its transfer to EF. The GST_C-like domain of ValRS from higher eukaryotes is likely involved in protein-protein interactions, to mediate the formation of the multi-aaRS complex that acts as a molecular hub to coordinate protein synthesis. ValRSs from prokaryotes and lower eukaryotes, such as fungi and plants, do not appear to contain this GST_C-like domain. 123 matched cddid_all.tbl CDD cd10295 cd10295 198328 GST_C_Sigma C-terminal, alpha helical domain of Class Sigma Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, Class Sigma; GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. Vertebrate class Sigma GSTs are characterized as GSH-dependent hematopoietic prostaglandin (PG) D synthases and are responsible for the production of PGD2 by catalyzing the isomerization of PGH2. The functions of PGD2 include the maintenance of body temperature, inhibition of platelet aggregation, bronchoconstriction, vasodilation, and mediation of allergy and inflammation. 100 matched cddid_all.tbl CDD cd10296 cd10296 198329 GST_C_CLIC4 C-terminal, alpha helical domain of Chloride Intracellular Channel 4. Glutathione S-transferase (GST) C-terminal domain family, Chloride Intracellular Channel (CLIC) 4 subfamily; CLICs are auto-inserting, self-assembling intracellular anion channels involved in a wide variety of functions including regulated secretion, cell division, and apoptosis. They can exist in both water-soluble and membrane-bound states and are found in various vesicles and membranes, and they may play roles in the maintenance of these intracellular membranes. The membrane localization domain is present in the N-terminal part of the protein. Structures of soluble CLICs reveal that they adopt a fold similar to GSTs, containing an N-terminal domain with a thioredoxin fold and a C-terminal alpha helical domain. CLIC4, also known as p64H1, is expressed ubiquitously and its localization varies depending on the nature of the cells and tissues, from the plasma membrane to subcellular compartments including the nucleus, mitochondria, ER, and the trans-Golgi network, among others. In response to cellular stress such as DNA damage and senescence, cytoplasmic CLIC4 translocates to the nucleus, where it acts on the TGF-beta pathway. Studies on knockout mice suggest that CLIC4 also plays an important role in angiogenesis, specifically in network formation, capillary sprouting, and lumen formation. CLIC4 has been found to induce apoptosis in several cell types and to retard the growth of grafted tumors in vivo. 141 matched cddid_all.tbl CDD cd10297 cd10297 198330 GST_C_CLIC5 C-terminal, alpha helical domain of Chloride Intracellular Channel 5. Glutathione S-transferase (GST) C-terminal domain family, Chloride Intracellular Channel (CLIC) 5 subfamily; CLICs are auto-inserting, self-assembling intracellular anion channels involved in a wide variety of functions including regulated secretion, cell division, and apoptosis. They can exist in both water-soluble and membrane-bound states and are found in various vesicles and membranes, and they may play roles in the maintenance of these intracellular membranes. The membrane localization domain is present in the N-terminal part of the protein. Structures of soluble CLICs reveal that they adopt a fold similar to GSTs, containing an N-terminal domain with a thioredoxin fold and a C-terminal alpha helical domain. CLIC5 exists in two alternatively-spliced isoforms, CLIC5A or CLIC5B (also called p64). It is expressed at high levels in hair cell stereocilia and is associated with the actin cytoskeleton and ezrin. A recessive mutation in the CLIC5 gene in mice led to the lack of coordination and deafness, due to a defect in the basal region of the hair bundle causing stereocilia to degrade. CLIC5 is therefore essential for normal inner ear function. CLIC5 is also highly expressed in podocytes where it is colocalized with the ezrin/radixin/moesin (ERM) complex. It is essential for foot process integrity, and for podocyte morphology and function. 141 matched cddid_all.tbl CDD cd10298 cd10298 198331 GST_C_CLIC2 C-terminal, alpha helical domain of Chloride Intracellular Channel 2. Glutathione S-transferase (GST) C-terminal domain family, Chloride Intracellular Channel (CLIC) 2 subfamily; CLICs are auto-inserting, self-assembling intracellular anion channels involved in a wide variety of functions including regulated secretion, cell division, and apoptosis. They can exist in both water-soluble and membrane-bound states and are found in various vesicles and membranes, and they may play roles in the maintenance of these intracellular membranes. The membrane localization domain is present in the N-terminal part of the protein. Structures of soluble CLICs reveal that they adopt a fold similar to GSTs, containing an N-terminal domain with a thioredoxin fold and a C-terminal alpha helical domain. CLIC2 contains an intramolecular disulfide bond and exists as a monomer regardless of redox conditions, in contrast to CLIC1 which forms a dimer under oxidizing conditions. It is expressed in most tissues except the brain, and is highly expressed in the lung, spleen, and in cardiac and skeletal muscles. CLIC2 interacts with ryanodine receptors (cardiac RyR2 and skeletal RyR1) and modulates their activity, suggesting that CLIC2 may function in the regulation of calcium release and signaling in cardiac and skeletal muscles. 138 matched cddid_all.tbl CDD cd10299 cd10299 198332 GST_C_CLIC3 C-terminal, alpha helical domain of Chloride Intracellular Channel 3. Glutathione S-transferase (GST) C-terminal domain family, Chloride Intracellular Channel (CLIC) 3 subfamily; CLICs are auto-inserting, self-assembling intracellular anion channels involved in a wide variety of functions including regulated secretion, cell division, and apoptosis. They can exist in both water-soluble and membrane-bound states and are found in various vesicles and membranes, and they may play roles in the maintenance of these intracellular membranes. The membrane localization domain is present in the N-terminal part of the protein. Structures of soluble CLICs reveal that they adopt a fold similar to GSTs, containing an N-terminal domain with a thioredoxin fold and a C-terminal alpha helical domain. CLIC3 is highly expressed in placental tissues, and may play a role in fetal development. 133 matched cddid_all.tbl CDD cd10300 cd10300 198333 GST_C_CLIC1 C-terminal, alpha helical domain of Chloride Intracellular Channel 1. Glutathione S-transferase (GST) C-terminal domain family, Chloride Intracellular Channel (CLIC) 1 subfamily; CLICs are auto-inserting, self-assembling intracellular anion channels involved in a wide variety of functions including regulated secretion, cell division, and apoptosis. They can exist in both water-soluble and membrane-bound states and are found in various vesicles and membranes, and they may play roles in the maintenance of these intracellular membranes. The membrane localization domain is present in the N-terminal part of the protein. Soluble CLIC1 is monomeric and adopts a fold similar to GSTs, containing an N-terminal domain with a thioredoxin fold and a C-terminal alpha helical domain. Upon oxidation, the N-terminal domain of CLIC1 undergoes a structural change to form a non-covalent dimer stabilized by the formation of an intramolecular disulfide bond between two cysteines that are far apart in the reduced form. The CLIC1 dimer bears no similarity to GST dimers. The redox-controlled structural rearrangement exposes a large hydrophobic surface, which is masked by dimerization in vitro. In vivo, this surface may represent the docking interface of CLIC1 in its membrane-bound state. The two cysteines in CLIC1 that form the disulfide bond in oxidizing conditions are essential for dimerization and chloride channel activity. CLIC1 is widely expressed in many tissues and its subcellular localization is dependent on cell type and cell cycle phase. It acts as a sensor of cell oxidation and appears to have a role in diseases that involve oxidative stress including tumorigenic and neurodegenerative diseases. 139 matched cddid_all.tbl CDD cd10301 cd10301 198334 GST_C_CLIC6 C-terminal, alpha helical domain of Chloride Intracellular Channel 6. Glutathione S-transferase (GST) C-terminal domain family, Chloride Intracellular Channel (CLIC) 6 subfamily; CLICs are auto-inserting, self-assembling intracellular anion channels involved in a wide variety of functions including regulated secretion, cell division, and apoptosis. They can exist in both water-soluble and membrane-bound states and are found in various vesicles and membranes, and they may play roles in the maintenance of these intracellular membranes. The membrane localization domain is present in the N-terminal part of the protein. Structures of soluble CLICs reveal that they adopt a fold similar to GSTs, containing an N-terminal domain with a thioredoxin fold and a C-terminal alpha helical domain. CLIC6 is expressed predominantly in the stomach, pituitary, and brain. It interacts with D2-like dopamine receptors directly and through scaffolding proteins. CLIC6 may be involved in the regulation of secretion, possibly through chloride ion transport regulation. 140 matched cddid_all.tbl CDD cd10302 cd10302 198335 GST_C_GDAP1L1 C-terminal, alpha helical domain of Ganglioside-induced differentiation-associated protein 1-like 1. Glutathione S-transferase (GST) C-terminal domain family, Ganglioside-induced differentiation-associated protein 1-like 1 (GDAP1L1) subfamily; GDAP1L1 is a paralogue of GDAP1 with about 56% sequence identity and 70% similarity. It's function is unknown. Like GDAP1, it does not exhibit GST activity using standard substrates. GDAP1 was originally identified as a highly expressed gene at the differentiated stage of GD3 synthase-transfected cells. More recently, mutations in GDAP1 have been reported to cause both axonal and demyelinating autosomal-recessive Charcot-Marie-Tooth (CMT) type 4A neuropathy. CMT is characterized by slow and progressive weakness and atrophy of muscles. Sequence analysis of GDAP1 shows similarities and differences with GSTs; it appears to contain both N-terminal thioredoxin-fold and C-terminal alpha helical domains of GSTs, however, it also contains additional C-terminal transmembrane domains unlike GSTs. GDAP1 is mainly expressed in neuronal cells and is localized in the mitochondria through its transmembrane domains. 111 matched cddid_all.tbl CDD cd10303 cd10303 198336 GST_C_GDAP1 C-terminal, alpha helical domain of Ganglioside-induced differentiation-associated protein 1. Glutathione S-transferase (GST) C-terminal domain family, Ganglioside-induced differentiation-associated protein 1 (GDAP1) subfamily; GDAP1 was originally identified as a highly expressed gene at the differentiated stage of GD3 synthase-transfected cells. More recently, mutations in GDAP1 have been reported to cause both axonal and demyelinating autosomal-recessive Charcot-Marie-Tooth (CMT) type 4A neuropathy. CMT is characterized by slow and progressive weakness and atrophy of muscles. Sequence analysis of GDAP1 shows similarities and differences with GSTs; it appears to contain both N-terminal thioredoxin-fold and C-terminal alpha helical domains of GSTs, however, it also contains additional C-terminal transmembrane domains unlike GSTs. GDAP1 is mainly expressed in neuronal cells and is localized in the mitochondria through its transmembrane domains. It does not exhibit GST activity using standard substrates. 111 matched cddid_all.tbl CDD cd10304 cd10304 198337 GST_C_Arc1p_N_like Glutathione S-transferase C-terminal-like, alpha helical domain of the Aminoacyl tRNA synthetase cofactor 1 and similar proteins. Glutathione S-transferase (GST) C-terminal domain family, Aminoacyl tRNA synthetase cofactor 1 (Arc1p)-like subfamily; Arc1p, also called GU4 nucleic binding protein 1 (G4p1) or p42, is a tRNA-aminoacylation and nuclear-export cofactor. It contains a domain in the N-terminal region with similarity to the C-terminal alpha helical domain of GSTs. This domain mediates the association of the aminoacyl tRNA synthetases (aaRSs), MetRS and GluRS, in yeast to form a stable stoichiometric ternany complex. The GST_C-like domain of Arc1p is a protein-protein interaction domain containing two binding sites which enable it to bind the two aaRSs simultaneously and independently. The MetRS-Arc1p-GluRS complex selectively recruits and aminoacylates its cognate tRNAs without additional cofactors. Arc1p also plays a role in the transport of tRNA from the nucleus to the cytoplasm. It may also control the subcellular distribution of GluRS in the cytoplasm, nucleoplasm, and the mitochondrial matrix. 100 matched cddid_all.tbl CDD cd10305 cd10305 198338 GST_C_AIMP3 Glutathione S-transferase C-terminal-like, alpha helical domain of Aminoacyl tRNA synthetase complex-Interacting Multifunctional Protein 3. Glutathione S-transferase (GST) C-terminal domain family, Aminoacyl tRNA synthetase complex-Interacting Multifunctional Protein (AIMP) 3 subfamily; AIMPs are non-enzymatic cofactors that play critical roles in the assembly and formation of a macromolecular multi-tRNA synthetase protein complex that functions as a molecular hub to coordinate protein synthesis. There are three AIMPs, named AIMP1-3, which play diverse regulatory roles. AIMP3, also called p18 or eukaryotic translation elongation factor 1 epsilon-1 (EEF1E1), contains a C-terminal domain with similarity to the C-terminal alpha helical domain of GSTs. It specifically interacts with methionyl-tRNA synthetase (MetRS) and is translocated to the nucleus during DNA synthesis or in response to DNA damage and oncogenic stress. In the nucleus, it interacts with ATM and ATR, which are upstream kinase regulators of p53. It appears to work against DNA damage in cooperation with AIMP2, and similar to AIMP2, AIMP3 is also a haploinsufficient tumor suppressor. AIMP3 transgenic mice have shorter lifespans than wild-type mice and they show characteristics of progeria, suggesting that AIMP3 may also be involved in cellular and organismal aging. 101 matched cddid_all.tbl CDD cd10306 cd10306 198339 GST_C_GluRS_N Glutathione S-transferase C-terminal-like, alpha helical domain of Glutamyl-tRNA synthetase. Glutathione S-transferase (GST) C-terminal domain family, Glutamyl-tRNA synthetase (GluRS) subfamily; This model characterizes the GST_C-like domain found in the N-terminal region of GluRS from lower eukaryotes. Aminoacyl-tRNA synthetases (aaRSs) comprise a family of enzymes that catalyze the coupling of amino acids with their matching tRNAs. This involves the formation of an aminoacyl adenylate using ATP, followed by the transfer of the activated amino acid to the 3'-adenosine moiety of the tRNA. AaRSs may also be involved in translational and transcriptional regulation, as well as in tRNA processing. The GST_C-like domain of GluRS is involved in protein-protein interactions. This domain mediates the formation of the MetRS-Arc1p-GluRS ternary complex found in lower eukaryotes, which is considered an evolutionary intermediate between prokaryotic aaRS and the multi-aaRS complex found in higher eukaryotes. AaRSs from prokaryotes, which are active as dimers, do not contain this GST_C-like domain. 87 matched cddid_all.tbl CDD cd10307 cd10307 198340 GST_C_MetRS_N Glutathione S-transferase C-terminal-like, alpha helical domain of Methionyl-tRNA synthetase from higher eukaryotes. Glutathione S-transferase (GST) C-terminal domain family, Methionyl-tRNA synthetase (MetRS) subfamily; This model characterizes the GST_C-like domain found in the N-terminal region of MetRS from higher eukaryotes. Aminoacyl-tRNA synthetases (aaRSs) comprise a family of enzymes that catalyze the coupling of amino acids with their matching tRNAs. This involves the formation of an aminoacyl adenylate using ATP, followed by the transfer of the activated amino acid to the 3'-adenosine moiety of the tRNA. AaRSs may also be involved in translational and transcriptional regulation, as well as in tRNA processing. MetRS is a class I aaRS, containing a Rossman fold catalytic core. It recognizes the initiator tRNA as well as the Met-tRNA for protein chain elongation. The GST_C-like domain of MetRS from higher eukaryotes is likely involved in protein-protein interactions, to mediate the formation of the multi-aaRS complex that acts as a molecular hub to coordinate protein synthesis. AaRSs from prokaryotes, which are active as dimers, do not contain this GST_C-like domain. 102 matched cddid_all.tbl CDD cd10308 cd10308 198341 GST_C_eEF1b_like Glutathione S-transferase C-terminal-like, alpha helical domain of eukaryotic translation Elongation Factor 1 beta. Glutathione S-transferase (GST) C-terminal domain family, eukaryotic translation Elongation Factor 1 beta (eEF1b) subfamily; eEF1b is a component of the eukaryotic translation elongation factor-1 (EF1) complex which plays a central role in the elongation cycle during protein biosynthesis. EF1 consists of two functionally distinct units, EF1A and EF1B. EF1A catalyzes the GTP-dependent binding of aminoacyl-tRNA to the ribosomal A site concomitant with the hydrolysis of GTP. The resulting inactive EF1A:GDP complex is recycled to the active GTP form by the guanine-nucleotide exchange factor EF1B, a complex composed of at least two subunits, alpha and gamma. Metazoan EFB1 contain a third subunit, beta. eEF1b contains a GST_C-like alpha helical domain at the N-terminal region and a C-terminal guanine nucleotide exchange domain. The GST_C-like domain likely functions as a protein-protein interaction domain, similar to the function of the GST_C-like domains of EF1Bgamma and various aminoacyl-tRNA synthetases (aaRSs) from higher eukaryotes. 82 matched cddid_all.tbl CDD cd10309 cd10309 198342 GST_C_GluProRS_N Glutathione S-transferase C-terminal-like, alpha helical domain of bifunctional Glutamyl-Prolyl-tRNA synthetase. Glutathione S-transferase (GST) C-terminal domain family, bifunctional GluRS-Prolyl-tRNA synthetase (GluProRS) subfamily; This model characterizes the GST_C-like domain found in the N-terminal region of GluProRS from higher eukaryotes. Aminoacyl-tRNA synthetases (aaRSs) comprise a family of enzymes that catalyze the coupling of amino acids with their matching tRNAs. This involves the formation of an aminoacyl adenylate using ATP, followed by the transfer of the activated amino acid to the 3'-adenosine moiety of the tRNA. AaRSs may also be involved in translational and transcriptional regulation, as well as in tRNA processing. The GST_C-like domain of GluProRS may be involved in protein-protein interactions, mediating the formation of the multi-aaRS complex in higher eukaryotes. The multi-aaRS complex acts as a molecular hub for protein synthesis. AaRSs from prokaryotes, which are active as dimers, do not contain this GST_C-like domain. 81 matched cddid_all.tbl CDD cd10310 cd10310 198343 GST_C_CysRS_N Glutathione S-transferase C-terminal-like, alpha helical domain of Cysteinyl-tRNA synthetase from higher eukaryotes. Glutathione S-transferase (GST) C-terminal domain family, Cysteinyl-tRNA synthetase (CysRS) subfamily; This model characterizes the GST_C-like domain found in the N-terminal region of CysRS from higher eukaryotes. Aminoacyl-tRNA synthetases (aaRSs) comprise a family of enzymes that catalyze the coupling of amino acids with their matching tRNAs. This involves the formation of an aminoacyl adenylate using ATP, followed by the transfer of the activated amino acid to the 3'-adenosine moiety of the tRNA. AaRSs may also be involved in translational and transcriptional regulation, as well as in tRNA processing. The GST_C-like domain of CysRS from higher eukaryotes is likely involved in protein-protein interactions, to mediate the formation of the multi-aaRS complex that acts as a molecular hub to coordinate protein synthesis. CysRSs from prokaryotes and lower eukaryotes do not appear to contain this GST_C-like domain. 73 matched cddid_all.tbl CDD cd10311 cd10311 197304 PLDc_N_DEXD_c N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. N-terminal putative catalytic domain of uncharacterized prokaryotic and archeal HKD family nucleases fused to a DEAD/DEAH box helicase domain. All members of this subfamily are uncharacterized. Other characterized members of the superfamily that have a related domain architecture ( containing a DEAD/DEAH box helicase domain), include the DNA/RNA helicase superfamily II (SF2) and Res-subunit of type III restriction endonucleases. In addition to the helicase-like region, members of this subfamily also contain one copy of the conserved HKD motif (H-x-K-x(4)-D, where x represents any amino acid residue) in the N-terminal putative catalytic domain. The HKD motif characterizes the phospholipase D (PLD, EC 3.1.4.4) superfamily. 156 matched cddid_all.tbl CDD cd10312 cd10312 197339 Deadenylase_CCR4b C-terminal deadenylase domain of CCR4b, also known as CCR4-NOT transcription complex subunit 6-like. This subfamily contains the C-terminal catalytic domain of the deadenylase, CCR4b, also known as CCR4-NOT transcription complex subunit 6-like (CNOT6L). CCR4 belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. CCR4 is the major deadenylase subunit of the CCR4-NOT transcription complex, which contains two deadenylase subunits and several noncatalytic subunits. The other deadenylase subunit, Caf1, is a DEDD-type protein and does not belong in this superfamily. There are two vertebrate CCR4 proteins, CCR4a (also called CCR4-NOT transcription complex subunit 6 or CNOT6) and CCR4b. CCR4b associates with other components, such as CNOT1-3 and Caf1, to form a CCR4-NOT multisubunit complex, which regulates transcription and mRNA degradation. The nuclease domain of CCR4b exhibits Mg2+-dependent deadenylase activity with strict specificity for poly (A) RNA as substrate. CCR4b is mainly localized in the cytoplasm. It regulates cell growth and influences cell cycle progression by regulating p27/Kip1 mRNA levels. It contributes to the prevention of cell death by regulating insulin-like growth factor-binding protein 5. 348 matched cddid_all.tbl CDD cd10313 cd10313 197340 Deadenylase_CCR4a C-terminal deadenylase domain of CCR4a, also known as CCR4-NOT transcription complex subunit 6. This subfamily contains the C-terminal catalytic domain of the deadenylase, CCR4a, also known as CCR4-NOT transcription complex subunit 6 (CNOT6). CCR4 belongs to the large EEP (exonuclease/endonuclease/phosphatase) superfamily that contains functionally diverse enzymes that share a common catalytic mechanism of cleaving phosphodiester bonds. CCR4 is the major deadenylase subunit of the CCR4-NOT transcription complex, which contains two deadenylase subunits and several noncatalytic subunits. The other deadenylase subunit, Caf1, is a DEDD-type protein and does not belong in this superfamily. There are two vertebrate CCR4 proteins, CCR4a and CCR4b (also called CNOT6-like or CNOT6L). CCR4a associates with other components, such as CNOT1-3 and Caf1, to form a CCR4-NOT multisubunit complex, which regulates transcription and mRNA degradation. The nuclease domain of CCR4a exhibits Mg2+-dependent deadenylase activity with specificity for poly (A) RNA as substrate. CCR4a is a component of P-bodies and is necessary for foci formation of various P-body components. It also plays a role in cellular responses to DNA damage, by regulating Chk2 activity. 350 matched cddid_all.tbl CDD cd10314 cd10314 198457 FAM20_C C-terminal putative kinase domain of FAM20 (family with sequence similarity 20) proteins. This family contains the C-terminal domain of FAM20A, -B, -C and related proteins. FAM20A may participate in enamel development and gingival homeostasis, FAM20B in proteoglycan production, and FAM20C in bone development. FAM20B is a xylose kinase that may regulate the number of glycosaminoglycan chains by phosphorylating the xylose residue in the glycosaminoglycan-protein linkage region of proteoglycans. FAM20C, also called Dentin Matrix Protein 4, is abundant in the dentin matrix, and may participate in the differentiation of mesenchymal precursor cells into functional odontoblast-like cells. Mutations in FAM20C are associated with lethal Osteosclerotic Bone Dysplasia (Raine Syndrome), and mutations in FAM20A with Amelogenesis imperfecta (AI) and Gingival Hyperplasia Syndrome. The C-terminal domains of members of this family are putative kinase domains, based on mutagenesis of the C-terminal domain of Drosophila Four-Jointed, a related Golgi kinase. This domain family is also known as DUF1193. 209 matched cddid_all.tbl CDD cd10315 cd10315 199215 CBM41_pullulanase Family 41 Carbohydrate-Binding Module from pullulanase-like enzymes. Pullulanases (EC 3.2.1.41) are a group of starch-debranching enzymes, catalyzing the hydrolysis of the alpha-1,6-glucosidic linkages of alpha-glucans, preferentially pullulan. Pullulan is a polysaccharide in which alpha-1,4 linked maltotriosyl units are combined via an alpha-1,6 linkage. These enzymes are of importance in the starch industry, where they are used to hydrolyze amylopectin starch. Pullulanases consist of multiple distinct domains, including a catalytic domain belonging to the glycoside hydrolase (GH) family 13 and carbohydrate-binding modules (CBM), including CBM41. 100 matched cddid_all.tbl CDD cd10316 cd10316 199904 RGL4_M Middle domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase. The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold. Both the middle domain represented by this model and the C-terminal domain are putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11. 92 matched cddid_all.tbl CDD cd10317 cd10317 199905 RGL4_C C-terminal domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase. The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold. Both the middle and the C-terminal domain are putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11. 161 matched cddid_all.tbl CDD cd10318 cd10318 199906 RGL11 Rhamnogalacturonan lyase of the polysaccharide lyase family 11. The rhamnogalacturonan lyase of the polysaccharide lyase family 11 (RGL11) cleaves glycoside bonds in polygalacturonan as well as RG (rhamnogalacturonan) type-I through a beta-elimination reaction. Functionally characterized members of this family, YesW and YesX from Bacillus subtilis, cleave glycoside bonds between rhamnose and galacturonic acid residues in the RG-I region of plant cell wall pectin. YesW and YesX work synergistically, with YesW cleaving the glycoside bond of the RG chain endolytically, and YesX converting the resultant oligosaccharides through an exotype reaction. This domain is sometimes found in architectures with non-catalytic carbohydrate-binding modules (CBMs). There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain through a beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11. 564 matched cddid_all.tbl CDD cd10319 cd10319 198439 EphR_LBD Ligand Binding Domain of Ephrin Receptors. Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). They are subdivided into 2 groups, A and B type receptors, depending on their ligand ephrin-A or ephrin-B, respectively. In general, class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. Class EphB receptors bind to transmembrane ephrin-B ligands. There are six vertebrate EhpB receptors (EphB1-6), which display promiscuous interactions with three ephrin-B ligands. One exception is EphB2, which also interacts with ephrin A5. EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). Ephrin/EphR interaction mainly results in cell-cell repulsion or adhesion, making it important in neural development and plasticity, cell morphogenesis, cell-fate determination, embryonic development, tissue patterning, and angiogenesis. 177 matched cddid_all.tbl CDD cd10320 cd10320 199907 RGL4_N N-terminal catalytic domain of rhamnogalacturonan lyase, a family 4 polysaccharide lyase. The rhamnogalacturonan lyase of the polysaccharide lyase family 4 (RGL4) is involved in the degradation of RG (rhamnogalacturonan) type-I, an important pectic plant cell wall polysaccharide, by cleaving the alpha-1,4 glycoside bond between L-rhamnose and D-galacturonic acids in the backbone of RG type-I through a beta-elimination reaction. RGL4 consists of three domains, an N-terminal catalytic domain, a middle domain with a FNIII type fold and a C-terminal domain with a jelly roll fold; the middle and C-terminal domains are both putative carbohydrate binding modules. There are two types of RG lyases, which both cleave the alpha-1,4 bonds of the RG-I main chain (RG chain) through the beta-elimination reaction, but belong to two structurally unrelated polysaccharide lyase (PL) families, 4 and 11. 265 matched cddid_all.tbl CDD cd10321 cd10321 199216 RNase_Ire1_like RNase domain (also known as the kinase extension nuclease domain) of Ire1 and RNase L. This RNase domain is found in the multi-functional protein Ire1; Ire1 also contains a type I transmembrane serine/threonine protein kinase (STK) domain, and a Luminal dimerization domain. Ire1 is essential for the endoplasmic reticulum (ER) unfolded protein response (UPR). The UPR is activated when protein misfolding is detected in the ER in order to reduce the synthesis of new proteins and increase the capacity of the ER to cope with the stress. IRE1 acts as an ER stress sensor; IRE1 dimerizes through its N-terminal luminal domain and forms oligomers, promoting trans-autophosphorylation by its cytosolic kinase domain which stimulates its endoribonuclease (RNase) activity and results in the cleavage of its mRNA substrate, Hac1 in yeast and Xbp1 in metazoans, thus promoting a splicing event that enables translation into a transcription factor which activates the UPR. This RNase domain is also found in Ribonuclease L (RNase L), sometimes referred to as the 2-5A-dependent RNase. RNase L is a highly regulated, latent endoribonuclease widely expressed in most mammalian tissues. It is involved in the mediation of the antiviral and pro-apoptotic activities of the interferon-inducible 2-5A system; the interferon (IFN)-inducible 2'-5'-oligoadenylate synthetase (OAS)/RNase L pathway blocks infections by certain types of viruses through cleavage of viral and cellular single-stranded RNA. RNase L has been shown to have an impact on the pathogenesis of prostate cancer; the RNase L gene, RNASEL, has been identified as a strong candidate for the hereditary prostate cancer 1 (HPC1) allele. 127 matched cddid_all.tbl CDD cd10322 cd10322 271357 SLC5sbd Solute carrier 5 family, sodium/glucose transporters and related proteins; solute-binding domain. This family represents the solute-binding domain of SLC5 proteins (also called the sodium/glucose cotransporter family or solute sodium symporter family) that co-transport Na+ with sugars, amino acids, inorganic ions or vitamins. Family members include: the human glucose (SGLT1, 2, 4, 5), chiro-inositol (SGLT5), myo-inositol (SMIT), choline (CHT), iodide (NIS), multivitamin (SMVT), and monocarboxylate (SMCT) cotransporters, as well as Vibrio parahaemolyticus glucose/galactose (vSGLT), and Escherichia coli proline (PutP) and pantothenate (PutF) cotransporters. Vibrio parahaemolyticus Na(+)/galactose cotransporter (vSGLT) has 13 transmembrane helices (TMs): TM-1, an inverted topology repeat: TMs1-5 and TMs6-10, and TMs 11-12 (TMs numbered to conform to the solute carrier 6 family Aquifex aeolicus LeuT). One member of this family, human SGLT3, has been characterized as a glucose sensor and not a transporter. Members of this family are important in human physiology and disease. 454 matched cddid_all.tbl CDD cd10323 cd10323 271358 SLC-NCS1sbd nucleobase-cation-symport-1 (NCS1) transporters; solute-binding domain. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. This family includes Microbacterium liquefaciens Mhp1, a transporter that mediates the uptake of indolyl methyl- and benzyl-hydantoins as part of a metabolic salvage pathway for their conversion to amino acids. It also includes various Saccharomyces cerevisiae transporters: Fcy21p (Purine-cytosine permease), vitamin B6 transporter Tpn1, nicotinamide riboside transporter 1 (Nrt1p, also called Thi71p), Dal4p (allantoin permease), Fui1p (uridine permease), and Fur4p (uracil permease). Mhp1 has 12 transmembrane (TM) helices (an inverted topology repeat: TMs1-5 and TMs6-10, and TMs11-12; TMs numbered to conform to the solute carrier 6 family Aquifex aeolicus LeuT). NCS1s belong to a superfamily which also contains the solute carrier 5 family sodium/glucose transporters (SLC5s), and SLC6 neurotransmitter transporters. 414 matched cddid_all.tbl CDD cd10324 cd10324 271359 SLC6sbd Solute carrier 6 family, neurotransmitter transporters; solute-binding domain. This family represents the solute-binding domain of SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporter family or Na+/Cl--dependent transporter family). These use sodium and chloride electrochemical gradients to catalyze the thermodynamically uphill movement of a variety of substrates, and include neurotransmitter transporters (NTTs). The latter are Na+/Cl--dependent plasma membrane transporters for the monoamine neurotransmitters serotonin (5-hydroxytryptamine), dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. NTTs are widely expressed in the mammalian brain, and are involved in regulating neurotransmitter signaling and homeostasis, through facilitating the uptake of released neurotransmitters from the extracellular space into neurons and glial cells. NTTs are the target of a range of therapeutic drugs for the treatment of psychiatric diseases, such as major depression, anxiety disorders, attention deficit hyperactivity disorder and epilepsy. In addition, they are the primary targets of cocaine, amphetamines and other psychostimulants. This family also includes Drosophila Blot which is expressed primarily in epithelial tissues of ectodermal origin and in the nervous system of the embryo and larvae, but in addition found in the developing oocyte and the freshly laid egg. A lack or reduction of Blot function during oogenesis results in early arrest of embryonic development. 12 transmembrane helices (TMs) appears to be common for eukaryotic and some prokaryotic and archaeal SLC6s, (a core inverted topology repeat, TM1-5 and TM6-10, plus TMs11-12; TMs numbered to conform to the SLC6 Aquifex aeolicus LeuT), although a majority of bacterial, and some archaeal SLC6s lack TM12, for example the functional Fusobacterium nucleatum tyrosine transporter Tyt1. 415 matched cddid_all.tbl CDD cd10325 cd10325 271360 SLC5sbd_vSGLT Vibrio parahaemolyticus Na(+)/galactose cotransporter (vSGLT) and related proteins; solute binding domain. vSGLT transports D-galactose, D-glucose, and alpha-D-fucose, with a sugar specificity in the order of D-galactose >D-fucose >D-glucose. It transports one Na+ ion for each sugar molecule, and appears to function as a monomer. vSGLT has 13 transmembrane helices (TMs): TM-1, an inverted topology repeat: TMs1-5 and TMs6-10, and TMs 11-12 (TMs numbered to conform to the solute carrier 6 family Aquifex aeolicus LeuT). This subfamily belongs to the solute carrier 5 (SLC5) transporter family. 523 matched cddid_all.tbl CDD cd10326 cd10326 271361 SLC5sbd_NIS-like Na(+)/iodide (NIS) and Na(+)/multivitamin (SMVT) cotransporters, and related proteins; solute binding domain. NIS (product of the SLC5A5 gene) transports I-, and other anions including ClO4-, SCN-, and Br-. SMVT (product of the SLC5A6 gene) transports biotin, pantothenic acid and lipoate. This subfamily also includes SMCT1 and 2. SMCT1(the product of the SLC5A8 gene) is a high-affinity transporter of various monocarboxylates including lactate and pyruvate, short-chain fatty acids, ketone bodies, nicotinate and its structural analogs, pyroglutamate, benzoate and its derivatives, and iodide. SMCT2 (product of the SLC5A12 gene) is a low-affinity transporter for short-chain fatty acids, lactate, pyruvate, and nicotinate. This subfamily belongs to the solute carrier 5 (SLC5) transporter family. 472 matched cddid_all.tbl CDD cd10327 cd10327 212037 SLC5sbd_PanF Na(+)/pantothenate cotransporters: PanF of Escherichia coli and related proteins; solute binding domain. PanF catalyzes the Na+-coupled uptake of extracellular pantothenate for coenzyme A biosynthesis in cells. This subfamily belongs to the solute carrier 5 (SLC5) transporter family. 472 matched cddid_all.tbl CDD cd10328 cd10328 271362 SLC5sbd_YidK uncharacterized SLC5 subfamily, Escherichia coli YidK-like; solute binding domain. Uncharacterized subfamily of the solute binding domain of the solute carrier 5 (SLC5) transporter family (also called the sodium/glucose cotransporter family or solute sodium symporter family) that co-transports Na+ with sugars, amino acids, inorganic ions or vitamins. One member of the SLC5 family, human SGLT3, has been characterized as a glucose sensor and not a transporter. This subfamily includes the uncharacterized Escherichia coli YidK protein, and belongs to the solute carrier 5 (SLC5) transporter family. 472 matched cddid_all.tbl CDD cd10329 cd10329 271363 SLC5sbd_SGLT1-like Na(+)/glucose cotransporter SGLT1 and related proteins; solute binding domain. This subfamily includes the solute-binding domain of SGLT proteins that cotransport Na+ with various solutes. Its members include: the human glucose (SGLT1, -2, -4, -5 ), chiro-inositol (SGLT5), and myo-inositol (SMIT) cotransporters. It also includes human SGLT3 which has been characterized as a glucose sensor and not a transporter. It belongs to the solute carrier 5 (SLC5) transporter family. 538 matched cddid_all.tbl CDD cd10332 cd10332 271364 SLC6sbd-B0AT-like System B(0) neutral amino acid transporter AT1, 2 and 3, and related proteins; solute-binding domain. This subgroup includes the solute-binding domain of transmembrane transporters, which transport, i) neutral amino acids: NTT4 (also called XT1), SBAT1 (also called B0AT2, v7-3, NTT7-3), and B0AT1 (also called HND); the human genes encoding these are SLC6A17, SLC6A15, and SLC6A19 respectively, ii) glycine: B0AT3 (also called Xtrp2, XT2), iii) imino acids, such as proline, pipecolate, MeAIB, and sarcosine: SIT1 (also called XTRP3, XT3, IMINO). The human genes encoding B0AT3 and SIT1 are SLC6A18 and SLC6A20 respectively. Transporters in this subgroup may play a role in disorders including major depression, Hartnup disorder, increased susceptibility to myocardial infarction, and iminoglycinuria. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 531 matched cddid_all.tbl CDD cd10333 cd10333 271365 LeuT-like_sbd Aquifex aeolicus LeuT and related proteins; solute binding domain. LeuT is a bacterial amino acid transporter with specificity for the hydrophobic amino acids glycine, alanine, methionine, and leucine. This subgroup belongs to the solute carrier 6 (SLC6) transporter family; LeuT has been used as a structural template for understanding fundamental aspects of SLC6 function. It has an arrangement of 12 transmembrane helices (TMs), which appears to be a common motif for eukaryotic and some prokaryotic and archaeal SLC6s: an inverted topology repeat: TMs1-5 and TMs6-10, and TMs11-12. 496 matched cddid_all.tbl CDD cd10334 cd10334 271366 SLC6sbd_u1 uncharacterized bacterial and archaeal solute carrier 6 subfamily; solute-binding domain. SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporter family or Na+/Cl--dependent transporter family) include neurotransmitter transporters (NTTs): these are sodium- and chloride-dependent plasma membrane transporters for the monoamine neurotransmitters serotonin (5-hydroxytryptamine), dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. These NTTs are widely expressed in the mammalian brain, involved in regulating neurotransmitter signaling and homeostasis, and the target of a range of therapeutic drugs for the treatment of psychiatric diseases. Bacterial members of the SLC6 family include the LeuT amino acid transporter. 480 matched cddid_all.tbl CDD cd10336 cd10336 271367 SLC6sbd_Tyt1-Like solute carrier 6 subfamily, Fusobacterium nucleatum Tyt1-like; solute-binding domain. SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporter family or Na+/Cl--dependent transporter family) include neurotransmitter transporters (NTTs): these are sodium- and chloride-dependent plasma membrane transporters for the monoamine neurotransmitters serotonin (5-hydroxytryptamine), dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. These NTTs are widely expressed in the mammalian brain, involved in regulating neurotransmitter signaling and homeostasis, and the target of a range of therapeutic drugs for the treatment of psychiatric diseases. Bacterial members of the SLC6 family include the LeuT amino acid transporter. An arrangement of 12 transmembrane (TM) helices appears to be as a common topological motif for eukaryotic and some prokaryotic and archaeal NTTs. However, this subfamily which contains the majority of bacterial members and some archaeal members, appears to contain only 11 TMs; for example the functional Fusobacterium nucleatum tyrosine transporter Tyt1. 440 matched cddid_all.tbl CDD cd10337 cd10337 198200 SH2_BCAR3 Src homology 2 (SH2) domain in the Breast Cancer Anti-estrogen Resistance protein 3. BCAR3 is part of a growing family of guanine nucleotide exchange factors is responsible for activation of Ras-family GTPases, including Sos1 and 2, GRF1 and 2, CalDAG-GEF/GRP1-4, C3G, cAMP-GEF/Epac 1 and 2, PDZ-GEFs, MR-GEF, RalGDS family members, RalGPS, RasGEF, Smg GDS, and phospholipase C(epsilon). 12102558 21262352 BCAR3 binds to the carboxy-terminus of BCAR1/p130Cas, a focal adhesion adapter protein. Over expression of BCAR1 (p130Cas) and BCAR3 induces estrogen independent growth in normally estrogen-dependent cell lines. They have been linked to resistance to anti-estrogens in breast cancer, Rac activation, and cell motility, though the BCAR3/p130Cas complex is not required for this activity in BCAR3. Many BCAR3-mediated signaling events in epithelial and mesenchymal cells are independent of p130Cas association. Structurally these proteins contain a single SH2 domain upstream of their RasGEF domain, which is responsible for the ability of BCAR3 to enhance p130Cas over-expression-induced migration. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 136 matched cddid_all.tbl CDD cd10338 cd10338 198201 SH2_SHA Src homology 2 (SH2) domain found in SH2 adaptor proteins A (SHA) Signal transducers. Signal transducing adaptor proteins are accessory to main proteins in a signal transduction pathway. These proteins lack intrinsic enzymatic activity, but mediate specific protein-protein interactions that drive the formation of protein complexes. Adaptor proteins usually contain several domains within their structure (e.g. SH2 and SH3 domains) which allow specific interactions with several other specific proteins. Not much is known about the SHA protein except that it is predicted to act as a transcription factor. Arabidopsis SHA pulled down a 120-kD tyrosine-phosphorylated protein in vitro. In addition to the SH2 domain there is a coiled-coil domain, a DNA binding domain, and a transactivation domain in the STAT proteins. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 106 matched cddid_all.tbl CDD cd10339 cd10339 198202 SH2_RIN_family Src homology 2 (SH2) domain found in Ras and Rab interactor (RIN)-family. The RIN (AKA Ras interaction/interference) family is composed of RIN1, RIN2 and RIN3. These proteins have multifunctional domains including SH2 and proline-rich (PR) domains in the N-terminal region, and RIN-family homology (RH), VPS9 and Ras-association (RA) domains in the C-terminal region. RIN proteins function as Rab5-GEFs, and RIN3 specifically functions as a Rab31-GEF. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 101 matched cddid_all.tbl CDD cd10340 cd10340 198203 SH2_N-SH2_SHP_like N-terminal Src homology 2 (N-SH2) domain found in SH2 domain Phosphatases (SHP) proteins. The SH2 domain phosphatases (SHP-1, SHP-2/Syp, Drosophila corkscrew (csw), and Caenorhabditis elegans Protein Tyrosine Phosphatase (Ptp-2)) are cytoplasmic signaling enzymes. They are both targeted and regulated by interactions of their SH2 domains with phosphotyrosine docking sites. These proteins contain two SH2 domains (N-SH2, C-SH2) followed by a tyrosine phosphatase (PTP) domain, and a C-terminal extension. Shp1 and Shp2 have two tyrosyl phosphorylation sites in their C-tails, which are phosphorylated differentially by receptor and nonreceptor PTKs. Csw retains the proximal tyrosine and Ptp-2 lacks both sites. Shp-binding proteins include receptors, scaffolding adapters, and inhibitory receptors. Some of these bind both Shp1 and Shp2 while others bind only one. Most proteins that bind a Shp SH2 domain contain one or more immuno-receptor tyrosine-based inhibitory motifs (ITIMs): [IVL]xpYxx[IVL]. Shp1 N-SH2 domain blocks the catalytic domain and keeps the enzyme in the inactive conformation, and is thus believed to regulate the phosphatase activity of SHP-1. Its C-SH2 domain is thought to be involved in searching for phosphotyrosine activators. The SHP2 N-SH2 domain is a conformational switch; it either binds and inhibits the phosphatase, or it binds phosphoproteins and activates the enzyme. The C-SH2 domain contributes binding energy and specificity, but it does not have a direct role in activation. Csw SH2 domain function is essential, but either SH2 domain can fulfill this requirement. The role of the csw SH2 domains during Sevenless receptor tyrosine kinase (SEV) signaling is to bind Daughter of Sevenless rather than activated SEV. Ptp-2 acts in oocytes downstream of sheath/oocyte gap junctions to promote major sperm protein (MSP)-induced MAP Kinase (MPK-1) phosphorylation. Ptp-2 functions in the oocyte cytoplasm, not at the cell surface to inhibit multiple RasGAPs, resulting in sustained Ras activation. It is thought that MSP triggers PTP-2/Ras activation and ROS production to stimulate MPK-1 activity essential for oocyte maturation and that secreted MSP domains and Cu/Zn superoxide dismutases function antagonistically to control ROS and MAPK signaling. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 99 matched cddid_all.tbl CDD cd10341 cd10341 199829 SH2_N-SH2_PLC_gamma_like N-terminal Src homology 2 (N-SH2) domain in Phospholipase C gamma. Phospholipase C gamma is a signaling molecule that is recruited to the C-terminal tail of the receptor upon autophosphorylation of a highly conserved tyrosine. PLCgamma is composed of a Pleckstrin homology (PH) domain followed by an elongation factor (EF) domain, 2 catalytic regions of PLC domains that flank 2 tandem SH2 domains (N-SH2, C-SH2), and ending with a SH3 domain and C2 domain. N-SH2 SH2 domain-mediated interactions represent a crucial step in transmembrane signaling by receptor tyrosine kinases. SH2 domains recognize phosphotyrosine (pY) in the context of particular sequence motifs in receptor phosphorylation sites. Both N-SH2 and C-SH2 have a very similar binding affinity to pY. But in growth factor stimulated cells these domains bind to different target proteins. N-SH2 binds to pY containing sites in the C-terminal tails of tyrosine kinases and other receptors. Recently it has been shown that this interaction is mediated by phosphorylation-independent interactions between a secondary binding site found exclusively on the N-SH2 domain and a region of the FGFR1 tyrosine kinase domain. This secondary site on the SH2 cooperates with the canonical pY site to regulate selectivity in mediating a specific cellular process. C-SH2 binds to an intramolecular site on PLCgamma itself which allows it to hydrolyze phosphatidylinositol-4,5-bisphosphate into diacylglycerol and inositol triphosphate. These then activate protein kinase C and release calcium. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 99 matched cddid_all.tbl CDD cd10342 cd10342 198205 SH2_SAP1 Src homology 2 (SH2) domain found in SLAM-associated protein (SAP)1. The X-linked lymphoproliferative syndrome (XLP) gene encodes SAP (also called SH2D1A/DSHP) a protein that consists of a 5 residue N-terminus, a single SH2 domain, and a short 25 residue C-terminal tail. XLP is characterized by an extreme sensitivity to Epstein-Barr virus. Both T and natural killer (NK) cell dysfunctions have been seen in XLP patients. SAP binds the cytoplasmic tail of Signaling lymphocytic activation molecule (SLAM), 2B4, Ly-9, and CD84. SAP is believed to function as a signaling inhibitor, by blocking or regulating binding of other signaling proteins. SAP and the SAP-like protein EAT-2 recognize the sequence motif TIpYXX[VI], which is found in the cytoplasmic domains of a restricted number of T, B, and NK cell surface receptors and are proposed to be natural inhibitors or regulators of the physiological role of a small family of receptors on the surface of these cells. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 103 matched cddid_all.tbl CDD cd10343 cd10343 198206 SH2_SHIP Src homology 2 (SH2) domain found in SH2-containing inositol-5'-phosphatase (SHIP) and SLAM-associated protein (SAP). The SH2-containing inositol-5'-phosphatase, SHIP (also called SHIP1/SHIP1a), is a hematopoietic-restricted phosphatidylinositide phosphatase that translocates to the plasma membrane after extracellular stimulation and hydrolyzes the phosphatidylinositol-3-kinase (PI3K)-generated second messenger PI-3,4,5-P3 (PIP3) to PI-3,4-P2. As a result, SHIP dampens down PIP3 mediated signaling and represses the proliferation, differentiation, survival, activation, and migration of hematopoietic cells. PIP3 recruits lipid-binding pleckstrin homology(PH) domain-containing proteins to the inner wall of the plasma membrane and activates them. PH domain-containing downstream effectors include the survival/proliferation enhancing serine/threonine kinase, Akt (protein kinase B), the tyrosine kinase, Btk, the regulator of protein translation, S6K, and the Rac and cdc42 guanine nucleotide exchange factor, Vav. SHIP is believed to act as a tumor suppressor during leukemogenesis and lymphomagenesis, and may play a role in activating the immune system to combat cancer. SHIP contains an N-terminal SH2 domain, a centrally located phosphatase domain that specifically hydrolyzes the 5'-phosphate from PIP3, PI-4,5-P2 and inositol-1,3,4,5- tetrakisphosphate (IP4), a C2 domain, that is an allosteric activating site when bound by SHIP's enzymatic product, PI-3,4-P2; 2 NPXY motifs that bind proteins with a phosphotyrosine binding (Shc, Dok 1, Dok 2) or an SH2 (p85a, SHIP2) domain; and a proline-rich domain consisting of four PxxP motifs that bind a subset of SH3-containing proteins including Grb2, Src, Lyn, Hck, Abl, PLCg1, and PIAS1. The SH2 domain of SHIP binds to the tyrosine phosphorylated forms of Shc, SHP-2, Doks, Gabs, CD150, platelet-endothelial cell adhesion molecule, Cas, c-Cbl, immunoreceptor tyrosine-based inhibitory motifs (ITIMs), and immunoreceptor tyrosine-based activation motifs (ITAMs). The X-linked lymphoproliferative syndrome (XLP) gene encodes SAP (also called SH2D1A/DSHP) a protein that consists of a 5 residue N-terminus, a single SH2 domain, and a short 25 residue C-terminal tail. XLP is characterized by an extreme sensitivity to Epstein-Barr virus. Both T and natural killer (NK) cell dysfunctions have been seen in XLP patients. SAP binds the cytoplasmic tail of Signaling lymphocytic activation molecule (SLAM), 2B4, Ly-9, and CD84. SAP is believed to function as a signaling inhibitor, by blocking or regulating binding of other signaling proteins. SAP and the SAP-like protein EAT-2 recognize the sequence motif TIpYXX(V/I), which is found in the cytoplasmic domains of a restricted number of T, B, and NK cell surface receptors and are proposed to be natural inhibitors or regulators of the physiological role of a small family of receptors on the surface of these cells. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 103 matched cddid_all.tbl CDD cd10344 cd10344 198207 SH2_SLAP Src homology 2 domain found in Src-like adaptor proteins. SLAP belongs to the subfamily of adapter proteins that negatively regulate cellular signaling initiated by tyrosine kinases. It has a myristylated N-terminus, SH3 and SH2 domains with high homology to Src family tyrosine kinases, and a unique C-terminal tail, which is important for c-Cbl binding. SLAP negatively regulates platelet-derived growth factor (PDGF)-induced mitogenesis in fibroblasts and regulates F-actin assembly for dorsal ruffles formation. c-Cbl mediated SLAP inhibition towards actin remodeling. Moreover, SLAP enhanced PDGF-induced c-Cbl phosphorylation by SFK. In contrast, SLAP mitogenic inhibition was not mediated by c-Cbl, but it rather involved a competitive mechanism with SFK for PDGF-receptor (PDGFR) association and mitogenic signaling. Accordingly, phosphorylation of the Src mitogenic substrates Stat3 and Shc were reduced by SLAP. Thus, we concluded that SLAP regulates PDGFR signaling by two independent mechanisms: a competitive mechanism for PDGF-induced Src mitogenic signaling and a non-competitive mechanism for dorsal ruffles formation mediated by c-Cbl. SLAP is a hematopoietic adaptor containing Src homology (SH)3 and SH2 motifs and a unique carboxy terminus. Unlike c-Src, SLAP lacks a tyrosine kinase domain. Unlike c-Src, SLAP does not impact resorptive function of mature osteoclasts but induces their early apoptosis. SLAP negatively regulates differentiation of osteoclasts and proliferation of their precursors. Conversely, SLAP decreases osteoclast death by inhibiting activation of caspase 3. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 104 matched cddid_all.tbl CDD cd10345 cd10345 198208 SH2_C-SH2_Zap70_Syk_like C-terminal Src homology 2 (SH2) domain found in Zeta-chain-associated protein kinase 70 (ZAP-70) and Spleen tyrosine kinase (Syk) proteins. ZAP-70 and Syk comprise a family of hematopoietic cell specific protein tyrosine kinases (PTKs) that are required for antigen and antibody receptor function. ZAP-70 is expressed in T and natural killer (NK) cells and Syk is expressed in B cells, mast cells, polymorphonuclear leukocytes, platelets, macrophages, and immature T cells. They are required for the proper development of T and B cells, immune receptors, and activating NK cells. They consist of two N-terminal Src homology 2 (SH2) domains and a C-terminal kinase domain separated from the SH2 domains by a linker or hinge region. Phosphorylation of both tyrosine residues within the Immunoreceptor Tyrosine-based Activation Motifs (ITAM; consensus sequence Yxx[LI]x(7,8)Yxx[LI]) by the Src-family PTKs is required for efficient interaction of ZAP-70 and Syk with the receptor subunits and for receptor function. ZAP-70 forms two phosphotyrosine binding pockets, one of which is shared by both SH2 domains. In Syk the two SH2 domains do not form such a phosphotyrosine-binding site. The SH2 domains here are believed to function independently. In addition, the two SH2 domains of Syk display flexibility in their relative orientation, allowing Syk to accommodate a greater variety of spacing sequences between the ITAM phosphotyrosines and singly phosphorylated non-classical ITAM ligands. This model contains the C-terminus SH2 domains of both Syk and Zap70. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 95 matched cddid_all.tbl CDD cd10346 cd10346 198209 SH2_SH2B_family Src homology 2 (SH2) domain found in SH2B adapter protein family. The SH2B adapter protein family has 3 members: SH2B1 (SH2-B, PSM), SH2B2 (APS), and SH2B3 (Lnk). SH2B family members contain a pleckstrin homology domain, at least one dimerization domain, and a C-terminal SH2 domain which binds to phosphorylated tyrosines in a variety of tyrosine kinases. SH2B1 and SH2B2 function in signaling pathways found downstream of growth hormone receptor and receptor tyrosine kinases, including the insulin, insulin-like growth factor-I (IGF-I), platelet-derived growth factor (PDGF), nerve growth factor, hepatocyte growth factor, and fibroblast growth factor receptors. SH2B2beta, a new isoform of SH2B2, is an endogenous inhibitor of SH2B1 and/or SH2B2 (SH2B2alpha), negatively regulating insulin signaling and/or JAK2-mediated cellular responses. SH2B3 negatively regulates lymphopoiesis and early hematopoiesis. The lnk-deficiency results in enhanced production of B cells, and expansion as well as enhanced function of hematopoietic stem cells (HSCs), demonstrating negative regulatory functions of Sh2b3/Lnk in cytokine signaling. Sh2b3/Lnk also functions in responses controlled by cell adhesion and in crosstalk between integrin- and cytokine-mediated signaling. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 97 matched cddid_all.tbl CDD cd10347 cd10347 198210 SH2_Nterm_shark_like N-terminal Src homology 2 (SH2) domain found in SH2 domains, ANK, and kinase domain (shark) proteins. These non-receptor protein-tyrosine kinases contain two SH2 domains, five ankyrin (ANK)-like repeats, and a potential tyrosine phosphorylation site in the carboxyl-terminal tail which resembles the phosphorylation site in members of the src family. Like, mammalian non-receptor protein-tyrosine kinases, ZAP-70 and syk proteins, they do not have SH3 domains. However, the presence of ANK makes these unique among protein-tyrosine kinases. Both tyrosine kinases and ANK repeats have been shown to transduce developmental signals, and SH2 domains are known to participate intimately in tyrosine kinase signaling. These tyrosine kinases are believed to be involved in epithelial cell polarity. The members of this family include the shark (SH2 domains, ANK, and kinase domain) gene in Drosophila and yellow fever mosquitos, as well as the hydra protein HTK16. Drosophila Shark is proposed to transduce intracellularly the Crumbs, a protein necessary for proper organization of ectodermal epithelia, intercellular signal. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 81 matched cddid_all.tbl CDD cd10348 cd10348 198211 SH2_Cterm_shark_like C-terminal Src homology 2 (SH2) domain found in SH2 domains, ANK, and kinase domain (shark) proteins. These non-receptor protein-tyrosine kinases contain two SH2 domains, five ankyrin (ANK)-like repeats, and a potential tyrosine phosphorylation site in its carboxyl-terminal tail which resembles the phosphorylation site in members of the src family. Like, mammalian non-receptor protein-tyrosine kinases, ZAP-70 and syk proteins, they do not have SH3 domains. However, the presence of ANK makes these unique among protein-tyrosine kinases. Both tyrosine kinases and ANK repeats have been shown to transduce developmental signals, and SH2 domains are known to participate intimately in tyrosine kinase signaling. These tyrosine kinases are believed to be involved in epithelial cell polarity. The members of this family include the shark (SH2 domains, ANK, and kinase domain) gene in Drosophila and yellow fever mosquitos, as well as the hydra protein HTK16. Drosophila Shark is proposed to transduce intracellularly the Crumbs, a protein necessary for proper organization of ectodermal epithelia, intercellular signal. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 86 matched cddid_all.tbl CDD cd10349 cd10349 199830 SH2_SH2D2A_SH2D7 Src homology 2 domain found in the SH2 domain containing protein 2A and 7 (SH2D2A and SH2D7). SH2D2A and SH7 both contain a single SH2 domain. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 77 matched cddid_all.tbl CDD cd10350 cd10350 198213 SH2_SH2D4A Src homology 2 domain found in the SH2 domain containing protein 4A (SH2D4A). SH2D4A contains a single SH2 domain. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 103 matched cddid_all.tbl CDD cd10351 cd10351 198214 SH2_SH2D4B Src homology 2 domain found in the SH2 domain containing protein 4B (SH2D4B). SH2D4B contains a single SH2 domain. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 103 matched cddid_all.tbl CDD cd10352 cd10352 198215 SH2_a2chimerin_b2chimerin Src homology 2 (SH2) domain found in alpha2-chimerin and beta2-chimerin proteins. Chimerins are a family of phorbol ester- and diacylglycerol-responsive GTPase-activating proteins. Alpha1-chimerin (formerly known as n-chimerin) and alpha2-chimerin are alternatively spliced products of a single gene, as are beta1- and beta2-chimerin. alpha1- and beta1-chimerin have a relatively short N-terminal region that does not encode any recognizable domains, whereas alpha2- and beta2-chimerin both include a functional SH2 domain that can bind to phosphotyrosine motifs within receptors. All of the isoforms contain a GAP domain with specificity in vitro for Rac1 and a diacylglycerol (DAG)-binding C1 domain which allows them to translocate to membranes in response to DAG signaling and anchors them in close proximity to activated Rac. Other C1 domain-containing diacylglycerol receptors including: PKC, Munc-13 proteins, phorbol ester binding scaffolding proteins involved in Ca2+-stimulated exocytosis, and RasGRPs, diacylglycerol-activated guanine-nucleotide exchange factors (GEFs) for Ras and Rap1. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 91 matched cddid_all.tbl CDD cd10353 cd10353 198216 SH2_Nterm_RasGAP N-terminal Src homology 2 (SH2) domain found in Ras GTPase-activating protein 1 (GAP). RasGAP is part of the GAP1 family of GTPase-activating proteins. The protein is located in the cytoplasm and stimulates the GTPase activity of normal RAS p21, but not its oncogenic counterpart. Acting as a suppressor of RAS function, the protein enhances the weak intrinsic GTPase activity of RAS proteins resulting in RAS inactivation, thereby allowing control of cellular proliferation and differentiation. Mutations leading to changes in the binding sites of either protein are associated with basal cell carcinomas. Alternative splicing results in two isoforms. The shorter isoform which lacks the N-terminal hydrophobic region, has the same activity, and is expressed in placental tissues. In general the longer isoform contains 2 SH2 domains, a SH3 domain, a pleckstrin homology (PH) domain, and a calcium-dependent phospholipid-binding C2 domain. The C-terminus contains the catalytic domain of RasGap which catalyzes the activation of Ras by hydrolyzing GTP-bound active Ras into an inactive GDP-bound form of Ras. This model contains the N-terminal SH2 domain. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 103 matched cddid_all.tbl CDD cd10354 cd10354 198217 SH2_Cterm_RasGAP C-terminal Src homology 2 (SH2) domain found in Ras GTPase-activating protein 1 (GAP). RasGAP is part of the GAP1 family of GTPase-activating proteins. The protein is located in the cytoplasm and stimulates the GTPase activity of normal RAS p21, but not its oncogenic counterpart. Acting as a suppressor of RAS function, the protein enhances the weak intrinsic GTPase activity of RAS proteins resulting in RAS inactivation, thereby allowing control of cellular proliferation and differentiation. Mutations leading to changes in the binding sites of either protein are associated with basal cell carcinomas. Alternative splicing results in two isoforms. The shorter isoform which lacks the N-terminal hydrophobic region, has the same activity, and is expressed in placental tissues. In general longer isoform contains 2 SH2 domains, a SH3 domain, a pleckstrin homology (PH) domain, and a calcium-dependent phospholipid-binding C2 domain. The C-terminus contains the catalytic domain of RasGap which catalyzes the activation of Ras by hydrolyzing GTP-bound active Ras into an inactive GDP-bound form of Ras. This model contains the C-terminal SH2 domain. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 77 matched cddid_all.tbl CDD cd10355 cd10355 198218 SH2_DAPP1_BAM32_like Src homology 2 domain found in dual adaptor for phosphotyrosine and 3-phosphoinositides ( DAPP1)/B lymphocyte adaptor molecule of 32 kDa (Bam32)-like proteins. DAPP1/Bam32 contains a putative myristoylation site at its N-terminus, followed by a SH2 domain, and a pleckstrin homology (PH) domain at its C-terminus. DAPP1 could potentially be recruited to the cell membrane by any of these domains. Its putative myristoylation site could facilitate the interaction of DAPP1 with the lipid bilayer. Its SH2 domain may also interact with phosphotyrosine residues on membrane-associated proteins such as activated tyrosine kinase receptors. And finally its PH domain exhibits a high-affinity interaction with the PtdIns(3,4,5)P(3) PtdIns(3,4)P(2) second messengers produced at the cell membrane following the activation of PI 3-kinases. DAPP1 is thought to interact with both tyrosine phosphorylated proteins and 3-phosphoinositides and therefore may play a role in regulating the location and/or activity of such proteins(s) in response to agonists that elevate PtdIns(3,4,5)P(3) and PtdIns(3,4)P(2). This protein is likely to play an important role in triggering signal transduction pathways that lie downstream from receptor tyrosine kinases and PI 3-kinase. It is likely that DAPP1 functions as an adaptor to recruit other proteins to the plasma membrane in response to extracellular signals. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 92 matched cddid_all.tbl CDD cd10356 cd10356 198219 SH2_ShkA_ShkC Src homology 2 (SH2) domain found in SH2 domain-bearing protein kinases A and C (ShkA and ShkC). SH2-bearing genes cloned from Dictyostelium include two transcription factors, STATa and STATc, and a signaling factor, SHK1 (shkA). A database search of the Dictyostelium discoideum genome revealed two additional putative STAT sequences, dd-STATb and dd-STATd, and four additional putative SHK genes, dd-SHK2 (shkB), dd-SHK3 (shkC), dd-SHK4 (shkD), and dd-SHK5 (shkE). This model contains members of shkA and shkC. All of the SHK members are most closely related to the protein kinases found in plants. However these kinases in plants are not conjugated to any SH2 or SH2-like sequences. Alignment data indicates that the SHK SH2 domains carry some features of the STAT SH2 domains in Dictyostelium. When STATc's linker domain was used for a BLAST search, the sequence between the protein kinase domain and the SH2 domain (the linker) of SHK was recovered, suggesting a close relationship among these molecules within this region. SHK's linker domain is predicted to contain an alpha-helix which is indeed homologous to that of STAT. Based on the phylogenetic alignment, SH2 domains can be grouped into two categories, STAT-type and Src-type. SHK family members are in between, but are closer to the STAT-type which indicates a close relationship between SHK and STAT families in their SH2 domains and further supports the notion that SHKs linker-SH2 domain evolved from STAT or STATL (STAT-like Linker-SH2) domain found in plants. In SHK, STAT, and SPT6, the linker-SH2 domains all reside exclusively in the C-terminal regions. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 113 matched cddid_all.tbl CDD cd10357 cd10357 198220 SH2_ShkD_ShkE Src homology 2 (SH2) domain found in SH2 domain-bearing protein kinases D and E (ShkD and ShkE). SH2-bearing genes cloned from Dictyostelium include two transcription factors, STATa and STATc, and a signaling factor, SHK1 (shkA). A database search of the Dictyostelium discoideum genome revealed two additional putative STAT sequences, dd-STATb and dd-STATd, and four additional putative SHK genes, dd-SHK2 (shkB), dd-SHK3 (shkC), dd-SHK4 (shkD), and dd-SHK5 (shkE). This model contains members of shkD and shkE. All of the SHK members are most closely related to the protein kinases found in plants. However these kinases in plants are not conjugated to any SH2 or SH2-like sequences. Alignment data indicates that the SHK SH2 domains carry some features of the STAT SH2 domains in Dictyostelium. When STATc's linker domain was used for a BLAST search, the sequence between the protein kinase domain and the SH2 domain (the linker) of SHK was recovered, suggesting a close relationship among these molecules within this region. SHK's linker domain is predicted to contain an alpha-helix which is indeed homologous to that of STAT. Based on the phylogenetic alignment, SH2 domains can be grouped into two categories, STAT-type and Src-type. SHK family members are in between, but are closer to the STAT-type which indicates a close relationship between SHK and STAT families in their SH2 domains and further supports the notion that SHKs linker-SH2 domain evolved from STAT or STATL (STAT-like Linker-SH2) domain found in plants. In SHK, STAT, and SPT6, the linker-SH2 domains all reside exclusively in the C-terminal regions. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 87 matched cddid_all.tbl CDD cd10358 cd10358 198221 SH2_PTK6_Brk Src homology 2 domain found in protein-tyrosine kinase-6 (PTK6) which is also known as breast tumor kinase (Brk). Human protein-tyrosine kinase-6 (PTK6, also known as breast tumor kinase (Brk)) is a member of the non-receptor protein-tyrosine kinase family and is expressed in two-thirds of all breast tumors. PTK6 (9). PTK6 contains a SH3 domain, a SH2 domain, and catalytic domains. For the case of the non-receptor protein-tyrosine kinases, the SH2 domain is typically involved in negative regulation of kinase activity by binding to a phosphorylated tyrosine residue near to the C terminus. The C-terminal sequence of PTK6 (PTSpYENPT where pY is phosphotyrosine) is thought to be a self-ligand for the SH2 domain. The structure of the SH2 domain resembles other SH2 domains except for a centrally located four-stranded antiparallel beta-sheet (strands betaA, betaB, betaC, and betaD). There are also differences in the loop length which might be responsible for PTK6 ligand specificity. There are two possible means of regulation of PTK6: autoinhibitory with the phosphorylation of Tyr playing a role in its negative regulation and autophosphorylation at this site, though it has been shown that PTK6 might phosphorylate signal transduction-associated proteins Sam68 and signal transducing adaptor family member 2 (STAP/BKS) in vivo. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 100 matched cddid_all.tbl CDD cd10359 cd10359 198222 SH2_SH3BP2 Src homology 2 domain found in c-Abl SH3 domain-binding protein-2 (SH3BP2). The adaptor protein 3BP2/SH3BP2 plays a regulatory role in signaling from immunoreceptors. The protein-tyrosine kinase Syk phosphorylates 3BP2 which results in the activation of Rac1 through the interaction with the SH2 domain of Vav1 and induces the binding to the SH2 domain of the upstream protein-tyrosine kinase Lyn and enhances its kinase activity. 3BP2 has a positive regulatory role in IgE-mediated mast cell activation. In lymphocytes, engagement of T cell or B cell receptors triggers tyrosine phosphorylation of 3BP2. Suppression of the 3BP2 expression by siRNA results in the inhibition of T cell or B cell receptor-mediated activation of NFAT. 3BP2 is required for the proliferation of B cells and B cell receptor signaling. Mutations in the 3BP2 gene are responsible for cherubism resulting in excessive bone resorption in the jaw. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 101 matched cddid_all.tbl CDD cd10360 cd10360 198223 SH2_Srm Src homology 2 (SH2) domain found in Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylation sites (srm). Srm is a nonreceptor protein kinase that has two SH2 domains, a SH3 domain, and a kinase domain with a tyrosine residue for autophosphorylation. However it lacks an N-terminal glycine for myristoylation and a C-terminal tyrosine which suppresses kinase activity when phosphorylated. Srm is most similar to members of the Tec family who other members include: Tec, Btk/Emb, and Itk/Tsk/Emt. However Srm differs in its N-terminal unique domain it being much smaller than in the Tec family and is closer to Src. Srm is thought to be a new family of nonreceptor tyrosine kinases that may be redundant in function. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 79 matched cddid_all.tbl CDD cd10361 cd10361 198224 SH2_Fps_family Src homology 2 (SH2) domain found in feline sarcoma, Fujinami poultry sarcoma, and fes-related (Fes/Fps/Fer) proteins. The Fps family consists of members Fps/Fes and Fer/Flk/Tyk3. They are cytoplasmic protein-tyrosine kinases implicated in signaling downstream from cytokines, growth factors and immune receptors. Fes/Fps/Fer contains three coiled-coil regions, an SH2 (Src-homology-2) and a TK (tyrosine kinase catalytic) domain signature. Members here include: Fps/Fes, Fer, Kin-31, and In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 90 matched cddid_all.tbl CDD cd10362 cd10362 198225 SH2_Src_Lck Src homology 2 (SH2) domain in lymphocyte cell kinase (Lck). Lck is a member of the Src non-receptor type tyrosine kinase family of proteins. It is expressed in the brain, T-cells, and NK cells. The unique domain of Lck mediates its interaction with two T-cell surface molecules, CD4 and CD8. It associates with their cytoplasmic tails on CD4 T helper cells and CD8 cytotoxic T cells to assist signaling from the T cell receptor (TCR) complex. When the T cell receptor is engaged by the specific antigen presented by MHC, Lck phosphorylase the intracellular chains of the CD3 and zeta-chains of the TCR complex, allowing ZAP-70 to bind them. Lck then phosphorylates and activates ZAP-70, which in turn phosphorylates Linker of Activated T cells (LAT), a transmembrane protein that serves as a docking site for proteins including: Shc-Grb2-SOS, PI3K, and phospholipase C (PLC). The tyrosine phosphorylation cascade culminates in the intracellular mobilization of a calcium ions and activation of important signaling cascades within the lymphocyte, including the Ras-MEK-ERK pathway, which goes on to activate certain transcription factors such as NFAT, NF-kappaB, and AP-1. These transcription factors regulate the production cytokines such as Interleukin-2 that promote long-term proliferation and differentiation of the activated lymphocytes. The N-terminal tail of Lck is myristoylated and palmitoylated and it tethers the protein to the plasma membrane of the cell. Lck also contains a SH3 domain, a SH2 domain, and a C-terminal tyrosine kinase domain. Lck has 2 phosphorylation sites, the first an autophosphorylation site that is linked to activation of the protein and the second which is phosphorylated by Csk, which inhibits it. Lck is also inhibited by SHP-1 dephosphorylation and by Cbl ubiquitin ligase, which is part of the ubiquitin-mediated pathway. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 101 matched cddid_all.tbl CDD cd10363 cd10363 198226 SH2_Src_HCK Src homology 2 (SH2) domain found in HCK. HCK is a member of the Src non-receptor type tyrosine kinase family of proteins and is expressed in hemopoietic cells. HCK is proposed to couple the Fc receptor to the activation of the respiratory burst. It may also play a role in neutrophil migration and in the degranulation of neutrophils. It has two different translational starts that have different subcellular localization. HCK has been shown to interact with BCR gene, ELMO1 Cbl gene, RAS p21 protein activator 1, RASA3, Granulocyte colony-stimulating factor receptor, ADAM15 and RAPGEF1. Like the other members of the Src family the SH2 domain in addition to binding the target, also plays an autoinhibitory role by binding to its C-terminal tail. In general SH2 domains are involved in signal transduction. HCK has a unique N-terminal domain, an SH3 domain, an SH2 domain, a kinase domain and a regulatory tail, as do the other members of the family. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 104 matched cddid_all.tbl CDD cd10364 cd10364 198227 SH2_Src_Lyn Src homology 2 (SH2) domain found in Lyn. Lyn is a member of the Src non-receptor type tyrosine kinase family of proteins and is expressed in the hematopoietic cells, in neural tissues, liver, and adipose tissue. There are two alternatively spliced forms of Lyn. Lyn plays an inhibitory role in myeloid lineage proliferation. Following engagement of the B cell receptors, Lyn undergoes rapid phosphorylation and activation, triggering a cascade of signaling events mediated by Lyn phosphorylation of tyrosine residues within the immunoreceptor tyrosine-based activation motifs (ITAM) of the receptor proteins, and subsequent recruitment and activation of other kinases including Syk, phospholipase C2 (PLC2) and phosphatidyl inositol-3 kinase. These kinases play critical roles in proliferation, Ca2+ mobilization and cell differentiation. Lyn plays an essential role in the transmission of inhibitory signals through phosphorylation of tyrosine residues within the immunoreceptor tyrosine-based inhibitory motifs (ITIM) in regulatory proteins such as CD22, PIR-B and FC RIIb1. Their ITIM phosphorylation subsequently leads to recruitment and activation of phosphatases such as SHIP-1 and SHP-1 which further down modulate signaling pathways, attenuate cell activation and can mediate tolerance. Lyn also plays a role in the insulin signaling pathway. Activated Lyn phosphorylates insulin receptor substrate 1 (IRS1) leading to an increase in translocation of Glut-4 to the cell membrane and increased glucose utilization. It is the primary Src family member involved in signaling downstream of the B cell receptor. Lyn plays an unusual, 2-fold role in B cell receptor signaling; it is essential for initiation of signaling but is also later involved in negative regulation of the signal. Lyn has a unique N-terminal domain, an SH3 domain, an SH2 domain, a kinase domain and a regulatory tail, as do the other members of the family. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 101 matched cddid_all.tbl CDD cd10365 cd10365 198228 SH2_Src_Src Src homology 2 (SH2) domain found in tyrosine kinase sarcoma (Src). Src is a member of the Src non-receptor type tyrosine kinase family of proteins. Src is thought to play a role in the regulation of embryonic development and cell growth. Members here include v-Src and c-Src. v-Src lacks the C-terminal inhibitory phosphorylation site and is therefore constitutively active as opposed to normal cellular src (c-Src) which is only activated under certain circumstances where it is required (e.g. growth factor signaling). v-Src is an oncogene whereas c-Src is a proto-oncogene. c-Src consists of three domains, an N-terminal SH3 domain, a central SH2 domain and a tyrosine kinase domain. The SH2 and SH3 domains work together in the auto-inhibition of the kinase domain. The phosphorylation of an inhibitory tyrosine near the c-terminus of the protein produces a binding site for the SH2 domain which then facilitates binding of the SH3 domain to a polyproline site within the linker between the SH2 domain and the kinase domain. Binding of the SH3 domain inactivates the enzyme. This allows for multiple mechanisms for c-Src activation: dephosphorylation of the C-terminal tyrosine by a protein tyrosine phosphatase, binding of the SH2 domain by a competitive phospho-tyrosine residue, or competitive binding of a polyproline binding site to the SH3 domain. Unlike most other Src members Src lacks cysteine residues in the SH4 domain that undergo palmitylation. Serine and threonine phosphorylation sites have also been identified in the unique domains of Src and are believed to modulate protein-protein interactions or regulate catalytic activity. Alternatively spliced forms of Src, which contain 6- or 11-amino acid insertions in the SH3 domain, are expressed in CNS neurons. c-Src has a unique N-terminal domain, an SH3 domain, an SH2 domain, a kinase domain and a regulatory tail, as do the other members of the family. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 101 matched cddid_all.tbl CDD cd10366 cd10366 198229 SH2_Src_Yes Src homology 2 (SH2) domain found in Yes. Yes is a member of the Src non-receptor type tyrosine kinase family of proteins. Yes is the cellular homolog of the Yamaguchi sarcoma virus oncogene. In humans it is encoded by the YES1 gene which maps to chromosome 18 and is in close proximity to thymidylate synthase. A corresponding Yes pseudogene has been found on chromosome 22. YES1 has been shown to interact with Janus kinase 2, CTNND1,RPL10, and Occludin. Yes1 has a unique N-terminal domain, an SH3 domain, an SH2 domain, a kinase domain and a regulatory tail, as do the other members of the family. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 101 matched cddid_all.tbl CDD cd10367 cd10367 198230 SH2_Src_Fgr Src homology 2 (SH2) domain found in Gardner-Rasheed feline sarcoma viral (v-fgr) oncogene homolog, Fgr. Fgr is a member of the Src non-receptor type tyrosine kinase family of proteins. The protein contains N-terminal sites for myristoylation and palmitoylation, a PTK domain, and SH2 and SH3 domains which are involved in mediating protein-protein interactions with phosphotyrosine-containing and proline-rich motifs, respectively. Fgr is expressed in B-cells and myeloid cells, localizes to plasma membrane ruffles, and functions as a negative regulator of cell migration and adhesion triggered by the beta-2 integrin signal transduction pathway. Multiple alternatively spliced variants, encoding the same protein, have been identified Fgr has been shown to interact with Wiskott-Aldrich syndrome protein. Fgr has a unique N-terminal domain, an SH3 domain, an SH2 domain, a kinase domain and a regulatory tail, as do the other members of the family. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 101 matched cddid_all.tbl CDD cd10368 cd10368 198231 SH2_Src_Fyn Src homology 2 (SH2) domain found in Fyn. Fyn is a member of the Src non-receptor type tyrosine kinase family of proteins. Fyn is involved in the control of cell growth and is required in the following pathways: T and B cell receptor signaling, integrin-mediated signaling, growth factor and cytokine receptor signaling, platelet activation, ion channel function, cell adhesion, axon guidance, fertilization, entry into mitosis, and differentiation of natural killer cells, oligodendrocytes and keratinocytes. The protein associates with the p85 subunit of phosphatidylinositol 3-kinase and interacts with the Fyn-binding protein. Alternatively spliced transcript variants encoding distinct isoforms exist. Fyn is primarily localized to the cytoplasmic leaflet of the plasma membrane. Tyrosine phosphorylation of target proteins by Fyn serves to either regulate target protein activity, and/or to generate a binding site on the target protein that recruits other signaling molecules. FYN has been shown to interact with a number of proteins including: BCAR1, Cbl, Janus kinase, nephrin, Sky, tyrosine kinase, Wiskott-Aldrich syndrome protein, and Zap-70. Fyn has a unique N-terminal domain, an SH3 domain, an SH2 domain, a kinase domain and a regulatory tail, as do the other members of the family. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 101 matched cddid_all.tbl CDD cd10369 cd10369 199831 SH2_Src_Frk Src homology 2 (SH2) domain found in the Fyn-related kinase (Frk). Frk is a member of the Src non-receptor type tyrosine kinase family of proteins. The Frk subfamily is composed of Frk/Rak and Iyk/Bsk/Gst. It is expressed primarily epithelial cells. Frk is a nuclear protein and may function during G1 and S phase of the cell cycle and suppress growth. Unlike the other Src members it lacks a glycine at position 2 of SH4 which is important for addition of a myristic acid moiety that is involved in targeting Src PTKs to cellular membranes. FRK and SHB exert similar effects when overexpressed in rat phaeochromocytoma (PC12) and beta-cells, where both induce PC12 cell differentiation and beta-cell proliferation. Under conditions that cause beta-cell degeneration these proteins augment beta-cell apoptosis. The FRK-SHB responses involve FAK and insulin receptor substrates (IRS) -1 and -2. Frk has been demonstrated to interact with retinoblastoma protein. Frk regulates PTEN protein stability by phosphorylating PTEN, which in turn prevents PTEN degradation. Frk also plays a role in regulation of embryonal pancreatic beta cell formation. Frk has a unique N-terminal domain, an SH3 domain, an SH2 domain, a kinase domain and a regulatory tail, as do the other members of the family. Like the other members of the Src family the SH2 domain in addition to binding the target, also plays an autoinhibitory role by binding to its activation loop. The tryosine involved is at the same site as the tyrosine involved in the autophosphorylation of Src. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 96 matched cddid_all.tbl CDD cd10370 cd10370 198233 SH2_Src_Src42 Src homology 2 (SH2) domain found in the Src oncogene at 42A (Src42). Src42 is a member of the Src non-receptor type tyrosine kinase family of proteins. The integration of receptor tyrosine kinase-induced RAS and Src42 signals by Connector eNhancer of KSR (CNK) as a two-component input is essential for RAF activation in Drosophila. Src42 is present in a wide variety of organisms including: California sea hare, pea aphid, yellow fever mosquito, honey bee, Panamanian leafcutter ant, and sea urchin. Src42 has a unique N-terminal domain, an SH3 domain, an SH2 domain, a kinase domain and a regulatory tail, as do the other members of the family. Like the other members of the Src family the SH2 domain in addition to binding the target, also plays an autoinhibitory role by binding to its C-terminal tail. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 96 matched cddid_all.tbl CDD cd10371 cd10371 198234 SH2_Src_Blk Src homology 2 (SH2) domain found in B lymphoid kinase (Blk). Blk is a member of the Src non-receptor type tyrosine kinase family of proteins. Blk is expressed in the B-cells. Unlike most other Src members Blk lacks cysteine residues in the SH4 domain that undergo palmitylation. Blk is required for the development of IL-17-producing gamma-delta T cells. Furthermore, Blk is expressed in lymphoid precursors and, in this capacity, plays a role in regulating thymus cellularity during ontogeny. Blk has a unique N-terminal domain, an SH3 domain, an SH2 domain, a kinase domain and a regulatory tail, as do the other members of the family. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 100 matched cddid_all.tbl CDD cd10372 cd10372 198235 SH2_STAT1 Src homology 2 (SH2) domain found in signal transducer and activator of transcription (STAT) 1 proteins. STAT1 is a member of the STAT family of transcription factors. STAT1 is involved in upregulating genes due to a signal by interferons. STAT1 forms homodimers or heterodimers with STAT3 that bind to the Interferon-Gamma Activated Sequence (GAS) promoter element in response to IFN-gamma stimulation. STAT1 forms a heterodimer with STAT2 that can bind Interferon Stimulated Response Element (ISRE) promoter element in response to either IFN-alpha or IFN-beta stimulation. Binding in both cases leads to an increased expression of ISG (Interferon Stimulated Genes). STAT1 has been shown to interact with protein kinase R, Src, IRF1, STAT3, MCM5, STAT2, CD117, Fanconi anemia, complementation group C, CREB-binding protein, Interleukin 27 receptor, alpha subunit, PIAS1, BRCA1, Epidermal growth factor receptor, PTK2, Mammalian target of rapamycin, IFNAR2, PRKCD, TRADD, C-jun, Calcitriol receptor, ISGF3G, and GNB2L1. STAT proteins mediate the signaling of cytokines and a number of growth factors from the receptors of these extracellular signaling molecules to the cell nucleus. STATs are specifically phosphorylated by receptor-associated Janus kinases, receptor tyrosine kinases, or cytoplasmic tyrosine kinases. The phosphorylated STAT molecules dimerize by reciprocal binding of their SH2 domains to the phosphotyrosine residues. These dimeric STATs translocate into the nucleus, bind to specific DNA sequences, and regulate the transcription of their target genes. However there are a number of unphosphorylated STATs that travel between the cytoplasm and nucleus and some STATs that exist as dimers in unstimulated cells that can exert biological functions independent of being activated. There are seven mammalian STAT family members which have been identified: STAT1, STAT2, STAT3, STAT4, STAT5 (STAT5A and STAT5B), and STAT6. There are 6 conserved domains in STAT: N-terminal domain (NTD), coiled-coil domain (CCD), DNA-binding domain (DBD), alpha-helical linker domain (LD), SH2 domain, and transactivation domain (TAD). NTD is involved in dimerization of unphosphorylated STATs monomers and for the tetramerization between STAT1, STAT3, STAT4 and STAT5 on promoters with two or more tandem STAT binding sites. It also plays a role in promoting interactions with transcriptional co-activators such as CREB binding protein (CBP)/p300, as well as being important for nuclear import and deactivation of STATs involving tyrosine de-phosphorylation. CCD interacts with other proteins, such as IFN regulatory protein 9 (IRF-9/p48) with STAT1 and c-JUN with STAT3 and is also thought to participate in the negative regulation of these proteins. Distinct genes are bound to STATs via their DBD domain. This domain is also involved in nuclear translocation of activated STAT1 and STAT3 phosphorylated dimers upon cytokine stimulation. LD links the DNA-binding and SH2 domains and is important for the transcriptional activation of STAT1 in response to IFN-gamma. It also plays a role in protein-protein interactions and has also been implicated in the constitutive nucleocytoplasmic shuttling of unphosphorylated STATs in resting cells. The SH2 domain is necessary for receptor association and tyrosine phosphodimer formation. Residues within this domain may be particularly important for some cellular functions mediated by the STATs as well as residues adjacent to this domain. The TAD interacts with several proteins, namely minichromosome maintenance complex component 5 (MCM5), breast cancer 1 (BRCA1) and CBP/p300. TAD also contains a modulatory phosphorylation site that regulates STAT activity and is necessary for maximal transcription of a number of target genes. The conserved tyrosine residue present in the C-terminus is crucial for dimerization via interaction with the SH2 domain upon the interaction of the ligand with the receptor. STAT activation by tyrosine phosphorylation also determines nuclear import and retention, DNA binding to specific DNA elements in the promoters of responsive genes, and transcriptional activation of STAT dimers. In addition to the SH2 domain there is a coiled-coil domain, a DNA binding domain, and a transactivation domain in the STAT proteins. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 151 matched cddid_all.tbl CDD cd10373 cd10373 198236 SH2_STAT2 Src homology 2 (SH2) domain found in signal transducer and activator of transcription (STAT) 2 proteins. STAT2 is a member of the STAT protein family. In response to interferon, STAT2 forms a complex with STAT1 and IFN regulatory factor family protein p48 (ISGF3G), in which this protein acts as a transactivator, but lacks the ability to bind DNA directly. Transcription adaptor P300/CBP (EP300/CREBBP) has been shown to interact specifically with STAT2, which is thought to be involved in the process of blocking IFN-alpha response by adenovirus. STAT2 has been shown to interact with MED14, CREB-binding protein, SMARCA4, STAT1, IFNAR2, IFNAR1, and ISGF3G. STAT proteins mediate the signaling of cytokines and a number of growth factors from the receptors of these extracellular signaling molecules to the cell nucleus. STATs are specifically phosphorylated by receptor-associated Janus kinases, receptor tyrosine kinases, or cytoplasmic tyrosine kinases. The phosphorylated STAT molecules dimerize by reciprocal binding of their SH2 domains to the phosphotyrosine residues. These dimeric STATs translocate into the nucleus, bind to specific DNA sequences, and regulate the transcription of their target genes. However there are a number of unphosphorylated STATs that travel between the cytoplasm and nucleus and some STATs that exist as dimers in unstimulated cells that can exert biological functions independent of being activated. There are seven mammalian STAT family members which have been identified: STAT1, STAT2, STAT3, STAT4, STAT5 (STAT5A and STAT5B), and STAT6. There are 6 conserved domains in STAT: N-terminal domain (NTD), coiled-coil domain (CCD), DNA-binding domain (DBD), alpha-helical linker domain (LD), SH2 domain, and transactivation domain (TAD). NTD is involved in dimerization of unphosphorylated STATs monomers and for the tetramerization between STAT1, STAT3, STAT4 and STAT5 on promoters with two or more tandem STAT binding sites. It also plays a role in promoting interactions with transcriptional co-activators such as CREB binding protein (CBP)/p300, as well as being important for nuclear import and deactivation of STATs involving tyrosine de-phosphorylation. CCD interacts with other proteins, such as IFN regulatory protein 9 (IRF-9/p48) with STAT1 and c-JUN with STAT3 and is also thought to participate in the negative regulation of these proteins. Distinct genes are bound to STATs via their DBD domain. This domain is also involved in nuclear translocation of activated STAT1 and STAT3 phosphorylated dimers upon cytokine stimulation. LD links the DNA-binding and SH2 domains and is important for the transcriptional activation of STAT1 in response to IFN-gamma. It also plays a role in protein-protein interactions and has also been implicated in the constitutive nucleocytoplasmic shuttling of unphosphorylated STATs in resting cells. The SH2 domain is necessary for receptor association and tyrosine phosphodimer formation. Residues within this domain may be particularly important for some cellular functions mediated by the STATs as well as residues adjacent to this domain. The TAD interacts with several proteins, namely minichromosome maintenance complex component 5 (MCM5), breast cancer 1 (BRCA1) and CBP/p300. TAD also contains a modulatory phosphorylation site that regulates STAT activity and is necessary for maximal transcription of a number of target genes. The conserved tyrosine residue present in the C-terminus is crucial for dimerization via interaction with the SH2 domain upon the interaction of the ligand with the receptor. STAT activation by tyrosine phosphorylation also determines nuclear import and retention, DNA binding to specific DNA elements in the promoters of responsive genes, and transcriptional activation of STAT dimers. In addition to the SH2 domain there is a coiled-coil domain, a DNA binding domain, and a transactivation domain in the STAT proteins. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 151 matched cddid_all.tbl CDD cd10374 cd10374 198237 SH2_STAT3 Src homology 2 (SH2) domain found in signal transducer and activator of transcription (STAT) 3 proteins. STAT3 encoded by this gene is a member of the STAT protein family. STAT3 mediates the expression of a variety of genes in response to cell stimuli, and plays a key role in many cellular processes such as cell growth and apoptosis. The small GTPase Rac1 regulates the activity of STAT3 and PIAS3 inhibits it. Three alternatively spliced transcript variants encoding distinct isoforms have been described. STAT 3 activation is required for self-renewal of embryonic stem cells (ESCs) and is essential for the differentiation of the TH17 helper T cells. Mutations in the STAT3 gene result in Hyperimmunoglobulin E syndrome and human cancers. STAT3 has been shown to interact with Androgen receptor, C-jun, ELP2, EP300, Epidermal growth factor receptor, Glucocorticoid receptor, HIF1A, Janus kinase 1, KHDRBS1, Mammalian target of rapamycin, MyoD, NDUFA13, NFKB1, Nuclear receptor coactivator 1, Promyelocytic leukemia protein, RAC1, RELA, RET proto-oncogene, RPA2, Src, STAT1, and TRIP10. STAT proteins mediate the signaling of cytokines and a number of growth factors from the receptors of these extracellular signaling molecules to the cell nucleus. STATs are specifically phosphorylated by receptor-associated Janus kinases, receptor tyrosine kinases, or cytoplasmic tyrosine kinases. The phosphorylated STAT molecules dimerize by reciprocal binding of their SH2 domains to the phosphotyrosine residues. These dimeric STATs translocate into the nucleus, bind to specific DNA sequences, and regulate the transcription of their target genes. However there are a number of unphosphorylated STATs that travel between the cytoplasm and nucleus and some STATs that exist as dimers in unstimulated cells that can exert biological functions independent of being activated. There are seven mammalian STAT family members which have been identified: STAT1, STAT2, STAT3, STAT4, STAT5 (STAT5A and STAT5B), and STAT6. There are 6 conserved domains in STAT: N-terminal domain (NTD), coiled-coil domain (CCD), DNA-binding domain (DBD), alpha-helical linker domain (LD), SH2 domain, and transactivation domain (TAD). NTD is involved in dimerization of unphosphorylated STATs monomers and for the tetramerization between STAT1, STAT3, STAT4 and STAT5 on promoters with two or more tandem STAT binding sites. It also plays a role in promoting interactions with transcriptional co-activators such as CREB binding protein (CBP)/p300, as well as being important for nuclear import and deactivation of STATs involving tyrosine de-phosphorylation. CCD interacts with other proteins, such as IFN regulatory protein 9 (IRF-9/p48) with STAT1 and c-JUN with STAT3 and is also thought to participate in the negative regulation of these proteins. Distinct genes are bound to STATs via their DBD domain. This domain is also involved in nuclear translocation of activated STAT1 and STAT3 phosphorylated dimers upon cytokine stimulation. LD links the DNA-binding and SH2 domains and is important for the transcriptional activation of STAT1 in response to IFN-gamma. It also plays a role in protein-protein interactions and has also been implicated in the constitutive nucleocytoplasmic shuttling of unphosphorylated STATs in resting cells. The SH2 domain is necessary for receptor association and tyrosine phosphodimer formation. Residues within this domain may be particularly important for some cellular functions mediated by the STATs as well as residues adjacent to this domain. The TAD interacts with several proteins, namely minichromosome maintenance complex component 5 (MCM5), breast cancer 1 (BRCA1) and CBP/p300. TAD also contains a modulatory phosphorylation site that regulates STAT activity and is necessary for maximal transcription of a number of target genes. The conserved tyrosine residue present in the C-terminus is crucial for dimerization via interaction with the SH2 domain upon the interaction of the ligand with the receptor. STAT activation by tyrosine phosphorylation also determines nuclear import and retention, DNA binding to specific DNA elements in the promoters of responsive genes, and transcriptional activation of STAT dimers. In addition to the SH2 domain there is a coiled-coil domain, a DNA binding domain, and a transactivation domain in the STAT proteins. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 162 matched cddid_all.tbl CDD cd10375 cd10375 198238 SH2_STAT4 Src homology 2 (SH2) domain found in signal transducer and activator of transcription (STAT) 4proteins. STAT4 mediate signals from the IL-12 receptors. STAT4 is mainly phosphorylated by IL-12-mediated signaling pathway in T cells. STAT4 expression is restricted in myeloid cells, thymus and testis. L-12 is the major cytokine that can activate STAT4, resulting in its tyrosine phosphorylation. The IL-12 receptor has two chains, termed IL-12R 1 and IL-12R 2, and ligand binding results in heterodimer formation and activation of the receptor associated JAK kinases, Jak2 and Tyk2. Phosphorylated STAT4 homo-dimerizes via its SH2 domain, and translocates into nucleus where it can recognize traditional N3 STAT target sequences in IL-12 responsive genes. STAT4 can also be phosphorylated in response to IFN-gamma stimulation through activation of Jak1 and Tyk2 in human. IL-17 can also activate STAT4 in human monocytic leukemia cell lines and IL-2 can induce Jak2 and Stat4 activation in NK cells but not in T cells. T helper 1 (Th1) cells produce IL-2 and IFNgamma, whereas Th2 cells secrete IL-4, IL-5, IL-6 and IL-13. Th1 cells are responsible for cell-mediated/inflammatory immunity and can enhance defenses against infectious agents and cancer, while Th2 cells are essential for humoral immunity and the clearance of parasitic antigens. The most potent factors that can promote Th1 and Th2 differentiation are the cytokines IL-12 and IL-4 respectively Although STAT4 is expressed both in Th1 and Th2 cells, STAT4 can only be phosphorylated by IL-12 which suggests that STAT4 plays an important role in Th1 cell function or development. STAT4 activation leads to Th1 differentiation, including the target genes of STAT4 such as ERM, a transcription factor that belongs to the Ets family of transcription factors. The expression of ERM is specifically induced by IL-12 in wild-type Th1 cells, but not in STAT4-deficient T cells. STAT proteins mediate the signaling of cytokines and a number of growth factors from the receptors of these extracellular signaling molecules to the cell nucleus. STATs are specifically phosphorylated by receptor-associated Janus kinases, receptor tyrosine kinases, or cytoplasmic tyrosine kinases. The phosphorylated STAT molecules dimerize by reciprocal binding of their SH2 domains to the phosphotyrosine residues. These dimeric STATs translocate into the nucleus, bind to specific DNA sequences, and regulate the transcription of their target genes. However there are a number of unphosphorylated STATs that travel between the cytoplasm and nucleus and some STATs that exist as dimers in unstimulated cells that can exert biological functions independent of being activated. There are seven mammalian STAT family members which have been identified: STAT1, STAT2, STAT3, STAT4, STAT5 (STAT5A and STAT5B), and STAT6. There are 6 conserved domains in STAT: N-terminal domain (NTD), coiled-coil domain (CCD), DNA-binding domain (DBD), alpha-helical linker domain (LD), SH2 domain, and transactivation domain (TAD). NTD is involved in dimerization of unphosphorylated STATs monomers and for the tetramerization between STAT1, STAT3, STAT4 and STAT5 on promoters with two or more tandem STAT binding sites. It also plays a role in promoting interactions with transcriptional co-activators such as CREB binding protein (CBP)/p300, as well as being important for nuclear import and deactivation of STATs involving tyrosine de-phosphorylation. CCD interacts with other proteins, such as IFN regulatory protein 9 (IRF-9/p48) with STAT1 and c-JUN with STAT3 and is also thought to participate in the negative regulation of these proteins. Distinct genes are bound to STATs via their DBD domain. This domain is also involved in nuclear translocation of activated STAT1 and STAT3 phosphorylated dimers upon cytokine stimulation. LD links the DNA-binding and SH2 domains and is important for the transcriptional activation of STAT1 in response to IFN-gamma. It also plays a role in protein-protein interactions and has also been implicated in the constitutive nucleocytoplasmic shuttling of unphosphorylated STATs in resting cells. The SH2 domain is necessary for receptor association and tyrosine phosphodimer formation. Residues within this domain may be particularly important for some cellular functions mediated by the STATs as well as residues adjacent to this domain. The TAD interacts with several proteins, namely minichromosome maintenance complex component 5 (MCM5), breast cancer 1 (BRCA1) and CBP/p300. TAD also contains a modulatory phosphorylation site that regulates STAT activity and is necessary for maximal transcription of a number of target genes. The conserved tyrosine residue present in the C-terminus is crucial for dimerization via interaction with the SH2 domain upon the interaction of the ligand with the receptor. STAT activation by tyrosine phosphorylation also determines nuclear import and retention, DNA binding to specific DNA elements in the promoters of responsive genes, and transcriptional activation of STAT dimers. In addition to the SH2 domain there is a coiled-coil domain, a DNA binding domain, and a transactivation domain in the STAT proteins. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 148 matched cddid_all.tbl CDD cd10376 cd10376 198239 SH2_STAT5 Src homology 2 (SH2) domain found in signal transducer and activator of transcription (STAT) 5 proteins. STAT5 is a member of the STAT family of transcription factors. Two highly related proteins, STAT5a and STAT5b are encoded by separate genes, but are 90% identical at the amino acid level. Both STAT5a and STAT5b are ubiquitously expressed and functionally interchangeable. Mice lacking either STAT5a or STAT5b have mild defects in prolactin dependent mammary differentiation or sexually dimorphic growth hormone-dependent effects, respectively. Mice lacking both STAT5a and STAT5b exhibit a perinatal lethal phenotype and have multiple defects, including anemia and a virtual absence of B and T lymphocytes. STAT proteins mediate the signaling of cytokines and a number of growth factors from the receptors of these extracellular signaling molecules to the cell nucleus. STATs are specifically phosphorylated by receptor-associated Janus kinases, receptor tyrosine kinases, or cytoplasmic tyrosine kinases. The phosphorylated STAT molecules dimerize by reciprocal binding of their SH2 domains to the phosphotyrosine residues. These dimeric STATs translocate into the nucleus, bind to specific DNA sequences, and regulate the transcription of their target genes. However there are a number of unphosphorylated STATs that travel between the cytoplasm and nucleus and some STATs that exist as dimers in unstimulated cells that can exert biological functions independent of being activated. There are seven mammalian STAT family members which have been identified: STAT1, STAT2, STAT3, STAT4, STAT5 (STAT5A and STAT5B), and STAT6. There are 6 conserved domains in STAT: N-terminal domain (NTD), coiled-coil domain (CCD), DNA-binding domain (DBD), alpha-helical linker domain (LD), SH2 domain, and transactivation domain (TAD). NTD is involved in dimerization of unphosphorylated STATs monomers and for the tetramerization between STAT1, STAT3, STAT4 and STAT5 on promoters with two or more tandem STAT binding sites. It also plays a role in promoting interactions with transcriptional co-activators such as CREB binding protein (CBP)/p300, as well as being important for nuclear import and deactivation of STATs involving tyrosine de-phosphorylation. CCD interacts with other proteins, such as IFN regulatory protein 9 (IRF-9/p48) with STAT1 and c-JUN with STAT3 and is also thought to participate in the negative regulation of these proteins. Distinct genes are bound to STATs via their DBD domain. This domain is also involved in nuclear translocation of activated STAT1 and STAT3 phosphorylated dimers upon cytokine stimulation. LD links the DNA-binding and SH2 domains and is important for the transcriptional activation of STAT1 in response to IFN-gamma. It also plays a role in protein-protein interactions and has also been implicated in the constitutive nucleocytoplasmic shuttling of unphosphorylated STATs in resting cells. The SH2 domain is necessary for receptor association and tyrosine phosphodimer formation. Residues within this domain may be particularly important for some cellular functions mediated by the STATs as well as residues adjacent to this domain. The TAD interacts with several proteins, namely minichromosome maintenance complex component 5 (MCM5), breast cancer 1 (BRCA1) and CBP/p300. TAD also contains a modulatory phosphorylation site that regulates STAT activity and is necessary for maximal transcription of a number of target genes. The conserved tyrosine residue present in the C-terminus is crucial for dimerization via interaction with the SH2 domain upon the interaction of the ligand with the receptor. STAT activation by tyrosine phosphorylation also determines nuclear import and retention, DNA binding to specific DNA elements in the promoters of responsive genes, and transcriptional activation of STAT dimers. In addition to the SH2 domain there is a coiled-coil domain, a DNA binding domain, and a transactivation domain in the STAT proteins. 137 matched cddid_all.tbl CDD cd10377 cd10377 198240 SH2_STAT6 Src homology 2 (SH2) domain found in signal transducer and activator of transcription (STAT) 6 proteins. STAT6 mediate signals from the IL-4 receptor. Unlike the other STAT proteins which bind an IFNgamma Activating Sequence (GAS), STAT6 stands out as having a unique binding site preference. This site consists of a palindromic sequence separated by a 3 bp spacer (TTCNNNG-AA)(N3 site). STAT6 is able to bind the GAS site but only at a low affinity. STAT6 may be an important regulator of mitogenesis when cells respond normally to IL-4. There is speculation that the inappropriate activation of STAT6 is involved in uncontrolled cell growth in an oncogenic state. IFNgamma is a negative regulator of STAT6 dependent transcription of target genes. Bcl-6 is another negative regulator of STAT6 activity. Bcl-6 is a transcriptional repressor normally expressed in germinal center B cells and some T cells. IL-4 signaling via STAT6 initially occurs unopposed, but is then dampened by a negative feedback mechanism through the IL-4/Stat6 dependent induction of SOCS1 expression. The IL-4 dependent aspect of Th2 differentiation requires the activation of STAT6. IL-4 signaling and STAT6 appear to play an important role in the immune response. Recently, it was shown that large scale chromatin remodeling of the IL-4 gene occurs as cells differentiate into Th2 effectors is STAT6 dependent. STAT proteins mediate the signaling of cytokines and a number of growth factors from the receptors of these extracellular signaling molecules to the cell nucleus. STATs are specifically phosphorylated by receptor-associated Janus kinases, receptor tyrosine kinases, or cytoplasmic tyrosine kinases. The phosphorylated STAT molecules dimerize by reciprocal binding of their SH2 domains to the phosphotyrosine residues. These dimeric STATs translocate into the nucleus, bind to specific DNA sequences, and regulate the transcription of their target genes. However there are a number of unphosphorylated STATs that travel between the cytoplasm and nucleus and some STATs that exist as dimers in unstimulated cells that can exert biological functions independent of being activated. There are seven mammalian STAT family members which have been identified: STAT1, STAT2, STAT3, STAT4, STAT5 (STAT5A and STAT5B), and STAT6. There are 6 conserved domains in STAT: N-terminal domain (NTD), coiled-coil domain (CCD), DNA-binding domain (DBD), alpha-helical linker domain (LD), SH2 domain, and transactivation domain (TAD). NTD is involved in dimerization of unphosphorylated STATs monomers and for the tetramerization between STAT1, STAT3, STAT4 and STAT5 on promoters with two or more tandem STAT binding sites. It also plays a role in promoting interactions with transcriptional co-activators such as CREB binding protein (CBP)/p300, as well as being important for nuclear import and deactivation of STATs involving tyrosine de-phosphorylation. CCD interacts with other proteins, such as IFN regulatory protein 9 (IRF-9/p48) with STAT1 and c-JUN with STAT3 and is also thought to participate in the negative regulation of these proteins. Distinct genes are bound to STATs via their DBD domain. This domain is also involved in nuclear translocation of activated STAT1 and STAT3 phosphorylated dimers upon cytokine stimulation. LD links the DNA-binding and SH2 domains and is important for the transcriptional activation of STAT1 in response to IFN-gamma. It also plays a role in protein-protein interactions and has also been implicated in the constitutive nucleocytoplasmic shuttling of unphosphorylated STATs in resting cells. The SH2 domain is necessary for receptor association and tyrosine phosphodimer formation. Residues within this domain may be particularly important for some cellular functions mediated by the STATs as well as residues adjacent to this domain. The TAD interacts with several proteins, namely minichromosome maintenance complex component 5 (MCM5), breast cancer 1 (BRCA1) and CBP/p300. TAD also contains a modulatory phosphorylation site that regulates STAT activity and is necessary for maximal transcription of a number of target genes. The conserved tyrosine residue present in the C-terminus is crucial for dimerization via interaction with the SH2 domain upon the interaction of the ligand with the receptor. STAT activation by tyrosine phosphorylation also determines nuclear import and retention, DNA binding to specific DNA elements in the promoters of responsive genes, and transcriptional activation of STAT dimers. In addition to the SH2 domain there is a coiled-coil domain, a DNA binding domain, and a transactivation domain in the STAT proteins. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 129 matched cddid_all.tbl CDD cd10378 cd10378 198241 SH2_Jak1 Src homology 2 (SH2) domain in the Janus kinase 1 (Jak1) proteins. Janus kinase 1 (JAK1), is a member of a class of protein-tyrosine kinases (PTK) characterized by the presence of a second phosphotransferase-related domain immediately N-terminal to the PTK domain. The second phosphotransferase domain bears all the hallmarks of a protein kinase, although its structure differs significantly from that of the PTK and threonine/serine kinase family members. JAK1 is a large, widely expressed membrane-associated phosphoprotein. JAK1 is involved in the interferon-alpha/beta and -gamma signal transduction pathways. The reciprocal interdependence between JAK1 and TYK2 activities in the interferon-alpha pathway, and between JAK1 and JAK2 in the interferon-gamma pathway, may reflect a requirement for these kinases in the correct assembly of interferon receptor complexes. These kinases couple cytokine ligand binding to tyrosine phosphorylation of various known signaling proteins and of a unique family of transcription factors termed the signal transducers and activators of transcription, or STATs. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 102 matched cddid_all.tbl CDD cd10379 cd10379 198242 SH2_Jak2 Src homology 2 (SH2) domain in the Janus kinase 2 (Jak2) proteins. Jak2 is a protein tyrosine kinase involved in a specific subset of cytokine receptor signaling pathways. It has been found to be constitutively associated with the prolactin receptor and is required for responses to gamma interferon. Mice that do not express an active protein for this gene exhibit embryonic lethality associated with the absence of definitive erythropoiesis. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 97 matched cddid_all.tbl CDD cd10380 cd10380 198243 SH2_Jak3 Src homology 2 (SH2) domain in the Janus kinase 3 (Jak3) proteins. Jak3 is a member of the Janus kinase (JAK) family of tyrosine kinases involved in cytokine receptor-mediated intracellular signal transduction. It is predominantly expressed in immune cells and transduces a signal in response to its activation via tyrosine phosphorylation by interleukin receptors. Mutations in this gene are associated with autosomal SCID (severe combined immunodeficiency disease). In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 96 matched cddid_all.tbl CDD cd10381 cd10381 198244 SH2_Jak_Tyk2 Src homology 2 (SH2) domain in Tyrosine Kinase 2 (Tyk2), a member of the Janus kinases (JAK). Tyk2 is a member of the tyrosine kinase and, more specifically, the Janus kinases (JAKs) protein families. This protein associates with the cytoplasmic domain of type I and type II cytokine receptors and promulgate cytokine signals by phosphorylating receptor subunits. It is also component of both the type I and type III interferon signaling pathways. As such, it may play a role in anti-viral immunity. A mutation in this gene has been associated with hyperimmunoglobulin E syndrome (HIES) - a primary immunodeficiency characterized by elevated serum immunoglobulin E. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 102 matched cddid_all.tbl CDD cd10382 cd10382 198245 SH2_SOCS1 Src homology 2 (SH2) domain found in suppressor of cytokine signaling (SOCS) proteins. SH2 domain found in SOCS proteins. SOCS was first recognized as a group of cytokine-inducible SH2 (CIS) domain proteins comprising eight family members in human (CIS and SOCS1-SOCS7). In addition to the SH2 domain, SOCS proteins have a variable N-terminal domain and a conserved SOCS box in the C-terminal domain. SOCS proteins bind to a substrate via their SH2 domain. The prototypical members, CIS and SOCS1-SOCS3, have been shown to regulate growth hormone signaling in vitro and in a classic negative feedback response compete for binding at phosphotyrosine sites in JAK kinase and receptor pathways to displace effector proteins and target bound receptors for proteasomal degradation. Loss of SOCS activity results in excessive cytokine signaling associated with a variety of hematopoietic, autoimmune, and inflammatory diseases and certain cancers. Members (SOCS4-SOCS7) were identified by their conserved SOCS box, an adapter motif of 3 helices that associates substrate binding domains, such as the SOCS SH2 domain, ankryin, and WD40 with ubiquitin ligase components. These show limited cytokine induction. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 98 matched cddid_all.tbl CDD cd10383 cd10383 198246 SH2_SOCS2 Src homology 2 (SH2) domain found in suppressor of cytokine signaling (SOCS) proteins. SH2 domain found in SOCS proteins. SOCS was first recognized as a group of cytokine-inducible SH2 (CIS) domain proteins comprising eight family members in human (CIS and SOCS1-SOCS7). In addition to the SH2 domain, SOCS proteins have a variable N-terminal domain and a conserved SOCS box in the C-terminal domain. SOCS proteins bind to a substrate via their SH2 domain. The prototypical members, CIS and SOCS1-SOCS3, have been shown to regulate growth hormone signaling in vitro and in a classic negative feedback response compete for binding at phosphotyrosine sites in JAK kinase and receptor pathways to displace effector proteins and target bound receptors for proteasomal degradation. Loss of SOCS activity results in excessive cytokine signaling associated with a variety of hematopoietic, autoimmune, and inflammatory diseases and certain cancers. Members (SOCS4-SOCS7) were identified by their conserved SOCS box, an adapter motif of 3 helices that associates substrate binding domains, such as the SOCS SH2 domain, ankryin, and WD40 with ubiquitin ligase components. These show limited cytokine induction. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 103 matched cddid_all.tbl CDD cd10384 cd10384 198247 SH2_SOCS3 Src homology 2 (SH2) domain found in suppressor of cytokine signaling (SOCS) proteins. SH2 domain found in SOCS proteins. SOCS was first recognized as a group of cytokine-inducible SH2 (CIS) domain proteins comprising eight family members in human (CIS and SOCS1-SOCS7). In addition to the SH2 domain, SOCS proteins have a variable N-terminal domain and a conserved SOCS box in the C-terminal domain. SOCS proteins bind to a substrate via their SH2 domain. The prototypical members, CIS and SOCS1-SOCS3, have been shown to regulate growth hormone signaling in vitro and in a classic negative feedback response compete for binding at phosphotyrosine sites in JAK kinase and receptor pathways to displace effector proteins and target bound receptors for proteasomal degradation. Loss of SOCS activity results in excessive cytokine signaling associated with a variety of hematopoietic, autoimmune, and inflammatory diseases and certain cancers. Members (SOCS4-SOCS7) were identified by their conserved SOCS box, an adapter motif of 3 helices that associates substrate binding domains, such as the SOCS SH2 domain, ankryin, and WD40 with ubiquitin ligase components. These show limited cytokine induction. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 101 matched cddid_all.tbl CDD cd10385 cd10385 198248 SH2_SOCS4 Src homology 2 (SH2) domain found in suppressor of cytokine signaling (SOCS) proteins. SH2 domain found in SOCS proteins. SOCS was first recognized as a group of cytokine-inducible SH2 (CIS) domain proteins comprising eight family members in human (CIS and SOCS1-SOCS7). In addition to the SH2 domain, SOCS proteins have a variable N-terminal domain and a conserved SOCS box in the C-terminal domain. SOCS proteins bind to a substrate via their SH2 domain. The prototypical members, CIS and SOCS1-SOCS3, have been shown to regulate growth hormone signaling in vitro and in a classic negative feedback response compete for binding at phosphotyrosine sites in JAK kinase and receptor pathways to displace effector proteins and target bound receptors for proteasomal degradation. Loss of SOCS activity results in excessive cytokine signaling associated with a variety of hematopoietic, autoimmune, and inflammatory diseases and certain cancers. Members (SOCS4-SOCS7) were identified by their conserved SOCS box, an adapter motif of 3 helices that associates substrate binding domains, such as the SOCS SH2 domain, ankryin, and WD40 with ubiquitin ligase components. These show limited cytokine induction. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 101 matched cddid_all.tbl CDD cd10386 cd10386 198249 SH2_SOCS5 Src homology 2 (SH2) domain found in suppressor of cytokine signaling (SOCS) family. SH2 domain found in SOCS proteins. SOCS was first recognized as a group of cytokine-inducible SH2 (CIS) domain proteins comprising eight family members in human (CIS and SOCS1-SOCS7). In addition to the SH2 domain, SOCS proteins have a variable N-terminal domain and a conserved SOCS box in the C-terminal domain. SOCS proteins bind to a substrate via their SH2 domain. The prototypical members, CIS and SOCS1-SOCS3, have been shown to regulate growth hormone signaling in vitro and in a classic negative feedback response compete for binding at phosphotyrosine sites in JAK kinase and receptor pathways to displace effector proteins and target bound receptors for proteasomal degradation. Loss of SOCS activity results in excessive cytokine signaling associated with a variety of hematopoietic, autoimmune, and inflammatory diseases and certain cancers. Members (SOCS4-SOCS7) were identified by their conserved SOCS box, an adapter motif of 3 helices that associates substrate binding domains, such as the SOCS SH2 domain, ankryin, and WD40 with ubiquitin ligase components. These show limited cytokine induction. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 81 matched cddid_all.tbl CDD cd10387 cd10387 198250 SH2_SOCS6 Src homology 2 (SH2) domain found in suppressor of cytokine signaling (SOCS) proteins. SH2 domain found in SOCS proteins. SOCS was first recognized as a group of cytokine-inducible SH2 (CIS) domain proteins comprising eight family members in human (CIS and SOCS1-SOCS7). In addition to the SH2 domain, SOCS proteins have a variable N-terminal domain and a conserved SOCS box in the C-terminal domain. SOCS proteins bind to a substrate via their SH2 domain. The prototypical members, CIS and SOCS1-SOCS3, have been shown to regulate growth hormone signaling in vitro and in a classic negative feedback response compete for binding at phosphotyrosine sites in JAK kinase and receptor pathways to displace effector proteins and target bound receptors for proteasomal degradation. Loss of SOCS activity results in excessive cytokine signaling associated with a variety of hematopoietic, autoimmune, and inflammatory diseases and certain cancers. Members (SOCS4-SOCS7) were identified by their conserved SOCS box, an adapter motif of 3 helices that associates substrate binding domains, such as the SOCS SH2 domain, ankryin, and WD40 with ubiquitin ligase components. These show limited cytokine induction. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 100 matched cddid_all.tbl CDD cd10388 cd10388 198251 SH2_SOCS7 Src homology 2 (SH2) domain found in suppressor of cytokine signaling (SOCS) proteins. SH2 domain found in SOCS proteins. SOCS was first recognized as a group of cytokine-inducible SH2 (CIS) domain proteins comprising eight family members in human (CIS and SOCS1-SOCS7). In addition to the SH2 domain, SOCS proteins have a variable N-terminal domain and a conserved SOCS box in the C-terminal domain. SOCS proteins bind to a substrate via their SH2 domain. The prototypical members, CIS and SOCS1-SOCS3, have been shown to regulate growth hormone signaling in vitro and in a classic negative feedback response compete for binding at phosphotyrosine sites in JAK kinase and receptor pathways to displace effector proteins and target bound receptors for proteasomal degradation. Loss of SOCS activity results in excessive cytokine signaling associated with a variety of hematopoietic, autoimmune, and inflammatory diseases and certain cancers. Members (SOCS4-SOCS7) were identified by their conserved SOCS box, an adapter motif of 3 helices that associates substrate binding domains, such as the SOCS SH2 domain, ankryin, and WD40 with ubiquitin ligase components. These show limited cytokine induction. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 101 matched cddid_all.tbl CDD cd10389 cd10389 198252 SH2_SHB Src homology 2 domain found in SH2 domain-containing adapter protein B (SHB). SHB functions in generating signaling compounds in response to tyrosine kinase activation. SHB contains proline-rich motifs, a phosphotyrosine binding (PTB) domain, tyrosine phosphorylation sites, and a SH2 domain. SHB mediates certain aspects of platelet-derived growth factor (PDGF) receptor-, fibroblast growth factor (FGF) receptor-, neural growth factor (NGF) receptor TRKA-, T cell receptor-, interleukin-2 (IL-2) receptor- and focal adhesion kinase- (FAK) signaling. SRC-like FYN-Related Kinase FRK/RAK (also named BSK/IYK or GTK) and SHB regulate apoptosis, proliferation and differentiation. SHB promotes apoptosis and is also required for proper mitogenicity, spreading and tubular morphogenesis in endothelial cells. SHB also plays a role in preventing early cavitation of embryoid bodies and reduces differentiation to cells expressing albumin, amylase, insulin and glucagon. SHB is a multifunctional protein that has difference responses in different cells under various conditions. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 97 matched cddid_all.tbl CDD cd10390 cd10390 198253 SH2_SHD Src homology 2 domain found in SH2 domain-containing adapter proteins D (SHD). The expression of SHD is restricted to the brain. SHD may be a physiological substrate of c-Abl and may function as an adapter protein in the central nervous system. It is also thought to be involved in apoptotic regulation. SHD contains five YXXP motifs, a substrate sequence preferred by Abl tyrosine kinases, in addition to a poly-proline rich region and a C-terminal SH2 domain. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 98 matched cddid_all.tbl CDD cd10391 cd10391 198254 SH2_SHE Src homology 2 domain found in SH2 domain-containing adapter protein E (SHE). SHE is expressed in heart, lung, brain, and skeletal muscle. SHE contains two pTry protein binding domains, protein interaction domain (PID) and a SH2 domain, followed by a glycine-proline rich region, all of which are N-terminal to the phosphotyrosine binding (PTB) domain. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 98 matched cddid_all.tbl CDD cd10392 cd10392 198255 SH2_SHF Src homology 2 domain found in SH2 domain-containing adapter protein F (SHF). SHF is thought to play a role in PDGF-receptor signaling and regulation of apoptosis. SHF is mainly expressed in skeletal muscle, brain, liver, prostate, testis, ovary, small intestine, and colon. SHF contains four putative tyrosine phosphorylation sites and an SH2 domain. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 98 matched cddid_all.tbl CDD cd10393 cd10393 198256 SH2_RIN1 Src homology 2 (SH2) domain found in Ras and Rab interactor 1 (RIN1)-like proteins. RIN1, a member of the RIN (AKA Ras interaction/interference) family, have multifunctional domains including SH2 and proline-rich (PR) domains in the N-terminal region, and RIN-family homology (RH), VPS9 and Ras-association (RA) domains in the C-terminal region. RIN proteins function as Rab5-GEFs. Previous studies showed that RIN1 interacts with EGF receptors via its SH2 domain and regulates trafficking and degradation of EGF receptors via its interaction with STAM, indicating a vital role for RIN1 in regulating endosomal trafficking of receptor tyrosine kinases (RTKs). RIN1 was first identified as a Ras-binding protein that suppresses the activated RAS2 allele in S. cerevisiae. RIN1 binds to the activated Ras through its carboxyl-terminal domain and this Ras-binding domain also binds to 14-3-3 proteins as Raf-1 does. The SH2 domain of RIN1 are thought to interact with the phosphotyrosine-containing proteins, but the physiological partners for this domain are unknown. The proline-rich domain in RIN1 is similar to the consensus SH3 binding regions. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 101 matched cddid_all.tbl CDD cd10394 cd10394 198257 SH2_RIN2 Src homology 2 (SH2) domain found in Ras and Rab interactor 2 (RIN2)-like proteins. RIN2, a member of the RIN (AKA Ras interaction/interference) family, have multifunctional domains including SH2 and proline-rich (PR) domains in the N-terminal region, and RIN-family homology (RH), VPS9 and Ras-association (RA) domains in the C-terminal region. RIN proteins function as Rab5-GEFs. Ras induces activation of Rab5 through RIN2, which is a direct downstream target of Ras and a direct upstream regulator of Rab5. In other words it is the binding of the GTP-bound form of Ras to the RA domain of RIN2 that enhances the GEF activity toward Rab5. It is thought that the RA domain negatively regulates the Rab5 GEF activity. In steady state, RIN2 is likely to form a closed conformation by an intramolecular interaction between the RA domain and the Vps9p-like (Rab5 GEF) domain, negatively regulating the Rab5 GEF activity. In the active state, the binding of Ras to the RA domain may reduce the intramolecular interaction and stabilize an open conformation of RIN2. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 100 matched cddid_all.tbl CDD cd10395 cd10395 198258 SH2_RIN3 Src homology 2 (SH2) domain found in Ras and Rab interactor 3 (RIN3)-like proteins. RIN3, a member of the RIN (AKA Ras interaction/interference) family, have multifunctional domains including SH2 and proline-rich (PR) domains in the N-terminal region, and RIN-family homology (RH), VPS9 and Ras-association (RA) domains in the C-terminal region. RIN proteins function as Rab5-GEFs. RIN3 stimulated the formation of GTP-bound Rab31, a Rab5-subfamily GTPase, and formed enlarged vesicles and tubular structures, where it colocalized with Rab31. Transferrin appeared to be transported partly through the RIN3-positive vesicles to early endosomes. RIN3 interacts via its Pro-rich domain with amphiphysin II, which contains SH3 domain and participates in receptor-mediated endocytosis. RIN3, a Rab5 and Rab31 GEF, plays an important role in the transport pathway from plasma membrane to early endosomes. Mutations in the region between the SH2 and RH domain of RIN3 specifically abolished its GEF action on Rab31, but not Rab5. RIN3 was also found to partially translocate the cation-dependent mannose 6-phosphate receptor from the trans-Golgi network to peripheral vesicles and that this is dependent on its Rab31-GEF activity. These data indicate that RIN3 specifically acts as a GEF for Rab31. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 101 matched cddid_all.tbl CDD cd10396 cd10396 198259 SH2_Tec_Itk Src homology 2 (SH2) domain found in Tec protein, IL2-inducible T-cell kinase (Itk). A member of the Tec protein tyrosine kinase Itk is expressed thymus, spleen, lymph node, T lymphocytes, NK and mast cells. It plays a role in T-cell proliferation and differentiation, analogous to Tec family kinases Txk. Itk has been shown to interact with Fyn, Wiskott-Aldrich syndrome protein, KHDRBS1, PLCG1, Lymphocyte cytosolic protein 2, Linker of activated T cells, Karyopherin alpha 2, Grb2, and Peptidylprolyl isomerase A. Most of the Tec family members have a PH domain (Txk and the short (type 1) splice variant of Drosophila Btk29A are exceptions), a Tec homology (TH) domain, a SH3 domain, a SH2 domain, and a protein kinase catalytic domain. The TH domain consists of a Zn2+-binding Btk motif and a proline-rich region. The Btk motif is found in Tec kinases, Ras GAP, and IGBP. It is crucial for the function of Tec PH domains and it's lack of presence in Txk is not surprising since it lacks a PH domain. The type 1 splice form of the Drosophila homolog also lacks both the PH domain and the Btk motif. The proline-rich regions are highly conserved for the most part with the exception of Bmx whose residues surrounding the PXXP motif are not conserved (TH-like) and Btk29A which is entirely unique with large numbers of glycine residues (TH-extended). Tec family members all lack a C-terminal tyrosine having an autoinhibitory function in its phosphorylated state. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 108 matched cddid_all.tbl CDD cd10397 cd10397 198260 SH2_Tec_Btk Src homology 2 (SH2) domain found in Tec protein, Bruton's tyrosine kinase (Btk). A member of the Tec protein tyrosine kinase Btk is expressed in bone marrow, spleen, all hematopoietic cells except T lymphocytes and plasma cells where it plays a crucial role in B cell maturation and mast cell activation. Btk has been shown to interact with GNAQ, PLCG2, protein kinase D1, B-cell linker, SH3BP5, caveolin 1, ARID3A, and GTF2I. Most of the Tec family members have a PH domain (Txk and the short (type 1) splice variant of Drosophila Btk29A are exceptions), a Tec homology (TH) domain, a SH3 domain, a SH2 domain, and a protein kinase catalytic domain. Btk is implicated in the primary immunodeficiency disease X-linked agammaglobulinemia (Bruton's agammaglobulinemia). The TH domain consists of a Zn2+-binding Btk motif and a proline-rich region. The Btk motif is found in Tec kinases, Ras GAP, and IGBP. It is crucial for the function of Tec PH domains and it's lack of presence in Txk is not surprising since it lacks a PH domain. The type 1 splice form of the Drosophila homolog also lacks both the PH domain and the Btk motif. The proline-rich regions are highly conserved for the most part with the exception of Bmx whose residues surrounding the PXXP motif are not conserved (TH-like) and Btk29A which is entirely unique with large numbers of glycine residues (TH-extended). Tec family members all lack a C-terminal tyrosine having an autoinhibitory function in its phosphorylated state. Two tyrosine phosphorylation (pY) sites have been identified in Btk: one located in the activation loop of the catalytic domain which regulates the transition between open (active) and closed (inactive) states and the other in its SH3 domain. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 106 matched cddid_all.tbl CDD cd10398 cd10398 198261 SH2_Tec_Txk Src homology 2 (SH2) domain found in Tec protein, Txk. A member of the Tec protein tyrosine kinase Txk is expressed in thymus, spleen, lymph node, T lymphocytes, NK cells, mast cell lines, and myeloid cell line. Txk plays a role in TCR signal transduction, T cell development, and selection which is analogous to the function of Itk. Txk has been shown to interact with IFN-gamma. Unlike most of the Tec family members Txk lacks a PH domain. Instead Txk has a unique region containing a palmitoylated cysteine string which has a similar membrane tethering function as the PH domain. Txk also has a zinc-binding motif, a SH3 domain, a SH2 domain, and a protein kinase catalytic domain. The TH domain consists of a Zn2+-binding Btk motif and a proline-rich region. The Btk motif is found in Tec kinases, Ras GAP, and IGBP and crucial to the function of the PH domain. It is not present in Txk which is not surprising since it lacks a PH domain. The type 1 splice form of the Drosophila homolog also lacks both the PH domain and the Btk motif. The proline-rich regions are highly conserved for the most part with the exception of Bmx whose residues surrounding the PXXP motif are not conserved (TH-like) and Btk29A which is entirely unique with large numbers of glycine residues (TH-extended). Tec family members all lack a C-terminal tyrosine having an autoinhibitory function in its phosphorylated state. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 106 matched cddid_all.tbl CDD cd10399 cd10399 198262 SH2_Tec_Bmx Src homology 2 (SH2) domain found in Tec protein, Bmx. A member of the Tec protein tyrosine kinase Bmx is expressed in the endothelium of large arteries, fetal endocardium, adult endocardium of the left ventricle, bone marrow, lung, testis, granulocytes, myeloid cell lines, and prostate cell lines. Bmx is involved in the regulation of Rho and serum response factor (SRF). Bmx has been shown to interact with PAK1, PTK2, PTPN21, and RUFY1. Most of the Tec family members have a PH domain (Txk and the short (type 1) splice variant of Drosophila Btk29A are exceptions), a Tec homology (TH) domain, a SH3 domain, a SH2 domain, and a protein kinase catalytic domain. The TH domain consists of a Zn2+-binding Btk motif and a proline-rich region. The Btk motif is found in Tec kinases, Ras GAP, and IGBP. It is crucial for the function of Tec PH domains. It is not present in Txk and the type 1 splice form of the Drosophila homolog. The proline-rich regions are highly conserved for the most part with the exception of Bmx whose residues surrounding the PXXP motif are not conserved (TH-like) and Btk29A which is entirely unique with large numbers of glycine residues (TH-extended). Tec family members all lack a C-terminal tyrosine having an autoinhibitory function in its phosphorylated state. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 106 matched cddid_all.tbl CDD cd10400 cd10400 198263 SH2_SAP1a Src homology 2 (SH2) domain found in SLAM-associated protein (SAP) 1a. The X-linked lymphoproliferative syndrome (XLP) gene encodes SAP (also called SH2D1A/DSHP) a protein that consists of a 5 residue N-terminus, a single SH2 domain, and a short 25 residue C-terminal tail. XLP is characterized by an extreme sensitivity to Epstein-Barr virus. Both T and natural killer (NK) cell dysfunctions have been seen in XLP patients. SAP binds the cytoplasmic tail of Signaling lymphocytic activation molecule (SLAM), 2B4, Ly-9, and CD84. SAP is believed to function as a signaling inhibitor, by blocking or regulating binding of other signaling proteins. SAP and the SAP-like protein EAT-2 recognize the sequence motif TIpYXX[VI], which is found in the cytoplasmic domains of a restricted number of T, B, and NK cell surface receptors and are proposed to be natural inhibitors or regulators of the physiological role of a small family of receptors on the surface of these cells. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 103 matched cddid_all.tbl CDD cd10401 cd10401 198264 SH2_C-SH2_Syk_like C-terminal Src homology 2 (SH2) domain found in Spleen tyrosine kinase (Syk) proteins. ZAP-70 and Syk comprise a family of hematopoietic cell specific protein tyrosine kinases (PTKs) that are required for antigen and antibody receptor function. ZAP-70 is expressed in T and natural killer (NK) cells and Syk is expressed in B cells, mast cells, polymorphonuclear leukocytes, platelets, macrophages, and immature T cells. They are required for the proper development of T and B cells, immune receptors, and activating NK cells. They consist of two N-terminal Src homology 2 (SH2) domains and a C-terminal kinase domain separated from the SH2 domains by a linker or hinge region. Phosphorylation of both tyrosine residues within the Immunoreceptor Tyrosine-based Activation Motifs (ITAM; consensus sequence Yxx[LI]x(7,8)Yxx[LI]) by the Src-family PTKs is required for efficient interaction of ZAP-70 and Syk with the receptor subunits and for receptor function. ZAP-70 forms two phosphotyrosine binding pockets, one of which is shared by both SH2 domains. In Syk the two SH2 domains do not form such a phosphotyrosine-binding site. The SH2 domains here are believed to function independently. In addition, the two SH2 domains of Syk display flexibility in their relative orientation, allowing Syk to accommodate a greater variety of spacing sequences between the ITAM phosphotyrosines and singly phosphorylated non-classical ITAM ligands. This model contains the C-terminus SH2 domains of Syk. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 99 matched cddid_all.tbl CDD cd10402 cd10402 198265 SH2_C-SH2_Zap70 C-terminal Src homology 2 (SH2) domain found in Zeta-chain-associated protein kinase 70 (ZAP-70). ZAP-70 and Syk comprise a family of hematopoietic cell specific protein tyrosine kinases (PTKs) that are required for antigen and antibody receptor function. ZAP-70 is expressed in T and natural killer (NK) cells and Syk is expressed in B cells, mast cells, polymorphonuclear leukocytes, platelets, macrophages, and immature T cells. They are required for the proper development of T and B cells, immune receptors, and activating NK cells. They consist of two N-terminal Src homology 2 (SH2) domains and a C-terminal kinase domain separated from the SH2 domains by a linker or hinge region. Phosphorylation of both tyrosine residues within the Immunoreceptor Tyrosine-based Activation Motifs (ITAM; consensus sequence Yxx[LI]x(7,8)Yxx[LI]) by the Src-family PTKs is required for efficient interaction of ZAP-70 and Syk with the receptor subunits and for receptor function. ZAP-70 forms two phosphotyrosine binding pockets, one of which is shared by both SH2 domains. In Syk the two SH2 domains do not form such a phosphotyrosine-binding site. The SH2 domains here are believed to function independently. In addition, the two SH2 domains of Syk display flexibility in their relative orientation, allowing Syk to accommodate a greater variety of spacing sequences between the ITAM phosphotyrosines and singly phosphorylated non-classical ITAM ligands. This model contains the C-terminus SH2 domains of Zap70. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 105 matched cddid_all.tbl CDD cd10403 cd10403 198266 SH2_STAP1 Src homology 2 domain found in Signal-transducing adaptor protein 1 (STAP1). STAP1 is a signal-transducing adaptor protein. It is composed of a Pleckstrin homology (PH) and SH2 domains along with several tyrosine phosphorylation sites. STAP-1 is an ortholog of BRDG1 (BCR downstream signaling 1). STAP1 protein functions as a docking protein acting downstream of Tec tyrosine kinase in B cell antigen receptor signaling. The protein is phosphorylated by Tec and participates in a positive feedback loop, increasing Tec activity. STAP1 has been shown to interact with C19orf2, an unconventional prefoldin RPB5 interactor. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 94 matched cddid_all.tbl CDD cd10404 cd10404 198267 SH2_STAP2 Src homology 2 domain found in Signal-transducing adaptor protein 2 (STAP2). STAP2 is a signal-transducing adaptor protein. It is composed of a Pleckstrin homology (PH) and SH2 domains along with several tyrosine phosphorylation sites. The STAP2 protein is the substrate of breast tumor kinase, an Src-type non-receptor tyrosine kinase that mediates the interactions linking proteins involved in signal transduction pathways. STAP2 has alternative splicing variants. STAP2 has been shown to interact with tyrosine-protein kinase 6 (PTK6). In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 97 matched cddid_all.tbl CDD cd10405 cd10405 198268 SH2_Vav1 Src homology 2 (SH2) domain found in the Vav1 proteins. Proto-oncogene vav is a member of the Dbl family of guanine nucleotide exchange factors (GEF) for the Rho family of GTP binding proteins. All vavs are activated by tyrosine phosphorylation leading to their activation. There are three Vav mammalian family members: Vav1 which is expressed in the hematopoietic system, and Vav2 and Vav3 are more ubiquitously expressed. Vav1 plays a role in T-cell and B-cell development and activation. It has been identified as the specific binding partner of Nef proteins from HIV-1, resulting in morphological changes, cytoskeletal rearrangements, and the JNK/SAPK signaling cascade, leading to increased levels of viral transcription and replication. Vav1 has been shown to interact with Ku70, PLCG1, Lymphocyte cytosolic protein 2, Janus kinase 2, SIAH2, S100B, Abl gene, ARHGDIB, SHB, PIK3R1, PRKCQ, Grb2, MAPK1, Syk, Linker of activated T cells, Cbl gene and EZH2. Vav proteins are involved in several processes that require cytoskeletal reorganization, such as the formation of the immunological synapse (IS), phagocytosis, platelet aggregation, spreading, and transformation. Vavs function as guanine nucleotide exchange factors (GEFs) for the Rho/Rac family of GTPases. Vav family members have several conserved motifs/domains including: a leucine-rich region, a leucine-zipper, a calponin homology (CH) domain, an acidic domain, a Dbl-homology (DH) domain, a pleckstrin homology (PH) domain, a cysteine-rich domain, 2 SH3 domains, a proline-rich region, and a SH2 domain. Vavs are the only known Rho GEFs that have both the DH/PH motifs and SH2/SH3 domains in the same protein. The leucine-rich helix-loop-helix (HLH) domain is thought to be involved in protein heterodimerization with other HLH proteins and it may function as a negative regulator by forming inactive heterodimers. The CH domain is usually involved in the association with filamentous actin, but in Vav it controls NFAT stimulation, Ca2+ mobilization, and its transforming activity. Acidic domains are involved in protein-protein interactions and contain regulatory tyrosines. The DH domain is a GDP-GTP exchange factor on Rho/Rac GTPases. The PH domain in involved in interactions with GTP-binding proteins, lipids and/or phosphorylated serine/threonine residues. The SH3 domain is involved in localization of proteins to specific sites within the cell interacting with protein with proline-rich sequences. The SH2 domain mediates a high affinity interaction with tyrosine phosphorylated proteins. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 103 matched cddid_all.tbl CDD cd10406 cd10406 198269 SH2_Vav2 Src homology 2 (SH2) domain found in the Vav2 proteins. Proto-oncogene vav is a member of the Dbl family of guanine nucleotide exchange factors (GEF) for the Rho family of GTP binding proteins. All vavs are activated by tyrosine phosphorylation leading to their activation. There are three Vav mammalian family members: Vav1 which is expressed in the hematopoietic system, and Vav2 and Vav3 are more ubiquitously expressed. Vav2 is a GEF for RhoA, RhoB and RhoG and may activate Rac1 and Cdc42. Vav2 has been shown to interact with CD19 and Grb2. Alternatively spliced transcript variants encoding different isoforms have been found for Vav2. Vav proteins are involved in several processes that require cytoskeletal reorganization, such as the formation of the immunological synapse (IS), phagocytosis, platelet aggregation, spreading, and transformation. Vavs function as guanine nucleotide exchange factors (GEFs) for the Rho/Rac family of GTPases. Vav family members have several conserved motifs/domains including: a leucine-rich region, a leucine-zipper, a calponin homology (CH) domain, an acidic domain, a Dbl-homology (DH) domain, a pleckstrin homology (PH) domain, a cysteine-rich domain, 2 SH3 domains, a proline-rich region, and a SH2 domain. Vavs are the only known Rho GEFs that have both the DH/PH motifs and SH2/SH3 domains in the same protein. The leucine-rich helix-loop-helix (HLH) domain is thought to be involved in protein heterodimerization with other HLH proteins and it may function as a negative regulator by forming inactive heterodimers. The CH domain is usually involved in the association with filamentous actin, but in Vav it controls NFAT stimulation, Ca2+ mobilization, and its transforming activity. Acidic domains are involved in protein-protein interactions and contain regulatory tyrosines. The DH domain is a GDP-GTP exchange factor on Rho/Rac GTPases. The PH domain in involved in interactions with GTP-binding proteins, lipids and/or phosphorylated serine/threonine residues. The SH3 domain is involved in localization of proteins to specific sites within the cell interacting with protein with proline-rich sequences. The SH2 domain mediates a high affinity interaction with tyrosine phosphorylated proteins. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 103 matched cddid_all.tbl CDD cd10407 cd10407 198270 SH2_Vav3 Src homology 2 (SH2) domain found in the Vav3 proteins. Proto-oncogene vav is a member of the Dbl family of guanine nucleotide exchange factors (GEF) for the Rho family of GTP binding proteins. All vavs are activated by tyrosine phosphorylation leading to their activation. There are three Vav mammalian family members: Vav1 which is expressed in the hematopoietic system, and Vav2 and Vav3 are more ubiquitously expressed. Vav3 preferentially activates RhoA, RhoG and, to a lesser extent, Rac1. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. VAV3 has been shown to interact with Grb2. Vav proteins are involved in several processes that require cytoskeletal reorganization, such as the formation of the immunological synapse (IS), phagocytosis, platelet aggregation, spreading, and transformation. Vavs function as guanine nucleotide exchange factors (GEFs) for the Rho/Rac family of GTPases. Vav family members have several conserved motifs/domains including: a leucine-rich region, a leucine-zipper, a calponin homology (CH) domain, an acidic domain, a Dbl-homology (DH) domain, a pleckstrin homology (PH) domain, a cysteine-rich domain, 2 SH3 domains, a proline-rich region, and a SH2 domain. Vavs are the only known Rho GEFs that have both the DH/PH motifs and SH2/SH3 domains in the same protein. The leucine-rich helix-loop-helix (HLH) domain is thought to be involved in protein heterodimerization with other HLH proteins and it may function as a negative regulator by forming inactive heterodimers. The CH domain is usually involved in the association with filamentous actin, but in Vav it controls NFAT stimulation, Ca2+ mobilization, and its transforming activity. Acidic domains are involved in protein-protein interactions and contain regulatory tyrosines. The DH domain is a GDP-GTP exchange factor on Rho/Rac GTPases. The PH domain in involved in interactions with GTP-binding proteins, lipids and/or phosphorylated serine/threonine residues. The SH3 domain is involved in localization of proteins to specific sites within the cell interacting with protein with proline-rich sequences. The SH2 domain mediates a high affinity interaction with tyrosine phosphorylated proteins. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 103 matched cddid_all.tbl CDD cd10408 cd10408 198271 SH2_Nck1 Src homology 2 (SH2) domain found in Nck. Nck proteins are adaptors that modulate actin cytoskeleton dynamics by linking proline-rich effector molecules to tyrosine kinases or phosphorylated signaling intermediates. There are two members known in this family: Nck1 (Nckalpha) and Nck2 (Nckbeta and Growth factor receptor-bound protein 4 (Grb4)). They are characterized by having 3 SH3 domains and a C-terminal SH2 domain. Nck1 and Nck2 have overlapping functions as determined by gene knockouts. Both bind receptor tyrosine kinases and other tyrosine-phosphorylated proteins through their SH2 domains. In addition they also bind distinct targets. Neuronal signaling proteins: EphrinB1, EphrinB2, and Disabled-1 (Dab-1) all bind to Nck-2 exclusively. And in the case of PDGFR, Tyr(P)751 binds to Nck1 while Tyr(P)1009 binds to Nck2. Nck1 and Nck2 have a role in the infection process of enteropathogenic Escherichia coli (EPEC). Their SH3 domains are involved in recruiting and activating the N-WASP/Arp2/3 complex inducing actin polymerization resulting in the production of pedestals, dynamic bacteria-presenting protrusions of the plasma membrane. A similar thing occurs in the vaccinia virus where motile plasma membrane projections are formed beneath the virus. Recently it has been shown that the SH2 domains of both Nck1 and Nck2 bind the G-protein coupled receptor kinase-interacting protein 1 (GIT1) in a phosphorylation-dependent manner. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 97 matched cddid_all.tbl CDD cd10409 cd10409 198272 SH2_Nck2 Src homology 2 (SH2) domain found in Nck. Nck proteins are adaptors that modulate actin cytoskeleton dynamics by linking proline-rich effector molecules to tyrosine kinases or phosphorylated signaling intermediates. There are two members known in this family: Nck1 (Nckalpha) and Nck2 (Nckbeta and Growth factor receptor-bound protein 4 (Grb4)). They are characterized by having 3 SH3 domains and a C-terminal SH2 domain. Nck1 and Nck2 have overlapping functions as determined by gene knockouts. Both bind receptor tyrosine kinases and other tyrosine-phosphorylated proteins through their SH2 domains. In addition they also bind distinct targets. Neuronal signaling proteins: EphrinB1, EphrinB2, and Disabled-1 (Dab-1) all bind to Nck-2 exclusively. And in the case of PDGFR, Tyr(P)751 binds to Nck1 while Tyr(P)1009 binds to Nck2. Nck1 and Nck2 have a role in the infection process of enteropathogenic Escherichia coli (EPEC). Their SH3 domains are involved in recruiting and activating the N-WASP/Arp2/3 complex inducing actin polymerization resulting in the production of pedestals, dynamic bacteria-presenting protrusions of the plasma membrane. A similar thing occurs in the vaccinia virus where motile plasma membrane projections are formed beneath the virus. Recently it has been shown that the SH2 domains of both Nck1 and Nck2 bind the G-protein coupled receptor kinase-interacting protein 1 (GIT1) in a phosphorylation-dependent manner. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 98 matched cddid_all.tbl CDD cd10410 cd10410 198273 SH2_SH2B1 Src homology 2 (SH2) domain found in SH2B adapter proteins (SH2B1, SH2B2, SH2B3). SH2B1 (SH2-B, PSM), like other members of the SH2B adapter protein family, contains a pleckstrin homology domain, at least one dimerization domain, and a C-terminal SH2 domain which binds to phosphorylated tyrosines in a variety of tyrosine kinases. SH2B1 and SH2B2 function in signaling pathways found downstream of growth hormone receptor and receptor tyrosine kinases, including the insulin, insulin-like growth factor-I (IGF-I), platelet-derived growth factor (PDGF), nerve growth factor, hepatocyte growth factor, and fibroblast growth factor receptors. SH2B2beta, a new isoform of SH2B2, is an endogenous inhibitor of SH2B1 and/or SH2B2 (SH2B2alpha), negatively regulating insulin signaling and/or JAK2-mediated cellular responses. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 97 matched cddid_all.tbl CDD cd10411 cd10411 198274 SH2_SH2B2 Src homology 2 (SH2) domain found in SH2B adapter proteins (SH2B1, SH2B2, SH2B3). SH2B2 (APS), like other members of the SH2B adapter protein family, contains a pleckstrin homology domain, at least one dimerization domain, and a C-terminal SH2 domain which binds to phosphorylated tyrosines in a variety of tyrosine kinases. SH2B1 and SH2B2 function in signaling pathways found downstream of growth hormone receptor and receptor tyrosine kinases, including the insulin, insulin-like growth factor-I (IGF-I), platelet-derived growth factor (PDGF), nerve growth factor, hepatocyte growth factor, and fibroblast growth factor receptors. SH2B2beta, a new isoform of SH2B2, is an endogenous inhibitor of SH2B1 and/or SH2B2 (SH2B2alpha), negatively regulating insulin signaling and/or JAK2-mediated cellular responses. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 97 matched cddid_all.tbl CDD cd10412 cd10412 198275 SH2_SH2B3 Src homology 2 (SH2) domain found in SH2B adapter proteins (SH2B1, SH2B2, SH2B3). SH2B3 (Lnk), like other members of the SH2B adapter protein family, contains a pleckstrin homology domain, at least one dimerization domain, and a C-terminal SH2 domain which binds to phosphorylated tyrosines in a variety of tyrosine kinases. SH2B3 negatively regulates lymphopoiesis and early hematopoiesis. The lnk-deficiency results in enhanced production of B cells, and expansion as well as enhanced function of hematopoietic stem cells (HSCs), demonstrating negative regulatory functions of Sh2b3/Lnk in cytokine signaling. Sh2b3/Lnk also functions in responses controlled by cell adhesion and in crosstalk between integrin- and cytokine-mediated signaling. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 97 matched cddid_all.tbl CDD cd10413 cd10413 198276 SH2_Grb7 Src homology 2 (SH2) domain found in the growth factor receptor bound, subclass 7 (Grb7) proteins. The Grb family binds to the epidermal growth factor receptor (EGFR, erbB1) via their SH2 domains. Grb7 is part of the Grb7 family of proteins which also includes Grb10, and Grb14. They are composed of an N-terminal Proline-rich domain, a Ras Associating-like (RA) domain, a Pleckstrin Homology (PH) domain, a phosphotyrosine interaction region (PIR, BPS) and a C-terminal SH2 domain. The SH2 domains of Grb7, Grb10 and Grb14 preferentially bind to a different RTK. Grb7 binds strongly to the erbB2 receptor, unlike Grb10 and Grb14 which bind weakly to it. Grb7 family proteins are phosphorylated on serine/threonine as well as tyrosine residues. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 108 matched cddid_all.tbl CDD cd10414 cd10414 198277 SH2_Grb14 Src homology 2 (SH2) domain found in the growth factor receptor bound, subclass 14 (Grb14) proteins. The Grb family binds to the epidermal growth factor receptor (EGFR, erbB1) via their SH2 domains. Grb14 is part of the Grb7 family of proteins which also includes Grb7, and Grb14. They are composed of an N-terminal Proline-rich domain, a Ras Associating-like (RA) domain, a Pleckstrin Homology (PH) domain, a phosphotyrosine interaction region (PIR, BPS) and a C-terminal SH2 domain. The SH2 domains of Grb7, Grb10 and Grb14 preferentially bind to a different RTK. Grb14 binds to Fibroblast Growth Factor Receptor (FGFR) and weakly to the erbB2 receptor. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 108 matched cddid_all.tbl CDD cd10415 cd10415 198278 SH2_Grb10 Src homology 2 (SH2) domain found in the growth factor receptor bound, subclass 10 (Grb10) proteins. The Grb family binds to the epidermal growth factor receptor (EGFR, erbB1) via their SH2 domains. Grb10 is part of the Grb7 family of proteins which also includes Grb7, and Grb14. They are composed of an N-terminal Proline-rich domain, a Ras Associating-like (RA) domain, a Pleckstrin Homology (PH) domain, a phosphotyrosine interaction region (PIR, BPS) and a C-terminal SH2 domain. The SH2 domains of Grb7, Grb10 and Grb14 preferentially bind to a different RTK. Grb10 has been shown to interact with many different proteins, including the insulin and IGF1 receptors, platelet-derived growth factor (PDGF) receptor-beta, Ret, Kit, Raf1 and MEK1, and Nedd4. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 108 matched cddid_all.tbl CDD cd10416 cd10416 198279 SH2_SH2D2A Src homology 2 domain found in the SH2 domain containing protein 2A (SH2D2A). SH2D2A contains a single SH2 domain. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 102 matched cddid_all.tbl CDD cd10417 cd10417 199832 SH2_SH2D7 Src homology 2 domain found in the SH2 domain containing protein 7 (SH2D7). SH2D7 contains a single SH2 domain. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 102 matched cddid_all.tbl CDD cd10418 cd10418 198281 SH2_Src_Fyn_isoform_a_like Src homology 2 (SH2) domain found in Fyn isoform a like proteins. Fyn is a member of the Src non-receptor type tyrosine kinase family of proteins. This cd contains the SH2 domain found in Fyn isoform a type proteins. Fyn is involved in the control of cell growth and is required in the following pathways: T and B cell receptor signaling, integrin-mediated signaling, growth factor and cytokine receptor signaling, platelet activation, ion channel function, cell adhesion, axon guidance, fertilization, entry into mitosis, and differentiation of natural killer cells, oligodendrocytes and keratinocytes. The protein associates with the p85 subunit of phosphatidylinositol 3-kinase and interacts with the Fyn-binding protein. Alternatively spliced transcript variants encoding distinct isoforms exist. Fyn is primarily localized to the cytoplasmic leaflet of the plasma membrane. Tyrosine phosphorylation of target proteins by Fyn serves to either regulate target protein activity, and/or to generate a binding site on the target protein that recruits other signaling molecules. FYN has been shown to interact with a number of proteins including: BCAR1, Cbl, Janus kinase, nephrin, Sky, tyrosine kinase, Wiskott-Aldrich syndrome protein, and Zap-70. Fyn has a unique N-terminal domain, an SH3 domain, an SH2 domain, a kinase domain and a regulatory tail, as do the other members of the family. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 101 matched cddid_all.tbl CDD cd10419 cd10419 198282 SH2_Src_Fyn_isoform_b_like Src homology 2 (SH2) domain found in Fyn isoform b like proteins. Fyn is a member of the Src non-receptor type tyrosine kinase family of proteins. This cd contains the SH2 domain found in Fyn isoform b type proteins. Fyn is involved in the control of cell growth and is required in the following pathways: T and B cell receptor signaling, integrin-mediated signaling, growth factor and cytokine receptor signaling, platelet activation, ion channel function, cell adhesion, axon guidance, fertilization, entry into mitosis, and differentiation of natural killer cells, oligodendrocytes and keratinocytes. The protein associates with the p85 subunit of phosphatidylinositol 3-kinase and interacts with the Fyn-binding protein. Alternatively spliced transcript variants encoding distinct isoforms exist. Fyn is primarily localized to the cytoplasmic leaflet of the plasma membrane. Tyrosine phosphorylation of target proteins by Fyn serves to either regulate target protein activity, and/or to generate a binding site on the target protein that recruits other signaling molecules. FYN has been shown to interact with a number of proteins including: BCAR1, Cbl, Janus kinase, nephrin, Sky, tyrosine kinase, Wiskott-Aldrich syndrome protein, and Zap-70. Fyn has a unique N-terminal domain, an SH3 domain, an SH2 domain, a kinase domain and a regulatory tail, as do the other members of the family. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 101 matched cddid_all.tbl CDD cd10420 cd10420 198283 SH2_STAT5b Src homology 2 (SH2) domain found in signal transducer and activator of transcription (STAT) 5b proteins. STAT5 is a member of the STAT family of transcription factors. Two highly related proteins, STAT5a and STAT5b are encoded by separate genes, but are 90% identical at the amino acid level. Both STAT5a and STAT5b are ubiquitously expressed and functionally interchangeable. Mice lacking either STAT5a or STAT5b have mild defects in prolactin dependent mammary differentiation or sexually dimorphic growth hormone-dependent effects, respectively. Mice lacking both STAT5a and STAT5b exhibit a perinatal lethal phenotype and have multiple defects, including anemia and a virtual absence of B and T lymphocytes. STAT proteins mediate the signaling of cytokines and a number of growth factors from the receptors of these extracellular signaling molecules to the cell nucleus. STATs are specifically phosphorylated by receptor-associated Janus kinases, receptor tyrosine kinases, or cytoplasmic tyrosine kinases. The phosphorylated STAT molecules dimerize by reciprocal binding of their SH2 domains to the phosphotyrosine residues. These dimeric STATs translocate into the nucleus, bind to specific DNA sequences, and regulate the transcription of their target genes. However there are a number of unphosphorylated STATs that travel between the cytoplasm and nucleus and some STATs that exist as dimers in unstimulated cells that can exert biological functions independent of being activated. There are seven mammalian STAT family members which have been identified: STAT1, STAT2, STAT3, STAT4, STAT5 (STAT5A and STAT5B), and STAT6. There are 6 conserved domains in STAT: N-terminal domain (NTD), coiled-coil domain (CCD), DNA-binding domain (DBD), alpha-helical linker domain (LD), SH2 domain, and transactivation domain (TAD). NTD is involved in dimerization of unphosphorylated STATs monomers and for the tetramerization between STAT1, STAT3, STAT4 and STAT5 on promoters with two or more tandem STAT binding sites. It also plays a role in promoting interactions with transcriptional co-activators such as CREB binding protein (CBP)/p300, as well as being important for nuclear import and deactivation of STATs involving tyrosine de-phosphorylation. CCD interacts with other proteins, such as IFN regulatory protein 9 (IRF-9/p48) with STAT1 and c-JUN with STAT3 and is also thought to participate in the negative regulation of these proteins. Distinct genes are bound to STATs via their DBD domain. This domain is also involved in nuclear translocation of activated STAT1 and STAT3 phosphorylated dimers upon cytokine stimulation. LD links the DNA-binding and SH2 domains and is important for the transcriptional activation of STAT1 in response to IFN-gamma. It also plays a role in protein-protein interactions and has also been implicated in the constitutive nucleocytoplasmic shuttling of unphosphorylated STATs in resting cells. The SH2 domain is necessary for receptor association and tyrosine phosphodimer formation. Residues within this domain may be particularly important for some cellular functions mediated by the STATs as well as residues adjacent to this domain. The TAD interacts with several proteins, namely minichromosome maintenance complex component 5 (MCM5), breast cancer 1 (BRCA1) and CBP/p300. TAD also contains a modulatory phosphorylation site that regulates STAT activity and is necessary for maximal transcription of a number of target genes. The conserved tyrosine residue present in the C-terminus is crucial for dimerization via interaction with the SH2 domain upon the interaction of the ligand with the receptor. STAT activation by tyrosine phosphorylation also determines nuclear import and retention, DNA binding to specific DNA elements in the promoters of responsive genes, and transcriptional activation of STAT dimers. In addition to the SH2 domain there is a coiled-coil domain, a DNA binding domain, and a transactivation domain in the STAT proteins. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 145 matched cddid_all.tbl CDD cd10421 cd10421 198284 SH2_STAT5a Src homology 2 (SH2) domain found in signal transducer and activator of transcription (STAT) 5a proteins. STAT5 is a member of the STAT family of transcription factors. Two highly related proteins, STAT5a and STAT5b are encoded by separate genes, but are 90% identical at the amino acid level. Both STAT5a and STAT5b are ubiquitously expressed and functionally interchangeable. Mice lacking either STAT5a or STAT5b have mild defects in prolactin dependent mammary differentiation or sexually dimorphic growth hormone-dependent effects, respectively. Mice lacking both STAT5a and STAT5b exhibit a perinatal lethal phenotype and have multiple defects, including anemia and a virtual absence of B and T lymphocytes. STAT proteins mediate the signaling of cytokines and a number of growth factors from the receptors of these extracellular signaling molecules to the cell nucleus. STATs are specifically phosphorylated by receptor-associated Janus kinases, receptor tyrosine kinases, or cytoplasmic tyrosine kinases. The phosphorylated STAT molecules dimerize by reciprocal binding of their SH2 domains to the phosphotyrosine residues. These dimeric STATs translocate into the nucleus, bind to specific DNA sequences, and regulate the transcription of their target genes. However there are a number of unphosphorylated STATs that travel between the cytoplasm and nucleus and some STATs that exist as dimers in unstimulated cells that can exert biological functions independent of being activated. There are seven mammalian STAT family members which have been identified: STAT1, STAT2, STAT3, STAT4, STAT5 (STAT5A and STAT5B), and STAT6. There are 6 conserved domains in STAT: N-terminal domain (NTD), coiled-coil domain (CCD), DNA-binding domain (DBD), alpha-helical linker domain (LD), SH2 domain, and transactivation domain (TAD). NTD is involved in dimerization of unphosphorylated STATs monomers and for the tetramerization between STAT1, STAT3, STAT4 and STAT5 on promoters with two or more tandem STAT binding sites. It also plays a role in promoting interactions with transcriptional co-activators such as CREB binding protein (CBP)/p300, as well as being important for nuclear import and deactivation of STATs involving tyrosine de-phosphorylation. CCD interacts with other proteins, such as IFN regulatory protein 9 (IRF-9/p48) with STAT1 and c-JUN with STAT3 and is also thought to participate in the negative regulation of these proteins. Distinct genes are bound to STATs via their DBD domain. This domain is also involved in nuclear translocation of activated STAT1 and STAT3 phosphorylated dimers upon cytokine stimulation. LD links the DNA-binding and SH2 domains and is important for the transcriptional activation of STAT1 in response to IFN-gamma. It also plays a role in protein-protein interactions and has also been implicated in the constitutive nucleocytoplasmic shuttling of unphosphorylated STATs in resting cells. The SH2 domain is necessary for receptor association and tyrosine phosphodimer formation. Residues within this domain may be particularly important for some cellular functions mediated by the STATs as well as residues adjacent to this domain. The TAD interacts with several proteins, namely minichromosome maintenance complex component 5 (MCM5), breast cancer 1 (BRCA1) and CBP/p300. TAD also contains a modulatory phosphorylation site that regulates STAT activity and is necessary for maximal transcription of a number of target genes. The conserved tyrosine residue present in the C-terminus is crucial for dimerization via interaction with the SH2 domain upon the interaction of the ligand with the receptor. STAT activation by tyrosine phosphorylation also determines nuclear import and retention, DNA binding to specific DNA elements in the promoters of responsive genes, and transcriptional activation of STAT dimers. In addition to the SH2 domain there is a coiled-coil domain, a DNA binding domain, and a transactivation domain in the STAT proteins. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 140 matched cddid_all.tbl CDD cd10422 cd10422 199217 RNase_Ire1 RNase domain (also known as the kinase extension nuclease domain) of Ire1. The model represents the C-terminal endoribonuclease domain of the multi-functional protein Ire1; Ire1 in addition contains a type I transmembrane serine/threonine protein kinase (STK) domain, and a Luminal dimerization domain. Ire1 is essential for the endoplasmic reticulum (ER) unfolded protein response (UPR), which acts as an ER stress sensor and is the oldest and most conserved component of the UPR in eukaryotes. During ER stress, IRE1 dimerizes through its N-terminal luminal domain and forms oligomers, promoting trans-autophosphorylation by its cytosolic kinase domain. This leads to a conformational change that stimulates its endoribonuclease (RNase) activity and results in the cleavage of its mRNA substrate, Hac1 in yeast and Xbp1 in metazoans, thus promoting a splicing event that enables translation into a transcription factor which activates the UPR. This RNase domain is homologous to the RNase domain of RNase L, and possesses a novel fold for a nuclease and appears to be rigid irrespective of the activation state of IRE1. Structural analysis and mutational studies have revealed that an early stage 'phosphoryl-transfer' competent conformation of IRE1 favors face-to-face dimerization of the kinase domains which precedes and is distinct from the RNase 'active' back-to-back conformation. Furthermore, in yeast IRE1, the flavonol quercetin activates the RNase and potentiates activation of the protein kinase by ADP, hinting at the possible existence of endogenous cytoplasmic ligands that may function along with stress signals from ER lumen in order to modulate IRE1 activity, thus identifying IRE1 as a target for development of ATP-competitive inhibitors to modulate the UPR with specific relevance for multiple myeloma. 129 matched cddid_all.tbl CDD cd10423 cd10423 199218 RNase_RNase-L RNase domain (also known as the kinase extension nuclease domain) of RNase L. Ribonuclease L (RNase L), sometimes referred to as the 2-5A-dependent RNase, is a highly regulated, latent endoribonuclease (thus the 'L' in RNase L) and is widely expressed in most mammalian tissues. It is involved in the mediation of the antiviral and pro-apoptotic activities of the interferon-inducible 2-5A system, which blocks infections by certain types of viruses through cleavage of viral and cellular single-stranded RNA. RNase L is unique in that it is composed of three major domains; N-terminus regulatory ankyrin repeat domain (ARD), followed by a linker, a protein kinase (PK)-like domain and a C-terminal ribonuclease (RNase) domain. The RNase domain has homology with IRE1, also containing both a kinase and an endoribonuclease, that functions in the unfolded protein response (UPR). RNase L has been shown to have an impact on the pathogenesis of prostate cancer; the RNase L gene, RNASEL, has been identified as a strong candidate for the hereditary prostate cancer 1 (HPC1) allele. The broad range of biological functions of RNase offers a possibility for RNase L as a therapeutic target. 119 matched cddid_all.tbl CDD cd10424 cd10424 198344 GST_C_9 C-terminal, alpha helical domain of an unknown subfamily 9 of Glutathione S-transferases. Glutathione S-transferase (GST) C-terminal domain family, unknown subfamily 9; composed of uncharacterized proteins with similarity to GSTs. GSTs are cytosolic dimeric proteins involved in cellular detoxification by catalyzing the conjugation of glutathione (GSH) with a wide range of endogenous and xenobiotic alkylating agents, including carcinogens, therapeutic drugs, environmental toxins, and products of oxidative stress. GSTs also show GSH peroxidase activity and are involved in the synthesis of prostaglandins and leukotrienes. The GST fold contains an N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain, with an active site located in a cleft between the two domains. GSH binds to the N-terminal domain while the hydrophobic substrate occupies a pocket in the C-terminal domain. 103 matched cddid_all.tbl CDD cd10425 cd10425 259896 Ephrin-A_Ectodomain Ectodomain of Ephrin A. Ephrins and their receptors EphR play an important role in cell communication in normal physiology, as well as in disease pathogenesis. Binding of the ephrin (Eph) ligand to EphR requires cell-cell contact, since both molecules are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling, depending on Eph kinase activity) and ephrin-expressing cells (reverse signaling). Eph signaling controls cell morphology, adhesion, migration and invasion. Ephrins can be subdivided into 2 groups, A and B, depending on their respective receptors EphA or EphB. The nine human EphA receptors bind to five GPI-linked ephrin-A ligands. Interactions are promiscuous within each class, and some Eph receptors can also bind to ephrins of the other class. All ephrin As contain a highly conserved receptor binding ectodomain described by this model. Although ephrin As do not have a cytoplasmic tail (in contrast to ephrin Bs), they are still capable of downstream activation of Src family kinases and phosphoinositide-3-kinases, most likely involving coreceptors such as neurotrophin receptors. 130 matched cddid_all.tbl CDD cd10426 cd10426 259897 Ephrin-B_Ectodomain Ectodomain of Ephrin B. Ephrin Bs have several conserved tyrosine phosphorylation sites in their cytoplasmic PDZ-like domain, which are important for signal transduction. Ephrins and their receptors EphR play an important role in cell communication in normal physiology, as well as in disease pathogenesis. Binding of the ephrin (Eph) ligand to EphR requires cell-cell contact, since both molecules are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling, depending on Eph kinase activity) and ephrin-expressing cells (reverse signaling). Eph signaling controls cell morphology, adhesion, migration and invasion. Ephrins can be subdivided into 2 groups, A and B, depending on their respective receptors EphA or EphB. The nine human EphA receptors bind to five GPI-linked ephrin-A ligands and the five EphB receptors bind to three transmembrane ephrin-B ligands. Interactions are promiscuous within each class, and some Eph receptors can also bind to ephrins of the other class. All ephrin Bs contain a highly conserved receptor binding ectodomain described in this model. 137 matched cddid_all.tbl CDD cd10428 cd10428 198410 LFG_like Proteins similar to and including lifeguard (LFG), a putative regulator of apoptosis. Lifeguard (LFG) inhibits Fas-mediated apoptosis and interacts with the death receptor FasR/CD95/Apo1. LFG has been shown to interact with Bax and is supposed to be integral to cellular membranes such as the ER. A close homolog, PP1201 or RECS1, appears located in the Golgi compartment and also interacts with the Fas receptor CD95/Apo1. PP1201 is expressed in response to shear stress. 217 matched cddid_all.tbl CDD cd10429 cd10429 198411 GAAP_like Golgi antiapoptotic protein. GAAP (or transmembrane BAX inhibitor motif containing 4) is a regulator of apoptosis that is related to the BAX inhibitor (BI)-1 like family of small transmembrane proteins, which have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. Human GAAP has been linked to the modulation of intracellular fluxes of Ca(2+), by suppressing influx from the extracellular medium and reducing release from intracellular stores. A viral homolog (vaccinia virus vGAAP) acts similar to its human counterpart in inhibiting apoptosis. 233 matched cddid_all.tbl CDD cd10430 cd10430 198412 BI-1 BAX inhibitor (BI)-1. Mammalian members of the BAX inhibitor (BI)-1 like family of small transmembrane proteins have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. Their broad tissue distribution and high degree of conservation suggests an important regulatory role. In plants, BI-1 like proteins play a role in pathogen resistance. 213 matched cddid_all.tbl CDD cd10431 cd10431 198413 GHITM Growth-hormone inducible transmembrane protein. GHITM appears to be ubiquitiously expressed in mammalian cells and expression has also been observed in various cancer cell lines. A cytoprotective function has been suggested. It is closely related to the BAX inhibitor (BI)-1 like family of small transmembrane proteins, which have been shown to have an antiapoptotic effect. 264 matched cddid_all.tbl CDD cd10432 cd10432 198414 BI-1-like_bacterial Bacterial BAX inhibitor (BI)-1/YccA-like proteins. This family is comprised of bacterial relatives of the mammalian members of the BAX inhibitor (BI)-1 like family of small transmembrane proteins, which have been shown to have an antiapoptotic effect either by stimulating the antiapoptotic function of Bcl-2, a well-characterized oncogene, or by inhibiting the proapoptotic effect of Bax, another member of the Bcl-2 family. In plants, BI-1 like proteins play a role in pathogen resistance. A characterized prokaryotic member, Escherichia coli YccA, has been shown to interact with ATP-dependent protease FtsH, which degrades abnormal membrane proteins as part of a quality control mechanism to keep the integrity of biological membranes. 211 matched cddid_all.tbl CDD cd10433 cd10433 198415 YccA_like YccA-like proteins. A prokaryotic member of the BAX inhibitor (BI)-1 like family of small transmembrane proteins, Escherichia coli YccA, has been shown to interact with ATP-dependent protease FtsH, which degrades abnormal membrane proteins as part of a quality control mechanism to keep the integrity of biological membranes. 205 matched cddid_all.tbl CDD cd10434 cd10434 198381 GIY-YIG_UvrC_Cho Catalytic GIY-YIG domain of nucleotide excision repair endonucleases UvrC, Cho, and similar proteins. UvrC is essential for nucleotide excision repair (NER). The N-terminal catalytic GIY-YIG domain of UvrC (also known as Uri domain) is responsible for the 3' incision reaction and the C-terminal half of UvrC, consisting of an UvrB-binding domain (UvrBb), EndoV-like nuclease domain and a helix-hairpin-helix (HhH) DNA-binding domain, contains the residues involved in 5' incision. The N- and C-terminal regions are joined by a common Cys-rich domain containing four conserved Cys residues. Besides UvrC, protein Cho (UvrC homolog) serves as a second endonuclease in E. coli NER. Cho contains GIY-YIG motif followed by a Cys-rich region and shares sequence homology with the N-terminal half of UvrC. It is capable of incising the DNA at the 3' side of a lesion in the presence of the UvrA and UvrB proteins during NER. The C-terminal half of Cho is a unique uncharacterized domain, which is distinct from that of UvrC. Moreover, unlike UvrC, Cho does not require the UvrC-binding domain of UvrB for the 3' incision reaction, which might cause the shift in incision position and the difference in incision efficiencies between Cho and UvrC on different damaged substrates. Due to this, the range of NER in E. coli can be broadened by combining action of Cho and UvrC. This family also includes many uncharacterized epsilon proofreading subunits of DNA polymerase III, which have an additional N-terminal ExoIII domain and a 3'-5' exonuclease domain homolog, fused to an UvrC-like region or a Cho-like region. The UvrC-like region includes a GIY-YIG motif, followed by a Cys-rich region, and an UvrB-binding domain (UvrBb), but lacks the EndoV-like nuclease domain and the helix-hairpin-helix (HhH) DNA-binding domain. The Cho-like region consists of a GIY-YIG motif, followed by the Cys-rich region, and the unique uncharacterized domain presenting in the C-terminal half of Cho. Some family members may not carry the Cys-rich region. This family also includes a specific Cho-like protein from G. violaceus, which possesses only UvrBb domain at the C-terminus, but lacks the additional N-terminal ExoIII domain. The oother two remote homologs of UvrC, Bacillus-I and -II, are included in this family as well. Both of them contain a GIY-YIG domain, but no Cys-rich region. Moreover, the whole C-terminal region of Bacillus-I is replaces by an unknown domain, and Bacillus-II possesses another unknown N-terminal extension. 81 matched cddid_all.tbl CDD cd10435 cd10435 198382 GIY-YIG_RE_Eco29kI_like Catalytic GIY-YIG domain of type II restriction endonucleases R.Eco29kI, R.Cfr42I, and similar proteins. This family corresponds to the catalytic GIY-YIG domain of a group of GGCGCC-specific type II restriction endonucleases R.Eco29kI, R.Cfr42I, and similar proteins. R.Eco29kI is encoded on plasmid pECO29 in the E. coli strain 29K. This enzyme recognizes the palindromic 5'-CCGC/GG-3' target and cuts between Cyt4 and Gua5 on each strand of the restriction site to generate 3'-staggered ends. R.Eco29kI forms a domain-swapped homodimeric catalytically active complex during DNA binding and cleavage. Each subunit contains one GIY-YIG catalytic motif. Restriction endonucleases R.Cfr42I is an isoschizomer of R.Eco29kI. Unlike R.Eco29kI, R.Cfr42I is functional as a homotetramer, binding and cleaving two cognate DNA molecules in a cooperative manner. Members in this family are single-domain proteins sharing sequence similarities with the catalytic domain of GIY-YIG endonucleases, such as homing endonuclease I-TevI. However, they utilize loop insertions and terminal extensions instead of the separate DNA-binding domain to interact with the target site 5'-CCGC/GG-3'. A divalent metal-ion cofactor is required for their catalysis, but not for substrate binding. This family also includes a hypothetical protein from Deinococcus radiodurans that corresponds to MraI, a type II restriction enzyme similar to GIY-YIG family of homing endonucleases. MraI is shown to be an isoschizomer of Eco29kI, Cfr42I recognizing the palindromic nucleotide sequence 5'-CCGC reduced GG-3'. The enzyme shows an absolute requirement of Mg2+, but is active in the absence of added 2-mercaptoethanol. MraI represents the first restriction enzyme from a bacterium whose DNA lacks modified methylated bases. 117 matched cddid_all.tbl CDD cd10436 cd10436 198383 GIY-YIG_EndoII_Hpy188I_like Catalytic GIY-YIG domain of coliphage T4 non-specific endonuclease II, type II restriction endonuclease R.Hpy188I, and similar proteins. This family includes two different GIY-YIG enzymes, coliphage T4 non-specific endonuclease II (EndoII), and type II restriction endonuclease R.Hpy188I. They display high sequence similarity to each other, and both of them contain an extra N-terminal hairpin that lacks counterparts in other GIY-YIG enzymes. EndoII encoded by gene denA catalyzes the initial step in degradation of host DNA, which permits scavenging of host-derived nucleotides for phage DNA synthesis. R.Hpy188I recognizes the unique sequence, 5'-TCNGA-3', and cleaves the DNA between nucleotides N and G in its recognition sequence to generate a single nucleotide 3'-overhang. EndoII binds to two DNA substrates as an X-shaped tetrameric structure composed as a dimer of dimers. In contrast, two subunits of R.Hpy188I form a dimer to embrace one bound DNA. Divalent metal-ion cofactors are required for their catalytic events, but not for the substrates binding. 97 matched cddid_all.tbl CDD cd10437 cd10437 198384 GIY-YIG_HE_I-TevI_like N-terminal catalytic domain of GIY-YIG intron endonuclease I-TevI, I-BmoI, I-BanI, I-BthII and similar proteins. I-TevI is a site-specific GIY-YIG homing endonuclease encoded within the group I intron of the thymidylate synthase gene (td) from Escherichia coli phage T4. It functions as an endonuclease that catalyzes the first step in intron homing by generating a double-strand break in the intronless td allele within a sequence designated the homing site. I-TevI recognizes its extensive 37 base pair DNA target in a site-specific, but sequence-tolerant manner. The cleavage site is located at 23 (upper strand) and 25 (lower strand) nucleotides upstream of the intron insertion site. A divalent cation, such as Mg2+, is required for the catalysis. I-TevI also acts as a repressor of its own transcription. It binds an operator that is located upstream of the I-TevI coding sequence and overlaps the T4 late promoter, which drives I-TevI expression from within the td intron. I-TevI binds the homing sites and the operator with the same affinity, but cleaves the homing site more efficiently than the operator. I-TevI consists of an N-terminal catalytic domain, containing the GIY-YIG motif, and a C-terminal DNA-binding domain that binds DNA as a monomer, joined by a flexible linker. The C-terminal domain includes three subdomains: a zinc finger, a minor-groove binding alpha-helix (NUMOD3, nuclease-associated modular domain 3), and a helix-turn-helix domain (HTH). The last two are responsible for DNA-binding. The zinc finger is part of the linker and not required for DNA-binding. It is implicated as a distance sensor to constrain the catalytic domain to cleave the homing site at a fixed position. None of other GIY-YIG endonucleases have been found to have the zinc finger motif. This family also includes a reduced activity isoschizomer of I-TevI, I-BmoI, which is encoded within the group I intron of the thymidylate synthase (TS) gene (thyA) from Bacillus mojavensis. I-BmoI catalyzes the first step in intron homing by generating a double-strand break in the intronless td allele within a sequence designated the homing site in the presence of a divalent cation cofactor, such as Mg2+. In the absence of Mg2+, I-Bmol only nicks one of the strands. Both I-BmoI and I-TevI bind a homologous stretch of TS-encoding DNA as monomers, but use different strategies to distinguish intronless from intron-containing substrates. I-TevI recognizes substrates at the level of DNA-binding. However, I-BmoI binds both intron-containing and intronless TS-encoding substrates, but efficiently cleaves only intronless substrate. Afterwards they cleave their respective intronless substrates in the same positions, and both require a critical G-C base pair adjacent to the top strand site for efficient cleavage. The C-terminal domain of I-BmoI has nuclease-associated modular DNA-binding domains (NUMODs), but lacks the zinc finger, which is different from that of I-TevI. Although the zinc finger implicated as a distance determination in I-TevI is absent, I-BmoI still possesses some cleavage distance discrimination. Besides I-TevI and I-BmoI, this family contains a putative GIY-YIG homing endonuclease, I-BanI, encoded within the self-splicing group I intron of nrdE gene from Bacillus anthracis. It contains two major domains, the N-terminal GIY-YIG domain and the C-terminal DNA-binding domain that consists of a minor-groove DNA binding alpha-helix motif and a helix-turn-helix (HTH) motif. I-BanI generates a double-strand break (DSB) in the intronless nrdE gene. The cleavage site is located at 5 and 7 nucleotides upstream of the intron insertion site, with 2-nucleotide 3' extensions. The recognition site is 35 to 40 base pairs and covers the cleavage site with a bias toward the downstream region including the (intervening sequence) IVS insertion site. Moreover, this family contains another putative GIY-YIG homing endonuclease, I-BthII, encoded within the self-splicing group I intron of nrdF gene from Bacillus thuringiensis ssp. pakistani. It contains a GIY-YIG motif that generates a double-strand break (DSB) in the intronless nrdF gene. The cleavage site is located at 7 and 9 nucleotides upstream of the intron insertion site, leaving 2-nucleotide 3' extensions. The recognition site is 27 to 29 base pairs with the DSB cleavage site at the 5'-end of the top strand, and with the intervening sequence (IVS) insertion site approximately in the middle of the recognition site. 90 matched cddid_all.tbl CDD cd10438 cd10438 198385 GIY-YIG_MSH Catalytic GIY-YIG domain of eukaryotic DNA mismatch repair protein MutS homologs. This family represents a putative GIY-YIG nuclease domain C-terminally fused to the DNA-repair ATPase on a small group of eukaryotic DNA mismatch repair protein mutS homologs (MSH). The MSH proteins in this family do not have the zinc finger domain, but have a predicted mitochondrial localization. They might play roles in the recognition and repair of errors made during the replication of DNA. The prototype of this family is the protein encoded by the chloroplast mutator (CHM) locus from Arabidopsis thaliana. It is suggested that this protein could be involved in the maintenance of mitochondrial genome stability. 72 matched cddid_all.tbl CDD cd10439 cd10439 198386 GIY-YIG_COG3410 GIY-YIG domain of uncharacterized bacterial protein structurally related to COG3410. This family contains a group of uncharacterized bacterial proteins. Although their function roles have not been recognized, these proteins contain a putative GIY-YIG domain in their N-terminus. Moreover, a conserved domain COG3410 with unknown function has been found in the C-terminus of most family members. 80 matched cddid_all.tbl CDD cd10440 cd10440 198387 GIY-YIG_COG3680 GIY-YIG domain of uncharacterized proteins from bacteria and their eukaryotic homologs. This family includes a group of functionally uncharacterized proteins from bacteria and their eukaryotic homologs which are present only in metazoa. These proteins might have nuclease activities and possibly be engaged in DNA repair or recombination, since they share sequence homology with the catalytic GIY-YIG domain of bacterial UvrC DNA repair proteins. Distinct from their prokaryotic relatives, the eukaryotic homologs contain an N-terminal extension that includes the region of approximately 3-4 ankyrin repeats, unique motifs mediating protein-protein interactions. Some of eukaryotic homologs do have an additional LEM domain located between ankyrin repeats region and GIY-YIG domain. The LEM domain, found in inner nuclear membrane proteins, may be involved in protein- or DNA-binding. The different domain composition of the eukaryotic homologs suggests that they might participate in interactions with multiple partners and implies important cellular function. 94 matched cddid_all.tbl CDD cd10441 cd10441 198388 GIY-YIG_COG1833 GIY-YIG domain of hypothetical proteins from archaea and their bacterial homologs. This family includes a group of functionally uncharacterized hypothetical proteins from archaea and their bacterial homologs. These proteins contain a putative GIY-YIG domain that shows sequence homology with bacterial UvrC DNA repair proteins. Meanwhile, all of them share a C-terminal extension with semi-conserved Cys and His residues, which suggests that the extended region may be a zinc-binding nucleic acid interaction domain. Although the majority of family members have a standalone GIY-YIG domain composition, some of them do have additional endonulcease III domain or sugar fermentation stimulation protein domain, both of which are N-terminally fused to the GIY-YIG domain. As a result, those proteins could perform some other role by cooperating with different domains, which remains to be determined in the future. 112 matched cddid_all.tbl CDD cd10442 cd10442 198389 GIY-YIG_PLEs Catalytic GIY-YIG endonuclease domain of penelope-like elements and similar proteins. This model corresponds to the EN domain of PLEs that contains catalytic module of the GIY-YIG endonucleases of group I bacterial/organellar introns, as well as bacterial UvrC DNA repair proteins. It can cleave DNA with low nucleotide sequence specificity. However, the PLEs EN domain is distinct from other GIY-YIG endonucleases by the presence of a well-conserved CCHH motif (CX(2-7)CX(33-39)HX(3-5)H, X can be any residue). The role of the CCHH motif has not yet been identified. Penelope-like elements (PLEs) represent a novel class of eukaryotic retroelements, which do not belong to either long terminal repeat (LTR) retrotransposons or non-LTR retrotransposons (often called LINEs), but instead form a sister clade to telomerase reverse transcriptases (TERTs), highly specialized non-mobile reverse transcriptases (RTs) which are responsible for the addition of telomeric repeats to the ends of eukaryotic chromosomes. The single open reading frame (ORF) encoded by PLE consists of two principal domains, RT domain and endonuclease (EN) domain, jointed by a linker region of variable length. Both of these two domains are functionally active. 92 matched cddid_all.tbl CDD cd10443 cd10443 198390 GIY-YIG_HE_Tlr8p_PBC-V_like GIY-YIG domain of uncharacterized hypothetical protein found in phycodnavirus PBCV-1 DNA virus, T. thermophila Tlr element eoncoding protein Tlr8p, and similar proteins found in bacteria. The family includes a group of diverse uncharacterized hypothetical proteins with a GIY-YIG domain that shows statistically significant similarity to the N-terminal catalytic domains of GIY-YIG family of intron-encoded homing endonuclease I-TevI. Similar to I-TevI, family members from phycodnavirus PBCV-1 DNA virus have nuclease-associated modular DNA-binding domains (NUMODs) and a helix-turn-helix (HTH) domain C-terminally fused to the GIY-YIG domain, which suggests that these PBCV-1 acquired the I-TevI-like homing endonucleases from phages by horizontal gene transfer. This family also includes proteins that appear to connect homing endonucleases with Penelope elements, such as Tetrahymena thermophila Tlr element encoding protein Tlr8p that possess additional N-terminal and central structural regions, followed by a putative superfamily 1 helicase domain and I-TevI-like GIY-YIG domain, but lacks the NUMOD domains and HTH domain. It is suggested that the Tlr8p element could have acquired its GIY-YIG domain w ithin the nucleus of the ciliate cell infected by the Phycodnavirus. Some family members only contain a standalone GIY-YIG domain and their biological functions are unclear. 90 matched cddid_all.tbl CDD cd10444 cd10444 198391 GIY-YIG_SegABCDEFG N-terminal catalytic GIY-YIG domain of bacteriophage T4 segABCDEFG gene encoding proteins. The prototypes of Seg family are proteins SegA, B, C, D, E, F, and G encoded by five seg genes segA, B, C, D, E, F, and G in the bacteriophage T4 genome, respectively. SegA, B, C, D, E, F, and G are not encoded by introns, but free-standing homologs of the GIY-YIG family of endonucleases encoded by group I introns, which are thought to initiate the homing of their own intron by cleaving the intronless DNA at or near the site of insertion. Both phage T4 intron-encoded and free-standing GIY-YIG endonucleases contribute to the exclusion of T2 markers from the progeny of mixed infections. SegA, encoded by the bacteriophage T4 segA gene, is a double-strand DNA endonulcease with a hierarchy of site specificity. The cleavage site of SegA is located in the uvsX gene of T4. Its cleaving activity requires the presence of Mg2+ and can be stimulated by the presence of ATP or ATPgammaS. Bacteriophage T4 segB gene encoding protein SegB is a site-specific endonuclease that recognizes a 27-bp sequence, cleaves DNA by introdu cing double-strand breaks in the adjacent gene 56 of T2 during mixed infection in the presence of Mg2+, Mn2+, or Ca2+ cations, and produces mostly 3' 2-nt protruding ends at its DNA cleavage site. It functions as a homing endonuclease to ensure spreading of its own gene and the surrounding tRNA genes among T4-related phages. Bacteriophage T4 segE gene encoding SegE is a site-specific endonuclease that preferentially cleaves DNA in a site located at the 5' end of the uvsW gene in the RB30 genome. It is responsible for a non-reciprocal genetic exchange between T-even-related phages. Bacteriophage T4 gene 69 encoding SegF is a site-specific double-strand DNA endonuclease that promotes marker exclusion. It preferentially introduces a double-strand break in the adjacent T2 gene 56 over T4 gene 56 both in vitro and in vivo during mixed infection, which results in the replacement of T2 gene 56 by T4 gene 56 in a process similar to group I intron homing. The cleavage site is located 210- and 212-bp upstream from its insertion site. Bacteriophage T4 segG gene (formerly gene 32.1) encoding SegG (also known as F-TevIV) is a double-strand DNA endonuclease adjacent to gene 32 of phage T4 that promotes marker exclusion. Although it is absent from phage T2, SegG preferentially introduces a double-strand break in T2 gene 32 during mixed infection, which results in replacement of T2 genetic markers by the corresponding T4 markers. The cleavage site is located 332- and 334-bp from its insertion site. 85 matched cddid_all.tbl CDD cd10445 cd10445 198392 GIY-YIG_bI1_like Catalytic GIY-YIG domain of putative intron-encoded endonuclease bI1 and similar proteins. The prototype of this family is a putative intron-encoded mitochondrial DNA endonuclease bI1 found in mitochondrion Ustilago maydis. This protein may arise from proteolytic cleavage of an in-frame translation of COB exon 1 plus intron 1, containing the bI1 open reading frame. It contains an N-terminal truncated non-functional cytochrome b region and a C-terminal intron-encoded endonuclease bI1 region. The bI1 region shows high sequence similarity to endonucleases of group I introns of fungi and phage and might be involved in intron homing. Many uncharacterized bI1 homologs existing in fungi and chlorophyta in this family do not contain the cytochrome b region, but have a standalone bI1-like region, which contains a GIY-YIG domain and a minor-groove binding alpha-helix nuclease-associated modular domain (NUMOD). This family also includes a Yarrowia lipolytica mobile group-II intron COX1-i1, also called intron alpha, encoding protein with reverse transcriptase activity. The group-II intron COX1-i1 may be involv ed both in the generation of the circular multimeric DNA molecules (senDNA alpha) which amplify during the senescence syndrome and in the generation of the site-specific deletion which accumulates in the premature-death syndrome. 88 matched cddid_all.tbl CDD cd10446 cd10446 198393 GIY-YIG_unchar_1 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria. The family includes a group of uncharacterized bacterial hypothetical proteins with a GIY-YIG domain that shows statistically significant similarity to the N-terminal catalytic domains of GIY-YIG family of intron-encoded homing endonuclease I-TevI and catalytic GIY-YIG domain of nucleotide excision repair endonuclease UvrC. 103 matched cddid_all.tbl CDD cd10447 cd10447 198394 GIY-YIG_unchar_2 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria and archaea. The family includes a group of uncharacterized hypothetical proteins, mainly found in bacteria and a few found in archaea, with a GIY-YIG domain that shows statistically significant similarity to the N-terminal catalytic domains of GIY-YIG family of intron-encoded homing endonuclease I-TevI and catalytic GIY-YIG domain of nucleotide excision repair endonuclease UvrC. 80 matched cddid_all.tbl CDD cd10448 cd10448 198395 GIY-YIG_unchar_3 GIY-YIG domain of uncharacterized hypothetical protein found in bacteria. The family includes a group of uncharacterized bacterial proteins with a GIY-YIG domain that shows statistically significant similarity to the N-terminal catalytic domains of GIY-YIG family of intron-encoded homing endonuclease I-TevI and catalytic GIY-YIG domain of nucleotide excision repair endonuclease UvrC. 87 matched cddid_all.tbl CDD cd10449 cd10449 198396 GIY-YIG_SLX1_like Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its homologs. Structure-specific endonuclease subunit SLX1 is a highly conserved protein from yeast to human, with an N-terminal GIY-YIG endonuclease domain and a C-terminal PHD-type zinc finger postulated to mediate protein-protein or protein-DNA interaction. SLX1 forms active heterodimeric complexes with its SLX4 partner, which has additional roles in the DNA damage response that are distinct from the function of the heterodimeric SLX1-SLX4 nuclease. In yeast, the SLX1-SLX4 complex functions as a 5' flap endonuclease that maintains ribosomal DNA copy number, where SLX1 and SLX4 are shown to be catalytic and regulatory subunits, respectively. This endonuclease introduces single-strand cuts in duplex DNA on the 3' side of junctions with single-strand DNA. In addition to 5' flap endonuclease activity, human SLX1-SLX4 complex has been identified as a Holliday junction resolvase that promotes symmetrical cleavage of static and migrating Holliday junctions. SLX1 also associates with MUS81, EME1, C20orf94, PLK1, and ERCC1. Some eukaryotic SLX1 homologs lack the zinc finger domain, but possess intrinsically unstructured extensions of unknown function. These unstructured segments might be involved in interactions with other proteins. 67 matched cddid_all.tbl CDD cd10450 cd10450 198397 GIY-YIG_AtGrxS16_like GIY-YIG domain found in CAXIP1-like proteins, iron-sulfur cluster assembly proteins, and similar proteins. The family includes CAX-interacting protein-1 (CXIP1)-like proteins and iron-sulfur cluster assembly proteins, both of which contain a GIY-YIG domain that shows statistically significant similarity to the N-terminal catalytic domains of GIY-YIG family of intron-encoded homing endonuclease I-TevI and catalytic GIY-YIG domain of nucleotide excision repair endonuclease UvrC. CAXIP1 is a novel PICOT (protein kinase C-interacting cousin of thioredoxin) domain-containing Arabidopsis protein that activates H+/Ca2+ exchanger CAX1, and its homolog CAX4, but not CAX2 or CAX3. Iron-sulfur cluster assembly proteins in this family also contain a C-terminal NifU-like domain that corresponds to a common region between the NifU protein from nitrogen-fixing bacteria and rhodobacterial species. The biochemical function of NifU is unknown. 70 matched cddid_all.tbl CDD cd10451 cd10451 198398 GIY-YIG_LuxR_like GIY-YIG domain of LuxR and ArsR family transcriptional regulators, and uncharacterized hypothetical proteins found in bacteria. The family includes some bacterial LuxR and ArsR family transcriptional regulators. The a C-terminal conserved domain shows sequence similarity to the N-terminal catalytic GIY-YIG domains of intron-encoded homing endonucleases. Besides, they have an N-terminally fused transcriptional regulators module, comprising the winged helix-turn-helix (wHTH) domain and uncharacterized domain DUF2087. At this point, they are distinct from GIY-YIG homing endonucleases, which typically contain a variety of C-terminally fused nuclease-associated modular DNA-binding domains (NUMODs). Moreover, some key residues relevant to catalysis in GIY-YIG endonucleases are mutanted or absent in this family, which suggests that members in this family might lose the catalytic function that GIY-YIG endonucleases possess. This family also includes many uncharacterized hypothetical proteins that consist of a standalone GIY-YIG like domain. 101 matched cddid_all.tbl CDD cd10452 cd10452 198399 GIY-YIG_RE_Eco29kI_NgoMIII Catalytic GIY-YIG domain of type II restriction enzyme R.Eco29kI, R.NgoMIII, and similar proteins. This family corresponds to the catalytic GIY-YIG domain of GGCGCC-specific type II restriction endonucleases R.Eco29kI, NgoMIII, and similar proteins. R.Eco29kI is encoded on plasmid pECO29 in the E. coli strain 29K. This enzyme recognizes the palindromic 5'-CCGC/GG-3' target and cuts between Cyt4 and Gua5 on each strand of the restriction site to generate 3'-staggered ends. R.Eco29kI forms a domain-swapped homodimeric catalytically active complex during DNA binding and cleavage. Each subunit contains one GIY-YIG catalytic motif. Restriction endonucleases R.NgoMIII is an isoschizomer of R.Eco29kI. Members in this family are single-domain proteins sharing sequence similarities with the catalytic domain of GIY-YIG endonucleases, such as homing endonuclease I-TevI. However, they utilize loop insertions and terminal extensions instead of the separate DNA-binding domain to interact with the target site 5'-CCGC/GG-3'. A divalent metal-ion cofactor is required for their catalysis, but not for their substrate binding. 204 matched cddid_all.tbl CDD cd10453 cd10453 198400 GIY-YIG_RE_Cfr42I Catalytic GIY-YIG domain of type II restriction enzyme R.Cfr42I and similar proteins. This family corresponds to the catalytic GIY-YIG domain of GGCGCC-specific type II restriction endonucleases R.Cfr42I and similar proteins. R.Cfr42I is encoded on plasmid pET21b(+) in the Citrobacter freundii RFL42 strain. This enzyme recognizes the palindromic 5'-CCGC/GG-3' target and cuts between Cyt4 and Gua5 on each strand of the restriction site to generate 3'-staggered ends. It is an isoschizomer of R.Eco29kI. Unlike R.Eco29kI, R.Cfr42I is functional as a homotetramer, binding and cleaving two cognate DNA molecules in a cooperative manner. Members in this family are single-domain proteins sharing sequence similarities with the catalytic domain of GIY-YIG endonucleases, such as homing endonuclease I-TevI. However, they utilize loop insertions and terminal extensions instead of the separate DNA-binding domain to interact with the target site 5'-CCGC/GG-3'. A divalent metal-ion cofactor is required for their catalysis. 156 matched cddid_all.tbl CDD cd10454 cd10454 198401 GIY-YIG_COG3680_Meta GIY-YIG domain of hypothetical proteins from Metazoa. Members of this family are functionally uncharacterized hypothetical proteins from Metazoa. They have bacterial homologs that display sequence homology with the catalytic GIY-YIG domain of bacterial UvrC DNA repair proteins. However, unlike their bacterial relatives, these Metazoan proteins contain an N-terminal extension that includes the region of approximately 3-4 ankyrin repeats, unique motifs mediating protein-protein interactions. Some of them do have an additional LEM domain located between ankyrin repeats region and GIY-YIG domain. The LEM domain, found in inner nuclear membrane proteins, may be involved in protein- or DNA-binding. The different domains composition suggests members in this subfamily might participate in interactions with multiple partners and imply some important cellular functions. 114 matched cddid_all.tbl CDD cd10455 cd10455 198402 GIY-YIG_SLX1 Catalytic GIY-YIG domain of yeast structure-specific endonuclease subunit SLX1 and its eukaryotic homologs. Structure-specific endonuclease subunit SLX1 is a highly conserved protein from yeast to human, with an N-terminal GIY-YIG endonuclease domain and a C-terminal PHD-type zinc finger postulated to mediate protein-protein or protein-DNA interaction. SLX1 forms active heterodimeric complexes with its SLX4 partner, which has additional roles in the DNA damage response that are distinct from the function of the heterodimeric SLX1-SLX4 nuclease. In yeast, the SLX1-SLX4 complex functions as a 5' flap endonuclease that maintains ribosomal DNA copy number, where SLX1 and SLX4 are shown to be catalytic and regulatory subunits, respectively. This endonuclease introduces single-strand cuts in duplex DNA on the 3' side of junctions with single-strand DNA. In addition to 5' flap endonuclease activity, human SLX1-SLX4 complex has been identified as a Holliday junction resolvase that promotes symmetrical cleavage of static and migrating Holliday junctions. SLX1 also associates with MUS81, EME1, C20orf94, PLK1, and ERCC1. Some eukaryotic SLX1 homologs lack the zinc finger domain, but possess intrinsically unstructured extensions of unknown function. These unstructured segments might be involved in interactions with other proteins. 76 matched cddid_all.tbl CDD cd10456 cd10456 198403 GIY-YIG_UPF0213 The GIY-YIG domain of uncharacterized protein family UPF0213 related to structure-specific endonuclease SLX1. This family contains a group of uncharacterized proteins found mainly in bacteria and several in dsDNA viruses. Although their function roles have not been recognized, these proteins show significant sequence similarities with the N-terminal GIY-YIG endonuclease domain of structure-specific endonuclease subunit SLX1, which binds another structure-specific endonuclease subunit SLX4 to form an active heterodimeric SLX1-SLX4 complex. This complex functions as a 5' flap endonuclease in yeast, and has also been identified as a Holliday junction resolvase in human. 68 matched cddid_all.tbl CDD cd10457 cd10457 198404 GIY-YIG_AtGrxS16 GIY-YIG domain found in CAXIP1-like proteins. The family includes CAX-interacting protein-1 (CXIP1)-like proteins which contain a GIY-YIG domain that shows statistically significant similarity to the N-terminal catalytic domains of GIY-YIG family of intron-encoded homing endonuclease I-TevI and catalytic GIY-YIG domain of nucleotide excision repair endonuclease UvrC. CAXIP1 is a novel PICOT (protein kinase C-interacting cousin of thioredoxin) domain-containing Arabidopsis protein that activates H+/Ca2+ exchanger CAX1, and its homolog CAX4, but not CAX2 or CAX3. 74 matched cddid_all.tbl CDD cd10458 cd10458 198405 GIY-YIG_NifU GIY-YIG domain found in iron-sulfur cluster assembly proteins. This family includes a group of uncharacterized iron-sulfur cluster assembly proteins that transiently bind the iron-sulfur cluster before transfer to target apoproteins. These iron-sulfur cluster assembly proteins contains a GIY-YIG domain that shows statistically significant similarity to the N-terminal catalytic domains of GIY-YIG family of intron-encoded homing endonuclease I-TevI and catalytic GIY-YIG domain of nucleotide excision repair endonuclease UvrC. They also contain a C-terminal NifU-like domain that corresponds to a common region between the NifU protein from nitrogen-fixing bacteria and rhodobacterial species. The biochemical function of NifU is unknown. 76 matched cddid_all.tbl CDD cd10459 cd10459 198417 PUB_PNGase PNGase/UBA or UBX (PUB) domain of the P97 adaptor protein Peptide:N-glycanase (PNGase). This PUB (PNGase/UBA or UBX) domain is found in the p97 adaptor protein PNGase (Peptide:N-glycanase). The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. Peptide:N-glycanase (PNGase), a deglycosylating enzyme that functions in proteasome-dependent degradation of misfolded glycoproteins which are translocated from the endoplasmic reticulum (ER) to the cytosol during ERAD, associates with the ubiquitin-proteasome system proteins mediated by the N-terminal PUB domain. PNGase is present in all eukaryotic organisms; however, the yeast PNGase ortholog does not contain the PUB domain. The mammalian PNGase binds a considerable number of proteins via its PUB domain; these include ERAD E3 enzyme, the autocrine motility factor receptor (AMFR or gp78), SAKS and Derlin-1. 93 matched cddid_all.tbl CDD cd10460 cd10460 198418 PUB_UBXD1 PNGase/UBA or UBX (PUB) domain of UBXD1. This PUB domain is found in p97 adaptor protein UBXD1 (UBX domain-containing protein 1, also called UBXD6). It functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The PUB domain in UBX-domain protein 1 (UBXD1), which is widely expressed in higher eukaryotes, except for fungi, and which is involved in substrate recruitment to p97, interacts strongly with the C-terminus of p97. UBXD1 also interacts with HRD1 and HERP, both components of the ERAD pathway, via p97. It is possibly involved in aggresome formation; aggresomes are perinuclear compartments that contain misfolded proteins colocalized with centrosome markers. 102 matched cddid_all.tbl CDD cd10461 cd10461 198419 PUB_UBA_plant PNGase/UBA or UBX (PUB) domain of plant Ubiquitin-associated (UBA) domain containing proteins. The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover. This family contains only plant UBA domain-containing proteins. 107 matched cddid_all.tbl CDD cd10462 cd10462 198420 PUB_UBA PNGase/UBA or UBX (PUB) domain of Ubiquitin-associated (UBA) domain containing proteins. The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover. 100 matched cddid_all.tbl CDD cd10463 cd10463 198421 PUB_WLM PNGase/UBA or UBX (PUB) domain of the Wss1p-like metalloprotease (WLM) family. The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. WLM domains are found mostly in plant proteins, belonging to the Zincin-like superfamily of Zn-dependent peptidases that are linked to the ubiquitin signaling pathway through its fusion with the ubiquitin-binding PUB, ubiquitin-like, and Little Finger domains. More specifically, genetic evidence implicates the WLM family in de-SUMOylation. 96 matched cddid_all.tbl CDD cd10464 cd10464 198422 PUB_RNF31 PNGase/UBA or UBX (PUB) domain of the RNF31 (or HOIP) protein. This PUB domain is found in the p97 adaptor protein RNF31 (RING finger protein 31). The PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. The RNF31 protein, also known as HOIP or Zibra, contains an N-terminal PUB domain similar to those in PNGase and UBXD1, suggesting its association with p97. RNF31 functions in a complex with another RING-finger protein (HOIL-IL), displaying E3 ubiquitin-protein ligase activity, and forming linear ubiquitin chain assembly complex (LUBAC) through linkages between the N- and C-termini of ubiquitin. LUBAC has been shown to activate the NF-kappaB pathway. 111 matched cddid_all.tbl CDD cd10466 cd10466 198456 FimH_man-bind Mannose binding domain of FimH and related proteins. This family, restricted to gammaproteobacteria, includes FimH, a mannose-specific adhesin of uropathogenic Escherichia coli strains. The domain appears to bind specifically to D-mannose and mediates cellular adhesion to mannosylated proteins, a prerequisite to colonization and subsequent invasion of epithelial tissues. 160 matched cddid_all.tbl CDD cd10467 cd10467 198458 FAM20_C_like C-terminal putative kinase domain of FAM20 (family with sequence similarity 20), Drosophila Four-jointed (Fj), and related proteins. Drosophila Fj is a Golgi kinase that phosphorylates Ser or Thr residues within extracellular cadherin domains of a transmembrane receptor Fat and its ligand, Dachsous (Ds). The Fat signaling pathway regulates growth, gene expression, and planar cell polarity (PCP). Defects from mutation in the Drosophila fj gene include loss of the intermediate leg joint, and a PCP defect in the eye. Fjx1, the murine homologue of Fj, has been shown to be involved in both the Fat and Hippo signaling pathways, these two pathways intersect at multiple points. The Hippo pathway is important in organ size control and in cancer. FAM20B is a xylose kinase that may regulate the number of glycosaminoglycan chains by phosphorylating the xylose residue in the glycosaminoglycan-protein linkage region of proteoglycans. This domain has homology to a kinase-active site, mutation of three conserved Asp residues at the Drosophila Fj putative active site abolished its ability to phosphorylate Ft and Ds cadherin domains. FAM20A may participate in enamel development and gingival homeostasis, FAM20B in proteoglycan production, and FAM20C in bone development. FAM20C, also called Dentin Matrix Protein 4, is abundant in the dentin matrix, and may participate in the differentiation of mesenchymal precursor cells into functional odontoblast-like cells. Mutations in FAM20C are associated with lethal Osteosclerotic Bone Dysplasia (Raine Syndrome), and mutations in FAM20A with Amelogenesis imperfecta (AI) and Gingival Hyperplasia Syndrome. This model includes the FAM20_C domain family, previously known as DUF1193; FAM20_C appears to be homologous to the catalytic domain of the phosphoinositide 3-kinase (PI3K)-like family. 210 matched cddid_all.tbl CDD cd10468 cd10468 198459 Four-jointed-like_C C-terminal kinase domain of Drosophila Four-jointed (Fj), mouse Fjx1, and related proteins. Drosophila Fj is a Golgi type II transmembrane protein that is partially secreted, and is a kinase that phosphorylates Ser or Thr residues within extracellular cadherin domains of a transmembrane receptor Fat and its ligand, Dachsous (Ds). Mutation of three conserved Asp residues at the Drosophila Fj putative active site abolished its ability to phosphorylate Ft and Ds cadherin domains. The Fat signaling pathway regulates growth, gene expression, and planar cell polarity (PCP). Defects from mutation in Drosophila Fj include loss of the intermediate leg joint, and a PCP defect in the eye. The expression of the Drospophila fj gene is modulated by Notch, Unpaired (JAK/STAT), and Wingless signals. Mouse Fjx1, has been shown to be involved in both the Fat and Hippo signaling pathways; these two pathways intersect at multiple points. The Hippo pathway is important in organ size control and in cancer. The expression of the mouse fjx1 gene is also Notch dependent; fjx1 is expressed in the brain, the peripheral nervous system, in epithelial structures of different organs, and during limb development. 286 matched cddid_all.tbl CDD cd10469 cd10469 198460 FAM20A_C C-terminal putative kinase domain of FAM20A. Human FAM20A may play a fundamental role in enamel development and gingival homeostasis as mutations in FAM20A may underlie the pathogenesis of the autosomal recessive Amelogenesis imperfecta (AI) and Gingival Hyperplasia Syndrome. It is expressed in ameloblasts and gingivae. AI refers to a heterogeneous group of disorders of biomineralization caused by a lack of normal enamel formation. Mouse FAM20A is a secreted protein and the gene encoding it is differentially expressed in hematopoietic cells undergoing myeloid differentiation. This protein has also been associated with growth disorder in mice. The C-terminal domain of FAM20A is a putative kinase domain, based on mutagenesis of the C-terminal domain of Drosophila Four-Jointed, a related Golgi kinase. This subfamily belongs to the FAM20_C (also known as DUF1193) domain family. 217 matched cddid_all.tbl CDD cd10470 cd10470 198461 FAM20B_C C-terminal putative kinase domain of FAM20B xylose kinase. Experiments with human FAM20B suggest that it is a xylose kinase that participates in proteoglycan production. It may regulate the number of glycosaminoglycan chains by phosphorylating the xylose residue in the glycosaminoglycan-protein linkage region of proteoglycans. The C-terminal domain of FAM20B is a putative kinase domain, based on mutagenesis of the C-terminal domain of Drosophila Four-Jointed, a related Golgi kinase. This subfamily belongs to the FAM20_C (also known as DUF1193) domain family. 206 matched cddid_all.tbl CDD cd10471 cd10471 198462 FAM20C_C C-terminal putative kinase domain of FAM20C (also known as Dentin Matrix Protein 4, DMP4). Mouse DMP4 is abundant in the dentin matrix, and is expressed in high levels in odontoblasts. These latter cells synthesize various nucleators or inhibitors of mineralization. The in vivo role of DMP4 in dentinogenesis is unclear. However, gain- and loss-of-function experiments suggest that it participates in the differentiation of mesenchymal precursor cells into functional odontoblast-like cells. In addition to this domain, DMP4 contains a Greek key calcium-binding domain. Human FAM20C participates in bone development; mutations in FAM20C are associated with lethal Osteosclerotic Bone Dysplasia (Raine Syndrome), an autosomal recessive disorder in which affected individuals die within days or weeks of birth, usually due to thoratic malformation resulting in respiratory failure. The C-terminal domain of FAM20C is a putative kinase domain, based on mutagenesis of the C-terminal domain of Drosophila Four-Jointed, a related Golgi kinase. This subfamily belongs to the FAM20_C (also known as DUF1193) domain family. 212 matched cddid_all.tbl CDD cd10472 cd10472 198440 EphR_LBD_B Ligand Binding Domain of Ephrin type-B receptors. Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). Class EphB receptors bind to transmembrane ephrin-B ligands. They play important roles in synapse formation and plasticity, spine morphogenesis, axon guidance, and angiogenesis. In the intestinal epithelium, EphB receptors are Wnt signaling target genes that control cell compartmentalization. They function as suppressors of colon cancer progression. There are six vertebrate EhpB receptors (EphB1-6), which display promiscuous interactions with three ephrin-B ligands. One exception is EphB2, which also interacts with ephrin A5. EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). Ephrin/EphR interaction mainly results in cell-cell repulsion or adhesion, making it important in neural development and plasticity, cell morphogenesis, cell-fate determination, embryonic development, tissue patterning, and angiogenesis. 176 matched cddid_all.tbl CDD cd10473 cd10473 198441 EphR_LBD_A Ligand Binding Domain of Ephrin type-A Receptors. Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). Class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). Ephrin/EphR interaction mainly results in cell-cell repulsion or adhesion, making it important in neural development and plasticity, cell morphogenesis, cell-fate determination, embryonic development, tissue patterning, and angiogenesis. 173 matched cddid_all.tbl CDD cd10474 cd10474 198442 EphR_LBD_B4 Ligand Binding Domain of Ephrin type-B Receptor 4. Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). Class EphB receptors bind to transmembrane ephrin-B ligands. There are six vertebrate EhpB receptors (EphB1-6), which display promiscuous interactions with three ephrin-B ligands. EphB4 plays a role in osteoblast differentiation and has been linked to multiple myeloma. EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). 180 matched cddid_all.tbl CDD cd10475 cd10475 198443 EphR_LBD_B6 Ligand Binding Domain of Ephrin type-B Receptor 6. Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). Class EphB receptors bind to transmembrane ephrin-B ligands. There are six vertebrate EhpB receptors (EphB1-6), which display promiscuous interactions with three ephrin-B ligands. EphB6, a kinase-defective member of this family, is downregulated in MDA-MB-231-breast cancer cells and myeloid cancers and upregulated in neuroblasoma and glioblastoma. EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). 180 matched cddid_all.tbl CDD cd10476 cd10476 198444 EphR_LBD_B1 Ligand Binding Domain of Ephrin type-B Receptor 1. Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). Class EphB receptors bind to transmembrane ephrin-B ligands. There are six vertebrate EhpB receptors (EphB1-6), which display promiscuous interactions with three ephrin-B ligands. Using EphB1 knockout-mice, EphB1 has been shown to be essential to the development of long-term potentiation (LTP), a cellular model of synaptic plasticity, learning and memory formation. EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). 176 matched cddid_all.tbl CDD cd10477 cd10477 198445 EphR_LBD_B2 Ligand Binding Domain of Ephrin type-B Receptor 2. Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). Class EphB receptors bind to transmembrane ephrin-B ligands. There are six vertebrate EhpB receptors (EphB1-6), which display promiscuous interactions with three ephrin-B ligands. EphB2 plays a role in cell positioning in the gastrointestinal tract by being expressed in proliferating progenitor cells. It also has been implicated in colorectal cancer. A loss of EphB2, as well as EphA4, also precedes memory decline in a murine model of Alzheimers disease. EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). 178 matched cddid_all.tbl CDD cd10478 cd10478 198446 EphR_LBD_B3 Ligand Binding Domain of Ephrin type-B Receptor 3. Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). Class EphB receptors bind to transmembrane ephrin-B ligands. There are six vertebrate EhpB receptors (EphB1-6), which display promiscuous interactions with three ephrin-B ligands. EphB3 plays a role in cell positioning in the gastrointestinal tract by being preferentially expressed in Paneth cells. It also has been implicated in early colorectal cancer and early stage squamous cell lung cancer. EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). 173 matched cddid_all.tbl CDD cd10479 cd10479 198447 EphR_LBD_A1 Ligand Binding Domain of Ephrin type-A Receptor 1. Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). Class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. EphA1 is downregulated in some advanced colorectal and myeloid cancers and upregulated in neuroblasoma and glioblastoma. EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). Ephrin/EphR interaction mainly results in cell-cell repulsion or adhesion. 177 matched cddid_all.tbl CDD cd10480 cd10480 198448 EphR_LBD_A2 Ligand Binding Domain of Ephrin type-A Receptor 2. EphRs comprise the largest subfamily of receptor tyr kinases (RTKs). Class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. EphA2 negatively regulates cell differentiation and has been shown to be overexpressed in tumor cells and tumor blood vessels in a variety of cancers including breast, prostate, lung, and colon. As a result, it is an attractive target for drug design since its inhibition could affect several aspects of tumor progression. EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). Ephrin/EphR interaction mainly results in cell-cell repulsion or adhesion. 174 matched cddid_all.tbl CDD cd10481 cd10481 198449 EphR_LBD_A3 Ligand Binding Domain of Ephrin type-A Receptor 3. Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). Class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. EphA3 has been implicated in leukemia, lung and other cancers. EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). Ephrin/EphR interaction mainly results in cell-cell repulsion or adhesion. 173 matched cddid_all.tbl CDD cd10482 cd10482 198450 EphR_LBD_A4 Ligand Binding Domain of Ephrin type-A Receptor 4. Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). Class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. A loss of EphA4, as well as EphB2, precedes memory decline in a murine model of Alzheimers disease. EphA4 has been shown to have a negative effect on axon regeneration and functional restoration in corticospinal lesions and is downregulated in some cervical cancers. EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). 174 matched cddid_all.tbl CDD cd10483 cd10483 198451 EphR_LBD_A5 Ligand Binding Domain of Ephrin type-A Receptor 5. Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). Class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. EphA5 is almost exclusively expressed in the nervous system. EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). 173 matched cddid_all.tbl CDD cd10484 cd10484 198452 EphR_LBD_A6 Ligand Binding Domain of Ephrin type-A Receptor 6. Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). Class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. EphA6, like other Eph receptors and their ephrin ligands, seems to play a role in neural development, underlying learning and memory. EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). 173 matched cddid_all.tbl CDD cd10485 cd10485 198453 EphR_LBD_A7 Ligand Binding Domain of Ephrin type-A Receptor 7. Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). Class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. EphA7 has been implicated in various cancers, including prostate, gastic and colorectal cancers. EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). 177 matched cddid_all.tbl CDD cd10486 cd10486 198454 EphR_LBD_A8 Ligand Binding Domain of Ephrin type-A Receptor 8. Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). Class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. EphA8 has been implicated in various cancers. EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). 173 matched cddid_all.tbl CDD cd10487 cd10487 198455 EphR_LBD_A10 Ligand Binding Domain of Ephrin type-A Receptor 10. Ephrin receptors (EphRs) comprise the largest subfamily of receptor tyrosine kinases (RTKs). Class EphA receptors bind GPI-anchored ephrin-A ligands. There are ten vertebrate EphA receptors (EphA1-10), which display promiscuous interactions with six ephrin-A ligands. EphA10, which contains an inactive tyr kinase domain, may function to attenuate signals of co-clustered active receptors. EphA10 is mainly expressed in the testis. EphRs contain a ligand binding domain and two fibronectin repeats extracellularly, a transmembrane segment, and a cytoplasmic tyrosine kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). Ephrin/EphR interaction results in cell-cell repulsion or adhesion. 173 matched cddid_all.tbl CDD cd10488 cd10488 199812 MH1_R-SMAD N-terminal Mad Homology 1 (MH1) domain of receptor regulated SMADs. The MH1 is a small DNA-binding domain present in SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. It binds to the major groove in an unusual manner via a beta hairpin structure. It negatively regulates the functions of the MH2 domain, the C-terminal domain of SMAD. This MH1 domain is found in all receptor regulated SMADs (R-SMADs) including SMAD1, SMAD2, SMAD3, SMAD5 and SMAD9. SMAD1 plays an essential role in bone development and postnatal bone formation through activation by bone morphogenetic protein (BMP) type 1 receptor kinase. SMAD2 regulates multiple cellular processes, such as cell proliferation, apoptosis and differentiation, while SMAD3 modulates signals of activin and TGF-beta. SMAD4, a common mediator SMAD (co-SMAD) binds R-SMADs, forming an oligomeric complex that binds to DNA and serves as a transcription factor. SMAD5 is involved in bone morphogenetic proteins (BMP) signal modulation, possibly playing a role in the pathway involving inhibition of hematopoietic progenitor cells by TGF-beta. SMAD9 (also known as SMAD8) can mediate the differentiation of mesenchymal stem cells (MSCs) into tendon-like cells by inhibiting the osteogenic pathway 123 matched cddid_all.tbl CDD cd10489 cd10489 199813 MH1_SMAD_6_7 N-terminal Mad Homology 1 (MH1) domain in SMAD6 and SMAD7. The MH1 is a small DNA-binding domain present in SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. MH1 binds to the DNA major groove in an unusual manner via a beta hairpin structure. It negatively regulates the functions of the MH2 domain, the C-terminal domain of SMAD. This MH1 domain is found in SMAD6 and SMAD7, both inhibitory SMADs (I-SMADs) and negative regulators of signaling mediated by TGF-beta superfamily. SMAD6 specifically inhibits bone morphogenetic protein (BMP) type I receptor mediated signaling while SMAD7 enhances muscle differentiation and is often associated with cancer, tissue fibrosis and inflammatory diseases. 119 matched cddid_all.tbl CDD cd10490 cd10490 199814 MH1_SMAD_1_5_9 N-terminal Mad Homology 1 (MH1) domain in SMAD1, SMAD5 and SMAD9 (also known as SMAD8). The MH1 is a small DNA-binding domain present in SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. MH1 binds to the DNA major groove in an unusual manner via a beta hairpin structure. It negatively regulates the functions of the MH2 domain, the C-terminal domain of SMAD. This MH1 domain is found in SMAD1, SMAD5 and SMAD9, all closely related receptor regulated SMADs (R-SMADs). SMAD1 plays an essential role in bone development and postnatal bone formation through activation by bone morphogenetic protein (BMP) type 1 receptor kinase. SMAD5 is involved in bone morphogenetic proteins (BMP) signal modulation and may also play a role in the pathway involving inhibition of hematopoietic progenitor cells by TGF-beta. SMAD9 mediates the differentiation of mesenchymal stem cells (MSCs) into tendon-like cells by inhibiting the osteogenic pathway. 124 matched cddid_all.tbl CDD cd10491 cd10491 199815 MH1_SMAD_2_3 N-terminal Mad Homology 1 (MH1) domain in SMAD2 and SMAD3. The MH1 is a small DNA-binding domain present in SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. MH1 binds to the DNA major groove in an unusual manner via a beta hairpin structure. It negatively regulates the functions of the MH2 domain, the C-terminal domain of SMAD. This MH1 is found in SMAD2 as well as SMAD3. SMAD2 mediates the signal of the transforming growth factor (TGF)-beta, and thereby regulates multiple cellular processes, such as cell proliferation, apoptosis, and differentiation. It plays a role in the transmission of extracellular signals from ligands of the TGF-beta superfamily growth factors into the cell nucleus. SMAD3 modulates signals of activin and TGF-beta. It binds SMAD4, enabling its transmigration into the nucleus where it forms complexes with other proteins and acts as a transcription factor. Increased SMAD3 activity has been implicated in the pathogenesis of scleroderma. 124 matched cddid_all.tbl CDD cd10492 cd10492 199816 MH1_SMAD_4 N-terminal Mad Homology 1 (MH1) domain in SMAD4. The MH1 is a small DNA-binding domain present in SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. MH1 binds to the DNA major groove in an unusual manner via a beta hairpin structure. It negatively regulates the functions of the MH2 domain, the C-terminal domain of SMAD. This MH1 belongs to SMAD4, a common mediator SMAD (co-SMAD), which belongs to the Dwarfin family of proteins and is involved in many cell functions such as differentiation, apoptosis, gastrulation, embryonic development and cell cycle. SMAD4 binds receptor regulated SMADs (R-SMADs) such as SMAD1 or SMAD2, and forms an oligomeric complex that binds to DNA and serves as a transcription factor. SMAD4 is often mutated in several cancers, such as multiploid colorectal cancer and pancreatic carcinoma, as well as in juvenile polyposis syndrome (JPS). 125 matched cddid_all.tbl CDD cd10493 cd10493 199817 MH1_SMAD_6 N-terminal Mad Homology 1 (MH1) domain in SMAD6. The MH1 is a small DNA-binding domain present in SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. MH1 binds to the DNA major groove in an unusual manner via a beta hairpin structure. It negatively regulates the functions of the MH2 domain, the C-terminal domain of SMAD. This MH1 belongs to SMAD6, an inhibitory SMAD (I-SMAD) or antagonistic SMAD, which acts as a negative regulator of signaling mediated by TGF-beta superfamily ligands, by competing with SMAD4 and preventing the transcription of SMAD4's gene products. SMAD6 specifically inhibits bone morphogenetic protein (BMP) type I receptor mediated signaling. 113 matched cddid_all.tbl CDD cd10494 cd10494 199818 MH1_SMAD_7 N-terminal Mad Homology 1 (MH1) domain in SMAD7. The MH1 is a small DNA-binding domain present in SMAD (small mothers against decapentaplegic) family of proteins. It binds to the major groove in an unusual manner via a beta hairpin structure. It negatively regulates the functions of the MH2 domain, the C-terminal domain of SMAD. This MH1 belongs to SMAD7, an inhibitory SMAD (I-SMAD) or antagonistic SMAD, which acts as a negative regulator of signaling mediated by TGF-beta superfamily ligands, by blocking TGF-beta type 1 and activin association with the receptor as well as access to SMAD2. SMAD7 enhances muscle differentiation, playing pivotal roles in embryonic development and adult homoeostasis. Altered expression of SMAD7 is often associated with cancer, tissue fibrosis and inflammatory diseases. 123 matched cddid_all.tbl CDD cd10495 cd10495 199820 MH2_R-SMAD C-terminal Mad Homology 2 (MH2) domain in receptor regulated SMADs. The MH2 domain is located at the C-terminus of the SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. The MH2 domain is responsible for type I receptor interaction, phosphorylation-triggered homo- and hetero-oligomerization, and transactivation. It is negatively regulated by the N-terminal MH1 domain. Receptor regulated SMADs (R-SMADs) include SMAD1, SMAD2, SMAD3, SMAD5 and SMAD9. SMAD1 plays an essential role in bone development and postnatal bone formation through activation by bone morphogenetic protein (BMP) type 1 receptor kinase. SMAD2 regulates multiple cellular processes, such as cell proliferation, apoptosis and differentiation, while SMAD3 modulates signals of activin and TGF-beta. SMAD5 is involved in BMP signal modulation, possibly playing a role in the pathway involving inhibition of hematopoietic progenitor cells by TGF-beta. SMAD9 (also known as SMAD8) can mediate the differentiation of mesenchymal stem cells into tendon-like cells by inhibiting the osteogenic pathway. 182 matched cddid_all.tbl CDD cd10496 cd10496 199821 MH2_I-SMAD C-terminal Mad Homology 2 (MH2) domain in Inhibitory SMADs. The MH2 domain is located at the C-terminus of the SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. The MH2 domain is responsible for type I receptor interaction, phosphorylation-triggered homo- and hetero-oligomerization, and transactivation. It is negatively regulated by the N-terminal MH1 domain, which prevents it from forming a complex with SMAD4. SMAD6 and SMAD7 are inhibitory SMADs (I-SMADs) that function as negative regulators of signaling mediated by the TGF-beta superfamily. SMAD6 specifically inhibits bone morphogenetic protein (BMP) type I receptor mediated signaling, while SMAD7 enhances muscle differentiation and is often associated with cancer, tissue fibrosis and inflammatory diseases. 165 matched cddid_all.tbl CDD cd10497 cd10497 199822 MH2_SMAD_1_5_9 C-terminal Mad Homology 2 (MH2) domain in SMAD1, SMAD5 and SMAD9. The MH2 domain is located at the C-terminus of the SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. The MH2 domain is responsible for type I receptor interaction, phosphorylation-triggered homo- and hetero-oligomerization, and transactivation. It is negatively regulated by the N-terminal MH1 domain, which prevents it from forming a complex with SMAD4. SMAD1, SMAD5 and SMAD9 (also known as SMAD8), are receptor regulated SMADs (R-SMADs). SMAD1 plays an essential role in bone development and postnatal bone formation through activation by bone morphogenetic protein (BMP) type 1 receptor kinase. SMAD5 is involved in BMP signal modulation and may also play a role in the pathway involving inhibition of hematopoietic progenitor cells by TGF-beta. SMAD9 mediates the differentiation of mesenchymal stem cells (MSCs) into tendon-like cells by inhibiting the osteogenic pathway. 201 matched cddid_all.tbl CDD cd10498 cd10498 199823 MH2_SMAD_4 C-terminal Mad Homology 2 (MH2) domain in SMAD4. The MH2 domain is located at the C-terminus of the SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. The MH2 domain is responsible for type I receptor interaction, phosphorylation-triggered homo- and hetero-oligomerization, and transactivation. It is negatively regulated by the N-terminal MH1 domain. SMAD4, which belongs to the Dwarfin family of proteins, is involved in many cell functions such as differentiation, apoptosis, gastrulation, embryonic development and the cell cycle. SMAD4 binds receptor regulated SMADs (R-SMADs) such as SMAD1 or SMAD2, and forms an oligomeric complex that binds to DNA and serves as a transcription factor. SMAD4 is often mutated in several cancers, such as multiploid colorectal cancer, cervical cancer and pancreatic carcinoma, as well as in juvenile polyposis syndrome. 222 matched cddid_all.tbl CDD cd10499 cd10499 199824 MH2_SMAD_6 C-terminal Mad Homology 2 (MH2) domain in SMAD6. The MH2 domain is located at the C-terminus of the SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. The MH2 domain is responsible for type I receptor interaction, phosphorylation-triggered homo- and hetero-oligomerization, and transactivation. It is negatively regulated by the N-terminal MH1 domain, which prevents it from forming a complex with SMAD4. SMAD6, an inhibitory or antagonistic SMAD (I-SMAD), acts as a negative regulator of signaling mediated by the TGF-beta superfamily of ligands, by competing with SMAD4 and preventing the transcription of SMAD4's gene products. SMAD6 specifically inhibits bone morphogenetic protein (BMP) type I receptor mediated signaling. SMAD6 and SMAD7 act as critical mediators for effective TGF-beta I-mediated suppression of Interleukin-1/Toll-like receptor (IL-1R/TLR) signaling through simultaneous binding to Pellino-1, an adaptor protein of interleukin-1 receptor associated kinase 1 (IRAK1), via their MH2 domains. 174 matched cddid_all.tbl CDD cd10500 cd10500 199825 MH2_SMAD_7 C-terminal Mad Homology 2 (MH2) domain in SMAD7. The MH2 domain is located at the C-terminus of the SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. The MH2 domain is responsible for type I receptor interaction, phosphorylation-triggered homo- and hetero-oligomerization, and transactivation. It is negatively regulated by the N-terminal MH1 domain, which prevents it from forming a complex with SMAD4. SMAD7, an inhibitory or antagonistic SMAD (I-SMAD), acts as a negative regulator of signaling mediated by the TGF-beta superfamily of ligands, by blocking TGF-beta type 1 and activin association with the receptor as well as access to SMAD2. SMAD7 enhances muscle differentiation, playing pivotal roles in embryonic development and adult homoeostasis. SMAD7 and SMAD6 act as critical mediators for effective TGF-beta I-mediated suppression of Interleukin-1/Toll-like receptor (IL-1R/TLR) signaling through simultaneous binding to Pellino-1, an adaptor protein of interleukin-1 receptor associated kinase 1(IRAK1), via their MH2 domains. Altered expression of SMAD7 is often associated with cancer, tissue fibrosis and inflammatory diseases. 171 matched cddid_all.tbl CDD cd10506 cd10506 259849 RNAP_IV_RPD1_N Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain. NRPD1 and NRPE1 are the largest subunits of plant DNA-dependent RNA polymerase IV and V that, together with second largest subunits (NRPD2 and NRPE2), form the active site region of the DNA entry and RNA exit channel. Higher plants have five multi-subunit nuclear RNA polymerases; RNAP I, RNAP II and RNAP III, which are essential for viability, plus the two isoforms of the non-essential polymerase RNAP IV and V, which specialize in small RNA-mediated gene silencing pathways. RNAP IV and/or V might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. The subunit compositions of RNAP IV and V reveal that they evolved from RNAP II. 744 matched cddid_all.tbl CDD cd10507 cd10507 259792 Zn-ribbon_RPA12 C-terminal zinc ribbon domain of RPA12 subunit of RNA polymerase I. The C-terminal zinc ribbon domain (C-ribbon) of subunit A12 (Zn-ribbon_RPA12) in RNA polymerase (Pol) I is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPA12 in Pol I, RPB9 in Pol II, RPC11 in Pol III and TFS in archaea are distantly related to each other and to the TFIIS elongation factor of Pol II. RPA12 has two zinc-binding domains separated by a flexible linker. 47 matched cddid_all.tbl CDD cd10508 cd10508 259793 Zn-ribbon_RPB9 C-terminal zinc ribbon domain of RPB9 subunit of RNA polymerase II. The C-terminal zinc ribbon domain (C-ribbon) of subunit B9 (Zn-ribbon_RPB9) in RNA polymerase (Pol) II is involved in intrinsic transcript cleavage. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPB9 have strong homology to RPA12 of Pol I and RPC11 of Pol III subunits but its intrinsic cleavage activity is weaker for Pol II. Zn-ribbon_RPB9 is homologous to Pol II elongation factor TFIIS domain III. The very weak cleavage activity of Pol II is stimulated by TFIIS. RPB9 has two zinc-binding domains separated by a flexible linker. 49 matched cddid_all.tbl CDD cd10509 cd10509 259794 Zn-ribbon_RPC11 C-terminal zinc ribbon domain of RPC11 subunit of RNA polymerase III. The C-terminal zinc ribbon domain (C-ribbon) of subunit C11 (Zn-ribbon_RPC11) in RNA polymerase (Pol) III is required for intrinsic transcript cleavage. RPC11 is also involved in Pol III termination. Eukaryote genomes are transcribed by three nuclear RNA polymerases (Pol I, II and III) that share some subunits. RPC11 has strong homology to RPB9 of Pol II and RPA12 of Pol I. Zn-ribbon_RPC11 is homologous to Pol II elongation factor TFIIS domain III. C11 has two zinc-binding domains separated by a flexible linker. 46 matched cddid_all.tbl CDD cd10511 cd10511 259795 Zn-ribbon_TFS C-terminal zinc ribbon domain of archaeal Transcription Factor S (TFS). TFS is an archaeal protein that stimulates the intrinsic cleavage activity of archaeal RNA polymerase. TFS C-terminal domain shows sequence similarity to the homologous C-terminal zinc ribbon domain of subunits A12.2, Rpb9, and C11 in eukaryotic RNA Polymerases (Pol) I, II, and III, respectively and domain III of TFIIS. TFS is not a subunit of archaeal RNA polymerase even though its domains arrangement is similar to A12.2, Rpb9, and C1. TFS is a transcription factor with a similar function to eukaryotic TFIIS. TFS has external cleavage induction activity and improves the fidelity of transcription. TFS has two zinc-binding domains. 47 matched cddid_all.tbl CDD cd10517 cd10517 380915 SET_SETDB1 SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and similar proteins. SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. 288 matched cddid_all.tbl CDD cd10518 cd10518 380916 SET_SETD1-like SET domain (including post-SET domain) found in SET domain-containing proteins (SETD1A/SETD1B), histone-lysine N-methyltransferases (KMT2A/KMT2B/KMT2C/KMT2D) and similar proteins. This family includes SET domain-containing protein 1A (SETD1A), 1B (SETD1B), as well as histone-lysine N-methyltransferase 2A (KMT2A), 2B (KMT2B), 2C (KMT2C), 2D (KMT2D). These proteins are histone-lysine N-methyltransferases (EC 2.1.1.43) that specifically methylate 'Lys-4' of histone H3 (H3K4me). 150 matched cddid_all.tbl CDD cd10519 cd10519 380917 SET_EZH SET domain found in enhancer of zeste homolog 1 (EZH1), zeste homolog 2 (EZH2) and similar proteins. The family includes EZH1 and EZH2. EZH1 (EC 2.1.1.43; also termed ENX-2, or histone-lysine N-methyltransferase EZH1) is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. EZH2 (EC 2.1.1.43; also termed lysine N-methyltransferase 6, ENX-1, or histone-lysine N-methyltransferase EZH2) is a catalytic subunit of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. Both, EZH1 and EZH2, can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. 117 matched cddid_all.tbl CDD cd10520 cd10520 380918 PR-SET_PRDM17 PR-SET domain found in PR domain zinc finger protein 17 (PRDM17) and similar proteins. PRDM17 (also termed zinc finger protein 408 (ZNF408)) may be involved in transcriptional regulation. 121 matched cddid_all.tbl CDD cd10521 cd10521 380919 SET_SMYD5 SET domain (including iSET domain and post-SET domain) found in SET and MYND domain-containing protein 5 (SMYD5) and similar proteins. SMYD5 (also termed protein NN8-4AG, or retinoic acid-induced protein 15) functions as histone lysine methyltransferase that mediates H4K20me3 at heterochromatin regions. It plays an important role in chromosome integrity by regulating heterochromatin and repressing endogenous repetitive DNA elements during differentiation. In zebrafish embryogenesis, it plays pivotal roles in both primitive and definitive hematopoiesis. 282 matched cddid_all.tbl CDD cd10522 cd10522 380920 SET_LegAS4-like SET domain found in Legionella pneumophila type IV secretion system effector LegAS4 and similar proteins. LegAS4 is a type IV secretion system effector of Legionella pneumophila. It contains a SET domain that is involved in the modification of Lys4 of histone H3 (H3K4) in the nucleolus of the host cell, thereby enhancing heterochromatic rDNA transcription. It also contains an ankyrin repeat domain of unknown function at its C-terminal region. 122 matched cddid_all.tbl CDD cd10523 cd10523 380921 SET_SETDB2 SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 2 (SETDB2) and similar proteins. SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis. 266 matched cddid_all.tbl CDD cd10524 cd10524 380922 SET_Suv4-20-like SET domain (including post-SET domain) found in Drosophila melanogaster suppressor of variegation 4-20 (Suv4-20) and similar proteins. Suv4-20 (also termed Su(var)4-20) is a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-20' of histone H4. It acts as a dominant suppressor of position-effect variegation. The family also includes Suv4-20 homologs, lysine N-methyltransferase 5B (KMT5B) and lysine N-methyltransferase 5C (KMT5C). Both KMT5B (also termed lysine-specific methyltransferase 5B, or suppressor of variegation 4-20 homolog 1, or Su(var)4-20 homolog 1, or Suv4-20h1) and KMT5C (also termed lysine-specific methyltransferase 5C, or suppressor of variegation 4-20 homolog 2, or Su(var)4-20 homolog 2, or Suv4-20h2) are histone methyltransferases that specifically trimethylate 'Lys-20' of histone H4 (H4K20me3). They play central roles in the establishment of constitutive heterochromatin in pericentric heterochromatin regions. 141 matched cddid_all.tbl CDD cd10525 cd10525 380923 SET_SUV39H1 SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 1 (SUV39H1) and similar proteins. SUV39H1 (EC 2.1.1.43; also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A (KMT1A), position-effect variegation 3-9 homolog (SUV39H), or Su(var)3-9 homolog 1) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. It mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions. 255 matched cddid_all.tbl CDD cd10526 cd10526 380924 SET_SMYD1 SET domain (including post-SET domain) found in SET and MYND domain-containing protein 1 (SMYD1) and similar proteins. SMYD1 (EC 2.1.1.43), also termed BOP, is a heart and muscle specific SET-MYND domain containing protein, which functions as a histone methyltransferase and regulates downstream gene transcription. It methylates histone H3 at 'Lys-4' (H3K4me), seems able to perform both mono-, di-, and trimethylation. SMYD1 plays a critical role in cardiomyocyte differentiation, cardiac morphogenesis and myofibril organization, as well as in the regulation of endothelial cells (ECs). It is expressed in vascular endothelial cells, it has beenshown that knockdown of SMYD1 in endothelial cells impairs EC migration and tube formation. 210 matched cddid_all.tbl CDD cd10527 cd10527 380925 SET_LSMT SET domain found in Rubisco large subunit methyltransferase (LSMT) and similar proteins. Rubisco LSMT is a non-histone protein methyl transferase responsible for the trimethylation of lysine14 in the large subunit of Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase). The family also includes SET domain-containing proteins, SETD3, SETD4 and SETD6, which belong to methyltransferase class VII that represents classical non-histone SET domain methyltransferases. Members in this family contain a SET domain and a C-terminal RubisCO LSMT substrate-binding (Rubis-subs-bind) domain. 236 matched cddid_all.tbl CDD cd10528 cd10528 380926 SET_SETD8 SET domain found in SET domain-containing protein 8 (SETD8) and similar proteins. SETD8 (EC 2.1.1.43; also termed N-lysine methyltransferase KMT5A, H4-K20-HMTase KMT5A, lysine N-methyltransferase 5A, lysine-specific methylase 5A, PR/SET domain-containing protein 07, PR-Set7 or PR/SET07) is a nucleosomal histone-lysine N-methyltransferase that specifically monomethylates 'Lys-20' of histone H4 (H4K20me1). It plays a central role in the silencing of euchromatic genes. 141 matched cddid_all.tbl CDD cd10529 cd10529 380927 SET_SETD5-like SET domain found in SET domain-containing protein 5 (SETD5), inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar proteins. SETD5 is a probable transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. KMT2E (also termed inactive lysine N-methyltransferase 2E or myeloid/lymphoid or mixed-lineage leukemia protein 5 (MLL5)) associates with chromatin regions downstream of transcriptional start sites of active genes and thus regulates gene transcription. The family also includes Saccharomyces cerevisiae SET domain-containing proteins, SET3 and SET4, and Schizosaccharomyces pombe SET3. Most of these family members contain a post-SET domain which harbors a zinc-binding site. 127 matched cddid_all.tbl CDD cd10530 cd10530 380928 SET_SETD7 SET domain found in SET domain-containing protein 7 (SETD7) and similar proteins. SETD7 (EC 2.1.1.43; also termed histone H3-K4 methyltransferase SETD7, H3-K4-HMTase SETD7, lysine N-methyltransferase 7 (KMT7) or SET7/9) is a histone-lysine N-methyltransferase that specifically monomethylates 'Lys-4' of histone H3. It plays a central role in the transcriptional activation of genes such as collagenase or insulin. Set7/9 also methylates non-histone proteins, including estrogen receptor alpha (ERa), suggesting it has a role in diverse biological processes. ERa methylation by Set7/9 stabilizes ERa and activates its transcriptional activities, which are involved in the carcinogenesis of breast cancer. In a high-throughput screen, treatment of human breast cancer cells (MCF7 cells) with cyproheptadine, a Set7/9 inhibitor, decreased the expression and transcriptional activity of ERa, thereby inhibiting estrogen-dependent cell growth. 130 matched cddid_all.tbl CDD cd10531 cd10531 380929 SET_SETD2-like SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2), nuclear SETD2 (NSD2), ASH1-like protein (ASH1L) and similar proteins. This family includes SET domain-containing protein 2 (SETD2), nuclear SETD2 (NSD2) and ASH1-like protein (ASH1L), which function as histone-lysine N-methyltransferases. SETD2 specifically trimethylates 'Lys-36' of histone H3 (H3K36me3) using demethylated 'Lys-36' (H3K36me2) as substrate. NSD2 shows histone H3 'Lys-27' (H3K27me) methyltransferase activity. ASH1L specifically methylates 'Lys-36' of histone H3 (H3K36me). The family also includes Arabidopsis thaliana ASH1-related protein 3 (ASHR3) and similar proteins. 136 matched cddid_all.tbl CDD cd10532 cd10532 380930 SET_SUV39H2 SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homolog 2 (SUV39H2) and similar proteins. SUV39H2 (EC 2.1.1.43; also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B (KMT1B), or Su(var)3-9 homolog 2) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. It mainly functions in heterochromatin regions, thereby playing a central role in the establishment of constitutive heterochromatin at pericentric and telomere regions. 243 matched cddid_all.tbl CDD cd10533 cd10533 380931 SET_EHMT2 SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase 2 (EHMT2) and similar proteins. EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C (KMT1C), or protein G9a) acts as a histone-lysine N-methyltransferase that specifically mono- and dimethylates 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. 239 matched cddid_all.tbl CDD cd10534 cd10534 380932 PR-SET_PRDM-like PR-SET domain found in PRDM (PRDI-BF1 and RIZ homology domain) family of proteins. PRDM family of proteins is defined based on the conserved N-terminal PR domain, which is closely related to the Su(var)3-9, enhancer of zeste, and trithorax (SET) domains of histone methyltransferases, and is specifically called PR-SET domain. The family consists of 17 members in primates. PRDMs play diverse roles in cell-cycle regulation, differentiation, and meiotic recombination. The family also contains zinc finger protein ZFPM1 and ZFPM2. ZFPM1 (also termed friend of GATA protein 1, FOG-1, friend of GATA 1, zinc finger protein 89A, or zinc finger protein multitype 1) functions as a transcription regulator that plays an essential role in erythroid and megakaryocytic cell differentiation. ZFPM2 (also termed friend of GATA protein 2, FOG-2, friend of GATA 2, zinc finger protein 89B, or zinc finger protein multitype 2) functions as a transcription regulator that plays a central role in heart morphogenesis and development of coronary vessels from epicardium, by regulating genes that are essential during cardiogenesis. 83 matched cddid_all.tbl CDD cd10535 cd10535 380933 SET_EHMT1 SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase 1 (EHMT1) and similar proteins. EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, or lysine N-methyltransferase 1D (KMT1D)) acts as a histone-lysine N-methyltransferase that specifically mono- and dimethylates 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. 231 matched cddid_all.tbl CDD cd10536 cd10536 380934 SET_SMYD4 SET domain (including iSET domain and post-SET domain) found in SET and MYND domain-containing protein 4 (SMYD4) and similar proteins. SMYD4 functions as a potential tumor suppressor that plays a critical role in breast carcinogenesis at least partly through inhibiting the expression of PDGFR-alpha. In zebrafish, SMYD4 is ubiquitously expressed in early embryos and becomes enriched in the developing heart; mutants show a strong defect in cardiomyocyte proliferation, which lead to a severe cardiac malformation. 218 matched cddid_all.tbl CDD cd10537 cd10537 380935 SET_SETD9 SET domain found in SET domain-containing protein 9 (SETD9) and similar proteins. SETD9 is an uncharacterized protein that belongs to the class V-like SAM-binding methyltransferase superfamily. 150 matched cddid_all.tbl CDD cd10538 cd10538 380936 SET_SETDB-like SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1) and 2 (SETDB2), suppressor of variegation 3-9 homologs, SUV39H1 and SUV39H2, euchromatic histone-lysine N-methyltransferase EHMT1 and EHMT2, and similar proteins. The family includes SET domain bifurcated 1 (SETDB1) and 2 (SETDB2), suppressor of variegation 3-9 homologs, SUV39H1 and SUV39H2, euchromatic histone-lysine N-methyltransferase EHMT1 and EHMT2. SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis. SUV39H1 (also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A, KMT1A, position-effect variegation 3-9 homolog, SUV39H, or Su(var)3-9 homolog 1) and SUV39H2 (also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B, KMT1B, or Su(var)3-9 homolog 2), both act as histone-lysine N-methyltransferases that specifically trimethylate 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. They mainly function in heterochromatin regions, thereby playing central roles in the establishment of constitutive heterochromatin at pericentric and telomere regions. EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, lysine N-methyltransferase 1D, or KMT1D) and EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C, KMT1C, or protein G9a), both act as histone-lysine N-methyltransferases that specifically mono- and dimethylate 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. This family also includes the pre-SET domain, which is found in a number of histone methyltransferases (HMTase), N-terminal to the SET domain. Pre-SET domain is a zinc binding motif which contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilizing SET domains. Most family members, except for Arabidopsis thaliana SUVH9, contain a post-SET domain which harbors a zinc-binding site. 217 matched cddid_all.tbl CDD cd10539 cd10539 380937 SET_ATXR5_6-like SET domain found in fungal protein lysine methyltransferase SET5 and similar protein. The family includes Arabidopsis thaliana ATXR5 and ATXR6. Both ATXR5 (also termed protein SET DOMAIN GROUP 15, or TRX-related protein 5) and ATXR6 (also termed protein SET DOMAIN GROUP 34, or TRX-related protein 6) function as histone methyltransferase that specifically monomethylates 'Lys-37' of histone H3 (H3K27me1). They are required for chromatin structure and gene silencing. 138 matched cddid_all.tbl CDD cd10540 cd10540 380938 SET_SpSet7-like SET domain found in Schizossacharomyces pombe Set7 and similar proteins. Schizosaccharomyces pombe Set7 is a novel histone-lysine N-methyltransferase. The family also includes a viral histone H3 lysine 27 methyltransferase from Paramecium bursaria Chlorella virus 1 (PBCV-1). 112 matched cddid_all.tbl CDD cd10541 cd10541 380939 SET_SETDB SET domain (including pre-SET and post-SET domains) found in SET domain bifurcated 1 (SETDB1), SET domain bifurcated 2 (SETDB2), and similar proteins. SETDB1 (EC 2.1.1.43; also termed ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. SETDB2 (EC 2.1.1.43; also termed chronic lymphocytic leukemia deletion region gene 8 protein (CLLD8), or lysine N-methyltransferase 1F (KMT1F)) acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It is involved in left-right axis specification in early development and mitosis. 236 matched cddid_all.tbl CDD cd10542 cd10542 380940 SET_SUV39H SET domain (including pre-SET and post-SET domains) found in suppressor of variegation 3-9 homologs, SUV39H1, SUV39H2 and similar proteins. This family includes SUV39H1 (also termed histone H3-K9 methyltransferase 1, H3-K9-HMTase 1, lysine N-methyltransferase 1A, KMT1A, position-effect variegation 3-9 homolog, SUV39H, or Su(var)3-9 homolog 1) and SUV39H2 (also termed histone H3-K9 methyltransferase 2, H3-K9-HMTase 2, lysine N-methyltransferase 1B, KMT1B, or Su(var)3-9 homolog 2), both act as histone-lysine N-methyltransferases that specifically trimethylate 'Lys-9' of histone H3 (H3K9me3) using monomethylated H3 'Lys-9' as substrate. They mainly function in heterochromatin regions, thereby playing central roles in the establishment of constitutive heterochromatin at pericentric and telomere regions. Also included are Schizosaccharomyces pombe H3K9 methyltransferase Clr4 (SUV39H homolog) and Neurospora crassa DIM-5, both of which also methylate 'Lys-9' of histone H3. 245 matched cddid_all.tbl CDD cd10543 cd10543 380941 SET_EHMT SET domain (including pre-SET and post-SET domains) found in euchromatic histone-lysine N-methyltransferase EHMT1, EHMT2 and similar proteins. This family includes EHMT1 (also termed Eu-HMTase1, G9a-like protein 1, GLP, GLP1, histone H3-K9 methyltransferase 5, H3-K9-HMTase 5, lysine N-methyltransferase 1D, or KMT1D) and EHMT2 (also termed Eu-HMTase2, HLA-B-associated transcript 8, histone H3-K9 methyltransferase 3, H3-K9-HMTase 3, lysine N-methyltransferase 1C, KMT1C, or protein G9a), both act as histone-lysine N-methyltransferases that specifically mono- and dimethylate 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. 231 matched cddid_all.tbl CDD cd10544 cd10544 380942 SET_SETMAR SET domain (including pre-SET and post-SET domains) found in SET domain and mariner transposase fusion protein (SETMAR) and similar proteins. SETMAR (also termed metnase) is a DNA-binding protein that is indirectly recruited to sites of DNA damage through protein-protein interactions. It has a sequence-specific DNA-binding activity recognizing the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element and displays a DNA nicking and end joining activity. SETMAR also acts as a histone-lysine N-methyltransferase that methylates 'Lys-4' and 'Lys-36' of histone H3. It specifically mediates dimethylation of H3 'Lys-36' at sites of DNA double-strand break and may recruit proteins required for efficient DSB repair through non-homologous end-joining. 254 matched cddid_all.tbl CDD cd10545 cd10545 380943 SET_AtSUVH-like SET domain found in Arabidopsis thaliana histone H3-K9 methyltransferases (SUVHs) and similar proteins. Arabidopsis thaliana SUVH protein (also termed suppressor of variegation 3-9 homolog protein) is a histone-lysine N-methyltransferase that methylates 'Lys-9' of histone H3. H3 'Lys-9' methylation represents a specific tag for epigenetic transcriptional repression. Some family members contain a post-SET domain which binds a Zn2+ ion. Most family members, except for Arabidopsis thaliana SUVH9, contain a post-SET domain which harbors a zinc-binding site. 232 matched cddid_all.tbl CDD cd10546 cd10546 240598 VKOR Vitamin K epoxide reductase (VKOR) family. VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. This family includes enzymes that are present in vertebrates, Drosophila, plants, bacteria, and archaea. All homologs of VKOR contain an active site CXXC motif, which is switched between reduced and disulfide-bonded states during the reaction cycle. In some plant and bacterial homologs, the VKOR domain is fused with domains of the thioredoxin family of oxidoreductases which may function as redox partners in initiating the reduction cascade. Warfarin, a widely used oral anticoagulant used in medicine as well as rodenticides, inhibits the activity of VKOR, resulting in decreased levels of reduced vitamin K, which is required for the function of several clotting factors. However, anticoagulation effect of warfarin is significantly associated with polymorphism of certain genes, including VKORC1. Interestingly, in rodents, an adaptive trait appears to have evolved convergently by selection on new or standing genetic polymorphisms in VKORC1 as well as by adaptive introgressive hybridization between species, likely brought about by human-mediated dispersal. 126 matched cddid_all.tbl CDD cd10547 cd10547 380415 cupin_BacB_C "Bacillus subtilis bacilysin and related proteins, C-terminal cupin domain. This model represents the C-terminal domain of bacilysin (BacB, also known as AerE in Microcystis aeruginosa), a non-ribosomally synthesized dipeptide antibiotic that is produced and excreted by certain strains of Bacillus subtilis. Bacilysin is an oxidase that catalyzes the synthesis of 2-oxo-3-(4-oxocyclohexa-2,5-dienyl)propanoic acid, a precursor to L-anticapsin. Each bacilysin monomer has two tandem cupin domains. It is active against a wide range of bacteria and some fungi. The antimicrobial activity of bacilysin is antagonized by glucosamine and N-acetyl glucosamine, indicating that bacilysin interferes with glucosamine synthesis, and thus, with the synthesis of microbial cell walls. AerE is thought to be involved in the formation of the 2-carboxy-6-hydroxyoctahydroindole (Choi) moiety found on all aeruginosin tetrapeptides, based on gene knock-out experiments. It is encoded by the aerE gene of the aerABCDEF aeruginosin biosynthesis gene cluster in Microcystis aeruginosa. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 92 matched cddid_all.tbl CDD cd10548 cd10548 380416 cupin_CDO "cysteine dioxygenase, cupin domain. This family contains cysteine dioxygenase (CDO; EC 1.13.11.20), which catalyzes the conversion of cysteine to cysteine sulfinic acid, the first step in the biosynthesis of essential oxidized cysteine metabolites such as sulfate, hypotaurine, and taurine. CDO also plays an important role in the regulation of intracellular cysteine levels in mammals; CDO expression is altered in cancer cells, and abnormal or deficient CDO activity has been linked to Parkinson's disease, Alzheimer's disease, and rheumatoid arthritis. CDO is an iron-dependent thiol dioxygenase that uses molecular oxygen to oxidize the sulfhydryl group of cysteine to generate cysteine sulfinic acid. The CDO active site contains an amino acid-derived cofactor. These enzymes are found in prokaryotes as well as eukaryotes and belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 100 matched cddid_all.tbl CDD cd10549 cd10549 319871 MtMvhB_like Uncharacterized polyferredoxin-like protein. This family contains uncharacterized polyferredoxin protein similar to Methanobacterium thermoautotrophicum MvhB. The mvhB is a gene of the methylviologen-reducing hydrogenase operon. It is predicted to contain 12 [4Fe-4S] clusters, and was therefore suggested to be a polyferredoxin. As a subfamily of the beta subunit of the DMSO Reductase (DMSOR) family, it is predicted to function as electron carrier in the reducing reaction. 128 matched cddid_all.tbl CDD cd10550 cd10550 319872 DMSOR_beta_like uncharacterized subfamily of DMSO Reductase beta subunit family. This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system. 130 matched cddid_all.tbl CDD cd10551 cd10551 319873 PsrB polysulfide reductase beta (PsrB) subunit. This family includes the beta subunit of bacterial polysulfide reductase (PsrABC), an integral membrane-bound enzyme responsible for quinone-coupled reduction of polysulfides, a process important in extreme environments such as deep-sea vents and hot springs. Polysulfide reductase contains three subunits: a catalytic subunit PsrA, an electron transfer PsrB subunit and the hydrophobic transmembrane PsrC subunit. PsrB belongs to the DMSO reductase superfamily that contains [4Fe-4S] clusters which transfer the electrons from the A subunit to the hydrophobic integral membrane C subunit via the B subunit. In Shewanella oneidensis, which has highly diverse anaerobic respiratory pathways, PsrABC is responsible for H2S generation as well as its regulation via respiration of sulfur species. PsrB transfers electrons from PsrC (serving as quinol oxidase) to the catalytic subunit PsrA for reduction of corresponding electron acceptors. It has been shown that T. thermophilus polysulfide reductase could be a key energy-conserving enzyme of the respiratory chain, using polysulfide as the terminal electron acceptor and pumping protons across the membrane. 185 matched cddid_all.tbl CDD cd10552 cd10552 319874 TH_beta_N N-terminal FeS domain of pyrogallol-phloroglucinol transhydroxylase (TH), beta subunit. This family includes the beta subunit of pyrogallol-phloroglucinol transhydroxylase (TH), a cytoplasmic molybdenum (Mo) enzyme from anaerobic microorganisms like Pelobacter acidigallici and Desulfitobacterium hafniense which catalyzes the conversion of pyrogallol to phloroglucinol, an important building block of plant polymers. TH belongs to the DMSO reductase (DMSOR) family; it is a heterodimer consisting of a large alpha catalytic subunit and a small beta FeS subunit. The beta subunit has two domains with the N-terminal domain containing three [4Fe-4S] centers and a seven-stranded, mainly antiparallel beta-barrel domain. In the anaerobic bacterium Pelobacter acidigallici, gallic acid, pyrogallol, phloroglucinol, or phloroglucinol carboxylic acid are fermented to three molecules of acetate (plus CO2), and TH is the key enzyme in the fermentation pathway, which converts pyrogallol to phloroglucinol in the absence of O2. 186 matched cddid_all.tbl CDD cd10553 cd10553 319875 PhsB_like uncharacterized beta subfamily of DMSO Reductase similar to Desulfonauticus sp PhsB. This family includes beta FeS subunits of anaerobic DMSO reductase (DMSOR) superfamily that have yet to be characterized. DMSOR consists of a large, periplasmic molybdenum-containing alpha subunit as well as a small beta FeS subunit, and may also have a small gamma subunit. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and the tungsten-containing formate dehydrogenase (FDH-T). Examples of heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system. 146 matched cddid_all.tbl CDD cd10554 cd10554 319876 HycB_like HycB, HydN and similar proteins. This family includes HycB, the FeS subunit of a membrane-associated formate hydrogenlyase system (FHL-1) in Escherichia coli that breaks down formate, produced during anaerobic fermentation, to H2 and CO2. FHL-1 consists of formate dehydrogenase H (FDH-H) and the hydrogenase 3 complex (Hyd-3). HycB is thought to code for the [4Fe-4S] ferredoxin subunit of hydrogenase 3, which functions as an intermediate electron carrier protein between hydrogenase 3 and formate dehydrogenase. HydN codes for the [4Fe-4S] ferredoxin subunit of FDH-H; a hydN in-frame deletion mutation causes only weak reduction in hydrogenase activity, but loss of more than 60% of FDH-H activity. This pathway is only active at low pH and high formate concentrations, and is thought to provide a detoxification/de-acidification system countering the buildup of formate during fermentation. 149 matched cddid_all.tbl CDD cd10555 cd10555 319877 EBDH_beta beta subunit of ethylbenzene-dehydrogenase (EBDH). This subfamily includes ethylbenzene dehydrogenase (EBDH, EC 1.17.99.2), a member of the DMSO reductase family. EBDH oxidizes the hydrocarbon ethylbenzene to (S)-1-phenylethanol. It is a heterotrimer, with the alpha subunit containing the catalytic center with a molybdenum held by two molybdopterin-guanine dinucleotides, the beta subunit containing four iron-sulfur clusters (the electron transfer subunit) and the gamma subunit containing a methionine and a lysine as axial heme ligands. During catalysis, electrons produced by substrate oxidation are transferred to a heme in the gamma subunit and then presumably to a separate cytochrome involved in nitrate respiration. 316 matched cddid_all.tbl CDD cd10556 cd10556 319878 SER_beta Beta subunit of selenate reductase. This subfamily includes beta FeS subunit of selenate reductase (SER), a member of the DMSO reductase family. SER catalyzes the reduction of selenate to selenite in bacterial species that can obtain energy by respiring anaerobically with selenate as the terminal electron acceptor. The enzyme comprises three subunits SerABC, forming a heterotrimer, with the catalytic component (alpha-subunit), iron-sulfur protein (beta-subunit) and monomeric b-type heme-containing gamma subunit. Beta subunit contains coordinating one [3Fe-4S] cluster and three [4Fe-4S] clusters and functions as electron carrier. 287 matched cddid_all.tbl CDD cd10557 cd10557 319879 NarH_beta-like beta subunit of nitrate reductase A (NarH) and similar proteins. This subfamily includes nitrate reductase A, a member of the DMSO reductase family. The respiratory nitrate reductase complex (NarGHI) from E. coli is a heterotrimer, with the catalytic subunit (NarG) with a molybdo-bis (molybdopterin guanine dinucleotide) cofactor and an [Fe-S] cluster, the electron transfer subunit (NarH) with four [Fe-S] clusters, and the integral membrane subunit (NarI) with two b-type hemes. Nitrate reductase A often forms a respiratory chain with the formate dehydrogenase via the lipid soluble quinol pool. Electron transfer from formate to nitrate is coupled to proton translocation across the cytoplasmic membrane generating proton motive force by a redox loop mechanism. Demethylmenaquinol (DMKH2) has been shown to be a good substrate for NarGHI in nitrate respiration in E. coli. 363 matched cddid_all.tbl CDD cd10558 cd10558 319880 FDH-N The beta FeS subunit of formate dehydrogenase-N (FDH-N). This subfamily contains beta FeS subunit of formate dehydrogenase-N (FDH-N), a member of the DMSO reductase family. FDH-N is involved in the major anaerobic respiratory pathway in the presence of nitrate, catalyzing the oxidation of formate to carbon dioxide at the expense of nitrate reduction to nitrite. Thus, FDH-N is a major component of nitrate respiration of Escherichia coli. This integral membrane enzyme forms a heterotrimer; the alpha-subunit (FDH-G) is the catalytic site of formate oxidation and membrane-associated, incorporating a selenocysteine (SeCys) residue and a [4Fe/4S] cluster in addition to two bis-MGD cofactors, the beta subunit (FDH-H) contains four [4Fe/4S] clusters which transfer the electrons from the alpha subunit to the gamma-subunit (FDH-I), a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. 208 matched cddid_all.tbl CDD cd10559 cd10559 319881 W-FDH tungsten-containing formate dehydrogenase, small subunit. This subfamily contains beta subunit of Tungsten-containing formate dehydrogenase (W-FDH), a member of the DMSO reductase family. W-FDH contains a tungsten instead of molybdenum at the catalytic center. This enzyme seems to be exclusively found in organisms such as hyperthermophilic archaea that live in extreme environments. It is a heterodimer of a large and a small subunit; the large subunit harbors the W site and one [4Fe-4S] center and the small subunit, containing three [4Fe-4S] clusters, functions to transfer electrons. 200 matched cddid_all.tbl CDD cd10560 cd10560 319882 FDH-O_like beta subunit of formate dehydrogenase O (FDH-O) and similar proteins. This subfamily includes beta subunit of formate dehydrogenase family O (FDH-O), which is highly homologous to formate dehydrogenase N (FDH-N), a member of the DMSO reductase family. In E. coli three formate dehydrogenases are synthesized that are capable of oxidizing formate; Fdh-H, couples formate disproportionation to hydrogen and CO2, and is part of the cytoplasmically oriented formate hydrogenlyase complex, while FDH-N and FDH-O indicate their respective induction after growth with nitrate and oxygen. Little is known about FDH-O, although it shows formate oxidase activity during aerobic growth and is also synthesized during nitrate respiration, similar to FDH-N. 225 matched cddid_all.tbl CDD cd10561 cd10561 319883 HybA_like the FeS subunit of hydrogenase 2. This subfamily includes the beta-subunit of hydrogenase 2 (Hyd-2), an enzyme that catalyzes the reversible oxidation of H2 to protons and electrons. Hyd-2 is membrane-associated and forms an unusual heterotetrameric [NiFe]-hydrogenase in that it lacks the typical cytochrome b membrane anchor subunit that transfers electrons to the quinone pool. The electron transfer subunit of Hyd-2 (HybA) which is predicted to contain four iron-sulfur clusters, is essential for electron transfer from Hyd-2 to menaquinone/demethylmenaquinone (MQ/DMQ) to couple hydrogen oxidation to fumarate reduction. 196 matched cddid_all.tbl CDD cd10562 cd10562 319884 FDH_b_like uncharacterized subfamily of beta subunit of formate dehydrogenase. This subfamily includes the beta-subunit of formate dehydrogenases that are as yet uncharacterized. Members of the DMSO reductase family include formate dehydrogenase N and O (FDH-N, FDH-O) and tungsten-containing formate dehydrogenase (W-FDH) and other similar proteins. FDH-N, a major component of nitrate respiration of Escherichia coli, is involved in the major anaerobic respiratory pathway in the presence of nitrate, catalyzing the oxidation of formate to carbon dioxide at the expense of nitrate reduction to nitrite. It forms a heterotrimer; the alpha-subunit (FDH-G) is the catalytic site of formate oxidation and membrane-associated, incorporating a selenocysteine (SeCys) residue and a [4Fe/4S] cluster in addition to two bis-MGD cofactors, the beta subunit (FDH-H) contains four [4Fe/4S] clusters which transfer the electrons from the alpha subunit to the gamma-subunit (FDH-I), a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. W-FDH contains a tungsten instead of molybdenum at the catalytic center. This enzyme seems to be exclusively found in organisms such as hyperthermophilic archaea that live in extreme environments. It is a heterodimer of a large and a small subunit; the large subunit harbors the W site and one [4Fe-4S] center and the small subunit, containing three [4Fe-4S] clusters, functions to transfer electrons. 161 matched cddid_all.tbl CDD cd10563 cd10563 319885 CooF_like CooF, iron-sulfur subunit of carbon monoxide dehydrogenase. This family includes CooF, the iron-sulfur subunit of carbon monoxide dehydrogenase (CODH), found in anaerobic bacteria and archaea. Carbon monoxide dehydrogenase is a key enzyme for carbon monoxide (CO) metabolism, where CooF is the proposed mediator of electron transfer between CODH and the CO-induced hydrogenase, catalyzing the reaction that uses CO as a single carbon and energy source, and producing only H2 and CO2. The ion-sulfur subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons in the protein complex during reaction. 140 matched cddid_all.tbl CDD cd10564 cd10564 319886 NapF_like NapF, iron-sulfur subunit of periplasmic nitrate reductase. This family contains NapF protein, the iron-sulfur subunit of periplasmic nitrate reductase. The periplasmic nitrate reductase NapABC of Escherichia coli likely functions during anaerobic growth in low-nitrate environments; napF operon expression is activated by cyclic AMP receptor protein (Crp). NapF is a subfamily of the beta subunit of DMSO reductase (DMSOR) family. DMSOR family members have a large, periplasmic molybdenum-containing alpha subunit as well as a small beta FeS subunit, and may also have a small gamma subunit. The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system. 139 matched cddid_all.tbl CDD cd10566 cd10566 349488 MDM2_like p53-binding domain found in E3 ubiquitin-protein ligase MDM2, MDM4, and similar proteins. MDM2 (also termed HDM2) and MDM4 (also termed MDMX or HDMX) are the primary negative regulators of p53 tumor suppressor. They have non-redundant roles in the regulation of p53. MDM2 mainly functions to control p53 stability, while MDM4 controls p53 transcriptional activity. Both MDM2 and MDM4 contain an N-terminal p53-binding domain, a RanBP2-type zinc finger (zf-RanBP2) domain near the central acidic region, and a C-terminal RING domain. Mdm2 can form homo-oligomers through its RING domain and display E3 ubiquitin ligase activity that catalyzes the attachment of ubiquitin to p53 as an essential step in the regulation of its level in cells. Despite its RING domain and structural similarity with MDM2, MDM4 does not homo-oligomerize and lacks ubiquitin-ligase function, but inhibits the transcriptional activity of p53. In addition, both their RING domains are responsible for the hetero-oligomerization, which is crucial for the suppression of p53 activity during embryonic development and the recruitment of E2 ubiquitin-conjugating enzymes. Moreover, MDM2 and MDM4 can be phosphorylated and destabilized in response to DNA damage stress. In response to ribosomal stress, MDM2-mediated p53 ubiquitination and degradation can be inhibited through the interaction with ribosomal proteins L5, L11 and L23. However, MDM4 is not bound to ribosomal proteins, suggesting its different response to regulation by small basic proteins such as ribosomal proteins and ARF. 75 matched cddid_all.tbl CDD cd10567 cd10567 349489 SWIB-MDM2_like SWIB/MDM2 domain found in SWIB/MDM2 homologous proteins. This family includes Schizosaccharomyces pombe upstream activation factor subunit spp27, Saccharomyces cerevisiae upstream activation factor subunit UAF30, Chlamydiae DNA topoisomerase/SWIB domain fusion protein, Arabidopsis thaliana zinc finger CCCH domain-containing proteins, AtC3H19 and AtC3H44, and similar proteins. S. pombe spp27, also termed upstream activation factor 27 KDa subunit (p27), or upstream activation factor 30 KDa subunit (p30), or upstream activation factor subunit uaf30, is a component of the UAF (upstream activation factor) complex which interacts with the upstream element of the RNA polymerase I promoter and forms a stable preinitiation complex. S. cerevisiae UAF30, also termed upstream activation factor 30 KDa subunit (p30), is a non-essential component of the UAF. It seems to play a role in silencing transcription by RNA polymerase II. The SWIB domain found in Chlamydiae DNA topoisomerase may play a role in chromatin condensation-decondensation, which is characteristic of the chlamydial developmental cycle and not found in any other types of bacteria. AtC3H19, also termed protein needed for RDR2-independent DNA methylation (NERD), is a plant-specific GW repeat- and PHD finger-containing protein that plays a central role in integrating RNA silencing and chromatin signals in 21 nt small-interfering RNA (siRNA)-dependent DNA methylation on the cytosine pathway, leading to transcriptional gene silencing of specific sequences. This family also includes many uncharacterized proteins containing two copies of SWIB/MDM2 domain. 71 matched cddid_all.tbl CDD cd10568 cd10568 349490 SWIB_like SWIB domain found in the 60 kda subunit of the ATP-dependent SWI/SNF chromatin-remodeling complexes and similar proteins. SWIB domain is a conserved region found within proteins in the SWI/SNF family of complexes. SWI/SNF complex proteins display helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors), among which the BAF60 subunit serves as a key link between the core complexes and specific transcriptional factors. The BAF60 subunit have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. The family also includes Saccharomyces cerevisiae transcription regulatory protein SNF12 and remodel the structure of chromatin complex subunit 6 (RSC6), and Schizosaccharomyces pombe SWI/SNF and RSC complexes subunit SSR3. SNF12, also termed 73-kDa subunit of the SWI/SNF transcriptional regulatory complex, or SWI/SNF complex component SWP73, is involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). RSC6 and SSR3 are components of the RSC, which is involved in transcription regulation and nucleosome positioning. RSC6 is essential for mitotic growth and suppresses formamide sensitivity of the RSC8 mutants. 69 matched cddid_all.tbl CDD cd10569 cd10569 269973 FERM_C_Talin FERM domain C-lobe/F3 of Talin. Talin (also called filopodin) plays an important role in initiating actin filament growth in motile cell protrusions. It is responsible for linking the cytoplasmic domains of integrins to the actin-based cytoskeleton, and is involved in vinculin, integrin and actin interactions. At the leading edge of motile cells, talin colocalises with the hyaluronan receptor layilin in transient adhesions, some of which become more stable focal adhesions (FA). During this maturation process, layilin is replaced with integrins, where localized production of PI(4,5)P(2) by type 1 phosphatidyl inositol phosphate kinase type 1gamma (PIPK1gamma) is thought to play a role in FA assembly. Talins are composed of a N-terminal region FERM domain which us made up of 3 subdomains (N, alpha-, and C-lobe; or- A-lobe, B-lobe, and C-lobe; or F1, F2, and F3) connected by short linkers, a talin rod which binds vinculin, and a conserved C-terminal region with actin- and integrin-binding sites. There are 2 additional actin-binding domains, one in the talin rod and the other in the FERM domain. Both the F2 and F3 FERM subdomains contribute to F-actin binding. Subdomain F3 of the FERM domain contains overlapping binding sites for integrin cytoplasmic domains and for the type 1 gamma isoform of PIP-kinase (phosphatidylinositol 4-phosphate 5-kinase). The FERM domain has a cloverleaf tripart structure . F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs) , the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 92 matched cddid_all.tbl CDD cd10570 cd10570 275393 PH-GRAM Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. 94 matched cddid_all.tbl CDD cd10571 cd10571 269975 PH_beta_spectrin Beta-spectrin pleckstrin homology (PH) domain. Beta spectrin binds actin and functions as a major component of the cytoskeleton underlying cellular membranes. Beta spectrin consists of multiple spectrin repeats followed by a PH domain, which binds to inositol-1,4,5-trisphosphate. The PH domain of beta-spectrin is thought to play a role in the association of spectrin with the plasma membrane of cells. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 106 matched cddid_all.tbl CDD cd10572 cd10572 269976 PH_RhoGEF3_XPLN Rho guanine nucleotide exchange factor 3 Pleckstrin homology (PH) domain. RhoGEF3/XPLN, a Rho family GEF, preferentially stimulates guanine nucleotide exchange on RhoA and RhoB, but not RhoC, RhoG, Rac1, or Cdc42 in vitro. It also possesses transforming activity. RhoGEF3/XPLN contains a tandem Dbl homology and PH domain, but lacks homology with other known functional domains or motifs. It is expressed in the brain, skeletal muscle, heart, kidney, platelets, and macrophage and neuronal cell lines. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 133 matched cddid_all.tbl CDD cd10573 cd10573 269977 PH_DAPP1 Dual Adaptor for Phosphotyrosine and 3-Phosphoinositides Pleckstrin homology (PH) domain. DAPP1 (also known as PHISH/3' phosphoinositide-interacting SH2 domain-containing protein or Bam32) plays a role in B-cell activation and has potential roles in T-cell and mast cell function. DAPP1 promotes B cell receptor (BCR) induced activation of Rho GTPases Rac1 and Cdc42, which feed into mitogen-activated protein kinases (MAPK) activation pathways and affect cytoskeletal rearrangement. DAPP1can also regulate BCR-induced activation of extracellular signal-regulated kinase (ERK), and c-jun NH2-terminal kinase (JNK). DAPP1 contains an N-terminal SH2 domain and a C-terminal pleckstrin homology (PH) domain with a single tyrosine phosphorylation site located centrally. DAPP1 binds strongly to both PtdIns(3,4,5)P3 and PtdIns(3,4)P2. The PH domain is essential for plasma membrane recruitment of PI3K upon cell activation. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 96 matched cddid_all.tbl CDD cd10574 cd10574 269978 EVH1_SPRED-like Sprouty-related EVH1 domain-containing-like proteins EVH1 domain. The Spred family has the following domains: an N-terminal EVH1 domain, a unique KBD (c-Kit kinase binding) domain which that is phosphorylated by the stem cell factor receptor c-Kit, and a C-terminal cysteine-rich SPR (Sprouty-related) domain which is involved in membrane localization. There are 3 Spred proteins: Spred1 which interacts with both Ras and Raf through its SPR domain; Spred2 which is the most abundant isoform; and Spred3 which has a non-functional KBD and maintains the inhibitory action on Raf. Legius syndrome is caused by heterozygous mutations in Spred1. Both EVH1 and SPR domains are involved in the inhibition of the MAP kinase pathway by Spred proteins. The specific function of the Spred2 EVH1 domain is unknown and there are no known interacting proteins to date. It is thought that its EVH1 domain will have a fourth distinct peptide binding mechanism within the EVH1 family. The EVH1 domains are part of the PH domain superamily. There are 5 EVH1 subfamilies: Enables/VASP, Homer/Vesl, WASP, Dcp1, and Spred. Ligands are known for three of the EVH1 subfamilies, all of which bind proline-rich sequences: the Enabled/VASP family binds to FPPPP peptides, the Homer/Vesl family binds PPxxF peptides, and the WASP family binds LPPPEP peptides. EVH1 has a PH-like fold, despite having minimal sequence similarity to PH or PTB domains. 113 matched cddid_all.tbl CDD cd10575 cd10575 276901 TNFRSF6B Tumor necrosis factor receptor superfamily member 6B (TNFRSF6B), also known as decoy receptor 3 (DcR3). The subfamily TNFRSF6B is also known as decoy receptor 3 (DcR3), M68, or TR6. This protein is a soluble receptor without death domain and cytoplasmic domain, and secreted by cells. It acts as a decoy receptor that competes with death receptors for ligand binding. It is a pleiotropic immunomodulator and biomarker for inflammatory diseases, autoimmune diseases, and cancer. Over-expression of this gene has been noted in several cancers, including pancreatic carcinoma, and gastrointestinal tract tumors. It can neutralize the biological effects of three tumor necrosis factor superfamily (TNFSF) members: TNFSF6 (Fas ligand/FasL/CD95L) and TNFSF14 (LIGHT) which are both involved in apoptosis and inflammation, and TNFSF15 (TNF-like molecule 1A/TL1A), which is a T cell co-stimulator and involved in gut inflammation. DcR3 is a novel inflammatory marker; higher DcR3 levels strongly correlate with inflammation and independently predict cardiovascular and all-cause mortality in chronic kidney disease (CKD) patients on hemodialysis. Increased synovial inflammatory cells infiltration in rheumatoid arthritis and ankylosing spondylitis is also associated with the elevated DcR3 expression. In cartilaginous fish, mRNA expression of DcR3 in the thymus and leydig, which are the representative lymphoid tissues of elasmobranchs, suggests that DcR3 may act as a modulator in the immune system. Interestingly, in banded dogfish (Triakis scyllia), DcR3 mRNA is strongly expressed in the gill, compared with human expression in the normal lung; both are respiratory organs, suggesting potential relevance of DcR3 to respiratory function. 163 matched cddid_all.tbl CDD cd10576 cd10576 276902 TNFRSF1A Tumor necrosis factor receptor superfamily member 1A (TNFRSF1A), also known as TNFR1. TNFRSF1A (also known as type I TNFR, TNFR1, DR1, TNFRSF1A, CD120a, p55) binds TNF-alpha, through the death domain (DD), and activates NF-kappaB, mediates apoptosis and activates signaling pathways controlling inflammatory, immune, and stress responses. It mediates signal transduction by interacting with antiapoptotic protein BCL2-associated athanogene 4 (BAG4/SODD) and adaptor proteins TRAF2 and TRADD that play regulatory roles. The human genetic disorder called tumor necrosis factor associated periodic syndrome (TRAPS), or periodic fever syndrome, is associated with germline mutations of the extracellular domains of this receptor, possibly due to impaired receptor clearance. TNFRSF1A polymorphisms rs1800693 and rs4149584 are associated with elevated risk of multiple sclerosis. Serum levels of TNFRSF1A are elevated in schizophrenia and bipolar disorder, and high levels are also associated with cognitive impairment and dementia. Patients with idiopathic recurrent acute pericarditis (IRAP), presumed to be an autoimmune process, have also been shown to carry rare mutations (R104Q and D12E) in the TNFRSF1A gene. 130 matched cddid_all.tbl CDD cd10577 cd10577 276903 TNFRSF1B Tumor necrosis factor receptor superfamily member 1B (TNFRSF1B), also known as TNFR2. TNFRSF1B (also known as TNFR2, type 2 TNFR, TNFBR, TNFR80, TNF-R75, TNF-R-II, p75, CD120b) binds TNF-alpha, but lacks the death domain (DD) that is associated with the cytoplasmic domain of TNFRSF1A (TNFR1). It is inducible and expressed exclusively by oligodendrocytes, astrocytes, T cells, thymocytes, myocytes, endothelial cells, and in human mesenchymal stem cells. TNFRSF1B protects oligodendrocyte progenitor cells (OLGs) against oxidative stress, and induces the up-regulation of cell survival genes. While pro-inflammatory and pathogen-clearing activities of TNF are mediated mainly through activation of TNFRSF1A, a strong activator of NF-kappaB, TNFRSF1B is more responsible for suppression of inflammation. Although the affinities of both receptors for soluble TNF are similar, TNFRSF1B is sometimes more abundantly expressed and thought to associate with TNF, thereby increasing its concentration near TNFRSF1A receptors, and making TNF available to activate TNFRSF1A (a ligand-passing mechanism). 163 matched cddid_all.tbl CDD cd10578 cd10578 276904 TNFRSF3 Tumor necrosis factor receptor superfamily member 3 (TNFRSF3), also known as lymphotoxin beta receptor (LTBR). TNFRSF3 (also known as lymphotoxin beta receptor, LTbetaR, CD18, TNFCR, TNFR3, D12S370, TNFR-RP, TNFR2-RP, LT-BETA-R, TNF-R-III) plays a role in signaling during development of lymphoid and other organs, lipid metabolism, immune response, and programmed cell death. Its ligands include lymphotoxin (LT) alpha/beta membrane form (heterotrimer) and tumor necrosis factor ligand superfamily member 14 (also known as LIGHT). TNFRSF3 agonism by these ligands initiates canonical, as well as non-canonical nuclear factor-kappaB (NF-kappaB) signaling, and preferentially results in the translocation of p52-RELB complexes into the nucleus. While these ligands are often expressed by T and B cells, TNFRSF3 is conspicuous absence on T and B lymphocytes and NK cells, suggesting that signaling may be unidirectional for TNFRSF3. Activity of this receptor has also been linked to carcinogenesis; it helps trigger apoptosis and can also lead to release of the interleukin 8 (IL8). Alternatively spliced transcript variants encoding multiple isoforms have been observed. 158 matched cddid_all.tbl CDD cd10579 cd10579 276905 TNFRSF6 Tumor necrosis factor receptor superfamily member 6 (TNFRSF6), also known as fas cell surface death receptor (Fas). TNFRSF6 (also known as fas cell surface death receptor (FasR) or Fas, APT1, CD95, FAS1, APO-1, FASTM, ALPS1A) contains a death domain and plays a central role in the physiological regulation of programmed cell death. It has been implicated in the pathogenesis of various malignancies and diseases of the immune system. The receptor interactions with the Fas ligand (FasL), allowing the formation of a death-inducing signaling complex that includes Fas-associated death domain protein (FADD), caspase 8, and caspase 10; autoproteolytic processing of the caspases in the complex triggers a downstream caspase cascade, leading to apoptosis. This receptor has also been shown to activate NF-kappaB, MAPK3/ERK1, and MAPK8/JNK, and is involved in transducing the proliferating signals in normal diploid fibroblast and T cells. Of the several alternatively spliced transcript variants, some are candidates for nonsense-mediated mRNA decay (NMD). Isoforms lacking the transmembrane domain may negatively regulate the apoptosis mediated by the full length isoform. 129 matched cddid_all.tbl CDD cd10580 cd10580 276906 TNFRSF10 Tumor necrosis factor receptor superfamily member 10 (TNFRSF10), includes TNFRSF10A (DR4), TNFRSF10B (DR5), TNFRSF10C (DcR1) and TNFRSF10D (DcR2). TNFRSF10 family contains TNFRSF10A (also known as DR4, Apo2, TRAIL-R1, CD261), TNFRSF10B (also known as DR5, KILLER, TRICK2A, TRAIL-R2, TRICKB, CD262), TNFRSF10C (also known as DcR1, TRAIL-R3, LIT, TRID, CD263), and TNFRSF10D (also known as DcR2, TRUNDD, TRAIL-R4, CD264). Tumor necrosis factor-related apoptosis inducing ligand (TNFSF10/TRAIL) binds to all 4 receptors. DR4 (TRAIL-R1) and DR5 (TRAIL-R2) are membrane-bound and contain a death domain in their intracellular portion, which is able to transmit an apoptotic signal, thus often called death receptors. In contrast, DcR1 (TRAIL-R3), which lacks the complete intracellular portion and DcR2 (TRAIL-R4), which has a truncated cytoplasmic death domain, do not transmit an apoptotic signal, thus known as decoy receptors. Apoptosis mediated by DR4 and DR5 requires Fas (TNFRSF6)-associated via death domain (FADD), a death domain containing adaptor protein. Two transcript variants encoding different isoforms and one non-coding transcript have been found for TNFRSF10B/DR5. DcR1 appears to function as an antagonistic receptor that protects cells from TRAIL-induced apoptosis; it has been found to be a p53-regulated DNA damage-inducible gene. The expression of this gene is detected in many normal tissues but not in most cancer cell lines, which may explain the specific sensitivity of cancer cells to the apoptosis-inducing activity of TRAIL. DcR2 has been shown to play an inhibitory role in TRAIL-induced cell apoptosis. The membrane expression of all of these receptors (DR4, DR5, DcR1, and DcR2) is greater in normal endometrium (NE) than in endometrioid adenocarcinoma (EAC). In EAC patients, membrane expression of these receptors are not independent predictors of survival. DcR1 and DcR2 expression is critical in cell growth and apoptosis in cutaneous or uveal melanoma; DcR1 and DcR2 are frequently methylated in both, leading to loss of gene expression and melanomagenesis. On the other hand, DR4 and DR5 methylation is rare in cutaneous melanoma and frequent in uveal melanoma; their expression is wholly independent of the promoter methylation status. DcR1 and DcR2 genes are also reported to be hyper-methylated in prostate cancer. The TRAIL ligand, a potent and specific inducer of apoptosis in cancer cells, has been explored as a therapeutic drug; experimental data has shown that DR4 specific TRAIL variants are more efficacious than wild-type TRAIL in pancreatic cancer. 103 matched cddid_all.tbl CDD cd10581 cd10581 276907 TNFRSF11B Tumor necrosis factor receptor superfamily member 11B (TNFRSF11B), also known as Osteoprotegerin (OPG). TNFRSF11B (also known as Osteoprotegerin, OPG, TR1, OCIF) is a secreted glycoprotein that regulates bone resorption. It binds to two ligands, RANKL (receptor activator of nuclear factor kappaB ligand, also known as osteoprotegerin ligand, OPGL, TRANCE, TNF-related activation induced cytokine), a critical cytokine for osteoclast differentiation, and TRAIL (TNF-related apoptosis-inducing ligand), involved in immune surveillance. Therefore, acting as a decoy receptor for RANKL and TRAIL, OPG inhibits the regulatory effects of nuclear factor-kappaB on inflammation, skeletal, and vascular systems, and prevents TRAIL-induced apoptosis. Studies in mice counterparts suggest that this protein and its ligand also play a role in lymph-node organogenesis and vascular calcification. Circulating OPG levels have emerged as independent biomarkers of cardiovascular disease (CVD) in patients with acute or chronic heart disease. OPG has also been implicated in various inflammations and linked to diabetes and poor glycemic control. Alternatively spliced transcript variants of this gene have been reported, although their full length nature has not been determined. 147 matched cddid_all.tbl CDD cd10582 cd10582 276908 TNFRSF14 Tumor necrosis factor receptor superfamily member 14 (TNFRSF14), also known as herpes virus entry mediator (HVEM). TNFRSF14 (also known as herpes virus entry mediator or HVEM, ATAR, CD270, HVEA, LIGHTR, TR2) regulates T-cell immune responses by activating inflammatory, as well as inhibitory signaling pathways. HVEM acts as a receptor for the canonical TNF-related ligand LIGHT (lymphotoxin-like), which exhibits inducible expression, and competes with herpes simplex virus glycoprotein D for HVEM. It also acts as a ligand for the immunoglobulin superfamily proteins BTLA (B and T lymphocyte attenuator) and CD160, a feature distinguishing HVEM from other immune regulatory molecules, thus, creating a functionally diverse set of intrinsic and bidirectional signaling pathways. HVEM is highly expressed in the gut epithelium. Genome-wide association studies have shown that Hvem is an inflammatory bowel disease (IBD) risk gene, suggesting that HVEM could have a regulatory role influencing the regulation of epithelial barrier, host defense, and the microbiota. Mouse models have revealed that HVEM is involved in colitis pathogenesis, mucosal host defense, and epithelial immunity, thus acting as a mucosal gatekeeper with multiple regulatory functions in the mucosa. HVEM plays a critical role in both tumor progression and resistance to antitumor immune responses, possibly through direct and indirect mechanisms. It is known to be expressed in several human malignancies, including esophageal squamous cell carcinoma, follicular lymphoma and melanoma. HVEM network may therefore be an attractive target for drug intervention. 101 matched cddid_all.tbl CDD cd10583 cd10583 276909 TNFRSF21 Tumor necrosis factor receptor superfamily member 21 (TNFRSF21), also known as death receptor (DR6). TNFRSF21 (also known as death receptor 6 (DR6), CD358, BM-018) is highly expressed in differentiating neurons as well as in the adult brain, and is upregulated in injured neurons. DR6 negatively regulates neurondendrocyte, axondendrocyte, and oligodendrocyte survival, hinders axondendrocyte and oligodendrocyte regeneration and its inhibition has a neuro-protective effect in nerve injury. It activates nuclear factor kappa-B (NFkB) and mitogen-activated protein kinase 8 (MAPK8, also called c-Jun N-terminal kinase 1), and induces cell apoptosis by associating with TNFRSF1A-associated via death domain (TRADD), which is known to mediate signal transduction of tumor necrosis factor receptors. TNFRSF21 plays a role in T-helper cell activation, and may be involved in inflammation and immune regulation. Its possible ligand is alpha-amyloid precursor protein (APP), hence probably involved in the development of Alzheimer's disease; when released, APP binds in an autocrine/paracrine manner to activate a caspase-dependent self-destruction program that removes unnecessary or connectionless axons. Increasing beta-catenin levels in brain endothelium upregulates TNFRSF21 and TNFRSF19, indicating that these death receptors are downstream target genes of Wnt/beta-catenin signaling, which has been shown to be required for blood-brain barrier development. DR6 is up-regulated in numerous solid tumors as well as in tumor vascular cells, including ovarian cancer and may be a clinically useful diagnostic and predictive serum biomarker for some adult sarcoma subtypes. 159 matched cddid_all.tbl CDD cd10585 cd10585 213020 CE4_SF Catalytic NodB homology domain of the carbohydrate esterase 4 superfamily. The carbohydrate esterase 4 (CE4) superfamily mainly includes chitin deacetylases (EC 3.5.1.41), bacterial peptidoglycan N-acetylglucosamine deacetylases (EC 3.5.1.-), and acetylxylan esterases (EC 3.1.1.72), which catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan, respectively. Members in this superfamily contain a NodB homology domain that adopts a deformed (beta/alpha)8 barrel fold, which encompasses a mononuclear metalloenzyme employing a conserved His-His-Asp zinc-binding triad, closely associated with the conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. The NodB homology domain of CE4 superfamily is remotely related to the 7-stranded beta/alpha barrel catalytic domain of the superfamily consisting of family 38 glycoside hydrolases (GH38), family 57 heat stable retaining glycoside hydrolases (GH57), lactam utilization protein LamB/YcsF family proteins, and YdjC-family proteins. 142 matched cddid_all.tbl CDD cd10718 cd10718 198285 SH2_CIS Src homology 2 (SH2) domain found in cytokine-inducible SH2-containing protein (CIS). CIS family members are known to be cytokine-inducible negative regulators of cytokine signaling. The expression of the CIS gene can be induced by IL2, IL3, GM-CSF and EPO in hematopoietic cells. Proteasome-mediated degradation of this protein has been shown to be involved in the inactivation of the erythropoietin receptor. Suppressor of cytokine signalling (SOCS) was first recognized as a group of cytokine-inducible SH2 (CIS) domain proteins comprising eight family members in human (CIS and SOCS1-SOCS7). In addition to the SH2 domain, SOCS proteins have a variable N-terminal domain and a conserved SOCS box in the C-terminal domain. SOCS proteins bind to a substrate via their SH2 domain. The prototypical members, CIS and SOCS1-SOCS3, have been shown to regulate growth hormone signaling in vitro and in a classic negative feedback response compete for binding at phosphotyrosine sites in JAK kinase and receptor pathways to displace effector proteins and target bound receptors for proteasomal degradation. Loss of SOCS activity results in excessive cytokine signaling associated with a variety of hematopoietic, autoimmune, and inflammatory diseases and certain cancers. In general SH2 domains are involved in signal transduction. They typically bind pTyr-containing ligands via two surface pockets, a pTyr and hydrophobic binding pocket, allowing proteins with SH2 domains to localize to tyrosine phosphorylated sites. 88 matched cddid_all.tbl CDD cd10719 cd10719 199908 DnaJ_zf Zinc finger domain of DnaJ and HSP40. Central/middle or CxxCxGxG-motif containing domain of DnaJ/Hsp40 (heat shock protein 40). DnaJ proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonin family. Hsp40 proteins are characterized by the presence of an N-terminal J domain, which mediates the interaction with Hsp70. This central domain contains four repeats of a CxxCxGxG motif and binds to two Zinc ions. It has been implicated in substrate binding. 65 matched cddid_all.tbl CDD cd10747 cd10747 199909 DnaJ_C C-terminal substrate binding domain of DnaJ and HSP40. The C-terminal region of the DnaJ/Hsp40 protein mediates oligomerization and binding to denatured polypeptide substrate. DnaJ/Hsp40 is a widely conserved heat-shock protein. It prevents the aggregation of unfolded substrate and forms a ternary complex with both substrate and DnaK/Hsp70; the N-terminal J-domain of DnaJ/Hsp40 stimulates the ATPase activity of DnaK/Hsp70. 158 matched cddid_all.tbl CDD cd10748 cd10748 199910 anti-TRAP anti-TRAP (AT) protein specific to Bacilli. In Bacillus subtilis and related bacteria, AT binds to the TRAP protein, (tryptophan-activated trp RNA-binding attenuation protein), effectively disrupting interaction of TRAP with mRNAs. Upon binding of tryptophan, TRAP (which forms a complex of 11 identical subunits) interacts with a specific location in the leader RNA and blocks translation of the tryptophan biosynthetic operon. AT, in turn, recognizes the tryptophan-activated TRAP complex and prevents RNA binding. AT is expressed in response to high levels of uncharged tryptophan tRNA. AT contains a zinc-binding motif that closely resembles the zinc-binding motifs in the zinc-finger region of DnaJ/Hsp40. AT has been shown to form homo-dodecameric assemblies, and can actually do that in two different relative orientations, resulting in two different dodecamers. Recent data suggest that the trimeric form of AT may be the biologically relevant active complex. 52 matched cddid_all.tbl CDD cd10785 cd10785 212097 GH38-57_N_LamB_YdjC_SF Catalytic domain of glycoside hydrolase (GH) families 38 and 57, lactam utilization protein LamB/YcsF family proteins, YdjC-family proteins, and similar proteins. The superfamily possesses strong sequence similarities across a wide range of all three kingdoms of life. It mainly includes four families, glycoside hydrolases family 38 (GH38), heat stable retaining glycoside hydrolases family 57 (GH57), lactam utilization protein LamB/YcsF family, and YdjC-family. The GH38 family corresponds to class II alpha-mannosidases (alphaMII, EC 3.2.1.24), which contain intermediate Golgi alpha-mannosidases II, acidic lysosomal alpha-mannosidases, animal sperm and epididymal alpha -mannosidases, neutral ER/cytosolic alpha-mannosidases, and some putative prokaryotic alpha-mannosidases. AlphaMII possess a-1,3, a-1,6, and a-1,2 hydrolytic activity, and catalyzes the degradation of N-linked oligosaccharides by employing a two-step mechanism involving the formation of a covalent glycosyl enzyme complex. GH57 is a purely prokaryotic family with the majority of thermostable enzymes from extremophiles (many of them are archaeal hyperthermophiles), which exhibit the enzyme specificities of alpha-amylase (EC 3.2.1.1), 4-alpha-glucanotransferase (EC 2.4.1.25), amylopullulanase (EC 3.2.1.1/41), and alpha-galactosidase (EC 3.2.1.22). This family also includes many hypothetical proteins with uncharacterized activity and specificity. GH57 cleaves alpha-glycosidic bond by employing a retaining mechanism, which involves a glycosyl-enzyme intermediate, allowing transglycosylation. Although the exact molecular function of LamB/YcsF family and YdjC-family remains unclear, they show high sequence and structure homology to the members of GH38 and GH57. Their catalytic domains adopt a similar parallel 7-stranded beta/alpha barrel, which is remotely related to catalytic NodB homology domain of the carbohydrate esterase 4 superfamily. 203 matched cddid_all.tbl CDD cd10786 cd10786 212098 GH38N_AMII_like N-terminal catalytic domain of class II alpha-mannosidases and similar proteins; glycoside hydrolase family 38 (GH38). Alpha-mannosidases (EC 3.2.1.24) are extensively found in eukaryotes and play important roles in the processing of newly formed N-glycans and in degradation of mature glycoproteins. A deficiency of this enzyme causes the lysosomal storage disease alpha-mannosidosis. Many bacterial and archaeal species also possess putative alpha-mannosidases, but their activity and specificity is largely unknown. Based on different functional characteristics and sequence homology, alpha-mannosidases have been organized into two classes (class I, belonging to glycoside hydrolase family 47, and class II, belonging to glycoside hydrolase family 38). Members of this family corresponds to class II alpha-mannosidases (alphaMII), which contain intermediate Golgi alpha-mannosidases II, acidic lysosomal alpha-mannosidases, animal sperm and epididymal alpha -mannosidases, neutral ER/cytosolic alpha-mannosidases, and some putative prokaryotic alpha-mannosidases. AlphaMII possess a-1,3, a-1,6, and a-1,2 hydrolytic activity, and catalyzes the degradation of N-linked oligosaccharides. The N-terminal catalytic domain of alphaMII adopts a structure consisting of parallel 7-stranded beta/alpha barrel. Members in this family are retaining glycosyl hydrolases of family GH38 that employs a two-step mechanism involving the formation of a covalent glycosyl enzyme complex. Two carboxylic acids positioned within the active site act in concert: one as a catalytic nucleophile and the other as a general acid/base catalyst. 251 matched cddid_all.tbl CDD cd10787 cd10787 212099 LamB_YcsF_like LamB/YcsF family of lactam utilization protein. The LamB/YbgL family includes the Aspergillus nidulans protein LamB, and its homologs from all three kingdoms of life. The lamb gene locates at the lam locus of Aspergillus nidulans, consisting of two divergently transcribed genes, lamA and lamB, needed for the utilization of lactams such as 2-pyrrolidinone. Both genes are under the control of the positive regulatory gene amdR and are subject to carbon and nitrogen metabolite repression. Although the exact molecular function of LamB is unknown, it might be required for conversion of exogenous 2-pyrrolidinone to endogenous GABA 238 matched cddid_all.tbl CDD cd10788 cd10788 212100 YdjC_like YdjC-family proteins. YdjC-family proteins are widely distributed, from human to bacteria. It is represented by an uncharacterised protein YdjC (also known as ChbG), encoded by the chb (N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel operon in Escherichia coli, which encodes enzymes involved in growth on an N,N'-diacetylchitobiose carbon source. This subfamily also includes hopanoid biosynthesis associated proteins HpnK and many uncharacterized YdjC homologs. Although the exact molecular function of the YdjC-family proteins remains unclear, it has been suggested that they play a role in the cleavage of cellobiosephosphate. 243 matched cddid_all.tbl CDD cd10789 cd10789 212101 GH38N_AMII_ER_cytosolic N-terminal catalytic domain of endoplasmic reticulum(ER)/cytosolic class II alpha-mannosidases; glycoside hydrolase family 38 (GH38). The subfamily is represented by Saccharomyces cerevisiae vacuolar alpha-mannosidase Ams1, rat ER/cytosolic alpha-mannosidase Man2C1, and similar proteins. Members in this family share high sequence similarity. None of them have any classical signal sequence or membrane spanning domains, which are typical of sorting or targeting signals. Ams1 functions as a second resident vacuolar hydrolase in S. cerevisiae. It aids in recycling macromolecular components of the cell through hydrolysis of terminal, non-reducing alpha-d-mannose residues. Ams1 utilizes both the cytoplasm to vacuole targeting (Cvt, nutrient-rich conditions) and autophagic (starvation conditions) pathways for biosynthetic delivery to the vacuole. Man2C1is involved in oligosaccharide catabolism in both the ER and cytosol. It can catalyze the cobalt-dependent cleavage of alpha 1,2-, alpha 1,3-, and alpha 1,6-linked mannose residues. Members in this family are retaining glycosyl hydrolases of family GH38 that employs a two-step mechanism involving the formation of a covalent glycosyl-enzyme complex. Two carboxylic acids positioned within the active site act in concert: one as a catalytic nucleophile and the other as a general acid/base catalyst. 252 matched cddid_all.tbl CDD cd10790 cd10790 212102 GH38N_AMII_1 N-terminal catalytic domain of putative prokaryotic class II alpha-mannosidases; glycoside hydrolase family 38 (GH38). This mainly bacterial subfamily corresponds to a group of putative class II alpha-mannosidases, including various proteins assigned as alpha-mannosidases, Streptococcus pyogenes (SpGH38) encoded by ORF spy1604. Escherichia coli MngB encoded by the mngB/ybgG gene, and Thermotoga maritime TMM, and similar proteins. SpGH38 targets alpha-1,3 mannosidic linkages. SpGH38 appears to exist as an elongated dimer and display alpha-1,3 mannosidase activity. It is active on disaccharides and some aryl glycosides. SpGH38 can also effectively deglycosylate human N-glycans in vitro. MngB exhibits alpha-mannosidase activity that catalyzes the conversion of 2-O-(6-phospho-alpha-mannosyl)-D-glycerate to mannose-6-phosphate and glycerate in the pathway which enables use of mannosyl-D-glycerate as a sole carbon source. TMM is a homodimeric enzyme that hydrolyzes p-nitrophenyl-alpha-D-mannopyranoside, alpha -1,2-mannobiose, alpha -1,3-mannobiose, alpha -1,4-mannobiose, and alpha -1,6-mannobiose. The GH38 family contains retaining glycosyl hydrolases that employ a two-step mechanism involving the formation of a covalent glycosyl enzyme complex. Two carboxylic acids positioned within the active site act in concert: one as a catalytic nucleophile and the other as a general acid/base catalyst. Divalent metal ions, such as zinc or cobalt ions, are suggested to be required for the catalytic activities of typical class II alpha-mannosidases. However, TMM requires the cobalt or cadmium for its activity. The cadmium ion dependency is unique to TMM. Moreover, TMM is inhibited by swainsonine but not 1-deoxymannojirimycin, which is in agreement with the features of cytosolic alpha-mannosidase. 273 matched cddid_all.tbl CDD cd10791 cd10791 212103 GH38N_AMII_like_1 N-terminal catalytic domain of mainly uncharacterized eukaryotic proteins similar to alpha-mannosidases; glycoside hydrolase family 38 (GH38). The subfamily of mainly uncharacterized eukaryotic proteins shows sequence homology with class II alpha-mannosidases (AlphaAMIIs). AlphaAMIIs possess a-1,3, a-1,6, and a-1,2 hydrolytic activity, and catalyze the degradation of N-linked oligosaccharides. The N-terminal catalytic domain of alphaMII adopts a structure consisting of parallel 7-stranded beta/alpha barrel. This subfamily belongs to the GH38 family of retaining glycosyl hydrolases, which employ a two-step mechanism involving the formation of a covalent glycosyl enzyme complex; two carboxylic acids positioned within the active site act in concert: one as a catalytic nucleophile and the other as a general acid/base catalyst. 254 matched cddid_all.tbl CDD cd10792 cd10792 212104 GH57N_AmyC_like N-terminal catalytic domain of alpha-amylase ( AmyC ) and similar proteins. Alpha-amylases (alpha-1,4-glucan-4-glucanohydrolases, EC 3.2.1.1) play essential roles in alpha-glucan metabolism by catalyzing the hydrolysis of polysaccharides such as amylose starch, and beta-limit dextrin. This subfamily is represented by a novel alpha-amylase (AmyC) encoded by hyperthermophilic organism Thermotoga maritime ORF tm1438, and its prokaryotic homologs. AmyC functions as a homotetramer and shows thermostable amylolytic activity. It is strongly inhibited by acarbose. AmyC is composed of a N-terminal catalytic domain, containing a distorted TIM-barrel structure with a characteristic (beta/alpha)7 fold motif, and two additional less conserved domains. There are other two canonical alpha-amylases encoded from T. maritime that lack the sequence similarity to AmyC, and belong to a different superfamily. 412 matched cddid_all.tbl CDD cd10793 cd10793 212105 GH57N_TLGT_like N-terminal catalytic domain of 4-alpha-glucanotransferase; glycoside hydrolase family 57 (GH57). 4-alpha-glucanotransferase (TLGT, EC 2.4.1.25) plays a key role in the maltose metabolism. It catalyzes the disproportionation of amylose and the formation of large cyclic alpha-1,4-glucan (cycloamylose) from linear amylose. TLGT functions as a homodimer. Each monomer is composed of two domains, an N-terminal catalytic domain with a (beta/alpha)7 barrel fold and a C-terminal domain with a twisted beta-sandwich fold. Some family members have been designated as alpha-amylases, such as the heat-stable eubacterial amylase from Dictyoglomus thermophilum (DtAmyA) and the extremely thermostable archaeal amylase from Pyrococcus furiosus(PfAmyA). However, both of these proteins are 4-alpha-glucanotransferases. DtAmyA was shown to have transglycosylating activity and PfAmyA exhibits 4-alpha-glucanotransferase activity. 279 matched cddid_all.tbl CDD cd10794 cd10794 212106 GH57N_PfGalA_like N-terminal catalytic domain of alpha-galactosidase; glycoside hydrolase family 57 (GH57). Alpha-galactosidases (GalA, EC 3.2.1.22) catalyze the hydrolysis of alpha-1,6-linked galactose residues from oligosaccharides and polymeric galactomannans. Based on sequence similarity, the majority of eukaryotic and bacterial GalAs have been classified into glycoside hydrolase family GH27, GH36, and GH4, respectively. This subfamily is represented by a novel type of GalA from Pyrococcus furiosus (PfGalA), which belongs to the GH57 family. PfGalA is an extremely thermo-active and thermostable GalA that functions as a bacterial-like GalA, however, without the capacity to hydrolyze polysaccharides. It specifically catalyzes the hydrolysis of para-nitrophenyl-alpha-galactopyranoside, and to some extent that of melibiose and raffinose. PfGalA has a pH optimum between 5.0-5.5. 305 matched cddid_all.tbl CDD cd10795 cd10795 212107 GH57N_MJA1_like N-terminal catalytic domain of a thermoactive alpha-amylase from Methanococcus jannaschii and similar proteins; glycoside hydrolase family 57 (GH57). The subfamily is represented by a thermostable alpha-amylase (MJA1, EC 3.2.1.1) encoded from the hyperthermophilic archaeon Methanococcus jannaschii locus, M J1611. MJA1 has a broad pH optimum 5.0-8.0. It exhibits extremely thermophilic alpha-amylase activity that catalyzes the hydrolysis of large sugar polymers with alpha-l,6 and alpha-l,4 linkages, and yields products including glucose polymers of 1-7 units. MJ1611 also encodes another alpha-amylase with catalytic features distinct from MJA1, which belongs to glycoside hydrolase family 13 (GH-13), and is not included here. This subfamily also includes many uncharacterized proteins found in bacteria and archaea. 306 matched cddid_all.tbl CDD cd10796 cd10796 212108 GH57N_APU N-terminal catalytic domain of thermoactive amylopullulanases; glycoside hydrolase family 57 (GH57). Pullulanases (EC 3.2.1.41) are capable of hydrolyzing the alpha-1,6 glucosidic bonds of pullulan, producing maltotriose. Amylopullulanases (APU, E.C 3.2.1.1/41) are type II pullulanases which can also degrade both the alpha-1,6 and alpha-1,4 glucosidic bonds of starch, producing oligosaccharides. This subfamily includes GH57 archaeal thermoactive APUs, which show both pullulanolytic and amylolytic activities. They have an acid pH optimum and the presence of Ca2+ might increase their activity, thermostability, and substrate affinity. Besides GH57 thermoactive APUs, all mesophilic and some thermoactive APUs belong to glycoside hydrolase family 13 with catalytic features distinct from GH57. This subfamily also includes many uncharacterized proteins found in bacteria and archaea. 313 matched cddid_all.tbl CDD cd10797 cd10797 212109 GH57N_APU_like_1 N-terminal putative catalytic domain of mainly uncharacterized prokaryotic proteins similar to archaeal thermoactive amylopullulanases; glycoside hydrolase family 57 (GH57). This subfamily of mainly uncharacterized bacterial proteins, shows high sequence homology to GH57 archaeal thermoactive amylopullulanases (APU, E.C 3.2.1.1/41). Thermoactive APUs are type II pullulanases with both pullulanolytic and amylolytic activities. They have an acid pH optimum and the presence of Ca2+ might increase their activity, thermostability, and substrate affinity. 327 matched cddid_all.tbl CDD cd10798 cd10798 212110 GH57N_like_1 Uncharacterized subfamily of glycoside hydrolase family 57 (GH57). This subfamily of uncharacterized bacterial proteins, shows high sequence homology to glycoside hydrolase family 57 (GH57). Glycoside hydrolase family 57(GH57) is a chiefly prokaryotic family with the majority of thermostable enzymes coming from extremophiles (many of these are archaeal hyperthermophiles), which exhibit the enzyme specificities of alpha-amylase (EC 3.2.1.1), 4-alpha-glucanotransferase (EC 2.4.1.25), amylopullulanase (EC 3.2.1.1/41), and alpha-galactosidase (EC 3.2.1.22). 330 matched cddid_all.tbl CDD cd10800 cd10800 212111 LamB_YcsF_YbgL_like Escherichia coli putative lactam utilization protein YbgL and similar proteins. This subfamily of the LamB/YbgL family is represented by the Escherichia coli putative lactam utilization protein YbgL. Although their molecular function of member of this subfamily is unknown, they show high sequence similarity to the Aspergillus nidulans lactam utilization protein LamB, which might be required for conversion of exogenous 2-pyrrolidinone to endogenous GABA. 240 matched cddid_all.tbl CDD cd10801 cd10801 212112 LamB_YcsF_like_1 uncharacterized proteins similar to the Aspergillus nidulans lactam utilization protein LamB. This mainly bacterial subfamily of the LamB/YbgL family, contains many well conserved uncharacterized proteins. Although their molecular function remains unknown, those proteins show high sequence similarity to the Aspergillus nidulans lactam utilization protein LamB, which might be required for conversion of exogenous 2-pyrrolidinone to endogenous GABA. 233 matched cddid_all.tbl CDD cd10802 cd10802 212113 YdjC_TTHB029_like Thermus thermophiles TTHB029 and similar proteins. This subfamily is represented by an YdjC-family protein TTHB029 from Thermus thermophilus HB8; it is similar to Escherichia coli YdjC, a hypothetical protein encoded by the celG gene. TTHB029 functions as a homodimer. Each of monomer consists of (beta/alpha)-barrel fold. The molecular function of TTHB029 is unclear. 251 matched cddid_all.tbl CDD cd10803 cd10803 212114 YdjC_EF3048_like Enterococcus faecalis EF3048 and similar proteins. This subfamily is represented by a putative cellobiose-phosphate cleavage protein EF3048 from Enterococcus faecalis v583. It is similar to Escherichia coli YdjC, a hypothetical protein encoded by the celG gene. EF3048 might function as a homodimer. Each of the monomers consists of a (beta/alpha)-barrel fold that forms an active homodimer. The molecular function of the EF3048 is unclear. 228 matched cddid_all.tbl CDD cd10804 cd10804 212115 YdjC_HpnK_like hopanoid biosynthesis associated protein HpnK and similar proteins. The subfamily includes some uncharacterized proteins annotated as hopanoid biosynthesis associated proteins, HpnK. They show high sequence similarity to proteins from the YdjC-family, the latter is represented by an uncharacterised protein YdjC (also known as ChbG) encoded by the chb (N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel operon in Escherichia coli, which encodes enzymes involved in growth on an N,N'-diacetylchitobiose carbon source. 261 matched cddid_all.tbl CDD cd10805 cd10805 212116 YdjC_like_1 uncharacterized YdjC-like family proteins from bacteria. The subfamily contains many hypothetical proteins, and belongs to the YdjC-like family of uncharacterized proteins from bacteria. The YdjC-family is represented by an uncharacterised protein YdjC (also known as ChbG) encoded by the chb (N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel operon in Escherichia coli, which encodes enzymes involved in growth on an N,N'-diacetylchitobiose carbon source. The molecular function of this subfamily is unclear. 251 matched cddid_all.tbl CDD cd10806 cd10806 212117 YdjC_like_2 uncharacterized YdjC-like family proteins from eukaryotes. This eukaryotic subfamily contains hypothetical and uncharacterized proteins, and belongs to the YdjC-like family of uncharacterized proteins. The YdjC-family is represented by an uncharacterised protein YdjC (also known as ChbG) encoded by the chb (N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel operon in Escherichia coli, which encodes enzymes involved in growth on an N,N'-diacetylchitobiose carbon source. The molecular function of this subfamily is unclear. 280 matched cddid_all.tbl CDD cd10807 cd10807 212118 YdjC_like_3 uncharacterized YdjC-like family proteins from bacteria. This subfamily contains many hypothetical proteins, and belongs to the YdjC-like family of uncharacterized proteins from bacteria. The YdjC-family is represented by an uncharacterised protein YdjC (also known as ChbG) encoded by the chb (N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel operon in Escherichia coli, which encodes enzymes involved in growth on an N,N'-diacetylchitobiose carbon source. The molecular function of this subfamily is unclear. 251 matched cddid_all.tbl CDD cd10808 cd10808 212119 YdjC Escherichia coli YdjC-like family of proteins. Uncharacterized subfamily of YdjC-like family of proteins. Included in this subfamily is the uncharacterized Escherichia coli protein YdjC (also known as ChbG), encoded by the chb (N,N'-diacetylchitobiose, also called [GlcNAc]2) or cel operon, which encodes enzymes involved in growth on an N,N'-diacetylchitobiose carbon source. The molecular function of this subfamily is unclear. 259 matched cddid_all.tbl CDD cd10809 cd10809 212120 GH38N_AMII_GMII_SfManIII_like N-terminal catalytic domain of Golgi alpha-mannosidase II, Spodoptera frugiperda Sf9 alpha-mannosidase III, and similar proteins; glycoside hydrolase family 38 (GH38). This subfamily is represented by Golgi alpha-mannosidase II (GMII, also known as mannosyl-oligosaccharide 1,3- 1,6-alpha mannosidase, EC 3.2.1.114, Man2A1), a monomeric, membrane-anchored class II alpha-mannosidase existing in the Golgi apparatus of eukaryotes. GMII plays a key role in the N-glycosylation pathway. It catalyzes the hydrolysis of the terminal both alpha-1,3-linked and alpha-1,6-linked mannoses from the high-mannose oligosaccharide GlcNAc(Man)5(GlcNAc)2 to yield GlcNAc(Man)3(GlcNAc)2(GlcNAc, N-acetylglucosmine), which is the committed step of complex N-glycan synthesis. GMII is activated by zinc or cobalt ions and is strongly inhibited by swainsonine. Inhibition of GMII provides a route to block cancer-induced changes in cell surface oligosaccharide structures. GMII has a pH optimum of 5.5-6.0, which is intermediate between those of acidic (lysosomal alpha-mannosidase) and neutral (ER/cytosolic alpha-mannosidase) enzymes. GMII is a retaining glycosyl hydrolase of family GH38 that employs a two-step mechanism involving the formation of a covalent glycosyl enzyme complex; two carboxylic acids positioned within the active site act in concert: one as a catalytic nucleophile and the other as a general acid/base catalyst. This subfamily also includes human alpha-mannosidase 2x (MX, also known as mannosyl-oligosaccharide 1,3- 1,6-alpha mannosidase, EC 3.2.1.114, Man2A2). MX is enzymatically and functionally very similar to GMII, and is thought to also function in the N-glycosylation pathway. Also found in this subfamily is class II alpha-mannosidase encoded by Spodoptera frugiperda Sf9 cell. This alpha-mannosidase is an integral membrane glycoprotein localized in the Golgi apparatus. It shows high sequence homology with mammalian Golgi alpha-mannosidase II(GMII). It can hydrolyze p-nitrophenyl alpha-D-mannopyranoside (pNP-alpha-Man), and it is inhibited by swainsonine. However, the Sf9 enzyme is stimulated by cobalt and can hydrolyze (Man)5(GlcNAc)2 to (Man)3(GlcNAc)2, but it cannot hydrolyze GlcNAc(Man)5(GlcNAc)2, which is distinct from that of GMII. Thus, this enzyme has been designated as Sf9 alpha-mannosidase III (SfManIII). It probably functions in an alternate N-glycan processing pathway in Sf9 cells. 340 matched cddid_all.tbl CDD cd10810 cd10810 212121 GH38N_AMII_LAM_like N-terminal catalytic domain of lysosomal alpha-mannosidase and similar proteins; glycoside hydrolase family 38 (GH38). The subfamily is represented by lysosomal alpha-mannosidase (LAM, Man2B1, EC 3.2.1.114), which is a broad specificity exoglycosidase hydrolyzing all known alpha 1,2-, alpha 1,3-, and alpha 1,6-mannosidic linkages from numerous high mannose type oligosaccharides. LAM is expressed in all tissues and in many species. In mammals, the absence of LAM can cause the autosomal recessive disease alpha-mannosidosis. LAM has an acidic pH optimum at 4.0-4.5. It is stimulated by zinc ion and is inhibited by cobalt ion and plant alkaloids, such as swainsonine (SW). LAM catalyzes hydrolysis by a double displacement mechanism in which a glycosyl-enzyme intermediate is formed and hydrolyzed via oxacarbenium ion-like transition states. A carboxylic acid in the active site acts as the catalytic nucleophile in the formation of the covalent intermediate while a second carboxylic acid acts as a general acid catalyst. The same residue is thought to assist in the hydrolysis (deglycosylation) step, this time acting as a general base. 278 matched cddid_all.tbl CDD cd10811 cd10811 212122 GH38N_AMII_Epman_like N-terminal catalytic domain of mammalian core-specific lysosomal alpha 1,6-mannosidase and similar proteins; glycoside hydrolase family 38 (GH38). The subfamily is represented by a novel human core-specific lysosomal alpha 1,6-mannosidase (Epman, Man2B2) and similar proteins. Although it was previously named as epididymal alpha-mannosidase, Epman has a broadly distributed transcript expression profile. Different from the major broad specificity lysosomal alpha-mannosidases (LAM, MAN2B1), Epman is not associated with genetic alpha-mannosidosis that is caused by the absence of LAM. Furthermore, Epman has unique substrate specificity. It can efficiently cleave only the alpha 1,6-linked mannose residue from (Man)3GlcNAc, but not (Man)3(GlcNAc)2 or other larger high mannose oligosaccharides, in the core of N-linked glycans. In contrast, the major LAM can cleave all of the alpha-linked mannose residues from high mannose oligosaccharides except the core alpha 1,6-linked mannose residue. Moreover, it is suggested that the catalytic activity of Epman is dependent on prior action by di-N-acetyl-chitobiase (chitobiase), which indicates there is a functional cooperation between these two enzymes for the full and efficient catabolism of mammalian lysosomal N-glycan core structures. Epman has an acidic pH optimum. It is strongly stimulated by cobalt or zinc ions and strongly inhibited by furanose analogues swainsonine (SW) and 1,4-dideoxy-1,4-imino-d-mannitol (DIM). 326 matched cddid_all.tbl CDD cd10812 cd10812 212123 GH38N_AMII_ScAms1_like N-terminal catalytic domain of yeast vacuolar alpha-mannosidases and similar proteins; glycoside hydrolase family 38 (GH38). The family is represented by Saccharomyces cerevisiae alpha-mannosidase (Ams1) and its eukaryotic homologs. Ams1 functions as a second resident vacuolar hydrolase in S. cerevisiae. It aids in recycling macromolecular components of the cell through hydrolysis of terminal, non-reducing alpha-d-mannose residues. Ams1 forms an oligomer in the cytoplasm and retains its oligomeric form during the import process. It utilizes both the Cvt (nutrient-rich conditions) and autophagic (starvation conditions) pathways for biosynthetic delivery to the vacuole. Mutants in either pathway are defective in Ams1 import. Members in this family show high sequence similarity with rat ER/cytosolic alpha-mannosidase Man2C1. 258 matched cddid_all.tbl CDD cd10813 cd10813 212124 GH38N_AMII_Man2C1 N-terminal catalytic domain of mammalian cytosolic alpha-mannosidase Man2C1 and similar proteins; glycoside hydrolase family 38 (GH38). The subfamily corresponds to cytosolic alpha-mannosidase Man2C1 (also known as ER-mannosidase II or neutral/cytosolic mannosidase), mainly found in various vertebrates, and similar proteins. Man2C1 plays an essential role in the catabolism of cytosolic free oligomannosides derived from dolichol intermediates and the degradation of newly synthesized glycoproteins in ER or cytosol. It can catalyze the cleavage of alpha 1,2-, alpha 1,3-, and alpha 1,6-linked mannose residues. Man2C1 is a cobalt-dependent enzyme belonging to alpha-mannosidase class II. It has a neutral pH optimum and is strongly inhitibed by furanose analogs swainsonine (SW) and 1,4-dideoxy-1,4-imino-D-mannitol (DIM), moderately by deoxymannojirimycin (DMM), but not by kifunensine (KIF). DMM and KIF, both pyranose analogs, are normally known to inhibit class I alpha-mannosidase. 252 matched cddid_all.tbl CDD cd10814 cd10814 212125 GH38N_AMII_SpGH38_like N-terminal catalytic domain of SPGH38, a putative alpha-mannosidase of Streptococcus pyogenes, and its prokaryotic homologs; glycoside hydrolase family 38 (GH38). The subfamily is represented by SpGH38 of Streptococcus pyogenes, which has been assigned as a putative alpha-mannosidase, and is encoded by ORF spy1604. SpGH38 appears to exist as an elongated dimer and display alpha-1,3 mannosidase activity. It is active on disaccharides and some aryl glycosides. SpGH38 can also effectively deglycosylate human N-glycans in vitro. A divalent metal ion, such as a zinc ion, is required for its activity. SpGH38 is inhibited by swainsonine. The absence of any secretion signal peptide suggests that SpGH38 may be intracellular. 271 matched cddid_all.tbl CDD cd10815 cd10815 212126 GH38N_AMII_EcMngB_like N-terminal catalytic domain of Escherichia coli alpha-mannosidase MngB and its bacterial homologs; glycoside hydrolase family 38 (GH38). The bacterial subfamily is represented by Escherichia coli alpha-mannosidase MngB, which is encoded by the mngB gene (previously called ybgG). MngB exhibits alpha-mannosidase activity that converts 2-O-(6-phospho-alpha-mannosyl)-D-glycerate to mannose-6-phosphate and glycerate in the pathway which enables use of mannosyl-D-glycerate as a sole carbon source. A divalent metal ion is required for its activity. 270 matched cddid_all.tbl CDD cd10816 cd10816 212127 GH57N_BE_TK1436_like N-terminal catalytic domain of Gh57 branching enzyme TK 1436 and similar proteins. The subfamily is represented by a novel branching-enzyme TK1436 of hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. Branching enzymes (BEs, EC 2.4.1.18) play a key role in synthesis of alpha-glucans and they generally are classified into glycoside hydrolase family 13 (GH13). However, TK1436 belongs to the GH57 family. It functions as a monomer and possesses BE activity. TK1436 is composed of a distorted N-terminal (beta/alpha)7-barrel domain and a C-terminal five alpha-helical domain, both of which participate in the formation of the active-site cleft. 423 matched cddid_all.tbl CDD cd10817 cd10817 467263 PDZ9_MUPP1-like PDZ domain 9 of multi-PDZ-domain protein 1 (MUPP1) and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 9 of MUPP1. MUPP1 and PATJ serve as scaffolding proteins linking different proteins and protein complexes involved in the organization of tight junctions and epithelial polarity. MUPP1 contains an L27 (Lin-2 and Lin-7 binding) domain and 13 PDZ domains. PATJ (also known as INAD-like) contains an L27 domain and ten PDZ domains. PATJ lacks 3 PDZ domains seen in MUPP1: PDZ6, PDZ9, and PDZ13. This MuPP1-like PDZ9 domain is therefore absent from PATJ. MUPP1 and PATJ share several binding partners, including junctional adhesion molecules (JAM), zonula occludens (ZO)-3, Pals1 (protein associated with Lin-7), Par (partitioning defective)-6 proteins, and nectins (adherence junction adhesion molecules). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MUPP1-like family PDZ9 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 79 matched cddid_all.tbl CDD cd10820 cd10820 467264 PDZ_SYNPO2-like PDZ domain of synaptopodin 2 (SYNPO2), synaptopodin 2-like protein (SYNPO2L), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SYNPO2, SYNPO2L, and related domains. SYNPO2 (also known as genethonin-2, myopodin) is a cytoskeleton adaptor protein. It participates in chaperone-assisted selective autophagy (CASA), a mechanism for the disposal of misfolded and damaged proteins and provides a link between the CASA chaperone complex and a membrane-tethering and fusion machinery that generates autophagosome membranes. The SYNPO2 PPxY motif binds CASA cochaperone BCL2-associated athanogene 3 (BAG3) and the SYNPO2 PDZ domain binds vacuolar protein sorting 18 homolog (VPS18). There are three isoforms of SYNPO2, which possess an amino-terminal PDZ domain (SYNPO2a, b, c); the short isoform SYNPO2d, lacks the PDZ domain. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SYNPO2-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 78 matched cddid_all.tbl CDD cd10822 cd10822 467265 PDZ_TAX1BP3-like PDZ domain of tax1-binding protein 3 (TAX1BP3), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of TAX1BP3, and related domains. TAX1BP3 (also known as glutaminase-interacting protein 3, tax interaction protein 1, TIP-1, tax-interacting protein 1) may regulate a number of protein-protein interactions by competing for PDZ domain binding sites. TAX1BP3 binds beta-catenin and may act as an inhibitor of the Wnt signaling pathway. It competes with LIN7A (also known as Lin-7A or LIN-7A) for inward rectifier potassium channel 4 (KCNJ4) binding, and thereby promotes KCNJ4 internalization. It may play a role in the Rho signaling pathway, and in the activation of CDC42 by the viral protein HPV16 E6. Binding partners of the TAX1BP3 PDZ domain include beta-catenin, KCNJ4, glutaminase liver isoform (GLS2), rho guanine nucleotide exchange factor 16 (ARHGEF16), rhotekin, and CDK5 regulatory subunit-associated protein 3 (also known as LAPZ). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This TAX1BP3-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 94 matched cddid_all.tbl CDD cd10823 cd10823 467635 cpPDZ_RseP_YlbL-like_arch circularly permuted PDZ domains of uncharacterized archaeal proteins related to Escherichia coli Regulator of sigma-E protease (RseP) and Bacillus subtilis YlbL protease. Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of uncharacterized archaeal proteins related to Escherichia coli ResP (also known as Site-2 protease RseP, and YaeL) and Bacillus subtilis YlbL protease. RseP participates in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmaE) protein RseA. YlbL is an S16 protease which participates with another unrelated S41 protease (CtpA) in a dual protease mechanism that promotes DNA damage checkpoint recovery. PDZ domains usually bind in sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP-YlbL archaeal family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus. 79 matched cddid_all.tbl CDD cd10824 cd10824 467636 cpPDZ_RseP_YlbL-like circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP), Bacillus subtilis YlbL protease, and related domains. Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL), Bacillus subtilis YlbL, and related domains, including archaeal and chloroplast PDZ domains. RseP participates in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmaE) protein RseA. YlbL is an S16 protease which participates with another unrelated S41 protease (CtpA) in a dual protease mechanism that promotes DNA damage checkpoint recovery. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP-YlbL family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus. 82 matched cddid_all.tbl CDD cd10827 cd10827 467627 cpPDZ3_ScNma111-like circularly permuted third PDZ domain (PDZ3) of Saccharomyces cerevisiae pro-apoptotic serine protease Nma111p and related domains. Third PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the HtrA-type protease Saccharomyces cerevisiae Nma111p (also known as Ynm3p), and related domains. Nma111p is a nuclear serine protease which mediates apoptosis through proteolysis of the apoptotic inhibitor Bir1p. Nma111p is composed of two protease domains and four PDZ domains; its N-terminal half is comprised of a protease domain, followed by two PDZ domains, and its C-terminal half has a similar domain arrangement. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This ScNma111-like PDZ3 domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation places both beta-strands A and B on the C-terminus. 87 matched cddid_all.tbl CDD cd10828 cd10828 467628 cpPDZ_Tricorn-protease circularly permuted PDZ domain of Tricorn protease, and related proteins. permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Tricorn protease, and related domains. The tricorn protease can degrade oligopeptides (which may have been generated by the proteasome) and channel the products to F1, F2 and F3 proteases which, in turn, catalyze the terminal degradation step yielding free amino acids. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. The tricorn family PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus. 93 matched cddid_all.tbl CDD cd10830 cd10830 467266 PDZ_MPP1-like PDZ domain of membrane palmitoylated protein1 (MPP1), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MPP1, and related domains. MPP1 (also known as MAGUK p55 subfamily member 1, erythrocyte membrane protein p55, EMP55) is a membrane-associated guanylate kinase (MAGUK)-like protein which forms a complex with protein 4.1 and glycophorin C (GPC) at the cytoplasmic face of the plasma membrane; this complex is essential for cytoskeleton-membrane linkage in erythrocytes and many non-erythroid cells, and participates in the determination of membrane stability and cell shape. MPP1, by interacting with various scaffold proteins and cytoskeletal proteins in the postsynaptic density, also plays an important role in organizing synaptic and non-synaptic structures. MPP1 is also a component of the Crumbs protein complex in the mammalian retina and may link the Usher protein network and the Crumbs protein complex. The MPP1 PDZ domain binding partners include GPC, ABCC4, and CADM1/Necl-2/SynCAM1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MPP1-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 81 matched cddid_all.tbl CDD cd10831 cd10831 467267 PDZ_CASK-like PDZ domain of peripheral plasma membrane protein CASK, Caenorhabditis Lin-2, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of CASK, Caenorhabditis elegans Lin-2, and related domains. CASK and Lin-2 are membrane-associated guanylate kinase (MAGUK)-like proteins. CASK (also known as Calcium/calmodulin-dependent protein kinase, CAKI, and Camguk) has a role in synaptic transmembrane protein anchoring and ion channel trafficking. CASK may regulate transmembrane proteins that bind calcium, calmodulin, or nucleotides; it regulates the Drosophila ether a go-go (eag) potassium channel, and also regulates autophosphorylation of CaMKII. CASK binding partners include the transcription factor TBR1, and cell-surface proteins, including amyloid precursor protein, neurexins, and syndecans. Lin-2, as a component of the CLin-10-Lin-2-Lin-7 complex, plays a role in controlling the basolateral localization of the EGF receptor Let-23; this complex also associates with the neuron-specific motor protein KIF17 to transport vesicles containing N-methyl-D-aspartate (NMDA) receptor 2B along microtubules. CASK may also function in targeting or scaffolding of the protein parkin which is selectively truncated by a Parkinson's disease-causing mutation; the C-terminus of parkin functions as a class II PDZ-binding motif that binds CASK. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MPP6-MPP2-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 81 matched cddid_all.tbl CDD cd10832 cd10832 467268 PDZ_MPP6-MPP2-like PDZ domain of membrane palmitoylated protein 6 (MPP6), MPP2, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MPP6, MPP2, and related domains. MPP6 (also known as MAGUK p55 subfamily member, Protein associated with Lin-7, 2 (PALS2), Veli-associated MAGUK 1, and VAM-1) is a membrane-associated guanylate kinase (MAGUK)-like protein. MPP6 is a regulator of Lin-7 expression and localization. MPP6 is also known to bind cell-adhesion protein, nectin-like molecule-2 (Necl-2), and localize to the basolateral plasma membrane in mammalian epithelial cells. MPP2 (also known as MAGUK p55 subfamily member 2) is a postsynaptic protein that links SynCAM1 cell adhesion molecules to core components of the postsynaptic density. Other members of this family include the Drosophila Vari protein, an essential basolateral septate junction protein which interacts with the cell-adhesion protein neurexin IV. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MPP6-MPP2-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 78 matched cddid_all.tbl CDD cd10833 cd10833 467269 PDZ1_PDZD7-like PDZ domain 1 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa. PDZD7 also forms homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the first PDZ domain of the canonical isoform of PDZD7- isoform 1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD7-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 84 matched cddid_all.tbl CDD cd10834 cd10834 467270 PDZ2_PDZD7-like PDZ domain 2 of the canonical isoform 1 of PDZ domain containing 7 (PDZD7), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of the long isoform 1 of PDZD7, and related domains. PDZD7 is critical for the organization of Usher syndrome type 2 (USH2) complex. Usher syndrome is the leading cause of hereditary sensory deaf-blindness in humans; USH2 is the most common sub-type. Formation of the USH2 complex is based upon heterodimerization between PDZD7 and whirlin (another PDZ domain-containing protein) and a subsequent dynamic interplay between USH2 proteins via their multiple PDZ domains. The PDZD7 PDZ2 domain binds GPR98 (also known as VLGR1) and usherin (USH2A). PDZD7 and whirlin form heterodimers through their multiple PDZ domains; whirlin and PDZD7 interact with usherin and GPR98 to form an interdependent ankle link complex. PDZD7 also interacts with myosin VIIa. PDZD7 also forms homodimers through its PDZ2 domain. Various isoforms of PDZD7 produced by alternative splicing have been identified; this subgroup includes the second PDZ domain of the canonical isoform of PDZD7- isoform 1. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD7-like family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 85 matched cddid_all.tbl CDD cd10838 cd10838 467629 cpPDZ_HhoA-like circularly permuted PDZ domain of Synechocystis sp. PCC 6803 putative serine proteases HhoA, HhoB, and HtrA and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of the cyanobacterial Synechocystis sp. PCC 6803 putative serine proteases HhoA, HhoB and HtrA, and related domains. These three proteases are functionally overlapping, and are involved in a number of key physiological responses, ranging from protection against light and heat stresses to phototaxis. HhoA assembles into trimers, mediated by its protease domain and further into a hexamer by a novel interaction between the PDZ domains of opposing trimers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This HhoA-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus. 104 matched cddid_all.tbl CDD cd10839 cd10839 467630 cpPDZ1_DegP-like circularly permuted first PDZ domain (PDZ1) of Escherichia coli periplasmic serine endoprotease DegP and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Escherichia coli DegP (also known as heat shock protein DegP and Protease Do) and related domains. DegP belongs to the HtrA family of housekeeping proteases. It acts as a protease, degrading transiently denatured and unfolded or misfolded proteins which accumulate in the periplasm following heat shock or other stress conditions, and as a molecular chaperone at low temperatures. DegP has two PDZ domains in addition to the protease domain; its PDZ1 domain is responsible for identifying the distinct substrate sequences that affect degradation (degron) of the substrate sequence, and its PDZ2 domain is responsible for combining with other DegP monomers to form a stable oligomer structure. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This DegP family PDZ domain 1 is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus. 91 matched cddid_all.tbl CDD cd10843 cd10843 380680 DSRM_DICER double-stranded RNA binding motif of endoribonuclease Dicer and similar proteins. Dicer (also known as helicase with RNase motif (HERNA), or helicase MOI) is a double-stranded RNA (dsRNA) endoribonuclease playing a central role in short dsRNA-mediated post-transcriptional gene silencing. It cleaves naturally occurring long dsRNAs and short hairpin pre-microRNAs (miRNA) into fragments of twenty-one to twenty-three nucleotides with 3' overhang of two nucleotides, producing respectively short interfering RNAs (siRNA) and mature microRNAs. Dicer contains a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 63 matched cddid_all.tbl CDD cd10844 cd10844 380681 DSRM_TARBP2_rpt2 second double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar proteins. TARBP2 (also known as TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)) participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. TARBP2 contains three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 67 matched cddid_all.tbl CDD cd10845 cd10845 380682 DSRM_RNAse_III_family double-stranded RNA binding motif of ribonuclease III (RNase III) and similar proteins. RNase III (EC 3.1.26.3; also known as ribonuclease 3) digests double-stranded RNA formed within single-strand substrates, but not RNA-DNA hybrids. It is involved in the processing of rRNA precursors, viral transcripts, some mRNAs, and at least 1 tRNA (metY, a minor form of tRNA-init-Met). It cleaves the 30S primary rRNA transcript to yield the immediate precursors to the 16S and 23S rRNAs. The cleavage can occur in assembled 30S, 50S, and even 70S subunits and is influenced by the presence of ribosomal proteins. The RNase III family also includes the mitochondrion-specific ribosomal protein mL44 subfamily, which is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). Members of this family contain an RNase III domain and a C-terminal double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 69 matched cddid_all.tbl CDD cd10909 cd10909 211315 ChtBD1_GH18_2 Hevein or type 1 chitin binding domain (ChtBD1) subfamily; in some members co-occurs with family 18 glycosyl hydrolases. This subfamily includes a Toxoplasma gondii ME49 protein annotated as a putative mannosyl-oligosaccharide glucosidase. ChtBD1 is a lectin domain found in proteins from plants and fungi that bind N-acetylglucosamine, plant endochitinases, wound-induced proteins such as hevein, a major IgE-binding allergen in natural rubber latex, and the alpha subunit of Kluyveromyces lactis killer toxin. This domain is involved in the recognition and/or binding of chitin subunits; it typically occurs N-terminal to glycosyl hydrolase domains in chitinases, together with other carbohydrate-binding domains, or by itself in tandem-repeat arrangements. 51 matched cddid_all.tbl CDD cd10910 cd10910 350234 PIN_limkain_b1_N_like N-terminal LabA-like PIN domain of limkain b1 and similar proteins. Limkain b1 is a human autoantigen, localized to a subset of ABCD3 and PXF marked peroxisomes. Limkain b1 may be a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. Limkain b1 contains multiple copies of LOTUS domains and a conserved RNA recognition motif, this and similar domain architectures are shared by several members of this family, and a function of these architectures in RNA binding or RNA metabolism has been suggested. The function of the N-terminal domain is unknown. This subfamily belongs to LabA-like PIN domain family which includes Synechococcus elongatus PCC 7942 LabA, human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like PIN family. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 126 matched cddid_all.tbl CDD cd10911 cd10911 350235 PIN_LabA PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins. This subfamily contains Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing, it is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system, and appears to be necessary for KaiC-dependent repression of gene expression. This subfamily belongs to the LabA-like domain family which includes the N-terminal domain of limkain b1, a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes. Also included in the LabA-like domain family are human ZNF451, uncharacterized Bacillus subtilis YqxD, uncharacterized Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously Pseudomonas putida S16 NicB , which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like family. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 154 matched cddid_all.tbl CDD cd10912 cd10912 350236 PIN_YacP-like PIN_domain of Bacillus subtilis YacP/Rae1 and related proteins. Bacillus subtilis YacP, also known as Rae1, is an endoribonuclease involved in ribosome-dependent mRNA decay. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. PIN domains were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 142 matched cddid_all.tbl CDD cd10913 cd10913 199211 Peptidase_C25_N_gingipain gingipain subgroup of the Peptidase C25 family N-terminal domain. Gingipain, produced by Porphyromonas gingivalis, exemplifies the Peptidase family C25, a unique class of cysteine proteases. P. gingivalis is one of the primary gram-negative pathogens that causes periodontitis, a disease also associated with other diseases such as diabetes and cardiovascular disease. The gingipain subgroup contains extracellular Arg- and Lys-specific proteinases called Arg-gingipain (Rgp) and Lys-gingipain (Kgp); RgpA and RgpB are homologous Arg-specific gingipains encoded by two closely related genes, rgpA and rgpB, while Lys-specific gingipain is encoded by the single kgp gene. Mutant studies have shown that, among the large quantities of proteolytic enzymes produced by P. gingivalis, these three proteases are major virulence factors of this bacterium. All three genes encode an N-terminal pre-pro fragment, followed by the protease domain; however, rgpA and kgp also encode additional C-terminal HA (hemaglutinin/adhesion) subunits which consist of several sequence-related adhesion domains. Although unique, their cysteine protease active site residues (His and Cys) forming the catalytic dyad, are well-conserved, cleaving the C-terminal peptide bond with Arg or Lys residues. Gingipains are evolutionarily related to other highly specific proteases including caspases, clostripain, legumains, and separase. Gingipains function by dysregulating host defense and inflammatory responses, and degrading host proteins, e.g. tissue, cells, matrix, plasma and immunological proteins. It has been suggested that they enhance gingival crevicular fluid (GCF) production through activation of the kallikrein/kinin pathways, thus increasing vascular permeability and causing gingival inflammation, a distinctive feature of periodontitis. RgpA and RgpB are also able to cleave and activate coagulation factors IX and X in order to activate prothrombin to produce thrombin, which in turn increases production of GCF. The gingipains also play a pivotal role in the survival of P. gingivalis in the host by attacking the host defense system through cleavage of several immunological molecules, while at the same time evading the host-immune response by dysregulating the cytokine network. 348 matched cddid_all.tbl CDD cd10914 cd10914 199212 Peptidase_C25_N_1 uncharacterized subgroup of the Peptidase C25 family N-terminal domain. Domains in this subgroup are uncharacterized members of the Peptidase family C25 N-terminal domain family. Peptidase family C25 is a unique class of cysteine proteases, exemplified by gingipain, which is produced by Porphyromonas gingivalis. P. gingivalis is one of the primary gram-negative pathogens that causes periodontitis, a disease that is also associated with other diseases such as diabetes and cardiovascular disease. Gingipains are a group of extracellular Arg- and Lys-specific proteinases called Arg-gingipain (Rgp) and Lys-gingipain (Kgp); RgpA and RgpB are homologous Arg-specific gingipains encoded by two closely related genes, rgpA and rgpB, while Lys-specific gingipain is encoded by the single kgp gene (also called prtK, prkP). Mutant studies have shown that, among the large quantities of proteolytic enzymes produced by P. gingivalis, these three proteases are major virulence factors of this bacterium. All three genes encode an N-terminal pre-pro fragment, followed by the protease domain; however, rgpA and kgp also encode additional C-terminal HA (hemaglutinin/adhesion) subunits which consist of several sequence-related adhesion domains. Although unique, their cysteine protease active site residues (His and Cys) forming the catalytic dyad are well-conserved, cleaving the C-terminal peptide bond with Arg or Lys residues. Gingipains are evolutionarily related to other highly specific proteases including caspases, clostripain, legumains, and separase. Gingipains function by dysregulating host defense and inflammatory responses, and degrading host proteins, e.g. tissue, cells, matrix, plasma and immunological proteins. They are proposed to enhance gingival crevicular fluid (GCF) production through activation of the kallikrein/kinin pathways, thus increasing vascular permeability and causing gingival inflammation, a distinctive feature of periodontitis. RgpA and RgpB are also able to cleave and activate coagulation factors IX and X in order to activate prothrombin to produce thrombin, which in turn increases production of GCF. The gingipains also play a pivotal role in the survival of P. gingivalis in the host by attacking the host defense system through cleavage of several immunological molecules, while at the same time evading the host-immune response by dysregulating the cytokine network. 365 matched cddid_all.tbl CDD cd10915 cd10915 199213 Peptidase_C25_N_2 uncharacterized subgroup of the Peptidase C25 family N-terminal domain. Domains in this subgroup are uncharacterized members of the Peptidase family C25 N-terminal domain family. Peptidases family C25 are a unique class of cysteine proteases, exemplified by gingipain, which is produced by Porphyromonas gingivalis. P. gingivalis is one of the primary gram-negative pathogens that causes periodontitis, a disease that is also associated with other diseases such as diabetes and cardiovascular disease. Gingipains are a group of extracellular Arg- and Lys-specific proteinases called Arg-gingipain (Rgp) and Lys-gingipain (Kgp); RgpA and RgpB are homologous Arg-specific gingipains encoded by two closely related genes, rgpA and rgpB, while Lys-specific gingipain is encoded by the single kgp gene. Mutant studies have shown that, among the large quantities of proteolytic enzymes produced by P. gingivalis, these three proteases are major virulence factors of this bacterium. All three genes encode an N-terminal pre-pro fragment, followed by the protease domain; however, rgpA and kgp also encode additional C-terminal HA (hemaglutinin/adhesion) subunits which consist of several sequence-related adhesion domains. Although unique, their cysteine protease active site residues (His and Cys) forming the catalytic dyad are well-conserved, cleaving the C-terminal peptide bond with Arg or Lys residues. Gingipains are evolutionarily related to other highly specific proteases including caspases, clostripain, legumains, and separase. Gingipains function by dysregulating host defense and inflammatory responses, and degrading host proteins, e.g. tissue, cells, matrix, plasma and immunological proteins. They are proposed to enhance gingival crevicular fluid (GCF) production through activation of the kallikrein/kinin pathways, thus increasing vascular permeability and causing gingival inflammation, a distinctive feature of periodontitis. RgpA and RgpB are also able to cleave and activate coagulation factors IX and X in order to activate prothrombin to produce thrombin, which in turn increases production of GCF. The gingipains also play a pivotal role in the survival of P. gingivalis in the host by attacking the host defense system through cleavage of several immunological molecules, while at the same time evading the host-immune response by dysregulating the cytokine network. 403 matched cddid_all.tbl CDD cd10916 cd10916 213021 CE4_PuuE_HpPgdA_like Catalytic domain of bacterial PuuE allantoinases, Helicobacter pylori peptidoglycan deacetylase (HpPgdA), and similar proteins. This family is a member of the very large and functionally diverse carbohydrate esterase 4 (CE4) superfamily. It contains bacterial PuuE (purine utilization E) allantoinases, a peptidoglycan deacetylase from Helicobacter pylori (HpPgdA), Escherichia coli ArnD, and many uncharacterized homologs from all three kingdoms of life. PuuE allantoinase appears to be metal-independent and specifically catalyzes the hydrolysis of (S)-allantoin into allantoic acid. Different from PuuE allantoinase, HpPgdA has the ability to bind a metal ion at the active site and is responsible for a peptidoglycan modification that counteracts the host immune response. Both PuuE allantoinase and HpPgdA function as a homotetramer. The monomer is composed of a 7-stranded barrel with detectable sequence similarity to the 6-stranded barrel NodB homology domain of polysaccharide deacetylase (DCA)-like proteins in the CE4 superfamily, which removes N-linked or O-linked acetyl groups from cell wall polysaccharides. However, in contrast with the typical DCAs, PuuE allantoinase and HpPgdA might not exhibit a solvent-accessible polysaccharide binding groove and only recognize a small substrate molecule. ArnD catalyzes the deformylation of 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol to 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol. 247 matched cddid_all.tbl CDD cd10917 cd10917 213022 CE4_NodB_like_6s_7s Catalytic NodB homology domain of rhizobial NodB-like proteins. This family belongs to the large and functionally diverse carbohydrate esterase 4 (CE4) superfamily, whose members show strong sequence similarity with some variability due to their distinct carbohydrate substrates. It includes many rhizobial NodB chitooligosaccharide N-deacetylase (EC 3.5.1.-)-like proteins, mainly from bacteria and eukaryotes, such as chitin deacetylases (EC 3.5.1.41), bacterial peptidoglycan N-acetylglucosamine deacetylases (EC 3.5.1.-), and acetylxylan esterases (EC 3.1.1.72), which catalyze the N- or O-deacetylation of substrates such as acetylated chitin, peptidoglycan, and acetylated xylan. All members of this family contain a catalytic NodB homology domain with the same overall topology and a deformed (beta/alpha)8 barrel fold with 6- or 7 strands. Their catalytic activity is dependent on the presence of a divalent cation, preferably cobalt or zinc, and they employ a conserved His-His-Asp zinc-binding triad closely associated with the conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. Several family members show diversity both in metal ion specificities and in the residues that coordinate the metal. 171 matched cddid_all.tbl CDD cd10918 cd10918 213023 CE4_NodB_like_5s_6s Putative catalytic NodB homology domain of PgaB, IcaB, and similar proteins which consist of a deformed (beta/alpha)8 barrel fold with 5- or 6-strands. This family belongs to the large and functionally diverse carbohydrate esterase 4 (CE4) superfamily, whose members show strong sequence similarity with some variability due to their distinct carbohydrate substrates. It includes bacterial poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, hemin storage system HmsF protein in gram-negative species, intercellular adhesion proteins IcaB, and many uncharacterized prokaryotic polysaccharide deacetylases. It also includes a putative polysaccharide deacetylase YxkH encoded by the Bacillus subtilis yxkH gene, which is one of six polysaccharide deacetylase gene homologs present in the Bacillus subtilis genome. Sequence comparison shows all family members contain a conserved domain similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, which consists of a deformed (beta/alpha)8 barrel fold with 6 or 7 strands. However, in this family, most proteins have 5 strands and some have 6 strands. Moreover, long insertions are found in many family members, whose function remains unknown. 157 matched cddid_all.tbl CDD cd10919 cd10919 200545 CE4_CDA_like Putative catalytic domain of chitin deacetylase-like proteins from insects and similar proteins. Chitin deacetylases (CDAs, EC 3.5.1.41) are secreted metalloproteins belonging to a family of extracellular chitin-modifying enzymes that catalyze the N-deacetylation of chitin, a beta-1,4-linked N-acetylglucosamine polymer, to form chitosan, a polymer of beta-(1,4)-linked d-glucosamine residues. CDAs have been isolated and characterized from various bacterial and fungal species and belong to the larger carbohydrate esterase family 4 (CE4). This family includes many CDA-like proteins, mainly from insects, which contain a putative CDA-like catalytic domain similar to the catalytic NodB homology domain of CE4 esterases. Some family members have an additional chitin binding domain (ChBD), or an additional low-density lipoprotein receptor class A domain (LDLa), or both. Due to the lack of some catalytically relevant residues, several insect CDA-like proteins are devoid of enzymatic activity and may simply bind to chitin and thus influence the mechanical or permeability properties of chitin-containing structures such as the cuticle or the peritrophic membrane. This family also includes many uncharacterized hypothetical proteins from bacteria, exhibiting high sequence similarity to insect CDA-like proteins. 273 matched cddid_all.tbl CDD cd10920 cd10920 200546 CE4_WbmS Catalytic domain of a putative polysaccharide deacetylase WbmS from Bordetella bronchiseptica and similar proteins. This family is represented by a putative polysaccharide deacetylase encoded by the O-antigen-related gene wbmS in Bordetella bronchiseptica. Although its precise function remains unknown, it has been suggested that WbmS might be involved in the biosynthesis of O-antigen, an important component of the gram-negative bacterial outer membrane, and may also play a role in sugar phosphate transfer. Structural superposition and sequence comparison show that WbmS consists of a conserved domain similar to the 7-stranded barrel catalytic domain of polysaccharide deacetylases (DACs) from the carbohydrate esterase 4 (CE4) superfamily, which removes N-linked acetyl groups from cell wall polysaccharides. 233 matched cddid_all.tbl CDD cd10921 cd10921 200547 CE4_MJ0505_like Putative catalytic domain of uncharacterized protein MJ0505 from Methanocaldococcus jannaschii and similar proteins. This family contains an uncharacterized protein MJ0505 from Methanocaldococcus jannaschii and its prokaryotic homologs. Although their biochemical properties remain to be determined, members in this family is composed of a seven-stranded barrel with a detectable sequence similarity to the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups of cell wall polysaccharides and belong to a larger carbohydrate esterase 4 (CE4) superfamily. 206 matched cddid_all.tbl CDD cd10922 cd10922 200548 CE4_PelA_like_C C-terminal Putative NodB-like catalytic domain of PelA-like uncharacterized hypothetical proteins found in bacteria. This family is represented by a protein PelA of unknown function that is encoded by a gene in the pelA-G gene cluster for pellicle production and biofilm formation in Pseudomonas aeruginosa. PelA and most of the family members contain a domain of unknown function, DUF297, in the N-terminus and a C-terminal domain that shows high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily. 266 matched cddid_all.tbl CDD cd10923 cd10923 200549 CE4_COG5298 Putative NodB-like catalytic domain of uncharacterized proteins found in bacteria. This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily. Some family members contain an additional copper amine oxidase N-terminal domain. 250 matched cddid_all.tbl CDD cd10924 cd10924 200550 CE4_COG4878 Putative NodB-like catalytic domain of uncharacterized proteins found in bacteria. The family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily. 273 matched cddid_all.tbl CDD cd10925 cd10925 200551 CE4_u1 Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily. This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily. 216 matched cddid_all.tbl CDD cd10926 cd10926 200552 CE4_u2 Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily. This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily. 253 matched cddid_all.tbl CDD cd10927 cd10927 200553 CE4_u3 Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily. This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily. 227 matched cddid_all.tbl CDD cd10928 cd10928 200554 CE4_u4 Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily. This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily. 222 matched cddid_all.tbl CDD cd10929 cd10929 200555 CE4_u5 Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily. This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily. 263 matched cddid_all.tbl CDD cd10930 cd10930 200556 CE4_u6 Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily. This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily. 240 matched cddid_all.tbl CDD cd10931 cd10931 200557 CE4_u7 Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily. This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily. 224 matched cddid_all.tbl CDD cd10932 cd10932 200558 CE4_u8 Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily. This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily. 324 matched cddid_all.tbl CDD cd10933 cd10933 200559 CE4_u9 Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily. This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily. 266 matched cddid_all.tbl CDD cd10934 cd10934 200560 CE4_cadherin_MopE_like_N N-terminal Putative NodB-like catalytic domain of hypothetical proteins containing C-terminal cadherin or MopE copper binding domains. The family includes several cadherin or MopE copper binding domain containing hypothetical proteins found in bacteria. Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium. They play a role in cell fate, signalling, proliferation, differentiation, and migration. The copper binding domain involves a tryptophan metabolite, kynurenine, in the protein MopE. Members of this family contain an additional conserved domain, which is N-terminally fused to the cadherin domain or the MopE copper binding domain. Although its function remains unclear, the conserved domain exhibits a seven-stranded barrel with a detectable sequence similarity to the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily. 267 matched cddid_all.tbl CDD cd10935 cd10935 200561 CE4_WalW Putative catalytic domain of lipopolysaccharide biosynthesis protein WalW and its bacterial homologs. This family corresponds to a group of uncharacterized lipopolysaccharide biosynthesis protein WalW found in bacteria. Although their biochemical properties remain to be determined, members of this family is composed of a seven-stranded barrel with detectable sequence similarity to the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily. 295 matched cddid_all.tbl CDD cd10936 cd10936 200562 CE4_DAC2 Putative catalytic domain of family 2 polysaccharide deacetylases (DACs) from bacteria. This family contains an uncharacterized protein BH1492 from Bacillus halodurans, an uncharacterized protein ATU2773 from Agrobacterium tumefaciens C58, and other bacterial hypothetical proteins. Although their functions are still unknown, structural superposition and sequence comparison suggest that BH1492 and ATU2773 might be divergently related to the 7-stranded barrel catalytic domain of polysaccharide deacetylases (DACs) from the carbohydrate esterase 4 (CE4) superfamily, which remove N-linked acetyl groups from cell wall polysaccharides. This family is designated as DAC family 2, a divergent DAC family. 215 matched cddid_all.tbl CDD cd10938 cd10938 200563 CE4_HpPgdA_like Catalytic domain of Helicobacter pylori peptidoglycan deacetylase (HpPgdA) and similar proteins. This family is represented by a peptidoglycan deacetylase (HP0310, HpPgdA) from the gram-negative pathogen Helicobacter pylori. HpPgdA has the ability to bind a metal ion at the active site and is responsible for a peptidoglycan modification that counteracts the host immune response. It functions as a homotetramer. The monomer is composed of a 7-stranded barrel with detectable sequence similarity to the 6-stranded barrel NodB homology domain of polysaccharide deacetylase (DCA)-like proteins in the CE4 superfamily, which removes N-linked or O-linked acetyl groups from cell wall polysaccharides. In contrast to typical NodB-like DCAs, HpPgdA does not exhibit a solvent-accessible polysaccharide binding groove, suggesting that the enzyme binds a small molecule at the active site. 258 matched cddid_all.tbl CDD cd10939 cd10939 200564 CE4_ArnD Catalytic domain of Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD and other bacterial homologs. This family is represented by Escherichia coli 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol deformylase ArnD (EC 3.5.1.n3). ArnD plays an important role in the biosynthesis of undecaprenyl phosphate alpha-4-amino-4-deoxy-L-arabinose (alpha-L-Ara4N). It catalyzes the deformylation of 4-deoxy-4-formamido-L-arabinose-phosphoundecaprenol to 4-amino-4-deoxy-L-arabinose-phosphoundecaprenol. The ArnD-dependent deformylation likely occurs on the inner leaflet of the inner membrane. This family also includes many uncharacterized bacterial polysaccharide deacetylases. All family members show high sequence homology to the catalytic domain of bacterial PuuE (purine utilization E) allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA), and are classified within the larger carbohydrate esterase 4 (CE4) superfamily. 290 matched cddid_all.tbl CDD cd10940 cd10940 200565 CE4_PuuE_HpPgdA_like_1 Putative catalytic domain of uncharacterized bacterial polysaccharide deacetylases similar to bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA). This family contains many uncharacterized bacterial polysaccharide deacetylases (DCAs) that show high sequence similarity to the catalytic domain of bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA). PuuE allantoinase appears to be metal-independent and specifically catalyzes the hydrolysis of (S)-allantoin into allantoic acid. Different from PuuE allantoinase, HpPgdA has the ability to bind a metal ion at the active site and is responsible for a peptidoglycan modification that counteracts the host immune response. Both PuuE allantoinase and HpPgdA function as homotetramers. The monomer is composed of a 7-stranded barrel with detectable sequence similarity to the 6-stranded barrel NodB homology domain of DCA-like proteins in the CE4 superfamily, which removes N-linked or O-linked acetyl groups from cell wall polysaccharides. In contrast to typical NodB-like DCAs, PuuE allantoinase and HpPgdA do not exhibit a solvent-accessible polysaccharide binding groove and might only bind a small molecule at the active site. 306 matched cddid_all.tbl CDD cd10941 cd10941 200566 CE4_PuuE_HpPgdA_like_2 Putative catalytic domain of uncharacterized prokaryotic polysaccharide deacetylases similar to bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA). This family contains many uncharacterized prokaryotic polysaccharide deacetylases (DCAs) that show high sequence similarity to the catalytic domain of bacterial PuuE allantoinases and Helicobacter pylori peptidoglycan deacetylase (HpPgdA). PuuE allantoinase appears to be metal-independent and specifically catalyzes the hydrolysis of (S)-allantoin into allantoic acid. Different from PuuE allantoinase, HpPgdA has the ability to bind a metal ion at the active site and is responsible for a peptidoglycan modification that counteracts the host immune response. Both PuuE allantoinase and HpPgdA function as homotetramers. The monomer is composed of a 7-stranded barrel with detectable sequence similarity to the 6-stranded barrel NodB homology domain of DCA-like proteins in the CE4 superfamily, which removes N-linked or O-linked acetyl groups from cell wall polysaccharides. In contrast to typical NodB-like DCAs, PuuE allantoinase and HpPgdA do not exhibit a solvent-accessible polysaccharide binding groove and might only bind a small molecule at the active site. 258 matched cddid_all.tbl CDD cd10942 cd10942 200567 CE4_u11 Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily. This family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily. 252 matched cddid_all.tbl CDD cd10943 cd10943 200568 CE4_NodB Putative catalytic domain of rhizobial NodB chitooligosaccharide N-deacetylase and its bacterial homologs. This family corresponds to rhizobial NodB chitooligosaccharide N-deacetylase (EC 3.5.1.-), encoded by nodB gene from the nodulation (nod) gene cluster that is responsible for the biosynthesis of bacterial nodulation signals, termed Nod factors. NodB is involved in de-N-acetylating the nonreducing N-acetylglucosamine residue of chitooligosaccharides to allow for the attachment of the fatty acyl group by the acyltransferase NodA. The monosaccharide N-acetylglucosamine cannot be deacetylated by NodB. NodB is composed of a 6-stranded barrel catalytic domain with detectable sequence similarity to the 7-stranded barrel homology domain of polysaccharide deacetylase (DCA)-like proteins in the larger carbohydrate esterase 4 (CE4) superfamily. 193 matched cddid_all.tbl CDD cd10944 cd10944 200569 CE4_SmPgdA_like Catalytic NodB homology domain of Streptococcus mutans polysaccharide deacetylase PgdA, Bacillus subtilis YheN, and similar proteins. This family is represented by a putative polysaccharide deacetylase PgdA from the oral pathogen Streptococcus mutans (SmPgdA) and Bacillus subtilis YheN (BsYheN), which are members of the carbohydrate esterase 4 (CE4) superfamily. SmPgdA is an extracellular metal-dependent polysaccharide deacetylase with a typical CE4 fold, with metal bound to a His-His-Asp triad. It possesses de-N-acetylase activity toward a hexamer of chitooligosaccharide N-acetylglucosamine, but not shorter chitooligosaccharides or a synthetic peptidoglycan tetrasaccharide. SmPgdA plays a role in tuning cell surface properties and in interactions with (salivary) agglutinin, an essential component of the innate immune system, most likely through deacetylation of an as-yet-unidentified polysaccharide. SmPgdA shows significant homology to the catalytic domains of peptidoglycan deacetylases from Streptococcus pneumoniae (SpPgdA) and Listeria monocytogenes (LmPgdA), both of which are involved in the bacterial defense mechanism against human mucosal lysozyme. The Bacillus subtilis genome contains six polysaccharide deacetylase gene homologs: pdaA, pdaB (previously known as ybaN), yheN, yjeA, yxkH and ylxY. The biological function of BsYheN is still unknown. This family also includes many uncharacterized polysaccharide deacetylases mainly found in bacteria. 189 matched cddid_all.tbl CDD cd10946 cd10946 200570 CE4_Mll8295_like Putative catalytic NodB homology domain of uncharacterized Mll8295 protein encoded from Rhizobium loti and its bacterial homologs. This family is represented by a putative polysaccharide deacetylase Mll8295 encoded from Rhizobium loti. Although its biological function still remains unknown, Mll8295 shows high sequence homology to the catalytic domain of Streptococcus pneumoniae polysaccharide deacetylase PgdA (SpPgdA), which is an extracellular metal-dependent polysaccharide deacetylase with de-N-acetylase activity toward a hexamer of chitooligosaccharide N-acetylglucosamine, but not shorter chitooligosaccharides or a synthetic peptidoglycan tetrasaccharide. Both Mll8295 and SpPgdA belong to the carbohydrate esterase 4 (CE4) superfamily. This family also includes many uncharacterized bacterial polysaccharide deacetylases. 217 matched cddid_all.tbl CDD cd10947 cd10947 200571 CE4_SpPgdA_BsYjeA_like Catalytic NodB homology domain of Streptococcus pneumoniae peptidoglycan deacetylase PgdA, Bacillus subtilis BsYjeA protein, and their bacterial homologs. This family is represented by Streptococcus pneumoniae peptidoglycan GlcNAc deacetylase (SpPgdA), a member of the carbohydrate esterase 4 (CE4) superfamily. SpPgdA protects gram-positive bacterial cell wall from host lysozymes by deacetylating peptidoglycan N-acetylglucosamine (GlcNAc) residues. It consists of three separate domains: N-terminal, middle and C-terminal (catalytic) domains. The catalytic NodB homology domain is similar to the deformed (beta/alpha)8 barrel fold adopted by other CE4 esterases, which harbors a mononuclear metalloenzyme employing a conserved His-His-Asp zinc-binding triad closely associated with conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. The enzyme is able to accept GlcNAc3 as a substrate, with the N-acetyl of the middle sugar being removed by the enzyme. This family also includes Bacillus subtilis BsYjeA protein encoded by the yjeA gene, which is one of the six polysaccharide deacetylase gene homologs (pdaA, pdaB/ybaN, yheN, yjeA, yxkH and ylxY) in the Bacillus subtilis genome. Although homology comparison shows that the BsYjeA protein contains a polysaccharide deacetylase domain, and was predicted to be a membrane-bound xylanase or a membrane-bound chitooligosaccharide deacetylase, more recent research indicates BsYjeA might be a novel non-specific secretory endonuclease which creates random nicks progressively on the two strands of dsDNA, resulting in highly distinguishable intermediates/products very different in chemical and physical compositions over time. In addition, BsYjeA shares several enzymatic properties with the well-understood DNase I endonuclease. Both enzymes are active on ssDNA and dsDNA, both generate random nicks, and both require Mg2+ or Mn2+ for hydrolytic activity. 177 matched cddid_all.tbl CDD cd10948 cd10948 200572 CE4_BsPdaA_like Catalytic NodB homology domain of Bacillus subtilis polysaccharide deacetylase PdaA, and its bacterial homologs. The Bacillus subtilis genome contains six polysaccharide deacetylase gene homologs: pdaA, pdaB (previously known as ybaN), yheN, yjeA, yxkH and ylxY. This family is represented by Bacillus subtilis pdaA gene encoding polysaccharide deacetylase BsPdaA, which is a member of the carbohydrate esterase 4 (CE4) superfamily. BsPdaA deacetylates peptidoglycan N-acetylmuramic acid (MurNAc) residues to facilitate the formation of muramic delta-lactam, which is required for recognition of germination lytic enzymes. BsPdaA deficiency leads to the absence of muramic delta-lactam residues in the spore cortex. Like other CE4 esterases, BsPdaA consists of a single catalytic NodB homology domain that appears to adopt a deformed (beta/alpha)8 barrel fold with a putative substrate binding groove harboring the majority of the conserved residues. It utilizes a general acid/base catalytic mechanism involving a tetrahedral transition intermediate, where a water molecule functions as the nucleophile tightly associated to the zinc cofactor. 223 matched cddid_all.tbl CDD cd10949 cd10949 200573 CE4_BsPdaB_like Putative catalytic NodB homology domain of Bacillus subtilis putative polysaccharide deacetylase PdaB, and its bacterial homologs. The Bacillus subtilis genome contains six polysaccharide deacetylase gene homologs: pdaA, pdaB (previously known as ybaN), yheN, yjeA, yxkH and ylxY. This family is represented by the putative polysaccharide deacetylase PdaB encoded by the pdaB gene on sporulation of Bacillus subtilis. Although its biochemical properties remain to be determined, the PdaB (YbaN) protein is essential for maintaining spores after the late stage of sporulation and is highly conserved in spore-forming bacteria. The glycans of the spore cortex may be candidate PdaB substrates. Based on sequence similarity, the family members are classified as carbohydrate esterase 4 (CE4) superfamily members. However, the classical His-His-Asp zinc-binding motif of CE4 esterases is missing in this family. 192 matched cddid_all.tbl CDD cd10950 cd10950 200574 CE4_BsYlxY_like Putative catalytic NodB homology domain of uncharacterized protein YlxY from Bacillus subtilis and its bacterial homologs. The Bacillus subtilis genome contains six polysaccharide deacetylase gene homologs: pdaA, pdaB (previously known as ybaN), yheN, yjeA, yxkH and ylxY. This family is represented by Bacillus subtilis putative polysaccharide deacetylase BsYlxY, encoded by the ylxY gene, which is a member of the carbohydrate esterase 4 (CE4) superfamily. Although its biological function still remains unknown, BsYlxY shows high sequence homology to the catalytic domain of Bacillus subtilis pdaB gene encoding a putative polysaccharide deacetylase (BsPdaB), which is essential for the maintenance of spores after the late stage of sporulation and is highly conserved in spore-forming bacteria. However, disruption of the ylxY gene in B. subtilis did not cause any sporulation defect. Moreover, the Asp residue in the classical His-His-Asp zinc-binding motif of CE4 esterases is mutated to a Val residue in this family. Other catalytically relevant residues of CE4 esterases are also not conserved, which suggest that members of this family may be inactive. 188 matched cddid_all.tbl CDD cd10951 cd10951 200575 CE4_ClCDA_like Catalytic NodB homology domain of Colletotrichum lindemuthianum chitin deacetylase and similar proteins. This family is represented by the chitin deacetylase (endo-chitin de-N-acetylase, ClCDA, EC 3.5.1.41) from Colletotrichum lindemuthianum (also known as Glomerella lindemuthiana), which is a member of the carbohydrate esterase 4 (CE4) superfamily. ClCDA catalyzes the hydrolysis of N-acetamido groups of N-acetyl-D-glucosamine residues in chitin, converting it to chitosan in fungal cell walls. It consists of a single catalytic domain similar to the deformed (alpha/beta)8 barrel fold adopted by other CE4 esterases, which encompasses a mononuclear metalloenzyme employing a conserved His-His-Asp zinc-binding triad closely associated with the conserved catalytic base (aspartic acid) and acid (histidine), to carry out acid/base catalysis. It possesses a highly conserved substrate-binding groove, with subtle alterations that influence substrate specificity and subsite affinity. Unlike its bacterial homologs, ClCDA contains two intramolecular disulfide bonds that may add stability to this secreted protein. The family also includes many uncharacterized deacetylases and hypothetical proteins mainly from eukaryotes, which show high sequence similarity to ClCDA. 197 matched cddid_all.tbl CDD cd10952 cd10952 200576 CE4_MrCDA_like Catalytic NodB homology domain of Mucor rouxii chitin deacetylase and similar proteins. This family is represented by the chitin deacetylase (MrCDA, EC 3.5.1.41) encoded from the fungus Mucor rouxii (also known as Amylomyces rouxii). MrCDA is an acidic glycoprotein with a very stringent specificity for beta1-4-linked N-acetylglucosamine homopolymers. It requires at least four residues (chitotetraose) for catalysis, and can achieve extensive deacetylation on chitin polymers. MrCDA shows high sequence similarity to Colletotrichum lindemuthianum chitin deacetylase (endo-chitin de-N-acetylase, ClCDA), which consists of a single catalytic domain similar to the deformed (beta/alpha)8 barrel fold adopted by the carbohydrate esterase 4 (CE4) superfamily, which encompasses a mononuclear metalloenzyme employing a conserved His-His-Asp zinc-binding triad closely associated with the conserved catalytic base (aspartic acid) and acid (histidine) to carry out acid/base catalysis. The family also includes some uncharacterized eukaryotic and bacterial homologs of MrCDA. 178 matched cddid_all.tbl CDD cd10953 cd10953 200577 CE4_SlAXE_like Catalytic NodB homology domain of Streptomyces lividans acetylxylan esterase and its bacterial homologs. This family is represented by Streptomyces lividans acetylxylan esterase (SlAXE, EC 3.1.1.72), a member of the carbohydrate esterase 4 (CE4) superfamily. SlAXE deacetylates O-acetylated xylan, a key component of plant cell walls. It shows no detectable activity on generic esterase substrates including para-nitrophenyl acetate. It is specific for sugar-based substrates and will precipitate acetylxylan as a result of deacetylation. SlAXE also functions as a chitin and chitooligosaccharide de-N-acetylase with equal efficiency to its activity on xylan. SlAXE forms a dimer. Each monomer contains a catalytic NodB homology domain with the same overall topology and a deformed (beta/alpha)8 barrel fold as other CE4 esterases, which encompasses a mononuclear metalloenzyme employing a conserved His-His-Asp zinc-binding triad closely associated with the conserved catalytic base (aspartic acid) and acid (histidine), to carry out acid/base catalysis. SlAXE possess a single metal center with a chemical preference for Co2+. 179 matched cddid_all.tbl CDD cd10954 cd10954 200578 CE4_CtAXE_like Catalytic NodB homology domain of Clostridium thermocellum acetylxylan esterase and its bacterial homologs. This family is represented by Clostridium thermocellum acetylxylan esterase (CtAXE, EC 3.1.1.72), a member of the carbohydrate esterase 4 (CE4) superfamily. CtAXE deacetylates O-acetylated xylan, a key component of plant cell walls. It shows no detectable activity on generic esterase substrates including para-nitrophenyl acetate. It is specific for sugar-based substrates and will precipitate acetylxylan, as a consequence of deacetylation. CtAXE is a monomeric protein containing a catalytic NodB homology domain with the same overall topology and a deformed (beta/alpha)8 barrel fold as other CE4 esterases. However, due to differences in the topography of the substrate-binding groove, the chemistry of the active center, and metal ion coordination, CtAXE has different metal ion preference and lacks activity on N-acetyl substrates. It is significantly activated by Co2+. Moreover, CtAXE displays distinctly different ligand coordination to the metal ion, utilizing an aspartate, a histidine, and four water molecules, as opposed to the conserved His-His-Asp zinc-binding triad of other CE4 esterases. 180 matched cddid_all.tbl CDD cd10955 cd10955 200579 CE4_BH0857_like Putative catalytic NodB homology domain of uncharacterized BH0857 protein from Bacillus halodurans and its bacterial homologs. This family is represented by a putative polysaccharide deacetylase BH0857 from Bacillus halodurans. Although its biological function still remains unknown, BH0857 shows high sequence homology to the catalytic NodB homology domain of Streptococcus pneumoniae polysaccharide deacetylase PgdA (SpPgdA), which is an extracellular metal-dependent polysaccharide deacetylase with de-N-acetylase activity toward a hexamer of chitooligosaccharide N-acetylglucosamine, but not shorter chitooligosaccharides or a synthetic peptidoglycan tetrasaccharide. Both BH0857 and SpPgdA belong to the carbohydrate esterase 4 (CE4) superfamily. This family also includes many uncharacterized bacterial polysaccharide deacetylases. 195 matched cddid_all.tbl CDD cd10956 cd10956 200580 CE4_BH1302_like Putative catalytic NodB homology domain of uncharacterized BH1302 protein from Bacillus halodurans and its bacterial homologs. This family is represented by a putative polysaccharide deacetylase BH1302 from Bacillus halodurans. Although its biological function is unknown, BH1302 shows high sequence homology to the catalytic NodB homology domain of Streptococcus pneumoniae polysaccharide deacetylase PgdA (SpPgdA), which is an extracellular metal-dependent polysaccharide deacetylase with de-N-acetylase activity toward a hexamer of chitooligosaccharide N-acetylglucosamine, but not shorter chitooligosaccharides or a synthetic peptidoglycan tetrasaccharide. Both BH1302 and SpPgdA belong to the carbohydrate esterase 4 (CE4) superfamily. This family also includes many uncharacterized bacterial polysaccharide deacetylases. 194 matched cddid_all.tbl CDD cd10958 cd10958 200581 CE4_NodB_like_2 Catalytic NodB homology domain of uncharacterized chitin deacetylases and hypothetical proteins. This family includes some uncharacterized chitin deacetylases and hypothetical proteins, mainly from eukaryotes. Although their biological function is unknown, members in this family show high sequence homology to the catalytic NodB homology domain of Colletotrichum lindemuthianum chitin deacetylase (endo-chitin de-N-acetylase, ClCDA, EC 3.5.1.41), which catalyzes the hydrolysis of N-acetamido groups of N-acetyl-D-glucosamine residues in chitin, converting it to chitosan in fungal cell walls. Like ClCDA, this family is a member the carbohydrate esterase 4 (CE4) superfamily. 190 matched cddid_all.tbl CDD cd10959 cd10959 200582 CE4_NodB_like_3 Catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases. This family includes many uncharacterized bacterial polysaccharide deacetylases. Although their biological function still remains unknown, members in this family show high sequence homology to the catalytic NodB homology domain of Streptococcus pneumoniae polysaccharide deacetylase PgdA (SpPgdA), which is an extracellular metal-dependent polysaccharide deacetylase with de-N-acetylase activity toward a hexamer of chitooligosaccharide N-acetylglucosamine, but not shorter chitooligosaccharides or a synthetic peptidoglycan tetrasaccharide. Like SpPgdA, this family is a member of the carbohydrate esterase 4 (CE4) superfamily. 187 matched cddid_all.tbl CDD cd10960 cd10960 200583 CE4_NodB_like_1 Catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases. This family includes many uncharacterized bacterial polysaccharide deacetylases. Although their biological function still remains unknown, members in this family show high sequence homology to the catalytic NodB homology domain of Streptococcus pneumoniae polysaccharide deacetylase PgdA (SpPgdA), which is an extracellular metal-dependent polysaccharide deacetylase with de-N-acetylase activity toward a hexamer of chitooligosaccharide N-acetylglucosamine, but not shorter chitooligosaccharides or a synthetic peptidoglycan tetrasaccharide. Like SpPgdA, this family is a member of the carbohydrate esterase 4 (CE4) superfamily. 238 matched cddid_all.tbl CDD cd10962 cd10962 200584 CE4_GT2-like Catalytic NodB homology domain of uncharacterized bacterial glycosyl transferase, group 2-like family proteins. This family includes many uncharacterized bacterial proteins containing an N-terminal GH18 (glycosyl hydrolase, family 18) domain, a middle NodB-like homology domain, and a C-terminal GT2-like (glycosyl transferase group 2) domain. Although their biological function is unknown, members in this family contain a middle NodB homology domain that is similar to the catalytic domain of Streptococcus pneumoniae polysaccharide deacetylase PgdA (SpPgdA), an extracellular metal-dependent polysaccharide deacetylase with de-N-acetylase activity toward a hexamer of chitooligosaccharide N-acetylglucosamine, but not shorter chitooligosaccharides or a synthetic peptidoglycan tetrasaccharide. Like SpPgdA, this family is a member of the carbohydrate esterase 4 (CE4) superfamily. The presence of three domains suggests that members of this family may be multifunctional. 196 matched cddid_all.tbl CDD cd10963 cd10963 200585 CE4_RC0012_like Putative catalytic NodB homology domain of uncharacterized protein RC0012 from Rickettsia conorii and its bacterial homologs. This family contains an uncharacterized protein RC0012 from Rickettsia conorii and its bacterial homologs. Although their biochemical properties remain to be determined, members in this family seems to be composed of a seven-stranded barrel with detectable sequence similarity to the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups from cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily. 182 matched cddid_all.tbl CDD cd10964 cd10964 200586 CE4_PgaB_5s N-terminal putative catalytic polysaccharide deacetylase domain of bacterial poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, and similar proteins. This family is represented by an outer membrane lipoprotein, poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase (PgaB, EC 3.5.1.-), encoded by Escherichia coli pgaB gene from the pgaABCD (formerly ycdSRQP) operon, which affects biofilm development by promoting abiotic surface binding and intercellular adhesion. PgaB catalyzes the N-deacetylation of poly-beta-1,6-N-acetyl-D-glucosamine (PGA), a biofilm adhesin polysaccharide that stabilizes biofilms of E. coli and other bacteria. PgaB contains an N-terminal NodB homology domain with a 5-stranded beta/alpha barrel, and a C-terminal carbohydrate binding domain required for PGA N-deacetylation, which may be involved in binding to unmodified poly-beta-1,6-GlcNAc and assisting catalysis by the deacetylase domain. This family also includes several orthologs of PgaB, such as the hemin storage system HmsF protein, encoded by Yersinia pestis hmsF gene from the hmsHFRS operon, which is essential for Y. pestis biofilm formation. Like PgaB, HmsF is an outer membrane protein with an N-terminal NodB homology domain, which is likely involved in the modification of the exopolysaccharide (EPS) component of the biofilm. HmsF also has a conserved but uncharacterized C-terminal domain that is present in other HmsF-like proteins in Gram-negative bacteria. This alignment model corresponds to the N-terminal NodB homology domain. 193 matched cddid_all.tbl CDD cd10965 cd10965 200587 CE4_IcaB_5s Putative catalytic polysaccharide deacetylase domain of bacterial intercellular adhesion protein IcaB and similar proteins. The family is represented by the surface-attached protein intercellular adhesion protein IcaB (Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase, EC 3.5.1.-), encoded by Staphylococcus epidermidis icaB gene from the icaABC gene cluster that is involved in the synthesis of polysaccharide intercellular adhesin (PIA), which is located mainly on the cell surface. IcaB is a secreted, cell wall-associated protein that plays a crucial role in exopolysaccharide modification in bacterial biofilm formation. It catalyzes the N-deacetylation of poly-beta-1,6-N-acetyl-D-glucosamine (PNAG, also referred to as PIA), a biofilm adhesin polysaccharide. IcaB shows high homology to the N-terminal NodB homology domain of Escherichia coli PgaB. At this point, they are classified in the same family. 172 matched cddid_all.tbl CDD cd10966 cd10966 213024 CE4_yadE_5s Putative catalytic polysaccharide deacetylase domain of uncharacterized protein yadE and similar proteins. This family contains an uncharacterized protein yadE from Escherichia coli and its bacterial homologs. Although its molecular function remains unknown, yadE shows high sequence similarity with the catalytic NodB homology domain of outer membrane lipoprotein PgaB and the surface-attached protein intercellular adhesion protein IcaB. Both PgaB and IcaB are essential in bacterial biofilm formation. 164 matched cddid_all.tbl CDD cd10967 cd10967 200589 CE4_GLA_like_6s Putative catalytic NodB homology domain of gellan lyase and similar proteins. This family is represented by the extracellular polysaccharide-degrading enzyme, gellan lyase (gellanase, EC 4.2.2.-), from Bacillus sp. The enzyme acts on gellan exolytically and releases a tetrasaccharide of glucuronyl-glucosyl-rhamnosyl-glucose with unsaturated glucuronic acid at the nonreducing terminus. The family also includes many uncharacterized prokaryotic polysaccharide deacetylases, which show high sequence similarity to Bacillus sp. gellan lyase. Although their biological functions remain unknown, all members of the family contain a conserved domain with a 6-stranded beta/alpha barrel, which is similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, belonging to the larger carbohydrate esterase 4 (CE4) superfamily. 202 matched cddid_all.tbl CDD cd10968 cd10968 213025 CE4_Mlr8448_like_5s Putative catalytic NodB homology domain of Mesorhizobium loti Mlr8448 protein and its bacterial homologs. This family contains Mesorhizobium loti Mlr8448 protein and its bacterial homologs. Although their biochemical properties are yet to be determined, members in this subfamily contain a conserved domain with a 5-stranded beta/alpha barrel, which is similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, belonging to the larger carbohydrate esterase 4 (CE4) superfamily. 161 matched cddid_all.tbl CDD cd10969 cd10969 213026 CE4_Ecf1_like_5s Putative catalytic NodB homology domain of a hypothetical protein Ecf1 from Escherichia coli and similar proteins. This family contains a hypothetical protein Ecf1 from Escherichia coli and its prokaryotic homologs. Although their biochemical properties remain to be determined, members in this family contain a conserved domain with a 5-stranded beta/alpha barrel, which is similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, belonging to the larger carbohydrate esterase 4 (CE4) superfamily. 218 matched cddid_all.tbl CDD cd10970 cd10970 213027 CE4_DAC_u1_6s Putative catalytic NodB homology domain of uncharacterized prokaryotic polysaccharide deacetylases which consist of a 6-stranded beta/alpha barrel. This family contains uncharacterized prokaryotic polysaccharide deacetylases. Although their biological functions remain unknown, all members of the family contain a conserved domain with a 6-stranded beta/alpha barrel, which is similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, belonging to the larger carbohydrate esterase 4 (CE4) superfamily. 194 matched cddid_all.tbl CDD cd10971 cd10971 200593 CE4_DAC_u2_5s Putative catalytic NodB homology domain of uncharacterized prokaryotic polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel. This family contains many uncharacterized prokaryotic polysaccharide deacetylases. Although their biological functions remain unknown, all members of this family are predicted to contain a conserved domain with a 5-stranded beta/alpha barrel, which is similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, belonging to the larger carbohydrate esterase 4 (CE4) superfamily. 198 matched cddid_all.tbl CDD cd10972 cd10972 200594 CE4_DAC_u3_5s Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel. This family contains uncharacterized bacterial polysaccharide deacetylases. Although their biological functions remain unknown, all members of the family are predicted to contain a conserved domain with a 5-stranded beta/alpha barrel, which is similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, belonging to the larger carbohydrate esterase 4 (CE4) superfamily. 216 matched cddid_all.tbl CDD cd10973 cd10973 213028 CE4_DAC_u4_5s Putative catalytic NodB homology domain of uncharacterized bacterial polysaccharide deacetylases which consist of a 5-stranded beta/alpha barrel. This family contains many uncharacterized bacterial polysaccharide deacetylases. Although their biological functions remain unknown, all members of the family are predicted to contain a conserved domain with a 5-stranded beta/alpha barrel, which is similar to the catalytic NodB homology domain of rhizobial NodB-like proteins, belonging to the larger carbohydrate esterase 4 (CE4) superfamily. 157 matched cddid_all.tbl CDD cd10974 cd10974 200596 CE4_CDA_like_1 Putative catalytic domain of chitin deacetylase-like proteins with additional chitin-binding peritrophin-A domain (ChBD) and/or a low-density lipoprotein receptor class A domain (LDLa). Chitin deacetylases (CDAs, EC 3.5.1.41) are secreted metalloproteins belonging to a family of extracellular chitin-modifying enzymes that catalyze the N-deacetylation of chitin, a beta-1,4-linked N-acetylglucosamine polymer, to form chitosan, a polymer of beta-(1,4)-linked d-glucosamine residues. CDAs have been isolated and characterized from various bacterial and fungal species and belong to the larger carbohydrate esterase 4 (CE4) superfamily. This family includes many CDA-like proteins mainly from insects, which contain a putative CDA-like catalytic domain similar to the catalytic NodB homology domain of CE4 esterases. In addition to the CDA-like domain, family members contain two additional domains, a chitin-binding peritrophin-A domain (ChBD) and a low-density lipoprotein receptor class A domain (LDLa), or have the ChBD domain but do not have the LDLa domain. 269 matched cddid_all.tbl CDD cd10975 cd10975 200597 CE4_CDA_like_2 Putative catalytic domain of chitin deacetylase-like proteins. Chitin deacetylases (CDAs, EC 3.5.1.41) are secreted metalloproteins belonging to a family of extracellular chitin-modifying enzymes that catalyze the N-deacetylation of chitin, a beta-1,4-linked N-acetylglucosamine polymer, to form chitosan, a polymer of beta-(1,4)-linked d-glucosamine residues. CDAs have been isolated and characterized from various bacterial and fungal species and belong to the larger carbohydrate esterase 4 (CE4) superfamily. This family includes many midgut-specific CDA-like proteins mainly from insects, such as Tribolium castaneum CDAs (TcCDA6-9). These proteins contain a putative CDA-like catalytic domain similar to the catalytic NodB homology domain of CE4 esterases. In addition to the CDA-like domain, some family members have an additional chitin-binding peritrophin-A domain (ChBD). 268 matched cddid_all.tbl CDD cd10976 cd10976 200598 CE4_CDA_like_3 Putative catalytic domain of uncharacterized bacterial hypothetical proteins similar to insect chitin deacetylase-like proteins. The family includes many uncharacterized bacterial hypothetical proteins that show high sequence similarity to insect chitin deacetylase-like proteins. Chitin deacetylases (CDAs, EC 3.5.1.41) are secreted metalloproteins belonging to a family of extracellular chitin-modifying enzymes that catalyze the N-deacetylation of chitin, a beta-1,4-linked N-acetylglucosamine polymer, to form chitosan, a polymer of beta-(1,4)-linked d-glucosamine residues. 299 matched cddid_all.tbl CDD cd10977 cd10977 200599 CE4_PuuE_SpCDA1 Catalytic domain of bacterial PuuE allantoinases, Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and similar proteins. Allantoinase (EC 3.5.2.5) can hydrolyze allantoin((2,5-dioxoimidazolidin-4-yl)urea), one of the most important nitrogen carrier for some plants, soil animals, and microorganisms, to allantoate. DAL1 gene from Saccharomyces cerevisiae encodes an allantoinase. However, some organisms possess allantoinase activity but lack DAL1 allantoinase. In those organisms, a defective allantoinase gene, named puuE (purine utilization E), encodes an allantoinase that specifically catalyzes the hydrolysis of (S)-allantoin into allantoic acid. PuuE allantoinase is related to polysaccharide deacetylase (DCA), one member of the carbohydrate esterase 4 (CE4) superfamily, that removes N-linked or O-linked acetyl groups of cell wall polysaccharides, and lacks sequence similarity with the known DAL1 allantoinase that belongs to the amidohydrolase superfamily. PuuE allantoinase functions as a homotetramer. Its monomer is composed of a 7-stranded barrel with detectable sequence similarity to the 6-stranded barrel NodB homology domain of DCAs. It appears to be metal-independent and acts on a small substrate molecule, which is distinct from the common features of DCAs that are normally metal ion dependent and recognize multimeric substrates. This family also includes a chitin deacetylase 1 (SpCDA1) encoded by the Schizosaccharomyces pombe cda1 gene. Although the general function of chitin deacetylase (CDA) is the synthesis of chitosan from chitin, a polymer of N-acetyl glucosamine, to build up the proper ascospore wall, the actual function of SpCDA1 might involve allantoin hydrolysis. It is likely orthologous to PuuE allantoinase, whereas it is more distantly related to the CDAs found in other fungi, such as Saccharomyces cerevisiae and Mucor rouxii. Those CDAs are similar with rizobial NodB protein and are not included in this family. 273 matched cddid_all.tbl CDD cd10978 cd10978 200600 CE4_Sll1306_like Putative catalytic domain of Synechocystis sp. Sll1306 protein and other bacterial homologs. The family contains Synechocystis sp. Sll1306 protein and uncharacterized bacterial polysaccharide deacetylases. Although their biological function remains unknown, they show very high sequence homology to the catalytic domain of bacterial PuuE (purine utilization E) allantoinases. PuuE allantoinase specifically catalyzes the hydrolysis of (S)-allantoin into allantoic acid. It functions as a homotetramer. Its monomer is composed of a 7-stranded barrel with detectable sequence similarity to the 6-stranded barrel NodB homology domain of polysaccharide deacetylase-like proteins in the CE4 superfamily, which removes N-linked or O-linked acetyl groups from cell wall polysaccharides. PuuE allantoinase appears to be metal-independent and acts on a small substrate molecule, which is distinct from the common feature of polysaccharide deacetylases that are normally metal ion dependent and recognize multimeric substrates. 271 matched cddid_all.tbl CDD cd10979 cd10979 200601 CE4_PuuE_like Putative catalytic domain of uncharacterized prokaryotic polysaccharide deacetylases similar to bacterial PuuE allantoinases. The family includes a group of uncharacterized prokaryotic polysaccharide deacetylases (DCAs) that show high sequence similarity to the catalytic domain of bacterial PuuE (purine utilization E) allantoinases. PuuE allantoinase specifically catalyzes the hydrolysis of (S)-allantoin into allantoic acid. It functions as a homotetramer. Its monomer is composed of a 7-stranded barrel with detectable sequence similarity to the 6-stranded barrel NodB homology domain of DCA-like proteins in the CE4 superfamily, which removes N-linked or O-linked acetyl groups from cell wall polysaccharides. PuuE allantoinase appears to be metal-independent and acts on a small substrate molecule, which is distinct from the common feature of DCAs which are normally metal ion dependent and recognize multimeric substrates. 281 matched cddid_all.tbl CDD cd10980 cd10980 200602 CE4_SpCDA1 Putative catalytic domain of Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), and similar proteins. This family is represented by Schizosaccharomyces pombe chitin deacetylase 1 (SpCDA1), encoded by the cda1 gene. The general function of chitin deacetylase (CDA) is the synthesis of chitosan from chitin, a polymer of N-acetyl glucosamine, to build up the proper ascospore wall. The actual function of SpCDA1 might be involved in allantoin hydrolysis. It is likely an ortholog to bacterial PuuE allantoinase, whereas it is more distantly related to the CDAs found in other fungi, such as Saccharomyces cerevisiae and Mucor rouxii. Those CDAs are similar with rizobial NodB protein and are not included in this family. 297 matched cddid_all.tbl CDD cd10981 cd10981 211380 ZnPC_S1P1 Zinc dependent phospholipase C/S1-P1 nuclease. This model describes both the bacterial and archeal zinc-dependent phospholipase C, a domain found in the alpha toxin of Clostridium perfringens, as well as S1/P1 nucleases, which predominantly act on single-stranded DNA and RNA. 238 matched cddid_all.tbl CDD cd10985 cd10985 199826 MH2_SMAD_2_3 C-terminal Mad Homology 2 (MH2) domain in SMAD2 and SMAD3. The MH2 domain is located at the C-terminus of the SMAD (small mothers against decapentaplegic) family of proteins, which are signal transducers and transcriptional modulators that mediate multiple signaling pathways. The MH2 domain is responsible for type I receptor interaction, phosphorylation-triggered homo- and hetero-oligomerization, and transactivation. It is negatively regulated by the N-terminal MH1 domain. SMAD2 and SMAD3 are receptor regulated SMADs (R-SMADs). SMAD2 regulates multiple cellular processes, such as cell proliferation, apoptosis and differentiation, while SMAD3 modulates signals of activin and TGF-beta. 191 matched cddid_all.tbl CDD cd11005 cd11005 199911 M35_like Peptidase M35 family. Family M35 Zn2+-metallopeptidase domain, also known as the deuterolysin family, contains fungal as well as bacterial metalloendopeptidases that include deuterolysin (EC2.4.24.39), peptidyl-Lys metalloendopeptidase (MEP), penicillolysin, as well as uncharacterized sequences. Typically, members of this family of extracellular peptidases contain a unique zinc-binding motif (the aspzincin motif), defined by the HExxH + D motif where an aspartic acid is the third zinc ligand and is found in a GTXDXXYG motif C-terminal to the His zinc ligands. Deuterolysins are highly active towards basic nuclear proteins such as histones and protamines, with a preference for a Lys or Arg residue in the P1' subsite. MEPs specifically cleave peptidyl-lysine bonds (-X-Lys-) in proteins and peptides. Penicillolysin, a thermolabile protease from Penicillium citrinum, strongly hydrolyzes nuclear proteins such as clupeine, salmine and histone. Many members of the M35 peptidases display unusual thermostabilities. 167 matched cddid_all.tbl CDD cd11006 cd11006 199912 M35_peptidyl-Lys_like Peptidase M35 domain of peptidyl-Lys metalloendopeptidases and related proteins. This family M35 Zn2+-metallopeptidase extracellular domain is mostly found in proteins characterized as peptidyl-Lys metalloendopeptidases (MEP; peptidyllysine metalloproteinase; EC 3.4.24.20), including some well-characterized domains in Aeromonas salmonicida subsp. Achromogenes (AsaP1) and Grifola frondosa (GfMEP). These proteins specifically cleave peptidyl-lysine bonds (-X-Lys- where X may even be Pro) in proteins and peptides. AsaP1 peptidase has been shown to be important in the virulence of A. salmonicida subsp. achromogenes, having a major role in the fish innate immune response. Members of this family contain a unique zinc-binding motif (the aspzincin motif), defined by the HExxH + D motif where an aspartic acid is the third zinc ligand and is found in a GTXDXXYG or similar motif C-terminal to the His zinc ligands. 163 matched cddid_all.tbl CDD cd11007 cd11007 199913 M35_like_1 Peptidase M35-like domain of uncharacterized proteins. This family contains proteins similar to the M35 Zn2+-metallopeptidases, also known as the deuterolysin family, presumably these are bacterial metalloendopeptidases that have yet to be characterized. Typically, members of this family of extracellular peptidases contain a unique zinc-binding motif (the aspzincin motif), defined by the HExxH + D motif where an aspartic acid is the third zinc ligand; however, members of this family do not contain the GTXDXXYG motif C-terminal to the His zinc ligands that is typical for the M35 proteases. Deuterolysins are highly active towards basic nuclear proteins such as histones and protamines, with a preference for a Lys or Arg residue in the P1' subsite. MEPs specifically cleave peptidyl-lysine bonds (-X-Lys-) in proteins and peptides. Many members of the M35 peptidases display unusual thermostabilities. 183 matched cddid_all.tbl CDD cd11008 cd11008 199914 M35_deuterolysin_like Peptidase M35 domain of deuterolysins and related proteins. This family M35 Zn2+-metallopeptidase extracellular domain is found in fungal deutrolysins (acid metalloproteinase, neutral proteinase II), including some well-characterized metallopeptidase domains in Aspergillus oryzae (NpII), Aspergillus fumigatus (MEP20), Penicillium roqueforti (protease II) and Emericella nidulans (PepJ peptidase). The neutral proteinase II from Aspergillus oryzae (NpII) unfolds reversibly upon incubation at higher temperatures, and loss in activity is mainly due to autoproteolysis. MEP20 is encoded by the mepB gene, which appears to be associated with the cytoplasmic degradation of small peptides. PepJ peptidase is a thermostable enzyme released under carbon starvation. Most members of this family contain a unique zinc-binding motif (the aspzincin motif), defined by the HExxH + D motif where an aspartic acid is the third zinc ligand and is found in a GTXDXXYG or similar motif C-terminal to the His zinc ligands. The aspzincin motif is poorly conserved in one subgroup, that includes Asp f2, a major allergen from Aspergillus fumigatus. This subgroup in addition lacks the key conserved Tyr residue which acts as a proton donor during catalysis, and no protease activity has been detected to date for Asp f2. 167 matched cddid_all.tbl CDD cd11009 cd11009 211381 Zn_dep_PLPC Zinc dependent phospholipase C (alpha toxin). This domain conveys a zinc dependent phospholipase C activity (EC 3.1.4.3). It is found in a monomeric phospholipase C of Bacillus cereus as well as in the alpha toxin of Clostridium perfringens and Clostridium bifermentans, which is involved in haemolysis and cell rupture. It is also found in a lecithinase of Listeria monocytogenes, which is involved in breaking the 2-membrane vacuoles that surround the bacterium. 218 matched cddid_all.tbl CDD cd11010 cd11010 211382 S1-P1_nuclease S1/P1 nucleases and related enzymes. This family summarizes both S1 and P1 nucleases (EC:3.1.30.1) which cleave RNA and single stranded DNA with no base specificity. S1 nuclease is more active on DNA than RNA. Its reaction products are oligonucleotides or single nucleotides with 5' phosphoryl groups. Although its primary substrate is single-stranded, it may also introduce single-stranded breaks in double-stranded DNA or RNA, or DNA-RNA hybrids. It is used as a reagent in nuclease protection assays and in removing single stranded tails from DNA molecules to create blunt ended molecules and opening hairpin loops generated during synthesis of double stranded cDNA. P1 nuclease cleaves its substrate at every position yielding nucleoside 5' monophosphates, and it does not recognize or act on double-stranded DNA. It is useful at removing single stranded strands hanging off the end of double stranded DNA and at completely cleaving melted DNA for simple DNA composition analysis. 249 matched cddid_all.tbl CDD cd11012 cd11012 259898 CuRO_6_ceruloplasmin The sixth cupredoxin domain of Ceruloplasmin. Ceruloplasmin is a multicopper oxidase essential for normal iron homeostasis and copper transport in blood. It also functions in amine oxidation and as an antioxidant preventing free radicals in serum. The protein has 6 cupredoxin domains with six copper centers; three mononuclear sites in domain 2, 4 and 6 and three in the form of trinuclear clusters at the interface of domains 1 and 6. Ceruloplasmin exhibits internal sequence homology that appears to have evolved from the triplication of a sequence unit composed of two tandem cupredoxin domains. This model represents the sixth cupredoxin domain of ceruloplasmin. 145 matched cddid_all.tbl CDD cd11013 cd11013 259899 Plantacyanin Plantacyanin is a subclass of phytocyanins, plant type I copper proteins. Plantacyanins belong to the phytocyanin family of blue copper proteins, a ubiquitous family of plant cupredoxins. Plantacyanin is involved in electron transfer reactions with the Cu center transitioning between the oxidized Cu(II) form and the reduced Cu(I) form. The exact function of plantacyanin is unknown. However plantacyanin is shown to play a role in reproduction in Arabidopsis. Plantacyanins may also be stress-related proteins and be involved in plant defense responses. 95 matched cddid_all.tbl CDD cd11014 cd11014 259900 Mavicyanin Mavicyanin is a subclass of phytocyanins, a plant blue copper protein. Mavicyanin is a glycosylated protein isolated from Cucurbita pepo medullosa (zucchini) peelings. It belongs to the phytocyanin family of blue copper proteins, a ubiquitous family of plant cupredoxins. Mavicyanin is involved in electron transfer reactions with the Cu center transitioning between the oxidized Cu(II) form and the reduced Cu(I) form. The copper is tetrahedrally coordinated by a cysteine, 2 histidines, and a glutamine residue, like in the case of stellacyanin. The biological roles of mavicyanin have not been elucidated yet. 101 matched cddid_all.tbl CDD cd11015 cd11015 259901 CuRO_2_FVIII_like The second cupredoxin domain of coagulation factor VIII and similar proteins. Factor VIII functions in the factor X-activating complex of the intrinsic coagulation pathway. It facilitates blood clotting by acting as a cofactor for factor IXa. In the presence of Ca2+ and phospholipids, Factor VIII and IXa form a complex that converts factor X to the activated form Xa. A variety of mutations in the Factor VIII gene can cause hemophilia A, which typically requires replacement therapy with purified protein. Factor VIII is synthesized as a single polypeptide with six cupredoxin domains and a domain structure of 1-2-3-4-B-5-6-C1-C2, where 1-6 are cupredoxin domains, B is a domain with no known structural homologs and is dispensible for coagulant activity, and C are domains distantly related to discoidin protein-fold family members. Factor VIII is initially processed through proteolysis to generate a heterodimer consisting of a heavy chain (1-2-3-4) and a light chain (5-6-C1-C2), which circulates in a tight complex with von Willebrand factor (VWF). Further processing of the heavy chain produces activated factor VIIIa, a heterotrimer composed of polypeptides (1-2), (3-4), and the light chain. This model represents the cupredoxin domain 2 of unprocessed Factor VIII or the heavy chain of circulating Factor VIII, and similar proteins. 134 matched cddid_all.tbl CDD cd11016 cd11016 259902 CuRO_4_FVIII_like The fourth cupredoxin domain of coagulation factor VIII and similar proteins. Factor VIII functions in the factor X-activating complex of the intrinsic coagulation pathway. It facilitates blood clotting by acting as a cofactor for factor IXa. In the presence of Ca2+ and phospholipids, Factor VIII and IXa form a complex that converts factor X to the activated form Xa. A variety of mutations in the Factor VIII gene can cause hemophilia A, which typically requires replacement therapy with purified protein. Factor VIII is synthesized as a single polypeptide with six cupredoxin domains and a domain structure of 1-2-3-4-B-5-6-C1-C2, where 1-6 are cupredoxin domains, B is a domain with no known structural homologs and is dispensible for coagulant activity, and C are domains distantly related to discoidin protein-fold family members. Factor VIII is initially processed through proteolysis to generate a heterodimer consisting of a heavy chain (1-2-3-4) and a light chain (5-6-C1-C2), which circulates in a tight complex with von Willebrand factor (VWF). Further processing of the heavy chain produces activated factor VIIIa, a heterotrimer composed of polypeptides (1-2), (3-4), and the light chain. This model represents the cupredoxin domain 4 of unprocessed Factor VIII or the heavy chain of circulating Factor VIII, and similar proteins. 143 matched cddid_all.tbl CDD cd11017 cd11017 259903 Phytocyanin_like_1 A subclass of phytocyanins, plant blue or type I copper proteins. Phytocyanins are plant blue or type I copper proteins. They are involved in electron transfer reactions with the Cu center transitioning between the oxidized Cu(II) form and the reduced Cu(I) form. Phytocyanins are classified into four groups: stellacyanin, plantacyanin, uclacyanin and early nodulin groups. Members of this unknown subgroup appear to have lost the T1 copper binding site. 99 matched cddid_all.tbl CDD cd11018 cd11018 259904 CuRO_6_FVIII_like The sixth cupredoxin domain of coagulation factor VIII and similar proteins. Factor VIII functions in the factor X-activating complex of the intrinsic coagulation pathway. It facilitates blood clotting by acting as a cofactor for factor IXa. In the presence of Ca2+ and phospholipids, Factor VIII and IXa form a complex that converts factor X to the activated form Xa. A variety of mutations in the Factor VIII gene can cause hemophilia A, which typically requires replacement therapy with purified protein. Factor VIII is synthesized as a single polypeptide with six cupredoxin domains and a domain structure of 1-2-3-4-B-5-6-C1-C2, where 1-6 are cupredoxin domains, B is a domain with no known structural homologs and is dispensible for coagulant activity, and C are domains distantly related to discoidin protein-fold family members. Factor VIII is initially processed through proteolysis to generate a heterodimer consisting of a heavy chain (1-2-3-4) and a light chain (5-6-C1-C2), which circulates in a tight complex with von Willebrand factor (VWF). Further processing of the heavy chain produces activated factor VIIIa, a heterotrimer composed of polypeptides (1-2), (3-4), and the light chain. This model represents the cupredoxin domain 6 of unprocessed Factor VIII or the second cupredoxin domain the light chain of circulating Factor VIII, and similar proteins. 144 matched cddid_all.tbl CDD cd11019 cd11019 259905 OsENODL1_like Early nodulin-like protein (OsENODL1) and similar proteins. This family includes early nodulin-like protein (OsENODL1) from Oryza sativa and similar proteins. It belongs to the phytocyanin family of blue copper proteins, a ubiquitous family of plant cupredoxins. Phytocyanin is involved in electron transfer reactions with the Cu center transitioning between the oxidized Cu(II) form and the reduced Cu(I) form. OsENODL1 expression occurs specifically at the late developmental stage of the seeds. Members of this subgroup appear to have lost the T1 copper binding site. 103 matched cddid_all.tbl CDD cd11020 cd11020 259906 CuRO_1_CuNIR Cupredoxin domain 1 of Copper-containing nitrite reductase. Copper-containing nitrite reductase (CuNIR), which catalyzes the reduction of NO2- to NO, is the key enzyme in the denitrification process in denitrifying bacteria. CuNIR contains at least one type 1 copper center and a type 2 copper center, which serves as the active site of the enzyme. A histidine, bound to the Type 2 Cu center, is responsible for binding and reducing nitrite. A Cys-His bridge plays an important role in facilitating rapid electron transfer from the type 1 center to the type 2 center. A reduced type I blue copper protein (pseudoazurin) was found to be a specific electron transfer donor for the copper-containing NIR in bacteria Alcaligenes faecalis. 119 matched cddid_all.tbl CDD cd11021 cd11021 259907 CuRO_2_ceruloplasmin The second cupredoxin domain of Ceruloplasmin. Ceruloplasmin is a multicopper oxidase essential for normal iron homeostasis and copper transport in blood. It also functions in amine oxidation and as an antioxidant preventing free radicals in serum. The protein has 6 cupredoxin domains with six copper centers; three mononuclear sites in domain 2, 4 and 6 and three in the form of trinuclear clusters at the interface of domains 1 and 6. Ceruloplasmin exhibits internal sequence homology that appears to have evolved from the triplication of a sequence unit composed of two tandem cupredoxin domains. This model represents the second cupredoxin domain of ceruloplasmin. 141 matched cddid_all.tbl CDD cd11022 cd11022 259908 CuRO_4_ceruloplasmin The fourth cupredoxin domain of Ceruloplasmin. Ceruloplasmin is a multicopper oxidase essential for normal iron homeostasis and copper transport in blood. It also functions in amine oxidation and as an antioxidant preventing free radicals in serum. The protein has 6 cupredoxin domains with six copper centers; three mononuclear sites in domain 2, 4 and 6 and three in the form of trinuclear clusters at the interface of domains 1 and 6. Ceruloplasmin exhibits internal sequence homology that appears to have evolved from the triplication of a sequence unit composed of two tandem cupredoxin domains. This model represents the fourth cupredoxin domain of ceruloplasmin. 144 matched cddid_all.tbl CDD cd11023 cd11023 259909 CuRO_2_ceruloplasmin_like_2 cupredoxin domain of ceruloplasmin homologs. Uncharacterized subfamily of ceruloplasmin homologous proteins. Ceruloplasmin (ferroxidase) is a multicopper oxidase essential for normal iron homeostasis. Ceruloplasmin also functions in copper transport, amine oxidase and as an antioxidant preventing free radicals in serum. The protein has 6 cupredoxin domains and exhibits internal sequence homology that appears to have evolved from the triplication of a sequence unit composed of two tandem cupredoxin domains. This model represents the first domain of the triplicated units. 118 matched cddid_all.tbl CDD cd11024 cd11024 259910 CuRO_1_2DMCO_NIR_like The cupredoxin domain 1 of a two-domain laccase related to nitrite reductase. The two-domain laccase (small laccase) in this family differs significantly from all laccases. It resembles the two domain nitrite reductase in both sequence and structure. It consists of two cupredoxin domains and forms trimers and hence resembles the quaternary structure of nitrite reductases more than that of large laccases. There are three trinuclear copper clusters in the enzyme localized between domains 1 and 2 of each pair of neighbor chains. Three copper ions of type 1 lie close to one another near the surface of the central part of the trimer, and, effectively, a trimeric substrate binding site is formed in their vicinity. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety of organic substrates coupled to the reduction of molecular oxygen to water. It displays broad substrate specificity, catalyzing the oxidation of a wide variety of aromatic, notably phenolic, and inorganic substances. Laccase has been implicated in a wide spectrum of biological activities. 119 matched cddid_all.tbl CDD cd11026 cd11026 410652 CYP2 cytochrome P450 family 2. The cytochrome P450 family 2 (CYP2 or Cyp2) is one of the largest, most diverse CYP families in vertebrates. It includes many subfamilies across vertebrate species but not all subfamilies are found in multiple vertebrate taxonomic classes. The CYP2U and CYP2R genes are present in the vertebrate ancestor and are shared across all vertebrate classes, whereas some subfamilies are lineage-specific, such as CYP2B and CYP2S in mammals. CYP2 enzymes play important roles in drug metabolism. The CYP2 family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 425 matched cddid_all.tbl CDD cd11027 cd11027 410653 CYP17A1-like cytochrome P450 family 17, subfamily A, polypeptide 1, and similar cytochrome P450s. This subfamily contains cytochrome P450 17A1 (CYP17A1 or Cyp17a1), cytochrome P450 21 (CYP21 or Cyp21) and similar proteins. CYP17A1, also called cytochrome P450c17, steroid 17-alpha-hydroxylase (EC 1.14.14.19)/17,20 lyase (EC 1.14.14.32), or 17-alpha-hydroxyprogesterone aldolase, catalyzes the conversion of pregnenolone and progesterone to their 17-alpha-hydroxylated products and subsequently to dehydroepiandrosterone (DHEA) and androstenedione; it catalyzes both the 17-alpha-hydroxylation and the 17,20-lyase reaction. This subfamily also contains CYP21, also called steroid 21-hydroxylase (EC 1.14.14.16) or cytochrome P-450c21 or CYP21A2, catalyzes the 21-hydroxylation of steroids and is required for the adrenal synthesis of mineralocorticoids and glucocorticoids. The CYP17A1-like subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 428 matched cddid_all.tbl CDD cd11028 cd11028 410654 CYP1 cytochrome P450 family 1. The cytochrome P450 family 1 (CYP1 or Cyp1) is composed of three functional human members: CYP1A1, CYP1A2 and CYP1B1, which are regulated by the aryl hydrocarbon receptor (AhR), ligand-activated transcriptional factor that dimerizes with AhR nuclear translocator (ARNT). CYP1 enzymes are involved in the metabolism of endogenous hormones, xenobiotics, and drugs. Included in the CYP1 family is CYP1D1 (cytochrome P450 family 1, subfamily D, polypeptide 1), which is not expressed in humans as its gene is pseudogenized due to five nonsense mutations in the putative coding region, but is functional in in other organisms including cynomolgus monkey. Zebrafish CYP1D1 expression is not regulated by AhR. The CYP1 family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 430 matched cddid_all.tbl CDD cd11029 cd11029 410655 CYP107-like cytochrome P450 family 107 and similar cytochrome P450s. This group contains bacterial cytochrome P450s from families 107 (CYP107), 154 (CYP154), 197 (CYP197), and similar proteins. Among the members of this group are: Pseudonocardia autotrophica vitamin D(3) 25-hydroxylase (also known as CYP197A; EC 1.14.15.15) that catalyzes the hydroxylation of vitamin D(3) into 25-hydroxyvitamin D(3) and 1-alpha,25-dihydroxyvitamin D(3), its physiologically active forms; Saccharopolyspora erythraea CYP107A1, also called P450eryF or 6-deoxyerythronolide B hydroxylase (EC 1.14.15.35), that catalyzes the conversion of 6-deoxyerythronolide B (6-DEB) to erythronolide B (EB) by the insertion of an oxygen at the 6S position of 6-DEB; Bacillus megaterium CYP107DY1 that displays C6-hydroxylation activity towards mevastatin to produce pravastatin; Streptomyces coelicolor CYP154C1 that shows activity towards 12- and 14-membered ring macrolactones in vitro and may be involved in catalyzing the site-specific oxidation of the precursors to macrolide antibiotics, which introduces regiochemical diversity into the macrolide ring system; and Nocardia farcinica CYP154C5 that acts on steroids with regioselectivity and stereoselectivity, converting various pregnans and androstans to yield 16 alpha-hydroxylated steroid products. Bacillus subtilis CYP107H1 is not included in this group. The CYP107-like group belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 384 matched cddid_all.tbl CDD cd11030 cd11030 410656 CYP105-like cytochrome P450 family 105 and similar cytochrome P450s. This group predominantly contains bacterial cytochrome P450s, including those belonging to families 105 (CYP105) and 165 (CYP165). Also included in this group are fungal family 55 proteins (CYP55). CYP105s are predominantly found in bacteria belonging to the phylum Actinobacteria and the order Actinomycetales, and are associated with a wide variety of pathways and processes, from steroid biotransformation to production of macrolide metabolites. CYP105A1 catalyzes two sequential hydroxylations of vitamin D3 with differing specificity and cytochrome P450-SOY (also known as CYP105D1) has been shown to be capable of both oxidation and dealkylation reactions. CYP105D6 and CYP105P1, from the filipin biosynthetic pathway, perform highly regio- and stereospecific hydroxylations. Other members of this group include, but are not limited to: CYP165D3 (also called OxyE) from the teicoplanin biosynthetic gene cluster of Actinoplanes teichomyceticus, which is responsible for the phenolic coupling of the aromatic side chains of the first and third peptide residues in the teicoplanin peptide; Micromonospora griseorubida cytochrome P450 MycCI that catalyzes hydroxylation at the C21 methyl group of mycinamicin VIII, the earliest macrolide form in the postpolyketide synthase tailoring pathway; and Fusarium oxysporum CYP55A1 (also called nitric oxide reductase cytochrome P450nor) that catalyzes an unusual reaction, the direct electron transfer from NAD(P)H to bound heme. The CYP105-like group belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 381 matched cddid_all.tbl CDD cd11031 cd11031 410657 Cyp158A-like cytochrome P450 family 158, subfamily A and similar cytochrome P450s. This family is composed of cytochrome P450s (CYPs) with similarity to Streptomyces coelicolor CYP158A1 and CYP158A2, Streptomyces natalensis PimD (also known as CYP107E), Mycobacterium tuberculosis CYP121, and Micromonospora griseorubida MycG (also known as CYP107B). CYP158A1 and CYP158A2 catalyze an unusual oxidative C-C coupling reaction to polymerize flaviolin and form highly conjugated pigments; CYP158A2 produces three isomers of biflaviolin and one triflaviolin while CYP158A1 produces only two isomers of biflaviolin. PimD is a cytochrome P450 monooxygenase with native epoxidase activity that is critical in the biosynthesis of the polyene macrolide antibiotic pimaricin. CYP121 is essential for the viability of M. tuberculosis and is a novel drug target for the inhibition of mycobacterial growth. MycG catalyzes both hydroxylation and epoxidation reactions in the biosynthesis of the 16-membered ring macrolide antibiotic mycinamicin II. This family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 380 matched cddid_all.tbl CDD cd11032 cd11032 410658 P450_EryK-like cytochrome P450 EryK and similar cytochrome P450s. This subfamily contains archaeal and bacterial CYPs including Saccharopolyspora erythraea P450 EryK, Saccharolobus solfataricus cytochrome P450 119 (CYP119), Picrophilus torridus CYP231A2, Bacillus subtilis CYP109, Streptomyces himastatinicus HmtT and HmtN, and Bacillus megaterium CYP106A2, among others. EryK, also called erythromycin C-12 hydroxylase, is active during the final steps of erythromycin A (ErA) biosynthesis. CYP106A2 catalyzes the hydroxylation of a variety of 3-oxo-delta(4)-steroids such as progesterone and deoxycorticosterone, mainly in the 15beta-position. It is also capable of hydroxylating a variety of terpenoids. HmtT and HmtN is involved in the post-tailoring of the cyclohexadepsipeptide backbone during the biosynthesis of the himastatin antibiotic. The EryK-like subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 368 matched cddid_all.tbl CDD cd11033 cd11033 410659 CYP142-like cytochrome P450 family 142 and similar cytochrome P450s. This family is composed of cytochrome P450s (CYPs) with similarity to Streptomyces sp. P450sky (also called CYP163B3), Sphingopyxis macrogoltabida P450pyr hydroxylase, Novosphingobium aromaticivorans CYP108D1, Pseudomonas sp. cytochrome P450-Terp (P450terp), and Amycolatopsis balhimycina P450 OxyD, as well as several Mycobacterium proteins CYP124, CYP125, CYP126, and CYP142. P450sky is involved in the hydroxylation of three beta-hydroxylated amino acid precursors required for the biosynthesis of the cyclic depsipeptide skyllamycin. P450pyr hydroxylase is an active and selective catalyst for the regio- and stereo-selective hydroxylation at non-activated carbon atoms with a broad substrate range. P450terp catalyzes the hydroxylation of alpha-terpineol as part of its catabolic assimilation. OxyD is involved in beta-hydroxytyrosine formation during vancomycin biosynthesis. CYP124 is a methyl-branched lipid omega-hydroxylase while CYP142 is a cholesterol 27-oxidase with likely roles in host response modulation and cholesterol metabolism. This family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 378 matched cddid_all.tbl CDD cd11034 cd11034 410660 P450cin-like P450cin and similar cytochrome P450s. This group is composed of Citrobacter braakii cytochrome P450cin (P450cin, also called CYP176A1) and similar proteins. P450cin is a bacterial P450 enzyme that catalyzes the enantiospecific hydroxylation of 1,8-cineole to (1R)-6beta-hydroxycineole; its natural reduction-oxidation partner is cindoxin. This family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 361 matched cddid_all.tbl CDD cd11035 cd11035 410661 P450cam-like P450cam and similar cytochrome P450s. This family is composed of cytochrome P450s (CYPs) with similarity to Pseudomonas putida P450cam and Cyp101 proteins from Novosphingobium aromaticivorans such as CYP101C1 and CYP101D2. P450cam catalyzes the hydroxylation of camphor in a process that involves two electron transfers from the iron-sulfur protein, putidaredoxin. CYP101D2 is capable of oxidizing camphor while CYP101C1 does not bind camphor but is capable of binding and hydroxylating ionone derivatives such as alpha- and beta-ionone and beta-damascone. This family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 359 matched cddid_all.tbl CDD cd11036 cd11036 410662 AknT-like AknT-like proteins. This family is composed of proteins similar to Streptomyces biosynthesis proteins including anthracycline biosynthesis proteins DnrQ and AknT, and macrolide antibiotic biosynthesis proteins TylM3 and DesVIII. Streptomyces peucetius DnrQ is involved in the biosynthesis of carminomycin and daunorubicin (daunomycin) while Streptomyces galilaeus AknT functions in the biosynthesis of aclacinomycin A. Streptomyces fradiae TylM3 is involved in the biosynthesis of tylosin derived from the polyketide lactone tylactone, and Streptomyces venezuelae functions in the biosynthesis of methymycin, neomethymycin, narbomycin, and pikromycin. These proteins are required for the glycosylation of specific substrates during the biosynthesis of specific anthracyclines and macrolide antibiotics. Although members of this family belong to the large cytochrome P450 (P450, CYP) superfamily and show significant similarity to cytochrome P450s, they lack heme-binding sites and are not functional cytochromes. 340 matched cddid_all.tbl CDD cd11037 cd11037 410663 CYP199A2-like cytochrome P450 family 199, subfamily A, polypeptide 2 and similar cytochrome P450s. This family is composed of cytochrome P450s (CYPs) with similarity to Rhodopseudomonas palustris CYP199A2 and CYP199A4. CYP199A2 catalyzes the oxidation of aromatic carboxylic acids including indole-2-carboxylic acid, 2-naphthoic acid and 4-ethylbenzoic acid. CYP199A4 catalyzes the hydroxylation of para-substituted benzoic acids. This family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 371 matched cddid_all.tbl CDD cd11038 cd11038 410664 CYP_AurH-like cytochrome P450 AurH and similar cytochrome P450s. This group includes Streptomyces thioluteus P450 monooxygenase AurH which is uniquely capable of forming a homochiral tetrahydrofuran ring, a vital component of the polyketide antibiotic aureothin. AurH catalyzes an unprecedented tandem oxygenation process: first, it catalyzes an asymmetric hydroxylation of deoxyaureothin to yield (7R)-7-hydroxydeoxyaureothin as an intermediate; and second, it mediates another C-O bond formation that leads to O-heterocyclization. The AurH-like subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 382 matched cddid_all.tbl CDD cd11039 cd11039 410665 P450-pinF2-like P450-pinF2 and similar cytochrome P450s. This family is composed of cytochrome P450s (CYPs) with similarity to Agrobacterium tumefaciens P450-pinF2, whose expression is induced by the presence of wounded plant tissue and by plant phenolic compounds such as acetosyringone. P450-pinF2 may be involved in the detoxification of plant protective agents at the site of wounding. This family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 372 matched cddid_all.tbl CDD cd11040 cd11040 410666 CYP7_CYP8-like cytochrome P450s similar to cytochrome P450 family 7, subfamily A, polypeptide 1, cytochrome P450 family 7, subfamily B, polypeptide 1, cytochrome P450 family 8, subfamily A, polypeptide 1. This family is composed of cytochrome P450s (CYPs) with similarity to the human P450s CYP7A1, CYP7B1, CYP8B1, CYP39A1 and prostacyclin synthase (CYP8A1). CYP7A1, CYP7B1, CYP8B1, and CYP39A1 are involved in the catabolism of cholesterol to bile acids (BAs) in two major pathways. CYP7A1 (cholesterol 7alpha-hydroxylase) and CYP8B1 (sterol 12-alpha-hydroxylase) function in the classic (or neutral) pathway, which leads to two bile acids: cholic acid (CA) and chenodeoxycholic acid (CDCA). CYP7B1 and CYP39A1 are 7-alpha-hydroxylases involved in the alternative (or acidic) pathway, which leads mainly to the formation of CDCA. Prostacyclin synthase (CYP8A1) catalyzes the isomerization of prostaglandin H2 to prostacyclin (or prostaglandin I2), a potent mediator of vasodilation and anti-platelet aggregation. This family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 432 matched cddid_all.tbl CDD cd11041 cd11041 410667 CYP503A1-like cytochrome P450 family 503, subfamily A, polypeptide 1 and similar cytochrome P450s. This family is composed of predominantly fungal cytochrome P450s (CYPs) with similarity to Fusarium fujikuroi Cytochrome P450 503A1 (CYP503A1, also called ent-kaurene oxidase or cytochrome P450-4), Aspergillus nidulans austinol synthesis protein I (ausI), Alternaria alternata tentoxin synthesis protein 1 (TES1), and Acanthamoeba polyphaga mimivirus cytochrome P450 51 (CYP51, also called P450-LIA1 or sterol 14-alpha demethylase). Ent-kaurene oxidase catalyzes three successive oxidations of the 4-methyl group of ent-kaurene to form kaurenoic acid, an intermediate in gibberellin biosynthesis. AusI and TES1 are cytochrome P450 monooxygenases that mediate the biosynthesis of the meroterpenoids, austinol and dehydroaustinol, and the phytotoxin tentoxin, respectively. P450-LIA1 catalyzes the 14-alpha demethylation of obtusifoliol and functions in steroid biosynthesis. This family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 441 matched cddid_all.tbl CDD cd11042 cd11042 410668 CYP51-like cytochrome P450 family 51 and similar cytochrome P450s. This family is composed of cytochrome P450 51 (CYP51 or sterol 14alpha-demethylase) and related cytochrome P450s. CYP51 is the only cytochrome P450 enzyme with a conserved function across animals, fungi, and plants, in the synthesis of essential sterols. In mammals, it is expressed in many different tissues, with highest expression in testis, ovary, adrenal gland, prostate, liver, kidney, and lung. In fungi, CYP51 is a significant drug target for treatment of human protozoan infections. In plants, it functions within a specialized defense-related metabolic pathway. CYP51 is also found in several bacterial species. This family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 416 matched cddid_all.tbl CDD cd11043 cd11043 410669 CYP90-like plant cytochrome P450s similar to cytochrome P450 family 90, subfamily A, polypeptide 1, cytochrome P450 family 90, subfamily B, polypeptide 1, and cytochrome P450 family 90, subfamily D, polypeptide 2. This family is composed of plant cytochrome P450s including: Arabidopsis thaliana cytochrome P450s 85A1 (CYP85A1 or brassinosteroid-6-oxidase 1), 90A1 (CYP90A1), 88A3 (CYP88A3 or ent-kaurenoic acid oxidase 1), 90B1 (CYP90B1 or Dwarf4 or steroid 22-alpha-hydroxylase), and 90C1 (CYP90C1 or 3-epi-6-deoxocathasterone 23-monooxygenase); Oryza sativa cytochrome P450s 90D2 (CYP90D2 or C6-oxidase), 87A3 (CYP87A3), and 724B1 (CYP724B1 or dwarf protein 11); and Taxus cuspidata cytochrome P450 725A2 (CYP725A2 or taxane 13-alpha-hydroxylase). These enzymes are monooxygenases that catalyze oxidation reactions involved in steroid or hormone biosynthesis. CYP85A1, CYP90D2, and CYP90C1 are involved in brassinosteroids biosynthesis, while CYP88A3 catalyzes three successive oxidations of ent-kaurenoic acid, which is a key step in the synthesis of gibberellins. This family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 408 matched cddid_all.tbl CDD cd11044 cd11044 410670 CYP120A1_CYP26-like cyanobacterial cytochrome P450 family 120, subfamily A, polypeptide 1 (CYP120A1), vertebrate cytochrome P450 family 26 enzymes, and similar cytochrome P450s. This family includes cyanobacterial CYP120A1 and vertebrate cytochrome P450s 26A1 (CYP26A1), 26B1 (CYP26B1), and 26C1 (CYP26C1). These are retinoic acid-metabolizing cytochromes that play key roles in retinoic acid (RA) metabolism. Human and zebrafish CYP26a1, as well as Synechocystis CYP120A1 are characterized as RA hydroxylases. RA is a critical signaling molecule that regulates gene transcription and the cell cycle. This family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 420 matched cddid_all.tbl CDD cd11045 cd11045 410671 CYP136-like putative cytochrome P450 family 136 and similar cytochrome P450s. This group is composed of Mycobacterium tuberculosis putative cytochrome P450 136 (CYP136) and similar proteins. It belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 407 matched cddid_all.tbl CDD cd11046 cd11046 410672 CYP97 cytochrome P450 family/clan 97. CYPs have been classified into families and subfamilies based on homology and phylogenetic criteria; family membership is defined as 40% amino acid sequence identity or higher. The plant CYPs have also been classified according to clans; land plants have 11 clans that form two groups: single-family clans (CYP51, CYP74, CYP97, CYP710, CYP711, CYP727, CYP746) and multi-family clans (CYP71, CYP72, CYP85, CYP86). Members of the CYP97 clan include Arabidopsis thaliana cytochrome P450s 97A3 (CYP97A3), CYP97B3, and CYP97C1. CYP97A3 is also called protein LUTEIN DEFICIENT 5 (LUT5) and CYP97C1 is also called carotene epsilon-monooxygenase or protein LUTEIN DEFICIENT 1 (LUT1). These cytochromes function as beta- and epsilon-ring carotenoid hydroxylases and are involved in the biosynthesis of xanthophylls. CYP97 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 441 matched cddid_all.tbl CDD cd11049 cd11049 410673 CYP170A1-like cytochrome P450 family 170, subfamily A, polypeptide 1-like actinobacterial cytochrome P450s. This subfamily is composed of Streptomyces coelicolor cytochrome P450 170A1 (CYP170A1), Streptomyces avermitilis pentalenene oxygenase, and similar actinobacterial cytochrome P450s. CYP170A1, also called epi-isozizaene 5-monooxygenase (EC 1.14.13.106)/(E)-beta-farnesene synthase (EC 4.2.3.47), catalyzes the two-step allylic oxidation of epi-isozizaene to albaflavenone, which is a sesquiterpenoid antibiotic. Pentalenene oxygenase (EC 1.14.15.32) catalyzes the conversion of pentalenene to pentalen-13-al by stepwise oxidation via pentalen-13-ol, a precursor of the neopentalenolactone antibiotic. The CYP170A1-like subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 415 matched cddid_all.tbl CDD cd11051 cd11051 410674 CYP59-like cytochrome P450 family 59 and similar cytochrome P450s. This family is composed of Aspergillus nidulans cytochrome P450 59 (CYP59), also called sterigmatocystin biosynthesis P450 monooxygenase stcS, and similar fungal proteins. CYP59 is required for the conversion of versicolorin A to sterigmatocystin. This family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 403 matched cddid_all.tbl CDD cd11052 cd11052 410675 CYP72_clan Plant cytochrome P450s, clan CYP72. CYPs have been classified into families and subfamilies based on homology and phylogenetic criteria; family membership is defined as 40% amino acid sequence identity or higher. The plant CYPs have also been classified according to clans; land plants have 11 clans that form two groups: single-family clans (CYP51, CYP74, CYP97, CYP710, CYP711, CYP727, CYP746) and multi-family clans (CYP71, CYP72, CYP85, CYP86). The CYP72 clan is associated with the metabolism of a diversity of fairly hydrophobic compounds including fatty acids and isoprenoids, with the catabolism of hormones (brassinosteroids and gibberellin, GA) and with the biosynthesis of cytokinins. This clan includes: CYP734 enzymes that are involved in brassinosteroid (BRs) catabolism and regulation of BRs homeostasis; CYP714 enzymes that are involved in the biosynthesis of gibberellins (GAs) and the mechanism to control their bioactive endogenous levels; and CYP72 family enzymes, among others. The CYP72 clan belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 427 matched cddid_all.tbl CDD cd11053 cd11053 410676 CYP110-like cytochrome P450 family 110 and similar cytochrome P450s. This group is composed of mostly uncharacterized proteins, including Nostoc sp. probable cytochrome P450 110 (CYP110) and putative cytochrome P450s 139 (CYP139), 138 (CYP138), and 135B1 (CYP135B1) from Mycobacterium bovis. CYP110 genes, unique to cyanobacteria, are widely distributed in heterocyst-forming cyanobacteria including nitrogen-fixing genera Nostoc and Anabaena. This family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 415 matched cddid_all.tbl CDD cd11054 cd11054 410677 CYP24A1-like cytochrome P450 family 24 subfamily A, polypeptide 1 and similar cytochrome P450s. This family is composed of vertebrate cytochrome P450 24A1 (CYP24A1) and similar proteins including several Drosophila proteins such as CYP315A1 (also called protein shadow) and CYP314A1 (also called ecdysone 20-monooxygenase), and vertebrate CYP11 and CYP27 subfamilies. Both CYP314A1 and CYP315A1, which has ecdysteroid C2-hydroxylase activity, are involved in the metabolism of insect hormones. CYP24A1 and CYP27B1 have roles in calcium homeostasis and metabolism, and the regulation of vitamin D. CYP24A1 catabolizes calcitriol (1,25(OH)2D), the physiologically active vitamin D hormone, by catalyzing its hydroxylation, while CYP27B1 is a calcidiol 1-monooxygenase that coverts 25-hydroxyvitamin D3 to calcitriol. The CYP24A1-like family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 426 matched cddid_all.tbl CDD cd11055 cd11055 410678 CYP3A-like cytochrome P450 family 3, subfamily A and similar cytochrome P450s. This family includes vertebrate CYP3A subfamily enzymes and CYP5a1, and similar proteins. CYP5A1, also called thromboxane-A synthase, converts prostaglandin H2 into thromboxane A2, a biologically active metabolite of arachidonic acid. CYP3A enzymes are drug-metabolizing enzymes embedded in the endoplasmic reticulum, where they can catalyze a wide variety of biochemical reactions including hydroxylation, N-demethylation, O-dealkylation, S-oxidation, deamination, or epoxidation of substrates. The CYP3A-like family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 422 matched cddid_all.tbl CDD cd11056 cd11056 410679 CYP6-like cytochrome P450 family 6 and similar cytochrome P450s. This family is composed of cytochrome P450s from insects and crustaceans, including the CYP6, CYP9 and CYP310 subfamilies, which are involved in the metabolism of insect hormones and xenobiotic detoxification. The CYP6-like family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 429 matched cddid_all.tbl CDD cd11057 cd11057 410680 CYP313-like cytochrome P450 family 313 and similar cytochrome P450s. This subfamily is composed of insect cytochrome P450s from families 313 (CYP313) and 318 (CYP318), and similar proteins. These proteins may be involved in the metabolism of insect hormones and in the breakdown of synthetic insecticides. Their specific function is yet unknown. They belong to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 427 matched cddid_all.tbl CDD cd11058 cd11058 410681 CYP60B-like cytochrome P450 family 60, subfamily B and similar cytochrome P450s. This family is composed of fungal cytochrome P450s including: Aspergillus nidulans cytochrome P450 60B (CYP60B), also called versicolorin B desaturase, which catalyzes the conversion of versicolorin B to versicolorin A during sterigmatocystin biosynthesis; Fusarium sporotrichioides cytochrome P450 65A1 (CYP65A1), also called isotrichodermin C-15 hydroxylase, which catalyzes the hydroxylation at C-15 of isotricodermin in trichothecene biosynthesis; and Penicillium aethiopicum P450 monooxygenase vrtK, also called viridicatumtoxin synthesis protein K, which catalyzes the spirocyclization of the geranyl moiety of previridicatumtoxin to produce viridicatumtoxin, a tetracycline-like fungal meroterpenoid. The CYP60B-like family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 419 matched cddid_all.tbl CDD cd11059 cd11059 410682 CYP_fungal unknown subfamily of fungal cytochrome P450s. This subfamily is composed of uncharacterized fungal cytochrome P450s. Cytochrome P450 (P450, CYP) is a large superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. Their monooxygenase activity relies on the reductive scission of molecular oxygen bound to the P450 heme iron, and the delivery of two electrons to the heme iron during the catalytic cycle. 422 matched cddid_all.tbl CDD cd11060 cd11060 410683 CYP57A1-like cytochrome P450 family 57, subfamily A, polypeptide 1 and similar cytochrome P450s. This family is composed of fungal cytochrome P450s including: Nectria haematococca cytochrome P450 57A1 (CYP57A1), also called pisatin demethylase, which detoxifies the phytoalexin pisatin; Penicillium aethiopicum P450 monooxygenase gsfF, also called griseofulvin synthesis protein F, which catalyzes the coupling of orcinol and phloroglucinol rings in griseophenone B to form desmethyl-dehydrogriseofulvin A during the biosynthesis of griseofulvin, a spirocyclic fungal natural product used to treat dermatophyte infections; and Penicillium aethiopicum P450 monooxygenase vrtE, also called viridicatumtoxin synthesis protein E, which catalyzes hydroxylation at C5 of the polyketide backbone during the biosynthesis of viridicatumtoxin, a tetracycline-like fungal meroterpenoid. The CYP57A1-like family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 425 matched cddid_all.tbl CDD cd11061 cd11061 410684 CYP67-like cytochrome P450 family 67 and similar cytochrome P450s. This subfamily includes Uromyces viciae-fabae cytochrome P450 67 (CYP67), also called planta-induced rust protein 16, Cystobasidium minutum (Rhodotorula minuta) cytochrome P450rm, and other fungal cytochrome P450s. P450rm catalyzes the formation of isobutene and 4-hydroxylation of benzoate. The gene encoding CYP67 is a planta-induced gene that is expressed in haustoria and rust-infected leaves. The CYP67-like subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 418 matched cddid_all.tbl CDD cd11062 cd11062 410685 CYP58-like cytochrome P450 family 58-like fungal cytochrome P450s. This group includes Fusarium sporotrichioides cytochrome P450 58 (CYP58, also known as Tri4 and trichodiene oxygenase), and similar fungal proteins. CYP58 catalyzes the oxygenation of trichodiene during the biosynthesis of trichothecenes, which are sesquiterpenoid toxins that act by inhibiting protein biosynthesis. The CYP58-like subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 425 matched cddid_all.tbl CDD cd11063 cd11063 410686 CYP52 cytochrome P450 family 52. Cytochrome P450 52 (CYP52), also called P450ALK, monooxygenases catalyze the first hydroxylation step in the assimilation of alkanes and fatty acids by filamentous fungi. The number of CYP52 proteins depend on the fungal species: for example, Candida tropicalis has seven, Candida maltose has eight, and Yarrowia lipolytica has twelve. The CYP52 family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 419 matched cddid_all.tbl CDD cd11064 cd11064 410687 CYP86A cytochrome P450 family 86, subfamily A. This subfamily includes several Arabidopsis thaliana cytochrome P450s (CYP86A1, CYP86A2, CYP86A4, among others), Petunia x hybrida CYP86A22, and Vicia sativa CYP94A1 and CYP94A2. They are P450-dependent fatty acid omega-hydroxylases that catalyze the omega-hydroxylation of various fatty acids. CYP86A2 acts on saturated and unsaturated fatty acids with chain lengths from C12 to C18; CYP86A22 prefers substrates with chain lengths of C16 and C18; and CYP94A1 acts on various fatty acids from 10 to 18 carbons. They play roles in the biosynthesis of extracellular lipids, cutin synthesis, and plant defense. The CYP86A subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 432 matched cddid_all.tbl CDD cd11065 cd11065 410688 CYP64-like cytochrome P450 family 64-like fungal cytochrome P450s. This group includes Aspergillus flavus cytochrome P450 64 (CYP64), also called O-methylsterigmatocystin (OMST) oxidoreductase or aflatoxin B synthase or aflatoxin biosynthesis protein Q, and similar fungal cytochrome P450s. CYP64 converts OMST to aflatoxin B1 and converts dihydro-O-methylsterigmatocystin (DHOMST) to aflatoxin B2 in the aflatoxin biosynthesis pathway. The CYP64-like subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 425 matched cddid_all.tbl CDD cd11066 cd11066 410689 CYP_PhacA-like fungal cytochrome P450s similar to Aspergillus nidulans phenylacetate 2-hydroxylase. This group includes Aspergillus nidulans phenylacetate 2-hydroxylase (encoded by the phacA gene) and similar fungal cytochrome P450s. PhacA catalyzes the ortho-hydroxylation of phenylacetate, the first step of A. nidulans phenylacetate catabolism. The PhacA-like subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 434 matched cddid_all.tbl CDD cd11067 cd11067 410690 CYP152 cytochrome P450 family 152, also called fatty acid hydroxylases or P450 peroxygenases. The cytochrome P450 152 (CYP152) family enzymes act as peroxygenases, converting fatty acids through oxidative decarboxylation, yielding terminal alkenes, and via alpha- and beta-hydroxylation to yield hydroxy-fatty acids. Included in this family are Bacillus subtilis CYP152A1, also called cytochrome P450BsBeta, that catalyzes the alpha- and beta-hydroxylation of long-chain fatty acids such as myristic acid in the presence of hydrogen peroxide, and Sphingomonas paucimobilis CYP152B1, also called cytochrome P450(SPalpha), that hydroxylates fatty acids with high alpha-regioselectivity. The CYP152 family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 400 matched cddid_all.tbl CDD cd11068 cd11068 410691 CYP120A1 cytochrome P450 family 102, subfamily A, polypeptide 1, also called bifunctional cytochrome P450/NADPH--P450 reductase. Cytochrome P450 102A1, also called cytochrome P450(BM-3) or P450BM-3, is a bifunctional cytochrome P450/NADPH--P450 reductase. These proteins fuse an N-terminal cytochrome p450 with a C-terminal cytochrome p450 reductase (CYPOR). It functions as a fatty acid monooxygenase, catalyzing the hydroxylation of fatty acids at omega-1, omega-2 and omega-3 positions, with activity towards fatty acids with a chain length of 9-18 carbons. Its NADPH-dependent reductase activity (via the C-terminal domain) allows electron transfer from NADPH to the heme iron of the N-terminal cytochrome P450. CYP120A1 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 430 matched cddid_all.tbl CDD cd11069 cd11069 410692 CYP_FUM15-like Fusarium verticillioides cytochrome P450 monooxygenase FUM15, and similar cytochrome P450s. Fusarium verticillioides cytochrome P450 monooxygenase FUM15, is also called fumonisin biosynthesis cluster protein 15. The FUM15 gene is part of the gene cluster that mediates the biosynthesis of fumonisins B1, B2, B3, and B4, which are carcinogenic mycotoxins. This FUM15-like subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 437 matched cddid_all.tbl CDD cd11070 cd11070 410693 CYP56-like cytochrome P450 family 56-like fungal cytochrome P450s. This group includes Saccharomyces cerevisiae cytochrome P450 56, also called cytochrome P450-DIT2, and similar fungal proteins. CYP56 is involved in spore wall maturation and is thought to catalyze the oxidation of tyrosine residues in the formation of LL-dityrosine-containing precursors of the spore wall. The CYP56-like subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 438 matched cddid_all.tbl CDD cd11071 cd11071 410694 CYP74 cytochrome P450 family 74. The cytochrome P450 74 (CYP74) family controls several enzymatic conversions of fatty acid hydroperoxides to bioactive oxylipins in plants, some invertebrates, and bacteria. It includes two dehydrases, namely allene oxide synthase (AOS) and divinyl ether synthase (DES), and two isomerases, hydroperoxide lyase (HPL) and epoxyalcohol synthase (EAS). AOS (EC 4.2.1.92, also called hydroperoxide dehydratase), such as Arabidopsis thaliana CYP74A acts on a number of unsaturated fatty-acid hydroperoxides, forming the corresponding allene oxides. DES (EC 4.2.1.121), also called colneleate synthase or CYP74D, catalyzes the selective removal of pro-R hydrogen at C-8 in the biosynthesis of colneleic acid. The linolenate HPL, Arabidopsis thaliana CYP74B2, is required for the synthesis of the green leaf volatiles (GLVs) hexanal and trans-2-hexenal. The fatty acid HPL, Solanum lycopersicum CYP74B, is involved in the biosynthesis of traumatin and C6 aldehydes. The epoxyalcohol synthase Ranunculus japonicus CYP74A88 (also known as RjEAS) specifically converts linoleic acid 9- and 13-hydroperoxides to oxiranyl carbinols 9,10-epoxy-11-hydroxy-12-octadecenoic acid and 11-hydroxy-12,13-epoxy-9-octadecenoic acid, respectively. The CYP74 family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 424 matched cddid_all.tbl CDD cd11072 cd11072 410695 CYP71-like cytochrome P450 family 71 and similar cytochrome P450s. The group includes plant cytochrome P450 family 71 (CYP71) proteins, as well as some CYPs designated as belonging to a different family including CYP99A1, CYP83B1, and CYP84A1, among others. Characterized CYP71 enzymes include: parsnip (Pastinaca sativa) CYP71AJ4, also called angelicin synthase, that converts (+)-columbianetin to angelicin, an angular furanocumarin; periwinkle (Catharanthus roseus) CYP71D351, also called tabersonine 16-hydroxylase 2, that is involved in the foliar biosynthesis of vindoline; sorghum CYP71E1, also called 4-hydroxyphenylacetaldehyde oxime monooxygenase, that catalyzes the conversion of p-hydroxyphenylacetaldoxime to p-hydroxymandelonitrile; as well as maize CYP71C1, CYP71C2, and CYP71C4, which are monooxygenases catalyzing the oxidation of 3-hydroxyindolin-2-one, indolin-2-one, and indole, respectively. CYPs within a single CYP71 subfamily, such as the C subfamily, usually metabolize similar/related compounds. The CYP71-like family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 428 matched cddid_all.tbl CDD cd11073 cd11073 410696 CYP76-like cytochrome P450 family 76 and similar cytochrome P450s. Characterized members of the plant cytochrome P450 family 76 (CYP76 or Cyp76) include: Catharanthus roseus CYP76B6, a multifunctional enzyme catalyzing two sequential oxidation steps leading to the formation of 8-oxogeraniol from geraniol; the Brassicaceae-specific CYP76C subfamily of enzymes that are involved in the metabolism of monoterpenols and phenylurea herbicides; and two P450s from Lamiaceae, CYP76AH and CYP76AK, that are involved in the oxidation of abietane diterpenes. CYP76AH produces ferruginol and 11-hydroxyferruginol, while CYP76AK catalyzes oxidations at the C20 position. Also included in this group is Berberis stolonifera Cyp80, also called berbamunine synthase or (S)-N-methylcoclaurine oxidase [C-O phenol-coupling], that catalyzes the phenol oxidation of N-methylcoclaurine to form the bisbenzylisoquinoline alkaloid berbamunine. The CYP76-like family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 435 matched cddid_all.tbl CDD cd11074 cd11074 410697 CYP73 cytochrome P450 family 73. Cytochrome P450 family 73 (CYP73 pr Cyp73), also called trans-cinnamate 4-monooxygenase (EC 1.14.14.91) or cinnamic acid 4-hydroxylase, catalyzes the regiospecific 4-hydroxylation of cinnamic acid to form precursors of lignin and many other phenolic compounds. It controls the general phenylpropanoid pathway, and controls carbon flux to pigments essential for pollination or UV protection. CYP73 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 434 matched cddid_all.tbl CDD cd11075 cd11075 410698 CYP77_89 cytochrome P450 families 77 and 89, and similar cytochrome P450s. This group includes cytochrome P450 families 73 (CYP77) and 89 (CYP89), which are sister families that share a common ancestor. CYP89, present only in angiosperms, is younger than CYP77, which is already found in lycopods; thus, CYP89 may have evolved from CYP77 after duplication and divergence. Also included in this group is ent-kaurene oxidase, called CYP701A3 in Arabidopsis thaliana and CYP701B1 in Physcomitrella patens, that catalyzes the oxidation of ent-kaurene to form ent-kaurenoic acid. CYP701A3 is sensitive to inhibitor uniconazole-P while CYP701B1 is not. This CYP77/89 group belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 433 matched cddid_all.tbl CDD cd11076 cd11076 410699 CYP78 cytochrome P450 family 78. Characterized cytochrome P450 family 78 (CYP78 or Cyp78) proteins include: CYP78A5, which is expressed in leaf, flora and embryo, and has been reported to stimulate plant organ growth in Arabidopsis thaliana and to regulate plant architecture, ripening time, and fruit mass in tomato; Glycine max CYP78A10 that functions in regulating seed size/weight and pod number; and Physcomitrella patens CYP78A27 or CYP78A28, which together, are essential in bud formation. The CYP78 family belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 426 matched cddid_all.tbl CDD cd11078 cd11078 410700 CYP130-like cytochrome P450 family 130-like and similar cytochrome P450s. This subfamily includes Mycobacterium tuberculosis cytochrome P450 130 (CYP130), Rhodococcus erythropolis CYP116, and similar bacterial proteins. CYP130 catalyzes the N-demethylation of dextromethorphan, and has also shown a natural propensity to bind primary arylamines. CYP116 is involved in the degradation of thiocarbamate herbicides. The CYP130-like subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 380 matched cddid_all.tbl CDD cd11079 cd11079 410701 Cyp_unk unknown subfamily of mostly bacterial cytochrome P450s. This subfamily is composed of uncharacterized cytochrome P450s, predominantly from bacteria. Cytochrome P450 (P450, CYP) is a large superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. Their monooxygenase activity relies on the reductive scission of molecular oxygen bound to the P450 heme iron, and the delivery of two electrons to the heme iron during the catalytic cycle. 350 matched cddid_all.tbl CDD cd11080 cd11080 410702 CYP134A1 cytochrome P450 family 134, subfamily A, polypeptide 1. Cytochrome P450 134A1 (CYP134A1, EC 1.14.15.13), also called pulcherriminic acid synthase or cyclo-L-leucyl-L-leucyl dipeptide oxidase or cytochrome P450 CYPX, catalyzes the oxidation of cyclo(L-Leu-L-Leu) (cLL) to yield pulcherriminic acid which forms the red pigment pulcherrimin via a non-enzymatic spontaneous reaction with Fe(3+). It belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 370 matched cddid_all.tbl CDD cd11082 cd11082 410703 CYP61_CYP710 C-22 sterol desaturase subfamily, such as fungal cytochrome P450 61 and plant cytochrome P450 710. C-22 sterol desaturase (EC 1.14.19.41), also called sterol 22-desaturase, is required for the formation of the C-22 double bond in the sterol side chain of delta22-unsaturated sterols, which are present specifically in fungi and plants. This enzyme is also called cytochrome P450 61 (CYP61) in fungi and cytochrome P450 710 (CYP710) in plants. The CYP61/CYP710 subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 415 matched cddid_all.tbl CDD cd11083 cd11083 410704 CYP_unk unknown subfamily of cytochrome P450s. This subfamily is composed of uncharacterized cytochrome P450s. Cytochrome P450 (P450, CYP) is a large superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. Their monooxygenase activity relies on the reductive scission of molecular oxygen bound to the P450 heme iron, and the delivery of two electrons to the heme iron during the catalytic cycle. 421 matched cddid_all.tbl CDD cd11234 cd11234 199893 E_set_GDE_N "N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme. E or ""early"" set domains are associated with the catalytic domain of the glycogen debranching enzyme at the N-terminal end. Glycogen debranching enzymes have both 4-alpha-glucanotransferase and amylo-1,6-glucosidase activities. As a transferase, it transfers a segment of a 1,4-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose or another 1,4-alpha-D-glucan. As a glucosidase, it catalyzes the endohydrolysis of 1,6-alpha-D-glucoside linkages at points of branching in chains of 1,4-linked alpha-D-glucose residues. The N-terminal domain of the glycogen debranching enzyme may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase. This domain is also a member of the CBM48 (Carbohydrate Binding Module 48) family whose members include pullulanase, maltooligosyl trehalose synthase, starch branching enzyme, glycogen branching enzyme, isoamylase, and the beta subunit of AMP-activated protein kinase." 101 matched cddid_all.tbl CDD cd11235 cd11235 200496 Sema_semaphorin The Sema domain, a protein interacting module, of semaphorins. Semaphorins are regulator molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. They can be divided into 7 classes. Vertebrates have members in classes 3-7, whereas classes 1 and 2 are known only in invertebrates. Class 2 and 3 semaphorins are secreted proteins; classes 1 and 4 through 6 are transmembrane proteins; and class 7 is membrane associated via glycosylphosphatidylinositol (GPI) linkage. The semaphorins exert their function through their receptors, the neuropilin and plexin families. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 437 matched cddid_all.tbl CDD cd11236 cd11236 200497 Sema_plexin_like The Sema domain, a protein interacting module, of Plexins and MET-like receptor tyrosine kinases. Plexins form a conserved family of transmembrane receptors for semaphorins and may be the ancestor of semaphorins. Ligand binding activates signal transduction pathways controlling axon guidance in the nervous system and other developmental processes including cell migration and morphogenesis, immune function, and tumor progression. Plexins are divided into four types (A-D) according to sequence similarity. In vertebrates, type A Plexins serve as the co-receptors for neuropilins to mediate the signalling of class 3 semaphorins except Sema3E, which signals through Plexin D1. Plexins serve as direct receptors for several other members of the semaphorin family: class 6 semaphorins signal through type A plexins and class 4 semaphorins through type B. Plexin C1 serves as the receptor of Sema7A and plays regulation roles in both immune and nervous systems. This family also includes the Met and RON receptor tyrosine kinases. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a ligand-recognition and -binding module. 401 matched cddid_all.tbl CDD cd11237 cd11237 200498 Sema_1A The Sema domain, a protein interacting module, of semaphorin 1A (Sema1A). Sema1A is a transmembrane protein. It has been shown to mediate the defasciculation of motor axon bundles at specific choice points. Sema1A binds to its receptor plexin A (PlexA), which in turn triggers downstream signaling events involving the receptor tyrosine kinase Otk, the evolutionarily conserved flavoprotein monooxygenase molecule interacting with CasL (MICAL), and the A kinase anchoring protein Nervy, leading to repulsive growth-cone response. Sema1A has also been shown to be involved in synaptic formation. It is a member of the semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 446 matched cddid_all.tbl CDD cd11238 cd11238 200499 Sema_2A The Sema domain, a protein interacting module, of semaphorin 2A (Sema2A). Sema2A, a secreted semaphorin, signals through its receptor plexin B (PlexB) to regulate central and peripheral axon pathfinding. In the Drosophila embryo, Sema2A secreted by oenocytes interacts with PlexB to guide sensory axons. Sema2A is a member of the semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 452 matched cddid_all.tbl CDD cd11239 cd11239 200500 Sema_3 The Sema domain, a protein interacting module, of class 3 semaphorins. Class 3 semaphorins (Sema3s) are secreted regulator molecules involved in the development of the nervous system, vasculogenesis, angiogenesis,and tumorigenesis. There are 7 distinct subfamilies named Sema3A to 3G. Sema3s function as repellent signals during axon guidance by repelling neurons away from the source of Sema3s. However, Sema3s that are secreted by tumor cells play an inhibitory role in tumor growth and angiogenesis (specifically Sema3B and Sema3F). Sema3s functions by forming complexes with neuropilins and A-type plexins, where neuropilins serve as the ligand binding moiety and the plexins function as signal transduction component. Sema3s primarily inhibit the cell motility and migration of tumor and endothelial cells by inducing collapse of the actin cytoskeleton via neuropilins and plexins. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 471 matched cddid_all.tbl CDD cd11240 cd11240 200501 Sema_4 "The Sema domain, a protein interacting module, of class 4 semaphorins (Sema4). Class 4 semaphorins (Sema4s) are transmembrane regulator molecules involved in the development of the nervous system, immune response, cytoskeletal organization, angiogenesis, and cell-cell interactions. There are 7 distinct subfamilies in class 4 semaphorins, named 4A to 4G. Several class 4 subfamilies play important roles in the immune system and are called ""immune semaphorins"". Sema4A plays critical roles in T cell-DC interactions in the immune response. Sema4D/CD100, expressed by lymphocytes, promotes the aggregation and survival of B lymphocytes and inhibits cytokine-induced migration of immune cells in vitro. It is required for normal activation of B and T lymphocytes. Sema4B negatively regulates basophil functions through T cell-basophil contacts and significantly inhibits IL-4 and IL-6 production from basophils in response to various stimuli, including IL-3 and papain. Sema4s not only influence the activation state of cells but also modulate their migration and survival. The effects of Sema4s on nonlymphoid cells are mediated by plexin D1 and plexin Bs. The Sema4G and Sema4C genes are expressed in the developing cerebellar cortex and are involved in neural tube closure and development of cerebellar granules cells through receptor plexin B2. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module." 456 matched cddid_all.tbl CDD cd11241 cd11241 200502 Sema_5 The Sema domain, a protein interacting module, of semaphorin 5 (Sema5). Class 5 semaphorins are transmembrane glycoproteins characterized by unique thrombospondin specific repeats in the extracellular region of the protein. There are three subfamilies in class 5 semaphorins, namely 5A, 5B and 5C. Sema5A and Sema5B function as guidance cues for optic and corticofugal nerve development, respectively. Sema5A-induced cell migration requires Met signaling. Sema5C is an early development gene and may play a role in odor-guided behavior. Sema5A is also implicated in cancer. In a screening model for metastasis, the Drosophila Sema5A ortholog, Dsema-5C, has been found to be required in tumorigenicity and metastasis. Sema5A is highly expressed in human pancreatic cancer cells and is associated with tumor growth, invasion and metastasis. Semaphorins are regulatory molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 438 matched cddid_all.tbl CDD cd11242 cd11242 200503 Sema_6 The Sema domain, a protein interacting module, of class 6 semaphorins (Sema6). Class 6 semaphorins (Sema6s) are membrane associated semaphorins. There are 6 subfamilies named 6A to 6D. Sema6s bind to plexin As in a neuropilin independent fashion. Sema6-plexin A signaling plays important roles in lamina-specific axon projections. Interactions between plexin A2, plexin A4, and Sema6A control lamina-restricted projection of hippocampal mossy fibers. Interactions between Sema6C, Sema6D and plexin A1 shape the stereotypic trajectories of sensory axons in the spinal cord. In addition to axon targeting, Sema6D-plexin A1 interactions influence a wide range of other biological processes. During cardiac development, Sema6D attracts or repels endothelial cells in the cardiac tube depending on the expression patterns of specific coreceptors in addition to plexin A1. Furthermore, Sema6D binds a receptor complex comprising of plexin A1, Trem2 (triggering receptor expressed on myeloid cells 2), and DAP12 on dendritic cells and osteoclasts to mediate T-cell-DC interactions and to control bone development, respectively. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 465 matched cddid_all.tbl CDD cd11243 cd11243 200504 Sema_7A The Sema domain, a protein interacting module, of semaphorin 7A (Sema7A, also called CD108). Sema7A plays regulatory roles in both immune and nervous systems. Unlike other semaphorins, which act as repulsive guidance cues, Sema7A enhances central and peripheral axon growth and is required for proper axon tract formation during embryonic development. Sema7A also plays a critical role in the negative regulation of T cell activation and function. Sema7A is a membrane-anchored member of the semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 414 matched cddid_all.tbl CDD cd11244 cd11244 200505 Sema_plexin_A The Sema domain, a protein interacting module, of Plexin A. Plexins serve as receptors of semaphorins and may be the ancestor of semaphorins. Members of the Plexin A subfamily are receptors for Sema1s, Sema3s, and Sema6s, and they mediate diverse biological functions including axon guidance, cardiovascular development, and immune function. Guanylyl cyclase Gyc76C and Off-track kinase (OTK), a putative receptor tyrosine kinase, modulate Sema1a-Plexin A mediated axon repulsion. Sema3s do not interact directly with plexin A receptors, but instead bind Neuropilin-1 or Neuropilin-2 toactivate neuropilin-plexin A holoreceptor complexes. In contrast to Sema3s, Sema6s do not require neuropilins for plexin A binding. In the complex, plexin As serve as signal-transducing subunits. An increasing number of molecules that interact with the intracellular region of Plexin A have been identified; among them are IgCAMs (in axon guidance events) and Trem2-DAP12 (in immune responses). The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a ligand-recognition and -binding module. 470 matched cddid_all.tbl CDD cd11245 cd11245 200506 Sema_plexin_B The Sema domain, a protein interacting module, of Plexin B. Plexins, which contain semaphorin domains, function as receptors of semaphorins and may be the ancestors of semaphorins. There are three members of the Plexin B subfamily, namely B1, B2 and B3. Plexins B1, B2 and B3 are receptors for Sema4D, Sema4C and Sema4G, and Sema5A, respectively. The activation of plexin B1 by Sema4D produces an acute collapse of axonal growth cones in hippocampal and retinal neurons over the early stages of neurite outgrowth and promotes branching and complexity. By signaling the effect of Sema4C and Sema4G, the plexin B2 receptor is critically involved in neural tube closure and cerebellar granule cell development. Plexin B3, the receptor of Sema5A, is a highly potent stimulator of neurite outgrowth of primary murine cerebellar neurons. Plexin B3 has been linked to verbal performance and white matter volume in human brain. Small GTPases play important roles in plexin B signaling. Plexin B1 activates Rho through Rho-specific guanine nucleotide exchange factors, leading to neurite retraction. Plexin B1 possesses an intrinsic GTPase-activating protein activity for R-Ras and induces growth cone collapse through R-Ras inactivation. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a ligand-recognition and -binding module. 440 matched cddid_all.tbl CDD cd11246 cd11246 200507 Sema_plexin_C1 The Sema domain, a protein interacting module, of Plexin C1. Plexins serve as semaphorin receptors. Plexin C1 has been identified as the receptor of semaphorin 7A, which plays regulation roles in both the immune and nervous systems. Unlike other semaphorins which act as repulsive guidance cues, Sema7A enhances central and peripheral axon growth and is required for proper axon tract formation during embryonic development. Plexin C1 is a potential tumor suppressor for melanoma progression. The expression of Plexin C1 is diminished or absent in human melanoma cell lines. Cofilin, an actin-binding protein involved in cell migration, is a downstream target of Sema7A-Plexin C1 signaling. Cofilin is not phosphorylated when Plexin C1 expression is silenced. Thus, melanoma invasion and metastasis may be promoted through the loss of Plexin C1 inhibitory signaling on cofilin activation. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a ligand-recognition and -binding module. 401 matched cddid_all.tbl CDD cd11247 cd11247 200508 Sema_plexin_D1 The Sema domain, a protein interacting module, of Plexin D1. Plexins are known as semaphorin receptors and Plexin D1 has been identified as the receptor of Sema3E. It binds to Sema3E directly with high affinity. Sema3E is implicated in axonal path finding and inhibition of developmental and post-ischemic angiogenesis. Plexin D1 is broadly expressed on tumor vessels and tumor cells in a number of different types of human tumors. Plexin D1-Sema3E interaction inhibits tumor growth but promotes invasiveness and metastasis. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a ligand-recognition and -binding module. 483 matched cddid_all.tbl CDD cd11248 cd11248 200509 Sema_MET_like The Sema domain, a protein interacting module, of MET and RON receptor tyrosine kinases. This family includes MET and RON receptor tyrosine kinases. MET is encoded by the c-met protooncogene. MET is the receptor for hepatocyte growth factor/scatter factor (HGF/SF). HGF/SF and MET regulates multiple cellular events and are essential for the development of several tissues and organs, including the placenta, liver, and several groups of skeletal muscles. RON receptor tyrosine kinase is a Macrophage-stimulating protein (MSP) receptor. Upon binding of MSP, RON is activated via autophosphorylation within its kinase catalytic domain, resulting in a variety of effects including proliferation, tubular morphogenesis, angiogenesis, cellular motility and invasiveness. By interacting with downstream signaling molecules, it regulates macrophage migration, phagocytosis, and nitric oxide production. MET and RON receptors have been implicated in cancer development and migration. They are composed of alpha-beta heterodimers. The extracellular alpha chain is disulfide linked to the beta chain, which contains an extracellular ligand-binding region with a Sema domain, a PSI domain and four IPT repeats, a transmembrane segment, and an intracellular catalytic tyrosine kinase domain. The Sema domain is necessary for receptor dimerization and activation. 467 matched cddid_all.tbl CDD cd11249 cd11249 200510 Sema_3A The Sema domain, a protein interacting module, of semaphorin 3A (Sema3A). Sema3A has been reported to inhibit the growth of certain experimental tumors and to regulate endothelial cell migration and apoptosis in vitro, as well as arteriogenesis in the muscle, skin vessel permeability, and tumor angiogenesis in vivo. The function of Sema3A is mediated through receptors neuropilin-1 (NP1) and plexins, although little is known about the requirement of specific plexins in its receptor complex. It is known however that Plexin-A4 is the receptor for Sema3A in the Toll-like receptor- and sepsis-induced cytokine storm during immune response. Sema3A is a member of the Class 3 semaphorin family of secreted proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 493 matched cddid_all.tbl CDD cd11250 cd11250 200511 Sema_3B The Sema domain, a protein interacting module, of semaphorin 3B (Sema3B). Sema3B is coexpressed with semaphorin 3F and both proteins are candidate tumor suppressors. Both Sema3B and Sema3F show high levels of expression in normal tissues and low-grade tumors but are down-regulated in highly metastatic tumors in the lung, melanoma cells, bladder carcinoma cells and prostate carcinoma. They are upregulated by estrogen and inhibit cell motility and invasiveness through decreased FAK phosphorylation and inhibition of MMP-2 and MMP-9 expression. Two receptor families, the neuropilins (NP) and plexins, have been implicated in mediating the actions of semaphorins 3B and 3F. Sema3B is a member of the class 3 semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 471 matched cddid_all.tbl CDD cd11251 cd11251 200512 Sema_3C The Sema domain, a protein interacting module, of semaphorin 3C (Sema3C). Sema3C is a secreted semaphorin expressed in and adjacent to cardiac neural crest cells, and causes impaired migration of neural crest cells to the developing cardiac outflow tract, resulting in the interruption of the aortic arch and persistent truncus arteriosus. It has been proposed that Sema3C acts as a guidance molecule, regulating migration of neural crest cells that express semaphorin receptors such as plexin A2. Sema3C may also participate in tumor progression. The cleavage of Sema3C induced by ADAMTS1 promotes the migration of breast cancer cells. Sema3C is a member of the class 3 semaphorin family of secreted proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 470 matched cddid_all.tbl CDD cd11252 cd11252 200513 Sema_3D The Sema domain, a protein interacting module, of semaphorin 3D (Sema3D). Sema3D is a secreted semaphorin expressed during the development of the nervous system. In zebrafish, Sema3D is expressed in the ventral tectum. It guides retinal axons along the dorsoventral axis of the tectum and guides the laterality of retinal ganglion cell (RGC) projections. Both Sema3D knockdown or its ubiquitous overexpression induced aberrant ipsilateral projections. Proper balance of Sema3D is needed at the midline for the progression of RGC axons from the chiasm midline into the contralateral optic tract. Sema3D is a member of the class 3 semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 474 matched cddid_all.tbl CDD cd11253 cd11253 200514 Sema_3E The Sema domain, a protein interacting module, of semaphorin 3E (Sema3E). Sema3E is a secreted molecule implicated in axonal path finding and inhibition of developmental and postischemic angiogenesis. It is also highly expressed in metastatic cancer cells. Sema3E signaling, through its high affinity functional receptor Plexin D1, drives cancer cell invasiveness and metastatic spreading. Sema3E is a member of the class 3 semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 471 matched cddid_all.tbl CDD cd11254 cd11254 200515 Sema_3F The Sema domain, a protein interacting module, of semaphorin 3F (Sema3F). Sema3F is coexpressed with semaphorin3B. Both Sema3B and Sema3F proteins are candidate tumor suppressors that are down-regulated in highly metastatic tumors. Two receptor families, the neuropilins and plexins, have been implicated in mediating the actions of semaphorins 3B and 3F. Sema3F is a member of the class 3 semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 470 matched cddid_all.tbl CDD cd11255 cd11255 200516 Sema_3G The Sema domain, a protein interacting module, of semaphorin 3G (Sema3G). Semaphorin 3G is identified as a primarily endothelial cell- expressed class 3 semaphorin that controls endothelial and smooth muscle cell functions in autocrine and paracrine manners, respectively. It is mainly expressed in the lung and kidney, and a little in the brain. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 474 matched cddid_all.tbl CDD cd11256 cd11256 200517 Sema_4A "The Sema domain, a protein interacting module, of semaphorin 4A (Sema4A). Sema4A is expressed in immune cells and is thus termed an ""immune semaphorin"". It plays critical roles in T cell-DC interactions in the immune response. It has been reported to enhance activation and differentiation of T cells in vitro and generation of antigen-specific T cells in vivo. The function of Sema4A in the immune response implicates its role in infectious and noninfectious diseases. Sema4A exerts its function through three receptors, namely Plexin B, Plexin D1, and Tim-2. Sema4A belongs to the class 4 transmembrane semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. TThe Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module." 447 matched cddid_all.tbl CDD cd11257 cd11257 200518 Sema_4B The Sema domain, a protein interacting module, of semaphorin 4B (Sema4B). Sema4B, expressed in T and B cells, is an immune semaphorin. It functions as a negative regulatory of basophils through T cell-basophil contacts and it significantly inhibits IL-4 and IL-6 production from basophils in response to various stimuli, including IL-3 and papain. In addition, T cell-derived Sema4B suppresses basophil-mediated Th2 skewing and humoral memory responses. Sema4B may be also involved in lung cancer cell mobility by inducing the degradation of CLCP1 (CUB, LCCL-homology, coagulation factor V/VIII homology domains protein). Sema4B is characterized by a PDZ-binding motif at the carboxy-terminus, which mediates interaction with the post-synaptic density protein PSD-95/SAP90, which is thought to play a central role during synaptogenesis and in the structure and function of post-synaptic specializations of excitatory synapses. Sema4B belongs to class 4 transmembrane semaphorin family proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 464 matched cddid_all.tbl CDD cd11258 cd11258 200519 Sema_4C The Sema domain, a protein interacting module, of semaphorin 4C (Sema4C). Sema4C acts as a Plexin B2 ligand to regulate the development of cerebellar granule cells and to modulate ureteric branching in the developing kidney. The binding of Sema4C to Plexin B2 results the phosphorylation of downstream regulator ErbB-2 and the plexin protein itself. The cytoplasmic region of Sema4C binds a neurite-outgrowth-related protein SFAP75, suggesting that Sema4C may also play a role in neural function. Sema4C belongs to the class 4 transmembrane semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 458 matched cddid_all.tbl CDD cd11259 cd11259 200520 Sema_4D "The Sema domain, a protein interacting module, of semaphorin 4D (Sema4D, also known as CD100). Sema4D/CD100 is expressed in immune cells and plays critical roles in immune response; it is thus termed an ""immune semaphorin"". It is expressed by lymphocytes and promotes the aggregation and survival of B lymphocytes and inhibits cytokine-induced migration of immune cells in vitro. Sema4D/CD100 knock-out mice demonstrate that Sema4D is required for normal activation of B and T lymphocytes. Sema4D increases B-cell and DC function using either Plexin B1 or CD72 as receptors. The function of Sema4D in immune response implicates its role in infectious and noninfectious diseases. Sema4D belongs to the class 4 transmembrane semaphorin family of proteins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module." 471 matched cddid_all.tbl CDD cd11260 cd11260 200521 Sema_4E The Sema domain, a protein interacting module, of semaphorin 4E (Sema4E). Sema4E is expressed in the epithelial cells that line the pharyngeal arches in zebrafish. It may act as a guidance molecule to restrict the branchiomotor axons to the mesenchymal cells. Gain-of-function and loss-of-function studies demonstrate that Sema4E is essential for the guidance of facial axons from the hindbrain into their pharyngeal arch targets and is sufficient for guidance of gill motor axons. Sema4E guides facial motor axons by a repulsive action. Sema4E belongs to the class 4 transmembrane semaphorin family of proteins. Semaphorins are regulatory molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 456 matched cddid_all.tbl CDD cd11261 cd11261 200522 Sema_4F The Sema domain, a protein interacting module, of semaphorin 4F (Sema4F). Sema4F plays role in heterotypic cell-cell contacts and controls cell proliferation and suppresses tumorigenesis. In neurofibromatosis type 1 (NF1) patients, reduced Sema4F level disrupts Schwann cell/axonal interactions. Experiments using a yeast two-hybrid system show that the extreme C-terminus of Sema4F interacts with the PDZ domains of post-synaptic density protein SAP90/PSD-95, indicating possible functional involvement of Semas4F at glutamatergic synapses. Recent work also suggests a role for Sema4F in the injury response of intramedullary axotomized motoneuron. Sema4F belongs to the class 4 transmembrane semaphorin family of proteins. Semaphorins are regulator molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 460 matched cddid_all.tbl CDD cd11262 cd11262 200523 Sema_4G The Sema domain, a protein interacting module, of semaphorin 4G (Sema4G). The Sema4G and Sema4C genes are expressed in the developing cerebellar cortex. Sema4G and Sema4C proteins specifically bind to Plexin B2 expressed in the cerebellar granule cells. Sema4G and Sema4C are involved in neural tube closure and cerebellar granule cell development through Plexin B2.Sema4G belongs to the class 4 transmembrane semaphorin family of proteins. Semaphorins are regulatory molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 457 matched cddid_all.tbl CDD cd11263 cd11263 200524 Sema_5A The Sema domain, a protein interacting module, of semaphorin 5A (Sema5A). Originally, mouse Sema5A was identified as a protein that induces inhibitory responses during optic nerve development. Recent studies show that Sema5A controls innate immunity in mice. It also has been identified as a candidate gene for causing idiopathic autism in humans. Plexin B3 functions as a binding partner and receptor for Sema5A. Furthermore, Sema5A is also implicated in cancer. The role of the Drosophila Sema5A ortholog, Dsema-5C, in tumorigenicity and metastasis has been reported. Sema5A is highly expressed in human pancreatic cancer cells and is associated with tumor growth, invasion and metastasis. Sema5A belongs to class 5 semaphorin family of proteins, which are transmembrane glycoproteins characterized by unique thrombospondin specific repeats in the extracellular region of the protein. Semaphorins are regulatory molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 436 matched cddid_all.tbl CDD cd11264 cd11264 200525 Sema_5B The Sema domain, a protein interacting module, of semaphorin 5B (Sema5B). Sema5B is expressed in regions of the basal telencephalon in rat. Sema5B is an inhibitory cue for corticofugal axons and acts as a source of repulsion for the appropriate guidance of cortical axons away from structures such as the ventricular zone as they navigate toward and within subcortical regions. In addition to its role as a guidance cue, Sema5B regulates the development and maintenance of synapse size and number in hippocampal neurons. In addition, the sema domain of Sema5B can be cleaved of the whole protein and exerts its function in regulation of synapse morphology. Sema5B belongs to the class 5 semaphorin family of proteins, which are transmembrane glycoproteins characterized by unique thrombospondin specific repeats in the extracellular region of the protein. Semaphorins are regulatory molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 437 matched cddid_all.tbl CDD cd11265 cd11265 200526 Sema_5C The Sema domain, a protein interacting module, of semaphorin 5C (sema5C). In Drosophila, Sema5C was identified as an early development gene, which is expressed in stage 2 embryos with a striped pattern emerging at later stages. Sema5c may play a role in odor-guided behavior and in tumorigenesis. Sema5C belongs to class 5 semaphorin family of proteins, which are transmembrane glycoproteins characterized by unique thrombospondin specific repeats in the extracellular region of the protein. Semaphorins are regulatory molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 433 matched cddid_all.tbl CDD cd11266 cd11266 200527 Sema_6A The Sema domain, a protein interacting module, of semaphorins 6A (Sema6A). In the cerebellum, Sema6A-plexin A2 signaling modulates granule cell migration by controlling centrosome positioning. Besides plexin A2, plexin A4 is also found to be a receptor of Sema6A. Interactions between plexin A2, plexin A4, and Sema6A control lamina-restricted projection of hippocampal mossy fibers. It is required for the clustering of boundary cap cells at the PNS/CNS interface and thus, prevents motoneurons from streaming out of the ventral spinal cord. At the dorsal root entry site, it organizes the segregation of dorsal roots. Sema6A may also be involved in axonal pathfinding processes in the periinfarct and homotopic contralateral cortex. Sema6A is a member of the class 6 semaphorin family of proteins, which are membrane associated semaphorins. Semaphorins are regulatory molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 466 matched cddid_all.tbl CDD cd11267 cd11267 200528 Sema_6B The Sema domain, a protein interacting module, of semaphorin 6B (Sema6B). Sema6B functions as repellents for axon growth; this repulsive activity is mediated by its receptor Plexin A4. Sema6B is expressed in CA3, and repels mossy fibers in a Plexin A4 dependent manner. In human, it was shown that peroxisome proliferator-activated receptors (PPARs) and 9-cis-retinoic acid receptor (RXR) regulate human semaphorin 6B (Sema6B) gene expression. Sema6B is a member of the class 6 semaphorin family of proteins, which are membrane associated semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 466 matched cddid_all.tbl CDD cd11268 cd11268 200529 Sema_6C The Sema domain, a protein interacting module, of semaphorin 6C (Sema6C, also called semaphorin Y). Sema6C is highly expressed in adult brain and skeletal muscle and it shows growth cone collapsing activity. It may play a role in the maintenance and remodelling of neuronal connections. In adult skeletal muscle, this role includes prevention of motor neuron sprouting and uncontrolled motor neuron growth. The expression of Sema6C in adult skeletal muscle is down-regulated following denervation. Sema6C is a member of the class 6 semaphorin family of proteins, which are membrane associated semaphorins. Semaphorins are regulatory molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 465 matched cddid_all.tbl CDD cd11269 cd11269 200530 Sema_6D The Sema domain, a protein interacting module, of semaphorin 6D (Sema6D). Sema6D is expressed predominantly in the nervous system during embryogenesis and it uses Plexin-A1 as a receptor. It displays repellent activity for dorsal root ganglion axons. Sema6D also acts as a regulator of late phase primary immune responses. In addition, Sema6D is overexpressed in gastric carcinoma, indicating that it may have an important role in the occurrence and development of the cancer. Sema6D is a member of the class 6 semaphorin family of proteins, which are membrane associated semaphorins. Semaphorins are regulatory molecules involved in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 465 matched cddid_all.tbl CDD cd11270 cd11270 200531 Sema_6E The Sema domain, a protein interacting module, semaphorin 6E (sema6E). Sema6E is expressed predominantly in the nervous system during embryogenesis. It binds Plexin A1 and might utilize it as a receptor to repel axons of specific types during development. Sema6E acts as a repellent to dorsal root ganglion axons as well as sympathetic axons. Sema6E is a member of the class 6 semaphorin family of proteins, which are membrane associated semaphorins. Semaphorins are regulatory molecules in the development of the nervous system and in axonal guidance. They also play important roles in other biological processes, such as angiogenesis, immune regulation, respiration systems and cancer. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a receptor-recognition and -binding module. 462 matched cddid_all.tbl CDD cd11271 cd11271 200532 Sema_plexin_A1 The Sema domain, a protein interacting module, of Plexin A1. Plexin A1 is found in both the nervous and immune systems. Its external Sema domain is also shared by semaphorin proteins. In the nervous system, Plexin A1 mediates Sema3A axon guidance function by interacting with the Sema3A coreceptor neuropilin, resulting in actin depolarization and cell repulsion. In the immune system, Plexin A1 mediates Sema6D signaling by binding to the Sema6D-Trem2-DAP12 complex on immune cells and osteoclasts to promote Rac activation and DAP12 phosphorylation. In gene profiling experiments, Plexin A1 was identified as a CIITA (class II transactivator) regulated gene in primary dendritic cells (DCs). The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a ligand-recognition and -binding module. 474 matched cddid_all.tbl CDD cd11272 cd11272 200533 Sema_plexin_A2 The Sema domain, a protein interacting module, of Plexin A2. Plexin A2 serves as a receptor for class 6 semaphorins. Interactions between Plexin A2, A4 and semaphorins 6A and 6B control the lamina-restricted projection of hippocampal mossy fibers. Sema6B also repels the growth of mossy fibers in a Plexin A4 dependent manner. Plexin A2 does not suppress Sema6B function. In addition, studies have shown that Plexin A2 may be related to anxiety and other psychiatric disorders. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a ligand-recognition and -binding module. 515 matched cddid_all.tbl CDD cd11273 cd11273 200534 Sema_plexin_A3 The Sema domain, a protein interacting module, of Plexin A3. Plexin-A3 forms a receptor complex with neuropilin-2 and transduces signals for class 3 semaphorins in the nervous system. Both plexins A3 and A4 are essential for normal sympathetic neuron development. They function cooperatively to regulate the migration of sympathetic neurons, and differentially to guide sympathetic axons. Both plexins A3 and A4 are not required for guiding neural crest precursors prior to reaching the sympathetic anlagen. Plexin A3 is a major driving force for intraspinal motor growth cone guidance. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a ligand-recognition and -binding module. 469 matched cddid_all.tbl CDD cd11274 cd11274 200535 Sema_plexin_A4 The Sema domain, a protein interacting module, of Plexin A4. Plexin A4 forms a receptor complex with neuropilins (NRPs) and transduces signals for class 3 semaphorins in the nervous system. It regulates facial nerve development by functioning as a receptor for Sema3A/NRP1. Both plexins A3 and A4 are essential for normal sympathetic development. They function both cooperatively, to regulate the migration of sympathetic neurons, and differentially, to guide sympathetic axons. Plexin A4 is also expressed in lymphoid tissues and functions in the immune system. It negatively regulates T lymphocyte responses. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a ligand-recognition and -binding module. 473 matched cddid_all.tbl CDD cd11275 cd11275 200536 Sema_plexin_B1 The Sema domain, a protein interacting module, of Plexin B1. Plexin B1 serves as the Semaphorin 4D receptor and functions as a regulator of developing neurons and a tumor suppressor protein for melanoma. The Sema4D-plexin B signaling complex regulates dendritic and axonal complexity. The activation of Plexin B1 by Sema4D produces an acute collapse of axonal growth cones in hippocampal and retinal neurons over the early stages of neurite outgrowth and promotes branching and complexity. As a tumor suppressor, plexin B1 abrogates activation of the oncogenic receptor, c-Met, by its ligand, hepatocyte growth factor (HGF), in melanoma. Furthermore, plexin B1 suppresses integrin-dependent migration and activation of pp125FAK and inhibits Rho activity. Plexin B1 is highly expressed in endothelial cells and its activation by Sema4D elicits a potent proangiogenic response. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a ligand-recognition and -binding module. 461 matched cddid_all.tbl CDD cd11276 cd11276 200537 Sema_plexin_B2 The Sema domain, a protein interacting module, of Plexin B2. Plexin B2 serves as the receptor of Sema4C and Sema4G. By signaling the effect of Sema4C and Sema4G, the plexin B2 receptor plays important roles in neural tube closure and cerebellar granule cell development. Mice lacking Plexin B2 demonstrated defects in closure of the neural tube and disorganization of the embryonic brain. In developing kidney, Sema4C-Plexin B2 signaling modulates ureteric branching. Plexin B2 is expressed both in the pretubular aggregates and the ureteric epithelium in the developing kidney. Deletion of Plexin B2 results in renal hypoplasia and occasional double ureters. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a ligand-recognition and -binding module. 449 matched cddid_all.tbl CDD cd11277 cd11277 200538 Sema_plexin_B3 The Sema domain, a protein interacting module, of Plexin B3. Plexin B3 is the receptor of semaphorin 5A. It is a highly potent stimulator of neurite outgrowth of primary murine cerebellar neurons. Plexin B3 has been linked to verbal performance and white matter volume in human brain. Furthermore, Sema5A and plexin B3 have been implicated in the progression of various types of cancer. They play an important role in the invasion and metastasis of gastric carcinoma. The stimulation of plexin B3 by Sema5A binding in human glioma cells results in the inhibition of cell migration and invasion. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as a ligand-recognition and -binding module. 434 matched cddid_all.tbl CDD cd11278 cd11278 200539 Sema_MET The Sema domain, a protein interacting module, of MET (also called hepatocyte growth factor receptor, HGFR). MET is encoded by the c-met protooncogene. MET is a receptor tyrosine kinase that binds its ligand, hepatocyte growth factor/scatter factor (HGF/SF). HGF/SF and MET are essential for the development of several tissues and organs, including the placenta, liver, and several groups of skeletal muscles. It also plays a major role in the abnormal migration of cancer cells as a result of overexpression or MET mutations. MET is composed of an alpha-beta heterodimer. The extracellular alpha chain is disulfide linked to the beta chain, which contains an extracellular ligand-binding region with a Sema domain, a PSI domain and four IPT repeats, a transmembrane segment, and an intracellular catalytic tyrosine kinase domain. The cytoplasmic C-terminal region acts as a docking site for multiple protein substrates, including Grb2, Gab1, STAT3, Shc, SHIP-1 and Src. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. The Sema domain of Met is necessary for receptor dimerization and activation. 492 matched cddid_all.tbl CDD cd11279 cd11279 200540 Sema_RON The Sema domain, a protein interacting module, of RON Receptor Tyrosine Kinase. RON receptor tyrosine kinase is a Macrophage-stimulating protein (MSP) receptor. Upon binding of MSP, RON is activated via autophosphorylation within its kinase catalytic domain, resulting in a wide range of effects, including proliferation, tubular morphogenesis, angiogenesis, cellular motility and invasiveness. By interacting with downstream signaling molecules, it regulates macrophage migration, phagocytosis, and nitric oxide production. RON has been implicated in cancers of the breast, colon, pancreas and ovaries because both splice variants and receptor overexpression have been identified in these tumors. The Sema domain is located at the N-terminus and contains four disulfide bonds formed by eight conserved cysteine residues. It serves as ligand recognition and binding model. RON is composed of an alpha-beta heterodimer. The extracellular alpha chain is disulfide linked to the beta chain, which contains an extracellular ligand-binding region with a Sema domain, a PSI domain and four IPT repeats, a transmembrane segment, and an intracellular catalytic tyrosine kinase domain. The Sema domain of RON may be necessary for receptor dimerization and activation. 493 matched cddid_all.tbl CDD cd11280 cd11280 200436 gelsolin_like Tandemly repeated domains found in gelsolin, severin, villin, and related proteins. Gelsolin repeats occur in gelsolin, severin, villin, advillin, villidin, supervillin, flightless, quail, fragmin, and other proteins, usually in several copies. They co-occur with villin headpiece domains, leucine-rich repeats, and several other domains. These gelsolin-related actin binding proteins (GRABPs) play regulatory roles in the assembly and disassembly of actin filaments; they are involved in F-actin capping, uncapping, severing, or the nucleation of actin filaments. Severing of actin filaments is Ca2+ dependent. Villins are also linked to generating bundles of F-actin with uniform filament polarity, which is most likely mediated by their extra villin headpiece domain. Many family members have also adopted functions in the nucleus, including the regulation of transcription. Supervillin, gelsolin, and flightless I are involved in intracellular signaling via nuclear hormone receptors. The gelsolin-like domain is distantly related to the actin depolymerizing domains found in cofilin and similar proteins. 88 matched cddid_all.tbl CDD cd11281 cd11281 200437 ADF_drebrin_like ADF homology domain of drebrin and actin-binding protein 1 (abp1). Actin depolymerization factor/cofilin-like domains (ADF domains) are present in a family of essential eukaryotic actin regulatory proteins. Many of these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments. Abp1 and drebrin (developmentally regulated brain protein) are multidomain proteins with an N-terminal ADF homology domain and one or more C-terminal SH3 domains. They have been shown to interact with polymeric F-actin, but not with monomeric G-actin, and do not appear to promote the disassembly of actin filaments. Drebrin rather stabilizes actin filaments by inducing changes in the helical twist and may promote or interfere with the interactions of other proteins with actin filaments. 136 matched cddid_all.tbl CDD cd11282 cd11282 200438 ADF_coactosin_like Coactosin-like members of the ADF homology domain family. Actin depolymerization factor/cofilin-like domains (ADF domains) are present in a family of essential eukaryotic actin regulatory proteins. Many of these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments. The function of coactosins is not well understood. They appear to interfere with the capping of actin filaments in Dictyostelium, and may not be able to bind monomeric globular actin. A role for coactosins as chaperones stabilizing 5-lipoxygenase (5LO) has been suggested; 5LO plays a crucial role in leukotriene synthesis. 114 matched cddid_all.tbl CDD cd11283 cd11283 200439 ADF_GMF-beta_like ADF-homology domain of glia maturation factor beta and related proteins. Actin depolymerization factor/cofilin-like domains (ADF domains) are present in a family of essential eukaryotic actin regulatory proteins. Most of these proteins enhance the turnover rate of actin and interact with actin monomers as well as actin filaments. The glia maturation factor (GMF), however, does not bind actin but interacts with the Arp2/3 complex (which contains actin-related proteins, amongst others) and suppresses Arp2/3 activity, inducing the dissociation of branched daughter filaments from their mother filaments. This family includes both mammalian GMF isoforms, GMF-beta and GMF-gamma. GMF-beta regulates cellular growth, fission, differentiation and apoptosis. GMF-gamma is important in myeloid cell development and is an important regulator for cell migration and polarity in neutrophils. 122 matched cddid_all.tbl CDD cd11284 cd11284 200440 ADF_Twf-C_like C-terminal ADF domain of twinfilin and related proteins. Actin depolymerization factor/cofilin-like domains (ADF domains) are present in a family of essential eukaryotic actin regulatory proteins. Twinfilin contains two ADF domains, and inhibits the assembly of actin filaments by strongly interacting with monomeric ADP-actin (ADP-G-actin) in a 1:1 stochiometry (with it's C-terminal ADF domain, Twf-C) and inhibiting the actin monomer's nucleotide exchange. Mammalian twinfilin may also cap the barbed ends of F-actin filaments and prevent further assembly (or disassembly), in a process which requires both ADF domains. The N-terminal ADF domain (Twf-N) binds G-actin with a lower affinity than Twf-C; Twf-C can also bind F-actin. During capping, Twf-N may interact with the terminal actin subunit, and Twf-C may bind between two adjacent subunits at the side of the filament. 132 matched cddid_all.tbl CDD cd11285 cd11285 200441 ADF_Twf-N_like N-terminal ADF domain of twinfilin and related proteins. Actin depolymerization factor/cofilin-like domains (ADF domains) are present in a family of essential eukaryotic actin regulatory proteins. Twinfilin contains two ADF domains, and inhibits the assembly of actin filaments by strongly interacting with monomeric ADP-actin (ADP-G-actin) in a 1:1 stochiometry (with it's C-terminal ADF domain, Twf-C) and inhibiting the actin monomer's nucleotide exchange. Mammalian twinfilin may also cap the barbed ends of F-actin filaments and prevent further assembly (or disassembly), in a process which requires both ADF domains. The N-terminal ADF domain (Twf-N) binds G-actin with a lower affinity than Twf-C; Twf-C can also bind F-actin. During capping, Twf-N may interact with the terminal actin subunit, and Twf-C may bind between two adjacent subunits at the side of the filament. 139 matched cddid_all.tbl CDD cd11286 cd11286 200442 ADF_cofilin_like Cofilin, Destrin, and related actin depolymerizing factors. Actin depolymerization factor/cofilin-like domains (ADF domains) are present in a family of essential eukaryotic actin regulatory proteins. These proteins enhance the turnover rate of actin, and interact with actin monomers (G-actin) as well as actin filaments (F-actin), typically with a preference for ADP-G-actin subunits. The basic function of cofilin is to promote disassembly of aged actin filaments. Vertebrates have three isoforms of cofilin: cofilin-1 (Cfl1, non-muscle cofilin), cofilin-2 (muscle cofilin), and ADF (destrin). When bound to actin monomers, cofilins inhibit their spontaneous exchange of nucleotides. The cooperative binding to (aged) ADP-F-actin induces a local change in the actin filament structure and further promotes aging. 133 matched cddid_all.tbl CDD cd11287 cd11287 200443 Sec23_C C-terminal Actin depolymerization factor-homology domain of Sec23. The C-terminal domain of the Sec23 subunit of the coat protein complex II (COPII) is distantly related to gelsolin-like repeats and the actin depolymerizing domains found in cofilin and similar proteins. Sec23 forms a tight complex with Sec24. The cytoplasmic Sec23/24 complex is recruited together with Sar1-GTP and Sec13/31 to induce coat polymerization and membrane deformation in the forming of COPII-coated endoplasmic reticulum vesicles. The function of the Sec23 C-terminal domain is unclear. 121 matched cddid_all.tbl CDD cd11288 cd11288 200444 gelsolin_S5_like Gelsolin sub-domain 5-like domain found in gelsolin, severin, villin, and related proteins. Gelsolin repeats occur in gelsolin, severin, villin, advillin, villidin, supervillin, flightless, quail, fragmin, and other proteins, usually in several copies. They co-occur with villin headpiece domains, leucine-rich repeats, and several other domains. These gelsolin-related actin binding proteins (GRABPs) play regulatory roles in the assembly and disassembly of actin filaments; they are involved in F-actin capping, uncapping, severing, or the nucleation of actin filaments. Severing of actin filaments is Ca2+ dependent. Villins are also linked to generating bundles of F-actin with uniform filament polarity, which is most likely mediated by their extra villin headpiece domain. Many family members have also adopted functions in the nucleus, including the regulation of transcription. Supervillin, gelsolin, and flightless I are involved in intracellular signaling via nuclear hormone receptors. The gelsolin-like domain is distantly related to the actin depolymerizing domains found in cofilin and similar proteins. 92 matched cddid_all.tbl CDD cd11289 cd11289 200445 gelsolin_S2_like Gelsolin sub-domain 2-like domain found in gelsolin, severin, villin, and related proteins. Gelsolin repeats occur in gelsolin, severin, villin, advillin, villidin, supervillin, flightless, quail, fragmin, and other proteins, usually in several copies. They co-occur with villin headpiece domains, leucine-rich repeats, and several other domains. These gelsolin-related actin binding proteins (GRABPs) play regulatory roles in the assembly and disassembly of actin filaments; they are involved in F-actin capping, uncapping, severing, or the nucleation of actin filaments. Severing of actin filaments is Ca2+ dependent. Villins are also linked to generating bundles of F-actin with uniform filament polarity, which is most likely mediated by their extra villin headpiece domain. Many family members have also adopted functions in the nucleus, including the regulation of transcription. Supervillin, gelsolin, and flightless I are involved in intracellular signaling via nuclear hormone receptors. The gelsolin-like domain is distantly related to the actin depolymerizing domains found in cofilin and similar proteins. 92 matched cddid_all.tbl CDD cd11290 cd11290 200446 gelsolin_S1_like Gelsolin sub-domain 1-like domain found in gelsolin, severin, villin, and related proteins. Gelsolin repeats occur in gelsolin, severin, villin, advillin, villidin, supervillin, flightless, quail, fragmin, and other proteins, usually in several copies. They co-occur with villin headpiece domains, leucine-rich repeats, and several other domains. These gelsolin-related actin binding proteins (GRABPs) play regulatory roles in the assembly and disassembly of actin filaments; they are involved in F-actin capping, uncapping, severing, or the nucleation of actin filaments. Severing of actin filaments is Ca2+ dependent. Villins are also linked to generating bundles of F-actin with uniform filament polarity, which is most likely mediated by their extra villin headpiece domain. Many family members have also adopted functions in the nucleus, including the regulation of transcription. Supervillin, gelsolin, and flightless I are involved in intracellular signaling via nuclear hormone receptors. The gelsolin_like domain is distantly related to the actin depolymerizing domains found in cofilin and similar proteins. 113 matched cddid_all.tbl CDD cd11291 cd11291 200447 gelsolin_S6_like Gelsolin sub-domain 6-like domain found in gelsolin, severin, villin, and related proteins. Gelsolin repeats occur in gelsolin, severin, villin, advillin, villidin, supervillin, flightless, quail, fragmin, and other proteins, usually in several copies. They co-occur with villin headpiece domains, leucine-rich repeats, and several other domains. These gelsolin-related actin binding proteins (GRABPs) play regulatory roles in the assembly and disassembly of actin filaments; they are involved in F-actin capping, uncapping, severing, or the nucleation of actin filaments. Severing of actin filaments is Ca2+ dependent. Villins are also linked to generating bundles of F-actin with uniform filament polarity, which is most likely mediated by their extra villin headpiece domain. Many family members have also adopted functions in the nucleus, including the regulation of transcription. Supervillin, gelsolin, and flightless I are involved in intracellular signaling via nuclear hormone receptors. The gelsolin-like domain is distantly related to the actin depolymerizing domains found in cofilin and similar proteins. 99 matched cddid_all.tbl CDD cd11292 cd11292 200448 gelsolin_S3_like Gelsolin sub-domain 3-like domain found in gelsolin, severin, villin, and related proteins. Gelsolin repeats occur in gelsolin, severin, villin, advillin, villidin, supervillin, flightless, quail, fragmin, and other proteins, usually in several copies. They co-occur with villin headpiece domains, leucine-rich repeats, and several other domains. These gelsolin-related actin binding proteins (GRABPs) play regulatory roles in the assembly and disassembly of actin filaments; they are involved in F-actin capping, uncapping, severing, or the nucleation of actin filaments. Severing of actin filaments is Ca2+ dependent. Villins are also linked to generating bundles of F-actin with uniform filament polarity, which is most likely mediated by their extra villin headpiece domain. Many family members have also adopted functions in the nucleus, including the regulation of transcription. Supervillin, gelsolin, and flightless I are involved in intracellular signaling via nuclear hormone receptors. The gelsolin-like domain is distantly related to the actin depolymerizing domains found in cofilin and similar proteins. 98 matched cddid_all.tbl CDD cd11293 cd11293 200449 gelsolin_S4_like Gelsolin sub-domain 4-like domain found in gelsolin, severin, villin, and related proteins. Gelsolin repeats occur in gelsolin, severin, villin, advillin, villidin, supervillin, flightless, quail, fragmin, and other proteins, usually in several copies. They co-occur with villin headpiece domains, leucine-rich repeats, and several other domains. These gelsolin-related actin binding proteins (GRABPs) play regulatory roles in the assembly and disassembly of actin filaments; they are involved in F-actin capping, uncapping, severing, or the nucleation of actin filaments. Severing of actin filaments is Ca2+ dependent. Villins are also linked to generating bundles of F-actin with uniform filament polarity, which is most likely mediated by their extra villin headpiece domain. Many family members have also adopted functions in the nucleus, including the regulation of transcription. Supervillin, gelsolin, and flightless I are involved in intracellular signaling via nuclear hormone receptors. The gelsolin-like domain is distantly related to the actin depolymerizing domains found in cofilin and similar proteins. 101 matched cddid_all.tbl CDD cd11294 cd11294 199894 E_set_Esterase_like_N "N-terminal Early set domain associated with the catalytic domain of putative esterases. E or ""early"" set domains are associated with the catalytic domain of esterase at the N-terminal end. Esterases catalyze the hydrolysis of organic esters to release an alcohol or thiol and acid. The term esterase can be applied to enzymes that hydrolyze carboxylate, phosphate and sulphate esters, but is more often restricted to the first class of substrate. The N-terminal domain of esterase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chitinase, among others." 83 matched cddid_all.tbl CDD cd11295 cd11295 199917 Mago_nashi Mago nashi proteins, integral members of the exon junction complex. Members of this family, which was originally identified in Drosophila and called mago nashi, are integral members of the exon junction complex (EJC). The EJC is a multiprotein complex that is deposited on spliced mRNAs after intron removal at a conserved position upstream of the exon-exon junction, and transported to the cytoplasm where it has been shown to influence translation, surveillance, and localization of the spliced mRNA. It consists of four core proteins (eIF4AIII, Barentsz [Btz], Mago, and Y14), mRNA, and ATP and is supposed to be a binding platform for more peripherally and transiently associated factors along mRNA travel. Mago and Y14 form a stable heterodimer that stabilizes the complex by inhibiting eIF4AIII's ATPase activity. In humans, but not Drosophila, EJC is involved in nonsense-mediated mRNA decay (NMD) via binding to Upf3b, a central NMD effector. EJC is stripped off the mRNA during the first round of translation and then the complex components are transported back into the nucleus and recycled. The Mago-Y14 heterodimer has been shown to interact with the cytoplasmic protein PYM, an EJC disassembly factor, and specifically binds to the karyopherin nuclear receptor importin 13. 143 matched cddid_all.tbl CDD cd11296 cd11296 211383 O-FucT_like GDP-fucose protein O-fucosyltransferase and related proteins. O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes. 206 matched cddid_all.tbl CDD cd11297 cd11297 350237 PIN_LabA-like_N_1 uncharacterized subfamily of N-terminal LabA-like PIN domains. This N-terminal LabA-like PIN domain is found in a well conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. LabA from Synechococcus elongatus PCC 7942, (which does not contain this C-terminal domain), has been shown to play a role in cyanobacterial circadian timing. The LabA-like C-terminal domains characteristic of this subfamily may be related to the LOTUS domain family (which also co-occurs with LabA-like N-terminal domains). The function of the N-terminal domain is unknown. The LabA-like PIN domain family also includes the N-terminal domain of limkain b1, a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes. Other members are the LabA-like PIN domains of human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like PIN family. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 117 matched cddid_all.tbl CDD cd11298 cd11298 211384 O-FucT-2 GDP-fucose protein O-fucosyltransferase 2. O-FucT-2 adds O-fucose to thrombospondin type 1 repeats (TSRs), and appears conserved in bilateria. The O-fucosylation of TSRs appears to play a role in regulating secretion of metalloproteases of the ADAMTS superfamily. O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes. 374 matched cddid_all.tbl CDD cd11299 cd11299 211385 O-FucT_plant GDP-fucose protein O-fucosyltransferase, plant specific subfamily. Some members of this plant-specific family of O-fucosyltransferases have been annotated as auxin-independent growth promotors. The function of the protein seems unclear. O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes. 290 matched cddid_all.tbl CDD cd11300 cd11300 211386 Fut8_like Alpha 1-6-fucosyltransferase. Alpha 1,6-fucosyltransferase (Fut8) transfers a fucose moiety from GDP-fucose to the reducing terminal N-acetylglucosamine of the core structure of Asn-linked oligosaccharides, in a process termed core fucosylation. Core fucosylation is essential for the function of growth factor receptors. O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes. 328 matched cddid_all.tbl CDD cd11301 cd11301 211387 Fut1_Fut2_like "Alpha-1,2-fucosyltransferase. Alpha-1,2-fucosyltransferases (Fut1, Fut2) catalyze the transfer of alpha-L-fucose to the terminal beta-D-galactose residue of glycoconjugates via an alpha-1,2-linkage, generating carbohydrate structures that exhibit H-antigenicity for blood-group carbohydrates. These structures also act as ligands for morphogenesis, the adhesion of microbes, and metastasizing cancer cells. Fut1 is responsible for producing the H antigen on red blood cells. Fut2 is expressed in epithelia of secretory tissues, and individuals termed ""secretors"" have at least one functional copy of the gene; they secrete H antigen which is further processed into A and/or B antigens depending on the ABO genotype. O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes." 265 matched cddid_all.tbl CDD cd11302 cd11302 211388 O-FucT-1 GDP-fucose protein O-fucosyltransferase 1. The protein O-fucosyltransferase 1 (Ofut1 or O-FucT-1) adds O-fucose to EGF (epidermal growth factor-like) repeats. The O-fucsosylation of the Notch receptor signaling protein is dependent on this enzyme, which requires GDP-fucose as a substrate. O-fucose residues added to the target of O-FucT-1 may be further elongated by other glycosyltransferases. On top of O-fucosylation, O-FucT-1 may have other functions such as the regulation of the Notch receptor exit from the ER. Six highly conserved cysteines are present in O-FucT-1, which is a soluble ER protein, as well as a DXD-like motif (ERD), conserved in mammals, Drosophila, and C. elegans. Both features are characteristic of several glycosyltransferase families. The membrane-bound pre-protein is released by proteolysis and, as for most glycosyltransferases, is strongly activated by manganese. O-FucT-1 is similar to family 1 glycosyltransferases (GT1). 347 matched cddid_all.tbl CDD cd11303 cd11303 206636 Dystroglycan_repeat Cadherin-like repeat domain of alpha dystroglycan. Dystroglycan is a glycoprotein widely distributed in skeletal muscle and other tissues; the pre-protein is cleaved into two subunits (alpha and beta) that form a complex which links the extracellular matrix to the cytoskeleton. Cadherin-like dystroglycan repeats are present in the extracellular alpha-dystroglycan subunit, which binds to the alpha-2-laminin G-domain in the basement membrane as part of the dystrophin-dystroglycan-complex (DGC). DGC has been shown to interact with other etxtracellular matrix components as well, such as perlecan and m-agrin, suggesting that the complex may play various different roles depending on the extracellular ligand. 99 matched cddid_all.tbl CDD cd11304 cd11304 206637 Cadherin_repeat Cadherin tandem repeat domain. Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. The cadherin repeat domains occur as tandem repeats in the extracellular regions, which are thought to mediate cell-cell contact when bound to calcium. They play numerous roles in cell fate, signalling, proliferation, differentiation, and migration; members include E-, N-, P-, T-, VE-, CNR-, proto-, and FAT-family cadherin, desmocollin, and desmoglein, a large variety of domain architectures with varying repeat copy numbers. Cadherin-repeat containing proteins exist as monomers, homodimers, or heterodimers. 98 matched cddid_all.tbl CDD cd11305 cd11305 206765 alpha_DG_C C-terminal domain of alpha dystroglycan. Dystroglycan is a glycoprotein widely distributed in skeletal muscle and other tissues; the pre-protein is cleaved into two subunits (alpha and beta) that form a complex which links the extracellular matrix to the cytoskeleton. This C-terminal domain of the alpha-subunit appears to contact neighboring cadherin-like repeats of alpha dystroglycan, and may also be involved in interactions with other components of the dystrophin-dystroglycan-complex (DGC). DGC has been shown to interact with extracellular matrix components such as laminin, perlecan and m-agrin, suggesting that the complex may play various different roles depending on the extracellular ligand. 124 matched cddid_all.tbl CDD cd11306 cd11306 199915 M35_peptidyl-Lys Peptidase M35 domain of peptidyl-Lys metalloendopeptidases. This family M35 Zn2+-metallopeptidase extracellular domain is mostly found in proteins characterized as peptidyl-Lys metalloendopeptidases (MEP; peptidyllysine metalloproteinase; EC 3.4.24.20), including some well-characterized domains in Aeromonas salmonicida subsp. Achromogenes (AsaP1) and Grifola frondosa (GfMEP). These proteins specifically cleave peptidyl-lysine bonds (-X-Lys- where X may even be Pro) in proteins and peptides. AsaP1 peptidase has been shown to be important in the virulence of A. salmonicida subsp. achromogenes, having a major role in the fish innate immune response. Members of this family contain a unique zinc-binding motif (the aspzincin motif), defined by the HExxH + D motif where an aspartic acid is the third zinc ligand and is found in a GTXDXXYG or similar motif C-terminal to the His zinc ligands. 160 matched cddid_all.tbl CDD cd11307 cd11307 199916 M35_Asp_f2_like "Peptidase M35 domain of Asp f2, a major allergen from Aspergillus fumigatus, and related proteins; non catalytic. In this domain subgroup the unique zinc-binding motif (the aspzincin motif, characteristic of the M35 deuterolysin family, and defined as the ""HEXXH + D"" motif: two His ligands and Asp as third ligand), is poorly conserved and may not bind Zinc. Members of this subgroup also lack a key conserved Tyr residue which acts as a proton donor during metallopeptidase catalysis. These include Asp f2, a major allergen from Aspergillus fumigatus, which reacts with serum from patients with ABPA (allergic bronchopulmonary aspergillosis), and pH-regulated antigen 1 (PRA1) from Candida albicans, which has a role in fungal morphogenesis and perhaps in the host-parasite interaction during candidal infection. No protease activity has been detected for Asp f2 to date. This subgroup also includes Saccharomyces cerevisiae Zps1p. The expression of the Zsp1 gene is increased in response to zinc deficiency; it is a target of the Zap1p transcription factor." 179 matched cddid_all.tbl CDD cd11308 cd11308 200604 Peptidase_M14NE-CP-C_like Peptidase associated domain: C-terminal domain of M14 N/E carboxypeptidase; putative folding, regulation, or interaction domain. This domain is found C-terminal to the M14 carboxypeptidase (CP) N/E subfamily containing zinc-binding enzymes that hydrolyze single C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. The N/E subfamily includes enzymatically active members (carboxypeptidase N, E, M, D, and Z), as well as non-active members (carboxypeptidase-like protein 1, -2, aortic CP-like protein, and adipocyte enhancer binding protein-1) which lack the critical active site and substrate-binding residues considered necessary for activity. The active N/E enzymes fulfill a variety of cellular functions, including prohormone processing, regulation of peptide hormone activity, alteration of protein-protein or protein-cell interactions and transcriptional regulation. For M14 CPs, it has been suggested that this domain may assist in folding of the CP domain, regulate enzyme activity, or be involved in interactions with other proteins or with membranes; for carboxypeptidase M, it may interact with the bradykinin 1 receptor at the cell surface. This domain may also be found in other peptidase families. 76 matched cddid_all.tbl CDD cd11309 cd11309 206763 14-3-3_fungi Fungal 14-3-3 protein domain. This family containing fungal 14-3-3 domains includes the yeasts Saccharomyces cerevisiae (BMH1 and BMH2) and Schizosaccharomyces pombe (rad24 and rad25) isoforms. They possess distinctively variant C-terminal segments that differentiate them from the mammalian isoforms; the C-terminus is longer and BMH1/2 isoforms contain polyglutamine (polyQ) sequences of unknown function. The C-terminal segments of yeast 14-3-3 isoforms may thus behave in a different manner compared to the higher eukaryote isoforms. Yeast 14-3-3 proteins bind to numerous proteins involved in a variety of yeast cellular processes making them excellent model organisms for elucidating the function of the 14-3-3 protein family. BMH1 and BMH2 are positive regulators of rapamycin-sensitive signaling via TOR kinases while they play an inhibitory role in Rtg3p-dependent transcription involved in retrograde signaling. 14-3-3 domains are an essential part of 14-3-3 proteins, a ubiquitous class of regulatory, phosphoserine/threonine-binding proteins found in all eukaryotic cells, including yeast, protozoa and mammalian cells. 231 matched cddid_all.tbl CDD cd11310 cd11310 206764 14-3-3_1 14-3-3 protein domain. This 14-3-3 domain family includes proteins in Caenorhabditis elegans, the silkworm (Bombyx mori) as well as barley (Hordeum vulgare). In C. elegans, 14-3-3 proteins are SIR-2.1 binding partners which induce transcriptional activation of DAF-16 during stress and are required for the life-span extension conferred by extra copies of sir-2.1. In B. mori, the 14-3-3 proteins are expressed widely in larval and adult tissues, including the brain, fat body, Malpighian tube, silk gland, midgut, testis, ovary, antenna, and pheromone gland, and interact with the N-terminal fragment of Hsp60, suggesting that 14-3-3 (a molecular adaptor) and Hsp60 (a molecular chaperone) work together to achieve a wide range of cellular functions in B. mori. In barley aleurone cells, 14-3-3 proteins and members of the ABF transcription factor family have a regulatory function in the gibberellic acid (GA) pathway since the balance of GA and abscisic acid (ABA) is a determining factor during transition of embryogenesis and seed germination. 14-3-3 is an essential part of 14-3-3 proteins, a ubiquitous class of regulatory, phosphoserine/threonine-binding proteins found in all eukaryotic cells, including yeast, protozoa and mammalian cells. 230 matched cddid_all.tbl CDD cd11313 cd11313 200452 AmyAc_arch_bac_AmyA Alpha amylase catalytic domain found in archaeal and bacterial Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC 3.2.1.1) catalyzes the hydrolysis of alpha-(1,4) glycosidic linkages of glycogen, starch, related polysaccharides, and some oligosaccharides. This group includes firmicutes, bacteroidetes, and proteobacteria. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 336 matched cddid_all.tbl CDD cd11314 cd11314 200453 AmyAc_arch_bac_plant_AmyA Alpha amylase catalytic domain found in archaeal, bacterial, and plant Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC 3.2.1.1) catalyzes the hydrolysis of alpha-(1,4) glycosidic linkages of glycogen, starch, related polysaccharides, and some oligosaccharides. This group includes AmyA from bacteria, archaea, water fleas, and plants. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 302 matched cddid_all.tbl CDD cd11315 cd11315 200454 AmyAc_bac1_AmyA Alpha amylase catalytic domain found in bacterial Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC 3.2.1.1) catalyzes the hydrolysis of alpha-(1,4) glycosidic linkages of glycogen, starch, related polysaccharides, and some oligosaccharides. This group includes Firmicutes, Proteobacteria, Actinobacteria, and Cyanobacteria. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 352 matched cddid_all.tbl CDD cd11316 cd11316 200455 AmyAc_bac2_AmyA Alpha amylase catalytic domain found in bacterial Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC 3.2.1.1) catalyzes the hydrolysis of alpha-(1,4) glycosidic linkages of glycogen, starch, related polysaccharides, and some oligosaccharides. This group includes Chloroflexi, Dictyoglomi, and Fusobacteria. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 403 matched cddid_all.tbl CDD cd11317 cd11317 200456 AmyAc_bac_euk_AmyA Alpha amylase catalytic domain found in bacterial and eukaryotic Alpha amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC 3.2.1.1) catalyzes the hydrolysis of alpha-(1,4) glycosidic linkages of glycogen, starch, related polysaccharides, and some oligosaccharides. This group includes AmyA proteins from bacteria, fungi, mammals, insects, mollusks, and nematodes. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 329 matched cddid_all.tbl CDD cd11318 cd11318 200457 AmyAc_bac_fung_AmyA Alpha amylase catalytic domain found in bacterial and fungal Alpha amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC 3.2.1.1) catalyzes the hydrolysis of alpha-(1,4) glycosidic linkages of glycogen, starch, related polysaccharides, and some oligosaccharides. This group includes bacterial and fungal proteins. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 391 matched cddid_all.tbl CDD cd11319 cd11319 200458 AmyAc_euk_AmyA Alpha amylase catalytic domain found in eukaryotic Alpha-amylases (also called 1,4-alpha-D-glucan-4-glucanohydrolase). AmyA (EC 3.2.1.1) catalyzes the hydrolysis of alpha-(1,4) glycosidic linkages of glycogen, starch, related polysaccharides, and some oligosaccharides. This group includes eukaryotic alpha-amylases including proteins from fungi, sponges, and protozoans. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 375 matched cddid_all.tbl CDD cd11320 cd11320 200459 AmyAc_AmyMalt_CGTase_like Alpha amylase catalytic domain found in maltogenic amylases, cyclodextrin glycosyltransferase, and related proteins. Enzymes such as amylases, cyclomaltodextrinase (CDase), and cyclodextrin glycosyltransferase (CGTase) degrade starch to smaller oligosaccharides by hydrolyzing the alpha-D-(1,4) linkages between glucose residues. In the case of CGTases, an additional cyclization reaction is catalyzed yielding mixtures of cyclic oligosaccharides which are referred to as alpha-, beta-, or gamma-cyclodextrins (CDs), consisting of six, seven, or eight glucose residues, respectively. CGTases are characterized depending on the major product of the cyclization reaction. Besides having similar catalytic site residues, amylases and CGTases contain carbohydrate binding domains that are distant from the active site and are implicated in attaching the enzyme to raw starch granules and in guiding the amylose chain into the active site. The maltogenic alpha-amylase from Bacillus is a five-domain structure, unlike most alpha-amylases, but similar to that of cyclodextrin glycosyltransferase. In addition to the A, B, and C domains, they have a domain D and a starch-binding domain E. Maltogenic amylase is an endo-acting amylase that has activity on cyclodextrins, terminally modified linear maltodextrins, and amylose. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 389 matched cddid_all.tbl CDD cd11321 cd11321 200460 AmyAc_bac_euk_BE Alpha amylase catalytic domain found in bacterial and eukaryotic branching enzymes. Branching enzymes (BEs) catalyze the formation of alpha-1,6 branch points in either glycogen or starch by cleavage of the alpha-1,4 glucosidic linkage yielding a non-reducing end oligosaccharide chain, and subsequent attachment to the alpha-1,6 position. By increasing the number of non-reducing ends, glycogen is more reactive to synthesis and digestion as well as being more soluble. This group includes bacterial and eukaryotic proteins. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 406 matched cddid_all.tbl CDD cd11322 cd11322 200461 AmyAc_Glg_BE Alpha amylase catalytic domain found in the Glycogen branching enzyme (also called 1,4-alpha-glucan branching enzyme). The glycogen branching enzyme catalyzes the third step of glycogen biosynthesis by the cleavage of an alpha-(1,4)-glucosidic linkage and the formation a new alpha-(1,6)-branch by subsequent transfer of cleaved oligosaccharide. They are part of a group called branching enzymes which catalyze the formation of alpha-1,6 branch points in either glycogen or starch. This group includes proteins from bacteria, eukaryotes, and archaea. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 402 matched cddid_all.tbl CDD cd11323 cd11323 200462 AmyAc_AGS Alpha amylase catalytic domain found in Alpha 1,3-glucan synthase (also called uridine diphosphoglucose-1,3-alpha-glucan glucosyltransferase and 1,3-alpha-D-glucan synthase). Alpha 1,3-glucan synthase (AGS, EC 2.4.1.183) is an enzyme that catalyzes the reversible chemical reaction of UDP-glucose and [alpha-D-glucosyl-(1-3)]n to form UDP and [alpha-D-glucosyl-(1-3)]n+1. AGS is a component of fungal cell walls. The cell wall of filamentous fungi is composed of 10-15% chitin and 10-35% alpha-1,3-glucan. AGS is triggered in fungi as a response to cell wall stress and elongates the glucan chains in cell wall synthesis. This group includes proteins from Ascomycetes and Basidomycetes. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 569 matched cddid_all.tbl CDD cd11324 cd11324 200463 AmyAc_Amylosucrase Alpha amylase catalytic domain found in Amylosucrase. Amylosucrase is a glucosyltransferase that catalyzes the transfer of a D-glucopyranosyl moiety from sucrose onto an acceptor molecule. When the acceptor is another saccharide, only alpha-1,4 linkages are produced. Unlike most amylopolysaccharide synthases, it does not require any alpha-D-glucosyl nucleoside diphosphate substrate. In the presence of glycogen it catalyzes the transfer of a D-glucose moiety onto a glycogen branch, but in its absence, it hydrolyzes sucrose and synthesizes polymers, smaller maltosaccharides, and sucrose isoforms. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 536 matched cddid_all.tbl CDD cd11325 cd11325 200464 AmyAc_GTHase Alpha amylase catalytic domain found in Glycosyltrehalose trehalohydrolase (also called Maltooligosyl trehalose Trehalohydrolase). Glycosyltrehalose trehalohydrolase (GTHase) was discovered as part of a coupled system for the production of trehalose from soluble starch. In the first half of the reaction, glycosyltrehalose synthase (GTSase), an intramolecular glycosyl transferase, converts the glycosidic bond between the last two glucose residues of amylose from an alpha-1,4 bond to an alpha-1,1 bond, making a non-reducing glycosyl trehaloside. In the second half of the reaction, GTHase cleaves the alpha-1,4 glycosidic bond adjacent to the trehalose moiety to release trehalose and malto-oligosaccharide. Like isoamylase and other glycosidases that recognize branched oligosaccharides, GTHase contains an N-terminal extension and does not have the conserved calcium ion present in other alpha amylase family enzymes. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. Glycosyltrehalose Trehalohydrolase Maltooligosyltrehalose Trehalohydrolase 436 matched cddid_all.tbl CDD cd11326 cd11326 200465 AmyAc_Glg_debranch Alpha amylase catalytic domain found in glycogen debranching enzymes. Debranching enzymes facilitate the breakdown of glycogen through glucosyltransferase and glucosidase activity. These activities are performed by a single enzyme in mammals, yeast, and some bacteria, but by two distinct enzymes in Escherichia coli and other bacteria. Debranching enzymes perform two activities: 4-alpha-D-glucanotransferase (EC 2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). 4-alpha-D-glucanotransferase catalyzes the endohydrolysis of 1,6-alpha-D-glucoside linkages at points of branching in chains of 1,4-linked alpha-D-glucose residues. Amylo-alpha-1,6-glucosidase catalyzes the endohydrolysis of 1,6-alpha-D-glucoside linkages at points of branching in chains of 1,4-linked alpha-D-glucose residues. In Escherichia coli, GlgX is the debranching enzyme and malQ is the 4-alpha-glucanotransferase. TreX, an archaeal glycogen-debranching enzyme has dual activities like mammals and yeast, but is structurally similar to GlgX. TreX exists in two oligomeric states, a dimer and tetramer. Isoamylase (EC 3.2.1.68) is one of the starch-debranching enzymes that catalyzes the hydrolysis of alpha-1,6-glucosidic linkages specific in alpha-glucans such as amylopectin or glycogen and their beta-limit dextrins. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 433 matched cddid_all.tbl CDD cd11327 cd11327 200466 AmyAc_Glg_debranch_2 Alpha amylase catalytic domain found in glycogen debranching enzymes. Debranching enzymes facilitate the breakdown of glycogen through glucosyltransferase and glucosidase activity. These activities are performed by a single enzyme in mammals, yeast, and some bacteria, but by two distinct enzymes in Escherichia coli and other bacteria. Debranching enzymes perform two activities, 4-alpha-D-glucanotransferase (EC 2.4.1.25) and amylo-1,6-glucosidase (EC 3.2.1.33). 4-alpha-D-glucanotransferase catalyzes the endohydrolysis of 1,6-alpha-D-glucoside linkages at points of branching in chains of 1,4-linked alpha-D-glucose residues. Amylo-alpha-1,6-glucosidase catalyzes the endohydrolysis of 1,6-alpha-D-glucoside linkages at points of branching in chains of 1,4-linked alpha-D-glucose residues. The catalytic triad (DED), which is highly conserved in other debranching enzymes, is not present in this group. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 478 matched cddid_all.tbl CDD cd11328 cd11328 200467 AmyAc_maltase "Alpha amylase catalytic domain found in maltase (also known as alpha glucosidase) and related proteins. Maltase (EC 3.2.1.20) hydrolyzes the terminal, non-reducing (1->4)-linked alpha-D-glucose residues in maltose, releasing alpha-D-glucose. In most cases, maltase is equivalent to alpha-glucosidase, but the term ""maltase"" emphasizes the disaccharide nature of the substrate from which glucose is cleaved, and the term ""alpha-glucosidase"" emphasizes the bond, whether the substrate is a disaccharide or polysaccharide. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase." 470 matched cddid_all.tbl CDD cd11329 cd11329 200468 AmyAc_maltase-like Alpha amylase catalytic domain family found in maltase. Maltase (EC 3.2.1.20) hydrolyzes the terminal, non-reducing (1->4)-linked alpha-D-glucose residues in maltose, releasing alpha-D-glucose. The catalytic triad (DED) which is highly conserved in the other maltase group is not present in this subfamily. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 477 matched cddid_all.tbl CDD cd11330 cd11330 200469 AmyAc_OligoGlu Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase) and related proteins. Oligo-1,6-glucosidase (EC 3.2.1.10) hydrolyzes the alpha-1,6-glucosidic linkage of isomalto-oligosaccharides, pannose, and dextran. Unlike alpha-1,4-glucosidases (EC 3.2.1.20), it fails to hydrolyze the alpha-1,4-glucosidic bonds of maltosaccharides. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 472 matched cddid_all.tbl CDD cd11331 cd11331 200470 AmyAc_OligoGlu_like Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase) and related proteins. Oligo-1,6-glucosidase (EC 3.2.1.10) hydrolyzes the alpha-1,6-glucosidic linkage of isomalto-oligosaccharides, pannose, and dextran. Unlike alpha-1,4-glucosidases (EC 3.2.1.20), it fails to hydrolyze the alpha-1,4-glucosidic bonds of maltosaccharides. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 450 matched cddid_all.tbl CDD cd11332 cd11332 200471 AmyAc_OligoGlu_TS Alpha amylase catalytic domain found in oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), trehalose synthase (also called maltose alpha-D-glucosyltransferase), and related proteins. Oligo-1,6-glucosidase (EC 3.2.1.10) hydrolyzes the alpha-1,6-glucosidic linkage of isomaltooligosaccharides, pannose, and dextran. Unlike alpha-1,4-glucosidases (EC 3.2.1.20), it fails to hydrolyze the alpha-1,4-glucosidic bonds of maltosaccharides. Trehalose synthase (EC 5.4.99.16) catalyzes the isomerization of maltose to produce trehalulose. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 481 matched cddid_all.tbl CDD cd11333 cd11333 200472 AmyAc_SI_OligoGlu_DGase Alpha amylase catalytic domain found in Sucrose isomerases, oligo-1,6-glucosidase (also called isomaltase; sucrase-isomaltase; alpha-limit dextrinase), dextran glucosidase (also called glucan 1,6-alpha-glucosidase), and related proteins. The sucrose isomerases (SIs) Isomaltulose synthase (EC 5.4.99.11) and Trehalose synthase (EC 5.4.99.16) catalyze the isomerization of sucrose and maltose to produce isomaltulose and trehalulose, respectively. Oligo-1,6-glucosidase (EC 3.2.1.10) hydrolyzes the alpha-1,6-glucosidic linkage of isomaltooligosaccharides, pannose, and dextran. Unlike alpha-1,4-glucosidases (EC 3.2.1.20), it fails to hydrolyze the alpha-1,4-glucosidic bonds of maltosaccharides. Dextran glucosidase (DGase, EC 3.2.1.70) hydrolyzes alpha-1,6-glucosidic linkages at the non-reducing end of panose, isomaltooligosaccharides and dextran to produce alpha-glucose.The common reaction chemistry of the alpha-amylase family enzymes is based on a two-step acid catalytic mechanism that requires two critical carboxylates: one acting as a general acid/base (Glu) and the other as a nucleophile (Asp). Both hydrolysis and transglycosylation proceed via the nucleophilic substitution reaction between the anomeric carbon, C1 and a nucleophile. Both enzymes contain the three catalytic residues (Asp, Glu and Asp) common to the alpha-amylase family as well as two histidine residues which are predicted to be critical to binding the glucose residue adjacent to the scissile bond in the substrates. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 428 matched cddid_all.tbl CDD cd11334 cd11334 200473 AmyAc_TreS Alpha amylase catalytic domain found in Trehalose synthetase. Trehalose synthetase (TreS) catalyzes the reversible interconversion of trehalose and maltose. The enzyme catalyzes the reaction in both directions, but the preferred substrate is maltose. Glucose is formed as a by-product of this reaction. It is believed that the catalytic mechanism may involve the cutting of the incoming disaccharide and transfer of a glucose to an enzyme-bound glucose. This enzyme also catalyzes production of a glucosamine disaccharide from maltose and glucosamine. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 447 matched cddid_all.tbl CDD cd11335 cd11335 200474 AmyAc_MTase_N Alpha amylase catalytic domain found in maltosyltransferase. Maltosyltransferase (MTase), a maltodextrin glycosyltransferase, acts on starch and maltooligosaccharides. It catalyzes the transfer of maltosyl units from alpha-1,4-linked glucans or maltooligosaccharides to other alpha-1,4-linked glucans, maltooligosaccharides or glucose. MTase is a homodimer. The catalytic core domain has the (beta/alpha) 8 barrel fold with the active-site cleft formed at the C-terminal end of the barrel. Substrate binding experiments have led to the location of two distinct maltose-binding sites: one lies in the active-site cleft and the other is located in a pocket adjacent to the active-site cleft. It is a member of the alpha-amylase family, but unlike typical alpha-amylases, MTase does not require calcium for activity and lacks two histidine residues which are predicted to be critical for binding the glucose residue adjacent to the scissile bond in the substrates. The common reaction chemistry of the alpha-amylase family of enzymes is based on a two-step acid catalytic mechanism that requires two critical carboxylates: one acting as a general acid/base (Glu) and the other as a nucleophile (Asp). Both hydrolysis and transglycosylation proceed via the nucleophilic substitution reaction between the anomeric carbon, C1 and a nucleophile. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 538 matched cddid_all.tbl CDD cd11336 cd11336 200475 AmyAc_MTSase Alpha amylase catalytic domain found in maltooligosyl trehalose synthase (MTSase). Maltooligosyl trehalose synthase (MTSase) domain. MTSase and maltooligosyl trehalose trehalohydrolase (MTHase) work together to produce trehalose. MTSase is responsible for converting the alpha-1,4-glucosidic linkage to an alpha,alpha-1,1-glucosidic linkage at the reducing end of the maltooligosaccharide through an intramolecular transglucosylation reaction, while MTHase hydrolyzes the penultimate alpha-1,4 linkage of the reducing end, resulting in the release of trehalose. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 660 matched cddid_all.tbl CDD cd11337 cd11337 200476 AmyAc_CMD_like Alpha amylase catalytic domain found in cyclomaltodextrinases and related proteins. Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase (NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC 3.2.1.133) catalyze the hydrolysis of alpha-(1,4) glycosidic linkages on a number of substrates including cyclomaltodextrins (CDs), pullulan, and starch. These enzymes hydrolyze CDs and starch to maltose and pullulan to panose by cleavage of alpha-1,4 glycosidic bonds whereas alpha-amylases essentially lack activity on CDs and pullulan. They also catalyze transglycosylation of oligosaccharides to the C3-, C4- or C6-hydroxyl groups of various acceptor sugar molecules. Since these proteins are nearly indistinguishable from each other, they are referred to as cyclomaltodextrinases (CMDs). This group of CMDs is mainly bacterial. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 328 matched cddid_all.tbl CDD cd11338 cd11338 200477 AmyAc_CMD Alpha amylase catalytic domain found in cyclomaltodextrinases and related proteins. Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase (NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC 3.2.1.133) catalyze the hydrolysis of alpha-(1,4) glycosidic linkages on a number of substrates including cyclomaltodextrins (CDs), pullulan, and starch. These enzymes hydrolyze CDs and starch to maltose and pullulan to panose by cleavage of alpha-1,4 glycosidic bonds whereas alpha-amylases essentially lack activity on CDs and pullulan. They also catalyze transglycosylation of oligosaccharides to the C3-, C4- or C6-hydroxyl groups of various acceptor sugar molecules. Since these proteins are nearly indistinguishable from each other, they are referred to as cyclomaltodextrinases (CMDs). The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 389 matched cddid_all.tbl CDD cd11339 cd11339 200478 AmyAc_bac_CMD_like_2 Alpha amylase catalytic domain found in bacterial cyclomaltodextrinases and related proteins. Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase (NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC 3.2.1.133) catalyze the hydrolysis of alpha-(1,4) glycosidic linkages on a number of substrates including cyclomaltodextrins (CDs), pullulan, and starch. These enzymes hydrolyze CDs and starch to maltose and pullulan to panose by cleavage of alpha-1,4 glycosidic bonds whereas alpha-amylases essentially lack activity on CDs and pullulan. They also catalyze transglycosylation of oligosaccharides to the C3-, C4- or C6-hydroxyl groups of various acceptor sugar molecules. Since these proteins are nearly indistinguishable from each other, they are referred to as cyclomaltodextrinases (CMDs). This group of CMDs is bacterial. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 344 matched cddid_all.tbl CDD cd11340 cd11340 200479 AmyAc_bac_CMD_like_3 Alpha amylase catalytic domain found in bacterial cyclomaltodextrinases and related proteins. Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase (NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC 3.2.1.133) catalyze the hydrolysis of alpha-(1,4) glycosidic linkages on a number of substrates including cyclomaltodextrins (CDs), pullulan, and starch. These enzymes hydrolyze CDs and starch to maltose and pullulan to panose by cleavage of alpha-1,4 glycosidic bonds whereas alpha-amylases essentially lack activity on CDs and pullulan. They also catalyze transglycosylation of oligosaccharides to the C3-, C4- or C6-hydroxyl groups of various acceptor sugar molecules. Since these proteins are nearly indistinguishable from each other, they are referred to as cyclomaltodextrinases (CMDs). This group of CMDs is bacterial. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 407 matched cddid_all.tbl CDD cd11341 cd11341 200480 AmyAc_Pullulanase_LD-like Alpha amylase catalytic domain found in Pullulanase (also called dextrinase; alpha-dextrin endo-1,6-alpha glucosidase), limit dextrinase, and related proteins. Pullulanase is an enzyme with action similar to that of isoamylase; it cleaves 1,6-alpha-glucosidic linkages in pullulan, amylopectin, and glycogen, and in alpha-and beta-amylase limit-dextrins of amylopectin and glycogen. Pullulanases are very similar to limit dextrinases, although they differ in their action on glycogen and the rate of hydrolysis of limit dextrins. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 406 matched cddid_all.tbl CDD cd11343 cd11343 200481 AmyAc_Sucrose_phosphorylase-like Alpha amylase catalytic domain found in sucrose phosphorylase (also called sucrose glucosyltransferase, disaccharide glucosyltransferase, and sucrose-phosphate alpha-D glucosyltransferase). Sucrose phosphorylase is a bacterial enzyme that catalyzes the phosphorolysis of sucrose to yield glucose-1-phosphate and fructose. These enzymes do not have the conserved calcium ion present in other alpha amylase family enzymes. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 445 matched cddid_all.tbl CDD cd11344 cd11344 200482 AmyAc_GlgE_like Alpha amylase catalytic domain found in GlgE-like proteins. GlgE is a (1,4)-a-D-glucan:phosphate a-D-maltosyltransferase, involved in a-glucan biosynthesis in bacteria. It is also an anti-tuberculosis drug target. GlgE isoform I from Streptomyces coelicolor has the same catalytic and very similar kinetic properties to GlgE from Mycobacterium tuberculosis. GlgE from Streptomyces coelicolor forms a homodimer with each subunit comprising five domains (A, B, C, N, and S) and 2 inserts. Domain A is a catalytic alpha-amylase-type domain that along with domain N, which has a beta-sandwich fold and forms the core of the dimer interface, binds cyclodextrins. Domain A, B, and the 2 inserts define a well conserved donor pocket that binds maltose. Cyclodextrins competitively inhibit the binding of maltooligosaccharides to the S. coelicolor enzyme, indicating that the hydrophobic patch overlaps with the acceptor binding site. This is not the case in M. tuberculosis GlgE because cyclodextrins do not inhibit this enzyme, despite acceptor length specificity being conserved. Domain C is hypothesized to help stabilize domain A and could be involved in substrate binding. Domain S is a helix bundle that is inserted within the N domain and it plays a role in the dimer interface and interacts directly with domain B. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 355 matched cddid_all.tbl CDD cd11345 cd11345 200483 AmyAc_SLC3A2 Alpha amylase catalytic domain found in solute carrier family 3 member 2 proteins. 4F2 cell-surface antigen heavy chain (hc) is a protein that in humans is encoded by the SLC3A2 gene. 4F2hc is a multifunctional type II membrane glycoprotein involved in amino acid transport and cell fusion, adhesion, and transformation. It is related to bacterial alpha-glycosidases, but lacks alpha-glycosidase activity. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 326 matched cddid_all.tbl CDD cd11346 cd11346 200484 AmyAc_plant_IsoA Alpha amylase catalytic domain family found in plant isoamylases. Two types of debranching enzymes exist in plants: isoamylase-type (EC 3.2.1.68) and a pullulanase-type (EC 3.2.1.41, also known as limit-dextrinase). These efficiently hydrolyze alpha-(1,6)-linkages in amylopectin and pullulan. This group does not contain the conserved catalytic triad present in other alpha-amylase-like proteins. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 347 matched cddid_all.tbl CDD cd11347 cd11347 200485 AmyAc_1 Alpha amylase catalytic domain found in an uncharacterized protein family. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 391 matched cddid_all.tbl CDD cd11348 cd11348 200486 AmyAc_2 Alpha amylase catalytic domain found in an uncharacterized protein family. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The catalytic triad (DED) is not present here. The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 429 matched cddid_all.tbl CDD cd11349 cd11349 200487 AmyAc_3 Alpha amylase catalytic domain found in an uncharacterized protein family. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 456 matched cddid_all.tbl CDD cd11350 cd11350 200488 AmyAc_4 Alpha amylase catalytic domain found in an uncharacterized protein family. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 390 matched cddid_all.tbl CDD cd11352 cd11352 200489 AmyAc_5 Alpha amylase catalytic domain found in an uncharacterized protein family. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 443 matched cddid_all.tbl CDD cd11353 cd11353 200490 AmyAc_euk_bac_CMD_like Alpha amylase catalytic domain found in eukaryotic and bacterial cyclomaltodextrinases and related proteins. Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase (NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC 3.2.1.133) catalyze the hydrolysis of alpha-(1,4) glycosidic linkages on a number of substrates including cyclomaltodextrins (CDs), pullulan, and starch. These enzymes hydrolyze CDs and starch to maltose and pullulan to panose by cleavage of alpha-1,4 glycosidic bonds whereas alpha-amylases essentially lack activity on CDs and pullulan. They also catalyze transglycosylation of oligosaccharides to the C3-, C4- or C6-hydroxyl groups of various acceptor sugar molecules. Since these proteins are nearly indistinguishable from each other, they are referred to as cyclomaltodextrinases (CMDs). This group of CMDs is mainly bacterial. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 366 matched cddid_all.tbl CDD cd11354 cd11354 200491 AmyAc_bac_CMD_like Alpha amylase catalytic domain found in bacterial cyclomaltodextrinases and related proteins. Cyclomaltodextrinase (CDase; EC3.2.1.54), neopullulanase (NPase; EC 3.2.1.135), and maltogenic amylase (MA; EC 3.2.1.133) catalyze the hydrolysis of alpha-(1,4) glycosidic linkages on a number of substrates including cyclomaltodextrins (CDs), pullulan, and starch. These enzymes hydrolyze CDs and starch to maltose and pullulan to panose by cleavage of alpha-1,4 glycosidic bonds whereas alpha-amylases essentially lack activity on CDs and pullulan. They also catalyze transglycosylation of oligosaccharides to the C3-, C4- or C6-hydroxyl groups of various acceptor sugar molecules. Since these proteins are nearly indistinguishable from each other, they are referred to as cyclomaltodextrinases (CMDs). This group of CMDs is bacterial. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 357 matched cddid_all.tbl CDD cd11355 cd11355 200492 AmyAc_Sucrose_phosphorylase Alpha amylase catalytic domain found in sucrose phosphorylase (also called sucrose glucosyltransferase, disaccharide glucosyltransferase, and sucrose-phosphate alpha-D glucosyltransferase). Sucrose phosphorylase is a bacterial enzyme that catalyzes the phosphorolysis of sucrose to yield glucose-1-phosphate and fructose. These enzymes do not have the conserved calcium ion present in other alpha amylase family enzymes. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 433 matched cddid_all.tbl CDD cd11356 cd11356 200493 AmyAc_Sucrose_phosphorylase-like_1 Alpha amylase catalytic domain found in sucrose phosphorylase-like proteins (also called sucrose glucosyltransferase, disaccharide glucosyltransferase, and sucrose-phosphate alpha-D glucosyltransferase). Sucrose phosphorylase is a bacterial enzyme that catalyzes the phosphorolysis of sucrose to yield glucose-1-phosphate and fructose. These enzymes do not have the conserved calcium ion present in other alpha amylase family enzymes. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 458 matched cddid_all.tbl CDD cd11358 cd11358 206766 RNase_PH RNase PH-like 3'-5' exoribonucleases. RNase PH-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Evolutionarily related members can be fond in prokaryotes, archaea, and eukaryotes. Bacterial ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain and is involved in mRNA degradation in a 3'-5' direction. Archaeal exosomes contain two individually encoded RNase PH-like 3'-5' exoribonucleases and are required for 3' processing of the 5.8S rRNA. The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits, but it is not a phosphorolytic enzyme per se; it directly associates with Rrp44 and Rrp6, which are hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. All members of the RNase PH-like family form ring structures by oligomerization of six domains or subunits, except for a total of 3 subunits with tandem repeats in the case of PNPase, with a central channel through which the RNA substrate must pass to gain access to the phosphorolytic active sites. 218 matched cddid_all.tbl CDD cd11359 cd11359 200494 AmyAc_SLC3A1 Alpha amylase catalytic domain found in Solute Carrier family 3 member 1 proteins. SLC3A1, also called Neutral and basic amino acid transport protein rBAT or NBAT, plays a role in amino acid and cystine absorption. Mutations in the gene encoding SLC3A1 causes cystinuria, an autosomal recessive disorder characterized by the failure of proximal tubules to reabsorb filtered cystine and dibasic amino acids. The Alpha-amylase family comprises the largest family of glycoside hydrolases (GH), with the majority of enzymes acting on starch, glycogen, and related oligo- and polysaccharides. These proteins catalyze the transformation of alpha-1,4 and alpha-1,6 glucosidic linkages with retention of the anomeric center. The protein is described as having 3 domains: A, B, C. A is a (beta/alpha) 8-barrel; B is a loop between the beta 3 strand and alpha 3 helix of A; C is the C-terminal extension characterized by a Greek key. The majority of the enzymes have an active site cleft found between domains A and B where a triad of catalytic residues (Asp, Glu and Asp) performs catalysis. Other members of this family have lost the catalytic activity as in the case of the human 4F2hc, or only have 2 residues that serve as the catalytic nucleophile and the acid/base, such as Thermus A4 beta-galactosidase with 2 Glu residues (GH42) and human alpha-galactosidase with 2 Asp residues (GH31). The family members are quite extensive and include: alpha amylase, maltosyltransferase, cyclodextrin glycotransferase, maltogenic amylase, neopullulanase, isoamylase, 1,4-alpha-D-glucan maltotetrahydrolase, 4-alpha-glucotransferase, oligo-1,6-glucosidase, amylosucrase, sucrose phosphorylase, and amylomaltase. 456 matched cddid_all.tbl CDD cd11362 cd11362 206767 RNase_PH_bact Ribonuclease PH. Ribonuclease PH (RNase PH)-like 3'-5' exoribonucleases are enzymes that catalyze the 3' to 5' processing and decay of RNA substrates. Structurally all members of this family form hexameric rings (trimers of dimers). Bacterial RNase PH forms a homohexameric ring, and removes nucleotide residues following the -CCA terminus of tRNA. 227 matched cddid_all.tbl CDD cd11363 cd11363 206768 RNase_PH_PNPase_1 Polyribonucleotide nucleotidyltransferase, repeat 1. Polyribonucleotide nucleotidyltransferase (PNPase) is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally, all members of this family form hexameric rings. In the case of PNPase the complex is a trimer, since each monomer contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction and in quality control of ribosomal RNA precursors. It is part of the RNA degradosome complex and binds to the scaffolding domain of the endoribonuclease RNase E. 229 matched cddid_all.tbl CDD cd11364 cd11364 206769 RNase_PH_PNPase_2 Polyribonucleotide nucleotidyltransferase, repeat 2. Polyribonucleotide nucleotidyltransferase (PNPase) is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally, all members of this family form hexameric rings. In the case of PNPase the complex is a trimer, since each monomer contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction and in quality control of ribosomal RNA precursors, with the second repeat containing the active site. PNPase is part of the RNA degradosome complex and binds to the scaffolding domain of the endoribonuclease RNase E. 223 matched cddid_all.tbl CDD cd11365 cd11365 206770 RNase_PH_archRRP42 RRP42 subunit of archaeal exosome. The RRP42 subunit of the archaeal exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of dimers). In archaea, the ring is formed by three Rrp41:Rrp42 dimers. The central chamber within the ring contains three phosphorolytic active sites located in an Rrp41 pocket at the interface between Rrp42 and Rrp41. The ring is capped by three copies of Rrp4 and/or Csl4 which contain putative RNA interaction domains. The archaeal exosome degrades single-stranded RNA (ssRNA) in the 3'-5' direction, but also can catalyze the reverse reaction of adding nucleoside diphosphates to the 3'-end of RNA which has been shown to lead to the formation of poly-A-rich tails on RNA. It is required for 3' processing of the 5.8S rRNA. 256 matched cddid_all.tbl CDD cd11366 cd11366 206771 RNase_PH_archRRP41 RRP41 subunit of archaeal exosome. The RRP41 subunit of the archaeal exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of dimers). In archaea, the ring is formed by three Rrp41:Rrp42 dimers. The central chamber within the ring contains three phosphorolytic active sites located in an Rrp41 pocket at the interface between Rrp42 and Rrp41. The ring is capped by three copies of Rrp4 and/or Csl4 which contain putative RNA interaction domains. The archaeal exosome degrades single-stranded RNA (ssRNA) in the 3'-5' direction, but also can catalyze the reverse reaction of adding nucleoside diphosphates to the 3'-end of RNA which has been shown to lead to the formation of poly-A-rich tails on RNA. 214 matched cddid_all.tbl CDD cd11367 cd11367 206772 RNase_PH_RRP42 RRP42 subunit of eukaryotic exosome. The RRP42 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. 272 matched cddid_all.tbl CDD cd11368 cd11368 206773 RNase_PH_RRP45 RRP45 subunit of eukaryotic exosome. The RRP45 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. 259 matched cddid_all.tbl CDD cd11369 cd11369 206774 RNase_PH_RRP43 RRP43 subunit of eukaryotic exosome. The RRP43 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. 261 matched cddid_all.tbl CDD cd11370 cd11370 206775 RNase_PH_RRP41 RRP41 subunit of eukaryotic exosome. The RRP41 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. 226 matched cddid_all.tbl CDD cd11371 cd11371 206776 RNase_PH_MTR3 MTR3 subunit of eukaryotic exosome. The MTR3 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. 210 matched cddid_all.tbl CDD cd11372 cd11372 206777 RNase_PH_RRP46 RRP46 subunit of eukaryotic exosome. The RRP46 subunit of eukaryotic exosome is a member of the RNase_PH family, named after the bacterial Ribonuclease PH, a 3'-5' exoribonuclease. Structurally all members of this family form hexameric rings (trimers of Rrp41-Rrp45, Rrp46-Rrp43, and Mtr3-Rrp42 dimers). The eukaryotic exosome core is composed of six individually encoded RNase PH-like subunits and three additional proteins (Rrp4, Csl4 and Rrp40) that form a stable cap and contain RNA-binding domains. The RNase PH-like subunits are no longer phosphorolytic enzymes, the exosome directly associates with Rrp44 and Rrp6, hydrolytic exoribonucleases related to bacterial RNase II/R and RNase D. The exosome plays an important role in RNA turnover. It plays a crucial role in the maturation of stable RNA species such as rRNA, snRNA and snoRNA, quality control of mRNA, and the degradation of RNA processing by-products and non-coding transcripts. 199 matched cddid_all.tbl CDD cd11374 cd11374 200603 CE4_u10 Putative catalytic domain of uncharacterized bacterial proteins from the carbohydrate esterase 4 superfamily. The family corresponds to a group of uncharacterized bacterial proteins with high sequence similarity to the catalytic domain of the six-stranded barrel rhizobial NodB-like proteins, which remove N-linked or O-linked acetyl groups of cell wall polysaccharides and belong to the larger carbohydrate esterase 4 (CE4) superfamily. 226 matched cddid_all.tbl CDD cd11375 cd11375 213029 Peptidase_M54 Peptidase family M54, also called archaemetzincins or archaelysins. Peptidase M54 (archaemetzincin or archaelysin) is a zinc-dependent aminopeptidase that contains the consensus zinc-binding sequence HEXXHXXGXXH/D and a conserved Met residue at the active site, and is thus classified as a metzincin. Archaemetzincins, first identified in archaea, are also found in bacteria and eukaryotes, including two human members, archaemetzincin-1 and -2 (AMZ1 and AMZ2). AMZ1 is mainly found in the liver and heart while AMZ2 is primarily expressed in testis and heart; both have been reported to degrade synthetic substrates and peptides. The Peptidase M54 family contains an extended metzincin concensus sequence of HEXXHXXGX3CX4CXMX17CXXC such that a second zinc ion is bound to four cysteines, thus resembling a zinc finger. Phylogenetic analysis of this family reveals a complex evolutionary process involving a series of lateral gene transfer, gene loss and genetic duplication events. 173 matched cddid_all.tbl CDD cd11376 cd11376 271138 Imelysin-like imelysin also called Peptidase M75. This family includes insulin-cleaving membrane protease (imelysin, ICMP), imelysin-like protein (IPPA from Psychrobacter arcticus), iron-regulated protein A (IrpA) and iron-transporter EfeO-like alginate-binding protein (Algp7). Imelysin is a membrane protein with the active site outside the cell envelope. It is also called the peptidase M75 since the HxxE sequence motif characteristic of the M14 peptidase is completely conserved. However, the overall structure and the GxHxxE motif region differ from the known HxxE metallopeptidases, suggesting that imelysin-like proteins may not be peptidases. Imelysin's cleavage of the oxidized insulin B chain shows a preference for aromatic hydrophobic amino acids at P1'. Imelysin was first identified in Pseudomonas aeruginosa and has also been shown to cleave fibrinogen. The tertiary structure shows a fold consisting of two domains, each consisting of a bundle of four helices that are similar to each other, implying an ancient gene duplication and fusion event. In addition to an imelysin-like domain, Algp7 typically contains an N-terminal cupredoxin (CUP) domain and has a deep cleft between the 4-helix bundles sufficiently large to accommodate macromolecules such as alginate polysaccharide. 253 matched cddid_all.tbl CDD cd11377 cd11377 206778 Pro-peptidase_S53 Activation domain of S53 peptidases. Members of this family are found in various subtilase propeptides, such as pro-kumamolysin and tripeptidyl peptidase I, and adopt a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptidase. 139 matched cddid_all.tbl CDD cd11378 cd11378 211390 DUF296 Domain of unknown function found in archaea, bacteria, and plants. This domain is found in proteins that contain AT-hook motifs, which suggests a role in DNA-binding for the proteins as a whole. Three conserved histidine residues appear to form a zinc-binding site, and the domain has been observed to form homotrimers. It co-occurs with a thioredoxin-like domain in uncharacterized cyanobacterial proteins. 113 matched cddid_all.tbl CDD cd11379 cd11379 211391 DUF4425 Uncharacterized protein conserved in Bacteroidetes. This family appears to form homodimers, the 3D structure has been determined by both NMR and X-ray crystallography. 119 matched cddid_all.tbl CDD cd11380 cd11380 211392 Ribosomal_S8e_like Eukaryotic/archaeal ribosomal protein S8e and similar proteins. This family contains the eukaryotic/archaeal ribosomal protein S8, a component of the small ribosomal subunits, as well as the NSA2 gene product. 138 matched cddid_all.tbl CDD cd11381 cd11381 211393 NSA2 pre-ribosomal protein NSA2 (Nop seven-associated 2). NSA2 appears to be a protein required for the maturation of 27S pre-rRNA in yeast; it has been characterized in mammalian cells as a nucleolar protein that might play a role in the regulation of the cell cycle and in cell proliferation. 257 matched cddid_all.tbl CDD cd11382 cd11382 211394 Ribosomal_S8e Eukaryotic/archaeal ribosomal protein S8e (RPS8). The eukaryotic/archaeal ribosomal protein S8 is a component of the small (40S in eukaryotes, 30S in archaea) ribosomal subunits and interacts tightly with 18S rRNA (16S rRNA in archaea, presumably). 122 matched cddid_all.tbl CDD cd11383 cd11383 206743 YfjP YfjP GTPase. The Era (E. coli Ras-like protein)-like YfjP subfamily includes several uncharacterized bacterial GTPases that are similar to Era. They generally show sequence conservation in the region between the Walker A and B motifs (G1 and G3 box motifs), to the exclusion of other GTPases. Era is characterized by a distinct derivative of the KH domain (the pseudo-KH domain) which is located C-terminal to the GTPase domain. 140 matched cddid_all.tbl CDD cd11384 cd11384 206744 RagA_like Rag GTPase, subfamily of Ras-related GTPases, includes Ras-related GTP-binding proteins A and B. RagA and RagB are closely related Rag GTPases (ras-related GTP-binding protein A and B) that constitute a unique subgroup of the Ras superfamily, and are functional homologs of Saccharomyces cerevisiae Gtr1. These domains function by forming heterodimers with RagC or RagD, and similarly, Gtr1 dimerizes with Gtr2, through the carboxy-terminal segments. They play an essential role in regulating amino acid-induced target of rapamycin complex 1 (TORC1) kinase signaling, exocytic cargo sorting at endosomes, and epigenetic control of gene expression. In response to amino acids, the Rag GTPases guide the TORC1 complex to activate the platform containing Rheb proto-oncogene by driving the relocalization of mTORC1 from discrete locations in the cytoplasm to a late endosomal and/or lysosomal compartment that is Rheb-enriched and contains Rab-7. 286 matched cddid_all.tbl CDD cd11385 cd11385 206745 RagC_like Rag GTPase, subfamily of Ras-related GTPases, includes Ras-related GTP-binding proteins C and D. RagC and RagD are closely related Rag GTPases (ras-related GTP-binding protein C and D) that constitute a unique subgroup of the Ras superfamily, and are functional homologs of Saccharomyces cerevisiae Gtr2. These domains form heterodimers with RagA or RagB, and similarly, Gtr2 dimerizes with Gtr1 in order to function. They play an essential role in regulating amino acid-induced target of rapamycin complex 1 (TORC1) kinase signaling, exocytic cargo sorting at endosomes, and epigenetic control of gene expression. In response to amino acids, the Rag GTPases guide the TORC1 complex to activate the platform containing Rheb proto-oncogene by driving the relocalization of mTORC1 from discrete locations in the cytoplasm to a late endosomal and/or lysosomal compartment that is Rheb-enriched and contains Rab-7. 175 matched cddid_all.tbl CDD cd11386 cd11386 206779 MCP_signal Methyl-accepting chemotaxis protein (MCP), signaling domain. Methyl-accepting chemotaxis proteins (MCPs or chemotaxis receptors) are an integral part of the transmembrane protein complex that controls bacterial chemotaxis, together with the histidine kinase CheA, the receptor-coupling protein CheW, receptor-modification enzymes, and localized phosphatases. MCPs contain a four helix trans membrane region, an N-terminal periplasmic ligand binding domain, and a C-terminal HAMP domain followed by a cytoplasmic signaling domain. This C-terminal signaling domain dimerizes into a four-helix bundle and interacts with CheA through the adaptor protein CheW. 200 matched cddid_all.tbl CDD cd11387 cd11387 381393 bHLHzip_USF_MITF basic Helix-Loop-Helix-zipper (bHLHzip) domain found in USF/MITF family. The USF (upstream stimulatory factor)/MITF (microphthalmia-associated transcription factor) family includes two bHLHzip transcription factor subfamilies. USFs are ubiquitously expressed and key regulators of a wide number of gene regulation networks, including the stress and immune responses, cell cycle and proliferation, lipid and glucid metabolism. USFs recruit chromatin remodeling enzymes and interact with co-activators and the members of the transcription pre-initiation complex. USFs interact with high affinity to E-box regulatory elements. The MITF (also known as microphthalmia-TFE, or MiT) subfamily comprises four genes in mammals (MITF, TFE3, TFEB, and TFEC); each gene has different functions. MITF is involved in neural crest melanocytes development as well as the pigmented retinal epithelium. TFEB is required for vascularization of the mouse placenta. TFE3 is involved in B cell function. TFEC regulates gene expression in macrophages. The MITF subfamily proteins can form homodimers or heterodimers with each other but not with other bHLH or bHLHzip proteins. 58 matched cddid_all.tbl CDD cd11388 cd11388 381394 bHLH_ScINO2_like basic helix-loop-helix (bHLH) domain found in Saccharomyces cerevisiae protein INO2 and similar proteins. INO2 is a positive regulatory factor required for depression of the co-regulated phospholipid biosynthetic enzymes in Saccharomyces cerevisiae. It is also involved in the expression of ITR1. 68 matched cddid_all.tbl CDD cd11389 cd11389 381395 bHLH-O_HERP_like basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES)-related repressor protein (HERP)-like family. The HERP-like family includes bHLH-O transcriptional regulators that are related to the Drosophila hairy and Enhancer-of-split proteins. They contain a basic helix-loop-helix (bHLH) domain with an invariant glycine residue in its basic region, an orange domain in the central region and YXXW sequence motif at its C-terminal region. HERP proteins (HEY1, HEY2 and HEYL) act as downstream effectors of Notch signaling. They are involved in cardiovascular development and have roles in somitogenesis, myogenesis and gliogenesis. Hairy and enhancer of split-related protein HELT is a transcriptional repressor expressed in the developing central nervous system. It binds preferentially to the canonical E box sequence 5'-CACGCG-3' and regulates neuronal differentiation and/or identity. Differentially expressed in chondrocytes proteins, DEC1 and DEC2, are widely expressed in both embryonic and adult tissues and have been implicated in apoptosis, cell proliferation, and circadian rhythms, as well as malignancy in various cancers. Drosophila melanogaster protein clockwork orange (Cwo) is also included in this family. It is involved in the regulation of Drosophila circadian rhythms. It functions as both an activator and a repressor of clock gene expression. 55 matched cddid_all.tbl CDD cd11390 cd11390 381396 bHLH_TS tissue specific basic helix-loop-helix (bHLH-TS) domain family. Tissue specific bHLH domain family includes transcription regulators whose expression are restricted to certain tissues. They are involved in cell-fate determination and process in neurogenesis, cardiogenesis, myogenesis, and hematopoiesis and include proteins from myogenic regulatory factor (MRF) family, twist-related protein (TWIST) family, scleraxis-like family, heart- and neural crest derivatives-expressed protein (HAND) family, helix-loop-helix protein (HEN) family, musculin-like family, germline alpha (FIGLA) family, T-cell acute lymphocytic leukemia protein/ lymphoblastic leukemia-derived sequence (TAL/LYL) family, ovary, uterus and testis protein (OUT) family, mesoderm posterior protein (Mesp) family, muscle, intestine and stomach expression 1 (MIST-1) family, protein atonal homologs (ATOH) family, neurogenin (NGN) family, neurogenic differentiation factor (NeuroD) family, achaete-scute complex-like (ASCL) family, Fer3-like protein (FERD3L)-like family, and Oligodendrocyte lineage genes (OLIG) family of transcription factors. 55 matched cddid_all.tbl CDD cd11391 cd11391 381397 bHLH_PAS basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain family. bHLH-PAS domain has been found in a large group of bHLH transcription regulators that are involved in gene expression responding to environmental change and controlling aspects of neural development, including proteins from aryl hydrocarbon receptor nuclear translocator (ARNT) family, hypoxia-inducible factor (HIF) family, aryl hydrocarbon receptor (AhR) family, neuronal PAS domain-containing protein (NPAS) family, Circadian locomotor output cycles protein kaput (CLOCK)-like family, and single-minded (SIM) family. bHLH-PAS transcriptional regulatory factors have a bHLH DNA-binding domain followed by two PAS domains and a C-terminal activation or repression domain. bHLH-PAS family members can be divided into class I and class II based on their dimerization partner. bHLH-PAS class I factors include AhR, HIF and SIM. The best characterized bHLH-PAS Class II protein is the ubiquitous ARNT. Some members of bHLH-PAS family act as transcriptional coactivators (such as NCoA) that lack the ability to dimerize and bind DNA. 55 matched cddid_all.tbl CDD cd11392 cd11392 381398 bHLH_ScPHO4_like basic helix-loop-helix (bHLH) domain found in Saccharomyces cerevisiae phosphate system positive regulatory protein PHO4 and similar proteins. PHO4 is a transcriptional activator that regulates the expression of repressible phosphatase under phosphate starvation conditions in Saccharomyces cerevisiae. The PHO4 protein has four functional domains with the bHLH domain at its carboxyl-terminal region. It regulates transcription by binding to promoter of the genes as a homodimer. 80 matched cddid_all.tbl CDD cd11393 cd11393 381399 bHLH_AtbHLH_like basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana genes coding transcription factors and similar proteins. bHLH proteins are the second largest class of plant transcription factors that regulate transcription of genes that are involve in many essential physiological and developmental process. bHLH proteins are transcriptional regulators that are found in organisms from yeast to humans. The Arabidopsis bHLH proteins that have been characterized so far have roles in regulation of fruit dehiscence, cell development (carpel, anther and epidermal), phytochrome signaling, flavonoid biosynthesis, hormone signaling and stress responses. 53 matched cddid_all.tbl CDD cd11394 cd11394 381400 bHLHzip_SREBP basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein (SREBP) family. The SREBP family includes SREBP1 and SREBP2, which are bHLHzip transcriptional activator of genes encoding proteins essential for cholesterol biosynthesis/uptake and fatty acid biosynthesis. SREBP1 and SREBP2 are principally found in the liver and in adipocytes and made up of an N-terminal transcription factor portion (composed of an activation domain, a bHLHzip domain, and a nuclear localization signal), a hydrophobic region containing two membrane spanning regions, and a C-terminal regulatory segment. They recognize a symmetric sterol regulatory element (TCACNCCAC) instead of E-box. 73 matched cddid_all.tbl CDD cd11395 cd11395 381401 bHLHzip_SREBP_like basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein (SREBP) family and similar proteins. The SREBP family includes SREBP1 and SREBP2, which are bHLHzip transcriptional activator of genes encoding proteins essential for cholesterol biosynthesis/uptake and fatty acid biosynthesis. SREBP1 and SREBP2 are principally found in the liver and in adipocytes and made up of an N-terminal transcription factor portion (composed of an activation domain, a bHLHzip domain, and a nuclear localization signal), a hydrophobic region containing two membrane spanning regions, and a C-terminal regulatory segment. They recognize a symmetric sterol regulatory element (TCACNCCAC) instead of E-box. The family also includes Saccharomyces cerevisiae transcription factor HMS1 (also termed high-copy MEP suppressor protein 1) and serine-rich protein TYE7. HMS1 is a putative bHLHzip transcription factor involved in exit from mitosis and pseudohyphal differentiation. TYE7, also termed basic-helix-loop-helix protein SGC1, is a putative bHLHzip transcription activator required for Ty1-mediated glycolytic gene expression. TYE7 N-terminal is extremely rich in serine residues. It binds DNA on E-box motifs, 5'-CANNTG-3'. TYE7 is not essential for growth. 87 matched cddid_all.tbl CDD cd11396 cd11396 381402 bHLHzip_USF basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factors, USF1, USF2 and similar proteins. Upstream stimulatory factor 1 and 2 (USF-1 and USF-2) are members of bHLHzip transcription factor family. USFs are ubiquitously expressed and key regulators of a wide number of gene regulation networks, including the stress and immune responses, cell cycle and proliferation, lipid and glucid metabolism. USFs recruit chromatin remodeling enzymes and interact with co-activators and the members of the transcription pre-initiation complex. USFs interact with high affinity to E-box regulatory elements. 58 matched cddid_all.tbl CDD cd11397 cd11397 381403 bHLHzip_MITF_like basic Helix-Loop-Helix-zipper (bHLHzip) domain found in the microphthalmia-associated transcription factor family (MITF) family. The MITF (also known as microphthalmia-TFE, or MiT) family is a small family that contain a basic helix loop helix domain associated with a leucine zipper (bHLHZip). The MITF family comprises four genes in mammals (MITF, TFE3, TFEB, and TFEC); each gene has different functions. MITF is involved in neural crest melanocytes development as well as the pigmented retinal epithelium. TFEB is required for vascularization of the mouse placenta. TFE3 is involved in B cell function. TFEC regulates gene expression in macrophages. The MITF family can form homodimers or heterodimers with each other but not with other bHLH or bHLHzip proteins. 69 matched cddid_all.tbl CDD cd11398 cd11398 381404 bHLHzip_scCBP1 basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Saccharomyces cerevisiae centromere-binding protein 1 (CBP-1) and similar proteins. CBP-1, also termed centromere promoter factor 1 (CPF1), or centromere-binding factor 1 (CBF1), is a bHLHzip protein that is required for chromosome stability and methionine prototrophy. It binds as a homodimer to the centromere DNA elements I (CDEI, GTCACATG) region of the centromere that is required for optimal centromere function. 89 matched cddid_all.tbl CDD cd11399 cd11399 381405 bHLHzip_scHMS1_like basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Saccharomyces cerevisiae transcription factor HMS1 and similar proteins. HMS1, also termed high-copy MEP suppressor protein 1, is a putative bHLHzip transcription factor involved in exit from mitosis and pseudohyphal differentiation. 96 matched cddid_all.tbl CDD cd11400 cd11400 381406 bHLHzip_Myc basic Helix-Loop-Helix-zipper (bHLHzip) domain found in the Myc family. The Myc family is a member of the bHLHzip family of transcription factors that play important roles in the control of normal cell proliferation, growth, survival and differentiation. All Myc isoforms contain two independently functioning polypeptide chain regions: N-terminal transactivating residues and a C-terminal bHLHzip segment. The bHLHzip family of bHLH transcription factors are characterized by a highly conserved N-terminal basic region that may bind DNA at a consensus hexanucleotide sequence known as the E-box (CANNTG) followed by HLH and leucine zipper motifs that may interact with other proteins to form homo- and heterodimers. Myc heterodimerizes with Max enabling specific binding to E-box DNA sequences in the promoters of target genes. The Myc proto-oncoprotein family includes at least five different functional members: c-, N-, L-, S- and B-Myc (which is lacking the bHLH domain). 80 matched cddid_all.tbl CDD cd11401 cd11401 381407 bHLHzip_Mad basic Helix-Loop-Helix-zipper (bHLHzip) domain found in the Mad family. Members of the Mad family (Mad1, Mxi, Mad3, and Mad4) bear the bHLHzip domain (also known as basic-helix-loop-helix-leucine-zipper or bHLH-LZ domain), which mediates heterodimerization to Max and the sequence-specific DNA binding ability to E-box DNA. Mad family proteins can repress transcription at the E-box through their interaction with co-repressors. Mad family proteins antagonize Myc function in transactivation and transformation and they are growth/tumor suppressors. The developmental phenotypes of the individual Mad family member knockout mice are relatively mild- all these mice have been shown to be viable and normal. 76 matched cddid_all.tbl CDD cd11402 cd11402 381408 bHLHzip_Mnt basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-binding protein Mnt and similar proteins. Mnt, also termed Class D basic helix-loop-helix protein 3 (bHLHd3), or Myc antagonist MNT, or protein ROX, is a bHLHZip transcriptional repressor that binds DNA as a heterodimer with MAX. It binds to the canonical E box sequence 5'-CACGTG-3' and, with higher affinity, to 5'-CACGCG-3'. Mnt has an important role as an antagonist and regulator of Myc activities and it is a potential tumor suppressor. Mnt is ubiquitously expressed. Mnt-deficient mice shown to exhibit early postnatal lethality. 77 matched cddid_all.tbl CDD cd11403 cd11403 381409 bHLH_scINO4_like basic Helix-Loop-Helix (bHLH) domain found in Saccharomyces cerevisiae INO4 and similar proteins. INO4 is a bHLH transcriptional activator of phospholipid synthetic genes (such as INO1, CHO1/PSS, CHO2/PEM1, OPI3/PEM2, etc.). It is required for de-repression of phospholipid biosynthetic gene expression in response to inositol deprivation in yeast. INO4 dimerizes with INO2 and binds to an UAS DNA element to control expression of the genes whose expression is inositol-responsive. 71 matched cddid_all.tbl CDD cd11404 cd11404 381410 bHLHzip_Mlx_like basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) family. Mlx, also termed Class D basic helix-loop-helix protein 13 (bHLHd13), or Max-like bHLHZip protein, or protein BigMax, or transcription factor-like protein 4, is a Max-like bHLHZip transcription regulator that interacts with the Max network of transcription factors. It forms a sequence-specific DNA-binding protein complex with some member of Mad family (Mad1 and Mad4) and Mondo family but not the Myc family and bind the E-box DNA to control transcription. The family also includes Saccharomyces cerevisiae INO4, which is a bHLH transcriptional activator of phospholipid synthetic genes (such as INO1, CHO1/PSS, CHO2/PEM1, OPI3/PEM2, etc.). It is required for de-repression of phospholipid biosynthetic gene expression in response to inositol deprivation in yeast. 70 matched cddid_all.tbl CDD cd11405 cd11405 381411 bHLHzip_MLXIP_like basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MLX-interacting protein (MLXIP), MLX-interacting protein-like (MLXIPL) and similar proteins. The family includes MLXIP and MLXIPL. MLXIP, also termed Class E basic helix-loop-helix protein 36 (bHLHe36), or transcriptional activator MondoA, is a bHLHZip transcriptional activator that binds DNA as a heterodimer with Mlx. It binds to the canonical E box sequence 5'-CACGTG-3' and plays a role in transcriptional activation of glycolytic target genes. MLXIP is most highly expressed in skeletal muscle and functions as an indirect glucose sensor, by sensing glucose 6-phosphate and shuttling between the nucleus and the cytoplasm. MLXIPL, also termed carbohydrate-responsive element-binding protein (ChREBP), or Class D basic helix-loop-helix protein 14 (bHLHd14), or MLX interactor, or WS basic-helix-loop-helix leucine zipper protein (WS-bHLH), or Williams-Beuren syndrome chromosomal region 14 protein (WBSCR14), is a bHLHZip transcriptional factor integral to the regulation of glycolysis and lipogenesis in the liver. It forms heterodimers with the bHLHZip protein Mlx to bind the DNA sequence 5'-CACGTG-3'. 74 matched cddid_all.tbl CDD cd11406 cd11406 381412 bHLHzip_Max basic Helix-Loop-Helix-zipper (bHLHzip) domain found in protein Max and similar proteins. Max, also termed Class D basic helix-loop-helix protein 4 (bHLHd4), or Myc-associated factor X, is a bHLHZip transcription regulator that forms a sequence-specific DNA-binding protein complex with MYC or MAD which recognizes the core sequence 5'-CAC[GA]TG-3'. The MYC:MAX complex is a transcriptional activator, whereas the MAD:MAX complex is a transcriptional repressor. Max homodimer bind DNA but is transcriptionally inactive. Targeted deletion of max results in early embryonic lethality in mice. 69 matched cddid_all.tbl CDD cd11407 cd11407 381413 bHLH-O_HERP basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES)-related repressor protein (HERP) family. HERP (also called Hey/Hesr/HRT/CHF/gridlock) proteins corresponds to a family of bHLH-O transcriptional repressors that are related to the Drosophila hairy and Enhancer-of-split proteins and act as downstream effectors of Notch signaling. They contain a basic helix-loop-helix (bHLH) domain with an invariant glycine residue in its basic region, an orange domain in the central region and YXXW sequence motif at its C-terminal region. HERP proteins are involved in cardiovascular development and have roles in somitogenesis, myogenesis and gliogenesis. 59 matched cddid_all.tbl CDD cd11408 cd11408 381414 bHLH-O_HELT basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split-related protein HELT and similar proteins. HELT, also termed HES/HEY-like transcription factor, is a bHLH-O transcriptional repressor expressed in the developing central nervous system. It binds preferentially to the canonical E box sequence 5'-CACGCG-3' and regulates neuronal differentiation and/or identity. HELT could homodimerize and heterodimerize with other bHLH-O protein such as HES-5 or HEY-2 and bound to E box to repress gene transcription. 56 matched cddid_all.tbl CDD cd11409 cd11409 381415 bHLH-O_DEC basic helix-loop-helix-orange (bHLH-O) domain found in differentially expressed in chondrocytes protein (DEC) family. The DEC family includes two bHLH-O transcriptional repressors, DEC1 and DEC2, which are widely expressed in both embryonic and adult tissues and have been implicated in apoptosis, cell proliferation, and circadian rhythms, as well as malignancy in various cancers. They mediate the circadian rhythm by negatively regulating the activity of the clock genes and clock-controlled genes. They are induced by CLOCK:BMAL1 heterodimer via the CACGTG E-box in the promoter. 75 matched cddid_all.tbl CDD cd11410 cd11410 381416 bHLH_O_HES basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split (HES) family. The HES family includes bHLH-O transcriptional regulators that are related to the Drosophila hairy and Enhancer-of-split (HES) proteins. They contain a basic helix-loop-helix (bHLH) domain with an invariant proline residue in its basic region, an orange domain in the central region and a conserved tetrapeptide motif, WRPW, at its C-terminal region. HES family proteins form heterodimers or homodimers via their HLH domain and bind DNA to repress gene transcription that play an essential role in development of both compartment and boundary cells of the central nervous system. 54 matched cddid_all.tbl CDD cd11411 cd11411 381417 bHLH_TS_MRF basic helix-loop-helix (bHLH) domain found in myogenic regulatory factor (MRF) family. MRFs are a family of muscle-specific bHLH transcription proteins (MyoD, Myf5, Mrf4 and MyoG) that plays an essential role in regulating skeletal muscle development and growth. MRFs are capable of binding to E-box motifs as a heterodimer with E-proteins to regulate transcription expression. 56 matched cddid_all.tbl CDD cd11412 cd11412 381418 bHLH_TS_TWIST1 basic helix-loop-helix (bHLH) domain found in twist-related protein 1 (TWIST1) and similar proteins. TWIST1, also termed Class A basic helix-loop-helix protein 38 (bHLHa38), or H-twist, is a bHLH transcriptional regulator that inhibits myogenesis by sequestrating E proteins, inhibiting trans-activation by MEF2, and inhibiting DNA-binding by MYOD1 through physical interaction. It also represses expression of proinflammatory cytokines such as TNFA and IL1B. In addition, TWIST1 is involved in cancer development and progression. 77 matched cddid_all.tbl CDD cd11413 cd11413 381419 bHLH_TS_TAL_LYL basic helix-loop-helix (bHLH) domain found in T-cell acute lymphocytic leukemia protein/ lymphoblastic leukemia-derived sequence (TAL/LYL) family. The TAL/LYL family includes a group of bHLH transcription factors (TAL1, TAL2 and LYL1) implicated in T cell acute leukaemia. They act as mediators of T cell leukaemogenesis. TAL-1, also termed Class A basic helix-loop-helix protein 17 (bHLHa17), or stem cell protein (SCL), or T-cell leukemia/lymphoma protein 5, is a hematopoietic-specific bHLH transcription factor that functions in embryonic and adult hematopoiesis in vertebrates. It is also required for embryonic vascular remodeling. It acts as a regulator of erythroid differentiation and binds to regulatory regions of a large cohort of erythroid genes as part of a complex with GATA-1, LMO2 and Ldb1. TAL-2, also termed Class A basic helix-loop-helix protein 19 (bHLHa19), is a bHLH transcription factor essential for the normal brain development. Lyl-1, also termed Class A basic helix-loop-helix protein 18 (bHLHa18), or lymphoblastic leukemia-derived sequence 1, is a proto-oncogenic bHLH transcription factor that plays an important role in hematopoietic stem cell function and is required for the late stages of postnatal angiogenesis to limit the formation of new blood vessels, notably by regulating the activity of the small GTPase Rap1. LYL-1 deficiency induces a stress erythropoiesis. 60 matched cddid_all.tbl CDD cd11414 cd11414 381420 bHLH_TS_HEN basic helix-loop-helix (bHLH) domain found in helix-loop-helix protein (HEN) family. The HEN family includes two neuron-specific bHLH transcription factors, HEN-1 (also known as Nhlh1 or bHLHa35 or NSCL-1) and HEN-2 (also known as Nhlh2 or bHLHa34 or NSCL-2). They may serve as DNA-binding protein that is involved in the control of cell-type determination, possibly within the developing nervous system. 57 matched cddid_all.tbl CDD cd11415 cd11415 381421 bHLH_TS_FERD3L_NATO3 basic helix-loop-helix (bHLH) domain found in Fer3-like protein (FERD3L) and similar proteins. FERD3L, also termed basic helix-loop-helix protein N-twist, or Class A basic helix-loop-helix protein 31 (bHLHa31), or nephew of atonal 3 (NATO3), or Neuronal twist (NTWIST), is a bHLH transcription factor expressed in the developing central nervous system (CNS). It regulates floor plate (FP) cells development. FP is a critical organizing center located at the ventral-most midline of the neural tube. FERD3L binds to the E-box and functions as inhibitor of transcription. 64 matched cddid_all.tbl CDD cd11416 cd11416 381422 bHLH_TS_ceHLH13_like basic helix-loop-helix (bHLH) domain found in Caenorhabditis elegans Helix-loop-helix protein 13 (HLH13) and similar proteins. Caenorhabditis elegans HLH13, also termed Fer3-like protein, or nephew of atonal 3, is a bHLH transcription factor that plays a role in the negative regulation of exit from L1 arrest and dauer diapause dependent on IIS signaling (insulin and insulin-like growth factor (IGF) signaling). 63 matched cddid_all.tbl CDD cd11417 cd11417 381423 bHLH_TS_PTF1A basic helix-loop-helix (bHLH) domain found in pancreas transcription factor 1 subunit alpha (PTF1A) and similar proteins. PTF1A, also termed Class A basic helix-loop-helix protein 29 (bHLHa29), or pancreas-specific transcription factor 1a, or bHLH transcription factor p48, or p48 DNA-binding subunit of transcription factor PTF1 (PTF1-p48), is a bHLH transcription factor implicated in the cell fate determination in various organs. It binds to the E-box consensus sequence 5'-CANNTG-3' and plays a role in early and late pancreas development and differentiation. 56 matched cddid_all.tbl CDD cd11418 cd11418 381424 bHLH_TS_ASCL basic helix-loop-helix (bHLH) domain found in achaete-scute complex-like (ASCL) family. The achaete-scute complex-like (ASCL, also known as achaete-scute complex homolog or ASH) family of bHLH transcription factors, ASCL1-5, have been implicated in cell fate specification and differentiation. They are critical for proper development of the nervous system. The deregulation of ASCL plays a key role in psychiatric and neurological disorders. ASCL-1, also termed Class A basic helix-loop-helix protein 46 (bHLHa46), or achaete-scute homolog 1 (ASH-1), or mammalian achaete-scute homolog 1 (Mash1), is a neural-specific bHLH transcription factor that is expressed in subsets of neural progenitors in both the central and peripheral nervous system. It plays a key role in neuronal differentiation and specification in the nervous system. ASCL-2, also termed achaete-scute homolog 2 (ASH-2), or Class A basic helix-loop-helix protein 45 (bHLHa45), or mammalian achaete-scute homolog 2 (Mash2), is a bHLH transcription factor that is involved in Schwann cell differentiation and control of proliferation in adult peripheral nerves. ASCL-3, also termed Class A basic helix-loop-helix protein 42 (bHLHa42), or bHLH transcriptional regulator Sgn-1, or achaete-scute homolog 3 (ASH-3), is a bHLH transcription factor specifically localized in the duct cells of the salivary glands. It may act as transcriptional repressor that inhibits myogenesis. The family also includes Drosophila melanogaster achaete-scute complex (AS-C) proteins, which consists of lethal of scute (also known as achaete-scute complex protein T3 or AST3), scute (also known as achaete-scute complex protein T4 or AST4), achaete (also known as achaete-scute complex protein T5 or AST5), and asense (also known as achaete-scute complex protein T8 or AST8). They are involved in the determination of the neuronal precursors in the peripheral nervous system and the central nervous system, as well as in sex determination and dosage compensation. 56 matched cddid_all.tbl CDD cd11419 cd11419 381425 bHLHzip_TFAP4 basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor AP-4 (TFAP4) and similar proteins. TFAP4, also termed activating enhancer-binding protein 4, or Class C basic helix-loop-helix protein 41 (bHLHc41), is a bHLHzip transcription factor that activates both viral and cellular genes involved in the regulation of cellular proliferation, stemness, and epithelial-mesenchymal transition by binding to the symmetrical DNA sequence 5'-CAGCTG-3'. 61 matched cddid_all.tbl CDD cd11420 cd11420 381426 bHLH_E-protein basic helix-loop-helix (bHLH) domain found in E proteins family. The E proteins family corresponds to class I bHLH proteins, which are widely expressed within the immune system and on which the majority of this chapter will be focused. Members in this family include E2A (also referred to as TCF-3), E47, TCF-12 (also referred to as HEB), and TCF-4 (also referred to as E2-2) in vertebrates, as well as the E protein ortholog, Daughterless (Da), from Drosophila melanogaster. E-proteins are expressed broadly and in certain complexes they are restricted to specific cell types. E-proteins homodimerize and heterodimerize with the tissue specific bHLH factors to bind DNA and regulate transcription and differentiation of cells during development. The activity of the E-proteins is regulated by two main mechanisms: first, the relative concentrations of E-proteins, tissue specific bHLH factors, and the Id proteins, and second, covalent modification. 47 matched cddid_all.tbl CDD cd11421 cd11421 381427 bHLH_TS_ATOH8 basic helix-loop-helix (bHLH) domain found in protein atonal homolog 8 (ATOH8) and similar proteins. ATOH8, also termed Class A basic helix-loop-helix protein 21 (bHLHa21), or helix-loop-helix protein hATH-6 (hATH6), is a bHLH shear-stress-responsive transcription factor expressed in activated satellite cells and proliferating myoblasts of human skeletal muscle tissue. It regulates endothelial cell proliferation, migration and tube-like structures formation. ATOH8 binds a palindromic (canonical) core consensus DNA sequence 5'-CANNTG- 3' known as an E-box element, possibly as a heterodimer with other bHLH proteins. 68 matched cddid_all.tbl CDD cd11422 cd11422 381428 bHLH_TS_FIGLA basic helix-loop-helix (bHLH) domain found in factor in the germline alpha (FIGLA) and similar proteins. FIGLA, also termed FIGalpha, or Class C basic helix-loop-helix protein 8 (bHLHc8), or folliculogenesis-specific basic helix-loop-helix protein, or transcription factor FIGa, is a germ-cell-specific bHLH transcription factor expressed abundantly in female and less so in male germ cells. It is essential for primordial follicle formation and expression of many genes required for folliculogenesis, fertilization and early embryonic survival. FIGLA knockout mice cannot form primordial follicles and lose oocytes rapidly after birth, whereas male gonads are unaffected. 56 matched cddid_all.tbl CDD cd11423 cd11423 381429 bHLH_TS_musculin_like basic helix-loop-helix (bHLH) domain found in musculin, transcription factor 21 (TCF-21) and similar proteins. The family includes two bHLH transcription factors, musculin and transcription factor 21 (TCF-21). Musculin, also termed activated B-cell factor 1 (ABF-1), or Class A basic helix-loop-helix protein 22 (bHLHa22), is a bHLH transcription factor expressed in activated B lymphocytes. It acts as a transcription repressor capable of inhibiting the transactivation capability of TCF3/E47. Musculin may play a role in regulating antigen-dependent B-cell differentiation. The mouse homolog, musculin, is suggested to be a repressor of myogenesis that is expressed in developing muscle and in the spleen. TCF-21, also termed capsulin, or Class A basic helix-loop-helix protein 23 (bHLHa23), or epicardin, or podocyte-expressed 1 (Pod-1), is a bHLH transcription factor expressed specifically in mesodermally-derived cells that surround the epithelium of the developing gastrointestinal, genitourinary and respiratory systems during mouse embryogenesis. It may play a role in the specification or differentiation of one or more subsets of epicardial cell types. 56 matched cddid_all.tbl CDD cd11424 cd11424 381430 bHLH_TS_OUT basic helix-loop-helix (bHLH) domain found in ovary, uterus and testis protein (OUT) family. The OUT family includes transcription factor 23 (TCF-23), transcription factor 24 (TCF-24) and similar proteins. TCF-23, also termed Class A basic helix-loop-helix protein 24 (bHLHa24), is a bHLH transcription factor that is essential for progesterone-dependent decidualization. The mouse homolog is also called ovary, uterus and testis protein (OUT), which is expressed predominantly in the reproductive organs such as the uterus, ovary and testis. It shows an Id-like inhibitory activity and functions as a negative regulator of bHLH factors through the formation of a functionally inactive heterodimeric complex. OUT inhibits the formation of TCF3 and MYOD1 homodimers and heterodimers, but lacks DNA binding activity. OUT is involved in the regulation or modulation of smooth muscle contraction of the uterus during pregnancy and particularly around the time of delivery. It also plays a role in the inhibition of myogenesis. Unlike typical bHLH factors, OUT proteins do not bind E-box (CANNTG) or N-box DNA sequences and inhibit DNA binding of homo- and heterodimers consisting of E12 and MyoD in gel mobility shift assays. TCF-24 is an uncharacterized bHLH transcription factor that shows high sequence similarity with TCF-23. 55 matched cddid_all.tbl CDD cd11425 cd11425 381431 bHLH_TS_Mesp_like basic helix-loop-helix (bHLH) domain found in mesoderm posterior protein (Mesp) family. Mesp, a bHLH tissue specific transcription factor, acts as a key regulator of the cardiovascular transcriptional network by inducing directly and/or indirectly the expression of the majority of key cardiovascular transcription factors. The Mesp family includes two bHLH transcription factors, Mesp1 and Mesp2. Mesp1, also termed Class C basic helix-loop-helix protein 5 (bHLHc5), promotes cardiovascular differentiation during embryonic development and embryonic stem cell differentiation. Mesp2, also termed Class C basic helix-loop-helix protein 6 (bHLHc6), plays an important role in somitogenesis. The family also includes mesogenin-1 (Msgn1) and similar proteins. Msgn1, also termed paraxial mesoderm-specific mesogenin1, or pMesogenin1 (pMsgn1), is a bHLH transcription factor required for maturation and segmentation of paraxial mesoderm. It may regulate the expression of T-box transcription factors essential for mesoderm formation and differentiation. 59 matched cddid_all.tbl CDD cd11426 cd11426 381432 bHLH_TS_MIST1_like basic helix-loop-helix (bHLH) domain found in muscle, intestine and stomach expression 1 (MIST-1) family. MIST-1, also termed Class A basic helix-loop-helix protein 15 (bHLHa15), or Class B basic helix-loop-helix protein 8 (bHLHb8), is a bHLH transcription factor expressed in pancreatic acinar cells and other serous exocrine cells. It is essential for cytoskeletal organization and secretory activity. It also functions as a potent endoplasmic reticulum (ER) stress-inducible transcriptional regulator. MIST-1 is capable of binding to E-box (CANNTG) motifs as a homodimer or a heterodimer with E-proteins (E12 and E47) to regulate transcription. The family also includes Drosophila melanogaster protein dimmed and similar proteins. Dimmed, also termed DIMM, is a bHLH transcription factor that regulates neurosecretory (NS) cell function and neuroendocrine cell fate in Drosophila. 56 matched cddid_all.tbl CDD cd11427 cd11427 381433 bHLH_TS_NeuroD basic helix-loop-helix (bHLH) domain found in neurogenic differentiation factor (NeuroD) family. The NeuroD family includes NeuroD1, NeuroD2, NeuroD4 and NeuroD6. NeuroD1, also termed Class A basic helix-loop-helix protein 3 (bHLHa3), is a neuronal bHLH transcription factor involved in the development and maintenance of the endocrine pancreas and neuronal elements. It acts as an essential regulator of glutamatergic neuronal differentiation. Loss of NeuroD1 causes ataxia, cerebellar hypoplasia, sensorineural deafness, and severe retinal dystrophy in mice. NeuroD2, also termed Class A basic helix-loop-helix protein 1 (bHLHa1), or NeuroD-related factor (NDRF), is a neuronal calcium-dependent bHLH transcription factor that induces neuronal differentiation and promotes neuronal survival. It plays a central role in thalamocortical synaptic maturation. NeuroD2 mediates calcium-dependent transcription activation by binding to E box-containing promoter. NeuroD4, also termed Class A basic helix-loop-helix protein 4 (bHLHa4), or protein atonal homolog 3 (ATH-3), or Atoh3, or Math-3, is a bHLH transcriptional activator that mediates neuronal differentiation. NeuroD6, also termed Class A basic helix-loop-helix protein 2 (bHLHa2), or protein atonal homolog 2 (ATH-2), or Atoh2, or Math2, or Nex1, is a neurogenic bHLH transcription factor involved in neuronal development, differentiation, and survival in Alzheimer's disease (AD) brains of both cohorts. It plays an integrative role in coordinating increase in mitochondrial mass with cytoskeletal remodeling, suggesting that it may act as a co-regulator of neuronal differentiation and energy metabolism. 55 matched cddid_all.tbl CDD cd11428 cd11428 381434 bHLH_TS_NGN basic helix-loop-helix (bHLH) domain found in neurogenin (NGN) family. The NGN family includes three neural-specific bHLH transcription factors, NGN1-3, which may function at neuroblast selection genes during the development of several neuronal lineages. NGN-1, also termed Class A basic helix-loop-helix protein 6 (bHLHa6), or neurogenic basic-helix-loop-helix protein, or neurogenic differentiation factor 3 (NeuroD3), is a neural-specific bHLH transcription factor involved in the initiation of neuronal differentiation. NGN-2, also termed Class A basic helix-loop-helix protein 8 (bHLHa8), or protein atonal homolog 4 (ATOH4), is a neural-specific bHLH transcription factor required for sensory neurogenesis. NGN-3, also termed Class A basic helix-loop-helix protein 7 (bHLHa7), or protein atonal homolog 5 (ATOH5), is a neural-specific bHLH transcription factor expressed in the developing central nervous system and the embryonic pancreas. It is involved in neurogenesis and plays an important role in spermatogenesis. 57 matched cddid_all.tbl CDD cd11429 cd11429 381435 bHLH_TS_OLIG basic helix-loop-helix (bHLH) domain found in Oligodendrocyte lineage genes (OLIG) family of transcription factors. The OLIG family includes three bHLH transcription factors, Oligo1-3, which are expressed in both the developing and mature central nervous system. Oligo1 and Oligo2 are expressed in a nervous tissue-specific manner, but Oligo3 is found mainly in non-neural tissues. Oligo (also known as Olig) have key roles in the specification of motor neurons, dorsal interneurons, and oligodendrocytes. Oligo1, also termed Class B basic helix-loop-helix protein 6 (bHLHb6), or Class E basic helix-loop-helix protein 21 (bHLHe21), promotes formation and maturation of oligodendrocytes, especially within the brain. Oligo2, also termed Class B basic helix-loop-helix protein 1 (bHLHb1), or Class E basic helix-loop-helix protein 19 (bHLHe19), or protein kinase C-binding protein 2, or protein kinase C-binding protein RACK17, is required for oligodendrocyte and motor neuron specification in the spinal cord, as well as for the development of somatic motor neurons in the hindbrain. It cooperates with OLIG1 to establish the MN progenitors (pMN) domain of the embryonic neural tube. Oligo3, also termed Class B basic helix-loop-helix protein 7 (bHLHb7), or Class E basic helix-loop-helix protein 20 (bHLHe20), is expressed in the ventricular zone of the dorsal alar plate of the hindbrain and involved in regulating the development of dorsal and ventral spinal cord. It may determine the distinct specification program of class A neurons in the dorsal part of the spinal cord and suppress specification of class B neurons. This family also includes two OLIG-related bHLH transcription factors, bHLHe22 and bHLHe23. bHLHe22, also termed Class B basic helix-loop-helix protein 5 (bHLHb5), or trinucleotide repeat-containing gene 20 protein, is a neural-specific transcriptional repressor that is expressed in both excitatory (unipolar brush cells) and inhibitory neurons (cartwheel cells) of the dorsal cochlear nucleus (DCN) during development. It is important for the proper development and/or survival of a number of neural cell types. bHLHe23, also termed Class B basic helix-loop-helix protein 4 (bHLHb4), is expressed in rod bipolar cells and is required for rod bipolar cell maturation. bHLHe23 have roles in spinal interneuron differentiation by mechanisms linked to the Notch signaling pathway. It modulates the expression of genes required for the differentiation and/or maintenance of pancreatic and neuronal cell types. 61 matched cddid_all.tbl CDD cd11430 cd11430 381436 bHLH_TS_ATOH1_like basic helix-loop-helix (bHLH) domain found in protein atonal homologs ATOH1, ATOH7 and similar proteins. The family includes ATOH1 and ATOH7. ATOH1, also termed Class A basic helix-loop-helix protein 14 (bHLHa14), or helix-loop-helix protein hATH-1 (hATH1), or Math1, or Cath1, is a proneural bHLH transcription factor that is essential for inner ear hair cell differentiation. It dimerizes with E47 and activates E-box (CANNTG) dependent transcription. ATOH1 is a mammalian homolog of the Drosophila melanogaster gene atonal and mouse atonal homolog 1 (Math1). ATOH7, also termed Class A basic helix-loop-helix protein 13 (bHLHa13), or helix-loop-helix protein hATH-5 (hATH5), or Math5, is a bHLH transcription factor involved in the differentiation of retinal ganglion cells. The family also includes protein Amos (also termed absent MD neurons and olfactory sensilla protein, or reduced olfactory organs protein, or rough eye protein). It is a bHLH transcription factor that promotes multiple dendritic neuron formation in the Drosophila peripheral nervous system. 56 matched cddid_all.tbl CDD cd11431 cd11431 381437 bHLH_TS_taxi_Dei basic helix-loop-helix (bHLH) domain found in Drosophila melanogaster protein taxi and similar proteins. Protein taxi, also termed protein delilah (Dei), is a bHLH transcription factor that is involved in regulation of cell adhesion and attachment that is expressed in specialized cells that provide anchoring sites to either muscles (tendon cells), or proprioceptors (chordotonal attachment cells) during embryonic development. It probably plays an important role in the differentiation of epidermal cells into the tendon cells that form the attachment sites for all muscles. 59 matched cddid_all.tbl CDD cd11432 cd11432 381438 bHLH-PAS_NPAS1_3_like basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing proteins, NPAS1, NPAS3 and similar proteins. The family includes neuronal PAS domain proteins NPAS1 and NPAS3, both of which are master regulators of neuropsychiatric function. NPAS1, also termed neuronal PAS1, or Basic-helix-loop-helix-PAS protein MOP5, or Class E basic helix-loop-helix protein 11 (bHLHe11), or member of PAS protein 5, or PAS domain-containing protein 5 (PASD5), is a bHLH-PAS transcriptional repressor expressed in the central nervous system and involved in neuronal differentiation. It is active during late embryogenesis and postnatal development. NPAS3, also termed neuronal PAS3, or Basic-helix-loop-helix-PAS protein MOP6, or Class E basic helix-loop-helix protein 12 (bHLHe12), or member of PAS protein 6, or PAS domain-containing protein 6 (PASD6), is a bHLH-PAS brain-enriched transcription factor that is involved in central nervous system development and neurogenesis. It is a replicated genetic risk factor for psychiatric disorders. Human chromosomal rearrangements that affect NPAS3 normal expression are associated with schizophrenia and mental retardation. 55 matched cddid_all.tbl CDD cd11433 cd11433 381439 bHLH-PAS_HIF basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor (HIF) family. The HIF family contains bHLH-PAS transcription regulators involved in oxygen homeostasis, including HIF1a, HIF2a, and HIF3a. They have been implicated in development, postnatal physiology as well as disease pathogenesis. HIF1a, also termed HIF-1-alpha, or HIF1-alpha, or ARNT-interacting protein, or Basic-helix-loop-helix-PAS protein MOP1, or Class E basic helix-loop-helix protein 78 (bHLHe78), or Member of PAS protein 1, or PAS domain-containing protein 8 (PASD8), functions as a master transcriptional regulator of the adaptive response to hypoxia. HIF2a, also termed HIF-2-alpha, or HIF2-alpha, or endothelial PAS domain-containing protein 1 (EPAS-1), or Basic-helix-loop-helix-PAS protein MOP2, or Class E basic helix-loop-helix protein 73 (bHLHe73), or Member of PAS protein 2, or PAS domain-containing protein 2 (PASD2), or HIF-1-alpha-like factor (HLF), is a bHLH-PAS transcription factor involved in the induction of oxygen regulated genes. HIF3a, also termed HIF-3-alpha, or HIF3-alpha, or endothelial PAS domain-containing protein 1 (EPAS-1), or Basic-helix-loop-helix-PAS protein MOP7, or Class E basic helix-loop-helix protein 17 (bHLHe17), or Member of PAS protein 7, or PAS domain-containing protein 7 (PASD7), or HIF3-alpha-1, or inhibitory PAS domain protein (IPAS), is a bHLH-PAS transcriptional regulator in adaptive response to low oxygen tension. It plays a role in the regulation of hypoxia-inducible gene expression. 58 matched cddid_all.tbl CDD cd11434 cd11434 381440 bHLH-PAS_SIM basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded (SIM) family. The SIM family includes Drosophila melanogaster protein SIM and its homologs from vertebrates, single-minded homolog 1 (SIM1) and single-minded homolog 2 (SIM2). SIM is a nuclear bHLH-PAS transcription factor that functions as a master developmental regulator controlling midline development of the ventral nerve cord in Drosophila. SIM1, also termed Class E basic helix-loop-helix protein 14 (bHLHe14), is a bHLH-PAS transcription factor that may have pleiotropic effects during embryogenesis and in the adult. SIM2, also termed Class E basic helix-loop-helix protein 15 (bHLHe15), is a bHLH-PAS transcription factor that may be a master gene of central nervous system (CNS) development in cooperation with ARNT. It may have pleiotropic effects in the tissues expressed during development. 61 matched cddid_all.tbl CDD cd11435 cd11435 381441 bHLH-PAS_AhRR basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor repressor (AhRR) and similar proteins. AhRR, also termed AhR repressor, or Class E basic helix-loop-helix protein 77 (bHLHe77), is a member of bHLH-PAS transcription factors that acts as a negative regulator of AhR (or Dioxin Receptor), playing key roles in development and environmental sensing. AhR is activated by Dioxin to control the expression of certain genes to influence biological processes such as apoptosis, proliferation, cell growth and differentiation. To form active DNA binding complexes, AhR dimerizes with a bHLH-PAS factor ARNT (Aryl hydrocarbon Nuclear Receptor Translocator). AhRR functions by competing with AhR for its partner ARNT. AhRR-ARNT complexes are transcriptionally inactive. 60 matched cddid_all.tbl CDD cd11436 cd11436 381442 bHLH-PAS_AhR basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor (AhR) and similar proteins. AhR, also termed Ah receptor, or Dioxin receptor (DR), or Class E basic helix-loop-helix protein 76 (bHLHe76), is the only member of bHLH-PAS transcription regulators that bind and be activated by small chemical ligands. It is activated by Dioxin to control the expression of certain genes to influence biological processes such as apoptosis, proliferation, cell growth and differentiation. To form active DNA binding complexes AhR dimerize with a bHLH-PAS factor ARNT (Aryl hydrocarbon Nuclear Receptor Translocator). 61 matched cddid_all.tbl CDD cd11437 cd11437 381443 bHLH-PAS_ARNT_like basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor nuclear translocator (ARNT) family. The ARNT family of bHLH-PAS transcription regulators includes ARNT, ARNT-like proteins (ARNTL and ARNTL2), and Drosophila melanogaster protein cycle. They act as the heterodimeric partner for bHLH-PAS proteins such as aryl hydrocarbon receptor (AhR), hypoxia-inducible factor (HIF), and single-minded (SIM). These bHLH-PAS transcription complexes are involved in transcriptional responses to xenobiotic, hypoxia, and developmental pathways. Heterodimerization of bHLH-PAS proteins with ARNT is mediated by contacts between both the bHLH and the tandem PAS domains. ARNT use bHLH and/or PAS domains to interact with several transcriptional coactivators. It is required for activity of the aryl hydrocarbon (dioxin) receptor. ARNTL, also termed Basic-helix-loop-helix-PAS protein MOP3, or brain and muscle ARNT-like 1 (BMAL1), or Class E basic helix-loop-helix protein 5 (bHLHe5), or member of PAS protein 3, or PAS domain-containing protein 3 (PASD3), or bHLH-PAS protein JAP3, is a member of the bHLH-PAS transcription factor family that forms heterodimers with another bHLH-PAS protein, CLOCK (circadian locomotor output cycle kaput), which regulates circadian rhythm. ARNTL-CLOCK heterodimer complex activates transcription from E-box (CANNTG) elements found in the promoter of circadian responsive genes. ARNTL is highly homologous to ARNT. ARNTL2, also termed Basic-helix-loop-helix-PAS protein MOP9, or brain and muscle ARNT-like 2 (BMAL2), or CYCLE-like factor (CLIF), or Class E basic helix-loop-helix protein 6 (bHLHe6), or member of PAS protein 9, or PAS domain-containing protein 9 (PASD9), is a neuronal bHLH-PAS transcriptional factor, regulating cell cycle progression and preventing cell death, whose sustained expression might ensure brain neuron survival. It also plays important roles in tumor angiogenesis. Protein cycle, also termed brain and muscle ARNT-like 1 (BMAL1), or MOP3, is a putative bHLH-PAS transcription factor involved in the generation of biological rhythms in Drosophila. It activates cycling transcription of Period (PER) and Timeless (TIM) by binding to the E-box (5'-CACGTG-3') present in their promoters. 58 matched cddid_all.tbl CDD cd11438 cd11438 381444 bHLH-PAS_ARNTL_PASD3 basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor nuclear translocator-like protein 1 (ARNTL) and similar proteins. ARNTL, also termed Basic-helix-loop-helix-PAS protein MOP3, or brain and muscle ARNT-like 1 (BMAL1), or Class E basic helix-loop-helix protein 5 (bHLHe5), or member of PAS protein 3, or PAS domain-containing protein 3 (PASD3), or bHLH-PAS protein JAP3, is a member of the bHLH-PAS transcription factor family that forms heterodimers with another bHLH-PAS protein, CLOCK (circadian locomotor output cycle kaput), which regulates circadian rhythm. ARNTL-CLOCK heterodimer complex activates transcription from E-box (CANNTG) elements found in the promoter of circadian responsive genes. ARNTL is highly homologous to ARNT. 64 matched cddid_all.tbl CDD cd11439 cd11439 381445 bHLH-PAS_SRC basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in steroid receptor coactivator (SRC) family. The SRC family of coactivators includes SRC-1 (NcoA-1/p160), SRC-2(TIF2/GRIP1/NcoA-2) and SRC-3(NcoA-3/pCIP/RAC3/ACTR/pCIP/AIB1/TRAM1), which are critical mediators of steroid receptor action. They contain bHLH-PAS domain at the N-terminal that is followed by receptor interacting domain and C-terminal transcriptional activation domain. SRC coactivators interact with nuclear receptors in a ligand-dependent manner and enhance transcriptional activation by the receptor via histone acetylation/methylation. 58 matched cddid_all.tbl CDD cd11440 cd11440 381446 bHLH-O_Cwo_like basic helix-loop-helix-orange (bHLH-O) domain found in Drosophila melanogaster protein clockwork orange (Cwo) and similar proteins. Cwo is a bHLH-O transcriptional regulator involved in the regulation of Drosophila circadian rhythms. It functions as both an activator and a repressor of clock gene expression. 60 matched cddid_all.tbl CDD cd11441 cd11441 381447 bHLH-PAS_CLOCK_like basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins. The family includes CLOCK, neuronal PAS domain-containing protein 2 (NPAS2) and non-mammalian circadian clock protein PASD1. CLOCK, also termed Class E basic helix-loop-helix protein 8 (bHLHe8), is a transcriptional activator which forms a core component of the circadian clock. NPAS2, also termed neuronal PAS2, or basic-helix-loop-helix-PAS protein MOP4, or Class E basic helix-loop-helix protein 9 (bHLHe9), or member of PAS protein 4, or PAS domain-containing protein 4, is a transcriptional activator which forms a core component of the circadian clock. PASD1 is evolutionarily related to Circadian locomotor output cycles protein kaput (CLOCK)and functions as a suppressor of the biological clock that drives the daily circadian rhythms of cells throughout the body. 54 matched cddid_all.tbl CDD cd11442 cd11442 381448 bHLH_AtPRE_like basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana paclobutrazol resistance (PRE) family. The PRE family includes several bHLH transcription factors from Arabidopsis thaliana, such as PRE1-6. PRE1 (also termed AtbHLH136, or protein banquo 1), PRE2 (also termed AtbHLH134, or protein banquo 2, or EN 52), PRE4 (also termed AtbHLH161, or protein banquo 3), and PRE5 (also termed AtbHLH164) are atypical and probable non DNA-binding bHLH transcription factors that integrate multiple signaling pathways to regulate cell elongation and plant development. PRE3 (also termed AtbHLH135, or protein activation-tagged BRI1 suppressor 1, or ATBS1, or protein target of MOOPTEROS 7, or EN 67) is an atypical and probable non DNA-binding bHLH transcription factor required for MONOPTEROS-dependent root initiation in embryo. It promotes the correct definition of the hypophysis cell division plane. PRE5 (also termed AtbHLH163, or protein KIDARI) is an atypical and probable non DNA-binding bHLH transcription factor that regulates light-mediated responses in day light conditions by binding and inhibiting the activity of the bHLH transcription factor HFR1, a critical regulator of light signaling and shade avoidance. 65 matched cddid_all.tbl CDD cd11443 cd11443 381449 bHLH_AtAMS_like basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein aborted microspores (AMS) and similar proteins. The family includes several bHLH transcription factors from Arabidopsis thaliana, such as AMS, ICE1 and SCREAM2. AMS, also termed AtbHLH21, or EN 48, plays a crucial role in tapetum development and it is required for male fertility and pollen differentiation. ICE1, also termed inducer of CBF expression 1, or AtbHLH116, or EN 45, or SCREAM, acts as a transcriptional activator that regulates the cold-induced transcription of CBF/DREB1 genes. It binds specifically to the MYC recognition sites (5'-CANNTG-3') found in the CBF3/DREB1A promoter. SCREAM2, also termed AtbHLH33, or EN 44, mediates stomatal differentiation in the epidermis probably by controlling successive roles of SPCH, MUTE, and FAMA. 72 matched cddid_all.tbl CDD cd11444 cd11444 381450 bHLH_AtIBH1_like basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana ILI1-BINDING BHLH 1 (IBH1) and similar proteins. The family includes several bHLH transcription factors from Arabidopsis thaliana, such as IBH1, UPBEAT1, PAR1 and PAR2. IBH1, also termed bHLH zeta, or AtbHLH158, is an atypical and probable non DNA-binding bHLH transcription factor that acts as transcriptional repressor that negatively regulates cell and organ elongation in response to gibberellin (GA) and brassinosteroid (BR) signaling. IBH1 forms heterodimer with BHLH49, thus inhibiting DNA binding of BHLH49, which is a transcriptional activator that regulates the expression of a subset of genes involved in cell expansion by binding to the G-box motif. UPBEAT1, also termed AtbHLH151, or EN 146, is a bHLH transcription factor that modulates the balance between cellular proliferation and differentiation in root growth. It does not act through cytokinin and auxin signaling, but by repressing peroxidase expression in the elongation zone. PAR1 (also termed AtbHLH165, or protein helix-loop-helix 1, or protein phytochrome rapidly regulated 1) and PAR2 (also termed AtbHLH166, or protein helix-loop-helix 2, or protein phytochrome rapidly regulated 2) are two atypical bHLH transcription factors that act as negative regulators of a variety of shade avoidance syndrome (SAS) responses, including seedling elongation and photosynthetic pigment accumulation. They act as direct transcriptional repressor of two auxin-responsive genes, SAUR15 and SAUR68. They may function in integrating shade and hormone transcriptional networks in response to light and auxin changes. 57 matched cddid_all.tbl CDD cd11445 cd11445 381451 bHLH_AtPIF_like basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana phytochrome interacting factors (PIFs) and similar proteins. The family includes several bHLH transcription factors from Arabidopsis thaliana, such as PIFs, ALC, PIL1, SPATULA, and UNE10. PIFs (PIF1, PIF3, PIF4, PIF5, PIF6 and PIF7) have been shown to control light-regulated gene expression. They directly bind to the photoactivated phytochromes and are degraded in response to light signals. ALC, also termed AtbHLH73, or protein ALCATRAZ, or EN 98, is required for the dehiscence of fruit, especially for the separation of the valve cells from the replum. It promotes the differentiation of a strip of labile non-lignified cells sandwiched between layers of lignified cells. PIL1, also termed AtbHLH124, or protein phytochrome interacting factor 3-like 1, or EN 110, is involved in responses to transient and long-term shade. It is required for the light-mediated inhibition of hypocotyl elongation and necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related gene APRR9. PIL1 seems to play a role in multiple PHYB responses, such as flowering transition and petiole elongation. SPATULA, also termed AtbHLH24, or EN 99, plays a role in floral organogenesis. It promotes the growth of carpel margins and of pollen tract tissues derived from them. UNE10, also termed AtbHLH16, or protein UNFERTILIZED EMBRYO SAC 10, or EN 99, is required during the fertilization of ovules by pollen. 64 matched cddid_all.tbl CDD cd11446 cd11446 381452 bHLH_AtILR3_like basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein IAA-leucine resistant 3 (ILR3) and similar proteins. ILR3, also termed AtbHLH105, or EN 133, is a bHLH transcription factor that plays a role in resistance to amide-linked indole-3-acetic acid (IAA) conjugates such as IAA-Leu and IAA-Phe. It may regulate gene expression in response to metal homeostasis changes. 76 matched cddid_all.tbl CDD cd11447 cd11447 381453 bHLH-O_HEYL basic helix-loop-helix-orange (bHLH-O) domain found in hairy/enhancer-of-split related with YRPW motif-like protein (HEYL) and similar proteins. HEYL, also termed Class B basic helix-loop-helix protein 33 (bHLHb33), or hairy-related transcription factor 3 (HRT-3), is a bHLH-O transcriptional repressor that is strongly expressed in the presomitic mesoderm, the somites, the peripheral nervous system and smooth muscle of all arteries and is a downstream effector of the Notch and transforming growth factor-beta pathways. It promotes neuronal differentiation by activating proneural genes and inhibiting other hairy and enhancer of split (HES) and hairy/enhancer-of-split related with YRPW motif protein (HEY) proteins. HEYL also functions as a tumor suppressor involved in the progression of human cancers. 74 matched cddid_all.tbl CDD cd11448 cd11448 381454 bHLH_AtFAMA_like basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein FAMA and similar proteins. The family includes several bHLH transcription factors from Arabidopsis thaliana, such as FAMA, MUTE and SPEECHLESS, which work together to regulate the sequential cell fate specification during stomatal development and differentiation. FAMA, also termed AtbHLH97, or EN 14, is a transcription activator required to promote differentiation and morphogenesis of stomatal guard cells and to halt proliferative divisions in their immediate precursors. It mediates the formation of stomata. MUTE, also termed AtbHLH45, or EN 20, is required for the differentiation of stomatal guard cells, by promoting successive asymmetric cell divisions and the formation of guard mother cells. It promotes the conversion of the leaf epidermis into stomata. SPEECHLESS, also termed AtbHLH98, or EN 19, is required for the initiation and the formation of stomata, by promoting the first asymmetric cell divisions. FAMA, MUTE and SPEECHLESS form heterodimers with SCREAM/ICE1 and SCRM2 to regulate transcription of genes during stomatal development. 74 matched cddid_all.tbl CDD cd11449 cd11449 381455 bHLH_AtAIB_like basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein ABA-INDUCIBLE bHLH-TYPE (AIB) and similar proteins. The family includes several bHLH transcription factors from Arabidopsis thaliana, such as AIB and MYC proteins (MYC2, MYC3 and MYC4). AIB, also termed AtbHLH17, or EN 35, is a transcription activator that regulates positively abscisic acid (ABA) response. MYC2, also termed protein jasmonate insensitive 1, or R-homologous Arabidopsis protein 1 (RAP-1), or AtbHLH6, or EN 38, or Z-box binding factor 1 protein, is a transcriptional activator involved in abscisic acid (ABA), jasmonic acid (JA), and light signaling pathways. MYC3, also termed protein altered tryptophan regulation 2, or AtbHLH5, or transcription factor ATR2, or EN 36, is a transcription factor involved in tryptophan, jasmonic acid (JA) and other stress-responsive gene regulation. MYC4, also termed AtbHLH4, or EN 37, is a transcription factor involved in jasmonic acid (JA) gene regulation. MYC2, together with MYC3 and MYC4, controls additively subsets of JA-dependent responses. 78 matched cddid_all.tbl CDD cd11450 cd11450 381456 bHLH_AtFIT_like basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana Fe-deficiency induced transcription factor 1 (FIT) and similar proteins. The family includes bHLH transcription factors from Arabidopsis thaliana, such as FIT and DYT1. FIT, also termed FER-like iron deficiency-induced transcription factor, or FER-like regulator of iron uptake, or AtbHLH29, or EN 43, is a bHLH transcription factor that is required for the iron deficiency response in plant. It regulates FRO2 at the level of mRNA accumulation and IRT1 at the level of protein accumulation. DYT1, also termed AtbHLH22, or protein dysfunctional tapetum 1, or EN 49, is a bHLH transcription factor involved in the control of tapetum development. It is required for male fertility and pollen differentiation, especially during callose deposition. 76 matched cddid_all.tbl CDD cd11451 cd11451 381457 bHLH_AtTT8_like basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein transparent testa 8 (TT8) and similar proteins. The family includes several bHLH transcription factors from Arabidopsis thaliana, such as TT8, EGL1, and GL3. TT8, also termed AtbHLH42, or EN 32, is involved in the control of flavonoid pigmentation and plays a key role in regulating leucoanthocyanidin reductase (BANYULS) and dihydroflavonol-4-reductase (DFR). EGL1, also termed AtbHLH2, or EN 30, or AtMYC146, or protein enhancer of GLABRA 3, is involved in epidermal cell fate specification and regulates negatively stomata formation but promotes trichome formation. GL3, also termed AtbHLH1, or AtMYC6, or protein shapeshifter, or EN 31, is involved in epidermal cell fate specification. It regulates negatively stomata formation, but, in association with TTG1 and MYB0/GL1, promotes trichome formation, branching and endoreplication. 75 matched cddid_all.tbl CDD cd11452 cd11452 381458 bHLH_AtNAI1_like basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein NAI1 and similar proteins. NAI1, also termed AtbHLH20, or EN 27, is a bHLH transcription activator that regulates the expression of at least NAI2, PYK10 and PBP1. It is required for and mediates the formation of endoplasmic reticulum bodies (ER bodies). It plays a role in the symbiotic interactions with the endophytes of the Sebacinaceae fungus family, such as Piriformospora indica and Sebacina. 75 matched cddid_all.tbl CDD cd11453 cd11453 381459 bHLH_AtBIM_like basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana BES1-interacting Myc-like proteins (BIMs) and similar proteins. The family includes Arabidopsis thaliana BIM1 and its homologs (BIM2 and BIM3), which are bHLH transcription factors that interact with BES1 to regulate transcription of Brassinosteroid (BR)-induced gene. BR regulates many growth and developmental processes such as cell elongation, vascular development, senescence stress responses, and photomorphogenesis. BIM1 heterodimerize with BES1 and bind to E-box sequences present in many BR-induced promoters to regulated BR-induced genes. 77 matched cddid_all.tbl CDD cd11454 cd11454 381460 bHLH_AtIND_like basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein INDEHISCENT (IND) and similar proteins. The family includes several bHLH transcription factors from Arabidopsis thaliana, such as IND, HEC proteins (HEC1, HEC2 and HEC3) and UNE12. IND, also termed AtbHLH40, or EN 120, is a bHLH transcription regulator required for seed dispersal. It is involved in the differentiation of all three cell types required for fruit dehiscence. HEC1 (also termed AtbHLH88, or protein HECATE 1, or EN 118), HEC2 (also termed AtbHLH37, or protein HECATE 2, or EN 117) and HEC3 (also termed AtbHLH43, or protein HECATE 3, or EN 119) are required for the female reproductive tract development and fertility. Both IND and HEC proteins have been implicated in regulation of auxin signaling. They heterodimerize with SPATULA (SPT) bHLH transcription factor to regulate reproductive tract development in plant. UNE12, also termed AtbHLH59, or protein UNFERTILIZED EMBRYO SAC 12, or EN 93, is required for ovule fertilization. 63 matched cddid_all.tbl CDD cd11455 cd11455 381461 bHLH_AtAIG1_like basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein AIG1 and similar proteins. AIG1, also termed AtbHLH32, or EN 54, or protein target of MOOPTEROS 5, is a transcription factor required for MONOPTEROS-dependent root initiation in embryo. 80 matched cddid_all.tbl CDD cd11456 cd11456 381462 bHLHzip_N-Myc_like basic Helix-Loop-Helix-zipper (bHLHzip) domain found in N-Myc and similar proteins. N-Myc, also termed Class E basic helix-loop-helix protein 37 (bHLHe37), is a bHLHZip proto-oncogene protein that positively regulates the transcription of MYCNOS in neuroblastoma cells. It is also essential during embryonic development. N-Myc has a critical role in regulating the switch between proliferation and differentiation of progenitor cells. It binds DNA as a heterodimer with MAX. The family also includes S-Myc, encoded by rat or mouse intronless myc gene, which has apoptosis-inducing activity. 87 matched cddid_all.tbl CDD cd11457 cd11457 381463 bHLHzip_L-Myc basic Helix-Loop-Helix-zipper (bHLHzip) domain found in L-Myc and similar proteins. L-Myc, also termed Class E basic helix-loop-helix protein 38 (bHLHe38), or protein L-Myc-1, or V-myc myelocytomatosis viral oncogene homolog, is a bHLHZip oncoprotein belonging to the Myc oncogene protein family. It binds DNA as a heterodimer with MAX. L-Myc is co-expressed with another Myc family member and has weaker transformation/transactivation activities. L-Myc knockout mouse did not exhibit any phenotypic abnormalities. 89 matched cddid_all.tbl CDD cd11458 cd11458 381464 bHLHzip_c-Myc basic Helix-Loop-Helix-zipper (bHLHzip) domain found in c-Myc and similar proteins. c-Myc, also termed Myc proto-oncogene protein, or Class E basic helix-loop-helix protein 39 (bHLHe39), or transcription factor p64, a bHLHZip proto-oncogene protein that functions as a transcription factor, which binds DNA in a non-specific manner, yet also specifically recognizes the core sequence 5'-CAC[GA]TG-3'. It activates the transcription of growth-related genes. 84 matched cddid_all.tbl CDD cd11459 cd11459 381465 bHLH-O_HES1_4 basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split HES-1, HES-4 and similar proteins. The family includes two bHLH-O transcriptional repressors, HES-1 and HES-4. HES-1, also termed Class B basic helix-loop-helix protein 39 (bHLHb39), or hairy homolog, or hairy-like protein (HL), plays an essential role in development of both compartment and boundary cells of the central nervous system. It regulates the maintenance of neural stem/progenitor cells by inhibiting proneural gene expression via Notch signaling. HES-4, also termed Class B basic helix-loop-helix protein 42 (bHLHb42), or bHLH factor Hes4, antagonizes the function of Twist-1 to regulate lineage commitment of bone marrow stromal/stem cells (BMSC). Epigenetic dysregulation of HES-4 is associated with striatal degeneration in postmortem Huntington brains. Both HES-1 and HES-4 are mammalian counterparts of the Hairy and Enhancer of split proteins that play a critical role in many physiological processes including cellular differentiation, cell cycle arrest, apoptosis and self-renewal ability. 63 matched cddid_all.tbl CDD cd11460 cd11460 381466 bHLH-O_HES6 basic helix-loop-helix-orange (bHLH-O) domain found in transcription factor HES-6 and similar proteins. HES-6, also termed Class B basic helix-loop-helix protein 41 (bHLHb41), or hairy and enhancer of split 6, or C-HAIRY1, is a bHLH-O transcription factor that is expressed in developing muscle and involved in angiogenesis, myogenesis, neural differentiation and neurogenesis. HES-6 antagonizes Notch signaling but is not regulated by Notch signaling. It is a transcription co-factor associated with stem cell characteristics in neural tissue. It may act as an inhibitor of Hes-1 during neuronal development and forms a heterodimer with HES-1 to prevent its association with transcriptional co-repressors. The overexpression of HES-6 has been reported in metastatic cancers of different origins. HES-6 is one mammalian counterpart of the Hairy and Enhancer of split proteins that play a critical role in many physiological processes including cellular differentiation, cell cycle arrest, apoptosis and self-renewal ability. 58 matched cddid_all.tbl CDD cd11461 cd11461 381467 bHLH-O_HES5 basic helix-loop-helix-orange (bHLH-O) domain found in transcription factor HES-5 and similar proteins. HES-5, also termed Class B basic helix-loop-helix protein 38 (bHLHb38), or hairy and enhancer of split 5, is a bHLH-O transcription factor that is involved in cell differentiation and proliferation in a variety of tissues. HES-5 is an essential effector for Notch signaling. It acts as a transducer of Notch signals in brain vascular development. It also acts as a key mediator of Wnt-3a-induced neuronal differentiation and plays a crucial role in normal inner ear hair cell development. HES-5 is one mammalian counterpart of the Hairy and Enhancer of split proteins that play a critical role in many physiological processes including cellular differentiation, cell cycle arrest, apoptosis and self-renewal ability. 59 matched cddid_all.tbl CDD cd11462 cd11462 381468 bHLH-O_HES7 basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split 7 (HES-7) and similar proteins. HES-7, also termed Class B basic helix-loop-helix protein 37 (bHLHb37), or bHLH factor Hes7, is a bHLH-O transcriptional repressor that is expressed in an oscillatory manner and acts as a key regulator of the pace of the segmentation clock. It is regulated by the Notch and Fgf/Mapk pathways. HES-7 is one mammalian counterpart of the Hairy and Enhancer of split proteins that play a critical role in many physiological processes including cellular differentiation, cell cycle arrest, apoptosis and self-renewal ability. 61 matched cddid_all.tbl CDD cd11463 cd11463 381469 bHLH-O_HES2 basic helix-loop-helix-orange (bHLH-O) domain found in hairy and enhancer of split 2 (HES-2) and similar proteins. HES-2, also termed Class B basic helix-loop-helix protein 40 (bHLHb40), is a bHLH-O transcriptional repressor of genes that require a bHLH protein for their transcription. It acts as a negative regulator through interaction with both E-box and N-box sequences. HES-2 is one mammalian counterpart of the Hairy and Enhancer of split proteins that play a critical role in many physiological processes including cellular differentiation, cell cycle arrest, apoptosis and self-renewal ability. 65 matched cddid_all.tbl CDD cd11464 cd11464 381470 bHLH_TS_TWIST basic helix-loop-helix (bHLH) domain found in twist-related protein (TWIST) family. The TWIST family includes TWIST1 and TWIST2, which are highly homologous bHLH transcription factors that promote epithelial-mesenchymal transition (EMT) during development and tumor metastasis. They are involved in the negative regulation of cellular determination and in the differentiation of several lineages, including myogenesis, osteogenesis, and neurogenesis. TWIST factors express in broad partially-overlapping patterns during embryo development and dimerize with a broad sets of dimer partners that form numerous unique transcriptional complexes to regulate embryonic development. 59 matched cddid_all.tbl CDD cd11465 cd11465 381471 bHLH_TS_scleraxis_like basic helix-loop-helix (bHLH) domain found in scleraxis, transcription factor 15 (TCF-15) and similar proteins. The family includes scleraxis and transcription factor 15 (TCF-15). Scleraxis, also termed SCX, or Class A basic helix-loop-helix protein 41 (bHLHa41), or Class A basic helix-loop-helix protein 48 (bHLHa48), is a bHLH transcription factor that is expressed in sclerotome limb bud cranial and body wall mesenchyme, pericardium and heart valves, ligaments and tendons. It is required for tendon formation ligaments, connective tissue, the diaphragm, and testis development. Scleraxis plays a central role in promoting fibroblast proliferation and matrix synthesis during the embryonic development of tendons. TCF-15, also termed Class A basic helix-loop-helix protein 40 (bHLHa40), or paraxis, or protein bHLH-EC2, is a bHLH transcription factor expressed in caudal lateral and paraxial mesoderm dermomyotome and sclerotome fore limb buds during embryo development. It may function as an early transcriptional regulator involved in the patterning of the mesoderm and in lineage determination of cell types derived from the mesoderm. 55 matched cddid_all.tbl CDD cd11466 cd11466 381472 bHLH_TS_HAND basic helix-loop-helix (bHLH) domain found in heart- and neural crest derivatives-expressed protein (HAND) family. The HAND family includes two bHLH transcription factors, HAND1 and HAND2. HAND1, also termed Class A basic helix-loop-helix protein 27 (bHLHa27), or extraembryonic tissues, heart, autonomic nervous system and neural crest derivatives-expressed protein 1 (eHAND), plays an essential role in both trophoblast-giant cells differentiation and in cardiac morphogenesis. HAND2, also termed Class A basic helix-loop-helix protein 26 (bHLHa26), or deciduum, heart, autonomic nervous system and neural crest derivatives-expressed protein 2 (dHAND), is essential for cardiac morphogenesis, particularly for the formation of the right ventricle and of the aortic arch arteries. 56 matched cddid_all.tbl CDD cd11467 cd11467 381473 bHLH_E-protein_Da_like basic helix-loop-helix (bHLH) domain found in Drosophila melanogaster protein daughterless (Da) and similar proteins. Da is a nuclear bHLH transcription factor that is a sole E protein ortholog essential for both neurogenesis and sex determination in Drosophila. Da is expressed in a broad range of tissues and is involved in diverse developmental processes such as oogenesis, sex determination and neurogenesis depending on its bHLH-binding partners. Da and achaete-scute complex (AS-C) form heterodimers that act as transcriptional activators of neural cell fates and are involved in sex determination. 70 matched cddid_all.tbl CDD cd11468 cd11468 381474 bHLH_TS_bHLHe22_like basic helix-loop-helix (bHLH) domain found in Class E basic helix-loop-helix protein bHLHe22, bHLHe23 and similar proteins. The family includes two OLIG-related bHLH transcription factors, bHLHe22 and bHLHe23. bHLHe22, also termed Class B basic helix-loop-helix protein 5 (bHLHb5), or trinucleotide repeat-containing gene 20 protein, is a neural-specific transcriptional repressor that is expressed in both excitatory (unipolar brush cells) and inhibitory neurons (cartwheel cells) of the dorsal cochlear nucleus (DCN) during development. It is important for the proper development and/or survival of a number of neural cell types. bHLHe23, also termed Class B basic helix-loop-helix protein 4 (bHLHb4), is expressed in rod bipolar cells and is required for rod bipolar cell maturation. bHLHe23 have roles in spinal interneuron differentiation by mechanisms linked to the Notch signaling pathway. It modulates the expression of genes required for the differentiation and/or maintenance of pancreatic and neuronal cell types. 62 matched cddid_all.tbl CDD cd11469 cd11469 381475 bHLH-PAS_ARNTL2_PASD9 basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor nuclear translocator-like protein 2 (ARNTL2) and similar proteins. ARNTL2, also termed Basic-helix-loop-helix-PAS protein MOP9, or brain and muscle ARNT-like 2 (BMAL2), or CYCLE-like factor (CLIF), or Class E basic helix-loop-helix protein 6 (bHLHe6), or member of PAS protein 9, or PAS domain-containing protein 9 (PASD9), is a neuronal bHLH-PAS transcriptional factor, regulating cell cycle progression and preventing cell death, whose sustained expression might ensure brain neuron survival. It also plays important roles in tumor angiogenesis. ARNT-2 heterodimerize with other bHLH-PAS proteins such as aryl hydrocarbon receptor (AhR), hypoxia-inducible factor (HIF), and single-minded (SIM). 60 matched cddid_all.tbl CDD cd11470 cd11470 381476 bHLH_TS_TCF15_paraxis basic helix-loop-helix (bHLH) domain found in transcription factor 15 (TCF-15) and similar proteins. TCF-15, also termed Class A basic helix-loop-helix protein 40 (bHLHa40), or paraxis, or protein bHLH-EC2, is a bHLH transcription factor expressed in caudal lateral and paraxial mesoderm dermomyotome and sclerotome fore limb buds during embryo development. It may function as an early transcriptional regulator involved in the patterning of the mesoderm and in lineage determination of cell types derived from the mesoderm. 66 matched cddid_all.tbl CDD cd11471 cd11471 381477 bHLH_TS_HAND2 basic helix-loop-helix (bHLH) domain found in heart- and neural crest derivatives-expressed protein 2 (HAND2) and similar proteins. HAND2, also termed Class A basic helix-loop-helix protein 26 (bHLHa26), or deciduum, heart, autonomic nervous system and neural crest derivatives-expressed protein 2 (dHAND), is a bHLH transcription factor that is essential for cardiac morphogenesis, particularly for the formation of the right ventricle and of the aortic arch arteries. 62 matched cddid_all.tbl CDD cd11473 cd11473 211395 W2 C-terminal domain of eIF4-gamma/eIF5/eIF2b-epsilon. This domain is found at the C-terminus of several translation initiation factors, including the epsilon chain of eIF2b, where it has been found to catalyze the conversion of eIF2.GDP to its active eIF2.GTP form. The structure of the domain resembles that of a set of concatenated HEAT repeats. 135 matched cddid_all.tbl CDD cd11474 cd11474 271368 SLC5sbd_CHT Na(+)- and Cl(-)-dependent choline cotransporter CHT and related proteins; solute-binding domain. Na+/choline co-transport by CHT is Cl- dependent. Human CHT (also called CHT1) is encoded by the SLC5A7 gene, and is expressed in the central nervous system. hCHT1-mediated choline uptake may be the rate-limiting step in acetylcholine synthesis, and essential for cholinergic transmission. Changes in this choline uptake in cortical neurons may contribute to Alzheimer's dementia. This subfamily belongs to the solute carrier 5 (SLC5) transporter family. 464 matched cddid_all.tbl CDD cd11475 cd11475 271369 SLC5sbd_PutP Na(+)/proline cotransporter PutP and related proteins; solute binding domain. Escherichia coli PutP catalyzes the Na+-coupled uptake of proline with a stoichiometry of 1:1. The putP gene is part of the put operon; this operon in addition encodes a proline dehydrogenase, allowing the use of proline as a source of nitrogen and/or carbon. This subfamily also includes the Bacillus subtilis Na+/proline cotransporter (OpuE) which has an osmoprotective instead of catabolic role. Expression of the opuE gene is under osmotic control and different sigma factors contribute to its regulation; it is also a putative CcpA-activated gene. This subfamily belongs to the solute carrier 5 (SLC5) transporter family. 464 matched cddid_all.tbl CDD cd11476 cd11476 271370 SLC5sbd_DUR3 Na(+)/urea-polyamine cotransporter DUR3, and related proteins; solute-binding domain. Dur3 is the yeast plasma membrane urea transporter. Saccharomyces cerevisiae DUR3 also transports polyamine. The polyamine uptake of S. cerevisiae DUR3 is activated upon its phosphorylation by polyamine transport protein kinase 2 (PTK2). S. cerevisiae DUR3 also appears to play a role in regulating the cellular boron concentration. This subfamily belongs to the solute carrier 5 (SLC5) transporter family. 493 matched cddid_all.tbl CDD cd11477 cd11477 271371 SLC5sbd_u1 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain. SLC5 (also called the sodium/glucose cotransporter family or solute sodium symporter family) is a family of proteins that co-transports Na+ with sugars, amino acids, inorganic ions or vitamins. Prokaryotic members of this family include Vibrio parahaemolyticus glucose/galactose (vSGLT), and Escherichia coli proline (PutP) and pantothenate (PutF) cotransporters. One member of the SLC5 family, human SGLT3, has been characterized as a glucose sensor and not a transporter. This subfamily belongs to the solute carrier 5 (SLC5) transporter family. 493 matched cddid_all.tbl CDD cd11478 cd11478 271372 SLC5sbd_u2 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain. SLC5 (also called the sodium/glucose cotransporter family or solute sodium symporter family) is a family of proteins that co-transports Na+ with sugars, amino acids, inorganic ions or vitamins. Prokaryotic members of this family include Vibrio parahaemolyticus glucose/galactose (vSGLT), and Escherichia coli proline (PutP) and pantothenate (PutF) cotransporters. One member of the SLC5 family, human SGLT3, has been characterized as a glucose sensor and not a transporter. This subfamily belongs to the solute carrier 5 (SLC5) transporter family. 496 matched cddid_all.tbl CDD cd11479 cd11479 271373 SLC5sbd_u3 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain. SLC5 (also called the sodium/glucose cotransporter family or solute sodium symporter family) is a family of proteins that co-transports Na+ with sugars, amino acids, inorganic ions or vitamins. Prokaryotic members of this family include Vibrio parahaemolyticus glucose/galactose (vSGLT), and Escherichia coli proline (PutP) and pantothenate (PutF) cotransporters. One member of the SLC5 family, human SGLT3, has been characterized as a glucose sensor and not a transporter. This subfamily belongs to the solute carrier 5 (SLC5) transporter family. 454 matched cddid_all.tbl CDD cd11480 cd11480 271374 SLC5sbd_u4 Uncharacterized bacterial solute carrier 5 subfamily; putative solute-binding domain. SLC5 (also called the sodium/glucose cotransporter family or solute sodium symporter family) is a family of proteins that co-transports Na+ with sugars, amino acids, inorganic ions or vitamins. Prokaryotic members of this family include Vibrio parahaemolyticus glucose/galactose (vSGLT), and Escherichia coli proline (PutP) and pantothenate (PutF) cotransporters. One member of the SLC5 family, human SGLT3, has been characterized as a glucose sensor and not a transporter. This subfamily belongs to the solute carrier 5 (SLC5) transporter family. 488 matched cddid_all.tbl CDD cd11482 cd11482 271375 SLC-NCS1sbd_NRT1-like nucleobase-cation-symport-1 (NCS1) transporter NRT1-like; solute-binding domain. This fungal NCS1 subfamily includes various Saccharomyces cerevisiae transporters: nicotinamide riboside transporter 1 (Nrt1p, also called Thi71p), Dal4p (allantoin permease), Fui1p (uridine permease), Fur4p (uracil permease), and Thi7p (thiamine transporter). NCS1s are essential components of salvage pathways for nucleobases and related metabolites. NCS1s belong to a superfamily which also contains the solute carrier 5 family sodium/glucose transporters, and solute carrier 6 family neurotransmitter transporters. 480 matched cddid_all.tbl CDD cd11483 cd11483 271376 SLC-NCS1sbd_Mhp1-like nucleobase-cation-symport-1 (NCS1) transporter Mhp1-like; solute-binding domain. This NCS1 subfamily includes Microbacterium liquefaciens Mhp1, and various uncharacterized NCS1s. Mhp1 mediates the uptake of indolyl methyl- and benzyl-hydantoins as part of a metabolic salvage pathway for their conversion to amino acids. Mhp1 has 12 transmembrane (TM) helices (an inverted topology repeat: TMs1-5 and TMs6-10, and TMs11-12; TMs numbered to conform to the Solute carrier 6 (SLC6) family Aquifex aeolicus LeuT). NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their other known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. NCS1s belong to a superfamily which also contains the solute carrier 5 family sodium/glucose transporters (SLC5s), and SLC6 neurotransmitter transporters. 451 matched cddid_all.tbl CDD cd11484 cd11484 271377 SLC-NCS1sbd_CobB-like nucleobase-cation-symport-1 (NCS1) transporter CobB-like; solute-binding domain. This NCS1 subfamily includes Escherichia coli CodB (cytosine permease), and the Saccharomyces cerevisiae transporters: Fcy21p (Purine-cytosine permease), and vitamin B6 transporter Tpn1. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. NCS1s belong to a superfamily which also contains the solute carrier 5 family sodium/glucose transporters (SLC5s), and solute carrier 6 family neurotransmitter transporters (SLC6s). 406 matched cddid_all.tbl CDD cd11485 cd11485 271378 SLC-NCS1sbd_YbbW-like uncharacterized nucleobase-cation-symport-1 (NCS1) transporter subfamily, YbbW-like; solute-binding domain. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. This subfamily includes the putative allantoin transporter Escherichia coli YbbW (also known as GlxB2). NCS1s belong to a superfamily which also contains the solute carrier 5 family sodium/glucose transporters (SLC5s), and solute carrier 6 family neurotransmitter transporters (SLC6s). 456 matched cddid_all.tbl CDD cd11486 cd11486 271379 SLC5sbd_SGLT1 Na(+)/glucose cotransporter SGLT1;solute binding domain. Human SGLT1 (hSGLT1) is a high-affinity/low-capacity glucose transporter, which can also transport galactose. In the transport mechanism, two Na+ ions first bind to the extracellular side of the transporter and induce a conformational change in the glucose binding site. This results in an increased affinity for glucose. A second conformational change in the transporter follows, bringing the Na+ and glucose binding sites to the inner surface of the membrane. Glucose is then released, followed by the Na+ ions. In the process, hSGLT1 is also able to transport water and urea and may be a major pathway for transport of these across the intestinal brush-border membrane. hSGLT1 is encoded by the SLC5A1 gene and expressed mostly in the intestine, but also in the trachea, kidney, heart, brain, testis, and prostate. The WHO/UNICEF oral rehydration solution (ORS) for the treatment of secretory diarrhea contains salt and glucose. The glucose, along with sodium ions, is transported by hSGLT1 and water is either co-transported along with these or follows by osmosis. Mutations in SGLT1 are associated with intestinal glucose galactose malabsorption (GGM). Up-regulation of intestinal SGLT1 may protect against enteric infections. SGLT1 is expressed in colorectal, head and neck, and prostate tumors. Epidermal growth factor receptor (EGFR) functions in cell survival by stabilizing SGLT1, and thereby maintaining intracellular glucose levels. SGLT1 is predicted to have 14 membrane-spanning regions. This subgroup belongs to the solute carrier 5 (SLC5)transporter family. 636 matched cddid_all.tbl CDD cd11487 cd11487 212056 SLC5sbd_SGLT2 Na(+)/glucose cotransporter SGLT2 and related proteins; solute-binding domain. Human SGLT2 (hSGLT2) is a high-capacity, low-affinity glucose transporter, that plays an important role in renal glucose reabsorption. It is encoded by the SLC5A2 gene and expressed almost exclusively in renal proximal tubule cells. Mutations in hSGLT2 cause Familial Renal Glucosuria (FRG), a rare autosomal defect in glucose transport. hSGLT2 is a major drug target for regulating blood glucose levels in diabetes. hSGLT2 is predicted to have 14 membrane-spanning regions. This subgroup belongs to the solute carrier 5 (SLC5) transporter family. 583 matched cddid_all.tbl CDD cd11488 cd11488 271380 SLC5sbd_SGLT4 Na(+)/glucose cotransporter SGLT4 and related proteins; solute-binding domain. Human SGLT4 (hSGLT4) has been reported to be a low-affinity glucose transporter with unusual sugar selectivity: it transports D-mannose but not galactose or 3-O-methyl-D-glucoside. It is encoded by the SLC5A9 gene and is expressed in intestine, kidney, liver, brain, lung, trachea, uterus, and pancreas. hSLGT4 is predicted to contain 14 membrane-spanning regions. This subgroup belongs to the solute carrier 5 (SLC5 )transporter family. 605 matched cddid_all.tbl CDD cd11489 cd11489 212058 SLC5sbd_SGLT5 Na(+)/glucose cotransporter SGLT5 and related proteins; solute-binding domain. Human SGLT5 is a glucose transporter, which also transports galactose. It is encoded by the SLC5A10 gene, and is exclusively expressed in the renal cortex. This subgroup belongs to the solute carrier 5 (SLC5) transporter family. 604 matched cddid_all.tbl CDD cd11490 cd11490 271381 SLC5sbd_SGLT6 Na(+)/chiro-inositol cotransporter SGLT6 and related proteins; solute-binding domain. Human SGLT6 (also called KST1, SMIT2) is a chiro-inositol transporter, which also transports myo-inositol. It is encoded by the SLC5A11 gene. Xenopus Na1-glucose cotransporter type 1 (SGLT-1)-like protein is predicted to contain 14 membrane-spanning regions. This subgroup belongs to the solute carrier 5 (SLC5) transporter family. 602 matched cddid_all.tbl CDD cd11491 cd11491 271382 SLC5sbd_SMIT Na(+)/myo-inositol cotransporter SMIT and related proteins; solute-binding domain. Human SMIT is a high-affinity myo-inositol transporter, and is expressed in brain, heart, kidney, and lung. Inhibition of myo-inositol uptake, through down-regulation of SMIT, may be a common mechanism of action of mood stabilizers, including lithium, carbamazepine, and valproate. SMIT is encoded by the SLC5A3 gene, which is a candidate gene for pathogenesis of nervous system dysfunction in Down syndrome (DS). The SNP, 21q22 near SLC5A3-MRPS6-KCNE2, has been associated with coronary heart disease, cardiovascular disease, and myocardial infarction. SMIT may also be involved in the pathogeneisis of congenital cataract. SMIT also plays roles in osteogenesis, bone formation, and bone mineral density determination. This subgroup belongs to the solute carrier 5 (SLC5) transporter family. 609 matched cddid_all.tbl CDD cd11492 cd11492 271383 SLC5sbd_NIS-SMVT Na(+)/iodide (NIS) and Na(+)/multivitamin (SMVT) cotransporters, and related proteins; solute binding domain. NIS (encoded by the SLC5A5 gene) transports I-, and other anions including ClO4-, SCN-, and Br-. SMVT (encoded by the SLC5A6 gene) transports biotin, pantothenic acid and lipoate. This subfamily also includes SMCT1 and -2. SMCT1(encoded by the SLC5A8 gene) is a high-affinity transporter of various monocarboxylates including lactate and pyruvate, short-chain fatty acids, ketone bodies, nicotinate and its structural analogs, pyroglutamate, benzoate and its derivatives, and iodide. SMCT2 (encoded by the SLC5A12 gene) is a low-affinity transporter for short-chain fatty acids, lactate, pyruvate, and nicotinate. This subgroup belongs to the solute carrier 5 (SLC5) transporter family. 522 matched cddid_all.tbl CDD cd11493 cd11493 271384 SLC5sbd_NIS-like_u1 uncharacterized subgroup of the Na(+)/iodide (NIS) cotransporter subfamily; putative solute-binding domain. Proteins belonging to the same subfamily as this uncharacterized subgroup include i) NIS, which transports I-, and other anions including ClO4-, SCN-, and Br-, ii) SMVT, which transports biotin, pantothenic acid and lipoate, and iii) the Na(+)/monocarboxylate cotransporters SMCT1 and 2. SMCT1 is a high-affinity transporter while SMCT2 is a low-affinity transporter. This subgroup belongs to the solute carrier 5 (SLC5) transporter family. 479 matched cddid_all.tbl CDD cd11494 cd11494 271385 SLC5sbd_NIS-like_u2 uncharacterized subgroup of the Na(+)/iodide (NIS) cotransporter subfamily; putative solute-binding domain. Proteins belonging to the same subfamily as this uncharacterized subgroup include i) NIS, which transports I-, and other anions including ClO4-, SCN-, and Br-, ii) SMVT, which transports biotin, pantothenic acid and lipoate, and iii) the Na(+)/monocarboxylate cotransporters, SMCT1 and 2. SMCT1 is a high-affinity transporter while SMCT2 is a low-affinity transporter. This subgroup belongs to the solute carrier 5 (SLC5) transporter family. 473 matched cddid_all.tbl CDD cd11495 cd11495 271386 SLC5sbd_NIS-like_u3 uncharacterized subgroup of the Na(+)/iodide (NIS) cotransporter subfamily; putative solute-binding domain. Proteins belonging to the same subfamily as this uncharacterized subgroup include i) NIS, which transports I-, and other anions including ClO4-, SCN-, and Br-, ii) SMVT, which transports biotin, pantothenic acid and lipoate, and iii) the Na(+)/monocarboxylate cotransporters SMCT1 and 2. SMCT1 is a high-affinity transporter while SMCT2 is a low-affinity transporter. This subgroup belongs to the solute carrier 5 (SLC5) transporter family. 473 matched cddid_all.tbl CDD cd11496 cd11496 271387 SLC6sbd-TauT-like Na(+)- and Cl(-)-dependent taurine transporter TauT, and related proteins; solute-binding domain. This subgroup represents the solute-binding domain of TauT-like Na(+)- and Cl(-)-dependent transporters. Family members include: human TauT which transports taurine, human GAT1, GAT2, and GAT3, and BGT1, which transport gamma-aminobutyric acid (GABA), and human CT1 which transports creatine. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 543 matched cddid_all.tbl CDD cd11497 cd11497 271388 SLC6sbd_SERT-like Na(+)- and Cl(-)-dependent monoamine transporters, SERT, NET, DAT1 and related proteins; solute binding domain. This subgroup represents the solute-binding domain of transmembrane transporters that transport monoamine neurotransmitters from synaptic spaces into presynaptic neurons. Members include: NET which transports norepinephrine, SERT which transports serotonin, and DAT1 which transports dopamine. These transporters may play a role in diseases including depression, anxiety disorders, attention-deficit hyperactivity disorder, and in the control of human behavior and emotional states. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 537 matched cddid_all.tbl CDD cd11498 cd11498 212067 SLC6sbd_GlyT1 Na(+)- and Cl(-)-dependent glycine transporter GlyT1; solute-binding domain. GlyT1 is a membrane-bound transporter that re-uptakes glycine from the synaptic cleft. Human GlyT1 is encoded by the SLC6A9 gene. GlyT1 is expressed in brain, pancreas, uterus, stomach, spleen, liver, and retina. GlyT1 may play a role in schizophrenia. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 585 matched cddid_all.tbl CDD cd11499 cd11499 271389 SLC6sbd_GlyT2 Na(+)- and Cl(-)-dependent glycine transporter GlyT2; solute-binding domain. GlyT2 (also called NET1) is a membrane-bound transporter that re-uptakes glycine from the synaptic cleft. Human GlyT2 is encoded by the SLC6A5 gene. GlyT2 is expressed in brain and spinal cord. GlyT2 may play a role in pain, and in spasticity. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 597 matched cddid_all.tbl CDD cd11500 cd11500 271390 SLC6sbd_PROT Na(+)- and Cl(-)-dependent L-proline transporter PROT; solute-binding domain. PROT is a high-affinity L-proline transporter that transports L-proline, and may have a role in excitatory neurotransmission. Human PROT is encoded by the SLC6A7 gene, a potential susceptible gene for asthma. PROT is expressed in the brain. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 541 matched cddid_all.tbl CDD cd11501 cd11501 271391 SLC6sbd_ATB0 Na(+)- and Cl(-)-dependent beta-alanine transporter ATB0+; solute-binding domain. ATB0+ (also known as the beta-alanine carrier) is a transmembrane transporter with a broad substrate specificity; it can transport non-alpha-amino acids such as beta-alanine with low affinity, and can transport dipolar and cationic amino acids such as leucine and lysine, with a higher affinity. It may have a role in the absorption of essential nutrients and drugs in the distal regions of the human gastrointestinal tract. Human ATB0+ is encoded by the SLC6A14 gene. ATB0+ is expressed in the lung, trachea, salivary gland, mammary gland, stomach, and pituitary gland. ATB0+ may play a role in obesity, and its upregulation may have a pathogenic role in colorectal cancer. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 602 matched cddid_all.tbl CDD cd11502 cd11502 271392 SLC6sbd_NTT5 Neurotransmitter transporter 5; solute-binding domain. Human NTT5 is encoded by the SLC6A16 gene. NTT5 is expressed in testis, pancreas, and prostate; its expression is predominantly intracellular, indicative of a vesicular location. Its substrates are unknown. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 535 matched cddid_all.tbl CDD cd11503 cd11503 271393 SLC5sbd_NIS Na(+)/iodide cotransporter NIS and related proteins; solute-binding domain. NIS (product of the SLC5A5 gene) transports I-, and other anions including ClO4-, SCN-, and Br-. NIS is expressed in the thyroid, colon, ovary, and in human breast cancers. It mediates the active transport and the concentration of iodide from the blood into thyroid follicular cells, a fundamental step in thyroid hormone biosynthesis, and is the basis of radioiodine therapy for thyroid cancer. Mutation in the SLC5A5 gene can result in a form of thyroid hormone dysgenesis. Human NIS exists mainly as a dimer stabilized by a disulfide bridge. This subgroup belongs to the solute carrier 5 (SLC5) transporter family. 535 matched cddid_all.tbl CDD cd11504 cd11504 271394 SLC5sbd_SMVT Na(+)/multivitamin cotransporter SMVT and related proteins; solute-binding domain. This multivitamin transporter SMVT (product of the SLC5A6 gene) transports biotin, pantothenic acid and lipoate, and is essential for mediating biotin uptake into mammalian cells. SMVT is expressed in the placenta, intestine, heart, brain, lung, liver, kidney and pancreas. Biotin may regulate its own cellular uptake through participation in holocarboxylase synthetase-dependent chromatin remodeling events at SMVT promoter loci. The cis regulatory elements, Kruppel-like factor 4 and activator protein-2, regulate the activity of the human SMVT promoter in the intestine. Glycosylation of the hSMVT is important for its transport function. This subgroup belongs to the solute carrier 5 (SLC5) transporter family. 527 matched cddid_all.tbl CDD cd11505 cd11505 271395 SLC5sbd_SMCT Na(+)/monocarboxylate cotransporters SMCT1 and 2 and related proteins; solute-binding domain. SMCT1 is a high-affinity transporter of various monocarboxylates including lactate and pyruvate, short-chain fatty acids, ketone bodies, nicotinate and its structural analogs, pyroglutamate, benzoate and its derivatives, and iodide. Human SMCT1 (hSMCT1, also called AIT) is encoded by the tumor suppressor gene SLC5A8. SMCT1 is expressed in the colon, small intestine, kidney, thyroid gland, retina, and brain. SMCT1 may contribute to the intestinal/colonic and oral absorption of monocarboxylate drugs. It also mediates iodide transport from thyrocyte into the colloid lumen in thyroid gland and, through transporting L-lactate and ketone bodies, helps maintain the energy status and the function of neurons. SMCT2 is a low-affinity transporter for short-chain fatty acids, lactate, pyruvate, and nicotinate. hSMCT2 is encoded by the SLC5A12 gene. SMCT2 is expressed in the kidney, small intestine, skeletal muscle, and retina. In the kidney, SMCT2 may initiate lactate absorption in the early parts of the tubule, SMCT1 in the latter parts of the tubule. In the retina, SMCT1 and SMCT2 may play a differential role in monocarboxylate transport in a cell type-specific manner. This subgroup belongs to the solute carrier 5 (SLC5) transporter family. 538 matched cddid_all.tbl CDD cd11506 cd11506 212075 SLC6sbd_GAT1 Na(+)- and Cl(-)-dependent GABA transporter 1; solute-binding domain. GAT1 transports gamma-aminobutyric acid (GABA). GABA is the main inhibitory neurotransmitter within the mammalian CNS. Human GAT1 is encoded by the SLC6A1 gene. GAT1 is expressed in brain and peripheral nervous system. The antiepileptic drug, Tiagabine, inhibits GAT1. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 598 matched cddid_all.tbl CDD cd11507 cd11507 271396 SLC6sbd_GAT2 Na(+)- and Cl(-)-dependent GABA transporter 2; solute-binding domain. This family includes human GAT2 (hGAT2) which transports gamma-aminobutyric acid (GABA). GABA is the main inhibitory neurotransmitter within the mammalian CNS. hGAT2 is encoded by the SLC6A13 gene, and is similar to mouse GAT-3, and rat GAT2. hGAT2 is expressed in brain, kidney, lung, and testis. hGAT2 is a potential drug target for treatment of epilepsy. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 544 matched cddid_all.tbl CDD cd11508 cd11508 212077 SLC6sbd_GAT3 Na(+)- and Cl(-)-dependent GABA transporter 3; solute-binding domain. This family includes human GAT3 (hGAT3) a high-affinity transporter of gamma-aminobutyric acid (GABA). GABA is the main inhibitory neurotransmitter within the mammalian CNS. hGAT3 is encoded by the SLC6A11 gene, and is similar to mouse GAT4, and rat GAT3/GATB. GAT3 is expressed primarily in the glia of the brain, and is a potential drug target for antiepileptic drugs. This subgroup belongs to the solute carrier 6 (SLC6) transporter family 542 matched cddid_all.tbl CDD cd11509 cd11509 271397 SLC6sbd_CT1 Na(+)- and Cl(-)-dependent creatine transporter 1; solute-binding domain. CT1 (also called CRTR, CRT) transports creatine. Human CT1 is encoded by the SLC6A8 gene. CT1 is ubiquitously expressed, with highest levels found in skeletal muscle and kidney. Creatine is absorbed from food or synthesized from arginine and plays an important role in energy metabolism. Deficiency in human CT1 leads to X-linked cerebral creatine transporter deficiency. In males, this disorder is characterized by language and speech delays, autistic-like behavior, seizures in about 50% of cases, and can also involve midfacial hypoplasia, and short stature. In females, it is characterized by mild cognitive impairment with behavior and learning problems. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 589 matched cddid_all.tbl CDD cd11510 cd11510 271398 SLC6sbd_TauT Na(+)- and Cl(-)-dependent taurine transporter; solute-binding domain. TauT is a Na(+)- and Cl(-)-dependent, high-affinity, low-capacity transporter of taurine and beta-alanine. Human TauT is encoded by the SLC6A6 gene. TauT is expressed in brain, retina, liver, kidney, heart, spleen, and pancreas. It may play a part in the supply of taurine to the intestinal epithelium and in the between-meal-capture of taurine. It may also participate in re-absorbing taurine that has been deconjugated from bile acids in the distal lumen. Functional TauT protects kidney cells from nephrotoxicity caused by the chemotherapeutic agent cisplatin; cisplatin down-regulates TauT in a p53-dependent manner. In mice, TauT has been shown to be important for the maintenance of skeletal muscle function and total exercise capacity. TauT-/- mice develop additional clinically important diseases, some of which are characterized by apoptosis, including vision loss, olfactory dysfunction, and chronic liver disease. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 542 matched cddid_all.tbl CDD cd11511 cd11511 212080 SLC6sbd_BGT1 Na(+)- and Cl(-)-dependent betaine/GABA transporter-1, and related proteins; solute-binding domain. BGT1 is a relatively low-affinity transporter of gamma-aminobutyric acid (GABA), and can also transport betaine. GABA is the main inhibitory neurotransmitter within the mammalian CNS. Human BGT1 is encoded by the SLC6A12 gene, and is similar to mouse GAT2. Mouse GAT2 plays a role in transporting GABA across the blood-brain barrier. In addition to being expressed in cells of the central nervous system, BGT1 is expressed in peripheral tissues, including kidney, liver, and heart. An association has been shown between the SLC6A12 gene and the occurrence of aspirin-intolerant asthma, and BGT1 is a drug target for antiepileptic drugs. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 541 matched cddid_all.tbl CDD cd11512 cd11512 212081 SLC6sbd_NET Na(+)- and Cl(-)-dependent norepinephrine transporter NET; solute-binding domain. NET (also called NAT1, NET1), is a transmembrane transporter that transports the neurotransmitter norepinephrine from synaptic spaces into presynaptic neurons. Human NET is encoded by the SLC6A2 gene. NET is expressed in brain, peripheral nervous system, adrenal gland, and placenta. NET may play a role in diseases or disorders including depression, orthostatic intolerance, anorexia nervosa, cardiovascular diseases, alcoholism, and attention-deficit hyperactivity disorder. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 560 matched cddid_all.tbl CDD cd11513 cd11513 271399 SLC6sbd_SERT Na(+)- and Cl(-)-dependent serotonin transporter SERT; solute-binding domain. SERT (also called 5-HTT), is a transmembrane transporter that transports the neurotransmitter serotonin from synaptic spaces into presynaptic neurons. The antiport of a K+ ion is believed to follow the transport of serotonin and promote the reorientation of SERT for another transport cycle. Human SERT is encoded by the SLC6A4 gene. SERT is expressed in brain, peripheral nervous system, placenta, epithelium, and platelets. SERT may play a role in diseases or disorders including anxiety, depression, autism, gastrointestinal disorders, premature ejaculation, and obesity. It may also have a role in social cognition. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 537 matched cddid_all.tbl CDD cd11514 cd11514 212083 SLC6sbd_DAT1 Na(+)- and Cl(-)-dependent dopamine transporter 1; solute-binding domain. DAT1 (also called DAT), is a plasma membrane transport protein that functions at the dopaminergic synapses to transport dopamine from the extracellular space back into the presynaptic nerve terminal. Human DAT1 is encoded by the SLC6A3 gene, and is expressed in the brain. DAT1 may play a role in diseases or disorders related to dopaminergic neurons, including attention-deficit hyperactivity disorder (ADHD), Tourette syndrome, Parkinson's disease, alcoholism, drug abuse, schizophrenia, extraversion, and risky behavior. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 555 matched cddid_all.tbl CDD cd11515 cd11515 271400 SLC6sbd_NTT4-like Na(+)-dependent neurotransmitter transporter 4, and related proteins; solute-binding domain. This subgroup includes the solute-binding domain of NTT4 (also called XT1) and SBAT1 (also called B0AT2, v7-3, NTT7-3); both these proteins can transport neutral amino acids. Human SBAT1 is encoded by the SLC6A15 gene, a susceptibility gene for major depression. SBAT1 is expressed in brain, and may have a role in transporting neurotransmitter precursors into neurons. Human NTT4 is encoded by the SLC6A17 gene. NTT4 is specifically expressed in the nervous system, in synaptic vesicles of glutamatergic and GABAergic neurons, and may play an important role in synaptic transmission. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 530 matched cddid_all.tbl CDD cd11516 cd11516 212085 SLC6sbd_B0AT1 Na(+)-dependent neutral amino acids transporter, B0AT1; solute-binding domain. B0AT1 (also called HND) transports neutral amino acids. Human B0AT1 is encoded by the SLC6A19 gene. B0AT1 is expressed primarily in the kidney and intestine; it requires collectrin for expression in the kidney, and angiotensin-converting enzyme 2 for expression in the intestine. Interaction with these two proteins implicates B0AT1 in more complex processes such as glomerular structure, exocytosis, and blood pressure control. The autosomal recessive disorder, Hartnup disorder, is caused by mutations in B0AT1. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 581 matched cddid_all.tbl CDD cd11517 cd11517 212086 SLC6sbd_B0AT3 glycine transporter, B0AT3; solute-binding domain. B0AT3 (also called Xtrp2, XT2) transports glycine. Human B0AT3 is encoded by the SLC6A18 gene. B0AT3 is expressed in the kidney. Mutations in the SLC6A18 gene may contribute to the autosomal recessive disorder iminoglycinuria and its related disorder hyperglycinuria. SLC6A18 or its neighboring genes are associated with increased susceptibility to myocardial infarction. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 576 matched cddid_all.tbl CDD cd11518 cd11518 271401 SLC6sbd_SIT1 Na(+)- and Cl(-)-dependent imino acid transporter SIT1; solute-binding domain. SIT1 (also called XTRP3, XT3, IMINO) transports imino acids, such as proline, pipecolate, MeAIB, and sarcosine. It has weak affinity for neutral amino acids such as phenylalanine. Human SIT1 is encoded by the SLC6A20 gene. SIT1 is expressed in brain, kidney, small intestine, thymus, spleen, ovary, and lung. SLC6A20 is a candidate gene for the rare disorder iminoglycinuria. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 576 matched cddid_all.tbl CDD cd11519 cd11519 271402 SLC5sbd_SMCT1 Na(+)/monocarboxylate cotransporter SMCT1 and related proteins; solute-binding domain. SMCT1 is a high-affinity transporter of various monocarboxylates including lactate and pyruvate, short-chain fatty acids, ketone bodies, nicotinate and its structural analogs, pyroglutamate, benzoate and its derivatives, and iodide. Human SMCT1 (hSMCT1, also called AIT) is encoded by the tumor suppressor gene SLC5A8. Its expression is under the control of the C/EBP transcription factor. Its tumor-suppressive role is related to uptake of butyrate, propionate, and pyruvate, these latter are inhibitors of histone deacetylases. SMCT1 is expressed in the colon, small intestine, kidney, thyroid gland, retina, and brain. SMCT1 may contribute to the intestinal/colonic and oral absorption of monocarboxylate drugs. SMCT1 also mediates iodide transport from thyrocyte into the colloid lumen in thyroid gland and through transporting l-lactate and ketone bodies helps maintain the energy status and the function of neurons. In the kidney its expression is limited to the S3 segment of the proximal convoluted tubule (in contrast to the low-affinity monocarboxylate transporter SMCT2, belonging to a different family, which is expressed along the entire length of the tubule). In the retina, SMCT1 and SMCT2 may play a differential role in monocarboxylate transport in a cell type-specific manner, SMCT1 is expressed predominantly in retinal neurons and in retinal pigmented epithelial (RPE) cells. This subgroup belongs to the solute carrier 5 (SLC5) transporter family. 542 matched cddid_all.tbl CDD cd11520 cd11520 212089 SLC5sbd_SMCT2 Na(+)/monocarboxylate cotransporter SMCT2 and related proteins; solute-binding domain. SMCT2 is a low-affinity transporter for short-chain fatty acids, lactate, pyruvate, and nicotinate. Human SMCT2 (hSMCT2) is encoded by the SLC5A12 gene. SMCT2 is expressed in the kidney, small intestine, skeletal muscle, and retina. In the kidney, it is expressed in the apical membrane of the proximal convoluted tubule, along the entire length of the tubule (in contrast to the high-affinity monocarboxylate transporter SMCT1, belonging to a different family, which is limited to the S3 segment of the tubule). SMCT2 may initiate lactate absorption in the early parts of the tubule. In the retina, SMCT1 and SMCT2 may play a differential role in monocarboxylate transport in a cell type-specific manner, SMCT2 is expressed exclusively in Muller cells. Nicotine transport by hSMCT2 is inhibited by several non-steroidal anti-inflammatory drugs. This subgroup belongs to the solute carrier 5 (SLC5) transporter family. 529 matched cddid_all.tbl CDD cd11521 cd11521 271403 SLC6sbd_NTT4 Na(+)-dependent neurotransmitter transporter 4; solute-binding domain. NTT4 (also called XT1) transports the neutral amino acids, proline, glycine, leucine, and alanine, and may play an important role in synaptic transmission. Human NTT4 is encoded by the SLC6A17 gene. NTT4 is specifically expressed in the nervous system, in synaptic vesicles of glutamatergic and GABAergic neurons. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 589 matched cddid_all.tbl CDD cd11522 cd11522 212091 SLC6sbd_SBAT1 Sodium-coupled branched-chain amino-acid transporter 1; solute-binding domain. SBAT1 (also called B0AT2, v7-3, NTT7-3) is a high-affinity Na(+)-dependent transporter for large neutral amino acids, including leucine, isoleucine, valine, proline and methionine. Human SBAT1 is encoded by the SLC6A15 gene, a susceptibility gene for major depression. SBAT1 is expressed in brain, and may have a role in transporting neurotransmitter precursors into neurons. This subgroup belongs to the solute carrier 6 (SLC6) transporter family. 580 matched cddid_all.tbl CDD cd11523 cd11523 212133 NTP-PPase Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain superfamily. This superfamily contains enzymes that hydrolyze the alpha-beta phosphodiester bond of all canonical NTPs into monophosphate derivatives and pyrophosphate (PPi). Divalent ions, such as Mg2+ ion(s), are essential to activate a proposed water nucleophile and stabilize the charged intermediates to facilitate catalysis. These enzymes share a conserved divalent ion-binding motif EXX[E/D] in their active sites. They also share a highly conserved four-helix bundle, where one face forms the active site, while the other participates in oligomer assembly. The four-helix bundle consists of two central antiparallel alpha-helices that can be contained within a single protomer or form upon dimerization. The superfamily members include dimeric dUTP pyrophosphatases (dUTPases; EC 3.6.1.23), the nonspecific NTP-PPase MazG proteins, HisE-encoded phosphoribosyl ATP pyrophosphohydolase (PRA-PH), fungal histidine biosynthesis trifunctional proteins, and several uncharacterized protein families. 72 matched cddid_all.tbl CDD cd11524 cd11524 211400 SYLF The SYLF domain (also called DUF500), a novel lipid-binding module. The SYLF domain is named after SH3YL1, Ysc84p/Lsb4p, Lsb3p, and plant FYVE, which are proteins that contain it. It is also called DUF500 and is highly conserved from bacteria to mammals. Some members, such as SH3YL1, Ysc84p, and Lsb3p, which represent the best characterized members of the family, also contain an SH3 domain, while family members from plants and stramenopiles also contain a FYVE zinc finger domain. Other members only contain a stand-alone SYLF domain. The SYLF domain of SH3YL1 binds phosphoinositides with high affinity, while the N-terminal SYLF domains of both Ysc84p and Lsb3p have been shown to bind and bundle actin filaments, as well as bind liposomes with high affinity. 194 matched cddid_all.tbl CDD cd11525 cd11525 211401 SYLF_SH3YL1_like The SYLF domain (also called DUF500), a novel lipid-binding module, of SH3 domain containing Ysc84-like 1 (SH3YL1) and similar proteins. This subfamily is composed of yeast Ysc84 (also called LAS17-binding protein 4, Lsb4p) and Lsb3p proteins, vertebrate SH3YL1 (SH3 domain containing Ysc84-like 1), and similar proteins. They contain an N-terminal SYLF domain (also called DUF500) and a C-terminal SH3 domain. SH3YL1 localizes to the plasma membrane and is required for dorsal ruffle formation. Ysc84p localizes to actin patches and plays an important role in actin polymerization during endocytosis. A study of the yeast SH3 domain interactome predicts that Lsb3p and Lsb4p may function as molecular hubs for the assembly of endocytic complexes. The SYLF domain of SH3YL1 binds phosphoinositides with high affinity, while the N-terminal SYLF domains of both Ysc84p and Lsb3p have been shown to bind and bundle actin filaments, as well as bind liposomes with high affinity. 199 matched cddid_all.tbl CDD cd11526 cd11526 211402 SYLF_FYVE The SYLF domain (also called DUF500), a novel lipid-binding module, of FYVE zinc finger domain containing proteins. This subfamily is composed of uncharacterized proteins from plants and stramenopiles containing a FYVE zinc finger domain followed by a SYLF domain (also called DUF500). The SYLF domain of the related protein, SH3YL1, binds phosphoinositides with high affinity, while the N-terminal SYLF domains of both Ysc84p and Lsb3p have been shown to bind and bundle actin filaments, as well as bind liposomes with high affinity. 201 matched cddid_all.tbl CDD cd11527 cd11527 212134 NTP-PPase_dUTPase Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in dimeric 2-Deoxyuridine 5'-triphosphate nucleotidohydrolase and similar proteins. dUTPase (dUTP pyrophosphatase; EC 3.6.1.23) catalyzes the hydrolysis of dUTP to dUMP and pyrophosphate. It acts to ensure chromosomal integrity by reducing the effective ratio of dUTP/dTTP. Members in this family are dimeric dUTPases, such as those from Leishmania major, Trypanosoma cruzi, and Campylobacter jejuni, which differ from the monomeric and trimeric forms and adopt an all-alpha topology. A central four-helix bundle, consisting of two alpha-helices from the rigid domain and two helices from the mobile domain and connecting loops, form the active site in dimeric dUTPase-like proteins, requiring the presence of metal ion cofactors to hydrolyze both dUTP and dUDP. 94 matched cddid_all.tbl CDD cd11528 cd11528 212135 NTP-PPase_MazG_Nterm Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) N-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs. MazG is a NTP-PPase that hydrolyzes all canonical NTPs into their corresponding nucleoside monophosphates and pyrophosphate. The prototype of this family is MazG proteins from Escherichia coli (EcMazG) that represents the most abundant form consisting two sequence-related domains in tandem, this family corresponding to the N-terminal MazG-like domain. EcMazG functions as a regulator of cellular response to starvation by lowering the cellular concentration of guanosine 3',5'-bispyrophosphate (ppGpp). EcMazG exists as a dimer; each monomer contains two tandem MazG-like domains with similarly folded globular structures. However, only the C-terminal domain has well-ordered active site and exhibits an NTPase activity responsible for the regulation of bacterial cell survival under nutritional stress. Divalent ions, such as Mg2+ or Mn2+, are required for activity; however, this domain does not exhibit an NTPase activity despite containing structural features such as the EEXX(E/D) motif and key basic catalytic residues responsible for nucleotide pyrophosphohydrolysis activity. It is suggested that the N-terminal domain of EcMazG might have a house-cleaning function by hydrolyzing noncanonical NTPs whose incorporation into the nascent DNA leads to increased mutagenesis and DNA damage. 114 matched cddid_all.tbl CDD cd11529 cd11529 212136 NTP-PPase_MazG_Cterm Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) C-terminal tandem-domain of MazG proteins from Escherichia coli and bacterial homologs'. MazG is a NTP-PPase that hydrolyzes all canonical NTPs into their corresponding nucleoside monophosphates and pyrophosphate. The prototype of this family is MazG proteins from Escherichia coli (EcMazG) that represents the most abundant form consisting two sequence-related domains in tandem, this family corresponding to the C-terminal MazG-like domain. EcMazG functions as a regulator of cellular response to starvation by lowering the cellular concentration of guanosine 3',5'-bispyrophosphate (ppGpp). EcMazG exists as a dimer. Each monomer contains two tandem MazG-like domains with similarly folded globular structures. However, only the C-terminal domain has well-ordered active sites and exhibits an NTPase activity responsible for the regulation of bacterial cell survival under nutritional stress. Divalent ions, such as Mg2+ or Mn2+, are required for activity, along with structural features such as EEXX(E/D) motifs and key basic catalytic residues. It has been shown that the C-terminus NTPase activity is responsible for regulation of bacterial cell survival under nutritional stress. 116 matched cddid_all.tbl CDD cd11530 cd11530 212137 NTP-PPase_DR2231_like Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Deinococcus radiodurans DR2231 protein and its bacterial homologs. This family includes a MazG-like NTP-PPase from Deinococcus radiodurans (DR2231), a putative NTP-PPase YP_001813558.1 from Exiguobacterium sibiricum and their bacterial homologs. DR2231 shows significant structural resemblance to MazG proteins, but is functionally related to the dimeric dUTPases. It can hydrolyze dUTP into dUMP. DR2231-like proteins contain a well conserved divalent ion binding motif, EXXEX(12-28)EXXD, which is the identity signature for the all-alpha-helical NTP-PPase superfamily. Unlike normal dimeric dUTPase-like proteins with a central four-helix bundle forming the active site, YP_001813558.1 displays a very unusual interlaced segment-swapped dimer. It potentially prefers to hydrolyze dCTPs or its derivatives. YP_001813558.1-like proteins contain a variant divalent ion binding motif, EXXEX(12-28)AXXD. 88 matched cddid_all.tbl CDD cd11531 cd11531 212138 NTP-PPase_BsYpjD Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain putative pyrophosphatase YpjD from Bacillus subtilis and its bacterial homologs. This family includes a putative pyrophosphatase Ypjd from Bacillus subtilis (BsYpjD) and its homologs. Although its biological role has not been described in detail, BsYpjD shows significant sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTP pyrophosphatase or dUTPase) and NTP-PPase MazG proteins. However, unlike typical tandem-domain MazG proteins, BsYpjD contains a single MazG-like domain. 93 matched cddid_all.tbl CDD cd11532 cd11532 212139 NTP-PPase_COG4997 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from archaea and bacteria. The family includes some uncharacterized hypothetical proteins from archaea and bacteria. Although their biological roles remain unclear, the family members show significant sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTP pyrophosphatase or dUTPase) and NTP-PPase MazG proteins. However, unlike typical tandem-domain MazG proteins, the family contains a single MazG-like domain. 95 matched cddid_all.tbl CDD cd11533 cd11533 212140 NTP-PPase_Af0060_like Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in uncharacterized protein from Archaeoglobus fulgidus (Af0060) and its bacterial homologs. This family includes an uncharacterized protein from Archaeoglobus fulgidus (Af0060) and its homologs from bacteria. Although its biological role remains unclear, Af0060 shows high sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTP pyrophosphatase or dUTPase) and NTP-PPase MazG proteins. However, unlike typical tandem-domain MazG proteins, members in this family consist of a single MazG-like domain that contains a well conserved divalent ion-binding motif EXX[E/D]. 75 matched cddid_all.tbl CDD cd11534 cd11534 212141 NTP-PPase_HisIE_like Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase (HisIE or PRATP-PH) and its homologs. This family includes Escherichia coli phosphoribosyl-ATP pyrophosphohydrolase, HisIE, and its homologs from all three kingdoms of life. E. coli HisIE is encoded by the hisIE gene, which is formed by hisE gene fused to hisl. HisIE is a bifunctional enzyme responsible for the second and third steps of the histidine-biosynthesis pathway. Its N-terminal and C-terminal domains have phosphoribosyl-AMP cyclohydrolase (HisI) and phosphoribosyl-ATP pyrophosphohydrolase (HisE or PRATP-PH) activity, respectively. This family corresponds to the C-terminal domain of HisIE and includes many hisE gene encoding proteins, all of which show significant sequence similarity to Mycobacterium tuberculosis phosphoribosyl-ATP pyrophosphohydrolase (HisE or PRATP-PH). These proteins may be responsible for only the second step in the histidine-biosynthetic pathway, irreversibly hydrolyzing phosphoribosyl-ATP (PRATP) to phosphoribosyl-AMP (PRAMP) and pyrophosphate. 84 matched cddid_all.tbl CDD cd11535 cd11535 212142 NTP-PPase_SsMazG Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Sulfolobus solfataricus (Ss) and its homologs from archaea and bacteria. This family includes a MazG-like protein from Sulfolobus solfataricus (SsMazG) and its homologs from archaea and bacteria. Although its biological roles remain still unclear, SsMazG shows significant sequence similarity to the NTP-PPase MazG proteins. However, unlike typical tandem-domain MazG proteins, SsMazG contains a single MazG-like domain. It is predicted that SsMazG might participate in house-cleaning by preventing incorporation of the oxidation product 2-oxo-(d)ATP (iso-dGTP), a mutagenic derivative of ATP, into DNA. 76 matched cddid_all.tbl CDD cd11536 cd11536 212143 NTP-PPase_iMazG Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in integron-associated MazG (iMazG) proteins. This family corresponds to the iMazG proteins representing a new subfamily of MazG NTP-PPases. iMazG is likely to act as a house-cleaning enzyme capable of removing aberrant dNTPs, preventing the incorporation of damaging non-canonical nucleotides into host-cell DNA. It can convert dNTP to dNMP and pyrophosphate by cleaving between the alpha- and beta-phosphates of its dNTP substrates, with a marked preference for dCTP and dATP. Unlike typical tandem-domain MazG proteins, iMazG contains a single MazG-like domain and functions as a tetramer (a dimer of dimers) with a typical four-helical bundle. The divalent ions, such as Mg2+, are required for its pyrophosphatase activity. 90 matched cddid_all.tbl CDD cd11537 cd11537 212144 NTP-PPase_RS21-C6_like Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in mouse RS21-C6 protein and its homologs. RS21-C6 proteins, highly expressed in all vertebrate genomes and green plants, act as house-cleaning enzymes, removing 5-methyl dCTP (m5dCTP) in order to prevent gene silencing. They show significant sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTP pyrophosphatase or dUTPase) and NTP-PPase MazG proteins. However, unlike typical tandem-domain MazG proteins, RS21-C6 contains a single MazG-like domain and functions as a tetramer (a dimer of dimers) with a typical four-helical bundle. Divalent ions, such as Mg2+, are required for its pyrophosphatase activity. This family also includes a pyrophosphatase from Archaeoglobus fulgidus (Af1178). Although its biological role remains unclear, Af1178 shows significant sequence similarity to the mouse RS21-C6 protein. 90 matched cddid_all.tbl CDD cd11538 cd11538 212145 NTP-PPase_u1 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from bacteria. This family corresponds to a group of uncharacterized hypothetical proteins from bacteria, showing a high sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTP pyrophosphatase or dUTPase) and NTP-PPase MazG proteins. However, unlike typical tandem-domain MazG proteins, members in this family consist of a single MazG-like domain that contains a well conserved divalent ion-binding motif EXX[E/D]. 97 matched cddid_all.tbl CDD cd11539 cd11539 212146 NTP-PPase_u2 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from bacteria and archaea. The family corresponds to a group of uncharacterized hypothetical proteins from bacteria and archaea, showing a high sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTP pyrophosphatase or dUTPase) and NTP-PPase MazG proteins. However, unlike typical tandem-domain MazG proteins, members in this family consist of a single MazG-like domain that contains a well conserved divalent ion-binding motif EXX[E/D]. 85 matched cddid_all.tbl CDD cd11540 cd11540 212147 NTP-PPase_u3 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from bacteria and archaea. This family corresponds to a group of uncharacterized hypothetical proteins from bacteria and archaea, showing a high sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTP pyrophosphatase or dUTPase) and NTP-PPase MazG proteins. However, unlike typical tandem-domain MazG proteins, members in this family consist of a single MazG-like domain that contains a well conserved divalent ion-binding motif EXX[E/D]. 76 matched cddid_all.tbl CDD cd11541 cd11541 212148 NTP-PPase_u4 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from bacteria and archaea. This family corresponds to a group of uncharacterized hypothetical proteins from bacteria, showing a high sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTP pyrophosphatase or dUTPase) and NTP-PPase MazG proteins. However, unlike typical tandem-domain MazG proteins, members in this family consist of a single MazG-like domain that contains a well conserved divalent ion-binding motif EXX[E/D]. 91 matched cddid_all.tbl CDD cd11542 cd11542 212149 NTP-PPase_u5 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from bacteria and archaea. This family corresponds to a group of uncharacterized hypothetical proteins from bacteria, showing a high sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTP pyrophosphatase or dUTPase) and NTP-PPase MazG proteins. However, unlike typical tandem-domain MazG proteins, members in this family consist of a single MazG-like domain that contains a well conserved divalent ion-binding motif EXX[E/D]. 99 matched cddid_all.tbl CDD cd11543 cd11543 212150 NTP-PPase_u6 Nucleoside Triphosphate Pyrophosphohydrolase EC 3.6.1.8) MazG-like domain found in a group of uncharacterized proteins from bacteria and archaea. This family corresponds to a group of uncharacterized hypothetical proteins from bacteria, showing a high sequence similarity to the dimeric 2-deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTP pyrophosphatase or dUTPase) and NTP-PPase MazG proteins. However, unlike typical tandem-domain MazG proteins, members in this family consist of a single MazG-like domain. 87 matched cddid_all.tbl CDD cd11544 cd11544 212151 NTP-PPase_DR2231 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Deinococcus radiodurans DR2231 protein and its bacterial homologs. This family corresponds to the DR2231 protein, a MazG-like NTP-PPase from Deinococcus radiodurans, and its bacterial homologs. All family members contain a well-conserved divalent ion binding motif, EXXEX(12-28)EXXD, which is the identity signature for all-alpha-helical NTP-PPase superfamily. DR2231 shows significant structural resemblance to MazG proteins, but is functionally related to the dimeric dUTPases. It might be an evolutionary precursor of dimeric dUTPases with very high specificity in hydrolyzing dUTP into dUMP, but an inability to hydrolyze dTTP, a typical feature of dUTPases. Moreover, unlike the dUPase monomer containing a single active site, the DR2231 protein dimer holds two putative active sites. 116 matched cddid_all.tbl CDD cd11545 cd11545 212152 NTP-PPase_YP_001813558 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Exiguobacterium sibiricum YP_001813558.1 protein and its bacterial homologs. This family contains a putative NTP_PPase (YP_001813558.1) from Exiguobacterium sibiricum and its bacterial homologs. Unlike normal dimeric dUTPase-like proteins with a central four-helix bundle forming the active site, YP_001813558.1 displays a very unusual interlaced segment-swapped dimer that might be important for it to adapt to an extremely cold environment. Moreover, structural analysis and comparisons indicate that YP_001813558.1 potentially prefers to hydrolyze dCTPs or its derivatives. 115 matched cddid_all.tbl CDD cd11546 cd11546 212153 NTP-PPase_His4 Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in His4-like fungal histidine biosynthesis trifunctional proteins and their homologs. This family includes fungal histidine biosynthesis trifunctional proteins and their homologs from eukaryotes and bacteria. Some family members contain three domains responsible for phosphoribosyl-AMP cyclohydrolase (PRAMP-CH), phosphoribosyl-ATP pyrophosphohydrolase (PRATP-PH), and histidinol dehydrogenase (Histidinol-DH) activity, respectively. Some others do not have Histidinol-DH domain, but have an additional N-terminal TIM phosphate binding domain. This family corresponds to the domain for PRATP-PH activity, which shows significant sequence similarity to Mycobacterium tuberculosis PRATP-PH that catalyzes the second step in the histidine-biosynthetic pathway, irreversibly hydrolyzing phosphoribosyl-ATP (PRATP) to phosphoribosyl-AMP (PRAMP) and pyrophosphate. 84 matched cddid_all.tbl CDD cd11547 cd11547 212154 NTP-PPase_HisE Nucleoside Triphosphate Pyrophosphohydrolase (EC 3.6.1.8) MazG-like domain found in Mycobacterium tuberculosis phosphoribosyl-ATP pyrophosphohydrolase (HisE or PRATP-PH) and its bacterial homologs. This family includes M. tuberculosis phosphoribosyl-ATP pyrophosphohydrolase (HisE or PRATP-PH) and its bacterial homologs. M. tuberculosis HisE is encoded by the hisE gene, which is a separate gene presenting in many bacteria and archaea but is fused to hisI in other bacteria, fungi and plants. HisE is responsible for the second step in the histidine-biosynthetic pathway. It can irreversibly hydrolyze phosphoribosyl-ATP (PRATP) to phosphoribosyl-AMP (PRAMP) and pyrophosphate. HisE dimerizes into a four alpha-helix bundle, forming two inferred PRATP active sites on the outer faces. M. tuberculosis HisE has been found to be essential for growth in vitro, thus making it a potential drug target for tuberculosis. 86 matched cddid_all.tbl CDD cd11548 cd11548 211389 NodZ_like Alpha 1,6-fucosyltransferase similar to Bradyrhizobium NodZ. Bradyrhizobium NodZ is an alpha 1,6-fucosyltransferase involved in the biosynthesis of the nodulation factor, a lipo-chitooligosaccharide formed by three-to-six beta-1,4-linked N-acetyl-d-glucosamine (GlcNAc) residues and a fatty acid acyl group attached to the nitrogen atom at the non-reducing end. NodZ transfers L-fucose from the GDP-beta-L-fucose donor to the reducing residue of the chitin oligosaccharide backbone, before the attachment of a fatty acid group. O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes. 287 matched cddid_all.tbl CDD cd11549 cd11549 211403 Serine_rich_CAS Serine rich Four helix bundle domain of CAS (Crk-Associated Substrate) scaffolding proteins; a protein interaction module. CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes including migration, chemotaxis, apoptosis, differentiation, and progenitor cell function. They mediate the signaling of integrins at focal adhesions where they localize, and thus, regulate cell invasion and survival. Over-expression of these proteins is implicated in poor prognosis, increased metastasis, and resistance to chemotherapeutics in many cancers such as breast, lung, melanoma, and glioblastoma. CAS proteins have also been linked to the pathogenesis of inflammatory disorders, Alzheimer's, Parkinson's, and developmental defects. They share a common domain structure containing protein interaction modules that enable their scaffolding function, including an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain. Vertebrates contain four CAS proteins: BCAR1 (or p130Cas), NEDD9 (or HEF1), EFS (or SIN), and CASS4 (or HEPL). CAS proteins associate with the 14-3-3 family; this interaction is regulated by integrin-mediated cell adhesion. The serine rich four helix bundle domain of BCAR1 has been shown to bind 14-3-3 in a phosphorylation-dependent manner. This domain is structurally similar to other helical bundles found in cell adhesion components such as alpha-catenin, vinculin, and FAK, and may bind other proteins in addition to the 14-3-3 family. 159 matched cddid_all.tbl CDD cd11550 cd11550 211404 Serine_rich_NEDD9 Serine rich Four helix bundle domain of CAS (Crk-Associated Substrate) scaffolding protein, Neural precursor cell Expressed, Developmentally Down-regulated 9; a protein interaction module. NEDD9 is also called human enhancer of filamentation 1 (HEF1) or CAS-L (Crk-associated substrate in lymphocyte). It was first described as a gene predominantly expressed in early embryonic brain, and was also isolated from a screen of human proteins that regulate filamentous budding in yeast, and as a tyrosine phosphorylated protein in lymphocytes. It promotes metastasis in different solid tumors. NEDD9 localizes in focal adhesions and associates with FAK and Abl kinase. It also interacts with SMAD3 and the proteasomal machinery which allows its rapid turnover; these interactions are not shared by other CAS proteins. CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes. They share a common domain structure containing protein interaction modules that enable their scaffolding function, including an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain. CAS proteins associate with the 14-3-3 family; this interaction is regulated by integrin-mediated cell adhesion. The serine rich four helix bundle domain of BCAR1, another CAS protein, has been shown to bind 14-3-3 in a phosphorylation-dependent manner. This domain is structurally similar to other helical bundles found in cell adhesion components such as alpha-catenin, vinculin, and FAK, and may bind other proteins in addition to the 14-3-3 family. 162 matched cddid_all.tbl CDD cd11551 cd11551 211405 Serine_rich_CASS4 Serine rich Four helix bundle domain of CAS (Crk-Associated Substrate) scaffolding protein family member 4; a protein interaction module. CASS4, also called HEPL (HEF1-EFS-p130Cas-like), localizes to focal adhesions and plays a role in regulating FAK activity, focal adhesion integrity, and cell spreading. It is most abundant in blood cells and lung tissue, and is also found in high levels in leukemia and ovarian cell lines. CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes. They share a common domain structure containing protein interaction modules that enable their scaffolding function, including an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain. CAS proteins associate with the 14-3-3 family; this interaction is regulated by integrin-mediated cell adhesion. The serine rich four helix bundle domain of BCAR1, another CAS protein, has been shown to bind 14-3-3 in a phosphorylation-dependent manner. This domain is structurally similar to other helical bundles found in cell adhesion components such as alpha-catenin, vinculin, and FAK, and may bind other proteins in addition to the 14-3-3 family. 159 matched cddid_all.tbl CDD cd11552 cd11552 211406 Serine_rich_BCAR1 Serine rich Four helix bundle domain of CAS (Crk-Associated Substrate) scaffolding protein, Breast Cancer Anti-estrogen Resistance 1; a protein interaction module. BCAR1, also called p130cas or CASS1, is the founding member of the CAS family of scaffolding proteins and was originally identified through its ability to associate with Crk. The name BCAR1 was designated because the human gene was identified in a screen for genes that promote resistance to tamoxifen. It is widely expressed and its deletion is lethal in mice. It plays a role in regulating cell motility, survival, proliferation, transformation, cancer progression, and bacterial pathogenesis. CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes. They share a common domain structure containing protein interaction modules that enable their scaffolding function, including an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain. CAS proteins associate with the 14-3-3 family; this interaction is regulated by integrin-mediated cell adhesion. The serine rich four helix bundle domain of BCAR1 has been shown to bind 14-3-3 in a phosphorylation-dependent manner. This domain is structurally similar to other helical bundles found in cell adhesion components such as alpha-catenin, vinculin, and FAK, and may bind other proteins in addition to the 14-3-3 family. 157 matched cddid_all.tbl CDD cd11554 cd11554 212092 SLC6sbd_u2 uncharacterized eukaryotic solute carrier 6 subfamily; solute-binding domain. SLC6 proteins (also called the sodium- and chloride-dependent neurotransmitter transporter family or Na+/Cl--dependent transporter family) include neurotransmitter transporters (NTTs): these are sodium- and chloride-dependent plasma membrane transporters for the monoamine neurotransmitters serotonin (5-hydroxytryptamine), dopamine, and norepinephrine, and the amino acid neurotransmitters GABA and glycine. These NTTs are widely expressed in the mammalian brain, and are involved in regulating neurotransmitter signaling and homeostasis, and are the target of a range of therapeutic drugs for the treatment of psychiatric diseases. Bacterial members of the SLC6 family include the LeuT amino acid transporter. 406 matched cddid_all.tbl CDD cd11555 cd11555 271404 SLC-NCS1sbd_u1 uncharacterized nucleobase-cation-symport-1 (NCS1) transporter subfamily; solute-binding domain. NCS1s are essential components of salvage pathways for nucleobases and related metabolites; their known substrates include allantoin, uracil, thiamine, and nicotinamide riboside. NCS1s belong to a superfamily which also contains the solute carrier 5 family sodium/glucose transporters (SLC5s), and solute carrier 6 family neurotransmitter transporters (SLC6s). 461 matched cddid_all.tbl CDD cd11556 cd11556 271405 SLC6sbd_SERT-like_u1 uncharacterized subgroup of the SERT-like Na(+)- and Cl(-)-dependent monoamine transporter subfamily; solute binding domain. SERT-like Na(+)- and Cl(-)-dependent monoamine transporters, transport monoamine neurotransmitters from synaptic spaces into presynaptic neurons. Members include: the norepinephrine transporter NET, the serotonin transporter SERT , and the dopamine transporter DAT1. These latter may play a role in diseases or disorders including depression, anxiety disorders, and attention-deficit hyperactivity disorder, and in the control of human behavior and emotional states. They belongs to the solute carrier 6 (SLC6) transporter family. Members of this subgroup are uncharacterized. 552 matched cddid_all.tbl CDD cd11557 cd11557 211407 ST7 Suppression of tumorigenicity 7. ST7 is a metazoan protein that behaves as a tumor suppressor in human cancer cells. It appears to localize to the cytoplasm and plasma membrane, and may mediate tumor suppression by regulating genes that are involved in oncogenic pathways and/or maintain cellular structure. It has been suggested that the suppression of tumorigenicity is associated with a function in mediating the remodeling of the extracellular matrix. However, somatic mutations of ST7 have not been observed as being commonly associated with molecular pathogenesis in various human neoplasias. 458 matched cddid_all.tbl CDD cd11558 cd11558 211396 W2_eIF2B_epsilon C-terminal W2 domain of eukaryotic translation initiation factor 2B epsilon. eIF2B is a heteropentameric complex which functions as a guanine nucleotide exchange factor in the recycling of eIF-2 during the initiation of translation in eukaryotes. The epsilon and gamma subunits are sequence similar and both are essential in yeast. Epsilon appears to be the catalytically active subunit, with gamma enhancing its activity. The C-terminal domain of the eIF2B epsilon subunit contains bipartite motifs rich in acidic and aromatic residues, which are responsible for the interaction with eIF2. The structure of the domain resembles that of a set of concatenated HEAT repeats. 169 matched cddid_all.tbl CDD cd11559 cd11559 211397 W2_eIF4G1_like C-terminal W2 domain of eukaryotic translation initiation factor 4 gamma 1 and similar proteins. eIF4G1 is a component of the multi-subunit eukaryotic translation initiation factor 4F, which facilitates recruitment of the mRNA to the ribosome, a rate-limiting step during translation initiation. This C-terminal domain, whose structure resembles that of a set of concatenated HEAT repeats, has been associated with binding to/recruiting the kinase Mnk1, which phosphorylates eIF4E. 134 matched cddid_all.tbl CDD cd11560 cd11560 211398 W2_eIF5C_like C-terminal W2 domain of the eukaryotic translation initiation factor 5C and similar proteins. eIF5C appears to be essential for the initiation of protein translation; its actual function, and specifically that of the C-terminal W2 domain, are not well understood. The Drosophila ortholog, kra (krasavietz) or exba (extra bases), may be involved in translational inhibition in neural development. The structure of this C-terminal domain resembles that of a set of concatenated HEAT repeats. 194 matched cddid_all.tbl CDD cd11561 cd11561 211399 W2_eIF5 C-terminal W2 domain of eukaryotic translation initiation factor 5. eIF5 functions as a GTPase acceleration protein (GAP), as well as a GDP dissociation inhibitor (GDI) during translational initiation in eukaryotes. The structure of this C-terminal domain resembles that of a set of concatenated HEAT repeats. 157 matched cddid_all.tbl CDD cd11564 cd11564 211408 FAT-like_CAS_C C-terminal FAT-like Four helix bundle domain, also called DUF3513, of CAS (Crk-Associated Substrate) scaffolding proteins; a protein interaction module. CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes including migration, chemotaxis, apoptosis, differentiation, and progenitor cell function. They mediate the signaling of integrins at focal adhesions where they localize, and thus, regulate cell invasion and survival. Over-expression of these proteins is implicated in poor prognosis, increased metastasis, and resistance to chemotherapeutics in many cancers such as breast, lung, melanoma, and glioblastoma. CAS proteins have also been linked to the pathogenesis of inflammatory disorders, Alzheimer's, Parkinson's, and developmental defects. They share a common domain structure containing protein interaction modules that enable their scaffolding function, including an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain. Vertebrates contain four CAS proteins: BCAR1 (or p130Cas), NEDD9 (or HEF1), EFS (or SIN), and CASS4 (or HEPL). The FAT-like C-terminal domain of CAS proteins binds to the C-terminal domain of NSPs (novel SH2-containing proteins) to form multidomain signaling modules that mediate cell migration and invasion. 126 matched cddid_all.tbl CDD cd11565 cd11565 467842 RWD_Spc24 RWD domain of the Spc24 component of the nuclear division cycle 80 (NDC80) kinetochore complex. The kinetochore protein Spc24 acts as a component of the essential kinetochore-associated NDC80 complex, which is involved in chromosome segregation and spindle checkpoint activity. Spc24 is required for kinetochore integrity and the organization of stable microtubule binding sites in the outer plate of the kinetochore. The NDC80 complex synergistically enhances the affinity of the SKA1 complex for microtubules and may allow the NDC80 complex to track depolymerizing microtubules. The model corresponds to the Spc24 RWD domain, which provides an interaction platform to mediate kinetochore assembly. 58 matched cddid_all.tbl CDD cd11566 cd11566 211318 eIF1_SUI1 Eukaryotic initiation factor 1. eIF1/SUI1 (eukaryotic initiation factor 1) plays an important role in accurate initiator codon recognition during translation initiation. eIF1 interacts with 18S rRNA in the 40S ribosomal subunit during eukaryotic translation initiation. Point mutations in the yeast eIF1 implicate the protein in maintaining accurate start-site selection but its mechanism of action is unknown. 84 matched cddid_all.tbl CDD cd11567 cd11567 211319 YciH_like Homologs of eIF1/SUI1 including Escherichia coli YciH. Members of the eIF1/SUI1 (eukaryotic initiation factor 1) family are found in eukaryotes, archaea, and some bacteria; eukaryotic members are understood to play an important role in accurate initiator codon recognition during translation initiation. The function of non-eukaryotic family members is unclear. Escherichia coli YciH is a non-essential protein and was reported to be able to perform some of the functions of IF3 in prokaryotic initiation. 76 matched cddid_all.tbl CDD cd11568 cd11568 211409 FAT-like_CASS4_C C-terminal FAT-like Four helix bundle domain, also called DUF3513, of CAS (Crk-Associated Substrate) scaffolding protein family member 4; a protein interaction module. CASS4, also called HEPL (HEF1-EFS-p130Cas-like), localizes to focal adhesions and plays a role in regulating FAK activity, focal adhesion integrity, and cell spreading. It is most abundant in blood cells and lung tissue, and is also found in high levels in leukemia and ovarian cell lines. CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes. They share a common domain structure containing protein interaction modules that enable their scaffolding function, including an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain, which binds to the C-terminal domain of NSPs (novel SH2-containing proteins) to form multidomain signaling modules that mediate cell migration and invasion. 123 matched cddid_all.tbl CDD cd11569 cd11569 211410 FAT-like_BCAR1_C C-terminal FAT-like Four helix bundle domain, also called DUF3513, of CAS (Crk-Associated Substrate) scaffolding protein, Breast Cancer Anti-estrogen Resistance 1; a protein interaction module. BCAR1, also called p130cas or CASS1, is the founding member of the CAS family of scaffolding proteins and was originally identified through its ability to associate with Crk. The name BCAR1 was designated because the human gene was identified in a screen for genes that promote resistance to tamoxifen. It is widely expressed and its deletion is lethal in mice. It plays a role in regulating cell motility, survival, proliferation, transformation, cancer progression, and bacterial pathogenesis. CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes. They share a common domain structure containing protein interaction modules that enable their scaffolding function, including an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain, which binds to the C-terminal domain of NSPs (novel SH2-containing proteins) to form multidomain signaling modules that mediate cell migration and invasion. 133 matched cddid_all.tbl CDD cd11570 cd11570 211411 FAT-like_NEDD9_C C-terminal FAT-like Four helix bundle domain, also called DUF3513, of CAS (Crk-Associated Substrate) scaffolding protein, Neural precursor cell Expressed, Developmentally Down-regulated 9; a protein interaction module. NEDD9 is also called human enhancer of filamentation 1 (HEF1) or CAS-L (Crk-associated substrate in lymphocyte). It was first described as a gene predominantly expressed in early embryonic brain, and was also isolated from a screen of human proteins that regulate filamentous budding in yeast, and as a tyrosine phosphorylated protein in lymphocytes. It promotes metastasis in different solid tumors. NEDD9 localizes in focal adhesions and associates with FAK and Abl kinase. It also interacts with SMAD3 and the proteasomal machinery which allows its rapid turnover; these interactions are not shared by other CAS proteins. CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes. They share a common domain structure containing protein interaction modules that enable their scaffolding function, including an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain, which binds to the C-terminal domain of NSPs (novel SH2-containing proteins) to form multidomain signaling modules that mediate cell migration and invasion. 128 matched cddid_all.tbl CDD cd11571 cd11571 211412 FAT-like_EFS_C C-terminal FAT-like Four helix bundle domain, also called DUF3513, of CAS (Crk-Associated Substrate) scaffolding protein, Embryonal Fyn-associated Substrate; a protein interaction module. EFS is also called HEFS, CASS3 (CAS scaffolding protein family member 3) or SIN (Src-interacting protein). It was identified based on interactions with the Src kinases, Fyn and Yes. It plays a role in thymocyte development and acts as a negative regulator of T cell proliferation. CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes. They share a common domain structure containing protein interaction modules that enable their scaffolding function, including an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain, which binds to the C-terminal domain of NSPs (novel SH2-containing proteins) to form multidomain signaling modules that mediate cell migration and invasion. 130 matched cddid_all.tbl CDD cd11572 cd11572 211413 RlmI_M_like Middle domain of the SAM-dependent methyltransferase RlmI and related proteins. This middle or central domain is typically found between an N-terminal PUA domain and a C-terminal SAM-dependent methyltransferase domain, such as in the Escherichia coli ribosomal RNA large subunit methyltransferase RlmI (YccW). It may be involved in binding to the RNA substrate. 99 matched cddid_all.tbl CDD cd11573 cd11573 211414 GH99_GH71_like Glycoside hydrolase families 71, 99, and related domains. This superfamily of glycoside hydrolases contains families GH71 and GH99 (following the CAZY nomenclature), as well as other members with undefined function and specificity. 284 matched cddid_all.tbl CDD cd11574 cd11574 211415 GH99 Glycoside hydrolase family 99, an endo-alpha-1,2-mannosidase. This family of glycoside hydrolases 99 (following the CAZY nomenclature) includes endo-alpha-1,2-mannosidase (EC 3.2.1.130), which is an important membrane-associated eukaryotic enzyme involved in the maturation of N-linked glycans. Specifically, it cleaves mannoside linkages internal to N-linked glycan chains by hydrolyzing an alpha-1,2-mannosidic bond between a glucose-substituted mannose and the remainder of the chain. The biological function and significance of the soluble bacterial orthologs, which may have obtained the genes via horizontal transfer, is not clear. 338 matched cddid_all.tbl CDD cd11575 cd11575 211416 GH99_GH71_like_3 Uncharacterized glycoside hydrolase family 99-like domain. This family of putative glycoside hydrolases resembles glycosyl hydrolase families 71 and 99 (following the CAZY nomenclature) and may share a similar catalytic site and mechanism. 376 matched cddid_all.tbl CDD cd11576 cd11576 211417 GH99_GH71_like_2 Uncharacterized glycoside hydrolase family 99-like domain. This family of putative glycoside hydrolases resembles glycosyl hydrolase families 71 and 99 (following the CAZY nomenclature) and may share a similar catalytic site and mechanism. The domain may co-occur with other domains involved in the binding/processing of glycans. 378 matched cddid_all.tbl CDD cd11577 cd11577 211418 GH71 Glycoside hydrolase family 71. This family of glycoside hydrolases 71 (following the CAZY nomenclature) function as alpha-1,3-glucanases (mutanases, EC 3.2.1.59). They appear to have an endo-hydrolytic mode of enzymatic activity and bacterial members are investigated as candidates for the development of dental caries treatments.The member from fission yeast, endo-alpha-1,3-glucanase Agn1p, plays a vital role in daughter cell separation, while Agn2p has been associated with endolysis of the ascus wall. 283 matched cddid_all.tbl CDD cd11578 cd11578 211419 GH99_GH71_like_1 Uncharacterized glycoside hydrolase family 99-like domain. This family of putative glycoside hydrolases resembles glycosyl hydrolase families 71 and 99 (following the CAZY nomenclature) and may share a similar catalytic site and mechanism. 313 matched cddid_all.tbl CDD cd11579 cd11579 211420 Glyco_tran_WbsX Glycosyl hydrolase family 99-like domain of WbsX-like glycosyltransferases. Members of this domain family are found in proteins within O-antigen biosynthesis clusters in Gram negative bacteria, where they may function as glycosyl hydrolases and typically co-occur with glycosyltransferase domains. They bear resemblance to GH71 and the GH99 family of alpha-1,2-mannosidases and may share a similar cataltyic site and mechanism. The O-antigens are essential lipopolysaccharides in gram-negative bacteria's outer membrane and have been linked to pathogenicity. 347 matched cddid_all.tbl CDD cd11580 cd11580 211421 eIF2D_N_like N-terminal domain of eIF2D, malignant T cell-amplified sequence 1 and related proteins. This N-terminal domain of various proteins co-occurs with a PUA domain. Members of this family are: (1) MCTS-1 (malignant T cell-amplified sequence 1) or MCT-1 (multiple copies T cell malignancies), which may play roles in the regulation of the cell cycle, (2) the eukayotic translation initiation factor 2D, and (3) an uncharacterized archaeal family. 72 matched cddid_all.tbl CDD cd11581 cd11581 212547 GINS_A Alpha-helical domain of GINS complex proteins; Sld5, Psf1, Psf2 and Psf3. The GINS complex is involved in both initiation and elongation stages of eukaryotic chromosome replication, with GINS being the component that most likely serves as the replicative helicase that unwinds duplex DNA ahead of the moving replication fork. In eukaryotes, GINS is a tetrameric arrangement of four subunits Sld5, Psf1, Psf2 and Psf3. The GINS complex has been found in eukaryotes and archaea, but not in bacteria. The four subunits of the complex are homologous and consist of two domains each, termed the alpha-helical (A) and beta-strand (B) domains. The A and B domains of Sld5/Psf1 are permuted with respect to Psf1/Psf3. 103 matched cddid_all.tbl CDD cd11582 cd11582 211424 Axin_TNKS_binding Tankyrase binding N-terminal segment of axin. This N-terminal region of axin mediates interactions with the ankyrin-repeat clusters 2 and 3 of tankyrase, which controls the turnover of axin via poly-ADP-ribosylation. Axin functions as a negative regulator of the WNT signaling pathway. 69 matched cddid_all.tbl CDD cd11583 cd11583 211425 Orc6_mid Middle domain of the origin recognition complex subunit 6. Orc6 is a subunit of the origin recognition complex in eukaryotes, and it may be involved in binding to DNA. This model describes the central or middle domain of Orc6, whose structure resembles that of TFIIB, a DNA-binding transcription factor. Orc6 appears to form distinct complexes with DNA, and a putative DNA-binding site has been identified. 94 matched cddid_all.tbl CDD cd11585 cd11585 211426 SATB1_N "N-terminal domain of SATB1 and similar proteins. SATB1, the special AT-rich sequence-binding protein 1, is involved in organizing chromosomal loci into distinct loops, creating a ""loopscape"" that has a direct bearing on gene expression. This N-terminal domain, which may be involved in various interactions with chromatin proteins, resembles a ubiquitin domain and has been shown to form tetramers, a function critical to SATB1-DNA interactions. The related Drosophila homeobox gene defective proventriculus (dve) plays a key role in the functional specification during endoderm development." 100 matched cddid_all.tbl CDD cd11586 cd11586 212155 VbhA_like VbhA antitoxin and related proteins. VbhA is the antitoxin to VbhT. The VbhT toxin of the mammalian pathogen Bartonella schoenbuchensis is responsible for the disruptive adenylation of host proteins. VbhT also induces FIC-domain-mediated growth arrest in bacteria; it is inhibited by this antitoxin which binds to block the ATP binding site of the VbhT FIC domain. 54 matched cddid_all.tbl CDD cd11587 cd11587 212536 Arginase-like Arginase types I and II and arginase-like family. This family includes arginase, also known as arginase-like amidino hydrolase family, and related proteins, found in bacteria, archaea and eykaryotes. Arginase is a binuclear Mn-dependent metalloenzyme and catalyzes hydrolysis of L-arginine to L-ornithine and urea (Arg, EC 3.5.3.1), the reaction being the fifth and final step in the urea cycle, providing the path for the disposal of nitrogenous compounds. Arginase controls cellular levels of arginine and ornithine which are involved in protein biosynthesis, and in production of creatine, polyamines, proline and nitric acid. In vertebrates, at least two isozymes have been identified: type I cytoplasmic or hepatic liver-type arginase and type II mitochondrial or non-hepatic arginase. Point mutations in human arginase gene lead to hyperargininemia with consequent mental disorders, retarded development and early death. Arginase is a therapeutic target to treat asthma, erectile dysfunction, atherosclerosis and cancer. 294 matched cddid_all.tbl CDD cd11589 cd11589 212537 Agmatinase_like_1 Agmatinase and related proteins. This family includes known and predicted bacterial agmatinase (agmatine ureohydrolase; AUH; SpeB; EC=3.5.3.11), a binuclear manganese metalloenzyme, belonging to the ureohydrolase superfamily. It is a key enzyme in the synthesis of polyamine putrescine; it catalyzes hydrolysis of agmatine to yield urea and putrescine, the precursor for biosynthesis of higher polyamines, spermidine, and spermine. Agmatinase from Deinococcus radiodurans shows approximately 33% of sequence identity to human mitochondrial agmatinase. An analysis of the evolutionary relationship among ureohydrolase superfamily enzymes indicates the pathway involving arginine decarboxylase and agmatinase evolved earlier than the arginase pathway of polyamine. 274 matched cddid_all.tbl CDD cd11592 cd11592 212538 Agmatinase_PAH Agmatinase-like family includes proclavaminic acid amidinohydrolase. This agmatinase subfamily contains bacterial and fungal/metazoan enzymes, including proclavaminic acid amidinohydrolase (PAH, EC 3.5.3.22) and Pseudomonas aeruginosa guanidinobutyrase (GbuA) and guanidinopropionase (GpuA). PAH hydrolyzes amidinoproclavaminate to yield proclavaminate and urea in clavulanic acid biosynthesis. Clavulanic acid is an effective inhibitor of beta-lactamases and is used in combination with amoxicillin to prevent the beta-lactam rings of the antibiotic from hydrolysis and, thus keeping the antibiotic biologically active. GbuA hydrolyzes 4-guanidinobutyrate (4-GB) into 4-aminobutyrate and urea while GpuA hydrolyzes 3-guanidinopropionate (3-GP) into beta-alanine and urea. Mutation studies show that significant variations in two active site loops in these two enzymes may be important for substrate specificity. This subfamily belongs to the ureohydrolase superfamily, which includes arginase, agmatinase, proclavaminate amidinohydrolase, and formiminoglutamase. 289 matched cddid_all.tbl CDD cd11593 cd11593 212539 Agmatinase-like_2 Agmatinase and related proteins. This family includes known and predicted bacterial and archaeal agmatinase (agmatine ureohydrolase; AUH; SpeB; EC=3.5.3.11), a binuclear manganese metalloenzyme that belongs to the ureohydrolase superfamily. It is a key enzyme in the synthesis of polyamine putrescine; it catalyzes hydrolysis of agmatine to yield urea and putrescine, the precursor for biosynthesis of higher polyamines, spermidine, and spermine. As compared to E. coli where two paths to putrescine exist, via decarboxylation of an amino acid, ornithine or arginine, a single path is found in Bacillus subtilis, where polyamine synthesis starts with agmatine; the speE and speB encode spermidine synthase and agmatinase, respectively. The level of agmatinase synthesis is very low, allowing strict control on the synthesis of putrescine and therefore, of all polyamines, consistent with polyamine levels in the cell. This subfamily belongs to the ureohydrolase superfamily, which includes arginase, agmatinase, proclavaminate amidinohydrolase, and formiminoglutamase. 263 matched cddid_all.tbl CDD cd11598 cd11598 212540 HDAC_Hos2 Class I histone deacetylases including ScHos2 and SpPhd1. This subfamily includes Class I histone deacetylase (HDAC) Hos2 from Saccharomyces cerevisiae as well as a histone deacetylase Phd1 from Schizosaccharomyces pombe. Hos2 binds to the coding regions of genes during gene activation, specifically it deacetylates the lysines in H3 and H4 histone tails. It is preferentially associated with genes of high activity genome-wide and is shown to be necessary for efficient transcription. Thus, Hos2 is directly required for gene activation in contrast to other class I histone deacetylases. Protein encoded by phd1 is inhibited by trichostatin A (TSA), a specific inhibitor of histone deacetylase, and is involved in the meiotic cell cycle in S. pombe. Class 1 HDACs are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues in histone amino termini to yield a deacetylated histone (EC 3.5.1.98). 311 matched cddid_all.tbl CDD cd11599 cd11599 212541 HDAC_classII_2 Histone deacetylases and histone-like deacetylases, classII. This subfamily includes eukaryotic as well as bacterial Class II histone deacetylase (HDAC) and related proteins. Deacetylases of class II are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) and possibly other proteins to yield deacetylated histones/other proteins. In D. discoideum, where four homologs (HdaA, HdaB, HdaC, HdaD) have been identified, HDAC activity is important for regulating the timing of gene expression during development. Also, inhibition of HDAC activity by trichostatin A is shown to cause hyperacetylation of the histone and a delay in cell aggregation and differentiation. 288 matched cddid_all.tbl CDD cd11600 cd11600 212542 HDAC_Clr3 Class II Histone deacetylase Clr3 and similar proteins. Clr3 is a class II Histone deacetylase Zn-dependent enzyme that catalyzes hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone (EC 3.5.1.98). Clr3 is the homolog of the class-II HDAC HdaI in S. cerevisiae, and is essential for silencing in heterochromatin regions, such as centromeric regions, ribosomal DNA, the mating-type region and telomeric loci. Clr3 has also been implicated in the regulation of stress-related genes; the histone acetyltransferase, Gcn5, in S. cerevisiae, preferentially acetylates global histone H3K14 while Clr3 preferentially deacetylates H3K14ac, and therefore, interplay between Gcn5 and Clr3 is crucial for the regulation of many stress-response genes. 313 matched cddid_all.tbl CDD cd11601 cd11601 409282 Nip7_N-like N-terminal domain of Nip7 and similar proteins. This domain of various proteins is often found N-terminal to a PUA (PseudoUridine synthase and Archaeosine transglycosylase) RNA binding domain. The family contains Nip7, a protein that was shown to be required for efficient biogenesis of the 60S ribosome subunit in Saccharomyces cerevisiae. Recently, it was demonstrated that human Nip7 is essential in the accurate processing of pre-rRNA. Also included are KD93, a human homolog of Nip7, as well as an archaeal homolog and bacterial RsmB/RsmF family ribosomal methyltransferases. 76 matched cddid_all.tbl CDD cd11602 cd11602 211427 Ndc10 Ndc10 component of the yeast centromere-binding factor 3. Ndc10 is a multidomain protein conserved in Saccharomycotina that interacts with kinetochore components. This model characterizes the majority of the protein; some family members may have an additional C-terminal domain that is homologous to transcriptional activators (GCR1_C). Ndc10 is part of the centromere-binding factor 3 (CBF3) complex in budding yeast. The CBF3 complex contains four essential proteins, Ndc10, Cep3, Ctf13, and Skp1. CBF3/Ndc10 is essential for the recruitment of the centromeric nucleosome and formation of the kinetochore. The Kinetochore is the large, multiprotein assembly that serves to connect condensed sister chromatids to the mitotic spindle. Ndc10 forms a dimer and it has non-sequence-specific DNA binding activity via the DNA backbone. Ndc10 also plays an important role in the coordination of cell division. It has been noted that the protein bears resemblance to the tyrosine recombinases (type IB topoisomerase/lambda-integrase). 413 matched cddid_all.tbl CDD cd11603 cd11603 211428 ThermoDBP Thermoproteales single-stranded DNA-binding (SSB) domain. ThermoDBP is a SSB protein of the Thermoproteales. SSB proteins are essential for the genome maintenance of all known cellular organisms. Many SSBs contain an OB fold domain, albeit with low sequence conservation and OB fold-containing SSB proteins have been detected in all three domains of life. However, one group of Crenarchaea, the Thermoproteales, lack SSB encoding genes. The Thermoproteales SSB protein, ThermoDBP, lacks the OB fold and binds specifically to ssDNA with low sequence specificity. Its three-dimensional structure resembles that of the Hut operon positive regulatory protein HutP. 141 matched cddid_all.tbl CDD cd11604 cd11604 211429 RTT106_N histone chaperone RTT106, regulator of Ty1 transposition protein 106; N-terminal homodimerization domain. This cd includes the N-terminal homodimerization domain of Saccharomyces cerevisiae Rtt106, a histone chaperone. In addition to this domain, Rtt106 contains two C-terminal pleckstrin-homology (PH) domains. The acetylation of lysine 56 in histone H3 (H3K56ac) is implicated in regulating nucleosome disassembly during gene transcription, and nucleosome assembly during DNA replication and repair. Rtt106 has been shown to aid in the efficient deposition of newly synthesized H3K56ac onto replicating DNA. The interaction of Rtt106 with (H3-H4)2, most likely in the form of a (H3-H4)2 tetramer, is important for gene silencing and for the DNA damage response. Data supports a combinatorial interaction: this N-terminal domain homodimerizes and intercalates between the two H3-H4 components of the (H3-H4)2 tetramer, independent of acetylation, and the two double PH domains bind the K56-containing region of H3. Acetylation of K56 increases the affinity of the interaction. Rtt106 also interacts with both the SWI/SNF and RSC chromatin remodeling complexes and is involved in their cell-cycle dependent recruitment to histone gene pairs regulated by the HIR co-repressor complex (HTA1-HTB1, HHT1-HHF1, and HHT2-HHF2). Saccharomyces cerevisiae Rtt106 also plays a role in a role in regulating Ty1 transposition. 54 matched cddid_all.tbl CDD cd11605 cd11605 467641 RWD_DRWD_ELF-like RWD, DRWD, and ELF domain family. The family includes the RWD, double-RWD (DRWD), and ELF domains. They belong to the ubiquitin-conjugating (UBC) superfamily that represents a structural domain with an alpha-beta(4)-alpha(3) core fold. The RWD domain (named after three major RWD-containing proteins: RING finger, WD-repeat-containing proteins and DEXD-like helicases) mediates protein-protein interactions in a variety of pathways in eukaryotes. The DRWD domain is responsible for substrate binding. It is involved in interactions with other kinetochore proteins. The ELF (N-terminal E2-like fold) domain is found in all Fanconi anemia group L protein (FANCL) homologs. It is required to promote efficient DNA damage-induced FANCD2 (Fanconi anemia group D2 protein) monoubiquitination in vertebrate cells. 94 matched cddid_all.tbl CDD cd11606 cd11606 212156 COE_DBD Colier/Olf/Early B-cell factor (EBF) DNA Binding Domain. COE_DBD is the amino-terminal DNA binding domain of the COE protein family. The COE transcription factor is a regulator of development in several organs and tissues that contain the DBD domain as well as IPT/TIG (immunoglobulin-like, Plexins, transcription factors/transcription factor immunoglobulin) and basic helix-loop-helix (bHLH) domains. COE has four members in mammals (COE1-4) with high sequence similarity at the amino-terminal region. COE_DBD requires a zinc ion to bind DNA and contains a zinc finger motif (H-X(3)-C-X(2)-C-X(5)-C) termed the zinc knuckle. COE is homo- or heterodimerized through the bHLH domain to bind DNA. COE1-4 each has a variant due to alternative splicing. However, this alternative splicing does not occur at the DBD domain. 212 matched cddid_all.tbl CDD cd11607 cd11607 211320 DENR_C C-terminal domain of DENR and related proteins. DENR (density regulated protein), together with MCT-1 (multiple copies T cell malignancies), has been shown to have similar function as eIF2D translation initiation factor (also known as ligatin), which is involved in the recruitment and delivery of aminoacyl-tRNAs to the P-site of the eukaryotic ribosome in a GTP-independent manner. 86 matched cddid_all.tbl CDD cd11608 cd11608 211321 eIF2D_C C-terminal domain of eIF2D and related proteins. eIF2D translation initiation factor (also known as ligatin) is involved in the recruitment and delivery of aminoacyl-tRNAs to the P-site of the eukaryotic ribosome in a GTP-independent manner. 85 matched cddid_all.tbl CDD cd11609 cd11609 211422 MCT1_N N-terminal domain of multiple copies T cell malignancies 1 and related proteins. This N-terminal domain of MCT-1 (multiple copies T cell malignancies 1), also known as MCTS-1 (malignant T cell-amplified sequence 1), co-occurs with a PUA domain. MCT-1, together with DENR (density regulated protein), has been shown to have similar function as eIF2D translation initiation factor (also known as ligatin), which is involved in the recruitment and delivery of aminoacyl-tRNAs to the P-site of the eukaryotic ribosome in a GTP-independent manner. 77 matched cddid_all.tbl CDD cd11610 cd11610 211423 eIF2D_N N-terminal domain of eIF2D and related proteins. This N-terminal domain of eIF2D co-occurs with a PUA domain. eIF2D translation initiation factor (also known as ligatin) is involved in the recruitment and delivery of aminoacyl-tRNAs to the P-site of the eukaryotic ribosome in a GTP-independent manner. 76 matched cddid_all.tbl CDD cd11611 cd11611 212157 SAF Domains similar to fish antifreeze type III protein. SAF domains are found in a wide variety of proteins with quite different functions. They are components of enzymes, such as D-altronate-dehydratases or sialic acid synthetases, of antifreeze proteins conserved in fish (where they bind to nascent ice crystals), and may act as periplasmic chaperones in bacterial flagella basal body P-ring formation. 56 matched cddid_all.tbl CDD cd11613 cd11613 212158 SAF_AH_GD Domains similar to fish antifreeze type III protein. Altronate dehydratase (EC 4.2.1.7) converts D-altronate into 2-dehydro-3-deoxy-D-gluconate and is part of a bacterial pathway for the degradation of D-galacturonate. D-galactarate dehydratase (EC 4.2.1.42) eliminates water from D-galactarate to yield 5-dehydro-4-deoxy-D-glucarate, initializing the degradation of D-galactarate. The function of the SAF domain in these enzymes is not clear. It may participate in dimerization. 80 matched cddid_all.tbl CDD cd11614 cd11614 212159 SAF_CpaB_FlgA_like SAF domains of the flagella basal body P-ring formation protein FlgA and the flp pilus assembly CpaB. FlgA is a putative periplasmic chaperone that assists in the formation of the flagellar P ring; CpaB is a protein invoved in the assembly of the flp pili, which are bacterial virulence factors mediating non-specific adherence to surfaces; these proteins appear to contain a single SAF domain. This intermediate family also contains the SAF domains of sialic acid synthetases and type III antifreeze proteins, which also share the same extensive core structure. 61 matched cddid_all.tbl CDD cd11615 cd11615 212160 SAF_NeuB_like C-terminal SAF domain of sialic acid synthetase. Sialic acid synthetase (N-acetylneuraminate synthase or N-acetylneuraminate-9-phosphate synthase) catalyzes the condensation of phosphoenolpyruvate with N-acetylmannosamine (ManNAc, in bacteria) or N-acetylmannosamine-6-phosphate (ManNAc-6P, in mammals), to yield N-acetylneuramic acid (NeuNAc) or N-acetylneuramic acid-9-phosphate (NeuNAc-9P), respectively. The N-terminal NeuB domain, a TIM-barrel-like structure, contains the catalytic site, the function of the SAF domain is not as clear. It may participate in domain-swapped dimerization and play a role in binding the substrate, in either domain-swapped dimers or by directly interacting with the N-terminal domain. Also included in the family are PEP-sugar pyruvyltransferases known as spore coat polysaccharide biosynthesis proteins (SpsE). 58 matched cddid_all.tbl CDD cd11616 cd11616 212161 SAF_DH_OX_like SAF domain of putative dehydrogenases or oxidoreductases. C-terminal SAF domain of an uncharacterized family of putative dehydrogenases or oxidoreductases, which are otherwise members of the NAD(P)-dependent Rossmann-fold superfamily. 80 matched cddid_all.tbl CDD cd11617 cd11617 212162 Antifreeze_III Type III antifreeze protein, may be specific to the Zoarcoidei. Antifreeze protein III inhibits the growth of ice crystals and protects fish from cold damage in sub-freezing temperatures. 62 matched cddid_all.tbl CDD cd11618 cd11618 211316 ChtBD1_1 Hevein or type 1 chitin binding domain; filamentous ascomycete subfamily. Hevein or type 1 chitin binding domain (ChtBD1), a lectin domain found in proteins from plants and fungi that bind N-acetylglucosamine, plant endochitinases, wound-induced proteins such as hevein, a major IgE-binding allergen in natural rubber latex, and the alpha subunit of Kluyveromyces lactis killer toxin. This domain is involved in the recognition and/or binding of chitin subunits; it typically occurs N-terminal to glycosyl hydrolase domains in chitinases, together with other carbohydrate-binding domains, or by itself in tandem-repeat arrangements. 44 matched cddid_all.tbl CDD cd11619 cd11619 212009 HR1_CIP4-like Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Cdc42-Interacting Protein 4 and similar proteins. This subfamily is composed of Cdc42-Interacting Protein 4 (CIP4), Formin Binding Protein 17 (FBP17), FormiN Binding Protein 1-Like (FNBP1L), and similar proteins. CIP4 and FNBP1L are Cdc42 effectors that bind Wiskott-Aldrich syndrome protein (WASP) and function in endocytosis. CIP4 and FBP17 bind to the Fas ligand and may be implicated in the inflammatory response. CIP4 may also play a role in phagocytosis. It functions downstream of Cdc42 in PDGF-dependent actin reorganization and cell migration, and also regulates the activity of PDGFRbeta. It uses Src as a substrate in regulating the invasiveness of breast tumor cells. CIP4 may also play a role in the pathogenesis of Huntington's disease. Members of this subfamily typically contain an N-terminal F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain, central HR1 domain, and a C-terminal SH3 domain. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family; the HR1 domain of CIP4 binds Cdc42 and TC10. Translocation of CIP4 is facilitated by its binding to TC10 at the plasma membrane. 77 matched cddid_all.tbl CDD cd11620 cd11620 212010 HR1_PKC-like_2_fungi Second Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of fungal Protein Kinase C-like proteins. This subfamily is composed of fungal PKC-like proteins including Pkc1p from Saccharomyces cerevisiae, and Pck1p and Pck2p from Schizosaccharomyces pombe. The yeast PKC-like proteins play a critical role in regulating cell wall biosynthesis and maintaining cell wall integrity. They contain two HR1 domains, C2 and C1 domains, and a kinase domain. This model characterizes the second HR1 domain. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family. The HR1 domains of Pck1p and Pck2p interact with GTP-bound Rho1p and Rho2p. 72 matched cddid_all.tbl CDD cd11621 cd11621 212011 HR1_PKC-like_1_fungi First Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of fungal Protein Kinase C-like proteins. This subfamily is composed of fungal PKC-like proteins including Pkc1p from Saccharomyces cerevisiae, and Pck1p and Pck2p from Schizosaccharomyces pombe. The yeast PKC-like proteins play a critical role in regulating cell wall biosynthesis and maintaining cell wall integrity. They contain two HR1 domains, C2 and C1 domains, and a kinase domain. This model characterizes the first HR1 domain. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family. The HR1 domains of Pck1p and Pck2p interact with GTP-bound Rho1p and Rho2p. 72 matched cddid_all.tbl CDD cd11622 cd11622 212012 HR1_PKN_1 First Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Protein Kinase N. PKN, also called Protein-kinase C-related kinase (PRK), is a serine/threonine protein kinase that can be activated by the small GTPase Rho, and by fatty acids such as arachidonic and linoleic acids. It is involved in many biological processes including cytoskeletal regulation, cell adhesion, vesicle transport, glucose transport, regulation of meiotic maturation and embryonic cell cycles, signaling to the nucleus, and tumorigenesis. In some vertebrates, there are three PKN isoforms from different genes (designated PKN1, PKN2, and PKN3), which show different enzymatic properties, tissue distribution, and varied functions. PKN proteins contain three HR1 domains, a C2 domain, and a kinase domain. This model characterizes the first HR1 domain of PKN. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family. 66 matched cddid_all.tbl CDD cd11623 cd11623 212013 HR1_PKN_2 Second Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Protein Kinase N. PKN, also called Protein-kinase C-related kinase (PRK), is a serine/threonine protein kinase that can be activated by the small GTPase Rho, and by fatty acids such as arachidonic and linoleic acids. It is involved in many biological processes including cytoskeletal regulation, cell adhesion, vesicle transport, glucose transport, regulation of meiotic maturation and embryonic cell cycles, signaling to the nucleus, and tumorigenesis. In some vertebrates, there are three PKN isoforms from different genes (designated PKN1, PKN2, and PKN3), which show different enzymatic properties, tissue distribution, and varied functions. PKN proteins contain three HR1 domains, a C2 domain, and a kinase domain. This model characterizes the second HR1 domain of PKN. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family. 71 matched cddid_all.tbl CDD cd11624 cd11624 212014 HR1_Rhophilin Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Rhophilin. Rhophilins are scaffolding proteins that function as effectors of the Rho family of small GTPases. Vertebrates harbor two proteins, Rhophilin-1 and Rhophilin-2, whose exact functions are yet to be determined. Rhophilin-1 has been implicated in sperm motility. Rhophilin-2 regulates the organization of the actin cytoskeleton. Rhophilins contain N-terminal HR1, central Bro1-like, and C-terminal PDZ domains; all are protein-interacting domains. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family; both Rhophilin-1 and Rhophilin-2 bind RhoA, and Rhophilin-2 has also been shown to bind RhoB. 76 matched cddid_all.tbl CDD cd11625 cd11625 212015 HR1_PKN_3 Third Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Protein Kinase N. PKN, also called Protein-kinase C-related kinase (PRK), is a serine/threonine protein kinase that can be activated by the small GTPase Rho, and by fatty acids such as arachidonic and linoleic acids. It is involved in many biological processes including cytoskeletal regulation, cell adhesion, vesicle transport, glucose transport, regulation of meiotic maturation and embryonic cell cycles, signaling to the nucleus, and tumorigenesis. In some vertebrates, there are three PKN isoforms from different genes (designated PKN1, PKN2, and PKN3), which show different enzymatic properties, tissue distribution, and varied functions. PKN proteins contain three HR1 domains, a C2 domain, and a kinase domain. This model characterizes the third HR1 domain of PKN. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family. 74 matched cddid_all.tbl CDD cd11626 cd11626 212016 HR1_ROCK Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Rho-associated coiled-coil containing protein kinase. ROCK is also referred to as Rho-associated kinase or simply as Rho kinase. It is a serine/threonine protein kinase that is activated via interaction with Rho GTPases and is involved in many cellular functions including contraction, adhesion, migration, motility, proliferation, and apoptosis. ROCKs are the best-described effectors of RhoA. There are two isoforms, ROCK1 and ROCK2, which may be functionally redundant in some systems, but exhibit different tissue distributions. Both isoforms are ubiquitously expressed in most tissues, but ROCK2 is more prominent in brain and skeletal muscle while ROCK1 is more pronounced in the liver, testes, and kidney. Studies in knockout mice result in different phenotypes, suggesting that the two isoforms do not compensate for each other during embryonic development. ROCK contains an N-terminal extension, a catalytic kinase domain, and a long C-terminal extension, which contains a Rho-binding HR1 domain and a pleckstrin homology (PH) domain. ROCK is auto-inhibited by HR1 and PH domains interacting with the catalytic domain. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family. 66 matched cddid_all.tbl CDD cd11627 cd11627 212017 HR1_Ste20-like Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Schizosaccharomyces pombe Ste20-like proteins. This group is composed of predominantly uncharacterized fungal proteins, which contain two known domains: HR1 at the N-terminal region and REM (Ras exchanger motif) at the C-terminal region. One member protein from Schizosaccharomyces pombe is named Ste16 while its gene is called ste20 (a target of rapamycin complex 2 subunit). It is a subunit in the protein kinase TOR complexes in fission yeast. The REM domain is usually found in nucleotide exchange factors for Ras-like small GTPases. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family. 71 matched cddid_all.tbl CDD cd11628 cd11628 212018 HR1_CIP4_FNBP1L Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of vertebrate Cdc42-Interacting Protein 4 and FormiN Binding Protein 1-Like. CIP4 and FNBP1L are Cdc42 effectors that bind Wiskott-Aldrich syndrome protein (WASP) and function in endocytosis. FNBP1L, also called Toca-1 (Transducer of Cdc42-dependent actin assembly 1), forms a complex with neural WASP; the complex induces the formation of filopodia and endocytic vesicles. FNBP1L is required for Cdc42-induced actin assembly and is essential for autophagy of intracellular pathogens. CIP4 may also play a role in phagocytosis. It functions downstream of Cdc42 in PDGF-dependent actin reorganization and cell migration, and also regulates the activity of PDGFRbeta. It uses Src as a substrate in regulating the invasiveness of breast tumor cells. CIP4 may also play a role in the pathogenesis of Huntington's disease. CIP4 and FNBP1L contain an N-terminal F-BAR domain, a central HR1 domain, and a C-terminal SH3 domain. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family; the HR1 domain of CIP4 binds Cdc42 and TC10. Translocation of CIP4 is facilitated by its binding to TC10 at the plasma membrane. 81 matched cddid_all.tbl CDD cd11629 cd11629 212019 HR1_FBP17 Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Formin Binding Protein 17. FBP17, also called FormiN Binding Protein 1 (FNBP1), is involved in dynamin-mediated endocytosis. It is recruited to clathrin-coated pits late in the endocytosis process and may play a role in the invagination and scission steps. FBP17 binds in vivo to tankyrase, a protein involved in telomere maintenance and mitogen activated protein kinase (MAPK) signaling. It also binds to the Fas ligand and may be implicated in the inflammatory response. FBP17 contains an N-terminal F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain, central HR1 domain, and a C-terminal SH3 domain. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family; the HR1 domain of the related protein, CIP4, binds Cdc42 and TC10. Translocation of CIP4 is facilitated by its binding to TC10 at the plasma membrane. 77 matched cddid_all.tbl CDD cd11630 cd11630 212020 HR1_PKN1_2 Second Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Protein Kinase N1. PKN1, also called PKNalpha or Protein-kinase C-related kinase 1 (PRK1), is a serine/threonine protein kinase that is activated by the Rho family of small GTPases, and by fatty acids such as arachidonic and linoleic acids. It is expressed ubiquitously and is the most abundant PKN isoform in neurons. PKN1 is implicated in a variety of functions including cytoskeletal reorganization, cardiac cell survival, cell adhesion, and glucose transport, among others. PKN1 contains three HR1 domains, a C2 domain, and a kinase domain. This model characterizes the second HR1 domain of PKN1. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family; PKN1 binds the GTPases RhoA, RhoB, and RhoC, and can also interact weakly with Rac. 78 matched cddid_all.tbl CDD cd11631 cd11631 212021 HR1_PKN2_2 Second Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Protein Kinase N2. PKN2, also called PKNgamma or Protein-kinase C-related kinase 2 (PRK2), is a serine/threonine protein kinase and an effector of the small GTPase Rho/Rac. It regulates G2/M cell cycle progression and the exit from cytokinesis. It also phosphorylates hepatitis C virus (HCV) RNA polymerase and thus, plays a role in HCV RNA replication. PKN2 shares a common domain architecture with other PKNs, containing three HR1 domains, a C2 domain, and a kinase domain. In addition, PKN2 contains a proline-rich region in between its C2 and kinase domains and has been shown to associate with SH3 domain containing proteins like NCK and Grb4. This model characterizes the second HR1 domain of PKN2. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family; PKN2 specifically binds to RhoA GTPase in a GTP-dependent manner. The HR1 domains of PKN2, together with its C2 domain, also facilitate the recruitment of PKN2 to primordial junctions at nascent cell-cell contacts, where it promotes junctional maturation. 74 matched cddid_all.tbl CDD cd11632 cd11632 212022 HR1_PKN3_2 Second Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Protein Kinase N3. PKN3, also called PKNbeta, is a serine/threonine protein kinase that is activated by the Rho family of small GTPases, preferentially by RhoC. Both PKN1 and RhoC show limited and barely detectable expression in normal tissues, but are both upregulated in cancer cells, particularly in late-stage malignancies. PKN3 has been implicated to play a role in the metastatic growth and invasiveness of cancer cells, downstream of the oncogenic phosphoinositide 3-kinase signaling network. PKN3 shares a common domain architecture with other PKNs, containing three HR1 domains, a C2 domain, and a kinase domain. In addition, PKN3 contains two proline-rich regions between its C2 and kinase domains, and has been shown to associate with SH3 domain containing proteins like GRAFs, GAP for RhoA, and Cdc42Hs. This model characterizes the second HR1 domain of PKN3. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family; PKN3 binds Rho family GTPases, preferentially RhoC. 74 matched cddid_all.tbl CDD cd11633 cd11633 212023 HR1_Rhophilin-1 Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Rhophilin-1. Rhophilin-1 is a scaffolding protein that functions as an effector of the Rho family of small GTPases. It has been implicated in sperm motility. Rhophilin-1 contains an N-terminal HR1, a central Bro1-like, and a C-terminal PDZ domain; all are protein-interacting domains. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family; Rhophilin-1 binds RhoA was isolated initially as a RhoA-binding protein. 85 matched cddid_all.tbl CDD cd11634 cd11634 212024 HR1_Rhophilin-2 Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Rhophilin-2. Rhophilin-2 is a scaffolding protein that functions as an effector of the Rho family of small GTPases. It plays a role in regulating the organization of the actin cytoskeleton. Rhophilin-2 contains an N-terminal HR1, a central Bro1-like, and a C-terminal PDZ domain; all are protein-interacting domains. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family; Rhophilin-2 has been shown to bind both RhoA and RhoB. 82 matched cddid_all.tbl CDD cd11635 cd11635 212025 HR1_PKN2_3 Third Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Protein Kinase N2. PKN2, also called PKNgamma or Protein-kinase C-related kinase 2 (PRK2), is a serine/threonine protein kinase and an effector of the small GTPase Rho/Rac. It regulates G2/M cell cycle progression and the exit from cytokinesis. It also phosphorylates hepatitis C virus (HCV) RNA polymerase and thus, plays a role in HCV RNA replication. PKN2 shares a common domain architecture with other PKNs, containing three HR1 domains, a C2 domain, and a kinase domain. In addition, PKN2 contains a proline-rich region in between its C2 and kinase domains and has been shown to associate with SH3 domain containing proteins like NCK and Grb4. This model characterizes the third HR1 domain of PKN2. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family; PKN2 specifically binds to RhoA GTPase in a GTP-dependent manner. The HR1 domains of PKN2, together with its C2 domain, also facilitate the recruitment of PKN2 to primordial junctions at nascent cell-cell contacts, where it promotes junctional maturation. 74 matched cddid_all.tbl CDD cd11636 cd11636 212026 HR1_PKN1_3 Third Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Protein Kinase N1. PKN1, also called PKNalpha or Protein-kinase C-related kinase 1 (PRK1), is a serine/threonine protein kinase that is activated by the Rho family of small GTPases, and by fatty acids such as arachidonic and linoleic acids. It is expressed ubiquitously and is the most abundant PKN isoform in neurons. PKN1 is implicated in a variety of functions including cytoskeletal reorganization, cardiac cell survival, cell adhesion, and glucose transport, among others. PKN1 contains three HR1 domains, a C2 domain, and a kinase domain. This model characterizes the third HR1 domain of PKN1. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family; PKN1 binds the GTPases RhoA, RhoB, and RhoC, and can also interact weakly with Rac. 74 matched cddid_all.tbl CDD cd11637 cd11637 212027 HR1_PKN3_3 Third Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Protein Kinase N3. PKN3, also called PKNbeta, is a serine/threonine protein kinase that is activated by the Rho family of small GTPases, preferentially by RhoC. Both PKN1 and RhoC show limited and barely detectable expression in normal tissues, but are both upregulated in cancer cells, particularly in late-stage malignancies. PKN3 has been implicated to play a role in the metastatic growth and invasiveness of cancer cells, downstream of the oncogenic phosphoinositide 3-kinase signaling network. PKN3 shares a common domain architecture with other PKNs, containing three HR1 domains, a C2 domain, and a kinase domain. In addition, PKN3 contains two proline-rich regions between its C2 and kinase domains, and has been shown to associate with SH3 domain containing proteins like GRAFs, GAP for RhoA, and Cdc42Hs. This model characterizes the third HR1 domain of PKN3. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family; PKN3 binds Rho family GTPases, preferentially RhoC. 74 matched cddid_all.tbl CDD cd11638 cd11638 212028 HR1_ROCK2 Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Rho-associated coiled-coil containing protein kinase 2. ROCK2 is a serine/threonine protein kinase and was the first identified target of activated RhoA. It plays a role in stress fiber and focal adhesion formation, and is prominently expressed in the brain, heart, and skeletal muscles. It is implicated in vascular and neurological disorders, such as hypertension and vasospasm of the coronary and cerebral arteries. ROCK2 is also activated by caspase-2 cleavage, resulting in thrombin-induced microparticle generation in response to cell activation. Mice deficient in ROCK2 show intrauterine growth retardation and embryonic lethality because of placental dysfunction. ROCK2 contains an N-terminal extension, a catalytic kinase domain, and a long C-terminal extension, which contains a Rho-binding HR1 domain and a pleckstrin homology (PH) domain. ROCK2 is auto-inhibited by HR1 and PH domains interacting with the catalytic domain. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family. 67 matched cddid_all.tbl CDD cd11639 cd11639 212029 HR1_ROCK1 Protein kinase C-related kinase homology region 1 (HR1) Rho-binding domain of Rho-associated coiled-coil containing protein kinase 1. ROCK1 is a serine/threonine kinase and is preferentially expressed in the liver, lung, spleen, testes, and kidney. It mediates signaling from Rho to the actin cytoskeleton. It is implicated in the development of cardiac fibrosis, cardiomyocyte apoptosis, and hyperglycemia. Mice deficient with ROCK1 display eyelids open at birth (EOB) and omphalocele phenotypes due to the disorganization of actin filaments in the eyelids and the umbilical ring. ROCK1 contains an N-terminal extension, a catalytic kinase domain, and a long C-terminal extension, which contains a Rho-binding HR1 domain and a pleckstrin homology (PH) domain. It is auto-inhibited by HR1 and PH domains interacting with the catalytic domain. HR1 domains are anti-parallel coiled-coil (ACC) domains that bind small GTPases from the Rho family. 66 matched cddid_all.tbl CDD cd11640 cd11640 212163 HutP Histidine Utilizing Protein, the hut operon positive regulatory protein. The HutP protein family regulates the expression of 'hut' structural genes in Bacillus and other bacteria. It forms an anti-termination complex, which recognizes three UAG triplet units, separated by four non-conserved nucleotides on the RNA terminator region. In an L-histidine and Mg2+ dependent manner, HutP binds to the nascent hut mRNA leader transcript, and the ensuing anti-termination complex inhibits formation of a stem-loop terminator, clearing the way for transcription of the hut structural genes. 134 matched cddid_all.tbl CDD cd11641 cd11641 381168 Precorrin-4_C11-MT Precorrin-4 C11-methyltransferase (CbiF/CobM). Precorrin-4 C11-methyltransferase participates in the pathway toward the biosynthesis of cobalamin (vitamin B12). There are two distinct cobalamin biosynthetic pathways in bacteria. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt insertion is the first committed step towards cobalamin synthesis. In the aerobic pathway, CobM catalyzes the methylation of precorrin-4 at C-11 to yield precorrin-5. In the anaerobic pathway, CibF catalyzes the methylation of cobalt-precorrin-4 to cobalt-precorrin-5. Both CibF and CobM, which are homologous, are included in this model. There are about 30 enzymes involved in vitamin B12 synthetic pathway. The enzymes involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Most of the enzymes are shared in both pathways and several of these enzymes are pathway-specific. 225 matched cddid_all.tbl CDD cd11642 cd11642 381169 SUMT Uroporphyrin-III C-methyltransferase (also known as S-Adenosyl-L-methionine:uroporphyrinogen III methyltransferase, SUMT). SUMT is an enzyme of the cobalamin and siroheme biosynthetic pathway. It catalyzes the first of three steps leading to the formation of siroheme from uroporphyrinogen III; it transfers two methyl groups from S-adenosyl-L-methionine to the C-2 and C-7 atoms of uroporphyrinogen III to yield precorrin-2 via the intermediate formation of precorrin-1. Precorrin-2 is also a precursor for the biosynthesis of vitamin B12, coenzyme F430, siroheme and heme d1. This family includes proteins in which the SUMT domain is fused to other functional domains, such as to a uroporphyrinogen-III synthase domain to form bifunctional uroporphyrinogen-III methylase/uroporphyrinogen-III synthase, or to a dual function dehydrogenase-chelatase domain, as in the case of the multifunctional S-adenosyl-L-methionine (SAM)-dependent bismethyltransferase/dehydrogenase/ferrochelatase CysG, which catalyzes all three steps that transform uroporphyrinogen III into siroheme. 228 matched cddid_all.tbl CDD cd11643 cd11643 381170 Precorrin-6A-synthase Precorrin-6A synthase (also named CobF). Precorrin-6A synthase participates in the pathway toward the biosynthesis of cobalamin (vitamin B12). There are two distinct cobalamin biosynthetic pathways in bacteria. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt insertion is the first committed step towards cobalamin synthesis. This model represents CobF, the precorrin-6A synthase, an enzyme specific to the aerobic pathway. After precorrin-4 is methylated at C-11 by CobM to produce precorrin-5, CobF catalyzes the removal of the extruded acyl group in the subsequent step, and the addition of a methyl group at C-1. The product of this reaction is precorrin-6A, which gets reduced by an NADH-dependent reductase to yield precorrin-6B. This family includes enzymes in GC-rich Gram-positive bacteria, alpha proteobacteria and Pseudomonas-related species. 244 matched cddid_all.tbl CDD cd11644 cd11644 381171 Precorrin-6Y-MT Precorrin-6Y methyltransferase (also named CbiE). CbiE (precorrin-6Y methyltransferase, also known as cobalt-precorrin-7 C(5)-methyltransferase, also known as cobalt-precorrin-6Y C(5)-methyltransferase) catalyzes the methylation of C-5 in cobalt-precorrin-7 to form cobalt-precorrin-8. It participates in the pathway toward the biosynthesis of cobalamin (vitamin B12). There are two distinct cobalamin biosynthetic pathways in bacteria. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt insertion is the first committed step towards cobalamin synthesis. CbiE functions in the anaerobic pathway, it is a subunit of precorrin-6Y C5,15-methyltransferase, a bifunctional enzyme: cobalt-precorrin-7 C(5)-methyltransferase (CbiE)/cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) (CbiT), that catalyzes two methylations (at C-5 and C-15) in precorrin-6Y, as well as the decarboxylation of the acetate side chain located in ring C, in order to generate precorrin-8X. CbiE and CbiT can be found fused (CbiET, also called CobL), or on separate protein chains (CbiE and CbiT). In the aerobic pathway, a single enzyme called CobL catalyzes the methylations at C-5 and C-15, and the decarboxylation of the C-12 acetate side chain of precorrin-6B. 198 matched cddid_all.tbl CDD cd11645 cd11645 381172 Precorrin_2_C20_MT Precorrin-2 C20-methyltransferase, also named CobI or CbiL. Precorrin-2 C20-methyltransferase (also known as S-adenosyl-L-methionine--precorrin-2 methyltransferase) participates in the pathway toward the biosynthesis of cobalamin (vitamin B12). There are two distinct cobalamin biosynthetic pathways in bacteria. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt insertion is the first committed step towards cobalamin synthesis. Precorrin-2 C20-methyltransferase catalyzes methylation at the C-20 position of a cyclic tetrapyrrole ring of precorrin-2 using S-adenosylmethionine as a methyl group source to produce precorrin-3A. In the anaerobic pathway, cobalt is inserted into precorrin-2 by CbiK to generate cobalt-precorrin-2, which is the substrate for CbiL, a C20 methyltransferase. In Clostridium difficile, CbiK and CbiL are fused into a bifunctional enzyme. In the aerobic pathway, the precorrin-2 C20-methyltransferase is named CobI. This family includes CbiL and CobI precorrin-2 C20-methyltransferases, both as stand-alone enzymes and when CbiL forms part of a bifunctional enzyme. 223 matched cddid_all.tbl CDD cd11646 cd11646 381173 Precorrin_3B_C17_MT Precorrin-3B C(17)-methyltransferase (also named CobJ or CbiH). Precorrin-3B C(17)-methyltransferase participates in the pathway toward the biosynthesis of cobalamin (vitamin B12). There are two distinct cobalamin biosynthetic pathways. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt insertion is the first committed step towards cobalamin synthesis. This model includes CobJ of the aerobic pathway and CbiH of the anaerobic pathway, both as stand-alone enzymes and when CobJ or CbiH form part of bifunctional enzymes, such as in Mycobacterium tuberculosis CobIJ where CobJ fuses with a precorrin-2 C(20)-methyltransferase domain, or Bacillus megaterium CbiH60, where CbiH is fused to a nitrite and sulfite reductase-like domain. In the aerobic pathway, once CobG has generated precorrin-3b, CobJ catalyzes the methylation of precorrin-3b at C-17 to form precorrin-4 (the extruded methylated C-20 fragment is left attached as an acyl group at C-1). In the corresponding anaerobic pathway, CbiH carries out this ring contraction, using cobalt-precorrin-3b as a substrate to generate a tetramethylated delta-lactone. 238 matched cddid_all.tbl CDD cd11647 cd11647 381174 DHP5_DphB diphthine methyl ester synthase and diphthine synthase. Eukaryotic diphthine methyl ester synthase (DHP5) and archaeal diphthamide synthase (DphB) participate in the second step of the biosynthetic pathway of diphthamide. The eukaryotic enzyme catalyzes four methylations of the modified target histidine residue in translation elongation factor 2 (EF-2), to form an intermediate called diphthine methyl ester; the archaeal enzyme, catalyzes only 3 methylations, producing diphthine. Diphtheria toxin ADP-ribosylates diphthamide leading to inhibition of protein synthesis in the eukaryotic host cells. 241 matched cddid_all.tbl CDD cd11648 cd11648 381175 RsmI Ribosomal RNA small subunit methyltransferase I (RsmI), also known as rRNA (cytidine-2'-O-)-methyltransferase. RsmI is an S-AdoMet (S-adenosyl-L-methionine or SAM)-dependent methyltransferase responsible for the 2'-O-methylation of cytidine 1402 (C1402) at the P site of bacterial 16S rRNA. Another S-AdoMet-dependent methyltransferase, RsmH (not included in this family), is responsible for N4-methylation at C1402. These methylation reactions may occur at a late step during 30S assembly in the cell. The dimethyl modification is believed to be conserved in bacteria, may play a role in fine-tuning the shape and functions of the P-site to increase the translation fidelity, and has been shown for Staphylococcus aureus, to contribute to virulence in host animals by conferring resistance to oxidative stress. 216 matched cddid_all.tbl CDD cd11649 cd11649 381176 RsmI_like uncharacterized subfamily of the tetrapyrrole methylase family similar to Ribosomal RNA small subunit methyltransferase I (RsmI). RsmI, also known as rRNA (cytidine-2'-O-)-methyltransferase, is an S-AdoMet (S-adenosyl-L-methionine or SAM)-dependent methyltransferase responsible for the 2'-O-methylation of cytidine 1402 (C1402) at the P site of bacterial 16S rRNA. Another S-AdoMet-dependent methyltransferase, RsmH (not included in this family), is responsible for N4-methylation at C1402. These methylation reactions may occur at a late step during 30S assembly in the cell. The dimethyl modification is believed to be conserved in bacteria, may play a role in fine-tuning the shape and functions of the P-site to increase the translation fidelity, and has been shown for Staphylococcus aureus, to contribute to virulence in host animals by conferring resistance to oxidative stress. 229 matched cddid_all.tbl CDD cd11650 cd11650 212164 AT4G37440_like Uncharacterized protein domain conserved in plants. This domain contains an extensive protein sequence fragment that appears conserved in a number of plant proteins, including the gene product of Arabidopsis thaliana locus AT4G37440, which has been identified in transcriptional profiling as expressed at different levels in white cabbage cultivars. 253 matched cddid_all.tbl CDD cd11651 cd11651 212165 YPK1_N_like Fungal protein kinase domain similar to the N-terminus of YPK1. This fungal domain family includes the N-terminal region of the Saccharomyces cerevisiae AGC kinases YPK1 and YPK2, which were found to be essential for the proliferation of yeast. YPK1 is required for cell growth and acts as a downstream kinase in the sphingolipid-mediated signaling pathway of yeast. It also plays a role in efficient endocytosis and in the maintenance of cell wall integrity. 174 matched cddid_all.tbl CDD cd11652 cd11652 212166 SSH-N "N-terminal domain conserved in slingshot (SSH) phosphatases. This domain or region conserved in Bilateria is found N-terminal to the DEK_C-like and catalytic domains of slingshot phosphatases. Slingshot is a cofilin-specific phosphatase. Dephosphorylation reactivates cofilin, which in turn depolymerizes actin and is thus required for actin filament reorganization. Slingshot is a member of the dual-specificity protein phosphatase family. This N-terminal SSH region may be involved in P-cofilin binding (the model C-terminus plus the DEK_C-like domain, which are characterized as the ""B"" domain in some of the literature), and may be required for the F-actin mediated activation of slingshot (the N-terminal region of this model, sometimes referred to as the ""A"" domain)." 233 matched cddid_all.tbl CDD cd11653 cd11653 212167 rap1_RCT C-terminal domain of RAP1 recruits proteins to telomeres. The RAP1 (repressor activator protein 1) C-terminal domain (RCT) mediates interactions with other proteins such as TRF2 (human), Rif1, Rif2, Sir3, Sir4 (Saccharomyces cerevisiae), and Taz1 (Schizosaccharomyces pombe) at telomeres and other loci. RAP1, identified in budding yeast as repressor/activator protein 1, is a well-conserved telomere binding protein, also found in fission yeast and mammals. In Saccharomyces cerevisiae, RAP1 directly binds DNA and is involved in transcriptional activation, gene silencing, as well as binding at numerous sites at each telemore, where it functions in telomere length regulation, telomeric position effect gene silencing and telomere end protection. Human RAP1 apparently does not bind telomeric DNA directly, but binds telomere repeat binding factor 2 (TRF2) via the RCT. RAP1 might act by suppressing nonhomologous end-joining. Yeast RAP1 has two myb-type DNA binding modules, and an RCT domain that recruits Sir proteins 3 and 4 (Sir3, Sir4) for gene silencing, and Rif1 and Rif2 for telomere length maintenance. Schizosaccharomyces pombe RAP1 (spRap1), like human RAP1, lacks direct DNA-binding activity and is localized to telomeres via Taz1, an ortholog of TRF1 and TRF2. The S. pompe RCT resembles the first 3-helix bundle of the yeast and human RCT forms, but is not included in this larger model. 100 matched cddid_all.tbl CDD cd11654 cd11654 212553 TRF2_RBM RAP1 binding motif of telomere repeat binding factor. TRF2 (Telomere repeat binding factor 2) functions as part of the 6-component shelterin complex. TRF2 binds DNA and recruits RAP1 (via binding to the RAP1 protein c-terminus (RCT)) and TIN2 in the protection of telomeres from DNA repair machinery. Metazoan shelterin consists of 3 DNA-binding proteins (TRF2, TRF1 and POT1) and 3 recruited proteins that bind to one or more of these DNA-binding proteins (RAP1, TIN2, TPP1). Human TRF1 and TRF2 bind double-stranded DNA. hTRF2 consists of a basic N-terminus, a TRF homology domain, the RAP1 binding motif (RBM) described by this model, the TIN2 binding motif (TBM), and a myb-like DNA binding domain. 42 matched cddid_all.tbl CDD cd11655 cd11655 212554 rap1_myb-like DNA-binding modules of yeast Rap1 and related proteins. Yeast Rap1 DNA-binding activity is mediated by a pair of DNA-binding modules comprised of 2 3-helix bundles with an N-terminal arm, closely matching the structure of homeodomain and myb-type proteins. Human Rap1 has a single myb-like module, and may not bind DNA directly. Rap1, identified in budding yeast as repressor-activator protein 1, is a conserved telomere binding protein, also identified in fission yeast and mammals. In Saccharomyces cerevisiae, Rap1 directly binds DNA and is involved in transcriptional activation, gene silencing, as well as binding at numerous binding sites at each telomere, where it functions in telomere length regulation, telomeric position effect gene silencing and telomere end protection. Human Rap1 apparently does not bind telomeric DNA directly, but binds telomere repeat binding factor 2 (TRF2) via the Rap C-terminal domain (RCT). Rap1 may act by suppressing non-homologous end-joining. Yeast Rap1 has 2 myb-type DNA binding modules, a BRCT domain, and a RCT domain that recruits Sir3 and Sir4 proteins for gene silencing and Rif1 and Rif2 for telomere length maintenance. Human Rap1 has a similar domain architecture but has a single myb-like domain. 57 matched cddid_all.tbl CDD cd11656 cd11656 212555 FBX4_GTPase_like C-terminal GTPase-like domain of F-Box Only Protein 4. F-box proteins are involved in substrate recognition as part of SCF (Skp1-Cul1-Rbx1-F-box protein) ubiquitin ligase complexes. Fbx4 (or Fbxo4) binds to the telomere repeat binding factor 1 (TRF1), whose activity at telomeres is regulated in part by selective ubiquitination and degradation. This ubiquitination of TRF1 is mediated by Fbx4, which binds to the TRFH domain of TRF1, via the C-terminal domain characterized by this model, a module resembling a small GTPase domain that lacks the GTP-binding site. When bound to telomeres, TIN2 acts to protect TRF1 from SCF-Fbx4 mediated ubiquitination. Tankyrase-mediated ADP-ribosylation releases TRF1 from telomeres, rendering them susceptible to ubiquitination and degradation, which in turn promotes telomere elongation. Fbx4 has also been reported to target cyclin D1 for degradation by the proteasome, a mechanism ensuring the fidelity of DNA replication. More recently, these findings have been disputed. 223 matched cddid_all.tbl CDD cd11657 cd11657 240667 TIN2_N N-terminal domain of TRF-interacting nuclear factor 2; shelterin complex protein of telomeres. TIN2 is one of the six proteins of shelterin complex, which acts to protect telomeres from DNA damage repair machinery. TIN2 binds directly to TRF1 and TRF2 and stabilizes TRF2 complex-telomere binding by tethering it to the TRF1 complex. TIN2 binding to TRF2 is primarily via the TRF binding motif (TBM) region and the N-terminus, while the far C-terminal region has lower affinity. The TIN2 TBM, but not the N-terminal region, is involved in TIN2 binding to TRF1. Truncation of the TIN2 N-terminus in mouse results in telomere elongation, suggesting a negative regulatory function of this region. Three shelterin components (TRF1, TRF2, POT1) bind DNA and 3 components (TIN2, RAP1, TPP1) are recruited by these DNA binding factors. TRF1 activity at telomeres is regulated in part by selective ubiquitination and degradation. Ubiquitination of TRF1 is mediated by Fbx4, which binds TRF1 in the TRFH domain, via a small GTPase module. When bound to telomeres, TIN2 acts to protect TRF1 from SCF-Fbx4 mediated ubiquitination. F-box proteins act in substrate recognition as part of Skp1-Cul1-Rbx1-F- box (SCF) protein complexes. Tankyrase-mediated ADP-ribosylation releases TRF1 from telomeres, rendering them susceptible to ubiquitination and degradation, promoting telomere elongation. TIN2 also binds PIP1, which recruits POT1 to telomeres. 188 matched cddid_all.tbl CDD cd11658 cd11658 212556 SANT_DMAP1_like SANT/myb-like domain of Human Dna Methyltransferase 1 Associated Protein 1-like. These proteins are members of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix bundle of the DNA-binding Myb domains and is found in a diverse set of proteins. 46 matched cddid_all.tbl CDD cd11659 cd11659 212557 SANT_CDC5_II SANT/myb-like DNA-binding domain of Cell Division Cycle 5-Like Protein repeat II. In humans, cell division cycle 5-like protein (CDC5) functions in pre-mRNA splicing in cell cycle control. The DNA-binding, myb-like domain of CDC5 is a member of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix bundle of DNA-binding Myb domains and is found in a diverse set of proteins. 53 matched cddid_all.tbl CDD cd11660 cd11660 212558 SANT_TRF Telomere repeat binding factor-like DNA-binding domains of the SANT/myb-like family. Human telomere repeat binding factors, TRF1 and TRF2, function as part of the 6 component shelterin complex. TRF2 binds DNA and recruits RAP1 (via binding to the RAP1 protein c-terminal (RCT)) and TIN2 in the protection of telomeres from DNA repair machinery. Metazoan shelterin consists of 3 DNA binding proteins (TRF2, TRF1, and POT1) and 3 recruited proteins that bind to one or more of these DNA-binding proteins (RAP1, TIN2, TPP1). Schizosaccharomyces pombe TAZ1 is an orthlog and binds RAP1. Human TRF1 and TRF2 bind double-stranded DNA. hTRF2 consists of a basic N-terminus, a TRF homology domain, the RAP1 binding motif (RBM), the TIN2 binding motif (TBM) and a myb-like DNA binding domain, SANT, named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. Tandem copies of the domain bind telomeric DNA tandem repeats as part of the capping complex. The single myb-like domain of TRF-type proteins is similar to the tandem myb_like domains found in yeast RAP1. 50 matched cddid_all.tbl CDD cd11661 cd11661 212559 SANT_MTA3_like Myb-Like Dna-Binding Domain of MTA3 and related proteins. Members in this SANT/myb family include domains found in mouse metastasis-associated protein 3 (MTA3) proteins and arginine-glutamic dipeptide (RERE) repeats proteins. SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domains are a diverse set of proteins that share a common 3 alpha-helix bundle. MTA3 has been shown to interact with nucleosome remodeling and deacetylase (NuRD) proteins CHD4 and HDAC1, and the core cohesin complex protein RAD21 in the ovary, and regulate G2/M progression in proliferating granulosa cells. RERE belongs to the atrophin family and has been identified as a nuclear receptor corepressor; altered expression levels of RERE are associated with cancer in humans while mutations of Rere in mice cause failure in closing the anterior neural tube and fusion of the telencephalic and optic vesicles during embryogenesis. 46 matched cddid_all.tbl CDD cd11662 cd11662 212560 apollo_TRF2_binding TRF2-binding region of apollo and similar proteins. Apollo protein, a DNA repair nuclease, is recruited to telomeres by TRF2 where it is associated with the principle components of the shelterin complex. Apollo is a member of the metallo-beta-lactamase family that is required for telomere integrity during S phase; its 5' exonuclease activity is regulated by binding to TRF2. Apollo and TRF2 also suppress damage to engineered interstitial telomere repeat tracts at the chromosome ends. TRF2, which binds preferentially to positively supercoiled DNA substrates, together with Apollo, negatively regulates the amount of DNA topoisomerases (TOP1, TOP2-alpha, and TOP2-beta) at telomeres since they also act in the same pathway of telomere protection. The shelterin complex protein identified in mammals is principally comprised of 6 factors that act to protect telomeres from DNA damage repair machinery. 3 components (TRF1, TRF2, POT1) bind DNA and 3 components are recruited by these factors (TIN2, RAP1, TPP1). 34 matched cddid_all.tbl CDD cd11663 cd11663 212128 GH119_BcIgtZ-like putative catalytic domain of glycoside hydrolase family 119 (GH119). The prokaryotic subgroup is represented by IgtZ, an alpha-amylase from a Bacillus circulans strain. The GH119 family is related to GH57, a chiefly prokaryotic family with the majority of thermostable enzymes coming from extremophiles (many of these are archaeal hyperthermophiles), which exhibit the enzyme specificities of alpha-amylase (EC 3.2.1.1), 4-alpha-glucanotransferase (EC 2.4.1.25), amylopullulanase (EC 3.2.1.1/41), and alpha-galactosidase (EC 3.2.1.22). GH57s cleave alpha-glycosidic bonds by employing a retaining mechanism, which involves a glycosyl-enzyme intermediate, allowing transglycosylation. 363 matched cddid_all.tbl CDD cd11664 cd11664 212129 LamB_YcsF_like_2 uncharacterized proteins similar to the Aspergillus nidulans lactam utilization protein LamB. This bacterial subfamily of the LamB/YbgL family, contains many well conserved uncharacterized proteins. Although their molecular function is unknown, those proteins show high sequence similarity to the Aspergillus nidulans lactam utilization protein LamB, which might be required for conversion of exogenous 2-pyrrolidinone to endogenous GABA. 238 matched cddid_all.tbl CDD cd11665 cd11665 212130 LamB_like Aspergillus nidulans lactam utilization protein LamB and similar proteins. This eukaryotic and bacterial subfamily of the LamB/YbgL family, includes Aspergillus nidulans protein LamB. The lamb gene locates at the lam locus of Aspergillus nidulans, consisting of two divergently transcribed genes, lamA and lamB, needed for the utilization of lactams such as 2-pyrrolidinone. Both genes are under the control of the positive regulatory gene amdR and are subject to carbon and nitrogen metabolite repression. Although the exact molecular function of lamb encoding protein LamB is unknown, it might be required for conversion of exogenous 2-pyrrolidinone to endogenous GABA. 238 matched cddid_all.tbl CDD cd11666 cd11666 212131 GH38N_Man2A1 N-terminal catalytic domain of Golgi alpha-mannosidase II and similar proteins; glycoside hydrolase family 38 (GH38). This subfamily is represented by Golgi alpha-mannosidase II (GMII, also known as mannosyl-oligosaccharide 1,3- 1,6-alpha mannosidase, EC 3.2.1.114, Man2A1), a monomeric, membrane-anchored class II alpha-mannosidase existing in the Golgi apparatus of eukaryotes. GMII plays a key role in the N-glycosylation pathway. It catalyzes the hydrolysis of the terminal of both alpha-1,3-linked and alpha-1,6-linked mannoses from the high-mannose oligosaccharide GlcNAc(Man)5(GlcNAc)2 to yield GlcNAc(Man)3(GlcNAc)2(GlcNAc, N-acetylglucosmine), which is the committed step of complex N-glycan synthesis. GMII is activated by zinc or cobalt ions and is strongly inhibited by swainsonine. Inhibition of GMII provides a route to block cancer-induced changes in cell surface oligosaccharide structures. GMII has a pH optimum of 5.5-6.0, which is intermediate between those of acidic (lysosomal alpha-mannosidase) and neutral (ER/cytosolic alpha-mannosidase) enzymes. GMII is a retaining glycosyl hydrolase of family GH38 that employs a two-step mechanism involving the formation of a covalent glycosyl enzyme complex; two carboxylic acids positioned within the active site act in concert: one as a catalytic nucleophile and the other as a general acid/base catalyst. 344 matched cddid_all.tbl CDD cd11667 cd11667 212132 GH38N_Man2A2 N-terminal catalytic domain of Golgi alpha-mannosidase IIx, and similar proteins; glycoside hydrolase family 38 (GH38). This subfamily is represented by human alpha-mannosidase 2x (MX, also known as mannosyl-oligosaccharide 1,3- 1,6-alpha mannosidase, EC 3.2.1.114, Man2A2). MX is enzymatically and functionally very similar to GMII (found in another subfamily), and as an isoenzyme of GMII. It is thought to also function in the N-glycosylation pathway. MX specifically hydrolyzes the same oligosaccharide substrate as does MII. It specifically removes two mannosyl residues from GlcNAc(Man)5(GlcNAc)2 to yield GlcNAc(Man)3(GlcNAc)2(GlcNAc, N-acetylglucosmine). 344 matched cddid_all.tbl CDD cd11669 cd11669 212168 TTHB210-like Hypothetical protein TTHB210, a sigma(E)-regulated gene product found in Thermus thermophilus, and similar proteins. TTHB210 is an uncharacterized protein found in Thermus thermophilus, and is controlled by the sigma(E) /anti-sigma(E) regulatory system. It is one of the five proteins of the extracytoplasmic function (ECF) sigma factor sigma(E)-regulated gene products whose physiological function have not been determined. Its crystallographic structure reveals a novel homodecamer although it is a dimer in solution. 115 matched cddid_all.tbl CDD cd11670 cd11670 212561 Sp_RAP1_RCT C-terminal domain of S. pombe RAP1 protein. The Schizosaccharomyces pombe RAP1 (repressor activator protein 1) protein C-terminal (RCT) domain structurally resembles the first 3-helix bundle found in yeast and human RAP1 RCT. S. pombe RAP1 (spRap1), like human RAP1, lacks direct DNA-binding activity and is localized to telomeres via Taz1, an ortholog of TRF1 and TRF2. The RAP1 RCT domain interacts with RAP1 binding motif (RBM) of TAZ1. RAP1, identified in budding yeast as repressor/activator protein 1 is a well-conserved telomere binding protein, found in budding yeast, fission yeast and mammals. In Saccharomyces cerevisiae, RAP1 directly binds DNA and is involved in transcriptional activation and mating type information gene silencing, as well as binding at numerous sites at each telomere, where it functions in telomere length regulation, telomeric position effect gene silencing and telomere end protection. Human RAP1 does not bind telomeric DNA directly, but binds telomere repeat binding factor 2 (TRF2) via the RAP C-terminal domain (RCT). Yeast RAP1 has 2 myb-type DNA binding modules, a BRCT domain, and a RCT domain that recruits Sir3 and Sir4 for gene silencing and Rif1 and Rif2 for telomere length maintenance. S. pombe RAP1 has a BRCT domain, 2 myb like domains, and the RCT. 52 matched cddid_all.tbl CDD cd11671 cd11671 212562 TAZ1_RBM RAP1 binding motif of Schizosaccharomyces pombe TAZ1. S. pombe TAZ1 recruits the spRAP1 protein to telomeres. The TAZ1 RAP1-binding motif (RBM) binds the RAP1 C-terminal domain (RCT), which structurally resembles the first 3-helix bundle found in yeast and human RAP1 RCT. TAZ1, an ortholog of TRF1 and TRF2, has a TRF homology (TRFH) domain, the RBM domain, a dimerization domain, and a myb-like C-terminus. RAP1, identified in budding yeast as repressor/activator protein 1, is a well-conserved telomere binding protein and is also found in fission yeast and mammals. In Saccharomyces cerevisiae, RAP1 directly binds DNA and is involved in transcriptional activation and mating type information gene silencing, as well as in binding to numerous binding sites at each telomere, where it functions in telomere length regulation, telomeric position effect gene silencing, and telomere end protection. Like S. pombe RAP1, human RAP1 does not bind telomeric DNA directly, but binds telomere repeat binding factor 2 (TRF2) through the RAP C-terminal domain (RCT). 49 matched cddid_all.tbl CDD cd11672 cd11672 277250 ADDz ATRX, Dnmt3 and Dnmt3l PHD-like zinc finger domain (ADDz). The ADDz zinc finger domain is present in the chromatin-associated proteins cytosine-5-methyltransferase 3 (Dnmt3) and ATRX, a SNF2 type transcription factor protein. The Dnmt3 family includes two active DNA methyltransferases, Dnmt3a and -3b, and one regulatory factor Dnmt3l. DNA methylation is an important epigenetic mechanism involved in diverse biological processes such as embryonic development, gene expression, and genomic imprinting. The ADDz domain is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif. 99 matched cddid_all.tbl CDD cd11673 cd11673 212563 hemoglobin_linker_C Globular domain of extracellular hemoglobin linker. This family of hemoglobin linker chains is restricted to annelid worms, and participates in the formation of the large erythrocruorin respiratory complex. Via its N-terminal coiled-coil segment (not included in this model), the molecule forms trimers, which are part of a scaffold organizing the overall complex architecture; the latter encompasses 36 linkers and 144 hemoglobins in total. This C-terminal globular domain is involved in trimerization, and also interacts with globins and other C-terminal globular linker domains of neighboring trimers. The structure resembles that of nitrophorins and lipocalins. 120 matched cddid_all.tbl CDD cd11674 cd11674 212564 lambda-1 inner capsid protein lambda-1 or VP3. The reovirus inner capsid protein lambda-1 displays nucleoside triphosphate phosphohydrolase (NTPase), RNA-5'-triphosphatase (RTPase), and RNA helicase activity and may play a role in the transcription of the virus genome, the unwinding or reannealing of double-stranded RNA during RNA synthesis. The RTPase activity constitutes the first step in the capping of RNA, resulting in a 5'-diphosphorylated RNA plus-strand. lambda1 is an Orthoreovirus core protein, VP3 is the homologous core protein in Aquareoviruses. 1166 matched cddid_all.tbl CDD cd11675 cd11675 212565 SCAB1_middle middle domain of the stomatal closure-related actin binding protein1. SCAB1 is a dimeric actin crosslinker conserved in plants. The three-dimensional structure of this domain resembles that of fibronectin type III repeat units and immunoglobulins. It is situated between a coiled-coil dimerization domain and a C-terminal pleckstrin homology-like module. SCAB1 appears to be required for normal actin dynamics in guard cells stomatal movement. The function of the middle domain is not clear. 85 matched cddid_all.tbl CDD cd11676 cd11676 212487 Gemin6 Gemin 6. Gemins 6, together with the survival motor neuron (SMN) protein, other Gemins, and Unr-interacting protein (UNRIP) form the SMN complex, which plays an important role in the Sm core assembly reaction, by binding directly to the Sm proteins, as well as UsnRNAs. Gemin 6 forms a heterodimer with Gemin 7, which serve as a surrogate for the SmB-SmD3 dimer during the formation of the heptameric Sm ring. 63 matched cddid_all.tbl CDD cd11677 cd11677 212488 Gemin7 Gemin 7. Gemins 7, together with the survival motor neuron (SMN) protein, other Gemins, and Unr-interacting protein (UNRIP) form the SMN complex, which plays an important role in the Sm core assembly reaction, by binding directly to the Sm proteins, as well as UsnRNAs. Gemin 7 forms a heterodimer with Gemin 6, which serve as a surrogate for the SmB-SmD3 dimer during the formation of the heptameric Sm ring. 77 matched cddid_all.tbl CDD cd11678 cd11678 212489 archaeal_LSm archaeal Like-Sm protein. The archaeal Sm-like (LSm): The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal LSm proteins are likely to represent the ancestral Sm domain. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes. 69 matched cddid_all.tbl CDD cd11679 cd11679 212490 archaeal_Sm_like archaeal Sm-related protein. Archaeal Sm-related proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain. 65 matched cddid_all.tbl CDD cd11680 cd11680 212543 HDAC_Hos1 Class I histone deacetylases Hos1 and related proteins. Saccharomyces cerevisiae Hos1 is responsible for Smc3 deacetylation. Smc3 is an important player during the establishment of sister chromatid cohesion. Hos1 belongs to the class I histone deacetylases (HDACs). HDACs are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues in histone amino termini to yield a deacetylated histone (EC 3.5.1.98). Enzymes belonging to this group participate in regulation of a number of processes through protein (mostly different histones) modification (deacetylation). Class I histone deacetylases in general act via the formation of large multiprotein complexes. Other class I HDACs are animal HDAC1, HDAC2, HDAC3, HDAC8, fungal RPD3 and HOS2, plant HDA9, protist, archaeal and bacterial (AcuC) deacetylases. Members of this class are involved in cell cycle regulation, DNA damage response, embryonic development, cytokine signaling important for immune response and in posttranslational control of the acetyl coenzyme A synthetase. 294 matched cddid_all.tbl CDD cd11681 cd11681 212544 HDAC_classIIa Histone deacetylases, class IIa. Class IIa histone deacetylases are Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine residues of histones (EC 3.5.1.98) to yield deacetylated histones. This subclass includes animal HDAC4, HDAC5, HDAC7, and HDCA9. Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. Histone deacetylases usually act via association with DNA binding proteins to target specific chromatin regions. Class IIa histone deacetylases are signal-dependent co-repressors, they have N-terminal regulatory domain with two or three conserved serine residues, phosphorylation of these residues is important for ability to shuttle between the nucleus and cytoplasm and act as transcriptional co-repressors. HDAC9 is involved in regulation of gene expression and dendritic growth in developing cortical neurons. It also plays a role in hematopoiesis. HDAC7 is involved in regulation of myocyte migration and differentiation. HDAC5 is involved in integration of chronic drug (cocaine) addiction and depression with changes in chromatin structure and gene expression. HDAC4 participates in regulation of chondrocyte hypertrophy and skeletogenesis. 377 matched cddid_all.tbl CDD cd11682 cd11682 212545 HDAC6-dom1 Histone deacetylase 6, domain 1. Histone deacetylases 6 are class IIb Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDACs usually act via association with DNA binding proteins to target specific chromatin regions. HDAC6 is the only histone deacetylase with internal duplication of two catalytic domains which appear to function independently of each other, and also has a C-terminal ubiquitin-binding domain. It is located in the cytoplasm and associates with microtubule motor complex, functioning as the tubulin deacetylase and regulating microtubule-dependent cell motility. Known interaction partners of HDAC6 are alpha tubulin (substrate) and ubiquitin-like modifier FAT10 (also known as Ubiquitin D or UBD). 337 matched cddid_all.tbl CDD cd11683 cd11683 212546 HDAC10 Histone deacetylase 10. Histone deacetylases 10 are class IIb Zn-dependent enzymes that catalyze hydrolysis of N(6)-acetyl-lysine of a histone to yield a deacetylated histone (EC 3.5.1.98). Histone acetylation/deacetylation process is important for mediation of transcriptional regulation of many genes. HDACs usually act via association with DNA binding proteins to target specific chromatin regions. HDAC10 has an N-terminal deacetylase domain and a C-terminal pseudo-repeat that shares significant similarity with its catalytic domain. It is located in the nucleus and cytoplasm, and is involved in regulation of melanogenesis. It transcriptionally down-regulates thioredoxin-interacting protein (TXNIP), leading to altered reactive oxygen species (ROS) signaling in human gastric cancer cells. Known interaction partners of HDAC10 are Pax3, KAP1, hsc70 and HDAC3 proteins. 337 matched cddid_all.tbl CDD cd11684 cd11684 212566 DHR2_DOCK Dock Homology Region 2, a GEF domain, of Dedicator of Cytokinesis proteins. DOCK proteins comprise a family of atypical guanine nucleotide exchange factors (GEFs) that lack the conventional Dbl homology (DH) domain. As GEFs, they activate the small GTPases Rac and Cdc42 by exchanging bound GDP for free GTP. They are also called the CZH (CED-5, Dock180, and MBC-zizimin homology) family, after the first family members identified. Dock180 was first isolated as a binding partner for the adaptor protein Crk. The Caenorhabditis elegans protein, Ced-5, is essential for cell migration and phagocytosis, while the Drosophila ortholog, Myoblast city (MBC), is necessary for myoblast fusion and dorsal closure. DOCKs are divided into four classes (A-D) based on sequence similarity and domain architecture: class A includes Dock1 (or Dock180), 2 and 5; class B includes Dock3 and 4; class C includes Dock6, 7, and 8; and class D includes Dock9, 10 and 11. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1, and DHR-2 (also called CZH2 or Docker). This alignment model represents the DHR-2 domain of DOCK proteins, which contains the catalytic GEF activity for Rac and/or Cdc42. 392 matched cddid_all.tbl CDD cd11685 cd11685 467408 UEV_TSG101-like ubiquitin E2 variant (UEV) domain of TSG101 and related proteins. This subfamily includes the UEV domain of eukaryotic tumor susceptibility gene 101 protein (TSG101, also known as ESCRT-I complex subunit TSG101, vacuolar protein-sorting protein 23, or Vps23) which functions in endocytic trafficking. TSG101 is a component of the ESCRT (endosomal sorting complex required for transport)-I complex, one of four complexes (ESCRT 0, -I, -II, -III) in the vacuolar protein sorting pathway. TSG101 also facilitates HIV-1 virus budding from infected cells, perhaps by linking the p6 domain of the viral structural Gag protein to the vacuolar protein sorting machinery. The UEV domain of TSG101 binds to an essential tetrapeptide motif within the p6 domain of the structural Gag protein and also to ubiquitin. UEVs are homologous to E2 ubiquitin ligases but lack the conserved cysteine residue required for catalytic activity. 126 matched cddid_all.tbl CDD cd11686 cd11686 467409 UBCc_UFC1 Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-fold modifier-conjugating enzyme 1 (UFC1) and related proteins. UFC1, also known as Ufm1-conjugating enzyme 1, participates in a ubiquitin-like (UBL) post translation modification enzymatic cascade known as UFMylation, that allows modification by a UBL-type modifier named ubiquitin-fold modifier (UFM1). UBLs are covalently attached to the target proteins or phospholipids through reaction cascades in a manner similar to the ubiquitination pathway. The UFMylation cascade consists of the ubiquitin-like modifier-activating enzyme (UBA5, an E1-like enzyme), UFM1-conjugating enzyme 1 (UFC1, an E2-like enzyme), and the UFM1-specific ligase (UFL1, an E3-like enzyme). UFM1 is synthesized in a precursor form which is then cleaved at the C-terminus to expose a Gly residue. The mature UFM1 is then activated by UBA5, then transferred to UFC1, and finally UFM1 is covalently conjugated with the target protein via UFL1. 151 matched cddid_all.tbl CDD cd11687 cd11687 212582 PpPFK_gamma Pichia pastoris 6-phosphofructokinase, gamma subunit. Pichia pastoris 6-phosphofructokinase (PpPfk) is the most complex and probably largest (1 MDa) eukaryotic Pfk. It forms a dodecamer of four alpha-beta-gamma trimers. The gamma unit is unique, in contrast to other eukaryotic ATP-dependent 6-phosphofructokinases, and participates in oligomerization of the alpha and beta chains. It is not essential for enzymatic activity, but it modulates the allosteric behavior of the enzyme. 346 matched cddid_all.tbl CDD cd11688 cd11688 212583 THUMP THUMP domain, predicted to bind RNA. The THUMP domain is named after THioUridine synthases, RNA Methyltransferases and Pseudo-uridine synthases. It is predicted to be an RNA-binding domain and probably functions by delivering a variety of RNA modification enzymes to their targets. 148 matched cddid_all.tbl CDD cd11689 cd11689 212588 SidM_DrrA_GEF guanine nucleotide-exchange factor domain of Legionella SidM/DrrA. Effector protein DrrA of Legionella pneumophila, an intracellular pathogen, is a potent guanine nucleotide-exchange factor (GEF) specific for the host Rab1 GTPase. It competes with endogenous exchange factors to recruit and activate Rab1 on plasma membrane-derived organelle, therefore effectively hijacking the host's vesicle trafficking to avoid phagosome-lysosome fusion. 187 matched cddid_all.tbl CDD cd11690 cd11690 212589 Tsi2_like Tse2 immunity protein Tsi2 and similar proteins. Tsi2 is an essential protein in Pseudomonas aeruginosa, providing protection from the activity of Tse2, most likely by directly interacting with Tse2. Tse2 is a toxin transported via the type VI secretion system and is targeted towards other bacteria in the environment. 72 matched cddid_all.tbl CDD cd11691 cd11691 212590 HRI1_like Tandem repeat domain of HRI1 and related proteins. Saccharomyces cerevisiae Hri1p (Hrr25-interacting protein 1, YLR301w) is a non-essential gene product named for its interaction with the yeast protein kinase Hrr25p. It has also been characterized as an interaction partner for Sec72p, but does not seem to be required for protein translocation into the ER. It may be a cytosolic protein. Hri1p contains a tandem repeat of a structural unit that forms a beta-barrel with structural similarity to nitrobindin. The two repeats are sequence dissimilar, and the second (c-terminal) repeat is missing several strands, forming an incomplete barrel. 101 matched cddid_all.tbl CDD cd11692 cd11692 212591 HRI1_N_like N-terminal domain of HRI1 and related proteins. Saccharomyces cerevisiae Hri1p (Hrr25-interacting protein 1, YLR301w) is a non-essential gene product named for its interaction with the yeast protein kinase Hrr25p. It has also been characterized as an interaction partner for Sec72p, but does not seem to be required for protein translocation into the ER. It may be a cytosolic protein. Hri1p contains a tandem repeat of a structural unit that forms a beta-barrel with structural similarity to nitrobindin. This N-terminal repeat is involved in homodimerization and may contain a ligand binding site. 134 matched cddid_all.tbl CDD cd11693 cd11693 212592 HRI1_C_like C-terminal domain of HRI1 and related proteins. Saccharomyces cerevisiae Hri1p (Hrr25-interacting protein 1, YLR301w) is a non-essential gene product named for its interaction with the yeast protein kinase Hrr25p. It has also been characterized as an interaction partner for Sec72p, but does not seem to be required for protein translocation into the ER. It may be a cytosolic protein. Hri1p contains a tandem repeat of a structural unit that forms a beta-barrel with structural similarity to nitrobindin. This C-terminal repeat is missing several strands and forms an incomplete barrel. 90 matched cddid_all.tbl CDD cd11694 cd11694 212567 DHR2_DOCK_D Dock Homology Region 2, a GEF domain, of Class D Dedicator of Cytokinesis proteins. DOCK proteins are atypical guanine nucleotide exchange factors (GEFs) that lack the conventional Dbl homology (DH) domain. As GEFs, they activate small GTPases by exchanging bound GDP for free GTP. They are divided into four classes (A-D) based on sequence similarity and domain architecture; class D, also called the Zizimin subfamily, includes Dock9, 10 and 11. Class D Docks are specific GEFs for Cdc42. Dock9 plays important roles in spine formation and dendritic growth. Dock10 and Dock11 are preferentially expressed in lymphocytes. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate. This alignment model represents the DHR-2 domain of class D DOCKs, which contains the catalytic GEF activity for Cdc42. Class D DOCKs also contain a Pleckstrin homology (PH) domain at the N-terminus. 376 matched cddid_all.tbl CDD cd11695 cd11695 212568 DHR2_DOCK_C Dock Homology Region 2, a GEF domain, of Class C Dedicator of Cytokinesis proteins. DOCK proteins are atypical guanine nucleotide exchange factors (GEFs) that lack the conventional Dbl homology (DH) domain. As GEFs, they activate small GTPases by exchanging bound GDP for free GTP. They are divided into four classes (A-D) based on sequence similarity and domain architecture; class C, also called the Zizimin-related (Zir) subfamily, includes Dock6, 7 and 8. Class C DOCKs have been shown to have GEF activity for both Rac and Cdc42. Dock6 regulates neurite outgrowth. Dock7 plays a critical roles in the early stages of axon formation, neuronal polarity, and myelination. Dock8 regulates T and B cell numbers and functions, and plays essential roles in humoral immune responses and the proper formation of B cell immunological synapses. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate. This alignment model represents the DHR-2 domain of Class C Docks, which contains the catalytic GEF activity for Rac and Cdc42. 368 matched cddid_all.tbl CDD cd11696 cd11696 212569 DHR2_DOCK_B Dock Homology Region 2, a GEF domain, of Class B Dedicator of Cytokinesis proteins. DOCK proteins are atypical guanine nucleotide exchange factors (GEFs) that lack the conventional Dbl homology (DH) domain. As GEFs, they activate small GTPases by exchanging bound GDP for free GTP. They are divided into four classes (A-D) based on sequence similarity and domain architecture; class B includes Dock3 and 4. Dock3 is a specific GEF for Rac and it regulates N-cadherin dependent cell-cell adhesion, cell polarity, and neuronal morphology. It promotes axonal growth by stimulating actin polymerization and microtubule assembly. Dock4 activates the Ras family GTPase Rap1, probably indirectly through interaction with Rap regulatory proteins. It plays a role in regulating dendritic growth and branching in hippocampal neurons, where it is highly expressed. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate. This alignment model represents the DHR-2 domain of class B DOCKs, which contains the catalytic GEF activity for Rac and/or Cdc42. Class B DOCKs also contain an SH3 domain at the N-terminal region and a PxxP motif at the C-terminus. 391 matched cddid_all.tbl CDD cd11697 cd11697 212570 DHR2_DOCK_A Dock Homology Region 2, a GEF domain, of Class A Dedicator of Cytokinesis proteins. DOCK proteins are atypical guanine nucleotide exchange factors (GEFs) that lack the conventional Dbl homology (DH) domain. As GEFs, they activate small GTPases by exchanging bound GDP for free GTP. They are divided into four classes (A-D) based on sequence similarity and domain architecture; class A includes Dock1, 2 and 5. Class A DOCKs are specific GEFs for Rac. Dock1 interacts with the scaffold protein Elmo and the resulting complex functions upstream of Rac in many biological events including phagocytosis of apoptotic cells, cell migration and invasion. Dock2 plays an important role in lymphocyte migration and activation, T-cell differentiation, neutrophil chemotaxis, and type I interferon induction. Dock5 functions upstream of Rac1 to regulate osteoclast function. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate. This alignment model represents the DHR-2 domain of class A DOCKs, which contains the catalytic GEF activity for Rac and/or Cdc42. Class A DOCKs also contain an SH3 domain at the N-terminal region and a PxxP motif at the C-terminus. 400 matched cddid_all.tbl CDD cd11698 cd11698 212571 DHR2_DOCK9 Dock Homology Region 2, a GEF domain, of Class D Dedicator of Cytokinesis 9. Dock9, also called Zizimin1, is an atypical guanine nucleotide exchange factor (GEF) that lacks the conventional Dbl homology (DH) domain. As a GEF, it activates the small GTPase Cdc42 by exchanging bound GDP for free GTP. It plays important roles in spine formation and dendritic growth. DOCK proteins are divided into four classes (A-D) based on sequence similarity and domain architecture; class D includes Dock9, 10 and 11. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate. This alignment model represents the DHR-2 domain of Dock9, which contains the catalytic GEF activity for Cdc42. Class D DOCKs also contain a Pleckstrin homology (PH) domain at the N-terminus. 415 matched cddid_all.tbl CDD cd11699 cd11699 212572 DHR2_DOCK10 Dock Homology Region 2, a GEF domain, of Class D Dedicator of Cytokinesis 10. Dock10, also called Zizimin3, is an atypical guanine nucleotide exchange factor (GEF) that lacks the conventional Dbl homology (DH) domain. As a GEF, it activates the small GTPase Cdc42 by exchanging bound GDP for free GTP. Dock10 is preferentially expressed in lymphocytes and may play a role in interleukin-4 induced activation of B cells. It may also play a role in the invasion of tumor cells. DOCK proteins are divided into four classes (A-D) based on sequence similarity and domain architecture; class D includes Dock9, 10 and 11. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate. This alignment model represents the DHR-2 domain of Dock10, which contains the catalytic GEF activity for Cdc42. Class D DOCKs also contain a Pleckstrin homology (PH) domain at the N-terminus. 446 matched cddid_all.tbl CDD cd11700 cd11700 212573 DHR2_DOCK11 Dock Homology Region 2, a GEF domain, of Class D Dedicator of Cytokinesis 11. Dock11, also called Zizimin2 or activated Cdc42-associated GEF (ACG), is an atypical guanine nucleotide exchange factor (GEF) that lacks the conventional Dbl homology (DH) domain. As a GEF, it activates the small GTPase Cdc42 by exchanging bound GDP for free GTP. Dock11 is predominantly expressed in lymphocytes and is found in high levels in germinal center B lymphocytes after T cell dependent antigen immunization. DOCK proteins are divided into four classes (A-D) based on sequence similarity and domain architecture; class D includes Dock9, 10 and 11. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate. This alignment model represents the DHR-2 domain of Dock11, which contains the catalytic GEF activity for Cdc42. Class D DOCKs also contain a Pleckstrin homology (PH) domain at the N-terminus. 413 matched cddid_all.tbl CDD cd11701 cd11701 212574 DHR2_DOCK8 Dock Homology Region 2, a GEF domain, of Class C Dedicator of Cytokinesis 8. Dock8, also called Zizimin-related 3 (Zir3), is an atypical guanine nucleotide exchange factor (GEF) that lacks the conventional Dbl homology (DH) domain. As a GEF, it activates the small GTPases Rac1 and Cdc42 by exchanging bound GDP for free GTP. Dock8 is highly expressed in the immune system and it regulates T and B cell numbers and functions. It plays essential roles in humoral immune responses and the proper formation of B cell immunological synapses. Dock8 deficiency is a primary immune deficiency that results in extreme susceptibility to cutaneous viral infections, elevated IgE levels, and eosinophilia. It was originally described as an autosomal recessive form of hyper IgE syndrome (AR-HIES). DOCK proteins are divided into four classes (A-D) based on sequence similarity and domain architecture; class C includes Dock6, 7 and 8. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate. This alignment model represents the DHR-2 domain of Dock8, which contains the catalytic GEF activity for Rac and/or Cdc42. 422 matched cddid_all.tbl CDD cd11702 cd11702 212575 DHR2_DOCK6 Dock Homology Region 2, a GEF domain, of Class C Dedicator of Cytokinesis 6. Dock6, also called Zizimin-related 1 (Zir1), is an atypical guanine nucleotide exchange factor (GEF) that lacks the conventional Dbl homology (DH) domain. As a GEF, it activates the small GTPases Rac and Cdc42 by exchanging bound GDP for free GTP. It is widely expressed and shows highest expression in the dorsal root ganglion and the brain. It regulates neurite outgrowth. DOCK proteins are divided into four classes (A-D) based on sequence similarity and domain architecture; class C includes Dock6, 7 and 8. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate. This alignment model represents the DHR-2 domain of Dock6, which contains the catalytic GEF activity for Rac and/or Cdc42. 423 matched cddid_all.tbl CDD cd11703 cd11703 212576 DHR2_DOCK7 Dock Homology Region 2, a GEF domain, of Class C Dedicator of Cytokinesis 7. Dock7, also called Zizimin-related 2 (Zir2), is an atypical guanine nucleotide exchange factor (GEF) that lacks the conventional Dbl homology (DH) domain. As a GEF, it activates the small GTPases Rac1 and Cdc42 by exchanging bound GDP for free GTP. It plays a critical role in the initial specification of axon formation in hippocampal neurons. It affects neuronal polarity by regulating microtubule dynamics. Dock7 also plays a role in controlling myelination by Schwann cells. It may also play important roles in the function and distribution of dermal and follicular melanocytes. DOCK proteins are divided into four classes (A-D) based on sequence similarity and domain architecture; class C includes Dock6, 7 and 8. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate. This alignment model represents the DHR-2 domain of Dock7, which contains the catalytic GEF activity for Rac and/or Cdc42. 473 matched cddid_all.tbl CDD cd11704 cd11704 212577 DHR2_DOCK3 Dock Homology Region 2, a GEF domain, of Class B Dedicator of Cytokinesis 3. Dock3, also called modifier of cell adhesion (MOCA), is an atypical guanine nucleotide exchange factor (GEF) that lacks the conventional Dbl homology (DH) domain. As a GEF, it activates small GTPases by exchanging bound GDP for free GTP. Dock3 is a specific GEF for Rac. It regulates N-cadherin dependent cell-cell adhesion, cell polarity, and neuronal morphology. It promotes axonal growth by stimulating actin polymerization and microtubule assembly. DOCK proteins are divided into four classes (A-D) based on sequence similarity and domain architecture; class B includes Dock3 and 4. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate. This alignment model represents the DHR-2 domain of Dock3, which contains the catalytic GEF activity for Rac and/or Cdc42. Class B DOCKs also contain an SH3 domain at the N-terminal region and a PxxP motif at the C-terminus. 392 matched cddid_all.tbl CDD cd11705 cd11705 212578 DHR2_DOCK4 Dock Homology Region 2, a GEF domain, of Class B Dedicator of Cytokinesis 4. Dock4 is an atypical guanine nucleotide exchange factor (GEF) that lacks the conventional Dbl homology (DH) domain. As a GEF, it activates small GTPases by exchanging bound GDP for free GTP. It plays a role in regulating dendritic growth and branching in hippocampal neurons, where it is highly expressed. It may also regulate spine morphology and synapse formation. Dock4 activates the Ras family GTPase Rap1, probably indirectly through interaction with Rap regulatory proteins. DOCK proteins are divided into four classes (A-D) based on sequence similarity and domain architecture; class B includes Dock3 and 4. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate. This alignment model represents the DHR-2 domain of Dock4, which contains the catalytic GEF activity for Rac and/or Cdc42. Class B DOCKs also contain an SH3 domain at the N-terminal region and a PxxP motif at the C-terminus. 391 matched cddid_all.tbl CDD cd11706 cd11706 212579 DHR2_DOCK2 Dock Homology Region 2, a GEF domain, of Class A Dedicator of Cytokinesis 2. Dock2 is a hematopoietic cell-specific, class A DOCK and is an atypical guanine nucleotide exchange factor (GEF) that lacks the conventional Dbl homology (DH) domain. As a GEF, it activates small GTPases by exchanging bound GDP for free GTP. It plays an important role in lymphocyte migration and activation, T-cell differentiation, neutrophil chemotaxis, and type I interferon induction. DOCK proteins are divided into four classes (A-D) based on sequence similarity and domain architecture; class A includes Dock1, 2 and 5. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate. This alignment model represents the DHR-2 domain of Dock2, which contains the catalytic GEF activity for Rac and/or Cdc42. Class A DOCKs, like Dock2, are specific GEFs for Rac and they contain an SH3 domain at the N-terminal region and a PxxP motif at the C-terminus. 421 matched cddid_all.tbl CDD cd11707 cd11707 212580 DHR2_DOCK1 Dock Homology Region 2, a GEF domain, of Class A Dedicator of Cytokinesis 1. Dock1, also called Dock180, is an atypical guanine nucleotide exchange factor (GEF) that lacks the conventional Dbl homology (DH) domain. As a GEF, it activates small GTPases by exchanging bound GDP for free GTP. Dock1 interacts with the scaffold protein Elmo and the resulting complex functions upstream of Rac in many biological events including phagocytosis of apoptotic cells, cell migration and invasion. In the nervous system, it mediates attractive responses to netrin-1 and thus, plays a role in axon outgrowth and pathfinding. DOCK proteins are divided into four classes (A-D) based on sequence similarity and domain architecture; class A includes Dock1, 2 and 5. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate. This alignment model represents the DHR-2 domain of Dock1, which contains the catalytic GEF activity for Rac and/or Cdc42. Class A DOCKs, like Dock1, are specific GEFs for Rac and they contain an SH3 domain at the N-terminal region and a PxxP motif at the C-terminus. 400 matched cddid_all.tbl CDD cd11708 cd11708 212581 DHR2_DOCK5 Dock Homology Region 2, a GEF domain, of Class A Dedicator of Cytokinesis 5. Dock5 is an atypical guanine nucleotide exchange factor (GEF) that lacks the conventional Dbl homology (DH) domain. As a GEF, it activates small GTPases by exchanging bound GDP for free GTP. It functions upstream of Rac1 to regulate osteoclast function. DOCK proteins are divided into four classes (A-D) based on sequence similarity and domain architecture; class A includes Dock1, 2 and 5. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate. This alignment model represents the DHR-2 domain of Dock5, which contains the catalytic GEF activity for Rac and/or Cdc42. Class A DOCKs, like Dock5, are specific GEFs for Rac and they contain an SH3 domain at the N-terminal region and a PxxP motif at the C-terminus. 400 matched cddid_all.tbl CDD cd11709 cd11709 293931 SPRY SPRY domain. SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). B30.2 also contains residues in the N-terminus that form a distinct PRY domain structure; i.e. B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil or RBCC core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). TRIM/RBCC proteins are involved in a variety of processes, including apoptosis, cell cycle regulation, cell growth, senescence, viral response, meiosis, cell differentiation, and vesicular transport. Genes belonging to this family are implicated in several human diseases that vary from cancer to rare genetic syndromes. The PRY-SPRY domain in these TRIM families is suggested to serve as the target binding site. While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Mutations found in the SPRY-containing proteins have shown to cause Mediterranean fever and Opitz syndrome. 118 matched cddid_all.tbl CDD cd11710 cd11710 212548 GINS_A_psf1 Alpha-helical domain of GINS complex protein Psf1. Psf1 is a component of the GINS tetrameric protein complex. Psf1 is mainly expressed in highly proliferative tissues, such as blastocysts, adult bone marrow, and testis, in which the stem cell system is active. Loss of Psf1 causes embryonic lethality. GINS is a complex of four subunits (Sld5, Psf1, Psf2 and Psf3) that is involved in both initiation and elongation stages of eukaryotic chromosome replication. Besides being essential for the maintenance of genomic integrity, GINS plays a central role in coordinating DNA replication with cell cycle checkpoints and is involved in cell growth. The eukaryotic GINS subunits are homologous and homologs are also found in the archaea; the complex is not found in bacteria. The four subunits of the complex consist of two domains each, termed the alpha-helical (A) and beta-strand (B) domains. The A and B domains of Sld5/Psf1 are permuted with respect to Psf1/Psf3. 129 matched cddid_all.tbl CDD cd11711 cd11711 212549 GINS_A_Sld5 Alpha-helical domain of GINS complex protein Sld5. Sld5 is a component of GINS tetrameric protein complex, and within the complex Sld5 interacts with Psf1 via its N-terminal A-domain, and with Psf2 through a combination of the A and B domains. Sld5 in Drosophila is required for normal cell cycle progression and the maintenance of genomic integrity. GINS is a complex of four subunits (Sld5, Psf1, Psf2 and Psf3) that is involved in both initiation and elongation stages of eukaryotic chromosome replication. Besides being essential for the maintenance of genomic integrity, GINS plays a central role in coordinating DNA replication with cell cycle checkpoints and is involved in cell growth. The eukaryotic GINS subunits are homologous and homologs are also found in the archaea; the complex is not found in bacteria. The four subunits of the complex consist of two domains each, termed the alpha-helical (A) and beta-strand (B) domains. The A and B domains of Sld5/Psf1 are permuted with respect to Psf1/Psf3. 119 matched cddid_all.tbl CDD cd11712 cd11712 212550 GINS_A_psf2 Alpha-helical domain of GINS complex protein Psf2 (partner of Sld5 2). Psf2 is a component of GINS tetrameric protein complex and has been found to play important roles in normal eye development in Xenopus laevis. GINS is a complex of four subunits (Sld5, Psf1, Psf2 and Psf3) that is involved in both initiation and elongation stages of eukaryotic chromosome replication. Besides being essential for the maintenance of genomic integrity, GINS plays a central role in coordinating DNA replication with cell cycle checkpoints and is involved in cell growth. The eukaryotic GINS subunits are homologous and homologs are also found in the archaea; the complex is not found in bacteria. The four subunits of the complex consist of two domains each, termed the alpha-helical (A) and beta-strand (B) domains. The A and B domains of Sld5/Psf1 are permuted with respect to Psf1/Psf3. 119 matched cddid_all.tbl CDD cd11713 cd11713 212551 GINS_A_psf3 Alpha-helical domain of GINS complex protein Psf3 (partner of Sld5 3). Psf3 is a component of GINS, a tetrameric protein complex. Psf3 expression is up regulated in malignant colon cancer and it might be involved in cancer cell proliferation. GINS is a complex of four subunits (Sld5, Psf1, Psf2 and Psf3) that is involved in both initiation and elongation stages of eukaryotic chromosome replication. Besides being essential for the maintenance of genomic integrity, GINS plays a central role in coordinating DNA replication with cell cycle checkpoints and is involved in cell growth. The eukaryotic GINS subunits are homologous and homologs are also found in the archaea; the complex is not found in bacteria. The four subunits of the complex consist of two domains each, termed the alpha-helical (A) and beta-strand (B) domains. The A and B domains of Sld5/Psf1 are permuted with respect to Psf1/Psf3. 109 matched cddid_all.tbl CDD cd11714 cd11714 212552 GINS_A_archaea Alpha-helical domain of archaeal GINS complex proteins. The GINS complex is involved in replication of archaeal and eukayotic genomes. The archaeal DNA replication system is a simplified version of that of the eukaryotes. Like its eukaryotic counterpart, the archaeal GINS complex is tetrameric, but instead of four different subunits (Sld5, Psf1, Psf2 and Psf3) it consists of two different proteins named Gins51 and Gins23. All GINS subunits are homologs and they can be classified into two groups. One group (the eukayotic Sld5 and Psf1, as well as the archaeal Gins51) has the alpha-helical (A) domain at the N-terminus and the beta-strand domain (B) at the C-terminus (this arrangement is called ABtype). The arrangement of the A and B domains is reversed in the second group (eukaryotic Psf2 and Psf3 and archaeal Gins23, also referred to as BAtype). The overall fold of each archaeal subunit and the overall tetrameric assembly of GINS are similar, but the relative locations of the C-terminal small domains are different with respect to the alpha helical domain characterized by this model, resulting in different subunit contacts in the archaeal GINS complex.Some archaea may have a homotetrameric GINS complex (4 copies of an AB-type module). 105 matched cddid_all.tbl CDD cd11715 cd11715 212584 THUMP_AdoMetMT THUMP domain associated with S-adenosylmethionine-dependent methyltransferases. Proteins of this family contain an N-terminal THUMP domain and a C-terminal S-adenosylmethionine-dependent methyltransferase domain. Members have been implicated in the modification of 23S RNA m2G2445, a highly conserved modification in bacteria and in the m2G6 modification of tRNA. The THUMP domain is named after thiouridine synthases, methylases and PSUSs. The domain consists of about 110 amino acid residues. It is predicted to be an RNA-binding domain and probably functions by delivering a variety of RNA modification enzymes to their targets. 152 matched cddid_all.tbl CDD cd11716 cd11716 212585 THUMP_ThiI THUMP domain of thiamine biosynthesis protein ThiI. ThiI is an enzyme responsible for the formation of the modified base S(4)U (4-thiouridine) found at position 8 in some prokaryotic tRNAs. This modification acts as a signal for UV exposure, triggering a response that provides protection against its damaging effects. ThiI consists of an N-terminal THUMP domain, followed by an NFLD domain, and a C-terminal PP-loop pyrophosphatase domain. The N-terminal THUMP domain has been implicated in the recognition of the acceptor-stem region. The THUMP domain is named after thiouridine synthases, methylases and PSUSs. The domain consists of about 110 amino acid residues. It is predicted to be an RNA-binding domain and probably functions by delivering a variety of RNA modification enzymes to their targets. 166 matched cddid_all.tbl CDD cd11717 cd11717 212586 THUMP_THUMPD1_like THUMP domain-containing protein 1-like. This family contains THUMP domain-only proteins including THUMP domain-containing protein 1 and Saccharomyces cerevisiae Tan1. Tan1 is non essential and has been shown to be required for the formation of the modified nucleoside N(4)-acetylcytidine (ac(4)C) in tRNA. To date, there is no functional information available about THUMPD1. The THUMP domain is named after thiouridine synthases, methylases and PSUSs. The domain consists of about 110 amino acid residues. It is predicted to be an RNA-binding domain and probably functions by delivering a variety of RNA modification enzymes to their targets. 158 matched cddid_all.tbl CDD cd11718 cd11718 212587 THUMP_SPOUT THUMP domain associated with SPOUT RNA Methylases. Members of this archaeal protein family are characterized by containing an N-terminal THUMP domain and a C-terminal SPOUT RNA methyltransferase domain. No functional information is available The THUMP domain is named after thiouridine synthases, methylases and PSUSs. The domain consists of about 110 amino acid residues. It is predicted to be an RNA-binding domain and probably functions by delivering a variety of RNA modification enzymes to their targets. 145 matched cddid_all.tbl CDD cd11719 cd11719 212593 FANC Fanconi anemia ID complex proteins FANCI and FANCD2. The Fanconi anemia ID complex consists of two subunits, Fanconi anemia I and Fanconi anemia D2 (FANCI-FANCD2) and plays a central role in the repair of DNA interstrand cross-links (ICLs). The complex is activated via DNA damage-induced phosphorylation by ATR (ataxia telangiectasia and Rad3-related) and monoubiquitination by the FA core complex ubiquitin ligase, and it binds to DNA at the ICL site, recognizing branched DNA structures. Defects in the complex cause Fanconi anemia, a cancer predisposition syndrome. 977 matched cddid_all.tbl CDD cd11720 cd11720 212594 FANCI Fanconi anemia I protein. The Fanconi anemia ID complex consists of two subunits, Fanconi anemia I and Fanconi anemia D2 (FANCI-FANCD2) and plays a central role in the repair of DNA interstrand cross-links (ICLs). The complex is activated via DNA damage-induced phosphorylation by ATR (ataxia telangiectasia and Rad3-related) and monoubiquitination by the FA core complex ubiquitin ligase, and it binds to DNA at the ICL site, recognizing branched DNA structures. Defects in the complex cause Fanconi anemia, a cancer predisposition syndrome. The phosphorylation of FANCI may function as a molecular switch to turn on the FA pathway. 1202 matched cddid_all.tbl CDD cd11721 cd11721 212595 FANCD2 Fanconi anemia D2 protein. The Fanconi anemia ID complex consists of two subunits, Fanconi anemia I and Fanconi anemia D2 (FANCI-FANCD2) and plays a central role in the repair of DNA interstrand cross-links (ICLs). The complex is activated via DNA damage-induced phosphorylation by ATR (ataxia telangiectasia and Rad3-related) and monoubiquitination by the FA core complex ubiquitin ligase, and it binds to DNA at the ICL site, recognizing branched DNA structures. Defects in the complex cause Fanconi anemia, a cancer predisposition syndrome. The phosphorylation of FANCD2 is required for DNA damage-induced intra-S phase checkpoint and for cellular resistance to DNA crosslinking agents. 1161 matched cddid_all.tbl CDD cd11722 cd11722 212596 SOAR STIM1 Orai1-activating region. STIM1 (stromal interaction module 1) is a metazoan transmembrane protein located in the endoplasmic reticulum (ER) membrane, which functions as a sensor for ER calcium ion levels and activates store-operated Ca2+ influx channels (SOCs), such as the Orai1 Ca2+ channel located in the plasma membrane. STIM1 has an N-terminal Ca-binding EF-hand domain, which is located in the ER lumen. Responding to the release of Ca2+ from the ER, STIM1 was found to aggregate near the plasma membrane and contact Orai1. This model describes a region near the C-terminus of STIM1, which has been shown to mediate the interaction with Orai1 and has been labeled SOAR (STIM1 Orai1-activating region). STIM1 has also been linked to sensing oxidative and temperature-variation stress and may play a rather general role in mediating calcium signaling in response to stress. Dimerization of STIM1 via the SOAR domain appears required for the activation of the Orai1 calcium channel. A model for STIM1 activation has been proposed, in which an inhibitory helix N-terminal to the SOAR domain prevents STIM1 clustering or aggregation, and in which conformational changes triggered by depletion of the calcium stores allow the clustering and activation of Orai1. 92 matched cddid_all.tbl CDD cd11723 cd11723 381177 YabN_N_like N-terminal S-AdoMet-dependent tetrapyrrole methylase domain of Bacillus subtilis YabN and similar domains. This family includes the S-AdoMet (S-adenosyl-L-methionine or SAM)-dependent tetrapyrrole methylase (TP-methylase) domain of Bacillus subtilis YabN, and similar domains. YabN is a fusion of an N-terminal TP-methylase and a C-terminal MazG-type nucleotide pyrophosphohydrolase domain. MazG-like NTP-PPases have been implicated in house-cleaning functions such as degrading abnormal (d)NTPs. TP-methylases use S-AdoMet in the methylation of diverse substrates. Most TP-methylase family members catalyze various methylation steps in cobalamin (vitamin B12) biosynthesis, other members like diphthine synthase and ribosomal RNA small subunit methyltransferase I (RsmI) act on other substrates. The specific function of YabN's TP-methylase domain is not known. 218 matched cddid_all.tbl CDD cd11724 cd11724 381178 TP_methylase uncharacterized family of the tetrapyrrole methylase superfamily. Members of this superfamily use S-AdoMet (S-adenosyl-L-methionine or SAM) in the methylation of diverse substrates. Most members catalyze various methylation steps in cobalamin (vitamin B12) biosynthesis. There are two distinct cobalamin biosynthetic pathways in bacteria. The aerobic pathway requires oxygen, and cobalt is inserted late in the pathway; the anaerobic pathway does not require oxygen, and cobalt insertion is the first committed step towards cobalamin synthesis. The enzymes involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Most of the enzymes are shared by both pathways and a few enzymes are pathway-specific. Diphthine synthase and Ribosomal RNA small subunit methyltransferase I (RsmI) are two superfamily members that are not involved in cobalamin biosynthesis. Diphthine synthase participates in the posttranslational modification of a specific histidine residue in elongation factor 2 (EF-2) of eukaryotes and archaea to diphthamide. RsmI catalyzes the 2-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA. Other superfamily members not involved in cobalamin biosynthesis include the N-terminal tetrapyrrole methylase domain of Bacillus subtilis YabN whose specific function is unknown, and Omphalotus olearius omphalotin methyltransferase which catalyzes the automethylation of its own C-terminus; this C terminus is subsequently released and macrocyclized to give Omphalotin A, a potent nematicide. 243 matched cddid_all.tbl CDD cd11725 cd11725 277251 ADDz_Dnmt3 ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3 (Dnmt3). Dnmt3 is a de novo DNA methyltransferase family that includes two active enzymes Dnmt3a and -3b and one regulatory factor Dnmt3l. The ADDz domain of Dnmt3 is located in the C-terminal region of Dnmt3, which is an active catalytic domain in Dnmt3a and -b, but lacks some residues for enzymatic activity in Dnmt3l. DNA methylation is an important epigenetic mechanism involved in diverse biological processes such as embryonic development, gene expression, and genomic imprinting. The ADDz_Dnmt3 domain is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif. 108 matched cddid_all.tbl CDD cd11726 cd11726 277252 ADDz_ATRX ADDz domain found in ATRX (alpha-thalassemia/mental retardation, X-linked). ADDz_ATRX is a PHD-like zinc finger domain of ATRX, which belongs to the SNF2 family of chromatin remodeling proteins. ATRX is a large chromatin-associated nuclear protein with two domains, ADDz_ATRX at the N-terminus, followed by a C-terminal ATPase/helicase domain. The ADDz_ATRX domain recognizes a specific methylated histone, and this interaction is required for heterochromatin localization of the ATRX protein. Missense mutations in either of the two ATRX domains lead to the X-linked alpha-thalassemia and mental retardation syndrome; however the mutations in the ADDz_ATRX domain produce a more severe disease phenotype that may also relate to disturbing unknown functions or interaction sites of this domain. The ADDz domain is also present in chromatin-associated proteins cytosine-5-methyltransferase 3 (Dnmt3); it is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif. 102 matched cddid_all.tbl CDD cd11727 cd11727 277253 ADDz_Dnmt3l ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3 like (Dnmt3l). Dnmt3l is a regulator of DNA methylation, which acts by recognizing unmethylated histone H3 tails and interacting with Dnmt3a to stimulate its de novo DNA methylation activity. The ADDz_Dnmt3l domain is located in the C-terminal region of Dnmt3l that otherwise lacks some residues required for DNA methyltransferase activity. DNA methylation is an important epigenetic mechanism involved in diverse biological processes such as embryonic development, gene expression, and genomic imprinting. Dnmt3l is also associating with HDAC1 and acts as a transcriptional repressor. The ADDz_Dnmt3l domain is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif. 123 matched cddid_all.tbl CDD cd11728 cd11728 277254 ADDz_Dnmt3b ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3b (Dnmt3b). ADDz_Dnmt3b is an active catalytic domain of Dnmt3b. Dnmt3b is a member of the Dnmt3 family and is a de novo DNA methyltransferases that has an N-terminal variable region followed by a conserved PWWP region and the cysteine-rich ADDz domain. DNA methylation is an important epigenetic mechanism involved in diverse biological processes such as embryonic development, gene expression, and genomic imprinting. The methyltransferase activity of Dnmt3a is not only responsible for the establishment of DNA methylation pattern, but is also essential for the inheritance of these patterns during mitosis. Dnmt3b is ubiquitously expressed in most adult tissues. The ADDz_Dnmt3 domain is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif. A knockout of Dnmt3b has been shown to be lethal in the mouse model. 120 matched cddid_all.tbl CDD cd11729 cd11729 277255 ADDz_Dnmt3a ADDz domain found in DNA (cytosine-5) methyltransferases (C5-MTases) 3a (Dnmt3a). Dnmt3a is a member of the Dnmt3 family and is a protein with de novo DNA methyltransferase activity. Dnmt3 family members are Dnmt3a, Dnmt3b, and Dnmt3l the non-enzymatic regulatory factor. Dnmt3a is recruited by Dnmt3l to unmethylated histone H3 and methylates the target. Dnmt3a has a variable region at the N-terminus, followed by a conserved PWWP region and the cysteine-rich ADDz domain. ADDz_Dnmt3a is an active catalytic domain of Dnmt3a. DNA methylation is an important epigenetic mechanism involved in diverse biological processes such as embryonic development, gene expression, and genomic imprinting. The methyltransferase activity of Dnmt3a is not only responsible for the establishment of DNA methylation pattern, but is also essential for the inheritance of these patterns during mitosis. The ADDz_Dnmt3 domain is a PHD-like zinc finger motif that contains two parts, a C2-C2 and a PHD-like zinc finger. PHD zinc finger domains have been identified in more than 40 proteins that are mainly involved in chromatin mediated transcriptional control; the classical PHD zinc finger has a C4-H-C3 motif that spans about 50-80 amino acids. In ADDz, the conserved histidine residue of the PHD finger is replaced by a cysteine, and an additional zinc finger C2-C2 like motif is located about twenty residues upstream of the C4-C-C3 motif. A knockout of Dnmt3a has been shown to be lethal in the mouse model. 128 matched cddid_all.tbl CDD cd11730 cd11730 212496 Tthb094_like_SDR_c Tthb094 and related proteins, classical (c) SDRs. Tthb094 from Thermus Thermophilus is a classical SDR which binds NADP. Members of this subgroup contain the YXXXK active site characteristic of SDRs. Also, an upstream Asn residue of the canonical catalytic tetrad is partially conserved in this subgroup of proteins of undetermined function. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human prostaglandin dehydrogenase (PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107, PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 206 matched cddid_all.tbl CDD cd11731 cd11731 212497 Lin1944_like_SDR_c Lin1944 and related proteins, classical (c) SDRs. Lin1944 protein from Listeria Innocua is a classical SDR, it contains a glycine-rich motif similar to the canonical motif of the SDR NAD(P)-binding site. However, the typical SDR active site residues are absent in this subgroup of proteins of undetermined function. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold (alpha/beta folding pattern with a central beta-sheet), an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Classical SDRs are typically about 250 residues long, while extended SDRs are approximately 350 residues. Sequence identity between different SDR enzymes are typically in the 15-30% range, but the enzymes share the Rossmann fold NAD-binding motif and characteristic NAD-binding and catalytic sequence patterns. These enzymes catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human prostaglandin dehydrogenase (PGDH) numbering). In addition to the Tyr and Lys, there is often an upstream Ser (Ser-138, PGDH numbering) and/or an Asn (Asn-107, PGDH numbering) contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Extended SDRs have additional elements in the C-terminal region, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Some atypical SDRs have lost catalytic activity and/or have an unusual NAD(P)-binding motif and missing or unusual active site residues. Reactions catalyzed within the SDR family include isomerization, decarboxylation, epimerization, C=N bond reduction, dehydratase activity, dehalogenation, Enoyl-CoA reduction, and carbonyl-alcohol oxidoreduction. 198 matched cddid_all.tbl CDD cd11732 cd11732 466838 ASKHA_NBD_HSP70_HSP105-110-like "nucleotide-binding domain (NBD) of the 105/110 kDa heat shock protein family. The 105/110 kDa heat shock proteins family includes the human proteins, HSPA4 (also known as 70-kDa heat shock protein 4; APG-2; HS24/P52; hsp70 RY; HSPH2), HSPA4L (also known as 70-kDa heat shock protein 4-like; APG-1; HSPH3; OSP94), and HSPH1 (also known as heat shock 105kDa/110kDa protein 1; HSP105; HSP105A; HSP105B; NY-CO-25), Saccharomyces cerevisiae Sse1p, Sse2p and a sea urchin sperm receptor. They all belong to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly and can direct incompetent ""client"" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. HSP70 chaperone activity is regulated by various co-chaperones: J-domain proteins and nucleotide exchange factors (NEFs)." 377 matched cddid_all.tbl CDD cd11733 cd11733 466839 ASKHA_NBD_HSP70_HSPA9 "nucleotide-binding domain (NBD) of human mitochondrial heat shock 70 kDa protein 9 (HSPA9) and similar proteins. This subgroup includes human mitochondrial HSPA9 (also known as mitochondrial stress-70 protein; mortalin; 75 kDa glucose-regulated protein/GRP-75; HSPA9B; MOT; peptide-binding protein 74/PBP74). It acts as a chaperone protein which plays an important role in mitochondrial iron-sulfur cluster (ISC) biogenesis. It interacts with and stabilizes ISC cluster assembly proteins FXN, NFU1, NFS1 and ISCU. HSPA9 regulates erythropoiesis via stabilization of ISC assembly. It may play a role in the control of cell proliferation and cellular aging. Members in this subgroup belong to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly, and can direct incompetent ""client"" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. Hsp70 chaperone activity is regulated by various co-chaperones: J-domain proteins and nucleotide exchange factors (NEFs)." 377 matched cddid_all.tbl CDD cd11734 cd11734 466840 ASKHA_NBD_HSP70_Ssc1_3 nucleotide-binding domain (NBD) of Saccharomyces cerevisiae mitochondrial heat shock protein Ssc1p and Ssc3p and similar proteins. This subgroup includes Saccharomyces cerevisiae Stress-Seventy subfamily C proteins, Ssc1p (also called import motor subunit, mitochondrial; endonuclease SceI 75 kDa subunit; mtHSP70; ENS1; endonuclease SceI 75 kDa subunit) and sc3p (also called extracellular mutant protein 10/Ecm10). Ssc1p is an essential component of the PAM complex, a complex required for the translocation of transit peptide-containing proteins from the inner membrane into the mitochondrial matrix in an ATP-dependent manner. It constitutes the ATP-driven core of the motor and binds the precursor preprotein. It is required for the import of the processed frataxin homolog YFH1 into the mitochondrion. Ssc1p also acts as a non-catalytic component of endonuclease SceI (endo.SceI), which cleaves specifically at multiple sites on mitochondrial DNA and produces double-stranded breaks. Ssc1p confers broader sequence specificity, greater stability, and higher activity on the catalytic subunit. Ssc3p plays a role in facilitating the assembly of some protein complexes inside the mitochondria. It may initiate the events that lead to refolding of imported precursors in the matrix space. 378 matched cddid_all.tbl CDD cd11735 cd11735 466841 ASKHA_NBD_HSP70_HSPA12A "nucleotide-binding domain (NBD) of heat shock 70 kDa protein 12A (HSPA12A) and similar proteins. HSPA12A is an adapter protein for SORL1, but not SORT1. It delays SORL1 internalization and affects SORL1 subcellular localization. HSPA12A belongs to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly, and can direct incompetent ""client"" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. HSP70 chaperone activity is regulated by various co-chaperones: J-domain proteins and nucleotide exchange factors (NEFs). No co-chaperones have yet been identified for HSPA12A." 413 matched cddid_all.tbl CDD cd11736 cd11736 466842 ASKHA_NBD_HSP70_HSPA12B "nucleotide-binding domain (NBD) of heat shock 70 kDa protein 12B (HSPA12B) and similar proteins. HSPA12B, predominantly expressed in endothelial cells, is required for angiogenesis, and may interact with known angiogenesis mediators. It may be important for host defense in microglia-mediated immune response. HSPA12B belongs to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly, and can direct incompetent ""client"" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. HSP70 chaperone activity is regulated by various co-chaperones: J-domain proteins and nucleotide exchange factors (NEFs). No co-chaperones have yet been identified for HSPA12B." 361 matched cddid_all.tbl CDD cd11737 cd11737 466843 ASKHA_NBD_HSP70_HSPA4 "nucleotide-binding domain (NBD) of heat shock 70 kDa protein 4 (HSPA4) and similar proteins. HSPA4, also called HSP70RY, , HS24/P52, hsp70 RY, and HSPH2, or heat shock 70-related protein APG-2, responds to acidic pH stress, is involved in the radioadaptive response, is required for normal spermatogenesis and is overexpressed in hepatocellular carcinoma. It participates in a pathway along with NBS1 (Nijmegen breakage syndrome 1, also known as p85 or nibrin), heat shock transcription factor 4b (HDF4b), and HSPA14 (belonging to a different HSP70 subfamily) that induces tumor migration, invasion, and transformation. HSPA4 expression in sperm was increased in men with oligozoospermia, especially in those with varicocele. HSPA4 belongs to the 105/110 kDa heat shock protein (HSP105/110) subfamily of the HSP70-like family. HSP105/110s are believed to function generally as co-chaperones of HSP70 chaperones, acting as nucleotide exchange factors (NEFs), to remove ADP from their HSP70 chaperone partners during the ATP hydrolysis cycle. HSP70 chaperones assist in protein folding and assembly, and can direct incompetent ""client"" proteins towards degradation. Like HSP70 chaperones, HSP105/110s have an N-terminal nucleotide-binding domain (NBD) and a C-terminal substrate-binding domain (SBD). For HSP70 chaperones, the nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. Hsp70 chaperone activity is also regulated by J-domain proteins." 381 matched cddid_all.tbl CDD cd11738 cd11738 466844 ASKHA_NBD_HSP70_HSPA4L "nucleotide-binding domain (NBD) of heat shock 70 kDa protein 4L (HSPA4L) and similar proteins. HSPA4L, also called heat shock 70-related protein APG-1, heat-shock protein family A member 4-like protein, HSPA4-like protein, osmotic stress protein 94, or HSPH3, possesses chaperone activity in vitro where it inhibits aggregation of citrate synthase. It is expressed ubiquitously and predominantly in the testis. It is required for normal spermatogenesis and plays a role in osmotolerance. HSPA4L belongs to the 105/110 kDa heat shock protein (HSP105/110) subfamily of the HSP70-like family. HSP105/110s are believed to function generally as co-chaperones of HSP70 chaperones, acting as nucleotide exchange factors (NEFs), to remove ADP from their HSP70 chaperone partners during the ATP hydrolysis cycle. HSP70 chaperones assist in protein folding and assembly, and can direct incompetent ""client"" proteins towards degradation. Like HSP70 chaperones, HSP105/110s have an N-terminal nucleotide-binding domain (NBD) and a C-terminal substrate-binding domain (SBD). For HSP70 chaperones, the nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. Hsp70 chaperone activity is also regulated by J-domain proteins." 383 matched cddid_all.tbl CDD cd11739 cd11739 466845 ASKHA_NBD_HSP70_HSPH1 "nucleotide-binding domain (NBD) of heat shock 105kDa/110kDa protein 1 (HSPH1) and similar proteins. HSPH1, also called heat shock protein 105 kDa, antigen NY-CO-25, heat shock 110 kDa protein, acts as a nucleotide-exchange factor (NEF) for chaperone proteins HSPA1A and HSPA1B, promoting the release of ADP from HSPA1A/B thereby triggering client/substrate protein release. It prevents the aggregation of denatured proteins in cells under severe stress, on which the ATP levels decrease markedly. It inhibits HSPA8/HSC70 ATPase and chaperone activities. HSPH1 belongs to the 105/110 kDa heat shock protein (HSP105/110) subfamily of the HSP70-like family. HSP105/110s are believed to function generally as co-chaperones of HSP70 chaperones, acting as nucleotide exchange factors (NEFs), to remove ADP from their HSP70 chaperone partners during the ATP hydrolysis cycle. HSP70 chaperones assist in protein folding and assembly, and can direct incompetent ""client"" proteins towards degradation. Like HSP70 chaperones, HSP105/110s have an N-terminal nucleotide-binding domain (NBD) and a C-terminal substrate-binding domain (SBD). For HSP70 chaperones, the nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. Hsp70 chaperone activity is also regulated by J-domain proteins." 380 matched cddid_all.tbl CDD cd11740 cd11740 213038 YajQ_like Proteins similar to Escherichia coli YajQ. In Pseudomonas syringae, YajQ functions as a host protein involved in the temporal control of bacteriophage Phi6 gene transcription. It has been shown to bind to the phage's major structural core protein P1, most likely activating transcription by acting indirectly on the RNA polymerase. YajQ may remain bound to the phage particles throughout the infection period. Earlier, YajQ was characterized as a putative nucleic acid-binding protein based on the similarity of its (ferredoxin-like) three-dimensional topology with that of RNP-like RNA-binding domains. 159 matched cddid_all.tbl CDD cd11741 cd11741 240666 TIN2_TBM TRF-binding motif region of TRF-Interacting Nuclear factor 2. The C-terminal region of TIN2 contains the TRF-binding motif (TBM), while the TIN2 N-terminal region acts in the modulation of TRF1 activity via the inhibition of tankyrase 1. TIN2 binding to TRF2 is primarily via the TRF binding motif (TBM) and the N-terminus, while the far C-terminal region interacts with lower affinity. The TIN2 TBM, but not the N-terminal region, is involved in TIN2 binding to TRF1. Truncation of the TIN2 N-terminus in mouse results in telomere elongation, suggesting a a negative regulatory function of this region. TIN2 is a shelterin complex protein identified in mammals, one of 6 factors that act to protect telomeres from DNA damage repair machinery. Three shelterin components (TRF1, TRF2, POT1) bind DNA and 3 components (TIN2, RAP1, TPP1) are recruited by these DNA binding factors. TIN2 binds directly to TRF1 and TRF2 and stabilizes TRF2 complex-telomere binding by tethering it to the TRF1 complex. TRF1 activity at telomeres is regulated in part by selective ubiquitination and degradation. Ubiquitination of TRF1 is mediated by Fbx4, which binds TRF1 in the TRFH domain, via a small GTPase module. When bound to telomeres, TIN2 acts to protect TRF1 from SCF-Fbx4 mediated ubiquitination. F-box proteins act in substrate recognition as part of SCF complexes (SCF: Skp1-Cul1-Rbx1-F- box protein). Tankyrase-mediated ADP-ribosylation releases TRF1 from telomeres, rendering them susceptible to ubiquitination and degradation, promoting telomere elongation. TIN2 also binds TPP1, which recruits POT1 to telomeres. 108 matched cddid_all.tbl CDD cd11743 cd11743 213039 Cthe_2751_like Uncharacterized protein domain similar to Clostridium thermocellum 2751. Cthe_2751 has been found to form homodimers. Based on structural similarity to other families, a role in processing nucleic acids was suggested, though interactions with DNA could not be demonstrated. 122 matched cddid_all.tbl CDD cd11744 cd11744 213354 MIT_CorA-like metal ion transporter CorA-like divalent cation transporter superfamily. This superfamily of essential membrane proteins is involved in transporting divalent cations (uptake or efflux) across membranes. They are found in most bacteria and archaea, and in some eukaryotes. It is a functionally diverse group which includes the Mg2+ transporters of Escherichia coli and Salmonella typhimurium CorAs (which can also transport Co2+, and Ni2+ ), the CorA Co2+ transporter from the hyperthermophilic Thermotoga maritima, and the Zn2+ transporter Salmonella typhimurium ZntB, which mediates the efflux of Zn2+ (and Cd2+). It includes five Saccharomyces cerevisiae members: i) two plasma membrane proteins, the Mg2+ transporter Alr1p/Swc3p and the putative Mg2+ transporter, Alr2p, ii) two mitochondrial inner membrane Mg2+ transporters: Mfm1p/Lpe10p, and Mrs2p, and iii) and the vacuole membrane protein Mnr2p, a putative Mg2+ transporter. It also includes a family of Arabidopsis thaliana members (AtMGTs), some of which are localized to distinct tissues, and not all of which can transport Mg2+. Thermotoga maritima CorA and Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, Mrs2p, and Alr1p. Natural variants such as GVN and GIN, as in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport. 286 matched cddid_all.tbl CDD cd11745 cd11745 213372 Yos9_DD C-terminal dimerization domain (DD) of Saccharomyces cerevisiae Yos9 and related proteins. Yos9 participates in the ER-associated protein degradation pathway that targets misfolded proteins for proteolysis. Yos9 is a component of the reductase degradation (HRD) ubiquitin-ligase complex, specifically part of the luminal submodule of the ligase. Yos9 scans proteins for specific oligosaccharide modifications, which are critical determinants of degradation signal. It has been shown to be involved in the degradation of glycosylated proteins and various nonglycosylated proteins. Yos9 functions as a homodimer where this domain is responsible for the self-association; it has an alphabeta-roll domain architecture, and is found at the C-terminus of the protein. The N-terminal portion of Yos9 which includes an MRH domain is required for binding to Hrd3p, another component of the HRD complex. The DD domain does not appear to be directly binding Hrd3p. 124 matched cddid_all.tbl CDD cd11746 cd11746 213062 GH94N_like N-terminal domain of glycoside hydrolase family 94 and related domains. The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes cellobiose phosphorylase (EC:2.4.1.20), cellodextrin phosphorylase (EC:2.4.1.49), chitobiose phosphorylase (EC:2.4.1.-), amongst other members. Their N-terminal domain is involved in oligomerization and may play a role in catalysis, but it is separate from the catalytic domain [an (alpha/alpha)(6) barrel]. This GH64N domain also occurs in tandem repeat arrangements (not at the N-terminus) in cyclic beta 1-2 glucan synthetase and related proteins, and as a standalone domain in distantly related proteins of unknown function. 179 matched cddid_all.tbl CDD cd11747 cd11747 213063 GH94N_like_1 Glycoside hydrolase family 94 N-terminal-like domain of uncharacterized function. The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes cellobiose phosphorylase and many other members. Their N-terminal domain is involved in oligomerization and may play a role in catalysis, but it is separate from the catalytic domain. This GH64N domain also occurs as a standalone domain in distantly related proteins of unknown function, as represented by this model, which also includes N-terminal GH94N-like domains of bacterial rhamnosidases and as found at the C-terminus of polygalacturonases. 204 matched cddid_all.tbl CDD cd11748 cd11748 213064 GH94N_NdvB_like Glycoside hydrolase family 94 N-terminal-like domain of NdvB-like proteins. The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes cellobiose phosphorylase (EC:2.4.1.20), cellodextrin phosphorylase (EC:2.4.1.49), chitobiose phosphorylase (EC:2.4.1.-), amongst other members. Their N-terminal domain is involved in oligomerization and may play a role in catalysis, but it is separate from the catalytic domain [an (alpha/alpha)(6) barrel)]. The GH64N domain, as represented by this model, is found at the N-terminus of largely uncharacterized proteins, some members from Xanthomonas campestris and related organisms are annotated as NdvB (nodule development B) gene products, glycosyltransferases required for the synthesis of cyclic beta-(1,2)-glucans, which play a role in interactions between bacteria and plants. 294 matched cddid_all.tbl CDD cd11749 cd11749 213065 GH94N_LBP_like N-terminal-like domain of Paenibacillus sp. YM-1 Laminaribiose Phosphorylase and similar proteins. The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes bacterial laminaribiose phosphorylase. This N-terminal domain is involved in oligomerization and may play a role in catalysis, but it is separate from the catalytic domain [an (alpha/alpha)(6) barrel]. Bacterial laminaribiose phosphorylase phosphorolyzes laminaribiose into alpha-glucose 1-phosphate and glucose, but does not phosphorolyze other glucobioses; it slightly phosphorolyzed laminaritriose and higher laminarioligosaccharides. The GH64N domain, as represented by this model, is also found at the N-terminus of GH94 members with uncharacterized specificities. 229 matched cddid_all.tbl CDD cd11750 cd11750 213066 GH94N_like_3 Glycoside hydrolase family 94 N-terminal-like domain of uncharacterized function. The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes cellobiose phosphorylase (EC:2.4.1.20), cellodextrin phosphorylase (EC:2.4.1.49), chitobiose phosphorylase (EC:2.4.1.-), amongst other members. Their N-terminal domain is involved in oligomerization and may play a role in catalysis, but it is separate from the catalytic domain [an (alpha/alpha)(6) barrel]. The GH64N domain, as represented by this model, is found at the N-terminus of GH94 members with uncharacterized specificities. 282 matched cddid_all.tbl CDD cd11751 cd11751 213067 GH94N_like_4 Glycoside hydrolase family 94 N-terminal-like domain of uncharacterized function. The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes cellobiose phosphorylase (EC:2.4.1.20), cellodextrin phosphorylase (EC:2.4.1.49), chitobiose phosphorylase (EC:2.4.1.-), amongst other members. Their N-terminal domain is involved in oligomerization and may play a role in catalysis, but it is separate from the catalytic domain [an (alpha/alpha)(6) barrel]. The GH64N domain, as represented by this model, is found near the N-terminus of GH94 members and related proteins with uncharacterized specificities. 223 matched cddid_all.tbl CDD cd11752 cd11752 213068 GH94N_CDP_like N-terminal domain of cellodextrin phosphorylase (CDP) and similar proteins. The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes cellodextrin phosphorylase (EC:2.4.1.49), also known as 1,4-beta-D-oligo-D-glucan:phosphate alpha-D-glucosyltransferase or CepB. This N-terminal domain is involved in oligomerization and may play a role in catalysis, but it is separate from the catalytic domain [an (alpha/alpha)(6) barrel]. Cellodextrin phosphorylase catalyzes the reversible and phosphate dependent removal of a single alpha-D-glucose-1-phosphate unit from a (1,4-beta-D-glucosyl) oligomer. 214 matched cddid_all.tbl CDD cd11753 cd11753 213069 GH94N_ChvB_NdvB_2_like Second GH94N domain of cyclic beta 1-2 glucan synthetase and similar domains. The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes cyclic beta 1-2 glucan synthetase (EC:2.4.1.20) or ChvB (encoded by the chromosomal chvB virulence gene). This second of two tandemly repeated GH94-N-terminal-like domains has not been characterized functionally. Some beta 1-2 glucan synthetases are annotated as NdvB (nodule development B) gene products, glycosyltransferases required for the synthesis of cyclic beta-(1,2)-glucans, which play a role in interactions between bacteria and plants. 336 matched cddid_all.tbl CDD cd11754 cd11754 213070 GH94N_CBP_like N-terminal domain of cellobiose phosphorylase (CBP) and similar proteins. The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes cellobiose phosphorylase (EC:2.4.1.20) or cellobiose:phosphate alpha-D-glucosyltransferase, or CepA. This N-terminal domain is involved in oligomerization and may play a role in catalysis, but it is separate from the catalytic domain [an (alpha/alpha)(6) barrel]. Cellobiose phosphorylase participates in the degradation of cellulose, it catalyzes the phosphate dependent hydrolysis of cellobiose into alpha-D-glucose-1-phosphate and D-glucose, a reversible reaction. 303 matched cddid_all.tbl CDD cd11755 cd11755 213071 GH94N_ChBP_like N-terminal domain of chitobiose phosphorylase (ChBP) and similar proteins. The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes chitobiose phosphorylase (EC:2.4.1.-). This N-terminal domain is involved in oligomerization and may play a role in catalysis, but it is separate from the catalytic domain [an (alpha/alpha)(6) barrel]. Chitobiose phosphorylase catalyzes the reversible phosphate dependent hydrolysis of chitobiose [(GlcNAc)2] into alpha-GlcNAc-1-phosphate and GlcNAc. In some organisms, ChBP may be involved in the production of GlcNac-6-phosphate in intracellular pathways. 300 matched cddid_all.tbl CDD cd11756 cd11756 213072 GH94N_ChvB_NdvB_1_like First GH94N domain of cyclic beta 1-2 glucan synthetase and similar domains. The glycoside hydrolase family 94 (previously known as glycosyltransferase family 36) includes cyclic beta 1-2 glucan synthetase (EC:2.4.1.20) or ChvB (encoded by the chromosomal chvB virulence gene). This first of two tandemly repeated GH94-N-terminal-like domains has not been characterized functionally. Some beta 1-2 glucan synthetases are annotated as NdvB (nodule development B) gene products, glycosyltransferases required for the synthesis of cyclic beta-(1,2)-glucans, which play a role in interactions between bacteria and plants. 284 matched cddid_all.tbl CDD cd11757 cd11757 212691 SH3_SH3BP4 Src Homology 3 domain of SH3 domain-binding protein 4. SH3 domain-binding protein 4 (SH3BP4) is also called transferrin receptor trafficking protein (TTP). SH3BP4 is an endocytic accessory protein that interacts with endocytic proteins including clathrin and dynamin, and regulates the internalization of the transferrin receptor (TfR). SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11758 cd11758 212692 SH3_CRK_N N-terminal Src Homology 3 domain of Ct10 Regulator of Kinase adaptor proteins. CRK adaptor proteins consists of SH2 and SH3 domains, which bind tyrosine-phosphorylated peptides and proline-rich motifs, respectively. They function downstream of protein tyrosine kinases in many signaling pathways started by various extracellular signals, including growth and differentiation factors. Cellular CRK (c-CRK) contains a single SH2 domain, followed by N-terminal and C-terminal SH3 domains. It is involved in the regulation of many cellular processes including cell growth, motility, adhesion, and apoptosis. CRK has been implicated in the malignancy of various human cancers. The N-terminal SH3 domain of CRK binds a number of target proteins including DOCK180, C3G, SOS, and cABL. The CRK family includes two alternatively spliced protein forms, CRKI and CRKII, that are expressed by the CRK gene, and the CRK-like (CRKL) protein, which is expressed by a distinct gene (CRKL). SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11759 cd11759 212693 SH3_CRK_C C-terminal Src Homology 3 domain of Ct10 Regulator of Kinase adaptor proteins. CRK adaptor proteins consists of SH2 and SH3 domains, which bind tyrosine-phosphorylated peptides and proline-rich motifs, respectively. They function downstream of protein tyrosine kinases in many signaling pathways started by various extracellular signals, including growth and differentiation factors. Cellular CRK (c-CRK) contains a single SH2 domain, followed by N-terminal and C-terminal SH3 domains. It is involved in the regulation of many cellular processes including cell growth, motility, adhesion, and apoptosis. CRK has been implicated in the malignancy of various human cancers. The C-terminal SH3 domain of CRK has not been shown to bind any target protein; it acts as a negative regulator of CRK function by stabilizing a structure that inhibits the access by target proteins to the N-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11760 cd11760 212694 SH3_MIA_like Src Homology 3 domain of Melanoma Inhibitory Activity protein and similar proteins. MIA is a single domain protein that adopts a SH3 domain-like fold; it contains an additional antiparallel beta sheet and two disulfide bonds compared to classical SH3 domains. MIA is secreted from malignant melanoma cells and it plays an important role in melanoma development and invasion. MIA is expressed by chondrocytes in normal tissues and may be important in the cartilage cell phenotype. Unlike classical SH3 domains, MIA does not bind proline-rich ligands. MIA is a member of the recently identified family that also includes MIA-like (MIAL), MIA2, and MIA3 (also called TANGO); the biological functions of this family are not yet fully understood. 76 matched cddid_all.tbl CDD cd11761 cd11761 212695 SH3_FCHSD_1 First Src Homology 3 domain of FCH and double SH3 domains proteins. This group is composed of FCH and double SH3 domains protein 1 (FCHSD1) and FCHSD2. These proteins have a common domain structure consisting of an N-terminal F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs), two SH3, and C-terminal proline-rich domains. They have only been characterized in silico and their functions remain unknown. This group also includes the insect protein, nervous wreck, which acts as a regulator of synaptic growth signaling. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11762 cd11762 212696 SH3_FCHSD_2 Second Src Homology 3 domain of FCH and double SH3 domains proteins. This group is composed of FCH and double SH3 domains protein 1 (FCHSD1) and FCHSD2. These proteins have a common domain structure consisting of an N-terminal F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs), two SH3, and C-terminal proline-rich domains. They have only been characterized in silico and their functions remain unknown. This group also includes the insect protein, nervous wreck, which acts as a regulator of synaptic growth signaling. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11763 cd11763 212697 SH3_SNX9_like Src Homology 3 domain of Sorting Nexin 9 and similar proteins. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. This subfamily consists of SH3 domain containing SNXs including SNX9, SNX18, SNX33, and similar proteins. SNX9 is localized to plasma membrane endocytic sites and acts primarily in clathrin-mediated endocytosis, while SNX18 is localized to peripheral endosomal structures, and acts in a trafficking pathway that is clathrin-independent but relies on AP-1 and PACS1. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11764 cd11764 212698 SH3_Eps8 Src Homology 3 domain of Epidermal growth factor receptor kinase substrate 8 and similar proteins. This group is composed of Eps8 and Eps8-like proteins including Eps8-like 1-3, among others. These proteins contain N-terminal Phosphotyrosine-binding (PTB), central SH3, and C-terminal effector domains. Eps8 binds either Abi1 (also called E3b1) or Rab5 GTPase activating protein RN-tre through its SH3 domain. With Abi1 and Sos1, it becomes part of a trimeric complex that is required to activate Rac. Together with RN-tre, it inhibits the internalization of EGFR. The SH3 domains of Eps8 and similar proteins recognize peptides containing a PxxDY motif, instead of the classical PxxP motif. SH3 domains are protein interaction domains that usually bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11765 cd11765 212699 SH3_Nck_1 First Src Homology 3 domain of Nck adaptor proteins. Nck adaptor proteins regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates. They contain three SH3 domains and a C-terminal SH2 domain. They function downstream of the PDGFbeta receptor and are involved in Rho GTPase signaling and actin dynamics. Vertebrates contain two Nck adaptor proteins: Nck1 (also called Nckalpha) and Nck2 (also called Nckbeta or Growth factor receptor-bound protein 4, Grb4), which show partly overlapping functions but also bind distinct targets. Their SH3 domains are involved in recruiting downstream effector molecules, such as the N-WASP/Arp2/3 complex, which when activated induces actin polymerization that results in the production of pedestals, or protrusions of the plasma membrane. The first SH3 domain of Nck proteins preferentially binds the PxxDY sequence, which is present in the CD3e cytoplasmic tail. This binding inhibits phosphorylation by Src kinases, resulting in the downregulation of TCR surface expression. SH3 domains are protein interaction domains that usually bind to proline-rich ligands with moderate affinity and selectivity, preferentially a PxxP motif. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 51 matched cddid_all.tbl CDD cd11766 cd11766 212700 SH3_Nck_2 Second Src Homology 3 domain of Nck adaptor proteins. Nck adaptor proteins regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates. They contain three SH3 domains and a C-terminal SH2 domain. They function downstream of the PDGFbeta receptor and are involved in Rho GTPase signaling and actin dynamics. Vertebrates contain two Nck adaptor proteins: Nck1 (also called Nckalpha) and Nck2 (also called Nckbeta or Growth factor receptor-bound protein 4, Grb4), which show partly overlapping functions but also bind distinct targets. Their SH3 domains are involved in recruiting downstream effector molecules, such as the N-WASP/Arp2/3 complex, which when activated induces actin polymerization that results in the production of pedestals, or protrusions of the plasma membrane. The second SH3 domain of Nck appears to prefer ligands containing the APxxPxR motif. SH3 domains are protein interaction domains that usually bind to proline-rich ligands with moderate affinity and selectivity, preferentially a PxxP motif. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11767 cd11767 212701 SH3_Nck_3 Third Src Homology 3 domain of Nck adaptor proteins. This group contains the third SH3 domain of Nck, the first SH3 domain of Caenorhabditis elegans Ced-2 (Cell death abnormality protein 2), and similar domains. Nck adaptor proteins regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates. They contain three SH3 domains and a C-terminal SH2 domain. They function downstream of the PDGFbeta receptor and are involved in Rho GTPase signaling and actin dynamics. Vertebrates contain two Nck adaptor proteins: Nck1 (also called Nckalpha) and Nck2 (also called Nckbeta or Growth factor receptor-bound protein 4, Grb4), which show partly overlapping functions but also bind distinct targets. Their SH3 domains are involved in recruiting downstream effector molecules, such as the N-WASP/Arp2/3 complex, which when activated induces actin polymerization that results in the production of pedestals, or protrusions of the plasma membrane. The third SH3 domain of Nck appears to prefer ligands with a PxAPxR motif. SH3 domains are protein interaction domains that usually bind to proline-rich ligands with moderate affinity and selectivity, preferentially a PxxP motif. Ced-2 is a cell corpse engulfment protein that interacts with Ced-5 in a pathway that regulates the activation of Ced-10, a Rac small GTPase. 56 matched cddid_all.tbl CDD cd11768 cd11768 212702 SH3_Tec_like Src Homology 3 domain of Tec-like Protein Tyrosine Kinases. The Tec (Tyrosine kinase expressed in hepatocellular carcinoma) subfamily is composed of Tec, Btk, Bmx (Etk), Itk (Tsk, Emt), Rlk (Txk), and similar proteins. They are cytoplasmic (or nonreceptor) tyr kinases containing Src homology protein interaction domains (SH3, SH2) N-terminal to the catalytic tyr kinase domain. Most Tec subfamily members (except Rlk) also contain an N-terminal pleckstrin homology (PH) domain, which binds the products of PI3K and allows membrane recruitment and activation. In addition, some members contain the Tec homology (TH) domain, which contains proline-rich and zinc-binding regions. Tec kinases are expressed mainly by haematopoietic cells, although Tec and Bmx are also found in endothelial cells. B-cells express Btk and Tec, while T-cells express Itk, Txk, and Tec. Collectively, Tec kinases are expressed in a variety of myeloid cells such as mast cells, platelets, macrophages, and dendritic cells. Each Tec kinase shows a distinct cell-type pattern of expression. The function of Tec kinases in lymphoid cells have been studied extensively. They play important roles in the development, differentiation, maturation, regulation, survival, and function of B-cells and T-cells. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11769 cd11769 212703 SH3_CSK Src Homology 3 domain of C-terminal Src kinase. CSK is a cytoplasmic (or nonreceptor) tyr kinase containing the Src homology domains, SH3 and SH2, N-terminal to the catalytic tyr kinase domain. They negatively regulate the activity of Src kinases that are anchored to the plasma membrane. To inhibit Src kinases, CSK is translocated to the membrane via binding to specific transmembrane proteins, G-proteins, or adaptor proteins near the membrane. CSK catalyzes the tyr phosphorylation of the regulatory C-terminal tail of Src kinases, resulting in their inactivation. It is expressed in a wide variety of tissues and plays a role, as a regulator of Src, in cell proliferation, survival, and differentiation, and consequently, in cancer development and progression. In addition, CSK also shows Src-independent functions. It is a critical component in G-protein signaling, and plays a role in cytoskeletal reorganization and cell migration. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11770 cd11770 212704 SH3_Nephrocystin Src Homology 3 domain of Nephrocystin (or Nephrocystin-1). Nephrocystin contains an SH3 domain involved in signaling pathways that regulate cell adhesion and cytoskeletal organization. It is a protein that in humans is associated with juvenile nephronophthisis, an inherited kidney disease characterized by renal fibrosis that lead to chronic renal failure in children. It is localized in cell-cell junctions in renal duct cells, and is known to interact with Ack1, an activated Cdc42-associated kinase. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11771 cd11771 212705 SH3_Pex13p_fungal Src Homology 3 domain of fungal peroxisomal membrane protein Pex13p. Pex13p, located in the peroxisomal membrane, contains two transmembrane regions and a C-terminal SH3 domain. It binds to the peroxisomal targeting type I (PTS1) receptor Pex5p and the docking factor Pex14p through its SH3 domain. It is essential for both PTS1 and PTS2 protein import pathways into the peroxisomal matrix. Pex13p binds Pex14p, which contains a PxxP motif, in a classical fashion to the proline-rich ligand binding site of its SH3 domain. It binds the WxxxF/Y motif of Pex5p in a novel site that does not compete with Pex14p binding. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 60 matched cddid_all.tbl CDD cd11772 cd11772 212706 SH3_OSTF1 Src Homology 3 domain of metazoan osteoclast stimulating factor 1. OSTF1, also named OSF or SH3P2, is a signaling protein containing SH3 and ankyrin-repeat domains. It acts through a Src-related pathway to enhance the formation of osteoclasts and bone resorption. It also acts as a negative regulator of cell motility. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11773 cd11773 212707 SH3_Sla1p_1 First Src Homology 3 domain of the fungal endocytic adaptor protein Sla1p. Sla1p facilitates endocytosis by playing a role as an adaptor protein in coupling components of the actin cytoskeleton to the endocytic machinery. It interacts with Abp1p, Las17p and Pan1p, which are activator proteins of actin-related protein 2/3 (Arp2/3). Sla1p contains multiple domains including three SH3 domains, a SAM (sterile alpha motif) domain, and a Sla1 homology domain 1 (SHD1), which binds to the NPFXD motif that is found in many integral membrane proteins such as the Golgi-localized Arf-binding protein Lsb5p and the P4-ATPases, Drs2p and Dnf1p. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11774 cd11774 212708 SH3_Sla1p_2 Second Src Homology 3 domain of the fungal endocytic adaptor protein Sla1p. Sla1p facilitates endocytosis by playing a role as an adaptor protein in coupling components of the actin cytoskeleton to the endocytic machinery. It interacts with Abp1p, Las17p and Pan1p, which are activator proteins of actin-related protein 2/3 (Arp2/3). Sla1p contains multiple domains including three SH3 domains, a SAM (sterile alpha motif) domain, and a Sla1 homology domain 1 (SHD1), which binds to the NPFXD motif that is found in many integral membrane proteins such as the Golgi-localized Arf-binding protein Lsb5p and the P4-ATPases, Drs2p and Dnf1p. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11775 cd11775 212709 SH3_Sla1p_3 Third Src Homology 3 domain of the fungal endocytic adaptor protein Sla1p. Sla1p facilitates endocytosis by playing a role as an adaptor protein in coupling components of the actin cytoskeleton to the endocytic machinery. It interacts with Abp1p, Las17p and Pan1p, which are activator proteins of actin-related protein 2/3 (Arp2/3). Sla1p contains multiple domains including three SH3 domains, a SAM (sterile alpha motif) domain, and a Sla1 homology domain 1 (SHD1), which binds to the NPFXD motif that is found in many integral membrane proteins such as the Golgi-localized Arf-binding protein Lsb5p and the P4-ATPases, Drs2p and Dnf1p. The third SH3 domain of Sla1p can bind ubiquitin while retaining the ability to bind proline-rich ligands; monoubiquitination of target proteins signals internalization and sorting through the endocytic pathway. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11776 cd11776 212710 SH3_PI3K_p85 Src Homology 3 domain of the p85 regulatory subunit of Class IA Phosphatidylinositol 3-kinases. Class I PI3Ks convert PtdIns(4,5)P2 to the critical second messenger PtdIns(3,4,5)P3. They are heterodimers and exist in multiple isoforms consisting of one catalytic subunit (out of four isoforms) and one of several regulatory subunits. Class IA PI3Ks associate with the p85 regulatory subunit family, which contains SH3, RhoGAP, and SH2 domains. The p85 subunits recruit the PI3K p110 catalytic subunit to the membrane, where p110 phosphorylates inositol lipids. Vertebrates harbor two p85 isoforms, called alpha and beta. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 72 matched cddid_all.tbl CDD cd11777 cd11777 212711 SH3_CIP4_Bzz1_like Src Homology 3 domain of Cdc42-Interacting Protein 4, Bzz1 and similar domains. This subfamily is composed of Cdc42-Interacting Protein 4 (CIP4) and similar proteins such as Formin Binding Protein 17 (FBP17) and FormiN Binding Protein 1-Like (FNBP1L), as well as yeast Bzz1 (or Bzz1p). CIP4 and FNBP1L are Cdc42 effectors that bind Wiskott-Aldrich syndrome protein (WASP) and function in endocytosis. CIP4 and FBP17 bind to the Fas ligand and may be implicated in the inflammatory response. CIP4 may also play a role in phagocytosis. Bzz1 is also a WASP/Las17-interacting protein involved in endocytosis and trafficking to the vacuole. It physically interacts with type I myosins and functions in the early steps of endocytosis. Members of this subfamily contain an N-terminal F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain as well as at least one C-terminal SH3 domain. Bzz1 contains a second SH3 domain at the C-terminus. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11778 cd11778 212712 SH3_Bzz1_2 Second Src Homology 3 domain of Bzz1 and similar domains. Bzz1 (or Bzz1p) is a WASP/Las17-interacting protein involved in endocytosis and trafficking to the vacuole. It physically interacts with type I myosins and functions in the early steps of endocytosis. Together with other proteins, it induces membrane scission in yeast. Bzz1 contains an N-terminal F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs), a central coiled-coil, and two C-terminal SH3 domains. This model represents the second C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 51 matched cddid_all.tbl CDD cd11779 cd11779 212713 SH3_Irsp53_BAIAP2L Src Homology 3 domain of Insulin Receptor tyrosine kinase Substrate p53, Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2 (BAIAP2)-Like proteins, and similar proteins. Proteins in this family include IRSp53, BAIAP2L1, BAIAP2L2, and similar proteins. They all contain an Inverse-Bin/Amphiphysin/Rvs (I-BAR) or IMD domain in addition to the SH3 domain. IRSp53, also known as BAIAP2, is a scaffolding protein that takes part in many signaling pathways including Cdc42-induced filopodia formation, Rac-mediated lamellipodia extension, and spine morphogenesis. IRSp53 exists as multiple splicing variants that differ mainly at the C-termini. BAIAP2L1, also called IRTKS (Insulin Receptor Tyrosine Kinase Substrate), serves as a substrate for the insulin receptor and binds the small GTPase Rac. It plays a role in regulating the actin cytoskeleton and colocalizes with F-actin, cortactin, VASP, and vinculin. IRSp53 and IRTKS also mediate the recruitment of effector proteins Tir and EspFu, which regulate host cell actin reorganization, to bacterial attachment sites. BAIAP2L2 co-localizes with clathrin plaques but its function has not been determined. The SH3 domains of IRSp53 and IRTKS have been shown to bind the proline-rich C-terminus of EspFu. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11780 cd11780 212714 SH3_Sorbs_3 Third (or C-terminal) Src Homology 3 domain of Sorbin and SH3 domain containing (Sorbs) proteins and similar domains. This family, also called the vinexin family, is composed predominantly of adaptor proteins containing one sorbin homology (SoHo) and three SH3 domains. Members include the third SH3 domains of Sorbs1 (or ponsin), Sorbs2 (or ArgBP2), Vinexin (or Sorbs3), and similar domains. They are involved in the regulation of cytoskeletal organization, cell adhesion, and growth factor signaling. Members of this family bind multiple partners including signaling molecules like c-Abl, c-Arg, Sos, and c-Cbl, as well as cytoskeletal molecules such as vinculin and afadin. They may have overlapping functions. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11781 cd11781 212715 SH3_Sorbs_1 First Src Homology 3 domain of Sorbin and SH3 domain containing (Sorbs) proteins and similar domains. This family, also called the vinexin family, is composed predominantly of adaptor proteins containing one sorbin homology (SoHo) and three SH3 domains. Members include the first SH3 domains of Sorbs1 (or ponsin), Sorbs2 (or ArgBP2), Vinexin (or Sorbs3), and similar domains. They are involved in the regulation of cytoskeletal organization, cell adhesion, and growth factor signaling. Members of this family bind multiple partners including signaling molecules like c-Abl, c-Arg, Sos, and c-Cbl, as well as cytoskeletal molecules such as vinculin and afadin. They may have overlapping functions. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11782 cd11782 212716 SH3_Sorbs_2 Second Src Homology 3 domain of Sorbin and SH3 domain containing (Sorbs) proteins and similar domains. This family, also called the vinexin family, is composed predominantly of adaptor proteins containing one sorbin homology (SoHo) and three SH3 domains. Members include the second SH3 domains of Sorbs1 (or ponsin), Sorbs2 (or ArgBP2), Vinexin (or Sorbs3), and similar domains. They are involved in the regulation of cytoskeletal organization, cell adhesion, and growth factor signaling. Members of this family bind multiple partners including signaling molecules like c-Abl, c-Arg, Sos, and c-Cbl, as well as cytoskeletal molecules such as vinculin and afadin. They may have overlapping functions. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11783 cd11783 212717 SH3_SH3RF_3 Third Src Homology 3 domain of SH3 domain containing ring finger 1 (SH3RF1), SH3RF3, and similar domains. SH3RF1 (or POSH) and SH3RF3 (or POSH2) are scaffold proteins that function as E3 ubiquitin-protein ligases. They contain an N-terminal RING finger domain and four SH3 domains. This model represents the third SH3 domain, located in the middle of SH3RF1 and SH3RF3, and similar domains. SH3RF1 plays a role in calcium homeostasis through the control of the ubiquitin domain protein Herp. It may also have a role in regulating death receptor mediated and JNK mediated apoptosis. SH3RF3 interacts with p21-activated kinase 2 (PAK2) and GTP-loaded Rac1. It may play a role in regulating JNK mediated apoptosis in certain conditions. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11784 cd11784 212718 SH3_SH3RF2_3 Third Src Homology 3 domain of SH3 domain containing ring finger 2. SH3RF2 is also called POSHER (POSH-eliminating RING protein) or HEPP1 (heart protein phosphatase 1-binding protein). It acts as an anti-apoptotic regulator of the JNK pathway by binding to and promoting the degradation of SH3RF1 (or POSH), a scaffold protein that is required for pro-apoptotic JNK activation. It may also play a role in cardiac functions together with protein phosphatase 1. SH3RF2 contains an N-terminal RING finger domain and three SH3 domains. This model represents the third SH3 domain, located in the middle, of SH3RF2. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11785 cd11785 212719 SH3_SH3RF_C C-terminal (Fourth) Src Homology 3 domain of SH3 domain containing ring finger 1 (SH3RF1), SH3RF3, and similar domains. SH3RF1 (or POSH) and SH3RF3 (or POSH2) are scaffold proteins that function as E3 ubiquitin-protein ligases. They contain an N-terminal RING finger domain and four SH3 domains. This model represents the fourth SH3 domain, located at the C-terminus of SH3RF1 and SH3RF3, and similar domains. SH3RF1 plays a role in calcium homeostasis through the control of the ubiquitin domain protein Herp. It may also have a role in regulating death receptor mediated and JNK mediated apoptosis. SH3RF3 interacts with p21-activated kinase 2 (PAK2) and GTP-loaded Rac1. It may play a role in regulating JNK mediated apoptosis in certain conditions. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11786 cd11786 212720 SH3_SH3RF_1 First Src Homology 3 domain of SH3 domain containing ring finger proteins. This model represents the first SH3 domain of SH3RF1 (or POSH), SH3RF2 (or POSHER), SH3RF3 (POSH2), and similar domains. Members of this family are scaffold proteins that function as E3 ubiquitin-protein ligases. They all contain an N-terminal RING finger domain and multiple SH3 domains; SH3RF1 and SH3RF3 have four SH3 domains while SH3RF2 has three. SH3RF1 plays a role in calcium homeostasis through the control of the ubiquitin domain protein Herp. It may also have a role in regulating death receptor mediated and JNK mediated apoptosis. SH3RF3 interacts with p21-activated kinase 2 (PAK2) and GTP-loaded Rac1. It may play a role in regulating JNK mediated apoptosis in certain conditions. SH3RF2 acts as an anti-apoptotic regulator of the JNK pathway by binding to and promoting the degradation of SH3RF1. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11787 cd11787 212721 SH3_SH3RF_2 Second Src Homology 3 domain of SH3 domain containing ring finger proteins. This model represents the second SH3 domain of SH3RF1 (or POSH), SH3RF2 (or POSHER), SH3RF3 (POSH2), and similar domains. Members of this family are scaffold proteins that function as E3 ubiquitin-protein ligases. They all contain an N-terminal RING finger domain and multiple SH3 domains; SH3RF1 and SH3RF3 have four SH3 domains while SH3RF2 has three. SH3RF1 plays a role in calcium homeostasis through the control of the ubiquitin domain protein Herp. It may also have a role in regulating death receptor mediated and JNK mediated apoptosis. SH3RF3 interacts with p21-activated kinase 2 (PAK2) and GTP-loaded Rac1. It may play a role in regulating JNK mediated apoptosis in certain conditions. SH3RF2 acts as an anti-apoptotic regulator of the JNK pathway by binding to and promoting the degradation of SH3RF1. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11788 cd11788 212722 SH3_RasGAP Src Homology 3 domain of Ras GTPase-Activating Protein 1. RasGAP, also called Ras p21 protein activator, RASA1, or p120RasGAP, is part of the GAP1 family of GTPase-activating proteins. It is a 120kD cytosolic protein containing an SH3 domain flanked by two SH2 domains at the N-terminal end, a pleckstrin homology (PH) domain, a calcium dependent phospholipid binding domain (CaLB/C2), and a C-terminal catalytic GAP domain. It stimulates the GTPase activity of normal RAS p21. It acts as a positive effector of Ras in tumor cells. It also functions as a regulator downstream of tyrosine receptors such as those of PDGF, EGF, ephrin, and insulin, among others. The SH3 domain of RasGAP is unable to bind proline-rich sequences but have been shown to interact with protein partners such as the G3BP protein, Aurora kinases, and the Calpain small subunit 1. The RasGAP SH3 domain is necessary for the downstream signaling of Ras and it also influences Rho-mediated cytoskeletal reorganization. SH3 domains are protein interaction domains that typically bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 59 matched cddid_all.tbl CDD cd11789 cd11789 212723 SH3_Nebulin_family_C C-terminal Src Homology 3 domain of the Nebulin family of proteins. Nebulin family proteins contain multiple nebulin repeats, and may contain an N-terminal LIM domain and/or a C-terminal SH3 domain. They have molecular weights ranging from 34 to 900 kD, depending on the number of nebulin repeats, and they all bind actin. They are involved in the regulation of actin filament architecture and function as stabilizers and scaffolds for cytoskeletal structures with which they associate, such as long actin filaments or focal adhesions. Nebulin family proteins that contain a C-terminal SH3 domain include the giant filamentous protein nebulin, nebulette, Lasp1, and Lasp2. Lasp2, also called LIM-nebulette, is an alternatively spliced variant of nebulette. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11790 cd11790 212724 SH3_Amphiphysin Src Homology 3 domain of Amphiphysin and related domains. Amphiphysins function primarily in endocytosis and other membrane remodeling events. They exist in several isoforms and mammals possess two amphiphysin proteins from distinct genes. Amphiphysin I proteins, enriched in the brain and nervous system, contain domains that bind clathrin, Adaptor Protein complex 2 (AP2), dynamin, and synaptojanin. They function in synaptic vesicle endocytosis. Human autoantibodies to amphiphysin I hinder GABAergic signaling and contribute to the pathogenesis of paraneoplastic stiff-person syndrome. Some amphiphysin II isoforms, also called Bridging integrator 1 (Bin1), are localized in many different tissues and may function in intracellular vesicle trafficking. In skeletal muscle, Bin1 plays a role in the organization and maintenance of the T-tubule network. Mutations in Bin1 are associated with autosomal recessive centronuclear myopathy. Amphiphysins contain an N-terminal BAR domain with an additional N-terminal amphipathic helix (an N-BAR), a variable central domain, and a C-terminal SH3 domain. The SH3 domain of amphiphysins bind proline-rich motifs present in binding partners such as dynamin, synaptojanin, and nsP3. It also belongs to a subset of SH3 domains that bind ubiquitin in a site that overlaps with the peptide binding site. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 64 matched cddid_all.tbl CDD cd11791 cd11791 212725 SH3_UBASH3 Src homology 3 domain of Ubiquitin-associated and SH3 domain-containing proteins, also called TULA (T cell Ubiquitin LigAnd) family of proteins. UBASH3 or TULA proteins are also referred to as Suppressor of T cell receptor Signaling (STS) proteins. They contain an N-terminal UBA domain, a central SH3 domain, and a C-terminal histidine phosphatase domain. They bind c-Cbl through the SH3 domain and to ubiquitin via UBA. In some vertebrates, there are two TULA family proteins, called UBASH3A (also called TULA or STS-2) and UBASH3B (also called TULA-2 or STS-1), which show partly overlapping as well as distinct functions. UBASH3B is widely expressed while UBASH3A is only found in lymphoid cells. UBASH3A facilitates apoptosis induced in T cells through its interaction with the apoptosis-inducing factor AIF. UBASH3B is an active phosphatase while UBASH3A is not. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 59 matched cddid_all.tbl CDD cd11792 cd11792 212726 SH3_Fut8 Src homology 3 domain of Alpha1,6-fucosyltransferase (Fut8). Fut8 catalyzes the alpha1,6-linkage of a fucose residue from a donor substrate to N-linked oligosaccharides on glycoproteins in a process called core fucosylation, which is crucial for growth factor receptor-mediated biological functions. Fut8-deficient mice show severe growth retardation, early death, and a pulmonary emphysema-like phenotype. Fut8 is also implicated to play roles in aging and cancer metastasis. It contains an N-terminal coiled-coil domain, a catalytic domain, and a C-terminal SH3 domain. The SH3 domain of Fut8 is located in the lumen and its role in glycosyl transfer is unclear. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11793 cd11793 212727 SH3_ephexin1_like Src homology 3 domain of ephexin-1-like SH3 domain containing Rho guanine nucleotide exchange factors. Members of this family contain RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), and C-terminal SH3 domains. They include the Rho guanine nucleotide exchange factors ARHGEF5, ARHGEF16, ARHGEF19, ARHGEF26, ARHGEF27 (also called ephexin-1), and similar proteins, and are also called ephexins because they interact directly with ephrin A receptors. GEFs interact with Rho GTPases via their DH domains to catalyze nucleotide exchange by stabilizing the nucleotide-free GTPase intermediate. They play important roles in neuronal development. The SH3 domains of ARHGEFs play an autoinhibitory role through intramolecular interactions with a proline-rich region N-terminal to the DH domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11794 cd11794 212728 SH3_DNMBP_N1 First N-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba. DNMBP or Tuba is a cdc42-specific guanine nucleotide exchange factor (GEF) that contains four N-terminal SH3 domains, a central RhoGEF [or Dbl homology (DH)] domain followed by a Bin/Amphiphysin/Rvs (BAR) domain, and two C-terminal SH3 domains. It provides a functional link between dynamin and key regulatory proteins of the actin cytoskeleton. It plays an important role in regulating cell junction configuration. The four N-terminal SH3 domains of DNMBP binds the GTPase dynamin, which plays an important role in the fission of endocytic vesicles. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 51 matched cddid_all.tbl CDD cd11795 cd11795 212729 SH3_DNMBP_N2 Second N-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba. DNMBP or Tuba is a cdc42-specific guanine nucleotide exchange factor (GEF) that contains four N-terminal SH3 domains, a central RhoGEF [or Dbl homology (DH)] domain followed by a Bin/Amphiphysin/Rvs (BAR) domain, and two C-terminal SH3 domains. It provides a functional link between dynamin and key regulatory proteins of the actin cytoskeleton. It plays an important role in regulating cell junction configuration. The four N-terminal SH3 domains of DNMBP binds the GTPase dynamin, which plays an important role in the fission of endocytic vesicles. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11796 cd11796 212730 SH3_DNMBP_N3 Third N-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba. DNMBP or Tuba is a cdc42-specific guanine nucleotide exchange factor (GEF) that contains four N-terminal SH3 domains, a central RhoGEF [or Dbl homology (DH)] domain followed by a Bin/Amphiphysin/Rvs (BAR) domain, and two C-terminal SH3 domains. It provides a functional link between dynamin and key regulatory proteins of the actin cytoskeleton. It plays an important role in regulating cell junction configuration. The four N-terminal SH3 domains of DNMBP binds the GTPase dynamin, which plays an important role in the fission of endocytic vesicles. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 51 matched cddid_all.tbl CDD cd11797 cd11797 212731 SH3_DNMBP_N4 Fourth N-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba. DNMBP or Tuba is a cdc42-specific guanine nucleotide exchange factor (GEF) that contains four N-terminal SH3 domains, a central RhoGEF [or Dbl homology (DH)] domain followed by a Bin/Amphiphysin/Rvs (BAR) domain, and two C-terminal SH3 domains. It provides a functional link between dynamin and key regulatory proteins of the actin cytoskeleton. It plays an important role in regulating cell junction configuration. The four N-terminal SH3 domains of DNMBP bind the GTPase dynamin, which plays an important role in the fission of endocytic vesicles. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 50 matched cddid_all.tbl CDD cd11798 cd11798 212732 SH3_DNMBP_C1 First C-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba. DNMBP or Tuba is a cdc42-specific guanine nucleotide exchange factor (GEF) that contains four N-terminal SH3 domains, a central RhoGEF [or Dbl homology (DH)] domain followed by a Bin/Amphiphysin/Rvs (BAR) domain, and two C-terminal SH3 domains. It provides a functional link between dynamin, Rho GTPase signaling, and actin dynamics. It plays an important role in regulating cell junction configuration. The C-terminal SH3 domains of DNMBP bind to N-WASP and Ena/VASP proteins, which are key regulatory proteins of the actin cytoskeleton. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11799 cd11799 212733 SH3_ARHGEF37_C1 First C-terminal Src homology 3 domain of Rho guanine nucleotide exchange factor 37. ARHGEF37 contains a RhoGEF [or Dbl homology (DH)] domain followed by a Bin/Amphiphysin/Rvs (BAR) domain, and two C-terminal SH3 domains. Its specific function is unknown. Its domain architecture is similar to the C-terminal half of DNMBP or Tuba, a cdc42-specific GEF that provides a functional link between dynamin, Rho GTPase signaling, and actin dynamics, and plays an important role in regulating cell junction configuration. GEFs activate small GTPases by exchanging bound GDP for free GTP. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11800 cd11800 212734 SH3_DNMBP_C2_like Second C-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba, and similar domains. DNMBP or Tuba is a cdc42-specific guanine nucleotide exchange factor (GEF) that contains four N-terminal SH3 domains, a central RhoGEF [or Dbl homology (DH)] domain followed by a Bin/Amphiphysin/Rvs (BAR) domain, and two C-terminal SH3 domains. It provides a functional link between dynamin, Rho GTPase signaling, and actin dynamics. It plays an important role in regulating cell junction configuration. The C-terminal SH3 domains of DNMBP bind to N-WASP and Ena/VASP proteins, which are key regulatory proteins of the actin cytoskeleton. Also included in this subfamily is the second C-terminal SH3 domain of Rho guanine nucleotide exchange factor 37 (ARHGEF37), whose function is still unknown. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11801 cd11801 212735 SH3_JIP1_like Src homology 3 domain of JNK-interacting proteins 1 and 2, and similar domains. JNK-interacting proteins (JIPs) function as scaffolding proteins for c-Jun N-terminal kinase (JNK) signaling pathways. They bind to components of Mitogen-activated protein kinase (MAPK) pathways such as JNK, MKK, and several MAP3Ks such as MLK and DLK. There are four JIPs (JIP1-4); all contain a JNK binding domain. JIP1 and JIP2 also contain SH3 and Phosphotyrosine-binding (PTB) domains. Both are highly expressed in the brain and pancreatic beta-cells. JIP1 functions as an adaptor linking motor to cargo during axonal transport and also is involved in regulating insulin secretion. JIP2 form complexes with fibroblast growth factor homologous factors (FHFs), which facilitates activation of the p38delta MAPK. The SH3 domain of JIP1 homodimerizes at the interface usually involved in proline-rich ligand recognition, despite the lack of this motif in the domain itself. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11802 cd11802 212736 SH3_Endophilin_B Src homology 3 domain of Endophilin-B. Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. They are classified into two types, A and B. Vertebrates contain two endophilin-B isoforms. Endophilin-B proteins are cytoplasmic proteins expressed mainly in the heart, placenta, and skeletal muscle. Endophilins contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11803 cd11803 212737 SH3_Endophilin_A Src homology 3 domain of Endophilin-A. Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. They are classified into two types, A and B. Vertebrates contain three endophilin-A isoforms (A1, A2, and A3). Endophilin-A proteins are enriched in the brain and play multiple roles in receptor-mediated endocytosis. They tubulate membranes and regulate calcium influx into neurons to trigger the activation of the endocytic machinery. They are also involved in the sorting of plasma membrane proteins, actin filament assembly, and the uncoating of clathrin-coated vesicles for fusion with endosomes. Endophilins contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11804 cd11804 212738 SH3_GRB2_like_N N-terminal Src homology 3 domain of Growth factor receptor-bound protein 2 (GRB2) and related proteins. This family includes the adaptor protein GRB2 and related proteins including Drosophila melanogaster Downstream of receptor kinase (DRK), Caenorhabditis elegans Sex muscle abnormal protein 5 (Sem-5), GRB2-related adaptor protein (GRAP), GRAP2, and similar proteins. Family members contain an N-terminal SH3 domain, a central SH2 domain, and a C-terminal SH3 domain. GRB2/Sem-5/DRK is a critical signaling molecule that regulates the Ras pathway by linking tyrosine kinases to the Ras guanine nucleotide releasing protein Sos (son of sevenless), which converts Ras to the active GTP-bound state. GRAP2 plays an important role in T cell receptor (TCR) signaling by promoting the formation of the SLP-76:LAT complex, which couples the TCR to the Ras pathway. GRAP acts as a negative regulator of T cell receptor (TCR)-induced lymphocyte proliferation by downregulating the signaling to the Ras/ERK pathway. The N-terminal SH3 domain of GRB2 binds to Sos and Sos-derived proline-rich peptides. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11805 cd11805 212739 SH3_GRB2_like_C C-terminal Src homology 3 domain of Growth factor receptor-bound protein 2 (GRB2) and related proteins. This family includes the adaptor protein GRB2 and related proteins including Drosophila melanogaster Downstream of receptor kinase (DRK), Caenorhabditis elegans Sex muscle abnormal protein 5 (Sem-5), GRB2-related adaptor protein (GRAP), GRAP2, and similar proteins. Family members contain an N-terminal SH3 domain, a central SH2 domain, and a C-terminal SH3 domain. GRB2/Sem-5/DRK is a critical signaling molecule that regulates the Ras pathway by linking tyrosine kinases to the Ras guanine nucleotide releasing protein Sos (son of sevenless), which converts Ras to the active GTP-bound state. GRAP2 plays an important role in T cell receptor (TCR) signaling by promoting the formation of the SLP-76:LAT complex, which couples the TCR to the Ras pathway. GRAP acts as a negative regulator of T cell receptor (TCR)-induced lymphocyte proliferation by downregulating the signaling to the Ras/ERK pathway. The C-terminal SH3 domains (SH3c) of GRB2 and GRAP2 have been shown to bind to classical PxxP motif ligands, as well as to non-classical motifs. GRB2 SH3c binds Gab2 (Grb2-associated binder 2) through epitopes containing RxxK motifs, while the SH3c of GRAP2 binds to the phosphatase-like protein HD-PTP via a RxxxxK motif. SH3 domains are protein interaction domains that typically bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11806 cd11806 212740 SH3_PRMT2 Src homology 3 domain of Protein arginine N-methyltransferase 2. PRMT2, also called HRMT1L1, belongs to the arginine methyltransferase protein family. It functions as a coactivator to both estrogen receptor alpha (ER-alpha) and androgen receptor (AR), presumably through arginine methylation. The ER-alpha transcription factor is involved in cell proliferation, differentiation, morphogenesis, and apoptosis, and is also implicated in the development and progression of breast cancer. PRMT2 and its variants are upregulated in breast cancer cells and may be involved in modulating the ER-alpha signaling pathway during formation of breast cancer. PRMT2 also plays a role in regulating the function of E2F transcription factors, which are critical cell cycle regulators, by binding to the retinoblastoma gene product (RB). It contains an N-terminal SH3 domain and an AdoMet binding domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11807 cd11807 212741 SH3_ASPP Src homology 3 domain of Apoptosis Stimulating of p53 proteins (ASPP). The ASPP family of proteins bind to important regulators of apoptosis (p53, Bcl-2, and RelA) and cell growth (APCL, PP1). They share similarity at their C-termini, where they harbor a proline-rich region, four ankyrin (ANK) repeats, and an SH3 domain. Vertebrates contain three members of the family: ASPP1, ASPP2, and iASPP. ASPP1 and ASPP2 activate the apoptotic function of the p53 family of tumor suppressors (p53, p63, and p73), while iASPP is an oncoprotein that specifically inhibits p53-induced apoptosis. The expression of ASPP proteins is altered in tumors; ASPP1 and ASPP2 are downregulated whereas iASPP is upregulated is some cancer types. ASPP proteins also bind and regulate protein phosphatase 1 (PP1), and this binding is competitive with p53 binding. The SH3 domain and the ANK repeats of ASPP contribute to the p53 binding site; they bind to the DNA binding domain of p53. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11808 cd11808 212742 SH3_Alpha_Spectrin Src homology 3 domain of Alpha Spectrin. Spectrin is a major structural component of the red blood cell membrane skeleton and is important in erythropoiesis and membrane biogenesis. It is a flexible, rope-like molecule composed of two subunits, alpha and beta, which consist of many spectrin-type repeats. Alpha and beta spectrin associate to form heterodimers and tetramers; spectrin tetramer formation is critical for red cell shape and deformability. Defects in alpha spectrin have been associated with inherited hemolytic anemias including hereditary spherocytosis (HSp), hereditary elliptocytosis (HE), and hereditary pyropoikilocytosis (HPP). Alpha spectrin contains a middle SH3 domain and a C-terminal EF-hand binding motif in addition to multiple spectrin repeats. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11809 cd11809 212743 SH3_srGAP Src homology 3 domain of Slit-Robo GTPase Activating Proteins. Slit-Robo GTPase Activating Proteins (srGAPs) are Rho GAPs that interact with Robo1, the transmembrane receptor of Slit proteins. Slit proteins are secreted proteins that control axon guidance and the migration of neurons and leukocytes. Vertebrates contain three isoforms of srGAPs (srGAP1-3), all of which are expressed during embryonic and early development in the nervous system but with different localization and timing. A fourth member has also been reported (srGAP4, also called ARHGAP4). srGAPs contain an N-terminal F-BAR domain, a Rho GAP domain, and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11810 cd11810 212744 SH3_RUSC1_like Src homology 3 domain of RUN and SH3 domain-containing proteins 1 and 2. RUSC1 and RUSC2, that were originally characterized in silico. They are adaptor proteins consisting of RUN, leucine zipper, and SH3 domains. RUSC1, also called NESCA (New molecule containing SH3 at the carboxy-terminus), is highly expressed in the brain and is translocated to the nuclear membrane from the cytoplasm upon stimulation with neurotrophin. It plays a role in facilitating neurotrophin-dependent neurite outgrowth. It also interacts with NEMO (or IKKgamma) and may function in NEMO-mediated activation of NF-kB. RUSC2, also called Iporin, is expressed ubiquitously with highest amounts in the brain and testis. It interacts with the small GTPase Rab1 and the Golgi matrix protein GM130, and may function in linking GTPases to certain intracellular signaling pathways. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 50 matched cddid_all.tbl CDD cd11811 cd11811 212745 SH3_CHK Src Homology 3 domain of CSK homologous kinase. CHK is also referred to as megakaryocyte-associated tyrosine kinase (Matk). It inhibits Src kinases using a noncatalytic mechanism by simply binding to them. As a negative regulator of Src kinases, Chk may play important roles in cell proliferation, survival, and differentiation, and consequently, in cancer development and progression. To inhibit Src kinases that are anchored to the plasma membrane, CHK is translocated to the membrane via binding to specific transmembrane proteins, G-proteins, or adaptor proteins near the membrane. CHK also plays a role in neural differentiation in a manner independent of Src by enhancing MAPK activation via Ras-mediated signaling. It is a cytoplasmic (or nonreceptor) tyr kinase containing the Src homology domains, SH3 and SH2, N-terminal to the catalytic tyr kinase domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 59 matched cddid_all.tbl CDD cd11812 cd11812 212746 SH3_AHI-1 Src Homology 3 domain of Abelson helper integration site-1 (AHI-1). AHI-1, also called Jouberin, is expressed in high levels in the brain, gonad tissues, and skeletal muscle. It is an adaptor protein that interacts with the small GTPase Rab8a and regulates it distribution and function, affecting cilium formation and vesicle transport. Mutations in the AHI-1 gene can cause Joubert syndrome, a disorder characterized by brainstem malformations, cerebellar aplasia/hypoplasia, and retinal dystrophy. AHI-1 variation is also associated with susceptibility to schizophrenia and type 2 diabetes mellitus progression. AHI-1 contains WD40 and SH3 domains. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11813 cd11813 212747 SH3_SGSM3 Src Homology 3 domain of Small G protein Signaling Modulator 3. SGSM3 is also called Merlin-associated protein (MAP), RUN and SH3 domain-containing protein (RUSC3), RUN and TBC1 domain-containing protein 3 (RUTBC3), Rab GTPase-activating protein 5 (RabGAP5), or Rab GAP-like protein (RabGAPLP). It is expressed ubiquitously and functions as a regulator of small G protein RAP- and RAB-mediated neuronal signaling. It is involved in modulating NGF-mediated neurite outgrowth and differentiation. It also interacts with the tumor suppressor merlin and may play a role in the merlin-associated suppression of cell growth. SGSM3 contains TBC, SH3, and RUN domains. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11814 cd11814 212748 SH3_Eve1_1 First Src homology 3 domain of ADAM-binding protein Eve-1. Eve-1, also called SH3 domain-containing protein 19 (SH3D19) or EEN-binding protein (EBP), exists in multiple alternatively spliced isoforms. The longest isoform contains five SH3 domain in the C-terminal region and seven proline-rich motifs in the N-terminal region. It is abundantly expressed in skeletal muscle and heart, and may be involved in regulating the activity of ADAMs (A disintegrin and metalloproteases). Eve-1 interacts with EEN, an endophilin involved in endocytosis and may be the target of the MLL-EEN fusion protein that is implicated in leukemogenesis. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 50 matched cddid_all.tbl CDD cd11815 cd11815 212749 SH3_Eve1_2 Second Src homology 3 domain of ADAM-binding protein Eve-1. Eve-1, also called SH3 domain-containing protein 19 (SH3D19) or EEN-binding protein (EBP), exists in multiple alternatively spliced isoforms. The longest isoform contains five SH3 domain in the C-terminal region and seven proline-rich motifs in the N-terminal region. It is abundantly expressed in skeletal muscle and heart, and may be involved in regulating the activity of ADAMs (A disintegrin and metalloproteases). Eve-1 interacts with EEN, an endophilin involved in endocytosis and may be the target of the MLL-EEN fusion protein that is implicated in leukemogenesis. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11816 cd11816 212750 SH3_Eve1_3 Third Src homology 3 domain of ADAM-binding protein Eve-1. Eve-1, also called SH3 domain-containing protein 19 (SH3D19) or EEN-binding protein (EBP), exists in multiple alternatively spliced isoforms. The longest isoform contains five SH3 domain in the C-terminal region and seven proline-rich motifs in the N-terminal region. It is abundantly expressed in skeletal muscle and heart, and may be involved in regulating the activity of ADAMs (A disintegrin and metalloproteases). Eve-1 interacts with EEN, an endophilin involved in endocytosis and may be the target of the MLL-EEN fusion protein that is implicated in leukemogenesis. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 51 matched cddid_all.tbl CDD cd11817 cd11817 212751 SH3_Eve1_4 Fourth Src homology 3 domain of ADAM-binding protein Eve-1. Eve-1, also called SH3 domain-containing protein 19 (SH3D19) or EEN-binding protein (EBP), exists in multiple alternatively spliced isoforms. The longest isoform contains five SH3 domain in the C-terminal region and seven proline-rich motifs in the N-terminal region. It is abundantly expressed in skeletal muscle and heart, and may be involved in regulating the activity of ADAMs (A disintegrin and metalloproteases). Eve-1 interacts with EEN, an endophilin involved in endocytosis and may be the target of the MLL-EEN fusion protein that is implicated in leukemogenesis. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 50 matched cddid_all.tbl CDD cd11818 cd11818 212752 SH3_Eve1_5 Fifth Src homology 3 domain of ADAM-binding protein Eve-1. Eve-1, also called SH3 domain-containing protein 19 (SH3D19) or EEN-binding protein (EBP), exists in multiple alternatively spliced isoforms. The longest isoform contains five SH3 domain in the C-terminal region and seven proline-rich motifs in the N-terminal region. It is abundantly expressed in skeletal muscle and heart, and may be involved in regulating the activity of ADAMs (A disintegrin and metalloproteases). Eve-1 interacts with EEN, an endophilin involved in endocytosis and may be the target of the MLL-EEN fusion protein that is implicated in leukemogenesis. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 50 matched cddid_all.tbl CDD cd11819 cd11819 212753 SH3_Cortactin_like Src homology 3 domain of Cortactin and related proteins. This subfamily includes cortactin, Abp1 (actin-binding protein 1), hematopoietic lineage cell-specific protein 1 (HS1), and similar proteins. These proteins are involved in regulating actin dynamics through direct or indirect interaction with the Arp2/3 complex, which is required to initiate actin polymerization. They all contain at least one C-terminal SH3 domain. Cortactin and HS1 bind Arp2/3 and actin through an N-terminal region that contains an acidic domain and several copies of a repeat domain found in cortactin and HS1. Abp1 binds actin via an N-terminal actin-depolymerizing factor (ADF) homology domain. Yeast Abp1 binds Arp2/3 directly through two acidic domains. Mammalian Abp1 does not directly interact with Arp2/3; instead, it regulates actin dynamics indirectly by interacting with dynamin and WASP family proteins. The C-terminal region of these proteins acts as an adaptor or scaffold that can connect membrane trafficking and signaling proteins that bind the SH3 domain within the actin network. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11820 cd11820 212754 SH3_STAM Src homology 3 domain of Signal Transducing Adaptor Molecules. STAMs were discovered as proteins that are highly phosphorylated following cytokine and growth factor stimulation. They function in cytokine signaling and surface receptor degradation, as well as regulate Golgi morphology. They associate with many proteins including Jak2 and Jak3 tyrosine kinases, Hrs, AMSH, and UBPY. STAM adaptor proteins contain VHS (Vps27, Hrs, STAM homology), ubiquitin interacting (UIM), and SH3 domains. There are two vertebrate STAMs, STAM1 and STAM2, which may be functionally redundant; vertebrate STAMs contain ITAM motifs. They are part of the endosomal sorting complex required for transport (ESCRT-0). STAM2 deficiency in mice did not cause any obvious abnormality, while STAM1 deficiency resulted in growth retardation. Loss of both STAM1 and STAM2 in mice proved lethal, indicating that STAMs are important for embryonic development. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11821 cd11821 212755 SH3_ASAP Src homology 3 domain of ArfGAP with SH3 domain, ankyrin repeat and PH domain containing proteins. ASAPs are Arf GTPase activating proteins (GAPs) and they function in regulating cell growth, migration, and invasion. They contain an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, ankyrin (ANK) repeats, and a C-terminal SH3 domain. Vertebrates contain at least three members, ASAP1, ASAP2, and ASAP3, but some ASAP3 proteins do not seem to harbor a C-terminal SH3 domain. ASAP1 and ASAP2 show GTPase activating protein (GAP) activity towards Arf1 and Arf5. They do not show GAP activity towards Arf6, but are able to mediate Arf6 signaling by binding stably to GTP-Arf6. ASAP3 is an Arf6-specific GAP. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11822 cd11822 212756 SH3_SASH_like Src homology 3 domain of SAM And SH3 Domain Containing Proteins. This subfamily, also called the SLY family, is composed of SAM And SH3 Domain Containing Protein 1 (SASH1), SASH2, SASH3, and similar proteins. These are adaptor proteins containing a central conserved region with a bipartite nuclear localization signal (NLS) as wells as SAM (sterile alpha motif) and SH3 domains. SASH1 is a potential tumor suppressor in breast and colon cancer. It is widely expressed in normal tissues (except lymphocytes and dendritic cells) and is localized in the nucleus and the cytoplasm. SASH1 interacts with the oncoprotein cortactin and is important in cell migration and adhesion. SASH2 (also called SAMSN-1, SLY2, HACS1 or NASH1) and SASH3 (also called SLY/SLY1) are expressed mainly in hematopoietic cells, although SASH2 is also found in endothelial cells as well as myeloid leukemias and myeloma. SASH2 was found to be differentially expressed in malignant haematopoietic cells and in colorectal tumors, and is a potential tumor suppressor in lung cancer. SASH3 is essential in the full activation of adaptive immunity and is involved in the signaling of T cell receptors. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11823 cd11823 212757 SH3_Nostrin Src homology 3 domain of Nitric Oxide Synthase TRaffic INducer. Nostrin is expressed in endothelial and epithelial cells and is involved in the regulation, trafficking and targeting of endothelial NOS (eNOS). It facilitates the endocytosis of eNOS by coordinating the functions of dynamin and the Wiskott-Aldrich syndrome protein (WASP). Increased expression of Nostrin may be correlated to preeclampsia. Nostrin contains an N-terminal F-BAR domain and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11824 cd11824 212758 SH3_PSTPIP1 Src homology 3 domain of Proline-Serine-Threonine Phosphatase-Interacting Protein 1. PSTPIP1, also called CD2 Binding Protein 1 (CD2BP1), is mainly expressed in hematopoietic cells. It is a binding partner of the cell surface receptor CD2 and PTP-PEST, a tyrosine phosphatase which functions in cell motility and Rac1 regulation. It also plays a role in the activation of the Wiskott-Aldrich syndrome protein (WASP), which couples actin rearrangement and T cell activation. Mutations in the gene encoding PSTPIP1 cause the autoinflammatory disorder known as PAPA (pyogenic sterile arthritis, pyoderma gangrenosum, and acne) syndrome. PSTPIP1 contains an N-terminal F-BAR domain, PEST motifs, and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11825 cd11825 212759 SH3_PLCgamma Src homology 3 domain of Phospholipase C (PLC) gamma. PLC catalyzes the hydrolysis of phosphatidylinositol (4,5)-bisphosphate [PtdIns(4,5)P2] to produce Ins(1,4,5)P3 and diacylglycerol (DAG) in response to various receptors. Ins(1,4,5)P3 initiates the calcium signaling cascade while DAG functions as an activator of PKC. PLCgamma catalyzes this reaction in tyrosine kinase-dependent signaling pathways. It is activated and recruited to its substrate at the membrane. Vertebrates contain two forms of PLCgamma, PLCgamma1, which is widely expressed, and PLCgamma2, which is primarily found in haematopoietic cells. PLCgamma contains a Pleckstrin homology (PH) domain followed by an elongation factor (EF) domain, two catalytic regions of PLC domains that flank two tandem SH2 domains, followed by a SH3 domain and C2 domain. The SH3 domain of PLCgamma1 directly interacts with dynamin-1 and can serve as a guanine nucleotide exchange factor (GEF). It also interacts with Cbl, inhibiting its phosphorylation and activity. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11826 cd11826 212760 SH3_Abi Src homology 3 domain of Abl Interactor proteins. Abl interactor (Abi) proteins are adaptor proteins serving as binding partners and substrates of Abl tyrosine kinases. They are involved in regulating actin cytoskeletal reorganization and play important roles in membrane-ruffling, endocytosis, cell motility, and cell migration. They localize to sites of actin polymerization in epithelial adherens junction and immune synapses, as well as to the leading edge of lamellipodia. Vertebrates contain two Abi proteins, Abi1 and Abi2. Abi1 displays a wide expression pattern while Abi2 is highly expressed in the eye and brain. Abi proteins contain a homeobox homology domain, a proline-rich region, and a SH3 domain. The SH3 domain of Abi binds to a PxxP motif in Abl. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11827 cd11827 212761 SH3_MyoIe_If_like Src homology 3 domain of Myosins Ie, If, and similar proteins. Myosins Ie (MyoIe) and If (MyoIf) are nonmuscle, unconventional, long tailed, class I myosins containing an N-terminal motor domain and a myosin tail with TH1, TH2, and SH3 domains. MyoIe interacts with the endocytic proteins, dynamin and synaptojanin-1, through its SH3 domain; it may play a role in clathrin-dependent endocytosis. In the kidney, MyoIe is critical for podocyte function and normal glomerular filtration. Mutations in MyoIe is associated with focal segmental glomerulosclerosis, a disease characterized by massive proteinuria and progression to end-stage kidney disease. MyoIf is predominantly expressed in the immune system; it plays a role in immune cell motility and innate immunity. Mutations in MyoIf may be associated with the loss of hearing. The MyoIf gene has also been found to be fused to the MLL (Mixed lineage leukemia) gene in infant acute myeloid leukemias (AML). SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11828 cd11828 212762 SH3_ARHGEF9_like Src homology 3 domain of ARHGEF9-like Rho guanine nucleotide exchange factors. Members of this family contain a SH3 domain followed by RhoGEF (also called Dbl-homologous or DH) and Pleckstrin Homology (PH) domains. They include the Rho guanine nucleotide exchange factors ARHGEF9, ASEF (also called ARHGEF4), ASEF2, and similar proteins. GEFs activate small GTPases by exchanging bound GDP for free GTP. ARHGEF9 specifically activates Cdc42, while both ASEF and ASEF2 can activate Rac1 and Cdc42. ARHGEF9 is highly expressed in the brain and it interacts with gephyrin, a postsynaptic protein associated with GABA and glycine receptors. ASEF plays a role in angiogenesis and cell migration. ASEF2 is important in cell migration and adhesion dynamics. ASEF exists in an autoinhibited form and is activated upon binding of the tumor suppressor APC (adenomatous polyposis coli), leading to the activation of Rac1 or Cdc42. In its autoinhibited form, the SH3 domain of ASEF forms an extensive interface with the DH and PH domains, blocking the Rac binding site. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11829 cd11829 212763 SH3_GAS7 Src homology 3 domain of Growth Arrest Specific protein 7. GAS7 is mainly expressed in the brain and is required for neurite outgrowth. It may also play a role in the protection and migration of embryonic stem cells. Treatment-related acute myeloid leukemia (AML) has been reported resulting from mixed-lineage leukemia (MLL)-GAS7 translocations as a complication of primary cancer treatment. GAS7 contains an N-terminal SH3 domain, followed by a WW domain, and a central F-BAR domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11830 cd11830 212764 SH3_VAV_2 C-terminal (or second) Src homology 3 domain of VAV proteins. VAV proteins function both as cytoplasmic guanine nucleotide exchange factors (GEFs) for Rho GTPases and scaffold proteins and they play important roles in cell signaling by coupling cell surface receptors to various effector functions. They play key roles in processes that require cytoskeletal reorganization including immune synapse formation, phagocytosis, cell spreading, and platelet aggregation, among others. Vertebrates have three VAV proteins (VAV1, VAV2, and VAV3). VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. The SH3 domain of VAV is involved in the localization of proteins to specific sites within the cell, by interacting with proline-rich sequences within target proteins. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11831 cd11831 212765 SH3_VAV_1 First Src homology 3 domain of VAV proteins. VAV proteins function both as cytoplasmic guanine nucleotide exchange factors (GEFs) for Rho GTPases and scaffold proteins and they play important roles in cell signaling by coupling cell surface receptors to various effector functions. They play key roles in processes that require cytoskeletal reorganization including immune synapse formation, phagocytosis, cell spreading, and platelet aggregation, among others. Vertebrates have three VAV proteins (VAV1, VAV2, and VAV3). VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. The SH3 domain of VAV is involved in the localization of proteins to specific sites within the cell, by interacting with proline-rich sequences within target proteins. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 62 matched cddid_all.tbl CDD cd11832 cd11832 212766 SH3_Shank Src homology 3 domain of SH3 and multiple ankyrin repeat domains (Shank) proteins. Shank proteins carry scaffolding functions through multiple sites of protein-protein interaction in its domain architecture, including ankyrin (ANK) repeats, a long proline rich region, as well as SH3, PDZ, and SAM domains. They bind a variety of membrane and cytosolic proteins, and exist in alternatively spliced isoforms. They are highly enriched in postsynaptic density (PSD) where they interact with the cytoskeleton and with postsynaptic membrane receptors including NMDA and glutamate receptors. They are crucial in the construction and organization of the PSD and dendritic spines of excitatory synapses. There are three members of this family (Shank1, Shank2, Shank3) which show distinct and cell-type specific patterns of expression. Shank1 is brain-specific; Shank2 is found in neurons, glia, endocrine cells, liver, and kidney; Shank3 is widely expressed. The SH3 domain of Shank binds GRIP, a scaffold protein that binds AMPA receptors and Eph receptors/ligands. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 50 matched cddid_all.tbl CDD cd11833 cd11833 212767 SH3_Stac_1 First C-terminal Src homology 3 domain of SH3 and cysteine-rich domain-containing (Stac) proteins. Stac proteins are putative adaptor proteins that contain a cysteine-rich C1 domain and one or two SH3 domains at the C-terminus. There are three mammalian members (Stac1, Stac2, and Stac3) of this family. Stac1 and Stac3 contain two SH3 domains while Stac2 contains a single SH3 domain at the C-terminus. This model represents the first C-terminal SH3 domain of Stac1 and Stac3, and the single C-terminal SH3 domain of Stac2. Stac1 and Stac2 have been found to be expressed differently in mature dorsal root ganglia (DRG) neurons. Stac1 is mainly expressed in peptidergic neurons while Stac2 is found in a subset of nonpeptidergic and all trkB+ neurons. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11834 cd11834 212768 SH3_Stac_2 Second C-terminal Src homology 3 domain of SH3 and cysteine-rich domain-containing proteins 1 and 3. This model represents the second C-terminal SH3 domain of Stac1 and Stac3. Stac proteins are putative adaptor proteins that contain a cysteine-rich C1 domain and one or two SH3 domains at the C-terminus. There are three mammalian members (Stac1, Stac2, and Stac3) of this family. Stac1 and Stac3 contain two SH3 domains while Stac2 contains a single SH3 domain at the C-terminus. Stac1 and Stac2 have been found to be expressed differently in mature dorsal root ganglia (DRG) neurons. Stac1 is mainly expressed in peptidergic neurons while Stac2 is found in a subset of nonpeptidergic and all trkB+ neurons. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 51 matched cddid_all.tbl CDD cd11835 cd11835 212769 SH3_ARHGAP32_33 Src homology 3 domain of Rho GTPase-activating proteins 32 and 33, and similar proteins. Members of this family contain N-terminal PX and Src Homology 3 (SH3) domains, a central Rho GAP domain, and C-terminal extensions. RhoGAPs (or ARHGAPs) bind to Rho proteins and enhance the hydrolysis rates of bound GTP. ARHGAP32 is also called RICS, PX-RICS, p250GAP, or p200RhoGAP. It is a Rho GTPase-activating protein for Cdc42 and Rac1, and is implicated in the regulation of postsynaptic signaling and neurite outgrowth. PX-RICS, a variant of RICS that contain PX and SH3 domains, is the main isoform expressed during neural development. It is involved in neural functions including axon and dendrite extension, postnatal remodeling, and fine-tuning of neural circuits during early brain development. ARHGAP33, also called sorting nexin 26 or TCGAP (Tc10/CDC42 GTPase-activating protein), is widely expressed in the brain where it is involved in regulating the outgrowth of axons and dendrites and is regulated by the protein tyrosine kinase Fyn. It is translocated to the plasma membrane in adipocytes in response to insulin and may be involved in the regulation of insulin-stimulated glucose transport. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11836 cd11836 212770 SH3_Intersectin_1 First Src homology 3 domain (or SH3A) of Intersectin. Intersectins (ITSNs) are adaptor proteins that function in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction. They are essential for initiating clathrin-coated pit formation. They bind to many proteins through their multidomain structure and facilitate the assembly of multimeric complexes. Vertebrates contain two ITSN proteins, ITSN1 and ITSN2, which exist in alternatively spliced short and long isoforms. The short isoforms contain two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoforms, in addition, contain RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. ITSN1 and ITSN2 are both widely expressed, with variations depending on tissue type and stage of development. The first SH3 domain (or SH3A) of ITSN1 has been shown to bind many proteins including Sos1, dynamin1/2, CIN85, c-Cbl, PI3K-C2, SHIP2, N-WASP, and CdGAP, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11837 cd11837 212771 SH3_Intersectin_2 Second Src homology 3 domain (or SH3B) of Intersectin. Intersectins (ITSNs) are adaptor proteins that function in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction. They are essential for initiating clathrin-coated pit formation. They bind to many proteins through their multidomain structure and facilitate the assembly of multimeric complexes. Vertebrates contain two ITSN proteins, ITSN1 and ITSN2, which exist in alternatively spliced short and long isoforms. The short isoforms contain two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoforms, in addition, contain RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. ITSN1 and ITSN2 are both widely expressed, with variations depending on tissue type and stage of development. The second SH3 domain (or SH3B) of ITSN1 has been shown to bind WNK and CdGAP. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11838 cd11838 212772 SH3_Intersectin_3 Third Src homology 3 domain (or SH3C) of Intersectin. Intersectins (ITSNs) are adaptor proteins that function in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction. They are essential for initiating clathrin-coated pit formation. They bind to many proteins through their multidomain structure and facilitate the assembly of multimeric complexes. Vertebrates contain two ITSN proteins, ITSN1 and ITSN2, which exist in alternatively spliced short and long isoforms. The short isoforms contain two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoforms, in addition, contain RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. ITSN1 and ITSN2 are both widely expressed, with variations depending on tissue type and stage of development. The third SH3 domain (or SH3C) of ITSN1 has been shown to bind many proteins including dynamin1/2, CIN85, c-Cbl, SHIP2, Reps1, synaptojanin-1, and WNK, among others. The SH3C of ITSN2 has been shown to bind the K15 protein of Kaposi's sarcoma-associated herpesvirus. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11839 cd11839 212773 SH3_Intersectin_4 Fourth Src homology 3 domain (or SH3D) of Intersectin. Intersectins (ITSNs) are adaptor proteins that function in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction. They are essential for initiating clathrin-coated pit formation. They bind to many proteins through their multidomain structure and facilitate the assembly of multimeric complexes. Vertebrates contain two ITSN proteins, ITSN1 and ITSN2, which exist in alternatively spliced short and long isoforms. The short isoforms contain two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoforms, in addition, contain RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. ITSN1 and ITSN2 are both widely expressed, with variations depending on tissue type and stage of development. The fourth SH3 domain (or SH3D) of ITSN1 has been shown to bind SHIP2, Numb, CdGAP, and N-WASP. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 58 matched cddid_all.tbl CDD cd11840 cd11840 212774 SH3_Intersectin_5 Fifth Src homology 3 domain (or SH3E) of Intersectin. Intersectins (ITSNs) are adaptor proteins that function in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction. They are essential for initiating clathrin-coated pit formation. They bind to many proteins through their multidomain structure and facilitate the assembly of multimeric complexes. Vertebrates contain two ITSN proteins, ITSN1 and ITSN2, which exist in alternatively spliced short and long isoforms. The short isoforms contain two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoforms, in addition, contain RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. ITSN1 and ITSN2 are both widely expressed, with variations depending on tissue type and stage of development. The fifth SH3 domain (or SH3E) of ITSN1 has been shown to bind many protein partners including SGIP1, Sos1, dynamin1/2, CIN85, c-Cbl, SHIP2, N-WASP, and synaptojanin-1, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11841 cd11841 212775 SH3_SH3YL1_like Src homology 3 domain of SH3 domain containing Ysc84-like 1 (SH3YL1) protein. SH3YL1 localizes to the plasma membrane and is required for dorsal ruffle formation. It binds phosphoinositides (PIs) with high affinity through its N-terminal SYLF domain (also called DUF500). In addition, SH3YL1 contains a C-terminal SH3 domain which has been reported to bind to N-WASP, dynamin 2, and SHIP2 (a PI 5-phosphatase). SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11842 cd11842 212776 SH3_Ysc84p_like Src homology 3 domain of Ysc84p and similar fungal proteins. This family is composed of the Saccharomyces cerevisiae proteins, Ysc84p (also called LAS17-binding protein 4, Lsb4p) and Lsb3p, and similar fungal proteins. They contain an N-terminal SYLF domain (also called DUF500) and a C-terminal SH3 domain. Ysc84p localizes to actin patches and plays an important in actin polymerization during endocytosis. The N-terminal domain of both Ysc84p and Lsb3p can bind and bundle actin filaments. A study of the yeast SH3 domain interactome predicts that the SH3 domains of Lsb3p and Lsb4p may function as molecular hubs for the assembly of endocytic complexes. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11843 cd11843 212777 SH3_PACSIN Src homology 3 domain of Protein kinase C and Casein kinase Substrate in Neurons (PACSIN) proteins. PACSINs, also called Synaptic dynamin-associated proteins (Syndapins), act as regulators of cytoskeletal and membrane dynamics. They bind both dynamin and Wiskott-Aldrich syndrome protein (WASP), and may provide direct links between the actin cytoskeletal machinery through WASP and dynamin-dependent endocytosis. Vetebrates harbor three isoforms with distinct expression patterns and specific functions. PACSINs contain an N-terminal F-BAR domain and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11844 cd11844 212778 SH3_CAS Src homology 3 domain of CAS (Crk-Associated Substrate) scaffolding proteins. CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes including migration, chemotaxis, apoptosis, differentiation, and progenitor cell function. They mediate the signaling of integrins at focal adhesions where they localize, and thus, regulate cell invasion and survival. Over-expression of these proteins is implicated in poor prognosis, increased metastasis, and resistance to chemotherapeutics in many cancers such as breast, lung, melanoma, and glioblastoma. CAS proteins have also been linked to the pathogenesis of inflammatory disorders, Alzheimer's, Parkinson's, and developmental defects. They share a common domain structure that includes an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain. Vertebrates contain four CAS proteins: BCAR1 (or p130Cas), NEDD9 (or HEF1), EFS (or SIN), and CASS4 (or HEPL). The SH3 domain of CAS proteins binds to diverse partners including FAK, FRNK, Pyk2, PTP-PEST, DOCK180, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd11845 cd11845 212779 SH3_Src_like Src homology 3 domain of Src kinase-like Protein Tyrosine Kinases. Src subfamily members include Src, Lck, Hck, Blk, Lyn, Fgr, Fyn, Yrk, Yes, and Brk. Src (or c-Src) proteins are cytoplasmic (or non-receptor) PTKs which are anchored to the plasma membrane. They contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). However, Brk lacks the N-terminal myristoylation sites. Src proteins are involved in signaling pathways that regulate cytokine and growth factor responses, cytoskeleton dynamics, cell proliferation, survival, and differentiation. They were identified as the first proto-oncogene products, and they regulate cell adhesion, invasion, and motility in cancer cells, and tumor vasculature, contributing to cancer progression and metastasis. Src kinases are overexpressed in a variety of human cancers, making them attractive targets for therapy. They are also implicated in acute inflammatory responses and osteoclast function. Src, Fyn, Yes, and Yrk are widely expressed, while Blk, Lck, Hck, Fgr, Lyn, and Brk show a limited expression pattern. This subfamily also includes Drosophila Src42A, Src oncogene at 42A (also known as Dsrc41) which accumulates at sites of cell-cell or cell-matrix adhesion, and participates in Drosphila development and wound healing. It has been shown to promote tube elongation in the tracheal system, is essential for proper cell-cell matching during dorsal closure, and regulates cell-cell contacts in developing Drosophila eyes. The SH3 domain of Src kinases contributes to substrate recruitment by binding adaptor proteins/substrates, and regulation of kinase activity through an intramolecular interaction. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11846 cd11846 212780 SH3_Srms Src homology 3 domain of Srms Protein Tyrosine Kinase. Src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylation sites (Srms) is a cytoplasmic (or non-receptor) PTK with limited homology to Src kinases. Src kinases in general contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr; they are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). However, Srms lacks the N-terminal myristoylation sites. Src proteins are involved in signaling pathways that regulate cytokine and growth factor responses, cytoskeleton dynamics, cell proliferation, survival, and differentiation. The SH3 domain of Src kinases contributes to substrate recruitment by binding adaptor proteins/substrates, and regulation of kinase activity through an intramolecular interaction. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11847 cd11847 212781 SH3_Brk Src homology 3 domain of Brk (Breast tumor kinase) Protein Tyrosine Kinase (PTK), also called PTK6. Brk is a cytoplasmic (or non-receptor) PTK with limited homology to Src kinases. It has been found to be overexpressed in a majority of breast tumors. It plays roles in normal cell differentiation, proliferation, survival, migration, and cell cycle progression. Brk substrates include RNA-binding proteins (SLM-1/2, Sam68), transcription factors (STAT3/5), and signaling molecules (Akt, paxillin, IRS-4). Src kinases in general contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr; they are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). However, Brk lacks the N-terminal myristoylation site. The SH3 domain of Src kinases contributes to substrate recruitment by binding adaptor proteins/substrates, and regulation of kinase activity through an intramolecular interaction. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 58 matched cddid_all.tbl CDD cd11848 cd11848 212782 SH3_SLAP-like Src homology 3 domain of Src-Like Adaptor Proteins. SLAPs are adaptor proteins with limited similarity to Src family tyrosine kinases. They contain an N-terminal SH3 domain followed by an SH2 domain, and a unique C-terminal sequence. They function in regulating the signaling, ubiquitination, and trafficking of T-cell receptor (TCR) and B-cell receptor (BCR) components. Vertebrates contain two SLAPs, named SLAP (or SLA1) and SLAP2 (or SLA2). SLAP has been shown to interact with the EphA receptor, EpoR, Lck, PDGFR, Syk, CD79a, among others, while SLAP2 interacts with CSF1R. Both SLAPs interact with c-Cbl, LAT, CD247, and Zap70. SLAP modulates TCR surface expression levels as well as surface and total BCR levels. As an adaptor to c-Cbl, SLAP increases the ubiquitination, intracellular retention, and targeted degradation of the BCR complex components. SLAP2 plays a role in c-Cbl-dependent regulation of CSF1R, a tyrosine kinase important for myeloid cell growth and differentiation. The SH3 domain of SLAP forms a complex with v-Abl. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11849 cd11849 212783 SH3_SPIN90 Src homology 3 domain of SH3 protein interacting with Nck, 90 kDa (SPIN90). SPIN90 is also called NCK interacting protein with SH3 domain (NCKIPSD), Dia-interacting protein (DIP), 54 kDa vimentin-interacting protein (VIP54), or WASP-interacting SH3-domain protein (WISH). It is an F-actin binding protein that regulates actin polymerization and endocytosis. It associates with the Arp2/3 complex near actin filaments and determines filament localization at the leading edge of lamellipodia. SPIN90 is expressed in the early stages of neuronal differentiation and plays a role in regulating growth cone dynamics and neurite outgrowth. It also interacts with IRSp53 and regulates cell motility by playing a role in the formation of membrane protrusions. SPIN90 contains an N-terminal SH3 domain, a proline-rich domain, and a C-terminal VCA (verprolin-homology and cofilin-like acidic) domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11850 cd11850 212784 SH3_Abl Src homology 3 domain of the Protein Tyrosine Kinase, Abelson kinase. Abl (or c-Abl) is a ubiquitously-expressed cytoplasmic (or nonreceptor) PTK that contains SH3, SH2, and tyr kinase domains in its N-terminal region, as well as nuclear localization motifs, a putative DNA-binding domain, and F- and G-actin binding domains in its C-terminal tail. It also contains a short autoinhibitory cap region in its N-terminus. Abl function depends on its subcellular localization. In the cytoplasm, Abl plays a role in cell proliferation and survival. In response to DNA damage or oxidative stress, Abl is transported to the nucleus where it induces apoptosis. In chronic myelogenous leukemia (CML) patients, an aberrant translocation results in the replacement of the first exon of Abl with the BCR (breakpoint cluster region) gene. The resulting BCR-Abl fusion protein is constitutively active and associates into tetramers, resulting in a hyperactive kinase sending a continuous signal. This leads to uncontrolled proliferation, morphological transformation and anti-apoptotic effects. BCR-Abl is the target of selective inhibitors, such as imatinib (Gleevec), used in the treatment of CML. Abl2, also known as ARG (Abelson-related gene), is thought to play a cooperative role with Abl in the proper development of the nervous system. The Tel-ARG fusion protein, resulting from reciprocal translocation between chromosomes 1 and 12, is associated with acute myeloid leukemia (AML). SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd11851 cd11851 212785 SH3_RIM-BP Src homology 3 domains of Rab3-interacting molecules (RIMs) binding proteins. RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3. RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery. RIM-BPs contain three SH3 domains and two to three fibronectin III repeats. Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3. RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis. The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 62 matched cddid_all.tbl CDD cd11852 cd11852 212786 SH3_Kalirin_1 First Src homology 3 domain of the RhoGEF kinase, Kalirin. Kalirin, also called Duo, Duet, or TRAD, is a large neuronal dual Rho guanine nucleotide exchange factor (RhoGEF) that activates Rac1, RhoA, and RhoG using two RhoGEF domains. Kalirin exists in many isoforms generated by alternative splicing and the use of multiple promoters; the major isoforms are kalirin-7, -9, and -12, which differ at their C-terminal ends. Kalirin-12, the longest isoform, contains an N-terminal Sec14p domain, spectrin-like repeats, two RhoGEF domains, two SH3 domains, as well as Ig, FNIII, and kinase domains at the C-terminal end. Kalirin-7 contains only a single RhoGEF domain and does not contain an SH3 domain. Kalirin, through its many isoforms, interacts with many different proteins and is able to localize to different locations within the cell. It influences neurite initiation, axon growth, dendritic morphogenesis, vesicle trafficking, neuronal maintenance, and neurodegeneration. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 62 matched cddid_all.tbl CDD cd11853 cd11853 212787 SH3_Kalirin_2 Second Src homology 3 domain of the RhoGEF kinase, Kalirin. Kalirin, also called Duo, Duet, or TRAD, is a large neuronal dual Rho guanine nucleotide exchange factor (RhoGEF) that activates Rac1, RhoA, and RhoG using two RhoGEF domains. Kalirin exists in many isoforms generated by alternative splicing and the use of multiple promoters; the major isoforms are kalirin-7, -9, and -12, which differ at their C-terminal ends. Kalirin-12, the longest isoform, contains an N-terminal Sec14p domain, spectrin-like repeats, two RhoGEF domains, two SH3 domains, as well as Ig, FNIII, and kinase domains at the C-terminal end. Kalirin-7 contains only a single RhoGEF domain and does not contain an SH3 domain. Kalirin, through its many isoforms, interacts with many different proteins and is able to localize to different locations within the cell. It influences neurite initiation, axon growth, dendritic morphogenesis, vesicle trafficking, neuronal maintenance, and neurodegeneration. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 59 matched cddid_all.tbl CDD cd11854 cd11854 212788 SH3_Fus1p Src homology 3 domain of yeast cell fusion protein Fus1p. Fus1p is required at the cell surface for cell fusion during the mating response in yeast. It requires Bch1p and Bud7p, which are Chs5p-Arf1p binding proteins, for localization to the plasma membrane. It acts as a scaffold protein to assemble a cell surface complex which is involved in septum degradation and inhibition of the NOG pathway to promote cell fusion. The SH3 domain of Fus1p interacts with Bin1p, a formin that controls the assembly of actin cables in response to Cdc42 signaling. It has been shown to bind the motif, R(S/T)(S/T)SL, instead of PxxP motifs. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd11855 cd11855 212789 SH3_Sho1p Src homology 3 domain of High osmolarity signaling protein Sho1p. Sho1p (or Sho1), also called SSU81 (Suppressor of SUA8-1 mutation), is a yeast membrane protein that regulates adaptation to high salt conditions by activating the HOG (high-osmolarity glycerol) pathway. High salt concentrations lead to the localization to the membrane of the MAPKK Pbs2, which is then activated by the MAPKK Ste11 and in turn, activates the MAPK Hog1. Pbs2 is localized to the membrane though the interaction of its PxxP motif with the SH3 domain of Sho1p. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11856 cd11856 212790 SH3_p47phox_like Src homology 3 domains of the p47phox subunit of NADPH oxidase and similar domains. This family is composed of the tandem SH3 domains of p47phox subunit of NADPH oxidase and Nox Organizing protein 1 (NoxO1), the four SH3 domains of Tks4 (Tyr kinase substrate with four SH3 domains), the five SH3 domains of Tks5, the SH3 domain of obscurin, Myosin-I, and similar domains. Most members of this group also contain Phox homology (PX) domains, except for obscurin and Myosin-I. p47phox and NoxO1 are regulators of the phagocytic NADPH oxidase complex (also called Nox2 or gp91phox) and nonphagocytic NADPH oxidase Nox1, respectively. They play roles in the activation of their respective NADPH oxidase, which catalyzes the transfer of electrons from NADPH to molecular oxygen to form superoxide. Tks proteins are Src substrates and scaffolding proteins that play important roles in the formation of podosomes and invadopodia, the dynamic actin-rich structures that are related to cell migration and cancer cell invasion. Obscurin is a giant muscle protein that plays important roles in the organization and assembly of the myofibril and the sarcoplasmic reticulum. Type I myosins (Myosin-I) are actin-dependent motors in endocytic actin structures and actin patches. They play roles in membrane traffic in endocytic and secretory pathways, cell motility, and mechanosensing. Myosin-I contains an N-terminal actin-activated ATPase, a phospholipid-binding TH1 (tail homology 1) domain, and a C-terminal extension which includes an F-actin-binding TH2 domain, an SH3 domain, and an acidic peptide that participates in activating the Arp2/3complex. The SH3 domain of myosin-I is required for myosin-I-induced actin polymerization. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11857 cd11857 212791 SH3_DBS Src homology 3 domain of DBL's Big Sister (DBS), a guanine nucleotide exchange factor. DBS, also called MCF2L (MCF2-transforming sequence-like protein) or OST, is a Rho GTPase guanine nucleotide exchange factor (RhoGEF), facilitating the exchange of GDP and GTP. It was originally isolated from a cDNA screen for sequences that cause malignant growth. It plays roles in regulating clathrin-mediated endocytosis and cell migration through its activation of Rac1 and Cdc42. Depending on cell type, DBS can also activate RhoA and RhoG. DBS contains a Sec14-like domain, spectrin-like repeats, a RhoGEF [or Dbl homology (DH)] domain, a Pleckstrin homology (PH) domain, and an SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11858 cd11858 212792 SH3_Myosin-I_fungi Src homology 3 domain of Type I fungal Myosins. Type I myosins (myosin-I) are actin-dependent motors in endocytic actin structures and actin patches. They play roles in membrane traffic in endocytic and secretory pathways, cell motility, and mechanosensing. Saccharomyces cerevisiae has two myosins-I, Myo3 and Myo5, which are involved in endocytosis and the polarization of the actin cytoskeleton. Myosin-I contains an N-terminal actin-activated ATPase, a phospholipid-binding TH1 (tail homology 1) domain, and a C-terminal extension which includes an F-actin-binding TH2 domain, an SH3 domain, and an acidic peptide that participates in activating the Arp2/3complex. The SH3 domain of myosin-I is required for myosin-I-induced actin polymerization. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11859 cd11859 212793 SH3_ZO Src homology 3 domain of the Tight junction proteins, Zonula occludens (ZO) proteins. ZO proteins are scaffolding proteins that associate with each other and with other proteins of the tight junction, zonula adherens, and gap junctions. They play roles in regulating cytoskeletal dynamics at these cell junctions. They are considered members of the MAGUK (membrane-associated guanylate kinase) protein family, which is characterized by the presence of a core of three domains: PDZ, SH3, and guanylate kinase (GuK). The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. Vertebrates contain three ZO proteins (ZO-1, ZO-2, and ZO-3) with redundant and non-redundant roles. They contain three PDZ domains, followed by SH3 and GuK domains; in addition, ZO-1 and ZO-2 contains a proline-rich (PR) actin binding domain at the C-terminus while ZO-3 contains this PR domain between the second and third PDZ domains. The C-terminal regions of the three ZO proteins are unique. The SH3 domain of ZO-1 has been shown to bind ZONAB, ZAK, afadin, and Galpha12. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 62 matched cddid_all.tbl CDD cd11860 cd11860 212794 SH3_DLG5 Src homology 3 domain of Disks Large homolog 5. DLG5 is a multifunctional scaffold protein that is located at sites of cell-cell contact and is involved in the maintenance of cell shape and polarity. Mutations in the DLG5 gene are associated with Crohn's disease (CD) and inflammatory bowel disease (IBD). DLG5 is a member of the MAGUK (membrane-associated guanylate kinase) protein family, which is characterized by the presence of a core of three domains: PDZ, SH3, and guanylate kinase (GuK). The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. DLG5 contains 4 PDZ domains as well as an N-terminal domain of unknown function. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 63 matched cddid_all.tbl CDD cd11861 cd11861 212795 SH3_DLG-like Src Homology 3 domain of Disks large homolog proteins. The DLG-like proteins are scaffolding proteins that cluster at synapses and are also called PSD (postsynaptic density)-95 proteins or SAPs (synapse-associated proteins). They play important roles in synaptic development and plasticity, cell polarity, migration and proliferation. They are members of the MAGUK (membrane-associated guanylate kinase) protein family, which is characterized by the presence of a core of three domains: PDZ, SH3, and guanylate kinase (GuK). The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. DLG-like proteins contain three PDZ domains and varying N-terminal regions. All DLG proteins exist as alternatively-spliced isoforms. Vertebrates contain four DLG proteins from different genes, called DLG1-4. DLG4 and DLG2 are found predominantly at postsynaptic sites and they mediate surface ion channel and receptor clustering. DLG3 is found axons and some presynaptic terminals. DLG1 interacts with AMPA-type glutamate receptors and is critical in their maturation and delivery to synapses. The SH3 domain of DLG4 binds and clusters the kainate subgroup of glutamate receptors via two proline-rich sequences in their C-terminal tail. It also binds AKAP79/150 (A-kinase anchoring protein). SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 61 matched cddid_all.tbl CDD cd11862 cd11862 212796 SH3_MPP Src Homology 3 domain of Membrane Protein, Palmitoylated (or MAGUK p55 subfamily member) proteins. The MPP/p55 subfamily of MAGUK (membrane-associated guanylate kinase) proteins includes at least eight vertebrate members (MPP1-7 and CASK), four Drosophila proteins (Stardust, Varicose, CASK and Skiff), and other similar proteins; they all contain one each of the core of three domains characteristic of MAGUK proteins: PDZ, SH3, and guanylate kinase (GuK). In addition, most members except for MPP1 contain N-terminal L27 domains and some also contain a Hook (Protein 4.1 Binding) motif in between the SH3 and GuK domains. CASK has an additional calmodulin-dependent kinase (CaMK)-like domain at the N-terminus. Members of this subfamily are scaffolding proteins that play important roles in regulating and establishing cell polarity, cell adhesion, and synaptic targeting and transmission, among others. The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 61 matched cddid_all.tbl CDD cd11863 cd11863 212797 SH3_CACNB Src Homology 3 domain of Voltage-dependent L-type calcium channel subunit beta. Voltage-dependent calcium channels (Ca(V)s) are multi-protein complexes that regulate the entry of calcium into cells. They impact muscle contraction, neuronal migration, hormone and neurotransmitter release, and the activation of calcium-dependent signaling pathways. They are composed of four subunits: alpha1, alpha2delta, beta, and gamma. The beta subunit is a soluble and intracellular protein that interacts with the transmembrane alpha1 subunit. It facilitates the trafficking and proper localization of the alpha1 subunit to the cellular plasma membrane. Vertebrates contain four different beta subunits from distinct genes (beta1-4); each exists as multiple splice variants. All are expressed in the brain while other tissues show more specific expression patterns. The beta subunits show similarity to MAGUK (membrane-associated guanylate kinase) proteins in that they contain SH3 and inactive guanylate kinase (GuK) domains; however, they do not appear to contain a PDZ domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 62 matched cddid_all.tbl CDD cd11864 cd11864 212798 SH3_PEX13_eumet Src Homology 3 domain of eumetazoan Peroxisomal biogenesis factor 13. PEX13 is a peroxin and is required for protein import into the peroxisomal matrix and membrane. It is an integral membrane protein that is essential for the localization of PEX14 and the import of proteins containing the peroxisome matrix targeting signals, PTS1 and PTS2. Mutations of the PEX13 gene in humans lead to a wide range of peroxisome biogenesis disorders (PBDs), the most severe of which is known as Zellweger syndrome (ZS), a severe multisystem disorder characterized by hypotonia, psychomotor retardation, and neuronal migration defects. PEX13 contains two transmembrane regions and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 58 matched cddid_all.tbl CDD cd11865 cd11865 212799 SH3_Nbp2-like Src Homology 3 domain of Saccharomyces cerevisiae Nap1-binding protein 2 and similar fungal proteins. This subfamily includes Saccharomyces cerevisiae Nbp2 (Nucleosome assembly protein 1 (Nap1)-binding protein 2), Schizosaccharomyces pombe Skb5, and similar proteins. Nbp2 interacts with Nap1, which is essential for maintaining proper nucleosome structures in transcription and replication. It is also the binding partner of the yeast type II protein phosphatase Ptc1p and serves as a scaffolding protein that brings seven kinases in close contact to Ptc1p. Nbp2 plays a role many cell processes including organelle inheritance, mating hormone response, cell wall stress, mitotic cell growth at elevated temperatures, and high osmolarity. Skb5 interacts with the p21-activated kinase (PAK) homolog Shk1, which is critical for fission yeast cell viability. Skb5 activates Shk1 and plays a role in regulating cell morphology and growth under hypertonic conditions. Nbp2 and Skb5 contain an SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11866 cd11866 212800 SH3_SKAP1-like Src Homology 3 domain of Src Kinase-Associated Phosphoprotein 1 and similar proteins. This subfamily is composed of SKAP1, SKAP2, and similar proteins. SKAP1 and SKAP2 are immune cell-specific adaptor proteins that play roles in T- and B-cell adhesion, respectively, and are thus important in the migration of T- and B-cells to sites of inflammation and for movement during T-cell conjugation with antigen-presenting cells. Both SKAP1 and SKAP2 bind to ADAP (adhesion and degranulation-promoting adaptor protein), among many other binding partners. They contain a pleckstrin homology (PH) domain, a C-terminal SH3 domain, and several tyrosine phosphorylation sites. The SH3 domain of SKAP1 is necessary for its ability to regulate T-cell conjugation with antigen-presenting cells and the formation of LFA-1 clusters. SKAP1 binds primarily to a proline-rich region of ADAP through its SH3 domain; its degradation is regulated by ADAP. A secondary interaction occurs via the ADAP SH3 domain and the RKxxYxxY motif in SKAP1. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11867 cd11867 212801 hSH3_ADAP Helically extended Src Homology 3 domain of Adhesion and Degranulation-promoting Adaptor Protein. ADAP, also called Fyn T-binding protein (FYB) or SLP-76-associated protein (SLAP), is expressed mainly in hematopoietic cells but not in B cells. It is required for the proliferation of mature T-cells and plays an important role in T-cell activation, TCR-induced integrin clustering, and T-cell adhesion. ADAP has been shown to bind many partners including SLP-76, Fyn, Src, SKAP1, SKAP2, dynein, Ena/VASP, Carma1, among others. It is connected to cytoskeleton via its binding to Ena and VASP, which impacts actin cytoskeletal remodeling upon TCR ligation. The SH3 domain of ADAP adopts an altered fold referred to as a helically extended SH3 (hSH3) domain characterized by clusters of positive charges. The hSH3 domain can no longer bind conventional proline-rich peptides, instead, it functions as a novel lipid interaction domain and can bind acidic lipids such as phosphatidylserine, phosphatidylinositol, phosphatidic acid, and polyphosphoinositides. 77 matched cddid_all.tbl CDD cd11869 cd11869 212802 SH3_p40phox Src Homology 3 domain of the p40phox subunit of NADPH oxidase. p40phox, also called Neutrophil cytosol factor 4 (NCF-4), is a cytosolic subunit of the phagocytic NADPH oxidase complex (also called Nox2 or gp91phox) which plays a crucial role in the cellular response to bacterial infection. NADPH oxidase catalyzes the transfer of electrons from NADPH to oxygen during phagocytosis forming superoxide and reactive oxygen species. p40phox positively regulates NADPH oxidase in both phosphatidylinositol-3-phosphate (PI3P)-dependent and PI3P-independent manner. It contains an N-terminal PX domain, a central SH3 domain, and a C-terminal PB1 domain that interacts with p67phox. The SH3 domain of p40phox binds to canonical polyproline and noncanonical motifs at the C-terminus of p47phox. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11870 cd11870 212803 SH3_p67phox-like_C C-terminal Src Homology 3 domain of the p67phox subunit of NADPH oxidase and similar proteins. This subfamily is composed of p67phox, NADPH oxidase activator 1 (Noxa1), and similar proteins. p67phox, also called Neutrophil cytosol factor 2 (NCF-2), and Noxa1 are homologs and are the cytosolic subunits of the phagocytic (Nox2) and nonphagocytic (Nox1) NADPH oxidase complexes, respectively. NADPH oxidase catalyzes the transfer of electrons from NADPH to oxygen during phagocytosis forming superoxide and reactive oxygen species. p67phox and Noxa1 play regulatory roles. p67phox contains N-terminal TPR, first SH3 (or N-terminal or central SH3), PB1, and C-terminal SH3 domains. Noxa1 has a similar domain architecture except it is lacking the N-terminal SH3 domain. The TPR domain of both binds activated GTP-bound Rac, while the C-terminal SH3 domain of p67phox and Noxa1 binds the polyproline motif found at the C-terminus of p47phox and Noxo1, respectively. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11871 cd11871 212804 SH3_p67phox_N N-terminal (or first) Src Homology 3 domain of the p67phox subunit of NADPH oxidase. p67phox, also called Neutrophil cytosol factor 2 (NCF-2), is a cytosolic subunit of the phagocytic NADPH oxidase complex (also called Nox2 or gp91phox) which plays a crucial role in the cellular response to bacterial infection. NADPH oxidase catalyzes the transfer of electrons from NADPH to oxygen during phagocytosis forming superoxide and reactive oxygen species. p67phox plays a regulatory role and contains N-terminal TPR, first SH3 (or N-terminal or central SH3), PB1, and C-terminal SH3 domains. It binds, via its C-terminal SH3 domain, to a proline-rich region of p47phox and upon activation, this complex assembles with flavocytochrome b558, the Nox2-p22phox heterodimer. Concurrently, RacGTP translocates to the membrane and interacts with the TPR domain of p67phox, which leads to the activation of NADPH oxidase. The PB1 domain of p67phox binds to its partner PB1 domain in p40phox, and this facilitates the assembly of p47phox-p67phox at the membrane. The N-terminal SH3 domain increases the affinity of p67phox for the oxidase complex. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11872 cd11872 212805 SH3_DOCK_AB Src Homology 3 domain of Class A and B Dedicator of Cytokinesis proteins. DOCK proteins are atypical guanine nucleotide exchange factors (GEFs) that lack the conventional Dbl homology (DH) domain. They are divided into four classes (A-D) based on sequence similarity and domain architecture: class A includes Dock1, 2 and 5; class B includes Dock3 and 4; class C includes Dock6, 7, and 8; and class D includes Dock9, 10 and 11. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate while DHR-2 contains the catalytic activity for Rac and/or Cdc42. This subfamily includes only Class A and B DOCKs, which also contain an SH3 domain at the N-terminal region and a PxxP motif at the C-terminus. Class A/B DOCKs are mostly specific GEFs for Rac, except Dock4 which activates the Ras family GTPase Rap1, probably indirectly through interaction with Rap regulatory proteins. The SH3 domain of class A/B DOCKs have been shown to bind Elmo, a scaffold protein that promotes GEF activity of DOCKs by releasing DHR-2 autoinhibition by the intramolecular SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd11873 cd11873 212806 SH3_CD2AP-like_1 First Src Homology 3 domain (SH3A) of CD2-associated protein and similar proteins. This subfamily is composed of the first SH3 domain (SH3A) of CD2AP, CIN85 (Cbl-interacting protein of 85 kDa), and similar domains. CD2AP and CIN85 are adaptor proteins that bind to protein partners and assemble complexes that have been implicated in T cell activation, kidney function, and apoptosis of neuronal cells. They also associate with endocytic proteins, actin cytoskeleton components, and other adaptor proteins involved in receptor tyrosine kinase (RTK) signaling. CD2AP and the main isoform of CIN85 contain three SH3 domains, a proline-rich region, and a C-terminal coiled-coil domain. All of these domains enable CD2AP and CIN85 to bind various protein partners and assemble complexes that have been implicated in many different functions. SH3A of both proteins bind to an atypical PXXXPR motif at the C-terminus of Cbl and the cytoplasmic domain of the cell adhesion protein CD2. CIN85 SH3A binds to internal proline-rich motifs within the proline-rich region; this intramolecular interaction serves as a regulatory mechanism to keep CIN85 in a closed conformation, preventing the recruitment of other proteins. CIN85 SH3A has also been shown to bind ubiquitin. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11874 cd11874 212807 SH3_CD2AP-like_2 Second Src Homology 3 domain (SH3B) of CD2-associated protein and similar proteins. This subfamily is composed of the second SH3 domain (SH3B) of CD2AP, CIN85 (Cbl-interacting protein of 85 kDa), and similar domains. CD2AP and CIN85 are adaptor proteins that bind to protein partners and assemble complexes that have been implicated in T cell activation, kidney function, and apoptosis of neuronal cells. They also associate with endocytic proteins, actin cytoskeleton components, and other adaptor proteins involved in receptor tyrosine kinase (RTK) signaling. CD2AP and the main isoform of CIN85 contain three SH3 domains, a proline-rich region, and a C-terminal coiled-coil domain. All of these domains enable CD2AP and CIN85 to bind various protein partners and assemble complexes that have been implicated in many different functions. SH3B of both proteins have been shown to bind to Cbl. In the case of CD2AP, its SH3B binds to Cbl at a site distinct from the c-Cbl/SH3A binding site. The CIN85 SH3B also binds ubiquitin. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11875 cd11875 212808 SH3_CD2AP-like_3 Third Src Homology 3 domain (SH3C) of CD2-associated protein and similar proteins. This subfamily is composed of the third SH3 domain (SH3C) of CD2AP, CIN85 (Cbl-interacting protein of 85 kDa), and similar domains. CD2AP and CIN85 are adaptor proteins that bind to protein partners and assemble complexes that have been implicated in T cell activation, kidney function, and apoptosis of neuronal cells. They also associate with endocytic proteins, actin cytoskeleton components, and other adaptor proteins involved in receptor tyrosine kinase (RTK) signaling. CD2AP and the main isoform of CIN85 contain three SH3 domains, a proline-rich region, and a C-terminal coiled-coil domain. All of these domains enable CD2AP and CIN85 to bind various protein partners and assemble complexes that have been implicated in many different functions. SH3C of both proteins have been shown to bind to ubiquitin. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11876 cd11876 212809 SH3_MLK Src Homology 3 domain of Mixed Lineage Kinases. MLKs are Serine/Threonine Kinases (STKs), catalyzing the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. MLKs act as mitogen-activated protein kinase kinase kinases (MAP3Ks, MKKKs, MAPKKKs), which phosphorylate and activate MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. MLKs play roles in immunity and inflammation, as well as in cell death, proliferation, and cell cycle regulation. Mammals have four MLKs (MLK1-4), mostly conserved in vertebrates, which contain an SH3 domain, a catalytic kinase domain, a leucine zipper, a proline-rich region, and a CRIB domain that mediates binding to GTP-bound Cdc42 and Rac. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 58 matched cddid_all.tbl CDD cd11877 cd11877 212810 SH3_PIX Src Homology 3 domain of Pak Interactive eXchange factors. PIX proteins are Rho guanine nucleotide exchange factors (GEFs), which activate small GTPases by exchanging bound GDP for free GTP. They act as GEFs for both Cdc42 and Rac 1, and have been implicated in cell motility, adhesion, neurite outgrowth, and cell polarity. Vertebrates contain two proteins from the PIX subfamily, alpha-PIX and beta-PIX. Alpha-PIX, also called ARHGEF6, is localized in dendritic spines where it regulates spine morphogenesis. Mutations in the ARHGEF6 gene cause X-linked intellectual disability in humans. Beta-PIX play roles in regulating neuroendocrine exocytosis, focal adhesion maturation, cell migration, synaptic vesicle localization, and insulin secretion. PIX proteins contain an N-terminal SH3 domain followed by RhoGEF (also called Dbl-homologous or DH) and Pleckstrin Homology (PH) domains, and a C-terminal leucine-zipper domain for dimerization. The SH3 domain of PIX binds to an atypical PxxxPR motif in p21-activated kinases (PAKs) with high affinity. The binding of PAKs to PIX facilitate the localization of PAKs to focal complexes and also localizes PAKs to PIX targets Cdc43 and Rac, leading to the activation of PAKs. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11878 cd11878 212811 SH3_Bem1p_1 First Src Homology 3 domain of Bud emergence protein 1 and similar domains. Members of this subfamily bear similarity to Saccharomyces cerevisiae Bem1p, containing two Src Homology 3 (SH3) domains at the N-terminus, a central PX domain, and a C-terminal PB1 domain. Bem1p is a scaffolding protein that is critical for proper Cdc42p activation during bud formation in yeast. During budding and mating, Bem1p migrates to the plasma membrane where it can serve as an adaptor for Cdc42p and some other proteins. Bem1p also functions as an effector of the G1 cyclin Cln3p and the cyclin-dependent kinase Cdc28p in promoting vacuolar fusion. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11879 cd11879 212812 SH3_Bem1p_2 Second Src Homology 3 domain of Bud emergence protein 1 and similar domains. Members of this subfamily bear similarity to Saccharomyces cerevisiae Bem1p, containing two Src Homology 3 (SH3) domains at the N-terminus, a central PX domain, and a C-terminal PB1 domain. Bem1p is a scaffolding protein that is critical for proper Cdc42p activation during bud formation in yeast. During budding and mating, Bem1p migrates to the plasma membrane where it can serve as an adaptor for Cdc42p and some other proteins. Bem1p also functions as an effector of the G1 cyclin Cln3p and the cyclin-dependent kinase Cdc28p in promoting vacuolar fusion. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd11880 cd11880 212813 SH3_Caskin Src Homology 3 domain of CASK interacting protein. Caskin proteins are multidomain adaptor proteins that contain six ankyrin repeats, a single SH3 domain, tandem sterile alpha motif (SAM) domains, and a long disordered proline-rich region. There are two Caskin proteins called Caskin1 and Caskin2. Caskin1 binds to the multidomain scaffolding protein CASK through the CaM domain in competition with Munc-interacting protein 1 (Mint1). CASK participates in one of two evolutionarily conserved tripartite complexes containing either Mint1 and Velis or Caskin1 and Velis. Caskin1 may play a role in infantile myoclonic epilepsy. There is not much known about Caskin2; despite sharing a domain architecture with Caskin1, Caskin2 does not bind CASK. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 61 matched cddid_all.tbl CDD cd11881 cd11881 212814 SH3_MYO7A Src Homology 3 domain of Myosin VIIa and similar proteins. Myo7A is an uncoventional myosin that is involved in organelle transport. It is required for sensory function in both Drosophila and mammals. Mutations in the Myo7A gene cause both syndromic deaf-blindness [Usher syndrome I (USH1)] and nonsyndromic (DFNB2 and DFNA11) deafness in humans. It contains an N-terminal motor domain, light chain-binding IQ motifs, a coiled-coil region for heavy chain dimerization, and a tail consisting of a pair of MyTH4-FERM tandems separated by a SH3 domain. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 64 matched cddid_all.tbl CDD cd11882 cd11882 212815 SH3_GRAF-like Src Homology 3 domain of GTPase Regulator Associated with Focal adhesion kinase and similar proteins. This subfamily is composed of Rho GTPase activating proteins (GAPs) with similarity to GRAF. Members contain an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. Although vertebrates harbor four Rho GAPs in the GRAF subfamily including GRAF, GRAF2, GRAF3, and Oligophrenin-1 (OPHN1), only three are included in this model. OPHN1 contains the BAR, PH and GAP domains, but not the C-terminal SH3 domain. GRAF and GRAF2 show GAP activity towards RhoA and Cdc42. GRAF influences Rho-mediated cytoskeletal rearrangements and binds focal adhesion kinase. GRAF2 regulates caspase-activated p21-activated protein kinase-2. The SH3 domain of GRAF and GRAF2 binds PKNbeta, a target of the small GTPase Rho. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11883 cd11883 212816 SH3_Sdc25 Src Homology 3 domain of Sdc25/Cdc25 guanine nucleotide exchange factors. This subfamily is composed of the Saccharomyces cerevisiae guanine nucleotide exchange factors (GEFs) Sdc25 and Cdc25, and similar proteins. These GEFs regulate Ras by stimulating the GDP/GTP exchange on Ras. Cdc25 is involved in the Ras/PKA pathway that plays an important role in the regulation of metabolism, stress responses, and proliferation, depending on available nutrients and conditions. Proteins in this subfamily contain an N-terminal SH3 domain as well as REM (Ras exchanger motif) and RasGEF domains at the C-terminus. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11884 cd11884 212817 SH3_MYO15 Src Homology 3 domain of Myosin XV. This subfamily is composed of proteins with similarity to Myosin XVa. Myosin XVa is an unconventional myosin that is critical for the normal growth of mechanosensory stereocilia of inner ear hair cells. Mutations in the myosin XVa gene are associated with nonsyndromic hearing loss. Myosin XVa contains a unique N-terminal extension followed by a motor domain, light chain-binding IQ motifs, and a tail consisting of a pair of MyTH4-FERM tandems separated by a SH3 domain, and a PDZ domain. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd11885 cd11885 212818 SH3_SH3TC Src Homology 3 domain of SH3 domain and tetratricopeptide repeat-containing (SH3TC) proteins and similar domains. This subfamily is composed of vertebrate SH3TC proteins and hypothetical fungal proteins containing BAR and SH3 domains. Mammals contain two SH3TC proteins, SH3TC1 and SH3TC2. The function of SH3TC1 is unknown. SH3TC2 is localized in Schwann cells in the peripheral nervous system, where it interacts with Rab11 and plays a role in peripheral nerve myelination. Mutations in SH3TC2 are associated with Charcot-Marie-Tooth disease type 4C, a severe hereditary peripheral neuropathy with symptoms that include progressive scoliosis, delayed age of walking, muscular atrophy, distal weakness, and reduced nerve conduction velocity. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11886 cd11886 212819 SH3_BOI Src Homology 3 domain of fungal BOI-like proteins. This subfamily includes the Saccharomyces cerevisiae proteins BOI1 and BOI2, and similar proteins. They contain an N-terminal SH3 domain, a Sterile alpha motif (SAM), and a Pleckstrin homology (PH) domain at the C-terminus. BOI1 and BOI2 interact with the SH3 domain of Bem1p, a protein involved in bud formation. They promote polarized cell growth and participates in the NoCut signaling pathway, which is involved in the control of cytokinesis. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11887 cd11887 212820 SH3_Bbc1 Src Homology 3 domain of Bbc1 and similar domains. This subfamily is composed of Saccharomyces cerevisiae Bbc1p, also called Mti1p (Myosin tail region-interacting protein), and similar proteins. Bbc1p interacts with and regulates type I myosins in yeast, Myo3p and Myo5p, which are involved in actin cytoskeletal reorganization. It also binds and inhibits Las17, a WASp family protein that functions as an activator of the Arp2/3 complex. Bbc1p contains an N-terminal SH3 domain. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 60 matched cddid_all.tbl CDD cd11888 cd11888 212821 SH3_ARHGAP9_like Src Homology 3 domain of Rho GTPase-activating protein 9 and similar proteins. This subfamily is composed of Rho GTPase-activating proteins including mammalian ARHGAP9, and vertebrate ARHGAPs 12 and 27. RhoGAPs (or ARHGAPs) bind to Rho proteins and enhance the hydrolysis rates of bound GTP. ARHGAP9 functions as a GAP for Rac and Cdc42, but not for RhoA. It negatively regulates cell migration and adhesion. It also acts as a docking protein for the MAP kinases Erk2 and p38alpha, and may facilitate cross-talk between the Rho GTPase and MAPK pathways to control actin remodeling. ARHGAP27, also called CAMGAP1, shows GAP activity towards Rac1 and Cdc42. It binds the adaptor protein CIN85 and may play a role in clathrin-mediated endocytosis. ARHGAP12 has been shown to display GAP activity towards Rac1. It plays a role in regulating HFG-driven cell growth and invasiveness. ARHGAPs in this subfamily contain SH3, WW, Pleckstin homology (PH), and RhoGAP domains. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11889 cd11889 212822 SH3_Cyk3p-like Src Homology 3 domain of Cytokinesis protein 3 and similar proteins. Cytokinesis protein 3 (Cyk3 or Cyk3p) is a component of the actomyosin ring independent cytokinesis pathway in yeast. It interacts with Inn1 and facilitates its recruitment to the bud neck, thereby promoting cytokinesis. Cyk3p contains an N-terminal SH3 domain and a C-terminal transglutaminase-like domain. The Cyk3p SH3 domain binds to the C-terminal proline-rich region of Inn1. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11890 cd11890 212823 MIA Melanoma Inhibitory Activity protein. MIA is a single domain protein that adopts a Src Homology 3 (SH3) domain-like fold; it contains an additional antiparallel beta sheet and two disulfide bonds compared to classical SH3 domains. MIA is secreted from malignant melanoma cells and it plays an important role in melanoma development and invasion. MIA is expressed by chondrocytes in normal tissues and may be important in the cartilage cell phenotype. Unlike classical SH3 domains, MIA does not bind proline-rich ligands. It binds peptide ligands with sequence similarity to type III human fibronectin repeats. 98 matched cddid_all.tbl CDD cd11891 cd11891 212824 MIAL Melanoma Inhibitory Activity-Like protein. MIAL is specifically expressed in the cochlea and the vestibule of the inner ear and may contribute to inner ear dysfunction in humans. MIAL is a member of the recently identified family that also includes MIA, MIA2, and MIA3 (also called TANGO); MIA is the most studied member of the family. MIA is a single domain protein that adopts a Src Homology 3 (SH3) domain-like fold; it contains an additional antiparallel beta sheet and two disulfide bonds compared to classical SH3 domains. MIA is secreted from malignant melanoma cells and it plays an important role in melanoma development and invasion. MIA is expressed by chondrocytes in normal tissues and may be important in the cartilage cell phenotype. Unlike classical SH3 domains, MIA does not bind proline-rich ligands. 83 matched cddid_all.tbl CDD cd11892 cd11892 212825 SH3_MIA2 Src Homology 3 domain of Melanoma Inhibitory Activity 2 protein. MIA2 is expressed specifically in hepatocytes and its expression is controlled by hepatocyte nuclear factor 1 binding sites in the MIA2 promoter. It inhibits the growth and invasion of hepatocellular carcinomas (HCC) and may act as a tumor suppressor. A mutation in MIA2 in mice resulted in reduced cholesterol and triglycerides. Since MIA2 localizes to ER exit sites, it may function as an ER-to-Golgi trafficking protein that regulates lipid metabolism. MIA2 contains an N-terminal SH3-like domain, similar to MIA. It is a member of the recently identified family that also includes MIA, MIAL, and MIA3 (also called TANGO). MIA is a single domain protein that adopts a SH3 domain-like fold; it contains an additional antiparallel beta sheet and two disulfide bonds compared to classical SH3 domains. Unlike classical SH3 domains, MIA does not bind proline-rich ligands. 73 matched cddid_all.tbl CDD cd11893 cd11893 212826 SH3_MIA3 Src Homology 3 domain of Melanoma Inhibitory Activity 3 protein. MIA3, also called TANGO or TANGO1, acts as a tumor suppressor of malignant melanoma. It is downregulated or lost in melanoma cells lines. Unlike other MIA family members, MIA3 is widely expressed except in hematopoietic cells. MIA3 is an ER resident transmembrane protein that is required for the loading of collagen VII into transport vesicles. SNPs in the MIA3 gene have been associated with coronary arterial disease and myocardial infarction. MIA3 contains an N-terminal SH3-like domain, similar to MIA. It is a member of the recently identified family that also includes MIA, MIAL, and MIA2. MIA is a single domain protein that adopts a SH3 domain-like fold; it contains an additional antiparallel beta sheet and two disulfide bonds compared to classical SH3 domains. Unlike classical SH3 domains, MIA does not bind proline-rich ligands. 73 matched cddid_all.tbl CDD cd11894 cd11894 212827 SH3_FCHSD2_2 Second Src Homology 3 domain of FCH and double SH3 domains protein 2. FCHSD2 has a domain structure consisting of an N-terminal F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs), two SH3, and C-terminal proline-rich domains. It has only been characterized in silico and its function is unknown. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd11895 cd11895 212828 SH3_FCHSD1_2 Second Src Homology 3 domain of FCH and double SH3 domains protein 1. FCHSD1 has a domain structure consisting of an N-terminal F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs), two SH3, and C-terminal proline-rich domains. It has only been characterized in silico and its function is unknown. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 58 matched cddid_all.tbl CDD cd11896 cd11896 212829 SH3_SNX33 Src Homology 3 domain of Sorting Nexin 33. SNX33 interacts with Wiskott-Aldrich syndrome protein (WASP) and plays a role in the maintenance of cell shape and cell cycle progression. It modulates the shedding and endocytosis of cellular prion protein (PrP(c)) and amyloid precursor protein (APP). SNXs are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNX33 also contains BAR and SH3 domains. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11897 cd11897 212830 SH3_SNX18 Src Homology 3 domain of Sorting nexin 18. SNX18 is localized to peripheral endosomal structures, and acts in a trafficking pathway that is clathrin-independent but relies on AP-1 and PACS1. It binds FIP5 and is required for apical lumen formation. It may also play a role in axonal elongation. SNXs are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNX18 also contains BAR and SH3 domains. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11898 cd11898 212831 SH3_SNX9 Src Homology 3 domain of Sorting nexin 9. Sorting nexin 9 (SNX9), also known as SH3PX1, is a cytosolic protein that interacts with proteins associated with clathrin-coated pits such as Cdc-42-associated tyrosine kinase 2 (ACK2). It binds class I polyproline sequences found in dynamin 1/2 and the WASP/N-WASP actin regulators. SNX9 is localized to plasma membrane endocytic sites and acts primarily in clathrin-mediated endocytosis. Its array of interacting partners suggests that SNX9 functions at the interface between endocytosis and actin cytoskeletal organization. SNXs are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNX9 also contains BAR and SH3 domains. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11899 cd11899 212832 SH3_Nck2_1 First Src Homology 3 domain of Nck2 adaptor protein. Nck2 (also called Nckbeta or Growth factor receptor-bound protein 4, Grb4) plays a crucial role in connecting signaling pathways of tyrosine kinase receptors and important effectors in actin dynamics and cytoskeletal remodeling. It binds neuronal signaling proteins such as ephrinB and Disabled-1 (Dab-1) exclusively. Nck adaptor proteins regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates. They contain three SH3 domains and a C-terminal SH2 domain. They function downstream of the PDGFbeta receptor and are involved in Rho GTPase signaling and actin dynamics. Vertebrates contain two Nck adaptor proteins: Nck1 (also called Nckalpha) and Nck2, which show partly overlapping functions but also bind distinct targets. The first SH3 domain of Nck2 binds the PxxDY sequence in the CD3e cytoplasmic tail; this binding inhibits phosphorylation by Src kinases, resulting in the downregulation of TCR surface expression. SH3 domains are protein interaction domains that usually bind to proline-rich ligands with moderate affinity and selectivity, preferentially a PxxP motif. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 58 matched cddid_all.tbl CDD cd11900 cd11900 212833 SH3_Nck1_1 First Src Homology 3 domain of Nck1 adaptor protein. Nck1 (also called Nckalpha) plays a crucial role in connecting signaling pathways of tyrosine kinase receptors and important effectors in actin dynamics and cytoskeletal remodeling. It binds and activates RasGAP, resulting in the downregulation of Ras. It is also involved in the signaling of endothilin-mediated inhibition of cell migration. Nck adaptor proteins regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates. They contain three SH3 domains and a C-terminal SH2 domain. They function downstream of the PDGFbeta receptor and are involved in Rho GTPase signaling and actin dynamics. Vertebrates contain two Nck adaptor proteins: Nck1 (also called Nckalpha) and Nck2, which show partly overlapping functions but also bind distinct targets. The first SH3 domain of Nck1 binds the PxxDY sequence in the CD3e cytoplasmic tail; this binding inhibits phosphorylation by Src kinases, resulting in the downregulation of TCR surface expression. SH3 domains are protein interaction domains that usually bind to proline-rich ligands with moderate affinity and selectivity, preferentially a PxxP motif. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 59 matched cddid_all.tbl CDD cd11901 cd11901 212834 SH3_Nck1_2 Second Src Homology 3 domain of Nck1 adaptor protein. Nck1 (also called Nckalpha) plays a crucial role in connecting signaling pathways of tyrosine kinase receptors and important effectors in actin dynamics and cytoskeletal remodeling. It binds and activates RasGAP, resulting in the downregulation of Ras. It is also involved in the signaling of endothilin-mediated inhibition of cell migration. Nck adaptor proteins regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates. They contain three SH3 domains and a C-terminal SH2 domain. They function downstream of the PDGFbeta receptor and are involved in Rho GTPase signaling and actin dynamics. Vertebrates contain two Nck adaptor proteins: Nck1 (also called Nckalpha) and Nck2, which show partly overlapping functions but also bind distinct targets. The second SH3 domain of Nck appears to prefer ligands containing the APxxPxR motif. SH3 domains are protein interaction domains that usually bind to proline-rich ligands with moderate affinity and selectivity, preferentially a PxxP motif. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11902 cd11902 212835 SH3_Nck2_2 Second Src Homology 3 domain of Nck2 adaptor protein. Nck2 (also called Nckbeta or Growth factor receptor-bound protein 4, Grb4) plays a crucial role in connecting signaling pathways of tyrosine kinase receptors and important effectors in actin dynamics and cytoskeletal remodeling. It binds neuronal signaling proteins such as ephrinB and Disabled-1 (Dab-1) exclusively. Nck adaptor proteins regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates. They contain three SH3 domains and a C-terminal SH2 domain. They function downstream of the PDGFbeta receptor and are involved in Rho GTPase signaling and actin dynamics. Vertebrates contain two Nck adaptor proteins: Nck1 (also called Nckalpha) and Nck2, which show partly overlapping functions but also bind distinct targets. The second SH3 domain of Nck appears to prefer ligands containing the APxxPxR motif. SH3 domains are protein interaction domains that usually bind to proline-rich ligands with moderate affinity and selectivity, preferentially a PxxP motif. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11903 cd11903 212836 SH3_Nck2_3 Third Src Homology 3 domain of Nck2 adaptor protein. Nck2 (also called Nckbeta or Growth factor receptor-bound protein 4, Grb4) plays a crucial role in connecting signaling pathways of tyrosine kinase receptors and important effectors in actin dynamics and cytoskeletal remodeling. It binds neuronal signaling proteins such as ephrinB and Disabled-1 (Dab-1) exclusively. Nck adaptor proteins regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates. They contain three SH3 domains and a C-terminal SH2 domain. They function downstream of the PDGFbeta receptor and are involved in Rho GTPase signaling and actin dynamics. Vertebrates contain two Nck adaptor proteins: Nck1 (also called Nckalpha) and Nck2, which show partly overlapping functions but also bind distinct targets. The third SH3 domain of Nck appears to prefer ligands with a PxAPxR motif. SH3 domains are protein interaction domains that usually bind to proline-rich ligands with moderate affinity and selectivity, preferentially a PxxP motif. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 59 matched cddid_all.tbl CDD cd11904 cd11904 212837 SH3_Nck1_3 Third Src Homology 3 domain of Nck1 adaptor protein. Nck1 (also called Nckalpha) plays a crucial role in connecting signaling pathways of tyrosine kinase receptors and important effectors in actin dynamics and cytoskeletal remodeling. It binds and activates RasGAP, resulting in the downregulation of Ras. It is also involved in the signaling of endothilin-mediated inhibition of cell migration. Nck adaptor proteins regulate actin cytoskeleton dynamics by linking proline-rich effector molecules to protein tyrosine kinases and phosphorylated signaling intermediates. They contain three SH3 domains and a C-terminal SH2 domain. They function downstream of the PDGFbeta receptor and are involved in Rho GTPase signaling and actin dynamics. Vertebrates contain two Nck adaptor proteins: Nck1 (also called Nckalpha) and Nck2, which show partly overlapping functions but also bind distinct targets. The third SH3 domain of Nck appears to prefer ligands with a PxAPxR motif. SH3 domains are protein interaction domains that usually bind to proline-rich ligands with moderate affinity and selectivity, preferentially a PxxP motif. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11905 cd11905 212838 SH3_Tec Src Homology 3 domain of Tec (Tyrosine kinase expressed in hepatocellular carcinoma). Tec is a cytoplasmic (or nonreceptor) tyr kinase containing Src homology protein interaction domains (SH3, SH2) N-terminal to the catalytic tyr kinase domain. It also contains an N-terminal pleckstrin homology (PH) domain, which binds the products of PI3K and allows membrane recruitment and activation, and the Tec homology (TH) domain, which contains proline-rich and zinc-binding regions. It is more widely-expressed than other Tec subfamily kinases. Tec is found in endothelial cells, both B- and T-cells, and a variety of myeloid cells including mast cells, erythroid cells, platelets, macrophages and neutrophils. Tec is a key component of T-cell receptor (TCR) signaling, and is important in TCR-stimulated proliferation, IL-2 production and phospholipase C-gamma1 activation. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd11906 cd11906 212839 SH3_BTK Src Homology 3 domain of Bruton's tyrosine kinase. BTK is a cytoplasmic (or nonreceptor) tyr kinase containing Src homology protein interaction domains (SH3, SH2) N-terminal to the catalytic tyr kinase domain. It also contains an N-terminal pleckstrin homology (PH) domain, which binds the products of PI3K and allows membrane recruitment and activation, and the Tec homology (TH) domain with proline-rich and zinc-binding regions. Btk is expressed in B-cells, and a variety of myeloid cells including mast cells, platelets, neutrophils, and dendrictic cells. It interacts with a variety of partners, from cytosolic proteins to nuclear transcription factors, suggesting a diversity of functions. Stimulation of a diverse array of cell surface receptors, including antigen engagement of the B-cell receptor (BCR), leads to PH-mediated membrane translocation of Btk and subsequent phosphorylation by Src kinase and activation. Btk plays an important role in the life cycle of B-cells including their development, differentiation, proliferation, survival, and apoptosis. Mutations in Btk cause the primary immunodeficiency disease, X-linked agammaglobulinaemia (XLA) in humans. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11907 cd11907 212840 SH3_TXK Src Homology 3 domain of TXK, also called Resting lymphocyte kinase (Rlk). TXK is a cytoplasmic (or nonreceptor) tyr kinase containing Src homology protein interaction domains (SH3, SH2) N-terminal to the catalytic tyr kinase domain. It also contains an N-terminal cysteine-rich region. Rlk is expressed in T-cells and mast cell lines, and is a key component of T-cell receptor (TCR) signaling. It is important in TCR-stimulated proliferation, IL-2 production and phospholipase C-gamma1 activation. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11908 cd11908 212841 SH3_ITK Src Homology 3 domain of Interleukin-2-inducible T-cell Kinase. ITK (also known as Tsk or Emt) is a cytoplasmic (or nonreceptor) tyr kinase containing Src homology protein interaction domains (SH3, SH2) N-terminal to the catalytic tyr kinase domain. It also contains an N-terminal pleckstrin homology (PH) domain, which binds the products of PI3K and allows membrane recruitment and activation, and the Tec homology (TH) domain, which contains proline-rich and zinc-binding regions. ITK is expressed in T-cells and mast cells, and is important in their development and differentiation. Of the three Tec kinases expressed in T-cells, ITK plays the predominant role in T-cell receptor (TCR) signaling. It is activated by phosphorylation upon TCR crosslinking and is involved in the pathway resulting in phospholipase C-gamma1 activation and actin polymerization. It also plays a role in the downstream signaling of the T-cell costimulatory receptor CD28, the T-cell surface receptor CD2, and the chemokine receptor CXCR4. In addition, ITK is crucial for the development of T-helper(Th)2 effector responses. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd11909 cd11909 212842 SH3_PI3K_p85beta Src Homology 3 domain of the p85beta regulatory subunit of Class IA Phosphatidylinositol 3-kinases. Class I PI3Ks convert PtdIns(4,5)P2 to the critical second messenger PtdIns(3,4,5)P3. They are heterodimers and exist in multiple isoforms consisting of one catalytic subunit (out of four isoforms) and one of several regulatory subunits. Class IA PI3Ks associate with the p85 regulatory subunit family, which contains SH3, RhoGAP, and SH2 domains. The p85 subunits recruit the PI3K p110 catalytic subunit to the membrane, where p110 phosphorylates inositol lipids. Vertebrates harbor two p85 isoforms, called alpha and beta. In addition to regulating the p110 subunit, p85beta binds CD28 and may be involved in the activation and differentiation of antigen-stimulated T cells. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 74 matched cddid_all.tbl CDD cd11910 cd11910 212843 SH3_PI3K_p85alpha Src Homology 3 domain of the p85alpha regulatory subunit of Class IA Phosphatidylinositol 3-kinases. Class I PI3Ks convert PtdIns(4,5)P2 to the critical second messenger PtdIns(3,4,5)P3. They are heterodimers and exist in multiple isoforms consisting of one catalytic subunit (out of four isoforms) and one of several regulatory subunits. Class IA PI3Ks associate with the p85 regulatory subunit family, which contains SH3, RhoGAP, and SH2 domains. The p85 subunits recruit the PI3K p110 catalytic subunit to the membrane, where p110 phosphorylates inositol lipids. Vertebrates harbor two p85 isoforms, called alpha and beta. In addition to regulating the p110 subunit, p85alpha interacts with activated FGFR3. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 75 matched cddid_all.tbl CDD cd11911 cd11911 212844 SH3_CIP4-like Src Homology 3 domain of Cdc42-Interacting Protein 4. This subfamily is composed of Cdc42-Interacting Protein 4 (CIP4), Formin Binding Protein 17 (FBP17), FormiN Binding Protein 1-Like (FNBP1L), and similar proteins. CIP4 and FNBP1L are Cdc42 effectors that bind Wiskott-Aldrich syndrome protein (WASP) and function in endocytosis. CIP4 and FBP17 bind to the Fas ligand and may be implicated in the inflammatory response. CIP4 may also play a role in phagocytosis. It functions downstream of Cdc42 in PDGF-dependent actin reorganization and cell migration, and also regulates the activity of PDGFRbeta. It uses Src as a substrate in regulating the invasiveness of breast tumor cells. CIP4 may also play a role in the pathogenesis of Huntington's disease. Members of this subfamily typically contain an N-terminal F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain, a central Cdc42-binding HR1 domain, and a C-terminal SH3 domain. The SH3 domain of CIP4 associates with Gapex-5, a Rab31 GEF. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11912 cd11912 212845 SH3_Bzz1_1 First Src Homology 3 domain of Bzz1 and similar domains. Bzz1 (or Bzz1p) is a WASP/Las17-interacting protein involved in endocytosis and trafficking to the vacuole. It physically interacts with type I myosins and functions in the early steps of endocytosis. Together with other proteins, it induces membrane scission in yeast. Bzz1 contains an N-terminal F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs), a central coiled-coil, and two C-terminal SH3 domains. This model represents the first C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11913 cd11913 212846 SH3_BAIAP2L1 Src Homology 3 domain of Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2-Like 1, also called Insulin Receptor Tyrosine Kinase Substrate (IRTKS). BAIAP2L1 or IRTKS is widely expressed, serves as a substrate for the insulin receptor, and binds the small GTPase Rac. It plays a role in regulating the actin cytoskeleton and colocalizes with F-actin, cortactin, VASP, and vinculin. BAIAP2L1 expression leads to the formation of short actin bundles, distinct from filopodia-like protrusions induced by the expression of the related protein IRSp53. IRTKS mediates the recruitment of effector proteins Tir and EspFu, which regulate host cell actin reorganization, to bacterial attachment sites. It contains an N-terminal IMD or Inverse-Bin/Amphiphysin/Rvs (I-BAR) domain, an SH3 domain, and a WASP homology 2 (WH2) actin-binding motif at the C-terminus. The SH3 domain of IRTKS has been shown to bind the proline-rich C-terminus of EspFu. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 58 matched cddid_all.tbl CDD cd11914 cd11914 212847 SH3_BAIAP2L2 Src Homology 3 domain of Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2-Like 2. BAIAP2L2 co-localizes with clathrin plaques but its function has not been determined. It contains an N-terminal IMD or Inverse-Bin/Amphiphysin/Rvs (I-BAR) domain, an SH3 domain, and a WASP homology 2 (WH2) actin-binding motif at the C-terminus. The related proteins, BAIAP2L1 and IRSp53, function as regulators of membrane dynamics and the actin cytoskeleton. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 59 matched cddid_all.tbl CDD cd11915 cd11915 212848 SH3_Irsp53 Src Homology 3 domain of Insulin Receptor tyrosine kinase Substrate p53. IRSp53 is also known as BAIAP2 (Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2). It is a scaffolding protein that takes part in many signaling pathways including Cdc42-induced filopodia formation, Rac-mediated lamellipodia extension, and spine morphogenesis. IRSp53 exists as multiple splicing variants that differ mainly at the C-termini. One variant (T-form) is expressed exclusively in human breast cancer cells. The gene encoding IRSp53 is a putative susceptibility gene for Gilles de la Tourette syndrome. IRSp53 can also mediate the recruitment of effector proteins Tir and EspFu, which regulate host cell actin reorganization, to bacterial attachment sites. It contains an N-terminal IMD, a CRIB (Cdc42 and Rac interactive binding motif), an SH3 domain, and a WASP homology 2 (WH2) actin-binding motif at the C-terminus. The SH3 domain of IRSp53 has been shown to bind the proline-rich C-terminus of EspFu. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 59 matched cddid_all.tbl CDD cd11916 cd11916 212849 SH3_Sorbs1_3 Third (or C-terminal) Src Homology 3 domain of Sorbin and SH3 domain containing 1 (Sorbs1), also called ponsin. Sorbs1 is also called ponsin, SH3P12, or CAP (c-Cbl associated protein). It is an adaptor protein containing one sorbin homology (SoHo) and three SH3 domains. It binds Cbl and plays a major role in regulating the insulin signaling pathway by enhancing insulin-induced phosphorylation of Cbl. Sorbs1, like vinexin, localizes at cell-ECM and cell-cell adhesion sites where it binds vinculin, paxillin, and afadin. It may function in the control of cell motility. Other interaction partners of Sorbs1 include c-Abl, Sos, flotillin, Grb4, ataxin-7, filamin C, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 59 matched cddid_all.tbl CDD cd11917 cd11917 212850 SH3_Sorbs2_3 Third (or C-terminal) Src Homology 3 domain of Sorbin and SH3 domain containing 2 (Sorbs2), also called Arg-binding protein 2 (ArgBP2). Sorbs2 or ArgBP2 is an adaptor protein containing one sorbin homology (SoHo) and three SH3 domains. It regulates actin-dependent processes including cell adhesion, morphology, and migration. It is expressed in many tissues and is abundant in the heart. Like vinexin, it is found in focal adhesion where it interacts with vinculin and afadin. It also localizes in epithelial cell stress fibers and in cardiac muscle cell Z-discs. Sorbs2 has been implicated to play roles in the signaling of c-Arg, Akt, and Pyk2. Other interaction partners of Sorbs2 include c-Abl, flotillin, spectrin, dynamin 1/2, synaptojanin, PTP-PEST, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 61 matched cddid_all.tbl CDD cd11918 cd11918 212851 SH3_Vinexin_3 Third (or C-terminal) Src Homology 3 domain of Vinexin, also called Sorbin and SH3 domain containing 3 (Sorbs3). Vinexin is also called Sorbs3, SH3P3, and SH3-containing adapter molecule 1 (SCAM-1). It is an adaptor protein containing one sorbin homology (SoHo) and three SH3 domains. Vinexin was first identified as a vinculin binding protein; it is co-localized with vinculin at cell-ECM and cell-cell adhesion sites. There are several splice variants of vinexin: alpha, which contains the SoHo and three SH3 domains and displays tissue-specific expression; and beta, which contains only the three SH3 domains and is widely expressed. Vinexin alpha stimulates the accumulation of F-actin at focal contact sites. Vinexin also promotes keratinocyte migration and wound healing. The SH3 domains of vinexin have been reported to bind a number of ligands including vinculin, WAVE2, DLG5, Abl, and Cbl. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 58 matched cddid_all.tbl CDD cd11919 cd11919 212852 SH3_Sorbs1_1 First Src Homology 3 domain of Sorbin and SH3 domain containing 1 (Sorbs1), also called ponsin. Sorbs1 is also called ponsin, SH3P12, or CAP (c-Cbl associated protein). It is an adaptor protein containing one sorbin homology (SoHo) and three SH3 domains. It binds Cbl and plays a major role in regulating the insulin signaling pathway by enhancing insulin-induced phosphorylation of Cbl. Sorbs1, like vinexin, localizes at cell-ECM and cell-cell adhesion sites where it binds vinculin, paxillin, and afadin. It may function in the control of cell motility. Other interaction partners of Sorbs1 include c-Abl, Sos, flotillin, Grb4, ataxin-7, filamin C, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11920 cd11920 212853 SH3_Sorbs2_1 First Src Homology 3 domain of Sorbin and SH3 domain containing 2 (Sorbs2), also called Arg-binding protein 2 (ArgBP2). Sorbs2 or ArgBP2 is an adaptor protein containing one sorbin homology (SoHo) and three SH3 domains. It regulates actin-dependent processes including cell adhesion, morphology, and migration. It is expressed in many tissues and is abundant in the heart. Like vinexin, it is found in focal adhesion where it interacts with vinculin and afadin. It also localizes in epithelial cell stress fibers and in cardiac muscle cell Z-discs. Sorbs2 has been implicated to play roles in the signaling of c-Arg, Akt, and Pyk2. Other interaction partners of Sorbs2 include c-Abl, flotillin, spectrin, dynamin 1/2, synaptojanin, PTP-PEST, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11921 cd11921 212854 SH3_Vinexin_1 First Src Homology 3 domain of Vinexin, also called Sorbin and SH3 domain containing 3 (Sorbs3). Vinexin is also called Sorbs3, SH3P3, and SH3-containing adapter molecule 1 (SCAM-1). It is an adaptor protein containing one sorbin homology (SoHo) and three SH3 domains. Vinexin was first identified as a vinculin binding protein; it is co-localized with vinculin at cell-ECM and cell-cell adhesion sites. There are several splice variants of vinexin: alpha, which contains the SoHo and three SH3 domains and displays tissue-specific expression; and beta, which contains only the three SH3 domains and is widely expressed. Vinexin alpha stimulates the accumulation of F-actin at focal contact sites. Vinexin also promotes keratinocyte migration and wound healing. The SH3 domains of vinexin have been reported to bind a number of ligands including vinculin, WAVE2, DLG5, Abl, and Cbl. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11922 cd11922 212855 SH3_Sorbs1_2 Second Src Homology 3 domain of Sorbin and SH3 domain containing 1 (Sorbs1), also called ponsin. Sorbs1 is also called ponsin, SH3P12, or CAP (c-Cbl associated protein). It is an adaptor protein containing one sorbin homology (SoHo) and three SH3 domains. It binds Cbl and plays a major role in regulating the insulin signaling pathway by enhancing insulin-induced phosphorylation of Cbl. Sorbs1, like vinexin, localizes at cell-ECM and cell-cell adhesion sites where it binds vinculin, paxillin, and afadin. It may function in the control of cell motility. Other interaction partners of Sorbs1 include c-Abl, Sos, flotillin, Grb4, ataxin-7, filamin C, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 58 matched cddid_all.tbl CDD cd11923 cd11923 212856 SH3_Sorbs2_2 Second Src Homology 3 domain of Sorbin and SH3 domain containing 2 (Sorbs2), also called Arg-binding protein 2 (ArgBP2). Sorbs2 or ArgBP2 is an adaptor protein containing one sorbin homology (SoHo) and three SH3 domains. It regulates actin-dependent processes including cell adhesion, morphology, and migration. It is expressed in many tissues and is abundant in the heart. Like vinexin, it is found in focal adhesion where it interacts with vinculin and afadin. It also localizes in epithelial cell stress fibers and in cardiac muscle cell Z-discs. Sorbs2 has been implicated to play roles in the signaling of c-Arg, Akt, and Pyk2. Other interaction partners of Sorbs2 include c-Abl, flotillin, spectrin, dynamin 1/2, synaptojanin, PTP-PEST, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11924 cd11924 212857 SH3_Vinexin_2 Second Src Homology 3 domain of Vinexin, also called Sorbin and SH3 domain containing 3 (Sorbs3). Vinexin is also called Sorbs3, SH3P3, and SH3-containing adapter molecule 1 (SCAM-1). It is an adaptor protein containing one sorbin homology (SoHo) and three SH3 domains. Vinexin was first identified as a vinculin binding protein; it is co-localized with vinculin at cell-ECM and cell-cell adhesion sites. There are several splice variants of vinexin: alpha, which contains the SoHo and three SH3 domains and displays tissue-specific expression; and beta, which contains only the three SH3 domains and is widely expressed. Vinexin alpha stimulates the accumulation of F-actin at focal contact sites. Vinexin also promotes keratinocyte migration and wound healing. The SH3 domains of vinexin have been reported to bind a number of ligands including vinculin, WAVE2, DLG5, Abl, and Cbl. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd11925 cd11925 212858 SH3_SH3RF3_3 Third Src Homology 3 domain of SH3 domain containing ring finger 3, an E3 ubiquitin-protein ligase. SH3RF3 is also called POSH2 (Plenty of SH3s 2) or SH3MD4 (SH3 multiple domains protein 4). It is a scaffold protein with E3 ubiquitin-protein ligase activity. It was identified in the screen for interacting partners of p21-activated kinase 2 (PAK2). It may play a role in regulating JNK mediated apoptosis in certain conditions. It also interacts with GTP-loaded Rac1. SH3RF3 is highly homologous to SH3RF1; it also contains an N-terminal RING finger domain and four SH3 domains. This model represents the third SH3 domain, located in the middle, of SH3RF3. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11926 cd11926 212859 SH3_SH3RF1_3 Third Src Homology 3 domain of SH3 domain containing ring finger 1, an E3 ubiquitin-protein ligase. SH3RF1 is also called POSH (Plenty of SH3s) or SH3MD2 (SH3 multiple domains protein 2). It is a scaffold protein that acts as an E3 ubiquitin-protein ligase. It plays a role in calcium homeostasis through the control of the ubiquitin domain protein Herp. It may also have a role in regulating death receptor mediated and JNK mediated apoptosis. SH3RF1 also enhances the ubiquitination of ROMK1 potassium channel resulting in its increased endocytosis. It contains an N-terminal RING finger domain and four SH3 domains. This model represents the third SH3 domain, located in the middle, of SH3RF1. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11927 cd11927 212860 SH3_SH3RF1_1 First Src Homology 3 domain of SH3 domain containing ring finger protein 1, an E3 ubiquitin-protein ligase. SH3RF1 is also called POSH (Plenty of SH3s) or SH3MD2 (SH3 multiple domains protein 2). It is a scaffold protein that acts as an E3 ubiquitin-protein ligase. It plays a role in calcium homeostasis through the control of the ubiquitin domain protein Herp. It may also have a role in regulating death receptor mediated and JNK mediated apoptosis. SH3RF1 also enhances the ubiquitination of ROMK1 potassium channel resulting in its increased endocytosis. It contains an N-terminal RING finger domain and four SH3 domains. This model represents the first SH3 domain, located at the N-terminal half, of SH3RF1. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11928 cd11928 212861 SH3_SH3RF3_1 First Src Homology 3 domain of SH3 domain containing ring finger 3, an E3 ubiquitin-protein ligase. SH3RF3 is also called POSH2 (Plenty of SH3s 2) or SH3MD4 (SH3 multiple domains protein 4). It is a scaffold protein with E3 ubiquitin-protein ligase activity. It was identified in the screen for interacting partners of p21-activated kinase 2 (PAK2). It may play a role in regulating JNK mediated apoptosis in certain conditions. It also interacts with GTP-loaded Rac1. SH3RF3 is highly homologous to SH3RF1; it also contains an N-terminal RING finger domain and four SH3 domains. This model represents the first SH3 domain, located at the N-terminal half, of SH3RF3. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11929 cd11929 212862 SH3_SH3RF2_1 First Src Homology 3 domain of SH3 domain containing ring finger 2. SH3RF2 is also called POSHER (POSH-eliminating RING protein) or HEPP1 (heart protein phosphatase 1-binding protein). It acts as an anti-apoptotic regulator of the JNK pathway by binding to and promoting the degradation of SH3RF1 (or POSH), a scaffold protein that is required for pro-apoptotic JNK activation. It may also play a role in cardiac functions together with protein phosphatase 1. SH3RF2 contains an N-terminal RING finger domain and three SH3 domains. This model represents the first SH3 domain, located at the N-terminal half, of SH3RF2. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11930 cd11930 212863 SH3_SH3RF1_2 Second Src Homology 3 domain of SH3 domain containing ring finger protein 1, an E3 ubiquitin-protein ligase. SH3RF1 is also called POSH (Plenty of SH3s) or SH3MD2 (SH3 multiple domains protein 2). It is a scaffold protein that acts as an E3 ubiquitin-protein ligase. It plays a role in calcium homeostasis through the control of the ubiquitin domain protein Herp. It may also have a role in regulating death receptor mediated and JNK mediated apoptosis. SH3RF1 also enhances the ubiquitination of ROMK1 potassium channel resulting in its increased endocytosis. It contains an N-terminal RING finger domain and four SH3 domains. This model represents the second SH3 domain, located C-terminal of the first SH3 domain at the N-terminal half, of SH3RF1. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11931 cd11931 212864 SH3_SH3RF3_2 Second Src Homology 3 domain of SH3 domain containing ring finger 3, an E3 ubiquitin-protein ligase. SH3RF3 is also called POSH2 (Plenty of SH3s 2) or SH3MD4 (SH3 multiple domains protein 4). It is a scaffold protein with E3 ubiquitin-protein ligase activity. It was identified in the screen for interacting partners of p21-activated kinase 2 (PAK2). It may play a role in regulating JNK mediated apoptosis in certain conditions. It also interacts with GTP-loaded Rac1. SH3RF3 is highly homologous to SH3RF1; it also contains an N-terminal RING finger domain and four SH3 domains. This model represents the second SH3 domain, located C-terminal of the first SH3 domain at the N-terminal half, of SH3RF3. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11932 cd11932 212865 SH3_SH3RF2_2 Second Src Homology 3 domain of SH3 domain containing ring finger 2. SH3RF2 is also called POSHER (POSH-eliminating RING protein) or HEPP1 (heart protein phosphatase 1-binding protein). It acts as an anti-apoptotic regulator of the JNK pathway by binding to and promoting the degradation of SH3RF1 (or POSH), a scaffold protein that is required for pro-apoptotic JNK activation. It may also play a role in cardiac functions together with protein phosphatase 1. SH3RF2 contains an N-terminal RING finger domain and three SH3 domains. This model represents the second SH3 domain, located C-terminal of the first SH3 domain at the N-terminal half, of SH3RF2. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11933 cd11933 212866 SH3_Nebulin_C C-terminal Src Homology 3 domain of Nebulin. Nebulin is a giant filamentous protein (600-900 kD) that is expressed abundantly in skeletal muscle. It binds to actin thin filaments and regulates its assembly and function. Nebulin was thought to be part of a molecular ruler complex that is critical in determining the lengths of actin thin filaments in skeletal muscle since its length, which varies due to alternative splicing, correlates with the length of thin filaments in various muscle types. Recent studies indicate that nebulin regulates thin filament length by stabilizing the filaments and preventing depolymerization. Mutations in nebulin can cause nemaline myopathy, characterized by muscle weakness which can be severe and can lead to neonatal lethality. Nebulin contains an N-terminal LIM domain, many nebulin repeats/super repeats, and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 58 matched cddid_all.tbl CDD cd11934 cd11934 212867 SH3_Lasp1_C C-terminal Src Homology 3 domain of LIM and SH3 domain protein 1. Lasp1 is a cytoplasmic protein that binds focal adhesion proteins and is involved in cell signaling, migration, and proliferation. It is overexpressed in several cancer cells including breast, ovarian, bladder, and liver. In cancer cells, it can be found in the nucleus; its degree of nuclear localization correlates with tumor size and poor prognosis. Lasp1 is a 36kD protein containing an N-terminal LIM domain, two nebulin repeats, and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 59 matched cddid_all.tbl CDD cd11935 cd11935 212868 SH3_Nebulette_C C-terminal Src Homology 3 domain of Nebulette and LIM-nebulette (or Lasp2). Nebulette is a cardiac-specific protein that localizes to the Z-disc. It interacts with tropomyosin and is important in stabilizing actin thin filaments in cardiac muscles. Polymorphisms in the nebulette gene are associated with dilated cardiomyopathy, with some mutations resulting in severe heart failure. Nebulette is a 107kD protein that contains an N-terminal acidic region, multiple nebulin repeats, and a C-terminal SH3 domain. LIM-nebulette, also called Lasp2 (LIM and SH3 domain protein 2), is an alternatively spliced variant of nebulette. Although it shares a gene with nebulette, Lasp2 is not transcribed from a muscle-specific promoter, giving rise to its multiple tissue expression pattern with highest amounts in the brain. It can crosslink actin filaments and it affects cell spreading. Lasp2 is a 34kD protein containing an N-terminal LIM domain, three nebulin repeats, and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 58 matched cddid_all.tbl CDD cd11936 cd11936 212869 SH3_UBASH3B Src homology 3 domain of Ubiquitin-associated and SH3 domain-containing protein B. UBASH3B, also called Suppressor of T cell receptor Signaling (STS)-1 or T cell Ubiquitin LigAnd (TULA)-2 is an active phosphatase that is expressed ubiquitously. The phosphatase activity of UBASH3B is essential for its roles in the suppression of TCR signaling and the regulation of EGFR. It also interacts with Syk and functions as a negative regulator of platelet glycoprotein VI signaling. TULA proteins contain an N-terminal UBA domain, a central SH3 domain, and a C-terminal histidine phosphatase domain. They bind c-Cbl through the SH3 domain and to ubiquitin via UBA. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 62 matched cddid_all.tbl CDD cd11937 cd11937 212870 SH3_UBASH3A Src homology 3 domain of Ubiquitin-associated and SH3 domain-containing protein A. UBASH3A is also called Cbl-Interacting Protein 4 (CLIP4), T cell Ubiquitin LigAnd (TULA), or T cell receptor Signaling (STS)-2. It is only found in lymphoid cells and exhibits weak phosphatase activity. UBASH3A facilitates T cell-induced apoptosis through interaction with the apoptosis-inducing factor AIF. It is involved in regulating the level of phosphorylation of the zeta-associated protein (ZAP)-70 tyrosine kinase. TULA proteins contain an N-terminal UBA domain, a central SH3 domain, and a C-terminal histidine phosphatase domain. They bind c-Cbl through the SH3 domain and to ubiquitin via UBA. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 60 matched cddid_all.tbl CDD cd11938 cd11938 212871 SH3_ARHGEF16_26 Src homology 3 domain of the Rho guanine nucleotide exchange factors ARHGEF16 and ARHGEF26. ARHGEF16, also called ephexin-4, acts as a GEF for RhoG, activating it by exchanging bound GDP for free GTP. RhoG is a small GTPase that is a crucial regulator of Rac in migrating cells. ARHGEF16 interacts directly with the ephrin receptor EphA2 and mediates cell migration and invasion in breast cancer cells by activating RhoG. ARHGEF26, also called SGEF (SH3 domain-containing guanine exchange factor), also activates RhoG. It is highly expressed in liver and may play a role in regulating membrane dynamics. ARHGEF16 and ARHGEF26 contain RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), and SH3 domains. The SH3 domains of ARHGEFs play an autoinhibitory role through intramolecular interactions with a proline-rich region N-terminal to the DH domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11939 cd11939 212872 SH3_ephexin1 Src homology 3 domain of the Rho guanine nucleotide exchange factor, ephexin-1 (also called NGEF or ARHGEF27). Ephexin-1, also called NGEF (neuronal GEF) or ARHGEF27, activates RhoA, Tac1, and Cdc42 by exchanging bound GDP for free GTP. It is expressed mainly in the brain in a region associated with movement control. It regulates the stability of postsynaptic acetylcholine receptor (AChR) clusters and thus, plays a critical role in the maturation and neurotransmission of neuromuscular junctions. Ephexin-1 directly interacts with the ephrin receptor EphA4 and their coexpression enhances the ability of ephexin-1 to activate RhoA. It is required for normal axon growth and EphA-induced growth cone collapse. Ephexin-1 contains RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), and SH3 domains. The SH3 domains of ARHGEFs play an autoinhibitory role through intramolecular interactions with a proline-rich region N-terminal to the DH domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11940 cd11940 212873 SH3_ARHGEF5_19 Src homology 3 domain of the Rho guanine nucleotide exchange factors ARHGEF5 and ARHGEF19. ARHGEF5, also called ephexin-3 or TIM (Transforming immortalized mammary oncogene), is a potent activator of RhoA and it plays roles in regulating cell shape, adhesion, and migration. It binds to the SH3 domain of Src and is involved in regulating Src-induced podosome formation. ARHGEF19, also called ephexin-2 or WGEF (weak-similarity GEF), is highly expressed in the intestine, liver, heart and kidney. It activates RhoA, Cdc42, and Rac 1, and has been shown to activate RhoA in the Wnt-PCP (planar cell polarity) pathway. It is involved in the regulation of cell polarity and cytoskeletal reorganization. ARHGEF5 and ARHGEF19 contain RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), and SH3 domains. The SH3 domains of ARHGEFs play an autoinhibitory role through intramolecular interactions with a proline-rich region N-terminal to the DH domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11941 cd11941 212874 SH3_ARHGEF37_C2 Second C-terminal Src homology 3 domain of Rho guanine nucleotide exchange factor 37. ARHGEF37 contains a RhoGEF [or Dbl homology (DH)] domain followed by a Bin/Amphiphysin/Rvs (BAR) domain, and two C-terminal SH3 domains. Its specific function is unknown. Its domain architecture is similar to the C-terminal half of DNMBP or Tuba, a cdc42-specific GEF that provides a functional link between dynamin, Rho GTPase signaling, and actin dynamics, and plays an important role in regulating cell junction configuration. GEFs activate small GTPases by exchanging bound GDP for free GTP. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11942 cd11942 212875 SH3_JIP2 Src homology 3 domain of JNK-interacting protein 2. JNK-interacting protein 2 (JIP2) is also called Mitogen-activated protein kinase 8-interacting protein 2 (MAPK8IP2) or Islet-brain-2 (IB2). It is widely expressed in the brain, where it forms complexes with fibroblast growth factor homologous factors (FHFs), which facilitates activation of the p38delta MAPK. JIP2 is enriched in postsynaptic densities and may play a role in motor and cognitive function. In addition to a JNK binding domain, JIP2 also contains SH3 and Phosphotyrosine-binding (PTB) domains. The SH3 domain of the related protein JIP1 homodimerizes at the interface usually involved in proline-rich ligand recognition, despite the lack of this motif in the domain itself. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11943 cd11943 212876 SH3_JIP1 Src homology 3 domain of JNK-interacting protein 1. JNK-interacting protein 1 (JIP1) is also called Islet-brain 1 (IB1) or Mitogen-activated protein kinase 8-interacting protein 1 (MAPK8IP1). It is highly expressed in neurons, where it functions as an adaptor linking motor to cargo during axonal transport. It also affects microtubule dynamics in neurons. JIP1 is also found in pancreatic beta-cells, where it is involved in regulating insulin secretion. In addition to a JNK binding domain, JIP1 also contains SH3 and Phosphotyrosine-binding (PTB) domains. Its SH3 domain homodimerizes at the interface usually involved in proline-rich ligand recognition, despite the lack of this motif in the domain itself. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11944 cd11944 212877 SH3_Endophilin_B2 Src homology 3 domain of Endophilin-B2. Endophilin-B2, also called SH3GLB2 (SH3-domain GRB2-like endophilin B2), is a cytoplasmic protein that interacts with the apoptosis inducer Bax. It is overexpressed in prostate cancer metastasis and has been identified as a cancer antigen with potential utility in immunotherapy. Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. They contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. Endophilin-B2 forms homo- and heterodimers (with endophilin-B1) through its BAR domain. The related protein endophilin-B1 interacts with amphiphysin 1 and dynamin 1 through its SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11945 cd11945 212878 SH3_Endophilin_B1 Src homology 3 domain of Endophilin-B1. Endophilin-B1, also called Bax-interacting factor 1 (Bif-1) or SH3GLB1 (SH3-domain GRB2-like endophilin B1), is localized mainly to the Golgi apparatus. It is involved in the regulation of many biological events including autophagy, tumorigenesis, nerve growth factor (NGF) trafficking, neurite outgrowth, mitochondrial outer membrane dynamics, and cell death. Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. They contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. Endophilin-B1 forms homo- and heterodimers (with endophilin-B2) through its BAR domain. It interacts with amphiphysin 1 and dynamin 1 through its SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 61 matched cddid_all.tbl CDD cd11946 cd11946 212879 SH3_GRB2_N N-terminal Src homology 3 domain of Growth factor receptor-bound protein 2. GRB2 is a critical signaling molecule that regulates the Ras pathway by linking tyrosine kinases to the Ras guanine nucleotide releasing protein Sos (son of sevenless), which converts Ras to the active GTP-bound state. It is ubiquitously expressed in all tissues throughout development and is important in cell cycle progression, motility, morphogenesis, and angiogenesis. In lymphocytes, GRB2 is associated with antigen receptor signaling components. GRB2 contains an N-terminal SH3 domain, a central SH2 domain, and a C-terminal SH3 domain. Its N-terminal SH3 domain binds to Sos and Sos-derived proline-rich peptides. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd11947 cd11947 212880 SH3_GRAP2_N N-terminal Src homology 3 domain of GRB2-related adaptor protein 2. GRAP2 is also called GADS (GRB2-related adapter downstream of Shc), GrpL, GRB2L, Mona, or GRID (Grb2-related protein with insert domain). It is expressed specifically in the hematopoietic system. It plays an important role in T cell receptor (TCR) signaling by promoting the formation of the SLP-76:LAT complex, which couples the TCR to the Ras pathway. It also have roles in antigen-receptor and tyrosine kinase mediated signaling. GRAP2 is unique from other GRB2-like adaptor proteins in that it can be regulated by caspase cleavage. It contains an N-terminal SH3 domain, a central SH2 domain, and a C-terminal SH3 domain. The N-terminal SH3 domain of the related protein GRB2 binds to Sos and Sos-derived proline-rich peptides. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11948 cd11948 212881 SH3_GRAP_N N-terminal Src homology 3 domain of GRB2-related adaptor protein. GRAP is a GRB-2 like adaptor protein that is highly expressed in lymphoid tissues. It acts as a negative regulator of T cell receptor (TCR)-induced lymphocyte proliferation by downregulating the signaling to the Ras/ERK pathway. It has been identified as a regulator of TGFbeta signaling in diabetic kidney tubules and may have a role in the pathogenesis of the disease. GRAP contains an N-terminal SH3 domain, a central SH2 domain, and a C-terminal SH3 domain. The N-terminal SH3 domain of the related protein GRB2 binds to Sos and Sos-derived proline-rich peptides. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11949 cd11949 212882 SH3_GRB2_C C-terminal Src homology 3 domain of Growth factor receptor-bound protein 2. GRB2 is a critical signaling molecule that regulates the Ras pathway by linking tyrosine kinases to the Ras guanine nucleotide releasing protein Sos (son of sevenless), which converts Ras to the active GTP-bound state. It is ubiquitously expressed in all tissues throughout development and is important in cell cycle progression, motility, morphogenesis, and angiogenesis. In lymphocytes, GRB2 is associated with antigen receptor signaling components. GRB2 contains an N-terminal SH3 domain, a central SH2 domain, and a C-terminal SH3 domain. The C-terminal SH3 domain of GRB2 binds to Gab2 (Grb2-associated binder 2) through epitopes containing RxxK motifs, as well as to the proline-rich C-terminus of FGRF2. SH3 domains are protein interaction domains that typically bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11950 cd11950 212883 SH3_GRAP2_C C-terminal Src homology 3 domain of GRB2-related adaptor protein 2. GRAP2 is also called GADS (GRB2-related adapter downstream of Shc), GrpL, GRB2L, Mona, or GRID (Grb2-related protein with insert domain). It is expressed specifically in the hematopoietic system. It plays an important role in T cell receptor (TCR) signaling by promoting the formation of the SLP-76:LAT complex, which couples the TCR to the Ras pathway. It also has roles in antigen-receptor and tyrosine kinase mediated signaling. GRAP2 is unique from other GRB2-like adaptor proteins in that it can be regulated by caspase cleavage. It contains an N-terminal SH3 domain, a central SH2 domain, and a C-terminal SH3 domain. The C-terminal SH3 domain of GRAP2 binds to different motifs found in substrate peptides including the typical PxxP motif in hematopoietic progenitor kinase 1 (HPK1), the RxxK motif in SLP-76 and HPK1, and the RxxxxK motif in phosphatase-like protein HD-PTP. SH3 domains are protein interaction domains that typically bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11951 cd11951 212884 SH3_GRAP_C C-terminal Src homology 3 domain of GRB2-related adaptor protein. GRAP is a GRB-2 like adaptor protein that is highly expressed in lymphoid tissues. It acts as a negative regulator of T cell receptor (TCR)-induced lymphocyte proliferation by downregulating the signaling to the Ras/ERK pathway. It has been identified as a regulator of TGFbeta signaling in diabetic kidney tubules and may have a role in the pathogenesis of the disease. GRAP contains an N-terminal SH3 domain, a central SH2 domain, and a C-terminal SH3 domain. The C-terminal SH3 domains (SH3c) of the related proteins, GRB2 and GRAP2, have been shown to bind to classical PxxP motif ligands, as well as to non-classical motifs. GRB2 SH3c binds Gab2 (Grb2-associated binder 2) through epitopes containing RxxK motifs, while the SH3c of GRAP2 binds to the phosphatase-like protein HD-PTP via a RxxxxK motif. SH3 domains are protein interaction domains that typically bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11952 cd11952 212885 SH3_iASPP Src Homology 3 (SH3) domain of Inhibitor of ASPP protein (iASPP). iASPP, also called RelA-associated inhibitor (RAI), is an oncoprotein that inhibits the apoptotic transactivation potential of p53. It is upregulated in human breast cancers expressing wild-type p53, in acute leukemias regardless of the p53 mutation status, as well as in ovarian cancer where it is associated with poor patient outcome and chemoresistance. iASPP is also a binding partner and negative regulator of p65RelA, which promotes cell proliferation and inhibits apoptosis; p65RelA has the opposite effect on cell growth compared to the p53 family. It contains a proline-rich region, four ankyrin (ANK) repeats, and an SH3 domain at its C-terminal half. The SH3 domain and the ANK repeats of iASPP contribute to the p53 binding site; they bind to the DNA binding domain of p53. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd11953 cd11953 212886 SH3_ASPP2 Src Homology 3 (SH3) domain of Apoptosis Stimulating of p53 protein 2. ASPP2 is the full length form of the previously-identified tumor supressor, p53-binding protein 2 (p53BP2). ASPP2 activates the apoptotic function of the p53 family of tumor suppressors (p53, p63, and p73). It plays a central role in regulating apoptosis and cell growth; ASPP2-deficient mice show postnatal death. Downregulated expression of ASPP2 is frequently found in breast tumors, lung cancer, and diffuse large B-cell lymphoma where it is correlated with a poor clinical outcome. ASPP2 contains a proline-rich region, four ankyrin (ANK) repeats, and an SH3 domain at its C-terminal half. The SH3 domain and the ANK repeats of ASPP2 contribute to the p53 binding site; they bind to the DNA binding domain of p53. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11954 cd11954 212887 SH3_ASPP1 Src Homology 3 domain of Apoptosis Stimulating of p53 protein 1. ASPP1, like ASPP2, activates the apoptotic function of the p53 family of tumor suppressors (p53, p63, and p73). In addition, it functions in the cytoplasm to regulate the nuclear localization of the transcriptional cofactors YAP and TAZ by inihibiting their phosphorylation; YAP and TAZ are important regulators of cell expansion, differentiation, migration, and invasion. ASPP1 is downregulated in breast tumors expressing wild-type p53. It contains a proline-rich region, four ankyrin (ANK) repeats, and an SH3 domain at its C-terminal half. The SH3 domain and the ANK repeats of ASPP1 contribute to the p53 binding site; they bind to the DNA binding domain of p53. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11955 cd11955 212888 SH3_srGAP1-3 Src homology 3 domain of Slit-Robo GTPase Activating Proteins 1, 2, and 3. srGAP1, also called Rho GTPase-Activating Protein 13 (ARHGAP13), is a Cdc42- and RhoA-specific GAP and is expressed later in the development of central nervous system tissues. srGAP2 is expressed in zones of neuronal differentiation. It plays a role in the regeneration of neurons and axons. srGAP3, also called MEGAP (MEntal disorder associated GTPase-Activating Protein), is a Rho GAP with activity towards Rac1 and Cdc42. It impacts cell migration by regulating actin and microtubule cytoskeletal dynamics. The association between srGAP3 haploinsufficiency and mental retardation is under debate. srGAPs are Rho GAPs that interact with Robo1, the transmembrane receptor of Slit proteins. Slit proteins are secreted proteins that control axon guidance and the migration of neurons and leukocytes. srGAPs contain an N-terminal F-BAR domain, a Rho GAP domain, and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11956 cd11956 212889 SH3_srGAP4 Src homology 3 domain of Slit-Robo GTPase Activating Protein 4. srGAP4, also called ARHGAP4, is highly expressed in hematopoietic cells and may play a role in lymphocyte differentiation. It is able to stimulate the GTPase activity of Rac1, Cdc42, and RhoA. In the nervous system, srGAP4 has been detected in differentiating neurites and may be involved in axon and dendritic growth. srGAPs are Rho GAPs that interact with Robo1, the transmembrane receptor of Slit proteins. Slit proteins are secreted proteins that control axon guidance and the migration of neurons and leukocytes. srGAPs contain an N-terminal F-BAR domain, a Rho GAP domain, and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11957 cd11957 212890 SH3_RUSC2 Src homology 3 domain of RUN and SH3 domain-containing protein 2. RUSC2, also called Iporin or Interacting protein of Rab1, is expressed ubiquitously with highest amounts in the brain and testis. It interacts with the small GTPase Rab1 and the Golgi matrix protein GM130, and may function in linking GTPases to certain intracellular signaling pathways. RUSC proteins are adaptor proteins consisting of RUN, leucine zipper, and SH3 domains. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11958 cd11958 212891 SH3_RUSC1 Src homology 3 domain of RUN and SH3 domain-containing protein 1. RUSC1, also called NESCA (New molecule containing SH3 at the carboxy-terminus), is highly expressed in the brain and is translocated to the nuclear membrane from the cytoplasm upon stimulation with neurotrophin. It plays a role in facilitating neurotrophin-dependent neurite outgrowth. It also interacts with NEMO (or IKKgamma) and may function in NEMO-mediated activation of NF-kB. RUSC proteins are adaptor proteins consisting of RUN, leucine zipper, and SH3 domains. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 51 matched cddid_all.tbl CDD cd11959 cd11959 212892 SH3_Cortactin Src homology 3 domain of Cortactin. Cortactin was originally identified as a substrate of Src kinase. It is an actin regulatory protein that binds to the Arp2/3 complex and stabilizes branched actin filaments. It is involved in cellular processes that affect cell motility, adhesion, migration, endocytosis, and invasion. It is expressed ubiquitously except in hematopoietic cells, where the homolog hematopoietic lineage cell-specific 1 (HS1) is expressed instead. Cortactin contains an N-terminal acidic domain, several copies of a repeat domain found in cortactin and HS1, a proline-rich region, and a C-terminal SH3 domain. The N-terminal region interacts with the Arp2/3 complex and F-actin, and is crucial in regulating branched actin assembly. Cortactin also serves as a scaffold and provides a bridge to the actin cytoskeleton for membrane trafficking and signaling proteins that bind to its SH3 domain. Binding partners for the SH3 domain of cortactin include dynamin2, N-WASp, MIM, FGD1, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11960 cd11960 212893 SH3_Abp1_eu Src homology 3 domain of eumetazoan Actin-binding protein 1. Abp1, also called drebrin-like protein, is an adaptor protein that functions in receptor-mediated endocytosis and vesicle trafficking. It contains an N-terminal actin-binding module, the actin-depolymerizing factor (ADF) homology domain, a helical domain, and a C-terminal SH3 domain. Mammalian Abp1, unlike yeast Abp1, does not contain an acidic domain that interacts with the Arp2/3 complex. It regulates actin dynamics indirectly by interacting with dynamin and WASP family proteins. Abp1 deficiency causes abnormal organ structure and function of the spleen, heart, and lung of mice. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11961 cd11961 212894 SH3_Abp1_fungi_C2 Second C-terminal Src homology 3 domain of Fungal Actin-binding protein 1. Abp1 is an adaptor protein that functions in receptor-mediated endocytosis and vesicle trafficking. It contains an N-terminal actin-binding module, the actin-depolymerizing factor (ADF) homology domain, a central proline-rich region, and a C-terminal SH3 domain (many yeast Abp1 proteins contain two C-terminal SH3 domains). Yeast Abp1 also contains two acidic domains that bind directly to the Arp2/3 complex, which is required to initiate actin polymerization. The SH3 domain of yeast Abp1 binds and localizes the kinases, Ark1p and Prk1p, which facilitate actin patch disassembly following vesicle internalization. It also mediates the localization to the actin patch of the synaptojanin-like protein, Sjl2p, which plays a key role in endocytosis. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11962 cd11962 212895 SH3_Abp1_fungi_C1 First C-terminal Src homology 3 domain of Fungal Actin-binding protein 1. Abp1 is an adaptor protein that functions in receptor-mediated endocytosis and vesicle trafficking. It contains an N-terminal actin-binding module, the actin-depolymerizing factor (ADF) homology domain, a central proline-rich region, and a C-terminal SH3 domain (many yeast Abp1 proteins contain two C-terminal SH3 domains). Yeast Abp1 also contains two acidic domains that bind directly to the Arp2/3 complex, which is required to initiate actin polymerization. The SH3 domain of yeast Abp1 binds and localizes the kinases, Ark1p and Prk1p, which facilitate actin patch disassembly following vesicle internalization. It also mediates the localization to the actin patch of the synaptojanin-like protein, Sjl2p, which plays a key role in endocytosis. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11963 cd11963 212896 SH3_STAM2 Src homology 3 domain of Signal Transducing Adaptor Molecule 2. STAM2, also called EAST (Epidermal growth factor receptor-associated protein with SH3 and TAM domain) or Hbp (Hrs binding protein), is part of the endosomal sorting complex required for transport (ESCRT-0). It plays a role in sorting mono-ubiquinated endosomal cargo for trafficking to the lysosome for degradation. It is also involved in the regulation of exocytosis. STAMs were discovered as proteins that are highly phosphorylated following cytokine and growth factor stimulation. They function in cytokine signaling and surface receptor degradation, as well as regulate Golgi morphology. They associate with many proteins including Jak2 and Jak3 tyrosine kinases, Hrs, AMSH, and UBPY. STAM adaptor proteins contain VHS (Vps27, Hrs, STAM homology), ubiquitin interacting (UIM), and SH3 domains. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11964 cd11964 212897 SH3_STAM1 Src homology 3 domain of Signal Transducing Adaptor Molecule 1. STAM1 is part of the endosomal sorting complex required for transport (ESCRT-0) and is involved in sorting ubiquitinated cargo proteins from the endosome. It may also be involved in the regulation of IL2 and GM-CSF mediated signaling, and has been implicated in neural cell survival. STAMs were discovered as proteins that are highly phosphorylated following cytokine and growth factor stimulation. They function in cytokine signaling and surface receptor degradation, as well as regulate Golgi morphology. They associate with many proteins including Jak2 and Jak3 tyrosine kinases, Hrs, AMSH, and UBPY. STAM adaptor proteins contain VHS (Vps27, Hrs, STAM homology), ubiquitin interacting (UIM), and SH3 domains. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11965 cd11965 212898 SH3_ASAP1 Src homology 3 domain of ArfGAP with SH3 domain, ankyrin repeat and PH domain containing protein 1. ASAP1 is also called DDEF1 (Development and Differentiation Enhancing Factor 1), AMAP1, centaurin beta-4, or PAG2. an Arf GTPase activating protein (GAP) with activity towards Arf1 and Arf5 but not Arf6. However, it has been shown to bind GTP-Arf6 stably without GAP activity. It has been implicated in cell growth, migration, and survival, as well as in tumor invasion and malignancy. It binds paxillin and cortactin, two components of invadopodia which are essential for tumor invasiveness. It also binds focal adhesion kinase (FAK) and the SH2/SH3 adaptor CrkL. ASAP1 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, ankyrin (ANK) repeats, and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11966 cd11966 212899 SH3_ASAP2 Src homology 3 domain of ArfGAP with SH3 domain, ankyrin repeat and PH domain containing protein 2. ASAP2 is also called DDEF2 (Development and Differentiation Enhancing Factor 2), AMAP2, centaurin beta-3, or PAG3. It mediates the functions of Arf GTPases vial dual mechanisms: it exhibits GTPase activating protein (GAP) activity towards class I (Arf1) and II (Arf5) Arfs; and it binds class III Arfs (GTP-Arf6) stably without GAP activity. It binds paxillin and is implicated in Fcgamma receptor-mediated phagocytosis in macrophages and in cell migration. ASAP2 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, ankyrin (ANK) repeats, and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd11967 cd11967 212900 SH3_SASH1 Src homology 3 domain of SAM And SH3 Domain Containing Protein 1. SASH1 is a potential tumor suppressor in breast and colon cancer. Its decreased expression is associated with aggressive tumor growth, metastasis, and poor prognosis. It is widely expressed in normal tissues (except lymphocytes and dendritic cells) and is localized in the nucleus and the cytoplasm. SASH1 interacts with the oncoprotein cortactin and is important in cell migration and adhesion. It is a member of the SLY family of proteins, which are adaptor proteins containing a central conserved region with a bipartite nuclear localization signal (NLS) as well as SAM (sterile alpha motif) and SH3 domains. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11968 cd11968 212901 SH3_SASH3 Src homology 3 domain of Sam And SH3 Domain Containing Protein 3. SASH3, also called SLY/SLY1 (SH3-domain containing protein expressed in lymphocytes), is expressed exclusively in lymhocytes and is essential in the full activation of adaptive immunity. It is involved in the signaling of T cell receptors. It was the first described member of the SLY family of proteins, which are adaptor proteins containing a central conserved region with a bipartite nuclear localization signal (NLS) as well as SAM (sterile alpha motif) and SH3 domains. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd11969 cd11969 212902 SH3_PLCgamma2 Src homology 3 domain of Phospholipase C (PLC) gamma 2. PLCgamma2 is primarily expressed in haematopoietic cells, specifically in B cells. It is activated by tyrosine phosphorylation by B cell receptor (BCR) kinases and is recruited to the plasma membrane where its substrate is located. It is required in pre-BCR signaling and in the maturation of B cells. PLCs catalyze the hydrolysis of phosphatidylinositol (4,5)-bisphosphate [PtdIns(4,5)P2] to produce Ins(1,4,5)P3 and diacylglycerol (DAG). Ins(1,4,5)P3 initiates the calcium signaling cascade while DAG functions as an activator of PKC. PLCgamma contains a Pleckstrin homology (PH) domain followed by an elongation factor (EF) domain, two catalytic regions of PLC domains that flank two tandem SH2 domains, followed by a SH3 domain and C2 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11970 cd11970 212903 SH3_PLCgamma1 Src homology 3 domain of Phospholipase C (PLC) gamma 1. PLCgamma1 is widely expressed and is essential in growth and development. It is activated by the TrkA receptor tyrosine kinase and functions as a key regulator of cell differentiation. It is also the predominant PLCgamma in T cells and is required for T cell and NK cell function. PLCs catalyze the hydrolysis of phosphatidylinositol (4,5)-bisphosphate [PtdIns(4,5)P2] to produce Ins(1,4,5)P3 and diacylglycerol (DAG). Ins(1,4,5)P3 initiates the calcium signaling cascade while DAG functions as an activator of PKC. PLCgamma contains a Pleckstrin homology (PH) domain followed by an elongation factor (EF) domain, two catalytic regions of PLC domains that flank two tandem SH2 domains, followed by a SH3 domain and C2 domain. The SH3 domain of PLCgamma1 directly interacts with dynamin-1 and can serve as a guanine nucleotide exchange factor (GEF). It also interacts with Cbl, inhibiting its phosphorylation and activity. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 60 matched cddid_all.tbl CDD cd11971 cd11971 212904 SH3_Abi1 Src homology 3 domain of Abl Interactor 1. Abi1, also called e3B1, is a central regulator of actin cytoskeletal reorganization through interactions with many protein complexes. It is part of WAVE, a nucleation-promoting factor complex, that links Rac 1 activation to actin polymerization causing lamellipodia protrusion at the plasma membrane. Abi1 interact with formins to promote protrusions at the leading edge of motile cells. It also is a target of alpha4 integrin, regulating membrane protrusions at sites of integrin engagement. Abi proteins are adaptor proteins serving as binding partners and substrates of Abl tyrosine kinases. They are involved in regulating actin cytoskeletal reorganization and play important roles in membrane-ruffling, endocytosis, cell motility, and cell migration. Abi proteins contain a homeobox homology domain, a proline-rich region, and a SH3 domain. The SH3 domain of Abi binds to a PxxP motif in Abl. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 59 matched cddid_all.tbl CDD cd11972 cd11972 212905 SH3_Abi2 Src homology 3 domain of Abl Interactor 2. Abi2 is highly expressed in the brain and eye. It regulates actin cytoskeletal reorganization at adherens junctions and dendritic spines, which is important in cell morphogenesis, migration, and cognitive function. Mice deficient with Abi2 show defects in orientation and migration of lens fibers, neuronal migration, dendritic spine morphology, as well as deficits in learning and memory. Abi proteins are adaptor proteins serving as binding partners and substrates of Abl tyrosine kinases. They are involved in regulating actin cytoskeletal reorganization and play important roles in membrane-ruffling, endocytosis, cell motility, and cell migration. Abi proteins contain a homeobox homology domain, a proline-rich region, and a SH3 domain. The SH3 domain of Abi binds to a PxxP motif in Abl. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 61 matched cddid_all.tbl CDD cd11973 cd11973 212906 SH3_ASEF Src homology 3 domain of APC-Stimulated guanine nucleotide Exchange Factor. ASEF, also called ARHGEF4, exists in an autoinhibited form and is activated upon binding of the tumor suppressor APC (adenomatous polyposis coli). GEFs activate small GTPases by exchanging bound GDP for free GTP. ASEF can activate Rac1 or Cdc42. Truncated ASEF, which is found in colorectal cancers, is constitutively active and has been shown to promote angiogenesis and cancer cell migration. ASEF contains a SH3 domain followed by RhoGEF (also called Dbl-homologous or DH) and Pleckstrin Homology (PH) domains. In its autoinhibited form, the SH3 domain of ASEF forms an extensive interface with the DH and PH domains, blocking the Rac binding site. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 73 matched cddid_all.tbl CDD cd11974 cd11974 212907 SH3_ASEF2 Src homology 3 domain of APC-Stimulated guanine nucleotide Exchange Factor 2. ASEF2, also called Spermatogenesis-associated protein 13 (SPATA13), is a GEF that localizes with actin at the leading edge of cells and is important in cell migration and adhesion dynamics. GEFs activate small GTPases by exchanging bound GDP for free GTP. ASEF2 can activate both Rac 1 and Cdc42, but only Rac1 activation is necessary for increased cell migration and adhesion turnover. Together with APC (adenomatous polyposis coli) and Neurabin2, a scaffold protein that binds F-actin, it is involved in regulating HGF-induced cell migration. ASEF2 contains a SH3 domain followed by RhoGEF (also called Dbl-homologous or DH) and Pleckstrin Homology (PH) domains. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11975 cd11975 212908 SH3_ARHGEF9 Src homology 3 domain of the Rho guanine nucleotide exchange factor ARHGEF9. ARHGEF9, also called PEM2 or collybistin, selectively activates Cdc42 by exchanging bound GDP for free GTP. It is highly expressed in the brain and it interacts with gephyrin, a postsynaptic protein associated with GABA and glycine receptors. Mutations in the ARHGEF9 gene cause X-linked mental retardation with associated features like seizures, hyper-anxiety, aggressive behavior, and sensory hyperarousal. ARHGEF9 contains a SH3 domain followed by RhoGEF (also called Dbl-homologous or DH) and Pleckstrin Homology (PH) domains. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 62 matched cddid_all.tbl CDD cd11976 cd11976 212909 SH3_VAV1_2 C-terminal (or second) Src homology 3 domain of VAV1 protein. VAV1 is expressed predominantly in the hematopoietic system and it plays an important role in the development and activation of B and T cells. It is activated by tyrosine phosphorylation to function as a guanine nucleotide exchange factor (GEF) for Rho GTPases following cell surface receptor activation, triggering various effects such as cytoskeletal reorganization, transcription regulation, cell cycle progression, and calcium mobilization. It also serves as a scaffold protein and has been shown to interact with Ku70, Socs1, Janus kinase 2, SIAH2, S100B, Abl gene, ZAP-70, SLP76, and Syk, among others. VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. The C-terminal SH3 domain of Vav1 interacts with a wide variety of proteins including cytoskeletal regulators (zyxin), RNA-binding proteins (Sam68), transcriptional regulators, viral proteins, and dynamin 2. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11977 cd11977 212910 SH3_VAV2_2 C-terminal (or second) Src homology 3 domain of VAV2 protein. VAV2 is widely expressed and functions as a guanine nucleotide exchange factor (GEF) for RhoA, RhoB and RhoG and also activates Rac1 and Cdc42. It is implicated in many cellular and physiological functions including blood pressure control, eye development, neurite outgrowth and branching, EGFR endocytosis and degradation, and cell cluster morphology, among others. It has been reported to associate with Nek3. VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. The SH3 domain of VAV is involved in the localization of proteins to specific sites within the cell, by interacting with proline-rich sequences within target proteins. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 58 matched cddid_all.tbl CDD cd11978 cd11978 212911 SH3_VAV3_2 C-terminal (or second) Src homology 3 domain of VAV3 protein. VAV3 is ubiquitously expressed and functions as a phosphorylation-dependent guanine nucleotide exchange factor (GEF) for RhoA, RhoG, and Rac1. It has been implicated to function in the hematopoietic, bone, cerebellar, and cardiovascular systems. VAV3 is essential in axon guidance in neurons that control blood pressure and respiration. It is overexpressed in prostate cancer cells and it plays a role in regulating androgen receptor transcriptional activity. VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. The SH3 domain of VAV is involved in the localization of proteins to specific sites within the cell, by interacting with proline-rich sequences within target proteins. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd11979 cd11979 212912 SH3_VAV1_1 First Src homology 3 domain of VAV1 protein. VAV1 is expressed predominantly in the hematopoietic system and it plays an important role in the development and activation of B and T cells. It is activated by tyrosine phosphorylation to function as a guanine nucleotide exchange factor (GEF) for Rho GTPases following cell surface receptor activation, triggering various effects such as cytoskeletal reorganization, transcription regulation, cell cycle progression, and calcium mobilization. It also serves as a scaffold protein and has been shown to interact with Ku70, Socs1, Janus kinase 2, SIAH2, S100B, Abl gene, ZAP-70, SLP76, and Syk, among others. VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. The first SH3 domain of Vav1 has been shown to bind the adaptor protein Grb2. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 63 matched cddid_all.tbl CDD cd11980 cd11980 212913 SH3_VAV2_1 First Src homology 3 domain of VAV2 protein. VAV2 is widely expressed and functions as a guanine nucleotide exchange factor (GEF) for RhoA, RhoB and RhoG and also activates Rac1 and Cdc42. It is implicated in many cellular and physiological functions including blood pressure control, eye development, neurite outgrowth and branching, EGFR endocytosis and degradation, and cell cluster morphology, among others. It has been reported to associate with Nek3. VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. The SH3 domain of VAV is involved in the localization of proteins to specific sites within the cell, by interacting with proline-rich sequences within target proteins. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 60 matched cddid_all.tbl CDD cd11981 cd11981 212914 SH3_VAV3_1 First Src homology 3 domain of VAV3 protein. VAV3 is ubiquitously expressed and functions as a phosphorylation-dependent guanine nucleotide exchange factor (GEF) for RhoA, RhoG, and Rac1. It has been implicated to function in the hematopoietic, bone, cerebellar, and cardiovascular systems. VAV3 is essential in axon guidance in neurons that control blood pressure and respiration. It is overexpressed in prostate cancer cells and it plays a role in regulating androgen receptor transcriptional activity. VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. The SH3 domain of VAV is involved in the localization of proteins to specific sites within the cell, by interacting with proline-rich sequences within target proteins. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 62 matched cddid_all.tbl CDD cd11982 cd11982 212915 SH3_Shank1 Src homology 3 domain of SH3 and multiple ankyrin repeat domains protein 1. Shank1, also called SSTRIP (Somatostatin receptor-interacting protein), is a brain-specific protein that plays a role in the construction of postsynaptic density (PSD) and the maturation of dendritic spines. Mice deficient in Shank1 show altered PSD composition, thinner PSDs, smaller dendritic spines, and weaker basal synaptic transmission, although synaptic plasticity is normal. They show increased anxiety and impaired fear memory, but also show better spatial learning. Shank proteins carry scaffolding functions through multiple sites of protein-protein interaction in its domain architecture, including ankyrin (ANK) repeats, a long proline rich region, as well as SH3, PDZ, and SAM domains. The SH3 domain of Shank binds GRIP, a scaffold protein that binds AMPA receptors and Eph receptors/ligands. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11983 cd11983 212916 SH3_Shank2 Src homology 3 domain of SH3 and multiple ankyrin repeat domains protein 2. Shank2, also called ProSAP1 (Proline-rich synapse-associated protein 1) or CortBP1 (Cortactin-binding protein 1), is found in neurons, glia, endocrine cells, liver, and kidney. It plays a role in regulating dendritic spine volume and branching and postsynaptic clustering. Mutations in the Shank2 gene are associated with autism spectrum disorder and mental retardation. Shank proteins carry scaffolding functions through multiple sites of protein-protein interaction in its domain architecture, including ankyrin (ANK) repeats, a long proline rich region, as well as SH3, PDZ, and SAM domains. The SH3 domain of Shank binds GRIP, a scaffold protein that binds AMPA receptors and Eph receptors/ligands. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11984 cd11984 212917 SH3_Shank3 Src homology 3 domain of SH3 and multiple ankyrin repeat domains protein 3. Shank3, also called ProSAP2 (Proline-rich synapse-associated protein 2), is widely expressed. It plays a role in the formation of dendritic spines and synapses. Haploinsufficiency of the Shank3 gene causes the 22q13 deletion/Phelan-McDermid syndrome, and variants of Shank3 have been implicated in autism spectrum disorder, schizophrenia, and intellectual disability. Shank proteins carry scaffolding functions through multiple sites of protein-protein interaction in its domain architecture, including ankyrin (ANK) repeats, a long proline rich region, as well as SH3, PDZ, and SAM domains. The SH3 domain of Shank binds GRIP, a scaffold protein that binds AMPA receptors and Eph receptors/ligands. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11985 cd11985 212918 SH3_Stac2_C C-terminal Src homology 3 domain of SH3 and cysteine-rich domain-containing protein 2 (Stac2). Stac proteins are putative adaptor proteins that contain a cysteine-rich C1 domain and one or two SH3 domains at the C-terminus. There are three mammalian members (Stac1, Stac2, and Stac3) of this family. Stac2 contains a single SH3 domain at the C-terminus unlike Stac1 and Stac3, which contain two C-terminal SH3 domains. Stac1 and Stac2 have been found to be expressed differently in mature dorsal root ganglia (DRG) neurons. Stac1 is mainly expressed in peptidergic neurons while Stac2 is found in a subset of nonpeptidergic and all trkB+ neurons. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11986 cd11986 212919 SH3_Stac3_1 First C-terminal Src homology 3 domain of SH3 and cysteine-rich domain-containing protein 3 (Stac3). Stac proteins are putative adaptor proteins that contain a cysteine-rich C1 domain and one or two SH3 domains at the C-terminus. There are three mammalian members (Stac1, Stac2, and Stac3) of this family. Stac1 and Stac3 contain two SH3 domains while Stac2 contains a single SH3 domain at the C-terminus. Stac1 and Stac2 have been found to be expressed differently in mature dorsal root ganglia (DRG) neurons. Stac1 is mainly expressed in peptidergic neurons while Stac2 is found in a subset of nonpeptidergic and all trkB+ neurons. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd11987 cd11987 212920 SH3_Intersectin1_1 First Src homology 3 domain (or SH3A) of Intersectin-1. Intersectin-1 (ITSN1) is an adaptor protein that functions in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction. It plays a role in clathrin-coated pit (CCP) formation. It binds to many proteins through its multidomain structure and facilitate the assembly of multimeric complexes. ITSN1 localizes in membranous organelles, CCPs, the Golgi complex, and may be involved in the cell membrane trafficking system. It exists in alternatively spliced short and long isoforms. The short isoform contains two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoform, in addition, contains RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. The first SH3 domain (or SH3A) of ITSN1 has been shown to bind many proteins including Sos1, dynamin1/2, CIN85, c-Cbl, PI3K-C2, SHIP2, N-WASP, and CdGAP, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd11988 cd11988 212921 SH3_Intersectin2_1 First Src homology 3 domain (or SH3A) of Intersectin-2. Intersectin-2 (ITSN2) is an adaptor protein that functions in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction. It plays a role in clathrin-coated pit (CCP) formation. It binds to many proteins through its multidomain structure and facilitate the assembly of multimeric complexes. ITSN2 also functions as a specific GEF for Cdc42 activation in epithelial morphogenesis, and is required in mitotic spindle orientation. It exists in alternatively spliced short and long isoforms. The short isoform contains two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoform, in addition, contains RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. The first SH3 domain (or SH3A) of ITSN2 is expected to bind many protein partners, similar to ITSN1 which has been shown to bind Sos1, dynamin1/2, CIN85, c-Cbl, PI3K-C2, SHIP2, N-WASP, and CdGAP, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd11989 cd11989 212922 SH3_Intersectin1_2 Second Src homology 3 domain (or SH3B) of Intersectin-1. Intersectin-1 (ITSN1) is an adaptor protein that functions in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction. It plays a role in clathrin-coated pit (CCP) formation. It binds to many proteins through its multidomain structure and facilitate the assembly of multimeric complexes. ITSN1 localizes in membranous organelles, CCPs, the Golgi complex, and may be involved in the cell membrane trafficking system. It exists in alternatively spliced short and long isoforms. The short isoform contains two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoform, in addition, contains RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. The second SH3 domain (or SH3B) of ITSN1 has been shown to bind WNK and CdGAP. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11990 cd11990 212923 SH3_Intersectin2_2 Second Src homology 3 domain (or SH3B) of Intersectin-2. Intersectin-2 (ITSN2) is an adaptor protein that functions in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction. It plays a role in clathrin-coated pit (CCP) formation. It binds to many proteins through its multidomain structure and facilitate the assembly of multimeric complexes. ITSN2 also functions as a specific GEF for Cdc42 activation in epithelial morphogenesis, and is required in mitotic spindle orientation. It exists in alternatively spliced short and long isoforms. The short isoform contains two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoform, in addition, contains RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. The second SH3 domain (or SH3B) of ITSN2 is expected to bind protein partners, similar to ITSN1 which has been shown to bind WNK and CdGAP. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11991 cd11991 212924 SH3_Intersectin1_3 Third Src homology 3 domain (or SH3C) of Intersectin-1. Intersectin-1 (ITSN1) is an adaptor protein that functions in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction. It plays a role in clathrin-coated pit (CCP) formation. It binds to many proteins through its multidomain structure and facilitate the assembly of multimeric complexes. ITSN1 localizes in membranous organelles, CCPs, the Golgi complex, and may be involved in the cell membrane trafficking system. It exists in alternatively spliced short and long isoforms. The short isoform contains two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoform, in addition, contains RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. The third SH3 domain (or SH3C) of ITSN1 has been shown to bind many proteins including dynamin1/2, CIN85, c-Cbl, SHIP2, Reps1, synaptojanin-1, and WNK, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11992 cd11992 212925 SH3_Intersectin2_3 Third Src homology 3 domain (or SH3C) of Intersectin-2. Intersectin-2 (ITSN2) is an adaptor protein that functions in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction. It plays a role in clathrin-coated pit (CCP) formation. It binds to many proteins through its multidomain structure and facilitate the assembly of multimeric complexes. ITSN2 also functions as a specific GEF for Cdc42 activation in epithelial morphogenesis, and is required in mitotic spindle orientation. It exists in alternatively spliced short and long isoforms. The short isoform contains two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoform, in addition, contains RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. The third SH3 domain (SH3C) of ITSN2 has been shown to bind the K15 protein of Kaposi's sarcoma-associated herpesvirus. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 52 matched cddid_all.tbl CDD cd11993 cd11993 212926 SH3_Intersectin1_4 Fourth Src homology 3 domain (or SH3D) of Intersectin-1. Intersectin-1 (ITSN1) is an adaptor protein that functions in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction. It plays a role in clathrin-coated pit (CCP) formation. It binds to many proteins through its multidomain structure and facilitate the assembly of multimeric complexes. ITSN1 localizes in membranous organelles, CCPs, the Golgi complex, and may be involved in the cell membrane trafficking system. It exists in alternatively spliced short and long isoforms. The short isoform contains two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoform, in addition, contains RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. The fourth SH3 domain (or SH3D) of ITSN1 has been shown to bind SHIP2, Numb, CdGAP, and N-WASP. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 65 matched cddid_all.tbl CDD cd11994 cd11994 212927 SH3_Intersectin2_4 Fourth Src homology 3 domain (or SH3D) of Intersectin-2. Intersectin-2 (ITSN2) is an adaptor protein that functions in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction. It plays a role in clathrin-coated pit (CCP) formation. It binds to many proteins through its multidomain structure and facilitate the assembly of multimeric complexes. ITSN2 also functions as a specific GEF for Cdc42 activation in epithelial morphogenesis, and is required in mitotic spindle orientation. It exists in alternatively spliced short and long isoforms. The short isoform contains two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoform, in addition, contains RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. The fourth SH3 domain (or SH3D) of ITSN2 is expected to bind protein partners, similar to ITSN1 which has been shown to bind SHIP2, Numb, CdGAP, and N-WASP. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 59 matched cddid_all.tbl CDD cd11995 cd11995 212928 SH3_Intersectin1_5 Fifth Src homology 3 domain (or SH3E) of Intersectin-1. Intersectin-1 (ITSN1) is an adaptor protein that functions in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction. It plays a role in clathrin-coated pit (CCP) formation. It binds to many proteins through its multidomain structure and facilitate the assembly of multimeric complexes. ITSN1 localizes in membranous organelles, CCPs, the Golgi complex, and may be involved in the cell membrane trafficking system. It exists in alternatively spliced short and long isoforms. The short isoform contains two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoform, in addition, contains RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. The fifth SH3 domain (or SH3E) of ITSN1 has been shown to bind many protein partners including SGIP1, Sos1, dynamin1/2, CIN85, c-Cbl, SHIP2, N-WASP, and synaptojanin-1, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11996 cd11996 212929 SH3_Intersectin2_5 Fifth Src homology 3 domain (or SH3E) of Intersectin-2. Intersectin-2 (ITSN2) is an adaptor protein that functions in exo- and endocytosis, actin cytoskeletal reorganization, and signal transduction. It plays a role in clathrin-coated pit (CCP) formation. It binds to many proteins through its multidomain structure and facilitate the assembly of multimeric complexes. ITSN2 also functions as a specific GEF for Cdc42 activation in epithelial morphogenesis, and is required in mitotic spindle orientation. It exists in alternatively spliced short and long isoforms. The short isoform contains two Eps15 homology domains (EH1 and EH2), a coiled-coil region and five SH3 domains (SH3A-E), while the long isoform, in addition, contains RhoGEF (also called Dbl-homologous or DH), Pleckstrin homology (PH) and C2 domains. The fifth SH3 domain (or SH3E) of ITSN2 is expected to bind protein partners, similar to ITSN1 which has been shown to bind many protein partners including SGIP1, Sos1, dynamin1/2, CIN85, c-Cbl, SHIP2, N-WASP, and synaptojanin-1, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd11997 cd11997 212930 SH3_PACSIN3 Src homology 3 domain of Protein kinase C and Casein kinase Substrate in Neurons 3 (PACSIN3). PACSIN 3 or Syndapin III (Synaptic dynamin-associated protein III) is expressed ubiquitously and regulates glucose uptake in adipocytes through its role in GLUT1 trafficking. It also modulates the subcellular localization and stimulus-specific function of the cation channel TRPV4. PACSINs act as regulators of cytoskeletal and membrane dynamics. Vetebrates harbor three isoforms with distinct expression patterns and specific functions. PACSINs contain an N-terminal F-BAR domain and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd11998 cd11998 212931 SH3_PACSIN1-2 Src homology 3 domain of Protein kinase C and Casein kinase Substrate in Neurons 1 (PACSIN1) and PACSIN 2. PACSIN 1 or Syndapin I (Synaptic dynamin-associated protein I) is expressed specifically in the brain and is localized in neurites and synaptic boutons. It binds the brain-specific proteins dynamin I, synaptojanin, synapsin I, and neural Wiskott-Aldrich syndrome protein (nWASP), and functions as a link between the cytoskeletal machinery and synaptic vesicle endocytosis. PACSIN 1 interacts with huntingtin and may be implicated in the neuropathology of Huntington's disease. PACSIN 2 or Syndapin II is expressed ubiquitously and is involved in the regulation of tubulin polymerization. It associates with Golgi membranes and forms a complex with dynamin II which is crucial in promoting vesicle formation from the trans-Golgi network. PACSINs act as regulators of cytoskeletal and membrane dynamics. Vetebrates harbor three isoforms with distinct expression patterns and specific functions. PACSINs contain an N-terminal F-BAR domain and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd11999 cd11999 212932 SH3_PACSIN_like Src homology 3 domain of an unknown subfamily of proteins with similarity to Protein kinase C and Casein kinase Substrate in Neurons (PACSIN) proteins. PACSINs, also called Synaptic dynamin-associated proteins (Syndapins), act as regulators of cytoskeletal and membrane dynamics. They bind both dynamin and Wiskott-Aldrich syndrome protein (WASP), and may provide direct links between the actin cytoskeletal machinery through WASP and dynamin-dependent endocytosis. Vetebrates harbor three isoforms with distinct expression patterns and specific functions. PACSINs contain an N-terminal F-BAR domain and a C-terminal SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd12000 cd12000 212933 SH3_CASS4 Src homology 3 domain of CAS (Crk-Associated Substrate) scaffolding protein family member 4. CASS4, also called HEPL (HEF1-EFS-p130Cas-like), localizes to focal adhesions and plays a role in regulating FAK activity, focal adhesion integrity, and cell spreading. It is most abundant in blood cells and lung tissue, and is also found in high levels in leukemia and ovarian cell lines. CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes. They share a common domain structure that includes an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain. The SH3 domain of CAS proteins binds to diverse partners including FAK, FRNK, Pyk2, PTP-PEST, DOCK180, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd12001 cd12001 212934 SH3_BCAR1 Src homology 3 domain of the CAS (Crk-Associated Substrate) scaffolding protein family member, Breast Cancer Anti-estrogen Resistance 1. BCAR1, also called p130cas or CASS1, is the founding member of the CAS family of scaffolding proteins and was originally identified through its ability to associate with Crk. The name BCAR1 was designated because the human gene was identified in a screen for genes that promote resistance to tamoxifen. It is widely expressed and its deletion is lethal in mice. It plays a role in regulating cell motility, survival, proliferation, transformation, cancer progression, and bacterial pathogenesis. CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes. They share a common domain structure that includes an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain. The SH3 domain of CAS proteins binds to diverse partners including FAK, FRNK, Pyk2, PTP-PEST, DOCK180, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 68 matched cddid_all.tbl CDD cd12002 cd12002 212935 SH3_NEDD9 Src homology 3 domain of CAS (Crk-Associated Substrate) scaffolding protein family member, Neural precursor cell Expressed, Developmentally Down-regulated 9. NEDD9 is also called human enhancer of filamentation 1 (HEF1) or CAS-L (Crk-associated substrate in lymphocyte). It was first described as a gene predominantly expressed in early embryonic brain, and was also isolated from a screen of human proteins that regulate filamentous budding in yeast, and as a tyrosine phosphorylated protein in lymphocytes. It promotes metastasis in different solid tumors. NEDD9 localizes in focal adhesions and associates with FAK and Abl kinase. It also interacts with SMAD3 and the proteasomal machinery which allows its rapid turnover; these interactions are not shared by other CAS proteins. CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes. They share a common domain structure that includes an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain. The SH3 domain of CAS proteins binds to diverse partners including FAK, FRNK, Pyk2, PTP-PEST, DOCK180, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd12003 cd12003 212936 SH3_EFS Src homology 3 domain of CAS (Crk-Associated Substrate) scaffolding protein family member, Embryonal Fyn-associated Substrate. EFS is also called HEFS, CASS3 (Cas scaffolding protein family member 3) or SIN (Src-interacting protein). It was identified based on interactions with the Src kinases, Fyn and Yes. It plays a role in thymocyte development and acts as a negative regulator of T cell proliferation. CAS proteins function as molecular scaffolds to regulate protein complexes that are involved in many cellular processes. They share a common domain structure that includes an N-terminal SH3 domain, an unstructured substrate domain that contains many YxxP motifs, a serine-rich four-helix bundle, and a FAT-like C-terminal domain. The SH3 domain of CAS proteins binds to diverse partners including FAK, FRNK, Pyk2, PTP-PEST, DOCK180, among others. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 62 matched cddid_all.tbl CDD cd12004 cd12004 212937 SH3_Lyn Src homology 3 domain of Lyn Protein Tyrosine Kinase. Lyn is a member of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) PTKs. Lyn is expressed in B lymphocytes and myeloid cells. It exhibits both positive and negative regulatory roles in B cell receptor (BCR) signaling. Lyn, as well as Fyn and Blk, promotes B cell activation by phosphorylating ITAMs (immunoreceptor tyr activation motifs) in CD19 and in Ig components of BCR. It negatively regulates signaling by its unique ability to phosphorylate ITIMs (immunoreceptor tyr inhibition motifs) in cell surface receptors like CD22 and CD5. Lyn also plays an important role in G-CSF receptor signaling by phosphorylating a variety of adaptor molecules. Src kinases contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). The SH3 domain of Src kinases contributes to substrate recruitment by binding adaptor proteins/substrates, and regulation of kinase activity through an intramolecular interaction. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd12005 cd12005 212938 SH3_Lck Src homology 3 domain of Lck Protein Tyrosine Kinase. Lck is a member of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) PTKs. Lck is expressed in T-cells and natural killer cells. It plays a critical role in T-cell maturation, activation, and T-cell receptor (TCR) signaling. Lck phosphorylates ITAM (immunoreceptor tyr activation motif) sequences on several subunits of TCRs, leading to the activation of different second messenger cascades. Phosphorylated ITAMs serve as binding sites for other signaling factor such as Syk and ZAP-70, leading to their activation and propagation of downstream events. In addition, Lck regulates drug-induced apoptosis by interfering with the mitochondrial death pathway. The apototic role of Lck is independent of its primary function in T-cell signaling. Src kinases contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). The SH3 domain of Src kinases contributes to substrate recruitment by binding adaptor proteins/substrates, and regulation of kinase activity through an intramolecular interaction. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd12006 cd12006 212939 SH3_Fyn_Yrk Src homology 3 domain of Fyn and Yrk Protein Tyrosine Kinases. Fyn and Yrk (Yes-related kinase) are members of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) PTKs. Fyn, together with Lck, plays a critical role in T-cell signal transduction by phosphorylating ITAM (immunoreceptor tyr activation motif) sequences on T-cell receptors, ultimately leading to the proliferation and differentiation of T-cells. In addition, Fyn is involved in the myelination of neurons, and is implicated in Alzheimer's and Parkinson's diseases. Yrk has been detected only in chickens. It is primarily found in neuronal and epithelial cells and in macrophages. It may play a role in inflammation and in response to injury. Src kinases contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). The SH3 domain of Src kinases contributes to substrate recruitment by binding adaptor proteins/substrates, and regulation of kinase activity through an intramolecular interaction. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd12007 cd12007 212940 SH3_Yes Src homology 3 domain of Yes Protein Tyrosine Kinase. Yes (or c-Yes) is a member of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) PTKs. c-Yes kinase is the cellular homolog of the oncogenic protein (v-Yes) encoded by the Yamaguchi 73 and Esh sarcoma viruses. It displays functional overlap with other Src subfamily members, particularly Src. It also shows some unique functions such as binding to occludins, transmembrane proteins that regulate extracellular interactions in tight junctions. Yes also associates with a number of proteins in different cell types that Src does not interact with, like JAK2 and gp130 in pre-adipocytes, and Pyk2 in treated pulmonary vein endothelial cells. Although the biological function of Yes remains unclear, it appears to have a role in regulating cell-cell interactions and vesicle trafficking in polarized cells. Src kinases contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). The SH3 domain of Src kinases contributes to substrate recruitment by binding adaptor proteins/substrates, and regulation of kinase activity through an intramolecular interaction. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 58 matched cddid_all.tbl CDD cd12008 cd12008 212941 SH3_Src Src homology 3 domain of Src Protein Tyrosine Kinase. Src (or c-Src) is a cytoplasmic (or non-receptor) PTK and is the vertebrate homolog of the oncogenic protein (v-Src) from Rous sarcoma virus. Together with other Src subfamily proteins, it is involved in signaling pathways that regulate cytokine and growth factor responses, cytoskeleton dynamics, cell proliferation, survival, and differentiation. Src also play a role in regulating cell adhesion, invasion, and motility in cancer cells, and tumor vasculature, contributing to cancer progression and metastasis. Elevated levels of Src kinase activity have been reported in a variety of human cancers. Several inhibitors of Src have been developed as anti-cancer drugs. Src is also implicated in acute inflammatory responses and osteoclast function. Src kinases contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). The SH3 domain of Src kinases contributes to substrate recruitment by binding adaptor proteins/substrates, and regulation of kinase activity through an intramolecular interaction. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd12009 cd12009 212942 SH3_Blk Src homology 3 domain of Blk Protein Tyrosine Kinase. Blk is a member of the Src subfamily of proteins, which are cytoplasmic (or non-receptor) PTKs. It is expressed specifically in B-cells and is involved in pre-BCR (B-cell receptor) signaling. Src kinases contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). The SH3 domain of Src kinases contributes to substrate recruitment by binding adaptor proteins/substrates, and regulation of kinase activity through an intramolecular interaction. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd12010 cd12010 212943 SH3_SLAP Src homology 3 domain of Src-Like Adaptor Protein. SLAP (or SLA1) modulates TCR surface expression levels as well as surface and total BCR levels. As an adaptor to c-Cbl, SLAP increases the ubiquitination, intracellular retention, and targeted degradation of the BCR complex components. SLAP has been shown to interact with the EphA receptor, EpoR, Lck, PDGFR, Syk, CD79a, c-Cbl, LAT, CD247, and Zap70, among others. SLAPs are adaptor proteins with limited similarity to Src family tyrosine kinases. They contain an N-terminal SH3 domain followed by an SH2 domain, and a unique C-terminal sequence. The SH3 domain of SLAP forms a complex with v-Abl. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd12011 cd12011 212944 SH3_SLAP2 Src homology 3 domain of Src-Like Adaptor Protein 2. SLAP2 plays a role in c-Cbl-dependent regulation of CSF1R, a tyrosine kinase important for myeloid cell growth and differentiation. It has been shown to interact with CSF1R, c-Cbl, LAT, CD247, and Zap70. SLAPs are adaptor proteins with limited similarity to Src family tyrosine kinases. They contain an N-terminal SH3 domain followed by an SH2 domain, and a unique C-terminal sequence. They function in regulating the signaling, ubiquitination, and trafficking of T-cell receptor (TCR) and B-cell receptor (BCR) components. The SH3 domain of SLAP forms a complex with v-Abl. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd12012 cd12012 212945 SH3_RIM-BP_2 Second Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins. RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3. RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery. RIM-BPs contain three SH3 domains and two to three fibronectin III repeats. Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3. RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis. The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 62 matched cddid_all.tbl CDD cd12013 cd12013 212946 SH3_RIM-BP_3 Third Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins. RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3. RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery. RIM-BPs contain three SH3 domains and two to three fibronectin III repeats. Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3. RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis. The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 61 matched cddid_all.tbl CDD cd12014 cd12014 212947 SH3_RIM-BP_1 First Src homology 3 domain of Rab3-interacting molecules (RIMs) binding proteins. RIMs binding proteins (RBPs, RIM-BPs) associate with calcium channels present in photoreceptors, neurons, and hair cells; they interact simultaneously with specific calcium channel subunits, and active zone proteins, RIM1 and RIM2. RIMs are part of the matrix at the presynaptic active zone and are associated with synaptic vesicles through their interaction with the small GTPase Rab3. RIM-BPs play a role in regulating synaptic transmission by serving as adaptors and linking calcium channels with the synaptic vesicle release machinery. RIM-BPs contain three SH3 domains and two to three fibronectin III repeats. Invertebrates contain one, while vertebrates contain at least two RIM-BPs, RIM-BP1 and RIM-BP2. RIM-BP1 is also called peripheral-type benzodiazapine receptor associated protein 1 (PRAX-1). Mammals contain a third protein, RIM-BP3. RIM-BP1 and RIM-BP2 are predominantly expressed in the brain where they display overlapping but distinct expression patterns, while RIM-BP3 is almost exclusively expressed in the testis and is essential in spermiogenesis. The SH3 domains of RIM-BPs bind to the PxxP motifs of RIM1, RIM2, and L-type (alpha1D) and N-type (alpha1B) calcium channel subunits. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 62 matched cddid_all.tbl CDD cd12015 cd12015 212948 SH3_Tks_1 First Src homology 3 domain of Tyrosine kinase substrate (Tks) proteins. Tks proteins are Src substrates and scaffolding proteins that play important roles in the formation of podosomes and invadopodia, the dynamic actin-rich structures that are related to cell migration and cancer cell invasion. Vertebrates contain two Tks proteins, Tks4 (Tyr kinase substrate with four SH3 domains) and Tks5 (Tyr kinase substrate with five SH3 domains), which display partially overlapping but non-redundant functions. Both associate with the ADAMs family of transmembrane metalloproteases, which function as sheddases and mediators of cell and matrix interactions. Tks5 interacts with N-WASP and Nck, while Tks4 is essential for the localization of MT1-MMP (membrane-type 1 matrix metalloproteinase) to invadopodia. Tks proteins contain an N-terminal Phox homology (PX) domain and four or five SH3 domains. This model characterizes the first SH3 domain of Tks proteins. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd12016 cd12016 212949 SH3_Tks_2 Second Src homology 3 domain of Tyrosine kinase substrate (Tks) proteins. Tks proteins are Src substrates and scaffolding proteins that play important roles in the formation of podosomes and invadopodia, the dynamic actin-rich structures that are related to cell migration and cancer cell invasion. Vertebrates contain two Tks proteins, Tks4 (Tyr kinase substrate with four SH3 domains) and Tks5 (Tyr kinase substrate with five SH3 domains), which display partially overlapping but non-redundant functions. Both associate with the ADAMs family of transmembrane metalloproteases, which function as sheddases and mediators of cell and matrix interactions. Tks5 interacts with N-WASP and Nck, while Tks4 is essential for the localization of MT1-MMP (membrane-type 1 matrix metalloproteinase) to invadopodia. Tks proteins contain an N-terminal Phox homology (PX) domain and four or five SH3 domains. This model characterizes the second SH3 domain of Tks proteins. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd12017 cd12017 212950 SH3_Tks_3 Third Src homology 3 domain of Tyrosine kinase substrate (Tks) proteins. Tks proteins are Src substrates and scaffolding proteins that play important roles in the formation of podosomes and invadopodia, the dynamic actin-rich structures that are related to cell migration and cancer cell invasion. Vertebrates contain two Tks proteins, Tks4 (Tyr kinase substrate with four SH3 domains) and Tks5 (Tyr kinase substrate with five SH3 domains), which display partially overlapping but non-redundant functions. Both associate with the ADAMs family of transmembrane metalloproteases, which function as sheddases and mediators of cell and matrix interactions. Tks5 interacts with N-WASP and Nck, while Tks4 is essential for the localization of MT1-MMP (membrane-type 1 matrix metalloproteinase) to invadopodia. Tks proteins contain an N-terminal Phox homology (PX) domain and four or five SH3 domains. This model characterizes the third SH3 domain of Tks proteins. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd12018 cd12018 212951 SH3_Tks4_4 Fourth (C-terminal) Src homology 3 domain of Tyrosine kinase substrate with four SH3 domains. Tks4, also called SH3 and PX domain-containing protein 2B (SH3PXD2B) or HOFI, is a Src substrate and scaffolding protein that plays an important role in the formation of podosomes and invadopodia, the dynamic actin-rich structures that are related to cell migration and cancer cell invasion. It is required in the formation of functional podosomes, EGF-induced membrane ruffling, and lamellipodia generation. It plays an important role in cellular attachment and cell spreading. Tks4 is essential for the localization of MT1-MMP (membrane-type 1 matrix metalloproteinase) to invadopodia. It contains an N-terminal Phox homology (PX) domain and four SH3 domains. This model characterizes the fourth (C-terminal) SH3 domain of Tks4. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd12019 cd12019 212952 SH3_Tks5_4 Fourth Src homology 3 domain of Tyrosine kinase substrate with five SH3 domains. Tks5, also called SH3 and PX domain-containing protein 2A (SH3PXD2A) or Five SH (FISH), is a scaffolding protein and Src substrate that is localized in podosomes, which are electron-dense structures found in Src-transformed fibroblasts, osteoclasts, macrophages, and some invasive cancer cells. It binds and regulates some members of the ADAMs family of transmembrane metalloproteases, which function as sheddases and mediators of cell and matrix interactions. It is required for podosome formation, degradation of the extracellular matrix, and cancer cell invasion. Tks5 contains an N-terminal Phox homology (PX) domain and five SH3 domains. This model characterizes the fourth SH3 domain of Tks5. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd12020 cd12020 212953 SH3_Tks5_5 Fifth (C-terminal) Src homology 3 domain of Tyrosine kinase substrate with five SH3 domains. Tks5, also called SH3 and PX domain-containing protein 2A (SH3PXD2A) or Five SH (FISH), is a scaffolding protein and Src substrate that is localized in podosomes, which are electron-dense structures found in Src-transformed fibroblasts, osteoclasts, macrophages, and some invasive cancer cells. It binds and regulates some members of the ADAMs family of transmembrane metalloproteases, which function as sheddases and mediators of cell and matrix interactions. It is required for podosome formation, degradation of the extracellular matrix, and cancer cell invasion. Tks5 contains an N-terminal Phox homology (PX) domain and five SH3 domains. This model characterizes the fifth (C-terminal) SH3 domain of Tks5. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd12021 cd12021 212954 SH3_p47phox_1 First or N-terminal Src homology 3 domain of the p47phox subunit of NADPH oxidase, also called Neutrophil Cytosolic Factor 1. p47phox, or NCF1, is a cytosolic subunit of the phagocytic NADPH oxidase complex (also called Nox2 or gp91phox), which plays a key role in the ability of phagocytes to defend against bacterial infections. NADPH oxidase catalyzes the transfer of electrons from NADPH to oxygen during phagocytosis forming superoxide and reactive oxygen species. p47phox is required for activation of NADH oxidase and plays a role in translocation. It contains an N-terminal Phox homology (PX) domain, tandem SH3 domains (N-SH3 and C-SH3), a polybasic/autoinhibitory region, and a C-terminal proline-rich region (PRR). This model characterizes the first SH3 domain (or N-SH3) of p47phox. In its inactive state, the tandem SH3 domains interact intramolecularly with the autoinhibitory region; upon activation, the tandem SH3 domains are exposed through a conformational change, resulting in their binding to the PRR of p22phox and the activation of NADPH oxidase. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd12022 cd12022 212955 SH3_p47phox_2 Second or C-terminal Src homology 3 domain of the p47phox subunit of NADPH oxidase, also called Neutrophil Cytosolic Factor 1. p47phox, or NCF1, is a cytosolic subunit of the phagocytic NADPH oxidase complex (also called Nox2 or gp91phox), which plays a key role in the ability of phagocytes to defend against bacterial infections. NADPH oxidase catalyzes the transfer of electrons from NADPH to oxygen during phagocytosis forming superoxide and reactive oxygen species. p47phox is required for activation of NADH oxidase and plays a role in translocation. It contains an N-terminal Phox homology (PX) domain, tandem SH3 domains (N-SH3 and C-SH3), a polybasic/autoinhibitory region, and a C-terminal proline-rich region (PRR). This model characterizes the second SH3 domain (or C-SH3) of p47phox. In its inactive state, the tandem SH3 domains interact intramolecularly with the autoinhibitory region; upon activation, the tandem SH3 domains are exposed through a conformational change, resulting in their binding to the PRR of p22phox and the activation of NADPH oxidase. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd12023 cd12023 212956 SH3_NoxO1_1 First or N-terminal Src homology 3 domain of Nox Organizing protein 1. Nox Organizing protein 1 (NoxO1) is a critical regulator of enzyme kinetics of the nonphagocytic NADPH oxidase Nox1, which catalyzes the transfer of electrons from NADPH to molecular oxygen to form superoxide. Nox1 is expressed in colon, stomach, uterus, prostate, and vascular smooth muscle cells. NoxO1 is involved in targeting activator subunits (such as NoxA1) to Nox1. It is co-localized with Nox1 in the membranes of resting cells and directs the subcellular localization of Nox1. NoxO1 contains an N-terminal Phox homology (PX) domain, tandem SH3 domains (N-SH3 and C-SH3), and a C-terminal proline-rich region (PRR). This model characterizes the first SH3 domain (or N-SH3) of NoxO1. The tandem SH3 domains of NoxO1 interact with the PRR of p22phox, which also complexes with Nox1. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd12024 cd12024 212957 SH3_NoxO1_2 Second or C-terminal Src homology 3 domain of NADPH oxidase (Nox) Organizing protein 1. Nox Organizing protein 1 (NoxO1) is a critical regulator of enzyme kinetics of the nonphagocytic NADPH oxidase Nox1, which catalyzes the transfer of electrons from NADPH to molecular oxygen to form superoxide. Nox1 is expressed in colon, stomach, uterus, prostate, and vascular smooth muscle cells. NoxO1 is involved in targeting activator subunits (such as NoxA1) to Nox1. It is co-localized with Nox1 in the membranes of resting cells and directs the subcellular localization of Nox1. NoxO1 contains an N-terminal Phox homology (PX) domain, tandem SH3 domains (N-SH3 and C-SH3), and a C-terminal proline-rich region (PRR). This model characterizes the second SH3 domain (or C-SH3) of NoxO1. The tandem SH3 domains of NoxO1 interact with the PRR of p22phox, which also complexes with Nox1. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd12025 cd12025 212958 SH3_Obscurin_like Src homology 3 domain of Obscurin and similar proteins. Obscurin is a giant muscle protein that is concentrated at the peripheries of Z-disks and M-lines. It binds small ankyrin I, a component of the sarcoplasmic reticulum (SR) membrane. It is associated with the contractile apparatus through binding with titin and sarcomeric myosin. It plays important roles in the organization and assembly of the myofibril and the SR. Obscurin has been observed as alternatively-spliced isoforms. The major isoform in sleletal muscle, approximately 800 kDa in size, is composed of many adhesion modules and signaling domains. It harbors 49 Ig and 2 FNIII repeats at the N-terminues, a complex middle region with additional Ig domains, an IQ motif, and a conserved SH3 domain near RhoGEF and PH domains, and a non-modular C-terminus with phosphorylation motifs. The obscurin gene also encodes two kinase domains, which are not part of the 800 kDa form of the protein, but is part of smaller spliced products that present in heart muscle. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 63 matched cddid_all.tbl CDD cd12026 cd12026 212959 SH3_ZO-1 Src homology 3 domain of the Tight junction protein, Zonula occludens protein 1. ZO-1 is a scaffolding protein that associates with other ZO proteins and other proteins of the tight junction, zonula adherens, and gap junctions. ZO proteins play roles in regulating cytoskeletal dynamics at these cell junctions. ZO-1 plays an essential role in embryonic development. It regulates the assembly and dynamics of the cortical cytoskeleton at cell-cell junctions. It is considered a member of the MAGUK (membrane-associated guanylate kinase) protein family, which is characterized by the presence of a core of three domains: PDZ, SH3, and guanylate kinase (GuK). The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. The C-terminal region of ZO-1 is the largest of the three ZO proteins and contains an actin-binding region and domains of unknown function designated alpha and ZU5. The SH3 domain of ZO-1 has been shown to bind ZONAB, ZAK, afadin, and Galpha12. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 65 matched cddid_all.tbl CDD cd12027 cd12027 212960 SH3_ZO-2 Src homology 3 domain of the Tight junction protein, Zonula occludens protein 2. ZO-2 is a scaffolding protein that associates with other ZO proteins and other proteins of the tight junction, zonula adherens, and gap junctions. ZO proteins play roles in regulating cytoskeletal dynamics at these cell junctions. ZO-2 plays an essential role in embryonic development. It is critical for the blood-testis barrier integrity and male fertility. It also regulates the expression of cyclin D1 and cell proliferation. It is considered a member of the MAGUK (membrane-associated guanylate kinase) protein family, which is characterized by the presence of a core of three domains: PDZ, SH3, and guanylate kinase (GuK). The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. The C-terminal region of ZO-2 contains an actin-binding region and a domain of unknown function designated beta. The SH3 domain of the related protein ZO-1 has been shown to bind ZONAB, ZAK, afadin, and Galpha12. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 63 matched cddid_all.tbl CDD cd12028 cd12028 212961 SH3_ZO-3 Src homology 3 domain of the Tight junction protein, Zonula occludens protein 3. ZO-3 is a scaffolding protein that associates with other ZO proteins and other proteins of the tight junction, zonula adherens, and gap junctions. ZO proteins play roles in regulating cytoskeletal dynamics at these cell junctions. ZO-3 is critical for epidermal barrier function. It regulates cyclin D1-dependent cell proliferation. It is considered a member of the MAGUK (membrane-associated guanylate kinase) protein family, which is characterized by the presence of a core of three domains: PDZ, SH3, and guanylate kinase (GuK). The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. The C-terminal region of ZO-3 is the smallest of the three ZO proteins. The SH3 domain of the related protein ZO-1 has been shown to bind ZONAB, ZAK, afadin, and Galpha12. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 65 matched cddid_all.tbl CDD cd12029 cd12029 212962 SH3_DLG3 Src Homology 3 domain of Disks Large homolog 3. DLG3, also called synapse-associated protein 102 (SAP102), is a scaffolding protein that clusters at synapses and plays an important role in synaptic development and plasticity. Mutations in DLG3 cause midgestational embryonic lethality in mice and may be associated with nonsyndromic X-linked mental retardation in humans. It interacts with the NEDD4 (neural precursor cell-expressed developmentally downregulated 4) family of ubiquitin ligases and promotes apical tight junction formation. DLG3 is a member of the MAGUK (membrane-associated guanylate kinase) protein family, which is characterized by the presence of a core of three domains: PDZ, SH3, and guanylate kinase (GuK). The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. DLG3 contains three PDZ domains. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 67 matched cddid_all.tbl CDD cd12030 cd12030 212963 SH3_DLG4 Src Homology 3 domain of Disks Large homolog 4. DLG4, also called postsynaptic density-95 (PSD95) or synapse-associated protein 90 (SAP90), is a scaffolding protein that clusters at synapses and plays an important role in synaptic development and plasticity. It is responsible for the membrane clustering and retention of many transporters and receptors such as potassium channels and PMCA4b, a P-type ion transport ATPase, among others. DLG4 is a member of the MAGUK (membrane-associated guanylate kinase) protein family, which is characterized by the presence of a core of three domains: PDZ, SH3, and guanylate kinase (GuK). The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. DLG4 contains three PDZ domains. The SH3 domain of DLG4 binds and clusters the kainate subgroup of glutamate receptors via two proline-rich sequences in their C-terminal tail. It also binds AKAP79/150 (A-kinase anchoring protein). SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 66 matched cddid_all.tbl CDD cd12031 cd12031 212964 SH3_DLG1 Src Homology 3 domain of Disks Large homolog 1. DLG1, also called synapse-associated protein 97 (SAP97), is a scaffolding protein that clusters at synapses and plays an important role in synaptic development and plasticity. DLG1 plays roles in regulating cell polarity, proliferation, migration, and cycle progression. It interacts with AMPA-type glutamate receptors and is critical in their maturation and delivery to synapses. It also interacts with PKCalpha and promotes wound healing. DLG1 is a member of the MAGUK (membrane-associated guanylate kinase) protein family, which is characterized by the presence of a core of three domains: PDZ, SH3, and guanylate kinase (GuK). The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. DLG1 contains three PDZ domains. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 67 matched cddid_all.tbl CDD cd12032 cd12032 212965 SH3_DLG2 Src Homology 3 domain of Disks Large homolog 2. DLG2, also called postsynaptic density-93 (PSD93) or Channel-associated protein of synapse-110 (chapsyn 110), is a scaffolding protein that clusters at synapses and plays an important role in synaptic development and plasticity. The DLG2 delta isoform binds inwardly rectifying potassium Kir2 channels, which determine resting membrane potential in neurons. It regulates the spatial and temporal distribution of Kir2 channels within neuronal membranes. DLG2 is a member of the MAGUK (membrane-associated guanylate kinase) protein family, which is characterized by the presence of a core of three domains: PDZ, SH3, and guanylate kinase (GuK). The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. DLG2 contains three PDZ domains. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 74 matched cddid_all.tbl CDD cd12033 cd12033 212966 SH3_MPP7 Src Homology 3 domain of Membrane Protein, Palmitoylated 7 (or MAGUK p55 subfamily member 7). MPP7 is a scaffolding protein that binds to DLG1 and promotes tight junction formation and epithelial cell polarity. Mutations in the MPP7 gene may be associated with the pathogenesis of diabetes and extreme bone mineral density. It is one of seven vertebrate homologs of the Drosophila Stardust protein, which is required in establishing cell polarity, and it contains two L27 domains followed by the core of three domains characteristic of MAGUK (membrane-associated guanylate kinase) proteins: PDZ, SH3, and guanylate kinase (GuK). The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 61 matched cddid_all.tbl CDD cd12034 cd12034 212967 SH3_MPP4 Src Homology 3 domain of Membrane Protein, Palmitoylated 4 (or MAGUK p55 subfamily member 4). MPP4, also called Disks Large homolog 6 (DLG6) or Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 5 protein (ALS2CR5), is a retina-specific scaffolding protein that plays a role in organizing presynaptic protein complexes in the photoreceptor synapse, where it localizes to the plasma membrane. It is required in the proper localization of calcium ATPases and for maintenance of calcium homeostasis. MPP4 is one of seven vertebrate homologs of the Drosophila Stardust protein, which is required in establishing cell polarity, and it contains two L27 domains followed by the core of three domains characteristic of MAGUK (membrane-associated guanylate kinase) proteins: PDZ, SH3, and guanylate kinase (GuK). The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 61 matched cddid_all.tbl CDD cd12035 cd12035 212968 SH3_MPP1-like Src Homology 3 domain of Membrane Protein, Palmitoylated 1 (or MAGUK p55 subfamily member 1)-like proteins. This subfamily includes MPP1, CASK (Calcium/calmodulin-dependent Serine protein Kinase), Caenorhabditis elegans lin-2, and similar proteins. MPP1 and CASK are scaffolding proteins from the MAGUK (membrane-associated guanylate kinase) protein family, which is characterized by the presence of a core of three domains: PDZ, SH3, and guanylate kinase (GuK). In addition, they also have the Hook (Protein 4.1 Binding) motif in between the SH3 and GuK domains. The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. CASK and lin-2 also contain an N-terminal calmodulin-dependent kinase (CaMK)-like domain and two L27 domains. MPP1 is ubiquitously-expressed and plays roles in regulating neutrophil polarity, cell shape, hair cell development, and neural development and patterning of the retina. CASK is highly expressed in the mammalian nervous system and plays roles in synaptic protein targeting, neural development, and gene expression regulation. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 62 matched cddid_all.tbl CDD cd12036 cd12036 212969 SH3_MPP5 Src Homology 3 domain of Membrane Protein, Palmitoylated 5 (or MAGUK p55 subfamily member 5). MPP5, also called PALS1 (Protein associated with Lin7) or Nagie oko protein in zebrafish or Stardust in Drosophila, is a scaffolding protein which associates with Crumbs homolog 1 (CRB1), CRB2, or CRB3 through its PDZ domain and with PALS1-associated tight junction protein (PATJ) or multi-PDZ domain protein 1 (MUPP1) through its L27 domain. The resulting tri-protein complexes are core proteins of the Crumb complex, which localizes at tight junctions or subapical regions, and is involved in the maintenance of apical-basal polarity in epithelial cells and the morphogenesis and function of photoreceptor cells. MPP5 is critical for the proper stratification of the retina and is also expressed in T lymphocytes where it is important for TCR-mediated activation of NFkB. Drosophila Stardust exists in several isoforms, some of which show opposing functions in photoreceptor cells, which suggests that the relative ratio of different Crumbs complexes regulates photoreceptor homeostasis. MPP5 contains two L27 domains followed by the core of three domains characteristic of MAGUK (membrane-associated guanylate kinase) proteins: PDZ, SH3, and guanylate kinase (GuK). In addition, it also contains the Hook (Protein 4.1 Binding) motif in between the SH3 and GuK domains. The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 63 matched cddid_all.tbl CDD cd12037 cd12037 212970 SH3_MPP2 Src Homology 3 domain of Membrane Protein, Palmitoylated 2 (or MAGUK p55 subfamily member 2). MPP2 is a scaffolding protein that interacts with the non-receptor tyrosine kinase c-Src in epithelial cells to negatively regulate its activity and morphological function. It is one of seven vertebrate homologs of the Drosophila Stardust protein, which is required in establishing cell polarity, and it contains two L27 domains followed by the core of three domains characteristic of MAGUK (membrane-associated guanylate kinase) proteins: PDZ, SH3, and guanylate kinase (GuK). In addition, it also contains the Hook (Protein 4.1 Binding) motif in between the SH3 and GuK domains. The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 59 matched cddid_all.tbl CDD cd12038 cd12038 212971 SH3_MPP6 Src Homology 3 domain of Membrane Protein, Palmitoylated 6 (or MAGUK p55 subfamily member 6). MPP6, also called Veli-associated MAGUK 1 (VAM-1) or PALS2, is a scaffolding protein that binds to Veli-1, a homolog of Caenorhabditis Lin-7. It is one of seven vertebrate homologs of the Drosophila Stardust protein, which is required in establishing cell polarity, and it contains two L27 domains followed by the core of three domains characteristic of MAGUK (membrane-associated guanylate kinase) proteins: PDZ, SH3, and guanylate kinase (GuK). In addition, it also contains the Hook (Protein 4.1 Binding) motif in between the SH3 and GuK domains. The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 61 matched cddid_all.tbl CDD cd12039 cd12039 212972 SH3_MPP3 Src Homology 3 domain of Membrane Protein, Palmitoylated 3 (or MAGUK p55 subfamily member 3). MPP3 is a scaffolding protein that colocalizes with MPP5 and CRB1 at the subdpical region adjacent to adherens junctions and may function in photoreceptor polarity. It interacts with some nectins and regulates their trafficking and processing. Nectins are cell-cell adhesion proteins involved in the establishment apical-basal polarity at cell adhesion sites. It is one of seven vertebrate homologs of the Drosophila Stardust protein, which is required in establishing cell polarity, and it contains two L27 domains followed by the core of three domains characteristic of MAGUK (membrane-associated guanylate kinase) proteins: PDZ, SH3, and guanylate kinase (GuK). The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 62 matched cddid_all.tbl CDD cd12040 cd12040 212973 SH3_CACNB2 Src Homology 3 domain of Voltage-dependent L-type calcium channel subunit beta2. The beta2 subunit of voltage-dependent calcium channels (Ca(V)s) is one of four beta subunits present in vertebrates. It is expressed in the heart and is present in specific neuronal cells including cerebellar Purkinje cells, hippocampal pyramidal neurons, and photoreceptors. Knockout of the beta2 gene in mice results in embryonic lethality, demonstrating its importance in development. Ca(V)s are multi-protein complexes that regulate the entry of calcium into cells. They impact muscle contraction, neuronal migration, hormone and neurotransmitter release, and the activation of calcium-dependent signaling pathways. They are composed of four subunits: alpha1, alpha2delta, beta, and gamma. The beta subunit is a soluble and intracellular protein that interacts with the transmembrane alpha1 subunit. It facilitates the trafficking and proper localization of the alpha1 subunit to the cellular plasma membrane. Vertebrates contain four different beta subunits from distinct genes (beta1-4); each exists as multiple splice variants. All are expressed in the brain while other tissues show more specific expression patterns. The beta subunits show similarity to MAGUK (membrane-associated guanylate kinase) proteins in that they contain SH3 and inactive guanylate kinase (GuK) domains; however, they do not appear to contain a PDZ domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 69 matched cddid_all.tbl CDD cd12041 cd12041 212974 SH3_CACNB1 Src Homology 3 domain of Voltage-dependent L-type calcium channel subunit beta-1. The beta1 subunit of voltage-dependent calcium channels (Ca(V)s) is one of four beta subunits present in vertebrates. It is the only beta subunit, as the beta1a variant, expressed in skeletal muscle; the beta1b variant is also widely expressed in other tissues including the heart and brain. Knockout of the beta1 gene in mice results in embryonic lethality, demonstrating its importance in development. Ca(V)s are multi-protein complexes that regulate the entry of calcium into cells. They impact muscle contraction, neuronal migration, hormone and neurotransmitter release, and the activation of calcium-dependent signaling pathways. They are composed of four subunits: alpha1, alpha2delta, beta, and gamma. The beta subunit is a soluble and intracellular protein that interacts with the transmembrane alpha1 subunit. It facilitates the trafficking and proper localization of the alpha1 subunit to the cellular plasma membrane. Vertebrates contain four different beta subunits from distinct genes (beta1-4); each exists as multiple splice variants. All are expressed in the brain while other tissues show more specific expression patterns. The beta subunits show similarity to MAGUK (membrane-associated guanylate kinase) proteins in that they contain SH3 and inactive guanylate kinase (GuK) domains; however, they do not appear to contain a PDZ domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 68 matched cddid_all.tbl CDD cd12042 cd12042 212975 SH3_CACNB3 Src Homology 3 domain of Voltage-dependent L-type calcium channel subunit beta3. The beta3 subunit of voltage-dependent calcium channels (Ca(V)s) is one of four beta subunits present in vertebrates. It is the main beta subunit present in smooth muscles and is strongly expressed in the brain; it is predominant in the olfactory bulb, cortex, and hippocampus. It may play a role in regulating the NMDAR (N-methyl-d-aspartate receptor) activity in the hippocampus and thus, activity-dependent synaptic plasticity and cognitive behaviors. Ca(V)s are multi-protein complexes that regulate the entry of calcium into cells. They impact muscle contraction, neuronal migration, hormone and neurotransmitter release, and the activation of calcium-dependent signaling pathways. They are composed of four subunits: alpha1, alpha2delta, beta, and gamma. The beta subunit is a soluble and intracellular protein that interacts with the transmembrane alpha1 subunit. It facilitates the trafficking and proper localization of the alpha1 subunit to the cellular plasma membrane. Vertebrates contain four different beta subunits from distinct genes (beta1-4); each exists as multiple splice variants. All are expressed in the brain while other tissues show more specific expression patterns. The beta subunits show similarity to MAGUK (membrane-associated guanylate kinase) proteins in that they contain SH3 and inactive guanylate kinase (GuK) domains; however, they do not appear to contain a PDZ domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 68 matched cddid_all.tbl CDD cd12043 cd12043 212976 SH3_CACNB4 Src Homology 3 domain of Voltage-dependent L-type calcium channel subunit beta4. The beta4 subunit of voltage-dependent calcium channels (Ca(V)s) is one of four beta subunits present in vertebrates. It is the only beta subunit expressed in the cochlea and is highly expressed in the brain, predominantly in the cerebellum. Ca(V)s are multi-protein complexes that regulate the entry of calcium into cells. They impact muscle contraction, neuronal migration, hormone and neurotransmitter release, and the activation of calcium-dependent signaling pathways. They are composed of four subunits: alpha1, alpha2delta, beta, and gamma. The beta subunit is a soluble and intracellular protein that interacts with the transmembrane alpha1 subunit. It facilitates the trafficking and proper localization of the alpha1 subunit to the cellular plasma membrane. Vertebrates contain four different beta subunits from distinct genes (beta1-4); each exists as multiple splice variants. All are expressed in the brain while other tissues show more specific expression patterns. The beta subunits show similarity to MAGUK (membrane-associated guanylate kinase) proteins in that they contain SH3 and inactive guanylate kinase (GuK) domains; however, they do not appear to contain a PDZ domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 68 matched cddid_all.tbl CDD cd12044 cd12044 212977 SH3_SKAP1 Src Homology 3 domain of Src Kinase-Associated Phosphoprotein 1. SKAP1, also called SKAP55 (Src kinase-associated protein of 55kDa), is an immune cell-specific adaptor protein that plays an important role in T-cell adhesion, migration, and integrin clustering. It is expressed exclusively in T-lymphocytes, mast cells, and macrophages. Binding partners include ADAP (adhesion and degranulation-promoting adaptor protein), Fyn, Riam, RapL, and RasGRP. It contains a pleckstrin homology (PH) domain, a C-terminal SH3 domain, and several tyrosine phosphorylation sites. The SH3 domain of SKAP1 is necessary for its ability to regulate T-cell conjugation with antigen-presenting cells and the formation of LFA-1 clusters. SKAP1 binds primarily to a proline-rich region of ADAP through its SH3 domain; its degradation is regulated by ADAP. A secondary interaction occurs via the ADAP SH3 domain and the RKxxYxxY motif in SKAP1. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd12045 cd12045 212978 SH3_SKAP2 Src Homology 3 domain of Src Kinase-Associated Phosphoprotein 2. SKAP2, also called SKAP55-Related (SKAP55R) or SKAP55 homolog (SKAP-HOM or SKAP55-HOM), is an immune cell-specific adaptor protein that plays an important role in adhesion and migration of B-cells and macrophages. Binding partners include ADAP (adhesion and degranulation-promoting adaptor protein), YopH, SHPS1, and HPK1. SKAP2 has also been identified as a substrate for lymphoid-specific tyrosine phosphatase (Lyp), which has been implicated in a wide variety of autoimmune diseases. It contains a pleckstrin homology (PH) domain, a C-terminal SH3 domain, and several tyrosine phosphorylation sites. Like SKAP1, SKAP2 is expected to bind primarily to a proline-rich region of ADAP through its SH3 domain; its degradation may be regulated by ADAP. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd12046 cd12046 212979 SH3_p67phox_C C-terminal (or second) Src Homology 3 domain of the p67phox subunit of NADPH oxidase. p67phox, also called Neutrophil cytosol factor 2 (NCF-2), is a cytosolic subunit of the phagocytic NADPH oxidase complex (also called Nox2 or gp91phox) which plays a crucial role in the cellular response to bacterial infection. NADPH oxidase catalyzes the transfer of electrons from NADPH to oxygen during phagocytosis forming superoxide and reactive oxygen species. p67phox plays a regulatory role and contains N-terminal TPR, first SH3 (or N-terminal or central SH3), PB1, and C-terminal SH3 domains. It binds, via its C-terminal SH3 domain, to a proline-rich region of p47phox and upon activation, this complex assembles with flavocytochrome b558, the Nox2-p22phox heterodimer. Concurrently, RacGTP translocates to the membrane and interacts with the TPR domain of p67phox, which leads to the activation of NADPH oxidase. The PB1 domain of p67phox binds to its partner PB1 domain in p40phox, and this facilitates the assembly of p47phox-p67phox at the membrane. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd12047 cd12047 212980 SH3_Noxa1_C C-terminal Src Homology 3 domain of NADPH oxidase activator 1. Noxa1 is a homolog of p67phox and is a cytosolic subunit of the nonphagocytic NADPH oxidase complex Nox1, which catalyzes the transfer of electrons from NADPH to molecular oxygen to form superoxide. Noxa1 is co-expressed with Nox1 in colon, stomach, uterus, prostate, and vascular smooth muscle cells, consistent with its regulatory role. It does not interact with p40phox, unlike p67phox, making Nox1 activity independent of p40phox, unlike Nox2. Noxa1 contains TPR, PB1, and C-terminal SH3 domains, but lacks the central SH3 domain that is present in p67phox. The TPR domain binds activated GTP-bound Rac. The C-terminal SH3 domain binds the polyproline motif found at the C-terminus of Noxo1, a homolog of p47phox. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd12048 cd12048 212981 SH3_DOCK3_B Src Homology 3 domain of Class B Dedicator of Cytokinesis 3. Dock3, also called modifier of cell adhesion (MOCA), and presenilin binding protein (PBP), is a class B DOCK and is an atypical guanine nucleotide exchange factor (GEF) that lacks the conventional Dbl homology (DH) domain. It regulates N-cadherin dependent cell-cell adhesion, cell polarity, and neuronal morphology. It promotes axonal growth by stimulating actin polymerization and microtubule assembly. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate while DHR-2 contains the catalytic activity for Rac and/or Cdc42. Class B DOCKs also contain an SH3 domain at the N-terminal region and a PxxP motif at the C-terminus; Dock3 is a specific GEFs for Rac. The SH3 domain of Dock3 binds to DHR-2 in an autoinhibitory manner; binding of the scaffold protein Elmo to the SH3 domain of Dock3 exposes the DHR-2 domain and promotes GEF activity. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd12049 cd12049 212982 SH3_DOCK4_B Src Homology 3 domain of Class B Dedicator of Cytokinesis 4. Dock4 is a class B DOCK and is an atypical guanine nucleotide exchange factor (GEF) that lacks the conventional Dbl homology (DH) domain. It plays a role in regulating dendritic growth and branching in hippocampal neurons, where it is highly expressed. It may also regulate spine morphology and synapse formation. Dock4 activates the Ras family GTPase Rap1, probably indirectly through interaction with Rap regulatory proteins. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate while DHR-2 contains the catalytic activity for Rac and/or Cdc42. Class B DOCKs also contain an SH3 domain at the N-terminal region and a PxxP motif at the C-terminus. The SH3 domain of Dock4 binds to DHR-2 in an autoinhibitory manner; binding of the scaffold protein Elmo to the SH3 domain of Dock4 exposes the DHR-2 domain and promotes GEF activity. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd12050 cd12050 212983 SH3_DOCK2_A Src Homology 3 domain of Class A Dedicator of Cytokinesis protein 2. Dock2 is a hematopoietic cell-specific, class A DOCK and is an atypical guanine nucleotide exchange factor (GEF) that lacks the conventional Dbl homology (DH) domain. It plays an important role in lymphocyte migration and activation, T-cell differentiation, neutrophil chemotaxis, and type I interferon induction. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate while DHR-2 contains the catalytic activity for Rac and/or Cdc42. Class A DOCKs also contain an SH3 domain at the N-terminal region and a PxxP motif at the C-terminus; they are specific GEFs for Rac. The SH3 domain of Dock2 binds to DHR-2 in an autoinhibitory manner; binding of the scaffold protein Elmo to the SH3 domain of Dock2 exposes the DHR-2 domain and promotes GEF activity. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd12051 cd12051 212984 SH3_DOCK1_5_A Src Homology 3 domain of Class A Dedicator of Cytokinesis proteins 1 and 5. Dock1, also called Dock180, and Dock5 are class A DOCKs and are atypical guanine nucleotide exchange factors (GEFs) that lack the conventional Dbl homology (DH) domain. Dock1 interacts with the scaffold protein Elmo and the resulting complex functions upstream of Rac in many biological events including phagocytosis of apoptotic cells, cell migration and invasion. Dock5 functions upstream of Rac1 to regulate osteoclast function. All DOCKs contain two homology domains: the DHR-1 (Dock homology region-1), also called CZH1 (CED-5, Dock180, and MBC-zizimin homology 1), and DHR-2 (also called CZH2 or Docker). The DHR-1 domain binds phosphatidylinositol-3,4,5-triphosphate while DHR-2 contains the catalytic activity for Rac and/or Cdc42. Class A DOCKs also contain an SH3 domain at the N-terminal region and a PxxP motif at the C-terminus; they are specific GEFs for Rac. The SH3 domain of Dock1 binds to DHR-2 in an autoinhibitory manner; binding of Elmo to the SH3 domain of Dock1 exposes the DHR-2 domain and promotes GEF activity. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd12052 cd12052 212985 SH3_CIN85_1 First Src Homology 3 domain (SH3A) of Cbl-interacting protein of 85 kDa. CIN85, also called SH3 domain-containing kinase-binding protein 1 (SH3KBP1) or CD2-binding protein 3 (CD2BP3) or Ruk, is an adaptor protein that is involved in the downregulation of receptor tyrosine kinases by facilitating endocytosis through interaction with endophilin-associated ubiquitin ligase Cbl proteins. It is also important in many other cellular processes including vesicle-mediated transport, cytoskeletal remodelling, apoptosis, cell adhesion and migration, and viral infection, among others. CIN85 exists as multiple variants from alternative splicing; the main variant contains three SH3 domains, a proline-rich region, and a C-terminal coiled-coil domain. All of these domains enable CIN85 to bind various protein partners and assemble complexes that have been implicated in many different functions. This alignment model represents the first SH3 domain (SH3A) of CIN85; SH3A binds to internal proline-rich motifs within the proline-rich region. This intramolecular interaction serves as a regulatory mechanism to keep CIN85 in a closed conformation, preventing the recruitment of other proteins. SH3A has also been shown to bind ubiquitin and to an atypical PXXXPR motif at the C-terminus of Cbl and the cytoplasmic end of the cell adhesion protein CD2. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd12053 cd12053 212986 SH3_CD2AP_1 First Src Homology 3 domain (SH3A) of CD2-associated protein. CD2AP, also called CMS (Cas ligand with Multiple SH3 domains) or METS1 (Mesenchyme-to-Epithelium Transition protein with SH3 domains), is a cytosolic adaptor protein that plays a role in regulating the cytoskeleton. It is critical in cell-to-cell union necessary for kidney function. It also stabilizes the contact between a T cell and antigen-presenting cells. It is primarily expressed in podocytes at the cytoplasmic face of the slit diaphragm and serves as a linker anchoring podocin and nephrin to the actin cytoskeleton. CD2AP contains three SH3 domains, a proline-rich region, and a C-terminal coiled-coil domain. All of these domains enable CD2AP to bind various protein partners and assemble complexes that have been implicated in many different functions. This alignment model represents the first SH3 domain (SH3A) of CD2AP. SH3A binds to the PXXXPR motif present in c-Cbl and the cytoplasmic domain of cell adhesion protein CD2. Its interaction with CD2 anchors CD2 at sites of cell contact. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd12054 cd12054 212987 SH3_CD2AP_2 Second Src Homology 3 domain (SH3B) of CD2-associated protein. CD2AP, also called CMS (Cas ligand with Multiple SH3 domains) or METS1 (Mesenchyme-to-Epithelium Transition protein with SH3 domains), is a cytosolic adaptor protein that plays a role in regulating the cytoskeleton. It is critical in cell-to-cell union necessary for kidney function. It also stabilizes the contact between a T cell and antigen-presenting cells. It is primarily expressed in podocytes at the cytoplasmic face of the slit diaphragm and serves as a linker anchoring podocin and nephrin to the actin cytoskeleton. CD2AP contains three SH3 domains, a proline-rich region, and a C-terminal coiled-coil domain. All of these domains enable CD2AP to bind various protein partners and assemble complexes that have been implicated in many different functions. This alignment model represents the second SH3 domain (SH3B) of CD2AP. SH3B binds to c-Cbl in a site (TPSSRPLR is the core binding motif) distinct from the c-Cbl/SH3A binding site. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd12055 cd12055 212988 SH3_CIN85_2 Second Src Homology 3 domain (SH3B) of Cbl-interacting protein of 85 kDa. CIN85, also called SH3 domain-containing kinase-binding protein 1 (SH3KBP1) or CD2-binding protein 3 (CD2BP3) or Ruk, is an adaptor protein that is involved in the downregulation of receptor tyrosine kinases by facilitating endocytosis through interaction with endophilin-associated ubiquitin ligase Cbl proteins. It is also important in many other cellular processes including vesicle-mediated transport, cytoskeletal remodelling, apoptosis, cell adhesion and migration, and viral infection, among others. CIN85 exists as multiple variants from alternative splicing; the main variant contains three SH3 domains, a proline-rich region, and a C-terminal coiled-coil domain. All of these domains enable CIN85 to bind various protein partners and assemble complexes that have been implicated in many different functions. This alignment model represents the second SH3 domain (SH3B) of CIN85. SH3B has been shown to bind Cbl proline-rich peptides and ubiquitin. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd12056 cd12056 212989 SH3_CD2AP_3 Third Src Homology 3 domain (SH3C) of CD2-associated protein. CD2AP, also called CMS (Cas ligand with Multiple SH3 domains) or METS1 (Mesenchyme-to-Epithelium Transition protein with SH3 domains), is a cytosolic adaptor protein that plays a role in regulating the cytoskeleton. It is critical in cell-to-cell union necessary for kidney function. It also stabilizes the contact between a T cell and antigen-presenting cells. It is primarily expressed in podocytes at the cytoplasmic face of the slit diaphragm and serves as a linker anchoring podocin and nephrin to the actin cytoskeleton. CD2AP contains three SH3 domains, a proline-rich region, and a C-terminal coiled-coil domain. All of these domains enable CD2AP to bind various protein partners and assemble complexes that have been implicated in many different functions. This alignment model represents the third SH3 domain (SH3C) of CD2AP. SH3C has been shown to bind ubiquitin. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd12057 cd12057 212990 SH3_CIN85_3 Third Src Homology 3 domain (SH3C) of Cbl-interacting protein of 85 kDa. CIN85, also called SH3 domain-containing kinase-binding protein 1 (SH3KBP1) or CD2-binding protein 3 (CD2BP3) or Ruk, is an adaptor protein that is involved in the downregulation of receptor tyrosine kinases by facilitating endocytosis through interaction with endophilin-associated ubiquitin ligase Cbl proteins. It is also important in many other cellular processes including vesicle-mediated transport, cytoskeletal remodelling, apoptosis, cell adhesion and migration, and viral infection, among others. CIN85 exists as multiple variants from alternative splicing; the main variant contains three SH3 domains, a proline-rich region, and a C-terminal coiled-coil domain. All of these domains enable CIN85 to bind various protein partners and assemble complexes that have been implicated in many different functions. This alignment model represents the third SH3 domain (SH3C) of CIN85. SH3C has been shown to bind ubiquitin. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd12058 cd12058 212991 SH3_MLK4 Src Homology 3 domain of Mixed Lineage Kinase 4. MLK4 is a Serine/Threonine Kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. MLKs act as mitogen-activated protein kinase kinase kinases (MAP3Ks, MKKKs, MAPKKKs), which phosphorylate and activate MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. MLKs play roles in immunity and inflammation, as well as in cell death, proliferation, and cell cycle regulation. The specific function of MLK4 is yet to be determined. Mutations in the kinase domain of MLK4 have been detected in colorectal cancers. MLK4 contains an SH3 domain, a catalytic kinase domain, a leucine zipper, a proline-rich region, and a CRIB domain that mediates binding to GTP-bound Cdc42 and Rac. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 58 matched cddid_all.tbl CDD cd12059 cd12059 212992 SH3_MLK1-3 Src Homology 3 domain of Mixed Lineage Kinases 1, 2, and 3. MLKs 1, 2, and 3 are Serine/Threonine Kinases (STKs), catalyzing the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. MLKs act as mitogen-activated protein kinase kinase kinases (MAP3Ks, MKKKs, MAPKKKs), which phosphorylate and activate MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. MLKs play roles in immunity and inflammation, as well as in cell death, proliferation, and cell cycle regulation. Little is known about the specific function of MLK1, also called MAP3K9. It is capable of activating the c-Jun N-terminal kinase pathway. Mice lacking both MLK1 and MLK2 are viable, fertile, and have normal life spans. MLK2, also called MAP3K10, is abundant in brain, skeletal muscle, and testis. It functions upstream of the MAPK, c-Jun N-terminal kinase. It binds hippocalcin, a calcium-sensor protein that protects neurons against calcium-induced cell death. Both MLK2 and hippocalcin may be associated with the pathogenesis of Parkinson's disease. MLK3, also called MAP3K11, is highly expressed in breast cancer cells and its signaling through c-Jun N-terminal kinase has been implicated in the migration, invasion, and malignancy of cancer cells. It also functions as a negative regulator of Inhibitor of Nuclear Factor-KappaB Kinase (IKK) and thus, impacts inflammation and immunity. MLKs contain an SH3 domain, a catalytic kinase domain, a leucine zipper, a proline-rich region, and a CRIB domain that mediates binding to GTP-bound Cdc42 and Rac. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 58 matched cddid_all.tbl CDD cd12060 cd12060 212993 SH3_alphaPIX Src Homology 3 domain of alpha-Pak Interactive eXchange factor. Alpha-PIX, also called Rho guanine nucleotide exchange factor 6 (ARHGEF6) or Cool (Cloned out of Library)-2, activates small GTPases by exchanging bound GDP for free GTP. It acts as a GEF for both Cdc42 and Rac 1, and is localized in dendritic spines where it regulates spine morphogenesis. It controls dendritic length and spine density in the hippocampus. Mutations in the ARHGEF6 gene cause X-linked intellectual disability in humans. PIX proteins contain an N-terminal SH3 domain followed by RhoGEF (also called Dbl-homologous or DH) and Pleckstrin Homology (PH) domains, and a C-terminal leucine-zipper domain for dimerization. The SH3 domain of PIX binds to an atypical PxxxPR motif in p21-activated kinases (PAKs) with high affinity. The binding of PAKs to PIX facilitate the localization of PAKs to focal complexes and also localizes PAKs to PIX targets Cdc43 and Rac, leading to the activation of PAKs. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 58 matched cddid_all.tbl CDD cd12061 cd12061 212994 SH3_betaPIX Src Homology 3 domain of beta-Pak Interactive eXchange factor. Beta-PIX, also called Rho guanine nucleotide exchange factor 7 (ARHGEF7) or Cool (Cloned out of Library)-1, activates small GTPases by exchanging bound GDP for free GTP. It acts as a GEF for both Cdc42 and Rac 1, and plays important roles in regulating neuroendocrine exocytosis, focal adhesion maturation, cell migration, synaptic vesicle localization, and insulin secretion. PIX proteins contain an N-terminal SH3 domain followed by RhoGEF (also called Dbl-homologous or DH) and Pleckstrin Homology (PH) domains, and a C-terminal leucine-zipper domain for dimerization. The SH3 domain of PIX binds to an atypical PxxxPR motif in p21-activated kinases (PAKs) with high affinity. The binding of PAKs to PIX facilitate the localization of PAKs to focal complexes and also localizes PAKs to PIX targets Cdc43 and Rac, leading to the activation of PAKs. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd12062 cd12062 212995 SH3_Caskin1 Src Homology 3 domain of CASK interacting protein 1. Caskin1 is a multidomain adaptor protein that contains six ankyrin repeats, a single SH3 domain, tandem sterile alpha motif (SAM) domains, and a long disordered proline-rich region. It is expressed at high levels in the brain and is localized in presynaptic regions. It binds to the multidomain scaffolding protein CASK through the CaMK domain in competition with Munc-interacting protein 1 (Mint1). CASK participates in one of two evolutionarily conserved tripartite complexes containing either Mint1 and Velis or Caskin1 and Velis. Caskin1 may play a role in infantile myoclonic epilepsy. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 62 matched cddid_all.tbl CDD cd12063 cd12063 212996 SH3_Caskin2 Src Homology 3 domain of CASK interacting protein 2. Caskin2 is a multidomain adaptor protein that contains six ankyrin repeats, a single SH3 domain, tandem sterile alpha motif (SAM) domains, and a long disordered proline-rich region. It shares a domain architecture with Caskin1, but does not bind CASK. The function of Caskin2 is still unknown. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 62 matched cddid_all.tbl CDD cd12064 cd12064 212997 SH3_GRAF Src Homology 3 domain of GTPase Regulator Associated with Focal adhesion kinase. GRAF, also called Rho GTPase activating protein 26 (ARHGAP26), Oligophrenin-1-like (OPHN1L) or GRAF1, is a GAP with activity towards RhoA and Cdc42 and is only weakly active towards Rac1. It influences Rho-mediated cytoskeletal rearrangements and binds focal adhesion kinase (FAK), which is a critical component of integrin signaling. It is essential for the major clathrin-independent endocytic pathway mediated by pleiomorphic membranes. GRAF contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. The SH3 domain of GRAF binds PKNbeta, a target of the small GTPase Rho. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 56 matched cddid_all.tbl CDD cd12065 cd12065 212998 SH3_GRAF2 Src Homology 3 domain of GTPase Regulator Associated with Focal adhesion kinase 2. GRAF2, also called Rho GTPase activating protein 10 (ARHGAP10) or PS-GAP, is a GAP with activity towards Cdc42 and RhoA. It regulates caspase-activated p21-activated protein kinase-2 (PAK-2p34). GRAF2 interacts with PAK-2p34, leading to its stabilization and decrease of cell death. It is highly expressed in skeletal muscle, and is involved in alpha-catenin recruitment at cell-cell junctions. GRAF2 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. The SH3 domain of GRAF binds PKNbeta, a target of the small GTPase Rho. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd12066 cd12066 212999 SH3_GRAF3 Src Homology 3 domain of GTPase Regulator Associated with Focal adhesion kinase 3. GRAF3 is also called Rho GTPase activating protein 42 (ARHGAP42) or ARHGAP10-like. Though its function has not been characterized, it may be a GAP with activity towards RhoA and Cdc42, based on its similarity to GRAF and GRAF2. It contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, a Rho GAP domain, and a C-terminal SH3 domain. The SH3 domain of GRAF and GRAF2 binds PKNbeta, a target of the small GTPase Rho. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd12067 cd12067 213000 SH3_MYO15A Src Homology 3 domain of Myosin XVa. Myosin XVa is an unconventional myosin that is critical for the normal growth of mechanosensory stereocilia of inner ear hair cells. Mutations in the myosin XVa gene are associated with nonsyndromic hearing loss. Myosin XVa contains a unique N-terminal extension followed by a motor domain, light chain-binding IQ motifs, and a tail consisting of a pair of MyTH4-FERM tandems separated by a SH3 domain, and a PDZ domain. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 80 matched cddid_all.tbl CDD cd12068 cd12068 213001 SH3_MYO15B Src Homology 3 domain of Myosin XVb. Myosin XVb, also called KIAA1783, was named based on its similarity with myosin XVa. It is a transcribed and unprocessed pseudogene whose predicted amino acid sequence contains mutated or deleted amino acid residues that are normally conserved and important for myosin function. The related myosin XVa is important for normal growth of mechanosensory stereocilia of inner ear hair cells. Myosin XVa contains a unique N-terminal extension followed by a motor domain, light chain-binding IQ motifs, and a tail consisting of a pair of MyTH4-FERM tandems separated by a SH3 domain, and a PDZ domain. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd12069 cd12069 213002 SH3_ARHGAP27 Src Homology 3 domain of Rho GTPase-activating protein 27. Rho GTPase-activating proteins (RhoGAPs or ARHGAPs) bind to Rho proteins and enhance the hydrolysis rates of bound GTP. ARHGAP27, also called CAMGAP1, shows GAP activity towards Rac1 and Cdc42. It binds the adaptor protein CIN85 and may play a role in clathrin-mediated endocytosis. It contains SH3, WW, Pleckstin homology (PH), and RhoGAP domains. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd12070 cd12070 213003 SH3_ARHGAP12 Src Homology 3 domain of Rho GTPase-activating protein 12. Rho GTPase-activating proteins (RhoGAPs or ARHGAPs) bind to Rho proteins and enhance the hydrolysis rates of bound GTP. ARHGAP12 has been shown to display GAP activity towards Rac1. It plays a role in regulating hepatocyte growth factor (HGF)-driven cell growth and invasiveness. It contains SH3, WW, Pleckstin homology (PH), and RhoGAP domains. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 60 matched cddid_all.tbl CDD cd12071 cd12071 213004 SH3_FBP17 Src Homology 3 domain of Formin Binding Protein 17. Formin Binding Protein 17 (FBP17), also called FormiN Binding Protein 1 (FNBP1), is involved in dynamin-mediated endocytosis. It is recruited to clathrin-coated pits late in the endocytosis process and may play a role in the invagination and scission steps. FBP17 binds in vivo to tankyrase, a protein involved in telomere maintenance and mitogen activated protein kinase (MAPK) signaling. It contains an N-terminal F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs) domain, a Cdc42-binding HR1 domain, and a C-terminal SH3 domain. The SH3 domain of the related protein, CIP4, associates with Gapex-5, a Rab31 GEF. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd12072 cd12072 213005 SH3_FNBP1L Src Homology 3 domain of Formin Binding Protein 1-Like. FormiN Binding Protein 1-Like (FNBP1L), also known as Toca-1 (Transducer of Cdc42-dependent actin assembly), forms a complex with neural Wiskott-Aldrich syndrome protein (N-WASP). The FNBP1L/N-WASP complex induces the formation of filopodia and endocytic vesicles. FNBP1L is required for Cdc42-induced actin assembly and is essential for autophagy of intracellular pathogens. It contains an N-terminal F-BAR domain, a central Cdc42-binding HR1 domain, and a C-terminal SH3 domain. The SH3 domain of the related protein, CIP4, associates with Gapex-5, a Rab31 GEF. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd12073 cd12073 213006 SH3_HS1 Src homology 3 domain of Hematopoietic lineage cell-specific protein 1. HS1, also called HCLS1 (hematopoietic cell-specific Lyn substrate 1), is a cortactin homolog expressed specifically in hematopoietic cells. It is an actin regulatory protein that binds the Arp2/3 complex and stabilizes branched actin filaments. It is required for cell spreading and signaling in lymphocytes. It regulates cytoskeletal remodeling that controls lymphocyte trafficking, and it also affects tissue invasion and infiltration of leukemic B cells. Like cortactin, HS1 contains an N-terminal acidic domain, several copies of a repeat domain found in cortactin and HS1, a proline-rich region, and a C-terminal SH3 domain. The N-terminal region binds the Arp2/3 complex and F-actin, while the C-terminal region acts as an adaptor or scaffold that can connect varied proteins that bind the SH3 domain within the actin network. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd12074 cd12074 213007 SH3_Tks5_1 First Src homology 3 domain of Tyrosine kinase substrate with five SH3 domains. Tks5, also called SH3 and PX domain-containing protein 2A (SH3PXD2A) or Five SH (FISH), is a scaffolding protein and Src substrate that is localized in podosomes, which are electron-dense structures found in Src-transformed fibroblasts, osteoclasts, macrophages, and some invasive cancer cells. It binds and regulates some members of the ADAMs family of transmembrane metalloproteases, which function as sheddases and mediators of cell and matrix interactions. It is required for podosome formation, degradation of the extracellular matrix, and cancer cell invasion. Tks5 contains an N-terminal Phox homology (PX) domain and five SH3 domains. This model characterizes the first SH3 domain of Tks5. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd12075 cd12075 213008 SH3_Tks4_1 First Src homology 3 domain of Tyrosine kinase substrate with four SH3 domains. Tks4, also called SH3 and PX domain-containing protein 2B (SH3PXD2B) or HOFI, is a Src substrate and scaffolding protein that plays an important role in the formation of podosomes and invadopodia, the dynamic actin-rich structures that are related to cell migration and cancer cell invasion. It is required in the formation of functional podosomes, EGF-induced membrane ruffling, and lamellipodia generation. It plays an important role in cellular attachment and cell spreading. Tks4 is essential for the localization of MT1-MMP (membrane-type 1 matrix metalloproteinase) to invadopodia. It contains an N-terminal Phox homology (PX) domain and four SH3 domains. This model characterizes the first SH3 domain of Tks4. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd12076 cd12076 213009 SH3_Tks4_2 Second Src homology 3 domain of Tyrosine kinase substrate with four SH3 domains. Tks4, also called SH3 and PX domain-containing protein 2B (SH3PXD2B) or HOFI, is a Src substrate and scaffolding protein that plays an important role in the formation of podosomes and invadopodia, the dynamic actin-rich structures that are related to cell migration and cancer cell invasion. It is required in the formation of functional podosomes, EGF-induced membrane ruffling, and lamellipodia generation. It plays an important role in cellular attachment and cell spreading. Tks4 is essential for the localization of MT1-MMP (membrane-type 1 matrix metalloproteinase) to invadopodia. It contains an N-terminal Phox homology (PX) domain and four SH3 domains. This model characterizes the second SH3 domain of Tks4. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd12077 cd12077 213010 SH3_Tks5_2 Second Src homology 3 domain of Tyrosine kinase substrate with five SH3 domains. Tks5, also called SH3 and PX domain-containing protein 2A (SH3PXD2A) or Five SH (FISH), is a scaffolding protein and Src substrate that is localized in podosomes, which are electron-dense structures found in Src-transformed fibroblasts, osteoclasts, macrophages, and some invasive cancer cells. It binds and regulates some members of the ADAMs family of transmembrane metalloproteases, which function as sheddases and mediators of cell and matrix interactions. It is required for podosome formation, degradation of the extracellular matrix, and cancer cell invasion. Tks5 contains an N-terminal Phox homology (PX) domain and five SH3 domains. This model characterizes the second SH3 domain of Tks5. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd12078 cd12078 213011 SH3_Tks4_3 Third Src homology 3 domain of Tyrosine kinase substrate with four SH3 domains. Tks4, also called SH3 and PX domain-containing protein 2B (SH3PXD2B) or HOFI, is a Src substrate and scaffolding protein that plays an important role in the formation of podosomes and invadopodia, the dynamic actin-rich structures that are related to cell migration and cancer cell invasion. It is required in the formation of functional podosomes, EGF-induced membrane ruffling, and lamellipodia generation. It plays an important role in cellular attachment and cell spreading. Tks4 is essential for the localization of MT1-MMP (membrane-type 1 matrix metalloproteinase) to invadopodia. It contains an N-terminal Phox homology (PX) domain and four SH3 domains. This model characterizes the third SH3 domain of Tks4. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 53 matched cddid_all.tbl CDD cd12079 cd12079 213012 SH3_Tks5_3 Third Src homology 3 domain of Tyrosine kinase substrate with five SH3 domains. Tks5, also called SH3 and PX domain-containing protein 2A (SH3PXD2A) or Five SH (FISH), is a scaffolding protein and Src substrate that is localized in podosomes, which are electron-dense structures found in Src-transformed fibroblasts, osteoclasts, macrophages, and some invasive cancer cells. It binds and regulates some members of the ADAMs family of transmembrane metalloproteases, which function as sheddases and mediators of cell and matrix interactions. It is required for podosome formation, degradation of the extracellular matrix, and cancer cell invasion. Tks5 contains an N-terminal Phox homology (PX) domain and five SH3 domains. This model characterizes the third SH3 domain of Tks5. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 54 matched cddid_all.tbl CDD cd12080 cd12080 213013 SH3_MPP1 Src Homology 3 domain of Membrane Protein, Palmitoylated 1 (or MAGUK p55 subfamily member 1). MPP1, also called 55 kDa erythrocyte membrane protein (p55), is a ubiquitously-expressed scaffolding protein that plays roles in regulating neutrophil polarity, cell shape, hair cell development, and neural development and patterning of the retina. It was originally identified as an erythrocyte protein that stabilizes the actin cytoskeleton to the plasma membrane by forming a complex with 4.1R protein and glycophorin C. MPP1 is one of seven vertebrate homologs of the Drosophila Stardust protein, which is required in establishing cell polarity, and it contains the three domains characteristic of MAGUK (membrane-associated guanylate kinase) proteins: PDZ, SH3, and guanylate kinase (GuK). In addition, it also contains the Hook (Protein 4.1 Binding) motif in between the SH3 and GuK domains. The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 62 matched cddid_all.tbl CDD cd12081 cd12081 213014 SH3_CASK Src Homology 3 domain of Calcium/calmodulin-dependent Serine protein Kinase. CASK is a scaffolding protein that is highly expressed in the mammalian nervous system and plays roles in synaptic protein targeting, neural development, and gene expression regulation. CASK interacts with many different binding partners including parkin, neurexin, syndecans, calcium channel proteins, caskin, among others, to perform specific functions in different subcellular locations. Disruption of the CASK gene in mice results in neonatal lethality while mutations in the human gene have been associated with X-linked mental retardation. Drosophila CASK is associated with both pre- and postsynaptic membranes and is crucial in synaptic transmission and vesicle cycling. CASK contains an N-terminal calmodulin-dependent kinase (CaMK)-like domain, two L27 domains, followed by the core of three domains characteristic of MAGUK (membrane-associated guanylate kinase) proteins: PDZ, SH3, and guanylate kinase (GuK). In addition, it also contains the Hook (Protein 4.1 Binding) motif in between the SH3 and GuK domains. The GuK domain in MAGUK proteins is enzymatically inactive; instead, the domain mediates protein-protein interactions and associates intramolecularly with the SH3 domain. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 62 matched cddid_all.tbl CDD cd12082 cd12082 240527 MATE_like Multidrug and toxic compound extrusion family and similar proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. MATE has also been identified as a large multigene family in plants, where the proteins are linked to disease resistance. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. 420 matched cddid_all.tbl CDD cd12083 cd12083 213373 DD_cGKI Dimerization/Docking domain of Cyclic GMP-dependent Protein Kinase I. Cyclic GMP-dependent Protein Kinase I (PKG1 or cGKI) is a Serine/Threonine Kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. cGKI exists as two splice variants, cGKI-alpha and cGKI-beta. They contain an N-terminal regulatory domain containing a dimerization/docking region and an autoinhibitory pseudosubstrate region, two cGMP-binding domains, and a C-terminal catalytic domain. Binding of cGMP to both binding sites releases the inhibition of the catalytic center by the pseudosubstrate region, allowing autophosphorylation and activation of the kinase. cGKI is a soluble protein expressed in all smooth muscles, platelets, cerebellum, and kidney. It is also expressed at lower concentrations in other tissues. It is involved in the regulation of smooth muscle tone, smooth cell proliferation, and platelet activation. The dimerization/docking (D/D) domain is a leucine/isoleucine zipper that mediates both homodimerization and interaction with isotype-specific G-kinase-anchoring proteins (GKAPs). The D/D domain of the two variants (alpha and beta) differ, allowing their targeting to different subcellular compartments and intracellular substrates. 48 matched cddid_all.tbl CDD cd12084 cd12084 438517 DD_RII_PKA-like dimerization/docking (D/D) domain of the type II Regulatory subunit of cAMP-dependent protein kinase and similar domains. cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence (IS), and two c-AMP binding domains. RI and RII subunits are distinguished by their IS; RII subunits contain a phosphorylation site and are both substrates and inhibitors while RI subunits are pseudo-substrates. RI subunits require ATP and Mg ions to form a stable holoenzyme while RII subunits do not. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis. 36 matched cddid_all.tbl CDD cd12085 cd12085 213374 DD_cGKI-alpha Dimerization/Docking domain of Cyclic GMP-dependent Protein Kinase I alpha. Cyclic GMP-dependent Protein Kinase I (PKG1 or cGKI) is a Serine/Threonine Kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. cGKI exists as two splice variants, cGKI-alpha and cGKI-beta. They contain an N-terminal regulatory domain containing a dimerization/docking region and an autoinhibitory pseudosubstrate region, two cGMP-binding domains, and a C-terminal catalytic domain. Binding of cGMP to both binding sites releases the inhibition of the catalytic center by the pseudosubstrate region, allowing autophosphorylation and activation of the kinase. cGKI is a soluble protein expressed in all smooth muscles, platelets, cerebellum, and kidney. It is involved in the regulation of smooth muscle tone, smooth cell proliferation, and platelet activation. The dimerization/docking (D/D) domain is a leucine/isoleucine zipper that mediates both homodimerization and interaction with isotype-specific G-kinase-anchoring proteins (GKAPs). The D/D domain of the two variants (alpha and beta) differ, allowing for their targeting to different subcellular compartments and intracellular substrates. cGKI-alpha specifically binds to myosin light chain phosphatase targeting subunit (MYPT1) and the regulator of G-protein signaling-2 (RGS-2). cGKI-alpha activates the phosphatase activity of MYPT1, resulting in vasorelaxation. It increases the activity of RGS-2 toward G proteins, with implications in the downstream signaling for vasoconstrictive agents. 48 matched cddid_all.tbl CDD cd12086 cd12086 213375 DD_cGKI-beta Dimerization/Docking domain of Cyclic GMP-dependent Protein Kinase I beta. Cyclic GMP-dependent Protein Kinase I (PKG1 or cGKI) is a Serine/Threonine Kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. cGKI exists as two splice variants, cGKI-alpha and cGKI-beta. They contain an N-terminal regulatory domain containing a dimerization/docking region and an autoinhibitory pseudosubstrate region, two cGMP-binding domains, and a C-terminal catalytic domain. Binding of cGMP to both binding sites releases the inhibition of the catalytic center by the pseudosubstrate region, allowing autophosphorylation and activation of the kinase. cGKI is a soluble protein expressed in all smooth muscles, platelets, cerebellum, and kidney. It is involved in the regulation of smooth muscle tone, smooth cell proliferation, and platelet activation. The dimerization/docking (D/D) domain is a leucine/isoleucine zipper that mediates both homodimerization and interaction with isotype-specific G-kinase-anchoring proteins (GKAPs). The D/D domain of the two variants (alpha and beta) differ, allowing for their targeting to different subcellular compartments and intracellular substrates. cGKI-beta binds specifically to inositol triphosphate receptor-associated PKG substrate (IRAG) and the transcriptional regulator TFII-I. Phosphorylation of IRAG by cGKI-beta contributes to smooth muscle relaxation while phosphorylation of TFII-I modulates its co-activator functions for serum response factor and Smad transcription factors. 52 matched cddid_all.tbl CDD cd12087 cd12087 213052 TM_EGFR-like Transmembrane domain of the Epidermal Growth Factor Receptor family of Protein Tyrosine Kinases. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. EGFR (HER, ErbB) subfamily members include EGFR (HER1, ErbB1), HER2 (ErbB2), HER3 (ErbB3), HER4 (ErbB4), and similar proteins. They are receptor PTKs (RTKs) containing an extracellular EGF-related ligand-binding region, a transmembrane (TM) helix, and a cytoplasmic region with a tyr kinase domain and a regulatory C-terminal tail. They are activated by ligand-induced dimerization, resulting in the phosphorylation of tyr residues in the C-terminal tail, which serve as binding sites for downstream signaling molecules. Collectively, they can recognize a variety of ligands including EGF, TGFalpha, and neuregulins, among others. All four subfamily members can form homo- or heterodimers. HER3 contains an impaired kinase domain and depends on its heterodimerization partner for activation. EGFR subfamily members are involved in signaling pathways leading to a broad range of cellular responses including cell proliferation, differentiation, migration, growth inhibition, and apoptosis. The TM domain not only serves as a membrane anchor, but also plays an important role in receptor dimerization and optimal activation. Mutations in the TM domain of EGFR family RTKs have been associated with increased breast cancer risk. 38 matched cddid_all.tbl CDD cd12088 cd12088 277187 helicase_insert_domain helicase_insert_domain. helicase_insert_domain; This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases, like archaeal Hef helicase, MDA5-like helicases and FancM-like helicases. The exact function of this domain is unknown, but seems to play a role in interaction with nucleotides and/or the stabilization of the nucleotide complex. 82 matched cddid_all.tbl CDD cd12089 cd12089 277188 Hef_ID insert domain of Archaeal Hef helicase/nuclease. Archaeal Hef helicase/nuclease, originally identified in the hyperthermophilic archaeon Pyrococcus furiosus, contains an N-terminal SF2 helicase domain and a C-terminal XPF/Mus81-type nuclease domain. Hef has been shown to process flap- or fork-DNA structures, and that both helicase and nuclease domain independently recognize branched DNA, with a strong preference for the forked DNA. The SF2 helicase domain is comprised of 3 structural domains, the 2 generally conserved helicase domains and a helical domain inserted between the two domains. This domain which is not present in all SF2 helicases, has been shown to play an important role in branched structure processing. 119 matched cddid_all.tbl CDD cd12090 cd12090 277189 MDA5_ID Insert domain of MDA5. MDA5 (melanoma-differentiation-associated gene 5, also known as IFIH1), as well as RIG-I (Retinoic acid Inducible Gene I, also known as DDX58) and LPG2 (also known as DHX58), contain two N-terminal CARD domains and a C-terminal SF2 helicase domain. They are cytoplasmic DEAD box RNA helicases acting as key innate immune pattern-recognition receptor (PRRs) that play an important role in host antiviral response by sensing incoming viral RNA. Their SF2 helicase domain is comprised of 3 structural domains, the 2 generally conserved helicase domains and a helical domain inserted between the two domains. The inserted domain is involved in conformational changes upon ligand binding. 120 matched cddid_all.tbl CDD cd12091 cd12091 277190 FANCM_ID Insert domain of FANCM and related proteins. FANCM and related proteins, like Mph1 and Fml1, are DNA junction-specific helicases/translocases that bind to and process perturbed replication forks and intermediates of homologous recombination. FANCM contains an N-terminal superfamily 2 helicase (SF2) domain, although FANCM, in contrast to other members of this family, does not exhibit DNA helicase activity. The SF2 helicase domain is comprised of 3 structural domains, the 2 generally conserved helicase domains and a helical domain inserted between the two domains. FANCM is a component of the Fanconi anaemia (FA) core complex. FA is a rare genetic disease in humans that is associated with progressive bone marrow failure, a variety of developmental abnormalities, and a high incidence of cancer. A key role of this complex is to monoubiquitination of FANCD2 and FANCI during S-phase and in response to DNA damage. The role of FANCM during this process seems to be the recruitment of the complex to chromatin. 116 matched cddid_all.tbl CDD cd12092 cd12092 213053 TM_ErbB4 Transmembrane domain of ErbB4, a Protein Tyrosine Kinase. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. ErbB4 (HER4) is a member of the EGFR (HER, ErbB) subfamily of proteins, which are receptor PTKs (RTKs) containing an extracellular EGF-related ligand-binding region, a transmembrane (TM) helix, and a cytoplasmic region with a tyr kinase domain and a regulatory C-terminal tail. It is activated by ligand-induced dimerization, leading to the phosphorylation of tyr residues in the C-terminal tail, which serve as binding sites for downstream signaling molecules. Ligands that bind ErbB4 fall into two groups, the neuregulins (or heregulins) and some EGFR (HER1, ErbB1) ligands including betacellulin, HBEGF, and epiregulin. All four neuregulins (NRG1-4) interact with ErbB4. Upon ligand binding, ErbB4 forms homo- or heterodimers with other ErbB proteins. The TM domain not only serves as a membrane anchor, but also plays an important role in receptor dimerization and optimal activation. Mutations in the TM domain of ErbB4 have been associated with increased breast cancer risk. ErbB4 is essential in embryonic development. It is implicated in mammary gland, cardiac, and neural development. As a postsynaptic receptor of NRG1, ErbB4 plays an important role in synaptic plasticity and maturation. The impairment of NRG1/ErbB4 signaling may contribute to schizophrenia. 44 matched cddid_all.tbl CDD cd12093 cd12093 213054 TM_ErbB1 Transmembrane domain of Epidermal Growth Factor Receptor or ErbB1, a Protein Tyrosine Kinase. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. EGFR (HER1, ErbB1) is a receptor PTK (RTK) containing an extracellular EGF-related ligand-binding region, a transmembrane (TM) helix, and a cytoplasmic region with a tyr kinase domain and a regulatory C-terminal tail. It is activated by ligand-induced dimerization, leading to the phosphorylation of tyr residues in the C-terminal tail, which serve as binding sites for downstream signaling molecules. Ligands for ErbB1 include EGF, heparin binding EGF-like growth factor (HBEGF), epiregulin, amphiregulin, TGFalpha, and betacellulin. Upon ligand binding, ErbB1 can form homo- or heterodimers with other EGFR/ErbB subfamily members. The TM domain not only serves as a membrane anchor, but also plays an important role in receptor dimerization and optimal activation. Mutations in the TM domain of ErbB1 have been associated with increased breast cancer risk. The ErbB1 signaling pathway is one of the most important pathways regulating cell proliferation, differentiation, survival, and growth. A number of monoclonal antibodies and small molecule inhibitors have been developed that target ErbB1, including the antibodies Cetuximab and Panitumumab, which are used in combination with other therapies for the treatment of colorectal cancer and non-small cell lung carcinoma (NSCLC). The small molecule inhibitors Gefitinib (Iressa) and Erlotinib (Tarceva), already used for NSCLC, are undergoing clinical trials for other types of cancer including gastrointestinal, breast, head and neck, and bladder. 44 matched cddid_all.tbl CDD cd12094 cd12094 213055 TM_ErbB2 Transmembrane domain of ErbB2, a Protein Tyrosine Kinase. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. ErbB2 (HER2, HER2/neu) is a member of the EGFR (HER, ErbB) subfamily of proteins, which are receptor PTKs (RTKs) containing an extracellular EGF-related ligand-binding region, a transmembrane (TM) helix, and a cytoplasmic region with a tyr kinase domain and a regulatory C-terminal tail. It is activated by ligand-induced dimerization, leading to the phosphorylation of tyr residues in the C-terminal tail, which serve as binding sites for downstream signaling molecules. ErbB2 does not bind to any known EGFR subfamily ligands, but contributes to the kinase activity of all possible heterodimers. It acts as the preferred partner of other ligand-bound EGFR proteins and functions as a signal amplifier, with the ErbB2-ErbB3 heterodimer being the most potent pair in mitogenic signaling. The TM domain not only serves as a membrane anchor, but also plays an important role in receptor dimerization and optimal activation. Mutations in the TM domain of ErbB2 have been associated with increased breast cancer risk. ErbB2 plays an important role in cell development, proliferation, survival and motility. Overexpression of ErbB2 results in its activation and downstream signaling, even in the absence of ligand. ErbB2 overexpression, mainly due to gene amplification, has been shown in a variety of human cancers. Its role in breast cancer is especially well-documented. ErbB2 is up-regulated in about 25% of breast tumors and is associated with increases in tumor aggressiveness, recurrence and mortality. ErbB2 is a target for monoclonal antibodies and small molecule inhibitors, which are being developed as treatments for cancer. The first humanized antibody approved for clinical use is Trastuzumab (Herceptin), which is being used in combination with other therapies to improve the survival rates of patients with HER2-overexpressing breast cancer. 44 matched cddid_all.tbl CDD cd12095 cd12095 213056 TM_ErbB3 Transmembrane domain of ErbB3, a Protein Tyrosine Kinase. ErbB3 (HER3) is a member of the EGFR (HER, ErbB) subfamily of proteins, which are receptor PTKs (RTKs) containing an extracellular EGF-related ligand-binding region, a transmembrane (TM) helix, and a cytoplasmic region with a tyr kinase domain and a regulatory C-terminal tail. ErbB receptors are activated by ligand-induced dimerization, leading to the phosphorylation of tyr residues in the C-terminal tail, which serve as binding sites for downstream signaling molecules. ErbB3 contains an impaired tyr kinase domain, which lacks crucial residues for catalytic activity against exogenous substrates but is still able to bind ATP and autophosphorylate. ErbB3 binds the neuregulin ligands, NRG1 and NRG2, and it relies on its heterodimerization partners for activity following ligand binding. The ErbB2-ErbB3 heterodimer constitutes a high affinity co-receptor capable of potent mitogenic signaling. The TM domain not only serves as a membrane anchor, but also plays an important role in receptor dimerization and optimal activation. Mutations in the TM domain of ErbB receptors have been associated with increased breast cancer risk. ErbB3 participates in a signaling pathway involved in the proliferation, survival, adhesion, and motility of tumor cells. 39 matched cddid_all.tbl CDD cd12097 cd12097 438518 DD_RI_PKA dimerization/docking (D/D) domain of the Type I Regulatory subunit of cAMP-dependent protein kinase. cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. RI subunits are pseudo-substrates as they do not contain a phosphorylation site in their inhibitory site unlike RII subunits. RIalpha function is required for normal development as its deletion is embryonically lethal. RIbeta is expressed highly in the brain and is associated with hippocampal function. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence, and two c-AMP binding domains. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis. 49 matched cddid_all.tbl CDD cd12098 cd12098 438519 DD_R_ScPKA-like dimerization/docking (D/D) domain found in Saccharomyces cerevisiae cAMP-dependent protein kinase regulatory subunit and similar domains. cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. The R subunit of fungal PKA is encoded by a single gene, which is called by various names in different organisms (for example: Yarrowia lipolytica RKA1, Saccharomyces cerevisiae Bcy1, and Schizosaccharomyces pombe Cgs1). Although most characterized PKA holoenzymes are tetramers, Y. lipolytica PKA has been reported to be a dimer of RKA1 and the catalytic subunit TPK1. RKA1 is essential and promotes hyphal growth. Cgs1 is essential for sexual differentiation of S. pombe; mutants with defective Cgs1 are partially sterile. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence, and two c-AMP binding domains. The D/D domain of metazoan R subunits dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs). The D/D domain of fungal R subunits may also serve as a dimerization domain, in the case of heterotetrameric PKAs. Fungal PKA plays a major role in controlling cell growth and metabolism in response to nutrients and stress conditions. 45 matched cddid_all.tbl CDD cd12099 cd12099 438520 DD_RII_PKA dimerization/docking (D/D) domain of the Type II Regulatory subunit of cAMP-dependent protein kinase. cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. RII subunits contain a phosphorylation site in their inhibitory site and are both substrates and inhibitors. RIIalpha plays a role in the association and dissociation of PKA with the centrosome during interphase and mitosis, respectively. RIIbeta plays an important role in adipocytes and neuronal tissues. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence, and two c-AMP binding domains. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis. 37 matched cddid_all.tbl CDD cd12100 cd12100 438521 DD_CABYR_SP17 dimerization/docking (D/D) domain of the sperm fibrous sheath proteins, Calcium-Binding tYrosine-phosphorylation Regulated protein and Sperm Protein 17. CABYR and SP17 are naturally located in the human sperm fibrous sheath (FS). CABYR was originally isolated from spermatoza and was thought to be testis-specific, but has recently been observed in lung and brain tumors. It is a polymorphic calcium binding protein that is phosphorylated during capacitation. SP17 plays an important role in the interaction of sperm with the zona pellucida during fertilization. It also promotes cell-cell adhesion. SP17 is found in various human tumors of unrelated histological origin including metastatic squamous cell carcinoma, multiple myeloma, ovarian cancer, and primary nervous system tumors, among others. Both CABYR and SP17 contain an N-terminal dimerization/docking (D/D) domain with similarity to the D/D domain of the R subunit of cAMP-dependent protein kinase (PKA). The D/D domain of the R subunit dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. The D/D domain of CABYR and SP17 have been shown to bind to AKAP3, a protein that is also associated to the FS of mammalian spermatozoa. 42 matched cddid_all.tbl CDD cd12101 cd12101 438522 DD_RIalpha_PKA dimerization/docking (D/D) domain of the Type I alpha Regulatory subunit of cAMP-dependent protein kinase. cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. RI subunits are pseudo-substrates as they do not contain a phosphorylation site in their inhibitory site unlike RII subunits. RIalpha is the key regulatory subunit responsible for maintaining cAMP control of the catalytic subunit. RIalpha function is required for normal development as its deletion is embryonically lethal due to failed cardiac morphogenesis. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence, and two c-AMP binding domains. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis. 50 matched cddid_all.tbl CDD cd12102 cd12102 438523 DD_RIbeta_PKA dimerization/docking (D/D) domain of the Type I beta Regulatory subunit of cAMP-dependent protein kinase. cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. RI subunits are pseudo-substrates as they do not contain a phosphorylation site in their inhibitory site unlike RII subunits. RIbeta is expressed highly in the brain and is associated with hippocampal function. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence, and two c-AMP binding domains. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis. 54 matched cddid_all.tbl CDD cd12103 cd12103 438524 DD_RIIalpha_PKA dimerization/docking (D/D) domain of the Type II alpha Regulatory subunit of cAMP-dependent protein kinase. cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. RII subunits contain a phosphorylation site in their inhibitory site and are both substrates and inhibitors. RIIalpha plays a role in the association and dissociation of PKA with the centrosome during interphase and mitosis, respectively. It is also involved in endosome-to-Golgi and Golgi-to-ER transport. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence, and two c-AMP binding domains. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis. 41 matched cddid_all.tbl CDD cd12104 cd12104 438525 DD_RIIbeta_PKA dimerization/docking (D/D) domain of the Type II beta Regulatory subunit of cAMP-dependent protein kinase. cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. RII subunits contain a phosphorylation site in their inhibitory site and are both substrates and inhibitors. RIIbeta plays an important role in adipocytes and neuronal tissues. Mice deficient with RIIbeta have small fat cells, and are resistant to obesity, diet-induced diabetes, and alcohol-induced motor defects. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence, and two c-AMP binding domains. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis. 43 matched cddid_all.tbl CDD cd12105 cd12105 213031 HmuY Bacterial proteins similar to Porphyromonas gingivalis HmuY. HmuY is a hemophore that scavenges heme from infected hosts and delivers it to the outer membrane receptor HmuR. Related but uncharacterized proteins do not appear to share the specific heme-binding site. 121 matched cddid_all.tbl CDD cd12106 cd12106 213061 PARMER_03128_N N-terminal domain of PARMER_03128. PARMER_03128 is an uncharacterized protein from Parabacteroides merdae. This model characterizes its N-terminal domain plus that of related proteins from Bacteroidetes. Structurally, they resemble domains found in streptococcal surface proteins such as SpaP. 137 matched cddid_all.tbl CDD cd12107 cd12107 213982 Hemerythrin "Hemerythrin. Hemerythrin (Hr) is a non-heme diiron oxygen transport protein found in four marine invertebrate phyla including priapulida, brachiopoda, sipunculida, and annelida, as well as in protozoa. Myohemerythrin (Mhr), a hemerythrin homolog, is found in the muscle tissue of sipunculids as well as in polycheate and oligocheate annelids. In addition to oxygen transport, Mhr proteins are involved in cadmium fixation and host anti-bacterial defense. Hr and Mhr proteins have the same ""four alpha helix bundle"" motif and active site structure. Hr forms oligomers, the octameric form being most prevalent, while Mhr is monomeric." 113 matched cddid_all.tbl CDD cd12108 cd12108 213983 Hr-like Hemerythrin-like domain. Hemerythrin (Hr) like domains have the same four alpha helix bundle and a similar, but slightly different active site structure than hemerythrin. They are non-heme diiron binding proteins mainly found in bacteria and eukaryotes. Like Hr, they may be involved in oxygen transport or like human FBXL5 (F-box and leucine-rich repeat protein 5), a member of this group, play a role in cellular iron homeostasis. 130 matched cddid_all.tbl CDD cd12109 cd12109 213984 Hr_FBXL5 Hemerythrin-like domain of FBXL5-like proteins. Human FBXL5 (F-box and leucine-rich repeat protein 5) protein plays a role in cellular iron homeostasis. It is part of an E3 ubiquitin ligase complex that targets the iron regulatory protein IRP2 for proteasomal degradation. The FBXL5's stability is regulated by iron concentration, with its iron- and oxygen-binding hemerythrin domain acting as a ligand-dependent regulatory switch. 158 matched cddid_all.tbl CDD cd12110 cd12110 213994 PHP_HisPPase_Hisj_like Polymerase and Histidinol Phosphatase domain of Histidinol phosphate phosphatase of Hisj like. Bacillus subtilis YtvP HisJ has strong histidinol phosphate phosphatase (HisPPase) activity. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to produce histidinol. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. The PHP domain of HisPPase is structurally homologous to other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. 244 matched cddid_all.tbl CDD cd12111 cd12111 213995 PHP_HisPPase_Thermotoga_like Polymerase and Histidinol Phosphatase domain of Thermotoga like. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. Thermotoga PHP is an uncharacterized protein. HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to give histidinol. The HisPPase can be classified into two types: the bifunctional HisPPase found in proteobacteria that belongs to the DDDD superfamily and the monofunctional Bacillus subtilis type that is a member of the PHP family. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. The PHP domain of HisPPase is structurally homologous to other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. 226 matched cddid_all.tbl CDD cd12112 cd12112 213996 PHP_HisPPase_Chlorobi_like Polymerase and Histidinol Phosphatase domain of Chlorobi like. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. Chlorobi PHP is uncharacterized protein. HisPPase catalyzes the eighth step of histidine biosynthesis, in which L-histidinol phosphate undergoes dephosphorylation to produce histidinol. The HisPPase can be classified into two types: the bifunctional Hisppase found in proteobacteria that belongs to the DDDD superfamily and the monofunctional Bacillus subtilis type that is a member of the PHP family. The PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination. The PHP domain of HisPPase is structurally homologous to other members of the PHP family that have a distorted (beta/alpha)7 barrel fold with a trinuclear metal site on the C-terminal side of the barrel. 235 matched cddid_all.tbl CDD cd12113 cd12113 213997 PHP_PolIIIA_DnaE3 Polymerase and Histidinol Phosphatase domain of alpha-subunit of bacterial polymerase III DnaE3. PolIIIAs that contain an N-terminal PHP domain have been classified into four basic groups based on genome composition, phylogenetic, and domain structural analysis: polC, dnaE1, dnaE2, and dnaE3. The PHP (also called histidinol phosphatase-2/HIS2) domain is associated with several types of DNA polymerases, such as PolIIIA and family X DNA polymerases, stand alone histidinol phosphate phosphatases (HisPPases), and a number of uncharacterized protein families. DNA polymerase III holoenzyme is one of the five eubacterial DNA polymerases that is responsible for the replication of the DNA duplex. The alpha subunit of DNA polymerase III core enzyme catalyzes the reaction for polymerizing both DNA strands. The PolIIIA PHP domain has four conserved sequence motifs and contains an invariant histidine that is involved in metal ion coordination, and like other PHP structures, the PolIIIA PHP exhibits a distorted (beta/alpha) 7 barrel and coordinates up to 3 metals. Initially, it was proposed that PHP region might be involved in pyrophosphate hydrolysis, but such an activity has not been found. It has been shown that the PHP of PolIIIA has a trinuclear metal complex and is capable of proofreading activity. Bacterial genome replication and DNA repair mechanisms is related to the GC content of its genomes. There is a correlation between GC content variations and the dimeric combinations of PolIIIA subunits. Eubacteria can be grouped into different GC variable groups: the full-spectrum or dnaE1 group, the high-GC or dnaE2-dnaE1 group, and the low GC or polC-dnaE3 group. 283 matched cddid_all.tbl CDD cd12114 cd12114 341279 A_NRPS_TlmIV_like The adenylation domain of nonribosomal peptide synthetases (NRPS), including Streptoalloteichus tallysomycin biosynthesis genes. The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. This family includes the TLM biosynthetic gene cluster from Streptoalloteichus that consists of nine NRPS genes; the N-terminal module of TlmVI (NRPS-5) and the starter module of BlmVI (NRPS-5) are comprised of the acyl CoA ligase (AL) and acyl carrier protein (ACP)-like domains, which are thought to be involved in the biosynthesis of the beta-aminoalaninamide moiety. 477 matched cddid_all.tbl CDD cd12115 cd12115 341280 A_NRPS_Sfm_like The adenylation domain of nonribosomal peptide synthetases (NRPS), including Saframycin A gene cluster from Streptomyces lavendulae. The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. This family includes the saframycin A gene cluster from Streptomyces lavendulae which implicates the NRPS system for assembling the unusual tetrapeptidyl skeleton in an iterative manner. It also includes saframycin Mx1 produced by Myxococcus xanthus NRPS. 447 matched cddid_all.tbl CDD cd12116 cd12116 341281 A_NRPS_Ta1_like The adenylation domain of nonribosomal peptide synthetases (NRPS), including salinosporamide A polyketide synthase. The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. This family includes the myxovirescin (TA) antibiotic biosynthetic gene in Myxococcus xanthus; TA production plays a role in predation. It also includes the salinosporamide A polyketide synthase which is involved in the biosynthesis of salinosporamide A, a marine microbial metabolite whose chlorine atom is crucial for potent proteasome inhibition and anticancer activity. 470 matched cddid_all.tbl CDD cd12117 cd12117 341282 A_NRPS_Srf_like The adenylation domain of nonribosomal peptide synthetases (NRPS), including Bacillus subtilis termination module Surfactin (SrfA-C). The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and, in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. This family includes the adenylation domain of the Bacillus subtilis termination module (Surfactin domain, SrfA-C) which recognizes a specific amino acid building block, which is then activated and transferred to the terminal thiol of the 4'-phosphopantetheine (Ppan) arm of the downstream peptidyl carrier protein (PCP) domain. 483 matched cddid_all.tbl CDD cd12118 cd12118 341283 ttLC_FACS_AEE21_like Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles and Arabidopsis. This family includes fatty acyl-CoA synthetases that can activate medium to long-chain fatty acids. These enzymes catalyze the ATP-dependent acylation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. Fatty acyl-CoA synthetases are responsible for fatty acid degradation as well as physiological regulation of cellular functions via the production of fatty acyl-CoA esters. The fatty acyl-CoA synthetase from Thermus thermophiles in this family has been shown to catalyze the long-chain fatty acid, myristoyl acid. Also included in this family are acyl activating enzymes from Arabidopsis, which contains a large number of proteins from this family with up to 63 different genes, many of which are uncharacterized. 486 matched cddid_all.tbl CDD cd12119 cd12119 341284 ttLC_FACS_AlkK_like Fatty acyl-CoA synthetases similar to LC-FACS from Thermus thermophiles. This family includes fatty acyl-CoA synthetases that can activate medium-chain to long-chain fatty acids. They catalyze the ATP-dependent acylation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. The fatty acyl-CoA synthetases are responsible for fatty acid degradation as well as physiological regulation of cellular functions via the production of fatty acyl-CoA esters. The fatty acyl-CoA synthetase from Thermus thermophiles in this family catalyzes the long-chain fatty acid, myristoyl acid, while another member in this family, the AlkK protein identified from Pseudomonas oleovorans, targets medium chain fatty acids. This family also includes uncharacterized FACS proteins. 518 matched cddid_all.tbl CDD cd12120 cd12120 213376 AMPKA_C_like C-terminal regulatory domain of 5'-AMP-activated protein kinase (AMPK) alpha subunit and similar domains. This family is composed of AMPKs, microtubule-associated protein/microtubule affinity regulating kinases (MARKs), yeast Kcc4p-like proteins, plant calcineurin B-Like (CBL)-interacting protein kinases (CIPKs), and similar proteins. They are serine/threonine protein kinases (STKs) that catalyze the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. AMPKs act as sensors for the energy status of the cell and are activated by cellular stresses that lead to ATP depletion such as hypoxia, heat shock, and glucose deprivation, among others. MARKs phosphorylate the tau protein and related microtubule-associated proteins (MAPs) on tubulin binding sites to induce detachment from microtubules, and are involved in the regulation of cell shape and polarity, cell cycle control, transport, and the cytoskeleton. Kcc4p and related proteins are septin-associated proteins that are involved in septin organization and in the yeast morphogenesis checkpoint coordinating the cell cycle with bud formation. CIPKs interact with the calcineurin B-like (CBL) calcium sensors to form a signaling network that decode specific calcium signals triggered by a variety of environmental stimuli including salinity, drought, cold, light, and mechanical perturbation, among others. All members of this family contain an N-terminal catalytic kinase domain and a C-terminal regulatory domain which is also called kinase associated domain 1 (KA1) in some cases. The C-terminal regulatory domain serves as a protein interaction domain in AMPKs and CIPKs. In MARKs and Kcc4p-like proteins, this domain binds phospholipids and may be involved in membrane localization. 95 matched cddid_all.tbl CDD cd12121 cd12121 213377 MARK_C_like C-terminal kinase associated domain 1 (KA1), a phospholipid binding domain, of microtubule affinity-regulating kinases, and similar domains. Microtubule-associated protein/microtubule affinity regulating kinases (MARKs), also called partition-defective (Par-1) kinases, are serine/threonine protein kinases (STKs) that catalyze the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. They phosphorylate the tau protein and related microtubule-associated proteins (MAPs) on tubulin binding sites to induce detachment from microtubules, and are involved in the regulation of cell shape and polarity, cell cycle control, transport, and the cytoskeleton. Mammals contain four proteins, MARK1-4, encoded by distinct genes belonging to this subfamily, with additional isoforms arising from alternative splicing. In yeast, MARK/Par-1 homologs are called Kin1/2 kinases. Kin1 is a membrane-associated kinase that is involved in regulating cytokinesis and the cell surface. MARKs contain an N-terminal catalytic kinase domain, a ubiquitin-associated domain (UBA), and a C-terminal kinase associated domain (KA1). The KA1 domain binds anionic phospholipids and may be involved in membrane localization as well as in auto-inhibition of the kinase domain. 96 matched cddid_all.tbl CDD cd12122 cd12122 213378 AMPKA_C C-terminal regulatory domain of 5'-AMP-activated protein kinase (AMPK) alpha catalytic subunit. AMPK, a serine/threonine protein kinase (STK), catalyzes the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. It acts as a sensor for the energy status of the cell and is activated by cellular stresses that lead to ATP depletion such as hypoxia, heat shock, and glucose deprivation, among others. AMPK is a heterotrimer of three subunits: alpha, beta, and gamma. Co-expression of the three subunits is required for kinase activity; in the absence of one, the other two subunits get degraded. The AMPK alpha subunit is the catalytic subunit and it contains an N-terminal kinase domain and a C-terminal regulatory domain (RD). Vertebrates contain two isoforms of the alpha subunit, alpha1 and alpha2, which are encoded by different genes, PRKAA1 and PRKAA2, respectively. The C-terminal RD of the AMPK alpha subunit is involved in AMPK heterotrimer formation. It mainly interacts with the C-terminal region of the beta subunit to form a tight alpha-beta complex that is associated with the gamma subunit. The AMPK alpha subunit RD also contains an auto-inhibitory region that interacts with the kinase domain; this inhibition is negated by the interaction with the AMPK gamma subunit. AMPK is conserved throughout evolution; the AMPK alpha subunit homologs in yeast and plants are called Snf1 and SnRK1 (Snf1 related kinase), respectively. 132 matched cddid_all.tbl CDD cd12124 cd12124 381264 Pgbs Protoglobins (Pgbs). Pgbs are single-domain globins of yet unknown biological function. Included in this subfamily are Pgbs from the strictly anaerobic methanogen Methanosarcina acetivorans (MaPgb) and from the obligate aerobic hyperthermophile Aeropyrum pernix (ApPgb). MaPgb is a dimeric globin which in addition to the 3-on-3 helical sandwich contains an N-terminal extension. This extension, along with other Pgb-specific loops buries the heme within the protein; two orthogonal apolar tunnels grant access of small ligand molecules to the heme. Like other globins, MaPgb can bind O2, CO and NO reversibly in vitro, however it has as unusually low O2 dissociation rate, along with a large structural distortion of the heme moiety. CO binding to and dissociation from the heme occurs through biphasic kinetics. ApPgb also contains heme, and can bind O2, CO and NO. This subfamily belongs to a family which includes the globin-coupled-sensors (GCSs) and single-domain sensor globins. It has been demonstrated that Pgbs and other single-domain globins can function as sensors, when coupled to an appropriate regulator domain. 185 matched cddid_all.tbl CDD cd12125 cd12125 381265 APC_alpha Allophycocyanin alpha subunit of the phycobilisome core. Phycobilisomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker polypeptides. PBPs have different numbers of chromophores, and the basic monomer component (alpha/beta heterodimers) can further oligomerize to ring-shaped trimers (heterohexamers) and hexamers (heterododecamers). Stacked PBP hexamers form both the core and the rods of the PBS; the core is mainly made up by allophycocyanin (APC) while the rods can be composed of the PBPs phycoerythrin (PE), phycocyanin (PC) and phycoerythrocyanin (PEC). 159 matched cddid_all.tbl CDD cd12126 cd12126 271281 APC_beta Allophycocyanin beta subunit of the phycobilisome core. Phycobilisomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker polypeptides. PBPs have different numbers of chromophores, and the basic monomer component (alpha/beta heterodimers) can further oligomerize to ring-shaped trimers (heterohexamers) and hexamers (heterododecamers). Stacked PBP hexamers form both the core and the rods of the PBS; the core is mainly made up by allophycocyanin (APC) while the rods can be composed of the PBPs phycoerythrin (PE), phycocyanin (PC) and phycoerythrocyanin (PEC). 163 matched cddid_all.tbl CDD cd12127 cd12127 381266 PE-PC-PEC_beta Beta subunits of phycocyanin, phycoerythrin and phycoerythrocyanin; phycobilisome rod components. phycobilisomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker polypeptides. PBPs have different numbers of chromophores, and the basic monomer component (alpha/beta heterodimers) can further oligomerize to ring-shaped trimers (heterohexamers) and hexamers (heterododecamers). Stacked PBP hexamers form both the core and the rods of the PBS; the core is mainly made up by allophycocyanin (APC) while the rods can be composed of the PBPs phycoerythrin (PE), phycocyanin (PC) and phycoerythrocyanin (PEC). This family also includes the beta subunits of Cryptophyte phycobiliproteins which represent another type of biliprotein antenna with different structure and organization. The beta subunits of cryptophyte PBPs share a high degree of sequence identity with both the alpha and beta subunits of the cyanobacterial and red algal PBPs, however the alpha cryptophyte subunits are shorter, and unrelated. There is only one type of PBP present in a single species, either phycocyanin or phycoerythrin, but not allophycocyanin. Structurally, phycoerythrin in cryptophytes is an alpha1alpha2betabeta dimer and not a trimer as in the PBS. 174 matched cddid_all.tbl CDD cd12128 cd12128 381267 PBP_PBS-LCM Phycobiliprotein-like domain of the phycobilisome core-membrane linker polypeptide. phycobilisomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae, they consist of a central core and radiating rods and function to harvest and channel light energy toward the photosynthetic reaction centers (RCs) within the membrane. They are comprised of phycobiliproteins or chromophorylated proteins (PBPs) maintained together by linker polypeptides. LCM is a chromophore-bearing PBS linker protein; it facilitates PBS assembly and functionally connects the PBS to the chlorophyll-containing core-complexes in the photosynthetic membrane. In addition to being a linker polypeptide that stabilizes the PBS architecture, the LCM also serves as a terminal energy acceptor. The single phycocyanobilin (PCB) chromophore of LCM are one of two terminal energy transmitters that transfer excitations from the hundreds of chromophores of the PBS to the RCs within the membrane. 172 matched cddid_all.tbl CDD cd12129 cd12129 271284 PE-PC-PEC_alpha Alpha subunits of phycoerythrin, phycocyanin and phycoerythrocyanin; phycobilisome rod components. phycobilisomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker polypeptides. PBPs have different numbers of chromophores, and the basic monomer component (alpha/beta heterodimers) can further oligomerize to ring-shaped trimers (heterohexamers) and hexamers (heterododecamers). Stacked PBP hexamers form both the core and the rods of the PBS; the core is mainly made up by allophycocyanin (APC) while the rods can be composed of the PBPs phycoerythrin (PE), phycocyanin (PC) and phycoerythrocyanin (PEC). 161 matched cddid_all.tbl CDD cd12130 cd12130 381268 Apl Allophycocyanin-like globins. phycobilisomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker polypeptides. PBPs have different numbers of chromophores, and the basic monomer component (alpha/beta heterodimers) can further oligomerize to ring-shaped trimers (heterohexamers) and hexamers (heterododecamers). Stacked PBP hexamers form both the core and the rods of the PBS; the core is mainly made up by allophycocyanin (APC) while the rods can be composed of the PBPs phycoerythrin (PE), phycocyanin (PC) and phycoerythrocyanin (PEC). This subfamily contains allophycocyanin-like proteins (Apls), which have conserved the residues critical for chromophore interactions, but may not maintain the proper alpha-beta subunit interactions and tertiary structure of phycobiliproteins. Indeed AplA isolated from Fremyella diplosiphon was not detected in phycobilisomes. As the genes encoding Apls cluster with light-responsive regulatory components, Apls may have photoresponsive regulatory role(s). 154 matched cddid_all.tbl CDD cd12131 cd12131 381269 HGbI-like Hell's gate globin I (HGbI) from Methylacidophilum infernorum and related proteins. HGbI is a single-domain heme-containing protein isolated from Methylacidiphilum infernorum, an aerobic acidophilic and thermophilic methanotroph. M. infernorum grows optimally at pH 2.0 and 60C and its home is New Zealand's Hell's Gate geothermal park. The physiological role of HGbI has yet to be determined. It has an extremely strong resistance to auto-oxidation, and has fast oxygen-binding/slow release characteristics. Its CO on-rate is comparable to the O2 on-rate, and it is able to bind acetate with high affinity in the ferric state. The coordination of the heme iron changes in the ferrous form from pentacoordinate at low pH to predominantly hexacoordinate at high pH; in the ferric form, it is predominantly hexacoordinate at all pH. 128 matched cddid_all.tbl CDD cd12137 cd12137 271287 GbX Globin_X (GbX). Zebrafish globin X (GbX) is expressed at low levels in neurons of the central nervous system, and appears to be associated with the sensory system. GbX is likely to be attached to the cell membrane via S-palmitoylation and N-myristoylation. It's unlikely to have a true respiratory function as it is membrane-associated. It has been suggested that it may protect the lipids in the cell membrane from oxidation or act as a redox-sensing or signaling protein. Zebrafish GbX is hexacoordinate, and displays cooperative O2 binding. 145 matched cddid_all.tbl CDD cd12139 cd12139 213015 SH3_Bin1 Src Homology 3 domain of Bridging integrator 1 (Bin1), also called Amphiphysin-2. Bin1 isoforms are localized in many different tissues and may function in intracellular vesicle trafficking. It plays a role in the organization and maintenance of the T-tubule network in skeletal muscle. Mutations in Bin1 are associated with autosomal recessive centronuclear myopathy. Bin1 contains an N-terminal BAR domain with an additional N-terminal amphipathic helix (an N-BAR) and a C-terminal SH3 domain. The SH3 domain of Bin1 forms transient complexes with actin, myosin filaments, and CDK5, to facilitate sarcomere organization and myofiber maturation. It also binds dynamin and prevents its self-assembly. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 72 matched cddid_all.tbl CDD cd12140 cd12140 213016 SH3_Amphiphysin_I Src Homology 3 domain of Amphiphysin I. Amphiphysins function primarily in endocytosis and other membrane remodeling events. They exist in several isoforms and mammals possess two amphiphysin proteins from distinct genes. Amphiphysin I proteins, enriched in the brain and nervous system, contain domains that bind clathrin, Adaptor Protein complex 2 (AP2), dynamin, and synaptojanin. They function in synaptic vesicle endocytosis. Human autoantibodies to amphiphysin I hinder GABAergic signaling and contribute to the pathogenesis of paraneoplastic stiff-person syndrome. Amphiphysins contain an N-terminal BAR domain with an additional N-terminal amphipathic helix (an N-BAR), a variable central domain, and a C-terminal SH3 domain. The SH3 domain of amphiphysins bind proline-rich motifs present in binding partners such as dynamin, synaptojanin, and nsP3. It also belongs to a subset of SH3 domains that bind ubiquitin in a site that overlaps with the peptide binding site. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 72 matched cddid_all.tbl CDD cd12141 cd12141 213017 SH3_DNMBP_C2 Second C-terminal Src homology 3 domain of Dynamin Binding Protein, also called Tuba, and similar domains. DNMBP or Tuba is a cdc42-specific guanine nucleotide exchange factor (GEF) that contains four N-terminal SH3 domains, a central RhoGEF [or Dbl homology (DH)] domain followed by a Bin/Amphiphysin/Rvs (BAR) domain, and two C-terminal SH3 domains. It provides a functional link between dynamin, Rho GTPase signaling, and actin dynamics. It plays an important role in regulating cell junction configuration. The C-terminal SH3 domains of DNMBP bind to N-WASP and Ena/VASP proteins, which are key regulatory proteins of the actin cytoskeleton. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd12142 cd12142 213018 SH3_D21-like Src Homology 3 domain of SH3 domain-containing protein 21 (SH3D21) and similar proteins. N-terminal SH3 domain of the uncharacterized protein SH3 domain-containing protein 21, and similar uncharacterized domains, it belongs to the CD2AP-like_3 subfamily of proteins. The CD2AP-like_3 subfamily is composed of the third SH3 domain (SH3C) of CD2AP, CIN85 (Cbl-interacting protein of 85 kDa), and similar domains. CD2AP and CIN85 are adaptor proteins that bind to protein partners and assemble complexes that have been implicated in T cell activation, kidney function, and apoptosis of neuronal cells. They also associate with endocytic proteins, actin cytoskeleton components, and other adaptor proteins involved in receptor tyrosine kinase (RTK) signaling. CD2AP and the main isoform of CIN85 contain three SH3 domains, a proline-rich region, and a C-terminal coiled-coil domain. All of these domains enable CD2AP and CIN85 to bind various protein partners and assemble complexes that have been implicated in many different functions. SH3C of both proteins have been shown to bind to ubiquitin. SH3 domains are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. They play versatile and diverse roles in the cell including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies. 55 matched cddid_all.tbl CDD cd12143 cd12143 213019 SH3_ARHGAP9 Src Homology 3 domain of Rho GTPase-activating protein 9 and similar proteins. Rho GTPase-activating proteins (RhoGAPs or ARHGAPs) bind to Rho proteins and enhance the hydrolysis rates of bound GTP. ARHGAP9 functions as a GAP for Rac and Cdc42, but not for RhoA. It negatively regulates cell migration and adhesion. It also acts as a docking protein for the MAP kinases Erk2 and p38alpha, and may facilitate cross-talk between the Rho GTPase and MAPK pathways to control actin remodeling. It contains SH3, WW, Pleckstin homology (PH), and RhoGAP domains. SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies. 57 matched cddid_all.tbl CDD cd12144 cd12144 213387 SDH_N_domain Saccharopine dehydrogenase N-terminal domain. SDH N-terminal domain is named due to its appearance at the N-terminal of SDH in eukaryotes, but can be found C-terminal of the SDH-like domain in other enzymes, such as the bifunctional lysine ketoglutarate reductase/saccharopine dehydrogenase enzyme. SDH catalyzes the final step in the reversible NAD-dependent oxidative deamination of saccharopine to alpha-ketoglutarate and lysine, in the alpha-aminoadipate pathway of L-lysine biosynthesis. SHD is structurally related to formate dehydrogenase and similar enzymes, having a 2-domain structure in which a Rossmann-fold NAD(P)-binding domain is inserted within the linear sequence of a catalytic domain of a related structure. 114 matched cddid_all.tbl CDD cd12145 cd12145 213388 Rev1_C C-terminal domain of the Y-family polymerase Rev1. Rev1 is a eukaryotic translesion synthesis (TLS) polymerase; TLS is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. The C-terminal domain modeled here is essential for TLS and has been shown to mediate interactions with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7), as well as with the RIRs (Rev1-interacting regions) of polymerases kappa, iota, and eta. Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment. 94 matched cddid_all.tbl CDD cd12146 cd12146 213389 STING_C C-terminal domain of STING. STING (stimulator of interferon genes, also known as MITA, ERIS, MPYS and TMEM173) is a master regulator that mediates cytokine production in response to microbial invasion by directly sensing bacterial secondary messengers such as the cyclic dinucleotide bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) and leading to the activation of IFN regulatory factor 3 (IRF3) through TANK-binding kinase 1 (TBK1) stimulation. STING is also a signaling adaptor in the IFN response to cytosolic DNA. This detection of foreign materials is the first step to a successful immune responses. STING is localized in the ER and comprised of an predicted N-terminal transmembrane region and a C-terminal c-di-GMP binding domain. 181 matched cddid_all.tbl CDD cd12147 cd12147 213390 Cep3_C C-terminal domain of the Cep3, a subunit of the yeast centromere-binding factor 3. Cep3, together with Skp1, Ctf13, and Ndc10, forms the yeast centromere-binding factor 3 (CBF3) which initiates kinetochore assembly by binding to the CDEIII locus of centromeric DNA. Cep3 is comprised of two domains, the N-terminal DNA-binding module, a Zn2Cys6-cluster, C-terminal domain, which dimerizes and is believed to be involved in the recruitment of the Skp1-Ctf1 heterodimer. 552 matched cddid_all.tbl CDD cd12148 cd12148 213391 fungal_TF_MHR fungal transcription factor regulatory middle homology region. This domain is present in the large family of fungal zinc cluster transcription factors that contain an N-terminal GAL4-like C6 zinc binuclear cluster DNA-binding domain. Examples of members of this large fungal group are the following Saccharomyces cerevisiae transcription factors, GAL4, STB5, DAL81, CAT8, RDR1, HAL9, PUT3, PPR1, ASG1, RSF2, PIP2, as well as the C-terminal domain of the Cep3, a subunit of the yeast centromere-binding factor 3. It has been suggested that this region plays a regulatory role. 410 matched cddid_all.tbl CDD cd12149 cd12149 213392 Flavi_E_C Immunoglobulin-like domain III (C-terminal domain) of Flavivirus envelope glycoprotein E. The C-terminal domain (domain III) of Flavivirus glycoprotein E appears to be involved in low-affinity interactions with negatively charged glycoaminoglycans on the host cell surface. Domain III may also play a role in interactions with alpha-v-beta-3 integrins in West Nile virus, Japanese encephalitis virus, and Dengue virus. The interface between domain I and domain III appears to be destabilized by the low-pH environment of the endosome, and domain III may play a vital role in the conformational changes of envelope glycoprotein E that follow the clathrin-mediated endocytosis of viral particles and are a prerequisite to membrane fusion. 91 matched cddid_all.tbl CDD cd12150 cd12150 213393 talin-RS rod-segment of the talin C-terminal domain. The talin rod-segment characterize by this model interacts with its N-terminal FERM domain to mask its integrin-binding site and interferes with interactions between the FERM domain and the cellular membrane. Talin is a large and ubiquitous cytoskeletal protein concentrated at focal adhesion sites. It is involved in linking integrins to the actin cytoskeleton. 172 matched cddid_all.tbl CDD cd12151 cd12151 213394 F1-ATPase_gamma mitochondrial ATP synthase gamma subunit. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain of F-ATPases is composed of alpha, beta, gamma, delta, and epsilon (not present in bacteria) subunits with a stoichiometry of 3:3:1:1:1. Alpha and beta subunit form the globular catalytic moiety, a hexameric ring of alternating subunits. Gamma, delta and epsilon subunits form a stalk, connecting F1 to F0, the integral membrane proton translocating domain. 282 matched cddid_all.tbl CDD cd12152 cd12152 213395 F1-ATPase_delta mitochondrial ATP synthase delta subunit. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinisic membrane domain, F1, is composed of alpha, beta, gamma, delta, and epsilon subunits with a stoichiometry of 3:3:1:1:1. Alpha and beta subunit form the globular catalytic moiety, a hexameric ring of alternating subunits. Gamma, delta and epsilon subunits form a stalk, connecting F1 to F0, the integral membrane proton translocating domain. In bacteria, which is lacking a eukaryotic epsilon subunit homolog, this subunit is called the epsilon subunit. 123 matched cddid_all.tbl CDD cd12153 cd12153 213396 F1-ATPase_epsilon eukaryotic mitochondrial ATP synthase epsilon subunit. The F-ATPase is found in bacterial plasma membranes, mitochondrial inner membranes, and in chloroplast thylakoid membranes. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinsic membrane domain, F1, is composed of alpha, beta, gamma, delta, and epsilon subunits (only found in eukaryotes, lacking in bacteria) with a stoichiometry of 3:3:1:1:1. Alpha and beta subunit form the globular catalytic moiety, a hexameric ring of alternating subunits. Gamma, delta and epsilon subunits form a stalk, connecting F1 to F0, the integral membrane proton translocating domain.The epsilon subunit is thought to be involved in the regulation of ATP synthase, since a null mutation increased oligomycin sensitivity and decreased inhibition by inhibitor protein IF1. 45 matched cddid_all.tbl CDD cd12154 cd12154 240631 FDH_GDH_like Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases. The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases. 310 matched cddid_all.tbl CDD cd12155 cd12155 240632 PGDH_1 Phosphoglycerate Dehydrogenase, 2-hydroxyacid dehydrogenase family. Phosphoglycerate Dehydrogenase (PGDH) catalyzes the NAD-dependent conversion of 3-phosphoglycerate into 3-phosphohydroxypyruvate, which is the first step in serine biosynthesis. Over-expression of PGDH has been implicated as supporting proliferation of certain breast cancers, while PGDH deficiency is linked to defects in mammalian central nervous system development. PGDH is a member of the 2-hydroxyacid dehydrogenase family, enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine Hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann-fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 314 matched cddid_all.tbl CDD cd12156 cd12156 240633 HPPR Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase. Hydroxy(phenyl)pyruvate reductase (HPPR) catalyzes the NADP-dependent reduction of hydroxyphenylpyruvates, hydroxypyruvate, or pyruvate to its respective lactate. HPPR acts as a dimer and is related to D-isomer-specific 2-hydroxyacid dehydrogenases, a superfamily that includes groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine Hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 301 matched cddid_all.tbl CDD cd12157 cd12157 240634 PTDH Thermostable Phosphite Dehydrogenase. Phosphite dehydrogenase (PTDH), a member of the D-specific 2-hydroxyacid dehydrogenase family, catalyzes the NAD-dependent formation of phosphate from phosphite (hydrogen phosphonate). PTDH has been suggested as a potential enzyme for cofactor regeneration systems. The D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD-binding domain. 318 matched cddid_all.tbl CDD cd12158 cd12158 240635 ErythrP_dh "D-Erythronate-4-Phosphate Dehydrogenase NAD-binding and catalytic domains. D-Erythronate-4-phosphate Dehydrogenase (E. coli gene PdxB), a D-specific 2-hydroxyacid dehydrogenase family member, catalyzes the NAD-dependent oxidation of erythronate-4-phosphate, which is followed by transamination to form 4-hydroxy-L-threonine-4-phosphate within the de novo biosynthesis pathway of vitamin B6. D-Erythronate-4-phosphate dehydrogenase has the common architecture shared with D-isomer specific 2-hydroxyacid dehydrogenases but contains an additional C-terminal dimerization domain in addition to an NAD-binding domain and the ""lid"" domain. The lid domain corresponds to the catalytic domain of phosphoglycerate dehydrogenase and other proteins of the D-isomer specific 2-hydroxyacid dehydrogenase family, which include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence." 343 matched cddid_all.tbl CDD cd12159 cd12159 240636 2-Hacid_dh_2 Putative D-isomer specific 2-hydroxyacid dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 303 matched cddid_all.tbl CDD cd12160 cd12160 240637 2-Hacid_dh_3 Putative D-isomer specific 2-hydroxyacid dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 310 matched cddid_all.tbl CDD cd12161 cd12161 240638 GDH_like_1 Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy dehydrogenase family. This group contains a variety of proteins variously identified as glycerate dehydrogenase (GDH, aka Hydroxypyruvate Reductase) and other enzymes of the 2-hydroxyacid dehydrogenase family. GDH catalyzes the reversible reaction of (R)-glycerate + NAD+ to hydroxypyruvate + NADH + H+. 2-hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann-fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 315 matched cddid_all.tbl CDD cd12162 cd12162 240639 2-Hacid_dh_4 Putative D-isomer specific 2-hydroxyacid dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 307 matched cddid_all.tbl CDD cd12163 cd12163 240640 2-Hacid_dh_5 Putative D-isomer specific 2-hydroxyacid dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 334 matched cddid_all.tbl CDD cd12164 cd12164 240641 GDH_like_2 Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy dehydrogenase family. This group contains a variety of proteins variously identified as glycerate dehydrogenase (GDH, also known as hydroxypyruvate reductase) and other enzymes of the 2-hydroxyacid dehydrogenase family. GDH catalyzes the reversible reaction of (R)-glycerate + NAD+ to hydroxypyruvate + NADH + H+. 2-hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann-fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 306 matched cddid_all.tbl CDD cd12165 cd12165 240642 2-Hacid_dh_6 Putative D-isomer specific 2-hydroxyacid dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 314 matched cddid_all.tbl CDD cd12166 cd12166 240643 2-Hacid_dh_7 Putative D-isomer specific 2-hydroxyacid dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 300 matched cddid_all.tbl CDD cd12167 cd12167 240644 2-Hacid_dh_8 Putative D-isomer specific 2-hydroxyacid dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 330 matched cddid_all.tbl CDD cd12168 cd12168 240645 Mand_dh_like D-Mandelate Dehydrogenase-like dehydrogenases. D-Mandelate dehydrogenase (D-ManDH), identified as an enzyme that interconverts benzoylformate and D-mandelate, is a D-2-hydroxyacid dehydrogenase family member that catalyzes the conversion of c3-branched 2-ketoacids. D-ManDH exhibits broad substrate specificities for 2-ketoacids with large hydrophobic side chains, particularly those with C3-branched side chains. 2-hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Glycerate dehydrogenase catalyzes the reaction (R)-glycerate + NAD+ to hydroxypyruvate + NADH + H+. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. 321 matched cddid_all.tbl CDD cd12169 cd12169 240646 PGDH_like_1 Putative D-3-Phosphoglycerate Dehydrogenases. Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily, which also include groups such as L-alanine dehydrogenase and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Many, not all, members of this family are dimeric. 308 matched cddid_all.tbl CDD cd12170 cd12170 240647 2-Hacid_dh_9 Putative D-isomer specific 2-hydroxyacid dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 294 matched cddid_all.tbl CDD cd12171 cd12171 240648 2-Hacid_dh_10 Putative D-isomer specific 2-hydroxyacid dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 310 matched cddid_all.tbl CDD cd12172 cd12172 240649 PGDH_like_2 Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains. Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily, which also include groups such as L-alanine dehydrogenase and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Many, not all, members of this family are dimeric. 306 matched cddid_all.tbl CDD cd12173 cd12173 240650 PGDH_4 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains. Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases. PGDH in E. coli and Mycobacterium tuberculosis form tetramers, with subunits containing a Rossmann-fold NAD binding domain. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. 304 matched cddid_all.tbl CDD cd12174 cd12174 240651 PGDH_like_3 Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains. Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily, which also include groups such as L-alanine dehydrogenase and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Many, not all, members of this family are dimeric. 305 matched cddid_all.tbl CDD cd12175 cd12175 240652 2-Hacid_dh_11 Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains. 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 311 matched cddid_all.tbl CDD cd12176 cd12176 240653 PGDH_3 Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains. Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases. PGDH in E. coli and Mycobacterium tuberculosis form tetramers, with subunits containing a Rossmann-fold NAD binding domain. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. 304 matched cddid_all.tbl CDD cd12177 cd12177 240654 2-Hacid_dh_12 Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains. 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 321 matched cddid_all.tbl CDD cd12178 cd12178 240655 2-Hacid_dh_13 Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains. 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 317 matched cddid_all.tbl CDD cd12179 cd12179 240656 2-Hacid_dh_14 Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains. 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 306 matched cddid_all.tbl CDD cd12180 cd12180 240657 2-Hacid_dh_15 Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains. 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 308 matched cddid_all.tbl CDD cd12181 cd12181 240658 ceo_syn N(5)-(carboxyethyl)ornithine synthase. N(5)-(carboxyethyl)ornithine synthase (ceo_syn) catalyzes the NADP-dependent conversion of N5-(L-1-carboxyethyl)-L-ornithine to L-ornithine + pyruvate. Ornithine plays a key role in the urea cycle, which in mammals is used in arginine biosynthesis, and is a precursor in polyamine synthesis. ceo_syn is related to the NAD-dependent L-alanine dehydrogenases. Like formate dehydrogenase and related enzymes, ceo_syn is comprised of 2 domains connected by a long alpha helical stretch, each resembling a Rossmann fold NAD-binding domain. The NAD-binding domain is inserted within the linear sequence of the more divergent catalytic domain. These ceo_syn proteins have a partially conserved NAD-binding motif and active site residues that are characteristic of related enzymes such as Saccharopine Dehydrogenase. 295 matched cddid_all.tbl CDD cd12183 cd12183 240659 LDH_like_2 D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains. D-Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate, and is a member of the 2-hydroxyacid dehydrogenase family. LDH is homologous to D-2-hydroxyisocaproic acid dehydrogenase (D-HicDH) and shares the 2-domain structure of formate dehydrogenase. D-2-hydroxyisocaproate dehydrogenase-like (HicDH) proteins are NAD-dependent members of the hydroxycarboxylate dehydrogenase family, and share the Rossmann fold typical of many NAD binding proteins. HicDH from Lactobacillus casei forms a monomer and catalyzes the reaction R-CO-COO(-) + NADH + H+ to R-COH-COO(-) + NAD+. D-HicDH, like the structurally distinct L-HicDH, exhibits low side-chain R specificity, accepting a wide range of 2-oxocarboxylic acid side chains. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. 328 matched cddid_all.tbl CDD cd12184 cd12184 240660 HGDH_like (R)-2-Hydroxyglutarate Dehydrogenase and related dehydrogenases, NAD-binding and catalytic domains. (R)-2-hydroxyglutarate dehydrogenase (HGDH) catalyzes the NAD-dependent reduction of 2-oxoglutarate to (R)-2-hydroxyglutarate. HGDH is a member of the D-2-hydroxyacid NAD(+)-dependent dehydrogenase family; these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. 330 matched cddid_all.tbl CDD cd12185 cd12185 240661 HGDH_LDH_like Putative Lactate dehydrogenase and (R)-2-Hydroxyglutarate Dehydrogenase-like proteins, NAD-binding and catalytic domains. This group contains various putative dehydrogenases related to D-lactate dehydrogenase (LDH), (R)-2-hydroxyglutarate dehydrogenase (HGDH), and related enzymes, members of the 2-hydroxyacid dehydrogenases family. LDH catalyzes the interconversion of pyruvate and lactate, and HGDH catalyzes the NAD-dependent reduction of 2-oxoglutarate to (R)-2-hydroxyglutarate. Despite often low sequence identity within this 2-hydroxyacid dehydrogenase family, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. 322 matched cddid_all.tbl CDD cd12186 cd12186 240662 LDH D-Lactate dehydrogenase and D-2-Hydroxyisocaproic acid dehydrogenase (D-HicDH), NAD-binding and catalytic domains. D-Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate, and is a member of the 2-hydroxyacid dehydrogenases family. LDH is homologous to D-2-hydroxyisocaproic acid dehydrogenase(D-HicDH) and shares the 2 domain structure of formate dehydrogenase. D-HicDH is a NAD-dependent member of the hydroxycarboxylate dehydrogenase family, and shares the Rossmann fold typical of many NAD binding proteins. HicDH from Lactobacillus casei forms a monomer and catalyzes the reaction R-CO-COO(-) + NADH + H+ to R-COH-COO(-) + NAD+. D-HicDH, like the structurally distinct L-HicDH, exhibits low side-chain R specificity, accepting a wide range of 2-oxocarboxylic acid side chains. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine Hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. 329 matched cddid_all.tbl CDD cd12187 cd12187 240663 LDH_like_1 D-Lactate and related Dehydrogenase like proteins, NAD-binding and catalytic domains. D-Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate, and is a member of the 2-hydroxyacid dehydrogenase family. LDH is homologous to D-2-Hydroxyisocaproic acid dehydrogenase(D-HicDH) and shares the 2 domain structure of formate dehydrogenase. D-2-hydroxyisocaproate dehydrogenase-like (HicDH) proteins are NAD-dependent members of the hydroxycarboxylate dehydrogenase family, and share the Rossmann fold typical of many NAD binding proteins. HicDH from Lactobacillus casei forms a monomer and catalyzes the reaction R-CO-COO(-) + NADH + H+ to R-COH-COO(-) + NAD+. D-HicDH, like the structurally distinct L-HicDH, exhibits low side-chain R specificity, accepting a wide range of 2-oxocarboxylic acid side chains. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine Hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. 329 matched cddid_all.tbl CDD cd12188 cd12188 240664 SDH Saccharopine Dehydrogenase NAD-binding and catalytic domains. Saccharopine Dehydrogenase (SDH) catalyzes the final step in the reversible NAD-dependent oxidative deamination of saccharopine to alpha-ketoglutarate and lysine, in the alpha-aminoadipate pathway of L-lysine biosynthesis. SHD is structurally related to formate dehydrogenase and similar enzymes, having a 2-domain structure in which a Rossmann-fold NAD(P)-binding domain is inserted within the linear sequence of a catalytic domain of related structure. 351 matched cddid_all.tbl CDD cd12189 cd12189 240665 LKR_SDH_like bifunctional lysine ketoglutarate reductase /saccharopine dehydrogenase enzyme. Bifunctional lysine ketoglutarate reductase /saccharopine dehydrogenase protein is a pair of enzymes linked on a single polypeptide chain that catalyze the initial, consecutive steps of lysine degradation. These proteins are related to the 2-domain saccharopine dehydrogenases. Along with formate dehydrogenase and similar enzymes, SDH consists paired domains resembling Rossmann folds in which the NAD-binding domain is inserted within the linear sequence of the catalytic domain. In this bifunctional enzyme, the LKR domain is N-terminal of the SDH domain. These proteins have a close match to the active site motif of SDHs, and an NAD-binding site motif that is a partial match to that found in SDH and other FDH-related proteins. 433 matched cddid_all.tbl CDD cd12190 cd12190 213397 Bacova_04320_like Uncharacterized proteins similar to Bacteroides ovatus 4320. This model characterized a family of proteins conserved in Bacteroidetes, similar to B. ovatus ATCC 8483 reading frame 04320. Structurally, the protein resembles members of the SRPBCC domain superfamily (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC). 159 matched cddid_all.tbl CDD cd12191 cd12191 213398 gal11_coact gall11 coactivator domain. Gall11/MED15 acts in the general regulation of GAL structural genes and is required for full expression for several genes in this pathway, including GALs 1,7, and 10 in Saccharomyces cerevisiae. GAL11 function is dependent on GCN4 functionality and binds GCN4 in a degenerate manner with multiple orientations found at the GCN4-Gal11 interface. 90 matched cddid_all.tbl CDD cd12192 cd12192 213399 GCN4_cent GCN4 central activation domain-like acidic activation domain. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain, comprised of a basic alpha-helical DNA-binding region and a coiled-coil dimerization region. 40 matched cddid_all.tbl CDD cd12193 cd12193 269833 bZIP_GCN4 Basic leucine zipper (bZIP) domain of General control protein GCN4: a DNA-binding and dimerization domain. GCN4 was identified in Saccharomyces cerevisiae from mutations in a deficiency in activation with the general amino acid control pathway. GCN4 encodes a trans-activator of amino acid biosynthetic genes containing 2 acidic activation domains and a C-terminal bZIP domain. In amino acid-deprived cells, GCN4 is up-regulated leading to transcriptional activation of genes encoding amino acid biosynthetic enzymes. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 54 matched cddid_all.tbl CDD cd12194 cd12194 213379 Kcc4p_like_C C-terminal kinase associated domain 1 (KA1), a phospholipid binding domain, of Kcc4p and similar proteins. This subfamily is composed of three Saccharomyces cerevisiae proteins, Kcc4p, Gin4p, and Hsl1p, as well as similar serine/threonine protein kinases (STKs). They catalyze the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. Kcc4p, Gin4p, and Hsl1p are septin-associated proteins that are involved in septin organization and in the yeast morphogenesis checkpoint coordinating the cell cycle with bud formation. They negatively regulate the Wee1-related kinase Swe1, which phosphorylates the cyclin-dependent kinase Cdc28, and is involved in regulating the entry of cells into mitosis. Kcc4p, Gin4p, and Hsl1p localize in the bud neck in a septin-dependent manner and display distinct but partially overlapping functions. They contain an N-terminal catalytic kinase domain and a C-terminal KA1 domain. The KA1 domain of Kcc4p, Gin4p, and Hsl1p binds acidic phospholipids including phosphatidylserine (PtdSer) and is required for bud neck localization. 122 matched cddid_all.tbl CDD cd12195 cd12195 213380 CIPK_C C-terminal regulatory domain of Calcineurin B-Like (CBL)-interacting protein kinases. CIPKs are serine/threonine protein kinases (STKs), catalyzing the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. They comprise a unique family in higher plants of proteins that interact with the calcineurin B-like (CBL) calcium sensors to form a signaling network that decode specific calcium signals triggered by a variety of environmental stimuli including salinity, drought, cold, light, and mechanical perturbation, among others. The specificity of the response relies on differences in expression and localization of both CBLs and CIPKs, as well as on the interaction specificity of CBL-CIPK combinations. There are 25, 30, and 43 CIPK genes identified in the Arabidopsis thaliana, Oryza sativa, and Zea mays genomes, respectively. The founding member of the CIPK family is Arabidopsis thaliana CIPK24, also called SOS2 (Salt Overlay Sensitive 2). CIPKs contain an N-terminal catalytic kinase domain and a C-terminal regulatory domain that contains the FISL (also called NAF for Asn-Ala-Phe) and PPI-binding motifs, which are involved in the interaction with CBLs and PP2C-type protein phosphatases, respectively. Studies using SOS2, SOS3, and ABI2 phosphatase show that the binding of CBL and PP2C-type protein phosphatase to CIPK is mutually exclusive. The binding of CBL to CIPK is inhibitory to kinase activity. 116 matched cddid_all.tbl CDD cd12196 cd12196 213381 MARK1-3_C C-terminal, kinase associated domain 1 (KA1), a phospholipid binding domain, of microtubule affinity-regulating kinases 1-3. Microtubule-associated protein/microtubule affinity regulating kinases (MARKs), also called partition-defective (Par-1) kinases, are serine/threonine protein kinases (STKs) that catalyze the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. They phosphorylate the tau protein and related microtubule-associated proteins (MAPs) on tubulin binding sites to induce detachment from microtubules, and are involved in the regulation of cell shape and polarity, cell cycle control, transport, and the cytoskeleton. Mammals contain four proteins, MARK1-4, encoded by distinct genes belonging to this subfamily, with additional isoforms arising from alternative splicing. MARK1/2, through their activation by death-associated protein kinase (DAPK), modulates polarized neurite outgrowth. MARK1, also called Par-1c, is also involved in axon-dendrite specification, and SNPs on the MARK1 gene is associated with autism spectrum disorders. MARK2, also called Par-1b, is implicated in many physiological processes including fertility, immune system homeostasis, learning and memory, growth, and metabolism. MARK3, also called Par-1a, is implicated in gluconeogenesis and adiposity; mice deficient with MARK3 display reduced adiposity, resistance to hepatic steatosis, and defective gluconeogensis. MARKs contain an N-terminal catalytic kinase domain, a ubiquitin-associated domain (UBA), and a C-terminal kinase associated domain (KA1). The KA1 domain binds anionic phospholipids and may be involved in membrane localization as well as in auto-inhibition of the kinase domain. 98 matched cddid_all.tbl CDD cd12197 cd12197 213382 MARK4_C C-terminal, kinase associated domain 1 (KA1), a phospholipid binding domain, of microtubule affinity-regulating kinase 4. Microtubule-associated protein/microtubule affinity regulating kinases (MARKs), also called partition-defective (Par-1) kinases, are serine/threonine protein kinases (STKs) that catalyze the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. They phosphorylate the tau protein and related microtubule-associated proteins (MAPs) on tubulin binding sites to induce detachment from microtubules, and are involved in the regulation of cell shape and polarity, cell cycle control, transport, and the cytoskeleton. Mammals contain four proteins, MARK1-4, encoded by distinct genes belonging to this subfamily, with additional isoforms arising from alternative splicing. MARK4 has two splicing isoforms: MARK4S, predominantly expressed in the brain; and MARK4L, expressed in all tissues. Unlike MARK1-3 that show cytoplasmic localization, MARK4 colocalizes with the centrosome and with microtubules. Decreased MARK4 expression in the brain may be involved in the pathogenesis of Prion diseases and may be correlated to PrP(Sc) deposits. MARK4 is also a component of the ectoplasmic specialization, a testis-specific adherens junction. MARKs contain an N-terminal catalytic kinase domain, a ubiquitin-associated domain (UBA), and a C-terminal kinase associated domain (KA1). The KA1 domain binds anionic phospholipids and may be involved in membrane localization as well as in auto-inhibition of the kinase domain. 99 matched cddid_all.tbl CDD cd12198 cd12198 213383 MELK_C C-terminal kinase associated domain 1 (KA1) of Maternal embryonic leucine zipper kinase. MELK, also called protein kinase 38 (PK38) or pEg3 kinase, is a cell cycle-regulated serine/threonine protein kinase (STK) that catalyzes the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. It is phosphorylated and maximally active during mitosis and is involved in regulating cell cycle progression, division, proliferation, tumor growth, and mRNA splicing. MELK shows a broad substrate specificity, including the zinc finger-like protein ZPR9, the transcription and splicing factor NIPP1, and the protein-tyrosine phosphatase Cdc25B, among others. MELK contains an N-terminal catalytic domain followed by a ubiquitin-associated (UBA) domain, a TP dipeptide-rich region, and a C-terminal KA1 domain. The KA1 domain of MELK, together with its TP dipeptide-rich region, functions as an autoinhibitory domain. The KA1 domain of the related microtubule affinity-regulating kinases (MARKs) has been shown to bind anionic phospholipids and may be involved in membrane localization. 96 matched cddid_all.tbl CDD cd12199 cd12199 213384 AMPKA1_C C-terminal regulatory domain of 5'-AMP-activated protein kinase (AMPK) alpha 1 catalytic subunit. AMPK, a serine/threonine protein kinase (STK), catalyzes the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. It acts as a sensor for the energy status of the cell and is activated by cellular stresses that lead to ATP depletion such as hypoxia, heat shock, and glucose deprivation, among others. AMPK is a heterotrimer of three subunits: alpha, beta, and gamma. Co-expression of the three subunits is required for kinase activity; in the absence of one, the other two subunits get degraded. The AMPK alpha subunit is the catalytic subunit and it contains an N-terminal kinase domain and a C-terminal regulatory domain (RD). Vertebrates contain two isoforms of the alpha subunit, alpha1 and alpha2, which are encoded by different genes, PRKAA1 and PRKAA2, respectively, and show varying expression patterns. AMPKalpha1 is the predominant isoform expressed in bone; it plays a role in bone remodeling in response to hormonal regulation. It is selectively regulated by nucleoside diphosphate kinase (NDPK)-A in an AMP-independent manner. AMPKalpha1 impacts the regulation of fat metabolism through its in vivo target, acetyl coenzyme A carboxylase (ACC). It also mediates the vasoprotective effects of estrogen through phosphorylation of another in vivo substrate, RhoA. The C-terminal RD of the AMPK alpha 1 subunit is involved in AMPK heterotrimer formation. It mainly interacts with the C-terminal region of the beta subunit to form a tight alpha-beta complex that is associated with the gamma subunit. The AMPK alpha subunit RD also contains an auto-inhibitory region that interacts with the kinase domain; this inhibition is negated by the interaction with the AMPK gamma subunit. 96 matched cddid_all.tbl CDD cd12200 cd12200 213385 AMPKA2_C C-terminal regulatory domain of 5'-AMP-activated serine/threonine kinase, subunit alpha. AMPK, a serine/threonine protein kinase (STK), catalyzes the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. It acts as a sensor for the energy status of the cell and is activated by cellular stresses that lead to ATP depletion such as hypoxia, heat shock, and glucose deprivation, among others. AMPK is a heterotrimer of three subunits: alpha, beta, and gamma. Co-expression of the three subunits is required for kinase activity; in the absence of one, the other two subunits get degraded. The AMPK alpha subunit is the catalytic subunit and it contains an N-terminal kinase domain and a C-terminal regulatory domain (RD). Vertebrates contain two isoforms of the alpha subunit, alpha1 and alpha2, which are encoded by different genes, PRKAA1 and PRKAA2, respectively, and show varying expression patterns. AMPKalpha2 shows cytoplasmic and nuclear localization, whereas AMPKalpha1 is localized only in the cytoplasm. The C-terminal RD of the AMPK alpha 1 subunit is involved in AMPK heterotrimer formation. It mainly interacts with the C-terminal region of the beta subunit to form a tight alpha-beta complex that is associated with the gamma subunit. The AMPK alpha subunit RD also contains an auto-inhibitory region that interacts with the kinase domain; this inhibition is negated by the interaction with the AMPK gamma subunit. 102 matched cddid_all.tbl CDD cd12201 cd12201 213386 MARK2_C C-terminal, kinase associated domain 1 (KA1), a phospholipid binding domain, of microtubule affinity-regulating kinase 2. Microtubule-associated protein/microtubule affinity regulating kinases (MARKs), also called partition-defective (Par-1) kinases, are serine/threonine protein kinases (STKs) that catalyze the transfer of the gamma-phosphoryl group from ATP to S/T residues on protein substrates. They phosphorylate the tau protein and related microtubule-associated proteins (MAPs) on tubulin binding sites to induce detachment from microtubules, and are involved in the regulation of cell shape and polarity, cell cycle control, transport, and the cytoskeleton. Mammals contain four proteins, MARK1-4, encoded by distinct genes belonging to this subfamily, with additional isoforms arising from alternative splicing. MARK2, also called Par-1b or ELKL motif kinase 1 (EMK-1), is implicated in many physiological processes including fertility, immune system homeostasis, learning and memory, growth, and metabolism. It also regulates axon formation and has been implicated in neurodegeneration. MARKs contain an N-terminal catalytic kinase domain, a ubiquitin-associated domain (UBA), and a C-terminal kinase associated domain (KA1). The KA1 domain binds anionic phospholipids and may be involved in membrane localization as well as in auto-inhibition of the kinase domain. 99 matched cddid_all.tbl CDD cd12202 cd12202 213401 CASP8AP2 Caspase 8-associated protein 2 myb-like domain. This domain is the SANT/myb-like domain of Caspase 8-associated protein 2 (CASP8AP2) / GON-4 like proteins. CASP8AP2 (aka Flice-Associated Huge Protein (FLASH)) is implicated in numerous gene regulatory roles including roles in embryogenesis, oncogenesis, down-regulation of replication-dependent histone genes, regulation of Caspase 8 activity at the death-inducing signaling complex (DISC), and as a useful marker in leukemia prognosis. Gon-4 is critical in Caenorhabditis elegans gonadogenesis. Danio rerio GON4 is a regulator of gene expression in hematopoietic development, possibly by repressing expression. These proteins are members of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix bundle of the DNA-binding Myb domains and is found in a diverse set of proteins. 66 matched cddid_all.tbl CDD cd12203 cd12203 213402 GT1 GT1, myb-like, SANT family. GT-1, a myb-like protein, is one of the GT trihelix transcription factors. GT-1 binds the GT cis-element of rbcS-3A, a light-induced gene, as a dimer. Arabidopsis GT-1 is a trans-activator and acts in the stabilization of components of the transcription pre-initiation complex comprised of TFIIA-TBP-TATA. The isolated GT-1 DNA-binding domain is sufficient to bind DNA. This region closely resembles the myb domain, but with longer helices. It has been proposed that GT-1 may respond to light signals via calcium-dependent phosphorylation to create a light-modulated molecular switch. These proteins are members of the SANT/myb group. SANT is named after 'SWI3, ADA2, N-CoR and TFIIIB', several factors that share this domain. The SANT domain resembles the 3 alpha-helix bundle of the DNA-binding Myb domains and is found in a diverse set of proteins. 66 matched cddid_all.tbl CDD cd12204 cd12204 213176 CBD_like Cellulose-binding domain, chitinase and related proteins. This group contains proteins related to the cellulose-binding domain of Erwinia chrysanthemi endoglucanase Z (EGZ) and Serratia marcescens chitinase B (ChiB). Gram negative plant parasite Erwinia chrysanthemi produces a variety of depolymerizing enzymes to metabolize pectin and cellulose on the host plant. Cellulase EGZ has a modular structure, with N-terminal catalytic domain linked to a C-terminal cellulose-binding domain (CBD). CBD mediates the secretion activity of EGZ. Chitinases allow certain bacteria to utilize chitin as a energy source. Typically, non-plant chitinases are of the glycosidase family 18. 48 matched cddid_all.tbl CDD cd12205 cd12205 213344 RasGAP_plexin Ras-GTPase Activating Domain of plexins. Plexins form a conserved family of transmembrane receptors for semaphorins and may be the ancestors of semaphorins. Ligand binding activates signal transduction pathways controlling axon guidance in the nervous system and other developmental processes, including cell migration and morphogenesis, immune function, and tumor progression. Plexins are divided into four types (A-D) according to sequence similarity. In vertebrates, type A Plexins serve as the co-receptors for neuropilins to mediate the signaling of class 3 semaphorins except Sema3E, which signals through Plexin D1. Plexins serve as direct receptors for several other members of the semaphorin family: class 6 semaphorins signal through type A plexins and class 4 semaphorins through type B. Plexin C1 serves as the receptor of Sema7A and plays regulation roles in both immune and nervous systems. Plexins contain a C-terminal RasGAP domain, which functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Plexins display GAP activity towards the Ras homolog Rap. Other proteins having a RasGAP domain include p120GAP, IQGAP, Rab5-activating protein 6, and Neurofibromin. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP show no sequence homology at their amino acid level. RasGTPases function as molecular switches in a large number of of signaling pathways. When bound to GTP they are in the on state and when bound to GDP they are in the off state. The RasGAP domain speeds up the hydrolysis of GTP in Ras-like proteins acting as a negative regulator. 382 matched cddid_all.tbl CDD cd12206 cd12206 213345 RasGAP_IQGAP_related Ras-GTPase Activating Domain of proteins related to IQGAPs. RasGAP: Ras-GTPase Activating Domain. RasGAP functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Proteins having a RasGAP domain include p120GAP, IQGAP, Rab5-activating protein 6, and Neurofibromin. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP show no sequence homology at their amino acid level. RasGTPases function as molecular switches in a myriad of signaling pathways. When bound to GTP they are in the on state and when bound to GDP they are in the off state. The RasGap domain speeds up the hydrolysis of GTP in Ras-like proteins acting as a negative regulator. 359 matched cddid_all.tbl CDD cd12207 cd12207 213346 RasGAP_IQGAP3 Ras-GTPase Activating Domain of IQ motif containing GTPase activating protein 3. This family represents the IQ motif containing GTPase activating protein 3 (IQGAP3), which associates with Ras GTP-binding proteins. A primary function of IQGAP proteins is to modulate cytoskeletal architecture. There are three known IQGAP family members: IQGAP1, IQGAP2 and IQGAP3. Human IQGAP1 and IQGAP2 share 62% identity. IQGAPs are multi-domain molecules having a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeats, a single WW domain, four IQ motifs that mediate interactions with calmodulin, and a RasGAP related domain that binds active Rho family GTPases. IQGAP is an essential regulator of cytoskeletal function. IQGAP1 negatively regulates Ras family GTPases by stimulating their intrinsic GTPase activity, the protein actually lacks GAP activity. Both IQGAP1 and IQGAP2 specifically bind to Cdc42 and Rac1, but not to RhoA. Despite of their similarities to part of the sequence of RasGAP, neither IQGAP1 nor IQGAP2 interacts with Ras. IQGAP3, only present in mammals, regulates the organization of the cytoskeleton under the regulation of Rac1 and Cdc42 in neuronal cells. The depletion of IQGAP3 is shown to impair neurite or axon outgrowth in neuronal cells with disorganized cytoskeleton. 350 matched cddid_all.tbl CDD cd12208 cd12208 411994 DIP1984-like DIP1984 family protein and similar proteins. DIP1984 is an uncharacterized protein from Corynebacterium diphtheriae. Some members of this family may have been misnamed as septicolysin. 150 matched cddid_all.tbl CDD cd12211 cd12211 213404 Bc2l-C_N N-Terminal Domain Of Bc2l-C Lectin. Lectin BC2L-C of Burkholderia cenocepacia is one of several lectins produced by this pathogen. BC2L-C has been shown to bind fucosylated human histo-blood group epitopes H-type 1, Lewis B, and Lewis Y. The C-terminal domain resembles BC2L-A, a calcium dependent mannose-binding protein. The N-terminal domain trimerizes and binds alpha-MeSeFuc in pockets between the monomeric units. The N-terminal domain has a similar structure to tumor necrosis factor (TNF). 131 matched cddid_all.tbl CDD cd12212 cd12212 276936 Fis1 Mitochondrial Fission Protein Fis1, cytosolic domain. Fis1, along with Dnm1 and Mdv1, is an essential protein in mediating mitochondrial fission. Dnm1 and Fis1 are highly conserved, with a common mechanism in disparate species. In mutants of these proteins, mitochondrial fission is impaired, resulting in networks of undivided mitochondria. The Fis1 N-terminus is cytosolic and tethered to the mitochondrial outer membrane via a C-terminal transmembrane domain. Fis1 appears to act via the recruitment of division complexes to the mitochondrial outer membrane, via interactions with Mdv1 or Caf4. Fis1 has tandem Tetratricopeptide repeat (TPR) motifs which are known to mediate protein-protein interactions. 115 matched cddid_all.tbl CDD cd12213 cd12213 213406 ABD Alpha-Mannosidase Binding Domain of Atg19/34. These proteins are related to the Alpha-mannosidase (Ams1) Binding Domain of Atg19/Atg34, a key component in the targeting pathway that directs alpha-mannosidase and aminopeptidase I to the vacuole, either through cytoplasm-to-vacuole trafficking or via autophagy in starvation conditions. Autophagy in a eukaryotic mechanism in which cytoplasm is enclosed in double-membraned autophagosomes which fuse with a vacuole for transport into the lumen. In Saccharomyces cerevisiae, alpha-mannosidase is selectively directed to the vacuole via the direct interaction with Atg19 (and paralog Atg34) in the Cvt pathway. Ams1 binding domains (ABD) Atg19/34 have a immunoglobulin fold with eight beta-strands. The ABD is responsible for Ams1 recognition, but its deletion does not affect the fusion of Atg19 with prApe1, and the transport of prApe1 to the vacuole. The Atg19 N-terminal region is a distinct coiled-coil domain. 112 matched cddid_all.tbl CDD cd12214 cd12214 213177 ChiA1_BD chitin-binding domain of Chi A1-like proteins. This group contains proteins related to the chitin binding domain of chitinase A1 (ChiA1) of Bacillus circulans WL-12. Glycosidase ChiA1 hydrolyzes chitin and is comprised of several domains: the C-terminal chitin binding domain, an N-terminal and catalytic domain, and 2 fibronectin type III-like domains. Chitinases function in invertebrates in the degradation of old exoskeletons, in fungi to utilize chitin in cell walls, and in bacteria which use chitin as an energy source. Bacillus circulans WL-12 ChiA1 facilitates invasion of fungal cell walls. The ChiAi chitin binding domain is required for the specific recognition of insoluble chitin. although topologically and structurally related, ChiA1 lacks the characteristic aromatic residues of Erwinia chrysanthemi endoglucanase Z (CBD(EGZ)). 45 matched cddid_all.tbl CDD cd12215 cd12215 213178 ChiC_BD Chitin-binding domain of chitinase C. Chitin-binding domain of chitinase C (ChiC) of Streptomyces griseus and related proteins. Chitinase C is a family 19 chitinase, and consists of a N-terminal chitin binding domain and a C-terminal chitin-catalytic domain that effects degradation. Chitinases function in invertebrates in the degradation of old exoskeletons, in fungi to utilize chitin in cell walls, and in bacteria which use chitin as an energy source. ChiC contains the characteristic chitin-binding aromatic residues. 42 matched cddid_all.tbl CDD cd12216 cd12216 213409 Csn2_like CRISPR/Cas system-associated protein Csn2. Csn2 is a Nmeni subtype-specific Cas protein, which may function in the adaptation process which mediates the incorporation of foreign nucleic acids into the microbial host genome. Csn 2 may interact directly with double-stranded DNA. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA. Csn2 has been predicted to be a functional analog of Cas4 based on anti-correlated phyletic patterns; also known as SPy1049 family. 217 matched cddid_all.tbl CDD cd12217 cd12217 213410 Stu0660_Csn2 Stu0660-like CRISPR/Cas system-associated protein Csn2. Csn2 is a Nmeni subtype-specific Cas protein, which may function in the adaptation process which mediates the incorporation of foreign nucleic acids into the microbial host genome. Csn 2 may interact directly with double-stranded DNA. This family of Csn2 proteins includes Stu0660, the proteins are larger than other (canonical) Csn2 proteins as they have an additional alpha-helical C-terminal domain. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA. Csn2 has been predicted to be a functional analog of Cas4 based on anti-correlated phyletic patterns; also known as SPy1049 family. 343 matched cddid_all.tbl CDD cd12218 cd12218 213411 Csn2 CRISPR/Cas system-associated protein Csn2. Csn2 is a Nmeni subtype-specific Cas protein, which may function in the adaptation process which mediates the incorporation of foreign nucleic acids into the microbial host genome. Csn 2 may interact directly with double-stranded DNA. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and associated Cas proteins comprise a system for heritable host defense by prokaryotic cells against phage and other foreign DNA. Csn2 has been predicted to be a functional analog of Cas4 based on anti-correlated phyletic patterns; also known as SPy1049 family. 219 matched cddid_all.tbl CDD cd12219 cd12219 340518 Ubl_TBK1_like ubiquitin-like (Ubl) domain found in non-canonical Inhibitor of kappa B kinases IKKepsilon and TBK1, and similar proteins. IKKepsilon and TBK1 (TRAF family member-associated NF-kappaB activator-binding kinase 1) are non-canonical members of IKK family. They have been characterized as activators of nuclear factor-kappaB (NF-kappaB), but they are not essential for NF-kappaB activation. They play critical roles in antiviral response via phosphorylation and activation of transcription factors IRF3, IRF7, STAT1 and STAT3. They are also involved in the survival, tumorigenesis and development of various cancers. Both IKKepsilon and TBK1 contain an N-terminal protein kinase domain followed a ubiquitin-like (Ubl) domain. The Ubl domain acts as a protein-protein interaction domain, and has been implicated in regulating kinase activity, which modulates interactions in the interferon pathway. 77 matched cddid_all.tbl CDD cd12220 cd12220 240617 Pesticin_RB Pesticin Translocation And Receptor Binding Domain. Pesticin (Pst) is a anti-bacterial toxin produced by Yersinia pestis that acts through uptake by the target related bacteria and the hydrolysis of peptidoglycan in the periplasm. Pst contains an N-terminal translocation domain, an intermediate receptor binding domain, and a phage-lysozyme like C-terminal activity domain. The N-terminal domain is further divided into the TonB box (which binds TonB) , the T (translocation domain) and the R (receptor binding domain). Bacteriocins such as pesticin are produced by gram-negative bacteria to attack related bacteria stains. Pst is transported to the periplasm via FyuA, an outer-membrane receptor of Y. pestis and E. coli, where it hydrolyzes peptidoglycan via the cleavage of N-acetylmuramic acid and C4 of N-acetylglucosamine. Disruption of the peptidoglycan layer renders the bacteria vulnerable to lysis via osmotic pressure. 166 matched cddid_all.tbl CDD cd12221 cd12221 240616 Cin1 Cellophane induced protein repeats of fungus Venturia inaequalis. Cin1 (cellulose induced protein 1) repeat protein of Venturia inaequalis, the fungus responsible for scab disease of apple, encodes 8 cysteine-rich repeats and is greatly upregulated within the plant and on cellophane membranes. The crystal structure reveals a pair of disulfide bridges in each repeat. The repeats have been described as adopting a beads-on-a-string organization. Cin1 function is undetermined, however the alpha-helical structure may be involved in protein-protein or protein-carbohydrate interactions in the extracellular matrix. 114 matched cddid_all.tbl CDD cd12222 cd12222 240615 Caa3-IV Caa3-Type Cytochrome Oxidase subunit 4 interacts with cyt c subunits I/III. Cytochrome c oxidase, a haem copper oxidase superfamily member, is the final step in the electron-transport chain, linking O2 reduction to transmembrane pumping in mitochondria and aerobic prokaryotes. Cytochrome c oxidase (aka Complex IV) catalyzes the reduction of O2 to 2H2O, and acts downstream of Complexes I-III: NADH-Q oxidoreductase, succinate-Q reductase, and Q-cytochrome c oxidoreductase. In Thermus thermophilus caa3-oxidase is comprised of subunit (SU) I/III, a fusion of classical SU I and SUIII, and IIc as well SU IV, which is composed of 2 connected transmembrane helices that interface with SU I/III. 63 matched cddid_all.tbl CDD cd12223 cd12223 409670 RRM_SR140 RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins. This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain). 84 matched cddid_all.tbl CDD cd12224 cd12224 409671 RRM_RBM22 RNA recognition motif (RRM) found in Pre-mRNA-splicing factor RBM22 and similar proteins. This subgroup corresponds to the RRM of RBM22 (also known as RNA-binding motif protein 22, or Zinc finger CCCH domain-containing protein 16), a newly discovered RNA-binding motif protein which belongs to the SLT11 gene family. SLT11 gene encoding protein (Slt11p) is a splicing factor in yeast, which is required for spliceosome assembly. Slt11p has two distinct biochemical properties: RNA-annealing and RNA-binding activities. RBM22 is the homolog of SLT11 in vertebrate. It has been reported to be involved in pre-splicesome assembly and to interact with the Ca2+-signaling protein ALG-2. It also plays an important role in embryogenesis. RBM22 contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a zinc finger of the unusual type C-x8-C-x5-C-x3-H, and a C-terminus that is unusually rich in the amino acids Gly and Pro, including sequences of tetraprolines. 74 matched cddid_all.tbl CDD cd12225 cd12225 409672 RRM1_2_CID8_like RNA recognition motif 1 and 2 (RRM1, RRM2) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins. This subgroup corresponds to the RRM domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. 76 matched cddid_all.tbl CDD cd12226 cd12226 409673 RRM_NOL8 RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins. This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells. 77 matched cddid_all.tbl CDD cd12227 cd12227 409674 RRM_SCAF4_SCAF8 RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4), SR-related and CTD-associated factor 8 (SCAF8) and similar proteins. This subfamily corresponds to the RRM in a new class of SCAFs (SR-like CTD-associated factors), including SCAF4, SCAF8 and similar proteins. The biological role of SCAF4 remains unclear, but it shows high sequence similarity to SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8). SCAF8 is a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. In addition, SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8 and SCAF4 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain), and serine/arginine-rich motifs. 77 matched cddid_all.tbl CDD cd12228 cd12228 409675 RRM_ENOX RNA recognition motif (RRM) found in the cell surface Ecto-NOX disulfide-thiol exchanger (ECTO-NOX or ENOX) proteins. This subgroup corresponds to the conserved RNA recognition motif (RRM) in ECTO-NOX proteins (also termed ENOX), comprising a family of plant and animal NAD(P)H oxidases exhibiting both, oxidative and protein disulfide isomerase-like, activities. They are growth-related and drive cell enlargement, and may play roles in aging and neurodegenerative diseases. ENOX proteins function as terminal oxidases of plasma membrane electron transport (PMET) through catalyzing electron transport from plasma membrane quinones to extracellular oxygen, forming water as a product. They are also hydroquinone oxidases that oxidize externally supplied NADH, hence NOX. ENOX proteins harbor a di-copper center that lack flavin. ENOX proteins display protein disulfide interchange activity that is also possessed by protein disulfide isomerase. In contrast to the classic protein disulfide isomerases, ENOX proteins lack the double CXXC motif. This family includes two ENOX proteins, ENOX1 and ENOX2. ENOX1, also termed candidate growth-related and time keeping constitutive hydroquinone [NADH] oxidase (cCNOX), or cell proliferation-inducing gene 38 protein, or Constitutive Ecto-NOX (cNOX), is the constitutively expressed cell surface NADH (ubiquinone) oxidase that is ubiquitous and refractory to drugs. ENOX2, also termed APK1 antigen, or cytosolic ovarian carcinoma antigen 1, or tumor-associated hydroquinone oxidase (tNOX), is a cancer-specific variant of ENOX1 and plays a key role in cell proliferation and tumor progression. In contrast to ENOX1, ENOX2 is drug-responsive and harbors a drug binding site to which the cancer-specific S-peptide tagged pan-ENOX2 recombinant (scFv) is directed. Moreover, ENOX2 is specifically inhibited by a variety of quinone site inhibitors that have anticancer activity and is unique to the surface of cancer cells. ENOX proteins contain many functional motifs. 84 matched cddid_all.tbl CDD cd12229 cd12229 409676 RRM_G3BP RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein G3BP1, G3BP2 and similar proteins. This subfamily corresponds to the RRM domain in the G3BP family of RNA-binding and SH3 domain-binding proteins. G3BP acts at the level of RNA metabolism in response to cell signaling, possibly as RNA transcript stabilizing factors or an RNase. Members include G3BP1, G3BP2 and similar proteins. These proteins associate directly with the SH3 domain of GTPase-activating protein (GAP), which functions as an inhibitor of Ras. They all contain an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing PXXP motif(s), an RNA recognition motif (RRM), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). 81 matched cddid_all.tbl CDD cd12230 cd12230 409677 RRM1_U2AF65 RNA recognition motif 1 (RRM1) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins. The subfamily corresponds to the RRM1 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. 82 matched cddid_all.tbl CDD cd12231 cd12231 409678 RRM2_U2AF65 RNA recognition motif 2 (RRM2) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins. This subfamily corresponds to the RRM2 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. 77 matched cddid_all.tbl CDD cd12232 cd12232 409679 RRM3_U2AF65 RNA recognition motif 3 (RRM3) found in U2 large nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65) and similar proteins. This subfamily corresponds to the RRM3 of U2AF65 and dU2AF50. U2AF65, also termed U2AF2, is the large subunit of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF), which has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF65 specifically recognizes the intron polypyrimidine tract upstream of the 3' splice site and promotes binding of U2 snRNP to the pre-mRNA branchpoint. U2AF65 also plays an important role in the nuclear export of mRNA. It facilitates the formation of a messenger ribonucleoprotein export complex, containing both the NXF1 receptor and the RNA substrate. Moreover, U2AF65 interacts directly and specifically with expanded CAG RNA, and serves as an adaptor to link expanded CAG RNA to NXF1 for RNA export. U2AF65 contains an N-terminal RS domain rich in arginine and serine, followed by a proline-rich segment and three C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The N-terminal RS domain stabilizes the interaction of U2 snRNP with the branch point (BP) by contacting the branch region, and further promotes base pair interactions between U2 snRNA and the BP. The proline-rich segment mediates protein-protein interactions with the RRM domain of the small U2AF subunit (U2AF35 or U2AF1). The RRM1 and RRM2 are sufficient for specific RNA binding, while RRM3 is responsible for protein-protein interactions. The family also includes Splicing factor U2AF 50 kDa subunit (dU2AF50), the Drosophila ortholog of U2AF65. dU2AF50 functions as an essential pre-mRNA splicing factor in flies. It associates with intronless mRNAs and plays a significant and unexpected role in the nuclear export of a large number of intronless mRNAs. 89 matched cddid_all.tbl CDD cd12233 cd12233 240679 RRM_Srp1p_AtRSp31_like RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins. This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus. 70 matched cddid_all.tbl CDD cd12234 cd12234 409680 RRM1_AtRSp31_like RNA recognition motif (RRM) found in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants. This subfamily corresponds to the RRM1in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. 72 matched cddid_all.tbl CDD cd12235 cd12235 409681 RRM_PPIL4 RNA recognition motif (RRM) found in peptidyl-prolyl cis-trans isomerase-like 4 (PPIase) and similar proteins. This subfamily corresponds to the RRM of PPIase, also termed cyclophilin-like protein PPIL4, or rotamase PPIL4, a novel nuclear RNA-binding protein encoded by cyclophilin-like PPIL4 gene. The precise role of PPIase remains unclear. PPIase contains a conserved N-terminal peptidyl-prolyl cistrans isomerase (PPIase) motif, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a lysine rich domain, and a pair of bipartite nuclear targeting sequences (NLS) at the C-terminus. 83 matched cddid_all.tbl CDD cd12236 cd12236 409682 RRM_snRNP70 RNA recognition motif (RRM) found in U1 small nuclear ribonucleoprotein 70 kDa (U1-70K) and similar proteins. This subfamily corresponds to the RRM of U1-70K, also termed snRNP70, a key component of the U1 snRNP complex, which is one of the key factors facilitating the splicing of pre-mRNA via interaction at the 5' splice site, and is involved in regulation of polyadenylation of some viral and cellular genes, enhancing or inhibiting efficient poly(A) site usage. U1-70K plays an essential role in targeting the U1 snRNP to the 5' splice site through protein-protein interactions with regulatory RNA-binding splicing factors, such as the RS protein ASF/SF2. Moreover, U1-70K protein can specifically bind to stem-loop I of the U1 small nuclear RNA (U1 snRNA) contained in the U1 snRNP complex. It also mediates the binding of U1C, another U1-specific protein, to the U1 snRNP complex. U1-70K contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region at the N-terminal half, and two serine/arginine-rich (SR) domains at the C-terminal half. The RRM is responsible for the binding of stem-loop I of U1 snRNA molecule. Additionally, the most prominent immunodominant region that can be recognized by auto-antibodies from autoimmune patients may be located within the RRM. The SR domains are involved in protein-protein interaction with SR proteins that mediate 5' splice site recognition. For instance, the first SR domain is necessary and sufficient for ASF/SF2 Binding. The family also includes Drosophila U1-70K that is an essential splicing factor required for viability in flies, but its SR domain is dispensable. The yeast U1-70k doesn't contain easily recognizable SR domains and shows low sequence similarity in the RRM region with other U1-70k proteins and therefore not included in this family. The RRM domain is dispensable for yeast U1-70K function. 91 matched cddid_all.tbl CDD cd12237 cd12237 409683 RRM_snRNP35 RNA recognition motif (RRM) found in U11/U12 small nuclear ribonucleoprotein 35 kDa protein (U11/U12-35K) and similar proteins. This subfamily corresponds to the RRM of U11/U12-35K, also termed protein HM-1, or U1 snRNP-binding protein homolog, and is one of the components of the U11/U12 snRNP, which is a subunit of the minor (U12-dependent) spliceosome required for splicing U12-type nuclear pre-mRNA introns. U11/U12-35K is highly conserved among bilateria and plants, but lacks in some organisms, such as Saccharomyces cerevisiae and Caenorhabditis elegans. Moreover, U11/U12-35K shows significant sequence homology to U1 snRNP-specific 70 kDa protein (U1-70K or snRNP70). It contains a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by an adjacent glycine-rich region, and Arg-Asp and Arg-Glu dipeptide repeats rich domain, making U11/U12-35K a possible functional analog of U1-70K. It may facilitate 5' splice site recognition in the minor spliceosome and play a role in exon bridging, interacting with components of the major spliceosome bound to the pyrimidine tract of an upstream U2-type intron. The family corresponds to the RRM of U11/U12-35K that may directly contact the U11 or U12 snRNA through the RRM domain. 94 matched cddid_all.tbl CDD cd12238 cd12238 409684 RRM1_RBM40_like RNA recognition motif 1 (RRM1) found in RNA-binding protein 40 (RBM40) and similar proteins. This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. 73 matched cddid_all.tbl CDD cd12239 cd12239 409685 RRM2_RBM40_like RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins. This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear. 82 matched cddid_all.tbl CDD cd12240 cd12240 409686 RRM_NCBP2 RNA recognition motif (RRM) found in nuclear cap-binding protein subunit 2 (CBP20) and similar proteins. This subfamily corresponds to the RRM of CBP20, also termed nuclear cap-binding protein subunit 2 (NCBP2), or cell proliferation-inducing gene 55 protein, or NCBP-interacting protein 1 (NIP1). CBP20 is the small subunit of the nuclear cap binding complex (CBC), which is a conserved eukaryotic heterodimeric protein complex binding to 5'-capped polymerase II transcripts and plays a central role in the maturation of pre-mRNA and uracil-rich small nuclear RNA (U snRNA). CBP20 is most likely responsible for the binding of capped RNA. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and interacts with the second and third domains of CBP80, the large subunit of CBC. 78 matched cddid_all.tbl CDD cd12241 cd12241 409687 RRM_SF3B14 RNA recognition motif (RRM) found in pre-mRNA branch site protein p14 (SF3B14) and similar proteins. This subfamily corresponds to the RRM of SF3B14 (also termed p14), a 14 kDa protein subunit of SF3B which is a multiprotein complex that is an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA and has been involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B14 associates directly with another SF3B subunit called SF3B155. It is also present in both U2- and U12-dependent spliceosomes and may contribute to branch site positioning in both the major and minor spliceosome. Moreover, SF3B14 interacts directly with the pre-mRNA branch adenosine early in spliceosome assembly and within the fully assembled spliceosome. SF3B14 contains one well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 77 matched cddid_all.tbl CDD cd12242 cd12242 409688 RRM_SLIRP RNA recognition motif (RRM) found in SRA stem-loop-interacting RNA-binding protein (SLIRP) and similar proteins. This subfamily corresponds to the RRM of SLIRP, a widely expressed small steroid receptor RNA activator (SRA) binding protein, which binds to STR7, a functional substructure of SRA. SLIRP is localized predominantly to the mitochondria and plays a key role in modulating several nuclear receptor (NR) pathways. It functions as a co-repressor to repress SRA-mediated nuclear receptor coactivation. It modulates SHARP- and SKIP-mediated co-regulation of NR activity. SLIRP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is required for SLIRP's corepression activities. 73 matched cddid_all.tbl CDD cd12243 cd12243 409689 RRM1_MSSP RNA recognition motif 1 (RRM1) found in the c-myc gene single-strand binding proteins (MSSP) family. This subfamily corresponds to the RRM1 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus, they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. Moreover, the family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. 71 matched cddid_all.tbl CDD cd12244 cd12244 409690 RRM2_MSSP RNA recognition motif 2 (RRM2) found in the c-myc gene single-strand binding proteins (MSSP) family. This subfamily corresponds to the RRM2 of c-myc gene single-strand binding proteins (MSSP) family, including single-stranded DNA-binding protein MSSP-1 (also termed RBMS1 or SCR2) and MSSP-2 (also termed RBMS2 or SCR3). All MSSP family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity. Both, MSSP-1 and -2, have been identified as protein factors binding to a putative DNA replication origin/transcriptional enhancer sequence present upstream from the human c-myc gene in both single- and double-stranded forms. Thus they have been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. Moreover, they family includes a new member termed RNA-binding motif, single-stranded-interacting protein 3 (RBMS3), which is not a transcriptional regulator. RBMS3 binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. In addition, a putative meiosis-specific RNA-binding protein termed sporulation-specific protein 5 (SPO5, or meiotic RNA-binding protein 1, or meiotically up-regulated gene 12 protein), encoded by Schizosaccharomyces pombe Spo5/Mug12 gene, is also included in this family. SPO5 is a novel meiosis I regulator that may function in the vicinity of the Mei2 dot. 82 matched cddid_all.tbl CDD cd12245 cd12245 409691 RRM_scw1_like RNA recognition motif (RRM) found in yeast cell wall integrity protein scw1 and similar proteins. This subfamily corresponds to the RRM of the family including yeast cell wall integrity protein scw1, yeast Whi3 protein, yeast Whi4 protein and similar proteins. The strong cell wall protein 1, scw1, is a nonessential cytoplasmic RNA-binding protein that regulates septation and cell-wall structure in fission yeast. It may function as an inhibitor of septum formation, such that its loss of function allows weak SIN signaling to promote septum formation. It's RRM domain shows high homology to two budding yeast proteins, Whi3 and Whi4. Whi3 is a dose-dependent modulator of cell size and has been implicated in cell cycle control in the yeast Saccharomyces cerevisiae. It functions as a negative regulator of ceroid-lipofuscinosis, neuronal 3 (Cln3), a G1 cyclin that promotes transcription of many genes to trigger the G1/S transition in budding yeast. It specifically binds the CLN3 mRNA and localizes it into discrete cytoplasmic loci that may locally restrict Cln3 synthesis to modulate cell cycle progression. Moreover, Whi3 plays a key role in cell fate determination in budding yeast. The RRM domain is essential for Whi3 function. Whi4 is a partially redundant homolog of Whi3, also containing one RRM. Some uncharacterized family members of this subfamily contain two RRMs; their RRM1 shows high sequence homology to the RRM of RNA-binding protein with multiple splicing (RBP-MS)-like proteins. 79 matched cddid_all.tbl CDD cd12246 cd12246 409692 RRM1_U1A_like "RNA recognition motif 1 (RRM1) found in the U1A/U2B""/SNF protein family. This subfamily corresponds to the RRM1 of U1A/U2B""/SNF protein family which contains Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B"" (U2 snRNP B"" or U2B""), all of which consist of two RNA recognition motifs (RRMs), connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B"", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B"" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. Moreover, U2B"" does not require an auxiliary protein for binding to RNA, and its nuclear transport is independent of U2 snRNA binding. " 78 matched cddid_all.tbl CDD cd12247 cd12247 409693 RRM2_U1A_like "RNA recognition motif 2 (RRM2) found in the U1A/U2B""/SNF protein family. This subfamily corresponds to the RRM2 of U1A/U2B""/SNF protein family, containing Drosophila sex determination protein SNF and its two mammalian counterparts, U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A) and U2 small nuclear ribonucleoprotein B"" (U2 snRNP B"" or U2B""), all of which consist of two RNA recognition motifs (RRMs) connected by a variable, flexible linker. SNF is an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila where it is essential in sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). U1A is an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. Moreover, U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins. U2B"", initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA, is a unique protein that comprises of the U2 snRNP. Additional research indicates U2B"" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B"" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent on U2 snRNA binding. " 72 matched cddid_all.tbl CDD cd12248 cd12248 409694 RRM_RBM44 RNA recognition motif (RRM) found in RNA-binding protein 44 (RBM44) and similar proteins. This subgroup corresponds to the RRM of RBM44, a novel germ cell intercellular bridge protein that is localized in the cytoplasm and intercellular bridges from pachytene to secondary spermatocyte stages. RBM44 interacts with itself and testis-expressed gene 14 (TEX14). Unlike TEX14, RBM44 does not function in the formation of stable intercellular bridges. It carries an RNA recognition motif (RRM) that could potentially bind a multitude of RNA sequences in the cytoplasm and help to shuttle them through the intercellular bridge, facilitating their dispersion into the interconnected neighboring cells. 77 matched cddid_all.tbl CDD cd12249 cd12249 409695 RRM1_hnRNPR_like RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins. This subfamily corresponds to the RRM1 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs); DND1 harbors only two RRMs. 78 matched cddid_all.tbl CDD cd12250 cd12250 409696 RRM2_hnRNPR_like RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins. This subfamily corresponds to the RRM2 in hnRNP R, hnRNP Q, APOBEC-1 complementation factor (ACF), and dead end protein homolog 1 (DND1). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. It has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. DND1 is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members in this family, except for DND1, contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains); DND1 harbors only two RRMs. 82 matched cddid_all.tbl CDD cd12251 cd12251 409697 RRM3_hnRNPR_like RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein R (hnRNP R) and similar proteins. This subfamily corresponds to the RRM3 in hnRNP R, hnRNP Q, and APOBEC-1 complementation factor (ACF). hnRNP R is a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches and has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP Q is also a ubiquitously expressed nuclear RNA-binding protein. It has been identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome, and has been implicated in the regulation of specific mRNA transport. ACF is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. This family also includes two functionally unknown RNA-binding proteins, RBM46 and RBM47. All members contain three conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 72 matched cddid_all.tbl CDD cd12252 cd12252 409698 RRM_DbpA RNA recognition motif (RRM) found in the DbpA subfamily of prokaryotic DEAD-box rRNA helicases. This subfamily corresponds to the C-terminal RRM homology domain of dbpA proteins implicated in ribosome biogenesis. They bind with high affinity and specificity to RNA substrates containing hairpin 92 of 23S rRNA (HP92), which is part of the ribosomal A-site. The majority of dbpA proteins contain two N-terminal ATPase catalytic domains and a C-terminal RNA binding domain, an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain). The catalytic domains bind to nearby regions of RNA to stimulate ATP hydrolysis and disrupt RNA structures. The C-terminal domain is responsible for the high-affinity RNA binding. Several members of this family lack specificity for 23S rRNA. These proteins can generally be distinguished by a basic region that extends beyond the C-terminal domain. 71 matched cddid_all.tbl CDD cd12253 cd12253 240699 RRM_PIN4_like RNA recognition motif (RRM) found in yeast RNA-binding protein PIN4, fission yeast RNA-binding post-transcriptional regulators cip1, cip2 and similar proteins. This subfamily corresponds to the RRM in PIN4, also termed psi inducibility protein 4 or modifier of damage tolerance Mdt1, a novel phosphothreonine (pThr)-containing protein that specifically interacts with the pThr-binding site of the Rad53 FHA1 domain. It is encoded by gene MDT1 (YBL051C) from yeast Saccharomyces cerevisiae. PIN4 is involved in normal G2/M cell cycle progression in the absence of DNA damage and functions as a novel target of checkpoint-dependent cell cycle arrest pathways. It contains an N-terminal RRM, a nuclear localization signal, a coiled coil, and a total of 15 SQ/TQ motifs. cip1 (Csx1-interacting protein 1) and cip2 (Csx1-interacting protein 2) are novel cytoplasmic RRM-containing proteins that counteract Csx1 function during oxidative stress. They are not essential for viability in fission yeast Schizosaccharomyces pombe. Both cip1 and cip2 contain one RRM. Like PIN4, Cip2 also possesses an R3H motif that may function in sequence-specific binding to single-stranded nucleic acids. 79 matched cddid_all.tbl CDD cd12254 cd12254 409699 RRM_hnRNPH_ESRPs_RBM12_like RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins. The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 73 matched cddid_all.tbl CDD cd12255 cd12255 409700 RRM1_LKAP RNA recognition motif 1 (RRM1) found in Limkain-b1 (LKAP) and similar proteins. This subfamily corresponds to the RRM1 of LKAP, a novel peroxisomal autoantigen that co-localizes with a subset of cytoplasmic microbodies marked by ABCD3 (ATP-binding cassette subfamily D member 3, known previously as PMP-70) and/or PXF (peroxisomal farnesylated protein, known previously as PEX19). It associates with LIM kinase 2 (LIMK2) and may serve as a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. LKAP contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). However, whether those RRMs are bona fide RNA binding sites remains unclear. Moreover, there is no evidence of LAKP localization in the nucleus. Therefore, if the RRMs are functional, their interaction with RNA species would be restricted to the cytoplasm and peroxisomes. 73 matched cddid_all.tbl CDD cd12256 cd12256 409701 RRM2_LKAP RNA recognition motif 2 (RRM2) found in Limkain-b1 (LKAP) and similar proteins. This subfamily corresponds to the RRM2 of LKAP, a novel peroxisomal autoantigen that co-localizes with a subset of cytoplasmic microbodies marked by ABCD3 (ATP-binding cassette subfamily D member 3, known previously as PMP-70) and/or PXF (peroxisomal farnesylated protein, known previously as PEX19). It associates with LIM kinase 2 (LIMK2) and may serve as a relatively common target of human autoantibodies reactive to cytoplasmic vesicle-like structures. LKAP contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). However, whether those RRMs are bona fide RNA binding sites remains unclear. Moreover, there is no evidence of LAKP localization in the nucleus. Therefore, if the RRMs are functional, their interaction with RNA species would be restricted to the cytoplasm and peroxisomes. 89 matched cddid_all.tbl CDD cd12257 cd12257 409702 RRM1_RBM26_like RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins. This subfamily corresponds to the RRM1 of RBM26, and the RRM of RBM27. RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. RBM27 contains only one RRM; its biological function remains unclear. 72 matched cddid_all.tbl CDD cd12258 cd12258 409703 RRM2_RBM26_like RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 26 (RBM26) and similar proteins. This subfamily corresponds to the RRM2 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. RBM26 contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. 72 matched cddid_all.tbl CDD cd12259 cd12259 409704 RRM_SRSF11_SREK1 RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11), splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins. This subfamily corresponds to the RRM domain of SRSF11 (SRp54 or p54), SREK1 ( SFRS12 or SRrp86) and similar proteins, a group of proteins containing regions rich in serine-arginine dipeptides (SR protein family). These are involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SR proteins have been identified as crucial regulators of alternative splicing. Different SR proteins display different substrate specificity, have distinct functions in alternative splicing of different pre-mRNAs, and can even negatively regulate splicing. All SR family members are characterized by the presence of one or two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and the C-terminal regions rich in serine and arginine dipeptides (SR domains). The RRM domain is responsible for RNA binding and specificity in both alternative and constitutive splicing. In contrast, SR domains are thought to be protein-protein interaction domains that are often interchangeable. 76 matched cddid_all.tbl CDD cd12260 cd12260 409705 RRM2_SREK1 RNA recognition motif 2 (RRM2) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins. This subfamily corresponds to the RRM2 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), which is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and it may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 contains two (some contain only one) RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1. It plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. 85 matched cddid_all.tbl CDD cd12261 cd12261 240707 RRM1_3_MRN1 RNA recognition motif 1 (RRM1) and 3 (RRM3) found in RNA-binding protein MRN1 and similar proteins. This subfamily corresponds to the RRM1 and RRM3 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 73 matched cddid_all.tbl CDD cd12262 cd12262 409706 RRM2_4_MRN1 RNA recognition motif 2 (RRM2) and 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins. This subgroup corresponds to the RRM2 and RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, and is an RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 78 matched cddid_all.tbl CDD cd12263 cd12263 409707 RRM_ABT1_like RNA recognition motif (RRM) found in activator of basal transcription 1 (ABT1) and similar proteins. This subfamily corresponds to the RRM of novel nuclear proteins termed ABT1 and its homologous counterpart, pre-rRNA-processing protein ESF2 (eighteen S factor 2), from yeast. ABT1 associates with the TATA-binding protein (TBP) and enhances basal transcription activity of class II promoters. Meanwhile, ABT1 could be a transcription cofactor that can bind to DNA in a sequence-independent manner. The yeast ABT1 homolog, ESF2, is a component of 90S preribosomes and 5' ETS-based RNPs. It is previously identified as a putative partner of the TATA-element binding protein. However, it is primarily localized to the nucleolus and physically associates with pre-rRNA processing factors. ESF2 may play a role in ribosome biogenesis. It is required for normal pre-rRNA processing, as well as for SSU processome assembly and function. Both ABT1 and ESF2 contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 98 matched cddid_all.tbl CDD cd12264 cd12264 409708 RRM_AKAP17A RNA recognition motif (RRM) found in A-kinase anchor protein 17A (AKAP-17A) and similar proteins. This subfamily corresponds to the RRM domain of AKAP-17A, also termed 721P, or splicing factor, arginine/serine-rich 17A (SFRS17A). It was originally reported as the pseudoautosomal or X inactivation escape gene 7 (XE7) and as B-lymphocyte antigen precursor. It has been suggested that AKAP-17A is an alternative splicing factor and an SR-related splicing protein that interacts with the classical SR protein ASF/SF2 and the SR-related factor ZNF265. Additional studies have indicated that AKAP-17A is a dual-specific protein kinase A anchoring protein (AKAP) that can bind both type I and type II protein kinase A (PKA) with high affinity and co-localizes with the catalytic subunit of PKA in nuclear speckles as well as the splicing factor SC35 in splicing factor compartments. It is involved in regulation of pre-mRNA splicing possibly by docking a pool of PKA in splicing factor compartments. AKAP-17A contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 122 matched cddid_all.tbl CDD cd12265 cd12265 409709 RRM_SLT11 RNA recognition motif (RRM) found in pre-mRNA-splicing factor SLT11 and similar proteins. This subfamily corresponds to the RRM of SLT11, also known as extracellular mutant protein 2, or synthetic lethality with U2 protein 11, and is a splicing factor required for spliceosome assembly in yeast. It contains a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). SLT11 can facilitate the cooperative formation of U2/U6 helix II in association with stem II in the yeast spliceosome by utilizing its RNA-annealing and -binding activities. 86 matched cddid_all.tbl CDD cd12266 cd12266 409710 RRM_like_XS RNA recognition motif (RRM)-like XS domain found in plants. This XS (named after rice gene X and SGS3) domain is a single-stranded RNA-binding domain (RBD) and possesses a unique version of a RNA recognition motif (RRM) fold. It is conserved in a family of plant proteins including gene X and SGS3. Although its function is still unknown, the plant SGS3 proteins are thought to be involved in post-transcriptional gene silencing (PTGS) pathways. In addition, they contain a conserved aspartate residue that may be functionally important. 107 matched cddid_all.tbl CDD cd12267 cd12267 409711 RRM_YRA1_MLO3 RNA recognition motif (RRM) found in yeast RNA annealing protein YRA1 (Yra1p), yeast mRNA export protein mlo3 and similar proteins. This subfamily corresponds to the RRM of Yra1p and mlo3. Yra1p is an essential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA1 gene. It belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. Yra1p possesses potent RNA annealing activity and interacts with a number of proteins involved in nuclear transport and RNA processing. It binds to the mRNA export factor Mex67p/TAP and couples transcription to export in yeast. Yra1p is associated with Pse1p and Kap123p, two members of the beta-importin family, further mediating transport of Yra1p into the nucleus. In addition, the co-transcriptional loading of Yra1p is required for autoregulation. Yra1p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This subfamily includes RNA-annealing protein mlo3, also termed mRNA export protein mlo3, which has been identified in fission yeast as a protein that causes defects in chromosome segregation when overexpressed. It shows high sequence similarity with Yra1p. 78 matched cddid_all.tbl CDD cd12268 cd12268 240714 RRM_Vip1 RNA recognition motif (RRM) found in fission yeast protein Vip1 and similar proteins. This subfamily corresponds to Vip1, an RNA-binding protein encoded by gene vip1 from fission yeast Schizosaccharomyces pombe. Its biological role remains unclear. Vip1 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 68 matched cddid_all.tbl CDD cd12269 cd12269 409712 RRM_Vip1_like RNA recognition motif (RRM) found in a group of uncharacterized plant proteins similar to fission yeast Vip1. This subfamily corresponds to the Vip1-like, uncharacterized proteins found in plants. Although their biological roles remain unclear, these proteins show high sequence similarity to the fission yeast Vip1. Like Vip1 protein, members in this family contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 69 matched cddid_all.tbl CDD cd12270 cd12270 409713 RRM_MTHFSD RNA recognition motif (RRM) found in vertebrate methenyltetrahydrofolate synthetase domain-containing proteins. This subfamily corresponds to methenyltetrahydrofolate synthetase domain (MTHFSD), a putative RNA-binding protein found in various vertebrate species. It contains an N-terminal 5-formyltetrahydrofolate cyclo-ligase domain and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of MTHFSD remains unclear. 72 matched cddid_all.tbl CDD cd12271 cd12271 409714 RRM1_PHIP1 RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins. This subfamily corresponds to the RRM1 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. 72 matched cddid_all.tbl CDD cd12272 cd12272 409715 RRM2_PHIP1 RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana phragmoplastin interacting protein 1 (PHIP1) and similar proteins. The CD corresponds to the RRM2 of PHIP1. A. thaliana PHIP1 and its homologs represent a novel class of plant-specific RNA-binding proteins that may play a unique role in the polarized mRNA transport to the vicinity of the cell plate. The family members consist of multiple functional domains, including a lysine-rich domain (KRD domain) that contains three nuclear localization motifs (KKKR/NK), two RNA recognition motifs (RRMs), and three CCHC-type zinc fingers. PHIP1 is a peripheral membrane protein and is localized at the cell plate during cytokinesis in plants. In addition to phragmoplastin, PHIP1 interacts with two Arabidopsis small GTP-binding proteins, Rop1 and Ran2. However, PHIP1 interacted only with the GTP-bound form of Rop1 but not the GDP-bound form. It also binds specifically to Ran2 mRNA. 73 matched cddid_all.tbl CDD cd12273 cd12273 409716 RRM1_NEFsp RNA recognition motif 1 (RRM1) found in vertebrate putative RNA exonuclease NEF-sp. This subfamily corresponds to the RRM1 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. 71 matched cddid_all.tbl CDD cd12274 cd12274 409717 RRM2_NEFsp RNA recognition motif 2 (RRM2) found in vertebrate putative RNA exonuclease NEF-sp. This subfamily corresponds to the RRM2 of NEF-sp., including uncharacterized putative RNA exonuclease NEF-sp found in vertebrates. Although its cellular functions remains unclear, NEF-sp contains an exonuclease domain and two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), suggesting it may possess both exonuclease and RNA-binding activities. 71 matched cddid_all.tbl CDD cd12275 cd12275 240721 RRM1_MEI2_EAR1_like RNA recognition motif 1 (RRM1) found in Mei2-like proteins and terminal EAR1-like proteins. This subfamily corresponds to the RRM1 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding protein family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. 71 matched cddid_all.tbl CDD cd12276 cd12276 409718 RRM2_MEI2_EAR1_like RNA recognition motif 2 (RRM2) found in Mei2-like proteins and terminal EAR1-like proteins. This subfamily corresponds to the RRM2 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. 71 matched cddid_all.tbl CDD cd12277 cd12277 409719 RRM3_MEI2_EAR1_like RNA recognition motif 3 (RRM3) found in Mei2-like proteins and terminal EAR1-like proteins. This subfamily corresponds to the RRM3 of Mei2-like proteins from plant and fungi, terminal EAR1-like proteins from plant, and other eukaryotic homologs. Mei2-like proteins represent an ancient eukaryotic RNA-binding proteins family whose corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. In the fission yeast Schizosaccharomyces pombe, the Mei2 protein is an essential component of the switch from mitotic to meiotic growth. S. pombe Mei2 stimulates meiosis in the nucleus upon binding a specific non-coding RNA. The terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) are mainly found in land plants. They may play a role in the regulation of leaf initiation. All members in this family are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition to the RRMs, the terminal EAR1-like proteins also contain TEL characteristic motifs that allow sequence and putative functional discrimination between them and Mei2-like proteins. 86 matched cddid_all.tbl CDD cd12278 cd12278 409720 RRM_eIF3B RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit B (eIF-3B) and similar proteins. This subfamily corresponds to the RRM domain in eukaryotic translation initiation factor 3 (eIF-3), a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3B, also termed eIF-3 subunit 9, or Prt1 homolog, eIF-3-eta, eIF-3 p110, or eIF-3 p116, is the major scaffolding subunit of eIF-3. It interacts with eIF-3 subunits A, G, I, and J. eIF-3B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is involved in the interaction with eIF-3J. The interaction between eIF-3B and eIF-3J is crucial for the eIF-3 recruitment to the 40 S ribosomal subunit. eIF-3B also binds directly to domain III of the internal ribosome-entry site (IRES) element of hepatitis-C virus (HCV) RNA through its N-terminal RRM, which may play a critical role in both cap-dependent and cap-independent translation. Additional research has shown that eIF-3B may function as an oncogene in glioma cells and can be served as a potential therapeutic target for anti-glioma therapy. This family also includes the yeast homolog of eIF-3 subunit B (eIF-3B, also termed PRT1 or eIF-3 p90) that interacts with the yeast homologs of eIF-3 subunits A(TIF32), G(TIF35), I(TIF34), J(HCR1), and E(Pci8). In yeast, eIF-3B (PRT1) contains an N-terminal RRM that is directly involved in the interaction with eIF-3A (TIF32) and eIF-3J (HCR1). In contrast to its human homolog, yeast eIF-3B (PRT1) may have potential to bind its total RNA through its RRM domain. 84 matched cddid_all.tbl CDD cd12279 cd12279 409721 RRM_TUT1 RNA recognition motif (RRM) found in speckle targeted PIP5K1A-regulated poly(A) polymerase (Star-PAP) and similar proteins. This subfamily corresponds to the RRM of Star-PAP, also termed RNA-binding motif protein 21 (RBM21), which is a ubiquitously expressed U6 snRNA-specific terminal uridylyltransferase (U6-TUTase) essential for cell proliferation. Although it belongs to the well-characterized poly(A) polymerase protein superfamily, Star-PAP is highly divergent from both, the poly(A) polymerase (PAP) and the terminal uridylyl transferase (TUTase), identified within the editing complexes of trypanosomes. Star-PAP predominantly localizes at nuclear speckles and catalyzes RNA-modifying nucleotidyl transferase reactions. It functions in mRNA biosynthesis and may be regulated by phosphoinositides. It binds to glutathione S-transferase (GST)-PIPKIalpha. Star-PAP preferentially uses ATP as a nucleotide substrate and possesses PAP activity that is stimulated by PtdIns4,5P2. It contains an N-terminal C2H2-type zinc finger motif followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a split PAP domain linked by a proline-rich region, a PAP catalytic and core domain, a PAP-associated domain, an RS repeat, and a nuclear localization signal (NLS). 74 matched cddid_all.tbl CDD cd12280 cd12280 409722 RRM_FET RNA recognition motif (RRM) found in the FET family of RNA-binding proteins. This subfamily corresponds to the RRM of FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA-binding proteins. This ubiquitously expressed family of similarly structured proteins predominantly localizing to the nuclear, includes FUS (also known as TLS or Pigpen or hnRNP P2), EWS (also known as EWSR1), TAF15 (also known as hTAFII68 or TAF2N or RPB56), and Drosophila Cabeza (also known as SARFH). The corresponding coding genes of these proteins are involved in deleterious genomic rearrangements with transcription factor genes in a variety of human sarcomas and acute leukemias. All FET proteins interact with each other and are therefore likely to be part of the very same protein complexes, which suggests a general bridging role for FET proteins coupling RNA transcription, processing, transport, and DNA repair. The FET proteins contain multiple copies of a degenerate hexapeptide repeat motif at the N-terminus. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a putative zinc-finger domain, and a conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is flanked by 3 arginine-glycine-glycine (RGG) boxes. FUS and EWS might have similar sequence specificity; both bind preferentially to GGUG-containing RNAs. FUS has also been shown to bind strongly to human telomeric RNA and to small low-copy-number RNAs tethered to the promoter of cyclin D1. To date, nothing is known about the RNA binding specificity of TAF15. 82 matched cddid_all.tbl CDD cd12281 cd12281 409723 RRM1_TatSF1_like RNA recognition motif 1 (RRM1) found in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins. This subfamily corresponds to the RRM1 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. 92 matched cddid_all.tbl CDD cd12282 cd12282 409724 RRM2_TatSF1_like RNA recognition motif 2 (RRM2) found in HIV Tat-specific factor 1 (Tat-SF1) and similar proteins. This subfamily corresponds to the RRM2 of Tat-SF1 and CUS2. Tat-SF1 is the cofactor for stimulation of transcriptional elongation by human immunodeficiency virus-type 1 (HIV-1) Tat. It is a substrate of an associated cellular kinase. Tat-SF1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a highly acidic carboxyl-terminal half. The family also includes CUS2, a yeast homolog of human Tat-SF1. CUS2 interacts with U2 RNA in splicing extracts and functions as a splicing factor that aids assembly of the splicing-competent U2 snRNP in vivo. CUS2 also associates with PRP11 that is a subunit of the conserved splicing factor SF3a. Like Tat-SF1, CUS2 contains two RRMs as well. 91 matched cddid_all.tbl CDD cd12283 cd12283 409725 RRM1_RBM39_like RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins. This subfamily corresponds to the RRM1 of RNA-binding protein 39 (RBM39), RNA-binding protein 23 (RBM23) and similar proteins. RBM39 (also termed HCC1) is a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. 73 matched cddid_all.tbl CDD cd12284 cd12284 409726 RRM2_RBM23_RBM39 RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein RBM23, RBM39 and similar proteins. This subfamily corresponds to the RRM2 of RBM39 (also termed HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Although the cellular function of RBM23 remains unclear, it shows high sequence homology to RBM39 and contains two RRMs. It may possibly function as a pre-mRNA splicing factor. 78 matched cddid_all.tbl CDD cd12285 cd12285 409727 RRM3_RBM39_like RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 39 (RBM39) and similar proteins. This subfamily corresponds to the RRM3 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, ia nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. 85 matched cddid_all.tbl CDD cd12286 cd12286 409728 RRM_Man1 RNA recognition motif (RRM) found in inner nuclear membrane protein Man1 (Man1) and similar proteins. This subfamily corresponds to the RRM of Man1, also termed LEM domain-containing protein 3 (LEMD3), an integral protein of the inner nuclear membrane that binds to nuclear lamins and emerin, thus playing a role in nuclear organization. It is part of a protein complex essential for chromatin organization and cell division. It also functions as an important negative regulator for the transforming growth factor (TGF) beta/activin/Nodal signaling pathway by directly interacting with chromatin-associated proteins and transcriptional regulators, including the R-Smads, Smad1, Smad2, and Smad3. Moreover, Man1 is a unique type of left-right (LR) signaling regulator that acts on the inner nuclear membrane. Man1 plays a crucial role in angiogenesis. The vascular remodeling can be regulated at the inner nuclear membrane through the interaction between Man1 and Smads. Man1 contains an N-terminal LEM domain, two putative transmembrane domains, a MAN1-Src1p C-terminal (MSC) domain, and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The LEM domain interacts with the DNA and chromatin-binding protein Barrier-to-Autointegration Factor, and is also necessary for efficient localization of MAN1 in the inner nuclear membrane. Research has indicated that C-terminal nucleoplasmic region of Man1 exhibits a DNA binding winged helix domain and is responsible for both DNA- and Smad-binding. 92 matched cddid_all.tbl CDD cd12287 cd12287 409729 RRM_U2AF35_like RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35) and similar proteins. This subfamily corresponds to the RRM in U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF) which has been implicated in the recruitment of U2 snRNP to pre-mRNAs. It is a highly conserved heterodimer composed of large and small subunits; this family includes the small subunit of U2AF (U2AF35 or U2AF1) and U2AF 35 kDa subunit B (U2AF35B or C3H60). U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF (U2AF65 or U2AF2). Although the biological role of U2AF35B remains unclear, it shows high sequence homolgy to U2AF35, which contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR) -rich segment interrupted by glycines. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants. 101 matched cddid_all.tbl CDD cd12288 cd12288 409730 RRM_La_like_plant RNA recognition motif (RRM) found in plant proteins related to the La autoantigen. This subfamily corresponds to the RRM of plant La-like proteins related to the La autoantigen. A variety of La-related proteins (LARPs or La ribonucleoproteins), with differing domain architecture, appear to function as RNA-binding proteins in eukaryotic cellular processes. Members in this family contain an LAM domain followed by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 90 matched cddid_all.tbl CDD cd12289 cd12289 409731 RRM_LARP6 RNA recognition motif (RRM) found in La-related protein 6 (LARP6) and similar proteins. This subfamily corresponds to the RRM of LARP6, also termed Acheron (Achn), a novel member of the lupus antigen (La) family. It is expressed predominantly in neurons and muscle in vertebrates. LARP6 functions as a key regulatory protein that may play a role in mediating a variety of developmental and homeostatic processes in animals, including myogenesis, neurogenesis and possibly metastasis. LARP6 binds to Ca2+/calmodulin-dependent serine protein kinase (CASK), and forms a complex with inhibitor of differentiation transcription factors. It is structurally related to the La autoantigen and contains a La motif (LAM), nuclear localization and export (NLS and NES) signals, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 93 matched cddid_all.tbl CDD cd12290 cd12290 409732 RRM1_LARP7 RNA recognition motif 1 (RRM1) found in La-related protein 7 (LARP7) and similar proteins. This subfamily corresponds to the RRM1 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. It plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. 79 matched cddid_all.tbl CDD cd12291 cd12291 409733 RRM1_La RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins. This subfamily corresponds to the RRM1 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. 73 matched cddid_all.tbl CDD cd12292 cd12292 409734 RRM2_La_like RNA recognition motif 2 in La autoantigen (La or SS-B or LARP3), La-related protein 7 (LARP7 or PIP7S) and similar proteins. This subfamily corresponds to the RRM2 of La and LARP7. La is a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. LARP7 is an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. It is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP), intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. LARP7 plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. Both La and LARP7 contain an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 74 matched cddid_all.tbl CDD cd12293 cd12293 410983 dRRM_Rrp7p deviant RNA recognition motif (dRRM) in yeast ribosomal RNA-processing protein 7 (Rrp7p) and similar proteins. Rrp7p is encoded by YCL031C gene from Saccharomyces cerevisiae. It is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. Rrp7p contains a deviant RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a RRP7 domain. The classic RRM fold has a topology of beta1-alpha1-beta2-beta3-alpha2-beta4 with juxtaposed N- and C-termini. By contrast, the N-terminal region of Rrp7 displays a cyclic permutation of RRM topology: the strand equivalent to RRM beta4 is shuffled to the N-terminus of the strand equivalent to RRM beta1. Moreover, Rrp7 has an extra strand beta1, which, together with other four beta-strands, forms an antiparallel five-stranded beta-sheet. 105 matched cddid_all.tbl CDD cd12294 cd12294 409735 RRM_Rrp7A RNA recognition motif in ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins. This subfamily corresponds to the RRM of Rrp7A, also termed gastric cancer antigen Zg14, a homolog of yeast ribosomal RNA-processing protein 7 (Rrp7p), and mainly found in Metazoa. Rrp7p is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. In contrast, the cellular function of Rrp7A remains unclear currently. Rrp7A harbors an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal Rrp7 domain. 103 matched cddid_all.tbl CDD cd12295 cd12295 409736 RRM_YRA2 RNA recognition motif in yeast RNA annealing protein YRA2 (Yra2p) and similar proteins. This subfamily corresponds to the RRM of Yra2p, a nonessential nuclear RNA-binding protein encoded by Saccharomyces cerevisiae YRA2 gene. It may share some overlapping functions with Yra1p, and is able to complement an YRA1 deletion when overexpressed in yeast. Yra2p belongs to the evolutionarily conserved REF (RNA and export factor binding proteins) family of hnRNP-like proteins. It is a major component of endogenous Yra1p complexes. It interacts with Yra1p and functions as a negative regulator of Yra1p. Yra2p consists of two highly conserved N- and C-terminal boxes and a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 74 matched cddid_all.tbl CDD cd12296 cd12296 409737 RRM1_Prp24 RNA recognition motif 1 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins. This subfamily corresponds to the RRM1 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. 71 matched cddid_all.tbl CDD cd12297 cd12297 409738 RRM2_Prp24 RNA recognition motif 2 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins. This subfamily corresponds to the RRM2 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. 78 matched cddid_all.tbl CDD cd12298 cd12298 409739 RRM3_Prp24 RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins. This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. 78 matched cddid_all.tbl CDD cd12299 cd12299 409740 RRM4_Prp24 RNA recognition motif 4 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins. This subfamily corresponds to the RRM4 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation. 71 matched cddid_all.tbl CDD cd12300 cd12300 409741 RRM1_PAR14 RNA recognition motif 1 in vertebrate poly [ADP-ribose] polymerase 14 (PARP-14). This subfamily corresponds to the RRM1 of PARP-14, also termed aggressive lymphoma protein 2, a member of the B aggressive lymphoma (BAL) family of macrodomain-containing PARPs. It is expressed in B lymphocytes and interacts with the IL-4-induced transcription factor Stat6. It plays a fundamental role in the regulation of IL-4-induced B-cell protection against apoptosis after irradiation or growth factor withdrawal. It mediates IL-4 effects on the levels of gene products that regulate cell survival, proliferation, and lymphomagenesis. PARP-14 acts as a transcriptional switch for Stat6-dependent gene activation. In the presence of IL-4, PARP-14 activates transcription by facilitating the binding of Stat6 to the promoter and release of HDACs from the promoter with an IL-4 signal. In contrast, in the absence of a signal, PARP-14 acts as a transcriptional repressor by recruiting HDACs. Moreover, the absence of PARP-14 protects against Myc-induced developmental block and lymphoma. Thus, PARP-14 may play an important role in Myc-induced oncogenesis. Research indicates that PARP-14 is also a binding partner with phosphoglucose isomerase (PGI)/ autocrine motility factor (AMF). It can inhibit PGI/AMF ubiquitination, thus contributing to its stabilization and secretion. PARP-14 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), three tandem macro domains, and C-terminal region with sequence homology to PARP catalytic domain. 82 matched cddid_all.tbl CDD cd12301 cd12301 409742 RRM1_2_PAR10_like RNA recognition motif 1 and 2 in poly [ADP-ribose] polymerase PARP-10, RNA recognition motif 2 in PARP-14, RNA recognition motif in N-myc-interactor (Nmi), interferon-induced 35 kDa protein (IFP 35), RNA-binding protein 43 (RBM43) and similar proteins. This subfamily corresponds to the RRM1 and RRM2 of PARP-10, RRM2 of PARP-14, RRM of N-myc-interactor (Nmi), interferon-induced 35 kDa protein (IFP 35) and RNA-binding protein 43 (RBM43). PARP-10 is a novel oncoprotein c-Myc-interacting protein with poly(ADP-ribose) polymerase activity. It is localized to the nuclear and cytoplasmic compartments. In addition to PARP activity, PARP-10 is also involved in the control of cell proliferation by inhibiting c-Myc- and E1A-mediated cotransformation of primary cells. PARP-10 may also play a role in nuclear processes including the regulation of chromatin, gene transcription, and nuclear/cytoplasmic transport. PARP-10 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two overlapping C-terminal domains composed of a glycine-rich region and a region with homology to catalytic domains of PARP enzymes (PARP domain). In addition, PARP-10 contains two ubiquitin-interacting motifs (UIM). PARP-14, also termed aggressive lymphoma protein 2, is a member of the B aggressive lymphoma (BAL) family of macrodomain-containing PARPs. Like PARP-10, PARP-14 also includes two RRMs at the N-terminus. Nmi, also termed N-myc and STAT interactor, is an interferon inducible protein that interacts with c-Myc, N-Myc, Max and c-Fos, and other transcription factors containing bHLH-ZIP, bHLH or ZIP domains. Besides binding Myc proteins, Nmi also associates with all the Stat family of transcription factors except Stat2. In response to cytokine (e.g. IL-2 and IFN-gamma) stimulation, Nmi can enhance Stat-mediated transcriptional activity through recruiting the Stat1 and Stat5 transcriptional coactivators, CREB-binding protein (CBP) and p300. IFP 35 is an interferon-induced leucine zipper protein that can specifically form homodimers. Distinct from known bZIP proteins, IFP 35 lacks a basic domain critical for DNA binding. In addition, IFP 35 may negatively regulate other bZIP transcription factors by protein-protein interaction. For instance, it can form heterodimers with B-ATF, a member of the AP1 transcription factor family. Both Nmi and IFP35 harbor one RRM. RBM43 is a putative RNA-binding protein containing one RRM, but its biological function remains unclear. 74 matched cddid_all.tbl CDD cd12302 cd12302 409743 RRM_scSet1p_like RNA recognition motif in budding yeast Saccharomyces cerevisiae SET domain-containing protein 1 (scSet1p) and similar proteins. This subfamily corresponds to the RRM of scSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, which is encoded by SET1 from the yeast S. cerevisiae. It is a nuclear protein that may play a role in both silencing and activating transcription. scSet1p is closely related to the SET domain proteins of multicellular organisms, which are implicated in diverse aspects of cell morphology, growth control, and chromatin-mediated transcriptional silencing. scSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. 110 matched cddid_all.tbl CDD cd12303 cd12303 409744 RRM_spSet1p_like RNA recognition motif in fission yeast Schizosaccharomyces pombe SET domain-containing protein 1 (spSet1p) and similar proteins. This subfamily corresponds to the RRM of spSet1p, also termed H3 lysine-4 specific histone-lysine N-methyltransferase, or COMPASS component SET1, or lysine N-methyltransferase 2, or Set1 complex component, is encoded by SET1 from the fission yeast S. pombe. It is essential for the H3 lysine-4 methylation. in vivo, and plays an important role in telomere maintenance and DNA repair in an ATM kinase Rad3-dependent pathway. spSet1p is the homology counterpart of Saccharomyces cerevisiae Set1p (scSet1p). However, it is more closely related to Set1 found in mammalian. Moreover, unlike scSet1p, spSet1p is not required for heterochromatin assembly in fission yeast. spSet1p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a conserved SET domain that may play a role in DNA repair and telomere function. 86 matched cddid_all.tbl CDD cd12304 cd12304 409745 RRM_Set1 RNA recognition motif in the Set1-like family of histone-lysine N-methyltransferases. This subfamily corresponds to the RRM of the Set1-like family of histone-lysine N-methyltransferases which includes Set1A and Set1B that are ubiquitously expressed vertebrates histone methyltransferases exhibiting high homology to yeast Set1. Set1A and Set1B proteins exhibit a largely non-overlapping subnuclear distribution in euchromatic nuclear speckles, strongly suggesting that they bind to a unique set of target genes and thus make non-redundant contributions to the epigenetic control of chromatin structure and gene expression. With the exception of the catalytic component, the subunit composition of the Set1A and Set1B histone methyltransferase complexes are identical. Each complex contains six human homologs of the yeast Set1/COMPASS complex, including Set1A or Set1B, Ash2 (homologous to yeast Bre2), CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). The genomic targeting of these complexes is determined by the identity of the catalytic subunit present in each histone methyltransferase complex. Thus, the Set1A and Set1B complexes may exhibit both overlapping and non-redundant properties. Both Set1A and Set1B contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. 93 matched cddid_all.tbl CDD cd12305 cd12305 409746 RRM_NELFE RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins. This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif. 75 matched cddid_all.tbl CDD cd12306 cd12306 409747 RRM_II_PABPs RNA recognition motif in type II polyadenylate-binding proteins. This subfamily corresponds to the RRM of type II polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 2 (PABP-2 or PABPN1), embryonic polyadenylate-binding protein 2 (ePABP-2 or PABPN1L) and similar proteins. PABPs are highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. ePABP-2 is predominantly located in the cytoplasm and PABP-2 is located in the nucleus. In contrast to the type I PABPs containing four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), the type II PABPs contains a single highly-conserved RRM. This subfamily also includes Saccharomyces cerevisiae RBP29 (SGN1, YIR001C) gene encoding cytoplasmic mRNA-binding protein Rbp29 that binds preferentially to poly(A). Although not essential for cell viability, Rbp29 plays a role in modulating the expression of cytoplasmic mRNA. Like other type II PABPs, Rbp29 contains one RRM only. 73 matched cddid_all.tbl CDD cd12307 cd12307 409748 RRM_NIFK_like RNA recognition motif in nucleolar protein interacting with the FHA domain of pKI-67 (NIFK) and similar proteins. This subgroup corresponds to the RRM of NIFK and Nop15p. NIFK, also termed MKI67 FHA domain-interacting nucleolar phosphoprotein, or nucleolar phosphoprotein Nopp34, is a putative RNA-binding protein interacting with the forkhead associated (FHA) domain of pKi-67 antigen in a mitosis-specific and phosphorylation-dependent manner. It is nucleolar in interphase but associates with condensed mitotic chromosomes. This family also includes Saccharomyces cerevisiae YNL110C gene encoding ribosome biogenesis protein 15 (Nop15p), also termed nucleolar protein 15. Both, NIFK and Nop15p, contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 74 matched cddid_all.tbl CDD cd12308 cd12308 409749 RRM1_Spen RNA recognition motif 1 (RRM1) found in the Spen (split end) protein family. This subfamily corresponds to the RRM1 domain in the Spen (split end) family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also known as one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong- to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. 78 matched cddid_all.tbl CDD cd12309 cd12309 240755 RRM2_Spen RNA recognition motif 2 (RRM2) found in the Spen (split end) protein family. This subfamily corresponds to the RRM2 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B), and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which share a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. 79 matched cddid_all.tbl CDD cd12310 cd12310 409750 RRM3_Spen RNA recognition motif 3 (RRM3) found in the Spen (split end) protein family. This subfamily corresponds to the RRM3 domain in the Spen (split end) protein family which includes RNA binding motif protein 15 (RBM15), putative RNA binding motif protein 15B (RBM15B) and similar proteins found in Metazoa. RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and is a novel component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possess mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also termed one twenty-two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. Members in this family belong to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. 72 matched cddid_all.tbl CDD cd12311 cd12311 409751 RRM_SRSF2_SRSF8 RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF2, SRSF8 and similar proteins. This subfamily corresponds to the RRM of SRSF2 and SRSF8. SRSF2, also termed protein PR264, or splicing component, 35 kDa (splicing factor SC35 or SC-35), is a prototypical SR protein that plays important roles in the alternative splicing of pre-mRNA. It is also involved in transcription elongation by directly or indirectly mediating the recruitment of elongation factors to the C-terminal domain of polymerase II. SRSF2 is exclusively localized in the nucleus and is restricted to nuclear processes. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. The RRM is responsible for the specific recognition of 5'-SSNG-3' (S=C/G) RNA. In the regulation of alternative splicing events, it specifically binds to cis-regulatory elements on the pre-mRNA. The RS domain modulates SRSF2 activity through phosphorylation, directly contacts RNA, and promotes protein-protein interactions with the spliceosome. SRSF8, also termed SRP46 or SFRS2B, is a novel mammalian SR splicing factor encoded by a PR264/SC35 functional retropseudogene. SRSF8 is localized in the nucleus and does not display the same activity as PR264/SC35. It functions as an essential splicing factor in complementing a HeLa cell S100 extract deficient in SR proteins. Like SRSF2, SRSF8 contains a single N-terminal RRM and a C-terminal RS domain. 73 matched cddid_all.tbl CDD cd12312 cd12312 240758 RRM_SRSF10_SRSF12 RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins. This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. 84 matched cddid_all.tbl CDD cd12313 cd12313 409752 RRM1_RRM2_RBM5_like RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins. This subfamily includes the RRM1 and RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37) and RNA-binding protein 10 (RBM10 or S1-1), and the RRM2 of RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). These RBMs share high sequence homology and may play an important role in regulating apoptosis. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM6 has been predicted to be a nuclear factor based on its nuclear localization signal. Both, RBM6 and RBM5, specifically bind poly(G) RNA. RBM10 is a paralog of RBM5. It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. All family members contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. 85 matched cddid_all.tbl CDD cd12314 cd12314 409753 RRM1_RBM6 RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 6 (RBM6). This subfamily corresponds to the RRM1 of RBM6, also termed lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, which has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has two additional unique domains: the decamer repeat occurring more than 20 times, and the POZ (poxvirus and zinc finger) domain. The POZ domain may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers. 78 matched cddid_all.tbl CDD cd12315 cd12315 409754 RRM1_RBM19_MRD1 RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19), yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins. This subfamily corresponds to the RRM1 of RBM19 and MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. 81 matched cddid_all.tbl CDD cd12316 cd12316 409755 RRM3_RBM19_RRM2_MRD1 RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 2 found in multiple RNA-binding domain-containing protein 1 (MRD1). This subfamily corresponds to the RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. 74 matched cddid_all.tbl CDD cd12317 cd12317 409756 RRM4_RBM19_RRM3_MRD1 RNA recognition motif 4 (RRM4) found in RNA-binding protein 19 (RBM19) and RNA recognition motif 3 (RRM3) found in multiple RNA-binding domain-containing protein 1 (MRD1). This subfamily corresponds to the RRM4 of RBM19 and the RRM3 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well conserved in yeast and its homologues exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. 72 matched cddid_all.tbl CDD cd12318 cd12318 409757 RRM5_RBM19_like RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins. This subfamily corresponds to the RRM5 of RBM19 and RRM4 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 80 matched cddid_all.tbl CDD cd12319 cd12319 409758 RRM4_MRD1 RNA recognition motif 4 (RRM4) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins. This subfamily corresponds to the RRM4 of MRD1which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. 84 matched cddid_all.tbl CDD cd12320 cd12320 409759 RRM6_RBM19_RRM5_MRD1 RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19 or RBD-1) and RNA recognition motif 5 (RRM5) found in multiple RNA-binding domain-containing protein 1 (MRD1). This subfamily corresponds to the RRM6 of RBM19 and RRM5 of MRD1. RBM19, also termed RNA-binding domain-1 (RBD-1), is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is essential for preimplantation development. It has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). MRD1 is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RRMs, which may play an important structural role in organizing specific rRNA processing events. 76 matched cddid_all.tbl CDD cd12321 cd12321 409760 RRM1_TDP43 RNA recognition motif 1 (RRM1) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins. This subfamily corresponds to the RRM1 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. 74 matched cddid_all.tbl CDD cd12322 cd12322 409761 RRM2_TDP43 RNA recognition motif 2 (RRM2) found in TAR DNA-binding protein 43 (TDP-43) and similar proteins. This subfamily corresponds to the RRM2 of TDP-43 (also termed TARDBP), a ubiquitously expressed pathogenic protein whose normal function and abnormal aggregation are directly linked to the genetic disease cystic fibrosis, and two neurodegenerative disorders: frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). TDP-43 binds both DNA and RNA, and has been implicated in transcriptional repression, pre-mRNA splicing and translational regulation. TDP-43 is a dimeric protein with two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal glycine-rich domain. The RRMs are responsible for DNA and RNA binding; they bind to TAR DNA and RNA sequences with UG-repeats. The glycine-rich domain can interact with the hnRNP family proteins to form the hnRNP-rich complex involved in splicing inhibition. It is also essential for the cystic fibrosis transmembrane conductance regulator (CFTR) exon 9-skipping activity. 71 matched cddid_all.tbl CDD cd12323 cd12323 240769 RRM2_MSI RNA recognition motif 2 (RRM2) found in RNA-binding protein Musashi homologs Musashi-1, Musashi-2 and similar proteins. This subfamily corresponds to the RRM2.in Musashi-1 (also termed Msi1), a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. 74 matched cddid_all.tbl CDD cd12324 cd12324 409762 RRM_RBM8 RNA recognition motif (RRM) found in RNA-binding protein RBM8A, RBM8B nd similar proteins. This subfamily corresponds to the RRM of RBM8, also termed binder of OVCA1-1 (BOV-1), or RNA-binding protein Y14, which is one of the components of the exon-exon junction complex (EJC). It has two isoforms, RBM8A and RBM8B, both of which are identical except that RBM8B is 16 amino acids shorter at its N-terminus. RBM8, together with other EJC components (such as Magoh, Aly/REF, RNPS1, Srm160, and Upf3), plays critical roles in postsplicing processing, including nuclear export and cytoplasmic localization of the mRNA, and the nonsense-mediated mRNA decay (NMD) surveillance process. RBM8 binds to mRNA 20-24 nucleotides upstream of a spliced exon-exon junction. It is also involved in spliced mRNA nuclear export, and the process of nonsense-mediated decay of mRNAs with premature stop codons. RBM8 forms a specific heterodimer complex with the EJC protein Magoh which then associates with Aly/REF, RNPS1, DEK, and SRm160 on the spliced mRNA, and inhibits ATP turnover by eIF4AIII, thereby trapping the EJC core onto RNA. RBM8 contains an N-terminal putative bipartite nuclear localization signal, one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), in the central region, and a C-terminal serine-arginine rich region (SR domain) and glycine-arginine rich region (RG domain). 88 matched cddid_all.tbl CDD cd12325 cd12325 409763 RRM1_hnRNPA_hnRNPD_like RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP A and hnRNP D subfamilies and similar proteins. This subfamily corresponds to the RRM1 in the hnRNP A subfamily which includes hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The hnRNP D subfamily includes hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus, plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this subfamily contain two putative RRMs and a glycine- and tyrosine-rich C-terminus. The family also contains DAZAP1 (Deleted in azoospermia-associated protein 1), RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. They all harbor two RRMs. 72 matched cddid_all.tbl CDD cd12326 cd12326 409764 RRM1_hnRNPA0 RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins. This subfamily corresponds to the RRM1 of hnRNP A0 which is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. 79 matched cddid_all.tbl CDD cd12327 cd12327 409765 RRM2_DAZAP1 RNA recognition motif 2 (RRM2) found in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins. This subfamily corresponds to the RRM2 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated is predominantly nuclear and the nonacetylated form is in cytoplasm. DAZAP1 also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. 80 matched cddid_all.tbl CDD cd12328 cd12328 409766 RRM2_hnRNPA_like RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A subfamily. This subfamily corresponds to the RRM2 of hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. 73 matched cddid_all.tbl CDD cd12329 cd12329 240775 RRM2_hnRNPD_like RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. This subfamily corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. It has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All memembers in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. 75 matched cddid_all.tbl CDD cd12330 cd12330 409767 RRM2_Hrp1p RNA recognition motif 2 (RRM2) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins. This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway; it binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. 78 matched cddid_all.tbl CDD cd12331 cd12331 409768 RRM_NRD1_SEB1_like RNA recognition motif (RRM) found in Saccharomyces cerevisiae protein Nrd1, Schizosaccharomyces pombe Rpb7-binding protein seb1 and similar proteins. This subfamily corresponds to the RRM of Nrd1 and Seb1. Nrd1 is a novel heterogeneous nuclear ribonucleoprotein (hnRNP)-like RNA-binding protein encoded by gene NRD1 (for nuclear pre-mRNA down-regulation) from yeast S. cerevisiae. It is implicated in 3' end formation of small nucleolar and small nuclear RNAs transcribed by polymerase II, and plays a critical role in pre-mRNA metabolism. Nrd1 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a short arginine-, serine-, and glutamate-rich segment similar to the regions rich in RE and RS dipeptides (RE/RS domains) in many metazoan splicing factors, and a proline- and glutamine-rich C-terminal domain (P+Q domain) similar to domains found in several yeast hnRNPs. Disruption of NRD1 gene is lethal to yeast cells. Its N-terminal domain is sufficient for viability, which may facilitate interactions with RNA polymerase II where Nrd1 may function as an auxiliary factor. By contrast, the RRM, RE/RS domains, and P+Q domain are dispensable. Seb1 is an RNA-binding protein encoded by gene seb1 (for seven binding) from fission yeast S. pombe. It is essential for cell viability and bound directly to Rpb7 subunit of RNA polymerase II. Seb1 is involved in processing of polymerase II transcripts. It also contains one RRM motif and a region rich in arginine-serine dipeptides (RS domain). 79 matched cddid_all.tbl CDD cd12332 cd12332 409769 RRM1_p54nrb_like RNA recognition motif 1 (RRM1) found in the p54nrb/PSF/PSP1 family. This subfamily corresponds to the RRM1 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. This subfamily also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. 71 matched cddid_all.tbl CDD cd12333 cd12333 409770 RRM2_p54nrb_like RNA recognition motif 2 (RRM2) found in the p54nrb/PSF/PSP1 family. This subfamily corresponds to the RRM2 of the p54nrb/PSF/PSP1 family, including 54 kDa nuclear RNA- and DNA-binding protein (p54nrb or NonO or NMT55), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF or POMp100), paraspeckle protein 1 (PSP1 or PSPC1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species, such as the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. All family members contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction module. PSF has an additional large N-terminal domain that differentiates it from other family members. 80 matched cddid_all.tbl CDD cd12334 cd12334 409771 RRM1_SF3B4 RNA recognition motif 1 (RRM1) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins. This subfamily corresponds to the RRM1 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. 74 matched cddid_all.tbl CDD cd12335 cd12335 409772 RRM2_SF3B4 RNA recognition motif 2 (RRM2) found in splicing factor 3B subunit 4 (SF3B4) and similar proteins. This subfamily corresponds to the RRM2 of SF3B4, also termed pre-mRNA-splicing factor SF3b 49 kDa (SF3b50), or spliceosome-associated protein 49 (SAP 49). SF3B4 is a component of the multiprotein complex splicing factor 3b (SF3B), an integral part of the U2 small nuclear ribonucleoprotein (snRNP) and the U11/U12 di-snRNP. SF3B is essential for the accurate excision of introns from pre-messenger RNA, and is involved in the recognition of the pre-mRNA's branch site within the major and minor spliceosomes. SF3B4 functions to tether U2 snRNP with pre-mRNA at the branch site during spliceosome assembly. It is an evolutionarily highly conserved protein with orthologs across diverse species. SF3B4 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It binds directly to pre-mRNA and also interacts directly and highly specifically with another SF3B subunit called SAP 145. 83 matched cddid_all.tbl CDD cd12336 cd12336 409773 RRM_RBM7_like RNA recognition motif (RRM) found in RNA-binding protein 7 (RBM7) and similar proteins. This subfamily corresponds to the RRM of RBM7, RBM11 and their eukaryotic homologous. RBM7 is an ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. It interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20, and may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM11 is a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. It is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. Both, RBM7 and RBM11, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. 75 matched cddid_all.tbl CDD cd12337 cd12337 409774 RRM1_SRSF4_like RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins. This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. 70 matched cddid_all.tbl CDD cd12338 cd12338 409775 RRM1_SRSF1_like RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins. This subgroup corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C), and plant pre-mRNA-splicing factor SF2 (SR1). SRSF1 is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9 has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. It can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. In contrast, SF2 contains two N-terminal RRMs and a C-terminal PSK domain rich in proline, serine and lysine residues. 72 matched cddid_all.tbl CDD cd12339 cd12339 409776 RRM2_SRSF1_4_like RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor SRSF1, SRSF4 and similar proteins. This subfamily corresponds to the RRM2 of several serine/arginine (SR) proteins that have been classified into two subgroups. The first subgroup consists of serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS) and serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). The second subgroup is composed of serine/arginine-rich splicing factor 1 (SRSF1 or ASF-1), serine/arginine-rich splicing factor 9 (SRSF9 or SRp30C) and plant pre-mRNA-splicing factor SF2 (SR1). These SR proteins are mainly involved in regulating constitutive and alternative pre-mRNA splicing. They also have been implicated in transcription, genomic stability, mRNA export and translation. All SR proteins in this family, except SRSF5, undergo nucleocytoplasmic shuttling, suggesting their widespread roles in gene expression. These SR proteins share a common domain architecture comprising two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. Both domains can directly contact with RNA. The RRMs appear to determine the binding specificity and the SR domain also mediates protein-protein interactions. In addition, this subfamily includes the yeast nucleolar protein 3 (Npl3p), also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. It is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein with two RRMs, separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. 70 matched cddid_all.tbl CDD cd12340 cd12340 409777 RBD_RRM1_NPL3 RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 3 (Npl3p) and similar proteins. This subfamily corresponds to the RRM1 of Npl3p, also termed mitochondrial targeting suppressor 1 protein, or nuclear polyadenylated RNA-binding protein 1. Npl3p is a major yeast RNA-binding protein that competes with 3'-end processing factors, such as Rna15, for binding to the nascent RNA, protecting the transcript from premature termination and coordinating transcription termination and the packaging of the fully processed transcript for export. It specifically recognizes a class of G/U-rich RNAs. Npl3p is a multi-domain protein containing two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a short linker and a C-terminal domain rich in glycine, arginine and serine residues. 69 matched cddid_all.tbl CDD cd12341 cd12341 409778 RRM_hnRNPC_like RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein C (hnRNP C)-related proteins. This subfamily corresponds to the RRM in the hnRNP C-related protein family, including hnRNP C proteins, Raly, and Raly-like protein (RALYL). hnRNP C proteins, C1 and C2, are produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex; they are involved in the packaging of the hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. Raly, also termed autoantigen p542, is an RNA-binding protein that may play a critical role in embryonic development. The biological role of RALYL remains unclear. It shows high sequence homology with hnRNP C proteins and Raly. Members of this family are characterized by an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. The Raly proteins contain a glycine/serine-rich stretch within the C-terminal regions, which is absent in the hnRNP C proteins. Thus, the Raly proteins represent a newly identified class of evolutionarily conserved autoepitopes. 68 matched cddid_all.tbl CDD cd12342 cd12342 240788 RRM_Nab3p RNA recognition motif (RRM) found in yeast nuclear polyadenylated RNA-binding protein 3 (Nab3p) and similar proteins. This subfamily corresponds to the RRM of Nab3p, an acidic nuclear polyadenylated RNA-binding protein encoded by Saccharomyces cerevisiae NAB3 gene that is essential for cell viability. Nab3p is predominantly localized within the nucleoplasm and essential for growth in yeast. It may play an important role in packaging pre-mRNAs into ribonucleoprotein structures amenable to efficient nuclear RNA processing. Nab3p contains an N-terminal aspartic/glutamic acid-rich region, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal region rich in glutamine and proline residues. 71 matched cddid_all.tbl CDD cd12343 cd12343 409779 RRM1_2_CoAA_like RNA recognition motif 1 (RRM1) and 2 (RRM2) found in RRM-containing coactivator activator/modulator (CoAA) and similar proteins. This subfamily corresponds to the RRM in CoAA (also known as RBM14 or PSP2) and RNA-binding protein 4 (RBM4). CoAA is a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner, and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. RBM4 is a ubiquitously expressed splicing factor with two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may also function as a translational regulator of stress-associated mRNAs as well as play a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RRMs, a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. This family also includes Drosophila RNA-binding protein lark (Dlark), a homolog of human RBM4. It plays an important role in embryonic development and in the circadian regulation of adult eclosion. Dlark shares high sequence similarity with RBM4 at the N-terminal region. However, Dlark has three proline-rich segments instead of three alanine-rich segments within the C-terminal region. 66 matched cddid_all.tbl CDD cd12344 cd12344 409780 RRM1_SECp43_like RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins. This subfamily corresponds to the RRM1 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. 82 matched cddid_all.tbl CDD cd12345 cd12345 409781 RRM2_SECp43_like RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43) and similar proteins. This subfamily corresponds to the RRM2 in tRNA selenocysteine-associated protein 1 (SECp43), yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8, and similar proteins. SECp43 is an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. Yeast proteins, NGR1 and NAM8, show high sequence similarity with SECp43. NGR1 is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA). It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains three RRMs, two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the C-terminus which also harbors a methionine-rich region. NAM8 is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. NAM8 also contains three RRMs. 80 matched cddid_all.tbl CDD cd12346 cd12346 409782 RRM3_NGR1_NAM8_like RNA recognition motif 3 (RRM3) found in yeast negative growth regulatory protein NGR1 (RBP1), yeast protein NAM8 and similar proteins. This subfamily corresponds to the RRM3 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both RNA and single-stranded DNA (ssDNA) in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. 72 matched cddid_all.tbl CDD cd12347 cd12347 409783 RRM_PPIE RNA recognition motif (RRM) found in cyclophilin-33 (Cyp33) and similar proteins. This subfamily corresponds to the RRM of Cyp33, also termed peptidyl-prolyl cis-trans isomerase E (PPIase E), or cyclophilin E, or rotamase E. Cyp33 is a nuclear RNA-binding cyclophilin with an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal PPIase domain. Cyp33 possesses RNA-binding activity and preferentially binds to polyribonucleotide polyA and polyU, but hardly to polyG and polyC. It binds specifically to mRNA, which can stimulate its PPIase activity. Moreover, Cyp33 interacts with the third plant homeodomain (PHD3) zinc finger cassette of the mixed lineage leukemia (MLL) proto-oncoprotein and a poly-A RNA sequence through its RRM domain. It further mediates downregulation of the expression of MLL target genes HOXC8, HOXA9, CDKN1B, and C-MYC, in a proline isomerase-dependent manner. Cyp33 also possesses a PPIase activity that catalyzes cis-trans isomerization of the peptide bond preceding a proline, which has been implicated in the stimulation of folding and conformational changes in folded and unfolded proteins. The PPIase activity can be inhibited by the immunosuppressive drug cyclosporin A. 75 matched cddid_all.tbl CDD cd12348 cd12348 409784 RRM1_SHARP RNA recognition motif 1 (RRM1) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins. This subfamily corresponds to the RRM1 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. 75 matched cddid_all.tbl CDD cd12349 cd12349 409785 RRM2_SHARP RNA recognition motif 2 (RRM2) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins. This subfamily corresponds to the RRM2 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. 74 matched cddid_all.tbl CDD cd12350 cd12350 409786 RRM3_SHARP RNA recognition motif 3 (RRM3) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins. This subfamily corresponds to the RRM3 of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. 74 matched cddid_all.tbl CDD cd12351 cd12351 409787 RRM4_SHARP RNA recognition motif 4 (RRM4) found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins. This subfamily corresponds to the RRM of SHARP, also termed Msx2-interacting protein (MINT), or SPEN homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs) and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain (Spen paralog and ortholog C-terminal domain), which is highly conserved among Spen proteins. 77 matched cddid_all.tbl CDD cd12352 cd12352 409788 RRM1_TIA1_like RNA recognition motif 1 (RRM1) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR. This subfamily corresponds to the RRM1 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. 73 matched cddid_all.tbl CDD cd12353 cd12353 409789 RRM2_TIA1_like RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins p40-TIA-1 and TIAR. This subfamily corresponds to the RRM2 of nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR), both of which are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. TIA-1 and TIAR share high sequence similarity. They are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis. TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both, TIA-1 and TIAR, bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. 75 matched cddid_all.tbl CDD cd12354 cd12354 409790 RRM3_TIA1_like RNA recognition motif 2 (RRM2) found in granule-associated RNA binding proteins (p40-TIA-1 and TIAR), and yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1. This subfamily corresponds to the RRM3 of TIA-1, TIAR, and PUB1. Nucleolysin TIA-1 isoform p40 (p40-TIA-1 or TIA-1) and nucleolysin TIA-1-related protein (TIAR) are granule-associated RNA binding proteins involved in inducing apoptosis in cytotoxic lymphocyte (CTL) target cells. They share high sequence similarity and are expressed in a wide variety of cell types. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis.TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. Both TIA-1 and TIAR bind specifically to poly(A) but not to poly(C) homopolymers. They are composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 and TIAR interact with RNAs containing short stretches of uridylates and their RRM2 can mediate the specific binding to uridylate-rich RNAs. The C-terminal auxiliary domain may be responsible for interacting with other proteins. In addition, TIA-1 and TIAR share a potential serine protease-cleavage site (Phe-Val-Arg) localized at the junction between their RNA binding domains and their C-terminal auxiliary domains. This subfamily also includes a yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1, termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein, which has been identified as both a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP). It may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RRMs, and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. 71 matched cddid_all.tbl CDD cd12355 cd12355 409791 RRM_RBM18 RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins. This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear. 80 matched cddid_all.tbl CDD cd12356 cd12356 409792 RRM_PPARGC1B RNA recognition motif (RRM) found in peroxisome proliferator-activated receptor gamma coactivator 1-beta (PGC-1-beta) and similar proteins. This subfamily corresponds to the RRM of PGC-1beta, also termed PPAR-gamma coactivator 1-beta, or PPARGC-1-beta, or PGC-1-related estrogen receptor alpha coactivator, which is one of the members of PGC-1 transcriptional coactivators family, including PGC-1alpha and PGC-1-related coactivator (PRC). PGC-1beta plays a nonredundant role in controlling mitochondrial oxidative energy metabolism and affects both, insulin sensitivity and mitochondrial biogenesis, and functions in a number of oxidative tissues. It is involved in maintaining baseline mitochondrial function and cardiac contractile function following pressure overload hypertrophy by preserving glucose metabolism and preventing oxidative stress. PGC-1beta induces hypertriglyceridemia in response to dietary fats through activating hepatic lipogenesis and lipoprotein secretion. It can stimulate apolipoprotein C3 (APOC3) expression, further mediating hypolipidemic effect of nicotinic acid. PGC-1beta also drives nuclear respiratory factor 1 (NRF-1) target gene expression and NRF-1 and estrogen related receptor alpha (ERRalpha)-dependent mitochondrial biogenesis. The modulation of the expression of PGC-1beta can trigger ERRalpha-induced adipogenesis. PGC-1beta is also a potent regulator inducing angiogenesis in skeletal muscle. The transcriptional activity of PGC-1beta can be increased through binding to host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. PGC-1beta is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, two glutamic/aspartic acid-rich acidic domains, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha, PGC-1beta lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. 97 matched cddid_all.tbl CDD cd12357 cd12357 409793 RRM_PPARGC1A_like RNA recognition motif (RRM) found in the peroxisome proliferator-activated receptor gamma coactivator 1A (PGC-1alpha) family of regulated coactivators. This subfamily corresponds to the RRM of PGC-1alpha, PGC-1beta, and PGC-1-related coactivator (PRC), which serve as mediators between environmental or endogenous signals and the transcriptional machinery governing mitochondrial biogenesis. They play an important integrative role in the control of respiratory gene expression through interacting with a number of transcription factors, such as NRF-1, NRF-2, ERR, CREB and YY1. All family members are multi-domain proteins containing the N-terminal activation domain, an LXXLL coactivator signature, a tetrapeptide motif (DHDY) responsible for HCF binding, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In contrast to PGC-1alpha and PRC, PGC-1beta possesses two glutamic/aspartic acid-rich acidic domains, but lacks most of the arginine/serine (SR)-rich domain that is responsible for the regulation of RNA processing. 91 matched cddid_all.tbl CDD cd12358 cd12358 240804 RRM1_VICKZ RNA recognition motif 1 (RRM1) found in the VICKZ family proteins. Thid subfamily corresponds to the RRM1 of IGF2BPs (or IMPs) found in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. 73 matched cddid_all.tbl CDD cd12359 cd12359 409794 RRM2_VICKZ RNA recognition motif 2 (RRM2) found in the VICKZ family proteins. This subfamily corresponds to the RRM2 of IGF-II mRNA-binding proteins (IGF2BPs or IMPs) in the VICKZ family that have been implicated in the post-transcriptional regulation of several different RNAs and in subcytoplasmic localization of mRNAs during embryogenesis. IGF2BPs are composed of two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and four hnRNP K homology (KH) domains. 76 matched cddid_all.tbl CDD cd12360 cd12360 409795 RRM_cwf2 RNA recognition motif (RRM) found in yeast pre-mRNA-splicing factor Cwc2 and similar proteins. This subfamily corresponds to the RRM of yeast protein Cwc2, also termed Complexed with CEF1 protein 2, or PRP19-associated complex protein 40 (Ntc40), or synthetic lethal with CLF1 protein 3, one of the components of the Prp19-associated complex [nineteen complex (NTC)] that can bind to RNA. NTC is composed of the scaffold protein Prp19 and a number of associated splicing factors, and plays a crucial role in intron removal during premature mRNA splicing in eukaryotes. Cwc2 functions as an RNA-binding protein that can bind both small nuclear RNAs (snRNAs) and pre-mRNA in vitro. It interacts directly with the U6 snRNA to link the NTC to the spliceosome during pre-mRNA splicing. In the N-terminal half, Cwc2 contains a CCCH-type zinc finger (ZnF domain), a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an intervening loop, also termed RNA-binding loop or RB loop, between ZnF and RRM, all of which are necessary and sufficient for RNA binding. The ZnF is also responsible for mediating protein-protein interaction. The C-terminal flexible region of Cwc2 interacts with the WD40 domain of Prp19. 79 matched cddid_all.tbl CDD cd12361 cd12361 409796 RRM1_2_CELF1-6_like RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA. This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain. 77 matched cddid_all.tbl CDD cd12362 cd12362 409797 RRM3_CELF1-6 RNA recognition motif 3 (RRM3) found in CELF/Bruno-like family of RNA binding proteins CELF1, CELF2, CELF3, CELF4, CELF5, CELF6 and similar proteins. This subgroup corresponds to the RRM3 of the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) proteins, a family of structurally related RNA-binding proteins involved in the regulation of pre-mRNA splicing in the nucleus and in the control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also termed BRUNOL-2, or CUG-BP1, or NAPOR, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR-2), CELF-3 (also termed BRUNOL-1, or TNRC4, or ETR-1, or CAGH4, or ER DA4), CELF-4 (also termed BRUNOL-4), CELF-5 (also termed BRUNOL-5), CELF-6 (also termed BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. 73 matched cddid_all.tbl CDD cd12363 cd12363 409798 RRM_TRA2 RNA recognition motif (RRM) found in transformer-2 protein homolog TRA2-alpha, TRA2-beta and similar proteins. This subfamily corresponds to the RRM of two mammalian homologs of Drosophila transformer-2 (Tra2), TRA2-alpha, TRA2-beta (also termed SFRS10), and similar proteins found in eukaryotes. TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Both, TRA2-alpha and TRA2-beta, contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. 80 matched cddid_all.tbl CDD cd12364 cd12364 409799 RRM_RDM1 RNA recognition motif (RRM) found in RAD52 motif-containing protein 1 (RDM1) and similar proteins. This subfamily corresponds to the RRM of RDM1, also termed RAD52 homolog B, a novel factor involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. RDM1 contains a small RD motif that shares with the recombination and repair protein RAD52, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RD motif is responsible for the acidic pH-dependent DNA-binding properties of RDM1. It interacts with ss- and dsDNA, and may act as a DNA-damage recognition factor by recognizing the distortions of the double helix caused by cisplatin-DNA adducts in vitro. In addition, due to the presence of RRM, RDM1 can bind to RNA as well as DNA. 81 matched cddid_all.tbl CDD cd12365 cd12365 409800 RRM_RNPS1 RNA recognition motif (RRM) found in RNA-binding protein with serine-rich domain 1 (RNPS1) and similar proteins. This subfamily corresponds to the RRM of RNPS1 and its eukaryotic homologs. RNPS1, also termed RNA-binding protein prevalent during the S phase, or SR-related protein LDC2, was originally characterized as a general pre-mRNA splicing activator, which activates both constitutive and alternative splicing of pre-mRNA in vitro.It has been identified as a protein component of the splicing-dependent mRNP complex, or exon-exon junction complex (EJC), and is directly involved in mRNA surveillance. Furthermore, RNPS1 is a splicing regulator whose activator function is controlled in part by CK2 (casein kinase II) protein kinase phosphorylation. It can also function as a squamous-cell carcinoma antigen recognized by T cells-3 (SART3)-binding protein, and is involved in the regulation of mRNA splicing. RNPS1 contains an N-terminal serine-rich (S) domain, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and the C-terminal arginine/serine/proline-rich (RS/P) domain. 73 matched cddid_all.tbl CDD cd12366 cd12366 409801 RRM1_RBM45 RNA recognition motif 1 (RRM1) found in RNA-binding protein 45 (RBM45) and similar proteins. This subfamily corresponds to the RRM1 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 81 matched cddid_all.tbl CDD cd12367 cd12367 409802 RRM2_RBM45 RNA recognition motif 2 (RRM2) found in RNA-binding protein 45 (RBM45) and similar proteins. This subfamily corresponds to the RRM2 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 74 matched cddid_all.tbl CDD cd12368 cd12368 409803 RRM3_RBM45 RNA recognition motif 3 (RRM3) found in RNA-binding protein 45 (RBM45) and similar proteins. This subfamily corresponds to the RRM3 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 75 matched cddid_all.tbl CDD cd12369 cd12369 409804 RRM4_RBM45 RNA recognition motif 4 (RRM4) found in RNA-binding protein 45 (RBM45) and similar proteins. This subfamily corresponds to the RRM4 of RBM45, also termed developmentally-regulated RNA-binding protein 1 (DRB1), a new member of RNA recognition motif (RRM)-type neural RNA-binding proteins, which expresses under spatiotemporal control. It is encoded by gene drb1 that is expressed in neurons, not in glial cells. RBM45 predominantly localizes in cytoplasm of cultured cells and specifically binds to poly(C) RNA. It could play an important role during neurogenesis. RBM45 carries four RRMs, also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 68 matched cddid_all.tbl CDD cd12370 cd12370 409805 RRM1_PUF60 RNA recognition motif 1 (RRM1) found in (U)-binding-splicing factor PUF60 and similar proteins. This subfamily corresponds to the RRM1 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. 76 matched cddid_all.tbl CDD cd12371 cd12371 409806 RRM2_PUF60 RNA recognition motif 2 (RRM2) found in (U)-binding-splicing factor PUF60 and similar proteins. This subfamily corresponds to the RRM2 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1). PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. Research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. 77 matched cddid_all.tbl CDD cd12372 cd12372 409807 RRM_CFIm68_CFIm59 RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6), pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7), and similar proteins. This subfamily corresponds to the RRM of cleavage factor Im (CFIm) subunits. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. Structurally related CFIm68 and CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59), are functionally redundant. Both contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. Their N-terminal RRM mediates the interaction with CFIm25, and also serves to enhance RNA binding and facilitate RNA looping. 76 matched cddid_all.tbl CDD cd12373 cd12373 409808 RRM_SRSF3_like RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins. This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. 73 matched cddid_all.tbl CDD cd12374 cd12374 409809 RRM_UHM_SPF45_PUF60 RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins. This subfamily corresponds to the RRM found in UHM domain of 45 kDa-splicing factor (SPF45 or RBM17), poly(U)-binding-splicing factor PUF60 (FIR or Hfp or RoBP1 or Siah-BP1), and similar proteins. SPF45 is an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. PUF60 is an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RRMs and a C-terminal UHM domain. 85 matched cddid_all.tbl CDD cd12375 cd12375 409810 RRM1_Hu_like RNA recognition motif 1 (RRM1) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins. This subfamily corresponds to the RRM1 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. This family also includes the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds to its own pre-mRNA and promotes female-specific alternative splicing. It contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. 76 matched cddid_all.tbl CDD cd12376 cd12376 240822 RRM2_Hu_like RNA recognition motif 2 (RRM2) found in the Hu proteins family, Drosophila sex-lethal (SXL), and similar proteins. This subfamily corresponds to the RRM2 of Hu proteins and SXL. The Hu proteins family represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. Also included in this subfamily is the sex-lethal protein (SXL) from Drosophila melanogaster. SXL governs sexual differentiation and X chromosome dosage compensation in flies. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RRMs that show high preference to bind single-stranded, uridine-rich target RNA transcripts. 79 matched cddid_all.tbl CDD cd12377 cd12377 409811 RRM3_Hu RNA recognition motif 3 (RRM3) found in the Hu proteins family. This subfamily corresponds to the RRM3 of the Hu proteins family which represent a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. 76 matched cddid_all.tbl CDD cd12378 cd12378 409812 RRM1_I_PABPs RNA recognition motif 1 (RRM1) found in type I polyadenylate-binding proteins. This subfamily corresponds to the RRM1 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammals, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. 80 matched cddid_all.tbl CDD cd12379 cd12379 409813 RRM2_I_PABPs RNA recognition motif 2 (RRM2) found found in type I polyadenylate-binding proteins. This subfamily corresponds to the RRM2 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is a ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. 77 matched cddid_all.tbl CDD cd12380 cd12380 409814 RRM3_I_PABPs RNA recognition motif 3 (RRM3) found found in type I polyadenylate-binding proteins. This subfamily corresponds to the RRM3 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in the regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. 80 matched cddid_all.tbl CDD cd12381 cd12381 409815 RRM4_I_PABPs RNA recognition motif 4 (RRM4) found in type I polyadenylate-binding proteins. This subfamily corresponds to the RRM4 of type I poly(A)-binding proteins (PABPs), highly conserved proteins that bind to the poly(A) tail present at the 3' ends of most eukaryotic mRNAs. They have been implicated in theThe CD corresponds to the RRM. regulation of poly(A) tail length during the polyadenylation reaction, translation initiation, mRNA stabilization by influencing the rate of deadenylation and inhibition of mRNA decapping. The family represents type I polyadenylate-binding proteins (PABPs), including polyadenylate-binding protein 1 (PABP-1 or PABPC1), polyadenylate-binding protein 3 (PABP-3 or PABPC3), polyadenylate-binding protein 4 (PABP-4 or APP-1 or iPABP), polyadenylate-binding protein 5 (PABP-5 or PABPC5), polyadenylate-binding protein 1-like (PABP-1-like or PABPC1L), polyadenylate-binding protein 1-like 2 (PABPC1L2 or RBM32), polyadenylate-binding protein 4-like (PABP-4-like or PABPC4L), yeast polyadenylate-binding protein, cytoplasmic and nuclear (PABP or ACBP-67), and similar proteins. PABP-1 is an ubiquitously expressed multifunctional protein that may play a role in 3' end formation of mRNA, translation initiation, mRNA stabilization, protection of poly(A) from nuclease activity, mRNA deadenylation, inhibition of mRNA decapping, and mRNP maturation. Although PABP-1 is thought to be a cytoplasmic protein, it is also found in the nucleus. PABP-1 may be involved in nucleocytoplasmic trafficking and utilization of mRNP particles. PABP-1 contains four copies of RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a less well conserved linker region, and a proline-rich C-terminal conserved domain (CTD). PABP-3 is a testis-specific poly(A)-binding protein specifically expressed in round spermatids. It is mainly found in mammalian and may play an important role in the testis-specific regulation of mRNA homeostasis. PABP-3 shows significant sequence similarity to PABP-1. However, it binds to poly(A) with a lower affinity than PABP-1. Moreover, PABP-1 possesses an A-rich sequence in its 5'-UTR and allows binding of PABP and blockage of translation of its own mRNA. In contrast, PABP-3 lacks the A-rich sequence in its 5'-UTR. PABP-4 is an inducible poly(A)-binding protein (iPABP) that is primarily localized to the cytoplasm. It shows significant sequence similarity to PABP-1 as well. The RNA binding properties of PABP-1 and PABP-4 appear to be identical. PABP-5 is encoded by PABPC5 gene within the X-specific subinterval, and expressed in fetal brain and in a range of adult tissues in mammalian, such as ovary and testis. It may play an important role in germ cell development. Moreover, unlike other PABPs, PABP-5 contains only four RRMs, but lacks both the linker region and the CTD. PABP-1-like and PABP-1-like 2 are the orthologs of PABP-1. PABP-4-like is the ortholog of PABP-5. Their cellular functions remain unclear. The family also includes the yeast PABP, a conserved poly(A) binding protein containing poly(A) tails that can be attached to the 3'-ends of mRNAs. The yeast PABP and its homologs may play important roles in the initiation of translation and in mRNA decay. Like vertebrate PABP-1, the yeast PABP contains four RRMs, a linker region, and a proline-rich CTD as well. The first two RRMs are mainly responsible for specific binding to poly(A). The proline-rich region may be involved in protein-protein interactions. 79 matched cddid_all.tbl CDD cd12382 cd12382 409816 RRM_RBMX_like RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins. This subfamily corresponds to the RRM domain of hnRNP G, also termed glycoprotein p43 or RBMX, an RNA-binding motif protein located on the X chromosome. It is expressed ubiquitously and has been implicated in the splicing control of several pre-mRNAs. Moreover, hnRNP G may function as a regulator of transcription for SREBP-1c and GnRH1. Research has shown that hnRNP G may also act as a tumor-suppressor since it upregulates the Txnip gene and promotes the fidelity of DNA end-joining activity. In addition, hnRNP G appears to play a critical role in proper neural development of zebrafish and frog embryos. The family also includes several paralogs of hnRNP G, such as hRBMY and hnRNP G-T (also termed RNA-binding motif protein, X-linked-like-2). Both, hRBMY and hnRNP G-T, are exclusively expressed in testis and critical for male fertility. Like hnRNP G, hRBMY and hnRNP G-T interact with factors implicated in the regulation of pre-mRNA splicing, such as hTra2-beta1 and T-STAR. Although members in this family share a high conserved N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), they appear to recognize different RNA targets. For instance, hRBMY interacts specifically with a stem-loop structure in which the loop is formed by the sequence CA/UCAA. In contrast, hnRNP G associates with single stranded RNA sequences containing a CCA/C motif. In addition to the RRM, hnRNP G contains a nascent transcripts targeting domain (NTD) in the middle region and a novel auxiliary RNA-binding domain (RBD) in its C-terminal region. The C-terminal RBD exhibits distinct RNA binding specificity, and would play a critical role in the regulation of alternative splicing by hnRNP G. 80 matched cddid_all.tbl CDD cd12383 cd12383 409817 RRM_RBM42 RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins. This subfamily corresponds to the RRM of RBM42 which has been identified as a heterogeneous nuclear ribonucleoprotein K (hnRNP K)-binding protein. It also directly binds the 3' untranslated region of p21 mRNA that is one of the target mRNAs for hnRNP K. Both, hnRNP K and RBM42, are components of stress granules (SGs). Under nonstress conditions, RBM42 predominantly localizes within the nucleus and co-localizes with hnRNP K. Under stress conditions, hnRNP K and RBM42 form cytoplasmic foci where the SG marker TIAR localizes, and may play a role in the maintenance of cellular ATP level by protecting their target mRNAs. RBM42 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 83 matched cddid_all.tbl CDD cd12384 cd12384 409818 RRM_RBM24_RBM38_like RNA recognition motif (RRM) found in eukaryotic RNA-binding protein RBM24, RBM38 and similar proteins. This subfamily corresponds to the RRM of RBM24 and RBM38 from vertebrate, SUPpressor family member SUP-12 from Caenorhabditis elegans and similar proteins. Both, RBM24 and RBM38, are preferentially expressed in cardiac and skeletal muscle tissues. They regulate myogenic differentiation by controlling the cell cycle in a p21-dependent or -independent manner. RBM24, also termed RNA-binding region-containing protein 6, interacts with the 3'-untranslated region (UTR) of myogenin mRNA and regulates its stability in C2C12 cells. RBM38, also termed CLL-associated antigen KW-5, or HSRNASEB, or RNA-binding region-containing protein 1(RNPC1), or ssDNA-binding protein SEB4, is a direct target of the p53 family. It is required for maintaining the stability of the basal and stress-induced p21 mRNA by binding to their 3'-UTRs. It also binds the AU-/U-rich elements in p63 3'-UTR and regulates p63 mRNA stability and activity. SUP-12 is a novel tissue-specific splicing factor that controls muscle-specific splicing of the ADF/cofilin pre-mRNA in C. elegans. All family members contain a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 76 matched cddid_all.tbl CDD cd12385 cd12385 409819 RRM1_hnRNPM_like RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins. This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. 76 matched cddid_all.tbl CDD cd12386 cd12386 409820 RRM2_hnRNPM_like RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins. This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. 74 matched cddid_all.tbl CDD cd12387 cd12387 409821 RRM3_hnRNPM_like RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein M (hnRNP M) and similar proteins. This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein M (hnRNP M), myelin expression factor 2 (MEF-2 or MyEF-2 or MST156) and similar proteins. hnRNP M is pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). MEF-2 is a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 shows high sequence homology with hnRNP M. It also contains three RRMs, which may be responsible for its ssDNA binding activity. 71 matched cddid_all.tbl CDD cd12388 cd12388 409822 RRM1_RAVER RNA recognition motif 1 (RRM1) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins. This subfamily corresponds to the RRM1 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. 70 matched cddid_all.tbl CDD cd12389 cd12389 409823 RRM2_RAVER RNA recognition motif 2 (RRM2) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins. This subfamily corresponds to the RRM2 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. 77 matched cddid_all.tbl CDD cd12390 cd12390 409824 RRM3_RAVER RNA recognition motif 3 (RRM3) found in ribonucleoprotein PTB-binding raver-1, raver-2 and similar proteins. This subfamily corresponds to the RRM3 of raver-1 and raver-2. Raver-1 is a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-2 is a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It shows high sequence homology to raver-1. Raver-2 exerts a spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Both, raver-1 and raver-2, contain three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. They binds to RNA through the RRMs. In addition, the two [SG][IL]LGxxP motifs serve as the PTB-binding motifs in raver1. However, raver-2 interacts with PTB through the SLLGEPP motif only. 91 matched cddid_all.tbl CDD cd12391 cd12391 409825 RRM1_SART3 RNA recognition motif 1 (RRM1) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins. This subfamily corresponds to the RRM1 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 72 matched cddid_all.tbl CDD cd12392 cd12392 409826 RRM2_SART3 RNA recognition motif 2 (RRM2) found in squamous cell carcinoma antigen recognized by T-cells 3 (SART3) and similar proteins. This subfamily corresponds to the RRM2 of SART3, also termed Tat-interacting protein of 110 kDa (Tip110), is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver. It is involved in the regulation of mRNA splicing probably via its complex formation with RNA-binding protein with a serine-rich domain (RNPS1), a pre-mRNA-splicing factor. SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication. In addition, SART3 is required for U6 snRNP targeting to Cajal bodies. It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro. SART3 contains an N-terminal half-a-tetratricopeptide repeat (HAT)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 81 matched cddid_all.tbl CDD cd12393 cd12393 409827 RRM_ZCRB1 RNA recognition motif (RRM) found in Zinc finger CCHC-type and RNA-binding motif-containing protein 1 (ZCRB1) and similar proteins. This subfamily corresponds to the RRM of ZCRB1, also termed MADP-1, or U11/U12 small nuclear ribonucleoprotein 31 kDa protein (U11/U12 snRNP 31 or U11/U12-31K), a novel multi-functional nuclear factor, which may be involved in morphine dependence, cold/heat stress, and hepatocarcinoma. It is located in the nucleoplasm, but outside the nucleolus. ZCRB1 is one of the components of U11/U12 snRNPs that bind to U12-type pre-mRNAs and form a di-snRNP complex, simultaneously recognizing the 5' splice site and branchpoint sequence. ZCRB1 is characterized by an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCHC-type Zinc finger motif. In addition, it contains core nucleocapsid motifs, and Lys- and Glu-rich domains. 76 matched cddid_all.tbl CDD cd12394 cd12394 409828 RRM1_RBM34 RNA recognition motif 1 (RRM1) found in RNA-binding protein 34 (RBM34) and similar proteins. This subfamily corresponds to the RRM1 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. 91 matched cddid_all.tbl CDD cd12395 cd12395 409829 RRM2_RBM34 RNA recognition motif 2 (RRM2) found in RNA-binding protein 34 (RBM34) and similar proteins. This subfamily corresponds to the RRM2 of RBM34, a putative RNA-binding protein containing two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Although the function of RBM34 remains unclear currently, its RRM domains may participate in mRNA processing. RBM34 may act as an mRNA processing-related protein. 73 matched cddid_all.tbl CDD cd12396 cd12396 409830 RRM1_Nop13p_fungi RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 13 (Nop13p) and similar proteins. This subfamily corresponds to the RRM1 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 85 matched cddid_all.tbl CDD cd12397 cd12397 409831 RRM2_Nop13p_fungi RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 13 (Nop13p) and similar proteins. This subfamily corresponds to the RRM2 of Nop13p encoded by YNL175c from Saccharomyces cerevisiae. It shares high sequence similarity with nucleolar protein 12 (Nop12p). Both Nop12p and Nop13p are not essential for growth. However, unlike Nop12p that is localized to the nucleolus, Nop13p localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent. Nop13p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 76 matched cddid_all.tbl CDD cd12398 cd12398 409832 RRM_CSTF2_RNA15_like RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. This subfamily corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. The family also includes yeast ortholog mRNA 3'-end-processing protein RNA15 and similar proteins. RNA15 is a core subunit of cleavage factor IA (CFIA), an essential transcriptional 3'-end processing factor from Saccharomyces cerevisiae. RNA recognition by CFIA is mediated by an N-terminal RRM, which is contained in the RNA15 subunit of the complex. The RRM of RNA15 has a strong preference for GU-rich RNAs, mediated by a binding pocket that is entirely conserved in both yeast and vertebrate RNA15 orthologs. 77 matched cddid_all.tbl CDD cd12399 cd12399 409833 RRM_HP0827_like RNA recognition motif (RRM) found in Helicobacter pylori HP0827 protein and similar proteins. This subfamily corresponds to the RRM of H. pylori HP0827, a putative ssDNA-binding protein 12rnp2 precursor, containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The ssDNA binding may be important in activation of HP0827. 75 matched cddid_all.tbl CDD cd12400 cd12400 409834 RRM_Nop6 RNA recognition motif (RRM) found in Saccharomyces cerevisiae nucleolar protein 6 (Nop6) and similar proteins. This subfamily corresponds to the RRM of Nop6, also known as Ydl213c, a component of 90S pre-ribosomal particles in yeast S. cerevisiae. It is enriched in the nucleolus and is required for 40S ribosomal subunit biogenesis. Nop6 is a non-essential putative RNA-binding protein with two N-terminal putative nuclear localisation sequences (NLS-1 and NLS-2) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It binds to the pre-rRNA early during transcription and plays an essential role in pre-rRNA processing. 74 matched cddid_all.tbl CDD cd12401 cd12401 409835 RRM_eIF4H RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4H (eIF-4H) and similar proteins. This subfamily corresponds to the RRM of eIF-4H, also termed Williams-Beuren syndrome chromosomal region 1 protein, which, together with elf-4B/eIF-4G, serves as the accessory protein of RNA helicase eIF-4A. eIF-4H contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It stimulates protein synthesis by enhancing the helicase activity of eIF-4A in the initiation step of mRNA translation. 84 matched cddid_all.tbl CDD cd12402 cd12402 409836 RRM_eIF4B RNA recognition motif (RRM) found in eukaryotic translation initiation factor 4B (eIF-4B) and similar proteins. This subfamily corresponds to the RRM of eIF-4B, a multi-domain RNA-binding protein that has been primarily implicated in promoting the binding of 40S ribosomal subunits to mRNA during translation initiation. It contains two RNA-binding domains; the N-terminal well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), binds the 18S rRNA of the 40S ribosomal subunit and the C-terminal basic domain (BD), including two arginine-rich motifs (ARMs), binds mRNA during initiation, and is primarily responsible for the stimulation of the helicase activity of eIF-4A. eIF-4B also contains a DRYG domain (a region rich in Asp, Arg, Tyr, and Gly amino acids) in the middle, which is responsible for both, self-association of eIF-4B and binding to the p170 subunit of eIF3. Additional research indicates that eIF-4B can interact with the poly(A) binding protein (PABP) in mammalian cells, which can stimulate both, the eIF-4B-mediated activation of the helicase activity of eIF-4A and binding of poly(A) by PABP. eIF-4B has also been shown to interact specifically with the internal ribosome entry sites (IRES) of several picornaviruses which facilitate cap-independent translation initiation. 81 matched cddid_all.tbl CDD cd12403 cd12403 409837 RRM1_NCL RNA recognition motif 1 (RRM1) found in vertebrate nucleolin. This subfamily corresponds to the RRM1 of ubiquitously expressed protein nucleolin, also termed protein C23. Nucleolin is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. RRM1, together with RRM2, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. 75 matched cddid_all.tbl CDD cd12404 cd12404 409838 RRM2_NCL RNA recognition motif 2 (RRM2) found in vertebrate nucleolin. This subfamily corresponds to the RRM2 of ubiquitously expressed protein nucleolin, also termed protein C23, a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines.RRM2, together with RRM1, binds specifically to RNA stem-loops containing the sequence (U/G)CCCG(A/G) in the loop. 77 matched cddid_all.tbl CDD cd12405 cd12405 409839 RRM3_NCL RNA recognition motif 3 (RRM3) found in vertebrate nucleolin. This subfamily corresponds to the RRM3 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. 72 matched cddid_all.tbl CDD cd12406 cd12406 409840 RRM4_NCL RNA recognition motif 4 (RRM4) found in vertebrate nucleolin. This subfamily corresponds to the RRM4 of ubiquitously expressed protein nucleolin, also termed protein C23, is a multifunctional major nucleolar phosphoprotein that has been implicated in various metabolic processes, such as ribosome biogenesis, cytokinesis, nucleogenesis, cell proliferation and growth, cytoplasmic-nucleolar transport of ribosomal components, transcriptional repression, replication, signal transduction, inducing chromatin decondensation, etc. Nucleolin exhibits intrinsic self-cleaving, DNA helicase, RNA helicase and DNA-dependent ATPase activities. It can be phosphorylated by many protein kinases, such as the major mitotic kinase Cdc2, casein kinase 2 (CK2), and protein kinase C-zeta. Nucleolin shares similar domain architecture with gar2 from Schizosaccharomyces pombe and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of nucleolin is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of nucleolin contains four closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which suggests that nucleolin is potentially able to interact with multiple RNA targets. The C-terminal RGG (or GAR) domain of nucleolin is rich in glycine, arginine and phenylalanine residues, and contains high levels of NG,NG-dimethylarginines. 78 matched cddid_all.tbl CDD cd12407 cd12407 409841 RRM_FOX1_like RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar proteins. This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 76 matched cddid_all.tbl CDD cd12408 cd12408 409842 RRM_eIF3G_like RNA recognition motif (RRM) found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins. This subfamily corresponds to the RRM of eIF-3G and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3, a large multisubunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. eIF-3G is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). eIF-3G contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G, plays an important role in the initiation phase of protein synthesis in yeast. It binds both, mRNA and rRNA, fragments due to an RRM near its C-terminus. 76 matched cddid_all.tbl CDD cd12409 cd12409 409843 RRM1_RRT5 RNA recognition motif 1 (RRM1) found in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins. This subfamily corresponds to the RRM1 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 84 matched cddid_all.tbl CDD cd12410 cd12410 409844 RRM2_RRT5 RNA recognition motif 2 (RRM2) found in yeast regulator of rDNA transcription protein 5 (RRT5) and similar proteins. This subfamily corresponds to the RRM2 of the lineage specific family containing a group of uncharacterized yeast regulators of rDNA transcription protein 5 (RRT5), which may play roles in the modulation of rDNA transcription. RRT5 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 93 matched cddid_all.tbl CDD cd12411 cd12411 409845 RRM_ist3_like RNA recognition motif (RRM) found in ist3 family. This subfamily corresponds to the RRM of the ist3 family that includes fungal U2 small nuclear ribonucleoprotein (snRNP) component increased sodium tolerance protein 3 (ist3), X-linked 2 RNA-binding motif proteins (RBMX2) found in Metazoa and plants, and similar proteins. Gene IST3 encoding ist3, also termed U2 snRNP protein SNU17 (Snu17p), is a novel yeast Saccharomyces cerevisiae protein required for the first catalytic step of splicing and for progression of spliceosome assembly. It binds specifically to the U2 snRNP and is an intrinsic component of prespliceosomes and spliceosomes. Yeast ist3 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). In the yeast pre-mRNA retention and splicing complex, the atypical RRM of ist3 functions as a scaffold that organizes the other two constituents, Bud13p (bud site selection 13) and Pml1p (pre-mRNA leakage 1). Fission yeast Schizosaccharomyces pombe gene cwf29 encoding ist3, also termed cell cycle control protein cwf29, is an RNA-binding protein complexed with cdc5 protein 29. It also contains one RRM. The biological function of RBMX2 remains unclear. It shows high sequence similarity to yeast ist3 protein and harbors one RRM as well. 89 matched cddid_all.tbl CDD cd12412 cd12412 409846 RRM_DAZL_BOULE RNA recognition motif (RRM) found in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. This subfamily corresponds to the RRM domain of two Deleted in AZoospermia (DAZ) autosomal homologs, DAZL (DAZ-like) and BOULE. BOULE is the founder member of the family and DAZL arose from BOULE in an ancestor of vertebrates. The DAZ gene subsequently originated from a duplication transposition of the DAZL gene. Invertebrates contain a single DAZ homolog, BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. The family members encode closely related RNA-binding proteins that are required for fertility in numerous organisms. These proteins contain an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a varying number of copies of a DAZ motif, believed to mediate protein-protein interactions. DAZL and BOULE contain a single copy of the DAZ motif, while DAZ proteins can contain 8-24 copies of this repeat. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. 81 matched cddid_all.tbl CDD cd12413 cd12413 409847 RRM1_RBM28_like RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins. This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. 79 matched cddid_all.tbl CDD cd12414 cd12414 409848 RRM2_RBM28_like RNA recognition motif 2 (RRM2) found in RNA-binding protein 28 (RBM28) and similar proteins. This subfamily corresponds to the RRM2 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. 76 matched cddid_all.tbl CDD cd12415 cd12415 409849 RRM3_RBM28_like RNA recognition motif 3 (RRM3) found in RNA-binding protein 28 (RBM28) and similar proteins. This subfamily corresponds to the RRM3 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. 83 matched cddid_all.tbl CDD cd12416 cd12416 409850 RRM4_RBM28_like RNA recognition motif 4 (RRM4) found in RNA-binding protein 28 (RBM28) and similar proteins. This subfamily corresponds to the RRM4 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs. 98 matched cddid_all.tbl CDD cd12417 cd12417 409851 RRM_SAFB_like RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family. This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM. 74 matched cddid_all.tbl CDD cd12418 cd12418 409852 RRM_Aly_REF_like RNA recognition motif (RRM) found in the Aly/REF family. This subfamily corresponds to the RRM of Aly/REF family which includes THO complex subunit 4 (THOC4, also termed Aly/REF), S6K1 Aly/REF-like target (SKAR, also termed PDIP3 or PDIP46) and similar proteins. THOC4 is an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus, and was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid, and might be a novel transcription cofactor for erythroid-specific genes. SKAR shows high sequence homology with THOC4 and possesses one RRM as well. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. 75 matched cddid_all.tbl CDD cd12419 cd12419 409853 RRM_Ssp2_like RNA recognition motif (RRM) found in yeast sporulation-specific protein 2 (Ssp2) and similar protein. This subfamily corresponds to the RRM of the lineage specific yeast sporulation-specific protein 2 (Ssp2) and similar proteins. Ssp2 is encoded by a sporulation-specific gene necessary for outer spore wall assembly in the yeast Saccharomyces cerevisiae. It localizes to the spore wall and may play an important role after meiosis II and during spore wall formation. Ssp2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 85 matched cddid_all.tbl CDD cd12420 cd12420 409854 RRM_RBPMS_like RNA recognition motif (RRM) found in RNA-binding protein with multiple splicing (RBP-MS)-like proteins. This subfamily corresponds to the RRM of RNA-binding proteins with multiple splicing (RBP-MS)-like proteins, including protein products of RBPMS genes (RBP-MS and its paralogue RBP-MS2), the Drosophila couch potato (cpo), and Caenorhabditis elegans Mec-8 genes. RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. It has also been shown to physically interact with Smad2, Smad3 and Smad4, and stimulates Smad-mediated transactivation. Cpo may play an important role in regulating normal function of the nervous system, whereas mutations in Mec-8 affect mechanosensory and chemosensory neuronal function. All members contain a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Some uncharacterized family members contain two RRMs; this subfamily includes their RRM1. Their RRM2 shows high sequence homology to the RRM of yeast proteins scw1, Whi3, and Whi4. 76 matched cddid_all.tbl CDD cd12421 cd12421 409855 RRM1_PTBP1_hnRNPL_like RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins. This subfamily corresponds to the RRM1 of the majority of family members that include polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. In addition, this family also includes RNA-binding motif protein 20 (RBM20) that is an alternative splicing regulator associated with dilated cardiomyopathy (DCM) and contains only one RRM. 74 matched cddid_all.tbl CDD cd12422 cd12422 409856 RRM2_PTBP1_hnRNPL_like RNA recognition motif (RRM) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), and similar proteins. This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), polypyrimidine tract-binding protein homolog 3 (PTBPH3), polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2), and similar proteins, and RRM3 of PTBPH1 and PTBPH2. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. Rod1 is a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL protein plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. This family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to other family members, all of which contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although their biological roles remain unclear, both PTBPH1 and PTBPH2 show significant sequence similarity to PTB. However, in contrast to PTB, they have three RRMs. 85 matched cddid_all.tbl CDD cd12423 cd12423 409857 RRM3_PTBP1_like RNA recognition motif 3 (RRM3) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins. This subfamily corresponds to the RRM3 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 74 matched cddid_all.tbl CDD cd12424 cd12424 409858 RRM3_hnRNPL_like RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins. This subfamily corresponds to the RRM3 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The family also includes polypyrimidine tract binding protein homolog 3 (PTBPH3) found in plant. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RRMs. 74 matched cddid_all.tbl CDD cd12425 cd12425 409859 RRM4_PTBP1_like RNA recognition motif 4 (RRM4) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins. This subfamily corresponds to the RRM4 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 76 matched cddid_all.tbl CDD cd12426 cd12426 409860 RRM4_PTBPH3 RNA recognition motif 4 (RRM4) found in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3). This subfamily corresponds to the RRM4 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 79 matched cddid_all.tbl CDD cd12427 cd12427 409861 RRM4_hnRNPL_like RNA recognition motif 4 (RRM4) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins. This subfamily corresponds to the RRM4 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 84 matched cddid_all.tbl CDD cd12428 cd12428 409862 RRM_PARN RNA recognition motif (RRM) found in poly(A)-specific ribonuclease PARN and similar proteins. The subfamily corresponds to the RRM of PARN, also termed deadenylating nuclease, or deadenylation nuclease, or polyadenylate-specific ribonuclease, a processive poly(A)-specific 3'-exoribonuclease involved in the decay of eukaryotic mRNAs. It specifically binds both, the poly(A) tail at the 3' end and the 7-methylguanosine (m7G) cap located at the 5' end of eukaryotic mRNAs, and catalyzes the 3'- to 5'-end deadenylation of single-stranded mRNA with a free 3' hydroxyl group both in the nucleus and in the cytoplasm. PARN belongs to the DEDD superfamily of exonucleases. It contains a nuclease domain, an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and an R3H domain. PARN exists as a homodimer. The nuclease domain is involved in the dimerization. RRM and R3H domains are essential for the RNA-binding. 66 matched cddid_all.tbl CDD cd12429 cd12429 409863 RRM_DNAJC17 RNA recognition motif (RRM) found in the DnaJ homolog subfamily C member 17. The CD corresponds to the RRM of some eukaryotic DnaJ homolog subfamily C member 17 and similar proteins. DnaJ/Hsp40 (heat shock protein 40) proteins are highly conserved and play crucial roles in protein translation, folding, unfolding, translocation, and degradation. They act primarily by stimulating the ATPase activity of Hsp70s, an important chaperonine family. Members in this family contains an N-terminal DnaJ domain or J-domain, which mediates the interaction with Hsp70. They also contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the C-terminus, which may play an essential role in RNA binding. 74 matched cddid_all.tbl CDD cd12430 cd12430 409864 RRM_LARP4_5_like RNA recognition motif (RRM) found in La-related protein 4 (LARP4), La-related protein 5 (LARP5 or LARP4B) and similar proteins. This subfamily corresponds to the RRM of LARP4 and LARP5. LARP4 is a cytoplasmic factor that can bind poly(A) RNA and interact with poly(A) binding protein (PABP). It may play a role in promoting translation by stabilizing mRNA. LARP5 is a cytosolic protein that co-sediments with polysomes and accumulates upon stress induction in cellular stress granules. It can interact with the cytosolic poly(A) binding protein 1 (PABPC1) and the receptor for activated C Kinase (RACK1), a component of the 40S ribosomal subunit. LARP5 may function as a stimulatory factor of translation through bridging mRNA factors of the 3' end with initiating ribosomes. Both, LARP4 and LARP5, are structurally related to the La autoantigen. Like other La-related proteins (LARPs) family members, LARP4 and LARP5 contain a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 76 matched cddid_all.tbl CDD cd12431 cd12431 409865 RRM_ALKBH8 RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins. This subfamily corresponds to the RRM of ALKBH8, also termed alpha-ketoglutarate-dependent dioxygenase ABH8, or S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8, expressed in various types of human cancers. It is essential in urothelial carcinoma cell survival mediated by NOX-1-dependent ROS signals. ALKBH8 has also been identified as a tRNA methyltransferase that catalyzes methylation of tRNA to yield 5-methylcarboxymethyl uridine (mcm5U) at the wobble position of the anticodon loop. Thus, ALKBH8 plays a crucial role in the DNA damage survival pathway through a distinct mechanism involving the regulation of tRNA modification. ALKBH8 localizes to the cytoplasm. It contains the characteristic AlkB domain that is composed of a tRNA methyltransferase motif, a motif homologous to the bacterial AlkB DNA/RNA repair enzyme, and a dioxygenase catalytic core domain encompassing cofactor-binding sites for iron and 2-oxoglutarate. In addition, unlike other AlkB homologs, ALKBH8 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal S-adenosylmethionine (SAM)-dependent methyltransferase (MT) domain. 80 matched cddid_all.tbl CDD cd12432 cd12432 409866 RRM_ACINU RNA recognition motif (RRM) found in apoptotic chromatin condensation inducer in the nucleus (acinus) and similar proteins. This subfamily corresponds to the RRM of Acinus, a caspase-3-activated nuclear factor that induces apoptotic chromatin condensation after cleavage by caspase-3 without inducing DNA fragmentation. It is essential for apoptotic chromatin condensation and may also participate in nuclear structural changes occurring in normal cells. Acinus contains a P-loop motif and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which indicates Acinus might have ATPase and DNA/RNA-binding activity. 90 matched cddid_all.tbl CDD cd12433 cd12433 409867 RRM_Yme2p_like RNA recognition motif (RRM) found in yeast mitochondrial escape protein 2 (Yme2p) and similar proteins. This subfamily corresponds to the RRM of Yme2p, also termed protein RNA12, an inner mitochondrial membrane protein that plays a critical role in mitochondrial DNA transactions. It may serve as a mediator of nucleoid structure and number in mitochondria of the yeast Saccharomyces cerevisiae. Yme2p contains an exonuclease domain, an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal domain. 86 matched cddid_all.tbl CDD cd12434 cd12434 409868 RRM_RCAN_like RNA recognition motif (RRM) found in regulators of calcineurin (RCANs) and similar proteins. This subfamily corresponds to the RRM of RCANs, a novel family of calcineurin regulators that are key factors contributing to Down syndrome in humans. They can stimulate and inhibit the Ca2+/calmodulin-dependent phosphatase calcineurin (also termed PP2B or PP3C) signaling in vivo through direct interactions with its catalytic subunit. Overexpressed RCANs may bind and inhibit calcineurin. In contrast, low levels of phosphorylated RCANs may stimulate the calcineurin signaling. RCANs are characterized by harboring a central short, unique serine-proline motif containing FLIISPPxSPP box, which is strongly conserved from yeast to human but is absent in bacteria. They consist of an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a highly conserved SP repeat domain containing the phosphorylation site by GSK-3, a well-known PxIxIT motif responsible for docking many substrates to calcineurin, and an unrecognized C-terminal TxxP motif of unknown function. 75 matched cddid_all.tbl CDD cd12435 cd12435 409869 RRM_GW182_like RNA recognition motif (RRM) found in the GW182 family proteins. This subfamily corresponds to the RRM of the GW182 family which includes three paralogs of TNRC6 (GW182-related) proteins comprising GW182/TNGW1, TNRC6B (containing three isoforms) and TNRC6C in mammal, a single Drosophila ortholog (dGW182, also called Gawky) and two Caenorhabditis elegans orthologs AIN-1 and AIN-2, which contain multiple miRNA-binding sites and have important functions in miRNA-mediated translational repression, as well as mRNA degradation in Metazoa. The GW182 family proteins directly interact with Argonaute (Ago) proteins, and thus function as downstream effectors in the miRNA pathway, responsible for inhibition of translation and acceleration of mRNA decay. Members in this family are characterized by an abnormally high content of glycine/tryptophan (G/W) repeats, one or more glutamine (Q)-rich motifs, and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The only exception is the worm protein that does not contain a recognizable RRM domain. The GW182 family proteins are recruited to miRNA targets through an interaction between their N-terminal domain and an Argonaute protein. Then they promote translational repression and/or degradation of miRNA targets through their C-terminal silencing domain. 71 matched cddid_all.tbl CDD cd12436 cd12436 409870 RRM1_2_MATR3_like RNA recognition motif 1 (RRM1) and 2 (RRM2) found in the matrin 3 family of nuclear proteins. This subfamily corresponds to the RRM of the matrin 3 family of nuclear proteins consisting of Matrin 3 (MATR3), nuclear protein 220 (NP220) and similar proteins. MATR3 is a highly conserved inner nuclear matrix protein that has been implicated in various biological processes. NP220 is a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). Both, Matrin 3 and NP220, contain two RNA recognition motif (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Cys2-His2 zinc finger-like motif at the C-terminal region. 76 matched cddid_all.tbl CDD cd12437 cd12437 409871 RRM_BRAP2_like RNA recognition motif (RRM) found in BRCA1-associated protein (BRAP2) and similar proteins. This subfamily corresponds to the RRM domain of BRAP2, also termed impedes mitogenic signal propagation (IMP), or ring finger protein 52, or renal carcinoma antigen NY-REN-63, a novel cytoplasmic protein interacting with the two functional nuclear localisation signal (NLS) motifs of BRCA1, a nuclear protein linked to breast cancer. It also binds to the SV40 large T antigen NLS motif and the bipartite NLS motif found in mitosin. BRAP2 may serve as a cytoplasmic retention protein and play a role in the regulation of nuclear protein transport. The family also includes RING finger protein ETP1 and its homologs found in fungi. ETP1, also termed BRAP2 homolog, or ethanol tolerance protein 1, is the yeast homolog of BRCA1-associated protein (BRAP2) found in vertebrates. It may be involved in ethanol and salt-induced transcriptional activation of the NHA1 promoter and heat shock protein genes (HSP12 and HSP26), and participate in ethanol-induced turnover of the low-affinity hexose transporter Hxt3p. Members in this family contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C3HC4-type ring finger domain and a UBP-type zinc finger. 82 matched cddid_all.tbl CDD cd12438 cd12438 409872 RRM_CNOT4 RNA recognition motif (RRM) found in Eukaryotic CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins. This subfamily corresponds to the RRM of NOT4, also termed CCR4-associated factor 4, or E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4Hp, a component of the CCR4-NOT complex, a global negative regulator of RNA polymerase II transcription. NOT4 functions as an ubiquitin-protein ligase (E3). It contains an N-terminal C4C4 type RING finger motif, followed by a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The RING fingers may interact with a subset of ubiquitin-conjugating enzymes (E2s), including UbcH5B, and mediate protein-protein interactions. T 98 matched cddid_all.tbl CDD cd12439 cd12439 409873 RRM_TRMT2A RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins. This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases. 79 matched cddid_all.tbl CDD cd12440 cd12440 409874 RRM_SYNJ RNA recognition motif (RRM) found in synaptojanin-1, synaptojanin-2 and similar proteins. This subfamily corresponds to the RRM of two active phosphatidylinositol phosphate phosphatases, synaptojanin-1 and synaptojanin-2. They have different interaction partners and are likely to have different biological functions. Synaptojanin-1 was originally identified as one of the major Grb2-binding proteins that may participate in synaptic vesicle endocytosis. It also acts as a Src homology 3 (SH3) domain-binding brain-specific inositol 5-phosphatase with a putative role in clathrin-mediated endocytosis. Synaptojanin-2 is a ubiquitously expressed homolog of synaptojanin-1. It is a novel Rac1 effector regulating the early step of clathrin-mediated endocytosis. Synaptojanin-2 directly and specifically interacts with Rac1 in a GTP-dependent manner. It mediates the inhibitory effect of Rac1 on endocytosis and plays an important role in the Rac1-mediated control of cell growth. Both, synaptojanin-1 and synaptojanin-2, have two tissue-specific alternative splicing isoforms, a shorter isoform expressed in brain and a longer isoform in peripheral tissues. Synaptojanin-1 contains an N-terminal domain homologous to the cytoplasmic portion of the yeast protein Sac1p, a central inositol 5-phosphatase domain followed by a putative RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal proline-rich region mediating the binding of synaptojanin-1 to various SH3 domain-containing proteins including amphiphysin, SH3p4, SH3p8, SH3p13, and Grb2. Synaptojanin-2 shows high sequence homology to the N-terminal Sac1p homology domain, the central inositol 5-phosphatase domain, the putative RNA recognition motif (RRM) of synaptojanin-1, but differs in the proline-rich region. 77 matched cddid_all.tbl CDD cd12441 cd12441 409875 RRM_Nup53_like RNA recognition motif (RRM) found in nucleoporin Nup53 and similar proteins. This subfamily corresponds to the RRM domain of nucleoporin Nup53, also termed mitotic phosphoprotein 44 (MP-44), or nuclear pore complex protein Nup53, required for normal cell growth and nuclear morphology in vertebrate. It tightly associates with the nuclear envelope membrane and the nuclear lamina where it interacts with lamin B. It may also interact with a group of nucleoporins including Nup93, Nup155, and Nup205 and play a role in the association of the mitotic checkpoint protein Mad1 with the nuclear pore complex (NPC). The family also includes Saccharomyces cerevisiae Nup53p, an ortholog of vertebrate nucleoporin Nup53. A unique property of yeast Nup53p is that it contains an additional Kap121p-binding domain and interacts specifically with the karyopherin Kap121p, which is involved in the assembly of Nup53p into NPCs. Both, vertebrate Nup35 and yeast Nup53p, contain an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a C-terminal amphipathic alpha-helix and several FG repeats. This family corresponds to the RRM domain which lacks the conserved residues that typically bind RNA in canonical RRM domains. 73 matched cddid_all.tbl CDD cd12442 cd12442 409876 RRM_RBM48 RNA recognition motif (RRM) found in RNA-binding protein 48 (RBM48) and similar proteins. This subfamily corresponds to the RRM of RBM48, a putative RNA-binding protein of unknown function. It contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 100 matched cddid_all.tbl CDD cd12443 cd12443 409877 RRM_MCM3A_like RNA recognition motif (RRM) found in 80 kDa MCM3-associated protein (Map80) and similar proteins. This subfamily corresponds to the RRM of Map80, also termed germinal center-associated nuclear protein (GANP), involved in the nuclear localization pathway of MCM3, a protein necessary for the initiation of DNA replication and also involves in controls that ensure DNA replication is initiated once per cell cycle. Map80 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 75 matched cddid_all.tbl CDD cd12444 cd12444 409878 RRM1_CPEBs RNA recognition motif 1 (RRM1) found in cytoplasmic polyadenylation element-binding protein CPEB-1, CPEB-2, CPEB-3, CPEB-4 and similar protiens. This subfamily corresponds to the RRM1 of the CPEB family of proteins that bind to defined groups of mRNAs and act as either translational repressors or activators to regulate their translation. CPEB proteins are well conserved in both, vertebrates and invertebrates. Based on sequence similarity, RNA-binding specificity, and functional regulation of translation, the CPEB proteins have been classified into two subfamilies. The first subfamily includes CPEB-1 and related proteins. CPEB-1 is an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bind to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. The second subfamily includes CPEB-2, CPEB-3, CPEB-4, and related protiens. Due to high sequence similarity, members in this subfamily may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. CPEB-2 impedes target RNA translation at elongation; it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All CPEB proteins are nucleus-cytoplasm shuttling proteins. They contain an N-terminal unstructured region, followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. CPEB-2, -3, and -4 have conserved nuclear export signals that are not present in CPEB-1. 95 matched cddid_all.tbl CDD cd12445 cd12445 409879 RRM2_CPEBs RNA recognition motif 2 (RRM2) found in cytoplasmic polyadenylation element-binding protein CPEB-1, CPEB-2, CPEB-3, CPEB-4 and similar protiens. This subfamily corresponds to the RRM2 of CPEB family of proteins that bind to defined groups of mRNAs and act as either translational repressors or activators to regulate their translation. CPEB proteins are well conserved in both, vertebrates and invertebrates. Based on sequence similarity, RNA-binding specificity, and functional regulation of translation, the CPEB proteins has been classified into two subfamilies. The first subfamily includes CPEB-1 and related proteins. CPEB-1 is an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bound to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. The second subfamily includes CPEB-2, CPEB-3, CPEB-4, and related protiens. Due to the high sequence similarity, members in this subfamily may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. Moreover, CPEB-2 impedes target RNA translation at elongation. It directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All CPEB proteins are nucleus-cytoplasm shuttling proteins. They contain an N-terminal unstructured region, followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. CPEB-2, -3, and -4 have conserved nuclear export signals that are not present in CPEB-1. 81 matched cddid_all.tbl CDD cd12446 cd12446 409880 RRM_RBM25 RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 25 and similar proteins. This subfamily corresponds to the RRM of RBM25, also termed Arg/Glu/Asp-rich protein of 120 kDa (RED120), or protein S164, or RNA-binding region-containing protein 7, an evolutionary-conserved splicing coactivator SRm160 (SR-related nuclear matrix protein of 160 kDa, )-interacting protein. RBM25 belongs to a family of RNA-binding proteins containing a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminus, a RE/RD-rich (ER) central region, and a C-terminal proline-tryptophan-isoleucine (PWI) motif. It localizes to the nuclear speckles and associates with multiple splicing components, including splicing cofactors SRm160/300, U snRNAs, assembled splicing complexes, and spliced mRNAs. It may play an important role in pre-mRNA processing by coupling splicing with mRNA 3'-end formation. Additional research indicates that RBM25 is one of the RNA-binding regulators that direct the alternative splicing of apoptotic factors. It can activate proapoptotic Bcl-xS 5'ss by binding to the exonic splicing enhancer, CGGGCA, and stabilize the pre-mRNA-U1 snRNP through interaction with hLuc7A, a U1 snRNP-associated factor. 83 matched cddid_all.tbl CDD cd12447 cd12447 409881 RRM1_gar2 RNA recognition motif 1 (RRM1) found in yeast protein gar2 and similar proteins. This subfamily corresponds to the RRM1 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. 76 matched cddid_all.tbl CDD cd12448 cd12448 409882 RRM2_gar2 RNA recognition motif 2 (RRM2) found in yeast protein gar2 and similar proteins. This subfamily corresponds to the RRM2 of yeast protein gar2, a novel nucleolar protein required for 18S rRNA and 40S ribosomal subunit accumulation. It shares similar domain architecture with nucleolin from vertebrates and NSR1 from Saccharomyces cerevisiae. The highly phosphorylated N-terminal domain of gar2 is made up of highly acidic regions separated from each other by basic sequences, and contains multiple phosphorylation sites. The central domain of gar2 contains two closely adjacent N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RGG (or GAR) domain of gar2 is rich in glycine, arginine and phenylalanine residues. 73 matched cddid_all.tbl CDD cd12449 cd12449 409883 RRM_CIRBP_RBM3 RNA recognition motif (RRM) found in cold inducible RNA binding protein (CIRBP), RNA binding motif protein 3 (RBM3) and similar proteins. This subfamily corresponds to the RRM domain of two structurally related heterogenous nuclear ribonucleoproteins, CIRBP (also termed CIRP or A18 hnRNP) and RBM3 (also termed RNPL), both of which belong to a highly conserved cold shock proteins family. The cold shock proteins can be induced after exposure to a moderate cold-shock and other cellular stresses such as UV radiation and hypoxia. CIRBP and RBM3 may function in posttranscriptional regulation of gene expression by binding to different transcripts, thus allowing the cell to response rapidly to environmental signals. However, the kinetics and degree of cold induction are different between CIRBP and RBM3. Tissue distribution of their expression is different. CIRBP and RBM3 may be differentially regulated under physiological and stress conditions and may play distinct roles in cold responses of cells. CIRBP, also termed glycine-rich RNA-binding protein CIRP, is localized in the nucleus and mediates the cold-induced suppression of cell cycle progression. CIRBP also binds DNA and possibly serves as a chaperone that assists in the folding/unfolding, assembly/disassembly and transport of various proteins. RBM3 may enhance global protein synthesis and the formation of active polysomes while reducing the levels of ribonucleoprotein complexes containing microRNAs. RBM3 may also serve to prevent the loss of muscle mass by its ability to decrease cell death. Furthermore, RBM3 may be essential for cell proliferation and mitosis. Both, CIRBP and RBM3, contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), that is involved in RNA binding, and C-terminal glycine-rich domain (RGG motif) that probably enhances RNA-binding via protein-protein and/or protein-RNA interactions. Like CIRBP, RBM3 can also bind to both RNA and DNA via its RRM domain. 80 matched cddid_all.tbl CDD cd12450 cd12450 409884 RRM1_NUCLs RNA recognition motif 1 (RRM1) found in nucleolin-like proteins mainly from plants. This subfamily corresponds to the RRM1 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 78 matched cddid_all.tbl CDD cd12451 cd12451 409885 RRM2_NUCLs RNA recognition motif 2 (RRM2) found in nucleolin-like proteins mainly from plants. This subfamily corresponds to the RRM2 of a group of plant nucleolin-like proteins, including nucleolin 1 (also termed protein nucleolin like 1) and nucleolin 2 (also termed protein nucleolin like 2, or protein parallel like 1). They play roles in the regulation of ribosome synthesis and in the growth and development of plants. Like yeast nucleolin, nucleolin-like proteins possess two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 79 matched cddid_all.tbl CDD cd12452 cd12452 409886 RRM_ARP_like RNA recognition motif (RRM) found in yeast asparagine-rich protein (ARP) and similar proteins. This subfamily corresponds to the RRM of ARP, also termed NRP1, encoded by Saccharomyces cerevisiae YDL167C. Although its exact biological function remains unclear, ARP contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), two Ran-binding protein zinc fingers (zf-RanBP), and an asparagine-rich region. It may possess RNA-binding and zinc ion binding activities. Additional research had indicated that ARP may function as a factor involved in the stress response. 83 matched cddid_all.tbl CDD cd12453 cd12453 409887 RRM1_RIM4_like RNA recognition motif 1 (RRM1) found in yeast meiotic activator RIM4 and similar proteins. This subfamily corresponds to the RRM1 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. 86 matched cddid_all.tbl CDD cd12454 cd12454 409888 RRM2_RIM4_like RNA recognition motif 2 (RRM2) found in yeast meiotic activator RIM4 and similar proteins. This subfamily corresponds to the RRM2 of RIM4, also termed regulator of IME2 protein 4, a putative RNA binding protein that is expressed at elevated levels early in meiosis. It functions as a meiotic activator required for both the IME1- and IME2-dependent pathways of meiotic gene expression, as well as early events of meiosis, such as meiotic division and recombination, in Saccharomyces cerevisiae. RIM4 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes a putative RNA-binding protein termed multicopy suppressor of sporulation protein Msa1. It is a putative RNA-binding protein encoded by a novel gene, msa1, from the fission yeast Schizosaccharomyces pombe. Msa1 may be involved in the inhibition of sexual differentiation by controlling the expression of Ste11-regulated genes, possibly through the pheromone-signaling pathway. Like RIM4, Msa1 also contains two RRMs, both of which are essential for the function of Msa1. 80 matched cddid_all.tbl CDD cd12455 cd12455 409889 RRM_like_Smg4_UPF3 RNA recognition motif (RRM)-like Smg4_UPF3 domain in yeast up-frameshift suppressor 3 (Upf3p), Caenorhabditis elegans SMG-4, their human orthologs Upf3A and Upf3B, and similar proteins. This subfamily corresponds to the RRM-like Smg4_UPF3 domain found in yeast up-frameshift suppressor 3 (Upf3p), Caenorhabditis elegans SMG-4, their human orthologs Upf3A and Upf3B, and similar proteins. Upf3p, also termed nonsense-mediated mRNA decay protein 3, or Sua6p, a surveillance factor encoded by UPF3 gene from Saccharomyces cerevisiae. It is required for nonsense-mediated mRNA decay (NMD) in yeast. Upf3p is primarily cytoplasmic but accumulates inside the nucleus. Its nuclear import is mediated by the Srp1p (importin-alpha)/beta heterodimer while its nuclear export is mediated by a leucine-rich nuclear export sequence (NES-A), but not the Crm1p exportin. C. elegans SMG-4 is a nuclear shuttling protein that shuttles between the cytoplasm and nucleus through nuclear import and export signals similar to that of the yeast Upf3p. It is regulated by phosphorylation. Human orthologs of yeast Upf3p and C. elegans SMG-4 include Upf3A and Upf3B, which derive from two genes, UPF3A and X-linked UPF3B, respectively. Both, Upf3A (Up-frameshift suppressor 3 homolog A, also termed regulator of nonsense transcripts 3A, or nonsense mRNA reducing factor 3A) and Upf3B (Up-frameshift suppressor 3 homolog B on chromosome X, also termed regulator of nonsense transcripts 3B, or nonsense mRNA reducing factor 3B), are nucleocytoplasmic shuttling proteins. They associate selectively with spliced beta-globin mRNA in vivo, and tethering of any human Upf protein to the 3'UTR of beta-globin mRNA prevents NMD. The function of the Upf proteins in identifying and targeting nonsense mRNAs for rapid decay is conserved among eukaryotes. Besides, all Upf proteins in this family contain a conserved Smg4_UPF3 domain with some similarity to an RNA recognition motif (RRM), indicating that they may be RNA binding proteins. 88 matched cddid_all.tbl CDD cd12456 cd12456 240902 RRM_p65 RNA recognition motif (RRM) found in the holoenzyme La family protein p65. This subfamily corresponds to the RRM of a lineage specific family containing the essential La family protein p65 found in Tetrahymena thermophila. It is a telomerase holoenzyme protein necessary for telomerase RNA (TER) accumulation in vivo. p65, together with TER and telomerase reverse transcriptase (TERT), comprise a ternary catalytic core complex of Tetrahymena telomerase, which is a ribonucleoprotein complex essential for maintenance of telomere DNA at linear chromosome ends. p65 harbors a cryptic, atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which displays high structural homology to the RRM in genuine La and LARP7 proteins. 76 matched cddid_all.tbl CDD cd12457 cd12457 409890 RRM_XMAS2 RNA recognition motif (RRM) found in X-linked male sterile 2 (Xmas-2) and similar proteins. This subfamily corresponds to the RRM in Xmas-2, the Drosophila homolog of yeast Sac3p protein, together with E(y)2, the Drosophila homologue of yeast Sus1p protein, forming an endogenous complex that is required in the regulation of mRNA transport and also involved in the efficient transcription regulation of the heat-shock protein 70 (hsp70) loci. All family members are found in insects and contain an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a PCI domain. 71 matched cddid_all.tbl CDD cd12458 cd12458 409891 RRM_AtC3H46_like RNA recognition motif (RRM) found in Arabidopsis thaliana zinc finger CCCH domain-containing protein 46 (AtC3H46) and similar proteins. This subfamily corresponds to the RRM domain in AtC3H46, a putative RNA-binding protein that contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a CCCH class of zinc finger, typically C-X8-C-X5-C-X3-H. It may possess ribonuclease activity. 70 matched cddid_all.tbl CDD cd12459 cd12459 409892 RRM1_CID8_like RNA recognition motif 1 (RRM1) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins. This subgroup corresponds to the RRM1 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. 80 matched cddid_all.tbl CDD cd12460 cd12460 409893 RRM2_CID8_like RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana CTC-interacting domain protein CID8, CID9, CID10, CID11, CID12, CID 13 and similar proteins. This subgroup corresponds to the RRM2 domains found in A. thaliana CID8, CID9, CID10, CID11, CID12, CID 13 and mainly their plant homologs. These highly related RNA-binding proteins contain an N-terminal PAM2 domain (PABP-interacting motif 2), two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a basic region that resembles a bipartite nuclear localization signal. The biological role of this family remains unclear. 82 matched cddid_all.tbl CDD cd12461 cd12461 409894 RRM_SCAF4 RNA recognition motif (RRM) found in SR-related and CTD-associated factor 4 (SCAF4) and similar proteins. The CD corresponds to the RRM of SCAF4 (also termed splicing factor, arginine/serine-rich 15 or SFR15, or CTD-binding SR-like protein RA4) that belongs to a new class of SCAFs (SR-like CTD-associated factors). Although its biological function remains unclear, SCAF4 shows high sequence similarity to SCAF8 that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II) and may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF4 and SCAF8 both contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs. 81 matched cddid_all.tbl CDD cd12462 cd12462 409895 RRM_SCAF8 RNA recognition motif (RRM) found in SR-related and CTD-associated factor 8 (SCAF8) and similar proteins. This subgroup corresponds to the RRM of SCAF8 (also termed CDC5L complex-associated protein 7, or RNA-binding motif protein 16, or CTD-binding SR-like protein RA8), a nuclear matrix protein that interacts specifically with a highly serine-phosphorylated form of the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II (pol II). The pol II CTD plays a role in coupling transcription and pre-mRNA processing. SCAF8 co-localizes primarily with transcription sites that are enriched in nuclear matrix fraction, which is known to contain proteins involved in pre-mRNA processing. Thus, SCAF8 may play a direct role in coupling with both, transcription and pre-mRNA processing, processes. SCAF8, together with SCAF4, represents a new class of SCAFs (SR-like CTD-associated factors). They contain a conserved N-terminal CTD-interacting domain (CID), an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and serine/arginine-rich motifs. 79 matched cddid_all.tbl CDD cd12463 cd12463 409896 RRM_G3BP1 RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein 1 (G3BP1) and similar proteins. This subgroup corresponds to the RRM of G3BP1, also termed ATP-dependent DNA helicase VIII (DH VIII), or GAP SH3 domain-binding protein 1, which has been identified as a phosphorylation-dependent endoribonuclease that interacts with the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity. The acidic RasGAP binding domain of G3BP1 harbors an arsenite-regulated phosphorylation site and dominantly inhibits stress granule (SG) formation. G3BP1 also contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). The RRM domain and RGG-rich region are canonically associated with RNA binding. G3BP1 co-immunoprecipitates with mRNAs. It binds to and cleaves the 3'-untranslated region (3'-UTR) of the c-myc mRNA in a phosphorylation-dependent manner. Thus, G3BP1 may play a role in coupling extra-cellular stimuli to mRNA stability. It has been shown that G3BP1 is a novel Dishevelled-associated protein that is methylated upon Wnt3a stimulation and that arginine methylation of G3BP1 regulates both Ctnnb1 mRNA and canonical Wnt/beta-catenin signaling. Furthermore, G3BP1 can be associated with the 3'-UTR of beta-F1 mRNA in cytoplasmic RNA-granules, demonstrating that G3BP1 may specifically repress the translation of the transcript. 80 matched cddid_all.tbl CDD cd12464 cd12464 409897 RRM_G3BP2 RNA recognition motif (RRM) found in ras GTPase-activating protein-binding protein 2 (G3BP2) and similar proteins. This subgroup corresponds to the RRM of G3BP2, also termed GAP SH3 domain-binding protein 2, a cytoplasmic protein that interacts with both IkappaBalpha and IkappaBalpha/NF-kappaB complexes, indicating that G3BP2 may play a role in the control of nucleocytoplasmic distribution of IkappaBalpha and cytoplasmic anchoring of the IkappaBalpha/NF-kappaB complex. G3BP2 contains an N-terminal nuclear transfer factor 2 (NTF2)-like domain, an acidic domain, a domain containing five PXXP motifs, an RNA recognition motif (RRM domain), and an Arg-Gly-rich region (RGG-rich region, or arginine methylation motif). It binds to the SH3 domain of RasGAP, a multi-functional protein controlling Ras activity, through its N-terminal NTF2-like domain. The acidic domain is sufficient for the interaction of G3BP2 with the IkappaBalpha cytoplasmic retention sequence. Furthermore, G3BP2 might influence stability or translational efficiency of particular mRNAs by binding to RNA-containing structures within the cytoplasm through its RNA-binding domain. 83 matched cddid_all.tbl CDD cd12465 cd12465 409898 RRM_UHMK1 RNA recognition motif (RRM) found in U2AF homology motif kinase 1 (UHMK1) and similar proteins. This subgroup corresponds to the RRM of UHMK1. UHMK1, also termed kinase interacting with stathmin (KIS) or P-CIP2, is a serine/threonine protein kinase functionally related to RNA metabolism and neurite outgrowth. It contains an N-terminal kinase domain and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), with high homology to the corresponding motif of the mammalian U2 small nuclear ribonucleoprotein auxiliary factor U2AF 65 kDa subunit (U2AF65 or U2AF2). UHMK1 targets two key regulators of cell proliferation and migration, the cyclin-dependent kinase (CDK) inhibitor p27Kip1 and the microtubule-destabilizing protein stathmin. It plays a critical role during vascular wound repair by preventing excessive vascular smooth muscle cell (VSMC) migration into the vascular lesion. Moreover, UHMK1 may control cell migration and neurite outgrowth by interacting with and phosphorylating the splicing factor SF1, thereby probably contributing to the control of protein expression. Furthermore, UHMK1 may be functionally related to microtubule dynamics and axon development. It localizes to RNA granules, interacts with three proteins found in RNA granules (KIF3A, NonO, and eEF1A), and further enhances the local translation. UHMK1 is highly expressed in regions of the brain implicated in schizophrenia and may play a role in susceptibility to schizophrenia. 88 matched cddid_all.tbl CDD cd12466 cd12466 409899 RRM2_AtRSp31_like RNA recognition motif 2 (RRM2) found in Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins from plants. This subgroup corresponds to the RRM2 in a family that represents a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at their N-terminus, and an RS domain at their C-terminus. 70 matched cddid_all.tbl CDD cd12467 cd12467 240913 RRM_Srp1p_like RNA recognition motif 1 (RRM1) found in fission yeast pre-mRNA-splicing factor Srp1p and similar proteins. This subgroup corresponds to the RRM domain in Srp1p encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but not essential for growth. Srp1p is closely related to the SR protein family found in metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. Some family members also contain another RRM domain. 78 matched cddid_all.tbl CDD cd12470 cd12470 409900 RRM1_MSSP1 RNA recognition motif 1 (RRM1) found in vertebrate single-stranded DNA-binding protein MSSP-1. This subgroup corresponds to the RRM1 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. 86 matched cddid_all.tbl CDD cd12471 cd12471 409901 RRM1_MSSP2 RNA recognition motif 1 (RRM1) found in vertebrate single-stranded DNA-binding protein MSSP-2. This subgroup corresponds to the RRM1 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3), a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. 84 matched cddid_all.tbl CDD cd12472 cd12472 409902 RRM1_RBMS3 RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3). This subgroup corresponds to the RRM1 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. 80 matched cddid_all.tbl CDD cd12473 cd12473 409903 RRM2_MSSP1 RNA recognition motif 2 (RRM2) found in vertebrate single-stranded DNA-binding protein MSSP-1. This subgroup corresponds to the RRM2 of MSSP-1, also termed RNA-binding motif, single-stranded-interacting protein 1 (RBMS1), or suppressor of CDC2 with RNA-binding motif 2 (SCR2). MSSP-1 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence CT(A/T)(A/T)T, and stimulates DNA replication in the system using SV40 DNA. MSSP-1 is identical with Scr2, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-1 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with c-MYC, the product of protooncogene c-myc. MSSP-1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. 85 matched cddid_all.tbl CDD cd12474 cd12474 409904 RRM2_MSSP2 RNA recognition motif 2 (RRM2) found in vertebrate single-stranded DNA-binding protein MSSP-2. This subgroup corresponds to the RRM2 of MSSP-2, also termed RNA-binding motif, single-stranded-interacting protein 2 (RBMS2), or suppressor of CDC2 with RNA-binding motif 3 (SCR3). MSSP-2 is a double- and single-stranded DNA binding protein that belongs to the c-myc single-strand binding proteins (MSSP) family. It specifically recognizes the sequence T(C/A)TT, and stimulates DNA replication in the system using SV40 DNA. MSSP-2 is identical with Scr3, a human protein which complements the defect of cdc2 kinase in Schizosaccharomyces pombe. MSSP-2 has been implied in regulating DNA replication, transcription, apoptosis induction, and cell-cycle movement, via the interaction with C-MYC, the product of protooncogene c-myc. MSSP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), both of which are responsible for the specific DNA binding activity as well as induction of apoptosis. 86 matched cddid_all.tbl CDD cd12475 cd12475 240919 RRM2_RBMS3 RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding motif, single-stranded-interacting protein 3 (RBMS3). This subgroup corresponds to the RRM2 of RBMS3, a new member of the c-myc gene single-strand binding proteins (MSSP) family of DNA regulators. Unlike other MSSP proteins, RBMS3 is not a transcriptional regulator. It binds with high affinity to A/U-rich stretches of RNA, and to A/T-rich DNA sequences, and functions as a regulator of cytoplasmic activity. RBMS3 contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and its C-terminal region is acidic and enriched in prolines, glutamines and threonines. 88 matched cddid_all.tbl CDD cd12476 cd12476 409905 RRM1_SNF RNA recognition motif 1 (RRM1) found in Drosophila melanogaster sex determination protein SNF and similar proteins. This subgroup corresponds to the RRM1 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. 85 matched cddid_all.tbl CDD cd12477 cd12477 409906 RRM1_U1A RNA recognition motif 1 (RRM1) found in vertebrate U1 small nuclear ribonucleoprotein A (U1A). This subgroup corresponds to the RRM1 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein and it also shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). It also binds to a flavivirus NS5 protein and plays an important role in virus replication. U1A contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and may be free to bind other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. 89 matched cddid_all.tbl CDD cd12478 cd12478 409907 RRM1_U2B "RNA recognition motif 1 in U2 small nuclear ribonucleoprotein B"" (U2B"") and similar proteins. This subgroup corresponds to the RRM1 of U2B"" (also termed U2 snRNP B"") a unique protein that comprises the U2 snRNP. It was initially identified as binding to stem-loop IV (SLIV) at the 3' end of U2 snRNA. Additional research indicates U2B"" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B"" does not require an auxiliary protein for binding to RNA. In addition, the nuclear transport of U2B"" is independent of U2 snRNA binding. U2B"" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B"" to the nucleus. " 91 matched cddid_all.tbl CDD cd12479 cd12479 240923 RRM2_SNF RNA recognition motif 2 (RRM2) found in Drosophila melanogaster sex determination protein SNF and similar proteins. This subgroup corresponds to the RRM2 of SNF (Sans fille), also termed U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A), an RNA-binding protein found in the U1 and U2 snRNPs of Drosophila. It is essential in Drosophila sex determination and possesses a novel dual RNA binding specificity. SNF binds with high affinity to both Drosophila U1 snRNA stem-loop II (SLII) and U2 snRNA stem-loop IV (SLIV). It can also bind to poly(U) RNA tracts flanking the alternatively spliced Sex-lethal (Sxl) exon, as does Drosophila Sex-lethal protein (SXL). SNF contains two RNA recognition motifs (RRMs); it can self-associate through RRM1, and each RRM can recognize poly(U) RNA binding independently. 80 matched cddid_all.tbl CDD cd12480 cd12480 409908 RRM2_U1A RNA recognition motif 2 (RRM2) found in vertebrate U1 small nuclear ribonucleoprotein A (U1 snRNP A or U1-A or U1A). This subgroup corresponds to the RRM2 of U1A (also termed U1 snRNP A or U1-A), an RNA-binding protein associated with the U1 snRNP, a small RNA-protein complex involved in pre-mRNA splicing. U1A binds with high affinity and specificity to stem-loop II (SLII) of U1 snRNA. It is predominantly a nuclear protein that shuttles between the nucleus and the cytoplasm independently of interactions with U1 snRNA. U1A may be involved in RNA 3'-end processing, specifically cleavage, splicing and polyadenylation, through interacting with a large number of non-snRNP proteins, including polypyrimidine tract binding protein (PTB), polypyrimidine-tract binding protein-associated factor (PSF), and non-POU-domain-containing, octamer-binding (NONO), DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 (DDX5). U1A also binds to a flavivirus NS5 protein and plays an important role in virus replication. It contains two RNA recognition motifs (RRMs); the N-terminal RRM (RRM1) binds tightly and specifically to the U1 snRNA SLII and its own 3'-UTR, while in contrast, the C-terminal RRM (RRM2) does not appear to associate with any RNA and it may be free for binding other proteins. U1A also contains a proline-rich region, and a nuclear localization signal (NLS) in the central domain that is responsible for its nuclear import. 86 matched cddid_all.tbl CDD cd12481 cd12481 240925 RRM2_U2B "RNA recognition motif 2 (RRM2) found in vertebrate U2 small nuclear ribonucleoprotein B"" (U2B""). This subgroup corresponds to the RRM1 of U2B"" (also termed U2 snRNP B""), a unique protein that comprises the U2 snRNP. It was initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA. Additional research indicates U2B"" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity. U2B"" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent of U2 snRNA binding. U2B"" contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B"" to the nucleus. " 80 matched cddid_all.tbl CDD cd12482 cd12482 409909 RRM1_hnRNPR RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R). This subgroup corresponds to the RRM1 of hnRNP R, which is a ubiquitously expressed nuclear RNA-binding protein that specifically binds mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. It is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, and in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; it binds RNA through its RRM domains. 79 matched cddid_all.tbl CDD cd12483 cd12483 409910 RRM1_hnRNPQ RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). This subgroup corresponds to the RRM1 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP, a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. 84 matched cddid_all.tbl CDD cd12484 cd12484 409911 RRM1_RBM46 RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 46 (RBM46). This subgroup corresponds to the RRM1 of RBM46, also termed cancer/testis antigen 68 (CT68), a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 78 matched cddid_all.tbl CDD cd12485 cd12485 240929 RRM1_RBM47 RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 47 (RBM47). This subgroup corresponds to the RRM1 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 78 matched cddid_all.tbl CDD cd12486 cd12486 409912 RRM1_ACF RNA recognition motif 1 (RRM1) found in vertebrate APOBEC-1 complementation factor (ACF). This subgroup corresponds to the RRM1 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. It contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. 78 matched cddid_all.tbl CDD cd12487 cd12487 409913 RRM1_DND1 RNA recognition motif 1 (RRM1) found in vertebrate dead end protein homolog 1 (DND1). This subgroup corresponds to the RRM1 of DND1, also termed RNA-binding motif, single-stranded-interacting protein 4, an RNA-binding protein that is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homolog 2 of Drosophila). It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts. DND1 may also impose another level of translational regulation to modulate expression of critical factors in embryonic stem (ES) cells. DND1 interacts specifically with apolipoprotein B editing complex 3 (APOBEC3), a multi-functional protein inhibiting retroviral replication. The DND1-APOBEC3 interaction may play a role in maintaining viability of germ cells and for preventing germ cell tumor development. DND1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 78 matched cddid_all.tbl CDD cd12488 cd12488 240932 RRM2_hnRNPR RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R). This subgroup corresponds to the RRM2 of hnRNP R, a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. It contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif. hnRNP R binds RNA through its RRM domains. 85 matched cddid_all.tbl CDD cd12489 cd12489 240933 RRM2_hnRNPQ RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. 85 matched cddid_all.tbl CDD cd12490 cd12490 409914 RRM2_ACF RNA recognition motif 2 (RRM2) found in vertebrate APOBEC-1 complementation factor (ACF). This subgroup corresponds to the RRM2 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. ACF contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. 89 matched cddid_all.tbl CDD cd12491 cd12491 409915 RRM2_RBM47 RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 47 (RBM47). This subgroup corresponds to the RRM2 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 95 matched cddid_all.tbl CDD cd12492 cd12492 240936 RRM2_RBM46 RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 46 (RBM46). This subgroup corresponds to the RRM2 of RBM46, also termed cancer/testis antigen 68 (CT68). It is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 85 matched cddid_all.tbl CDD cd12493 cd12493 409916 RRM2_DND1 RNA recognition motif 2 (RRM2) found in vertebrate dead end protein homolog 1 (DND1). This subgroup corresponds to the RRM2 of DND1, also termed RNA-binding motif, single-stranded-interacting protein 4. It is an RNA-binding protein that is essential for maintaining viable germ cells in vertebrates. It interacts with the 3'-untranslated region (3'-UTR) of multiple messenger RNAs (mRNAs) and prevents micro-RNA (miRNA) mediated repression of mRNA. For instance, DND1 binds cell cycle inhibitor, P27 (p27Kip1, CDKN1B), and cell cycle regulator and tumor suppressor, LATS2 (large tumor suppressor, homolog 2 of Drosophila). It helps maintain their protein expression through blocking the inhibitory function of microRNAs (miRNA) from these transcripts. DND1 may also impose another level of translational regulation to modulate expression of critical factors in embryonic stem (ES) cells. Moreover, DND1 interacts specifically with apolipoprotein B editing complex 3 (APOBEC3), a multi-functional protein inhibiting retroviral replication. The DND1-APOBEC3 interaction may play a role in maintaining viability of germ cells and for preventing germ cell tumor development. DND1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 83 matched cddid_all.tbl CDD cd12494 cd12494 409917 RRM3_hnRNPR RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein R (hnRNP R). This subgroup corresponds to the RRM3 of hnRNP R. a ubiquitously expressed nuclear RNA-binding protein that specifically bind mRNAs with a preference for poly(U) stretches. Upon binding of RNA, hnRNP R forms oligomers, most probably dimers. hnRNP R has been implicated in mRNA processing and mRNA transport, and also acts as a regulator to modify binding to ribosomes and RNA translation. hnRNP R is predominantly located in axons of motor neurons and to a much lower degree in sensory axons. In axons of motor neurons, it also functions as a cytosolic protein and interacts with wild type of survival motor neuron (SMN) proteins directly, further providing a molecular link between SMN and the spliceosome. Moreover, hnRNP R plays an important role in neural differentiation and development, as well as in retinal development and light-elicited cellular activities. hnRNP R contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP R binds RNA through its RRM domains. 72 matched cddid_all.tbl CDD cd12495 cd12495 409918 RRM3_hnRNPQ RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). This subgroup corresponds to the RRM3 of hnRNP Q, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NASP1), or synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP). It is a ubiquitously expressed nuclear RNA-binding protein identified as a component of the spliceosome complex, as well as a component of the apobec-1 editosome. As an alternatively spliced version of NSAP, it acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport. hnRNP Q has also been identified as SYNCRIP that is a dual functional protein participating in both viral RNA replication and translation. As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton. Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli. hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains. 72 matched cddid_all.tbl CDD cd12496 cd12496 409919 RRM3_RBM46 RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 46 (RBM46). This subgroup corresponds to the RRM3 of RBM46, also termed cancer/testis antigen 68 (CT68), is a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM46 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 74 matched cddid_all.tbl CDD cd12497 cd12497 409920 RRM3_RBM47 RNA recognition motif 3 (RRM3) found in vertebrate RNA-binding protein 47 (RBM47). This subgroup corresponds to the RRM3 of RBM47, a putative RNA-binding protein that shows high sequence homology with heterogeneous nuclear ribonucleoprotein R (hnRNP R) and heterogeneous nuclear ribonucleoprotein Q (hnRNP Q). Its biological function remains unclear. Like hnRNP R and hnRNP Q, RBM47 contains two well defined and one degenerated RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 74 matched cddid_all.tbl CDD cd12498 cd12498 409921 RRM3_ACF RNA recognition motif 3 (RRM3) found in vertebrate APOBEC-1 complementation factor (ACF). This subgroup corresponds to the RRM3 of ACF, also termed APOBEC-1-stimulating protein, an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing. It may also act as an apoB mRNA recognition factor and chaperone and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus. ACF contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which display high affinity for an 11 nucleotide AU-rich mooring sequence 3' of the edited cytidine in apoB mRNA. All three RRMs may be required for complementation of editing activity in living cells. RRM2/3 are implicated in ACF interaction with APOBEC-1. 83 matched cddid_all.tbl CDD cd12499 cd12499 409922 RRM_EcCsdA_like RNA recognition motif (RRM) found in Escherichia coli cold-shock DEAD box protein A (CsdA) and similar proteins. This subgroup corresponds to the C-terminal RRM homology domain of E. coli CsdA, also termed ATP-dependent RNA helicase deaD, or translation factor W2, a member of the DbpA subfamily of prokaryotic DEAD-box rRNA helicases that have been implicated in ribosome biogenesis. CsdA may be involved in translation initiation, gene regulation after cold-shock, mRNA decay and biogenesis of the large or small ribosomal subunit. It contains two N-terminal ATPase catalytic domains and a C-terminal RNA binding domain, an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain). The catalytic domains bind to nearby regions of RNA to stimulate ATP hydrolysis and disrupt RNA structures. The C-terminal domain is responsible for the high-affinity RNA binding. 73 matched cddid_all.tbl CDD cd12500 cd12500 409923 RRM_BsYxiN_like RNA recognition motif (RRM) found in Bacillus subtilis ATP-dependent RNA helicase YxiN and similar proteins. This subgroup corresponds to the C-terminal RRM homology domain of YxiN. B. subtilis YxiN is a member of the DbpA subfamily of prokaryotic DEAD-box rRNA helicases that have been implicated in ribosome biogenesis. It binds with high affinity and specificity to RNA substrates containing hairpin 92 of 23S rRNA (HP92) with either 3' or 5' extensions in an ATP-dependent manner. YxiN contains two N-terminal ATPase catalytic domains and a C-terminal RNA binding domain, an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain). The catalytic domains bind to nearby regions of RNA to stimulate ATP hydrolysis and disrupt RNA structures. The C-terminal domain is responsible for the high-affinity RNA binding. 73 matched cddid_all.tbl CDD cd12501 cd12501 409924 RRM_EcDbpA_like RNA recognition motif (RRM) found in Escherichia coli RNA helicase dbpA and similar proteins. This subgroup corresponds to the C-terminal RRM homology domain of dbpA. E. coli dbpA is a member of the DbpA subfamily of prokaryotic DEAD-box rRNA helicases that have been implicated in ribosome biogenesis. It binds with high affinity and specificity for RNA substrates containing hairpin 92 of 23S rRNA (HP92) with either 3' or 5' extensions. As a non-processive ATP-dependent helicase, DbpA destabilizes and unwinds short <9bp (base pairs) RNA duplexes as well as long duplex RNA stretches. It disrupts RNA helices exclusively in a 3'- 5' direction and requires a single-stranded loading site 3' of the substrate helix. dbpA contains two N-terminal ATPase catalytic domains and a C-terminal RNA binding domain, an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNPs (ribonucleoprotein domain). The catalytic domains bind to nearby regions of RNA to stimulate ATP hydrolysis and disrupt RNA structures. The C-terminal domain binds specifically to hairpin 92. 73 matched cddid_all.tbl CDD cd12502 cd12502 409925 RRM2_RMB19 RNA recognition motif 2 (RRM2) found in RNA-binding protein 19 (RBM19) and similar proteins. This subfamily corresponds to the RRM2 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA and is also essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 72 matched cddid_all.tbl CDD cd12503 cd12503 409926 RRM1_hnRNPH_GRSF1_like RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, G-rich sequence factor 1 (GRSF-1) and similar proteins. This subfamily corresponds to the RRM1 of hnRNP H proteins and GRSF-1. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. These proteins have similar RNA binding affinities and specifically recognize the sequence GGGA. They can either stimulate or repress splicing upon binding to a GGG motif. hnRNP H binds to the RNA substrate in the presence or absence of these proteins, whereas hnRNP F binds to the nuclear mRNA only in the presence of cap-binding proteins. hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. hnRNP H3 may be involved in splicing arrest induced by heat shock. Most family members contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and play an important role in efficiently silencing the exon. Members in this family can regulate the alternative splicing of fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. Members in this family have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. They also include a cytoplasmic poly(A)+ mRNA binding protein, GRSF-1, which interacts with RNA in a G-rich element-dependent manner. They may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RRMs responsible for the RNA binding, and two auxiliary domains (an acidic alpha-helical domain and an N-terminal alanine-rich region) that may play a role in protein-protein interactions and provide binding specificity. 77 matched cddid_all.tbl CDD cd12504 cd12504 409927 RRM2_hnRNPH_CRSF1_like RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family. This subfamily corresponds to the RRM2 of hnRNP H protein family which includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9). They represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing, having similar RNA binding affinities and specifically recognizing the sequence GGGA. They can either stimulate or repress splicing upon binding to a GGG motif. hnRNP H binds to the RNA substrate in the presence or absence of these proteins, whereas hnRNP F binds to the nuclear mRNA only in the presence of cap-binding proteins. Furthermore, hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. hnRNP H3 may be involved in the splicing arrest induced by heat shock. Most family members contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. Members in this family can regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. The family also includes a cytoplasmic poly(A)+ mRNA binding protein, GRSF-1, which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 also contains three potential RRMs responsible for the RNA binding, and two auxiliary domains (an acidic alpha-helical domain and an N-terminal alanine-rich region) that may play a role in protein-protein interactions and provide binding specificity. 77 matched cddid_all.tbl CDD cd12505 cd12505 409928 RRM2_GRSF1 RNA recognition motif 2 (RRM2) found in G-rich sequence factor 1 (GRSF-1) and similar proteins. This subfamily corresponds to the RRM2 of GRSF-1, a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic alpha-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity. 77 matched cddid_all.tbl CDD cd12506 cd12506 409929 RRM3_hnRNPH_CRSF1_like RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H protein family, G-rich sequence factor 1 (GRSF-1) and similar proteins. This subfamily corresponds to the RRM3 of hnRNP H proteins and GRSF-1. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. These proteins have similar RNA binding affinities and specifically recognize the sequence GGGA. They can either stimulate or repress splicing upon binding to a GGG motif. hnRNP H binds to the RNA substrate in the presence or absence of these proteins, whereas hnRNP F binds to the nuclear mRNA only in the presence of cap-binding proteins. hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. hnRNP H3 may be involved in the splicing arrest induced by heat shock. Most family members contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. For instance, members in this family can regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. The family also includes a cytoplasmic poly(A)+ mRNA binding protein, GRSF-1, which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 also contains three potential RRMs responsible for the RNA binding, and two auxiliary domains (an acidic alpha-helical domain and an N-terminal alanine-rich region) that may play a role in protein-protein interactions and provide binding specificity. 75 matched cddid_all.tbl CDD cd12507 cd12507 240951 RRM1_ESRPs_Fusilli RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein ESRP1, ESRP2, Drosophila RNA-binding protein Fusilli and similar proteins. This subfamily corresponds to the RRM1 of ESRPs and Fusilli. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B). These are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. They are highly conserved paralogs and specifically bind to GU-rich binding site. ESRP1 and ESRP2 contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes Drosophila fusilli (fus) gene encoding RNA-binding protein Fusilli. Loss of fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous fibroblast growth factor receptor 2 (FGFR2) splicing and functions as a splicing factor. It shows high sequence homology to ESRPs and contains three RRMs as well. It also has an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine. 75 matched cddid_all.tbl CDD cd12508 cd12508 409930 RRM2_ESRPs_Fusilli RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein ESRP1, ESRP2, Drosophila RNA-binding protein Fusilli and similar proteins. This subfamily corresponds to the RRM2 of ESRPs and Fusilli. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. They are highly conserved paralogs and specifically bind to GU-rich binding site. ESRP1 and ESRP2 contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes Drosophila fusilli (fus) gene encoding RNA-binding protein Fusilli.Loss of fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous FGFR2 splicing and functions as a splicing factor. It shows high sequence homology to ESRPs and contains three RRMs as well. It also has an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine. 80 matched cddid_all.tbl CDD cd12509 cd12509 409931 RRM3_ESRPs_Fusilli RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2, Drosophila RNA-binding protein Fusilli and similar proteins. This subfamily corresponds to the RRM3 of ESRPs and Fusilli. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. They are highly conserved paralogs and specifically bind to GU-rich binding site. ESRP1 and ESRP2 contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The family also includes Drosophila fusilli (fus) gene encoding RNA-binding protein Fusilli. Loss of fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous FGFR2 splicing and functions as a splicing factor. Fusilli shows high sequence homology to ESRPs and contains three RRMs as well. It also has an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine. 81 matched cddid_all.tbl CDD cd12510 cd12510 409932 RRM1_RBM12_like RNA recognition motif 1 (RRM1) found in RNA-binding protein RBM12, RBM12B and similar proteins. This subfamily corresponds to the RRM1 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear. 74 matched cddid_all.tbl CDD cd12511 cd12511 409933 RRM2_RBM12_like RNA recognition motif 2 (RRM2) found in RNA-binding protein RBM12, RBM12B and similar proteins. This subfamily corresponds to the RRM2 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B shows high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear. 73 matched cddid_all.tbl CDD cd12512 cd12512 409934 RRM3_RBM12 RNA recognition motif 3 (RRM3) found in RNA-binding protein 12 (RBM12) and similar proteins. This subfamily corresponds to the RRM3 of RBM12. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. The biological role of RBM12 remains unclear. 101 matched cddid_all.tbl CDD cd12513 cd12513 409935 RRM3_RBM12B RNA recognition motif 3 (RRM3) found in RNA-binding protein 12B (RBM12B) and similar proteins. This subgroup corresponds to the RRM3 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear. 81 matched cddid_all.tbl CDD cd12514 cd12514 409936 RRM4_RBM12_like RNA recognition motif 4 (RRM4) found in RNA-binding protein RBM12, RBM12B and similar proteins. This subfamily corresponds to the RRM4 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear. 73 matched cddid_all.tbl CDD cd12515 cd12515 409937 RRM5_RBM12_like RNA recognition motif 5 (RRM5) found in RNA-binding protein RBM12, RBM12B and similar proteins. This subfamily corresponds to the RRM5 of RBM12 and RBM12B. RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. RBM12B show high sequence semilarity with RBM12. It contains five distinct RRMs as well. The biological roles of both RBM12 and RBM12B remain unclear. 75 matched cddid_all.tbl CDD cd12516 cd12516 409938 RRM1_RBM26 RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 26 (RBM26). This subgroup corresponds to the RRM1 of RBM26, also known as cutaneous T-cell lymphoma (CTCL) tumor antigen se70-2, which represents a cutaneous lymphoma (CL)-associated antigen. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The RRMs may play some functional roles in RNA-binding or protein-protein interactions. 76 matched cddid_all.tbl CDD cd12517 cd12517 409939 RRM_RBM27 RNA recognition motif (RRM) found in vertebrate RNA-binding protein 27 (RBM27). This subgroup corresponds to the RRM of RBM27 which contains a single RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although the specific function of the RRM in RBM27 remains unclear, it shows high sequence similarity with RRM1of RBM26, which functions as a cutaneous lymphoma (CL)-associated antigen. 76 matched cddid_all.tbl CDD cd12518 cd12518 409940 RRM_SRSF11 RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 11 (SRSF11) and similar proteins. This subgroup corresponds to the RRM of SRSF11, also termed arginine-rich 54 kDa nuclear protein (SRp54 or p54), which belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family). It is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. SRSF11 has been identified as a tau exon 10 splicing repressor. It interacts with a purine-rich element in exon 10, and suppresses exon 10 inclusion by antagonizing Tra2beta, an SR-domain-containing protein that enhances exon 10 inclusion. SRSF11 is a unique SR family member and may regulate the alternative splicing in a tissue- and substrate-dependent manner. It can directly interact with the U2 auxiliary factor 65-kDa subunit (U2AF65), a protein associated with the 3' splice site. In addition, unlike the typical SR proteins, SRSF11 associates with other SR proteins but not with the U1 small nuclear ribonucleoprotein U1-70K or the U2 auxiliary factor 35-kDa subunit (U2AF35). SREK1 has unique properties in regulating alternative splicing of different pre-mRNAs; it promotes the use of the distal 5' splice site in E1A pre-mRNA alternative splicing. It also inhibits cryptic splice site selection on the beta-globin pre-mRNA containing competing 5' splice sites. SREK1 contains an RNA recognition motif (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and one serine-arginine (SR)-rich domains (SR domains). 80 matched cddid_all.tbl CDD cd12519 cd12519 409941 RRM1_SREK1 RNA recognition motif 1 (RRM1) found in splicing regulatory glutamine/lysine-rich protein 1 (SREK1) and similar proteins. This subgroup corresponds to the RRM1 of SREK1, also termed serine/arginine-rich-splicing regulatory protein 86-kDa (SRrp86), or splicing factor arginine/serine-rich 12 (SFRS12), or splicing regulatory protein 508 amino acid (SRrp508). SREK1 belongs to a family of proteins containing regions rich in serine-arginine dipeptides (SR proteins family), and is involved in bridge-complex formation and splicing by mediating protein-protein interactions across either introns or exons. It is a unique SR family member and may play a crucial role in determining tissue specific patterns of alternative splicing. SREK1 can alter splice site selection by both positively and negatively modulating the activity of other SR proteins. For instance, SREK1 can activate SRp20 and repress SC35 in a dose-dependent manner both in vitro and in vivo. In addition, SREK1 generally contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and two serine-arginine (SR)-rich domains (SR domains) separated by an unusual glutamic acid-lysine (EK) rich region. The RRM and SR domains are highly conserved among other members of the SR superfamily. However, the EK domain is unique to SREK1; plays a modulatory role controlling SR domain function by involvement in the inhibition of both constitutive and alternative splicing and in the selection of splice-site. 80 matched cddid_all.tbl CDD cd12520 cd12520 240964 RRM1_MRN1 RNA recognition motif 1 (RRM1) found in RNA-binding protein MRN1 and similar proteins. This subgroup corresponds to the RRM1 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa,which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 74 matched cddid_all.tbl CDD cd12521 cd12521 240965 RRM3_MRN1 RNA recognition motif 3 (RRM3) found in RNA-binding protein MRN1 and similar proteins. This subgroup corresponds to the RRM3 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 74 matched cddid_all.tbl CDD cd12522 cd12522 409942 RRM4_MRN1 RNA recognition motif 4 (RRM4) found in RNA-binding protein MRN1 and similar proteins. This subgroup corresponds to the RRM4 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 81 matched cddid_all.tbl CDD cd12523 cd12523 409943 RRM2_MRN1 RNA recognition motif 2 (RRM2) found in RNA-binding protein MRN1 and similar proteins. This subgroup corresponds to the RRM2 of MRN1, also termed multicopy suppressor of RSC-NHP6 synthetic lethality protein 1, or post-transcriptional regulator of 69 kDa, which is a RNA-binding protein found in yeast. Although its specific biological role remains unclear, MRN1 might be involved in translational regulation. Members in this family contain four copies of conserved RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 78 matched cddid_all.tbl CDD cd12524 cd12524 409944 RRM1_MEI2_like RNA recognition motif 1 (RRM1) found in plant Mei2-like proteins. This subgroup corresponds to the RRM1 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and it is highly conserved between plants and fungi. Up to date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. 77 matched cddid_all.tbl CDD cd12525 cd12525 409945 RRM1_MEI2_fungi RNA recognition motif 1 (RRM1) found in fungal Mei2-like proteins. This subgroup corresponds to the RRM1 of fungal Mei2-like proteins. The Mei2 protein is an essential component of the switch from mitotic to meiotic growth in the fission yeast Schizosaccharomyces pombe. It is an RNA-binding protein that contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In the nucleus, S. pombe Mei2 stimulates meiosis upon binding a specific non-coding RNA through its C-terminal RRM motif. 91 matched cddid_all.tbl CDD cd12526 cd12526 409946 RRM1_EAR1_like RNA recognition motif 1 (RRM1) found in terminal EAR1-like proteins. This subgroup corresponds to the RRM1 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. 71 matched cddid_all.tbl CDD cd12527 cd12527 409947 RRM2_EAR1_like RNA recognition motif 2 (RRM2) found in terminal EAR1-like proteins. This subgroup corresponds to the RRM2 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. 71 matched cddid_all.tbl CDD cd12528 cd12528 240972 RRM2_MEI2_fungi RNA recognition motif 2 (RRM2) found in fungal Mei2-like proteins. This subgroup corresponds to the RRM2 of fungal Mei2-like proteins.The Mei2 protein is an essential component of the switch from mitotic to meiotic growth in the fission yeast Schizosaccharomyces pombe. It is an RNA-binding protein that contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In the nucleus, S. pombe Mei2 stimulates meiosis upon binding a specific non-coding RNA through its C-terminal RRM motif. 81 matched cddid_all.tbl CDD cd12529 cd12529 409948 RRM2_MEI2_like RNA recognition motif 2 (RRM2) found in plant Mei2-like proteins. This subgroup corresponds to the RRM2 of Mei2-like proteins that represent an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. 71 matched cddid_all.tbl CDD cd12530 cd12530 240974 RRM3_EAR1_like RNA recognition motif 3 (RRM3) found in terminal EAR1-like proteins. This subgroup corresponds to the RRM3 of terminal EAR1-like proteins, including terminal EAR1-like protein 1 and 2 (TEL1 and TEL2) found in land plants. They may play a role in the regulation of leaf initiation. The terminal EAR1-like proteins are putative RNA-binding proteins carrying three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and TEL characteristic motifs that allow sequence and putative functional discrimination between the terminal EAR1-like proteins and Mei2-like proteins. 101 matched cddid_all.tbl CDD cd12531 cd12531 240975 RRM3_MEI2_like RNA recognition motif 3 (RRM3) found in plant Mei2-like proteins. This subgroup corresponds to the RRM3 of Mei2-like proteins, representing an ancient eukaryotic RNA-binding proteins family. Their corresponding Mei2-like genes appear to have arisen early in eukaryote evolution, been lost from some lineages such as Saccharomyces cerevisiae and metazoans, and diversified in the plant lineage. The plant Mei2-like genes may function in cell fate specification during development, rather than as stimulators of meiosis. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The C-terminal RRM (RRM3) is unique to Mei2-like proteins and is highly conserved between plants and fungi. To date, the intracellular localization, RNA target(s), cellular interactions and phosphorylation states of Mei2-like proteins in plants remain unclear. 86 matched cddid_all.tbl CDD cd12532 cd12532 409949 RRM3_MEI2_fungi RNA recognition motif 3 (RRM3) found in fungal Mei2-like proteins. This subgroup corresponds to the RRM3 of fungal Mei2-like proteins. The Mei2 protein is an essential component of the switch from mitotic to meiotic growth in the fission yeast Schizosaccharomyces pombe. It is an RNA-binding protein that contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In the nucleus, S. pombe Mei2 stimulates meiosis upon binding a specific non-coding RNA through its C-terminal RRM motif. 90 matched cddid_all.tbl CDD cd12533 cd12533 409950 RRM_EWS RNA recognition motif (RRM) found in vertebrate Ewing Sarcoma Protein (EWS). This subgroup corresponds to the RRM of EWS, also termed Ewing sarcoma breakpoint region 1 protein, a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multifunctional protein and may play roles in transcription and RNA processing. EWS is involved in transcriptional regulation by interacting with the preinitiation complex TFIID and the RNA polymerase II (RNAPII) complexes. It is also associated with splicing factors, such as the U1 snRNP protein U1C, suggesting its implication in pre-mRNA splicing. Additionally, EWS has been shown to regulate DNA damage-induced alternative splicing (AS). Like other members in the FET family, EWS contains an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. EWS specifically binds to poly G and poly U RNA. It also binds to the proximal-element DNA of the macrophage-specific promoter of the CSF-1 receptor gene. 84 matched cddid_all.tbl CDD cd12534 cd12534 240978 RRM_SARFH RNA recognition motif (RRM) found in Drosophila melanogaster RNA-binding protein cabeza and similar proteins. This subgroup corresponds to the RRM in cabeza, also termed P19, or sarcoma-associated RNA-binding fly homolog (SARFH). It is a putative homolog of human RNA-binding proteins FUS (also termed TLS or Pigpen or hnRNP P2), EWS (also termed EWSR1), TAF15 (also termed hTAFII68 or TAF2N or RPB56), and belongs to the of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a nuclear RNA binding protein that may play an important role in the regulation of RNA metabolism during fly development. Cabeza contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 83 matched cddid_all.tbl CDD cd12535 cd12535 409951 RRM_FUS_TAF15 RNA recognition motif (RRM) found in vertebrate fused in Ewing's sarcoma protein (FUS), TATA-binding protein-associated factor 15 (TAF15) and similar proteins. This subgroup corresponds to the RRM of FUS and TAF15. FUS (TLS or Pigpen or hnRNP P2), also termed 75 kDa DNA-pairing protein (POMp75), or oncoprotein TLS (Translocated in liposarcoma), is a member of the FET (previously TET) (FUS/TLS, EWS, TAF15) family of RNA- and DNA-binding proteins whose expression is altered in cancer. It is a multi-functional protein and has been implicated in pre-mRNA splicing, chromosome stability, cell spreading, and transcription. FUS was originally identified in human myxoid and round cell liposarcomas as an oncogenic fusion with the stress-induced DNA-binding transcription factor CHOP (CCAAT enhancer-binding homologous protein) and later as hnRNP P2, a component of hnRNP H complex assembled on pre-mRNA. It can form ternary complexes with hnRNP A1 and hnRNP C1/C2. Additional research indicates that FUS binds preferentially to GGUG-containing RNAs. In the presence of Mg2+, it can bind both single- and double-stranded DNA (ssDNA/dsDNA) and promote ATP-independent annealing of complementary ssDNA and D-loop formation in superhelical dsDNA. FUS has been shown to be recruited by single stranded noncoding RNAs to the regulatory regions of target genes such as cyclin D1, where it represses transcription by disrupting complex formation. TAF15 (TAFII68), also termed TATA-binding protein-associated factor 2N (TAF2N), or RNA-binding protein 56 (RBP56), originally identified as a TAF in the general transcription initiation TFIID complex, is a novel RNA/ssDNA-binding protein with homology to the proto-oncoproteins FUS and EWS (also termed EWSR1), belonging to the FET family as well. TAF15 likely functions in RNA polymerase II (RNAP II) transcription by interacting with TFIID and subunits of RNAP II itself. TAF15 is also associated with U1 snRNA, chromatin and RNA, in a complex distinct from the Sm-containing U1 snRNP that functions in splicing. Like other members in the FET family, both FUS and TAF15 contain an N-terminal Ser, Gly, Gln and Tyr-rich region composed of multiple copies of a degenerate hexapeptide repeat motif. The C-terminal region consists of a conserved nuclear import and retention signal (C-NLS), a C2/C2 zinc-finger motif, a conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and at least 1 arginine-glycine-glycine (RGG)-repeat region. 86 matched cddid_all.tbl CDD cd12536 cd12536 409952 RRM1_RBM39 RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 39 (RBM39). This subgroup corresponds to the RRM1 of RBM39, also termed hepatocellular carcinoma protein 1, or RNA-binding region-containing protein 2, or splicing factor HCC1, a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). An octapeptide sequence called the RS-ERK motif is repeated six times in the RS region of RBM39. Based on the specific domain composition, RBM39 has been classified into a family of non-snRNP (small nuclear ribonucleoprotein) splicing factors that are usually not complexed to snRNAs. 83 matched cddid_all.tbl CDD cd12537 cd12537 409953 RRM1_RBM23 RNA recognition motif 1 (RRM1) found in vertebrate probable RNA-binding protein 23 (RBM23). This subgroup corresponds to the RRM1 of RBM23, also termed RNA-binding region-containing protein 4, or splicing factor SF2, which may function as a pre-mRNA splicing factor. It shows high sequence homology to RNA-binding protein 39 (RBM39 or HCC1), a nuclear autoantigen that contains an N-terminal arginine/serine rich (RS) motif and three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In contrast to RBM39, RBM23 contains only two RRMs. 85 matched cddid_all.tbl CDD cd12538 cd12538 409954 RRM_U2AF35 RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor U2AF 35 kDa subunit (U2AF35). This subgroup corresponds to the RRM of U2AF35, also termed U2AF1, which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. U2AF35 directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. It promotes U2 snRNP binding to the branch-point sequences of introns through association with the large subunit of U2AF, U2AF65 (also termed U2AF2). U2AF35 contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich segment interrupted by glycines. U2AF35 binds both U2AF65 and the pre-mRNA through its RRM domain. 104 matched cddid_all.tbl CDD cd12539 cd12539 409955 RRM_U2AF35B RNA recognition motif (RRM) found in splicing factor U2AF 35 kDa subunit B (U2AF35B). This subgroup corresponds to the RRM of U2AF35B, also termed zinc finger CCCH domain-containing protein 60 (C3H60), which is one of the small subunits of U2 small nuclear ribonucleoprotein (snRNP) auxiliary factor (U2AF). It has been implicated in the recruitment of U2 snRNP to pre-mRNAs and is a highly conserved heterodimer composed of large and small subunits. Members in this family are mainly found in plant. They show high sequence homology to vertebrates U2AF35 that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. U2AF35B contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain. In contrast to U2AF35, U2AF35B has a plant-specific conserved C-terminal region containing SERE motif(s), which may have an important function specific to higher plants. 102 matched cddid_all.tbl CDD cd12540 cd12540 409956 RRM_U2AFBPL RNA recognition motif (RRM) found in U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL) and similar proteins. This subgroup corresponds to the RRM of U2AFBPL, a human homolog of the imprinted mouse gene U2afbp-rs, which encodes a U2 small nuclear ribonucleoprotein auxiliary factor 35 kDa subunit-related protein 1 (U2AFBPL), also termed CCCH type zinc finger, RNA-binding motif and serine/arginine rich protein 1 (U2AF1RS1), or U2 small nuclear RNA auxiliary factor 1-like 1 (U2AF1L1). Although the biological role of U2AFBPL remains unclear, it shows high sequence homology to splicing factor U2AF 35 kDa subunit (U2AF35 or U2AF1) that directly binds to the 3' splice site of the conserved AG dinucleotide and performs multiple functions in the splicing process in a substrate-specific manner. Like U2AF35, U2AFBPL contains two N-terminal zinc fingers, a central RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal arginine/serine (SR)-rich domain. 105 matched cddid_all.tbl CDD cd12541 cd12541 409957 RRM2_La RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins. This subgroup corresponds to the RRM2 of La autoantigen, also termed Lupus La protein, or La ribonucleoprotein, or Sjoegren syndrome type B antigen (SS-B), a highly abundant nuclear phosphoprotein and well conserved in eukaryotes. It specifically binds the 3'-terminal UUU-OH motif of nascent RNA polymerase III transcripts and protects them from exonucleolytic degradation by 3' exonucleases. In addition, La can directly facilitate the translation and/or metabolism of many UUU-3' OH-lacking cellular and viral mRNAs, through binding internal RNA sequences within the untranslated regions of target mRNAs. La contains an N-terminal La motif (LAM), followed by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). In addition, it possesses a short basic motif (SBM) and a nuclear localization signal (NLS) at the C-terminus. 77 matched cddid_all.tbl CDD cd12542 cd12542 409958 RRM2_LARP7 RNA recognition motif 2 in La-related protein 7 (LARP7) and similar proteins. This subgroup corresponds to the RRM2 of LARP7, also termed La ribonucleoprotein domain family member 7, or P-TEFb-interaction protein for 7SK stability (PIP7S), an oligopyrimidine-binding protein that binds to the highly conserved 3'-terminal U-rich stretch (3' -UUU-OH) of 7SK RNA. LARP7 is a stable component of the 7SK small nuclear ribonucleoprotein (7SK snRNP). It intimately associates with all the nuclear 7SK and is required for 7SK stability. LARP7 also acts as a negative transcriptional regulator of cellular and viral polymerase II genes, acting by means of the 7SK snRNP system. LARP7 plays an essential role in the inhibition of positive transcription elongation factor b (P-TEFb)-dependent transcription, which has been linked to the global control of cell growth and tumorigenesis. LARP7 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), at the N-terminal region, which mediates binding to the U-rich 3' terminus of 7SK RNA. LARP7 also carries another putative RRM domain at its C-terminus. 78 matched cddid_all.tbl CDD cd12543 cd12543 409959 RRM2_PAR14 RNA recognition motif 2 in vertebrate poly [ADP-ribose] polymerase 14 (PARP-14). This subgroup corresponds to the RRM2 of PARP-14, also termed aggressive lymphoma protein 2, a member of the B aggressive lymphoma (BAL) family of macrodomain-containing PARPs. It is expressed in B lymphocytes and interacts with the IL-4-induced transcription factor Stat6. It plays a fundamental role in the regulation of IL-4-induced B-cell protection against apoptosis after irradiation or growth factor withdrawal. It mediates IL-4 effects on the levels of gene products that regulate cell survival, proliferation, and lymphomagenesis. PARP-14 acts as a transcriptional switch for Stat6-dependent gene activation. In the presence of IL-4, PARP-14 activates transcription by facilitating the binding of Stat6 to the promoter and release of HDACs from the promoter with an IL-4 signal. In contrast, in the absence of a signal, PARP-14 acts as a transcriptional repressor by recruiting HDACs. Absence of PARP-14 protects against Myc-induced developmental block and lymphoma. Thus, PARP-14 may play an important role in Myc-induced oncogenesis. Additional research indicates that PARP-14 is also a binding partner with phosphoglucose isomerase (PGI)/ autocrine motility factor (AMF). It can inhibit PGI/AMF ubiquitination, thus contributing to its stabilization and secretion. PARP-14 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), three tandem macro domains, and C-terminal region with sequence homology to PARP catalytic domain. 75 matched cddid_all.tbl CDD cd12544 cd12544 409960 RRM_NMI RNA recognition motif in N-myc-interactor (Nmi) and similar proteins. This subgroup corresponds to the RRM.in Nmi, also termed N-myc and STAT interactor, an interferon inducible protein that interacts with c-Myc, N-Myc, Max and c-Fos, and other transcription factors containing bHLH-ZIP, bHLH or ZIP domains. In addition to binding Myc proteins, Nmi also associates with all the Stat family of transcription factors except Stat2. In response to cytokines (e.g. IL-2 and IFN-gamma) stimulation, Nmi can enhance Stat-mediated transcriptional activity through recruiting the Stat1 and Stat5 transcriptional coactivators, CREB-binding protein (CBP) and p300. Nmi contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 81 matched cddid_all.tbl CDD cd12545 cd12545 409961 RRM_IN35 RNA recognition motif in interferon-induced 35 kDa protein (IFP 35) and similar proteins. This subgroup corresponds to the RRM in IFP 35, an interferon-induced leucine zipper protein that can specifically form homodimers. Distinct from known bZIP proteins, IFP 35 lacks a basic domain critical for DNA binding. IFP 35 may negatively regulate other bZIP transcription factors by protein-protein interaction. For instance, it can form heterodimers with B-ATF, a member of the AP1 transcription factor family. IFP 35 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 79 matched cddid_all.tbl CDD cd12546 cd12546 409962 RRM_RBM43 RNA recognition motif in vertebrate RNA-binding protein 43 (RBM43). This subgroup corresponds to the RRM of RBM43, a putative RNA-binding protein containing one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). Although its biological function remains unclear, RBM43 shows high sequence homology to poly [ADP-ribose] polymerase 10 (PARP-10), which is a novel oncoprotein c-Myc-interacting protein with poly(ADP-ribose) polymerase activity. 77 matched cddid_all.tbl CDD cd12547 cd12547 409963 RRM1_2_PAR10 RNA recognition motif 1 and 2 in poly [ADP-ribose] polymerase 10 (PARP-10) and similar proteins. This subgroup corresponds to the RRM1 and RRM2 of PARP-10, a novel oncoprotein c-Myc-interacting protein with poly(ADP-ribose) polymerase activity. It is localized to the nuclear and cytoplasmic compartments. In addition to the PARP activity, PARP-10 is also involved in the control of cell proliferation by inhibiting c-Myc- and E1A-mediated cotransformation of primary cells. PARP-10 may play a role in nuclear processes including the regulation of chromatin, gene transcription, and nuclear/cytoplasmic transport. It contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two overlapping C-terminal domains composed of a glycine-rich region and a region with homology to catalytic domains of PARP enzymes (PARP domain). In addition, PARP-10 contains two ubiquitin-interacting motifs (UIM). 72 matched cddid_all.tbl CDD cd12548 cd12548 409964 RRM_Set1A RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1A (Set1A). This subgroup corresponds to the RRM of Setd1A, also termed SET domain-containing protein 1A (Set1A), or lysine N-methyltransferase 2F, or Set1/Ash2 histone methyltransferase complex subunit Set1, a ubiquitously expressed vertebrates histone methyltransferase that exhibits high homology to yeast Set1. Set1A is localized to euchromatic nuclear speckles and associates with a complex containing six human homologs of the yeast Set1/COMPASS complex, including CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). Set1A contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. In contrast to Set1B, Set1A additionally contains an HCF-1 binding motif that interacts with HCF-1 in vivo. 95 matched cddid_all.tbl CDD cd12549 cd12549 409965 RRM_Set1B RNA recognition motif in vertebrate histone-lysine N-methyltransferase Setd1B (Set1B). This subgroup corresponds to the RRM of Setd1B, also termed SET domain-containing protein 1B (Set1B), or lysine N-methyltransferase 2G, a ubiquitously expressed vertebrates histone methyltransferase that exhibits high homology to yeast Set1. Set1B is localized to euchromatic nuclear speckles and associates with a complex containing six human homologs of the yeast Set1/COMPASS complex, including CXXC finger protein 1 (CFP1; homologous to yeast Spp1), Rbbp5 (homologous to yeast Swd1), Ash2 (homologous to yeast Bre2), Wdr5 (homologous to yeast Swd3), and Wdr82 (homologous to yeast Swd2). Set1B complex is a histone methyltransferase that produces trimethylated histone H3 at Lys4. Set1B contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), an N- SET domain, and a C-terminal catalytic SET domain followed by a post-SET domain. 93 matched cddid_all.tbl CDD cd12550 cd12550 409966 RRM_II_PABPN1 RNA recognition motif in type II polyadenylate-binding protein 2 (PABP-2) and similar proteins. This subgroup corresponds to the RRM of PABP-2, also termed poly(A)-binding protein 2, or nuclear poly(A)-binding protein 1 (PABPN1), or poly(A)-binding protein II (PABII), which is a ubiquitously expressed type II nuclear poly(A)-binding protein that directs the elongation of mRNA poly(A) tails during pre-mRNA processing. Although PABP-2 binds poly(A) with high affinity and specificity as type I poly(A)-binding proteins, it contains only one highly conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, PABP-2 possesses an acidic N-terminal domain that is essential for the stimulation of PAP, and an arginine-rich C-terminal domain. 76 matched cddid_all.tbl CDD cd12551 cd12551 409967 RRM_II_PABPN1L RNA recognition motif in vertebrate type II embryonic polyadenylate-binding protein 2 (ePABP-2). This subgroup corresponds to the RRM of ePABP-2, also termed embryonic poly(A)-binding protein 2, or poly(A)-binding protein nuclear-like 1 (PABPN1L). ePABP-2 is a novel embryonic-specific cytoplasmic type II poly(A)-binding protein that is expressed during the early stages of vertebrate development and in adult ovarian tissue. It may play an important role in the poly(A) metabolism of stored mRNAs during early vertebrate development. ePABP-2 shows significant sequence similarity to the ubiquitously expressed nuclear polyadenylate-binding protein 2 (PABP-2 or PABPN1). Like PABP-2, ePABP-2 contains one RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), which is responsible for the poly(A) binding. In addition, it possesses an acidic N-terminal domain predicted to form a coiled-coil and an arginine-rich C-terminal domain. 77 matched cddid_all.tbl CDD cd12552 cd12552 409968 RRM_Nop15p RNA recognition motif in yeast ribosome biogenesis protein 15 (Nop15p) and similar proteins. This subgroup corresponds to the RRM of Nop15p, also termed nucleolar protein 15, which is encoded by YNL110C from Saccharomyces cerevisiae, and localizes to the nucleoplasm and nucleolus. Nop15p has been identified as a component of a pre-60S particle. It interacts with RNA components of the early pre-60S particles. Furthermore, Nop15p binds directly to a pre-rRNA transcript in vitro and is required for pre-rRNA processing. It functions as a ribosome synthesis factor required for the 5' to 3' exonuclease digestion that generates the 5' end of the major, short form of the 5.8S rRNA as well as for processing of 27SB to 7S pre-rRNA. Nop15p also play a specific role in cell cycle progression. Nop15p contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 77 matched cddid_all.tbl CDD cd12553 cd12553 409969 RRM1_RBM15 RNA recognition motif 1 (RRM1) found in vertebrate RNA binding motif protein 15 (RBM15). This subgroup corresponds to the RRM1 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contains three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. 78 matched cddid_all.tbl CDD cd12554 cd12554 409970 RRM1_RBM15B RNA recognition motif 1 (RRM1) found in putative RNA binding motif protein 15B (RBM15B) from vertebrate. This subfamily corresponds to the RRM1 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. 80 matched cddid_all.tbl CDD cd12555 cd12555 409971 RRM2_RBM15 RNA recognition motif 2 (RRM2) found in vertebrate RNA binding motif protein 15 (RBM15). This subgroup corresponds to the RRM2 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. 87 matched cddid_all.tbl CDD cd12556 cd12556 409972 RRM2_RBM15B RNA recognition motif 2 (RRM2) found in putative RNA binding motif protein 15B (RBM15B) from vertebrate. This subgroup corresponds to the RRM2 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. 85 matched cddid_all.tbl CDD cd12557 cd12557 409973 RRM3_RBM15 RNA recognition motif 3 (RRM3) found in vertebrate RNA binding motif protein 15 (RBM15). This subgroup corresponds to the RRM3 of RBM15, also termed one-twenty two protein 1 (OTT1), conserved in eukaryotes, a novel mRNA export factor component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contains three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralogue and ortholog C-terminal) domain. This family also includes a RBM15-MKL1 (OTT-MAL) fusion protein that RBM15 is N-terminally fused to megakaryoblastic leukemia 1 protein (MKL1) at the C-terminus in a translocation involving chromosome 1 and 22, resulting in acute megakaryoblastic leukemia. The fusion protein could interact with the mRNA export machinery. Although it maintains the specific transactivator function of MKL1, the fusion protein cannot activate RTE-mediated mRNA expression and has lost the post-transcriptional activator function of RBM15. However, it has transdominant suppressor function contributing to its oncogenic properties. 73 matched cddid_all.tbl CDD cd12558 cd12558 409974 RRM3_RBM15B RNA recognition motif 3 (RRM3) found in putative RNA-binding protein 15B (RBM15B) from vertebrate. This subgroup corresponds to the RRM3 of RBM15B, also termed one twenty-two 3 (OTT3), a paralog of RNA binding motif protein 15 (RBM15), also known as One-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. 76 matched cddid_all.tbl CDD cd12559 cd12559 409975 RRM_SRSF10 RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 10 (SRSF10) and similar proteins. This subgroup corresponds to the RRM of SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). SRSF10 is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. 95 matched cddid_all.tbl CDD cd12560 cd12560 409976 RRM_SRSF12 RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 12 (SRSF12) and similar proteins. This subgroup corresponds to the RRM of SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19). SRSF12 is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. SRSF12 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides. 84 matched cddid_all.tbl CDD cd12561 cd12561 409977 RRM1_RBM5_like RNA recognition motif 1 (RRM1) found in RNA-binding protein 5 (RBM5) and similar proteins. This subgroup corresponds to the RRM1 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. 81 matched cddid_all.tbl CDD cd12562 cd12562 409978 RRM2_RBM5_like RNA recognition motif 2 (RRM2) found in RNA-binding protein 5 (RBM5) and similar proteins. This subgroup corresponds to the RRM2 of RNA-binding protein 5 (RBM5 or LUCA15 or H37), RNA-binding protein 10 (RBM10 or S1-1) and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both, RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. 86 matched cddid_all.tbl CDD cd12563 cd12563 409979 RRM2_RBM6 RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 6 (RBM6). This subgroup corresponds to the RRM2 of RBM6, also termed lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, which has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both, RBM6 and RBM5, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has two additional unique domains: the decamer repeat occurring more than 20 times, and the POZ (poxvirus and zinc finger) domain. The POZ domain may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers. 87 matched cddid_all.tbl CDD cd12564 cd12564 409980 RRM1_RBM19 RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins. This subgroup corresponds to the RRM1 of RBM19, also termed RNA-binding domain-1 (RBD-1), a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 76 matched cddid_all.tbl CDD cd12565 cd12565 409981 RRM1_MRD1 RNA recognition motif 1 (RRM1) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins. This subgroup corresponds to the RRM1 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. 76 matched cddid_all.tbl CDD cd12566 cd12566 409982 RRM2_MRD1 RNA recognition motif 2 (RRM2) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins. This subgroup corresponds to the RRM2 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. MRD1 contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. 79 matched cddid_all.tbl CDD cd12567 cd12567 409983 RRM3_RBM19 RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins. This subgroup corresponds to the RRM3 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 79 matched cddid_all.tbl CDD cd12568 cd12568 241012 RRM3_MRD1 RNA recognition motif 3 (RRM3) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins. This subgroup corresponds to the RRM3 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. 72 matched cddid_all.tbl CDD cd12569 cd12569 409984 RRM4_RBM19 RNA recognition motif 4 (RRM4) found in RNA-binding protein 19 (RBM19) and similar proteins. This subgroup corresponds to the RRM4 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 72 matched cddid_all.tbl CDD cd12570 cd12570 241014 RRM5_MRD1 RNA recognition motif 5 (RRM5) found in yeast multiple RNA-binding domain-containing protein 1 (MRD1) and similar proteins. This subgroup corresponds to the RRM5 of MRD1 which is encoded by a novel yeast gene MRD1 (multiple RNA-binding domain). It is well-conserved in yeast and its homologs exist in all eukaryotes. MRD1 is present in the nucleolus and the nucleoplasm. It interacts with the 35 S precursor rRNA (pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). MRD1 is essential for the initial processing at the A0-A2 cleavage sites in the 35 S pre-rRNA. It contains 5 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may play an important structural role in organizing specific rRNA processing events. 76 matched cddid_all.tbl CDD cd12571 cd12571 409985 RRM6_RBM19 RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19) and similar proteins. This subgroup corresponds to the RRM6 of RBM19, also termed RNA-binding domain-1 (RBD-1), which is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. RBM19 has a unique domain organization containing 6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 79 matched cddid_all.tbl CDD cd12572 cd12572 409986 RRM2_MSI1 RNA recognition motif 2 (RRM2) found in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins. This subgroup corresponds to the RRM2 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1) and has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. It represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. 74 matched cddid_all.tbl CDD cd12573 cd12573 409987 RRM2_MSI2 RNA recognition motif 2 (RRM2) found in RNA-binding protein Musashi homolog 2 (Musashi-2) and similar proteins. This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. 76 matched cddid_all.tbl CDD cd12574 cd12574 409988 RRM1_DAZAP1 RNA recognition motif 1 (RRM1) found in Deleted in azoospermia-associated protein 1 (DAZAP1) and similar proteins. This subfamily corresponds to the RRM1 of DAZAP1 or DAZ-associated protein 1, also termed proline-rich RNA binding protein (Prrp), a multi-functional ubiquitous RNA-binding protein expressed most abundantly in the testis and essential for normal cell growth, development, and spermatogenesis. DAZAP1 is a shuttling protein whose acetylated form is predominantly nuclear and the nonacetylated form is in cytoplasm. It also functions as a translational regulator that activates translation in an mRNA-specific manner. DAZAP1 was initially identified as a binding partner of Deleted in Azoospermia (DAZ). It also interacts with numerous hnRNPs, including hnRNP U, hnRNP U like-1, hnRNPA1, hnRNPA/B, and hnRNP D, suggesting DAZAP1 might associate and cooperate with hnRNP particles to regulate adenylate-uridylate-rich elements (AU-rich element or ARE)-containing mRNAs. DAZAP1 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal proline-rich domain. 82 matched cddid_all.tbl CDD cd12575 cd12575 409989 RRM1_hnRNPD_like RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. This subfamily corresponds to the RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar proteins. hnRNP D0 is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP A/B is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP DL (or hnRNP D-like) is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. All members in this family contain two putative RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. 72 matched cddid_all.tbl CDD cd12576 cd12576 409990 RRM1_MSI RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog Musashi-1, Musashi-2 and similar proteins. This subfamily corresponds to the RRM1 in Musashi-1 and Musashi-2. Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells, and associated with asymmetric divisions in neural progenitor cells. It is evolutionarily conserved from invertebrates to vertebrates. Musashi-1 is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). It has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, Musashi-1 represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-2 (also termed Msi2) has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Both, Musashi-1 and Musashi-2, contain two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. 76 matched cddid_all.tbl CDD cd12577 cd12577 409991 RRM1_Hrp1p RNA recognition motif 1 (RRM1) found in yeast nuclear polyadenylated RNA-binding protein 4 (Hrp1p or Nab4p) and similar proteins. This subfamily corresponds to the RRM1 of Hrp1p and similar proteins. Hrp1p or Nab4p, also termed cleavage factor IB (CFIB), is a sequence-specific trans-acting factor that is essential for mRNA 3'-end formation in yeast Saccharomyces cerevisiae. It can be UV cross-linked to RNA and specifically recognizes the (UA)6 RNA element required for both, the cleavage and poly(A) addition, steps. Moreover, Hrp1p can shuttle between the nucleus and the cytoplasm, and play an additional role in the export of mRNAs to the cytoplasm. Hrp1p also interacts with Rna15p and Rna14p, two components of CF1A. In addition, Hrp1p functions as a factor directly involved in modulating the activity of the nonsense-mediated mRNA decay (NMD) pathway. It binds specifically to a downstream sequence element (DSE)-containing RNA and interacts with Upf1p, a component of the surveillance complex, further triggering the NMD pathway. Hrp1p contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an arginine-glycine-rich region harboring repeats of the sequence RGGF/Y. 76 matched cddid_all.tbl CDD cd12578 cd12578 409992 RRM1_hnRNPA_like RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A subfamily. This subfamily corresponds to the RRM1 in hnRNP A0, hnRNP A1, hnRNP A2/B1, hnRNP A3 and similar proteins. hnRNP A0 is a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A1 is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A2/B1 is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A3 is also a RNA trafficking response element-binding protein that participates in the trafficking of A2RE-containing RNA. The hnRNP A subfamily is characterized by two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. 78 matched cddid_all.tbl CDD cd12579 cd12579 409993 RRM2_hnRNPA0 RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A0 (hnRNP A0) and similar proteins. This subgroup corresponds to the RRM2 of hnRNP A0, a low abundance hnRNP protein that has been implicated in mRNA stability in mammalian cells. It has been identified as the substrate for MAPKAP-K2 and may be involved in the lipopolysaccharide (LPS)-induced post-transcriptional regulation of tumor necrosis factor-alpha (TNF-alpha), cyclooxygenase 2 (COX-2) and macrophage inflammatory protein 2 (MIP-2). hnRNP A0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. 80 matched cddid_all.tbl CDD cd12580 cd12580 409994 RRM2_hnRNPA1 RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins. This subgroup corresponds to the RRM2 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. Moreover, hnRNP A1, together with the scaffold protein septin 6, serves as host proteins to form a complex with NS5b and viral RNA, and further play important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. 77 matched cddid_all.tbl CDD cd12581 cd12581 409995 RRM2_hnRNPA2B1 RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins. This subgroup corresponds to the RRM2 of hnRNP A2/B1, an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. 80 matched cddid_all.tbl CDD cd12582 cd12582 409996 RRM2_hnRNPA3 RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins. This subgroup corresponds to the RRM2 of hnRNP A3, a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. 80 matched cddid_all.tbl CDD cd12583 cd12583 241027 RRM2_hnRNPD RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins. This subgroup corresponds to the RRM2 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. 75 matched cddid_all.tbl CDD cd12584 cd12584 409997 RRM2_hnRNPAB RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins. This subgroup corresponds to the RRM2 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. 80 matched cddid_all.tbl CDD cd12585 cd12585 409998 RRM2_hnRPDL RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP DL) and similar proteins. This subgroup corresponds to the RRM2 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. 75 matched cddid_all.tbl CDD cd12586 cd12586 409999 RRM1_PSP1 RNA recognition motif 1 (RRM1) found in vertebrate paraspeckle protein 1 (PSP1). This subgroup corresponds to the RRM1 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Its cellular function remains unknown currently, however, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. 71 matched cddid_all.tbl CDD cd12587 cd12587 410000 RRM1_PSF RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF). This subgroup corresponds to the RRM1 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Besides, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. Additionally, PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. 71 matched cddid_all.tbl CDD cd12588 cd12588 410001 RRM1_p54nrb RNA recognition motif 1 (RRM1) found in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb). This subgroup corresponds to the RRM1 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. p54nrb binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manneras well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. 71 matched cddid_all.tbl CDD cd12589 cd12589 410002 RRM2_PSP1 RNA recognition motif 2 (RRM2) found in vertebrate paraspeckle protein 1 (PSP1 or PSPC1). This subgroup corresponds to the RRM2 of PSPC1, also termed paraspeckle component 1 (PSPC1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO), which localizes to paraspeckles in an RNA-dependent manner. PSPC1 contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. 80 matched cddid_all.tbl CDD cd12590 cd12590 410003 RRM2_PSF RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF). This subgroup corresponds to the RRM2 of PSF, also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex, a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also both single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. It promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NonO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. 80 matched cddid_all.tbl CDD cd12591 cd12591 410004 RRM2_p54nrb RNA recognition motif 2 (RRM2) found in vertebrate 54 kDa nuclear RNA- and DNA-binding protein (p54nrb). This subgroup corresponds to the RRM2 of p54nrb, also termed non-POU domain-containing octamer-binding protein (NonO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. It is ubiquitously expressed and highly conserved in vertebrates. It binds both, single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer with polypyrimidine tract-binding protein-associated-splicing factor (PSF). p54nrb contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), at the N-terminus. 80 matched cddid_all.tbl CDD cd12592 cd12592 410005 RRM_RBM7 RNA recognition motif (RRM) found in vertebrate RNA-binding protein 7 (RBM7). This subfamily corresponds to the RRM of RBM7, a ubiquitously expressed pre-mRNA splicing factor that enhances messenger RNA (mRNA) splicing in a cell-specific manner or in a certain developmental process, such as spermatogenesis. RBM7 interacts with splicing factors SAP145 (the spliceosomal splicing factor 3b subunit 2) and SRp20. It may play a more specific role in meiosis entry and progression. Together with additional testis-specific RNA-binding proteins, RBM7 may regulate the splicing of specific pre-mRNA species that are important in the meiotic cell cycle. RBM7 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. 75 matched cddid_all.tbl CDD cd12593 cd12593 410006 RRM_RBM11 RNA recognition motif (RRM) found in vertebrate RNA-binding protein 11 (RBM11). This subfamily corresponds to the RRM or RBM11, a novel tissue-specific splicing regulator that is selectively expressed in brain, cerebellum and testis, and to a lower extent in kidney. RBM11 is localized in the nucleoplasm and enriched in SRSF2-containing splicing speckles. It may play a role in the modulation of alternative splicing during neuron and germ cell differentiation. RBM11 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region lacking known homology at the C-terminus. The RRM of RBM11 is responsible for RNA binding, whereas the C-terminal region permits nuclear localization and homodimerization. 75 matched cddid_all.tbl CDD cd12594 cd12594 410007 RRM1_SRSF4 RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 4 (SRSF4). This subgroup corresponds to the RRM1 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4). SRSF4 is a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFSF4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, it activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal SR domains rich in serine-arginine dipeptides. 87 matched cddid_all.tbl CDD cd12595 cd12595 410008 RRM1_SRSF5 RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 5 (SRSF5). This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. 70 matched cddid_all.tbl CDD cd12596 cd12596 410009 RRM1_SRSF6 RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 6 (SRSF6). This subfamily corresponds to the RRM1 of SRSF6, also termed pre-mRNA-splicing factor SRp55, which is an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal SR domains rich in serine-arginine dipeptides. 72 matched cddid_all.tbl CDD cd12597 cd12597 410010 RRM1_SRSF1 RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins. This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides. 79 matched cddid_all.tbl CDD cd12598 cd12598 241042 RRM1_SRSF9 RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 9 (SRSF9). This subgroup corresponds to the RRM1 of SRSF9, also termed pre-mRNA-splicing factor SRp30C. SRSF9 is an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. 72 matched cddid_all.tbl CDD cd12599 cd12599 410011 RRM1_SF2_plant_like RNA recognition motif 1 (RRM1) found in plant pre-mRNA-splicing factor SF2 and similar proteins. This subgroup corresponds to the RRM1 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. 72 matched cddid_all.tbl CDD cd12600 cd12600 410012 RRM2_SRSF4_like RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins. This subfamily corresponds to the RRM2 of three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and is essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. 72 matched cddid_all.tbl CDD cd12601 cd12601 410013 RRM2_SRSF1_like RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor SRSF1, SRSF9 and similar proteins. This subfamily corresponds to the RRM2 of serine/arginine-rich splicing factor SRSF1, SRSF9 and similar proteins. SRSF1, also termed ASF-1, is a shuttling SR protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF9, also termed SRp30C, has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. Both, SRSF1 and SRSF9, contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal RS domains rich in serine-arginine dipeptides. 74 matched cddid_all.tbl CDD cd12602 cd12602 410014 RRM2_SF2_plant_like RNA recognition motif 2 (RRM2) found in plant pre-mRNA-splicing factor SF2 and similar proteins. This subfamily corresponds to the RRM2 of SF2, also termed SR1 protein, a plant serine/arginine (SR)-rich phosphoprotein similar to the mammalian splicing factor SF2/ASF. It promotes splice site switching in mammalian nuclear extracts. SF2 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal domain rich in proline, serine and lysine residues (PSK domain), a composition reminiscent of histones. This PSK domain harbors a putative phosphorylation site for the mitotic kinase cyclin/p34cdc2. 76 matched cddid_all.tbl CDD cd12603 cd12603 410015 RRM_hnRNPC RNA recognition motif (RRM) found in vertebrate heterogeneous nuclear ribonucleoprotein C1/C2 (hnRNP C1/C2). This subgroup corresponds to the RRM of heterogeneous nuclear ribonucleoprotein C (hnRNP) proteins C1 and C2, produced by a single coding sequence. They are the major constituents of the heterogeneous nuclear RNA (hnRNA) ribonucleoprotein (hnRNP) complex in vertebrates. They bind hnRNA tightly, suggesting a central role in the formation of the ubiquitous hnRNP complex. They are involved in the packaging of hnRNA in the nucleus and in processing of pre-mRNA such as splicing and 3'-end formation. hnRNP C proteins contain two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes the variable region, the basic region and the KSG box rich in repeated Lys-Ser-Gly sequences, the leucine zipper, and the acidic region. The RRM is capable of binding poly(U). The KSG box may bind to RNA. The leucine zipper may be involved in dimer formation. The acidic and hydrophilic C-teminus harbors a putative nucleoside triphosphate (NTP)-binding fold and a protein kinase phosphorylation site. 84 matched cddid_all.tbl CDD cd12604 cd12604 410016 RRM_RALY RNA recognition motif (RRM) found in vertebrate RNA-binding protein Raly. This subgroup corresponds to the RRM of Raly, also termed autoantigen p542, or heterogeneous nuclear ribonucleoprotein C-like 2, or hnRNP core protein C-like 2, or hnRNP associated with lethal yellow protein homolog, an RNA-binding protein that may play a critical role in embryonic development. It is encoded by Raly, a ubiquitously expressed gene of unknown function. Raly shows a high degree of identity with the 5' sequences of p542 gene encoding autoantigen, which can cross-react with EBNA-1 of the Epstein Barr virus. Raly contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain that includes a unique glycine/serine-rich stretch. 76 matched cddid_all.tbl CDD cd12605 cd12605 410017 RRM_RALYL RNA recognition motif (RRM) found in vertebrate RNA-binding Raly-like protein (RALYL). This subgroup corresponds to the RRM of RALYL, also termed heterogeneous nuclear ribonucleoprotein C-like 3, or hnRNP core protein C-like 3, a putative RNA-binding protein that shows high sequence homology with Raly, an RNA-binding protein playing a critical role in embryonic development. The biological role of RALYL remains unclear. Like Raly, RALYL contains two distinct domains, an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal auxiliary domain. 69 matched cddid_all.tbl CDD cd12606 cd12606 410018 RRM1_RBM4 RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 4 (RBM4). This subgroup corresponds to the RRM1 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. 67 matched cddid_all.tbl CDD cd12607 cd12607 410019 RRM2_RBM4 RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 4 (RBM4). This subgroup corresponds to the RRM2 of RBM4, a ubiquitously expressed splicing factor that has two isoforms, RBM4A (also known as Lark homolog) and RBM4B (also known as RBM30), which are very similar in structure and sequence. RBM4 may function as a translational regulator of stress-associated mRNAs and also plays a role in micro-RNA-mediated gene regulation. RBM4 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), a CCHC-type zinc finger, and three alanine-rich regions within their C-terminal regions. The C-terminal region may be crucial for nuclear localization and protein-protein interaction. The RRMs, in combination with the C-terminal region, are responsible for the splicing function of RBM4. 67 matched cddid_all.tbl CDD cd12608 cd12608 410020 RRM1_CoAA RNA recognition motif 1 (RRM1) found in vertebrate RRM-containing coactivator activator/modulator (CoAA). This subgroup corresponds to the RRM1 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. 69 matched cddid_all.tbl CDD cd12609 cd12609 410021 RRM2_CoAA RNA recognition motif 2 (RRM2) found in vertebrate RRM-containing coactivator activator/modulator (CoAA). This subgroup corresponds to the RRM2 of CoAA, also termed RNA-binding protein 14 (RBM14), or paraspeckle protein 2 (PSP2), or synaptotagmin-interacting protein (SYT-interacting protein), a heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein identified as a nuclear receptor coactivator. It mediates transcriptional coactivation and RNA splicing effects in a promoter-preferential manner and is enhanced by thyroid hormone receptor-binding protein (TRBP). CoAA contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a TRBP-interacting domain. It stimulates transcription through its interactions with coactivators, such as TRBP and CREB-binding protein CBP/p300, via the TRBP-interacting domain and interaction with an RNA-containing complex, such as DNA-dependent protein kinase-poly(ADP-ribose) polymerase complexes, via the RRMs. 68 matched cddid_all.tbl CDD cd12610 cd12610 410022 RRM1_SECp43 RNA recognition motif 1 (RRM1) found in tRNA selenocysteine-associated protein 1 (SECp43). This subgroup corresponds to the RRM1 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. 84 matched cddid_all.tbl CDD cd12611 cd12611 410023 RRM1_NGR1_NAM8_like RNA recognition motif 1 (RRM1) found in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins. This subgroup corresponds to the RRM1 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two of which are followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The subgroup also includes NAM8, a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. 84 matched cddid_all.tbl CDD cd12612 cd12612 410024 RRM2_SECp43 RNA recognition motif 2 (RRM2) found in tRNA selenocysteine-associated protein 1 (SECp43). This subgroup corresponds to the RRM2 of SECp43, an RNA-binding protein associated specifically with eukaryotic selenocysteine tRNA [tRNA(Sec)]. It may play an adaptor role in the mechanism of selenocysteine insertion. SECp43 is located primarily in the nucleus and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal polar/acidic region. 82 matched cddid_all.tbl CDD cd12613 cd12613 410025 RRM2_NGR1_NAM8_like RNA recognition motif 2 (RRM2) found in yeast negative growth regulatory protein NGR1, yeast protein NAM8 and similar proteins. This subgroup corresponds to the RRM2 of NGR1 and NAM8. NGR1, also termed RNA-binding protein RBP1, is a putative glucose-repressible protein that binds both, RNA and single-stranded DNA (ssDNA), in yeast. It may function in regulating cell growth in early log phase, possibly through its participation in RNA metabolism. NGR1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a glutamine-rich stretch that may be involved in transcriptional activity. In addition, NGR1 has an asparagine-rich region near the carboxyl terminus which also harbors a methionine-rich region. The family also includes protein NAM8, which is a putative RNA-binding protein that acts as a suppressor of mitochondrial splicing deficiencies when overexpressed in yeast. It may be a non-essential component of the mitochondrial splicing machinery. Like NGR1, NAM8 contains two RRMs. 80 matched cddid_all.tbl CDD cd12614 cd12614 410026 RRM1_PUB1 RNA recognition motif 1 (RRM1) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins. This subgroup corresponds to the RRM1 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. 74 matched cddid_all.tbl CDD cd12615 cd12615 410027 RRM1_TIA1 RNA recognition motif 1 (RRM1) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins. This subgroup corresponds to the RRM1 of TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and functions as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. 74 matched cddid_all.tbl CDD cd12616 cd12616 410028 RRM1_TIAR RNA recognition motif 1 (RRM1) found in nucleolysin TIAR and similar proteins. This subgroup corresponds to the RRM1 of nucleolysin TIAR, also termed TIA-1-related protein, and a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. 81 matched cddid_all.tbl CDD cd12617 cd12617 410029 RRM2_TIAR RNA recognition motif 2 (RRM2) found in nucleolysin TIAR and similar proteins. This subgroup corresponds to the RRM2 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal, highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. 80 matched cddid_all.tbl CDD cd12618 cd12618 410030 RRM2_TIA1 RNA recognition motif 2 (RRM2) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins. This subgroup corresponds to the RRM2 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1), and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. 78 matched cddid_all.tbl CDD cd12619 cd12619 410031 RRM2_PUB1 RNA recognition motif 2 (RRM2) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins. This subgroup corresponds to the RRM2 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. It is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA). However, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. 80 matched cddid_all.tbl CDD cd12620 cd12620 241064 RRM3_TIAR RNA recognition motif 3 (RRM3) found in nucleolysin TIAR and similar proteins. This subgroup corresponds to the RRM3 of nucleolysin TIAR, also termed TIA-1-related protein, a cytotoxic granule-associated RNA-binding protein that shows high sequence similarity with 40-kDa isoform of T-cell-restricted intracellular antigen-1 (p40-TIA-1). TIAR is mainly localized in the nucleus of hematopoietic and nonhematopoietic cells. It is translocated from the nucleus to the cytoplasm in response to exogenous triggers of apoptosis. TIAR possesses nucleolytic activity against cytolytic lymphocyte (CTL) target cells. It can trigger DNA fragmentation in permeabilized thymocytes, and thus may function as an effector responsible for inducing apoptosis. TIAR is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. It interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. 73 matched cddid_all.tbl CDD cd12621 cd12621 410032 RRM3_TIA1 RNA recognition motif 3 (RRM3) found in nucleolysin TIA-1 isoform p40 (p40-TIA-1) and similar proteins. This subgroup corresponds to the RRM3 of p40-TIA-1, the 40-kDa isoform of T-cell-restricted intracellular antigen-1 (TIA-1) and a cytotoxic granule-associated RNA-binding protein mainly found in the granules of cytotoxic lymphocytes. TIA-1 can be phosphorylated by a serine/threonine kinase that is activated during Fas-mediated apoptosis, and function as the granule component responsible for inducing apoptosis in cytolytic lymphocyte (CTL) targets. It is composed of three N-terminal highly homologous RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glutamine-rich C-terminal auxiliary domain containing a lysosome-targeting motif. TIA-1 interacts with RNAs containing short stretches of uridylates and its RRM2 can mediate the specific binding to uridylate-rich RNAs. 72 matched cddid_all.tbl CDD cd12622 cd12622 410033 RRM3_PUB1 RNA recognition motif 3 (RRM3) found in yeast nuclear and cytoplasmic polyadenylated RNA-binding protein PUB1 and similar proteins. This subfamily corresponds to the RRM3 of yeast protein PUB1, also termed ARS consensus-binding protein ACBP-60, or poly uridylate-binding protein, or poly(U)-binding protein. PUB1 has been identified as both, a heterogeneous nuclear RNA-binding protein (hnRNP) and a cytoplasmic mRNA-binding protein (mRNP), which may be stably bound to a translationally inactive subpopulation of mRNAs within the cytoplasm. PUB1 is distributed in both, the nucleus and the cytoplasm, and binds to poly(A)+ RNA (mRNA or pre-mRNA). Although it is one of the major cellular proteins cross-linked by UV light to polyadenylated RNAs in vivo, PUB1 is nonessential for cell growth in yeast. PUB1 also binds to T-rich single stranded DNA (ssDNA); however, there is no strong evidence implicating PUB1 in the mechanism of DNA replication. PUB1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a GAR motif (glycine and arginine rich stretch) that is located between RRM2 and RRM3. 74 matched cddid_all.tbl CDD cd12623 cd12623 410034 RRM_PPARGC1A RNA recognition motif (RRM) found in peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1alpha, or PPARGC-1-alpha) and similar proteins. This subgroup corresponds to the RRM of PGC-1alpha, also termed PPARGC-1-alpha, or ligand effect modulator 6, a member of a family of transcription coactivators that plays a central role in the regulation of cellular energy metabolism. As an inducible transcription coactivator, PGC-1alpha can interact with a broad range of transcription factors involved in a wide variety of biological responses, such as adaptive thermogenesis, skeletal muscle fiber type switching, glucose/fatty acid metabolism, and heart development. PGC-1alpha stimulates mitochondrial biogenesis and promotes oxidative metabolism. It participates in the regulation of both carbohydrate and lipid metabolism and plays a role in disorders such as obesity, diabetes, and cardiomyopathy. PGC-1alpha is a multi-domain protein containing an N-terminal activation domain region, a central region involved in the interaction with at least a nuclear receptor, and a C-terminal domain region. The N-terminal domain region consists of three leucine-rich motifs (L1, NR box 2 and 3), among which the two last are required for interaction with nuclear receptors, potential nuclear localization signals (NLS), and a proline-rich region overlapping a putative repression domain. The C-terminus of PGC-1alpha is composed of two arginine/serine-rich regions (SR domains), a putative dimerization domain, and an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). PGC-1alpha could interact favorably with single-stranded RNA. 91 matched cddid_all.tbl CDD cd12624 cd12624 410035 RRM_PRC RNA recognition motif (RRM) found in peroxisome proliferator-activated receptor gamma coactivator-related protein 1 (PRC) and similar proteins. This subgroup corresponds to the RRM of PRC, also termed PGC-1-related coactivator, one of the members of PGC-1 transcriptional coactivators family, including peroxisome proliferator-activated receptor gamma coactivators PGC-1alpha and PGC-1beta. Unlike PGC-1alpha and PGC-1beta, PRC is ubiquitous and more abundantly expressed in proliferating cells than in growth-arrested cells. PRC has been implicated in the regulation of several metabolic pathways, mitochondrial biogenesis, and cell growth. It functions as a growth-regulated transcriptional cofactor activating many nuclear genes specifying mitochondrial respiratory function. PRC directly interacts with nuclear transcriptional factors implicated in respiratory chain expression including nuclear respiratory factors 1 and 2 (NRF-1 and NRF-2), CREB (cAMP-response element-binding protein), and estrogen-related receptor alpha (ERRalpha). It interacts indirectly with the NRF-2beta subunit through host cell factor (HCF), a cellular protein involved in herpes simplex virus (HSV) infection and cell cycle regulation. Furthermore, like PGC-1alpha and PGC-1beta, PRC can transactivate a number of NRF-dependent nuclear genes required for mitochondrial respiratory function, including those encoding cytochrome c, 5-aminolevulinate synthase, Tfam, and TFB1M, and TFB2M. Further research indicates that PRC may also act as a sensor of metabolic stress that orchestrates a redox-sensitive program of inflammatory gene expression. PRC is a multi-domain protein containing an N-terminal activation domain, an LXXLL coactivator signature, a central proline-rich region, a tetrapeptide motif (DHDY) responsible for HCF binding, a C-terminal arginine/serine-rich (SR) domain, and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 91 matched cddid_all.tbl CDD cd12625 cd12625 241069 RRM1_IGF2BP1 RNA recognition motif 1 (RRM1) found in vertebrate insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1). This subgroup corresponds to the RRM1 of IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also termed coding region determinant-binding protein (CRD-BP), or VICKZ family member 1, or zipcode-binding protein 1 (ZBP-1). IGF2BP1 is a multi-functional regulator of RNA metabolism that has been implicated in the control of aspects of localization, stability, and translation for many mRNAs. It is predominantly located in cytoplasm and was initially identified as a trans-acting factor that interacts with the zipcode in the 3'- untranslated region (UTR) of the beta-actin mRNA, which is important for its localization and translational regulation. It inhibits IGF-II mRNA translation through binding to the 5'-UTR of the transcript. IGF2BP1 also acts as human immunodeficiency virus type 1 (HIV-1) Gag-binding factor that interacts with HIV-1 Gag protein and blocks the formation of infectious HIV-1 particles. IGF2BP1 promotes mRNA stabilization; it functions as a coding region determinant (CRD)-binding protein that binds to the coding region of betaTrCP1 mRNA and prevents miR-183-mediated degradation of betaTrCP1 mRNA. It also promotes c-myc mRNA stability by associating with the CRD and stabilizes CD44 mRNA via interaction with the 3'-UTR of the transcript. In addition, IGF2BP1 specifically interacts with both Hepatitis C virus (HCV) 5'-UTR and 3'-UTR, further recruiting eIF3 and enhancing HCV internal ribosome entry site (IRES)-mediated translation initiation via the 3'-UTR. IGF2BP1 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. It also contains two putative nuclear export signals (NESs) and a putative nuclear localization signal (NLS). 77 matched cddid_all.tbl CDD cd12626 cd12626 241070 RRM1_IGF2BP2 RNA recognition motif 1 (RRM1) found in vertebrate insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2). This subgroup corresponds to the RRM1 of IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also termed hepatocellular carcinoma autoantigen p62, or VICKZ family member 2, which is a ubiquitously expressed RNA-binding protein involved in the stimulation of insulin action. It is predominantly nuclear. SNPs in IGF2BP2 gene are implicated in susceptibility to type 2 diabetes. IGF2BP2 plays an important role in cellular motility; it regulates the expression of PINCH-2, an important mediator of cell adhesion and motility, and MURF-3, a microtubule-stabilizing protein, through direct binding to their mRNAs. IGF2BP2 may be involved in the regulation of mRNA stability through the interaction with the AU-rich element-binding factor AUF1. IGF2BP2 binds initially to nascent beta-actin transcripts and facilitates the subsequent binding of the shuttling IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. 77 matched cddid_all.tbl CDD cd12627 cd12627 410036 RRM1_IGF2BP3 RNA recognition motif 1 (RRM1) found in vertebrate insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3). This subgroup corresponds to the RRM1 of IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also termed KH domain-containing protein overexpressed in cancer (KOC), or VICKZ family member 3, an RNA-binding protein that plays an important role in the differentiation process during early embryogenesis. It is known to bind to and repress the translation of IGF2 leader 3 mRNA. IGF2BP3 also acts as a Glioblastoma-specific proproliferative and proinvasive marker acting through IGF2 resulting in the activation of oncogenic phosphatidylinositol 3-kinase/mitogen-activated protein kinase (PI3K/MAPK) pathways. IGF2BP3 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. 77 matched cddid_all.tbl CDD cd12628 cd12628 410037 RRM2_IGF2BP1 RNA recognition motif 2 (RRM2) found in vertebrate insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1). This subgroup corresponds to the RRM2 of IGF2BP1 (IGF2 mRNA-binding protein 1 or IMP-1), also termed coding region determinant-binding protein (CRD-BP), or VICKZ family member 1, or zipcode-binding protein 1 (ZBP-1). IGF2BP1 is a multi-functional regulator of RNA metabolism that has been implicated in the control of aspects of localization, stability, and translation for many mRNAs. It is predominantly located in cytoplasm and was initially identified as a trans-acting factor that interacts with the zipcode in the 3'- untranslated region (UTR) of the beta-actin mRNA, which is important for its localization and translational regulation. It inhibits IGF-II mRNA translation through binding to the 5'-UTR of the transcript. IGF2BP1 also acts as human immunodeficiency virus type 1 (HIV-1) Gag-binding factor that interacts with HIV-1 Gag protein and blocks the formation of infectious HIV-1 particles. It promotes mRNA stabilization and functions as a coding region determinant (CRD)-binding protein that binds to the coding region of betaTrCP1 mRNA and prevents miR-183-mediated degradation of betaTrCP1 mRNA. It also promotes c-myc mRNA stability by associating with the CRD. It stabilizes CD44 mRNA via interaction with the 3'-UTR of the transcript. In addition, IGF2BP1 specifically interacts with both Hepatitis C virus (HCV) 5'-UTR and 3'-UTR, further recruiting eIF3 and enhancing HCV internal ribosome entry site (IRES)-mediated translation initiation via the 3'-UTR. IGF2BP1 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. It also contains two putative nuclear export signals (NESs) and a putative nuclear localization signal (NLS). 76 matched cddid_all.tbl CDD cd12629 cd12629 410038 RRM2_IGF2BP2 RNA recognition motif 2 (RRM2) found in vertebrate insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2). This subgroup corresponds to the RRM2 of IGF2BP2 (IGF2 mRNA-binding protein 2 or IMP-2), also termed hepatocellular carcinoma autoantigen p62, or VICKZ family member 2, a ubiquitously expressed RNA-binding protein involved in the stimulation of insulin action. It is predominantly nuclear. SNPs in IGF2BP2 gene are implicated in susceptibility to type 2 diabetes. IGF2BP2 plays an important role in cellular motility; it regulates the expression of PINCH-2, an important mediator of cell adhesion and motility, and MURF-3, a microtubule-stabilizing protein, through direct binding to their mRNAs. IGF2BP2 may be involved in the regulation of mRNA stability through the interaction with the AU-rich element-binding factor AUF1. In addition, IGF2BP2 binds initially to nascent beta-actin transcripts and facilitates the subsequent binding of the shuttling IGF2BP1. IGF2BP2 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. 76 matched cddid_all.tbl CDD cd12630 cd12630 410039 RRM2_IGF2BP3 RNA recognition motif 2 (RRM2) found in vertebrate insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3). This subgroup corresponds to the RRM2 of IGF2BP3 (IGF2 mRNA-binding protein 3 or IMP-3), also termed KH domain-containing protein overexpressed in cancer (KOC), or VICKZ family member 3, an RNA-binding protein that plays an important role in the differentiation process during early embryogenesis. It is known to bind to and repress the translation of IGF2 leader 3 mRNA. IGF2BP3 also acts as a Glioblastoma-specific proproliferative and proinvasive marker acting through IGF2 resulting in the activation of oncogenic phosphatidylinositol 3-kinase/mitogen-activated protein kinase (PI3K/MAPK) pathways. IGF2BP3 contains four hnRNP K-homology (KH) domains, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a RGG RNA-binding domain. 76 matched cddid_all.tbl CDD cd12631 cd12631 410040 RRM1_CELF1_2_Bruno RNA recognition motif 1 (RRM1) found in CUGBP Elav-like family member CELF-1, CELF-2, Drosophila melanogaster Bruno protein and similar proteins. This subgroup corresponds to the RRM1 of CELF-1, CELF-2 and Bruno protein. CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR) belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in regulation of pre-mRNA splicing, and control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. The human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. This subgroup also includes Drosophila melanogaster Bruno protein, which plays a central role in regulation of Oskar (Osk) expression in flies. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. 84 matched cddid_all.tbl CDD cd12632 cd12632 410041 RRM1_CELF3_4_5_6 RNA recognition motif 1 (RRM1) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins. This subfamily corresponds to the RRM1 of CELF-3, CELF-4, CELF-5, CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In additiona to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. 87 matched cddid_all.tbl CDD cd12633 cd12633 241077 RRM1_FCA RNA recognition motif 1 (RRM1) found in plant flowering time control protein FCA and similar proteins. This subgroup corresponds to the RRM1 of FCA, a gene controlling flowering time in Arabidopsis, encoding a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. 80 matched cddid_all.tbl CDD cd12634 cd12634 410042 RRM2_CELF1_2 RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins. This subgroup corresponds to the RRM2 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP), CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It binds specifically to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it preferentially binds to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contains three highly conserved RRMs. It binds to RNA via the first two RRMs, which are also important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. 81 matched cddid_all.tbl CDD cd12635 cd12635 410043 RRM2_CELF3_4_5_6 RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins. This subgroup corresponds to the RRM2 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, being highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contain three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. On the other hand, both RRM1 and RRM2 of CELF-4 can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, being strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in a muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. 81 matched cddid_all.tbl CDD cd12636 cd12636 410044 RRM2_Bruno_like RNA recognition motif 2 (RRM2) found in Drosophila melanogaster Bruno protein and similar proteins. This subgroup corresponds to the RRM2 of Bruno, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. 81 matched cddid_all.tbl CDD cd12637 cd12637 410045 RRM2_FCA RNA recognition motif 2 (RRM2) found in plant flowering time control protein FCA and similar proteins. This subgroup corresponds to the RRM2 of FCA, a gene controlling flowering time in Arabidopsis, which encodes a flowering time control protein that functions in the posttranscriptional regulation of transcripts involved in the flowering process. The flowering time control protein FCA contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNP (ribonucleoprotein domains), and a WW protein interaction domain. 81 matched cddid_all.tbl CDD cd12638 cd12638 241082 RRM3_CELF1_2 RNA recognition motif 3 (RRM3) found in CUGBP Elav-like family member CELF-1, CELF-2 and similar proteins. This subgroup corresponds to the RRM3 of CELF-1 (also termed BRUNOL-2, or CUG-BP1, or EDEN-BP) and CELF-2 (also termed BRUNOL-3, or ETR-3, or CUG-BP2, or NAPOR), both of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-1 is strongly expressed in all adult and fetal tissues tested. Human CELF-1 is a nuclear and cytoplasmic RNA-binding protein that regulates multiple aspects of nuclear and cytoplasmic mRNA processing, with implications for onset of type 1 myotonic dystrophy (DM1), a neuromuscular disease associated with an unstable CUG triplet expansion in the 3'-UTR (3'-untranslated region) of the DMPK (myotonic dystrophy protein kinase) gene; it preferentially targets UGU-rich mRNA elements. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. The Xenopus homolog embryo deadenylation element-binding protein (EDEN-BP) mediates sequence-specific deadenylation of Eg5 mRNA. It specifically binds to the EDEN motif in the 3'-untranslated regions of maternal mRNAs and targets these mRNAs for deadenylation and translational repression. CELF-1 contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The two N-terminal RRMs of EDEN-BP are necessary for the interaction with EDEN as well as a part of the linker region (between RRM2 and RRM3). Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. CELF-2 is expressed in all tissues at some level, but highest in brain, heart, and thymus. It has been implicated in the regulation of nuclear and cytoplasmic RNA processing events, including alternative splicing, RNA editing, stability and translation. CELF-2 shares high sequence identity with CELF-1, but shows different binding specificity; it binds preferentially to sequences with UG repeats and UGUU motifs. It has been shown to bind to a Bruno response element, a cis-element involved in translational control of oskar mRNA in Drosophila, and share sequence similarity to Bruno, the Drosophila protein that mediates this process. It also binds to the 3'-UTR of cyclooxygenase-2 messages, affecting both translation and mRNA stability, and binds to apoB mRNA, regulating its C to U editing. CELF-2 also contain three highly conserved RRMs. It binds to RNA via the first two RRMs, which are important for localization in the cytoplasm. The splicing activation or repression activity of CELF-2 on some specific substrates is mediated by RRM1/RRM2. Both, RRM1 and RRM2 of CELF-2, can activate cardiac troponin T (cTNT) exon 5 inclusion. In addition, CELF-2 possesses a typical arginine and lysine-rich nuclear localization signal (NLS) in the C-terminus, within RRM3. 92 matched cddid_all.tbl CDD cd12639 cd12639 241083 RRM3_CELF3_4_5_6 RNA recognition motif 2 (RRM2) found in CUGBP Elav-like family member CELF-3, CELF-4, CELF-5, CELF-6 and similar proteins. This subgroup corresponds to the RRM3 of CELF-3, CELF-4, CELF-5, and CELF-6, all of which belong to the CUGBP1 and ETR-3-like factors (CELF) or BRUNOL (Bruno-like) family of RNA-binding proteins that display dual nuclear and cytoplasmic localizations and have been implicated in the regulation of pre-mRNA splicing and in the control of mRNA translation and deadenylation. CELF-3, expressed in brain and testis only, is also known as bruno-like protein 1 (BRUNOL-1), or CAG repeat protein 4, or CUG-BP- and ETR-3-like factor 3, or embryonic lethal abnormal vision (ELAV)-type RNA-binding protein 1 (ETR-1), or expanded repeat domain protein CAG/CTG 4, or trinucleotide repeat-containing gene 4 protein (TNRC4). It plays an important role in the pathogenesis of tauopathies. CELF-3 contains three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein.The effect of CELF-3 on tau splicing is mediated mainly by the RNA-binding activity of RRM2. The divergent linker region might mediate the interaction of CELF-3 with other proteins regulating its activity or involved in target recognition. CELF-4, highly expressed throughout the brain and in glandular tissues, moderately expressed in heart, skeletal muscle, and liver, is also known as bruno-like protein 4 (BRUNOL-4), or CUG-BP- and ETR-3-like factor 4. Like CELF-3, CELF-4 also contains three highly conserved RRMs. The splicing activation or repression activity of CELF-4 on some specific substrates is mediated by its RRM1/RRM2. Both, RRM1 and RRM2 of CELF-4, can activate cardiac troponin T (cTNT) exon 5 inclusion. CELF-5, expressed in brain, is also known as bruno-like protein 5 (BRUNOL-5), or CUG-BP- and ETR-3-like factor 5. Although its biological role remains unclear, CELF-5 shares same domain architecture with CELF-3. CELF-6, strongly expressed in kidney, brain, and testis, is also known as bruno-like protein 6 (BRUNOL-6), or CUG-BP- and ETR-3-like factor 6. It activates exon inclusion of a cardiac troponin T minigene in transient transfection assays in an muscle-specific splicing enhancer (MSE)-dependent manner and can activate inclusion via multiple copies of a single element, MSE2. CELF-6 also promotes skipping of exon 11 of insulin receptor, a known target of CELF activity that is expressed in kidney. In addition to three highly conserved RRMs, CELF-6 also possesses numerous potential phosphorylation sites, a potential nuclear localization signal (NLS) at the C terminus, and an alanine-rich region within the divergent linker region. 79 matched cddid_all.tbl CDD cd12640 cd12640 241084 RRM3_Bruno_like RNA recognition motif 3 (RRM3) found in Drosophila melanogaster Bruno protein and similar proteins. This subgroup corresponds to the RRM3 of Bruno protein, a Drosophila RNA recognition motif (RRM)-containing protein that plays a central role in regulation of Oskar (Osk) expression. It mediates repression by binding to regulatory Bruno response elements (BREs) in the Osk mRNA 3' UTR. The full-length Bruno protein contains three RRMs, two located in the N-terminal half of the protein and the third near the C-terminus, separated by a linker region. 79 matched cddid_all.tbl CDD cd12641 cd12641 410046 RRM_TRA2B RNA recognition motif (RRM) found in Transformer-2 protein homolog beta (TRA-2 beta) and similar proteins. This subgroup corresponds to the RRM of TRA2-beta or TRA-2-beta, also termed splicing factor, arginine/serine-rich 10 (SFRS10), or transformer-2 protein homolog B, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-beta is a serine/arginine-rich (SR) protein that controls the pre-mRNA alternative splicing of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. It contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. TRA2-beta specifically binds to two types of RNA sequences, the CAA and (GAA)2 sequences, through the RRMs in different RNA binding modes. 87 matched cddid_all.tbl CDD cd12642 cd12642 410047 RRM_TRA2A RNA recognition motif (RRM) found in transformer-2 protein homolog alpha (TRA-2 alpha) and similar proteins. This subgroup corresponds to the RRM of TRA2-alpha or TRA-2-alpha, also termed transformer-2 protein homolog A, a mammalian homolog of Drosophila transformer-2 (Tra2). TRA2-alpha is a 40-kDa serine/arginine-rich (SR) protein (SRp40) that specifically binds to gonadotropin-releasing hormone (GnRH) exonic splicing enhancer on exon 4 (ESE4) and is necessary for enhanced GnRH pre-mRNA splicing. It strongly stimulates GnRH intron A excision in a dose-dependent manner. In addition, TRA2-alpha can interact with either 9G8 or SRp30c, which may also be crucial for ESE-dependent GnRH pre-mRNA splicing. TRA2-alpha contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), flanked by the N- and C-terminal arginine/serine (RS)-rich regions. 84 matched cddid_all.tbl CDD cd12643 cd12643 410048 RRM_CFIm68 RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 68 kDa subunit (CFIm68 or CPSF6) and similar proteins. This subgroup corresponds to the RRM of CFIm68. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. Two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. The family includes CFIm68, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF6), or cleavage and polyadenylation specificity factor 68 kDa subunit (CPSF68), or protein HPBRII-4/7. CFIm68 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. The N-terminal RRM of CFIm68 mediates the interaction with CFIm25. It also serves to enhance RNA binding and facilitate RNA looping. 77 matched cddid_all.tbl CDD cd12644 cd12644 410049 RRM_CFIm59 RNA recognition motif (RRM) found in pre-mRNA cleavage factor Im 59 kDa subunit (CFIm59 or CPSF7) and similar proteins. This subgroup corresponds to the RRM of CFIm59. Cleavage factor Im (CFIm) is a highly conserved component of the eukaryotic mRNA 3' processing machinery that functions in UGUA-mediated poly(A) site recognition, the regulation of alternative poly(A) site selection, mRNA export, and mRNA splicing. It is a complex composed of a small 25 kDa (CFIm25) subunit and a larger 59/68/72 kDa subunit. The two separate genes, CPSF6 and CPSF7, code for two isoforms of the large subunit, CFIm68 and CFIm59. The family includes CFIm59, also termed cleavage and polyadenylation specificity factor subunit 6 (CPSF7), or cleavage and polyadenylation specificity factor 59 kDa subunit (CPSF59). CFIm59 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a central proline-rich region, and a C-terminal RS-like domain. The N-terminal RRM of CFIm59 mediates the interaction with CFIm25. It also serves to enhance RNA binding and facilitate RNA looping. 90 matched cddid_all.tbl CDD cd12645 cd12645 241089 RRM_SRSF3 RNA recognition motif (RRM) found in vertebrate serine/arginine-rich splicing factor 3 (SRSF3). This subgroup corresponds to the RRM of SRSF3, also termed pre-mRNA-splicing factor SRp20, a splicing regulatory serine/arginine (SR) protein that modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation and tumor induction and maintenance. SRSF3 can shuttle between the nucleus and cytoplasm. It contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. 81 matched cddid_all.tbl CDD cd12646 cd12646 410050 RRM_SRSF7 RNA recognition motif (RRM) found in vertebrate serine/arginine-rich splicing factor 7 (SRSF7). This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions. 77 matched cddid_all.tbl CDD cd12647 cd12647 410051 RRM_UHM_SPF45 RNA recognition motif (RRM) found in UHM domain of 45 kDa-splicing factor (SPF45) and similar proteins. This subgroup corresponds to the RRM of SPF45, also termed RNA-binding motif protein 17 (RBM17), an RNA-binding protein consisting of an unstructured N-terminal region, followed by a G-patch motif and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and an Arg-Xaa-Phe sequence motif. SPF45 regulates alternative splicing of the apoptosis regulatory gene FAS (also known as CD95). It induces exon 6 skipping in FAS pre-mRNA through the UHM domain that binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) present in the 3' splice site-recognizing factors U2AF65, SF1 and SF3b155. 95 matched cddid_all.tbl CDD cd12648 cd12648 410052 RRM3_UHM_PUF60 RNA recognition motif 3 (RRM3) found in UHM domain of poly(U)-binding-splicing factor PUF60 and similar proteins. This subgroup corresponds to the RRM3 of PUF60, also termed FUSE-binding protein-interacting repressor (FBP-interacting repressor or FIR), or Ro-binding protein 1 (RoBP1), or Siah-binding protein 1 (Siah-BP1), an essential splicing factor that functions as a poly-U RNA-binding protein required to reconstitute splicing in depleted nuclear extracts. Its function is enhanced through interaction with U2 auxiliary factor U2AF65. PUF60 also controls human c-myc gene expression by binding and inhibiting the transcription factor far upstream sequence element (FUSE)-binding-protein (FBP), an activator of c-myc promoters. PUF60 contains two central RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a C-terminal U2AF (U2 auxiliary factor) homology motifs (UHM) that harbors another RRM and binds to tryptophan-containing linear peptide motifs (UHM ligand motifs, ULMs) in several nuclear proteins. The research indicates that PUF60 binds FUSE as a dimer, and only the first two RRM domains participate in the single-stranded DNA recognition. 98 matched cddid_all.tbl CDD cd12649 cd12649 241093 RRM1_SXL RNA recognition motif 1 (RRM1) found in Drosophila sex-lethal (SXL) and similar proteins. This subfamily corresponds to the RRM1 of SXL which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. 81 matched cddid_all.tbl CDD cd12650 cd12650 410053 RRM1_Hu RNA recognition motif 1 (RRM1) found in the Hu proteins family. This subfamily corresponds to the RRM1 of the Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. 77 matched cddid_all.tbl CDD cd12651 cd12651 410054 RRM2_SXL RNA recognition motif 2 (RRM2) found in Drosophila sex-lethal (SXL) and similar proteins. This subfamily corresponds to the RRM2 of the sex-lethal protein (SXL) which governs sexual differentiation and X chromosome dosage compensation in Drosophila melanogaster. It induces female-specific alternative splicing of the transformer (tra) pre-mRNA by binding to the tra uridine-rich polypyrimidine tract at the non-sex-specific 3' splice site during the sex-determination process. SXL binds also to its own pre-mRNA and promotes female-specific alternative splicing. SXL contains an N-terminal Gly/Asn-rich domain that may be responsible for the protein-protein interaction, and tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that show high preference to bind single-stranded, uridine-rich target RNA transcripts. 81 matched cddid_all.tbl CDD cd12652 cd12652 410055 RRM2_Hu RNA recognition motif 2 (RRM2) found in the Hu proteins family. This subfamily corresponds to the RRM2 of Hu proteins family which represents a group of RNA-binding proteins involved in diverse biological processes. Since the Hu proteins share high homology with the Drosophila embryonic lethal abnormal vision (ELAV) protein, the Hu family is sometimes referred to as the ELAV family. Drosophila ELAV is exclusively expressed in neurons and is required for the correct differentiation and survival of neurons in flies. The neuronal members of the Hu family include Hu-antigen B (HuB or ELAV-2 or Hel-N1), Hu-antigen C (HuC or ELAV-3 or PLE21), and Hu-antigen D (HuD or ELAV-4), which play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. Hu-antigen R (HuR or ELAV-1 or HuA) is the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. Moreover, HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Hu proteins perform their cytoplasmic and nuclear molecular functions by coordinately regulating functionally related mRNAs. In the cytoplasm, Hu proteins recognize and bind to AU-rich RNA elements (AREs) in the 3' untranslated regions (UTRs) of certain target mRNAs, such as GAP-43, vascular epithelial growth factor (VEGF), the glucose transporter GLUT1, eotaxin and c-fos, and stabilize those ARE-containing mRNAs. They also bind and regulate the translation of some target mRNAs, such as neurofilament M, GLUT1, and p27. In the nucleus, Hu proteins function as regulators of polyadenylation and alternative splicing. Each Hu protein contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. 79 matched cddid_all.tbl CDD cd12653 cd12653 410056 RRM3_HuR RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen R (HuR). This subgroup corresponds to the RRM3 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. 85 matched cddid_all.tbl CDD cd12654 cd12654 241098 RRM3_HuB RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen B (HuB). This subgroup corresponds to the RRM3 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. 86 matched cddid_all.tbl CDD cd12655 cd12655 410057 RRM3_HuC RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen C (HuC). This subgroup corresponds to the RRM3 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. 85 matched cddid_all.tbl CDD cd12656 cd12656 241100 RRM3_HuD RNA recognition motif 3 (RRM3) found in vertebrate Hu-antigen D (HuD). This subgroup corresponds to the RRM3 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells. And it also regulates the neurite elongation and morphological differentiation. HuD specifically bound poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. 86 matched cddid_all.tbl CDD cd12657 cd12657 410058 RRM1_hnRNPM RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M). This subgroup corresponds to the RRM1 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). 76 matched cddid_all.tbl CDD cd12658 cd12658 410059 RRM1_MYEF2 RNA recognition motif 1 (RRM1) found in vertebrate myelin expression factor 2 (MEF-2). This subgroup corresponds to the RRM1 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. 76 matched cddid_all.tbl CDD cd12659 cd12659 410060 RRM2_hnRNPM RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M). This subgroup corresponds to the RRM2 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. It functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). 76 matched cddid_all.tbl CDD cd12660 cd12660 410061 RRM2_MYEF2 RNA recognition motif 2 (RRM2) found in vertebrate myelin expression factor 2 (MEF-2). This subgroup corresponds to the RRM2 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. 76 matched cddid_all.tbl CDD cd12661 cd12661 410062 RRM3_hnRNPM RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein M (hnRNP M). This subgroup corresponds to the RRM3 of hnRNP M, a pre-mRNA binding protein that may play an important role in the pre-mRNA processing. It also preferentially binds to poly(G) and poly(U) RNA homopolymers. Moreover, hnRNP M is able to interact with early spliceosomes, further influencing splicing patterns of specific pre-mRNAs. hnRNP M functions as the receptor of carcinoembryonic antigen (CEA) that contains the penta-peptide sequence PELPK signaling motif. In addition, hnRNP M and another splicing factor Nova-1 work together as dopamine D2 receptor (D2R) pre-mRNA-binding proteins. They regulate alternative splicing of D2R pre-mRNA in an antagonistic manner. hnRNP M contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an unusual hexapeptide-repeat region rich in methionine and arginine residues (MR repeat motif). 77 matched cddid_all.tbl CDD cd12662 cd12662 410063 RRM3_MYEF2 RNA recognition motif 3 (RRM3) found in vertebrate myelin expression factor 2 (MEF-2). This subgroup corresponds to the RRM3 of MEF-2, also termed MyEF-2 or MST156, a sequence-specific single-stranded DNA (ssDNA) binding protein that binds specifically to ssDNA derived from the proximal (MB1) element of the myelin basic protein (MBP) promoter and represses transcription of the MBP gene. MEF-2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which may be responsible for its ssDNA binding activity. 77 matched cddid_all.tbl CDD cd12663 cd12663 410064 RRM1_RAVER1 RNA recognition motif 1 (RRM1) found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1). This subgroup corresponds to the RRM1 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. 71 matched cddid_all.tbl CDD cd12664 cd12664 410065 RRM1_RAVER2 RNA recognition motif 1 (RRM1) found in vertebrate ribonucleoprotein PTB-binding 2 (raver-2). This subgroup corresponds to the RRM1 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. 70 matched cddid_all.tbl CDD cd12665 cd12665 410066 RRM2_RAVER1 RNA recognition motif 2 (RRM2) found found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1). This subgroup corresponds to the RRM2 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. 77 matched cddid_all.tbl CDD cd12666 cd12666 410067 RRM2_RAVER2 RNA recognition motif 2 (RRM2) found in vertebrate ribonucleoprotein PTB-binding 2 (raver-2). This subgroup corresponds to the RRM2 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. 77 matched cddid_all.tbl CDD cd12667 cd12667 410068 RRM3_RAVER1 RNA recognition motif 3 (RRM3) found in vertebrate ribonucleoprotein PTB-binding 1 (raver-1). This subgroup corresponds to the RRM3 of raver-1, a ubiquitously expressed heterogeneous nuclear ribonucleoprotein (hnRNP) that serves as a co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. It shuttles between the cytoplasm and the nucleus and can accumulate in the perinucleolar compartment, a dynamic nuclear substructure that harbors PTB. Raver-1 also modulates focal adhesion assembly by binding to the cytoskeletal proteins, including alpha-actinin, vinculin, and metavinculin (an alternatively spliced isoform of vinculin) at adhesion complexes, particularly in differentiated muscle tissue. Raver-1 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two PTB-binding [SG][IL]LGxxP motifs. Raver1 binds to PTB through the PTB-binding motifs at its C-terminal half, and binds to other partners, such as RNA having the sequence UCAUGCAGUCUG, through its N-terminal RRMs. Interestingly, the 12-nucleotide RNA having the sequence UCAUGCAGUCUG with micromolar affinity is found in vinculin mRNA. Additional research indicates that the RRM1 of raver-1 directs its interaction with the tail domain of activated vinculin. Then the raver1/vinculin tail (Vt) complex binds to vinculin mRNA, which is permissive for vinculin binding to F-actin. 92 matched cddid_all.tbl CDD cd12668 cd12668 410069 RRM3_RAVER2 RNA recognition motif 3 (RRM3) found found in vertebrate ribonucleoprotein PTB-binding 2 (raver-2). This subgroup corresponds to the RRM3 of raver-2, a novel member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family. It is present in vertebrates and shows high sequence homology to raver-1, a ubiquitously expressed co-repressor of the nucleoplasmic splicing repressor polypyrimidine tract-binding protein (PTB)-directed splicing of select mRNAs. In contrast, raver-2 exerts a distinct spatio-temporal expression pattern during embryogenesis and is mainly limited to differentiated neurons and glia cells. Although it displays nucleo-cytoplasmic shuttling in heterokaryons, raver2 localizes to the nucleus in glia cells and neurons. Raver-2 can interact with PTB and may participate in PTB-mediated RNA-processing. However, there is no evidence indicating that raver-2 can bind to cytoplasmic proteins. Raver-2 contains three N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two putative nuclear localization signals (NLS) at the N- and C-termini, a central leucine-rich region, and a C-terminal region harboring two [SG][IL]LGxxP motifs. Raver-2 binds to PTB through the SLLGEPP motif only, and binds to RNA through its RRMs. 98 matched cddid_all.tbl CDD cd12669 cd12669 410070 RRM1_Nop12p_like RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 12 (Nop12p) and similar proteins. This subgroup corresponds to the RRM1 of Nop12p which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 100 matched cddid_all.tbl CDD cd12670 cd12670 410071 RRM2_Nop12p_like RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 12 (Nop12p) and similar proteins. This subgroup corresponds to the RRM2 of Nop12p, which is encoded by YOL041C from Saccharomyces cerevisiae. It is a novel nucleolar protein required for pre-25S rRNA processing and normal rates of cell growth at low temperatures. Nop12p shares high sequence similarity with nucleolar protein 13 (Nop13p). Both, Nop12p and Nop13p, are not essential for growth. However, unlike Nop13p that localizes primarily to the nucleolus but is also present in the nucleoplasm to a lesser extent, Nop12p is localized to the nucleolus. Nop12p contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 77 matched cddid_all.tbl CDD cd12671 cd12671 410072 RRM_CSTF2_CSTF2T RNA recognition motif (RRM) found in cleavage stimulation factor subunit 2 (CSTF2), cleavage stimulation factor subunit 2 tau variant (CSTF2T) and similar proteins. This subgroup corresponds to the RRM domain of CSTF2, its tau variant and eukaryotic homologs. CSTF2, also termed cleavage stimulation factor 64 kDa subunit (CstF64), is the vertebrate conterpart of yeast mRNA 3'-end-processing protein RNA15. It is expressed in all somatic tissues and is one of three cleavage stimulatory factor (CstF) subunits required for polyadenylation. CstF64 contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a CstF77-binding domain, a repeated MEARA helical region and a conserved C-terminal domain reported to bind the transcription factor PC-4. During polyadenylation, CstF interacts with the pre-mRNA through the RRM of CstF64 at U- or GU-rich sequences within 10 to 30 nucleotides downstream of the cleavage site. CSTF2T, also termed tauCstF64, is a paralog of the X-linked cleavage stimulation factor CstF64 protein that supports polyadenylation in most somatic cells. It is expressed during meiosis and subsequent haploid differentiation in a more limited set of tissues and cell types, largely in meiotic and postmeiotic male germ cells, and to a lesser extent in brain. The loss of CSTF2T will cause male infertility, as it is necessary for spermatogenesis and fertilization. Moreover, CSTF2T is required for expression of genes involved in morphological differentiation of spermatids, as well as for genes having products that function during interaction of motile spermatozoa with eggs. It promotes germ cell-specific patterns of polyadenylation by using its RRM to bind to different sequence elements downstream of polyadenylation sites than does CstF64. 85 matched cddid_all.tbl CDD cd12672 cd12672 410073 RRM_DAZL RNA recognition motif (RRM) found in vertebrate deleted in azoospermia-like (DAZL) proteins. This subgroup corresponds to the RRM of DAZL, also termed SPGY-like-autosomal, encoded by the autosomal homolog of DAZ gene, DAZL. It is ancestral to the deleted in azoospermia (DAZ) protein. DAZL is germ-cell-specific RNA-binding protein that contains a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a DAZ motif, a protein-protein interaction domain. Although their specific biochemical functions remain to be investigated, DAZL proteins may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. 82 matched cddid_all.tbl CDD cd12673 cd12673 410074 RRM_BOULE RNA recognition motif (RRM) found in protein BOULE. This subgroup corresponds to the RRM of BOULE, the founder member of the human DAZ gene family. Invertebrates contain a single BOULE, while vertebrates, other than catarrhine primates, possess both BOULE and DAZL genes. The catarrhine primates possess BOULE, DAZL, and DAZ genes. BOULE encodes an RNA-binding protein containing an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a single copy of the DAZ motif. Although its specific biochemical functions remains to be investigated, BOULE protein may interact with poly(A)-binding proteins (PABPs), and act as translational activators of specific mRNAs during gametogenesis. 81 matched cddid_all.tbl CDD cd12674 cd12674 410075 RRM1_Nop4p RNA recognition motif 1 (RRM1) found in yeast nucleolar protein 4 (Nop4p) and similar proteins. This subgroup corresponds to the RRM1 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 80 matched cddid_all.tbl CDD cd12675 cd12675 410076 RRM2_Nop4p RNA recognition motif 2 (RRM2) found in yeast nucleolar protein 4 (Nop4p) and similar proteins. This subgroup corresponds to the RRM2 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 83 matched cddid_all.tbl CDD cd12676 cd12676 410077 RRM3_Nop4p RNA recognition motif 3 (RRM3) found in yeast nucleolar protein 4 (Nop4p) and similar proteins. This subgroup corresponds to the RRM3 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 107 matched cddid_all.tbl CDD cd12677 cd12677 410078 RRM4_Nop4p RNA recognition motif 4 (RRM4) found in yeast nucleolar protein 4 (Nop4p) and similar proteins. This subgroup corresponds to the RRM4 of Nop4p (also known as Nop77p), encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 158 matched cddid_all.tbl CDD cd12678 cd12678 410079 RRM_SLTM RNA recognition motif (RRM) found in Scaffold attachment factor (SAF)-like transcription modulator (SLTM) and similar proteins. This subgroup corresponds to the RRM domain of SLTM, also termed modulator of estrogen-induced transcription, which shares high sequence similarity with scaffold attachment factor B1 (SAFB1). It contains a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. To a large extent, SLTM co-localizes with SAFB1 in the nucleus, which suggests that they share similar functions, such as the inhibition of an oestrogen reporter gene. However, rather than mediating a specific inhibitory effect on oestrogen action, SLTM is shown to exert a generalized inhibitory effect on gene expression associated with induction of apoptosis in a wide range of cell lines. 74 matched cddid_all.tbl CDD cd12679 cd12679 410080 RRM_SAFB1_SAFB2 RNA recognition motif (RRM) found in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins. This subgroup corresponds to RRM of SAFB1, also termed scaffold attachment factor B (SAF-B), heat-shock protein 27 estrogen response element ERE and TATA-box-binding protein (HET), or heterogeneous nuclear ribonucleoprotein hnRNP A1- associated protein (HAP), a large multi-domain protein with well-described functions in transcriptional repression, RNA splicing and metabolism, and a proposed role in chromatin organization. Based on the numerous functions, SAFB1 has been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. SAFB1 specifically binds to AT-rich scaffold or matrix attachment region DNA elements (S/MAR DNA) by using its N-terminal scaffold attachment factor-box (SAF-box, also known as SAP domain), a homeodomain-like DNA binding motif. The central region of SAFB1 is composed of an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a nuclear localization signal (NLS). The C-terminus of SAFB1 contains Glu/Arg- and Gly-rich regions that might be involved in protein-protein interaction. Additional studies indicate that the C-terminal region contains a potent and transferable transcriptional repression domain. Another family member is SAFB2, a homolog of SAFB1. Both SAFB1 and SAFB2 are ubiquitously coexpressed and share very high sequence similarity, suggesting that they might function in a similar manner. However, unlike SAFB1, exclusively existing in the nucleus, SAFB2 is also present in the cytoplasm. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1. 76 matched cddid_all.tbl CDD cd12680 cd12680 410081 RRM_THOC4 RNA recognition motif (RRM) found in THO complex subunit 4 (THOC4) and similar proteins. This subgroup corresponds to the RRM of THOC4, also termed transcriptional coactivator Aly/REF, or ally of AML-1 and LEF-1, or bZIP-enhancing factor BEF, an mRNA transporter protein with a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It is involved in RNA transportation from the nucleus. THOC4 was initially identified as a transcription coactivator of LEF-1 and AML-1 for the TCRalpha enhancer function. In addition, THOC4 specifically binds to rhesus (RH) promoter in erythroid. It might be a novel transcription cofactor for erythroid-specific genes. 75 matched cddid_all.tbl CDD cd12681 cd12681 410082 RRM_SKAR RNA recognition motif (RRM) found in S6K1 Aly/REF-like target (SKAR) and similar proteins. This subgroup corresponds to the RRM of SKAR, also termed polymerase delta-interacting protein 3 (PDIP3), 46 kDa DNA polymerase delta interaction protein (PDIP46), belonging to the Aly/REF family of RNA binding proteins that have been implicated in coupling transcription with pre-mRNA splicing and nucleo-cytoplasmic mRNA transport. SKAR is widely expressed and localizes to the nucleus. It may be a critical player in the function of S6K1 in cell and organism growth control by binding the activated, hyperphosphorylated form of S6K1 but not S6K2. Furthermore, SKAR functions as a protein partner of the p50 subunit of DNA polymerase delta. In addition, SKAR may have particular importance in pancreatic beta cell size determination and insulin secretion. SKAR contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 69 matched cddid_all.tbl CDD cd12682 cd12682 410083 RRM_RBPMS RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing (RBP-MS). This subfamily corresponds to the RRM of RBP-MS, also termed heart and RRM expressed sequence (hermes), an RNA-binding proteins found in various vertebrate species. It contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RBP-MS physically interacts with Smad2, Smad3 and Smad4 and plays a role in regulation of Smad-mediated transcriptional activity. In addition, RBP-MS may be involved in regulation of mRNA translation and localization during Xenopus laevis development. 76 matched cddid_all.tbl CDD cd12683 cd12683 410084 RRM_RBPMS2 RNA recognition motif (RRM) found in vertebrate RNA-binding protein with multiple splicing 2 (RBP-MS2). This subfamily corresponds to the RRM of RBP-MS2, encoded by RBPMS2 gene, a paralog of RNA-binding protein with multiple splicing (RBP-MS). The biological function of RBP-MS2 remains unclear. Like RBP-MS, RBP-MS2 contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 76 matched cddid_all.tbl CDD cd12684 cd12684 410085 RRM_cpo RNA recognition motif (RRM) found in Drosophila couch potato (cpo) coding RNA-binding protein and similar proteins. This subfamily corresponds to the RRM of Cpo, an RNA-binding protein encoded by Drosophila couch potato (cpo) gene. Cpo contains a well conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It may control the processing of RNA molecules required for the proper functioning of the peripheral nervous system (PNS). 83 matched cddid_all.tbl CDD cd12685 cd12685 410086 RRM_RBM20 RNA recognition motif (RRM) found in vertebrate RNA-binding protein 20 (RBM20). This subfamily corresponds to the RRM of RBM20, an alternative splicing regulator associated with dilated cardiomyopathy (DCM). It contains only one copy of RNA-recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 76 matched cddid_all.tbl CDD cd12686 cd12686 410087 RRM1_PTBPH1_PTBPH2 RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2). This subfamily corresponds to the RRM1 of PTBPH1 and PTBPH2. Although their biological roles remain unclear, PTBPH1 and PTBPH2 show significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Both, PTBPH1 and PTBPH2, contain three RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 81 matched cddid_all.tbl CDD cd12687 cd12687 410088 RRM1_PTBPH3 RNA recognition motif 1 (RRM1) found in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3). This subfamily corresponds to the RRM1 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 75 matched cddid_all.tbl CDD cd12688 cd12688 410089 RRM1_PTBP1_like RNA recognition motif 1 (RRM1) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins. This subfamily corresponds to the RRM1 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and functions at several aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein and negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 81 matched cddid_all.tbl CDD cd12689 cd12689 410090 RRM1_hnRNPL_like RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins. This subfamily corresponds to the RRM1 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 80 matched cddid_all.tbl CDD cd12690 cd12690 410091 RRM3_PTBPH1_PTBPH2 RNA recognition motif 3 (RRM3) found in plant polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2). This subfamily corresponds to the RRM3 of PTBPH1 and PTBPH2. Although their biological roles remain unclear, PTBPH1 and PTBPH2 show significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Both, PTBPH1 and PTBPH2, contain three RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 97 matched cddid_all.tbl CDD cd12691 cd12691 241135 RRM2_PTBPH1_PTBPH2 RNA recognition motif 2 (RRM2) found in plant polypyrimidine tract-binding protein homolog 1 and 2 (PTBPH1 and PTBPH2). This subfamily corresponds to the RRM2 of PTBPH1 and PTBPH2. Although their biological roles remain unclear, PTBPH1 and PTBPH2 show significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Both, PTBPH1 and PTBPH2, contain three RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 95 matched cddid_all.tbl CDD cd12692 cd12692 410092 RRM2_PTBPH3 RNA recognition motif 2 (RRM2) found in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3). This subfamily corresponds to the RRM2 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 88 matched cddid_all.tbl CDD cd12693 cd12693 410093 RRM2_PTBP1_like RNA recognition motif 2 (RRM2) found in polypyrimidine tract-binding protein 1 (PTB or hnRNP I) and similar proteins. This subfamily corresponds to the RRM2 of polypyrimidine tract-binding protein 1 (PTB or hnRNP I), polypyrimidine tract-binding protein 2 (PTBP2 or nPTB), regulator of differentiation 1 (Rod1), and similar proteins found in Metazoa. PTB is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTBP2 is highly homologous to PTB and is perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 also contains four RRMs. ROD1 coding protein Rod1 is a mammalian PTB homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It may play a role controlling differentiation in mammals. All members in this family contain four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 96 matched cddid_all.tbl CDD cd12694 cd12694 410094 RRM2_hnRNPL_like RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein L (hnRNP-L) and similar proteins. This subfamily corresponds to the RRM2 of heterogeneous nuclear ribonucleoprotein L (hnRNP-L), heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL), and similar proteins. hnRNP-L is a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both nuclear and cytoplasmic roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-LL plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to hnRNP-L, which contains three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 86 matched cddid_all.tbl CDD cd12695 cd12695 410095 RRM3_PTBP1 RNA recognition motif 3 (RRM3) found in vertebrate polypyrimidine tract-binding protein 1 (PTB). This subgroup corresponds to the RRM3 of PTB, also known as 58 kDa RNA-binding protein PPTB-1 or heterogeneous nuclear ribonucleoprotein I (hnRNP I), an important negative regulator of alternative splicing in mammalian cells. PTB also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTB contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RRM1 and RRM2 are independent from each other and separated by flexible linkers. By contrast, there is an unusual and conserved interdomain interaction between RRM3 and RRM4. It is widely held that only RRMs 3 and 4 are involved in RNA binding and RRM2 mediates PTB homodimer formation. However, new evidence show that the RRMs 1 and 2 also contribute substantially to RNA binding. Moreover, PTB may not always dimerize to repress splicing. It is a monomer in solution. 93 matched cddid_all.tbl CDD cd12696 cd12696 410096 RRM3_PTBP2 RNA recognition motif 3 (RRM3) found in vertebrate polypyrimidine tract-binding protein 2 (PTBP2). This subgroup corresponds to the RRM3 of PTBP2, also known as neural polypyrimidine tract-binding protein or neurally-enriched homolog of PTB (nPTB), highly homologous to polypyrimidine tract binding protein (PTB) and perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 contains four RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 107 matched cddid_all.tbl CDD cd12697 cd12697 410097 RRM3_ROD1 RNA recognition motif 3 (RRM3) found in vertebrate regulator of differentiation 1 (Rod1). This subgroup corresponds to the RRM3 of ROD1 coding protein Rod1, a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. Rod1 contains four repeats of RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and does have RNA binding activities. 76 matched cddid_all.tbl CDD cd12698 cd12698 410098 RRM3_PTBPH3 RNA recognition motif 3 (RRM3) found in plant polypyrimidine tract-binding protein homolog 3 (PTBPH3). This subgroup corresponds to the RRM3 of PTBPH3. Although its biological roles remain unclear, PTBPH3 shows significant sequence similarity to polypyrimidine tract binding protein (PTB) that is an important negative regulator of alternative splicing in mammalian cells and also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. Like PTB, PTBPH3 contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 76 matched cddid_all.tbl CDD cd12699 cd12699 410099 RRM3_hnRNPL RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein L (hnRNP-L). This subgroup corresponds to the RRM3 of hnRNP-L, a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-L shows significant sequence homology with polypyrimidine tract-binding protein (PTB or hnRNP I). Both, hnRNP-L and PTB, are localized in the nucleus but excluded from the nucleolus. hnRNP-L is an RNA-binding protein with three RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 77 matched cddid_all.tbl CDD cd12700 cd12700 410100 RRM3_hnRPLL RNA recognition motif 3 (RRM3) found in vertebrate heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL). The subgroup corresponds to the RRM3 of hnRNP-LL which plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to heterogeneous nuclear ribonucleoprotein L (hnRNP-L), which is an abundant nuclear, multifunctional RNA-binding protein with three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 74 matched cddid_all.tbl CDD cd12701 cd12701 410101 RRM4_PTBP1 RNA recognition motif 4 (RRM4) found in vertebrate polypyrimidine tract-binding protein 1 (PTB). This subgroup corresponds to the RRM4 of PTB, also known as 58 kDa RNA-binding protein PPTB-1 or heterogeneous nuclear ribonucleoprotein I (hnRNP I), an important negative regulator of alternative splicing in mammalian cells. PTB also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTB contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RRM1 and RRM2 are independent from each other and separated by flexible linkers. By contrast, there is an unusual and conserved interdomain interaction between RRM3 and RRM4. It is widely held that only RRMs 3 and 4 are involved in RNA binding and RRM2 mediates PTB homodimer formation. However, new evidence shows that the RRMs 1 and 2 also contribute substantially to RNA binding. Moreover, PTB may not always dimerize to repress splicing. It is a monomer in solution. 76 matched cddid_all.tbl CDD cd12702 cd12702 241146 RRM4_PTBP2 RNA recognition motif 4 (RRM4) found in vertebrate polypyrimidine tract-binding protein 2 (PTBP2). This subgroup corresponds to the RRM4 of PTBP2, also known as neural polypyrimidine tract-binding protein or neurally-enriched homolog of PTB (nPTB), highly homologous to polypyrimidine tract binding protein (PTB) and perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 contains four RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 80 matched cddid_all.tbl CDD cd12703 cd12703 410102 RRM4_ROD1 RNA recognition motif 4 (RRM4) found in vertebrate regulator of differentiation 1 (Rod1). This subgroup corresponds to the RRM4 of ROD1 coding protein Rod1, a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein that negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. Rod1 contains four repeats of RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and does have RNA binding activities. 91 matched cddid_all.tbl CDD cd12704 cd12704 410103 RRM4_hnRNPL RNA recognition motif 4 (RRM4) found in vertebrate heterogeneous nuclear ribonucleoprotein L (hnRNP-L). This subgroup corresponds to the RRM4 of hnRNP-L, a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-L shows significant sequence homology with polypyrimidine tract-binding protein (PTB or hnRNP I). Both hnRNP-L and PTB are localized in the nucleus but excluded from the nucleolus. hnRNP-L is an RNA-binding protein with three RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 84 matched cddid_all.tbl CDD cd12705 cd12705 410104 RRM4_hnRPLL RNA recognition motif 4 (RRM4) found in vertebrate heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL). The subgroup corresponds to the RRM4 of hnRNP-LL which plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to heterogeneous nuclear ribonucleoprotein L (hnRNP-L), which is an abundant nuclear, multifunctional RNA-binding protein with three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 85 matched cddid_all.tbl CDD cd12706 cd12706 410105 RRM_LARP5 RNA recognition motif (RRM) found in vertebrate La-related protein 5 (LARP5 or LARP4B). This subgroup corresponds to the RRM of LARP5, a cytosolic protein that co-sediments with polysomes and accumulates upon stress induction in cellular stress granules. It can interact with the cytosolic poly(A) binding protein 1 (PABPC1) and the receptor for activated C Kinase (RACK1), a component of the 40S ribosomal subunit. LARP5 may function as a stimulatory factor of translation through bridging mRNA factors of the 3' end with initiating ribosomes. Like other La-related proteins (LARPs) family members, LARP5 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 77 matched cddid_all.tbl CDD cd12707 cd12707 410106 RRM_LARP4 RNA recognition motif (RRM) found in vertebrate La-related protein 4 (LARP4). This subgroup corresponds to the RRM of LARP4, a cytoplasmic factor that can bind poly(A) RNA and interact with poly(A) binding protein (PABP). It may play a role in promoting translation by stabilizing mRNA. LARP4 is structurally related to the La autoantigen. Like other La-related proteins (LARPs) family members, LARP4 contains a La motif (LAM) and an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 77 matched cddid_all.tbl CDD cd12708 cd12708 410107 RRM_RCAN1 RNA recognition motif (RRM) found in vertebrate regulator of calcineurin 1 (RCAN1). This subgroup corresponds to the RRM of RCAN1, also termed calcipressin-1, or Adapt78, or Down syndrome critical region protein 1, or myocyte-enriched calcineurin-interacting protein 1 (MCIP1), encoded by the Down syndrome critical region 1 (DSCR1) gene that is abundantly expressed in human brain, heart and muscles. Overexpressed RCAN1 functions as an inhibitor of the Ca2+/calmodulin-dependent phosphatase calcineurin (also termed PP2B or PP3C), and is associated with Alzheimer's disease (AD) and Down syndrome (DS). RCAN1 can be phosphorylated by several kinases such as big MAP kinase 1 (BMK1), glycogen synthase kinase-3 (GSK-3), NF-kappaB inducing kinase (NIK), and protein kinase A (PKA). The phosphorylation of RCAN1 can positively or negatively regulate calcineurin-mediated gene transcription, and also affect its protein stability in the ubiquitin-proteasome pathway. RCAN1 consists of an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a highly conserved SP repeat domain containing the phosphorylation site by GSK-3, a well-known PxIxIT motif responsible for docking many substrates to calcineurin, and an unrecognized C-terminal TxxP motif of unknown function. 93 matched cddid_all.tbl CDD cd12709 cd12709 410108 RRM_RCAN2 RNA recognition motif (RRM) found in vertebrate regulator of calcineurin 2 (RCAN2). This subgroup corresponds to the RRM of RCAN2, also termed calcipressin-2, or Down syndrome candidate region 1-like 1 (DSCR1L1), or myocyte-enriched calcineurin-interacting protein 2 (MCIP2), or thyroid hormone-responsive protein ZAKI-4, encoded by a novel thyroid hormone-responsive gene ZAKI-4 that is abundantly expressed in human brain, heart and muscles. RCAN2 binds to the catalytic subunit of Ca2+/calmodulin-dependent phosphatase calcineurin (also termed PP2B or PP3C), calcineurin A, and inhibits its phosphatase activity through its C-terminal region. RCAN2 consists of an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a highly conserved SP repeat domain containing the phosphorylation site by GSK-3, a well-known PxIxIT motif responsible for docking many substrates to calcineurin, and an unrecognized C-terminal TxxP motif of unknown function. 77 matched cddid_all.tbl CDD cd12710 cd12710 410109 RRM_RCAN3 RNA recognition motif (RRM) found in vertebrate regulator of calcineurin 3 (RCAN3). This subgroup corresponds to the RRM of RCAN3, also termed calcipressin-3, or Down syndrome candidate region 1-like protein 2 (DSCR1L2), or myocyte-enriched calcineurin-interacting protein 3 (MCIP3), encoded by a ubiquitously expressed DSCR1L2 gene. Overexpressed RCAN3 binds and inhibits the Ca2+/calmodulin-dependent phosphatase calcineurin (also termed PP2B or PP3C), and further down-regulates nuclear factor of activated T cells (NFAT)-dependent cytokine gene expression in activated human Jurkat T cells. Moreover, RCAN3 interacts with cardiac troponin I (TNNI3), a heart-specific inhibitory subunit of the troponin complex, and may play a role in cardiac contraction. RCAN3 consists of an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a highly conserved SP repeat domain containing the phosphorylation site by GSK-3, a well-known PxIxIT motif responsible for docking many substrates to calcineurin, and an unrecognized C-terminal TxxP motif of unknown function. 77 matched cddid_all.tbl CDD cd12711 cd12711 410110 RRM_TNRC6A RNA recognition motif (RRM) found in vertebrate GW182 autoantigen. This subgroup corresponds to the RRM of the GW182 autoantigen, also termed trinucleotide repeat-containing gene 6A protein (TNRC6A), or CAG repeat protein 26, or EMSY interactor protein, or protein GW1, or glycine-tryptophan protein of 182 kDa, a phosphorylated cytoplasmic autoantigen involved in stabilizing and/or regulating translation and/or storing several different mRNAs. GW182 is characterized by multiple glycine/tryptophan (G/W) repeats and is a critical component of GW bodies (GWBs, also called mammalian processing bodies, or P bodies). The mRNAs associated with GW182 are presumed to reside within GWBs. GW182 has been shown to bind multiple Ago-miRNA complexes, and thus plays a key role in miRNA-mediated translational repression and mRNA degradation. In the absence of Ago2, GW182 may induce translational silencing effect. GW182 is composed of an N-terminal G/W-rich region containing an Ago hook responsible for Ago protein-binding; a ubiquitin-associated (UBA) domain and a glutamine (Q)-rich region in the middle region; a middle G/W-rich region, a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal G/W-rich region, at the C-terminus. A bipartite C-terminal region including the middle and C-terminal G/W-rich regions is referred to as silencing domain that triggers silencing of bound transcripts by inhibiting protein expression and promoting mRNA decay via deadenylation. 92 matched cddid_all.tbl CDD cd12712 cd12712 410111 RRM_TNRC6B RNA recognition motif (RRM) found in vertebrate trinucleotide repeat-containing gene 6B protein (TNRC6B). This subgroup corresponds to the RRM of TNRC6B, one of three GW182 paralogs in mammalian genomes. It is involved in miRNA-mediated mRNA degradation. TNRC6B is composed of an N-terminal glycine/tryptophan (G/W)-rich region; a ubiquitin-associated (UBA) domain and a glutamine (Q)-rich region in the middle region; a middle G/W-rich region, a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal G/W-rich region, at the C-terminus. TNRC6B directly interacts with Argonaute (Ago) proteins through its N-terminal glycine/tryptophan (G/W)-rich region that is called Ago protein-binding domain. TNRC6B is enriched in P-bodies and its Q-rich domain is responsible for P-body localization. A bipartite C-terminal region including the middle and C-terminal G/W-rich regions is referred as silencing domain that triggers silencing of bound transcripts by inhibiting protein expression and promoting mRNA decay via deadenylation. The C-terminal half of TNRC6B comprising an RRM domain exerts a strong translation inhibition potential, which does not require either association with Agos or localization to P-bodies. 83 matched cddid_all.tbl CDD cd12713 cd12713 410112 RRM_TNRC6C RNA recognition motif (RRM) found in vertebrate trinucleotide repeat-containing gene 6C protein (TNRC6C). This subgroup corresponds to the RRM of TNRC6C, one of three GW182 paralogs in mammalian genomes. It is enriched in P-bodies and important for efficient miRNA-mediated repression. TNRC6C is composed of an N-terminal glycine/tryptophan (G/W)-rich region containing an Ago hook responsible for Ago protein-binding; a ubiquitin-associated (UBA) domain and a glutamine (Q)-rich region in the middle region; a middle G/W-rich region, a RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal G/W-rich region, at the C-terminus. A bipartite C-terminal region including the middle and C-terminal G/W-rich regions is referred as silencing domain that triggers silencing of bound transcripts by inhibiting protein expression and promoting mRNA decay via deadenylation. The C-terminal half containing the RRM domain functions as a key effector domain mediating protein synthesis repression by TNRC6C. 88 matched cddid_all.tbl CDD cd12714 cd12714 410113 RRM1_MATR3 RNA recognition motif 1 (RRM1) found in vertebrate matrin-3. This subgroup corresponds to the RRM1 of Matrin 3 (MATR3 or P130), a highly conserved inner nuclear matrix protein with a bipartite nuclear localization signal (NLS), two zinc finger domains predicted to bind DNA, and two RNA recognition motifs (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that are known to interact with RNA. MATR3 has been implicated in various biological processes. It is involved in RNA processing by interacting with other nuclear proteins to anchor hyperedited RNAs to the nuclear matrix. It plays a role in mRNA stabilization through maintaining the stability of certain mRNA species. Besides, it modulates the activity of proximal promoters by binding to highly repetitive sequences of matrix/scaffold attachment region (MAR/SAR). The phosphorylation of MATR3 is assumed to cause neuronal death. It is phosphorylated by the protein kinase ATM, which activates the cellular response to double strand breaks in the DNA. Its phosphorylation by protein kinase A (PKA) is responsible for the activation of the N-methyl-d-aspartic acid (NMDA) receptor. Furthermore, MATR3 has been identified as both a Ca2+-dependent CaM-binding protein and a downstream substrate of caspases. Additional research indicates that matrin 3 also binds Rev/Rev responsive element (RRE)-containing viral RNA and functions as a cofactor that mediates the post-transcriptional regulation of HIV-1. 76 matched cddid_all.tbl CDD cd12715 cd12715 410114 RRM2_MATR3 RNA recognition motif 2 (RRM2) found in vertebrate matrin-3. This subgroup corresponds to the RRM2 of Matrin 3 (MATR3 or P130), a highly conserved inner nuclear matrix protein with a bipartite nuclear localization signal (NLS), two zinc finger domains predicted to bind DNA, and two RNA recognition motifs (RRM), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), that are known to interact with RNA. MATR3 has been implicated in various biological processes. It is involved in RNA processing by interacting with other nuclear proteins to anchor hyperedited RNAs to the nuclear matrix. It plays a role in mRNA stabilization through maintaining the stability of certain mRNA species. Besides, it modulates the activity of proximal promoters by binding to highly repetitive sequences of matrix/scaffold attachment region (MAR/SAR). The phosphorylation of MATR3 is assumed to cause neuronal death. It is phosphorylated by the protein kinase ATM, which activates the cellular response to double strand breaks in the DNA. Its phosphorylation by protein kinase A (PKA) is responsible for the activation of the N-methyl-d-aspartic acid (NMDA) receptor. Furthermore, MATR3 has been identified as both a Ca2+-dependent CaM-binding protein and a downstream substrate of caspases. Additional research indicates that matrin 3 also binds Rev/Rev responsive element (RRE)-containing viral RNA and functions as a cofactor that mediates the post-transcriptional regulation of HIV-1. 80 matched cddid_all.tbl CDD cd12716 cd12716 410115 RRM1_2_NP220 RNA recognition motif 1 (RRM1) and 2 (RRM2) found in vertebrate nuclear protein 220 (NP220). This subgroup corresponds to RRM1 and RRM2 of NP220, also termed zinc finger protein 638 (ZN638), or cutaneous T-cell lymphoma-associated antigen se33-1, or zinc finger matrin-like protein, a large nucleoplasmic DNA-binding protein that binds to cytidine-rich sequences, such as CCCCC (G/C), in double-stranded DNA (dsDNA). NP220 contains multiple domains, including MH1, MH2, and MH3, domains homologous to the acidic nuclear protein matrin 3; RS, an arginine/serine-rich domain commonly found in pre-mRNA splicing factors; PstI-HindIII, a domain essential for DNA binding; acidic repeat, a domain with nine repeats of the sequence LVTVDEVIEEEDL; and a Cys2-His2 zinc finger-like motif that is also present in matrin 3. It may be involved in packaging, transferring, or processing transcripts. This subgroup corresponds to the domain of MH2 that contains two tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 76 matched cddid_all.tbl CDD cd12717 cd12717 410116 RRM_ETP1 RNA recognition motif (RRM) found in yeast RING finger protein ETP1 and similar proteins. This subgroup corresponds to the RRM of ETP1, also termed BRAP2 homolog, or ethanol tolerance protein 1, the yeast homolog of BRCA1-associated protein (BRAP2) found in vertebrates. It may be involved in ethanol and salt-induced transcriptional activation of the NHA1 promoter and heat shock protein genes (HSP12 and HSP26), and participate in ethanol-induced turnover of the low-affinity hexose transporter Hxt3p. ETP1 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C3HC4-type ring finger domain and a UBP-type zinc finger. 83 matched cddid_all.tbl CDD cd12718 cd12718 410117 RRM_BRAP2 RNA recognition motif (RRM) found in BRCA1-associated protein (BRAP2). This subgroup corresponds to the RRM of BRAP2, also termed impedes mitogenic signal propagation (IMP), or ring finger protein 52, or renal carcinoma antigen NY-REN-63, a novel cytoplasmic protein interacting with the two functional nuclear localisation signal (NLS) motifs of BRCA1, a nuclear protein linked to breast cancer. It also binds to the SV40 large T antigen NLS motif and the bipartite NLS motif found in mitosin. BRAP2 may serve as a cytoplasmic retention protein and play a role in the regulation of nuclear protein transport. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C3HC4-type ring finger domain and a UBP-type zinc finger. 84 matched cddid_all.tbl CDD cd12719 cd12719 410118 RRM_SYNJ1 RNA recognition motif (RRM) found in synaptojanin-1 and similar proteins. This subgroup corresponds to the RRM of synaptojanin-1, also termed synaptojanin, or synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1, originally identified as one of the major Grb2-binding proteins that may participate in synaptic vesicle endocytosis. It also acts as a Src homology 3 (SH3) domain-binding brain-specific inositol 5-phosphatase with a putative role in clathrin-mediated endocytosis. Synaptojanin-1 contains an N-terminal domain homologous to the cytoplasmic portion of the yeast protein Sac1p, a central inositol 5-phosphatase domain followed by a putative RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal proline-rich region mediating the binding of synaptojanin-1 to various SH3 domain-containing proteins including amphiphysin, SH3p4, SH3p8, SH3p13, and Grb2. Synaptojanin-1 has two tissue-specific alternative splicing isoforms, synaptojanin-145 expressed in brain and synaptojanin-170 expressed in peripheral tissues. Synaptojanin-145 is very abundant in nerve terminals and may play an essential role in the clathrin-mediated endocytosis of synaptic vesicles. In contrast to synaptojanin-145, synaptojanin-170 contains three unique asparagine-proline-phenylalanine (NPF) motifs in the C-terminal region and may functions as a potential binding partner for Eps15, a clathrin coat-associated protein acting as a major substrate for the tyrosine kinase activity of the epidermal growth factor receptor. 77 matched cddid_all.tbl CDD cd12720 cd12720 410119 RRM_SYNJ2 RNA recognition motif (RRM) found in synaptojanin-2 and similar proteins. This subgroup corresponds to the RRM of synaptojanin-2, also termed synaptic inositol-1,4,5-trisphosphate 5-phosphatase 2, an ubiquitously expressed central regulatory enzyme in the phosphoinositide-signaling cascade. As a novel Rac1 effector regulating the early step of clathrin-mediated endocytosis, synaptojanin-2 acts as a polyphosphoinositide phosphatase directly and specifically interacting with Rac1 in a GTP-dependent manner. It mediates the inhibitory effect of Rac1 on endocytosis and plays an important role in the Rac1-mediated control of cell growth. Synaptojanin-2 shows high sequence homology to the N-terminal Sac1p homology domain, the central inositol 5-phosphatase domain, the putative RNA recognition motif (RRM) of synaptojanin-1, but differs in the proline-rich region. 78 matched cddid_all.tbl CDD cd12721 cd12721 410120 RRM_Nup53p_fungi RNA recognition motif (RRM) found in yeast nucleoporin Nup53p and similar proteins. This subgroup corresponds to the RRM of Saccharomyces cerevisiae Nup53p, the ortholog of vertebrate nucleoporin Nup53. A unique property of yeast Nup53p is that it contains an additional Kap121p-binding domain and interacts specifically with the karyopherin Kap121p, which is involved in the assembly of Nup53p into NPCs. Like vertebrate Nup35, yeast Nup53p contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a C-terminal amphipathic alpha-helix and several FG repeats. The RRM domain lacks the conserved residues that typically bind RNA in canonical RRM domains. 86 matched cddid_all.tbl CDD cd12722 cd12722 410121 RRM_Nup53 RNA recognition motif (RRM) found in nucleoporin Nup53. This subgroup corresponds to the RRM of nucleoporin Nup53, also termed mitotic phosphoprotein 44 (MP-44), or nuclear pore complex protein Nup53, required for normal cell growth and nuclear morphology in vertebrate. It tightly associates with the nuclear envelope membrane and the nuclear lamina where it interacts with lamin B. It may also interact with a group of nucleoporins including Nup93, Nup155, and Nup205 and play a role in the association of the mitotic checkpoint protein Mad1 with the nuclear pore complex (NPC). Nup35 contains an atypical RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a C-terminal amphipathic alpha-helix and several FG repeats. This RRM lacks the conserved residues that typically bind RNA in canonical RRM domains. 74 matched cddid_all.tbl CDD cd12723 cd12723 410122 RRM1_CPEB1 RNA recognition motif 1 (RRM1) found in cytoplasmic polyadenylation element-binding protein 1 (CPEB-1) and similar proteins. This subgroup corresponds to the RRM2 of CPEB-1 (also termed CPE-BP1 or CEBP), an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bound to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. CPEB-1 contains an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. Both of the RRMs and the Zn finger are required for CPEB-1 to bind CPE. The N-terminal regulatory region may be responsible for CPEB-1 interacting with other proteins. 101 matched cddid_all.tbl CDD cd12724 cd12724 410123 RRM1_CPEB2_like RNA recognition motif 1 (RRM1) found in cytoplasmic polyadenylation element-binding protein CPEB-2, CPEB-3, CPEB-4 and similar protiens. This subgroup corresponds to the RRM1 of the paralog proteins CPEB-2, CPEB-3 and CPEB-4, all well-conserved in both, vertebrates and invertebrates. Due to the high sequence similarity, members in this family may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. Moreover, CPEB-2 impedes target RNA translation at elongation; it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All family members contain an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. In addition, they do have conserved nuclear export signals that are not present in CPEB-1. 92 matched cddid_all.tbl CDD cd12725 cd12725 410124 RRM2_CPEB1 RNA recognition motif 2 (RRM2) found in cytoplasmic polyadenylation element-binding protein 1 (CPEB-1) and similar proteins. This subgroup corresponds to the RRM2 of CPEB-1 (also termed CPE-BP1 or CEBP), an RNA-binding protein that interacts with the cytoplasmic polyadenylation element (CPE), a short U-rich motif in the 3' untranslated regions (UTRs) of certain mRNAs. It functions as a translational regulator that plays a major role in the control of maternal CPE-containing mRNA in oocytes, as well as of subsynaptic CPE-containing mRNA in neurons. Once phosphorylated and recruiting the polyadenylation complex, CPEB-1 may function as a translational activator stimulating polyadenylation and translation. Otherwise, it may function as a translational inhibitor when dephosphorylated and bound to a protein such as maskin or neuroguidin, which blocks translation initiation through interfering with the assembly of eIF-4E and eIF-4G. Although CPEB-1 is mainly located in cytoplasm, it can shuttle between nucleus and cytoplasm. CPEB-1 contains an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. Both of the RRMs and the Zn finger are required for CPEB-1 to bind CPE. The N-terminal regulatory region may be responsible for CPEB-1 interacting with other proteins. 84 matched cddid_all.tbl CDD cd12726 cd12726 410125 RRM2_CPEB2_like RNA recognition motif 2 (RRM2) found in cytoplasmic polyadenylation element-binding protein CPEB-2, CPEB-3, CPEB-4 and similar protiens. This subgroup corresponds to the RRM2 of the paralog proteins CPEB-2, CPEB-3 and CPEB-4, all well conserved in both, vertebrates and invertebrates. Due to the high sequence similarity, members in this family may share similar expression patterns and functions. CPEB-2 is an RNA-binding protein that is abundantly expressed in testis and localized in cytoplasm in transfected HeLa cells. It preferentially binds to poly(U) RNA oligomers and may regulate the translation of stored mRNAs during spermiogenesis. Moreover, CPEB-2 impedes target RNA translation at elongation; it directly interacts with the elongation factor, eEF2, to reduce eEF2/ribosome-activated GTP hydrolysis in vitro and inhibit peptide elongation of CPEB2-bound RNA in vivo. CPEB-3 is a sequence-specific translational regulatory protein that regulates translation in a polyadenylation-independent manner. It functions as a translational repressor that governs the synthesis of the AMPA receptor GluR2 through binding GluR2 mRNA. It also represses translation of a reporter RNA in transfected neurons and stimulates translation in response to NMDA. CPEB-4 is an RNA-binding protein that mediates meiotic mRNA cytoplasmic polyadenylation and translation. It is essential for neuron survival and present on the endoplasmic reticulum (ER). It is accumulated in the nucleus upon ischemia or the depletion of ER calcium. CPEB-4 is overexpressed in a large variety of tumors and is associated with many mRNAs in cancer cells. All family members contain an N-terminal unstructured region, two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a Zn-finger motif. In addition, they do have conserved nuclear export signals that are not present in CPEB-1. 81 matched cddid_all.tbl CDD cd12727 cd12727 410126 RRM_like_Smg4_UPF3A RNA recognition motif (RRM)-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog A (Upf3A). This subgroup corresponds to the RRM-like Smg4_UPF3 domain in Upf3A, also termed regulator of nonsense transcripts 3A, or nonsense mRNA reducing factor 3A, a human ortholog of yeast Upf3p and Caenorhabditis elegans SMG-4. It derives from gene UPF3A and is required for nonsense-mediated mRNA decay (NMD) in human. Upf3A is a nucleocytoplasmic shuttling protein that associates selectively with spliced beta-globin mRNA in vivo. Like other Upf3 proteins, Upf3A contains nuclear import and export signals, and a conserved Smg4_UPF3 domain with some similarity to an RNA recognition motif (RRM), indicating that it may be an RNA binding protein. 87 matched cddid_all.tbl CDD cd12728 cd12728 410127 RRM_like_Smg4_UPF3B RNA recognition motif (RRM)-like Smg4_UPF3 domain in up-frameshift suppressor 3 homolog B on chromosome X (Upf3B). This subgroup corresponds to the RRM-like Smg4_UPF3 domain in Upf3B, also termed regulator of nonsense transcripts 3B, or nonsense mRNA reducing factor 3B, a human ortholog of yeast Upf3p and Caenorhabditis elegans SMG-4. It derives from X-linked gene UPF3B and is required for nonsense-mediated mRNA decay (NMD) in human. Upf3B is a nucleocytoplasmic shuttling protein that associates selectively with spliced beta-globin mRNA in vivo. Like other Upf3 proteins, Upf3B contains nuclear import and export signals, and a conserved Smg4_UPF3 domain with some similarity to an RNA recognition motif (RRM), indicating that it may be an RNA binding protein. 89 matched cddid_all.tbl CDD cd12729 cd12729 410128 RRM1_hnRNPH_hnRNPH2_hnRNPF RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP H2, hnRNP F and similar proteins. This subgroup corresponds to the RRM1 of hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and hnRNP F. These represent a group of nuclear RNA binding proteins that play important roles in the regulation of alternative splicing decisions. hnRNP H and hnRNP F are two closely related proteins, both of which bind to the RNA sequence DGGGD. They are present in a complex with the tissue-specific splicing factor Fox2, and regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts. The presence of Fox 2 can allows hnRNP H and hnRNP F to better compete with the SR protein ASF/SF2 for binding to FGFR2 exon IIIc. Thus, hnRNP H and hnRNP F can function as potent silencers of FGFR2 exon IIIc inclusion through an interaction with the exonic GGG motifs. Furthermore, hnRNP H and hnRNP H2 are almost identical. Both of them have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. 79 matched cddid_all.tbl CDD cd12730 cd12730 410129 RRM1_GRSF1 RNA recognition motif 1 (RRM1) found in G-rich sequence factor 1 (GRSF-1) and similar proteins. This subgroup corresponds to the RRM1 of GRSF-1, a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic alpha-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity. 79 matched cddid_all.tbl CDD cd12731 cd12731 410130 RRM2_hnRNPH_hnRNPH2_hnRNPF RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein hnRNP H, hnRNP H2, hnRNP F and similar proteins. This subgroup corresponds to the RRM2 of hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and hnRNP F. These represent a group of nuclear RNA binding proteins that play important roles in the regulation of alternative splicing decisions. hnRNP H and hnRNP F are two closely related proteins, both of which bind to the RNA sequence DGGGD. They are present in a complex with the tissue-specific splicing factor Fox2, and regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts. The presence of Fox 2 can allows hnRNP H and hnRNP F to better compete with the SR protein ASF/SF2 for binding to FGFR2 exon IIIc. Thus, hnRNP H and hnRNP F can function as potent silencers of FGFR2 exon IIIc inclusion through an interaction with the exonic GGG motifs. Furthermore, hnRNP H and hnRNP H2 are almost identical; both have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. 90 matched cddid_all.tbl CDD cd12732 cd12732 410131 RRM2_hnRNPH3 RNA recognition motif 2 (RRM2) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) and similar proteins. This subgroup corresponds to the RRM2 of hnRNP H3 (also termed hnRNP 2H9), a nuclear RNA binding protein that belongs to the hnRNP H protein family that also includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and hnRNP F. This family is involved in mRNA processing and exhibit extensive sequence homology. Currently, little is known about the functions of hnRNP H3 except for its role in the splicing arrest induced by heat shock. In addition, the typical hnRNP H proteins contain contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and play an important role in efficiently silencing the exon. Members in this family can regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. In addition, like other hnRNP H protein family members, hnRNP H3 has an extensive glycine-rich region near the C-terminus, which may allow it to homo- or heterodimerize. 96 matched cddid_all.tbl CDD cd12733 cd12733 410132 RRM3_GRSF1 RNA recognition motif 3 (RRM3) found in G-rich sequence factor 1 (GRSF-1) and similar proteins. This subgroup corresponds to the RRM3 of G-rich sequence factor 1 (GRSF-1), a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. GRSF-1 contains three potential RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for the RNA binding. In addition, GRSF-1 has two auxiliary domains, an acidic alpha-helical domain and an N-terminal alanine-rich region, that may play a role in protein-protein interactions and provide binding specificity. 75 matched cddid_all.tbl CDD cd12734 cd12734 410133 RRM3_hnRNPH_hnRNPH2_hnRNPF RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein hnRNP H , hnRNP H2, hnRNP F and similar proteins. This subgroup corresponds to the RRM3 of hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H') and hnRNP F, which represent a group of nuclear RNA binding proteins that play important roles in the regulation of alternative splicing decisions. hnRNP H and hnRNP F are two closely related proteins, both of which bind to the RNA sequence DGGGD. They are present in a complex with the tissue-specific splicing factor Fox2, and regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts. The presence of Fox 2 can allows hnRNP H and hnRNP F to better compete with the SR protein ASF/SF2 for binding to FGFR2 exon IIIc. Thus, hnRNP H and hnRNP F can function as potent silencers of FGFR2 exon IIIc inclusion through an interaction with the exonic GGG motifs. Furthermore, hnRNP H and hnRNP H2 are almost identical; bothe have been found to bind nuclear-matrix proteins. hnRNP H activates exon inclusion by binding G-rich intronic elements downstream of the 5' splice site in the transcripts of c-src, human immunodeficiency virus type 1 (HIV-1), Bcl-X, GRIN1, and myelin. It silences exons when bound to exonic elements in the transcripts of beta-tropomyosin, HIV-1, and alpha-tropomyosin. hnRNP H2 has been implicated in pre-mRNA 3' end formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. In addition, the family members have an extensive glycine-rich region near the C-terminus, which may allow them to homo- or heterodimerize. 76 matched cddid_all.tbl CDD cd12735 cd12735 241179 RRM3_hnRNPH3 RNA recognition motif 3 (RRM3) found in heterogeneous nuclear ribonucleoprotein H3 (hnRNP H3) and similar proteins. This subgroup corresponds to the RRM3 of hnRNP H3 (also termed hnRNP 2H9), a nuclear RNA binding protein that belongs to the hnRNP H protein family that also includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), and hnRNP F. This family is involved in mRNA processing and exhibit extensive sequence homology. Currently, little is known about the functions of hnRNP H3 except for its role in the splicing arrest induced by heat shock. In addition, the typical hnRNP H proteins contain contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), except for hnRNP H3, in which the RRM1 is absent. RRM1 and RRM2 are responsible for the binding to the RNA at DGGGD motifs, and they play an important role in efficiently silencing the exon. Members in this family can regulate the alternative splicing of the fibroblast growth factor receptor 2 (FGFR2) transcripts, and function as silencers of FGFR2 exon IIIc through an interaction with the exonic GGG motifs. The lack of RRM1 could account for the reduced silencing activity within hnRNP H3. In addition, like other hnRNP H protein family members, hnRNP H3 has an extensive glycine-rich region near the C-terminus, which may allow it to homo- or heterodimerize. 75 matched cddid_all.tbl CDD cd12736 cd12736 410134 RRM1_ESRP1 RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 1 (ESRP1) and similar proteins. This subgroup corresponds to the RRM1 of ESRP1, also termed RNA-binding motif protein 35A (RBM35A), which has been identified as an epithelial cell type-specific regulator of fibroblast growth factor receptor 2 (FGFR2) splicing. It is required for expression of epithelial FGFR2-IIIb and the regulation of CD44, CTNND1 (p120-Catenin) and ENAH (hMena) splicing. It enhances epithelial-specific exons of CD44 and ENAH, silences mesenchymal exons of CTNND1, or both within FGFR2. Additional research indicated that ESRP1 functions as a tumor suppressor in colon cancer cells. It may be involved in posttranscriptional regulation of various genes by exerting a differential effect on protein translation via 5' untranslated regions (UTRs) of mRNAs. ESRP1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 93 matched cddid_all.tbl CDD cd12737 cd12737 410135 RRM1_ESRP2 RNA recognition motif 1 (RRM1) found in epithelial splicing regulatory protein 2 (ESRP2) and similar proteins. This subgroup corresponds to the RRM1 of ESRP2, also termed RNA-binding motif protein 35B (RBM35B), which has been identified as an epithelial cell type-specific regulator of fibroblast growth factor receptor 2 (FGFR2) splicing. It is required for expression of epithelial FGFR2-IIIb and the regulation of CD44, CTNND1 (also termed p120-Catenin) and ENAH (also termed hMena) splicing. It enhances epithelial-specific exons of CD44 and ENAH, silences mesenchymal exons of CTNND1, or both within FGFR2. ESRP2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 80 matched cddid_all.tbl CDD cd12738 cd12738 241182 RRM1_Fusilli RNA recognition motif 1 (RRM1) found in Drosophila RNA-binding protein Fusilli and similar proteins. This subgroup corresponds to the RRM1 of RNA-binding protein Fusilli which is encoded by Drosophila fusilli (fus) gene. Loss of Fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous fibroblast growth factor receptor 2 (FGFR2) splicing and functions as a splicing factor. Fusilli contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine. 80 matched cddid_all.tbl CDD cd12739 cd12739 410136 RRM2_ESRP1 RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 1 (ESRP1) and similar proteins. This subgroup corresponds to the RRM2 of ESRP1, also termed RNA-binding motif protein 35A (RBM35A), which has been identified as an epithelial cell type-specific regulator of fibroblast growth factor receptor 2 (FGFR2) splicing. It is required for expression of epithelial FGFR2-IIIb and the regulation of CD44, CTNND1 (also termed p120-Catenin) and ENAH (also termed hMena) splicing. It enhances epithelial-specific exons of CD44 and ENAH, silences mesenchymal exons of CTNND1, or both within FGFR2. Additional research indicated that ESRP1 functions as a tumor suppressor in colon cancer cells. It may be involved in posttranscriptional regulation of various genes by exerting a differential effect on protein translation via 5' untranslated regions (UTRs) of mRNAs. ESRP1 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 111 matched cddid_all.tbl CDD cd12740 cd12740 241184 RRM2_ESRP2 RNA recognition motif 2 (RRM2) found in epithelial splicing regulatory protein 2 (ESRP2) and similar proteins. This subgroup corresponds to the RRM2 of ESRP2, also termed RNA-binding motif protein 35B (RBM35B), which has been identified as an epithelial cell type-specific regulator of fibroblast growth factor receptor 2 (FGFR2) splicing. It is required for expression of epithelial FGFR2-IIIb and the regulation of CD44, CTNND1 (also termed p120-Catenin) and ENAH (also termed hMena) splicing. It enhances epithelial-specific exons of CD44 and ENAH, silences mesenchymal exons of CTNND1, or both within FGFR2. ESRP2 contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 107 matched cddid_all.tbl CDD cd12741 cd12741 410137 RRM2_Fusilli RNA recognition motif 2 (RRM2) found in Drosophila RNA-binding protein Fusilli and similar proteins. This subgroup corresponds to the RRM2 of RNA-binding protein Fusilli which is encoded by Drosophila fusilli (fus) gene. Loss of Fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous fibroblast growth factor receptor 2 (FGFR2) splicing and functions as a splicing factor. Fusilli contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine. 99 matched cddid_all.tbl CDD cd12742 cd12742 410138 RRM3_ESRP1_ESRP2 RNA recognition motif 3 (RRM3) found in epithelial splicing regulatory protein ESRP1, ESRP2 and similar proteins. This subgroup corresponds to the RRM3 of ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B). These are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. They are highly conserved paralogs and specifically bind to GU-rich binding site. ESRP1 and ESRP2 contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). 81 matched cddid_all.tbl CDD cd12743 cd12743 241187 RRM3_Fusilli RNA recognition motif 3 (RRM3) found in Drosophila RNA-binding protein Fusilli and similar proteins. This subgroup corresponds to the RRM3 of RNA-binding protein Fusilli which is encoded by Drosophila fusilli (fus) gene. Loss of Fusilli activity causes lethality during embryogenesis in flies. Drosophila Fusilli can regulate endogenous fibroblast growth factor receptor 2 (FGFR2) splicing and functions as a splicing factor. Fusilli contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an N-terminal domain with unknown function and a C-terminal domain particularly rich in alanine, glutamine, and serine. 85 matched cddid_all.tbl CDD cd12744 cd12744 410139 RRM1_RBM12B RNA recognition motif 1 (RRM1) found in RNA-binding protein 12B (RBM12B) and similar proteins. This subgroup corresponds to the RRM1 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear. 79 matched cddid_all.tbl CDD cd12745 cd12745 241189 RRM1_RBM12 RNA recognition motif 1 (RRM1) found in RNA-binding protein 12 (RBM12) and similar proteins. This subgrup corresponds to the RRM1 of RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. The biological role of RBM12 remains unclear. 92 matched cddid_all.tbl CDD cd12746 cd12746 410140 RRM2_RBM12B RNA recognition motif 2 (RRM2) found in RNA-binding protein 12B (RBM12B) and similar proteins. This subgroup corresponds to the RRM2 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear. 86 matched cddid_all.tbl CDD cd12747 cd12747 410141 RRM2_RBM12 RNA recognition motif 2 (RRM2) found in RNA-binding protein 12 (RBM12) and similar proteins. This subgroup corresponds to the RRM2 of RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), which is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. The biological role of RBM12 remains unclear. 75 matched cddid_all.tbl CDD cd12748 cd12748 410142 RRM4_RBM12B RNA recognition motif 4 (RRM4) found in RNA-binding protein 12B (RBM12B) and similar proteins. This subgroup corresponds to the RRM4 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear. 76 matched cddid_all.tbl CDD cd12749 cd12749 410143 RRM4_RBM12 RNA recognition motif 4 (RRM4) found in RNA-binding protein 12 (RBM12) and similar proteins. This subgroup corresponds to the RRM4 of RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), which is ubiquitously expressed. It contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. The biological role of RBM12 remains unclear. 88 matched cddid_all.tbl CDD cd12750 cd12750 410144 RRM5_RBM12B RNA recognition motif 5 (RRM5) found in RNA-binding protein 12B (RBM12B) and similar proteins. This subgroup corresponds to the RRM5 of RBM12B which contains five distinct RNA binding motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). Its biological role remains unclear. 77 matched cddid_all.tbl CDD cd12751 cd12751 410145 RRM5_RBM12 RNA recognition motif 5 (RRM5) found in RNA-binding protein 12 (RBM12) and similar proteins. This subgroup corresponds to the RRM5 of RBM12, also termed SH3/WW domain anchor protein in the nucleus (SWAN), which is ubiquitously expressed. It contains five distinct RNA binding motifs (RBMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two proline-rich regions, and several putative transmembrane domains. The biological role of RBM12 remains unclear. 76 matched cddid_all.tbl CDD cd12752 cd12752 410146 RRM1_RBM5 RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 5 (RBM5). This subgroup corresponds to the RRM1 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. 87 matched cddid_all.tbl CDD cd12753 cd12753 410147 RRM1_RBM10 RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 10 (RBM10). This subgroup corresponds to the RRM1 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. 84 matched cddid_all.tbl CDD cd12754 cd12754 410148 RRM2_RBM10 RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 10 (RBM10). This subgroup corresponds to the RRM2 of RBM10, also termed G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), a paralog of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 is structurally related to RBM5 and RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, and a G-patch/D111 domain. 87 matched cddid_all.tbl CDD cd12755 cd12755 410149 RRM2_RBM5 RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 5 (RBM5). This subgroup corresponds to the RRM2 of RBM5, also termed protein G15, or putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9, a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both, RBM5 and RBM6, specifically bind poly(G) RNA. They contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. 86 matched cddid_all.tbl CDD cd12756 cd12756 410150 RRM1_hnRNPD RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D0 (hnRNP D0) and similar proteins. This subgroup corresponds to the RRM1 of hnRNP D0, also termed AU-rich element RNA-binding protein 1, which is a UUAG-specific nuclear RNA binding protein that may be involved in pre-mRNA splicing and telomere elongation. hnRNP D0 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), in the middle and an RGG box rich in glycine and arginine residues in the C-terminal part. Each of RRMs can bind solely to the UUAG sequence specifically. 74 matched cddid_all.tbl CDD cd12757 cd12757 410151 RRM1_hnRNPAB RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A/B (hnRNP A/B) and similar proteins. This subgroup corresponds to the RRM1 of hnRNP A/B, also termed APOBEC1-binding protein 1 (ABBP-1), which is an RNA unwinding protein with a high affinity for G- followed by U-rich regions. hnRNP A/B has also been identified as an APOBEC1-binding protein that interacts with apolipoprotein B (apoB) mRNA transcripts around the editing site and thus plays an important role in apoB mRNA editing. hnRNP A/B contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long C-terminal glycine-rich domain that contains a potential ATP/GTP binding loop. 80 matched cddid_all.tbl CDD cd12758 cd12758 410152 RRM1_hnRPDL RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein D-like (hnRNP D-like or hnRNP DL) and similar proteins. This subgroup corresponds to the RRM1 of hnRNP DL (or hnRNP D-like), also termed AU-rich element RNA-binding factor, or JKT41-binding protein (protein laAUF1 or JKTBP), which is a dual functional protein that possesses DNA- and RNA-binding properties. It has been implicated in mRNA biogenesis at the transcriptional and post-transcriptional levels. hnRNP DL binds single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) in a non-sequencespecific manner, and interacts with poly(G) and poly(A) tenaciously. It contains two putative two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a glycine- and tyrosine-rich C-terminus. 76 matched cddid_all.tbl CDD cd12759 cd12759 241203 RRM1_MSI1 RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog 1 (Musashi-1) and similar proteins. This subgroup corresponds to the RRM1 of Musashi-1. The mammalian MSI1 gene encoding Musashi-1 (also termed Msi1) is a neural RNA-binding protein putatively expressed in central nervous system (CNS) stem cells and neural progenitor cells and associated with asymmetric divisions in neural progenitor cells. Musashi-1 is evolutionarily conserved from invertebrates to vertebrates. It is a homolog of Drosophila Musashi and Xenopus laevis nervous system-specific RNP protein-1 (Nrp-1). Musashi-1 has been implicated in the maintenance of the stem-cell state, differentiation, and tumorigenesis. It translationally regulates the expression of a mammalian numb gene by binding to the 3'-untranslated region of mRNA of Numb, encoding a membrane-associated inhibitor of Notch signaling, and further influences neural development. Moreover, it represses translation by interacting with the poly(A)-binding protein and competes for binding of the eukaryotic initiation factor-4G (eIF-4G). Musashi-1 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. 77 matched cddid_all.tbl CDD cd12760 cd12760 410153 RRM1_MSI2 RNA recognition motif 1 (RRM1) found in RNA-binding protein Musashi homolog 2 (Musashi-2 ) and similar proteins. This subgroup corresponds to the RRM2 of Musashi-2 (also termed Msi2) which has been identified as a regulator of the hematopoietic stem cell (HSC) compartment and of leukemic stem cells after transplantation of cells with loss and gain of function of the gene. It influences proliferation and differentiation of HSCs and myeloid progenitors, and further modulates normal hematopoiesis and promotes aggressive myeloid leukemia. Musashi-2 contains two conserved N-terminal tandem RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), along with other domains of unknown function. 93 matched cddid_all.tbl CDD cd12761 cd12761 410154 RRM1_hnRNPA1 RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) and similar proteins. This subgroup corresponds to the RRM1 of hnRNP A1, also termed helix-destabilizing protein, or single-strand RNA-binding protein, or hnRNP core protein A1, and is an abundant eukaryotic nuclear RNA-binding protein that may modulate splice site selection in pre-mRNA splicing. hnRNP A1 has been characterized as a splicing silencer, often acting in opposition to an activating hnRNP H. It silences exons when bound to exonic elements in the alternatively spliced transcripts of c-src, HIV, GRIN1, and beta-tropomyosin. hnRNP A1 can shuttle between the nucleus and the cytoplasm. Thus, it may be involved in transport of cellular RNAs, including the packaging of pre-mRNA into hnRNP particles and transport of poly A+ mRNA from the nucleus to the cytoplasm. The cytoplasmic hnRNP A1 has high affinity with AU-rich elements, whereas the nuclear hnRNP A1 has high affinity with a polypyrimidine stretch bordered by AG at the 3' ends of introns. hnRNP A1 is also involved in the replication of an RNA virus, such as mouse hepatitis virus (MHV), through an interaction with the transcription-regulatory region of viral RNA. hnRNP A1, together with the scaffold protein septin 6, serves as host protein to form a complex with NS5b and viral RNA, and further plays important roles in the replication of Hepatitis C virus (HCV). hnRNP A1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. The RRMs of hnRNP A1 play an important role in silencing the exon and the glycine-rich domain is responsible for protein-protein interactions. 81 matched cddid_all.tbl CDD cd12762 cd12762 410155 RRM1_hnRNPA2B1 RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1) and similar proteins. This subgroup corresponds to the RRM1 of hnRNP A2/B1 which is an RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE). Many mRNAs, such as myelin basic protein (MBP), myelin-associated oligodendrocytic basic protein (MOBP), carboxyanhydrase II (CAII), microtubule-associated protein tau, and amyloid precursor protein (APP) are trafficked by hnRNP A2/B1. hnRNP A2/B1 also functions as a splicing factor that regulates alternative splicing of the tumor suppressors, such as BIN1, WWOX, the antiapoptotic proteins c-FLIP and caspase-9B, the insulin receptor (IR), and the RON proto-oncogene among others. Moreover, the overexpression of hnRNP A2/B1 has been described in many cancers. It functions as a nuclear matrix protein involving in RNA synthesis and the regulation of cellular migration through alternatively splicing pre-mRNA. It may play a role in tumor cell differentiation. hnRNP A2/B1 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. 81 matched cddid_all.tbl CDD cd12763 cd12763 410156 RRM1_hnRNPA3 RNA recognition motif 1 (RRM1) found in heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3) and similar proteins. This subgroup corresponds to the RRM1 of hnRNP A3 which is a novel RNA trafficking response element-binding protein that interacts with the hnRNP A2 response element (A2RE) independently of hnRNP A2 and participates in the trafficking of A2RE-containing RNA. hnRNP A3 can shuttle between the nucleus and the cytoplasm. It contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a long glycine-rich region at the C-terminus. 81 matched cddid_all.tbl CDD cd12764 cd12764 410157 RRM2_SRSF4 RNA recognition motif 2 (RRM2) found in vertebrate serine/arginine-rich splicing factor 4 (SRSF4). This subgroup corresponds to the RRM2 of SRSF4, also termed pre-mRNA-splicing factor SRp75, or SRP001LB, or splicing factor, arginine/serine-rich 4 (SFRS4), a splicing regulatory serine/arginine (SR) protein that plays an important role in both constitutive splicing and alternative splicing of many pre-mRNAs. For instance, it interacts with heterogeneous nuclear ribonucleoproteins, hnRNP G and hnRNP E2, and further regulates the 5' splice site of tau exon 10, whose misregulation causes frontotemporal dementia. SFRS4 also induces production of HIV-1 vpr mRNA through the inhibition of the 5'-splice site of exon 3. In addition, SRSF4 activates splicing of the cardiac troponin T (cTNT) alternative exon by direct interactions with the cTNT exon 5 enhancer RNA. SRSF4 can shuttle between the nucleus and cytoplasm. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine-rich region, an internal region homologous to the RRM, and a very long, highly phosphorylated C-terminal RS domains rich in serine-arginine dipeptides. 97 matched cddid_all.tbl CDD cd12765 cd12765 410158 RRM2_SRSF5 RNA recognition motif 2 (RRM2) found in vertebrate serine/arginine-rich splicing factor 5 (SRSF5). This subgroup corresponds to the RRM2 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5), is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain. 81 matched cddid_all.tbl CDD cd12766 cd12766 410159 RRM2_SRSF6 RNA recognition motif 2 (RRM2) found found in vertebrate serine/arginine-rich splicing factor 6 (SRSF6). This subgroup corresponds to the RRM2 of SRSF6, also termed pre-mRNA-splicing factor SRp55, an essential splicing regulatory serine/arginine (SR) protein that preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. For instance, it does not bind to the purine-rich sequence in the calcitonin-specific ESE, but binds to a region adjacent to the purine tract. Moreover, cellular levels of SRSF6 may control tissue-specific alternative splicing of the calcitonin/ calcitonin gene-related peptide (CGRP) pre-mRNA. SRSF6 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. 73 matched cddid_all.tbl CDD cd12767 cd12767 410160 RRM2_SRSF1 RNA recognition motif 2 (RRM2) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins. This subgroup corresponds to the RRM2 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit, a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal SR domains rich in serine-arginine dipeptides. 84 matched cddid_all.tbl CDD cd12768 cd12768 410161 RRM2_SRSF9 RNA recognition motif 2 (RRM2) found in vertebrate serine/arginine-rich splicing factor 9 (SRSF9). This subgroup corresponds to the RRM2 of SRSF9, also termed pre-mRNA-splicing factor SRp30C, an essential splicing regulatory serine/arginine (SR) protein that has been implicated in the activity of many elements that control splice site selection, the alternative splicing of the glucocorticoid receptor beta in neutrophils and in the gonadotropin-releasing hormone pre-mRNA. SRSF9 can also interact with other proteins implicated in alternative splicing, including YB-1, rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by an unusually short C-terminal RS domains rich in serine-arginine dipeptides. 84 matched cddid_all.tbl CDD cd12769 cd12769 410162 RRM1_HuR RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen R (HuR). This subgroup corresponds to the RRM1 of HuR, also termed ELAV-like protein 1 (ELAV-1), a ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response; it binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. Meanwhile, HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. 82 matched cddid_all.tbl CDD cd12770 cd12770 410163 RRM1_HuD RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen D (HuD). This subgroup corresponds to the RRM1 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells, as well as the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. 81 matched cddid_all.tbl CDD cd12771 cd12771 410164 RRM1_HuB RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen B (HuB). This subgroup corresponds to the RRM1 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads and is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. 83 matched cddid_all.tbl CDD cd12772 cd12772 410165 RRM1_HuC RNA recognition motif 1 (RRM1) found in vertebrate Hu-antigen C (HuC). This subgroup corresponds to the RRM1 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. 85 matched cddid_all.tbl CDD cd12773 cd12773 410166 RRM2_HuR RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen R (HuR). This subgroup corresponds to the RRM2 of HuR, also termed ELAV-like protein 1 (ELAV-1), the ubiquitously expressed Hu family member. It has a variety of biological functions mostly related to the regulation of cellular response to DNA damage and other types of stress. HuR has an anti-apoptotic function during early cell stress response. It binds to mRNAs and enhances the expression of several anti-apoptotic proteins, such as p21waf1, p53, and prothymosin alpha. HuR also has pro-apoptotic function by promoting apoptosis when cell death is unavoidable. Furthermore, HuR may be important in muscle differentiation, adipogenesis, suppression of inflammatory response and modulation of gene expression in response to chronic ethanol exposure and amino acid starvation. Like other Hu proteins, HuR contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. 84 matched cddid_all.tbl CDD cd12774 cd12774 410167 RRM2_HuD RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen D (HuD). This subgroup corresponds to the RRM2 of HuD, also termed ELAV-like protein 4 (ELAV-4), or paraneoplastic encephalomyelitis antigen HuD, one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuD has been implicated in various aspects of neuronal function, such as the commitment and differentiation of neuronal precursors as well as synaptic remodeling in mature neurons. HuD also functions as an important regulator of mRNA expression in neurons by interacting with AU-rich RNA element (ARE) and stabilizing multiple transcripts. Moreover, HuD regulates the nuclear processing/stability of N-myc pre-mRNA in neuroblastoma cells and also regulates the neurite elongation and morphological differentiation. HuD specifically binds poly(A) RNA. Like other Hu proteins, HuD contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an ARE. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. 84 matched cddid_all.tbl CDD cd12775 cd12775 410168 RRM2_HuB RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen B (HuB). This subgroup corresponds to the RRM2 of HuB, also termed ELAV-like protein 2 (ELAV-2), or ELAV-like neuronal protein 1, or nervous system-specific RNA-binding protein Hel-N1 (Hel-N1), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. HuB is also expressed in gonads. It is up-regulated during neuronal differentiation of embryonic carcinoma P19 cells. Like other Hu proteins, HuB contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. 84 matched cddid_all.tbl CDD cd12776 cd12776 241220 RRM2_HuC RNA recognition motif 2 (RRM2) found in vertebrate Hu-antigen C (HuC). This subgroup corresponds to the RRM2 of HuC, also termed ELAV-like protein 3 (ELAV-3), or paraneoplastic cerebellar degeneration-associated antigen, or paraneoplastic limbic encephalitis antigen 21 (PLE21), one of the neuronal members of the Hu family. The neuronal Hu proteins play important roles in neuronal differentiation, plasticity and memory. Like other Hu proteins, HuC contains three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). RRM1 and RRM2 may cooperate in binding to an AU-rich RNA element (ARE). The AU-rich element binding of HuC can be inhibited by flavonoids. RRM3 may help to maintain the stability of the RNA-protein complex, and might also bind to poly(A) tails or be involved in protein-protein interactions. 81 matched cddid_all.tbl CDD cd12777 cd12777 410169 RRM1_PTBP1 RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 1 (PTB). This subgroup corresponds to the RRM1 of PTB, also known as 58 kDa RNA-binding protein PPTB-1 or heterogeneous nuclear ribonucleoprotein I (hnRNP I), an important negative regulator of alternative splicing in mammalian cells. PTB also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTB contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RRM1 and RRM2 are independent from each other and separated by flexible linkers. By contrast, there is an unusual and conserved interdomain interaction between RRM3 and RRM4. It is widely held that only RRMs 3 and 4 are involved in RNA binding and RRM2 mediates PTB homodimer formation. However, new evidence shows that the RRMs 1 and 2 also contribute substantially to RNA binding. Moreover, PTB may not always dimerize to repress splicing. It is a monomer in solution. 81 matched cddid_all.tbl CDD cd12778 cd12778 410170 RRM1_PTBP2 RNA recognition motif 1 (RRM1) found in vertebrate polypyrimidine tract-binding protein 2 (PTBP2). This subgroup corresponds to the RRM1 of PTBP2, also known as neural polypyrimidine tract-binding protein or neurally-enriched homolog of PTB (nPTB), highly homologous to polypyrimidine tract binding protein (PTB) and perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 contains four RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 82 matched cddid_all.tbl CDD cd12779 cd12779 410171 RRM1_ROD1 RNA recognition motif 1 (RRM1) found in vertebrate regulator of differentiation 1 (Rod1). This subgroup corresponds to the RRM1 of ROD1 coding protein Rod1, a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein that negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. Rod1 contains four repeats of RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and does have RNA binding activities. 90 matched cddid_all.tbl CDD cd12780 cd12780 410172 RRM1_hnRNPL RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein L (hnRNP-L). This subgroup corresponds to the RRM1 of hnRNP-L, a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-L shows significant sequence homology to polypyrimidine tract-binding protein (PTB or hnRNP I). Both, hnRNP-L and PTB, are localized in the nucleus but excluded from the nucleolus. hnRNP-L is an RNA-binding protein with three RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 80 matched cddid_all.tbl CDD cd12781 cd12781 410173 RRM1_hnRPLL RNA recognition motif 1 (RRM1) found in vertebrate heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL). This subgroup corresponds to the RRM1 of hnRNP-LL, which plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to heterogeneous nuclear ribonucleoprotein L (hnRNP-L), which is an abundant nuclear, multifunctional RNA-binding protein with three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 84 matched cddid_all.tbl CDD cd12782 cd12782 410174 RRM2_PTBP1 RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein 1 (PTB). This subgroup corresponds to the RRM2 of PTB, also known as 58 kDa RNA-binding protein PPTB-1 or heterogeneous nuclear ribonucleoprotein I (hnRNP I), an important negative regulator of alternative splicing in mammalian cells. PTB also functions at several other aspects of mRNA metabolism, including mRNA localization, stabilization, polyadenylation, and translation. PTB contains four RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). RRM1 and RRM2 are independent from each other and separated by flexible linkers. By contrast, there is an unusual and conserved interdomain interaction between RRM3 and RRM4. It is widely held that only RRMs 3 and 4 are involved in RNA binding and RRM2 mediates PTB homodimer formation. However, new evidence shows that the RRMs 1 and 2 also contribute substantially to RNA binding. Moreover, PTB may not always dimerize to repress splicing. It is a monomer in solution. 108 matched cddid_all.tbl CDD cd12783 cd12783 410175 RRM2_PTBP2 RNA recognition motif 2 (RRM2) found in vertebrate polypyrimidine tract-binding protein 2 (PTBP2). This subgroup corresponds to the RRM2 of PTBP2, also known as neural polypyrimidine tract-binding protein or neurally-enriched homolog of PTB (nPTB), highly homologous to polypyrimidine tract binding protein (PTB) and perhaps specific to the vertebrates. Unlike PTB, PTBP2 is enriched in the brain and in some neural cell lines. It binds more stably to the downstream control sequence (DCS) RNA than PTB does but is a weaker repressor of splicing in vitro. PTBP2 also greatly enhances the binding of two other proteins, heterogeneous nuclear ribonucleoprotein (hnRNP) H and KH-type splicing-regulatory protein (KSRP), to the DCS RNA. The binding properties of PTBP2 and its reduced inhibitory activity on splicing imply roles in controlling the assembly of other splicing-regulatory proteins. PTBP2 contains four RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 107 matched cddid_all.tbl CDD cd12784 cd12784 410176 RRM2_ROD1 RNA recognition motif 2 (RRM2) found in vertebrate regulator of differentiation 1 (Rod1). This subgroup corresponds to the RRM2 of ROD1 coding protein Rod1, a mammalian polypyrimidine tract binding protein (PTB) homolog of a regulator of differentiation in the fission yeast Schizosaccharomyces pombe, where the nrd1 gene encodes an RNA binding protein and negatively regulates the onset of differentiation. ROD1 is predominantly expressed in hematopoietic cells or organs. It might play a role controlling differentiation in mammals. Rod1 contains four repeats of RNA recognition motifs (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain) and does have RNA binding activities. 108 matched cddid_all.tbl CDD cd12785 cd12785 410177 RRM2_hnRNPL RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein L (hnRNP-L). This subgroup corresponds to the RRM2 of hnRNP-L, a higher eukaryotic specific subunit of human KMT3a (also known as HYPB or hSet2) complex required for histone H3 Lys-36 trimethylation activity. It plays both, nuclear and cytoplasmic, roles in mRNA export of intronless genes, IRES-mediated translation, mRNA stability, and splicing. hnRNP-L shows significant sequence homology to polypyrimidine tract-binding protein (PTB or hnRNP I). Both hnRNP-L and PTB are localized in the nucleus but excluded from the nucleolus. hnRNP-L is an RNA-binding protein with three RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 100 matched cddid_all.tbl CDD cd12786 cd12786 241230 RRM2_hnRPLL RNA recognition motif 2 (RRM2) found in vertebrate heterogeneous nuclear ribonucleoprotein L-like (hnRNP-LL). The subgroup corresponds to the RRM2 of hnRNP-LL which plays a critical and unique role in the signal-induced regulation of CD45 and acts as a global regulator of alternative splicing in activated T cells. It is closely related in domain structure and sequence to heterogeneous nuclear ribonucleoprotein L (hnRNP-L), which is an abundant nuclear, multifunctional RNA-binding protein with three RNA-recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 96 matched cddid_all.tbl CDD cd12787 cd12787 213347 RasGAP_plexin_B Ras-GTPase Activating Domain of type B plexins. Plexins form a conserved family of transmembrane receptors for semaphorins and may be the ancestors of semaphorins. Plexins are divided into four types (A-D) according to sequence similarity.There are three members of the Plexin-B subfamily, namely B1, B2 and B3. Plexins-B1, B2 and B3 are receptors for Sema4D, Sema4C and Sema4G, and Sema5A, respectively. The activation of plexin-B1 by Sema4D produces an acute collapse of axonal growth cones in hippocampal and retinal neurons over the early stages of neurite outgrowth and promotes branching and complexity. By signaling the effect of Sema4C and Sema4G, the plexin-B2 receptor is critically involved in neural tube closure and cerebellar granule cell development. Plexin-B3, the receptor of Sema5A, is a highly potent stimulator of neurite outgrowth of primary murine cerebellar neurons. Plexin-B3 has been linked to verbal performance and white matter volume in human brain. Small GTPases play important roles in plexin-B signaling. Plexin-B1 activates Rho through Rho-specific guanine nucleotide exchange factors, leading to neurite retraction. Plexin-B1 possesses an intrinsic GTPase-activating protein activity for R-Ras and induces growth cone collapse through R-Ras inactivation. Plexins contain a C-terminal RasGAP domain, which functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Plexins display GAP activity towards the Ras homolog Rap. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP show no sequence homology at their amino acid level. RasGTPases function as molecular switches in a large number of of signaling pathways. When bound to GTP they are in the on state and when bound to GDP they are in the off state. The RasGAP domain speeds up the hydrolysis of GTP in Ras-like proteins acting as a negative regulator. 391 matched cddid_all.tbl CDD cd12788 cd12788 213348 RasGAP_plexin_D1 Ras-GTPase Activating Domain of plexin-D1. Plexins form a conserved family of transmembrane receptors for semaphorins and may be the ancestors of semaphorins. Plexins are divided into four types (A-D) according to sequence similarity. Plexin-D1 has been identified as the receptor of Sema3E. It binds to Sema3E directly with high affinity. Sema3E is implicated in axonal path finding and inhibition of developmental and postischemic angiogenesis. Plexin-D1 is broadly expressed on tumor vessels and tumor cells in a number of different types of human tumors. The Plexin-D1 and Sema3E interaction inhibits tumor growth but promotes invasiveness and metastasis. Plexins contain a C-terminal RasGAP domain, which functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Plexins display GAP activity towards the Ras homolog Rap. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP show no sequence homology at their amino acid level. RasGTPases function as molecular switches in a large number of of signaling pathways. When bound to GTP they are in the on state and when bound to GDP they are in the off state. The RasGAP domain speeds up the hydrolysis of GTP in Ras-like proteins acting as a negative regulator. 419 matched cddid_all.tbl CDD cd12789 cd12789 213349 RasGAP_plexin_C1 Ras-GTPase Activating Domain of plexin-C1. Plexins form a conserved family of transmembrane receptors for semaphorins and may be the ancestors of semaphorins. Plexins are divided into four types (A-D) according to sequence similarity. Plexin-C1 has been identified as the receptor of semaphorin 7A, which plays regulatory roles in both the immune and nervous systems. Unlike other semaphorins which act as repulsive guidance cues, Sema7A enhances central and peripheral axon growth and is required for proper axon tract formation during embryonic development. Plexin-C1 is a potential tumor suppressor for melanoma progression. The expression of Plexin-C1 is diminished or absent in human melanoma cell lines. Cofilin, an actin-binding protein involved in cell migration, is a downstream target of Sema7A and Plexin-C1 signaling. Melanoma invasion and metastasis may be promoted through the loss of Plexin-C1 inhibitory signaling on cofilin activation. Plexins contain a C-terminal RasGAP domain, which functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Plexins display GAP activity towards the Ras homolog Rap. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP show no sequence homology at their amino acid level. RasGTPases function as molecular switches in a large number of of signaling pathways. When bound to GTP they are in the on state and when bound to GDP they are in the off state. The RasGAP domain speeds up the hydrolysis of GTP in Ras-like proteins acting as a negative regulator. 393 matched cddid_all.tbl CDD cd12790 cd12790 213350 RasGAP_plexin_A Ras-GTPase Activating Domain of type A plexins. Plexins form a conserved family of transmembrane receptors for semaphorins and may be the ancestors of semaphorins. They are divided into four types (A-D) according to sequence similarity. In vertebrates, there are four type A plexins (A1-A4) that serve as the co-receptors for neuropilins to mediate the signaling of class 3 semaphorins except Sema3E, which signals through Plexin-D1. Plexins serve as direct receptors for several other members of the semaphorin family: class 1 and class 6 semaphorins signal through type A plexins, which mediate diverse biological functions including axon guidance, cardiovascular development, and immune function. Guanylyl cyclase Gyc76C and Off-track kinase (OTK), a putative receptor tyrosine kinase, modulate Sema1a and Plexin-A mediated axon repulsion. In their complex with Sema6s, type A plexins serve as signal-transducing subunits. An increasing number of molecules that interact with the intracellular region of Plexin-A have been identified; among them are IgCAMs (in axon guidance events) and Trem2-DAP12 (in immune responses). Plexins contain a C-terminal RasGAP domain, which functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Plexins display GAP activity towards the Ras homolog Rap. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP show no sequence homology at their amino acid level. RasGTPases function as molecular switches in a large number of of signaling pathways. When bound to GTP they are in the on state and when bound to GDP they are in the off state. The RasGAP domain speeds up the hydrolysis of GTP in Ras-like proteins acting as a negative regulator. 385 matched cddid_all.tbl CDD cd12791 cd12791 213351 RasGAP_plexin_B3 Ras-GTPase Activating Domain of plexin-B3. Plexins form a conserved family of transmembrane receptors for semaphorins and may be the ancestors of semaphorins. Plexins are divided into four types (A-D) according to sequence similarity. Plexin-B3 is the receptor of semaphorin 5A. It is a highly potent stimulator of neurite outgrowth of primary murine cerebellar neurons. Plexin-B3 has been linked to verbal performance and white matter volume in human brain. Furthermore, Sema5A and plexin-B3 have been implicated in the progression of various types of cancer. They play an important role in the invasion and metastasis of gastric carcinoma. The protein and mRNA expression of Sema5A and its receptor plexin-B3 increased gradually in non-neoplastic mucosa, primary gastric carcinoma, and lymph node metastasis, and their expression is correlated. The stimulation of plexin-B3 by Sema5A binding in human glioma cells results in the inhibition of cell migration and invasion. Plexins contain a C-terminal RasGAP domain, which functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Plexins display GAP activity towards the Ras homolog Rap. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP show no sequence homology at their amino acid level. RasGTPases function as molecular switches in a large number of of signaling pathways. When bound to GTP they are in the on state and when bound to GDP they are in the off state. The RasGAP domain speeds up the hydrolysis of GTP in Ras-like proteins acting as a negative regulator. 397 matched cddid_all.tbl CDD cd12792 cd12792 213352 RasGAP_plexin_B2 Ras-GTPase Activating Domain of plexin-B2. Plexins form a conserved family of transmembrane receptors for semaphorins and may be the ancestors of semaphorins. Plexins are divided into four types (A-D) according to sequence similarity. Plexin-B2 serves as the receptor of Sema4C and Sema4G. By signaling the effect of Sema4C and Sema4G, the plexin-B2 receptor is critically involved in neural tube closure and cerebellar granule cell development. Mice lacking Plexin-B2 demonstrated defects in closure of the neural tube and disorganization of the embryonic brain. In developing kidney, Sema4C and Plexin-B2 signaling modulates ureteric branching. Plexin-B2 is expressed both in the pretubular aggregates and the ureteric epithelium in the developing kidney. Deletion of Plexin-B2 results in renal hypoplasia and occasional double ureters. Plexins contain a C-terminal RasGAP domain, which functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Plexins display GAP activity towards the Ras homolog Rap. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP show no sequence homology at their amino acid level. RasGTPases function as molecular switches in a large number of of signaling pathways. When bound to GTP they are in the on state and when bound to GDP they are in the off state. The RasGAP domain speeds up the hydrolysis of GTP in Ras-like proteins acting as a negative regulator. 400 matched cddid_all.tbl CDD cd12793 cd12793 213353 RasGAP_plexin_B1 Ras-GTPase Activating Domain of plexin-B1. Plexins form a conserved family of transmembrane receptors for semaphorins and may be the ancestors of semaphorins. Plexins are divided into four types (A-D) according to sequence similarity. Plexin-B1 serves as the Semaphorin 4D receptor and functions as a regulator of developing neurons and a tumor suppressor protein for melanoma. The Sema4D and plexin-B1 signaling complex regulates dendritic and axonal complexity. The activation of Plexin-B1 by Sema4D produces an acute collapse of axonal growth cones in hippocampal and retinal neurons over the early stages of neurite outgrowth and promotes branching and complexity. As a tumor suppressor, plexin-B1 abrogates activation of the oncogenic receptor, c-Met, by its ligand, hepatocyte growth factor (HGF), in melanoma. Furthermore, plexin-B1 suppresses integrin-dependent migration and activation of pp125FAK and inhibits Rho activity. Plexin-B1 is highly expressed in endothelial cells and its activation by Sema4D elicits a potent proangiogenic response. Plexins contain a C-terminal RasGAP domain, which functions as an enhancer of the hydrolysis of GTP that is bound to Ras-GTPases. Plexins display GAP activity towards the Ras homolog Rap. Although the Rho (Ras homolog) GTPases are most closely related to members of the Ras family, RhoGAP and RasGAP show no sequence homology at their amino acid level. RasGTPases function as molecular switches in a large number of of signaling pathways. When bound to GTP they are in the on state and when bound to GDP they are in the off state. The RasGAP domain speeds up the hydrolysis of GTP in Ras-like proteins acting as a negative regulator. 394 matched cddid_all.tbl CDD cd12794 cd12794 240614 Hsm3_like Hsm3 is a yeast Proteasome chaperone of the 19S regulatory particle and related proteins. This group contains proteins related to the Hsm3 protein (Yeast Proteasome Interacting Protein) of Saccharomyces cerevisiae. S. cerevisiae Hsm3 is a chaperone of regulatory particles involved in proteasome assembly. The 26S Proteasome is a large, 2.5 MDa complex comprised of at least 33 subunits, and relies on chaperones to facilitate correct assembly. The proteasome contains a cylindrical 20S core particle and 1-2 19S regulatory particles, comprised of AAA-ATPase and non-ATPase subunits. The proteasome acts in ubiquitin-dependent proteolysis. The 19S RP targets and opens the the ubiquitin-tagged substrate and releases ubiquitin. Hsm3 acts as a 19S chaperone, binding to the C-terminal domain of Rpt1 (the 6 ATPase subunits of the 19 S regulatory particle(s). Hsm3 has a C-shape composed of 11 HEAT repeats. Mutations in the Hsm3-Rpt interface disrupt formation of the 26 S Proteasome complex. 455 matched cddid_all.tbl CDD cd12795 cd12795 240613 FILIA_N_like FILIA-N KH-like domain. This group contains the N-terminal atypical KH domain of FILIA and related domains. FILIA is expressed in oocytes and embryo, and contains an atypical KH domain at the N-terminus with an N-terminal extension that interacts with RNA. RNA-binding may mediate RNA transcript regulation in oogenesis and embryogenesis. FILIA-N differs from typical KH domains by forming a stable dimer in solution and crystal structure. 114 matched cddid_all.tbl CDD cd12796 cd12796 240609 LbR_Ice_bind Ice-binding protein, left-handed beta-roll. The ice-binding protein of the grass Lolium perenne (LpIBP) discourages the recrystallization of ice. Ice-binding proteins produced by organisms to prevent the growing of ice are termed to anti-freeze proteins. LpIBP consists of an unusual left-handed beta roll. Ice-binding is mediated by a flat beta-sheet on one side of the helix. 114 matched cddid_all.tbl CDD cd12797 cd12797 410984 M23_peptidase M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins. This model describes the metallopeptidase M23 family, which includes beta-lytic metallopeptidase and lysostaphin. Members of this family are zinc endopeptidases that lyse bacterial cell wall peptidoglycans; they cleave either the N-acylmuramoyl-Ala bond between the cell wall peptidoglycan and the cross-linking peptide (e.g. beta-lytic endopeptidase) or a bond within the cross-linking peptide (e.g. stapholysin, and lysostaphin). Beta-lytic metallopeptidase, formerly known as beta-lytic protease, has a preference for cleavage of Gly-X bonds and favors hydrophobic or apolar residues on either side. It inhibits growth of sensitive organisms and may potentially serve as an antimicrobial agent. Lysostaphin, produced by Staphylococcus genus, cleaves pentaglycine cross-bridges of cell wall peptidoglycan, acting as autolysins to maintain cell wall metabolism or as toxins and weapons against competing strains. Staphylolysin (also known as LasA) is implicated in a range of processes related to Pseudomonas virulence, including stimulating shedding of the ectodomain of cell surface heparan sulphate proteoglycan syndecan-1, and elastin degradation in connective tissue. Its active site is less constricted and contains a five-coordinate zinc ion with trigonal bipyramidal geometry and two metal-bound water molecules, possibly contributing to its activity against a wider range of substrates than those used by related lytic enzymes, consistent with its multiple roles in Pseudomonas virulence. The family includes members that do not appear to have the conserved zinc-binding site and might be lipoproteins lacking proteolytic activity. 85 matched cddid_all.tbl CDD cd12798 cd12798 213998 Alt_A1 Alternaria alternata allergen Alt a 1. Alt a 1 defines a new homologous protein family with unknown function exclusively found in fungi. The unique structure of Alt a 1 contains intramolecular disulfide bonds that are conserved among the Alt a 1 homologs. Residues reported to be IgE antibody-binding epitopes are exposed through dimerization via a conserved disulfide bond and hydrophobic and polar interactions. Further mechanistic structure/function studies will give insight into immunologic studies directed toward new forms of immunotherapy for Alternaria species-sensitive allergic patients. 132 matched cddid_all.tbl CDD cd12799 cd12799 340366 pesticin_lyz-like lysozyme-like C-terminal domain of pesticin and related proteins. Pesticin (Pst) is an anti-bacterial toxin produced by Yersinia pestis that acts through uptake by the target related bacteria and the hydrolysis of peptidoglycan in the periplasm. Pst contains an N-terminal translocation domain, an intermediate receptor binding domain, and a phage-lysozyme like C-terminal activity domain. Bacteriocins such as pesticin are produced by gram-negative bacteria to attack related bacterial stains. Pst is transported to the periplasm via FyuA, an outer-membrane receptor of Y. pestis and E. coli, where it hydrolyzes peptidoglycan via the cleavage of N-acetylmuramic acid and C4 of N-acetylglucosamine. Disruption of the peptidoglycan layer renders the bacteria vulnerable to lysis via osmotic pressure. The pesticin C-terminal domain resembles the lysozyme-like family, which includes soluble lytic transglycosylases (SLT), goose egg-white lysozymes (GEWL), hen egg-white lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases. All the members are involved in the hydrolysis of beta-1,4- linked polysaccharides. 129 matched cddid_all.tbl CDD cd12800 cd12800 213999 Sol_i_2 Sol i 2, a major allergen from fire ant venom. Sol i 2, one of four known potent allergens from the venom of red imported fire ant, is a powerful trigger of anaphylaxis. It causes production of IgE antibody in many individuals stung by fire ants. The closest structure homolog of Sol I 2 is the sequence-unrelated odorant binding protein and pheromone binding protein LUSH of the fruit fly Drosophila, suggesting a possible similar biological function. 118 matched cddid_all.tbl CDD cd12801 cd12801 214000 HopAB_KID Kinase-interacting domains of the HopAB family of Type III Effector proteins. HopAB family members are type III effector proteins that are secreted by the plant pathogen Pseudomonas syringae into the host plant to inhibit its immune system and facilitate the spread of the pathogen. AvrPtoB, also called HopAB3, is the best studied member of the family. It suppresses host basal defenses by interfering with PAMP (pathogen-associated molecular signature)-triggered immunity (PTI) through binding and inhibiting BAK1, a kinase which serves to activate defense signaling. It also recognizes the kinase Pto to activate effector-triggered immunity (ETI). AvrPtoB contains an N-terminal region that contains two kinase-interacting domains (KID) and a C-terminal E3 ligase domain. The first KID recognizes the PTI-associated kinase Bti9 as well as Pto, and is referred to as the Pto-binding domain (PID). The second KID interacts with BAK1 and FLS2, which are leucine-rich repeat-containing receptor-like kinases, and is called the BAK1-interacting domain (BID). This family also contains a unique member, HopPmaL, which is shorter and lacks the C-terminal E3 ligase domain. 77 matched cddid_all.tbl CDD cd12802 cd12802 214001 HopAB_PID Pto-interacting domain of the HopAB family of Type III Effector proteins. HopAB family members are type III effector proteins that are secreted by the plant pathogen Pseudomonas syringae into the host plant to inhibit its immune system and facilitate the spread of the pathogen. AvrPtoB, also called HopAB3, is the best studied member of the family. It suppresses host basal defenses by interfering with PAMP (pathogen-associated molecular signature)-triggered immunity (PTI) through binding and inhibiting BAK1, a kinase which serves to activate defense signaling. It also recognizes the kinase Pto to activate effector-triggered immunity (ETI). AvrPtoB contains an N-terminal region that contains two kinase-interacting domains (KID) and a C-terminal E3 ligase domain. The first KID recognizes the PTI-associated kinase Bti9 as well as Pto, and is referred to as the Pto-binding domain (PID). The second KID interacts with BAK1 and FLS2, which are leucine-rich repeat-containing receptor-like kinases, and is called the BAK1-interacting domain (BID). This family also contains a unique member, HopPmaL, which is shorter and lacks the C-terminal E3 ligase domain. 79 matched cddid_all.tbl CDD cd12803 cd12803 214002 HopAB_BID BAK1-interacting domain of the HopAB family of Type III Effector proteins. HopAB family members are type III effector proteins that are secreted by the plant pathogen Pseudomonas syringae into the host plant to inhibit its immune system and facilitate the spread of the pathogen. AvrPtoB, also called HopAB3, is the best studied member of the family. It suppresses host basal defenses by interfering with PAMP (pathogen-associated molecular signature)-triggered immunity (PTI) through binding and inhibiting BAK1, a kinase which serves to activate defense signaling. It also recognizes the kinase Pto to activate effector-triggered immunity (ETI). AvrPtoB contains an N-terminal region that contains two kinase-interacting domains (KID) and a C-terminal E3 ligase domain. The first KID recognizes the PTI-associated kinase Bti9 as well as Pto, and is referred to as the Pto-binding domain (PID). The second KID interacts with BAK1 and FLS2, which are leucine-rich repeat-containing receptor-like kinases, and is called the BAK1-interacting domain (BID). This family also contains a unique member, HopPmaL, which is shorter and lacks the C-terminal E3 ligase domain. 80 matched cddid_all.tbl CDD cd12804 cd12804 214003 AKAP10_AKB PKA-binding (AKB) domain of A Kinase Anchor Protein 10. AKAPs coordinate the specificity of PKA signaling by facilitating the localization of the kinase to subcellular sites through their binding to regulatory (R) subunits of PKA. AKAP-10, also called PRKA10 or Dual-specific AKAP 2 (D-AKAP2), is a multisubunit protein containing two regulator of G protein signaling (RGS)-like domains and a PKA-binding (AKB) domain. The AKB domain of AKAP10 can bind to the dimerization/docking (D/D) domains of both RI and RII regulatory subunits of PKA. This model also includes a C-terminal PDZ-binding motif that binds to PDZK1 and NHERF-1, allowing AKAP10 to link indirectly to membrane proteins. Mutations in AKAP10 can alter its binding to R subunits, which may alter the targeting of PKA; some AKAP10 mutations are associated with abnormalities including hypertension, increased risk of severe arrhythmias during kidney transplantation, and familial breast cancer. 45 matched cddid_all.tbl CDD cd12805 cd12805 214004 Allergen_V_VI Group V, VI major allergens from grass, including Phlp 5, Phlp 6, Pha a 5 and Lol p 5. This family contains major allergens from various grass pollen, including Phl p 5 and Phl p 6 (timothy grass), Lol p 5 (rye grass) and Pha a 5 (canary grass). They induce allergic rhinitis and bronchial asthma in millions of allergic patients worldwide. These group V and group VI grass-pollen allergens belong to a new class of protease-resistant four-helix-bundle domains, which also have internal helix-turn-helix homology pointing to a special type of four-helix bundle topology, defined as twinned two-helix bundle. IgE binding experiments with recombinant Phl p 6 fragments indicated that the N terminus of the allergen is required for IgE recognition. Immunotherapy treatment for these allergies generally involves administration of grass pollen extracts which induce an initial rise in specific immunoglobulin E (sIgE) production followed by a progressive decline during the treatment. 85 matched cddid_all.tbl CDD cd12806 cd12806 214005 Esterase_713_like Novel bacterial esterase that cleaves esters on halogenated cyclic compounds. This family contains proteins similar to a novel bacterial esterase (Alcaligenes esterase 713) with the alpha/beta hydrolase fold but does not contain the GXSXXG pentapeptide around the active site serine residue as commonly seen in other enzymes of this class. Esterase 713 shows negligible sequence homology to other esterase and lipase enzymes. It is active as a dimer and cleaves esters on halogenated cyclic compounds though its natural substrate is unknown. This enzyme is possibly exported from the cytosol to the periplasmic space. A large majority of sequences in this family have yet to be characterized. 261 matched cddid_all.tbl CDD cd12807 cd12807 214006 Esterase_713 Novel bacterial esterase 713 that cleaves esters on halogenated cyclic compounds. This family contains proteins similar to a novel bacterial esterase (esterase 713) with the alpha/beta hydrolase fold that cleaves esters on halogenated cyclic compounds. This Alcaligenes esterase, however, does not contain the GXSXXG pentapeptide around the active site serine residue as seen in other esterase families. This enzyme is active as a dimer though its natural substrate is unknown. It has two distinct disulfide bridges; one formed between adjacent cysteines appears to facilitate the correct formation of the oxyanion cleft in the catalytic site. Esterase 713 also resembles human pancreatic lipase in its location of the acidic residue of the catalytic triad. It is possibly exported from the cytosol to the periplasmic space. A large majority of sequences in this family have yet to be characterized. 315 matched cddid_all.tbl CDD cd12808 cd12808 214007 Esterase_713_like-1 Uncharacterized enzymes similar to novel bacterial esterase that cleaves esters on halogenated cyclic compounds. This family contains uncharacterized proteins similar to a novel bacterial esterase (Alcaligenes esterase 713) with the alpha/beta hydrolase fold but does not contain the GXSXXG pentapeptide around the active site serine residue as commonly seen in other enzymes of this class. Esterase 713 shows negligible sequence homology to other esterase and lipase enzymes. It is active as a dimer and cleaves esters on halogenated cyclic compounds though its natural substrate is unknown. 309 matched cddid_all.tbl CDD cd12809 cd12809 214008 Esterase_713_like-2 Uncharacterized enzymes similar to novel bacterial esterase that cleaves esters on halogenated cyclic compounds. This family contains uncharacterized proteins similar to a novel bacterial esterase (Alcaligenes esterase 713) with the alpha/beta hydrolase fold but does not contain the GXSXXG pentapeptide around the active site serine residue as commonly seen in other enzymes of this class. Esterase 713 shows negligible sequence homology to other esterase and lipase enzymes. It is active as a dimer and cleaves esters on halogenated cyclic compounds though its natural substrate is unknown. 280 matched cddid_all.tbl CDD cd12810 cd12810 214009 Esterase_713_like-3 Uncharacterized enzymes similar to novel bacterial esterase that cleaves esters on halogenated cyclic compounds. This family contains uncharacterized proteins similar to a novel bacterial esterase (Alcaligenes esterase 713) with the alpha/beta hydrolase fold but does not contain the GXSXXG pentapeptide around the active site serine residue as commonly seen in other enzymes of this class. Esterase 713 shows negligible sequence homology to other esterase and lipase enzymes. It is active as a dimer and cleaves esters on halogenated cyclic compounds though its natural substrate is unknown. 328 matched cddid_all.tbl CDD cd12811 cd12811 411995 MALA Mala s 1 allergenic protein and similar proteins. This family includes the yeast Malassezia sympodialis allergen Mala s 1 which is localized in the cell wall and exposed on the cell surface. It can elicit specific IgE and T-cell activity in patients with atopic eczema (AE), a chronic inflammatory disease. Mala s 1 does not show any significant sequence homology to characterized proteins. However, its structure is a beta-propeller which is a novel fold among allergens. 304 matched cddid_all.tbl CDD cd12812 cd12812 214010 BPSL1549 Burkholderia Lethal Factor 1. BPSL1549, also suggested to be called Burkholderia lethal factor 1, is a protein of unknown function from Burkholderia pseudomallei, a causative agent of melioidosis (also called Whitmore's disease). This protein shows similarity to Escherichia coli cytotoxic necrotizing factor 1 which has been found to act as a potent cytotoxin against eukaryotic cells and is lethal when administered to mice. BPSL1549 expression levels correlate with suppression or promotion of pathogenic conditions. BPSL1549 inhibits helicase activity of translation initiation factor eIF4A. As yet, there is no vaccine and the organism is multidrug resistant. 203 matched cddid_all.tbl CDD cd12813 cd12813 240610 LbR-like Left-handed beta-roll, including virulence factors and various other proteins. This family contains a variety of protein domains with a left-handed beta-roll structure including cell surface adhesion proteins, bacterial virulence factors, and ice-binding proteins, and other activities. UspA1 Head And Neck Domain and YadA of Yersinia are part of a class of pathogenicity factors that act as cell surface adhesion molecules, in which N-terminal head and neck domains extend from the bacterial outer membrane. The UspA1 head domain of Moraxella catarrhalis, is formed from trimeric beta-rolls of 14-16 amino acid repeats. The UspA1 head domain connects to a neck region of large extended, charged loops that maybe be ligand binding, which is in turn connected to an extended coiled coil domain that tethers the head and neck region to the cell surface via a transmembrane region. The collagen-binding domain virulence factor YadA an adhesion proteins of several Yersinia species, and related cell surface proteins. The collagen-binding portion is found in the hydrophobic N-terminal region. YadA forms a matrix on the bacterial outer membrane, which mediates binding to collagen and epithelial cells. YadA inhibits the complement-activating pathway with the coating of the cell surface with factor H, which impedes C3b molecules. The ice-binding protein of the grass Lolium perenne (LpIBP) discourages the recrystallization of ice. Ice-binding proteins produced by organisms to prevent the growing of ice are termed to anti-freeze proteins. LpIBP consists of an unusual left-handed beta roll. Ice-binding is mediated by a flat beta-sheet on one side of the helix. These domains form a left handed beta roll made up of a series of short repeated elements. 99 matched cddid_all.tbl CDD cd12819 cd12819 240611 LbR_vir_like Cell adhesion-like domain, left-handed beta-roll. This group contains proteins of unknown function related to characterized cell surface adhesion proteins with a left-handed beta-roll, like the UspA1 Head And Neck Domain and YadA of Yersinia. UspA1 and UspA2 are part of a class of pathogenicity factors that act as cell surface adhesion molecules, in which N-terminal head and neck domains extend from the bacterial outer membrane. The UspA1 head domain of Moraxella catarrhalis, is formed from trimeric beta-helices of 14-16 amino acid repeats. The UspA1 head domain connects to a neck region of large extended, charged loops that maybe be ligand binding, which is in turn connected to an extended coiled coil domain that tethers the head and neck region to the cell surface via a transmembrane region. The collagen-binding domain virulence factor YadA an adhesion proteins of several Yersinia species, and related cell surface proteins. The collagen-binding portion is found in the hydrophobic N-terminal region. YadA forms a matrix on the bacterial outer membrane, which mediates binding to collagen and epithelial cells. YadA inhibits the complement-activating pathway with the coating of the cell surface with factor H, which impedes C3b molecules. These domains form a left handed beta roll made up of a series of short repeated elements. 111 matched cddid_all.tbl CDD cd12820 cd12820 240612 LbR_YadA-like YadA-like, left-handed beta-roll. This group contains the collagen-binding domain virulence factor YadA an adhesion proteins of several Yersinia species, and related cell surface proteins, including Moraxella catarrhalis UspA-like proteins. The collagen-binding portion is found in the hydrophobic N-terminal region. YadA forms a matrix on the bacterial outer membrane, which mediates binding to collagen and epithelial cells. YadA inhibits the complement-activating pathway with the coating of the cell surface with factor H, which impedes C3b molecules. These domains form a left handed beta roll made up of a series of short repeated elements. UspA1 and UspA2 are part of a class of pathogenicity factors that act as cell surface adhesion molecules, in which N-terminal head and neck domains extend from the bacterial outer membrane. The UspA1 head domain of Moraxella catarrhalis, is formed from trimeric left-handed parallel beta-helices of 14-16 amino acid repeats. The UspA1 head domain connects to a neck region of large extended, charged loops that maybe be ligand binding, which is in turn connected to an extended coiled coil domain that tethers the head and neck region to the cell surface via a transmembrane region. 126 matched cddid_all.tbl CDD cd12821 cd12821 213355 EcCorA_ZntB-like Escherichia coli CorA-Salmonella typhimurium ZntB_like family. A family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. Members of this family are found in all three kingdoms of life. It is a functionally diverse family, including the Mg2+ transporters Escherichia coli and Salmonella typhimurium CorAs (which can also transport Co2+, and Ni2+ ), and the Zn2+ transporter Salmonella typhimurium ZntB which mediates the efflux of Zn2+ (and Cd2+). It also includes two Saccharomyces cerevisiae members: the inner membrane Mg2+ transporters Mfm1p/Lpe10p, and Mrs2p, and a family of Arabidopsis thaliana members (AtMGTs) some of which are localized to distinct tissues, and not all of which can transport Mg2+. Structures of the intracellular domain of Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, and Mrs2p. Natural variants such as GVN and GIN, such as occur in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport. 285 matched cddid_all.tbl CDD cd12822 cd12822 213356 TmCorA-like Thermotoga maritima CorA-like family. This family belongs to the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. Members of the Thermotoga maritima CorA_like family are found in all three kingdoms of life. It is a functionally diverse family, in addition to the CorA Co2+ transporter from the hyperthermophilic Thermotoga maritima, it includes three Saccharomyces cerevisiae members: two plasma membrane proteins, the Mg2+ transporter Alr1p/Swc3p and the putative Mg2+ transporter, Alr2p, and the vacuole membrane protein Mnr2p, a putative Mg2+ transporter. Thermotoga maritima CorA forms funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport by Alr1p. Natural variants in this signature sequence may be associated with the transport of different divalent cations. The functional diversity of the MIT superfamily may also be due to minor structural differences regulating gating, substrate selection, and transport. 289 matched cddid_all.tbl CDD cd12823 cd12823 213357 Mrs2_Mfm1p-like Saccharomyces cerevisiae inner mitochondrial membrane Mg2+ transporters Mfm1p and Mrs2p-like family. A eukaryotic subfamily belonging to the Escherichia coli CorA-Salmonella typhimurium ZntB_like family (EcCorA_ZntB-like) family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. This functionally diverse subfamily includes the inner mitochondrial membrane Mg2+ transporters Saccharomyces cerevisiae Mfm1p/Lpe10p, Mrs2p, and human MRS2/ MRS2L. It also includes a family of Arabidopsis thaliana proteins (AtMGTs) some of which are localized to distinct tissues, and not all of which can transport Mg2+. Structures of the intracellular domain of two EcCorA_ZntB-like family transporters: Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, and Mrs2p. Natural variants such as GVN and GIN, as in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport. 323 matched cddid_all.tbl CDD cd12824 cd12824 213358 ZntB-like Salmonella typhimurium Zn2+ transporter ZntB-like subfamily. A bacterial subfamily belonging to the Escherichia coli CorA-Salmonella typhimurium ZntB_like family (EcCorA_ZntB-like) family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. This subfamily includes the Zn2+ transporter Salmonella typhimurium ZntB which mediates the efflux of Zn2+ (and Cd2+). Structures of the intracellular domain of Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, and Mrs2p. Natural variants such as GVN and GIN, which occur in proteins belonging to this subfamily, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport. 290 matched cddid_all.tbl CDD cd12825 cd12825 213359 EcCorA-like Escherichia coli Mg2+ transporter CorA_like subfamily. A bacterial subfamily of the Escherichia coli CorA-Salmonella typhimurium ZntB_like(EcCorA_ZntB-like) family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. This subfamily includes the Mg2+ transporters Escherichia coli, Salmonella typhimurium, and Helicobacter pylori CorAs (which can also transport Co2+, and Ni2+). Structures of the intracellular domain of Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, and Mrs2p. Natural variants such as GVN and GIN, such as occur in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport. 287 matched cddid_all.tbl CDD cd12826 cd12826 213360 EcCorA_ZntB-like_u1 uncharacterized bacterial subfamily of the Escherichia coli CorA-Salmonella typhimurium ZntB family. A uncharacterized subfamily of the Escherichia coli CorA-Salmonella typhimurium ZntB (EcCorA-ZntB_like) family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. The EcCorA-ZntB_like family includes the Mg2+ transporters Escherichia coli and Salmonella typhimurium CorAs, which can also transport Co2+, and Ni2+. Structures of the intracellular domain of EcCorA-ZntB_like family members, Vibrio parahaemolyticus and Salmonella typhimurium ZntB, form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA. Natural variants such as GVN and GIN, as in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport. 281 matched cddid_all.tbl CDD cd12827 cd12827 213361 EcCorA_ZntB-like_u2 uncharacterized bacterial subfamily of the Escherichia coli CorA-Salmonella typhimurium ZntB family. A uncharacterized subfamily of the Escherichia coli CorA-Salmonella typhimurium ZntB (EcCorA-ZntB_like) family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes.The EcCorA-ZntB-like family includes the Mg2+ transporters Escherichia coli and Salmonella typhimurium CorAs, which can also transport Co2+, and Ni2+. Structures of the intracellular domain of EcCorA-ZntB-like family members, Vibrio parahaemolyticus and Salmonella typhimurium ZntB, form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA. Natural variants such as GVN and GIN, such as occur in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport. 289 matched cddid_all.tbl CDD cd12828 cd12828 213362 TmCorA-like_1 Thermotoga maritima CorA_like subfamily. This subfamily belongs to the Thermotoga maritima CorA (TmCorA)-family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. Members of this subfamily are found in all three kingdoms of life. It is functionally diverse subfamily, in addition to the CorA Co2+ transporter from the hyperthermophilic Thermotoga maritima, it includes Methanosarcina mazei CorA which may be involved in transport of copper and/or other divalent metal ions. Thermotoga maritima CorA forms funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport by a related protein, Saccharomyces cerevisiae Alr1p. Natural variants in this signature sequence may be associated with the transport of different divalent cations. The functional diversity of the MIT superfamily may also be due to minor structural differences regulating gating, substrate selection, and transport. 294 matched cddid_all.tbl CDD cd12829 cd12829 213363 Alr1p-like Saccharomyces cerevisiae Alr1p-like subfamily. This eukaryotic subfamily belongs to the Thermotoga maritima CorA (TmCorA)-family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. This subfamily includes three Saccharomyces cerevisiae members: two plasma membrane proteins, the Mg2+ transporter Alr1p/Swc3p and the putative Mg2+ transporter, Alr2p, and the vacuole membrane protein Mnr2p, a putative Mg2+ transporter. Thermotoga maritima CorA forms funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport by Alr1p. Natural variants in this signature sequence may be associated with the transport of different divalent cations. The functional diversity of the MIT superfamily may also be due to minor structural differences regulating gating, substrate selection, and transport. 305 matched cddid_all.tbl CDD cd12830 cd12830 213364 MtCorA-like Mycobacterium tuberculosis CorA-like subfamily. This bacterial subfamily belongs to the Thermotoga maritima CorA (TmCorA)-like family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. This subfamily includes the Mg2+ transporter Mycobacterium tuberculosis CorA (which also transports Co2+). Thermotoga maritima CorA forms funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport by a related protein, Saccharomyces cerevisiae Alr1p. Natural variants in this signature sequence may be associated with the transport of different divalent cations. The functional diversity of the MIT superfamily may also be due to minor structural differences regulating gating, substrate selection, and transport. 292 matched cddid_all.tbl CDD cd12831 cd12831 213365 TmCorA-like_u2 Uncharacterized bacterial subfamily of the Thermotoga maritima CorA-like family. This subfamily belongs to the Thermotoga maritima CorA (TmCorA)-like family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. Members of the TmCorA-like family are found in all three kingdoms of life. It is a functionally diverse family which includes the CorA Co2+ transporter from the hyperthermophilic Thermotoga maritima, and three Saccharomyces cerevisiae proteins: two located in the plasma membrane: the Mg2+ transporter Alr1p/Swc3p and the putative Mg2+ transporter, Alr2p, and the vacuole membrane protein Mnr2p, a putative Mg2+ transporter. Thermotoga maritima CorA forms funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport by a related protein, Saccharomyces cerevisiae Alr1p. Natural variants in this signature sequence may be associated with the transport of different divalent cations. The functional diversity of the MIT superfamily may also be due to minor structural differences regulating gating, substrate selection, and transport. 287 matched cddid_all.tbl CDD cd12832 cd12832 213366 TmCorA-like_u3 Uncharacterized subfamily of the Thermotoga maritima CorA-like family. This subfamily belongs to the Thermotoga maritima CorA (TmCorA)-like family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. Members of the TmCorA-like family are found in all three kingdoms of life. It is a functionally diverse family which includes the CorA Co2+ transporter from the hyperthermophilic Thermotoga maritima, and three Saccharomyces cerevisiae proteins: two located in the plasma membrane: the Mg2+ transporter Alr1p/Swc3p and the putative Mg2+ transporter, Alr2p, and the vacuole membrane protein Mnr2p, a putative Mg2+ transporter. Thermotoga maritima CorA forms funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport by a related protein, Saccharomyces cerevisiae Alr1p. Natural variants in this signature sequence may be associated with the transport of different divalent cations. The functional diversity of the MIT superfamily may also be due to minor structural differences regulating gating, substrate selection, and transport. 287 matched cddid_all.tbl CDD cd12833 cd12833 213367 ZntB-like_1 Salmonella typhimurium Zn2+ transporter ZntB-like subgroup. A bacterial subgroup belonging to the Escherichia coli CorA-Salmonella typhimurium ZntB_like family (EcCorA_ZntB-like) of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. This subgroup includes the Zn2+ transporter Salmonella typhimurium ZntB which mediates the efflux of Zn2+ (and Cd2+). Structures of the intracellular domain of Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, and Mrs2p. Natural variants such as GVN and GIN, which occur in proteins belonging to this subfamily, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport. 290 matched cddid_all.tbl CDD cd12834 cd12834 213368 ZntB_u1 Uncharacterized bacterial subgroup of the Salmonella typhimurium Zn2+ transporter ZntB-like subfamily. The MIT superfamily of essential membrane proteins is involved in transporting divalent cations (uptake or efflux) across membranes. The ZntB-like subfamily includes the Zn2+ transporter Salmonella typhimurium ZntB which mediates the efflux of Zn2+ (and Cd2+). Structures of the intracellular domain of Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, and Mrs2p. Natural variants such as GVN and GIN which occur in proteins belonging to this subfamily, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport. 290 matched cddid_all.tbl CDD cd12835 cd12835 213369 EcCorA-like_1 Escherichia coli Mg2+ transporter CorA_like subgroup. A bacterial subgroup of the Escherichia coli CorA-Salmonella typhimurium ZntB_like (EcCorA_ZntB-like) family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. This subgroup includes the Mg2+ transporters Escherichia coli CorA and Salmonella typhimurium CorA (which can also transport Co2+, and Ni2+). Structures of the intracellular domain of Vibrio parahaemolyticus and Salmonella typhimurium ZntB form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, and Mrs2p. Natural variants such as GVN and GIN, such as occur in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport. 287 matched cddid_all.tbl CDD cd12836 cd12836 213370 HpCorA-like Mg2+ transporter Helicobacter pylori CorA-like subgroup. A bacterial subgroup of the Escherichia coli CorA-Salmonella typhimurium ZntB_like (EcCorA_ZntB-like) family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. This subgroup includes the Mg2+ transporter Helicobacter pylori CorAs (which can also transport Co2+, and Ni2+); CorA plays an important role in the viability of this pathogen. Structures of the intracellular domain of Vibrio parahaemolyticus and Salmonella typhimurium ZntB (members of the EcCorA_ZntB-like family) form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA, and Mrs2p. Natural variants such as GVN and GIN, such as occur in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport. 288 matched cddid_all.tbl CDD cd12837 cd12837 213371 EcCorA-like_u1 uncharacterized subgroup of the Escherichia coli Mg2+ transporter CorA_like subfamily. A uncharacterized subgroup of the Escherichia coli CorA-Salmonella typhimurium ZntB_like family (EcCorA_ZntB-like) family of the MIT superfamily of essential membrane proteins involved in transporting divalent cations (uptake or efflux) across membranes. The EcCorA_ZntB-like family includes the Mg2+ transporters Escherichia coli and Salmonella typhimurium CorAs, which can also transport Co2+, and Ni2+. Structures of the intracellular domain of EcCorA_ZntB-like family members, Vibrio parahaemolyticus and Salmonella typhimurium ZntB, form funnel-shaped homopentamers, the tip of the funnel is formed from two C-terminal transmembrane (TM) helices from each monomer, and the large opening of the funnel from the N-terminal cytoplasmic domains. The GMN signature motif of the MIT superfamily occurs just after TM1, mutation within this motif is known to abolish Mg2+ transport through Salmonella typhimurium CorA. Natural variants such as GVN and GIN, such as occur in some ZntB family proteins, may be associated with the transport of different divalent cations, such as zinc and cadmium. The functional diversity of MIT transporters may also be due to minor structural differences regulating gating, substrate selection, and transport. 298 matched cddid_all.tbl CDD cd12838 cd12838 214011 Killer_toxin_alpha Alpha subunit of killer toxin from halotolerant yeast. This family contains the alpha subunit of killer toxins that are secreted by several strains of yeasts and fungi. These toxins are proteinous substances that kill sensitive strains. The halotolerant yeast Pichia farinosa KK1 strain produces the SMK toxin, with maximum killer activity under acidic pH and high salt concentration. This toxin is composed of alpha and beta subunits that interact tightly with each other under acidic conditions but easily dissociated and lose activity under neutral conditions. It shares topology to that of the fungal killer toxin, KP4, which contains a rare structural motif, suggesting that these toxins may be evolutionally and/or functionally related. 62 matched cddid_all.tbl CDD cd12839 cd12839 214012 Killer_toxin_beta Beta subunit of killer toxin from halotolerant yeast. This family contains the beta subunit of killer toxins that are secreted by several strains of yeasts and fungi. These toxins are proteinous substances that kill sensitive strains. The halotolerant yeast Pichia farinosa KK1 strain produces the SMK toxin, with maximum killer activity under acidic pH and high salt concentration. This toxin is composed of alpha and beta subunits that interact tightly with each other under acidic conditions but easily dissociated and loose activity under neutral conditions. It shares topology to that of the fungal killer toxin, KP4, which contains a rare structural motif, suggesting that these toxins may be evolutionally and/or functionally related. 74 matched cddid_all.tbl CDD cd12840 cd12840 214013 CarS Antirepressor CarS. CarS, an antirepressor present in Cystobacterineae, recognizes repressors to turn on the photo-inducible promoter P(B). In the dark, access to the P(B) promoter is blocked by the repressor CarA. Blue light causes expression of CarS, leading the way to the CarA-CarS interaction which dismantles the CarA-operator complex, resulting in the derepression of the P(B) promoter. A parallel pathway for regulating P(B) involves the interaction of CarS with the repressor CarH, which shares the domain architecture of CarA. CarH and CarA contain an N-terminal, MerR-type winged-helix DNA-binding domain that recognizes CarS. CarS adopts an SH3-like fold with loop length variations and acts as an operator DNA mimic. 80 matched cddid_all.tbl CDD cd12841 cd12841 214014 TM_EphA1 Transmembrane domain of Ephrin Receptor A1 Protein Tyrosine Kinase. Ephrin receptors (EphRs) comprise the largest subfamily of receptor PTKs, and are classified into two classes (EphA and EphB), corresponding to binding preferences for either GPI-anchored ephrin-A ligands or transmembrane ephrin-B ligands. Vertebrates have ten EphA and six EphB receptors, which display promiscuous ligand interactions within each class. EphA1 has been associated with late-onset Alzheimer's disease and certain cancers such as colorectal and gastric carcinomas. EphRs contain an ephrin binding domain and two fibronectin repeats extracellularly, a single-span transmembrane (TM) domain, and a cytoplasmic tyr kinase domain. Binding of the ephrin ligand to EphR requires cell-cell contact since both are anchored to the plasma membrane. This allows ephrin/EphR dimers to form, leading to the activation of the intracellular tyr kinase domain. The resulting downstream signals occur bidirectionally in both EphR-expressing cells (forward signaling) and ephrin-expressing cells (reverse signaling). The main effect of ephrin/EphR interaction is cell-cell repulsion or adhesion. Ephrin/EphR signaling is important in neural development and plasticity, cell morphogenesis and proliferation, cell-fate determination, embryonic development, tissue patterning, and angiogenesis. The TM domain mediates dimerization. 38 matched cddid_all.tbl CDD cd12842 cd12842 410985 IGCP_Hfx_cass2 integron gene cassette protein (IGCP) Hfx_cass2 and similar proteins. This family contains the unique integron gene cassette protein Hfx_cass2 and similar proteins that have yet to be characterized. The structure of Hfx_cass2 depicts a homodimer incorporating a compact all-alpha fold of six helical segments with a core central bundle of helices. It has a surface cleft reminiscent of an enzyme active site. This family may allow an assessment of the impact of the integron/gene cassette system on the emergence of new phenotypes, such as drug resistance or virulence. 110 matched cddid_all.tbl CDD cd12843 cd12843 240608 Bvu_2165_C_like The C-terminal domain of uncharacterized bacterial proteins. This family contains the C-terminal domain of uncharacterized hypothetical proteins from bacteria, including Bacteroides vulgatus Bvu_2165. The structure of Bvu_2165 is dimeric, with an extensive binding interface. 105 matched cddid_all.tbl CDD cd12869 cd12869 240607 MqsR Motility quorum-sensing regulator (MqsR). This family includes domains similar to the motility quorum-sensing regulator MqsR, a toxin that is highly upregulated in persisters (dormant cells found in biofilms that are a source of antibiotic resistance). MqsR pairs with its antitoxin MqsA, forming a unique family of toxin:antitoxin (TA) systems. MqsR has been found to be structurally homologous to the bacterial ribonuclease (RelE) toxins; however, its sequence is not similar to any other known toxins and therefore its molecular function is as yet unknown. 98 matched cddid_all.tbl CDD cd12870 cd12870 240606 MqsA antitoxin MqsA for MqsR toxin. This family includes domains similar to the antitoxin MqsA that binds motility quorum-sensing regulator MqsR, a toxin that is highly upregulated in persisters (dormant cells found in biofilms that are a source of antibiotic resistance), thus forming a unique toxin:antitoxin (TA) pair. MqsA neutralizes MsqR toxicity. It binds its own promoter as well as those of genes important for E. coli physiology, such as mcbR and spy. It also binds zinc and has been shown to coordinate DNA via its C-terminal domain. This family also includes the B. subtilis YokU protein, which is functionally uncharacterized. 66 matched cddid_all.tbl CDD cd12871 cd12871 214015 Bacuni_01323_like Uncharacterized protein conserved in Bacteroidetes. A well-conserved family of 16-stranded beta barrels resembling outer membrane porins. The interior of the barrels is mostly occupied by an insert with partially helical structure. 231 matched cddid_all.tbl CDD cd12872 cd12872 293932 SPRY_Ash2 SPRY domain in Ash2. This SPRY domain is found at the C-terminus of Ash2 (absent, small, or homeotic discs 2) -like proteins, core components of all mixed-lineage leukemia (MLL) family histone methyltransferases. Ash2 is a member of the trithorax group of transcriptional regulators of the Hox genes. Recent studies show that the SPRY domain of Ash2 mediates the interaction with RbBP5 and has an important role in regulating the methyltransferase activity of MLL complexes. In yeast, Ash2 is involved in histone methylation and is required for the earliest stages of embryogenesis. 150 matched cddid_all.tbl CDD cd12873 cd12873 293933 SPRY_DDX1 SPRY domain associated with DEAD box gene DDX1. This SPRY domain is associated with the DEAD box gene, DDX1, an RNA-dependent ATPase involved in HIV-1 Rev function and virus replication. It is suggested that DDX1 acts as a cellular cofactor by promoting oligomerization of Rev on the Rev response element (RRE). DDX1 RNA is overexpressed in breast cancer, data showing a strong and independent association between poor prognosis and deregulation of the DEAD box protein DDX1, thus potentially serving as an effective prognostic biomarker for early recurrence in primary breast cancer. DDX1 also interacts with RelA and enhances nuclear factor kappaB-mediated transcription. DEAD-box proteins are associated with all levels of RNA metabolism and function, and have been implicated in translation initiation, transcription, RNA splicing, ribosome assembly, RNA transport, and RNA decay. 155 matched cddid_all.tbl CDD cd12874 cd12874 293934 SPRY_PRY PRY/SPRY domain, also known as B30.2. This domain contains residues in the N-terminus that form a distinct PRY domain structure such that the B30.2 domain consists of PRY and SPRY subdomains. B30.2 domains comprise the C-terminus of three protein families: BTNs (receptor glycoproteins of immunoglobulin superfamily); several TRIM proteins (composed of RING/B-box/coiled-coil core); Stonutoxin (secreted poisonous protein of the stonefish Synanceia horrida). While SPRY domains are evolutionarily ancient, B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. Among the TRIM proteins, also known as the N-terminal RING finger/B-box/coiled coil (RBCC) family, only Classes I and II contain the B30.2 domain that has evolved under positive selection. Class I TRIM proteins include multiple members involved in antiviral immunity at various levels of interferon signaling cascade. Among the 75 human TRIMs, roughly half enhance immune response, which they do at multiple levels in signaling pathways. The PRY-SPRY domain in these TRIM families is suggested to serve as the target binding site. 168 matched cddid_all.tbl CDD cd12875 cd12875 293935 SPRY_SOCS_Fbox SPRY domain in Fbxo45 and suppressors of cytokine signaling (SOCS) proteins. This family consists of the SPRY domain-containing SOCS box protein family (SPSB1-4, also known as SSB-1 to -4) as well as F-box protein 45 (Fbxo45), a novel synaptic E3 and ubiquitin ligase. The SPSB protein is composed of a central SPRY protein interaction domain and a C-terminal SOCS box. SPSB1, SPSB2, and SPSB4 interact with prostate apoptosis response protein 4 (Par-4) and are negative regulators that recruit the ECS E3 ubiquitin ligase complex to polyubiquitinate inducible nitric-oxide synthase (iNOS), resulting in its proteasomal degradation. Fbxo45 is related to this family; it is located N-terminal to the SPRY domain, and known to induce the degradation of a synaptic vesicle-priming factor, Munc13-1, via the SPRY domain, thus playing an important role in the regulation of neurotransmission by modulating Munc13-1 at the synapse. Suppressor of cytokine signaling (SOCS) proteins negatively regulate signaling from JAK-associated cytokine receptor complexes, and play key roles in the regulation of immune homeostasis. 169 matched cddid_all.tbl CDD cd12876 cd12876 293936 SPRY_SOCS3 SPRY domain in the suppressor of cytokine signaling 3 (SOCS3) family. The SPRY domain-containing SOCS box protein family (SPSB1-4, also known as SSB-1 to -4) is composed of a central SPRY protein interaction domain and a C-terminal SOCS box. All four SPSB proteins interact with c-Met, the hepatocyte growth factor receptor, but SOCS3 regulates cellular response to a variety of cytokines such as leukemia inhibitory factor (LIF) and interleukin 6. SOCS3, along with SOCS1, are expressed by immune cells and cells of the central nervous system (CNS) and have the potential to impact immune processes within the CNS. In non-small cell lung cancer (NSCLC), SOCS3 is silenced and proline-rich tyrosine kinase 2 (Pyk2) is over-expressed; it has been suggested that SOCS3 could be an effective way to prevent the progression of NSCLC due to its role in regulating Pyk2 expression. 185 matched cddid_all.tbl CDD cd12877 cd12877 240457 SPRY1_RyR SPRY domain 1 (SPRY1) of ryanodine receptor (RyR). This SPRY domain is the first of three structural repeats in all three isoforms of the ryanodine receptor (RyR), which are the major Ca2+ release channels in the membranes of sarcoplasmic reticulum (SR). There are three RyR genes in mammals; the skeletal RyR1, the cardiac RyR2 and the brain RyR3. The three SPRY domains are located in the N-terminal part of the cytoplasmic region of the RyRs, but no specific function has been found for this first SPRY domain of the RyRs. 151 matched cddid_all.tbl CDD cd12878 cd12878 240458 SPRY2_RyR SPRY domain 2 (SPRY2) of ryanodine receptor (RyR). This SPRY domain (SPRY2) is the second of three structural repeats in all three isoforms of the ryanodine receptor (RyR), which are the major Ca2+ release channels in the membranes of sarcoplasmic reticulum (SR). There are three RyR genes in mammals; the skeletal RyR1, the cardiac RyR2 and the brain RyR3. The three SPRY domains are located in the N-terminal part of the cytoplasmic region of the RyRs, The SPRY2 domain has been shown to bind to the dihydropryidine receptor (DHPR) II-III loop and the ASI region of RyR1 133 matched cddid_all.tbl CDD cd12879 cd12879 293937 SPRY3_RyR SPRY domain 3 (SPRY3) of ryanodine receptor (RyR). This SPRY domain (SPRY3) is the third of three structural repeats in all three isoforms of the ryanodine receptor (RyR), which are the major Ca2+ release channels in the membranes of sarcoplasmic reticulum (SR). There are three RyR genes in mammals; the skeletal RyR1, the cardiac RyR2 and the brain RyR3. The three SPRY domains are located in the N-terminal part of the cytoplasmic region of the RyRs, but no specific function has been found for this third SPRY domain of the RyRs. 151 matched cddid_all.tbl CDD cd12880 cd12880 293938 SPRYD7 SPRY domain-containing protein 7. This family contains SPRY domain-containing protein 7 (also known as SPRY domain-containing protein 7 or CLL deletion region gene 6 protein homolog or CLLD6 or chronic lymphocytic leukemia deletion region gene 6 protein homolog). In humans, CLLD6 is highly expressed in heart, skeletal muscle, and testis as well as cancer cell lines. It also has cross-species conservation, suggesting that it is likely to carry out important cellular processes. 160 matched cddid_all.tbl CDD cd12881 cd12881 293939 SPRY_HERC1 SPRY domain in HERC1. This SPRY domain is found in the HERC1, a large protein related to chromosome condensation regulator RCC1. It is widely expressed in many tissues, playing an important role in intracellular membrane trafficking in the cytoplasm as well as Golgi apparatus. HERC1 also interacts with tuberous sclerosis 2 (TSC2, tuberin), which suppresses cell growth, and results in the destabilization of TSC2. However, the biological function of HERC1 has yet to be defined. 162 matched cddid_all.tbl CDD cd12882 cd12882 293940 SPRY_RNF123 SPRY domain at N-terminus of ring finger protein 123. This SPRY domain is found at the N-terminus of RING finger protein 123 domain (also known as E3 ubiquitin-protein ligase RNF123). The ring finger domain motif is present in a variety of functionally distinct proteins and known to be involved in protein-protein and protein-DNA interactions. RNF123 displays E3 ubiquitin ligase activity toward the cyclin-dependent kinase inhibitor p27 (Kip1). 128 matched cddid_all.tbl CDD cd12883 cd12883 293941 SPRY_RING SPRY domain at N-terminus of Really Interesting New Gene (RING) finger domain. This SPRY domain is found at the N-terminus of RING finger domains which are present in a variety of functionally distinct proteins and known to be involved in protein-protein and protein-DNA interactions. RING-finger domain is a type of Zn-finger that binds two Zn atoms and is identified in proteins with a wide range of functions such as viral replication, signal transduction, and development. 121 matched cddid_all.tbl CDD cd12884 cd12884 293942 SPRY_hnRNP SPRY domain in heterogeneous nuclear ribonucleoprotein U-like (hnRNP) protein 1. This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of heterogeneous nuclear ribonucleoprotein U-like (hnRNP) protein 1 (also known as HNRPUL1 ) which is a major constituent of nuclear matrix or scaffold and binds directly to DNA sequences through the N-terminal acidic region named serum amyloid P (SAP). Its function is specifically modulated by E1B-55kDa in adenovirus-infected cells. HNRPUL1 also participates in ATR protein kinase signaling pathways during adenovirus infection. Two transcript variants encoding different isoforms have been found for this gene. When associated with bromodomain-containing protein 7 (BRD7), it activates transcription of glucocorticoid-responsive promoter in the absence of ligand-stimulation. 177 matched cddid_all.tbl CDD cd12885 cd12885 293943 SPRY_RanBP_like SPRY domain in Ran binding proteins, SSH4, HECT E3 and SPRYD3. This family includes SPRY domains found in Ran binding proteins (RBP or RanBPM) 9 and 10, SSH4 (suppressor of SHR3 null mutation protein 4), SPRY domain-containing protein 3 (SPRYD3) as well as HECT, a C-terminal catalytic domain of a subclass of ubiquitin-protein ligase (E3). RanBP9 and RanBP10 act as androgen receptor (AR) coactivators. Both consist of the N-terminal proline- and glutamine-rich regions, the SPRY domain, and LisH-CTLH and CRA motifs. The SPRY domain in SSH4 may be involved in cargo recognition, either directly or by combination with other adaptors, possibly leading to a higher selectivity. SPRYD3 is highly expressed in most tissues in humans, possibly involved in important cellular processes. HECT E3 mediates the direct transfer of ubiquitin from E2 to substrate. 132 matched cddid_all.tbl CDD cd12886 cd12886 293944 SPRY_like SPRY domain-like in bacteria. This family contains SPRY-like domains that are found only in bacterial and are mostly uncharacterized. SPRY domains, first identified in the SP1A kinase of Dictyostelium and rabbit Ryanodine receptor (hence the name), are homologous to B30.2. SPRY domains have been identified in at least 11 eukaryotic protein families, covering a wide range of functions, including regulation of cytokine signaling (SOCS), RNA metabolism (DDX1 and hnRNP), immunity to retroviruses (TRIM5alpha), intracellular calcium release (ryanodine receptors or RyR) and regulatory and developmental processes (HERC1 and Ash2L). 129 matched cddid_all.tbl CDD cd12887 cd12887 293945 SPRY_NHR_like SPRY domain in neuralized homology repeat. This family contains the neuralized homology repeat 1 (NHR1) domain similar to the SPRY domain (known to mediate specific protein-protein interactions) at the C-terminus of a conserved region within eukaryotic neuralized and neuralized-like proteins. In Drosophila, the neuralized protein (Neur) belongs to a group of ubiquitin ligases and is required in a subset of Notch pathway-mediated cell fate decisions during development of the nervous system. Neur binds to the Notch receptor ligand Delta through its first NHR1 domain and mediates its ubiquitination for endocytosis. Multiple copies of this region are found in some members of the family. 161 matched cddid_all.tbl CDD cd12888 cd12888 293946 SPRY_PRY_TRIM7_like PRY/SPRY domain in tripartite motif-binding protein 7 (TRIM7)-like, including TRIM7, TRIM10, TRIM15, TRIM26, TRIM39, TRIM41. This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of several tripartite motif-containing (TRIM) proteins, including TRIM7 (also referred to as glycogenin-interacting protein, RING finger protein 90 or RNF90), TRIM10, TRIM15, TRIM26, TRIM39 and TRIM41. TRIM7 or GNIP interacts with glycogenin and stimulates its self-glucosylating activity via its SPRY domain. TRIM10 (also known as hematopoietic RING finger 1 (HERF1) or TRIM10/HERF1) plays a key role in definitive erythroid development; downregulation of the Spi-1/PU.1 oncogene induces the expression of TRIM10/HERF1, a key factor required for terminal erythroid cell differentiation and survival. Antiviral activity of TRIM15 is dependent on the ability of its B-box to interact with the MLV Gag precursor protein; downregulation of TRIM15, along with TRIM11, enhances virus release suggesting that these proteins contribute to the endogenous restriction of retroviruses in cells. Tripartite motif-containing 26 (TRIM26) function is as yet unknown; however, since it is localized in the human histocompatibility complex (MHC) class I region, TRIM26 may play a role in immune response although studies show no association between TRIM26 polymorphisms and the risk of aspirin-exacerbated respiratory disease. TRIM39 is a MOAP-1 (Modulator of Apoptosis)-binding protein that stabilizes MOAP-1 through inhibition of its poly-ubiquitination process. TRIM41 (also known as RING finger-interacting protein with C kinase or RINCK) functions as an E3 ligase that catalyzes the ubiquitin-mediated degradation of protein kinase C. 169 matched cddid_all.tbl CDD cd12889 cd12889 293947 SPRY_PRY_TRIM67_9 PRY/SPRY domain in tripartite motif-containing proteins, TRIM9 and TRIM67. This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM9 proteins. TRIM9 protein is expressed mainly in the cerebral cortex, and functions as an E3 ubiquitin ligase. It has been shown that TRIM9 is localized to the neurons in the normal human brain and its immunoreactivity in affected brain areas in Parkinson's disease and dementia with Lewy bodies is severely decreased, possibly playing an important role in the regulation of neuronal function and participating in pathological process of Lewy body disease through its ligase. TRIM67 negatively regulates Ras activity via degradation of 80K-H, leading to neural differentiation, including neuritogenesis. 172 matched cddid_all.tbl CDD cd12890 cd12890 293948 SPRY_PRY_TRIM16 PRY/SPRY domain in tripartite motif-containing protein 16 (TRIM16). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM16 and TRIM-like proteins. TRIM16 (also known as estrogen-responsive B box protein or EBBP) does not possess a RING domain like the other TRIM proteins, but contains two B-box domains and can heterodimerize with other TRIM proteins such as TRIM24, Promyelocytic leukemia (PML) protein and Midline-1 (MID1 or TRIM18). It is a regulator of keratinocyte differentiation and a tumor suppressor in retinoid-sensitive neuroblastoma. It has been shown that loss of TRIM16 expression plays an important role in the development of cutaneous squamous cell carcinoma (SCC) and is a determinant of retinoid sensitivity. TRIM16 also has E3 ubiquitin ligase activity. 182 matched cddid_all.tbl CDD cd12891 cd12891 293949 SPRY_PRY_C-I_2 PRY/SPRY domain in tripartite motif-containing (TRIM) proteins, including TRIM14-like, TRIM16-like, TRIM25-like, TRIM47-like, TRIM65 and RNF135, and stonustoxin. This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of several Class I TRIM proteins, including TRIM14, TRIM16 and TRIM25, TRIM47 as well as RING finger protein RNF135 and stonustoxin, a secreted poisonous protein of the stonefish Synanceja horrida. TRIM16 (also known as estrogen-responsive B box protein or EBBP) has E3 ubiquitin ligase activity. It is a regulator of keratinocyte differentiation and a tumor suppressor in retinoid-sensitive neuroblastoma. TRIM25 (also called Efp) ubiquitinates the N terminus of the viral RNA receptor retinoic acid-inducible gene-I (RIG-I) in response to viral infection, leading to activation of the RIG-I signaling pathway, thus resulting in type I interferon production to limit viral replication. It has been shown that the influenza A virus targets TRIM25 and disables its antiviral function. TRIM47, also known as GOA (Gene overexpressed in astrocytoma protein) or RNF100 (RING finger protein 100), is highly expressed in kidney tubular cells, but low expressed in most tissue. It is overexpressed in astrocytoma tumor cells and plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. RNF135 ubiquitinates RIG-I (retinoic acid-inducible gene-I) to promote interferon-beta induction during the early phase of viral infection. Stonustoxin (STNX) is a hypotensive and lethal protein factor that also possesses other biological activities such as species-specific hemolysis (due to its ability to form pores in the cell membrane) and platelet aggregation, edema-induction, and endothelium-dependent vasorelaxation (mediated by the nitric oxide pathway and activation of potassium channels). The PRY-SPRY domain in these TRIM families is suggested to serve as the target binding site. 167 matched cddid_all.tbl CDD cd12892 cd12892 240472 SPRY_PRY_TRIM18 PRY/SPRY domain of TRIM18/MID1, also known as FXY or RNF59. This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is at the C-terminus of the overall domain architecture of MID1 (also known as FXY, RNF59, TRIM18) gene represented by a RING finger domain (RING), two B-box motifs (BBOX), coiled-coil C-terminal to Bbox domain (BBC) and fibronectin type 3 domain (FN3). Mutations in the human MID1 gene result in X-linked Opitz G/BBB syndrome (OS), a disorder affecting development of midline structures, causing craniofacial, urogenital, gastrointestinal and cardiovascular abnormalities. A unique MID1 gene mutation located in a variable loop in the SPRY domain alters conformation of the binding pocket and may affect the binding affinity to the PRY/SPRY domain. 177 matched cddid_all.tbl CDD cd12893 cd12893 293950 SPRY_PRY_TRIM35 PRY/SPRY domain in tripartite motif-containing protein 35 (TRIM35). This PRY/SPRY domain is found at the C-terminus of the overall domain architecture of tripartite motif 35, TRIM35 (also known as hemopoietic lineage switch protein), which includes a RING finger domain (RING) and a B-box motif (BBOX). TRIM35 may play a role as a tumor suppressor and is implicated in the cell death mechanism. 171 matched cddid_all.tbl CDD cd12894 cd12894 293951 SPRY_PRY_TRIM36 PRY/SPRY domain in tripartite motif-containing protein 36 (TRIM36). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM36, a Class I TRIM protein. TRIM36 (also known as Haprin or RNF98) has a ubiquitin ligase activity and interacts with centromere protein-H, one of the kinetochore proteins. It has been shown that TRIM36 is potentially associated with chromosome segregation and that an excess of TRIM36 may cause chromosomal instability. In Xenopus laevis, TRIM36 is expressed during early embryogenesis and plays an important role in the arrangement of somites during their formation. 204 matched cddid_all.tbl CDD cd12895 cd12895 293952 SPRY_PRY_TRIM46 PRY/SPRY domain in tripartite motif-containing protein 46 (TRIM46). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM46 proteins (composed of RING/B-box/coiled-coil core and also known as RBCC proteins). The SPRY/PRY combination is a possible component of immune defense. This protein family has not yet been characterized. 209 matched cddid_all.tbl CDD cd12896 cd12896 293953 SPRY_PRY_TRIM65 PRY/SPRY domain in tripartite motif-containing domain 65 (TRIM65). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM65 proteins (composed of RING/B-box/coiled-coil core and also known as RBCC proteins). The SPRY/PRY combination is a possible component of immune defense. This protein family has not been characterized. 182 matched cddid_all.tbl CDD cd12897 cd12897 293954 SPRY_PRY_TRIM50_72 PRY/SPRY domain in tripartite motif-binding (TRIM) proteins TRIM50 and TRIM72. This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of several TRIM proteins, including TRIM72 and TRIM50. TRIM72 (also known as MG53) has been shown to perform a critical function in membrane repair following acute muscle injury by nucleating the assembly of the repair machinery at injury sites. It is expressed specifically in skeletal muscle and heart, and tethered to the plasma membrane and cytoplasmic vesicles via its interaction with phosphatidylserine. TRIM50, an E3 ubiquitin ligase, is deleted in Williams-Beuren (WBS) syndrome, a multi-system neurodevelopmental disorder caused by the deletion of contiguous genes at chromosome region 7q11.23. 191 matched cddid_all.tbl CDD cd12898 cd12898 293955 SPRY_PRY_TRIM76 PRY/SPRY domain in tripartite motif-containing protein 76 (TRIM76), also called cardiomyopathy-associated protein 5. This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM76, a Class I TRIM protein. TRIM76 (also known as cardiomyopathy-associated protein 5 or CMYA5 or myospryn or SPRYD2) is a muscle-specific member of the TRIM superfamily, but lacks the RING domain. It has been suggested that TRIM76 is involved in two distinct processes, protein kinase A signaling and vesicular trafficking. It has also been implicated in Duchenne muscular dystrophy and cardiac disease; gene polymorphism of TRIM76 is associated with left ventricular wall thickness in patients with hypertension while its interactions with M-band titin and calpain 3 link it to tibial and limb-girdle muscular dystrophies. 171 matched cddid_all.tbl CDD cd12899 cd12899 293956 SPRY_PRY_TRIM76_like PRY/SPRY domain in tripartite motif-containing protein 76 (TRIM76)-like. This domain is similar to the distinct PRY/SPRY subdomain found at the C-terminus of TRIM76, a Class I TRIM protein. TRIM76 (also known as cardiomyopathy-associated protein 5 or CMYA5 or myospryn or SPRYD2) is a muscle-specific member of the TRIM superfamily, but lacks the RING domain. It has been suggested that TRIM76 is involved in two distinct processes, protein kinase A signaling and vesicular trafficking. 176 matched cddid_all.tbl CDD cd12900 cd12900 293957 SPRY_PRY_TRIM21 PRY/SPRY domain in tripartite motif-binding protein 21 (TRIM21) also known as 52kD Ribonucleoprotein Autoantigen (Ro52). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM21, which is also known as Sjogren Syndrome Antigen A (SSA), SSA1, 52kD Ribonucleoprotein Autoantigen (Ro52, Ro/SSA, SS-A/Ro) or RING finger protein 81 (RNF81). TRIM21 domains are composed of RING/B-box/coiled-coil core and also known as RBCC proteins. As an E3 ligase, TRIM21 mediates target specificity in ubiquitination; it regulates type 1 interferon and proinflammatory cytokines via ubiquitination of interferon regulatory factors (IRFs). It is up-regulated at the site of autoimmune inflammation, such as cutaneous lupus lesions, indicating a central role in the tissue destructive inflammatory process. It interacts with auto-antigens in patients with Sjogren syndrome and systemic lupus erythematosus, a chronic systemic autoimmune disease characterized by the presence of autoantibodies against the protein component of the human intracellular ribonucleoprotein-RNA complexes and more specifically TRIM21, Ro60/TROVE2 and La/SSB proteins. It binds the Fc part of IgG molecules via its PRY-SPRY domain with unexpectedly high affinity. 180 matched cddid_all.tbl CDD cd12901 cd12901 293958 SPRY_PRY_FSD1 Fibronectin type III and SPRY containing 1 (FSD1) domain includes PRY at the N-terminus. This domain is part of the fibronectin type III and SPRY domain containing 1 (FSD1) and FSD1-like (FSD1L) proteins. These are centrosome-associated proteins that are characterized by an N-terminal coiled-coil region downstream of B-box (BBC) domain, a central fibronectin type III (FN3) domain, and C-terminal repeats in PRY/SPRY domain. The FSD1 protein associates with a subset of microtubules and may be involved in the stability and organization of microtubules during cytokinesis. 207 matched cddid_all.tbl CDD cd12902 cd12902 293959 SPRY_PRY_RNF135 PRY/SPRY domain in RING finger protein RNF135. This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of the RING finger protein RNF135 (also known as Riplet/RNF135), which ubiquitinates RIG-I (retinoic acid-inducible gene-I) to promote interferon-beta induction during the early phase of viral infection. Normally, RIG-I is activated by TRIM25 in response to viral infection, leading to activation of the RIG-I signaling pathway, thus resulting in type I interferon production to limit viral replication. However, RNF135, consisting of an N-terminal RING finger domain, C-terminal SPRY and PRY motifs and showing sequence similarity to TRIM25, acts as an alternative factor that promotes RIG-I activation independent of TRIM25. 168 matched cddid_all.tbl CDD cd12903 cd12903 293960 SPRY_PRY_SPRYD4 PRY/SPRY domain containing protein 4 (SPRYD4). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain and is encoded by the SPRYD4 gene. SPRYD4 (SPRY containing domain 4) is ubiquitously expressed in many human tissues, most strongly in kidney, bladder, brain, thymus and stomach. Subcellular localization demonstrates that SPRYD4 protein is localized in the nucleus when overexpressed in COS-7 green monkey cell. It has remained uncharacterized thus far. 169 matched cddid_all.tbl CDD cd12904 cd12904 293961 SPRY_BSPRY SPRY domain in Ro-Ret family. This domain, named BSPRY, has been identified in the Ro-Ret family, since the protein is composed of a B-box, an alpha-helical coiled coil and a SPRY domain. The gene for BSPRY resides on human chromosome 9 and is specifically expressed in testis. The function of BSPRY is not known, but several related proteins of the RING-Box-coiled-coil (RBCC) family have been implicated in cell transformation. 171 matched cddid_all.tbl CDD cd12905 cd12905 293962 SPRY_PRY_A33L zinc-binding protein A33-like. This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM69 and TRIM proteins NF7 and bloodthirsty (bty). TRIM69 is a novel testis E3 ubiquitin ligase that may function to ubiquitinate its particular substrates during spermatogenesis. In humans, TRIM69 localizes in the cytoplasm and nucleus, and requires an intact RING finger domain to function. TRIM protein NF7, which also contains a chromodomain (CHD) at the N-terminus and an RFP (Ret finger protein)-like domain at the C-terminus, is required for its association with transcriptional units of RNA polymerase II which is mediated by a trimeric B box. In Xenopus oocyte, xNF7 has been identified as a nuclear microtubule-associated protein (MAP) whose microtubule-bundling activity, but not E3-ligase activity, contributes to microtubule organization and spindle integrity. Bloodthirsty (bty) is a novel gene identified in zebrafish and has been shown to likely play a role in in regulation of the terminal steps of erythropoiesis. 178 matched cddid_all.tbl CDD cd12906 cd12906 293963 SPRY_SOCS1-2-4 SPRY domain in the suppressor of cytokine signaling 1, 2, 4 families (SOCS1, SOCS2, SOCS4). The SPRY domain-containing SOCS box protein family (SPSB1-4, also known as SSB-1 to -4) is composed of a central SPRY protein interaction domain and a C-terminal SOCS box. All four SPSB proteins interact with c-Met, the hepatocyte growth factor receptor, but only SPSB1, SPSB2, and SPSB4 interact with prostate apoptosis response protein 4 (Par-4). They are negative regulators that recruit the ECS E3 ubiquitin ligase complex to polyubiquitinate inducible nitric-oxide synthase (iNOS), resulting in its proteasomal degradation, thus contributing to protection against the cytotoxic effect of iNOS in activated macrophages. It has been shown that SPSB1 and SPSB4 induce the degradation of iNOS more strongly than SPSB2. The Drosophila melanogaster SPSB1 homolog, GUSTAVUS, interacts with the DEAD box RNA helicase Vasa. Suppressor of cytokine signaling (SOCS) proteins negatively regulate signaling from JAK-associated cytokine receptor complexes, and play key roles in the regulation of immune homeostasis. 174 matched cddid_all.tbl CDD cd12907 cd12907 293964 SPRY_Fbox SPRY domain in the F-box family Fbxo45. Fbxo45 is a novel synaptic E3 and ubiquitin ligase, related to the suppressor of cytokine signaling (SOCS) proteins and located N-terminal to a SPRY (SPla and the ryanodine receptor) domain. Fbxo45 induces the degradation of a synaptic vesicle-priming factor, Munc13-1, via the SPRY domain, thus playing an important role in the regulation of neurotransmission by modulating Munc13-1 at the synapse. F-box motifs are found in proteins that function as the substrate recognition component of SCF E3 complexes. 175 matched cddid_all.tbl CDD cd12908 cd12908 293965 SPRYD3 SPRY domain-containing protein 3. This family contains SPRY domain-containing protein 3 (SPRYD3). In humans, it is highly expressed in most tissues, including brain, kidney, heart, intestine, skeletal muscle, and testis. It also has cross-species conservation, suggesting that it is likely to carry out important cellular processes. 171 matched cddid_all.tbl CDD cd12909 cd12909 293966 SPRY_RanBP9_10 SPRY domain in Ran binding proteins 9 and 10. This family includes SPRY domain in Ran binding protein (RBP or RanBPM) 9 and 10, and similar proteins. RanBP9 (also known as RanBPM), a binding partner of Ran, is a small Ras-like GTPase that exerts multiple functions via interactions with various proteins. RanBP9 and RanBP10 also act as androgen receptor (AR) coactivators. Both consist of the N-terminal proline- and glutamine-rich regions, the SPRY domain, and LisH-CTLH and CRA motifs. SPRY domain of RanBPM forms a complex with CD39, a prototypic member of the NTPDase family, thus down-regulating activity substantially. RanBP10 enhances the transcriptional activity of AR in a ligand-dependent manner and exhibits a protein expression pattern different from RanBPM in various cell lines. RanBP10 is highly expressed in AR-positive prostate cancer LNCaP cells, while RanBPM is abundant in WI-38 and MCF-7 cells. 144 matched cddid_all.tbl CDD cd12910 cd12910 293967 SPRY_SSH4_like SPRY domain in SSH4 and similar proteins. This family includes SPRY domain in SSH4 (suppressor of SHR3 null mutation protein 4) and similar proteins. SSH4 is a component of the endosome-vacuole trafficking pathway that regulates nutrient transport and may be involved in processes determining whether plasma membrane proteins are degraded or routed to the plasma membrane. The SPRY domain in SSH4 may be involved in cargo recognition, either directly or by combination with other adaptors, possibly leading to a higher selectivity. In yeast, SSH4 and the homologous protein EAR1 (endosomal adapter of RSP5) recruit Rsp5p, an essential ubiquitin ligase of the Nedd4 family, and assist it in its function at multivesicular bodies by directing the ubiquitylation of specific cargoes. 192 matched cddid_all.tbl CDD cd12911 cd12911 350336 HK_sensor Sensor domains of Histidine Kinase receptors. Histidine kinase (HK) receptors are part of two-component systems (TCS) in bacteria that play a critical role for sensing and adapting to environmental changes. Typically, HK receptors contain an extracellular sensing domain flanked by two transmembrane helices, an intracellular dimerization histidine phosphorylation domain (DHp), and a C-terminal kinase domain, with many variations on this theme. HK receptors in this family contain double PDC (PhoQ/DcuS/CitA) sensor domains. Signals detected by the sensor domain are transmitted through DHp to the kinase domain, resulting in the phosphorylation of a conserved histidine residue in DHp; phosphotransfer to a conserved aspartate in its cognate response regulator (RR) follows, which leads to the activation of genes for downstream cellular responses. The HK family includes not just histidine kinase receptors but also sensors for chemotaxis proteins and diguanylate cyclase receptors, implying a combinatorial molecular evolution. 100 matched cddid_all.tbl CDD cd12912 cd12912 350337 PDC2_MCP_like second PDC (PhoQ/DcuS/CitA) domain of methyl-accepting chemotaxis proteins and similar domains. Members of this subfamily display varying domain architectures but all contain double PDC (PhoQ/DcuS/CitA) sensor domains. This model represents the second PDC domain of Methyl-accepting chemotaxis proteins (MCPs), Histidine kinases (HKs), and other similar domains. Many members contain both HAMP (HK, Adenylyl cyclase, MCP, and Phosphatase) and MCP domains, which are signalling domains that interact with protein partners to relay a signal. MCPs are part of a transmembrane protein complex that controls bacterial chemotaxis. HK receptors are part of two-component systems (TCS) in bacteria that play a critical role for sensing and adapting to environmental changes. Typically, HK receptors contain an extracellular sensing domain flanked by two transmembrane helices, an intracellular dimerization histidine phosphorylation domain (DHp), and a C-terminal kinase domain, with many variations on this theme. In the case of HKs, signals detected by the sensor domain are transmitted through DHp to the kinase domain, resulting in the phosphorylation of a conserved histidine residue in DHp; phosphotransfer to a conserved aspartate in its cognate response regulator (RR) follows, which leads to the activation of genes for downstream cellular responses. 92 matched cddid_all.tbl CDD cd12913 cd12913 350338 PDC1_MCP_like first PDC (PhoQ/DcuS/CitA) domain of methyl-accepting chemotaxis proteins and similar domains. Members of this subfamily display varying domain architectures but all contain double PDC (PhoQ/DcuS/CitA) sensor domains. This model represents the first PDC domain of Methyl-accepting chemotaxis proteins (MCPs), Histidine kinases (HKs), and other similar domains. Many members contain both HAMP (HK, Adenylyl cyclase, MCP, and Phosphatase) and MCP domains, which are signalling domains that interact with protein partners to relay a signal. MCPs are part of a transmembrane protein complex that controls bacterial chemotaxis. HK receptors are part of two-component systems (TCS) in bacteria that play a critical role for sensing and adapting to environmental changes. Typically, HK receptors contain an extracellular sensing domain flanked by two transmembrane helices, an intracellular dimerization histidine phosphorylation domain (DHp), and a C-terminal kinase domain, with many variations on this theme. In the case of HKs, signals detected by the sensor domain are transmitted through DHp to the kinase domain, resulting in the phosphorylation of a conserved histidine residue in DHp; phosphotransfer to a conserved aspartate in its cognate response regulator (RR) follows, which leads to the activation of genes for downstream cellular responses. 139 matched cddid_all.tbl CDD cd12914 cd12914 350339 PDC1_DGC_like first PDC (PhoQ/DcuS/CitA) domain of diguanylate-cyclase and similar domains. Members of this subfamily display varying domain architectures but all contain double PDC (PhoQ/DcuS/CitA) sensor domains. This model represents the first PDC domain of Diguanylate-cyclases (DGCs), Histidine kinases (HKs), and other similar domains. Many members of this subfamily contain a C-terminal DGC (also called GGDEF) domain. DGCs regulate the turnover of cyclic diguanosine monophosphate. HK receptors are part of two-component systems (TCS) in bacteria that play a critical role for sensing and adapting to environmental changes. Typically, HK receptors contain an extracellular sensing domain flanked by two transmembrane helices, an intracellular dimerization histidine phosphorylation domain (DHp), and a C-terminal kinase domain, with many variations on this theme. In the case of HKs, signals detected by the sensor domain are transmitted through DHp to the kinase domain, resulting in the phosphorylation of a conserved histidine residue in DHp; phosphotransfer to a conserved aspartate in its cognate response regulator (RR) follows, which leads to the activation of genes for downstream cellular responses. 123 matched cddid_all.tbl CDD cd12915 cd12915 350340 PDC2_DGC_like second PDC (PhoQ/DcuS/CitA) domain of diguanylate-cyclase and similar domains. Members of this subfamily display varying domain architectures but all contain double PDC (PhoQ/DcuS/CitA) sensor domains. This model represents the second PDC domain of Diguanylate-cyclases (DGCs), Histidine kinases (HKs), and other similar domains. Many members of this subfamily contain a C-terminal DGC (also called GGDEF) domain. DGCs regulate the turnover of cyclic diguanosine monophosphate. HK receptors are part of two-component systems (TCS) in bacteria that play a critical role for sensing and adapting to environmental changes. Typically, HK receptors contain an extracellular sensing domain flanked by two transmembrane helices, an intracellular dimerization histidine phosphorylation domain (DHp), and a C-terminal kinase domain, with many variations on this theme. In the case of HKs, signals detected by the sensor domain are transmitted through DHp to the kinase domain, resulting in the phosphorylation of a conserved histidine residue in DHp; phosphotransfer to a conserved aspartate in its cognate response regulator (RR) follows, which leads to the activation of genes for downstream cellular responses. 96 matched cddid_all.tbl CDD cd12916 cd12916 240599 VKOR_1 Vitamin K epoxide reductase family in bacteria and plants. This family includes vitamin K epoxide reductase (VKOR) present in bacteria and plant. VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. All homologs of VKOR contain an active site CXXC motif, which is switched between reduced and disulfide-bonded states during the reaction cycle. In some plant and bacterial homologs, the VKOR domain is fused with domains of the thioredoxin family of oxidoreductases which may function as redox partners in initiating the reduction cascade. 133 matched cddid_all.tbl CDD cd12917 cd12917 240600 VKOR_euk Vitamin K epoxide reductase family in eukaryotes, excluding plants. This family includes vitamin K epoxide reductase (VKOR) present in bacteria and plant. VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. All homologs of VKOR contain an active site CXXC motif, which is switched between reduced and disulfide-bonded states during the reaction cycle. Warfarin, a widely used oral anticoagulant used in medicine as well as rodenticides, inhibits the activity of VKOR, resulting in decreased levels of reduced vitamin K, which is required for the function of several clotting factors. However, anticoagulation effect of warfarin is significantly associated with polymorphism of certain genes, including VKORC1. Interestingly, in rodents, an adaptive trait appears to have evolved convergently by selection on new or standing genetic polymorphisms in VKORC1 as well as by adaptive introgressive hybridization between species, likely brought about by human-mediated dispersal. 140 matched cddid_all.tbl CDD cd12918 cd12918 240601 VKOR_arc Vitamin K epoxide reductase family in archaea and some bacteria. This family includes vitamin K epoxide reductase (VKOR) mostly present in archaea and some bacteria. VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. All homologs of VKOR contain an active site CXXC motif, which is switched between reduced and disulfide-bonded states during the reaction cycle. In some bacterial homologs, the VKOR domain is fused with domains of the thioredoxin family of oxidoreductases which may function as redox partners in initiating the reduction cascade. 126 matched cddid_all.tbl CDD cd12919 cd12919 240602 VKOR_2 Vitamin K epoxide reductase family in bacteria. This family includes vitamin K epoxide reductase (VKOR) present only in bacteria. VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. All homologs of VKOR contain an active site CXXC motif, which is switched between reduced and disulfide-bonded states during the reaction cycle. In some bacterial homologs, the VKOR domain is fused with domains of the thioredoxin family of oxidoreductases which may function as redox partners in initiating the reduction cascade. 169 matched cddid_all.tbl CDD cd12920 cd12920 240603 VKOR_3 Vitamin K epoxide reductase family in bacteria. This family includes vitamin K epoxide reductase (VKOR) present in proteobacteria and spirochetes. VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. All homologs of VKOR contain an active site CXXC motif, which is switched between reduced and disulfide-bonded states during the reaction cycle. In some bacterial homologs, the VKOR domain is fused with domains of the thioredoxin family of oxidoreductases which may function as redox partners in initiating the reduction cascade. 134 matched cddid_all.tbl CDD cd12921 cd12921 240604 VKOR_4 Vitamin K epoxide reductase (VKOR) family in bacteria. This family includes vitamin K epoxide reductase (VKOR) present only in bacteria. VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. All homologs of VKOR contain an active site CXXC motif, which is switched between reduced and disulfide-bonded states during the reaction cycle. In some bacterial homologs, the VKOR domain is fused with domains of the thioredoxin family of oxidoreductases which may function as redox partners in initiating the reduction cascade. This family also has a cysteine peptidase domain present at the N-terminus of the VKOR domain. 128 matched cddid_all.tbl CDD cd12922 cd12922 240605 VKOR_5 Vitamin K epoxide reductase family in bacteria. This family includes vitamin K epoxide reductase (VKOR) mostly present in actinobacteria. VKOR (also named VKORC1) is an integral membrane protein that catalyzes the reduction of vitamin K 2,3-epoxide and vitamin K to vitamin K hydroquinone, an essential co-factor subsequently used in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. All homologs of VKOR contain an active site CXXC motif, which is switched between reduced and disulfide-bonded states during the reaction cycle. In some bacterial homologs, the VKOR domain is fused with domains of the thioredoxin family of oxidoreductases which may function as redox partners in initiating the reduction cascade. 133 matched cddid_all.tbl CDD cd12923 cd12923 214016 iSH2_PI3K_IA_R Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation, and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. In vertebrates, there are three genes (PIK3R1, PIK3R2, and PIK3R3) that encode for different Class IA PI3K R subunits. 152 matched cddid_all.tbl CDD cd12924 cd12924 214017 iSH2_PIK3R1 Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunit 1, PIK3R1, also called p85alpha. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. In addition, p85alpha, also called PIK3R1, contains N-terminal SH3 and GAP domains. p85alpha carry functions independent of its PI3K regulatory role. It can independently stimulate signaling pathways involved in cytoskeletal rearrangements. Insulin-sensitive tissues express splice variants of the PIK3R1 gene, p50alpha and p55alpha, which may play important roles in insulin signaling during lipid and glucose metabolism. Mice deficient with PIK3R1 die perinatally, indicating its importance in development. 161 matched cddid_all.tbl CDD cd12925 cd12925 214018 iSH2_PIK3R3 Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunit 3, PIK3R3, also called p55gamma. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation, and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. p55gamma, also called PIK3R3 or p55PIK, also contains a unique N-terminal 24-amino acid residue (N24) that interacts with cell cycle modulators to promote cell cycle progression. 161 matched cddid_all.tbl CDD cd12926 cd12926 214019 iSH2_PIK3R2 Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunit 2, PIK3R2, also called p85beta. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. They play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation, and apoptosis. They are classified according to their substrate specificity, regulation, and domain structure. Class IA PI3Ks are heterodimers of a p110 catalytic (C) subunit and a p85-related regulatory (R) subunit. The R subunit down-regulates PI3K basal activity, stabilizes the C subunit, and plays a role in the activation downstream of tyrosine kinases. All R subunits contain two SH2 domains that flank an intervening helical domain (iSH2), which binds to the N-terminal adaptor-binding domain (ABD) of the catalytic subunit. p85beta, also called PIK3R2, contains N-terminal SH3 and GAP domains. It is expressed ubiquitously but at lower levels than p85alpha. Its expression is increased in breast and colon cancer, correlates with tumor progression, and enhanced invasion. During viral infection, the viral nonstructural (NS1) protein binds p85beta specifically, which leads to PI3K activation and the promotion of viral replication. Mice deficient with PIK3R2 develop normally and exhibit moderate metabolic and immunological defects. 161 matched cddid_all.tbl CDD cd12927 cd12927 240571 MMP_TTHA0227_like Minimal MMP-like domain found in Thermus thermophilus TTHA0227, Acidothermus cellulolyticus ACEL2062 and similar proteins. The family includes hypothetical proteins from bacteria that contain a minimal metalloprotease (MMP)-like domain consisting of 3-stranded mixed 2-beta sheets.These proteins may belong to a superfamily of bacterial zinc metallo-peptidases, which is characterized by a conserved HExxHxxGxxD (x could be any amino acid) motif. However, some family members carry a shorter HExxHxxG motif or HExxH motif. Some others do not have such a motif, but still share very high sequence similarity. 97 matched cddid_all.tbl CDD cd12929 cd12929 240592 GUCT RNA-binding GUCT domain found in the RNA helicase II/Gu protein family. This family includes vertebrate RNA helicase II/Gualpha (RH-II/Gualpha) and RNA helicase II/Gubeta (RH-II/Gubeta), both of which consist of a DEAD box helicase domain (DEAD), a helicase conserved C-terminal domain, and a Gu C-terminal (GUCT) domain. They localize to nucleoli, suggesting roles in ribosomal RNA production, but RH-II/Gubeta also localizes to nuclear speckles containing the splicing factor SC35, suggesting its possible involvement in pre-mRNA splicing. In contrast to RH-II/Gualpha, RH-II/Gubeta has RNA-unwinding activity, but no RNA-folding activity. The family also contains plant DEAD-box ATP-dependent RNA helicase 7 (RH7 or PRH75), Thermus thermophilus heat resistant RNA-dependent ATPase (Hera) and similar proteins. RH7 is a new nucleus-localized member of the DEAD-box protein family from higher plants. It displays a weak ATPase activity which is barely stimulated by RNA ligands. RH7 contains an N-terminal KDES domain rich in lysine, glutamic acid, aspartic acid, and serine residues, seven highly conserved helicase motifs in the central region, a GUCT domain, and a C-terminal GYR domain harboring a large number of glycine residues interrupted by either arginines or tyrosines. Thermus thermophilus Hera is a DEAD box helicase that binds fragments of 23S rRNA and RNase P RNA via its C-terminal domain. It contains a helicase core that harbors two RecA-like domains termed RecA_N and RecA_C, a dimerization domain (DD), and a C-terminal RNA-binding domain (RBD) that reveals a compact, RRM-like fold and shows sequence similarity with the typical GUCT domain found in the RNA helicase II/Gu protein family. 72 matched cddid_all.tbl CDD cd12930 cd12930 410577 GAT_SF GAT domain found in eukaryotic GGAs, metazoan Tom1-like proteins, metazoan STAMs, fungal Vps27, and similar proteins. The GAT (GGA and Tom1) domain superfamily includes the canonical GAT domain found in ADP-ribosylation factor (Arf)-binding proteins (GGAs) from eukaryotes, myb protein 1 (Tom1)-like proteins from metazoa, and LAS seventeen-binding protein 5 (Lsb5p)-like proteins from fungi. The canonical GAT domain is a monomeric three-helix bundle that binds ubiquitin. GGAs, also called Golgi-localized gamma-ear-containing Arf-binding proteins, belong to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. GGAs play important roles in ubiquitin-dependent sorting of cargo proteins both in biosynthetic and endocytic pathways. Tom1 and its related proteins, Tom1L1 and Tom1L2, form a protein family sharing an N-terminal VHS-domain followed by a GAT domain. Tom1 family proteins bind to ubiquitin, ubiquitinated proteins, and Toll-interacting protein (Tollip) through its GAT domain. They do not associate with either Arf GTPases through its GAT domain nor with acidic cluster-dileucine sequences through its VHS domain. The GAT domain superfamily also includes the non-canonical GAT domain found in several components of the ESCRT-0 complex, including signal transducing adapter molecules (STAMs) and hepatocyte growth factor-regulated tyrosine kinase substrate (Hrs) from metazoa, as well as vacuolar protein sorting-associated protein 27 (Vps27) and class E vacuolar protein-sorting machinery protein Hse1 from fungi. Hrs, together with STAM, forms a Hrs/STAM core complex. Vps27, together with Hse1, forms a Vps27/Hse1 core complex. Those complexes consist of two intertwined GAT domains, each consisting of two helices from one subunit, and one from the other subunit. The intertwined GAT heterodimer acts as a scaffold for binding of ubiquitinated cargo proteins and coordinating ubiquitination and deubiquitination reactions that regulate sorting. 77 matched cddid_all.tbl CDD cd12931 cd12931 240579 eNOPS_SF NOPS domain, including C-terminal helical extension region, in the p54nrb/PSF/PSP1 family. All members in this family contain a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRM1 and RRM2), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction NOPS (NONA and PSP1) domain with a long helical C-terminal extension. The NOPS domain specifically binds to RRM2 domain of the partner DBHS protein via a substantial interaction surface. Its highly conserved C-terminal residues are critical for functional DBHS dimerization while the highly conserved C-terminal helical extension, forming a right-handed antiparallel heterodimeric coiled-coil, is essential for localization of these proteins to subnuclear bodies. PSF has an additional large N-terminal domain that differentiates it from other family members. The p54nrb/PSF/PSP1 family includes 54 kDa nuclear RNA- and DNA-binding protein (p54nrb), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and paraspeckle protein 1 (PSP1), which are ubiquitously expressed and are well conserved in vertebrates. p54nrb, also termed NONO or NMT55, is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF, also termed POMp100, is also a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSP1, also termed PSPC1, is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSP1 remains unknown currently. The family also includes some p54nrb/PSF/PSP1 homologs from invertebrate species. For instance, the Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA) and Chironomus tentans hrp65 gene encoding protein Hrp65. D. melanogaster NONA is involved in eye development and behavior and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans Hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. 90 matched cddid_all.tbl CDD cd12932 cd12932 240576 RRP7_like RRP7 domain ribosomal RNA-processing protein 7 (Rrp7p), ribosomal RNA-processing protein 7 homolog A (Rrp7A), and similar proteins. This CD corresponds to the RRP7 domain of Rrp7p and Rrp7A. Rrp7p is encoded by YCL031C gene from Saccharomyces cerevisiae. It is an essential yeast protein involved in pre-rRNA processing and ribosome assembly, and is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. Rrp7A, also termed gastric cancer antigen Zg14, is the Rrp7p homolog mainly found in Metazoans. The cellular function of Rrp7A remains unclear currently. Both Rrp7p and Rrp7A harbor an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RRP7 domain. 118 matched cddid_all.tbl CDD cd12933 cd12933 240597 eIF3G eIF3G domain found in eukaryotic translation initiation factor 3 subunit G (eIF-3G) and similar proteins. eIF-3G, also termed eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or eIF3-p44, is the RNA-binding subunit of eIF3. eIF3 is a large multi-subunit complex that plays a central role in the initiation of translation by binding to the 40 S ribosomal subunit and promoting the binding of methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. Besides, eIF-3G is one of the cytosolic targets; it interacts with mature apoptosis-inducing factor (AIF). This family also includes yeast eIF3-p33, a homolog of vertebrate eIF-3G; it plays an important role in the initiation phase of protein synthesis in yeast. It binds both mRNA and rRNA fragments due to an RNA recognition motif near its C-terminus. 114 matched cddid_all.tbl CDD cd12934 cd12934 240585 LEM LEM (Lap2/Emerin/Man1) domain found in emerin, lamina-associated polypeptide 2 (LAP2), inner nuclear membrane protein Man1 and similar proteins. The family corresponds to a group of inner nuclear membrane proteins containing LEM domain. Emerin occurs in four phosphorylated forms and plays a role in cell cycle-dependent events. It is absent from the inner nuclear membrane in most patients with X-linked muscular dystrophy. Emerin interacts with A-type and B-type lamins. Man1, also termed LEM domain-containing protein 3 (LEMD3) is an integral protein of the inner nuclear membrane that binds to nuclear lamins and emerin, thus playing a role in nuclear organization. LAP2, also termed thymopoietin (TP), or thymopoietin-related peptide (TPRP), is composed of isoform alpha and isoforms beta/gamma and may be involved in chromatin organization and post-mitotic reassembly. Some LAP2 isoforms are inner nuclear membrane proteins that can bind to nuclear lamins and chromatin, while others are non-membrane nuclear polypeptides. This family also contains LEM domain-containing protein LEMP-1 and LEM2. LEMP-1, also termed cancer/testis antigen 50 (CT50), is encoded by LEMD1, a novel testis-specific gene expressed in colorectal cancers. LEMP-1 may function as a cancer-testis antigen for immunotherapy of colorectal carcinoma (CRC). LEM2, also termed LEMD2, is a novel Man1-related ubiquitously expressed inner nuclear membrane protein required for normal nuclear envelope morphology. Association with lamin A is required for its proper nuclear envelope localization while its binding to lamin C plays an important role in the organization of lamin A/C complexes. Some uncharacterized LEM domain-containing proteins are also included in this family. Unlike other family members, these harbor an ankyrin repeat region that may mediate protein-protein interactions. 37 matched cddid_all.tbl CDD cd12935 cd12935 240596 LEM_like LEM-like domain of lamina-associated polypeptide 2 (LAP2) and similar proteins. LAP2, also termed thymopoietin (TP), or thymopoietin-related peptide (TPRP), is composed of isoform alpha and isoforms beta/gamma and may be involved in chromatin organization and postmitotic reassembly. Some of the LAP2 isoforms are inner nuclear membrane proteins that can bind to nuclear lamins and chromatin, while others are nonmembrane nuclear polypeptides. All LAP2 isoforms contain an N-terminal lamina-associated polypeptide-Emerin-MAN1 (LEM)-domain that is connected to a highly divergent LEM-like domain by an unstructured linker. Both LEM and LEM-like domains share the same structural fold, mainly composed of two large parallel alpha helices. However, their biochemical nature of the solvent-accessible residues is completely different, which indicates the two domains may target different protein surfaces. The LEM domain is responsible for the interaction with the nonspecific DNA binding protein barrier-to-autointegration factor (BAF), and the LEM-like domain is involved in chromosome binding. The family also includes the yeast helix-extension-helix domain-containing proteins, Heh1p (formerly called Src1p) and Heh2p, and their uncharacterized homologs found mainly in fungi and several in bacteria. Heh1p and Heh2p are inner nuclear membrane proteins that might interact with nuclear pore complexes (NPCs). Heh1p is involved in mitosis. It functions at the interface between subtelomeric gene expression and transcription export (TREX)-dependent messenger RNA export through NPCs. The function of Heh2p remains ill-defined. Both Heh1p and Heh2p contain a LEM-like domain (also termed HeH domain), but lack a LEM domain. 36 matched cddid_all.tbl CDD cd12936 cd12936 240593 GUCT_RHII_Gualpha_beta RNA-binding GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA helicase II/Gubeta (RH-II/Gubeta) and similar proteins. This subfamily corresponds to the Gu C-terminal (GUCT) domain of RH-II/Gualpha and RH-II/Gubeta, two paralogues found in vertebrates. RH-II/Gualpha, also termed nucleolar RNA helicase 2, or DEAD box protein 21, or nucleolar RNA helicase Gu, is a bifunctional enzyme that displays independent RNA-unwinding and RNA-folding activities. It unwinds double-stranded RNA in the 5' to 3' direction in the presence of Mg2+ through the domains in its N-terminal region. In contrast, it folds single-stranded RNA in an ATP-dependent manner and its C-terminal region is responsible for the Mg2+ independent RNA-foldase activity. RH-II/Gualpha consists of a DEAD box helicase domain (DEAD), a helicase conserved C-terminal domain (helicase_C), and a GUCT followed by three FRGQR repeats and one PRGQR sequence. The DEAD and helicase_C domains may play critical roles in the RNA-helicase activity of RH-II/Gualpha. The function of GUCT domain remains unclear. The C-terminal region responsible for the RNA-foldase activity does not overlap with the GUCT domain. RH-II/Gubeta, also termed ATP-dependent RNA helicase DDX50, or DEAD box protein 50, or nucleolar protein Gu2, shows significant sequence homology with RH-II/Gualpha. It contains a DEAD domain, a helicase_C domain, and a GUCT domain followed by an arginine-serine-rich sequence but not (F/P)RGQR repeats in RH-II/Gualpha. Both RH-II/Gualpha and RH-II/Gubeta localize to nucleoli, suggesting roles in ribosomal RNA production, but RH-II/Gubeta also localizes to nuclear speckles containing the splicing factor SC35, suggesting its possible involvement in pre-mRNA splicing. In contrast to RH-II/Gualpha, RH-II/Gubeta has RNA-unwinding activity, but no RNA-folding activity. 93 matched cddid_all.tbl CDD cd12937 cd12937 240594 GUCT_RH7_like RNA-binding GUCT domain found in plant DEAD-box ATP-dependent RNA helicase 7 (RH7) and similar proteins. This subfamily corresponds to the Gu C-terminal (GUCT) domain of RH7 and similar proteins. RH7, also termed plant RNA helicase 75 (PRH75), is a new nucleus-localized member of the DEAD-box protein family from higher plants. It displays a weak ATPase activity which is barely stimulated by RNA ligands. RH7 contains an N-terminal KDES domain rich in lysine, glutamic acid, aspartic acid, and serine residues, seven highly conserved helicase motifs in the central region, a GUCT domain, and a C-terminal GYR domain harboring a large number of glycine residues interrupted by either arginines or tyrosines. RH7 is RNA specific and harbors two possible RNA-binding motifs, the helicase motif VI (HRIGRTGR) and the C-terminal glycine-rich GYR domain. 86 matched cddid_all.tbl CDD cd12938 cd12938 240595 GUCT_Hera RNA-binding GUCT-like domain found in Thermus thermophilus heat resistant RNA-dependent ATPase (Hera) and similar proteins. This subfamily corresponds to the Gu C-terminal (GUCT)-like domain of Hera and similar proteins. Thermus thermophilus Hera is a DEAD box helicase that binds fragments of 23S rRNA and RNase P RNA via its C-terminal domain. It contains a helicase core that harbors two RecA-like domains termed RecA_N and RecA_C, a dimerization domain (DD), and a C-terminal RNA-binding domain (RBD) that reveals a compact, RRM-like fold and shows sequence similarity with GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA helicase II/Gubeta (RH-II/Gubeta) and plant DEAD-box ATP-dependent RNA helicase 7 (RH7 or PRH75). 74 matched cddid_all.tbl CDD cd12939 cd12939 240586 LEM_emerin LEM (Lap2/Emerin/Man1) domain found in emerin. This CD corresponds to the LEM domain that is critical for binding to lamin A/C and is also involved in interaction with the DNA binding protein barrier-to-autointegration factor (BAF). Emerin is an inner nuclear membrane protein that occurs in four differently phosphorylated forms and plays a role in cell cycle-dependent events. It is absent from the inner nuclear membrane in most patients with X-linked muscular dystrophy. Emerin interacts with A-type and B-type lamins. It contains an N-terminal LEM domain followed by a poly-serine segment, a region rich in hydrophobic amino acids comprising the nuclear localization signal (NLS) followed by another poly-serine segment, and a C-terminal transmembrane region. 43 matched cddid_all.tbl CDD cd12940 cd12940 240587 LEM_LAP2_LEMD1 LEM (Lap2/Emerin/Man1) domain found in lamina-associated polypeptide 2 (LAP2), LEM domain-containing protein 1 (LEMP-1) and similar proteins. This CD corresponds to the LEM domain of LAP2, LEMP-1 and similar proteins. LAP2, also termed thymopoietin (TP), or thymopoietin-related peptide (TPRP), is composed of isoform alpha and isoforms beta/gamma and may be involved in chromatin organization and post-mitotic reassembly. Some of LAP2 isoforms are inner nuclear membrane proteins that can bind to nuclear lamins and chromatin, while others are non-membrane nuclear polypeptides. All LAP2 isoforms contain an N-terminal LEM domain that is connected to a highly divergent LEM-like domain by an unstructured linker. Although LEM and LEM-like domains share the same structural fold composed of two large parallel alpha helices, the biochemical nature of the solvent-accessible residues is completely different, indicating that the two domains may target different protein surfaces. The LEM domain interacts with the nonspecific DNA binding protein barrier-to-autointegration factor (BAF) while the LEM-like domain is involved in chromosome binding. LEMP-1, also termed cancer/testis antigen 50 (CT50), is encoded by LEMD1, a novel testis-specific gene expressed in colorectal cancers. It may function as a cancer-testis antigen for immunotherapy of colorectal carcinoma (CRC). LEMP-1 contains an N-terminal LEM domain. 42 matched cddid_all.tbl CDD cd12941 cd12941 240588 LEM_LEMD2 LEM (Lap2/Emerin/Man1) domain found in LEM domain-containing protein 2 (LEM2). This CD corresponds to the LEM domain that is responsible for the interaction with chromatin protein barrier-to-autointegration factor (BAF). LEM2, also termed LEMD2, is a novel Man1-related ubiquitously expressed inner nuclear membrane protein required for normal nuclear envelope morphology. Association with lamin A is required for its proper nuclear envelope localization. It also binds to lamin C and plays an important role in the organization of lamin A/C complexes. LEM2 contains an N-terminal LEM domain, two putative transmembrane domains and a MAN1-Src1p C-terminal (MSC) domain, but lacks the Man1-specific C-terminal RNA recognition motif (RRM). 38 matched cddid_all.tbl CDD cd12942 cd12942 240589 LEM_Man1 LEM (Lap2/Emerin/Man1) domain found in inner nuclear membrane protein Man1. This CD corresponds to the LEM domain of Man1 and similar proteins. Man1, also termed LEM domain-containing protein 3 (LEMD3), is an integral protein of the inner nuclear membrane that binds to nuclear lamins and emerin, thus playing a role in nuclear organization. It is part of a protein complex essential for chromatin organization and cell division. It also functions as an important negative regulator for the transforming growth factor beta (TGF-beta) /activin/Nodal signaling pathway and bone morphogenetic protein (BMP) signaling pathway by directly interacting with chromatin-associated proteins and transcriptional regulators, including the R-Smads, Smad1, Smad2, and Smad3. Man1 is a unique type of left/right (LR) signaling regulator that acts on the inner nuclear membrane. Furthermore, Man1 plays a crucial role in angiogenesis. The vascular remodeling can be regulated at the inner nuclear membrane through interactions between Man1 and Smads. Man1 contains an N-terminal LEM domain, two putative transmembrane domains, a Man1-Src1p C-terminal (MSC) domain, and a C-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The LEM domain interacts with DNA and chromatin-binding protein Barrier-to-Autointegration Factor, and is also necessary for efficient localization of Man1 in the inner nuclear membrane. It has been shown that the C-terminal nucleoplasmic region of Man1 exhibits a DNA binding winged helix domain and is responsible for both, DNA- and Smad-binding. 44 matched cddid_all.tbl CDD cd12943 cd12943 240590 LEM_ANKL1 LEM (Lap2/Emerin/Man1) domain found in ankyrin repeat and LEM domain-containing protein 1 (ANKL1). The family includes ANKL1, also termed ankyrin repeat domain-containing protein 41 (ANKRD41), or LEM-domain containing protein 3 (LEM3), and similar proteins. Although their biological roles remain unclear, the family members contain an N-terminal ankyrin repeat region, LEM domain and C-terminal GIY-YIG nuclease domain. The ankyrin repeats are unique motifs mediating protein-protein interactions. The LEM domain, mainly found in inner nuclear membrane proteins, may be involved in protein- or DNA-binding. 38 matched cddid_all.tbl CDD cd12944 cd12944 240591 LEM_ANKL2 LEM (Lap2/Emerin/Man1) domain found in ankyrin repeat and LEM domain-containing protein 2 (ANKL2). The family includes ANKL2 and similar proteins. Although their biological roles remain unclear, the family members share an N-terminal LEM domain and an ankyrin repeat region. The LEM domain, mainly found in inner nuclear membrane proteins, may be involved in protein- or DNA-binding. The ankyrin repeats are unique motifs mediating protein-protein interactions. 43 matched cddid_all.tbl CDD cd12945 cd12945 240580 NOPS_NONA_like NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSP1 homologs from invertebrate species. The family contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction NOPS (NONA and PSP1) domain. This model corresponds to the NOPS domain, with a long helical C-terminal extension , found in Drosophila melanogaster gene no-ontransient A (nonA) encoding puff-specific protein Bj6 (also termed NONA), Chironomus tentans hrp65 gene encoding protein Hrp65 and similar proteins. D. melanogaster NONA is involved in eye development and behavior, and may play a role in circadian rhythm maintenance, similar to vertebrate p54nrb. C. tentans hrp65 is a component of nuclear fibers associated with ribonucleoprotein particles in transit from the gene to the nuclear pore. The NOPS domain specifically binds to the second RNA recognition motif (RRM2) domain of the partner DBHS protein via a substantial interaction surface. Its highly conserved C-terminal residues are critical for functional DBHS dimerization while the highly conserved C-terminal helical extension, forming a right-handed antiparallel heterodimeric coiled-coil, is essential for localization of these proteins to subnuclear bodies. 100 matched cddid_all.tbl CDD cd12946 cd12946 240581 NOPS_p54nrb_PSF_PSPC1 NOPS domain, including C-terminal coiled-coil region, in p54nrb/PSF/PSPC1 family proteins. The family contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction NOPS (NONA and PSP1) domain. This model corresponds to the NOPS domain, with a long helical C-terminal extension, found in the p54nrb/PSF/PSPC1 proteins. The NOPS domain specifically binds to the second RNA recognition motif (RRM2) domain of the partner DBHS protein via a substantial interaction surface. Its highly conserved C-terminal residues are critical for functional DBHS dimerization while the highly conserved C-terminal helical extension, forming a right-handed antiparallel heterodimeric coiled-coil, is essential for localization of these proteins to subnuclear bodies. Members in the family include 54 kDa nuclear RNA- and DNA-binding protein (p54nrb), polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and paraspeckle protein component 1 (PSPC1 or PSP1), which are ubiquitously expressed and are conserved in vertebrates. p54nrb, also termed NONO or NMT55, is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. PSF, also termed POMp100, is a multi-functional protein that binds RNA, single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and many factors, and mediates diverse activities in the cell. PSPC1 is a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. The cellular function of PSPC1 remains unknown currently. PSF has an additional large N-terminal domain that differentiates it from other family members. 93 matched cddid_all.tbl CDD cd12947 cd12947 240582 NOPS_p54nrb NOPS domain, including C-terminal coiled-coil region, in 54 kDa nuclear RNA- and DNA-binding protein (p54nrb) and similar proteins. The family contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction NOPS (NONA and PSP1) domain. This model corresponds to the NOPS domain, with a long helical C-terminal extension, found in p54nrb, also termed non-POU domain-containing octamer-binding protein (NONO), or 55 kDa nuclear protein (NMT55), or DNA-binding p52/p100 complex 52 kDa subunit. It is a multi-functional protein involved in numerous nuclear processes including transcriptional regulation, splicing, DNA unwinding, nuclear retention of hyperedited double-stranded RNA, viral RNA processing, control of cell proliferation, and circadian rhythm maintenance. p54nrb is ubiquitously expressed and highly conserved in vertebrates. It binds both single- and double-stranded RNA and DNA, and also possesses inherent carbonic anhydrase activity. p54nrb forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner. It also forms a heterodimer with polypyrimidine tract-binding protein-associated-splicing factor (PSF). The NOPS domain specifically binds to the second RNA recognition motif (RRM2) domain of the partner DBHS protein via a substantial interaction surface. Its highly conserved C-terminal residues are critical for functional DBHS dimerization while the highly conserved C-terminal helical extension, forming a right-handed antiparallel heterodimeric coiled-coil, is essential for paraspeckle localization to subnuclear bodies. 94 matched cddid_all.tbl CDD cd12948 cd12948 240583 NOPS_PSF NOPS domain, including C-terminal coiled-coil region, in polypyrimidine tract-binding protein (PTB)-associated-splicing factor (PSF) and similar proteins. This model contains the NOPS (NONA and PSP1) domain PSF (also termed proline- and glutamine-rich splicing factor, or 100 kDa DNA-pairing protein (POMp100), or 100 kDa subunit of DNA-binding p52/p100 complex), with a long helical C-terminal extension. PSF is a multifunctional protein that mediates diverse activities in the cell. It is ubiquitously expressed and highly conserved in vertebrates. PSF binds not only RNA but also single-stranded DNA (ssDNA) as well as double-stranded DNA (dsDNA) and facilitates the renaturation of complementary ssDNAs. Additionally, it promotes the formation of D-loops in superhelical duplex DNA, and is involved in cell proliferation. PSF can also interact with multiple factors. It is an RNA-binding component of spliceosomes and binds to insulin-like growth factor response element (IGFRE). Moreover, PSF functions as a transcriptional repressor interacting with Sin3A and mediating silencing through the recruitment of histone deacetylases (HDACs) to the DNA binding domain (DBD) of nuclear hormone receptors. As an RNA-binding component of spliceosomes, PSF binds to the insulin-like growth factor response element (IGFRE), and acts as an independent negative regulator of the transcriptional activity of the porcine P-450 cholesterol side-chain cleavage enzyme gene (P450scc) IGFRE. PSF is an essential pre-mRNA splicing factor and is dissociated from PTB and binds to U1-70K and serine-arginine (SR) proteins during apoptosis. In addition, PSF forms a heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NONO). The PSF/p54nrb complex displays a variety of functions, such as DNA recombination and RNA synthesis, processing, and transport. PSF contains two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), which are responsible for interactions with RNA and for the localization of the protein in speckles. It also contains an N-terminal region rich in proline, glycine, and glutamine residues, which may play a role in interactions recruiting other molecules. The NOPS domain specifically binds to the second RNA recognition motif (RRM2) domain of the partner DBHS protein via a substantial interaction surface. Its highly conserved C-terminal residues are critical for functional DBHS dimerization while the highly conserved C-terminal helical extension, forming a right-handed antiparallel heterodimeric coiled-coil, is essential for localization of these proteins to subnuclear bodies. 97 matched cddid_all.tbl CDD cd12949 cd12949 240584 NOPS_PSPC1 NOPS domain, including C-terminal coiled-coil region, in paraspeckle protein component 1 (PSPC1) and similar proteins. The family contains a DBHS domain (for Drosophila behavior, human splicing), which comprises two conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and a charged protein-protein interaction NOPS (NONA and PSP1) domain. This model corresponds to the NOPS domain, with a long helical C-terminal extension, of paraspeckle component 1 (PSPC1, also termed PSP1), a novel nucleolar factor that accumulates within a new nucleoplasmic compartment, termed paraspeckles, and diffusely distributes in the nucleoplasm. It is ubiquitously expressed and highly conserved in vertebrates. Although its cellular function remains unknown currently, PSPC1 forms a novel heterodimer with the nuclear protein p54nrb, also known as non-POU domain-containing octamer-binding protein (NONO), which localizes to paraspeckles in an RNA-dependent manner. The NOPS domain specifically binds to the second RNA recognition motif (RRM2) domain of the partner DBHS protein via a substantial interaction surface. Its highly conserved C-terminal residues are critical for functional DBHS dimerization while the highly conserved C-terminal helical extension, forming a right-handed antiparallel heterodimeric coiled-coil, is essential for localization of these proteins to subnuclear bodies. 94 matched cddid_all.tbl CDD cd12950 cd12950 240577 RRP7_Rrp7p RRP7 domain ribosomal RNA-processing protein 7 (Rrp7p) and similar proteins. This CD corresponds to the RRP7 domain of Rrp7p. Rrp7p is encoded by YCL031C gene from Saccharomyces cerevisiae. It is an essential yeast protein involved in pre-rRNA processing and ribosome assembly. Rrp7p contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RRP7 domain. 128 matched cddid_all.tbl CDD cd12951 cd12951 240578 RRP7_Rrp7A RRP7 domain ribosomal RNA-processing protein 7 homolog A (Rrp7A) and similar proteins. The family corresponds to the RRP7 domain of Rrp7A, also termed gastric cancer antigen Zg14, and similar proteins which are yeast ribosomal RNA-processing protein 7 (Rrp7p) homologs mainly found in Metazoans. The cellular function of Rrp7A remains unclear currently. Rrp7A harbors an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RRP7 domain. 129 matched cddid_all.tbl CDD cd12952 cd12952 240572 MMP_ACEL2062 Minimal MMP-like domain found in Acidothermus cellulolyticus hypothetical protein ACEL2062 and similar protein. The subfamily includes an uncharacterized protein from Acidothermus cellulolyticus (ACEL2062) and its homologs from bacteria. Although its biological role remains unclear, ACEL2062 contains a minimal metalloprotease (MMP)-like domain consisting of 3-stranded mixed 2-beta sheets and a HExxHxxGxxD/S (x could be any amino acid) motif. It may belong to a superfamily of bacterial zinc metallo-peptidases, which is characterized by a conserved HExxHxxGxxD motif. 117 matched cddid_all.tbl CDD cd12953 cd12953 240573 MMP_TTHA0227 Minimal MMP-like domain found in Thermus thermophilus hypothetical protein TTHA0227 and similar proteins. The subfamily includes an uncharacterized protein from Thermus thermophilus (TTHA0227) and its homologs from bacteria. Although its biological role remains unclear, TTHA0227 contains a minimal metalloprotease (MMP)-like domain consisting of 3-stranded mixed 2-beta sheets and a HExxH (x could be any amino acid) motif. It may belong to a superfamily of bacterial zinc metallo-peptidases, which is characterized by a conserved HExxHxxGxxD motif. 112 matched cddid_all.tbl CDD cd12954 cd12954 240574 MMP_TTHA0227_like_1 Minimal MMP-like domain found in a group of hypothetical proteins from alphaproteobacteria and actinobacteria. The subfamily includes some uncharacterized bacterial proteins which show high sequence similarity with Thermus thermophilus hypothetical protein TTHA0227. However, they do not contain the conserved HExxH (x could be any amino acid) motif. They may not have any zinc metallo-peptidase activity. 99 matched cddid_all.tbl CDD cd12955 cd12955 214020 SKA2 Spindle and kinetochore-associated protein 2. SKA2, also called FAM33A, is a component of the SKA complex, which is formed by the association of three subunits (SKA1, SKA2, annd SKA3). The SKA complex is essential for accurate cell division. It functions with the Ndc80 network to establish stable kinetochore-microtubule interactions, which are crucial for the highly orchestrated chromosome movements during mitosis. The biological unit is a W-shaped homodimer of the three-subunit complex. SKA2 has also been identified as a glucocorticoid receptor-interacting protein and may be involved in regulating cancer cell proliferation. 116 matched cddid_all.tbl CDD cd12956 cd12956 240562 CBM_SusE-F_like carbohydrate-binding modules from Bacteroides thetaiotaomicron SusE, SusF and similar proteins. This group includes five starch-specific CBMs (carbohydrate-binding modules) of SusE and SusF, two cell surface lipoproteins within the Sus (Starch-utilization system) system of the human gut symbiont Bacteroides thetaiotaomicron. These CBMs have no enzymatic activity. The precise mechanistic roles of SusE and SusF in starch metabolism are unclear. Both proteins contain an N-terminal domain which may belong to the immunoglobulin superfamily (IgSF), followed by two or three tandem starch-binding CBMs. SusF has three CBMs (CBM-Fa, -Fb, and -Fc; F denotes SusF, and they are labeled alphabetically from the N- to C- terminus). SusE has two CBMs (CBM-Eb and -Ec, corresponding to CBM-Fb and -Fc). Each starch-binding site contains an arc of aromatic amino acids for hydrophobic stacking with glucose, and hydrogen-bonding acceptors and donors for interacting with the O-2 and O-3 of glucose. These five CBMs show differences in their affinity for various different starch oligosaccharides, and they also contribute differently to binding insoluble starch. CBM-Fa (the CBM unique to SusF), does not bind insoluble starch; CBM-Fb and CBM-Fc both do, deletion of one or the other results in a decrease in the overall affinity of SusF for starch. Both CBM-Eb and CBM-Ec are needed for SusE to bind tightly to starch. CBM-Ec has an additional starch-binding loop that may mediate interactions with partially unwound single helical forms of starch or small starch-breakdown products. Proteins in this group are present in the species of the Gram-negative Bacteroidetes phylum. 93 matched cddid_all.tbl CDD cd12957 cd12957 240570 SKA3_N Spindle and kinetochore-associated protein 3, N-terminal domain. SKA3, also called RAMA1 or C13orf3, is a component of the SKA complex, which is formed by the association of three subunits (SKA1, SKA2, and SKA3). The SKA complex is essential for accurate cell division. It functions with the Ndc80 network to establish stable kinetochore-microtubule interactions, which are crucial for the highly orchestrated chromosome movements during mitosis. The biological unit is a W-shaped homodimer of the three-subunit complex. SKA3 contributes to SAC (spindle-assembly checkpoint) signaling through its interaction with Bub3. This model represents the N-terminal domain of SKA3, which is involved in interactions with SKA1 and SKA2 to form the SKA complex. The C-terminal portion of SKA3 is involved in creating a microtubule-binding surface. 100 matched cddid_all.tbl CDD cd12958 cd12958 214021 SKA1_N Spindle and kinetochore-associated protein 1, N-terminal domain. SKA1 is a component of the SKA complex, which is formed by the association of three subunits (SKA1, SKA2, annd SKA3). The SKA complex is essential for accurate cell division. It functions with the Ndc80 network to establish stable kinetochore-microtubule interactions, which are crucial for the highly orchestrated chromosome movements during mitosis. The biological unit is a W-shaped homodimer of the three-subunit complex. This model represents the N-terminal domain of SKA1, which is involved in interactions with SKA2 and SKA3 to form the SKA complex. The C-terminal portion of SKA1 is involved in creating a microtubule-binding surface. 89 matched cddid_all.tbl CDD cd12959 cd12959 214022 MMACHC-like Methylmalonic aciduria and homocystinuria type C protein and similar proteins. MMACHC, also called CblC, is involved in the intracellular processing of vitamin B12 by catalyzing two reactions: the reductive decyanation of cyanocobalamin in the presence of a flavoprotein oxidoreductase and the dealkylation of alkylcobalamins through the nucleophilic displacement of the alkyl group by glutathione. Mutations in MMACHC cause combined methylmalonic acidemia/aciduria and homocystinuria (CblC type), the most common inherited disorder of cobalamin metabolism. The structure of MMACHC reveals it to be the most divergent member of the NADPH-dependent flavin reductase family that can use FMN or FAD to catalyze reductive decyanation; it is also the first enzyme with glutathione transferase (GST) activity that is unrelated to the GST superfamily in structure and sequence. 226 matched cddid_all.tbl CDD cd12960 cd12960 240575 Spider_toxin Spider neurotoxins including agatoxin, purotoxin and ctenitoxin. This domain family contains spider toxins that include the omega-Aga-IVB, a P-type calcium channel antagonist from venom of the funnel web spider, Agelenopsis aperta, as well as purotoxin-1 (PT1), a spider peptide venom of the Central Asian spider Geolycosa sp., which specifically exerts inhibitory action on P2X3 purinoreceptors at nanomolar concentrations. These spider toxins, which are ion channel blockers, share a common structural motif composed of a triple-stranded antiparallel beta-sheet, stabilized by internal disulfide bonds known as cystine knots. 36 matched cddid_all.tbl CDD cd12961 cd12961 240569 CBM58_SusG Carbohydrate-binding module 58 from Bacteroides thetaiotaomicron SusG and similar CBMs. This group includes the starch-specific CBM (carbohydrate-binding module) of SusG, a cell surface lipoprotein within the Sus (Starch-utilization system) system of the Human gut symbiont Bacteroides thetaiotaomicron. It represents the CBM58 class of CBMs in the carbohydrate active enzymes (CAZy) database. SusG is an alpha-amylase, and is essential for growth on high molecular weight starch. SusG-CBM58 binds maltooligosaccharide distal to, and on the opposite side of, the amylase catalytic site; it is one of two starch-binding sites in SusG, the other being adjacent to the active site. SusG-CBM58 is required for efficient degradation of insoluble starch by the purified enzyme. Its starch-binding site contains an arc of aromatic amino acids for hydrophobic stacking with glucose, and hydrogen-bonding acceptors and donors for interacting with the O-2 and O-3 of glucose. It may play a role in product exchange with other Sus components. 110 matched cddid_all.tbl CDD cd12962 cd12962 240568 X25_BaPul_like X25 domain of Bacillus acidopullulyticus pullulanase and similar proteins. Pullulanase (EC 3.2.1.41) cleaves 1,6-alpha-glucosidic linkages in pullulan, amylopectin, and glycogen, and in alpha-and beta-amylase limit-dextrins of amylopectin and glycogen. BaPul is used industrially in the production of high fructose corn syrup, high maltose content syrups and low calorie and ''light'' beers. Pullulanases, in addition to the catalytic domain, include several carbohydrate-binding domains (CBMs) as well as domains of unknown function (termed ''X'' modules). X25 was identified in Bacillus acidopullulyticus pullulanase, and splits another domain of unknown function (X45). X25 is present in multiple copy in some pullulanases. It has been suggested that X25 and X45 are CBMs which target mixed alpha-1,6/alpha-1,4 linked D-glucan polysaccharides. 95 matched cddid_all.tbl CDD cd12963 cd12963 240567 X45_BaPul_like X45 domain of Bacillus acidopullulyticus pullulanase and similar proteins. Pullulanase (EC 3.2.1.41) cleaves 1,6-alpha-glucosidic linkages in pullulan, amylopectin, and glycogen, and in alpha-and beta-amylase limit-dextrins of amylopectin and glycogen. BaPul is used industrially in the production of high fructose corn syrup, high maltose content syrups and low calorie and ''light'' beers. Pullulanases, in addition to the catalytic domain, include several carbohydrate-binding domains (CBMs) as well as domains of unknown function (termed ''X'' modules). X45 was identified in Bacillus acidopullulyticus pullulanase, it is interupted by another domain of unknown function (X25). It has been suggested that X25 and X45 are CBMs which target mixed alpha-1,6/alpha-1,4 linked D-glucan polysaccharides. 89 matched cddid_all.tbl CDD cd12964 cd12964 240563 CBM-Fa carbohydrate-binding module Fa from Bacteroides thetaiotaomicron SusE, and similar CBMs. CBM-Fa is the first of three starch-specific CBM (carbohydrate-binding modules) of SusF, a cell surface lipoproteins within the Sus (Starch-utilization system) system of the human gut symbiont Bacteroides thetaiotaomicron. The precise mechanistic role of SusF in starch metabolism is unclear. SusF has an N-terminal domain which may belong to the immunoglobulin superfamily (IgSF), followed by three tandem starch-binding CBMs: CBM-Fa, -Fb, and -Fc; F denotes SusF, and they are labeled alphabetically from the N- to C- terminus. These CBMs have no enzymatic activity. Each starch-binding site contains an arc of aromatic amino acids for hydrophobic stacking with glucose, and hydrogen-bonding acceptors and donors for interacting with the O-2 and O-3 of glucose. These three CBMs show differences in their affinity for various different starch oligosaccharides, and they contribute differently to binding insoluble starch. CBM-Fa does not bind insoluble starch, and can bind smaller maltooligosaccharides. Proteins in this subgroup are present in the species of the Gram-negative Bacteroidetes phylum. 110 matched cddid_all.tbl CDD cd12965 cd12965 240564 CBM-Eb_CBM-Fb carbohydrate-binding modules Eb and Fb from SusE and SusF, respectively, and similar CBMs. Included in this subgroup are CBM-Eb and CBM-Fb, starch-specific carbohydrate-binding modules of SusE and SusF, cell surface lipoproteins within the Sus (Starch-utilization system)system of the human gut symbiont Bacteroides thetaiotaomicron. These CBMs have no enzymatic activity. The precise mechanistic roles of SusE and SusF in starch metabolism are unclear. Both proteins have an N-terminal domain which may belong to the immunoglobulin superfamily (IgSF), followed by two or three tandem starch-binding CBMs. SusF has three CBMs (CBM-Fa, -Fb, and -Fc; F denotes SusF, and they are labeled alphabetically from the N- to C- terminus). SusE has two CBMs (CBM-Eb and -Ec, corresponding to CBM-Fb and -Fc). Each starch-binding site contains an arc of aromatic amino acids for hydrophobic stacking with glucose, and hydrogen-bonding acceptors and donors for interacting with the O-2 and O-3 of glucose. These five CBMs show differences in their affinity for various different starch oligosaccharides, and they contribute differently to binding insoluble starch. CBM-Fb and CBM-Fc both bind insoluble starch, deletion of one or the other results in a decrease in the overall affinity of SusF for starch. Both CBM-Eb and CBM-Ec are needed for SusE to bind tightly to starch. Proteins in this group are present in the species of the Gram-negative Bacteroidetes phylum. 98 matched cddid_all.tbl CDD cd12966 cd12966 240565 CBM-Ec_CBM-Fc carbohydrate-binding modules Ec and Fc from SusE and SusF, respectively, and similar CBMs. Included in this subgroup are CBM-Ec and CBM-Fc, starch-specific carbohydrate-binding modules of SusE and SusF, cell surface lipoproteins within the Sus (Starch-utilization system) system of the human gut symbiont Bacteroides thetaiotaomicron. These CBMs have no enzymatic activity. The precise mechanistic roles of SusE and SusF in starch metabolism are unclear. Both proteins have an N-terminal domain which may belong to the immunoglobulin superfamily (IgSF), followed by two or three tandem starch-binding CBMs. SusF has three CBMs (CBM-Fa, -Fb, and -Fc; F denotes SusF, and they are labeled alphabetically from the N- to C- terminus). SusE has two CBMs (CBM-Eb and -Ec, corresponding to CBM-Fb and -Fc). Each starch-binding site contains an arc of aromatic amino acids for hydrophobic stacking with glucose, and hydrogen-bonding acceptors and donors for interacting with the O-2 and O-3 of glucose. These five CBMs show differences in their affinity for various different starch oligosaccharides, and they contribute differently to binding insoluble starch. CBM-Fb and CBM-Fc both bind insoluble starch, deletion of one or the other results in a decrease in the overall affinity of SusF for starch. Both CBM-Eb and CBM-Ec are needed for SusE to bind tightly to starch. Proteins in this group are present in the species of the Gram-negative Bacteroidetes phylum. 98 matched cddid_all.tbl CDD cd12967 cd12967 240566 CBM_SusE-F_like_u1 Uncharacterized subgroup of the CBM-SusE-F_like superfamily. The CBM SusE-F_like superfamily includes starch-specific CBMs (carbohydrate-binding modules) of SusE and SusF, two cell surface lipoproteins within the Sus (Starch-utilization system) system of the human gut symbiont Bacteroides thetaiotaomicron. These CBMs have no enzymatic activity. The precise mechanistic roles of SusE and SusF in starch metabolism are unclear. Both proteins have an N-terminal domain which may belong to the immunoglobulin superfamily (IgSF), followed by two or three tandem starch-binding CBMs. SusF has three CBMs (CBM-Fa, -Fb, and -Fc; F denotes SusF, and they are labeled alphabetically from the N- to C- terminus). SusE has two CBMs (CBM-Eb and -Ec, corresponding to CBM-Fb and -Fc). Each starch-binding site contains an arc of aromatic amino acids for hydrophobic stacking with glucose, and hydrogen-bonding acceptors and donors for interacting with the O-2 and O-3 of glucose. These five CBMs show differences in their affinity for various different starch oligosaccharides, and they also contribute differently to binding insoluble starch. Proteins in this group are present in the species of the Gram-negative Bacteroidetes phylum. 91 matched cddid_all.tbl CDD cd13112 cd13112 240556 POLO_box Polo-box domain (PBD), a C-terminal tandemly repeated region of polo-like kinases. The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a C-terminal single repeat), which appears to be involved in autoinhibition and in mediating the subcellular localization. The latter may be controlled via interactions between the polo-box domain and phospho-peptide motifs. The phosphopeptide binding site is formed at the interface between the two tandemly repeated PBDs. The PBDs of Plk4/Sak appear unique in participating in homodimer interactions, though it is not clear whether and how they interact with phosphopeptides. 76 matched cddid_all.tbl CDD cd13113 cd13113 381706 Wnt Wnt domain found in the WNT signaling gene family, also called Wingless-type mouse mammary tumor virus (MMTV) integration site family. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about the structure of Wnt proteins, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. Wnt signaling mediated by Wnt proteins orchestrates and influences a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 288 matched cddid_all.tbl CDD cd13114 cd13114 240557 POLO_box_Plk4_1 First (cryptic) polo-box domain (PBD) of polo-like kinase 4 (Plk4/Sak). The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a C-terminal single repeat), which appears to be involved in autoinhibition and in mediating the subcellular localization. The latter may be controlled via interactions between the polo-box domain and phospho-peptide motifs. The phosphopeptide binding site is formed at the interface between the two tandemly repeated PBDs. The PBDs of Plk4/Sak appear unique in participating in homodimer interactions, though it is not clear whether and how they interact with phosphopeptides. 112 matched cddid_all.tbl CDD cd13115 cd13115 240558 POLO_box_Plk4_2 Second (cryptic) polo-box domain (PBD) of polo-like kinase 4 (Plk4/Sak). The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a C-terminal single repeat), which appears to be involved in autoinhibition and in mediating the subcellular localization. The latter may be controlled via interactions between the polo-box domain and phospho-peptide motifs. The phosphopeptide binding site is formed at the interface between the two tandemly repeated PBDs. The PBDs of Plk4/Sak appear unique in participating in homodimer interactions, though it is not clear whether and how they interact with phosphopeptides. 108 matched cddid_all.tbl CDD cd13116 cd13116 240559 POLO_box_Plk4_3 C-terminal (third) polo-box domain (PBD) of polo-like kinase 4 (Plk4/Sak). The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a C-terminal single repeat), which appears to be involved in autoinhibition and in mediating the subcellular localization. The latter may be controlled via interactions between the polo-box domain and phospho-peptide motifs. The phosphopeptide binding site is formed at the interface between the two tandemly repeated PBDs. The PBDs of Plk4/Sak appear unique in participating in homodimer interactions, though it is not clear whether and how they interact with phosphopeptides. 81 matched cddid_all.tbl CDD cd13117 cd13117 240560 POLO_box_2 Second polo-box domain (PBD) of polo-like kinases Plk1, Plk2, Plk3, and Plk5. The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a C-terminal single repeat), which appears to be involved in autoinhibition and in mediating the subcellular localization. The latter may be controlled via interactions between the polo-box domain and phospho-peptide motifs. The phosphopeptide binding site is formed at the interface between the two tandemly repeated PBDs. The PBDs of Plk4/Sak appear unique in participating in homodimer interactions, though it is not clear whether and how they interact with phosphopeptides. 81 matched cddid_all.tbl CDD cd13118 cd13118 240561 POLO_box_1 First polo-box domain (PBD) of polo-like kinases Plk1, Plk2, Plk3, and Plk5. The polo-like Ser/Thr kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the inactive kinase Plk5) play various roles in cytokinesis and mitosis. At their C-terminus, they contain a tandemly repeated polo-box domain (in the case of Plk4, a tandem repeat of cryptic PBDs is found in the middle of the protein followed by a C-terminal single repeat), which appears to be involved in autoinhibition and in mediating the subcellular localization. The latter may be controlled via interactions between the polo-box domain and phospho-peptide motifs. The phosphopeptide binding site is formed at the interface between the two tandemly repeated PBDs. The PBDs of Plk4/Sak appear unique in participating in homodimer interactions, though it is not clear whether and how they interact with phosphopeptides. 91 matched cddid_all.tbl CDD cd13119 cd13119 240524 BF2867_like Tandemly repeated domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins. Two structurally similar domains with low sequence similarity form a protein that may have a role in cell adhesion. This family also includes BF1858 and overlaps with DUF3988. 115 matched cddid_all.tbl CDD cd13120 cd13120 240525 BF2867_like_N N-terminal domain found in Bacteroides fragilis Nctc 9343 BF2867 and related proteins. Two structurally similar domains with low sequence similarity in a tandem repeat arrangement form a protein that may have a role in cell adhesion. This family overlaps with DUF3988. 156 matched cddid_all.tbl CDD cd13121 cd13121 240526 BF2867_like_C C-terminal domain found in Bacteroides fragilisNctc 9343 BF2867 and related proteins. Two structurally similar domains with low sequence similarity in a tandem repeat arrangement form a protein that may have a role in cell adhesion. This family overlaps with DUF3988. 138 matched cddid_all.tbl CDD cd13122 cd13122 240555 MSL2_CXC DNA-binding cysteine-rich domain of male-specific lethal 2 and related proteins. The CXC domain of Drosophila melanogaster MSL2 forms a Zn(3)Cys(9) cluster and is involved in recruiting members of the dosage compensation complex (DCC) to sites on the X chromosome. 50 matched cddid_all.tbl CDD cd13123 cd13123 240528 MATE_MurJ_like MurJ/MviN, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins. Escherichia coli MurJ (MviN) has been identified as essential for murein biosynthesis. It has been suggested that MurJ functions as the peptidoglycan lipid II flippase which is involved in translocation of lipid-anchored peptidoglycan precursors across the cytoplasmic membrane, though results obtained in Bacillus subtilis seem to indicate that its MurJ homologs are not essential for growth. Some MviN family members (e.g. in Mycobacterium tuberculosis) possess an extended C-terminal region that contains an intracellular pseudo-kinase domain and an extracellular domain resembling carbohydrate-binding proteins. Proteins from the MATE family are involved in exporting metabolites across the cell membrane and are often responsible for multidrug resistance (MDR). 420 matched cddid_all.tbl CDD cd13124 cd13124 240529 MATE_SpoVB_like Stage V sporulation protein B, also known as Stage III sporulation protein F, and related proteins. The integral membrane protein SpoVB has been implicated in the biosynthesis of the peptidoglycan component of the spore cortex in Bacillus subtilis. This model represents a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins. Proteins from the MATE family are involved in exporting metabolites across the cell membrane and are often responsible for multidrug resistance (MDR). 434 matched cddid_all.tbl CDD cd13125 cd13125 240530 MATE_like_10 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. This family might function as a translocase for lipopolysaccharides, such as O-antigen. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. 409 matched cddid_all.tbl CDD cd13126 cd13126 240531 MATE_like_11 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. This family might function as a translocase for lipopolysaccharides, such as O-antigen. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. 396 matched cddid_all.tbl CDD cd13127 cd13127 240532 MATE_tuaB_like Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. This family might function as a translocase for lipopolysaccharides and participate in the biosynthesis of cell wall components such as teichuronic acid. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. 406 matched cddid_all.tbl CDD cd13128 cd13128 240533 MATE_Wzx_like Wzx, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins. Escherichia coli Wzx and related proteins from other gram-negative bacteria are thought to act as flippases, assisting in the membrane translocation of lipopolysaccharides including those containing O-antigens. Proteins from the MATE family are involved in exporting metabolites across the cell membrane and are often responsible for multidrug resistance (MDR). 402 matched cddid_all.tbl CDD cd13129 cd13129 240534 MATE_epsE_like Multidrug and toxic compound extrusion family and similar proteins. This model represents a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins, including Ralstonia solanaceraum GMI1000 epsE, which may be involved in exporting exopolysaccharide EPS I, a virulence factor. Proteins from the MATE family are involved in exporting metabolites across the cell membrane and are often responsible for multidrug resistance (MDR). 411 matched cddid_all.tbl CDD cd13130 cd13130 240535 MATE_rft1 Rft1-like subfamily of the multidrug and toxic compound extrusion family (MATE). This eukaryotic family may function as a transporter, shuttling phospholipids, lipopolysaccharides or oligosaccharides from cytoplasmic to the lumenal side of the endoplasmic reticulum. Proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. MATE has also been identified as a large multigene family in plants, where the proteins are linked to disease resistance. 441 matched cddid_all.tbl CDD cd13131 cd13131 240536 MATE_NorM_like Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Vibrio cholerae NorM. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. This subfamily includes Vibrio cholerae NorM and functions most likely as a multidrug efflux pump, removing xenobiotics from the interior of the cell. The pump utilizes a cation gradient across the membrane to facilitate the export process. NorM appears to bind monovalent cations in an outward-facing conformation and may subsequently cycle through an inward-facing and outward-facing conformation to capture and release its substrate. 435 matched cddid_all.tbl CDD cd13132 cd13132 240537 MATE_eukaryotic Eukaryotic members of the multidrug and toxic compound extrusion (MATE) family. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. MATE has also been identified as a large multigene family in plants, where the proteins are linked to disease resistance. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. This subfamily, which is restricted to eukaryotes, contains vertebrate solute transporters responsible for secretion of cationic drugs across the brush border membranes, yeast proteins located in the vacuole membrane, and plant proteins involved in disease resistance and iron homeostatis under osmotic stress. 436 matched cddid_all.tbl CDD cd13133 cd13133 240538 MATE_like_7 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. 438 matched cddid_all.tbl CDD cd13134 cd13134 240539 MATE_like_8 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. 438 matched cddid_all.tbl CDD cd13135 cd13135 240540 MATE_like_9 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. 429 matched cddid_all.tbl CDD cd13136 cd13136 240541 MATE_DinF_like DinF and similar proteins, a subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins. Escherichia coli DinF is a membrane protein that has been found to protect cells against oxidative stress and bile salts. The expression of DinF is regulated as part of the SOS system. It may act by detoxifying oxidizing molecules that have the potential to damage DNA. Some member of this family have been reported to enhance the virulence of plant pathogenic bacteria by enhancing their ability to grow in the presence of toxic compounds. Proteins from the MATE family are involved in exporting metabolites across the cell membrane and are often responsible for multidrug resistance (MDR). 424 matched cddid_all.tbl CDD cd13137 cd13137 240542 MATE_NorM_like Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Thermotoga marina NorM. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. 432 matched cddid_all.tbl CDD cd13138 cd13138 240543 MATE_yoeA_like Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Bacillus subtilis yoeA. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. 431 matched cddid_all.tbl CDD cd13139 cd13139 240544 MATE_like_14 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. 448 matched cddid_all.tbl CDD cd13140 cd13140 240545 MATE_like_1 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. MATE has also been identified as a large multigene family in plants, where the proteins are linked to disease resistance. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. 435 matched cddid_all.tbl CDD cd13141 cd13141 240546 MATE_like_13 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. 443 matched cddid_all.tbl CDD cd13142 cd13142 240547 MATE_like_12 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. 444 matched cddid_all.tbl CDD cd13143 cd13143 240548 MATE_MepA_like Subfamily of the multidrug and toxic compound extrusion (MATE)-like proteins similar to Streptococcus aureus MepA. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. This subfamily includes Streptococcus aureus MepA and Vibrio vulnificus VmrA and functions most likely as a multidrug efflux pump. 426 matched cddid_all.tbl CDD cd13144 cd13144 240549 MATE_like_4 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. 434 matched cddid_all.tbl CDD cd13145 cd13145 240550 MATE_like_5 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. 440 matched cddid_all.tbl CDD cd13146 cd13146 240551 MATE_like_6 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. 433 matched cddid_all.tbl CDD cd13147 cd13147 240552 MATE_MJ0709_like Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins, similar to Methanocaldococcus jannaschii MJ0709. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. 441 matched cddid_all.tbl CDD cd13148 cd13148 240553 MATE_like_3 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. 441 matched cddid_all.tbl CDD cd13149 cd13149 240554 MATE_like_2 Uncharacterized subfamily of the multidrug and toxic compound extrusion (MATE) proteins. The integral membrane proteins from the MATE family are involved in exporting metabolites across the cell membrane and are responsible for multidrug resistance (MDR) in many bacteria and animals. A number of family members are involved in the synthesis of peptidoglycan components in bacteria. 434 matched cddid_all.tbl CDD cd13150 cd13150 240523 DAXX_histone_binding Histone binding domain of the death-domain associated protein (DAXX). DAXX is a nuclear protein that modulates transcription of various genes and is involved in cell death and/or the suppression of growth. DAXX is also a histone chaperone conserved in Metazoa that acts specifically on histone H3.3. This alignment models a functional domain of DAXX that interacts with the histone H3.3-H4 dimer, and in doing so competes with DNA binding and interactions between the histone chaperone ASF1/CIA and the H3-H4 dimer. 198 matched cddid_all.tbl CDD cd13151 cd13151 240522 DAXX_helical_bundle Helical bundle domain of the death-domain associated protein (DAXX). DAXX is a nuclear protein that modulates transcription of various genes and is involved in cell death and/or the suppression of growth. DAXX is also a histone chaperone conserved in Metazoa that acts specifically on histone H3.3. This alignment models the N-terminal helical bundle domain of DAXX, which was shown to interact with the tumor suppressor Ras-association domain family 1C (RASSF1C). 88 matched cddid_all.tbl CDD cd13152 cd13152 240516 KOW_GPKOW_A "KOW motif of the ""G-patch domain and KOW motifs-containing protein"" (GPKOW) repeat A. GPKOW contains one G-patch domain and two KOW motifs. GPKOW is a nuclear protein that regulated by catalytic (C) subunit of Protein Kinase A (PKA) and bind RNA in vivo. PKA may be involved in regulating multiple steps in post-transcriptional processing of pre-mRNAs. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. GPKOW is also known as T54 protein or MOS2 homolog." 57 matched cddid_all.tbl CDD cd13153 cd13153 240517 KOW_GPKOW_B "KOW motif of the ""G-patch domain and KOW motifs-containing protein"" (GPKOW) repeat B. GPKOW contains one G-patch domain and two KOW motifs. GPKOW is a nuclear protein that regulated by catalytic (C) subunit of Protein Kinase A (PKA) and bind RNA in vivo. PKA may be involved in regulating multiple steps in post-transcriptional processing of pre-mRNAs. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. GPKOW is also known as the T54 protein or MOS2 homolog." 51 matched cddid_all.tbl CDD cd13154 cd13154 240518 KOW_Mtr4 KOW_Mtr4 is an inserted domain in Mtr4 globular domain. Mtr4 is a conserved helicase with a core DExH region that cooperates with the eukaryotic nuclear exosome in RNA processing and degradation. KOW_Mtr4 motif might be involved in presenting RNA substrates to the helicase core. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KOW motif is located at the extended insertion of Mtr4 protein. 129 matched cddid_all.tbl CDD cd13155 cd13155 240519 KOW_KIN17 KOW_Kin17 is a RNA-binding motif. KOW domain of the KIN17protein contributes to the RNA-binding properties of the whole protein. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. KIN17 is conserved from yeast to human that ubiquitously expressed at low levels in mammals tissue and have functions in DNA replication, DNA repair and cell cycle control. 54 matched cddid_all.tbl CDD cd13156 cd13156 240520 KOW_RPL6 KOW motif of Ribosomal Protein L6. RPL6 contains KOW motif that has an extra ribosomal role as an oncogenic. KOW domain is known as an RNA-binding motif that is shared so far among some families of ribosomal proteins, the essential bacterial transcriptional elongation factor NusG, the eukaryotic chromatin elongation factor Spt5, the higher eukaryotic KIN17 proteins and Mtr4. 152 matched cddid_all.tbl CDD cd13157 cd13157 269979 PTB_tensin-related Tensin-related Phosphotyrosine-binding (PTB) domain. Tensin plays critical roles in renal function, muscle regeneration, and cell migration. It binds to actin filaments and interacts with the cytoplasmic tails of beta-integrin via its PTB domain, allowing tensin to link actin filaments to integrin receptors. Tensin functions as a platform for assembly and disassembly of signaling complexes at focal adhesions by recruiting tyrosine-phosphorylated signaling molecules, and also by providing interaction sites for other proteins. In addition to its PTB domain, it contains a C-terminal SH2 domain. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. 129 matched cddid_all.tbl CDD cd13158 cd13158 269980 PTB_APPL Adaptor protein containing PH domain, PTB domain, and Leucine zipper motif (APPL; also called DCC-interacting protein (DIP)-13alpha) Phosphotyrosine-binding (PTB) domain. APPL interacts with oncoprotein serine/threonine kinase AKT2, tumor suppressor protein DCC (deleted in colorectal cancer), Rab5, GIPC (GAIP-interacting protein, C terminus), human follicle-stimulating hormone receptor (FSHR), and the adiponectin receptors AdipoR1 and AdipoR2. There are two isoforms of human APPL: APPL1 and APPL2, which share about 50% sequence identity. APPL has a BAR and a PH domain near its N terminus, and the two domains are thought to function as a unit (BAR-PH domain). C-terminal to this is a PTB domain. Lipid binding assays show that the BAR, PH, and PTB domains can bind phospholipids. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. 135 matched cddid_all.tbl CDD cd13159 cd13159 269981 PTB_LDLRAP-mammal-like Low Density Lipoprotein Receptor Adaptor Protein 1 (LDLRAP1) in mammals and similar proteins Phosphotyrosine-binding (PTB) PH-like fold. The null mutations in the LDL receptor adaptor protein 1 (LDLRAP1) gene, which serves as an adaptor for LDLR endocytosis in the liver, causes autosomal recessive hypercholesterolemia (ARH). LDLRAP1 contains a single PTB domain. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd contains mammals, insects, and sponges. 123 matched cddid_all.tbl CDD cd13160 cd13160 269982 PTB_LDLRAP_insect-like Low Density Lipoprotein Receptor Adaptor Protein 1 (LDLRAP1) in insects and similar proteins Phosphotyrosine-binding (PTB) PH-like fold. The null mutations in the LDL receptor adaptor protein 1 (LDLRAP1) gene, which serves as an adaptor for LDLR endocytosis in the liver, causes autosomal recessive hypercholesterolemia (ARH). LDLRAP1 contains a single PTB domain. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd contains insects, ticks, sea urchins, and nematodes. 125 matched cddid_all.tbl CDD cd13161 cd13161 269983 PTB_TK_HMTK Tyrosine-specific kinase/HM-motif TK (TM/HMTK) Phosphotyrosine-binding (PTB) PH-like fold. TK kinases catalyzes the transfer of the terminal phosphate of ATP to a specific tyrosine residue on its target protein. TK kinases play significant roles in development and cell division. Tyrosine-protein kinases can be divided into two subfamilies: receptor tyrosine kinases, which have an intracellular tyrosine kinase domain, a transmembrane domain and an extracellular ligand-binding domain; and non-receptor (cytoplasmic) tyrosine kinases, which are soluble, cytoplasmic kinases. In HMTK the conserved His-Arg-Asp sequence within the catalytic loop is replaced by a His-Met sequence. TM/HMTK have are 2-3 N-terminal PTB domains. PTB domains in TKs are thought to function analogously to the membrane targeting (PH, myristoylation) and pTyr binding (SH2) domains of Src subgroup kinases. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Dab-like subgroup. 120 matched cddid_all.tbl CDD cd13162 cd13162 269984 PTB_RGS12 Regulator of G-protein signaling 12 Phosphotyrosine-binding (PTB) PH-like fold. RGS12 functions as a GTPase-activating protein and a transcriptional repressor. It is thought to play a role in tumorigenesis. RGS12 specifically interacts with guanine nucleotide-binding protein G(i), alpha-1 subunit and guanine nucleotide-binding protein G(k) subunit alpha. RGS proteins are multi-functional, GTPase-accelerating proteins that promote GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signalling pathways. Upon activation by GPCRs, heterotrimeric G proteins exchange GDP for GTP, are released from the receptor, and dissociate into free, active GTP-bound alpha subunit and beta-gamma dimer, both of which activate downstream effectors. The response is terminated upon GTP hydrolysis by the alpha subunit, which can then bind the beta-gamma dimer and the receptor. RGS proteins markedly reduce the lifespan of GTP-bound alpha subunits by stabilizing the G protein transition state. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Dab-like subgroup. 131 matched cddid_all.tbl CDD cd13163 cd13163 269985 PTB_ICAP1 Integrin beta-1-binding protein 1 Phosphotyrosine-binding (PTB) PH-like fold. ICAP1 (also called Integrin cytoplasmic domain-associated protein 1) binds specifically to the beta1 integrin subunit cytoplasmic domain and the cerebral cavernous malformation (CCM) protein CCM1. It regulates beta1 integrin-dependent cell migration by affecting the pattern of focal adhesion formation. ICAP1 recruits CCM1 to the cell membrane and activates CCM1 by changing its conformation. Since CCM1 plays role in cardiovascular development, it is hypothesized ICAP1 is involved in vascular differentiation. ICAP-1 has an N-terminal domain that rich in serine and threonine and a C-terminal PTB domain. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Dab-like subgroup. 129 matched cddid_all.tbl CDD cd13164 cd13164 241318 PTB_DOK4_DOK5_DOK6 Downstream of tyrosine kinase 4, 5, and 6 proteins phosphotyrosine-binding domain (PTBi). The Dok family adapters are phosphorylated by different protein tyrosine kinases. Dok proteins are involved in processes such as modulation of cell differentiation and proliferation, as well as in control of the cell spreading and migration The Dok protein contains an N-terminal pleckstrin homology (PH) domain followed by a central phosphotyrosine binding (PTB) domain, which has a PH-like fold, and a proline- and tyrosine-rich C-terminal tail. The PH domain binds to acidic phospholids and localizes proteins to the plasma membrane, while the PTB domain mediates protein-protein interactions by binding to phosphotyrosine-containing motifs. The C-terminal part of Dok contains multiple tyrosine phosphorylation sites that serve as potential docking sites for Src homology 2-containing proteins such as ras GTPase-activating protein and Nck, leading to inhibition of ras signaling pathway activation and the c-Jun N-terminal kinase (JNK) and c-Jun activation, respectively. There are 7 mammalian Dok members: Dok-1 to Dok-7. Dok-1 and Dok-2 act as negative regulators of the Ras-Erk pathway downstream of many immunoreceptor-mediated signaling systems, and it is believed that recruitment of p120 rasGAP by Dok-1 and Dok-2 is critical to their negative regulation. Dok-3 is a negative regulator of the activation of JNK and mobilization of Ca2+ in B-cell receptor-mediated signaling, interacting with SHIP-1 and Grb2. Dok-4- 6 play roles in protein tyrosine kinase(PTK)-mediated signaling in neural cells and Dok-7 is the key cytoplasmic activator of MuSK (Muscle-Specific Protein Tyrosine Kinase). PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the IRS-like subgroup. 103 matched cddid_all.tbl CDD cd13165 cd13165 269986 PTB_DOK7 Downstream of tyrosine kinase 7 phosphotyrosine-binding domain (PTBi). The Dok family adapters are phosphorylated by different protein tyrosine kinases. Dok proteins are involved in processes such as modulation of cell differentiation and proliferation, as well as in control of the cell spreading and migration The Dok protein contains an N-terminal pleckstrin homology (PH) domain followed by a central phosphotyrosine binding (PTB) domain, which has a PH-like fold, and a proline- and tyrosine-rich C-terminal tail. The PH domain is binds to acidic phospholids and localizes proteins to the plasma membrane, while the PTB domain mediates protein-protein interactions by binding to phosphotyrosine-containing motifs. The C-terminal part of Dok contains multiple tyrosine phosphorylation sites that serve as potential docking sites for Src homology 2-containing proteins such as ras GTPase-activating protein and Nck, leading to inhibition of ras signaling pathway activation and the c-Jun N-terminal kinase (JNK) and c-Jun activation, respectively. There are 7 mammalian Dok members: Dok-1 to Dok-7. Dok-1 and Dok-2 act as negative regulators of the Ras-Erk pathway downstream of many immunoreceptor-mediated signaling systems, and it is believed that recruitment of p120 rasGAP by Dok-1 and Dok-2 is critical to their negative regulation. Dok-3 is a negative regulator of the activation of JNK and mobilization of Ca2+ in B-cell receptor-mediated signaling, interacting with SHIP-1 and Grb2. Dok-4- 6 play roles in protein tyrosine kinase(PTK)-mediated signaling in neural cells and Dok-7 is the key cytoplasmic activator of MuSK (Muscle-Specific Protein Tyrosine Kinase). PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the IRS-like subgroup. 101 matched cddid_all.tbl CDD cd13166 cd13166 269987 PTB_CCM2 Cerebral cavernous malformation 2 FERM domain C-lobe. CCM2 (also called malcavernin; C7orf22/chromosome 7 open reading frame 22; OSM) along with CCM1 and CCM3 constitutes a set of proteins which when mutated are responsible for cerebral cavernous malformations, an autosomal dominant neurovascular disease characterized by cerebral hemorrhages and vascular malformations in the central nervous system. CCM2 plays many functional roles. CCM2 functions as a scaffold involved in small GTPase Rac-dependent p38 mitogen-activated protein kinase (MAPK) activation when the cell is under hyperosmotic stress. It associates with CCM1 in the signalling cascades that regulate vascular integrity and participates in HEG1 (the transmembrane receptor heart of glass 1) mediated endothelial cell junctions. CCM proteins also inhibit the activation of small GTPase RhoA and its downstream effector Rho kinase (ROCK) to limit vascular permeability. CCM2 mediates TrkA-dependent cell death via its N-terminal PTB domain in pediatric neuroblastic tumours. CCM2 possesses an N-terminal PTB domain and a C-terminal Karet domain. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Dab-like subgroup. 193 matched cddid_all.tbl CDD cd13167 cd13167 269988 PTB_P-CLI1 PTB-containing, cubilin and LRP1-interacting protein Phosphotyrosine-binding (PTB) PH-like fold. P-CLI1 (also called Phosphotyrosine interaction domain-containing protein 1) increases proliferation of preadipocytes without affecting adipocytic differentiation. It forms a complex with PID1/PCLI1, LRP1 and CUBNI. It is found in subcutaneous fat, heart, skeletal muscle, brain, colon, thymus, spleen, kidney, liver, small intestine, placenta, lung and peripheral blood leukocyte. P-CLI1 contains a single PTB domain. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. 139 matched cddid_all.tbl CDD cd13168 cd13168 269989 PTB_LOC417372 uncharacterized protein LOC417372 Phosphotyrosine-binding (PTB) PH-like fold. The function of LOC417372 and its related proteins are unknown to date. Members here contain a N-terminal RUN domain, followed by a PDZ domain, and a C-terminal PTB domain. The RUN domain is involved in Ras-like GTPase signaling. The PDZ domain (also called DHR/Dlg homologous region or GLGF after its conserved sequence motif) binds C-terminal polypeptides, internal (non-C-terminal) polypeptides, and lipids. PTB domains have a common PH-like fold and are found in various eukaryotic signaling molecules. This domain was initially shown to binds peptides with a NPXY motif with differing requirements for phosphorylation of the tyrosine, although more recent studies have found that some types of PTB domains can bind to peptides lack tyrosine residues altogether. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. PTB domains are classified into three groups: phosphotyrosine-dependent Shc-like, phosphotyrosine-dependent IRS-like, and phosphotyrosine-independent Dab-like PTB domains. This cd is part of the Dab-like subgroup. 125 matched cddid_all.tbl CDD cd13169 cd13169 269990 RanBD_NUP50_plant Ran-binding protein 2, repeat 1. RanBP2 (also called E3 SUMO-protein ligase RanBP2, 358 kDa nucleoporin, and nuclear pore complex (NPC) protein Nup358) is a giant nucleoporin that localizes to the cytosolic face of the NPC. RanBP2 contains a leucine-rich region, 8 zinc-finger motifs, a cyclophilin A homologous domain, and 4 RanBDs. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran. All eukaryotic cells contain RanBP1, but in vertebrates however, the main RanBP seems to be RanBP2. There is no RanBP2 ortholog in yeast. Transport complex disassembly is accomplished by a small ubiquitin-related modifier-1 (SUMO-1)-modified version of RanGAP that is bound to RanBP2. RanBP1 acts as a second line of defense against exported RanGTP#importin complexes which have escaped from dissociation by RanBP2. RanBP2 also interacts with the importin subunit beta-1. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity. The first RanBD2 is present in this hierarchy. 117 matched cddid_all.tbl CDD cd13170 cd13170 269991 RanBD_NUP50 Nucleoporin 50 Ran-binding domain. NUP50 acts as a cofactor for the importin-alpha:importin-beta heterodimer, which allows for transportation of many nuclear-targeted proteins through nuclear pore complexes. It is thought to function primarily at the terminal stages of nuclear protein import to coordinate import complex disassembly and importin recycling. NUP50 is composed of a N-terminal NUP50 domain which binds the C-terminus of importin-beta, a central domain which binds importin-beta, and a C-terminal RanBD which binds importin-beta through Ran-GTP. NUP50:importin-alpha then binds cargo and can stimulate nuclear import. The N-terminal domain of NUP50 is also able to displace nuclear localization signals from importin-alpha. NUP50 interacts with cyclin-dependent kinase inhibitor 1B which binds to cyclin E-CDK2 or cyclin D-CDK4 complexes and prevents its activation, thereby controling the cell cycle progression at G1. Fungal Nup2 transiently associates with nuclear pore complexes (NPCs) and when artificially tethered to DNA, can prevent the spread of transcriptional activation or repression between flanking genes, a function termed boundary activity (BA). Nup2 and the Ran guanylyl-nucleotide exchange factor, Prp20, interact at specific chromatin regions and enable the NPC to play an active role in chromatin organization. Nup60p, the nup responsible for anchoring Nup2 and the Mlp proteins to the NPC is required for Nup2-dependent BA. Nup2 contains an N-terminal Nup50 family domain and a C-terminal RanBD. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity. 111 matched cddid_all.tbl CDD cd13171 cd13171 269992 RanBD1_RanBP2_insect-like Ran-binding protein 2, Ran binding domain repeat 1. RanBP2 (also called E3 SUMO-protein ligase RanBP2, 358 kDa nucleoporin, and nuclear pore complex (NPC) protein Nup358) is a giant nucleoporin that localizes to the cytosolic face of the NPC. RanBP2 contains a leucine-rich region, 8 zinc-finger motifs, a cyclophilin A homologous domain, and 4 RanBDs. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran. All eukaryotic cells contain RanBP1, but in vertebrates however, the main RanBP seems to be RanBP2. There is no RanBP2 ortholog in yeast. Transport complex disassembly is accomplished by a small ubiquitin-related modifier-1 (SUMO-1)-modified version of RanGAP that is bound to RanBP2. RanBP1 acts as a second line of defense against exported RanGTP-importin complexes which have escaped from dissociation by RanBP2. RanBP2 also interacts with the importin subunit beta-1. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity. The members here include insects and nematodes. RanBD repeat 1 is present in this hierarchy. 117 matched cddid_all.tbl CDD cd13172 cd13172 269993 RanBD2_RanBP2_insect-like Ran-binding protein 2, Ran binding domain repeat 2. RanBP2 (also called E3 SUMO-protein ligase RanBP2, 358 kDa nucleoporin, and nuclear pore complex (NPC) protein Nup358) is a giant nucleoporin that localizes to the cytosolic face of the NPC. RanBP2 contains a leucine-rich region, 8 zinc-finger motifs, a cyclophilin A homologous domain, and 4 RanBDs. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran. All eukaryotic cells contain RanBP1, but in vertebrates however, the main RanBP seems to be RanBP2. There is no RanBP2 ortholog in yeast. Transport complex disassembly is accomplished by a small ubiquitin-related modifier-1 (SUMO-1)-modified version of RanGAP that is bound to RanBP2. RanBP1 acts as a second line of defense against exported RanGTP-importin complexes which have escaped from dissociation by RanBP2. RanBP2 also interacts with the importin subunit beta-1. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity. The members here include insects and nematodes. RanBD repeat 2 is present in this hierarchy. 118 matched cddid_all.tbl CDD cd13173 cd13173 269994 RanBD3_RanBP2_insect-like Ran-binding protein 2, Ran binding domain repeat 3. RanBP2 (also called E3 SUMO-protein ligase RanBP2, 358 kDa nucleoporin, and nuclear pore complex (NPC) protein Nup358) is a giant nucleoporin that localizes to the cytosolic face of the NPC. RanBP2 contains a leucine-rich region, 8 zinc-finger motifs, a cyclophilin A homologous domain, and 4 RanBDs. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran. All eukaryotic cells contain RanBP1, but in vertebrates however, the main RanBP seems to be RanBP2. There is no RanBP2 ortholog in yeast. Transport complex disassembly is accomplished by a small ubiquitin-related modifier-1 (SUMO-1)-modified version of RanGAP that is bound to RanBP2. RanBP1 acts as a second line of defense against exported RanGTP-importin complexes which have escaped from dissociation by RanBP2. RanBP2 also interacts with the importin subunit beta-1. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity. The members here include insects and nematodes. RanBD repeat 3 is present in this hierarchy. 115 matched cddid_all.tbl CDD cd13174 cd13174 269995 RanBD4_RanBP2_insect-like Ran-binding protein 2, Ran binding domain repeat 4. RanBP2 (also called E3 SUMO-protein ligase RanBP2, 358 kDa nucleoporin, and nuclear pore complex (NPC) protein Nup358) is a giant nucleoporin that localizes to the cytosolic face of the NPC. RanBP2 contains a leucine-rich region, 8 zinc-finger motifs, a cyclophilin A homologous domain, and 4 RanBDs. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran. All eukaryotic cells contain RanBP1, but in vertebrates however, the main RanBP seems to be RanBP2. There is no RanBP2 ortholog in yeast. Transport complex disassembly is accomplished by a small ubiquitin-related modifier-1 (SUMO-1)-modified version of RanGAP that is bound to RanBP2. RanBP1 acts as a second line of defense against exported RanGTP-importin complexes which have escaped from dissociation by RanBP2. RanBP2 also interacts with the importin subunit beta-1. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity. The members here include insects and nematodes. RanBD repeat 4 is present in this hierarchy. 118 matched cddid_all.tbl CDD cd13175 cd13175 269996 RanBD5_RanBP2_insect-like Ran-binding protein 2, Ran binding domain repeat 5. RanBP2 (also called E3 SUMO-protein ligase RanBP2, 358 kDa nucleoporin, and nuclear pore complex (NPC) protein Nup358) is a giant nucleoporin that localizes to the cytosolic face of the NPC. RanBP2 contains a leucine-rich region, 8 zinc-finger motifs, a cyclophilin A homologous domain, and 4 RanBDs. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran. All eukaryotic cells contain RanBP1, but in vertebrates however, the main RanBP seems to be RanBP2. There is no RanBP2 ortholog in yeast. Transport complex disassembly is accomplished by a small ubiquitin-related modifier-1 (SUMO-1)-modified version of RanGAP that is bound to RanBP2. RanBP1 acts as a second line of defense against exported RanGTP-importin complexes which have escaped from dissociation by RanBP2. RanBP2 also interacts with the importin subunit beta-1. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity. The members here include insects and nematodes. RanBD repeat 5 is present in this hierarchy. 114 matched cddid_all.tbl CDD cd13176 cd13176 269997 RanBD_RanBP2-like Ran-binding protein 2, Ran binding domains. RanBP2 (also called E3 SUMO-protein ligase RanBP2, 358 kDa nucleoporin, and nuclear pore complex (NPC) protein Nup358) is a giant nucleoporin that localizes to the cytosolic face of the NPC. RanBP2 contains a leucine-rich region, 8 zinc-finger motifs, a cyclophilin A homologous domain, and 4 RanBDs. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran. All eukaryotic cells contain RanBP1, but in vertebrates however, the main RanBP seems to be RanBP2. There is no RanBP2 ortholog in yeast. Transport complex disassembly is accomplished by a small ubiquitin-related modifier-1 (SUMO-1)-modified version of RanGAP that is bound to RanBP2. RanBP1 acts as a second line of defense against exported RanGTP-importin complexes which have escaped from dissociation by RanBP2. RanBP2 also interacts with the importin subunit beta-1. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity. The members here include human, chicken, frog, tunicates, sea urchins, ticks, sea anemones, and sponges. RanBD repeats 1 and 3 are present in this hierarchy. 117 matched cddid_all.tbl CDD cd13177 cd13177 269998 RanBD2_RanBP2-like Ran-binding protein 2, Ran binding domain repeat 2. RanBP2 (also called E3 SUMO-protein ligase RanBP2, 358 kDa nucleoporin, and nuclear pore complex (NPC) protein Nup358) is a giant nucleoporin that localizes to the cytosolic face of the NPC. RanBP2 contains a leucine-rich region, 8 zinc-finger motifs, a cyclophilin A homologous domain, and 4 RanBDs. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran. All eukaryotic cells contain RanBP1, but in vertebrates however, the main RanBP seems to be RanBP2. There is no RanBP2 ortholog in yeast. Transport complex disassembly is accomplished by a small ubiquitin-related modifier-1 (SUMO-1)-modified version of RanGAP that is bound to RanBP2. RanBP1 acts as a second line of defense against exported RanGTP-importin complexes which have escaped from dissociation by RanBP2. RanBP2 also interacts with the importin subunit beta-1. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity. The members here include human, chicken, frog, tunicates, sea urchins, ticks, sea anemones, and sponges. RanBD repeat 2 is present in this hierarchy. 117 matched cddid_all.tbl CDD cd13178 cd13178 269999 RanBD4_RanBP2-like Ran-binding protein 2, Ran binding domain repeat 4. RanBP2 (also called E3 SUMO-protein ligase RanBP2, 358 kDa nucleoporin, and nuclear pore complex (NPC) protein Nup358) is a giant nucleoporin that localizes to the cytosolic face of the NPC. RanBP2 contains a leucine-rich region, 8 zinc-finger motifs, a cyclophilin A homologous domain, and 4 RanBDs. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran. All eukaryotic cells contain RanBP1, but in vertebrates however, the main RanBP seems to be RanBP2. There is no RanBP2 ortholog in yeast. Transport complex disassembly is accomplished by a small ubiquitin-related modifier-1 (SUMO-1)-modified version of RanGAP that is bound to RanBP2. RanBP1 acts as a second line of defense against exported RanGTP-importin complexes which have escaped from dissociation by RanBP2. RanBP2 also interacts with the importin subunit beta-1. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity. The members here include human, chicken, frog, tunicates, sea urchins, ticks, sea anemones, and sponges. RanBD repeat 4 is present in this hierarchy. 117 matched cddid_all.tbl CDD cd13179 cd13179 270000 RanBD_RanBP1 Ran-binding domain. RanBP1 interacts specifically with GTP-charged Ran. RanBP1 does not activate GTPase activity of Ran, but does markedly increase GTP hydrolysis by the RanGTPase-activating protein (RanGAP1). In both mammalian cells and in yeast, RanBP1 acts as a negative regulator of Regulator of chromosome condensation 1 (RCC1) by inhibiting RCC1-stimulated guanine nucleotide release from Ran. In addition to Ran, RanBP1 has been shown to interact with Exportin-1 and Importin subunit beta-1 which docks the NPC at the cytoplasmic side of the nuclear pore complex. RabBP1 contains a single RanBD. The RanBD is present in RanBD1, RanBD2, RanBD3, Nuc2, and Nuc50. Most of these proteins have a single RanBD, with the exception of RanBD2 which has 4 RanBDs. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran. The Ran-binding domain is found in multiple copies in Nuclear pore complex proteins. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity. 136 matched cddid_all.tbl CDD cd13180 cd13180 270001 RanBD_RanBP3 Ran-binding protein 3 Ran-binding domain. RanBP3, a Ran-interacting nuclear protein, unlike the related proteins RanBP1 and RanBP2, which promote disassembly of the export complex in the cytosol, acts as a CRM1 cofactor, enhancing nuclear export signal (NES) export by stabilizing the export complex in the nucleus. CRM1/Exportin1 is responsible for exporting many proteins and ribonucleoproteins from the nucleus to the cytosol. RanBP3 also alters the cargo selectivity of CRM1, promoting recognition of the NES of HIV-1 Rev and of other cargos while deterring recognition of the import adaptor protein Snurportin1. RanBP3 contains a N-terminal nuclear localization signal (NLS), 2 FxFG motifs, and a single RanBD. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity. 113 matched cddid_all.tbl CDD cd13181 cd13181 270002 RanBD_NUP2 Nucleoporin 2 Ran-binding domain. Yeast protein Nup2 transiently associates with Nuclear pore complexes (NPCs) and when artificially tethered to DNA, can prevent the spread of transcriptional activation or repression between flanking genes, a function termed boundary activity (BA). Nup2 and the Ran guanylyl-nucleotide exchange factor, Prp20, interact at specific chromatin regions and enable the NPC to play an active role in chromatin organization. Nup60p, the nup responsible for anchoring Nup2 and the Mlp proteins to the NPC is required for Nup2-dependent BA. Nup2 contains an N-terminal Nup50 family domain and a C-terminal RanBD. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity. 115 matched cddid_all.tbl CDD cd13182 cd13182 270003 EVH1-like_Dcp1 Decapping enzyme EVH1-like domain. Dcp1 is a small protein containing an EVH1 domain. The Dcp1-Dcp2 complex plays a critical step in mRNA degradation with the removal of the 50 cap structure. Dcp1 stimulates the activity of Dcp2 by promoting and/or stabilizing the closed complex. The interface of Dcp1 and Dcp2 is not fully conserved and in higher eukaryotes it requires an additional factor. The proline-rich sequence (PRS)-binding sites in Dcp1p indicates that it belongs to a novel class of EVH1 domains. Dcp1 has 2 prominent sites,one required for the function of the Dcp1p-Dcp2p complex, and the other, the PRS-binding site of EVH1 domains, a binding site for decapping regulatory proteins. It also has a conserved hydrophobic patch is shown to be critical for decapping. The EVH1 domains are part of the PH domain superamily. 116 matched cddid_all.tbl CDD cd13183 cd13183 270004 FERM_C_FRMPD1_FRMPD3_FRMPD4 FERM domain C-lobe of FERM and PDZ domain containing proteins 1, 3, and 4 (FRMPD1, 3, 4). The function of FRMPD1, FRMPD3, and FRMPD4 is unknown at present. These proteins contain an N-terminal PDZ (post synaptic density protein (PSD95), Drosophila disc large tumor suppressor (Dlg1), and zonula occludens-1 protein (zo-1) domain and a C-terminal FERM domain. PDZ (also known as DHR (Dlg homologous region) or GLGF (glycine-leucine-glycine-phenylalanine) domains) help anchor transmembrane proteins to the cytoskeleton and hold together signaling complexes. PDZ domains bind to a short region of the C-terminus of other specific proteins. The FERM domain is composed of three subdomains: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3), which form a clover leaf fold. The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs) , the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 105 matched cddid_all.tbl CDD cd13184 cd13184 270005 FERM_C_4_1_family FERM domain C-lobe of Protein 4.1 family. The protein 4.1 family includes four well-defined members: erythroid protein 4.1 (4.1R), the best known and characterized member, 4.1G (general), 4.1N (neuronal), and 4.1 B (brain). The less well understood 4.1O/FRMD3 is not a true member of this family and is not included in this hierarchy. Besides three highly conserved domains, FERM, SAB (spectrin and actin binding domain) and CTD (C-terminal domain), the proteins from this family contain several unique domains: U1, U2 and U3. FERM domains like other members of the FERM domain superfamily have a cloverleaf architecture with three distinct lobes: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The brain is a particularly rich source of protein 4.1 isoforms. The various 4.1R, 4.1G, 4.1N, and 4.1B mRNAs are all expressed in distinct patterns within the brain. It is likely that 4.1 proteins play important functional roles in the brain including motor coordination and spatial learning, postmitotic differentiation, and synaptic architecture and function. In addition they are found in nonerythroid, nonneuronal cells where they may play a general structural role in nuclear architecture and/or may interact with splicing factors. The FERM C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs) , the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 94 matched cddid_all.tbl CDD cd13185 cd13185 270006 FERM_C_FRMD1_FRMD6 FERM domain C-lobe of FERM domain containing 1 and 6 proteins. FRMD6 (also called willin and hEx/human expanded) is localized throughout the cytoplasm or along the plasma membrane. The Drosophilla protein Ex is a regulator of the Hippo/SWH (Sav/Wts/Hpo) signaling pathway, a signaling pathway that plays a pivotal role in organ size control and is tumor suppression by restricting proliferation and promoting apoptosis. Surprisingly, hEx is thought to function independently of the Hippo pathway. Instead it is hypothesized that hEx inhibits progression through the S phase of the cell cycle by upregulating p21(Cip1) and downregulating Cyclin A. It is also implicated in the progression of Alzheimer disease. Not much is known about FRMD1 to date. Both FRMD1 and FRMD6 contains a single FERM domain which has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe is a member of the PH superfamily. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs) , the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 107 matched cddid_all.tbl CDD cd13186 cd13186 270007 FERM_C_NBL4_NBL5 FERM domain C-lobe of Novel band 4.1-like protein 4 and 5 (NBL4 and 5). NBL4 (also called Erythrocyte protein band 4.1-like 4; Epb4 1l4) plays a role the beta-catenin/Tcf signaling pathway and is thought to be involved in establishing the cell polarity or proliferation. NBL4 may be also involved in adhesion, in cell motility and/or in cell-to-cell communication. No role for NBL5 has been proposed to date. Both NBL4 and NBL5 contain a N-terminal FERM domain which has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe is a member of the PH superfamily. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs) , the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 92 matched cddid_all.tbl CDD cd13187 cd13187 270008 FERM_C_PTPH13 FERM domain C-lobe of Protein tyrosine phosphatase non-receptor 13 (PTPH13). There are many functions of PTPN13 (also called PTPL1, PTP-BAS, hPTP1E, FAP1, or PTPL1). Mice lacking PTPN13 activity have abnormal regulation of signal transducer and activator of transcription signaling in their T cells, mild impairment of motor nerve repair, and a significant reduction in the growth of retinal glia cultures. It also plays a role in adipocyte differentiation. PTPN13 contains a kinase non-catalytic C-lobe domain (KIND), a FERM domain with two potential phosphatidylinositol 4,5-biphosphate [PtdIns(4,5)P2]-binding motifs, 5 PDZ domains, and a carboxy-terminal catalytic domain. There is an nteraction between the FERM domain of PTPL1 and PtdIns(4,5)P2 which is thought to regulate the membrane localization of PTPN13. PDZ are protein/protein interaction domains so there is the potential for numerous partners that can actively participate in the regulation of its phosphatase activity or can permit direct or indirect recruitment of tyrosine phosphorylated PTPL1 substrates. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 103 matched cddid_all.tbl CDD cd13188 cd13188 270009 FERM_C_PTPN14_PTPN21 FERM domain C-lobe of Protein tyrosine phosphatase non-receptor proteins 14 and 21 (PTPN14 and 21). This CD contains PTP members: pez/PTPN14 and PTPN21. A number of mutations in Pez have been shown to be associated with breast and colorectal cancer. The PTPN protein family belong to larger family of PTPs. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. The members are composed of a N-terminal FERM domain and a C-terminal PTP catalytic domain. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. Like most other ERM members they have a phosphoinositide-binding site in their FERM domain. The FERM C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs) , the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 91 matched cddid_all.tbl CDD cd13189 cd13189 270010 FERM_C_PTPN4_PTPN3_like FERM domain C-lobe of Protein tyrosine phosphatase non-receptor proteins 3 and 4 (PTPN4 and PTPN3). PTPN4 (also called PTPMEG, protein tyrosine phosphatase, megakaryocyte) is a cytoplasmic protein-tyrosine phosphatase (PTP) thought to play a role in cerebellar function. PTPMEG-knockout mice have impaired memory formation and cerebellar long-term depression. PTPN3/PTPH1 is a membrane-associated PTP that is implicated in regulating tyrosine phosphorylation of growth factor receptors, p97 VCP (valosin-containing protein, or Cdc48 in Saccharomyces cerevisiae), and HBV (Hepatitis B Virus) gene expression; it is mutated in a subset of colon cancers. PTPMEG and PTPN3/PTPH1 contains a N-terminal FERM domain, a middle PDZ domain, and a C-terminal phosphatase domain. PTP1/Tyrosine-protein phosphatase 1 from nematodes and a FERM_C repeat 1 from Tetraodon nigroviridis are also included in this cd. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs) , the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 95 matched cddid_all.tbl CDD cd13190 cd13190 270011 FERM_C_FAK1 FERM domain C-lobe of Focal Adhesion Kinase 1 and 2. FAK1 (also called FRNK/Focal adhesion kinase-related nonkinase; p125FAK/pp125FAK;PTK2/Protein-tyrosine kinase 2 protein tyrosine kinase 2 (PTK2) is a non-receptor tyrosine kinase that localizes to focal adhesions in adherent cells. It has been implicated in diverse cellular roles including cell locomotion, mitogen response and cell survival. The N-terminal region of FAK1 contains a FERM domain, a linker, a kinase domain, and a C-terminal FRNK (FAK-related-non-kinase) domain. Three subdomains of FERM: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3), form a cloverleaf fold, similar to those of known FERM structures despite the low sequence conservation. The C-lobe/F3 within the FERM domain is part of the PH domain family. The phosphoinositide-binding site found in ERM family proteins is not present in the FERM domain of FAK1. The adjacent Src SH3 and SH2 binding sites in the linker of FAK1 associates with the F3 and F1 lobes and are thought to be involved in regulation. The FERM domain of FAK1 can inhibit enzymatic activity and repress FAK signaling. In an inactive state of FAK1, the FERM domain is thought to interact with the catalytic domain of FAK1 to repress its activity. Upon activation this interaction is disrupted and its kinase activity restored. The FRNK domain is thought to function as a negative regulator of kinase activity. The C-lobe/F3 is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs) , the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 111 matched cddid_all.tbl CDD cd13191 cd13191 270012 FERM_C_FRMD4A_FRMD4B FERM domain C-lobe of FERM domain-containing protein 4A and 4B (FRMD4A and 4B). FRMD4A is part of the Par-3/FRMD4A/cytohesin-1 complex that activates Arf6, a central player in actin cytoskeleton dynamics and membrane trafficking, during junctional remodeling and epithelial polarization. The Par-3/Par-6/aPKC/Cdc42 complex regulates the conversion of primordial adherens junctions (AJs) into belt-like AJs and the formation of linear actin cables. When primordial AJs are formed, Par-3 recruits scaffolding protein FRMD4A which connects Par-3 and the Arf6 guanine-nucleotide exchange factor (GEF), cytohesin-1. FRMD4B (also called GRP1-binding protein, GRSP1) is a novel member of GRP1 signaling complexes that are recruited to plasma membrane ruffles in response to insulin receptor signaling. The GRSP1/FRMD4B protein contains a FERM protein domain as well as two coiled coil domains and may function as a scaffolding protein. GRP1 and GRSP1 interact through the coiled coil domains in the two proteins. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs) , the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 113 matched cddid_all.tbl CDD cd13192 cd13192 270013 FERM_C_FRMD3_FRMD5 FERM domain C-lobe of FERM domain-containing protein 3 and 5 (FRMD3 and 5). FRMD3 (also called Band 4.1-like protein 4O/4.1O though it is not a true member of that family) is a novel putative tumor suppressor gene that is implicated in the origin and progression of lung cancer. In humans there are 5 isoforms that are produced by alternative splicing. Less is known about FRMD5, though there are 2 isoforms of the human protein are produced by alternative splicing. Both FRMD3 and FRMD5 contain a N-terminal FERM domain, followed by a FERM adjacent (FA) domain, and 4.1 protein C-terminal domain (CTD). The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 105 matched cddid_all.tbl CDD cd13193 cd13193 270014 FERM_C_FARP1-like FERM domain C-lobe of FERM, RhoGEF and pleckstrin domain-containing protein 1 and related proteins. Members here include FARP1 (also called Chondrocyte-derived ezrin-like protein; PH domain-containing family C member 2), FARP2 (also called FIR/FERM domain including RhoGEF; FGD1-related Cdc42-GEF/FRG), and FRMD7(FERM domain containing 7). FARP1 and FARP2 are members of the Dbl family guanine nucleotide exchange factors (GEFs) which are upstream positive regulators of Rho GTPases. FARP1 has increased expression in differentiated chondrocytes. FARP2 is thought to regulate neurite remodeling by mediating the signaling pathways from membrane proteins to Rac. It is found in brain, lung, and testis, as well as embryonic hippocampal and cortical neurons. These members are composed of a N-terminal FERM domain, a proline-rich (PR) domain, Dbl-homology (DH), and two C-terminal PH domains. Other members in this family do not contain the DH domains such as the Human FERM domain containing protein 7 and Caenorhabditis elegans CFRM3, both of which have unknown functions. They contain an N-terminal FERM domain, a PH domain, followed by a FA (FERM adjacent) domain. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 122 matched cddid_all.tbl CDD cd13194 cd13194 270015 FERM_C_ERM FERM domain C-lobe/F3 of the ERM family. The ERM family includes ezrin, radixin, moesin and merlin. They are composed of a N-terminal FERM (ERM) domain (also called N-ERMAD (N-terminal ERM association domain)), a coiled coil region (CRR), and a C-terminal domain CERMAD (C-terminal ERM association domain) which has an F-actin-binding site (ABD). Two actin-binding sites have been identified in the middle and N-terminal domains. Merlin is structurally similar to the ERM proteins, but instead of an actin-binding domain (ABD), it contains a C-terminal domain (CTD), just like the proteins from the 4.1 family. Activated ezrin, radixin and moesin are thought to be involved in the linking of actin filaments to CD43, CD44, ICAM1-3 cell adhesion molecules, various membrane channels and receptors, such as the Na+/H+ exchanger-3 (NHE3), cystic fibrosis transmembrane conductance regulator (CFTR), and the beta2-adrenergic receptor. The ERM proteins exist in two states, a dormant state in which the FERM domain binds to its own C-terminal tail and thereby precludes binding of some partner proteins, and an activated state, in which the FERM domain binds to one of many membrane binding proteins and the C-terminal tail binds to F-actin. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain of ERM is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 97 matched cddid_all.tbl CDD cd13195 cd13195 270016 FERM_C_MYLIP_IDOL FERM domain C-lobe of E3 ubiquitin ligase myosin regulatory light chain-interacting protein (MYLIP; also called inducible degrader of the LDL receptor, IDOL). MYLIP/IDOL is a regulator of the LDL receptor (LDLR) pathway via the nuclear receptor liver X receptor (LXR). In response to cellular cholesterol loading, the activation of LXR leads to the induction of MYLIP expression. MYLIP stimulates ubiquitination of the LDLR on its cytoplasmic tail, directing its degradation. The LXR-MYLIP-LDLR pathway provides a complementary pathway to sterol regulatory element-binding proteins for the feedback inhibition of cholesterol uptake. MYLIP has an N-terminal FERM domain and in some cases a C-terminal RING domain. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 111 matched cddid_all.tbl CDD cd13196 cd13196 275394 FERM_C_JAK FERM domain C-lobe of Janus kinase (JAK). JAK (also called Just Another Kinase) is a family of intracellular, non-receptor tyrosine kinases that transduce cytokine-mediated signals via the JAK-STAT pathway. The JAK family in mammals consists of 4 members: JAK1, JAK2, JAK3 and TYK2. JAKs are composed of seven JAK homology (JH) domains (JH1-JH7) . The C-terminal JH1 domain is the main catalytic domain, followed by JH2, which is often referred to as a pseudokinase domain, followed by JH3-JH4 which is homologous to the SH2 domain, and lastly JH5-JH7 which is a FERM domain. Named after Janus, the two-faced Roman god of doorways, JAKs possess two near-identical phosphate-transferring domains; one which displays the kinase activity (JH1), while the other negatively regulates the kinase activity of the first (JH2). The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 109 matched cddid_all.tbl CDD cd13197 cd13197 270018 FERM_C_CCM1 FERM domain C-lobe of Cerebral cavernous malformation 1. CCM1 (also called KRIT-1/Krev interaction trapped 1;ankyrin repeat-containing protein Krit1; CAM), a Rap1-binding protein, is expressed in endothelial cells where it is present in cell-cell junctions and associated with junctional proteins. Together with CCM2/MGC4607 and CCM3/PDCD10, KRIT1 constitutes a set of proteins, mutations of which are found in cerebral cavernous malformations which are characterized by cerebral hemorrhages and vascular malformations in the central nervous system. KRIT-1 possesses four ankyrin repeats, a FERM domain, and multiple NPXY sequences, one of which is essential for integrin cytoplasmic domain-associated protein-1alpha (ICAP1alpha) binding and all of which mediate binding of CCM2. KRIT-1 localization is mediated by its FERM domain. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 100 matched cddid_all.tbl CDD cd13198 cd13198 270019 FERM_C1_MyoVII FERM domain C-lobe, repeat 1, of Myosin VII (MyoVII/Myo7). MyoVII, a MyTH-FERM myosin, is an actin-based motor protein essential for a variety of biological processes in the actin cytoskeleton function. Mutations in MyoVII leads to problems in sensory perception: deafness and blindness in humans (Usher Syndrome), retinal defects and deafness in mice (shaker 1), and aberrant auditory and vestibular function in zebrafish. Myosin VIIAs have plus (barbed) end-directed motor activity on actin filaments and a characteristic actin-activated ATPase activity. MyoVII consists of a conserved spectrin-like, SH3 subdomain N-terminal region, a motor/head region, a neck made of 4-5 IQ motifs, and a tail consisting of a coiled-coil domain, followed by a tandem repeat of myosin tail homology 4 (MyTH4) domains and partial FERM domains that are separated by an SH3 subdomain and are thought to mediate dimerization and binding to other proteins or cargo. Members include: MyoVIIa, MyoVIIb, and MyoVII members that do not have distinct myosin VIIA and myosin VIIB genes. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs) , the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 99 matched cddid_all.tbl CDD cd13199 cd13199 270020 FERM_C2_MyoVII FERM domain C-lobe, repeat 2, of Myosin VII (MyoVII, Myo7). MyoVII, a MyTH-FERM myosin, is an actin-based motor protein essential for a variety of biological processes in the actin cytoskeleton function. Mutations in MyoVII leads to problems in sensory perception: deafness and blindness in humans (Usher Syndrome), retinal defects and deafness in mice (shaker 1), and aberrant auditory and vestibular function in zebrafish. Myosin VIIAs have plus (barbed) end-directed motor activity on actin filaments and a characteristic actin-activated ATPase activity. MyoVII consists of a conserved spectrin-like, SH3 subdomain N-terminal region, a motor/head region, a neck made of 4-5 IQ motifs, and a tail consisting of a coiled-coil domain, followed by a tandem repeat of myosin tail homology 4 (MyTH4) domains and partial FERM domains that are separated by an SH3 subdomain and are thought to mediate dimerization and binding to other proteins or cargo. Members include: MyoVIIa, MyoVIIb, and MyoVII members that do not have distinct myosin VIIA and myosin VIIB genes. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 96 matched cddid_all.tbl CDD cd13200 cd13200 270021 FERM_C_KCBP FERM domain C-lobe of Kinesin-like calmodulin binding protein. KCBPs (also called KIPK/Kinesin-like Calmodulin-Binding Protein-Interacting Protein Kinase), a member of the Kinesin-14 family, is a C-terminal microtubule motor with three unique domains including a myosin tail homology region 4 (MyTH4), a talin-like domain, and a calmodulin-binding domain (CBD). Binding of the Ca2+-activated calmodulin to KCBP causes the motor to dissociate from microtubules. The microtubule binding of KCBP is controlled by the calcium binding protein KIC containing a single EF-hand motif. KCBPs are unique to land plants and green algae. The MyTH4 and talin-like domains are not found in other kinesins, while the CBD domain is also only found in Strongylocentrotus purpuratus kinesin-C (SpKinC). The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 109 matched cddid_all.tbl CDD cd13201 cd13201 270022 FERM_C_MyoXV FERM domain C-lobe of Myosin XV (MyoXV/Myo15). MyoXV, a MyTH-FERM myosin, are actin-based motor proteins essential for a variety of biological processes in actin cytoskeleton function. Specifically MyoXV functions in the actin organization in hair cells of the organ of Corti. Mutations in Human MyoXVa causes non-syndromic deafness, DFNB3 and the mouse shaker-2 mutation. MyoXV consists of a N-terminal motor/head region, a neck made of 1-3 IQ motifs, and a tail that consists of either a myosin tail homology 4 (MyTH4) domains, followed by an SH3 domain, and a MyTH-FERM domains as in rat Myo15 or two MyTH-FERM domains separated by a SH3 domain as in human Myo15A. The MyTH-FERM domains are thought to mediate dimerization and binding to other proteins or cargo. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 101 matched cddid_all.tbl CDD cd13202 cd13202 270023 FERM_C_MyoX FERM domain C-lobe of Myosin X (MyoX, Myo10). MyoX, a MyTH-FERM myosin, is a molecular motor that has crucial functions in the transport and/or tethering of integrins in the actin-based extensions known as filopodia, microtubule binding, and in netrin-mediated axon guidance. It functions as a dimer. MyoX walks on bundles of actin, rather than single filaments, unlike the other unconventional myosins. MyoX is present in organisms ranging from humans to choanoflagellates, but not in Drosophila and Caenorhabditis elegans.MyoX consists of a N-terminal motor/head region, a neck made of 3 IQ motifs, and a tail consisting of a coiled-coil domain, a PEST region, 3 PH domains, a myosin tail homology 4 (MyTH4), and a FERM domain at its very C-terminus. The MyoX FERM domain binds to the NPXY motif of several beta-integrins, a key family of cell surface receptors that are involved in cell adhesion and migration. In addition the FERM domain binds to the cytoplasmic domains of the netrin receptors DCC (deleted in colorectal cancer) and neogenin. The FERM domain also forms a supramodule with its MyTH4 domain which binds to the negatively charged E-hook region in the tails of alpha- and beta-tubulin forming a proposed motorized link between actin filaments and microtubules. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 90 matched cddid_all.tbl CDD cd13203 cd13203 270024 FERM_C1_myosin_like FERM domain C-lobe, repeat 1, of Myosin-like proteins. These myosin-like proteins are unidentified though they are sequence similar to myosin 1/myo1, myosin 7/myoVII, and myosin 10/myoX. These myosin-like proteins contain an N-terminal motor/head region and a C-terminal tail consisting of two myosin tail homology 4 (MyTH4) and twos FERM domains. In myoX the FERM domain forms a supramodule with its MyTH4 domain which binds to the negatively charged E-hook region in the tails of alpha- and beta-tubulin forming a proposed motorized link between actin filaments and microtubules and a similar thing might happen in these myosins. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The first FERM_N repeat is present in this hierarchy. The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 97 matched cddid_all.tbl CDD cd13204 cd13204 270025 FERM_C2_myosin_like FERM domain C-lobe, repeat 2, of Myosin-like proteins. These myosin-like proteins are unidentified though they are sequence similar to myosin 1/myo1, myosin 7/myoVII, and myosin 10/myoX. These myosin-like proteins contain an N-terminal motor/head region and a C-terminal tail consisting of two myosin tail homology 4 (MyTH4) and twos FERM domains. In myoX the FERM domain forms a supramodule with its MyTH4 domain which binds to the negatively charged E-hook region in the tails of alpha- and beta-tubulin forming a proposed motorized link between actin filaments and microtubules and a similar thing might happen in these myosins. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The second FERM_N repeat is present in this hierarchy. The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 93 matched cddid_all.tbl CDD cd13205 cd13205 270026 FERM_C_fermitin FERM domain C-lobe of the Fermitin family. Fermitin functions as a mediator of integrin inside-out signalling. The recruitment of Fermitin proteins and Talin to the membrane mediates the terminal event of integrin signalling, via interaction with integrin beta subunits. Fermatin has FERM domain interrupted with a pleckstrin homology (PH) domain. Fermitin family homologs (Fermt1, 2, and 3, also known as Kindlins) are each encoded by a different gene. In mammalian studies, Fermt1 is generally expressed in epithelial cells, Fermt2 is expressed inmuscle tissues, and Fermt3 is expressed in hematopoietic lineages. Specifically Fermt2 is expressed in smooth and striated muscle tissues in mice and in the somites (a trunk muscle precursor) and neural crest in Xenopus embryos. As such it has been proposed that Fermt2 plays a role in cardiomyocyte and neural crest differentiation. Expression of mammalian Fermt3 is associated with hematopoietic lineages: the anterior ventral blood islands, vitelline veins, and early myeloid cells. In Xenopus embryos this expression, also include the notochord and cement gland. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). This cd is not included in the C-lobe hierarchy based on its position in the tree. One thing to note is that unlike the other members of the C-lobe hierarchy it contains 2 FERM M domains which might also reflect a difference in its evolutionary history. The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 91 matched cddid_all.tbl CDD cd13206 cd13206 241360 FERM_C-lobe_PLEKHH1_PLEKHH2 FERM domain C-lobe of Pleckstrin homology domain-containing family H. PLEKHH1 and PLEKHH2 (also called PLEKHH1L) are thought to function in phospholipid binding and signal transduction. There are 3 Human PLEKHH genes: PLEKHH1, PLEKHH2, and PLEKHH3. There are many isoforms, the longest of which contain a FERM domain, a MyTH4 domain, two PH domains, a peroximal domain, a vacuolar domain, and a coiled coil stretch. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 100 matched cddid_all.tbl CDD cd13207 cd13207 275395 FERM-like_C_SNX Atypical FERM-like domain C-lobe of Sorting nexin family. Sorting nexins function in regulating recycling from endosomes to the cell surface. SNX17, SNX27, and SNX31 contain a N-terminal PX domain, a FERM-like domain, and a unique C-terminal region. All three proteins are able to bind the Ras GTPase through their FERM-like domains. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. These interactions place the PX-FERM-like proteins at a hub of endosomal sorting and signaling processes. These proteins participate in a network of interactions that will impact on both endosomal protein trafficking and compartment specific Ras signaling cascades. The typical FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. FERM domains are found in cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 116 matched cddid_all.tbl CDD cd13208 cd13208 275396 PH-GRAM_MTMR5_MTMR13 Myotubularian (MTM) related 5 and 13 proteins (MTMR5 and MTMR13) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTMR5 is a catalytically inactive phosphatase that plays a role as an adapter for the phosphatase myotubularin to regulate myotubularintracellular location. It lacks several amino acids in the dsPTPase catalytic pocket which renders it catalytically inactive as a phosphatase. MTMR5 is the most well-studied inactive member of this family and has been implicated in cellular growth control and oncogenic transformation. MTMR13 is a catalytically inactive phosphatase that plays a role as an adapter for the phosphatase myotubularin to regulate myotubularintracellular location. It contains a Leu residue instead of a conserved Cys residue in the dsPTPase catalytic loop which renders it catalytically inactive as a phosphatase. MTMR13 has high sequence similarity to MTMR5 and has recently been shown to be a second gene mutated in type 4B Charcot-Marie-Tooth syndrome. Both MTMR5 and MTMR13 contain an N-terminal DENN domain, a PH-GRAM domain, an inactive PTP domain, a SET interaction domain, a coiled-coil domain, and a C-terminal PH domain. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The PH domain family possesses multiple functions including the ability to bind phosphoinositides via its beta1/beta2, beta3/beta4, and beta6/beta7 connecting loops and to other proteins. However, no phosphoinositide binding sites have been found for the MTMRs to date. Although the majority of the sequences are MTMR 5 and 13, this cd also contains MTM5 nematode sequences. 120 matched cddid_all.tbl CDD cd13209 cd13209 275397 PH-GRAM_MTMR3_MTMR4 Myotubularian (MTM) related 3 and 4 proteins (MTMR3 and MTMR4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTMR3 is a member of the myotubularin dual specificity protein phosphatase gene family. MTMR3 binds to phosphoinositide lipids through its PH-GRAM domain, and can hydrolyze phosphatidylinositol(3)-phosphate and phosphatidylinositol(3,5)-biphosphate in vitro. The protein can self-associate and also form heteromers with MTMR4. MTMR4, a member of the myotubularin dual specificity protein phosphatase gene family. MTMR4 binds to phosphoinositide lipids through its PH-GRAM domain, and can hydrolyze phosphatidylinositol(3)-phosphate and phosphatidylinositol(3,5)-biphosphate in vitro. The protein form heteromers with MTMR3. Both MTMR3 and MTMR4 contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an active PTP domain, a SET-interaction domain, a coiled-coil region, and a C-terminal lipid-binding FYVE domain which binds phosphotidylinositol-3-phosphate. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The PH domain family possesses multiple functions including the ability to bind phosphoinositides via its beta1/beta2, beta3/beta4, and beta6/beta7 connecting loops and to other proteins. However, no phosphoinositide binding sites have been found for the MTMRs to date. 94 matched cddid_all.tbl CDD cd13210 cd13210 270030 PH-GRAM_MTMR6-like Myotubularian (MTM) related (MTMR) 7 and 8 proteins Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTMR6, MTMR7, and MRMR8 are all member of the myotubularin dual specificity protein phosphatase gene family. They bind to phosphoinositide lipids through its PH-GRAM domain. These proteins also interact with each other as well as MTMR9. They contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an active PTP domain, a SET-interaction domain, and a C-terminal coiled-coil region. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The lipid-binding FYVE domain has been shown to bind phosphotidylinositol-3-phosphate. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The PH domain family possesses multiple functions including the ability to bind phosphoinositides via its beta1/beta2, beta3/beta4, and beta6/beta7 connecting loops and to other proteins. However, no phosphoinositide binding sites have been found for the MTMRs to date. 98 matched cddid_all.tbl CDD cd13211 cd13211 275398 PH-GRAM_MTMR9 Myotubularian (MTM) related 9 protein (MTMR9) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTMR9 is a catalytically inactive phosphatase that plays a role as an adapter for the phosphatase myotubularin to regulate myotubularintracellular location. It contains a Gly residue instead of a conserved Cys residue in the dsPTPase catalytic loop which renders it catalytically inactive as a phosphatase. MTMR9 contains an N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an inactive PTP domain, a SET interaction domain, and a C-terminal coiled-coil region. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The PH domain family possesses multiple functions including the ability to bind phosphoinositides via its beta1/beta2, beta3/beta4, and beta6/beta7 connecting loops and to other proteins. However, no phosphoinositide binding sites have been found for the MTMRs to date. 99 matched cddid_all.tbl CDD cd13212 cd13212 275399 PH-GRAM_MTMR10-like Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTMR10, MTMR11, and MTMR12 are catalytically inactive phosphatases that play a role as an adapter for the phosphatase myotubularin to regulate myotubularintracellular location. They contains a Glu residue instead of a conserved Cys residue in the dsPTPase catalytic loop which renders it catalytically inactive as a phosphatase. They contains an N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an inactive PTP domain, a SET interaction domain, and a C-terminal coiled-coil domain. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. 125 matched cddid_all.tbl CDD cd13213 cd13213 275400 PH-GRAM_MTMR14 Myotubularian (MTM) related 14 protein (MTMR14) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTMR14 is a member of the myotubularin protein phosphatase gene family. MTMR14 binds to phosphoinositide lipids through its PH-GRAM domain, and can hydrolyze phosphatidylinositol(3)-phosphate and phosphatidylinositol(3,5)-biphosphate in vitro. MTMR14 plays a role in the regulation of autophagy and mutations in MTMR14 result in autosomal dominant centronuclear myopathy. MTMR14 contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an active PTP domain, a SET-interaction domain (SID), a coiled-coil region, and a C-terminal PDZ domain. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain (SID), and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The PH domain family possesses multiple functions including the ability to bind phosphoinositides via its beta1/beta2, beta3/beta4, and beta6/beta7 connecting loops and to other proteins. However, no phosphoinositide binding sites have been found for the MTMRs to date. 116 matched cddid_all.tbl CDD cd13214 cd13214 275401 PH-GRAM_WBP2 WW binding protein 2 (WB2) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. WBP2 plays a number of roles including: acting as a tyrosine kinase substrate, activation of estrogen receptor alpha (ERalpha)/progesterone receptor (PR) transcription, and playing a role in breast cancer. WBP2 contain a N-terminal PH-GRAM domain and a C-terminal WWbp domain. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The WWbp domain is characterized by several short PY and PT-like motifs of the PPPPY form and binds to WW domains. WW domains contain two highly conserved tryptophans that are spaced 20-23 residues apart. They bind proline-rich peptide motifs [AP]-P-P-[AP]-Y, and/or phosphoserine- phosphothreonine-containing motifs. 103 matched cddid_all.tbl CDD cd13215 cd13215 275402 PH-GRAM1_AGT26 Autophagy-related protein 26/Sterol 3-beta-glucosyltransferase Pleckstrin homology (PH) domain, repeat 1. ATG26 (also called UGT51/UDP-glycosyltransferase 51), a member of the glycosyltransferase 28 family, resulting in the biosynthesis of sterol glucoside. ATG26 in decane metabolism and autophagy. There are 32 known autophagy-related (ATG) proteins, 17 are components of the core autophagic machinery essential for all autophagy-related pathways and 15 are the additional components required only for certain pathways or species. The core autophagic machinery includes 1) the ATG9 cycling system (ATG1, ATG2, ATG9, ATG13, ATG18, and ATG27), 2) the phosphatidylinositol 3-kinase complex (ATG6/VPS30, ATG14, VPS15, and ATG34), and 3) the ubiquitin-like protein system (ATG3, ATG4, ATG5, ATG7, ATG8, ATG10, ATG12, and ATG16). Less is known about how the core machinery is adapted or modulated with additional components to accommodate the nonselective sequestration of bulk cytosol (autophagosome formation) or selective sequestration of specific cargos (Cvt vesicle, pexophagosome, or bacteria-containing autophagosome formation). The pexophagosome-specific additions include the ATG30-ATG11-ATG17 receptor-adaptors complex, the coiled-coil protein ATG25, and the sterol glucosyltransferase ATG26. ATG26 is necessary for the degradation of medium peroxisomes. It contains 2 GRAM domains and a single PH domain. PH domains are only found in eukaryotes. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 116 matched cddid_all.tbl CDD cd13216 cd13216 275403 PH-GRAM2_AGT26 Autophagy-related protein 26/Sterol 3-beta-glucosyltransferase Pleckstrin homology (PH) domain, repeat 2. ATG26 (also called UGT51/UDP-glycosyltransferase 51), a member of the glycosyltransferase 28 family, resulting in the biosynthesis of sterol glucoside. ATG26 in decane metabolism and autophagy. There are 32 known autophagy-related (ATG) proteins, 17 are components of the core autophagic machinery essential for all autophagy-related pathways and 15 are the additional components required only for certain pathways or species. The core autophagic machinery includes 1) the ATG9 cycling system (ATG1, ATG2, ATG9, ATG13, ATG18, and ATG27), 2) the phosphatidylinositol 3-kinase complex (ATG6/VPS30, ATG14, VPS15, and ATG34), and 3) the ubiquitin-like protein system (ATG3, ATG4, ATG5, ATG7, ATG8, ATG10, ATG12, and ATG16). Less is known about how the core machinery is adapted or modulated with additional components to accommodate the nonselective sequestration of bulk cytosol (autophagosome formation) or selective sequestration of specific cargos (Cvt vesicle, pexophagosome, or bacteria-containing autophagosome formation). The pexophagosome-specific additions include the ATG30-ATG11-ATG17 receptor-adaptors complex, the coiled-coil protein ATG25, and the sterol glucosyltransferase ATG26. ATG26 is necessary for the degradation of medium peroxisomes. It contains 2 GRAM domains and a single PH domain. PH domains are only found in eukaryotes. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 93 matched cddid_all.tbl CDD cd13217 cd13217 275404 PH-GRAM1_TCB1D8_TCB1D9_family TCB1D8 and TCB1D9 family Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain, repeat 1. TBC1D8, TBC1D8B, TBC1D9 and TBC1D9B may act as a GTPase-activating proteins for Rab family protein(s). They all contain an N-terminal PH-GRAM domain and a C-terminal Rab-GTPase-TBC (Tre-2, BUB2p, and Cdc16p) domain. This cd contains the first repeat of the PH-GRAM domain. The GRAM domain is found in glucosyltransferases, myotubularins and other putative membrane-associated proteins. The GRAM domain is part of a larger motif with a pleckstrin homology (PH) domain fold. 99 matched cddid_all.tbl CDD cd13218 cd13218 275405 PH-GRAM2_TCB1D8_TCB1D9_family TCB1D8 and TCB1D9 family Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain, repeat 2. TBC1D8, TBC1D8B, TBC1D9 and TBC1D9B may act as a GTPase-activating proteins for Rab family protein(s). They all contain an N-terminal PH-GRAM domain and a C-terminal Rab-GTPase-TBC (Tre-2, BUB2p, and Cdc16p) domain. This cd contains the second repeat of the PH-GRAM domain. The GRAM domain is found in glucosyltransferases, myotubularins and other putative membrane-associated proteins. The GRAM domain is part of a larger motif with a pleckstrin homology (PH) domain fold. 96 matched cddid_all.tbl CDD cd13219 cd13219 270039 PH-GRAM_C2-GRAM C2 and GRAM domain-containing protein Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. C2GRAM contains two N-terminal C2 domains followed by a single PH-GRAM domain. Since it contains both of these domains it is assumed that this gene cross-links both calcium and phosphoinositide signaling pathways. In general he C2 domain is involved in binding phospholipids in a calcium dependent manner or calcium independent manner. The GRAM domain is found in glucosyltransferases, myotubularins and other putative membrane-associated proteins. The GRAM domain is part of a larger motif with a pleckstrin homology (PH) domain fold. 111 matched cddid_all.tbl CDD cd13220 cd13220 275406 PH-GRAM_GRAMDC GRAM domain-containing protein (GRAMDC) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. The GRAMDC proteins are membrane proteins. Nothing is known about its function. Members include: GRAMDC1A, GRAMDC1B, GRAMDC1C, GRAMDC2, GRAMDC3, GRAMDC4, and GRAMDC-like proteins. All of the members, except for GRAMDC4 are included in this hierarchy. Each contains a single PH-GRAM domain at their N-terminus. The GRAM domain is found in glucosyltransferases, myotubularins and other putative membrane-associated proteins. The GRAM domain is part of a larger motif with a pleckstrin homology (PH) domain fold. 94 matched cddid_all.tbl CDD cd13221 cd13221 270041 PH-GRAM_GRAMDC4 GRAM domain-containing protein 4 (GRAMDC4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. GRAMDC4 is a membrane protein. Nothing is known about its function. Paralogs include: GRAMDC1A, GRAMDC1B, GRAMDC1C, GRAMDC2, GRAMDC3, and GRAMDC-like proteins. It contains a single PH-GRAM domain at its N-terminus. The GRAM domain is found in glucosyltransferases, myotubularins and other putative membrane-associated proteins. The GRAM domain is part of a larger motif with a pleckstrin homology (PH) domain fold. 104 matched cddid_all.tbl CDD cd13222 cd13222 270042 PH-GRAM_GEM GLABRA 2 expression modulator (GEM) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. GEM interacts with CDT1, a pre-replication complex component that is involved in DNA replication, and with TTG1 (Transparent Testa GLABRA 1), a transcriptional regulator of epidermal cell fate. GEM controls the level of histone H3K9 methylation at the promoters of the GLABRA 2 and CAPRICE (CPC) genes, which are essential for epidermis patterning. GEM also regulates cell division in different root cell types. GEM regulates proliferation-differentiation decisions by integrating DNA replication, cell division and transcriptional controls. The GRAM domain is found in glucosyltransferases, myotubularins and other putative membrane-associated proteins. The GRAM domain is part of a larger motif with a pleckstrin homology (PH) domain fold. 109 matched cddid_all.tbl CDD cd13223 cd13223 275407 PH-GRAM_MTM-like Myotubularian 1 and related proteins Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase. MTM1, MTMR1, and MTMR2 are members of the myotubularin protein phosphatase gene family. They contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an active PTP domain, a SET-interaction domain, and a C-terminal coiled-coil region. In addition MTMR1 (Myotubularian related 1 protein) and MTMR2 (Myotubularian related 2 protein) contain a C-terminal PDZ domain. Mutations in MTMR2 are a cause of Charcot-Marie-Tooth disease type 4B, an autosomal recessive demyelinating neuropathy. The protein can self-associate and form heteromers with MTMR5 and MTMR12. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The PH domain family possesses multiple functions including the ability to bind phosphoinositides via its beta1/beta2, beta3/beta4, and beta6/beta7 connecting loops and to other proteins. However, no phosphoinositide binding sites have been found for the MTMRs to date. 100 matched cddid_all.tbl CDD cd13224 cd13224 270044 PH_Net1 Neuroepithelial cell transforming 1 Pleckstrin homology (PH) domain. Net1 (also called ArhGEF8) is part of the family of Rho guanine nucleotide exchange factors. Members of this family activate Rho proteins by catalyzing the exchange of GDP for GTP. The protein encoded by this gene interacts with RhoA within the cell nucleus and may play a role in repairing DNA damage after ionizing radiation. Net1 binds to caspase activation and recruitment domain (CARD)- and membrane-associated guanylate kinase-like domain-containing (CARMA) proteins and regulates nuclear factor kB activation. Net1 contains a RhoGEF domain N-terminal to a single PH domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 135 matched cddid_all.tbl CDD cd13225 cd13225 270045 PH-like_bacteria Pleckstrin homology (PH)-like domains in bacteria (PHb). Pleckstrin homology (PH) domains were first identified in eukaryotic proteins. Recently PH-like domains have been identified in bacteria as well. These PHb form dome-shaped oligomeric rings with a conserved hydrophilic surface at the intersection of the beta-strands of adjacent protomers that likely mediates protein-protein interactions. It is now thought that the PH domain superfamily is more widespread than previous thought and appears to have existed before prokaryotes and eukaryotes diverged. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 95 matched cddid_all.tbl CDD cd13226 cd13226 275408 PH-GRAM-like_Eap45 Pleckstrin homology-like domain or GLUE (GRAM-like ubiquitin-binding in Eap45) domain of Eap45. ESCRT complexes form the main machinery driving protein sorting from endosomes to lysosomes. Human/yeast ESCRT-I consists of Tsg101/Vps23, Vps28/Vps28, and a Vps37 homolog/Vps37. Human/yeast ESCRT-II is composed of EAP20/Vps25, EAP30/Vps22, and EAP45/Vps36. Yeast ESCRT-III consists Vps2, Vps20, Vps24, and Snf7 subunits. In contrast, there are three Human paralogs of Snf7 (hSnf7-1/CHMP4A, hSnf7-2/CHMP4B, and hSnf7-3/CHMP4C) and two paralogs of Vps2 (CHMP2A and CHMP2B). Yeast ESCRT-I links directly to ESCRT-II, through a tight interaction of Vps28 (ESCRT-I) with the yeast-specific zinc-finger insertion within the GLUE domain of Vps36. The Vps36 subunit (ESCRT-II) binds ubiquitin using one of its two NZF zinc fingers in its N-terminal region. Human Vps36, EAP45, also binds ubiquitin despite having no NZF domain. Instead, mammalian ESCRT-II interacts with Ub through the Eap45 GLUE domain directly. While yeast Vps36 GLUE shows a preference for the singly phosphorylated PI(3)P, while Eap45 GLUE preferentially binds the triply phosphorylated phosphatidylinositol PI(3,4,5)P3. Structurally, Eap45 GLUE only has a PH-like fold since it lacks the secondary structure element corresponding to the 4 strand, unlike that of yeast Vps36 GLUE. ESCRT-II also interacts with ESCRT-III via a EAP20(Vps25)/CHMP6(Vps20) interaction. The interactions of ESCRT-II GLUE domain with membranes, ESCRT-I, and ubiquitin are critical for ubiquitinated cargo progression from early to late endosomes. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 129 matched cddid_all.tbl CDD cd13227 cd13227 275409 PH-GRAM-like_Vps36 Pleckstrin homology-like domain or GLUE (GRAM-like ubiquitin-binding in Eap45) domain of Vps36. ESCRT complexes form the main machinery driving protein sorting from endosomes to lysosomes. Yeast/human ESCRT-I consists of Vps23/Tsg101, Vps28/Vps28, and Vps37/Vps37 homolog. Yeast/human ESCRT-II is composed of Vps25/EAP20, Vps22/EAP30, and Vps36/EAP45. Yeast ESCRT-III consists Vps2, Vps20, Vps24, and Snf7 subunits. In contrast, there are three human paralogs of Snf7 (hSnf7-1/CHMP4A, hSnf7-2/CHMP4B, and hSnf7-3/CHMP4C) and two paralogs of Vps2 (CHMP2A and CHMP2B). Yeast ESCRT-I links directly to ESCRT-II, through a tight interaction of Vps28 (ESCRT-I) with the yeast-specific zinc-finger insertion within the GLUE domain of Vps36. The Vps36 subunit (ESCRT-II) binds ubiquitin using one of its two NZF zinc fingers in its N-terminal region. Human Vps36, EAP45, also binds ubiquitin despite having no NZF domain. Instead, mammalian ESCRT-II interacts with Ub through the Eap45 GLUE domain itself. The yeast Vps36 GLUE has a complete PH domain, wherease Eap45 GLUE only has a PH-like fold since it lacks the secondary structure element corresponding to the 4 strand. ESCRT-II also interacts with ESCRT-III via a Vps25(EAP20)/Vps20(CHMP6) interaction. Structure 2CAY is missing this insertion that contains 2 NZF zinc fingers. It is a split PH domain, with a noncanonical lipid binding pocket that binds PI(3)P. The interactions of ESCRT-II GLUE domain with membranes, ESCRT-I, and ubiquitin are critical for ubiquitinated cargo progression from early to late endosomes. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 119 matched cddid_all.tbl CDD cd13228 cd13228 270048 PHear_NECAP NECAP (adaptin-ear-binding coat-associated protein) Plextrin Homology (PH) fold with ear-like function (PHear) domain. NECAPs are alpha-ear-binding proteins that enrich on clathrin-coated vesicles (CCVs). NECAP 1 is expressed in brain and non-neuronal tissues and cells while NECAP 2 is ubiquitously expressed. The PH-like domain of NECAPs is a protein-binding interface that mimics the FxDxF motif binding properties of the alpha-ear and is called PHear (PH fold with ear-like function) domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 120 matched cddid_all.tbl CDD cd13229 cd13229 270049 PH_TFIIH Transcription Factor II H (TFIIH) Pleckstrin homology (PH) domain. The transcription factor II H (TFIIH) is one of the general transcription factors (GTFs) known to be a target of the transactivation domain (TAD) of p53. Human TFIIH and its homologous yeast counterpart (factor b) are composed of ten subunits that can be divided into two groups, the core TFIIH (XPB/Ssl2, p62/Tfb1, p52/Tfb2, p44/Ssl1, p34/Tfb4, and TTDA/Tfb5 in human/yeast) and the CAK complex (cdk7/Kin28, cyclin H/Ccl1, and MAT1/Tfb3). These two complexes are linked by the XPD/Rad3 subunit. The helicase activities of XPB and XPD are essential to the formation of the open complex during transcription initiation and the kinase activity of cdk7 phosphorylates the C-terminal domain (CTD) of the RNA Pol II largest subunit, enabling RNA Pol II to progress from the initiation phase to the elongation phase of transcription. The PH domain of p62/Tfb1 has been shown to interact with herpes simplex virus protein 16 (VP16) TAD and the binding of p53 TAD is mediated by the TAD2 subdomain. TFIIE recruits TFIIH to complete the preinitiation complex (PIC) formation and regulates enzymatic activities of TFIIH. The PH domain of the human TFIIH p62 subunit binds to the C-terminal acidic (AC) domain of the human TFIIEalpha subunit. This interaction could be a switch to replace p53 with TFIIE on TFIIH in transcription. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 93 matched cddid_all.tbl CDD cd13230 cd13230 270050 PH1_SSRP1-like Structure Specific Recognition protein 1 (SSRP1) Pleckstrin homology (PH) domain, repeat 1. SSRP1 is a component of FACT (facilitator of chromatin transcription), an essential chromatin reorganizing factor. In yeast FACT (yFACT) is composed of three proteins: Spt16/Cdc68, Pob3, and Nhp6. In metazoans the Pob3 and Nhp6 orthologs are fused to form SSRP1/T160 in human and mouse, respectively. The middle domain of the Pob3 subunit (Pob3-M) has an unusual double pleckstrin homology (PH) architecture. yFACT interacts in a physiologically important way with the central single-strand DNA binding factor RPA to promote a step in DNA Replication. Coordinated function by yFACT and RPA is important during nucleosome deposition. These results support the model that the FACT family has an essential role in constructing nucleosomes during DNA replication, and suggest that RPA contributes to this process. Members of this cd are composed of the first PH-like repeat. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 137 matched cddid_all.tbl CDD cd13231 cd13231 270051 PH2_SSRP1-like Structure Specific Recognition protein 1 (SSRP1) Pleckstrin homology (PH) domain, repeat 2. SSRP1 is a component of FACT (facilitator of chromatin transcription), an essential chromatin reorganizing factor. In yeast FACT (yFACT) is composed of three proteins: Spt16/Cdc68, Pob3, and Nhp6. In metazoans the Pob3 and Nhp6 orthologs are fused to form SSRP1/T160 in human and mouse, respectively.The middle domain of the Pob3 subunit (Pob3-M) has an unusual double pleckstrin homology (PH) architecture. yFACT interacts in a physiologically important way with the central single-strand DNA binding factor RPA to promote a step in DNA Replication. Coordinated function by yFACT and RPA is important during nucleosome deposition. These results support the model that the FACT family has an essential role in constructing nucleosomes during DNA replication, and suggest that RPA contributes to this process. Members of this cd are composed of the second PH-like repeat. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 100 matched cddid_all.tbl CDD cd13232 cd13232 270052 Ig-PH_SCAB1 Stomatal Closure Related Actin-Binding Protein 1 Pleckstrin homology-like domain. SCAB1 is an actin-binding protein that interacts with actin filaments and regulates stomatal movement. SCAB1 is composed of an actin-binding domain, two coiled-coil (CC) domains, and a fused immunoglobulin (Ig) and PH (Ig-PH) domain. SCAB1 homologs are widely present, often in multiple copies (three in Arabidopsis), in plants including eudicots, monocots, ferns and mosses, but are not found in algae and non-plant species. The C-terminal PH domain binds weakly with inositol phosphates via an atypical basic surface patch. SCAB1 forms a dimeric structure via its coiled-coil domains. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 119 matched cddid_all.tbl CDD cd13233 cd13233 270053 PH_ARHGAP9-like Beta-spectrin pleckstrin homology (PH) domain. ARHGAP family genes encode Rho/Rac/Cdc42-like GTPase activating proteins with RhoGAP domain. The ARHGAP members here all have a PH domain upstream of their C-terminal RhoGAP domain. Some have additional N-terminal SH3 and WW domains. The members here include: ARHGAP9, ARHGAP12, ARHGAP15, and ARHGAP27. ARHGAP27 and ARHGAP12 shared the common-domain structure, consisting of SH3, WW, PH, and RhoGAP domains. The PH domain of ArhGAP9 employs a non-canonical phosphoinositide binding mechanism, a variation of the spectrin- Ins(4,5)P2-binding mode, that gives rise to a unique PI binding profile, namely a preference for both PI(4,5)P2 and the PI 3-kinase products PI(3,4,5)P3 and PI(3,4)P2. This lipid binding mechanism is also employed by the PH domain of Tiam1 and Slm1. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 110 matched cddid_all.tbl CDD cd13234 cd13234 270054 PHsplit_PLC_gamma Phospholipase C-gamma Split pleckstrin homology (PH) domain. PLC-gamma (PLCgamma) is activated by receptor and non-receptor tyrosine kinases due to the presence of its SH2 and SH3 domains. There are two main isoforms of PLC-gamma expressed in human specimens, PLC-gamma1 and PLC-gamma2. PLC-gamma consists of an N-terminal PH domain, a EF hand domain, a catalytic domain split into X and Y halves internal to which is a PH domain split by two SH2 domains and a single SH3 domain, and a C-terminal C2 domain. The split PH domain is present in this hierarchy. PLCs (EC 3.1.4.3) play a role in the initiation of cellular activation, proliferation, differentiation and apoptosis. They are central to inositol lipid signalling pathways, facilitating intracellular Ca2+ release and protein kinase C (PKC) activation. Specificaly, PLCs catalyze the cleavage of phosphatidylinositol-4,5-bisphosphate (PIP2) and result in the release of 1,2-diacylglycerol (DAG) and inositol 1,4,5-triphosphate (IP3). These products trigger the activation of protein kinase C (PKC) and the release of Ca2+ from intracellular stores. There are fourteen kinds of mammalian phospholipase C proteins which are are classified into six isotypes (beta, gamma, delta, epsilon, zeta, eta). PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 105 matched cddid_all.tbl CDD cd13235 cd13235 270055 PH2_FARP1-like FERM, RhoGEF and pleckstrin domain-containing protein 1 and related proteins Pleckstrin Homology (PH) domain, repeat 2. Members here include FARP1 (also called Chondrocyte-derived ezrin-like protein; PH domain-containing family C member 2), FARP2 (also called FIR/FERM domain including RhoGEF; FGD1-related Cdc42-GEF/FRG), and FARP6 (also called Zinc finger FYVE domain-containing protein 24). They are members of the Dbl family guanine nucleotide exchange factors (GEFs) which are upstream positive regulators of Rho GTPases. Little is known about FARP1 and FARP6, though FARP1 has increased expression in differentiated chondrocytes. FARP2 is thought to regulate neurite remodeling by mediating the signaling pathways from membrane proteins to Rac. It is found in brain, lung, and testis, as well as embryonic hippocampal and cortical neurons. FARP1 and FARP2 are composed of a N-terminal FERM domain, a proline-rich (PR) domain, Dbl-homology (DH), and two C-terminal PH domains. FARP6 is composed of Dbl-homology (DH), and two C-terminal PH domains separated by a FYVE domain. This hierarchy contains the second PH repeat. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 98 matched cddid_all.tbl CDD cd13236 cd13236 270056 PH2_FGD1-4 FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins pleckstrin homology (PH) domain, C-terminus. In general, FGDs have a RhoGEF (DH) domain, followed by an N-terminal PH domain, a FYVE domain and a C-terminal PH domain. All FGDs are guanine nucleotide exchange factors that activates the Rho GTPase Cdc42, an important regulator of membrane trafficking. The RhoGEF domain is responsible for GEF catalytic activity, while the N-terminal PH domain is involved in intracellular targeting of the DH domain. Not much is known about FGD2. FGD1 is the best characterized member of the group with mutations here leading to the X-linked disorder known as faciogenital dysplasia (FGDY). Both FGD1 and FGD3 are targeted by the ubiquitin ligase SCF(FWD1/beta-TrCP) upon phosphorylation of two serine residues in its DSGIDS motif and subsequently degraded by the proteasome. However, FGD1 and FGD3 induced significantly different morphological changes in HeLa Tet-Off cells and while FGD1 induced long finger-like protrusions, FGD3 induced broad sheet-like protrusions when the level of GTP-bound Cdc42 was significantly increased by the inducible expression of FGD3. They also reciprocally regulated cell motility in inducibly expressed in HeLa Tet-Off cells, FGD1 stimulated cell migration while FGD3 inhibited it. FGD1 and FGD3 therefore play different roles to regulate cellular functions, even though their intracellular levels are tightly controlled by the same destruction pathway through SCF(FWD1/beta-TrCP). FGD4 is one of the genes associated with Charcot-Marie-Tooth neuropathy type 4 (CMT4), a group of progressive motor and sensory axonal and demyelinating neuropathies that are distinguished from other forms of CMT by autosomal recessive inheritance. Those affected have distal muscle weakness and atrophy associated with sensory loss and, frequently, pes cavus foot deformity. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 105 matched cddid_all.tbl CDD cd13237 cd13237 270057 PH2_FGD5_FGD6 FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins 5 and 6 pleckstrin homology (PH) domain, C-terminus. FGD5 regulates promotes angiogenesis of vascular endothelial growth factor (VEGF) in vascular endothelial cells, including network formation, permeability, directional movement, and proliferation. The specific function of FGD6 is unknown. In general, FGDs have a RhoGEF (DH) domain, followed by a PH domain, a FYVE domain and a C-terminal PH domain. All FGDs are guanine nucleotide exchange factors that activate the Rho GTPase Cdc42, an important regulator of membrane trafficking. The RhoGEF domain is responsible for GEF catalytic activity, while the PH domain is involved in intracellular targeting of the DH domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 91 matched cddid_all.tbl CDD cd13238 cd13238 270058 PH2_FGD4_insect-like FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 4 pleckstrin homology (PH) domain, C-terminus, in insect and related arthropods. In general, FGDs have a RhoGEF (DH) domain, followed by an N-terminal PH domain, a FYVE domain and a C-terminal PH domain. All FGDs are guanine nucleotide exchange factors that activates the Rho GTPase Cdc42, an important regulator of membrane trafficking. The RhoGEF domain is responsible for GEF catalytic activity, while the N-terminal PH domain is involved in intracellular targeting of the DH domain. FGD4 is one of the genes associated with Charcot-Marie-Tooth neuropathy type 4 (CMT4), a group of progressive motor and sensory axonal and demyelinating neuropathies that are distinguished from other forms of CMT by autosomal recessive inheritance. Those affected have distal muscle weakness and atrophy associated with sensory loss and, frequently, pes cavus foot deformity. This cd contains insects, crustaceans, and chelicerates. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 97 matched cddid_all.tbl CDD cd13239 cd13239 270059 PH_Obscurin Obscurin pleckstrin homology (PH) domain. Obscurin (also called Obscurin-RhoGEF; Obscurin-myosin light chain kinase/Obscurin-MLCK) is a giant muscle protein that is concentrated at the peripheries of Z-disks and M-lines. It binds small ankyrin I, a component of the sarcoplasmic reticulum (SR) membrane. It is associated with the contractile apparatus through binding with titin and sarcomeric myosin. It plays important roles in the organization and assembly of the myofibril and the SR. Obscurin has been observed as alternatively-spliced isoforms. The major isoform in sleletal muscle, approximately 800 kDa in size, is composed of many adhesion modules and signaling domains. It harbors 49 Ig and 2 FNIII repeats at the N-terminues, a complex middle region with additional Ig domains, an IQ motif, and a conserved SH3 domain near RhoGEF and PH domains, and a non-modular C-terminus with phosphorylation motifs. The obscurin gene also encodes two kinase domains, which are not part of the 800 kDa form of the protein, but is part of smaller spliced products that present in heart muscle. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 125 matched cddid_all.tbl CDD cd13240 cd13240 270060 PH1_Kalirin_Trio_like Triple functional domain pleckstrin homology pleckstrin homology (PH) domain, repeat 1. RhoGEFs, Kalirin and Trio, the mammalian homologs of Drosophila Trio and Caenorhabditis elegans UNC-73 regulate a novel step in secretory granule maturation. Their signaling modulates the extent to which regulated cargo enter and remain in the regulated secretory pathway. This allows for fine tuning of peptides released by a single secretory cell type with impaired signaling leading to pathological states. Trio plays an essential role in regulating the actin cytoskeleton during axonal guidance and branching. Kalirin and Trio are encoded by separate genes in mammals and by a single one in invertebrates. Kalirin and Trio share the same complex multidomain structure and display several splice variants. The longest Kalirin and Trio proteins have a Sec14 domain, a stretch of spectrin repeats, a RhoGEF(DH)/PH cassette (also called GEF1), an SH3 domain, a second RhoGEF(DH)/PH cassette (also called GEF2), a second SH3 domain, Ig/FNIII domains, and a kinase domain. The first RhoGEF(DH)/PH cassette catalyzes exchange on Rac1 and RhoG while the second RhoGEF(DH)/PH cassette is specific for RhoA. Kalirin and Trio are closely related to p63RhoGEF and have PH domains of similar function. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. 123 matched cddid_all.tbl CDD cd13241 cd13241 270061 PH2_Kalirin_Trio_p63RhoGEF p63RhoGEF pleckstrin homology (PH) domain, repeat 2. The guanine nucleotide exchange factor p63RhoGEF is an effector of the heterotrimeric G protein, Galphaq and linking Galphaq-coupled receptors (GPCRs) to the activation of RhoA. The Dbl(DH) and PH domains of p63RhoGEF interact with the effector-binding site and the C-terminal region of Galphaq and appear to relieve autoinhibition of the catalytic DH domain by the PH domain. Trio, Duet, and p63RhoGEF are shown to constitute a family of Galphaq effectors that appear to activate RhoA both in vitro and in intact cells. Dbs is a guanine nucleotide exchange factor (GEF), which contains spectrin repeats, a rhoGEF (DH) domain and a PH domain. The Dbs PH domain participates in binding to both the Cdc42 and RhoA GTPases. Trio plays an essential role in regulating the actin cytoskeleton during axonal guidance and branching. Trio is a multidomain signaling protein that contains two RhoGEF(DH)-PH domains in tandem. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 140 matched cddid_all.tbl CDD cd13242 cd13242 270062 PH_puratrophin-1 Puratrophin-1 pleckstrin homology (PH) domain. Puratrophin-1 (also called Purkinje cell atrophy-associated protein 1 or PLEKHG4/Pleckstrin homology domain-containing family G member 4) contains a spectrin repeat, a RhoGEF (DH) domain, and a PH domain. It is thought to function in intracellular signaling and cytoskeleton dynamics at the Golgi. Puratrophin-1 is expressed in kidney, Leydig cells in the testis, epithelial cells in the prostate gland and Langerhans islet in the pancreas. A single nucleotide substitution in the puratrophin-1 gene were once thought to result in autosomal dominant cerebellar ataxia (ADCA), but now it has been demonstrated that this ataxia is a result of defects in the BEAN gene. Puratrophin contains a domain architecture similar to that of Dbl family members Dbs and Trio. Dbs is a guanine nucleotide exchange factor (GEF), which contains spectrin repeats, a RhoGEF (DH) domain and a PH domain. The Dbs PH domain participates in binding to both the Cdc42 and RhoA GTPases. Trio plays an essential role in regulating the actin cytoskeleton during axonal guidance and branching. Trio is a multidomain signaling protein that contains two RhoGEF(DH)-PH domains in tandem. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 136 matched cddid_all.tbl CDD cd13243 cd13243 270063 PH_PLEKHG1_G2_G3 Pleckstrin homology domain-containing family G members 1, 2, and 3 pleckstrin homology (PH) domain. PLEKHG1 (also called ARHGEF41), PLEKHG2 (also called ARHGEF42 or CLG/common-site lymphoma/leukemia guanine nucleotide exchange factor2), and PLEKHG3 (also called ARHGEF43) have RhoGEF DH/double-homology domains in tandem with a PH domain which is involved in phospholipid binding. They function as a guanine nucleotide exchange factor (GEF) and are involved in the regulation of Rho protein signal transduction. Mutations in PLEKHG1 have been associated panic disorder (PD), an anxiety disorder characterized by panic attacks and anticipatory anxiety. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 147 matched cddid_all.tbl CDD cd13244 cd13244 270064 PH_PLEKHG5_G6 Pleckstrin homology domain-containing family G member 5 and 6 pleckstrin homology (PH) domain. PLEKHG5 has a RhoGEF DH/double-homology domain in tandem with a PH domain which is involved in phospholipid binding. PLEKHG5 activates the nuclear factor kappa B (NFKB1) signaling pathway. Mutations in PLEKHG5 are associated with autosomal recessive distal spinal muscular atrophy. PLEKHG6 (also called MyoGEF) has no known function to date. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 100 matched cddid_all.tbl CDD cd13245 cd13245 270065 PH_PLEKHG7 Pleckstrin homology domain-containing family G member 7 pleckstrin homology (PH) domain. PLEKHG7 has a RhoGEF DH/double-homology domain in tandem with a PH domain which is involved in phospholipid binding. PLEKHG7 is proposed to functions as a guanine nucleotide exchange factor (GEF) and is involved in the regulation of Rho protein signal transduction. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 128 matched cddid_all.tbl CDD cd13246 cd13246 270066 PH_Scd1 Shape and Conjugation Deficiency 1 Pleckstrin homology (PH) domain. Fission yeast Scd1 is an exchange factor for Cdc42 and an effector of Ras1, the homolog of the human H-Ras. Scd2/Bem1 mediates Cdc42 activation by binding to Scd1/Cdc24 and to Cdc42. Ras1 regulates Scd1/Cdc24/Ral1, which is a putative guanine nucleotide exchange factor for Cdc42, a member of the Rho family of Ras-like proteins. Cdc42 then activates the Shk1/Orb2 protein kinase. Scd1 interacts with Klp5 and Klp6 kinesins to mediate cytokinesis. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 148 matched cddid_all.tbl CDD cd13247 cd13247 270067 BAR-PH_APPL Adaptor protein containing PH domain, PTB domain, and Leucine zipper motif Bin1/amphiphysin/Rvs167 (BAR)-Pleckstrin homology (PH) domain. APPL (also called DCC-interacting protein (DIP)-13alpha) interacts with oncoprotein serine/threonine kinase AKT2, tumor suppressor protein DCC (deleted in colorectal cancer), Rab5, GIPC (GAIP-interacting protein, C terminus), human follicle-stimulating hormone receptor (FSHR), and the adiponectin receptors AdipoR1 and AdipoR2. There are two isoforms of human APPL: APPL1 and APPL2, which share about 50% sequence identity. APPL has a BAR and a PH domain near its N terminus, and the two domains are thought to function as a unit (BAR-PH domain). C-terminal to this is a PTB domain. Lipid binding assays show that the BAR, PH, and PTB domains can bind phospholipids. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 125 matched cddid_all.tbl CDD cd13248 cd13248 270068 PH_PEPP1_2_3 Phosphoinositol 3-phosphate binding proteins 1, 2, and 3 pleckstrin homology (PH) domain. PEPP1 (also called PLEKHA4/PH domain-containing family A member 4 and RHOXF1/Rhox homeobox family member 1), and related homologs PEPP2 (also called PLEKHA5/PH domain-containing family A member 5) and PEPP3 (also called PLEKHA6/PH domain-containing family A member 6), have PH domains that interact specifically with PtdIns(3,4)P3. Other proteins that bind PtdIns(3,4)P3 specifically are: TAPP1 (tandem PH-domain-containing protein-1) and TAPP2], PtdIns3P AtPH1, and Ptd- Ins(3,5)P2 (centaurin-beta2). All of these proteins contain at least 5 of the 6 conserved amino acids that make up the putative phosphatidylinositol 3,4,5- trisphosphate-binding motif (PPBM) located at their N-terminus. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 104 matched cddid_all.tbl CDD cd13249 cd13249 270069 PH_rhotekin2 Anillin Pleckstrin homology (PH) domain. Anillin (Rhotekin/RTKN; also called PLEKHK/Pleckstrin homology domain-containing family K) is an actin binding protein involved in cytokinesis. It interacts with GTP-bound Rho proteins and results in the inhibition of their GTPase activity. Dysregulation of the Rho signal transduction pathway has been implicated in many forms of cancer. Anillin proteins have a N-terminal HRI domain/ACC (anti-parallel coiled-coil) finger domain or Rho-binding domain binds small GTPases from the Rho family. The C-terminal PH domain helps target anillin to ectopic septin containing foci. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 111 matched cddid_all.tbl CDD cd13250 cd13250 270070 PH_ACAP ArfGAP with coiled-coil, ankyrin repeat and PH domains Pleckstrin homology (PH) domain. ACAP (also called centaurin beta) functions both as a Rab35 effector and as an Arf6-GTPase-activating protein (GAP) by which it controls actin remodeling and membrane trafficking. ACAP contain an NH2-terminal bin/amphiphysin/Rvs (BAR) domain, a phospholipid-binding domain, a PH domain, a GAP domain, and four ankyrin repeats. The AZAPs constitute a family of Arf GAPs that are characterized by an NH2-terminal pleckstrin homology (PH) domain and a central Arf GAP domain followed by two or more ankyrin repeats. On the basis of sequence and domain organization, the AZAP family is further subdivided into four subfamilies: 1) the ACAPs contain an NH2-terminal bin/amphiphysin/Rvs (BAR) domain (a phospholipid-binding domain that is thought to sense membrane curvature), a single PH domain followed by the GAP domain, and four ankyrin repeats; 2) the ASAPs also contain an NH2-terminal BAR domain, the tandem PH domain/GAP domain, three ankyrin repeats, two proline-rich regions, and a COOH-terminal Src homology 3 domain; 3) the AGAPs contain an NH2-terminal GTPase-like domain (GLD), a split PH domain, and the GAP domain followed by four ankyrin repeats; and 4) the ARAPs contain both an Arf GAP domain and a Rho GAP domain, as well as an NH2-terminal sterile-a motif (SAM), a proline-rich region, a GTPase-binding domain, and five PH domains. PMID 18003747 and 19055940 Centaurin can bind to phosphatidlyinositol (3,4,5)P3. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 98 matched cddid_all.tbl CDD cd13251 cd13251 270071 PH_ASAP ArfGAP with SH3 domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain. ASAPs (ASAP1, ASAP2, and ASAP3) function as an Arf-specific GAPs, participates in rhodopsin trafficking, is associated with tumor cell metastasis, modulates phagocytosis, promotes cell proliferation, facilitates vesicle budding, Golgi exocytosis, and regulates vesicle coat assembly via a Bin/Amphiphysin/Rvs domain. ASAPs contain an NH2-terminal BAR domain, a tandem PH domain/GAP domain, three ankyrin repeats, two proline-rich regions, and a COOH-terminal Src homology 3 (SH3) domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 108 matched cddid_all.tbl CDD cd13252 cd13252 270072 PH1_ADAP ArfGAP with dual PH domains Pleckstrin homology (PH) domain, repeat 1. ADAP (also called centaurin alpha) is a phophatidlyinositide binding protein consisting of an N-terminal ArfGAP domain and two PH domains. In response to growth factor activation, PI3K phosphorylates phosphatidylinositol 4,5-bisphosphate to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 1 is recruited to the plasma membrane following growth factor stimulation by specific binding of its PH domain to phosphatidylinositol 3,4,5-trisphosphate. Centaurin alpha 2 is constitutively bound to the plasma membrane since it binds phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol 3,4,5-trisphosphate with equal affinity. This cd contains the first PH domain repeat. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 109 matched cddid_all.tbl CDD cd13253 cd13253 270073 PH1_ARAP ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 1. ARAP proteins (also called centaurin delta) are phosphatidylinositol 3,4,5-trisphosphate-dependent GTPase-activating proteins that modulate actin cytoskeleton remodeling by regulating ARF and RHO family members. They bind phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) and phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4,5)P2) binding. There are 3 mammalian ARAP proteins: ARAP1, ARAP2, and ARAP3. All ARAP proteins contain a N-terminal SAM (sterile alpha motif) domain, 5 PH domains, an ArfGAP domain, 2 ankyrin domain, A RhoGap domain, and a Ras-associating domain. This hierarchy contains the first PH domain in ARAP. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 94 matched cddid_all.tbl CDD cd13254 cd13254 270074 PH2_ARAP ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 2. ARAP proteins (also called centaurin delta) are phosphatidylinositol 3,4,5-trisphosphate-dependent GTPase-activating proteins that modulate actin cytoskeleton remodeling by regulating ARF and RHO family members. They bind phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) and phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4,5)P2) binding. There are 3 mammalian ARAP proteins: ARAP1, ARAP2, and ARAP3. All ARAP proteins contain a N-terminal SAM (sterile alpha motif) domain, 5 PH domains, an ArfGAP domain, 2 ankyrin domain, A RhoGap domain, and a Ras-associating domain. This hierarchy contains the second PH domain in ARAP. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 90 matched cddid_all.tbl CDD cd13255 cd13255 270075 PH_TAAP2-like Tandem PH-domain-containing protein 2 Pleckstrin homology (PH) domain. The binding of TAPP2 (also called PLEKHA2) adaptors to PtdIns(3,4)P(2), but not PI(3,4, 5)P3, function as negative regulators of insulin and PI3K signalling pathways (i.e. TAPP/utrophin/syntrophin complex). TAPP2 contains two sequential PH domains in which the C-terminal PH domain specifically binds PtdIns(3,4)P2 with high affinity. The N-terminal PH domain does not interact with any phosphoinositide tested. They also contain a C-terminal PDZ-binding motif that interacts with several PDZ-binding proteins, including PTPN13 (known previously as PTPL1 or FAP-1) as well as the scaffolding proteins MUPP1 (multiple PDZ-domain-containing protein 1), syntrophin and utrophin. The members here are most sequence similar to TAPP2 proteins, but may not be actual TAPP2 proteins. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 110 matched cddid_all.tbl CDD cd13256 cd13256 270076 PH3_ARAP ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 3. ARAP proteins (also called centaurin delta) are phosphatidylinositol 3,4,5-trisphosphate-dependent GTPase-activating proteins that modulate actin cytoskeleton remodeling by regulating ARF and RHO family members. They bind phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) and phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4,5)P2) binding. There are 3 mammalian ARAP proteins: ARAP1, ARAP2, and ARAP3. All ARAP proteins contain a N-terminal SAM (sterile alpha motif) domain, 5 PH domains, an ArfGAP domain, 2 ankyrin domain, A RhoGap domain, and a Ras-associating domain. This hierarchy contains the third PH domain in ARAP. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 110 matched cddid_all.tbl CDD cd13257 cd13257 270077 PH4_ARAP ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 4. ARAP proteins (also called centaurin delta) are phosphatidylinositol 3,4,5-trisphosphate-dependent GTPase-activating proteins that modulate actin cytoskeleton remodeling by regulating ARF and RHO family members. They bind phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) and phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4,5)P2) binding. There are 3 mammalian ARAP proteins: ARAP1, ARAP2, and ARAP3. All ARAP proteins contain a N-terminal SAM (sterile alpha motif) domain, 5 PH domains, an ArfGAP domain, 2 ankyrin domain, A RhoGap domain, and a Ras-associating domain. This hierarchy contains the fourth PH domain in ARAP. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 91 matched cddid_all.tbl CDD cd13258 cd13258 270078 PH_PLEKHJ1 Pleckstrin homology domain containing, family J member 1 Pleckstrin homology (PH) domain. PLEKHJ1 (also called GNRPX2/Guanine nucleotide-releasing protein x ). It contains a single PH domain. Very little information is known about PLEKHJ1. PLEKHJ1 has been shown to interact with IKBKG (inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase gamma) and KRT33B (keratin 33B). PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 123 matched cddid_all.tbl CDD cd13259 cd13259 270079 PH5_ARAP ArfGAP with RhoGAP domain, ankyrin repeat and PH domain Pleckstrin homology (PH) domain, repeat 5. ARAP proteins (also called centaurin delta) are phosphatidylinositol 3,4,5-trisphosphate-dependent GTPase-activating proteins that modulate actin cytoskeleton remodeling by regulating ARF and RHO family members. They bind phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) and phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4,5)P2) binding. There are 3 mammalian ARAP proteins: ARAP1, ARAP2, and ARAP3. All ARAP proteins contain a N-terminal SAM (sterile alpha motif) domain, 5 PH domains, an ArfGAP domain, 2 ankyrin domain, A RhoGap domain, and a Ras-associating domain. This hierarchy contains the five PH domain in ARAP. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 121 matched cddid_all.tbl CDD cd13260 cd13260 270080 PH_RASA1 RAS p21 protein activator (GTPase activating protein) 1 Pleckstrin homology (PH) domain. RASA1 (also called RasGap1 or p120) is a member of the RasGAP family of GTPase-activating proteins. RASA1 contains N-terminal SH2-SH3-SH2 domains, followed by two C2 domains, a PH domain, a RasGAP domain, and a BTK domain. Splice variants lack the N-terminal domains. It is a cytosolic vertebrate protein that acts as a suppressor of RAS via its C-terminal GAP domain function, enhancing the weak intrinsic GTPase activity of RAS proteins resulting in the inactive GDP-bound form of RAS, allowing control of cellular proliferation and differentiation. Additionally, it is involved in mitogenic signal transmission towards downstream interacting partners through its N-terminal SH2-SH3-SH2 domains. RASA1 interacts with a number of proteins including: G3BP1, SOCS3, ANXA6, Huntingtin, KHDRBS1, Src, EPHB3, EPH receptor B2, Insulin-like growth factor 1 receptor, PTK2B, DOK1, PDGFRB, HCK, Caveolin 2, DNAJA3, HRAS, GNB2L1 and NCK1. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 103 matched cddid_all.tbl CDD cd13261 cd13261 270081 PH_RasGRF1_2 Ras-specific guanine nucleotide-releasing factors 1 and 2 Pleckstrin homology (PH) domain. RasGRF1 (also called GRF1; CDC25Mm/Ras-specific nucleotide exchange factor CDC25; GNRP/Guanine nucleotide-releasing protein) and RasGRF2 (also called GRF2; Ras guanine nucleotide exchange factor 2) are a family of guanine nucleotide exchange factors (GEFs). They both promote the exchange of Ras-bound GDP by GTP, thereby regulating the RAS signaling pathway. RasGRF1 and RasGRF2 form homooligomers and heterooligomers. GRF1 has 3 isoforms and GRF2 has 2 isoforms. The longest isoforms of RasGRF1 and RasGRF2 contain the following domains: a Rho-GEF domain sandwiched between 2 PH domains, IQ domains, a REM (Ras exchanger motif) domain, and a Ras-GEF domainwhich gives them the capacity to activate both Ras and Rac GTPases in response to signals from a variety of neurotransmitter receptors. Their IQ domains allow them to act as calcium sensors to mediate the actions of NMDA-type and calcium-permeable AMPA-type glutamate receptors. GRF1 also mediates the action of dopamine receptors that signal through cAMP. GRF1 and GRF2 play strikingly different roles in regulating MAP kinase family members, neuronal synaptic plasticity, specific forms of learning and memory, and behavioral responses to psychoactive drugs. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 136 matched cddid_all.tbl CDD cd13262 cd13262 270082 PH_RasSynGAP-like Synaptic Ras-GTPase activating protein family Pleckstrin homology (PH) domain. The RasSynGAP family is composed of members: DAB2IP, nGAP, and SynGAP. Neuronal growth-associated proteins (nGAPs) are growth cone markers found in multiple types of neurons. There are many nGAPs including Cap1 (Adenylate cyclase-associated protein 1), Capzb (Capping protein (actin filament) muscle Z-line, beta), Clptm1 (Cleft lip and palate associated transmembrane protein 1), Cotl1 (Coactosin-like 1), Crmp1 (Collapsin response mediator protein 1), Cyfip1 (Cytoplasmic FMR1 interacting protein 1), Fabp7 (Fatty acid binding protein 7, brain), Farp2 (FERM, RhoGEF and pleckstrin domain protein 2), Gap43 (Growth associated protein 43), Gnao1 (Guanine nucleotide binding protein (G protein), alpha activating activity polypeptide O), Gnai2 (Guanine nucleotide binding protein (G protein), alpha inhibiting 2), Pacs1 (Phosphofurin acidic cluster sorting protein 1), Rtn1 (Reticulon 1), Sept2 (Septin 2), Snap25 (Synaptosomal-associated protein 25), Strap (Serine/threonine kinase receptor associated protein), Stx7 (Syntaxin 7), and Tmod2 (Tropomodulin 2). SynGAP, a neuronal Ras-GAP, has been shown display both Ras-GAP activity and Ras-related protein (Rap)-GAP activity. Saccharomyces cerevisiae Bud2 and GAP1 members CAPRI (Ca2+-promoted Ras inactivator) and RASAL (Ras-GTPase-activating-like protein) also possess this dual activity. Human DOC-2/DAB2-interacting protein (DAB2IP) is encoded by a tumor suppressor gene and a newly recognized member of the Ras-GTPase-activating family. DAB2IP is a critical component of many signal transduction pathways mediated by Ras and tumor necrosis factors including apoptosis pathways, and it is involved in the formation of many types of tumors. DAB2IP participates in regulation of gene expression and pluripotency of cells. It has been reported that DAB2IP was expressed in different tumor tissues. Little information is available concerning the expression levels of DAB2IP in normal tissues and cells, however, and no studies of its expression patterns during the development of human embryos have been reported. DAB2IP was expressed primarily in cell cytoplasm throughout the fetal development. The expression levels varied among tissues and different gestational ages. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 125 matched cddid_all.tbl CDD cd13263 cd13263 270083 PH_RhoGap25-like Rho GTPase activating protein 25 and related proteins Pleckstrin homology (PH) domain. RhoGAP25 (also called ArhGap25) like other RhoGaps are involved in cell polarity, cell morphology and cytoskeletal organization. They act as GTPase activators for the Rac-type GTPases by converting them to an inactive GDP-bound state and control actin remodeling by inactivating Rac downstream of Rho leading to suppress leading edge protrusion and promotes cell retraction to achieve cellular polarity and are able to suppress RAC1 and CDC42 activity in vitro. Overexpression of these proteins induces cell rounding with partial or complete disruption of actin stress fibers and formation of membrane ruffles, lamellipodia, and filopodia. This hierarchy contains RhoGAP22, RhoGAP24, and RhoGAP25. Members here contain an N-terminal PH domain followed by a RhoGAP domain and either a BAR or TATA Binding Protein (TBP) Associated Factor 4 (TAF4) domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 114 matched cddid_all.tbl CDD cd13264 cd13264 270084 PH_ITSN Intersectin Pleckstrin homology (PH) domain. ITSNs, an adaptor protein family, play a role in endo- and exocytosis, actin cytoskeleton rearrangement and signal transduction. There are two human ITSN genes: ITSN1 and ITSN2. They share significant sequence identity and a similar domain structure having both short and long isoforms produced by alternative splicing. The short isoform (ITSN-S) consists of two Eps15 homology domains (EH1 and EH2), a coiled-coil region (CCR) and five Src homology 3 domains (SH3A-E). The EH domains bind to Asn-Pro-Phe motifs and are implicated in endocytosis and vesicle transport. The SH3 domains bind to proline-rich sequences and are commonly found in proteins implicated in cell signalling pathways, cytoskeletal organization and membrane traffic. The long isoform (ITSN-L) contains three additional C-terminal domains, a Dbl homology domain (DH), a Pleckstrin homology domain (PH) and a C2 domain. The tandem DH-PH domains are present in all Dbl family of GEFs. ITSN acts specifically on Cdc42 through its DH domain with no portion of the PH domain making contact with Cdc42. This is in contrast to Dbs which requires the PH domain for full catalytic activity. The ITSN PH domain binds phosphoinositides. C2 domains are usually involved in Ca2+-dependent and Ca2+-independent phospholipid binding. There are more than 30 proteins that interact with ITSNs. ITSN-S is present in mammals, frogs, flies and nematodes, while ITSN-L is present only in vertebrates. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 132 matched cddid_all.tbl CDD cd13265 cd13265 270085 PH_evt Evectin Pleckstrin homology (PH) domain. There are 2 members of the evectin family (also called pleckstrin homology domain containing, family B): evt-1 (also called PLEKHB1) and evt-2 (also called PLEKHB2). evt-1 is specific to the nervous system, where it is expressed in photoreceptors and myelinating glia. evt-2 is widely expressed in both neural and nonneural tissues. Evectins possess a single N-terminal PH domain and a C-terminal hydrophobic region. evt-1 is thought to function as a mediator of post-Golgi trafficking in cells that produce large membrane-rich organelles. It is a candidate gene for the inherited human retinopathy autosomal dominant familial exudative vitreoretinopathy and a susceptibility gene for multiple sclerosis. evt-2 is essential for retrograde endosomal membrane transport from the plasma membrane (PM) to the Golgi. Two membrane trafficking pathways pass through recycling endosomes: a recycling pathway and a retrograde pathway that links the PM to the Golgi/ER. Its PH domain that is unique in that it specifically recognizes phosphatidylserine (PS), but not polyphosphoinositides. PS is an anionic phospholipid class in eukaryotic biomembranes, is highly enriched in the PM, and plays key roles in various physiological processes such as the coagulation cascade, recruitment and activation of signaling molecules, and clearance of apoptotic cells. PH domains are only found in eukaryotes. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 108 matched cddid_all.tbl CDD cd13266 cd13266 270086 PH_Skap_family Src kinase-associated phosphoprotein family Pleckstrin homology (PH) domain. Skap adaptor proteins couple receptors to cytoskeletal rearrangements. Src kinase-associated phosphoprotein of 55 kDa (Skap55)/Src kinase-associated phosphoprotein 1 (Skap1), Skap2, and Skap-homology (Skap-hom) have an N-terminal coiled-coil conformation, a central PH domain and a C-terminal SH3 domain. Their PH domains bind 3'-phosphoinositides as well as directly affecting targets such as in Skap55 where it directly affecting integrin regulation by ADAP and NF-kappaB activation or in Skap-hom where the dimerization and PH domains comprise a 3'-phosphoinositide-gated molecular switch that controls ruffle formation. PH domains are only found in eukaryotes. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 106 matched cddid_all.tbl CDD cd13267 cd13267 270087 PH_DOCK-D Dedicator of cytokinesis-D subfamily Pleckstrin homology (PH) domain. DOCK-D subfamily (also called Zizimin subfamily) consists of Dock9/Zizimin1, Dock10/Zizimin3, and Dock11/Zizimin2. DOCK-D has a N-terminal DUF3398 domain, a PH-like domain, a Dock Homology Region 1, DHR1 (also called CZH1), a C2 domain, and a C-terminal DHR2 domain (also called CZH2). Zizimin1 is enriched in the brain, lung, and kidney; zizimin2 is found in B and T lymphocytes, and zizimin3 is enriched in brain, lung, spleen and thymus. Zizimin1 functions in autoinhibition and membrane targeting. Zizimin2 is an immune-related and age-regulated guanine nucleotide exchange factor, which facilitates filopodial formation through activation of Cdc42, which results in activation of cell migration. No function has been determined for Zizimin3 to date. The N-terminal half of zizimin1 binds to the GEF domain through three distinct areas, including CZH1, to inhibit the interaction with Cdc42. In addition its PH domain binds phosphoinositides and mediates zizimin1 membrane targeting. DOCK is a family of proteins involved in intracellular signalling networks. They act as guanine nucleotide exchange factors for small G proteins of the Rho family, such as Rac and Cdc42. There are 4 subfamilies of DOCK family proteins based on their sequence homology: A-D. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 126 matched cddid_all.tbl CDD cd13268 cd13268 270088 PH_Brdg1 BCR downstream signaling 1 Pleckstrin homology (PH) domain. Brdg1 is thought to function as a docking protein acting downstream of Tec, a protein tyrosine kinases (PTK), in B-cell antigen receptor (BCR) signaling. BRDG1 contains a proline-rich (PR) motif which is thought to bind SH3 or WW domains, a PH domain, and multiple tyrosine residues which are potential target sites for SH2 domains. Since PH domains bind phospholipids it is thought to be involved in the tethering of Tec and BRDG1 to the cell membrane.Tec and Pyk2, but not Btk, Bmx, Lyn, Syk, or c-Abl, induces phosphorylation of BRDG1 on tyrosine residues. Efficient phosphorylation requires both the PH and SH2 domains of BRDG1 and the kinase domain of Tec. The overexpression of BRDG1 increases theBCR-mediated activation of cAMP-response element binding protein (CREB). Phosphorylated BRDG1 is hypothesized to recruit CREB either directly or through its recruitment of downstream effectors which then recruit CREB. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 127 matched cddid_all.tbl CDD cd13269 cd13269 241423 PH_alsin Alsin Pleckstrin homology (PH) domain. The ALS2 gene encodes alsin, a GEF, that has dual specificity for Rac1 and Rab5 GTPases. Alsin mutations in the form of truncated proteins are responsible for motor function disorders including juvenile-onset amyotrophic lateral sclerosis, familial juvenile primary lateral sclerosis, and infantile-onset ascending hereditary spastic paralysis. The alsin protein is widely expressed in the developing CNS including neurons of the cerebral cortex, brain stem, spinal cord, and cerebellum. Alsin contains a regulator of chromosome condensation 1 (RCC1) domain, a Rho guanine nucleotide exchanging factor (RhoGEF) domain, a PH domain, a Membrane Occupation and Recognition Nexus (MORN), a vacuolar protein sorting 9 (Vps9) domain, and a Dbl homology (DH) domain. Alsin interacts with Rab5 through its Vps9 domain and through this interaction modulates early endosome fusion and trafficking. The GEF activity of alsin towards Rab5 is regulated by Rac1 function. The GEF activity of alsin for Rac1 occurs via its DH domain and this interaction plays a role in promoting spinal motor neuron survival via multiple Rac-dependent signaling pathways. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 106 matched cddid_all.tbl CDD cd13270 cd13270 270089 PH1_TAPP1_2 Tandem PH-domain-containing proteins 1 and 2 Pleckstrin homology (PH) domain, N-terminal repeat. The binding of TAPP1 (also called PLEKHA1/pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1) and TAPP2 (also called PLEKHA2) adaptors to PtdIns(3,4)P(2), but not PI(3,4, 5)P3, function as negative regulators of insulin and PI3K signalling pathways (i.e. TAPP/utrophin/syntrophin complex). TAPP1 and TAPP2 contain two sequential PH domains in which the C-terminal PH domain binds PtdIns(3,4)P2. They also contain a C-terminal PDZ-binding motif that interacts with several PDZ-binding proteins, including PTPN13 (known previously as PTPL1 or FAP-1) as well as the scaffolding proteins MUPP1 (multiple PDZ-domain-containing protein 1), syntrophin and utrophin. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 118 matched cddid_all.tbl CDD cd13271 cd13271 270090 PH2_TAPP1_2 Tandem PH-domain-containing proteins 1 and 2 Pleckstrin homology (PH) domain, C-terminal repeat. The binding of TAPP1 (also called PLEKHA1/pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 1) and TAPP2 (also called PLEKHA2) adaptors to PtdIns(3,4)P(2), but not PI(3,4, 5)P3, function as negative regulators of insulin and PI3K signalling pathways (i.e. TAPP/utrophin/syntrophin complex). TAPP1 and TAPP2 contain two sequential PH domains in which the C-terminal PH domain specifically binds PtdIns(3,4)P2 with high affinity. The N-terminal PH domain does not interact with any phosphoinositide tested. They also contain a C-terminal PDZ-binding motif that interacts with several PDZ-binding proteins, including PTPN13 (known previously as PTPL1 or FAP-1) as well as the scaffolding proteins MUPP1 (multiple PDZ-domain-containing protein 1), syntrophin and utrophin. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 114 matched cddid_all.tbl CDD cd13272 cd13272 270091 PH_INPP4A_INPP4B Type I inositol 3,4-bisphosphate 4-phosphatase and Type II inositol 3,4-bisphosphate 4-phosphatase Pleckstrin homology (PH) domain. INPP4A (also called Inositol polyphosphate 4-phosphatase type I) and INPP4B (also called Inositol polyphosphate 4-phosphatase type II) both catalyze the hydrolysis of the 4-position phosphate of phosphatidylinositol 3,4-bisphosphate and inositol 1,3,4-trisphosphate. They differ in that INPP4A additionally catalyzes the hydrolysis of the 4-position phosphate of inositol 3,4-bisphosphate, while INPP4B catalyzes the hydrolysis of the 4-position phosphate of inositol 1,4-bisphosphate. They both have a single PH domain followed by a C2 domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 144 matched cddid_all.tbl CDD cd13273 cd13273 270092 PH_SWAP-70 Switch-associated protein-70 Pleckstrin homology (PH) domain. SWAP-70 (also called Differentially expressed in FDCP 6/DEF-6 or IRF4-binding protein) functions in cellular signal transduction pathways (in conjunction with Rac), regulates cell motility through actin rearrangement, and contributes to the transformation and invasion activity of mouse embryo fibroblasts. Metazoan SWAP-70 is found in B lymphocytes, mast cells, and in a variety of organs. Metazoan SWAP-70 contains an N-terminal EF-hand motif, a centrally located PH domain, and a C-terminal coiled-coil domain. The PH domain of Metazoan SWAP-70 contains a phosphoinositide-binding site and a nuclear localization signal (NLS), which localize SWAP-70 to the plasma membrane and nucleus, respectively. The NLS is a sequence of four Lys residues located at the N-terminus of the C-terminal a-helix; this is a unique characteristic of the Metazoan SWAP-70 PH domain. The SWAP-70 PH domain binds PtdIns(3,4,5)P3 and PtdIns(4,5)P2 embedded in lipid bilayer vesicles. There are additional plant SWAP70 proteins, but these are not included in this hierarchy. Rice SWAP70 (OsSWAP70) exhibits GEF activity toward the its Rho GTPase, OsRac1, and regulates chitin-induced production of reactive oxygen species and defense gene expression in rice. Arabidopsis SWAP70 (AtSWAP70) plays a role in both PAMP- and effector-triggered immunity. Plant SWAP70 contains both DH and PH domains, but their arrangement is the reverse of that in typical DH-PH-type Rho GEFs, wherein the DH domain is flanked by a C-terminal PH domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 110 matched cddid_all.tbl CDD cd13274 cd13274 270093 PH_DGK_type2 Type 2 Diacylglycerol kinase Pleckstrin homology (PH) domain. DGK (also called DAGK) catalyzes the conversion of diacylglycerol (DAG) to phosphatidic acid (PA) utilizing ATP as a source of the phosphate. In non-stimulated cells, DGK activity is low and DAG is used for glycerophospholipid biosynthesis. Upon receptor activation of the phosphoinositide pathway, DGK activity increases which drives the conversion of DAG to PA. DGK acts as a switch by terminating the signalling of one lipid while simultaneously activating signalling by another. There are 9 mammalian DGK isoforms all with conserved catalytic domains and two cysteine rich domains. These are further classified into 5 groups according to the presence of additional functional domains and substrate specificity: Type 1 - DGK-alpha, DGK-beta, DGK-gamma - contain EF-hand motifs and a recoverin homology domain; Type 2 - DGK-delta, DGK-eta, and DGK-kappa- contain a pleckstrin homology domain, two cysteine-rich zinc finger-like structures, and a separated catalytic region; Type 3 - DGK-epsilon - has specificity for arachidonate-containing DAG; Type 4 - DGK-zeta, DGK-iota- contain a MARCKS homology domain, ankyrin repeats, a C-terminal nuclear localization signal, and a PDZ-binding motif; Type 5 - DGK-theta - contains a third cysteine-rich domain, a pleckstrin homology domain and a proline rich region. The type 2 DGKs are present as part of this Metazoan DGK hierarchy. They have a N-terminal PH domain, two cysteine rich domains, followed by bipartite catalytic domains, and a C-terminal SAM domain. Their catalytic domains and perhaps other DGK catalytic domains may function as two independent units in a coordinated fashion. They may also require other motifs for maximal activity because several DGK catalytic domains have very little DAG kinase activity when expressed as isolated subunits. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 97 matched cddid_all.tbl CDD cd13275 cd13275 270094 PH_M-RIP Myosin phosphatase-RhoA Interacting Protein Pleckstrin homology (PH) domain. M-RIP is proposed to play a role in myosin phosphatase regulation by RhoA. M-RIP contains 2 PH domains followed by a Rho binding domain (Rho-BD), and a C-terminal myosin binding subunit (MBS) binding domain (MBS-BD). The amino terminus of M-RIP with its adjacent PH domains and polyproline motifs mediates binding to both actin and Galpha. M-RIP brings RhoA and MBS into close proximity where M-RIP can target RhoA to the myosin phosphatase complex to regulate the myosin phosphorylation state. M-RIP does this via its C-terminal coiled-coil domain which interacts with the MBS leucine zipper domain of myosin phosphatase, while its Rho-BD, directly binds RhoA in a nucleotide-independent manner. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 104 matched cddid_all.tbl CDD cd13276 cd13276 270095 PH_AtPH1 Arabidopsis thaliana Pleckstrin homolog (PH) 1 (AtPH1) PH domain. AtPH1 is expressed in all plant tissue and is proposed to be the plant homolog of human pleckstrin. Pleckstrin consists of two PH domains separated by a linker region, while AtPH has a single PH domain with a short N-terminal extension. AtPH1 binds PtdIns3P specifically and is thought to be an adaptor molecule since it has no obvious catalytic functions. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 106 matched cddid_all.tbl CDD cd13277 cd13277 270096 PH_Bem3 Bud emergence protein 3 (Bem3) Pleckstrin homology (PH) domain. Bud emergence in Saccharomyces cerevisiae involves cell cycle-regulated reorganizations of cortical cytoskeletal elements and requires the action of the Rho-type GTPase Cdc42. Bem3 contains a RhoGAP domain and a PH domain. Though Bem3 and Bem2 both contain a RhoGAP, but only Bem3 is able to stimulate the hydrolysis of GTP on Cdc42. Bem3 is thought to be the GAP for Cdc42. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 111 matched cddid_all.tbl CDD cd13278 cd13278 241432 PH_Bud4 Bud4 Pleckstrin homology (PH) domain. Bud4 is an anillin-like yeast protein involved in the formation and the disassembly of the double ring structure formed by the septins during cytokinesis. Bud4 acts with Bud3 and and in parallel with septin phosphorylation by the p21-activated kinase Cla4 and the septin-dependent kinase Gin4. Bud4 is regulated by the cyclin-dependent protein kinase Cdk1, the master regulator of cell cycle progression. Bud4 contains an anillin-like domain followed by a PH domain. In addition there are two consensus Cdk phosphorylation sites: one at the N-terminus and one right before the C-terminal PH domain. Anillins also have C-terminal PH domains. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 139 matched cddid_all.tbl CDD cd13279 cd13279 270097 PH_Cla4_Ste20 Pleckstrin homology (PH) domain. Budding yeast contain two main p21-activated kinases (PAKs), Cla4 and Ste20. The yeast Ste20 protein kinase is involved in pheromone response, though the function of Ste20 mammalian homologs is unknown. Cla4 is involved in budding and cytokinesis and interacts with Cdc42, a GTPase required for polarized cell growth as is Pak. Cla4 and Ste20 kinases share a function in localizing cell growth with respect to the septin ring. They both contain a PH domain, a Cdc42/Rac interactive binding (CRIB) domain, and a C-terminal Protein Kinase catalytic (PKc) domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 92 matched cddid_all.tbl CDD cd13280 cd13280 270098 PH_SIP3 Snf1p-interacting protein 3 Pleckstrin homology (PH) domain. SIP3 interacts with SNF1 protein kinase and activates transcription when anchored to DNA. It may function in the SNF1 pathway. SIP3 contain an N-terminal Bin/Amphiphysin/Rvs (BAR) domain followed by a PH domain. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 105 matched cddid_all.tbl CDD cd13281 cd13281 270099 PH_PLEKHD1 Pleckstrin homology (PH) domain containing, family D (with coiled-coil domains) member 1 PH domain. Human PLEKHD1 (also called UPF0639, pleckstrin homology domain containing, family D (with M protein repeats) member 1) is a single transcript and contains a single PH domain. PLEKHD1 is conserved in human, chimpanzee, , dog, cow, mouse, chicken, zebrafish, and Caenorhabditis elegans. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 139 matched cddid_all.tbl CDD cd13282 cd13282 241436 PH1_PLEKHH1_PLEKHH2 Pleckstrin homology (PH) domain containing, family H (with MyTH4 domain) members 1 and 2 (PLEKHH1) PH domain, repeat 1. PLEKHH1 and PLEKHH2 (also called PLEKHH1L) are thought to function in phospholipid binding and signal transduction. There are 3 Human PLEKHH genes: PLEKHH1, PLEKHH2, and PLEKHH3. There are many isoforms, the longest of which contain a FERM domain, a MyTH4 domain, two PH domains, a peroximal domain, a vacuolar domain, and a coiled coil stretch. The FERM domain has a cloverleaf tripart structure (FERM_N, FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 96 matched cddid_all.tbl CDD cd13283 cd13283 270100 PH_GPBP Goodpasture antigen binding protein Pleckstrin homology (PH) domain. The GPBP (also called Collagen type IV alpha-3-binding protein/hCERT; START domain-containing protein 11/StARD11; StAR-related lipid transfer protein 11) is a kinase that phosphorylates an N-terminal region of the alpha 3 chain of type IV collagen, which is commonly known as the goodpasture antigen. Its splice variant the ceramide transporter (CERT) mediates the cytosolic transport of ceramide. There have been additional splice variants identified, but all of them function as ceramide transport proteins. GPBP and CERT both contain an N-terminal PH domain, followed by a serine rich domain, and a C-terminal START domain. However, GPBP has an additional serine rich domain just upstream of its START domain. They are members of the oxysterol binding protein (OSBP) family which includes OSBP, OSBP-related proteins (ORP), Goodpasture antigen binding protein (GPBP), and Four phosphate adaptor protein 1 (FAPP1). They have a wide range of purported functions including sterol transport, cell cycle control, pollen development and vessicle transport from Golgi recognize both PI lipids and ARF proteins. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 100 matched cddid_all.tbl CDD cd13284 cd13284 270101 PH_OSBP_ORP4 Human Oxysterol binding protein and OSBP-related protein 4 Pleckstrin homology (PH) domain. Human OSBP is proposed to function is sterol-dependent regulation of ERK dephosphorylation and sphingomyelin synthesis as well as modulation of insulin signaling and hepatic lipogenesis. It contains a N-terminal PH domain, a FFAT motif (two phenylalanines in an acidic tract), and a C-terminal OSBP-related domain. OSBPs and Osh1p PH domains specifically localize to the Golgi apparatus in a PtdIns4P-dependent manner. ORP4 is proposed to function in Vimentin-dependent sterol transport and/or signaling. Human ORP4 has 2 forms, a long (ORP4L) and a short (ORP4S). ORP4L contains a N-terminal PH domain, a FFAT motif (two phenylalanines in an acidic tract), and a C-terminal OSBP-related domain. ORP4S is truncated and contains only an OSBP-related domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. They are members of the oxysterol binding protein (OSBP) family which includes OSBP, OSBP-related proteins (ORP), Goodpasture antigen binding protein (GPBP), and Four phosphate adaptor protein 1 (FAPP1). They have a wide range of purported functions including sterol transport, cell cycle control, pollen development and vessicle transport from Golgi recognize both PI lipids and ARF proteins. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 99 matched cddid_all.tbl CDD cd13285 cd13285 270102 PH_ORP1 Human Oxysterol binding protein related protein 1 Pleckstrin homology (PH) domain. Human ORP1 has 2 forms, a long (ORP1L) and a short (ORP1S). ORP1L contains 3 N-terminal ankyrin repeats, followed by a PH domain, a FFAT motif (two phenylalanines in an acidic tract), and a C-terminal OSBP-related domain. ORP1S is truncated and contains only an OSBP-related domain. ORP1L is proposed to function in motility and distribution of late endosomes, autophagy, and macrophage lipid metabolism. ORP1S is proposed to function in vesicle transport from Golgi. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. In general OSBPs and ORPs have been found to be involved in the transport and metabolism of cholesterol and related lipids in eukaryotes. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. They are members of the oxysterol binding protein (OSBP) family which includes OSBP, OSBP-related proteins (ORP), Goodpasture antigen binding protein (GPBP), and Four phosphate adaptor protein 1 (FAPP1). They have a wide range of purported functions including sterol transport, cell cycle control, pollen development and vessicle transport from Golgi recognize both PI lipids and ARF proteins. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 125 matched cddid_all.tbl CDD cd13286 cd13286 270103 PH_OPR5_ORP8 Human Oxysterol binding protein related proteins 5 and 8 Pleckstrin homology (PH) domain. Human ORP5 is proposed to function in efficient nonvesicular transfer of low-density lipoproteins-derived cholesterol (LDL-C) from late endosomes/lysosomes to the endoplasmic reticulum (ER). Human ORP8 is proposed to modulate lipid homeostasis and sterol regulatory element binding proteins (SREBP) activity. Both ORP5 and ORP8 contain a N-terminal PH domain, a C-terminal OSBP-related domain, followed by a transmembrane domain that localizes ORP5 to the ER. Unlike all the other human OSBP/ORPs they lack a FFAT motif (two phenylalanines in an acidic tract). Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. In general OSBPs and ORPs have been found to be involved in the transport and metabolism of cholesterol and related lipids in eukaryotes. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. They are members of the oxysterol binding protein (OSBP) family which includes OSBP, OSBP-related proteins (ORP), Goodpasture antigen binding protein (GPBP), and Four phosphate adaptor protein 1 (FAPP1). They have a wide range of purported functions including sterol transport, cell cycle control, pollen development and vessicle transport from Golgi recognize both PI lipids and ARF proteins. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 130 matched cddid_all.tbl CDD cd13287 cd13287 270104 PH_ORP3_ORP6_ORP7 Human Oxysterol binding protein related proteins 3, 6, and 7 Pleckstrin homology (PH) domain. Human ORP3 is proposed to function in regulating the cell-matrix and cell-cell adhesion. A proposed specific function for Human ORP6 was not found at present. Human ORP7is proposed to function in negatively regulating the Golgi soluble NSF attachment protein receptor (SNARE) of 28kDa (GS28) protein stability via sequestration of Golgi-associated ATPase enhancer of 16 kDa (GATE-16). ORP3 has 2 isoforms: the longer ORP3(1) and the shorter ORP3(2). ORP3(1), ORP6, and ORP7 all contain a N-terminal PH domain, a FFAT motif (two phenylalanines in an acidic tract), and a C-terminal OSBP-related domain. The shorter ORP3(2) is missing the C-terminal portion of its OSBP-related domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. In general OSBPs and ORPs have been found to be involved in the transport and metabolism of cholesterol and related lipids in eukaryotes. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. They are members of the oxysterol binding protein (OSBP) family which includes OSBP, OSBP-related proteins (ORP), Goodpasture antigen binding protein (GPBP), and Four phosphate adaptor protein 1 (FAPP1). They have a wide range of purported functions including sterol transport, cell cycle control, pollen development and vessicle transport from Golgi recognize both PI lipids and ARF proteins. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 123 matched cddid_all.tbl CDD cd13288 cd13288 270105 PH_Ses Sesquipedalian family Pleckstrin homology (PH) domain. The sesquipedalian family has 2 mammalian members: Ses1 and Ses2, which are also callled 7 kDa inositol polyphosphate phosphatase-interacting protein 1 and 2. They play a role in endocytic trafficking and are required for receptor recycling from endosomes, both to the trans-Golgi network and the plasma membrane. Members of this family form homodimers and heterodimers. Sesquipedalian interacts with inositol polyphosphate 5-phosphatase OCRL-1 (INPP5F) also known as Lowe oculocerebrorenal syndrome protein, a phosphatase enzyme that is involved in actin polymerization and is found in the trans-Golgi network and INPP5B. Sesquipedalian contains a single PH domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 120 matched cddid_all.tbl CDD cd13289 cd13289 241443 PH_Osh3p_yeast Yeast oxysterol binding protein homolog 3 Pleckstrin homology (PH) domain. Yeast Osh3p is proposed to function in sterol transport and regulation of nuclear fusion during mating and of pseudohyphal growth as well as sphingolipid metabolism. Osh3 contains a N-GOLD (Golgi dynamics) domain, a PH domain, a FFAT motif (two phenylalanines in an acidic tract), and a C-terminal OSBP-related domain. GOLD domains are thought to mediate protein-protein interactions, but their role in ORPs are unknown. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. In general OSBPs and ORPs have been found to be involved in the transport and metabolism of cholesterol and related lipids in eukaryotes. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. They are members of the oxysterol binding protein (OSBP) family which includes OSBP, OSBP-related proteins (ORP), Goodpasture antigen binding protein (GPBP), and Four phosphate adaptor protein 1 (FAPP1). They have a wide range of purported functions including sterol transport, cell cycle control, pollen development and vessicle transport from Golgi recognize both PI lipids and ARF proteins. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 90 matched cddid_all.tbl CDD cd13290 cd13290 241444 PH_ORP9 Human Oxysterol binding protein related protein 9 Pleckstrin homology (PH) domain. Human ORP9 is proposed to function in regulation of Akt phosphorylation. ORP9 has 2 forms, a long (ORP9L) and a short (ORP9S). ORP9L contains an N-terminal PH domain, a FFAT motif (two phenylalanines in an acidic tract), and a C-terminal OSBP-related domain. ORP1S is truncated and contains a FFAT motif and an OSBP-related domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. In general OSBPs and ORPs have been found to be involved in the transport and metabolism of cholesterol and related lipids in eukaryotes. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. They are members of the oxysterol binding protein (OSBP) family which includes OSBP, OSBP-related proteins (ORP), Goodpasture antigen binding protein (GPBP), and Four phosphate adaptor protein 1 (FAPP1). They have a wide range of purported functions including sterol transport, cell cycle control, pollen development and vessicle transport from Golgi recognize both PI lipids and ARF proteins. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 102 matched cddid_all.tbl CDD cd13291 cd13291 270106 PH_ORP10_ORP11 Human Oxysterol binding protein (OSBP) related proteins 10 and 11 (ORP10 and ORP11) Pleckstrin homology (PH) domain. Human ORP10 is involvedt in intracellular transport or organelle positioning and is proposed to function as a regulator of cellular lipid metabolism. Human ORP11 localizes at the Golgi-late endosome interface and is thought to form a dimer with ORP9 functioning as an intracellular lipid sensor or transporter. Both ORP10 and ORP11 contain a N-terminal PH domain, a FFAT motif (two phenylalanines in an acidic tract), and a C-terminal OSBP-related domain. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. In general OSBPs and ORPs have been found to be involved in the transport and metabolism of cholesterol and related lipids in eukaryotes. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. They are members of the oxysterol binding protein (OSBP) family which includes OSBP, OSBP-related proteins (ORP), Goodpasture antigen binding protein (GPBP), and Four phosphate adaptor protein 1 (FAPP1). They have a wide range of purported functions including sterol transport, cell cycle control, pollen development and vessicle transport from Golgi recognize both PI lipids and ARF proteins. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 107 matched cddid_all.tbl CDD cd13292 cd13292 241446 PH_Osh1p_Osh2p_yeast Yeast oxysterol binding protein homologs 1 and 2 Pleckstrin homology (PH) domain. Yeast Osh1p is proposed to function in postsynthetic sterol regulation, piecemeal microautophagy of the nucleus, and cell polarity establishment. Yeast Osh2p is proposed to function in sterol metabolism and cell polarity establishment. Both Osh1p and Osh2p contain 3 N-terminal ankyrin repeats, a PH domain, a FFAT motif (two phenylalanines in an acidic tract), and a C-terminal OSBP-related domain. OSBP andOsh1p PH domains specifically localize to the Golgi apparatus in a PtdIns4P-dependent manner. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. In general OSBPs and ORPs have been found to be involved in the transport and metabolism of cholesterol and related lipids in eukaryotes. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. They are members of the oxysterol binding protein (OSBP) family which includes OSBP, OSBP-related proteins (ORP), Goodpasture antigen binding protein (GPBP), and Four phosphate adaptor protein 1 (FAPP1). They have a wide range of purported functions including sterol transport, cell cycle control, pollen development and vessicle transport from Golgi recognize both PI lipids and ARF proteins. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 103 matched cddid_all.tbl CDD cd13293 cd13293 241447 PH_CpORP2-like Cryptosporidium-like Oxysterol binding protein related protein 2 Pleckstrin homology (PH) domain. There are 2 types of ORPs found in Cryptosporidium: CpORP1 and CpORP2. Cryptosporium differs from other apicomplexans like Plasmodium, Toxoplasma, and Eimeria which possess only a single long-type ORP consisting of an N-terminal PH domain followed by a C-terminal ligand binding (LB) domain. CpORP2 is like this, but CpORP1 differs and has a truncated N-terminus resulting in only having a LB domain present. The exact functions of these proteins are largely unknown though CpORP1 is thought to be involved in lipid transport across the parasitophorous vacuole membrane. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. In general OSBPs and ORPs have been found to be involved in the transport and metabolism of cholesterol and related lipids in eukaryotes. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. They are members of the oxysterol binding protein (OSBP) family which includes OSBP, OSBP-related proteins (ORP), Goodpasture antigen binding protein (GPBP), and Four phosphate adaptor protein 1 (FAPP1). They have a wide range of purported functions including sterol transport, cell cycle control, pollen development and vessicle transport from Golgi recognize both PI lipids and ARF proteins. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 88 matched cddid_all.tbl CDD cd13294 cd13294 241448 PH_ORP_plant Plant Oxysterol binding protein related protein Pleckstrin homology (PH) domain. Plant ORPs contain a N-terminal PH domain and a C-terminal OSBP-related domain. Not much is known about its specific function in plants to date. Members here include: Arabidopsis, spruce, and petunia. Oxysterol binding proteins are a multigene family that is conserved in yeast, flies, worms, mammals and plants. In general OSBPs and ORPs have been found to be involved in the transport and metabolism of cholesterol and related lipids in eukaryotes. They all contain a C-terminal oxysterol binding domain, and most contain an N-terminal PH domain. OSBP PH domains bind to membrane phosphoinositides and thus likely play an important role in intracellular targeting. They are members of the oxysterol binding protein (OSBP) family which includes OSBP, OSBP-related proteins (ORP), Goodpasture antigen binding protein (GPBP), and Four phosphate adaptor protein 1 (FAPP1). They have a wide range of purported functions including sterol transport, cell cycle control, pollen development and vessicle transport from Golgi recognize both PI lipids and ARF proteins. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 100 matched cddid_all.tbl CDD cd13295 cd13295 270107 PH_EFA6 Exchange Factor for ARF6 Pleckstrin homology (PH) domain. EFA6 (also called PSD/pleckstrin and Sec7 domain containing) is an guanine nucleotide exchange factor for ADP ribosylation factor 6 (ARF6), which is involved in membrane recycling. EFA6 has four structurally related polypeptides: EFA6A, EFA6B, EFA6C and EFA6D. It consists of a N-terminal proline rich region (PR), a SEC7 domain, a PH domain, a PR, a coiled-coil region, and a C-terminal PR. The EFA6 PH domain regulates its association with the plasma membrane. EFA6 activates Arf6 through its Sec7 catalytic domain and modulates this activity through its C-terminal domain, which rearranges the actin cytoskeleton in fibroblastic cell lines. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 126 matched cddid_all.tbl CDD cd13296 cd13296 270108 PH2_MyoX Myosin X Pleckstrin homology (PH) domain, repeat 2. MyoX, a MyTH-FERM myosin, is a molecular motor that has crucial functions in the transport and/or tethering of integrins in the actin-based extensions known as filopodia, microtubule binding, and in netrin-mediated axon guidance. It functions as a dimer. MyoX walks on bundles of actin, rather than single filaments, unlike the other unconventional myosins. MyoX is present in organisms ranging from humans to choanoflagellates, but not in Drosophila and Caenorhabditis elegans.MyoX consists of a N-terminal motor/head region, a neck made of 3 IQ motifs, and a tail consisting of a coiled-coil domain, a PEST region, 3 PH domains, a myosin tail homology 4 (MyTH4), and a FERM domain at its very C-terminus. The first PH domain in the MyoX tail is a split-PH domain, interupted by the second PH domain such that PH 1a and PH 1b flanks PH 2. The third PH domain (PH 3) follows the PH 1b domain. This cd contains the second PH repeat. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 103 matched cddid_all.tbl CDD cd13297 cd13297 270109 PH3_MyoX-like Myosin X-like Pleckstrin homology (PH) domain, repeat 3. MyoX, a MyTH-FERM myosin, is a molecular motor that has crucial functions in the transport and/or tethering of integrins in the actin-based extensions known as filopodia, microtubule binding, and in netrin-mediated axon guidance. It functions as a dimer. MyoX walks on bundles of actin, rather than single filaments, unlike the other unconventional myosins. MyoX is present in organisms ranging from humans to choanoflagellates, but not in Drosophila and Caenorhabditis elegans.MyoX consists of a N-terminal motor/head region, a neck made of 3 IQ motifs, and a tail consisting of a coiled-coil domain, a PEST region, 3 PH domains, a myosin tail homology 4 (MyTH4), and a FERM domain at its very C-terminus. The first PH domain in the MyoX tail is a split-PH domain, interupted by the second PH domain such that PH 1a and PH 1b flanks PH 2. The third PH domain (PH 3) follows the PH 1b domain. This cd contains the third MyoX PH repeat. PLEKHH3/Pleckstrin homology (PH) domain containing, family H (with MyTH4 domain) member 3 is also part of this CD and like MyoX contains a FERM domain, a MyTH4 domain, and a single PH domain. Not much is known about the function of PLEKHH3. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 126 matched cddid_all.tbl CDD cd13298 cd13298 270110 PH1_PH_fungal Fungal proteins Pleckstrin homology (PH) domain, repeat 1. The functions of these fungal proteins are unknown, but they all contain 2 PH domains. This cd represents the first PH repeat. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 106 matched cddid_all.tbl CDD cd13299 cd13299 270111 PH2_PH_fungal Fungal proteins Pleckstrin homology (PH) domain, repeat 2. The functions of these fungal proteins are unknown, but they all contain 2 PH domains. This cd represents the second PH repeat. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 102 matched cddid_all.tbl CDD cd13300 cd13300 270112 PH1_TECPR1 Tectonin beta-propeller repeat-containing protein 1 Pleckstrin homology (PH) domain, repeat 1. TECPR1 is a tethering factor involved in autophagy. It promotes the autophagosome fusion with lysosomes by associating with both the ATG5-ATG12 conjugate and phosphatidylinositol-3-phosphate (PtdIns3P) present at the surface of autophagosomes. TECPR1 is also involved in selective autophagy against bacterial pathogens, by being required for phagophore/preautophagosomal structure biogenesis and maturation. It contains 2 DysFN (Dysferlin domains of unknown function, N-terminal), 2 Hyd_WA domains that is a probably beta-propeller, a PH-like domain, a TECPR domain, and a DysFC (C-terminal). The PH domain mediates the binding to phosphatidylinositol-3-phosphate (PtdIns3P). Binding to the ATG5-ATG12 conjugate exposes the PH domain, allowing the association with PtdIns3P. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 122 matched cddid_all.tbl CDD cd13301 cd13301 270113 PH1_Pleckstrin_2 Pleckstrin 2 Pleckstrin homology (PH) domain, repeat 1. Pleckstrin is a protein found in platelets. This name is derived from platelet and leukocyte C kinase substrate and the KSTR string of amino acids. Pleckstrin 2 contains two PH domains and a DEP (dishvelled, egl-10, and pleckstrin) domain. Unlike pleckstrin 1, pleckstrin 2 does not contain obvious sites of PKC phosphorylation. Pleckstrin 2 plays a role in actin rearrangement, large lamellipodia and peripheral ruffle formation, and may help orchestrate cytoskeletal arrangement. The PH domains of pleckstrin 2 are thought to contribute to lamellipodia formation. This cd contains the first PH domain repeat. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 108 matched cddid_all.tbl CDD cd13302 cd13302 270114 PH2_Pleckstrin_2 Pleckstrin 2 Pleckstrin homology (PH) domain, repeat 2. Pleckstrin is a protein found in platelets. This name is derived from platelet and leukocyte C kinase substrate and the KSTR string of amino acids. Pleckstrin 2 contains two PH domains and a DEP (dishvelled, egl-10, and pleckstrin) domain. Unlike pleckstrin 1, pleckstrin 2 does not contain obvious sites of PKC phosphorylation. Pleckstrin 2 plays a role in actin rearrangement, large lamellipodia and peripheral ruffle formation, and may help orchestrate cytoskeletal arrangement. The PH domains of pleckstrin 2 are thought to contribute to lamellipodia formation. This cd contains the second PH domain repeat. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 109 matched cddid_all.tbl CDD cd13303 cd13303 241457 PH1-like_Rtt106 Pleckstrin homology-like domain, repeat 1, of Histone chaperone RTT106 (regulator of Ty1 transposition protein 106). Rtt106 is a histone chaperone. The binding of Rtt106 to H3K56-acetylated (H3-H4)2 tetramers contributes to nucleosome assembly in terms of DNA replication, gene silencing and maintenance of genomic stability. Rtt106 contains an N-terminal homodimerization domain and two C-terminal pleckstrin-homology (PH) domains (PH1 and PH2). The N-terminal domain homodimerizes homodimerizes and interacts with H3-H4 independently of acetylation while the double PH domain binds the K56-containing region of H3. Rtt106 also interacts with both the SWI/SNF and RSC chromatin remodeling complexes and is involved in their cell-cycle dependent recruitment to histone gene pairs regulated by the HIR co-repressor complex (HTA1-HTB1, HHT1-HHF1, and HHT2-HHF2). This model contains the first PH-like domain repeat. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 139 matched cddid_all.tbl CDD cd13304 cd13304 241458 PH2-like_Rtt106 Pleckstrin homology-like domain, repeat 2, of Histone chaperone RTT106 (regulator of Ty1 transposition protein 106). Rtt106 is a histone chaperone. Rtt106 contains an N-terminal homodimerization domain and two C-terminal pleckstrin-homology (PH) domains (PH1 and PH2). The binding of Rtt106 to H3K56-acetylated (H3-H4)2 tetramers contributes to nucleosome assembly in terms of DNA replication, gene silencing and maintenance of genomic stability. The N-terminal domain homodimerizes homodimerizes and interacts with H3-H4 independently of acetylation while the double PH domain binds the K56-containing region of H3. Rtt106 also interacts with both the SWI/SNF and RSC chromatin remodeling complexes and is involved in their cell-cycle dependent recruitment to histone gene pairs regulated by the HIR co-repressor complex (HTA1-HTB1, HHT1-HHF1, and HHT2-HHF2). This model contains the second PH-like domain repeat. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 89 matched cddid_all.tbl CDD cd13305 cd13305 270115 PH_SHARPIN SHANK-associated RH domain interacting protein Pleckstrin homology (PH) domain. SHARPIN has a variety of roles including: a role as a scaffolding partner of anchoring/scaffold proteins Shank1, a role in carcinogenesis through the interaction with FYN binding protein (FYB), which binds to oncogene FYN, a role in apoptosis by interacting with AIFM1, a mitochondrial regulator of cell death, CAPN13, and NSD1, as well as a role in immune disease and inflammation. SHARPIN has at its N-terminus a PH domain, followed by a E3 ubiquitin ligase domain, and a C-terminal RanBP-type and C3HC4-type zinc finger containing 1 domain (RBCK1, also known as HOIP which functions as a protein kinase C (PKC) binding protein as well as a transcriptional activator. SHARPIN's PH domain functions as a dimerization module, rather than a ligand recognition domain. Instead it acts as a dimerization module extending the functional applications of this superfold. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 114 matched cddid_all.tbl CDD cd13306 cd13306 270116 PH1_AFAP Actin filament associated protein family Pleckstrin homology (PH) domain, repeat 1. There are 3 members of the AFAP family of adaptor proteins: AFAP1, AFAP1L1, and AFAP1L2/XB130. AFAP1 is a cSrc binding partner and actin cross-linking protein. AFAP1L1 is thought to play a similar role to AFAP1 in terms of being an actin cross-linking protein, but it preferentially binds to cortactin and not cSrc, thereby playing a role in invadosome formation. AFAP1L2 is a cSrc binding protein, but does not bind to actin filaments. AFAP1L2 acts as an intermediary between the RET/PTC kinase and PI-3kinase pathway in the thyroid. The AFAPs share a similar structure of a SH3 binding motif, 3 SH2 binding motifs, 2 PH domains, a coiled-coil region corresponding to the AFAP1 leucine zipper, and an actin binding domain. The amino terminal PH1 domain of AFAP1 has been known to function in intra-molecular regulation of AFAP1. In addition, the PH1 domain is a binding partner for PKCa and phospholipids. This cd is the first PH domain of AFAP. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 107 matched cddid_all.tbl CDD cd13307 cd13307 270117 PH2_AFAP Actin filament associated protein family Pleckstrin homology (PH) domain, repeat 2. There are 3 members of the AFAP family of adaptor proteins: AFAP1, AFAP1L1, and AFAP1L2/XB130. AFAP1 is a cSrc binding partner and actin cross-linking protein. AFAP1L1 is thought to play a similar role to AFAP1 in terms of being an actin cross-linking protein, but it preferentially binds to cortactin and not cSrc, thereby playing a role in invadosome formation. AFAP1L2 is a cSrc binding protein, but does not bind to actin filaments. AFAP1L2 acts as an intermediary between the RET/PTC kinase and PI-3kinase pathway in the thyroid. The AFAPs share a similar structure of a SH3 binding motif, 3 SH2 binding motifs, 2 PH domains, a coiled-coil region corresponding to the AFAP1 leucine zipper, and an actin binding domain. This cd is the second PH domain of AFAP. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 101 matched cddid_all.tbl CDD cd13308 cd13308 270118 PH_3BP2 SH3 domain-binding protein 2 Pleckstrin homology (PH) domain. SH3BP2 (the gene that encodes the adaptor protein 3BP2), HD, ITU, IT10C3, and ADD1 are located near the Huntington's Disease Gene on Human Chromosome 4pl6.3. SH3BP2 lies in a region that is often missing in individuals with Wolf-Hirschhorn syndrome (WHS). Gain of function mutations in SH3BP2 causes enhanced B-cell antigen receptor (BCR)-mediated activation of nuclear factor of activated T cells (NFAT), resulting in a rare, genetic disorder called cherubism. This results in an increase in the signaling complex formation with Syk, phospholipase C-gamma2 (PLC-gamma2), and Vav1. It was recently discovered that Tankyrase regulates 3BP2 stability through ADP-ribosylation and ubiquitylation by the E3-ubiquitin ligase. Cherubism mutations uncouple 3BP2 from Tankyrase-mediated protein destruction, which results in its stabilization and subsequent hyperactivation of the Src, Syk, and Vav signaling pathways. SH3BP2 is also a potential negative regulator of the abl oncogene. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 113 matched cddid_all.tbl CDD cd13309 cd13309 270119 PH_SKIP SifA and kinesin-interacting protein Pleckstrin homology (PH) domain. SKIP (also called PLEKHM2/Pleckstrin homology domain-containing family M member 2) is a soluble cytosolic protein that contains a RUN domain and a PH domain separated by a unstructured linker region. SKIP is a target of the Salmonella effector protein SifA and the SifA-SKIP complex regulates kinesin-1 on the bacterial vacuole. The PH domain of SKIP binds to the N-terminal region of SifA while the N-terminus of SKIP is proposed to bind the TPR domain of the kinesin light chain. The opposite side of the SKIP PH domain is proposed to bind phosphoinositides. TSifA, SKIP, SseJ, and RhoA family GTPases are also thought to promote host membrane tubulation. Recently, it was shown that the lysosomal GTPase Arl8 binds to the kinesin-1 linker SKIP and that both are required for the normal intracellular distribution of lysosomes. Interestingly, two kinesin light chain binding motifs (WD) in SKIP have now been identified to match a consensus sequence for a kinesin light chain binding site found in several proteins including calsyntenin-1/alcadein, caytaxin, and vaccinia virus A36. SKIP has also been shown to interact with Rab1A. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 103 matched cddid_all.tbl CDD cd13310 cd13310 270120 PH_RalGPS1_2 Ral GEF with PH domain and SH3 binding motif 1 and 2 Pleckstrin homology (PH) domain. RalGPS1 (also called Ral GEF with PH domain and SH3 binding motif 1;RALGEF2/ Ral guanine nucleotide exchange factor 2; RalA exchange factor RalGPS1; Ral guanine nucleotide exchange factor RalGPS1A2; ras-specific guanine nucleotide-releasing factor RalGPS1) and RalGPS2 (also called Ral GEF with PH domain and SH3 binding motif 2; Ral-A exchange factor RalGPS2; ras-specific guanine nucleotide-releasing factor RalGPS22). They activate small GTPase Ral proteins such as RalA and RalB by stimulating the exchange of Ral bound GDP to GTP, thereby regulating various downstream cellular processes. Structurally they contain an N-terminal Cdc25-like catalytic domain, followed by a PXXP motif and a C-terminal PH domain. The Cdc25-like catalytic domain interacts with Ral and its PH domain ensures the correct membrane localization. Its PXXP motif is thought to interact with the SH3 domain of Grb2. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 116 matched cddid_all.tbl CDD cd13311 cd13311 270121 PH_Slm1 Slm1 Pleckstrin homology (PH) domain. Slm1 is a component of the target of rapamycin complex 2 (TORC2) signaling pathway. It plays a role in the regulation of actin organization and is a target of sphingolipid signaling during the heat shock response. Slm1 contains a single PH domain that binds PtdIns(4,5)P2, PtdIns(4)P, and dihydrosphingosine 1-phosphate (DHS-1P). Slm1 possesses two binding sites for anionic lipids. The non-canonical binding site of the PH domain of Slm1 is used for ligand binding, and it is proposed that beta-spectrin, Tiam1 and ArhGAP9 also have this type of phosphoinositide binding site. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 110 matched cddid_all.tbl CDD cd13312 cd13312 270122 PH_USP37_like Pleckstrin homology-like domain of Ubiquitin carboxyl-terminal hydrolase 37. Members here include USP37, USP29, and USP26. All of these contain a single PH-like domain. USP37 (also called ubiquitin carboxyl-terminal hydrolase 37, ubiquitin thiolesterase 37, deubiquitinating enzyme 37, and tmp_locus_50) is a deubiquitinase that antagonizes the anaphase-promoting complex (APC/C) during G1/S transition by mediating deubiquitination of cyclin-A (CCNA1 and CCNA2), resulting in promoting S phase entry. USP37 mediates deubiquitination of 'Lys-11'-linked polyubiquitin chains, a specific ubiquitin-linkage type mediated by the APC/C complex and 'Lys-48'-linked polyubiquitin chains in vitro. Phosphorylation at Ser-628 during G1/S phase maximizes the deubiquitinase activity, leading to prevent degradation of cyclin-A (CCNA1 and CCNA2). USP29 (also called ubiquitin carboxyl-terminal hydrolase 29, ubiquitin thiolesterase 29, deubiquitinating enzyme 29, and HOM-TES-84/86) plays a role in apoptosis and oxidative stress. In response to oxidative stress, JTV1 dissociates from the ARS complex, translocates to the nucleus, associates with far upstream element binding protein (FBP) and co-activates the transcription of USP29 which binds to, cleaves poly-ubiquitin chains from, and stabilizes p53 leading to apoptosis. The X-linked deubiquitination enzyme USP26 (also called ubiquitin carboxyl-terminal hydrolase 26, ubiquitin thiolesterase 26, and deubiquitinating enzyme 26) is a regulator of androgen receptor (AR) signaling. It binds to AR using three nuclear receptor interaction motifs (LXXLL, FXXLF and FXXFF) and modulates AR ubiquitination. Polymorphism of Usp26 correlates with idiopathic male infertility. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 103 matched cddid_all.tbl CDD cd13313 cd13313 270123 PH_NF1 Neurofibromin-1 Pleckstrin homology-like domain. Neurofibromin (NF1) contains a N-terminal RasGAP domain, followed by a Sec14-like domain, and a PH domain. Surprisingly, in neurofibromin the PH domain alone is not sufficient for phospholipid binding and instead requires the presence of the Sec-14 domain. The Sec-14 domain has been shown to bind 1-(3-sn-phosphatidyl)-sn-glycerol (PtdGro), (3-sn-phosphatidyl)-ethanolamine (PtdEtn) and -choline (PtdCho) and to a minor extent to (3-sn-phosphatidyl)-l-serine (PtdSer) and 1-(3-sn-phosphatidyl)-d-myo-inositol (PtdIns). Neurofibromatosis type 1 (also known as von Recklinghausen neurofibromatosis or NF1) is a genetic disorder caused by alterations in the tumor suppressor gene NF1. Hallmark symptoms include neural crest derived tumors, pigmentation anomalies, bone deformations, and learning disabilities. Mutations of the tumour suppressor gene NF1 are responsible for disease pathogenesis, with 90% of the alterations being nonsense codons. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 110 matched cddid_all.tbl CDD cd13314 cd13314 270124 PH_Rpn13 Pleckstrin homology-like domain of Regulatory Particle Non-ATPase 13. Targeted protein degradation is performed to a great extent by the ubiquitin-proteasome pathway, in which substrate proteins are marked by covalently attached ubiquitin chains that mediate recognition by the proteasome. Rpn13(also called ADRM1/ARM1) is one of the two major ubiquitin receptors of the proteasome, the other being S5a/Rpn10 which is not essential for ubiquitin-mediated protein degradation in budding yeast2. S5a has two ubiquitin interacting motifs (UIMs) that bind simultaneously to ubiquitin moieties to increase affinity while Rpn13 binds ubiquitin with a single, high affinity surface within its N-terminal PH domain. Rpn13 also binds and activates deubiquitinating enzyme Uch37, one of the proteasome's three deubiquitinating enzymes. Recently it was discovered that the ubiquitin-binding domain (BD) and Uch37 BD of human (h) Rpn13 pack against each other when it is not incorporated into the proteasome reducing hRpn13's affinity for ubiquitin. However when hRpn13 binds to hRpn2/S1 this abrogates its interdomain interactions, thus activating hRpn13 for ubiquitin binding. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 105 matched cddid_all.tbl CDD cd13315 cd13315 270125 PH_Sec3 Sec 3 Pleckstrin homology-like domain. The Sec3 subunit of the exocyst, a complex involved in polarized exocytosis, bind phospholipids and GTPase Cdc42 and therefore functions as a coincidence detector at the plasma membrane. Unlike most PH domains, Sec3 contains an additional alpha-helix at its N-terminus and two beta-strands at its C-terminus that mediate dimerization through domain swapping. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 141 matched cddid_all.tbl CDD cd13316 cd13316 270126 PH_Boi "Boi family Pleckstrin homology domain. Yeast Boi proteins Boi1 and Boi2 are functionally redundant and important for cell growth with Boi mutants displaying defects in bud formation and in the maintenance of cell polarity.They appear to be linked to Rho-type GTPase, Cdc42 and Rho3. Boi1 and Boi2 display two-hybrid interactions with the GTP-bound (""active"") form of Cdc42, while Rho3 can suppress of the lethality caused by deletion of Boi1 and Boi2. These findings suggest that Boi1 and Boi2 are targets of Cdc42 that promote cell growth in a manner that is regulated by Rho3. Boi proteins contain a N-terminal SH3 domain, followed by a SAM (sterile alpha motif) domain, a proline-rich region, which mediates binding to the second SH3 domain of Bem1, and C-terminal PH domain. The PH domain is essential for its function in cell growth and is important for localization to the bud, while the SH3 domain is needed for localization to the neck. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes." 97 matched cddid_all.tbl CDD cd13317 cd13317 270127 PH_PLEKHO1_PLEKHO2 Pleckstrin homology domain-containing family O Pleckstrin homology domain. The PLEKHO family members are PLEKHO1 (also called CKIP-1/Casein kinase 2-interacting protein 1/CK2-interacting protein 1) and PLEKHO2 (PLEKHQ1/PH domain-containing family Q member 1). They both contain a single PH domain. PLEKHO1 acts as a scaffold protein that functions in plasma membrane recruitment, transcriptional activity modulation, and posttranscriptional modification regulation. As an adaptor protein it is involved in signaling pathways, apoptosis, differentiation, cytoskeleton, and bone formation. Not much is know about PLEKHO2. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 102 matched cddid_all.tbl CDD cd13318 cd13318 270128 PH_IQSEC IQ motif and SEC7 domain-containing protein family Pleckstrin homology domain. The IQSEC (also called BRAG/Brefeldin A-resistant Arf-gunanine nucleotide exchange factor) family are a subset of Arf GEFs that have been shown to activate Arf6, which acts in the endocytic pathway to control the trafficking of a subset of cargo proteins including integrins and have key roles in the function and organization of distinct excitatory and inhibitory synapses in the retina. The family consists of 3 members: IQSEC1 (also called BRAG2/GEP100), IQSEC2 (also called BRAG1), and IQSEC3 (also called SynArfGEF, BRAG3, or KIAA1110). IQSEC1 interacts with clathrin and modulates cell adhesion by regulating integrin surface expression and in addition to Arf6, it also activates the class II Arfs, Arf4 and Arf5. Mutations in IQSEC2 cause non-syndromic X-linked intellectual disability as well as reduced activation of Arf substrates (Arf1, Arf6). IQSEC3 regulates Arf6 at inhibitory synapses and associates with the dystrophin-associated glycoprotein complex and S-SCAM. These members contains a IQ domain that may bind calmodulin, a PH domain that is thought to mediate membrane localization by binding of phosphoinositides, and a SEC7 domain that can promote GEF activity on ARF. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 128 matched cddid_all.tbl CDD cd13319 cd13319 270129 PH_RARhoGAP RA and RhoGAP domain-containing protein Pleckstrin homology PH domain. RARhoGAP (also called Rho GTPase-activating protein 20 and ARHGAP20 ) is thought to function in rearrangements of the cytoskeleton and cell signaling events that occur during spermatogenesis. RARhoGAP was also shown to be activated by Rap1 and to induce inactivation of Rho, resulting in the neurite outgrowth. Recent findings show that ARHGAP20, even although it is located in the middle of the MDR on 11q22-23, is expressed at higher levels in chronic lymphocytic leukemia patients with 11q22-23 and/or 13q14 deletions and its expression pattern suggests a functional link between cases with 11q22-23 and 13q14 deletions. The mechanism needs to be further studied. RARhoGAP contains a PH domain, a Ras-associating domain, a Rho-GAP domain, and ANXL repeats. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 97 matched cddid_all.tbl CDD cd13320 cd13320 270130 PH_OCRL-like oculocerebrorenal syndrome of Lowe family Pleckstrin homology-like domain. The OCRL family has two members: OCRL1 (also called INPP5F, LOCR, NPHL2, or phosphatidylinositol polyphosphate 5-phosphatase) and OCRL2 ( also called IPNNB5, inositol polyphosphate-5-phosphatase, phosphoinositide 5-phosphatase, 5PTase, or type II inositol-1,4,5-trisphosphate 5-phosphatase). The OCRL proteins hydrolyze phosphatidylinositol 4,5-bisphosphate (PtIns(4,5)P2) and the signaling molecule phosphatidylinositol 1,4,5-trisphosphate (PtIns(1,4,5)P3), and thereby modulates cellular signaling events. They interact with APPL1, FAM109A and FAM109B and several Rab GTPases which might both target them to the specific membranes and as well as stimulating the phosphatase activity. All OCRL family members contain a PH domain and a Rho-GAP domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 105 matched cddid_all.tbl CDD cd13321 cd13321 241475 PH_PLEKHM1 Pleckstrin homology domain-containing family M member 1 Pleckstrin homology (PH) domain. PLEKHM1 is thought to function in vesicular transport in osteoclasts. Mutations in the PLEKHM1 gene are associated with osteopetrosis OPTB6. PLEKHM1 contains an N-terminal RUN domain (RPIP8/RaP2 interacting protein 8, UNC-14 and NESCA/new molecule containing SH3 at the carboxyl-terminus), followed by a PH domain, and either a C1 domain or a DUF4206 domain at its C-terminus. The RUN domain is thought to be involved in Rab-mediated membrane trafficking, possibly as a Rab-binding site. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 132 matched cddid_all.tbl CDD cd13322 cd13322 270131 PH_PHLPP-like PH domain leucine-rich repeat protein phosphatase family Pleckstrin homology-like domain. The PHLPP family has members PHLPP1 (also called hSCOP/Suprachiasmatic nucleus circadian oscillatory protein; PLEKHE1/Pleckstrin homology domain-containing family E member 1) and PHLPP2 (PHLPP-like/PHLPPL). The PHLPP family of novel Ser/Thr phosphatases serve as important regulators of cell survival and apoptosis. PHLPP isozymes catalyze the dephosphorylation of a conserved regulatory motif, the hydrophobic motif, on the AGC kinases Akt, PKC, and S6 kinase, as well as an inhibitory site on the kinase Mst1, to inhibit cellular proliferation and induce apoptosis and negatively regulates ERK1/2 activation. Reductions in their expression have been detected in several cancers and linked to cancer progression. PHLPP1 and PHLPP2 both contain an N-terminal PH domain, followed by 21 LRR (leucine-rich) repeats, and a C-terminal PP2C-like domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 95 matched cddid_all.tbl CDD cd13323 cd13323 270132 PH_PLEKHN1 Pleckstrin homology domain containing family N member 1Pleckstrin homology-like domain. Not much is known about PLEKHN1. It is found in a wide range of animals including humans, green anole, frog, and zebrafish. It contains a single PH domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 121 matched cddid_all.tbl CDD cd13324 cd13324 270133 PH_Gab-like Grb2-associated binding protein family Pleckstrin homology (PH) domain. Gab proteins are scaffolding adaptor proteins, which possess N-terminal PH domains and a C-terminus with proline-rich regions and multiple phosphorylation sites. Following activation of growth factor receptors, Gab proteins are tyrosine phosphorylated and activate PI3K, which generates 3-phosphoinositide lipids. By binding to these lipids via the PH domain, Gab proteins remain in proximity to the receptor, leading to further signaling. While not all Gab proteins depend on the PH domain for recruitment, it is required for Gab activity. There are 3 families: Gab1, Gab2, and Gab3. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 112 matched cddid_all.tbl CDD cd13325 cd13325 270134 PH_unc89 unc89 pleckstrin homology (PH) domain. unc89 is a myofibrillar protein. unc89-B the largest isoform is composed of 53 immunoglobulin (Ig) domains, 2 Fn3 domains, a triplet of SH3, DH and PH domains at its N-terminus, and 2 protein kinase domains (PK1 and PK2) at its C-terminus. unc-89 mutants display disorganization of muscle A-bands, and usually lack M-lines. The COOH-terminal region of obscurin, the human homolog of unc89, interacts via two specific Ig-like domains with the NH(2)-terminal Z-disk region of titin, a protein that connects the Z line to the M line in the sarcomere and contributes to the contraction of striated muscle. obscurin is also thought to be involved in Ca2+/calmodulin via its IQ domains, as well as G protein-coupled signal transduction in the sarcomere via its RhoGEF/DH domain. The DH-PH region of OBSCN and unc89, the C. elegans homolog, has exchange activity for RhoA and Rho-1 respectively, but not for the small GTPases homologous to Cdc42 or Rac. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 114 matched cddid_all.tbl CDD cd13326 cd13326 270135 PH_CNK_insect-like Connector enhancer of KSR (Kinase suppressor of ras) (CNK) pleckstrin homology (PH) domain. CNK family members function as protein scaffolds, regulating the activity and the subcellular localization of RAS activated RAF. There is a single CNK protein present in Drosophila and Caenorhabditis elegans in contrast to mammals which have 3 CNK proteins (CNK1, CNK2, and CNK3). All of the CNK members contain a sterile a motif (SAM), a conserved region in CNK (CRIC) domain, and a PSD-95/DLG-1/ZO-1 (PDZ) domain, and a PH domain. A CNK2 splice variant CNK2A also has a PDZ domain-binding motif at its C terminus and Drosophila CNK (D-CNK) also has a domain known as the Raf-interacting region (RIR) that mediates binding of the Drosophila Raf kinase. This cd contains CNKs from insects, spiders, mollusks, and nematodes. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 91 matched cddid_all.tbl CDD cd13327 cd13327 270136 PH_PLEKHM3_2 Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 2. PLEKHM3 (also called differentiation associated protein/DAPR)(also called differentiation associated protein/DAPR) exists as three alternatively spliced isoforms that participate in metal ion binding. It contains 2 PH domains and 1 phorbol-ester/DAG-type zinc finger domain. PLEKHM3 is found in Humans, canines, bovine, mouse, rat, chicken and zebrafish. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 88 matched cddid_all.tbl CDD cd13328 cd13328 275410 PH1_FDG_family FYVE, RhoGEF and PH domain containing/faciogenital dysplasia family proteins, N-terminal Pleckstrin homology (PH) domain. In general, FGDs have a RhoGEF (DH) domain, followed by an N-terminal PH domain, a FYVE domain and a C-terminal PH domain. All FGDs are guanine nucleotide exchange factors that activates the Rho GTPase Cdc42, an important regulator of membrane trafficking. The RhoGEF domain is responsible for GEF catalytic activity, while the N-terminal PH domain is involved in intracellular targeting of the DH domain. Mutations in the FGD1 gene are responsible for the X-linked disorder known as faciogenital dysplasia (FGDY). PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 92 matched cddid_all.tbl CDD cd13329 cd13329 275411 PH_RhoGEF Rho guanine nucleotide exchange factor Pleckstrin homology domain. RhoGEFs belongs to regulator of G-protein signaling (RGS) domain-containing RhoGEFs that are RhoA-selective and directly activated by the Galpha12/13 family of heterotrimeric G proteins. The members here all contain Dbl homology (DH)-PH domains. In addition some members contain N-terminal C1 (Protein kinase C conserved region 1) domains, PDZ (also called DHR/Dlg homologous regions) domains, ANK (ankyrin) domains, and RGS (Regulator of G-protein signalling) domains or C-terminal ATP-synthase B subunit. The DH-PH domains bind and catalyze the exchange of GDP for GTP on RhoA. RhoGEF2/Rho guanine nucleotide exchange factor 2, p114RhoGEF/p114 Rho guanine nucleotide exchange factor, p115RhoGEF, p190RhoGEF, PRG/PDZ Rho guanine nucleotide exchange factor, RhoGEF 11, RhoGEF 12, RhoGEF 18, AKAP13/A-kinase anchoring protein 13, and LARG/Leukemia-associated Rho guanine nucleotide exchange factor are included in this CD. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 109 matched cddid_all.tbl CDD cd13330 cd13330 241484 PH_CARM1 Coactivator-Associated Methyltransferase 1 Pleckstrin homology (PH) domain. CARM1 (also known as protein arginine methyltransferase 4/PRMT4) is a protein arginine methyltransferase recruited by several transcription factors. It methylates a variety of proteins and plays a role in gene expression. The N-terminal domain of CARM1 contains a N-terminal PH domain, a catalytic core module composed of two parts (a Rossmann fold topology (RF) and a beta-barrel), and a C-terminal domain. The N-terminal and the C-terminal end of CARM1 catalytic module contain molecular switches that may explain how CARM1 regulates its biological activities by protein-protein interactions. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 107 matched cddid_all.tbl CDD cd13331 cd13331 270139 PH_Avo1 Avo1 Pleckstrin homology (PH) domain. Target of rapamycin (TOR) is a highly conserved serine/threonine protein kinase and a central controller of the growth, metabolism and ageing of eukaryotic cells. TOR assembles into two protein complexes termed TOR complex 1 (TORC1) and TOR complex 2 (TORC2) which function as central nodes in a complex network of signal transduction pathways that are involved in normal physiological as well as pathogenic events. TORC1 mediates the rapamycin-sensitive signalling branch, which positively regulates anabolic processes and negatively regulates catabolic processes. TORC2 signalling is rapamycinin insensitive and is involved in the spatial aspects of cell growth by controlling the actin cytoskeleton and cell polarity. In Saccharomyces cerevisiae, TORC2 is involved in the regulation of ceramide metabolism. In S. cerevisiae, TORC1 consists of the proteins Kog1, Lst8, Tco89 and either Tor1 or Tor2, while TORC2 consists of the proteins Avo1, Avo2, Avo3, Bit61, Lst8 and Tor2. The C-terminal domain of the Saccharomyces cerevisiae TORC2 component Avo1 is required for plasma-membrane localization of TORC2 and is essential for yeast viability. The C-termini of Avo1 and Sin1, its Human ortholog, both have the pleckstrin homology (PH) domain fold. Comparison with known PH-domain structures suggests a putative binding site for phosphoinositides. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 108 matched cddid_all.tbl CDD cd13332 cd13332 275412 FERM_C_JAK1 FERM domain C-lobe of Janus kinase 1. JAK1 is a tyrosine kinase protein essential in signaling type I and type II cytokines. It interacts with the gamma chain of type I cytokine receptors to elicit signals from the IL-2 receptor family, the IL-4 receptor family, the gp130 receptor family, ciliary neurotrophic factor receptor (CNTF-R), neurotrophin-1 receptor (NNT-1R) and Leptin-R). It also is involved in transducing a signal by type I (IFN-alpha/beta) and type II (IFN-gamma) interferons, and members of the IL-10 family via type II cytokine receptors. JAK (also called Just Another Kinase) is a family of intracellular, non-receptor tyrosine kinases that transduce cytokine-mediated signals via the JAK-STAT pathway. The JAK family in mammals consists of 4 members: JAK1, JAK2, JAK3 and TYK2. JAKs are composed of seven JAK homology (JH) domains (JH1-JH7) . The C-terminal JH1 domain is the main catalytic domain, followed by JH2, which is often referred to as a pseudokinase domain, followed by JH3-JH4 which is homologous to the SH2 domain, and lastly JH5-JH7 which is a FERM domain. Named after Janus, the two-faced Roman god of doorways, JAKs possess two near-identical phosphate-transferring domains; one which displays the kinase activity (JH1), while the other negatively regulates the kinase activity of the first (JH2). The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 144 matched cddid_all.tbl CDD cd13333 cd13333 270141 FERM_C_JAK2 FERM domain C-lobe of Janus kinase (JAK) 2. JAK2 has been implicated in signaling by members of the type II cytokine receptor family, the GM-CSF receptor family, the gp130 receptor family, and the single chain receptors. JAK2 orthologs have been identified in all mammals. Mutations in JAK2 have been implicated in polycythemia vera, essential thrombocythemia, myelofibrosis as well as other myeloproliferative disorders. JAK2 gene fusions with the PCM1 and TEL(ETV6) (TEL-JAK2) genes have been found in leukemia patients. Researcher are targetting JAK2 inhibitors in the treatment of patients with prostate cancer. JAK2 has been shown to interact with a variety of proteins including growth hormone receptor, STAT5A, STAT5B, interleukin 5 receptor alpha subunit, interleukin 12 receptor, SOCS3, PTPN6,PTPN11, Grb2, VAV1, and YES1. JAK (also called Just Another Kinase) is a family of intracellular, non-receptor tyrosine kinases that transduce cytokine-mediated signals via the JAK-STAT pathway. The JAK family in mammals consists of 4 members: JAK1, JAK2, JAK3 and TYK2. JAKs are composed of seven JAK homology (JH) domains (JH1-JH7) . The C-terminal JH1 domain is the main catalytic domain, followed by JH2, which is often referred to as a pseudokinase domain, followed by JH3-JH4 which is homologous to the SH2 domain, and lastly JH5-JH7 which is a FERM domain. Named after Janus, the two-faced Roman god of doorways, JAKs possess two near-identical phosphate-transferring domains; one which displays the kinase activity (JH1), while the other negatively regulates the kinase activity of the first (JH2). The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 113 matched cddid_all.tbl CDD cd13334 cd13334 275413 FERM_C_JAK3 FERM domain C-lobe of Janus kinase (JAK) 3. JAK3 functions in signal transduction and interacts with members of the STAT (signal transduction and activators of transcription) family. It is required for signaling of the type I receptors that use the common gamma chain: IL-2, IL-4, IL-7, IL-9, IL-15 and IL-21. Cytokine binding induces the association of separate cytokine receptor subunits and the activation of the receptor-associated JAKs. In the absence of cytokine, JAKs lack protein tyrosine kinase activity. Once activated, the JAKs create docking sites for the STAT transcription factors by phosphorylation of specific tyrosine residues on the cytokine receptor subunits. Unlike the ubiquitous expression of JAK1, JAK2 and Tyk2, JAK3 is predominantly expressed in hematopoietic cells, such as NK cells, T cells and B cells. Mutations of JAK3 result in severe combined immunodeficiency (SCID). In addition to its well-known roles in T cells and NK cells, JAK3 has recently been found to inhibits IL-8-mediated chemotaxis. JAK3 interacts with CD247, TIAF1, and IL2RG. JAK (also called Just Another Kinase) is a family of intracellular, non-receptor tyrosine kinases that transduce cytokine-mediated signals via the JAK-STAT pathway. The JAK family in mammals consists of 4 members: JAK1, JAK2, JAK3 and TYK2. JAKs are composed of seven JAK homology (JH) domains (JH1-JH7) . The C-terminal JH1 domain is the main catalytic domain, followed by JH2, which is often referred to as a pseudokinase domain, followed by JH3-JH4 which is homologous to the SH2 domain, and lastly JH5-JH7 which is a FERM domain. Named after Janus, the two-faced Roman god of doorways, JAKs possess two near-identical phosphate-transferring domains; one which displays the kinase activity (JH1), while the other negatively regulates the kinase activity of the first (JH2). The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 110 matched cddid_all.tbl CDD cd13335 cd13335 275414 FERM_C_TYK2 FERM domain C-lobe of Non-receptor tyrosine-protein kinase TYK2. Tyk2 functions primarily in IL-12 and type I-IFN signaling as well as transduction of IL-23, IL-10, and IL-6 signals. A mutation in the Tyk2 gene has been associated with hyperimmunoglobulin E syndrome (HIES), a primary immunodeficiency characterized by elevated serum immunoglobulin E. Tyk2 has been shown to interact with FYN, PTPN6, IFNAR1, Ku80 and GNB2L1. JAK (also called Just Another Kinase) is a family of intracellular, non-receptor tyrosine kinases that transduce cytokine-mediated signals via the JAK-STAT pathway. The JAK family in mammals consists of 4 members: JAK1, JAK2, JAK3 and TYK2. JAKs are composed of seven JAK homology (JH) domains (JH1-JH7) . The C-terminal JH1 domain is the main catalytic domain, followed by JH2, which is often referred to as a pseudokinase domain, followed by JH3-JH4 which is homologous to the SH2 domain, and lastly JH5-JH7 which is a FERM domain. Named after Janus, the two-faced Roman god of doorways, JAKs possess two near-identical phosphate-transferring domains; one which displays the kinase activity (JH1), while the other negatively regulates the kinase activity of the first (JH2). The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 158 matched cddid_all.tbl CDD cd13336 cd13336 275415 FERM-like_C_SNX31 Atypical FERM-like domain C-lobe of Sorting nexin 31. SNX31 functions in regulating recycling from endosomes to the cell surface. SNX31 contains a N-terminal PX domain, a FERM-like domain, and a unique C-terminal region. It bind Ras GTPase through its FERM-like domains. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. These interactions place the PX-FERM-like proteins at a hub of endosomal sorting and signaling processes. These proteins participate in a network of interactions that will impact on both endosomal protein trafficking and compartment specific Ras signaling cascades. The typical FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. FERM domains are found in cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 113 matched cddid_all.tbl CDD cd13337 cd13337 270145 FERM-like_C_SNX17 Atypical FERM-like domain C-lobe of Sorting nexin 17. SNX17 is a beta1-integrin-tail-binding protein that interacts with the free kindlin-binding site in endosomes to stabilize beta1 integrins, resulting in their recycling to the cell surface where they can be reused. SNX17 contains a N-terminal PX domain, a FERM-like domain, and a unique C-terminal region. SNX17 binds Ras GTPase through its FERM-like domains. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. These interactions place the PX-FERM-like proteins at a hub of endosomal sorting and signaling processes. These proteins participate in a network of interactions that will impact on both endosomal protein trafficking and compartment specific Ras signaling cascades. The typical FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. FERM domains are found in cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 113 matched cddid_all.tbl CDD cd13338 cd13338 270146 FERM-like_C_SNX27 Atypical FERM-like domain C-lobe of Sorting nexin 27. SNX27 is localized to early endosomes and known to regulate the intracellular trafficking of ion channels and receptors. SNX27 contain a N-terminal PDZ domain, a PX domain, and a FERM-like domain. SNX27 regulates trafficking of a PAK interacting exchange factor-G protein-coupled receptor kinase interacting protein complex via its PDZ domain interaction. Sorting nexin 27 interacts with multidrug resistance-associated protein 4 (MRP4). SNX27 binds Ras GTPase through its FERM-like domains. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. These interactions place the PX-FERM-like proteins at a hub of endosomal sorting and signaling processes. These proteins participate in a network of interactions that will impact on both endosomal protein trafficking and compartment specific Ras signaling cascades. The typical FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. FERM domains are found in cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs), the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites. 102 matched cddid_all.tbl CDD cd13339 cd13339 275416 PH-GRAM_MTMR13 Myotubularian (MTM) related 13 protein Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTMR13 (also called SBF2/SET binding factor 2) is a catalytically inactive phosphatase that plays a role as an adapter for the phosphatase myotubularin to regulate myotubularintracellular location. It contains a Leu residue instead of a conserved Cys residue in the dsPTPase catalytic loop which renders it catalytically inactive as a phosphatase. MTMR13 has high sequence similarity to MTMR5 and has recently been shown to be a second gene mutated in type 4B Charcot-Marie-Tooth syndrome. Both MTMR5 and MTMR13 contain an N-terminal DENN domain, a PH-GRAM domain, an inactive PTP domain, a SET interaction domain, a coiled-coil domain, and a C-terminal PH domain. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The PH domain family possesses multiple functions including the ability to bind phosphoinositides via its beta1/beta2, beta3/beta4, and beta6/beta7 connecting loops and to other proteins. However, no phosphoinositide binding sites have been found for the MTMRs to date. 119 matched cddid_all.tbl CDD cd13340 cd13340 275417 PH-GRAM_MTMR5 Myotubularian (MTM) related 5 protein (MTMR5) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTMR5 (also called SBF1/SET binding factor 1) is a catalytically inactive phosphatase that plays a role as an adapter for the phosphatase myotubularin to regulate myotubularintracellular location. It lacks several amino acids in the dsPTPase catalytic pocket which renders it catalytically inactive as a phosphatase. MTMR5 is the most well-studied inactive member of this family and has been implicated in cellular growth control and oncogenic transformation. MTMR5 and MTMR13 contain an N-terminal DENN domain, a PH-GRAM domain, an inactive PTP domain, a SET interaction domain, a coiled-coil domain, and a C-terminal PH domain. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The PH domain family possesses multiple functions including the ability to bind phosphoinositides via its beta1/beta2, beta3/beta4, and beta6/beta7 connecting loops and to other proteins. However, no phosphoinositide binding sites have been found for the MTMRs to date. 119 matched cddid_all.tbl CDD cd13341 cd13341 270149 PH-GRAM_MTMR3 Myotubularian (MTM) related 3 protein (MTMR3) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTMR3 is a member of the myotubularin dual specificity protein phosphatase gene family. MTMR3 binds to phosphoinositide lipids through its PH-GRAM domain, and can hydrolyze phosphatidylinositol(3)-phosphate and phosphatidylinositol(3,5)-biphosphate in vitro. The protein can self-associate and also form heteromers with MTMR4. Both MTMR3 and MTMR4 contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an active PTP domain, a SET-interaction domain, a coiled-coil region, and a C-terminal lipid-binding FYVE domain which binds phosphotidylinositol-3-phosphate. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The PH domain family possesses multiple functions including the ability to bind phosphoinositides via its beta1/beta2, beta3/beta4, and beta6/beta7 connecting loops and to other proteins. However, no phosphoinositide binding sites have been found for the MTMRs to date. 94 matched cddid_all.tbl CDD cd13342 cd13342 270150 PH-GRAM_MTMR4 Myotubularian (MTM) related 4 protein (MTMR4) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTMR4 is a member of the myotubularin dual specificity protein phosphatase gene family. MTMR4 binds to phosphoinositide lipids through its PH-GRAM domain, and can hydrolyze phosphatidylinositol(3)-phosphate and phosphatidylinositol(3,5)-biphosphate in vitro. The protein form heteromers with MTMR3. Both MTMR3 and MTMR4 contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an active PTP domain, a SET-interaction domain, a coiled-coil region, and a C-terminal lipid-binding FYVE domain which binds phosphotidylinositol-3-phosphate. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The PH domain family possesses multiple functions including the ability to bind phosphoinositides via its beta1/beta2, beta3/beta4, and beta6/beta7 connecting loops and to other proteins. However, no phosphoinositide binding sites have been found for the MTMRs to date. 114 matched cddid_all.tbl CDD cd13343 cd13343 270151 PH-GRAM_MTMR6 Myotubularian (MTM) related (MTMR) 6 protein Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTMR6 is a member of the myotubularin dual specificity protein phosphatase gene family. MTMR6 binds to phosphoinositide lipids through its PH-GRAM domain. It acts as a negative regulator of KCNN4/KCa3.1 channel activity in CD4+ T-cells possibly by decreasing intracellular levels of phosphatidylinositol-3 phosphatase and negatively regulates proliferation of reactivated CD4+ T-cells MTMR6 interacts with MTMR7, MTMR8 and MTMR9. MTMR6 contains a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an active PTP domain, a SET-interaction domain, and a C-terminal coiled-coil region. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The PH domain family possesses multiple functions including the ability to bind phosphoinositides via its beta1/beta2, beta3/beta4, and beta6/beta7 connecting loops and to other proteins. However, no phosphoinositide binding sites have been found for the MTMRs to date. 101 matched cddid_all.tbl CDD cd13344 cd13344 270152 PH-GRAM_MTMR7 Myotubularian (MTM) related 7 protein (MTMR7) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTMR7 is a member of the myotubularin dual specificity protein phosphatase gene family. MTMR6 binds to phosphoinositide lipids through its PH-GRAM domain and can hydrolyze phosphatidylinositol(3)-phosphate and phosphatidylinositol(3,5)-biphosphate. MTMR7 interacts with MTMR6, MTMR8 and MTMR9. MTMR7 contains a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an active PTP domain, a SET-interaction domain, and a C-terminal coiled-coil region. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The PH domain family possesses multiple functions including the ability to bind phosphoinositides via its beta1/beta2, beta3/beta4, and beta6/beta7 connecting loops and to other proteins. However, no phosphoinositide binding sites have been found for the MTMRs to date. 103 matched cddid_all.tbl CDD cd13345 cd13345 270153 PH-GRAM_MTMR8 Myotubularian (MTM) related 8 protein (MTMR8) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTMR8 is a member of the myotubularin dual specificity protein phosphatase gene family. MTMR8 binds to phosphoinositide lipids through its PH-GRAM domain. MTMR8 can self associate and interacts with MTMR6, MTMR7 and MTMR9. MTMR8 contains a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an active PTP domain, a SET-interaction domain, and a C-terminal coiled-coil region. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The PH domain family possesses multiple functions including the ability to bind phosphoinositides via its beta1/beta2, beta3/beta4, and beta6/beta7 connecting loops and to other proteins. However, no phosphoinositide binding sites have been found for the MTMRs to date. 103 matched cddid_all.tbl CDD cd13346 cd13346 270154 PH-GRAM_MTMR10 Myotubularian (MTM) related 10 protein (MTMR10) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTMR10 is a catalytically inactive phosphatase that plays a role as an adapter for the phosphatase myotubularin to regulate myotubularintracellular location. It contains a Glu residue instead of a conserved Cys residue in the dsPTPase catalytic loop which renders it catalytically inactive as a phosphatase. MTMR10 contains an N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an inactive PTP domain, and a SET interaction domain. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The PH domain family possesses multiple functions including the ability to bind phosphoinositides via its beta1/beta2, beta3/beta4, and beta6/beta7 connecting loops and to other proteins. However, no phosphoinositide binding sites have been found for the MTMRs to date. 177 matched cddid_all.tbl CDD cd13348 cd13348 275418 PH-GRAM_MTMR12 Myotubularian (MTM) related 12 protein (MTMR12) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTMR12 is a catalytically inactive phosphatase that plays a role as an adapter for the phosphatase myotubularin to regulate myotubularintracellular location. It contains a Glu residue instead of a conserved Cys residue in the dsPTPase catalytic loop which renders it catalytically inactive as a phosphatase. MTMR12 contains an N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an inactive PTP domain, a SET interaction domain, and a C-terminal a coiled-coil domain. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The PH domain family possesses multiple functions including the ability to bind phosphoinositides via its beta1/beta2, beta3/beta4, and beta6/beta7 connecting loops and to other proteins. However, no phosphoinositide binding sites have been found for the MTMRs to date. 178 matched cddid_all.tbl CDD cd13349 cd13349 270156 PH-GRAM1_TBC1D8 TBC1 domain family member 8 (TBC1D8; also called Vascular Rab-GAP/TBC-containing protein) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain, repeat 1. TBC1D8 may act as a GTPase-activating protein for Rab family protein(s). TBC1D8 contains an N-terminal PH-GRAM domain and a C-terminal Rab-GTPase-TBC (Tre-2, BUB2p, and Cdc16p) domain. This cd contains the first repeat of the PH-GRAM domain. The GRAM domain is found in glucosyltransferases, myotubularins and other putative membrane-associated proteins. The GRAM domain is part of a larger motif with a pleckstrin homology (PH) domain fold. 99 matched cddid_all.tbl CDD cd13350 cd13350 275419 PH-GRAM1_TBC1D8B TBC1 domain family member 8B (TBC1D8B) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain, repeat 1. TBC1D8B may act as a GTPase-activating protein for Rab family protein(s). TBC1D8B contains an N-terminal PH-GRAM domain and a C-terminal Rab-GTPase-TBC (Tre-2, BUB2p, and Cdc16p) domain. This cd contains the first repeat of the PH-GRAM domain. The GRAM domain is found in glucosyltransferases, myotubularins and other putative membrane-associated proteins. The GRAM domain is part of a larger motif with a pleckstrin homology (PH) domain fold. 99 matched cddid_all.tbl CDD cd13351 cd13351 275420 PH-GRAM1_TCB1D9_TCB1D9B TBC1 domain family members 9 and 9B (TBC1D9 and TBC1D9B) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain, repeat 1. TBC1D9 and TCB1D9B may act as a GTPase-activating proteins for Rab family protein(s). TBC1D9 and TCB1D9B contain two N-terminal PH-GRAM domain and a C-terminal Rab-GTPase-TBC (Tre-2, BUB2p, and Cdc16p) domain. This cd contains the first repeat of the PH-GRAM domain. The GRAM domain is found in glucosyltransferases, myotubularins and other putative membrane-associated proteins. The GRAM domain is part of a larger motif with a pleckstrin homology (PH) domain fold. 99 matched cddid_all.tbl CDD cd13352 cd13352 270159 PH-GRAM2_TBC1D8B TBC1 domain family member 8B (TBC1D8B) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain, repeat 2. TBC1D8B may act as a GTPase-activating protein for Rab family protein(s). TBC1D8B contains an N-terminal PH-GRAM domain and a C-terminal Rab-GTPase-TBC (Tre-2, BUB2p, and Cdc16p) domain. This cd contains the second repeat of the PH-GRAM domain. The GRAM domain is found in glucosyltransferases, myotubularins and other putative membrane-associated proteins. The GRAM domain is part of a larger motif with a pleckstrin homology (PH) domain fold. 93 matched cddid_all.tbl CDD cd13353 cd13353 270160 PH-GRAM2_TBC1D8 TBC1 domain family member 8 (TBC1D8; also called Vascular Rab-GAP/TBC-containing protein) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain, repeat 2. TBC1D8 may act as a GTPase-activating protein for Rab family protein(s). TBC1D8 contains two N-terminal PH-GRAM domain and a C-terminal Rab-GTPase-TBC (Tre-2, BUB2p, and Cdc16p) domain. This cd contains the second repeat of the PH-GRAM domain. The GRAM domain is found in glucosyltransferases, myotubularins and other putative membrane-associated proteins. The GRAM domain is part of a larger motif with a pleckstrin homology (PH) domain fold. 96 matched cddid_all.tbl CDD cd13354 cd13354 270161 PH-GRAM2_TCB1D9_TCB1D9B TBC1 domain family members 9 and 9B (TBC1D9 and TBC1D9B) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain, repeat 2. TBC1D9 and TCB1D9B may act as a GTPase-activating proteins for Rab family protein(s). TBC1D9 and TCB1D9B contain two N-terminal PH-GRAM domain and a C-terminal Rab-GTPase-TBC (Tre-2, BUB2p, and Cdc16p) domain. This cd contains the second repeat of the PH-GRAM domain. The GRAM domain is found in glucosyltransferases, myotubularins and other putative membrane-associated proteins. The GRAM domain is part of a larger motif with a pleckstrin homology (PH) domain fold. 97 matched cddid_all.tbl CDD cd13355 cd13355 270162 PH-GRAM_MTM1 Myotubularian 1 protein (MTM1) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTM1 is a member of the myotubularin protein phosphatase gene family. It is required for muscle cell differentiation and mutations in this gene have been identified as being responsible for X-linked myotubular myopathy, a severe congenital muscle disorder characterized by defective muscle cell development. Since its initial discovery, there have been an additional 14 myotubularin-related proteins identified. MTM1 binds to phosphoinositide lipids through its PH-GRAM domain, and can hydrolyze phosphatidylinositol(3)-phosphate and phosphatidylinositol(3,5)-biphosphate in vitro. The protein can self-associate and form heteromers with MTMR12. MTM1 contains a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an active PTP domain, a SET-interaction domain, and a C-terminal coiled-coil region. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. All MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE and PH domains C-terminal to the coiled-coil region. 100 matched cddid_all.tbl CDD cd13356 cd13356 270163 PH-GRAM_MTMR2_mammal-like Myotubularian related 2 protein (MTMR2) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTMR2 is a member of the myotubularin protein phosphatase gene family. MTMR2 binds to phosphoinositide lipids through its PH-GRAM domain, and can hydrolyze phosphatidylinositol(3)-phosphate and phosphatidylinositol(3,5)-biphosphate in vitro. Mutations in MTMR2 are a cause of Charcot-Marie-Tooth disease type 4B, an autosomal recessive demyelinating neuropathy. The protein can self-associate and form heteromers with MTMR5 and MTMR12. MTMR2 contains a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an active PTP domain, a SET-interaction domain, a coiled-coil region, and a C-terminal PDZ domain. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The PH domain family possesses multiple functions including the ability to bind phosphoinositides via its beta1/beta2, beta3/beta4, and beta6/beta7 connecting loops and to other proteins. However, no phosphoinositide binding sites have been found for the MTMRs to date.Members in this cd include mammals, chickens, anoles, human body lice, and aphids. 115 matched cddid_all.tbl CDD cd13357 cd13357 270164 PH-GRAM_MTMR2_insect-like Myotubularian related 2 protein (MTMR2) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTMR2 is a member of the myotubularin protein phosphatase gene family. MTMR2 binds to phosphoinositide lipids through its PH-GRAM domain, and can hydrolyze phosphatidylinositol(3)-phosphate and phosphatidylinositol(3,5)-biphosphate in vitro. Mutations in MTMR2 are a cause of Charcot-Marie-Tooth disease type 4B, an autosomal recessive demyelinating neuropathy. The protein can self-associate and form heteromers with MTMR5 and MTMR12. MTMR2 contains a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an active PTP domain, a SET-interaction domain, a coiled-coil region, and a C-terminal PDZ domain. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The PH domain family possesses multiple functions including the ability to bind phosphoinositides via its beta1/beta2, beta3/beta4, and beta6/beta7 connecting loops and to other proteins. However, no phosphoinositide binding sites have been found for the MTMRs to date. Members in this cd include Drosophila, sea urchins, mosquitos, bees, ticks, and anemones. 100 matched cddid_all.tbl CDD cd13358 cd13358 270165 PH-GRAM_MTMR1 Myotubularian related 1 protein (MTMR1) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTMR1 is a member of the myotubularin protein phosphatase gene family. MTMR1 binds to phosphoinositide lipids through its PH-GRAM domain, and can hydrolyze phosphatidylinositol(3)-phosphate and phosphatidylinositol(3,5)-biphosphate in vitro. MTMR1 contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an active PTP domain, a SET-interaction domain, a coiled-coil region, and a C-terminal PDZ domain. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. The PH domain family possesses multiple functions including the ability to bind phosphoinositides via its beta1/beta2, beta3/beta4, and beta6/beta7 connecting loops and to other proteins. However, no phosphoinositide binding sites have been found for the MTMRs to date. 100 matched cddid_all.tbl CDD cd13359 cd13359 270166 PH_ELMO1_CED-12 Engulfment and cell motility protein 1 pleckstrin homology (PH) domain. DOCK2 (Dedicator of cytokinesis 2), a hematopoietic cell-specific, atypical GEF, controls lymphocyte migration through Rac activation. A DOCK2-ELMO1 complex s necessary for DOCK2-mediated Rac signaling. DOCK2 contains a SH3 domain at its N-terminus, followed by a lipid binding DHR1 domain, and a Rac-binding DHR2 domain at its C-terminus. ELMO1, a mammalian homolog of C. elegans CED-12, contains the N-terminal RhoG-binding region, the ELMO domain, the PH domain, and the C-terminal sequence with three PxxP motifs. The C-terminal region of ELMO1, including the Pro-rich sequence, binds the SH3-containing region of DOCK2 forming a intermolecular five-helix bundle along with the PH domain of ELMO1. Autoinhibition of ELMO1 and DOCK2 is accomplished by the interactions of the EID and EAD domains and SH3 and DHR2 domains, respectively. The interaction of DOCK2 and ELMO1 mutually relieve their autoinhibition and results in the activation of Rac1. The PH domain of ELMO1 does not bind phosphoinositides due to the absence of key binding residues. It more closely resembles the FERM domain rather than other PH domains. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 126 matched cddid_all.tbl CDD cd13360 cd13360 241514 PH_PLC_fungal Fungal Phospholipase C (PLC) pleckstrin homology (PH) domain. Fungal PLC have mostly been characterized in the yeast Saccharomyces cerevisiae via deletion studies which resulted in a pleiotropic phenotype, with defects in growth, carbon source utilization, and sensitivity to osmotic stress and high temperature. Unlike Saccharomyces several other fungi including Neurospora crassa, Cryphonectria parasitica , and Magnaporthe oryzae (Mo) have several PLC proteins, some of which lack a PH domain, with varied functions. MoPLC1-mediated regulation of Ca2+ level is important for conidiogenesis and appressorium formation while both MoPLC2 and MoPLC3 are required for asexual reproduction, cell wall integrity, appressorium development, and pathogenicity. The fungal PLCs in this hierarchy contain an N-terminal PH domain, a EF hand domain, a catalytic domain split into X and Y halves, and a C-terminal C2 domain. PLCs (EC 3.1.4.3) play a role in the initiation of cellular activation, proliferation, differentiation and apoptosis. They are central to inositol lipid signalling pathways, facilitating intracellular Ca2+ release and protein kinase C (PKC) activation. Specificaly, PLCs catalyze the cleavage of phosphatidylinositol-4,5-bisphosphate (PIP2) and result in the release of 1,2-diacylglycerol (DAG) and inositol 1,4,5-triphosphate (IP3). These products trigger the activation of protein kinase C (PKC) and the release of Ca2+ from intracellular stores. There are fourteen kinds of mammalian phospholipase C proteins which are are classified into six isotypes (beta, gamma, delta, epsilon, zeta, eta). PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 118 matched cddid_all.tbl CDD cd13361 cd13361 270167 PH_PLC_beta Phospholipase C-beta (PLC-beta) pleckstrin homology (PH) domain. PLC-beta (PLCbeta) is regulated by heterotrimeric G protein-coupled receptors through their C2 domain and long C-terminal extension which forms an autoinhibitory helix. There are four isoforms: PLC-beta1-4. The PH domain of PLC-beta2 and PLC-beta3 plays a dual role, much like PLC-delta1, by binding to the plasma membrane, as well as the interaction site for the catalytic activator. However, PLC-beta binds to the lipid surface independent of PIP2. PLC-beta1 seems to play unspecified roles in cellular proliferation and differentiation. PLC-beta consists of an N-terminal PH domain, a EF hand domain, a catalytic domain split into X and Y halves, a C2 domain and a C-terminal PDZ. Members of the Rho GTPase family (e.g., Rac1, Rac2, Rac3, and cdc42) have been implicated in their activation by binding to an alternate site on the N-terminal PH domain. A basic amino acid region within the enzyme's long C-terminal tail appears to function as a Nuclear Localization Signal for import into the nucleus. PLCs (EC 3.1.4.3) play a role in the initiation of cellular activation, proliferation, differentiation and apoptosis. They are central to inositol lipid signalling pathways, facilitating intracellular Ca2+ release and protein kinase C (PKC) activation. Specificaly, PLCs catalyze the cleavage of phosphatidylinositol-4,5-bisphosphate (PIP2) and result in the release of 1,2-diacylglycerol (DAG) and inositol 1,4,5-triphosphate (IP3). These products trigger the activation of protein kinase C (PKC) and the release of Ca2+ from intracellular stores. There are fourteen kinds of mammalian phospholipase C proteins which are are classified into six isotypes (beta, gamma, delta, epsilon, zeta, eta). PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.the plasma membrane, but only a few (less than 10%) display strong specificity in binding inositol phosphates. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinases, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, cytoskeletal associated molecules, and in lipid associated enzymes. 127 matched cddid_all.tbl CDD cd13362 cd13362 270168 PH_PLC_gamma Phospholipase C-gamma (PLC-gamma) pleckstrin homology (PH) domain. PLC-gamma (PLCgamma) is activated by receptor and non-receptor tyrosine kinases due to the presence of its SH2 and SH3 domains. There are two main isoforms of PLC-gamma expressed in human specimens, PLC-gamma1 and PLC-gamma2. PLC-gamma consists of an N-terminal PH domain, a EF hand domain, a catalytic domain split into X and Y halves internal to which is a PH domain split by two SH2 domains and a single SH3 domain, and a C-terminal C2 domain. Only the first PH domain is present in this hierarchy. PLCs (EC 3.1.4.3) play a role in the initiation of cellular activation, proliferation, differentiation and apoptosis. They are central to inositol lipid signalling pathways, facilitating intracellular Ca2+ release and protein kinase C (PKC) activation. Specificaly, PLCs catalyze the cleavage of phosphatidylinositol-4,5-bisphosphate (PIP2) and result in the release of 1,2-diacylglycerol (DAG) and inositol 1,4,5-triphosphate (IP3). These products trigger the activation of protein kinase C (PKC) and the release of Ca2+ from intracellular stores. There are fourteen kinds of mammalian phospholipase C proteins which are are classified into six isotypes (beta, gamma, delta, epsilon, zeta, eta). PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 121 matched cddid_all.tbl CDD cd13363 cd13363 270169 PH_PLC_delta "Phospholipase C-delta (PLC-delta) pleckstrin homology (PH) domain. The PLC-delta (PLCdelta) consists of three family members, delta 1, 2, and 3. PLC-delta1 is the most well studied. PLC-delta is activated by high calcium levels generated by other PLC family members, and functions as a calcium amplifier within the cell. PLC-delta consists of an N-terminal PH domain, a EF hand domain, a catalytic domain split into X and Y halves, and a C-terminal C2 domain. The PH domain binds PIP2 and promotes activation of the catalytic core as well as tethering the enzyme to the plasma membrane. The C2 domain has been shown to mediate calcium-dependent phospholipid binding as well. The PH and C2 domains operate in concert as a ""tether and fix"" apparatus necessary for processive catalysis by the enzyme. Its leucine-rich nuclear export signal (NES) in its EF hand motif, as well as a Nuclear localization signal within its linker region allow PLC-delta 1 to actively translocate into and out of the nucleus. PLCs (EC 3.1.4.3) play a role in the initiation of cellular activation, proliferation, differentiation and apoptosis. They are central to inositol lipid signalling pathways, facilitating intracellular Ca2+ release and protein kinase C (PKC) activation. Specificaly, PLCs catalyze the cleavage of phosphatidylinositol-4,5-bisphosphate (PIP2) and result in the release of 1,2-diacylglycerol (DAG) and inositol 1,4,5-triphosphate (IP3). These products trigger the activation of protein kinase C (PKC) and the release of Ca2+ from intracellular stores. There are fourteen kinds of mammalian phospholipase C proteins which are are classified into six isotypes (beta, gamma, delta, epsilon, zeta, eta). PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes." 117 matched cddid_all.tbl CDD cd13364 cd13364 270170 PH_PLC_eta Phospholipase C-eta (PLC-eta) pleckstrin homology (PH) domain. PLC-eta (PLCeta) consists of two enzymes, PLCeta1 and PLCeta2. They hydrolyze phosphatidylinositol 4,5-bisphosphate, are more sensitive to Ca2+ than other PLC isozymes, and involved in PKC activation in the brain and neuroendocrine systems. PLC-eta consists of an N-terminal PH domain, a EF hand domain, a catalytic domain split into X and Y halves by a variable linker, a C2 domain, and a C-terminal PDZ domain. PLCs (EC 3.1.4.3) play a role in the initiation of cellular activation, proliferation, differentiation and apoptosis. They are central to inositol lipid signalling pathways, facilitating intracellular Ca2+ release and protein kinase C (PKC) activation. Specificaly, PLCs catalyze the cleavage of phosphatidylinositol-4,5-bisphosphate (PIP2) and result in the release of 1,2-diacylglycerol (DAG) and inositol 1,4,5-triphosphate (IP3). These products trigger the activation of protein kinase C (PKC) and the release of Ca2+ from intracellular stores. There are fourteen kinds of mammalian phospholipase C proteins which are are classified into six isotypes (beta, gamma, delta, epsilon, zeta, eta). PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes.involved in targeting proteins to the plasma membrane, but only a few (less than 10%) display strong specificity in binding inositol phosphates. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinases, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, cytoskeletal associated molecules, and in lipid associated enzymes. 109 matched cddid_all.tbl CDD cd13365 cd13365 270171 PH_PLC_plant-like Plant-like Phospholipase C (PLC) pleckstrin homology (PH) domain. PLC-gamma (PLCgamma) was the second class of PLC discovered. PLC-gamma consists of an N-terminal PH domain, a EF hand domain, a catalytic domain split into X and Y halves internal to which is a PH domain split by two SH2 domains and a single SH3 domain, and a C-terminal C2 domain. PLCs (EC 3.1.4.3) play a role in the initiation of cellular activation, proliferation, differentiation and apoptosis. They are central to inositol lipid signalling pathways, facilitating intracellular Ca2+ release and protein kinase C (PKC) activation. Specificaly, PLCs catalyze the cleavage of phosphatidylinositol-4,5-bisphosphate (PIP2) and result in the release of 1,2-diacylglycerol (DAG) and inositol 1,4,5-triphosphate (IP3). These products trigger the activation of protein kinase C (PKC) and the release of Ca2+ from intracellular stores. There are fourteen kinds of mammalian phospholipase C proteins which are are classified into six isotypes (beta, gamma, delta, epsilon, zeta, eta). This cd contains PLC members from fungi and plants. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 115 matched cddid_all.tbl CDD cd13366 cd13366 270172 PH_ABR Active breakpoint cluster region-related protein pleckstrin homology (PH) domain. The ABR protein contains multiple domains including a RhoGEF domain, a PH domain, a C1 domain, a C2 domain, and a C-terminal RhoGAP domain. It is related to a slightly larger protein, BCR, which is structurally similar, but has an additional N-terminal kinase domain. ABR has GAP activity for both Rac and Cdc42. It promotes the exchange of RAC or CDC42-bound GDP by GTP, thereby activating them. It is highly enriched in the brain and found to a lesser extent in heart, lung and muscle. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 185 matched cddid_all.tbl CDD cd13367 cd13367 270173 PH_BCR_vertebrate Breakpoint Cluster Region-related pleckstrin homology (PH) domain. The BCR gene is one of the two genes in the BCR-ABL complex, which is associated with the Philadelphia chromosome, a product of a reciprocal translocation between chromosomes 22 and 9. BCR is a GTPase-activating protein (GAP) for RAC1 (primarily) and CDC42. The Dbl region of BCR has the most RhoGEF activity for Cdc42, and less activity towards Rac and Rho. Since BCR possesses both GAP and GEF activities, it may function to temporally regulate the activity of these GTPases. It also displays serine/threonine kinase activity. The BCR protein contains multiple domains including an N-terminal kinase domain, a RhoGEF domain, a PH domain, a C1 domain, a C2 domain, and a C-terminal RhoGAP domain. This hierarchy is composed of vertebrate BCRs. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 194 matched cddid_all.tbl CDD cd13368 cd13368 270174 PH_BCR_arthropod Breakpoint Cluster Region-related pleckstrin homology (PH) domain. The BCR gene is one of the two genes in the BCR-ABL complex, which is associated with the Philadelphia chromosome, a product of a reciprocal translocation between chromosomes 22 and 9. BCR is a GTPase-activating protein (GAP) for RAC1 (primarily) and CDC42. The Dbl region of BCR has the most RhoGEF activity for Cdc42, and less activity towards Rac and Rho. Since BCR possesses both GAP and GEF activities, it may function to temporally regulate the activity of these GTPases. It also displays serine/threonine kinase activity. The BCR protein contains multiple domains including an N-terminal kinase domain, a RhoGEF domain, a PH domain, a C1 domain, a C2 domain, and a C-terminal RhoGAP domain. This hierarchy is composed of arthropod BCRs. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 180 matched cddid_all.tbl CDD cd13369 cd13369 270175 PH_RASAL1 Ras-GTPase-activating-like protein pleckstrin homology (PH) domain. RASAL1 is a member of the GAP1 family of GTPase-activating proteins, along with GAP1(m), GAP1(IP4BP) and CAPRI. RASAL1 contains two C2 domains, a PH domain, a RasGAP domain, and a BTK domain. RASAL1 contains two fully conserved C2 domains, a PH domain, a RasGAP domain, and a BTK domain. Its catalytic GAP domain has dual RasGAP and RapGAP activities, while its C2 domains bind phospholipids in the presence of Ca2+. Both CAPRI and RASAL1 are calcium-activated RasGAPs that inactivate Ras at the plasma membrane. Thereby enhancing the weak intrinsic GTPase activity of RAS proteins resulting in the inactive GDP-bound form of RAS and allowing control of cellular proliferation and differentiation. CAPRI and RASAL1 differ in that CAPRI is an amplitude sensor while RASAL1 senses calcium oscillations. This difference between them resides not in their C2 domains, but in their PH domains leading to speculation that this might reflect an association with either phosphoinositides and/or proteins. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 138 matched cddid_all.tbl CDD cd13370 cd13370 241521 PH_GAP1m_mammal-like GTPase activating protein 1 m pleckstrin homology (PH) domain. GAP1(m) (also called RASA2/RAS p21 protein activator (GTPase activating protein) 2) is a member of the GAP1 family of GTPase-activating proteins, along with RASAL1, GAP1(IP4BP), and CAPRI. With the notable exception of GAP1(m), they all possess an arginine finger-dependent GAP activity on the Ras-related protein Rap1. GAP1(m) contains two C2 domains, a PH domain, a RasGAP domain, and a BTK domain. Its C2 domains, like those of GAP1IP4BP, do not contain the C2 motif that is known to be required for calcium-dependent phospholipid binding. GAP1(m) is regulated by the binding of its PH domains to phophoinositides, PIP3 (phosphatidylinositol 3,4,5-trisphosphate). It suppresses RAS, enhancing the weak intrinsic GTPase activity of RAS proteins resulting in the inactive GDP-bound form of RAS, allowing control of cellular proliferation and differentiation. GAP1(m) binds inositol tetrakisphosphate (IP4). PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 133 matched cddid_all.tbl CDD cd13371 cd13371 241522 PH_GAP1_mammal-like GAP1(IP4BP) pleckstrin homology (PH) domain. GAP1 (also called IP4BP, RASA3/Ras GTPase-activating protein 3, and RAS p21 protein activator (GTPase activating protein) 3/GAPIII/MGC46517/MGC47588)) is a member of the GAP1 family of GTPase-activating proteins, along with RASAL1, GAP1(m), and CAPRI. With the notable exception of GAP1(m), they all possess an arginine finger-dependent GAP activity on the Ras-related protein Rap1. GAP1(IP4BP) contains two C2 domains, a PH domain, a RasGAP domain, and a BTK domain. Its C2 domains, like those of GAP1M, do not contain the C2 motif that is known to be required for calcium-dependent phospholipid binding. GAP1(IP4BP) is regulated by the binding of its PH domains to phophoinositides, PIP3 (phosphatidylinositol 3,4,5-trisphosphate) and PIP2 (phosphatidylinositol 4,5-bisphosphate). It suppresses RAS, enhancing the weak intrinsic GTPase activity of RAS proteins resulting in the inactive GDP-bound form of RAS, allowing control of cellular proliferation and differentiation. GAP1(IP4BP) binds tyrosine-protein kinase, HCK. Members here include humans, chickens, frogs, and fish. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 125 matched cddid_all.tbl CDD cd13372 cd13372 241523 PH_CAPRI Ca2+ promoted Ras inactivator pleckstrin homology (PH) domain. CAPRI (also called RASA4/RAS p21 protein activator (GTPase activating protein) 4/GAPL/FLJ59070/KIAA0538/MGC131890) is a member of the GAP1 family of GTPase-activating proteins. CAPRI contains two fully conserved C2 domains, a PH domain, a RasGAP domain, and a BTK domain. Its catalytic GAP domain has dual RasGAP and RapGAP activities, while its C2 domains bind phospholipids in the presence of Ca2+. Both CAPRI and RASAL are calcium-activated RasGAPs that inactivate Ras at the plasma membrane. Thereby enhancing the weak intrinsic GTPase activity of RAS proteins resulting in the inactive GDP-bound form of RAS and allowing control of cellular proliferation and differentiation. CAPRI and RASAL differ in that CAPRI is an amplitude sensor while RASAL senses calcium oscillations. This difference between them resides not in their C2 domains, but in their PH domains leading to speculation that this might reflect an association with either phosphoinositides and/or proteins. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 140 matched cddid_all.tbl CDD cd13373 cd13373 270176 PH_nGAP Neuronal growth-associated proteins Pleckstrin homology (PH) domain. nGAP (also called RASAL2/RAS protein activator like-3) is a member of the RasSynGAP family along with DOC-2/DAB2-interacting protein (DAB2IP) and synaptic RasGAP (SynGAP). nGAPs are growth cone markers found in multiple types of neurons. There are many nGAPs including Cap1 (Adenylate cyclase-associated protein 1), Capzb (Capping protein (actin filament) muscle Z-line, beta), Clptm1 (Cleft lip and palate associated transmembrane protein 1), Cotl1 (Coactosin-like 1), Crmp1 (Collapsin response mediator protein 1), Cyfip1 (Cytoplasmic FMR1 interacting protein 1), Fabp7 (Fatty acid binding protein 7, brain), Farp2 (FERM, RhoGEF and pleckstrin domain protein 2), Gap43 (Growth associated protein 43), Gnao1 (Guanine nucleotide binding protein (G protein), alpha activating activity polypeptide O), Gnai2 (Guanine nucleotide binding protein (G protein), alpha inhibiting 2), Pacs1 (Phosphofurin acidic cluster sorting protein 1), Rtn1 (Reticulon 1), Sept2 (Septin 2), Snap25 (Synaptosomal-associated protein 25), Strap (Serine/threonine kinase receptor associated protein), Stx7 (Syntaxin 7), and Tmod2 (Tropomodulin 2). PH domains are only found in eukaryotes. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 138 matched cddid_all.tbl CDD cd13374 cd13374 270177 PH_RASAL3 RAS protein activator like-3 Pleckstrin homology (PH) domain. RASAL3 is thought to be a Ras GTPase-activating protein. It is involved in positive regulation of Ras GTPase activity and of small GTPase mediated signal transduction as well as negative regulation of Ras protein signal transduction. It contains a PH domain, a C2 domain, and a Ras-GAP domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 146 matched cddid_all.tbl CDD cd13375 cd13375 270178 PH_SynGAP Synaptic Ras-GTPase activating protein Pleckstrin homology (PH) domain. SynGAP is a member of the RasSynGAP family along with DOC-2/DAB2-interacting protein (DAB2IP) and neuronal growth-associated protein (nGAP/RASAL2). SynGAP, a neuronal Ras-GAP, has been shown display both Ras-GAP activity and Ras-related protein (Rap)-GAP activity. Saccharomyces cerevisiae Bud2 and GAP1 members CAPRI (Ca2+-promoted Ras inactivator) and RASAL (Ras-GTPase-activating-like protein) also possess this dual activity. Human DOC-2/DAB2-interacting protein (DAB2IP) is encoded by a tumor suppressor gene and a newly recognized member of the Ras-GTPase-activating family. Members here include mammals, amphibians, and bony fish. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 189 matched cddid_all.tbl CDD cd13376 cd13376 270179 PH_DAB2IP DOC-2/Disabled homolog 2-interacting protein Pleckstrin homology (PH) domain. DAB2IP (also called AIP1/ASK1-interacting protein-1 and DIP1/2) is a member of the RasSynGAP family along with Synaptic Ras-GTPase activating protein (SynGAP) and neuronal growth-associated protein (nGAP/RASAL2). DAB2IP is a critical component of many signal transduction pathways mediated by Ras and tumor necrosis factors including apoptosis pathways, and it is involved in the formation of many types of tumors. DAB2IP participates in regulation of gene expression and pluripotency of cells. Human DAB2IP is expressed in the adrenal gland, pancreas, endocardium, stomach, kidney, testis, small intestine, liver, trachea, skin, ovary, endometrium, lung, esophagus and bladder. No expression was observed in the cerebrum, parotid gland, thymus, thyroid gland and spleen. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 182 matched cddid_all.tbl CDD cd13378 cd13378 241529 PH_RhoGAP2 Rho GTPase activating protein 2 Pleckstrin homology (PH) domain. RhoGAP2 (also called RhoGap22 or ArhGap22) are involved in cell polarity, cell morphology and cytoskeletal organization. They activate a GTPase belonging to the RAS superfamily of small GTP-binding proteins. The encoded protein is insulin-responsive, is dependent on the kinase Akt, and requires the Akt-dependent 14-3-3 binding protein which binds sequentially to two serine residues resulting in regulation of cell motility. Members here contain an N-terminal PH domain followed by a RhoGAP domain and either a BAR or TATA Binding Protein (TBP) Associated Factor 4 (TAF4) domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 116 matched cddid_all.tbl CDD cd13379 cd13379 241530 PH_RhoGap24 Rho GTPase activating protein 24 Pleckstrin homology (PH) domain. RhoGap24 (also called ARHGAP24, p73RhoGAp, and Filamin-A-associated RhoGAP) like other RhoGAPs are involved in cell polarity, cell morphology and cytoskeletal organization. They act as GTPase activators for the Rac-type GTPases by converting them to an inactive GDP-bound state and control actin remodeling by inactivating Rac downstream of Rho leading to suppress leading edge protrusion and promotes cell retraction to achieve cellular polarity and are able to suppress RAC1 and CDC42 activity in vitro. Overexpression of these proteins induces cell rounding with partial or complete disruption of actin stress fibers and formation of membrane ruffles, lamellipodia, and filopodia. Members here contain an N-terminal PH domain followed by a RhoGAP domain and either a BAR or TATA Binding Protein (TBP) Associated Factor 4 (TAF4) domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 114 matched cddid_all.tbl CDD cd13380 cd13380 270180 PH_Skap1 Src kinase-associated phosphoprotein 1 Pleckstrin homology (PH) domain. Adaptor protein Skap1 (also called Skap55/Src kinase-associated phosphoprotein of 55 kDa) and its partner, ADAP (adhesion and degranulation promoting adapter protein) help reorganize the cytoskeleton and/or promote integrin-mediated adhesion upon immunoreceptor activation. Skap1 is also involved in T Cell Receptor (TCR)-induced RapL-Rap1 complex formation and LFA-1 activation. Skap1 has an N-terminal coiled-coil conformation which is proposed to be involved in homodimer formation, a central PH domain and a C-terminal SH3 domain that associates with ADAP. The Skap1 PH domain plays a role in controlling integrin function via recruitment of ADAP-SKAP complexes to integrins as well as in controlling the ability of ADAP to interact with the CBM signalosome and regulate NF-kappaB. SKAP1 is necessary for RapL binding to membranes in a PH domain-dependent manner and the PI3K pathway. Skap adaptor proteins couple receptors to cytoskeletal rearrangements. Skap55/Skap1, Skap2, and Skap-homology (Skap-hom) have an N-terminal coiled-coil conformation, a central PH domain and a C-terminal SH3 domain. Their PH domains bind 3'-phosphoinositides as well as directly affecting targets such as in Skap55 where it directly affecting integrin regulation by ADAP and NF-kappaB activation or in Skap-hom where the dimerization and PH domains comprise a 3'-phosphoinositide-gated molecular switch that controls ruffle formation. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 106 matched cddid_all.tbl CDD cd13381 cd13381 270181 PH_Skap-hom_Skap2 Src kinase-associated phosphoprotein homolog and Skap 2 Pleckstrin homology (PH) domain. Adaptor protein Skap-hom, a homolog of Skap55, which interacts with actin and with ADAP (adhesion and degranulation promoting adapter protein) undergoes tyrosine phosphorylation in response to plating of bone marrow-derived macrophages on fibronectin. Skap-hom has an N-terminal coiled-coil conformation that is involved in homodimer formation, a central PH domain and a C-terminal SH3 domain that associates with ADAP. The Skap-hom PH domain regulates intracellular targeting; its interaction with the DM domain inhibits Skap-hom actin-based ruffles in macrophages and its binding to 3'-phosphoinositides reverses this autoinhibition. The Skap-hom PH domain binds PI[3,4]P2 and PI[3,4,5]P3, but not to PI[3]P, PI[5]P, or PI[4,5]P2. Skap2 is a downstream target of Heat shock transcription factor 4 (HSF4) and functions in the regulation of actin reorganization during lens differentiation. It is thought that SKAP2 anchors the complex of tyrosine kinase adaptor protein 2 (NCK20/focal adhesion to fibroblast growth factor receptors at the lamellipodium in lens epithelial cells. Skap2 has an N-terminal coiled-coil conformation which interacts with the SH2 domain of NCK2, a central PH domain and a C-terminal SH3 domain that associates with ADAP (adhesion and degranulation promoting adapter protein)/FYB (the Fyn binding protein). Skap2 PH domain binds to membrane lipids. Skap adaptor proteins couple receptors to cytoskeletal rearrangements. Src kinase-associated phosphoprotein of 55 kDa (Skap55)/Src kinase-associated phosphoprotein 1 (Skap1), Skap2, and Skap-hom have an N-terminal coiled-coil conformation, a central PH domain and a C-terminal SH3 domain. Their PH domains bind 3'-phosphoinositides as well as directly affecting targets such as in Skap55 where it directly affecting integrin regulation by ADAP and NF-kappaB activation or in Skap-hom where the dimerization and PH domains comprise a 3'-phosphoinositide-gated molecular switch that controls ruffle formation. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 106 matched cddid_all.tbl CDD cd13382 cd13382 270182 PH_OCRL1 oculocerebrorenal syndrome of Lowe 1 Pleckstrin homology-like domain. OCRL1 (also called INPP5F, LOCR, NPHL2, or phosphatidylinositol polyphosphate 5-phosphatase) hydrolyzes phosphatidylinositol 4,5-bisphosphate (PtIns(4,5)P2) and the signaling molecule phosphatidylinositol 1,4,5-trisphosphate (PtIns(1,4,5)P3), and thereby modulates cellular signaling events. It interact with APPL1, FAM109A and FAM109B and several Rab GTPases which might both target them to the specific membranes and as well as stimulating the phosphatase activity. OCRL1 contains a PH domain and a Rho-GAP domain. Patients with Lowe syndrome suffer primarily from congenital cataracts, neonatal hypotonia, intellectual disability and Fanconi syndrome. Mutations in OCRL are also found in a subset of patients with type 2 Dent disease, who selectively suffer from renal proximal tubular dysfunction. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 105 matched cddid_all.tbl CDD cd13383 cd13383 270183 PH_OCRL2 oculocerebrorenal syndrome of Lowe 2 Pleckstrin homology-like domain. OCRL2 ( also called IPNNB5, inositol polyphosphate-5-phosphatase, phosphoinositide 5-phosphatase, 5PTase, or type II inositol-1,4,5-trisphosphate 5-phosphatase) hydrolyzes phosphatidylinositol 4,5-bisphosphate (PtIns(4,5)P2) and the signaling molecule phosphatidylinositol 1,4,5-trisphosphate (PtIns(1,4,5)P3), and thereby modulates cellular signaling events. It interact with APPL1, FAM109A and FAM109B and several Rab GTPases which might both target them to the specific membranes and as well as stimulating the phosphatase activity. OCRL2 contains a PH domain and a Rho-GAP domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 108 matched cddid_all.tbl CDD cd13384 cd13384 241535 PH_Gab2_2 Grb2-associated binding protein family pleckstrin homology (PH) domain. The Gab subfamily includes several Gab proteins, Drosophila DOS and C. elegans SOC-1. They are scaffolding adaptor proteins, which possess N-terminal PH domains and a C-terminus with proline-rich regions and multiple phosphorylation sites. Following activation of growth factor receptors, Gab proteins are tyrosine phosphorylated and activate PI3K, which generates 3-phosphoinositide lipids. By binding to these lipids via the PH domain, Gab proteins remain in proximity to the receptor, leading to further signaling. While not all Gab proteins depend on the PH domain for recruitment, it is required for Gab activity. Members here include insect, nematodes, and crustacean Gab2s. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 115 matched cddid_all.tbl CDD cd13385 cd13385 270184 PH_Gab3 Grb2-associated binding protein 3 pleckstrin homology (PH) domain. The Gab subfamily includes several Gab proteins, Drosophila DOS and C. elegans SOC-1. They are scaffolding adaptor proteins, which possess N-terminal PH domains and a C-terminus with proline-rich regions and multiple phosphorylation sites. Following activation of growth factor receptors, Gab proteins are tyrosine phosphorylated and activate PI3K, which generates 3-phosphoinositide lipids. By binding to these lipids via the PH domain, Gab proteins remain in proximity to the receptor, leading to further signaling. While not all Gab proteins depend on the PH domain for recruitment, it is required for Gab activity. The members in this cd include the Gab1, Gab2, and Gab3 proteins. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 125 matched cddid_all.tbl CDD cd13386 cd13386 275421 PH1_FGD2 FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 2, N-terminal Pleckstrin homology (PH) domain. In general, FGDs have a RhoGEF (DH) domain, followed by an N-terminal PH domain, a FYVE domain and a C-terminal PH domain. All FGDs are guanine nucleotide exchange factors that activates the Rho GTPase Cdc42, an important regulator of membrane trafficking. The RhoGEF domain is responsible for GEF catalytic activity, while the N-terminal PH domain is involved in intracellular targeting of the DH domain. Not much is known about FGD2. FGD1 is the best characterized member of the group with mutations here leading to the X-linked disorder known as faciogenital dysplasia (FGDY). PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 108 matched cddid_all.tbl CDD cd13387 cd13387 275422 PH1_FGD3 FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 3, N-terminal Pleckstrin homology (PH) domain. In general, FGDs have a RhoGEF (DH) domain, followed by an N-terminal PH domain, a FYVE domain and a C-terminal PH domain. All FGDs are guanine nucleotide exchange factors that activates the Rho GTPase Cdc42, an important regulator of membrane trafficking. The RhoGEF domain is responsible for GEF catalytic activity, while the N-terminal PH domain is involved in intracellular targeting of the DH domain. Both FGD1 and FGD3 are targeted by the ubiquitin ligase SCF(FWD1/beta-TrCP) upon phosphorylation of two serine residues in its DSGIDS motif and subsequently degraded by the proteasome. However, FGD1 and FGD3 induced significantly different morphological changes in HeLa Tet-Off cells and while FGD1 induced long finger-like protrusions, FGD3 induced broad sheet-like protrusions when the level of GTP-bound Cdc42 was significantly increased by the inducible expression of FGD3. They also reciprocally regulated cell motility in inducibly expressed in HeLa Tet-Off cells, FGD1 stimulated cell migration while FGD3 inhibited it. FGD1 and FGD3 therefore play different roles to regulate cellular functions, even though their intracellular levels are tightly controlled by the same destruction pathway through SCF(FWD1/beta-TrCP). PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 108 matched cddid_all.tbl CDD cd13388 cd13388 275423 PH1_FGD1-4_like FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins 1-4 and similar proteins, N-terminal Pleckstrin homology (PH) domain. In general, FGDs have a RhoGEF (DH) domain, followed by an N-terminal PH domain, a FYVE domain and a C-terminal PH domain. All FGDs are guanine nucleotide exchange factors that activates the Rho GTPase Cdc42, an important regulator of membrane trafficking. The RhoGEF domain is responsible for GEF catalytic activity, while the N-terminal PH domain is involved in intracellular targeting of the DH domain. Mutations in the FGD1 gene are responsible for the X-linked disorder known as faciogenital dysplasia (FGDY). Both FGD1 and FGD3 are targeted by the ubiquitin ligase SCF(FWD1/beta-TrCP) upon phosphorylation of two serine residues in its DSGIDS motif and subsequently degraded by the proteasome. They play different roles to regulate cellular functions, even though their intracellular levels are tightly controlled by the same destruction pathway. FGD4 is one of the genes associated with Charcot-Marie-Tooth neuropathy type 4 (CMT4), a group of progressive motor and sensory axonal and demyelinating neuropathies that are distinguished from other forms of CMT by autosomal recessive inheritance. Those affected have distal muscle weakness and atrophy associated with sensory loss and, frequently, pes cavus foot deformity. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 94 matched cddid_all.tbl CDD cd13389 cd13389 275424 PH1_FGD5_FGD6 FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins 5 and 6, N-terminal Pleckstrin Homology (PH) domain. FGD5 regulates promotes angiogenesis of vascular endothelial growth factor (VEGF) in vascular endothelial cells, including network formation, permeability, directional movement, and proliferation. The specific function of FGD6 is unknown. In general, FGDs have a RhoGEF (DH) domain, followed by a PH domain, a FYVE domain and a C-terminal PH domain. All FGDs are guanine nucleotide exchange factors that activate the Rho GTPase Cdc42, an important regulator of membrane trafficking. The RhoGEF domain is responsible for GEF catalytic activity, while the PH domain is involved in intracellular targeting of the DH domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 124 matched cddid_all.tbl CDD cd13390 cd13390 275425 PH_LARG Leukemia-associated Rho guanine nucleotide exchange factor Pleckstrin homology (PH) domain. LARG (also called RhoGEF12) belongs to regulator of G-protein signaling (RGS) domain-containing RhoGEFs that are RhoA-selective and directly activated by the Galpha12/13 family of heterotrimeric G proteins. RhoGEFs activate Rho GTPases regulating cytoskeletal structure, gene transcription, and cell migration. LARG contains a N-terminal extension, followed by Dbl homology (DH)-PH domains which bind and catalyze the exchange of GDP for GTP on RhoA in addition to a RGS domain. The active site of RhoA adopts two distinct GDP-excluding conformations among the four unique complexes in the asymmetric unit. The LARG PH domain also contains a potential protein-docking site. LARG forms a homotetramer via its DH domains. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 138 matched cddid_all.tbl CDD cd13391 cd13391 275426 PH_PRG PDZ Rho guanine nucleotide exchange factor Pleckstrin homology (PH) domain. PRG (also called RhoGEF11) belongs to regulator of G-protein signaling (RGS) domain-containing RhoGEFs that are RhoA-selective and directly activated by the Galpha12/13 family of heterotrimeric G proteins. RhoGEFs activate Rho GTPases regulating cytoskeletal structure, gene transcription, and cell migration. PRG contains an N-terminal PDZ domain, a regulators of G-protein signaling-like (RGSL) domain, a linker region, and a C-terminal Dbl-homology (DH) and pleckstrin-homology (PH) domains which bind and catalyze the exchange of GDP for GTP on RhoA. As is the case in p115-RhoGEF, it is thought that the PRG activated by relieving autoinhibition caused by the linker region. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 142 matched cddid_all.tbl CDD cd13392 cd13392 275427 PH_AKAP13 A-kinase anchoring protein 13 Pleckstrin homology (PH) domain. The Rho-specific GEF activity of AKAP13 (also called Brx-1, AKAP-Lbc, and proto-Lbc) mediates signaling downstream of G-protein coupled receptors and Toll-like receptor 2. It plays a role in cell growth, cell development and actin fiber formation. Protein kinase A (PKA) binds and phosphorylates AKAP13, regulating its Rho-GEF activity. Alternative splicing of this gene in humans has at least 3 transcript variants encoding different isoforms (i.e. proto-/onco-Lymphoid blast crisis, Lbc and breast cancer nuclear receptor-binding auxiliary protein, Brx) containing a dbl oncogene homology (DH) domain and PH domain which are required for full transforming activity. The DH domain is associated with guanine nucleotide exchange activation while the PH domain has multiple functions including determine protein sub-cellular localisation via phosphoinositide interactions, while others bind protein partners. Other ligands include protein kinase C which is bound by the PH domain of AKAP13, serving to activate protein kinase D and mobilize a cardiac hypertrophy signaling pathway. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 103 matched cddid_all.tbl CDD cd13393 cd13393 275428 PH_ARHGEF2 Rho guanine nucleotide exchange factor 2 Pleckstrin homology (PH) domain. ARHGEF2, also called GEF-H1, acts as guanine nucleotide exchange factor (GEF) for RhoA GTPases. It is thought to play a role in actin cytoskeleton reorganization in different tissues since its activation induces formation of actin stress fibers. ARHGEF2 contains a C1 domain followed by Dbl-homology (DH) and pleckstrin-homology (PH) domains which bind and catalyze the exchange of GDP for GTP on RhoA. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 116 matched cddid_all.tbl CDD cd13394 cd13394 240521 Syo1_like Fungal symportin 1 (syo1) and similar proteins. This family of eukaryotic proteins includes Saccharomyces cerevisiae Ydl063c and Chaetomium thermophilum Syo1, which mediate the co-import of two ribosomal proteins, Rpl5 and Rpl11 (which both interact with 5S rRNA) into the nucleus. Import precedes their association with rRNA and subsequent ribosome assembly in the nucleolus. The primary structure of syo1 is a mixture of Armadillo- (ARM, N-terminal part of syo1) and HEAT-repeats (C-terminal part of syo1). 597 matched cddid_all.tbl CDD cd13395 cd13395 466846 ASKHA_NBD_Arp4_ACTL6-like nucleotide-binding domain (NBD) of the actin-related protein 4 (Arp4)-like subfamily. The Arp4-like subfamily includes Arp4, also called actin-like protein 4, from fungi and plants. Saccharomyces cerevisiae Arp4 acts synergistically with Arp8 to depolymerize F-actin; it binds ATP, but unlike conventional actin, does not form filaments. It is a component of the NuA4 histone acetyltransferase complex, the chromatin-remodeling INO80 complex and the SWR1 chromatin remodeling complex. Arabidopsis thaliana Arp4 is involved in several developmental processes including organization of plant organs, flowering time, anther development, flower senescence and fertility, probably by regulating the chromatin structure. This family also includes human homologs of yeast and plant, which are actin-like protein 6A (encoded by the ACTL6A gene; also known as ArpNbeta, 53 kDa BRG1-associated factor A/BRG1-associated factor 53A/BAF35A, and INO80 complex subunit K/INO80K) and actin-like protein 6B (encoded by the ACTL6B gene; also known as ArpNalpha, 53 kDa BRG1-associated factor B/BRG1-associated factor 53B/BAF35B). ACTL6A and ACTL6B are involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). They are components of numerous complexes with chromatin remodeling and histone acetyltransferase activity. ACTL6A is also a putative core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair. Schizosaccharomyces pombe actin-related protein 42 (Arp42) is also included in this family. It is also a component of SWI/SNF and RSC complexes. 413 matched cddid_all.tbl CDD cd13396 cd13396 466847 ASKHA_NBD_AtArp8-like nucleotide-binding domain (NBD) of Arabidopsis thaliana actin-related protein 8 (AtArp8) and similar proteins. Arabidopsis thaliana ARP8, also called F-box protein ARP8, is an F-Box protein localized to the nucleolus. It is ubiquitously expressed in all organs and cell types and has a cell cycle-dependent subcellular pattern of distribution: it is localized to the nucleolus in interphase cells and dispersed in the cytoplasm in mitotic cells. 332 matched cddid_all.tbl CDD cd13397 cd13397 466848 ASKHA_NBD_actin_Arp-T1-3 nucleotide-binding domain (NBD) of actin, actin-related proteins T1-T3 (Arp-T1-3), and similar proteins. The family includes actin and human actin-related proteins T1, T2, and T3. Actin is a ubiquitous protein involved in the formation of filaments that are major components of the cytoskeleton. It is a highly dynamic structural protein network involved in processes such as cell contraction, cell motility, vesicle trafficking, intracellular organization, cytokinesis, endocytosis and apoptosis. Arp-T1, encoded by ACTRT1/ARPT1 gene expressed in testis, negatively regulates the Hedgehog (SHH) signaling, binds to the promoter of the SHH signaling mediator, GLI1, and inhibits its expression. Arp-T2 (also called actin-related protein M2; encoded by ACTRT2/ARPM2 gene expressed in testis and various other cell types) and Arp-T3 (also called actin-related protein M1; encoded by ACTRT3/ARPM1 gene expressed in all tested human tissues) play general roles in the organization of the cytoskeleton like other cytoplasmic actin-related proteins. 359 matched cddid_all.tbl CDD cd13399 cd13399 381602 Slt35-like "Slt35-like lytic transglycosylase. Lytic transglycosylase similar to Escherichia coli lytic transglycosylase Slt35 and Pseudomonas aeruginosa Sltb1. Lytic transglycosylase (LT) catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc) as do ""goose-type"" lysozymes. However, in addition to this, they also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue. Proteins similar to this this family include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as the eukaryotic ""goose-type"" lysozymes (goose egg-white lysozyme; GEWL)." 108 matched cddid_all.tbl CDD cd13400 cd13400 381603 LT_IagB-like "Escherichia coli invasion protein IagB and similar proteins. Lytic transglycosylase-like protein, similar to Escherichia coli invasion protein IagB. IagB is encoded within a pathogenicity island in Salmonella enterica and has been shown to degrade polymeric peptidoglycan. IagB-like invasion proteins are implicated in the invasion of eukaryotic host cells by bacteria. Lytic transglycosylase (LT) catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), as do ""goose-type"" lysozymes. However, in addition to this, they also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue. Members of this family resemble the soluble and insoluble membrane-bound LTs in bacteria and the LTs in bacteriophage lambda." 109 matched cddid_all.tbl CDD cd13401 cd13401 381604 Slt70-like "70kDa soluble lytic transglycosylase (Slt70) and similar proteins. Catalytic domain of the 70kda soluble lytic transglycosylase (LT)-like proteins, which also have an N-terminal U-shaped U-domain and a linker L-domain. LTs catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), as do ""goose-type"" lysozymes. However, in addition to this, they also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue. Proteins similar to this family include the soluble and insoluble membrane-bound LTs in bacteria and the LTs in bacteriophage lambda." 152 matched cddid_all.tbl CDD cd13402 cd13402 381605 LT_TF-like "lytic transglycosylase-like domain of tail fiber-like proteins and similar domains. These tail fiber-like proteins are multi-domain proteins that include a lytic transglycosylase (LT) domain. Members of the LT family include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, and the eukaryotic ""goose-type"" lysozymes (goose egg-white lysozyme; GEWL). LTs catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), as do ""goose-type"" lysozymes. However, in addition to this, they also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue." 117 matched cddid_all.tbl CDD cd13403 cd13403 381606 MLTF-like membrane-bound lytic murein transglycosylase F (MLTF) and similar proteins. This subfamily includes membrane-bound lytic murein transglycosylase F (MltF, murein lyase F) that degrades murein glycan strands. It is responsible for catalyzing the release of 1,6-anhydromuropeptides from peptidoglycan. Lytic transglycosylase catalyzes the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc) as do goose-type lysozymes. However, in addition, it also makes a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue. 161 matched cddid_all.tbl CDD cd13404 cd13404 259831 UreI_AmiS_like "UreI/AmiS family, proton-gated urea channel and putative amide transporters. This family includes UreI proton-gated urea channels as well as putative amide transporters (AmiS of the amidase gene cluster). Helicobacter pylori UreI (HpUreI), a proton-gated inner membrane urea channel opens in acidic pH to allow urea influx to the cytoplasm. There urea is metabolized, producing NH3 and CO2, leading to buffering of the periplasm. This action is essential for the survival of H. pylori in the stomach, and has been identified as a mechanism that could be clinically targeted to prevent various illnesses associated with infection by H. pylori. UreI and the related amide channels (AmiS) appear to function as hexamers, and have 6 predicted transmembrane segments. UreI has also been shown have a lipid ""plug"" in the center of the hexamer. Urea enters at the periplasmic opening of UreI and must pass 2 constriction sites, one on each side of a conserved Glu (Glu 177, H. pylori numbering), to reach the cytoplasm. Urea/thiourea selectivity is diminished by mutation of a conserved Trp to Ala or Phe in constriction site 2 (cytoplasmic). Channel functionality is greatly diminished by mutation of a conserved Trp in constriction site 1 (periplasmic) and a conserved Tyr in constriction site 2, and to a lesser extent a conserved Phe in site 1. In the cytoplasm, urease hydrolyzes urea to form ammonia and carbamate, which decomposes to carbonic acid. UreI is fully open at pH 5.0 to facilitate urea influx, but closes at neutral pH, preventing over-alkalization. Glu 177 (H. pylori numbering) is present in urea channel proteins, but absent in the related amide channels, suggesting that it plays a role in urea specificity." 167 matched cddid_all.tbl CDD cd13405 cd13405 276910 TNFRSF14_teleost Tumor necrosis factor receptor superfamily member 14 (TNFRSF14) in teleost; also known as herpes virus entry mediator (HVEM). This subfamily of TNFRSF14 (also known as herpes virus entry mediator or HVEM, ATAR, CD270, HVEA, LIGHTR, TR2) is found in teleosts, many of which are as yet uncharacterized. It regulates T-cell immune responses by activating inflammatory as well as inhibitory signaling pathways. HVEM acts as a receptor for the canonical TNF-related ligand LIGHT (lymphotoxin-like), which exhibits inducible expression, and competes with herpes simplex virus glycoprotein D for HVEM. It also acts as a ligand for the immunoglobulin superfamily proteins BTLA (B and T lymphocyte attenuator) and CD160, a feature distinguishing HVEM from other immune regulatory molecules, thus, creating a functionally diverse set of intrinsic and bidirectional signaling pathways. HVEM is highly expressed in the gut epithelium. Genome-wide association studies have shown that HVEM is an inflammatory bowel disease (IBD) risk gene, suggesting that HVEM could have a regulatory role influencing the regulation of epithelial barrier, host defense, and the microbiota. Mouse models have revealed that HVEM is involved in colitis pathogenesis, mucosal host defense, and epithelial immunity, thus acting as a mucosal gatekeeper with multiple regulatory functions in the mucosa. HVEM plays a critical role in both tumor progression and resistance to antitumor immune responses, possibly through direct and indirect mechanisms. It is known to be expressed in several human malignancies, including esophageal squamous cell carcinoma, follicular lymphoma, and melanoma. HVEM network may therefore be an attractive target for drug intervention. In Asian seabass, the up-regulation of differentially expressed TNFRSF14 gene has been observed. 111 matched cddid_all.tbl CDD cd13406 cd13406 276911 TNFRSF4 Tumor necrosis factor receptor superfamily member 4 (TNFRSF4), also known as CD134 or OXO40. TNFRSF4 (also known as OX40, ACT35, CD134, IMD16, TXGP1L) activates NF-kappaB through its interaction with adaptor proteins TRAF2 and TRAF5. It also promotes the expression of apoptosis inhibitors BCL2 and BCL2lL1/BCL2-XL, and thus suppresses apoptosis. It is primarily expressed on activated CD4+ and CD8+ T cells, where it is transiently expressed and upregulated on the most recently antigen-activated T cells within inflammatory lesions. This makes it an attractive target to modulate immune responses, i.e. TNFRSF4 (OX40) blocking agents to inhibit adverse inflammation or agonists to enhance immune responses. An artificially created biologic fusion protein, OX40-immunoglobulin (OX40-Ig), prevents OX40 from reaching the T-cell receptors, thus reducing the T-cell response. Some single nucleotide polymorphisms (SNPs) of its natural ligand OX40 ligand (OX40L, CD252), which is also found on activated T cells, have been associated with systemic lupus erythematosus. 142 matched cddid_all.tbl CDD cd13407 cd13407 276912 TNFRSF5 Tumor necrosis factor receptor superfamily member 5 (TNFRSF5), also known as CD40. TNFRSF5 (commonly known as CD40 and also as CDW40, p50, Bp50) is widely expressed in diverse cell types including B lymphocytes, dendritic cells, platelets, monocytes, endothelial cells, and fibroblasts. It is essential in mediating a wide variety of immune and inflammatory responses, including T cell-dependent immunoglobulin class switching, memory B cell development, and germinal center formation. Its natural immunomodulating ligand is CD40L, and a primary defect in the CD40/CD40L system is associated with X-linked hyper-IgM (XHIM) syndrome. It is also involved in tumorigenesis; CD40 expression is significantly higher in gastric carcinomas and it is associated with the lymphatic metastasis of cancer cells and their tumor node metastasis (TNM) classification. Upregulated levels of CD40/CD40L on B cells and T cells may play an important role in the immune pathogenesis of breast cancer. Consequently, the CD40/CD40L system serves as a link between tumorigenesis, atherosclerosis, and the immune system, and offers a potential target for drug therapy for related diseases, such as cancer, atherosclerosis, diabetes mellitus, and immunological rejection. 161 matched cddid_all.tbl CDD cd13408 cd13408 276913 TNFRSF7 Tumor necrosis factor receptor superfamily member 7 (TNFRSF7), also known as CD27. TNFRSF7 (also known as CD27, T14, S152, Tp55, S152, LPFS2) has a key role in the generation of immunological memory via effects on T-cell expansion and survival, and B cell development. It binds to ligand CD70, and plays a key role in regulating B-cell activation and immunoglobulin synthesis. CD27 transduces signals that lead to the activation of NF-kappaB and MAPK8/JNK, and mediates the signaling process through adaptor proteins TRAF2 and TRAF5. CD27-binding protein (SIVA), a pro-apoptotic protein, can bind to CD27 and may play an important role in the apoptosis induced by this receptor. The potential role of the CD27/CD70 pathway in the course of inflammatory diseases, such as arthritis, and inflammatory bowel disease, suggests that CD70 may be a target for immune intervention. The expression of CD27 and CD44 molecules correlates with the differentiation stage of B cell precursors and has been shown to have a biological significance in acute lymphoblastic leukemia. 121 matched cddid_all.tbl CDD cd13409 cd13409 276914 TNFRSF8 Tumor necrosis factor receptor superfamily member 8 (TNFRSF8), also known as CD30. TNFRSF8 (also known as CD30, Ki-1, D1S166E) is expressed by activated T and B cells. It transduces signals that lead to the activation of NF-kappaB, mediated by the adaptor proteins TRAF2 and TRAF5. This receptor is a positive regulator of apoptosis, and has been shown to limit the proliferative potential of auto-reactive CD8 effector T cells and protect the body against autoimmunity. Two alternatively spliced transcript variants of this gene encoding distinct isoforms have been reported. CD30 is expressed in malignant Hodgkin and Reed-Sternberg cells on the surface of extracellular vesicles, facilitating CD30-CD30L interaction between cell types. This receptor is also associated with anaplastic large cell lymphoma. It is expressed in embryonal carcinoma, but not in seminoma, making it a useful marker in distinguishing between these germ cell tumors. Since CD30 has restricted expression in normal tissues, it is an optimal target for selectively eliminating CD30-expressing neoplastic cells by specific toxin-conjugated monoclonal antibodies (mAbs). 130 matched cddid_all.tbl CDD cd13410 cd13410 276915 TNFRSF9 Tumor necrosis factor receptor superfamily member 9 (TNFRSF9), also known as CD137. TNFRSF9 (also known as CD137, ILA, 4-1BB) plays a role in the immunobiology of human cancer where it is preferentially expressed on tumor-reactive subset of tumor-infiltrating lymphocytes. It can be expressed by activated T cells, but to a larger extent on CD8 than on CD4 T cells. In addition, CD137 expression is found on dendritic cells, follicular dendritic cells, natural killer cells, granulocytes and cells of blood vessel walls at sites of inflammation. It transduces signals that lead to the activation of NF-kappaB, mediated by the TRAF adaptor proteins. CD137 contributes to the clonal expansion, survival, and development of T cells. It can also induce proliferation in peripheral monocytes, enhance T cell apoptosis induced by TCR/CD3 triggered activation, and regulate CD28 co-stimulation to promote Th1 cell responses. CD137 is modulated by SAHA treatment in breast cancer cells, suggesting that the combination of SAHA with this receptor could be a new therapeutic approach for the treatment of tumors. 138 matched cddid_all.tbl CDD cd13411 cd13411 276916 TNFRSF11A Tumor necrosis factor receptor superfamily member 11A (TNFRSF11A), also known as receptor activator of nuclear factor-kappaB (RANK). TNFRSF11A (also known as RANK, FEO, OFE, ODFR, OSTS, PDB2, CD26, OPTB7, TRANCER, LOH18CR1) induces the activation of NF-kappa B and MAPK8/JNK through interactions with various TRAF adaptor proteins. This receptor and its ligand are important regulators of the interaction between T cells and dendritic cells. The receptor is also an essential mediator for osteoclast and lymph node development. Mutations at this locus have been associated with familial expansile osteolysis, autosomal recessive osteopetrosis, and Juvenile Paget's disease (JPD) of bone. Alternatively spliced transcript variants have been described for this locus. Mutation analysis may improve diagnosis, prognostication, recurrence risk assessment, and perhaps treatment selection among the monogenic disorders of RANKL/OPG/RANK activation. 163 matched cddid_all.tbl CDD cd13412 cd13412 276917 TNFRSF11B_teleost Tumor necrosis factor receptor superfamily 11B (TNFRSF11B) in teleost; also known as Osteoprotegerin (OPG). This subfamily of TNFRSF11B (also known as Osteoprotegerin, OPG, TR1, OCIF) is found in teleosts. It is a secreted glycoprotein that regulates bone resorption. It binds to two ligands, RANKL (receptor activator of nuclear factor kappaB ligand, also known as osteoprotegerin ligand, OPGL, TRANCE, TNF-related activation induced cytokine), a critical cytokine for osteoclast differentiation, and TRAIL (TNF-related apoptosis-inducing ligand), involved in immune surveillance. Therefore, acting as a decoy receptor for RANKL and TRAIL, OPG inhibits the regulatory effects of nuclear factor-kappaB on inflammation, skeletal, and vascular systems, and prevents TRAIL-induced apoptosis. Studies in mice counterparts suggest that this protein and its ligand also play a role in lymph-node organogenesis and vascular calcification. Circulating OPG levels have emerged as independent biomarkers of cardiovascular disease (CVD) in patients with acute or chronic heart disease. OPG has also been implicated in various inflammations and linked to diabetes and poor glycemic control. Alternatively spliced transcript variants of this gene have been reported, although their full length nature has not been determined. Genetic analysis of the Japanese rice fish medaka (Oryzias latipes) has shown that entire networks for bone formation are conserved between teleosts and mammals; enabling medaka to be used as a genetic model to monitor bone homeostasis in vivo. 129 matched cddid_all.tbl CDD cd13413 cd13413 276918 TNFRSF12A Tumor necrosis factor receptor superfamily member 12A (TNFRSFA), also known as receptor fibroblast growth factor inducible 14 (FN14). TNFRSF12A (also known as receptor fibroblast growth factor inducible 14, FN14, CD266, TWEAKR) is induced by a large variety of growth factors including Fibroblast Growth Factor 1 (FGF1), FGF2, Platelet-Derived Growth Factor (PDGF), Epidermal Growth Factor (EGF) and Vascular Endothelial Growth Factor (VEGF), as well as cytokines such as tumor necrosis factor alpha (TNFalpha), Interleukin-1beta (IL-1beta), Interferon gamma (IFNgamma), and transforming growth factor-beta (TGF-beta). FN14 is expressed on a wide variety of different cell types and binds the ligand TWEAK (tumor necrosis factor-like weak inducer of apoptosis) to activate several signaling cascades through activation of NF-kappaB signaling mediated by adaptor TRAF proteins. The FN14/TWEAK pathway controls a range of cellular activities such as proliferation, differentiation, and apoptosis, and has diverse biological functions in pathological mechanisms like inflammation and fibrosis that are associated with cardiovascular diseases (CVDs). The complex is a positive regulator of cardiac hypertrophy and it has been shown that deletion of FN14 receptor protects from right heart fibrosis and dysfunction; the TWEAK/Fn14 axis could be a potential new therapeutic target for achieving cardiac protection in patients with CVDs. FN14 expression is also stimulated under specific atrophic conditions, such as denervation, immobilization, and starvation, leading to activation of TWEAK/Fn14 signaling and eventually skeletal muscle atrophy. FN14 is also a factor that promotes prostate cancer bone metastasis. 117 matched cddid_all.tbl CDD cd13414 cd13414 276919 TNFRSF17 Tumor necrosis factor receptor superfamily member 17 (TNFRSF17), also known as B cell maturation antigen (BCMA), as well as TNFRSF13A. TNFRSF17 (also known as TNFRSF13A, B cell maturation antigen or BCMA, CD269) is predominantly expressed on terminally differentiated B cells, including multiple myeloma cells, and is important for B cell development and autoimmune response. Upon binding to its ligands, B cell activator of the TNF family (BAFF, also known as TNSF13B, TALL-1, BLyS, zTNF4), and a proliferation inducing ligand (APRIL), BCMA activates NF-kappaB and MAPK8/JNK; it has a higher affinity for APRIL than for BAFF. This receptor may transduce signals for cell survival and proliferation by binding to TRAF1, TRAF2, and TRAF3. BCMA expression has also been linked to a number of cancers, autoimmune disorders, and infectious diseases. It has been shown that although BCMA does not play a role in normal B cell homeostasis, it is critical for the long-term survival of bone marrow plasma cells. BCMA is expressed in a number of hematologic malignancies, including both Hodgkin's and non-Hodgkin's lymphomas, as well as primary tumor cells and cell lines of multiple myeloma, playing a critical role in protecting myeloma cells from apoptosis. BCMA has been identified as a promising chimeric antigen receptor (CAR) target for multiple myeloma; CARs are synthetic transmembrane proteins used to redirect autologous T cells with a new specificity for antigens on the surface of cancer cells. BCMA may also be implicated in the context of both viral and fungal infections; peripheral blood B cells isolated from HIV+ viremic patients have increased expression levels of BCMA, and significant decreased levels are found during fungal infection with C. neoformans. BCMA has been linked to mucosal immunity; its signaling in B cells and non-B cells is important for driving protective IgA responses. Also, abnormal expression or signaling of BCMA in the gut may be relevant to diseases, such as irritable bowel disease and ulcerative colitis. 165 matched cddid_all.tbl CDD cd13415 cd13415 276920 TNFRSF13B Tumor necrosis factor receptor superfamily member 13B (TNFRSF13B), also known as transmembrane activator and calcium modulator and cyclophilin ligand interactor (TACI). TNFRSF13B (also known as transmembrane activator and calcium modulator and cyclophilin ligand interactor (TACI), CVID, RYZN, CD267, CVID2, TNFRSF14B) is mainly expressed on B cells and binds strongly to B cell activating factor (BAFF) and weakly to a proliferation-inducing ligand (APRIL). TACI-APRIL interactions induce B-cell differentiation, whereas TACI-BAFF ligation negatively regulates B-cell functions. In humans, TACI is expressed on memory B cells and TACI mutations are detected in 8-10% of common variable immunodeficiency (CVID) patients, making it the most frequently mutated gene for the disease. Coexisting morbidities in CVID include bronchiectasis, autoimmunity, and malignancies. However, TNFRSF13B/TACI defects alone do not result in CVID but may also be found frequently in distinct clinical phenotypes, including benign lymphoproliferation and IgG subclass deficiencies. Over-expression of TACI has been detected in multiple myeloma and thyroid carcinoma; correlative analyses suggest that TACI expression is a useful prognostic marker for lymphoma. 212 matched cddid_all.tbl CDD cd13416 cd13416 276921 TNFRSF16 Tumor necrosis factor receptor superfamily member 16 (TNFRSF16), also known as p75 neurotrophin receptor (p75NTR) or CD271. TNFRSF16 (also known as nerve growth factor receptor (NGFR) or p75 neurotrophin receptor (p75NTR or p75(NTR)), CD271, Gp80-LNGFR) is a common receptor for both neurotrophins and proneurotrophins, and plays a diverse role in many tissues, including the nervous system. It has been shown to be expressed in various types of stem cells and has been used to prospectively isolate stem cells with different degrees of potency. p75NTR owes its signaling to the recruitment of intracellular binding proteins, leading to the activation of different signaling pathways. It binds nerve growth factor (NGF) and the complex can initiate a signaling cascade which has been associated with both neuronal apoptosis and neuronal survival of discrete populations of neurons, depending on the presence or absence of intracellular signaling molecules downstream of p75NTR (e.g. NF-kB, JNK, or p75NTR intracellular death domain). p75NTR can also bind NGF in concert with the neurotrophic tyrosine kinase receptor type 1 (TrkA) protein where it is thought to modulate the formation of the high-affinity neurotrophin binding complex. On melanoma cell, p75NTR is an immunosuppressive factor, induced by interferon (IFN)-gamma, and mediates down-regulation of melanoma antigens. It can interact with the aggregated form of amyloid beta (Abeta) peptides, and plays an important role in etiopathogenesis of Alzheimer's disease by influencing protein tau hyper-phosphorylation. p75(NTR) is involved in the formation and progression of retina diseases; its expression is induced in retinal pigment epithelium (RPE) cells and its knockdown rescues RPE cell proliferation activity and inhibits RPE apoptosis induced by hypoxia. It can therefore be a potential therapeutic target for RPE hypoxia or oxidative stress diseases. 159 matched cddid_all.tbl CDD cd13417 cd13417 276922 TNFRSF18 Tumor necrosis factor receptor superfamily member 18 (TNFRSF18), also known as glucocorticoid-induced tumor necrosis factor receptor family-related protein (GITR). TNFRSF18 (also known as activation-inducible TNF receptor (AITR), glucocorticoid-induced tumor necrosis factor receptor family-related protein (GITR), CD357, GITR-D) has increased expression upon T-cell activation, and is thought to play a key role in dominant immunological self-tolerance maintained by CD25(+)CD4(+) regulatory T cells. In inflammatory cells, GITR expression indicates a possible molecular link between steroid use and complicated acute sigmoid diverticulitis; increased MMP-9 expression by GITR signaling might explain morphological changes in the colonic wall in diverticulitis. Its ligand, GITRL, activates GITR which could then influence the activity of effector and regulatory T cells, participating in the development of several autoimmune and inflammatory diseases, including autoimmune thyroid disease and rheumatoid arthritis. In systemic lupus erythematosus (SLE) patients, serum GITRL levels are increased compared with healthy controls. GITR and its ligand, GITRL, are possibly involved in the pathogenesis of primary Sjogren's syndrome (pSS). GITR is inactivated during tumor progression in Multiple Myeloma (MM); restoration of GITR expression in GITR deficient MM cells leads to inhibition of MM proliferation and induction of apoptosis, thus playing a pivotal role in MM pathogenesis and disease progression. Regulatory T-cells (Tregs) in liver tumor up-regulate the expression of GITR compared with Tregs in tumor-free liver tissue and blood. Regulatory single nucleotide polymorphisms (SNPs) in the promoter regions of the TNFRSF18 gene have been identified in a group of male Gabonese individuals exposed to a wide array of parasitic diseases such as malaria, filariasis and schistosomiasis, and may serve as a basis to study parasite susceptibility in association studies. 130 matched cddid_all.tbl CDD cd13418 cd13418 276923 TNFRSF19 Tumor necrosis factor receptor superfamily member 19 (TNFRSF19), also known as TROY. TNFRSF19 (also known as TAJ; TROY; TRADE; TAJ-alpha) is expressed in progenitor cells of the hippocampus, thalamus, and cerebral cortex and highly expressed during embryonic development. It has been shown to interact with TRAF family members, and to activate JNK signaling pathway when overexpressed in cells. It is frequently overexpressed in colorectal cancer cell lines and primary colorectal carcinomas. TNFRSF19 is a beta-catenin target gene, in mesenchymal stem cells, and also activates NF-kappaB signaling, showing that beta-catenin regulates NF-kappaB activity via TNFRSF19. Since Wnt/beta-catenin signaling plays a crucial role in the regulation of colon tissue regeneration and the development of colon tumors, TNFRSF19 may contribute to the development of colorectal tumors. These findings define a role for death receptors DR6 and TROY in CNS-specific vascular development. TNFRSF19 has been shown to promote glioblastoma (GBM) survival signaling and therefore targeting it may increase tumor vulnerability and improve therapeutic response in glioblastoma. It may play an important role in myelin-associated inhibitory factors (MAIFs)-induced inhibition of neurite outgrowth in the postnatal central nervous system (CNS) or on axon regeneration following CNS injury. 117 matched cddid_all.tbl CDD cd13419 cd13419 276924 TNFRSF19L tumor necrosis factor receptor superfamily member 19-like (TNFRSF19L), also known as receptor expressed in lymphoid tissues (RELT). TNFRSF19L (also known as receptor expressed in lymphoid tissues (RELT)) is especially abundant in hematologic tissues and can stimulate the proliferation of T-cells. It serves as a substrate for the closely related kinases, odd-skipped related transcription factor 1 (OSR1) and STE20/SPS1-related proline/alanine-rich kinase (SPAK); RELT binds SPAK and uses it to mediate p38 and JNK activation, rather than rely on the canonical TRAF pathways for its function. RELT is capable of stimulating T-cell proliferation in the presence of CD3 signaling, which suggests its regulatory role in immune response. It interacts with phospholipid scramblase 1 (PLSCR1), an interferon-inducible protein that mediates antiviral activity against DNA and RNA viruses; PLSCR1 is a regulator of hepatitis B virus X (HBV X) protein. RELT and PLSCR1 co-localize in intracellular regions of human embryonic kidney-293 cells, with RELT over-expression appearing to alter the localization of PLSCR1. 91 matched cddid_all.tbl CDD cd13420 cd13420 276925 TNFRSF25 tumor necrosis factor receptor superfamily member 25 (TNFRSF25), also known as death receptor 3 (DR3). TNFRSF25 (also known as death receptor 3 (DR3), death domain receptor 3 (DDR3), apoptosis-mediating receptor, lymphocyte associated receptor of death (LARD), apoptosis inducing receptor (AIR), APO-3, translocating chain-association membrane protein (TRAMP), WSL-1, WSL-LR or TNFRSF12) is preferentially expressed in thymocytes and lymphocytes, and may play a role in regulating lymphocyte homeostasis. It has been detected in lymphocyte-rich tissues such as colon, intestine, thymus and spleen, as well as in the prostate. Various death domain containing adaptor proteins mediate the signal transduction of this receptor; it activates nuclear factor kappa-B (NFkB) and induces cell apoptosis by associating with TNFRSF1A-associated via death domain (TRADD), which is known to mediate signal transduction of tumor necrosis factor receptors. DR3 associates with tumor necrosis factor (TNF)-like cytokine 1A (TL1A also known as TNFSF15) on activated lymphocytes and induces pro-inflammatory signals; TL1A also binds decoy receptor DcR3 (also known as TNFRSF6B). DR3/DcR3/TL1A expression is increased in both serum and inflamed tissues in autoimmune diseases such as in several autoimmune diseases, including inflammatory bowel disease (IBD), rheumatoid arthritis (RA), allergic asthma, experimental autoimmune encephalomyelitis, type 1 diabetes, ankylosing spondylitis (AS), and primary biliary cirrhosis (PBC), making modulation of TL1A-DR3 interaction a potential therapeutic target. 114 matched cddid_all.tbl CDD cd13421 cd13421 276926 TNFRSF_EDAR Tumor necrosis factor receptor superfamily member ectodysplasin A receptor (EDAR). Ectodysplasin A receptor (EDAR, also known as DL, ED3, ED5, ED1R, EDA3, HRM1, EDA1R, ECTD10A, ECTD10B, EDA-A1R) binds the soluble ligand ectodysplasin A and can activate the nuclear factor-kappaB, JNK, and caspase-independent cell death pathways. It is required for the development of hair, teeth, and other ectodermal derivatives. Mutations in this gene result in autosomal dominant and recessive forms of hypohidrotic ectodermal dysplasia. Patients present defects in the development of ectoderm-derived structures resulting in sparse hair, too few teeth (oligodontia), the absence or reduction in the ability to sweat as well as problems with mucous and saliva and the production and formation of pigment cells. 136 matched cddid_all.tbl CDD cd13422 cd13422 276927 TNFRSF5_teleost Tumor necrosis factor receptor superfamily member 5 (TNFRSF5) in teleosts; also known as CD40. TNFRSF5 (commonly known as CD40 and also as CDW40, p50, Bp50) is widely expressed in diverse cell types including B lymphocytes, dendritic cells, platelets, monocytes, endothelial cells, and fibroblasts. It is essential in mediating a wide variety of immune and inflammatory responses, including T cell-dependent immunoglobulin class switching, memory B cell development, and germinal center formation. Its natural immunomodulating ligand is CD40L, and a primary defect in the CD40/CD40L system is associated with X-linked hyper-IgM (XHIM) syndrome. It is also involved in tumorigenesis; CD40 expression is significantly higher in gastric carcinomas and it is associated with the lymphatic metastasis of cancer cells and their tumor node metastasis (TNM) classification. Upregulated levels of CD40/CD40L on B cells and T cells may play an important role in the immune pathogenesis of breast cancer. Consequently, the CD40/CD40L system serves as a link between tumorigenesis, atherosclerosis, and the immune system, and offers a potential target for drug therapy for related diseases, such as cancer, atherosclerosis, diabetes mellitus, and immunological rejection. Salmon CD40 and CD40L are widely expressed, particularly in immune tissues, and their importance for the immune response is indicated by their relatively high expression in salmon lymphoid organs and gills. 161 matched cddid_all.tbl CDD cd13423 cd13423 276928 TNFRSF6_teleost Tumor necrosis factor receptor superfamily member 6 (TNFRSF6) in teleosts; also known as fas cell surface death receptor (FasR). This subfamily of TNFRSF6 (also known as fas cell surface death receptor (FasR) or Fas; APT1; CD95; FAS1; APO-1; FASTM; ALPS1A) is found in teleosts. It contains a death domain and plays a central role in the physiological regulation of programmed cell death. In humans, it has been implicated in the pathogenesis of various malignancies and diseases of the immune system. The receptor interactions with the Fas ligand (FasL), allowing the formation of a death-inducing signaling complex that includes Fas-associated death domain protein (FADD), caspase 8, and caspase 10; autoproteolytic processing of the caspases in the complex triggers a downstream caspase cascade, leading to apoptosis. This receptor has also been shown to activate NF-kappaB, MAPK3/ERK1, and MAPK8/JNK, and is involved in transducing the proliferating signals in normal diploid fibroblast and T cells. In channel catfish and the Japanese rice fish, medaka, homologs of Fas receptor (FasR), as well as FADD and caspase 8, have been identified and characterized, and likely constitute the teleost equivalent of the death-inducing signaling complex (DISC). FasL/FasR are involved in the initiation of apoptosis and suggest that mechanisms of cell-mediated cytotoxicity in teleosts are similar to those used by mammals; presumably, the mechanism of apoptosis induction via death receptors was evolutionarily established during the appearance of vertebrates. 103 matched cddid_all.tbl CDD cd13424 cd13424 276929 TNFRSF9_teleost Tumor necrosis factor receptor superfamily member 9 (TNFRSF9) in teleosts; also known as CD137. This subfamily of TNFRSF9 (also known as CD137, ILA, 4-1BB) is found in teleosts. CD137 plays a role in the immunobiology of human cancer where it is preferentially expressed on tumor-reactive subset of tumor-infiltrating lymphocytes. It can be expressed by activated T cells, but to a larger extent on CD8 than on CD4 T cells. In addition, CD137 expression is found on dendritic cells, follicular dendritic cells, natural killer cells, granulocytes and cells of blood vessel walls at sites of inflammation. It transduces signals that lead to the activation of NF-kappaB, mediated by the TRAF adaptor proteins. CD137 contributes to the clonal expansion, survival, and development of T cells. It can also induce proliferation in peripheral monocytes, enhance T cell apoptosis induced by TCR/CD3 triggered activation, and regulate CD28 co-stimulation to promote Th1 cell responses. CD137 is modulated by SAHA treatment in breast cancer cells, suggesting that the combination of SAHA with this receptor could be a new therapeutic approach for the treatment of tumors. Mostly, CD137 in teleosts have not been characterized. 150 matched cddid_all.tbl CDD cd13425 cd13425 240448 Peptidase_G1_like Peptidases of the G1 family and homologs that might lack peptidase activity. Some members of this family had been classified earlier as carboxyl peptidases insensitive to pepstatin, and the family has also been called the eqolisin family, due to the fact that the conserved catalytic dyad of the family consists of a glutamate (E) and glutamine (Q) residue. The family is found in fungi and bacteria. This family also includes homologous uncharacterized proteins that might lack peptidase activity. 195 matched cddid_all.tbl CDD cd13426 cd13426 240449 Peptidase_G1 Peptidases of the G1 family, including scytalidoglutamic peptidase and aspergillopepsin. Some members of this family had been classified earlier as carboxyl peptidases insensitive to pepstatin, and the family has also been called the eqolisin family, due to the fact that the conserved catalytic dyad of the family consists of a glutamate (E) and glutamine (Q) residue. The family is found in fungi and bacteria. 206 matched cddid_all.tbl CDD cd13427 cd13427 240450 YncM_like Uncharacterized proteins similar to Bacillus subtilis YncM. Members of this family share close structural similarity with peptidases of the Peptidase_G1 family and may be homologous. They do not appear to share the peptidases' active site, though a bound sulfate ion in the single available structure suggests a functional site at a matching location. 204 matched cddid_all.tbl CDD cd13428 cd13428 259832 UreI_AmiS "UreI/Amis family, proton-gated urea channel and putative amide transporters. This subfamily includes UreI proton-gated urea channels as well as putative amide transporters (AmiS of the amidase gene cluster). Helicobacter pylori UreI (HpUreI), a proton-gated inner membrane urea channel opens in acidic pH to allow urea influx to the cytoplasm. There urea is metabolized, producing NH3 and Co2, leading to buffering of the periplasm. This action is essential for the survival of H. pylori in the stomach, and has been identified as a mechanism that could be clinically targeted to prevent various illnesses associated with infection by H. pylori. UreI and the related amide channels (AmiS) appear to function as hexamers, and have 6 predicted transmembrane segments. UreI has also been shown have a lipid ""plug"" in the center of the hexamer. Urea enters at the periplasmic opening of UreI and must pass 2 constriction sites, one on each side of a conserved Glu (Glu 177, H. pylori numbering), to reach the cytoplasm. Urea/thiourea selectivity is diminished by mutation of a conserved Trp to Ala or Phe in constriction site 2 (cytoplasmic). Channel functionality is greatly diminished by mutation of a conserved Trp in constriction site 1 (periplasmic) and a conserved Tyr in constriction site 2, and to a lesser extent a conserved Phe in site 1. In the cytoplasm, urease hydrolyzes urea to form ammonia and carbamate, which decomposes to carbonic acid. UreI is fully open at pH 5.0 to facilitate urea influx, but closes at neutral pH, preventing over-alkalization. Glu 177 (H. pylori numbering) is present in urea channel proteins, but absent in the related amide channels, suggesting that it plays a role in urea specificity." 162 matched cddid_all.tbl CDD cd13429 cd13429 259833 UreI_AmiS_like_2 "UreI/AmiS family, subgroup 2. Putative transporters related to proton-gated urea channel and putative amide transporters. This subfamily includes putative UreI proton-gated urea channels and putative amide transporters (AmiS of the amidase gene cluster). Helicobacter pylori UreI (HpUreI), a proton-gated inner membrane urea channel opens in acidic pH to allow urea influx to the cytoplasm. There urea is metabolized, producing NH3 and Co2, leading to buffering of the periplasm. This action is essential for the survival of H. pylori in the stomach, and has been identified as a mechanism that could be clinically targeted to prevent various illnesses associated with infection by H. pylori. UreI and the related amide channels (AmiS) appear to function as hexamers, and have 6 predicted transmembrane segments. UreI has also been shown have a lipid ""plug"" in the center of the hexamer. Urea enters at the periplasmic opening of UreI and must pass 2 constriction sites, one on each side of a conserved Glu (Glu 177, H. pylori numbering), to reach the cytoplasm. Urea/thiourea selectivity is diminished by mutation of a conserved Trp to Ala or Phe in constriction site 2 (cytoplasmic). Channel functionality is greatly diminished by mutation of a conserved Trp in constriction site 1 (periplasmic) and a conserved Tyr in constriction site 2, and to a lesser extent a conserved Phe in site 1. In the cytoplasm, urease hydrolyzes urea to form ammonia and carbamate, which decomposes to carbonic acid. UreI is fully open at pH 5.0 to facilitate urea influx, but closes at neutral pH, preventing over-alkalization. Glu 177 (H. pylori numbering) is present in urea channel proteins, but absent in the related amide channels, suggesting that it plays a role in urea specificity." 165 matched cddid_all.tbl CDD cd13430 cd13430 240445 LDT_IgD_like IgD-like repeat domain of mycobacterial L,D-transpeptidases. Immunoglobulin-like domain found in actinobacterial L,D-transpeptidases, including Mycobacterium tuberculosis LdtMt2, which is a non-classical transpeptidase that generates 3->3 transpeptide linkages. LdtMt2 is associated with virulence and resistance to amoxicillin. This domain may occur in a tandem-repeat arrangement and is found N-terminal to the catalytic L,D-transpeptidase domain. 98 matched cddid_all.tbl CDD cd13431 cd13431 240446 LDT_IgD_like_1 IgD-like repeat domain of mycobacterial L,D-transpeptidases. Immunoglobulin-like domain found in actinobacterial L,D-transpeptidases, including Mycobacterium tuberculosis LdtMt2, which is a non-classical transpeptidase that generates 3->3 transpeptide linkages. LdtMt2 is associated with virulence and resistance to amoxicillin. This domain may occur in a tandem-repeat arrangement and is found N-terminal to the catalytic L,D-transpeptidase domain; this model represents the first (N-terminal) repeat in LdtMt2 and related proteins. 95 matched cddid_all.tbl CDD cd13432 cd13432 240447 LDT_IgD_like_2 IgD-like repeat domain of mycobacterial L,D-transpeptidases. Immunoglobulin-like domain found in actinobacterial L,D-transpeptidases, including Mycobacterium tuberculosis LdtMt2, which is a non-classical transpeptidase that generates 3->3 transpeptide linkages. LdtMt2 is associated with virulence and resistance to amoxicillin. This domain may occur in a tandem-repeat arrangement and is found N-terminal to the catalytic L,D-transpeptidase domain; this model represents the repeat adjacent to the catalytic domain. 99 matched cddid_all.tbl CDD cd13433 cd13433 240441 Na_channel_gate Inactivation gate of the voltage-gated sodium channel alpha subunits. This region is part of the intracellular linker between domains III and IV of the alpha subunits of voltage-gated sodium channels. It is responsible for fast inactivation of the channel and essential for proper physiological function. 54 matched cddid_all.tbl CDD cd13434 cd13434 259812 SPFH_SLPs Stomatin-like proteins (slipins) family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model summarizes proteins similar to stomatin, podocin, and other members of the stomatin-like protein family (SLPs or slipins). The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Individual proteins of the SPFH superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Stomatin interacts with and regulates members of the degenerin/epithelia Na+ channel family in mechanosensory cells of Caenorhabditis elegans and vertebrate neurons and participates in trafficking of Glut1 glucose transporters. Mutations in the podocin gene give rise to autosomal recessive steroid resistant nephritic syndrome. Bacterial and archaebacterial SLPs and many of the eukaryotic family members remain uncharacterized. 108 matched cddid_all.tbl CDD cd13435 cd13435 259813 SPFH_SLP-4 Slipin-4 (SLP-4), an uncharacterized subgroup of the stomatin-like proteins (slipins) family; belonging to the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model summarizes a subgroup of the stomatin-like protein family (SLPs or slipins) that is found in arthropods. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Individual proteins of the SPFH superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Members of this divergent slipin subgroup remain largely uncharacterized. It contains Drosophila Mec2, the gene for which was identified in a screen for genes required for nephrocyte function; it may function together with Sns in maintaining nephrocyte diaphragm. 208 matched cddid_all.tbl CDD cd13436 cd13436 259814 SPFH_SLP-1 Stomatin-like protein 1 (SLP-1), a subgroup of the stomatin-like proteins (slipins) family; belonging to the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model summarizes a subgroup of the stomatin-like protein family (SLPs or slipins) that is found in animals. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Individual proteins of the SPFH superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. The family contains human SLP-1, which has been found to be expressed in the brain, and Caenorhabditis elegans UNC-24, which is a lipid raft-associated protein required for normal locomotion. It may mediate the correct localization of UNC-1. Mutations in the unc-24 gene result in abnormal motion and altered patterns of sensitivity to volatile anesthetics. 131 matched cddid_all.tbl CDD cd13437 cd13437 259815 SPFH_alloslipin Alloslipin, a subgroup of the stomatin-like proteins (slipins) family; belonging to the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model summarizes a subgroup of the stomatin-like protein family (SLPs or slipins) that is found in some eukaryotes and viruses. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Individual proteins of the SPFH superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. This diverse subgroup of the SLPs remains largely uncharacterized. 222 matched cddid_all.tbl CDD cd13438 cd13438 259816 SPFH_eoslipins_u2 Uncharacterized prokaryotic subgroup of the stomatin-like proteins (slipins) family; belonging to the SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily. This model summarizes a subgroup of the stomatin-like protein family (SLPs or slipins) that is found in bacteria. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Individual proteins of the SPFH superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Bacterial SLPs remain uncharacterized. 215 matched cddid_all.tbl CDD cd13439 cd13439 240442 CamS_repeat Repeat domain of CamS sex pheromone cAM373 precursor and related proteins. This family includes CamS, from which Staphylococcus aureus sex pheromone staph-cAM373 is processed. The protein contains two structurally similar repeats in a tandem arrangement. The heptapeptide cAM373 is a Streptococcus faecalis pheromone, secreted by recipient cells, which induces a mating response in donor cells that contain particular conjugative plasmids. cAM373 is also excreted by Staphylococcus aureus. The family also contains sex hormone precursors from other bacteria and an uncharacterized protein with a single repeat from Desulfovibrio piger, which is structurally similar and might be homologous. 106 matched cddid_all.tbl CDD cd13440 cd13440 240443 CamS_repeat_2 C-terminal repeat domain of CamS sex pheromone cAM373 precursor. This family includes CamS, from which Staphylococcus aureus sex pheromone staph-cAM373 is processed. The protein contains two structurally similar repeats in a tandem arrangement. The heptapeptide cAM373 is a Streptococcus faecalis pheromone, secreted by recipient cells, which induces a mating response in donor cells that contain particular conjugative plasmids. cAM373 is also excreted by Staphylococcus aureus. The family also contains sex hormone precursors from other bacteria. 115 matched cddid_all.tbl CDD cd13441 cd13441 240444 CamS_repeat_1 N-terminal repeat domain of CamS sex pheromone cAM373 precursor. This family includes CamS, from which Staphylococcus aureus sex pheromone staph-cAM373 is processed. The protein contains two structurally similar repeats in a tandem arrangement. The heptapeptide cAM373 is a Streptococcus faecalis pheromone, secreted by recipient cells, which induces a mating response in donor cells that contain particular conjugative plasmids. cAM373 is also excreted by Staphylococcus aureus. The family also contains sex hormone precursors from other bacteria. 204 matched cddid_all.tbl CDD cd13442 cd13442 412041 CDI_toxin_Bp1026b-like C-terminal (CT) toxin domain of the contact-dependent growth inhibition (CDI) system of Burkholderia pseudomallei 1026b, and related proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. This model represents the C-terminal (CT) toxin domain of CdiA effector proteins. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via the C-terminal domain. A wide variety of C-terminal toxin domains appear to exist; this particular example from Burkholderia pseudomallei 1026b and other bacteria appears to function as a Mg2+-dependent RNAse cleaving tRNA, most likely in the aminoacyl acceptor stem. This CdiA-Ct is structurally similar to another CDI toxin domain from B. pseudomallei E479 which is unrelated in sequence but has a similar nuclease domain, and shares similar fold and active-site architecture; it contains a core alpha/beta-fold that is characteristic of PD(D/E)XK superfamily nucleases. 129 matched cddid_all.tbl CDD cd13443 cd13443 259836 CDI_inhibitor_Bp1026b_like Inhibitor of the contact-dependent growth inhibition (CDI) system of Burkholderia pseudomallei 1026b, and related proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. This model represents the inhibitor of the CdiA effector protein from Burkholderia pseudomallei 1026b (which is a tRNAse). CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered. The inhibitors are intracellular proteins that inactivate the toxin/effector protein. 100 matched cddid_all.tbl CDD cd13444 cd13444 259837 CDI_toxin_EC869_like Zn-dependent DNAse of the contact-dependent growth inhibition (CDI) system of Escherichia coli EC869, and related proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring bacteria. This model represents the C-terminal toxin domain of CdiA effector proteins. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered. A wide variety of C-terminal toxin domains appear to exist; this particular example from Escherichia coli EC869 and other bacteria appears to function as a Zn2+-dependent DNAse degrading the genome of target cells. 143 matched cddid_all.tbl CDD cd13445 cd13445 259838 CDI_inhibitor_EC869_like Inhibitor of the contact-dependent growth inhibition (CDI) system of Escherichia coli EC869, and related proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring bacteria. This model represents the inhibitor of the CdiA effector protein from Escherichia coli EC869 (which is a DNAse). CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered. The inhibitors are intracellular proteins that inactivate the toxin/effector protein. This domain is also known as DUF1436. 157 matched cddid_all.tbl CDD cd13516 cd13516 259825 HHD_CCM2 harmonin-homology domain (harmonin_N_like domain) of malcavernin (CCM2). CCM2 (also called malcavernin; C7orf22/chromosome 7 open reading frame 22; OSM) along with CCM1 and CCM3 constitutes a set of proteins which when mutated are responsible for cerebral cavernous malformations, an autosomal dominant neurovascular disease characterized by cerebral hemorrhages and vascular malformations in the central nervous system. CCM2 plays many functional roles. CCM2 functions as a scaffold involved in small GTPase Rac-dependent p38 mitogen-activated protein kinase (MAPK) activation when the cell is under hyperosmotic stress. It associates with CCM1 in the signaling cascades that regulate vascular integrity and participates in HEG1 (the transmembrane receptor heart of glass 1) mediated endothelial cell junctions. CCM proteins also inhibit the activation of small GTPase RhoA and its downstream effector Rho kinase (ROCK) to limit vascular permeability. CCM2 mediates TrkA-dependent cell death via its N-terminal PTB domain in pediatric neuroblastic tumours. CCM2 possesses an N-terminal PTB domain. The C-terminal domain of malcavernin, which is represented here, appears similar to the N-terminal domain of the scaffolding protein harmonin. It has also been referred to as the Karet domain. 97 matched cddid_all.tbl CDD cd13517 cd13517 270235 PBP2_ModA3_like Substrate binding domain of molybdate binding protein-like (ModA3), a member of the type 2 periplasmic binding fold superfamily. This subfamily contains molybdate binding protein-like (ModA3) domain of an ABC-type transporter. Molybdate transport system is comprised of a periplasmic binding protein, an integral membrane protein, and an energizer protein. These three proteins are coded by modA, modB, and modC genes, respectively. ModA proteins serve as initial receptors in the ABC transport of molybdate mostly in eubacteria and archaea. ModA transporters import molybdenum and tungsten from the environment in the form of the oxyanions molybdate (MoO(4) (2-)) and tungstate (WO(4) (2-)). After binding molybdate with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. In contrast to the structure of the two ModA homologs from Escherichia coli and Azotobacter vinelandii, where the oxygen atoms are tetrahedrally arrangted around the metal center, the structure of Pyrococcus furiosus ModA/WtpA (PfModA) has shown that a binding site for molybdate and tungstate where the central metal atom is in a hexacoordinate configuration. The ModA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 223 matched cddid_all.tbl CDD cd13518 cd13518 270236 PBP2_Fe3_thiamine_like Substrate binding domain of iron and thiamine transporters-like, a member of the type 2 periplasmic binding fold superfamily. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. On the other hand, thiamin is an essential cofactor in all living systems. Thiamin diphosphate (ThDP)-dependent enzymes play an important role in carbohydrate and branched-chain amino acid metabolism. Most prokaryotes, plants, and fungi can synthesize thiamin, but it is not synthesized in vertebrates. These periplasmic domains have high affinities for their respective substrates and serve as the primary receptor for transport. After binding iron and thiamine with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The iron- and thiamine-binding proteins belong to the PBPI2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 260 matched cddid_all.tbl CDD cd13519 cd13519 270237 PBP2_PEB3_AcfC Ligand-binding domain of a glycoprotein adhesion and an accessory colonization factor, a member of the type 2 periplasmic binding fold superfamily. PEB3 is a glycoprotein adhesion from Campylobacter jejuni whose structure suggests a functional role in transport, and resembles PEB1a, an Asp/Glu transporter and an adhesin. The overall structure of PEB3 is a dimer and is similar to that of other type 2 periplasmic transport proteins such as the molybdate/tungstate, sulfate, and ferric iron transporters. PEB3 has high sequence identity to Paa, an Escherichia coli adhesin, and to AcfC, an accessory colonization factor from Vibrio cholera. 227 matched cddid_all.tbl CDD cd13520 cd13520 270238 PBP2_TAXI_TRAP Substrate binding domain of TAXI proteins of the tripartite ATP-independent periplasmic transporters; the type 2 periplasmic binding protein fold. This group includes Thermus thermophilus GluBP (TtGluBP) of TAXI-TRAP family and closely related proteins. TRAP transporters are ubiquitous in prokaryotes, but absent from eukaryotes. They are comprised of an SBP (substrate-binding protein) of the DctP or TAXI families and two unequally sized integral membrane components. Although TtGluBP is predicted to be an L-glutamate and/or an L-glutamine-binding protein, the substrate spectrum of TAXI proteins remains to be defined. A sequence-homology search also shows that TtGluBP shares low sequence homology with putative immunogenic proteins of uncharacterized function. The substrate-binding domain of TAXI proteins belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and tworeceptor cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 285 matched cddid_all.tbl CDD cd13521 cd13521 270239 PBP2_AlgQ_like Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold. This family represents the periplasmic-binding component of high molecular weight (HMW) alginate uptake system found in gram-negative soil bacteria and related proteins. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. In Sphingomonas sp. A1, the transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins AlgQ1 and AlgQ2. Alginate is an anionic polysaccharide that is made up of alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide. 483 matched cddid_all.tbl CDD cd13522 cd13522 270240 PBP2_ABC_oligosaccharides The periplasmic-binding component of ABC transport systems specific for maltose and related oligosaccharides; possess type 2 periplasmic binding fold. This family represents the periplasmic binding component of ABC transport systems involved in uptake of oligosaccharides including maltose, trehalose, maltodextrin, and cyclodextrin. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 368 matched cddid_all.tbl CDD cd13523 cd13523 270241 PBP2_polyamines The periplasmic-binding component of ABC transporters involved in uptake of polyamines; possess the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding proteins that function as the primary high-affinity receptors of ABC-type polyamine transport systems. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, as well as plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 268 matched cddid_all.tbl CDD cd13524 cd13524 270242 PBP2_Thiaminase_I Thiaminase-I has high structural homology to the type 2 periplasmic binding proteins of active transport systems. Thiaminase-I, a thiamin-(vitamin B1) degrading enzyme, is a monomer in its biologically active form, with two distinct globular domains (N- and C-domains) separated by a deep groove. It has a structural topology similar to the periplasmic substrate-domains of ABC-type transport systems, such as thiamin-binding protein (TbpA), that possess the type 2 periplasmic binding protein fold. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. 363 matched cddid_all.tbl CDD cd13525 cd13525 270243 PBP2_ATP-Prtase_HisG The catalytic domain of ATP phosphoribosyltransferase contains the type 2 periplasmic substrate-binding fold. Encoded by the hisG gene, the ATP phosphoribosyltransferase (ATP-PRT, EC 2.4.2.17) is the first enzyme in histidine biosynthetic pathway that catalyzes the condensation of ATP and PRPP (5'-phosphoribosyl 1'-pyrophosphate), and is regulated by a feedback inhibition from the product histidine. ATP-PRT has two distinct forms: a hexameric long form, HisGL, containing two catalytic domains and a C-terminal regulatory domain; and a hetero-octomeric short form, HisGs, without the regulatory domain. HisGL is catalytically competent, but the hetero-octameric HisGs requires the second subunit HisZ, a paralog to the catalytic domain of functional histidyl-tRNA synthetases (HisRSs), for the enzyme activity. This catalytic domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. 208 matched cddid_all.tbl CDD cd13526 cd13526 270244 PBP2_lipoprotein_MetQ_like The periplasmic-binding component of ABC-type methionine uptake transporter system and its related lipoproteins; the type 2 periplasmic-binding protein fold. This family represents the periplasmic substrate-binding domain of ATP-binding cassette (ABC) transporter involved in uptake of methionine (MetQ) and its related homologs. Members of the MetQ-like family include the 32-kilodalton lipoprotein (Tp32) from Treponema pallidum, the membrane-associated lipoprotein-9 GmpC from Staphylococcus aureus, and Toll-like receptor 2-activating lipoprotein IlpA from Vibrio vulnificus. They all function as a receptor for methionine. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. 228 matched cddid_all.tbl CDD cd13527 cd13527 270245 PBP2_TRAP Substrate-binding component of Tripartite ATP-independent Periplasmic transporters and related proteins; contains the type 2 periplasmic-binding protein fold. This family represents the TRAP Transporters that are specific to various ligands, including sialic acid (N-acetyl neuraminic acid), glutamate, ectoine, xylulose, C4-dicarboxylates such as succinate, malate and fumarate, and keto acids such as pyruvate and alpha-ketobutyrate. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. This family also includes some eukaryotic homologs that have not been functionally characterized. TRAP transporters are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 301 matched cddid_all.tbl CDD cd13528 cd13528 270246 PBP2_osmoprotectants Substrate-binding domain of osmoregulatory ABC-type transporters; the type 2 periplasmic-binding protein fold. This family represents the periplasmic substrate-binding component of ABC transport systems that are involved in uptake of osmoprotectants (also termed compatible solutes) such as betaine, choline, proline betaine, carnitine, and L-proline. To counteract the efflux of water, bacteria and archaea accumulate the compatible solutes for a sustained adjustment to high osmolarity surroundings. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 264 matched cddid_all.tbl CDD cd13529 cd13529 270247 PBP2_transferrin Transferrin family of the type 2 periplasmic-binding protein superfamily. Transferrins are iron-binding blood plasma glycoproteins that regulate the level of free iron in biological fluids. Vertebrate transferrins are made of a single polypeptide chain with a molecular weight of about 80 kDa. The polypeptide is folded into two homologous lobes (the N-lobe and C-lobe), and each lobe is further subdivided into two similar alpha helical and beta sheet domains separated by a deep cleft that forms the binding site for ferric iron. Thus, the transferrin protein contains two homologous metal-binding sites with high affinities for ferric iron. The modern transferrin proteins are thought to be evolved from an ancestral gene coding for a protein of 40 kDa containing a single binding site by means of a gene duplication event. Vertebrate transferrins are found in a variety of bodily fluids, including serum transferrins, ovotransferrins, lactoferrins, and melanotransferrins. Transferrin-like proteins are also found in the circulatory fluid of certain invertebrates. The transferrins have the same structural fold as the type 2 periplasmic-binding proteins, many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. 298 matched cddid_all.tbl CDD cd13530 cd13530 270248 PBP2_peptides_like Peptide-binding protein and related homologs; type 2 periplasmic binding protein fold. This domain is found in solute binding proteins that serve as initial receptors in the ABC transport, signal transduction and channel gating. The PBP2 proteins share the same architecture as periplasmic binding proteins type 1, but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. 217 matched cddid_all.tbl CDD cd13531 cd13531 270249 PBP2_MxaJ Methanol oxidation system protein MoxJ; the type 2 periplasmic binding fold. This predicted periplasmic protein, called MoxJ or MxaJ, is required for methanol oxidation in Methylobacterium extorquens. Homology suggests it is the substrate-binding protein of an ABC transporter associated with methanol oxidation. Other evidence also suggests that MoxJ is an accessory factor or additional subunit of methanol dehydrogenase itself. Mutational studies show a dependence on this protein for expression of the PQQ-dependent, two-subunit methanol dehydrogenase (MxaF and MxaI) in Methylobacterium extorquens, as if it is a chaperone for enzyme assembly or a third subunit. A homologous N-terminal sequence was found in Paracoccus denitrificans as a 32Kd third subunit. MoxJ may be both, a component of a periplasmic enzyme that converts methanol to formaldehyde and a component of an ABC transporter that delivers the resulting formaldehyde to the cell's interior. 242 matched cddid_all.tbl CDD cd13532 cd13532 270250 PBP2_PDT_like Catalytic domain of prephenate dehydratase and similar proteins; the type 2 periplasmic binding protein fold. Prephenate dehydratase (PDT, EC:4.2.1.51) converts prephenate to phenylpyruvate through dehydration and decarboxylation reactions. PDT plays a key role in the biosynthesis of L-Phe in organisms that utilize the shikimate pathway. PDT is allosterically regulated by L-Phe and other amino acids. The catalytic PDT domain consists of two similar subdomains with a cleft in between, which hosts the highly conserved active site. In gram-postive bacteria and archaea, PDT is a monofunctional enzyme, consisting of a catalytic domain (PDT domain) and a regulatory domain (ACT) (aspartokinase, chorismate mustase domain). In gram-negative bacteria, PDT exists as fusion protein with chorismate mutase (CM), forming a bifunctional enzyme, P-protein (PheA). The CM in the P-protein catalyzes the pericycle isomerization of chorismate to prephenate that serves as a substrate for PDT. The CM and PDT are essentail enzymes for the biosynthesis of aromatic amino acids in microorganisms but are not found in humans. Thus, both CM and PDT can potentially serve as drug targets against microbial pathogens. The PDT domain has the same structural fold as the type 2 periplasmic binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 184 matched cddid_all.tbl CDD cd13533 cd13533 270251 PBP2_Yhfz Substrate-binding domain of uncharacterized protein Yhfz from Shigella Flexneri; the type 2 periplasmic-binding protein fold. This subfamily contains periplasmic binding protein type II (BPBII). This domain is found in solute binding proteins that serve as initial receptors in the ABC transport, signal transduction and channel gating. The PBPII proteins share the same architecture as periplasmic binding proteins type I (PBPI), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBPII proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. 222 matched cddid_all.tbl CDD cd13534 cd13534 270252 PBP2_MqnD_like Menaquinone biosynthetic enzyme and related hypothetical proteins; the type 2 periplasmic-binding protein fold. This family represents MqnD, an enzyme within the alternative menaquinone biosynthetic pathway, and related conserved hypothetical proteins. Menaquinone (MK; vitamin K) is an essential lipid-soluble carrier that shuttles electrons between membrane-bound protein complexes in the electron transport chain. The members include Ttha1568, MqnD from Thermus thermophiles HB8, and the conserved hypothetical proteins SCO4506 from Streptomyces coelicolor, Af1704 from Archaeoglobus DSM 4304, Dr0370 from Deinococcus radiodurans, and Ca3427 from candida albicans. They all have significant structural homology with the members of type 2 periplasmic-binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 261 matched cddid_all.tbl CDD cd13535 cd13535 270253 PBP2_Osm_BCP_like Substrate binding domain of osmoregulatory ABC-type glycine betaine/choline/L-proline transport system and related proteins; the type 2 periplasmic binding protein fold. This family is part of a high affinity multicomponent binding-protein-dependent ATP-binding cassette transport system specific to certain quaternary ammonium compounds for osmoregulation. The periplasmic substrate-binding domain, which is often fused to the permease component of the ATP-binding cassette transporter complex, is involved in uptake of osmoprotectants (also termed compatible solutes) such as betaines, choline, and L-proline. Many microorganisms accumulate these compatible solutes in response to high osmolarity to offset the loss of cell water. This domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 277 matched cddid_all.tbl CDD cd13536 cd13536 270254 PBP2_EcModA Substrate binding domain of ModA from Escherichia coli and its closest homologs;the type 2 periplasmic binding protein fold. This subfamily contains domains found in ModA proteins that serve as initial receptors in the ABC transport of molybdate in eubacteria and archaea. After binding molybdate with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ModA proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 227 matched cddid_all.tbl CDD cd13537 cd13537 270255 PBP2_YvgL_like Substrate binding domain of putative molybdate-binding protein YvgL and similar proteins;the type 2 periplasmic binding protein fold. This subfamily contains domains found in ModA proteins of putative ABC-type transporter. ModA proteins serve as initial receptors in the ABC transport of molybdate in eubacteria and archaea. Bacteria and archaea import molybdenum and tungsten from the environment in the form of the oxyanions molybdate (MoO(4) (2-)) and tungstate (WO(4) (2-)). After binding molybdate and tungstate with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ModA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 225 matched cddid_all.tbl CDD cd13538 cd13538 270256 PBP2_ModA_like_1 Substrate binding domain of putative molybdate-binding protein;the type 2 periplasmic binding protein fold. This subfamily contains domains found in ModA proteins of putative ABC-type transporter. Molybdate transport system is comprised of a periplasmic binding protein, an integral membrane protein, and an energizer protein. These three proteins are coded by modA, modB, and modC genes, respectively. ModA proteins serve as initial receptors in the ABC transport of molybdate mostly in eubacteria and archaea. After binding molybdate with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ModA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 230 matched cddid_all.tbl CDD cd13539 cd13539 270257 PBP2_AvModA Substrate binding domain of ModA/WtpA from Azotobacter vinelandii and its closest homologs;the type 2 periplasmic binding protein fold. This subfamily contains domains found in ModA proteins that serve as initial receptors in the ABC transport of molybdate in eubacteria and archaea. Bacteria and archaea import molybdenum and tungsten from the environment in the form of the oxyanions molybdate (MoO(4) (2-)) and tungstate (WO(4) (2-)). After binding molybdate with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. In contrast to the structure of the two ModA homologs from Escherichia coli and Azotobacter vinelandii, where the oxygen atoms are tetrahedrally arranged around the metal center, the structure of Pyrococcus furiosus ModA/WtpA (PfModA) has shown that a binding site for molybdate and tungstate is where the central metal atom is in a hexacoordinate configuration. This octahedral geometry was rather unexpected. The ModA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 226 matched cddid_all.tbl CDD cd13540 cd13540 270258 PBP2_ModA_WtpA Substrate binding domain of ModA/WtpA from Pyrococcus furiosus and its closest homologs;the type 2 periplasmic binding protein fold. This subfamily contains domains found in ModA proteins that serve as initial receptors in the ABC transport of molybdate in eubacteria and archaea. Bacteria and archaea import molybdenum and tungsten from the environment in the form of the oxyanions molybdate (MoO(4) (2-)) and tungstate (WO(4) (2-)). After binding molybdate with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. In contrast to the structure of the two ModA homologs from Escherichia coli and Azotobacter vinelandii, where the oxygen atoms are tetrahedrally arranged around the metal center, the structure of Pyrococcus furiosus ModA/WtpA (PfModA) has shown that a binding site for molybdate and tungstate where the central metal atom is in a hexacoordinate configuration. The ModA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 263 matched cddid_all.tbl CDD cd13541 cd13541 270259 PBP2_ModA_like_2 Substrate binding domain of molybdate-binding proteins;the type 2 periplasmic binding protein fold. This subfamily contains domains found in ModA proteins of putative ABC-type transporter. ModA proteins serve as initial receptors in the ABC transport of molybdate in eubacteria and archaea. Bacteria and archaea import molybdenum and tungsten from the environment in the form of the oxyanions molybdate (MoO(4) (2-)) and tungstate (WO(4) (2-)). After binding molybdate and tungstate with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ModA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 238 matched cddid_all.tbl CDD cd13542 cd13542 270260 PBP2_FutA1_ilke Substrate binding domain of ferric iron-binding protein, a member of the type 2 periplasmic binding fold superfamily. FutA1 is the periplasmic component of an ABC-type iron transporter and serves as the primary receptor in Synerchosystis species. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria and is critical for survival of these pathogens within the host. After binding iron with high affinity, FutA1 interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The iron- and thiamine-binding proteins belong to the PBPI2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 314 matched cddid_all.tbl CDD cd13543 cd13543 270261 PBP2_Fbp Substrate binding domain of ferric iron transporter, a member of the type 2 periplasmic binding fold superfamily. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. This periplasmic protein (Fbp) has high affinities for ferric iron and serves as the primary receptor for transport. After binding iron with high affinity, Fbp interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ferric iron-binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 306 matched cddid_all.tbl CDD cd13544 cd13544 270262 PBP2_Fbp_like_1 Substrate binding domain of a putative ferric iron transporter, a member of the type 2 periplasmic binding fold superfamily. The substrate domain of this group shows a high homology to the periplasmic component of ferric iron transporter (Fbp), but its biochemical characterization has not been performed. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. After binding iron with high affinity, Fbp interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ferric iron-binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 292 matched cddid_all.tbl CDD cd13545 cd13545 270263 PBP2_TbpA Substrate binding domain of thiamin transporter, a member of the type 2 periplasmic binding fold superfamily. Thiamin-binding protein TbpA is the periplasmic component of ABC-type transporter in E. coli, while the transmembrane permease and ATPase are ThiP and ThiQ, respectively. Thiamin (vitamin B1) is an essential confactor in all living systems that most prokaryotes, plants, and fungi can synthesized thiamin. However, in vertebrates, thiamine cannot be synthesized and must therefore be obtained through dietary absorption. In addition to thiamin biosynthesis, most organisms can import thiamin using specific transporters. After binding thiamine with high affinity, TbpA interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The thiamine-binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 269 matched cddid_all.tbl CDD cd13546 cd13546 270264 PBP2_BitB Substrate binding domain of a putative iron transporter BitB, a member of the type 2 periplasmic binding fold superfamily. The substrate domain of this group shows a high homology to the periplasmic component of ferric iron transporter (Fbp), but its biochemical characterization has not been performed. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. After binding iron with high affinity, Fbp interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ferric iron-binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 258 matched cddid_all.tbl CDD cd13547 cd13547 270265 PBP2_Fbp_like_2 Substrate binding domain of an uncharacterized ferric iron transporter, a member of the type 2 periplasmic binding fold superfamily. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. This periplasmic domain (Fbp) has high affinity for ferric iron and serves as the primary receptor for transport. After binding iron with high affinity, Fbp interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ferric iron-binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 259 matched cddid_all.tbl CDD cd13548 cd13548 270266 PBP2_AEPn_like Substrate binding domain of a putative 2-amnioethylphosphonate-bindinig transporter, a member of the type 2 periplasmic binding fold superfamily. The substrate domain of this group shows a high homology to the periplasmic component of ferric iron transporter (Fbp), but its biochemical characterization has not been performed. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. After binding iron with high affinity, Fbp interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ferric iron-binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 310 matched cddid_all.tbl CDD cd13549 cd13549 270267 PBP2_Fbp_like_3 Substrate binding domain of an uncharacterized ferric iron transporter, a member of the type 2 periplasmic binding fold superfamily. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. This periplasmic domain (Fbp) has high affinity for ferric iron and serves as the primary receptor for transport. After binding iron with high affinity, Fbp interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ferric iron-binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 263 matched cddid_all.tbl CDD cd13550 cd13550 270268 PBP2_Fbp_like_4 Substrate binding domain of an uncharacterized ferric iron transporter, a member of the type 2 periplasmic binding fold superfamily. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. This periplasmic domain (Fbp) has high affinity for ferric iron and serves as the primary receptor for transport. After binding iron with high affinity, Fbp interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ferric iron-binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 265 matched cddid_all.tbl CDD cd13551 cd13551 270269 PBP2_Fbp_like_5 Substrate binding domain of an uncharacterized ferric iron transporter, a member of the type 2 periplasmic binding fold superfamily. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. This periplasmic domain (Fbp) has high affinity for ferric iron and serves as the primary receptor for transport. After binding iron with high affinity, Fbp interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ferric iron-binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 267 matched cddid_all.tbl CDD cd13552 cd13552 270270 PBP2_Fbp_like_6 Substrate binding domain of an uncharacterized ferric iron transporter, a member of the type 2 periplasmic binding fold superfamily. The periplasmic iron binding protein plays an essential role in the iron uptake pathway of Gram-negative pathogenic bacteria from the Pasteurellaceae and Neisseriaceae families and is critical for survival of these pathogens within the host. This periplasmic domain (Fbp) has high affinity for ferric iron and serves as the primary receptor for transport. After binding iron with high affinity, Fbp interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ferric iron-binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 266 matched cddid_all.tbl CDD cd13553 cd13553 270271 PBP2_NrtA_CpmA_like Substrate binding domain of ABC-type nitrate/bicarbonate transporters, a member of the type 2 periplasmic binding fold superfamily. This subfamily includes nitrate (NrtA) and bicarbonate (CmpA) receptors. These domains are found in eubacterial perisplamic-binding proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding their ligand with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. These binding proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 212 matched cddid_all.tbl CDD cd13554 cd13554 270272 PBP2_DszB Substrate binding domain of 2'-hydroxybiphenyl-2-sulfinate desulfinase, a member of the type 2 periplasmic binding fold superfamily. This subfamily includes DszB, which converts 2'-hydroxybiphenyl-2-sulfinate to 2-hydroxybiphenyl and sulfinate at the rate-limiting step of the microbial dibenzothiophene desulfurization pathway. The overall fold of DszB is highly similar to those of periplasmic substrate-binding proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates. After binding their ligand with high affinity, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The DszB protein belongs to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 246 matched cddid_all.tbl CDD cd13555 cd13555 270273 PBP2_sulfate_ester_like Sulfate ester binding protein-like, the type 2 periplasmic binding protein fold. This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The SsuA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 268 matched cddid_all.tbl CDD cd13556 cd13556 270274 PBP2_SsuA_like_1 Substrate binding domain of putative sulfonate binding protein, a member of the type 2 periplasmic binding fold superfamily. This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The SsuA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 265 matched cddid_all.tbl CDD cd13557 cd13557 270275 PBP2_SsuA Substrate binding domain of sulfonate binding protein, a member of the type 2 periplasmic binding fold superfamily. This subfamily includes the sulfonate binding domains SsuA found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The SsuA proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 275 matched cddid_all.tbl CDD cd13558 cd13558 270276 PBP2_SsuA_like_2 Putative substrate binding domain of sulfonate binding protein, the type 2 periplasmic binding protein fold. This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The SsuA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 267 matched cddid_all.tbl CDD cd13559 cd13559 270277 PBP2_SsuA_like_3 Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic binding protein fold. This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The SsuA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 258 matched cddid_all.tbl CDD cd13560 cd13560 270278 PBP2_taurine Taurine-binding periplasmic protein; the type 2 periplasmic binding protein fold. This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The SsuA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 218 matched cddid_all.tbl CDD cd13561 cd13561 270279 PBP2_SsuA_like_4 Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic binding protein fold. This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The SsuA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 212 matched cddid_all.tbl CDD cd13562 cd13562 270280 PBP2_SsuA_like_5 Putative substrate binding domain of sulfonate binding protein-like, the type 2 periplasmic binding protein fold. This subfamily includes sulfonate binding domains found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The SsuA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 215 matched cddid_all.tbl CDD cd13563 cd13563 270281 PBP2_SsuA_like_6 Putative substrate binding domain of sulfonate binding protein-like, a member of the type 2 periplasmic binding protein fold. This subfamily includes the periplasmic component of putative ABC-type sulfonate transport system similar to SsuA. These domains are found in eubacterial SsuA proteins that serve as initial receptors in the ABC transport of bicarbonate, nitrate, taurine, or a wide range of aliphatic sulfonates, while other closest homologs are involved in thiamine (vitamin B1) biosynthetic pathway and desulfurization (DszB). After binding the ligand, SsuA interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The SsuA proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 208 matched cddid_all.tbl CDD cd13564 cd13564 270282 PBP2_ThiY_THI5_like Substrate binding domain of ABC-type transporter for thiamin biosynthetic pathway intermediates and similar proteins; the type 2 periplasmic binding protein fold. ThiY is the periplasmic N-formyl-4-amino-5-(aminomethyl)-2-methylpyrimidine (FAMP) binding component of the ABC transport system (ThiXYZ). FAMP is imported into cell by the transporter, where it is then incorporated into the thiamin biosynthetic pathway. The closest structural homologs of ThiY are THI5, which is responsible for the synthesis of 4-amino-5-(hydroxymethyl)-2-methylpyrimidine phosphate (HMP-P) in the thiamin biosynthetic pathway of eukaryotes, and periplasmic binding proteins involved in alkanesulfonate/nitrate and bicarbonate transport. After binding the ligand, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ThiY/THI5 proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 214 matched cddid_all.tbl CDD cd13565 cd13565 270283 PBP2_PstS Substrate binding domain of ABC-type phosphate transporter, a member of the type 2 periplasmic-binding fold superfamily. This subfamily contians phosphate binding domain found in PstS proteins that serve as initial receptors in the ABC transport of phosphate in eubacteria and archaea. After binding the ligand, PstS interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The PstS proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 254 matched cddid_all.tbl CDD cd13566 cd13566 270284 PBP2_phosphate Substrate binding domain of putative ABC-type phosphate transporter, a member of the type 2 periplasmic binding fold superfamily. This subfamily contains uncharacterized phosphate binding domains found in PstS proteins that serve as initial receptors in the ABC transport of phosphate in eubacteria and archaea. After binding the ligand, PstS interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The PstS proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 245 matched cddid_all.tbl CDD cd13567 cd13567 270285 PBP2_TtGluBP Substrate binding domain of Thermus thermophilus GluBP (TtGluBP) of TAXI family of the tripartite ATP-independent periplasmic transporters; contains the type 2 periplasmic binding protein fold. This subgroup includes TtGluBP of TAXI-TRAP family and closely related proteins. TRAP transporters are comprised of an SBP (substrate-binding protein) and two unequally sized integral membrane components. Although TtGluBP is predicted to be an L-glutamate and/or an L-glutamine-binding protein, the substrate spectrum of TAXI proteins remains to be defined. A sequence-homology search also shows that TtGluBP shares low sequence homology with putative immunogenic proteins of uncharacterized function. 284 matched cddid_all.tbl CDD cd13568 cd13568 270286 PBP2_TAXI_TRAP_like_3 Substrate binding domain of putative TAXI proteins of the tripartite ATP-independent periplasmic transporters; the type 2 periplasmic binding protein fold. This subgroup includes uncharacterized periplasmic binding proteins that are related to Thermus thermophilus GluBP (TtGluBP) of TAXI-TRAP family. TRAP transporters are comprised of an SBP (substrate-binding protein) and two unequally sized integral membrane components. Although TtGluBP is predicted to be an L-glutamate and/or an L-glutamine-binding protein, the substrate spectrum of TAXI proteins remains to be defined. A sequence-homology search also shows that TtGluBP shares low sequence homology with putative immunogenic proteins of uncharacterized function. 289 matched cddid_all.tbl CDD cd13569 cd13569 270287 PBP2_TAXI_TRAP_like_1 Substrate binding domain of putative TAXI proteins of the tripartite ATP-independent periplasmic transporters; the type 2 periplasmic binding protein fold. This subgroup includes uncharacterized periplasmic binding proteins that are related to Thermus thermophilus GluBP (TtGluBP) of TAXI-TRAP family. TRAP transporters are comprised of an SBP (substrate-binding protein) and two unequally sized integral membrane components. Although TtGluBP is predicted to be an L-glutamate and/or an L-glutamine-binding protein, the substrate spectrum of TAXI proteins remains to be defined. A sequence-homology search also shows that TtGluBP shares low sequence homology with putative immunogenic proteins of uncharacterized function. 283 matched cddid_all.tbl CDD cd13570 cd13570 270288 PBP2_TAXI_TRAP_like_2 Substrate binding domain of putative TAXI proteins of the tripartite ATP-independent periplasmic transporters; the type 2 periplasmic binding protein fold. This subgroup includes uncharacterized periplasmic binding proteins that are related to Thermus thermophilus GluBP (TtGluBP) of TAXI-TRAP family. TRAP transporters are comprised of an SBP (substrate-binding protein) and two unequally sized integral membrane components. Although TtGluBP is predicted to be an L-glutamate and/or an L-glutamine-binding protein, the substrate spectrum of TAXI proteins remains to be defined. A sequence-homology search also shows that TtGluBP shares low sequence homology with putative immunogenic proteins of uncharacterized function. 281 matched cddid_all.tbl CDD cd13571 cd13571 270289 PBP2_PnhD_1 Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold. This subfamily includes putative periplasmic binding components of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. They belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 253 matched cddid_all.tbl CDD cd13572 cd13572 270290 PBP2_PnhD_2 Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold. This subfamily includes putative periplasmic binding component of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. They belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 249 matched cddid_all.tbl CDD cd13573 cd13573 270291 PBP2_PnhD_3 Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold. This subfamily includes putative periplasmic binding component of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. They belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 253 matched cddid_all.tbl CDD cd13574 cd13574 270292 PBP2_PnhD_4 Substrate binding domain of uncharacterized ABC-type phosphonate-like transporter; contains the type 2 periplasmic binding fold. This subfamily includes putative periplasmic binding component of an ABC transport system similar to alkylphosphonate binding domain PnhD. These domains are found in PnhD-like proteins that are predicted to function as initial receptors in hypophosphite, phosphonate, or phosphate ABC transport in archaea and eubacteria. They belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 250 matched cddid_all.tbl CDD cd13575 cd13575 270293 PBP2_PnhD Substrate binding domain of ABC-type phosphonate uptake system; contains the type 2 periplasmic binding fold. This subfamily includes the Escherichia coli PhnD (EcPhnD) which exhibits high affinity for the environmentally abundant 2-aminoethylphosphonate (2-AEP), a precursor in the biosynthesis of phosphonolipids, phosphonoproteins, and phosphonoglycans. The Escherichia coli phn operon encodes 14 genes involved in binding, uptake and metabolism of phosphonate, and is activated under phophophate-limiting conditions. PhnD belongs to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. The PBP2 have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. PhnD is the periplasmic binding component of an ABC-type phosphonate uptake system (PhnCDE) that recognizes and binds phosphonate. 259 matched cddid_all.tbl CDD cd13576 cd13576 270294 PBP2_BugD_Asp Aspartic acid transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold. The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) receptors present in a number of bacterial species, but mainly in proteobacteria. Bug proteins are the PBP components of the tripartite carboxylate transporters (TTT). Their expansive expansion in proteobacteria indicates a large functional diversity. The best studied examples are Bordetella pertussis BugD, which is an aspartic acid transporter, and BugE, which is glutamate transporter. 294 matched cddid_all.tbl CDD cd13577 cd13577 270295 PBP2_BugE_Glu Glutamate transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold. The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) receptors present in a number of bacterial species, but mainly in proteobacteria. Bug proteins are the PBP components of the tripartite carboxylate transporters (TTT). Their expansive expansion in proteobacteria indicates a large functional diversity. The best studied examples are Bordetella pertussis BugD, which is an aspartic acid transporter, and BugE, which is glutamate transporter. 292 matched cddid_all.tbl CDD cd13578 cd13578 270296 PBP2_Bug27 Aromatic solutes transporter of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold. Bug27 binds non-carboxylated solute nicotinamide, in contrast to BugD (aspartic acid transporter) and BugE (glutamate transporter) which both bind aliphatic carboxylated ligands. The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) receptors present in a number of bacterial species, but mainly in proteobacteria. Bug proteins are the PBP components of the tripartite carboxylate transporters (TTT). Their expansive expansion in proteobacteria indicates a large functional diversity. 291 matched cddid_all.tbl CDD cd13579 cd13579 270297 PBP2_Bug_NagM Uncharacterized NagM-like protein of Bug (Bordetella uptake gene) protein family; contains the type 2 periplasmic binding fold. The Bug (Bordetella uptake gene) protein family is a large family of periplasmic solute-binding (PBP) receptors present in a number of bacterial species, but mainly in proteobacteria. Bug proteins are the PBP components of the tripartite carboxylate transporters (TTT). Their expansive expansion in proteobacteria indicates a large functional diversity. The best studied examples are Bordetella pertussis BugD, which is an aspartic acid transporter, and BugE, which is glutamate transporter. 292 matched cddid_all.tbl CDD cd13580 cd13580 270298 PBP2_AlgQ_like_1 Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold. This subgroup includes uncharacterized periplasmic-binding proteins that are closely related to high molecular weight (HMW) alginate bining proteins (AlgQ1 and AlgQ2) found in gram-negative soil bacteria. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins (AlgQ1 and AlgQ2). Alginate is an anionic polysaccharide that is made up of alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide. 471 matched cddid_all.tbl CDD cd13581 cd13581 270299 PBP2_AlgQ_like_2 Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold. This subgroup includes uncharacterized periplasmic-binding proteins that are closely related to high molecular weight (HMW) alginate bining proteins (AlgQ1 and AlgQ2) found in gram-negative soil bacteria. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins (AlgQ1 and AlgQ2). Alginate is an anionic polysaccharide that is made up of alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide. 490 matched cddid_all.tbl CDD cd13582 cd13582 270300 PBP2_AlgQ_like_3 Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold. This subgroup includes uncharacterized periplasmic-binding proteins that are closely related to high molecular weight (HMW) alginate bining proteins (AlgQ1 and AlgQ2) found in gram-negative soil bacteria. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins (AlgQ1 and AlgQ2). Alginate is an anionic polysaccharide that is made up of alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide. 504 matched cddid_all.tbl CDD cd13583 cd13583 270301 PBP2_AlgQ_like_4 Periplasmic-binding component of alginate-specific ABC uptake system-like; contains the type 2 periplasmic binding fold. This subgroup includes uncharacterized periplasmic-binding proteins that are closely related to high molecular weight (HMW) alginate bining proteins (AlgQ1 and AlgQ2) found in gram-negative soil bacteria. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins (AlgQ1 and AlgQ2). Alginate is an anionic polysaccharide that is made up of alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide. 478 matched cddid_all.tbl CDD cd13584 cd13584 270302 PBP2_AlgQ1_2 Periplasmic-binding component of alginate-specific ABC uptake system; contains the type 2 periplasmic binding fold. This group represents the periplasmic-binding component of high molecular weight (HMW) alginate uptake system found in gram-negative soil bacteria such as Sphingomonas sp. A1. The HMW alginate uptake system is composed of a novel pit formed on the cell surface and a pit-dependent ATP-binding cassette (ABC) transporter in the inner membrane. The transportation of HMW alginate from the pit to the ABC transporter is mediated by periplasmic HMW alginate-binding proteins (AlgQ1 and AlgQ2). Alginate is an anionic polysaccharide that includes alpha-L-mannuronate and its 5'-epimer, alpha-L-guluronate. Alginate is present in the cell walls of brown seaweeds, where it forms a viscous gum by binding water. Alginate is also produced by two bacteria genera Pseudomonas and Azotobacter. AlgQ1 and AlgQ2 belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. However, unlike other bacterial periplasmic-binding proteins that deliver small solutes to ABC transporters, AlgQ1/2 can bind a macromolecule and may have specificity for either sugar or a certain type of polysaccharide. 481 matched cddid_all.tbl CDD cd13585 cd13585 270303 PBP2_TMBP_like The periplasmic-binding component of ABC transport systems specific for trehalose/maltose and similar oligosaccharides; possess type 2 periplasmic binding fold. This family includes the periplasmic trehalose/maltose-binding component of an ABC transport system and related proteins from archaea and bacteria. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 383 matched cddid_all.tbl CDD cd13586 cd13586 270304 PBP2_Maltose_binding_like The periplasmic-binding component of ABC transport systems specific for maltose and related polysaccharides; possess type 2 periplasmic binding fold. This subfamily represents the periplasmic binding component of ABC transport systems involved in uptake of polysaccharides including maltose, maltodextrin, and cyclodextrin. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 367 matched cddid_all.tbl CDD cd13587 cd13587 270305 PBP2_polyamine_2 The periplasmic-binding component of an uncharacterized ABC transporter involved in uptake of polyamines; contains the type 2 periplasmic binding fold. This family represents the periplasmic binding domain that functions as the primary polyamine receptor of an uncharacterized ABC-type transport system. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 292 matched cddid_all.tbl CDD cd13588 cd13588 270306 PBP2_polyamine_1 The periplasmic-binding component of an uncharacterized ABC transporter involved in uptake of polyamines; contains the type 2 periplasmic binding fold. This group represents the periplasmic binding domain that functions as the primary high-affinity receptor of an uncharactertized ABC-type polyamine transport system. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 279 matched cddid_all.tbl CDD cd13589 cd13589 270307 PBP2_polyamine_RpCGA009 The periplasmic-binding component of an uncharacterized ABC transport system from Rhodopseudomonas palustris CGA009 and related proteins; contains the type 2 periplasmic-binding fold. This group represents the periplasmic binding domain that serves as the primary high-affinity receptor of an uncharacterized ABC-type polyamine transporter from Rhodopseudomonas palustris Cga009 and related proteins from other bacteria. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 268 matched cddid_all.tbl CDD cd13590 cd13590 270308 PBP2_PotD_PotF_like The periplasmic-binding component of ABC transporters involved in uptake of polyamines; possess the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain that functions as the primary high-affinity receptors of ABC-type polyamine transport systems. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 315 matched cddid_all.tbl CDD cd13591 cd13591 270309 PBP2_HisGL1 The catalytic domain of hexameric long form HisGL1; contains the type 2 periplasmic binding protein fold. Encoded by the hisG gene, the ATP phosphoribosyltransferase (ATP-PRT, EC 2.4.2.17) is the first enzyme in histidine biosynthetic pathway that catalyzes the condensation of ATP and PRPP (5'-phosphoribosyl 1'-pyrophosphate), and is regulated by a feedback inhibition from the product histidine. ATP-PRT has two distinct forms: a hexameric long form, HisGL, containing two catalytic domains and a C-terminal regulatory domain; and a hetero-octomeric short form, HisGs, without the regulatory domain. HisGL is catalytically competent, but the hetero-octameric HisGs requires the second subunit HisZ, a paralog to the catalytic domain of functional histidyl-tRNA synthetases (HisRSs), for the enzyme activity. This catalytic domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. 204 matched cddid_all.tbl CDD cd13592 cd13592 270310 PBP2_HisGL2 The catalytic domain of hexameric long form HisGL2; contains the type 2 periplasmic binding protein fold. Encoded by the hisG gene, the ATP phosphoribosyltransferase (ATP-PRT, EC 2.4.2.17) is the first enzyme in histidine biosynthetic pathway that catalyzes the condensation of ATP and PRPP (5'-phosphoribosyl 1'-pyrophosphate), and is regulated by a feedback inhibition from the product histidine. ATP-PRT has two distinct forms: a hexameric long form, HisGL, containing two catalytic domains and a C-terminal regulatory domain; and a hetero-octomeric short form, HisGs, without the regulatory domain. HisGL is catalytically competent, but the hetero-octameric HisGs requires the second subunit HisZ, a paralog to the catalytic domain of functional histidyl-tRNA synthetases (HisRSs), for the enzyme activity. This catalytic domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. 208 matched cddid_all.tbl CDD cd13593 cd13593 270311 PBP2_HisGL3 The catalytic domain of hexameric long form HisGL3; contains the type 2 periplasmic binding protein fold. Encoded by the hisG gene, the ATP phosphoribosyltransferase (ATP-PRT, EC 2.4.2.17) is the first enzyme in histidine biosynthetic pathway that catalyzes the condensation of ATP and PRPP (5'-phosphoribosyl 1'-pyrophosphate), and is regulated by a feedback inhibition from the product histidine. ATP-PRT has two distinct forms: a hexameric long form, HisGL, containing two catalytic domains and a C-terminal regulatory domain; and a hetero-octomeric short form, HisGs, without the regulatory domain. HisGL is catalytically competent, but the hetero-octameric HisGs requires the second subunit HisZ, a paralog to the catalytic domain of functional histidyl-tRNA synthetases (HisRSs), for the enzyme activity. This catalytic domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. 220 matched cddid_all.tbl CDD cd13594 cd13594 270312 PBP2_HisGL4 The catalytic domain of hexameric long form HisGL4; contains the type 2 periplasmic binding fold. Encoded by the hisG gene, the ATP phosphoribosyltransferase (ATP-PRT, EC 2.4.2.17) is the first enzyme in histidine biosynthetic pathway that catalyzes the condensation of ATP and PRPP (5'-phosphoribosyl 1'-pyrophosphate), and is regulated by a feedback inhibition from the product histidine. ATP-PRT has two distinct forms: a hexameric long form, HisGL, containing two catalytic domains and a C-terminal regulatory domain; and a hetero-octomeric short form, HisGs, without the regulatory domain. HisGL is catalytically competent, but the hetero-octameric HisGs requires the second subunit HisZ, a paralog to the catalytic domain of functional histidyl-tRNA synthetases (HisRSs), for the enzyme activity. This catalytic domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. 207 matched cddid_all.tbl CDD cd13595 cd13595 270313 PBP2_HisGs The catalytic domain of hetero-octomeric short form HisGs; contains the type 2 periplasmic binding protein fold. Encoded by the hisG gene, the ATP phosphoribosyltransferase (ATP-PRT, EC 2.4.2.17) is the first enzyme in histidine biosynthetic pathway that catalyzes the condensation of ATP and PRPP (5'-phosphoribosyl 1'-pyrophosphate), and is regulated by a feedback inhibition from the product histidine. ATP-PRT has two distinct forms: a hexameric long form, HisGL, containing two catalytic domains and a C-terminal regulatory domain; and a hetero-octomeric short form, HisGs, without the regulatory domain. HisGL is catalytically competent, but the hetero-octameric HisGs requires the second subunit HisZ, a paralog to the catalytic domain of functional histidyl-tRNA synthetases (HisRSs), for the enzyme activity. This catalytic domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. 205 matched cddid_all.tbl CDD cd13596 cd13596 270314 PBP2_lipoprotein_GmpC The periplasmic substrate-binding domain of the membrane-associated lipoprotein-9 GmpC; contains the type 2 periplasmic-binding protein fold. This group includes the membrane-associated lipoprotein-9 from Staphylococcus aureus that binds the dipeptide glycylmethionine (GlyMet). The lipoprotein-9 has both structural and sequential homology to the MetQ family of substrate-binding protein. The GlyMet binding protein belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. 230 matched cddid_all.tbl CDD cd13597 cd13597 270315 PBP2_lipoprotein_Tp32 The substrate-binding domain of the 32-kilodalton lipoprotein (Tp32) from Treponema pallidum binds L-methionine; the type 2 periplasmic-binding protein fold. This group includes the lipoprotein Tp32, a periplasmic component of a methionine uptake transporter system, and its closely related homologs. The Tp32 has both structural and sequential homology to the MetQ family of substrate-binding protein, and thus it belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. 236 matched cddid_all.tbl CDD cd13598 cd13598 270316 PBP2_lipoprotein_IlpA_like Toll-like receptor 2-activating lipoprotein IlpA from Vibrio vulnificus and similar lipoproteins; the type 2 periplasmic binding protein fold. This group includes the IlpA protein which has both structural and sequential homology to the MetQ family of substrate-binding protein, and thus belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. 227 matched cddid_all.tbl CDD cd13599 cd13599 270317 PBP2_lipoprotein_Gna1946 The membrane-associated lipoprotein Gna1946 from Neisseria meningitidis; the type 2 periplasmic binding protein fold. Gna1946 shares significant structural and sequence homology with the periplasmic substrate-binding domain of ATP-binding cassette (ABC) transporter involved in uptake of methionine (MetQ). The members of the MetQ-like family include the 32-kilodalton lipoprotein (Tp32) from Treponema pallidum, the membrane-associated lipoprotein-9 GmpC from Staphylococcus aureus, and Toll-like receptor 2-activating lipoprotein IlpA from Vibrio vulnificus. They all function as a receptor for methionine. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. 228 matched cddid_all.tbl CDD cd13600 cd13600 270318 PBP2_lipoprotein_like_1 Putative periplasmic-binding component of ABC-type methionine uptake transporter system-like; the type 2 periplasmic binding protein fold. This subgroup shares significant sequence homology with the periplasmic substrate-binding domain of ATP-binding cassette (ABC) transporter involved in uptake of methionine (MetQ). The members of the MetQ-like family include the 32-kilodalton lipoprotein (Tp32) from Treponema pallidum, the membrane-associated lipoprotein-9 GmpC from Staphylococcus aureus, and Toll-like receptor 2-activating lipoprotein IlpA from Vibrio vulnificus. They all function as a receptor for methionine. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. 228 matched cddid_all.tbl CDD cd13601 cd13601 270319 PBP2_TRAP_DctP1_3_4_like Periplasmic substrate-binding component of uncharacterized TRAP-type C4-dicarboxylate transporter subfamilies; the type 2 periplasmic-binding protein fold. This model includes uncharacterized DctP subfamilies of the TRAP Transporters. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 302 matched cddid_all.tbl CDD cd13602 cd13602 270320 PBP2_TRAP_BpDctp6_7 Substrate-binding domain of a pyroglutamic acid binding DctP subfamily of the tripartite ATP-independent periplasmic transporters; contains the type 2 periplasmic binding protein fold. DctP6 and DctP7 groups of the TRAP transporters that involved in pyroglutamic acid transport. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 300 matched cddid_all.tbl CDD cd13603 cd13603 270321 PBP2_TRAP_Siap_TeaA_like Substrate-binding domain of a sialic acid binding Tripartite ATP-independent Periplasmic transport system (SiaP) and related proteins; the type 2 periplasmic-binding protein fold. This subfamily includes the periplasmic-binding component of TRAP transport systems such as SiaP (a sialic acid binding virulence factor), TeaA (an ectoine binding protein), and an uncharacterized TM0322 from hyperthermophilic bacterium Thermotoga maritima. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process and a smaller membrane of unknown function. The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 297 matched cddid_all.tbl CDD cd13604 cd13604 270322 PBP2_TRAP_ketoacid_lactate_like Substrate-binding domain of an alpha-keto acid binding Tripartite ATP-independent Periplasmic transporter and related proteins; the type 2 periplasmic-binding protein fold. This family constitutes TRAP transporters that bind to ketoacids such as pyruvate and alpha-ketobutyrate, xylulose, and other unknown ligands. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 306 matched cddid_all.tbl CDD cd13605 cd13605 270323 PBP2_TRAP_DctP_like_2 Substrate-binding component of uncharacterized Tripartite ATP-independent Periplasmic transporter; the type 2 periplasmic-binding protein fold. This family represents the TRAP Transporters that are specific to various ligands, including sialic acid (N-acetyl neuraminic acid), glutamate, ectoine, xylulose, C4-dicarboxylates such as succinate, malate and fumarate, and keto acids such as pyruvate and alpha-ketobutyrate. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. This CD also included some eukaryotic homologs that have not been functionally characterized. TRAP transporters are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 303 matched cddid_all.tbl CDD cd13606 cd13606 270324 PBP2_ProX_like Bacterial substrate-binding protein ProX of ABC-type osmoregulated transporter and its related proteins; the type 2 periplasmic-binding protein fold. This group includes periplasmic substrate-binding component of ABC transport systems from gram-negative and -positive bacteria that are involved in uptake of osmoprotectants (also termed compatible solutes) such as betaine, choline, proline betaine, carnitine, and L-proline. To counteract the efflux of water, many microorganisms accumulate the compatible solutes for a sustained adjustment to high osmolarity surroundings. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 260 matched cddid_all.tbl CDD cd13607 cd13607 270325 PBP2_AfProX_like Substrate-binding protein ProX of ABC-type osmoregulatory transporter from Archaeoglobus fulgidus and its related proteins; the type 2 periplasmic-binding protein fold. This subfamily includes the periplasmic substrate-binding protein ProX from the hyperthermophilic archaeon Archaeoglobus fulgidus and its related proteins. AfProX is involved in uptake of compatible solutes such as the trimethylammonium compound glycine betaine and the dimethylammonium compound proline betaine, but the relative substrate preference is not known. To counteract the efflux of water, many microorganisms accumulate the compatible solutes for a sustained adjustment to high osmolarity surroundings. AfProX belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 261 matched cddid_all.tbl CDD cd13608 cd13608 270326 PBP2_OpuCC_like Substrate-binding protein OpuCC of ABC-type osmoregulatory transporter and related proteins; the type 2 periplasmic-binding protein fold. This subfamily includes the periplasmic substrate-binding protein OpuCC of the ABC transporter OpuC (where Opu is osmoprotectant uptake), which can recognize a broad spectrum of compatible solutes, and its paralog OpuBC that can solely bind choline. To counteract the efflux of water, many microorganisms accumulate the compatible solutes for a sustained adjustment to high osmolarity surroundings. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 265 matched cddid_all.tbl CDD cd13609 cd13609 270327 PBP2_Opu_like_1 Substrate-binding domain of putative ABC-type osmoprotectant uptake system; the type 2 periplasmic-binding protein fold. This group includes the periplasmic substrate-binding component of a putative ABC transport system that is predicted to be involved in uptake of osmoprotectants (also termed compatible solutes) such as betaine, choline, proline betaine, carnitine, and L-proline. The relative substrate preference of this group is not known. To counteract the efflux of water, many microorganisms accumulate the compatible solutes for a sustained adjustment to high osmolarity surroundings. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 263 matched cddid_all.tbl CDD cd13610 cd13610 270328 PBP2_ChoS Substrate-binding domain ChoS of an osmoregulated ABC-type transporter and related proteins; type 2 periplasmic-binding protein fold. Osmoprotectant binding lipoprotein ChoS of Lactococcus lactis is predicted to be involved in uptake of compatible solutes such as choline and glycine betaine, but the relative substrate preference is not known. To counteract the efflux of water, microorganisms accumulate the compatible solutes for a sustained adjustment to high osmolarity surroundings. ChoS belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 264 matched cddid_all.tbl CDD cd13611 cd13611 270329 PBP2_YehZ Substrate-binding domain YehZ of an osmoregulated ABC-type transporter; the type 2 periplasmic-binding protein fold. Osmoprotectant binding lipoprotein YehZ of Clostridium sticklandii is predicted to be involved in uptake of compatible solutes such as choline, L-proline and glycine betaine, but the relative substrate preference is not known. To counteract the efflux of water, microorganisms accumulate the compatible solutes for a sustained adjustment to high osmolarity surroundings. YehZ belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 267 matched cddid_all.tbl CDD cd13612 cd13612 270330 PBP2_ProWX Substrate-binding protein ProWX of ABC-type osmoregulated transporter and its related proteins; the type 2 periplasmic-binding protein fold. Osmoprotectant binding lipoprotein ProWX of Helicobacter pylori is predicted to be involved in uptake of compatible solutes such as choline, L-proline and glycine betaine, but the relative substrate preference is not known. To counteract the efflux of water, microorganisms accumulate the compatible solutes for a sustained adjustment to high osmolarity surroundings. ProWX belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 267 matched cddid_all.tbl CDD cd13613 cd13613 270331 PBP2_Opu_like_2 Substrate-binding domain of putative ABC-type osmoprotectant uptake system; the type 2 periplasmic-binding protein fold. This group includes the periplasmic substrate-binding component of a putative ABC transport system that is predicted to be involved in uptake of osmoprotectants (also termed compatible solutes) such as betaine, choline, proline betaine, carnitine, and L-proline. The relative substrate preference of this group is not known. To counteract the efflux of water, many microorganisms accumulate the compatible solutes for a sustained adjustment to high osmolarity surroundings. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 264 matched cddid_all.tbl CDD cd13614 cd13614 270332 PBP2_QAT_like Substrate-binding domain of quaternary amine ABC-type transporter; the type 2 periplasmic-binding protein fold. This group includes the periplasmic substrate-binding component of a putative quaternary amine ABC transport system that is predicted to be involved in uptake of osmoprotectants (also termed compatible solutes) such as betaine, choline, proline betaine, carnitine, and L-proline. The relative substrate preference of this group is not known. To counteract the efflux of water, many microorganisms accumulate the compatible solutes for a sustained adjustment to high osmolarity surroundings. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 264 matched cddid_all.tbl CDD cd13615 cd13615 270333 PBP2_ProWY Substrate-binding domain of ABC-type osmoregulated transporter; the type 2 periplasmic-binding protein fold. Osmoprotectant binding lipoprotein ProWY of Streptococcus thermophilus is predicted to be involved in uptake of compatible solutes such as choline, L-proline and glycine betaine, but the relative substrate preference is not known. To counteract the efflux of water, microorganisms accumulate the compatible solutes for a sustained adjustment to high osmolarity surroundings. ProWY belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 262 matched cddid_all.tbl CDD cd13616 cd13616 270334 PBP2_OsmF Substrate-binding domain OsmF of an osmoregulated ABC-type transporter; the type 2 periplasmic-binding protein fold. Osmoprotectant binding lipoprotein OsmF of an ABC transporter (YehZYXW) from Escherichia coli is predicted to be involved in uptake of compatible solutes such as choline, L-proline and glycine betaine, but the relative substrate preference is not known. To counteract the efflux of water, microorganisms accumulate the compatible solutes for a sustained adjustment to high osmolarity surroundings. OsmF belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 274 matched cddid_all.tbl CDD cd13617 cd13617 270335 PBP2_transferrin_C The C-lobe of transferrin, a member of the type 2 periplasmic binding protein fold superfamily. Transferrins are iron-binding blood plasma glycoproteins that regulate the level of free iron in biological fluids. Vertebrate transferrins are made of a single polypeptide chain with a molecular weight of about 80 kDa. The polypeptide is folded into two homologous lobes (the N-lobe and C-lobe), and each lobe is further subdivided into two similar alpha helices and beta sheets domains separated by a deep cleft that forms the binding site for ferric iron. Thus, the transferrin protein contains two homologous metal-binding sites with high affinities for ferric iron. The modern transferrin proteins are thought to be evolved from an ancestral gene coding for a protein of 40 kDa containing a single binding site by means of a gene duplication event. Vertebrate transferrins are found in a variety of bodily fluids, including serum transferrins, ovotransferrins, lactoferrins, and melanotransferrins. Transferrin-like proteins are also found in the circulatory fluid of certain invertebrates. The transferrins have the same structural fold as the type 2 periplasmic-binding proteins, many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. 331 matched cddid_all.tbl CDD cd13618 cd13618 270336 PBP2_transferrin_N The N-lobe of transferrin, a member of the type 2 periplasmic binding protein fold superfamily. Transferrins are iron-binding blood plasma glycoproteins that regulate the level of free iron in biological fluids. Vertebrate transferrins are made of a single polypeptide chain with a molecular weight of about 80 kDa. The polypeptide is folded into two homologous lobes (the N-lobe and C-lobe), and each lobe is further subdivided into two similar alpha helices and beta sheets domains separated by a deep cleft that forms the binding site for ferric iron. Thus, the transferrin protein contains two homologous metal-binding sites with high affinities for ferric iron. The modern transferrin proteins are thought to be evolved from an ancestral gene coding for a protein of 40 kDa containing a single binding site by means of a gene duplication event. Vertebrate transferrins are found in a variety of bodily fluids, including serum transferrins, ovotransferrins, lactoferrins, and melanotransferrins. Transferrin-like proteins are also found in the circulatory fluid of certain invertebrates. The transferrins have the same structural fold as the type 2 periplasmic-binding proteins, many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. 324 matched cddid_all.tbl CDD cd13619 cd13619 270337 PBP2_GlnP Glutamine-binding domain of ABC transporter, a member of the type 2 periplasmic binding fold protein superfamily. Periplasmic glutamine binding domain GlnP serves as an initial receptor in the ABC transport of glutamine in eubacteria. GlnP belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 220 matched cddid_all.tbl CDD cd13620 cd13620 270338 PBP2_GltS Substrate binding domain of glutamate or arginine ABC transporter, a member of the type 2 periplasmic binding fold protein superfamily. This family comprises of the periplasmic-binding protein component (GltS) of an ABC transporter specific for glutamate or arginine from Lactococcus lactis, as well as its closely related proteins. The GltS domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis 227 matched cddid_all.tbl CDD cd13621 cd13621 270339 PBP2_AA_binding_like_3 Substrate-binding domain of putative amino acid-binding protein; the type 2 periplasmic-binding protein fold. This putative amino acid-binding protein belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 229 matched cddid_all.tbl CDD cd13622 cd13622 270340 PBP2_Arg_3 Substrate binding domain of an arginine 3rd transport system; the type 2 periplasmic binding fold. This subgroup is similar to the HisJ-like family that comprises the periplasmic substrate-binding proteins, including the lysine-, arginine-, ornithine-binding protein (LAO) and the histidine-binding protein (HisJ), which serve as initial receptors for active transport. HisJ and LAO proteins belong to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 222 matched cddid_all.tbl CDD cd13623 cd13623 270341 PBP2_AA_hypothetical Substrate-binding domain of putative amino-acid transport system; the type 2 periplasmic binding protein fold. This putative amino acid-binding protein belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 220 matched cddid_all.tbl CDD cd13624 cd13624 270342 PBP2_Arg_Lys_His Substrate binding domain of the arginine-, lysine-, histidine-binding protein ArtJ; the type 2 periplasmic binding protein fold. This group includes the periplasmic substrate-binding protein ArtJ of the ATP-binding cassette (ABC) transport system from the thermophilic bacterium Geobacillus stearothermophilus, which is specific for arginine, lysine, and histidine. ArtJ belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 219 matched cddid_all.tbl CDD cd13625 cd13625 270343 PBP2_AA_binding_like_1 Substrate-binding domain of putative amino acid-binding protein; the type 2 periplasmic-binding protein fold. This putative amino acid-binding protein belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 230 matched cddid_all.tbl CDD cd13626 cd13626 270344 PBP2_Cystine_like Substrate binding domain of cystine ABC transporters; the type 2 periplasmic binding protein fold. Cystine-binding domain of periplasmic receptor-dependent ATP-binding cassette (ABC) transporters. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Also, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 219 matched cddid_all.tbl CDD cd13627 cd13627 270345 PBP2_AA_binding_like_2 Substrate-binding domain of putative amino acid-binding protein; the type 2 periplasmic-binding protein fold. This putative amino acid-binding protein belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 243 matched cddid_all.tbl CDD cd13628 cd13628 270346 PBP2_Ala Periplasmic substrate binding domain of ABC-type transporter specific to alanine; the type 2 periplasmic binding protein. This periplasmic substrate component serves as an initial receptor in the ABC transport of glutamine in eubacteria and archaea. After binding the alanine with high affinity, this domain Interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. This alanine specific domain belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 219 matched cddid_all.tbl CDD cd13629 cd13629 270347 PBP2_Dsm1740 Amino acid-binding domain of the type 2 periplasmic binding fold superfamily. This subfamily includes the periplasmic binding protein type II (BPBII). This domain is found in solute binding proteins that serve as initial receptors in the ABC transport, signal transduction and channel gating. The PBPII proteins share the same architecture as periplasmic binding proteins type I (PBPI), but have a different topology. They are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBPII proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the family includes ionotropic glutamate receptors and unorthodox sensor proteins involved in signal transduction. 221 matched cddid_all.tbl CDD cd13630 cd13630 270348 PBP2_PDT_1 Catalytic domain of prephenate dehydratase and similar proteins, subgroup 1; the type 2 periplasmic binding protein fold. Prephenate dehydratase (PDT, EC:4.2.1.51) converts prephenate to phenylpyruvate through dehydration and decarboxylation reactions. PDT plays a key role in the biosynthesis of L-Phe in organisms that utilize the shikimate pathway. PDT is allosterically regulated by L-Phe and other amino acids. The catalytic PDT domain consists of two similar subdomains with a cleft in between, which hosts the highly conserved active site. In gram-postive bacteria and archaea, PDT is a monofunctional enzyme, consisting of a catalytic domain (PDT domain) and a regulatory domain (ACT) (aspartokinase, chorismate mustase domain). In gram-negative bacteria, PDT exists as fusion protein with chorismate mutase (CM), forming a bifunctional enzyme, P-protein (PheA). The CM in the P-protein catalyzes the pericycle isomerization of chorismate to prephenate that serves as a substrate for PDT. The CM and PDT are essentail enzymes for the biosynthesis of aromatic amino acids in microorganisms but are not found in humans. Thus, both CM and PDT can potentially serve as drug targets against microbial pathogens. The PDT domain has the same structural fold as the type 2 periplasmic binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 180 matched cddid_all.tbl CDD cd13631 cd13631 270349 PBP2_Ct-PDT_like Catalytic domain of prephenate dehydratase from Chlorobium tepidum and similar proteins, subgroup 2; the type 2 periplasmic binding protein fold. Prephenate dehydratase (PDT, EC:4.2.1.51) converts prephenate to phenylpyruvate through dehydration and decarboxylation reactions. PDT plays a key role in the biosynthesis of L-Phe in organisms that utilize the shikimate pathway. PDT is allosterically regulated by L-Phe and other amino acids. The catalytic PDT domain consists of two similar subdomains with a cleft in between, which hosts the highly conserved active site. In gram-postive bacteria and archaea, PDT is a monofunctional enzyme, consisting of a catalytic domain (PDT domain) and a regulatory domain (ACT) (aspartokinase, chorismate mustase domain). In gram-negative bacteria, PDT exists as fusion protein with chorismate mutase (CM), forming a bifunctional enzyme, P-protein (PheA). The CM in the P-protein catalyzes the pericycle isomerization of chorismate to prephenate that serves as a substrate for PDT. The CM and PDT are essentail enzymes for the biosynthesis of aromatic amino acids in microorganisms but are not found in humans. Thus, both CM and PDT can potentially serve as drug targets against microbial pathogens. The PDT domain has the same structural fold as the type 2 periplasmic binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 182 matched cddid_all.tbl CDD cd13632 cd13632 270350 PBP2_Aa-PDT_like Catalytic domain of prephenate dehydratase from Arthrobacter aurescens and similar proteins, subgroup 3; the type 2 periplasmic binding protein fold. Prephenate dehydratase (PDT, EC:4.2.1.51) converts prephenate to phenylpyruvate through dehydration and decarboxylation reactions. PDT plays a key role in the biosynthesis of L-Phe in organisms that utilize the shikimate pathway. PDT is allosterically regulated by L-Phe and other amino acids. The catalytic PDT domain consists of two similar subdomains with a cleft in between, which hosts the highly conserved active site. In gram-postive bacteria and archaea, PDT is a monofunctional enzyme, consisting of a catalytic domain (PDT domain) and a regulatory domain (ACT) (aspartokinase, chorismate mustase domain). In gram-negative bacteria, PDT exists as fusion protein with chorismate mutase (CM), forming a bifunctional enzyme, P-protein (PheA). The CM in the P-protein catalyzes the pericycle isomerization of chorismate to prephenate that serves as a substrate for PDT. The CM and PDT are essentail enzymes for the biosynthesis of aromatic amino acids in microorganisms but are not found in humans. Thus, both CM and PDT can potentially serve as drug targets against microbial pathogens. The PDT domain has the same structural fold as the type 2 periplasmic binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 183 matched cddid_all.tbl CDD cd13633 cd13633 270351 PBP2_Sa-PDT_like Catalytic domain of prephenate dehydratase from Staphylococcus aureus and similar proteins, subgroup 4; the type 2 periplasmic binding protein fold. Prephenate dehydratase (PDT, EC:4.2.1.51) converts prephenate to phenylpyruvate through dehydration and decarboxylation reactions. PDT plays a key role in the biosynthesis of L-Phe in organisms that utilize the shikimate pathway. PDT is allosterically regulated by L-Phe and other amino acids. The catalytic PDT domain consists of two similar subdomains with a cleft in between, which hosts the highly conserved active site. In gram-postive bacteria and archaea, PDT is a monofunctional enzyme, consisting of a catalytic domain (PDT domain) and a regulatory domain (ACT) (aspartokinase, chorismate mustase domain). In gram-negative bacteria, PDT exists as fusion protein with chorismate mutase (CM), forming a bifunctional enzyme, P-protein (PheA). The CM in the P-protein catalyzes the pericycle isomerization of chorismate to prephenate that serves as a substrate for PDT. The CM and PDT are essentail enzymes for the biosynthesis of aromatic amino acids in microorganisms but are not found in humans. Thus, both CM and PDT can potentially serve as drug targets against microbial pathogens. The PDT domain has the same structural fold as the type 2 periplasmic binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 184 matched cddid_all.tbl CDD cd13634 cd13634 270352 PBP2_Sco4506 The conserved hypothetical protein SCO4506 exhibits the type 2 periplasmic-binidng protein fold. This group includes the SCO4506 protein from Streptomyces coelicolor and related hypothetical proteins. SCO4506 is an ortholog of Ttha1568 (MqnD) from Thermus thermophilies HB8. MqnD is an enzyme within an alternative menaquinone biosynthetic pathway that catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate. Menaquinone (MK; vitamin K) is an essential lipid-soluble carrier that shuttles electrons between membrane-bound protein complexes in the electron transport chain. SCO4506 has significant structural homology with the members of type 2 periplasmic-binding fold protein superfamily. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 256 matched cddid_all.tbl CDD cd13635 cd13635 270353 PBP2_Ttha1568_Mqnd A menaquinone biosynthetic enzyme exhibits the type 2 periplasmic-binding protein fold. This group includes Ttha1568 (MqnD) from Thermus thermophilies HB8, an enzyme within an alternative menaquinone biosynthetic pathway that catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate. Menaquinone (MK; vitamin K) is an essential lipid-soluble carrier that shuttles electrons between membrane-bound protein complexes in the electron transport chain. Ttha1568 has significant structural homology with the members of type 2 periplasmic-binding fold protein superfamily. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 260 matched cddid_all.tbl CDD cd13636 cd13636 270354 PBP2_Af1704 The conserved hypothetical protein Af1704 exhibits the type 2 periplasmic-binding protein fold. This group includes the Af1704 protein from from Archaeoglobus fulgidus DSM 4304, which is an ortholog of Ttha1568 (MqnD) from Thermus thermophilies HB8. MqnD is an enzyme within an alternative menaquinone biosynthetic pathway that catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate. Menaquinone (MK; vitamin K) is an essential lipid-soluble carrier that shuttles electrons between membrane-bound protein complexes in the electron transport chain. Af1704 has significant structural homology with the members of type 2 periplasmic-binding fold protein superfamily. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 259 matched cddid_all.tbl CDD cd13637 cd13637 270355 PBP2_Ca3427_like The conserved hypothetical protein Ca3427 exhibits the type 2 periplasmic-binding protein fold. This group includes the Ca3427 protein from candida albicans, which is an ortholog of Ttha1568 (MqnD) from Thermus thermophilies HB8, and other related hypothetical proteins. MqnD is an enzyme within an alternative menaquinone biosynthetic pathway that catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate. Menaquinone (MK; vitamin K) is an essential lipid-soluble carrier that shuttles electrons between membrane-bound protein complexes in the electron transport chain. Ca3427 has significant structural homology with the members of type 2 periplasmic-binding fold protein superfamily. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 273 matched cddid_all.tbl CDD cd13638 cd13638 270356 PBP2_EcProx_like Substrate binding domain of Escherichia coli betaine transport system-like; the type 2 periplasmic binding protein fold. This group includes the periplasmic substrate-binding protein ProX. ProX from the Escherichia coli ATP-binding cassette transport system ProU binds the compatible solutes glycine betaine and proline betaine with high affinity and specificity. Many microorganisms accumulate these compatible solutes in response to high osmolarity to offset the loss of cell water. The ProX belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 299 matched cddid_all.tbl CDD cd13639 cd13639 270357 PBP2_OpuAC_like Substrate binding domain of Lactococcus lactis ABC-type transporter OpuA and related proteins; the type 2 periplasmic binding protein fold. This subfamily is part of a high affinity multicomponent binding-protein-dependent transport system specific to betaine compounds for osmoregulation. The periplasmic substrate-binding domain, which is often fused to the permease component of the ATP-binding cassette transporter complex, is involved in uptake of osmoprotectants (also termed compatible solutes) such as glycine betaine and proline betaine. Many microorganisms accumulate these compatible solutes in response to high osmolarity to offset the loss of cell water. This domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 254 matched cddid_all.tbl CDD cd13640 cd13640 270358 PBP2_ChoX Substrate binding domain of ABC-type choline transport system; the type 2 periplasmic binding protein fold. This subfamily is part of a high affinity multicomponent binding-protein-dependent transport system specific to choline and acetylcholine for osmoregulation. The periplasmic substrate-binding domain, which is often fused to the permease component of the ATP-binding cassette transporter complex, is involved in uptake of osmoprotectants (also termed compatible solutes) such as choline and betaines. Choline is necessary for the biosynthesis of glycine betaine. Many microorganisms accumulate these compatible solutes in response to high osmolarity to offset the loss of cell water. In the case of the Sinorhizobium meliloti choline uptake system ChoVWX, ChoV is the nucleotide-binding domain that provides energy for the transport process via ATP hydrolysis, ChoW is the integral transmembrane protein that forms the substrate translaocation pathway, and ChoX is the substrate-binding domain. ChoX belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 266 matched cddid_all.tbl CDD cd13641 cd13641 270359 PBP2_HisX_like Substrate-binding domain of ABC-type histidine transporter involves in betaine and proline uptake; the type 2 periplasmic-binding protein fold. This subfamily is part of a high affinity multicomponent binding-protein-dependent transport system specific to certain quaternary ammonium compounds for osmoregulation. The periplasmic substrate-binding domain, which is often fused to the permease component of the ATP-binding cassette transporter complex, is involved in uptake of osmoprotectants (also termed compatible solutes) such as glycine betaine, proline betaine, choline, and carnitine. Many microorganisms accumulate these compatible solutes in response to high osmolarity to offset the loss of cell water. This domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 261 matched cddid_all.tbl CDD cd13642 cd13642 270360 PBP2_BCP_1 Substrate-binding domain of osmoregulatory ABC-type glycine betaine/choline/L-proline transport system-like; the type 2 periplasmic-binding protein fold. This subfamily is part of a high affinity multicomponent binding-protein-dependent transport system specific to certain quaternary ammonium compounds for osmoregulation. The periplasmic substrate-binding domain, which is often fused to the permease component of the ATP-binding cassette transporter complex, is involved in uptake of osmoprotectants (also termed compatible solutes) such as glycine betaine, proline betaine, choline, and carnitine. Many microorganisms accumulate these compatible solutes in response to high osmolarity to offset the loss of cell water. This domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 292 matched cddid_all.tbl CDD cd13643 cd13643 270361 PBP2_BCP_2 Substrate-binding domain of osmoregulatory ABC-type glycine betaine/choline/L-proline transport system-like; the type 2 periplasmic-binding protein fold. This subfamily is part of a high affinity multicomponent binding-protein-dependent transport system specific to certain quaternary ammonium compounds for osmoregulation. The periplasmic substrate-binding domain, which is often fused to the permease component of the ATP-binding cassette transporter complex, is involved in uptake of osmoprotectants (also termed compatible solutes) such as glycine betaine, proline betaine, choline, and carnitine. Many microorganisms accumulate these compatible solutes in response to high osmolarity to offset the loss of cell water. This domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 283 matched cddid_all.tbl CDD cd13644 cd13644 270362 PBP2_HemC_archaea Archaeal HemC of hydroxymethylbilane synthase family; the type 2 periplasmic binding protein fold. Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This subfamily includes the three domains of HMBS. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. 273 matched cddid_all.tbl CDD cd13645 cd13645 270363 PBP2_HuPBGD_like Human porphobilinogen deaminase possess type 2 periplasmic binding protein fold. Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This subfamily includes the three domains of human PBGD and its closely related proteins. Mutations in human PBGD cause AIP (acute intermittent porphyria), an inherited autosomal dominant disorder. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. 282 matched cddid_all.tbl CDD cd13646 cd13646 270364 PBP2_EcHMBS_like cd00494. Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This subfamily includes the three domains of Escherichia coli HMBS and its closely related proteins. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. 274 matched cddid_all.tbl CDD cd13647 cd13647 270365 PBP2_PBGD_2 An uncharacterized subgroup of the PBGD family; the type 2 periplasmic binding protein fold. Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This subfamily includes the three domains of HMBS. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. 282 matched cddid_all.tbl CDD cd13648 cd13648 270366 PBP2_PBGD_1 An uncharacterized subgroup of the PBGD family; the type 2 periplasmic binding protein fold. Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophyll, and vitamin B12. HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB). This subfamily includes the three domains of HMBS. The enzyme is believed to bind substrate through a hinge-bending motion of domains 1 and 2. The C-terminal domain 3 contains an invariant cysteine that forms the covalent attachment site for the DPM (dipyrromethane) cofactor. HMBS is found in all organisms except viruses. The domains 1 and 2 have the same overall topology as found in the type 2 periplasmic-binding proteins (PBP2), many of which are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. 278 matched cddid_all.tbl CDD cd13649 cd13649 270367 PBP2_Cae31940 Substrate binding domain of an uncharacterized protein similar to ABC-type transporter for thiamin biosynthetic pathway intermediates; a member of the type 2 periplasmic binding fold superfamily. This subfamily includes the periplamic-binding protein Cae31940 which is phylogenetically similar to the ThiY/THI5 family. ThiY is the periplasmic N-formyl-4-amino-5-(aminomethyl)-2-methylpyrimidine (FAMP) binding component of the ABC transport system (ThiXYZ). FAMP is imported into cell by the transporter, where it is then incorporated into the thiamin biosynthetic pathway. The closest structural homologs of ThiY are THI5, which is responsible for the synthesis of 4-amino-5-(hydroxymethyl)-2-methylpyrimidine phosphate (HMP-P) in the thiamin biosynthetic pathway of eukaryotes, and periplasmic binding proteins involved in alkanesulfonate/nitrate and bicarbonate transport. After binding the ligand, They interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ThiY/THI5 proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 223 matched cddid_all.tbl CDD cd13650 cd13650 270368 PBP2_THI5 Substrate binding domain of ABC-type transporters for thiamin biosynthetic pathway intermediates; a member of the type 2 periplasmic binding fold superfamily. ThiY is the periplasmic N-formyl-4-amino-5-(aminomethyl)-2-methylpyrimidine (FAMP) binding component of the ABC transport system (ThiXYZ). FAMP is imported into cell by the transporter, where it is then incorporated into the thiamin biosynthetic pathway. The closest structural homologs of ThiY are periplasmic binding proteins involved in alkanesulfonate/nitrate and bicarbonate transport , as well as THI5 which is responsible for the synthesis of 4-amino-5-(hydroxymethyl)-2-methylpyrimidine phosphate (HMP-P) in the thiamin biosynthetic pathway of eukaryotes. After binding the ligand, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ThiY/THI5 proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 251 matched cddid_all.tbl CDD cd13651 cd13651 270369 PBP2_ThiY Substrate binding domain of ABC-type transporters for thiamin biosynthetic pathway intermediates; a member of the type 2 periplasmic binding fold superfamily. ThiY is the periplasmic N-formyl-4-amino-5-(aminomethyl)-2-methylpyrimidine (FAMP) binding component of the ABC transport system (ThiXYZ). FAMP is imported into cell by the transporter, where it is then incorporated into the thiamin biosynthetic pathway. The closest structural homologs of ThiY are periplasmic binding proteins involved in alkanesulfonate/nitrate and bicarbonate transport , as well as THI5 which is responsible for the synthesis of 4-amino-5-(hydroxymethyl)-2-methylpyrimidine phosphate (HMP-P) in the thiamin biosynthetic pathway of eukaryotes. After binding the ligand, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ThiY/THI5 proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 214 matched cddid_all.tbl CDD cd13652 cd13652 270370 PBP2_ThiY_THI5_like_1 Putative substrate binding domain of an ABC-type transporter similar to ThiY/THI5; the type 2 periplasmic binding protein fold. This subfamily is phylogenetically similar to ThiY, which is the periplasmic N-formyl-4-amino-5-(aminomethyl)-2-methylpyrimidine (FAMP) binding component of the ABC transport system (ThiXYZ). FAMP is imported into cell by the transporter, where it is then incorporated into the thiamin biosynthetic pathway. The closest structural homologs of ThiY are THI5, which is responsible for the synthesis of 4-amino-5-(hydroxymethyl)-2-methylpyrimidine phosphate (HMP-P) in the thiamin biosynthetic pathway of eukaryotes, and periplasmic binding proteins involved in alkanesulfonate/nitrate and bicarbonate transport. After binding the ligand, they interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The ThiY/THI5 proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 217 matched cddid_all.tbl CDD cd13653 cd13653 270371 PBP2_phosphate_like_1 Substrate binding domain of putative ABC-type phosphate transporter, a member of the type 2 periplasmic binding fold superfamily. This subfamily contains uncharacterized phosphate binding domains found in PstS proteins that serve as initial receptors in the ABC transport of phosphate in eubacteria and archaea. After binding the ligand, PstS interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The PstS proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 240 matched cddid_all.tbl CDD cd13654 cd13654 270372 PBP2_phosphate_like_2 Substrate binding domain of putative ABC-type phosphate transporter, a member of the type 2 periplasmic binding fold superfamily. This subfamily contains uncharacterized phosphate binding domains found in PstS proteins that serve as initial receptors in the ABC transport of phosphate in eubacteria and archaea. After binding the ligand, PstS interacts with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. The PstS proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 259 matched cddid_all.tbl CDD cd13655 cd13655 270373 PBP2_oligosaccharide_1 The periplasmic binding component of ABC tansport system specific for an unknown oligosaccharide; possess the type 2 periplasmic binidng fold. This group represents an uncharacterized periplasmic-binding protein of an ATP-binding cassette transporter predicted to be involved in uptake of an unknown oligosaccharide molecule. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 363 matched cddid_all.tbl CDD cd13656 cd13656 270374 PBP2_MBP The periplasmic binding component of ABC tansport system specific for maltose; possess the type 2 periplasmic binidng fold. This group includes the periplasmic maltose-binding protein of an ATP-binding cassette transporter. Maltose is a disaccharide formed from two units of glucose. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 364 matched cddid_all.tbl CDD cd13657 cd13657 270375 PBP2_Maltodextrin The periplasmic binding component of ABC transport system specific for maltodextrin. This group includes the periplasmic maltodextrin-binding protein of a binding protein-dependent ATP-binding cassette transporter. Maltodextrin is a polysaccharide that is used as a food addtive and can be enzymatically produced from any starch . Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 368 matched cddid_all.tbl CDD cd13658 cd13658 270376 PBP2_CMBP The periplasmic binding component of ABC transport systems specific for cyclo/maltodextrin; possess the type 2 periplasmic binding fold. This group includes the periplasmic cyclo/maltodextrin-binding protein of Thermoactinomyces vulgaris ATP-binding cassette transporter and related proteins. Cyclodextrins are a family of compounds composed of glucose units connected by 1, 4 glycosidic linkages to form a series of oligosaccharide rings, and their cavity is hydrophibic which allows cyclodextrins to accomodate hydrophobic molecules/moieties in the cavity. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 372 matched cddid_all.tbl CDD cd13659 cd13659 270377 PBP2_PotF The periplasmic substrate-binding component of an ABC putrescine transport system and related proteins; contains the type 2 periplasmic-binding fold. This group represents the periplasmic substrate-binding domain that serves as the primary polyamine receptor of ABC-type putrescine-preferential transporter from gram-negative bacteria. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 331 matched cddid_all.tbl CDD cd13660 cd13660 270378 PBP2_PotD The periplasmic substrate-binding component of an active spermidine-preferential transport system; contains the type 2 periplasmic binding fold. This group represents the periplasmic binding domain that serves as the primary polyamine receptor of ABC-type spermindine-preferential transport system from gram-negative bacteria. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 315 matched cddid_all.tbl CDD cd13661 cd13661 270379 PBP2_PotD_PotF_like_1 The periplasmic substrate-binding component of an uncharacterized active transport system closely related to spermidine and putrescine transporters; contains the type 2 periplasmic binding fold. This group represents the periplasmic binding domain that serves as a primary polyamine receptor of an uncharacterized ABC-type transport system from plants and plant-symbiotic cyanobacteria. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, as well as plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 319 matched cddid_all.tbl CDD cd13662 cd13662 270380 PBP2_TpPotD_like The periplasmic substrate-binding component of an ABC-type polyamine transport system from Treponema pallidum and related proteins; contains the type 2 periplasmic binding fold. This group includes the polyamine-binding component of an ABC-type polyamine transport system from Treponema pallidum and closely related proteins, which is homologous to the spermidine-preferring periplasmic substrate-binding protein component (PotD)of ABC transport system. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, as well as plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 312 matched cddid_all.tbl CDD cd13663 cd13663 270381 PBP2_PotD_PotF_like_2 The periplasmic substrate-binding component of an uncharacterized active transport system closely related to spermidine and putrescine transporters; contains the type 2 periplasmic binding fold. This group represents the periplasmic substrate-binding domain that serves as a primary polyamine receptor of an uncharacterized ABC-type transport system from gram-negative bacteria. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, as well as plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 323 matched cddid_all.tbl CDD cd13664 cd13664 270382 PBP2_PotD_PotF_like_3 TThe periplasmic substrate-binding component of an uncharacterized active transport system closely related to spermidine and putrescine transporters; contains the type 2 periplasmic binding fold. This family represents the periplasmic substrate-binding domain that functions as the primary high-affinity receptors of ABC-type polyamine transport systems. Polyamine transport plays an essential role in the regulation of intracellular polyamine levels which are known to be elevated in rapidly proliferating cells and tumors. Natural polyamines are putrescine, spermindine, and spermine. They are polycations that play multiple roles in cell growth, survival and proliferation, and plant stress and disease resistance. They can interact with negatively charged molecules, such as nucleic acids, to modulate their functions. Members of this family belong to the type 2 periplasmic-binding fold superfamily. PBP2 is comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 315 matched cddid_all.tbl CDD cd13665 cd13665 270383 PBP2_TRAP_Dctp3_4 Periplasmic substrate-binding component of TRAP-type C4-dicarboxylate transport system DctP3 and DctP4; the type 2 periplasmic-binding protein fold. This group includes uncharacterized DctP3 and DctP 4 subfamilies of TRAP Transporters specific to C4-dicarboxylates such as succinate, malate and fumarate. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. This CD also included some eukaryotic homologs that have not been functionally characterized. TRAP transporters are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 302 matched cddid_all.tbl CDD cd13666 cd13666 270384 PBP2_TRAP_DctP_like_1 Substrate-binding component of an uncharacterized TRAP-type C4-dicarboxylate transport system; the type 2 periplasmic-binding protein fold. This group includes a DctP subfamily of TRAP Transporters specific to C4-dicarboxylates such as succinate, malate and fumarate. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. This CD also included some eukaryotic homologs that have not been functionally characterized. TRAP transporters are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 303 matched cddid_all.tbl CDD cd13667 cd13667 270385 PBP2_TRAP_DctP1 Periplasmic substrate-binding component of an uncharacterized TRAP-type C4-dicarboxylate transport system DctP1; contains the type 2 periplasmic-binding protein fold. This group includes an uncharacterized DctP1 subfamily of the TRAP Transporters. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 295 matched cddid_all.tbl CDD cd13668 cd13668 270386 PBP2_TRAP_UehA_TeaA Periplasmic substrate-binding component of osmoregulatory TRAP transporters TeaA and UehA; the type 2 periplasmic-binding protein fold. This subfamily includes the periplasmic-binding component of the ectoine-specific TRAP transporters TeaA from Halomonas elongata and UehA from Ruegeria pomeroyi. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process and a smaller membrane of unknown function. The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 305 matched cddid_all.tbl CDD cd13669 cd13669 270387 PBP2_TRAP_TM0322_like Periplasmic component of TRAP-type C4-dicarboxylate transport system TM0322 from Thermotoga maritima and similar proteins; the type 2 periplasmic binding protein fold. This subgroup includes the hyperthermophilic bacterium Thermotoga maritima TRAP-type C4-dicarboxylate transport system TM0322 and its closely related proteins. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 296 matched cddid_all.tbl CDD cd13670 cd13670 270388 PBP2_TRAP_Tp0957_like Uncharacterized substrate-binding protein of the Tripartite ATP-independent Periplasmic transporter family; the type 2 periplasmic-binding protein fold. This subfamily includes the putative periplasmic substrate-binding protein Tp0957 from Treponema pallidum, which is similar to TRAP transport systems such as SiaP (a sialic acid binding virulence factor) and TeaA (an ectoine binding protein). TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process and a smaller membrane of unknown function. The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 298 matched cddid_all.tbl CDD cd13671 cd13671 270389 PBP2_TRAP_SBP_like_3 Uncharacterized substrate-binding protein of the Tripartite ATP-independent Periplasmic transporter family; the type 2 periplasmic-binding protein fold. This subfamily includes uncharacterized periplasmic substrate-binding proteins similar to TRAP transport systems such as SiaP (a sialic acid binding virulence factor) and TeaA (an ectoine binding protein). TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process and a smaller membrane of unknown function. The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 296 matched cddid_all.tbl CDD cd13672 cd13672 270390 PBP2_TRAP_Siap Substrate-binding domain of a sialic acid binding Tripartite ATP-independent Periplasmic transport system (SiaP); the type 2 periplasmic-binding protein fold. This subfamily represents the periplasmic-binding component of TRAP transport system SiaP, a sialic acid binding virulence factor. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process and a smaller membrane of unknown function. The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 295 matched cddid_all.tbl CDD cd13673 cd13673 270391 PBP2_TRAP_SBP_like_2 Uncharacterized substrate-binding protein of the Tripartite ATP-independent Periplasmic transporter family; the type 2 periplasmic-binding protein fold. This subfamily includes uncharacterized periplasmic substrate-binding proteins similar to TRAP transport systems such as SiaP (a sialic acid binding virulence factor) and TeaA (an ectoine binding protein). TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process and a smaller membrane of unknown function. The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 301 matched cddid_all.tbl CDD cd13674 cd13674 270392 PBP2_TRAP_SBP_like_1 Uncharacterized substrate-binding protein of the Tripartite ATP-independent Periplasmic transporter family; the type 2 periplasmic-binding protein fold. This subfamily includes uncharacterized periplasmic substrate-binding proteins similar to TRAP transport systems such as SiaP (a sialic acid binding virulence factor) and TeaA (an ectoine binding protein). TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process and a smaller membrane of unknown function. The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 299 matched cddid_all.tbl CDD cd13675 cd13675 270393 PBP2_TRAP_SBP_like_5 Uncharacterized substrate-binding protein of the Tripartite ATP-independent Periplasmic transporter family; the type 2 periplasmic-binding protein fold. This subfamily includes uncharacterized periplasmic substrate-binding proteins similar to TRAP transport systems such as SiaP (a sialic acid binding virulence factor) and TeaA (an ectoine binding protein). TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process and a smaller membrane of unknown function. The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 296 matched cddid_all.tbl CDD cd13676 cd13676 270394 PBP2_TRAP_DctP2_like Substrate-binding component of Tripartite ATP-independent Periplasmic transporter DctP2 and related proteins; the type 2 periplasmic-binding protein fold. This subgroup includes TRAP transporter DctP2 and its similar proteins. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 297 matched cddid_all.tbl CDD cd13677 cd13677 270395 PBP2_TRAP_SBP_like_6 Uncharacterized substrate-binding protein of the Tripartite ATP-independent Periplasmic transporter family; the type 2 periplasmic-binding protein fold. This subfamily includes uncharacterized periplasmic substrate-binding proteins similar to TRAP transport systems such as SiaP (a sialic acid binding virulence factor) and TeaA (an ectoine binding protein). TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process and a smaller membrane of unknown function. The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 304 matched cddid_all.tbl CDD cd13678 cd13678 270396 PBP2_TRAP_DctP10 Substrate-binding component of Tripartite ATP-independent Periplasmic transporter DctP10; the type 2 periplasmic-binding protein fold. This subgroup includes TRAP transporter DctP10 and its similar proteins. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 300 matched cddid_all.tbl CDD cd13679 cd13679 270397 PBP2_TRAP_YiaO_like Substrate-binding domain of 2,3-diketo-L-gulonate-binding Tripartite ATP-independent Periplasmic transport system and related proteins; the type 2 periplasmic-binding protein fold. This subfamily includes the solute receptor protein YiaO of TRAP transport system. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process and a smaller membrane of unknown function. The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 298 matched cddid_all.tbl CDD cd13680 cd13680 270398 PBP2_TRAP_SBP_like_4 Uncharacterized substrate-binding protein of the Tripartite ATP-independent Periplasmic transporter family; the type 2 periplasmic-binding protein fold. This subfamily includes uncharacterized periplasmic substrate-binding proteins similar to TRAP transport systems such as SiaP (a sialic acid binding virulence factor) and TeaA (an ectoine binding protein). TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process and a smaller membrane of unknown function. The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 300 matched cddid_all.tbl CDD cd13681 cd13681 270399 PBP2_TRAP_lactate Substrate-binding component of a lactate binding Tripartite ATP-independent Periplasmic transporter and related proteins; the type 2 periplasmic-binding protein fold. This subgroup includes a lactate binding TRAP transporter and its similar proteins. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 311 matched cddid_all.tbl CDD cd13682 cd13682 270400 PBP2_TRAP_alpha-ketoacid Substrate-binding component of an alpha-keto acid binding Tripartite ATP-independent Periplasmic transporter and related proteins; contains the type 2 periplasmic-binding protein fold. This subgroup includes TRAP transporters that bind to ketoacids such as pyruvate and alpha-ketobutyrate, xylulose, and other unknown ligands. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 323 matched cddid_all.tbl CDD cd13683 cd13683 270401 PBP2_TRAP_DctP6_7 Substrate-binding domain of Tripartite ATP-independent Periplasmic transporter DctP6 and DctP7; type 2 periplasmic-binding protein fold. This subgroup includes TRAP-type mannitol/chloroaromatic compound transport system (Dctp6) and similar proteins. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process and a smaller membrane of unknown function. The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the PBP2 superfamily. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 304 matched cddid_all.tbl CDD cd13684 cd13684 270402 PBP2_TRAP_Dctp5_like Substrate-binding component of Tripartite ATP-independent Periplasmic transporter DctP5 and related proteins; the type 2 periplasmic-binding protein fold. This subgroup includes TRAP transporter DctP5 and its similar proteins. TRAP transporters are a large family of solute transporters ubiquitously found in bacteria and archaea. They are comprised of a periplasmic substrate-binding protein (SBP; often called the P subunit) and two unequally sized integral membrane components: a large transmembrane subunit involved in the translocation process (the M subunit) and a smaller membrane of unknown function (the Q subunit). The driving force of TRAP transporters is provided by electrochemical ion gradients (either protons or sodium ions) across the cytoplasmic membrane, rather than ATP hydrolysis. This substrate-binding domain belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 314 matched cddid_all.tbl CDD cd13685 cd13685 270403 PBP2_iGluR_non_NMDA_like The ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate receptors, a member of the type 2 periplasmic-binding fold protein superfamily. This subfamily represents the ligand-binding domain of non-NMDA (N-methyl-D-aspartate) type ionotropic glutamate receptors including AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) receptors (GluR1-4), kainate receptors (GluR5-7 and KA1/2), and orphan receptors delta 1/2. iGluRs form tetrameric ligand-gated ion channels, which are concentrated at postsynaptic sites in excitatory synapses where they fulfill a variety of different functions. While this ligand-binding domain of iGluRs is structurally homologous to the periplasmic binding fold type II superfamily, the N-terminal leucine/isoleucine/valine#binding protein (LIVBP)-like domain belongs to the periplasmic-binding fold type I. 252 matched cddid_all.tbl CDD cd13686 cd13686 270404 GluR_Plant Plant glutamate receptor domain; the type 2 periplasmic binding protein fold. This subfamily contains the glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. Animal iGluRs mediate the ion flux in the synapses of the CNS and can be subdivided into several classes depending on the neurotransmitter specificity and ion conductance properties. Their plant homologs have been shown to function in light signal transduction and calcium homeostasis. The GluR proteins belong to the PBP2 superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 232 matched cddid_all.tbl CDD cd13687 cd13687 270405 PBP2_iGluR_NMDA The ligand-binding domain of the NMDA (N-methyl-D-aspartate) subtype of ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily. The ligand-binding domain of the ionotropic NMDA subtype is structurally homologous to the periplasmic-binding fold type II superfamily, while the N-terminal domain belongs to the periplasmic-binding fold type I. The function of the NMDA subtype receptor serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer comprising two NR1 and two NR2 (A, B, C, and D) or NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain. 239 matched cddid_all.tbl CDD cd13688 cd13688 270406 PBP2_GltI_DEBP Substrate-binding domain of ABC aspartate-glutamate transporter; the type 2 periplasmic binding protein fold. This subfamily represents the periplasmic-binding protein component of ABC transporter specific for carboxylic amino acids, including GtlI from Escherichia coli. The aspartate-glutamate binding domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 238 matched cddid_all.tbl CDD cd13689 cd13689 270407 PBP2_BsGlnH Substrate binding domain of ABC glutamine transporter from Bacillus subtilis; the type 2 periplasmic-bindig protein fold. This group includes periplasmic glutamine-binding domain GlnP from Bacillus subtilis and its related proteins. The GlnP domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 229 matched cddid_all.tbl CDD cd13690 cd13690 270408 PBP2_GluB Substrate binding domain of ABC glutamate transporter; the type 2 periplasmic binding protein fold. This group includes periplasmic glutamate-binding domain GluB from Corynebacterium efficiens and its related proteins. The GluB domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 231 matched cddid_all.tbl CDD cd13691 cd13691 270409 PBP2_Peb1a_like Substrate binding domain of an ABC aspartate/glutamate transporter; the type 2 periplasmic-binding protein fold. This group includes periplasmic aspartate/glutamate binding domain Peb1a and its closely related protein. The Peb1a is an important virulence factor in the food-borne human pathogen Campylobacter jejuni, which has a major role in adherence and host colonization. The Peb1a domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 228 matched cddid_all.tbl CDD cd13692 cd13692 270410 PBP2_BztA Substrate bindng domain of ABC glutamate/glutamine/aspartate/asparagine transporter; the type 2 periplasmic binding protein fold. BztA is the periplamic-binding protein component of ABC transporter specific for carboxylic amino acids, glutamine and asparagine. The BZtA domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 236 matched cddid_all.tbl CDD cd13693 cd13693 270411 PBP2_polar_AA Substrate binding domain of polar amino-acid uptake ABC transporter; the type 2 periplasmic binding protein fold. This group includes the periplamic-binding protein component of putative polar amino acid ABC transporter. The polar amino-acid binding domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 228 matched cddid_all.tbl CDD cd13694 cd13694 270412 PBP2_Cysteine Substrate binding domain of ABC cysteine transporter; the type 2 periplasmic binding protein fold. This subfamily comprises of the periplasmic-binding protein component of ABC transporter specific for cysteine and its closely related proteins. The cysteine-binding domains belong to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 229 matched cddid_all.tbl CDD cd13695 cd13695 270413 PBP2_Mlr3796_like The substrate-binding domain of putative amino aicd transporter; the type 2 periplasmic binding protein fold. This group includes the periplamic-binding protein component of a putative amino acid ABC transporter from Mesorhizobium loti and its related proteins. The putative Mlr3796-like domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 232 matched cddid_all.tbl CDD cd13696 cd13696 270414 PBP2_Atu4678_like The substrate binding domain of putative amino acid transporter; the type 2 periplasmic binding protein fold. This group includes the periplamic-binding protein component of a putative amino acid ABC transporter from Agrobacterium tumefaciens and its related proteins. The putative Atu4678-like domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 227 matched cddid_all.tbl CDD cd13697 cd13697 270415 PBP2_ArtJ_like Putative substrate-binding domain of ABC arginine transporter; the type 2 periplasmic-binding protein fold. The ArtJ domain belongs to the type 2 periplasmic binding protein fold superfamily (PBP2), whose many members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 228 matched cddid_all.tbl CDD cd13698 cd13698 270416 PBP2_HisGluGlnArgOpine Substrate binding domain of ABC-type histidine/glutamate/glutamine/arginine/opine transporter; the type 2 periplasmic-binding protein fold. This group includes periplasmic-binding component of His/Glu/Gln/Arg/Opine ATP-binding cassette transport system. This substrate-binding domain belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 214 matched cddid_all.tbl CDD cd13699 cd13699 270417 PBP2_OccT_like Substrate binding domain of ABC-type octopine transporter-like; the type 2 periplasmic-binding protein fold. This group includes periplasmic octopine-binding protein and related proteins. This group belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 211 matched cddid_all.tbl CDD cd13700 cd13700 270418 PBP2_Arg_STM4351 Substrate binding domain of arginine-specific ABC transporter; type 2 periplasmic-binding protein fold. This group includes domains similar to Escherichia coli arginine third transport system. STM4351 is the high arginine specific periplasmic-binding protein of ABC transport system. STM4351 belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 222 matched cddid_all.tbl CDD cd13701 cd13701 270419 PBP2_ml15202_like Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the type 2 periplasmic-binding protein fold. This group includes uncharacterized periplasmic substrate-binding protein similar to HisJ and LAO proteins which are involved in the ABC transport of histidine-, arginine, and lysine-arginine-ornithine amino acids. This group belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 227 matched cddid_all.tbl CDD cd13702 cd13702 270420 PBP2_mlr5654_like Substrate binding domain of ABC-type histidine/lysine/arginine/ornithine transporter-like; the type 2 periplasmic-binding protein fold. This group includes uncharacterized periplasmic substrate-binding protein similar to HisJ and LAO proteins which serve as initial receptors in the ABC transport of histidine-, arginine, and lysine-arginine-ornithine amino acids. This group belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 223 matched cddid_all.tbl CDD cd13703 cd13703 270421 PBP2_HisJ_LAO Substrate binding domain of ABC-type histidine- and lysine/arginine/ornithine transporters; the type 2 periplasmic-binding protein fold. This subgroup includes the periplasmic-binding proteins, HisJ and LAO, that serve as initial receptors in the ABC transport of histidine and lysine-arginine-ornithine amino acids. They are belong to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 229 matched cddid_all.tbl CDD cd13704 cd13704 270422 PBP2_HisK The periplasmic sensor domain of histidine kinase receptors; the type 2 periplasmic binding fold protein. This subfamily includes the periplasmic sensor domain of the histidine kinase receptors (HisK) which are elements of the two-component signal transduction systems commonly found in bacteria and lower eukaryotes. Typically, the two-component system consists of a membrane-spanning histidine kinase sensor and a cytoplasmic response regulator. The two-component systems serve as a stimulus-response coupling mechanism to enable microorganisms to sense and respond to changes in environmental conditions. Extracellular stimuli such as small molecule ligands and ions are detected by the N-terminal periplasmic sensing domain of the sensor kinase receptor, which regulate the catalytic activity of the cytoplasmic kinase domain and promote ATP-dependent autophosphorylation of a conserved histidine residue. The phosphate is then transferred to a conserved aspartate in the response regulator through a phospho-transfer mechanism, and the activity of the response regulator is in turn regulated. The sensor domain belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space through their function as an initial high-affinity binding component. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 220 matched cddid_all.tbl CDD cd13705 cd13705 270423 PBP2_BvgS_D1 The first of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 peripasmic-binding fold protein. This group contains the first domain of the periplasmic solute-binding domains of BvgS and related proteins. BvgS is composed of two periplasmic domains homologous to bacterial periplasmic-binding proteins (PBPs), a transmembrane region followed successively by a cytoplasmic PAS (Per/ARNT/SIM), a histidine-kinase (HK), a receiver and a histidine phosphotransfer (Hpt) domains. The sensor protein BvgS can autophosphorylate and phosphorylate the response regulator BvgA. The BvgAS phosphorelay controls the expression of virulence factors in response to certain environmental stimuli in Bordetella pertussis. Its close homologs, Escherichia coli EvgS and Klebsiella pneumoniae KvgS, appear to be involved in the transcriptional regulation of drug efflux pumps and in countering free radical stresses and sensing iron limiting conditions, respectively. The periplasmic sensor domain of BvgS belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 221 matched cddid_all.tbl CDD cd13706 cd13706 270424 PBP2_HisK_like_1 Putative sensor domain similar to HisK; the type 2 periplasmic binding fold protein. This group includes periplasmic sensor domain of the histidine kinase receptors (HisK) which are elements of the two-component signal transduction systems commonly found in bacteria and lower eukaryotes. Typically, the two-component system consists of a membrane-spanning histidine kinase sensor and a cytoplasmic response regulator. The two-component systems serve as a stimulus-response coupling mechanism to enable microorganisms to sense and respond to changes in environmental conditions. Extracellular stimuli such as small molecule ligands and ions are detected by the N-terminal periplasmic sensing domain of the sensor kinase receptor, which regulate the catalytic activity of the cytoplasmic kinase domain and promote ATP-dependent autophosphorylation of a conserved histidine residue. The phosphate is then transferred to a conserved aspartate in the response regulator through a phospho-transfer mechanism, and the activity of the response regulator is in turn regulated. The sensor domain belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space through their function as an initial high-affinity binding component. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 219 matched cddid_all.tbl CDD cd13707 cd13707 270425 PBP2_BvgS_D2 The second of the two tandem periplasmic domains of sensor-kinase BvgS; the type 2 peripasmic-binding fold protein. This group contains the second domain of the periplasmic solute-binding domains of BvgS and related proteins. BvgS is composed of two periplasmic domains homologous to bacterial periplasmic-binding proteins (PBPs), a transmembrane region followed successively by a cytoplasmic PAS (Per/ARNT/SIM), a Histidine-kinase (HK), a receiver and a Histidine phosphotransfer (Hpt) domains. The sensor protein BvgS can autophosphorylate and phosphorylate the response regulator BvgA. The BvgAS phosphorelay controls the expression of virulence factors in response to certain environmental stimuli in Bordetella pertussis. Its close homologs, Escherichia coli EvgS and Klebsiella pneumoniae KvgS, appear to be involved in the transcriptional regulation of drug efflux pumps and in countering free radical stresses and sensing iron limiting conditions, respectively. The periplasmic sensor domain of BvgS belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 221 matched cddid_all.tbl CDD cd13708 cd13708 270426 PBP2_BvgS_like_1 Putative sensor domain similar to BvgS; the type 2 periplasmic binding protein domain. BvgS is composed of two periplasmic domains homologous to bacterial periplasmic-binding proteins (PBPs), a transmembrane region followed successively by a cytoplasmic PAS (Per/ARNT/SIM), a Histidine-kinase (HK), a receiver and a Histidine phosphotransfer (Hpt) domains. The sensor protein BvgS can autophosphorylate and phosphorylate the response regulator BvgA. The BvgAS phosphorelay controls the expression of virulence factors in response to certain environmental stimuli in Bordetella pertussis. Its close homologs, Escherichia coli EvgS and Klebsiella pneumoniae KvgS, appear to be involved in the transcriptional regulation of drug efflux pumps and in countering free radical stresses and sensing iron limiting conditions, respectively. The periplasmic sensor domain of BvgS belongs to the type 2 periplasmic-binding fold protein (PBP2) superfamily, whose members are involved in chemotaxis and uptake of nutrients and other small molecules from the extracellular space as a primary receptor. PBP2 typically comprises of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 220 matched cddid_all.tbl CDD cd13709 cd13709 270427 PBP2_YxeM Substrate binding domain of an ABC transporter YxeMNO; the type 2 periplasmic binding protein fold. This group contains cystine-binding domain (YxeM) of a periplasmic receptor-dependent ATP-binding cassette transporter and its closely related proteins. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Likewise, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 227 matched cddid_all.tbl CDD cd13710 cd13710 270428 PBP2_TcyK Substrate binding domain of an ABC transporter TcyJKLMN; the type 2 periplasmic binding protein fold. This group contains periplasmic cystine-binding domain (TcyK) of an ATP-binding cassette transporter from Bacillus subtilus and its closely related proteins. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Likewise, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 233 matched cddid_all.tbl CDD cd13711 cd13711 270429 PBP2_Ngo0372_TcyA Substrate binding domain of ABC transporters involved in cystine import; the type 2 periplasmic binding protein fold. This subgroup includes cystine-binding domain of periplasmic receptor-dependent ATP-binding cassette transporters from Neisseria gonorrhoeae and Bacillus subtilis and their related proteins. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Likewise, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 222 matched cddid_all.tbl CDD cd13712 cd13712 270430 PBP2_FliY Substrate binding domain of an Escherichia coli ABC transporter; the type 2 periplasmic binding protein fold. This group contains cystine binding domain FliY and its related proteins. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Likewise, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 219 matched cddid_all.tbl CDD cd13713 cd13713 270431 PBP2_Cystine_like_1 Substrate binding domain of putative ABC transporters involved in cystine import; the type 2 periplasmic binding protein fold. This group contains uncharacterized periplasmic cystine-binding domain of ATP-binding cassette (ABC) transporters. Cystine is an oxidized dimeric form of cysteine that is required for optimal bacterial growth. In Bacillus subtilis, three ABC transporters, TcyJKLMN (YtmJKLMN), TcyABC (YckKJI), and YxeMNO are involved in uptake of cystine. Likewise, three uptake systems were identified in Salmonella enterica serovar Typhimurium, while in Escherichia coli, two transport systems seem to be involved in cystine uptake. Moreover, L-cystine limitation was shown to prevent virulence of Neisseria gonorrhoeae; thus, its L-cystine solute receptor (Ngo0372) may be suited as target for an antimicrobial vaccine. The cystine receptor belongs to the type 2 periplasmic binding fold protein superfamily (PBP2). The PBP2 proteins are typically comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two receptor cytoplasmically-located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 218 matched cddid_all.tbl CDD cd13714 cd13714 270432 PBP2_iGluR_Kainate Kainate receptor of the type 2 periplasmic-binding fold superfamily. This group contains glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. Animal iGluRs mediate the ion flux in the synapses of the CNS and can be subdivided into several classes depending on the neurotransmitter specificity and ion conductance properties. Their plant homologs have been shown to function in light signal transduction and calcium homeostasis. The GluR proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 251 matched cddid_all.tbl CDD cd13715 cd13715 270433 PBP2_iGluR_AMPA The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) subtypes of ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily. This family represents the ligand-binding domain of the AMPA receptor subunits, a member of non-NMDA (N-methyl-D-aspartate) type iGluRs which are ligand-gated ion channels that mediate excitatory synaptic transmission in the central nervous system. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of AMPA receptors belongs to the periplasmic-binding fold type I. They consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. 261 matched cddid_all.tbl CDD cd13716 cd13716 270434 PBP2_iGluR_delta_like The ligand-binding domain of the delta family of ionotropic glutamate receptors, a member of the type 2 periplasmic-binding fold protein superfamily. This subfamily represents the ligand-binding domain of an orphan family of delta receptors, GluRdelta1 and GluRdelta2. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of iGluRs belongs to the periplasmic-binding fold type I. Although the delta receptors are members of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetical analysis shows that both GluRdelta1 and GluRalpha2 are more homologous to non-NMDA receptors. GluRdelta2 was shown to function as an AMPA-like receptor by mutation analysis. Moreover, targeted disruption of GluRdelta2 gene caused motor coordination impairment, Purkinje cell maturation, and long-term depression of synaptic transmission. It has been suggested that GluRdelta2 is the receptor for cerebellin 1, a glycoprotein of the Clq, and the tumor necrosis factor family which is secreted from cerebellar granule cells. Furthermore, recent studies have shown that the orphan GluRdelta1 plays an essential role in high-frequency hearing and ionic homeostasis in the basal cochlea and that the locus encoding GluRdelta1 may be involved in congenial or acquired high-frequency hearing loss in humans. 257 matched cddid_all.tbl CDD cd13717 cd13717 270435 PBP2_iGluR_putative The ligand-binding domain of putative ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily. This group contains glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. Animal iGluRs mediate the ion flux in the synapses of the CNS and can be subdivided into several classes depending on the neurotransmitter specificity and ion conductance properties. Their plant homologs have been shown to function in light signal transduction and calcium homeostasis. The GluR proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 360 matched cddid_all.tbl CDD cd13718 cd13718 270436 PBP2_iGluR_NMDA_Nr2 The ligand-binding domain of the NR2 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily. This group contains the ligand-binding domain of the NR2 subunit of NMDA receptor family. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain. 283 matched cddid_all.tbl CDD cd13719 cd13719 270437 PBP2_iGluR_NMDA_Nr1 The ligand-binding domain of the NR1 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily. This group contains the ligand binding domain of the NR1, an essential channel-forming subunit of the NMDA receptor. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer ccomposed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. When co-expressed with NR1, the NR3 subunits form receptors that are activated by glycine alone and therefore can be classified as excitatory glycine receptors. NR1/NR3 receptors are calcium-impermeable and unaffected by ligands acting at the NR2 glutamate-binding site. 277 matched cddid_all.tbl CDD cd13720 cd13720 270438 PBP2_iGluR_NMDA_Nr3 The ligand-binding domain of the NR3 subunit of ionotropic NMDA (N-methyl-D-aspartate) glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily. This group contains the ligand-binding domain of the NR3 subunit of NMDA receptor family. The ionotropic N-methyl-d-asparate (NMDA) subtype of glutamate receptors serves critical functions in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer composed of two NR1 and two NR2 (A, B, C, and D) or of NR3 (A and B) subunits. The receptor controls a cation channel that is highly permeable to monovalent ions and calcium and exhibits voltage-dependent inhibition by magnesium. Dual agonists, glutamate and glycine, are required for efficient activation of the NMDA receptor. Among NMDA receptor subtypes, the NR2B subunit containing receptors appear particularly important for pain perception; thus NR2B-selective antagonists may be useful in the treatment of chronic pain. 283 matched cddid_all.tbl CDD cd13721 cd13721 270439 PBP2_iGluR_Kainate_GluR6 GluR6 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily. This group contains glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. Animal iGluRs mediate the ion flux in the synapses of the CNS and can be subdivided into several classes depending on the neurotransmitter specificity and ion conductance properties. Their plant homologs have been shown to function in light signal transduction and calcium homeostasis. The GluR proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 251 matched cddid_all.tbl CDD cd13722 cd13722 270440 PBP2_iGluR_Kainate_GluR5 GluR5 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily. This group contains glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. Animal iGluRs mediate the ion flux in the synapses of the CNS and can be subdivided into several classes depending on the neurotransmitter specificity and ion conductance properties. Their plant homologs have been shown to function in light signal transduction and calcium homeostasis. The GluR proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 250 matched cddid_all.tbl CDD cd13723 cd13723 270441 PBP2_iGluR_Kainate_GluR7 GluR7 subtype of kainate receptor, type 2 periplasmic-binding fold superfamily. This group contains glutamate receptor domain GluR. These domains are found in the GluR proteins that have been shown to function as L-glutamate activated potassium channels, also known ionotropic glutamate receptors or iGluRs. In addition to two ligand binding core domains, iGluRs typically have a channel-like domain inserted in the middle of the GluR-like domain. Animal iGluRs mediate the ion flux in the synapses of the CNS and can be subdivided into several classes depending on the neurotransmitter specificity and ion conductance properties. Their plant homologs have been shown to function in light signal transduction and calcium homeostasis. The GluR proteins belong to the PBPII superfamily of periplasmic binding proteins that differ in size and ligand specificity, but have similar tertiary structures consisting of two globular subdomains connected by a flexible hinge. They have been shown to bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. 369 matched cddid_all.tbl CDD cd13724 cd13724 270442 PBP2_iGluR_kainate_KA1 The ligand-binding domain of the kainate subtype KA1 of ionotropic glutamate receptors, a member of the type 2 periplasmic-binding fold protein superfamily. This group contains the ligand-binding domain of the KA1 subunit of kainate receptor. While this ligand-binding domain is structurally homologous to the periplasmic binding fold type II superfamily, the N_terminal domain of kainate receptors belongs to the periplasmic-binding fold type I. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated by kainate and glutamate when expressed in heterologous systems. Kainate receptors are involved in excitatory neurotransmission by activating postsynaptic receptors and in inhibitory neurotransmission by modulating release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. Kainate receptors are closely related to AMAP receptors. In contrast of AMPA receptors, kainate receptors play only a minor role in signaling at synapses and their function is not well defined. 333 matched cddid_all.tbl CDD cd13725 cd13725 270443 PBP2_iGluR_kainate_KA2 The ligand-binding domain of the kainate subtype KA2 of ionotropic glutamate receptors, a member of the type 2 periplasmic-binding fold protein superfamily. This group contains the ligand-binding domain of the KA2 subunit of kainate receptor. While this ligand-binding domain is structurally homologous to the periplasmic binding fold type II superfamily, the N_terminal domain of kainate receptors belongs to the periplasmic-binding fold type I. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated by kainate and glutamate when expressed in heterologous systems. Kainate receptors are involved in excitatory neurotransmission by activating postsynaptic receptors and in inhibitory neurotransmission by modulating release of the inhibitory neurotransmitter GABA through a presynaptic mechanism. Kainate receptors are closely related to AMAP receptors. In contrast of AMPA receptors, kainate receptors play only a minor role in signaling at synapses and their function is not well defined. 250 matched cddid_all.tbl CDD cd13726 cd13726 270444 PBP2_iGluR_AMPA_GluR2 The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) subtype GluR2 of ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily. This group contains the ligand-binding domain of the AMPA receptor subunit GluR2, a member of non-NMDA (N-methyl-D-aspartate) type iGluRs which are ligand-gated ion channels that mediate excitatory synaptic transmission in the central nervous system. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of AMPA receptors belongs to the periplasmic-binding fold type I. The AMPA receptors are the most commonly found receptor in the nervous system and sensitive to the artificial glutamate analog, AMPA. They consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. 259 matched cddid_all.tbl CDD cd13727 cd13727 270445 PBP2_iGluR_AMPA_GluR4 The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) subtype GluR4 of ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily. This group contains the ligand-binding domain of the AMPA receptor subunit GluR4, a member of non-NMDA (N-methyl-D-aspartate) type iGluRs which are ligand-gated ion channels that mediate excitatory synaptic transmission in the central nervous system. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of AMPA receptors belongs to the periplasmic-binding fold type I.The AMPA receptors are the most commonly found receptor in the nervous system and sensitive to the artificial glutamate analog, AMPA. They consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. 259 matched cddid_all.tbl CDD cd13728 cd13728 270446 PBP2_iGluR_AMPA_GluR3 The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) subtype GluR3 of ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily. This group contains the ligand-binding domain of the AMPA receptor subunit GluR3, a member of non-NMDA (N-methyl-D-aspartate) type iGluRs which are ligand-gated ion channels that mediate excitatory synaptic transmission in the central nervous system. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of AMPA receptors belongs to the periplasmic-binding fold type I. The AMPA receptors are the most commonly found receptor in the nervous system and sensitive to the artificial glutamate analog, AMPA. They consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current 259 matched cddid_all.tbl CDD cd13729 cd13729 270447 PBP2_iGluR_AMPA_GluR1 The ligand-binding domain of the AMPA (alpha-amino-3-hydroxyl-5-methyl-4-isoxazolepropionic acid) subtype GluR1 of ionotropic glutamate receptors, a member of the type 2 periplasmic binding fold protein superfamily. This group contains the ligand-binding domain of the AMPA receptor subunit GluR1, a member of non-NMDA (N-methyl-D-aspartate) type iGluRs which are ligand-gated ion channels that mediate excitatory synaptic transmission in the central nervous system. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of AMPA receptors belongs to the periplasmic-binding fold type I. The AMPA receptors are the most commonly found receptor in the nervous system and sensitive to the artificial glutamate analog, AMPA. They consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. 260 matched cddid_all.tbl CDD cd13730 cd13730 270448 PBP2_iGluR_delta_1 The ligand-binding domain of an orphan ionotropic glutamate receptor delta-1, a member of the type 2 periplasmic-binding fold protein superfamily. This group contains the ligand-binding domain of the delta1 receptor of an orphan glutamate receptor family. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of delta receptors belongs to the periplasmic-binding fold type I. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetical analysis shows that both GluRdelta1 and GluRdelta2 are more homologous to non-NMDA receptors. GluRdelta2 was shown to function as an AMPA-like receptor by mutation analysis. Moreover, targeted disruption of GluRdelta2 gene caused motor coordination impairment, Purkinje cell maturation, and long-term depression of synaptic transmission. It has been suggested that GluRdelta2 is the receptor for cerebellin 1, a glycoprotein of the Clq, and the tumor necrosis factor family which is secreted from cerebellar granule cells. Furthermore, recent studies have shown that the orphan GluRdelta1 plays an essential role in high-frequency hearing and ionic homeostasis in the basal cochlea and that the locus encoding GluRdelta1 may be involved in congenial or acquired high-frequency hearing loss in humans. 257 matched cddid_all.tbl CDD cd13731 cd13731 270449 PBP2_iGluR_delta_2 The ligand-binding domain of an orphan ionotropic glutamate receptor delta-2, a member of the type 2 periplasmic-binding fold protein superfamily. This group contains the ligand-binding domain of the delta-2 receptor of an orphan glutamate receptor family. While this ligand-binding domain is structurally homologous to the periplasmic-binding fold type II superfamily, the N-terminal domain of delta receptors belongs to the periplasmic-binding fold type I. Although the delta receptors are a member of the ionotropic glutamate receptor family, they cannot be activated by AMPA, kainate, NMDA, glutamate, or any other ligands. Phylogenetical analysis shows that both GluRdelta1 and GluRalpha2 are more homologous to non-NMDA receptors. GluRdelta2 was shown to function as an AMPA-like receptor by mutation analysis. Moreover, targeted disruption of GluRdelta2 gene caused motor coordination impairment, Purkinje cell maturation, and long-term depression of synaptic transmission. It has been suggested that GluRdelta2 is the receptor for cerebellin 1, a glycoprotein of the Clq, and the tumor necrosis factor family which is secreted from cerebellar granule cells. Furthermore, recent studies have shown that the orphan GluRdelta1 plays an essential role in high-frequency hearing and ionic homeostasis in the basal cochlea and that the locus encoding GluRdelta1 may be involved in congenial or acquired high-frequency hearing loss in humans. 257 matched cddid_all.tbl CDD cd13732 cd13732 467029 HFD_CENP-W histone-fold domain found in centromere protein W (CENP-W) and similar proteins. CENP-W, also called cancer-up-regulated gene 2 protein (CUG2), is a component of the CENPA-NAC (nucleosome-associated) complex, which plays a central role in the assembly of kinetochore proteins, mitotic progression and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENP-A into centromeres. CENP-W is also part of a nucleosome-associated complex that binds specifically to histone H3-containing nucleosomes at the centromere, as opposed to nucleosomes containing CENP-A. Moreover, CENP-W forms a heterodimer with CENP-T. This dimer co-assembles with CENP-S-CENP-X heterodimers at centromeres to form the tetrameric CENP-T-W-S-X complex, which is a subcomplex of the large constitutive centromere-associated network (CCAN, also known as the interphase centromere complex or ICEN). The heterotetrameric CENP-T-W-S-X complex binds and supercoils DNA and plays an important role in kinetochore assembly. CENP-W has a fundamental role in kinetochore assembly and function. It is one of the inner kinetochore proteins, with most further proteins binding downstream. It is required for normal chromosome organization and normal progress through mitosis. 74 matched cddid_all.tbl CDD cd13733 cd13733 293968 SPRY_PRY_C-I_1 PRY/SPRY domain in tripartite motif-containing (TRIM) proteins, including TRIM5, TRIM6, TRIM7, TRIM10, TRIM11, TRIM17, TRIM20, TRIM21, TRIM27, TRIM35, TRIM38, TRIM41, TRIM50, TRIM58, TRIM60, TRIM62, TRIM69, TRIM72, NF7 and bloodthirsty. This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of several Class IV TRIM proteins, including TRIM7, TRIM35, TRIM41, TRIM50, TRIM62, TRIM69, TRIM72, TRIM protein NF7 and bloodthirsty (bty). TRIM7 interacts with glycogenin and stimulates its self-glucosylating activity via its SPRY domain. TRIM35 may play a role as a tumor suppressor and is implicated in the cell death mechanism. TRIM41 is localized to speckles in the cytoplasm and nucleus, and functions as an E3 ligase that catalyzes the ubiquitin-mediated degradation of protein kinase C. TRIM50, an E3 ubiquitin ligase, is deleted in Williams-Beuren (WBS) syndrome, a multi-system neurodevelopmental disorder caused by the deletion of contiguous genes at chromosome region 7q11.23. TRIM62 is involved in the morphogenesis of the mammary gland; loss of TRIM62 gene expression in breast is associated with increased risk of recurrence in early-onset breast cancer. TRIM69 is a novel testis E3 ubiquitin ligase that may function to ubiquitinate its particular substrates during spermatogenesis. In humans, TRIM69 localizes in the cytoplasm and nucleus, and requires an intact RING finger domain to function. TRIM protein NF7, which also contains a chromodomain (CHD) at the N-terminus and an RFP (Ret finger protein)-like domain at the C-terminus, is required for its association with transcriptional units of RNA polymerase II which is mediated by a trimeric B box. In Xenopus oocyte, xNF7 has been identified as a nuclear microtubule-associated protein (MAP) whose microtubule-bundling activity, but not E3-ligase activity, contributes to microtubule organization and spindle integrity. Bloodthirsty (bty) is a novel gene identified in zebrafish and has been shown to likely play a role in in regulation of the terminal steps of erythropoiesis. TRIM72 has been shown to perform a critical function in membrane repair following acute muscle injury by nucleating the assembly of the repair machinery at injury sites. The PRY-SPRY domain in these TRIM families is suggested to serve as the target binding site. 174 matched cddid_all.tbl CDD cd13734 cd13734 293969 SPRY_PRY_C-II PRY/SPRY domain in tripartite motif-containing proteins 1, 9, 18, 36, 46, 67,76 (TRIM1, TRIM9, TRIM18, TRIM36, TRIM46, TRIM67, TRIM76). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of several Class I TRIM proteins, including TRIM1, TRIM9, TRIM18, TRIM36, TRIM46, TRIM67 and TRIM76. TRIM1 (also known as MID2) and its close homolog, TRIM18 (also known as MID1), both contain a B30.2-like domain at their C-terminus and a single fibronectin type III (FN3) motif between it and their N-terminal RBCC domain. Their coiled-coil motifs mediate both homo- and heterodimerization, a prerequisite for association of the rapamycin-sensitive PP2A regulatory subunit Alpha 4 with microtubules. Mutations in TRIM18 have shown to cause Opitz syndrome, a disorder causing congenital anomalies such as cleft lip and palate as well as heart defects. TRIM9 is expressed mainly in the cerebral cortex, and functions as an E3 ubiquitin ligase. Its immunoreactivity is severely decreased in affected brain areas in Parkinson's disease and dementia with Lewy bodies, possibly playing an important role in the regulation of neuronal function and participating in pathological process of Lewy body disease through its ligase. TRIM36 interacts with centromere protein-H, one of the kinetochore proteins and possibly associates with chromosome segregation; an excess of TRIM36 may cause chromosomal instability. TRIM46 has not yet been characterized. TRIM67 negatively regulates Ras activity via degradation of 80K-H, leading to neural differentiation, including neuritogenesis. TRIM76 (also known as cardiomyopathy-associated protein 5 or CMYA5) is a muscle-specific member of the TRIM superfamily, but lacks the RING domain. It is possibly involved in protein kinase A signaling as well as vesicular trafficking. It has also been implicated in Duchenne muscular dystrophy and cardiac disease. The PRY-SPRY domain in these TRIM families is suggested to serve as the target binding site. 166 matched cddid_all.tbl CDD cd13735 cd13735 293970 SPRY_HECT_like SPRY domain in HECT E3. This domain consists of the SPRY subdomain similar to those found at the N-terminus of the HECT (homologous to the E6AP carboxyl terminus) protein, a C-terminal catalytic domain of a subclass of ubiquitin-protein ligase (E3). HECT E3 binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ubiquitin molecules to the end of growing ubiquitin chains. It has a prominent role in protein trafficking and immune response, and is involved in crucial signaling pathways implicated in tumorigenesis. 150 matched cddid_all.tbl CDD cd13736 cd13736 293971 SPRY_PRY_TRIM25 PRY/SPRY domain in tripartite motif-containing domain 25 (TRIM25). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM25 proteins (composed of RING/B-box/coiled-coil core and also known as RBCC proteins). TRIM25 (also called Efp) ubiquitinates the N terminus of the viral RNA receptor retinoic acid-inducible gene-I (RIG-I) in response to viral infection, leading to activation of the RIG-I signaling pathway, thus resulting in type I interferon production to limit viral replication. It has been shown that the influenza A virus targets TRIM25 and disables its antiviral function. 169 matched cddid_all.tbl CDD cd13737 cd13737 293972 SPRY_PRY_TRIM25-like PRY/SPRY domain in tripartite motif-containing domain 25 (TRIM25)-like. This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of proteins similar to TRIM25 (composed of RING/B-box/coiled-coil core and also known as RBCC proteins). TRIM25 (also called Efp) ubiquitinates the N terminus of the viral RNA receptor retinoic acid-inducible gene-I (RIG-I) in response to viral infection, leading to activation of the RIG-I signaling pathway, thus resulting in type I interferon production to limit viral replication. It has been shown that the influenza A virus targets TRIM25 and disables its antiviral function. 172 matched cddid_all.tbl CDD cd13738 cd13738 293973 SPRY_PRY_TRIM14 PRY/SPRY domain of tripartite motif-binding protein 14 (TRIM14). This is a TRIM14 domain family contains residues in the N-terminus that form a distinct PRY domain structure such that the B30.2 domain consists of PRY and SPRY subdomains. TRIM14 domains have yet to be characterized. These B30.2 domains are a more recent adaptation where the SPRY/PRY combination is a possible component of immune defense. It belongs to Class IV TRIM protein family which has members involved in antiviral immunity at various levels of interferon signaling cascade. 173 matched cddid_all.tbl CDD cd13739 cd13739 293974 SPRY_PRY_TRIM1 PRY/SPRY domain of tripartite motif-binding protein 1 (TRIM1) or MID2. This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM1 (also known as MID2 or midline 2). MID2 and its close homolog, TRIM18 (also known as MID1), both contain a B30.2-like domain at their C-terminus and a single fibronectin type III (FN3) motif between it and their N-terminal RBCC domain. MID2 and MID1 coiled-coil motifs mediate both homo- and heterodimerization, a prerequisite for association of the rapamycin-sensitive PP2A regulatory subunit Alpha 4 with microtubules. Mutations in MID1 have shown to cause Opitz syndrome, a disorder causing congenital anomalies such as cleft lip and palate as well as heart defects. 170 matched cddid_all.tbl CDD cd13740 cd13740 293975 SPRY_PRY_TRIM7 PRY/SPRY domain in tripartite motif-binding protein 7 (TRIM7). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of tripartite motif-containing protein 7 (TRIM7), also referred to as glycogenin-interacting protein (GNIP) or RING finger protein 90 (RNF90). TRIM7 or GNIP interacts with glycogenin and stimulates its self-glucosylating activity via its SPRY domain. The GNIP gene encodes at least four distinct isoforms of GNIP, of which three (GNIP1, GNIP2, and GNIP3) have the B30.2 domain. 169 matched cddid_all.tbl CDD cd13741 cd13741 240499 SPRY_PRY_TRIM41 PRY/SPRY domain in tripartite motif-binding protein 41 (TRIM41). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of tripartite motif-containing protein 41 (TRIM41). TRIM41 (also known as RING finger-interacting protein with C kinase or RINCK) is localized to speckles in the cytoplasm and nucleus, and functions as an E3 ligase that catalyzes the ubiquitin-mediated degradation of protein kinase C. 199 matched cddid_all.tbl CDD cd13742 cd13742 293976 SPRY_PRY_TRIM72 PRY/SPRY domain in tripartite motif-binding protein 72 (TRIM72). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM72. Muscle-specific TRIM72 (also known as Mitsugumin 53 or MG53) has been shown to perform a critical function in membrane repair following acute muscle injury by nucleating the assembly of the repair machinery at injury sites. It is expressed specifically in skeletal muscle and heart, and tethered to the plasma membrane and cytoplasmic vesicles via its interaction with phosphatidylserine. TRIM72 interacts with dysferlin, a sarcolemmal protein whose deficiency causes Miyoshi myopathy (MM) and limb girdle muscular dystrophy type 2B (LGMD2B); this coordination plays an important role in the repair of sarcolemma damage. 192 matched cddid_all.tbl CDD cd13743 cd13743 293977 SPRY_PRY_TRIM50 PRY/SPRY domain in tripartite motif-binding protein 50 (TRIM50). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM50. TRIM50, an E3 ubiquitin ligase, is deleted in Williams-Beuren (WBS) syndrome, a multi-system neurodevelopmental disorder caused by the deletion of contiguous genes at chromosome region 7q11.23. It is specifically expressed in gastric parietal cells and may play an essential role in tubulovesicular dynamics. It also interacts with and increases the level of p62, a multifunctional adaptor protein that is implicated in various cellular processes such as the autophagy clearance of polyubiquitinated protein aggregates. 189 matched cddid_all.tbl CDD cd13744 cd13744 293978 SPRY_PRY_TRIM62 PRY/SPRY domain in tripartite motif-binding protein 62 (TRIM62). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM62. It is also called DEAR1 ductal epithelium (associated RING chromosome 1) and is involved in the morphogenesis of the mammary gland; loss of TRIM62 gene expression in breast is associated with increased risk of recurrence in early-onset breast cancer and thus, making TRIM62 a predictive biomarker. Non-small cell lung cancer lesions show a step-wise loss of TRIM62 levels during disease progression, indicating that it may play a role in the evolution of lung cancer. Decreased levels of TRIM62 also represent an independent adverse prognostic factor in AML. 188 matched cddid_all.tbl CDD cd13745 cd13745 293979 SPRY_PRY_TRIM39 PRY/SPRY domain in tripartite motif-binding protein 39 (TRIM39) and TRIM39-like. This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of pyrin, several tripartite motif-containing proteins (TRIMs), including E3 ubiquitin-protein ligase (TRIM21), RET finger protein (RFP)/tripartite motif protein 27 (TRIM27), as well as butyrophilin (Btns) and butyrophilin-like (Btnl) family members, with the exception of Btnl2. Btn and Btnl family members are novel regulators of immune responses, with many of the genes located within the MHC. They are implicated in T-cell inhibition and modulation of epithelial cell-T cell interactions. TRIM21 (also known as RO52, SSA1 or RNF81) is a major autoantigen in autoimmune diseases such as rheumatoid arthritis, systemic lupus erythematosus, and Sjorgen's syndrome. TRIM27 (also known as Ret finger protein, RFP or RNF76) negatively regulates CD4 T-cells by ubiquitinating and inhibiting the class II phosphatidylinositol 3 kinase C2beta (PI3K-C2beta), a kinase critical for KCa3.1 channel activation. The PRY/SPRY domain of Pyrin, which is mutated in familial Mediterranean fever patients, interacts with inflammasome components and inhibits proIL-1beta processing. 177 matched cddid_all.tbl CDD cd13746 cd13746 259839 Sir4p-SID_like The SID domain of Saccharomyces cerevisiae silent information regulator 4, a Sir2p interaction domain; and related domains. Saccharomyces cerevisiae Sir2p, Sir3p, and Sir4p form a heterotrimeric complex which binds chromatin and represses transcription at the homothallic mating type (HM) loci and at subtelomeric regions. This domain model spans residues 742-893 of Sir4p. Sir4p forms a stable heterodimer with Sir2p, mediated by Sir4p residues included in this domain, and a pocket between Sir2p's catalytic domain and its non-conserved N-terminus. Sir4p also interacts with an array of additional factors, including Yku80p, a subunit of the telomeric Ku complex (Yku70p-Yku80p), which binds two sites within Sir4p, one at the N-terminus and one in the C-terminal residues, 731-1358. Other interaction factors include Esc1p (Establishes silent chromatin 1) which binds the Sir4p PAD domain (partitioning and anchoring domain, residues 950-1262), and Sir3p, Yku70p, and Rap1p (Repressor Activator Protein) which bind in its C-terminal coiled-coil (residues 1257-1358). Other Sir4p interacting factors include the Ty5 retrotransposon. Additional roles for Sir4p include roles in DNA repair, and in aging. A SIR4 mutant having a truncated Sir4p lacking a C-terminal coiled-coil domain, has an extended mean life span; deletion of the SIR4 gene leads to a decreased mean life span. 115 matched cddid_all.tbl CDD cd13747 cd13747 259834 UreI_AmiS_like_1 "UreI/Amis family, subgroup 1. Putative proton-gated urea channel and putative amide transporters. This subfamily includes putative UreI proton-gated urea channels and putative amide transporters (AmiS of the amidase gene cluster). Helicobacter pylori UreI (HpUreI), a proton-gated inner membrane urea channel opens in acidic pH to allow urea influx to the cytoplasm. There urea is metabolized, producing NH3 and Co2, leading to buffering of the periplasm. This action is essential for the survival of H. pylori in the stomach, and has been identified as a mechanism that could be clinically targeted to prevent various illnesses associated with infection by H. pylori. UreI and the related amide channels (AmiS) appear to function as hexamers, and have 6 predicted transmembrane segments. UreI has also been shown have a lipid ""plug"" in the center of the hexamer. Urea enters at the periplasmic opening of UreI and must pass 2 constriction sites, one on each side of a conserved Glu (Glu 177, H. pylori numbering), to reach the cytoplasm. Urea/thiourea selectivity is diminished by mutation of a conserved Trp to Ala or Phe in constriction site 2 (cytoplasmic). Channel functionality is greatly diminished by mutation of a conserved Trp in constriction site 1 (periplasmic) and a conserved Tyr in constriction site 2, and to a lesser extent a conserved Phe in site 1. In the cytoplasm, urease hydrolyzes urea to form ammonia and carbamate, which decomposes to carbonic acid. UreI is fully open at pH 5.0 to facilitate urea influx, but closes at neutral pH, preventing over-alkalization. Glu 177 (H. pylori numbering) is present in urea channel proteins, but absent in the related amide channels, suggesting that it plays a role in urea specificity." 167 matched cddid_all.tbl CDD cd13748 cd13748 259840 CBM29_CBM65 family 29 and family 65 carbohydrate binding modules. Members of this family bind to polysaccharides that are components of plant cell walls. CBM29 is present in cell-wall degrading multi-enzyme complexes from the anaerobic fungus Piromyces equi, CBM65 can be found in endoglucanases expressed by Eubacterium cellulosolvens and has a preference for xyloglucans. 106 matched cddid_all.tbl CDD cd13749 cd13749 259796 Zn-ribbon_TFIIS domain III/zinc ribbon domain of Transcription Factor IIS. TFIIS is a zinc-containing transcription factor. It has been shown in vitro to have distinct biochemical activities, including binding to RNA polymerases, stimulation of transcript elongation, and activation of a nascent RNA cleavage activity in the RNA polymerase II (Pol II) elongation complex. TFIIS consists of three domains. Domain II and III are sufficient for all known TFIIS activities. Domain III is a zinc ribbon that separated from domain II by a long linker and is indispensable for TFIIS function. The TFIIS homologs, subunits A12.2, B9, and C11, of Pol I, II, and III respectively, are required for RNA cleavage by the polymerases. In a single organism, there are tissue-specific TFIIS related proteins. 47 matched cddid_all.tbl CDD cd13750 cd13750 381628 TGF_beta_GDNF_like transforming growth factor beta (TGF-beta) like domain found in the glial cell-line-derived neurotrophic factor (GDNF) family of ligands. GDNF family of ligands includes GDNF, Artemin, Neurturin, and Persephin. They plays an important role in the development and maintenance of the central and peripheral nervous system, renal morphogenesis, and spermatogenesis. 95 matched cddid_all.tbl CDD cd13751 cd13751 381629 TGF_beta_GDF8_like transforming growth factor beta (TGF-beta) like domain found in growth/differentiation factors, GDF8 and GDF11, and similar proteins. The family includes GDF8 and GDF11. GDF8, also termed myostatin, acts specifically as a negative regulator of skeletal muscle growth. GDF11, also termed bone morphogenetic protein 11 (BMP-11), is a secreted signal that acts globally to specify positional identity along the anterior/posterior axis during development. 96 matched cddid_all.tbl CDD cd13752 cd13752 381630 TGF_beta_INHB transforming growth factor beta (TGF-beta) like domain found in inhibin beta A chain (INHBA), B chain (INHBB), C chain (INHBC), E chain (INHBE) and similar proteins. The family includes inhibin beta A chain (INHBA), B chain (INHBB), C chain (INHBC), and E chain (INHBE). INHBA, also termed activin beta-A chain, or erythroid differentiation protein (EDF), is a component of inhibin A, activin A, or activin AB. Inhibins and activins inhibit and activate, respectively, the secretion of follitropin by the pituitary gland. INHBB, also termed activin beta-B chain, is a component of inhibin B, activin A, or activin AB. Inhibins and activins inhibit and activate, respectively, the secretion of follitropin by the pituitary gland. INHBC, also termed activin beta-C chain, might play important roles in carcinogenesis. It may function as a negative regulator of liver growth. INHBE, also termed activin beta-E chain, is a possible insulin resistance-associated hepatokine with hepatic gene expression that positively correlated with insulin resistance and body mass index in humans. It also acts as a possible new marker for drug-induced endoplasmic reticulum stress. 100 matched cddid_all.tbl CDD cd13753 cd13753 381631 TGF_beta_TGFbeta1_2_3 transforming growth factor beta (TGF-beta) like domain found in transforming growth factor beta-1 (TGF-beta-1), beta-2 (TGF-beta-2), beta-3 (TGF-beta-3) and similar proteins. The family includes TGF-beta-1, TGF-beta-2 and TGF-beta-3, which are polypeptide members of the transforming growth factor beta superfamily of cytokines. TGF-beta-1 is a secreted protein that performs many cellular functions, including the control of cell growth, cell proliferation, cell differentiation, and apoptosis. TGF-beta-2 is a secreted protein that performs many cellular functions and has a vital role during embryonic development. It can suppress the effects of interleukin-2 dependent T-cell growth. TGF-beta-3 is involved in embryogenesis and cell differentiation. It regulates molecules involved in cellular adhesion and extracellular matrix (ECM) formation during the process of palate development. 97 matched cddid_all.tbl CDD cd13754 cd13754 381632 TGF_beta_INHA transforming growth factor beta (TGF-beta) like domain found in inhibin alpha chain (INHA) and similar proteins. INHA is a component of inhibins (inhibin A or inhibin B) that inhibit the secretion of follitropin by the pituitary gland. 89 matched cddid_all.tbl CDD cd13755 cd13755 381633 TGF_beta_maverick transforming growth factor beta (TGF-beta) like domain found in Drosophila melanogaster maverick and similar proteins. Maverick, also termed MAV, is a novel member of the TGF-beta superfamily in Drosophila. It's a bone morphogenetic protein (BMP)/TGF-beta related ligand. 102 matched cddid_all.tbl CDD cd13756 cd13756 381634 TGF_beta_BMPs_GDFs transforming growth factor beta (TGF-beta) like domain found in the BMP/GDF family. The BMP/GDF family consists of bone morphogenetic proteins (BMPs), growth and differentiation factors (GDFs) and similar proteins. BMPs are a group of growth factors also known as cytokines and as metabologens. They induce the formation of bone and cartilage and functions as pivotal morphogenetic signals, orchestrating tissue architecture throughout the body. GDFs have functions predominantly in development. 102 matched cddid_all.tbl CDD cd13757 cd13757 381635 TGF_beta_AMH transforming growth factor beta (TGF-beta) like domain found in anti-Muellerian hormone (AMH) and similar proteins. AMH, also termed Muellerian-inhibiting factor, or Muellerian-inhibiting substance (MIS), is a glycoprotein that causes regression of the Muellerian duct. It can also inhibit the growth of tumors derived from tissues of Muellerian duct origin. 99 matched cddid_all.tbl CDD cd13758 cd13758 381636 TGF_beta_LEFTY1_2 transforming growth factor beta (TGF-beta) like domain found in left-right determination factor 1 (lefty-1), factor 2 (lefty-2) and similar proteins. Lefty-1, also termed left-right determination factor B, or protein lefty-B, is required for left-right axis determination as a regulator of Lefty-2 and NODAL. Lefty-2, also termed endometrial bleeding-associated factor, or left-right determination factor A, or protein lefty-A, or transforming growth factor beta-4 (TGF-beta-4), is required for left-right (L-R) asymmetry determination of organ systems in mammals. It may play a role in endometrial bleeding. 90 matched cddid_all.tbl CDD cd13759 cd13759 381637 TGF_beta_NODAL transforming growth factor beta (TGF-beta) like domain found in Nodal (NODAL)-related proteins. NODAL is essential for mesoderm formation and axial patterning during embryonic development. 103 matched cddid_all.tbl CDD cd13760 cd13760 381638 TGF_beta_BMP2_like transforming growth factor beta (TGF-beta) like domain found in bone morphogenetic protein 2 (BMP-2), 4 (BMP-4) and similar proteins. The family includes BMP2 and BMP4 (also known as BMP2B), both of which induce cartilage and bone formation. BMP-2 stimulates the differentiation of myoblasts into osteoblasts via the EIF2AK3-EIF2A- ATF4 pathway. BMP-4 acts in mesoderm induction, tooth development, limb formation and fracture repair. 102 matched cddid_all.tbl CDD cd13761 cd13761 381639 TGF_beta_BMP5_like transforming growth factor beta (TGF-beta) like domain found in bone morphogenetic proteins BMP-5, BMP-6, BMP-7, BMP-8A/B and similar proteins. The family includes BMP-5, BMP-6, BMP-7 and BMP-8A/B, which may induce cartilage and bone formation. 103 matched cddid_all.tbl CDD cd13762 cd13762 381640 TGF_beta_GDP9_9B_like transforming growth factor beta (TGF-beta) like domain found in growth/differentiation factor 9 (GDF-9), growth/differentiation factor 9B (GDF-9B) and similar proteins. The family includes GDF-9B (also known as BMP15) and GDF9. GDF-9B acts as oocyte-specific growth/differentiation factor that stimulates folliculogenesis and granulosa cell (GC) growth. GDF-9 is required for ovarian folliculogenesis. It promotes primordial follicle development and stimulates granulosa cell proliferation. 104 matched cddid_all.tbl CDD cd13763 cd13763 381641 TGF_beta_BMP3_like transforming growth factor beta (TGF-beta) like domain found in bone morphogenetic protein 3 (BMP-3), growth/differentiation factor 10 (GDF10) and similar proteins. The family includes BMP-3 (also known as BMP-3A or osteogenin) and GDF10 (also known as BMP-3B). BMP-3 negatively regulates bone density. It antagonizes the ability of certain osteogenic BMPs to induce osteoprogenitor differentitation and ossification. GDF10 is a growth factor involved in osteogenesis and adipogenesis. 103 matched cddid_all.tbl CDD cd13764 cd13764 381642 TGF_beta_GDF1_3_like transforming growth factor beta (TGF-beta) like domain found in embryonic growth/differentiation factor 1 (GDF1), factor 3 (GDF3) and similar proteins. The family includes GDF-1 and GDF-3. GDF1 may mediate cell differentiation events during embryonic development. GDF3 is a growth factor involved in early embryonic development and adipose-tissue homeostasis. The family also contains protein DVR-1, also termed vegetal hemisphere VG1 protein (VG-1), which serves to facilitate the differentiation of either mesoderm or endoderm either as a cofactor in an instructive signal or by providing permissive environment. 102 matched cddid_all.tbl CDD cd13765 cd13765 381643 TGF_beta_ADMP transforming growth factor beta (TGF-beta) like domain found in anti-dorsalizing morphogenetic protein (ADMP) and similar proteins. ADMP is a bone morphogenetic protein (BMP)-like transforming growth factor beta ligand, functions in the trunk organizer to antagonize head formation, thereby regulating organizer patterning. It negatively affects the formation of the organizer, although it is robustly expressed within the organizer itself. The organizer-promoting signal of ADMP is mediated by the activin A type I receptor, ACVR1 (also known as activin receptor-like kinase-2, ALK2). 105 matched cddid_all.tbl CDD cd13766 cd13766 381644 TGF_beta_GDF5_6_7 transforming growth factor beta (TGF-beta) like domain found in growth/differentiation factor 5 (GDF5), factor 6 (GDF6), factor 7 (GDF7) and similar proteins. The family includes GDF5, GDF6 and GDF7. GDF5, also termed bone morphogenetic protein 14 (BMP-14), or cartilage-derived morphogenetic protein 1 (CDMP-1), or lipopolysaccharide-associated protein 4 (LAP-4), or LPS-associated protein 4, or radotermin, is a growth factor involved in bone and cartilage formation. GDF6, also termed bone morphogenetic protein 13 (BMP-13), or growth/differentiation factor 16, is a growth factor that controls proliferation and cellular differentiation in the retina and bone formation. GDF7, also termed bone morphogenetic protein 12 (BMP-12), may play an active role in the motor area of the primate neocortex. 102 matched cddid_all.tbl CDD cd13767 cd13767 381645 TGF_beta_BMP9_like transforming growth factor beta (TGF-beta) like domain found in bone morphogenetic proteins, BMP-9, BMP-10 and similar proteins. The family includes BMP9 (also known as GDF2) and BMP10. BMP-9 is a potent circulating inhibitor of angiogenesis. It signals through the type I activin receptor ACVRL1 but not other activin receptor-like kinases (ALKs). BMP-10 is required for maintaining the proliferative activity of embryonic cardiomyocytes by preventing premature activation of the negative cell cycle regulator CDKN1C/p57KIP and maintaining the required expression levels of cardiogenic factors such as MEF2C and NKX2-5. It inhibits endothelial cell migration and growth. It may reduce cell migration and cell matrix adhesion in breast cancer cell lines. 105 matched cddid_all.tbl CDD cd13768 cd13768 259841 DSS1_Sem1 proteasome complex subunit DSS1/Sem1. The evolutionarily conserved deleted in split hand/split foot protein 1 (DSS1)/Sem1 is a subunit of the regulatory particle (RP) of the proteasome. It is implicated in ubiquitin-mediated proteolysis, is required for the maintenance of genomic stability, and functions in DNA damage response. DSS1/Sem1 also displays RP-independent functions; it serves as a functional component of the nuclear pore associated TREX-2 transcription-export complex and is required for proper nuclear export of mRNA. In mammalian cells, DSS1 binds and stabilizes the tumor suppressor BRCA2, and contributes to its function in mediating homologous recombinational repair. In yeast, Sem1 also complexes with the COP9 signalosome, which is involved in de-neddylation. DSS1/Sem1 may be a versatile protein which contributes to the functional integrity of multiple protein complexes involved in various biological processes. 61 matched cddid_all.tbl CDD cd13769 cd13769 259842 ApoLp-III_like Apolipophorin-III and similar insect proteins. Exchangeable apolipoproteins play vital roles in the transport of lipids and lipoprotein metabolism. Apolipophorin III (apoLp-III) assists in the loading of diacylglycerol, generated from triacylglycerol stores in the fat body through the action of adipokinetic hormone, into lipophorin, the hemolymph lipoprotein. ApoLp-III increases the lipid carrying capacity of lipophorin by covering the expanding hydrophobic surface resulting from diacylglycerol uptake. It plays a critical role in the transport of lipids during insect flight, and may also play a role in defense mechanisms and innate immunity. 158 matched cddid_all.tbl CDD cd13775 cd13775 259817 SPFH_eoslipins_u3 Uncharacterized prokaryotic subfamily of the stomatin-like proteins (slipins), a subgroup of the SPFH family (stomatin, prohibitin, flotillin, and HflK/C). This model summarizes a subgroup of the stomatin-like protein family (SLPs or slipins) that is found in bacteria and archaebacteria. The conserved domain common to the SPFH superfamily has also been referred to as the Band 7 domain. Individual proteins of the SPFH superfamily may cluster to form membrane microdomains which may in turn recruit multiprotein complexes. Bacterial and archaebacterial SLPs remain uncharacterized. 177 matched cddid_all.tbl CDD cd13777 cd13777 260099 Aar2_N N-terminal domain of Aar2, a U5 small nuclear ribonucleoprotein particle assembly factor. This family consists of the N-terminal domain of eukaryotic Aar2 and Aar2-like proteins. Aar2 is a U5 small nuclear ribonucleoprotein (snRNP) particle assembly factor and part of Prp8, which forms a large complex containing U5 snRNA, Snu114, and seven Sm proteins (B, D1, D2, D3, E, F and G). Upon import of the complex into the nucleus, Aar2 phosphorylation leads to its release from Prp8 and replacement by Brr2p, thus playing an important role in Brr2p regulation and possibly safeguarding against non-specific RNA binding to Prp8. Aar2p binds directly with the RNaseH-like domain in the C-terminal region of Prp8p. In yeast, Aar2 protein is involved in splicing pre-mRNA of the a1 cistron and other genes important for cell growth. 126 matched cddid_all.tbl CDD cd13778 cd13778 260100 Aar2_C C-terminal domain of Aar2, a U5 small nuclear ribonucleoprotein particle assembly factor. This family consists of the C-terminal domain of eukaryotic Aar2 and Aar2-like proteins. Aar2 is a U5 small nuclear ribonucleoprotein (snRNP) particle assembly factor and part of Prp8, which forms a large complex containing U5 snRNA, Snu114, and seven Sm proteins (B, D1, D2, D3, E, F and G). Upon import of the complex into the nucleus, Aar2 phosphorylation leads to its release from Prp8 and replacement by Brr2p, thus playing an important role in Brr2p regulation and possibly safeguarding against non-specific RNA binding to Prp8. Aar2p binds directly with the RNaseH-like domain in the C-terminal region of Prp8p. In yeast, Aar2 protein is involved in splicing pre-mRNA of the a1 cistron and other genes important for cell growth. 155 matched cddid_all.tbl CDD cd13783 cd13783 260101 SPACA1 Sperm acrosome membrane-associated protein 1. SPACA1 (aka SAMP32, due to its 32kDa M.W.) is localized to the acrosome of spermatozoa. The acrosome is an organelle transformed from the Golgi apparatus to form a cap over the anterior portion of the spermatozoa head, which contains the sperm nucleus. Mammalian acrosomes contain digestive enzymes that degrade the ovum outer membrane (zona pellucida) to allow fusion of the sperm and ovum nuclei via the acrosomal reaction. In mammals, the acrosome releases hyaluronidase and acrosin. Antibodies generated against recombinant SPACA1 have been shown to inhibit human sperm binding and membrane fusion in vitro vs. zona-free hamster ova. Male mice lacking SPACA1 are infertile, and exhibit globozoospermia-like misformed sperm heads. SPACA1 content has been reported to be diminished in a comparison of round-headed vs normal spermatozoa. 248 matched cddid_all.tbl CDD cd13784 cd13784 260102 SP_1775_like Uncharacterized protein conserved in Streptococci. Streptococcus pneumoniae SP_1775 and related proteins from other Streptococci; may form homooctamers that may bind hydrophobic ligands. 67 matched cddid_all.tbl CDD cd13785 cd13785 260079 CARD_BinCARD_like BinCARD (Bcl10-interacting protein with CARD). BinCARD was ubiquitously expressed CRAD (Caspase activation and recruitment domain) protein in all tissues. CARD proteins play important role in apoptosis by functioning as direct regulators of death-inducing caspases. BinCARD interacts with apoptosis inducer CARD protein Bcl10 through CARD. It inhibits Bcl10-mediated activation of NF-kappa B and to suppress Bcl10 phosphorylation. Caspase activation and recruitment domains (CARDs) are death domains (DDs) found associated with caspases. In general, DDs domains are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. 86 matched cddid_all.tbl CDD cd13831 cd13831 259853 HU histone-like DNA-binding protein HU. This subfamily includes HU and HU-like domains. HU is a conserved nucleoid-associated protein (NAP) which binds non-specifically to duplex DNA with a particular preference for targeting nicked and bent DNA. It is highly basic and contributes to chromosomal compaction and maintenance of negative supercoiling, thus often referred to as histone-like protein. HU can induce DNA bends, condense DNA in a fiber and also interact with single stranded DNA. It contains two homologous subunits, alpha and beta, typically forming homodimers (alpha-alpha and beta-beta), except in E. coli and other enterobacteria, which form heterodimers (alpha-beta). In E. coli, HU binds uniformly to the chromosome, with a preference for damaged or distorted DNA structures and can introduce negative supercoils into closed circular DNA in the presence of topoisomerase I. Anabaena HU (AHU) shows preference for A/T-rich region in the center of its DNA binding site. 86 matched cddid_all.tbl CDD cd13832 cd13832 259854 IHF Integration host factor (IHF) and similar proteins. This subfamily includes integration host factor (IHF) and IHF-like domains. IHF is a nucleoid-associated protein (NAP) that binds and sharply bends many DNA targets in a sequence specific manner. It is a heterodimeric protein composed of two highly homologous subunits IHFA (IHF-alpha) and IHFB (IHF-beta). It is known to act as a transcription factor at many gene regulatory regions in E. coli. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). IHF is also involved in formation as well as maintenance of bacterial biofilms since it is found in complex with extracellular DNA (eDNA) within the extracellular polymeric substances (EPS) matrix of many biofilms. This subfamily also includes the protein Hbb from tick-borne spirochete Borrelia burgdorferi, responsible for causing Lyme disease in humans. Hbb, a homodimer, shows DNA sequence preferences that are related, yet distinct from those of IHF. 85 matched cddid_all.tbl CDD cd13833 cd13833 259855 HU_IHF_like Uncharacterized proteins similar to DNA sequence specific (IHF) and non-specific (HU) domains. This subfamily consists of uncharacterized proteins similar to integration host factor (IHF) and HU domains, including hypothetical protein Bvu_2165 from Bacteroides vulgatus. IHF is a nucleoid-associated protein (NAP) that binds and sharply bends many DNA targets in a sequence specific manner. It is a heterodimeric protein composed of two highly homologous subunits IHFA (IHF-alpha) and IHFB (IHF-beta). It is known to act as a transcription factor at many gene regulatory regions in E. coli. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). IHF is also involved in formation as well as maintenance of bacterial biofilms since it is found in complex with extracellular DNA (eDNA) within the extracellular polymeric substances (EPS) matrix of many biofilms. 97 matched cddid_all.tbl CDD cd13834 cd13834 259856 HU_like DNA-binding proteins similar to HU domains. This subfamily consists of DNA-binding proteins similar to HU domains. HU is a conserved nucleoid-associated protein (NAP) which binds non-specifically to duplex DNA with a particular preference for targeting nicked and bent DNA. It is highly basic and contributes to chromosomal compaction and maintenance of negative supercoiling, thus often referred to as histone-like protein. HU can induce DNA bends, condense DNA in a fiber and also interact with single stranded DNA. It contains two homologous subunits, alpha and beta, typically forming homodimers (alpha-alpha and beta-beta), except in E. coli and other enterobacteria, which form heterodimers (alpha-beta). 94 matched cddid_all.tbl CDD cd13835 cd13835 259857 IHF_A Alpha subunit of integration host factor (IHFA). This subfamily consists of the alpha subunit of integration host factor (IHF) and IHF-like domains. IHF is a nucleoid-associated protein (NAP) that binds and sharply bends many DNA targets in a sequence specific manner. It is a heterodimeric protein composed of two highly homologous subunits IHFA (IHF-alpha) and IHFB (IHF-beta). It is known to act as a transcription factor at many gene regulatory regions in E. coli. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). IHF is also involved in formation as well as maintenance of bacterial biofilms since it is found in complex with extracellular DNA (eDNA) within the extracellular polymeric substances (EPS) matrix of many biofilms. 88 matched cddid_all.tbl CDD cd13836 cd13836 259858 IHF_B Beta subunit of integration host factor (IHFB). This subfamily consists of the beta subunit of integration host factor (IHF) and IHF-like domains. IHF is a nucleoid-associated protein (NAP) that binds and sharply bends many DNA targets in a sequence specific manner. It is a heterodimeric protein composed of two highly homologous subunits IHFA (IHF-alpha) and IHFB (IHF-beta). It is known to act as a transcription factor at many gene regulatory regions in E. coli. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). IHF is also involved in formation as well as maintenance of bacterial biofilms since it is found in complex with extracellular DNA (eDNA) within the extracellular polymeric substances (EPS) matrix of many biofilms. 89 matched cddid_all.tbl CDD cd13838 cd13838 260013 RNase_H_like_Prp8_IV Ribonuclease-like Prp8 domain IV core. This family contains Prp8 domain IV, which adopts a RNase H like fold within its core structure but with little sequence similarity. Prp8, a spliceosome protein, interacts directly with the splice sites and branch regions of precursor-mRNAs and spliceosomal RNAs associated with catalysis of the two steps of splicing. Catalysis of RNA cleavage by RNase H-like proteins involves a two-metal mechanism in which adjacently-bound divalent magnesium ions promote hydrolysis by activation of a water nucleophile and stabilization of the transition-state. However, the Prp8 domain IV contains only one of the canonical metal-binding sites and the coordinating side chains are spatially conserved with respect to Mg2+-coordinating residues within the RNase H fold. 251 matched cddid_all.tbl CDD cd13839 cd13839 260103 MEF2_binding Mycocyte enhancer factor-2 (MEF2) binding domain of the calcineurin-binding protein cabin-1. The myocyte enhancer factor-2 (MEF2) binding domain, as found in the calcineurin-binding protein cabin-1, adopts an amphipathic alpha-helical structure, which allows it to bind to a hydrophobic groove on the MEF2S domain, forming a triple-helical interaction. Interaction of this domain with MEF2 causes repression of transcription. Cabin-1 inhibits calcineurin-mediated signal transduction in T-cell receptor-mediated signalling pathways, by binding to the activated form of calcineurin. Cabin-1 acts as a co-repressor of MEF2, the mycocyte enhancer factor-2, which regulates transcription in a calcium-dependent manner and plays vital roles in T-cell development and function. 35 matched cddid_all.tbl CDD cd13840 cd13840 260104 SMBP_like Small metal-binding protein conserved in proteobacteria. This periplasmic protein appears capable of binding multiple equivalents of a variety of divalent and trivalent metals, including Cu(2+) and Fe(3+) but also Mn(2+), Ni(2+), Mg(2+), and Zn(2+). It has been suggested that SMBP is a metal scavenging protein that plays a role in cellular copper management in Nitrosomonas europaea. 89 matched cddid_all.tbl CDD cd13841 cd13841 260105 ABBA-PTs ABBA-type aromatic prenyltransferases (PTases). ABBA-type aromatic prenyltransferases (PTases) are a subgroup of prenyltransferases that are characterized by an unusual type of beta/alpha fold with antiparallel beta strands. They lack the (N/D)DxxD motif which is characteristic for many other prenyltransferases. Generally, aromatic prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties onto aromatic substrates, forming C-C bonds between C-1 or C-3 of the isoprenoid substrate and one of the aromatic carbons of the acceptor substrate by an electrophilic alkylation, or Friedel-Crafts alkylation mechanism. 294 matched cddid_all.tbl CDD cd13842 cd13842 259911 CuRO_HCO_II_like Cupredoxin domain of Heme-copper oxidase subunit II. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is diverse in terms of electron donors, subunit composition, and heme types. The number of subunits varies from two to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian cytochrome c oxidase (CcO) are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. It has been proposed that archaea acquired heme-copper oxidases through gene transfer from gram-positive bacteria. Subunit II is found in CcO, ubiquinol oxidase, and the ba3-like oxidases, while the cbb3 oxidases contain alternative additional subunits. Additionally, nitrous oxide reductase contains the globular portion of subunit II as a domain within its structure. In some families, subunit II contains a copper-copper binuclear center that is involved in the transfer of electrons from the substrate to the binuclear center (active site) in subunit I. 95 matched cddid_all.tbl CDD cd13843 cd13843 259912 Azurin_like Azurin and similar redox proteins. Azurin is a bacterial blue copper-binding protein. It serves as a redox partner to enzymes such as nitrite reductase or arsenite oxidase. The copper of Azurin is tetrahedrally coordinated by a cysteine, 2 histidines, and a methionine residue. The electron transfer reactions are carried out with the Cu center transitioning between the oxidized Cu(II) form and the reduced Cu(I) form. Azurin can function as tumor suppressor; it forms a complex with p53 that triggers apoptosis in various human cancer cells. Auracyanins A and B are from photosynthetic bacteria. They are very similar blue copper proteins with 38% sequence identity and they are homologous to the bacterial redox protein Azurin. However, auracyanin A is expressed only when C. aurantiacus cells are grown in light, whereas auracyanin B is expressed under dark and in light. Thus, auracyanin A may function as a redox partner in photosynthesis, while auracyanin B may function in aerobic respiration. 124 matched cddid_all.tbl CDD cd13844 cd13844 259913 CuRO_1_BOD_CotA_like The first Cupredoxin domain of Bilirubin oxidase (BOD), the bacterial endospore coat component CotA, and similar proteins. Bilirubin oxidase (BOD) catalyzes the oxidation of bilirubin to biliverdin and the four-electron reduction of molecular oxygen to water. CotA protein is an abundant component of the outer coat layer in bacterial endospore coat and it is required for spore resistance against hydrogen peroxide and UV light. Also included in this subfamily are phenoxazinone synthase (PHS), which catalyzes the oxidative coupling of substituted o-aminophenols to produce phenoxazinones. PHS has been shown to participate in diverse biological functions such as spore pigmentation and biosynthesis of the antibiotic grixazone. These are Laccase-like multicopper oxidases (MCOs) that are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 162 matched cddid_all.tbl CDD cd13845 cd13845 259914 CuRO_1_AAO The first cupredoxin domain of plant Ascorbate oxidase. Ascorbate oxidase catalyzes the oxidation of ascorbic acid to dehydroascorbic acid. This multicopper oxidase (MCO) is found in cucurbitaceous plants such as pumpkin, cucumber, and melon. It can detect levels of ascorbic acid and eliminate it. The biological function of ascorbate oxidase is still not clear. Ascorbate oxidase belongs to MCO family which couple oxidation of substrates with reduction of dioxygen to water. MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 120 matched cddid_all.tbl CDD cd13846 cd13846 259915 CuRO_1_AAO_like_1 The first cupredoxin domain of plant Ascorbate oxidase homologs. This subfamily is composed of plant pollen multicopper oxidase homologous to ascorbate oxidase. Ascorbate oxidase catalyzes the oxidation of ascorbic acid to dehydroascorbic acid. This multicopper oxidase (MCO) is found in cucurbitaceous plants such as pumpkin, cucumber, and melon. It can detect levels of ascorbic acid and eliminate it. The biological function of ascorbate oxidase is still not clear. Ascorbate oxidase belongs to MCO family which couple oxidation of substrates with reduction of dioxygen to water. MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. This subfamily does not harbor trinuclear copper binding histidines. 118 matched cddid_all.tbl CDD cd13847 cd13847 259916 CuRO_1_AAO_like_2 The first cupredoxin domain of Ascorbate oxidase homologs. This family includes fungal proteins with similarity to ascorbate oxidase. Ascorbate oxidase catalyzes the oxidation of ascorbic acid to dehydroascorbic acid. It can detect levels of ascorbic acid and eliminate it. The biological function of ascorbate oxidase is still not clear. Ascorbate oxidase belongs to multicopper oxidase (MCO) family which couple oxidation of substrates with reduction of dioxygen to water. MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 117 matched cddid_all.tbl CDD cd13848 cd13848 259917 CuRO_1_CopA The first cupredoxin domain of CopA copper resistance protein family. CopA is a multicopper oxidase (MCO) related to laccase and L-ascorbate oxidase, both copper-containing enzymes. It is part of the copper-regulatory cue operon, which employs a cytosolic metalloregulatory protein CueR that induces expression of CopA and CueO under copper stress conditions. CopA is a copper efflux P-type ATPase that is located in the inner cell membrane and is involved in copper resistance in bacteria. CopA mutant causes a loss of function including copper tolerance and oxidase activity, and copA transcription is inducible in the presence of copper. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 116 matched cddid_all.tbl CDD cd13849 cd13849 259918 CuRO_1_LCC_plant The first cupredoxin domain of plant laccases. Laccase is a blue multicopper oxidase (MCO) which catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. Laccase has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism. Plants usually express multiple laccase genes, but their precise physiological/biochemical roles remain largely unclear. MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 117 matched cddid_all.tbl CDD cd13850 cd13850 259919 CuRO_1_Abr2_like The first cupredoxin domain of a group of fungal Laccases similar to Abr2 from Aspergillus fumigatus. Abr2 is involved in conidial pigment biosynthesis in Aspergillus fumigatus. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. Laccase has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism in fungi and plants. Like other related multicopper oxidases (MCOs), laccase is composed of three cupredoxin domains that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 117 matched cddid_all.tbl CDD cd13851 cd13851 259920 CuRO_1_Fet3p The first Cupredoxin domain of multicopper oxidase Fet3P. Fet3p catalyzes the ferroxidase reaction, which couples the oxidation of Fe(II) to Fe(III) and a four-electron reduction of molecular oxygen to water. Fet3p is a type I membrane protein with the amino-terminal oxidase domain in the exocellular space and the carboxyl terminus in the cytoplasm. The periplamic produced Fe(III) is transferred to the permease Ftr1p for import into the cytosol. The four copper ions are inserted post-translationally and are essential for catalytic activity, thus linking copper and iron homeostasis. Like other related multicopper oxidases (MCOs), Fet3p is composed of three cupredoxin domains that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 121 matched cddid_all.tbl CDD cd13852 cd13852 259921 CuRO_1_McoP_like The first cupredoxin domain of multicopper oxidase McoP and similar proteins. This family includes archaeal and bacterial multicopper oxidases (MCOs), represented by the extremely thermostable McoP from the hyperthermophilic archaeon Pyrobaculum aerophilum. McoP is an efficient metallo-oxidase that catalyzes the oxidation of cuprous and ferrous ions. It is noteworthy that McoP has three-fold higher catalytic efficiency when using nitrous oxide as the electron acceptor than when using dioxygen, the typical oxidizing substrate of MCOs. McoP may function as a novel archaeal nitrous oxide reductase that is probably involved in the denitrification pathway in archaea. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 114 matched cddid_all.tbl CDD cd13853 cd13853 259922 CuRO_1_Tth-MCO_like The first cupredoxin domain of the bacterial laccases similar to Tth-MCO from Thermus Thermophilus. The subfamily of bacterial laccases includes Tth-MCO and similar proteins. Tth-MCO is a hyperthermophilic multicopper oxidase (MCO) from thermus thermophilus HB27. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. It has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism in fungi and plants. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 139 matched cddid_all.tbl CDD cd13854 cd13854 259923 CuRO_1_MaLCC_like The first cupredoxin domain of the fungal laccases similar to Ma-LCC from Melanocarpus albomyces. The subfamily of fungal laccases includes Ma-LCC and similar proteins. Ma-LCC is a multicopper oxidase (MCO) from Melanocarpus albomyces. Its crystal structure contains all four coppers at the mono- and trinuclear copper centers. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. It has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism in fungi and plants. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 122 matched cddid_all.tbl CDD cd13855 cd13855 259924 CuRO_1_McoC_like The first cupredoxin domain of a multicopper oxidase McoC and similar proteins. This family includes bacteria multicopper oxidases (MCOs) represented by McoC from pathogenic bacterium Campylobacter jejuni. McoC is a periplasmic multicopper oxidase, which has been characterized to be associated with copper homeostasis. McoC may also function to protect against oxidative stress as it may convert metallic ions into their less toxic form. MCOs are multi-domain enzymes that are able to couple oxidation of substrates with reduction of dioxygen to water. They are capable of oxidizing a vast range of substrates, varying from aromatic compunds to inorganic compounds such as metals. Most MCOs have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 121 matched cddid_all.tbl CDD cd13856 cd13856 259925 CuRO_1_Tv-LCC_like The first cupredoxin domain of fungal laccases similar to Tv-LCC from Trametes versicolor. This subfamily of fungal laccases includes Tv-LCC from Trametes versicolor and Rs-LCC2 from plant pathogenic fungus Rhizoctonia solani. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. It has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 125 matched cddid_all.tbl CDD cd13857 cd13857 259926 CuRO_1_Diphenol_Ox The first cupredoxin domain of fungal laccase, diphenol oxidase. Diphenol oxidase belongs to the laccase family. It catalyzes the initial steps in melanin biosynthesis from diphenols. Melanin is one of the virulence factors of infectious fungi. In the pathogenesis of C. neoformans, melanin pigments have been shown to protect the fungal cells from oxidative and microbicidal activities of host defense systems. Laccase is a blue multicopper oxidase (MCO) which catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. It has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 119 matched cddid_all.tbl CDD cd13858 cd13858 259927 CuRO_1_tcLCC2_insect_like The first cupredoxin domain of insect laccases similar to laccase 2 in Tribolium castaneum. This multicopper oxidase (MCO) family includes the majority of insect laccases. One member of the family is laccase 2 from Tribolium castaneum. Laccase 2 is required for beetle cuticle tanning. Laccase (polyphenol oxidase EC 1.10.3.2) is a blue multi-copper enzyme that catalyzes the oxidation of a variety of organic substrates coupled to the reduction of molecular oxygen to water. It displays broad substrate specificity, catalyzing the oxidation of a wide variety of aromatic - notably phenolic and inorganic substances. Laccase has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism in fungi, plants and insects. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 105 matched cddid_all.tbl CDD cd13859 cd13859 259928 CuRO_D1_2dMcoN_like The first cupredoxin domain of bacterial two domain multicopper oxidase McoN and similar proteins. This family includes bacterial two domain multicopper oxidases (2dMCOs) represented by the McoN from Nitrosomonas europaea. McoN is a trimeric type C blue copper oxidase. Each subunit houses a type 1 copper site in domain 1 and a type 2/type 3 trinuclear copper cluster at the subunit-subunit interface. The 2dMCO is proposed to be a key intermediate in the evolution of three domain MCOs. Its biological function has not been characterized. Multicopper oxidases couple oxidation of substrates with reduction of dioxygen to water. These MCOs are capable of oxidizing a vast range of substrates, varying from aromatic to inorganic compounds such as metals. 122 matched cddid_all.tbl CDD cd13860 cd13860 259929 CuRO_1_2dMco_1 The first cupredoxin domain of bacteria two domain multicopper oxidase. This subfamily includes bacterial two domain multicopper oxidases (2dMCOs) with similarity to McoN from Nitrosomonas europaea. 2dMCO is a trimeric type C blue copper oxidase. Each subunit houses a type 1 copper site in domain 1 and a type 2/type 3 trinuclear copper cluster at the subunit-subunit interface. The 2dMCO is proposed to be a key intermediate in the evolution of three domain MCOs. Multicopper oxidases couple oxidation of substrates with reduction of dioxygen to water. These MCOs are capable of oxidizing a vast range of substrates, varying from aromatic to inorganic compounds such as metals. 119 matched cddid_all.tbl CDD cd13861 cd13861 259930 CuRO_1_CumA_like The first cupredoxin domain of CumA like multicopper oxidase. This multicopper oxidase (MCO) subfamily includes CumA from Pseudomonas putida, which is involved in the oxidation of Mn(II). However, the cumA gene has been identified in a variety of bacterial species, including both Mn(II)-oxidizing and non-Mn(II)-oxidizing strains. Thus, the proteins in this family may catalyze the oxidation of other substrates. MCO catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water and has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 119 matched cddid_all.tbl CDD cd13862 cd13862 259931 CuRO_1_MCO_like_1 The first cupredoxin domain of uncharacterized multicopper oxidase. Multicopper Oxidases (MCOs) are multi-domain enzymes that are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre which binds a dioxygen. The dioxygen, following the transfer of four electrons, is reduced to two molecules of water. These MCOs are capable of oxidizing a vast range of substrates, varying from aromatic to inorganic compounds such as metals. This subfamily of MCOs is composed of three cupredoxin domains. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 123 matched cddid_all.tbl CDD cd13864 cd13864 259932 CuRO_1_MCO_like_2 The second cupredoxin domain of uncharacterized multicopper oxidase. Multicopper Oxidases (MCOs) are multi-domain enzymes that are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre which binds a dioxygen. The dioxygen, following the transfer of four electrons, is reduced to two molecules of water. These MCOs are capable of oxidizing a vast range of substrates, varying from aromatic to inorganic compounds such as metals. This subfamily of MCOs is composed of three cupredoxin domains. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 139 matched cddid_all.tbl CDD cd13865 cd13865 259933 CuRO_1_LCC_like_3 The second cupredoxin domain of uncharacterized multicopper oxidase. Multicopper Oxidases (MCOs) are multi-domain enzymes that are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre which binds a dioxygen. The dioxygen, following the transfer of four electrons, is reduced to two molecules of water. These MCOs are capable of oxidizing a vast range of substrates, varying from aromatic to inorganic compounds such as metals. This subfamily of MCOs is composed of three cupredoxin domains. The cupredoxin domain 1 of 3-domain MCOs contains part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 115 matched cddid_all.tbl CDD cd13866 cd13866 259934 CuRO_2_BOD The second cupredoxin domain of Bilirubin oxidase (BOD). Bilirubin oxidase (BOD) catalyzes the oxidation of bilirubin to biliverdin and the four-electron reduction of molecular oxygen to water. It is used in diagnosing jaundice through the determination of bilirubin in serum. BOD is a member of the multicopper oxidase (MCO) family that also includes laccase, ascorbate oxidase and ceruloplasmin. MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 152 matched cddid_all.tbl CDD cd13867 cd13867 259935 CuRO_2_CueO_FtsP The second Cupredoxin domain of the multicopper oxidase CueO, the cell division protein FtsP, and similar proteins. CueO is a multicopper oxidase (MCO) that is part of the copper-regulatory cue operon, which employs a cytosolic metalloregulatory protein CueR that induces expression of CopA and CueO under copper stress conditions. CueO is a periplasmic multicopper oxidase that is stimulated by exogenous copper(II). FtsP (also named SufI) is a component of the cell division apparatus. It is involved in protecting or stabilizing the assembly of divisomes under stress conditions. FtsP belongs to the multicopper oxidase superfamily but lacks metal cofactors. The protein is localized at septal rings and may serve as a scaffolding function. Members of this subfamily contain three cupredoxin domains and this model represents the second domain. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 146 matched cddid_all.tbl CDD cd13868 cd13868 259936 CuRO_2_CotA_like The second Cupredoxin domain of bacterial laccases including CotA, a bacterial endospore coat component. CotA protein is an abundant component of the outer coat layer in bacterial endospore coat and it is required for spore resistance against hydrogen peroxide and UV light. Laccase is composed of three cupredoxin-like domains and includes one mononuclear and one trinuclear copper center. It is a member of the multicopper oxidase (MCO) family, which couples the oxidation of a substrate with a four-electron reduction of molecular oxygen to water. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 155 matched cddid_all.tbl CDD cd13869 cd13869 259937 CuRO_2_PHS The second Cupredoxin domain of phenoxazinone synthase (PHS). Phenoxazinone synthase (PHS, 2-aminophenol:oxygen oxidoreductase) catalyzes the oxidative coupling of substituted o-aminophenols to produce phenoxazinones. PHS participates in diverse biological functions such as spore pigmentation and biosynthesis of the antibiotic grixazone. It is a member of the multicopper oxidase (MCO) family, which couples the oxidation of a substrate with a four-electron reduction of molecular oxygen to water. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 166 matched cddid_all.tbl CDD cd13870 cd13870 259938 CuRO_2_CopA_like_1 The second cupredoxin domain of CopA copper resistance protein like family. The members of this family are copper resistance protein (CopA) homologs. CopA is multicopper oxidase (MCO) related to laccase and L-ascorbate oxidase, both copper-containing enzymes. CopA is involved in copper resistance in bacteria. CopA mutant causes a loss of function, including copper tolerance and oxidase activity, and copA transcription is inducible in the presence of copper. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 117 matched cddid_all.tbl CDD cd13871 cd13871 259939 CuRO_2_AAO The second cupredoxin domain of plant Ascorbate oxidase. Ascorbate oxidase catalyzes the oxidation of ascorbic acid to dehydroascorbic acid. This multicopper oxidase (MCO) is found in cucurbitaceous plants such as pumpkin, cucumber, and melon. It can detect levels of ascorbic acid and eliminate it. The biological function of ascorbate oxidase is still not clear. MCOs couple oxidation of substrates with reduction of dioxygen to water. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 166 matched cddid_all.tbl CDD cd13872 cd13872 259940 CuRO_2_AAO_like_1 The second cupredoxin domain of plant pollen multicopper oxidase homologous to ascorbate oxidase. The proteins in this subfamily are expressed in plant pollen. They share homology to ascorbate oxidase and other members of the blue copper oxidase family. The expression of the protein is detected during germination and pollen tube growth. Ascorbate oxidase catalyzes the oxidation of ascorbic acid to dehydroascorbic acid. It is a member of the multicopper oxidase (MCO) family that couples oxidation of substrates with reduction of dioxygen to water. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 141 matched cddid_all.tbl CDD cd13873 cd13873 259941 CuRO_2_AAO_like_2 The second cupredoxin domain of plant Ascorbate oxidase homologs. This family includes plant laccases similar to ascorbate oxidase. Ascorbate oxidase catalyzes the oxidation of ascorbic acid to dehydroascorbic acid. It can detect levels of ascorbic acid and eliminate it. The biological function of ascorbate oxidase is still not clear. Ascorbate oxidase belongs to multicopper oxidase (MCO) family which couples oxidation of substrates with reduction of dioxygen to water. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 161 matched cddid_all.tbl CDD cd13874 cd13874 259942 CuRO_2_CopA The second cupredoxin domain of CopA copper resistance protein family. CopA is a multicopper oxidase (MCO) related to laccase and L-ascorbate oxidase, both copper-containing enzymes. It is part of the copper-regulatory cue operon, which employs a cytosolic metalloregulatory protein CueR that induces expression of CopA and CueO under copper stress conditions. CopA is a copper efflux P-type ATPase that is located in the inner cell membrane and is is involved in copper resistance in bacteria. CopA mutant causes a loss of function including copper tolerance and oxidase activity and copA transcription is inducible in the presence of copper. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 112 matched cddid_all.tbl CDD cd13875 cd13875 259943 CuRO_2_LCC_plant The second cupredoxin domain of the plant laccases. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. Laccase has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism. Plants usually express multiple laccase genes, but their precise physiological/biochemical roles remain largely unclear. Like other related multicopper oxidases (MCOs), laccase is composed of three cupredoxin domains that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 148 matched cddid_all.tbl CDD cd13876 cd13876 259944 CuRO_2_Abr2_like The second cupredoxin domain of a group of fungal Laccases similar to Abr2 from Aspergillus fumigatus. Abr2 is involved in conidial pigment biosynthesis in Aspergillus fumigatus. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. Laccase has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism in fungi and plants. Like other related multicopper oxidases (MCOs), laccase is composed of three cupredoxin domains that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 138 matched cddid_all.tbl CDD cd13877 cd13877 259945 CuRO_2_Fet3p_like The second Cupredoxin domain of multicopper oxidase Fet3P. Fet3p catalyzes the ferroxidase reaction, which couples the oxidation of Fe(II) to Fe(III) with the four-electron reduction of molecular oxygen to water. Fet3p is a type I membrane protein with the amino-terminal oxidase domain in the extracellular space and the carboxyl terminus in the cytoplasm. The periplasmic produced Fe(III) is transferred to the permease Ftr1p for import into the cytosol. The four copper ions are inserted post-translationally and are essential for catalytic activity, thus linking copper and iron homeostasis. Like other related multicopper oxidases (MCOs), Fet3p is composed of three cupredoxin domains that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 148 matched cddid_all.tbl CDD cd13879 cd13879 259946 CuRO_2_McoP_like The second cupredoxin domain of multicopper oxidase McoP and similar proteins. This family includes archaeal and bacterial multicopper oxidases (MCOs), represented by the extremely thermostable McoP from the hyperthermophilic archaeon Pyrobaculum aerophilum. McoP is an efficient metallo-oxidase that catalyzes the oxidation of cuprous and ferrous ions. It is noteworthy that McoP has three-fold higher catalytic efficiency when using nitrous oxide as electron acceptor than when using dioxygen, the typical oxidizing substrate of multicopper oxidases. McoP may function as a novel archaeal nitrous oxide reductase that is probably involved in the denitrification pathway in archaea. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 162 matched cddid_all.tbl CDD cd13880 cd13880 259947 CuRO_2_MaLCC_like The second cupredoxin domain of the fungal laccases similar to Ma-LCC from Melanocarpus albomyces. The subfamily of fungal laccases includes Ma-LCC and similar proteins. Ma-LCC is a multicopper oxidase (MCO) from Melanocarpus albomyces. Its crystal structure contains all four coppers at the mono- and trinuclear copper centers. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. It has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism in fungi and plants. Laccase is composed of three cupredoxin domains that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 167 matched cddid_all.tbl CDD cd13881 cd13881 259948 CuRO_2_McoC_like The second cupredoxin domain of a multicopper oxidase McoC and similar proteins. This family includes bacterial multicopper oxidases (MCOs) represented by McoC from the pathogenic bacterium Campylobacter jejuni. McoC is a periplasmic MCO, which has been characterized to be associated with copper homeostasis. McoC may also function to protect against oxidative stress as it may convert metallic ions into their less toxic form. MCOs are multi-domain enzymes that are able to couple oxidation of substrates with the reduction of dioxygen to water. These MCOs are capable of oxidizing a vast range of substrates, varying from aromatic to inorganic compounds such as metals. They are composed of three cupredoxin domains that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 142 matched cddid_all.tbl CDD cd13882 cd13882 259949 CuRO_2_Tv-LCC_like The second cupredoxin domain of the fungal laccases similar to Tv-LCC from Trametes versicolor. This subfamily of fungal laccases includes Tv-LCC from Trametes versicolor and Rs-LCC2 from plant pathogenic fungus Rhizoctonia solani. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. It has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism. Laccase is a multicopper oxidase (MCO) composed of three cupredoxin domains that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 159 matched cddid_all.tbl CDD cd13883 cd13883 259950 CuRO_2_Diphenol_Ox The second cupredoxin domain of fungal laccase, diphenol oxidase. Diphenol oxidase belongs to the laccase family. It catalyzes the initial steps in melanin biosynthesis from diphenols. Melanin is one of the virulence factors of infectious fungi. In the pathogenesis of C. neoformans, melanin pigments have been shown to protect the fungal cells from oxidative and microbicidal activities of host defense systems. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. It has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism. Laccase is a multicopper oxidase (MCO) composed of three cupredoxin domains that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 164 matched cddid_all.tbl CDD cd13884 cd13884 259951 CuRO_2_tcLCC_insect_like The second cupredoxin domain of the insect laccases similar to laccase 2 in Tribolium castaneum. This multicopper oxidase (MCO) subfamily includes the majority of insect laccases. One member is laccase 2 from Tribolium castaneum, which is required for beetle cuticle tanning. Laccase (polyphenol oxidase EC 1.10.3.2) is a blue multi-copper enzyme that catalyzes the oxidation of a variety of organic substrates coupled to the reduction of molecular oxygen to water. It displays broad substrate specificity, catalyzing the oxidation of a wide variety of aromatic - notably phenolic and inorganic substances. Laccase has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism in fungi, plants and insects. Laccase is composed of three cupredoxin domains that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 150 matched cddid_all.tbl CDD cd13885 cd13885 259952 CuRO_2_CumA_like The second cupredoxin domain of CumA like multicopper oxidase. This multicopper oxidase (MCO) subfamily includes CumA from Pseudomonas putida. CumA is involved in the oxidation of Mn(II) in Pseudomonas putida; however, the cumA gene has been identified in a variety of bacterial species, including both Mn(II)-oxidizing and non-Mn(II)-oxidizing strains. Thus, the proteins in this family may catalyze the oxidation of other substrates. MCOs catalyze the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water and has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism. The MCOs in this subfamily are composed of three cupredoxin domains that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 132 matched cddid_all.tbl CDD cd13886 cd13886 259953 CuRO_2_MCO_like_1 The second cupredoxin domain of uncharacterized multicopper oxidase. Multicopper Oxidases (MCOs) are multi-domain enzymes that are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre which binds a dioxygen. The dioxygen, following the transfer of four electrons, is reduced to two molecules of water. These MCOs are capable of oxidizing a vast range of substrates, varying from aromatic to inorganic compounds such as metals. This family of MCOs is composed of three cupredoxin domains that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 163 matched cddid_all.tbl CDD cd13887 cd13887 259954 CuRO_2_MCO_like_2 The second cupredoxin domain of uncharacterized multicopper oxidase. Multicopper Oxidases (MCOs) are multi-domain enzymes that are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs oxidise their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre which binds a dioxygen. The dioxygen, following the transfer of four electrons, is reduced to two molecules of water. These MCOs are capable of oxidizing a vast range of substrates, varying from aromatic to inorganic compounds such as metals. This family of MCOs is composed of three cupredoxin domains that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 114 matched cddid_all.tbl CDD cd13888 cd13888 259955 CuRO_3_McoP_like The third cupredoxin domain of multicopper oxidase McoP and similar proteins. This subfamily includes archaeal and bacterial multicopper oxidases (MCOs), represented by the extremely thermostable McoP from the hyperthermophilic archaeon Pyrobaculum aerophilum. McoP is an efficient metallo-oxidase that catalyzes the oxidation of cuprous and ferrous ions. It is noteworthy that McoP has three-fold higher catalytic efficiency when using nitrous oxide as electron acceptor than when using dioxygen, the typical oxidizing substrate of multicopper oxidases. McoP may function as a novel archaeal nitrous oxide reductase that is probably involved in the denitrification pathway in archaea. Members of this subfamily contain three cupredoxin domain repeats. The copper ions are bound in several sites; Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 139 matched cddid_all.tbl CDD cd13889 cd13889 259956 CuRO_3_BOD The third cupredoxin domain of Bilirubin oxidase (BOD). Bilirubin oxidase (BOD) catalyzes the oxidation of bilirubin to biliverdin and the four-electron reduction of molecular oxygen to water. It is used in diagnosing jaundice through the determination of bilirubin in serum. BOD is a member of the multicopper oxidase (MCO) family that also includes laccase, ascorbate oxidase and ceruloplasmin. MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 124 matched cddid_all.tbl CDD cd13890 cd13890 259957 CuRO_3_CueO_FtsP The third Cupredoxin domain of the multicopper oxidase CueO, the cell division protein FtsP, and similar proteins. CueO is a multicopper oxidase (MCO) that is part of the copper-regulatory cue operon, which employs a cytosolic metalloregulatory protein CueR that induces expression of CopA and CueO under copper stress conditions. CueO is a periplasmic multicopper oxidase that is stimulated by exogenous copper(II). FtsP (also named SufI) is a component of the cell division apparatus. It is involved in protecting or stabilizing the assembly of divisomes under stress conditions. FtsP belongs to the multicopper oxidase superfamily but lacks metal cofactors. The protein is localized at septal rings and may serve as a scaffolding function. Members of this subfamily contain three cupredoxin domains and this model represents the first domain. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. FtsP does not contain any copper binding sites. 124 matched cddid_all.tbl CDD cd13891 cd13891 259958 CuRO_3_CotA_like The third Cupredoxin domain of bacterial laccases including CotA, a bacterial endospore coat component. CotA protein is an abundant component of the outer coat layer in bacterial endospore coat and is required for spore resistance against hydrogen peroxide and UV light. CotA belongs to the laccase-like multicopper oxidase (MCO) family, which are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 143 matched cddid_all.tbl CDD cd13892 cd13892 259959 CuRO_3_PHS The third Cupredoxin domain of phenoxazinone synthase (PHS). Phenoxazinone synthase (PHS, 2-aminophenol:oxygen oxidoreductase) catalyzes the oxidative coupling of substituted o-aminophenols to produce phenoxazinones. PHS has been shown to participate in diverse biological functions such as spore pigmentation and biosynthesis of the antibiotic grixazone. PHS is a member of the laccase-like multicopper oxidase (MCO) family, which are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 184 matched cddid_all.tbl CDD cd13893 cd13893 259960 CuRO_3_AAO The third cupredoxin domain of plant Ascorbate oxidase. Ascorbate oxidase catalyzes the oxidation of ascorbic acid to dehydroascorbic acid. This multicopper oxidase (MCO) is found in cucurbitaceous plants such as pumpkin, cucumber, and melon. It can detect levels of ascorbic acid and eliminate it. The biological function of ascorbate oxidase is still not clear. Ascorbate oxidase belongs to MCO family which couple oxidation of substrates with reduction of dioxygen to water. MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 155 matched cddid_all.tbl CDD cd13894 cd13894 259961 CuRO_3_AAO_like_1 The third cupredoxin domain of plant Ascorbate oxidase homologs. This subfamily is composed of plant pollen multicopper oxidase homologous to ascorbate oxidase. Ascorbate oxidase catalyzes the oxidation of ascorbic acid to dehydroascorbic acid. This multicopper oxidase (MCO) is found in cucurbitaceous plants such as pumpkin, cucumber, and melon. It can detect levels of ascorbic acid and eliminate it. The biological function of ascorbate oxidase is still not clear. Ascorbate oxidase belongs to MCO family which couple oxidation of substrates with reduction of dioxygen to water. MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. This subfamily does not harbor T1 copper or trinuclear copper binding sites. 123 matched cddid_all.tbl CDD cd13895 cd13895 259962 CuRO_3_AAO_like_2 The third cupredoxin domain of Ascorbate oxidase homologs. This family includes fungal proteins with similarity to ascorbate oxidase. Ascorbate oxidase catalyzes the oxidation of ascorbic acid to dehydroascorbic acid. It can detect levels of ascorbic acid and eliminate it. The biological function of ascorbate oxidase is still not clear. Ascorbate oxidase belongs to multicopper oxidase (MCO) family which couple oxidation of substrates with reduction of dioxygen to water. MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 188 matched cddid_all.tbl CDD cd13896 cd13896 259963 CuRO_3_CopA The third cupredoxin domain of CopA copper resistance protein family. CopA is a multicopper oxidase (MCO) related to laccase and L-ascorbate oxidase, both copper-containing enzymes. It is part of the copper-regulatory cue operon, which employs a cytosolic metalloregulatory protein CueR that induces expression of CopA and CueO under copper stress conditions. CopA is a copper efflux P-type ATPase that is located in the inner cell membrane and is is involved in copper resistance in bacteria. CopA mutant causes a loss of function including copper tolerance and oxidase activity and copA transcription is inducible in the presence of copper. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 115 matched cddid_all.tbl CDD cd13897 cd13897 259964 CuRO_3_LCC_plant The third cupredoxin domain of the plant laccases. Laccase is a blue multicopper oxidase (MCO) which catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. Laccase has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism. Plants usually express multiple laccase genes, but their precise physiological/biochemical roles remain largely unclear. MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 139 matched cddid_all.tbl CDD cd13898 cd13898 259965 CuRO_3_Abr2_like The third cupredoxin domain of a group of fungal Laccases similar to Abr2 from Aspergillus fumigatus. Abr2 is involved in conidial pigment biosynthesis in Aspergillus fumigatus. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. Laccase has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism in fungi and plants. Like other related multicopper oxidases (MCOs), laccase is composed of three cupredoxin domains that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 164 matched cddid_all.tbl CDD cd13899 cd13899 259966 CuRO_3_Fet3p The third Cupredoxin domain of multicopper oxidase Fet3p. Fet3p catalyzes the ferroxidase reaction, which couples the oxidation of Fe(II) to Fe(III) with the four-electron reduction of molecular oxygen to water. Fet3p is a type I membrane protein with the amino-terminal oxidase domain in the extracellular space and the carboxyl terminus in the cytoplasm. The periplasmic produced Fe(III) is transferred to the permease Ftr1p for import into the cytosol. The four copper ions are inserted post-translationally and are essential for catalytic activity, thus linking copper and iron homeostasis. Like other related multicopper oxidases (MCOs), Fet3p is composed of three cupredoxin domains that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 160 matched cddid_all.tbl CDD cd13900 cd13900 259967 CuRO_3_Tth-MCO_like The third cupredoxin domain of the bacterial laccases similar to Tth-MCO from Thermus Thermophilus. The subfamily of bacterial laccases includes Tth-MCO and similar proteins. Tth-MCO is a hyperthermophilic multicopper oxidase (MCO) from thermus thermophilus HB27. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. It has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism in fungi and plants. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 123 matched cddid_all.tbl CDD cd13901 cd13901 259968 CuRO_3_MaLCC_like The third cupredoxin domain of the fungal laccases similar to Ma-LCC from Melanocarpus albomyces. The subfamily of fungal laccases includes Ma-LCC and similar proteins. Ma-LCC is a multicopper oxidase (MCO) from Melanocarpus albomyces. Its crystal structure contains all four coppers at the mono- and trinuclear copper centers. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. It has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism in fungi and plants. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 157 matched cddid_all.tbl CDD cd13902 cd13902 259969 CuRO_3_McoC_like The third cupredoxin domain of a multicopper oxidase McoC and similar proteins. This family includes bacteria multicopper oxidases (MCOs) represented by McoC from pathogenic bacterium Campylobacter jejuni. McoC is a periplasmic multicopper oxidase, which has been characterized to be associated with copper homeostasis. McoC may also function to protect against oxidative stress as it may convert metallic ions into their less toxic form. MCOs are multi-domain enzymes that are able to couple oxidation of substrates with reduction of dioxygen to water. They are capable of oxidizing a vast range of substrates, varying from aromatic compunds to inorganic compounds such as metals. Most MCOs have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 125 matched cddid_all.tbl CDD cd13903 cd13903 259970 CuRO_3_Tv-LCC_like The third cupredoxin domain of the fungal laccases similar to Tv-LCC from Trametes Versicolor. This subfamily of fungal laccases includes Tv-LCC from Trametes versicolor and Rs-LCC2 from plant pathogenic fungus Rhizoctonia solani. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. It has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 147 matched cddid_all.tbl CDD cd13904 cd13904 259971 CuRO_3_Diphenol_Ox The third cupredoxin domain of fungal laccase, diphenol oxidase. Diphenol oxidase belongs to the laccase family. It catalyzes the initial steps in melanin biosynthesis from diphenols. Melanin is one of the virulence factors of infectious fungi. In the pathogenesis of C. neoformans, melanin pigments have been shown to protect the fungal cells from oxidative and microbicidal activities of host defense systems. Laccase is a blue multicopper oxidase (MCO) which catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water. It has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 158 matched cddid_all.tbl CDD cd13905 cd13905 259972 CuRO_3_tcLLC2_insect_like The third cupredoxin domain of the insect laccases similar to laccase 2 in Tribolium castaneum. This multicopper oxidase (MCO) family includes the majority of insect laccases. One member of the family is laccase 2 from Tribolium castaneum. Laccase 2 is required for beetle cuticle tanning. Laccase (polyphenol oxidase EC 1.10.3.2) is a blue multi-copper enzyme that catalyzes the oxidation of a variety of organic substrates coupled to the reduction of molecular oxygen to water. It displays broad substrate specificity, catalyzing the oxidation of a wide variety of aromatic - notably phenolic and inorganic substances. Laccase has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism in fungi, plants and insects. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 174 matched cddid_all.tbl CDD cd13906 cd13906 259973 CuRO_3_CumA_like The third cupredoxin domain of CumA like multicopper oxidase. This multicopper oxidase (MCO) subfamily includes CumA from Pseudomonas putida, which is involved in the oxidation of Mn(II). However, the cumA gene has been identified in a variety of bacterial species, including both Mn(II)-oxidizing and non-Mn(II)-oxidizing strains. Thus, the proteins in this family may catalyze the oxidation of other substrates. MCO catalyzes the oxidation of a variety aromatic - notably phenolic and inorganic substances coupled to the reduction of molecular oxygen to water and has been implicated in a wide spectrum of biological activities and, in particular, plays a key role in morphogenesis, development and lignin metabolism. Although MCOs have diverse functions, majority of them have three cupredoxin domain repeats that include one mononuclear and one trinuclear copper center. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 138 matched cddid_all.tbl CDD cd13907 cd13907 259974 CuRO_3_MCO_like_1 The third cupredoxin domain of uncharacterized multicopper oxidase. Multicopper Oxidases (MCOs) are multi-domain enzymes that are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre which binds a dioxygen. The dioxygen, following the transfer of four electrons, is reduced to two molecules of water. These MCOs are capable of oxidizing a vast range of substrates, varying from aromatic to inorganic compounds such as metals. This subfamily of MCOs is composed of three cupredoxin domains. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 154 matched cddid_all.tbl CDD cd13908 cd13908 259975 CuRO_3_MCO_like_2 The third cupredoxin domain of uncharacterized multicopper oxidase. Multicopper Oxidases (MCOs) are multi-domain enzymes that are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre which binds a dioxygen. The dioxygen, following the transfer of four electrons, is reduced to two molecules of water. These MCOs are capable of oxidizing a vast range of substrates, varying from aromatic to inorganic compounds such as metals. This subfamily of MCOs is composed of three cupredoxin domains. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 122 matched cddid_all.tbl CDD cd13909 cd13909 259976 CuRO_3_MCO_like_3 The third cupredoxin domain of uncharacterized multicopper oxidase. Multicopper Oxidases (MCOs) are multi-domain enzymes that are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre which binds a dioxygen. The dioxygen, following the transfer of four electrons, is reduced to two molecules of water. These MCOs are capable of oxidizing a vast range of substrates, varying from aromatic to inorganic compounds such as metals. This subfamily of MCOs is composed of three cupredoxin domains. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 137 matched cddid_all.tbl CDD cd13910 cd13910 259977 CuRO_3_MCO_like_4 The third cupredoxin domain of uncharacterized multicopper oxidase. Multicopper Oxidases (MCOs) are multi-domain enzymes that are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre which binds a dioxygen. The dioxygen, following the transfer of four electrons, is reduced to two molecules of water. These MCOs are capable of oxidizing a vast range of substrates, varying from aromatic to inorganic compounds such as metals. This subfamily of MCOs is composed of three cupredoxin domains. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 166 matched cddid_all.tbl CDD cd13911 cd13911 259978 CuRO_3_MCO_like_5 The third cupredoxin domain of uncharacterized multicopper oxidase. Multicopper Oxidases (MCOs) are multi-domain enzymes that are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs oxidize their substrate by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear copper centre which binds a dioxygen. The dioxygen, following the transfer of four electrons, is reduced to two molecules of water. These MCOs are capable of oxidizing a vast range of substrates, varying from aromatic to inorganic compounds such as metals. This subfamily of MCOs is composed of three cupredoxin domains. The cupredoxin domain 3 of 3-domain MCOs contains the Type 1 (T1) copper binding site and part the trinuclear copper binding site, which is located at the interface of domains 1 and 3. 119 matched cddid_all.tbl CDD cd13912 cd13912 259979 CcO_II_C C-terminal domain of Cytochrome c Oxidase subunit II. Cytochrome c Oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Only subunits I and II are essential for function. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Subunit II contains a copper-copper binuclear site called CuA, which is believed to be involved in electron transfer from cytochrome c to the binuclear center (active site) in subunit I. 130 matched cddid_all.tbl CDD cd13913 cd13913 259980 ba3_CcO_II_C C-terminal cupredoxin domain of Ba3-like heme-copper oxidase subunit II. The ba3 family of heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and some archaea, which catalyze the reduction of O2 and simultaneously pump protons across the membrane. It has been proposed that archaea acquired heme-copper oxidases through gene transfer from gram-positive bacteria. The ba3 family contains oxidases that lack the conserved residues that form the D- and K-pathways in CcO and ubiquinol oxidase. Instead, they contain a potential alternative K-pathway. Additional proton channels have been proposed for this family of oxidases but none have been identified definitively. 99 matched cddid_all.tbl CDD cd13914 cd13914 259981 CuRO_HCO_II_like_3 Uncharacterized subfamily with similarity to Heme-copper oxidase subunit II cupredoxin domain. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is diverse in terms of electron donors, subunit composition, and heme types. The number of subunits varies from two to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian cytochrome c oxidase (CcO) are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. It has been proposed that archaea acquired heme-copper oxidases through gene transfer from gram-positive bacteria. Subunit II is found in CcO, ubiquinol oxidase, and the ba3-like oxidases, while the cbb3 oxidases contain alternative additional subunits. Additionally, nitrous oxide reductase contains the globular portion of subunit II as a domain within its structure. In some families, subunit II contains a copper-copper binuclear center that is involved in the transfer of electrons from the substrate to the binuclear center (active site) in subunit I. 108 matched cddid_all.tbl CDD cd13915 cd13915 259982 CuRO_HCO_II_like_2 Uncharacterized subfamily with similarity to Heme-copper oxidase subunit II cupredoxin domain. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is diverse in terms of electron donors, subunit composition, and heme types. The number of subunits varies from two to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian cytochrome c oxidase (CcO) are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. It has been proposed that archaea acquired heme-copper oxidases through gene transfer from gram-positive bacteria. Subunit II is found in CcO, ubiquinol oxidase, and the ba3-like oxidases, while the cbb3 oxidases contain alternative additional subunits. Additionally, nitrous oxide reductase contains the globular portion of subunit II as a domain within its structure. In some families, subunit II contains a copper-copper binuclear center that is involved in the transfer of electrons from the substrate to the binuclear center (active site) in subunit I. 98 matched cddid_all.tbl CDD cd13916 cd13916 259983 CuRO_HCO_II_like_1 Uncharacterized subfamily with similarity to Heme-copper oxidase subunit II cupredoxin domain. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is diverse in terms of electron donors, subunit composition, and heme types. The number of subunits varies from two to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian cytochrome c oxidase (CcO) are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. It has been proposed that archaea acquired heme-copper oxidases through gene transfer from gram-positive bacteria. Subunit II is found in CcO, ubiquinol oxidase, and the ba3-like oxidases, while the cbb3 oxidases contain alternative additional subunits. Additionally, nitrous oxide reductase contains the globular portion of subunit II as a domain within its structure. In some families, subunit II contains a copper-copper binuclear center that is involved in the transfer of electrons from the substrate to the binuclear center (active site) in subunit I. 93 matched cddid_all.tbl CDD cd13917 cd13917 259984 CuRO_HCO_II_like_4 Uncharacterized subfamily with similarity to Heme-copper oxidase subunit II cupredoxin domain. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is diverse in terms of electron donors, subunit composition, and heme types. The number of subunits varies from two to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian cytochrome c oxidase (CcO) are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. It has been proposed that archaea acquired heme-copper oxidases through gene transfer from gram-positive bacteria. Subunit II is found in CcO, ubiquinol oxidase, and the ba3-like oxidases, while the cbb3 oxidases contain alternative additional subunits. Additionally, nitrous oxide reductase contains the globular portion of subunit II as a domain within its structure. In some families, subunit II contains a copper-copper binuclear center that is involved in the transfer of electrons from the substrate to the binuclear center (active site) in subunit I. 88 matched cddid_all.tbl CDD cd13918 cd13918 259985 CuRO_HCO_II_like_6 Uncharacterized subfamily with similarity to Heme-copper oxidase subunit II cupredoxin domain. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is diverse in terms of electron donors, subunit composition, and heme types. The number of subunits varies from two to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian cytochrome c oxidase (CcO) are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. It has been proposed that archaea acquired heme-copper oxidases through gene transfer from gram-positive bacteria. Subunit II is found in CcO, ubiquinol oxidase, and the ba3-like oxidases, while the cbb3 oxidases contain alternative additional subunits. Additionally, nitrous oxide reductase contains the globular portion of subunit II as a domain within its structure. In some families, subunit II contains a copper-copper binuclear center that is involved in the transfer of electrons from the substrate to the binuclear center (active site) in subunit I. 139 matched cddid_all.tbl CDD cd13919 cd13919 259986 CuRO_HCO_II_like_5 Uncharacterized subfamily with similarity to Heme-copper oxidase subunit II cupredoxin domain. Heme-copper oxidases are transmembrane protein complexes in the respiratory chains of prokaryotes and mitochondria which catalyze the reduction of O2 and simultaneously pump protons across the membrane. The superfamily is diverse in terms of electron donors, subunit composition, and heme types. The number of subunits varies from two to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian cytochrome c oxidase (CcO) are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. It has been proposed that archaea acquired heme-copper oxidases through gene transfer from gram-positive bacteria. Subunit II is found in CcO, ubiquinol oxidase, and the ba3-like oxidases, while the cbb3 oxidases contain alternative additional subunits. Additionally, nitrous oxide reductase contains the globular portion of subunit II as a domain within its structure. In some families, subunit II contains a copper-copper binuclear center that is involved in the transfer of electrons from the substrate to the binuclear center (active site) in subunit I. 107 matched cddid_all.tbl CDD cd13920 cd13920 259987 Stellacyanin Stellacyanin is a subclass of phytocyanins, a plant type I copper protein. Stellacyanin is a subclass of the phytocyanins, a ubiquitous family of plant cupredoxins. Stellacyanin is involved in electron transfer reactions with the Cu center transitioning between the oxidized Cu(II) form and the reduced Cu(I) form. The copper is tetrahedrally coordinated by a cysteine, 2 histidines, and a glutamine residue. The glutamine residue substitutes for a methione ligand typically found in other blue copper proteins. The exact function of stellacyanin is unknown. However, stellacyanin appears to be associated with the plant cell wall; it may be involved in oxidative reactions to build polymeric material making up the cell wall. 101 matched cddid_all.tbl CDD cd13921 cd13921 259988 Amicyanin Amicyanin is a type I blue copper protein that plays an essential role in electron transfer. In Paracoccus denitrificans bacteria, amicyanin acts as an intermediary of a three-member redox complex along with methylamine dehydrogenase (MADH) and cytochrome c-551i. The electron is transferred from the active site of MADH via the amicyanin copper ion to the cytochrome heme iron. The electron transfer from MADH to cytochrome c-551i does not involve a ternary complex but occurs via a ping-pong mechanism in which amicyanin uses the same interface for the reactions with MADH and cytochrome c-551i. 81 matched cddid_all.tbl CDD cd13922 cd13922 259989 Azurin Azurin is a redox partner for enzymes such as nitrite reductase or arsenite oxidase. Azurin is a bacterial blue copper-binding protein. It serves as a redox partner to enzymes such as nitrite reductase or arsenite oxidase. The copper of Azurin is tetrahedrally coordinated by a cysteine, 2 histidines, and a methionine residue. The electron transfer reactions are carried out with the Cu center transitioning between the oxidized Cu(II) form and the reduced Cu(I) form. Azurin can function as a tumor suppressor; it forms a complex with p53 that triggers apoptosis in various human cancer cells. 125 matched cddid_all.tbl CDD cd13925 cd13925 381607 RPF core lysozyme-like domain of resuscitation-promoting factor proteins. Resuscitation-promoting factor (RPF) proteins, found in various (G+C)-rich Gram-positive bacteria, act to reactivate cultures from stationary phase. This protein shares elements of the structural core of lysozyme and related proteins. Furthermore, it shares a conserved active site glutamate which is required for activity, and has a polysaccharide binding cleft that corresponds to the peptidoglycan binding cleft of lysozyme. Muralytic activity of Rpf in Micrococcus luteus correlates with resuscitation, supporting a mechanism dependent on cleavage of peptidoglycan by RPF. 71 matched cddid_all.tbl CDD cd13926 cd13926 381608 N-acetylmuramidase_GH108 N-acetylmuramidase domain of the glycosyl hydrolase 108 family. This domain acts as a lysozyme (N-acetylmuramidase), EC:3.2.1.17. It contains a conserved EGGY motif near the N-terminus, the glutamic acid within this motif is essential for catalytic activity. In bacteria, it may activate the secretion of large proteins via the breaking and rearrangement of the peptidoglycan layer during secretion. It is frequently found at the N-terminus of proteins containing a peptidoglycan binding domain. 91 matched cddid_all.tbl CDD cd13929 cd13929 260106 PT-DMATS_CymD aromatic prenyltransferases (PTases) of the DMATS/CymD familiy. Members of the DMATS/CymD family of ABBA prenyltransferases prenylate indole, tyrosine, and xanthone derivatives. This family of fungal proteins includes cyclic dipeptide N-prenyltransferase (CdpNPT), Brevianamide F prenyltransferase (ftmPT1), fumigaclavine C synthase (FgaPT1), dimethylallyltryptophan synthase (DMATS) and related proteins. CdpNPT accepts a variety of tryptophan-containing cyclic dipeptides, including L-tryptophan itself, and prenylates these substrates inverse at the N-1 position of the indole group. FtmPT1 catalyzes the prenylation of brevianamide F in the biosynthesis of fumitremorgin-type alkaloids. FgaPT1 catalyses the prenylation of fumigaclavine A. Dimethylallyltryptophan synthases (DMATS) catalyzes the prenylation of L-tryptophan at C-4 of the indole ring during the biosynthesis of ergot alkaloids. 392 matched cddid_all.tbl CDD cd13930 cd13930 260107 PT-Tnase Aromatic Prenyltransferases (PTases) associated with tryptophanase. This group of bacterial and fungal proteins shows homology to the DMATS/CymD family of ABBA prenyltransferases, which prenylates indole, tyrosine, and xanthone derivatives. Some of the members, mostly fungal proteins, are associated with tryptophanase-like domains (Tnase) which catalyzes the degradation of L-tryptophan to yield indole, pyruvate and ammonia, or the degradation of L-tyrosine to yield phenol, pyruvate and ammonia. This suggest that these otherwise uncharacterized proteins may exhibit multiple functions. 348 matched cddid_all.tbl CDD cd13931 cd13931 260108 PT-CloQ_NphB Aromatic Prenyltransferases (PTases) of the CloQ/NphB family. Members of the CloQ/NphB family of ABBA prenyltransferases catalyze the prenylation of phenols, naphthalenes, and phenazines. This family of fungal and bacterial proteins includes dihydrophenazine-1-carboxylate dimethylallyltransferase PpzP, the aromatic prenyltransferase from the clorobiocin biosynthetic pathway CloQ, and related proteins. CloQ catalyzes the attachment of a dimethylallyl moiety to 4-hydroxyphenylpyruvate, part of the biosynthetic pathway of the Streptomyces roseochromogenes antibiotic clorobiocin. PpzP, as well as EpzP, are important for the biosynthesis of endophenazines; they catalyze the prenylation of 5,10-dihydrophenazine-1-carboxylic acid (dhPCA). Streptomyces NphB catalyzes the addition of a 10-carbon geranyl group to small organic aromatic substrates and is involved in the biosynthesis of the antioxidant naphterpin. Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties onto aromatic substrates in biosynthetic pathways of microbial secondary metabolites. 274 matched cddid_all.tbl CDD cd13932 cd13932 259826 HN_RTEL1 harmonin_N_like domain of regulator of telomere elongation helicase 1 (also known as RTEL). Mouse Rtel is an essential protein required for the maintenance of both telomeric and genomic stability. RTEL1 appears to maintain genome stability by suppressing homologous recombination (HR). In vitro, purified human and insect RTEL1 have been shown to promote the disassembly of D loop recombination intermediates, in a reaction dependent upon ATP hydrolysis. Human RTEL1 is implicated in the etiology of Dyskeratosis congenital (DC, is an inherited bone marrow failure and cancer predisposition syndrome). Point mutations in its helicase domains, and truncations which result in loss of its C-terminus have been discovered in DC families. RTEL1 is also a candidate gene influencing glioma susceptibility. The C-terminal domain of RTEL1, represented here, appears similar to the N-terminal domain of the scaffolding protein harmonin. 99 matched cddid_all.tbl CDD cd13933 cd13933 259827 harmonin_N_like_u1 domain similar to the N-terminal protein-binding module of harmonin; uncharacterized subgroup. This domain is a putative protein-binding module based on its sequence similarity to the N-terminal domain of harmonin. Harmonin (not belonging to this group) is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein, which organizes the Usher protein network of the inner ear and the retina. This domain is also related to domains found in several other scaffold proteins which organize supramolecular complexes. 78 matched cddid_all.tbl CDD cd13934 cd13934 260014 RNase_H_Dikarya_like Fungal (dikarya) Ribonuclease H, uncharacterized. This family contains dikarya RNase H, many of which are uncharacterized. Ribonuclease H (RNase H) enzymes are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. It is widely present in various organisms, including bacteria, archaea and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. An important RNase H function is to remove Okazaki fragments during DNA replication. 153 matched cddid_all.tbl CDD cd13935 cd13935 260015 RNase_H_bacteria_like RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner. This family includes bacterial ribonuclease H (RNase H) enzymes. RNases are divided into two major families, Type 1 and Type 2, based on amino acid sequence similarities and biochemical properties. RNase H is an endonuclease that cleaves the RNA strand of an RNA/DNA hybrid in a sequence non-specific manner in the presence of divalent cations. RNase H is widely present in various organisms, including bacteria, archaea and eukaryotes. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes. Despite the lack of amino acid sequence homology, type 1 and type 2 RNase H share a main-chain fold and steric configurations of the four acidic active-site residues and have the same catalytic mechanism and functions in cells. RNase H is involved in DNA replication, repair and transcription. One of the important functions of RNase H is to remove Okazaki fragments during DNA replication. RNase H inhibitors have been explored as an anti-HIV drug target because RNase H inactivation inhibits reverse transcription. 133 matched cddid_all.tbl CDD cd13936 cd13936 260110 PANDER_like Domains similar to the Pancreatic-derived factor. FAM3B or PANDER (PANcreatic DERived factor) has been identifed as a regulator of glucose homeostasis and beta cell function. The protein is expressed in the endocrine pancreas and co-secreted with insulin in response to glucose, particularly under conditions of insulin resistance. The protein had initially been predicted to be a member of the four-helical cytokine family, hence the FAM3B designation. This wider family contains FAM3B and FAM4C, N-terminal domains of N-acetylglucosaminyltransferases, and domains in poorly characterized proteins that have been associated with deafness and the progression of cancer. 149 matched cddid_all.tbl CDD cd13937 cd13937 260111 PANDER_GnT-1_2_like PANDER-like domain of N-acetylglucosaminyltransferases. O-linked-mannose beta-1,2-N-acetylglucosaminyltransferase 1 participates in O-mannosyl glycosylation and may be responsible for creating GlcNAc(beta1-2)Man(alpha1-)O-Ser/Thr moieties on alpha dystroglycan and other O-mannosylated proteins. The domain characterized by this model lies N-terminal to the catalytic domain. Its function has not been determined. 148 matched cddid_all.tbl CDD cd13938 cd13938 260112 PANDER_like_TMEM2 PANDER-like domain of the transmembrane protein TMEM2. TMEM2 has been characterized as a transmembrane protein that maps to the DFNB7-DFNB11 deafness locus on human chromosome 9. It contains a domain similar to the Pancreatic-derived factor PANDER, C-terminal to a glycine rich G8-domain. The function of the PANDER-like domain in TMEM2 has not been characterized. 168 matched cddid_all.tbl CDD cd13939 cd13939 260113 PANDER_FAM3B Pancreatic derived factor. FAM3B or PANDER (PANcreatic DERived factor) has been identifed as a regulator of glucose homeostasis and beta cell function. The protein is expressed in the endocrine pancreas and co-secreted with insulin in response to glucose, particularly under conditions of insulin resistance. The protein had initially been predicted to be a member of the four-helical cytokine family, hence the FAM3B designation. PANDER induces apoptosis of insulin-secreting beta-cells when over-expressed in vitro. It has been associated with the progression of type 2 diabetes by downregulating beta cell function as well as insulin sensitivity in the liver. 175 matched cddid_all.tbl CDD cd13940 cd13940 260114 ILEI_FAM3C Interleukin-like EMT inducer. The secreted factor FAM3C or ILEI (InterLeukin-like Emt Inducer) has been identifed as a protein involved in the epithelial-mesenchymal transition (EMT) and in processes associated with metastasis formation and the progression of cancer. The protein had initially been predicted to be a member of the four-helical cytokine family, hence the FAM3C designation. ILEI has been found to be widely expressed, and to be involved in retinal development. 171 matched cddid_all.tbl CDD cd13941 cd13941 260115 PANDER_like_KIAA1199 PANDER-like domain of KIAA1199 and similar proteins. KIAA1199 has been characterized as a protein associated with poor survival when upregulated in human cancer, as well as with nonsyndromic loss of hearing when mutated. It contains a C-terminal domain similar to the Pancreatic-derived factor PANDER; the function of this PANDER-like domain has not been characterized. 157 matched cddid_all.tbl CDD cd13944 cd13944 260116 lytB_ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase. The 4-hydroxy-3-methylbut-2-enyl diphosphate (HMBPP) reductase (called lytB or ispH) is the terminal enzyme of the mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway, one of the two metabolic routes for isoprenoid biosynthesis. The MEP pathway is essential in many eubacteria, plants, and the malaria parasite. LytB converts HMBPP into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). 275 matched cddid_all.tbl CDD cd13945 cd13945 260117 Chs5_N N-terminal dimerization domain of Chs5 and similar proteins. Chs5/6 is a multi-protein complex conserved in fungi that interacts with chitin synthase III (Chs3p) and is involved in its transport to the cell surface from the trans-Golgi network, functioning as an exomer cargo adapter. Chs5p appears to form a complex with Chs6p and its paralogs Bch1p, Bud7p, and Bch2p. In this complex, Chs5p may act as a central scaffold. The N-terminal domain characterized by this model forms a homodimer and has been shown to interact with Chs6p and Bch1p. It may function as a flexible hinge domain that allows the exomer to interact with both proteins and the Golgi membrane as the latter undergoes changes in curvature during the formation of transport vesicles. The dimerization domain sits N-terminally to a conserved FBE (FN3-BRCT) unit, which binds Arf1 an is involved in the recruitment of the exomer to the membrane. 73 matched cddid_all.tbl CDD cd13946 cd13946 260118 LysW Lysine biosynthesis protein LysW. LysW functions as a carrier protein in the biosynthesis pathway of lysine. The C-terminal glutamate sidechain of LysW attaches to the amino group of alpha-aminoadipate (AAA); this peptide bond formation is catalyzed by the ligase LysX. AAA remains associated with LysW throughout its biosynthetic conversion to lysine. LysW also acts to protect the amino group of glutamate in arginine biosynthesis. 54 matched cddid_all.tbl CDD cd13949 cd13949 320087 7tm_V1R_pheromone vomeronasal organ pheromone receptor type-1 family, member of the seven-transmembrane G protein-coupled receptor superfamily. This family represents vomeronasal type-1 receptors (V1Rs) that are specifically expressed in the vomeronasal organ (VNO), which is the sensory organ of the accessory olfactory system present in amphibians, reptiles, and non-primate mammals such as mice and rodents, but it is non-functional or absent in humans, apes and monkeys. The VNO detects pheromones, chemicals released from animals that can influence social and reproductive behaviors, such as male-male aggression or sexual mating, in other members of the same species. On the other hand, the olfactory epithelium, which contains olfactory receptor neurons inside the nasal cavity, is responsible for detecting odor molecules (smells). There are two types of vertebrate pheromones: (1) small volatile molecules such as 2-heptanone, a substance in the urine of both male and female that extends estrous cycle length in female mice; and (2) water-soluble molecules such as the major histocompatibility complex (HMC) class-I peptide, which can induce the pregnancy block effect, the tendency for female rodents to abort their pregnancies upon exposure to the scent of an unknown male. While V1Rs and G-alpha(i2) protein are co-expressed in the apical neurons of the VNO, V2Rs (type-2 vomeronasal receptors) and G-alpha(o) protein are coexpressed in the basal layer of the VNO. Activation of V1R or V2R causes stimulation of phospholipase pathway, generating diacylglycerol (DAG) and inositol 1,4,5-triphosphate (IP3). V1Rs have a short N-terminal extracellular domain, whereas V2Rs contain a long N-terminal extracellular domain, which is believed to bind pheromones. Although V1Rs share the seven-transmembrane domain structure with V1Rs and olfactory receptors, they share little sequence similarity with each other. 295 matched cddid_all.tbl CDD cd13950 cd13950 320088 7tm_TAS2R mammalian taste receptors type 2, member of the seven-transmembrane G protein-coupled receptor superfamily. This group represents a family of mammalian taste receptors (TAS2Rs), which function as bitter taste receptors. The human TAS2R family contains about 25 functional members, which are glycoproteins and have the ability to form both homomeric and heteromeric receptor complexes. Five basic tastes are perceived by animals: bitter, sweet, sour, salty, and umami (the taste of glutamate, MSG). Among these, sour and salty are mediated by ion channels, while the perception of umami and sweet tastes is mediated by the TAS1R taste receptors, which belong to the class C GPCR family. The TAS2Rs in humans have a short extracellular N-terminus and the ligand binds within the transmembrane domain, whereas the TAS1Rs have a large N-terminal extracellular domain composed of the Venus flytrap module that forms the orthosteric (primary) ligand binding site. Signal transduction of bitter taste involves binding of bitter compounds to TAS2Rs linked to the alpha-subunit of gustducin, a heterotrimeric G protein expressed in taste receptor cells. This G-alpha subunit stimulates phosphodiesterase and decreases cAMP and cGMP levels. Further steps in the signaling cascade is still unknown. The beta-gamma-subunit of gustducin also mediates bitter taste transduction by activating phospholipase C, which leads to an increased formation of IP3 (inositol triphosphate) and DAG (diacylglycerol), thereby causing release of Ca2+ from intracellular stores and enhanced neurotransmitter release. 288 matched cddid_all.tbl CDD cd13951 cd13951 320089 7tmF_Frizzled_SMO class F frizzled/smoothened family, member of the 7-transmembrane G protein-coupled receptor superfamily. The class F G protein-coupled receptors includes the frizzled (FZD) family of seven-transmembrane proteins consisting of 10 isoforms (FZD1-10) in mammals. The FZDs are activated by the wingless/int-1 (WNT) family of secreted lipoglycoproteins and preferentially couple to stimulatory G proteins of the Gs family, which activate adenylate cyclase, but can also couple to G proteins of the Gi/Gq families. In the WNT/beta-catenin signaling pathway, the WNT ligand binds to FZD and a lipoprotein receptor-related protein (LRP) co-receptor. This leads to the stabilization and translocation of beta-catenin to the nucleus, where it induces the activation of TCF/LEF family transcription factors. The conserved cytoplasmic motif of FZD, Lys-Thr-X-X-X-Trp, is required for activation of the WNT/beta-catenin pathway, and for membrane localization and phosphorylation of Dsh (dishevelled) protein, a key component of the WNT pathway that relays the WNT signals from the activated receptor to downstream effector proteins. Also included in the class F family is the closely related smoothened (SMO), which is a transmembrane G protein-coupled receptor that acts as the transducer of the hedgehog (HH) signaling pathway. SMO is activated by the hedgehog (HH) family of proteins acting on the 12-transmembrane domain receptor patched (PTCH), which constitutively inhibits SMO. Thus, in the absence of HH proteins, PTCH inhibits SMO signaling. On the other hand, binding of HH to the PTCH receptor activates its internalization and degradation, thereby releasing the PTCH inhibition of SMO. This allows SMO to trigger intracellular signaling and the subsequent activation of the Gli family of zinc finger transcriptional factors and induction of HH target gene expression (PTCH, Gli1, cyclin, Bcl-2, etc). The WNT and HH signaling pathways play critical roles in many developmental processes, such as cell-fate determination, cell proliferation, neural patterning, stem cell renewal, tissue homeostasis and repair, and tumorigenesis, among many others. 314 matched cddid_all.tbl CDD cd13952 cd13952 410627 7tm_classB class B family of seven-transmembrane G protein-coupled receptors. The class B of seven-transmembrane GPCRs is classified into three major subfamilies: subfamily B1 (secretin-like receptor family), B2 (adhesion family), and B3 (Methuselah-like family). The class B receptors have been identified in all the vertebrates, from fishes to mammals, as well as invertebrates including Caenorhabditis elegans and Drosophila melanogaster, but are not present in plants, fungi or prokaryotes. The B1 subfamily comprises receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, glucagon, glucagon-like peptide (GLP), calcitonin gene-related peptide, parathyroid hormone (PTH), and corticotropin-releasing factor. These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. All members of the subfamily B1 receptors preferentially couple to G proteins of G(s) family, which positively stimulate adenylate cyclase, leading to increased intracellular cAMP formation and calcium influx. The subfamily B2 consists of cell-adhesion receptors with 33 members in humans and vertebrates. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing a variety of structural motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, linked to a class B seven-transmembrane domain. These include, for example, EGF (epidermal growth factor)-like domains in CD97, Celsr1 (cadherin family member), Celsr2, Celsr3, EMR1 (EGF-module-containing mucin-like hormone receptor-like 1), EMR2, EMR3, and Flamingo; two laminin A G-type repeats and nine cadherin domains in Flamingo and its human orthologs Celsr1, Celsr2 and Celsr3; olfactomedin-like domains in the latrotoxin receptors; and five or four thrombospondin type 1 repeats in BAI1 (brain-specific angiogenesis inhibitor 1), BAI2 and BAI3. Almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. Furthermore, the subfamily B3 includes Methuselah (Mth) protein, which was originally identified in Drosophila as a GPCR affecting stress resistance and aging, and its closely related proteins. 260 matched cddid_all.tbl CDD cd13953 cd13953 320091 7tm_classC_mGluR-like metabotropic glutamate receptor-like class C family of seven-transmembrane G protein-coupled receptors superfamily. The class C GPCRs consist of glutamate receptors (mGluR1-8), the extracellular calcium-sensing receptors (caSR), the gamma-amino-butyric acid type B receptors (GABA-B), the vomeronasal type-2 pheromone receptors (V2R), the type 1 taste receptors (TAS1R), and the promiscuous L-alpha-amino acid receptor (GPRC6A), as well as several orphan receptors. Structurally, these receptors are typically composed of a large extracellular domain containing a Venus flytrap module which possesses the orthosteric agonist-binding site, a cysteine-rich domain (CRD) with the exception of GABA-B receptors, and the seven-transmembrane domains responsible for G protein activation. Moreover, the Venus flytrap module shows high structural homology with bacterial periplasmic amino acid-binding proteins, which serve as primary receptors in transport of a variety of soluble substrates such as amino acids and polysaccharides, among many others. The class C GPCRs exist as either homo- or heterodimers, which are essential for their function. The GABA-B1 and GABA-B2 receptors form a heterodimer via interactions between the N-terminal Venus flytrap modules and the C-terminal coiled-coiled domains. On the other hand, heterodimeric CaSRs and Tas1Rs and homodimeric mGluRs utilize Venus flytrap interactions and intermolecular disulphide bonds between cysteine residues located in the cysteine-rich domain (CRD), which can also acts as a molecular link to mediate the signal between the Venus flytrap and the 7TMs. Furthermore, members of the class C GPCRs bind a variety of endogenous ligands, ranging from amino acids, ions, to pheromones and sugar molecules, and play important roles in many physiological processes such as synaptic transmission, calcium homeostasis, and the sensation of sweet and umami tastes. 251 matched cddid_all.tbl CDD cd13954 cd13954 320092 7tmA_OR olfactory receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 270 matched cddid_all.tbl CDD cd13956 cd13956 260119 PT_UbiA UbiA family of prenyltransferases (PTases). Many characterized members of the UbiA prenyltransferase family are aromatic prenyltransferases and play an important role in the biosynthesis of heme, chlorophyll, vitamin E, and vitamin K. They contain two copies of a motif similar to the active site DxxD motif of trans-prenyltransferases and are potentially related. Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties onto a wide variety of substrates and play an important role in many biosynthetic pathways. 271 matched cddid_all.tbl CDD cd13957 cd13957 260120 PT_UbiA_Cox10 Protoheme IX farnesyltransferase. Protoheme IX farnesyltransferase (also called heme O synthase, heme A:farnesyltransferase, cytochrome c oxidase subunit X [Cox10]) converts heme B (protoheme IX) to heme O by substitution of the vinyl group on carbon 2 of the heme B porphyrin ring with a hydroxyethyl farnesyl side group. It is localized at the mitochondrial inner membrane. Eukaryotic Cox10 is important for the maturation of the heme A prosthetic group of cytochrome c oxidase (COX), the terminal component of the mitochondrial respiratory chain, that catalyzes the electron transfer from reduced cytochrome c to oxygen. Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties onto a wide variety of substrates and play an important role in many biosynthetic pathways. 271 matched cddid_all.tbl CDD cd13958 cd13958 260121 PT_UbiA_chlorophyll Bacteriochlorophyll/chlorophyll synthetase. Chlorophyll synthase catalyzes the last step of chlorophyll (Chl) biosynthesis, the addition of the tetraprenyl (phytyl or geranylgeranyl) side chain. In plant chloroplast, the chlorophyll synthase is located in thylakoid membrane and has been shown to also have a regulatory or channeling function. Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties onto a wide variety of substrates and play an important role in many biosynthetic pathways. 277 matched cddid_all.tbl CDD cd13959 cd13959 260122 PT_UbiA_COQ2 4-Hydroxybenzoate polyprenyltransferase. 4-Hydroxybenzoate polyprenyltransferase, also known as Coq2, catalyzes the prenylation of p-hydroxybenzoate with an all-trans polyprenyl group, an important step in ubiquinone (CoQ) biosynthesis. Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties onto a wide variety of substrates and play an important role in many biosynthetic pathways. 272 matched cddid_all.tbl CDD cd13960 cd13960 260123 PT_UbiA_HPT1 Tocopherol phytyltransferase. Tocopherol polyprenyltransferase (TPT1), also known as homogentisate phytyltransferase 1 (HPT1), tocopherol phytyltransferase, or VTE2, catalyzes the first step in the biosynthesis of the tocopherol forms of vitamin E, which involves the prenylation of homogentisate using phytyl diphosphate (PDP) as the prenyl donor. Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties onto a wide variety of substrates and play an important role in many biosynthetic pathways. 289 matched cddid_all.tbl CDD cd13961 cd13961 260124 PT_UbiA_DGGGPS Geranylgeranylglycerol-phosphate geranylgeranyltransferase. Digeranylgeranylglyceryl phosphate synthase (DGGGPS) transfers a geranylgeranyl group from geranylgeranyl diphosphate to (S)-3-O-geranylgeranylglyceryl phosphate to form (S)-2,3-di-O-geranylgeranylglyceryl phosphate, as part of the isoprenoid ether lipid biosynthesis. Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties onto a wide variety of substrates and play an important role in many biosynthetic pathways. 270 matched cddid_all.tbl CDD cd13962 cd13962 260125 PT_UbiA_UBIAD1 1,4-Dihydroxy-2-naphthoate octaprenyltransferase. Human UBIAD1 is an enzyme involved in the synthesis of MK-4. Menaquinones (MKs, also called bacterial forms) are one of the two forms of natural vitamin K, the other being the plant form, phylloquinone (PK). All forms of vitamin K have a 2-methyl-1,4-naphthoquinone (menadione; K3) ring structure in common. At the 3-position of the ring, PK has a phytyl side chain while MKs have several repeating prenyl units. Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties onto a wide variety of substrates and play an important role in many biosynthetic pathways. 283 matched cddid_all.tbl CDD cd13963 cd13963 260126 PT_UbiA_2 UbiA family of prenyltransferases (PTases), Unknown subgroup. Many characterized members of the UbiA prenyltransferase family are aromatic prenyltransferases and play an important role in the biosynthesis of heme, chlorophyll, vitamin E, and vitamin K. They contain two copies of a motif similar to the active site DxxD motif of trans-prenyltransferases and are potentially related. Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties onto a wide variety of substrates and play an important role in many biosynthetic pathways. The function of this subgroup is unknown. 278 matched cddid_all.tbl CDD cd13964 cd13964 260127 PT_UbiA_1 UbiA family of prenyltransferases (PTases), Unknown subgroup. Many characterized members of the UbiA prenyltransferase family are aromatic prenyltransferases and play an important role in the biosynthesis of heme, chlorophyll, vitamin E, and vitamin K. They contain two copies of a motif similar to the active site DxxD motif of trans-prenyltransferases and are potentially related. Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties onto a wide variety of substrates and play an important role in many biosynthetic pathways. The function of this subgroup is unknown. 282 matched cddid_all.tbl CDD cd13965 cd13965 260128 PT_UbiA_3 UbiA family of prenyltransferases (PTases), Unknown subgroup. Many characterized members of the UbiA prenyltransferase family are aromatic prenyltransferases and play an important role in the biosynthesis of heme, chlorophyll, vitamin E, and vitamin K. They contain two copies of a motif similar to the active site DxxD motif of trans-prenyltransferases and are potentially related. Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties onto a wide variety of substrates and play an important role in many biosynthetic pathways. The function of this subgroup is unknown. 273 matched cddid_all.tbl CDD cd13966 cd13966 260129 PT_UbiA_4 UbiA family of prenyltransferases (PTases), Unknown subgroup. Many characterized members of the UbiA prenyltransferase family are aromatic prenyltransferases and play an important role in the biosynthesis of heme, chlorophyll, vitamin E, and vitamin K. They contain two copies of a motif similar to the active site DxxD motif of trans-prenyltransferases and are potentially related. Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties onto a wide variety of substrates and play an important role in many biosynthetic pathways. The function of this subgroup is unknown. 272 matched cddid_all.tbl CDD cd13967 cd13967 260130 PT_UbiA_5 UbiA family of prenyltransferases (PTases), Unknown subgroup. Many characterized members of the UbiA prenyltransferase family are aromatic prenyltransferases and play an important role in the biosynthesis of heme, chlorophyll, vitamin E, and vitamin K. They contain two copies of a motif similar to the active site DxxD motif of trans-prenyltransferases and are potentially related. Prenyltransferases (PTs) catalyze the regioselective transfer of prenyl moieties onto a wide variety of substrates and play an important role in many biosynthetic pathways. The function of this subgroup is unknown. 277 matched cddid_all.tbl CDD cd13968 cd13968 270870 PKc_like Catalytic domain of the Protein Kinase superfamily. The PK superfamily contains the large family of typical PKs that includes serine/threonine kinases (STKs), protein tyrosine kinases (PTKs), and dual-specificity PKs that phosphorylate both serine/threonine and tyrosine residues of target proteins, as well as pseudokinases that lack crucial residues for catalytic activity and/or ATP binding. It also includes phosphoinositide 3-kinases (PI3Ks), aminoglycoside 3'-phosphotransferases (APHs), choline kinase (ChoK), Actin-Fragmin Kinase (AFK), and the atypical RIO and Abc1p-like protein kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to their target substrates; these include serine/threonine/tyrosine residues in proteins for typical or atypical PKs, the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives for PI3Ks, the 4-hydroxyl of PtdIns for PI4Ks, and other small molecule substrates for APH/ChoK and similar proteins such as aminoglycosides, macrolides, choline, ethanolamine, and homoserine. 136 matched cddid_all.tbl CDD cd13969 cd13969 270871 ADCK1-like aarF domain containing kinase 1 and similar proteins. This subfamily is composed of uncharacterized ABC1 kinase-like proteins including the human protein called aarF domain containing kinase 1 (ADCK1). Eukaryotes contain at least three ABC1-like proteins: in humans, these are ADCK3 and the putative protein kinases named ADCK1 and ADCK2. Yeast Abc1p and its human homolog ADCK3 are atypical protein kinases required for the biosynthesis of Coenzyme Q (ubiquinone or Q), which is an essential lipid component in respiratory electron and proton transport. In algae and higher plants, ABC1 kinases have proliferated to more than 15 subfamilies, most of which are located in plastids or mitochondria. Plant subfamilies 14 and 15 (ABC1K14-15) belong to the same group of ABC1 kinases as human ADCK1. ABC1 kinases are not related to the ATP-binding cassette (ABC) membrane transporter family. 253 matched cddid_all.tbl CDD cd13970 cd13970 270872 ABC1_ADCK3 Activator of bc1 complex (ABC1) kinases, also called aarF domain containing kinase 3. This subfamily is composed of the atypical yeast protein kinase Abc1p, its human homolog ADCK3 (also called CABC1), and similar proteins. Abc1p (also called Coq8p) is required for the biosynthesis of Coenzyme Q (ubiquinone or Q), which is an essential lipid component in respiratory electron and proton transport. It is necessary for the formation of a multi-subunit Q-biosynthetic complex and may also function in the regulation of Q synthesis. Human ADCK3 is able to rescue defects in Q synthesis and the phosphorylation state of Coq proteins in yeast Abc1 (or Coq8) mutants. Mutations in ADCK3 cause progressive cerebellar ataxia and atrophy due to Q10 deficiency. In algae and higher plants, ABC1 kinases have proliferated to more than 15 subfamilies, most of which are located in plastids or mitochondria. Subfamily 13 (ABC1K13) of plant ABC1 kinases belongs in this subfamily with yeast Abc1p and human ADCK3. ABC1 kinases are not related to the ATP-binding cassette (ABC) membrane transporter family. 251 matched cddid_all.tbl CDD cd13971 cd13971 270873 ADCK2-like aarF domain containing kinase 2 and similar proteins. This subfamily is composed of uncharacterized ABC1 kinase-like proteins including the human protein called aarF domain containing kinase 2 (ADCK2). Eukaryotes contain at least three ABC1-like proteins; in humans, these are ADCK3 and the putative protein kinases named ADCK1 and ADCK2. Yeast Abc1p and its human homolog ADCK3 are atypical protein kinases required for the biosynthesis of Coenzyme Q (ubiquinone or Q), which is an essential lipid component in respiratory electron and proton transport. In algae and higher plants, ABC1 kinases have proliferated to more than 15 subfamilies, most of which are located in plastids or mitochondria. Plant subfamily 10 (ABC1K10) belong to the same group of ABC1 kinases as human ADCK2. ABC1 kinases are not related to the ATP-binding cassette (ABC) membrane transporter family. 298 matched cddid_all.tbl CDD cd13972 cd13972 270874 UbiB Ubiquinone biosynthetic protein UbiB. UbiB is the prokaryotic homolog of yeast Abc1p and human ADCK3 (aarF domain containing kinase 3). It is required for the biosynthesis of Coenzyme Q (ubiquinone or Q), which is an essential lipid component in respiratory electron and proton transport. It is required in the first monooxygenase step in Q biosynthesis. Mutant strains with disrupted ubiB genes lack Q and accumulate octaprenylphenol, a Q biosynthetic intermediate. 247 matched cddid_all.tbl CDD cd13973 cd13973 270875 PK_MviN-like Pseudokinase domain of the peptidoglycan biosynthetic protein MviN. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. This family is composed of the mycobacterial protein MviN and similar proteins. MviN is an integral membrane protein that is essential for growth and is required for cell wall integrity and peptidogylcan (PG) biosynthesis. It comprises of 14 predicted transmembrane (TM) helices at the N-terminus, followed by an intracellular pseudokinase domain linked through a single TM helix to a carbohydrate binding extracellular domain. Phosphorylation of the MviN pseudokinase domain by the PG-sensitive serine/threonine protein kinase PknB recruits a forkhead associated (FHA) domain protein FhaA, which modulates local PG synthesis at cell poles and the septum. The MviN pseudokinase forms a canonical receptor kinase dimer. 236 matched cddid_all.tbl CDD cd13974 cd13974 270876 STKc_SHIK Catalytic domain of the Serine/Threonine kinase, SINK-homologous inhibitory kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. SHIK, also referred to as STK40 or LYK4, is a cytoplasmic and nuclear protein that is involved in the negative regulation of NF-kappaB- and p53-mediated transcription. It was identified as a protein related to SINK, a p65-interacting protein that inhibits p65 phosphorylation by the catalytic subunit of PKA, thereby inhibiting transcriptional competence of NF-kappaB. The SHIK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 290 matched cddid_all.tbl CDD cd13975 cd13975 270877 PKc_Dusty Catalytic domain of the Dual-specificity Protein Kinase, Dusty. Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine as well as tyrosine residues on protein substrates. Dusty protein kinase is also called Receptor-interacting protein kinase 5 (RIPK5 or RIP5) or RIP-homologous kinase. It is widely distributed in the central nervous system, and may be involved in inducing both caspase-dependent and caspase-independent cell death. The Dusty subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine PKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 262 matched cddid_all.tbl CDD cd13976 cd13976 270878 PK_TRB Pseudokinase domain of Tribbles Homolog proteins. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. Tribbles Homolog (TRB) proteins interact with many proteins involved in signaling pathways. They play scaffold-like regulatory functions and affect many cellular processes such as mitosis, apoptosis, differentiation, and gene expression. TRB proteins bind to the middle kinase in mitogen activated protein kinase (MAPK) signaling cascades, MAPK kinases. They regulate the activity of MAPK kinases, and thus, affect MAPK signaling. In Drosophila, Tribbles regulates String, the ortholog of mammalian Cdc25, during morphogenesis. String is implicated in the progression of mitosis during embryonic development. Vertebrates contain three TRB proteins encoded by three separate genes: Tribbles-1 (TRB1 or TRIB1), Tribbles-2 (TRB2 or TRIB2), and Tribbles-3 (TRB3 or TRIB3). The TRB subfamily is part of a larger superfamily that includes the catalytic domains of serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 242 matched cddid_all.tbl CDD cd13977 cd13977 270879 STKc_PDIK1L Catalytic domain of the Serine/Threonine kinase, PDLIM1 interacting kinase 1 like. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PDIK1L is also called STK35 or CLIK-1. It is predominantly a nuclear protein which is capable of autophosphorylation. Through its interaction with the PDZ-LIM protein CLP-36, it is localized to actin stress fibers. The PDIK1L subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). 322 matched cddid_all.tbl CDD cd13978 cd13978 270880 STKc_RIP Catalytic domain of the Serine/Threonine kinase, Receptor Interacting Protein. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. RIP kinases serve as essential sensors of cellular stress. They are involved in regulating NF-kappaB and MAPK signaling, and are implicated in mediating cellular processes such as apoptosis, necroptosis, differentiation, and survival. RIP kinases contain a homologous N-terminal kinase domain and varying C-terminal domains. Higher vertebrates contain multiple RIP kinases, with mammals harboring at least five members. RIP1 and RIP2 harbor C-terminal domains from the Death domain (DD) superfamily while RIP4 contains ankyrin (ANK) repeats. RIP3 contain a RIP homotypic interaction motif (RHIM) that facilitates binding to RIP1. RIP1 and RIP3 are important in apoptosis and necroptosis, while RIP2 and RIP4 play roles in keratinocyte differentiation and inflammatory immune responses. The RIP subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 263 matched cddid_all.tbl CDD cd13979 cd13979 270881 STKc_Mos Catalytic domain of the Serine/Threonine kinase, Oocyte maturation factor Mos. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Mos (or c-Mos) is a germ-cell specific kinase that plays roles in both the release of primary arrest and the induction of secondary arrest in oocytes. It is expressed towards the end of meiosis I and is quickly degraded upon fertilization. It is a component of the cytostatic factor (CSF), which is responsible for metaphase II arrest. In addition, Mos activates a phoshorylation cascade that leads to the activation of the p34 subunit of MPF (mitosis-promoting factor or maturation promoting factor), a cyclin-dependent kinase that is responsible for the release of primary arrest in meiosis I. The Mos subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 265 matched cddid_all.tbl CDD cd13980 cd13980 270882 STKc_Vps15 Catalytic domain of the Serine/Threonine kinase, Vacuolar protein sorting-associated protein 15. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Vps15 is a large protein consisting of an N-terminal kinase domain, a C-terminal WD-repeat containing domain, and an intermediate bridge domain that contain HEAT repeats. The kinase domain is necessary for the signaling functions of Vps15. Human Vps15 was previously called p150. It associates and regulates Vps34, also called Class III phosphoinositide 3-kinase (PI3K), which catalyzes the phosphorylation of D-myo-phosphatidylinositol (PtdIns). Vps34 is the only PI3K present in yeast. It plays an important role in the regulation of protein and vesicular trafficking and sorting, autophagy, trimeric G-protein signaling, and phagocytosis. The Vps15 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and PI3K. 278 matched cddid_all.tbl CDD cd13981 cd13981 270883 STKc_Bub1_BubR1 Catalytic domain of the Serine/Threonine kinases, Spindle assembly checkpoint proteins Bub1 and BubR1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of Bub1 (Budding uninhibited by benzimidazoles 1), BubR1, and similar proteins. They contain an N-terminal Bub1/Mad3 homology domain essential for Cdc20 binding and a C-terminal kinase domain. Bub1 and BubR1 are involved in SAC, a surveillance system that delays metaphase to anaphase transition by blocking the activity of APC/C (the anaphase promoting complex) until all chromosomes achieve proper attachments to the mitotic spindle, to avoid chromosome missegregation. Impaired SAC leads to genomic instabilities and tumor development. Bub1 and BubR1 facilitate the localization of SAC proteins to kinetochores and regulate kinetochore-microtubule (K-MT) attachments. Repression studies of Bub1 and BubR1 show that they exert an additive effect in misalignment phenotypes and may function cooperatively or in parallel pathways in regulating K-MT attachments. The Bub1/BubR1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 298 matched cddid_all.tbl CDD cd13982 cd13982 270884 STKc_IRE1 Catalytic domain of the Serine/Threonine kinase, Inositol-requiring protein 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. IRE1, also called Endoplasmic reticulum (ER)-to-nucleus signaling protein (or ERN), is an ER-localized type I transmembrane protein with kinase and endoribonuclease domains in the cytoplasmic side. It acts as an ER stress sensor and is the oldest and most conserved component of the unfolded protein response (UPR) in eukaryotes. The UPR is activated when protein misfolding is detected in the ER in order to decrease the synthesis of new proteins and increase the capacity of the ER to cope with the stress. During ER stress, IRE1 dimerizes and forms oligomers, allowing the kinase domain to undergo trans-autophosphorylation. This leads to a conformational change that stimulates its endoribonuclease activity and results in the cleavage of its mRNA substrate, HAC1 in yeast and XBP1 in metazoans, promoting a splicing event that enables translation into a transcription factor which activates the UPR. Mammals contain two IRE1 proteins, IRE1alpha (or ERN1) and IRE1beta (or ERN2). The Ire1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 269 matched cddid_all.tbl CDD cd13983 cd13983 270885 STKc_WNK Catalytic domain of the Serine/Threonine kinase, With No Lysine (WNK) kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. WNKs comprise a subfamily of STKs with an unusual placement of a catalytic lysine relative to all other protein kinases. They are critical in regulating ion balance and are thus, important components in the control of blood pressure. They are also involved in cell signaling, survival, proliferation, and organ development. WNKs are activated by hyperosmotic or low-chloride hypotonic stress and they function upstream of SPAK and OSR1 kinases, which regulate the activity of cation-chloride cotransporters through direct interaction and phosphorylation. There are four vertebrate WNKs which show varying expression patterns. WNK1 and WNK2 are widely expressed while WNK3 and WNK4 show a more restricted expression pattern. Because mutations in human WNK1 and WNK4 cause PseudoHypoAldosteronism type II (PHAII), characterized by hypertension (due to increased sodium reabsorption) and hyperkalemia (due to impaired renal potassium secretion), there are more studies conducted on these two proteins, compared to WNK2 and WNK3. The WNK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 258 matched cddid_all.tbl CDD cd13984 cd13984 270886 PK_NRBP1_like Pseudokinase domain of Nuclear Receptor Binding Protein 1 and similar proteins. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity and/or ATP binding. This subfamily is composed of NRBP1, also called MLF1-adaptor molecule (MADM), and MADML. NRBP1 was originally named based on the presence of nuclear binding and localization motifs prior to functional analyses. It is expressed ubiquitously and is found to localize in the cytoplasm, not the nucleus. NRBP1 is an adaptor protein that interacts with myeloid leukemia factor 1 (MLF1), an oncogene that enhances myeloid development of hematopoietic cells. It also interacts with the small GTPase Rac3. NRBP1 may also be involved in Golgi to ER trafficking. MADML (for MADM-Like) has been shown to be expressed throughout development in Xenopus laevis with highest expression found in the developing lens and retina. The NRBP1-like subfamily is part of a larger superfamily that includes the catalytic domains of serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd13985 cd13985 270887 STKc_GAK_like Catalytic domain of cyclin G-Associated Kinase-like proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily includes cyclin G-Associated Kinase (GAK), Drosophila melanogaster Numb-Associated Kinase (NAK)-like proteins, and similar protein kinases. GAK plays regulatory roles in clathrin-mediated membrane trafficking, the maintenance of centrosome integrity and chromosome congression, neural patterning, survival of neurons, and immune responses. NAK plays a role in asymmetric cell division through its association with Numb. It also regulates the localization of Dlg, a protein essential for septate junction formation. The GAK-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 272 matched cddid_all.tbl CDD cd13986 cd13986 270888 STKc_16 Catalytic domain of Serine/Threonine Kinase 16. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. STK16 is associated with many names including Myristylated and Palmitylated Serine/threonine Kinase 1 (MPSK1), Kinase related to cerevisiae and thaliana (Krct), and Protein Kinase expressed in day 12 fetal liver (PKL12). It is widely expressed in mammals with highest levels found in liver, testis, and kidney. It is localized in the Golgi but is translocated to the nucleus upon disorganization of the Golgi. STK16 is constitutively active and is capable of phosphorylating itself and other substrates. It may be involved in regulating stromal-epithelial interactions during mammary gland ductal morphogenesis. It may also function as a transcriptional co-activator of type-C natriuretic peptide and VEGF. The STK16 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 282 matched cddid_all.tbl CDD cd13987 cd13987 270889 STKc_SBK1 Catalytic domain of the Serine/Threonine kinase, SH3 Binding Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. SBK1, also called BSK146, is predominantly expressed in the brain. Its expression is increased in the developing brain during the late embryonic stage, coinciding with dramatic neuronal proliferation, migration, and maturation. SBK1 may play an important role in regulating brain development. The SBK1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 259 matched cddid_all.tbl CDD cd13988 cd13988 270890 STKc_TBK1 Catalytic domain of the Serine/Threonine kinase, TANK Binding Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TBK1 is also called T2K and NF-kB-activating kinase. It is widely expressed in most cell types and acts as an IkappaB kinase (IKK)-activating kinase responsible for NF-kB activation in response to growth factors. It plays a role in modulating inflammatory responses through the NF-kB pathway. TKB1 is also a major player in innate immune responses since it functions as a virus-activated kinase necessary for establishing an antiviral state. It phosphorylates IRF-3 and IRF-7, which are important transcription factors for inducing type I interferon during viral infection. In addition, TBK1 may also play roles in cell transformation and oncogenesis. The TBK1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 316 matched cddid_all.tbl CDD cd13989 cd13989 270891 STKc_IKK Catalytic domain of the Serine/Threonine kinase, Inhibitor of Nuclear Factor-KappaB Kinase (IKK). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The IKK complex functions as a master regulator of Nuclear Factor-KappaB (NF-kB) proteins, a family of transcription factors which are critical in many cellular functions including inflammatory responses, immune development, cell survival, and cell proliferation, among others. It is composed of two kinases, IKKalpha and IKKbeta, and the regulatory subunit IKKgamma or NEMO (NF-kB Essential MOdulator). IKKs facilitate the release of NF-kB dimers from an inactive state, allowing them to migrate to the nucleus where they regulate gene transcription. There are two IKK pathways that regulate NF-kB signaling, called the classical (involving IKKbeta and NEMO) and non-canonical (involving IKKalpha) pathways. The classical pathway regulates the majority of genes activated by NF-kB. The IKK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). 289 matched cddid_all.tbl CDD cd13990 cd13990 270892 STKc_TLK Catalytic domain of the Serine/Threonine kinase, Tousled-Like Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TLKs play important functions during the cell cycle and are implicated in chromatin remodeling, DNA replication and repair, and mitosis. They phosphorylate and regulate Anti-silencing function 1 protein (Asf1), a histone H3/H4 chaperone that helps facilitate the assembly of chromatin following DNA replication during S phase. TLKs also phosphorylate the H3 histone tail and are essential in transcription. Vertebrates contain two subfamily members, TLK1 and TLK2. The TLK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 279 matched cddid_all.tbl CDD cd13991 cd13991 270893 STKc_NIK Catalytic domain of the Serine/Threonine kinase, NF-kappaB Inducing Kinase (NIK). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. NIK, also called mitogen activated protein kinase kinase kinase 14 (MAP3K14), phosphorylates and activates Inhibitor of NF-KappaB Kinase (IKK) alpha, which is a regulator of NF-kB proteins, a family of transcription factors which are critical in many cellular functions including inflammatory responses, immune development, cell survival, and cell proliferation, among others. NIK is essential in the IKKalpha-mediated non-canonical NF-kB signaling pathway, in which IKKalpha processes the IkB-like C-terminus of NF-kB2/p100 to produce p52, allowing the p52/RelB dimer to migrate to the nucleus where it regulates gene transcription. NIK also plays an important role in Toll-like receptor 7/9 signaling cascades. The NIK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 268 matched cddid_all.tbl CDD cd13992 cd13992 270894 PK_GC Pseudokinase domain of membrane Guanylate Cyclase receptors. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. Membrane (or particulate) GCs consist of an extracellular ligand-binding domain, a single transmembrane region, and an intracellular tail that contains a PK-like domain, an amphiphatic region and a catalytic GC domain that catalyzes the conversion of GTP into cGMP and pyrophosphate. Membrane GCs act as receptors that transduce an extracellular signal to the intracellular production of cGMP, which has been implicated in many processes including cell proliferation, phototransduction, and muscle contractility, through its downstream effectors such as PKG. The PK-like domain of GCs lack a critical aspartate involved in ATP binding and does not exhibit kinase activity. It functions as a negative regulator of the catalytic GC domain and may also act as a docking site for interacting proteins such as GC-activating proteins. The GC subfamily is part of a larger superfamily that includes the catalytic domains of protein serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 268 matched cddid_all.tbl CDD cd13993 cd13993 270895 STKc_Pat1_like Catalytic domain of Fungal Pat1-like Serine/Threonine kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of Schizosaccharomyces pombe Pat1 (also called Ran1), Saccharomyces cerevisiae VHS1 and KSP1, and similar fungal STKs. Pat1 blocks Mei2, an RNA-binding protein which is indispensable in the initiation of meiosis. Pat1 is inactivated and Mei2 activated, which initiates meiosis, under nutrient-deprived conditions through a signaling cascade involving Ste11. Meiosis induced by Pat1 inactivation may show different characteristics than normal meiosis including aberrant positioning of centromeres. VHS1 was identified in a screen for suppressors of cell cycle arrest at the G1/S transition, while KSP1 may be involved in regulating PRP20, which is required for mRNA export and maintenance of nuclear structure. The Pat1-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 267 matched cddid_all.tbl CDD cd13994 cd13994 270896 STKc_HAL4_like Catalytic domain of Fungal Halotolerance protein 4-like Serine/Threonine kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of HAL4, Saccharomyces cerevisiae Ptk2/Stk2, and similar fungal proteins. Proteins in this subfamily are involved in regulating ion transporters. In budding and fission yeast, HAL4 promotes potassium ion uptake, which increases cellular resistance to other cations such as sodium, lithium, and calcium ions. HAL4 stabilizes the major high-affinity K+ transporter Trk1 at the plasma membrane under low K+ conditions, which prevents endocytosis and vacuolar degradation. Budding yeast Ptk2 phosphorylates and regulates the plasma membrane H+ ATPase, Pma1. The HAL4-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 265 matched cddid_all.tbl CDD cd13995 cd13995 270897 STKc_MAP3K8 Catalytic domain of the Serine/Threonine kinase, Mitogen-Activated Protein Kinase (MAPK) Kinase Kinase 8. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MAP3K8 is also called Tumor progression locus 2 (Tpl2) or Cancer Osaka thyroid (Cot), and was first identified as a proto-oncogene in T-cell lymphoma induced by MoMuL virus and in breast carcinoma induced by MMTV. Activated MAP3K8 induces various MAPK pathways including Extracellular Regulated Kinase (ERK) 1/2, c-Jun N-terminal kinase (JNK), and p38. It plays a pivotal role in innate immunity, linking Toll-like receptors to the production of TNF and the activation of ERK in macrophages. It is also required in interleukin-1beta production and is critical in host defense against Gram-positive bacteria. MAP3Ks (MKKKs or MAPKKKs) phosphorylate and activate MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. The MAP3K8 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd13996 cd13996 270898 STKc_EIF2AK Catalytic domain of the Serine/Threonine kinase, eukaryotic translation Initiation Factor 2-Alpha Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. EIF2AKs phosphorylate the alpha subunit of eIF-2, resulting in the downregulation of protein synthesis. eIF-2 phosphorylation is induced in response to cellular stresses including virus infection, heat shock, nutrient deficiency, and the accummulation of unfolded proteins, among others. There are four distinct kinases that phosphorylate eIF-2 and control protein synthesis under different stress conditions: General Control Non-derepressible-2 (GCN2) which is activated during amino acid or serum starvation; protein kinase regulated by RNA (PKR) which is activated by double stranded RNA; heme-regulated inhibitor kinase (HRI) which is activated under heme-deficient conditions; and PKR-like endoplasmic reticulum kinase (PERK) which is activated when misfolded proteins accumulate in the ER. The EIF2AK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 273 matched cddid_all.tbl CDD cd13997 cd13997 270899 PKc_Wee1_like Catalytic domain of the Wee1-like Protein Kinases. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine or tyrosine residues on protein substrates. This subfamily is composed of the dual-specificity kinase Myt1, the protein tyrosine kinase Wee1, and similar proteins. These proteins are cell cycle checkpoint kinases that are involved in the regulation of cyclin-dependent kinase CDK1, the master engine for mitosis. CDK1 is kept inactivated through phosphorylation of N-terminal thr (T14 by Myt1) and tyr (Y15 by Myt1 and Wee1) residues. Mitosis progression is ensured through activation of CDK1 by dephoshorylation and inactivation of Myt1/Wee1. The Wee1-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine PKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 252 matched cddid_all.tbl CDD cd13998 cd13998 270900 STKc_TGFbR-like Catalytic domain of Transforming Growth Factor beta Receptor-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of receptors for the TGFbeta family of secreted signaling molecules including TGFbeta, bone morphogenetic proteins (BMPs), activins, growth and differentiation factors (GDFs), and anti-Mullerian hormone, among others. These receptors contain an extracellular domain that binds ligands, a single transmembrane (TM) region, and a cytoplasmic catalytic kinase domain. There are two types of TGFbeta receptors included in this subfamily, I and II, that play different roles in signaling. For signaling to occur, the ligand first binds to the high-affinity type II receptor, which is followed by the recruitment of the low-affinity type I receptor to the complex and its activation through trans-phosphorylation by the type II receptor. The active type I receptor kinase starts intracellular signaling to the nucleus by phosphorylating SMAD proteins. Type I receptors contain an additional domain located between the TM and kinase domains called the the GS domain, which contains the activating phosphorylation site and confers preference for specific SMAD proteins. Different ligands interact with various combinations of types I and II receptors to elicit a specific signaling pathway. Activins primarily signal through combinations of ACVR1b/ALK7 and ACVR2a/b; myostatin and GDF11 through TGFbR1/ALK4 and ACVR2a/b; BMPs through ACVR1/ALK1 and BMPR2; and TGFbeta through TGFbR1 and TGFbR2. The TGFbR-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 289 matched cddid_all.tbl CDD cd13999 cd13999 270901 STKc_MAP3K-like Catalytic domain of Mitogen-Activated Protein Kinase (MAPK) Kinase Kinase-like Serine/Threonine kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed mainly of MAP3Ks and similar proteins, including TGF-beta Activated Kinase-1 (TAK1, also called MAP3K7), MAP3K12, MAP3K13, Mixed lineage kinase (MLK), MLK-Like mitogen-activated protein Triple Kinase (MLTK), and Raf (Rapidly Accelerated Fibrosarcoma) kinases. MAP3Ks (MKKKs or MAPKKKs) phosphorylate and activate MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. Also included in this subfamily is the pseudokinase Kinase Suppressor of Ras (KSR), which is a scaffold protein that functions downstream of Ras and upstream of Raf in the Extracellular signal-Regulated Kinase (ERK) pathway. 245 matched cddid_all.tbl CDD cd14000 cd14000 270902 STKc_LRRK Catalytic domain of the Serine/Threonine kinase, Leucine-Rich Repeat Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. LRRKs are also classified as ROCO proteins because they contain a ROC (Ras of complex proteins)/GTPase domain followed by a COR (C-terminal of ROC) domain of unknown function. In addition, LRRKs contain a catalytic kinase domain and protein-protein interaction motifs including a WD40 domain, LRRs and ankyrin (ANK) repeats. LRRKs possess both GTPase and kinase activities, with the ROC domain acting as a molecular switch for the kinase domain, cycling between a GTP-bound state which drives kinase activity and a GDP-bound state which decreases the activity. Vertebrates contain two members, LRRK1 and LRRK2, which show complementary expression in the brain. Mutations in LRRK2 are linked to both familial and sporadic forms of Parkinson's disease. The normal roles of LRRKs are not clearly defined. They may be involved in mitogen-activated protein kinase (MAPK) pathways, protein translation control, programmed cell death pathways, and cytoskeletal dynamics. The LRRK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 275 matched cddid_all.tbl CDD cd14001 cd14001 270903 PKc_TOPK Catalytic domain of the Dual-specificity protein kinase, Lymphokine-activated killer T-cell-originated protein kinase. Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine as well as tyrosine residues on protein substrates. TOPK, also called PDZ-binding kinase (PBK), is activated at the early stage of mitosis and plays a critical role in cytokinesis. It partly functions as a mitogen-activated protein kinase (MAPK) kinase and is capable of phosphorylating p38, JNK1, and ERK2. TOPK also plays a role in DNA damage sensing and repair through its phosphorylation of histone H2AX. It contributes to cancer development and progression by downregulating the function of tumor suppressor p53 and reducing cell-cycle regulatory proteins. TOPK is found highly expressed in breast and skin cancer cells. The TOPK subfamily is part of a larger superfamily that includes the catalytic domains of other protein kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 292 matched cddid_all.tbl CDD cd14002 cd14002 270904 STKc_STK36 Catalytic domain of Serine/Threonine Kinase 36. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. STK36, also called Fused (or Fu) kinase, is involved in the Hedgehog signaling pathway. It is activated by the Smoothened (SMO) signal transducer, resulting in the stabilization of GLI transcription factors and the phosphorylation of SUFU to facilitate the nuclear accumulation of GLI. In Drosophila, Fused kinase is maternally required for proper segmentation during embryonic development and for the development of legs and wings during the larval stage. In mice, STK36 is not necessary for embryonic development, although mice deficient in STK36 display growth retardation postnatally. The STK36 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 253 matched cddid_all.tbl CDD cd14003 cd14003 270905 STKc_AMPK-like Catalytic domain of AMP-activated protein kinase-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The AMPK-like subfamily is composed of AMPK, MARK, BRSK, NUAK, MELK, SNRK, TSSK, and SIK, among others. LKB1 serves as a master upstream kinase that activates AMPK and most AMPK-like kinases. AMPK, also called SNF1 (sucrose non-fermenting1) in yeasts and SnRK1 (SNF1-related kinase1) in plants, is a heterotrimeric enzyme composed of a catalytic alpha subunit and two regulatory subunits, beta and gamma. It is a stress-activated kinase that serves as master regulator of glucose and lipid metabolism by monitoring carbon and energy supplies, via sensing the cell's AMP:ATP ratio. MARKs phosphorylate tau and related microtubule-associated proteins (MAPs), and regulates microtubule-based intracellular transport. They are involved in embryogenesis, epithelial cell polarization, cell signaling, and neuronal differentiation. BRSKs play important roles in establishing neuronal polarity. TSSK proteins are almost exclusively expressed postmeiotically in the testis and play important roles in spermatogenesis and/or spermiogenesis. The AMPK-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 252 matched cddid_all.tbl CDD cd14004 cd14004 270906 STKc_PASK Catalytic domain of the Serine/Threonine kinase, Per-ARNT-Sim (PAS) domain Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PASK (or PASKIN) is a nutrient and energy sensor and thus, plays an important role in maintaining cellular energy homeostasis. It coordinates the utilization of glucose in response to metabolic demand. It contains an N-terminal PAS domain which directly interacts and inhibits a C-terminal catalytic kinase domain. The PAS domain serves as a sensory module for different environmental signals such as light, redox state, and various metabolites. Binding of ligands to the PAS domain causes structural changes which leads to kinase activation and the phosphorylation of substrates to trigger the appropriate cellular response. The PASK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd14005 cd14005 270907 STKc_PIM Catalytic domain of the Serine/Threonine kinase, Proviral Integration Moloney virus (PIM) kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The PIM gene locus was discovered as a result of the cloning of retroviral intergration sites in murine Moloney leukemia virus, leading to the identification of PIM kinases. They are constitutively active STKs with a broad range of cellular targets and are overexpressed in many haematopoietic malignancies and solid cancers. Vertebrates contain three distinct PIM kinase genes (PIM1-3); each gene may result in mutliple protein isoforms. There are two PIM1 and three PIM2 isoforms as a result of alternative translation initiation sites, while there is only one PIM3 protein. Compound knockout mice deficient of all three PIM kinases that survive the perinatal period show a profound reduction in body size, indicating that PIMs are important for body growth. The PIM subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 255 matched cddid_all.tbl CDD cd14006 cd14006 270908 STKc_MLCK-like Catalytic kinase domain of Myosin Light Chain Kinase-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This family is composed of MLCKs and related MLCK-like kinase domains from giant STKs such as titin, obscurin, SPEG, Unc-89, Trio, kalirin, and Twitchin. Also included in this family are Death-Associated Protein Kinases (DAPKs) and Death-associated protein kinase-Related Apoptosis-inducing protein Kinase (DRAKs). MLCK phosphorylates myosin regulatory light chain and controls the contraction of all muscle types. Titin, obscurin, Twitchin, and SPEG are muscle proteins involved in the contractile apparatus. The giant STKs are multidomain proteins containing immunoglobulin (Ig), fibronectin type III (FN3), SH3, RhoGEF, PH and kinase domains. Titin, obscurin, Twitchin, and SPEG contain many Ig domain repeats at the N-terminus, while Trio and Kalirin contain spectrin-like repeats. The MLCK-like family is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 247 matched cddid_all.tbl CDD cd14007 cd14007 270909 STKc_Aurora Catalytic domain of the Serine/Threonine kinase, Aurora kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Aurora kinases are key regulators of mitosis and are essential for the accurate and equal division of genomic material from parent to daughter cells. Yeast contains only one Aurora kinase while most higher eukaryotes have two. Vertebrates contain at least 2 Aurora kinases (A and B); mammals contains a third Aurora kinase gene (C). Aurora-A regulates cell cycle events from the late S-phase through the M-phase including centrosome maturation, mitotic entry, centrosome separation, spindle assembly, chromosome alignment, cytokinesis, and mitotic exit. Aurora-A activation depends on its autophosphorylation and binding to the microtubule-associated protein TPX2. Aurora-B is most active at the transition during metaphase to the end of mitosis. It is critical for accurate chromosomal segregation, cytokinesis, protein localization to the centrosome and kinetochore, correct microtubule-kinetochore attachments, and regulation of the mitotic checkpoint. Aurora-C is mainly expressed in meiotically dividing cells; it was originally discovered in mice as a testis-specific STK called Aie1. Both Aurora-B and -C are chromosomal passenger proteins that can form complexes with INCENP and survivin, and they may have redundant cellular functions. The Aurora subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 253 matched cddid_all.tbl CDD cd14008 cd14008 270910 STKc_LKB1_CaMKK Catalytic domain of the Serine/Threonine kinases, Liver Kinase B1, Calmodulin Dependent Protein Kinase Kinase, and similar proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Both LKB1 and CaMKKs can phosphorylate and activate AMP-activated protein kinase (AMPK). LKB1, also called STK11, serves as a master upstream kinase that activates AMPK and most AMPK-like kinases. LKB1 and AMPK are part of an energy-sensing pathway that links cell energy to metabolism and cell growth. They play critical roles in the establishment and maintenance of cell polarity, cell proliferation, cytoskeletal organization, as well as T-cell metabolism, including T-cell development, homeostasis, and effector function. CaMKKs are upstream kinases of the CaM kinase cascade that phosphorylate and activate CaMKI and CamKIV. They may also phosphorylate other substrates including PKB and AMPK. Vertebrates contain two CaMKKs, CaMKK1 (or alpha) and CaMKK2 (or beta). CaMKK1 is involved in the regulation of glucose uptake in skeletal muscles. CaMKK2 is involved in regulating energy balance, glucose metabolism, adiposity, hematopoiesis, inflammation, and cancer. The LKB1/CaMKK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 267 matched cddid_all.tbl CDD cd14009 cd14009 270911 STKc_ATG1_ULK_like Catalytic domain of the Serine/Threonine kinases, Autophagy-related protein 1 and Unc-51-like kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily includes yeast ATG1 and metazoan homologs including vertebrate ULK1-3. The ATG1/ULK complex is conserved from yeast to humans and it plays a critical role in the initiation of autophagy, the intracellular system that leads to the lysosomal degradation of cellular components and their recycling into basic metabolic units. It is involved in nutrient sensing and signaling, the assembly of autophagy factors and the execution of autophagy. In metazoans, ATG1 homologs display additional functions. Unc-51 and ULKs have been implicated in neuronal and axonal development. The ATG1/ULK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 251 matched cddid_all.tbl CDD cd14010 cd14010 270912 STKc_ULK4 Catalytic domain of the Serine/Threonine kinase, Unc-51-like kinase 4. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. ULK4 is a functionally uncharacterized kinase that shows similarity to ATG1/ULKs. The ATG1/ULK complex is conserved from yeast to humans and it plays a critical role in the initiation of autophagy, the intracellular system that leads to the lysosomal degradation of cellular components and their recycling into basic metabolic units. The ULK4 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 269 matched cddid_all.tbl CDD cd14011 cd14011 270913 PK_SCY1_like Pseudokinase domain of Scy1-like proteins. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. This subfamily is composed of the catalytically inactive kinases with similarity to yeast Scy1. It includes four mammalian proteins called SCY1-like protein 1 (SCYL1), SCYL2, SCYL3, as well as Testis-EXpressed protein 14 (TEX14). SCYL1 binds to and co-localizes with the membrane trafficking coatomer I (COPI) complex, and regulates COPI-mediated vesicle trafficking. Null mutations in the SCYL1 gene are responsible for the pathology in mdf (muscle-deficient) mice which display progressive motor neuropathy. SCYL2, also called coated vesicle-associated kinase of 104 kDa (CVAK104), is involved in the trafficking of clathrin-coated vesicles. It also binds the HIV-1 accessory protein Vpu and acts as a regulatory factor that promotes the dephosphorylation of Vpu, facilitating the restriction of HIV-1 release. SCYL3, also called ezrin-binding protein PACE-1, may be involved in regulating cell adhesion and migration. TEX14 is required for spermatogenesis and male fertility. It localizes to kinetochores (KT) during mitosis and is a target of the mitotic kinase PLK1. It regulates the maturation of the outer KT and the KT-microtubule attachment. The SCY1-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 287 matched cddid_all.tbl CDD cd14012 cd14012 270914 PK_eIF2AK_GCN2_rpt1 Pseudokinase domain, repeat 1, of eukaryotic translation Initiation Factor 2-Alpha Kinase 4 or General Control Non-derepressible-2. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. EIF2AKs phosphorylate the alpha subunit of eIF-2, resulting in the overall downregulation of protein synthesis. eIF-2 phosphorylation is induced in response to cellular stresses including virus infection, heat shock, nutrient deficiency, and the accummulation of unfolded proteins, among others. There are four distinct kinases that phosphorylate eIF-2 and control protein synthesis under different stress conditions: GCN2, protein kinase regulated by RNA (PKR), heme-regulated inhibitor kinase (HRI), and PKR-like endoplasmic reticulum kinase (PERK). GCN2 is activated by amino acid or serum starvation and UV irradiation. It induces GCN4, a transcriptional activator of amino acid biosynthetic genes, leading to increased production of amino acids under amino acid-deficient conditions. In serum-starved cells, GCN2 activation induces translation of the stress-responsive transcription factor ATF4, while under UV stress, GCN2 triggers transcriptional rescue via NF-kappaB signaling. GCN2 contains an N-terminal RWD, a degenerate kinase-like (repeat 1), the catalytic kinase (repeat 2), a histidyl-tRNA synthetase (HisRS)-like, and a C-terminal ribosome-binding and dimerization (RB/DD) domains. The degenerate pseudokinase domain of GCN2 may function as a regulatory domain. The GCN2 subfamily is part of a larger superfamily that includes the catalytic domains of serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 254 matched cddid_all.tbl CDD cd14013 cd14013 270915 STKc_SNT7_plant Catalytic domain of the Serine/Threonine kinase, Plant SNT7. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. SNT7 is a plant thylakoid-associated kinase that is essential in short- and long-term acclimation responses to cope with various light conditions in order to maintain photosynthetic redox poise for optimal photosynthetic performance. Short-term response involves state transitions over periods of minutes while the long-term response (LTR) occurs over hours to days and involves changing the relative amounts of photosystems I and II. SNT7 acts as a redox sensor and a signal transducer for both responses, which are triggered by the redox state of the plastoquinone (PQ) pool. It is positioned at the top of a phosphorylation cascade that induces state transitions by phosphorylating light-harvesting complex II (LHCII), and triggers the LTR through the phosphorylation of chloroplast proteins. The SNT7 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 318 matched cddid_all.tbl CDD cd14014 cd14014 270916 STKc_PknB_like Catalytic domain of bacterial Serine/Threonine kinases, PknB and similar proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily includes many bacterial eukaryotic-type STKs including Staphylococcus aureus PknB (also called PrkC or Stk1), Bacillus subtilis PrkC, and Mycobacterium tuberculosis Pkn proteins (PknB, PknD, PknE, PknF, PknL, and PknH), among others. S. aureus PknB is the only eukaryotic-type STK present in this species, although many microorganisms encode for several such proteins. It is important for the survival and pathogenesis of S. aureus as it is involved in the regulation of purine and pyrimidine biosynthesis, cell wall metabolism, autolysis, virulence, and antibiotic resistance. M. tuberculosis PknB is essential for growth and it acts on diverse substrates including proteins involved in peptidoglycan synthesis, cell division, transcription, stress responses, and metabolic regulation. B. subtilis PrkC is located at the inner membrane of endospores and functions to trigger spore germination. Bacterial STKs in this subfamily show varied domain architectures. The well-characterized members such as S. aureus and M. tuberculosis PknB, and B. subtilis PrkC, contain an N-terminal cytosolic kinase domain, a transmembrane (TM) segment, and mutliple C-terminal extracellular PASTA domains. The PknB subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 260 matched cddid_all.tbl CDD cd14015 cd14015 270917 STKc_VRK Catalytic domain of the Serine/Threonine protein kinase, Vaccinia Related Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. VRKs were initially discovered due to its similarity to vaccinia virus B1R STK, which is important for viral replication. They play important roles in cell signaling, nuclear envelope dynamics, apoptosis, and stress responses. Vertebrates contain three VRK proteins (VRK1, VRK2, and VRK3) while invertebrates, specifically fruit flies and nematodes, seem to carry only a single ortholog. Mutations of VRK in Drosophila and Caenorhabditis elegans showed varying phenotypes ranging from embryonic lethality to mitotic and meiotic defects resulting in sterility. In vertebrates, VRK1 is implicated in cell cycle progression and proliferation, nuclear envelope assembly, and chromatin condensation. VRK2 is involved in modulating JNK signaling. VRK3 is an inactive pseudokinase that inhibits ERK signaling. The VRK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 300 matched cddid_all.tbl CDD cd14016 cd14016 270918 STKc_CK1 Catalytic domain of the Serine/Threonine protein kinase, Casein Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CK1 phosphorylates a variety of substrates including enzymes, transcription and splice factors, cytoskeletal proteins, viral oncogenes, receptors, and membrane-associated proteins. There are mutliple isoforms of CK1 and in mammals, seven isoforms (alpha, beta, gamma1-3, delta, and epsilon) have been characterized. These isoforms differ mainly in the length and structure of their C-terminal non-catalytic region. Some isoforms have several splice variants such as the long (L) and short (S) variants of CK1alpha. CK1 proteins are involved in the regulation of many cellular processes including membrane transport processes, circadian rhythm, cell division, apoptosis, and the development of cancer and neurodegenerative diseases. The CK1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 266 matched cddid_all.tbl CDD cd14017 cd14017 270919 STKc_TTBK Catalytic domain of the Serine/Threonine protein kinase, Tau-Tubulin Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TTBK is a neuron-specific kinase that phosphorylates the microtubule-associated protein tau and promotes its aggregation. Higher vertebrates contain two TTBK proteins, TTBK1 and TTBK2, both of which have been implicated in neurodegeneration. TTBK1 has been linked to Alzheimer's disease (AD) while TTBK2 is associated with spinocerebellar ataxia type 11 (SCA11). Both AD and SCA11 patients show the presence of neurofibrillary tangles in the brain. The Drosophila TTBK homolog, Asator, is an essential protein that localizes to the mitotic spindle during mitosis and may be involved in regulating microtubule dynamics and function. The TTBK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 263 matched cddid_all.tbl CDD cd14018 cd14018 270920 STKc_PINK1 Catalytic domain of the Serine/Threonine protein kinase, Pten INduced Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PINK1 contains an N-terminal mitochondrial targeting sequence, a catalytic domain, and a C-terminal regulatory region. It plays an important role in maintaining mitochondrial homeostasis. It protects cells against oxidative stress-induced apoptosis by phosphorylating the chaperone TNFR-associated protein 1 (TRAP1), also called Hsp75. Phosphorylated TRAP1 prevents cytochrome c release and peroxide-induced apoptosis. PINK1 interacts with Omi/HtrA2, a serine protease, and Parkin, an E3 ubiquitin ligase, in different pathways to promote mitochondrial health. The parkin gene is the most commonly mutated gene in autosomal recessive familial parkinsonism. Mutations within the catalytic domain of PINK1 are also associated with Parkinson's disease. The PINK1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 313 matched cddid_all.tbl CDD cd14019 cd14019 270921 STKc_Cdc7 Catalytic domain of the Serine/Threonine Kinase, Cell Division Cycle 7 kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Cdc7 kinase (or Hsk1 in fission yeast) is a critical regulator in the initiation of DNA replication. It forms a complex with a Dbf4-related regulatory subunit, a cyclin-like molecule that activates the kinase in late G1 phase, and is also referred to as Dbf4-dependent kinase (DDK). Its main targets are mini-chromosome maintenance (MCM) proteins. Cdc7 kinase may also have additional roles in meiosis, checkpoint responses, the maintenance and repair of chromosome structures, and cancer progression. The Cdc7 kinase subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 252 matched cddid_all.tbl CDD cd14020 cd14020 270922 STKc_KIS Catalytic domain of the Serine/Threonine Kinase, Kinase Interacting with Stathmin (also called U2AF homology motif (UHM) kinase 1). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. KIS (or UHMK1) contains an N-terminal kinase domain and a C-terminal domain with a UHM motif, a protein interaction motif initially found in the pre-mRNA splicing factor U2AF. It phosphorylates the splicing factor SF1, which enhances binding to the splice site to promote spliceosome assembly. KIS was first identified as a kinase that interacts with stathmin, a phosphoprotein that plays a role in axon development and microtubule dynamics. It localizes in RNA granules in neurons and is important in neurite outgrowth. The KIS/UHMK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 285 matched cddid_all.tbl CDD cd14021 cd14021 270923 ChoK-like_euk Euykaryotic Choline Kinase and similar proteins. This group is composed of eukaryotic choline kinase, ethanolamine kinase, and similar proteins. ChoK catalyzes the transfer of the gamma-phosphoryl group from ATP (or CTP) to its substrate, choline, producing phosphorylcholine (PCho), a precursor to the biosynthesis of two major membrane phospholipids, phosphatidylcholine (PC), and sphingomyelin (SM). Although choline is the preferred substrate, ChoK also shows substantial activity towards ethanolamine and its N-methylated derivatives. ETNK catalyzes the transfer of the gamma-phosphoryl group from CTP to ethanolamine (Etn), the first step in the CDP-Etn pathway for the formation of the major phospholipid, phosphatidylethanolamine (PtdEtn). Unlike ChoK, ETNK shows specific activity for its substrate and displays negligible activity towards N-methylated derivatives of Etn. ChoK plays an important role in cell signaling pathways and the regulation of cell growth. The ChoK subfamily is part of a larger superfamily that includes the catalytic domains of other kinases, such as the typical serine/threonine/tyrosine protein kinases (PKs), RIO kinases, actin-fragmin kinase (AFK), and phosphoinositide 3-kinase (PI3K). 229 matched cddid_all.tbl CDD cd14022 cd14022 270924 PK_TRB2 Pseudokinase domain of Tribbles Homolog 2. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. TRB2 binds and negatively regulates the mitogen activated protein kinase (MAPK) kinases, MKK7 and MEK1, which are activators of the MAPKs, ERK and JNK. It controls the activation of inflammatory monocytes, which is essential in innate immune responses and the pathogenesis of inflammatory diseases such as atherosclerosis. TRB2 expression is down-regulated in human acute myeloid leukaemia (AML), which may lead to enhanced cell survival and pathogenesis of the disease. TRB2 is one of three Tribbles Homolog (TRB) proteins present in vertebrates that are encoded by three separate genes. TRB proteins interact with many proteins involved in signalling pathways. They play scaffold-like regulatory functions and affect many cellular processes such as mitosis, apoptosis, and gene expression. The TRB2 subfamily is part of a larger superfamily that includes the catalytic domains of serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 242 matched cddid_all.tbl CDD cd14023 cd14023 270925 PK_TRB1 Pseudokinase domain of Tribbles Homolog 1. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. TRB1 interacts directly with the mitogen activated protein kinase (MAPK) kinase MKK4, an activator of JNK. It regulates vascular smooth muscle cell proliferation and chemotaxis through the JNK signaling pathway. It is found to be down-regulated in human acute myeloid leukaemia (AML) and may play a role in the pathogenesis of the disease. It has also been identified as a potential biomarker for antibody-mediated allograft failure. TRB1 is one of three Tribbles Homolog (TRB) proteins present in vertebrates that are encoded by three separate genes. TRB proteins interact with many proteins involved in signalling pathways. They play scaffold-like regulatory functions and affect many cellular processes such as mitosis, apoptosis, and gene expression. The TRB1 subfamily is part of a larger superfamily that includes the catalytic domains of serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 242 matched cddid_all.tbl CDD cd14024 cd14024 270926 PK_TRB3 Pseudokinase domain of Tribbles Homolog 3. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. TRB3 binds and regulates ATF4, p65/RelA, and PKB (or Akt). It negatively regulates ATF4-mediated gene expression including that of CHOP (C/EBP homologous protein) and HO-1, which are both involved in modulating apoptosis. It also inhibits insulin-mediated phosphorylation of PKB and is a possible determinant of insulin resistance and related disorders. In osteoarthritic chondrocytes where it inhibits insulin-like growth factor 1-mediated cell survival, TRB3 is overexpressed, resulting in increased cell death. TRB3 is one of three Tribbles Homolog (TRB) proteins present in vertebrates that are encoded by three separate genes. TRB proteins interact with many proteins involved in signalling pathways. They play scaffold-like regulatory functions and affect many cellular processes such as mitosis, apoptosis, and gene expression. The TRB3 subfamily is part of a larger superfamily that includes the catalytic domains of serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 242 matched cddid_all.tbl CDD cd14025 cd14025 270927 STKc_RIP4_like Catalytic domain of the Serine/Threonine kinases, Receptor Interacting Protein 4 and similar proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of RIP4, ankyrin (ANK) repeat and kinase domain containing 1 (ANKK1), and similar proteins, all of which harbor C-terminal ANK repeats. RIP4, also called Protein Kinase C-associated kinase (PKK), regulates keratinocyte differentiation and cutaneous inflammation. It activates NF-kappaB and is important in the survival of diffuse large B-cell lymphoma cells. The ANKK1 protein, also called PKK2, has not been studied extensively. The ANKK1 gene, located less than 10kb downstream of the D2 dopamine receptor (DRD2) locus, is altered in the Taq1 A1 polymorphism, which is related to a reduced DRD2 binding affinity and consequently, to mental disorders. The RIP4-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 267 matched cddid_all.tbl CDD cd14026 cd14026 270928 STKc_RIP2 Catalytic domain of the Serine/Threonine kinase, Receptor Interacting Protein 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. RIP2, also called RICK or CARDIAK, harbors a C-terminal Caspase Activation and Recruitment domain (CARD) belonging to the Death domain (DD) superfamily. It functions as an effector kinase downstream of the pattern recognition receptors from the Nod-like (NLR) family, Nod1 and Nod2, which recognizes bacterial peptidoglycans released upon infection. RIP2 may also be involved in regulating wound healing and keratinocyte proliferation. RIP kinases serve as essential sensors of cellular stress. The RIP2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 284 matched cddid_all.tbl CDD cd14027 cd14027 270929 STKc_RIP1 Catalytic domain of the Serine/Threonine kinase, Receptor Interacting Protein 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. RIP1 harbors a C-terminal Death domain (DD), which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 can also recruit other kinases including MEKK1, MEKK3, and RIP3 through an intermediate domain (ID) that bears a RIP homotypic interaction motif (RHIM). RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accummulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. RIP kinases serve as essential sensors of cellular stress. The RIP1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 267 matched cddid_all.tbl CDD cd14028 cd14028 270930 STKc_Bub1_vert Catalytic domain of the Serine/Threonine kinase, Vertebrate Spindle assembly checkpoint protein Bub1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Bub1 (Budding uninhibited by benzimidazoles 1) contains an N-terminal Bub1/Mad3 homology domain essential for Cdc20 binding, a GLEBS motif for Bub3/kinetochore binding, and a C-terminal kinase domain. It is involved in SAC, a surveillance system that delays metaphase to anaphase transition by blocking the activity of APC/C (the anaphase promoting complex) until all chromosomes achieve proper attachments to the mitotic spindle, to avoid chromosome missegregation. Bub1 contributes to the inhibition of APC/C by phosphorylating its crucial cofactor, Cdc20, rendering it unable to activate APC/C. In addition, Bub1 facilitates the localization to kinetochores of other SAC and motor proteins including Mad1, Mad2, BubR1, and Plk1. It acts as the master organizer of the functional inner centromere. Bub1 also play roles in protecting sister chromatid cohesion and normal metaphase congression. The Bub1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 290 matched cddid_all.tbl CDD cd14029 cd14029 270931 STKc_BubR1_vert Catalytic domain of the Serine/Threonine kinase, Vertebrate Spindle assembly checkpoint protein BubR1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. BubR1 (Budding uninhibited by benzimidazoles R1) is also called Bub1 beta (Bub1b). It contains an N-terminal Bub1/Mad3 homology domain essential for Cdc20 binding and a C-terminal kinase domain. It is involved in SAC, a surveillance system that delays metaphase to anaphase transition by blocking the activity of APC/C (the anaphase promoting complex) until all chromosomes achieve proper attachments to the mitotic spindle, to avoid chromosome missegregation. BubR1 inhibits APC/C through direct binding. It also plays an important role in stabilizing kinetochore-microtubule attachments. Mutant mice expressing only 10% normal BubR1 protein are viable and develop into adult mice, but display many early aging-associated phenotypes including reduced lifespan, muscle atrophy, cataracts, impaired wound healing, and infertility. The BubR1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 304 matched cddid_all.tbl CDD cd14030 cd14030 270932 STKc_WNK1 Catalytic domain of the Serine/Threonine protein kinase, With No Lysine (WNK) 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. WNK1 is widely expressed and is most abundant in the testis. In hyperosmotic or hypotonic low-chloride stress conditions, WNK1 is activated and it phosphorylates its substrates including SPAK and OSR1 kinases, which regulate the activity of cation-chloride cotransporters through direct interaction and phosphorylation. Mutations in WNK1 cause PseudoHypoAldosteronism type II (PHAII), characterized by hypertension and hyperkalemia. WNK1 negates WNK4-mediated inhibition of the sodium-chloride cotransporter NCC and activates the epithelial sodium channel ENaC by activating SGK1. WNK1 also decreases the surface expression of renal outer medullary potassium channel (ROMK) by stimulating their endocytosis. Hypertension and hyperkalemia in PHAII patients with WNK1 mutations may be due partly to increased activity of NCC and ENaC, and impaired renal potassium secretion by ROMK, respectively. In addition, WNK1 interacts with MEKK2/3 and acts as an activator of extracellular signal-regulated kinase (ERK) 5. It also negatively regulates TGFbeta signaling. WNKs comprise a subfamily of STKs with an unusual placement of the catalytic lysine relative to all other protein kinases. The WNK1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 289 matched cddid_all.tbl CDD cd14031 cd14031 270933 STKc_WNK3 Catalytic domain of the Serine/Threonine protein kinase, With No Lysine (WNK) 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. WNK3 shows a restricted expression pattern; it is found at high levels in the pituary glands and is also expressed in the kidney and brain. It has been shown to regulate many ion transporters including members of the SLC12A family of cation-chloride cotransporters such as NCC and NKCC2, the renal potassium channel ROMK, and the epithelial calcium channels TRPV5 and TRPV6. WNK3 appears to sense low-chloride hypotonic stress and under these conditions, it activates SPAK, which directly interacts and phosphorylates cation-chloride cotransporters. WNK3 has also been shown to promote cell survival, possibly through interaction with procaspase-3 and HSP70. WNKs comprise a subfamily of STKs with an unusual placement of the catalytic lysine relative to all other protein kinases. The WNK3 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 275 matched cddid_all.tbl CDD cd14032 cd14032 270934 STKc_WNK2_like Catalytic domain of With No Lysine (WNK) 2-like Serine/Threonine kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. WNK2 is widely expressed and has been shown to be epigenetically silenced in gliomas. It inhibits cell growth by acting as a negative regulator of MEK1-ERK1/2 signaling. WNK2 modulates growth factor-induced cancer cell proliferation, suggesting that it may be a tumor suppressor gene. WNKs comprise a subfamily of STKs with an unusual placement of the catalytic lysine relative to all other protein kinases. They are critical in regulating ion balance and are thus, important components in the control of blood pressure. The WNK2-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 266 matched cddid_all.tbl CDD cd14033 cd14033 270935 STKc_WNK4 Catalytic domain of the Serine/Threonine protein kinase, With No Lysine (WNK) 4. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. WNK4 shows a restricted expression pattern and is usually found in epithelial cells. It is expressed in nephrons and in extrarenal tissues including intestine, eye, mammary glands, and prostate. WNK4 regulates a variety of ion transport proteins including apical or basolateral ion transporters, ion channels in the transcellular pathway, and claudins in the paracellular pathway. Mutations in WNK4 cause PseudoHypoAldosteronism type II (PHAII), characterized by hypertension and hyperkalemia. WNK4 inhibits the activity of the thiazide-sensitive Na-Cl cotransporter (NCC), which is responsible for about 15% of NaCl reabsorption in the kidney. It also inhibits the renal outer medullary potassium channel (ROMK) and decreases its surface expression. Hypertension and hyperkalemia in PHAII patients with WNK4 mutations may be partly due to increased NaCl reabsorption through NCC and impaired renal potassium secretion by ROMK, respectively. The WNK4 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 261 matched cddid_all.tbl CDD cd14034 cd14034 270936 PK_NRBP1 Pseudokinase domain of Nuclear Receptor Binding Protein 1. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity and/or ATP binding. NRBP1, also called MLF1-adaptor molecule (MADM), was originally named based on the presence of nuclear binding and localization motifs prior to functional analyses. It is expressed ubiquitously and is found to localize in the cytoplasm, not the nucleus. NRBP1 is an adaptor protein that interacts with myeloid leukemia factor 1 (MLF1), an oncogene that enhances myeloid development of hematopoietic cells. It also interacts with the small GTPase Rac3. NRBP1 may also be involved in Golgi to ER trafficking and actin dynamics. The NRBP1-like subfamily is part of a larger superfamily that includes the catalytic domains of serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 277 matched cddid_all.tbl CDD cd14035 cd14035 270937 PK_MADML Pseudokinase domain of MLF1-ADaptor Molecule-Like. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity and/or ATP binding. MADML has been shown to be expressed throughout development in Xenopus laevis with highest expression found in the developing lens and retina. It may play an important role in embryonic eye development. The MADML subfamily is part of a larger superfamily that includes the catalytic domains of serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 263 matched cddid_all.tbl CDD cd14036 cd14036 270938 STKc_GAK Catalytic domain of the Serine/Threonine protein kinase, cyclin G-Associated Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. GAK, also called auxilin-2, contains an N-terminal kinase domain that phosphorylates the mu subunits of adaptor protein (AP) 1 and AP2. In addition, it contains an auxilin-1-like domain structure consisting of PTEN-like, clathrin-binding, and J domains. Like auxilin-1, GAK facilitates Hsc70-mediated dissociation of clathrin from clathrin-coated vesicles. GAK is expressed ubiquitously and is enriched in the Golgi, unlike auxilin-1 which is nerve-specific. GAK also plays regulatory roles outside of clathrin-mediated membrane traffic including the maintenance of centrosome integrity and chromosome congression, neural patterning, survival of neurons, and immune responses through interaction with the interleukin 12 receptor. It also interacts with the androgen receptor, acting as a transcriptional coactivator, and its expression is significantly increased with the progression of prostate cancer. The GAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 282 matched cddid_all.tbl CDD cd14037 cd14037 270939 STKc_NAK_like Catalytic domain of Numb-Associated Kinase (NAK)-like Serine/Threonine kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of Drosophila melanogaster NAK, human BMP-2-inducible protein kinase (BMP2K or BIKe) and similar vertebrate proteins, as well as the Saccharomyces cerevisiae proteins Prk1, Actin-regulating kinase 1 (Ark1), and Akl1. NAK was the first characterized member of this subfamily. It plays a role in asymmetric cell division through its association with Numb. It also regulates the localization of Dlg, a protein essential for septate junction formation. BMP2K contains a nuclear localization signal and a kinase domain that is capable of phosphorylating itself and myelin basic protein. The expression of the BMP2K gene is increase during BMP-2-induced osteoblast differentiation. It may function to control the rate of differentiation. Prk1, Ark1, and Akl1 comprise a subfamily of yeast proteins that are important regulators of the actin cytoskeleton and endocytosis. They share an N-terminal kinase domain but no significant homology in other regions of their sequences. The NAK-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 277 matched cddid_all.tbl CDD cd14038 cd14038 270940 STKc_IKK_beta Catalytic domain of the Serine/Threonine kinase, Inhibitor of Nuclear Factor-KappaB Kinase (IKK) beta. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. IKKbeta is involved in the classical pathway of regulating Nuclear Factor-KappaB (NF-kB) proteins, a family of transcription factors which are critical in many cellular functions including inflammatory responses, immune development, cell survival, and cell proliferation, among others. The classical pathway regulates the majority of genes activated by NF-kB including those encoding cytokines, chemokines, leukocyte adhesion molecules, and anti-apoptotic factors. It involves NEMO (NF-kB Essential MOdulator)- and IKKbeta-dependent phosphorylation and degradation of the Inhibitor of NF-kB (IkB), which liberates NF-kB dimers (typified by the p50-p65 heterodimer) from an inactive IkB/dimeric NF-kB complex, enabling them to migrate to the nucleus where they regulate gene transcription. The IKKbeta subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 290 matched cddid_all.tbl CDD cd14039 cd14039 270941 STKc_IKK_alpha Catalytic domain of the Serine/Threonine kinase, Inhibitor of Nuclear Factor-KappaB Kinase (IKK) alpha. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. IKKalpha is involved in the non-canonical or alternative pathway of regulating Nuclear Factor-KappaB (NF-kB) proteins, a family of transcription factors which are critical in many cellular functions including inflammatory responses, immune development, cell survival, and cell proliferation, among others. The non-canonical pathway functions in cells lacking NEMO (NF-kB Essential MOdulator) and IKKbeta. It is induced by a subset of TNFR family members including CD40, RANK, and B cell-activating factor receptor. IKKalpha processes the Inhibitor of NF-kB (IkB)-like C-terminus of NF-kB2/p100 to produce p52, allowing the p52/RelB dimer to migrate to the nucleus. This pathway is dependent on NIK (NF-kB Inducing Kinase) which phosphorylates and activates IKKalpha. The IKKalpha subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 289 matched cddid_all.tbl CDD cd14040 cd14040 270942 STKc_TLK1 Catalytic domain of the Serine/Threonine kinase, Tousled-Like Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. A splice variant of TLK1, called TLK1B, is expressed in the presence of double strand breaks (DSBs). It lacks the N-terminal part of TLK1, but is expected to phosphorylate the same substrates. TLK1/1B interacts with Rad9, which is critical in DNA damage-activated checkpoint response, and plays a role in the repair of linearized DNA with incompatible ends. TLKs play important functions during the cell cycle and are implicated in chromatin remodeling, DNA replication and repair, and mitosis. The TLK1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 299 matched cddid_all.tbl CDD cd14041 cd14041 270943 STKc_TLK2 Catalytic domain of the Serine/Threonine kinase, Tousled-Like Kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TLKs play important functions during the cell cycle and are implicated in chromatin remodeling, DNA replication and repair, and mitosis. They phosphorylate and regulate Anti-silencing function 1 protein (Asf1), a histone H3/H4 chaperone that helps facilitate the assembly of chromatin following DNA replication during S phase. TLKs also phosphorylate the H3 histone tail and are essential in transcription. Vertebrates contain two subfamily members, TLK1 and TLK2. The TLK2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). 309 matched cddid_all.tbl CDD cd14042 cd14042 270944 PK_GC-A_B Pseudokinase domain of the membrane Guanylate Cyclase receptors, GC-A and GC-B. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity and/or ATP binding. GC-A binds and is activated by the atrial and B-type natriuretic peptides, ANP and BNP, which are important in blood pressure regulation and cardiac pathophysiology. GC-B binds the C-type natriuretic peptide, CNP, which is a potent vasorelaxant and functions in vascular remodeling and bone growth regulation. Membrane (or particulate) GCs consist of an extracellular ligand-binding domain, a single transmembrane region, and an intracellular tail that contains a PK-like domain, an amphiphatic region and a catalytic GC domain that catalyzes the conversion of GTP into cGMP and pyrophosphate. Membrane GCs act as receptors that transduce an extracellular signal to the intracellular production of cGMP, which has been implicated in many processes including cell proliferation, phototransduction, and muscle contractility, through its downstream effectors such as PKG. The PK-like domain of GCs functions as a negative regulator of the catalytic GC domain and may also act as a docking site for interacting proteins such as GC-activating proteins. The GC-A/B subfamily is part of a larger superfamily that includes the catalytic domains of protein serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 279 matched cddid_all.tbl CDD cd14043 cd14043 270945 PK_GC-2D Pseudokinase domain of the membrane Guanylate Cyclase receptor, GC-2D. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity and/or ATP binding. GC-2D is allso called Retinal Guanylyl Cyclase 1 (RETGC-1) or Rod Outer Segment membrane Guanylate Cyclase (ROS-GC). It is found in the photoreceptors of the retina where it anchors the reciprocal feedback loop between calcium and cGMP, which regulates the dark, light, and recovery phases in phototransduction. It is also found in other sensory neurons and may be a universal transduction component that plays a role in the perception of all senses. Membrane (or particulate) GCs consist of an extracellular ligand-binding domain, a single transmembrane region, and an intracellular tail that contains a PK-like domain, an amphiphatic region and a catalytic GC domain that catalyzes the conversion of GTP into cGMP and pyrophosphate. Membrane GCs act as receptors that transduce an extracellular signal to the intracellular production of cGMP, which has been implicated in many processes including cell proliferation, phototransduction, and muscle contractility, through its downstream effectors such as PKG. The PK-like domain of GCs functions as a negative regulator of the catalytic GC domain and may also act as a docking site for interacting proteins such as GC-activating proteins. The GC-2D subfamily is part of a larger superfamily that includes the catalytic domains of protein serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 267 matched cddid_all.tbl CDD cd14044 cd14044 270946 PK_GC-C Pseudokinase domain of the membrane Guanylate Cyclase receptor, GC-C. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity and/or ATP binding. GC-C binds and is activated by the intestinal hormones, guanylin (GN) and uroguanylin (UGN), which are secreted after salty meals to inhibit sodium absorption and induce the secretion of chloride, bicarbonate, and water. GN and UGN are also present in the kidney, where they induce increased salt and water secretion. This prevents the development of hypernatremia and hypervolemia after ingestion of high amounts of salt. Membrane (or particulate) GCs consist of an extracellular ligand-binding domain, a single transmembrane region, and an intracellular tail that contains a PK-like domain, an amphiphatic region and a catalytic GC domain that catalyzes the conversion of GTP into cGMP and pyrophosphate. Membrane GCs act as receptors that transduce an extracellular signal to the intracellular production of cGMP, which has been implicated in many processes including cell proliferation, phototransduction, and muscle contractility, through its downstream effectors such as PKG. The PK-like domain of GCs functions as a negative regulator of the catalytic GC domain and may also act as a docking site for interacting proteins such as GC-activating proteins. The GC-C subfamily is part of a larger superfamily that includes the catalytic domains of protein serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 271 matched cddid_all.tbl CDD cd14045 cd14045 270947 PK_GC_unk Pseudokinase domain of the unknown subfamily of membrane Guanylate Cyclase receptors. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. Membrane (or particulate) GCs consist of an extracellular ligand-binding domain, a single transmembrane region, and an intracellular tail that contains a PK-like domain, an amphiphatic region and a catalytic GC domain that catalyzes the conversion of GTP into cGMP and pyrophosphate. Membrane GCs act as receptors that transduce an extracellular signal to the intracellular production of cGMP, which has been implicated in many processes including cell proliferation, phototransduction, and muscle contractility, through its downstream effectors such as PKG. The PK-like domain of GCs lack a critical aspartate involved in ATP binding and does not exhibit kinase activity. It functions as a negative regulator of the catalytic GC domain and may also act as a docking site for interacting proteins such as GC-activating proteins. The GC subfamily is part of a larger superfamily that includes the catalytic domains of protein serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 269 matched cddid_all.tbl CDD cd14046 cd14046 270948 STKc_EIF2AK4_GCN2_rpt2 Catalytic domain, repeat 2, of the Serine/Threonine kinase, eukaryotic translation Initiation Factor 2-Alpha Kinase 4 or General Control Non-derepressible-2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. GCN2 (or EIF2AK4) is activated by amino acid or serum starvation and UV irradiation. It induces GCN4, a transcriptional activator of amino acid biosynthetic genes, leading to increased production of amino acids under amino acid-deficient conditions. In serum-starved cells, GCN2 activation induces translation of the stress-responsive transcription factor ATF4, while under UV stress, GCN2 triggers transcriptional rescue via NF-kB signaling. GCN2 contains an N-terminal RWD, a degenerate kinase-like (repeat 1), the catalytic kinase (repeat 2), a histidyl-tRNA synthetase (HisRS)-like, and a C-terminal ribosome-binding and dimerization (RB/DD) domains. Its kinase domain is activated via conformational changes as a result of the binding of uncharged tRNA to the HisRS-like domain. EIF2AKs phosphorylate the alpha subunit of eIF-2, resulting in the overall downregulation of protein synthesis. The GCN2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 278 matched cddid_all.tbl CDD cd14047 cd14047 270949 STKc_EIF2AK2_PKR Catalytic domain of the Serine/Threonine kinase, eukaryotic translation Initiation Factor 2-Alpha Kinase 2 or Protein Kinase regulated by RNA. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PKR (or EIF2AK2) contains an N-terminal double-stranded RNA (dsRNA) binding domain and a C-terminal catalytic kinase domain. It is activated by dsRNA, which is produced as a replication intermediate in virally infected cells. It plays a key role in mediating innate immune responses to viral infection. PKR is also directly activated by PACT (protein activator of PKR) and heparin, and is inhibited by viral proteins and RNAs. PKR also regulates transcription and signal transduction in diseased cells, playing roles in tumorigenesis and neurodegenerative diseases. EIF2AKs phosphorylate the alpha subunit of eIF-2, resulting in the downregulation of protein synthesis. The PKR subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 267 matched cddid_all.tbl CDD cd14048 cd14048 270950 STKc_EIF2AK3_PERK Catalytic domain of the Serine/Threonine kinase, eukaryotic translation Initiation Factor 2-Alpha Kinase 3 or PKR-like Endoplasmic Reticulum Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PERK (or EIF2AK3) is a type-I ER transmembrane protein containing a luminal domain bound with the chaperone BiP under unstressed conditions and a cytoplasmic catalytic kinase domain. In response to the accumulation of misfolded or unfolded proteins in the ER, PERK is activated through the release of BiP, allowing it to dimerize and autophosphorylate. It functions as the central regulator of translational control during the Unfolded Protein Response (UPR) pathway. In addition to the eIF-2 alpha subunit, PERK also phosphorylates Nrf2, a leucine zipper transcription factor which regulates cellular redox status and promotes cell survival during the UPR. EIF2AKs phosphorylate the alpha subunit of eIF-2, resulting in the downregulation of protein synthesis. The PERK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 281 matched cddid_all.tbl CDD cd14049 cd14049 270951 STKc_EIF2AK1_HRI Catalytic domain of the Serine/Threonine kinase, eukaryotic translation Initiation Factor 2-Alpha Kinase 2 or Heme-Regulated Inhibitor kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. HRI (or EIF2AK1) contains an N-terminal regulatory heme-binding domain and a C-terminal catalytic kinase domain. It is suppressed under normal conditions by binding of the heme iron, and is activated during heme deficiency. It functions as a critical regulator that ensures balanced synthesis of globins and heme, in order to form stable hemoglobin during erythroid differentiation and maturation. HRI also protects cells and enhances survival under iron-deficient conditions. EIF2AKs phosphorylate the alpha subunit of eIF-2, resulting in the downregulation of protein synthesis. The HRI subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 284 matched cddid_all.tbl CDD cd14050 cd14050 270952 PKc_Myt1 Catalytic domain of the Dual-specificity protein kinase, Myt1. Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine as well as tyrosine residues on protein substrates. Myt1 is a cytoplasmic cell cycle checkpoint kinase that can keep the cyclin-dependent kinase CDK1 in an inactive state through phosphorylation of N-terminal thr (T14) and tyr (Y15) residues, leading to the delay of meiosis I entry. Meiotic progression is ensured by a two-step inhibition and downregulation of Myt1 by CDK1/XRINGO and p90Rsk during oocyte maturation. In addition, Myt1 targets cyclin B1/B2 and is essential for Golgi and ER assembly during telophase. In Drosophila, Myt1 may be a downstream target of Notch during eye development. The Myt1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine PKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 249 matched cddid_all.tbl CDD cd14051 cd14051 270953 PTKc_Wee1 Catalytic domain of the Protein Tyrosine Kinase, Wee1. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Wee1 is a nuclear cell cycle checkpoint kinase that helps keep the cyclin-dependent kinase CDK1 in an inactive state through phosphorylation of an N-terminal tyr (Y15) residue. During the late G2 phase, CDK1 is activated and mitotic entry is promoted by the removal of this inhibitory phosphorylation by the phosphatase Cdc25. Although Wee1 is functionally a tyr kinase, it is more closely related to serine/threonine kinases (STKs). It contains a catalytic kinase domain sandwiched in between N- and C-terminal regulatory domains. It is regulated by phosphorylation and degradation, and its expression levels are also controlled by circadian clock proteins. There are two distinct Wee1 proteins in vertebrates showing different expression patterns, called Wee1a and Wee1b. They are functionally dstinct and are implicated in different steps of egg maturation and embryo development. The Wee1 subfamily is part of a larger superfamily that includes the catalytic domains of STKs, other PTKs, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 275 matched cddid_all.tbl CDD cd14052 cd14052 270954 PTKc_Wee1_fungi Catalytic domain of the Protein Tyrosine Kinases, Fungal Wee1 proteins. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. This subfamily is composed of fungal Wee1 proteins, also called Swe1 in budding yeast and Mik1 in fission yeast. Yeast Wee1 is required to control cell size. Wee1 is a cell cycle checkpoint kinase that helps keep the cyclin-dependent kinase CDK1 in an inactive state through phosphorylation of an N-terminal tyr (Y15) residue. During the late G2 phase, CDK1 is activated and mitotic entry is promoted by the removal of this inhibitory phosphorylation by the phosphatase Cdc25. Although Wee1 is functionally a tyr kinase, it is more closely related to serine/threonine kinases (STKs). It contains a catalytic kinase domain sandwiched in between N- and C-terminal regulatory domains. It is regulated by phosphorylation and degradation, and its expression levels are also controlled by circadian clock proteins. The fungal Wee1 subfamily is part of a larger superfamily that includes the catalytic domains of STKs, other PTKs, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 278 matched cddid_all.tbl CDD cd14053 cd14053 270955 STKc_ACVR2 Catalytic domain of the Serine/Threonine Kinase, Activin Type II Receptor. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. ACVR2 belongs to a group of receptors for the TGFbeta family of secreted signaling molecules that includes TGFbeta, bone morphogenetic proteins (BMPs), activins, growth and differentiation factors (GDFs), and anti-Mullerian hormone, among others. These receptors contain an extracellular domain that binds ligands, a single transmembrane region, and a cytoplasmic catalytic kinase domain. Type II receptors, such as ACVR2, are high-affinity receptors which bind ligands, autophosphorylate, as well as trans-phosphorylate and activate low-affinity type I receptors. ACVR2 acts primarily as the receptors for activins, nodal, myostatin, GDF11, and a subset of BMPs. ACVR2 signaling impacts many cellular and physiological processes including reproductive and gonadal functions, myogenesis, bone remodeling and tooth development, kidney organogenesis, apoptosis, fibrosis, inflammation, and neurogenesis. Vertebrates contain two ACVR2 proteins, ACVR2a (or ActRIIA) and ACVR2b (or ActRIIB). The ACVR2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 290 matched cddid_all.tbl CDD cd14054 cd14054 270956 STKc_BMPR2_AMHR2 Catalytic domain of the Serine/Threonine Kinases, Bone Morphogenetic Protein and Anti-Muellerian Hormone Type II Receptors. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. BMPR2 and AMHR2 belong to a group of receptors for the TGFbeta family of secreted signaling molecules that includes TGFbeta, BMPs, activins, growth and differentiation factors (GDFs), and AMH, among others. These receptors contain an extracellular domain that binds ligands, a single transmembrane region, and a cytoplasmic catalytic kinase domain. Type II receptors are high-affinity receptors which bind ligands, autophosphorylate, as well as trans-phosphorylate and activate low-affinity type I receptors. BMPR2 and AMHR2 act primarily as a receptor for BMPs and AMH, respectively. BMPs induce bone and cartilage formation, as well as regulate tooth, kidney, skin, hair, haematopoietic, and neuronal development. Mutations in BMPR2A is associated with familial pulmonary arterial hypertension. AMH is mainly responsible for the regression of Mullerian ducts during male sex differentiation. It is expressed exclusively by somatic cells of the gonads. Mutations in either AMH or AMHR2 cause persistent Mullerian duct syndrome (PMDS), a rare form of male pseudohermaphroditism characterized by the presence of Mullerian derivatives (ovary and tubes) in otherwise normally masculine males. The BMPR2/AMHR2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 300 matched cddid_all.tbl CDD cd14055 cd14055 270957 STKc_TGFbR2_like Catalytic domain of the Serine/Threonine Kinase, Transforming Growth Factor beta Type II Receptor. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TGFbR2 belongs to a group of receptors for the TGFbeta family of secreted signaling molecules that includes TGFbeta, bone morphogenetic proteins, activins, growth and differentiation factors, and anti-Mullerian hormone, among others. These receptors contain an extracellular domain that binds ligands, a single transmembrane region, and a cytoplasmic catalytic kinase domain. Type II receptors, such as TGFbR2, are high-affinity receptors which bind ligands, autophosphorylate, as well as trans-phosphorylate and activate low-affinity type I receptors. TGFbR2 acts as the receptor for TGFbeta, which is crucial in growth control and homeostasis in many different tissues. It plays roles in regulating apoptosis and in maintaining the balance between self renewal and cell loss. It also plays a key role in maintaining vascular integrity and in regulating responses to genotoxic stress. Mutations in TGFbR2 can cause aortic aneurysm disorders such as Loeys-Dietz and Marfan syndromes. The TGFbR2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 295 matched cddid_all.tbl CDD cd14056 cd14056 270958 STKc_TGFbR_I Catalytic domain of the Serine/Threonine Kinases, Transforming Growth Factor beta family Type I Receptors. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of type I receptors for the TGFbeta family of secreted signaling molecules including TGFbeta, bone morphogenetic proteins, activins, growth and differentiation factors, and anti-Mullerian hormone, among others. These receptors contain an extracellular domain that binds ligands, a single transmembrane (TM) region, and a cytoplasmic catalytic kinase domain. Type I receptors are low-affinity receptors that bind ligands only after they are recruited by the ligand/type II high-affinity receptor complex. Following activation through trans-phosphorylation by type II receptors, they start intracellular signaling to the nucleus by phosphorylating SMAD proteins. Type I receptors contain an additional domain located between the TM and kinase domains called the GS domain, which contains the activating phosphorylation site and confers preference for specific SMAD proteins. They are inhibited by the immunophilin FKBP12, which is thought to control leaky signaling caused by receptor oligomerization in the absence of ligand. The TGFbR-I subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 287 matched cddid_all.tbl CDD cd14057 cd14057 270959 PK_ILK Pseudokinase domain of Integrin Linked Kinase. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. ILK contains N-terminal ankyrin repeats, a Pleckstrin Homology (PH) domain, and a C-terminal pseudokinase domain. It is a component of the IPP (ILK/PINCH/Parvin) complex that couples beta integrins to the actin cytoskeleton, and plays important roles in cell adhesion, spreading, invasion, and migration. ILK was initially thought to be an active kinase despite the lack of key conserved residues because of in vitro studies showing that it can phosphorylate certain protein substrates. However, in vivo experiments in Caenorhabditis elegans, Drosophila melanogaster, and mice (ILK-null and knock-in) proved that ILK is not an active kinase. In addition to actin cytoskeleton regulation, ILK also influences the microtubule network and mitotic spindle orientation. The pseudokinase domain of ILK binds several adaptor proteins including the parvins and paxillin. The ILK subfamily is part of a larger superfamily that includes the catalytic domains of protein serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 251 matched cddid_all.tbl CDD cd14058 cd14058 270960 STKc_TAK1 Catalytic domain of the Serine/Threonine Kinase, Transforming Growth Factor beta Activated Kinase-1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TAK1 is also known as mitogen-activated protein kinase kinase kinase 7 (MAPKKK7 or MAP3K7), TAK, or MEKK7. As a MAPKKK, it is an important mediator of cellular responses to extracellular signals. It regulates both the c-Jun N-terminal kinase and p38 MAPK cascades by activating the MAPK kinases, MKK4 and MKK3/6. In addition, TAK1 plays diverse roles in immunity and development, in different biological contexts, through many signaling pathways including TGFbeta/BMP, Wnt/Fz, and NF-kB. It is also implicated in the activation of the tumor suppressor kinase, LKB1. The TAK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 253 matched cddid_all.tbl CDD cd14059 cd14059 270961 STKc_MAP3K12_13 Catalytic domain of the Serine/Threonine Kinases, Mitogen-Activated Protein Kinase Kinase Kinases 12 and 13. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MAP3K12 is also called MAPK upstream kinase (MUK), dual leucine zipper-bearing kinase (DLK) or leucine-zipper protein kinase (ZPK). It is involved in the c-Jun N-terminal kinase (JNK) pathway that directly regulates axonal regulation through the phosphorylation of microtubule-associated protein 1B (MAP1B). It also regulates the differentiation of many cell types including adipocytes and may play a role in adipogenesis. MAP3K13, also called leucine zipper-bearing kinase (LZK), directly phosphorylates and activates MKK7, which in turn activates the JNK pathway. It also activates NF-kB through IKK activation and this activity is enhanced by antioxidant protein-1 (AOP-1). MAP3Ks (MKKKs or MAPKKKs) phosphorylate and activate MAP2Ks (MAPKKs or MKKs), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. The MAP3K12/13 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 237 matched cddid_all.tbl CDD cd14060 cd14060 270962 STKc_MLTK Catalytic domain of the Serine/Threonine Kinase, Mixed lineage kinase-Like mitogen-activated protein Triple Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MLTK, also called zipper sterile-alpha-motif kinase (ZAK), contains a catalytic kinase domain and a leucine zipper. There are two alternatively-spliced variants, MLTK-alpha and MLTK-beta. MLTK-alpha contains a sterile-alpha-motif (SAM) at the C-terminus. MLTK regulates the c-Jun N-terminal kinase, extracellular signal-regulated kinase, p38 MAPK, and NF-kB pathways. ZAK is the MAP3K involved in the signaling cascade that leads to the ribotoxic stress response initiated by cellular damage due to Shiga toxins and ricin. It may also play a role in cell transformation and cancer development. MAP3Ks (MKKKs or MAPKKKs) phosphorylate and activate MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals.The MLTK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 242 matched cddid_all.tbl CDD cd14061 cd14061 270963 STKc_MLK Catalytic domain of the Serine/Threonine Kinases, Mixed Lineage Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MLKs act as mitogen-activated protein kinase kinase kinases (MAP3Ks, MKKKs, MAPKKKs), which phosphorylate and activate MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. Mammals have four MLKs (MLK1-4), mostly conserved in vertebrates, which contain an SH3 domain, a catalytic kinase domain, a leucine zipper, a proline-rich region, and a CRIB domain that mediates binding to GTP-bound Cdc42 and Rac. MLKs play roles in immunity and inflammation, as well as in cell death, proliferation, and cell cycle regulation. The MLK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 258 matched cddid_all.tbl CDD cd14062 cd14062 270964 STKc_Raf Catalytic domain of the Serine/Threonine Kinases, Raf (Rapidly Accelerated Fibrosarcoma) kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Raf kinases act as mitogen-activated protein kinase kinase kinases (MAP3Ks, MKKKs, MAPKKKs), which phosphorylate and activate MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. They function in the linear Ras-Raf-MEK-ERK pathway that regulates many cellular processes including cycle regulation, proliferation, differentiation, survival, and apoptosis. Aberrant expression or activation of components in this pathway are associated with tumor initiation, progression, and metastasis. Raf proteins contain a Ras binding domain, a zinc finger cysteine-rich domain, and a catalytic kinase domain. Vertebrates have three Raf isoforms (A-, B-, and C-Raf) with different expression profiles, modes of regulation, and abilities to function in the ERK cascade, depending on cellular context and stimuli. They have essential and non-overlapping roles during embryo- and organogenesis. Knockout of each isoform results in a lethal phenotype or abnormality in most mouse strains. The Raf subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 253 matched cddid_all.tbl CDD cd14063 cd14063 270965 PK_KSR Pseudokinase domain of Kinase Suppressor of Ras. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. KSR is a scaffold protein that functions downstream of Ras and upstream of Raf in the Extracellular signal-Regulated Kinase (ERK) pathway that regulates many cellular processes including cycle regulation, proliferation, differentiation, survival, and apoptosis. KSR proteins regulate the assembly and activation of the Raf/MEK/ERK module upon Ras activation at the membrane by direct association of its components. They are widely regarded as pseudokinases, but there is some debate in this designation as a few groups have reported detecting kinase catalytic activity for KSRs, specifically KSR1. Vertebrates contain two KSR proteins, KSR1 and KSR2. The KSR subfamily is part of a larger superfamily that includes the catalytic domains of other protein kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 271 matched cddid_all.tbl CDD cd14064 cd14064 270966 PKc_TNNI3K Catalytic domain of the Dual-specificity protein kinase, TNNI3-interacting kinase. Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine as well as tyrosine residues on protein substrates. TNNI3K, also called cardiac ankyrin repeat kinase (CARK), is a cardiac-specific troponin I-interacting kinase that promotes cardiac myogenesis, improves cardiac performance, and protects the myocardium from ischemic injury. It contains N-terminal ankyrin repeats, a catalytic kinase domain, and a C-terminal serine-rich domain. TNNI3K exerts a disease-accelerating effect on cardiac dysfunction and reduced survival in mouse models of cardiomyopathy. The TNNI3K subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine PKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 254 matched cddid_all.tbl CDD cd14065 cd14065 270967 PKc_LIMK_like Catalytic domain of the LIM domain kinase-like protein kinases. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine or tyrosine residues on protein substrates. Members of this subfamily include LIMK, Testicular or testis-specific protein kinase (TESK), and similar proteins. LIMKs are characterized as serine/threonine kinases (STKs) while TESKs are dual-specificity protein kinases. Both LIMK and TESK phosphorylate and inactivate cofilin, an actin depolymerizing factor, to induce the reorganization of the actin cytoskeleton. They are implicated in many cellular functions including cell spreading, motility, morphogenesis, meiosis, mitosis, and spermatogenesis. The LIMK-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 252 matched cddid_all.tbl CDD cd14066 cd14066 270968 STKc_IRAK Catalytic domain of the Serine/Threonine kinases, Interleukin-1 Receptor Associated Kinases and related STKs. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. IRAKs are involved in Toll-like receptor (TLR) and interleukin-1 (IL-1) signalling pathways, and are thus critical in regulating innate immune responses and inflammation. Some IRAKs may also play roles in T- and B-cell signaling, and adaptive immunity. Vertebrates contain four IRAKs (IRAK-1, -2, -3 (or -M), and -4) that display distinct functions and patterns of expression and subcellular distribution, and can differentially mediate TLR signaling. IRAK-1, -2, and -4 are ubiquitously expressed and are active kinases, while IRAK-M is only induced in monocytes and macrophages and is an inactive kinase. Variations in IRAK genes are linked to diverse diseases including infection, sepsis, cancer, and autoimmune diseases. IRAKs contain an N-terminal Death domain (DD), a proST region (rich in serines, prolines, and threonines), a central kinase domain (a pseudokinase domain in the case of IRAK3), and a C-terminal domain; IRAK-4 lacks the C-terminal domain. This subfamily includes plant receptor-like kinases (RLKs) including Arabidopsis thaliana BAK1 and CLAVATA1 (CLV1). BAK1 functions in BR (brassinosteroid)-regulated plant development and in pathways involved in plant resistance to pathogen infection and herbivore attack. CLV1, directly binds small signaling peptides, CLAVATA3 (CLV3) and CLAVATA3/EMBRYO SURROUNDING REGI0N (CLE), to restrict stem cell proliferation: the CLV3-CLV1-WUS (WUSCHEL) module influences stem cell maintenance in the shoot apical meristem, and the CLE40 (CLAVATA3/EMBRYO SURROUNDING REGION40) -ACR4 (CRINKLY4) -CLV1- WOX5 (WUSCHEL-RELATED HOMEOBOX5) module at the root apical meristem. The IRAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 272 matched cddid_all.tbl CDD cd14067 cd14067 270969 STKc_LRRK1 Catalytic domain of the Serine/Threonine Kinase, Leucine-Rich Repeat Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. LRRK1 is one of two vertebrate LRRKs which show complementary expression in the brain. It can form heterodimers with LRRK2, and may influence the age of onset of LRRK2-associated Parkinson's disease. LRRKs are also classified as ROCO proteins because they contain a ROC (Ras of complex proteins)/GTPase domain followed by a COR (C-terminal of ROC) domain of unknown function. In addition, LRRKs contain a catalytic kinase domain and protein-protein interaction motifs including a WD40 domain, LRRs and ankyrin (ANK) repeats. LRRKs possess both GTPase and kinase activities, with the ROC domain acting as a molecular switch for the kinase domain, cycling between a GTP-bound state which drives kinase activity and a GDP-bound state which decreases the activity. The LRRK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 276 matched cddid_all.tbl CDD cd14068 cd14068 270970 STKc_LRRK2 Catalytic domain of the Serine/Threonine Kinase, Leucine-Rich Repeat Kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. LRRK2 is one of two vertebrate LRRKs which show complementary expression in the brain. Mutations in LRRK2, found in the kinase, ROC-COR, and WD40 domains, are linked to both familial and sporadic forms of Parkinson's disease. The most prevalent mutation, G2019S located in the activation loop of the kinase domain, increases kinase activity. The R1441C/G mutations in the GTPase domain have also been reported to influence kinase activity. LRRKs are also classified as ROCO proteins because they contain a ROC (Ras of complex proteins)/GTPase domain followed by a COR (C-terminal of ROC) domain of unknown function. In addition, LRRKs contain a catalytic kinase domain and protein-protein interaction motifs including a WD40 domain, LRRs and ankyrin (ANK) repeats. LRRKs possess both GTPase and kinase activities, with the ROC domain acting as a molecular switch for the kinase domain, cycling between a GTP-bound state which drives kinase activity and a GDP-bound state which decreases the activity. The LRRK2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 252 matched cddid_all.tbl CDD cd14069 cd14069 270971 STKc_Chk1 Catalytic domain of the Serine/Threonine kinase, Checkpoint kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Chk1 is implicated in many major checkpoints of the cell cycle, providing a link between upstream sensors and the cell cycle engine. It plays an important role in DNA damage response and maintaining genomic stability. Chk1 acts as an effector of the sensor kinase, ATR (ATM and Rad3-related), a member of the PI3K family, which is activated upon DNA replication stress. Chk1 delays mitotic entry in response to replication blocks by inhibiting cyclin dependent kinase (Cdk) activity. In addition, Chk1 contributes to the function of centrosome and spindle-based checkpoints, inhibits firing of origins of DNA replication (Ori), and represses transcription of cell cycle proteins including cyclin B and Cdk1. The Chk1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 261 matched cddid_all.tbl CDD cd14070 cd14070 270972 STKc_HUNK Catalytic domain of the Serine/Threonine Kinase, Hormonally up-regulated Neu-associated kinase (also called MAK-V). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. HUNK/MAK-V was identified from a mammary tumor in an MMTV-neu transgenic mouse. It is required for the metastasis of c-myc-induced mammary tumors, but is not necessary for c-myc-induced primary tumor formation or normal development. It is required for HER2/neu-induced tumor formation and maintenance of the cells' tumorigenic phenotype. It is over-expressed in aggressive subsets of ovary, colon, and breast carcinomas. HUNK interacts with synaptopodin, and may also play a role in synaptic plasticity. The HUNK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 262 matched cddid_all.tbl CDD cd14071 cd14071 270973 STKc_SIK Catalytic domain of the Serine/Threonine Kinases, Salt-Inducible kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. SIKs are part of a complex network that regulates Na,K-ATPase to maintain sodium homeostasis and blood pressure. Vertebrates contain three forms of SIKs (SIK1-3) from three distinct genes, which display tissue-specific effects. SIK1, also called SNF1LK, controls steroidogenic enzyme production in adrenocortical cells. In the brain, both SIK1 and SIK2 regulate energy metabolism. SIK2, also called QIK or SNF1LK2, is involved in the regulation of gluconeogenesis in the liver and lipogenesis in adipose tissues, where it phosphorylates the insulin receptor substrate-1. In the liver, SIK3 (also called QSK) regulates cholesterol and bile acid metabolism. In addition, SIK2 plays an important role in the initiation of mitosis and regulates the localization of C-Nap1, a centrosome linker protein. The SIK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 253 matched cddid_all.tbl CDD cd14072 cd14072 270974 STKc_MARK Catalytic domain of the Serine/Threonine Kinases, MAP/microtubule affinity-regulating kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MARKs, also called Partitioning-defective 1 (Par1) proteins, function as regulators of diverse cellular processes in nematodes, Drosophila, yeast, and vertebrates. They are involved in embryogenesis, epithelial cell polarization, cell signaling, and neuronal differentiation. MARKs phosphorylate tau and related microtubule-associated proteins (MAPs), and regulates microtubule-based intracellular transport. Vertebrates contain four isoforms, namely MARK1 (or Par1c), MARK2 (or Par1b), MARK3 (Par1a), and MARK4 (or MARKL1). Known substrates of MARKs include the cell cycle-regulating phosphatase Cdc25, tyrosine phosphatase PTPH1, MAPK scaffolding protein KSR1, class IIa histone deacetylases, and plakophilin 2. The MARK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 253 matched cddid_all.tbl CDD cd14073 cd14073 270975 STKc_NUAK Catalytic domain of the Serine/Threonine Kinase, novel (nua) kinase family NUAK. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. NUAK proteins are classified as AMP-activated protein kinase (AMPK)-related kinases, which like AMPK are activated by the major tumor suppressor LKB1. Vertebrates contain two NUAK proteins, called NUAK1 and NUAK2. NUAK1, also called ARK5 (AMPK-related protein kinase 5), regulates cell proliferation and displays tumor suppression through direct interaction and phosphorylation of p53. It is also involved in cell senescence and motility. High NUAK1 expression is associated with invasiveness of nonsmall cell lung cancer (NSCLC) and breast cancer cells. NUAK2, also called SNARK (Sucrose, non-fermenting 1/AMP-activated protein kinase-related kinase), is involved in energy metabolism. It is activated by hyperosmotic stress, DNA damage, and nutrients such as glucose and glutamine. NUAK2-knockout mice develop obesity, altered serum lipid profiles, hyperinsulinaemia, hyperglycaemia, and impaired glucose tolerance. The NUAK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 254 matched cddid_all.tbl CDD cd14074 cd14074 270976 STKc_SNRK Catalytic domain of the Serine/Threonine Kinase, SNF1-related kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. SNRK is a kinase highly expressed in testis and brain that is found inactive in cells that lack the LKB1 tumour suppressor protein kinase. The regulatory subunits STRAD and MO25 are required for LKB1 to activate SNRK. The SNRK mRNA is increased 3-fold when granule neurons are cultured in low potassium, and may thus play a role in the survival responses in these cells. In some vertebrates, a second SNRK gene (snrkb or snrk-1) has been sequenced and/or identified. Snrk-1 is expressed specifically in embryonic zebrafish vasculature; it plays an essential role in angioblast differentiation, maintenance, and migration. The SNRK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 258 matched cddid_all.tbl CDD cd14075 cd14075 270977 STKc_NIM1 Catalytic domain of the Serine/Threonine Kinase, NIM1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. NIM1 is a widely-expressed kinase belonging to the AMP-activated protein kinase (AMPK) subfamily. Although present in most tissues, NIM1 kinase activity is only observed in the brain and testis. NIM1 is capable of autophosphorylating and activating itself, but may be present in other tissues in the inactive form. The physiological function of NIM1 has yet to be elucidated. The NIM1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 255 matched cddid_all.tbl CDD cd14076 cd14076 270978 STKc_Kin4 Catalytic domain of the yeast Serine/Threonine Kinase, Kin4. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Kin4 is a central component of the spindle position checkpoint (SPOC), which monitors spindle position and regulates the mitotic exit network (MEN). Kin4 associates with spindle pole bodies in mother cells to inhibit MEN signaling and delay mitosis until the anaphase nucleus is properly positioned along the mother-bud axis. Kin4 activity is regulated by both the bud neck-associated kinase Elm1 and protein phosphatase 2A. The Kin4 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 270 matched cddid_all.tbl CDD cd14077 cd14077 270979 STKc_Kin1_2 Catalytic domain of Kin1, Kin2, and simlar Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of yeast Kin1, Kin2, and similar proteins. Fission yeast Kin1 is a membrane-associated kinase that is involved in regulating cell surface cohesiveness during interphase. It also plays a role during mitosis, linking actomyosin ring assembly with septum synthesis and membrane closure to ensure separation of daughter cells. Budding yeast Kin1 and Kin2 act downstream of the Rab-GTPase Sec4 and are associated with the exocytic apparatus; they play roles in the secretory pathway. The Kin1/2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 267 matched cddid_all.tbl CDD cd14078 cd14078 270980 STKc_MELK Catalytic domain of the Serine/Threonine Kinase, Maternal Embryonic Leucine zipper Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MELK is a cell cycle dependent protein which functions in cytokinesis, cell cycle, apoptosis, cell proliferation, and mRNA processing. It is found upregulated in many types of cancer cells, playing an indispensable role in cancer cell survival. It makes an attractive target in the design of inhibitors for use in the treatment of a wide range of human cancer. The MELK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 257 matched cddid_all.tbl CDD cd14079 cd14079 270981 STKc_AMPK_alpha Catalytic domain of the Alpha subunit of the Serine/Threonine Kinase, AMP-activated protein kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. AMPK, also called SNF1 (sucrose non-fermenting1) in yeasts and SnRK1 (SNF1-related kinase1) in plants, is a heterotrimeric enzyme composed of a catalytic alpha subunit and two regulatory subunits, beta and gamma. It is a stress-activated kinase that serves as master regulator of glucose and lipid metabolism by monitoring carbon and energy supplies, via sensing the cell's AMP:ATP ratio. In response to decreased ATP levels, it enhances energy-producing processes and inhibits energy-consuming pathways. Once activated, AMPK phosphorylates a broad range of downstream targets, with effects in carbohydrate metabolism and uptake, lipid and fatty acid biosynthesis, carbon energy storage, and inflammation, among others. Defects in energy homeostasis underlie many human diseases including Type 2 diabetes, obesity, heart disease, and cancer. As a result, AMPK has emerged as a therapeutic target in the treatment of these diseases. The AMPK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd14080 cd14080 270982 STKc_TSSK-like Catalytic domain of testis-specific serine/threonine kinases and similar proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TSSK proteins are almost exclusively expressed postmeiotically in the testis and play important roles in spermatogenesis and/or spermiogenesis. There are five mammalian TSSK proteins which show differences in their localization and timing of expression. TSSK1 and TSSK2 are expressed specifically in meiotic and postmeiotic spermatogenic cells, respectively. TSSK3 has been reported to be expressed in the interstitial Leydig cells of adult testis. TSSK4, also called TSSK5, is expressed in testis from haploid round spermatids to mature spermatozoa. TSSK6, also called SSTK, is expressed at the head of elongated sperm. TSSK1/TSSK2 double knock-out and TSSK6 null mice are sterile without manifesting other defects, making these kinases viable targets for male contraception. The TSSK-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 262 matched cddid_all.tbl CDD cd14081 cd14081 270983 STKc_BRSK1_2 Catalytic domain of Brain-specific serine/threonine-protein kinases 1 and 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. BRSK1, also called SAD-B or SAD1 (Synapses of Amphids Defective homolog 1), and BRSK2, also called SAD-A, are highly expressed in mammalian forebrain. They play important roles in establishing neuronal polarity. BRSK1/2 double knock-out mice die soon after birth, showing thin cerebral cortices due to disordered subplate layers and neurons that lack distinct axons and dendrites. BRSK1 regulates presynaptic neurotransmitter release. Its activity fluctuates during cell cysle progression and it acts as a regulator of centrosome duplication. BRSK2 is also abundant in pancreatic islets, where it is involved in the regulation of glucose-stimulated insulin secretion. The BRSK1/2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 255 matched cddid_all.tbl CDD cd14082 cd14082 270984 STKc_PKD Catalytic domain of the Serine/Threonine kinase, Protein Kinase D. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PKDs are important regulators of many intracellular signaling pathways such as ERK and JNK, and cellular processes including the organization of the trans-Golgi network, membrane trafficking, cell proliferation, migration, and apoptosis. They contain N-terminal cysteine-rich zinc binding C1 (PKC conserved region 1), central PH (Pleckstrin Homology), and C-terminal catalytic kinase domains. Mammals harbor three types of PKDs: PKD1 (or PKCmu), PKD2, and PKD3 (or PKCnu). PKDs are activated in a PKC-dependent manner by many agents including diacylglycerol (DAG), PDGF, neuropeptides, oxidative stress, and tumor-promoting phorbol esters, among others. The PKD subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 260 matched cddid_all.tbl CDD cd14083 cd14083 270985 STKc_CaMKI Catalytic domain of the Serine/Threonine kinase, Calcium/calmodulin-dependent protein kinase Type I. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CaMKs are multifunctional calcium and calmodulin (CaM) stimulated STKs involved in cell cycle regulation. There are several types of CaMKs including CaMKI, CaMKII, and CaMKIV. In vertebrates, there are four CaMKI proteins encoded by different genes (alpha, beta, gamma, and delta), each producing at least one variant. CaMKs contain an N-terminal catalytic domain and a C-terminal regulatory domain that harbors a CaM binding site. CaMKI proteins are monomeric and they play pivotal roles in the nervous system, including long-term potentiation, dendritic arborization, neurite outgrowth, and the formation of spines, synapses, and axons. In addition, they may be involved in osteoclast differentiation and bone resorption. The CaMKI subfamily is part of a larger superfamily that includes the catalytic domains of other protein kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 259 matched cddid_all.tbl CDD cd14084 cd14084 270986 STKc_Chk2 Catalytic domain of the Serine/Threonine kinase, Cell cycle Checkpoint Kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Checkpoint Kinase 2 (Chk2) plays an important role in cellular responses to DNA double-strand breaks and related lesions. It is phosphorylated and activated by ATM kinase, resulting in its dissociation from sites of damage to phosphorylate downstream targets such as BRCA1, p53, cell cycle transcription factor E2F1, the promyelocytic leukemia protein (PML) involved in apoptosis, and CDC25 phosphatases, among others. Mutations in Chk2 is linked to a variety of cancers including familial breast cancer, myelodysplastic syndromes, prostate cancer, lung cancer, and osteosarcomas. Chk2 contains an N-terminal SQ/TQ cluster domain (SCD), a central forkhead-associated (FHA) domain, and a C-terminal catalytic kinase domain. The Chk2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 275 matched cddid_all.tbl CDD cd14085 cd14085 270987 STKc_CaMKIV Catalytic domain of the Serine/Threonine kinase, Calcium/calmodulin-dependent protein kinase Type IV. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CaMKs are multifunctional calcium and calmodulin (CaM) stimulated STKs involved in cell cycle regulation. There are several types of CaMKs including CaMKI, CaMKII, and CaMKIV. CaMKs contain an N-terminal catalytic domain and a C-terminal regulatory domain that harbors a CaM binding site. CaMKIV is found predominantly in neurons and immune cells. It is activated by the binding of calcium/CaM and phosphorylation by CaMKK (alpha or beta). The CaMKK-CaMKIV cascade participates in regulating several transcription factors like CREB, MEF2, and retinoid orphan receptors. It also is implicated in T-cell development and signaling, cytokine secretion, and signaling through Toll-like receptors, and is thus, pivotal in immune response and inflammation. The CaMKIV subfamily is part of a larger superfamily that includes the catalytic domains of other protein kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 294 matched cddid_all.tbl CDD cd14086 cd14086 270988 STKc_CaMKII Catalytic domain of the Serine/Threonine kinase, Calcium/calmodulin-dependent protein kinase Type II. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CaMKs are multifunctional calcium and calmodulin (CaM) stimulated STKs involved in cell cycle regulation. There are several types of CaMKs including CaMKI, CaMKII, and CaMKIV. CaMKs contain an N-terminal catalytic domain followed by a regulatory domain that harbors a CaM binding site. In addition, CaMKII contains a C-terminal association domain that facilitates oligomerization. There are four CaMKII proteins (alpha, beta, gamma, delta) encoded by different genes; each gene undergoes alternative splicing to produce more than 30 isoforms. CaMKII-alpha and -beta are enriched in neurons while CaMKII-gamma and -delta are predominant in myocardium. CaMKII is a signaling molecule that translates upstream calcium and reactive oxygen species (ROS) signals into downstream responses that play important roles in synaptic function and cardiovascular physiology. It is a major component of the postsynaptic density and is critical in regulating synaptic plasticity including long-term potentiation. It is critical in regulating ion channels and proteins involved in myocardial excitation-contraction and excitation-transcription coupling. Excessive CaMKII activity promotes processes that contribute to heart failure and arrhythmias. The CaMKII subfamily is part of a larger superfamily that includes the catalytic domains of other protein kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 292 matched cddid_all.tbl CDD cd14087 cd14087 270989 STKc_PSKH1 Catalytic domain of the Protein Serine/Threonine kinase H1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PSKH1 is an autophosphorylating STK that is expressed ubiquitously and exhibits multiple intracellular localizations including the centrosome, Golgi apparatus, and splice factor compartments. It contains a catalytic kinase domain and an N-terminal SH4-like motif that is acylated to facilitate membrane attachment. PSKH1 plays a rile in the maintenance of the Golgi apparatus, an important organelle within the secretory pathway. It may also function as a novel splice factor and a regulator of prostate cancer cell growth. The PSKH1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 259 matched cddid_all.tbl CDD cd14088 cd14088 270990 STKc_CaMK_like Catalytic domain of an Uncharacterized group of Serine/Threonine kinases with similarity to Calcium/calmodulin-dependent protein kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of uncharacterized STKs with similarity to CaMKs, which are multifunctional calcium and calmodulin (CaM) stimulated STKs involved in cell cycle regulation. The CaMK family includes CaMKI, CaMKII, CaMKIV, and CaMK kinase (CaMKK). CaMKs contain an N-terminal catalytic domain followed by a regulatory domain that harbors a CaM binding site. This uncharacterized subfamily is part of a larger superfamily that includes the catalytic domains of other protein kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 265 matched cddid_all.tbl CDD cd14089 cd14089 270991 STKc_MAPKAPK Catalytic domain of the Serine/Threonine kinases, Mitogen-activated protein kinase-activated protein kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of the MAPK-activated protein kinases MK2, MK3, MK5 (also called PRAK for p38-regulated/activated protein kinase), and related proteins. These proteins contain a catalytic kinase domain followed by a C-terminal autoinhibitory region that contains nuclear localization (NLS) and nuclear export (NES) signals with a p38 MAPK docking motif that overlaps the NLS. In addition, MK2 and MK3 contain an N-terminal proline-rich region that can bind to SH3 domains. MK2 and MK3 are bonafide substrates for the MAPK p38, while MK5 plays a functional role in the p38 MAPK pathway although their direct interaction has been difficult to detect. MK2 and MK3 are closely related and show, thus far, indistinguishable substrate specificity, while MK5 shows a distinct spectrum of substrates. MK2 and MK3 are mainly involved in the regulation of gene expression and they participate in diverse cellular processes such as endocytosis, cytokine production, cytoskeletal reorganization, cell migration, cell cycle control and chromatin remodeling. They are implicated in inflammation and cance and their substrates include mRNA-AU-rich-element (ARE)-binding proteins (TTP and hnRNP A0), Hsp proteins (Hsp27 and Hsp25) and RSK, among others. MK2/3 are both expressed ubiquitously but MK2 is expressed at significantly higher levels. MK5 is a ubiquitous protein that is implicated in neuronal morphogenesis, cell migration, and tumor angiogenesis. It interacts with PKA, which induces cytoplasmic translocation of MK5. Its substrates includes p53, ERK3/4, Hsp27, and cytosolic phospholipase A2 (cPLA2). The MAPKAPK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 263 matched cddid_all.tbl CDD cd14090 cd14090 270992 STKc_Mnk Catalytic domain of the Serine/Threonine kinases, Mitogen-activated protein kinase signal-integrating kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MAPK signal-integrating kinases (Mnks) are MAPK-activated protein kinases and is comprised by a group of four proteins, produced by alternative splicing from two genes (Mnk1 and Mnk2). The isoforms of Mnk1 (1a/1b) and Mnk2 (2a/2b) differ at their C-termini, with the a-form having a longer C-terminus containing a MAPK-binding region. All Mnks contain a catalytic kinase domain and a polybasic region at the N-terminus which binds importin and the eukaryotic initiation factor eIF4G. The best characterized Mnk substrate is eIF4G, whose phosphorylation may promote the export of certain mRNAs from the nucleus. Mnk also phosphorylate substrates that bind to AU-rich elements that regulate mRNA stability and translation. Mnks have also been implicated in tyrosine kinase receptor signaling, inflammation, and cell prolieration or survival. The Mnk subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 289 matched cddid_all.tbl CDD cd14091 cd14091 270993 STKc_RSK_C C-terminal catalytic domain of the Serine/Threonine Kinases, Ribosomal S6 kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. RSKs contain an N-terminal kinase domain (NTD) from the AGC family and a C-terminal kinase domain (CTD) from the CAMK family. They are activated by signaling inputs from extracellular regulated kinase (ERK) and phosphoinositide dependent kinase 1 (PDK1). ERK phosphorylates and activates the CTD of RSK, serving as a docking site for PDK1, which phosphorylates and activates the NTD, which in turn phosphorylates all known RSK substrates. RSKs act as downstream effectors of mitogen-activated protein kinase (MAPK) and play key roles in mitogen-activated cell growth, differentiation, and survival. Mammals possess four RSK isoforms (RSK1-4) from distinct genes. RSK proteins are also referred to as MAP kinase-activated protein kinases (MAPKAPKs), 90 kDa ribosomal protein S6 kinases (p90-RSKs), or p90S6Ks. The RSK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 291 matched cddid_all.tbl CDD cd14092 cd14092 270994 STKc_MSK_C C-terminal catalytic domain of the Serine/Threonine Kinase, Mitogen and stress-activated kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MSKs contain an N-terminal kinase domain (NTD) from the AGC family and a C-terminal kinase domain (CTD) from the CAMK family. MSKs are activated by two major signaling cascades, the Ras-MAPK and p38 stress kinase pathways, in response to various stimuli such as growth factors, hormones, neurotransmitters, cellular stress, and pro-inflammatory cytokines. This triggers phosphorylation in the activation loop (A-loop) of the CTD of MSK. The active CTD phosphorylates the hydrophobic motif (HM) in the C-terminal extension of NTD, which facilitates the phosphorylation of the A-loop and activates the NTD, which in turn phosphorylates downstream targets. MSKs are predominantly nuclear proteins. They are widely expressed in many tissues including heart, brain, lung, liver, kidney, and pancreas. There are two isoforms of MSK, called MSK1 and MSK2. The MSK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 311 matched cddid_all.tbl CDD cd14093 cd14093 270995 STKc_PhKG Catalytic domain of the Serine/Threonine Kinase, Phosphorylase kinase Gamma subunit. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Phosphorylase kinase (PhK) catalyzes the phosphorylation of inactive phosphorylase b to form the active phosphorylase a. It coordinates hormonal, metabolic, and neuronal signals to initiate the breakdown of glycogen stores, which enables the maintenance of blood-glucose homeostasis during fasting, and is also used as a source of energy for muscle contraction. PhK is one of the largest and most complex protein kinases, composed of a heterotetramer containing four molecules each of four subunit types: one catalytic (gamma) and three regulatory (alpha, beta, and delta). Each subunit has tissue-specific isoforms or splice variants. Vertebrates contain two isoforms of the gamma subunit (gamma 1 and gamma 2). The gamma subunit, when isolated, is constitutively active and does not require phosphorylation of the A-loop for activity. The regulatory subunits restrain this kinase activity until signals are received to relieve this inhibition. For example, the kinase is activated in response to hormonal stimulation, after autophosphorylation or phosphorylation by cAMP-dependent kinase of the alpha and beta subunits. The high-affinity binding of ADP to the beta subunit also stimulates kinase activity, whereas calcium relieves inhibition by binding to the delta (calmodulin) subunit. The PhKG subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 272 matched cddid_all.tbl CDD cd14094 cd14094 270996 STKc_CASK Catalytic domain of the Serine/Threonine Kinase, Calcium/calmodulin-dependent serine protein kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CASK belongs to the MAGUK (membrane-associated guanylate kinase) protein family, which functions as multiple domain adaptor proteins and is characterized by the presence of a core of three domains: PDZ, SH3, and guanylate kinase (GuK). The enzymatically inactive GuK domain in MAGUK proteins mediates protein-protein interactions and associates intramolecularly with the SH3 domain. In addition, CASK contains a catalytic kinase and two L27 domains. It is highly expressed in the nervous system and plays roles in synaptic protein targeting, neural development, and regulation of gene expression. Binding partners include parkin (a Parkinson's disease molecule), neurexin (adhesion molecule), syndecans, calcium channel proteins, CINAP (nucleosome assembly protein), transcription factor Tbr-1, and the cytoplasmic adaptor proteins Mint1, Veli/mLIN-7/MALS, SAP97, caskin, and CIP98. Deletion or mutations in the CASK gene have been implicated in X-linked mental retardation. The CASK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 300 matched cddid_all.tbl CDD cd14095 cd14095 270997 STKc_DCKL Catalytic domain of the Serine/Threonine Kinase, Doublecortin-like kinase (also called Doublecortin-like and CAM kinase-like). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. DCKL (or DCAMKL) proteins belong to the doublecortin (DCX) family of proteins which are involved in neuronal migration, neurogenesis, and eye receptor development, among others. Family members typically contain tandem doublecortin (DCX) domains at the N-terminus; DCX domains can bind microtubules and serve as protein-interaction platforms. In addition, DCKL proteins contain a C-terminal kinase domain with similarity to CAMKs. They are involved in the regulation of cAMP signaling. Vertebrates contain three DCKL proteins (DCKL1-3); DCKL1 and 2 also contain a serine, threonine, and proline rich domain (SP), while DCKL3 contains only a single DCX domain instead of tandem domains. The DCKL subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 258 matched cddid_all.tbl CDD cd14096 cd14096 270998 STKc_RCK1-like Catalytic domain of RCK1-like Serine/Threonine Kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of fungal STKs including Saccharomyces cerevisiae RCK1 and RCK2, Schizosaccharomyces pombe Sty1-regulated kinase 1 (Srk1), and similar proteins. RCK1, RCK2 (or Rck2p), and Srk1 are MAPK-activated protein kinases. RCK1 and RCK2 are involved in oxidative and metal stress resistance in budding yeast. RCK2 also regulates rapamycin sensitivity in both S. cerevisiae and Candida albicans. Srk1 is activated by Sty1/Spc1 and is involved in negatively regulating cell cycle progression by inhibiting Cdc25. The RCK1-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 295 matched cddid_all.tbl CDD cd14097 cd14097 270999 STKc_STK33 Catalytic domain of Serine/Threonine Kinase 33. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. STK33 is highly expressed in the testis and is present in low levels in most tissues. It may be involved in spermatogenesis and organ ontogenesis. It interacts with and phosphorylates vimentin and may be involved in regulating intermediate filament cytoskeletal dynamics. Its role in promoting the cell viability of KRAS-dependent cancer cells is under debate; some studies have found STK33 to promote cancer cell viability, while other studies have found it to be non-essential. KRAS is the most commonly mutated human oncogene, thus, studies on the role of STK33 in KRAS mutant cancer cells are important. The STK33 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 266 matched cddid_all.tbl CDD cd14098 cd14098 271000 STKc_Rad53_Cds1 Catalytic domain of the yeast Serine/Threonine Kinases, Rad53 and Cds1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Rad53 and Cds1 are the checkpoint kinase 2 (Chk2) homologs found in budding and fission yeast, respectively. They play a central role in the cell's response to DNA lesions to prevent genome rearrangements and maintain genome integrity. They are phosphorylated in response to DNA damage and incomplete replication, and are essential for checkpoint control. They help promote DNA repair by stalling the cell cycle prior to mitosis in the presence of DNA damage. The Rad53/Cds1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 265 matched cddid_all.tbl CDD cd14099 cd14099 271001 STKc_PLK Catalytic domain of the Serine/Threonine Kinases, Polo-like kinases. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PLKs play important roles in cell cycle progression and in DNA damage responses. They regulate mitotic entry, mitotic exit, and cytokinesis. In general PLKs contain an N-terminal catalytic kinase domain and a C-terminal regulatory polo box domain (PBD), which is comprised by two bipartite polo-box motifs (or polo boxes) and is involved in protein interactions. PLKs derive their names from homology to polo, a kinase first identified in Drosophila. There are five mammalian PLKs (PLK1-5) from distinct genes. There is good evidence that PLK1 may function as an oncogene while PLK2-5 have tumor suppressive properties. PLK1 functions as a positive regulator of mitosis, meiosis, and cytokinesis. PLK2 functions in G1 progression, S-phase arrest, and centriole duplication. PLK3 regulates angiogenesis and responses to DNA damage. PLK4 is required for late mitotic progression, cell survival, and embryonic development. PLK5 was first identified as a pseudogene containing a stop codon within the kinase domain, however, both murine and human genes encode expressed proteins. PLK5 functions in cell cycle arrest. 258 matched cddid_all.tbl CDD cd14100 cd14100 271002 STKc_PIM1 Catalytic domain of the Serine/Threonine kinase, Proviral Integration Moloney virus (PIM) kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The PIM gene locus was discovered as a result of the cloning of retroviral intergration sites in murine Moloney leukemia virus, leading to the identification of PIM kinases. They are constitutively active STKs with a broad range of cellular targets and are overexpressed in many haematopoietic malignancies and solid cancers. Vertebrates contain three distinct PIM kinase genes (PIM1-3); each gene may result in mutliple protein isoforms. There are two PIM1 isoforms resulting from alternative translation initiation sites. PIM1 is the founding member of the PIM subfamily. It is involved in regulating cell growth, differentiation, and apoptosis. It promotes cancer development when overexpressed by inhibiting apoptosis, promoting cell proliferation, and promoting genomic instability. The PIM1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 254 matched cddid_all.tbl CDD cd14101 cd14101 271003 STKc_PIM2 Catalytic domain of the Serine/Threonine kinase, Proviral Integration Moloney virus (PIM) kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The PIM gene locus was discovered as a result of the cloning of retroviral intergration sites in murine Moloney leukemia virus, leading to the identification of PIM kinases. They are constitutively active STKs with a broad range of cellular targets and are overexpressed in many haematopoietic malignancies and solid cancers. Vertebrates contain three distinct PIM kinase genes (PIM1-3); each gene may result in mutliple protein isoforms. There are three PIM2 isoforms resulting from alternative translation initiation sites. PIM2 is highly expressed in leukemia and lymphomas and has been shown to promote the survival and proliferation of tumor cells. The PIM2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 257 matched cddid_all.tbl CDD cd14102 cd14102 271004 STKc_PIM3 Catalytic domain of the Serine/Threonine kinase, Proviral Integration Moloney virus (PIM) kinase 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The PIM gene locus was discovered as a result of the cloning of retroviral intergration sites in murine Moloney leukemia virus, leading to the identification of PIM kinases. They are constitutively active STKs with a broad range of cellular targets and are overexpressed in many haematopoietic malignancies and solid cancers. Vertebrates contain three distinct PIM kinase genes (PIM1-3). PIM3 can inhibit apoptosis and promote cell survival and protein translation, therefore, it can enhance the proliferation of normal and cancer cells. Mice deficient with PIM3 show minimal effects, suggesting that PIM3 msy not be essential. Since its expression is enhanced in several cancers, it may make a good molecular target for cancer drugs. The PIM3 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 253 matched cddid_all.tbl CDD cd14103 cd14103 271005 STKc_MLCK Catalytic domain of the Serine/Threonine Kinase, Myosin Light Chain Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MLCK phosphorylates myosin regulatory light chain and controls the contraction of all muscle types. In vertebrates, different MLCKs function in smooth (MLCK1), skeletal (MLCK2), and cardiac (MLCK3) muscles. A fourth protein, MLCK4, has also been identified through comprehensive genome analysis although it has not been biochemically characterized. The MLCK1 gene expresses three transcripts in a cell-specific manner: a short MLCK1 which contains three immunoglobulin (Ig)-like and one fibronectin type III (FN3) domains, PEVK and actin-binding regions, and a kinase domain near the C-terminus; a long MLCK1 containing six additional Ig-like domains at the N-terminus compared to the short MLCK1; and the C-terminal Ig module. MLCK2, MLCK3, and MLCK4 share a simpler domain architecture of a single kinase domain near the C-terminus and the absence of Ig-like or FN3 domains. The MLCK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 250 matched cddid_all.tbl CDD cd14104 cd14104 271006 STKc_Titin Catalytic domain of the Giant Serine/Threonine Kinase Titin. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Titin, also called connectin, is a muscle-specific elastic protein and is the largest known protein to date. It contains multiple immunoglobulin (Ig)-like and fibronectin type III (FN3) domains, and a single kinase domain near the C-terminus. It spans half of the sarcomere, the repeating contractile unit of striated muscle, and performs mechanical and catalytic functions. Titin contributes to the passive force generated when muscle is stretched during relaxation. Its kinase domain phosphorylates and regulates the muscle protein telethonin, which is required for sarcomere formation in differentiating myocytes. In addition, titin binds many sarcomere proteins and acts as a molecular scaffold for filament formation during myofibrillogenesis. The Titin subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 277 matched cddid_all.tbl CDD cd14105 cd14105 271007 STKc_DAPK Catalytic domain of the Serine/Threonine Kinase, Death-Associated Protein Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. DAPKs mediate cell death and act as tumor suppressors. They are necessary to induce cell death and their overexpression leads to death-associated changes including membrane blebbing, cell rounding, and formation of autophagic vesicles. Vertebrates contain three subfamily members with different domain architecture, localization, and function. DAPK1 is the prototypical member of the subfamily and is also simply referred to as DAPK. DAPK2 is also called DAPK-related protein 1 (DRP-1), while DAPK3 has also been named DAP-like kinase (DLK) and zipper-interacting protein kinase (ZIPk). These proteins are ubiquitously expressed in adult tissues, are capable of cross talk with each other, and may act synergistically in regulating cell death. The DAPK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 269 matched cddid_all.tbl CDD cd14106 cd14106 271008 STKc_DRAK Catalytic domain of the Serine/Threonine Kinase, Death-associated protein kinase-Related Apoptosis-inducing protein Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. DRAKs, also called STK17, were named based on their similarity (around 50% identity) to the kinase domain of DAPKs. They contain an N-terminal kinase domain and a C-terminal regulatory domain. Vertebrates contain two subfamily members, DRAK1 and DRAK2. Both DRAKs are localized to the nucleus, autophosphorylate themselves, and phosphorylate myosin light chain as a substrate. They may play a role in apoptotic signaling. The DRAK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 268 matched cddid_all.tbl CDD cd14107 cd14107 271009 STKc_obscurin_rpt1 Catalytic kinase domain, first repeat, of the Giant Serine/Threonine Kinase Obscurin. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Obscurin, approximately 800 kDa in size, is one of three giant proteins expressed in vetebrate striated muscle, together with titin and nebulin. It is a multidomain protein composed of tandem adhesion and signaling domains, including 49 immunoglobulin (Ig) and 2 fibronectin type III (FN3) domains at the N-terminus followed by a more complex region containing more Ig domains, a conserved SH3 domain near a RhoGEF and PH domains, non-modular regions, as well as IQ and phosphorylation motifs. The obscurin gene also encode two kinase domains, which are not expressed as part of the 800 kDa protein, but as a smaller, alternatively spliced product present mainly in the heart muscle, also called obscurin-MLCK. Obscurin is localized at the peripheries of Z-disks and M-lines, where it is able to communicate with the surrounding myoplasm. It interacts with diverse proteins including sAnk1, myosin, titin, and MyBP-C. It may act as a scaffold for the assembly of elements of the contractile apparatus. The obscurin subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 257 matched cddid_all.tbl CDD cd14108 cd14108 271010 STKc_SPEG_rpt1 Catalytic kinase domain, first repeat, of Giant Serine/Threonine Kinase Striated muscle preferentially expressed protein kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The Striated muscle preferentially expressed gene (SPEG) generates 4 different isoforms through alternative promoter use and splicing in a tissue-specific manner: SPEGalpha and SPEGbeta are expressed in cardiac and skeletal striated muscle; Aortic Preferentially Expressed Protein-1 (APEG-1) is expressed in vascular smooth muscle; and Brain preferentially expressed gene (BPEG) is found in the brain and aorta. SPEG proteins have mutliple immunoglobulin (Ig), 2 fibronectin type III (FN3), and two kinase domains. They are necessary for cardiac development and survival. The SPEG subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 255 matched cddid_all.tbl CDD cd14109 cd14109 271011 PK_Unc-89_rpt1 Pseudokinase domain, first repeat, of the Giant Serine/Threonine Kinase Uncoordinated protein 89. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. The nematode Unc-89 gene, through alternative promoter use and splicing, encodes at least six major isoforms (Unc-89A to Unc-89F) of giant muscle proteins that are homologs for the vetebrate obscurin. In flies, five isoforms of Unc-89 have been detected: four in the muscles of adult flies (two in the indirect flight muscle and two in other muscles) and another isoform in the larva. Unc-89 in nematodes is required for normal muscle cell architecture. In flies, it is necessary for the development of a symmetrical sarcomere in the flight muscles. Unc-89 proteins contain several adhesion and signaling domains including multiple copies of the immunoglobulin (Ig) domain, as well as fibronectin type III (FN3), SH3, RhoGEF, and PH domains. The nematode Unc-89 isoforms D, C, D, and F contain two kinase domain with B and F having two complete kinase domains while the first repeat of C and D are partial domains. Homology modeling suggests that the first kinase repeat of Unc-89 may be catalytically inactive, a pseudokinase, while the second kinase repeat may be active. The pseudokinase domain may function as a regulatory domain or a protein interaction domain. The Unc-89 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 255 matched cddid_all.tbl CDD cd14110 cd14110 271012 STKc_obscurin_rpt2 Catalytic kinase domain, second repeat, of the Giant Serine/Threonine Kinase Obscurin. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Obscurin, approximately 800 kDa in size, is one of three giant proteins expressed in vetebrate striated muscle, together with titin and nebulin. It is a multidomain protein composed of tandem adhesion and signaling domains, including 49 immunoglobulin (Ig) and 2 fibronectin type III (FN3) domains at the N-terminus followed by a more complex region containing more Ig domains, a conserved SH3 domain near a RhoGEF and PH domains, non-modular regions, as well as IQ and phosphorylation motifs. The obscurin gene also encode two kinase domains, which are not expressed as part of the 800 kDa protein, but as a smaller, alternatively spliced product present mainly in the heart muscle, also called obscurin-MLCK. Obscurin is localized at the peripheries of Z-disks and M-lines, where it is able to communicate with the surrounding myoplasm. It interacts with diverse proteins including sAnk1, myosin, titin, and MyBP-C. It may act as a scaffold for the assembly of elements of the contractile apparatus. The obscurin subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 257 matched cddid_all.tbl CDD cd14111 cd14111 271013 STKc_SPEG_rpt2 Catalytic kinase domain, second repeat, of Giant Serine/Threonine Kinase Striated muscle preferentially expressed protein kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The Striated muscle preferentially expressed gene (SPEG) generates 4 different isoforms through alternative promoter use and splicing in a tissue-specific manner: SPEGalpha and SPEGbeta are expressed in cardiac and skeletal striated muscle; Aortic Preferentially Expressed Protein-1 (APEG-1) is expressed in vascular smooth muscle; and Brain preferentially expressed gene (BPEG) is found in the brain and aorta. SPEG proteins have mutliple immunoglobulin (Ig), 2 fibronectin type III (FN3), and two kinase domains. They are necessary for cardiac development and survival. The SPEG subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 257 matched cddid_all.tbl CDD cd14112 cd14112 271014 STKc_Unc-89_rpt2 Catalytic kinase domain, second repeat, of the Giant Serine/Threonine Kinase Uncoordinated protein 89. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The nematode Unc-89 gene, through alternative promoter use and splicing, encodes at least six major isoforms (Unc-89A to Unc-89F) of giant muscle proteins that are homologs for the vetebrate obscurin. In flies, five isoforms of Unc-89 have been detected: four in the muscles of adult flies (two in the indirect flight muscle and two in other muscles) and another isoform in the larva. Unc-89 in nematodes is required for normal muscle cell architecture. In flies, it is necessary for the development of a symmetrical sarcomere in the flight muscles. Unc-89 proteins contain several adhesion and signaling domains including multiple copies of the immunoglobulin (Ig) domain, as well as fibronectin type III (FN3), SH3, RhoGEF, and PH domains. The nematode Unc-89 isoforms D, C, D, and F contain two kinase domain with B and F having two complete kinase domains while the first repeat of C and D are partial domains. Homology modeling suggests that the first kinase repeat of Unc-89 may be catalytically inactive, a pseudokinase, while the second kinase repeat may be active. The Unc-89 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 259 matched cddid_all.tbl CDD cd14113 cd14113 271015 STKc_Trio_C C-terminal kinase domain of the Large Serine/Threonine Kinase and Rho Guanine Nucleotide Exchange Factor, Triple functional domain protein. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Triple functional domain protein (Trio), also called PTPRF-interacting protein, is a large multidomain protein containing a series of spectrin-like repeats, two each of RhoGEF and SH3 domains, an immunoglobulin-like (Ig) domain and a C-terminal kinase. Trio plays important roles in neuronal cell migration and axon guidance. It was originally identified as an interacting partner of the of the receptor-like tyrosine phosphatase (RPTP) LAR (leukocyte-antigen-related protein), a family of receptors that function in the signaling to the actin cytoskeleton during development. Trio functions as a GEF for Rac1, RhoG, and RhoA, and is involved in the regulation of lamellipodia formation, mediating Rac1-dependent cell spreading and migration. The Trio subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 263 matched cddid_all.tbl CDD cd14114 cd14114 271016 STKc_Twitchin_like The catalytic domain of the Giant Serine/Threonine Kinases, Twitchin and Projectin. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily is composed of Caenorhabditis elegans and Aplysia californica Twitchin, Drosophila melanogaster Projectin, and similar proteins. These are very large muscle proteins containing multiple immunoglobulin (Ig)-like and fibronectin type III (FN3) domains and a single kinase domain near the C-terminus. Twitchin and Projectin are both associated with thick filaments. Twitchin is localized in the outer parts of A-bands and is involved in regulating muscle contraction. It interacts with the myofibrillar proteins myosin and actin in a phosphorylation-dependent manner, and may be involved in regulating the myosin cross-bridge cycle. The kinase activity of Twitchen is activated by Ca2+ and the Ca2+ binding protein S100A1. Projectin is associated with the end of thick filaments and is a component of flight muscle connecting filaments. The kinase domain of Projectin may play roles in autophosphorylation and transphosphorylation, which impact the formation of myosin filaments. The Twitchin-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 259 matched cddid_all.tbl CDD cd14115 cd14115 271017 STKc_Kalirin_C C-terminal kinase domain of the Large Serine/Threonine Kinase and Rho Guanine Nucleotide Exchange Factor, Kalirin. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Kalirin, also called Duo or Duet, is a large multidomain protein containing a series of spectrin-like repeats, two each of RhoGEF and SH3 domains, an immunoglobulin-like (Ig) domain and a C-terminal kinase. As a GEF, it activates Rac1, RhoA, and RhoG. It is highly expressed in neurons and is required for spine formation. The kalirin gene produces at least 10 isoforms from alternative promoter use and splicing. Of the major isoforms (Kalirin-7, -9, and -12), only kalirin-12 contains the C-terminal kinase domain. Kalirin-12 is highly expressed during embryonic development and it plays an important role in axon outgrowth. The Kalirin subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 248 matched cddid_all.tbl CDD cd14116 cd14116 271018 STKc_Aurora-A Catalytic domain of the Serine/Threonine kinase, Aurora-A kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Aurora kinases are key regulators of mitosis and are essential for the accurate and equal division of genomic material from parent to daughter cells. Vertebrates contain at least 2 Aurora kinases (A and B); mammals contains a third Aurora kinase gene (C). Aurora-A regulates cell cycle events from the late S-phase through the M-phase including centrosome maturation, mitotic entry, centrosome separation, spindle assembly, chromosome alignment, cytokinesis, and mitotic exit. Aurora-A activation depends on its autophosphorylation and binding to the microtubule-associated protein TPX2, which also localizes the kinase to spindle microtubules. Aurora-A is overexpressed in many cancer types such as prostate, ovarian, breast, bladder, gastric, and pancreatic. The Aurora subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 258 matched cddid_all.tbl CDD cd14117 cd14117 271019 STKc_Aurora-B_like Catalytic domain of the Serine/Threonine kinase, Aurora-B kinase and similar proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Aurora kinases are key regulators of mitosis and are essential for the accurate and equal division of genomic material from parent to daughter cells. Vertebrates contain at least 2 Aurora kinases (A and B); mammals contains a third Aurora kinase gene (C). This subfamily includes Aurora-B and Aurora-C. Aurora-B is most active at the transition during metaphase to the end of mitosis. It associates with centromeres, relocates to the midzone of the central spindle, and concentrates at the midbody during cell division. It is critical for accurate chromosomal segregation, cytokinesis, protein localization to the centrosome and kinetochore, correct microtubule-kinetochore attachments, and regulation of the mitotic checkpoint. Aurora-C is mainly expressed in meiotically dividing cells; it was originally discovered in mice as a testis-specific STK called Aie1. Both Aurora-B and -C are chromosomal passenger proteins that can form complexes with INCENP and survivin, and they may have redundant cellular functions. INCENP participates in the activation of Aurora-B in a two-step process: first by binding to form an intermediate state of activation and the phosphorylation of its C-terminal TSS motif to generate the fully active kinase. The Aurora-B subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 270 matched cddid_all.tbl CDD cd14118 cd14118 271020 STKc_CAMKK Catalytic domain of the Serine/Threonine kinase, Calmodulin Dependent Protein Kinase Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CaMKKs are upstream kinases of the CaM kinase cascade that phosphorylate and activate CaMKI and CamKIV. They may also phosphorylate other substrates including PKB and AMP-activated protein kinase (AMPK). Vertebrates contain two CaMKKs, CaMKK1 (or alpha) and CaMKK2 (or beta). CaMKK1 is involved in the regulation of glucose uptake in skeletal muscles. CaMKK2 is involved in regulating energy balance, glucose metabolism, adiposity, hematopoiesis, inflammation, and cancer. The CaMKK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 275 matched cddid_all.tbl CDD cd14119 cd14119 271021 STKc_LKB1 Catalytic domain of the Serine/Threonine kinase, Liver Kinase B1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. LKB1, also called STK11, was first identified as a tumor suppressor responsible for Peutz-Jeghers syndrome, a disorder that leads to an increased risk of spontaneous epithelial cancer. It serves as a master upstream kinase that activates AMP-activated protein kinase (AMPK) and most AMPK-like kinases. LKB1 and AMPK are part of an energy-sensing pathway that links cell energy to metabolism and cell growth. They play critical roles in the establishment and maintenance of cell polarity, cell proliferation, cytoskeletal organization, as well as T-cell metabolism, including T-cell development, homeostasis, and effector function. To be activated, LKB1 requires the adaptor proteins STe20-Related ADaptor (STRAD) and mouse protein 25 (MO25). The LKB1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 255 matched cddid_all.tbl CDD cd14120 cd14120 271022 STKc_ULK1_2-like Catalytic domain of the Serine/Threonine kinases, Unc-51-like kinases 1 and 2, and similar proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The ATG1/ULK complex is conserved from yeast to humans and it plays a critical role in the initiation of autophagy, the intracellular system that leads to the lysosomal degradation of cellular components and their recycling into basic metabolic units. ULK1 is required for efficient amino acid starvation-induced autophagy and mitochondrial clearance. ULK2 is ubiquitously expressed and is essential in autophagy induction. ULK1 and ULK2 have unique and cell-type specific roles, but also display partially redundant roles in starvation-induced autophagy. They both display neuron-specific functions: ULK1 is involved in non-clathrin-coated endocytosis in growth cones, filopodia extension, and axon branching; ULK2 plays a role in axon development. The ULK1/2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd14121 cd14121 271023 STKc_ULK3 Catalytic domain of the Serine/Threonine kinase, Unc-51-like kinase 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The ATG1/ULK complex is conserved from yeast to humans and it plays a critical role in the initiation of autophagy, the intracellular system that leads to the lysosomal degradation of cellular components and their recycling into basic metabolic units. ULK3 mRNA is up-regulated in fibroblasts after Ras-induced senescence, and its overexpression induces both autophagy and senescence in a fibroblast cell line. ULK3, through its kinase activity, positively regulates Gli proteins, mediators of the Sonic hedgehog (Shh) signaling pathway that is implicated in tissue homeostasis maintenance and neurogenesis. It is inhibited by binding to Suppressor of Fused (Sufu). The ULK3 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 252 matched cddid_all.tbl CDD cd14122 cd14122 271024 STKc_VRK1 Catalytic domain of the Serine/Threonine protein kinase, Vaccinia Related Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. VRKs were initially discovered due to its similarity to vaccinia virus B1R STK, which is important for viral replication. Vertebrates contain three VRK proteins. Human VRK1 is implicated in the regulation of many cellular processes including cell cycle progression and proliferation, stress responses, nuclear envelope assembly and chromatin condensation. It regulates cell cycle progression during the DNA replication period by inducing cyclin D1 expression. VRK1 also phosphorylates and regulates some transcription factors including p53, c-Jun, ATF2, and nuclear factor BAF. VRK1 stabilizes p53 by interfering with its mdm2-mediated degradation. Accumulation of p53, which blocks cell growth and division, is modulated by an autoregulatory loop between p53 and VRK1 (accumulated p53 downregulates VRK1). This autoregulatory loop has been found to be nonfunctional in some lung carcinomas. The VRK1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 301 matched cddid_all.tbl CDD cd14123 cd14123 271025 STKc_VRK2 Catalytic domain of the Serine/Threonine protein kinase, Vaccinia Related Kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. VRKs were initially discovered due to its similarity to vaccinia virus B1R STK, which is important for viral replication. They play important roles in cell signaling, nuclear envelope dynamics, apoptosis, and stress responses. Vertebrates contain three VRK proteins. VRK2 exists as two alternative splice forms, A and B, which differ in their C-terminal regions. VRK2A, the predominant isoform, contains a hydrophobic tail and is anchored to the ER and mitochondria. It is expressed in all cell types. VRK2B lacks a membrane-anchor tail and is detected in the cytosol and the nucleus. Like VRK1, it can stabilize p53. VRK2B functionally replaces VRK1 in the nucleus of cell types where VRK1 is absent. VRK2 modulates hypoxia-induced stress responses by interacting with TAK1, an atypical MAPK kinase kinase which triggers cascades that activate JNK following oxidative stress. VRK2 also interacts with JIP1, a scaffold protein that assembles three consecutive members of a MAPK pathway. This interaction prevents the association of JNK with the signaling complex, leading to reduced phosphorylation and AP1-dependent transcription. The VRK2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 302 matched cddid_all.tbl CDD cd14124 cd14124 271026 PK_VRK3 Pseudokinase domain of Vaccinia Related Kinase 3. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. VRKs were initially discovered due to its similarity to vaccinia virus B1R STK, which is important for viral replication. They play important roles in cell signaling, nuclear envelope dynamics, apoptosis, and stress responses. Vertebrates contain three VRK proteins. VRK3 is an inactive pseudokinase that is unable to bind ATP. It achieves its regulatory function through protein-protein interactions. It negatively regulates ERK signaling by binding directly and enhancing the activity of the MAPK phosphatase VHR (vaccinia H1-related), which dephosphorylates and inactivates ERK. The VRK3 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 298 matched cddid_all.tbl CDD cd14125 cd14125 271027 STKc_CK1_delta_epsilon Catalytic domain of the Serine/Threonine protein kinases, Casein Kinase 1 delta and epsilon. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CK1 phosphorylates a variety of substrates including enzymes, transcription and splice factors, cytoskeletal proteins, viral oncogenes, receptors, and membrane-associated proteins. There are mutliple isoforms of CK1 and in mammals, seven isoforms (alpha, beta, gamma1-3, delta, and epsilon) have been characterized. These isoforms differ mainly in the length and structure of their C-terminal non-catalytic region. The delta and epsilon isoforms of CK1 play important roles in circadian rhythm and cell growth. They phosphorylate PERIOD proteins (PER1-3), which are circadian clock proteins that fulfill negative regulatory functions. PER phosphorylation leads to its degradation. However, CRY proteins form a complex with PER and CK1delta/epsilon that protects PER from degradation and leads to nuclear accummulation of the complex, which inhibits BMAL1-CLOCK dependent transcription activation. CK1delta/epsilon also phosphorylate the tumor suppressor p53 and the cellular oncogene Mdm2, which are key regulators of cell growth, genome integrity, and the development of cancer. This subfamily also includes the CK1 fungal proteins Saccharomyces cerevisiae HRR25 and Schizosaccharomyces pombe HHP1. These fungal proteins are involved in DNA repair. The CK1 delta/epsilon subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 275 matched cddid_all.tbl CDD cd14126 cd14126 271028 STKc_CK1_gamma Catalytic domain of the Serine/Threonine protein kinase, Casein Kinase 1 gamma. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CK1 phosphorylates a variety of substrates including enzymes, transcription and splice factors, cytoskeletal proteins, viral oncogenes, receptors, and membrane-associated proteins. There are mutliple isoforms of CK1 and in mammals, seven isoforms (alpha, beta, gamma1-3, delta, and epsilon) have been characterized. These isoforms differ mainly in the length and structure of their C-terminal non-catalytic region. CK1gamma proteins are unique within the CK1 subfamily in that they are palmitoylated at the C-termini and are anchored to the plasma membrane. CK1gamma is involved in transducing the signaling of LDL-receptor-related protein 6 (LRP6) through direct phosphorylation following Wnt stimulation, resulting in the recruitment of the scaffold protein Axin. In Xenopus embryos, CK1gamma is required during anterio-posterior patterning. In higher vertebrates, three CK1gamma (gamma1-3) isoforms exist. In mammalian cells, CK1gamma2 has been implicated in regulating the synthesis of sphingomyelin, a phospholipid that is found in the outer leaflet of the plasma membrane, by hyperphosphorylating and inactivating the ceramide transfer protein CERT. CK1gamma2 also phosphorylates the transcription factor Smad-3 resulting in its ubiquitination and degradation. It inhibits Smad-3 mediated responses of Transforming Growth Factor-beta (TGF-beta) including cell growth arrest. The CK1 gamma subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 288 matched cddid_all.tbl CDD cd14127 cd14127 271029 STKc_CK1_fungal Catalytic domain of the Serine/Threonine protein kinase, Fungal Casein Kinase 1 homolog 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CK1 phosphorylates a variety of substrates including enzymes, transcription and splice factors, cytoskeletal proteins, viral oncogenes, receptors, and membrane-associated proteins. There are mutliple isoforms of CK1 and in mammals, seven isoforms (alpha, beta, gamma1-3, delta, and epsilon) have been characterized. These isoforms differ mainly in the length and structure of their C-terminal non-catalytic region. This subfamily is composed of fungal CK1 homolog 1 proteins, also called Yck1 in Saccharomyces cerevisiae and Cki1 in Schizosaccharomyces pombe. Yck1 (or Yck1p) and Cki1 are plasma membrane-anchored proteins. Yck1 phosphorylates and regulates Khd1p, a RNA-binding protein that represses translation of bud-localized mRNA. Cki1 phosphorylates and regulates phosphatidylinositol (PI)-(4)P-5-kinase, which catalyzes the last step in the sythesis of PI(4,5)P2, which is involved in actin cytoskeleton remodeling and membrane traffic. The fungal CK1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 277 matched cddid_all.tbl CDD cd14128 cd14128 271030 STKc_CK1_alpha Catalytic domain of the Serine/Threonine protein kinases, Casein Kinase 1 alpha. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CK1 phosphorylates a variety of substrates including enzymes, transcription and splice factors, cytoskeletal proteins, viral oncogenes, receptors, and membrane-associated proteins. There are mutliple isoforms of CK1 and in mammals, seven isoforms (alpha, beta, gamma1-3, delta, and epsilon) have been characterized. These isoforms differ mainly in the length and structure of their C-terminal non-catalytic region. CK1alpha plays a role in cell cycle progression, spindle dynamics, and chromosome segregation. It is also involved in regulating apoptosis mediated by Fas or the retinoid X receptor (RXR), and is a positive regulator of Wnt signaling. CK1alpha phosphorylates the NS5A protein of flaviviruses such as the Hepatitis C virus (HCV) and yellow fever virus (YFV), and influences flaviviral replication. The CK1 alpha subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 266 matched cddid_all.tbl CDD cd14129 cd14129 271031 STKc_TTBK2 Catalytic domain of the Serine/Threonine protein kinase, Tau-Tubulin Kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TTBK is a neuron-specific kinase that phosphorylates the microtubule-associated protein tau and promotes its aggregation. Higher vertebrates contain two TTBK proteins, TTBK1 and TTBK2, both of which have been implicated in neurodegeneration. Mutations in TTBK2 is associated with the development of spinocerebellar ataxia type 11, belonging to a group of neurodegenerative disorders characterized by progressive incoordination, dysarthria and impairment of eye movements. Brain tissues of SCA11 patients show the presence of neurofibrillary tangles and tau deposition in the brain, similar to Alzheimer's disease (AD) patients. The TTBK2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 262 matched cddid_all.tbl CDD cd14130 cd14130 271032 STKc_TTBK1 Catalytic domain of the Serine/Threonine protein kinase, Tau-Tubulin Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TTBK is a neuron-specific kinase that phosphorylates the microtubule-associated protein tau and promotes its aggregation. Higher vertebrates contain two TTBK proteins, TTBK1 and TTBK2, both of which have been implicated in neurodegeneration. Genetic variations in TTBK1 are linked to Alzheimer's disease (AD). Hyperphosphorylated tau is a major component of paired helical filaments that accumulate in the brain of AD patients. Studies in transgenic mice show that TTBK1 is involved in the phosphorylation-dependent pathogenic aggregation of tau. The TTBK1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 262 matched cddid_all.tbl CDD cd14131 cd14131 271033 PKc_Mps1 Catalytic domain of the Dual-specificity Mitotic checkpoint protein kinase, Monopolar spindle 1 (also called TTK). Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine as well as tyrosine residues on protein substrates. TTK/Mps1 is a spindle checkpoint kinase that was first discovered due to its necessity in centrosome duplication in budding yeast. It was later found to function in the spindle assembly checkpoint, which monitors the proper attachment of chromosomes to the mitotic spindle. In yeast, substrates of Mps1 include the spindle pole body components Spc98p, Spc110p, and Spc42p. The TTK/Mps1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine PKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 271 matched cddid_all.tbl CDD cd14132 cd14132 271034 STKc_CK2_alpha Catalytic subunit (alpha) of the Serine/Threonine Kinase, Casein Kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CK2 is a tetrameric protein with two catalytic (alpha) and two regulatory (beta) subunits. It is constitutively active and ubiquitously expressed, and is found in the cytoplasm, nucleus, as well as in the plasma membrane. It phosphorylates a wide variety of substrates including gylcogen synthase, cell cycle proteins, nuclear proteins (e.g. DNA topoisomerase II), and ion channels (e.g. ENaC), among others. It may be considered a master kinase controlling the activity or lifespan of many other kinases and exerting its effect over cell fate, gene expression, protein synthesis and degradation, and viral infection. CK2 is implicated in every stage of the cell cycle and is required for cell cycle progression. It plays crucial roles in cell differentiation, proliferation, and survival, and is thus implicated in cancer. CK2 is not an oncogene by itself but elevated CK2 levels create an environment that enhances the survival of tumor cells. The CK2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 306 matched cddid_all.tbl CDD cd14133 cd14133 271035 PKc_DYRK_like Catalytic domain of Dual-specificity tYrosine-phosphorylated and -Regulated Kinase-like protein kinases. Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (S/T) as well as tyrosine residues on protein substrates. This subfamily is composed of the dual-specificity DYRKs and YAK1, as well as the S/T kinases (STKs), HIPKs. DYRKs and YAK1 autophosphorylate themselves on tyrosine residues and phosphorylate their substrates exclusively on S/T residues. Proteins in this subfamily play important roles in cell proliferation, differentiation, survival, growth, and development. The DYRK-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 262 matched cddid_all.tbl CDD cd14134 cd14134 271036 PKc_CLK "Catalytic domain of the Dual-specificity protein kinases, CDC-like kinases. Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (S/T) as well as tyrosine residues on protein substrates. CLKs are involved in the phosphorylation and regulation of serine/arginine-rich (SR) proteins, which play a crucial role in pre-mRNA splicing by directing splice site selection. SR proteins are phosphorylated first by SR protein kinases (SRPKs) at the N-terminus, which leads to its assembly into nuclear speckles where splicing factors are stored. CLKs phosphorylate the C-terminal part of SR proteins, causing the nuclear speckles to dissolve and splicing factors to be recruited at sites of active transcription. Based on a conserved ""EHLAMMERILG"" signature motif which may be crucial for substrate specificity, CLKs are also referred to as LAMMER kinases. CLKs autophosphorylate at tyrosine residues and phosphorylate their substrates exclusively on S/T residues. In Drosophila, the CLK homolog DOA (Darkener of apricot) is essential for embryogenesis and its mutation leads to defects in sexual differentiation, eye formation, and neuronal development. In fission yeast, the CLK homolog Lkh1 is a negative regulator of filamentous growth and asexual flocculation, and is also involved in oxidative stress response. Vertebrates contain mutliple CLK proteins and mammals have four (CLK1-4). The CLK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase." 332 matched cddid_all.tbl CDD cd14135 cd14135 271037 STKc_PRP4 Catalytic domain of the Serine/Threonine Kinase, Pre-mRNA-Processing factor 4. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PRP4 phosphorylates a number of factors involved in the formation of active spliceosomes, which catalyze pre-mRNA splicing. It phosphorylates PRP6 and PRP31, components of the U4/U6-U5 tri-small nuclear ribonucleoprotein (snRNP), during spliceosomal complex formation. In fission yeast, PRP4 phosphorylates the splicing factor PRP1 (U5-102 kD in mammals). Thus, PRP4 plays a key role in regulating spliceosome assembly and pre-mRNA splicing. It also plays an important role in mitosis by acting as a spindle assembly checkpoint kinase that is required for chromosome alignment and the recruitment of the checkpoint proteins MPS1, MAD1, and MAD2 at kinetochores. The PRP4 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 318 matched cddid_all.tbl CDD cd14136 cd14136 271038 STKc_SRPK Catalytic domain of the Serine/Threonine Kinase, Serine-aRginine Protein Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. SRPKs phosphorylate and regulate splicing factors from the SR protein family by specifically phosphorylating multiple serine residues residing in SR/RS dipeptide motifs (also known as RS domains). Phosphorylation of the RS domains enhances interaction with transportin SR and facilitates entry of the SR proteins into the nucleus. SRPKs contain a nonconserved insert domain, within the well-conserved catalytic kinase domain, that regulates their subcellular localization. They play important roles in mediating pre-mRNA processing and mRNA maturation, as well as other cellular functions such as chromatin reorganization, cell cycle and p53 regulation, and metabolic signaling. Vertebrates contain three distinct SRPKs, called SRPK1-3. The SRPK homolog in budding yeast, Sky1p, recognizes and phosphorylates its substrate Npl3p, which lacks a classic RS domain but contains a single RS dipeptide at the C-terminus of its RGG domain. Npl3p is a shuttling heterogeneous nuclear ribonucleoprotein (hnRNP) that exports a distinct class of mRNA from the nucleus to the cytoplasm. The SRPK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 320 matched cddid_all.tbl CDD cd14137 cd14137 271039 STKc_GSK3 The catalytic domain of the Serine/Threonine Kinase, Glycogen Synthase Kinase 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. GSK3 is a mutifunctional kinase involved in many cellular processes including cell division, proliferation, differentiation, adhesion, and apoptosis. In plants, GSK3 plays a role in the response to osmotic stress. In Caenorhabditis elegans, it plays a role in regulating normal oocyte-to-embryo transition and response to oxidative stress. In Chlamydomonas reinhardtii, GSK3 regulates flagellar length and assembly. In mammals, there are two isoforms, GSK3alpha and GSK3beta, which show both distinct and redundant functions. The two isoforms differ mainly in their N-termini. They are both involved in axon formation and in Wnt signaling.They play distinct roles in cardiogenesis, with GSKalpha being essential in cardiomyocyte survival, and GSKbeta regulating heart positioning and left-right symmetry. GSK3beta was first identified as a regulator of glycogen synthesis, but has since been determined to play other roles. It regulates the degradation of beta-catenin and IkB. Beta-catenin is the main effector of Wnt, which is involved in normal haematopoiesis and stem cell function. IkB is a central inhibitor of NF-kB, which is critical in maintaining leukemic cell growth. GSK3beta is enriched in the brain and is involved in regulating neuronal signaling pathways. It is implicated in the pathogenesis of many diseases including Type II diabetes, obesity, mood disorders, Alzheimer's disease, osteoporosis, and some types of cancer, among others. The GSK3 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 293 matched cddid_all.tbl CDD cd14138 cd14138 271040 PTKc_Wee1a Catalytic domain of the Protein Tyrosine Kinase, Wee1a. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. This subfamily is composed of human Wee1a, Xenopus laevis Wee1b (XeWee1b) and similar vertebrate proteins. Members of this subfamily show a wide expression pattern. XeWee1b functions after the first zygotic cell divisions. It is expressed in all tissues and is also present after the gastrulation stage of embryos. Wee1 is a cell cycle checkpoint kinase that helps keep the cyclin-dependent kinase CDK1 in an inactive state through phosphorylation of an N-terminal tyr (Y15) residue. During the late G2 phase, CDK1 is activated and mitotic entry is promoted by the removal of this inhibitory phosphorylation by the phosphatase Cdc25. Although Wee1 is functionally a tyr kinase, it is more closely related to serine/threonine kinases (STKs). It contains a catalytic kinase domain sandwiched in between N- and C-terminal regulatory domains. It is regulated by phosphorylation and degradation, and its expression levels are also controlled by circadian clock proteins. The Wee1a subfamily is part of a larger superfamily that includes the catalytic domains of STKs, other PTKs, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 276 matched cddid_all.tbl CDD cd14139 cd14139 271041 PTKc_Wee1b Catalytic domain of the Protein Tyrosine Kinase, Wee1b. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. This subfamily is composed of human Wee1b (also called Wee2), Xenopus laevis Wee1a (XeWee1a) and similar vertebrate proteins. XeWee1a accumulates after exiting the metaphase II stage in oocytes and in early mitotic cells. It functions during the first zygotic cell division and not during subsequent divisions. Mammalian Wee2/Wee1b is an oocyte-specific inhibitor of meiosis that functions downstream of cAMP. Wee1 is a cell cycle checkpoint kinase that helps keep the cyclin-dependent kinase CDK1 in an inactive state through phosphorylation of an N-terminal tyr (Y15) residue. During the late G2 phase, CDK1 is activated and mitotic entry is promoted by the removal of this inhibitory phosphorylation by the phosphatase Cdc25. Although Wee1 is functionally a tyr kinase, it is more closely related to serine/threonine kinases (STKs). It contains a catalytic kinase domain sandwiched in between N- and C-terminal regulatory domains. It is regulated by phosphorylation and degradation, and its expression levels are also controlled by circadian clock proteins. The Wee1b subfamily is part of a larger superfamily that includes the catalytic domains of STKs, other PTKs, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 274 matched cddid_all.tbl CDD cd14140 cd14140 271042 STKc_ACVR2b Catalytic domain of the Serine/Threonine Kinase, Activin Type IIB Receptor. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. ACVR2b (or ActRIIB) belongs to a group of receptors for the TGFbeta family of secreted signaling molecules that includes TGFbeta, bone morphogenetic proteins (BMPs), activins, growth and differentiation factors (GDFs), and anti-Mullerian hormone, among others. These receptors contain an extracellular domain that binds ligands, a single transmembrane region, and a cytoplasmic catalytic kinase domain. ACVR2b is one of two ACVR2 receptors found in vertebrates. Type II receptors are high-affinity receptors which bind ligands, autophosphorylate, as well as trans-phosphorylate and activate low-affinity type I receptors. ACVR2 acts primarily as the receptors for activins, nodal, myostatin, GDF11, and a subset of BMPs. ACVR2 signaling impacts many cellular and physiological processes including reproductive and gonadal functions, myogenesis, bone remodeling and tooth development, kidney organogenesis, apoptosis, fibrosis, inflammation, and neurogenesis. The ACVR2b subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 291 matched cddid_all.tbl CDD cd14141 cd14141 271043 STKc_ACVR2a Catalytic domain of the Serine/Threonine Kinase, Activin Type IIA Receptor. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. ACVR2a (or ActRIIA) belongs to a group of receptors for the TGFbeta family of secreted signaling molecules that includes TGFbeta, bone morphogenetic proteins (BMPs), activins, growth and differentiation factors (GDFs), and anti-Mullerian hormone, among others. These receptors contain an extracellular domain that binds ligands, a single transmembrane region, and a cytoplasmic catalytic kinase domain. ACVR2b is one of two ACVR2 receptors found in vertebrates. Type II receptors are high-affinity receptors which bind ligands, autophosphorylate, as well as trans-phosphorylate and activate low-affinity type I receptors. ACVR2 acts primarily as the receptors for activins, nodal, myostatin, GDF11, and a subset of BMPs. ACVR2 signaling impacts many cellular and physiological processes including reproductive and gonadal functions, myogenesis, bone remodeling and tooth development, kidney organogenesis, apoptosis, fibrosis, inflammation, and neurogenesis. The ACVR2a subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 290 matched cddid_all.tbl CDD cd14142 cd14142 271044 STKc_ACVR1_ALK1 Catalytic domain of the Serine/Threonine Kinases, Activin Type I Receptor and Activin receptor-Like Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. ACVR1, also called Activin receptor-Like Kinase 2 (ALK2), and ALK1 act as receptors for bone morphogenetic proteins (BMPs) and they activate SMAD1/5/8. ACVR1 is widely expressed while ALK1 is limited mainly to endothelial cells. The specificity of BMP binding to type I receptors is affected by type II receptors. ACVR1 binds BMP6/7/9/10 and can also bind anti-Mullerian hormone (AMH) in the presence of AMHR2. ALK1 binds BMP9/10 as well as TGFbeta in endothelial cells. A missense mutation in the GS domain of ACVR1 causes fibrodysplasia ossificans progressiva, a complex and disabling disease characterized by congenital skeletal malformations and extraskeletal bone formation. ACVR1 belongs to a group of receptors for the TGFbeta family of secreted signaling molecules that includes TGFbeta, BMPs, activins, growth and differentiation factors, and AMH, among others. These receptors contain an extracellular domain that binds ligands, a single transmembrane (TM) region, and a cytoplasmic catalytic kinase domain. Type I receptors, like ACVR1 and ALK1, are low-affinity receptors that bind ligands only after they are recruited by the ligand/type II high-affinity receptor complex. Following activation, they start intracellular signaling to the nucleus by phosphorylating SMAD proteins. Type I receptors contain an additional domain located between the TM and kinase domains called the GS domain, which contains the activating phosphorylation site and confers preference for specific SMAD proteins. The ACVR1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 298 matched cddid_all.tbl CDD cd14143 cd14143 271045 STKc_TGFbR1_ACVR1b_ACVR1c Catalytic domain of the Serine/Threonine Kinases, Transforming Growth Factor beta Type I Receptor and Activin Type IB/IC Receptors. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TGFbR1, also called Activin receptor-Like Kinase 5 (ALK5), functions as a receptor for TGFbeta and phoshorylates SMAD2/3. TGFbeta proteins are cytokines that regulate cell growth, differentiation, and survival, and are critical in the development and progression of many human cancers. Mutations in TGFbR1 (and TGFbR2) can cause aortic aneurysm disorders such as Loeys-Dietz and Marfan syndromes. ACVR1b (also called ALK4) and ACVR1c (also called ALK7) act as receptors for activin A and B, respectively. TGFbR1, ACVR1b, and ACVR1c belong to a group of receptors for the TGFbeta family of secreted signaling molecules that includes TGFbeta, bone morphogenetic proteins, activins, growth and differentiation factors, and anti-Mullerian hormone, among others. These receptors contain an extracellular domain that binds ligands, a single transmembrane (TM) region, and a cytoplasmic catalytic kinase domain. Type I receptors, like TGFbR1, ACVR1b, and ACVR1c, are low-affinity receptors that bind ligands only after they are recruited by the ligand/type II high-affinity receptor complex. Following activation, they start intracellular signaling to the nucleus by phosphorylating SMAD proteins. Type I receptors contain an additional domain located between the TM and kinase domains called the GS domain, which contains the activating phosphorylation site and confers preference for specific SMAD proteins. The TGFbR1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 288 matched cddid_all.tbl CDD cd14144 cd14144 271046 STKc_BMPR1 Catalytic domain of the Serine/Threonine Kinase, Bone Morphogenetic Protein Type I Receptor. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. BMPR1 functions as a receptor for morphogenetic proteins (BMPs), which are involved in the regulation of cell proliferation, survival, differentiation, and apoptosis. BMPs are able to induce bone, cartilage, ligament, and tendon formation, and may play roles in bone diseases and tumors. Vertebrates contain two type I BMP receptors, BMPR1a and BMPR1b. BMPR1 belongs to a group of receptors for the TGFbeta family of secreted signaling molecules that also includes TGFbeta, activins, growth and differentiation factors, and anti-Mullerian hormone, among others. These receptors contain an extracellular domain that binds ligands, a single transmembrane (TM) region, and a cytoplasmic catalytic kinase domain. Type I receptors, like BMPR1, are low-affinity receptors that bind ligands only after they are recruited by the ligand/type II high-affinity receptor complex. Following activation, they start intracellular signaling to the nucleus by phosphorylating SMAD proteins. Type I receptors contain an additional domain located between the TM and kinase domains called the GS domain, which contains the activating phosphorylation site and confers preference for specific SMAD proteins. The BMPR1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 287 matched cddid_all.tbl CDD cd14145 cd14145 271047 STKc_MLK1 Catalytic domain of the Serine/Threonine Kinase, Mixed Lineage Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MLK1 is a mitogen-activated protein kinase kinase kinase (MAP3K, MKKK, MAPKKK) and is also called MAP3K9. MAP3Ks phosphorylate and activate MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. Little is known about the specific function of MLK1. It is capable of activating the c-Jun N-terminal kinase pathway. Mice lacking both MLK1 and MLK2 are viable, fertile, and have normal life spans. There could be redundancy in the function of MLKs. Mammals have four MLKs, mostly conserved in vertebrates, which contain an SH3 domain, a catalytic kinase domain, a leucine zipper, a proline-rich region, and a CRIB domain that mediates binding to GTP-bound Cdc42 and Rac. MLKs play roles in immunity and inflammation, as well as in cell death, proliferation, and cell cycle regulation. The MLK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 270 matched cddid_all.tbl CDD cd14146 cd14146 271048 STKc_MLK4 Catalytic domain of the Serine/Threonine Kinase, Mixed Lineage Kinase 4. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MLK4 is a mitogen-activated protein kinase kinase kinase (MAP3K, MKKK, MAPKKK), which phosphorylates and activates MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. The specific function of MLK4 is yet to be determined. Mutations in the kinase domain of MLK4 have been detected in colorectal cancers. Mammals have four MLKs, mostly conserved in vertebrates, which contain an SH3 domain, a catalytic kinase domain, a leucine zipper, a proline-rich region, and a CRIB domain that mediates binding to GTP-bound Cdc42 and Rac. MLKs play roles in immunity and inflammation, as well as in cell death, proliferation, and cell cycle regulation.The MLK4 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 268 matched cddid_all.tbl CDD cd14147 cd14147 271049 STKc_MLK3 Catalytic domain of the Serine/Threonine Kinase, Mixed Lineage Kinase 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MLK3 is a mitogen-activated protein kinase kinase kinases (MAP3K, MKKK, MAPKKK), which phosphorylates and activates MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. MLK3 activates multiple MAPK pathways and plays a role in apoptosis, proliferation, migration, and differentiation, depending on the cellular context. It is highly expressed in breast cancer cells and its signaling through c-Jun N-terminal kinase has been implicated in the migration, invasion, and malignancy of cancer cells. MLK3 also functions as a negative regulator of Inhibitor of Nuclear Factor-KappaB Kinase (IKK) and consequently, it also impacts inflammation and immunity. Mammals have four MLKs, mostly conserved in vertebrates, which contain an SH3 domain, a catalytic kinase domain, a leucine zipper, a proline-rich region, and a CRIB domain that mediates binding to GTP-bound Cdc42 and Rac. MLKs play roles in immunity and inflammation, as well as in cell death, proliferation, and cell cycle regulation.The MLK3 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 267 matched cddid_all.tbl CDD cd14148 cd14148 271050 STKc_MLK2 Catalytic domain of the Serine/Threonine Kinase, Mixed Lineage Kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MLK2 is a mitogen-activated protein kinase kinase kinase (MAP3K, MKKK, MAPKKK) and is also called MAP3K10. MAP3Ks phosphorylate and activate MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. MLK2 is abundant in brain, skeletal muscle, and testis. It functions upstream of the MAPK, c-Jun N-terminal kinase. It binds hippocalcin, a calcium-sensor protein that protects neurons against calcium-induced cell death. Both MLK2 and hippocalcin may be associated with the pathogenesis of Parkinson's disease. MLK2 also binds to normal huntingtin (Htt), which is important in neuronal transcription, development, and survival. MLK2 does not bind to the polyglutamine-expanded Htt, which is implicated in the pathogeneis of Huntington's disease, leading to neuronal toxicity. Mammals have four MLKs, mostly conserved in vertebrates, which contain an SH3 domain, a catalytic kinase domain, a leucine zipper, a proline-rich region, and a CRIB domain that mediates binding to GTP-bound Cdc42 and Rac. MLKs play roles in immunity and inflammation, as well as in cell death, proliferation, and cell cycle regulation. The MLK2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). 258 matched cddid_all.tbl CDD cd14149 cd14149 271051 STKc_C-Raf Catalytic domain of the Serine/Threonine Kinase, C-Raf (Rapidly Accelerated Fibrosarcoma) kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. C-Raf, also known as Raf-1 or c-Raf-1, is ubiquitously expressed and was the first Raf identified. It was characterized as the acquired oncogene from an acutely transforming murine sarcoma virus (3611-MSV) and the transforming agent from the avian retrovirus MH2. C-Raf-deficient mice embryos die around midgestation with increased apoptosis of embryonic tissues, especially in the fetal liver. One of the main functions of C-Raf is restricting caspase activation to promote survival in response to specific stimuli such as Fas stimulation, macrophage apoptosis, and erythroid differentiation. C-Raf is a mitogen-activated protein kinase kinase kinase (MAP3K, MKKK, MAPKKK), which phosphorylates and activates MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. It functions in the linear Ras-Raf-MEK-ERK pathway that regulates many cellular processes including cycle regulation, proliferation, differentiation, survival, and apoptosis. The C-Raf subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 283 matched cddid_all.tbl CDD cd14150 cd14150 271052 STKc_A-Raf Catalytic domain of the Serine/Threonine Kinase, A-Raf (Rapidly Accelerated Fibrosarcoma) kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. A-Raf cooperates with C-Raf in regulating ERK transient phosphorylation that is associated with cyclin D expression and cell cycle progression. Mice deficient in A-Raf are born alive but show neurological and intestinal defects. A-Raf demonstrates low kinase activity to MEK, compared with B- and C-Raf, and may also have alternative functions other than in the ERK signaling cascade. It regulates the M2 type pyruvate kinase, a key glycolytic enzyme. It also plays a role in endocytic membrane trafficking. A-Raf is a mitogen-activated protein kinase kinase kinase (MAP3K, MKKK, MAPKKK), which phosphorylates and activates MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. It functions in the linear Ras-Raf-MEK-ERK pathway that regulates many cellular processes including cycle regulation, proliferation, differentiation, survival, and apoptosis. The A-Raf subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 265 matched cddid_all.tbl CDD cd14151 cd14151 271053 STKc_B-Raf Catalytic domain of the Serine/Threonine Kinase, B-Raf (Rapidly Accelerated Fibrosarcoma) kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. B-Raf activates ERK with the strongest magnitude, compared with other Raf kinases. Mice embryos deficient in B-Raf die around midgestation due to vascular hemorrhage caused by apoptotic endothelial cells. Mutations in B-Raf have been implicated in initiating tumorigenesis and tumor progression, and are found in malignant cutaneous melanoma, papillary thyroid cancer, as well as in ovarian and colorectal carcinomas. Most oncogenic B-Raf mutations are located at the activation loop of the kinase and surrounding regions; the V600E mutation accounts for around 90% of oncogenic mutations. The V600E mutant constitutively activates MEK, resulting in sustained activation of ERK. B-Raf is a mitogen-activated protein kinase kinase kinase (MAP3K, MKKK, MAPKKK), which phosphorylates and activates MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. They function in the linear Ras-Raf-MEK-ERK pathway that regulates many cellular processes including cycle regulation, proliferation, differentiation, survival, and apoptosis. The B-Raf subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 274 matched cddid_all.tbl CDD cd14152 cd14152 271054 STKc_KSR1 Catalytic domain of the Serine/Threonine Kinase, Kinase Suppressor of Ras 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. KSR1 functions as a transducer of TNFalpha-stimulated C-Raf activation of ERK1/2 and NF-kB. Detected activity of KSR1 is cell type specific and context dependent. It is inactive in normal colon epithelial cells and becomes activated at the onset of inflammatory bowel disease (IBD). Similarly, KSR1 activity is undetectable prior to stimulation by EGF or ceramide in COS-7 or YAMC cells, respectively. KSR proteins are widely regarded as pseudokinases, however, this matter is up for debate as catalytic activity has been detected for KSR1 in some systems. The KSR1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 279 matched cddid_all.tbl CDD cd14153 cd14153 271055 PK_KSR2 Pseudokinase domain of Kinase Suppressor of Ras 2. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. KSR2 interacts with the protein phosphatase calcineurin and functions in calcium-mediated ERK signaling. It also functions in energy metabolism by regulating AMP kinase and AMPK-dependent processes such as glucose uptake and fatty acid oxidation. KSR proteins act as scaffold proteins that function downstream of Ras and upstream of Raf in the Extracellular signal-Regulated Kinase (ERK) pathway that regulates many cellular processes including cycle regulation, proliferation, differentiation, survival, and apoptosis. KSR proteins regulate the assembly and activation of the Raf/MEK/ERK module upon Ras activation at the membrane by direct association of its components. They are widely regarded as pseudokinases. The KSR2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 270 matched cddid_all.tbl CDD cd14154 cd14154 271056 STKc_LIMK Catalytic domain of the Serine/Threonine Kinase, LIM domain kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. LIMKs phosphorylate and inactivate cofilin, an actin depolymerizing factor, to induce the reorganization of the actin cytoskeleton. They act downstream of Rho GTPases and are expressed ubiquitously. As regulators of actin dynamics, they contribute to diverse cellular functions such as cell motility, morphogenesis, differentiation, apoptosis, meiosis, mitosis, and neurite extension. LIMKs contain the LIM (two repeats), PDZ, and catalytic kinase domains. Vertebrate have two members, LIMK1 and LIMK2. The LIMK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 272 matched cddid_all.tbl CDD cd14155 cd14155 271057 PKc_TESK Catalytic domain of the Dual-specificity protein kinase, Testicular protein kinase. Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine as well as tyrosine residues on protein substrates. TESK proteins phosphorylate cofilin and induce actin cytoskeletal reorganization. In the Drosphila eye, TESK is required for epithelial cell organization. Mammals contain two TESK proteins, TESK1 and TESK2, which are highly expressed in testis and play roles in spermatogenesis. TESK1 is found in testicular germ cells while TESK2 is expressed mainly in nongerminal Sertoli cells. TESK1 is stimulated by integrin-mediated signaling pathways. It regulates cell spreading and focal adhesion formation. The TESK subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine PKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 253 matched cddid_all.tbl CDD cd14156 cd14156 271058 PKc_LIMK_like_unk Catalytic domain of an unknown subfamily of LIM domain kinase-like protein kinases. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine or tyrosine residues on protein substrates. This group is composed of uncharacterized proteins with similarity to LIMK and Testicular or testis-specific protein kinase (TESK). LIMKs are characterized as serine/threonine kinases (STKs) while TESKs are dual-specificity protein kinases. Both LIMK and TESK phosphorylate and inactivate cofilin, an actin depolymerizing factor, to induce the reorganization of the actin cytoskeleton. They are implicated in many cellular functions including cell spreading, motility, morphogenesis, meiosis, mitosis, and spermatogenesis. The LIMK-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd14157 cd14157 271059 STKc_IRAK2 Catalytic domain of the Serine/Threonine kinase, Interleukin-1 Receptor Associated Kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. IRAKs are involved in Toll-like receptor (TLR) and interleukin-1 (IL-1) signalling pathways, and are thus critical in regulating innate immune responses and inflammation. IRAKs contain an N-terminal Death domain (DD), a proST region (rich in serines, prolines, and threonines), a central kinase domain, and a C-terminal domain; IRAK-4 lacks the C-terminal domain. Vertebrates contain four IRAKs (IRAK-1, -2, -3 (or -M), and -4) that display distinct functions and patterns of expression and subcellular distribution, and can differentially mediate TLR signaling. IRAK2 plays a role in mediating NFkB activation by TLR3, TLR4, and TLR8. It is specifically targeted by the viral protein A52, which is important for virulence, to inhibit all IL-1/TLR pathways, indicating that IRAK2 has a predominant role in NFkB activation. It is redundant with IRAK1 in early signaling but is critical for late and sustained activation. The IRAK2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 289 matched cddid_all.tbl CDD cd14158 cd14158 271060 STKc_IRAK4 Catalytic domain of the Serine/Threonine kinase, Interleukin-1 Receptor Associated Kinase 4. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. IRAKs are involved in Toll-like receptor (TLR) and interleukin-1 (IL-1) signalling pathways, and are thus critical in regulating innate immune responses and inflammation. IRAKs contain an N-terminal Death domain (DD), a proST region (rich in serines, prolines, and threonines), a central kinase domain, and a C-terminal domain; IRAK-4 lacks the C-terminal domain. Vertebrates contain four IRAKs (IRAK-1, -2, -3 (or -M), and -4) that display distinct functions and patterns of expression and subcellular distribution, and can differentially mediate TLR signaling. IRAK4 plays a critical role in NFkB activation by its interaction with MyD88, which acts as a scaffold that enables IRAK4 to phosphorylate and activate IRAK1 and/or IRAK2. It also plays an important role in type I IFN production induced by TLR7/8/9. The IRAK4 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 288 matched cddid_all.tbl CDD cd14159 cd14159 271061 STKc_IRAK1 Catalytic domain of the Serine/Threonine kinase, Interleukin-1 Receptor Associated Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. IRAKs are involved in Toll-like receptor (TLR) and interleukin-1 (IL-1) signalling pathways, and are thus critical in regulating innate immune responses and inflammation. IRAKs contain an N-terminal Death domain (DD), a proST region (rich in serines, prolines, and threonines), a central kinase domain, and a C-terminal domain; IRAK-4 lacks the C-terminal domain. Vertebrates contain four IRAKs (IRAK-1, -2, -3 (or -M), and -4) that display distinct functions and patterns of expression and subcellular distribution, and can differentially mediate TLR signaling. IRAK1 plays a role in the activation of IRF3/7, STAT, and NFkB. It mediates IL-6 and IFN-gamma responses following IL-1 and IL-18 stimulation, respectively. It also plays an essential role in IFN-alpha induction downstream of TLR7 and TLR9. The IRAK1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 296 matched cddid_all.tbl CDD cd14160 cd14160 271062 PK_IRAK3 Pseudokinase domain of Interleukin-1 Receptor Associated Kinase 3. The pseudokinase domain shows similarity to protein kinases but lacks crucial residues for catalytic activity. IRAKs are involved in Toll-like receptor (TLR) and interleukin-1 (IL-1) signalling pathways, and are thus critical in regulating innate immune responses and inflammation. IRAKs contain an N-terminal Death domain (DD), a proST region (rich in serines, prolines, and threonines), a central kinase domain (a pseudokinase in the case of IRAK3), and a C-terminal domain; IRAK-4 lacks the C-terminal domain. Vertebrates contain four IRAKs (IRAK-1, -2, -3 (or -M), and -4) that display distinct functions and patterns of expression and subcellular distribution, and can differentially mediate TLR signaling. IRAK3 (or IRAK-M) is the only IRAK that does not show kinase activity. It is found only in monocytes and macrophages in humans, and functions as a negative regulator of TLR signaling including TLR-2 induced p38 activation. It also negatively regulates the alternative NFkB pathway in a TLR-2 specific manner. IRAK3 is downregulated in the monocytes of obese people, and is associated with high SOD2, a marker of mitochondrial oxidative stress. It is an important inhibitor of inflammation in association with obesity and metabolic syndrome. The IRAK3 subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 276 matched cddid_all.tbl CDD cd14161 cd14161 271063 STKc_NUAK2 Catalytic domain of the Serine/Threonine Kinase, novel (nua) kinase family NUAK 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. NUAK proteins are classified as AMP-activated protein kinase (AMPK)-related kinases, which like AMPK are activated by the major tumor suppressor LKB1. Vertebrates contain two NUAK proteins, called NUAK1 and NUAK2. NUAK2, also called SNARK (Sucrose, non-fermenting 1/AMP-activated protein kinase-related kinase), is involved in energy metabolism. It is activated by hyperosmotic stress, DNA damage, and nutrients such as glucose and glutamine. NUAK2-knockout mice develop obesity, altered serum lipid profiles, hyperinsulinaemia, hyperglycaemia, and impaired glucose tolerance. NUAK2 is implicated in regulating actin stress fiber assembly through its association with myosin phosphatase Rho-interacting protein (MRIP), which leads to an increase in myosin regulatory light chain (MLC) phosphorylation. It is also associated with tumor growth, migration, and oncogenicity of melanoma cells. The NUAK2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 255 matched cddid_all.tbl CDD cd14162 cd14162 271064 STKc_TSSK4-like Catalytic domain of testis-specific serine/threonine kinase 4 and similar proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TSSK proteins are almost exclusively expressed postmeiotically in the testis and play important roles in spermatogenesis and/or spermiogenesis. There are five mammalian TSSK proteins which show differences in their localization and timing of expression. TSSK4, also called TSSK5, is expressed in testis from haploid round spermatids to mature spermatozoa. It phosphorylates Cre-Responsive Element Binding protein (CREB), facilitating the binding of CREB to the specific cis cAMP responsive element (CRE), which is important in activating genes related to germ cell differentiation. Mutations in the human TSSK4 gene is associated with infertile Chinese men with impaired spermatogenesis. The TSSK4-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 259 matched cddid_all.tbl CDD cd14163 cd14163 271065 STKc_TSSK3-like Catalytic domain of testis-specific serine/threonine kinase 3 and similar proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TSSK proteins are almost exclusively expressed postmeiotically in the testis and play important roles in spermatogenesis and/or spermiogenesis. There are five mammalian TSSK proteins which show differences in their localization and timing of expression. TSSK3 has been reported to be expressed in the interstitial Leydig cells of adult testis. Its mRNA levels is low at birth, increases at puberty, and remains high throughout adulthood. The TSSK3-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 257 matched cddid_all.tbl CDD cd14164 cd14164 271066 STKc_TSSK6-like Catalytic domain of testis-specific serine/threonine kinase 6 and similar proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TSSK proteins are almost exclusively expressed postmeiotically in the testis and play important roles in spermatogenesis and/or spermiogenesis. There are five mammalian TSSK proteins which show differences in their localization and timing of expression. TSSK6, also called SSTK, is expressed at the head of elongated sperm. It can phosphorylate histones and associate with heat shock protens HSP90 and HSC70. Male mice deficient in TSSK6 are infertile, showing spermatogenic impairment including reduced sperm counts, impaired DNA condensation, abnormal morphology and decreased motility rates. The TSSK6-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd14165 cd14165 271067 STKc_TSSK1_2-like Catalytic domain of testis-specific serine/threonine kinase 1, TSSK2, and similar proteins. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. TSSK proteins are almost exclusively expressed postmeiotically in the testis and play important roles in spermatogenesis and/or spermiogenesis. There are five mammalian TSSK proteins which show differences in their localization and timing of expression. TSSK1 and TSSK2 are expressed specifically in meiotic and postmeiotic spermatogenic cells, respectively. TSSK2 is localized in the sperm neck, equatorial segment, and mid-piece of the sperm tail. Both TSSK1 and TSSK2 phosphorylate their common substrate TSKS (testis-specific-kinase-substrate). TSSK1/TSSK2 double knock-out mice are sterile without manifesting other defects, making these kinases viable targets for male contraception. The TSSK1/2-like subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 263 matched cddid_all.tbl CDD cd14166 cd14166 271068 STKc_CaMKI_gamma Catalytic domain of the Serine/Threonine kinase, Calcium/calmodulin-dependent protein kinase Type I gamma. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CaMKs are multifunctional calcium and calmodulin (CaM) stimulated STKs involved in cell cycle regulation. The CaMK family includes CaMKI, CaMKII, CaMKIV, and CaMK kinase (CaMKK). In vertebrates, there are four CaMKI proteins encoded by different genes (alpha, beta, gamma, and delta), each producing at least one variant. CaMKs contain an N-terminal catalytic domain and a C-terminal regulatory domain that harbors a CaM binding site. CaMKI proteins are monomeric and they play pivotal roles in the nervous system, including long-term potentiation, dendritic arborization, neurite outgrowth, and the formation of spines, synapses, and axons. In addition, they may be involved in osteoclast differentiation and bone resorption. The CaMKI-gamma subfamily is part of a larger superfamily that includes the catalytic domains of other protein kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 285 matched cddid_all.tbl CDD cd14167 cd14167 271069 STKc_CaMKI_alpha Catalytic domain of the Serine/Threonine kinase, Calcium/calmodulin-dependent protein kinase Type I alpha. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CaMKs are multifunctional calcium and calmodulin (CaM) stimulated STKs involved in cell cycle regulation. The CaMK family includes CaMKI, CaMKII, CaMKIV, and CaMK kinase (CaMKK). In vertebrates, there are four CaMKI proteins encoded by different genes (alpha, beta, gamma, and delta), each producing at least one variant. CaMKs contain an N-terminal catalytic domain and a C-terminal regulatory domain that harbors a CaM binding site. CaMKI proteins are monomeric and they play pivotal roles in the nervous system, including long-term potentiation, dendritic arborization, neurite outgrowth, and the formation of spines, synapses, and axons. In addition, they may be involved in osteoclast differentiation and bone resorption. The CaMKI-alpha subfamily is part of a larger superfamily that includes the catalytic domains of other protein kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 263 matched cddid_all.tbl CDD cd14168 cd14168 271070 STKc_CaMKI_delta Catalytic domain of the Serine/Threonine kinase, Calcium/calmodulin-dependent protein kinase Type I delta. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CaMKs are multifunctional calcium and calmodulin (CaM) stimulated STKs involved in cell cycle regulation. The CaMK family includes CaMKI, CaMKII, CaMKIV, and CaMK kinase (CaMKK). In vertebrates, there are four CaMKI proteins encoded by different genes (alpha, beta, gamma, and delta), each producing at least one variant. CaMKs contain an N-terminal catalytic domain and a C-terminal regulatory domain that harbors a CaM binding site. CaMKI proteins are monomeric and they play pivotal roles in the nervous system, including long-term potentiation, dendritic arborization, neurite outgrowth, and the formation of spines, synapses, and axons. In addition, they may be involved in osteoclast differentiation and bone resorption. The CaMKI-delta subfamily is part of a larger superfamily that includes the catalytic domains of other protein kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 301 matched cddid_all.tbl CDD cd14169 cd14169 271071 STKc_CaMKI_beta Catalytic domain of the Serine/Threonine kinase, Calcium/calmodulin-dependent protein kinase Type I beta. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CaMKs are multifunctional calcium and calmodulin (CaM) stimulated STKs involved in cell cycle regulation. The CaMK family includes CaMKI, CaMKII, CaMKIV, and CaMK kinase (CaMKK). In vertebrates, there are four CaMKI proteins encoded by different genes (alpha, beta, gamma, and delta), each producing at least one variant. CaMKs contain an N-terminal catalytic domain and a C-terminal regulatory domain that harbors a CaM binding site. CaMKI proteins are monomeric and they play pivotal roles in the nervous system, including long-term potentiation, dendritic arborization, neurite outgrowth, and the formation of spines, synapses, and axons. In addition, they may be involved in osteoclast differentiation and bone resorption. The CaMKI-beta subfamily is part of a larger superfamily that includes the catalytic domains of other protein kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 277 matched cddid_all.tbl CDD cd14170 cd14170 271072 STKc_MAPKAPK2 Catalytic domain of the Serine/Threonine kinase, Mitogen-activated protein kinase-activated protein kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MAPK-activated protein kinase 2 (MAPKAP2 or MK2) contains an N-terminal proline-rich region that can bind to SH3 domains, a catalytic kinase domain followed by a C-terminal autoinhibitory region that contains nuclear localization (NLS) and nuclear export (NES) signals with a p38 MAPK docking motif that overlaps the NLS. MK2 is a bonafide substrate for the MAPK p38. It is closely related to MK3 and thus far, MK2/3 show indistinguishable substrate specificity. They are mainly involved in the regulation of gene expression and they participate in diverse cellular processes such as endocytosis, cytokine production, cytoskeletal reorganization, cell migration, cell cycle control and chromatin remodeling. They are implicated in inflammation and cance and their substrates include mRNA-AU-rich-element (ARE)-binding proteins (TTP and hnRNP A0), Hsp proteins (Hsp27 and Hsp25) and RSK, among others. MK2/3 are both expressed ubiquitously but MK2 is expressed at significantly higher levels. The MK2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 303 matched cddid_all.tbl CDD cd14171 cd14171 271073 STKc_MAPKAPK5 Catalytic domain of the Serine/Threonine kinase, Mitogen-activated protein kinase-activated protein kinase 5. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MAPK-activated protein kinase 5 (MAPKAP5 or MK5) is also called PRAK (p38-regulated/activated protein kinase). It contains a catalytic kinase domain followed by a C-terminal autoinhibitory region that contains nuclear localization (NLS) and nuclear export (NES) signals with a p38 MAPK docking motif that overlaps the NLS. MK5 is a ubiquitous protein that is implicated in neuronal morphogenesis, cell migration, and tumor angiogenesis. It interacts with PKA, which induces cytoplasmic translocation of MK5. Its substrates includes p53, ERK3/4, Hsp27, and cytosolic phospholipase A2 (cPLA2). The MAPKAPK subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 289 matched cddid_all.tbl CDD cd14172 cd14172 271074 STKc_MAPKAPK3 Catalytic domain of the Serine/Threonine kinase, Mitogen-activated protein kinase-activated protein kinase 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MAPK-activated protein kinase 3 (MAPKAP3 or MK3) contains an N-terminal proline-rich region that can bind to SH3 domains, a catalytic kinase domain followed by a C-terminal autoinhibitory region that contains nuclear localization (NLS) and nuclear export (NES) signals with a p38 MAPK docking motif that overlaps the NLS. MK3 is a bonafide substrate for the MAPK p38. It is closely related to MK2 and thus far, MK2/3 show indistinguishable substrate specificity. They are mainly involved in the regulation of gene expression and they participate in diverse cellular processes such as endocytosis, cytokine production, cytoskeletal reorganization, cell migration, cell cycle control and chromatin remodeling. They are implicated in inflammation and cance and their substrates include mRNA-AU-rich-element (ARE)-binding proteins (TTP and hnRNP A0), Hsp proteins (Hsp27 and Hsp25) and RSK, among others. MK2/3 are both expressed ubiquitously but MK2 is expressed at significantly higher levels. MK3 activity is only significant when MK2 is absent. The MK3 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 267 matched cddid_all.tbl CDD cd14173 cd14173 271075 STKc_Mnk2 Catalytic domain of the Serine/Threonine kinase, Mitogen-activated protein kinase signal-integrating kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MAPK signal-integrating kinases (Mnks) are MAPK-activated protein kinases and is comprised by a group of four proteins, produced by alternative splicing from two genes (Mnk1 and Mnk2). The isoforms of Mnk1 (1a/1b) and Mnk2 (2a/2b) differ at their C-termini, with the a-form having a longer C-terminus containing a MAPK-binding region. All Mnks contain a catalytic kinase domain and a polybasic region at the N-terminus which binds importin and the eukaryotic initiation factor eIF4G. The best characterized Mnk substrate is eIF4G, whose phosphorylation may promote the export of certain mRNAs from the nucleus. Mnk also phosphorylate substrates that bind to AU-rich elements that regulate mRNA stability and translation. Mnks have also been implicated in tyrosine kinase receptor signaling, inflammation, and cell prolieration or survival. The Mnk subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 288 matched cddid_all.tbl CDD cd14174 cd14174 271076 STKc_Mnk1 Catalytic domain of the Serine/Threonine kinase, Mitogen-activated protein kinase signal-integrating kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MAPK signal-integrating kinases (Mnks) are MAPK-activated protein kinases and is comprised by a group of four proteins, produced by alternative splicing from two genes (Mnk1 and Mnk2). The isoforms of Mnk1 (1a/1b) and Mnk2 (2a/2b) differ at their C-termini, with the a-form having a longer C-terminus containing a MAPK-binding region. All Mnks contain a catalytic kinase domain and a polybasic region at the N-terminus which binds importin and the eukaryotic initiation factor eIF4G. The best characterized Mnk substrate is eIF4G, whose phosphorylation may promote the export of certain mRNAs from the nucleus. Mnk also phosphorylate substrates that bind to AU-rich elements that regulate mRNA stability and translation. Mnks have also been implicated in tyrosine kinase receptor signaling, inflammation, and cell prolieration or survival. The Mnk subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 289 matched cddid_all.tbl CDD cd14175 cd14175 271077 STKc_RSK1_C C-terminal catalytic domain of the Serine/Threonine Kinase, Ribosomal S6 kinase 1 (also called Ribosomal protein S6 kinase alpha-1 or 90kDa ribosomal protein S6 kinase 1). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. RSK1 is also called S6K-alpha-1, RPS6KA1, p90RSK1 or MAPK-activated protein kinase 1a (MAPKAPK-1a). It is a component of the insulin transduction pathway, regulating the function of IRS1. It also interacts with PKA and promotes its inactivation. RSK1 is one of four RSK isoforms (RSK1-4) from distinct genes present in vertebrates. RSKs contain an N-terminal kinase domain (NTD) from the AGC family and a C-terminal kinase domain (CTD) from the CAMK family. They are activated by signaling inputs from extracellular regulated kinase (ERK) and phosphoinositide dependent kinase 1 (PDK1). ERK phosphorylates and activates the CTD of RSK, serving as a docking site for PDK1, which phosphorylates and activates the NTD, which in turn phosphorylates all known RSK substrates. RSKs act as downstream effectors of mitogen-activated protein kinase (MAPK) and play key roles in mitogen-activated cell growth, differentiation, and survival. The RSK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 291 matched cddid_all.tbl CDD cd14176 cd14176 271078 STKc_RSK2_C C-terminal catalytic domain of the Serine/Threonine Kinase, Ribosomal S6 kinase 2 (also called 90kDa ribosomal protein S6 kinase 3 or Ribosomal protein S6 kinase alpha-3). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. RSK2 is also called p90RSK3, RPS6KA3, S6K-alpha-3, or MAPK-activated protein kinase 1b (MAPKAPK-1b). RSK2 is expressed highly in the regions of the brain with high synaptic activity. It plays a role in the maintenance and consolidation of excitatory synapses. It is a specific modulator of phospholipase D in calcium-regulated exocytosis. Mutations in the RSK2 gene, RPS6KA3, cause Coffin-Lowry syndrome (CLS), a rare syndromic form of X-linked mental retardation characterized by growth and psychomotor retardation and skeletal abnormalities. RSK2 is one of four RSK isoforms (RSK1-4) from distinct genes present in vertebrates. RSKs contain an N-terminal kinase domain (NTD) from the AGC family and a C-terminal kinase domain (CTD) from the CAMK family. They are activated by signaling inputs from extracellular regulated kinase (ERK) and phosphoinositide dependent kinase 1 (PDK1). ERK phosphorylates and activates the CTD of RSK, serving as a docking site for PDK1, which phosphorylates and activates the NTD, which in turn phosphorylates all known RSK substrates. RSKs act as downstream effectors of mitogen-activated protein kinase (MAPK) and play key roles in mitogen-activated cell growth, differentiation, and survival. The RSK2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 339 matched cddid_all.tbl CDD cd14177 cd14177 271079 STKc_RSK4_C C-terminal catalytic domain of the Serine/Threonine Kinase, Ribosomal S6 kinase 4 (also called Ribosomal protein S6 kinase alpha-6 or 90kDa ribosomal protein S6 kinase 6). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. RSK4 is also called S6K-alpha-6, RPS6KA6, p90RSK6 or pp90RSK4. RSK4 is a substrate of ERK and is a modulator of p53-dependent proliferation arrest in human cells. Deletion of the RSK4 gene, RPS6KA6, frequently occurs in patients of X-linked deafness type 3, mental retardation and choroideremia. Studies of RSK4 in cancer cells and tissues suggest that it may be oncogenic or tumor suppressive depending on many factors. RSK4 is one of four RSK isoforms (RSK1-4) from distinct genes present in vertebrates. RSKs contain an N-terminal kinase domain (NTD) from the AGC family and a C-terminal kinase domain (CTD) from the CAMK family. They are activated by signaling inputs from extracellular regulated kinase (ERK) and phosphoinositide dependent kinase 1 (PDK1). ERK phosphorylates and activates the CTD of RSK, serving as a docking site for PDK1, which phosphorylates and activates the NTD, which in turn phosphorylates all known RSK substrates. RSKs act as downstream effectors of mitogen-activated protein kinase (MAPK) and play key roles in mitogen-activated cell growth, differentiation, and survival. The RSK4 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 295 matched cddid_all.tbl CDD cd14178 cd14178 271080 STKc_RSK3_C C-terminal catalytic domain of the Serine/Threonine Kinase, Ribosomal S6 kinase 3 (also called Ribosomal protein S6 kinase alpha-2 or 90kDa ribosomal protein S6 kinase 2). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. RSK3 is also called S6K-alpha-2, RPS6KA2, p90RSK2 or MAPK-activated protein kinase 1c (MAPKAPK-1c). RSK3 binds muscle A-kinase anchoring protein (mAKAP)-b directly and regulates concentric cardiac myocyte growth. The RSK3 gene, RPS6KA2, is a putative tumor suppressor gene in sporadic epithelial ovarian cancer and variations to the gene may be associated with rectal cancer risk. RSK3 is one of four RSK isoforms (RSK1-4) from distinct genes present in vertebrates. RSKs contain an N-terminal kinase domain (NTD) from the AGC family and a C-terminal kinase domain (CTD) from the CAMK family. They are activated by signaling inputs from extracellular regulated kinase (ERK) and phosphoinositide dependent kinase 1 (PDK1). ERK phosphorylates and activates the CTD of RSK, serving as a docking site for PDK1, which phosphorylates and activates the NTD, which in turn phosphorylates all known RSK substrates. RSKs act as downstream effectors of mitogen-activated protein kinase (MAPK) and play key roles in mitogen-activated cell growth, differentiation, and survival. The RSK3 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 293 matched cddid_all.tbl CDD cd14179 cd14179 271081 STKc_MSK1_C C-terminal catalytic domain of the Serine/Threonine Kinase, Mitogen and stress-activated kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MSK1 plays a role in the regulation of translational control and transcriptional activation. It phosphorylates the transcription factors, CREB and NFkB. It also phosphorylates the nucleosomal proteins H3 and HMG-14. Increased phosphorylation of MSK1 is associated with the development of cerebral ischemic/hypoxic preconditioning. MSKs contain an N-terminal kinase domain (NTD) from the AGC family and a C-terminal kinase domain (CTD) from the CAMK family. MSKs are activated by two major signaling cascades, the Ras-MAPK and p38 stress kinase pathways, which trigger phosphorylation in the activation loop (A-loop) of the CTD of MSK. The active CTD phosphorylates the hydrophobic motif (HM) of NTD, which facilitates the phosphorylation of the A-loop and activates the NTD, which in turn phosphorylates downstream targets. The MSK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 310 matched cddid_all.tbl CDD cd14180 cd14180 271082 STKc_MSK2_C C-terminal catalytic domain of the Serine/Threonine Kinase, Mitogen and stress-activated kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MSK2 and MSK1 play nonredundant roles in activating histone H3 kinases, which play pivotal roles in compaction of the chromatin fiber. MSK2 is the required H3 kinase in response to stress stimuli and activation of the p38 MAPK pathway. MSK2 also plays a role in the pathogenesis of psoriasis. MSKs contain an N-terminal kinase domain (NTD) from the AGC family and a C-terminal kinase domain (CTD) from the CAMK family, similar to 90 kDa ribosomal protein S6 kinases (RSKs). MSKs are activated by two major signaling cascades, the Ras-MAPK and p38 stress kinase pathways, which trigger phosphorylation in the activation loop (A-loop) of the CTD of MSK. The active CTD phosphorylates the hydrophobic motif (HM) of NTD, which facilitates the phosphorylation of the A-loop and activates the NTD, which in turn phosphorylates downstream targets. The MSK2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 309 matched cddid_all.tbl CDD cd14181 cd14181 271083 STKc_PhKG2 Catalytic domain of the Serine/Threonine Kinase, Phosphorylase kinase Gamma 2 subunit. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Phosphorylase kinase (PhK) catalyzes the phosphorylation of inactive phosphorylase b to form the active phosphorylase a. It coordinates hormonal, metabolic, and neuronal signals to initiate the breakdown of glycogen stores, which enables the maintenance of blood-glucose homeostasis during fasting, and is also used as a source of energy for muscle contraction. PhK is one of the largest and most complex protein kinases, composed of a heterotetramer containing four molecules each of four subunit types: one catalytic (gamma) and three regulatory (alpha, beta, and delta). The gamma 2 subunit (PhKG2) is also referred to as the testis/liver gamma isoform. Mutations in its gene cause autosomal-recessive glycogenosis of the liver. The gamma subunit, when isolated, is constitutively active and does not require phosphorylation of the A-loop for activity. The regulatory subunits restrain this kinase activity until signals are received to relieve this inhibition. For example, the kinase is activated in response to hormonal stimulation, after autophosphorylation or phosphorylation by cAMP-dependent kinase of the alpha and beta subunits. The high-affinity binding of ADP to the beta subunit also stimulates kinase activity, whereas calcium relieves inhibition by binding to the delta (calmodulin) subunit. The PhKG2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 279 matched cddid_all.tbl CDD cd14182 cd14182 271084 STKc_PhKG1 Catalytic domain of the Serine/Threonine Kinase, Phosphorylase kinase Gamma 1 subunit. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Phosphorylase kinase (PhK) catalyzes the phosphorylation of inactive phosphorylase b to form the active phosphorylase a. It coordinates hormonal, metabolic, and neuronal signals to initiate the breakdown of glycogen stores, which enables the maintenance of blood-glucose homeostasis during fasting, and is also used as a source of energy for muscle contraction. PhK is one of the largest and most complex protein kinases, composed of a heterotetramer containing four molecules each of four subunit types: one catalytic (gamma) and three regulatory (alpha, beta, and delta). The gamma 1 subunit (PhKG1) is also referred to as the muscle gamma isoform. The gamma subunit, when isolated, is constitutively active and does not require phosphorylation of the A-loop for activity. The regulatory subunits restrain this kinase activity until signals are received to relieve this inhibition. For example, the kinase is activated in response to hormonal stimulation, after autophosphorylation or phosphorylation by cAMP-dependent kinase of the alpha and beta subunits. The high-affinity binding of ADP to the beta subunit also stimulates kinase activity, whereas calcium relieves inhibition by binding to the delta (calmodulin) subunit. The PhKG1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 276 matched cddid_all.tbl CDD cd14183 cd14183 271085 STKc_DCKL1 Catalytic domain of the Serine/Threonine Kinase, Doublecortin-like kinase 1 (also called Doublecortin-like and CAM kinase-like 1). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. DCKL1 (or DCAMKL1) belongs to the doublecortin (DCX) family of proteins which are involved in neuronal migration, neurogenesis, and eye receptor development, among others. Family members typically contain tandem doublecortin (DCX) domains at the N-terminus; DCX domains can bind microtubules and serve as protein-interaction platforms. In addition, DCKL1 contains a serine, threonine, and proline rich domain (SP) and a C-terminal kinase domain with similarity to CAMKs. DCKL1 interacts with tubulin, glucocorticoid receptor, dynein, JIP1/2, caspases (3 and 8), and calpain, among others. It plays roles in neurogenesis, neuronal migration, retrograde transport, and neuronal apoptosis. The DCKL1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 268 matched cddid_all.tbl CDD cd14184 cd14184 271086 STKc_DCKL2 Catalytic domain of the Serine/Threonine Kinase, Doublecortin-like kinase 2 (also called Doublecortin-like and CAM kinase-like 2). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. DCKL2 (or DCAMKL2) belongs to the doublecortin (DCX) family of proteins which are involved in neuronal migration, neurogenesis, and eye receptor development, among others. Family members typically contain tandem doublecortin (DCX) domains at the N-terminus; DCX domains can bind microtubules and serve as protein-interaction platforms. In addition, DCKL2 contains a serine, threonine, and proline rich domain (SP) and a C-terminal kinase domain with similarity to CAMKs. DCKL2 has been shown to interact with tubulin, JIP1/2, JNK, neurabin 2, and actin. It is associated with the terminal segments of axons and dendrites, and may function as a phosphorylation-dependent switch to control microtubule dynamics in neuronal growth cones. The DCKL2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 259 matched cddid_all.tbl CDD cd14185 cd14185 271087 STKc_DCKL3 Catalytic domain of the Serine/Threonine Kinase, Doublecortin-like kinase 3 (also called Doublecortin-like and CAM kinase-like 3). STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. DCKL3 (or DCAMKL3) belongs to the doublecortin (DCX) family of proteins which are involved in neuronal migration, neurogenesis, and eye receptor development, among others. Family members typically contain tandem doublecortin (DCX) domains at the N-terminus; DCX domains can bind microtubules and serve as protein-interaction platforms. DCKL3 contains a single DCX domain (instead of a tandem) and a C-terminal kinase domain with similarity to CAMKs. It has been shown to interact with tubulin and JIP1/2. The DCKL3 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 258 matched cddid_all.tbl CDD cd14186 cd14186 271088 STKc_PLK4 Catalytic domain of the Serine/Threonine Kinase, Polo-like kinase 4. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PLKs play important roles in cell cycle progression and in DNA damage responses. They regulate mitotic entry, mitotic exit, and cytokinesis. In general PLKs contain an N-terminal catalytic kinase domain and a C-terminal regulatory polo box domain (PBD), which is comprised by two bipartite polo-box motifs (or polo boxes) and is involved in protein interactions. There are five mammalian PLKs (PLK1-5) from distinct genes. PLK4, also called SAK or STK18, is structurally different from other PLKs in that it contains only one polo box that can form two adjacent polo boxes and a functional PDB by homodimerization. It is required for late mitotic progression, cell survival, and embryonic development. It localizes to centrosomes and is required for centriole duplication and chromosomal stability. Overexpression of PLK4 may be associated with colon tumors. The PLK4 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd14187 cd14187 271089 STKc_PLK1 Catalytic domain of the Serine/Threonine Kinase, Polo-like kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PLKs play important roles in cell cycle progression and in DNA damage responses. They regulate mitotic entry, mitotic exit, and cytokinesis. In general PLKs contain an N-terminal catalytic kinase domain and a C-terminal regulatory polo box domain (PBD), which is comprised by two bipartite polo-box motifs (or polo boxes) and is involved in protein interactions. There are five mammalian PLKs (PLK1-5) from distinct genes. PLK1 functions as a positive regulator of mitosis, meiosis, and cytokinesis. Its localization changes during mitotic progression; associating first with centrosomes in prophase, with kinetochores in prometaphase and metaphase, at the central spindle in anaphase, and in the midbody during telophase. It carries multiple functions throughout the cell cycle through interactions with differrent substrates at these specific subcellular locations. PLK1 is overexpressed in many human cancers and is associated with poor prognosis. The PLK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 265 matched cddid_all.tbl CDD cd14188 cd14188 271090 STKc_PLK2 Catalytic domain of the Serine/Threonine Kinase, Polo-like kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PLKs play important roles in cell cycle progression and in DNA damage responses. They regulate mitotic entry, mitotic exit, and cytokinesis. In general PLKs contain an N-terminal catalytic kinase domain and a C-terminal regulatory polo box domain (PBD), which is comprised by two bipartite polo-box motifs (or polo boxes) and is involved in protein interactions. There are five mammalian PLKs (PLK1-5) from distinct genes. PLK2, also called Snk (serum-inducible kinase), functions in G1 progression, S-phase arrest, and centriole duplication. Its gene is responsive to both growth factors and cellular stress, is a transcriptional target of p53, and activates a G2-M checkpoint. The PLK2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 255 matched cddid_all.tbl CDD cd14189 cd14189 271091 STKc_PLK3 Catalytic domain of the Serine/Threonine Kinase, Polo-like kinase 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. PLKs play important roles in cell cycle progression and in DNA damage responses. They regulate mitotic entry, mitotic exit, and cytokinesis. In general PLKs contain an N-terminal catalytic kinase domain and a C-terminal regulatory polo box domain (PBD), which is comprised by two bipartite polo-box motifs (or polo boxes) and is involved in protein interactions. There are five mammalian PLKs (PLK1-5) from distinct genes. PLK3, also called Prk or Fnk (FGF-inducible kinase), regulates angiogenesis and responses to DNA damage. Activated PLK3 mediates Chk2 phosphorylation by ATM and the resulting checkpoint activation. PLK3 phosphorylates DNA polymerase delta and may be involved in DNA repair. It also inhibits Cdc25c, thereby regulating the onset of mitosis. The PLK3 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 255 matched cddid_all.tbl CDD cd14190 cd14190 271092 STKc_MLCK2 Catalytic domain of the Serine/Threonine Kinase, Myosin Light Chain Kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MLCK2 (or MYLK2) phosphorylates myosin regulatory light chain and controls the contraction of skeletal muscles. MLCK2 contains a single kinase domain near the C-terminus followed by a regulatory segment containing an autoinhibitory Ca2+/calmodulin binding site. The MLCK2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 261 matched cddid_all.tbl CDD cd14191 cd14191 271093 STKc_MLCK1 Catalytic domain of the Serine/Threonine Kinase, Myosin Light Chain Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MLCK1 (or MYLK1) phosphorylates myosin regulatory light chain and controls the contraction of smooth muscles. The MLCK1 gene expresses three transcripts in a cell-specific manner: a short MLCK1 which contains three immunoglobulin (Ig)-like and one fibronectin type III (FN3) domains, PEVK and actin-binding regions, and a kinase domain near the C-terminus followed by a regulatory segment containing an autoinhibitory Ca2+/calmodulin binding site; a long MLCK1 containing six additional Ig-like domains at the N-terminus compared to the short MLCK1; and the C-terminal Ig module which results in the expression of telokin in phasic smooth muscles, leading to Ca2+ desensitization by cyclic nucleotides of smooth muscle force. MLCK1 is also responsible for myosin regulatory light chain phosphorylation in nonmuscle cells and may play a role in regulating myosin II ATPase activity. The MLCK1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 259 matched cddid_all.tbl CDD cd14192 cd14192 271094 STKc_MLCK3 Catalytic domain of the Serine/Threonine Kinase, Myosin Light Chain Kinase 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MLCK3 (or MYLK3) phosphorylates myosin regulatory light chain 2 and controls the contraction of cardiac muscles. It is expressed specifically in both the atrium and ventricle of the heart and its expression is regulated by the cardiac protein Nkx2-5. MLCK3 plays an important role in cardiogenesis by regulating the assembly of cardiac sarcomeres, the repeating contractile unit of striated muscle. MLCK3 contains a single kinase domain near the C-terminus and a unique N-terminal half, and unlike MLCK1/2, it does not appear to be regulated by Ca2+/calmodulin. The MLCK3 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 261 matched cddid_all.tbl CDD cd14193 cd14193 271095 STKc_MLCK4 Catalytic domain of the Serine/Threonine Kinase, Myosin Light Chain Kinase 4. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. MLCK phosphorylates myosin regulatory light chain and controls the contraction of all muscle types. In vertebrates, different MLCKs function in smooth (MLCK1), skeletal (MLCK2), and cardiac (MLCK3) muscles. A fourth protein, MLCK4, has also been identified through comprehensive genome analysis although it has not been biochemically characterized. MLCK4 (or MYLK4 or SgK085) contains a single kinase domain near the C-terminus. The MLCK4 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 261 matched cddid_all.tbl CDD cd14194 cd14194 271096 STKc_DAPK1 Catalytic domain of the Serine/Threonine Kinase, Death-Associated Protein Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. DAPKs mediate cell death and act as tumor suppressors. They are necessary to induce cell death and their overexpression leads to death-associated changes including membrane blebbing, cell rounding, and formation of autophagic vesicles. Vertebrates contain three subfamily members with different domain architecture, localization, and function. DAPK1 is the prototypical member of the subfamily and is also simply referred to as DAPK. It is Ca2+/calmodulin (CaM)-regulated and actin-associated protein that contains an N-terminal kinase domain followed by an autoinhibitory CaM binding region and a large C-terminal extension with multiple functional domains including ankyrin (ANK) repeats, a cytoskeletal binding domain, a Death domain, and a serine-rich tail. Loss of DAPK1 expression, usually because of DNA methylation, is implicated in many tumor types. DAPK1 is highly abundant in the brain and has also been associated with neurodegeneration. The DAPK1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 269 matched cddid_all.tbl CDD cd14195 cd14195 271097 STKc_DAPK3 Catalytic domain of the Serine/Threonine Kinase, Death-Associated Protein Kinase 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. DAPKs mediate cell death and act as tumor suppressors. They are necessary to induce cell death and their overexpression leads to death-associated changes including membrane blebbing, cell rounding, and formation of autophagic vesicles. Vertebrates contain three subfamily members with different domain architecture, localization, and function. DAPK3, also called DAP-like kinase (DLK) and zipper-interacting protein kinase (ZIPk), contains an N-terminal kinase domain and a C-terminal region with nuclear localization signals (NLS) and a leucine zipper motif that mediates homodimerization and interaction with other leucine zipper proteins. It interacts with Par-4, a protein that contains a death domain and interacts with actin filaments. DAPK3 is present in both the cytoplasm and nucleus. Its co-expression with Par-4 results in the co-localization of the two proteins to actin filaments. In addition to cell death, DAPK3 is also implicated in mediating cell motility and the contraction of smooth muscles. The DAPK3 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 271 matched cddid_all.tbl CDD cd14196 cd14196 271098 STKc_DAPK2 Catalytic domain of the Serine/Threonine Kinase, Death-Associated Protein Kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. DAPKs mediate cell death and act as tumor suppressors. They are necessary to induce cell death and their overexpression leads to death-associated changes including membrane blebbing, cell rounding, and formation of autophagic vesicles. Vertebrates contain three subfamily members with different domain architecture, localization, and function. DAPK2, also called DAPK-related protein 1 (DRP-1), is a Ca2+/calmodulin (CaM)-regulated protein containing an N-terminal kinase domain, a CaM autoinhibitory site and a dimerization module. It lacks the cytoskeletal binding regions of DAPK1 and the exogenous protein has been shown to be soluble and cytoplasmic. FLAG-tagged DAPK2, however, accumulated within membrane-enclosed autophagic vesicles. It is unclear where endogenous DAPK2 is localized. DAPK2 participates in TNF-alpha and FAS-receptor induced cell death and enhances neutrophilic maturation in myeloid leukemic cells. It contributes to the induction of anoikis and its down-regulation is implicated in the beta-catenin induced resistance of malignant epithelial cells to anoikis. The DAPK2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 269 matched cddid_all.tbl CDD cd14197 cd14197 271099 STKc_DRAK1 Catalytic domain of the Serine/Threonine Kinase, Death-associated protein kinase-Related Apoptosis-inducing protein Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. DRAKs were named based on their similarity (around 50% identity) to the kinase domain of DAPKs. They contain an N-terminal kinase domain and a C-terminal regulatory domain. Vertebrates contain two subfamily members, DRAK1 (also called STK17A) and DRAK2. Both DRAKs are localized to the nucleus, autophosphorylate themselves, and phosphorylate myosin light chain as a substrate. Rabbit DRAK1 has been shown to induce apoptosis in osteoclasts and overexpressio of human DRAK1 induces apoptosis in cultured fibroblast cells. DRAK1 may be involved in apoptotic signaling. The DRAK1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 271 matched cddid_all.tbl CDD cd14198 cd14198 271100 STKc_DRAK2 The catalytic domain of the Serine/Threonine Kinase, Death-associated protein kinase-Related Apoptosis-inducing protein Kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. DRAKs were named based on their similarity (around 50% identity) to the kinase domain of DAPKs. They contain an N-terminal kinase domain and a C-terminal regulatory domain. Vertebrates contain two subfamily members, DRAK1 and DRAK2 (also called STK17B). Both DRAKs are localized to the nucleus, autophosphorylate themselves, and phosphorylate myosin light chain as a substrate. DRAK2 has been implicated in inducing or enhancing apoptosis in beta cells, fibroblasts, and lymphoid cells, where it is highly expressed. It is involved in regulating many immune processes including the germinal center (GC) reaction, responses to thymus-dependent antigens, activated T cell survival, memory T cell responses. It may be involved in the development of autoimmunity. The DRAK2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 270 matched cddid_all.tbl CDD cd14199 cd14199 271101 STKc_CaMKK2 Catalytic domain of the Serine/Threonine kinase, Calmodulin Dependent Protein Kinase Kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CaMKKs are upstream kinases of the CaM kinase cascade that phosphorylate and activate CaMKI and CamKIV. They may also phosphorylate other substrates including PKB and AMP-activated protein kinase (AMPK). CaMKK2, also called CaMKK beta, is one of the most versatile CaMKs. It is involved in regulating energy balance, glucose metabolism, adiposity, hematopoiesis, inflammation, and cancer. CaMKK2 contains unique N- and C-terminal domains and a central catalytic kinase domain that is followed by a regulatory domain that bears overlapping autoinhibitory and CaM-binding regions. It can be activated by signaling through G-coupled receptors, IP3 receptors, plasma membrane ion channels, and Toll-like receptors. Thus, CaMKK2 acts as a molecular hub that is capable of receiving and decoding signals from diverse pathways. The CaMKK2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 286 matched cddid_all.tbl CDD cd14200 cd14200 271102 STKc_CaMKK1 Catalytic domain of the Serine/Threonine kinase, Calmodulin Dependent Protein Kinase Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. CaMKKs are upstream kinases of the CaM kinase cascade that phosphorylate and activate CaMKI and CamKIV. They may also phosphorylate other substrates including PKB and AMP-activated protein kinase (AMPK). CaMKK1, also called CaMKK alpha, is involved in the regulation of glucose uptake in skeletal muscles, independently of AMPK and PKB activation. It also play roles in learning and memory. Studies on CaMKK1 knockout mice reveal deficits in fear conditioning. The CaMKK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 284 matched cddid_all.tbl CDD cd14201 cd14201 271103 STKc_ULK2 Catalytic domain of the Serine/Threonine kinase, Unc-51-like kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The ATG1/ULK complex is conserved from yeast to humans and it plays a critical role in the initiation of autophagy, the intracellular system that leads to the lysosomal degradation of cellular components and their recycling into basic metabolic units. ULK2 is ubiquitously expressed and is essential in autophagy induction. It displays partially redundant functions with ULK1 and is able to compensate for the loss of ULK1 in non-selective autophagy. It also displays neuron-specific functions and is important in axon development. The ULK2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 271 matched cddid_all.tbl CDD cd14202 cd14202 271104 STKc_ULK1 Catalytic domain of the Serine/Threonine kinase, Unc-51-like kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The ATG1/ULK complex is conserved from yeast to humans and it plays a critical role in the initiation of autophagy, the intracellular system that leads to the lysosomal degradation of cellular components and their recycling into basic metabolic units. ULK1 is required for efficient amino acid starvation-induced autophagy and mitochondrial clearance. It associates with three autophagy-related proteins (Atg13, FIP200 amd Atg101) to form the ULK1 complex. All fours proteins are essential for autophagosome formation. ULK1 is regulated by both mammalian target-of rapamycin complex 1 (mTORC1) and AMP-activated protein kinase (AMPK). mTORC1 negatively regulates the ULK1 complex in a nutrient-dependent manner while AMPK stimulates autophagy by inhibiting mTORC1. ULK1 also plays neuron-specific roles and is involved in non-clathrin-coated endocytosis in growth cones, filopodia extension, neurite extension, and axon branching. The ULK1 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 267 matched cddid_all.tbl CDD cd14203 cd14203 271105 PTKc_Src_Fyn_like Catalytic domain of a subset of Src kinase-like Protein Tyrosine Kinases. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. This subfamily includes a subset of Src-like PTKs including Src, Fyn, Yrk, and Yes, which are all widely expressed. Yrk has been detected only in chickens. It is primarily found in neuronal and epithelial cells and in macrophages. It may play a role in inflammation and in response to injury. Src (or c-Src) proteins are cytoplasmic (or non-receptor) PTKs which are anchored to the plasma membrane. They contain an N-terminal SH4 domain with a myristoylation site, followed by SH3 and SH2 domains, a tyr kinase domain, and a regulatory C-terminal region containing a conserved tyr. They are activated by autophosphorylation at the tyr kinase domain, but are negatively regulated by phosphorylation at the C-terminal tyr by Csk (C-terminal Src Kinase). Src proteins are involved in signaling pathways that regulate cytokine and growth factor responses, cytoskeleton dynamics, cell proliferation, survival, and differentiation. They were identified as the first proto-oncogene products, and they regulate cell adhesion, invasion, and motility in cancer cells and tumor vasculature, contributing to cancer progression and metastasis. They are also implicated in acute inflammatory responses and osteoclast function. The Src/Fyn-like subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 248 matched cddid_all.tbl CDD cd14204 cd14204 271106 PTKc_Mer Catalytic Domain of the Protein Tyrosine Kinase, Mer. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Mer (or Mertk) is named after its original reported expression pattern (monocytes, epithelial, and reproductive tissues). It is required for the ingestion of apoptotic cells by phagocytes such as macrophages, retinal pigment epithelial cells, and dendritic cells. Mer is also important in maintaining immune homeostasis. Mer is a member of the TAM subfamily, composed of receptor PTKs (RTKs) containing an extracellular ligand-binding region with two immunoglobulin-like domains followed by two fibronectin type III repeats, a transmembrane segment, and an intracellular catalytic domain. Binding to their ligands, Gas6 and protein S, leads to receptor dimerization, autophosphorylation, activation, and intracellular signaling. The Mer subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 284 matched cddid_all.tbl CDD cd14205 cd14205 271107 PTKc_Jak2_rpt2 Catalytic (repeat 2) domain of the Protein Tyrosine Kinase, Janus kinase 2. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Jak2 is widely expressed in many tissues and is essential for the signaling of hormone-like cytokines such as growth hormone, erythropoietin, thrombopoietin, and prolactin, as well as some IFNs and cytokines that signal through the IL-3 and gp130 receptors. Disruption of Jak2 in mice results in an embryonic lethal phenotype with multiple defects including erythropoietic and cardiac abnormalities. It is the only Jak gene that results in a lethal phenotype when disrupted in mice. A mutation in the pseudokinase domain of Jak2, V617F, is present in many myeloproliferative diseases, including almost all patients with polycythemia vera, and 50% of patients with essential thrombocytosis and myelofibrosis. Jak2 is a member of the Janus kinase (Jak) subfamily of proteins, which are cytoplasmic (or nonreceptor) PTKs containing an N-terminal FERM domain, followed by a Src homology 2 (SH2) domain, a pseudokinase domain, and a C-terminal catalytic tyr kinase domain. Jaks are crucial for cytokine receptor signaling. They are activated by autophosphorylation upon cytokine-induced receptor aggregation, and subsequently trigger downstream signaling events such as the phosphorylation of signal transducers and activators of transcription (STATs). The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 284 matched cddid_all.tbl CDD cd14206 cd14206 271108 PTKc_Aatyk3 Catalytic domain of the Protein Tyrosine Kinases, Apoptosis-associated tyrosine kinase 3. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Aatyk3, also called lemur tyrosine kinase 3 (Lmtk3) is a receptor kinase containing a transmembrane segment and a long C-terminal cytoplasmic tail with a catalytic domain. The function of Aatyk3 is still unknown. The Aatyk3 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). 276 matched cddid_all.tbl CDD cd14207 cd14207 271109 PTKc_VEGFR1 Catalytic domain of the Protein Tyrosine Kinases, Vascular Endothelial Growth Factor Receptors. PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. VEGFR1 (or Flt1) binds VEGFA, VEGFB, and placenta growth factor (PLGF). It regulates monocyte and macrophage migration, vascular permeability, haematopoiesis, and the recruitment of haematopietic progenitor cells from the bone marrow. VEGFR1 is a member of the VEGFR subfamily of proteins, which are receptor PTKs (RTKs) containing an extracellular ligand-binding region with seven immunoglobulin (Ig)-like domains, a transmembrane segment, and an intracellular catalytic domain. The binding of VEGFRs to their ligands, the VEGFs, leads to receptor dimerization, activation, and intracellular signaling. The VEGFR1 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 340 matched cddid_all.tbl CDD cd14208 cd14208 271110 PTK_Jak3_rpt1 Pseudokinase (repeat 1) domain of the Protein Tyrosine Kinase, Janus kinase 3. Jak3 is expressed only in hematopoietic cells. It binds the shared receptor subunit, common gamma chain and thus, is essential in the signaling of cytokines that use it such as IL-2, IL-4, IL-7, IL-9, IL-15, and IL-21. Jak3 is important in lymphoid development and myeloid cell differentiation. Inactivating mutations in Jak3 have been reported in humans with severe combined immunodeficiency (SCID). Jak3 is a cytoplasmic (or nonreceptor) PTK containing an N-terminal FERM domain, followed by a Src homology 2 (SH2) domain, a pseudokinase domain, and a C-terminal tyr kinase domain. The pseudokinase domain shows similarity to tyr kinases but lacks crucial residues for catalytic activity and ATP binding. It modulates the kinase activity of the C-terminal catalytic domain. Jaks are activated by autophosphorylation upon cytokine-induced receptor aggregation, and subsequently trigger downstream signaling events such as the phosphorylation of signal transducers and activators of transcription (STATs). The Jak3 subfamily is part of a larger superfamily that includes the catalytic domains of other kinases such as serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 260 matched cddid_all.tbl CDD cd14209 cd14209 271111 STKc_PKA Catalytic subunit of the Serine/Threonine Kinase, cAMP-dependent protein kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis. The PKA subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 290 matched cddid_all.tbl CDD cd14210 cd14210 271112 PKc_DYRK Catalytic domain of the protein kinase, Dual-specificity tYrosine-phosphorylated and -Regulated Kinase. Protein Kinases (PKs), Dual-specificity tYrosine-phosphorylated and -Regulated Kinase (DYRK) subfamily, catalytic (c) domain. Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (S/T) as well as tyrosine residues on protein substrates. The DYRK subfamily is part of a larger superfamily that includes the catalytic domains of other protein S/T PKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). DYRKs autophosphorylate themselves on tyrosine residues and phosphorylate their substrates exclusively on S/T residues. They play important roles in cell proliferation, differentiation, survival, and development. Vertebrates contain multiple DYRKs (DYRK1-4) and mammals contain two types of DYRK1 proteins, DYRK1A and DYRK1B. DYRK1A is involved in neuronal differentiation and is implicated in the pathogenesis of DS (Down syndrome). DYRK1B plays a critical role in muscle differentiation by regulating transcription, cell motility, survival, and cell cycle progression. It is overexpressed in many solid tumors where it acts as a tumor survival factor. DYRK2 promotes apoptosis in response to DNA damage by phosphorylating the tumor suppressor p53, while DYRK3 promotes cell survival by phosphorylating SIRT1 and promoting p53 deacetylation. DYRK4 is a testis-specific kinase that may function during spermiogenesis. 311 matched cddid_all.tbl CDD cd14211 cd14211 271113 STKc_HIPK Catalytic domain of the Serine/Threonine Kinase, Homeodomain-Interacting Protein Kinase. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. HIPKs, originally identified by their ability to bind homeobox factors, are nuclear proteins containing catalytic kinase and homeobox-interacting domains as well as a PEST region overlapping with the speckle-retention signal (SRS). They show speckled localization in the nucleus, apart from the nucleoles. They play roles in the regulation of many nuclear pathways including gene transcription, cell survival, proliferation, differentiation, development, and DNA damage response. Vertebrates contain three HIPKs (HIPK1-3) and mammals harbor an additional family member HIPK4, which does not contain a homeobox-interacting domain and is localized in the cytoplasm. HIPK2, the most studied HIPK, is a coregulator of many transcription factors and cofactors and it regulates gene transcription during development and in DNA damage response. The HIPK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 329 matched cddid_all.tbl CDD cd14212 cd14212 271114 PKc_YAK1 Catalytic domain of the Dual-specificity protein kinase, YAK1. Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (S/T) as well as tyrosine residues on protein substrates. This subfamily is composed of proteins with similarity to Saccharomyces cerevisiae YAK1 (or Yak1p), a dual-specificity kinase that autophosphorylates at tyrosine residues and phosphorylates substrates on S/T residues. YAK1 phosphorylates and activates the transcription factors Hsf1 and Msn2, which play important roles in cellular homeostasis during stress conditions including heat shock, oxidative stress, and nutrient deficiency. It also phosphorylates the protein POP2, a component of a complex that regulates transcription, under glucose-deprived conditions. It functions as a part of a glucose-sensing system that is involved in controlling growth in yeast. The YAK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 330 matched cddid_all.tbl CDD cd14213 cd14213 271115 PKc_CLK1_4 "Catalytic domain of the Dual-specificity protein kinases, CDC-like kinases 1 and 4. Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine as well as tyrosine residues on protein substrates. CLK1 plays a role in neuronal differentiation. CLKs are involved in the phosphorylation and regulation of serine/arginine-rich (SR) proteins, which play a crucial role in pre-mRNA splicing by directing splice site selection. SR proteins are phosphorylated first by SR protein kinases (SRPKs) at the N-terminus, which leads to its assembly into nuclear speckles where splicing factors are stored. CLKs phosphorylate the C-terminal part of SR proteins, causing the nuclear speckles to dissolve and splicing factors to be recruited at sites of active transcription. Based on a conserved ""EHLAMMERILG"" signature motif which may be crucial for substrate specificity, CLKs are also referred to as LAMMER kinases. CLKs autophosphorylate at tyrosine residues and phosphorylate their substrates exclusively on serine/threonine residues. The CLK1/4 subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine PKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase." 330 matched cddid_all.tbl CDD cd14214 cd14214 271116 PKc_CLK3 "Catalytic domain of the Dual-specificity protein kinase, CDC-like kinase 3. Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine as well as tyrosine residues on protein substrates. CLK3 is predominantly expressed in mature spermatozoa, and might play a role in the fertilization process. CLKs are involved in the phosphorylation and regulation of serine/arginine-rich (SR) proteins, which play a crucial role in pre-mRNA splicing by directing splice site selection. SR proteins are phosphorylated first by SR protein kinases (SRPKs) at the N-terminus, which leads to its assembly into nuclear speckles where splicing factors are stored. CLKs phosphorylate the C-terminal part of SR proteins, causing the nuclear speckles to dissolve and splicing factors to be recruited at sites of active transcription. Based on a conserved ""EHLAMMERILG"" signature motif which may be crucial for substrate specificity, CLKs are also referred to as LAMMER kinases. CLKs autophosphorylate at tyrosine residues and phosphorylate their substrates exclusively on serine/threonine residues. The CLK3 subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine PKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase." 331 matched cddid_all.tbl CDD cd14215 cd14215 271117 PKc_CLK2 "Catalytic domain of the Dual-specificity protein kinase, CDC-like kinase 2. Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine as well as tyrosine residues on protein substrates. CLK2 plays a role in hepatic insulin signaling and glucose metabolism. It is induced by the insulin/Akt pathway as part of the hepatic refeeding reponse, and it directly phosphorylates the SR domain of PGC-1alpha, which results in decreased gluconeogenic gene expression and glucose output. CLKs are involved in the phosphorylation and regulation of serine/arginine-rich (SR) proteins, which play a crucial role in pre-mRNA splicing by directing splice site selection. SR proteins are phosphorylated first by SR protein kinases (SRPKs) at the N-terminus, which leads to its assembly into nuclear speckles where splicing factors are stored. CLKs phosphorylate the C-terminal part of SR proteins, causing the nuclear speckles to dissolve and splicing factors to be recruited at sites of active transcription. Based on a conserved ""EHLAMMERILG"" signature motif which may be crucial for substrate specificity, CLKs are also referred to as LAMMER kinases. CLKs autophosphorylate at tyrosine residues and phosphorylate their substrates exclusively on serine/threonine residues. The CLK2 subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine PKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase." 330 matched cddid_all.tbl CDD cd14216 cd14216 271118 STKc_SRPK1 Catalytic domain of the Serine/Threonine Kinase, Serine-aRginine Protein Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. SRPK1 binds with high affinity the alternative splicing factor, SRSF1 (serine/arginine-rich splicing factor 1), and regiospecifically phosphorylates 10-12 serines in its RS domain. It plays a role in the regulation of pre-mRNA splicing, chromatin structure, and germ cell development. SRPKs phosphorylate and regulate splicing factors from the SR protein family by specifically phosphorylating multiple serine residues residing in SR/RS dipeptide motifs (also known as RS domains). Phosphorylation of the RS domains enhances interaction with transportin SR and facilitates entry of the SR proteins into the nucleus. SRPKs contain a nonconserved insert domain, within the well-conserved catalytic kinase domain, that regulates their subcellular localization. The SRPK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 349 matched cddid_all.tbl CDD cd14217 cd14217 271119 STKc_SRPK2 Catalytic domain of the Serine/Threonine Kinase, Serine-aRginine Protein Kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. SRPK2 mediates neuronal cell cycle and cell death through regulation of nuclear cyclin D1. It has also been found to promote leukemia cell proliferation by regulating cyclin A1. SRPK2 also plays a role in regulating pre-mRNA splicing and is required for spliceosomal B complex formation. SRPKs phosphorylate and regulate splicing factors from the SR protein family by specifically phosphorylating multiple serine residues residing in SR/RS dipeptide motifs (also known as RS domains). Phosphorylation of the RS domains enhances interaction with transportin SR and facilitates entry of the SR proteins into the nucleus. SRPKs contain a nonconserved insert domain, within the well-conserved catalytic kinase domain, that regulates their subcellular localization. The SRPK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 366 matched cddid_all.tbl CDD cd14218 cd14218 271120 STKc_SRPK3 Catalytic domain of the Serine/Threonine Kinase, Serine-aRginine Protein Kinase 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. SRPK3 is highly expressed in the heart and skeletal muscles, and is controlled by a muscle-specific enhancer that is regulated by MEF2. It may play an important role in muscle development. SRPKs phosphorylate and regulate splicing factors from the SR protein family by specifically phosphorylating multiple serine residues residing in SR/RS dipeptide motifs (also known as RS domains). Phosphorylation of the RS domains enhances interaction with transportin SR and facilitates entry of the SR proteins into the nucleus. SRPKs contain a nonconserved insert domain, within the well-conserved catalytic kinase domain, that regulates their subcellular localization. The SRPK subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 365 matched cddid_all.tbl CDD cd14219 cd14219 271121 STKc_BMPR1b Catalytic domain of the Serine/Threonine Kinase, Bone Morphogenetic Protein Type IB. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. BMPR1b, also called Activin receptor-Like Kinase 6 (ALK6), functions as a receptor for bone morphogenetic proteins (BMPs), which are involved in the regulation of cell proliferation, survival, differentiation, and apoptosis. BMPs are able to induce bone, cartilage, ligament, and tendon formation, and may play roles in bone diseases and tumors. Mutations in BMPR1b that led to inhibition of chondrogenesis can cause Brachydactyly (BD) type A2, a dominant hand malformation characterized by shortening and lateral deviation of the index fingers. A point mutation in the BMPR1b kinase domain is also associated with the Booroola phenotype, characterized by precocious differentiation of ovarian follicles. BMPR1b belongs to a group of receptors for the TGFbeta family of secreted signaling molecules that includes TGFbeta, BMPs, activins, growth and differentiation factors, and anti-Mullerian hormone, among others. These receptors contain an extracellular domain that binds ligands, a single transmembrane (TM) region, and a cytoplasmic catalytic kinase domain. Type I receptors, like BMPR1b, are low-affinity receptors that bind ligands only after they are recruited by the ligand/type II high-affinity receptor complex. Following activation, they start intracellular signaling to the nucleus by phosphorylating SMAD proteins. Type I receptors contain an additional domain located between the TM and kinase domains called the GS domain, which contains the activating phosphorylation site and confers preference for specific SMAD proteins. The BMPR1b subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 305 matched cddid_all.tbl CDD cd14220 cd14220 271122 STKc_BMPR1a Catalytic domain of the Serine/Threonine Kinase, Bone Morphogenetic Protein Type IA Receptor. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. BMPR1a, also called Activin receptor-Like Kinase 3 (ALK3), functions as a receptor for bone morphogenetic proteins (BMPs), which are involved in the regulation of cell proliferation, survival, differentiation, and apoptosis. BMPs are able to induce bone, cartilage, ligament, and tendon formation, and may play roles in bone diseases and tumors. Germline mutations in BMPR1a are associated with an increased risk to Juvenile Polyposis Syndrome, a hamartomatous disorder that may lead to gastrointestinal cancer. BMPR1a may also play an indirect role in the development of hematopoietic stem cells (HSCs) as osteoblasts are a major component of the HSC niche within the bone marrow. BMPR1a belongs to a group of receptors for the TGFbeta family of secreted signaling molecules that includes TGFbeta, BMPs, activins, growth and differentiation factors, and anti-Mullerian hormone, among others. These receptors contain an extracellular domain that binds ligands, a single transmembrane (TM) region, and a cytoplasmic catalytic kinase domain. Type I receptors, like BMPR1a, are low-affinity receptors that bind ligands only after they are recruited by the ligand/type II high-affinity receptor complex. Following activation, they start intracellular signaling to the nucleus by phosphorylating SMAD proteins. Type I receptors contain an additional domain located between the TM and kinase domains called the GS domain, which contains the activating phosphorylation site and confers preference for specific SMAD proteins. The BMPR1a subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 287 matched cddid_all.tbl CDD cd14221 cd14221 271123 STKc_LIMK1 Catalytic domain of the Serine/Threonine Kinase, LIM domain kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. LIMK1 activation is induced by bone morphogenic protein, vascular endothelial growth factor, and thrombin. It plays roles in microtubule disassembly and cell cycle progression, and is critical in the regulation of neurite outgrowth. LIMK1 knockout mice show abnormalities in dendritic spine morphology and synaptic function. LIMK1 is one of the genes deleted in patients with Williams Syndrome, which is characterized by distinct craniofacial features, cardiovascular problems, as well as behavioral and neurological abnormalities. LIMKs phosphorylate and inactivate cofilin, an actin depolymerizing factor, to induce the reorganization of the actin cytoskeleton. They act downstream of Rho GTPases and are expressed ubiquitously. As regulators of actin dynamics, they contribute to diverse cellular functions such as cell motility, morphogenesis, differentiation, apoptosis, meiosis, mitosis, and neurite extension. LIMKs contain the LIM (two repeats), PDZ, and catalytic kinase domains. The LIMK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 267 matched cddid_all.tbl CDD cd14222 cd14222 271124 STKc_LIMK2 Catalytic domain of the Serine/Threonine Kinase, LIM domain kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. LIMK2 activation is induced by transforming growth factor-beta l (TGFb-l) and shares the same subcellular location as the cofilin family member twinfilin, which may be its biological substrate. LIMK2 plays a role in spermatogenesis, and may contribute to tumor progression and metastasis formation in some cancer cells. LIMKs phosphorylate and inactivate cofilin, an actin depolymerizing factor, to induce the reorganization of the actin cytoskeleton. They act downstream of Rho GTPases and are expressed ubiquitously. As regulators of actin dynamics, they contribute to diverse cellular functions such as cell motility, morphogenesis, differentiation, apoptosis, meiosis, mitosis, and neurite extension. LIMKs contain the LIM (two repeats), PDZ, and catalytic kinase domains. The LIMK2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 272 matched cddid_all.tbl CDD cd14223 cd14223 271125 STKc_GRK2 Catalytic domain of the Serine/Threonine Kinase, G protein-coupled Receptor Kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. GRK2, also called beta-adrenergic receptor kinase (beta-ARK) or beta-ARK1, is important in regulating several cardiac receptor responses. It plays a role in cardiac development and in hypertension. Deletion of GRK2 in mice results in embryonic lethality, caused by hypoplasia of the ventricular myocardium. GRK2 also plays important roles in the liver (as a regulator of portal blood pressure), in immune cells, and in the nervous system. Altered GRK2 expression has been reported in several disorders including major depression, schizophrenia, bipolar disorder, and Parkinsonism. GRK2 contains an N-terminal RGS homology (RH) domain, a central catalytic domain, and C-terminal pleckstrin homology (PH) domain that mediates PIP2 and G protein betagamma-subunit translocation to the membrane. GRKs phosphorylate and regulate G protein-coupled receptors (GPCRs), the largest superfamily of cell surface receptors which regulate some part of nearly all physiological functions. Phosphorylated GPCRs bind to arrestins, which prevents further G protein signaling despite the presence of activating ligand. TheGRK2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 321 matched cddid_all.tbl CDD cd14224 cd14224 271126 PKc_DYRK2_3 Catalytic domain of the protein kinases, Dual-specificity tYrosine-phosphorylated and -Regulated Kinases 2 and 3. Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (S/T) as well as tyrosine residues on protein substrates. This subfamily is composed of DYRK2 and DYRK3, and similar proteins. Drosophila DYRK2 interacts and phosphorylates the chromatin remodelling factor, SNR1 (Snf5-related 1), and also interacts with the essential chromatin component, trithorax. It may play a role in chromatin remodelling. Vertebrate DYRK2 phosphorylates and regulates the tumor suppressor p53 to induce apoptosis in response to DNA damage. It can also phosphorylate the transcription factor, nuclear factor of activated T cells (NFAT). DYRK2 is overexpressed in lung adenocarcinoma and esophageal carcinomas, and is a predictor for favorable prognosis in lung adenocarcinoma. DYRK3, also called regulatory erythroid kinase (REDK), is highly expressed in erythroid cells and the testis, and is also present in adult kidney and liver. It promotes cell survival by phosphorylating and activating SIRT1, an NAD(+)-dependent protein deacetylase, which promotes p53 deacetylation, resulting in the inhibition of apoptosis. DYRKs autophosphorylate themselves on tyrosine residues and phosphorylate their substrates exclusively on S/T residues. The DYRK2/3 subfamily is part of a larger superfamily that includes the catalytic domains of other S/T kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 380 matched cddid_all.tbl CDD cd14225 cd14225 271127 PKc_DYRK4 Catalytic domain of the protein kinase, Dual-specificity tYrosine-phosphorylated and -Regulated Kinase 4. Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (S/T) as well as tyrosine residues on protein substrates. DYRK4 is a testis-specific kinase with restricted expression to postmeiotic spermatids. It may function during spermiogenesis, however, it is not required for male fertility. DYRK4 has also been detected in a human teratocarcinoma cell line induced to produce postmitotic neurons. It may have a role in neuronal differentiation. DYRKs autophosphorylate themselves on tyrosine residues and phosphorylate their substrates exclusively on S/T residues. They play important roles in cell proliferation, differentiation, survival, and development. The DYRK4 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 341 matched cddid_all.tbl CDD cd14226 cd14226 271128 PKc_DYRK1 Catalytic domain of the protein kinase, Dual-specificity tYrosine-phosphorylated and -Regulated Kinase 1. Dual-specificity PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine (S/T) as well as tyrosine residues on protein substrates. Mammals contain two types of DYRK1 proteins, DYRK1A and DYRK1B. DYRK1A was previously called minibrain kinase homolog (MNBH) or dual-specificity YAK1-related kinase. It phosphorylates various substrates and is involved in many cellular events. It phosphorylates and inhibits the transcription factors, nuclear factor of activated T cells (NFAT) and forkhead in rhabdomyosarcoma (FKHR). It regulates neuronal differentiation by targetting CREB (cAMP response element-binding protein). It also targets many endocytic proteins including dynamin and amphiphysin and may play a role in the endocytic pathway. The gene encoding DYRK1A is located in the DSCR (Down syndrome critical region) of human chromosome 21 and DYRK1A has been implicated in the pathogenesis of DS. DYRK1B, also called minibrain-related kinase (MIRK), is highly expressed in muscle and plays a critical role in muscle differentiation by regulating transcription, cell motility, survival, and cell cycle progression. It is overexpressed in many solid tumors where it acts as a tumor survival factor. DYRKs autophosphorylate themselves on tyrosine residues and phosphorylate their substrates exclusively on S/T residues. The DYRK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 339 matched cddid_all.tbl CDD cd14227 cd14227 271129 STKc_HIPK2 Catalytic domain of the Serine/Threonine Kinase, Homeodomain-Interacting Protein Kinase 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. HIPK2, the most studied HIPK, is a coregulator of many transcription factors and cofactors including homeodomain proteins (Nkx and HOX families), Smad1-4, Pax6, c-Myb, AML1, the histone acetyltransferase p300, and the tumor repressor p53, among others. It regulates gene transcription during development and in DNA damage response (DDR), and mediates cell processes such as apoptosis, survival, differentiation, and proliferation. HIPK2 mediates apoptosis by phosphorylating and activating p53 during DDR, resulting in the activation of apoptotic genes. In the absence of p53, HIPK2 targets the anti-apoptotic corepressor C-terminal binding protein (CtBP), leading to CtBP's degradation and the promotion of apoptosis. HIPKs, originally identified by their ability to bind homeobox factors, are nuclear proteins containing catalytic kinase and homeobox-interacting domains as well as a PEST region overlapping with the speckle-retention signal (SRS). The HIPK2 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 355 matched cddid_all.tbl CDD cd14228 cd14228 271130 STKc_HIPK1 Catalytic domain of the Serine/Threonine Kinase, Homeodomain-Interacting Protein Kinase 1. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. HIPK1 has been implicated in regulating eye size, lens formation, and retinal morphogenesis during late embryogenesis. It also contributes to the regulation of haematopoiesis and leukaemogenesis by phosphorylating and repressing the transcription factor c-Myb, which is crucial in T- and B-cell development. In glucose-deprived conditions, HIPK1 phosphorylates Daxx, leading to its relocalization from the nucleus to the cytoplasm, where it binds and stabilizes ASK1 (apoptosis signal-regulating kinase 1), a mitogen-activated protein kinase (MAPK) kinase kinase that activates the JNK and p38 MAPK pathways. HIPKs, originally identified by their ability to bind homeobox factors, are nuclear proteins containing catalytic kinase and homeobox-interacting domains as well as a PEST region overlapping with the speckle-retention signal (SRS). The HIPK1 subfamily is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 355 matched cddid_all.tbl CDD cd14229 cd14229 271131 STKc_HIPK3 Catalytic domain of the Serine/Threonine Kinase, Homeodomain-Interacting Protein Kinase 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. HIPK3 is a Fas-interacting protein that induces FADD (Fas-associated death domain) phosphorylation and mediates FasL-induced JNK activation. Overexpression of HIPK3 does not affect cell death, however its expression in prostate cancer cells contributes to increased resistance to Fas receptor-mediated apoptosis. HIPK3 also plays a role in regulating steroidogenic gene expression. In response to cAMP, HIPK3 activates the phosphorylation of JNK and c-Jun, leading to increased activity of the transcription factor SF-1 (Steroidogenic factor 1), a key regulator for steroid biosynthesis in the gonad and adrenal gland. HIPKs, originally identified by their ability to bind homeobox factors, are nuclear proteins containing catalytic kinase and homeobox-interacting domains as well as a PEST region overlapping with the speckle-retention signal (SRS). The HIPK3 subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). 330 matched cddid_all.tbl CDD cd14230 cd14230 410578 GAT_GGA canonical GAT domain found in metazoan and fungal ADP-ribosylation factor (Arf)-binding proteins (GGAs). GGAs, also called Golgi-localized gamma-ear-containing Arf-binding proteins, belong to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. GGAs also play important roles in ubiquitin-dependent sorting of cargo proteins both in biosynthetic and endocytic pathways. The family includes three GGAs (GGA1, GGA2, and GGA3) identified in mammals and two GGAs (Gga1p and Gga2p) identified in the budding yeast Saccharomyces cerevisiae. All these GGAs have a multidomain structure consisting of: an N-terminal VHS (Vps27/Hrs/Stam) domain that binds acidic-cluster dileucine (DxxLL)-type sorting signals (where x is any amino acid) found in the cytoplasmic tail of TGN sorting receptors; a GAT (GGA and TOM) domain that interacts with class I GTP-bound form of Arf proteins, Rabaptin-5, ubiquitin, and the tumor susceptibility gene 101 product (TSG101); a largely unstructured hinge region that contains clathrin-binding motifs; and a C-terminal GAE (gamma-adaptin ear homology) domain that binds accessory proteins. In contrast to other GGAs-like proteins, members of this family contain a GAT N-terminal region, a helix-loop-helix in the complex with Arf1-GTP. 80 matched cddid_all.tbl CDD cd14231 cd14231 410579 GAT_GGA-like_plant canonical GAT domain found in uncharacterized Golgi-localized gamma ear-containing Arf-binding protein (GGA)-like proteins mainly found in plants. The family includes a group of uncharacterized plant proteins containing an N-terminal VHS (Vps27p/Hrs/STAM)-domain and a GAT (GGA and TOM1) domain. Both domains are also present in Golgi-localized gamma ear-containing Arf-binding proteins (GGAs), which belong to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. In contrast to GGA proteins, members in this family do not have either a GAE (gamma-adaptin ear homology) domain or a clathrin-binding motif. The canonical GAT domain is a monomeric three-helix bundle that binds ubiquitin. 79 matched cddid_all.tbl CDD cd14232 cd14232 410580 GAT_LSB5 canonical GAT domain found in yeast LAS seventeen-binding protein 5 (Lsb5p) and similar proteins. Lsb5p, also called LAS17-binding protein 5, is a Golgi-localized gamma ear-containing Arf-binding protein (GGA)-like protein located to the plasma membrane in an actin-independent manner. It plays important roles in membrane-trafficking events through association with the actin regulators, the yeast Wiskott-Aldrich syndrome protein (WASP) homologue Las17p and the cortical protein Sla1p, the yeast Arf3p (orthologous with mammalian Arf6), and ubiquitin. Lsb5p contains an N-terminal VHS (Vps27p/Hrs/STAM)-domain and a GAT (GGA and TOM1) domain. In contrast to GGA proteins, Lsb5p harbors a C-terminal NPF (Asn-Pro-Phe) motif, but does not have either a GAE (gamma-adaptin ear homology) domain or a clathrin-binding motif. The canonical GAT domain is a monomeric three-helix bundle that binds ubiquitin. 78 matched cddid_all.tbl CDD cd14233 cd14233 410581 GAT_TOM1_like canonical GAT domain found in target of myb protein 1 (Tom1) protein family. Tom1 and its related proteins, Tom1L1 and Tom1L2, form a protein family sharing an N-terminal VHS (Vps27p/Hrs/STAM)-domain followed by a GAT (GGA and TOM1) domain, both of which are also conserved in Golgi-localized gamma ear-containing Arf-binding proteins (GGAs). In contrast to GGAs, the Tom1 family proteins bind to ubiquitin, ubiquitinated proteins, and Toll-interacting protein (Tollip) through its GAT domain, but do not associate with Arf GTPases through its GAT domain nor with acidic cluster-dileucine sequences through its VHS domain. In addition, the Tom1 family proteins recruit clathrin onto endosomes through their C-terminal region. In their C-terminal clathrin-binding regions, Tom1 and Tom1L2 are similar to each other, but distinguishable from Tom1L1. The yeast S. cerevisiae does not contain homologous proteins of the Tom1 family. The canonical GAT domain is a monomeric three-helix bundle that binds ubiquitin. 87 matched cddid_all.tbl CDD cd14234 cd14234 410582 GAT_GGA_meta canonical GAT domain found in metazoan ADP-ribosylation factor (Arf)-binding proteins (GGAs). GGAs, also called Golgi-localized gamma-ear-containing Arf-binding proteins, belong to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. Moreover, GGAs play important roles in ubiquitin-dependent sorting of cargo proteins both in biosynthetic and endocytic pathways. Three GGAs (GGA1, GGA2, and GGA3) have been identified in mammals. They may appear to behave similarly, since all of them have a multidomain structure consisting of: an N-terminal VHS (Vps27/Hrs/Stam) domain that binds the acidic-cluster dileucine (DxxLL)-type sorting signals (where x is any amino acid) found in the cytoplasmic tail of TGN sorting receptors; a GAT (GGA and TOM) domain that interacts with class I GTP-bound form of Arf proteins, Rabaptin-5, ubiquitin, and the tumor susceptibility gene 101 product (TSG101); a largely unstructured hinge region that contains clathrin-binding motifs; and a C-terminal GAE (gamma-adaptin ear homology) domain that binds accessory proteins. However, the three GGAs have some differences, which suggest they may possess their own distinct roles. For instance, both GGA1 and GGA3, but not GGA2, contains an internal DxxLL motif that binds to it own VHS domain. Only a portion of the VHS domain of GGA2 possesses distant structural homology to that of GGA1 or GGA3. Moreover, the binding affinity of GGA2 to ubiquitin is quite lower than that of GGA1 or GGA3. In addition, GGA3 has a short splicing variant that is predominantly expressed in human cell lines and tissues except the brain. It does have a VHS domain, but it is unable to bind to the DxxLL motif. GGA2 and GGA3 undergo epidermal growth factor (EGF)-induced phosphorylation. 84 matched cddid_all.tbl CDD cd14235 cd14235 410583 GAT_GGA_fungi canonical GAT domain found in fungal ADP-ribosylation factor (Arf)-binding proteins (GGAs). GGAs, also called Golgi-localized gamma-ear-containing Arf-binding proteins, belong to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. Two GGAs (Gga1p and Gga2p) have been identified in the budding yeast Saccharomyces cerevisiae. Yeast GGAs play important roles in the carboxypeptidase Y (CPY) pathway, vacuole biogenesis, alpha-factor maturation, and interactions with clathrin. They have a multidomain structure consisting of VHS (Vps27/Hrs/ STAM), GAT (GGA and TOM), hinge, and GAE (gamma-adaptin ear) domains. Both Gga1p and Gga2p function as effectors of Arf in yeast. They interact with Arf1p and Arf2p in a GTP-dependent manner. Moreover, Gga2p mediates sequential ubiquitin-independent and ubiquitin-dependent steps in the trafficking of ARN1, a ferrichrome transporter in S. cerevisiae, from the TGN to the vacuole. It also acts as a phosphatidylinositol 4-phosphate effector at the Golgi exit, which binds directly to the TGN PtdIns(4)-kinase Pik1p and contributes to Pik1p recruitment. In addition, Gga2p is required for sorting of the yeast siderophore iron transporter1 (Sit1) to the vacuolar pathway. The GAT domain of GGAs interacts with class I GTP-bound form of Arf proteins, Rabaptin-5, ubiquitin, and/or the tumor susceptibility gene 101 product (TSG101). 92 matched cddid_all.tbl CDD cd14236 cd14236 260094 GAT_TOM1 canonical GAT domain found in target of Myb protein 1 (Tom1). Tom1 was originally identified by its induced expression by the v-Myb oncogene. It is predominantly present in the cytosol and can interact with clathrin, endofin, Toll-interacting protein (Tollip), and ubiquitinated proteins. It acts as a linker protein to regulate the ability of endofin to recruit clathrin onto the sorting endosome. Moreover, Tom1 functions as a negative regulator of IL-1beta and tumor necrosis factor (TNF)-alpha-induced signaling pathways. It also plays a role in the TLR2/4 signaling pathways. Tom1 contains an N-terminal VHS (Vps27p/Hrs/STAM)-domain, a GAT (GGA and TOM1) domain and a C-terminal clathrin-binding region, both of which are conserved in Golgi-localized gamma ear-containing Arf-binding proteins (GGAs). In contrast to GGAs, Tom1 binds to ubiquitin, ubiquitinated proteins, and Tollip through its GAT domain, but does not associate with Arf GTPases through its GAT domain nor with acidic cluster-dileucine sequences through its VHS domain. The canonical GAT domain is a monomeric three-helix bundle that binds ubiquitin. 95 matched cddid_all.tbl CDD cd14237 cd14237 410584 GAT_TM1L1 canonical GAT domain found in target of Myb-like protein 1 (Tom1L1). Tom1L1, also called Src-activating and signaling molecule protein (Srcasm), was identified as a substrate of the Src family of protein kinases. It is tyrosine-phosphorylated by Src family kinases and modulates growth factor and Src-mediated signaling pathways. It also plays a potential role in endosomal sorting and ligand-stimulated endocytosis of EGF receptors (EGFR). Tom1L1 is predominantly present in the cytosol and can interact with Toll-interacting protein (Tollip), Hrs or TSG101, clathrin, and ubiquitinated proteins. It contains an N-terminal VHS (Vps27p/Hrs/STAM)-domain, a GAT (GGA and TOM1) domain, and a C-terminal clathrin-binding region, both of which are conserved in Golgi-localized gamma ear-containing Arf-binding proteins (GGAs). It interacts with Tollip through their GAT domain and recuits clathrin onto endosomes through their C-terminal region. However, in the C-terminal clathrin-binding region, Tom1 and Tom1L2 are similar to each other, but distinguishable from Tom1L1. The canonical GAT domain is a monomeric three-helix bundle that binds ubiquitin. 92 matched cddid_all.tbl CDD cd14238 cd14238 410585 GAT_TM1L2 canonical GAT domain found in target of Myb-like protein 2 (Tom1L2). Tom1L2, together with Myb protein 1 (Tom1) and target of Myb-like protein 1 (Tom1L1), constitute the Tom1 family. Tom1L2 can interact with Toll-interacting protein (Tollip), clathrin, and ubiquitin. It may play a potential role in endosomal sorting, as well as in the regulation of membrane trafficking that is linked to immunity and cell proliferation. Tom1L2 contains an N-terminal VHS (Vps27p/Hrs/STAM)-domain, a GAT (GGA and TOM1) domain, and a C-terminal clathrin-binding region, both of which are conserved in Golgi-localized gamma ear-containing Arf-binding proteins (GGAs). It interacts with Tollip through their GAT domain and recuits clathrin onto endosomes through their C-terminal region. However, in the C-terminal clathrin-binding region, Tom1 and Tom1L2 are similar to each other, but distinguishable from Tom1L1. The canonical GAT domain is a monomeric three-helix bundle that binds ubiquitin. 92 matched cddid_all.tbl CDD cd14239 cd14239 410586 GAT_GGA1_GGA2 canonical GAT domain found in ADP-ribosylation factor (Arf)-binding proteins GGA1 and GGA2. This subfamily includes GGA1 and GGA2, both of which belong to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. GGA1, also called gamma-adaptin-related protein 1, or Golgi-localized gamma ear-containing Arf-binding protein 1, regulates the low-density lipoprotein and sorting receptor LR11/SorLA endocytic traffic and further alters amyloid-beta precursor protein (APP) intracellular distribution and amyloid-beta production. It is also critical for the effects of beta-site APP-cleaving enzyme-1 (BACE1) on amyloid-beta generation. It interacts with BACE1 and promotes its traffic from early endosomes to late endocytic compartments or the TGN. Moreover, GGA1 acts as a clathrin assembly protein with the ability to polymerize clathrin into tubules. GGA2, also called gamma-adaptin-related protein 2, Golgi-localized gamma ear-containing Arf-binding protein 2, or VHS domain and ear domain of gamma-adaptin (Vear), interacts with the acidic cluster-dileucine motif in the cytoplasmic tail of the cation-independent mannose 6-phosphate receptor (CI-MPR) and further plays a major role in the sorting of lysosomal enzymes. It also mediates a vital function that cannot be compensated for by GGA1 and/or GGA3. Both GGA1 and GGA2 have a multidomain structure consisting of an N-terminal VHS (Vps27/Hrs/Stam) domain, a GAT (GGA and TOM) domain, a largely unstructured hinge region that contains clathrin-binding motifs, and a C-terminal GAE (gamma-adaptin ear homology) domain. The GAT domain of GGAs interacts with class I GTP-bound form of Arf proteins, Rabaptin-5, ubiquitin, and/or the tumor susceptibility gene 101 product (TSG101). 88 matched cddid_all.tbl CDD cd14240 cd14240 410587 GAT_GGA3 canonical GAT domain found in ADP-ribosylation factor-binding protein GGA3. GGA3, also called Golgi-localized gamma ear-containing Arf-binding protein 3, belongs to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. GGA3 interacts selectively with the Met/Hepatocyte Growth Factor receptor tyrosine kinase (RTK) when stimulated. It functions as a specific cargo adaptor to target the Met RTK into recycling tubules, and further coordinates the recycling, signaling and degradative fates of the Met RTK. Moreover, GGA3, together with PACS-1 and the protein kinase CK2, forms a complex that regulates cation-independent mannose-6-phosphate receptor (CI-MPR) trafficking. Furthermore, GGA3 has been identified as an interacting protein of the beta-site APP-cleaving enzyme-1 (BACE1), a stress-related protease that is involved in Alzheimer's disease (AD) pathology. GGA3 has a multidomain structure consisting of an N-terminal VHS (Vps27/Hrs/Stam) domain, a GAT (GGA and TOM) domain, a largely unstructured hinge region that contains clathrin-binding motifs, and a C-terminal GAE (gamma-adaptin ear homology) domain. The GAT domain of GGAs interacts with class I GTP-bound form of Arf proteins, Rabaptin-5, ubiquitin, and/or the tumor susceptibility gene 101 product (TSG101). 87 matched cddid_all.tbl CDD cd14241 cd14241 260131 PAD Phenolic Acid Decarboxylase. This family of bacterial and fungal phenolic acid decarboxylases catalyzes the non-oxidative decarboxylation of phenolic acids to produce 4-vinyl derivates. Phenolic acid, like ferulic, p-coumaric, and caffeic acids, are important lignin-related aromatic acids and are natural constituents of plant cell walls. They act as crosslinkers between lignin polymers and hemicellulose/cellulose in plants. Their degradation is important from a biotechnological viewpoint. 144 matched cddid_all.tbl CDD cd14243 cd14243 260109 PT-AcyF_like Putative ABBA-type prenyltransferases acting on cyanobactins. Members of this family are found in gene clusters responsible for the production and posttranslational modification of cyanobactins, small ribosomal cyclic peptides produced by cyanobacteria. The AcyF_like proteins are structurally similar to the ABBA-type aromatic prenyltransferases, and may be responsible for the reverse- and forward-O-prenylation of tyrosine, serine, and theronine in cyanobactins. ABBA-type aromatic prenyltransferases (PTases) are a subgroup of prenyltransferases that are characterized by an unusual type of beta/alpha fold with antiparallel beta strands. They lack the (N/D)DxxD motif which is characteristic for many other prenyltransferases. 294 matched cddid_all.tbl CDD cd14244 cd14244 271203 GH_101_like Endo-a-N-acetylgalactosaminidase and related glcyosyl hydrolases. This family contains the enzymatically active domain of cell surface proteins that specifically cleave Gal-beta-1,3-GalNAc-alpha-Ser/Thr (T-antigen, galacto-N-biose), the core 1 type O-linked glycan common to mucin glycoproteins (EC:3.2.1.97). It has been classified as glycosyl hydrolase family 101 in the Cazy resource. Virulence of pathogenic organisms such as the Gram-positive Streptococcus pneumoniae and other commensal human bacteria is largely determined by their ability to degrade host glycoproteins and to metabolize the resultant carbohydrates. 298 matched cddid_all.tbl CDD cd14245 cd14245 271204 DMP12 Putative DNA mimic protein DMP12. The Neisseria sp. protein DMP12 has been shown to interact with the bacterial histone-like protein HU and may do so by acting as a DNA mimic. It is likely to play a regulatory role, but not via direct competition for binding of HU, which is involved in maintenance of the bacterial nucleoid structure. 114 matched cddid_all.tbl CDD cd14246 cd14246 271205 ADAM17_MPD Membrane-proximal domain of a disintegrin and metalloprotease 17 (ADAM17). ADAM17 is a multi-domain protein that acts as a sheddase; is involved in the cleavage and release of the soluble ectodomain of tumor necrosis factor alpha from the cell surface and in the trans-Golgi network, as well as in the release of various other targets such as cytokines and cell adhesion molecules. This links ADAM17 to a variety of biological processes, including cellular differentiation and the progression of cancer. It was shown that the enzymatic activity of ADAM17 is regulated via a protein-disulfide isomerase (PDI). Specifically, the disulfide bridges within a CxxC motif of the membrane-proximal domain (MPD) are isomerized by PDI; the conversion triggers a conformational change between a closed and an opened form of the MPD, which may constitute a molecular switch that triggers the shedding activity of ADAM17. 60 matched cddid_all.tbl CDD cd14247 cd14247 271206 Lmo2686_like Uncharacterized hexameric protein conserved in Bacilli. This family conserved in bacilli contains proteins that form an unusual hexameric arrangement via circular domain-swapping of a beta-hairpin-beta unit. 138 matched cddid_all.tbl CDD cd14248 cd14248 271207 ESP Exocrine gland-secreting peptide 1 (ESP1) and similar pheromones. ESP1 is a peptide pheromone found in male mouse tear fluid, which is recognized by a specific G-protein-coupled receptor in the vomeronasal sensory neurons and affects female mouse sexual receptive behaviour. This small family appears restricted to rodents. ESP36 is expressed only in the female mouse extraorbital lacrimal gland. The juvenile pheromone ESP22 is secreted from the lacrimal gland and released into the tears of 2-3 week old mice; it activates the vomeronasal response pathway, and inhibits male sexual behavior. Information regarding other members of this family is not yet available. 52 matched cddid_all.tbl CDD cd14249 cd14249 271208 ESP1_like Exocrine gland-secreting peptide 1 (ESP1) and similar pheromones. ESP1 is a peptide pheromone found in male mouse tear fluid, which is recognized by a specific G-protein-coupled receptor in the vomeronasal sensory neurons and affects female mouse sexual receptive behaviour. This small family appears restricted to rodents; the functions of members other than mouse ESP1 have not yet been determined. 46 matched cddid_all.tbl CDD cd14250 cd14250 271209 ESP36_like Exocrine gland-secreting peptide 36 (ESP36) and similar pheromones. ESP36 is a peptide pheromone expressed only in the female mouse extraorbital lacrimal gland. This family also includes the juvenile pheromone ESP22 which is secreted from the lacrimal gland and released into the tears of 2-3 week old mice. ESP22 activates the vomeronasal response pathway, and inhibits male sexual behavior. This small family appears restricted to rodents; the functions of other members have not yet been determined. 55 matched cddid_all.tbl CDD cd14251 cd14251 271210 PL-6 Polysaccharide Lyase Family 6. Polysaccharide Lyase Family 6 is a family of beta-helical polysaccharide lyases. Members include alginate lyase (EC 4.2.2.3) and chondroitinase B (EC 4.2.2.19). Chondroitinase B is an enzyme that only cleaves the beta-(1,4)-linkage of dermatan sulfate (DS), leading to 4,5-unsaturated dermatan sulfate disaccharides as the product. DS is a highly sulfated, unbranched polysaccharide belonging to a family of glycosaminoglycans (GAGs) composed of alternating hexosamine (gluco- or galactosamine) and uronic acid (D-glucuronic or L-iduronic acid) moieties. DS contains alternating 1,4-beta-D-galactosamine (GalNac) and 1,3-alpha-L-iduronic acid units. The related chondroitin sulfate (CS) contains alternating GalNac and 1,3-beta-D-glucuronic acid units. Alginate lyases (known as either mannuronate (EC 4.2.2.3) or guluronate lyases (EC 4.2.2.11) catalyze the degradation of alginate, a copolymer of alpha-L-guluronate and its C5 epimer beta-D-mannuronate. 369 matched cddid_all.tbl CDD cd14252 cd14252 271211 Dockerin_like Dockerin repeat domains and domains resembling dockerin repeats. Dockerins are modules in the cellulosome complex that often anchor catalytic subunits by binding to cohesin domains of scaffolding proteins. Three types of dockerins and their corresponding cohesin have been described in the literature. This alignment models two consecutive dockerin repeats, the functional unit. 57 matched cddid_all.tbl CDD cd14253 cd14253 271212 Dockerin Dockerin repeat domain. Dockerins are modules in the cellulosome complex that often anchor catalytic subunits by binding to cohesin domains of scaffolding proteins. Three types of dockerins and their corresponding cohesin have been described in the literature. This alignment models two consecutive dockerin repeats, the functional unit. 56 matched cddid_all.tbl CDD cd14254 cd14254 271213 Dockerin_II Type II dockerin repeat domain. Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. The cellulosome consists of scaffoldin, a noncatalytic scaffolding polypeptide, that comprises repeating cohesion modules and a single carbohydrate-binding module (CBM). Specific calcium-dependent interactions between cohesins and dockerins appear to be essential for cellulosome assembly. This subfamily represents type II dockerins, which are responsible for mediating attachment of the cellulosome complex to the bacterial cell wall. 54 matched cddid_all.tbl CDD cd14255 cd14255 271214 Dockerin_III Type III dockerin repeat domain. Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. Two specific calcium-dependent interactions between cohesin and dockerin appear to be essential for cellulosome assembly, type I and type II. This subfamily represents the atypical type III dockerins and related domains. 65 matched cddid_all.tbl CDD cd14256 cd14256 271215 Dockerin_I Type I dockerin repeat domain. Bacterial cohesin domains bind to a complementary protein domain named dockerin, and this interaction is required for the formation of the cellulosome, a cellulose-degrading complex. The cellulosome consists of scaffoldin, a noncatalytic scaffolding polypeptide, that comprises repeating cohesion modules and a single carbohydrate-binding module (CBM). Specific calcium-dependent interactions between cohesins and dockerins appear to be essential for cellulosome assembly. This subfamily represents type I dockerins, which are responsible for anchoring a variety of enzymatic domains to the complex. 57 matched cddid_all.tbl CDD cd14257 cd14257 271221 CttA_X X module of the carbohydrate-binding protein CttA and similar proteins. This model represents a putative carbohydrate-binding domain conserved in Ruminococcus, which sits N-terminal to a dockerin repeat; the protein may be a component of the Ruminococcus cellulosome system. This X module does not share similarities with other known X modules from cellulolytic bacteria and may have a structural role. 116 matched cddid_all.tbl CDD cd14259 cd14259 271222 PUFD_like PCGF Ub-like fold discriminator and related domains. The PUFD domain binds the RAWUL (RING finger and WD40-associated ubiquitin-like) domain of the polycomb-group RING finger homologs PCGF1 and PCGF3. PUFD was characterized as a domain of the BCL6 corepressor BCOR. It does not appear to bind to PCGF2 and PCGF4. PCGF1 is a component of the Polycomb group (PcG) multi-protein BCOR complex, which is involved in repressing the transcription of BCL6 and CDKN1A. The BCL-6 corepressor (BCOR) is a transcriptional repressor required for germinal center formation and is possibly involved in apoptosis. 106 matched cddid_all.tbl CDD cd14260 cd14260 271223 PUFD_like_1 PCGF Ub-like fold discriminator of BCOR-like 1. The PUFD domain binds the RAWUL (RING finger and WD40-associated ubiquitin-like) domain of the polycomb-group RING finger homologs PCGF1 and PCGF3. PUFD was characterized as a domain of the BCL6 corepressor BCOR. It does not appear to bind to PCGF2 and PCGF4. PCGF1 is a component of the Polycomb group (PcG) multi-protein BCOR complex, which is involved in repressing the transcription of BCL6 and CDKN1A. The BCL-6 corepressor-like protein 1 (BCoR-L1) is largely uncharacterized; it contains ankyrin repeats. 115 matched cddid_all.tbl CDD cd14261 cd14261 271224 PUFD PCGF Ub-like fold discriminator of BCOR. The PUFD domain binds the RAWUL (RING finger and WD40-associated ubiquitin-like) domain of the polycomb-group RING finger homologs PCGF1 and PCGF3. PUFD was characterized as a domain of the BCL6 corepressor BCOR. It does not appear to bind to PCGF2 and PCGF4. PCGF1 is a component of the Polycomb group (PcG) multi-protein BCOR complex, which is involved in repressing the transcription of BCL6 and CDKN1A. The BCL-6 corepressor (BCOR) is a transcriptional repressor required for germinal center formation and is possibly involved in apoptosis. 117 matched cddid_all.tbl CDD cd14262 cd14262 271354 VirB5_like VirB5 protein family. This family contains VirB5 domains, including TraC, a VirB5 homolog encoded by the pKM101 plasmid, and similar proteins. VirB5 is one of 11 conserved proteins (VirB1-VirB11) in Agrobacterium tumefaciens, the causative agent of crown gall disease, that span the inner and the outer membrane, and is involved in type IV DNA secretion systems (T4SS) which mediate the translocation of virulence factors (proteins and/or DNA) from Gram-negative bacteria into eukaryotic cells. VirB5 assembles extracellular pili by interacting with several essential proteins. VirB2-VirB5 complex formation precedes incorporation into pili; it depends on the inner membrane protein VirB4 to interact directly with and stabilize VirB8 in order for VirB5 to bind to VirB8 and VirB10. Mutagenesis studies show that VirB5 proteins participate in protein-protein interactions important for pilus assembly and function. 173 matched cddid_all.tbl CDD cd14263 cd14263 260132 DAGK_IM_like Integral membrane diacylglycerol kinase and similar enzymes. This mostly bacterial family of homo-trimeric integral membrane enzymes, the products of the dgkA gene, catalyzes the ATP-dependent phosphorylation of substrates such as diacylglycerol to phosphatidic acid or of undecaprenol to undecaprenyl phosphate. They are not related other cytosolic or membrane-associated kinases, including the eukaryotic diacylglycerol kinases. 106 matched cddid_all.tbl CDD cd14264 cd14264 260133 DAGK_IM Integral membrane diacylglycerol kinase. This mostly bacterial family of homo-trimeric integral membrane enzymes, the products of the dgkA gene, catalyzes the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid. Escherichia coli DAGK participates in the membrane-derived oligosaccharide cycle (MDO cycle) by recycling lipids to restore phosphatidylglycerols that were used up in the biosynthesis of MDOs. DAGK also recycles diacylglycerols that are produced during the biosynthesis of lipopolysaccharides (LPS) back to phospholipids. DAGK is not the main source of phosphatidic acid in de-novo biosynthesis of glycerophospholipids. Escherichia coli DAGK has low activity as an undecaprenol kinase. 109 matched cddid_all.tbl CDD cd14265 cd14265 260134 UDPK_IM_like Integral membrane undecaprenol kinase and similar enzymes. This mostly bacterial family of homo-trimeric integral membrane enzymes, the products of the dgkA gene, catalyzes the ATP-dependent phosphorylation of undecaprenol to undecaprenyl phosphate. C55-isoprenyl (undecaprenyl) pyroposphate acts as a scaffold for the assembly of peptidoglycan components; undecaprenol kinase (UDPK) is involved in recycling undecaprenyl units for re-use in the peptidoglycan biosynthesis. UDPK does not participate in the de-novo biosynthesis of undecaprenyl phosphate. Gram-positive bacteria have a large pool of free undecaprenol, in contrast to gram-negative bacteria. UDPK may also play a role in a stress-induced pathway that affects the function of ribosomes. In Streptococcus mutans, UDPK has been shown to be required for biofilm formation, such as in the case of smooth surface dental caries. Members of the UDPK family have low activity as diacylglycerol kinases (DAGK), and many of them are annotated as DAGKs. 106 matched cddid_all.tbl CDD cd14266 cd14266 260135 UDPK_IM_PAP2_like Integral membrane undecaprenol kinase domain co-occurring with type 2 phosphatidic acid phosphatase-like domains. This bacterial family of homo-trimeric integral membrane enzyme domains catalyzes the ATP-dependent phosphorylation of of undecaprenol to undecaprenyl phosphate. They sit N-terminally to phosphatase domains that are members of the type 2 phosphatidic acid phosphatase superfamily, and the function of members of this domain architecture was determined to be undecaprenyl pyrophosphate phosphatases. The bi-functional enzymes might generate undecaprenyl phosphate via two mechanisms - the phosphorylation of undecaprenol or the cleavage of the terminal phosphate group of undecaprenyl pyrophosphate. 106 matched cddid_all.tbl CDD cd14267 cd14267 341312 Rif1_CTD_C-II_like Saccharomyces cerevisiae Rap1-interacting factor 1 CTD domain, metazoan Rif1 C-II domains and related domains. This model includes Saccharomyces cerevisiae Rif1_CTD (carboxy-terminal domain) and metazoan Rif1 C-II (C-terminal subdomain II). Rif1 was originally identified in S. cerevisiae where it negatively regulates telomere length homeostasis via interaction with the C-terminal domain of Rap1. A protective capping structure (telosome) comprised of Rap1, Rif1, and Rif2, inhibits telomerase, counteracts SIR-mediated transcriptional silencing, and prevents inadvertent recognition of telomeres as DNA double-strand breaks (DSBs). S. cerevisiae Rif1 has two Rap1 binding sites: the Rap1-binding module (RBM), and the CTD domain. The latter, represented here, has a lower Rap1 affinity, and provides trans binding through tetramerization. In mammals, Rif1 has been implicated in various cellular processes including pluripotency of stem cells, breast cancer development, and DSB repair pathway choice. A mutual antagonism between the nonhomologous end joining factors (53BP1-RIF1) and the homologous recombination factors (BRCA1 -CtIP) ensures correct repair pathway choice. 46 matched cddid_all.tbl CDD cd14270 cd14270 270456 UBA UBA domain found in proteins involved in ubiquitin-mediated proteolysis. The ubiquitin-associated (UBA) domains are commonly occurring sequence motifs found in proteins involved in ubiquitin-mediated proteolysis. They contribute to ubiquitin (Ub) binding or ubiquitin-like (UbL) domain binding. However, some kinds of UBA domains can only the bind UbL domain, but not the Ub domain. UBA domains are normally comprised of compact three-helix bundles which contain a conserved GF/Y-loop. They can bind polyubiquitin with high affinity. They also bind monoubiquitin and other proteins. Most UBA domain-containing proteins have one UBA domain, but some harbor two or three UBA domains. 30 matched cddid_all.tbl CDD cd14271 cd14271 270457 UBA_YLR419W_like UBA domain found in Saccharomyces cerevisiae putative ATP-dependent RNA helicase YLR419W and similar proteins. The group includes some uncharacterized hypothetical proteins which show a high level of sequence similarity with Saccharomyces cerevisiae putative ATP-dependent RNA helicase YLR419W. All family members contain a ubiquitin-associated (UBA) domain, RWD domain, DEAD-box (DEXDc), helicase superfamily c-terminal domain (HELICc), Helicase associated domain (HA2), and a C-terminal oligonucleotide/oligosaccharide-binding (OB)-fold. 41 matched cddid_all.tbl CDD cd14272 cd14272 270458 UBA_AMPK-RKs UBA domain of AMPK related kinases. The AMPK-RK family comprises AMP-activated protein kinases (AMPKs), MAP/microtubule affinity-regulating kinases (MARKs), Brain-specific kinases (BRSKs), Salt inducible kinases (SIKs), maternal embryonic leucine zipper kinase (MELK), and SNF-related serine/threonine-protein kinase (SNRK). It is the only kinase family in the human genome containing an ubiquitin-associated (UBA) or UBA-like domain which is located immediately C-terminal to their N-terminal protein kinase catalytic domain. In addition, most of family members contain a C-terminal regulatory domain of 5'-AMP-activated protein kinase (AMPK), but some are lack of this region. AMPK-RKs play central roles in metabolic control, energy homeostasis and stress responses in eukaryotes. They require phosphorylation by liver kinase B1 (LKB1) for full activity. Normally, AMPK-RKs appear to exist as heterotrimeric complexes consisting of a catalytic alpha-subunit and regulatory beta- and gamma-subunits. This model corresponds to the catalytic subunit. The UBA domain, previously called SNF1 homology (SNH) domain, regulates the conformation, LKB1-mediated phosphorylation and activation, and localization of the AMPK-RKs, but does not interact with ubiquitin-like molecules. In AMPKalpha subunits, the UBA-like autoinhibitory domain (AID) is responsible for AMPKalpha subunit autoinhibition. Due to the lack of UBA domain, NUAK1 kinase, also called ARK5 (AMPK-related kinase 5), and NUAK2 kinase, also called SNARK (SNF1/AMPK-related kinase), are not included in this family. 38 matched cddid_all.tbl CDD cd14273 cd14273 270459 UBA_TAP-C_like UBA-like domain found in the NXF family of mRNA nuclear export factors and similar proteins. This family includes nuclear RNA export factors (NXF1/NXF2), FAS-associated factors (FAF1/2), tyrosyl-DNA phosphodiesterase 2 (TDP2), OTU domain-containing proteins (OTU7A/OTU7B), NSFL1 cofactor p47, defective in cullin neddylation protein 1 (DCN1)-like protein (DCNL1/DCNL2), yeast defective in cullin neddylation protein 1 (DCN1) and similar proteins. NXF proteins can stimulate nuclear export of mRNAs and facilitate the export of unspliced viral mRNA containing the constitutive transport element. FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF2 is the translation product of a highly expressed gene in the T-cells and eosinophils of atopic dermatitis patients compared with those of normal individuals. Its biological function remains unclear. TDP2 is a 5'-Tyr-DNA phosphodiesterase required for the efficient repair of topoisomerase II-induced DNA double strand breaks. OTU7A and OTU7B are zinc finger proteins that function as deubiquitinating enzymes. p47 is a major cofactor of the cytosolic AAA ATPase p97. It is required for the p97-regulated membrane reassembly of the endoplasmic reticulum (ER), the nuclear envelope and the Golgi apparatus. DCNL1 plays an essential role in the neddylation E3 complex and participates in the release of inhibitory effects of CAND1 on cullin-RING ligase E3 complex assembly and activity. The biological function of DCNL2 remains unclear. Yeast DCN1 is a scaffold-type E3 ligase for cullin neddylation. It can bind directly to cullins and the ubiquitin-like protein Nedd8-specific E2 (Ubc12), and regulate cullin neddylation and thus display ubiquitin ligase activity. 31 matched cddid_all.tbl CDD cd14274 cd14274 270460 UBA_ACK1 UBA domain found in activated Cdc42 kinase 1 (ACK1) and similar proteins. ACK1, also called tyrosine kinase non-receptor protein 2, is an intracellular non-receptor tyrosine kinase that specifically interacts with Cdc42 and act as Cdc42 effectors. It forms a signaling complex with Cdc42, p130(Cas), and Crk, and mediates Cdc42-dependent cell migration and signaling to p130(Cas). Ack1 also stimulates prostate tumorigenesis in part by inhibiting the proapoptotic tumor suppressor WW domain containing oxidoreductase (Wwox). Moreover, ACK1 associates directly with the heavy chain of clathrin and further participates in trafficking, underlying an ability to increase receptor-mediated transferrin uptake. It may functions as a regulator of the guanine nucleotide exchange factor Dbl that can activate Rho family proteins. ACK1 consists of an N-terminal tyrosine kinase catalytic domain followed by an SH3 domain, a Cdc42/Rac interactive binding (CRIB) domain, a proline-rich region, and a C-terminal ubiquitin-association (UBA) domain. The proline-rich region of ACK1 is responsible for the binding to the adaptor proteins Nck, Grb2, sorting nexin protein 9 (SH3PX1), and Hck. 45 matched cddid_all.tbl CDD cd14275 cd14275 270461 UBA_EF-Ts UBA domain found in elongation factor Ts (EF-Ts) from bacteria, chloroplasts and mitochondria of eukaryotes. EF-Ts functions as a nucleotide exchange factor in the functional cycle of EF-Tu, another translation elongation factor that facilitates the binding of aminoacylated transfer RNAs (aminoacyl-tRNA) to the ribosomal A site as a ternary complex with guanosine triphosphate during the elongation cycle of protein biosynthesis, and then catalyzes the hydrolysis of GTP and release itself in GDP-bound form. EF-Ts forms complex with EF-Tu and catalyzes the nucleotide exchange reaction promoting the formation of EF-Tu in GTP-bound form from EF-Tu in GDP-bound form. EF-Ts from Thermus thermophiles is shorter than EF-Ts from Escherichia coli, but it has higher thermostability. The mitochondrial translational EF-Ts from chloroplasts and mitochondria display high similarity to the bacterial EF-Ts. The majority of family members contain one ubiquitin-associated (UBA) domain, but some family members from plants harbor two tandem UBA domains. 37 matched cddid_all.tbl CDD cd14276 cd14276 270462 UBA_UBP25_like UBA domain found in ubiquitin carboxyl-terminal hydrolase UBP25, UBP28, and similar proteins. UBP25, also called deubiquitinating enzyme 25, USP on chromosome 21, ubiquitin thioesterase 25, or ubiquitin-specific-processing protease 25, belongs to the deubiquitinating enzyme (DUB) family that specifically hydrolyzes ubiquitin chains on ubiquitin-conjugated proteins. USP25 has one muscular isoform and two ubiquitous isoforms. The longer muscular isoform can bind to muscle-restricted cytoskeletal and sarcomeric proteins, such as myosin binding protein C1 (MyBPC1), actin alpha-1 (ACTA1) and filamin C (FLNC), and further prevent their degradation. USP25 harbors three potential ubiquitin-binding domains (UBDs), one ubiquitin-associated (UBA) domain and two ubiquitin-interacting motifs (UIMs) in the N-terminal region. Its C-terminal tyrosine-rich region is responsible for the binding of the second SH2 domain of SYK, a non-receptor tyrosine kinase that specifically phosphorylates USP25 and alters its cellular levels. UBP28, also called deubiquitinating enzyme 28, ubiquitin thioesterase 28, or ubiquitin-specific-processing protease 28, is also an ubiquitin-specific protease belonging to the DUB family. UBP28 can form a ternary complex with nucleoplasmic Fbw7alpha, an F-box protein that is part of an SCF-type ubiquitin ligase, and MYC, a transcription factor encoded by MYC proto-oncogene. UBP28 is required for the stability of MYC, and this stabilization is necessary for tumour-cell proliferation. Besides, UBP28 plays a critical role in the regulation of the Chk2-p53-PUMA pathway. It specifically interacts with 53BP1 and is essential to stabilize Chk2 and 53BP1 in response to DNA damage. 38 matched cddid_all.tbl CDD cd14277 cd14277 270463 UBA_UBP2_like UBA domain found in ubiquitin-associated protein 2 (UBAP-2) like proteins. The family contains some uncharacterized ubiquitin-associated proteins, including UBAP-2 and its homolog, UBAP2-like [UBP2L, also called protein NICE-4 (for newly identified cDNA from the epidermal differentiation complex EDC)], both of which contain an N-terminal ubiquitin-associated (UBA) domain along with a highly conserved, but function unknown domain (DUF3697). 38 matched cddid_all.tbl CDD cd14278 cd14278 270464 UBA_NAC_like UBA-like domain found in nascent polypeptide-associated complex subunit alpha (NACA) and similar proteins. The family contains nascent polypeptide-associated complex subunit alpha (NACA), putative NACA-like protein (NACP1), nascent polypeptide-associated complex subunit alpha domain-containing protein 1 (NACAD), and similar proteins found in archaea and bacteria. NACA, also called NAC-alpha or Alpha-NAC, together with BTF3, also called Beta-NAC, form the nascent polypeptide-associated complex (NAC) which is a cytosolic protein chaperone that contacts the nascent polypeptide chains as they emerge from the ribosome. Besides, NACA has a high affinity for nucleic acids and exists as part of several protein complexes playing a role in proliferation, apoptosis, or degradation. It is a cytokine-modulated specific transcript in the human TF-1 erythroleukemic cell line. It also acts as a transcriptional co-activator in osteoblasts by binding to phosphorylated c-Jun, a member of the activator-protein-1 (AP-1) family. Moreover, NACA binds to and regulates the adaptor protein Fas-associated death domain (FADD). In addition, NACA functions as a novel factor participating in the positive regulation of human erythroid-cell differentiation. The biological function of NACP1 (also called Alpha-NAC pseudogene 1 or NAC-alpha pseudogene 1) and NACAD remain unclear. The family also includes huntingtin-interacting protein K (HYPK), also called Huntingtin yeast partner K or Huntingtin yeast two-hybrid protein K. It is an intrinsically unstructured Huntingtin (HTT)-interacting protein with chaperone-like activity. It may be involved in regulating cell growth, cell cycle, unfolded protein response and cell death. All members in this family contain an ubiquitin-associated (UBA) domain. 37 matched cddid_all.tbl CDD cd14279 cd14279 270465 CUE CUE domain found in ubiquitin-binding CUE proteins. This family includes many coupling of ubiquitin conjugation to endoplasmic reticulum degradation (CUE) domain containing proteins that are characterized by an FP and a di-leucine-like sequence and bind to monoubiquitin with varying affinities. Some higher eukaryotic CUE domain proteins do not bind monoubiquitin efficiently, since they carry LP, rather than FP among CUE domains. CUE domains form three-helix bundle structures and are distantly related to the ubiquitin-associated (UBA) domains which are widely occurring ubiquitin-binding motifs found in a broad range of cellular proteins in species ranging from yeast to human. The majority of family members contain one CUE domain, but some family members from fungi harbor two CUE domains. 38 matched cddid_all.tbl CDD cd14280 cd14280 270466 UBA1_Rad23_like UBA1 domain of Rad23 proteins found in eukaryotes. The Rad23 family includes the yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe), their mammalian orthologs HR23A and HR23B, and putative DNA repair proteins from plants. Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ubiquitinylated proteins and participate in translocating polyubiquitinated proteins to the proteasome. Rad23 proteins carry a ubiquitin-like (UBL) and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. UBL domain is responsible for the binding to proteasome. UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates which suggests Rad23 proteins might be involved in certain pathways of ubiquitin metabolism. Both UBL domain and XPC-binding domain are necessary for efficient NER function of Rad23 proteins. This model corresponds to the UBA1 domain. 39 matched cddid_all.tbl CDD cd14281 cd14281 270467 UBA2_Rad23_like UBA2 domain of Rad23 proteins found in eukaryotes. The Rad23 family includes the yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe), their mammalian orthologs HR23A and HR23B, and putative DNA repair proteins from plants. Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ubiquitinylated proteins and participate in translocating polyubiquitinated proteins to the proteasome. Rad23 proteins carry a ubiquitin-like (UBL) and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. UBL domain is responsible for the binding to proteasome. UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates which suggests Rad23 proteins might be involved in certain pathways of ubiquitin metabolism. Both UBL domain and XPC-binding domain are necessary for efficient NER function of Rad23 proteins. This model corresponds to the UBA2 domain. 38 matched cddid_all.tbl CDD cd14282 cd14282 270468 UBA_TDRD3 UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins. TDRD3 is a modular protein containing Tudor domain, a DUF/OB-fold motif and a ubiquitin-associated (UBA) domain. It shows both nucleic acid- and methyl-binding properties and can interact with methylated RNA-binding proteins, such as fragile X mental retardation protein (FMRP) and DEAD/H box-3 (also known as DDX3X/Y, DBX/Y, HLP2 and DDX14) which is implicated in human genetic diseases. At this point, TDRD3 may play a central role in RNA processing regulatory pathways involving arginine methylation. TDRD3 localizes predominantly to the cytoplasm stress granules (SGs). The Tudor domain is essential and sufficient for its recruitment to SGs. 39 matched cddid_all.tbl CDD cd14283 cd14283 270469 UBA_TNR6C UBA domain found in trinucleotide repeat-containing gene 6C protein (TNRC6C) and similar proteins. TNRC6C is one of three GW182 paralogs in mammalian genomes. It is enriched in P-bodies and important for efficient miRNA-mediated repression. TNRC6C is composed of an N-terminal glycine/tryptophan (G/W)-rich region containing an Ago hook responsible for Ago protein-binding; a ubiquitin-associated (UBA) domain and a glutamine (Q)-rich region in the middle region; a middle G/W-rich region, a RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal G/W-rich region, at the C-terminus. A bipartite C-terminal region including the middle and C-terminal G/W-rich regions is referred as silencing domain that triggers silencing of bound transcripts by inhibiting protein expression and promoting mRNA decay via deadenylation. The C-terminal half containing the RRM domain functions as a key effector domain mediating protein synthesis repression by TNRC6C. 38 matched cddid_all.tbl CDD cd14284 cd14284 270470 UBA_GAWKY UBA domain found in Drosophila melanogaster protein Gawky (GW) and similar proteins. GW is the D. melanogaster GW182 homolog (dGW182) which belongs to the GW182 protein family. The GW182 proteins directly interact with Argonaute (Ago) proteins, and thus function as downstream effectors in the miRNA pathway, responsible for inhibition of translation and acceleration of mRNA decay. They are characterized by an abnormally high content of glycine/tryptophan (G/W) repeats, one or more glutamine (Q)-rich motifs, and a C-terminal RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The GW182 proteins are recruited to miRNA targets through an interaction between their N-terminal domain and an Argonaute protein. Then they promote translational repression and/or degradation of miRNA targets through their C-terminal silencing domain. In addition to a G/W repeats region, a Q-rich region, and a RRM domain, GW also contains a ubiquitin-associated domain (UBA). 35 matched cddid_all.tbl CDD cd14285 cd14285 270471 UBA_scEDE1_like UBA domain found in Saccharomyces cerevisiae EH domain-containing and endocytosis protein 1 (Ede1) and similar proteins. Ede1, also bud site selection protein 15, is the mammalian protein Eps15 homolog found in yeast and functions at the internalization step of endocytosis. Both Ede1 and Eps15 are endocytic scaffold proteins that may involve in stabilization of the adaptor-cargo complex. They both contain contains three N-terminal Eps15 homology (EH) domains and C-terminal ubiquitin-binding motifs. Whereas Eps15 has two ubiquitin interacting motifs (UIM), Ede1 harbors a single ubiquitin-associated (UBA) domain. This model corresponds to Ede1 UBA domain that is responsible for the binding of monoubiquitinated proteins and negatively regulates EH domain-mediated protein-protein interactions. 35 matched cddid_all.tbl CDD cd14286 cd14286 270472 UBA_UBP24 UBA domain found in ubiquitin carboxyl-terminal hydrolase 24 (UBP24) and similar proteins. UBP24, also called deubiquitinating enzyme 24, ubiquitin thioesterase 24, or ubiquitin-specific-processing protease 24, is a deubiquitinating protein that interacts with damage-specific DNA-binding protein 2 (DDB2) and regulates DDB2 stability. It may also play a role in the pathogenesis of Parkinson's disease (PD). UBP24 proteins contain an N-terminal ubiquitin-associated (UBA) domain and a C-terminal peptidase C19 domain. 37 matched cddid_all.tbl CDD cd14287 cd14287 270473 UBA_At3g58460_like UBA domain found in uncharacterized protein At3g58460 from Arabidopsis thaliana and its homologs from other plants. The uncharacterized protein At3g58460 from Arabidopsis thaliana is also known as rhomboid-like protein 15 which is encoded by RBL15 gene. Although the biological function of the family members remains unclear, they all contain an N-terminal rhomboid-like domain and a C-terminal ubiquitin-associated (UBA) domain. 36 matched cddid_all.tbl CDD cd14288 cd14288 270474 UBA_HUWE1 UBA domain found in eukaryotic E3 ubiquitin-protein ligase HUWE1 and similar proteins. HUWE1, also called ARF-binding protein 1 (ARF-BP1), HECT, UBA and WWE domain-containing protein 1, homologous to E6AP carboxyl terminus homologs protein 9 (HectH9), large structure of UREB1 (LASU1), Mcl-1 ubiquitin ligase E3 (Mule), upstream regulatory element-binding protein 1 (URE-B1), or URE-binding protein 1, may function as a ubiquitin-protein ligase that involves in the ubiquitination cascade that targets specific substrate proteins in proteolysis. It can ubiquitylate DNA polymerase beta (Pol beta), the major BER DNA polymerase and modulates base excision repair (BER). HUWE1 also acts as a critical mediator of both the p53-independent and p53-dependent tumor suppressor functions of ARF tumor suppressor in p53 regulation. Moreover, HUWE1 is both required and sufficient for the polyubiquitination of Mcl-1, an anti-apoptotic Bcl-2 family member involving in DNA damage-induced apoptosis. Furthermore, HUWE1 plays an important role in the regulation of Cdc6 stability after DNA damage. In addition, HUWE1 works as a partner of N-Myc oncoprotein in neural cells. It ubiquitinates N-Myc and primes it for proteasomal-mediated degradation. HUWE1 contains a ubiquitin-associated (UBA) domain, a WWE domain, and a Bcl-2 homology region 3 (BH3) domain at the N-terminus and a HECT domain at the C-terminus. WWE domain plays a role in the regulation of specific protein-protein interactions in a ubiquitin conjugation system. BH3 domain is responsible for the specific binding to Mcl-1. HECT domain involves in the inhibition of the transcriptional activity of p53 via a ubiquitin-dependent degradation pathway. It also controls neural differentiation and proliferation by destabilizing the N-Myc oncoprotein. 40 matched cddid_all.tbl CDD cd14289 cd14289 270475 UBA_RHBD3 UBA domain found in vertebrate rhomboid domain-containing protein 3 (RHBD3). RHBD3 is encoded by a novel chromosome 22 CpG island-associated gene (C22orf3) that is not expressed in a significant proportion of pituitary tumors. C22orf3 is also called pituitary tumor apoptosis gene (PTAG) or RHBDD3 which is located directly upstream of EWSR1. Although its biological function remains unclear, RHBD3 contains an N-terminal rhomboid domain and a C-terminal ubiquitin-associated (UBA) domain. 44 matched cddid_all.tbl CDD cd14290 cd14290 270476 UBA_PUB_plant UBA domain found in plant PNGase/UBA or UBX (PUB) domain-containing proteins. This family includes some uncharacterized hypothetical proteins found in plants. Although their biological function remain unclear, all family members contain an N-terminal ubiquitin-associated (UBA) domain and a C-terminal PUB domain. UBA domain, along with UBL (ubiquitin-like) domain, has been implicated in proteasomal degradation by associating with substrates destined for degradation as well as with subunits of the proteasome, thus regulating protein turnover. PUB domain functions as a p97 (also known as valosin-containing protein or VCP) adaptor by interacting with the D1 and/or D2 ATPase domains. The type II AAA+ ATPase p97 is involved in a variety of cellular processes such as the deglycosylation of ERAD substrates, membrane fusion, transcription factor activation and cell cycle regulation through differential binding to specific adaptor proteins. 49 matched cddid_all.tbl CDD cd14291 cd14291 270477 UBA1_NUB1_like UBA1 domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins. NUB1, also called negative regulator of ubiquitin-like proteins 1, renal carcinoma antigen NY-REN-18, or protein BS4, is a NEDD8-interacting protein that can be induced by interferon. It functions as a strong post-transcriptional down-regulator of the NEDD8 expression and plays critical roles in regulating many biological events, such as cell growth, NF-kappaB signaling, and biological responses to hypoxia. NUB1 can also interact with aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) which may function in the regulation of cell cycle progression. NUB1 contains three ubiquitin-associated domains (UBA), a bipartite nuclear localization signal (NLS) and a PEST motif. This model corresponds to UBA1 domain. 36 matched cddid_all.tbl CDD cd14292 cd14292 270478 UBA2_NUB1 UBA2 domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins. NUB1, also called negative regulator of ubiquitin-like proteins 1, renal carcinoma antigen NY-REN-18, or protein BS4, is a NEDD8-interacting protein that can be induced by interferon. It functions as a strong post-transcriptional down-regulator of the NEDD8 expression and plays critical roles in regulating many biological events, such as cell growth, NF-kappaB signaling, and biological responses to hypoxia. NUB1 can also interact with aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) which may function in the regulation of cell cycle progression. NUB1 contains three ubiquitin-associated domains (UBA), a bipartite nuclear localization signal (NLS) and a PEST motif. This model corresponds to UBA2 domain. 35 matched cddid_all.tbl CDD cd14293 cd14293 270479 UBA3_NUB1 UBA3 domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins. NUB1, also called negative regulator of ubiquitin-like proteins 1, renal carcinoma antigen NY-REN-18, or protein BS4, is a NEDD8-interacting protein that can be induced by interferon. It functions as a strong post-transcriptional down-regulator of the NEDD8 expression and plays critical roles in regulating many biological events, such as cell growth, NF-kappaB signaling, and biological responses to hypoxia. NUB1 can also interact with aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) which may function in the regulation of cell cycle progression. NUB1 contains three ubiquitin-associated domains (UBA), a bipartite nuclear localization signal (NLS) and a PEST motif. This model corresponds to UBA3 domain. 36 matched cddid_all.tbl CDD cd14294 cd14294 270480 UBA1_UBP5_like UBA1 domain found in ubiquitin carboxyl-terminal hydrolase UBP5, UBP13 and similar proteins. UBP5, also called deubiquitinating enzyme 5, Isopeptidase T (IsoT), ubiquitin thioesterase 5, or ubiquitin-specific-processing protease 5, is a deubiquitinating enzyme largely responsible for the disassembly of the majority of unanchored polyubiquitin in the cell. Zinc is required for its catalytic activity. UBP5 contains four ubiquitin (Ub)-binding sites including an N-terminal zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. ZnF domain binds the proximal ubiquitin. UBP domain forms the active site. UBA domains are involved in binding linear or K48-linked polyubiquitin. UBP13, also called deubiquitinating enzyme 13, Isopeptidase T-3 (isoT3), ubiquitin thioesterase 13, or ubiquitin-specific-processing protease 13, is an ortholog of UBP5. It has similar domain architecture, but functions differently from USP5 in cellular deubiquitination processes. It exhibits a weak deubiquitinating activity preferring to Lys63-linked polyubiquitin in a non-activation manner. Moreover, the zinc finger (ZnF) domain of USP13 cannot bind to Ub. Its tandem UBA domains can bind with different types of diUb but preferentially with K63-linked.USP13 can also regulate the protein level of CD3delta in cells via its UBA domains. This model corresponds to the UBA1 domain. 44 matched cddid_all.tbl CDD cd14295 cd14295 270481 UBA1_atUBP14 UBA1 domain found in Arabidopsis thaliana ubiquitin carboxyl-terminal hydrolase 14 (atUBP14) and similar proteins. atUBP14, also called deubiquitinating enzyme 14, TITAN-6 protein, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, is related to the isopeptidase T class of deubiquitinating enzymes that recycle polyubiquitin chains following protein degradation. atUBP14 is essential for early plant development. It can disassemble multi-ubiquitin chains linked internally via epsilon-amino isopeptide bonds using Lys48 and can process some, but not all, translational fusions of ubiquitin linked via alpha-amino peptide bonds. atUBP14 contains two ubiquitin-association (UBA) domains. This model corresponds to the UBA1 domain. 45 matched cddid_all.tbl CDD cd14296 cd14296 270482 UBA1_scUBP14_like UBA1 domain found in Saccharomyces cerevisiae ubiquitin carboxyl-terminal hydrolase 14 (scUBP14) and similar proteins. scUBP14, also called deubiquitinating enzyme 14, glucose-induced degradation protein 6, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, is the yeast ortholog of human Isopeptidase T (USP5), a deubiquitinating enzyme known to bind the 29-linked polyubiquitin chains. scUBP14 has been identified as a K29-linked polyubiquitin binding protein as well. It is involved in K29-linked polyubiquitin metabolism by binding to the 29-linked Ub4 resin and serving as an internal positive control in budding yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA1 domain. 39 matched cddid_all.tbl CDD cd14297 cd14297 270483 UBA2_spUBP14_like UBA2 domain found in Schizosaccharomyces pombe ubiquitin carboxyl-terminal hydrolase 14 (spUBP14) and similar proteins. spUBP14, also called deubiquitinating enzyme 14, UBA domain-containing protein 2, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, functions as a deubiquitinating enzyme that is involved in protein degradation in fission yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA2 domain. 39 matched cddid_all.tbl CDD cd14298 cd14298 270484 UBA2_scUBP14_like UBA2 domain found in Saccharomyces cerevisiae ubiquitin carboxyl-terminal hydrolase 14 (scUBP14) and similar proteins. scUBP14, also called deubiquitinating enzyme 14, glucose-induced degradation protein 6, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, is the yeast ortholog of human Isopeptidase T (USP5), a deubiquitinating enzyme known to bind the 29-linked polyubiquitin chains. scUBP14 has been identified as a K29-linked polyubiquitin binding protein as well. It is involved in K29-linked polyubiquitin metabolism by binding to the 29-linked Ub4 resin and serving as an internal positive control in budding yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA2 domain. 38 matched cddid_all.tbl CDD cd14300 cd14300 270485 UBA_UBS3A_like UBA domain found in ubiquitin-associated and SH3 domain-containing protein A (UBS3A) and similar proteins. UBS3A, also called Cbl-interacting protein 4 (CLIP4), suppressor of T-cell receptor signaling 2 (Sts-2), or T-cell ubiquitin ligand 1 (TULA-1), is a lymphoid protein only detected in thymus, spleen, and bone marrow. UBS3A exhibits extremely low phosphatase activity, but is capable of promoting T-cell apoptosis independent of either T cell receptor (TCR)/CD3-mediated signaling or caspase activity. It functions as a negative regulator of TCR signaling. UBS3A can also inhibit HIV-1 biogenesis through the binding of ATP-binding cassette protein family E member 1 (ABCE-1), a host factor of HIV-1 assembly. Moreover, UBS3A acts as the Cbl- and ubiquitin-interacting protein that can inhibit endocytosis and downregulation of ligand-activated epidermal growth factor receptor (EGFR) by impairing Cbl-induced ubiquitination, as well as inhibit clathrin-dependent endocytosis in general. This family also includes Arabidopsis thaliana ubiquitin carboxyl-terminal hydrolase 14 (atUBP14) and some uncharacterized AAA-type ATPase-like proteins found in plants. 37 matched cddid_all.tbl CDD cd14301 cd14301 270486 UBA_UBS3B UBA domain found in ubiquitin-associated and SH3 domain-containing protein B (UBS3B) and similar proteins. UBS3B, or Cbl-interacting protein p70, suppressor of T-cell receptor signaling 1 (Sts-1), T-cell ubiquitin ligand 2 (TULA-2), or tyrosine-protein phosphatase STS1/TULA2, is ubiquitously expressed in mammalian tissues in a variety of cell types. It exhibits high phosphatase activity, but demonstrates no proapoptotic activity. It negatively regulates the tyrosine kinase Zap-70 activation and T cell receptor (TCR) signaling pathways that modulate T cell activation. Moreover, UBS3B acts as a Cbl- and ubiquitin-interacting protein that inhibits endocytosis of epidermal growth factor receptor (EGFR) and platelet-derived growth factor receptor. 38 matched cddid_all.tbl CDD cd14302 cd14302 270487 UBA_UBXN1 UBA domain found in UBX domain-containing protein 1 (UBXN1) and similar proteins. UBXN1, also called SAPK substrate protein 1 (SAKS1) or UBA/UBX 33.3 kDa protein, is a widely expressed protein containing an N-terminal ubiquitin-associated (UBA) domain, a coiled-coil region, and a C-terminal ubiquitin-like (UBX) domain. It binds polyubiquitin and valosin-containing protein (VCP), and has been identified as a substrate for stress-activated protein kinases (SAPKs). Moreover, UBXN1 specifically binds to Homer2b. It may also interact with ubiquitin (Ub) and may be involved in the Ub-proteasome proteolytic pathways. In addition, UBXN1 can associate with autoubiquitinated BRCA1 tumor suppressor and inhibit its enzymatic function through its UBA domain. 41 matched cddid_all.tbl CDD cd14303 cd14303 270488 UBA1_KPC2 UBA1 domain found in Kip1 ubiquitination-promoting complex protein 2 (KPC2) and similar proteins. KPC2, also called ubiquitin-associated domain-containing protein 1 (UBAC1), or glialblastoma cell differentiation-related protein 1, is one of two subunits of Kip1 ubiquitination-promoting complex (KPC), a novel E3 ubiquitin-protein ligase that also contains KPC1 subunit and regulates the ubiquitin-dependent degradation of the cyclin-dependent kinase (CDK) inhibitor p27 at G1 phase. KPC2 contains a ubiquitin-like (UBL) domain and two ubiquitin-associated (UBA) domains. This model corresponds to the UBA1 domain. 41 matched cddid_all.tbl CDD cd14304 cd14304 270489 UBA2_KPC2 UBA2 domain found in Kip1 ubiquitination-promoting complex protein 2 (KPC2) and similar proteins. KPC2, also called ubiquitin-associated domain-containing protein 1 (UBAC1), or glialblastoma cell differentiation-related protein 1, is one of two subunits of Kip1 ubiquitination-promoting complex (KPC), a novel E3 ubiquitin-protein ligase that also contains KPC1 subunit and regulates the ubiquitin-dependent degradation of the cyclin-dependent kinase (CDK) inhibitor p27 at G1 phase. KPC2 contains a ubiquitin-like (UBL) domain and two ubiquitin-associated (UBA) domains. This model corresponds to the UBA2 domain. 39 matched cddid_all.tbl CDD cd14305 cd14305 270490 UBA_UBAC2 UBA domain found in ubiquitin-associated domain-containing protein 2 (UBAC2) and similar proteins. UBAC2, also called phosphoglycerate dehydrogenase-like protein 1, is a ubiquitin-associated domain (UBA)-domain containing protein encoded by gene UBAC2 (or PHGDHL1), a risk gene for Behcet's disease (BD). It may play an important role in the development of BD through its transcriptional modulation. Members in this family contain an N-terminal rhomboid-like domain and a C-terminal UBA domain. 38 matched cddid_all.tbl CDD cd14306 cd14306 270491 UBA_VP13D UBA domain found in vacuolar protein sorting-associated protein 13D (VP13D) and similar proteins. VP13D is a chorea-acanthocytosis (CHAC)-similar protein encoded by gene VPS13D. it contains two putative domains, ubiquitin-associated (UBA) domain and lectin domain of ricin B chain profile (ricin-B-lectin), suggesting it may interact with, and be involved in the trafficking of, proteins modified with ubiquitin and/or carbohydrate molecules. Further investigation is required. 36 matched cddid_all.tbl CDD cd14307 cd14307 270492 UBA_RUP1p UBA domain found in yeast UBA domain-containing protein RUP1p and similar proteins. RUP1p is a ubiquitin-associated (UBA) domain-containing protein encoded by a nonessential yeast gene RUP1. It can mediate the association of Rsp5 and Ubp2. The N-terminal UBA domain is responsible for antagonizing Rsp5 function, as well as bridging the Rsp5-Ubp2 interaction. No other characterized functional domains or motifs are found in RUP1p. 38 matched cddid_all.tbl CDD cd14308 cd14308 270493 UBA_Mud1_like UBA domain found in Schizosaccharomyces pombe UBA domain-containing protein mud1 and similar proteins. Schizosaccharomyces pombe mud1 is an ortholog of the Saccharomyces cerevisiae DNA-damage response protein Ddi1. S. cerevisiae Ddi1, also called v-SNARE-master 1 (Vsm1), belongs to a family of proteins known as the ubiquitin receptors which can bind ubiquitinated substrates and the proteasome. It is involved in the degradation of the F-box protein Ufo1, involved in the G1/S transition. It also participates in Mec1-mediated degradation of Ho endonuclease. Both S. pombe mud1 and S. cerevisiae Ddi1 contain an N-terminal ubiquitin-like (UBL) domain, an aspartyl protease-like domain, and a C-terminal ubiquitin-associated (UBA) domain. S. pombe mud1 binds to K48-linked polyubiquitin (polyUb) through UBA domain. 36 matched cddid_all.tbl CDD cd14309 cd14309 270494 UBA_scDdi1_like UBA domain found in Saccharomyces cerevisiae DNA-damage response protein Ddi1 and similar proteins. Ddi1, also called v-SNARE-master 1 (Vsm1), is a ubiquitin receptor involved in regulation of the cell cycle and late secretory pathway in Saccharomyces cerevisiae. It functions as a ubiquitin association domain (UBA)- ubiquitin-like-domain (UBL) shuttle protein that is required for the proteasome to enable ubiquitin-dependent degradation of its ligands. For instance, Ddi1 plays an essential role in the final stages of proteasomal degradation of Ho endonuclease and of its cognate FBP, Ufo1. Moreover, Ddi1 and its associated protein Rad23p play a cooperative role as negative regulators in yeast PHO pathway. Ddi1 contains an N-terminal UBL domain and a C-terminal UBA domain. It also harbors a central retroviral aspartyl-protease-like domain (RVP) which may be important in cell-cycle control. At this point, Ddi1 may function proteolytically during regulated protein turnover in the cell. This family also includes mammalian regulatory solute carrier protein family 1 member 1 (RSC1A1), also called transporter regulator RS1 (RS1) which mediates transcriptional and post-transcriptional regulation of Na(+)-D-glucose cotransporter SGLT1. 36 matched cddid_all.tbl CDD cd14310 cd14310 270495 UBA_cnDdi1_like UBA domain found in Cryptococcus neoformans DNA-damage response protein Ddi1 and similar proteins. The family includes some uncharacterized Ddi and similar proteins which show a high level of sequence similarity with yeast Ddi1. Ddi1, also called v-SNARE-master 1 (Vsm1), is a ubiquitin receptor involved in regulation of the cell cycle and late secretory pathway in yeast. It functions as a ubiquitin association domain (UBA)- ubiquitin-like-domain (UBL) shuttle protein that is required for the proteasome to enable ubiquitin-dependent degradation of its ligands. Ddi1 contains an N-terminal UBL domain and a C-terminal UBA domain. It also harbors a central retroviral aspartyl-protease-like domain (RVP) which may be important in cell-cycle control. At this point, Ddi1 may function proteolytically during regulated protein turnover in the cell. 30 matched cddid_all.tbl CDD cd14311 cd14311 270496 UBA_II_E2_UBC1 UBA domain of yeast ubiquitin-conjugating enzyme E2 1 (UBC1) and similar proteins. UBC1, also called ubiquitin-conjugating enzyme E2-24 kDa, or ubiquitin-protein ligase, is the yeast homolog of mammalian ubiquitin-conjugating enzyme E2 K (UBE2K or E2-25K). UBC1 and UBE2K are unique class II E2 conjugating enzymes, both of which contain a C-terminal ubiquitin-associated (UBA) domain in addition to an N-terminal catalytic ubiquitin-conjugating enzyme E2 (UBCc) domain. The yeast UBC1 plays an important role in the degradation of short-lived proteins especially during the G0-G1 transition accompanying spore germination. 48 matched cddid_all.tbl CDD cd14312 cd14312 270497 UBA_II_E2_UBC27_like UBA domain found in plant ubiquitin-conjugating enzyme E2 27 and similar proteins. UBC27, also called ubiquitin carrier protein 27, functions as a class II ubiquitin-conjugating (UBC) enzyme (E2). E2, together with E1 (ubiquitin-activating enzyme UBA) and E3 (ubiquitin ligase), is required in the multi-step reaction of ubiquitin conjugation. Unlike other Arabidopsis UBCs, in addition to an N-terminal ubiquitin-conjugating enzyme E2 catalytic domain (UBCc), UBC27 has an additional C-terminal ubiquitin-associated domain (UBA). 36 matched cddid_all.tbl CDD cd14313 cd14313 270498 UBA_II_E2_UBE2K_like UBA domain found in vertebrate ubiquitin-conjugating enzyme E2 K (UBE2K), Drosophila melanogaster ubiquitin-conjugating enzyme E2-22 kDa (UbcD4) and similar proteins. UBE2K, also called Huntingtin-interacting protein 2 (HIP-2), ubiquitin carrier protein, ubiquitin-conjugating enzyme E2-25 kDa (E2-25K), or ubiquitin-protein ligase, is a multi-ubiquitinating enzyme with the ability to synthesize Lys48-linked polyubiquitin chains which is involved in the ubiquitin (Ub)-dependent proteolytic pathway. It interacts with the frameshift mutant of ubiquitin B and functions as a crucial factor regulating amyloid-beta neurotoxicity. It has also been characterized as Huntingtin-interacting protein that modulates the neurotoxicity of Amyloid-beta (Abeta), the principal protein involved in Alzheimer's disease pathogenesis. Moreover, E2-25K increases aggregate the formation of expanded polyglutamine proteins and polyglutamine-induced cell death in the pathology of polyglutamine diseases. UbcD4, also called ubiquitin carrier protein, or ubiquitin-protein ligase, is encoded by Drosophila E2 gene which is only expressed in pole cells in embryos. It is a putative E2 enzyme homologous to the Huntingtin interacting protein-2 (HIP2) of human. UbcD4 specifically interacts with the polyubiquitin-binding subunit of the proteasome. This family also includes a putative ubiquitin conjugating enzyme from plasmodium Yoelii (pyUCE). It shows a high level of sequence similarity with UBE2K and may also plays a role in the ubiquitin-mediated protein degradation pathway. All family members are class II E2 conjugating enzymes which contain a C-terminal ubiquitin-associated (UBA) domain in addition to an N-terminal catalytic ubiquitin-conjugating enzyme E2 (UBCc) domain. 36 matched cddid_all.tbl CDD cd14314 cd14314 270499 UBA_II_E2_pyUCE_like UBA domain found in a putative ubiquitin conjugating enzyme from plasmodium Yoelii (pyUCE) and similar proteins. P. Yoelii ubiquitin-conjugating enzyme and other uncharacterized family members show high sequence similarity to the human Huntingtin interacting protein-2 (HIP2) which belongs to a class II E2 ubiquitin-conjugating enzyme family. These proteins may play roles in the ubiquitin-mediated protein degradation pathway. They all contain a C-terminal ubiquitin-associated (UBA) domain in addition to an N-terminal catalytic ubiquitin-conjugating enzyme E2 (UBCc) domain. 37 matched cddid_all.tbl CDD cd14315 cd14315 270500 UBA1_UBAP1 UBA1 domain found in vertebrate ubiquitin-associated protein 1 (UBAP-1). UBAP-1, also called nasopharyngeal carcinoma-associated gene 20 protein, is a ubiquitously expressed protein that may play an important role in the ubiquitin pathway and cell progression. It co-localizes with TDP-43 proteins in neuronal cytoplasmic inclusions and acts as a genetic risk factor for frontotemporal lobar degeneration (FTLD). Moreover, UBAP-1, together with VPS37A, forms an endosome-specific endosomal sorting complexes I required for transport (ESCRT-I) complex that displays a restricted cellular function, ubiquitin-dependent endosomal sorting and multivesicular body (MVB) biogenesis. UBAP-1 contains an N-terminal UBAP-1-MVB12-associated (UMA) domain, and two tandem ubiquitin-associated (UBA) domains that may be responsible for the binding of ubiquitin-conjugating enzymes. This model corresponds to UBA1 domain. 43 matched cddid_all.tbl CDD cd14316 cd14316 270501 UBA2_UBAP1_like UBA2 domain found in ubiquitin-associated protein 1 (UBAP-1) and similar proteins. UBAP-1, also called nasopharyngeal carcinoma-associated gene 20 protein, is a ubiquitously expressed protein that may play an important role in the ubiquitin pathway and cell progression. It co-localizes with TDP-43 proteins in neuronal cytoplasmic inclusions and acts as a genetic risk factor for frontotemporal lobar degeneration (FTLD). Moreover, UBAP-1, together with VPS37A, forms an endosome-specific endosomal sorting complexes I required for transport (ESCRT-I) complex that displays a restricted cellular function, ubiquitin-dependent endosomal sorting and multivesicular body (MVB) biogenesis. UBAP-1 contains an N-terminal UBAP-1-MVB12-associated (UMA) domain, and two tandem ubiquitin-associated (UBA) domains that may be responsible for the binding of ubiquitin-conjugating enzymes. This model corresponds to UBA2 domain. 37 matched cddid_all.tbl CDD cd14317 cd14317 270502 UBA_DHX57 UBA domain found in putative ATP-dependent RNA helicase DHX57 and similar proteins. DHX57, also called DEAH box protein 57, is a multi-domain protein with an N-terminal ubiquitin-association (UBA) domain, a Zinc finger domain, a RWD domain, a DEAD-like helicase domain and two C-terminal helicase associated domains. Although the precise biological function of DHX57 remains unclear, it may function as a putative ATP-dependent RNA helicase. 38 matched cddid_all.tbl CDD cd14318 cd14318 270503 UBA_Cbl_like UBA domain found in casitas B-lineage lymphoma (Cbl) proteins. The Cbl adaptor proteins family contains a small class of RING-type E3 ubiquitin ligases with oncogenic activity which is represented by three mammalian members, c-Cbl, Cbl-b and Cbl-3. Cbl proteins function as potent negative regulators of various signaling cascades in a wide range of cell types. They play roles in ubiquitinating the activated tyrosine kinases and targeting them for degradation. Cbl proteins in this family consists of a highly conserved N-terminal half that includes a tyrosine-kinase-binding (TKB) domain and a RING finger domain, both of which are required for Cbl-mediated downregulation of RTKs, and a C-terminal half that includes a ubiquitin-associated (UBA) domain and other protein interaction motifs. The UBA domain contains leucine/isoleucine repeats and may play a role in dimerization of Cbl proteins. In addition, although both c-Cbl and Cbl-b have the C-terminal UBA domain, only the UBA domain from Cbl-b can bind ubiquitin. 40 matched cddid_all.tbl CDD cd14319 cd14319 270504 UBA_NBR1 UBA domain of next to BRCA1 gene 1 protein (NBR1) and similar proteins. NBR1, also called cell migration-inducing gene 19 protein, membrane component chromosome 17 surface marker 2, neighbor of BRCA1 gene 1 protein, or protein 1A1-3B, is a scaffold protein that may be involved in signal transmission downstream of the serine/protein kinase from the giant muscle protein titin. Moreover, NBR1 functions as an autophagic receptor for ubiquitinated cargo. It interacts with ATG8-family proteins for its degradation by autophagy. NBR1 contains an N-terminal Phox and Bem1p (PB1) domain that plays a critical role in mediating protein-protein interactions with both titin kinase and with another scaffold protein, p62. NBR1 also has a LC3-interaction region (LIR) and a ubiquitin-associated (UBA) domain. The LIR is required for the autophagic clearance of NBR1. UBA domain is responsible for the ubiquitin binding which is necessary for the puromycin-induced formation of ubiquitinated protein aggregates. 39 matched cddid_all.tbl CDD cd14320 cd14320 270505 UBA_SQSTM UBA domain of sequestosome-1 (SQSTM) and similar proteins. SQSTM, also called EBI3-associated protein of 60 kDa (EBIAP /p60), phosphotyrosine-independent ligand for the Lck SH2 domain of 62 kDa, or ubiquitin-binding protein p62, is a widely expressed multifunctional cytoplasmic protein that is able to noncovalently bind ubiquitin and several signaling proteins, suggesting a regulatory role connected to the ubiquitin-proteasome pathway. It functions as a scaffolding protein that regulates a diverse range of signaling pathways leading to activation of the nuclear factor kappa B (NF-kappaB) family of transcription factors. It also plays a novel role in connecting receptor signals with the endosomal signaling network required for mediating TrkA-induced differentiation. SQSTM contains a PB1 dimerization domain, a tumor necrosis factor receptor-associated factor 6 (TRAF6) binding site, and a C-terminal ubiquitin-associated (UBA) domain that mediates the recognition of polyubiquitin chains and ubiquitylated substrates. 40 matched cddid_all.tbl CDD cd14321 cd14321 270506 UBA_IAPs UBA domain found in inhibitor of apoptosis proteins (IAPs). IAPs are frequently overexpressed in cancer and associated with tumor cell survival, chemoresistance, disease progression and poor prognosis. They function primarily as negative regulators of cell death. They regulate caspases and apoptosis through the inhibition of specific members of the caspase family of cysteine proteases. In addition, IAPs has been implicated in a multitude of other cellular processes, including inflammatory signalling and immunity, mitogenic kinase signalling, proliferation and mitosis, as well as cell invasion and metastasis. IAPs in this family includes cellular inhibitor of apoptosis protein c-IAP1 and c-IAP2, XIAP, and BIRC8, all of which contain three N-terminal baculoviral IAP repeat (BIR) domains that enable interactions with proteins, a ubiquitin-association (UBA) domain that is responsible for the binding of binds polyubiquitin (polyUb), and a RING domain at the carboxyl terminus that is required for ubiquitin ligase activity. c-IAPs contains an additional caspase activation and recruitment domain (CARD) between UBA and RING domains. CARD domain may serve as a protein interaction surface. 44 matched cddid_all.tbl CDD cd14322 cd14322 270507 UBA_LATS UBA domain found in serine/threonine-protein kinase LATS and similar proteins. The LATS proteins family consists of two isoforms, LATS1 and LATS2, both of which are mammalian homologs of the Drosophila tumor suppressor gene lats/warts. LATS1, also called large tumor suppressor homolog 1, or WARTS protein kinase (warts), is a serine/threonine-protein kinase that highly conserved from fly to human. LATS2, also called kinase phosphorylated during mitosis protein, or large tumor suppressor homolog 2, or serine/threonine-protein kinase KPM, or Warts-like kinase, inhibits the G1/S transition and is essential for embryonic development, proliferation control and genomic integrity. LATS proteins contain an N-terminal ubiquitin-associated (UBA) domain and a C-terminal protein kinase domain. 39 matched cddid_all.tbl CDD cd14323 cd14323 270508 UBA_PLCs_like UBA domain of eukaryotic protein linking integrin-associated protein with cytoskeleton (PLIC) proteins, Saccharomyces cerevisiae proteins Dsk2p and Gts1p, and similar proteins. The PLIC proteins (or ubiquilins) family contains human homologs of the yeast ubiquitin-like Dsk2 protein, PLIC-1 (also called ubiquilin-1), PLIC-2 (also called ubiquilin-2 or Chap1), PLIC-3 (also called ubiquilin-3) and PLIC-4 (also called ubiquilin-4, Ataxin-1 interacting ubiquitin-like protein, A1Up, Connexin43-interacting protein of 75 kDa, or CIP75), and mouse PLIC proteins. They are ubiquitin-binding adaptor proteins involved in all protein degradation pathways through delivering ubiquitinated substrates to proteasomes. They also promote autophagy-dependent cell survival during nutrient starvation. Saccharomyces cerevisiae Dsk2p is a nuclear-enriched protein that may involve in the ubiquitin-proteasome proteolytic pathway through interacting with K48-linked polyubiquitin and the proteasome. Gts1p, also called protein LSR1, is encoded by a pleiotropic gene GTS1 in budding yeast. The formation of Gts1p-mediated protein aggregates may induce reactive oxygen species (ROS) production and apoptosis. Gts1p also plays an important role in the regulation of heat and other stress responses under glucose-limited or -depleted conditions in either batch or continuous culture. 39 matched cddid_all.tbl CDD cd14324 cd14324 270509 UBA_Dsk2p_like UBA domain of Saccharomyces cerevisiae proteasome interacting protein Dsk2p and its homologs found in fungi. The family contains several fungal multi-ubiquitin receptors, including Saccharomyces cerevisiae Dsk2p and Schizosaccharomyces pombe Dph1p, both of which have been characterized as shuttle proteins transporting ubiquitinated substrates destined for degradation from the E3 ligase to the 26S proteasome. They interact with the proteasome through their N-terminal ubiquitin-like domain (UBL) and with ubiquitin (Ub) through their C-terminal ubiquitin-associated domain (UBA). S. cerevisiae Dsk2p is a nuclear-enriched protein that may involve in the ubiquitin-proteasome proteolytic pathway through interacting with K48-linked polyubiquitin and the proteasome. Moreover, it has been implicated in spindle pole duplication through assisting in Cdc31 assembly into the new spindle pole body (SPB). S. pombe Dph1p is a ubiquitin receptor working in concert with the class V myosin, Myo52, to target the degradation of the S. pombe CLIP-170 homolog, Tip1. It also can protect ubiquitin chains against disassembly by deubiquitinating enzymes. 42 matched cddid_all.tbl CDD cd14325 cd14325 270510 UBA_RNF31 UBA domain found in E3 ubiquitin-protein ligase RING finger protein 31 and similar proteins. RNF31, also called HOIL-1-interacting protein (HOIP), or zinc in-between-RING-finger ubiquitin-associated domain protein, together with HOIL-1 and SHARPIN, forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis. RNF31 contains a central ubiquitin-associated (UBA) domain that is responsible for the interaction with the N-terminal ubiquitin-like domain (UBL) of HOIL-1L. In addition, RNF31 can interact with the atypical mammalian orphan receptor DAX-1, trigger DAX-1 ubiquitination and stabilization, and participate in repressing steroidogenic gene expression. 55 matched cddid_all.tbl CDD cd14326 cd14326 270511 UBA_UBL7 UBA domain found in ubiquitin-like protein 7 (UBL7) and similar proteins. UBL7, also called bone marrow stromal cell ubiquitin-like protein (BMSC-UbP), or ubiquitin-like protein SB132, is a novel ubiquitin-like protein that may play roles in regulation of bone marrow stromal cell (BMSC) function or cell differentiation via an evocator-associated and cell-specific pattern. UBL7 contains an N-terminal ubiquitin domain (UBQ) and a C-terminal ubiquitin-associated (UBA) domain. UBQ domain interacts with 26S proteasome-dependent degradation, and UBA domain links cellular processes and the ubiquitin system. 38 matched cddid_all.tbl CDD cd14327 cd14327 270512 UBA_atUPL1_2_like UBA domain found in Arabidopsis thaliana E3 ubiquitin-protein ligase UPL1 (atUPL1), UPL2 (atUPL2) and similar proteins. The family includes two highly similar 405-kDa HECT E3 ubiquitin-protein ligases (UPLs), UPL1 and UPL2, from Arabidopsis thaliana. The HECT E3 UPL family plays a prominent role in the ubiquitination of plant proteins. The biological functions of UPL1 and UPL2 remain unclear. Both of them contain a ubiquitin-associated (UBA) domain and a C-terminal HECT domain. UBA domain may be involved in ubiquitin metabolism. HECT domain is necessary and sufficient for their E3 catalytic activity, but requires ATP, E1 and an E2 of the Arabidopsis UBC8 family to ubiquitinate proteins. 38 matched cddid_all.tbl CDD cd14328 cd14328 270513 UBA_TNK1 UBA domain found in non-receptor tyrosine-protein kinase TNK1 and similar proteins. TNK1, also called CD38 negative kinase 1, is a non-receptor protein tyrosine kinase (NRPTK) that has been implicated in the regulation of apoptosis, cell growth, nuclear factor-kappaB, and Ras. It associates with phospholipase C (PLC)-gamma1 and may play a role in phospholipid signal transduction. TNK1 contains an NH2-terminal kinase, a Src Homology 3 (SH3) domain, a proline-rich (PR) region, and a C-terminal ubiquitin-association (UBA) domain. 40 matched cddid_all.tbl CDD cd14329 cd14329 270514 UBA_SWA2p_like UBA domain found in yeast auxilin-like clathrin uncoating factor SWA2 (Swa2p) and similar proteins. The lineage specific group includes Swa2p and other uncharacterized hypothetical proteins from Saccharomyces. Swa2p, also called bud site selection protein 24, DnaJ-related protein SWA2, or synthetic lethal with ARF1 protein 2, is the yeast auxilin ortholog that is a multifunctional protein with three N-terminal clathrin-binding (CB) motifs, a ubiquitin-association (UBA) domain, a tetratricopeptide repeat (TPR) domain, and a C-terminal J-domain. It is required for disassembly of clathrin-coated vesicles (CCVs) in an ATP-dependent manner, as well as for cortical endoplasmic reticulum (ER) inheritance. 36 matched cddid_all.tbl CDD cd14330 cd14330 270515 UBA_atDRM2_like UBA domain found in Arabidopsis thaliana DNA (cytosine-5)-methyltransferase DRM2 (atDRM2) and similar proteins. atDRM2, also called protein domains rearranged methylase 2, is a homolog of the mammalian de novo methyltransferase DNMT3. It is the major de novo methyltransferase targeted to DNA by small interfering RNAs (siRNAs) in the RNA-directed DNA methylation (RdDM) pathway in Arabidopsis thaliana. atDRM2 is a part of the RdDM effector complex and plays a catalytic role in RdDM. It contains an N-terminal UBA domains and a C-terminal methyltransferase domain, both of which are required for normal RdDM. 37 matched cddid_all.tbl CDD cd14331 cd14331 270516 UBA_HERC1_2 UBA domain found in probable E3 ubiquitin-protein ligase HERC1, HERC2 and similar proteins. HERC1, also called HECT domain and RCC1-like domain-containing protein 1, p532, or p619, is an ubiquitously expressed giant protein involved in ubiquitin-dependent intracellular membrane trafficking through its interaction with vesicle coat proteins such as clathrin and ARF. Moreover, it has been identified as a tuberous sclerosis complex TSC2-interacting protein that may play a role in TSC-mTOR (mammalian target of rapamycin) pathway. HERC2, also called HECT domain and RCC1-like domain-containing protein 2, is a SUMO-regulated E3 ubiquitin ligase that plays an important role in the SUMO-dependent pathway which orchestrates the DNA double-strand break (DSB) response. Moreover, HERC2 functions as a RNF8 auxiliary factor that regulates ubiquitin-dependent retention of repair proteins on damaged chromosomes. HERC1 and HERC2 are multi-domain proteins with different domain organizations. Both of them contain a ubiquitin-association (UBA) domain, more than one RCC1-like domains (RLDs) and a C-terminal HECT E3 ubiquitin ligase domain. 40 matched cddid_all.tbl CDD cd14332 cd14332 270517 UBA_RuvA_C C-terminal UBA-like domain of holliday junction ATP-dependent DNA helicase RuvA. RuvA, along with RuvB and RuvC proteins, is involved in branch migration of heteroduplex DNA in homologous recombination that is a crucial process for maintaining genomic integrity and generating biological diversity in all living organisms. RuvA has a tetrameric architecture in which each subunit comprised of three distinct domains. This model corresponds to the C-terminal domain of RuvA which is distantly related to the ubiquitin-associated (UBA) domain. It plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB. Within the Holliday junction, the C-terminal domain makes no interaction with DNA. 45 matched cddid_all.tbl CDD cd14333 cd14333 270518 UBA_unchar_Eumetazoa UBA domain found in some hypothetical proteins from Eumetazoa. The family includes some uncharacterized Eumetazoan proteins. Although their biological function remain unclear, they all contain a very conserved ubiquitin-associated (UBA) domain which is a commonly occurring sequence motif found in proteins involved in ubiquitin-mediated proteolysis. 38 matched cddid_all.tbl CDD cd14334 cd14334 270519 UBA_SNF1_fungi UBA domain of yeast carbon catabolite-derepressing protein kinases (Snf1) and similar proteins found in fungi. Snf1, also called yeast adenosine monophosphate (AMP)-activated protein kinase (AMPK), is a global regulator of carbon metabolism in the yeast Saccharomyces cerevisiae. Its phosphorylation is essential for the regulation by carbon catabolite repression in eukaryotic cells. Snf1 is involved in the cellular responses to nutrient stress, as well as other environmental stresses, including sodium ion stress, heat shock, alkaline pH, oxidative stress, and genotoxic stress. It plays roles in various nutrient-responsive, cellular developmental processes, including meiosis and sporulation, aging, haploid invasive growth, and diploid pseudohyphal growth. It is required for transcription of glucose-repressed genes, glycogen storage, thermotolerance, and peroxisome biogenesis. The catalytic activity of Snf1 can be regulated by upstream kinases, Sak1, Elm1, and Tos3, by the Reg1-Glc7 protein phosphatase 1, and by autoinhibition. In addition to an N-terminal protein kinase domain and a C-terminal regulatory domain of 5'-AMP-activated protein kinase (AMPK), Snf1 contains an ubiquitin-associated (UBA) domain, previously called SNF1 homology (SNH) domain, in the middle region. 48 matched cddid_all.tbl CDD cd14335 cd14335 270520 UBA_SnRK1_plant UBA domain found in the plant sucrose nonfermenting-1-related kinase (SnRK1) proteins. The plant SnRK1 proteins (also known as AKIN10/11) family contains plant orthologs of the yeast sucrose non-fermenting (Snf1) kinase and mammalian AMP-activated protein kinase (AMPK), including two catalytic alpha-subunits of plant Snf1-related kinases (SnRKs): SNF1-related protein kinase catalytic subunit alpha KIN10 (also called AKIN10 or AKIN alpha2) and SNF1-related protein kinase catalytic subunit alpha KIN11 (also called AKIN11 or AKIN alpha1). AKIN10 and AKIN11 function as central integrators of sugar, metabolic, stress, and developmental signals in plants. They form different complexes with the regulatory AKINbeta2, a plant ortholog of conserved Snf1/AMPK beta-subunits. In addition to an N-terminal protein kinase domain and a C-terminal regulatory domain of 5'-AMP-activated protein kinase (AMPK), Snf1 contains an ubiquitin-associated (UBA) domain, previously called SNF1 homology (SNH) domain, in the middle region. 41 matched cddid_all.tbl CDD cd14336 cd14336 270521 UBA_AID_AMPKalpha UBA-like autoinhibitory domain (AID) found in vertebrate 5'-AMP-activated protein kinase catalytic alpha (AMPKalpha) subunits. The family corresponds to the catalytic subunits of adenosine monophosphate (AMP)-activated protein kinase (AMPK) which includes two isoforms encoded by two distinct genes, AMPKalpha-1 (PRKAA1) and AMPKalpha-2 (PRKAA2). Skeletal muscle predominantly expresses the AMPKalpha-2, whereas the liver expresses approximately equal amounts of both AMPKalpha subunits. One AMPKalpha subunit and two regulatory subunits, beta (beta1, beta2, beta3) and gamma (gamma1, gamma2, gamma3) form a heterotrimeric AMPK complex that plays a central role in the regulation of cellular energy metabolism, activates energy-producing pathways and inhibits energy-consuming processes through responding to a fall in intracellular ATP levels. It is activated in beta-cells at low glucose concentrations, but inhibited as glucose levels increase. AMPKalpha subunits show significant similarity in the catalytic core region, but have divergent COOH-terminal tails, suggesting they may interact with different proteins within this region. Both of AMPKalpha subunits have an N-terminal Ser/Thr kinase domain followed by an ubiquitin-associated (UBA)-like AID, and a C-terminal AMPK regulatory domain. The Ser/Thr kinase domain contains a conserved Thr residue that must be phosphorylated for activity in the activation loop. The AID is responsible for AMPKalpha subunits autoinhibition. The C-terminal regulatory domain of the alpha-subunit is essential for binding the beta- and gamma-subunits. 65 matched cddid_all.tbl CDD cd14337 cd14337 270522 UBA_MARK_Par1 UBA domain found in microtubule-associated protein (MAP)/microtubule affinity-regulating kinase (MARK)/ partitioning-defective 1 (Par-1) and similar proteins. The MARK/Par-1 subfamily contains serine/threonine-protein kinases including mammal MARKs, and polarity kinases Par-1 found in Caenorhabditis elegans and Drosophila melanogaster. Those proteins are frequently found associated with membrane structures and participate in diverse processes from control of the cell cycle and polarity to intracellular signaling and microtubule stability. They are involved in nematode embryogenesis, cell cycle control, epithelial cell polarization, cell signaling, and neuronal migration and differentiation. The mammals MARKs have been implicated in carcinomas, Alzheimer's disease (through tau hyperphosphorylation), and autism. Four MARK isoforms exist in humans. Members in this subfamily contain an N-terminal protein kinase catalytic domain, followed by an ubiquitin-associated (UBA) domain and a C-terminal regulatory domain of 5'-AMP-activated protein kinase (AMPK). 40 matched cddid_all.tbl CDD cd14338 cd14338 270523 UBA_SIK UBA domain found in salt-inducible kinase SIK1, SIK2, SIK3 and similar proteins. Salt-inducible kinase SIK1, SIK2, SIK3 are serine/threonine kinases that belong to the AMP-activated protein kinases (AMPK) family involved in the regulation of metabolism during energy stress. SIK1, also called serine/threonine-protein kinase SNF1-like kinase 1 (SNF1LK), is required for myogenic differentiation. It is degraded by the proteasome in myoblasts which is regulated by cAMP signaling. Moreover, SIK1 acts as a class II histone deacetylase (HDAC) kinase, triggering the cytoplasmic export of the HDACs and activation of myocyte enhancer factor 2 (MEF2)-dependent transcription. It also regulates transcription through inhibitory phosphorylation of a family of cAMP responsive element binding protein (CREB) coactivators, called TORCs/CRTCs. In addition, SIK1 links LKB1 to p53-dependent anoikis and suppresses metastasis. It is also involved in a cell sodium-sensing network that regulates active sodium transport through a calcium-dependent process. SIK2, also called Qin-induced kinase or serine/threonine-protein kinase SNF1-like kinase 2 (SNF1LK2), plays an important role in the insulin-signaling pathway during adipocyte differentiation, as well as in autophagy progression. Moreover, SIK2 plays a critical role in neuronal survival and modulates cAMP responsive element binding protein (CREB)-mediated gene expression in response to hormones and nutrients. SIK2 acts as a critical determinant in autophagy progression. In addition, SIK2 localizes at the centrosome and functions as a centrosome kinase required for bipolar mitotic spindle formation. It is involved in the initiation of mitosis, and regulates the localization of the centrosome linker protein, C-Nap1, through S2392 phosphorylation. SIK3, also called salt-inducible kinase 3 or serine/threonine-protein kinase QSK, acts as a novel energy regulator that modulates cholesterol and bile acid metabolism by coupling with retinoid metabolism. It also play an essential role in facilitating chondrocyte hypertrophy during skeletogenesis and growth plate maintenance. Members in this family contain an N-terminal protein kinase catalytic domain followed by an ubiquitin-associated (UBA) domain. 45 matched cddid_all.tbl CDD cd14339 cd14339 270524 UBA_SNRK UBA domain of SNF-related serine/threonine-protein kinase (SNRK) and similar proteins mainly found in metazoa. SNRK, also called Sucrose nonfermenting 1 (Snf1)-related kinase, is a serine/threonine kinase highly expressed in the testis. It is a distant member of the largely adenosine monophosphate (AMP)-activated protein kinase (AMPK) family. SNRK can be phosphorylated and activated by LKB1 and may mediate cellular effects regulated by LKB1. It is also involved in the regulation of colon cancer cell proliferation and beta-catenin signaling. It inhibits colon cancer cell proliferation through calcyclin-binding protein (CacyBP)-dependent reduction of beta-catenin. In addition to an N-terminal protein kinase domain, it harbors an ubiquitin-associated (UBA) domain, previously called SNF1 homology (SNH) domain which is conserved in other Snf1-related kinases, but not in any other protein kinase. 48 matched cddid_all.tbl CDD cd14340 cd14340 270525 UBA_BRSK UBA domain found in serine/threonine-protein kinase BRSK1, BRSK2 and similar proteins. The family includes brain-specific kinases BRSK1 and BRSK2. They are AMP-activated protein kinase (AMPK)-related kinases that are highly expressed in mammalian forebrain and crucial for establishing neuronal polarity.BRSK1, also called brain-selective kinase 1, brain-specific serine/threonine-protein kinase 1, BR serine/threonine-protein kinase 1, serine/threonine-protein kinase SAD-B, or synapses of Amphids Defective homolog 1 (SAD1 homolog), is associated with synaptic vesicles and is tightly associated with the presynaptic cytomatrix in nerve terminals. It can regulate neurotransmitter release presynaptically. BRSK2, also called brain-selective kinase 2, brain-specific serine/threonine-protein kinase 2, BR serine/threonine-protein kinase 2, serine/threonine-protein kinase 29, or serine/threonine-protein kinase SAD-A is an AMP-activated protein kinase (AMPK)-related kinase exclusively expressed in brain and pancreas. It plays an essential role in neuronal polarization. It interacts with CDK-related protein kinase PCTAIRE1, a kinase involved in neurite outgrowth and neurotransmitter release, and further negatively regulates glucose-stimulated insulin secretion (GSIS) in pancreatic beta-cells through activation of p21-activated kinase-1 (PAK1). BRSK2 also regulates cell-cycle progression controlled by APC/C(Cdh1) through the ubiquitin-proteasome pathway. Moreover, BRSK2 is regulated by endoplasmic reticulum (ER) stress in protein level and involved in ER stress-induced apoptosis. Both BRSK1 and BRSK2 contain an N-terminal protein kinase catalytic domain followed by an ubiquitin-associated (UBA) domain. 54 matched cddid_all.tbl CDD cd14341 cd14341 270526 UBA_MELK UBA domain found in maternal embryonic leucine zipper kinase (MELK) and similar proteins. MELK, also called protein kinase Eg3 (pEg3 kinase), protein kinase PK38 (PK38), or tyrosine-protein kinase MELK, is a cell cycle dependent protein kinase involved in diverse cell processes including stem cell renewal, cell cycle progression, cell proliferation, apoptosis and mRNA processing. It is expressed in normal tissues and especially in cancer cells. It is upregulated in cancer tissues and thus may act as potential anticancer target in diverse tumor entities. MELK comprises an N-terminal protein kinase catalytic domain, followed by an ubiquitin-associated (UBA) domain, and a C-terminal autoinhibitory domain of 5'-AMP-activated protein kinase (AMPK). 52 matched cddid_all.tbl CDD cd14342 cd14342 270527 UBA_TAP-C UBA-like domain found in nuclear RNA export factor NXF1, NXF2 and similar proteins. The NXF family of mRNA nuclear export factors including vertebrate NXF1 (also called tip-associated protein or mRNA export factor TAP), NXF2 (also called cancer/testis antigen CT39 or TAP-like protein TAPL-2), Caenorhabditis elegans NXF1 (ceNXF1), Saccharomyces cerevisiae mRNA nuclear export factor Mex67p and similar proteins. NXF proteins can stimulate nuclear export of mRNAs and facilitate the export of unspliced viral mRNA containing the constitutive transport element. It is a multi-domain protein with a nuclear localization sequence (NLS), a non-canonical mRNA-binding domain, and four leucine-rich repeats (LLR) at the N-terminal region. Its C-terminal part contains a NTF2-like domain and a ubiquitin-associated (UBA)-like domain, joined by flexible Pro-rich linker. Caenorhabditis elegans NXF1 are essential for the nuclear export of poly(A)+mRNA. In budding yeast, Mex67p binds mRNAs through its adaptor Yra1/REF. It also interacts directly with Nab2, an essential shuttling mRNA-binding protein required for export. Moreover, Mex67p associates with both nuclear pore protein (nucleoporin) FG repeats and Hpr1, a component of the TREX/THO complex linking transcription and export. 51 matched cddid_all.tbl CDD cd14343 cd14343 270528 UBA_F100B_like UBA-like domain found in protein FAM100B. The family corresponds to the uncharacterized protein FAM100B and its homologs mainly found in Metazoa. Although their biological roles remain unclear, all family members contain a ubiquitin-associated (UBA)-like domain that may be involved in the binding of ubiquitin. 39 matched cddid_all.tbl CDD cd14344 cd14344 270529 UBA_TYDP2 UBA-like domain found in tyrosyl-DNA phosphodiesterase 2 (TDP2) and similar proteins. TDP2, also called ETS1-associated protein II (EAPII) or TRAF and TNF receptor-associated protein (Ttrap), is a 5'-Tyr-DNA phosphodiesterase, a member of the Mg(2+)/Mn(2+)-dependent family of phosphodiesterases which contains an N-terminal ubiquitin-associated (UBA)-like domain and a C-terminal phosphodiesterase domain. TDP2 is required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini needed for subsequent DNA ligation and hence repair of the break. Tyrosyl-DNA phosphodiesterase 1 (TDP1), an enzyme that cleaves 3'-phosphotyrosyl bonds, and TDP2 are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TDP2 has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation. It can associate with CD40, tumor necrosis factor receptor-75 (TNF-R75) and TNF receptor-associated factors (TRAFs) and may inhibit the activation of nuclear factor-kappa B (NF-kappaB). 37 matched cddid_all.tbl CDD cd14345 cd14345 270530 UBA_UBXD7 UBA-like domain found in UBX domain-containing protein 7 (UBXD7) and similar proteins. UBXD7, also known as UBXN7, functions as a ubiquitin-binding adaptor that mediates the interaction between the AAA+ ATPase p97 (also known as VCP or Cdc48) and the transcription factor HIF1alpha. It binds only to the active, NEDD8- or Rub1-modified form of cullins. UBXD7 contains the ubiquitin-associated (UBA), ubiquitin-associating (UAS), ubiquitin regulatory X (UBX), and ubiquitin-interacting motif (UIM) domains. Either UBA or UIM could serve as a docking site for neddylated-cullins. Moreover, UBA-like domain is required for binding ubiquitylated-protein substrates, UIM motif is responsible for the binding to cullin RING ligases (CRLs), and UBX domain is essential for p97 binding. 37 matched cddid_all.tbl CDD cd14346 cd14346 270531 UBA_Ubx5_like UBA-like domain found in Saccharomyces cerevisiae UBX domain-containing protein 5 (Ubx5) and similar proteins. Ubx5 is a ubiquitin regulatory X (UBX) domain-containing protein encoded by the open reading frame (ORF) YDR330W in yeast. As the yeast ortholog of mammalian UBXD7, Ubx5 functions as the cofactor of AAA+ ATPase p97, also known as VCP or Cdc48. It binds only to the active, NEDD8- or Rub1-modified form of cullins. Ubx5 contains the ubiquitin-associated (UBA), ubiquitin-associating (UAS), ubiquitin regulatory X (UBX) and ubiquitin-interacting motif (UIM) domains and its UIM domain is required to promote UV-dependent degradation of polyubiquitinated Rpb1. 39 matched cddid_all.tbl CDD cd14347 cd14347 270532 UBA_Cezanne_like UBA-like domain found in OTU domain-containing proteins OTU7A, OTU7B and similar proteins. OTU7A, also called zinc finger protein Cezanne 2, belongs to a family of proteins that have been characterized as highly specific ubiquitin iso-peptidases removing ubiquitin from proteins. OTU7B, also called cellular zinc finger anti-NF-kappaB protein, zinc finger A20 domain-containing protein 1, or zinc finger protein Cezanne, is a novel deubiquitinating enzyme that acts as a negative regulator of NF-kappaB and may play a role in the control of the inflammatory process. Both OTU7A and OTU7B contain an N-terminal ubiquitin-associated (UBA)-like domain, followed by an ovarian tumor (OTU) domain and a ubiquitin binding domain, A20-like zinc finger. In addition, they both display proteolytic activity. 43 matched cddid_all.tbl CDD cd14348 cd14348 270533 UBA_p47 UBA-like domain found in NSFL1 cofactor p47 and similar proteins. p47, also called UBX domain-containing protein 2C, is a major cofactor of the cytosolic AAA ATPase p97. It is required for the p97-regulated membrane reassembly of the endoplasmic reticulum (ER), the nuclear envelope and the Golgi apparatus. p47, together with p97, forms the p97-p47 complex that plays an important role in regulation of membrane fusion events. p47 contains an N-terminal ubiquitin-associated (UBA)-like domain, a central SEP (named after shp1, eyc and p47) domain, and a ubiquitin-like (UBX) domain. UBA-like domain is responsible for forming a highly stable complex with ubiquitin. SEP domain and UBX domain may involve in p47 trimerization or forms a stable complex with the p97 N-terminal domain. 40 matched cddid_all.tbl CDD cd14349 cd14349 270534 UBA_CF106 UBA-like domain found in uncharacterized protein C6orf106 and similar proteins. The family corresponds to a group of uncharacterized protein C6orf106 and its homologs mainly found in Metazoa. All family members contain a ubiquitin-associated (UBA)-like domain. 41 matched cddid_all.tbl CDD cd14350 cd14350 270535 UBA_DCNL UBA-like domain found in DCN1-like protein DCNL1, DCNL2 and similar proteins. DCNL1 (defective in cullin neddylation protein 1-like protein 1), also called DCUN1 domain-containing protein 1, is encoded by squamous cell carcinoma-related oncogene SCCRO (DCUN1D1). It interacts with known cullin isoforms as well as ROC1, Ubc12 and CAND1, the components of the neddylation pathway. It plays an essential role in the neddylation E3 complex and participates in the release of inhibitory effects of CAND1 on cullin-RING ligase E3 complex assembly and activity. DCNL1 contains an N-terminal ubiquitin-associated (UBA)-like domain and a C-terminal cullin binding domain that binds to cullins and Rbx-1, components of an E3 ubiquitin ligase complex for neddylation. DCNL2 (defective in cullin neddylation protein 1-like protein 2), also called DCUN1 domain-containing protein 2, is encoded by gene DCUN1D2. Although its biological function remains unclear, DCNL2 shows high sequence similarity with DCNL1 and may also contribute to neddylation of cullin components of SCF-type E3 ubiquitin ligase complexes. Like DCNL1, DCNL2 contains an N-terminal UBA-like domain and a C-terminal cullin binding domain. 42 matched cddid_all.tbl CDD cd14351 cd14351 270536 UBA_Ubx1_like UBA-like domain found in yeast UBX domain-containing protein 1 (Ubx1) and similar proteins. Ubx1, also called suppressor of high-copy PP1 protein (Shp1), is the substrate-recruiting cofactor of AAA-adenosine triphosphatase Cdc48 in Saccharomyces cerevisiae. In concert with ubiquitin-like Atg8, Cdc48 and Ubx1 are involved in the regulation of autophagosome biogenesis. Ubx1 also functions as a regulator of phosphoprotein phosphatase 1 (PP1) with differential effects on glycogen metabolism, meiotic differentiation, and mitotic cell cycle progression. All family members contain an N-terminal ubiquitin-associated (UBA)-like domain. 37 matched cddid_all.tbl CDD cd14352 cd14352 270537 UBA_DCN1 UBA-like domain found in yeast defective in cullin neddylation protein 1 (DCN1) and similar proteins. DCN1 is a scaffold-type E3 ligase for cullin neddylation. It can bind directly to cullins and the ubiquitin-like protein Nedd8-specific E2 (Ubc12), and regulate cullin neddylation and thus display ubiquitin ligase activity. It contains an N-terminal ubiquitin-associated (UBA)-like domain and a unique C-terminal PONY domain that is essential for the neddylation function of DCN1. 36 matched cddid_all.tbl CDD cd14353 cd14353 270538 UBA_FAF UBA-like domain found in FAS-associated factor FAF1, FAF2 and similar proteins. FAF1, also called UBX domain-containing protein 12 or UBX domain-containing protein 3A, is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF1 is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kappaB (NF-kappaB) by interfering with the nuclear translocation of the p65 subunit. Although the precise role of FAF1 in the ubiquitination pathway remains unclear, FAF1 interacts with valosin-containing protein (VCP) which is involved in the ubiquitin-proteosome pathway. FAF2, also called protein ETEA, UBX domain-containing protein 3B, or UBX domain-containing protein 8, is the translation product of a highly expressed gene in the T-cells and eosinophils of atopic dermatitis patients compared with those of normal individuals. FAF2 shows homology to Fas-associated factor 1 (FAF1). Both of them contain N-terminal ubiquitin-associated (UBA)-like domain, UAS and ubiquitin-like (UBX) domains. Compared to FAF1, however, FAF2 lacks the nuclear targeting domain. The function of FAF2 remains unclear. A yeast two-hybrid assay showed that it can interact with Fas. Because of its homology to FAF1, it is postulated that FAF2 could be involved in modulating Fas-mediated apoptosis of T-cells and eosinophils of atopic dermatitis patients, making them more resistant to apoptosis. 32 matched cddid_all.tbl CDD cd14354 cd14354 270539 UBA_UBP25 UBA domain found in ubiquitin carboxyl-terminal hydrolase 25 (UBP25) and similar proteins. UBP25, also called deubiquitinating enzyme 25, USP on chromosome 21, ubiquitin thioesterase 25, or ubiquitin-specific-processing protease 25, belongs to the deubiquitinating enzyme (DUB) family that specifically hydrolyzes ubiquitin chains on ubiquitin-conjugated proteins. USP25 has one muscular isoform and two ubiquitous isoforms. The longer muscular isoform can bind to muscle-restricted cytoskeletal and sarcomeric proteins, such as myosin binding protein C1 (MyBPC1), actin alpha-1 (ACTA1) and filamin C (FLNC), and further prevent their degradation. USP25 harbors three potential ubiquitin-binding domains (UBDs), one ubiquitin-associated (UBA) domain and two ubiquitin-interacting motifs (UIMs) in the N-terminal region. Its C-terminal tyrosine-rich region is responsible for the binding of the second SH2 domain of SYK, a non-receptor tyrosine kinase that specifically phosphorylates USP25 and alters its cellular levels. 46 matched cddid_all.tbl CDD cd14355 cd14355 270540 UBA_UBP28 UBA domain found in ubiquitin carboxyl-terminal hydrolase 28 (UBP28) and similar proteins. UBP28, also called deubiquitinating enzyme 28, ubiquitin thioesterase 28, or ubiquitin-specific-processing protease 28, is an ubiquitin-specific protease that belongs to the deubiquitinating enzyme (DUB) family which specifically hydrolyzes ubiquitin chains on ubiquitin-conjugated proteins. UBP28 can form a ternary complex with nucleoplasmic Fbw7alpha, an F-box protein that is part of an SCF-type ubiquitin ligase, and MYC, a transcription factor encoded by MYC proto-oncogene. UBP28 is required for the stability of MYC, and this stabilization is necessary for tumour-cell proliferation. Besides, UBP28 plays a critical role in the regulation of the Chk2-p53-PUMA pathway. It specifically interacts with 53BP1 and is essential to stabilize Chk2 and 53BP1 in response to DNA damage. 42 matched cddid_all.tbl CDD cd14358 cd14358 270541 UBA_NAC_euk UBA-like domain found in nascent polypeptide-associated complex subunit alpha (NACA) and its homologs mainly found in eukaryotes. The subfamily contains nascent polypeptide-associated complex subunit alpha (NACA), putative NACA-like protein (NACP1), nascent polypeptide-associated complex subunit alpha domain-containing protein 1 (NACAD), and similar proteins. NACA, also called NAC-alpha or Alpha-NAC, together with BTF3, also called Beta-NAC, form the nascent polypeptide-associated complex (NAC) which is a cytosolic protein chaperone that contacts the nascent polypeptide chains as they emerge from the ribosome. Besides, NACA has a high affinity for nucleic acids and exists as part of several protein complexes playing a role in proliferation, apoptosis, or degradation. It is a cytokine-modulated specific transcript in the human TF-1 erythroleukemic cell line. It also acts as a transcriptional co-activator in osteoblasts by binding to phosphorylated c-Jun, a member of the activator-protein-1 (AP-1) family. Moreover, NACA binds to and regulates the adaptor protein Fas-associated death domain (FADD). In addition, NACA functions as a novel factor participating in the positive regulation of human erythroid-cell differentiation. The biological function of NACP1 (also called Alpha-NAC pseudogene 1 or NAC-alpha pseudogene 1) and NACAD remain unclear. All family members contain an NAC domain and a C-terminal ubiquitin-associated (UBA) domain. 37 matched cddid_all.tbl CDD cd14359 cd14359 270542 UBA_AeNAC UBA-like domain found in archaeal nascent polypeptide-associated complex homolog from Methanothermobacter marburgensis (AeNAC) and similar proteins. AeNAC is a functional archaeal homolog of eukaryotic nascent polypeptide-associated complex (NAC). Both AeNAC and eukaryotic NAC function as the cytosolic chaperone that can bind to ribosomal RNA, interact with the nascent polypeptide chains as they emerge from the ribosome, and assist in post-translational processes. They all contain a NAC domain and an ubiquitin-associated (UBA) domain in the C-terminus. However, unlike eukaryotic NAC, AeNAC forms a ribosome associated homodimer, but not heterodimer. The NAC domain of AeNAC is responsible for the homodimer formation. 40 matched cddid_all.tbl CDD cd14360 cd14360 270543 UBA_NAC_like_bac UBA-like domain found in uncharacterized bacteria proteins similar to eukaryotic nascent polypeptide-associated complex proteins (NAC). This subfamily contains a group of uncharacterized proteins found in bacteria. They all contain an N-terminal ubiquitin-associated (UBA) that shows high sequence similarity with that of eukaryotic nascent polypeptide-associated complex proteins (NAC) which is one of the cytosolic chaperones that contact the nascent polypeptide chains as they emerge from the ribosome and assist in post-translational processes. 38 matched cddid_all.tbl CDD cd14361 cd14361 270544 UBA_HYPK UBA-like domain found in Huntingtin-interacting protein K (HYPK) and similar proteins. HYPK, also called Huntingtin yeast partner K or Huntingtin yeast two-hybrid protein K, is an intrinsically unstructured Huntingtin (HTT)-interacting protein with chaperone-like activity. It is involved in regulating cell growth, cell cycle, unfolded protein response, and cell death. All members in this subfamily contain an N-terminal ubiquitin-associated (UBA) that shows high sequence similarity with that of eukaryotic nascent polypeptide-associated complex proteins (NAC) which is one of the cytosolic chaperones that contact the nascent polypeptide chains as they emerge from the ribosome and assist in post-translational processes. 41 matched cddid_all.tbl CDD cd14362 cd14362 270545 CUE_TAB2_TAB3 CUE domain found in the N-terminal of TGF-beta-activated kinase 1 and MAP3K7-binding proteins TAB2, TAB3 and similar proteins. TAB2, also called mitogen-activated protein kinase kinase kinase 7-interacting protein 2, TAK1-binding protein 2, or TGF-beta-activated kinase 1-binding protein 2, is an adaptor protein that regulates activation of TAK1, a MAP kinase kinase kinase (MAPKKK), through linking TAK1 to TRAF6 in the Interleukin-1 (IL-1) induced NF-kappaB activation pathway. TAB3, also called mitogen-activated protein kinase kinase kinase 7-interacting protein 3, NF-kappa-B-activating protein 1, TAK1-binding protein 3, or TGF-beta-activated kinase 1-binding protein 3, is a TAB2-like TAK1-binding protein that activates NF-kappaB similar to TAB2. It activates TAK1 and regulates its association with TRAF2 and TRAF6. Moreover, TAB3 interacts with TRAF6 and TRAF2 in an IL-1- and a TNF-dependent manner, respectively. In summary, TAB2 and TAB3 function redundantly as mediators of TAK1 activation in IL-1 and TNF signal transduction. Both of them contain an N-terminal CUE domain, a coiled-coil (CC) region, a TAK1-binding domain and a C-terminal Npl4 zinc finger (NZF) ubiquitin-binding domain (UBD). 42 matched cddid_all.tbl CDD cd14363 cd14363 270546 CUE_TOLIP CUE domain found in the C-terminal of toll-interacting protein (Tollip) and similar proteins. Tollip is a new component of the IL-1RI pathway which contains an N-terminal C2 domain and a C-terminal CUE domain. Tollip binds to the cytoplasmic TIR domain of IL-1Rs after IL-1 stimulation. It is sufficient for recruitment of IRAK to IL-1Rs and negatively regulates IL-1-induced signaling by inhibiting IRAK phosphorylation. In addition, Tollip directly interacts with toll-like receptors TLR2 and TLR4, and plays an inhibitory role in TLR-mediated cell activation through suppressing phosphorylation and kinase activity of IRAK. Moreover, Tollip can associate with GAT domains of Tom1 and its related proteins Tom1L1 and Tom1L2, and facilitate the recruitment of clathrin onto endosomes. 41 matched cddid_all.tbl CDD cd14364 cd14364 270547 CUE_ASCC2 CUE domain found in activating signal cointegrator 1 complex subunit 2 (ASCC2) and similar proteins. ASCC2, also called ASC-1 complex subunit p100 or Trip4 complex subunit p100, together with ASCC1 (also called p50) and ASCC3 (also called p300), form the activating signal cointegrator complex (ASCC). ASCC plays an essential role in activating protein 1 (AP-1), serum response factor (SRF), and nuclear factor kappaB (NF-kappaB) transactivation. It acts as a transcriptional coactivator of nuclear receptors and regulates the transrepression between nuclear receptors and either AP-1 or NF-kappaB in vivo. Members in this family all contain a CUE domain. 40 matched cddid_all.tbl CDD cd14365 cd14365 270548 CUE_N4BP2 CUE domain found in NEDD4-binding protein 2 (N4BP2) and similar proteins. N4BP2 has been identified as an oncogene bcl-3 coding protein BCL-3-binding protein (B3BP) that participates in connecting transcriptional activation and genetic recombination of the Ig gene. In addition to BCL-3, it also interacts with p300/CBP histone acetyltransferases. N4BP2 shows intrinsic ATP binding and hydrolyzing activity. It contains an N-terminal ATP-binding region that is responsible for the interaction with BCL-3 and p300/CBP. N4BP2 also functions as a 5'-polynucleotide kinase that can transfer a phosphate group to the 5' end of DNA and RNA substrates. Moreover, N4BP2 contains a C-terminal MutS-related domain that possesses nicking endonuclease activity and may play a role in DNA mismatch repair (MMR). This model corresponds to CUE domain in the N-terminus of N4BP2. 42 matched cddid_all.tbl CDD cd14366 cd14366 270549 CUE_CUED1 CUE domain found in CUE domain-containing protein 1 (CUED1) and similar proteins. The subfamily includes a group of uncharacterized CUE domain-containing protein termed CUED1. Their biological function remains unknown. 42 matched cddid_all.tbl CDD cd14367 cd14367 270550 CUE_CUED2 CUE domain found in CUE domain-containing protein 2 (CUED2) and similar proteins. CUEDC2 is a novel negative regulator of progesterone receptor (PR) and functions to promote the progesterone-induced PR degradation by the ubiquitin-proteasome pathway. It also acts as the regulator of JAK1/STAT3 signaling through inhibiting cytokine-induced phosphorylation of JAK1 and STAT3 and the subsequent STAT3 transcriptional activity. All members in this subfamily contain a CUE domain. 42 matched cddid_all.tbl CDD cd14368 cd14368 270551 CUE_DEF1_like CUE domain found in fungal RNA polymerase II degradation factor 1 (DEF1) and similar proteins. DEF1, also called RRM3-interacting protein 1, is a RNA Polymerase II (RNAPII) degradation factor that may be required to couple arrested RNAPII to the proteasome to facilitate its degradation. It contains a CUE domain that is responsible for the binding of ubiquitin. The family also includes many uncharacterized hypothetical proteins. They show a high level of sequence similarity with DEF1. 41 matched cddid_all.tbl CDD cd14369 cd14369 270552 CUE_VPS9_like CUE domain found in vacuolar protein sorting-associated protein 9 (VPS9) and similar proteins. VPS9, also called vacuolar protein-targeting protein 9, is a cytosolic yeast protein required for localization of vacuolar proteins, such as the soluble vacuolar hydrolases CPY and PrA. It may bind and act as an effector of a rab GTPase and plays a role in vacuolar protein sorting (VPS) pathway. VPS9 contains a region called GBH domain that is related to mammalian Ras-binding proteins, Rin1 and JC265, and may negatively regulate Ras-mediated signaling in yeast Saccharomyces cerevisiae. This model corresponds to the N-terminal CUE domain that interacts specifically with monoubiquitin and regulates intramolecular monoubiquitylation. 42 matched cddid_all.tbl CDD cd14370 cd14370 270553 CUE_DMA CUE-like DMA domain found in the DM domain gene family encodes putative transcription factors DMRTA1, DMRTA2 and DMRTA3. The DM domain proteins are related to the sexual regulators doublesex from Drosophila melanogaster and MAB-3 from Caenorhabditis elegans. Thus, they have been named as doublesex- and mab-3-related transcription factors and may be involved in sexual development or in somite development. All DM domain proteins contain a DM domain which is an unusual zinc finger motif. In addition to an N-terminal DM domain, members in this family, including DMRTA1, DMRTA2 and DMRTA3, also harbor additional CUE-like DMA domain. DMRTA1 is encoded by gene DMRT1, a vertebrate equivalent of the D. melanogaster master sex regulator gene, doublesex. In D. melanogaster, doublesex controls the terminal switch of the pathway leading to sex fate choice. DMRT1 may function as regulator of sex differentiation in vertebrate. Especially, it is required for testis differentiation, but is not involved in the gonadal sex fate choice. DMRTA2, also called Doublesex- and mab-3-related transcription factor 5 (DMRT5), is encoded by gene DMRT2. In the zebrafish, DMRT2 is involved in somite development. DMRTA2 may act as an activator of cyclin-dependent kinase inhibitor 2C (cdkn2c) during spermatogenesis. It may also play significant roles in embryonic neurogenesis. DMRTA3 is encoded by tumor suppressor gene DMRT3 which serves as a novel potential target for homozygous deletion in squamous cell carcinoma of the lung. 40 matched cddid_all.tbl CDD cd14371 cd14371 270554 CUE_CID7_like CUE domain found in CTC-interacting domain proteins CID5, CID6, CID7 and similar proteins. CID7 is encoded by ubiquitously expressed gene CID7. It contains an N-terminal PABC-interacting domain (PAM2 or PABP-interacting motif 2) which is also found in the human Paip1 and Paip2. At this point, it functions as an interaction partner of the PABC domain of Arabidopsis thaliana Poly(A)-binding proteins. It also harbors an ubiquitin-associated (UBA)-like CUE domain and a C-terminal small MutS-related (SMR) domain. CID5 and CID6 are encoded by gene CID5, CID6, respectively. CID5 is only expressed in immature siliques. The biological function of CID5 and CID6 remain unclear. 43 matched cddid_all.tbl CDD cd14372 cd14372 270555 CUE_Cue5p_like CUE domain found in yeast ubiquitin-binding protein CUE5 (Cue5p), donuts protein 1 (DON1p) and similar proteins. Cue5p, also called coupling of ubiquitin conjugation to ER degradation protein 5, is encoded by the open reading frame (ORF) Yor042. It contains a CUE domain which exhibits weak ubiquitin binding properties. Donuts protein 1 (DON1p) is encoded by the ORF YDR273w. It localizes specifically to the prospore membrane and is expressed exclusively during meiosis. DON1p may function as a unique marker to investigate the defects associated with the impaired function of the meiotic plaque in the mpc- mutants. 45 matched cddid_all.tbl CDD cd14373 cd14373 270556 CUE_Cue3p_like CUE domain found in yeast ubiquitin-binding protein CUE3 (Cue3p) and similar proteins. Cue3p, also called coupling of ubiquitin conjugation to ER degradation protein 3, is encoded by the open reading frame (ORF) YGL110C. It is involved in the intramolecular monoubiquitination that serves as a regulatory signal in a variety of cellular processes in yeast. Cue3p contains a CUE domain. 41 matched cddid_all.tbl CDD cd14374 cd14374 270557 CUE1_Cue2p_like CUE1 domain found in yeast ubiquitin-binding protein CUE2 (Cue2p) and similar proteins. Cue2p, also called coupling of ubiquitin conjugation to ER degradation protein 2, is encoded by the open reading frame (ORF) YKL090W. It is involved in the intramolecular monoubiquitination that serves as a regulatory signal in a variety of cellular processes in yeast. Cue2p contains two tandem CUE domains at the N-terminus. Both of them can bind monoubiquitin independently. This model corresponds to the first CUE domain. 42 matched cddid_all.tbl CDD cd14375 cd14375 270558 CUE2_Cue2p_like CUE2 domain found in yeast ubiquitin-binding protein CUE2 (Cue2p) and similar proteins. Cue2p, also called coupling of ubiquitin conjugation to ER degradation protein 2, is encoded by the open reading frame (ORF) YKL090W. It is involved in the intramolecular monoubiquitination that serves as a regulatory signal in a variety of cellular processes in yeast. Cue2p contains two tandem CUE domains at the N-terminus. Both of them can bind monoubiquitin independently. This model corresponds to the second CUE domain. 38 matched cddid_all.tbl CDD cd14376 cd14376 270559 CUE_AUP1_AMFR_like CUE domain found in ancient ubiquitous protein 1 (AUP1), autocrine motility factor receptor (AMFR) and similar proteins. AUP1 is a component of the HRD1-SEL1L endoplasmic reticulum (ER) quality control complex and is essential for US11-mediated dislocation of class I MHC heavy chains. AMFR is an internalizing cell surface glycoprotein that is localized in both plasma membrane caveolae and the ER, and involves in the regulation of cellular adhesion, proliferation, motility and apoptosis, as well as in the process of learning and memory. Cue1p is an N-terminally membrane-anchored endoplasmic reticulum (ER) protein essential for the activity of the two major yeast RING finger ubiquitin ligases (E3s) implicated in ER-associated degradation (ERAD). This family also includes plant E3 ubiquitin protein ligases RIN2, RIN3, and similar proteins. Comparing with other CUE domain-containing proteins, some family members from higher eukaryotes do not bind monoubiquitin efficiently, since they carry LP, rather than FP among CUE domains. 37 matched cddid_all.tbl CDD cd14377 cd14377 270560 UBA1_Rad23 UBA1 domain of Rad23 proteins found in metazoa. The family includes mammalian orthologs of yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe). Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ubiquitinylated proteins and participate in translocating polyubiquitinated proteins to the proteasome. Rad23 proteins carry a ubiquitin-like (UBL) and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. UBL domain is responsible for the binding to proteasome. UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates which suggests Rad23 proteins might be involved in certain pathways of ubiquitin metabolism. Both UBL domain and XPC-binding domain are necessary for efficient NER function of Rad23 proteins. This model corresponds to the UBA1 domain. 40 matched cddid_all.tbl CDD cd14378 cd14378 270561 UBA1_Rhp23p_like UBA1 domain of Schizosaccharomyces pombe UV excision repair protein Rhp23p and its homologs. The subfamily contains several fungal multi-ubiquitin receptors, including Schizosaccharomyces pombe Rhp23p and Saccharomyces cerevisiae Rad23p, both of which are orthologs of human HR23A. They play roles in nucleotide excision repair (NER) and in cell cycle regulation. They also function as shuttle proteins transporting ubiquitinated substrates destined for degradation from the E3 ligase to the 26S proteasome. For instance, S. pombe Rhp23p forms a complex with Rhp41p to recognize photolesions and help initiate DNA repair, and it also protects ubiquitin chains against disassembly by deubiquitinating enzymes. Like human HR23A, members in this subfamily interact with the proteasome through their N-terminal ubiquitin-like domain (UBL), and with ubiquitin (Ub), or multi-ubiquitinated substrates, through their two ubiquitin-associated domains (UBA), termed internal UBA1 and C-terminal UBA2. In addition, they contain a xeroderma pigmentosum group C (XPC) protein-binding domain that might be necessary for its efficient NER function. This model corresponds to the UBA1 domain. 47 matched cddid_all.tbl CDD cd14379 cd14379 270562 UBA1_Rad23_plant UBA1 domain of putative DNA repair proteins Rad23 found in plant. The radiation sensitive 23 (Rad23) subfamily consists of four isoforms of putative DNA repair proteins from Arabidopsis thaliana and similar proteins from other plants. The nuclear-enriched Rad23 proteins function in the cell cycle, morphology, and fertility of plants through their delivery of ubiquitin (Ub)/26S proteasome system (UPS) substrates to the 26S proteasome. Rad23 proteins contain an N-terminal ubiquitin-like (UBL) domain that associates with the 26S proteasome Ub receptor RPN10, and two C-terminal ubiquitin-associated (UBA) domains that bind Ub conjugates. This model corresponds to the UBA1 domain. 50 matched cddid_all.tbl CDD cd14380 cd14380 270563 UBA2_Rad23 UBA2 domain of Rad23 proteins found in metazoa. The family includes mammalian orthologs of yeast nucleotide excision repair (NER) proteins, Rad23p (in Saccharomyces cerevisiae) and Rhp23p (in Schizosaccharomyces pombe). Rad23 proteins play dual roles in DNA repair as well as in proteosomal degradation. They have affinity for both the proteasome and ubiquitinylated proteins and participate in translocating polyubiquitinated proteins to the proteasome. Rad23 proteins carry a ubiquitin-like (UBL) and two ubiquitin-associated (UBA) domains, as well as a xeroderma pigmentosum group C (XPC) protein-binding domain. UBL domain is responsible for the binding to proteasome. UBA domains are important for binding of ubiquitin (Ub) or multi-ubiquitinated substrates which suggests Rad23 proteins might be involved in certain pathways of ubiquitin metabolism. Both UBL domain and XPC-binding domain are necessary for efficient NER function of Rad23 proteins. This model corresponds to the UBA2 domain. 39 matched cddid_all.tbl CDD cd14381 cd14381 270564 UBA2_Rhp23p_like UBA2 domain of Schizosaccharomyces pombe UV excision repair protein Rhp23p and its fungal homologs. The subfamily contains several fungal multiubiquitin receptors, including Schizosaccharomyces pombe Rhp23p and Saccharomyces cerevisiae Rad23p, both of which are orthologs of human HR23A. They play roles in nucleotide excision repair (NER) and in cell cycle regulation. They also function as shuttle proteins transporting ubiquitinated substrates destined for degradation from the E3 ligase to the 26S proteasome. For instance, S. pombe Rhp23p forms a complex with Rhp41p to recognize photolesions and help initiate DNA repair, and it also protects ubiquitin chains against disassembly by deubiquitinating enzymes. Like human HR23A, members in this subfamily interact with the proteasome through their N-terminal ubiquitin-like domain (UBL), and with ubiquitin (Ub), or multi-ubiquitinated substrates, through their two ubiquitin-associated domains (UBA), termed internal UBA1 and C-terminal UBA2. In addition, they contain a xeroderma pigmentosum group C (XPC) protein-binding domain that might be necessary for its efficient NER function. This model corresponds to the UBA2 domain. 40 matched cddid_all.tbl CDD cd14382 cd14382 270565 UBA2_RAD23_plant UBA2 domain of putative DNA repair proteins RAD23 found in plant. The radiation sensitive 23 (RAD23) subfamily consists of four isoforms of putative DNA repair proteins from Arabidopsis thaliana and similar proteins from other plants. The nuclear-enriched RAD23 proteins function in the cell cycle, morphology, and fertility of plants through their delivery of ubiquitin (Ub)/26S proteasome system (UPS) substrates to the 26S proteasome. RAD23 proteins contain an N-terminal ubiquitin-like (UBL) domain that associates with the 26S proteasome Ub receptor RPN10, and two C-terminal ubiquitin-associated (UBA) domains that bind Ub conjugates. This model corresponds to the UBA2 domain. 43 matched cddid_all.tbl CDD cd14383 cd14383 270566 UBA1_UBP5 UBA1 domain found in ubiquitin carboxyl-terminal hydrolase 5 (UBP5). UBP5, also called deubiquitinating enzyme 5, Isopeptidase T (IsoT), ubiquitin thioesterase 5, or ubiquitin-specific-processing protease 5, is a deubiquitinating enzyme largely responsible for the disassembly of the majority of unanchored polyubiquitin in the cell. Zinc is required for its catalytic activity. UBP5 contains four ubiquitin (Ub)-binding sites including an N-terminal zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. ZnF domain binds the proximal ubiquitin. UBP domain forms the active site. UBA domains are involved in binding linear or K48-linked polyubiquitin. This model corresponds to the UBA1 domain. 49 matched cddid_all.tbl CDD cd14384 cd14384 270567 UBA1_UBP13 UBA1 domain found in ubiquitin carboxyl-terminal hydrolase 13 (UBP13). UBP13, also called deubiquitinating enzyme 13, Isopeptidase T-3 (isoT3), ubiquitin thioesterase 13, or ubiquitin-specific-processing protease 13, is an ortholog of UBP5 implicated in catalyzing hydrolysis of various ubiquitin (Ub)-chains. It contains a zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. Due to the non-activating catalysis for K63-polyubiquitin chains, UBP13 may function differently from USP5 in cellular deubiquitination processes. Moreover, the zinc finger (ZnF) domain of USP13 cannot bind to Ub. Its tandem UBA domains can bind with different types of diUb but preferentially with K63-linked.USP13 can also regulate the protein level of CD3delta in cells via its UBA domains. This model corresponds to the UBA1 domain. 49 matched cddid_all.tbl CDD cd14385 cd14385 270568 UBA1_spUBP14_like UBA1 domain found in Schizosaccharomyces pombe ubiquitin carboxyl-terminal hydrolase 14 (spUBP14) and similar proteins. spUBP14, also called deubiquitinating enzyme 14, UBA domain-containing protein 2, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, functions as a deubiquitinating enzyme that is involved in protein degradation in fission yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA1 domain. 47 matched cddid_all.tbl CDD cd14386 cd14386 270569 UBA2_UBP5 UBA2 domain found in ubiquitin carboxyl-terminal hydrolase 5 (UBP5). UBP5, also called deubiquitinating enzyme 5, Isopeptidase T (IsoT), ubiquitin thioesterase 5, or ubiquitin-specific-processing protease 5, is a deubiquitinating enzyme largely responsible for the disassembly of the majority of unanchored polyubiquitin in the cell. Zinc is required for its catalytic activity. UBP5 contains four ubiquitin (Ub)-binding sites including an N-terminal zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. ZnF domain binds the proximal ubiquitin. UBP domain forms the active site. UBA domains are involved in binding linear or K48-linked polyubiquitin. This model corresponds to the UBA2 domain. 43 matched cddid_all.tbl CDD cd14387 cd14387 270570 UBA2_UBP13 UBA2 domain found in ubiquitin carboxyl-terminal hydrolase 13 (UBP13). UBP13, also called deubiquitinating enzyme 13, Isopeptidase T-3 (isoT3), ubiquitin thioesterase 13, or ubiquitin-specific-processing protease 13 is an ortholog of UBP5 implicated in catalyzing hydrolysis of various ubiquitin (Ub)-chains. It contains a zinc finger (ZnF) domain, a catalytic ubiquitin-specific processing protease (UBP) domain (catalytic C-box and H-box), and two ubiquitin-associated (UBA) domains. Due to the non-activating catalysis for K63-polyubiquitin chains, UBP13 may function differently from USP5 in cellular deubiquitination processes. Moreover, the zinc finger (ZnF) domain of USP13 cannot bind to Ub. Its tandem UBA domains can bind with different types of diUb but preferentially with K63-linked.USP13 can also regulate the protein level of CD3delta in cells via its UBA domains. This model corresponds to the UBA2 domain. 35 matched cddid_all.tbl CDD cd14388 cd14388 270571 UBA2_atUBP14 UBA2 domain found in Arabidopsis thaliana ubiquitin carboxyl-terminal hydrolase 14 (atUBP14) and similar proteins. atUBP14, also called deubiquitinating enzyme 14, TITAN-6 protein, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, is related to the isopeptidase T class of deubiquitinating enzymes that recycle polyubiquitin chains following protein degradation. atUBP14 is essential for early plant development. It can disassemble multi-ubiquitin chains linked internally via epsilon-amino isopeptide bonds using Lys48 and can process some, but not all, translational fusions of ubiquitin linked via alpha-amino peptide bonds. atUBP14 contains two ubiquitin-association (UBA) domains. This model corresponds to the UBA2 domain which show a high level of sequence similarity with mammalian ubiquitin-associated and SH3 domain-containing protein A (UBS3A). 38 matched cddid_all.tbl CDD cd14389 cd14389 270572 UBA_AAA_plant UBA domain found in plant AAA-type ATPase-like proteins. This family includes some uncharacterized AAA-type ATPase-like proteins found in plant. The AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. Members in this family contains an N-terminal ubiquitin-association (UBA) domain, a AAA-type ATPase domain and a C-terminal MgsA AAA+ ATPase domain. This model corresponds to the UBA domain which show a high level of sequence similarity with mammalian ubiquitin-associated and SH3 domain-containing protein A (UBS3A). 37 matched cddid_all.tbl CDD cd14390 cd14390 270573 UBA_II_E2_UBE2K UBA domain of vertebrate ubiquitin-conjugating enzyme E2 K (UBE2K). UBE2K, also called Huntingtin-interacting protein 2 (HIP-2), ubiquitin carrier protein, ubiquitin-conjugating enzyme E2-25 kDa (E2-25K), or ubiquitin-protein ligase is a multi-ubiquitinating enzyme with the ability to synthesize Lys48-linked polyubiquitin chains which is involved in the ubiquitin (Ub)-dependent proteolytic pathway. It interacts with the frameshift mutant of ubiquitin B and functions as a crucial factor regulating amyloid-beta neurotoxicity. It has also been characterized as Huntingtin-interacting protein that modulates the neurotoxicity of Amyloid-beta (Abeta), the principal protein involved in Alzheimer's disease pathogenesis. Moreover, E2-25K increases aggregate the formation of expanded polyglutamine proteins and polyglutamine-induced cell death in the pathology of polyglutamine diseases. UBE2K and its yeast homolog UBC1 are unique class II E2 conjugating enzymes, both of which contain a C-terminal ubiquitin-associated (UBA) domain in addition to an N-terminal catalytic ubiquitin-conjugating enzyme E2 (UBCc) domain. 38 matched cddid_all.tbl CDD cd14391 cd14391 270574 UBA_II_E2_UBCD4 UBA domain found in Drosophila melanogaster ubiquitin-conjugating enzyme E2-22 kDa (UbcD4) and similar proteins. UbcD4, also called ubiquitin carrier protein or ubiquitin-protein ligase, is a class II E2 ubiquitin-conjugating enzyme encoded by Drosophila E2 gene which is only expressed in pole cells in embryos. It is a putative E2 enzyme homologous to the Huntingtin interacting protein-2 (HIP2) of human. UbcD4 specifically interacts with the polyubiquitin-binding subunit of the proteasome. It contains a C-terminal ubiquitin-associated (UBA) domain in addition to an N-terminal catalytic ubiquitin-conjugating enzyme E2 (UBCc) domain. 36 matched cddid_all.tbl CDD cd14392 cd14392 270575 UBA_Cbl-b UBA domain found in E3 ubiquitin-protein ligase Cbl-b and similar proteins. Cbl-b, also called casitas B-lineage lymphoma proto-oncogene b, RING finger protein 56, SH3-binding protein Cbl-b, or signal transduction protein Cbl-b, has been identified as a regulator of antigen-specific, T cell-intrinsic, peripheral immune tolerance (a state also called clonal anergy). It may inhibit activation of the p85 subunit of phosphoinositide 3-kinase (PI3K), protein kinase C-theta (PKC-theta), and phospholipase C-gamma1 (PLC-gamma1) and negatively regulates T-cell receptor-induced transcription factor nuclear factor-kappaB (NF-kappaB) activation. In addition, Cbl-b may target multiple signaling molecules involved in transforming growth factor (TGF)-beta-mediated transactivation pathways. Cbl-b contains a proline rich domain, a nuclear localization signal, a C3HC4 zinc finger and a ubiquitin-associated (UBA) domain. 41 matched cddid_all.tbl CDD cd14393 cd14393 270576 UBA_c-Cbl UBA domain found in E3 ubiquitin-protein ligase Cbl and similar proteins. Cbl, also called casitas B-lineage lymphoma proto-oncogene, proto-oncogene c-Cbl, RING finger protein 55, or signal transduction protein Cbl, is a multi-domain protein that acts as a key negative regulator of various receptor and non-receptor tyrosine kinases signaling. It contains a tyrosine kinase-binding domain (TKB), a proline-rich domain, a RING domain, and a ubiquitin-associated (UBA) domain. The TKB is responsible for the interactions with many tyrosine kinases, such as the colony-stimulating factor-1 (CSF-1) receptor, Syk/ZAP-70 and Src-family of protein tyrosine kinases. The proline-rich domain can recruit proteins with SH3 domain. Moreover, Cbl functions as an E3 ubiquitin ligase that can bind ubiquitin-conjugating enzymes (E2s) through RING domain. 40 matched cddid_all.tbl CDD cd14394 cd14394 270577 UBA_BIRC2_3 UBA domain found in baculoviral IAP repeat-containing protein BIRC2, BIRC3 and similar proteins. The subfamily includes cellular inhibitor of apoptosis protein 1 (c-IAP1) and c-IAP2. c-IAPs function as ubiquitin E3 ligases that mediate the ubiquitination of the substrates involved in apoptosis, nuclear factor-kappaB (NF-kappaB)signaling, and oncogenesis. Unlike other apoptosis proteins (IAPs), such as XIAP, c-IAPs exhibit minimal binding to caspases and may not play an important role in the inhibition of these proteases. c-IAP1, also called baculoviral IAP repeat-containing protein BIRC2, IAP-2, RING finger protein 48, or TNFR2-TRAF-signaling complex protein 2, is a potent regulator of the tumor necrosis factor (TNF) receptor family and NF-kappaB signaling pathways in the cytoplasm. It can also regulate E2F1 transcription factor-mediated control of cyclin transcription in the nucleus. c-IAP2, also called BIRC3, IAP-1, apoptosis inhibitor 2 (API2), or IAP homolog C, also influences ubiquitin-dependent pathways that modulate innate immune signalling by activation of NF-kappaB. c-IAPs contain three N-terminal baculoviral IAP repeat (BIR) domains that enable interactions with proteins, a ubiquitin-association (UBA) domain that is responsible for the binding of binds polyubiquitin (polyUb), a caspase activation and recruitment domain (CARD) that serves as a protein interaction surface, and a RING domain at the carboxyl terminus that is required for ubiquitin ligase activity. 50 matched cddid_all.tbl CDD cd14395 cd14395 270578 UBA_BIRC4_8 UBA domain found in E3 ubiquitin-protein ligase XIAP, baculoviral IAP repeat-containing protein 8 (BIRC8) and similar proteins. XIAP, also called baculoviral IAP repeat-containing protein 4 (BIRC4), IAP-like protein (ILP), inhibitor of apoptosis protein 3 (IAP-3), or X-linked inhibitor of apoptosis protein (X-linked IAP), is a potent suppressor of apoptosis that directly inhibits specific members of the caspase family of cysteine proteases, including caspase-3, -7, and -9. It promotes proteasomal degradation of caspase-3 and enhances its anti-apoptotic effect in Fas-induced cell death. The ubiquitin-protein ligase (E3) activity of XIAP also exhibits in the ubiquitination of second mitochondria-derived activator of caspases (Smac). The mitochondrial proteins, Smac/DIABLO and Omi/HtrA2, can inhibit the antiapoptotic activity of XIAP. XIAP has also been implicated in several intracellular signaling cascades involved in the cellular response to stress, such as the c-Jun N-terminal kinase (JNK) pathway, the nuclear factor-kappaB (NF-kappaB) pathway, and the transforming growth factor-beta (TGF-beta) pathway. Moreover, XIAP can regulate copper homeostasis through interacting with MURR1. BIRC8, also called inhibitor of apoptosis-like protein 2 (IAP-like protein 2 or ILP-2), or testis-specific inhibitor of apoptosis, is a tissue-specific homolog of E3 ubiquitin-protein ligase XIAP. It has been implicated in the control of apoptosis in the testis by direct inhibition of caspase 9. Both XIAP and BIRC8 contain three N-terminal baculoviral IAP repeat (BIR) domains, a ubiquitin-association (UBA) domain and a RING domain at the carboxyl terminus. 50 matched cddid_all.tbl CDD cd14396 cd14396 270579 UBA_XtBIRC7_like UBA domain found in Xenopus tropicalis baculoviral IAP repeat-containing protein BIRC7, BIRC71A and similar proteins. X. tropicalis BIRC7, also called E3 ubiquitin-protein ligase EIAP, embryonic/Egg IAP (xEIAP/XLX), inhibitor of apoptosis (IAP)-like protein, XIAP homolog XLX, is a weak apoptosis inhibitor that exhibits caspase inhibition and autoubiquitylation. It is uniquely modified by MAPK- and Cdc2/Cyclin B-dependent phosphorylation during oocyte maturation. Its caspase-dependent cleavage is altered when it is phosphorylated. X. tropicalis BIRC7 contains two N-terminal baculoviral IAP repeats (BIRs) and a C-terminal RING domain. Based on sequence homology, it also harbors a ubiquitin-associated (UBA) domain which is not detected in human BIRC7. 44 matched cddid_all.tbl CDD cd14397 cd14397 270580 UBA_LATS1 UBA domain found in vertebrate serine/threonine-protein kinase LATS1. LATS1, also called large tumor suppressor homolog 1 or WARTS protein kinase (warts), is a serine/threonine-protein kinase that highly conserved from fly to human. It plays a crucial role in the prevention of tumor formation by controlling mitosis progression. Human LATS1 is the mammalian homologs of Drosophila lats/warts gene that could suppress tumor growth and rescue all developmental defects in flies, including embryonic lethality. It forms a regulatory complex with zyxin, a regulator of actin filament assembly. The LATS1/zyxin complex plays a role in controlling mitosis progression on mitotic apparatus. LATS1 is phosphorylated in a cell-cycle-dependent manner and complexes with CDC2 in early mitosis. It can negatively modulates tumor cell growth by inducing G(2)/M cell cycle transition or apoptosis. It also functions as a mitotic exit network kinase interacting with MOB1A, a protein whose homolog in budding yeast associates with kinases involved in mitotic exit. Moreover, LATS1 acts as a novel cytoskeleton regulator that affects cytokinesis by regulating actin polymerization through inhibiting LIMK1. LATS1 can also inhibit transcription regulation and transformation functions of oncogene YAP by inhibiting its nuclear translocation through phosphorylation. In addition, LATS1 can regulate the transcriptional activity of forkhead L2 (FOXL2) via phosphorylation. It also acts as an acting-binding protein that can negatively regulate the actin polymerization. LATS1 contains an N-terminal ubiquitin-associated (UBA) domain and a C-terminal protein kinase domain. 41 matched cddid_all.tbl CDD cd14398 cd14398 270581 UBA_LATS2 UBA domain found in vertebrate serine/threonine-protein kinase LATS2. LATS2, also called kinase phosphorylated during mitosis protein, or large tumor suppressor homolog 2, or serine/threonine-protein kinase KPM, or Warts-like kinase, is a novel mammalian homolog of the Drosophila tumor suppressor gene lats/warts. It inhibits the G1/S transition and is essential for embryonic development, proliferation control, and genomic integrity. LATS2 is a serine/threonine kinase that negatively regulates CyclinE/CDK2 and plays a role in tumor suppression. It also acts as the negative regulator of androgen receptor (AR) through inhibiting androgen-regulated gene expression and thus plays an important role in AR -regulated transcription and in the development of prostate cancer. Moreover, LATS2 induces apoptosis via down-regulation of anti-apoptotic proteins, BCL-2 and BCL-x(L), in human lung cancer cells. It is a centrosomal protein and forms a complex with Ajuba, a LIM protein, to regulate organization of the spindle apparatus through recruitment of gamma-tubulin to the centrosome during mitosis. Furthermore, LATS2 interacts with Mdm2 to inhibit p53 ubiquitination and promote p53 activation. It stabilizes the cellular protein level of Snail1, a central regulator of epithelial cell adhesion and movement in epithelial-to-mesenchymal transitions (EMTs) during embryo development, and enhances its EMT activity. LATS2 contains an N-terminal ubiquitin-associated (UBA) domain and a C-terminal protein kinase domain. 41 matched cddid_all.tbl CDD cd14399 cd14399 270582 UBA_PLICs UBA domain of eukaryotic protein linking integrin-associated protein (IAP, also known as CD47) with cytoskeleton (PLIC) proteins. The PLIC proteins (or ubiquilins) family contains human homologs of the yeast ubiquitin-like Dsk2 protein, PLIC-1 (also called ubiquilin-1), PLIC-2 (also called ubiquilin-2 or Chap1), PLIC-3 (also called ubiquilin-3) and PLIC-4 (also called ubiquilin-4, Ataxin-1 interacting ubiquitin-like protein, A1Up, Connexin43-interacting protein of 75 kDa, or CIP75), and mouse PLIC proteins. They are ubiquitin-binding adaptor proteins involved in all protein degradation pathways through delivering ubiquitinated substrates to proteasomes. They also promote autophagy-dependent cell survival during nutrient starvation. PLIC-1 regulates the function of the thrombospondin receptor CD47 and G protein signaling. It plays a role in TLR4-mediated signaling through interacting with the Toll/interleukin-1 receptor (TIR) domain of TLR4. It also inhibits the TLR3-Trif antiviral pathway by reducing the abundance of Trif. Moreover, PLIC-1 binds to gamma-aminobutyric acid receptors (GABAARs) and modulates the ubiquitin-dependent, proteasomal degradation of GABAARs. Furthermore, PLIC-1 acts as a molecular chaperone regulating amyloid precursor protein (APP) biosynthesis, trafficking, and degradation by stimulating K63-linked polyubiquitination of lysine 688 in the APP intracellular domain. In addition, PLIC-1 is involved in the protein aggregation-stress pathway via associating with the ubiquitin-interacting motif (UIM) proteins ataxin 3, HSJ1a, and epidermal growth factor substrate 15 (EPS15). PLIC-2 is a protein that binds the ATPase domain of the HSP70-like Stch protein. It functions as a negative regulator of G protein-coupled receptor (GPCR) endocytosis. It also involved in amyotrophic lateral sclerosis (ALS)-related dementia. PLIC-3 is encoded by UBQLN3, a testis-specific gene. It shows high sequence similarity with the Xenopus protein XDRP1, a nuclear phosphoprotein that binds to the N-terminus of cyclin A and inhibits Ca2+-induced degradation of cyclin A, but not cyclin B. PLIC-4 is a ubiquitin-like nuclear protein that interacts with ataxin-1 and further links ataxin-1 with the chaperone and ubiquitin-proteasome pathways. It also binds to the non-ubiquitinated gap junction protein connexin43 (Cx43) and regulates the turnover of Cx43 through the proteasomal pathway. PLIC proteins contain an N-terminal ubiquitin-like (UBL) domain that is responsible for the binding of ubiquitin-interacting motifs (UIMs) expressed by proteasomes and endocytic adaptors, and C-terminal ubiquitin-associated (UBA) domain that interacts with ubiquitin chains present on proteins destined for proteasomal degradation. In addition, mammalian PLIC2 proteins have an extra collagen-like motif region which is absent in other PLIC proteins and the yeast Dsk2 protein. 40 matched cddid_all.tbl CDD cd14400 cd14400 270583 UBA_Gts1p_like UBA domain found in Saccharomyces cerevisiae protein GTS1 (Gts1p) and similar proteins. Gts1p, also called protein LSR1, is encoded by a pleiotropic gene GTS1 in budding yeast. The formation of Gts1p-mediated protein aggregates may induce reactive oxygen species (ROS) production and apoptosis. Gts1p also plays an important role in the regulation of heat and other stress responses under glucose-limited or -depleted conditions in either batch or continuous culture. Gts1p contains an N-terminal zinc finger motif similar to that of GATA-transcription factors, a ubiquitin-associated (UBA) domain and a C-terminal glutamine-rich strand. The zinc finger is responsible for the binding to the glycolytic enzyme glyceraldehydes-3-phosphate dehydrogenase (GAPDH) which is required for the maintenance of the metabolic oscillations of budding yeast. The polyglutamine sequence is indispensable for the pleiotropy and nuclear localization of Gts1p. It is essential for the transcriptional activation, whereas Gts1p lacks DNA binding activity. 39 matched cddid_all.tbl CDD cd14401 cd14401 270584 UBA_HERC1 UBA domain found in probable E3 ubiquitin-protein ligase HERC1 and similar proteins. HERC1, also called HECT domain and RCC1-like domain-containing protein 1, or p532, or p619, is an ubiquitously expressed multi-domain protein involved in ubiquitin-dependent intracellular membrane trafficking through its interaction with vesicle coat proteins such as clathrin and ARF. Moreover, it has been identified as a tuberous sclerosis complex TSC2-interacting protein that may play a role in TSC-mTOR (mammalian target of rapamycin) pathway. In addition to a ubiquitin-association (UBA) domain, HERC1 contains more than one RCC1-like domains (RLDs) and a C-terminal HECT E3 ubiquitin ligase domain. At this point, it may function as both E3 ubiquitin ligases and guanine nucleotide exchange factors (GEFs). 44 matched cddid_all.tbl CDD cd14402 cd14402 270585 UBA_HERC2 UBA domain found in probable E3 ubiquitin-protein ligase HERC2 and similar proteins. HERC2, also called HECT domain and RCC1-like domain-containing protein 2, is a SUMO-regulated E3 ubiquitin ligase that plays an important role in the SUMO-dependent pathway which orchestrates the DNA double-strand break (DSB) response. Moreover, HERC2 functions as a RNF8 auxiliary factor that regulates ubiquitin-dependent retention of repair proteins on damaged chromosomes. In addition to a ubiquitin-association (UBA) domain, HERC2 contains more than one RCC1-like domains (RLDs) and a C-terminal HECT E3 ubiquitin ligase domain. 45 matched cddid_all.tbl CDD cd14403 cd14403 270586 UBA_AID_AAPK1 UBA-like autoinhibitory domain (AID) found in vertebrate 5'-AMP-activated protein kinase catalytic subunit alpha-1 (AMPKalpha-1). AMPKalpha-1, also called acetyl-CoA carboxylase kinase (ACACA kinase), hydroxymethylglutaryl-CoA reductase kinase (HMGCR kinase), or Tau-protein kinase PRKAA1, is one of the catalytic subunits of adenosine monophosphate (AMP)-activated protein kinase (AMPK). It has been implicated in a number of important cellular processes. For instance, it functions as a glucose sensor controlling CD8 T-cell memory, as well as a new kinase for RhoA and a new mediator of the vasoprotective effects of estrogen. It also plays a significant role in cervical malignant growth, in regulating oxidative stress and life span in erythrocytes, in modulating the antioxidant status of vascular endothelial cells, in limiting skeletal muscle overgrowth during hypertrophy through inhibition of the mammalian target of rapamycin (mTOR)-signaling pathway. AMPKalpha-1 has an N-terminal Ser/Thr kinase domain followed by an ubiquitin-associated (UBA)-like AID and a C-terminal AMPK regulatory domain. The Ser/Thr kinase domain contains a conserved Thr residue that must be phosphorylated for activity in the activation loop. The AID is responsible for AMPKalpha subunit autoinhibition. The C-terminal regulatory domain of the alpha1-subunit is essential for binding the beta1- and gamma1-subunits. 65 matched cddid_all.tbl CDD cd14404 cd14404 270587 UBA_AID_AAPK2 UBA-like autoinhibitory domain (AID) found in vertebrate 5'-AMP-activated protein kinase catalytic subunit alpha-2 (AMPKalpha-2). AMPKalpha-2, also called acetyl-CoA carboxylase kinase (ACACA kinase) or hydroxymethylglutaryl-CoA reductase kinase (HMGCR kinase), is one of the catalytic subunits of adenosine monophosphate (AMP)-activated protein kinase (AMPK). It shows a wide expression pattern and is highly expressed in skeletal muscle, heart, and liver. It may be involved in the regulation of glucose and lipid metabolism and protein synthesis in peripheral tissues, as well as in regulation of energy intake and body weight. AMPKalpha-2 has an N-terminal Ser/Thr kinase domain followed by an ubiquitin-associated (UBA)-like AID, and a C-terminal AMPK regulatory domain. The Ser/Thr kinase domain contains a conserved Thr residue that must be phosphorylated for activity in the activation loop. The AID is responsible for AMPKalpha subunit autoinhibition. The C-terminal regulatory domain is essential for binding the beta- and gamma-subunits. 65 matched cddid_all.tbl CDD cd14405 cd14405 270588 UBA_MARK1 UBA domain found in serine/threonine-protein kinase MARK1 and similar proteins. MARK1, also called MAP/microtubule affinity-regulating kinase 1 or PAR1 homolog c (Par-1c), is a kinase-regulating microtubule-dependent transport in axons and dendrites. It is involved in the specification of neuronal polarity, in axon-dendrite specification, and in the synaptic plasticity in adult neurons. It has been implicated in Alzheimer's disease, cancer, and autism. 41 matched cddid_all.tbl CDD cd14406 cd14406 270589 UBA_MARK2 UBA domain found in serine/threonine-protein kinase MARK2 and similar proteins. MARK2, also called ELKL motif kinase 1 (EMK-1), MAP/microtubule affinity-regulating kinase 2, PAR1 homolog, or PAR1 homolog b (Par-1b), is enriched in brain. It belongs to the AMPK family of Ser/Thr kinases. MARK2 has been implicated in regulating fertility, immune homeostasis, learning, and memory as well as adiposity, insulin hypersensitivity, and glucose metabolism. The activity of MARK2 is necessary for the outgrowth of cell processes, neurites, and dendritic spines. It is a TORC2 (also known as Crtc2) Ser-275 kinase that blocks TORC2-induced cAMP response element binding protein (CREB) activity. It regulates axon formation via phosphorylation of a kinesin-like motor protein GAKIN/KIF13B. It also acts as a positive regulator of Wnt-beta-catenin signaling. 42 matched cddid_all.tbl CDD cd14407 cd14407 270590 UBA_MARK3_4 UBA domain found in MAP/microtubule affinity-regulating kinase MARK3, MARK4, and similar proteins. MARK3, also called C-TAK1, Cdc25C-associated protein kinase 1, ELKL motif kinase 2 (EMK-2), protein kinase STK10, Ser/Thr protein kinase PAR-1 (Par-1a), or serine/threonine-protein kinase p78, is a known regulator of KSR1, a molecular scaffold of the Raf/MEK/ERK MAP kinase cascade that regulates the intensity and duration of ERK activation. It binds plakophilin 2 (PKP2), phosphorylates human Cdc25C on serine 216, and promotes 14-3-3 protein binding and protein localization. It also interacts with microphthalmia-associated transcription factor, Mitf which is necessary for regulating genes involved in osteoclast differentiation. Moreover, MARK3 is involved in regulating localization and activity of class IIa histone deacetylases. The lack of MARK3 leads to reduced adiposity, resistance to hepatic steatosis, and defective gluconeogenesis. MARK4, also called MAP/microtubule affinity-regulating kinase-like 1 (MARKL1), or Par-1d, is a member of the AMP-activated protein kinase (AMPK)-related family of kinases. It plays a key role in energy metabolism and may act as a novel drug target for the treatment of obesity and type 2 diabetes. MARK4 also functions as the substrate of ubiquitin specific protease-9 (USP9X) and can be regulated by unusual Lys(29)/Lys(33)-linked polyubiquitin chains. Furthermore, MARK4 may play some role in hepatocellular carcinogenesis. 43 matched cddid_all.tbl CDD cd14408 cd14408 270591 UBA_SIK1 UBA domain found in salt-inducible kinase 1 (SIK1). SIK1, also called serine/threonine-protein kinase SNF1-like kinase 1 (SNF1LK), is a serine/threonine kinase abundant in adrenal glands. It belongs to the AMP-activated protein kinases (AMPK) family involved in the regulation of metabolism during energy stress. SIK1 is required for myogenic differentiation. It is degraded by the proteasome in myoblasts which is regulated by cAMP signaling. Moreover, SIK1 acts as a class II histone deacetylase (HDAC) kinase, triggering the cytoplasmic export of the HDACs and activation of myocyte enhancer factor 2 (MEF2)-dependent transcription. It also regulates transcription through inhibitory phosphorylation of a family of cAMP responsive element binding protein (CREB) coactivators, called TORCs/CRTCs. In addition, SIK1 links LKB1 to p53-dependent anoikis and suppresses metastasis. It is also involved in a cell sodium-sensing network that regulates active sodium transport through a calcium-dependent process. SIK1 contains an N-terminal protein kinase catalytic domain followed by an ubiquitin-associated (UBA) domain and a putative PEST domain. 50 matched cddid_all.tbl CDD cd14409 cd14409 270592 UBA_SIK2 UBA domain found in salt-inducible kinase 2 (SIK2). SIK2, also called Qin-induced kinase or serine/threonine-protein kinase SNF1-like kinase 2 (SNF1LK2), is a serine/threonine kinase highly expressed in adipocytes. It belongs to the AMP-activated protein kinases (AMPK) family involved in the regulation of metabolism during energy stress. It plays an important role in the insulin-signaling pathway during adipocyte differentiation, as well as in autophagy progression. Moreover, SIK2 plays a critical role in neuronal survival and modulates cAMP responsive element binding protein (CREB)-mediated gene expression in response to hormones and nutrients. SIK2 acts as a critical determinant in autophagy progression. In addition, SIK2 localizes at the centrosome and functions as a centrosome kinase required for bipolar mitotic spindle formation. It is involved in the initiation of mitosis, and regulates the localization of the centrosome linker protein, C-Nap1, through S2392 phosphorylation. SIK2 contains an N-terminal protein kinase catalytic domain followed by an ubiquitin-associated (UBA) domain. 45 matched cddid_all.tbl CDD cd14410 cd14410 270593 UBA_SIK3 UBA domain found in salt-inducible kinase 3 (SIK3). SIK3, also called salt-inducible kinase 3 or serine/threonine-protein kinase QSK, is a serine/threonine kinase ubiquitously expressed. It belongs to the AMP-activated protein kinases (AMPK) family involved in the regulation of metabolism during energy stress. It acts as a novel energy regulator that modulates cholesterol and bile acid metabolism by coupling with retinoid metabolism. It also play an essential role in facilitating chondrocyte hypertrophy during skeletogenesis and growth plate maintenance. SIK3 contains an N-terminal protein kinase catalytic domain followed by an ubiquitin-associated (UBA) domain. 45 matched cddid_all.tbl CDD cd14411 cd14411 270594 UBA_DCNL1 UBA-like domain found in DCN1-like protein 1 (DCNL1) and similar proteins. DCNL1 (defective in cullin neddylation protein 1-like protein 1), also called DCUN1 domain-containing protein 1, is encoded by squamous cell carcinoma-related oncogene SCCRO (DCUN1D1). It interacts with known cullin isoforms as well as ROC1, Ubc12 and CAND1, the components of the neddylation pathway. It plays an essential role in the neddylation E3 complex and participates in the release of inhibitory effects of CAND1 on cullin-RING ligase E3 complex assembly and activity. DCNL1 contains an N-terminal ubiquitin-associated (UBA)-like domain and a C-terminal cullin binding domain that binds to cullins and Rbx-1, components of an E3 ubiquitin ligase complex for neddylation. 51 matched cddid_all.tbl CDD cd14412 cd14412 270595 UBA_DCNL2 UBA-like domain found in DCN1-like protein 2 (DCNL2) and similar proteins. DCNL2 (defective in cullin neddylation protein 1-like protein 2), also called DCUN1 domain-containing protein 2, is encoded by gene DCUN1D2. Although its biological function remains unclear, DCNL2 shows high sequence similarity with DCNL1, a protein that plays an essential role in the neddylation E3 complex and participates in the release of inhibitory effects of CAND1 on cullin-RING ligase E3 complex assembly and activity. At this point, DCNL2 may also contribute to neddylation of cullin components of SCF-type E3 ubiquitin ligase complexes. Like DCNL1, DCNL2 contains an N-terminal ubiquitin-associated (UBA)-like domain and a C-terminal cullin binding domain that is responsible for the binding to cullins and Rbx-1, components of an E3 ubiquitin ligase complex for neddylation. 47 matched cddid_all.tbl CDD cd14413 cd14413 270596 UBA_FAF1 UBA-like domain found in FAS-associated factor 1 (FAF1) and similar proteins. FAF1, also called UBX domain-containing protein 12 or UBX domain-containing protein 3A, is a multi-functional Fas associating protein that contains an N-terminal ubiquitin-associated (UBA)-like domain, UAS and ubiquitin-like (UBX) domains, p150 subunit of a chromatin assembly factor like domain (CAF) and a novel nuclear localization signal (NLS). FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF1 is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kappaB (NF-kappaB) by interfering with the nuclear translocation of the p65 subunit. Although the precise role of FAF1 in the ubiquitination pathway remains unclear, FAF1 interacts with valosin-containing protein (VCP) which is involved in the ubiquitin-proteosome pathway. 33 matched cddid_all.tbl CDD cd14414 cd14414 270597 UBA_FAF2 UBA-like TAP-C domain found in FAS-associated factor 2 (FAF2) and similar proteins. FAF2, also called protein ETEA, UBX domain-containing protein 3B, or UBX domain-containing protein 8, is the translation product of a highly expressed gene in the T-cells and eosinophils of atopic dermatitis patients compared with those of normal individuals. FAF2 shows homology to Fas-associated factor 1 (FAF1). Both of them contain N-terminal ubiquitin-associated (UBA)-like domain, UAS and ubiquitin-like (UBX) domains. Compared to FAF1, however, FAF2 lacks the nuclear targeting domain. The function of FAF2 remains unclear. A yeast two-hybrid assay showed that it can interact with Fas. Because of its homology to FAF1, it is postulated that FAF2 could be involved in modulating Fas-mediated apoptosis of T-cells and eosinophils of atopic dermatitis patients, making them more resistant to apoptosis. 38 matched cddid_all.tbl CDD cd14415 cd14415 270598 UBA_NACA_NACP1 UBA-like domain found in nascent polypeptide-associated complex subunit alpha (NACA) and putative NACA-like protein (NACP1). NACA, also called NAC-alpha or alpha-NAC, together with BTF3, also called Beta-NAC, form the nascent polypeptide-associated complex (NAC) which is a cytosolic protein chaperone that contacts the nascent polypeptide chains as they emerge from the ribosome. Besides, NACA has a high affinity for nucleic acids and exists as part of several protein complexes playing a role in proliferation, apoptosis, or degradation. It is a cytokine-modulated specific transcript in the human TF-1 erythroleukemic cell line. It also acts as a transcriptional co-activator in osteoblasts by binding to phosphorylated c-Jun, a member of the activator-protein-1 (AP-1) family. Moreover, NACA binds to and regulates the adaptor protein Fas-associated death domain (FADD). In addition, NACA functions as a novel factor participating in the positive regulation of human erythroid-cell differentiation. Both NACA and BTF3 harbor an NAC domain that mediates the dimerization of the two subunits. By contrast, NACA has an extra ubiquitin-associated (UBA) domain in the C-terminus. In addition to NACA, the family includes NACP1, also called Alpha-NAC pseudogene 1 or NAC-alpha pseudogene 1. The biological function of NACP1 remains unclear. 46 matched cddid_all.tbl CDD cd14416 cd14416 270599 UBA_NACAD UBA-like domain found in nascent polypeptide-associated complex subunit alpha domain-containing protein 1 (NACAD). The subfamily includes a group of uncharacterized proteins mainly found in vertebrates. Their biological function remains unknown, but they show high sequence similarity to the nascent polypeptide-associated complex (NAC) subunit alpha (NACA) that exists as part of several protein complexes playing a role in proliferation, apoptosis, or degradation. Like NACA, NACAD contains an NAC domain and a C-terminal ubiquitin-associated (UBA) domain. 44 matched cddid_all.tbl CDD cd14417 cd14417 270600 CUE_DMA_DMRTA1 CUE-like DMA domain found in doublesex- and mab-3-related transcription factor A1 (DMRTA1) and similar proteins. DMRTA1 is encoded by gene DMRT1, a vertebrate equivalent of the Drosophila melanogaster master sex regulator gene, doublesex. In D. melanogaster, doublesex controls the terminal switch of the pathway leading to sex fate choice. DMRT1 may function as regulator of sex differentiation in vertebrate. Especially, it is required for testis differentiation, but is not involved in the gonadal sex fate choice. 40 matched cddid_all.tbl CDD cd14418 cd14418 270601 CUE_DMA_DMRTA2 CUE-like DMA domain found in doublesex- and mab-3-related transcription factor A2 (DMRTA2). DMRTA2, also called Doublesex- and mab-3-related transcription factor 5 (DMRT5), is encoded by gene DMRT2. In the zebrafish, DMRT2 is involved in somite development. DMRTA2 may act as an activator of cyclin-dependent kinase inhibitor 2C (cdkn2c) during spermatogenesis. It may also play significant roles in embryonic neurogenesis. 42 matched cddid_all.tbl CDD cd14419 cd14419 270602 CUE_DMA_DMRTA3 CUE-like DMA domain found in doublesex- and mab-3-related transcription factor 3 (DMRTA3). DMRTA3 is encoded by tumor suppressor gene DMRT3 which serves as a novel potential target for homozygous deletion in squamous cell carcinoma of the lung. 43 matched cddid_all.tbl CDD cd14420 cd14420 270603 CUE_AUP1 CUE domain found in ancient ubiquitous protein 1 (AUP1) and similar proteins. AUP1 is a component of the HRD1-SEL1L endoplasmic reticulum (ER) quality control complex and is essential for US11-mediated dislocation of class I MHC heavy chains. It also binds to the membrane-proximal KVGFFKR motif of the cytoplasmic tail of the integrin alphaCTs that plays a crucial role in the inside-out signaling of alpha(IIb)beta(3). AUP1 is found in both the ER and in lipid droplets. It contains two conserved cytoplasmic domains, an acyltransferase domain, a CUE domain and an E2 ubiquitin conjugase G2 (Ube2g2)-binding domain (G2BR). The acyltransferase domain transfers fatty acids onto phospholipids and CUE domain participates in ubiquitin binding or in recruitment of ubiquitin-conjugating enzymes to the site of dislocation. 45 matched cddid_all.tbl CDD cd14421 cd14421 270604 CUE_AMFR CUE domain found in autocrine motility factor receptor (AMFR) and similar proteins. AMFR is an internalizing cell surface glycoprotein that is localized in both plasma membrane caveolae and the endoplasmic reticulum (ER), and involves in the regulation of cellular adhesion, proliferation, motility and apoptosis, as well as in the process of learning and memory. It is also called ER-protein gp78 that has been identified as a RING finger-dependent ubiquitin protein ligase (E3) implicated in degradation from the ER. AMFR contains an N-terminal RING-finger domain and a C-terminal CUE domain. 41 matched cddid_all.tbl CDD cd14422 cd14422 270605 CUE_RIN3_plant CUE domain found in plant E3 ubiquitin protein ligases RIN2, RIN3 and similar proteins. RIN2 and RIN3 are two closely related RPM1-interacting proteins conserved in higher eukaryotes. They are orthologs of the mammalian autocrine motility factor receptor (AMFR), a cytokine receptor localized in both plasma membrane caveolae and the endoplasmic reticulum (ER). RIN2 and RIN3 have been identified as membrane-bound RING-finger type ubiquitin ligases with six apparent transmembrane domains, a RING-finger domain and a CUE domain. They act as positive regulators of RPM1- and RPS2-dependent hypersensitive response (HR). 38 matched cddid_all.tbl CDD cd14423 cd14423 270606 CUE_UBR5 CUE domain found in E3 ubiquitin-protein ligase UBR5 and similar proteins. UBR5, also called E3 ubiquitin-protein ligase, HECT domain-containing 1, hyperplastic discs protein homolog (HYD), progestin-induced protein, EDD, or Rat100, belongs to the E3 protein family of HECT (homologous to E6-AP C-terminus) ligases. It is frequently overexpressed in breast and ovarian cancer, suggesting a role in cancer development. UBR5 is involved in DNA-damage signaling. It can ubiquitinate DNA topoisomerase II-binding protein 1 (TopBP1) in the presence of the E2 enzyme UBCH4. It also activates the DNA-damage checkpoint kinase CHK2. Moreover, UBR5 interacts with the calcium and integrin-binding protein (CIB) in a DNA-damage-dependent manner. It functions as the substrate of the extracellular signal-regulated kinases (ERKs) 1 and 2. It also acts as a ubiquitin ligase that controls the levels of poly(A)-binding protein-interacting protein 2. In addition, UBR5 ubiquitinates and up-regulates beta-catenin, regulates transcription, and activates smooth-muscle differentiation through its ability to stabilize myocardin. UBR5 contains an N-terminal CUE domain, a zinc-finger-like domain termed the ubiquitin-recognin (UBR) box, a MLLE (mademoiselle) domain, and a C-terminal catalytic HECT domain. 47 matched cddid_all.tbl CDD cd14424 cd14424 270607 CUE_Cue1p_like CUE domain found in yeast ubiquitin-binding protein CUE1 (Cue1p), CUE4 (Cue4p) and similar proteins. Cue1p, also called coupling of ubiquitin conjugation to ER degradation protein 1 or kinetochore-defect suppressor 4, is encoded by the open reading frame (ORF) YMR264W in yeast. It is an N-terminally membrane-anchored endoplasmic reticulum (ER) protein essential for the activity of the two major yeast RING finger ubiquitin ligases (E3s) implicated in ER-associated degradation (ERAD). It interacts with the ERAD ubiquitin-conjugating enzyme (E2) Ubc7p in vivo, stimulates Ubc7p E2 activity, and further activates ER-associated protein degradation. Cue1p contains a CUE domain which binds ubiquitin much more weakly than those of other CUE domain containing proteins. It also has an Ubc7p binding-domain at the C-terminal region which is required for Ubc7p-dependent ubiquitylation and for degradation of substrates in the ER. This family also includes Cue4p, also called coupling of ubiquitin conjugation to ER degradation protein 4. It is encoded by the open reading frame (ORF) YML101C in yeast. Cue4p contains a CUE domain which shows high level of similarity with that of Cue1p. 37 matched cddid_all.tbl CDD cd14425 cd14425 270608 UBA1_HR23A UBA1 domain of UV excision repair protein RAD23 homolog A (HR23A) found in vertebrates. HR23A, also called Rad23A, is a DNA repair protein that binds to 19S subunit of the 26S proteasome and shuttles ubiquitinated proteins to the proteasome for degradation which is required for efficient nucleotide excision repair (NER), a primary mechanism for removing UV-induced DNA lesions. HR23A also plays a critical role in the interaction of HIV-1 viral protein R (Vpr) with proteasome, especially facilitating Vpr to promote protein poly-ubiquitination. HR23A contains an N-terminal ubiquitin-like (UBL) domain that binds proteasomes and two C-terminal ubiquitin-associated (UBA) domains that bind ubiquitin or multi-ubiquitinated substrates. In addition, it has a XPC protein-binding domain that might be necessary for its efficient NER function. This model corresponds to the UBA1 domain. 40 matched cddid_all.tbl CDD cd14426 cd14426 270609 UBA1_HR23B UBA1 domain of UV excision repair protein RAD23 homolog B (HR23B) found in vertebrates. HR23B, also called xeroderma pigmentosum group C (XPC) repair-complementing complex 58 kDa protein (p58), is tightly complexed with XPC protein to form the XPC-HR23B complex. Although it displays a high affinity for both single- and double-stranded DNA, the XPC-HR23B complex functions as a global genome repair (GGR)-specific repair factor that is specifically involved in global genome but not transcription-coupled nucleotide excision repair (NER). HR23B also interacts specifically with S5a subunit of the human 26 S proteasome, and plays an important role in shuttling ubiquitinated cargo proteins to the proteasome. HR23B contains an N-terminal ubiquitin-like (UBL) domain that binds proteasomes and two C-terminal ubiquitin-associated (UBA) domains that bind ubiquitin or multi-ubiquitinated substrates. In addition, it has a XPC protein-binding domain that might be necessary for its efficient NER function. This model corresponds to the UBA1 domain. 46 matched cddid_all.tbl CDD cd14427 cd14427 270610 UBA2_HR23A UBA2 domain of UV excision repair protein RAD23 homolog A (HR23A) found in vertebrates. HR23A, also called Rad23A, is a DNA repair protein that binds to 19S subunit of the 26S proteasome and shuttles ubiquitinated proteins to the proteasome for degradation which is required for efficient nucleotide excision repair (NER), a primary mechanism for removing UV-induced DNA lesions. HR23A also plays a critical role in the interaction of HIV-1 viral protein R (Vpr) with proteasome, especially facilitating Vpr to promote protein poly-ubiquitination. HR23A contains an N-terminal ubiquitin-like (UBL) domain that binds proteasomes and two C-terminal ubiquitin-associated (UBA) domains that bind ubiquitin or multi-ubiquitinated substrates. In addition, it has a XPC protein-binding domain that might be necessary for its efficient NER function. This model corresponds to the UBA2 domain. 41 matched cddid_all.tbl CDD cd14428 cd14428 270611 UBA2_HR23B UBA2 domain of UV excision repair protein RAD23 homolog B (HR23B) found in vertebrates. HR23B, also called xeroderma pigmentosum group C (XPC) repair-complementing complex 58 kDa protein (p58), is tightly complexed with XPC protein to form the XPC-HR23B complex. Although it displays a high affinity for both single- and double-stranded DNA, the XPC-HR23B complex functions as a global genome repair (GGR)-specific repair factor that is specifically involved in global genome but not transcription-coupled nucleotide excision repair (NER). HR23B also interacts specifically with S5a subunit of the human 26 S proteasome, and plays an important role in shuttling ubiquitinated cargo proteins to the proteasome. HR23B contains an N-terminal ubiquitin-like (UBL) domain that binds proteasomes and two C-terminal ubiquitin-associated (UBA) domains that bind ubiquitin or multi-ubiquitinated substrates. In addition, it has a XPC protein-binding domain that might be necessary for its efficient NER function. This model corresponds to the UBA2 domain. 45 matched cddid_all.tbl CDD cd14435 cd14435 259859 SPO1_TF1_like Bacteriophage SPO1-encoded TF1 binds and bends DNA. This group contains proteins related to bacillus phage SPO1-encoded transcription factor 1 (TF1), a type II DNA-binding protein related to the DNA sequence specific (IHF) and non-specific (HU) domains. Type II DNA-binding proteins bind and bend DNA as dimers. Like IHF, TF1 binds DNA specifically and bends DNA sharply. Bacteriophage SPO1-encoded TF1 recognizes SPO1 phage DNA containing 5-(hydroxymethyl)-2'-deoxyuridine as opposed to thymine, Related family members includes integration host factor (IHF) and HU, also called type II DNA-binding proteins (DNABII), which are small dimeric proteins that specifically bind the DNA minor groove, inducing large bends in the DNA and serving as architectural factors in a variety of cellular processes such as recombination, initiation of replication/transcription and gene regulation. IHF binds DNA in a sequence specific manner while HU displays little or no sequence preference. IHF homologs are usually heterodimers, while HU homologs are typically homodimers (except HU heterodimers from E. coli and other enterobacteria). HU is highly basic and contributes to chromosomal compaction and maintenance of negative supercoiling, thus often referred to as histone-like protein. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). 87 matched cddid_all.tbl CDD cd14436 cd14436 271226 LepB Legionella Rab1-specific GAP LepB. LepB of Legionella, a human pathogen, is a specific RabGAP for Rab1, a member of the largest subfamily of small GTPases. RabGTPases play a role in the control of vesicular trafficking and are switched off by GTPase-activating enzymes (GAPs) that stimulate the intrinsic GTP hydrolysis activity. Legionella LepB is unrelated to the TBC family of human Rab1 RabGAPs. 272 matched cddid_all.tbl CDD cd14437 cd14437 271227 nt01cx_1156_like Uncharacterized proteins conserved in Clostridia. Some members of this uncharacterized protein family have been annotated as putative lipoproteins. The structure resembles that of a partial beta-propeller (3 out of 6 blades), suggesting that family members might form dimers. 199 matched cddid_all.tbl CDD cd14438 cd14438 271228 Hip_N N-terminal dimerization domain of the Hsp70-interacting protein (Hip) and similar proteins. The Hsc70/Hsp70-interacting protein (Hip, also p48 or suppressor of tumorigenicity ST13) functions as a regulator of the cyclic action of Hsp70. Hip forms homodimers, and this model characterizes the N-terminal dimerization domain, which may not be directly involved in its regulatory function. A central domain of Hip that contains TPR repeats binds the ATPase domain of Hsp70 and slows the release of ADP. 41 matched cddid_all.tbl CDD cd14439 cd14439 270205 AlgX_N_like N-terminal catalytic domain of putative alginate O-acetyltranferase and similar proteins. The alginate biosynthesis protein AlgX appears to be directly involved in the O-acetylation of alginate, an exopolysaccharide that is associated with the formation of persistent biofilms, such as those by mucoid strains of Pseudomonas aeruginosa that affect patients suffering from cystic fibrosis. Its N-terminal catalytic domain resembles SGNH hydrolases, though with a permuted topology. The active site matches that of the SGNH hydrolases, is well conserved, and has been verified experimentally. This wider family includes AlgX, AlgJ, AlgV, and a number of uncharacterized families, some of which may have been mis-annotated in sequence databases. 316 matched cddid_all.tbl CDD cd14440 cd14440 270206 AlgX_N_like_3 Uncharacterized proteins similar to putative alginate O-acetyltransferase. The alginate biosynthesis protein AlgX appears to be directly involved in the O-acetylation of alginate, an exopolysaccharide that is associated with the formation of persistent biofilms, such as those by mucoid strains of Pseudomonas aeruginosa that affect patients suffering from cystic fibrosis. Its N-terminal catalytic domain resembles SGNH hydrolases, though with a permuted topology. The active site matches that of the SGNH hydrolases, is well conserved, and has been verified experimentally. Members of this uncharacterized protein family resemble AlgX_N. 315 matched cddid_all.tbl CDD cd14441 cd14441 270207 AlgX_N N-terminal catalytic domain of the putative alginate O-acetyltranferase AlgX. The alginate biosynthesis protein AlgX appears to be directly involved in the O-acetylation of alginate, an exopolysaccharide that is associated with the formation of persistent biofilms, such as those by mucoid strains of Pseudomonas aeruginosa that affect patients suffering from cystic fibrosis. This N-terminal catalytic domain resembles SGNH hydrolases, though with a permuted topology. The active site matches that of the SGNH hydrolases, is well conserved, and has been verified experimentally. AlgX contains a C-terminal carbohydrate binding domain that belongs to the wider family of CBM6-CBM35-CBM36_like domains. 310 matched cddid_all.tbl CDD cd14442 cd14442 270208 AlgJ_like putative alginate O-acetyltranferases AlgJ, AlgV, and similar proteins. The alginate biosynthesis protein AlgX appears to be directly involved in the O-acetylation of alginate, an exopolysaccharide that is associated with the formation of persistent biofilms, such as those by mucoid strains of Pseudomonas aeruginosa that affect patients suffering from cystic fibrosis. Its N-terminal catalytic domain resembles SGNH hydrolases, though with a permuted topology. The active site matches that of the SGNH hydrolases, is well conserved, and has been verified experimentally. Members of this family have been annotated as AlgJ or AlgV, and they closely resemble AlgX in sequence and function, although they lack the C-terminal carbohydrate binding domain of AlgX. 321 matched cddid_all.tbl CDD cd14443 cd14443 270209 AlgX_N_like_2 Uncharacterized proteins similar to putative alginate O-acetyltranferase. The alginate biosynthesis protein AlgX appears to be directly involved in the O-acetylation of alginate, an exopolysaccharide that is associated with the formation of persistent biofilms, such as those by mucoid strains of Pseudomonas aeruginosa that affect patients suffering from cystic fibrosis. Its N-terminal catalytic domain resembles SGNH hydrolases, though with a permuted topology. The active site matches that of the SGNH hydrolases, is well conserved, and has been verified experimentally. Some members of this uncharacterized family, which resembles AlgX_N, have been annotated as twin-arginine translocation signal, although they share little or no similarity with experimentally characterized proteins that bear the same name. 313 matched cddid_all.tbl CDD cd14444 cd14444 270210 AlgX_N_like_1 Uncharacterized proteins similar to putative alginate O-acetyltranferase. The alginate biosynthesis protein AlgX appears to be directly involved in the O-acetylation of alginate, an exopolysaccharide that is associated with the formation of persistent biofilms, such those as by mucoid strains of Pseudomonas aeruginosa that affect patients suffering from cystic fibrosis. Its N-terminal catalytic domain resembles SGNH hydrolases, though with a permuted topology. The active site matches that of the SGNH hydrolases, is well conserved, and has been verified experimentally. Members of this uncharacterized family similar to AlgX_N have been annotated as cell division proteins FtsQ, although they share little or no similarity with experimentally characterized members of the FtsQ family. 298 matched cddid_all.tbl CDD cd14445 cd14445 271220 RILP-like Rab interacting lysosomal protein-like 1 and 2 (Rilpl1 and Rilpl2). This domain is found in Rab interacting lysosomal protein-like 1 and 2, and appears to be conserved in Bilateria. The Rilp-like proteins regulate the concentration of ciliary membrane proteins in the primary cilium. Rilpl2 interacts with myosin-Va and has been linked to the regulation of cellular morphology in neurons; it forms a complex with Rac1 and activates Rac1-Pak signaling, dependent on myosin-Va. 89 matched cddid_all.tbl CDD cd14446 cd14446 271219 bt3222_like Uncharacterized proteins similar to Bacteriodes thetaiotaomicron bt3222. This family appears to be specific to Bacteroidetes; the two-domain protein forms a homodimer. 266 matched cddid_all.tbl CDD cd14447 cd14447 269894 SPX Domain found in Syg1, Pho81, XPR1, and related proteins. This region has been named the SPX domain after (Syg1, Pho81 and XPR1). This domain is found at the amino terminus of a variety of proteins. In the yeast protein Syg1, the N-terminus directly binds to the G-protein beta subunit and inhibits transduction of the mating pheromone signal. Similarly, the N-terminus of the human XPR1 protein binds directly to the beta subunit of the G-protein heterotrimer leading to increased production of cAMP. These findings suggest that members of this family are involved in G-protein associated signal transduction. The N-termini of several proteins involved in the regulation of phosphate transport, including the putative phosphate level sensors Pho81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa, are also members of this family. The SPX domain of S. cerevisiae low-affinity phosphate transporters Pho87 and Pho90 auto-regulates uptake and prevents efflux. This SPX dependent inhibition is mediated by the physical interaction with Spl2. NUC-2 contains several ankyrin repeats. Several members of this family are annotated as XPR1 proteins: the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with xenotropic and polytropic murine leukaemia viruses (MLV). Infection by these retroviruses can inhibit XPR1-mediated cAMP signaling and result in cell toxicity and death. The similarity between Syg1, phosphate regulators and XPR1 sequences has been previously noted, as has the additional similarity to several predicted proteins, of unknown function, from Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Schizosaccharomyces pombe, S. cerevisiae, and many other diverse organisms. 143 matched cddid_all.tbl CDD cd14448 cd14448 259990 CuRO_2_BOD_CotA_like Cupredoxin domain 2 of Bilirubin oxidase (BOD), the bacterial endospore coat component CotA, and similar proteins. Bilirubin oxidase (BOD) catalyzes the oxidation of bilirubin to biliverdin and the four-electron reduction of molecular oxygen to water. CotA protein is an abundant component of the outer coat layer in bacterial endospore coat and is required for spore resistance against hydrogen peroxide and UV light. Also included in this subfamily are phenoxazinone synthase (PHS), which catalyzes the oxidative coupling of substituted o-aminophenols to produce phenoxazinones, and FtsP (also named SufI), which is a component of the cell division apparatus. These proteins are laccase-like multicopper oxidases (MCOs) that are able to couple oxidation of substrates with reduction of dioxygen to water. MCOs are capable of oxidizing a vast range of substrates, varying from aromatic compounds to inorganic compounds such as metals. Although the members of this family have diverse functions, majority of them have three cupredoxin domain repeats. The copper ions are bound in several sites: Type 1, Type 2, and/or Type 3. The ensemble of types 2 and 3 copper is called a trinuclear cluster. MCOs oxidize their substrate by accepting electrons at a mononuclear copper center and transferring them to the active site trinuclear copper center. The cupredoxin domain 2 of 3-domain MCOs has lost the ability to bind copper. 144 matched cddid_all.tbl CDD cd14449 cd14449 259991 CuRO_1_2DMCO_NIR_like_2 The cupredoxin domain 1 of a two-domain laccase related to nitrite reductase. The two-domain laccase (small laccase) in this family differs significantly from all laccases. It resembles the two domain nitrite reductase in both sequence and structure. It consists of two cupredoxin domains and forms trimers, and hence resembles the quaternary structure of nitrite reductases more than that of large laccases. There are three trinuclear copper clusters in the enzyme localized between domains 1 and 2 of each pair of neighbor chains. Laccase is a blue multi-copper enzyme that catalyzes the oxidation of a variety of organic substrates coupled to the reduction of molecular oxygen to water. It displays broad substrate specificity, catalyzing the oxidation of a wide variety of aromatic, notably phenolic, and inorganic substances. Laccase has been implicated in a wide spectrum of biological activities. This subfamily has lost the type 1 (T1) copper binding site in domain 1 that is present in other two-domain laccases. 135 matched cddid_all.tbl CDD cd14450 cd14450 259992 CuRO_3_FV_like The third cupredoxin domain of coagulation factor V and similar proteins. Factor V is an essential coagulation protein with both pro- and anti-coagulant functions. Aberrant expression of human factor V can lead to bleeding or thromboembolic disease, which may be life-threatening. Bovine factor Va serves as the cofactor in the prothrombinase complex that results in a 300,000-fold increase in the rate of thrombin generation. Factor V is synthesized as a single polypeptide with six cupredoxin domains and a domain structure of 1-2-3-4-B-5-6-C1-C2, where 1-6 are cupredoxin domains, B is a domain with no known structural homologs and is dispensible for coagulant activity, and C are domains distantly related to discoidin protein-fold family members. Factor V has little activity prior to proteolytic cleavage by thrombin or FXa upon secretion. The resulting Factor Va is a heterodimer consisting of a heavy chain (1-2-3-4) and a light chain (5-6-C1-C2). This model represents the cupredoxin domain 3 of unprocessed Factor V or the heavy chain of Factor Va, and similar proteins including pseutarin C non-catalytic subunit. Pseutarin C is a prothrombin activator from Pseudonaja textilis venom. 181 matched cddid_all.tbl CDD cd14451 cd14451 259993 CuRO_5_FV_like The fifth cupredoxin domain of coagulation factor V and similar proteins. Factor V is an essential coagulation protein with both pro- and anti-coagulant functions. Aberrant expression of human factor V can lead to bleeding or thromboembolic disease, which may be life-threatening. Bovine factor Va serves as the cofactor in the prothrombinase complex that results in a 300,000-fold increase in the rate of thrombin generation. Factor V is synthesized as a single polypeptide with six cupredoxin domains and a domain structure of 1-2-3-4-B-5-6-C1-C2, where 1-6 are cupredoxin domains, B is a domain with no known structural homologs and is dispensible for coagulant activity, and C are domains distantly related to discoidin protein-fold family members. Factor V has little activity prior to proteolytic cleavage by thrombin or FXa upon secretion. The resulting Factor Va is a heterodimer consisting of a heavy chain (1-2-3-4) and a light chain (5-6-C1-C2). This model represents the cupredoxin domain 5 of unprocessed Factor V or the first cupredoxin domain of the light chain of coagulation factor Va, and similar proteins including pseutarin C non-catalytic subunit. Pseutarin C is a prothrombin activator from Pseudonaja textilis venom. 173 matched cddid_all.tbl CDD cd14452 cd14452 259994 CuRO_1_FVIII_like The first cupredoxin domain of coagulation factor VIII and similar proteins. Factor VIII functions in the factor X-activating complex of the intrinsic coagulation pathway. It facilitates blood clotting by acting as a cofactor for factor IXa. In the presence of Ca2+ and phospholipids, Factor VIII and IXa form a complex that converts factor X to the activated form Xa. A variety of mutations in the Factor VIII gene can cause hemophilia A, which typically requires replacement therapy with purified protein. Factor VIII is synthesized as a single polypeptide with six cupredoxin domains and a domain structure of 1-2-3-4-B-5-6-C1-C2, where 1-6 are cupredoxin domains, B is a domain with no known structural homologs and is dispensible for coagulant activity, and C are domains distantly related to discoidin protein-fold family members. Factor VIII is initially processed through proteolysis to generate a heterodimer consisting of a heavy chain (1-2-3-4) and a light chain (5-6-C1-C2), which circulates in a tight complex with von Willebrand factor (VWF). Further processing of the heavy chain produces activated factor VIIIa, a heterotrimer composed of polypeptides (1-2), (3-4), and the light chain. This model represents the cupredoxin domain 1 of unprocessed Factor VIII or the heavy chain of circulating Factor VIII, and similar proteins. 173 matched cddid_all.tbl CDD cd14453 cd14453 259995 CuRO_2_FV_like The second cupredoxin domain of coagulation factor V and similar proteins. Factor V is an essential coagulation protein with both pro- and anti-coagulant functions. Aberrant expression of human factor V can lead to bleeding or thromboembolic disease, which may be life-threatening. Bovine factor Va serves as the cofactor in the prothrombinase complex that results in a 300,000-fold increase in the rate of thrombin generation. Factor V is synthesized as a single polypeptide with six cupredoxin domains and a domain structure of 1-2-3-4-B-5-6-C1-C2, where 1-6 are cupredoxin domains, B is a domain with no known structural homologs and is dispensible for coagulant activity, and C are domains distantly related to discoidin protein-fold family members. Factor V has little activity prior to proteolytic cleavage by thrombin or FXa upon secretion. The resulting Factor Va is a heterodimer consisting of a heavy chain (1-2-3-4) and a light chain (5-6-C1-C2). This model represents the cupredoxin domain 2 of unprocessed Factor V or the heavy chain of Factor Va, and similar proteins including pseutarin C non-catalytic subunit. Pseutarin C is a prothrombin activator from Pseudonaja textilis venom. 123 matched cddid_all.tbl CDD cd14454 cd14454 259996 CuRO_4_FV_like The fourth cupredoxin domain of coagulation factor V and similar proteins. Factor V is an essential coagulation protein with both pro- and anti-coagulant functions. Aberrant expression of human factor V can lead to bleeding or thromboembolic disease, which may be life-threatening. Bovine factor Va serves as the cofactor in the prothrombinase complex that results in a 300,000-fold increase in the rate of thrombin generation. Factor V is synthesized as a single polypeptide with six cupredoxin domains and a domain structure of 1-2-3-4-B-5-6-C1-C2, where 1-6 are cupredoxin domains, B is a domain with no known structural homologs and is dispensible for coagulant activity, and C are domains distantly related to discoidin protein-fold family members. Factor V has little activity prior to proteolytic cleavage by thrombin or FXa upon secretion. The resulting Factor Va is a heterodimer consisting of a heavy chain (1-2-3-4) and a light chain (5-6-C1-C2). This model represents the cupredoxin domain 4 of unprocessed Factor V or the heavy chain of Factor Va, and similar proteins including pseutarin C non-catalytic subunit. Pseutarin C is a prothrombin activator from Pseudonaja textilis venom. 144 matched cddid_all.tbl CDD cd14455 cd14455 259997 CuRO_6_FV_like The sixth cupredoxin domain of coagulation factor V and similar proteins. Factor V is an essential coagulation protein with both pro- and anti-coagulant functions. Aberrant expression of human factor V can lead to bleeding or thromboembolic disease, which may be life-threatening. Bovine factor Va serves as the cofactor in the prothrombinase complex that results in a 300,000-fold increase in the rate of thrombin generation. Factor V is synthesized as a single polypeptide with six cupredoxin domains and a domain structure of 1-2-3-4-B-5-6-C1-C2, where 1-6 are cupredoxin domains, B is a domain with no known structural homologs and is dispensible for coagulant activity, and C are domains distantly related to discoidin protein-fold family members. Factor V has little activity prior to proteolytic cleavage by thrombin or FXa upon secretion. The resulting Factor Va is a heterodimer consisting of a heavy chain (1-2-3-4) and a light chain (5-6-C1-C2). This model represents the cupredoxin domain 6 of unprocessed Factor V or the second cupredoxin domain of the light chain of coagulation factor Va, and similar proteins including pseutarin C non-catalytic subunit. Pseutarin C is a prothrombin activator from Pseudonaja textilis venom. 140 matched cddid_all.tbl CDD cd14456 cd14456 271218 Menin Scaffolding protein menin encoded by the MEN1 gene. MEN1 is the gene responsible for multiple endocrine neoplasia type 1, and it has been characterized as a tumor suppressor gene that encodes a protein called menin. Menin is mostly found in the nucleus and can regulate gene expression in a positive and in a negative way, and it has been shown to interact with transcription activators, transcription repressors, cell signaling proteins, and various other proteins. It plays major roles in DNA repair, the regulation of the cell cycle, and chromatin remodeling. 437 matched cddid_all.tbl CDD cd14458 cd14458 271217 DP_DD Dimerization domain of DP. DP functions as a binding partner for E2F transcription factors. DP and E2F form heterodimers and play important roles in regulating genes involved in DNA synthesis, cell cycle progression, proliferation and apoptosis. The transcriptional activity of E2F is inhibited by the retinoblastoma protein (Rb) which binds to the E2F-DP heterodimer, blocks the transactivation domain, and negatively regulates the G1-S transition. DP is distantly related to E2F. In humans, there are at least six closely related E2F and two DP family members, all containing a DNA binding domain, a coiled-coil (CC) region, and a marked-box domain. E2F1 to E2F5 also contain a C-terminal transactivation domain. 105 matched cddid_all.tbl CDD cd14472 cd14472 270615 mltA_B_like Domain B insert of mltA_like lytic transglycosylases. Escherichia coli MltA is a membrane-bound lytic transglycosylase comprised of two domains separated by a large groove, where the peptidoglycan strand binds. Domain A is made up of an N-terminal and a C-terminal portion, which correspond to the 3D domain, named for 3 conserved aspartate residues. Domain B is inserted within the linear sequence of domain A. MltA is distinct from other bacterial lytic transglycosylases (LTs), which are similar to each other. Escherichia coli peptidoglycan lytic transglycosylase (LT) initiates cell wall recycling in response to damage, during bacterial fission, and cleaves peptidoglycan (PG) to create functional spaces in its wall. PG chains (also known as murein), the major components of the bacterial cell wall, are comprised of alternating beta-1-4-linked N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), and lytic transglycosylases cleave this beta-1-4 bond. Typically, peptidoglycan lytic transglycosylases (LT) are exolytic, releasing Metabolite 1 (GlcNAc-anhMurNAc-L-Ala-D-Glu-m-Dap-D-Ala-D-Ala) from the ends of the PG strands. In contrast, MltE is endolytic , cleaving in the middle of PG strands, with further processing to Metabolite 1 accomplished by other LTs. In E. coli, there are six membrane-bound LTs: MltA-MltF and soluble Slt70. Slt35 is a soluble fragment cleaved from MltB. Bacterial LTs are classified in 4 families: Family 1 includes slt70 MltC-MltF, Family 2 includes MltA, Family 3 includes MltB, and Family 4 of bacteriophage origin. While most of the LT family members are similar in structure and sequence with a lysozyme-like fold, Family 2 (including mltA) is distinct. 134 matched cddid_all.tbl CDD cd14473 cd14473 271216 FERM_B-lobe FERM domain B-lobe. The FERM domain has a cloverleaf tripart structure (FERM_N, FERM_M, FERM_C/N, alpha-, and C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3). The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases, the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the pleckstrin homology (PH) and phosphotyrosine binding (PTB) domains and consequently is capable of binding to both peptides and phospholipids at different sites. 99 matched cddid_all.tbl CDD cd14474 cd14474 269895 SPX_YDR089W SPX domain of the yeast protein YDR089W and related proteins. This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. The uncharacterized yeast protein YDR089W has not been shown to be involved in phosphate homeostasis, in contrast to most of the other SPX-domain containing proteins. 144 matched cddid_all.tbl CDD cd14475 cd14475 269896 SPX_SYG1_like SPX domain of the yeast plasma protein Syg1 and related proteins. This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. In the yeast protein Syg1, the N-terminus binds directly to the G-protein beta subunit and inhibits transduction of the mating pheromone signal, and it co-occurs with a C-terminal domain from the EXS family. 139 matched cddid_all.tbl CDD cd14476 cd14476 269897 SPX_PHO1_like SPX domain of the plant protein PHOSPHATE1 (PHO1). This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. The PHO1 gene family conserved in plants is involved in a variety of processes, most notably the transport of inorganic phosphate from the root to the shoot of the plant and mediating the response to low levels of inorganic phosphate. More recently it has become evident that PHO1 gene families have diverged in various plants and may play roles in stress response as well as the stomatal response to abscisic acid. 139 matched cddid_all.tbl CDD cd14477 cd14477 269898 SPX_XPR1_like SPX domain of the xenotropic and polytropic retrovirus receptor 1 (XPR1) and related proteins. This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. The N-terminus of the human XPR1 protein (xenotropic and polytropic retrovirus receptor 1) binds directly to the beta subunit of the G-protein heterotrimer leading to increased production of cAMP. These findings suggest that all members of this family are involved in G-protein associated signal transduction. Several members of this family are annotated as XPR1 proteins: the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with xenotropic and polytropic murine leukaemia viruses (MLV). Infection by these retroviruses can inhibit XPR1-mediated cAMP signaling and result in cell toxicity and death. Similarity between Syg1, phosphate regulators and XPR1 sequences has been previously noted, as has the additional similarity to several predicted proteins, of unknown function, from Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Schizosaccharomyces pombe, and Saccharomyces cerevisiae, and many other diverse organisms. 161 matched cddid_all.tbl CDD cd14478 cd14478 269899 SPX_PHO87_PHO90_like SPX domain of the phosphate transporters Pho87, Pho90, Pho91, and related proteins. This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. The SPX domain of the Saccharomyces cerevisiae membrane-localized low-affinity phosphate transporters Pho87 and Pho90 auto-regulates uptake and prevents efflux. This SPX dependent inhibition is mediated by the physical interaction with Spl2. Pho91 is involved in the export of inorganic phosphate from the vacuole to the cytosol. While both, Pho87 and Pho90, transport phosphate into the cell, only Pho87 appears to also function as a sensor for high extracellular phosphate concentrations. 148 matched cddid_all.tbl CDD cd14479 cd14479 269900 SPX-MFS_plant SPX domain of proteins found in plants and stramenopiles; most have a C-terminal MFS domain. This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The SPX domain is found at the amino terminus of a variety of proteins. This family, mostly found in plants, contains a C-terminal MFS domain (major facilitator superfamily), suggesting a function as a secondary transporter. The function of this N-terminal region is unclear, although it might be involved in regulating transport. 140 matched cddid_all.tbl CDD cd14480 cd14480 269901 SPX_VTC2_like SPX domain of the vacuolar transport chaperone Vtc2 and similar proteins. This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. Vtc2 is part of the Saccharomyces cerevisiae membrane-integral VTC complex, together with Vtc1, Vtc3, and Vtc4. It contains an N-terminal SPX domain next to a central polyphosphate polymerase domain and a C-terminal domain of unknown function. 135 matched cddid_all.tbl CDD cd14481 cd14481 269902 SPX_AtSPX1_like SPX domain of the plant protein SPX1 and similar proteins. This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. This family of plant proteins contains a single SPX domain. Arabidopsis thaliana SPX1 and SPX3 have been reported to play roles in the adaptation to low-phosphate conditions, SPX3 may be involved in the regulation of SPX1 activity. Oryza sativa SPX1 suppresses the regulation of expression of OsPT2, a low-affinity phosphate transporter, by the MYB-like OsPHR2. 149 matched cddid_all.tbl CDD cd14482 cd14482 269903 SPX_BAH1-like SPX domain of the E3 ubiquitin-protein ligase BAH1/NLA and similar proteins. This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. BAH1 (benzoic acid hypersensitive 1) appears to function as an E3 ubiquitin ligase; the protein contains an SPX and a RING finger domain. It has been suggested that BAH1/NLA is involved in the regulation of plant immune responses, probably via a pathway of salicylic acid biosynthesis that includes benzoic acid as an intermediate. 156 matched cddid_all.tbl CDD cd14483 cd14483 269904 SPX_PHO81_NUC-2_like SPX domain of Pho81, NUC-2, and similar proteins. This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. The N-termini of several proteins involved in the regulation of phosphate transport, including the putative phosphate level sensors Pho81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa, are also members of this family. NUC-2 plays an important role in the phosphate-regulated signal transduction pathway in N. crassa. It shows high similarity to a cyclin-dependent kinase inhibitory protein Pho81, which is part of the phosphate regulatory cascade in S. cerevisiae. Both, NUC-2 and Pho81, have multi-domain architecture, including the SPX N-terminal domain following by several ankyrin repeats and a putative C-terminal glycerophosphodiester phosphodiesterase domain (GDPD) with unknown function. 162 matched cddid_all.tbl CDD cd14484 cd14484 269905 SPX_GDE1_like SPX domain of Gde1 and similar proteins. This region has been named the SPX domain after (Syg1, Pho81 and XPR1). The domain is found at the amino terminus of a variety of proteins. The N-termini of several proteins involved in the regulation of phosphate transport, including the putative phosphate level sensors Pho81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa, are also members of this family. The yeast protein Gde1/Ypl110c is similar to both, NUC-2 and Pho81, in sharing their multi-domain architecture, which includes the SPX N-terminal domain followed by several ankyrin repeats and a C-terminal glycerophosphodiester phosphodiesterase domain (GDPD). Gde1 hydrolyzes intracellular glycerophosphocholine into glycerolphosphate and choline, and plays a role in the utilization of glycerophosphocholine as a source for phosphate. 134 matched cddid_all.tbl CDD cd14485 cd14485 270618 mltA_like_LT_A Domain A of MltA and related lytic transglycosylase; domain A is interrupted by domain B. Escherichia coli MltA is a membrane-bound lytic transglycosylase comprised of two domains separated by a large groove, where the peptidoglycan strand binds. Domain A is made up of an N-terminal and a C-terminal portion, which correspond to the 3D domain, named for 3 conserved aspartate residues. Domain B is inserted within the linear sequence of domain A. MltA is distinct from other bacterial lytic transglycosylases (LTs), which are similar to each other. Escherichia coli peptidoglycan lytic transglycosylase (LT) initiates cell wall recycling in response to damage, during bacterial fission, and cleaves peptidoglycan (PG) to create functional spaces in its wall. PG chains (also known as murein), the major components of the bacterial cell wall, are comprised of alternating beta-1-4-linked N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), and lytic transglycosylases cleave this beta-1-4 bond. Typically, peptidoglycan lytic transglycosylases (LT) are exolytic, releasing Metabolite 1 (GlcNAc-anhMurNAc-L-Ala-D-Glu-m-Dap-D-Ala-D-Ala) from the ends of the PG strands. In contrast, MltE is endolytic , cleaving in the middle of PG strands, with further processing to Metabolite 1 accomplished by other LTs. In E. coli, there are six membrane-bound LTs: MltA-MltF and soluble Slt70. Slt35 is a soluble fragment cleaved from MltB. Bacterial LTs are classified in 4 families: Family 1 includes slt70 MltC-MltF, Family 2 includes MltA, Family 3 includes MltB, and Family 4 of bacteriophage origin. While most of the LT family members are similar in structure and sequence with a lysozyme-like fold, Family 2 (including mltA) is distinct. 159 matched cddid_all.tbl CDD cd14486 cd14486 270619 3D_domain 3D domain, named for 3 conserved aspartate residues, is found in mltA-like lytic transglycosylases and numerous other contexts. This family contains the 3D domain, named for its 3 conserved aspartates. It is found in conjunction with numerous other domains such as MltA (membrane-bound lytic murein transglycosylase A). These aspartates are critical active site residues of mltA-like lytic transglycosylases. Escherichia coli peptidoglycan lytic transglycosylase (LT) initiates cell wall recycling in response to damage, during bacterial fission, and cleaves peptidoglycan (PG) to create functional spaces in its wall. MltA has 2 domains, separated by a large groove, where the peptidoglycan strand binds. The C-terminus has a double-psi beta barrel fold within the 3D domain, which forms the larger A domain along with the N-terminal region of Mlts, but is also found in various other domain architectures. Peptigoglycan (also known as murein) chains, the primary structural component of bacterial cells walls, are comprised of alternating beta-1-4-linked N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc); lytic transglycosylases (LTs) cleave this beta-1-4 bond. Typically, LTs are exolytic, releasing Metabolite 1 (GlcNAc-anhMurNAc-L-Ala-D-Glu-m-Dap-D-Ala-D-Ala) from the ends of the PG strands. In contrast, membrane-bound lytic murein transglycosylase E (MltE) is endolytic , cleaving in the middle of PG strands, with further processing to Metabolite 1 accomplished by other LTs. In E. coli, there are six membrane- bound LTs: MltA-MltF and soluble Slt70. Slt35 is a soluble fragment cleaved from MltB. Bacterial LTs are classified in 4 families: Family 1 includes slt70 MltC-MltF, Family 2 includes MltA, Family 3 includes MltB, and family 4 of bacteriophage origin. While most LTs are related members of the lysozyme-like lytic transglycosylase family, MltA represents a distinct fold and sequence conservation. 104 matched cddid_all.tbl CDD cd14487 cd14487 271153 AlgX_C C-terminal carbohydrate-binding domain of the alginate O-acetyltranferase AlgX. The alginate biosynthesis protein AlgX appears to be directly involved in the O-acetylation of alginate, an exopolysaccharide that is associated with the formation of persistent biofilms, such as those by mucoid strains of Pseudomonas aeruginosa that affect patients suffering from cystic fibrosis. This N-terminal catalytic domain resembles SGNH hydrolases, though with a permuted topology. The active site matches that of the SGNH hydrolases, is well conserved, and has been verified experimentally. AlgX contains a C-terminal carbohydrate binding domain that belongs to the wider family of CBM6-CBM35-CBM36_like domains. 128 matched cddid_all.tbl CDD cd14488 cd14488 271154 CBM6-CBM35-CBM36_like_2 uncharacterized members of the carbohydrate binding module 6 (CBM6) and CBM35_like superfamily. Carbohydrate binding module family 6 (CBM6, family 6 CBM), also known as cellulose binding domain family VI (CBD VI), and related CBMs (CBM35 and CBM36). These are non-catalytic carbohydrate binding domains found in a range of enzymes that display activities against a diverse range of carbohydrate targets, including mannan, xylan, beta-glucans, cellulose, agarose, and arabinans. These domains facilitate the strong binding of the appended catalytic modules to their dedicated, insoluble substrates. Many of these CBMs are associated with glycoside hydrolase (GH) domains. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold. CBM36s are calcium-dependent xylan binding domains. CBM35s display conserved specificity through extensive sequence similarity, but divergent function through their appended catalytic modules. 132 matched cddid_all.tbl CDD cd14489 cd14489 271155 CBM_SBP_bac_1_like Putative Carbohydrate Binding Module (CBM) of extracellular solute-binding protein family 1. Domains in this family co-occur with extracellular solute-binding domains which are periplasmic components of ABC-type sugar transport systems involved in carbohydrate transport and metabolism. Carbohydrate binding modules of family 6 (CBM6), also known as cellulose binding domain family VI (CBD VI), and related CBMs (CBM35 and CBM36) are non-catalytic carbohydrate binding domains found in a range of enzymes that display activities against a diverse range of carbohydrate targets, including mannan, xylan, beta-glucans, cellulose, agarose, and arabinans. These domains facilitate the strong binding of co-occuring (catalytic) modules to their insoluble substrates. 150 matched cddid_all.tbl CDD cd14490 cd14490 271156 CBM6-CBM35-CBM36_like_1 uncharacterized members of the carbohydrate binding module 6 (CBM6) and CBM35_like superfamily. Carbohydrate binding module family 6 (CBM6, family 6 CBM), also known as cellulose binding domain family VI (CBD VI), and related CBMs (CBM35 and CBM36). These are non-catalytic carbohydrate binding domains found in a range of enzymes that display activities against a diverse range of carbohydrate targets, including mannan, xylan, beta-glucans, cellulose, agarose, and arabinans. These domains facilitate the strong binding of the appended catalytic modules to their dedicated, insoluble substrates. Many of these CBMs are associated with glycoside hydrolase (GH) domains. CBM6 is an unusual CBM as it represents a chimera of two distinct binding sites with different modes of binding: binding site I within the loop regions and binding site II on the concave face of the beta-sandwich fold. CBM36s are calcium-dependent xylan binding domains. CBM35s display conserved specificity through extensive sequence similarity, but divergent function through their appended catalytic modules. 156 matched cddid_all.tbl CDD cd14491 cd14491 381186 lipocalin_MxiM-like Shigella pilot protein MxiM and similar proteins. Shigella flexneri MxiM, is a pilot protein for S. flexneri MxiD, an outer membrane (OM)-associated ring-forming secretin and component of the type-III secretion system. MxiM, also an OM protein, binds lipids and MxiD. MxiM binds and affects several features of the secretin MxiD, including its stability in the periplasm, OM association, as well as assembly into multimeric structure. This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 134 matched cddid_all.tbl CDD cd14492 cd14492 381187 lipocalin_MxiM-like MxiM-like lipocalin found in Bacteroidetes. Uncharacterized proteins in this family conserved in Bacteroidetes are similar to Shigella flexneri MxiM, a pilot protein for S. flexneri MxiD, an outer membrane (OM)-associated ring-forming secretin and component of the type-III secretion system. MxiM, also an OM protein, binds lipids and MxiD. This subgroup belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 142 matched cddid_all.tbl CDD cd14493 cd14493 381188 lipocalin_MxiM Shigella Pilot protein MxiM. Shigella flexneri MxiM is a pilot protein for S. flexneri MxiD, an outer membrane (OM)-associated ring-forming secretin. MxiM, also an OM protein, binds lipids and MxiD. MixD is a component of the type-III secretion system that translocates proteins through both membranes of gram-negative bacterial pathogens into host cells and requires the formation of an integral OM secretin ring. MxiM binds and affects several features of the secretin MxiD, including its stability in the periplasm, OM association, as well as assembly into multimeric structure. MxiM belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 115 matched cddid_all.tbl CDD cd14494 cd14494 350344 PTP_DSP_cys cys-based protein tyrosine phosphatase and dual-specificity phosphatase superfamily. This superfamily is composed of cys-based phosphatases, which includes classical protein tyrosine phosphatases (PTPs) as well as dual-specificity phosphatases (DUSPs or DSPs). They are characterized by a CxxxxxR conserved catalytic loop (where C is the catalytic cysteine, x is any amino acid, and R is an arginine). PTPs are part of the tyrosine phosphorylation/dephosphorylation regulatory mechanism, and are important in the response of the cells to physiologic and pathologic changes in their environment. DUSPs show more substrate diversity (including RNA and lipids) and include pTyr, pSer, and pThr phosphatases. 113 matched cddid_all.tbl CDD cd14495 cd14495 350345 PTPLP-like Protein tyrosine phosphatase-like domains of phytases and similar domains. This subfamily contains the tandem protein tyrosine phosphatase (PTP)-like domains of protein tyrosine phosphatase-like phytases (PTPLPs) and similar domains including the PTP domain of Pseudomonas syringae tyrosine-protein phosphatase hopPtoD2. PTPLPs, also known as cysteine phytases, are one of four known classes of phytases, enzymes that degrade phytate (inositol hexakisphosphate [InsP(6)]) to less-phosphorylated myo-inositol derivatives. Phytate is the most abundant cellular inositol phosphate and plays important roles in a broad scope of cellular processes, including DNA repair, RNA processing and export, development, apoptosis, and pathogenicity. PTPLPs adopt a PTP fold, including the active-site signature sequence (CX5R(S/T)) and utilize a classical PTP reaction mechanism. However, these enzymes display no catalytic activity against classical PTP substrates due to several unique structural features that confer specificity for myo-inositol polyphosphates. 278 matched cddid_all.tbl CDD cd14496 cd14496 350346 PTP_paladin protein tyrosine phosphatase-like domains of paladin. Paladin is a putative phosphatase, which in mouse is expressed in endothelial cells during embryonic development and in arterial smooth muscle cells in adults. It has been suggested to be an antiphosphatase that regulates the activity of specific neural crest regulatory factors and thus, modulates neural crest cell formation and migration. Paladin contains two protein tyrosine phosphatase (PTP)-like domains. This model represents both repeats. 185 matched cddid_all.tbl CDD cd14497 cd14497 350347 PTP_PTEN-like protein tyrosine phosphatase-like domain of phosphatase and tensin homolog and similar proteins. Phosphatase and tensin homolog (PTEN) is a tumor suppressor that acts as a dual-specificity protein phosphatase and as a lipid phosphatase. It dephosphorylates phosphoinositide trisphosphate. In addition to PTEN, this family includes tensins, voltage-sensitive phosphatases (VSPs), and auxilins. They all contain a protein tyrosine phosphatase-like domain although not all are active phosphatases. Tensins are intracellular proteins that act as links between the extracellular matrix and the cytoskeleton, and thereby mediate signaling for cell shape and motility, and they may or may not have phosphatase activity. VSPs are phosphoinositide phosphatases with substrates that include phosphatidylinositol-4,5-diphosphate and phosphatidylinositol-3,4,5-trisphosphate. Auxilins are J domain-containing proteins that facilitate Hsc70-mediated dissociation of clathrin from clathrin-coated vesicles, and they do not exhibit phosphatase activity. 160 matched cddid_all.tbl CDD cd14498 cd14498 350348 DSP dual-specificity phosphatase domain. The dual-specificity phosphatase domain is found in typical and atypical dual-specificity phosphatases (DUSPs), which function as protein-serine/threonine phosphatases (EC 3.1.3.16) and protein-tyrosine-phosphatases (EC 3.1.3.48). Typical DUSPs, also called mitogen-activated protein kinase (MAPK) phosphatases (MKPs), deactivate MAPKs by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. All MKPs contain an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. Atypical DUSPs contain the catalytic dual specificity phosphatase domain but lack the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. Also included in this family are dual specificity phosphatase-like domains of catalytically inactive members such as serine/threonine/tyrosine-interacting protein (STYX) and serine/threonine/tyrosine interacting like 1 (STYXL1), as well as active phosphatases with substrates that are not phosphoproteins such as PTP localized to the mitochondrion 1 (PTPMT1), which is a lipid phosphatase, and laforin, which is a glycogen phosphatase. 135 matched cddid_all.tbl CDD cd14499 cd14499 350349 CDC14_C C-terminal dual-specificity phosphatase domain of CDC14 family proteins. The cell division control protein 14 (CDC14) family is highly conserved in all eukaryotes, although the roles of its members seem to have diverged during evolution. Yeast Cdc14, the best characterized member of this family, is a dual-specificity phosphatase that plays key roles in cell cycle control. It preferentially dephosphorylates cyclin-dependent kinase (CDK) targets, which makes it the main antagonist of CDK in the cell. Cdc14 functions at the end of mitosis and it triggers the events that completely eliminates the activity of CDK and other mitotic kinases. It is also involved in coordinating the nuclear division cycle with cytokinesis through the cytokinesis checkpoint, and in chromosome segregation. Cdc14 phosphatases also function in DNA replication, DNA damage checkpoint, and DNA repair. Vertebrates may contain more than one Cdc14 homolog; humans have three (CDC14A, CDC14B, and CDC14C). CDC14 family proteins contain a highly conserved N-terminal pseudophosphatase domain that contributes to substrate specificity and a C-terminal catalytic dual-specificity phosphatase domain with the PTP signature motif. 174 matched cddid_all.tbl CDD cd14500 cd14500 350350 PTP-IVa protein tyrosine phosphatase type IVA family. Protein tyrosine phosphatases type IVA (PTP-IVa), also known as protein-tyrosine phosphatases of regenerating liver (PRLs) constitute a family of small, prenylated phosphatases that are the most oncogenic of all PTPs. They stimulate progression from G1 into S phase during mitosis and enhances cell proliferation, cell motility and invasive activity, and promotes cancer metastasis. They associate with magnesium transporters of the cyclin M (CNNM) family, which results in increased intracellular magnesium levels that promote oncogenic transformation. Vertebrates contain three members: PRL-1, PRL-2, and PRL-3. 156 matched cddid_all.tbl CDD cd14501 cd14501 350351 PFA-DSP plant and fungi atypical dual-specificity phosphatase. Plant and fungi atypical dual-specificity phosphatases (PFA-DSPs) are a group of atypical DSPs present in plants, fungi, kinetoplastids, and slime molds. They share structural similarity with atypical- and lipid phosphatase DSPs from mammals. The PFA-DSP group is composed of active as well as inactive phosphatases. The best characterized member is Saccharomyces Siw14, also known as Oca3, which plays a role in actin filament organization and endocytosis. Siw14 has been shown to be an inositol pyrophosphate phosphatase, hydrolyzing the beta-phosphate from 5-diphosphoinositol pentakisphosphate (5PP-IP5or IP7). 149 matched cddid_all.tbl CDD cd14502 cd14502 350352 RNA_5'-triphosphatase RNA 5'-triphosphatase domain. This family of RNA-specific cysteine phosphatases includes baculovirus RNA 5'-triphosphatase, dual specificity protein phosphatase 11 (DUSP11), and the RNA triphosphatase domains of metazoan and plant mRNA capping enzymes. RNA/polynucleotide 5'-triphosphatase (EC 3.1.3.33) catalyzes the removal of the gamma-phosphate from the 5'-triphosphate end of nascent mRNA to yield a diphosphate end. mRNA capping enzyme is a bifunctional enzyme that catalyzes the first two steps of cap formation. DUSP11 has RNA 5'-triphosphatase and diphosphatase activity, but only poor protein-tyrosine phosphatase activity. 167 matched cddid_all.tbl CDD cd14503 cd14503 350353 PTP-bact bacterial tyrosine-protein phosphataseS similar to Neisseria NMA1982. This subfamily is composed of bacterial tyrosine-protein phosphatases similar to Neisseria meningitidis NMA1982, which displays phosphatase activity but whose biological function is still unknown. 136 matched cddid_all.tbl CDD cd14504 cd14504 350354 DUSP23 dual specificity phosphatase 23. Dual specificity phosphatase 23 (DUSP23), also known as VH1-like phosphatase Z (VHZ) or low molecular mass dual specificity phosphatase 3 (LDP-3), functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). It deactivates its MAPK substrates by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. DUSP23 is an atypical DUSP; it contains the catalytic dual specificity phosphatase domain but lacks the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. It is able to enhance activation of JNK and p38 MAPK, and has been shown to dephosphorylate p44-ERK1 (MAPK3) in vitro. It has been associated with cell growth and human primary cancers. It has also been identified as a cell-cell adhesion regulatory protein; it promotes the dephosphorylation of beta-catenin at Tyr 142 and enhances the interaction between alpha- and beta-catenin. 142 matched cddid_all.tbl CDD cd14505 cd14505 350355 CDKN3-like cyclin-dependent kinase inhibitor 3 and similar proteins. This family is composed of eukaryotic cyclin-dependent kinase inhibitor 3 (CDKN3) and related archaeal and bacterial proteins. CDKN3 is also known as kinase-associated phosphatase (KAP), CDK2-associated dual-specificity phosphatase, cyclin-dependent kinase interactor 1 (CDI1), or cyclin-dependent kinase-interacting protein 2 (CIP2). It has been characterized as dual-specificity phosphatase, which function as a protein-serine/threonine phosphatase (EC 3.1.3.16) and protein-tyrosine-phosphatase (EC 3.1.3.48). It dephosphorylates CDK2 at a threonine residue in a cyclin-dependent manner, resulting in the inhibition of G1/S cell cycle progression. It also interacts with CDK1 and controls progression through mitosis by dephosphorylating CDC2. CDKN3 may also function as a tumor suppressor; its loss of function was found in a variety of cancers including glioblastoma and hepatocellular carcinoma. However, it has also been found over-expressed in many cancers such as breast, cervical, lung and prostate cancers, and may also have an oncogenic function. 163 matched cddid_all.tbl CDD cd14506 cd14506 350356 PTP_PTPDC1 protein tyrosine phosphatase domain of PTP domain-containing protein 1. protein tyrosine phosphatase domain-containing protein 1 (PTPDC1) is an uncharacterized non-receptor class protein-tyrosine phosphatase (PTP). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. Small interfering RNA (siRNA) knockdown of the ptpdc1 gene is associated with elongated cilia. 206 matched cddid_all.tbl CDD cd14507 cd14507 350357 PTP-MTM-like protein tyrosine phosphatase-like domain of myotubularins. Myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. They dephosphorylate the D-3 position of phosphatidylinositol 3-phosphate [PI(3)P] and phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2], generating phosphatidylinositol and phosphatidylinositol 5-phosphate [PI(5)P], respectively. Not all members are catalytically active proteins, some function as adaptors for the active members. 226 matched cddid_all.tbl CDD cd14508 cd14508 350358 PTP_tensin protein tyrosine phosphatase-like domain of tensins. The tensin family of intracellular proteins (tensin-1, -2, -3 and -4) act as links between the extracellular matrix and the cytoskeleton, and thereby mediate signaling for cell shape and motility. Dysregulation of tensin expression has been implicated in human cancer. Tensin-1, -2, and -3 contain an N-terminal region with a protein tyrosine phosphatase (PTP)-like domain followed by a protein kinase 2 (C2) domain, and a C-terminal region with SH2 and pTyr binding (PTB) domains. In addition, tensin-2 contains a zinc finger N-terminal to its PTP domain. Tensin-4 is not included in this model as it does not contain a PTP-like domain. 159 matched cddid_all.tbl CDD cd14509 cd14509 350359 PTP_PTEN protein tyrosine phosphatase-like catalytic domain of phosphatase and tensin homolog. Phosphatase and tensin homolog (PTEN), also phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN or mutated in multiple advanced cancers 1 (MMAC1), is a tumor suppressor that acts as a dual-specificity protein phosphatase and as a lipid phosphatase. It is a critical endogenous inhibitor of phosphoinositide signaling. It dephosphorylates phosphoinositide trisphosphate, and therefore, has the function of negatively regulating Akt. The PTEN/PI3K/AKT pathway regulates the signaling of multiple biological processes such as apoptosis, metabolism, cell proliferation, and cell growth. PTEN contains an N-terminal PIP-binding domain, a protein tyrosine phosphatase (PTP)-like catalytic domain, a regulatory C2 domain responsible for its cellular location, a C-tail containing phosphorylation sites, and a C-terminal PDZ domain. 158 matched cddid_all.tbl CDD cd14510 cd14510 350360 PTP_VSP_TPTE protein tyrosine phosphatase-like catalytic domain of voltage-sensitive phosphatase/transmembrane phosphatase with tensin homology. Voltage-sensitive phosphatase (VSP) proteins comprise a family of phosphoinositide phosphatases with substrates that include phosphatidylinositol-4,5-diphosphate and phosphatidylinositol-3,4,5-trisphosphate. This family is conserved in deuterostomes; VSP was first identified as a sperm flagellar plasma membrane protein in Ciona intestinalis. Gene duplication events in primates resulted in the presence of paralogs, transmembrane phosphatase with tensin homology (TPTE) and TPTE2, that retain protein domain architecture but, in the case of TPTE, have lost catalytic activity. TPTE, also called cancer/testis antigen 44 (CT44), may play a role in the signal transduction pathways of the endocrine or spermatogenic function of the testis. TPTE2, also called TPTE and PTEN homologous inositol lipid phosphatase (TPIP), occurs in several differentially spliced forms; TPIP alpha displays phosphoinositide 3-phosphatase activity and is localized on the endoplasmic reticulum, while TPIP beta is cytosolic and lacks detectable phosphatase activity. VSP/TPTE proteins contain an N-terminal voltage sensor consisting of four transmembrane segments, a protein tyrosine phosphatase (PTP)-like phosphoinositide phosphatase catalytic domain, followed by a regulatory C2 domain. 177 matched cddid_all.tbl CDD cd14511 cd14511 350361 PTP_auxilin-like protein tyrosine phosphatase-like domain of auxilin and similar proteins. This subfamily contains proteins similar to auxilin, characterized by also containing a J domain. It includes auxilin, also called auxilin-1, and cyclin-G-associated kinase (GAK), also called auxilin-2. Auxilin-1 and -2 facilitate Hsc70-mediated dissociation of clathrin from clathrin-coated vesicles. GAK is expressed ubiquitously and is enriched in the Golgi, while auxilin-1 which is nerve-specific. Both proteins contain a protein tyrosine phosphatase (PTP)-like domain similar to the PTP-like domain of PTEN (a phosphoinositide 3-phosphatase), and a C-terminal region with clathrin-binding and J domains. In addition, GAK contains an N-terminal protein kinase domain that phosphorylates the mu subunits of adaptor protein (AP) 1 and AP2. 164 matched cddid_all.tbl CDD cd14512 cd14512 350362 DSP_MKP dual specificity phosphatase domain of mitogen-activated protein kinase phosphatase. Mitogen-activated protein kinase (MAPK) phosphatases (MKPs) are eukaryotic dual-specificity phosphatases (DUSPs) that act on MAPKs, which are involved in gene regulation, cell proliferation, programmed cell death and stress responses, as an important feedback control mechanism that limits MAPK cascades. MKPs, also referred to as typical DUSPs, function as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). They deactivate MAPKs by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. All MKPs contain an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. Based on sequence homology, subcellular localization and substrate specificity, 10 MKPs can be subdivided into three subfamilies (class I-III). 136 matched cddid_all.tbl CDD cd14513 cd14513 350363 DSP_slingshot dual specificity phosphatase domain of slingshot family phosphatases. The slingshot (SSH) family of dual specificity protein phosphatases is composed of Drosophila slingshot phosphatase and its vertebrate homologs: SSH1, SSH2 and SSH3. Its members specifically dephosphorylate and reactivate Ser-3-phosphorylated cofilin (P-cofilin), an actin-binding protein that plays an essential role in actin filament dynamics. In Drosophila, loss of ssh gene function causes prominent elevation in the levels of P-cofilin and filamentous actin and disorganized epidermal cell morphogenesis, including bifurcation phenotypes of bristles and wing hairs. SSH family phosphatases contain an N-terminal, SSH family-specific non-catalytic (SSH-N) domain, followed by a short domain with similarity to the C-terminal domain of the chromatin-associated protein DEK, and a dual specificity phosphatase catalytic domain. In addition, many members contain a C-terminal tail. The SSH-N domain plays critical roles in P-cofilin recognition, F-actin-mediated activation, and subcellular localization of SSHs. 139 matched cddid_all.tbl CDD cd14514 cd14514 350364 DUSP14-like dual specificity protein phosphatases 14, 18, 21, 28 and similar proteins. This family is composed of dual specificity protein phosphatase 14 (DUSP14, also known as MKP-6), 18 (DUSP18), 21 (DUSP21), 28 (DUSP28), and similar proteins. They function as protein-serine/threonine phosphatases (EC 3.1.3.16) and protein-tyrosine-phosphatases (EC 3.1.3.48), and are atypical DUSPs. They contain the catalytic dual specificity phosphatase domain but lack the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. DUSP14 directly interacts and dephosphorylates TGF-beta-activated kinase 1 (TAK1)-binding protein 1 (TAB1) in T cells, and negatively regulates TCR signaling and immune responses. DUSP18 has been shown to interact and dephosphorylate SAPK/JNK, and may play a role in regulating the SAPK/JNK pathway. DUSP18 and DUSP21 target to opposing sides of the mitochondrial inner membrane. DUSP28 has been implicated in hepatocellular carcinoma progression and in migratory activity and drug resistance of pancreatic cancer cells. 133 matched cddid_all.tbl CDD cd14515 cd14515 350365 DUSP3-like dual specificity protein phosphatases 3, 13, 26, 27, and similar domains. This family is composed of dual specificity protein phosphatase 3 (DUSP3, also known as VHR), 13B (DUSP13B, also known as TMDP), 26 (DUSP26, also known as MPK8), 13A (DUSP13A, also known as MDSP), dual specificity phosphatase and pro isomerase domain containing 1 (DUPD1), and inactive DUSP27. In general, DUSPs function as protein-serine/threonine phosphatases (EC 3.1.3.16) and protein-tyrosine-phosphatases (EC 3.1.3.48). Members of this family are atypical DUSPs; they contain the catalytic dual specificity phosphatase domain but lack the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. Inactive DUSP27 contains a dual specificity phosphatase-like domain with the active site cysteine substituted to serine. 148 matched cddid_all.tbl CDD cd14516 cd14516 350366 DSP_fungal_PPS1 dual specificity phosphatase domain of fungal dual specificity protein phosphatase PPS1-like. This subfamily contains fungal proteins with similarity to dual specificity protein phosphatase PPS1 from Saccharomyces cerevisiae, which has a role in the DNA synthesis phase of the cell cycle. As a dual specificity protein phosphatase, PPS1 functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). It contains a C-terminal catalytic dual specificity phosphatase domain. 177 matched cddid_all.tbl CDD cd14517 cd14517 350367 DSP_STYXL1 dual specificity phosphatase-like domain of serine/threonine/tyrosine interacting like 1. Serine/threonine/tyrosine interacting like 1 (STYXL1), also known as DUSP24 and MK-STYX, is a catalytically inactive phosphatase with homology to the mitogen-activated protein kinase (MAPK) phosphatases (MKPs). STYXL1 plays a role in regulating pathways by competing with active phosphatases for binding to MAPKs. Similar to MKPs, STYXL1 contains an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, however its C-terminal dual specificity phosphatase-like domain is a pseudophosphatase missing the catalytic cysteine. 155 matched cddid_all.tbl CDD cd14518 cd14518 350368 DSP_fungal_YVH1 dual specificity phosphatase domain of fungal YVH1-like dual specificity protein phosphatase. This family is composed of Saccharomyces cerevisiae dual specificity protein phosphatase Yvh1 and similar fungal proteins. Yvh1 could function as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). It regulates cell growth, sporulation, and glycogen accumulation. It plays an important role in ribosome assembly. Yvh1 associates transiently with late pre-60S particles and is required for the release of the nucleolar/nuclear pre-60S factor Mrt4, which is necessary to construct a translation-competent 60S subunit and mature ribosome stalk. Yvh1 contains an N-terminal catalytic dual specificity phosphatase domain and a C-terminal tail. 153 matched cddid_all.tbl CDD cd14519 cd14519 350369 DSP_DUSP22_15 dual specificity phosphatase domain of dual specificity protein phosphatase 22, 15, and similar proteins. Dual specificity protein phosphatase 22 (DUSP22, also known as VHX) and 15 (DUSP15, also known as VHY) function as protein-serine/threonine phosphatases (EC 3.1.3.16) and protein-tyrosine-phosphatases (EC 3.1.3.48). They are atypical DUSPs; they contain the catalytic dual specificity phosphatase domain but lack the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. The both contain N-terminal myristoylation recognition sequences and myristoylation regulates their subcellular location. DUSP22 negatively regulates the estrogen receptor-alpha-mediated signaling pathway and the IL6-leukemia inhibitory factor (LIF)-STAT3-mediated signaling pathway. DUSP15 has been identified as a regulator of oligodendrocyte differentiation. DUSP22 is a single domain protein containing only the catalytic dual specificity phosphatase domain while DUSP15 contains a short C-terminal tail. 136 matched cddid_all.tbl CDD cd14520 cd14520 350370 DSP_DUSP12 dual specificity phosphatase domain of dual specificity protein phosphatase 12 and similar proteins. Dual specificity protein phosphatase 12 (DUSP12), also called YVH1, functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). It deactivates its MAPK substrates by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. DUSP12 is an atypical DUSP; it contains the catalytic dual specificity phosphatase domain but lacks the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. It targets p38 MAPK to regulate macrophage response to bacterial infection. It also ameliorates cardiac hypertrophy in response to pressure overload through c-Jun N-terminal kinase (JNK) inhibition. DUSP12 has been identified as a modulator of cell cycle progression, a function independent of phosphatase activity and mediated by its C-terminal zinc-binding domain. 144 matched cddid_all.tbl CDD cd14521 cd14521 350371 DSP_fungal_SDP1-like dual specificity phosphatase domain of fungal dual specificity protein phosphatase SDP1, MSG5, and similar proteins. This family is composed of fungal dual specificity protein phosphatases (DUSPs) including Saccharomyces cerevisiae SDP1 and MSG5, and Schizosaccharomyces pombe Pmp1. function as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). They deactivate MAPKs by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. SDP1 is oxidative stress-induced and dephosphorylates MAPK substrates such as SLT2. MSG5 dephosphorylates the Fus3 and Slt2 MAPKs operating in the mating and cell wall integrity (CWI) pathways, respectively. Pmp1 is responsible for dephosphorylating the CWI MAPK Pmk1. These phosphatases bind to their target MAPKs through a conserved IYT motif located outside of the dual specificity phosphatase domain. 155 matched cddid_all.tbl CDD cd14522 cd14522 350372 DSP_STYX dual specificity phosphatase-like domain of serine/threonine/tyrosine-interacting protein. Serine/threonine/tyrosine-interacting protein (STYX), also called protein tyrosine phosphatase-like protein, is a catalytically inactive member of the protein tyrosine phosphatase family that plays an integral role in regulating pathways by competing with active phosphatases for binding to MAPKs. It acts as a nuclear anchor for MAPKs, affecting their nucleocytoplasmic shuttling. 151 matched cddid_all.tbl CDD cd14523 cd14523 350373 DSP_DUSP19 dual specificity phosphatase domain of dual specificity protein phosphatase 19. Dual specificity protein phosphatase 19 (DUSP19), also called low molecular weight dual specificity phosphatase 3 (LMW-DSP3) or stress-activated protein kinase (SAPK) pathway-regulating phosphatase 1 (SKRP1), functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). It is an atypical DUSP; it contains the catalytic dual specificity phosphatase domain but lacks the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. DUSP19 interacts with the MAPK kinase MKK7, a JNK activator, and inactivates the JNK MAPK pathway. 137 matched cddid_all.tbl CDD cd14524 cd14524 350374 PTPMT1 protein-tyrosine phosphatase mitochondrial 1. Protein-tyrosine phosphatase mitochondrial 1 or PTP localized to the mitochondrion 1 (PTPMT1), also called phosphoinositide lipid phosphatase (PLIP), phosphatidylglycerophosphatase and protein-tyrosine phosphatase 1, or PTEN-like phosphatase, is a lipid phosphatase or phosphatidylglycerophosphatase (EC 3.1.3.27) which dephosphorylates phosphatidylglycerophosphate (PGP) to phosphatidylglycerol (PG). It is targeted to the mitochondrion by an N-terminal signal sequence and is found anchored to the matrix face of the inner membrane. It is essential for the biosynthesis of cardiolipin, a mitochondrial-specific phospholipid regulating the membrane integrity and activities of the organelle. PTPMT1 also plays a crucial role in hematopoietic stem cell (HSC) function, and has been shown to display activity toward phosphoprotein substrates. 149 matched cddid_all.tbl CDD cd14526 cd14526 350375 DSP_laforin-like dual specificity phosphatase domain of laforin and similar domains. This family is composed of glucan phosphatases including vertebrate dual specificity protein phosphatase laforin, also called lafora PTPase (LAFPTPase), and plant starch excess4 (SEX4). Laforin is a glycogen phosphatase; its gene is mutated in Lafora progressive myoclonus epilepsy or Lafora disease (LD), a fatal autosomal recessive neurodegenerative disorder characterized by the presence of progressive neurological deterioration, myoclonus, and epilepsy. One characteristic of LD is the accumulation of insoluble glucans. Laforin prevents LD by at least two mechanisms: by preventing hyperphosphorylation of glycogen by dephosphorylating it, allowing proper glycogen formation, and by promoting the ubiquitination of proteins involved in glycogen metabolism via its interaction with malin. Laforin contains an N-terminal CBM20 (carbohydrate-binding module, family 20) domain and a C-terminal catalytic dual specificity phosphatase (DSP) domain. Plant SEX4 regulate starch metabolism by selectively dephosphorylating glucose moieties within starch glucan chains. It contains an N-terminal catalytic DSP domain and a C-terminal Early (E) set domain. 146 matched cddid_all.tbl CDD cd14527 cd14527 350376 DSP_bac unknown subfamily of bacterial and plant dual specificity protein phosphatases. This subfamily is composed of uncharacterized bacterial and plant dual-specificity protein phosphatases. DUSPs function as a protein-serine/threonine phosphatases (EC 3.1.3.16) and a protein-tyrosine-phosphatases (EC 3.1.3.48). 136 matched cddid_all.tbl CDD cd14528 cd14528 350377 PFA-DSP_Siw14 atypical dual specificity phosphatases similar to yeast Siw14. This subfamily contains Saccharomyces Siw14 and a novel phosphatase from the Arabidopsis thaliana gene locus At1g05000. Siw14, also known as Oca3, plays a role in actin filament organization and endocytosis. Siw14 has been shown to be an inositol pyrophosphate phosphatase, hydrolyzing the beta-phosphate from 5-diphosphoinositol pentakisphosphate (5PP-IP5or IP7). The At1g05000 protein, also called AtPFA-DSP1, has been shown to have highest activity toward olyphosphate (poly-P(12-13)) and deoxyribo- and ribonucleoside triphosphates, and less activity toward phosphoenolpyruvate, phosphotyrosine, phosphotyrosine-containing peptides, and phosphatidylinositols. This subfamily belongs to a group of atypical DSPs present in plants, fungi, kinetoplastids, and slime molds called plant and fungi atypical dual-specificity phosphatases (PFA-DSPs). 148 matched cddid_all.tbl CDD cd14529 cd14529 350378 TpbA-like bacterial protein tyrosine and dual-specificity phosphatases related to Pseudomonas aeruginosa TpbA. This subfamily contains bacterial protein tyrosine phosphatases (PTPs) and dual-specificity phosphatases (DUSPs) related to Pseudomonas aeruginosa TpbA, a DUSP that negatively regulates biofilm formation by converting extracellular quorum sensing signals and to Mycobacterium tuberculosis PtpB, a PTP virulence factor that attenuates host immune defenses by interfering with signal transduction pathways in macrophages. PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides, while DUSPs function as protein-serine/threonine phosphatases (EC 3.1.3.16) and PTPs. 158 matched cddid_all.tbl CDD cd14531 cd14531 350379 PFA-DSP_Oca1 atypical dual specificity phosphatases similar to oxidant-induced cell-cycle arrest protein 1. Oxidant-induced cell-cycle arrest protein 1 (Oca1) is an atypical dual specificity phosphatase whose gene is required for G1 arrest in response to the lipid oxidation product linoleic acid hydroperoxide. It may function in linking growth, stress responses, and the cell cycle. Oca1 belongs to a group of atypical DSPs present in plants, fungi, kinetoplastids, and slime molds called plant and fungi atypical dual-specificity phosphatases (PFA-DSPs). 149 matched cddid_all.tbl CDD cd14532 cd14532 350380 PTP-MTMR6-like protein tyrosine phosphatase-like domain of myotubularin related phosphoinositide phosphatases 6, 7, and 8. This subgroup of enzymatically active phosphatase domains of myotubularins consists of MTMR6, MTMR7 and MTMR8, and related domains. Beside the phosphatase domain, they contain a C-terminal coiled-coil domain and an N-terminal PH-GRAM domain. In general, myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. They dephosphorylate the D-3 position of phosphatidylinositol 3-phosphate [PI(3)P] and phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2], generating phosphatidylinositol and phosphatidylinositol 5-phosphate [PI(5)P], respectively. MTMR6, MTMR7 and MTMR8 form complexes with catalytically inactive MTMR9, and display differential substrate preferences. In cells, the MTMR6/R9 complex significantly increases the cellular levels of PtdIns(5)P, the product of PI(3,5)P(2) dephosphorylation, whereas the MTMR8/R9 complex reduces cellular PtdIns(3)P levels. The MTMR6/R9 complex serves to inhibit stress-induced apoptosis while the MTMR8/R9 complex inhibits autophagy. 301 matched cddid_all.tbl CDD cd14533 cd14533 350381 PTP-MTMR3-like protein tyrosine phosphatase-like domain of myotubularin related phosphoinositide phosphatases 3 and 4. This subgroup of enzymatically active phosphatase domains of myotubularins consists of MTMR3, also known as ZFYVE10, and MTMR4, also known as ZFYVE11, and related domains. Beside the phosphatase domain, they contain a C-terminal FYVE domain and an N-terminal PH-GRAM domain. In general, myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. They dephosphorylate the D-3 position of phosphatidylinositol 3-phosphate [PI(3)P] and phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2], generating phosphatidylinositol and phosphatidylinositol 5-phosphate [PI(5)P], respectively. 229 matched cddid_all.tbl CDD cd14534 cd14534 350382 PTP-MTMR5-like protein tyrosine phosphatase-like pseudophosphatase domain of myotubularin related phosphoinositide phosphatases 5 and 13. This subgroup of enzymatically inactive phosphatase domains of myotubularins consists of MTMR5, also known as SET binding factor 1 (SBF1) and MTMR13, also known as SET binding factor 2 (SBF2), and similar domains. Beside the pseudophosphatase domain, they contain a variety of other domains, including a DENN and a PH-like domain. In general, myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. MTMR5 and MTMR13 are pseudophosphatases that lack the catalytic cysteine in their catalytic pocket. Mutations in MTMR13 causes Charcot-Marie-Tooth type 4B2, a severe childhood-onset neuromuscular disorder, characterized by demyelination and redundant loops of myelin known as myelin outfoldings, a similar phenotype as mutations in MTMR2. Mutations in the MTMR5 gene cause Charcot-Marie-tooth disease type 4B3. MTMR5 and MTMR13 interact with MTMR2 and stimulate its phosphatase activity. 274 matched cddid_all.tbl CDD cd14535 cd14535 350383 PTP-MTM1-like protein tyrosine phosphatase-like domain of myotubularin, and myotubularin related phosphoinositide phosphatases 1 and 2. This subgroup of enzymatically active phosphatase domains of myotubularins consists of MTM1, MTMR1 and MTMR2. All contain an additional N-terminal PH-GRAM domain and C-terminal coiled-coiled domain and PDZ binding site. In general, myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. They dephosphorylate the D-3 position of phosphatidylinositol 3-phosphate [PI(3)P] and phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2], generating phosphatidylinositol and phosphatidylinositol 5-phosphate [PI(5)P], respectively. 249 matched cddid_all.tbl CDD cd14536 cd14536 350384 PTP-MTMR9 protein tyrosine phosphatase-like pseudophosphatase domain of myotubularin related phosphoinositide phosphatase 9. Myotubularin related phosphoinositide phosphatase 9 (MTMR9) is enzymatically inactive and contains a C-terminal coiled-coil domain and an N-terminal PH-GRAM domain. Mutations have been associated with obesity and metabolic syndrome. In general, myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. MTMR9 is a pseudophosphatase that lacks the catalytic cysteine in its catalytic pocket. It forms complexes with catalytically active MTMR6, MTMR7 and MTMR8, and regulates their activities; the complexes display differential substrate preferences. The MTMR6/R9 complex serves to inhibit stress-induced apoptosis while the MTMR8/R9 complex inhibits autophagy. 224 matched cddid_all.tbl CDD cd14537 cd14537 350385 PTP-MTMR10-like protein tyrosine phosphatase-like pseudophosphatase domain of myotubularin related phosphoinositide phosphatases 10, 11, and 12. This subgroup of enzymatically inactive phosphatase domains of myotubularins consists of MTMR10, MTMR11, MTMR12, and similar proteins. Beside the phosphatase domain, they contain an N-terminal PH-GRAM domain. In general, myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. MTMR10, MTMR11, and MTMR12 are pseudophosphatases that lack the catalytic cysteine in their catalytic pocket. MTMR12 functions as an adapter for the catalytically active myotubularin to regulate its intracellular location. 200 matched cddid_all.tbl CDD cd14538 cd14538 350386 PTPc-N20_13 catalytic domain of tyrosine-protein phosphatase non-receptor type 20 and type 13. Tyrosine-protein phosphatase non-receptor type 20 (PTPN20) and type 13 (PTPN13, also known as PTPL1) belong to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. Human PTPN20 is a widely expressed phosphatase with a dynamic subcellular distribution that is targeted to sites of actin polymerization. Human PTPN13 is an important regulator of tumor aggressiveness. 207 matched cddid_all.tbl CDD cd14539 cd14539 350387 PTP-N23 PTP-like domain of tyrosine-protein phosphatase non-receptor type 23. Tyrosine-protein phosphatase non-receptor type 23 (PTPN23), also called His domain-containing protein tyrosine phosphatase (HD-PTP) or protein tyrosine phosphatase TD14 (PTP-TD14), is a catalytically inactive member of the tyrosine-specific protein tyrosine phosphatase (PTP) family. Human PTPN23 may be involved in the regulation of small nuclear ribonucleoprotein assembly and pre-mRNA splicing by modifying the survival motor neuron (SMN) complex. It plays a role in ciliogenesis and is part of endosomal sorting complex required for transport (ESCRT) pathways. PTPN23 contains five domains: a BRO1-like domain that plays a role in endosomal sorting; a V-domain that interacts with Lys63-linked polyubiquitinated substrates; a central proline-rich region that might recruit SH3-containing proteins; a PTP-like domain; and a proteolytic degradation-targeting motif, also known as a PEST sequence. 205 matched cddid_all.tbl CDD cd14540 cd14540 350388 PTPc-N21_14 catalytic domain of tyrosine-protein phosphatase non-receptor type 21 and type 14. Tyrosine-protein phosphatase non-receptor type 21 (PTPN21) and type 14 (PTPN14) belong to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. Both PTPN21 and PTPN14 contain an N-terminal FERM domain and a C-terminal catalytic PTP domain, separated by a long intervening sequence. 219 matched cddid_all.tbl CDD cd14541 cd14541 350389 PTPc-N3_4 catalytic domain of tyrosine-protein phosphatase non-receptor type 21 and type 14. Tyrosine-protein phosphatase non-receptor type 3 (PTPN3) and type 4 (PTPN4) belong to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPN3 and PTPN4 are large modular proteins containing an N-terminal FERM domain, a PDZ domain and a C-terminal catalytic PTP domain. PTPN3 interacts with mitogen-activated protein kinase p38gamma and serves as its specific phosphatase. PTPN4 functions in TCR cell signaling, apoptosis, cerebellar synaptic plasticity, and innate immune responses. 212 matched cddid_all.tbl CDD cd14542 cd14542 350390 PTPc-N22_18_12 catalytic domain of tyrosine-protein phosphatase non-receptor type 22, type 18 and type 12. Tyrosine-protein phosphatase non-receptor type 22 (PTPN22), type 18 (PTPN18) and type 12 (PTPN12) belong to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPN22 is expressed in hematopoietic cells and it functions as a key regulator of immune homeostasis by inhibiting T-cell receptor signaling through the direct dephosphorylation of Src family kinases (Lck and Fyn), ITAMs of the TCRz/CD3 complex, and other signaling molecules. TPN18 regulates HER2-mediated cellular functions through defining both its phosphorylation and ubiquitination states. PTPN12 is characterized as a tumor suppressor and a pivotal regulator of EGFR/HER2 signaling. 202 matched cddid_all.tbl CDD cd14543 cd14543 350391 PTPc-N9 catalytic domain of tyrosine-protein phosphatase non-receptor type 9. Tyrosine-protein phosphatase non-receptor type 9 (PTPN9), also called protein-tyrosine phosphatase MEG2, belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPN9 plays an important role in promoting intracellular secretary vesicle fusion in hematopoietic cells and promotes the dephosphorylation of ErbB2 and EGFR in breast cancer cells, leading to impaired activation of STAT5 and STAT3. It also directly dephosphorylates STAT3 at the Tyr705 residue, resulting in its inactivation. PTPN9 has been found to be dysregulated in various human cancers, including breast, colorectal, and gastric cancer. 271 matched cddid_all.tbl CDD cd14544 cd14544 350392 PTPc-N11_6 catalytic domain of tyrosine-protein phosphatase non-receptor type 11 and type 6. Tyrosine-protein phosphatase non-receptor type 11 (PTPN11) and type 6 (PTPN6) belong to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPN11 and PTPN6, are also called SH2 domain-containing tyrosine phosphatase 2 (SHP2) and 1 (SHP1), respectively. They contain two tandem SH2 domains: a catalytic PTP domain, and a C-terminal tail with regulatory properties. Although structurally similar, they have different localization and different roles in signal transduction. PTPN11/SHP2 is expressed ubiquitously and plays a positive role in cell signaling, leading to cell activation, while PTPN6/SHP1 expression is restricted mainly to hematopoietic and epithelial cells and functions as a negative regulator of signaling events. 251 matched cddid_all.tbl CDD cd14545 cd14545 350393 PTPc-N1_2 catalytic domain of tyrosine-protein phosphatase non-receptor type 1 and type 2. Tyrosine-protein phosphatase non-receptor type 1 (PTPN1) type 2 (PTPN2) belong to the family of classical tyrosine-specific protein tyrosine phosphatases, (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPN1 (or PTP-1B) is the first PTP to be purified and characterized and is the prototypical intracellular PTP found in a wide variety of human tissues. It dephosphorylates and regulates the activity of a number of receptor tyrosine kinases, including the insulin receptor, the EGF receptor, and the PDGF receptor. PTPN2 (or TCPTP), a tumor suppressor, dephosphorylates and inactivates EGFRs, Src family kinases, Janus-activated kinases (JAKs)-1 and -3, and signal transducer and activators of transcription (STATs)-1, -3 and -5, in a cell type and context-dependent manner. 231 matched cddid_all.tbl CDD cd14546 cd14546 350394 R-PTP-N-N2 PTP-like domain of receptor-type tyrosine-protein phosphatase-like N and N2. Receptor-type tyrosine-protein phosphatase-like N (PTPRN) and N2 (PTPRN2) belong to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). They consist of a large ectodomain that contains a RESP18HD (regulated endocrine-specific protein 18 homology domain), followed by a transmembrane segment, and a single, catalytically-impaired, PTP domain. They are mainly expressed in neuropeptidergic neurons and peptide-secreting endocrine cells, including insulin-producing pancreatic beta-cells, and are involved in involved in the generation, cargo storage, traffic, exocytosis and recycling of insulin secretory granules, as well as in beta-cell proliferation. They also are major autoantigens in type 1 diabetes and are involved in the regulation of insulin secretion. 208 matched cddid_all.tbl CDD cd14547 cd14547 350395 PTPc-KIM catalytic domain of the kinase interaction motif (KIM) family of protein-tyrosine phosphatases. The kinase interaction motif (KIM) family of protein-tyrosine phosphatases (PTPs) includes tyrosine-protein phosphatases non-receptor type 7 (PTPN7) and non-receptor type 5 (PTPN5), and protein-tyrosine phosphatase receptor type R (PTPRR). PTPN7 is also called hematopoietic protein-tyrosine phosphatase (HePTP) while PTPN5 is also called striatal-enriched protein-tyrosine phosphatase (STEP). They belong to the family of classical tyrosine-specific PTPs (EC 3.1.3.48) that catalyze the dephosphorylation of phosphotyrosine peptides. KIM-PTPs are characterized by the presence of a 16-amino-acid KIM that binds specifically to members of the MAPK (mitogen-activated protein kinase) family. They are highly specific to the MAPKs ERK1/2 (extracellular-signal-regulated kinase 1/2) and p38, over JNK (c-Jun N-terminal kinase); they dephosphorylate these kinases and thereby critically modulate cell proliferation and differentiation. 224 matched cddid_all.tbl CDD cd14548 cd14548 350396 R3-PTPc catalytic domain of R3 subfamily receptor-type tyrosine-protein phosphatases and similar proteins. R3 subfamily receptor-type phosphotyrosine phosphatases (RPTP) are characterized by a unique modular composition consisting of multiple extracellular fibronectin type III (FN3) repeats and a single (most RPTP subtypes have two) cytoplasmic catalytic PTP domain. Vertebrate members include receptor-type tyrosine-protein phosphatase-like O (PTPRO), J (PTPRJ), Q (PTPRQ), B (PTPRB), V (PTPRV) and H (PTPRH). They belong to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. Most members are PTPs, except for PTPRQ, which dephosphorylates phosphatidylinositide substrates. PTPRV is characterized only in rodents; its function has been lost in humans. Both vertebrate and invertebrate R3 subfamily RPTPs are involved in the control of a variety of cellular processes, including cell growth, differentiation, mitotic cycle and oncogenic transformation. 222 matched cddid_all.tbl CDD cd14549 cd14549 350397 R5-PTPc-1 catalytic domain of R5 subfamily receptor-type tyrosine-protein phosphatases, repeat 1. The R5 subfamily of receptor-type phosphotyrosine phosphatases (RPTP) is composed of receptor-type tyrosine-protein phosphatase Z (PTPRZ) and G (PTPRG). They belong to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. They are type 1 integral membrane proteins consisting of an extracellular region with a carbonic anhydrase-like (CAH) and a fibronectin type III (FN3) domains, and an intracellular region with a catalytic PTP domain (repeat 1) proximal to the membrane, and a catalytically inactive PTP-fold domain (repeat 2) distal to the membrane. This model represents the catalytic PTP domain (repeat 1). 204 matched cddid_all.tbl CDD cd14550 cd14550 350398 R5-PTP-2 PTP-like domain of R5 subfamily receptor-type tyrosine-protein phosphatases, repeat 2. The R5 subfamily of receptor-type phosphotyrosine phosphatases (RPTP) is composed of receptor-type tyrosine-protein phosphatase Z (PTPRZ) and G (PTPRG). They belong to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. They are type 1 integral membrane proteins consisting of an extracellular region with a carbonic anhydrase-like (CAH) and a fibronectin type III (FN3) domains, and an intracellular region with a catalytic PTP domain (repeat 1) proximal to the membrane, and a catalytically inactive PTP-fold domain (repeat 2) distal to the membrane. This model represents the inactive PTP-like domain (repeat 2). 200 matched cddid_all.tbl CDD cd14551 cd14551 350399 R-PTPc-A-E-1 catalytic domain of receptor-type tyrosine-protein phosphatase A and E, repeat 1. Receptor-type tyrosine-protein phosphatase A (PTPRA) and E (PTPRE) belong to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRA and PTPRE share several functions including regulation of Src family kinases and voltage-gated potassium (Kv) channels. They both contain a small extracellular domain, a transmembrane segment, and an intracellular region containing two tandem catalytic PTP domains. This model represents the first catalytic PTP domain (repeat 1). 202 matched cddid_all.tbl CDD cd14552 cd14552 350400 R-PTPc-A-E-2 catalytic domain of receptor-type tyrosine-protein phosphatase A and E, repeat 2. Receptor-type tyrosine-protein phosphatase A (PTPRA) and E (PTPRE) belong to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRA and PTPRE share several functions including regulation of Src family kinases and voltage-gated potassium (Kv) channels. They both contain a small extracellular domain, a transmembrane segment, and an intracellular region containing two tandem catalytic PTP domains. This model represents the second PTP domain (repeat 2). 202 matched cddid_all.tbl CDD cd14553 cd14553 350401 R-PTPc-LAR-1 catalytic domain of LAR family receptor-type tyrosine-protein phosphatases, repeat 1. The LAR (leukocyte common antigen-related) family of receptor-type tyrosine-protein phosphatases (RPTPs) include three vertebrate members: LAR (or PTPRF), R-PTP-delta (or PTPRD), and R-PTP-sigma (or PTPRS). They belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. LAR-RPTPs are synaptic adhesion molecules; they bind to distinct synaptic membrane proteins and are physiologically responsible for mediating presynaptic development by shaping various synaptic adhesion pathways. They play roles in various aspects of neuronal development, including axon guidance, neurite extension, and synapse formation and function. LAR-RPTPs contain an extracellular region with three immunoglobulin-like (Ig) domains and four to eight fibronectin type III (FN3) repeats (determined by alternative splicing), a single transmembrane domain, followed by an intracellular region with a membrane-proximal catalytic PTP domain (repeat 1, also called D1) and a membrane-distal non-catalytic PTP-like domain (repeat 2, also called D2). This model represents the catalytic PTP domain (repeat 1). 238 matched cddid_all.tbl CDD cd14554 cd14554 350402 R-PTP-LAR-2 PTP-like domain of the LAR family receptor-type tyrosine-protein phosphatases, repeat 2. The LAR (leukocyte common antigen-related) family of receptor-type tyrosine-protein phosphatases (RPTPs) include three vertebrate members: LAR (or PTPRF), R-PTP-delta (or PTPRD), and R-PTP-sigma (or PTPRS). They belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. LAR-RPTPs are synaptic adhesion molecules; they bind to distinct synaptic membrane proteins and are physiologically responsible for mediating presynaptic development by shaping various synaptic adhesion pathways. They play roles in various aspects of neuronal development, including axon guidance, neurite extension, and synapse formation and function. LAR-RPTPs contain an extracellular region with three immunoglobulin-like (Ig) domains and four to eight fibronectin type III (FN3) repeats (determined by alternative splicing), a single transmembrane domain, followed by an intracellular region with a membrane-proximal catalytic PTP domain (repeat 1, also called D1) and a membrane-distal non-catalytic PTP-like domain (repeat 2, also called D2). This model represents the non-catalytic PTP-like domain (repeat 2). 238 matched cddid_all.tbl CDD cd14555 cd14555 350403 R-PTPc-typeIIb-1 catalytic domain of type IIb (or R2B) subfamily receptor-type tyrosine-protein phosphatases, repeat 1. The type II (or R2B) subfamily of receptor protein tyrosine phosphatases (RPTPs) include the prototypical member PTPmu (or PTPRM), PCP-2 (or PTPRU), PTPrho (or PTPRT), and PTPkappa (or PTPRK). They belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. Type IIb RPTPs mediate cell-cell adhesion though homophilic interactions; their ligand is an identical molecule on an adjacent cell. No heterophilic interactions between the subfamily members have been observed. They also commonly function as tumor suppressors. They contain an extracellular region with an Meprin-A5 (neuropilin)-mu (MAM) domain, an immunoglobulin (Ig) domain, and four fibronectin type III (FN3) repeats, a transmembrane domain, and an intracellular segment with a juxtamembrane domain similar to the cytoplasmic domain of classical cadherins and two tandem PTP domains. This model represents the first (repeat 1) PTP domain. 204 matched cddid_all.tbl CDD cd14556 cd14556 350404 R-PTPc-typeIIb-2 PTP domain of type IIb (or R2B) subfamily receptor-type tyrosine-protein phosphatases, repeat 2. The type IIb (or R2B) subfamily of receptor protein tyrosine phosphatases (RPTPs) include the prototypical member PTPmu (or PTPRM), PCP-2 (or PTPRU), PTPrho (or PTPRT), and PTPkappa (or PTPRK). They belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. Type IIb RPTPs mediate cell-cell adhesion though homophilic interactions; their ligand is an identical molecule on an adjacent cell. No heterophilic interactions between the subfamily members have been observed. They also commonly function as tumor suppressors. They contain an extracellular region with an Meprin-A5 (neuropilin)-mu (MAM) domain, an immunoglobulin (Ig) domain, and four fibronectin type III (FN3) repeats, a transmembrane domain, and an intracellular segment with a juxtamembrane domain similar to the cytoplasmic domain of classical cadherins and two tandem PTP domains. This model represents the second (repeat 2) PTP domain. 201 matched cddid_all.tbl CDD cd14557 cd14557 350405 R-PTPc-C-1 catalytic domain of receptor-type tyrosine-protein phosphatase C, repeat 1. Receptor-type tyrosine-protein phosphatase C (PTPRC), also known as CD45, leukocyte common antigen (LCA) or GP180, belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRC/CD45 is found in all nucleated hematopoietic cells and is an essential regulator of T- and B-cell antigen receptor signaling. It controls immune response, both positively and negatively, by dephosphorylating a number of signaling molecules such as the Src family kinases, the CD3zeta chain of TCY, and ZAP-70 kinase. Mutations in the human PTPRC/CD45 gene are associated with severe combined immunodeficiency (SCID) and multiple sclerosis. PTPRC/CD45 contains an extracellular receptor-like region with fibronectin type III (FN3) repeats, a short transmembrane segment, and a cytoplasmic region comprising of a membrane proximal catalytically active PTP domain (repeat 1 or D1) and a membrane distal catalytically impaired PTP-like domain (repeat 2, or D2). This model represents repeat 1. 201 matched cddid_all.tbl CDD cd14558 cd14558 350406 R-PTP-C-2 PTP-like domain of receptor-type tyrosine-protein phosphatase C, repeat 2. Receptor-type tyrosine-protein phosphatase C (PTPRC), also known as CD45, leukocyte common antigen (LCA) or GP180, belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRC/CD45 is found in all nucleated hematopoietic cells and is an essential regulator of T- and B-cell antigen receptor signaling. It controls immune response, both positively and negatively, by dephosphorylating a number of signaling molecules such as the Src family kinases, the CD3zeta chain of TCY, and ZAP-70 kinase. Mutations in the human PTPRC/CD45 gene are associated with severe combined immunodeficiency (SCID) and multiple sclerosis. PTPRC/CD45 contains an extracellular receptor-like region with fibronectin type III (FN3) repeats, a short transmembrane segment, and a cytoplasmic region comprising of a membrane proximal catalytically active PTP domain (repeat 1 or D1) and a membrane distal catalytically impaired PTP-like domain (repeat 2, or D2). This model represents repeat 2. 203 matched cddid_all.tbl CDD cd14559 cd14559 350407 PTP_YopH-like YopH and related bacterial protein tyrosine phosphatases. Yersinia outer protein H (YopH) belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. YopH is an essential virulence determinant of the pathogenic bacterium by dephosphorylating several focal adhesion proteins including p130Cas in human epithelial cells, resulting in the disruption of focal adhesions and cell detachment from the extracellular matrix. It contains an N-terminal domain that contains signals required for TTSS-mediated delivery of YopH into host cells and a C-terminal catalytic PTP domain. 227 matched cddid_all.tbl CDD cd14560 cd14560 350408 PTP_tensin-1 protein tyrosine phosphatase-like domain of tensin-1. Tensin-1 (TNS1) is part of the tensin family of intracellular proteins (tensin-1, -2, -3 and -4), which act as links between the extracellular matrix and the cytoskeleton, and thereby mediate signaling for cell shape and motility. It plays an essential role in TGF-beta-induced myofibroblast differentiation and myofibroblast-mediated formation of extracellular fibronectin and collagen matrix. It also positively regulates RhoA activity through its interaction with DLC1, a RhoGAP-containing tumor suppressor; the tensin-1-DLC1-RhoA signaling axis is critical in regulating cellular functions that lead to angiogenesis. Tensin-1 contains an N-terminal region with a protein tyrosine phosphatase (PTP)-like domain followed by a protein kinase 2 (C2) domain, and a C-terminal region with SH2 and pTyr binding (PTB) domains. 159 matched cddid_all.tbl CDD cd14561 cd14561 350409 PTP_tensin-3 protein tyrosine phosphatase-like domain of tensin-3. Tensin-3 (TNS3) is also called tensin-like SH2 domain-containing protein 1 (TENS1) or tumor endothelial marker (TEM6). It is part of the tensin family of intracellular proteins (tensin-1, -2, -3 and -4), which act as links between the extracellular matrix and the cytoskeleton, and thereby mediate signaling for cell shape and motility. Tensin-3 contributes to cell migration, anchorage-independent growth, tumorigenesis, and metastasis of cancer cells. It cooperates with Dock5, an exchange factor for the small GTPase Rac, for osteoclast activity to ensure the correct organization of podosomes. Tensin-3 contains an N-terminal region with a protein tyrosine phosphatase (PTP)-like domain followed by a protein kinase 2 (C2) domain, and a C-terminal region with SH2 and pTyr binding (PTB) domains. 159 matched cddid_all.tbl CDD cd14562 cd14562 350410 PTP_tensin-2 protein tyrosine phosphatase-like domain of tensin-2. Tensin-2 (TNS2) is also called tensin-like C1 domain-containing phosphatase (TENC1) or C1 domain-containing phosphatase and tensin homolog (C1-TEN). It is part of the tensin family of intracellular proteins (tensin-1, -2, -3 and -4), which act as links between the extracellular matrix and the cytoskeleton, and thereby mediate signaling for cell shape and motility. Tensin-2 is an essential component for the maintenance of glomerular basement membrane (GBM) structures. It also modulates cell contractility and remodeling of collagen fibers through the DLC1, a RhoGAP that binds to tensins in focal adhesions. Tensin-2 may have phosphatase activity; it reduces AKT1 phosphorylation. It contains an N-terminal region with a zinc finger, a protein tyrosine phosphatase (PTP)-like domain and a protein kinase 2 (C2) domain, and a C-terminal region with SH2 and pTyr binding (PTB) domains. 159 matched cddid_all.tbl CDD cd14563 cd14563 350411 PTP_auxilin_N N-terminal protein tyrosine phosphatase-like domain of auxilin. Auxilin, also called auxilin-1 or DnaJ homolog subfamily C member 6 (DNAJC6), is a J-domain containing protein that recruits the ATP-dependent chaperone Hsc70 to newly budded clathrin-coated vesicles and promotes uncoating of clathrin-coated vesicles, driving the clathrin assembly#disassembly cycle. Mutations in the DNAJC6 gene, encoding auxilin, are associated with early-onset Parkinson's disease. Auxilin contains an N-terminal protein tyrosine phosphatase (PTP)-like domain similar to the PTP-like domain of PTEN, a phosphoinositide 3-phosphatase, and a C-terminal region with clathrin-binding and J domains. 163 matched cddid_all.tbl CDD cd14564 cd14564 350412 PTP_GAK protein tyrosine phosphatase-like domain of cyclin-G-associated kinase. cyclin-G-associated kinase (GAK), also called auxilin-2, contains an N-terminal protein kinase domain that phosphorylates the mu subunits of adaptor protein (AP) 1 and AP2. In addition, it contains an auxilin-1-like domain structure consisting of a protein tyrosine phosphatase (PTP)-like domain similar to the PTP-like domain of PTEN (a phosphoinositide 3-phosphatase), and a C-terminal region with clathrin-binding and J domains. Like auxilin-1, GAK facilitates Hsc70-mediated dissociation of clathrin from clathrin-coated vesicles. GAK is expressed ubiquitously and is enriched in the Golgi, unlike auxilin-1 which is nerve-specific. GAK also plays regulatory roles outside of clathrin-mediated membrane traffic including the maintenance of centrosome integrity and chromosome congression, neural patterning, survival of neurons, and immune responses through interaction with the interleukin 12 receptor. 163 matched cddid_all.tbl CDD cd14565 cd14565 350413 DSP_MKP_classI dual specificity phosphatase domain of class I mitogen-activated protein kinase phosphatase. Mitogen-activated protein kinase (MAPK) phosphatases (MKPs) are eukaryotic dual-specificity phosphatases (DUSPs) that act on MAPKs and function as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). They deactivate MAPKs by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. Based on sequence homology, subcellular localization and substrate specificity, 10 MKPs can be subdivided into three subfamilies (class I-III). Class I MKPs consist of DUSP1/MKP-1, DUSP2 (PAC1), DUSP4/MKP-2 and DUSP5. They are all mitogen- and stress-inducible nuclear MKPs. All MKPs contain an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. 138 matched cddid_all.tbl CDD cd14566 cd14566 350414 DSP_MKP_classII dual specificity phosphatase domain of class II mitogen-activated protein kinase phosphatase. Mitogen-activated protein kinase (MAPK) phosphatases (MKPs) are eukaryotic dual-specificity phosphatases (DUSPs) that act on MAPKs and function as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). They deactivate MAPKs by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. Based on sequence homology, subcellular localization and substrate specificity, 10 MKPs can be subdivided into three subfamilies (class I-III). Class II MKPs consist of DUSP6/MKP-3, DUSP7/MKP-X and DUSP9/MKP-4, and are ERK-selective cytoplasmic MKPs. All MKPs contain an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. 137 matched cddid_all.tbl CDD cd14567 cd14567 350415 DSP_DUSP10 dual specificity phosphatase domain of dual specificity protein phosphatase 10. Dual specificity protein phosphatase 10 (DUSP10), also called mitogen-activated protein kinase (MAPK) phosphatase 5 (MKP-5), functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). Like other MKPs, it deactivates its MAPK substrates by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. It belongs to the class III subfamily and is a JNK/p38-selective cytoplasmic MKP. DUSP10/MKP-5 coordinates skeletal muscle regeneration by negatively regulating mitochondria-mediated apoptosis. It is also an important regulator of intestinal epithelial barrier function and a suppressor of colon tumorigenesis. DUSP10/MKP-5 contains an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. 152 matched cddid_all.tbl CDD cd14568 cd14568 350416 DSP_MKP_classIII dual specificity phosphatase domain of class III mitogen-activated protein kinase phosphatase. Mitogen-activated protein kinase (MAPK) phosphatases (MKPs) are eukaryotic dual-specificity phosphatases (DUSPs) that act on MAPKs and function as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). They deactivate MAPKs by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. Based on sequence homology, subcellular localization and substrate specificity, 10 MKPs can be subdivided into three subfamilies (class I-III). Class III MKPs consist of DUSP8, DUSP10/MKP-5 and DUSP16/MKP-7, and are JNK/p38-selective phosphatases, which are found in both the cell nucleus and cytoplasm. All MKPs contain an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. 140 matched cddid_all.tbl CDD cd14569 cd14569 350417 DSP_slingshot_2 dual specificity phosphatase domain of slingshot homolog 2. Dual specificity protein phosphatase slingshot homolog 2 (SSH2), also called SSH-like protein 2, is part of the slingshot (SSH) family, whose members specifically dephosphorylate and reactivate Ser-3-phosphorylated cofilin (P-cofilin), an actin-binding protein that plays an essential role in actin filament dynamics. SSH2 has been identified as a target of protein kinase D1 that regulates cofilin phosphorylation and remodeling of the actin cytoskeleton during neutrophil chemotaxis. There are at least two human SSH2 isoforms reported: hSSH-2L (long) and hSSH-2. As SSH family phosphatases, they contain an N-terminal, SSH family-specific non-catalytic (SSH-N) domain, followed by a short domain with similarity to the C-terminal domain of the chromatin-associated protein DEK, and a dual specificity phosphatase catalytic domain. In addition, hSSH-2L contains a long C-terminal tail while hSSH-2 does not. 144 matched cddid_all.tbl CDD cd14570 cd14570 350418 DSP_slingshot_1 dual specificity phosphatase domain of slingshot homolog 1. Dual specificity protein phosphatase slingshot homolog 1 (SSH1), also called SSH-like protein 1, is part of the slingshot (SSH) family, whose members specifically dephosphorylate and reactivate Ser-3-phosphorylated cofilin (P-cofilin), an actin-binding protein that plays an essential role in actin filament dynamics. SSH1 links NOD1 signaling to actin remodeling, facilitating the changes that leads to NF-kappaB activation and innate immune responses. There are at least two human SSH1 isoforms reported: hSSH-1L (long) and hSSH-1S (short). As SSH family phosphatases, they contain an N-terminal, SSH family-specific non-catalytic (SSH-N) domain, followed by a short domain with similarity to the C-terminal domain of the chromatin-associated protein DEK, and a dual specificity phosphatase catalytic domain. They also contain C-terminal tails, differing in the lengths of the tail. 144 matched cddid_all.tbl CDD cd14571 cd14571 350419 DSP_slingshot_3 dual specificity phosphatase domain of slingshot homolog 3. Dual specificity protein phosphatase slingshot homolog 3 (SSH3), also called SSH-like protein 3, is part of the slingshot (SSH) family, whose members specifically dephosphorylate and reactivate Ser-3-phosphorylated cofilin (P-cofilin), an actin-binding protein that plays an essential role in actin filament dynamics. The Xenopus homolog (xSSH) is involved in the gastrulation movement. Mouse SSH3 dephosphorylates actin-depolymerizing factor (ADF) and cofilin but is dispensable for development. There are at least two human SSH3 isoforms reported: hSSH-3L (long) and hSSH-3. As SSH family phosphatases, they contain an N-terminal, SSH family-specific non-catalytic (SSH-N) domain, followed by a short domain with similarity to the C-terminal domain of the chromatin-associated protein DEK, and a dual specificity phosphatase catalytic domain. In addition, hSSH-3L contains a C-terminal tail while hSSH-3 does not. 144 matched cddid_all.tbl CDD cd14572 cd14572 350420 DUSP14 dual specificity protein phosphatase 14. dual specificity protein phosphatase 14 (DUSP14), also called mitogen-activated protein kinase (MAPK) phosphatase 6 (MKP-6) or MKP-1-like protein tyrosine phosphatase (MKP-L), functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). It deactivates its MAPK substrates by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. DUSP14 is an atypical DUSP; it contains the catalytic dual specificity phosphatase domain but lacks the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. DUSP14 dephosphorylates JNK, ERK, and p38 in vitro. It also directly interacts and dephosphorylates TGF-beta-activated kinase 1 (TAK1)-binding protein 1 (TAB1) in T cells, and negatively regulates TCR signaling and immune responses. 150 matched cddid_all.tbl CDD cd14573 cd14573 350421 DUSP18_21 dual specificity protein phosphatases 18 and 21. This subfamily contains dual specificity protein phosphatase 18 (DUSP18), dual specificity protein phosphatase 21 (DUSP21), and similar proteins. They function as protein-serine/threonine phosphatases (EC 3.1.3.16) and protein-tyrosine-phosphatases (EC 3.1.3.48), and are atypical DUSPs. They contain the catalytic dual specificity phosphatase domain but lack the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. DUSP18, also called low molecular weight dual specificity phosphatase 20 (LMW-DSP20), is a catalytically active phosphatase with a preference for phosphotyrosine over phosphoserine/threonine oligopeptides in vitro. In vivo, it has been shown to interact and dephosphorylate SAPK/JNK, and may play a role in regulating the SAPK/JNK pathway. DUSP21 is also called low molecular weight dual specificity phosphatase 21 (LMW-DSP21). Its gene has been identified as a potential therapeutic target in human hepatocellular carcinoma. DUSP18 and DUSP21 target to opposing sides of the mitochondrial inner membrane. 158 matched cddid_all.tbl CDD cd14574 cd14574 350422 DUSP28 dual specificity protein phosphatase 28. Dual specificity protein phosphatase 28 (DUSP28), also called VHP, functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). It is an atypical DUSP that contains the catalytic dual specificity phosphatase domain but lacks the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. It has been implicated in hepatocellular carcinoma progression and in migratory activity and drug resistance of pancreatic cancer cells. DUSP28 has an exceptionally low phosphatase activity due to the presence of bulky residues in the active site pocket resulting in low accessibility. 140 matched cddid_all.tbl CDD cd14575 cd14575 350423 DUPD1 dual specificity phosphatase and pro isomerase domain containing 1. Dual specificity phosphatase and pro isomerase domain containing 1 (DUPD1) was initially named as such because computational prediction appeared to encode a protein of 446 amino acids in length that included two catalytic domains: a proline isomerase and a dual specificity phosphatase (DUSP). However, it was subsequently shown that the true open reading frame only encompassed the DUSP domain and the gene product was therefore renamed DUSP27. This is distinct from inactive DUSP27. DUSPs function as protein-serine/threonine phosphatases (EC 3.1.3.16) and protein-tyrosine-phosphatases (EC 3.1.3.48). DUPD1/DUSP27 has been shown to have catalytic activity with preference for phosphotyrosine over phosphothreonine and phosphoserine residues. It associates with the short form of the prolactin (PRL) receptor and plays a role in PRL-mediated MAPK inhibition in ovarian cells. 160 matched cddid_all.tbl CDD cd14576 cd14576 350424 DSP_iDUSP27 dual specificity phosphatase-like domain of inactive dual specificity protein phosphatase 27. Inactive dual specificity protein phosphatase 27 (DUSP27) may play a role in myofiber maturation. It is a pseudophosphatase containing a substitution of the active site cysteine into a serine. It is a large protein of more than 1000 amino acids in length with an N-terminal dual specificity phosphatase-like domain. 159 matched cddid_all.tbl CDD cd14577 cd14577 350425 DUSP13B dual specificity protein phosphatase 13 isoform B. Dual specificity protein phosphatase 13 isoform B (DUSP13B), also called testis- and skeletal-muscle-specific DSP (TMDP) or dual specificity phosphatase SKRP4, functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). It deactivates its MAPK substrates by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. DUSP13B is an atypical DUSP; it contains the catalytic dual specificity phosphatase domain but lacks the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. DUSP13B inactivates MAPK activation in the order of selectivity, JNK = p38 > ERK in cells. It may play a role in protection from external stress during spermatogenesis. 163 matched cddid_all.tbl CDD cd14578 cd14578 350426 DUSP26 dual specificity protein phosphatase 26. Dual specificity protein phosphatase 26 (DUSP26), also called mitogen-activated protein kinase (MAPK) phosphatase 8 (MKP-8) or low-molecular-mass dual-specificity phosphatase 4 (LDP-4), functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). It deactivates its MAPK substrates by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. DUSP26 is an atypical DUSP; it contains the catalytic dual specificity phosphatase domain but lacks the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. It is a brain phosphatase highly overexpressed in neuroblastoma and has also been identified as a p53 phosphatase, dephosphorylating phospho-Ser20 and phospho-Ser37 in the p53 transactivation domain. 144 matched cddid_all.tbl CDD cd14579 cd14579 350427 DUSP3 dual specificity protein phosphatase 3. Dual specificity protein phosphatase 3 (DUSP3), also called vaccinia H1-related phosphatase (VHR), functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). It deactivates its MAPK substrates by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. DUSP3 is an atypical DUSP; it contains the catalytic dual specificity phosphatase domain but lacks the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. It favors bisphosphorylated substrates over monophosphorylated ones, and prefers pTyr peptides over pSer/pThr peptides. Reported physiological substrates includes MAPKs ERK1/2, JNK, and p38, as well as STAT5, EGFR, and ErbB2. DUSP3 has been linked to breast and prostate cancer, and may also play a role in thrombosis. 168 matched cddid_all.tbl CDD cd14580 cd14580 350428 DUSP13A dual specificity protein phosphatase 13 isoform A. Dual specificity protein phosphatase 13 isoform A (DUSP13A), also called branching-enzyme interacting DSP or muscle-restricted DSP (MDSP), functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). It deactivates its MAPK substrates by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. DUSP13A is an atypical DUSP; it contains the catalytic dual specificity phosphatase domain but lacks the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. DUSP13A also functions as a regulator of apoptosis signal-regulating kinase 1 (ASK1), a MAPK kinase kinase, by interacting with its N-terminal domain and inducing ASK1-mediated apoptosis through the activation of caspase-3. This function is independent of phosphatase activity. 145 matched cddid_all.tbl CDD cd14581 cd14581 350429 DUSP22 dual specificity protein phosphatase 22. Dual specificity protein phosphatase 22 (DUSP22), also called JNK-stimulatory phosphatase-1 (JSP-1), low molecular weight dual specificity phosphatase 2 (LMW-DSP2), mitogen-activated protein kinase phosphatase x (MKP-x) or VHR-related MKPx (VHX), functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). It deactivates its MAPK substrates by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. DUSP22 is an atypical DUSP; it contains the catalytic dual specificity phosphatase domain but lacks the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. DUSP22 negatively regulates the estrogen receptor-alpha-mediated signaling pathway and the IL6-leukemia inhibitory factor (LIF)-STAT3-mediated signaling pathway. It also regulates cell death by acting as a scaffold protein for the ASK1-MKK7-JNK signal transduction pathway independently of its phosphatase activity. 149 matched cddid_all.tbl CDD cd14582 cd14582 350430 DSP_DUSP15 dual specificity phosphatase domain of dual specificity protein phosphatase 15. Dual specificity protein phosphatase 15 (DUSP15), also called Vaccinia virus VH1-related dual-specific protein phosphatase Y (VHY) or VH1-related member Y, functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). DUSP15 is an atypical DUSP; it contains the catalytic dual specificity phosphatase domain but lacks the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs or MKPs. It is highly expressed in the testis and is located in the plasma membrane in a myristoylation-dependent manner. It may be involved in the regulation of meiotic signal transduction in testis cells. It is also expressed in the brain and has been identified as a regulator of oligodendrocyte differentiation. DUSP15 contains an N-terminal catalytic dual specificity phosphatase domain and a short C-terminal tail. 146 matched cddid_all.tbl CDD cd14583 cd14583 350431 PTP-MTMR7 protein tyrosine phosphatase-like domain of myotubularin related phosphoinositide phosphatase 7. Myotubularin related phosphoinositide phosphatase 7 (MTMR7) is enzymatically active and contains a C-terminal coiled-coil domain and an N-terminal PH-GRAM domain. In general, myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. They dephosphorylate the D-3 position of phosphatidylinositol 3-phosphate [PI(3)P] and phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2], generating phosphatidylinositol and phosphatidylinositol 5-phosphate [PI(5)P], respectively. In neuronal cells, MTMR7 forms a complex with catalytically inactive MTMR9 and dephosphorylates phosphatidylinositol 3-phosphate and Ins(1,3)P2. 302 matched cddid_all.tbl CDD cd14584 cd14584 350432 PTP-MTMR8 protein tyrosine phosphatase-like domain of myotubularin related phosphoinositide phosphatase 8. Myotubularin related phosphoinositide phosphatase 8 (MTMR8) is enzymatically active and contains a C-terminal coiled-coil domain and an N-terminal PH-GRAM domain. In general, myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. They dephosphorylate the D-3 position of phosphatidylinositol 3-phosphate [PI(3)P] and phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2], generating phosphatidylinositol and phosphatidylinositol 5-phosphate [PI(5)P], respectively. MTMR8 forms a complex with catalytically inactive MTMR9 and preferentially dephosphorylates PtdIns(3)P; the MTMR8/R9 complex inhibits autophagy. In zebrafish, it cooperates with PI3K to regulate actin filament modeling and muscle development. 308 matched cddid_all.tbl CDD cd14585 cd14585 350433 PTP-MTMR6 protein tyrosine phosphatase-like domain of myotubularin related phosphoinositide phosphatase 6. Myotubularin related phosphoinositide phosphatase 6 is enzymatically active and contains a C-terminal coiled-coil domain and an N-terminal PH-GRAM domain. In general, myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. They dephosphorylate the D-3 position of phosphatidylinositol 3-phosphate [PI(3)P] and phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2], generating phosphatidylinositol and phosphatidylinositol 5-phosphate [PI(5)P], respectively. MTMR6 forms a complex with catalytically inactive MTMR9 and preferentially dephosphorylates PtdIns(3,5)P(2); the MTMR6/R9 complex serves to inhibit stress-induced apoptosis. 302 matched cddid_all.tbl CDD cd14586 cd14586 350434 PTP-MTMR3 protein tyrosine phosphatase-like domain of myotubularin related phosphoinositide phosphatase 3. Myotubularin related phosphoinositide phosphatase 3 (MTMR3), also known as FYVE domain-containing dual specificity protein phosphatase 1 (FYVE-DSP1) or Zinc finger FYVE domain-containing protein 10 (ZFYVE10), is enzymatically active and contains a C-terminal FYVE domain and an N-terminal PH-GRAM domain. In general, myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. They dephosphorylate the D-3 position of phosphatidylinositol 3-phosphate [PI(3)P] and phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2], generating phosphatidylinositol and phosphatidylinositol 5-phosphate [PI(5)P], respectively. Together with phosphoinositide 5-kinase PIKfyve, phosphoinositide 3-phosphatase MTMR3 constitutes a phosphoinositide loop that produces PI(5)P via PI(3,5)P2 and regulates cell migration. 317 matched cddid_all.tbl CDD cd14587 cd14587 350435 PTP-MTMR4 protein tyrosine phosphatase-like domain of myotubularin related phosphoinositide phosphatase 4. Myotubularin related phosphoinositide phosphatase 4 (MTMR4), also known as FYVE domain-containing dual specificity protein phosphatase 2 (FYVE-DSP2) or zinc finger FYVE domain-containing protein 11 (ZFYVE11), is enzymatically active and contains a C-terminal FYVE domain and an N-terminal PH-GRAM domain. In general, myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. They dephosphorylate the D-3 position of phosphatidylinositol 3-phosphate [PI(3)P] and phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2], generating phosphatidylinositol and phosphatidylinositol 5-phosphate [PI(5)P], respectively. MTMR4 localizes at the interface of early and recycling endosomes to regulate trafficking through this pathway. It plays a role in bacterial pathogenesis by stabilizing the integrity of bacteria-containing vacuoles. 308 matched cddid_all.tbl CDD cd14588 cd14588 350436 PTP-MTMR5 protein tyrosine phosphatase-like pseudophosphatase domain of myotubularin related phosphoinositide phosphatase 5. Myotubularin related phosphoinositide phosphatase 5 (MTMR5), also known as SET binding factor 1 (SBF1), is enzymatically inactive and contains a variety of other domains, including a DENN and a PH-like domain. Mutations in the MTMR5 gene cause Charcot-Marie-tooth disease type 4B3. In general, myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. MTMR5 is a pseudophosphatase that lacks the catalytic cysteine in its catalytic pocket. It interacts with MTMR2, an active myotubularin related phosphatidylinositol phosphatase, regulates its enzymatic activity and subcellular location. 291 matched cddid_all.tbl CDD cd14589 cd14589 350437 PTP-MTMR13 protein tyrosine phosphatase-like pseudophosphatase domain of myotubularin related phosphoinositide phosphatase 13. Myotubularin related phosphoinositide phosphatase 13 (MTMR13), also known as SET binding factor 2 (SBF2), is enzymatically inactive and contains a variety of other domains, including a DENN and a PH-like domain. Mutations in MTMR13 causes Charcot-Marie-Tooth type 4B2, a severe childhood-onset neuromuscular disorder, characterized by demyelination and redundant loops of myelin known as myelin outfoldings, a similar phenotype as mutations in MTMR2. In general, myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. MTMR13 is a pseudophosphatase that lacks the catalytic cysteine in its catalytic pocket. It is believed to interact with MTMR2 and stimulate its phosphatase activity. It is also a guanine nucleotide exchange factor (GEF) which may activate RAB28, promoting the exchange of GDP to GTP and converting inactive GDP-bound Rab proteins into their active GTP-bound form. 297 matched cddid_all.tbl CDD cd14590 cd14590 350438 PTP-MTMR2 protein tyrosine phosphatase-like domain of myotubularin related phosphoinositide phosphatase 2. Myotubularin related phosphoinositide phosphatase 2 (MTMR2) is enzymatically active and contains an additional N-terminal PH-GRAM domain and C-terminal coiled-coiled domain and PDZ binding site. Mutations in MTMR2 causes Charcot-Marie-Tooth type 4B1, a severe childhood-onset neuromuscular disorder, characterized by demyelination and redundant loops of myelin known as myelin outfoldings, a similar phenotype as mutations in MTMR13. MTMR13, an inactive phosphatase, is believed to interact with MTMR2 and stimulate its phosphatase activity. In general, myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. They dephosphorylate the D-3 position of phosphatidylinositol 3-phosphate [PI(3)P] and phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2], generating phosphatidylinositol and phosphatidylinositol 5-phosphate [PI(5)P], respectively. 262 matched cddid_all.tbl CDD cd14591 cd14591 350439 PTP-MTM1 protein tyrosine phosphatase-like domain of myotubularin phosphoinositide phosphatase 1. Myotubularin phosphoinositide phosphatase 1 (MTM1), also called myotubularin, is enzymatically active and contains an N-terminal PH-GRAM domain and C-terminal coiled-coiled domain and PDZ binding site. Mutations in MTM1 cause X-linked myotubular myopathy. In general, myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. They dephosphorylate the D-3 position of phosphatidylinositol 3-phosphate [PI(3)P] and phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2], generating phosphatidylinositol and phosphatidylinositol 5-phosphate [PI(5)P], respectively. 249 matched cddid_all.tbl CDD cd14592 cd14592 350440 PTP-MTMR1 protein tyrosine phosphatase-like domain of myotubularin related phosphoinositide phosphatase 1. Myotubularin-related phosphoinositide phosphatase 1 (MTMR1) is enzymatically active and contains an N-terminal PH-GRAM domain, a C-terminal coiled-coiled domain and a PDZ binding site. MTMR1 is associated with myotonic dystrophy. In general, myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. They dephosphorylate the D-3 position of phosphatidylinositol 3-phosphate [PI(3)P] and phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2], generating phosphatidylinositol and phosphatidylinositol 5-phosphate [PI(5)P], respectively. 249 matched cddid_all.tbl CDD cd14593 cd14593 350441 PTP-MTMR10 protein tyrosine phosphatase-like pseudophosphatase domain of myotubularin related phosphoinositide phosphatase 10. Myotubularin related phosphoinositide phosphatase 10 (MTMR10) is enzymatically inactive and contains an N-terminal PH-GRAM domain. In general, myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. MTMR10 is a pseudophosphatase that lacks the catalytic cysteine in its catalytic pocket. 195 matched cddid_all.tbl CDD cd14594 cd14594 350442 PTP-MTMR12 protein tyrosine phosphatase-like pseudophosphatase domain of myotubularin related phosphoinositide phosphatase 12. Myotubularin related phosphoinositide phosphatase 12 (MTMR12), also called phosphatidylinositol 3 phosphate 3-phosphatase adapter subunit (3-PAP), is enzymatically inactive and contains a C-terminal coiled-coil domain and an N-terminal PH-GRAM domain. In general, myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. MTMR12 is a pseudophosphatase that lacks the catalytic cysteine in its catalytic pocket. It functions as an adapter for the catalytically active myotubularin to regulate its intracellular location. 203 matched cddid_all.tbl CDD cd14595 cd14595 350443 PTP-MTMR11 protein tyrosine phosphatase-like pseudophosphatase domain of myotubularin related phosphoinositide phosphatase 11. Myotubularin related phosphoinositide phosphatase 11 (MTMR11), also called cisplatin resistance-associated protein (hCRA) in humans, is enzymatically inactive and contains a C-terminal coiled-coil domain and an N-terminal PH-GRAM domain. In general, myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. MTMR11 is a pseudophosphatase that lacks the catalytic cysteine in its catalytic pocket. 195 matched cddid_all.tbl CDD cd14596 cd14596 350444 PTPc-N20 catalytic domain of tyrosine-protein phosphatase non-receptor type 20. Tyrosine-protein phosphatase non-receptor type 20 (PTPN20) belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. Human PTPN20 is a widely expressed phosphatase with a dynamic subcellular distribution that is targeted to sites of actin polymerization. 207 matched cddid_all.tbl CDD cd14597 cd14597 350445 PTPc-N13 catalytic domain of tyrosine-protein phosphatase non-receptor type 13. Tyrosine-protein phosphatase non-receptor type 13 (PTPN13, also known as PTPL1) belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. Human PTPN13 is an important regulator of tumor aggressiveness. It regulates breast cancer cell aggressiveness through direct inactivation of Src kinase. In hepatocellular carcinoma, PTPN13 is a tumor suppressor. PTPN13 contains a FERM domain, five PDZ domains, and a C-terminal catalytic PTP domain. With its PDZ domains, PTPN13 has numerous interacting partners that can actively participate in the regulation of its phosphatase activity or can permit direct or indirect recruitment of tyrosine phosphorylated substrates. Its FERM domain is necessary for localization to the membrane. 234 matched cddid_all.tbl CDD cd14598 cd14598 350446 PTPc-N21 catalytic domain of tyrosine-protein phosphatase non-receptor type 21. Tyrosine-protein phosphatase non-receptor type 21 (PTPN21), also called protein-tyrosine phosphatase D1, belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPN21 is a component of a multivalent scaffold complex nucleated by focal adhesion kinase (FAK) at specific intracellular sites. It promotes cytoskeleton events that induce cell adhesion and migration by modulating Src-FAK signaling. It can also selectively associate with and stimulate Tec family kinases and modulate Stat3 activation. Human PTPN21 may also play a pathologic role in gastrointestinal tract tumorigenesis. PTPN21 contains an N-terminal FERM domain and a C-terminal catalytic PTP domain, separated by a long intervening sequence. 220 matched cddid_all.tbl CDD cd14599 cd14599 350447 PTPc-N14 catalytic domain of tyrosine-protein phosphatase non-receptor type 14. Tyrosine-protein phosphatase non-receptor type 14 (PTPN14), also called protein-tyrosine phosphatase pez, belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPN14 is a potential tumor suppressor and plays a regulatory role in the Hippo and Wnt/beta-catenin signaling pathways. It contains an N-terminal FERM domain and a C-terminal catalytic PTP domain, separated by a long intervening sequence. 287 matched cddid_all.tbl CDD cd14600 cd14600 350448 PTPc-N3 catalytic domain of tyrosine-protein phosphatase non-receptor type 3. Tyrosine-protein phosphatase non-receptor type 3 (PTPN3), also called protein-tyrosine phosphatase H1 (PTP-H1), belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPN3 interacts with mitogen-activated protein kinase p38gamma and serves as its specific phosphatase. PTPN3 and p38gamma cooperate to promote Ras-induced oncogenesis. PTPN3 is a large modular protein containing an N-terminal FERM domain, a PDZ domain and a C-terminal catalytic PTP domain. Its PDZ domain binds with the PDZ-binding motif of p38gamma and enables efficient tyrosine dephosphorylation. 274 matched cddid_all.tbl CDD cd14601 cd14601 350449 PTPc-N4 catalytic domain of tyrosine-protein phosphatase non-receptor type 4. Tyrosine-protein phosphatase non-receptor type 4 (PTPN4), also called protein-tyrosine phosphatase MEG1, belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPN4 functions in TCR cell signaling, apoptosis, cerebellar synaptic plasticity, and innate immune responses. It specifically inhibits the TRIF-dependent TLR4 pathway by suppressing tyrosine phosphorylation of TRAM. It is a large modular protein containing an N-terminal FERM domain, a PDZ domain and a C-terminal catalytic PTP domain; the PDZ domain regulates the catalytic activity of PTPN4. 212 matched cddid_all.tbl CDD cd14602 cd14602 350450 PTPc-N22 catalytic domain of tyrosine-protein phosphatase non-receptor type 22. Tyrosine-protein phosphatase non-receptor type 22 (PTPN22), also called lymphoid phosphatase (LyP), PEST-domain phosphatase (PEP), or hematopoietic cell protein-tyrosine phosphatase 70Z-PEP, belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPN22 is expressed in hematopoietic cells and it functions as a key regulator of immune homeostasis by inhibiting T-cell receptor signaling through the direct dephosphorylation of Src family kinases (Lck and Fyn), ITAMs of the TCRz/CD3 complex, and other signaling molecules. Mutations in the PTPN22 gene are associated with multiple connective tissue and autoimmune diseases including type 1 diabetes mellitus, rheumatoid arthritis, and systemic lupus erythematosus. PTPN22 contains an N-terminal catalytic PTP domain and four proline-rich regions at the C-terminus. 234 matched cddid_all.tbl CDD cd14603 cd14603 350451 PTPc-N18 catalytic domain of tyrosine-protein phosphatase non-receptor type 18. Tyrosine-protein phosphatase non-receptor type 18 (PTPN18), also called brain-derived phosphatase, belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPN18 regulates HER2-mediated cellular functions through defining both its phosphorylation and ubiquitination states. The N-terminal catalytic PTP domain of PTPN18 blocks lysosomal routing and delays the degradation of HER2 by dephosphorylation, and its C-terminal PEST domain promotes K48-linked HER2 ubiquitination and its destruction via the proteasome pathway. 266 matched cddid_all.tbl CDD cd14604 cd14604 350452 PTPc-N12 catalytic domain of tyrosine-protein phosphatase non-receptor type 12. Tyrosine-protein phosphatase non-receptor type 12 (PTPN12), also called PTP-PEST or protein-tyrosine phosphatase G1 (PTPG1), belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPN12 is characterized as a tumor suppressor and a pivotal regulator of EGFR/HER2 signaling. It regulates various physiological processes, including cell migration, immune response, and neuronal activity, by dephosphorylating multiple substrates including HER2, FAK, PYK2, PSTPIP, WASP, p130Cas, paxillin, Shc, catenin, c-Abl, ArgBP2, p190RhoGAP, RhoGDI, cell adhesion kinase beta, and Rho GTPase. 297 matched cddid_all.tbl CDD cd14605 cd14605 350453 PTPc-N11 catalytic domain of tyrosine-protein phosphatase non-receptor type 11. Tyrosine-protein phosphatase non-receptor type 11 (PTPN11), also called SH2 domain-containing tyrosine phosphatase 2 (SHP-2 or SHP2), belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPN11 promotes the activation of the RAS/Mitogen-Activated Protein Kinases (MAPK) Extracellular-Regulated Kinases 1/2 (ERK1/2) pathway, a canonical signaling cascade that plays key roles in various cellular processes, including proliferation, survival, differentiation, migration, or metabolism. It also regulates the phosphoinositide 3-kinase (PI3K)/AKT pathway, a fundamental cascade that functions in cell survival, proliferation, migration, morphogenesis, and metabolism. PTPN11 dysregulation is associated with several developmental diseases and malignancies, such as Noonan syndrome and juvenile myelomonocytic leukemia. It contains two tandem SH2 domains, a catalytic PTP domain, and a C-terminal tail with regulatory properties. 253 matched cddid_all.tbl CDD cd14606 cd14606 350454 PTPc-N6 catalytic domain of tyrosine-protein phosphatase non-receptor type 6. Tyrosine-protein phosphatase non-receptor type 6 (PTPN6), also called SH2 domain-containing protein-tyrosine phosphatase 1 (SHP1 or SHP-1), belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPN6 expression is restricted mainly to hematopoietic and epithelial cells. It is an important regulator of hematopoietic cells, downregulating pathways that promote cell growth, survival, adhesion, and activation. It regulates glucose homeostasis by modulating insulin signalling in the liver and muscle, and it also negatively regulates bone resorption, affecting both the formation and the function of osteoclasts. PTPN6 contains two tandem SH2 domains, a catalytic PTP domain, and a C-terminal tail with regulatory properties. 266 matched cddid_all.tbl CDD cd14607 cd14607 350455 PTPc-N2 catalytic domain of tyrosine-protein phosphatase non-receptor type 2. Tyrosine-protein phosphatase non-receptor type 2 (PTPN2), also called T-cell protein-tyrosine phosphatase (TCPTP), belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPN2, a tumor suppressor, dephosphorylates and inactivates EGFRs, Src family kinases, Janus-activated kinases (JAKs)-1 and -3, and signal transducer and activators of transcription (STATs)-1, -3 and -5, in a cell type and context-dependent manner. It is deleted in 6% of all T-cell acute lymphoblastic leukemias and is associated with constitutive JAK1/STAT5 signaling and tumorigenesis. 257 matched cddid_all.tbl CDD cd14608 cd14608 350456 PTPc-N1 catalytic domain of tyrosine-protein phosphatase non-receptor type 1. Tyrosine-protein phosphatase non-receptor type 1 (PTPN1), also called protein-tyrosine phosphatase 1B (PTP-1B), belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPN1/PTP-1B is the first PTP to be purified and characterized and is the prototypical intracellular PTP found in a wide variety of human tissues. It contains an N-terminal catalytic PTP domain, followed by two tandem proline-rich motifs that mediate interaction with SH3-domain-containing proteins, and a small hydrophobic stretch that localizes the enzyme to the endoplasmic reticulum (ER). It dephosphorylates and regulates the activity of a number of receptor tyrosine kinases, including the insulin receptor, the EGF receptor, and the PDGF receptor. 277 matched cddid_all.tbl CDD cd14609 cd14609 350457 R-PTP-N PTP-like domain of receptor-type tyrosine-protein phosphatase N. Receptor-type tyrosine-protein phosphatase-like N (PTPRN or R-PTP-N), also called islet cell antigen 512 (ICA512) or PTP IA-2, belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). It consists of a large ectodomain that contains a RESP18HD (regulated endocrine-specific protein 18 homology domain), followed by a transmembrane segment, and a single, catalytically-impaired, PTP domain. PTPRN is located in secretory granules of neuroendocrine cells and is involved in the generation, cargo storage, traffic, exocytosis and recycling of insulin secretory granules, as well as in beta-cell proliferation. It is a major autoantigen in type 1 diabetes and is involved in the regulation of insulin secretion. 281 matched cddid_all.tbl CDD cd14610 cd14610 350458 R-PTP-N2 PTP-like domain of receptor-type tyrosine-protein phosphatase N2. Receptor-type tyrosine-protein phosphatase N2 (PTPRN2 or R-PTP-N2), also called islet cell autoantigen-related protein (IAR), ICAAR, phogrin, or IA-2beta, belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). It consists of a large ectodomain that contains a RESP18HD (regulated endocrine-specific protein 18 homology domain), followed by a transmembrane segment, and a single, catalytically-impaired, PTP domain. It is mainly expressed in neuropeptidergic neurons and peptide-secreting endocrine cells, including insulin-producing pancreatic beta-cells. It may function as a phosphatidylinositol phosphatase to regulate insulin secretion. It is also required for normal accumulation of the neurotransmitters norepinephrine, dopamine and serotonin in the brain. 283 matched cddid_all.tbl CDD cd14611 cd14611 350459 R-PTPc-R catalytic domain of receptor-type tyrosine-protein phosphatase R. Receptor-type tyrosine-protein phosphatase-like R (PTPRR or R-PTP-R), also called protein-tyrosine phosphatase PCPTP1, belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRR is a kinase interaction motif (KIM)-PTP, characterized by the presence of a 16-amino-acid KIM that binds specifically to members of the MAPK (mitogen-activated protein kinase) family. The human and mouse PTPRR gene produces multiple neuronal protein isoforms of varying sizes (in human, PTPPBS-alpha, beta, gamma and delta). All isoforms contain the KIM motif and the catalytic PTP domain. PTPRR-deficient mice show significant defects in fine motor coordination and balance skills that are reminiscent of a mild ataxia. 226 matched cddid_all.tbl CDD cd14612 cd14612 350460 PTPc-N7 catalytic domain of tyrosine-protein phosphatase non-receptor type 7. Tyrosine-protein phosphatase non-receptor type 7 (PTPN7), also called hematopoietic protein-tyrosine phosphatase (HePTP) or LC-PTP. belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPN7/HePTP is a kinase interaction motif (KIM)-PTP, characterized by the presence of a 16-amino-acid KIM that binds specifically to members of the MAPK (mitogen-activated protein kinase) family. PTPN7/HePTP is found exclusively in the white blood cells in bone marrow, thymus, spleen, lymph nodes and all myeloid and lymphoid cell lines. It negatively regulates T-cell activation and proliferation, and is often dysregulated in the preleukemic disorder myelodysplastic syndrome, as well as in acute myelogenous leukemia. 247 matched cddid_all.tbl CDD cd14613 cd14613 350461 PTPc-N5 catalytic domain of tyrosine-protein phosphatase non-receptor type 5. Tyrosine-protein phosphatase non-receptor type 5 (PTPN5), also called striatum-enriched protein-tyrosine phosphatase (STEP) or neural-specific PTP, belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPN5/STEP is a kinase interaction motif (KIM)-PTP, characterized by the presence of a 16-amino-acid KIM that binds specifically to members of the MAPK (mitogen-activated protein kinase) family. It is a CNS-enriched protein that regulates key signaling proteins required for synaptic strengthening, as well as NMDA and AMPA receptor trafficking. PTPN5 is implicated in multiple neurologic and neuropsychiatric disorders, such as Alzheimer's disease, Parkinson's disease, schizophrenia, and fragile X syndrome. 258 matched cddid_all.tbl CDD cd14614 cd14614 350462 R-PTPc-O catalytic domain of receptor-type tyrosine-protein phosphatase O. Receptor-type tyrosine-protein phosphatase O (PTPRO or R-PTP-O), also known as glomerular epithelial protein 1 or protein tyrosine phosphatase U2 (PTP-U2), belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRO is a member of the R3 subfamily of receptor-type phosphotyrosine phosphatases (RPTP), characterized by a unique modular composition consisting of multiple extracellular fibronectin type III (FN3) repeats and a single (most RPTP subtypes have two) cytoplasmic catalytic PTP domain. It is essential for sustaining the structure and function of foot processes by regulating tyrosine phosphorylation of podocyte proteins. It has been identified as a synaptic cell adhesion molecule (CAM) that serves as a potent initiator of synapse formation. It is also a tumor suppressor in several types of cancer, such as hepatocellular carcinoma, lung cancer, and breast cancer. 245 matched cddid_all.tbl CDD cd14615 cd14615 350463 R-PTPc-J catalytic domain of receptor-type tyrosine-protein phosphatase J. Receptor-type tyrosine-protein phosphatase J (PTPRJ or R-PTP-J), also known as receptor-type tyrosine-protein phosphatase eta (R-PTP-eta) or density-enhanced phosphatase 1 (DEP-1) OR CD148, belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRJ is a member of the R3 subfamily of receptor-type phosphotyrosine phosphatases (RPTP), characterized by a unique modular composition consisting of multiple extracellular fibronectin type III (FN3) repeats (eight in PTPRJ) and a single (most RPTP subtypes have two) cytoplasmic catalytic PTP domain. It is expressed in various cell types including epithelial, hematopoietic, and endothelial cells. It plays a role in cell adhesion, migration, proliferation and differentiation. It dephosphorylates or contributes to the dephosphorylation of various substrates including protein kinases such as FLT3, PDGFRB, MET, RET (variant MEN2A), VEGFR-2, LYN, SRC, MAPK1, MAPK3, and EGFR, as well as PIK3R1 and PIK3R2. 229 matched cddid_all.tbl CDD cd14616 cd14616 350464 R-PTPc-Q catalytic domain of receptor-type tyrosine-protein phosphatase Q. Receptor-type tyrosine-protein phosphatase Q (PTPRQ or R-PTP-Q), also called phosphatidylinositol phosphatase PTPRQ, belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRQ is a member of the R3 subfamily of receptor-type phosphotyrosine phosphatases (RPTP), characterized by a unique modular composition consisting of multiple extracellular fibronectin type III (FN3) repeats (18 in PTPRQ) and a single (most RPTP subtypes have two) cytoplasmic catalytic PTP domain. It displays low tyrosine-protein phosphatase activity; rather, it functions as a phosphatidylinositol phosphatase required for auditory processes. It regulates the levels of phosphatidylinositol 4,5-bisphosphate (PIP2) in the basal region of hair bundles. It can dephosphorylate a broad range of phosphatidylinositol phosphates, including phosphatidylinositol 3,4,5-trisphosphate and most phosphatidylinositol monophosphates and diphosphates. 224 matched cddid_all.tbl CDD cd14617 cd14617 350465 R-PTPc-B catalytic domain of receptor-type tyrosine-protein phosphatase B. Receptor-type tyrosine-protein phosphatase B (PTPRB), also known as receptor-type tyrosine-protein phosphatase beta (R-PTP-beta) or vascular endothelial protein tyrosine phosphatase(VE-PTP), belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRB/VE-PTP is a member of the R3 subfamily of receptor-type phosphotyrosine phosphatases (RPTP), characterized by a unique modular composition consisting of multiple extracellular fibronectin type III (FN3) repeats and a single (most RPTP subtypes have two) cytoplasmic catalytic PTP domain. It is expressed specifically in vascular endothelial cells and it plays an important role in blood vessel remodeling and angiogenesis. 228 matched cddid_all.tbl CDD cd14618 cd14618 350466 R-PTPc-V catalytic domain of receptor-type tyrosine-protein phosphatase V. Receptor-type tyrosine-protein phosphatase V (PTPRV or R-PTP-V), also known as embryonic stem cell protein-tyrosine phosphatase (ES cell phosphatase) or osteotesticular protein-tyrosine phosphatase (OST-PTP), belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRV is a member of the R3 subfamily of receptor-type phosphotyrosine phosphatases (RPTP), characterized by a unique modular composition consisting of multiple extracellular fibronectin type III (FN3) repeats and a single (most RPTP subtypes have two) cytoplasmic catalytic PTP domain. In rodents, it may play a role in the maintenance of pluripotency and may function in signaling pathways during bone remodeling. It is the only PTP whose function has been lost between rodent and human. The human OST-PTP gene is a pseudogene. 230 matched cddid_all.tbl CDD cd14619 cd14619 350467 R-PTPc-H catalytic domain of receptor-type tyrosine-protein phosphatase H. Receptor-type tyrosine-protein phosphatase H (PTPRH or R-PTP-H), also known as stomach cancer-associated protein tyrosine phosphatase 1 (SAP-1), belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRH is a member of the R3 subfamily of receptor-type phosphotyrosine phosphatases (RPTP), characterized by a unique modular composition consisting of multiple extracellular fibronectin type III (FN3) repeats and a single (most RPTP subtypes have two) cytoplasmic catalytic PTP domain. It is localized specifically at microvilli of the brush border in gastrointestinal epithelial cells. It plays a role in intestinal immunity by regulating CEACAM20 through tyrosine dephosphorylation. It is also a negative regulator of integrin-mediated signaling and may contribute to contact inhibition of cell growth and motility. 233 matched cddid_all.tbl CDD cd14620 cd14620 350468 R-PTPc-E-1 catalytic domain of receptor-type tyrosine-protein phosphatase E, repeat 1. Receptor-type tyrosine-protein phosphatase E (PTPRE), also known as receptor-type tyrosine-protein phosphatase epsilon (R-PTP-epsilon), belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. The PTPRE gene contains two distinct promoters that generate the two major isoforms: transmembrane (receptor type RPTPe or PTPeM) and cytoplasmic (cyt-PTPe or PTPeC). Receptor type RPTPe plays a critical role in signaling transduction pathways and phosphoprotein network topology in red blood cells, and may also play a role in osteoclast formation and function. It also negatively regulates PDGFRbeta-mediated signaling pathways that are crucial for the pathogenesis of atherosclerosis. cyt-PTPe acts as a negative regulator of insulin receptor signaling in skeletal muscle. It regulates insulin-induced phosphorylation of proteins downstream of the insulin receptor. Receptor type RPTPe contains a small extracellular region, a single transmembrane segment, and an intracellular region two tandem catalytic PTP domains. This model represents the first PTP domain (repeat 1). 229 matched cddid_all.tbl CDD cd14621 cd14621 350469 R-PTPc-A-1 catalytic domain of receptor-type tyrosine-protein phosphatase A, repeat 1. Receptor-type tyrosine-protein phosphatase A (PTPRA), also known as receptor-type tyrosine-protein phosphatase alpha (R-PTP-alpha), belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRA is a positive regulator of Src and Src family kinases via dephosphorylation of the Src-inhibitory tyrosine 527. Thus, it affects transformation and tumorigenesis, inhibition of proliferation, cell cycle arrest, integrin signaling, neuronal differentiation and outgrowth, and ion channel activity. It is also involved in interleukin-1 signaling in fibroblasts through its interaction with the focal adhesion targeting domain of focal adhesion kinase. PTPRA comprises a small extracellular domain, a transmembrane segment, and an intracellular region containing two tandem catalytic PTP domains. This model represents the first catalytic PTP domain (repeat 1). 296 matched cddid_all.tbl CDD cd14622 cd14622 350470 R-PTPc-E-2 catalytic domain of receptor-type tyrosine-protein phosphatase E, repeat 2. Receptor-type tyrosine-protein phosphatase E (PTPRE), also known as receptor-type tyrosine-protein phosphatase epsilon (R-PTP-epsilon), belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. The PTPRE gene contains two distinct promoters that generate the two major isoforms: transmembrane (receptor type RPTPe or PTPeM) and cytoplasmic (cyt-PTPe or PTPeC). Receptor type RPTPe plays a critical role in signaling transduction pathways and phosphoprotein network topology in red blood cells, and may also play a role in osteoclast formation and function. It also negatively regulates PDGFRbeta-mediated signaling pathways that are crucial for the pathogenesis of atherosclerosis. cyt-PTPe acts as a negative regulator of insulin receptor signaling in skeletal muscle. It regulates insulin-induced phosphorylation of proteins downstream of the insulin receptor. Receptor type RPTPe contains a small extracellular region, a single transmembrane segment, and an intracellular region two tandem catalytic PTP domains. This model represents the second PTP domain (repeat 2). 205 matched cddid_all.tbl CDD cd14623 cd14623 350471 R-PTPc-A-2 catalytic domain of receptor-type tyrosine-protein phosphatase A, repeat 2. Receptor-type tyrosine-protein phosphatase A (PTPRA), also known as receptor-type tyrosine-protein phosphatase alpha (R-PTP-alpha), belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRA is a positive regulator of Src and Src family kinases via dephosphorylation of the Src-inhibitory tyrosine 527. Thus, it affects transformation and tumorigenesis, inhibition of proliferation, cell cycle arrest, integrin signaling, neuronal differentiation and outgrowth, and ion channel activity. It is also involved in interleukin-1 signaling in fibroblasts through its interaction with the focal adhesion targeting domain of focal adhesion kinase. PTPRA comprises a small extracellular domain, a transmembrane segment, and an intracellular region containing two tandem catalytic PTP domains. This model represents the second PTP domain (repeat 2). 228 matched cddid_all.tbl CDD cd14624 cd14624 350472 R-PTPc-D-1 catalytic domain of receptor-type tyrosine-protein phosphatase D, repeat 1. Receptor-type tyrosine-protein phosphatase D (PTPRD), also known as receptor-type tyrosine-protein phosphatase delta (R-PTP-delta), belongs to the LAR (leukocyte common antigen-related) family of receptor-type tyrosine-protein phosphatases (RPTPs), which belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. LAR-RPTPs are synaptic adhesion molecules that play roles in various aspects of neuronal development, including axon guidance, neurite extension, and synapse formation and function. PTPRD is involved in pre-synaptic differentiation through interaction with SLITRK2. It contains an extracellular region with three immunoglobulin-like (Ig) domains and four to eight fibronectin type III (FN3) repeats (determined by alternative splicing), a single transmembrane domain, followed by an intracellular region with a membrane-proximal catalytic PTP domain (repeat 1, also called D1) and a membrane-distal non-catalytic PTP-like domain (repeat 2, also called D2). This model represents the catalytic PTP domain (repeat 1). 284 matched cddid_all.tbl CDD cd14625 cd14625 350473 R-PTPc-S-1 catalytic domain of receptor-type tyrosine-protein phosphatase S, repeat 1. Receptor-type tyrosine-protein phosphatase S (PTPRS), also known as receptor-type tyrosine-protein phosphatase sigma (R-PTP-sigma), belongs to the LAR (leukocyte common antigen-related) family of receptor-type tyrosine-protein phosphatases (RPTPs), which belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRS is a receptor for glycosaminoglycans, including heparan sulfate proteoglycan and neural chondroitin sulfate proteoglycans (CSPGs), which present a barrier to axon regeneration. It also plays a role in stimulating neurite outgrowth in response to the heparan sulfate proteoglycan GPC2. PTPRS contains an extracellular region with three immunoglobulin-like (Ig) domains and four to eight fibronectin type III (FN3) repeats (determined by alternative splicing), a single transmembrane domain, followed by an intracellular region with a membrane-proximal catalytic PTP domain (repeat 1, also called D1) and a membrane-distal non-catalytic PTP-like domain (repeat 2, also called D2). This model represents the catalytic PTP domain (repeat 1). 282 matched cddid_all.tbl CDD cd14626 cd14626 350474 R-PTPc-F-1 catalytic domain of receptor-type tyrosine-protein phosphatase F, repeat 1. Receptor-type tyrosine-protein phosphatase F (PTPRF), also known as leukocyte common antigen related (LAR), is the prototypical member of the LAR family of receptor-type tyrosine-protein phosphatases (RPTPs), which belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRF/LAR plays a role for LAR in cadherin complexes where it associates with and dephosphorylates beta-catenin, a pathway which may be critical for cadherin complex stability and cell-cell association. It also regulates focal adhesions through cyclin-dependent kinase-1 and is involved in axon guidance in the developing nervous system. It also functions in regulating insulin signaling. PTPRF contains an extracellular region with three immunoglobulin-like (Ig) domains and four to eight fibronectin type III (FN3) repeats (determined by alternative splicing), a single transmembrane domain, followed by an intracellular region with a membrane-proximal catalytic PTP domain (repeat 1, also called D1) and a membrane-distal non-catalytic PTP-like domain (repeat 2, also called D2). This model represents the catalytic PTP domain (repeat 1). 276 matched cddid_all.tbl CDD cd14627 cd14627 350475 R-PTP-S-2 PTP-like domain of receptor-type tyrosine-protein phosphatase S, repeat 2. Receptor-type tyrosine-protein phosphatase S (PTPRS), also known as receptor-type tyrosine-protein phosphatase sigma (R-PTP-sigma), belongs to the LAR (leukocyte common antigen-related) family of receptor-type tyrosine-protein phosphatases (RPTPs), which belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRS is a receptor for glycosaminoglycans, including heparan sulfate proteoglycan and neural chondroitin sulfate proteoglycans (CSPGs), which present a barrier to axon regeneration. It also plays a role in stimulating neurite outgrowth in response to the heparan sulfate proteoglycan GPC2. PTPRS contains an extracellular region with three immunoglobulin-like (Ig) domains and four to eight fibronectin type III (FN3) repeats (determined by alternative splicing), a single transmembrane domain, followed by an intracellular region with a membrane-proximal catalytic PTP domain (repeat 1, also called D1) and a membrane-distal non-catalytic PTP-like domain (repeat 2, also called D2). This model represents the non-catalytic PTP-like domain (repeat 2). Although described as non-catalytic, this domain contains the catalytic cysteine and the active site signature motif, HCSAGxGRxG. 290 matched cddid_all.tbl CDD cd14628 cd14628 350476 R-PTP-D-2 PTP-like domain of receptor-type tyrosine-protein phosphatase D, repeat 2. Receptor-type tyrosine-protein phosphatase-like D (PTPRD), also known as receptor-type tyrosine-protein phosphatase delta (R-PTP-delta), belongs to the LAR (leukocyte common antigen-related) family of receptor-type tyrosine-protein phosphatases (RPTPs), which belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. LAR-RPTPs are synaptic adhesion molecules that play roles in various aspects of neuronal development, including axon guidance, neurite extension, and synapse formation and function. PTPRD is involved in pre-synaptic differentiation through interaction with SLITRK2. It contains an extracellular region with three immunoglobulin-like (Ig) domains and four to eight fibronectin type III (FN3) repeats (determined by alternative splicing), a single transmembrane domain, followed by an intracellular region with a membrane-proximal catalytic PTP domain (repeat 1, also called D1) and a membrane-distal non-catalytic PTP-like domain (repeat 2, also called D2). This model represents the non-catalytic PTP-like domain (repeat 2). Although described as non-catalytic, this domain contains the catalytic cysteine and the active site signature motif, HCSAGxGRxG. 292 matched cddid_all.tbl CDD cd14629 cd14629 350477 R-PTP-F-2 PTP-like domain of receptor-type tyrosine-protein phosphatase F, repeat 2. Receptor-type tyrosine-protein phosphatase F (PTPRF), also known as leukocyte common antigen related (LAR), is the prototypical member of the LAR family of receptor-type tyrosine-protein phosphatases (RPTPs), which belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRF/LAR plays a role for LAR in cadherin complexes where it associates with and dephosphorylates beta-catenin, a pathway which may be critical for cadherin complex stability and cell-cell association. It also regulates focal adhesions through cyclin-dependent kinase-1 and is involved in axon guidance in the developing nervous system. It also functions in regulating insulin signaling. PTPRF contains an extracellular region with three immunoglobulin-like (Ig) domains and four to eight fibronectin type III (FN3) repeats (determined by alternative splicing), a single transmembrane domain, followed by an intracellular region with a membrane-proximal catalytic PTP domain (repeat 1, also called D1) and a membrane-distal non-catalytic PTP-like domain (repeat 2, also called D2). This model represents the non-catalytic PTP-like domain (repeat 2). Although described as non-catalytic, this domain contains the catalytic cysteine and the active site signature motif, HCSAGxGRxG. 291 matched cddid_all.tbl CDD cd14630 cd14630 350478 R-PTPc-T-1 catalytic domain of receptor-type tyrosine-protein phosphatase T, repeat 1. Receptor-type tyrosine-protein phosphatase T (PTPRT), also known as receptor-type tyrosine-protein phosphatase rho (RPTP-rho or PTPrho), belongs to the type IIb subfamily of receptor protein tyrosine phosphatases (RPTPs), which belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRT is highly expressed in the nervous system and it plays a critical role in regulation of synaptic formation and neuronal development. It dephosphorylates a specific tyrosine residue in syntaxin-binding protein 1, a key component of synaptic vesicle fusion machinery, and regulates its binding to syntaxin 1. PTPRT has been identified as a potential candidate gene for autism spectrum disorder (ASD) susceptibility. It contains an extracellular region with an Meprin-A5 (neuropilin)-mu (MAM) domain, an immunoglobulin (Ig) domain, and four fibronectin type III (FN3) repeats, a transmembrane domain, and an intracellular segment with a juxtamembrane domain similar to the cytoplasmic domain of classical cadherins and two tandem PTP domains. This model represents the first (repeat 1) PTP domain. 237 matched cddid_all.tbl CDD cd14631 cd14631 350479 R-PTPc-K-1 catalytic domain of receptor-type tyrosine-protein phosphatase K, repeat 1. Receptor-type tyrosine-protein phosphatase K (PTPRK), also known as receptor-type tyrosine-protein phosphatase kappa (RPTP-kappa or PTPkappa), belongs to the type IIb subfamily of receptor protein tyrosine phosphatases (RPTPs), which belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRK is widely expressed and has been shown to stimulate cell motility and neurite outgrowth. It is required for anti-proliferative and pro-migratory effects of TGF-beta, suggesting a role in regulation, maintenance, and restoration of cell adhesion. It is a potential tumour suppressor in primary central nervous system lymphomas, colorectal cancer, and breast cancer. It contains an extracellular region with an Meprin-A5 (neuropilin)-mu (MAM) domain, an immunoglobulin (Ig) domain, and four fibronectin type III (FN3) repeats, a transmembrane domain, and an intracellular segment with a juxtamembrane domain similar to the cytoplasmic domain of classical cadherins and two tandem PTP domains. This model represents the first (repeat 1) PTP domain. 218 matched cddid_all.tbl CDD cd14632 cd14632 350480 R-PTPc-U-1 catalytic domain of receptor-type tyrosine-protein phosphatase U, repeat 1. Receptor-type tyrosine-protein phosphatase U (PTPRU), also known as pancreatic carcinoma phosphatase 2 (PCP-2), belongs to the type IIb subfamily of receptor protein tyrosine phosphatases (RPTPs), which belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRU/PCP-2 is the most distant member of the type IIb subfamily and may have a distinct biological function other than cell-cell aggregation. It localizes to the adherens junctions and directly binds and dephosphorylates beta-catenin, and regulates the balance between signaling and adhesive beta-catenin. It plays an important role in the maintenance of epithelial integrity. PTPRU contains an extracellular region with an Meprin-A5 (neuropilin)-mu (MAM) domain, an immunoglobulin (Ig) domain, and four fibronectin type III (FN3) repeats, a transmembrane domain, and an intracellular segment with a juxtamembrane domain similar to the cytoplasmic domain of classical cadherins and two tandem PTP domains. This model represents the first (repeat 1) PTP domain. 205 matched cddid_all.tbl CDD cd14633 cd14633 350481 R-PTPc-M-1 catalytic domain of receptor-type tyrosine-protein phosphatase M, repeat 1. Receptor-type tyrosine-protein phosphatase M (PTPRM), also known as protein-tyrosine phosphatase mu (R-PTP-mu or PTPmu), belongs to the type IIb subfamily of receptor protein tyrosine phosphatases (RPTPs), which belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRM/PTPmu is a homophilic cell adhesion molecule expressed in CNS neurons and glia. It is required for E-, N-, and R-cadherin-dependent neurite outgrowth. Loss of PTPmu contributes to tumor cell migration and dispersal of human glioblastomas. PTPRM contains an extracellular region with an Meprin-A5 (neuropilin)-mu (MAM) domain, an immunoglobulin (Ig) domain, and four fibronectin type III (FN3) repeats, a transmembrane domain, and an intracellular segment with a juxtamembrane domain similar to the cytoplasmic domain of classical cadherins and two tandem PTP domains. This model represents the first (repeat 1) PTP domain. 273 matched cddid_all.tbl CDD cd14634 cd14634 350482 R-PTPc-T-2 PTP domain of receptor-type tyrosine-protein phosphatase T, repeat 2. Receptor-type tyrosine-protein phosphatase T (PTPRT), also known as receptor-type tyrosine-protein phosphatase rho (RPTP-rho or PTPrho), belongs to the type IIb subfamily of receptor protein tyrosine phosphatases (RPTPs), which belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRT is highly expressed in the nervous system and it plays a critical role in regulation of synaptic formation and neuronal development. It dephosphorylates a specific tyrosine residue in syntaxin-binding protein 1, a key component of synaptic vesicle fusion machinery, and regulates its binding to syntaxin 1. PTPRT has been identified as a potential candidate gene for autism spectrum disorder (ASD) susceptibility. It contains an extracellular region with an Meprin-A5 (neuropilin)-mu (MAM) domain, an immunoglobulin (Ig) domain, and four fibronectin type III (FN3) repeats, a transmembrane domain, and an intracellular segment with a juxtamembrane domain similar to the cytoplasmic domain of classical cadherins and two tandem PTP domains. This model represents the second (repeat 2) PTP domain. 206 matched cddid_all.tbl CDD cd14635 cd14635 350483 R-PTPc-M-2 PTP domain of receptor-type tyrosine-protein phosphatase M, repeat 2. Receptor-type tyrosine-protein phosphatase M (PTPRM), also known as protein-tyrosine phosphatase mu (R-PTP-mu or PTPmu), belongs to the type IIb subfamily of receptor protein tyrosine phosphatases (RPTPs), which belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRM/PTPmu is a homophilic cell adhesion molecule expressed in CNS neurons and glia. It is required for E-, N-, and R-cadherin-dependent neurite outgrowth. Loss of PTPmu contributes to tumor cell migration and dispersal of human glioblastomas. PTPRM contains an extracellular region with an Meprin-A5 (neuropilin)-mu (MAM) domain, an immunoglobulin (Ig) domain, and four fibronectin type III (FN3) repeats, a transmembrane domain, and an intracellular segment with a juxtamembrane domain similar to the cytoplasmic domain of classical cadherins and two tandem PTP domains. This model represents the second (repeat 2) PTP domain. 206 matched cddid_all.tbl CDD cd14636 cd14636 350484 R-PTPc-K-2 PTP domain of receptor-type tyrosine-protein phosphatase K, repeat 2. Receptor-type tyrosine-protein phosphatase K (PTPRK), also known as receptor-type tyrosine-protein phosphatase kappa (RPTP-kappa or PTPkappa), belongs to the type IIb subfamily of receptor protein tyrosine phosphatases (RPTPs), which belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRK is widely expressed and has been shown to stimulate cell motility and neurite outgrowth. It is required for anti-proliferative and pro-migratory effects of TGF-beta, suggesting a role in regulation, maintenance, and restoration of cell adhesion. It is a potential tumour suppressor in primary central nervous system lymphomas, colorectal cancer, and breast cancer. It contains an extracellular region with an Meprin-A5 (neuropilin)-mu (MAM) domain, an immunoglobulin (Ig) domain, and four fibronectin type III (FN3) repeats, a transmembrane domain, and an intracellular segment with a juxtamembrane domain similar to the cytoplasmic domain of classical cadherins and two tandem PTP domains. This model represents the second (repeat 2) PTP domain. 206 matched cddid_all.tbl CDD cd14637 cd14637 350485 R-PTPc-U-2 PTP domain of receptor-type tyrosine-protein phosphatase U, repeat 2. Receptor-type tyrosine-protein phosphatase U (PTPRU), also known as pancreatic carcinoma phosphatase 2 (PCP-2), belongs to the type IIb subfamily of receptor protein tyrosine phosphatases (RPTPs), which belong to the larger family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRU/PCP-2 is the most distant member of the type IIb subfamily and may have a distinct biological function other than cell-cell aggregation. It localizes to the adherens junctions and directly binds and dephosphorylates beta-catenin, and regulates the balance between signaling and adhesive beta-catenin. It plays an important role in the maintenance of epithelial integrity. PTPRU contains an extracellular region with an Meprin-A5 (neuropilin)-mu (MAM) domain, an immunoglobulin (Ig) domain, and four fibronectin type III (FN3) repeats, a transmembrane domain, and an intracellular segment with a juxtamembrane domain similar to the cytoplasmic domain of classical cadherins and two tandem PTP domains. This model represents the second (repeat 2) PTP domain. 207 matched cddid_all.tbl CDD cd14638 cd14638 350486 DSP_DUSP1 dual specificity phosphatase domain of dual specificity protein phosphatase 1. Dual specificity protein phosphatase 1 (DUSP1), also called mitogen-activated protein kinase (MAPK) phosphatase 1 (MKP-1), functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). Like other MKPs, it deactivates its MAPK substrates by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. It belongs to the class I subfamily and is a mitogen- and stress-inducible nuclear MKP. Human MKP-1 dephosphorylates MAPK1/ERK2, regulating its activity during the meiotic cell cycle. Although initially MKP-1 was considered to be ERK-specific, it has been shown that MKP-1 also dephosphorylates both JNK and p38 MAPKs. DUSP1/MKP-1 is involved in various functions, including proliferation, differentiation, and apoptosis in normal cells. It is a central regulator of a variety of functions in the immune, metabolic, cardiovascular, and nervous systems. It contains an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. 151 matched cddid_all.tbl CDD cd14639 cd14639 350487 DSP_DUSP5 dual specificity phosphatase domain of dual specificity protein phosphatase 5. Dual specificity protein phosphatase 5 (DUSP5) functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). Like other mitogen-activated protein kinase (MAPK) phosphatases (MKPs), it deactivates its MAPK substrates by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. It belongs to the class I subfamily and is a mitogen- and stress-inducible nuclear MKP. DUSP5 preferentially dephosphorylates extracellular signal-regulated kinase (ERK), and is involved in ERK signaling and ERK-dependent inflammatory gene expression in adipocytes. It also plays a role in regulating pressure-dependent myogenic cerebral arterial constriction, which is crucial for the maintenance of constant cerebral blood flow to the brain. DUSP5 contains an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. 138 matched cddid_all.tbl CDD cd14640 cd14640 350488 DSP_DUSP4 dual specificity phosphatase domain of dual specificity protein phosphatase 4. Dual specificity protein phosphatase 4 (DUSP4), also called mitogen-activated protein kinase (MAPK) phosphatase 2 (MKP-2), functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). Like other MKPs, it deactivates its MAPK substrates by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. It belongs to the class I subfamily and is a mitogen- and stress-inducible nuclear MKP. DUSP4 regulates either ERK or c-JUN N-terminal kinase (JNK), depending on the cell type. It dephosphorylates nuclear JNK and induces apoptosis in diffuse large B cell lymphoma (DLBCL) cells. It acts as a negative regulator of macrophage M1 activation and inhibits inflammation during macrophage-adipocyte interaction. It has been linked to different aspects of cancer: it may have a role in the development of ovarian cancers, oesophagogastric rib metastasis, and pancreatic tumours; it may also be a candidate tumor suppressor gene, with its deletion implicated in breast cancer, prostate cancer, and gliomas. DUSP4/MKP-2 contains an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. 141 matched cddid_all.tbl CDD cd14641 cd14641 350489 DSP_DUSP2 dual specificity phosphatase domain of dual specificity protein phosphatase 2. Dual specificity protein phosphatase 2 (DUSP2), also called dual specificity protein phosphatase PAC-1, functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). Like other mitogen-activated protein kinase (MAPK) phosphatases (MKPs), it deactivates its MAPK substrates by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. It belongs to the class I subfamily and is a mitogen- and stress-inducible nuclear MKP. DUSP2 can preferentially dephosphorylate ERK1/2 and p38, but not JNK in vitro. It is predominantly expressed in hematopoietic tissues with high T-cell content, such as thymus, spleen, lymph nodes, peripheral blood and other organs such as the brain and liver. It has a critical and positive role in inflammatory responses. DUSP2 mRNA and protein are significantly reduced in most solid cancers including breast, colon, lung, ovary, kidney and prostate, and the suppression of DUSP2 is associated with tumorigenesis and malignancy. DUSP2 contains an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. 144 matched cddid_all.tbl CDD cd14642 cd14642 350490 DSP_DUSP6 dual specificity phosphatase domain of dual specificity protein phosphatase 6. Dual specificity protein phosphatase 6 (DUSP6), also called mitogen-activated protein kinase (MAPK) phosphatase 3 (MKP-3) or dual specificity protein phosphatase PYST1, functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). Like other MKPs, it deactivates its MAPK substrates by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. It belongs to the class II subfamily and is an ERK-selective cytoplasmic MKP. DUSP6/MKP-3 plays an important role in obesity-related hyperglycemia by promoting hepatic glucose output. MKP-3 deficiency attenuates body weight gain induced by a high-fat diet, protects mice from developing obesity-related hepatosteatosis, and reduces adiposity, possibly by repressing adipocyte differentiation. It also contributes to p53-controlled cellular senescence. It contains an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. 143 matched cddid_all.tbl CDD cd14643 cd14643 350491 DSP_DUSP7 dual specificity phosphatase domain of dual specificity protein phosphatase 7. Dual specificity protein phosphatase 7 (DUSP7), also called mitogen-activated protein kinase (MAPK) phosphatase X (MKP-X) or dual specificity protein phosphatase PYST2, functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). Like other MKPs, it deactivates its MAPK substrates by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. It belongs to the class II subfamily and is an ERK-selective cytoplasmic MKP. DUSP7 has been shown as an essential regulator of multiple steps in oocyte meiosis. Due to alternative promoter usage, the PYST2 gene gives rise to two isoforms, PYST2-S and PYST2-L. PYST2-L is over-expressed in leukocytes derived from AML and ALL patients as well as in some solid tumors and lymphoblastoid cell lines; it plays a role in cell-crowding. It contains an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. 149 matched cddid_all.tbl CDD cd14644 cd14644 350492 DSP_DUSP9 dual specificity phosphatase domain of dual specificity protein phosphatase 9. Dual specificity protein phosphatase 9 (DUSP9), also called mitogen-activated protein kinase (MAPK) phosphatase 4 (MKP-4), functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). Like other MKPs, it deactivates its MAPK substrates by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. It belongs to the class II subfamily and is an ERK-selective cytoplasmic MKP. DUSP9 is a mediator of bone morphogenetic protein (BMP) signaling to control the appropriate ERK activity critical for the determination of embryonic stem cell fate. Down-regulation of DUSP9 expression has been linked to severe pre-eclamptic placenta as well as cancers such as hepatocellular carcinoma. DUSP9 contains an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. 145 matched cddid_all.tbl CDD cd14645 cd14645 350493 DSP_DUSP8 dual specificity phosphatase domain of dual specificity protein phosphatase 8. Dual specificity protein phosphatase 8 (DUSP8), also called DUSP hVH-5 or M3/6, functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). Like other MKPs, it deactivates its MAPK substrates by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. It belongs to the class III subfamily and is a JNK/p38-selective cytoplasmic MKP. DUSP8 controls basal and acute stress-induced ERK1/2 signaling in adult cardiac myocytes, which impacts contractility, ventricular remodeling, and disease susceptibility. It also plays a role in decreasing ureteric branching morphogenesis by inhibiting p38MAPK. DUSP8 contains an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. 151 matched cddid_all.tbl CDD cd14646 cd14646 350494 DSP_DUSP16 dual specificity phosphatase domain of dual specificity protein phosphatase 16. Dual specificity protein phosphatase 16 (DUSP16), also called mitogen-activated protein kinase (MAPK) phosphatase 7 (MKP-7), functions as a protein-serine/threonine phosphatase (EC 3.1.3.16) and a protein-tyrosine-phosphatase (EC 3.1.3.48). Like other MKPs, it deactivates its MAPK substrates by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. It belongs to the class III subfamily and is a JNK/p38-selective cytoplasmic MKP. DUSP16/MKP-7 plays an essential role in perinatal survival and selectively controls the differentiation and cytokine production of myeloid cells. It is acetylated by Mycobacterium tuberculosis Eis protein, which leads to the inhibition of JNK-dependent autophagy, phagosome maturation, and ROS generation, and thus, initiating suppression of host immune responses. DUSP16/MKP-7 contains an N-terminal Cdc25/rhodanese-like domain, which is responsible for MAPK-binding, and a C-terminal catalytic dual specificity phosphatase domain. 145 matched cddid_all.tbl CDD cd14651 cd14651 271236 ZIP_Put3 Leucine zipper Dimerization domain of transcription factor Put3. Put3p activates the transcription of PUT1 and PUT2 genes in the presence of proline, allowing yeast cells to use proline as a nitrogen source. These genes encode for proteins that convert proline to glutamate, which is a metabolically more useful form of nitrogen. Put3p is a member of the Gal4p family of transcriptional activators which contain an N-terminal DNA-binding domain with a Zn2Cys6 binuclear cluster that interact with CCG triplets and a leucine zipper-like heptad repeat that dimerizes. Dimerization allows binding of targets which contain two CCG motifs oriented in an inverted (CGG-CCG), direct (CCG-CCG), or everted (CCG-CGG) manner. 31 matched cddid_all.tbl CDD cd14653 cd14653 271237 ZIP_Gal4p-like Leucine zipper Dimerization domain of Gal4p-like transcription factors. The Gal4p family of transcriptional activators contain an N-terminal DNA-binding domain with a Zn2Cys6 binuclear cluster that interact with CCG triplets and a leucine zipper-like heptad repeat that dimerizes. Dimerization allows binding of targets which contain two CCG motifs oriented in an inverted (CGG-CCG), direct (CCG-CCG), or everted (CCG-CGG) manner. Included in this family are Saccharomyces cerevisiae Gal4p, Hap1p, Put3p, Ppr1p and Sip4p, Neurospora crassa acu-15, and Colletotrichum acutatum Nir1, among others. Gal4p functions in the induction of GAL genes in the presence of galactose; GAL proteins are responsible for the transport of galactose into the cell and for its metabolism through the glycolytic pathway. Hap1p promotes transcription of genes required for respiration and controlling oxidative damage in response to heme. Put3p activates the transcription of the PUT1 and PUT2 genes in the presence of proline, allowing yeast cells to use proline as a nitrogen source. Ppr1p activates transcription of the URA1, URA3, and URA4 genes, which encode enzymes involved in the regulation of pyrimidine levels. Sip4p activates target genes under conditions of glucose deprivation. Acu-15 is involved in regulating acetate utilization while Nir1 plays a role during nitrogen-starvation conditions. 24 matched cddid_all.tbl CDD cd14654 cd14654 271238 ZIP_Gal4 Leucine zipper Dimerization domain of transcription factor Gal4 and similar fungal proteins. Gal4p is one of several GAL proteins required for the growth of yeast on galactose; GAL proteins are responsible for the transport of galactose into the cell and for its metabolism through the glycolytic pathway. Gal4p functions in the induction of GAL genes in the presence of galactose through an upstream activating sequence (UAS) present in their promoters. The Gal4p family of transcriptional activators contain an N-terminal DNA binding domain with a Zn2Cys6 binuclear cluster that interact with CCG triplets and a leucine zipper-like heptad repeat that dimerizes. Dimerization allows binding of targets which contain two CCG motifs oriented in an inverted (CGG-CCG), direct (CCG-CCG), or everted (CCG-CGG) manner. 47 matched cddid_all.tbl CDD cd14655 cd14655 271239 ZIP_Hap1 Leucine zipper Dimerization domain of transcription factor Hap1 and similar fungal proteins. Hap1p mediates oxygen sensing and heme signaling in yeast. In response to heme, it promotes transcription of genes required for respiration and controlling oxidative damage. It is a member of the Gal4/Gal4p family of transcriptional activators which contain an N-terminal DNA binding domain with a Zn2Cys6 binuclear cluster that interact with CCG triplets and a leucine zipper-like heptad repeat that dimerizes. Dimerization allows binding of targets which contain two CCG motifs oriented in an inverted (CGG-CCG), direct (CCG-CCG), or everted (CCG-CGG) manner. Hap1p binds to DNA containing a direct repeat of two CGG triplets. It is a large protein that contains repression modules (RPMs) and heme-responsive motifs (HRMs) in addition to the DNA-binding and dimerization domains. 32 matched cddid_all.tbl CDD cd14656 cd14656 271139 Imelysin-like_EfeO EfeO is a component of the EfeUOB operon. This family includes the EfeO domain, an essential component of the EfeUOB operon which is highly conserved in bacteria. However, its biochemical function is unknown. EfeO contains an N-terminal cupredoxin (CUP)-like domain and C-terminal imelysin-like domain that may bind iron. Algp7, a member of EfeO family protein from Sphingomonas sp. A1, is found to bind alginate at neutral pH, but does not contain the CUP domain, thus having a role that does not seem to be related to iron uptake. Some members of this family are fused to an N-terminal putative EfeU ion permease domain. The imelysin-like domain of this family also contains the GxHxxE sequence motif and a highly conserved functional site, suggesting a similar role to other imelysin family proteins containing the same motif. 239 matched cddid_all.tbl CDD cd14657 cd14657 271140 Imelysin_IrpA-like Imelysin-like iron-regulated protein A-like. This family includes putative iron-regulated protein A (IrpA) mainly from Bacteriodes, proteobacteria and cyanobacteria, as well as uncharacterized proteins with domains similar to insulin-cleaving membrane protease (imelysin, ICMP) protein. IrpA has been shown to be essential for growth under iron-deficient conditions in the cyanobacteria Synechococcus sp. The conserved GxHxxE motif is similar to other known imelysin-like proteins that are regulated by iron, such as ICMP, IrpA and EfeO. Imelysin is a membrane protein with the active site outside the cell envelope. The tertiary structure shows a fold consisting of two domains, each of which consists of a bundle of four helices that are similar to each other, implying an ancient gene duplication and fusion event. 345 matched cddid_all.tbl CDD cd14658 cd14658 271141 Imelysin-like_IrpA Imelysin-like domain in iron-regulated protein A. This family includes putative iron-regulated protein A (IrpA) mainly from Bacteriodes, proteobacteria and cyanobacteria, with domain similar to insulin-cleaving membrane protease (imelysin, ICMP) protein. It has been shown to be essential for growth under iron-deficient conditions in the cyanobacteria Synechococcus sp. The conserved GxHxxE motif is similar to other known imelysin-like proteins that are regulated by iron, such as ICMP, IrpA and EfeO. Imelysin is a membrane protein with the active site outside the cell envelope. The tertiary structure shows a fold consisting of two domains, each of which consists of a bundle of four helices that are similar to each other, implying an ancient gene duplication and fusion event. 282 matched cddid_all.tbl CDD cd14659 cd14659 271142 Imelysin-like_IPPA Imelysin-like protein. This family includes insulin-cleaving membrane protease (imelysin, ICMP)-like protein (IPPA from Psychrobacter arcticus), the Pseudomonas aeruginosa PA4372 and Vibrio cholera VC1266 Fur-regulated imelysin-like protein. They share the overall fold and a similar functional site as the insulin-cleaving membrane protease (ICMP). However, IPPA adopts a structure distinctive from the known HxxE metallopeptidases or iron-binding proteins, suggesting this protein may not be a peptidase; the histidine in the GxHxxE motif region is no longer conserved (GxxxxE), indicating a possible loss of enzymatic function or a change in substrate preference (compared to imelysin and IrpA families). A putative functional site for this non-peptidase homolog is located at the domain interface. The tertiary structure shows a fold consisting of two domains, each of which consists of a bundle of four helices that are similar to each other, implying an ancient gene duplication and fusion event. 331 matched cddid_all.tbl CDD cd14660 cd14660 271137 E2F_DD Dimerization domain of E2F transcription factors. E2F transcription factors are involved in the regulation of DNA synthesis, cell cycle progression, proliferation and apoptosis. It associates with the retinoblastoma (Rb) protein, negatively regulating the G1-S transition until cyclin-dependent kinases phosphorylate Rb, which causes E2F release. E2F forms heterodimers with DP, a distantly related protein. Heterodimerization enhances the Rb binding, DNA binding, and transactivation activities of E2Fs. In humans, there are at least six closely related E2F and two DP family members, all containing a DNA-binding domain, a coiled-coil (CC) region, and a marked-box domain. E2F1 to E2F5 also contain a C-terminal transactivation domain. 104 matched cddid_all.tbl CDD cd14661 cd14661 271136 Imelysin_like_PIBO Permuted imelysin-like protein from Bacteroides ovatus (PIBO) and similar proteins. This family includes imelysin-like proteins such as imelysin-like protein from gut bacteria Bacteroides ovatus (PIBO) that have a circularly permuted topology compared with the canonical imelysin fold, such that the N-terminal and C-terminal regions are swapped in the primary sequence. PIBO is highly similar to imelysin-like protein from Psychrobacter arcticus (IPPA) despite low sequence similarity and circular permutation. PIBO is functionally equivalent to insulin-cleaving membrane protease (ICMP or imelysin), although the permutation results in the conserved GxHxxE motif to be at the C-terminus. It may have a conserved role in iron uptake although it adopts a structure distinctive from known metallopeptidases or iron-binding proteins. 347 matched cddid_all.tbl CDD cd14662 cd14662 271132 STKc_SnRK2 Catalytic domain of the Serine/Threonine Kinases, Sucrose nonfermenting 1-related protein kinase subfamily 2. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The SnRKs form three different subfamilies designated SnRK1-3. SnRK2 is represented in this cd. SnRK2s are involved in plant response to abiotic stresses and abscisic acid (ABA)-dependent plant development. The SnRK2s subfamily is in turn classed into three subgroups, all 3 of which are represented in this CD. Group 1 comprises kinases not activated by ABA, group 2 - kinases not activated or activated very weakly by ABA (depending on plant species), and group 3 - kinases strongly activated by ABA. The SnRKs belong to a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 257 matched cddid_all.tbl CDD cd14663 cd14663 271133 STKc_SnRK3 Catalytic domain of the Serine/Threonine Kinases, Sucrose nonfermenting 1-related protein kinase subfamily 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The SnRKs form three different subfamilies designated SnRK1-3. SnRK3 is represented in this cd. The SnRK3 group contains members also known as CBL-interacting protein kinase, salt overly sensitive 2, SOS3-interacting proteins and protein kinase S. These kinases interact with calcium-binding proteins such as SOS3, SCaBPs, and CBL proteins, and are involved in responses to salt stress and in sugar and ABA signaling. The SnRKs belong to a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 256 matched cddid_all.tbl CDD cd14664 cd14664 271134 STK_BAK1_like Catalytic domain of the Serine/Threonine Kinase, BRI1 associated kinase 1 and related STKs. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. This subfamily includes three leucine-rich repeat receptor-like kinases (LRR-RLKs): Arabidopsis thaliana BAK1 and CLAVATA1 (CLV1), and Physcomitrella patens CLL1B clavata1-like receptor S/T protein kinase. BAK1 functions in various signaling pathways. It plays a role in BR (brassinosteroid)-regulated plant development as a co-receptor of BRASSINOSTEROID (BR) INSENSITIVE 1 (BRI1), the receptor for BRs, and is required for full activation of BR signaling. It also modulates pathways involved in plant resistance to pathogen infection (pattern-triggered immunity, PTI) and herbivore attack (wound- or herbivore feeding-induced accumulation of jasmonic acid (JA) and JA-isoleucine. CLV1, directly binds small signaling peptides, CLAVATA3 (CLV3) and CLAVATA3/EMBRYO SURROUNDING REGI0N (CLE), to restrict stem cell proliferation: the CLV3-CLV1-WUS (WUSCHEL) module influences stem cell maintenance in the shoot apical meristem, and the CLE40 (CLAVATA3/EMBRYO SURROUNDING REGION40) -ACR4 (CRINKLY4) -CLV1- WOX5 (WUSCHEL-RELATED HOMEOBOX5) module at the root apical meristem. The STK_BAK1-like subfamily is part of a larger superfamily that includes the catalytic domains of other protein STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 270 matched cddid_all.tbl CDD cd14665 cd14665 271135 STKc_SnRK2-3 Catalytic domain of the Serine/Threonine Kinases, Sucrose nonfermenting 1-related protein kinase subfamily 2, group 3. STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The SnRKs form three different subfamilies designated SnRK1-3. SnRK2 is represented in this cd. SnRK2s are involved in plant response to abiotic stresses and abscisic acid (ABA)-dependent plant development. The SnRK2s subfamily is in turn classed into three subgroups, all 3 of which are represented in this CD. Group 1 comprises kinases not activated by ABA, group 2 - kinases not activated or activated very weakly by ABA (depending on plant species), and group 3 - kinases strongly activated by ABA. The SnRKs belong to a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. 257 matched cddid_all.tbl CDD cd14667 cd14667 270620 3D_containing_proteins Non-mltA associated 3D domain containing proteins, named for 3 conserved aspartate residues. This family contains the 3D domain, named for its 3 conserved aspartates, including similar uncharacterized proteins. These proteins contain the critical active site aspartate of mltA-like lytic transglycosylases where the 3D domain forms a larger domain with the N-terminal region. This domain is also found in conjunction with numerous other domains such as the Escherichia coli MltA, a membrane-bound lytic transglycosylase comprised of 2 domains separated by a large groove, where the peptidoglycan strand binds. Domain A is made up of an N-terminal and a C-terminal portion, corresponding to the 3D domain and Domain B is inserted within the linear sequence of domain A. MltA is distinct from other bacterial LTs, which are similar to each other. Escherichia coli peptidoglycan lytic transglycosylase (LT) initiates cell wall recycling in response to damage, during bacterial fission, and cleaves peptidoglycan (PG) to create functional spaces in its wall. PG chains (also known as murein), the major components of the bacterial cell wall, are comprised of alternating beta-1-4-linked N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), and lytic transglycosylases cleave this beta-1-4 bond. 90 matched cddid_all.tbl CDD cd14668 cd14668 270616 mlta_B Domain B insert of mltA_like lytic transglycosylases. Escherichia coli MltA is a membrane-bound lytic transglycosylase comprised of two domains separated by a large groove, where the peptidoglycan strand binds. Domain A is made up of an N-terminal and a C-terminal portion, which correspond to the 3D domain, named for 3 conserved aspartate residues. Domain B is inserted within the linear sequence of domain A. MltA is distinct from other bacterial lytic transglycosylases (LTs), which are similar to each other. Escherichia coli peptidoglycan lytic transglycosylase (LT) initiates cell wall recycling in response to damage, during bacterial fission, and cleaves peptidoglycan (PG) to create functional spaces in its wall. PG chains (also known as murein), the major components of the bacterial cell wall, are comprised of alternating beta-1-4-linked N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), and lytic transglycosylases cleave this beta-1-4 bond. Typically, peptidoglycan lytic transglycosylases (LT) are exolytic, releasing Metabolite 1 (GlcNAc-anhMurNAc-L-Ala-D-Glu-m-Dap-D-Ala-D-Ala) from the ends of the PG strands. In contrast, MltE is endolytic , cleaving in the middle of PG strands, with further processing to Metabolite 1 accomplished by other LTs. In E. coli, there are six membrane-bound LTs: MltA-MltF and soluble Slt70. Slt35 is a soluble fragment cleaved from MltB. Bacterial LTs are classified in 4 families: Family 1 includes slt70 MltC-MltF, Family 2 includes MltA, Family 3 includes MltB, and Family 4 of bacteriophage origin. While most of the LT family members are similar in structure and sequence with a lysozyme-like fold, Family 2 (including mltA) is distinct. 159 matched cddid_all.tbl CDD cd14669 cd14669 270617 mlta_related_B putative domain B insert of mltA_type lytic transglycosylases. Escherichia coli MltA is a membrane-bound lytic transglycosylase comprised of two domains separated by a large groove, where the peptidoglycan strand binds. Domain A is made up of an N-terminal and a C-terminal portion, which correspond to the 3D domain, named for 3 conserved aspartate residues. Domain B is inserted within the linear sequence of domain A. MltA is distinct from other bacterial lytic transglycosylases (LTs), which are similar to each other. Escherichia coli peptidoglycan lytic transglycosylase (LT) initiates cell wall recycling in response to damage, during bacterial fission, and cleaves peptidoglycan (PG) to create functional spaces in its wall. PG chains (also known as murein), the major components of the bacterial cell wall, are comprised of alternating beta-1-4-linked N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), and lytic transglycosylases cleave this beta-1-4 bond. Typically, peptidoglycan lytic transglycosylases (LT) are exolytic, releasing Metabolite 1 (GlcNAc-anhMurNAc-L-Ala-D-Glu-m-Dap-D-Ala-D-Ala) from the ends of the PG strands. In contrast, MltE is endolytic , cleaving in the middle of PG strands, with further processing to Metabolite 1 accomplished by other LTs. In E. coli, there are six membrane-bound LTs: MltA-MltF and soluble Slt70. Slt35 is a soluble fragment cleaved from MltB. Bacterial LTs are classified in 4 families: Family 1 includes slt70 MltC-MltF, Family 2 includes MltA, Family 3 includes MltB, and Family 4 of bacteriophage origin. While most of the LT family members are similar in structure and sequence with a lysozyme-like fold, Family 2 (including mltA) is distinct. 128 matched cddid_all.tbl CDD cd14670 cd14670 270614 BslA_like "Bacterial immunoglobulin-like hydrophobin BslA and similar proteins. BslA (YuaB) is a protein from Bacillus subtilis acting as a hydrophobin, which forms surface layers around biofilms and participates in biofilm assembly. BslA contains an unusually hydrophobic ""cap structure"", which is essential for its activity and for the ability of bacteria to form hydrophobic, non-wetting biofilms. A number of domains in various proteins from Bacilli and other bacterial lineages appear related to BslA, but do not conserve the hydrophobic cap." 128 matched cddid_all.tbl CDD cd14671 cd14671 269821 PAAR_like proline-alanine-alanine-arginine (PAAR) repeat superfamily. This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat superfamily, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey cells. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. The PAAR-repeat proteins form a diverse superfamily with several subgroups extended both N- and C-terminally by domains with various predicted functions; the termini are exposed to solution, and do not distort the VgrG binding site. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. It has been shown that PAAR proteins are essential for T6SS-mediated secretion and target cell killing by Vibrio cholerae (encodes two PAAR proteins) and Acinetobacter baylyi (encodes three PAAR proteins); inactivation of all these PAAR genes results in inactivation of Hcp secretion as well as T6SS-dependent killing of E. coli. 77 matched cddid_all.tbl CDD cd14672 cd14672 270612 UBA_ceTYDP2_like UBA-like domain found in Caenorhabditis elegans tyrosyl-DNA phosphodiesterase 2 (TDP2) and similar proteins. The family includes C. elegans TDP2 and its homologs found in bilateria. TDP2 (also known as TTRAP or EAPII) belongs to the Mg(2+)/Mn(2+)-dependent family of phosphodiesterases which contains an N-terminal ubiquitin-associated (UBA)-like domain and a C-terminal phosphodiesterase domain. It required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini needed for subsequent DNA ligation and hence repair of the break. Tyrosyl-DNA phosphodiesterase 1 (TDP1), an enzyme that cleaves 3'-phosphotyrosyl bonds, and TDP2 are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TDP2 has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation. 37 matched cddid_all.tbl CDD cd14673 cd14673 270192 PH_PHLDB1_2 Pleckstrin homology-like domain-containing family B member 2 pleckstrin homology (PH) domain. PHLDB2 (also called LL5beta) and PHLDB1 (also called LL5alpha) are cytoskeleton- and membrane-associated proteins. PHLDB2 has been identified as a key component of the synaptic podosomes that play an important role in in postsynaptic maturation. Both are large proteins containing an N-terminal pleckstrin (PH) domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 105 matched cddid_all.tbl CDD cd14674 cd14674 270193 PH_PLEKHM3_1 Pleckstrin homology domain-containing family M member 3 Pleckstrin homology domain 1. PLEKHM3 (also called differentiation associated protein/DAPR) exists as three alternatively spliced isoforms that participate in metal ion binding. It contains 2 PH domains and 1 phorbol-ester/DAG-type zinc finger domain. PLEKHM3 is found in Humans, canines, bovine, mouse, rat, chicken and zebrafish. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2, or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 90 matched cddid_all.tbl CDD cd14675 cd14675 270194 PH-SEC3_like PH-like domain of Sec3-like protein. Fungal Sec3, as well as its homolog in higher eukaryotes Exocyst complex component 1 (EXOC1) are part of the exocyst is a conserved octameric complex involved in the docking of post-Golgi transport vesicles to sites of membrane remodeling during cellular processes such as polarization, migration, and division. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 115 matched cddid_all.tbl CDD cd14676 cd14676 270195 PH_DOK1,2,3 Pleckstrin homology (PH) domain of Downstream of tyrosine kinase 1, 2, and 3. The Dok family adapters are phosphorylated by different protein tyrosine kinases. Dok proteins are involved in processes such as modulation of cell differentiation and proliferation, as well as in control of the cell spreading and migration The Dok protein contains an N-terminal pleckstrin homology (PH) domain followed by a central phosphotyrosine binding (PTB) domain, which has a PH-like fold, and a proline- and tyrosine-rich C-terminal tail. The PH domain is binds to acidic phospholids and localizes proteins to the plasma membrane. There are 7 mammalian Dok members: Dok-1 to Dok-7. Dok-1 and Dok-2 act as negative regulators of the Ras-Erk pathway downstream of many immunoreceptor-mediated signaling systems, and it is believed that recruitment of p120 rasGAP by Dok-1 and Dok-2 is critical to their negative regulation. Dok-3 is a negative regulator of the activation of JNK and mobilization of Ca2+ in B-cell receptor-mediated signaling, interacting with SHIP-1 and Grb2. In general, PH domains have diverse functions, but are generally involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 113 matched cddid_all.tbl CDD cd14677 cd14677 270196 PH_DOK7 Pleckstrin homology (PH) domain of Downstream of tyrosine kinase 7. The Dok family adapters are phosphorylated by different protein tyrosine kinases. Dok proteins are involved in processes such as modulation of cell differentiation and proliferation, as well as in control of the cell spreading and migration The Dok protein contains an N-terminal pleckstrin homology (PH) domain followed by a central phosphotyrosine binding (PTB) domain, which has a PH-like fold, and a proline- and tyrosine-rich C-terminal tail. The PH domain is binds to acidic phospholids and localizes proteins to the plasma membrane. There are 7 mammalian Dok members: Dok-1 to Dok-7. Dok-7 is the key cytoplasmic activator of MuSK (Muscle-Specific Protein Tyrosine Kinase). In general, PH domains have diverse functions, but are generally involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 102 matched cddid_all.tbl CDD cd14678 cd14678 270197 PH_DOK4_DOK5_DOK6 Pleckstrin homology (PH) domain of Downstream of tyrosine kinase 4, 5, and 6 proteins. The Dok family adapters are phosphorylated by different protein tyrosine kinases. Dok proteins are involved in processes such as modulation of cell differentiation and proliferation, as well as in control of the cell spreading and migration The Dok protein contains an N-terminal pleckstrin homology (PH) domain followed by a central phosphotyrosine binding (PTB) domain, which has a PH-like fold, and a proline- and tyrosine-rich C-terminal tail. The PH domain binds to acidic phospholids and localizes proteins to the plasma membrane, while the PTB domain mediates protein-protein interactions by binding to phosphotyrosine-containing motifs. The C-terminal part of Dok contains multiple tyrosine phosphorylation sites that serve as potential docking sites for Src homology 2-containing proteins such as ras GTPase-activating protein and Nck, leading to inhibition of ras signaling pathway activation and the c-Jun N-terminal kinase (JNK) and c-Jun activation, respectively. There are 7 mammalian Dok members: Dok-1 to Dok-7. Dok-1 and Dok-2 act as negative regulators of the Ras-Erk pathway downstream of many immunoreceptor-mediated signaling systems, and it is believed that recruitment of p120 rasGAP by Dok-1 and Dok-2 is critical to their negative regulation. Dok-3 is a negative regulator of the activation of JNK and mobilization of Ca2+ in B-cell receptor-mediated signaling, interacting with SHIP-1 and Grb2. Dok-4- 6 play roles in protein tyrosine kinase(PTK)-mediated signaling in neural cells and Dok-7 is the key cytoplasmic activator of MuSK (Muscle-Specific Protein Tyrosine Kinase). In general, PH domains have diverse functions, but are generally involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 105 matched cddid_all.tbl CDD cd14679 cd14679 275429 PH_p115RhoGEF Rho guanine nucleotide exchange factor Pleckstrin homology domain. p115RhoGEF (also called LSC, GEF1 or LBCL2) belongs to regulator of G-protein signaling (RGS) domain-containing RhoGEFs that are RhoA-selective and directly activated by the Galpha12/13 family of heterotrimeric G proteins. In addition to the Dbl homology (DH)-PH domain, p115RhoGEF contains an N-terminal RGS (Regulator of G-protein signalling) domain. The DH-PH domains bind and catalyze the exchange of GDP for GTP on RhoA. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 125 matched cddid_all.tbl CDD cd14680 cd14680 275430 PH_p190RhoGEF Rho guanine nucleotide exchange factor Pleckstrin homology domain. p190RhoGEF (also called RIP2 or ARHGEF28) belongs to regulator of G-protein signaling (RGS) domain-containing RhoGEFs that are RhoA-selective and directly activated by the Galpha12/13 family of heterotrimeric G proteins. In addition to the Dbl homology (DH)-PH domain, p190RhoGEF contains an N-terminal C1 (Protein kinase C conserved region 1) domain. The DH-PH domains bind and catalyze the exchange of GDP for GTP on RhoA. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 101 matched cddid_all.tbl CDD cd14681 cd14681 270200 PH-STXBP6 PH-like domain of Syntaxin binding protein 6. Syntaxin binding protein 6 (STXBP6, also called Amisyn) contains, beside the N-terminal PH-like domain, a C-terminal R-SNARE-like domain, which allows it to assemble into SNARE complexes, which in turn makes the complexes inactive and inhibits exocytosis. SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, with STXBP6 being a R-SNARE. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 130 matched cddid_all.tbl CDD cd14682 cd14682 270201 PH-EXOC1_like PH-like domain of Exocyst complex component 1-like. Exocyst complex component 1-like proteins are short, higher eukaryotic proteins that show homology to the PH-domain of higher eukaryotic EXOC1 and yeast SEC3 which are part of the exocyst complex involved in the docking of post-Golgi transport vesicles to sites of membrane remodeling during cellular processes such as polarization, migration, and division. Their function is unknown. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 118 matched cddid_all.tbl CDD cd14683 cd14683 270202 PH-EXOC1 PH-like domain of Exocyst complex component 1. Exocyst complex component 1 (EXOC1, also known as SEC3) is the higher eukaryotes homolog of yeast Sec3. The Exocyst is a conserved octameric complex involved in the docking of post-Golgi transport vesicles to sites of membrane remodeling during cellular processes such as polarization, migration, and division. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 117 matched cddid_all.tbl CDD cd14684 cd14684 270203 RanBD1_RanBP2-like Ran-binding protein 2, Ran binding domain repeat 1. RanBP2 (also called E3 SUMO-protein ligase RanBP2, 358 kDa nucleoporin, and nuclear pore complex (NPC) protein Nup358) is a giant nucleoporin that localizes to the cytosolic face of the NPC. RanBP2 contains a leucine-rich region, 8 zinc-finger motifs, a cyclophilin A homologous domain, and 4 RanBDs. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran. All eukaryotic cells contain RanBP1, but in vertebrates however, the main RanBP seems to be RanBP2. There is no RanBP2 ortholog in yeast. Transport complex disassembly is accomplished by a small ubiquitin-related modifier-1 (SUMO-1)-modified version of RanGAP that is bound to RanBP2. RanBP1 acts as a second line of defense against exported RanGTP-importin complexes which have escaped from dissociation by RanBP2. RanBP2 also interacts with the importin subunit beta-1. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity. The members here include human, chicken, frog, tunicates, sea urchins, ticks, sea anemones, and sponges. RanBD repeat 1 is present in this hierarchy. 117 matched cddid_all.tbl CDD cd14685 cd14685 270204 RanBD3_RanBP2-like Ran-binding protein 2, Ran binding domain repeat 3. RanBP2 (also called E3 SUMO-protein ligase RanBP2, 358 kDa nucleoporin, and nuclear pore complex (NPC) protein Nup358) is a giant nucleoporin that localizes to the cytosolic face of the NPC. RanBP2 contains a leucine-rich region, 8 zinc-finger motifs, a cyclophilin A homologous domain, and 4 RanBDs. Ran is a Ras-like nuclear small GTPase, which regulates receptor-mediated transport between the nucleus and the cytoplasm. RanGTP hydrolysis is stimulated by RanGAP together with the Ran-binding domain containing acessory proteins RanBP1 and RanBP2. These accessory proteins stabilize the active GTP-bound form of Ran. All eukaryotic cells contain RanBP1, but in vertebrates however, the main RanBP seems to be RanBP2. There is no RanBP2 ortholog in yeast. Transport complex disassembly is accomplished by a small ubiquitin-related modifier-1 (SUMO-1)-modified version of RanGAP that is bound to RanBP2. RanBP1 acts as a second line of defense against exported RanGTP-importin complexes which have escaped from dissociation by RanBP2. RanBP2 also interacts with the importin subunit beta-1. RabBD shares structural similarity to the PH domain, but lacks detectable sequence similarity. The members here include human, chicken, frog, tunicates, sea urchins, ticks, sea anemones, and sponges. RanBD repeats 3 is present in this hierarchy. 117 matched cddid_all.tbl CDD cd14686 cd14686 269834 bZIP Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain. Basic leucine zipper (bZIP) factors comprise one of the most important classes of enhancer-type transcription factors. They act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes including cell survival, learning and memory, lipid metabolism, and cancer progression, among others. They also play important roles in responses to stimuli or stress signals such as cytokines, genotoxic agents, or physiological stresses. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 52 matched cddid_all.tbl CDD cd14687 cd14687 269835 bZIP_ATF2 Basic leucine zipper (bZIP) domain of Activating Transcription Factor-2 (ATF-2) and similar proteins: a DNA-binding and dimerization domain. ATF-2 is a sequence-specific DNA-binding protein that belongs to the Basic leucine zipper (bZIP) family of transcription factors. In response to stress, it activates a variety of genes including cyclin A, cyclin D, and c-Jun. ATF-2 also plays a role in the DNA damage response that is independent of its transcriptional activity. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 61 matched cddid_all.tbl CDD cd14688 cd14688 269836 bZIP_YAP Basic leucine zipper (bZIP) domain of Yeast Activator Protein (YAP) and similar proteins: a DNA-binding and dimerization domain. This subfamily is composed predominantly of AP-1-like transcription factors including Saccharomyces cerevisiae YAPs, Schizosaccharomyces pombe PAP1, and similar proteins. Members of this subfamily belong to the Basic leucine zipper (bZIP) family of transcription factors. The YAP subfamily is composed of eight members (YAP1-8) which may all be involved in stress responses. YAP1 is the major oxidative stress regulator and is also involved in iron metabolism (like YAP5) and detoxification of arsenic (like YAP8). YAP2 is involved in cadmium stress responses while YAP4 and YAP6 play roles in osmotic stress. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 63 matched cddid_all.tbl CDD cd14689 cd14689 269837 bZIP_CREB3 Basic leucine zipper (bZIP) domain of Cyclic AMP-responsive element-binding protein 3 (CREB3) and similar proteins: a DNA-binding and dimerization domain. This subfamily is composed of CREB3 (also called LZIP or Luman), and the CREB3-like proteins CREB3L1 (or OASIS), CREB3L2, CREB3L3 (or CREBH), and CREB3L4 (or AIbZIP). They are type II membrane-associated members of the Basic leucine zipper (bZIP) family of transcription factors, with their N-termini facing the cytoplasm and their C-termini penetrating through the ER membrane. They contain an N-terminal transcriptional activation domain followed bZIP and transmembrane domains, and a C-terminal tail. They play important roles in ER stress and the unfolded protein response (UPR), as well as in many other biological processes such as cell secretion, bone and cartilage formation, and carcinogenesis. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 61 matched cddid_all.tbl CDD cd14690 cd14690 269838 bZIP_CREB1 Basic leucine zipper (bZIP) domain of Cyclic AMP-responsive element-binding protein 1 (CREB1) and similar proteins: a DNA-binding and dimerization domain. CREB1 is a Basic leucine zipper (bZIP) transcription factor that plays a role in propagating signals initiated by receptor activation through the induction of cAMP-responsive genes. Because it responds to many signal transduction pathways, CREB1 is implicated to function in many processes including learning, memory, circadian rhythm, immune response, and reproduction, among others. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 55 matched cddid_all.tbl CDD cd14691 cd14691 269839 bZIP_XBP1 Basic leucine zipper (bZIP) domain of X-box binding protein 1 (XBP1) and similar proteins: a DNA-binding and dimerization domain. XBP1, a member of the Basic leucine zipper (bZIP) family, is the key transcription factor that orchestrates the unfolded protein response (UPR). It is the most conserved component of the UPR and is critical for cell fate determination in response to ER stress. The inositol-requiring enzyme 1 (IRE1)-XBP1 pathway is one of the three major sensors at the ER membrane that initiates the UPR upon activation. IRE1, a type I transmembrane protein kinase and endoribonuclease, oligomerizes upon ER stress leading to its increased activity. It splices the XBP1 mRNA, producing a variant that translocates to the nucleus and activates its target genes, which are involved in protein folding, degradation, and trafficking. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 58 matched cddid_all.tbl CDD cd14692 cd14692 269840 bZIP_ATF4 Basic leucine zipper (bZIP) domain of Activating Transcription Factor-4 (ATF-4) and similar proteins: a DNA-binding and dimerization domain. ATF-4 was also isolated and characterized as the cAMP-response element binding protein 2 (CREB2). It is a Basic leucine zipper (bZIP) transcription factor that has been reported to act as both an activator or repressor. It is a critical component in both the unfolded protein response (UPR) and amino acid response (AAR) pathways. Under certain stress conditions, ATF-4 transcription is increased; accumulation of ATF-4 induces the expression of genes involved in amino acid metabolism and transport, mitochondrial function, redox chemistry, and others that ensure protein synthesis and recovery from stress. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 63 matched cddid_all.tbl CDD cd14693 cd14693 269841 bZIP_CEBP Basic leucine zipper (bZIP) domain of CCAAT/enhancer-binding protein (CEBP) and similar proteins: a DNA-binding and dimerization domain. CEBPs (or C/EBPs) are Basic leucine zipper (bZIP) transcription factors that regulate the cell cycle, differentiation, growth, survival, energy metabolism, innate and adaptive immunity, and inflammation, among others. They are also associated with cancer and viral disease. There are six CEBP proteins in mammalian cells including CEBPA (alpha), CEBPB (beta), CEBPG (gamma), CEBPD (delta), and CEBPE (epsilon), which all contain highly conserved bZIP domains at their C-termini and variations at their N-terminal regions. Each possesses unique properties to regulate cell type-specific growth and differentiation. The sixth isoform, CEBPZ (zeta), lacks an intact DNA-binding domain and is excluded from this subfamily. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 60 matched cddid_all.tbl CDD cd14694 cd14694 269842 bZIP_NFIL3 Basic leucine zipper (bZIP) domain of Nuclear factor interleukin-3-regulated protein (NFIL3): a DNA-binding and dimerization domain. NFIL3, also called E4 promoter-binding protein 4 (E4BP4), is a Basic leucine zipper (bZIP) transcription factor that was independently identified as a transactivator of the IL3 promoter in T-cells and as a transcriptional repressor that binds to a DNA sequence site in the adenovirus E4 promoter. Its expression levels are regulated by cytokines and it plays crucial functions in the immune system. It is required for the development of natural killer cells and CD8+ conventional dendritic cells. In B-cells, NFIL3 mediates immunoglobulin heavy chain class switching that is required for IgE production, thereby influencing allergic and pathogenic immune responses. It is also involved in the polarization of T helper responses. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 60 matched cddid_all.tbl CDD cd14695 cd14695 269843 bZIP_HLF Basic leucine zipper (bZIP) domain of Hepatic leukemia factor (HLF) and similar proteins: a DNA-binding and dimerization domain. HLF, also called vitellogenin gene-binding protein (VBP) in birds, is a circadian clock-controlled Basic leucine zipper (bZIP) transcription factor which is a direct transcriptional target of CLOCK/BMAL1. It is implicated, together with bZIPs DBP and TEF, in the regulation of genes involved in the metabolism of endobiotic and xenobiotic agents. Triple knockout mice display signs of early aging and suffer premature death, likely due to impaired defense against xenobiotic stress. A leukemogenic translocation results in the chimeric fusion protein E2A-HLF that results in a rare form of pro-B-cell acute lymphoblastic leukemia (ALL). bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 60 matched cddid_all.tbl CDD cd14696 cd14696 269844 bZIP_Jun Basic leucine zipper (bZIP) domain of Jun proteins and similar proteins: a DNA-binding and dimerization domain. Jun is a member of the activator protein-1 (AP-1) complex, which is mainly composed of Basic leucine zipper (bZIP) dimers of the Jun and Fos families, and to a lesser extent, the activating transcription factor (ATF) and musculoaponeurotic fibrosarcoma (Maf) families. The broad combinatorial possibilities for various dimers determine binding specificity, affinity, and the spectrum of regulated genes. The AP-1 complex is implicated in many cell functions including proliferation, apoptosis, survival, migration, tumorigenesis, and morphogenesis, among others. There are three Jun proteins: c-Jun, JunB, and JunD. c-Jun is the most potent transcriptional activator of the AP-1 proteins. Both c-Jun and JunB are essential during development; deletion of either results in embryonic lethality in mice. c-Jun is essential in hepatogenesis and liver erythropoiesis, while JunB is required in vasculogenesis and angiogenesis in extraembryonic tissues. While JunD is dispensable in embryonic development, it is involved in transcription regulation of target genes that help cells to cope with environmental signals. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 61 matched cddid_all.tbl CDD cd14697 cd14697 269845 bZIP_Maf Basic leucine zipper (bZIP) domain of musculoaponeurotic fibrosarcoma (Maf) proteins: a DNA-binding and dimerization domain. Maf proteins are Basic leucine zipper (bZIP) transcription factors that may participate in the activator protein-1 (AP-1) complex, which is implicated in many cell functions including proliferation, apoptosis, survival, migration, tumorigenesis, and morphogenesis, among others. Maf proteins fall into two groups: small and large. The large Mafs (c-Maf, MafA, MafB, NRL) contain an N-terminal transactivation domain, a linker region of varying size, an anxillary DNA-binding domain, and a C-terminal bZIP domain. They function as critical regulators of terminal differentiation in the blood and in many tissues such as bone, brain, kidney, pancreas, and retina. The small Mafs (MafF, MafK, MafG) do not contain a transactivation domain. They form dimers with cap'n'collar (CNC) proteins that harbor transactivation domains, and they act either as activators or repressors depending on their dimerization partner. They play roles in stress response and detoxification pathways. They have been implicated in various diseases such as diabetes, neurological diseases, thrombocytopenia and cancer. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 70 matched cddid_all.tbl CDD cd14698 cd14698 269846 bZIP_CNC Basic leucine zipper (bZIP) domain of Cap'n'Collar (CNC) transcription factors: a DNA-binding and dimerization domain. CNC proteins form a subfamily of Basic leucine zipper (bZIP) transcription factors that are defined by a conserved 43-amino acid region (called the CNC domain) located N-terminal to the bZIP DNA-binding domain. This subfamily includes Drosophila Cnc and four vertebrate counterparts, NFE2 (nuclear factor, erythroid-derived 2), NFE2-like 1 or NFE2-related factor 1 (NFE2L1 or Nrf1), NFE2L2 (or Nrf2), and NFE2L3 (or Nrf3). It also includes BACH1 and BACH2, which contain an additional BTB domain (Broad complex###Tramtrack###Bric-a-brac domain, also known as the POZ [poxvirus and zinc finger] domain). CNC proteins function during development and/or contribute in maintaining homeostasis during stress responses. In flies, Cnc functions both in development and in stress responses. In vertebrates, several CNC proteins encoded by distinct genes show varying functions and expression patterns. NFE2 is required for the proper development of platelets while the three Nrfs function in stress responses. Nrf2, the most extensively studied member of this subfamily, acts as a xenobiotic-activated receptor that regulates the adaptive response to oxidants and electrophiles. BACH1 forms heterodimers with small Mafs such as MafK to function as a repressor of heme oxygenase-1 (HO-1) gene (Hmox-1) enhancers. BACH2 is a B-cell specific transcription factor that plays a critical role in oxidative stress-mediated apoptosis. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 68 matched cddid_all.tbl CDD cd14699 cd14699 269847 bZIP_Fos_like Basic leucine zipper (bZIP) domain of the oncogene Fos (Fos)-like transcription factors: a DNA-binding and dimerization domain. This subfamily is composed of Fos proteins (c-Fos, FosB, Fos-related antigen 1 (Fra-1), and Fra-2), Activating Transcription Factor-3 (ATF-3), and similar proteins. Fos proteins are members of the activator protein-1 (AP-1) complex, which is mainly composed of bZIP dimers of the Jun and Fos families, and to a lesser extent, ATF and musculoaponeurotic fibrosarcoma (Maf) families. The broad combinatorial possibilities for various dimers determine binding specificity, affinity, and the spectrum of regulated genes. The AP-1 complex is implicated in many cell functions including proliferation, apoptosis, survival, migration, tumorigenesis, and morphogenesis, among others. ATF3 is induced by various stress signals such as cytokines, genotoxic agents, or physiological stresses. It is implicated in cancer and host defense against pathogens. It negatively regulates the transcription of pro-inflammatory cytokines and is critical in preventing acute inflammatory syndromes. ATF3 dimerizes with Jun and other ATF proteins; the heterodimers function either as activators or repressors depending on the promoter context. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 59 matched cddid_all.tbl CDD cd14700 cd14700 269848 bZIP_ATF6 Basic leucine zipper (bZIP) domain of Activating Transcription Factor-6 (ATF-6) and similar proteins: a DNA-binding and dimerization domain. ATF-6 is a type I membrane-bound Basic leucine zipper (bZIP) transcription factor that binds to the consensus ER stress response element (ERSE) and enhances the transcription of genes encoding glucose-regulated proteins Grp78, Grp94, and calreticulum. ATF-6 is one of three sensors of the unfolded protein response (UPR) in metazoans; the others being the kinases Ire1 and PERK. It contains an ER-lumenal domain that detects unfolded proteins. In response to ER stress, ATF-6 translocates from the ER to the Golgi with simultaneous cleavage in a process called regulated intramembrane proteolysis (Rip) to its transcriptionally competent form, which enters the nucleus and upregulates target UPR genes. The three UPR sensor branches cross-communicate to form a signaling network. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 52 matched cddid_all.tbl CDD cd14701 cd14701 269849 bZIP_BATF Basic leucine zipper (bZIP) domain of BATF proteins: a DNA-binding and dimerization domain. Basic leucine zipper (bZIP) transcription factor ATF-like (BATF or SFA2), BATF2 (or SARI) and BATF3 form heterodimers with Jun proteins. They function as inhibitors of AP-1-driven transcription. Unlike most bZIP transcription factors that contain additional domains, BATF and BATF3 contain only the the bZIP DNA-binding and dimerization domain. BATF2 contains an additional C-terminal domain of unknown function. BATF:Jun hetrodimers preferentially bind to TPA response elements (TREs) with the consensus sequence TGA(C/G)TCA, and can also bind to a TGACGTCA cyclic AMP response element (CRE). In addition to negative regulation, BATF proteins also show positive transcriptional activities in the development of classical dendritic cells and T helper cell subsets, and in antibody production. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 58 matched cddid_all.tbl CDD cd14702 cd14702 269850 bZIP_plant_GBF1 Basic leucine zipper (bZIP) domain of Plant G-box binding factor 1 (GBF1)-like transcription factors: a DNA-binding and dimerization domain. This subfamily is composed of plant bZIP transciption factors including Arabidopsis thaliana G-box binding factor 1 (GBF1), Zea mays Opaque-2 and Ocs element-binding factor 1 (OCSBF-1), Triticum aestivum Histone-specific transcription factor HBP1 (or HBP-1a), Petroselinum crispum Light-inducible protein CPRF3 and CPRF6, and Nicotiana tabacum BZI-3, among many others. bZIP G-box binding factors (GBFs) contain an N-terminal proline-rich domain in addition to the bZIP domain. GBFs are involved in developmental and physiological processes in response to stimuli such as light or hormones. Opaque-2 plays a role in affecting lysine content and carbohydrate metabolism, acting indirectly on starch/amino acid ratio. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 52 matched cddid_all.tbl CDD cd14703 cd14703 269851 bZIP_plant_RF2 Basic leucine zipper (bZIP) domain of Plant RF2-like transcription factors: a DNA-binding and dimerization domain. This subfamily is composed of plant bZIP transciption factors with similarity to Oryza sativa RF2a and RF2b, which are important for plant development. They interact with, as homodimers or heterodimers with each other, and activate transcription from the RTBV (rice tungro bacilliform virus) promoter, which is regulated by sequence-specific DNA-binding proteins that bind to the essential cis element BoxII. RF2a and RF2b show differences in binding affinities to BoxII, expression patterns in different rice organs, and subcellular localization. Transgenic rice with increased RF2a and RF2b display increased resistance to rice tungro disease (RTD) with no impact on plant development. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 52 matched cddid_all.tbl CDD cd14704 cd14704 269852 bZIP_HY5-like Basic leucine zipper (bZIP) domain of Plant Elongated/Long Hypocotyl5 (HY5)-like transcription factors and similar proteins: a DNA-binding and dimerization domain. This subfamily is predominantly composed of plant Basic leucine zipper (bZIP) transcription factors with similarity to Solanum lycopersicum and Arabidopsis thaliana HY5. Also included are the Dictyostelium discoideum bZIP transcription factors E and F. HY5 plays an important role in seedling development and is a positive regulator of photomorphogenesis. Plants with decreased levels of HY5 show defects in light responses including inhibited photomorphogenesis, loss of alkaloid organization, and reduced carotenoid accumulation. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 52 matched cddid_all.tbl CDD cd14705 cd14705 269853 bZIP_Zip1 Basic leucine zipper (bZIP) domain of Fungal Zip1-like transcription factors: a DNA-binding and dimerization domain. This subfamily is composed of fungal bZIP transcription factors including Schizosaccharomyces pombe Zip1, Saccharomyces cerevisiae Methionine-requiring protein 28 (Met28p), and Neurospora crassa cys-3, among others. Zip1 is required for the production of key proteins involved in sulfur metabolism and also plays a role in cadmium response. Met28p acts as a cofactor of Met4p, a transcriptional activator of the sulfur metabolic network; it stabilizes DNA:Met4 complexes. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 55 matched cddid_all.tbl CDD cd14706 cd14706 269854 bZIP_CREBZF Basic leucine zipper (bZIP) domain of CREBZF/Zhangfei transcription factor and similar proteins: a DNA-binding and dimerization domain. CREBZF (also called Zhangfei, ZF, LAZip, or SMILE) is a neuronal bZIP transcription factor that is involved in the infection cycle of herpes simplex virus (HSV) and related cellular processes. It suppresses the ability of the HSV transactivator VP16 to initiate the viral replicative cycle. CREBZF has also been implicated in the regulation of the human nerve growth factor receptor trkA and the tumor suppressor p53. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 54 matched cddid_all.tbl CDD cd14707 cd14707 269855 bZIP_plant_BZIP46 Basic leucine zipper (bZIP) domain of uncharaterized Plant BZIP transcription factors: a DNA-binding and dimerization domain. This subfamily is composed of uncharacterized plant bZIP transciption factors with similarity to Glycine max BZIP46, which may be a drought-responsive gene. Plant bZIPs are involved in developmental and physiological processes in response to stimuli/stresses such as light, hormones, and temperature changes. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 55 matched cddid_all.tbl CDD cd14708 cd14708 269856 bZIP_HBP1b-like Basic leucine zipper (bZIP) domain of uncharaterized BZIP transcription factors with similarity to Triticum aestivum HBP-1b: a DNA-binding and dimerization domain. This subfamily is composed primarily of uncharacterized bZIP transciption factors from flowering plants, mosses, clubmosses, and algae. Included in this subfamily is wheat HBP-1b, which contains a C-terminal DOG1 domain, which is a specific plant regulator for seed dormancy. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 53 matched cddid_all.tbl CDD cd14709 cd14709 269857 bZIP_CREBL2 Basic leucine zipper (bZIP) domain of Cyclic AMP-responsive element-binding protein-like 2 (CREBL2): a DNA-binding and dimerization domain. CREBL2 is a bZIP transcription factor that interacts with CREB and plays a critical role in adipogenesis and lipogenesis. Its overexpression upregulates the expression of PPARgamma and CEBPalpha to promote adipogenesis as well as accelerate lipogenesis by increasing GLUT1 and GLUT4. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 56 matched cddid_all.tbl CDD cd14710 cd14710 269858 bZIP_HAC1-like Basic leucine zipper (bZIP) domain of Fungal HAC1-like transcription factors: a DNA-binding and dimerization domain. HAC1 (also called Hac1p or HacA) is a bZIP transcription factor that plays a critical role in the unfolded protein response (UPR). The UPR is initiated by the ER-resident protein kinase and endonuclease IRE1, which promotes non-conventional splicing of the HAC1 mRNA, facilitating its translation. HAC1 binds to and activates promoters of genes that encode chaperones and other targets of the UPR. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 53 matched cddid_all.tbl CDD cd14711 cd14711 269859 bZIP_CEBPA Basic leucine zipper (bZIP) domain of CCAAT/enhancer-binding protein alpha (CEBPA): a DNA-binding and dimerization domain. CEPBA is a critical regulator of myeloid development; it directs granulocyte and monocyte differentiation. It is highly expressed in early myeloid progenitors and is found mutated in over half of patients with acute myeloid leukemia (AML). It is also a key regulator in energy homeostasis; mice deficient of CEBPA show abnormalities in glycogen/lipid synthesis and storage. CEPBA is the longest CEBP protein containing two transactivation domains at the N-terminus followed by a regulatory domain, a bZIP domain, and C-terminal tail. CEBPs (or C/EBPs) are Basic leucine zipper (bZIP) transcription factors that regulate many cellular processes. There are six CEBP proteins in mammalian cells including CEBPA (alpha), CEBPB (beta), CEBPG (gamma), CEBPD (delta), and CEBPE (epsilon), which all contain highly conserved bZIP domains at their C-termini and variations at their N-terminal regions. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 61 matched cddid_all.tbl CDD cd14712 cd14712 269860 bZIP_CEBPB Basic leucine zipper (bZIP) domain of CCAAT/enhancer-binding protein beta (CEBPB): a DNA-binding and dimerization domain. CEBPB is a key regulator of metabolism, adipocyte differentiation, myogenesis, and macrophage activation. It is expressed as three distinct isoforms from an intronless gene through alternative translation initiation: CEBPB1 (or liver-enriched activator protein 1, LAP1); CEBPB2 (OR LAP2); and CEBPB3 (or liver-enriched inhibitory protein, LIP). LAP1/2 function as transcriptional activators while LIP is a repressor due to its lack of a transactivation domain. The relative expression of LAP and LIP has effects on inflammation, ER stress, and insulin resistance. CEBPs (or C/EBPs) are Basic leucine zipper (bZIP) transcription factors that regulate many cellular processes. There are six CEBP proteins in mammalian cells including CEBPA (alpha), CEBPB (beta), CEBPG (gamma), CEBPD (delta), and CEBPE (epsilon), which all contain highly conserved bZIP domains at their C-termini and variations at their N-terminal regions. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 71 matched cddid_all.tbl CDD cd14713 cd14713 269861 bZIP_CEBPG Basic leucine zipper (bZIP) domain of CCAAT/enhancer-binding protein gamma (CEBPG): a DNA-binding and dimerization domain. CEBPG is an important regulator of cellular senescence; mouse embryonic fibroblasts deficient of CEBPG proliferated poorly, entered senescence prematurely, and expressed elevated levels of proinflammatory genes. It is also the primary transcription factor that regulates antioxidant and DNA repair transcripts in normal bronchial epithelial cells. In a subset of AML patients with CEBPA hypermethylation, CEBPG is significantly overexpressed. CEBPG is the shortest CEBP protein and it lacks a transactivation domain. It acts as a regulator and buffering reservoir against the transcriptional activities of other CEBP proteins. CEBPs (or C/EBPs) are Basic leucine zipper (bZIP) transcription factors that regulate many cellular processes. There are six CEBP proteins in mammalian cells including CEBPA (alpha), CEBPB (beta), CEBPG (gamma), CEBPD (delta), and CEBPE (epsilon), which all contain highly conserved bZIP domains at their C-termini and variations at their N-terminal regions. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 61 matched cddid_all.tbl CDD cd14714 cd14714 269862 bZIP_CEBPD Basic leucine zipper (bZIP) domain of CCAAT/enhancer-binding protein delta (CEBPD): a DNA-binding and dimerization domain. CEBPD is an inflammatory response gene that is induced by Toll-like receptor 4 (TLR4) and is essential in the expression of many lipopolysaccharide (LPS)-induced genes and the clearance of bacterial infection. Its expression is increased in response to various extracellular stimuli and it induces growth arrest and apoptosis in cancer cells. It is thought to function as a tumor suppressor and its expression is found reduced by site-specific methylation in many cancers including breast, cervical, and hepatocellular carcinoma. CEBPs (or C/EBPs) are Basic leucine zipper (bZIP) transcription factors that regulate many cellular processes. There are six CEBP proteins in mammalian cells including CEBPA (alpha), CEBPB (beta), CEBPG (gamma), CEBPD (delta), and CEBPE (epsilon), which all contain highly conserved bZIP domains at their C-termini and variations at their N-terminal regions. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 65 matched cddid_all.tbl CDD cd14715 cd14715 269863 bZIP_CEBPE Basic leucine zipper (bZIP) domain of CCAAT/enhancer-binding protein epsilon (CEBPE): a DNA-binding and dimerization domain. CEBPE is a critical regulator of terminal granulocyte differentiation or granulopoiesis. It is expressed only in myeloid cells. Mice deficient with CEBPE are normal at birth and fertile, but they do not produce normal neutrophils or eosinophils, and show impaired inflammatory and bacteriocidal responses. Functional loss of CEBPE causes the rare congenital disorder, Neutrophil-specific granule deficiency (SGD), which is characterized by patients' neutrophils with atypical nuclear morphology, abnormal migration and bactericidal activity, and the lack of specific granules. Patients with SGD suffer from severe and frequent bacterial infections. CEBPs (or C/EBPs) are Basic leucine zipper (bZIP) transcription factors that regulate many cellular processes. There are six CEBP proteins in mammalian cells including CEBPA (alpha), CEBPB (beta), CEBPG (gamma), CEBPD (delta), and CEBPE (epsilon), which all contain highly conserved bZIP domains at their C-termini and variations at their N-terminal regions. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 61 matched cddid_all.tbl CDD cd14716 cd14716 269864 bZIP_CEBP-like_1 Basic leucine zipper (bZIP) domain of CCAAT/enhancer-binding protein (CEBP)-like proteins: a DNA-binding and dimerization domain. This group is an uncharacterized subfamily of CEBP-like proteins. CEBPs (or C/EBPs) are Basic leucine zipper (bZIP) transcription factors that regulate the cell cycle, differentiation, growth, survival, energy metabolism, innate and adaptive immunity, and inflammation, among others. They are also associated with cancer and viral disease. There are six CEBP proteins in mammalian cells including CEBPA (alpha), CEBPB (beta), CEBPG (gamma), CEBPD (delta), and CEBPE (epsilon), which all contain highly conserved bZIP domains at their C-termini and variations at their N-terminal regions. Each possesses unique properties to regulate cell type-specific growth and differentiation. The sixth isoform, CEBPZ (zeta), lacks an intact DNA-binding domain and is excluded from this subfamily. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 60 matched cddid_all.tbl CDD cd14717 cd14717 269865 bZIP_Maf_small Basic leucine zipper (bZIP) domain of small musculoaponeurotic fibrosarcoma (Maf) proteins: a DNA-binding and dimerization domain. Maf proteins are Basic leucine zipper (bZIP) transcription factors that may participate in the activator protein-1 (AP-1) complex, which is implicated in many cell functions including proliferation, apoptosis, survival, migration, tumorigenesis, and morphogenesis, among others. Maf proteins fall into two groups: small and large. The small Mafs (MafF, MafK, and MafG) do not contain a transactivation domain but do harbor the anxillary DNA-binding domain and a C-terminal bZIP domain. They form dimers with cap'n'collar (CNC) proteins that harbor transactivation domains, and they act either as activators or repressors depending on their dimerization partner. CNC transcription factors include NFE2 (nuclear factor, erythroid-derived 2) and similar proteins NFE2L1 (NFE2-like 1), NFE2L2, and NFE2L3, as well as BACH1 and BACH2. Small Mafs play roles in stress response and detoxification pathways. They also regulate the expression of betaA-globin and other genes activated during erythropoiesis. They have been implicated in various diseases such as diabetes, neurological diseases, thrombocytopenia and cancer. Triple deletion of the three small Mafs is embryonically lethal. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 70 matched cddid_all.tbl CDD cd14718 cd14718 269866 bZIP_Maf_large Basic leucine zipper (bZIP) domain of large musculoaponeurotic fibrosarcoma (Maf) proteins: a DNA-binding and dimerization domain. Maf proteins are Basic leucine zipper (bZIP) transcription factors that may participate in the activator protein-1 (AP-1) complex, which is implicated in many cell functions including proliferation, apoptosis, survival, migration, tumorigenesis, and morphogenesis, among others. Maf proteins fall into two groups: small and large. The large Mafs (c-Maf, MafA, MafB, and neural retina leucine zipper or NRL) contain an N-terminal transactivation domain, a linker region of varying size, an anxillary DNA-binding domain, a C-terminal bZIP domain. They function as critical regulators of terminal differentiation in the blood and in many tissues such as bone, brain, kidney, pancreas, and retina. MafA and MafB also play crucial roles in islet beta cells; they regulate genes essential for glucose sensing and insulin secretion cooperatively and sequentially. Large Mafs are also implicated in oncogenesis; MafB and c-Maf chromosomal translocations result in multiple myelomas. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 70 matched cddid_all.tbl CDD cd14719 cd14719 269867 bZIP_BACH Basic leucine zipper (bZIP) domain of BTB and CNC homolog (BACH) proteins: a DNA-binding and dimerization domain. BACH proteins are Cap'n'Collar (CNC) Basic leucine zipper (bZIP) transcription factors that are defined by a conserved 43-amino acid region (called the CNC domain) located N-terminal to the bZIP DNA-binding domain. In addition, they contain a BTB domain (Broad complex-Tramtrack-Bric-a-brac domain, also known as the POZ [poxvirus and zinc finger] domain) that is absent in other CNC proteins. Veterbrates contain two members, BACH1 and BACH2. BACH1 forms heterodimers with small Mafs such as MafK to function as a repressor of heme oxygenase-1 (HO-1) gene (Hmox-1) enhancers. It has also been implicated as the master regulator of breast cancer bone metastasis. The BACH1 bZIP transcription factor should not be confused with the protein originally named as BRCA1-Associated C-terminal Helicase1 (BACH1), which has been renamed BRIP1 (BRCA1 Interacting Protein C-terminal Helicase1) and also called FANCJ. BACH2 is a B-cell specific transcription factor that plays a critical role in oxidative stress-mediated apoptosis. It plays an important role in class switching and somatic hypermutation of immunoglobulin genes. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 71 matched cddid_all.tbl CDD cd14720 cd14720 269868 bZIP_NFE2-like Basic leucine zipper (bZIP) domain of Nuclear Factor, Erythroid-derived 2 (NFE2) and similar proteins: a DNA-binding and dimerization domain. This subfamily is composed of NFE2 and NFE2-like proteins including NFE2-like 1 or NFE2-related factor 1 (NFE2L1 or Nrf1), NFE2L2 (or Nrf2), and NFE2L3 (or Nrf3). These are Cap'n'Collar (CNC) Basic leucine zipper (bZIP) transcription factors that are defined by a conserved 43-amino acid region (called the CNC domain) located N-terminal to the bZIP DNA-binding domain. NFE2 functions in development; it is required for the proper development of platelets. The three Nrfs function in stress responses. Nrf2, the most extensively studied member of this subfamily, acts as a xenobiotic-activated receptor that regulates the adaptive response to oxidants and electrophiles. As the master regulator of the antioxidant defense pathway, it plays roles in the biology of inflammation, obesity, and cancer. Nrf1 is an essential protein that binds to the antioxidant response element (ARE) and is also involved in regulating oxidative stress. In addition, it also regulates genes involved in cell and tissue differentiation, inflammation, and hepatocyte homeostasis. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 68 matched cddid_all.tbl CDD cd14721 cd14721 269869 bZIP_Fos Basic leucine zipper (bZIP) domain of the oncogene Fos (Fos): a DNA-binding and dimerization domain. Fos proteins are members of the activator protein-1 (AP-1) complex, which is mainly composed of Basic leucine zipper (bZIP) dimers of the Jun and Fos families, and to a lesser extent, the activating transcription factor (ATF) and musculoaponeurotic fibrosarcoma (Maf) families. The broad combinatorial possibilities for various dimers determine binding specificity, affinity, and the spectrum of regulated genes. The AP-1 complex is implicated in many cell functions including proliferation, apoptosis, survival, migration, tumorigenesis, and morphogenesis, among others. There are four Fos proteins: c-Fos, FosB, Fos-related antigen 1 (Fra-1), and Fra-2. In addition, FosB also exists as smaller splice variants FosB2 and deltaFosB2. They all contain an N-terminal region and a bZIP domain. c-Fos and FosB also contain a C-terminal transactivation domain which is absent in Fra-1/2 and the smaller FosB variants. Fos proteins can only heterodimerize with Jun and other AP-1 proteins, but cannot homodimerize. Fos:Jun heterodimers are more stable and can bind DNA with more affinity that Jun:Jun homodimers. Fos proteins can enhance the trans-activating and transforming properties of Jun proteins. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 62 matched cddid_all.tbl CDD cd14722 cd14722 269870 bZIP_ATF3 Basic leucine zipper (bZIP) domain of Activating Transcription Factor-3 (ATF-3) and similar proteins: a DNA-binding and dimerization domain. ATF-3 is a Basic leucine zipper (bZIP) transcription factor that is induced by various stress signals such as cytokines, genetoxic agents, or physiological stresses. It is implicated in cancer and host defense against pathogens. It negatively regulates the transcription of pro-inflammatory cytokines and is critical in preventing acute inflammatory syndromes. Mice deficient with ATF3 display increased susceptibility to endotoxic shock induced death. ATF3 dimerizes with Jun and other ATF proteins; the heterodimers function either as activators or repressors depending on the promoter context. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 62 matched cddid_all.tbl CDD cd14723 cd14723 271240 ZIP_Ppr1 Leucine zipper Dimerization coil of Ppr1-like transcription factors. Ppr1/Ppr1p activates transcription of the URA1, URA3, and URA4 genes, which encode enzymes involved in the regulation of pyrimidine levels. Also included in this subfamily is Colletotrichum acutatum Nir1 which plays a role during nitrogen-starvation conditions. Proteins in this subfamily are members of the Gal4p family of transcriptional activators which contain an N-terminal DNA-binding domain with a Zn2Cys6 binuclear cluster that interact with CCG triplets and a leucine zipper-like heptad repeat that dimerizes. Dimerization allows binding of targets which contain two CCG motifs oriented in an inverted (CGG-CCG), direct (CCG-CCG), or everted (CCG-CGG) manner. 25 matched cddid_all.tbl CDD cd14724 cd14724 271241 ZIP_Gal4-like_1 Leucine zipper Dimerization domain of Gal4-like transcription factors. The Gal4p family of transcriptional activators contain an N-terminal DNA-binding domain with a Zn2Cys6 binuclear cluster that interact with CCG triplets and a leucine zipper-like heptad repeat that dimerizes. Dimerization allows binding of targets which contain two CCG motifs oriented in an inverted (CGG-CCG), direct (CCG-CCG), or everted (CCG-CGG) manner. Gal4p family members are involved in the activation of genes in response to a specific signal. Gal4p functions in the induction of GAL genes in the presence of galactose; GAL proteins are responsible for the transport of galactose into the cell and for its metabolism through the glycolytic pathway. Hap1p promotes transcription of genes required for respiration and controlling oxidative damage in response to heme. Put3p activates the transcription of PUT1 and PUT2 genes in the presence of proline, allowing yeast cells to use proline as a nitrogen source. Sip4p activates target genes under conditions of glucose deprivation while Nir1 plays a role during nitrogen-starvation conditions. This subfamily is composed of uncharacterized members of the Gal4p family. 24 matched cddid_all.tbl CDD cd14725 cd14725 271242 ZIP_Gal4-like_2 Leucine zipper Dimerization coil of Gal4-like transcription factors. The Gal4p family of transcriptional activators contain an N-terminal DNA-binding domain with a Zn2Cys6 binuclear cluster that interact with CCG triplets and a leucine zipper-like heptad repeat that dimerizes. Dimerization allows binding of targets which contain two CCG motifs oriented in an inverted (CGG-CCG), direct (CCG-CCG), or everted (CCG-CGG) manner. Gal4p family members are involved in the activation of genes in response to a specific signal. Gal4p functions in the induction of GAL genes in the presence of galactose; GAL proteins are responsible for the transport of galactose into the cell and for its metabolism through the glycolytic pathway. Hap1p promotes transcription of genes required for respiration and controlling oxidative damage in response to heme. Put3p activates the transcription of the PUT1 and PUT2 genes in the presence of proline, allowing yeast cells to use proline as a nitrogen source. Sip4p activates target genes under conditions of glucose deprivation while Nir1 plays a role during nitrogen-starvation conditions. This subfamily is composed of uncharacterized members of the Gal4p family. 24 matched cddid_all.tbl CDD cd14726 cd14726 350608 TraB_PrgY-like TraB/PryY confer plasmid-borne pheromone resistance. TraB/PrgY proteins, identified in gut bacterium Enterococcus faecalis, are plasmid-borne homologs that are induced by pheromones. Induction rends the host bacterium insensitive to self-induction by its own pheromones, and prevents the transfer of the pheromone-inducible conjugative plasmids to bacteria that already contain it. Based on homology to Tiki activity, it has been proposed that TraB acts as a protease in the inactivation of mating pheromone, cleaving at the amino-terminus. The pheromones are small peptides (7-8 residues) encoded by the bacterial genome, and are specific for particular plasmids, or class of plasmids, which may contain several virulence factors and disseminate rapidly. Plasmid-borne antibiotic resistance and virulence determinants make these elements important contributors to medical problems. Trab/PrygY is a member of a Tiki-like superfamily. Tiki is a membrane-associated metalloprotease (MEROPS family M96) that inhibits Wnt via the cleavage of its amino terminus. Wnt is essential in animal development and homeostasis. In Xenopus, Tiki is critical in head development. In human cells, Tiki inhibits Wnt-signaling. Tiki proteins are also related to erythromycin esterase, gumN plant pathogens, RtxA containing toxins, and Campylobacter Jejuni ChaN heme-binding protein. 177 matched cddid_all.tbl CDD cd14727 cd14727 350609 ChanN-like ChaN is an iron-regulated, heme-binding protein. This family represents a domain found in ChaN, a heme-binding/iron-regulated lipoprotein from Campylobacter jejuni. ChaN, possibly involved in the uptake of heme-iron, contains a pair of cofacial heme groups situated between two ChaN monomers. A single tyrosine residue contacts the heme-bound iron atom while the heme-binding regions of each monomer also have contacts to the heme in the complementary monomer. ChaN presumably associates with an outer membrane-associated receptor, ChaR. Campylobacter jejuni is an important cause of food-borne illness, and is dependent on iron uptake from the host. ChaN like proteins are related to the Tiki/TraB like family of proteases. Proteins containing this domain also include protein reticulata-related from Arabidopsis which may play a role in leaf development. 211 matched cddid_all.tbl CDD cd14728 cd14728 350610 Ere-like Erythromycin esterase and succinoglycan biosynthesis related proteins. This group contains erythromycin esterase, which shares conserved active site residues of the Tiki/TraB family. Erythromycin esterases (EreA and EreB) disrupt erythromycin via the hydrolysis of the macrolactone ring. A critical catalytic histidine acts as a general base in the activation of a water molecule. Macrolides act by inhibiting bacterial protein synthesis by binding at the exit tunnel of ribosomal subunit 50s, blocking the translation of the polypeptide. Erythromycin esterase, typically found in integrons and transposons, confers antibiotic resistance through the disruption of the drug ring structure. EreB substrate profile is substantially broader than that for EreA, being able to also metabolize semisynthetic derivatives such as azalide azithromycin. 367 matched cddid_all.tbl CDD cd14729 cd14729 350611 RtxA-like C2-2 like domain of various multidomain toxins, including RTX-containing like proteins. This group contains mostly poorly-characterized C2-2 like domains of multidomain bacterial toxins, including Pasteurella multocida toxin PMT (also known as dermonecrotic toxin), MARTX (multifunctional-autoprocessing repeats-in-toxin holotoxin RtxA) proteins from Vibrio vulnificus, as well as bacterial effector protein from Pseudomonas syringae (type III effector HopAC1). MARTX domains at the N- and C- termini act in the translocation of the central domain across the eukaryotic plasma membrane, where it is proteolytically released. These are related to Pasteurella multicida toxin, which has structural and sequence similarity to the TIKI/TraB family of proteases. However, while this group of multidomain proteins shows fairly strong conservation of the active site residues of this family, the Pasteurella multicida toxin does not. 170 matched cddid_all.tbl CDD cd14730 cd14730 269830 LodA_like L-lysine epsilon-oxidase from Marinomonas mediterranea and similar proteins. L-lysine epsilon-oxidase is responsible for oxidative deamination of L-lysine, producing L-2-aminoadipate-6-semialdehyde. Hydrogen peroxide is a side-product of this enzymatic reaction, which requires the cofactor CTQ (cysteine tryptophylquinone). CTQ most likely forms a Schiff base with the free amino acid substrate. The protein is also called marinocine, for its broad-spectrum antibacterial activity; the latter is most likely caused by hydrogen peroxide synthesis. Homologs of LodA have been detected in various gram-negative bacteria, and they appear to be associated with the formation of biofilms. 509 matched cddid_all.tbl CDD cd14731 cd14731 269831 LodA_like_1 Uncharacterized proteins similar to L-lysine epsilon-oxidase from Marinomonas mediterranea. L-lysine epsilon-oxidase is responsible for oxidative deamination of L-lysine, producing L-2-aminoadipate-6-semialdehyde. Hydrogen peroxide is a side-product of this enzymatic reaction, which requires the cofactor CTQ (cysteine tryptophylquinone). CTQ most likely forms a Schiff base with the free amino acid substrate. The protein is known for its broad-spectrum antibacterial activity; the latter is most likely caused by hydrogen peroxide synthesis. Although members of this related family share features of the active site, their functions are not known. Homologs of LodA have been detected in various gram-negative bacteria, and they appear to be associated with the formation of biofilms. 587 matched cddid_all.tbl CDD cd14732 cd14732 269832 LodA L-lysine epsilon-oxidase from Marinomonas mediterranea and similar proteins. L-lysine epsilon-oxidase is responsible for oxidative deamination of L-lysine, producing L-2-aminoadipate-6-semialdehyde. Hydrogen peroxide is a side-product of this enzymatic reaction, which requires the cofactor CTQ (cysteine tryptophylquinone). CTQ most likely forms a Schiff base with the free amino acid substrate. The protein is also called marinocine, for its broad-spectrum antibacterial activity; the latter is most likely caused by hydrogen peroxide synthesis. The dimerization interface observed in the available 3D structure does not seem to be conserved. Homologs of LodA have been detected in various gram-negative bacteria, and they appear to be associated with the formation of biofilms. 639 matched cddid_all.tbl CDD cd14733 cd14733 350515 BACK BACK (BTB and C-terminal Kelch) domain. The BACK domain is found in architectures C-terminal to a BTB domain, in a diverse set of architectures together with Kelch, MATH, and/or TAZ domains. It is involved in interactions with the Cullin3 (Cul3) ubiquitin ligase complex, as well as in homo-oligomerization. Most proteins containing the BACK domain are understood to function as adaptor proteins that play a role in ubiquitination of various substrates. 55 matched cddid_all.tbl CDD cd14736 cd14736 350516 BACK_AtBPM-like BACK (BTB and C-terminal Kelch) domain found in plant BTB/POZ-MATH (BPM) protein family. The BPM protein family includes Arabidopsis thaliana BTB/POZ and MATH domain-containing proteins, AtBPM1-6, and similar proteins. BPM protein, also termed protein BTB-POZ and MATH domain, may act as a substrate-specific adaptor of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. 62 matched cddid_all.tbl CDD cd14737 cd14737 269822 PAAR_1 proline-alanine-alanine-arginine (PAAR) domain. This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey cells. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. It has been shown that PAAR proteins are essential for T6SS-mediated secretion and target cell killing by Vibrio cholerae (encodes two PAAR proteins) and Acinetobacter baylyi (encodes three PAAR proteins); inactivation of all these PAAR genes results in inactivation of Hcp secretion as well as T6SS-dependent killing of E. coli. 94 matched cddid_all.tbl CDD cd14738 cd14738 269823 PAAR_2 proline-alanine-alanine-arginine (PAAR) domain. This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey cells. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. It has been shown that PAAR proteins are essential for T6SS-mediated secretion and target cell killing by Vibrio cholerae (encodes two PAAR proteins) and Acinetobacter baylyi (encodes three PAAR proteins); inactivation of all these PAAR genes results in inactivation of Hcp secretion as well as T6SS-dependent killing of E. coli. 94 matched cddid_all.tbl CDD cd14739 cd14739 269824 PAAR_3 proline-alanine-alanine-arginine (PAAR) domain. This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey cells. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. It has been shown that PAAR proteins are essential for T6SS-mediated secretion and target cell killing by Vibrio cholerae (encodes two PAAR proteins) and Acinetobacter baylyi (encodes three PAAR proteins); inactivation of all these PAAR genes results in inactivation of Hcp secretion as well as T6SS-dependent killing of E. coli. 90 matched cddid_all.tbl CDD cd14740 cd14740 269825 PAAR_4 proline-alanine-alanine-arginine (PAAR) domain. This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of bacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). A few members contains C-terminal domain extensions corresponding to Rearrangement hotspot (Rhs) protein repeats and conserved Rhs repeat-associated unique core sequences as well as uncharacterized domains such as DUF4150. However, these terminal domains are exposed to solution, and do not distort the binding site of VgrG. Rhs and related YD-peptide repeat proteins are widely distributed in bacteria. Rhs shares similar architecture with distantly related WapA proteins of Bacillus and Listeria species, suggesting intercellular growth inhibition as its primary function. Additionally, a plasmid-encoded Rhs protein has been implicated in bacteriocin production in Pseudomonas savastanoi. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. 121 matched cddid_all.tbl CDD cd14741 cd14741 269826 PAAR_5 proline-alanine-alanine-arginine (PAAR) domain. This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family in bacteria as well as some archaea, where it forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). The T6SS is responsible for translocation of a wide variety of toxic effector molecules, allowing predatory cells to kill prokaryotic as well as eukaryotic prey cells. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. It has been shown that PAAR proteins are essential for T6SS-mediated secretion and target cell killing by Vibrio cholerae (encodes two PAAR proteins) and Acinetobacter baylyi (encodes three PAAR proteins); inactivation of all these PAAR genes results in inactivation of Hcp secretion as well as T6SS-dependent killing of E. coli. 95 matched cddid_all.tbl CDD cd14742 cd14742 269827 PAAR_RHS proline-alanine-alanine-arginine (PAAR) domain, also containing C-terminal Rearrangement hotspot (Rhs) extensions. This PAAR (proline-alanine-alanine-arginine) repeat subfamily, which forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS), contains C- and N-terminal domain extensions. These include Rearrangement hotspot (Rhs) protein repeats and conserved Rhs repeat-associated unique core sequences at the C-terminal, and various predicted functions at N- and C-terminal extensions. However, these terminal domains are exposed to solution, and do not distort the binding site of VgrG. Rhs and related YD-peptide repeat proteins are widely distributed in bacteria. Rhs shares similar architecture with distantly related WapA proteins of Bacillus and Listeria species, suggesting intercellular growth inhibition as its primary function. Additionally, a plasmid-encoded Rhs protein has been implicated in bacteriocin production in Pseudomonas savastanoi. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. 86 matched cddid_all.tbl CDD cd14743 cd14743 269828 PAAR_CT_1 proline-alanine-alanine-arginine (PAAR) domain with C-terminal extension. This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of mostly gamma-proteobacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). Some members contains C-terminal domain extensions corresponding to Rearrangement hotspot (Rhs) protein repeats and conserved Rhs repeat-associated unique core sequences as well as uncharacterized domains. However, these terminal domains are exposed to solution, and do not distort the binding site of VgrG. Rhs and related YD-peptide repeat proteins are widely distributed in bacteria. Rhs shares similar architecture with distantly related WapA proteins of Bacillus and Listeria species, suggesting intercellular growth inhibition as its primary function. Additionally, a plasmid-encoded Rhs protein has been implicated in bacteriocin production in Pseudomonas savastanoi. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. 78 matched cddid_all.tbl CDD cd14744 cd14744 269829 PAAR_CT_2 proline-alanine-alanine-arginine (PAAR) domain with uncharacterized C-terminal extension. This domain is found in the PAAR (proline-alanine-alanine-arginine) repeat family of mostly beta- and gamma-proteobacteria, and forms a sharp conical extension on the VgrG spike, a trimeric protein complex of the bacterial type VI secretion system (T6SS). Most members contain C-terminal domain extensions corresponding to several uncharacterized domains such as S-type pyocin, DUF2235, DUF2345 and cytotoxic proteins. However, these terminal domains are exposed to solution, and do not distort the binding site of VgrG. The pointed tip of the PAAR domain is stabilized by a zinc atom positioned close to the cone's vertex and is likely to be important for its integrity during penetration of the target cell envelope. VgrG proteins are orthologous to the central baseplate spikes of bacteriophages with contractile tails, and genes encoding proteins with PAAR motifs have been frequently found immediately downstream from vgrG-like genes. 78 matched cddid_all.tbl CDD cd14745 cd14745 270613 GH66 Glycoside Hydrolase Family 66. Glycoside Hydrolase Family 66 contains proteins characterized as cycloisomaltooligosaccharide glucanotransferase (CITase) and dextranases from a variety of bacteria. CITase cyclizes part of a (1-6)-alpha-D-glucan (dextrans) chain by formation of a (1-6)-alpha-D-glucosidic bond. Dextranases catalyze the endohydrolysis of (1-6)-alpha-D-glucosidic linkages in dextran. Some members contain Carbohydrate Binding Module 35 (CBM35) domains, either C-terminal or inserted in the domain or both. 331 matched cddid_all.tbl CDD cd14747 cd14747 270450 PBP2_MalE Maltose-binding protein MalE; possesses type 2 periplasmic binding fold. This group includes the periplasmic maltose-binding component of an ABC transport system from the phytopathogen Xanthomonas citri and its related bacterial proteins. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 386 matched cddid_all.tbl CDD cd14748 cd14748 270451 PBP2_UgpB The periplasmic-binding component of ABC transport system specific for sn-glycerol-3-phosphate; possesses type 2 periplasmic binding fold. This group includes the periplasmic component of an ABC transport system specific for sn-glycerol-3-phosphate (G3P) and closely related proteins from archaea and bacteria. Under phophate starvation conditions, Escherichia coli can utilize G3P as phosphate source when exclusively imported by an ATP-binding cassette (ABC) transporter composed of the periplasmic binding protein, UgpB, the transmembrane subunits, UgpA and UgpE, and a homodimer of the nucleotide binding subunit, UgpC. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 385 matched cddid_all.tbl CDD cd14749 cd14749 270452 PBP2_XBP1_like The periplasmic-binding component of ABC transport systems specific for xylo-oligosaccharides; possesses type 2 periplasmic binding fold. This group represents the periplasmic component of an ABC transport system XBP1 that shows preference for xylo-oligosaccharides in the order of xylotriose > xylobiose > xylotetraose. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 388 matched cddid_all.tbl CDD cd14750 cd14750 270453 PBP2_TMBP The periplasmic-binding component of ABC transport systems specific for trehalose/maltose; possesses type 2 periplasmic binding fold. This group represents the periplasmic trehalose/maltose-binding component of an ABC transport system and related proteins from archaea and bacteria. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 385 matched cddid_all.tbl CDD cd14751 cd14751 270454 PBP2_GacH The periplasmic-binding component of the putative oligosacchride ABC transporter GacHFG; possesses type 2 periplasmic binding fold. This group represents the periplasmic component GacH of an ABC import system. GacH is identified as a maltose/maltodextrin-binding protein with a low affinity for acarbose. Members of this group belong to the type 2 periplasmic-binding fold superfamily. PBP2 proteins are comprised of two globular subdomains connected by a flexible hinge and bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. The majority of PBP2 proteins function in the uptake of small soluble substrates in eubacteria and archaea. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. 376 matched cddid_all.tbl CDD cd14752 cd14752 270212 GH31_N N-terminal domain of glycosyl hydrolase family 31 (GH31). This family is found N-terminal to the glycosyl-hydrolase domain of Glycoside hydrolase family 31 (GH31). GH31 includes the glycoside hydrolases alpha-glucosidase (EC 3.2.1.20), alpha-1,3-glucosidase (EC 3.2.1.84), alpha-xylosidase (EC 3.2.1.177), sucrase-isomaltase (EC 3.2.1.48 and EC 3.2.1.10), as well as alpha-glucan lyase (EC 4.2.2.13). All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. In most cases, the pyranose moiety recognized in subsite-1 of the substrate binding site is an alpha-D-glucose, though some GH31 family members show a preference for alpha-D-xylose. Several GH31 enzymes can accommodate both glucose and xylose and different levels of discrimination between the two have been observed. Most characterized GH31 enzymes are alpha-glucosidases. In mammals, GH31 members with alpha-glucosidase activity are implicated in at least three distinct biological processes. The lysosomal acid alpha-glucosidase (GAA) is essential for glycogen degradation and a deficiency or malfunction of this enzyme causes glycogen storage disease II, also known as Pompe disease. In the endoplasmic reticulum, alpha-glucosidase II catalyzes the second step in the N-linked oligosaccharide processing pathway that constitutes part of the quality control system for glycoprotein folding and maturation. The intestinal enzymes sucrase-isomaltase (SI) and maltase-glucoamylase (MGAM) play key roles in the final stage of carbohydrate digestion, making alpha-glucosidase inhibitors useful in the treatment of type 2 diabetes. GH31 alpha-glycosidases are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues of the catalytic domain have been identified as the catalytic nucleophile and the acid/base, respectively. A loop of the N-terminal beta-sandwich domain is part of the active site pocket. 122 matched cddid_all.tbl CDD cd14755 cd14755 271288 GS_BA2291-HK-like Non-heme globin sensor domain of BA2291 histidine kinase and related domains. This subfamily includes the sensor domain of Bacillus anthracis BA2291 histidine kinase. BA2291 is one of the most active kinases in promoting sporulation, and is found in most members of the Bacillus cereus subfamily of the genus Bacillus, which includes B. anthracis and Bacillus thuringiensis, but not Bacillus subtilis. This subfamily also includes two sensor-only plasmid encoded sporulation inhibitors pXO1-118 and pXO2-61 found only in B. anthracis and various strains of Bacillus cereus having similar plasmids. The pXO1-118 and pXO2-61 sensor domains form homodimers, and in vitro bind fatty acid and halide, and not heme; there may be roles for fatty acid (or similar molecule), chloride ion, and possibly pH, as signaling cues. It has been proposed that BA2291 senses the same environmental cue in vivo, and that pXO1-118 and pXO2-61 act by titrating out an environmental signal that might cause an ill-timed sporulation. 132 matched cddid_all.tbl CDD cd14756 cd14756 381270 TrHb Truncated Mb-fold globins, T family. The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. They are classified into three main groups based on their structural properties and named after Mycobacterium sp. genes glbN, glbO, and glbP: TrHb1s (N), TrHb2s (O) and TrHb3s (P). Typical of the TrHb1s (N) group is a protein matrix tunnel. An example of a TrHb1 is Mycobacterium tuberculosis TrHb1/Mt-trHbN which is expressed during the Mycobacterium stationary phase, and plays a specific defense role against nitrosative stress. TrHb2s include the dimeric Arabidopsis thaliana TrHb2 AtGLB3. GLB3 is likely to have a function distinct from other plant globins: it exhibits a low O2 affinity, an unusual concentration-independent binding of O2 and CO, and does not respond to any of the treatments that induce plant 3-on-3 globins. TrHb3s include Campylobacter jejuni Ctb, encoded by Cj0465c, which may play a role in moderating O2 flux within C. jejuni. 111 matched cddid_all.tbl CDD cd14757 cd14757 381271 GS_EcDosC-like_GGDEF Globin sensor domain of Escherichia coli Direct Oxygen Sensing Cyclase and related proteins; coupled to a C-terminal GGDEF domain. Globin-coupled-sensors belonging to this subfamily have a C-terminal diguanylate cyclase (DGC/GGDEF) domain coupled to the globin sensor domain. DGC/GGDEF likely functions as a c-di-GMP cyclase in the synthesis of the second messenger cyclic-di-GMP (c-di-GMP). Members include Escherichia coli DosC (also known as YddV), the gene for which is found in a two-gene operon, dosCP. In DosC, the sensory globin domain is coupled to a GGDEF-class diguanylate cyclase, while in DosP, a heme-containing PAS domain is coupled to an EAL-class c-di-GMP phosphodiesterase. DosP and DosC associate in a di-GMP-responsive Escherichia coli RNA processing complex along with polynucleotide phosphorylase (PNPase), enolase, RNase E, and RNA. 149 matched cddid_all.tbl CDD cd14758 cd14758 381272 GS_GGDEF_1 Globin sensor domain, coupled to DGC/GGDEF domains; uncharacterized subgroup. Globin-coupled-sensors belonging to this subfamily have a sensor domain coupled to a C-terminal diguanylate cyclase (DGC/GGDEF) domain. DGC/GGDEF likely functions as a c-di-GMP cyclase in the synthesis of the second messenger cyclic-di-GMP (c-di-GMP). 148 matched cddid_all.tbl CDD cd14759 cd14759 381273 GS_GGDEF_2 Globin sensor domain, coupled to DGC/GGDEF domains; uncharacterized subgroup. The majority of globin-coupled-sensors in this subfamily have diguanylate cyclase (DGC/GGDEF) domains N-terminal to the globin sensor domain and/or C-terminal EAL domains, DGC/GGDEF and EAL domains are involved in the synthesis and degradation of the secondary messenger c-di-GMP, respectively. Some members have GAF small-molecule-binding domains in addition. 150 matched cddid_all.tbl CDD cd14760 cd14760 271293 GS_PAS-GGDEF-EAL Globin sensor domain; coupled to PAS, DGC/GGDEF and EAL domains. In addition to the N-terminal sensing domain, globin-coupled-sensors in this bacterial subfamily have a signal-sensing PAS domain, and diguanylate cyclase (DGC/GGDEF) and EAL domains. The latter two domains are involved in the synthesis and degradation of c-di-GMP, respectively, and may be involved in regulating cell surface adhesiveness, and in the transition between planktonic and biofilm growth modes. 148 matched cddid_all.tbl CDD cd14761 cd14761 381274 GS_GsGCS-like Globin sensor domain of Geobacter sulfurreducens globin-coupled-sensor and related proteins. GsGCS is a GCS of unknown function, comprised of an N-terminal globin sensor domain and a C- terminal transmembrane signal-transduction domain. For GCSs in general, the first signal O2 binds to/dissociates from the heme iron complex inducing a structural change in the globin domain, which is then transduced to the functional domain, switching on (or off) the function of the latter. Ferric GsGCS is bis-histidyl hexa-coordinated (provided by a His residue located at the E11 topological site, as distinct from the E7 site). Ferrous GsGCS is a penta- and hexa-coordinated mixture. The C-terminal domains of other members of this subfamily include histidine kinase, and PsiE domains. 149 matched cddid_all.tbl CDD cd14762 cd14762 381275 GS_STAS Globin sensor domain; coupled to a STAS domain. Globin-coupled-sensors in this subfamily have a C-terminal sulphate transporter and anti-sigma factor antagonist (STAT) domain coupled to the globin sensor domain. 143 matched cddid_all.tbl CDD cd14763 cd14763 381276 SSDgbs_1 Sensor single-domain globins; uncharacterized bacterial subgroup. This subfamily of sensor single-domain globins, belongs to a family that includes GCSs (globin-coupled-sensors) and single-domain protoglobins (Pgbs). For GCSs, an N-terminal heme-bound oxygen-sensing/binding globin domain is coupled to a C-terminal functional/signaling domain. The first signal O2 binds to/dissociates from the heme in its sensor domain inducing a conformational change in that domain and ultimately in the signaling domain. It has been demonstrated that the Pgbs and other single domain globins can function as sensors, when coupled to an appropriate regulatory domain. 144 matched cddid_all.tbl CDD cd14764 cd14764 381277 SSDgbs_2 Sensor single-domain globins; uncharacterized subgroup. This subfamily of sensor single-domain globins, belongs to a family that includes GCSs (globin-coupled-sensors) and single-domain protoglobins (Pgbs). For GCSs, an N-terminal heme-bound oxygen-sensing/binding globin domain is coupled to a C-terminal functional/signaling domain. The first signal O2 binds to/dissociates from the heme in its sensor domain inducing a conformational change in that domain and ultimately in the signaling domain. It has been demonstrated that the Pgbs and other single domain globins can function as sensors, when coupled to an appropriate regulatory domain. 145 matched cddid_all.tbl CDD cd14765 cd14765 381278 Hb Hemoglobins. Hb is the oxygen transport protein of erythrocytes. It is an allosterically modulated heterotetramer. Hemoglobin A (HbA) is the most common Hb in adult humans, and is formed from two alpha-chains and two beta-chains (alpha2beta2). An equilibrium exists between deoxygenated/unliganded/T(tense state) Hb having low oxygen affinity, and oxygenated /liganded/R(relaxed state) Hb having a high oxygen affinity. Various endogenous heterotropic effectors bind Hb to modulate its oxygen affinity and cooperative behavior, e.g. hydrogen ions, chloride ions, carbon dioxide and 2,3-bisphosphoglycerate. Hb is also an allosterically regulated nitrite reductase; the plasma nitrite anion may be activated by hemoglobin in areas of hypoxia to bring about vasodilation. Other Hb types are: HbA2 (alpha2delta2) which, in normal individuals, is naturally expressed at a low level; Hb Portland-1 (zeta2gamma2), Hb Gower-1 (zeta2epsilon2), and Hb Gower-2 (alpha2epsilon2), which are Hbs present during the embryonic period; and fetal hemoglobin (HbF, alpha2gamma2), the primary Hb throughout most of gestation. These Hb types have differences in O2 affinity and in their interactions with allosteric effectors. 131 matched cddid_all.tbl CDD cd14766 cd14766 381279 CeGLB25-like Caenorhabditis elegans globin GLB-25, and related globins. The C. elegans genome contains 33 genes encoding globins that are all transcribed. These are very diverse in gene and protein structure and are localized in a variety of cells. The C. elegans globin GLB-25 (locus tag T06A1.3), like the majority of them, was expressed in neuronal cells in the head and tail portions of the body and in the nerve cord. 137 matched cddid_all.tbl CDD cd14767 cd14767 271300 PE_beta-like Phycoerythrin beta subunit, a component of the phycobilisome rod; and related proteins. phycobilisomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker polypeptides. PBPs have different numbers of chromophores, and the basic monomer component (alpha/beta heterodimers) can further oligomerize to ring-shaped trimers (heterohexamers) and hexamers (heterododecamers). Stacked PBP hexamers form both the core and the rods of the PBS; the core is mainly made up by allophycocyanin (APC) while the rods can be composed of the PBPs phycoerythrin (PE), phycocyanin (PC) and phycoerythrocyanin (PEC). This subfamily also includes the beta subunits of Cryptophyte phycobiliproteins which represent another type of biliprotein antenna with different structure and organization. The beta subunits of cryptophyte PBPs share a high degree of sequence identity with both the alpha and beta subunits of the cyanobacterial and red algal PBPs, however the alpha cryptophyte subunits are shorter, and unrelated. There is only one type of PBP present in a single species, either phycocyanin or phycoerythrin, but not allophycocyanin. Structurally, phycoerythrin in cryptophytes is an alpha1alpha2betabeta dimer and not a trimer as in the PBS. 176 matched cddid_all.tbl CDD cd14768 cd14768 271301 PC_PEC_beta Beta subunits of phycoerythrin and phycoerythrocyanin; phycobilisome rod components. phycobilisomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker polypeptides. PBPs have different numbers of chromophores, and the basic monomer component (alpha/beta heterodimers) can further oligomerize to ring-shaped trimers (heterohexamers) and hexamers (heterododecamers). Stacked PBP hexamers form both the core and the rods of the PBS; the core is mainly made up by allophycocyanin (APC) while the rods can be composed of the PBPs phycoerythrin (PE), phycocyanin (PC) and phycoerythrocyanin (PEC). 171 matched cddid_all.tbl CDD cd14769 cd14769 271302 PE_alpha Phycoerythrin alpha subunit, a phycobilisome rod component. phycobilisomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker polypeptides. PBPs have different numbers of chromophores, and the basic monomer component (alpha/beta heterodimers) can further oligomerize to ring-shaped trimers (heterohexamers) and hexamers (heterododecamers). Stacked PBP hexamers form both the core and the rods of the PBS; the core is mainly made up by allophycocyanin (APC) while the rods can be composed of the PBPs phycoerythrin (PE), phycocyanin (PC) and phycoerythrocyanin (PEC). 164 matched cddid_all.tbl CDD cd14770 cd14770 271303 PC-PEC_alpha Alpha subunits of phycoerythrin and phycoerythrocyanin; phycobilisome rod components. phycobilisomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker polypeptides. PBPs have different numbers of chromophores, and the basic monomer component (alpha/beta heterodimers) can further oligomerize to ring-shaped trimers (heterohexamers) and hexamers (heterododecamers). Stacked PBP hexamers form both the core and the rods of the PBS; the core is mainly made up by allophycocyanin (APC) while the rods can be composed of the PBPs phycoerythrin (PE), phycocyanin (PC) and phycoerythrocyanin (PEC). 162 matched cddid_all.tbl CDD cd14771 cd14771 381280 TrHb2_Mt-trHbO-like_O Truncated hemoglobins, group 2 (O); Mycobacterium tuberculosis hemoglobin O like. The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. TrHbs are classified into three main groups based on their structural properties and named after Mycobacterium sp. genes glbN, glbO, and glbP: TrHb1s (N), TrHb2s (O) and TrHb3s (P). This group includes a Mycobacterium tuberculosis TrHb2, Mt-trHbO, encoded by the Mycobacterium tuberculosis glbO gene, which is expressed throughout the Mycobacterium growth phase. It also includes a TrHb2 from the thermophilic Thermobifida fusca ( Tf-trHb) which has a high thermostability and at the optimal growth temperature for Thermobifida fusca (between 55 and 60 degrees C ), it is capable of efficient O2 binding and release. Tf-trHb shares a relatively slow rate of oxygen binding with Mt-trHbO. 119 matched cddid_all.tbl CDD cd14772 cd14772 381281 TrHb2_Bs-trHb-like_O Truncated hemoglobins, group 2 (O); Bacillus subtilis TrHb like. The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. TrHbs are classified into three main groups based on their structural properties and named after Mycobacterium sp. genes glbN, glbO, and glbP: TrHb1s (N), TrHb2s (O) and TrHb3s (P). TrHb2's belonging to this group include monomeric Bacillus subtilis trHb (Bs-trHb), which exhibits an extremely high oxygen affinity, and a dimeric TrHb2 from the thermophilic aerobic spore forming bacterium Geobacillus stearothermophilus(Gs-trHb). 116 matched cddid_all.tbl CDD cd14773 cd14773 381282 TrHb2_PhHbO-like_O Truncated hemoglobins, group 2 (O); Pseudoalteromonas haloplanktis PhHbO like. The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. TrHbs are classified into three main groups based on their structural properties and named after Mycobacterium sp. genes glbN, glbO, and glbP: TrHb1s (N), TrHb2s (O) and TrHb3s (P). TrHb2's belonging to this group include Pseudoalteromonas haloplanktis PhHbO (encoded by the PSHAa0030 gene) which appears to be involved in oxidative and nitrosative stress resistance. 119 matched cddid_all.tbl CDD cd14774 cd14774 381283 TrHb2_HGbIV-like_O hell's gate globin IV and similar truncated hemoglobins, group 2 (O). The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. TrHbs are classified into three main groups based on their structural properties and named after Mycobacterium sp. genes glbN, glbO, and glbP: TrHb1s (N), TrHb2s (O) and TrHb3s (P). 131 matched cddid_all.tbl CDD cd14775 cd14775 381284 TrHb2_O-like Truncated hemoglobins, group 2 (O); uncharacterized subgroup. The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. TrHbs are classified into three main groups based on their structural properties and named after Mycobacterium sp. genes glbN, glbO, and glbP: TrHb1s (N), TrHb2s (O) and TrHb3s (P). 119 matched cddid_all.tbl CDD cd14776 cd14776 271309 HmpEc-globin-like Globin domain of Escherichia coli flavohemoglobin (Hmp) and related proteins. Flavohemoglobins (flavoHbs) function primarily as nitric oxide dioxygenases (NODs, EC 1.14.12.17), converting NO and O2 to inert NO3- (nitrate). They have an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD- and FAD-binding domain, and use the reducing power of cellular NAD(P)H to drive regeneration of the ferrous heme. They protect from nitrosative stress (the broad range of cellular toxicities caused by NO), and modulate NO signaling pathways. This subfamily includes Vibrio fischeri Hmp and E.coli Hmp. NO scavenging by flavoHb affects the swarming behavior of Escherichia coli, and protects against NO during initiation of the squid-Vibrio symbiosis. E.coli Hmp can catalyze the reduction of several alkylhydroperoxide substrates into their corresponding alcohols using NADH as an electron donor, and it has been suggested that it participates in the repair of the lipid membrane oxidative damage generated during oxidative/nitrosative stress. 138 matched cddid_all.tbl CDD cd14777 cd14777 381285 Yhb1-globin-like Globin domain of Saccharomyces cerevisiae flavohemoglobin (Yhb1p) and related domains. FlavoHbs function primarily as nitric oxide dioxygenases (NODs, EC 1.14.12.17), converting NO and O2 to inert NO3- (nitrate). They have an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD- and FAD-binding domain, and use the reducing power of cellular NAD(P)H to drive regeneration of the ferrous heme. They protect from nitrosative stress (the broad range of cellular toxicities caused by NO), and modulate NO signaling pathways. S. cerevisiae Yhb1p has been shown to protect against nitrosative stress and to control ferric reductase activity; it may participate in regulating the activity of plasma membrane ferric reductase(s). Also included in this subfamily is Dictyostelium discoideum FlavoHb, the expression of which affects D. discoideum development. 140 matched cddid_all.tbl CDD cd14778 cd14778 381286 VtHb-like_SDgb Vitreoscilla stercoraria hemoglobin and related proteins; single-domain globins. VtHb is homodimeric, and may both transport oxygen to terminal respiratory oxidases, and provide resistance to nitrosative stress. It has medium oxygen affinity and displays cooperative ligand-binding properties. VHb has biotechnological application, its expression in heterologous hosts (bacteria and plants) has improved growth and productivity under microaerobic conditions. Another member of this subfamily Campylobacter jejuni hemoglobin (Cgb) is monomeric, and plays a role in detoxifying NO. Along with a truncated globin Ctb, it is up-regulated by the transcription factor NssR in response to nitrosative stress. 140 matched cddid_all.tbl CDD cd14779 cd14779 381287 FHP_Ae-globin-like Globin domain of Alcaligenes eutrophus flavohemoglobin (FHP) and related proteins. Flavohemoglobins (flavoHbs) function primarily as nitric oxide dioxygenases (NODs, EC 1.14.12.17), converting NO and O2 to inert NO3- (nitrate). They have an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD- and FAD-binding domain, and use the reducing power of cellular NAD(P)H to drive regeneration of the ferrous heme. They protect from nitrosative stress (the broad range of cellular toxicities caused by NO), and modulate NO signaling pathways. NO scavenging by flavoHb maintains Medicago truncatula-Sinorhizobium meliloti symbiosis. Alcaligenes eutrophus FHP contains a phospholipid-binding site. 140 matched cddid_all.tbl CDD cd14780 cd14780 381288 HmpPa-globin-like Globin domain of Pseudomonas aeruginosa flavohemoglobin (HmpPa) and related proteins. Flavohemoglobins (flavoHbs) function primarily as nitric oxide dioxygenases (NODs, EC 1.14.12.17), converting NO and O2 to inert NO3- (nitrate). They have an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD- and FAD-binding domain, and use the reducing power of cellular NAD(P)H to drive regeneration of the ferrous heme. They protect from nitrosative stress (the broad range of cellular toxicities caused by NO), and modulate NO signaling pathways. The physiological role of HmpPa is thought to be detoxification of NO under aerobic conditions. 140 matched cddid_all.tbl CDD cd14781 cd14781 381289 FHb-globin_1 Globin domain of flavohemoglobins (flavoHbs); uncharacterized subgroup. FlavoHbs function primarily as nitric oxide dioxygenases (NODs, EC 1.14.12.17), converting NO and O2 to inert NO3- (nitrate). They have an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD- and FAD-binding domain, and use the reducing power of cellular NAD(P)H to drive regeneration of the ferrous heme. They protect from nitrosative stress (the broad range of cellular toxicities caused by NO), and modulate NO signaling pathways. This subfamily may contain some single-domain goblins (SDgbs). 139 matched cddid_all.tbl CDD cd14782 cd14782 381290 FHb-globin_2 Globin domain of flavohemoglobins (flavoHbs); uncharacterized subgroup. FlavoHbs function primarily as nitric oxide dioxygenases (NODs, EC 1.14.12.17), converting NO and O2 to inert NO3- (nitrate). They have an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD- and FAD-binding domain, and use the reducing power of cellular NAD(P)H to drive regeneration of the ferrous heme. They protect from nitrosative stress (the broad range of cellular toxicities caused by NO), and modulate NO signaling pathways. 143 matched cddid_all.tbl CDD cd14783 cd14783 271316 FHb-globin_3 Globin domain of flavohemoglobins (flavoHbs); uncharacterized subgroup. FlavoHbs function primarily as nitric oxide dioxygenases (NODs, EC 1.14.12.17), converting NO and O2 to inert NO3- (nitrate). They have an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD- and FAD-binding domain, and use the reducing power of cellular NAD(P)H to drive regeneration of the ferrous heme. They protect from nitrosative stress (the broad range of cellular toxicities caused by NO), and modulate NO signaling pathways. 140 matched cddid_all.tbl CDD cd14784 cd14784 381291 class1_nsHb-like Class 1 nonsymbiotic hemoglobins and related proteins. Class1 nsHbs include the dimeric hexacoordinate Trema tomentosa nsHb and the dimeric hexacoordinate nsHb from monocot barley. This subfamily also includes ParaHb, a dimeric pentacoordinate Hb from the root nodules of Parasponia andersonii, a non-legume capable of symbiotic nitrogen fixation. ParaHb is unusual in that it has different heme redox potentials for each subunit. 149 matched cddid_all.tbl CDD cd14785 cd14785 270211 V-ATPase_C Subunit C of vacuolar H+-ATPase (V-ATPase). This family contains subunit C of vacuolar H+-ATPase (V-ATPase), a protein that plays a crucial role in the vacuolar system of eukaryotic cells. The main function of V-ATPase is to generate a proton-motive force at the expense of ATP and to cause limited acidification in the internal space (lumen) of several organelles of the vacuolar system. V-ATPases are multi-subunit protein complexes made up of two distinct structures: a peripheral catalytic sector (V1) and a hydrophobic membrane sector (V0) responsible for driving protons; subunit C is one of five polypeptides composing V1. The key function of the C subunit is intimately involved in the reversible dissociation of the V1 and V0 structures. It has also been identified as a mediator of the acidic microenvironment of tumors which it controls by proton extrusion to the extracellular medium. The acidic environment causes tissue damage, activates destructive enzymes in the extracellular matrix, and acquires metastatic cell phenotypes. 368 matched cddid_all.tbl CDD cd14786 cd14786 341075 STAT_CCD Coiled-coil domain of Signal Transducer and Activator of Transcription (STAT), also called alpha domain. This family consists of the coiled-coil (alpha) domain of the STAT proteins (Signal Transducer and Activator of Transcription, or Signal Transduction And Transcription), which are latent cytoplasmic transcriptional factors that play an important role in cytokine and growth factor signaling. STAT proteins regulate several aspects of growth, survival and differentiation in cells. The transcription factors of this family are activated by JAK (Janus kinase) and dysregulation of this pathway is frequently observed in primary tumors and leads to immunosuppression, increased angiogenesis and enhanced survival of tumors. There are seven mammalian STAT family members that have been identified: STAT1, STAT2, STAT3, STAT4, STAT5A, STAT5B and STAT6. STAT proteins consist of six structural regions: N-domain (ND)/protein interaction domain, coiled-coil domain (CCD)/STAT all alpha domain, DNA-binding domain (DBD), linker domain (LK), a Src homology 2 (SH2) domain, and C-terminal transcriptional activation domain (TA) that includes two conserved phosphorylation sites (tyrosine and serine residues). The coiled-coil or alpha domain is an interacting region with other proteins, including IRF-9/p48 for STAT1, c-Jun, StIP1, and GRIM-19 for STAT3, and SMRT with STAT5A and STAT5B. A functional STAT1 mutant (phenylalanine to serine) in this domain region shows significantly decreased protein expression caused by translational/post-translational mechanisms independent of proteasome machinery. The phenylalanine is not conserved in STAT4 and STAT6 that have tight specificity, suggesting a novel potential mechanism of specific activation of STAT proteins. Specifically, STAT3, STAT5, and STAT6, which are continually imported to the nucleus independent of tyrosine phosphorylation, require the conformational structure of their coiled-coil domains. 125 matched cddid_all.tbl CDD cd14787 cd14787 350612 Tiki_TraB-like diverse proteins related to the Tiki and TraB protease domains. The extracellular domain of Tiki family proteins shares homology with bacterial TraB/PrgY proteins which are known for their roles in the inhibition of mating pheromones. Tiki and TraB/PrgY proteins share limited sequence identity, but their predicted secondary structures reveal that several catalytic residues are anchored in a similar manner, consistent with a common evolutionary origin. Tiki domains are related to the erythromycin esterase, gumN plant pathogens, RtxA toxins, and Campylobacter Jejuni heme-binding, ChaN-like proteins. Tiki is a membrane-associated metalloprotease (MEROPS family M96) that inhibits Wnt via the cleavage of its amino terminus, diminishing Wnt's binding to receptors. Wnt is essential in animal development and homeostasis. In Xenopus, Tiki is critical in head development. In human cells, Tiki inhibits Wnt-signaling, which is important in embryogenesis, homeostasis, and regeneration. Deregulation of Wnt contributes to birth defects, cancer and various diseases. TraB/PrgY protein has been identified in gut bacterium Enterococcus faecalis, but its function has not been well characterized. Plasmid-borne TraB has been implicated in the regulation of pheromone sensitivity and specificity. Based on homology to Tiki activity, it has been proposed that TraB acts as a metalloprotease in the inactivation of mating pheromone. Pasteurella multicida toxin has structural and sequence similarity to the Tiki/TraB family of proteases. However, unlike related multidomain toxins in this family, they do not exhibit conservation of the typical active site residues. 127 matched cddid_all.tbl CDD cd14788 cd14788 350613 GumN poorly characterized family of proteins related to gumN pathogenicity factor of Xanthomonas. GumN, a poorly characterized protein, is part of the large gum cluster of pathogenicity factors of the plant pathogen Xanthomonas. Except for GumN, the gum cluster is conserved, and proteins of this operon are involved in the production of xanthan, an extracellular polysaccharide that promotes plant disease. Xanthomonas campestri is responsible for 'black rot' disease in certain crop plants. GumN has sequence similarity to the Tiki/TraB protease family, but lacks the typical conserved residues of the active site. 286 matched cddid_all.tbl CDD cd14789 cd14789 350614 Tiki Tiki homology domain antagonizes Wnt function via cleavage of amino-terminal residues. Tiki is a membrane-associated metalloprotease that inhibits Wnt via the cleavage of its amino terminus, diminishing Wnt's binding to receptors. Wnt is essential in animal development and homeostasis. In xenopus, tiki is critical in head development. In human cells, TIKI inhibits Wnt-signaling, which is important in embryogenesis, homeostasis, and regeneration. Deregulation of WNT contributes to birth defects, cancer and various diseases. TIKI homology domains are part of the TraB family and are related to the Erythromycin esterase, GumN plant pathogens, RtxA toxins, and Campylobacter Jejuni heme-binding, Chan-like proteins. TraB/PrgY are identified in gut bacterium Enterococcus faecalis, but its function has not been well characterized. Plasmid-borne, TraB has been implicated in the regulation of pheromone sensitivity and specificity. Based on homology to TIKI activity, it has been proposed that TraB acts as a metalloprotease in the inactivation of mating pheromone. The TIKI/TraB family has 2 conserved GxxH motifs and conserved glutamate and arginine residues that may be catalytic. 259 matched cddid_all.tbl CDD cd14790 cd14790 269891 GH_D Glycoside hydrolases, clan D. This group of glycosyl hydrolase families is comprised of glycosyl hydrolase family 31 (GH31), family 36 (GH36), and family 27 (GH27). These structurally and mechanistically related protein families are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively. They have a wide range of functions including alpha-glucosidase, alpha-xylosidase, 6-alpha-glucosyltransferase, 3-alpha-isomaltosyltransferase, alpha-N-acetylgalactosaminidase, stachyose synthase, raffinose synthase, and alpha-1,4-glucan lyase. 253 matched cddid_all.tbl CDD cd14791 cd14791 269892 GH36 glycosyl hydrolase family 36 (GH36). GH36 enzymes occur in prokaryotes, eukaryotes, and archaea with a wide range of hydrolytic activities, including alpha-galactosidase, alpha-N-acetylgalactosaminidase, stachyose synthase, and raffinose synthase. All GH36 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. GH36 members are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively. 299 matched cddid_all.tbl CDD cd14792 cd14792 269893 GH27 glycosyl hydrolase family 27 (GH27). GH27 enzymes occur in eukaryotes, prokaryotes, and archaea with a wide range of hydrolytic activities, including alpha-glucosidase (glucoamylase and sucrase-isomaltase), alpha-N-acetylgalactosaminidase, and 3-alpha-isomalto-dextranase. All GH27 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. GH27 members are retaining enzymes that cleave their substrates via an acid/base-catalyzed, double-displacement mechanism involving a covalent glycosyl-enzyme intermediate. Two aspartic acid residues have been identified as the catalytic nucleophile and the acid/base, respectively. 271 matched cddid_all.tbl CDD cd14793 cd14793 269816 DUF302_like Domains similar to DUF302 and the N-terminal domains found in some bacterial RNAses. DUF302 is an uncharacterized domain with widespread phylogenetic distribution. It appears homologous to the N-terminal domains of RNAse H3 and the Escherichia coli toxin RnlA. 81 matched cddid_all.tbl CDD cd14794 cd14794 269817 RNLA_N_1 N-terminal repeat domain of toxin RnlA; first out of two repeats. The Escherichia coli toxin RnlA functions as an mRNA endoribonuclease and is part of a two-component toxin-antitoxin system that promotes resistance to phage infections, together with the antitoxin RnlB. RNAse activity is located in the C-terminal domain. This N-terminal domain appears to participate in homodimerization and is the first out of two repeats. 90 matched cddid_all.tbl CDD cd14795 cd14795 269818 RNLA_N_2 N-terminal repeat domain of toxin RnlA; second out of two repeats. The Escherichia coli toxin RnlA functions as an mRNA endoribonuclease and is part of a two-component toxin-antitoxin system that promotes resistance to phage infections, together with the antitoxin RnlB. RNAse activity is located in the C-terminal domain. This N-terminal domain appears to participate in homodimerization and is the second out of two repeats. 87 matched cddid_all.tbl CDD cd14796 cd14796 269819 RNAse_HIII_N N-terminal domain of ribonuclease H3. RNAse H3 (HIII) is a bacterial type 2 ribonuclease, which endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, and plays a role in DNA replication and repair. The N-terminal domain characterized by this model has been shown to be important in substrate binding; it might form initial contacts with the substrate and not be part of the active complex that involves the C-terminal ribonuclease domain. This domain has also been characterized as DUF3378. 66 matched cddid_all.tbl CDD cd14797 cd14797 269820 DUF302 Uncharacterized domain family DUF302. These domains are mostly found in bacterial single-domain proteins and have been shown to form homodimers; they may also bind zinc. Also characterized as COG3439. 124 matched cddid_all.tbl CDD cd14798 cd14798 271353 RX-CC_like Coiled-coil domain of the potato virux X resistance protein and similar proteins. The potato virus X resistance protein (RX) confers resistance against potato virus X. It is a member of a family of resistance proteins with a domain architecture that includes an N-terminal coiled-coil domain (modeled here), a nucleotide-binding domain, and leucine-rich repeats (CC-NB-LRR). These intracellular resistance proteins recognize pathogen effector proteins and will subsequently trigger a response that may be as severe as localized cell death. The N-terminal coiled-coil domain of RX has been shown to interact with RanGAP2, which is a necessary co-factor in the resistance response. 124 matched cddid_all.tbl CDD cd14799 cd14799 438995 BRcat_Rcat_RBR BRcat (benign-catalytic) and Rcat (required-for-catalysis) domains, part of the RBR (RING1-BRcat-Rcat) domain. The RBR family of RING-type E3 ligases are characterized by containing an RBR (RING1-BRcat-Rcat) domain, which was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. It is composed of an extended RING domain (RING1) followed by an in-between RING (IBR) domain and the catalytic domain, which is structurally an IBR domain but is commonly designated as RING2. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBRs has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis), where the IBR and RING2 domains have been renamed as BRcat and Rcat domains, respectively. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. The BRcat domain adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. 37 matched cddid_all.tbl CDD cd14801 cd14801 341082 STAT_DBD DNA-binding domain of Signal Transducer and Activator of Transcription (STAT). This family consists of the DNA binding domain (DBD) of the STAT proteins (Signal Transducer and Activator of Transcription, or Signal Transduction And Transcription), which are latent cytoplasmic transcriptional factors that play an important role in cytokine and growth factor signaling. STAT proteins regulate several aspects of growth, survival and differentiation in cells. The transcription factors of this family are activated by JAK (Janus kinase) and dysregulation of this pathway is frequently observed in primary tumors and leads to immunosuppression, increased angiogenesis and enhanced survival of tumors. There are seven mammalian STAT family members that have been identified: STAT1, STAT2, STAT3, STAT4, STAT5A, STAT5B and STAT6. STAT proteins consist of six structural regions: N-terminal domain (ND)/protein interaction domain, coiled-coil domain (CCD)/STAT all alpha domain, DNA-binding domain (DBD), linker domain (LK), a Src homology 2 (SH2) domain, and C-terminal transcriptional activation domain (TA) that includes two conserved phosphorylation sites (tyrosine and serine residues). STAT1 and STAT3 have the greatest diversity of biological functions among the 7 known members of the STAT family. The DNA binding domain of STAT has an Ig-like fold. DNA binding specificity experiments of different STAT proteins show that STAT5A specificity is more similar to that of STAT6 than that of STAT1, as also seen from the evolutionary relationships. 157 matched cddid_all.tbl CDD cd14803 cd14803 269812 RAP Receptor-associated protein (RAP). Receptor-associated protein, RAP, is an antagonist and a specialized chaperone in the endoplasmic reticulum that binds tightly to members of the low-density lipoprotein (LDL) receptor family and prevents them from associating with other ligands. RAP associates with (LDL) receptor-related protein (LRP) early in the secretory pathway, reducing its ligand binding capacity, and then dissociates from LRP in the low-pH environment of the Golgi; studies have shown that histidine residues in RAP D3 serve as a switch that facilitates its uncoupling from the receptor. RAP is a modular protein identified as having an internal triplication, with domains, D1, D2, and D3, each thought to have distinct functions; these domains are independent and do not interact. The carboxyl-terminal domain (D3) of RAP is required for folding and trafficking of LRP, while the amino-terminal tandem D1D2 domains of RAP are essential for blocking LRP from binding of certain ligands, such as activated forms of alpha2-macroglobulin. 97 matched cddid_all.tbl CDD cd14804 cd14804 271351 Tra_M TraM mediates signalling between transferosome and relaxosome. TraM is a plasmid encoded DNA-binding protein that is essential for conjugative transfer of F-like plasmids (e.g. F, R1, R100 and pED208) between bacterial cells. Bacterial conjugation, a form of horizontal gene transfer between cells, is an important contributor to bacterial genetic diversity, enabling virulence and antibiotics resistance factors to rapidly spread in medically important human pathogens. Mutation studies have shown that TraM is required for normal levels of transfer gene expression as well as for efficient site-specific single-stranded DNA cleavage at the origin of transfer (oriT). TraM tetramers bridge oriT to a key component of the conjugative pore, the coupling protein TraD. The N-terminal ribbon-helix-helix (RHH) domain of TraM is able to cooperatively bind DNA in a staggered arrangement without interaction between tetramers. This allows the C-terminal TraM tetramerization domains to be free to make multiple interactions with TraD, thus driving plasmid recruitment to the conjugative pore. 122 matched cddid_all.tbl CDD cd14805 cd14805 271348 Translin-like Translin and translin-associated factor-X (TRAX). Translin (also known as TB-RBP), and its binding partner protein TRAX (translin-associated factor-X) are a paralogous pair of conserved proteins, and oligomeric complexes of TRAX and translin are known as C3PO proteins (for component 3 promoter of RNA-induced silencing complex or RISC). The Translin-Trax complex enhances the removal of the passenger strand in RNAi and the formation of active RISC. Translin and Trax participate in a variety of nucleic acid metabolism pathways in addition to RNAi and have been implicated in a wide range of biological activities, including mRNA processing, cell growth regulation, spermatogenesis, neuronal development/function, genome stability regulation and carcinogenesis; however, their precise role in some of the processes remains unclear. It has been shown that Trax subunit, but not Translin, possesses a Glu-Glu-Asp catalytic center with the capacity to digest RNA as well as DNA; this catalytic activity is required for passenger-strand removal and RISC activation in RNAi. In Archaeoglobus fulgidus, Trax-like-subunits assemble into an octameric structure, highly similar to human C3PO; its complex with duplex RNA reveals that the octamer entirely encapsulates a single 13-base-pair RNA duplex inside a large inner cavity. 197 matched cddid_all.tbl CDD cd14806 cd14806 269813 RAP_D1 Receptor-associated protein (RAP), Domain 1. This subfamily is the N-terminal domain (D1) of receptor-associated protein, RAP, an antagonist and a specialized chaperone in the endoplasmic reticulum that binds tightly to members of the low-density lipoprotein (LDL) receptor family and prevents them from associating with other ligands. D1 as well as domain 2 (D2) are essential for blocking low-density lipoprotein receptor-related protein (LRP) from binding of certain ligands, such as activated forms of alpha2-macroglobulin; D1 and D2 each bind LRP weakly but the tandem D1D2 binds much more tightly, suggesting the avidity effects arising from amino acid residues contributed from each domain. The double module of complement type repeats, CR56, of LRP binds many ligands including alpha2-macroglobulin, which promotes the catabolism of the Abeta-peptide implicated in Alzheimer's disease. 71 matched cddid_all.tbl CDD cd14807 cd14807 269814 RAP_D2 Domain 2 of receptor-associated protein (RAP). This subfamily is the N-terminal domain (D2) of receptor-associated protein, RAP, an antagonist and a specialized chaperone in the endoplasmic reticulum that binds tightly to members of the low-density lipoprotein (LDL) receptor family and prevents them from associating with other ligands. D2, along with RAP domain 1 (D1), is essential for blocking low-density lipoprotein receptor-related protein (LRP) from binding of certain ligands, such as alpha2-macroglobulin; D1 and D2 each bind LRP weakly but the tandem D1D2 binds much more tightly to the second and the fourth ligand-binding clusters present on LRP, suggesting the avidity effects arising from amino acid residues contributed from each domain. Also, RAP has regions that interact weakly with heparin, one located in D2 and two located in D3. The double module of complement type repeats, CR56, of LRP binds many ligands including alpha2-macroglobulin, which promotes the catabolism of the Abeta-peptide implicated in Alzheimer's disease. 98 matched cddid_all.tbl CDD cd14808 cd14808 269815 RAP_D3 C-terminal receptor-associated protein (RAP), Domain 3. This subfamily is the C-terminal domain (D3) of receptor-associated protein, RAP, an antagonist and a specialized chaperone in the endoplasmic reticulum that binds tightly to members of the low-density lipoprotein (LDL) receptor family and prevents them from associating with other ligands. D3 is required for folding and trafficking of low-density lipoprotein receptor-related protein (LRP). In the mildly acidic pH of the Golgi, unfolding of RAP-D3 helical bundle facilitates dissociation of RAP from the LDL receptor type A (LA) repeats of LDLR family proteins. Also, RAP has 3 regions that interact weakly with heparin, two regions located in D3 and one in RAP domain 2 (D2). The double module of complement type repeats, CR56, of LRP binds many ligands including alpha2-macroglobulin, which promotes the catabolism of the Abeta-peptide implicated in Alzheimer's disease. 100 matched cddid_all.tbl CDD cd14809 cd14809 269871 bZIP_AUREO-like Basic leucine zipper (bZIP) domain of blue light (BL) receptor aureochrome (AUREO) and similar bZIP domains. AUREO is a BL-activated transcription factor specific to phototrophic stramenopiles. It has a bZIP and a BL-sensing light-oxygen voltage (LOV) domain. It has been shown to mediate BL-induced branching and regulate the development of the sex organ in Vaucheria frigida. bZIP factors act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. This subgroup also includes the Epstein-Barr virus (EBV) immediate-early transcription factor ZEBRA (BZLF1, Zta, Z, EB1). ZEBRA exhibits a variant of the bZIP fold, it has a unique dimer interface and a substantial hydrophobic pocket; it has a C-terminal moiety which stabilizes the coiled coil involved in dimer formation. ZEBRA functions to trigger the switch of EBV's biphasic infection cycle from latent to lytic infection. It activates the promoters of EBV lytic genes by binding ZEBRA response elements (ZREs) and inducing a cascade of expression of over 50 viral genes. It also down regulates latency-associated promoters, is an essential replication factor, induces host cell cycle arrest, and alters cellular immune responses and transcription factor activity. 52 matched cddid_all.tbl CDD cd14810 cd14810 269872 bZIP_u1 Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain; uncharacterized subfamily. Basic leucine zipper (bZIP) factors comprise one of the most important classes of enhancer-type transcription factors. They act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes including cell survival, learning and memory, lipid metabolism, and cancer progression, among others. They also play important roles in responses to stimuli or stress signals such as cytokines, genotoxic agents, or physiological stresses. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 52 matched cddid_all.tbl CDD cd14811 cd14811 269873 bZIP_u2 Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain; uncharacterized subfamily. Basic leucine zipper (bZIP) factors comprise one of the most important classes of enhancer-type transcription factors. They act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes including cell survival, learning and memory, lipid metabolism, and cancer progression, among others. They also play important roles in responses to stimuli or stress signals such as cytokines, genotoxic agents, or physiological stresses. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 52 matched cddid_all.tbl CDD cd14812 cd14812 269874 bZIP_u3 Basic leucine zipper (bZIP) domain of bZIP transcription factors: a DNA-binding and dimerization domain; uncharacterized subfamily. Basic leucine zipper (bZIP) factors comprise one of the most important classes of enhancer-type transcription factors. They act in networks of homo and heterodimers in the regulation of a diverse set of cellular processes including cell survival, learning and memory, lipid metabolism, and cancer progression, among others. They also play important roles in responses to stimuli or stress signals such as cytokines, genotoxic agents, or physiological stresses. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 52 matched cddid_all.tbl CDD cd14813 cd14813 269875 bZIP_BmCbz-like Basic leucine zipper (bZIP) domain of Bombyx mori chorion b-ZIP transcription factor and similar bZIP domains. Bombyx mori chorion b-ZIP transcription factor, is encoded by the Cbz gene. The bZIP structural motif contains a basic region and a leucine zipper, composed of alpha helices with leucine residues 7 amino acids apart, which stabilize dimerization with a parallel leucine zipper domain. Dimerization of leucine zippers creates a pair of the adjacent basic regions that bind DNA and undergo conformational change. Dimerization occurs in a specific and predictable manner resulting in hundreds of dimers having unique effects on transcription. 52 matched cddid_all.tbl CDD cd14814 cd14814 350615 Peptidase_M15 Metalloproteases including zinc D-Ala-D-Ala carboxypeptidase, L-Ala-D-Glu peptidase, L,D-carboxypeptidase, bacteriophage endolysins, and related proteins. This family summarizes zinc-binding metallopeptidases which are mostly carboxypeptidases and dipeptidases, and includes zinc-dependent D-Ala-D-Ala carboxypeptidases, VanX, L-Ala-D-Glu peptidase, L,D-carboxypeptidase and bacteriophage endolysins, amongst other family members. These peptidases belong to MEROPS family M15 which are involved in bacterial cell wall biosynthesis and metabolism. 111 matched cddid_all.tbl CDD cd14815 cd14815 271352 BA_2398_like Putative Bacillus anthracis lipoprotein and related proteins. Uncharacterized protein family found in Bacilli and Gammaproteobacteria 145 matched cddid_all.tbl CDD cd14817 cd14817 350616 D-Ala-D-Ala_dipeptidase_VanX D-Ala-D-Ala dipeptidase VanX. D-Ala-D-Ala dipeptidase (also known as D-alanyl-D-alanine dipeptidase vanX; VanX; EC 3.4.13.22) is a Zn2+-dependent enzyme that mediates resistance to the antibiotic vancomycin in Enterococci and other bacteria (both Gram-positive and Gram-negative). It is part of a gene cluster that affects cell-wall biosynthesis. The operon triggers the termination of peptidoglycan precursors by D-Ala-(R)-lactate instead of D-Ala-D-Ala dipeptides. The enzyme is stereospecific, as L-Ala-L-Ala, D-Ala-L-Ala and L-Ala-D-Ala are not substrates. It belongs in the MEROPS peptidase family M15, subfamily D. 199 matched cddid_all.tbl CDD cd14818 cd14818 341426 longin-like Longin-like domains. Longin-like domains are small protein domains present in a variety of proteins and members of protein complexes involved in or required for different steps during the transport of proteins from the ribosome to the ER to the plasma membrane, via the Golgi apparatus. Examples are mu and sigma subunits of the heterotetrameric adaptor protein (AP) complex, zeta and delta subunits of the heterotetrameric F-COPI complex, a subgroup of R-SNARE proteins, a subfamily of the transport protein particle (TRAPP), and the signal recognition particle receptor subunit alpha (SR-alpha). 117 matched cddid_all.tbl CDD cd14819 cd14819 271349 Translin Translin, also known as TB-RBP (testis brain RNA-binding protein). Translin (also known as TB-RBP for Testis Brain RNA-binding protein, a mouse ortholog), is a paralog of its binding partner protein TRAX (translin-associated factor-X) and together they form oligomeric complexes known as C3PO proteins (for component 3 promoter of RNA-induced silencing complex or RISC). DNA damage has been proposed to stimulate transport of Translin into nuclei. It binds to RNA and single-stranded DNA, and its selectivity is modulated by interactions with GTP and TRAX. Translin may also regulate dendritic trafficking of BDNF RNAs as well as function as a key activator of siRNA-mediated silencing in drosophila. Translin and Trax participate in a variety of nucleic acid metabolism pathways in addition to RNAi and have been implicated in a wide range of biological activities, including mRNA processing, cell growth regulation, spermatogenesis, neuronal development/function, genome stability regulation and carcinogenesis; however, their precise role in some of the processes remains unclear. 206 matched cddid_all.tbl CDD cd14820 cd14820 271350 TRAX Translin-associated factor-X (TRAX). TRAX (translin-associated factor-X) is a paralog of its binding partner protein Translin and together they form oligomeric complexes known as C3PO proteins (for component 3 promoter of RNA-induced silencing complex or RISC). TRAX complexed with Translin is possibly involved in dendritic RNA processing and in DNA double-strand break repair as an interacting partner with C1D, an activator of the DNA-dependent protein kinase involved in the repair of DNA-double strand breaks. It has been shown that Trax subunit, but not Translin, possesses a Glu-Glu-Asp catalytic center with the capacity to digest RNA; this catalytic activity is required for passenger-strand removal and RISC activation in RNAi. In Archaeoglobus fulgidus, Trax-like-subunits assemble into an octameric structure, highly similar to human C3PO; its complex with duplex RNA reveals that the octamer entirely encapsulates a single 13-base-pair RNA duplex inside a large inner cavity. Translin and Trax participate in a variety of nucleic acid metabolism pathways in addition to RNAi and have been implicated in a wide range of biological activities, including mRNA processing, cell growth regulation, spermatogenesis, neuronal development/function, genome stability regulation and carcinogenesis; however, their precise role in some of the processes remains unclear. 182 matched cddid_all.tbl CDD cd14821 cd14821 350517 BACK_SPOP_like BACK (BTB and C-terminal Kelch) domain found in speckle-type POZ protein (SPOP) and similar proteins. This family includes speckle-type POZ protein (SPOP), speckle-type POZ protein-like (SPOPL), TD and POZ domain-containing proteins (TDPOZ), Drosophila melanogaster protein roadkill, and similar proteins. Both SPOP and SPOPL serve as adaptors of cullin-RING-based BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex that mediates the ubiquitination and proteasomal degradation of target proteins. TDPOZ is a family of bipartite animal and plant proteins that contain a tumor necrosis factor receptor-associated factor (TRAF) domain (TD) and a POZ/BTB domain. TDPOZ proteins may be nuclear scaffold proteins involved in transcription regulation in early development and other cellular processes. Drosophila melanogaster protein roadkill, also termed Hh-induced MATH and BTB domain-containing protein (HIB), is a hedgehog-induced BTB protein that modulates hedgehog signaling by degrading Ci/Gli transcription factor. 59 matched cddid_all.tbl CDD cd14822 cd14822 350518 BACK_BTBD9 BACK (BTB and C-terminal Kelch) domain found in BTB/POZ domain-containing protein 9 (BTBD9). BTBD9 is a risk factor for Restless Legs Syndrome (RLS) encoding a Cullin-3 substrate adaptor. The BTBD9 gene may be associated with antipsychotic-induced RLS in schizophrenia. Mutations in BTBD9 lead to reduced dopamine, increased locomotion and sleep fragmentation. 101 matched cddid_all.tbl CDD cd14823 cd14823 341427 AP_longin-like Longin-like domains of AP complex subunits. AP complex sigma subunits are part of the heterotetrameric adaptor protein (AP) complex which consists of one large subunit (alpha-, gamma-, delta- or epsilon), one beta-, one mu-, and one sigma-subunit. In general, AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. In most cases the coat protein is clathrin (AP1 and AP2 complex), but some of the other members of the AP complex family are associated with nonclathrin coats. The sigma subunit is comprised of a single longin domain and plays a role in binding dileucine-based sorting signals. 131 matched cddid_all.tbl CDD cd14824 cd14824 341428 Longin longin domain. Longin-domain is N-terminal domain of a subgroup of R-SNARE proteins, including VAMP7, Ykt6, and Sec22. Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex. Longins are the only R-SNAREs that are common to all eukaryotes, and they are characterized by a conserved N-terminal domain with a profilin-like fold called a longin domain. 122 matched cddid_all.tbl CDD cd14825 cd14825 341429 TRAPPC2_sedlin Trafficking protein particle complex subunit 2. Trafficking protein particle complex subunit 2 (TRAPPC2), also known as Sedlin (SEDL) or TRS20, has been identified as a component of the transport protein particle (TRAPP), required for tethering endoplasmic reticulum (ER)-derived vesicles to Golgi membranes and for Golgi traffic. In humans, deletions or point mutations in the SEDL gene cause the genetic disease spondyloepiphyseal dysplasia tarda (SEDT), an X-linked skeletal disorder. 135 matched cddid_all.tbl CDD cd14826 cd14826 341430 SR_alpha_SRX SRX domain of signal recognition particle receptor subunit alpha. Signal recognition particle receptor subunit alpha (SR-alpha) is part of the membrane-associated heterodimeric receptor for the signal recognition particle (SRP). The signal recognition particle (SRP) pathway is highly conserved and plays an important role in the translocation of proteins across and insertion into membranes by targeting the translating ribosome to the endoplasmic reticulum. The N-terminal SRX domain of SR-alpha has a profilin-like fold and has been shown to be the interaction site with the second subunit, SR-beta. 118 matched cddid_all.tbl CDD cd14827 cd14827 341431 AP_sigma AP complex subunit sigma. AP complex sigma subunits are part of the heterotetrameric adaptor protein (AP) complex which consists of one large subunit (alpha-, gamma-, delta- or epsilon), one beta-, one mu-, and one sigma-subunit. In general, AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. In most cases the coat protein is clathrin (AP1 and AP2 complex), but some of the other members of the AP complex family are associated with nonclathrin coats. The sigma subunit is comprised of a single longin domain and plays a role in binding dileucine-based sorting signals. 138 matched cddid_all.tbl CDD cd14828 cd14828 341432 AP_Mu_N AP complex subunit mu N-terminal domain. AP complex mu subunits are part of the heterotetrameric adaptor protein (AP) complex which consists of one large subunit (alpha-, gamma-, delta- or epsilon), one beta-, one mu-, and one sigma-subunit. In general, AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. In most cases the coat protein is clathrin (AP1 and AP2 complex), but some of the other members of the AP complex family are associated with nonclathrin coats. The mu subunit is comprised of an N-terminal longin domain followed by a C-terminal domain which is involved in the binding of the Y-X-X-Phi sorting signal. 136 matched cddid_all.tbl CDD cd14829 cd14829 341433 Zeta-COP zeta subunit of the F-COPI complex. Zeta subunit of the heterotetrameric F-COPI complex, which consists of one beta-, one gamma-, one delta-, and one zeta subunit, where beta- and gamma- subunits are related to the large adaptor protein (AP) complex subunits, and delta- and zeta- subunits are related to the medium and small AP subunits, respectively. F-COPI forms a coatomer together with the B-COPI subcomplex, which assembles with a small GTPase, ADP-ribosylation factor 1 (ARF1), playing an important role in the formation of COPI complex-coated vesicles. COPI complex-coated vesicles function in the early secretory pathway mediating the retrograde transport from the Golgi to the ER, and intra-Golgi transport. 132 matched cddid_all.tbl CDD cd14830 cd14830 341434 Delta_COP_N delta subunit of the F-COPI complex, N-terminal domain. Delta subunit of the heterotetrameric F-COPI complex, which consists of one beta-, one gamma-, one delta-, and one zeta subunit, where beta- and gamma- subunits are related to the large adaptor protein (AP) complex subunits, and delta- and zeta- subunits are related to the medium and small AP subunits, respectively. F-COPI forms a coatomer together with the B-COPI subcomplex, which assembles with a small GTPase, ADP-ribosylation factor 1 (ARF1), playing an important role in the formation of COPI complex-coated vesicles. COPI complex-coated vesicles function in the early secretory pathway mediating the retrograde transport from the Golgi to the ER, and intra-Golgi transport. 130 matched cddid_all.tbl CDD cd14831 cd14831 341435 AP1_sigma AP-1 complex subunit sigma. AP-1 complex sigma subunit is part of the heterotetrameric adaptor protein (AP)-1 complex which consists of one large gamma-, one beta-, one mu-, and one sigma-subunit. AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. In the case of AP-1 the coat protein is clathrin. AP-1 binds the phospholipid PI(4)P which plays a role in its localisation to the trans-Golgi network (TGN)/endosome. The sigma subunit is comprised of a single longin domain and plays a role in binding dileucine-based sorting signals. 143 matched cddid_all.tbl CDD cd14832 cd14832 341436 AP4_sigma AP-4 complex subunit sigma. AP-4 complex sigma subunit is part of the heterotetrameric adaptor protein (AP)-1 complex which consists of one large epsilon-, one beta-, one mu-, and one sigma-subunit. AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. AP-4 does not bind the coat protein clathrin, it is associated with nonclathrin coats. Its phospholipid binding partner is unknown and it is localized in the trans-Golgi network (TGN). The sigma subunit is comprised of a single longin domain and plays a role in binding dileucine-based sorting signals. 138 matched cddid_all.tbl CDD cd14833 cd14833 341437 AP2_sigma AP-2 complex subunit sigma. AP-2 complex sigma subunit is part of the heterotetrameric adaptor protein (AP)-2 complex which consists of one large alpha-, one beta-, one mu-, and one sigma-subunit. AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. In the case of AP-2 the coat protein is clathrin. AP-2 binds the phospholipid PI(4,5)P2 which is important for its localisation to the plasma membrane. The sigma subunit is comprised of a single longin domain and plays a role in binding dileucine-based sorting signals. 141 matched cddid_all.tbl CDD cd14834 cd14834 341438 AP3_sigma AP-3 complex subunit sigma. AP-3 complex sigma subunit is part of the heterotetrameric adaptor protein (AP)-1 complex which consists of one large delta-, one beta-, one mu-, and one sigma-subunit. AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. AP-3 binds the coat protein clathrin and the phospholipid PI(3)P and it is localized in the endosome. The sigma subunit is comprised of a single longin domain and plays a role in binding dileucine-based sorting signals. 146 matched cddid_all.tbl CDD cd14835 cd14835 341439 AP1_Mu_N AP-1 complex subunit mu N-terminal domain. AP-1 complex mu subunit is part of the heterotetrameric adaptor protein (AP)-1 complex which consists of one large gamma-, one beta-, one mu-, and one sigma-subunit. AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. In the case of AP-1 the coat protein is clathrin. AP-1 binds the phospholipid PI(4)P which plays a role in its localisation to the trans-Golgi network (TGN)/endosome. The mu subunit is comprised of an N-terminal longin domain followed by a C-terminal domain which is involved in the binding of the Y-X-X-Phi sorting signal. 139 matched cddid_all.tbl CDD cd14836 cd14836 341440 AP2_Mu_N AP-2 complex subunit mu N-terminal domain. AP-2 complex mu subunit is part of the heterotetrameric adaptor protein (AP)-2 complex which consists of one large alpha-, one beta-, one mu-, and one sigma-subunit. AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. In the case of AP-2 the coat protein is clathrin. AP-2 binds the phospholipid PI(4,5)P2 which is important for its localisation to the plasma membrane. The mu subunit is comprised of an N-terminal longin domain followed by a C-terminal domain which is involved in the binding of the Y-X-X-Phi sorting signal. 140 matched cddid_all.tbl CDD cd14837 cd14837 341441 AP3_Mu_N AP-3 complex subunit mu N-terminal domain. AP-3 complex mu subunit is part of the heterotetrameric adaptor protein (AP)-1 complex which consists of one large delta-, one beta-, one mu-, and one sigma-subunit. AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. AP-3 binds the coat protein clathrin and the phospholipid PI(3)P and it is localized in the endosome. The mu subunit is comprised of an N-terminal longin domain followed by a C-terminal domain which is involved in the binding of the Y-X-X-Phi sorting signal. 139 matched cddid_all.tbl CDD cd14838 cd14838 341442 AP4_Mu_N AP-4 complex subunit mu N-terminal domain. AP-4 complex mu subunit is part of the heterotetrameric adaptor protein (AP)-1 complex which consists of one large epsilon-, one beta-, one mu-, and one sigma-subunit. AP complexes link the cytosolic domains of the cargo proteins to the protein coat that induces vesicle budding in the donor compartment during vesicle transport. AP-4 does not bind the coat protein clathrin, it is associated with nonclathrin coats. Its phospholipid binding partner is unknown and it is localized in the trans-Golgi network (TGN). The mu subunit is comprised of an N-terminal longin domain followed by a C-terminal domain which is involved in the binding of the Y-X-X-Phi sorting signal. 137 matched cddid_all.tbl CDD cd14840 cd14840 350617 D-Ala-D-Ala_dipeptidase_Aad D-Ala-D-Ala dipeptidase (includes Lactobacillus plantarum Aad peptidase). D-Ala-D-Ala dipeptidase (also known as D-alanyl-D-alanine dipeptidase vanX; VanX; EC 3.4.13.22) is a Zn2+-dependent enzyme that mediates resistance to the antibiotic vancomycin in Enterococci and other bacteria (both Gram-positive and Gram-negative). It is part of a gene cluster that affects cell-wall biosynthesis. The operon triggers the termination of peptidoglycan precursors by D-Ala-(R)-lactate instead of D-Ala-D-Ala dipeptides. The enzyme is stereospecific, as L-Ala-L-Ala, D-Ala-L-Ala and L-Ala-D-Ala are not substrates. This subfamily includes Lactobacillus Aad peptidase and belongs in the MEROPS peptidase family M15, subfamily D. 158 matched cddid_all.tbl CDD cd14843 cd14843 350618 D-Ala-D-Ala_dipeptidase_like D-Ala-D-Ala dipeptidase, includes uncharacterized enzymes. This subfamily of D-Ala-D-Ala dipeptidase (also known as D-alanyl-D-alanine dipeptidase vanX; VanX; EC 3.4.13.22) also includes several uncharacterized proteins. This is a Zn2+-dependent enzyme that mediates resistance to the antibiotic vancomycin in Enterococci and other bacteria (both Gram-positive and Gram-negative). It is part of a gene cluster that affects cell-wall biosynthesis. The operon triggers the termination of peptidoglycan precursors by D-Ala-(R)-lactate instead of D-Ala-D-Ala dipeptides. The enzyme is stereospecific, as L-Ala-L-Ala, D-Ala-L-Ala and L-Ala-D-Ala are not substrates. It belongs in the MEROPS peptidase family M15, subfamily D. 160 matched cddid_all.tbl CDD cd14844 cd14844 350619 Zn-DD-carboxypeptidase_like Proteins similar to the zinc-containing D-Ala-D-Ala dipeptidase. The zinc D-Ala-D-Ala carboxypeptidase (Streptomyces-type) (also known as D-alanyl-D-alanine hydrolase; D-alanyl-D-alanine-cleaving carboxypeptidase; DD-carboxypeptidase; DD-carboxypeptidase-transpeptidase; Zn2+ G peptidase; G enzyme; EC 3.4.17.14) is a zinc enzyme that belongs to the peptidase M15 subfamily A. The enzyme catalyzes carboxypeptidation but not transpeptidation reactions involved in bacterial cell wall metabolism. Its specificity with substrates of the type Xaa-Yaa-Zaa shows that the enzyme requires the substrate N-terminus to be blocked and C-terminus to be free, and Yaa and Zaa should be in the D-configuration. It is weakly inhibited by beta-lactams most likely caused by the enzyme active site geometry. 108 matched cddid_all.tbl CDD cd14845 cd14845 350620 L-Ala-D-Glu_peptidase_like L-Ala-D-Glu peptidase, also known as L-alanyl-D-glutamate endopeptidase. This L-Ala-D-Glu peptidase family includes L-alanyl-D-glutamate peptidase (bacteriophage T5) (also known as L-alanoyl-D-glutamate endopeptidase), and Ply118 and Ply500 L-Ala-D-Glu peptidase. Bacteriophage endolysin degrades the peptidoglycan of the bacterial host from within, leading to cell lysis and release of progeny virions. The bacteriophage endolysin Ply118 cleaves between L-Ala and D-Glu residues of Listeria cell wall peptidoglycan. This family belongs to the MEROPS peptidase M15 subfamily C. 126 matched cddid_all.tbl CDD cd14846 cd14846 350621 Peptidase_M15_like Uncharacterized family of the peptidase family M15, subfamily B. This family of uncharacterized proteins, similar to endolysin lys (Clavibacter phage CMP1) and VanYn peptidase, are zinc-binding enzymes that belong to the peptidase M15 subfamily B, involved in bacterial cell wall metabolism. 104 matched cddid_all.tbl CDD cd14847 cd14847 350622 DD-carboxypeptidase_like Uncharacterized proteins of the MEROPS peptidase family M15, subfamily B. This family of uncharacterized proteins similar to D-Ala-D-Ala carboxypeptidase pdcA (Myxococcus-type) are zinc-binding enzymes that belong to the peptidase M15 subfamily B. The enzyme D-Ala-D-Ala carbozypeptidase catalyzes carboxypeptidation reactions involved in bacterial cell wall metabolism. 162 matched cddid_all.tbl CDD cd14849 cd14849 350623 DD-dipeptidase_VanXYc D-Ala-D-Ala dipeptidase/D-Ala-D-Ala carboxypeptidase (VanXYc) and related proteins. VanXYc peptidase (also known as vanXY(C) peptidase, D-alanyl-D-alanine carboxypeptidase D,D-dipeptidase/D,D-carboxypeptidase, vancomycin resistance D,D-dipeptidase) is a Zn2+-dependent enzyme that mediates resistance to the antibiotic vancomycin in Enterococci. Some of the vancomycin resistance operons encode VanXY D,D-carboxypeptidase which hydrolyzes both, dipeptide (D-Ala-D-Ala) or pentapeptide (UDP-MurNac-L-Ala-D-Glu-L-Lys-D-Ala-D-Ala). It is a bifunctional enzyme that catalyzes D,D-peptidase and D,D-carboxypeptidase activities. VanXY has higher sequence similarity to VanY than with VanX and hydrolyzes D,D-dipeptides such as D-Ala-D-Ala, whereas VanY is inactive against this substrate; thus having a less restrictive active site to accommodate larger substrates such as UDP-MurNAc-pentapeptide[Ala]. This family belongs to the MEROPS family M15, subfamily B, and includes the D,D-dipeptidases VanXYg and VanXYe. 127 matched cddid_all.tbl CDD cd14852 cd14852 350624 LD-carboxypeptidase L,D-carboxypeptidase DacB and LdcB, and related proteins. This L,D-carboxypeptidase family includes LdcB LD-Carboxypeptidase from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis, and L,D-carboxypeptidase DacB from Streptococcus pneumonia and Lactococcus lactis. These enzymes are active against cell-wall-derived tetrapeptides and synthetic tetrapeptides lacking the sugar moiety but are inactive against tetrapeptides terminating in L-alanine. L,D-carboxypeptidase DacB plays a key role in the remodeling of S. pneumoniae peptidoglycan during cell division. It adopts a zinc-dependent carboxypeptidase fold and acts as an L,D-carboxypeptidase towards the tetrapeptide L-Ala-D-iGln-L-Lys-D-Ala of the peptidoglycan stem. This family also includes vanY D-Ala-D-Ala carboxypeptidase which is vancomycin-inducible and penicillin-resistant. VanY hydrolyzes depsipeptide- and D-alanyl-D-alanine-containing peptidoglycan precursors; it is insensitive to beta-lactams. All these enzymes belong to the MEROPS family M15 subfamily B. 162 matched cddid_all.tbl CDD cd14853 cd14853 341443 TRAPPC_longin-like Longin-like domains of Trafficking protein particle complex. Longin-like domains of a subfamily of core components of the trafficking protein particle complex (TRAPP), including TRAPPC2, TRAPPC4, TRAPPC1 and a TRAPPC2L, whose function is not known. TRAPP complexes are required for tethering endoplasmic reticulum (ER)-derived vesicles to Golgi membranes and for Golgi traffic. 132 matched cddid_all.tbl CDD cd14854 cd14854 341444 TRAPPC2L Trafficking protein particle complex subunit 2-like. Trafficking protein particle complex subunit 2-like (TRAPPC2L) is related to TRAPPC2. Its function is not known, but there are indications that it is part of the TRAPP II complex, which is required for distinct tethering events at Golgi membranes. TRAPPC2 has been identified as a general component of transport protein particle (TRAPP), required for tethering endoplasmic reticulum (ER)-derived vesicles to Golgi membranes and for Golgi traffic. 135 matched cddid_all.tbl CDD cd14855 cd14855 341445 TRAPPC1_MUM2 Trafficking protein particle complex subunit 1. Trafficking protein particle complex subunit 1 (TRAPPC1), also known as MUM2 and BET5, has been identified as a component of the transport protein particle (TRAPP), required for tethering endoplasmic reticulum (ER)-derived vesicles to Golgi membranes and for Golgi traffic. 132 matched cddid_all.tbl CDD cd14856 cd14856 341446 TRAPPC4_synbindin Trafficking protein particle complex subunit 4. Trafficking protein particle complex subunit 4 (TRAPPC4), also known as synbindin or TRS23, has been identified as a component of the transport protein particle (TRAPP), required for tethering endoplasmic reticulum (ER)-derived vesicles to Golgi membranes and for Golgi traffic. 127 matched cddid_all.tbl CDD cd14858 cd14858 410986 TrmE_N N-terminal domain of TrmE, a tRNA modification GTPase. This family contains the N-terminal domain of TrmE (also known as MnmE, ThdF, MSS1), a guanine nucleotide-binding protein conserved in all three kingdoms of life. It is involved in the modification of uridine bases (U34) at the first anticodon (wobble) position of tRNAs decoding two-family box triplets. TrmE is a three-domain protein comprising an N-terminal alpha/beta domain, a helical domain, and the GTPase domain which is nested within the helical domain. The N-terminal domain induces dimerization for self-assembly and is topologically homologous to the tetrahydrofolate (THF)-binding domain of N,N-dimethylglycine oxidase (DMGO). However, the THF-binding site in DMGO is encoded on a single polypeptide, while homodimerization would be required to create a similar THF-binding site in TrmE. Dimerization also creates a second, symmetry-related THF-binding site. Biochemical and structural studies show that TrmE indeed binds formyl-THF. A cysteine residue, necessary for modification of U34, is located close to the C1-group donor 5-formyl-tetrahydrofolate, suggesting a direct role of TrmE in the modification analogous to DNA modification enzymes. 117 matched cddid_all.tbl CDD cd14859 cd14859 275438 PMEI_like pectin methylesterase inhibitor and related proteins. Pectin methylesterase (PME; Pectinesterase; EC 3.1.1.11; CAZy class 8 of carbohydrate esterases) catalyzes the demethylesterification of homogalacturonans in the cell wall. Its activity is regulated by the proteinaceous PME inhibitor (PMEI) which inhibits PME and invertase through formation of a non-covalent 1:1 complex. Depending on the mode of demethylesterification, PMEI activity results in either loosening or rigidification of the cell wall. PMEI has been implicated in the regulation of fruit development, carbohydrate metabolism and cell wall extension. It may also be involved in inhibiting microbial pathogen PMEs. Thus, PMEI probably plays an important physiological role in PME regulation in plants, possessing several potential applications in a food-technological context. CIF (cell-wall inhibitor of beta-fructosidase from tobacco) is structurally similar to PMEI and these members are also included in this model. Comparison of the CIF/INV1 structure with the complex between PMEI/PME suggests a common targeting mechanism in PMEI and CIF. However, CIF and PMEI use distinct surface areas to selectively inhibit very different enzymatic scaffolds. 140 matched cddid_all.tbl CDD cd14860 cd14860 341482 4HBD_NAD 4-hydroxybutyrate dehydrogenase, also called gamma-hydroxybutyrate dehydrogenase, catalyzes the reduction of succinic simialdehyde to 4-hydroxybutyrate in the succinic degradation pathway. 4-hydroxybutyrate dehydrogenase (4HBD) is an iron-containing (type III) NAD-dependent alcohol dehydrogenase. It plays a role in the succinate metabolism biochemical pathway. It catalyzes the reduction of succinic simialdehide to 4-hydroxybutyrate in the succinate degradation pathway This succinate degradation pathway is present in some bacteria which can use succinate as sole carbon source. 371 matched cddid_all.tbl CDD cd14861 cd14861 341483 Fe-ADH-like Iron-containing alcohol dehydrogenases-like. This family contains proteins similar to iron-containing alcohol dehydrogenase (Fe-ADH), most of which have not been characterized. Their specific function is unknown. The protein structure represents a dehydroquinate synthase-like fold and belongs to the alcohol dehydrogenase-like superfamily. It is distinct from other alcohol dehydrogenases which contain different protein domains. Alcohol dehydrogenase catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. 374 matched cddid_all.tbl CDD cd14862 cd14862 341484 Fe-ADH-like iron-containing alcohol dehydrogenases (Fe-ADH)-like. This family contains iron-containing alcohol dehydrogenase (Fe-ADH) which catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. It is distinct from other alcohol dehydrogenases which contains different protein domains. Proteins of this family have not been characterized. 375 matched cddid_all.tbl CDD cd14863 cd14863 341485 Fe-ADH-like iron-containing alcohol dehydrogenases (Fe-ADH)-like. This family contains iron-containing alcohol dehydrogenase (Fe-ADH) which catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. It is distinct from other alcohol dehydrogenases which contains different protein domains. Proteins of this family have not been characterized. 380 matched cddid_all.tbl CDD cd14864 cd14864 341486 Fe-ADH-like iron-containing alcohol dehydrogenases (Fe-ADH)-like. This family contains iron-containing alcohol dehydrogenase (Fe-ADH) which catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. It is distinct from other alcohol dehydrogenases which contains different protein domains. Proteins of this family have not been characterized. 376 matched cddid_all.tbl CDD cd14865 cd14865 341487 Fe-ADH-like iron-containing alcohol dehydrogenases (Fe-ADH)-like. This family contains iron-containing alcohol dehydrogenase (Fe-ADH) which catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. It is distinct from other alcohol dehydrogenases which contains different protein domains. Proteins of this family have not been characterized. 383 matched cddid_all.tbl CDD cd14866 cd14866 341488 Fe-ADH-like iron-containing alcohol dehydrogenases (Fe-ADH)-like. This family contains iron-containing alcohol dehydrogenase (Fe-ADH) which catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. It is distinct from other alcohol dehydrogenases which contains different protein domains. Proteins of this family have not been characterized. 384 matched cddid_all.tbl CDD cd14867 cd14867 271246 uS7_Eukaryote Eukaryota homolog of Ribosomal Protein S7. uS7, also known as Ribosomal protein (RP)S7, is an important part of the translation process which is universally present in the small subunit of prokaryotic and eukaryotic ribosomes. Eukaryotic RPS7 (also named RPS5) have variable N-terminal regions that affect the efficiency of initiation translation process by impacting small ribosomal subunit to function. The ribosome small subunit is one of the two subunits of ribosome organelles that use mRNA as a template for protein synthesis in a process called translation. The small subunits of bacteria and eukaryotes have the same shape of head, body, platform, beak, and shoulder. RPS7 is located at the head of the small subunit which is a primary ribosomal RNA (rRNA) binding protein that assists in rRNA folding and the binding of other proteins during small subunit assembly in all species. RPS7 is also involved in the formation of the mRNA exit channel at the interface of the large and small subunits. Some ribosomal proteins have extra ribosomal functions in cell differentiation and apoptosis. 185 matched cddid_all.tbl CDD cd14868 cd14868 271247 uS7_Mitochondria_Fungi Fungal Mitochondrial homolog of Ribosomal Protein S7. uS7, also known as Ribosomal protein (RP)S7, is an important part of the translation process which is universally present in the small subunit of prokaryotic and eukaryotic ribosomes. Fungal and plants mitochondrial RPS7 shows less homology to the mammalian than to bacterial RPS7. The ribosome small subunit is one of the two subunits of ribosome organelles that use mRNA as a template for protein synthesis in a process called translation. The small subunits of bacteria and eukaryotes have the same shape of head, body, platform, beak, and shoulder. RPS7 is located at the head of the small subunit. RPS7 is a primary ribosomal RNA (rRNA) binding protein that assists in rRNA folding and the binding of other proteins during small subunit assembly in all species. RPS7 is also involved in the formation of the mRNA exit channel at the interface of the large and small subunits. Some ribosomal proteins have extra ribosomal functions in cell differentiation and apoptosis. 151 matched cddid_all.tbl CDD cd14869 cd14869 271248 uS7_Bacteria Bacterial homolog of Ribosomal Protein S7. uS7, also known as Ribosomal protein (RP)S7, is an important part of the translation process which is universally present in the small subunit of prokaryotic and eukaryotic ribosomes. Prokaryotic RPS7 is lacking the variable N-terminal region of eukaryotic RPS7. The ribosome small subunit is one of the two subunits of ribosome organelles that use mRNA as a template for protein synthesis in a process called translation. The small subunits of bacteria and eukaryotes have the same shape of head, body, platform, beak, and shoulder. RPS7 is located at the head of the small subunit which is a primary ribosomal RNA (rRNA) binding protein that assists in rRNA folding and the binding of other proteins during small subunit assembly in all species. RPS7 is also involved in the formation of the mRNA exit channel at the interface of the large and small subunits. Some ribosomal proteins have extra ribosomal functions in cell differentiation and apoptosis. 138 matched cddid_all.tbl CDD cd14870 cd14870 271249 uS7_Mitochondria_Mammalian Mammalian Mitochondrial homolog of Ribosomal Protein S7. uS7, also known as Ribosomal protein (RP)S7, is an important part of the translation process which is universally present in the small subunit of prokaryotic and eukaryotic ribosomes. MRPS7 shows more homology to bacterial RPS7 than mitochondrial proteins from plants and fungi. The ribosome small subunit is one of the two subunits of ribosome organelles that use mRNA as a template for protein synthesis in a process called translation. The ribosomes present in mammalian mitochondria have more proteins and low percentage of ribosomal RNA than bacterial ribosomes. The small subunits of bacteria and eukaryotes have the same shape of head, body, platform, beak, and shoulder. RPS7 is located at the head of the small subunit. RPS7 is a primary ribosomal RNA (rRNA) binding protein that assists in rRNA folding and the binding of other proteins during small subunit assembly in all species. RPS7 is also involved in the formation of the mRNA exit channel at the interface of the large and small subunits. Some ribosomal proteins have extra ribosomal functions in cell differentiation and apoptosis. 199 matched cddid_all.tbl CDD cd14871 cd14871 271250 uS7_Chloroplast Chloroplast homolog of Ribosomal Protein S7. Chloroplast RPS7 has both general and specific regulatory roles in chloroplast translation process. uS7, also known as Ribosomal protein (RP)S7, is universally present in the small subunit of prokaryotic and eukaryotic ribosomes. The chloroplasts of plants and algae have bacterial ancestry, but it has adopted novel mechanisms in order to execute its roles within a eukaryotic cell. Chloroplast RPS7 is more homologous to bacterial RPS7 than other eukaryotic mitochondrial proteins. The ribosome small subunit is one of the two subunits of ribosome organelles that use mRNA as a template for protein synthesis in a process called translation. The chloroplast translation regulation is more complex than in bacteria with additional RNA and chloroplast-unique proteins. The small subunits of bacteria and eukaryotes have the same shape of head, body, platform, beak, and shoulder. RPS7 is located at the head of the small subunit. RPS7 is a primary ribosomal RNA (rRNA) binding protein that assists in rRNA folding and the binding of other proteins during small subunit assembly in all species. RPS7 is also involved in the formation of the mRNA exit channel at the interface of the large and small subunits. Some ribosomal proteins have extra ribosomal functions in cell differentiation and apoptosis. 146 matched cddid_all.tbl CDD cd14872 cd14872 276839 MYSc_Myo4 class IV myosin, motor domain. These myosins all possess a WW domain either N-terminal or C-terminal to their motor domain and a tail with a MyTH4 domain followed by a SH3 domain in some instances. The monomeric Acanthamoebas were the first identified members of this group and have been joined by Stramenopiles. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 644 matched cddid_all.tbl CDD cd14873 cd14873 276840 MYSc_Myo10 class X myosin, motor domain. Myosin X is an unconventional myosin motor that functions as a monomer. In mammalian cells, the motor is found to localize to filopodia. Myosin X walks towards the barbed ends of filaments and is thought to walk on bundles of actin, rather than single filaments, a unique behavior. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. C-terminal to the head domain are a variable number of IQ domains, 2 PH domains, a MyTH4 domain, and a FERM domain. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 651 matched cddid_all.tbl CDD cd14874 cd14874 276841 MYSc_Myo12 class XXXIII myosin, motor domain. Little is known about the XXXIII class of myosins. They are found predominately in nematodes. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 628 matched cddid_all.tbl CDD cd14875 cd14875 276842 MYSc_Myo13 class XIII myosin, motor domain. These myosins have an N-terminal motor domain, a light-chain binding domain, and a C-terminal GPA/Q-rich domain. There is little known about the function of this myosin class. Two of the earliest members identified in this class are green alga Acetabularia cliftonii, Aclmyo1 and Aclmyo2. They are striking with their short tail of Aclmyo1 of 18 residues and the maximum of 7 IQ motifs in Aclmyo2. It is thought that these myosins are involved in organelle transport and tip growth. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 664 matched cddid_all.tbl CDD cd14876 cd14876 276843 MYSc_Myo14 class XIV myosin, motor domain. These myosins localize to plasma membranes of the intracellular parasites and may be involved in the cell invasion process. Their known functions include: transporting phagosomes to the nucleus and perturbing the developmentally regulated elimination of the macronucleus during conjugation. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. C-terminal to their motor domain these myosins have a MyTH4-FERM protein domain combination. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 649 matched cddid_all.tbl CDD cd14878 cd14878 276844 MYSc_Myo16 class XVI myosin, motor domain. These XVI type myosins are also known as Neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adapter 3/NYAP3. Myo16 is thought to play a regulatory role in cell cycle progression and has been recently implicated in Schizophrenia. Class XVI myosins are characterized by an N-terminal ankyrin repeat domain and some with chitin synthase domains that arose independently from the ones in the class XVII fungal myosins. They bind protein phosphatase 1 catalytic subunits 1alpha/PPP1CA and 1gamma/PPP1CC. Human Myo16 interacts with ACOT9, ARHGAP26 and PIK3R2 and with components of the WAVE1 complex, CYFIP1 and NCKAP1. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 656 matched cddid_all.tbl CDD cd14879 cd14879 276845 MYSc_Myo17 class XVII myosin, motor domain. This fungal myosin which is also known as chitin synthase uses its motor domain to tether its vesicular cargo to peripheral actin. It works in opposition to dynein, contributing to the retention of Mcs1 vesicles at the site of cell growth and increasing vesicle fusion necessary for polarized growth. Class 17 myosins consist of a N-terminal myosin motor domain with Cyt-b5, chitin synthase 2, and a DEK_C domains at it C-terminus. The chitin synthase region contains several transmembrane domains by which myosin 17 is thought to bind secretory vesicles. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 647 matched cddid_all.tbl CDD cd14880 cd14880 276846 MYSc_Myo19 class XIX myosin, motor domain. Monomeric myosin-XIX (Myo19) functions as an actin-based motor for mitochondrial movement in vertebrate cells. It contains a variable number of IQ domains. Human myo19 contains a motor domain, three IQ motifs, and a short tail. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 658 matched cddid_all.tbl CDD cd14881 cd14881 276847 MYSc_Myo20 class XX myosin, motor domain. These class 20 myosins are primarily insect myosins with such members as Drosophila, Daphnia, and mosquitoes. These myosins contain a single IQ motif in the neck region. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 633 matched cddid_all.tbl CDD cd14882 cd14882 276848 MYSc_Myo21 class XXI myosin, motor domain. The myosins here are comprised of insects. Leishmania class XXI myosins do not group with them. Myo21, unlike other myosin proteins, contains UBA-like protein domains and has no structural or functional relationship with the myosins present in other organisms possessing cilia or flagella. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. They have diverse tails with IQ, WW, PX, and Tub domains. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 642 matched cddid_all.tbl CDD cd14883 cd14883 276849 MYSc_Myo22 class XXII myosin, motor domain. These myosins possess an extended neck with multiple IQ motifs such as found in class V, VIII, XI, and XIII myosins. These myosins are defined by two tandem MyTH4 and FERM domains. The apicomplexan, but not diatom myosins contain 4-6 WD40 repeats near the end of the C-terminal tail which suggests a possible function of these myosins in signal transduction and transcriptional regulation. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 661 matched cddid_all.tbl CDD cd14884 cd14884 276850 MYSc_Myo23 class XXIII myosin, motor domain. These myosins are predicted to have a neck region with 1-2 IQ motifs and a single MyTH4 domain in its C-terminal tail. The lack of a FERM domain here is odd since MyTH4 domains are usually found alongside FERM domains where they bind to microtubules. At any rate these Class XXIII myosins are still proposed to function in the apicomplexan microtubule cytoskeleton. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 685 matched cddid_all.tbl CDD cd14886 cd14886 276851 MYSc_Myo25 class XXV myosin, motor domain. These myosins are MyTH-FERM myosins that play a role in cell adhesion and filopodia formation. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 650 matched cddid_all.tbl CDD cd14887 cd14887 276852 MYSc_Myo26 class XXVI myosin, motor domain. These MyTH-FERM myosins are thought to be related to the other myosins that have a MyTH4 domain such as class III, VII, IX, X , XV, XVI, XVII, XX, XXII, XXV, and XXXIV. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 725 matched cddid_all.tbl CDD cd14888 cd14888 276853 MYSc_Myo27 class XXVII myosin, motor domain. Not much is known about this myosin class. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 667 matched cddid_all.tbl CDD cd14889 cd14889 276854 MYSc_Myo28 class XXVIII myosin, motor domain. These myosins are found in fish, chicken, and mollusks. The tail regions of these class-XXVIII myosins consist of an IQ motif, a short coiled-coil region, and an SH2 domain. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 659 matched cddid_all.tbl CDD cd14890 cd14890 276855 MYSc_Myo29 class XXIX myosin, motor domain. Class XXIX myosins are comprised of Stramenopiles and have very long tail domains consisting of three IQ motifs, short coiled-coil regions, up to 18 CBS domains, a PB1 domain, and a carboxy-terminal transmembrane domain. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 662 matched cddid_all.tbl CDD cd14891 cd14891 276856 MYSc_Myo30 class XXX myosin, motor domain. Myosins of class XXX are composed of an amino-terminal SH3-like domain, two IQ motifs, a coiled-coil region and a PX domain. The myosin classes XXX to XXXIV contain members from Phytophthora species and Hyaloperonospora parasitica. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 645 matched cddid_all.tbl CDD cd14892 cd14892 276857 MYSc_Myo31 class XXXI myosin, motor domain. Class XXXI myosins have a very long neck region consisting of 17 IQ motifs and 2 tandem ANK repeats that are separated by a PH domain. The myosin classes XXX to XXXIV contain members from Phytophthora species and Hyaloperonospora parasitica. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 656 matched cddid_all.tbl CDD cd14893 cd14893 276858 MYSc_Myo32 class XXXII myosin, motor domain. Class XXXII myosins do not contain any IQ motifs, but possess tandem MyTH4 and FERM domains. The myosin classes XXX to XXXIV contain members from Phytophthora species and Hyaloperonospora parasitica. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 741 matched cddid_all.tbl CDD cd14894 cd14894 276859 MYSc_Myo33 class myosin, motor domain. Class XXXIII myosins have variable numbers of IQ domain and 2 tandem ANK repeats that are separated by a PH domain. The myosin classes XXX to XXXIV contain members from Phytophthora species and Hyaloperonospora parasitica. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 871 matched cddid_all.tbl CDD cd14895 cd14895 276860 MYSc_Myo34 class XXXIV myosin, motor domain. Class XXXIV myosins are composed of an IQ motif, a short coiled-coil region, 5 tandem ANK repeats, and a carboxy-terminal FYVE domain. The myosin classes XXX to XXXIV contain members from Phytophthora species and Hyaloperonospora parasitica. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 704 matched cddid_all.tbl CDD cd14896 cd14896 276861 MYSc_Myo35 class XXXV myosin, motor domain. This class of metazoan myosins contains 2 IQ motifs, 2 MyTH4 domains, a single FERM domain, and an SH3 domain. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 644 matched cddid_all.tbl CDD cd14897 cd14897 276862 MYSc_Myo36 class XXXVI myosin, motor domain. This class of molluscan myosins contains a motor domain followed by a GlcAT-I (Beta1,3-glucuronyltransferase I) domain. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 635 matched cddid_all.tbl CDD cd14898 cd14898 276863 MYSc_Myo37 class XXXVII myosin, motor domain. The class XXXVIII myosins are comprised of fungi. Not much is known about this myosin class. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 578 matched cddid_all.tbl CDD cd14899 cd14899 276864 MYSc_Myo38 class XXXVIII myosin. The class XXXVIII myosins are comprised of Stramenopiles. Not much is known about this myosin class. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 717 matched cddid_all.tbl CDD cd14900 cd14900 276865 MYSc_Myo39 class XXXIX myosin, motor domain. The class XXXIX myosins are found in Stramenopiles. Not much is known about this myosin class. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 627 matched cddid_all.tbl CDD cd14901 cd14901 276866 MYSc_Myo40 class XL myosin, motor domain. The class XL myosins are comprised of Stramenopiles. Not much is known about this myosin class. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 655 matched cddid_all.tbl CDD cd14902 cd14902 276867 MYSc_Myo41 class XLI myosin, motor domain. The class XLI myosins are comprised of Stramenopiles. Not much is known about this myosin class. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 716 matched cddid_all.tbl CDD cd14903 cd14903 276868 MYSc_Myo42 class XLII myosin, motor domain. The class XLII myosins are comprised of Stramenopiles. Not much is known about this myosin class. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 658 matched cddid_all.tbl CDD cd14904 cd14904 276869 MYSc_Myo43 class XLIII myosin, motor domain. The class XLIII myosins are comprised of Stramenopiles. Not much is known about this myosin class. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 653 matched cddid_all.tbl CDD cd14905 cd14905 276870 MYSc_Myo44 class XLIV myosin, motor domain. There is little known about the function of the myosin XLIV class. Members here include cellular slime mold Polysphondylium and soil-living amoeba Dictyostelium. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 673 matched cddid_all.tbl CDD cd14906 cd14906 276871 MYSc_Myo45 class XLV myosin, motor domain. The class XLVI myosins are comprised of slime molds Dictyostelium and Polysphondylium. Not much is known about this myosin class. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 715 matched cddid_all.tbl CDD cd14907 cd14907 276872 MYSc_Myo46 class XLVI myosin, motor domain. The class XLVI myosins are comprised of Alveolata. Not much is known about this myosin class. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 669 matched cddid_all.tbl CDD cd14908 cd14908 276873 MYSc_Myo47 class XLVII myosin, motor domain. The class XLVII myosins are comprised of Stramenopiles. Not much is known about this myosin class. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 682 matched cddid_all.tbl CDD cd14909 cd14909 276874 MYSc_Myh1_insects_crustaceans "class II myosin heavy chain 1, motor domain. Myosin motor domain of type IIx skeletal muscle myosin heavy chain 1 (also called MYHSA1, MYHa, MyHC-2X/D, MGC133384) in insects and crustaceans. Myh1 is a type I skeletal muscle myosin that in Humans is encoded by the MYH1 gene. Class II myosins, also called conventional myosins, are the myosin type responsible for producing actomyosin contraction in metazoan muscle and non-muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy." 666 matched cddid_all.tbl CDD cd14910 cd14910 276875 MYSc_Myh1_mammals "class II myosin heavy chain 1, motor domain. Myosin motor domain of type IIx skeletal muscle myosin heavy chain 1 (also called MYHSA1, MYHa, MyHC-2X/D, MGC133384) in mammals. Class II myosins, also called conventional myosins, are the myosin type responsible for producing actomyosin contraction in metazoan muscle and non-muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy." 671 matched cddid_all.tbl CDD cd14911 cd14911 276876 MYSc_Myh2_insects_mollusks "class II myosin heavy chain 2, motor domain. Myosin motor domain of type IIa skeletal muscle myosin heavy chain 2 (also called MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A) in insects and mollusks. This gene encodes a member of the class II or conventional myosin heavy chains, and functions in skeletal muscle contraction. Mutations in this gene results in inclusion body myopathy-3 and familial congenital myopathy. Class II myosins, also called conventional myosins, are the myosin type responsible for producing actomyosin contraction in metazoan muscle and non-muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy." 674 matched cddid_all.tbl CDD cd14912 cd14912 276877 MYSc_Myh2_mammals "class II myosin heavy chain 2, motor domain. Myosin motor domain of type IIa skeletal muscle myosin heavy chain 2 (also called MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A) in mammals. Mutations in this gene results in inclusion body myopathy-3 and familial congenital myopathy. Class II myosins, also called conventional myosins, are the myosin type responsible for producing actomyosin contraction in metazoan muscle and non-muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy." 673 matched cddid_all.tbl CDD cd14913 cd14913 276878 MYSc_Myh3 "class II myosin heavy chain 3, motor domain. Myosin motor domain of fetal skeletal muscle myosin heavy chain 3 (MYHC-EMB, MYHSE1, HEMHC, SMHCE) in tetrapods including mammals, lizards, and frogs. This gene is a member of the MYH family and encodes a protein with an IQ domain and a myosin head-like domain. Mutations in this gene have been associated with two congenital contracture (arthrogryposis) syndromes, Freeman-Sheldon syndrome and Sheldon-Hall syndrome. Class II myosins, also called conventional myosins, are the myosin type responsible for producing actomyosin contraction in metazoan muscle and non-muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy." 668 matched cddid_all.tbl CDD cd14915 cd14915 276879 MYSc_Myh4 "class II myosin heavy chain 4, motor domain. Myosin motor domain of skeletal muscle myosin heavy chain 4 (also called MYH2B, MyHC-2B, MyHC-IIb). Class II myosins, also called conventional myosins, are the myosin type responsible for producing actomyosin contraction in metazoan muscle and non-muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy." 671 matched cddid_all.tbl CDD cd14916 cd14916 276880 MYSc_Myh6 "class II myosin heavy chain 6, motor domain. Myosin motor domain of alpha (or fast) cardiac muscle myosin heavy chain 6. Cardiac muscle myosin is a hexamer consisting of two heavy chain subunits, two light chain subunits, and two regulatory subunits. This gene encodes the alpha heavy chain subunit of cardiac myosin. Mutations in this gene cause familial hypertrophic cardiomyopathy and atrial septal defect. Class II myosins, also called conventional myosins, are the myosin type responsible for producing actomyosin contraction in metazoan muscle and non-muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy." 670 matched cddid_all.tbl CDD cd14917 cd14917 276881 MYSc_Myh7 "class II myosin heavy chain 7, motor domain. Myosin motor domain of beta (or slow) type I cardiac muscle myosin heavy chain 7 (also called CMH1, MPD1, and CMD1S). Muscle myosin is a hexameric protein containing 2 heavy chain subunits, 2 alkali light chain subunits, and 2 regulatory light chain subunits. It is expressed predominantly in normal human ventrical and in skeletal muscle tissues rich in slow-twitch type I muscle fibers. Changes in the relative abundance of this protein and the alpha (or fast) heavy subunit of cardiac myosin correlate with the contractile velocity of cardiac muscle. Its expression is also altered during thyroid hormone depletion and hemodynamic overloading. Mutations in this gene are associated with familial hypertrophic cardiomyopathy, myosin storage myopathy, dilated cardiomyopathy, and Laing early-onset distal myopathy. Class II myosins, also called conventional myosins, are the myosin type responsible for producing actomyosin contraction in metazoan muscle and non-muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy." 668 matched cddid_all.tbl CDD cd14918 cd14918 276882 MYSc_Myh8 "class II myosin heavy chain 8, motor domain. Myosin motor domain of perinatal skeletal muscle myosin heavy chain 8 (also called MyHC-peri, MyHC-pn). Myosin is a hexameric protein composed of a pair of myosin heavy chains (MYH) and two pairs of nonidentical light chains. A mutation in this gene results in trismus-pseudocamptodactyly syndrome. Class II myosins, also called conventional myosins, are the myosin type responsible for producing actomyosin contraction in metazoan muscle and non-muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy." 668 matched cddid_all.tbl CDD cd14919 cd14919 276883 MYSc_Myh9 "class II myosin heavy chain 9, motor domain. Myosin motor domain of non-muscle myosin heavy chain 9 (also called NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS, and DFNA17). Myosin is a hexameric protein composed of a pair of myosin heavy chains (MYH) and two pairs of nonidentical light chains. The encoded protein is a myosin IIA heavy chain that contains an IQ domain and a myosin head-like domain which is involved in several important functions, including cytokinesis, cell motility and maintenance of cell shape. Defects in this gene have been associated with non-syndromic sensorineural deafness autosomal dominant type 17, Epstein syndrome, Alport syndrome with macrothrombocytopenia, Sebastian syndrome, Fechtner syndrome and macrothrombocytopenia with progressive sensorineural deafness. Class II myosins, also called conventional myosins, are the myosin type responsible for producing actomyosin contraction in metazoan muscle and non-muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy." 670 matched cddid_all.tbl CDD cd14920 cd14920 276952 MYSc_Myh10 "class II myosin heavy chain 10, motor domain. Myosin motor domain of non-muscle myosin heavy chain 10 (also called NMMHCB). Mutations in this gene have been associated with May-Hegglin anomaly and developmental defects in brain and heart. Multiple transcript variants encoding different isoforms have been found for this gene. Class II myosins, also called conventional myosins, are the myosin type responsible for producing actomyosin contraction in metazoan muscle and non-muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy." 673 matched cddid_all.tbl CDD cd14921 cd14921 276885 MYSc_Myh11 "class II myosin heavy chain 11, motor domain. Myosin motor domain of smooth muscle myosin heavy chain 11 (also called SMMHC, SMHC). The gene product is a subunit of a hexameric protein that consists of two heavy chain subunits and two pairs of non-identical light chain subunits. It functions as a major contractile protein, converting chemical energy into mechanical energy through the hydrolysis of ATP. The gene encoding a human ortholog of rat NUDE1 is transcribed from the reverse strand of this gene, and its 3' end overlaps with that of the latter. Inversion of the MYH11 locus is one of the most frequent chromosomal aberrations found in acute myeloid leukemia. Alternative splicing generates isoforms that are differentially expressed, with ratios changing during muscle cell maturation. Mutations in MYH11 have been described in individuals with thoracic aortic aneurysms leading to acute aortic dissections with patent ductus arteriosus. MYH11 mutations are also thought to contribute to human colorectal cancer and are also associated with Peutz-Jeghers syndrome. The mutations found in human intestinal neoplasia result in unregulated proteins with constitutive motor activity, similar to the mutant myh11 zebrafish. Class II myosins, also called conventional myosins, are the myosin type responsible for producing actomyosin contraction in metazoan muscle and non-muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy." 673 matched cddid_all.tbl CDD cd14923 cd14923 276887 MYSc_Myh13 "class II myosin heavy chain 13, motor domain. Myosin motor domain of skeletal muscle myosin heavy chain 13 (also called MyHC-eo) in mammals, chicken, and green anole. Myh13 is a myosin whose expression is restricted primarily to the extrinsic eye muscles which are specialized for function in eye movement. Class II myosins, also called conventional myosins, are the myosin type responsible for producing muscle contraction in muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy." 671 matched cddid_all.tbl CDD cd14927 cd14927 276953 MYSc_Myh7b "class II myosin heavy chain 7b, motor domain. Myosin motor domain of cardiac muscle, beta myosin heavy chain 7b (also called KIAA1512, dJ756N5.1, MYH14, MHC14). MYH7B is a slow-twitch myosin. Mutations in this gene result in one form of autosomal dominant hearing impairment. Multiple transcript variants encoding different isoforms have been found for this gene. Class II myosins, also called conventional myosins, are the myosin type responsible for producing actomyosin contraction in metazoan muscle and non-muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy." 676 matched cddid_all.tbl CDD cd14929 cd14929 276892 MYSc_Myh15_mammals "class II myosin heavy chain 15, motor domain. Myosin motor domain of sarcomeric myosin heavy chain 15 in mammals (also called KIAA1000) . MYH15 is a slow-twitch myosin. Myh15 is a ventricular myosin heavy chain. Myh15 is absent in embryonic and fetal muscles and is found in orbital layer of extraocular muscles at birth. Class II myosins, also called conventional myosins, are the myosin type responsible for producing actomyosin contraction in metazoan muscle and non-muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy." 662 matched cddid_all.tbl CDD cd14930 cd14930 276893 MYSc_Myh14_mammals "class II myosin heavy chain 14 motor domain. Myosin motor domain of non-muscle myosin heavy chain 14 (also called FLJ13881, KIAA2034, MHC16, MYH17). Its members include mammals, chickens, and turtles. Class II myosins, also called conventional myosins, are the myosin type responsible for producing actomyosin contraction in metazoan muscle and non-muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. Some of the data used for this classification were produced by the CyMoBase team at the Max-Planck-Institute for Biophysical Chemistry. The sequence names are composed of the species abbreviation followed by the protein abbreviation and optional protein classifier and variant designations." 670 matched cddid_all.tbl CDD cd14932 cd14932 276895 MYSc_Myh18 "class II myosin heavy chain 18, motor domain. Myosin motor domain of muscle myosin heavy chain 18. Class II myosins, also called conventional myosins, are the myosin type responsible for producing actomyosin contraction in metazoan muscle and non-muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy." 676 matched cddid_all.tbl CDD cd14934 cd14934 276896 MYSc_Myh16 "class II myosin heavy chain 16, motor domain. Myosin motor domain of myosin heavy chain 16 pseudogene (also called MHC20, MYH16, and myh5), encoding a sarcomeric myosin heavy chain expressed in nonhuman primate masticatory muscles, is inactivated in humans. This cd contains Myh16 in mammals. MYH16 has intermediate fibres between that of slow type 1 and fast 2B fibres, but exert more force than any other fibre type examined. Class II myosins, also called conventional myosins, are the myosin type responsible for producing actomyosin contraction in metazoan muscle and non-muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. Some of the data used for this classification were produced by the CyMoBase team at the Max-Planck-Institute for Biophysical Chemistry. The sequence names are composed of the species abbreviation followed by the protein abbreviation and optional protein classifier and variant designations." 659 matched cddid_all.tbl CDD cd14937 cd14937 276897 MYSc_Myo24A class XXIV A myosin, motor domain. These myosins have a 1-2 IQ motifs in their neck and a coiled-coil region in their C-terminal tail. The function of the class XXIV myosins remain elusive. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 637 matched cddid_all.tbl CDD cd14938 cd14938 276898 MYSc_Myo24B class XXIV B myosin, motor domain. These myosins have a 1-2 IQ motifs in their neck and a coiled-coil region in their C-terminal tail. The functions of these myosins remain elusive. The catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy. 713 matched cddid_all.tbl CDD cd14939 cd14939 320093 7tmD_STE2 fungal alpha-factor pheromone receptor STE2, member of the class D family of seven-transmembrane G protein-coupled receptors. This subfamily represents the alpha-factor pheromone receptor encoded by the STE2 gene, which is required for pheromone sensing and mating in haploid cells of the yeast Saccharomyces cerevisiae. The STE2-encoded seven-transmembrane domain receptor is a member of the class D GPCRs. Class D receptors are composed of two major subfamilies: Ste2 and Ste3. These two GPCRs (Ste2 and Ste3) sense the polypeptide mating pheromones, alpha-factor and a-factor, which activate a G protein-coupled receptors on the surface of the opposite yeast-mating haploid-types (MATa and MAT-alpha), respectively. Activation of these receptors by pheromones leads to activation of the mitogen-activated protein kinase (MAPK) signal transduction cascades, G1 cell cycle arrest, and polarized cell growth in the direction of the partner cell (a process called shmooing), which ultimately induces cell-cell fusion and the formation of a diploid zygote. Like all GPCRs, these pheromone mating factor receptors possess the same basic architecture of seven-transmembrane (7TM) domains and share common signaling mechanisms; however, there is no significant sequence similarity either between Ste2 and Ste3, or between these two receptors and the other 7TM GPCRs. Thus, STE2 and STE3 represent phylogenetically distinct groups. 265 matched cddid_all.tbl CDD cd14940 cd14940 320094 7tmE_cAMP_R_Slime_mold slime mold cyclic AMP receptor, member of the class E family of seven-transmembrane G protein-coupled receptors. This family represents the class E of seven-transmembrane G-protein coupled receptors found in soil-living amoebas, commonly referred to as slime molds. The class E family includes cAMP receptors (cAR1-4) and cAMP receptors-like proteins (CrlA-C) from Dictyostelium discoideum, and their highly homologous cAMP receptors (TasA and TasB) from Polysphondylium pallidum. So far, four subtypes of cAMP receptors (cAR1-4) have been identified that play an essential role in the detection and transmit of the periodic extracellular cAMP waves that regulate chemotactic cell movement during Dictyostelium development, from the unicellular amoeba aggregate into many multicellular slugs and then differentiate into a sporocarp, a fruiting body with cells specialized for different functions. These four subtypes differ in their expression levels and patterns during development. cAR1 is high-affinity receptor that is the first one to be expressed highly during early aggregation and continues to be expressed at low levels during later developmental stages. cAR1 detects extracellular cAMP and is coupled to G-alpha2 protein. Cells lacking cAR1 fail to aggregate, demonstrating that cAR1 is responsible for aggregation. During later aggregation the high-affinity cAR3 receptor is expressed at low levels. Nonetheless, cells lacking cAR3 do not show an obviously altered pattern of development and are still able to aggregate into fruiting bodies. In contrast, cAR2 and cAR4 are low affinity receptors expressed predominantly after aggregation in pre-stalk cells. cAR2 is essential for normal tip formation and deletion of the receptor arrests development at the mound stage. On the other hand, CAR4 regulates axial patterning and cellular differentiation, and deletion of the receptor results in defects during culmination. Furthermore, three cAMP receptor-like proteins (CrlA-C) were identified in Dictyostelium that show limited sequence similarity to the cAMP receptors. Of these CrlA is thought to be required for normal cell growth and tip formation in developing aggregates. 256 matched cddid_all.tbl CDD cd14941 cd14941 271344 TRAPPC_bet3-like Bet3-like domains of TRAPP. Bet3-like domains of a subfamily of core components of the trafficking protein particle complex (TRAPP) include TRAPPC3, TRAPPC5, and TRAPPC6A. TRAPP complexes play a key role in the regulation of ER-to-Golgi and intra-Golgi transport by tethering the vesicle membrane to the target membrane. TRAPPs are large multimeric protein complexes which contain six core subunits that belong to two distinct structural families, the bet3-like family and the sedlin-like family. 152 matched cddid_all.tbl CDD cd14942 cd14942 271345 TRAPPC3_bet3 Bet3-TRAPPC3 subunit of the TRAPP complex. Bet3 (also known as TRAPPC3) subunit of the trafficking protein particle complex (TRAPP). Bet3 is one of the six core subunits of TRAPP complexes which play a key role in the regulation of ER-to-Golgi and intra-Golgi transport by tethering the vesicle membrane to the target membrane. TRAPPC3 has also been shown to be additionally important for membrane fusion during the formation of vesicular tubular clusters (VTC). In its core, Bet3 forms a hydrophobic channel that also contains a conserved acylation site. 155 matched cddid_all.tbl CDD cd14943 cd14943 271346 TRAPPC5_Trs31 Trs31 subunit of the TRAPP complex. TRS31 (also known as TRAPPC5) subunit of the trafficking protein particle complex (TRAPP). TRS31 is one of the six core subunits of TRAPP complexes which play a key role in the regulation of ER-to-Golgi and intra-Golgi transport by tethering the vesicle membrane to the target membrane. 158 matched cddid_all.tbl CDD cd14944 cd14944 271347 TRAPPC6A_Trs33 Trs33 subunit of the TRAPP complex. TRS33 (also known as TRAPPC6A) subunit of the trafficking protein particle complex (TRAPP). TRS33 is one of the six core subunits of TRAPP complexes which play a key role in the regulation of ER-to-Golgi and intra-Golgi transport by tethering the vesicle membrane to the target membrane. In mammals, mutations in TRAPPC6a cause mosaic loss of coat pigment. 167 matched cddid_all.tbl CDD cd14945 cd14945 271253 Myo5-like_CBD Cargo binding domain of myosin 5 and similar proteins. Class V myosins are well studied unconventional myosins, represented by three paralogs (Myo5 a,b,c) in vertebrates and two (myo2 and myo4) in fungi and related to plant class XI myosins. Their C-terminal cargo binding domains is important for the binding of a diverse set of cargos, including membrane vesicles, organelles, proteins and mRNA. MyoV-CBDs interact with several adaptor proteins that in turn interact with the cargo. 288 matched cddid_all.tbl CDD cd14946 cd14946 380670 Tet_JBP oxygenase domain of ten-eleven translocation (TET) enzymes, J-binding proteins (JBPs), and similar proteins. TET proteins are involved in DNA demethylation through iteratively oxidizing 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). TET proteins contain a C-terminal catalytic domain which consists of a cysteine-rich region and a double-stranded beta-helix (DSBH) fold. Alterations in TET protein function have been linked to cancer, and TETs influence many cell differentiation processes. J binding protein (JBP) 1 and JBP2 are thymidine hydroxylases that catalyze the first step of base J biosynthesis: the hydroxylation of thymine in DNA to form 5-hydroxymethyluracil (hmU). Base J (beta-d-glucopyranosyloxymethyluracil) is a hyper-modified DNA base found in the DNA of kinetoplastids (Trypanosoma brucei, Trypanosoma cruzi, and Leishmania). JBP1 and JBP2 each contain a J-DNA binding domain and a thymidine hydroxylase domain. Members of this TET/JBP family of dioxygenases require Fe2+ and alpha-ketoglutarate (also known as 2-oxoglutarate) for activity. 264 matched cddid_all.tbl CDD cd14947 cd14947 271343 NBR1_like Functionally uncharacterized domain in neighbor of Brca1 Gene 1 and related proteins. NBR1 has been characterized as a specific late endosomal protein, which might play a role in receptor (RTK) trafficking. Specifically, NBR1 was shown to inhibit ligand-mediated receptor internalization from the cell surface. The region covered by this domain model may be involved in that function, as the C-terminus (which contains a UBA domain) was shown to be essential but not sufficient by itself. In an earlier yeast two-hybrid study, the region in mouse NBR1 covered by this domain has been shown to interact with CIB (calcium and integrin-binding protein) and FEZ1 (fasciculation and elongation protein zeta-1). Thus, NBR1 may play a role in cellular signalling pathways and possibly in neural development. 112 matched cddid_all.tbl CDD cd14948 cd14948 271342 BACON Bacteroidetes-Associated Carbohydrate-binding (putative) Often N-terminal (BACON) domain. The BACON domain is found in diverse domain architectures and accociated with a wide variety of domains, including carbohydrate-active enzymes and proteases. It was named for its suggested function of carbohydrate binding; the latter was inferred from domain architectures, sequence conservation, and phyletic distribution. However, recent experimental data suggest that its primary function in Bacteroides ovatus endo-xyloglucanase BoGH5A is to distance the catalytic module from the cell surface and confer additional mobility to the catalytic domain for attack of the polysaccharide. No evidence for a direct role in carbohydrate binding could be found in that case. The large majority of BACON domains are found in Bacteroidetes. 83 matched cddid_all.tbl CDD cd14949 cd14949 271340 Asparaginase_2_like_3 Uncharacterized bacterial subfamily of the L-Asparaginase type 2-like enzymes, an Ntn-hydrolase family. The wider family of Asparaginase 2-like enzymes includes Glycosylasparaginase, Taspase 1, and L-Asparaginase type 2. Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked glycoprotein. Taspase1 catalyzes the cleavage of the Mix Lineage Leukemia (MLL) nuclear protein and transcription factor TFIIA. L-Asparaginase type 2 hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzymes of this family undergo autoproteolytic cleavage before a threonine to generate alpha and beta subunits. The threonine becomes the N-terminal residue of the beta subunit and is the catalytic residue. 280 matched cddid_all.tbl CDD cd14950 cd14950 271341 Asparaginase_2_like_2 Uncharacterized archaebacterial subfamily of the L-Asparaginase type 2-like enzymes, an Ntn-hydrolase family. The wider family of Asparaginase 2-like enzymes includes Glycosylasparaginase, Taspase 1, and L-Asparaginase type 2. Glycosylasparaginase catalyzes the hydrolysis of the glycosylamide bond of asparagine-linked glycoprotein. Taspase1 catalyzes the cleavage of the Mix Lineage Leukemia (MLL) nuclear protein and transcription factor TFIIA. L-Asparaginase type 2 hydrolyzes L-asparagine to L-aspartate and ammonia. The proenzymes of this family undergo autoproteolytic cleavage before a threonine to generate alpha and beta subunits. The threonine becomes the N-terminal residue of the beta subunit and is the catalytic residue. 251 matched cddid_all.tbl CDD cd14951 cd14951 271321 NHL-2_like NHL repeat domain of NHL repeat-containing protein 2 and similar proteins. NHL repeat-containing protein 2 (NHLRC2) and related bacterial proteins; members of this eukaryotic and bacterial family are uncharacterized, the NHL repeat domain is found C-terminally of a thioredoxin domain. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. 334 matched cddid_all.tbl CDD cd14952 cd14952 271322 NHL_PKND_like NHL repeat domain of the protein kinase PknD. PknD is a mycobacterial transmembrane protein with a cytosolic kinase domain and an extracellular sensor domain that contains NHL repeats. It plays a key role in the development of central nervous system tuberculosis, by mediating the invasion of host brain endothelia. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. 247 matched cddid_all.tbl CDD cd14953 cd14953 271323 NHL_like_1 Uncharacterized NHL-repeat domain in bacterial proteins. This bacterial family of NHL-repeat domains is found in a variety of domain architectures. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. 323 matched cddid_all.tbl CDD cd14954 cd14954 271324 NHL_TRIM71_like NHL repeat domain of the tripartite motif-containing protein 71 (TRIM71) and related proteins. The E3 ubiquitin-protein ligase TRIM71 (LIN-41) is a RING-finger domain containing protein that has been associated with a variety of activities. The NHL repeat domain appears responsible for targeting TRIM71 to mRNAs, and TRIM71 appears responsible for translational repression and mRNA decay. Together with BRAT, TRIM71 may be part of a family of mRNA repressors that regulate proliferation and differentiation. TRIM has been shown to negatively regulate stability of Lin28B, which inhibits the pre-let-7 miRNA precursor from maturing by recruiting the terminal uriyltransferase TUT4. This family also contains the Caenorhabditis elegans NHL repeat containing 1 (NHL-1), a RING-finger-containing protein that was shown to interact with E2 ubiquitin conjugating enzymes in two-hybrid screens. Its domain architecture resembles that of the E3 ubiquitin protein ligases TRIM2, TRIM32, and TRIM71. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. 285 matched cddid_all.tbl CDD cd14955 cd14955 271325 NHL_like_4 Uncharacterized NHL-repeat domain in bacterial and archaeal proteins. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. 279 matched cddid_all.tbl CDD cd14956 cd14956 271326 NHL_like_3 Uncharacterized NHL-repeat domain in bacterial proteins. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. 274 matched cddid_all.tbl CDD cd14957 cd14957 271327 NHL_like_2 Uncharacterized NHL-repeat domain in bacterial and archaeal proteins. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. 280 matched cddid_all.tbl CDD cd14958 cd14958 271328 NHL_PAL_like Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL, EC 4.3.2.5). PAL catalyzes the N-dealkylation of peptidyl-alpha-hydroxyglycine, which results in an alpha-amidated peptide and glyoxylate. Amidation of the C-terminus is required for the activity of many peptide hormones and neuropeptides. The catalytic residues of PAL are located on several NHL-repeats. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. 300 matched cddid_all.tbl CDD cd14959 cd14959 271329 NHL_brat_like NHL repeat domain of the Drosophila brain-tumor protein (brat) and similar proteins. Drosophila brain-tumor (brat) has been identified as a tumor suppressor that negatively regulates cell proliferation during development of the Drosophila larval brain. It appears to be recruited to the 3'-untranslated region of hunchback RNA and regulates its translation by forming a complex with Pumilio (Pum) and Nanos (Nos). The NHL domain of brat appears to be involved by interacting with the RNA-binding Puf repeats of Pumilio, a sequence-specific RNA binding protein. This family also contains the Caenorhabditis elegans homolog NCL-1. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. 274 matched cddid_all.tbl CDD cd14960 cd14960 271330 NHL_TRIM2_like NHL repeat domain of the tripartite motif-containing protein 2 (TRIM2) and related proteins. The E3 ubiquitin-protein ligase TRIM2 is responsible for ubiquinating the apoptosis-inducing Bcl-2-interacting mediator of cell death (Bim), when the latter is phosphorylated by p42/p44 MAPK. TRIM2 regulates the ubiquitination of neurofilament light subunit (NF-L), deficiencies in TRIM2 result in increased NF-L levels in axons and subsequent axonopathy. TRIM2 is also involved in regulating axon outgrowth during development; it contains RING and BBOX domains, the NHL repeat domain is located at its C-terminus. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. 274 matched cddid_all.tbl CDD cd14961 cd14961 271331 NHL_TRIM32_like NHL repeat domain of the tripartite motif-containing protein 32 (TRIM32) and related proteins. The E3 ubiquitin-protein ligase TRIM32 (HT2A) is widely expressed and is responsible for ubiquinating a large variety of targets, including dysbindin (DTNBP1), NPHP7/Glis2, TAp73, and others. TRIM32 promotes disassociation of the plakoglobin-PI3K complex and reduces PI3K-Akt-FoxO signaling. Mutations in TRIM32 have been implemented in the two diverse diseases limb-girdle muscular dystrophy type 2H (LGMD2H) or sarcotubular myopathy (STM) and Bardet-Biedl syndrome type 11 (BBS11). The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. 273 matched cddid_all.tbl CDD cd14962 cd14962 271332 NHL_like_6 Uncharacterized NHL-repeat domain in bacterial proteins. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. 271 matched cddid_all.tbl CDD cd14963 cd14963 271333 NHL_like_5 Uncharacterized NHL-repeat domain in bacterial proteins. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies, typically as 6 instances. It is about 40 residues long and resembles the WD repeat and other beta-propeller structures. 268 matched cddid_all.tbl CDD cd14964 cd14964 410628 7tm_GPCRs seven-transmembrane G protein-coupled receptor superfamily. This hierarchical evolutionary model represents the seven-transmembrane (7TM) receptors, often referred to as G protein-coupled receptors (GPCRs), which transmit physiological signals from the outside of the cell to the inside via G proteins. GPCRs constitute the largest known superfamily of transmembrane receptors across the three kingdoms of life that respond to a wide variety of extracellular stimuli including peptides, lipids, neurotransmitters, amino acids, hormones, and sensory stimuli such as light, smell and taste. All GPCRs share a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. However, some 7TM receptors, such as the type 1 microbial rhodopsins, do not activate G proteins. Based on sequence similarity, GPCRs can be divided into six major classes: class A (the rhodopsin-like family), class B (the Methuselah-like, adhesion and secretin-like receptor family), class C (the metabotropic glutamate receptor family), class D (the fungal mating pheromone receptors), class E (the cAMP receptor family), and class F (the frizzled/smoothened receptor family). Nearly 800 human GPCR genes have been identified and are involved essentially in all major physiological processes. Approximately 40% of clinically marketed drugs mediate their effects through modulation of GPCR function for the treatment of a variety of human diseases including bacterial infections. 267 matched cddid_all.tbl CDD cd14965 cd14965 410629 7tm_Opsins_type1 type 1 opsins, member of the seven-transmembrane GPCR superfamily. This group represents the microbial rhodopsin family, also known as type 1 rhodopsins, which can function as light-dependent ion pumps, cation channels, and sensors. They have been found in various single-celled microorganisms from all three domains of life, including halophile archaea, gamma-proteobacteria, cyanobacteria, fungi, and green algae. Members of the type I rhodopsin family include: light-driven inward chloride pump halorhodopsin (HR); light-driven outward proton pump bacteriorhodopsin (BR); light-gated cation channel channelrhodopsin (ChR); light-sensor activating transmembrane transducer proteins, sensory rhodopsin I and II (SRI and II); light-sensor activating soluble transducer protein Anabaena sensory rhodopsin (ASR); and other light-driven proton pumps such as blue-light-absorbing and green-light absorbing proteorhodopsins, among others. While microbial (type 1) and animal (type 2) rhodopsins have no sequence similarity with each other, they share a common architecture consisting of seven-transmembrane alpha-helices (TM) connected by extracellular loops and intracellular loops. Both types of rhodopsins consist of opsin and a covalently attached retinal (the aldehyde of vitamin A), a photoreactive chromophore, via a protonated Schiff base linkage to an amino group of lysine in the middle of the seventh transmembrane helix (TM7). Upon the absorption of light, microbial rhodopsins undergo light-induced photoisomerization of all-trans retinal into the 13-cis isomer, whereas the photoisomerization of 11-cis retinal to all-trans isomer occurs in the animal rhodopsins. While animal visual rhodopsins are activated by light to catalyze GDP/GTP exchange in the alpha subunit of the retinal G protein transducin (Gt), microbial rhodopsins do not activate G proteins. 214 matched cddid_all.tbl CDD cd14966 cd14966 320097 7tmD_STE3 fungal a-factor pheromone receptor STE3, member of the class D family of seven-transmembrane G protein-coupled receptors. This subfamily represents the a-factor pheromone receptor encoded by the STE3 gene, which is required for pheromone sensing and mating in haploid cells of the yeast Saccharomyces cerevisiae. The STE3-encoded seven-transmembrane domain receptor is a member of the class D GPCRs. Class D receptors are composed of two major subfamilies: Ste2 and Ste3. These two GPCRs (Ste2 and Ste3) sense the polypeptide mating pheromones, alpha-factor and a-factor, which activate a G protein-coupled receptors on the surface of the opposite yeast-mating haploid-types (MATa and MAT-alpha), respectively. Activation of these receptors by pheromones leads to activation of the mitogen-activated protein kinase (MAPK) signal transduction cascades, G1 cell cycle arrest, and polarized cell growth in the direction of the partner cell (a process called shmooing), which ultimately induces cell-cell fusion and the formation of a diploid zygote. Like all GPCRs, these pheromone mating factor receptors possess the same basic architecture of seven-transmembrane (7TM) domains and share common signaling mechanisms; however, there is no significant sequence similarity either between Ste2 and Ste3, or between these two receptors and the other 7TM GPCRs. Thus, STE2 and STE3 represent phylogenetically distinct groups. 259 matched cddid_all.tbl CDD cd14967 cd14967 320098 7tmA_amine_R-like amine receptors and similar proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. Amine receptors of the class A family of GPCRs include adrenoceptors, 5-HT (serotonin) receptors, muscarinic cholinergic receptors, dopamine receptors, histamine receptors, and trace amine receptors. The receptors of amine subfamily are major therapeutic targets for the treatment of neurological disorders and psychiatric diseases. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 259 matched cddid_all.tbl CDD cd14968 cd14968 341316 7tmA_Adenosine_R adenosine receptor subfamily, member of the class A family of seven-transmembrane G protein-coupled receptors. The adenosine receptors (or P1 receptors), a family of G protein-coupled purinergic receptors, bind adenosine as their endogenous ligand. There are four types of adenosine receptors in human, designated as A1, A2A, A2B, and A3. Each type is encoded by a different gene and has distinct functions with some overlap. For example, both A1 and A2A receptors are involved in regulating myocardial oxygen consumption and coronary blood flow in the heart, while the A2A receptor also has a broad spectrum of anti-inflammatory effects in the body. These two receptors also expressed in the brain, where they have important roles in the release of other neurotransmitters such as dopamine and glutamate, while the A2B and A3 receptors found primarily in the periphery and play important roles in inflammation and immune responses. The A1 and A3 receptors preferentially interact with G proteins of the G(i/o) family, thereby lowering the intracellular cAMP levels, whereas the A2A and A2B receptors interact with G proteins of the G(s) family, activating adenylate cyclase to elevate cAMP levels. 285 matched cddid_all.tbl CDD cd14969 cd14969 381741 7tmA_Opsins_type2_animals type 2 opsins in animals, member of the class A family of seven-transmembrane G protein-coupled receptors. This rhodopsin family represents the type 2 opsins found in vertebrates and invertebrates except sponge. Type 2 opsins primarily function as G protein coupled receptors and are responsible for vision as well as for circadian rhythm and pigment regulation. On the contrary, type 1 opsins such as bacteriorhodopsin and proteorhodopsin are found in both prokaryotic and eukaryotic microbes, functioning as light-gated ion channels, proton pumps, sensory receptors and in other unknown functions. Although these two opsin types share seven-transmembrane domain topology and a conserved lysine reside in the seventh helix, type 1 opsins do not activate G-proteins and are not evolutionarily related to type 2. Type 2 opsins can be classified into six distinct subfamilies including the vertebrate opsins/encephalopsins, the G(o) opsins, the G(s) opsins, the invertebrate G(q) opsins, the photoisomerases, and the neuropsins. 284 matched cddid_all.tbl CDD cd14970 cd14970 320101 7tmA_Opioid_R-like opioid receptors and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes opioid receptors, somatostatin receptors, melanin-concentrating hormone receptors (MCHRs), and neuropeptides B/W receptors. Together they constitute the opioid receptor-like family, members of the class A G-protein coupled receptors. Opioid receptors are coupled to inhibitory G proteins of the G(i/o) family and are involved in regulating a variety of physiological functions such as pain, addiction, mood, stress, epileptic seizure, and obesity, among many others. G protein-coupled somatostatin receptors (SSTRs), which display strong sequence similarity with opioid receptors, binds somatostatin (somatotropin release inhibiting factor), a polypeptide hormone that regulates a wide variety of physiological functions such as neurotransmission, cell proliferation, contractility of smooth muscle cells, and endocrine signaling as well as inhibition of the release of many secondary hormones. MCHR binds melanin concentrating hormone and is presumably involved in the neuronal regulation of food intake. Despite strong homology with somatostatin receptors, MCHR does not appear to bind somatostatin. Neuropeptides B/W receptors are primarily expressed in the CNS and stimulate the cortisol secretion by activating the adenylate cyclase- and the phospholipase C-dependent signaling pathways. 282 matched cddid_all.tbl CDD cd14971 cd14971 320102 7tmA_Galanin_R-like galanin receptor and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This subfamily includes G-protein coupled galanin receptors, kisspeptin receptor and allatostatin-A receptor (AstA-R) in insects. These receptors, which are members of the class A of seven transmembrane GPCRs, share a high degree of sequence homology among themselves. The galanin receptors bind galanin, a neuropeptide that is widely expressed in the brain, peripheral tissues, and endocrine glands. Galanin is implicated in numerous neurological and psychiatric diseases including Alzheimer's disease, eating disorders, and epilepsy, among many others. KiSS1-derived peptide receptor (also known as GPR54 or kisspeptin receptor) binds the peptide hormone kisspeptin (metastin), which encoded by the metastasis suppressor gene (KISS1) expressed in various endocrine and reproductive tissues. AstA-R is a G-protein coupled receptor that binds allatostatin A. Three distinct types of allatostatin have been identified in the insects and crustaceans: AstA, AstB, and AstC. They both inhibit the biosynthesis of juvenile hormone and exert an inhibitory influence on food intake. Therefore, allatostatins are considered as potential targets for insect control. 281 matched cddid_all.tbl CDD cd14972 cd14972 341317 7tmA_EDG-like endothelial differentiation gene family, member of the class A family of seven-transmembrane G protein-coupled receptors. This group represents the endothelial differentiation gene (Edg) family of G-protein coupled receptors, melanocortin/ACTH receptors, and cannabinoid receptors as well as their closely related receptors. The Edg GPCRs bind blood borne lysophospholipids including sphingosine-1-phosphate (S1P) and lysophosphatidic acid (LPA), which are involved in the regulation of cell proliferation, survival, migration, invasion, endothelial cell shape change and cytoskeletal remodeling. The Edg receptors are classified into two subfamilies: the lysophosphatidic acid subfamily that includes LPA1 (Edg2), LPA2 (Edg4), and LPA3 (Edg7); and the S1P subfamily that includes S1P1 (Edg1), S1P2 (Edg5), S1P3 (Edg3), S1P4 (Edg6), and S1P5 (Edg8). Melanocortin receptors bind a group of pituitary peptide hormones known as melanocortins, which include adrenocorticotropic hormone (ACTH) and the different isoforms of melanocyte-stimulating hormones. Two types of cannabinoid receptors, CB1 and CB2, are activated by naturally occurring endocannabinoids, cannabis plant-derived cannabinoids such as tetrahydrocannabinol, or synthetic cannabinoids. The CB receptors are involved in the various physiological processes such as appetite, mood, memory, and pain sensation. CB1 receptor is expressed predominantly in central and peripheral neurons, while CB2 receptor is found mainly in the immune system. 275 matched cddid_all.tbl CDD cd14973 cd14973 320104 7tmA_Mrgpr mas-related G protein-coupled receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. The Mas-related G-protein coupled receptor (Mrgpr) family constitutes a group of orphan receptors exclusively expressed in nociceptive primary sensory neurons and mast cells in the skin. Members of the Mrgpr family have been implicated in the modulation of nociception, pruritus (itching), and mast cell degranulation. The Mrgpr family in rodents and humans contains more than 50 members that can be grouped into 9 distinct subfamilies: MrgprA, B, C (MrgprX1), D, E, F, G, H (GPR90), and the primate-specific MrgprX subfamily. Some Mrgprs can be activated by endogenous ligands such as beta-alanine, adenine (a cell metabolite and potential transmitter), RF-amide related peptides, or salusin-beta (a bioactive peptide). However, the effects of these agonists are not clearly understood, and the physiological role of the individual receptor family members remains to be determined. Also included in this family is Mas-related G-protein coupled receptor 1-like (MAS1L) which is only found in primates. The angiotensin-II metabolite angiotensin is an endogenous ligand for MAS1L. 272 matched cddid_all.tbl CDD cd14974 cd14974 320105 7tmA_Anaphylatoxin_R-like anaphylatoxin receptors and related G protein-coupled chemokine receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. This subfamily of G-protein coupled receptors includes anaphylatoxin receptors, formyl peptide receptors (FPR), prostaglandin D2 receptor 2, GPR1, and related chemokine receptors. The anaphylatoxin receptors are a group of G-protein coupled receptors that bind anaphylatoxins. The members of this group include C3a and C5a receptors. The formyl peptide receptors (FPRs) are chemoattractant GPCRs that involved in mediating immune responses to infection. They are expressed mainly on polymorphonuclear and mononuclear phagocytes and bind N-formyl-methionyl peptides (FMLP), which are derived from the mitochondrial proteins of ruptured host cells or invading pathogens. Chemokine receptor-like 1 (also known as chemerin receptor 23) is a GPCR for the chemoattractant adipokine chemerin, also known as retinoic acid receptor responder protein 2 (RARRES2), and for the omega-3 fatty acid derived molecule resolvin E1. Interaction with chemerin induces activation of the MAPK and PI3K signaling pathways leading to downstream functional effects, such as a decrease in immune responses, stimulation of adipogenesis, and angiogenesis. On the other hand, resolvin E1 negatively regulates the cytokine production in macrophages by reducing the activation of MAPK1/3 and NF-kB pathways. Prostaglandin D2 receptor, also known as CRTH2, is a chemoattractant G-protein coupled receptor expressed on T helper type 2 cells that binds prostaglandin D2 (PGD2). PGD2 functions as a mast cell-derived mediator to trigger asthmatic responses and also causes vasodilation. PGD2 exerts its inflammatory effects by binding to two G-protein coupled receptors, the D-type prostanoid receptor (DP) and PD2R2 (CRTH2). PD2R2 couples to the G protein G(i/o) type which leads to a reduction in intracellular cAMP levels and an increase in intracellular calcium. GPR1 is an orphan receptor that can be activated by the leukocyte chemoattractant chemerin, thereby suggesting that some of the anti-inflammatory actions of chemerin may be mediated through GPR1. 274 matched cddid_all.tbl CDD cd14975 cd14975 320106 7tmA_LTB4R leukotriene B4 receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Leukotriene B4 (LTB4), a metabolite of arachidonic acid, is a powerful chemotactic activator for granulocytes and macrophages. Two receptors for LTB4 have been identified: a high-affinity receptor (LTB4R1 or BLT1) and a low-affinity receptor (TB4R2 or BLT2). Both BLT1 and BLT2 receptors belong to the rhodopsin-like G-protein coupled receptor superfamily and primarily couple to G(i) proteins, which lead to chemotaxis, calcium mobilization, and inhibition of adenylate cyclase. In some cells, they can also couple to the G(q)-like protein, G16, and activate phospholipase C. LTB4 is involved in mediating inflammatory processes, immune responses, and host defense against infection. Studies have shown that LTB4 stimulates leukocyte extravasation, neutrophil degranulation, lysozyme release, and reactive oxygen species generation. 278 matched cddid_all.tbl CDD cd14976 cd14976 320107 7tmA_RNL3R relaxin-3 like peptide receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. This G protein-coupled receptor subfamily is composed of the relaxin-3 like peptide receptors, RNL3R1 and RNL3R2, and similar proteins. The relaxin-3 like peptide family includes relaxin-1, -2, -3, as well as insulin-like (INSL) peptides 3 to 6. RNL3/relaxin-3 and INSL5 are the endogenous ligands for RNL3R1 and RNL3R2, respectively. RNL3R1, also called GPCR135 or RXFP3, is predominantly expressed in the brain and is implicated in stress, anxiety, feeding, and metabolism. Insulin-like peptide 5 (INSL5), the endogenous ligand for RNL3R2 (also called GPCR142 or RXFP4), plays a role in fat and glucose metabolism. INSL5 is highly expressed in human rectal and colon tissues. Both RNL3R1 and RNL3R2 signal through G(i) protein and inhibit adenylate cyclase, thereby inhibit cAMP accumulation. RNL3R1 is shown to activate Erk1/2 signaling pathway. 290 matched cddid_all.tbl CDD cd14977 cd14977 320108 7tmA_ET_R-like endothelin receptors and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This subfamily of G-protein coupled receptors includes endothelin receptors, bombesin receptor subtype 3 (BRS-3), gastrin-releasing peptide receptor (GRPR), neuromedin B receptor (NMB-R), endothelin B receptor-like 2 (ETBR-LP-2), and GRP37. The endothelin receptors and related proteins are members of the seven transmembrane rhodopsin-like G-protein coupled receptor family (class A GPCRs) which activate multiple effectors via different types of G protein. 292 matched cddid_all.tbl CDD cd14978 cd14978 410630 7tmA_FMRFamide_R-like FMRFamide (Phe-Met-Arg-Phe) receptors and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes Drosophila melanogaster G-protein coupled FMRFamide (Phe-Met-Arg-Phe-NH2) receptor DrmFMRFa-R and related invertebrate receptors, as well as the vertebrate proteins GPR139 and GPR142. DrmFMRFa-R binds with high affinity to FMRFamide and intrinsic FMRFamide-related peptides. FMRFamide is a neuropeptide from the family of FMRFamide-related peptides (FaRPs), which all containing a C-terminal RFamide (Arg-Phe-NH2) motif and have diverse functions in the central and peripheral nervous systems. FMRFamide is an important neuropeptide in many types of invertebrates such as insects, nematodes, molluscs, and worms. In invertebrates, the FMRFamide-related peptides are involved in the regulation of heart rate, blood pressure, gut motility, feeding behavior, and reproduction. On the other hand, in vertebrates such as mice, they play a role in the modulation of morphine-induced antinociception. Orphan receptors GPR139 and GPR142 are very closely related G protein-coupled receptors, but they have different expression patterns in the brain and in other tissues. These receptors couple to inhibitory G proteins and activate phospholipase C. Studies suggested that dimer formation may be required for their proper function. GPR142 is predominantly expressed in pancreatic beta-cells and mediates enhancement of glucose-stimulated insulin secretion, whereas GPR139 is mostly expressed in the brain and is suggested to play a role in the control of locomotor activity. Tryptophan and phenylalanine have been identified as putative endogenous ligands of GPR139. 299 matched cddid_all.tbl CDD cd14979 cd14979 320110 7tmA_NTSR-like neurotensin receptors and related G protein-coupled receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. This subfamily includes the neurotensin receptors and related G-protein coupled receptors, including neuromedin U receptors, growth hormone secretagogue receptor, motilin receptor, the putative GPR39 and the capa receptors from insects. These receptors all bind peptide hormones with diverse physiological effects. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 300 matched cddid_all.tbl CDD cd14980 cd14980 320111 7tmA_Glycoprotein_LRR_R-like glycoprotein hormone receptors and leucine-rich repeats containing G protein-coupled receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. This subfamily includes the glycoprotein hormone receptors (GPHRs), vertebrate receptors containing 17 leucine-rich repeats (LGR4-6), and the relaxin family peptide receptors (also known as LGR7 and LGR8). They are seven transmembrane domain receptors with a very large extracellular N-terminal domain containing many leucine-rich repeats responsible for hormone recognition and binding. The glycoprotein hormone receptor family contains receptors for the pituitary hormones, thyrotropin (thyroid-stimulating hormone receptor), follitropin (follicle-stimulating hormone receptor), and lutropin (luteinizing hormone receptor). Glycoprotein hormone receptors couple primarily to the G(s)-protein and promotes cAMP production, but also to the G(i)- or G(q)-protein. Two orphan GPCRs, LGR7 and LGR8, have been recently identified as receptors for the relaxin peptide hormones. 286 matched cddid_all.tbl CDD cd14981 cd14981 320112 7tmA_Prostanoid_R G protein-coupled receptors for prostanoids, member of the class A family of seven-transmembrane G protein-coupled receptors. Prostanoids are the cyclooxygenase (COX) metabolites of arachidonic acid, which include the prostaglandins (PGD2, PGE2, PGF2alpha), prostacyclin (PGI2), and thromboxane A2 (TxA2). These five major bioactive prostanoids acts as mediators or modulators in a wide range of physiological and pathophysiological processes within the kidney and play important roles in inflammation, platelet aggregation, and vasoconstriction/relaxation, among many others. They act locally by preferentially interacting with G protein-coupled receptors designated DP, EP. FP, IP, and TP, respectively. The phylogenetic tree suggests that the prostanoid receptors can be grouped into two major branches: G(s)-coupled (DP1, EP2, EP4, and IP) and G(i)- (EP3) or G(q)-coupled (EP1, FP, and TP), forming three clusters. 288 matched cddid_all.tbl CDD cd14982 cd14982 341318 7tmA_purinoceptor-like purinoceptor and its related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. Members of this subfamily include lysophosphatidic acid receptor, P2 purinoceptor, protease-activated receptor, platelet-activating factor receptor, Epstein-Barr virus induced gene 2, proton-sensing G protein-coupled receptors, GPR35, and GPR55, among others. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 283 matched cddid_all.tbl CDD cd14983 cd14983 320114 7tmA_FFAR free fatty acid receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. This subfamily includes the free fatty acid receptors (FFARs) which bind free fatty acids (FFAs). They belong to the class A G-protein coupled receptors and are composed of three members, each encoded by a separate gene (FFAR1, FFAR2, and FFAR3). These genes and a fourth pseudogene, GPR42, are localized together on chromosome 19. FFAR1 is a receptor for medium- and long-chain FFAs, whereas FFAR2 and FFAR3 are receptors for short chain FFAs (SCFAs), which have different ligand affinities. FFAR1 directly mediates FFA stimulation of glucose-stimulated insulin secretion and also indirectly increases insulin secretion by enhancing the release of incretin. FFAR2 activation by SCFA suppresses adipose insulin signaling, which leads to the inhibition of fat accumulation in adipose tissue. FAAR3 is expressed in intestinal L cells, which produces glucagon-like peptide 1 (GLP-1) and peptide YY (PYY), suggesting that this receptor may be involved in energy homeostasis. FFARs are considered important components of the body's nutrient sensing mechanism, and therefore, these receptors are potential therapeutic targets for the treatment of metabolic disorders, such as type 2 diabetes and obesity. 278 matched cddid_all.tbl CDD cd14984 cd14984 341319 7tmA_Chemokine_R classical and atypical chemokine receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Chemokines are principal regulators for leukocyte trafficking, recruitment, and activation. Chemokine family membership is defined on the basis of sequence homology and on the presence of variations on a conserved cysteine motif, which allows the family to further divide into four subfamilies (CC, CXC, XC, and CX3C). Chemokines interact with seven-transmembrane receptors which are typically coupled to G protein for signaling. Currently, there are ten known receptors for CC chemokines, seven for CXC chemokines, and single receptors for the XC and CX3C chemokines. In addition to these classical chemokine receptors, there exists a subfamily of atypical chemokine receptors (ACKRs) that are unable to couple to G-proteins and, instead, they preferentially mediate beta-arrestin dependent processes, such as receptor internalization, after ligand binding. The classical chemokine receptors contain a conserved DRYLAIV motif in the second intracellular loop, which is required for G-protein coupling. However, the ACKRs lack this conserved motif and fail to couple to G-proteins and induce classical GPCR signaling. Five receptors have been identified for the ACKR family, including CC-chemokine receptors like 1 and 2 (CCRL1 and CCRL2), CXCR7, Duffy antigen receptor for chemokine (DARC), and D6. Both ACKR1 (DARC) and ACKR3 (CXCR7) show low sequence homology to the classic chemokine receptors. 278 matched cddid_all.tbl CDD cd14985 cd14985 341320 7tmA_Angiotensin_R-like angiotesin receptor family and its related G protein-coupled receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes the angiotensin receptors, the bradykinin receptors, apelin receptor as well as putative G-protein coupled receptors (GPR15 and GPR25). Angiotensin II (Ang II), the main effector in the renin-angiotensin system, plays a crucial role in the regulation of cardiovascular homeostasis through its type 1 (AT1) and type 2 (AT2) receptors. Ang II contributes to cardiovascular diseases such as hypertension and atherosclerosis via AT1R activation. Ang II increases blood pressure through Gq-mediated activation of phospholipase C, resulting in phosphoinositide (PI) hydrolysis and increased intracellular calcium levels. Through the AT2 receptor, Ang II counteracts the vasoconstrictor action of AT1R and thereby induces vasodilation, sodium excretion, and reduction of blood pressure. Bradykinins (BK) are pro-inflammatory peptides that mediate various vascular and pain responses to tissue injury through its B1 and B2 receptors. Apelin (APJ) receptor binds the endogenous peptide ligands, apelin and Toddler/Elabela. APJ is an adipocyte-derived hormone that is ubiquitously expressed throughout the human body, and Toddler/Elabela is a short secretory peptide that is required for normal cardiac development in zebrafish. Activation of APJ receptor plays key roles in diverse physiological processes including vasoconstriction and vasodilation, cardiac muscle contractility, angiogenesis, and regulation of water balance and food intake. Orphan receptors, GPR15 and GPR25, share strong sequence homology to the angiotensin II type AT1 and AT2 receptors. 284 matched cddid_all.tbl CDD cd14986 cd14986 320117 7tmA_Vasopressin-like vasopressin receptors and its related G protein-coupled receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Members of this group form a subfamily within the class A G-protein coupled receptors (GPCRs), which includes the vasopressin and oxytocin receptors, the gonadotropin-releasing hormone receptors (GnRHRs), the neuropeptide S receptor (NPSR), and orphan GPR150. These receptors share significant sequence homology with each other, suggesting that they have a common evolutionary origin. Vasopressin, also known as arginine vasopressin or anti-diuretic hormone, is a neuropeptide synthesized in the hypothalamus. The actions of vasopressin are mediated by the interaction of this hormone with three tissue-specific subtypes: V1AR, V1BR, and V2R. Although vasopressin differs from oxytocin by only two amino acids, they have divergent physiological functions. Vasopressin is involved in regulating osmotic and cardiovascular homeostasis, whereas oxytocin plays an important role in the uterus during childbirth and in lactation. GnRHR, also known as luteinizing hormone releasing hormone receptor (LHRHR), plays an central role in vertebrate reproductive function; its activation by binding to GnRH leads to the release of follicle stimulating hormone (FSH) and luteinizing hormone (LH) from the pituitary gland. Neuropeptide S (NPS) promotes arousal and anxiolytic-like effects by activating its cognate receptor NPSR. NPSR has also been associated with asthma and allergy. GPR150 is an orphan receptor closely related to the oxytocin and vasopressin receptors. 295 matched cddid_all.tbl CDD cd14987 cd14987 320118 7tmA_ACKR3_CXCR7 CXC chemokine receptor 7, member of the class A family of seven-transmembrane G protein-coupled receptors. ACKR3, also known as CXCR7, is an atypical chemokine receptor for CXCL12 and CXCR11. Unlike the classical chemokine receptors, ACKR3 contains a DRYLSIT-sequence instead of the conserved DRYLAIV motif in the second intracellular loop, which is required for G-protein coupling. Thus, ACKR3 does not activate classical GPCR signaling, instead induces beta-arrestin recruitment which is leading to ligand internalization and MAP-kinase activation. It is acting as a scavenger for CXCL12 and, to a lesser degree, for CXCL11. ACKR3 is highly expressed by blood vascular endothelial cells in brain, in numerous embryonic and neonatal tissues, in inflamed tissues and in a variety of cancers such as lymphomas, sarcomas, prostate and breast cancers, and gliomas. Five receptors have been identified for the ACKR family, including CC-Chemokine Receptors like 1 and 2 (CCRL1 and CCRL2), CXCR7, DARC, and D6. Both ACKR1 (DARC) and ACKR3 (CXCR7) show low sequence homology to the classic chemokine receptors. 282 matched cddid_all.tbl CDD cd14988 cd14988 320119 7tmA_GPR182 G protein-coupled receptor 182, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR182 is an orphan G-protein coupled receptor that belongs to the class A of seven-transmembrane GPCR superfamily. When GPR182 gene was first cloned, it was proposed to encode an adrenomedullin receptor. However when the corresponding protein was expressed, it was found not to respond to adrenomedullin (ADM). All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 278 matched cddid_all.tbl CDD cd14989 cd14989 320120 7tmA_GPER1 G protein-coupled estrogen receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors. G-protein coupled estrogen receptor 1 (GPER1), also known as the G-protein coupled receptor 30 (GPR30), is a high affinity receptor for estrogen. This receptor is a member of the class A of seven-transmembrane GPCRs. Estrogen binding results in intracellular calcium mobilization and synthesis of phosphatidylinositol (3,4,5)-trisphosphate in the nucleus. GPR30 plays an important role in development of tamoxifen resistance in breast cancer cells. The distribution of GPR30 is well established in the rodent, with high expression observed in the hypothalamus, pituitary gland, adrenal medulla, kidney medulla and developing follicles of the ovary. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 276 matched cddid_all.tbl CDD cd14990 cd14990 320121 7tmA_GPR146 G protein-coupled receptor 146, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR146 is an orphan G-protein coupled receptor that belongs to the class A of seven-transmembrane GPCR superfamily. The endogenous ligand for GPR146 is not known. It has been suggested that GPR146 may be a part of the C-peptide signaling complex. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 280 matched cddid_all.tbl CDD cd14991 cd14991 320122 7tmA_HCAR-like hydroxycarboxylic acid receptors and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes the hydroxycarboxylic acid receptors (HCARs) as well as their closely related receptors, GPR31 and oxoeicosanoid receptor 1 (OXER1). HCARs are members of the class A family of G-protein coupled receptors (GPCRs). HCAR subfamily contain three receptor subtypes: HCAR1, HCAR2, and HCAR3. The endogenous ligand of HCAR1 (also known as lactate receptor 1, GPR104, or GPR81) is L-lactic acid. The endogenous ligands of HCAR2 (also known as niacin receptor 1, GPR109A, nicotinic acid receptor) and HCAR3 (also known as niacin receptor 2, orGPR109B) are 3-hydroxybutyric acid and 3-hydroxyoctanoic acid, respectively. All three HCA receptors are expressed in adipocytes, and are coupled to G(i)-proteins mediating anti-lipolytic effects in fat cells. OXER1 is a receptor for eicosanoids and polyunsaturated fatty acids such as 5-oxo-6E,8Z,11Z,14Z-eicosatetraenoic acid (5-OXO-ETE), 5(S)-hydroperoxy-6E,8Z,11Z,14Z-eicosatetraenoic acid (5(S)-HPETE) and arachidonic acid, whereas GPR31 is a high-affinity receptor for 12-(S)-hydroxy-5,8,10,14-eicosatetraenoic acid (12-S-HETE). 280 matched cddid_all.tbl CDD cd14992 cd14992 320123 7tmA_TACR_family tachykinin receptor and closely related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This subfamily includes G-protein coupled receptors for a variety of neuropeptides of the tachykinin (TK) family as well as closely related receptors. The tachykinins are widely distributed throughout the mammalian central and peripheral nervous systems and act as excitatory transmitters on neurons and cells in the gastrointestinal tract. The TKs are characterized by a common five-amino acid C-terminal sequence, Phe-X-Gly-Leu-Met-NH2, where X is a hydrophobic residue. The three major mammalian tachykinins are substance P (SP), neurokinin A (NKA), and neurokinin B (NKB). The physiological actions of tachykinins are mediated through three types of receptors: neurokinin receptor type 1 (NK1R), NK2R, and NK3R. SP is a high-affinity endogenous ligand for NK1R, which interacts with the Gq protein and activates phospholipase C, leading to elevation of intracellular calcium. NK2R is a high-affinity receptor for NKA, the tachykinin neuropeptide substance K. SP and NKA are found in the enteric nervous system and mediate in the regulation of gastrointestinal motility, secretion, vascular permeability, and pain perception. NK3R is activated by its high-affinity ligand, NKB, which is primarily involved in the central nervous system and plays a critical role in the regulation of gonadotropin hormone release and the onset of puberty. 291 matched cddid_all.tbl CDD cd14993 cd14993 320124 7tmA_CCKR-like cholecystokinin receptors and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group represents four G-protein coupled receptors that are members of the RFamide receptor family, including cholecystokinin receptors (CCK-AR and CCK-BR), orexin receptors (OXR), neuropeptide FF receptors (NPFFR), and pyroglutamylated RFamide peptide receptor (QRFPR). These RFamide receptors are activated by their endogenous peptide ligands that share a common C-terminal arginine (R) and an amidated phenylanine (F) motif. CCK-AR (type A, alimentary; also known as CCK1R) is found abundantly on pancreatic acinar cells and binds only sulfated CCK-peptides with very high affinity, whereas CCK-BR (type B, brain; also known as CCK2R), the predominant form in the brain and stomach, binds CCK or gastrin and discriminates poorly between sulfated and non-sulfated peptides. CCK is implicated in regulation of digestion, appetite control, and body weight, and is involved in neurogenesis via CCK-AR. There is some evidence to support that CCK and gastrin, via their receptors, are involved in promoting cancer development and progression, acting as growth and invasion factors. Orexins (OXs; also referred to as hypocretins) are neuropeptide hormones that regulate the sleep-wake cycle and potently influence homeostatic systems regulating appetite and feeding behavior or modulating emotional responses such as anxiety or panic. OXs are synthesized as prepro-orexin (PPO) in the hypothalamus and then proteolytically cleaved into two forms of isoforms: orexin-A (OX-A) and orexin-B (OX-B). OXA is a 33 amino-acid peptide with N-terminal pyroglutamyl residue and two intramolecular disulfide bonds, whereas OXB is a 28 amino-acid linear peptide with no disulfide bonds. OX-A binds orexin receptor 1 (OX1R) with high-affinity, but also binds with somewhat low-affinity to OX2R, and signals primarily to Gq coupling, whereas OX-B shows a strong preference for the orexin receptor 2 (OX2R) and signals through Gq or Gi/o coupling. The 26RFa, also known as QRFP (Pyroglutamylated RFamide peptide), is a 26-amino acid residue peptide that exerts similar orexigenic activity including the regulation of feeding behavior in mammals. It is the ligand for G-protein coupled receptor 103 (GPR103), which is predominantly expressed in paraventricular (PVN) and ventromedial (VMH) nuclei of the hypothalamus. GPR103 shares significant protein sequence homology with orexin receptors (OX1R and OX2R), which have recently shown to produce a neuroprotective effect in Alzheimer's disease by forming a functional heterodimer with GPR103. Neuropeptide FF (NPFF) is a mammalian octapeptide that has been implicated in a wide range of physiological functions in the brain including pain sensitivity, insulin release, food intake, memory, blood pressure, and opioid-induced tolerance and hyperalgesia. The effects of NPFF are mediated through neuropeptide FF1 and FF2 receptors (NPFF1-R and NPFF2-R) which are predominantly expressed in the brain. NPFF induces pro-nociceptive effects, mainly through the NPFF1-R, and anti-nociceptive effects, mainly through the NPFF2-R. 296 matched cddid_all.tbl CDD cd14994 cd14994 320125 7tmA_GPR141 orphan G protein-coupled receptor 141, member of the class A family of seven-transmembrane G protein-coupled receptors. This subgroup represents the G-protein coupled receptor 141 of unknown function. Several ESTs for GPR141 were found in marrow and cancer cells. GPR141 is a member of the rhodopsin-like, class A GPCRs, which is a widespread protein family that includes the light-sensitive rhodopsin as well as receptors for biogenic amines, lipids, nucleotides, odorants, peptide hormones, and a variety of other ligands. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 275 matched cddid_all.tbl CDD cd14995 cd14995 320126 7tmA_TRH-R thyrotropin-releasing hormone receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. TRH-R is a member of the class A rhodopsin-like G protein-coupled receptors, which binds the tripeptide thyrotropin releasing hormone. The TRH-R activates phosphoinositide metabolism through a pertussis-toxin-insensitive G-protein, the G(q)/G(11) class. TRH stimulates the synthesis and release of thyroid-stimulating hormone in the anterior pituitary. TRH is produced in many other tissues, especially within the nervous system, where it appears to act as a neurotransmitter/neuromodulator. It also stimulates the synthesis and release of prolactin. In the CNS, TRH stimulates a number of behavioral and pharmacological actions, including increased turnover of catecholamines in the nucleus accumbens. There are two thyrotropin-releasing hormone receptors in some mammals, thyrotropin-releasing hormone receptor 1 (TRH1) which has been found in a number of species including rat, mouse, and human and thyrotropin-releasing hormone receptor 2 (TRH2) which has, only been found in rodents. These TRH receptors are found in high levels in the anterior pituitary, and are also found in the retina and in certain areas of the brain. 269 matched cddid_all.tbl CDD cd14996 cd14996 320127 7tmA_GPR82 orphan G protein-coupled receptor 82, member of the class A family of seven-transmembrane G protein-coupled receptors. This subgroup represents the G-protein coupled receptor 82 of unknown function. GPR82 is a member of the rhodopsin-like, class A GPCRs, which is a widespread protein family that includes the light-sensitive rhodopsin as well as receptors for biogenic amines, lipids, nucleotides, odorants, peptide hormones, and a variety of other ligands. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 305 matched cddid_all.tbl CDD cd14997 cd14997 320128 7tmA_ETH-R ecdysis-triggering hormone receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. This subgroup represents the ecdysis-triggering hormone receptors found in insects, which are members of the class A family of seven-transmembrane G-protein coupled receptors. Ecdysis-triggering hormones are vital regulatory signals that govern the stereotypic physiological sequence leading to cuticle shedding in insects. Thus, the ETH signaling system has been a target for the design of more sophisticated insect-selective pest control strategies. Two subtypes of ecdysis-triggering hormone receptor were identified in Drosophila melanogaster. Blood-borne ecdysis-triggering hormone (ETH) activates the behavioral sequence through direct actions on the central nervous system. In insects, ecdysis is thought to be controlled by the interaction between peptide hormones; in particular between ecdysis-triggering hormone (ETH) from the periphery and eclosion hormone (EH) and crustacean cardioactive peptide (CCAP) from the central nervous system. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 294 matched cddid_all.tbl CDD cd14998 cd14998 320129 7tmA_GPR153_GPR162-like orphan G protein-coupled receptors 153 and 162, member of the class A family of seven-transmembrane G protein-coupled receptors. This group contains the G-protein coupled receptor 153 (GPR153), GPR162, and similar proteins. These are orphan GCPRs with unknown endogenous ligand and function. GPR153 and GPR163 are widely expressed in the central nervous system (CNS) and share a common evolutionary ancestor due to a gene duplication event. Although categorized as members of the rhodopsin-like class A GPCRs, both GPR162 and GPR153 contain an HRM-motif instead of the highly conserved Asp-Arg-Tyr (DRY) motif found in the third transmembrane helix (TM3) of class A receptors which is important for efficient G protein-coupled signal transduction. Moreover, the LPxF motif, a variant of NPxxY motif that plays a crucial role during receptor activation, is found at the end of TM7 in both GPR162 and GPR153. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 301 matched cddid_all.tbl CDD cd14999 cd14999 320130 7tmA_UII-R urotensin-II receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. The urotensin-II receptor (UII-R, also known as the hypocretin receptor) is a member of the class A rhodopsin-like G-protein coupled receptors, which binds the peptide hormone urotensin-II. Urotensin II (UII) is a vasoactive somatostatin-like or cortistatin-like peptide hormone. However, despite the apparent structural similarity to these peptide hormones, they are not homologous to UII. Urotensin II was first identified in fish spinal cord, but later found in humans and other mammals. In fish, UII is secreted at the back part of the spinal cord, in a neurosecretory centre called uroneurapophysa, and is involved in the regulation of the renal and cardiovascular systems. In mammals, urotensin II is the most potent mammalian vasoconstrictor identified to date and causes contraction of arterial blood vessels, including the thoracic aorta. The urotensin II receptor is a rhodopsin-like G-protein coupled receptor, which binds urotensin-II. The receptor was previously known as GPR14, or sensory epithelial neuropeptide-like receptor (SENR). The UII receptor is expressed in the CNS (cerebellum and spinal cord), skeletal muscle, pancreas, heart, endothelium and vascular smooth muscle. It is involved in the pathophysiological control of cardiovascular function and may also influence CNS and endocrine functions. Binding of urotensin II to the receptor leads to activation of phospholipase C, through coupling to G(q/11) family proteins. The resulting increase in intracellular calcium may cause the contraction of vascular smooth muscle. 282 matched cddid_all.tbl CDD cd15000 cd15000 320131 7tmA_BNGR-A34-like putative neuropeptide receptor BNGR-A34 and similar proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This subgroup includes putative neuropeptide receptor BNGR-A34 found in silkworm and its closely related proteins from invertebrates. They are members of the class A rhodopsin-like GPCRs, which represent a widespread protein family that includes the light-sensitive rhodopsin as well as receptors for biogenic amines, lipids, nucleotides, odorants, peptide hormones, and a variety of other ligands. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 285 matched cddid_all.tbl CDD cd15001 cd15001 320132 7tmA_GPRnna14-like GPRnna14 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes the orphan G-protein coupled receptor GPRnna14 found in body louse (Pediculus humanus humanus) as well as its closely related proteins of unknown function. These receptors are members of the class A rhodopsin-like G-protein coupled receptors. As an obligatory parasite of humans, the body louse is an important vector for human diseases, including epidemic typhus, relapsing fever, and trench fever. GPRnna14 shares significant sequence similarity with the members of the neurotensin receptor family. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 266 matched cddid_all.tbl CDD cd15002 cd15002 320133 7tmA_GPR151 G protein-coupled receptor 151, member of the class A family of seven-transmembrane G protein-coupled receptors. G-protein coupled receptor 151 (GRP151) is an orphan receptor of unknown function. Its expression is conserved in habenular axonal projections of vertebrates and may be a promising novel target for psychiatric drug development. GPR151 shows high sequence similarity with galanin receptors (GALR). GPR151 is a member of the class A rhodopsin-like GPCRs, which represent a widespread protein family that includes the light-sensitive rhodopsin as well as receptors for biogenic amines, lipids, nucleotides, odorants, peptide hormones, and a variety of other ligands. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 280 matched cddid_all.tbl CDD cd15005 cd15005 320134 7tmA_SREB-like super conserved receptor expressed in brain and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. The SREB (super conserved receptor expressed in brain) subfamily consists of at least three members, named SREB1 (GPR27), SREB2 (GPR85), and SREB3 (GPR173). They are very highly conserved G protein-coupled receptors throughout vertebrate evolution, however no endogenous ligands have yet been identified. SREB2 is greatly expressed in brain regions involved in psychiatric disorders and cognition, such as the hippocampal dentate gyrus. Genetic studies in both humans and mice have shown that SREB2 influences brain size and negatively regulates hippocampal adult neurogenesis and neurogenesis-dependent cognitive function, all of which are suggesting a potential link between SREB2 and schizophrenia. All three SREB genes are highly expressed in differentiated hippocampal neural stem cells. Furthermore, all GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 329 matched cddid_all.tbl CDD cd15006 cd15006 320135 7tmA_GPR176 orphan G protein-coupled receptor 176, member of the rhodopsin-like class A GPCR family. GPR176 is a putative G protein-coupled receptor that belongs to the class A GPCR superfamily; no endogenous ligand for GPR176 has yet been identified. The class A rhodopsin-like GPCRs represent a widespread protein family that includes the light-sensitive rhodopsin as well as receptors for biogenic amines, lipids, nucleotides, odorants, peptide hormones, and a variety of other ligands. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 289 matched cddid_all.tbl CDD cd15007 cd15007 320136 7tmA_GPR75 G protein-coupled receptor 75, member of the class A family of seven-transmembrane G protein-coupled receptors. G-protein coupled receptor 75 (GPR75) is an atypical chemokine receptor that is expressed by mouse and human islets. Although GPR75 shows low sequence homology to C-C chemokine receptors, chemokine (C-C motif) ligand 5 (CCL5) has been shown to act as an endogenous ligand for GPR75. CCL5 plays a key role in recruiting lymphocytes to sites of inflammatory and infection through promiscuous binding to the C-C chemokine G-protein-coupled receptors. Although categorized as a member of the rhodopsin-like class A GPCRs, GPR75 contains HRL-motif instead of the highly conserved Asp-Arg-Tyr (DRY) motif found in the third transmembrane helix (TM3) of class A receptors and important for efficient G protein-coupled signal transduction. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, which then activate the heterotrimeric G proteins. GPR75 is coupled to the G-protein G(q), which elevates intracellular calcium. 261 matched cddid_all.tbl CDD cd15008 cd15008 320137 7tmA_GPR19 G protein-coupled receptor 19, member of the class A family of seven-transmembrane G protein-coupled receptors. G-protein coupled receptor 19 is an orphan receptor that is expressed predominantly in neuronal cells during mouse embryogenesis. Its mRNA is found frequently over-expressed in patients with small cell lung cancer. GPR19 shares a significant amino acid sequence identity with the D2 dopamine and neuropeptide Y families of receptors. Human GPR19 gene, intronless in the coding region, also has a distribution in brain overlapping that of the D2 dopamine receptor gene, and is located on chromosome 12. GPR19 is a member of the class A family of GPCRs, which represents a widespread protein family that includes the light-sensitive rhodopsin as well as receptors for biogenic amines, lipids, nucleotides, odorants, peptide hormones, and a variety of other ligands. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 275 matched cddid_all.tbl CDD cd15010 cd15010 410631 7tmA_ACKR1_DARC Duffy antigen receptor for chemokines, member of the class A family of seven-transmembrane G protein-coupled receptors. Atypical chemokine receptor 1 (ACKR1), also known as DARC (Duffy antigen receptor for chemokines) or Fy glycoprotein (GpFy), was originally identified on erythrocytes. ACKR1 is also ubiquitously expressed by endothelial cells of venules and is highly promiscuous among all chemokine receptor. It binds many proinflammatory chemokines from both the CC and CXC subfamilies, including CCL2, CCL5, CCL7, CCL11, CXCL1, CXCL2, CXCL3, and CXCL5. Erythrocyte ACKR1 is thought to act as a chemokine sink, limiting the levels of circulating chemokines, thereby controlling leukocyte activation. ACKR1-deficient erythrocytes are shown to confer resistance to the malarial parasite, Plasmodium vivax. On the other hand, ACKR1-expressing endothelial cells can internalize chemokines. ACKR1-internalized chemokines can be moved intact across the endothelium and promotes neutrophil transmigration. Unlike the classical chemokine receptors that contain a conserved DRYLAIV motif in the second intracellular loop, which is required for G-protein coupling, the ACKRs lack this conserved motif and fail to couple to G-proteins and induce classical GPCR signaling. Five receptors have been identified for the ACKR family, including CC-Chemokine Receptors like 1 and 2 (CCRL1 and CCRL2), CXCR7, DARC, and D6. Both ACKR1 (DARC) and ACKR3 (CXCR7) show low sequence homology to the classic chemokine receptors. 257 matched cddid_all.tbl CDD cd15011 cd15011 320139 7tmA_GPR149 G protein-coupled receptor 149, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR149 is predominantly expressed in the ovary and is present at low levels in the brain and the digestive tract (stomach and small intestine). GPR149-null mice are viable and have normal maturation of the ovarian follicle, but show enhanced fertility and ovulation. Additionally, the null mice showed increased expression levels of growth differentiation factor 9 (Gdf9) in oocytes, and upregulated expression of cyclin D2, a downstream target of FSH (follicle-stimulating hormone) receptor signaling pathways that promotes granulosa cell proliferation. GPR149 is an orphan receptor with no known endogenous ligand as yet identified. Although categorized as a member of the class A GPCRs, GPR149 lacks the first two charged amino acids of the highly conserved Asp-Arg-Tyr (DRY) motif found in the third transmembrane helix (TM3) of class A receptors which is important for efficient G protein-coupled signal transduction. Moreover, the transmembrane domains and carboxyl terminus of GPR149 show low similarities to other GPCRs. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 256 matched cddid_all.tbl CDD cd15012 cd15012 320140 7tmA_Trissin_R trissin receptor and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This subgroup represents the Drosophila melanogaster trissin receptor and closely related invertebrate proteins which are a member of the class A family of seven-transmembrane G-protein coupled receptors. The cysteine-rich trissin has been shown to be an endogenous ligand for the orphan CG34381 in Drosophila melanogaster. Trissin is a peptide composed of 28 amino acids with three intrachain disulfide bonds with no significant structural similarities to known endogenous peptides. Cysteine-rich peptides are known to have antimicrobial or toxicant activities, although frequently their mechanism of action is poorly understood. Since the expression of trissin and its receptor is reported to predominantly localize to the brain and thoracicoabdominal ganglion, trissin is predicted to behave as a neuropeptide. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 277 matched cddid_all.tbl CDD cd15013 cd15013 320141 7tm_TAS2R4 mammalian taste receptor 2, subtype 4, member of the seven-transmembrane G protein-coupled receptor superfamily. This group includes the mammalian taste receptor 2 (TAS2R) subtype 4, which functions as a bitter taste receptor. The human TAS2R family contains about 25 functional members, which are glycoproteins and have the ability to form both homomeric and heteromeric receptor complexes. Five basic tastes are perceived by animals: bitter, sweet, sour, salty, and umami (the taste of glutamate, MSG). Among these, sour and salty are mediated by ion channels, while the perception of umami and sweet tastes is mediated by the TAS1R taste receptors, which belong to the class C GPCR family. The TAS2Rs in humans have a short extracellular N-terminus and the ligand binds within the transmembrane domain, whereas the TAS1Rs have a large N-terminal extracellular domain composed of the Venus flytrap module that forms the orthosteric (primary) ligand binding site. Signal transduction of bitter taste involves binding of bitter compounds to TAS2Rs linked to the alpha-subunit of gustducin, a heterotrimeric G protein expressed in taste receptor cells. This G-alpha subunit stimulates phosphodiesterase and decreases cAMP and cGMP levels. Further steps in the signaling cascade is still unknown. The beta-gamma-subunit of gustducin also mediates bitter taste transduction by activating phospholipase C, which leads to an increased formation of IP3 (inositol triphosphate) and DAG (diacylglycerol), thereby causing release of Ca2+ from intracellular stores and enhanced neurotransmitter release. 286 matched cddid_all.tbl CDD cd15014 cd15014 320142 7tm_TAS2R40 mammalian taste receptor 2, subtype 40, member of the seven-transmembrane G-protein coupled receptor superfamily. This group includes the mammalian taste receptor 2 (T2R) subtype 40, which functions as a bitter taste receptor. The human TAS2R family contains about 25 functional members, which are glycoproteins and have the ability to form both homomeric and heteromeric receptor complexes. Five basic tastes are perceived by animals: bitter, sweet, sour, salty, and umami (taste of glutamate MSG). Among these, sour and salty are mediated by ion channels, while the perception of umami and sweet tastes is mediated by the TAS1R taste receptors, which belong to the class C GPCR family. The TAS2Rs in humans have a short extracellular N-terminus and the ligand binds within the transmembrane domain, whereas the TAS1Rs have a large N-terminal extracellular domain composed of the Venus flytrap module that forms the orthosteric (primary) ligand binding site. Signal transduction of bitter taste involves binding of bitter compounds to TAS2Rs linked to the alpha-subunit of gustducin, a heterotrimeric G protein expressed in taste receptor cells. This G-alpha subunit stimulates phosphodiesterase and decreases cAMP and cGMP levels. Further steps in the signaling cascade is still unknown. The beta-gamma-subunit of gustducin also mediates bitter taste transduction by activating phospholipase C, which leads to an increased formation of IP3 (inositol triphosphate) and DAG (diacylglycerol), thereby causing release of Ca2+ from intracellular stores and enhanced neurotransmitter release. 290 matched cddid_all.tbl CDD cd15015 cd15015 320143 7tm_TAS2R39 mammalian taste receptor 2, subtype 39, member of the seven-transmembrane G protein-coupled receptor superfamily. This group includes the mammalian taste receptor 2 (T2R) subtype 39, which functions as a bitter taste receptor. The human TAS2R family contains about 25 functional members, which are glycoproteins and have the ability to form both homomeric and heteromeric receptor complexes. Five basic tastes are perceived by animals: bitter, sweet, sour, salty, and umami (taste of glutamate MSG). Among these, sour and salty are mediated by ion channels, while the perception of umami and sweet tastes is mediated by the TAS1R taste receptors, which belong to the class C GPCR family. The TAS2Rs in humans have a short extracellular N-terminus and the ligand binds within the transmembrane domain, whereas the TAS1Rs have a large N-terminal extracellular domain composed of the Venus flytrap module that forms the orthosteric (primary) ligand binding site. Signal transduction of bitter taste involves binding of bitter compounds to TAS2Rs linked to the alpha-subunit of gustducin, a heterotrimeric G protein expressed in taste receptor cells. This G-alpha subunit stimulates phosphodiesterase and decreases cAMP and cGMP levels. Further steps in the signaling cascade is still unknown. The beta-gamma-subunit of gustducin also mediates bitter taste transduction by activating phospholipase C, which leads to an increased formation of IP3 (inositol triphosphate) and DAG (diacylglycerol), thereby causing release of Ca2+ from intracellular stores and enhanced neurotransmitter release. 289 matched cddid_all.tbl CDD cd15016 cd15016 320144 7tm_TAS2R1 mammalian taste receptor 2, subtype 1, member of the seven-transmembrane G protein-coupled receptor superfamily. This group includes the mammalian taste receptor 2 (TAS2R) subtype 1, which functions as a bitter taste receptor. The human TAS2R family contains about 25 functional members, which are glycoproteins and have the ability to form both homomeric and heteromeric receptor complexes. Five basic tastes are perceived by animals: bitter, sweet, sour, salty, and umami (the taste of glutamate, MSG). Among these, sour and salty are mediated by ion channels, while the perception of umami and sweet tastes is mediated by the TAS1R taste receptors, which belong to the class C GPCR family. The TAS2Rs in humans have a short extracellular N-terminus and the ligand binds within the transmembrane domain, whereas the TAS1Rs have a large N-terminal extracellular domain composed of the Venus flytrap module that forms the orthosteric (primary) ligand binding site. Signal transduction of bitter taste involves binding of bitter compounds to TAS2Rs linked to the alpha-subunit of gustducin, a heterotrimeric G protein expressed in taste receptor cells. This G-alpha subunit stimulates phosphodiesterase and decreases cAMP and cGMP levels. Further steps in the signaling cascade is still unknown. The beta-gamma-subunit of gustducin also mediates bitter taste transduction by activating phospholipase C, which leads to an increased formation of IP3 (inositol triphosphate) and DAG (diacylglycerol), thereby causing release of Ca2+ from intracellular stores and enhanced neurotransmitter release. 283 matched cddid_all.tbl CDD cd15017 cd15017 320145 7tm_TAS2R16 mammalian taste receptor 2, subtype 16, member of the seven-transmembrane G protein-coupled receptor superfamily. This group includes the mammalian taste receptor 2 (TAS2R) subtype 16, which functions as a bitter taste receptor. The human TAS2R family contains about 25 functional members, which are glycoproteins and have the ability to form both homomeric and heteromeric receptor complexes. Five basic tastes are perceived by animals: bitter, sweet, sour, salty, and umami (the taste of glutamate, MSG). Among these, sour and salty are mediated by ion channels, while the perception of umami and sweet tastes is mediated by the TAS1R taste receptors, which belong to the class C GPCR family. The TAS2Rs in humans have a short extracellular N-terminus and the ligand binds within the transmembrane domain, whereas the TAS1Rs have a large N-terminal extracellular domain composed of the Venus flytrap module that forms the orthosteric (primary) ligand binding site. Signal transduction of bitter taste involves binding of bitter compounds to TAS2Rs linked to the alpha-subunit of gustducin, a heterotrimeric G protein expressed in taste receptor cells. This G-alpha subunit stimulates phosphodiesterase and decreases cAMP and cGMP levels. Further steps in the signaling cascade is still unknown. The beta-gamma-subunit of gustducin also mediates bitter taste transduction by activating phospholipase C, which leads to an increased formation of IP3 (inositol triphosphate) and DAG (diacylglycerol), thereby causing release of Ca2+ from intracellular stores and enhanced neurotransmitter release. 285 matched cddid_all.tbl CDD cd15018 cd15018 320146 7tm_TAS2R41-like mammalian taste receptor 2, subtype 41, member of the seven-transmembrane G protein-coupled receptor superfamily. This group includes the mammalian taste receptor 2 (TAS2R) subtype 41, which functions as a bitter taste receptor. Also included is the closely related TAS2R60. The human TAS2R family contains about 25 functional members, which are glycoproteins and have the ability to form both homomeric and heteromeric receptor complexes. Five basic tastes are perceived by animals: bitter, sweet, sour, salty, and umami (the taste of glutamate, MSG). Among these, sour and salty are mediated by ion channels, while the perception of umami and sweet tastes is mediated by the TAS1R taste receptors, which belong to the class C GPCR family. The TAS2Rs in humans have a short extracellular N-terminus and the ligand binds within the transmembrane domain, whereas the TAS1Rs have a large N-terminal extracellular domain composed of the Venus flytrap module that forms the orthosteric (primary) ligand binding site. Signal transduction of bitter taste involves binding of bitter compounds to TAS2Rs linked to the alpha-subunit of gustducin, a heterotrimeric G protein expressed in taste receptor cells. This G-alpha subunit stimulates phosphodiesterase and decreases cAMP and cGMP levels. Further steps in the signaling cascade is still unknown. The beta-gamma-subunit of gustducin also mediates bitter taste transduction by activating phospholipase C, which leads to an increased formation of IP3 (inositol triphosphate) and DAG (diacylglycerol), thereby causing release of Ca2+ from intracellular stores and enhanced neurotransmitter release. 290 matched cddid_all.tbl CDD cd15019 cd15019 320147 7tm_TAS2R14-like mammalian taste receptor 2, subtype 14, member of the seven-transmembrane G protein-coupled receptor superfamily. This group includes the mammalian taste receptor 2 (TAS2R) subtype 14, which functions as a bitter taste receptor. The human TAS2R family contains about 25 functional members, which are glycoproteins and have the ability to form both homomeric and heteromeric receptor complexes. Five basic tastes are perceived by animals: bitter, sweet, sour, salty, and umami (the taste of glutamate, MSG). Among these, sour and salty are mediated by ion channels, while the perception of umami and sweet tastes is mediated by the TAS1R taste receptors, which belong to the class C GPCR family. The TAS2Rs in humans have a short extracellular N-terminus and the ligand binds within the transmembrane domain, whereas the TAS1Rs have a large N-terminal extracellular domain composed of the Venus flytrap module that forms the orthosteric (primary) ligand binding site. Signal transduction of bitter taste involves binding of bitter compounds to TAS2Rs linked to the alpha-subunit of gustducin, a heterotrimeric G protein expressed in taste receptor cells. This G-alpha subunit stimulates phosphodiesterase and decreases cAMP and cGMP levels. Further steps in the signaling cascade is still unknown. The beta-gamma-subunit of gustducin also mediates bitter taste transduction by activating phospholipase C, which leads to an increased formation of IP3 (inositol triphosphate) and DAG (diacylglycerol), thereby causing release of Ca2+ from intracellular stores and enhanced neurotransmitter release. 290 matched cddid_all.tbl CDD cd15020 cd15020 320148 7tm_TAS2R3 mammalian taste receptor 2, subtype 3, member of the seven-transmembrane G protein-coupled receptor superfamily. This group includes the mammalian taste receptor 2 (TAS2R) subtype 3, which functions as a bitter taste receptor. The human TAS2R family contains about 25 functional members, which are glycoproteins and have the ability to form both homomeric and heteromeric receptor complexes. Five basic tastes are perceived by animals: bitter, sweet, sour, salty, and umami (the taste of glutamate, MSG). Among these, sour and salty are mediated by ion channels, while the perception of umami and sweet tastes is mediated by the TAS1R taste receptors, which belong to the class C GPCR family. The TAS2Rs in humans have a short extracellular N-terminus and the ligand binds within the transmembrane domain, whereas the TAS1Rs have a large N-terminal extracellular domain composed of the Venus flytrap module that forms the orthosteric (primary) ligand binding site. Signal transduction of bitter taste involves binding of bitter compounds to TAS2Rs linked to the alpha-subunit of gustducin, a heterotrimeric G protein expressed in taste receptor cells. This G-alpha subunit stimulates phosphodiesterase and decreases cAMP and cGMP levels. Further steps in the signaling cascade is still unknown. The beta-gamma-subunit of gustducin also mediates bitter taste transduction by activating phospholipase C, which leads to an increased formation of IP3 (inositol triphosphate) and DAG (diacylglycerol), thereby causing release of Ca2+ from intracellular stores and enhanced neurotransmitter release. 290 matched cddid_all.tbl CDD cd15021 cd15021 320149 7tm_TAS2R10 mammalian taste receptor 2, subtype 10, member of the seven-transmembrane G protein-coupled receptor superfamily. This group includes the mammalian taste receptor 2 (TAS2R) subtype 10, which functions as a bitter taste receptor. The human TAS2R family contains about 25 functional members, which are glycoproteins and have the ability to form both homomeric and heteromeric receptor complexes. Five basic tastes are perceived by animals: bitter, sweet, sour, salty, and umami (the taste of glutamate, MSG). Among these, sour and salty are mediated by ion channels, while the perception of umami and sweet tastes is mediated by the TAS1R taste receptors, which belong to the class C GPCR family. The TAS2Rs in humans have a short extracellular N-terminus and the ligand binds within the transmembrane domain, whereas the TAS1Rs have a large N-terminal extracellular domain composed of the Venus flytrap module that forms the orthosteric (primary) ligand binding site. Signal transduction of bitter taste involves binding of bitter compounds to TAS2Rs linked to the alpha-subunit of gustducin, a heterotrimeric G protein expressed in taste receptor cells. This G-alpha subunit stimulates phosphodiesterase and decreases cAMP and cGMP levels. Further steps in the signaling cascade is still unknown. The beta-gamma-subunit of gustducin also mediates bitter taste transduction by activating phospholipase C, which leads to an increased formation of IP3 (inositol triphosphate) and DAG (diacylglycerol), thereby causing release of Ca2+ from intracellular stores and enhanced neurotransmitter release. 285 matched cddid_all.tbl CDD cd15022 cd15022 320150 7tm_TAS2R8 mammalian taste receptor 2, subtype 8, member of the seven-transmembrane G protein-coupled receptor superfamily. This group includes the mammalian taste receptor 2 (TAS2R) subtype 8, which functions as a bitter taste receptor. The human TAS2R family contains about 25 functional members, which are glycoproteins and have the ability to form both homomeric and heteromeric receptor complexes. Five basic tastes are perceived by animals: bitter, sweet, sour, salty, and umami (the taste of glutamate, MSG). Among these, sour and salty are mediated by ion channels, while the perception of umami and sweet tastes is mediated by the TAS1R taste receptors, which belong to the class C GPCR family. The TAS2Rs in humans have a short extracellular N-terminus and the ligand binds within the transmembrane domain, whereas the TAS1Rs have a large N-terminal extracellular domain composed of the Venus flytrap module that forms the orthosteric (primary) ligand binding site. Signal transduction of bitter taste involves binding of bitter compounds to TAS2Rs linked to the alpha-subunit of gustducin, a heterotrimeric G protein expressed in taste receptor cells. This G-alpha subunit stimulates phosphodiesterase and decreases cAMP and cGMP levels. Further steps in the signaling cascade is still unknown. The beta-gamma-subunit of gustducin also mediates bitter taste transduction by activating phospholipase C, which leads to an increased formation of IP3 (inositol triphosphate) and DAG (diacylglycerol), thereby causing release of Ca2+ from intracellular stores and enhanced neurotransmitter release. 292 matched cddid_all.tbl CDD cd15023 cd15023 320151 7tm_TAS2R7-like mammalian taste receptor 2, subtypes 7 and 9, member of the seven-transmembrane G protein-coupled receptor superfamily. This group includes the mammalian taste receptor 2 (TAS2R) subtypes 7 and 9, which function as bitter taste receptors. The human TAS2R family contains about 25 functional members, which are glycoproteins and have the ability to form both homomeric and heteromeric receptor complexes. Five basic tastes are perceived by animals: bitter, sweet, sour, salty, and umami (the taste of glutamate, MSG). Among these, sour and salty are mediated by ion channels, while the perception of umami and sweet tastes is mediated by the TAS1R taste receptors, which belong to the class C GPCR family. The TAS2Rs in humans have a short extracellular N-terminus and the ligand binds within the transmembrane domain, whereas the TAS1Rs have a large N-terminal extracellular domain composed of the Venus flytrap module that forms the orthosteric (primary) ligand binding site. Signal transduction of bitter taste involves binding of bitter compounds to TAS2Rs linked to the alpha-subunit of gustducin, a heterotrimeric G protein expressed in taste receptor cells. This G-alpha subunit stimulates phosphodiesterase and decreases cAMP and cGMP levels. Further steps in the signaling cascade is still unknown. The beta-gamma-subunit of gustducin also mediates bitter taste transduction by activating phospholipase C, which leads to an increased formation of IP3 (inositol triphosphate) and DAG (diacylglycerol), thereby causing release of Ca2+ from intracellular stores and enhanced neurotransmitter release. 291 matched cddid_all.tbl CDD cd15024 cd15024 320152 7tm_TAS2R42 mammalian taste receptor 2, subtype 42, member of the seven-transmembrane G protein-coupled receptor superfamily. This group includes the mammalian taste receptor 2 (TAS2R) subtype 42, which functions as a bitter taste receptor. The human TAS2R family contains about 25 functional members, which are glycoproteins and have the ability to form both homomeric and heteromeric receptor complexes. Five basic tastes are perceived by animals: bitter, sweet, sour, salty, and umami (the taste of glutamate, MSG). Among these, sour and salty are mediated by ion channels, while the perception of umami and sweet tastes is mediated by the TAS1R taste receptors, which belong to the class C GPCR family. The TAS2Rs in humans have a short extracellular N-terminus and the ligand binds within the transmembrane domain, whereas the TAS1Rs have a large N-terminal extracellular domain composed of the Venus flytrap module that forms the orthosteric (primary) ligand binding site. Signal transduction of bitter taste involves binding of bitter compounds to TAS2Rs linked to the alpha-subunit of gustducin, a heterotrimeric G protein expressed in taste receptor cells. This G-alpha subunit stimulates phosphodiesterase and decreases cAMP and cGMP levels. Further steps in the signaling cascade is still unknown. The beta-gamma-subunit of gustducin also mediates bitter taste transduction by activating phospholipase C, which leads to an increased formation of IP3 (inositol triphosphate) and DAG (diacylglycerol), thereby causing release of Ca2+ from intracellular stores and enhanced neurotransmitter release. 288 matched cddid_all.tbl CDD cd15025 cd15025 320153 7tm_TAS2R38 mammalian taste receptor 2, subtype 38, member of the seven-transmembrane G protein-coupled receptor superfamily. This group includes the mammalian taste receptor 2 (T2R) subtype 38, which functions as a bitter taste receptor. Genetic variants of human TAS2R38 influence the ability to taste synthetic compounds 6-n-propylthiouracil (PROP) and phenylthiocarbamide (PTC). Thus, sensitivity to the bitter taste of PROP is often used as a marker for individual differences in taste perception that can affect food preferences and intake. The human TAS2R family contains about 25 functional members, which are glycoproteins and have the ability to form both homomeric and heteromeric receptor complexes. Five basic tastes are perceived by animals: bitter, sweet, sour, salty, and umami (the taste of glutamate, MSG). Among these, sour and salty are mediated by ion channels, while the perception of umami and sweet tastes is mediated by the TAS1R taste receptors, which belong to the class C GPCR family. The TAS2Rs in humans have a short extracellular N-terminus and the ligand binds within the transmembrane domain, whereas the TAS1Rs have a large N-terminal extracellular domain composed of the Venus flytrap module that forms the orthosteric (primary) ligand binding site. Signal transduction of bitter taste involves binding of bitter compounds to TAS2Rs linked to the alpha-subunit of gustducin, a heterotrimeric G protein expressed in taste receptor cells. This G-alpha subunit stimulates phosphodiesterase and decreases cAMP and cGMP levels. Further steps in the signaling cascade is still unknown. The beta-gamma-subunit of gustducin also mediates bitter taste transduction by activating phospholipase C, which leads to an increased formation of IP3 (inositol triphosphate) and DAG (diacylglycerol), thereby causing release of Ca2+ from intracellular stores and enhanced neurotransmitter release. 293 matched cddid_all.tbl CDD cd15026 cd15026 320154 7tm_TAS2R13 mammalian taste receptor 2, subtype 13, member of the seven-transmembrane G protein-coupled receptor superfamily. This group includes the mammalian taste receptor 2 (TAS2R) subtype 13, which functions as a bitter taste receptor. The human TAS2R family contains about 25 functional members, which are glycoproteins and have the ability to form both homomeric and heteromeric receptor complexes. Five basic tastes are perceived by animals: bitter, sweet, sour, salty, and umami (the taste of glutamate, MSG). Among these, sour and salty are mediated by ion channels, while the perception of umami and sweet tastes is mediated by the TAS1R taste receptors, which belong to the class C GPCR family. The TAS2Rs in humans have a short extracellular N-terminus and the ligand binds within the transmembrane domain, whereas the TAS1Rs have a large N-terminal extracellular domain composed of the Venus flytrap module that forms the orthosteric (primary) ligand binding site. Signal transduction of bitter taste involves binding of bitter compounds to TAS2Rs linked to the alpha-subunit of gustducin, a heterotrimeric G protein expressed in taste receptor cells. This G-alpha subunit stimulates phosphodiesterase and decreases cAMP and cGMP levels. Further steps in the signaling cascade is still unknown. The beta-gamma-subunit of gustducin also mediates bitter taste transduction by activating phospholipase C, which leads to an increased formation of IP3 (inositol triphosphate) and DAG (diacylglycerol), thereby causing release of Ca2+ from intracellular stores and enhanced neurotransmitter release. 287 matched cddid_all.tbl CDD cd15027 cd15027 320155 7tm_TAS2R43-like mammalian taste receptor 2, subtype 43, and related proteins, member of the seven-transmembrane G protein-coupled receptor superfamily. This group includes the mammalian taste receptor 2 (T2R) subtype 43, which functions as a bitter taste receptor. Also included are the closely related taste receptors TAS2R19, TAS2R20, TAS2R30, TAS2R31, TAS2R45 and TAS2R50. The human TAS2R family contains about 25 functional members, which are glycoproteins and have the ability to form both homomeric and heteromeric receptor complexes. Five basic tastes are perceived by animals: bitter, sweet, sour, salty, and umami (the taste of glutamate, MSG). Among these, sour and salty are mediated by ion channels, while the perception of umami and sweet tastes is mediated by the TAS1R taste receptors, which belong to the class C GPCR family. The TAS2Rs in humans have a short extracellular N-terminus and the ligand binds within the transmembrane domain, whereas the TAS1Rs have a large N-terminal extracellular domain composed of the Venus flytrap module that forms the orthosteric (primary) ligand binding site. Signal transduction of bitter taste involves binding of bitter compounds to TAS2Rs linked to the alpha-subunit of gustducin, a heterotrimeric G protein expressed in taste receptor cells. This G-alpha subunit stimulates phosphodiesterase and decreases cAMP and cGMP levels. Further steps in the signaling cascade is still unknown. The beta-gamma-subunit of gustducin also mediates bitter taste transduction by activating phospholipase C, which leads to an increased formation of IP3 (inositol triphosphate) and DAG (diacylglycerol), thereby causing release of Ca2+ from intracellular stores and enhanced neurotransmitter release. 292 matched cddid_all.tbl CDD cd15028 cd15028 320156 7tm_Opsin-1_euk proton pumping rhodopsins in fungi and algae, member of the seven-transmembrane GPCR superfamily. This subgroup represents uncharacterized proton pumping rhodopsins found in fungi and algae. They belong to the microbial rhodopsin family, also known as type I rhodopsins, consisting of the light-driven inward chloride pump halorhodopsin (HR), the outward proton pump bacteriorhodopsin (BR), the light-gated cation channel channelrhodopsin (ChR), the light-sensor activating transmembrane transducer protein sensory rhodopsin II (SRII), and the other light-driven proton pumps such as blue-light absorbing and green-light absorbing proteorhodopsins, among others. Microbial rhodopsins have been found in various single-celled microorganisms from all three domains of life, including halophile archaea, gamma-proteobacteria, cyanobacteria, fungi, and green algae. While microbial (type 1) and animal (type 2) rhodopsins have no sequence similarity with each other, they share a common architecture consisting of seven-transmembrane alpha-helices (TM) connected by extracellular loops and intracellular loops. Both types of rhodopsins consist of opsin and a covalently attached retinal (the aldehyde of vitamin A), a photoreactive chromophore, via a protonated Schiff base linkage to an amino group of lysine in the middle of the seventh transmembrane helix (TM7). Upon the absorption of light, microbial rhodopsins undergo light-induced photoisomerization of all-trans retinal into the 13-cis isomer, whereas the photoisomerization of 11-cis retinal to all-trans isomer occurs in the animal rhodopsins. While animal visual rhodopsins are activated by light to catalyze GDP/GTP exchange in the alpha subunit of the retinal G protein transducin (Gt), microbial rhodopsins do not activate G proteins, but instead can function as light-dependent ion pumps, cation channels, and sensors. 231 matched cddid_all.tbl CDD cd15029 cd15029 320157 7tm_SRI_SRII light-sensor activating transmembrane transducer protein sensory rhodopsin I and II; member of the seven-transmembrane GPCR superfamily. This subgroup includes the light-sensor activating transmembrane transducer proteins, sensory rhodopsin I (SRI) and II (SRII, also called phoborhodopsin). SRI and SRII are responsible for positive (attractive) and negative (repellent) phototaxis in halobacteria, respectively, thereby controlling the cell's directional movement in response to changes in light intensity by swimming either towards or away from the light. Both sensory rhodopsins belong to the family of microbial rhodopsins, also known as type I rhodopsins, consisting of the light-driven inward chloride pump halorhodopsin (HR), the outward proton pump bacteriorhodopsin (BR), the light-gated cation channel channelrhodopsin (ChR), and the other light-driven proton pumps such as blue-light absorbing and green-light absorbing proteorhodopsins, among others. Microbial rhodopsins have been found in various single-celled microorganisms from all three domains of life, including halophile archaea, gamma-proteobacteria, cyanobacteria, fungi, and green algae. While microbial (type 1) and animal (type 2) rhodopsins have no sequence similarity with each other, they share a common architecture consisting of seven-transmembrane alpha-helices (TM) connected by extracellular loops and intracellular loops. Both types of rhodopsins consist of opsin and a covalently attached retinal (the aldehyde of vitamin A), a photoreactive chromophore, via a protonated Schiff base linkage to an amino group of lysine in the middle of the seventh transmembrane helix (TM7). Upon the absorption of light, microbial rhodopsins undergo light-induced photoisomerization of all-trans retinal into the 13-cis isomer, whereas the photoisomerization of 11-cis retinal to all-trans isomer occurs in the animal rhodopsins. While animal visual rhodopsins are activated by light to catalyze GDP/GTP exchange in the alpha subunit of the retinal G protein transducin (Gt), microbial rhodopsins do not activate G proteins, but instead can function as light-dependent ion pumps, cation channels, and sensors. 214 matched cddid_all.tbl CDD cd15030 cd15030 320158 7tmF_SMO_homolog class F smoothened family membrane region, a homolog of frizzled receptors. This group represents smoothened (SMO), a transmembrane G protein-coupled receptor that acts as the transducer of the hedgehog (HH) signaling pathway. SMO is activated by the hedgehog (HH) family of proteins acting on the 12-transmembrane domain receptor patched (PTCH), which constitutively inhibits SMO. Thus, in the absence of HH proteins, PTCH inhibits SMO signaling. On the other hand, binding of HH to the PTCH receptor activates its internalization and degradation, thereby releasing the PTCH inhibition of SMO. This allows SMO to trigger intracellular signaling and the subsequent activation of the Gli family of zinc finger transcriptional factors and induction of HH target gene expression (PTCH, Gli1, cyclin, Bcl-2, etc). SMO is closely related to the frizzled (FZD) family of seven transmembrane-spanning proteins, which constitute a novel and separate family of G-protein coupled receptors. The FZDs are activated by the wingless/int-1 (WNT) family of secreted lipoglycoproteins and preferentially couple to stimulatory G proteins of the Gs family, which activate adenylate cyclase, but can also couple to G proteins of the Gi/Gq families. In the WNT/beta-catenin signaling pathway, the WNT ligand binds to FZD and a lipoprotein receptor-related protein (LRP) co-receptor. This leads to the stabilization and translocation of beta-catenin to the nucleus, where it induces the activation of TCF/LEF family transcription factors. The WNT and HH signaling pathways play critical roles in many developmental processes, such as cell-fate determination, cell proliferation, neural patterning, stem cell renewal, tissue homeostasis and repair, and tumorigenesis, among many others. 331 matched cddid_all.tbl CDD cd15031 cd15031 320159 7tmF_FZD3_insect class F insect frizzled subfamily 3, member of 7-transmembrane G protein-coupled receptors. This group represents subfamily 3 of the frizzled (FZD) family of seven transmembrane-spanning G protein-coupled proteins that is found in insects such as Drosophila melanogaster. This class F protein family consists of 10 isoforms (FZD1-10) in mammals. The FZDs are activated by the wingless/int-1 (WNT) family of secreted lipoglycoproteins and preferentially couple to stimulatory G proteins of the Gs family, which activate adenylate cyclase, but can also couple to G proteins of the Gi/Gq families. In the WNT/beta-catenin signaling pathway, the WNT ligand binds to FZD and a lipoprotein receptor-related protein (LRP) co-receptor. This leads to the stabilization and translocation of beta-catenin to the nucleus, where it induces the activation of TCF/LEF family transcription factors. The conserved cytoplasmic motif of FZD, Lys-Thr-X-X-X-Trp, is required for activation of the WNT/beta-catenin pathway, and for membrane localization and phosphorylation of Dsh (dishevelled) protein, a key component of the WNT pathway that relays the WNT signals from the activated receptor to downstream effector proteins. The WNT pathway plays a critical role in many developmental processes, such as cell-fate determination, cell proliferation, neural patterning, stem cell renewal, tissue homeostasis and repair, and tumorigenesis, among many others. 311 matched cddid_all.tbl CDD cd15032 cd15032 320160 7tmF_FZD6 class F frizzled subfamily 6, member of 7-transmembrane G protein-coupled receptors. This group includes subfamily 6 of the frizzled (FZD) family of seven transmembrane-spanning proteins, which constitute a novel and separate class of GPCRs, and its closely related proteins. This class F protein family consists of 10 isoforms (FZD1-10) in mammals. The FZDs are activated by the wingless/int-1 (WNT) family of secreted lipoglycoproteins and preferentially couple to stimulatory G proteins of the Gs family, which activate adenylate cyclase, but can also couple to G proteins of the Gi/Gq families. In the WNT/beta-catenin signaling pathway, the WNT ligand binds to FZD and a lipoprotein receptor-related protein (LRP) co-receptor. This leads to the stabilization and translocation of beta-catenin to the nucleus, where it induces the activation of TCF/LEF family transcription factors. The conserved cytoplasmic motif of FZD, Lys-Thr-X-X-X-Trp, is required for activation of the WNT/beta-catenin pathway, and for membrane localization and phosphorylation of Dsh (dishevelled) protein, a key component of the WNT pathway that relays the WNT signals from the activated receptor to downstream effector proteins. The WNT pathway plays a critical role in many developmental processes, such as cell-fate determination, cell proliferation, neural patterning, stem cell renewal, tissue homeostasis and repair, and tumorigenesis, among many others. 321 matched cddid_all.tbl CDD cd15033 cd15033 320161 7tmF_FZD3 class F frizzled subfamily 3, member of 7-transmembrane G protein-coupled receptors. This group includes subfamily 3 of the frizzled (FZD) family of seven transmembrane-spanning proteins, which constitute a novel and separate class of GPCRs, and its closely related proteins. This class F protein family consists of 10 isoforms (FZD1-10) in mammals. The FZDs are activated by the wingless/int-1 (WNT) family of secreted lipoglycoproteins and preferentially couple to stimulatory G proteins of the Gs family, which activate adenylate cyclase, but can also couple to G proteins of the Gi/Gq families. In the WNT/beta-catenin signaling pathway, the WNT ligand binds to FZD and a lipoprotein receptor-related protein (LRP) co-receptor. This leads to the stabilization and translocation of beta-catenin to the nucleus, where it induces the activation of TCF/LEF family transcription factors. The conserved cytoplasmic motif of FZD, Lys-Thr-X-X-X-Trp, is required for activation of the WNT/beta-catenin pathway, and for membrane localization and phosphorylation of Dsh (dishevelled) protein, a key component of the WNT pathway that relays the WNT signals from the activated receptor to downstream effector proteins. The WNT pathway plays a critical role in many developmental processes, such as cell-fate determination, cell proliferation, neural patterning, stem cell renewal, tissue homeostasis and repair, and tumorigenesis, among many others. 321 matched cddid_all.tbl CDD cd15034 cd15034 320162 7tmF_FZD1_2_7-like class F frizzled subfamilies 1, 2 and 7; member of 7-transmembrane G protein-coupled receptors. This group includes subfamilies 1, 2 and 7 of the frizzled (FZD) family of seven transmembrane-spanning proteins, which constitute a novel and separate class of G-protein coupled receptors, as well as their closely related proteins. This class F protein family consists of 10 isoforms (FZD1-10) in mammals. The FZDs are activated by the wingless/int-1 (WNT) family of secreted lipoglycoproteins and preferentially couple to stimulatory G proteins of the Gs family, which activate adenylate cyclase, but can also couple to G proteins of the Gi/Gq families. In the WNT/beta-catenin signaling pathway, the WNT ligand binds to FZD and a lipoprotein receptor-related protein (LRP) co-receptor. This leads to the stabilization and translocation of beta-catenin to the nucleus, where it induces the activation of TCF/LEF family transcription factors. The conserved cytoplasmic motif of FZD, Lys-Thr-X-X-X-Trp, is required for activation of the WNT/beta-catenin pathway, and for membrane localization and phosphorylation of Dsh (dishevelled) protein, a key component of the WNT pathway that relays the WNT signals from the activated receptor to downstream effector proteins. The WNT pathway plays a critical role in many developmental processes, such as cell-fate determination, cell proliferation, neural patterning, stem cell renewal, tissue homeostasis and repair, and tumorigenesis, among many others. 322 matched cddid_all.tbl CDD cd15035 cd15035 320163 7tmF_FZD5_FZD8-like class F frizzled subfamilies 5, 8 and related proteins; member of 7-transmembrane G protein-coupled receptors. This group includes subfamilies 5 and 8 of the frizzled (FZD) family of seven transmembrane-spanning proteins, which constitute a novel and separate class of GPCRs, as well as their closely related proteins. This class F protein family consists of 10 isoforms (FZD1-10) in mammals. The FZDs are activated by the wingless/int-1 (WNT) family of secreted lipoglycoproteins and preferentially couple to stimulatory G proteins of the Gs family, which activate adenylate cyclase, but can also couple to G proteins of the Gi/Gq families. In the WNT/beta-catenin signaling pathway, the WNT ligand binds to FZD and a lipoprotein receptor-related protein (LRP) co-receptor. This leads to the stabilization and translocation of beta-catenin to the nucleus, where it induces the activation of TCF/LEF family transcription factors. The conserved cytoplasmic motif of FZD, Lys-Thr-X-X-X-Trp, is required for activation of the WNT/beta-catenin pathway, and for membrane localization and phosphorylation of Dsh (dishevelled) protein, a key component of the WNT pathway that relays the WNT signals from the activated receptor to downstream effector proteins. The WNT pathway plays a critical role in many developmental processes, such as cell-fate determination, cell proliferation, neural patterning, stem cell renewal, tissue homeostasis and repair, and tumorigenesis, among many others. 307 matched cddid_all.tbl CDD cd15036 cd15036 320164 7tmF_FZD9 class F frizzled subfamily 9, member of 7-transmembrane G protein-coupled receptors. This group includes subfamily 9 of the frizzled (FZD) family of seven transmembrane-spanning proteins, which constitute a novel and separate class of GPCRs, and its closely related proteins. This class F protein family consists of 10 isoforms (FZD1-10) in mammals. The FZDs are activated by the wingless/int-1 (WNT) family of secreted lipoglycoproteins and preferentially couple to stimulatory G proteins of the Gs family, which activate adenylate cyclase, but can also couple to G proteins of the Gi/Gq families. In the WNT/beta-catenin signaling pathway, the WNT ligand binds to FZD and a lipoprotein receptor-related protein (LRP) co-receptor. This leads to the stabilization and translocation of beta-catenin to the nucleus, where it induces the activation of TCF/LEF family transcription factors. The conserved cytoplasmic motif of FZD, Lys-Thr-X-X-X-Trp, is required for activation of the WNT/beta-catenin pathway, and for membrane localization and phosphorylation of Dsh (dishevelled) protein, a key component of the WNT pathway that relays the WNT signals from the activated receptor to downstream effector proteins. The WNT pathway plays a critical role in many developmental processes, such as cell-fate determination, cell proliferation, neural patterning, stem cell renewal, tissue homeostasis and repair, and tumorigenesis, among many others. 320 matched cddid_all.tbl CDD cd15037 cd15037 320165 7tmF_FZD10 class F frizzled subfamily 10, member of 7-transmembrane G protein-coupled receptors. This group includes subfamily 10 of the frizzled (FZD) family of seven transmembrane-spanning proteins, which constitute a novel and separate class of GPCRs, and its closely related proteins. This class F protein family consists of 10 isoforms (FZD1-10) in mammals. The FZDs are activated by the wingless/int-1 (WNT) family of secreted lipoglycoproteins and preferentially couple to stimulatory G proteins of the Gs family, which activate adenylate cyclase, but can also couple to G proteins of the Gi/Gq families. In the WNT/beta-catenin signaling pathway, the WNT ligand binds to FZD and a lipoprotein receptor-related protein (LRP) co-receptor. This leads to the stabilization and translocation of beta-catenin to the nucleus, where it induces the activation of TCF/LEF family transcription factors. The conserved cytoplasmic motif of FZD, Lys-Thr-X-X-X-Trp, is required for activation of the WNT/beta-catenin pathway, and for membrane localization and phosphorylation of Dsh (dishevelled) protein, a key component of the WNT pathway that relays the WNT signals from the activated receptor to downstream effector proteins. The WNT pathway plays a critical role in many developmental processes, such as cell-fate determination, cell proliferation, neural patterning, stem cell renewal, tissue homeostasis and repair, and tumorigenesis, among many others. 320 matched cddid_all.tbl CDD cd15038 cd15038 320166 7tmF_FZD4 class F frizzled subfamily 4, member of 7-transmembrane G protein-coupled receptors. This group includes subfamily 4 of the frizzled (FZD) family of seven transmembrane-spanning proteins, which constitute a novel and separate class of GPCRs, and its closely related proteins. This class F protein family consists of 10 isoforms (FZD1-10) in mammals. The FZDs are activated by the wingless/int-1 (WNT) family of secreted lipoglycoproteins and preferentially couple to stimulatory G proteins of the Gs family, which activate adenylate cyclase, but can also couple to G proteins of the Gi/Gq families. In the WNT/beta-catenin signaling pathway, the WNT ligand binds to FZD and a lipoprotein receptor-related protein (LRP) co-receptor. This leads to the stabilization and translocation of beta-catenin to the nucleus, where it induces the activation of TCF/LEF family transcription factors. The conserved cytoplasmic motif of FZD, Lys-Thr-X-X-X-Trp, is required for activation of the WNT/beta-catenin pathway, and for membrane localization and phosphorylation of Dsh (dishevelled) protein, a key component of the WNT pathway that relays the WNT signals from the activated receptor to downstream effector proteins. The WNT pathway plays a critical role in many developmental processes, such as cell-fate determination, cell proliferation, neural patterning, stem cell renewal, tissue homeostasis and repair, and tumorigenesis, among many others. 304 matched cddid_all.tbl CDD cd15039 cd15039 410632 7tmB3_Methuselah-like Methuselah-like subfamily B3, member of the class B family of seven-transmembrane G protein-coupled receptors. The subfamily B3 of class B GPCRs consists of Methuselah (Mth) and its closely related proteins found in bilateria. Mth was originally identified in Drosophila as a GPCR affecting stress resistance and aging. In addition to the seven transmembrane helices, Mth contains an N-terminal extracellular domain involved in ligand binding, and a third intracellular loop (IC3) required for the specificity of G-protein coupling. Drosophila Mth mutants showed an increase in average lifespan by 35% and greater resistance to a variety of stress factors, including starvation, high temperature, and paraquat-induced oxidative toxicity. Moreover, mutations in two endogenous peptide ligands of Methuselah, Stunted A and B, showed an increased in lifespan and resistance to oxidative stress induced by dietary paraquat. These results strongly suggest that the Stunted-Methuselah system plays important roles in stress response and aging. 270 matched cddid_all.tbl CDD cd15040 cd15040 320168 7tmB2_Adhesion adhesion receptors, subfamily B2 of the class B family of seven-transmembrane G protein-coupled receptors. The B2 subfamily of class B GPCRs consists of cell-adhesion receptors with 33 members in humans and vertebrates. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing a variety of structural motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, linked to a class B seven-transmembrane domain. These include, for example, EGF (epidermal growth factor)-like domains in CD97, Celsr1 (cadherin family member), Celsr2, Celsr3, EMR1 (EGF-module-containing mucin-like hormone receptor-like 1), EMR2, EMR3, and Flamingo; two laminin A G-type repeats and nine cadherin domains in Flamingo and its human orthologs Celsr1, Celsr2 and Celsr3; olfactomedin-like domains in the latrotoxin receptors; and five or four thrombospondin type 1 repeats in BAI1 (brain-specific angiogenesis inhibitor 1), BAI2 and BAI3. Furthermore, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 253 matched cddid_all.tbl CDD cd15041 cd15041 341321 7tmB1_hormone_R The subfamily B1 of hormone receptors (secretin-like), member of the class B family seven-transmembrane G protein-coupled receptors. The B1 subfamily of class B GPCRs, also referred to as secretin-like receptor family, includes receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, glucagon, glucagon-like peptide (GLP), calcitonin gene-related peptide, parathyroid hormone (PTH), and corticotropin-releasing factor. These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. All members of this subfamily preferentially couple to G proteins of G(s) family, which positively stimulate adenylate cyclase, leading to increased intracellular cAMP formation and calcium influx. Moreover, the B1 subfamily receptors play key roles in hormone homeostasis and are promising drug targets in various human diseases including diabetes, osteoporosis, obesity, neurodegenerative conditions (Alzheimer###s and Parkinson's), cardiovascular disease, migraine, and psychiatric disorders (anxiety, depression). Furthermore, the subfamilies B2 and B3 consist of receptors that are capable of interacting with epidermal growth factors (EGF) and the Drosophila melanogaster Methuselah gene product (Mth), respectively. The class B GPCRs have been identified in all the vertebrates, from fishes to mammals, as well as invertebrates including Caenorhabditis elegans and Drosophila melanogaster, but are not present in plants, fungi, or prokaryotes. 273 matched cddid_all.tbl CDD cd15042 cd15042 320170 7tmC_Boss Bride of sevenless, member of the class C family of seven-transmembrane G protein-coupled receptors. Bride of Sevenless (Boss) is a putative Drosophila melanogaster G protein-coupled receptor that functions as a glucose-responding receptor to regulate energy metabolism. Boss is expressed predominantly in the fly's fat body, a nutrient-sensing tissue functionally analogous to the mammalian liver and adipose tissues, and in photoreceptor cells. Boss, which is expressed on the surface of R8 photoreceptor cell, binds and activates the Sevenless receptor tyrosine kinase on the neighboring R7 precursor cell. Activation of Sevenless results in phosphorylation of the Sevenless, triggering a signaling transduction cascade through Ras pathway that ultimately leads to the differentiation of the R7 precursor into a fully functional R7 photoreceptor, the last of eight photoreceptors to differentiate in each ommatidium of the developing Drosophila eye. In the absence of either of Sevenless or Boss, the R7 precursor fails to differentiate as a photoreceptor and instead develops into a non-neuronal cone cell. Moreover, Boss mutants in Drosophila showed elevated food intake, but reduced stored triglyceride levels, suggesting that Boss may play a role in regulating energy homeostasis in nutrient sensing tissues. Furthermore, GPRC5B, a mammalian Boss homolog, activates obesity-associated inflammatory signaling in adipocytes, and that the GPRC5B knockout mice showed resistance to high-fat diet-induced obesity and insulin resistance. 238 matched cddid_all.tbl CDD cd15043 cd15043 320171 7tmC_RAIG_GPRC5 retinoic acid-inducible orphan G-protein-coupled receptors; class C family of seven-transmembrane G protein-coupled receptors, group 5. Retinoic acid-inducible G-protein-coupled receptors (RAIGs), also referred to as GPCR class C group 5, are a group consisting of four orphan receptors RAIG1 (GPRC5A), RAIG2 (GPRC5B), RAIG3 (GPRC5C), and RAIG4 (GPRC5D). Unlike other members of the class C GPCRs which contain a large N-terminal extracellular domain, RAIGs have a shorter N-terminus. Thus, it is unlikely that RAIGs bind an agonist at its N-terminus domain. Instead, agonists may bind to the seven-transmembrane domain of these receptors. In addition, RAIG2 and RAIG3 contain a cleavable signal peptide whereas RAIG1 and RAIG4 do not. Although their expression is induced by retinoic acid (vitamin A analog), their biological function is not clearly understood. To date, no ligand is known for the members of RAIG family. Three receptor types (RAIG1-3) are found in vertebrates, while RAIG4 is only present in mammals. They show distinct tissue distribution with RAIG1 being primarily expressed in the lung, RAIG2 in the brain and placenta, RAIG3 in the brain, kidney and liver, and RAIG4 in the skin. RAIG1 is evolutionarily conserved from mammals to fish. RAIG1 has been to shown to act as a tumor suppressor in non-small cell lung carcinoma as well as oral squamous cell carcinoma, but it could also act as an oncogene in breast cancer, colorectal cancer, and pancreatic cancer. Studies have shown that overexpression of RAIG1 decreases intracellular cAMP levels. Moreover, knocking out RAIG1 induces the activation of the NF-kB and STAT3 signaling pathways leading to cell proliferation and resistance to apoptosis. RAIG2 (GPRC5B), a mammalian Boss (Bride of sevenless) homolog, activates obesity-associated inflammatory signaling in adipocytes, and GPRC5B knockout mice show resistance to high-fat diet-induced obesity and insulin resistance. The specific functions of RAIG3 and RAIG4 are unknown; however, they may play roles in mediating the effects of retinoic acid on embryogenesis, differentiation, and tumorigenesis through interactions with G-protein signaling pathways. 248 matched cddid_all.tbl CDD cd15044 cd15044 320172 7tmC_V2R_AA_sensing_receptor-like vomeronasal type-2 pheromone receptors, amino acid-sensing receptors and closely related proteins; member of the class C family of seven-transmembrane G protein-coupled receptors. This group is composed of vomeronasal type-2 pheromone receptors (V2Rs), a subgroup of broad-spectrum amino-acid sensing receptors including calcium-sensing receptor (CaSR) and GPRC6A, as well as their closely related proteins. Members of the V2R family of vomeronasal GPCRs are involved in detecting protein pheromones for social and sexual cues between the same species. V2Rs and G-alpha(o) protein are co-expressed in the basal layer of the vomeronasal organ (VNO), which is the sensory organ of the accessory olfactory system present in amphibians, reptiles, and non-primate mammals such as mice and rodents, but it is non-functional or absent in humans, apes, and monkeys. On the other hand, members of the V1R receptor family and G-alpha(i2) protein are co-expressed in the apical neurons of the VNO. Activation of V1R or V2R causes activation of phospholipase pathway, producing the second messengers diacylglycerol (DAG) and IP3. However, in contrast to V1Rs, V2Rs contain the long N-terminal extracellular domain, which is believed to bind pheromones. CaSR is a widely expressed GPCR that is involved in sensing small changes in extracellular levels of calcium ion to maintain a constant level of the extracellular calcium via modulating the synthesis and secretion of calcium regulating hormones, such as parathyroid hormone (PTH), in order to regulate Ca(2+)transport into or out of the extracellular fluid via kidney, intestine, and/or bone. For instance, when Ca2+ is high, CaSR downregulates PTH synthesis and secretion, leading to an increase in renal Ca2+ excretion, a decrease in intestinal Ca2+ absorption, and a reduction in release of skeletal Ca2+. GRPC6A (GPCR, class C, group 6, subtype A) is a widely expressed amino acid-sensing GPCR that is most closely related to CaSR. GPRC6A is most potently activated by the basic amino acids L-arginine, L-lysine, and L-ornithine and less potently by small aliphatic amino acids. Moreover, the receptor can be either activated or modulated by divalent cations such as Ca2+. GPRC6A is expressed in the testis, but not the ovary and specifically also binds to the osteoblast-derived hormone osteocalcin (OCN), which regulates testosterone production by the testis and male fertility independently of the hypothalamic-pituitary axis. Furthermore, GPRC6A knockout studies suggest that GRPC6A is involved in regulation of bone metabolism, male reproduction, energy homeostasis, glucose metabolism, and in activation of inflammation response, as well as prostate cancer growth and progression, among others. 251 matched cddid_all.tbl CDD cd15045 cd15045 320173 7tmC_mGluRs metabotropic glutamate receptors, member of the class C family of seven-transmembrane G protein-coupled receptors. The metabotropic glutamate receptors (mGluRs) are homodimeric class C G-protein coupled receptors which are activated by glutamate, the major excitatory neurotransmitter of the CNS. mGluRs are involved in regulating neuronal excitability and synaptic transmission via intracellular activation of second messenger signaling pathways. While the ionotropic glutamate receptor subtypes (AMPA, NMDA, and kainite) mediate fast excitatory postsynaptic transmission, mGluRs are known to mediate slower excitatory postsynaptic responses and to be involved in synaptic plasticity in the mammalian brain. In addition to seven-transmembrane helices, the class C GPCRs are characterized by a large N-terminal extracellular Venus flytrap-like domain, which is composed of two adjacent lobes separated by a cleft which binds an endogenous ligand. Moreover, they exist as either homo- or heterodimers, which are essential for their function. For instance, mGluRs form homodimers via interactions between the N-terminal Venus flytrap domains and the intermolecular disulphide bonds between cysteine residues located in the cysteine-rich domain (CRD). At least eight different subtypes of metabotropic receptors (mGluR1-8) have been identified and further classified into three groups based on their sequence homology, pharmacological properties, and signaling pathways. Group 1 (mGluR1 and mGluR5) receptors are predominantly located postsynaptically on neurons and are involved in long-term synaptic plasticity in the brain, including long-term potentiation (LTP) in the hippocampus and long-term depression (LTD) in the cerebellum. They are coupled to G(q/11) proteins, thereby activating phospholipase C to generate inositol-1,4,5-triphosphate (IP3) and diacyglycerol (DAG), which in turn lead to Ca2+ release and protein kinase C activation, respectively. Group I mGluR expression is shown to be strongly upregulated in animal models of epilepsy, brain injury, inflammatory, and neuropathic pain, as well as in patients with amyotrophic lateral sclerosis or multiple sclerosis. Group 2 (mGluR2 and mGluR3) and 3 (mGluR4, mGluR6, mGluR7, and mGluR8) receptors are predominantly localized presynaptically in the active region of neurotransmitter release. They are coupled to (Gi/o) proteins, which leads to inhibition of adenylate cyclase activity and cAMP formation, and consequently to a decrease in protein kinase A (PKA) activity. Ultimately, activation of these receptors leads to inhibition of neurotransmitter release such as glutamate and GABA via inhibition of Ca2+ channels and activation of K+ channels. Furthermore, while activation of Group 1 mGluRs increases NMDA (N-methyl-D-aspartate) receptor activity and risk of neurotoxicity, Group 2 and 3 mGluRs decrease NMDA receptor activity and prevent neurotoxicity. 253 matched cddid_all.tbl CDD cd15046 cd15046 320174 7tmC_TAS1R type 1 taste receptors, member of the class C of seven-transmembrane G protein-coupled receptors. This subfamily represents the type I taste receptors (TAS1Rs) that belongs to the class C family of G protein-coupled receptors. The functional TAS1Rs are obligatory heterodimers built from three known members, TAS1R1-3. TAS1R1 combines with TAS1R3 to form an umami taste receptor, which is responsible for the perception of savory taste, such as the food additive mono-sodium glutamate (MSG); whereas the combination of TAS1R2-TAS1R3 forms a sweet-taste receptor for sugars and D-amino acids. On the other hand, the type II taste receptors (TAS2Rs), which belong to the class A family of GPCRs, recognize bitter tasting compounds. In the case of sweet, for example, the TAS1R2-TAS1R3 heterodimer activates phospholipase C (PLC) via alpha-gustducin, a heterodimeric G protein that is involved in perception of sweet and bitter tastes. This activation leads to generation of inositol (1, 4, 5)-trisphosphate (IP3) and diacylglycerol (DAG), and consequently increases intracellular Ca2+ mobilization and activates a cation channel, TRPM5. In contrast to the TAS1R2-TAS1R3 heterodimer, TAS1R3 alone could activate adenylate cyclase leading to cAMP formation in the absence of alpha-gustducin. Each TAS1R contains a large extracellular Venus flytrap-like domain in the N-terminus, cysteine-rich domain (CRD) and seven-transmembrane (7TM) domain, which are characteristics of the class C GPCRs. The Venus flytrap-like domain shares strong sequence homology to bacterial periplasmic binding proteins and possess the orthosteric amino acid and calcium binding sites for members of the class C, including CaSR, GABA-B1, GPRC6A, mGlu, and TAS1R receptors. 253 matched cddid_all.tbl CDD cd15047 cd15047 320175 7tmC_GABA-B-like gamma-aminobutyric acid type B receptor and related proteins, member of the class C family of seven-transmembrane G protein-coupled receptors. The type B receptor for gamma-aminobutyric acid, GABA-B, is activated by its endogenous ligand GABA, the principal inhibitory neurotransmitter. The functional GABA-B receptor is an obligatory heterodimer composed of two related subunits, GABA-B1, which is primarily involved in GABA ligand binding, and GABA-B2, which is responsible for both G-protein coupling and trafficking of the heterodimer to the plasma membrane. Activation of GABA-B couples to G(i/o)-type G proteins, which in turn modulate three major downstream effectors: adenylate cyclase, voltage-sensitive Ca2+ channels, and inwardly-rectifying K+ channels. Consequently, GABA-B receptor produces slow and sustained inhibitory responses by decreased neurotransmitter release via inhibition of Ca2+ channels and by postsynaptic hyperpolarization via the activation of K+ channels through the G-protein beta-gamma dimer. The GABA-B is expressed in both pre- and postsynaptic sites of glutamatergic and GABAergic neurons in the brain where it regulates synaptic activity. Thus, the GABA-B receptor agonist, baclofen, is used to treat muscle tightness and cramping caused by spasticity in multiple sclerosis patients. Moreover, GABA-B antagonists improves cognitive performance in mammals, while GABA-B agonists suppress cognitive behavior. In most of the class C family members, the extracellular Venus-flytrap domain in the N-terminus is connected to the seven-transmembrane (7TM) via a cysteine-rich domain (CRD). However, in the GABA-B receptor, the CRD is absent in both subunits and the Venus-flytrap ligand-binding domain is directly connected to the 7TM via a 10-15 amino acids linker, suggesting that GABA-B receptor may utilize a different activation mechanism. Also included in this group are orphan receptors, GPR156 and GPR158, which are closely related to the GABA-B receptor family. 263 matched cddid_all.tbl CDD cd15048 cd15048 320176 7tmA_Histamine_H3R_H4R histamine receptor subtypes H3R and H4R, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes histamine subtypes H3R and H4R, members of the histamine receptor family, which belong to the class A of GPCRs. Histamine plays a key role as chemical mediator and neurotransmitter in various physiological and pathophysiological processes in the central and peripheral nervous system. Histamine exerts its functions by binding to four different G protein-coupled receptors (H1-H4). The H3 and H4 receptors couple to the G(i)-proteins, which leading to the inhibition of cAMP formation. The H3R receptor functions as a presynaptic autoreceptors controlling histamine release and synthesis. The H4R plays an important role in histamine-mediated chemotaxis in mast cells and eosinophils. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 296 matched cddid_all.tbl CDD cd15049 cd15049 341322 7tmA_mAChR muscarinic acetylcholine receptor subfamily, member of the class A family of seven-transmembrane G protein-coupled receptors. Muscarinic acetylcholine receptors (mAChRs) regulate the activity of many fundamental central and peripheral functions. The mAChR family consists of 5 subtypes M1-M5, which can be further divided into two major groups according to their G-protein coupling preference. The M1, M3 and M5 receptors selectively interact with G proteins of the G(q/11) family, whereas the M2 and M4 receptors preferentially link to the G(i/o) types of G proteins. Activation of mAChRs by agonist (acetylcholine) leads to a variety of biochemical and electrophysiological responses. In general, the exact nature of these responses and the subsequent physiological effects mainly depend on the molecular and pharmacological identity of the activated receptor subtype(s). All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 262 matched cddid_all.tbl CDD cd15050 cd15050 320178 7tmA_Histamine_H1R histamine subtype H1 receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes histamine receptor subtype H1R, a member of histamine receptor family, which belongs to the class A of GPCRs. Histamine plays a key role as chemical mediator and neurotransmitter in various physiological and pathophysiological processes in the central and peripheral nervous system. Histamine exerts its functions by binding to four different G protein-coupled receptors (H1-H4). H1R selectively interacts with the G(q)-type G protein that activates phospholipase C and the phosphatidylinositol pathway. Antihistamines, a widely used anti-allergy medication, act on the H1 subtype and produce drowsiness as a side effect. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 263 matched cddid_all.tbl CDD cd15051 cd15051 320179 7tmA_Histamine_H2R histamine subtype H2 receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes histamine receptor subtype H2R, a member of histamine receptor family, which belongs to the class A of GPCRs. Histamine plays a key role as chemical mediator and neurotransmitter in various physiological and pathophysiological processes in the central and peripheral nervous system. Histamine exerts its functions by binding to four different G protein-coupled receptors (H1-H4). The H2R subtype selectively interacts with the G(s)-type G protein that activates adenylate cyclase, leading to increased cAMP production and activation of Protein Kinase A. H2R is found in various tissues such as the brain, stomach, and heart. Its most prominent role is in histamine-induced gastric acid secretion. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 287 matched cddid_all.tbl CDD cd15052 cd15052 320180 7tmA_5-HT2 serotonin receptor subtype 2, member of the class A family of seven-transmembrane G protein-coupled receptors. The 5-HT2 receptors are a subfamily of serotonin receptors that bind the neurotransmitter serotonin (5HT; 5-hydroxytryptamine) in the central nervous system (CNS). The 5-HT2 subfamily is composed of three subtypes that mediate excitatory neurotransmission: 5-HT2A, 5-HT2B, and 5-HT2C. They are selectively linked to G proteins of the G(q/11) family and activate phospholipase C, which leads to activation of protein kinase C and calcium release. In the CNS, serotonin is involved in the regulation of appetite, mood, sleep, cognition, learning and memory, as well as implicated in diseases such as migraine, schizophrenia, and depression. Indeed, 5-HT2 receptors are attractive targets for a variety of psychoactive drugs, ranging from atypical antipsychotic drugs, antidepressants, and anxiolytics, which have an antagonistic action on 5-HT2 receptors, to hallucinogens, which act as agonists at postsynaptic 5-HT2 receptors. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 262 matched cddid_all.tbl CDD cd15053 cd15053 320181 7tmA_D2-like_dopamine_R D2-like dopamine receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Dopamine receptors are members of the class A G protein-coupled receptors that are involved in many neurological processes in the central nervous system (CNS). The neurotransmitter dopamine is the primary endogenous agonist for dopamine receptors. Dopamine receptors consist of at least five subtypes: D1, D2, D3, D4, and D5. The D1 and D5 subtypes are members of the D1-like family of dopamine receptors, whereas the D2, D3 and D4 subtypes are members of the D2-like family. The D1-like family receptors are coupled to G proteins of the G(s) family, which activate adenylate cyclase, causing cAMP formation and activation of protein kinase A. In contrast, activation of D2-like family receptors is linked to G proteins of the G(i) family, which inhibit adenylate cyclase. Dopamine receptors are major therapeutic targets for neurological and psychiatric disorders such as drug abuse, depression, schizophrenia, or Parkinson's disease. 263 matched cddid_all.tbl CDD cd15054 cd15054 320182 7tmA_5-HT6 serotonin receptor subtype 6, member of the class A family of seven-transmembrane G protein-coupled receptors. The 5-HT6 receptors are a subfamily of serotonin receptors that bind the neurotransmitter serotonin (5HT; 5-hydroxytryptamine) in the mammalian central nervous system (CNS). 5-HT6 receptors are selectively linked to G proteins of the G(s) family, which positively stimulate adenylate cyclase, causing cAMP formation and activation of protein kinase A. The 5-HT6 receptors mediates excitatory neurotransmission and are involved in learning and memory; thus they are promising targets for the treatment of cognitive impairment. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 267 matched cddid_all.tbl CDD cd15055 cd15055 320183 7tmA_TAARs trace amine-associated receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. The trace amine-associated receptors (TAARs) are a distinct subfamily within the class A G protein-coupled receptor family. Trace amines are endogenous amines of unknown function that have strong structural and metabolic similarity to classical monoamine neurotransmitters (serotonin, noradrenaline, adrenaline, dopamine, and histamine), which play critical roles in human and animal physiological activities such as cognition, consciousness, mood, motivation, perception, and autonomic responses. However, trace amines are found in the mammalian brain at very low concentrations compared to classical monoamines. Trace amines, including p-tyramine, beta-phenylethylamine, and tryptamine, are also thought to act as chemical messengers to exert their biological effects in vertebrates. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 285 matched cddid_all.tbl CDD cd15056 cd15056 320184 7tmA_5-HT4 serotonin receptor subtype 4, member of the class A family of seven-transmembrane G protein-coupled receptors. The 5-HT4 subtype is a member of the serotonin receptor family that belongs to the class A G protein-coupled receptors, and binds the neurotransmitter serotonin (5HT; 5-hydroxytryptamine) in the mammalian central nervous system (CNS). 5-HT4 receptors are selectively linked to G proteins of the G(s) family, which positively stimulate adenylate cyclase, causing cAMP formation and activation of protein kinase A. 5-HT4 receptor-specific agonists have been shown to enhance learning and memory in animal studies. Moreover, hippocampal 5-HT4 receptor expression has been reported to be inversely correlated with memory performance in humans. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 294 matched cddid_all.tbl CDD cd15057 cd15057 320185 7tmA_D1-like_dopamine_R D1-like family of dopamine receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Dopamine receptors are members of the class A G protein-coupled receptors that are involved in many neurological processes in the central nervous system (CNS). The neurotransmitter dopamine is the primary endogenous agonist for dopamine receptors. Dopamine receptors consist of at least five subtypes: D1, D2, D3, D4, and D5. The D1 and D5 subtypes are members of the D1-like family of dopamine receptors, whereas the D2, D3 and D4 subtypes are members of the D2-like family. The D1-like family receptors are coupled to G proteins of the G(s) family, which activate adenylate cyclase, causing cAMP formation and activation of protein kinase A. In contrast, activation of D2-like family receptors is linked to G proteins of the G(i) family, which inhibit adenylate cyclase. Dopamine receptors are major therapeutic targets for neurological and psychiatric disorders such as drug abuse, depression, schizophrenia, or Parkinson's disease. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 299 matched cddid_all.tbl CDD cd15058 cd15058 320186 7tmA_Beta_AR beta adrenergic receptors (adrenoceptors), member of the class A family of seven-transmembrane G protein-coupled receptors. The beta adrenergic receptor (beta adrenoceptor), also known as beta AR, is activated by hormone adrenaline (epinephrine) and plays important roles in regulating cardiac function and heart rate, as well as pulmonary physiology. The human heart contains three subtypes of the beta AR: beta-1 AR, beta-2 AR, and beta-3 AR. Beta-1 AR and beta-2 AR, which expressed at about a ratio of 70:30, are the major subtypes involved in modulating cardiac contractility and heart rate by positively stimulating the G(s) protein-adenylate cyclase-cAMP-PKA signaling pathway. In contrast, beta-3 AR produces negative inotropic effects by activating inhibitory G(i) proteins. The aberrant expression of beta-ARs can lead to cardiac dysfunction such as arrhythmias or heart failure. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 305 matched cddid_all.tbl CDD cd15059 cd15059 320187 7tmA_alpha2_AR alpha-2 adrenergic receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. The alpha-2 adrenergic receptors (or adrenoceptors) are a subfamily of the class A rhodopsin-like GPCRs that share a common architecture of seven transmembrane helices. This subfamily consists of three highly homologous receptor subtypes that have a key role in neurotransmitter release: alpha-2A, alpha-2B, and alpha-2C. In addition, a fourth subtype, alpha-2D is present in ray-finned fishes and amphibians, but is not found in humans. The alpha-2 receptors are found in both central and peripheral nervous system and serve to produce inhibitory functions through the G(i) proteins. Thus, the alpha-2 receptors inhibit adenylate cyclase, which decreases cAMP production and thereby decreases calcium influx during the action potential. Consequently, lowered levels of calcium will lead to a decrease in neurotransmitter release by negative feedback. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 261 matched cddid_all.tbl CDD cd15060 cd15060 320188 7tmA_tyramine_octopamine_R-like tyramine/octopamine receptor-like, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes tyramine/octopamine receptors and similar proteins found in insects and other invertebrates. Both octopamine and tyramine mediate their actions via G protein-coupled receptors (GPCRs) and are the invertebrate equivalent of vertebrate adrenergic neurotransmitters. In Drosophila, octopamine is involved in ovulation by mediating an egg release from the ovary, while a physiological role for tyramine in this process is not fully understood. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 260 matched cddid_all.tbl CDD cd15061 cd15061 320189 7tmA_tyramine_R-like tyramine receptors and similar proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes tyramine-specific receptors and similar proteins found in insects and other invertebrates. These tyramine receptors form a distinct receptor family that is phylogenetically different from the other tyramine/octopamine receptors which also found in invertebrates. Both octopamine and tyramine mediate their actions via G protein-coupled receptors (GPCRs) and are the invertebrate equivalent of vertebrate adrenergic neurotransmitters. In Drosophila, octopamine is involved in ovulation by mediating an egg release from the ovary, while a physiological role for tyramine in this process is not fully understood. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 256 matched cddid_all.tbl CDD cd15062 cd15062 320190 7tmA_alpha1_AR alpha-1 adrenergic receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. The alpha-1 adrenergic receptors (or adrenoceptors) are a subfamily of the class A rhodopsin-like GPCRs that share a common architecture of seven transmembrane helices. This subfamily consists of three highly homologous receptor subtypes that primarily mediate smooth muscle contraction: alpha-1A, alpha-1B, and alpha-1D. Activation of alpha-1 receptors by catecholamines such as norepinephrine and epinephrine couples to the G(q) protein, which then activates the phospholipase C pathway, leading to an increase in IP3 and calcium. Consequently, the elevation of intracellular calcium concentration leads to vasoconstriction in smooth muscle of blood vessels. In addition, activation of alpha-1 receptors by phenylpropanolamine (PPA) produces anorexia and may induce appetite suppression in rats. 261 matched cddid_all.tbl CDD cd15063 cd15063 320191 7tmA_Octopamine_R octopamine receptors in invertebrates, member of the class A family of seven-transmembrane G protein-coupled receptors. G-protein coupled receptor for octopamine (OA), which functions as a neurotransmitter, neurohormone, and neuromodulator in invertebrate nervous system. Octopamine (also known as beta, 4-dihydroxyphenethylamine) is an endogenous trace amine that is highly similar to norepinephrine, but lacks a hydroxyl group, and has effects on the adrenergic and dopaminergic nervous systems. Based on the pharmacological and signaling profiles, the octopamine receptors can be classified into at least two groups: OA1 receptors elevate intracellular calcium levels in muscle, whereas OA2 receptors activate adenylate cyclase and increase cAMP production. 266 matched cddid_all.tbl CDD cd15064 cd15064 320192 7tmA_5-HT1_5_7 serotonin receptor subtypes 1, 5 and 7, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes serotonin receptor subtypes 1, 5, and 7 that are activated by the neurotransmitter serotonin. The 5-HT1 and 5-HT5 receptors mediate inhibitory neurotransmission by coupling to G proteins of the G(i/o) family. The 5-HT1 receptor subfamily includes 5-HT1A, 5-HT1B, 5-HT1D, 5-HT1E, and 5-HT1F. There is no 5-HT1C receptor subtype, as it has been reclassified as 5-HT2C receptor. The 5-HT5A and 5-HT5B receptors have been cloned from rat and mouse, but only the 5-HT5A isoform has been identified in human because of the presence of premature stop codons in the human 5-HT5B gene, which prevents a functional receptor from being expressed. The 5-HT7 receptor is coupled to Gs, which positively stimulates adenylate cyclase activity, leading to increased intracellular cAMP formation and calcium influx. In the CNS, serotonin is involved in the regulation of appetite, mood, sleep, cognition, learning and memory, as well as implicated in neurologic disorders such as migraine, schizophrenia, and depression. 258 matched cddid_all.tbl CDD cd15065 cd15065 320193 7tmA_Ap5-HTB1-like serotonin receptor subtypes B1 and B2 from Aplysia californica and similar proteins; member of the class A family of seven-transmembrane G protein-coupled receptors. This subfamily includes Aplysia californica serotonin receptors Ap5-HTB1 and Ap5-HTB2, and similar proteins from bilateria including insects, mollusks, annelids, and worms. Ap5-HTB1 is one of the several different receptors for 5-hydroxytryptamine (5HT, serotonin). In Aplysia, serotonin plays important roles in a variety of behavioral and physiological processes mediated by the central nervous system. These include circadian clock, feeding, locomotor movement, cognition and memory, synaptic growth and synaptic plasticity. Both Ap5-HTB1 and Ap5-HTB2 receptors are coupled to G-proteins that stimulate phospholipase C, leading to the activation of phosphoinositide metabolism. Ap5-HTB1 is expressed in the reproductive system, whereas Ap5-HTB2 is expressed in the central nervous system. 300 matched cddid_all.tbl CDD cd15066 cd15066 320194 7tmA_DmOct-betaAR-like Drosophila melanogaster beta-adrenergic receptor-like octopamine receptors and similar receptors in bilateria; member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes Drosophila beta-adrenergic-like octopamine receptors and similar proteins. The biogenic amine octopamine is the invertebrate equivalent of vertebrate adrenergic neurotransmitters and exerts its effects through different G protein-coupled receptor types. Insect octopamine receptors are involved in the modulation of carbohydrate metabolism, muscular tension, cognition and memory. The activation of octopamine receptors mediating these actions leads to an increase in adenylate cyclase activity, thereby increasing cAMP levels. In Drosophila melanogaster, three subgroups have been classified on the basis of their structural homology and functional equivalents with vertebrate beta-adrenergic receptors: DmOctBeta1R, DmOctBeta2R, and DmOctBeta3R. 265 matched cddid_all.tbl CDD cd15067 cd15067 320195 7tmA_Dop1R2-like dopamine 1-like receptor 2 from Drosophila melanogaster and similar proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. G protein-coupled dopamine 1-like receptor 2 is expressed in Drosophila heads and it shows significant sequence similarity with vertebrate and invertebrate dopamine receptors. Although the Drosophila Dop1R2 receptor does not cluster into the D1-like structural group, it does show pharmacological properties similar to D1-like receptors. As shown in vertebrate D1-like receptors, agonist stimulation of Dop1R2 activates adenylyl cyclase to increase cAMP levels and also generates a calcium signal through stimulation of phospholipase C. 262 matched cddid_all.tbl CDD cd15068 cd15068 320196 7tmA_Adenosine_R_A2A adenosine receptor subtype A2A, member of the class A family of seven-transmembrane G protein-coupled receptors. The A2A receptor, a member of the adenosine receptor family of G protein-coupled receptors, binds adenosine as its endogenous ligand and is involved in regulating myocardial oxygen consumption and coronary blood flow. High-affinity A2A and low-affinity A2B receptors are preferentially coupled to G proteins of the stimulatory (Gs) family, which lead to activation of adenylate cyclase and thereby increasing the intracellular cAMP levels. The A2A receptor activation protects against tissue injury and acts as anti-inflammatory agent. In human skin endothelial cells, activation of A2B receptor, but not the A2A receptor, promotes angiogenesis. Alternatively, activated A2A receptor, but not the A2B receptor, promotes angiogenesis in human umbilical vein and lung microvascular endothelial cells. The A2A receptor alters cardiac contractility indirectly by modulating the anti-adrenergic effect of A1 receptor, while the A2B receptor exerts direct effects on cardiac contractile function, but does not modulate beta-adrenergic or A1 anti-adrenergic effects. 293 matched cddid_all.tbl CDD cd15069 cd15069 320197 7tmA_Adenosine_R_A2B adenosine receptor subtype 2AB, member of the class A family of seven-transmembrane G protein-coupled receptors. The A2B receptor, a member of the adenosine receptor family of G protein-coupled receptors, binds adenosine as its endogenous ligand and is involved in regulating myocardial oxygen consumption and coronary blood flow. High-affinity A2A and low-affinity A2B receptors are preferentially coupled to G proteins of the stimulatory (Gs) family, which lead to activation of adenylate cyclase and thereby increasing the intracellular cAMP levels. The A2A receptor activation protects against tissue injury and acts as anti-inflammatory agent. In human skin endothelial cells, activation of A2B receptor, but not the A2A receptor, promotes angiogenesis. Alternatively, activated A2A receptor, but not the A2B receptor, promotes angiogenesis in human umbilical vein and lung microvascular endothelial cells. The A2A receptor alters cardiac contractility indirectly by modulating the anti-adrenergic effect of A1 receptor, while the A2B receptor exerts direct effects on cardiac contractile function, but does not modulate beta-adrenergic or A1 anti-adrenergic effects. 294 matched cddid_all.tbl CDD cd15070 cd15070 320198 7tmA_Adenosine_R_A3 adenosine receptor subtype A3, member of the class A family of seven-transmembrane G protein-coupled receptors. The A3 receptor, a member of the adenosine receptor family of G protein-coupled receptors, is coupled to G proteins of the inhibitory G(i) family, which lead to inhibition of adenylate cyclase and thereby lowering the intracellular cAMP levels. The A3 receptor has a sustained protective function in the heart during cardiac ischemia and contributes to inhibition of neutrophil degranulation in neutrophil-mediated tissue injury. Moreover, activation of A3 receptor by adenosine protects astrocytes from cell death induced by hypoxia. 280 matched cddid_all.tbl CDD cd15071 cd15071 341323 7tmA_Adenosine_R_A1 adenosine receptor subtype A1, member of the class A family of seven-transmembrane G protein-coupled receptors. The adenosine A1 receptor, a member of the adenosine receptor family of G protein-coupled receptors, binds adenosine as its endogenous ligand. The A1 receptor has primarily inhibitory function on the tissues in which it is located. The A1 receptor slows metabolic activity in the brain and has a strong anti-adrenergic effects in the heart. Thus, it antagonizes beta1-adrenergic receptor-induced stimulation and thereby reduces cardiac contractility. The A1 receptor preferentially couples to G proteins of the G(i/o) family, which lead to inhibition of adenylate cyclase and thereby lowering the intracellular cAMP levels. 290 matched cddid_all.tbl CDD cd15072 cd15072 320200 7tmA_Retinal_GPR retinal G protein coupled receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. This group represents the retinal G-protein coupled receptor (RGR) found exclusively in retinal pigment epithelium (RPE) and Muller cells. RGR is a member of the class A rhodopsin-like receptor family. As with other opsins, RGR binds all-trans retinal and contains a conserved lysine reside on the seventh helix. RGR functions as a photoisomerase to catalyze the conversion of all-trans-retinal to 11-cis-retinal. Two mutations in RGR gene are found in patients with retinitis pigmentosa, indicating that RGR is essential to the visual process. 260 matched cddid_all.tbl CDD cd15073 cd15073 320201 7tmA_Peropsin retinal pigment epithelium-derived rhodopsin homolog, member of the class A family of seven-transmembrane G protein-coupled receptors. Peropsin, also known as a retinal pigment epithelium-derived rhodopsin homolog (RRH), is a visual pigment-like protein found exclusively in the apical microvilli of the retinal pigment epithelium. Peropsin belongs to the type 2 opsin family of the class A G-protein coupled receptors. Peropsin presumably plays a physiological role in the retinal pigment epithelium either by detecting light directly or monitoring the levels of retinoids, the primary light absorber in visual perception, or other pigment-related compounds in the eye. 280 matched cddid_all.tbl CDD cd15074 cd15074 320202 7tmA_Opsin5_neuropsin neuropsin (Opsin-5), member of the class A family of seven-transmembrane G protein-coupled receptors. Neuropsin, also known as Opsin-5, is a photoreceptor protein expressed in the retina, brain, testes, and spinal cord. Neuropsin belongs to the type 2 opsin family of the class A G-protein coupled receptors. Mammalian neuropsin activates Gi protein-mediated photo-transduction pathway in a UV-dependent manner, whereas, in non-mammalian vertebrates, neuropsin is involved in regulating the photoperiodic control of seasonal reproduction in birds such as quail. As with other opsins, it may also act as a retinal photoisomerase. 284 matched cddid_all.tbl CDD cd15075 cd15075 320203 7tmA_Parapinopsin non-visual parapinopsin, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes the non-visual pineal pigment, parapinopsin, which is a member of the class A of the seven transmembrane G protein-coupled receptors. Parapinopsin serves as a UV-sensitive pigment for the wavelength discrimination in the pineal-related organs of lower vertebrates such as reptiles, amphibians, and fish. Although parapinopsin is phylogenetically related to vertebrate visual pigments such as rhodopsin, which releases its retinal chromophore and bleaches, the parapinopsin photoproduct is stable and does not bleach. The vertebrate non-visual opsin family includes pinopsins, parapinopsin, VA (vertebrate ancient) opsins, and parietopsins. These non-visual opsins are expressed in various extra-retinal tissues and/or in non-rod, non-cone retinal cells. 279 matched cddid_all.tbl CDD cd15076 cd15076 320204 7tmA_SWS1_opsin short wave-sensitive 1 opsins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes Short Wave-Sensitive opsin 1 (SWS1), which mediates visual transduction in response to light at short wavelengths (ultraviolet to blue). Vertebrate cone opsins are expressed in cone photoreceptor cells of the retina and involved in mediating photopic vision, which allows color perception. The cone opsins can be classified into four classes according to their peak absorption wavelengths: SWS1 (ultraviolet sensitive), SWS2 (short wave-sensitive), MWS/LWS (medium/long wave-sensitive), and RH2 (medium wave-sensitive, rhodopsin-like opsins). Members of this group belong to the class A of the G protein-coupled receptors and possess seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. 280 matched cddid_all.tbl CDD cd15077 cd15077 320205 7tmA_SWS2_opsin short wave-sensitive 2 opsins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes Short Wave-Sensitive opsin 2 (SWS2), which mediates visual transduction in response to light at short wavelengths (violet to blue). Vertebrate cone opsins are expressed in cone photoreceptor cells of the retina and involved in mediating photopic vision, which allows color perception. The cone opsins can be classified into four classes according to their peak absorption wavelengths: SWS1 (ultraviolet sensitive), SWS2 (short wave-sensitive), MWS/LWS (medium/long wave-sensitive), and RH2 (medium wave-sensitive, rhodopsin-like opsins). Members of this group belong to the class A of the G protein-coupled receptors and possess seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. 280 matched cddid_all.tbl CDD cd15078 cd15078 320206 7tmA_Encephalopsin encephalopsins (opsin-3), member of the class A family of seven-transmembrane G protein-coupled receptors. Encephalopsin, also called Opsin-3 or Panopsin, is a mammalian extra-retinal opsin that is highly localized in the brain. It is thought to play a role in encephalic photoreception. Encephalopsin belongs to the class A of the G protein-coupled receptors and shows strong homology to the vertebrate visual opsins. 279 matched cddid_all.tbl CDD cd15079 cd15079 320207 7tmA_photoreceptors_insect insect photoreceptors R1-R6 and similar proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes the insect photoreceptors and their closely related proteins. The Drosophila eye is composed of about 800 unit eyes called ommatidia, each of which contains eight photoreceptor cells (R1-R8). The six outer photoreceptors (R1-R6) function like the vertebrate rods and are responsible for motion detection in dim light and image formation. The R1-R6 photoreceptors express a blue-absorbing pigment, Rhodopsin 1(Rh1). The inner photoreceptors (R7 and R8) are considered the equivalent of the color-sensitive vertebrate cone cells, which express a range of different pigments. The R7 photoreceptors express one of two different UV absorbing pigments, either Rh3 or Rh4. Likewise, the R8 photoreceptors express either the blue absorbing pigment Rh5 or green absorbing pigment Rh6. These photoreceptors belong the class A of the G protein-coupled receptors and possess seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. 292 matched cddid_all.tbl CDD cd15080 cd15080 381742 7tmA_MWS_opsin medium wave-sensitive opsins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes Medium Wave-Sensitive opsin, which mediates visual transduction in response to light at medium wavelengths (green). Vertebrate cone opsins are expressed in cone photoreceptor cells of the retina and involved in mediating photopic vision, which allows color perception. The cone opsins can be classified into four classes according to their peak absorption wavelengths: SWS1 (ultraviolet sensitive), SWS2 (short wave-sensitive), MWS/LWS (medium/long wave-sensitive), and RH2 (medium wave-sensitive, rhodopsin-like opsins). Members of this group belong to the class A of the G protein-coupled receptors and possess seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. 280 matched cddid_all.tbl CDD cd15081 cd15081 320209 7tmA_LWS_opsin long wave-sensitive opsins, member of the class A family of seven-transmembrane G protein-coupled receptors. Long Wave-Sensitive opsin is also called red-sensitive opsin or red cone photoreceptor pigment, which mediates visual transduction in response to light at long wavelengths. Vertebrate cone opsins are expressed in cone photoreceptor cells of the retina and involved in mediating photopic vision, which allows color perception. The cone opsins can be classified into four classes according to their peak absorption wavelengths: SWS1 (ultraviolet sensitive), SWS2 (short wave-sensitive), MWS/LWS (medium/long wave-sensitive), and RH2 (medium wave-sensitive, rhodopsin-like opsins). Members of this group belong to the class A of the G protein-coupled receptors and possess seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. 292 matched cddid_all.tbl CDD cd15082 cd15082 320210 7tmA_VA_opsin non-visual VA (vertebrate ancient) opsins, member of the class A family of seven-transmembrane G protein-coupled receptors. The vertebrate ancient (VA) opsin photopigments were originally identified in salmon and they appear to have diverged early in the evolution of vertebrate opsins. VA opsins are localized in the inner retina and the brain in teleosts. The vertebrate non-visual opsin family includes pinopsins, parapinopsin, VA (vertebrate ancient) opsins, and parietopsins. These non-visual opsins are expressed in various extraretinal tissues and/or in non-rod, non-cone retinal cells. They are thought to be involved in light-dependent physiological functions such as photo-entrainment of circadian rhythm, photoperiodicity, and body color change. The VA opsins belong the class A of the G protein-coupled receptors and possess seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. 291 matched cddid_all.tbl CDD cd15083 cd15083 320211 7tmA_Melanopsin-like vertebrate melanopsins and related opsins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group represent the Gq-coupled rhodopsin subfamily consists of melanopsins, insect photoreceptors R1-R6, invertebrate Gq opsins as well as their closely related opsins. Melanopsins (also called Opsin-4) are the primary photoreceptor molecules for non-visual functions such as the photo-entrainment of the circadian rhythm and pupillary constriction in mammals. Mammalian melanopsins are expressed only in the inner retina, whereas non-mammalian vertebrate melanopsins are localized in various extra-retinal tissues such as iris, brain, pineal gland, and skin. The outer photoreceptors (R1-R6) are the insect Drosophila equivalent to the vertebrate rods and are responsible for image formation and motion detection. The invertebrate G(q) opsins includes the arthropod and mollusk visual opsins as well as invertebrate melanopsins, which are also found in vertebrates. Arthropods possess color vision by the use of multiple opsins sensitive to different light wavelengths. Members of this subfamily belong to the class A of the G protein-coupled receptors and have seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. 291 matched cddid_all.tbl CDD cd15084 cd15084 320212 7tmA_Pinopsin non-visual pinopsins, member of the class A family of seven-transmembrane G protein-coupled receptors. Pinopsins are found in the pineal organ of birds, reptiles and amphibians, but are absent from teleosts and mammals. The vertebrate non-visual opsin family includes pinopsins, parapinopsin, VA (vertebrate ancient) opsins, and parietopsins. These non-visual opsins are expressed in various extra-retinal tissues and/or in non-rod, non-cone retinal cells. They are thought to be involved in light-dependent physiological functions such as photo-entrainment of circadian rhythm, photoperiodicity and body color change. Pinopsins belong the class A of the G protein-coupled receptors and possess seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. 295 matched cddid_all.tbl CDD cd15085 cd15085 320213 7tmA_Parietopsin non-visual parietopsins, member of the class A family of seven-transmembrane G protein-coupled receptors. Parietopsin is a non-visual green light-sensitive opsin that was initially identified in the parietal eye of lizards. The vertebrate non-visual opsin family includes pinopsins, parapinopsin, VA (vertebrate ancient) opsins, and parietopsins. These non-visual opsins are expressed in various extra-retinal tissues and/or in non-rod, non-cone retinal cells. They are thought to be involved in light-dependent physiological functions such as photo-entrainment of circadian rhythm, photoperiodicity and body color change. Parietopsin belongs to the class A of the G protein-coupled receptors and shows strong homology to the vertebrate visual opsins. 280 matched cddid_all.tbl CDD cd15086 cd15086 320214 7tmA_tmt_opsin teleost multiple tissue (tmt) opsin, member of the class A family of seven-transmembrane G protein-coupled receptors. Teleost multiple tissue (tmt) opsins are homologs of encephalopsin. Mouse encephalopsin (or panopsin) is highly expressed in the brain and testes, whereas the teleost homologs are localized to multiple tissues. The exact functions of the encephalopsins and tmt-opsins are unknown. The vertebrate non-visual opsin family includes pinopsins, parapinopsin, VA (vertebrate ancient) opsins, and parietopsins. These non-visual opsins are expressed in various extra-retinal tissues and/or in non-rod, non-cone retinal cells. They are thought to be involved in light-dependent physiological functions such as photo-entrainment of circadian rhythm, photoperiodicity and body color change. Tmt opsins belong to the class A of the G protein-coupled receptors and show strong homology to the vertebrate visual opsins. 276 matched cddid_all.tbl CDD cd15087 cd15087 320215 7tmA_NPBWR neuropeptide B/W receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Neuropeptide B/W receptor 1 and 2 are members of the class A G-protein coupled receptors that bind the neuropeptides B and W, respectively. NPBWR1 (previously known as GPR7) is expressed predominantly in cerebellum and frontal cortex, while NPBWR2 (previously known as GPR8) is located mostly in the frontal cortex and is present in human, but not in rat and mice. These receptors are suggested to be involved in the regulation of food intake, neuroendocrine function, and modulation of inflammatory pain, among many others. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 282 matched cddid_all.tbl CDD cd15088 cd15088 320216 7tmA_MCHR-like melanin concentrating hormone receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. Melanin-concentrating hormone receptor (MCHR) binds melanin concentrating hormone and is presumably involved in the neuronal regulation of food intake and energy homeostasis. Despite strong homology with somatostatin receptors, MCHR does not appear to bind somatostatin. Two MCHRs have been characterized in vertebrates, MCHR1 and MCHR2. MCHR1 is expressed in all mammals, whereas MCHR2 is only expressed in the higher order mammals, such as humans, primates, and dogs, and is not found in rodents. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 278 matched cddid_all.tbl CDD cd15089 cd15089 320217 7tmA_Delta_opioid_R opioid receptor subtype delta, member of the class A family of seven-transmembrane G protein-coupled receptors. The delta-opioid receptor binds the endogenous pentapeptide ligands such as enkephalins and produces antidepressant-like effects. The opioid receptor family is composed of four major subtypes: mu (MOP), delta (DOP), kappa (KOP) opioid receptors, and the nociceptin/orphanin FQ peptide receptor (NOP). They are distributed widely in the central nervous system and respond to classic alkaloid opiates, such as morphine and heroin, as well as to endogenous peptide ligands, which include dynorphins, enkephalins, endorphins, endomorphins, and nociceptin. Opioid receptors are coupled to inhibitory G proteins of the G(i/o) family and involved in regulating a variety of physiological functions such as pain, addiction, mood, stress, epileptic seizure, and obesity, among many others. 281 matched cddid_all.tbl CDD cd15090 cd15090 320218 7tmA_Mu_opioid_R opioid receptor subtype mu, member of the class A family of seven-transmembrane G protein-coupled receptors. The mu-opioid receptor binds endogenous opioids such as beta-endorphin and endomorphin. The opioid receptor family is composed of four major subtypes: mu (MOP), delta (DOP), kappa (KOP) opioid receptors, and the nociceptin/orphanin FQ peptide receptor (NOP). They are distributed widely in the central nervous system and respond to classic alkaloid opiates, such as morphine and heroin, as well as to endogenous peptide ligands, which include dynorphins, enkephalins, endorphins, endomorphins, and nociceptin. Opioid receptors are coupled to inhibitory G proteins of the G(i/o) family and involved in regulating a variety of physiological functions such as pain, addiction, mood, stress, epileptic seizure, and obesity, among many others. 279 matched cddid_all.tbl CDD cd15091 cd15091 320219 7tmA_Kappa_opioid_R opioid receptor subtype kappa, member of the class A family of seven-transmembrane G protein-coupled receptors. The kappa-opioid receptor binds the opioid peptide dynorphin as the primary endogenous ligand. The opioid receptor family is composed of four major subtypes: mu (MOP), delta (DOP), kappa (KOP) opioid receptors, and the nociceptin/orphanin FQ peptide receptor (NOP). They are distributed widely in the central nervous system and respond to classic alkaloid opiates, such as morphine and heroin, as well as to endogenous peptide ligands, which include dynorphins, enkephalins, endorphins, endomorphins, and nociceptin. Opioid receptors are coupled to inhibitory G proteins of the G(i/o) family and involved in regulating a variety of physiological functions such as pain, addiction, mood, stress, epileptic seizure, and obesity, among many others. 282 matched cddid_all.tbl CDD cd15092 cd15092 320220 7tmA_NOFQ_opioid_R nociceptin/orphanin FQ peptide receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. The nociceptin (NOP) receptor binds nociceptin or orphanin FQ, a 17 amino acid endogenous neuropeptide. The NOP receptor is involved in the modulation of various brain activities including instinctive and emotional behaviors. The opioid receptor family is composed of four major subtypes: mu (MOP), delta (DOP), kappa (KOP) opioid receptors, and the nociceptin/orphanin FQ peptide receptor (NOP). They are distributed widely in the central nervous system and respond to classic alkaloid opiates, such as morphine and heroin, as well as to endogenous peptide ligands, which include dynorphins, enkephalins, endorphins, endomorphins, and nociceptin. Opioid receptors are coupled to inhibitory G proteins of the G(i/o) family and involved in regulating a variety of physiological functions such as pain, addiction, mood, stress, epileptic seizure, and obesity, among many others. 279 matched cddid_all.tbl CDD cd15093 cd15093 320221 7tmA_SSTR somatostatin receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. G protein-coupled somatostatin receptors (SSTRs) are composed of five distinct subtypes (SSTR1-5) that display strong sequence similarity with opioid receptors. All five receptor subtypes bind the natural somatostatin (somatotropin release inhibiting factor), a polypeptide hormone that regulates a wide variety of physiological functions such as neurotransmission, cell proliferation, contractility of smooth muscle cells, and endocrine signaling as well as inhibition of the release of many secondary hormones. They share common signaling cascades such as inhibition of adenylyl cyclase, activation of phosphotyrosine phosphatase activity, and G-protein-dependent regulation of MAPKs. 280 matched cddid_all.tbl CDD cd15094 cd15094 320222 7tmA_AstC_insect somatostatin-like receptor for allatostatin C, member of the class A family of seven-transmembrane G protein-coupled receptors. G protein-coupled somatostatin receptors (SSTRs) are composed of five distinct subtypes (SSTR1-5) that display strong sequence similarity with opioid receptors. All five receptor subtypes bind the natural somatostatin (somatotropin release inhibiting factor), a polypeptide hormone that regulates a wide variety of physiological functions such as neurotransmission, cell proliferation, contractility of smooth muscle cells, and endocrine signaling as well as inhibition of the release of many secondary hormones. In Drosophila melanogaster and other insects, a 15-amino-acid peptide named allatostatin C(AstC) binds the somatostatin-like receptors. Two AstC receptors have been identified in Drosophila with strong sequence homology to human somatostatin and opioid receptors. 282 matched cddid_all.tbl CDD cd15095 cd15095 320223 7tmA_KiSS1R KiSS1-derived peptide (kisspeptin) receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. The G protein-coupled KiSS1-derived peptide receptor (GPR54 or kisspeptin receptor) binds the peptide hormone kisspeptin (previously known as metastin), which encoded by the metastasis suppressor gene (KISS1) expressed in various endocrine and reproductive tissues. The KiSS1 receptor is coupled to G proteins of the G(q/11) family, which lead to activation of phospholipase C and increase of intracellular calcium. This signaling cascade plays an important role in reproduction by regulating the secretion of gonadotropin-releasing hormone. 288 matched cddid_all.tbl CDD cd15096 cd15096 320224 7tmA_AstA_R_insect allatostatin-A receptor in insects, member of the class A family of seven-transmembrane G protein-coupled receptors. The G protein-coupled AstA receptor binds allatostatin A. Three distinct types of allatostatin have been identified in the insects and crustaceans: AstA, AstB, and AstC. They both inhibit the biosynthesis of juvenile hormone and exert an inhibitory influence on food intake. Therefore, allatostatins are considered as potential targets for insect control. 284 matched cddid_all.tbl CDD cd15097 cd15097 320225 7tmA_Gal2_Gal3_R galanin receptor subtypes 2 and 3, member of the class A family of seven-transmembrane G protein-coupled receptors. The G protein-coupled galanin receptors bind galanin, a neuropeptide that is widely expressed in the brain, peripheral tissues, and endocrine glands. Three receptors subtypes have been so far identified: GAL1, GAL2, and GAL3. The specific functions of each subtype remains mostly unknown, although galanin is thought to be involved in a variety of neuronal functions such as hormone release and food intake. Galanin is implicated in numerous neurological and psychiatric diseases including Alzheimer's disease, depression, eating disorders, epilepsy and stroke, among many others. 279 matched cddid_all.tbl CDD cd15098 cd15098 320226 7tmA_Gal1_R galanin receptor subtype 1, member of the class A family of seven-transmembrane G protein-coupled receptors. The G protein-coupled galanin receptors bind galanin, a neuropeptide that is widely expressed in the brain, peripheral tissues, and endocrine glands. Three receptors subtypes have been so far identified: GAL1, GAL2, and GAL3. The specific functions of each subtype remains mostly unknown, although galanin is thought to be involved in a variety of neuronal functions such as hormone release and food intake. Galanin is implicated in numerous neurological and psychiatric diseases including Alzheimer's disease, depression, eating disorders, epilepsy and stroke, among many others. 282 matched cddid_all.tbl CDD cd15099 cd15099 320227 7tmA_Cannabinoid_R cannabinoid receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Cannabinoid receptors belong to the class A G-protein coupled receptor superfamily. Two types of cannabinoid receptors, CB1 and CB2, have been identified so far. They are activated by naturally occurring endocannabinoids, cannabis plant-derived cannabinoids such as tetrahydrocannabinol, or synthetic cannabinoids. The CB receptors are involved in the various physiological processes such as appetite, mood, memory, and pain sensation. CB1 receptor is expressed predominantly in central and peripheral neurons, while CB2 receptor is found mainly in the immune system. 281 matched cddid_all.tbl CDD cd15100 cd15100 320228 7tmA_GPR3_GPR6_GPR12-like G protein-coupled receptors 3, 6, 12, and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR3, GPR6, and GPR12 form a subfamily of constitutively active G-protein coupled receptors with dual coupling to G(s) and G(i) proteins. These three orphan receptors are involved in the regulation of cell proliferation and survival, neurite outgrowth, cell clustering, and maintenance of meiotic prophase arrest. They constitutively activate adenylate cyclase to a similar degree as that seen with fully activated G(s)-coupled receptors, and are also able to constitutively activate inhibitory G(i/o) proteins. Lysophospholipids such as sphingosine 1-phosphate (S1P) and sphingosylphosphorylcholine have been detected as the high-affinity ligands for Gpr6 and Gpr12, respectively, which show high sequence homology with GPR3. Also included in this subfamily is GPRx, also known as GPR185, which involved in the maintenance of meiotic arrest in frog oocytes. 268 matched cddid_all.tbl CDD cd15101 cd15101 341325 7tmA_LPAR lysophosphatidic acid receptor subfamily, member of the class A family of seven-transmembrane G protein-coupled receptors. The endothelial differentiation gene (Edg) family of G-protein coupled receptors binds blood borne lysophospholipids including sphingosine-1-phosphate (S1P) and lysophosphatidic acid (LPA), which are involved in the regulation of cell proliferation, survival, migration, invasion, endothelial cell shape change and cytoskeletal remodeling. The Edg receptors are classified into two subfamilies: the lysophosphatidic acid subfamily that includes LPA1 (Edg2), LPA2 (Edg4), and LPA3 (Edg7); and the S1P subfamily that includes S1P1 (Edg1), S1P2 (Edg5), S1P3 (Edg3), S1P4 (Edg6), and S1P5 (Edg8). The Edg receptors couple and activate at least three different G protein subtypes including G(i/o), G(q/11), and G(12/13). 274 matched cddid_all.tbl CDD cd15102 cd15102 320230 7tmA_S1PR sphingosine-1-phosphate receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. The endothelial differentiation gene (Edg) family of G-protein coupled receptors binds blood borne lysophospholipids including sphingosine-1-phosphate (S1P) and lysophosphatidic acid (LPA), which are involved in the regulation of cell proliferation, survival, migration, invasion, endothelial cell shape change and cytoskeletal remodeling. The Edg receptors are classified into two subfamilies: the lysophosphatidic acid subfamily that includes LPA1 (Edg2), LPA2 (Edg4), and LPA3 (Edg7); and the S1P subfamily that includes S1P1 (Edg1), S1P2 (Edg5), S1P3 (Edg3), S1P4 (Edg6), and S1P5 (Edg8). The Edg receptors couple and activate at least three different G protein subtypes including G(i/o), G(q/11), and G(12/13). 270 matched cddid_all.tbl CDD cd15103 cd15103 320231 7tmA_MCR melanocortin receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. The melanocortin receptor (MCR) subfamily is a member of the class A family of seven-transmembrane G-protein coupled receptors. MCRs bind a group of pituitary peptide hormones known as melanocortins, which include adrenocorticotropic hormone (ACTH) and the different isoforms of melanocyte-stimulating hormones. There are five known subtypes of the MCR subfamily. MC1R is involved in regulating skin pigmentation and hair color. ACTH (adrenocorticotropic hormone) is the only endogenous ligand for MC2R, which shows low sequence similarity with other melanocortin receptors. Mutations in MC2R cause familial glucocorticoid deficiency type 1, in which patients have elevated plasma ACTH and low cortisol levels. MC3R is expressed in many parts of the brain and peripheral tissues and involved in the regulation of energy homeostasis. MC4R is expressed primarily in the central nervous system and involved in both eating behavior and sexual function. MC5R is widely expressed in peripheral tissues and is mainly involved in the regulation of exocrine gland function. 270 matched cddid_all.tbl CDD cd15104 cd15104 320232 7tmA_GPR119_R_insulinotropic_receptor G protein-coupled receptor 119, also called glucose-dependent insulinotropic receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR119 is activated by oleoylethanolamide (OEA), a naturally occurring bioactive lipid with hypophagic and anti-obesity effects. Immunohistochemistry and double-immunofluorescence studies revealed the predominant GPR119 localization in pancreatic polypeptide (PP)-cells of islets. In addition, GPR119 expression is elevated in islets of obese hyperglycemic mice as compared to control islets, suggesting a possible involvement of this receptor in the development of obesity and diabetes. GPR119 has a significant sequence similarity with the members of the endothelial differentiation gene family. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 283 matched cddid_all.tbl CDD cd15105 cd15105 320233 7tmA_MrgprA mas-related G protein-coupled receptor subtype A, member of the class A family of seven-transmembrane G protein-coupled receptors. The Mas-related G-protein coupled receptor (Mrgpr) family constitutes a group of orphan receptors exclusively expressed in nociceptive primary sensory neurons and mast cells in the skin. Members of the Mrgpr family have been implicated in the modulation of nociception, pruritus (itching), and mast cell degranulation. The Mrgpr family in rodents and humans contains more than 50 members that can be grouped into 9 distinct subfamilies: MrgprA, B, C (MrgprX1), D, E, F, G, H (GPR90), and the primate-specific MrgprX subfamily. Some Mrgprs can be activated by endogenous ligands such as beta-alanine, adenine (a cell metabolite and potential transmitter), RF-amide related peptides, or salusin-beta (a bioactive peptide). However, the effects of these agonists are not clearly understood, and the physiological role of the individual receptor family members remains to be determined. 276 matched cddid_all.tbl CDD cd15106 cd15106 320234 7tmA_MrgprX-like primate-specific mas-related G protein-coupled receptor subtype X-like, member of the class A family of seven-transmembrane G protein-coupled receptors. The Mas-related G-protein coupled receptor (Mrgpr) family constitutes a group of orphan receptors exclusively expressed in nociceptive primary sensory neurons and mast cells in the skin. Members of the Mrgpr family have been implicated in the modulation of nociception, pruritus (itching), and mast cell degranulation. The Mrgpr family in rodents and humans contains more than 50 members that can be grouped into 9 distinct subfamilies: MrgprA, B, C (MrgprX1), D, E, F, G, H (GPR90), and the primate-specific MrgprX subfamily. Some Mrgprs can be activated by endogenous ligands such as beta-alanine, adenine (a cell metabolite and potential transmitter), RF-amide related peptides, or salusin-beta (a bioactive peptide). However, the effects of these agonists are not clearly understood, and the physiological role of the individual receptor family members remains to be determined. 274 matched cddid_all.tbl CDD cd15107 cd15107 320235 7tmA_MrgprB mas-related G protein-coupled receptor subtype B, member of the class A family of seven-transmembrane G protein-coupled receptors. The Mas-related G-protein coupled receptor (Mrgpr) family constitutes a group of orphan receptors exclusively expressed in nociceptive primary sensory neurons and mast cells in the skin. Members of the Mrgpr family have been implicated in the modulation of nociception, pruritus (itching), and mast cell degranulation. The Mrgpr family in rodents and humans contains more than 50 members that can be grouped into 9 distinct subfamilies: MrgprA, B, C (MrgprX1), D, E, F, G, H (GPR90), and the primate-specific MrgprX subfamily. Some Mrgprs can be activated by endogenous ligands such as beta-alanine, adenine (a cell metabolite and potential transmitter), RF-amide related peptides, or salusin-beta (a bioactive peptide). However, the effects of these agonists are not clearly understood, and the physiological role of the individual receptor family members remains to be determined. 276 matched cddid_all.tbl CDD cd15108 cd15108 320236 7tmA_MrgprD mas-related G protein-coupled receptor subtype D, member of the class A family of seven-transmembrane G protein-coupled receptors. The Mas-related G-protein coupled receptor (Mrgpr) family constitutes a group of orphan receptors exclusively expressed in nociceptive primary sensory neurons and mast cells in the skin. Members of the Mrgpr family have been implicated in the modulation of nociception, pruritus (itching), and mast cell degranulation. The Mrgpr family in rodents and humans contains more than 50 members that can be grouped into 9 distinct subfamilies: MrgprA, B, C (MrgprX1), D, E, F, G, H (GPR90), and the primate-specific MrgprX subfamily. Some Mrgprs can be activated by endogenous ligands such as beta-alanine, adenine (a cell metabolite and potential transmitter), RF-amide related peptides, or salusin-beta (a bioactive peptide). However, the effects of these agonists are not clearly understood, and the physiological role of the individual receptor family members remains to be determined. 276 matched cddid_all.tbl CDD cd15109 cd15109 320237 7tmA_MrgprF mas-related G protein-coupled receptor subtype F, member of the class A family of seven-transmembrane G protein-coupled receptors. The Mas-related G-protein coupled receptor (Mrgpr) family constitutes a group of orphan receptors exclusively expressed in nociceptive primary sensory neurons and mast cells in the skin. Members of the Mrgpr family have been implicated in the modulation of nociception, pruritus (itching), and mast cell degranulation. The Mrgpr family in rodents and humans contains more than 50 members that can be grouped into 9 distinct subfamilies: MrgprA, B, C (MrgprX1), D, E, F, G, H (GPR90), and the primate-specific MrgprX subfamily. Some Mrgprs can be activated by endogenous ligands such as beta-alanine, adenine (a cell metabolite and potential transmitter), RF-amide related peptides, or salusin-beta (a bioactive peptide). However, the effects of these agonists are not clearly understood, and the physiological role of the individual receptor family members remains to be determined. 274 matched cddid_all.tbl CDD cd15110 cd15110 320238 7tmA_MrgprH mas-related G protein-coupled receptor subtype H, member of the class A family of seven-transmembrane G protein-coupled receptors. The Mas-related G-protein coupled receptor (Mrgpr) family constitutes a group of orphan receptors exclusively expressed in nociceptive primary sensory neurons and mast cells in the skin. Members of the Mrgpr family have been implicated in the modulation of nociception, pruritus (itching), and mast cell degranulation. The Mrgpr family in rodents and humans contains more than 50 members that can be grouped into 9 distinct subfamilies: MrgprA, B, C (MrgprX1), D, E, F, G, H (GPR90), and the primate-specific MrgprX subfamily. Some Mrgprs can be activated by endogenous ligands such as beta-alanine, adenine (a cell metabolite and potential transmitter), RF-amide related peptides, or salusin-beta (a bioactive peptide). However, the effects of these agonists are not clearly understood, and the physiological role of the individual receptor family members remains to be determined. 274 matched cddid_all.tbl CDD cd15111 cd15111 320239 7tmA_MrgprG mas-related G protein-coupled receptor subtype G, member of the class A family of seven-transmembrane G protein-coupled receptors. The Mas-related G-protein coupled receptor (Mrgpr) family constitutes a group of orphan receptors exclusively expressed in nociceptive primary sensory neurons and mast cells in the skin. Members of the Mrgpr family have been implicated in the modulation of nociception, pruritus (itching), and mast cell degranulation. The Mrgpr family in rodents and humans contains more than 50 members that can be grouped into 9 distinct subfamilies: MrgprA, B, C (MrgprX1), D, E, F, G, H (GPR90), and the primate-specific MrgprX subfamily. Some Mrgprs can be activated by endogenous ligands such as beta-alanine, adenine (a cell metabolite and potential transmitter), RF-amide related peptides, or salusin-beta (a bioactive peptide). However, the effects of these agonists are not clearly understood, and the physiological role of the individual receptor family members remains to be determined. 263 matched cddid_all.tbl CDD cd15112 cd15112 320240 7tmA_MrgprE mas-related G protein-coupled receptor subtype E, member of the class A family of seven-transmembrane G protein-coupled receptors. The Mas-related G-protein coupled receptor (Mrgpr) family constitutes a group of orphan receptors exclusively expressed in nociceptive primary sensory neurons and mast cells in the skin. Members of the Mrgpr family have been implicated in the modulation of nociception, pruritus (itching), and mast cell degranulation. The Mrgpr family in rodents and humans contains more than 50 members that can be grouped into 9 distinct subfamilies: MrgprA, B, C (MrgprX1), D, E, F, G, H (GPR90), and the primate-specific MrgprX subfamily. Some Mrgprs can be activated by endogenous ligands such as beta-alanine, adenine (a cell metabolite and potential transmitter), RF-amide related peptides, or salusin-beta (a bioactive peptide). However, the effects of these agonists are not clearly understood, and the physiological role of the individual receptor family members remains to be determined. 272 matched cddid_all.tbl CDD cd15113 cd15113 320241 7tmA_MAS1L mas-related G protein-coupled receptor 1-like (MAS1L), member of the class A family of seven-transmembrane G protein-coupled receptors. MAS1L is also called MAS1 oncogene-like (MAS1-like) or mas-related G-protein coupled receptor MRG. MAS1L is a G protein-coupled receptor that only found in primates. The angiotensin-II metabolite angiotensin is an endogenous ligand for MAS1L. The Mas-related G-protein coupled receptor (Mrgpr) family constitutes a group of orphan receptors exclusively expressed in nociceptive primary sensory neurons and mast cells in the skin. Members of the Mrgpr family have been implicated in the modulation of nociception, pruritus (itching), and mast cell degranulation. The Mrgpr family in rodents and humans contains more than 50 members that can be grouped into 9 distinct subfamilies: MrgprA, B, C (MrgprX1), D, E, F, G, H (GPR90), and the primate-specific MrgprX subfamily. Some Mrgprs can be activated by endogenous ligands such as beta-alanine, adenine (a cell metabolite and potential transmitter), RF-amide related peptides, or salusin-beta (a bioactive peptide). However, the effects of these agonists are not clearly understood, and the physiological role of the individual receptor family members remains to be determined. 265 matched cddid_all.tbl CDD cd15114 cd15114 320242 7tmA_C5aR complement component 5a anaphylatoxin chemotactic receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. The anaphylatoxin receptors are a group of G-protein coupled receptors which bind anaphylatoxins; members of this group include C3a receptors and C5a receptors. Anaphylatoxins are also known as complement peptides (C3a, C4a and C5a) that are produced from the activation of the complement system cascade. These complement anaphylatoxins can trigger degranulation of endothelial cells, mast cells, or phagocytes, which induce a local inflammatory response and stimulate smooth muscle cell contraction, histamine release, and increased vascular permeability. They are potent mediators involved in chemotaxis, inflammation, and generation of cytotoxic oxygen-derived free radicals. In humans, a single receptor for C3a (C3AR1) and two receptors for C5a (C5AR1 and C5AR2, also known as C5L2 or GPR77) have been identified, but there is no known receptor for C4a. 274 matched cddid_all.tbl CDD cd15115 cd15115 320243 7tmA_C3aR complement component 3a anaphylatoxin chemotactic receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. The anaphylatoxin receptors are a group of G-protein coupled receptors which bind anaphylatoxins; members of this group include C3a receptors and C5a receptors. Anaphylatoxins are also known as complement peptides (C3a, C4a and C5a) that are produced from the activation of the complement system cascade. These complement anaphylatoxins can trigger degranulation of endothelial cells, mast cells, or phagocytes, which induce a local inflammatory response and stimulate smooth muscle cell contraction, histamine release, and increased vascular permeability. They are potent mediators involved in chemotaxis, inflammation, and generation of cytotoxic oxygen-derived free radicals. In humans, a single receptor for C3a (C3AR1) and two receptors for C5a (C5AR1 and C5AR2, also known as C5L2 or GPR77) have been identified, but there is no known receptor for C4a. 265 matched cddid_all.tbl CDD cd15116 cd15116 320244 7tmA_CMKLR1 chemokine-like receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors. Chemokine receptor-like 1 (also known as Chemerin receptor 23) is a GPCR for the chemoattractant adipokine chemerin, also known as retinoic acid receptor responder protein 2 (RARRES2), and for the omega-3 fatty acid derived molecule resolvin E1. Interaction with chemerin induces activation of the MAPK and PI3K signaling pathways leading to downstream functional effects, such as a decrease in immune responses, stimulation of adipogenesis, and angiogenesis. On the other hand, resolvin E1 negatively regulates the cytokine production in macrophages by reducing the activation of MAPK1/3 and NF-kB pathways. CMKLR1 is prominently expressed in dendritic cells and macrophages. 284 matched cddid_all.tbl CDD cd15117 cd15117 320245 7tmA_FPR-like N-formyl peptide receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. The formyl peptide receptors (FPRs) are chemoattractant GPCRs that involved in mediating immune responses to infection. They are expressed at elevated levels on polymorphonuclear and mononuclear phagocytes. FPRs bind N-formyl peptides, which are derived from the mitochondrial proteins of ruptured host cells or invading pathogens. Activation of FPRs by N-formyl peptides such as N-formyl-Met-Leu-Phe (FMLP) triggers a signaling cascade that stimulates neutrophil accumulation, phagocytosis and superoxide production. These responses are mediated through a pertussis toxin-sensitive G(i) protein that activates a PLC-IP3-calcium signaling pathway. While FPRs are involved in host defense responses to bacterial infection, they can also suppress the immune system under certain conditions. Yet, the physiological role of the FPR family is not fully understood. 288 matched cddid_all.tbl CDD cd15118 cd15118 320246 7tmA_PD2R2_CRTH2 prostaglandin D2 receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. Prostaglandin D2 receptor, also known as CRTH2, is a chemoattractant G-protein coupled receptor expressed on T helper type 2 cells that binds prostaglandin D2 (PGD2). PGD2 functions as a mast cell-derived mediator to trigger asthmatic responses and also causes vasodilation. PGD2 exerts its inflammatory effects by binding to two G-protein coupled receptors, the D-type prostanoid receptor (DP) and PD2R2 (CRTH2). PD2R2 couples to the G protein G(i/o) type which leads to a reduction in intracellular cAMP levels and an increase in intracellular calcium. PD2R2 is involved in mediating chemotaxis of Th2 cells, eosinophils, and basophils generated during allergic inflammatory processes. CRTH2 (PD2R2), but not DP receptor, undergoes agonist-induced internalization which is one of key processes that regulates the signaling of the GPCR. 284 matched cddid_all.tbl CDD cd15119 cd15119 320247 7tmA_GPR1 G protein-coupled receptor 1 for chemerin, member of the class A family of seven-transmembrane G protein-coupled receptors. G-protein coupled receptor 1 (GPR1) belongs to the class A of the seven transmembrane domain receptors. This is an orphan receptor that can be activated by the leukocyte chemoattractant chemerin, thereby suggesting that some of the anti-inflammatory actions of chemerin may be mediated through GPR1. GPR1 is most closely related to another chemerin receptor CMKLR1. In an in-vitro study, GPR1 has been shown to act as a co-receptor to allow replication of HIV viruses. 278 matched cddid_all.tbl CDD cd15120 cd15120 320248 7tmA_GPR33 orphan receptor GPR33, member of the class A family of seven-transmembrane G protein-coupled receptors. G-protein coupled receptor GPR33, an orphan member of the chemokine-like receptor family, was originally identified as a pseudogene in humans as well as in several apes and rodent species. Although the intact GPR33 allele is still present in a small fraction of the human population, the human GPR33 contains a premature stop codon. The amino acid sequence of GPR33 shares a high degree of sequence identity with the members of the chemokine and chemoattractant receptors that control leukocyte chemotaxis. The human GPR33 is expressed in spleen, lung, heart, kidney, pancreas, thymus, gonads, and leukocytes. 282 matched cddid_all.tbl CDD cd15121 cd15121 320249 7tmA_LTB4R1 leukotriene B4 receptor subtype 1 (LTB4R1 or BLT1), member of the class A family of seven-transmembrane G protein-coupled receptors. Leukotriene B4 (LTB4), a metabolite of arachidonic acid, is a powerful chemotactic activator for granulocytes and macrophages. Two receptors for LTB4 have been identified: a high-affinity receptor (LTB4R1 or BLT1) and a low-affinity receptor (TB4R2 or BLT2). Both BLT1 and BLT2 receptors belong to the rhodopsin-like G-protein coupled receptor superfamily and primarily couple to G(i) proteins, which lead to chemotaxis, calcium mobilization, and inhibition of adenylate cyclase. In some cells, they can also couple to the Gq-like protein, G16, and activate phospholipase C. LTB4 is involved in mediating inflammatory processes, immune responses, and host defense against infection. Studies have shown that LTB4 stimulates leukocyte extravasation, neutrophil degranulation, lysozyme release, and reactive oxygen species generation. 278 matched cddid_all.tbl CDD cd15122 cd15122 320250 7tmA_LTB4R2 leukotriene B4 receptor subtype 2 (LTB4R2 or BLT2), member of the class A family of seven-transmembrane G protein-coupled receptors. Leukotriene B4 (LTB4), a metabolite of arachidonic acid, is a powerful chemotactic activator for granulocytes and macrophages. Two receptors for LTB4 have been identified: a high-affinity receptor (LTB4R1 or BLT1) and a low-affinity receptor (TB4R2 or BLT2). Both BLT1 and BLT2 receptors belong to the rhodopsin-like G-protein coupled receptor superfamily and primarily couple to G(i) proteins, which lead to chemotaxis, calcium mobilization, and inhibition of adenylate cyclase. In some cells, they can also couple to the Gq-like protein, G16, and activate phospholipase C. LTB4 is involved in mediating inflammatory processes, immune responses, and host defense against infection. Studies have shown that LTB4 stimulates leukocyte extravasation, neutrophil degranulation, lysozyme release, and reactive oxygen species generation. 281 matched cddid_all.tbl CDD cd15123 cd15123 320251 7tmA_BRS-3 bombesin receptor subtype 3, member of the class A family of seven-transmembrane G protein-coupled receptors. BRS-3 is classified as an orphan receptor and belongs to the bombesin subfamily of G-protein coupled receptors, whose members also include neuromedin B receptor (NMBR) and gastrin-releasing peptide receptor (GRPR). Bombesin is a tetradecapeptide, originally isolated from frog skin. Mammalian bombesin-related peptides are widely distributed in the gastrointestinal and central nervous systems. The bombesin family receptors couple primarily to the G proteins of G(q/11) family. BRS-3 interacts with known naturally-occurring bombesin-related peptides with low affinity; however, no endogenous high-affinity ligand to the receptor has been identified. BRS-3 is suggested to play a role in sperm cell division and maturation. 294 matched cddid_all.tbl CDD cd15124 cd15124 320252 7tmA_GRPR gastrin-releasing peptide receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. The gastrin-releasing peptide receptor (GRPR) is a G-protein coupled receptor whose endogenous ligand is gastrin releasing peptide. GRP shares high sequence homology with the neuropeptide neuromedin B in the C-terminal region. This receptor is high glycosylated and couples to a pertussis-toxin-insensitive G protein of the family of Gq/11, which leads to the activation of phospholipase C. Gastrin-releasing peptide (GRP) is a potent mitogen for neoplastic tissues and involved in regulating multiple functions of the gastrointestinal and central nervous systems. These include the release of gastrointestinal hormones, the contraction of smooth muscle cells, and the proliferation of epithelial cells. GRPR belongs to the bombesin subfamily of G-protein coupled receptors, whose members also include neuromedin B receptor (NMBR) and bombesin receptor subtype 3 (BRS-3). Bombesin is a tetradecapeptide, originally isolated from frog skin. 293 matched cddid_all.tbl CDD cd15125 cd15125 320253 7tmA_NMBR neuromedin B receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. The neuromedin B receptor (NMBR), also known as BB1, is a G-protein coupled receptor whose endogenous ligand is the neuropeptide neuromedin B. Neuromedin B is a potent mitogen and growth factor for normal and cancerous lung and for gastrointestinal epithelial tissues. NMBR is widely distributed in the CNS, with especially high levels in olfactory nucleus and thalamic regions. The receptor couples primarily to a pertussis-toxin-insensitive G protein of the Gq/11 family, which leads to the activation of phospholipase C. NMBR belongs to the bombesin subfamily of G-protein coupled receptors, whose members also include gastrin-releasing peptide receptor (GRPR) and bombesin receptor subtype 3 (BRS-3). Bombesin is a tetradecapeptide, originally isolated from frog skin. 292 matched cddid_all.tbl CDD cd15126 cd15126 320254 7tmA_ETBR-LP2 endothelin B receptor-like protein 2, member of the class A family of seven-transmembrane G protein-coupled receptors. Endothelin B receptor-like protein 2, also called GPR37L1, is almost exclusively expressed in the nervous system. It has recently been shown to act as a receptor for the neuropeptide prosaptide, the active fragment of the secreted neuroprotective and glioprotective factor prosaposin (also called sulfated glycoprotein-1). Both prosaptide and prosaposin protect primary astrocytes against oxidative stress. GPR37L1 is part of the class A family of GPCRs that includes receptors for hormones, neurotransmitters, sensory stimuli, and a variety of other ligands. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 298 matched cddid_all.tbl CDD cd15127 cd15127 320255 7tmA_GPR37 G protein-coupled receptor 37, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR37, also called parkin-associated endothelin-like receptor (Pael-R), was isolated from a set of human brain frontal lobe expressed sequence tags. It is highly expressed in the mammalian CNS. It is a substrate of parkin and is involved in the pathogenesis of Parkinson's disease. GPR37 has recently been shown to act as a receptor for the neuropeptide prosaptide, the active fragment of the secreted neuroprotective and glioprotective factor prosaposin (also called sulfated glycoprotein-1). Both prosaptide and prosaposin protect primary astrocytes against oxidative stress. GPR37 is part of the class A family of GPCRs that includes receptors for hormones, neurotransmitters, sensory stimuli, and a variety of other ligands. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 298 matched cddid_all.tbl CDD cd15128 cd15128 320256 7tmA_ET_R endothelin receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Endothelins are 21-amino acid peptides which able to activate a number of signal transduction processes including phospholipase A2, phospholipase C, and phospholipase D, as well as cytosolic protein kinase activation. They play an important role in the regulation of the cardiovascular system and are the most potent vasoconstrictors identified, stimulating cardiac contraction, regulating the release of vasoactive substances, and stimulating mitogenesis in blood vessels. Two endothelin receptor subtypes have been isolated and identified in vertebrates, endothelin A receptor (ET-A) and endothelin B receptor (ET-B), and are members of the seven transmembrane class A G-protein coupled receptor family which activate multiple effectors via different types of G protein. Some vertebrates contain a third subtype, endothelin A receptor (ET-C). ET-A receptors are mainly located on vascular smooth muscle cells, whereas ET-B receptors are present on endothelial cells lining the vessel wall. Endothelin receptors have also been found in the brain. 300 matched cddid_all.tbl CDD cd15129 cd15129 320257 7tmA_GPR142 G-protein-coupled receptor GPR142, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR142, a vertebrate orphan receptor, is very closely related to GPR139, but they have different expression patterns in the brain and in other tissues. These receptors couple to inhibitory G proteins and activate phospholipase C. Studies suggested that dimer formation may be required for their proper function. GPR142 is predominantly expressed in pancreatic beta-cells and plays an important role in mediating enhancement of glucose-stimulated insulin secretion and maintaining glucose homeostasis, whereas GPR139 is expressed almost exclusively in the brain and is suggested to play a role in the control of locomotor activity. These orphan receptors are phylogenetically clustered with invertebrate FMRFamide receptors such as Drosophila melanogaster DrmFMRFa-R. 270 matched cddid_all.tbl CDD cd15130 cd15130 320258 7tmA_NTSR neurotensin receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Neurotensin (NTS) is a 13 amino-acid neuropeptide that functions as both a neurotransmitter and a hormone in the nervous system and peripheral tissues, respectively. NTS exerts various biological activities through activation of the G protein-coupled neurotensin receptors, NTSR1 and NTSR2. In the brain, NTS is involved in the modulation of dopamine neurotransmission, opioid-independent analgesia, hypothermia, and the inhibition of food intake, while in the periphery NTS promotes the growth of various normal and cancer cells and acts as a paracrine and endocrine modulator of the digestive tract. The third neurotensin receptor, NTSR3 or also called sortilin, is not a G protein-coupled receptor. 281 matched cddid_all.tbl CDD cd15131 cd15131 320259 7tmA_GHSR growth hormone secretagogue receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. Growth hormone secretagogue receptor, GHSR, is also known as GH-releasing peptide receptor (GHRP) or Ghrelin receptor. Ghrelin, the endogenous ligand for GHSR, is an acylated 28-amino acid peptide hormone produced by ghrelin cells in the gastrointestinal tract. Ghrelin, also called hunger hormone, is involved in the regulation of growth hormone release, appetite and feeding, gut motility, lipid and glucose metabolism, and energy balance. It also plays a role in the cardiovascular, immune, and reproductive systems. GHSR couples to G-alpha-11 proteins. Both ghrelin and GHSR are expressed in a wide range of cancer tissues. Recent studies suggested that ghrelin may play a role in processes associated with cancer progression, including cell proliferation, metastasis, apoptosis, and angiogenesis. 291 matched cddid_all.tbl CDD cd15132 cd15132 320260 7tmA_motilin_R motilin receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. Motilin receptor, also known as GPR38, is a G-protein coupled receptor that binds the endogenous ligand motilin. Motilin is a 22 amino acid peptide hormone expressed throughout the gastrointestinal tract and stimulates contraction of gut smooth muscle. Motilin is also called as the housekeeper of the gut because it is responsible for the proper filling and emptying of the gastrointestinal tract in response to food intake, and for stimulating the production of pepsin. Motilin receptor shares significant amino acid sequence identity with the growth hormone secretagogue receptor (GHSR) and neurotensin receptors (NTS-R1 and 2). 289 matched cddid_all.tbl CDD cd15133 cd15133 320261 7tmA_NMU-R neuromedin U receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Neuromedin U (NMU) is a highly conserved neuropeptide with a common C-terminal heptapeptide sequence (FLFRPRN-amide) found at the highest levels in the gastrointestinal tract and pituitary gland of mammals. Disruption or replacement of residues in the conserved heptapeptide region can result in the reduced ability of NMU to stimulate smooth-muscle contraction. Two G-protein coupled receptor subtypes, NMU-R1 and NMU-R2, with a distinct expression pattern, have been identified to bind NMU. NMU-R1 is expressed primarily in the peripheral nervous system, while NMU-R2 is mainly found in the central nervous system. Neuromedin S, a 36 amino-acid neuropeptide that shares a conserved C-terminal heptapeptide sequence with NMU, is a highly potent and selective NMU-R2 agonist. Pharmacological studies have shown that both NMU and NMS inhibit food intake and reduce body weight, and that NMU increases energy expenditure. 298 matched cddid_all.tbl CDD cd15134 cd15134 320262 7tmA_capaR neuropeptide capa receptor and similar invertebrate proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. CapaR is a G-protein coupled receptor for the Drosophila melanogaster capa neuropeptides (Drm-capa-1 and -2), which act on the Malpighian tubules to increase fluid transport. The capa peptides are evolutionarily related to vertebrate Neuromedin U neuropeptide and contain a C-terminal FPRXamide motif. CapaR regulates fluid homeostasis through its ligands, thereby acts as a desiccation stress-responsive receptor. CapaR undergoes desensitization, with internalization mediated by beta-arrestin-2. 298 matched cddid_all.tbl CDD cd15135 cd15135 320263 7tmA_GPR39 G protein-coupled receptor 39, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR39 is an orphan G protein-coupled receptor that belongs to the growth hormone secretagogue and neurotensin receptor subfamily. GPR39 is expressed in peripheral tissues such as pancreas, gut, gastrointestinal tract, liver, kidney as well as certain regions of the brain. The divalent metal ion Zn(2+) has been shown to be a ligand capable of activating GPR39. Thus, it has been suggested that GPR39 function as a G(q)-coupled Zn(2+)-sensing receptor which involved in the regulation of endocrine pancreatic function, body weight, gastrointestinal mobility, and cell death. 320 matched cddid_all.tbl CDD cd15136 cd15136 320264 7tmA_Glyco_hormone_R glycoprotein hormone receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. The glycoprotein hormone receptors (GPHRs) are seven transmembrane domain receptors with a very large extracellular N-terminal domain containing many leucine-rich repeats responsible for hormone recognition and binding. The glycoprotein hormone family includes three gonadotropins: luteinizing hormone (LH), follicle-stimulating hormone (FSH), chorionic gonadotropin (CG) and a pituitary thyroid-stimulating hormone (TSH). The glycoprotein hormones exert their biological functions by interacting with their cognate GPCRs. Both LH and CG bind to the same receptor, the luteinizing hormone-choriogonadotropin receptor (LHCGR); FSH binds to FSH-R and TSH to TSH-R. GPHRs couple primarily to the G(s)-protein and promotes cAMP production, but also to the G(i)- or G(q)-protein. 275 matched cddid_all.tbl CDD cd15137 cd15137 320265 7tmA_Relaxin_R relaxin family peptide receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes relaxin/insulin-like family peptide receptor 1 (RXFP1 or LGR7) and 2 (RXFP2 or LGR8), which contain a very large extracellular N-terminal domain with numerous leucine-rich repeats responsible for hormone recognition and binding. Relaxin is a member of the insulin superfamily that has diverse actions in both reproductive and non-reproductive tissues. The relaxin-like peptide family includes relaxin-1, relaxin-2, and the insulin-like (INSL) peptides such as INSL3, INSL4, INSL5 and INSL6. The relaxin family peptides share high structural but low sequence similarity, and exert their physiological functions by activating a group of four GPCRs, RXFP1-4. Relaxin and INSL3 are the endogenous ligands for RXFP1 and RXFP2, respectively. Upon receptor binding, relaxin activates a variety of signaling pathways to produce second messengers such as cAMP. 284 matched cddid_all.tbl CDD cd15138 cd15138 320266 7tmA_LRR_GPR orphan leucine-rich repeat-containing G protein-coupled receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes leucine-rich repeat-containing G-protein coupled receptor 4 (LGR4), 5 (LGR5), and 6 (LGR6). These receptors contain a subfamily of receptors related to the glycoprotein hormone receptor family, which includes the luteinizing hormone (LH) receptor, the follicle-stimulating hormone (FSH) receptor, and the pituitary thyroid-stimulating hormone (TSH) receptor. LGR4-6 are receptors for the R-spondin (Rspo) family of secreted proteins containing two N-terminal furin-like repeats and a thrombospondin domain. The RSPO proteins are involved in regulating proliferation and differentiation of adult stem cells by potently enhancing the WNT-stimulated beta-catenin signaling. LGR4 is broadly expressed in proliferating cells, and its deficient mice display development defects in multiple organs. LGR5 acts as a marker for resident stem cell in numerous epithelial cell layers, including small intestine, colon, stomach, and kidney. LGR6 also serves as a marker of multipotent stem cells in the hair follicle that generate all skin cell lineages. Members of this group are characterized by a very large extracellular N-terminal domain containing 17 leucine-rich repeats (LRRs), flanked by cysteine-rich N- and C-terminal capping domains, and the extracellular domain is responsible for high-affinity binding with the Rspo proteins. 274 matched cddid_all.tbl CDD cd15139 cd15139 320267 7tmA_PGE2_EP2 prostaglandin E2 receptor EP2 subtype, member of the class A family of seven-transmembrane G protein-coupled receptors. Prostaglandin E2 receptor EP2, also called prostanoid EP2 receptor, is one of four receptor subtypes whose endogenous physiological ligand is prostaglandin E2 (PGE2). Each of these subtypes (EP1-EP4) have unique but overlapping tissue distributions that activate different intracellular signaling pathways. Stimulation of the EP2 receptor by PGE2 causes cAMP accumulation through G(s) protein activation, which subsequently produces smooth muscle relaxation and mediates the systemic vasodepressor response to PGE2. Prostanoids are the cyclooxygenase (COX) metabolites of arachidonic acid, which include the prostaglandins (PGD2, PGE2, PGF2alpha), prostacyclin (PGI2), and thromboxane A2 (TxA2). These five major bioactive prostanoids acts as mediators or modulators in a wide range of physiological and pathophysiological processes within the kidney and play important roles in inflammation, platelet aggregation, and vasoconstriction/relaxation, among many others. They act locally by preferentially interacting with G protein-coupled receptors designated DP, EP. FP, IP, and TP, respectively. The phylogenetic tree suggests that the prostanoid receptors can be grouped into two major branches: G(s)-coupled (DP1, EP2, EP4, and IP) and G(i)- (EP3) or G(q)-coupled (EP1, FP, and TP), forming three clusters. 299 matched cddid_all.tbl CDD cd15140 cd15140 320268 7tmA_PGD2 prostaglandin D2 receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. Prostaglandin D2 receptor (also called prostanoid DP receptor, DP1, or PGD2R1) is a G-protein coupled receptor whose endogenous ligand is prostaglandin D2 (PGD2). PGD2, the major cyclooxygenase metabolite of arachidonic acid produced by mast cells, mediates inflammatory reactions in response to allergen challenge and causes peripheral vasodilation. PGD2 exerts its biological effects by binding to two types of cell surface receptors: a DP1 receptor that belongs to the prostanoid receptor family and a chemoattractant receptor-homologous molecule expressed on the T-helper type 2 cells (CRTH2 or PD2R2). 312 matched cddid_all.tbl CDD cd15141 cd15141 320269 7tmA_PGI2 prostaglandin I2 receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. Prostaglandin I2 receptor (also called prostacyclin receptor or prostanoid IP receptor) is a class A, G protein-coupled receptor whose endogenous ligand is prostacyclin, which is the major product of cyclooxygenase metabolite of arachidonic acid that found predominantly in platelets and vascular smooth muscle cells (VSMCs). The PGI2 receptor is coupled to both G(s) and G(q) protein subtypes, resulting in increased cAMP formation, phosphoinositide turnover, and Ca2+ signaling. PGI2 receptor activation by prostacyclin induces VSMC differentiation and produces a potent vasodilation and inhibition of platelet aggregation. 301 matched cddid_all.tbl CDD cd15142 cd15142 320270 7tmA_PGE2_EP4 prostaglandin E2 receptor EP4 subtype, member of the class A family of seven-transmembrane G protein-coupled receptors. Prostaglandin E2 receptor EP4, also called prostanoid EP4 receptor, is one of four receptor subtypes whose endogenous physiological ligand is prostaglandin E2 (PGE2). Each of these subtypes (EP1-EP4) have unique but overlapping tissue distributions that activate different intracellular signaling pathways. Like the EP2 receptor, stimulation of the EP4 receptor by PGE2 causes cAMP accumulation through G(s) protein activation. Knockout studies in mice suggest that EP4 receptor may be involved in the maintenance of bone mass and fracture healing. Prostanoids are the cyclooxygenase (COX) metabolites of arachidonic acid, which include the prostaglandins (PGD2, PGE2, PGF2alpha), prostacyclin (PGI2), and thromboxane A2 (TxA2). These five major bioactive prostanoids acts as mediators or modulators in a wide range of physiological and pathophysiological processes within the kidney and play important roles in inflammation, platelet aggregation, and vasoconstriction/relaxation, among many others. They act locally by preferentially interacting with G protein-coupled receptors designated DP, EP. FP, IP, and TP, respectively. The phylogenetic tree suggests that the prostanoid receptors can be grouped into two major branches: G(s)-coupled (DP1, EP2, EP4, and IP) and G(i)- (EP3) or G(q)-coupled (EP1, FP, and TP), forming three clusters. 302 matched cddid_all.tbl CDD cd15143 cd15143 320271 7tmA_TXA2_R thromboxane A2 receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. The thromboxane receptor, also known as the prostanoid TP receptor, is a class A G-protein coupled receptor whose endogenous ligand is thromboxane A2 (TXA2). TXA2 is the major product of cyclooxygenase metabolite of arachidonic acid that found predominantly in platelets and stimulates platelet aggregation, Ca2+ influx into platelets, and also causes vasoconstriction. TXA2 has been shown to be involved in immune regulation, angiogenesis and metastasis, among many others. Activation of TXA2 receptor is coupled to G(q) and G(13), resulting in the activations of phospholipase C and RhoGEF, respectively. TXA2 receptor is widely distributed in the body and is abundantly expressed in thymus and spleen. 296 matched cddid_all.tbl CDD cd15144 cd15144 320272 7tmA_PGE2_EP1 prostaglandin E2 receptor EP1 subtype, member of the class A family of seven-transmembrane G protein-coupled receptors. Prostaglandin E2 receptor EP1, also called prostanoid EP1 receptor, is one of four receptor subtypes whose endogenous physiological ligand is prostaglandin E2 (PGE2). Each of these subtypes (EP1-EP4) have unique but overlapping tissue distributions that activate different intracellular signaling pathways. It has been shown that stimulation of the EP1 receptor by PGE2 causes smooth muscle contraction and increased intracellular Ca2+ levels; however, it is still unclear whether EP1 receptor is exclusively coupled to G(q/11), which leading to activation of phospholipase C and phosphatidylinositol hydrolysis. Prostanoids are the cyclooxygenase (COX) metabolites of arachidonic acid, which include the prostaglandins (PGD2, PGE2, PGF2alpha), prostacyclin (PGI2), and thromboxane A2 (TxA2). These five major bioactive prostanoids acts as mediators or modulators in a wide range of physiological and pathophysiological processes within the kidney and play important roles in inflammation, platelet aggregation, and vasoconstriction/relaxation, among many others. They act locally by preferentially interacting with G protein-coupled receptors designated DP, EP. FP, IP, and TP, respectively. The phylogenetic tree suggests that the prostanoid receptors can be grouped into two major branches: G(s)-coupled (DP1, EP2, EP4, and IP) and G(i)- (EP3) or G(q)-coupled (EP1, FP, and TP), forming three clusters. 294 matched cddid_all.tbl CDD cd15145 cd15145 320273 7tmA_FP prostaglandin F2-alpha receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. The PGF2-alpha receptor, also called prostanoid FP receptor, is a class A G-protein coupled receptor whose endogenous ligand is prostaglandin F2-alpha. PGF2-alpha binding to this receptor is coupled to the stimulation of phospholipase C (PLC) pathway via G-protein subunit G(q). This leads to the release of inositol trisphosphate (IP3) and diacylglycerol (DAG) which results in increased intracellular Ca2+ levels and activation of PKC. The receptor activation primarily induces uterine contraction and bronchoconstriction, and stimulates luteolysis. Like most prostanoid receptors, the PGF2-alpha receptor has also been implicated in tumor angiogenesis and metastasis. 290 matched cddid_all.tbl CDD cd15146 cd15146 320274 7tmA_PGE2_EP3 prostaglandin E2 receptor EP3 subtype, member of the class A family of seven-transmembrane G protein-coupled receptors. Prostaglandin E2 receptor EP3, also called prostanoid EP3 receptor, is one of four receptor subtypes whose endogenous physiological ligand is prostaglandin E2 (PGE2). Each of these subtypes (EP1-EP4) have unique but overlapping tissue distributions that activate different intracellular signaling pathways. Stimulation of the EP3 receptor by PGE2 preferentially couples to G(i) protein. This leads to a decrease in adenylate cyclase activity, thereby decreasing cAMP levels, which subsequently produces smooth muscle contraction. Knockout mice studies suggest that the EP3 receptor may act as a systemic vasopressor. Prostanoids are the cyclooxygenase (COX) metabolites of arachidonic acid, which include the prostaglandins (PGD2, PGE2, PGF2alpha), prostacyclin (PGI2), and thromboxane A2 (TxA2). These five major bioactive prostanoids acts as mediators or modulators in a wide range of physiological and pathophysiological processes within the kidney and play important roles in inflammation, platelet aggregation, and vasoconstriction/relaxation, among many others. They act locally by preferentially interacting with G protein-coupled receptors designated DP, EP. FP, IP, and TP, respectively. The phylogenetic tree suggests that the prostanoid receptors can be grouped into two major branches: G(s)-coupled (DP1, EP2, EP4, and IP) and G(i)- (EP3) or G(q)-coupled (EP1, FP, and TP), forming three clusters. 308 matched cddid_all.tbl CDD cd15147 cd15147 320275 7tmA_PAFR platelet-activating factor receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. The platelet-activating factor receptor is a G(q/11)-protein coupled receptor, which is linked to p38 MAPK and PI3K signaling pathways. PAF is a phospholipid (1-0-alkyl-2-acetyl-sn-glycero-3-phosphorylcholine) which is synthesized by cells especially involved in host defense such as platelets, macrophages, neutrophils, and monocytes. PAF is well-known for its ability to induce platelet aggregation and anaphylaxis, and also plays important roles in allergy, asthma, and inflammatory responses, among many others. 291 matched cddid_all.tbl CDD cd15148 cd15148 320276 7tmA_GPR34-like putative G protein-coupled receptor 34, member of the class A family of seven-transmembrane G protein-coupled receptors. This subgroup represents the G-protein coupled receptor 34 of unknown function. Orphan GPR34 is a member of the rhodopsin-like, class A GPCRs, which is a widespread protein family that includes the light-sensitive rhodopsin as well as receptors for biogenic amines, lipids, nucleotides, odorants, peptide hormones, and a variety of other ligands. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 282 matched cddid_all.tbl CDD cd15149 cd15149 320277 7tmA_P2Y14 P2Y purinoceptor 14, member of the class A family of seven-transmembrane G protein-coupled receptors. The P2Y14 receptor is activated by UDP-sugars and belongs to the G(i) class of the P2Y family of purinergic G-protein coupled receptors. The P2Y receptor family is composed of eight subtypes, which are activated by naturally occurring extracellular nucleotides such as ATP, ADP, UTP, UDP, and UDP-sugars. These eight receptors are ubiquitous in human tissues and can be further classified into two subfamilies based on sequence homology and second messenger coupling: a subfamily of five P2Y1-like receptors (P2Y1, P2Y2, P2Y4, P2Y6, and P2Y11Rs) that are coupled to G(q) protein to activate phospholipase C (PLC) and a second subfamily of three P2Y12-like receptors (P2Y12, P2YR13, and P2Y14Rs) that are coupled to G(i) protein to inhibit adenylate cyclase. Several cloned subtypes, such as P2Y3, P2Y5 and P2Y7-10, are not functional mammalian nucleotide receptors. The native agonists for P2Y receptors are: ATP (P2Y2, P2Y12), ADP (P2Y1, P2Y12 and P2Y13), UTP (P2Y2, P2Y4), UDP (P2Y6, P2Y14), and UDP-sugars (P2Y14). P2Y14 receptor has been reported to be involved in a diverse set of physiological responses in many epithelia as well as in immune and inflammatory cells. 284 matched cddid_all.tbl CDD cd15150 cd15150 341326 7tmA_P2Y12 P2Y purinoceptor 12, member of the class A family of seven-transmembrane G protein-coupled receptors. The P2Y12 receptor (P2Y12R) is found predominantly on the surface of blood platelets and is activated by adenosine diphosphate (ADP). P2Y12R plays an important role in the regulation of blood clotting and belongs to the G(i) class of the P2Y family of purinergic G protein-coupled receptors. P2Y receptor family is composed of eight subtypes, which are activated by naturally occurring extracellular nucleotides such as ATP, ADP, UTP, UDP, and UDP-sugars. These eight receptors are ubiquitous in human tissues and can be further classified into two subfamilies based on sequence homology and second messenger coupling: a subfamily of five P2Y1-like receptors (P2Y1, P2Y2, P2Y4, P2Y6, and P2Y11Rs) that are coupled to G(q) protein to activate phospholipase C (PLC) and a second subfamily of three P2Y12-like receptors (P2Y12, P2YR13, and P2Y14Rs) that are coupled to G(i) protein to inhibit adenylate cyclase. Several cloned subtypes, such as P2Y3, P2Y5 and P2Y7-10, are not functional mammalian nucleotide receptors. The native agonists for P2Y receptors are: ATP (P2Y2, P2Y12), ADP (P2Y1, P2Y12 and P2Y13), UTP (P2Y2, P2Y4), UDP (P2Y6, P2Y14), and UDP-sugars (P2Y14). 285 matched cddid_all.tbl CDD cd15151 cd15151 341327 7tmA_P2Y13 P2Y purinoceptor 13, member of the class A family of seven-transmembrane G protein-coupled receptors. The P2Y13 receptor (P2Y13R) is activated by adenosine diphosphate (ADP) and belongs to the G(i) class of the P2Y family of purinergic G protein-coupled receptors. P2Y receptor family is composed of eight subtypes, which are activated by naturally occurring extracellular nucleotides such as ATP, ADP, UTP, UDP, and UDP-sugars. These eight receptors are ubiquitous in human tissues and can be further classified into two subfamilies based on sequence homology and second messenger coupling: a subfamily of five P2Y1-like receptors (P2Y1, P2Y2, P2Y4, P2Y6, and P2Y11Rs) that are coupled to G(q) protein to activate phospholipase C (PLC) and a second subfamily of three P2Y12-like receptors (P2Y12, P2YR13, and P2Y14Rs) that are coupled to G(i) protein to inhibit adenylate cyclase. Several cloned subtypes, such as P2Y3, P2Y5 and P2Y7-10, are not functional mammalian nucleotide receptors. The native agonists for P2Y receptors are: ATP (P2Y2, P2Y12), ADP (P2Y1, P2Y12 and P2Y13), UTP (P2Y2, P2Y4), UDP (P2Y6, P2Y14), and UDP-sugars (P2Y14). 284 matched cddid_all.tbl CDD cd15152 cd15152 320280 7tmA_GPR174-like putative purinergic receptor GPR174, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR174 has been recently identified as a lysophosphatidylserine receptor that enhances intracellular cAMP formation by coupling to a G(s) protein. GPR174 is a member of the rhodopsin-like, class A GPCRs, which is a widespread protein family that includes the light-sensitive rhodopsin as well as receptors for biogenic amines, lipids, nucleotides, odorants, peptide hormones, and a variety of other ligands. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 282 matched cddid_all.tbl CDD cd15153 cd15153 320281 7tmA_P2Y10 P2Y purinoceptor 10, member of the class A family of seven-transmembrane G protein-coupled receptors. P2Y10 receptor is a G-protein coupled receptor that is activated by both sphingosine-1-phosphate (S1P) and lysophosphatidic acid (LPA). Phylogenetic analysis of the class A GPCRs shows that P2Y10 is grouped into the cluster comprising nucleotide and lipid receptors. Although the mouse P2Y10 was found to be expressed in brain, lung, reproductive organs, and skeletal muscle, the physiological function of this receptor is not yet known. S1P and LPA are bioactive lipid molecules that induce a variety of cellular responses through G proteins: adhesion, invasion, cell migration and proliferation, among many others. 283 matched cddid_all.tbl CDD cd15154 cd15154 320282 7tmA_LPAR5 lysophosphatidic acid receptor 5, member of the class A family of seven-transmembrane G protein-coupled receptors. Lysophosphatidic acid receptor 5 (LPAR5) is a G protein-coupled receptor that binds the bioactive lipid lysophosphatidic acid (LPA) and is involved in maintenance of human hair growth. Phylogenetic analysis of the class A GPCRs shows that LAPR5 is classified into the cluster consisting receptors that are preferentially activated by adenosine and uridine nucleotides. Although LPA6 (P2Y5) is expressed in human hair follicle cells, LPA4 and LPA5 are not. These three receptors are highly homologous and mediate an increase in intracellular cAMP production. Activation of LPAR5 is coupled to G(q) and G(12/13) proteins. 285 matched cddid_all.tbl CDD cd15155 cd15155 320283 7tmA_LPAR4 lysophosphatidic acid receptor 4, member of the class A family of seven-transmembrane G protein-coupled receptors. Lysophosphatidic acid receptor 4 (LPAR4) is a G protein-coupled receptor that binds and is activated by the bioactive lipid lysophosphatidic acid (LPA), which is released by activated platelets and constitutively found in serum. Phylogenetic analysis of the class A GPCRs shows that LAPR4 is classified into the cluster consisting receptors that are preferentially activated by adenosine and uridine nucleotides. Although LPA6 (P2Y5) is expressed in human hair follicle cells, LPA4 and LPA5 are not. These three receptors are highly homologous and mediate an increase in intracellular cAMP production. Activation of LPAR5 is coupled to G(12/13) proteins, leading to neurite retraction and stress fiber formation, whereas coupling to G(q) protein leads to increases in calcium levels. 283 matched cddid_all.tbl CDD cd15156 cd15156 320284 7tmA_LPAR6_P2Y5 lysophosphatidic acid receptor 6, member of the class A family of seven-transmembrane G protein-coupled receptors. Lysophosphatidic acid receptor 6 (LPAR6), also known as P2Y5, is a G(i), G(12/13) G protein-coupled receptor that is activated by the bioactive lipid lysophosphatidic acid (LPA), which is released by activated platelets and constitutively present in serum. LPAR6 plays an important role in maintenance of human hair growth. Thus, mutations in the receptor are responsible for both autosomal recessive wooly hair and hypotrichosis. Phylogenetic analysis of the class A GPCRs shows that LAPR6 (P2Y5) is classified into the cluster consisting of receptors that are preferentially activated by adenosine and uridine nucleotides. Although LPA6 (P2Y5) is expressed in human hair follicle cells, LPA4 and LPA5 are not. These three receptors are highly homologous and mediate an increase in intracellular cAMP production. 285 matched cddid_all.tbl CDD cd15157 cd15157 320285 7tmA_CysLTR2 cysteinyl leukotriene receptor 2, member of the class A family of seven-transmembrane G protein-coupled receptors. Cysteinyl leukotrienes (LTC4, LTD4, and LTE4) are the most potent inflammatory lipid mediators that play an important role in human asthma. They are synthesized in the leucocytes (cells of immune system) from arachidonic acid by the actions of 5-lipoxygenase and induce bronchial constriction through G protein-coupled receptors, CysLTR1 and CysLTR2. Activation of CysLTR1 by LTD4 induces airway smooth muscle contraction and proliferation, eosinophil migration, and damage to the lung tissue. They belong to the class A GPCR superfamily, which all have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 278 matched cddid_all.tbl CDD cd15158 cd15158 320286 7tmA_CysLTR1 cysteinyl leukotriene receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors. Cysteinyl leukotrienes (LTC4, LTD4, and LTE4) are the most potent inflammatory lipid mediators that play an important role in human asthma. They are synthesized in the leucocytes (cells of immune system) from arachidonic acid by the actions of 5-lipoxygenase and induce bronchial constriction through G protein-coupled receptors, CysLTR1 and CysLTR2. Activation of CysLTR1 by LTD4 induces airway smooth muscle contraction and proliferation, eosinophil migration, and damage to the lung tissue. They belong to the class A GPCR superfamily, which all have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 285 matched cddid_all.tbl CDD cd15159 cd15159 320287 7tmA_EBI2 Epstein-Barr virus (EBV)-induced gene 2, member of the class A family of seven-transmembrane G protein-coupled receptors. Epstein-Barr virus-induced G-protein coupled receptor 2 (EBI2), also called GPR183, is activated by 7alpha, 25-dihydroxyxcholesterol (7alpha, 25-OHC), an oxysterol. EBI2 was originally identified as one of major genes induced in the Burkitt's lymphoma cell line BL41by EBV infection. EBI2 is involved in regulating B cell migration and responses, and is also implicated in human diseases such as type I diabetes, multiple sclerosis, and cancers. 286 matched cddid_all.tbl CDD cd15160 cd15160 320288 7tmA_Proton-sensing_R proton-sensing G protein-coupled receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Proton/pH-sensing G-protein coupled receptors sense pH of 7.6 to 6.0. They mediate a variety of biological activities in neutral and mildly acidic pH conditions, whereas the acid-sensing ionotropic ion channels typically sense strong acidic pH. The proton/pH-sensing receptor family includes the G2 accumulation receptor (G2A, also known as GPR132), the T cell death associated gene-8 (TDAG8, GPR65) receptor, ovarian cancer G-protein receptor 1 (OGR-1, GPR68), and G-protein-coupled receptor 4 (GPR4). 280 matched cddid_all.tbl CDD cd15161 cd15161 320289 7tmA_GPR17 G protein-coupled receptor 17, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR17 is a Forkhead box protein O1 (FOXO1) target and abundantly expressed in agouti-related peptide (AGRP) neurons. FOXO1 is a transcription factor that plays key roles in regulation of gluconeogenesis and glycogenolysis by insulin signaling. For instance, food intake and body weight increase when hypothalamic FOXO1 is activated, whereas they both decrease when FOXO1 is inhibited. However, a recent study has been reported that GPR17 deficiency in mice did not affect food intake or glucose homeostasis. Thus, GPR17 may not play a role in the control of food intake, body weight, or glycemic control. GPR17 is phylogenetically closely related to purinergic P2Y and cysteinyl-leukotriene receptors. 277 matched cddid_all.tbl CDD cd15162 cd15162 341328 7tmA_PAR protease-activated receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. This subfamily includes purinergic receptor P2Y8 and protease-activated receptors. P2Y8 (or P2RY8) expression is often increased in leukemia patients, and it plays a role in the pathogenesis of acute leukemia. P2Y8 is phylogenetically closely related to the protease-activated receptors (PARs), which are activated by serine proteases such as thrombin, trypsin, and tryptase. These proteases cleave the extracellular domain of the receptor to form a new N-terminus, which in turn functions as a tethered ligand. The newly-formed tethered ligand binds intramolecularly to activate the receptor and triggers G-protein binding and intracellular signaling. Four different types of the protease-activated receptors have been identified (PAR1-4) and are predominantly expressed in platelets. PAR1, PAR3, and PAR4 are activated by thrombin, whereas PAR2 is activated by trypsin. The PARs are known to couple with several G-proteins including Gi (cAMP inhibitory), G12/13 (Rho and Ras activation), and Gq (calcium signaling) to activate downstream signaling messengers which induces numerous cellular and physiological effects. 280 matched cddid_all.tbl CDD cd15163 cd15163 320291 7tmA_GPR20 G protein-coupled receptor 20, member of the class A family of seven-transmembrane G protein-coupled receptors. Orphan GPR20 is phylogenetically related to the P2Y family of purinergic G protein-coupled receptors. The P2Y receptor family is composed of eight subtypes, which are activated by naturally occurring extracellular nucleotides such as ATP, ADP, UTP, UDP, and UDP-glucose. GPR20 has been shown to constitutively activate G(i) proteins in the absence of a ligand; however its functional role is not known. GPR20 is a member of the class A G protein-coupled receptor superfamily, which all have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A common feature of GPCR signaling is agonist-induced conformational changes in the receptors, which then activate the heterotrimeric G proteins. G-proteins regulate a variety of cellular functions including metabolic enzymes, ion channels, and transporters, among many others. 258 matched cddid_all.tbl CDD cd15164 cd15164 320292 7tmA_GPR35-like G protein-coupled receptor 35 and similar proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR35 shares closest homology with GPR55, and they belong to the class A G protein-coupled receptor superfamily, which all have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A number of studies have suggested that GPR35 may play important physiological roles in hypertension, atherosclerosis, nociception, asthma, glucose homeostasis and diabetes, and inflammatory bowel disease. GPR35 is thought to be responsible for brachydactyly mental retardation syndrome, which is associated with a deletion comprising chromosome 2q37 in human, and is also implicated as a potential oncogene in stomach cancer. Several endogenous ligands for GPR35 have been identified including kynurenic acid, 2-oleoyl lysophosphatidic acid, and zaprinast. GPR35 couples to G(13) and G(i/o) proteins. 272 matched cddid_all.tbl CDD cd15165 cd15165 320293 7tmA_GPR55-like G protein-coupled receptor 55 and similar proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR55 shares closest homology with GPR35, and they belong to the class A G protein-coupled receptor superfamily, which all have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. GPR55 has been reported to couple to G(13), G(12), or G(q) proteins. Activation of GPR55 leads to activation of phospholipase C, RhoA, ROCK, ERK, p38MAPK, and calcium release. Lysophosphatidylinositol (LPI) is currently considered as the endogenous ligand for GPR55, although the receptor was initially de-orphanized as a cannabinoid receptor and binds many cannabinoid ligands. 277 matched cddid_all.tbl CDD cd15166 cd15166 320294 7tmA_NAGly_R_GPR18 N-arachidonyl glycine receptor, GPR18, member of the class A family of seven-transmembrane G protein-coupled receptors. N-arachidonyl glycine (NAGly), an endogenous metabolite of the endocannabinoid anandamide, has been identified as an endogenous ligand of the G(i/o) protein-coupled receptor 18 (GPR18). NAGly is involved in directing microglial migration in the CNS through activation of GPR18. NAGly-GPR18 signaling is thought to play an important role in microglial-neuronal communication. Recent studies also show that GPR18 functions as the abnormal cannabidiol (Abn-CBD) receptor. Abn-CBD is a synthetic isomer of cannabidiol and is inactive at cannabinoid receptors (CB1 or CB2), but acts as a selective agonist at GPR18. The NAGly receptor is a member of the class A G protein-coupled receptor superfamily, which all have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, which then activate the heterotrimeric G proteins. G-proteins regulate a variety of cellular functions including metabolic enzymes, ion channels, and transporters, among many others. 275 matched cddid_all.tbl CDD cd15167 cd15167 320295 7tmA_GPR171 orphan G protein-coupled receptor 171, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR171 is phylogenetically related to the P2Y family of purinergic G protein-coupled receptors. The P2Y receptor family is composed of eight subtypes, which are activated by naturally occurring extracellular nucleotides such as ATP, ADP, UTP, UDP, and UDP-glucose. A recent study has been reported that the peptide LENSSPQAPARRLLPP (BigLEN) activates GPR17 to regulate body weight in mice; however the biological role of the receptor remains unknown. GPR171 is a member of the class A G protein-coupled receptor superfamily, which all have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A common feature of GPCR signaling is agonist-induced conformational changes in the receptors, which then activate the heterotrimeric G proteins. G-proteins regulate a variety of cellular functions including metabolic enzymes, ion channels, and transporters, among many others. 282 matched cddid_all.tbl CDD cd15168 cd15168 341329 7tmA_P2Y1-like P2Y purinoceptors 1, 2, 4, 6, 11 and similar proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. The P2Y receptor family is composed of eight subtypes, which are activated by naturally occurring extracellular nucleotides such as ATP, ADP, UTP, UDP, and UDP-glucose. These eight receptors are ubiquitous in human tissues and can be further classified into two subfamilies based on sequence homology and second messenger coupling: a subfamily of five P2Y1-like receptors (P2Y1, P2Y2, P2Y4, P2Y6, and P2Y11Rs) that are coupled to G(q) protein to activate phospholipase C (PLC) and a second subfamily of three P2Y12-like receptors (P2Y12, P2YR13, and P2Y14Rs) that are coupled to G(i) protein to inhibit adenylate cyclase. Several cloned subtypes, such as P2Y3, P2Y5, and P2Y7-10, are not functional mammalian nucleotide receptors. The native agonists for P2Y receptors are: ATP (P2Y2, P2Y12), ADP (P2Y1, P2Y12, and P2Y13), UTP (P2Y2, P2Y4), UDP (P2Y6, P2Y14), and UDP-glucose (P2Y14). This cluster only includes P2Y1-like receptors as well as other closely related orphan receptors, such as GPR91 (a succinate receptor) and GPR80/GPR99 (an alpha-ketoglutarate receptor). 284 matched cddid_all.tbl CDD cd15169 cd15169 320297 7tmA_FFAR1 free fatty acid receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors. This subgroup includes the mammalian free fatty acid receptor 1 (FFAR1), also called GPR40. FFAR1 is a cell-surface receptor for medium- and long-chain free fatty acids (FFAs). The receptor is most potently activated by eicosatrienoic acid (C20:3), but can also be activated at micromolar concentrations of various fatty acids. FFAR1 directly mediates FFA stimulation of glucose-stimulated insulin secretion and indirectly increases insulin secretion by enhancing the release of incretin. Free fatty acid receptors (FFARs) belong to the class A G-protein coupled receptors and are comprised of three members, each encoded by a separate gene (FFAR1, FFAR2, and FFAR3). These genes and a fourth pseudogene, GPR42, are localized together on chromosome 19. FFARs are considered important components of the body's nutrient sensing mechanism, and therefore, these receptors are potential therapeutic targets for the treatment of metabolic disorders, such as type 2 diabetes and obesity. 284 matched cddid_all.tbl CDD cd15170 cd15170 320298 7tmA_FFAR2_FFAR3 free fatty acid receptors 2, 3, and similar proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This subgroup includes free fatty acid receptor 2 (FFAR2), FFAR3, and similar proteins. They are a member of the class A G-protein coupled receptors that bind free fatty acids. The FFAR subfamily is composed of three receptors, each encoded by a separate gene (FFAR1, FFAR2, and FFAR3). These genes and a fourth pseudogene, GPR42, are localized together on chromosome 19. FFAR2 and FFAR3 are cell-surface receptors for short chain FFAs (SCFAs) with different ligand affinities, whereas FFAR1 is a receptor for medium- and long-chain FFAs. FFAR2 activation by SCFA suppresses adipose insulin signaling, which leads to inhibition of fat accumulation in adipose tissue. FAAR3 is expressed in intestinal L cells, which produces glucagon-like peptide 1 (GLP-1) and peptide YY (PYY), thus suggesting that this receptor may be involved in energy homeostasis. FFARs are considered important components of the body's nutrient sensing mechanism, and therefore, these receptors are potential therapeutic targets for the treatment of metabolic disorders, such as type 2 diabetes and obesity. 278 matched cddid_all.tbl CDD cd15171 cd15171 320299 7tmA_CCRL2 CC chemokine receptor-like 2, member of the class A family of seven-transmembrane G protein-coupled receptors. Chemokine (CC-motif) receptor-like 2 (CCRL2) is a member of the atypical chemokine receptor family. CCRL2, like other atypical receptors, has an alteration in the conserved DRYLAIV motif in the third intracellular loop, which is essential for GPCR coupling and signaling. CCR2L is expressed in most hematopoietic cells and many lymphoid organs as well as in heart and lung. CCRL2 was initially reported to promote chemotaxis and calcium fluxes in responses to chemokines (CCL2, CCL5, CCL7, and CCL8); however, these results are still controversial. More recently, chemerin, a chemotactic agonist of CMKLR1 (chemokine-like receptor-1) and GPR1, was identified as a novel non-signaling ligand for both human and mouse CCRL2. Chemokines are principal regulators for leukocyte trafficking, recruitment, and activation. Chemokine family membership is defined on the basis of sequence homology and on the presence of variations on a conserved cysteine motif, which allows the family to further divide into four subfamilies (CC, CXC, XC, and CX3C). 279 matched cddid_all.tbl CDD cd15172 cd15172 341330 7tmA_CCR6 CC chemokine receptor type 6, member of the class A family of seven-transmembrane G protein-coupled receptors. CCR6 is the only known receptor identified for the chemokine CCL20 (also known as macrophage inflammatory protein-3alpha, MIP-3alpha). CCR6 is expressed by all mature human B cells, effector memory T-cells, and dendritic cells found in the gut mucosal immune system. CCL20 contributes to recruitment of CCR6-expressing cells to Peyer's patches and isolated lymphoid follicles in the intestine, thereby promoting the assembly and maintenance of organized lymphoid structures. Also, CCL20 expression is highly inducible in response to inflammatory signals. Thus, CCL20 is involved in both inflammatory and homeostatic functions in the immune system. Chemokines are principal regulators for leukocyte trafficking, recruitment, and activation. Chemokine family membership is defined on the basis of sequence homology and on the presence of variations on a conserved cysteine motif, which allows the family to further divide into four subfamilies (CC, CXC, XC, and CX3C). Chemokines interact with seven-transmembrane receptors which are typically coupled to G protein for signaling. Currently, there are ten known receptors for CC chemokines, seven for CXC chemokines, and single receptors for the XC and CX3C chemokines. The CC chemokine receptors are all activating the G protein Gi. 281 matched cddid_all.tbl CDD cd15173 cd15173 320301 7tmA_CXCR6 CXC chemokine receptor type 6, member of the class A family of seven-transmembrane G protein-coupled receptors. CXCR6 binds specifically to the chemokine CXCL16, which is expressed on dendritic cells, monocyte/macrophages, activated T cells, fibroblastic reticular cells, and cancer cells. CXCR6 is phylogenetically more closely related to CC-type chemokine receptors (CCR6 and CCR9) than other CXC receptors. Chemokines are principal regulators for leukocyte trafficking, recruitment, and activation. Chemokine family membership is defined on the basis of sequence homology and on the presence of variations on a conserved cysteine motif, which allows the family to further divide into four subfamilies (CC, CXC, XC, and CX3C). Chemokines interact with seven-transmembrane receptors which are typically coupled to G protein for signaling. Currently, there are ten known receptors for CC chemokines, seven for CXC chemokines, and single receptors for the XC and CX3C chemokines. 270 matched cddid_all.tbl CDD cd15174 cd15174 320302 7tmA_CCR9 CC chemokine receptor type 9, member of the class A family of seven-transmembrane G protein-coupled receptors. CCR9 is a homeostatic receptor specific for CCL25 (formerly known as thymus expressed chemokine) and is highly expressed on both immature and mature thymocytes as well as on intestinal homing T Lymphocytes and mucosal Lymphocytes. In cutaneous melanoma, activation of CCR9-CCL25 has been shown to stimulate metastasis to the small intestine. Chemokines are principal regulators for leukocyte trafficking, recruitment, and activation. Chemokine family membership is defined on the basis of sequence homology and on the presence of variations on a conserved cysteine motif, which allows the family to further divide into four subfamilies (CC, CXC, XC, and CX3C). Chemokines interact with seven-transmembrane receptors which are typically coupled to G protein for signaling. Currently, there are ten known receptors for CC chemokines, seven for CXC chemokines, and single receptors for the XC and CX3C chemokines. The CC chemokine receptors are all activating the G protein Gi. 280 matched cddid_all.tbl CDD cd15175 cd15175 341331 7tmA_CCR7 CC chemokine receptor type 7, member of the class A family of seven-transmembrane G protein-coupled receptors. CCR7 is a major homeostatic receptor responsible for lymph node development and effective adaptive immune responses and plays a critical role in trafficking of dendritic cells and B and T lymphocytes. Its only two ligands, CCL and CCl21, are primarily produced by stromal cells in the T cell zones of lymph nodes and spleen. Chemokines are principal regulators for leukocyte trafficking, recruitment, and activation. Chemokine family membership is defined on the basis of sequence homology and on the presence of variations on a conserved cysteine motif, which allows the family to further divide into four subfamilies (CC, CXC, XC, and CX3C). Chemokines interact with seven-transmembrane receptors which are typically coupled to G protein for signaling. Currently, there are ten known receptors for CC chemokines, seven for CXC chemokines, and single receptors for the XC and CX3C chemokines. The CC chemokine receptors are all activating the G protein Gi. 278 matched cddid_all.tbl CDD cd15176 cd15176 320304 7tmA_ACKR4_CCR11 atypical chemokine receptor 4, member of the class A family of seven-transmembrane G protein-coupled receptors. ACKR4 was first reported to bind several CC chemokines including CCL19, CCL21, and CCL25 and was originally designated CCR11. AKCR4 is unable to couple to G-protein and, instead, it preferentially mediates beta-arrestin dependent processes, such as receptor internalization, after ligand binding. Thus, ACKR4 may act as a scavenger receptor to suppress the effects of proinflammatory chemokines. Unlike the classical chemokine receptors that contain a conserved DRYLAIV motif in the second intracellular loop, which is required for G-protein coupling, the ACKRs lack this conserved motif and fail to couple to G-proteins and induce classical GPCR signaling. Five receptors have been identified for the ACKR family, including CC-chemokine receptors like 1 and 2 (CCRL1 and CCRL2), CXCR7, Duffy antigen receptor for chemokine (DARC), and D6. Both ACKR1 (DARC) and ACKR3 (CXCR7) show low sequence homology to the classic chemokine receptors. 276 matched cddid_all.tbl CDD cd15177 cd15177 341332 7tmA_CCR10 CC chemokine receptor type 10, member of the class A family of seven-transmembrane G protein-coupled receptors. CCR10 is a homeostatic receptor specific for two C-C motif chemokines, CCL27 and CCL28. Activation of CCR10 by its two ligands mediates diverse activities, ranging from leukocyte trafficking to skin cancer. Chemokines are principal regulators for leukocyte trafficking, recruitment, and activation. Chemokine family membership is defined on the basis of sequence homology and on the presence of variations on a conserved cysteine motif, which allows the family to further divide into four subfamilies (CC, CXC, XC, and CX3C). Chemokines interact with seven-transmembrane receptors which are typically coupled to G protein for signaling. Currently, there are ten known receptors for CC chemokines, seven for CXC chemokines, and single receptors for the XC and CX3C chemokines. The CC chemokine receptors are all activating the G protein Gi. 280 matched cddid_all.tbl CDD cd15178 cd15178 341333 7tmA_CXCR1_2 CXC chemokine receptor types 1 and 2, member of the class A family of seven-transmembrane G protein-coupled receptors. CXCR1 and CXCR2 are closely related chemotactic receptors for a group of CXC chemokines distinguished by the presence of the amino acid motif ELR immediately adjacent to their CXC motif. Expression of CXCR1 and CXCR2 is strictly controlled in neutrophils by external stimuli such as lipopolysaccharide (LPS), tumor necrosis factor (TNF)-alpha, Toll-like receptor agonists, and nitric oxide. CXCL8 (formerly known as interleukin-8) binds with high-affinity and activates both receptors. CXCR1 also binds CXCL7 (neutrophil-activating protein-2), whereas CXCR2 non-selectively binds to all seven ELR-positive chemokines (CXCL1-7). Chemokines are principal regulators for leukocyte trafficking, recruitment, and activation. Chemokine family membership is defined on the basis of sequence homology and on the presence of variations on a conserved cysteine motif, which allows the family to further divide into four subfamilies (CC, CXC, XC, and CX3C). Chemokines interact with seven-transmembrane receptors which are typically coupled to G protein for signaling. Currently, there are ten known receptors for CC chemokines, seven for CXC chemokines, and single receptors for the XC and CX3C chemokines. 279 matched cddid_all.tbl CDD cd15179 cd15179 341334 7tmA_CXCR4 CXC chemokine receptor type 4, member of the class A family of seven-transmembrane G protein-coupled receptors. CXCR4 is the only known G protein-coupled chemokine receptor for the key homeostatic ligand CXCL12, which is constitutively secreted by bone marrow stromal cells. Atypical chemokine receptor CXCR7 (ACKR3) also binds CXCL12, but activates signaling in a G protein-independent manner. CXCR4 is also a co-receptor for HIV infection and plays critical roles in the development of immune system during both lymphopoiesis and myelopoiesis. Chemokines are principal regulators for leukocyte trafficking, recruitment, and activation. Chemokine family membership is defined on the basis of sequence homology and on the presence of variations on a conserved cysteine motif, which allows the family to further divide into four subfamilies (CC, CXC, XC, and CX3C). Chemokines interact with seven-transmembrane receptors which are typically coupled to G protein for signaling. Currently, there are ten known receptors for CC chemokines, seven for CXC chemokines, and single receptors for the XC and CX3C chemokines. 278 matched cddid_all.tbl CDD cd15180 cd15180 341335 7tmA_CXCR3 CXC chemokine receptor type 3, member of the class A family of seven-transmembrane G protein-coupled receptors. CXCR3 is an inflammatory chemotactic receptor for a group of CXC chemokines distinguished by the presence of the amino acid motif ELR immediately adjacent to their CXC motif. CXCR3 specifically binds three chemokines CXCL9 (monokine induced by gamma-interferon), CXCL10 (interferon induced protein of 10 kDa), and CXCL11 (interferon inducible T-cell alpha-chemoattractant, I-TAC). CXC3R is expressed on CD4+ Th1 and CD8+ cytotoxic T lymphocytes as well as highly on innate lymphocytes, such as NK cells and NK T cells, where it may mediate the recruitment of these cells to the sites of infection and inflammation. Chemokines are principal regulators for leukocyte trafficking, recruitment, and activation. Chemokine family membership is defined on the basis of sequence homology and on the presence of variations on a conserved cysteine motif, which allows the family to further divide into four subfamilies (CC, CXC, XC, and CX3C). Chemokines interact with seven-transmembrane receptors which are typically coupled to G protein for signaling. Currently, there are ten known receptors for CC chemokines, seven for CXC chemokines, and single receptors for the XC and CX3C chemokines. 280 matched cddid_all.tbl CDD cd15181 cd15181 341336 7tmA_CXCR5 CXC chemokine receptor type 5, member of the class A family of seven-transmembrane G protein-coupled receptors. CXCR5 is a B-cell selective receptor that binds specifically to the homeostatic chemokine CXCL13 and regulates adaptive immunity. The receptor is found on all peripheral blood and tonsillar B cells and is involved in lymphocyte migration (homing) to specific tissues and development of normal lymphoid tissue. Chemokines are principal regulators for leukocyte trafficking, recruitment, and activation. Chemokine family membership is defined on the basis of sequence homology and on the presence of variations on a conserved cysteine motif, which allows the family to further divide into four subfamilies (CC, CXC, XC, and CX3C). Chemokines interact with seven-transmembrane receptors which are typically coupled to G protein for signaling. Currently, there are ten known receptors for CC chemokines, seven for CXC chemokines, and single receptors for the XC and CX3C chemokines. 281 matched cddid_all.tbl CDD cd15182 cd15182 341337 7tmA_XCR1 XC chemokine receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors. XCR1 is a chemokine receptor specific for XCL1 and XCL2 (previously called lymphotactin alpha/beta), which differ in only two amino acids. XCL1/2 is the only member of the C chemokine subfamily, which is unique as containing only two of the four cysteines that are found in other chemokine families. Human XCL1/2 has been shown to be secreted by activated CD8+ T cells and upon activation of the innate immune system. Chemokines are principal regulators for leukocyte trafficking, recruitment, and activation. Chemokine family membership is defined on the basis of sequence homology and on the presence of variations on a conserved cysteine motif, which allows the family to further divide into four subfamilies (CC, CXC, XC, and CX3C). Chemokines interact with seven-transmembrane receptors which are typically coupled to G protein for signaling. 271 matched cddid_all.tbl CDD cd15183 cd15183 320311 7tmA_CCR1 CC chemokine receptor type 1, member of the class A family of seven-transmembrane G protein-coupled receptors. CCR1 is widely expressed on both hematopoietic and non-hematopoietic cells and binds to the inflammatory CC chemokines CCL3, CCL5, CCL6, CCL9, CCL15, and CCL23. CCR1 activates the typical chemokine signaling pathway through the G(i/o) type of G proteins, causing inhibition of adenylate cyclase and stimulation of phospholipase C, PKC, calcium flux, and PLA2. Chemokines are principal regulators for leukocyte trafficking, recruitment, and activation. Chemokine family membership is defined on the basis of sequence homology and on the presence of variations on a conserved cysteine motif, which allows the family to further divide into four subfamilies (CC, CXC, XC, and CX3C). Chemokines interact with seven-transmembrane receptors which are typically coupled to G protein for signaling. Currently, there are ten known receptors for CC chemokines, seven for CXC chemokines, and single receptors for the XC and CX3C chemokines. 278 matched cddid_all.tbl CDD cd15184 cd15184 341338 7tmA_CCR5_CCR2 CC chemokine receptor types 5 and 2, member of the class A family of seven-transmembrane G protein-coupled receptors. CCR2 and CCR5 share very high amino acid sequence identity. Both receptors play important roles in the trafficking of monocytes/macrophages and are implicated in the pathogenesis of immunologic diseases (rheumatoid arthritis, celiac disease, and transplant rejection) and cardiovascular diseases (atherosclerosis and autoimmune hepatitis). CCR2 is a receptor specific for members of the monocyte chemotactic protein family, including CCL2, CCL7, and CCL13. Conversely, CCR5 is a major co-receptor for HIV infection and binds many CC chemokine ligands, including CC chemokine ligands including CCL2, CCL3, CCL4, CCL5, CCL11, CCL13, CCL14, and CCL16. CCR2 is expressed primarily on blood monocytes and memory T cells, whereas CCR5 is expressed on antigen-presenting cells (macrophages and dendritic cells) and activated T effector cells. Chemokines are principal regulators for leukocyte trafficking, recruitment, and activation. Chemokine family membership is defined on the basis of sequence homology and on the presence of variations on a conserved cysteine motif, which allows the family to further divide into four subfamilies (CC, CXC, XC, and CX3C). Chemokines interact with seven-transmembrane receptors which are typically coupled to G protein for signaling. Currently, there are ten known receptors for CC chemokines, seven for CXC chemokines, and single receptors for the XC and CX3C chemokines. 278 matched cddid_all.tbl CDD cd15185 cd15185 341339 7tmA_CCR3 CC chemokine receptor type 3, member of the class A family of seven-transmembrane G protein-coupled receptors. CCR3 is a highly promiscuous receptor that binds a variety of inflammatory CC-type chemokines, including CCL11 (eotaxin-1), CCL3L1, CCL5 (regulated on activation, normal T cell expressed and secreted; RANTES), CCL7 (monocyte-specific chemokine 3 or MCP-3), CCL8 (MCP-2), CCL11, CCL13 (MCP-4), CCL15, CCL24 (eotaxin-2), CCL26 (eotaxin-3), and CCL28. Among these, the eosinophil chemotactic chemokines (CCL11, CCL24, and CCL26) are the most potent and specific ligands. In addition to eosinophil, CCR3 is expressed on cells involved in allergic responses, such as basophils, Th2 lymphocytes, and mast cells. Chemokines are principal regulators for leukocyte trafficking, recruitment, and activation. Chemokine family membership is defined on the basis of sequence homology and on the presence of variations on a conserved cysteine motif, which allows the family to further divide into four subfamilies (CC, CXC, XC, and CX3C). Chemokines interact with seven-transmembrane receptors which are typically coupled to G protein for signaling. Currently, there are ten known receptors for CC chemokines, seven for CXC chemokines, and single receptors for the XC and CX3C chemokines. 278 matched cddid_all.tbl CDD cd15186 cd15186 320314 7tmA_CX3CR1 CX3C chemokine receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors. CX3CR1 is an inflammatory receptor specific for CX3CL1 (also known as fractalkine in human), which is involved in the adhesion and migration of leukocytes. The CX3C chemokine subfamily is only represented by CX3CL1, which exists in both soluble and membrane-anchored forms. Membrane-anchored form promotes strong adhesion of receptor-bearing leukocytes to CX3CL1-expressing endothelial cells. On the other hand, soluble CX3CL1, which is released by the proteolytic cleavage of membrane-anchored CX3CL1, is a potent chemoattractant for CX3CR1-expressing T cells and monocytes. Chemokine family membership is defined on the basis of sequence homology and on the presence of variations on a conserved cysteine motif, which allows the family to further divide into four subfamilies (CC, CXC, XC, and CX3C). Chemokines interact with seven-transmembrane receptors which are typically coupled to G protein for signaling. 273 matched cddid_all.tbl CDD cd15187 cd15187 320315 7tmA_CCR8 CC chemokine receptor type 8, member of the class A family of seven-transmembrane G protein-coupled receptors. CCR8, the receptor for the CC chemokines CCL1 and CC16, is highly expressed on allergen-specific T-helper type 2 cells, and is implicated in the pathogenesis of human asthma. CCL1- and CCR8-expressing CD4+ effector T lymphocytes are shown to have a critical role in lung mucosal inflammatory responses. CCR8 is also a functional receptor for CCL16, a liver-expressed CC chemokine that involved in attracting lymphocytes, dendritic cells, and monocytes. Chemokines are principal regulators for leukocyte trafficking, recruitment, and activation. Chemokine family membership is defined on the basis of sequence homology and on the presence of variations on a conserved cysteine motif, which allows the family to further divide into four subfamilies (CC, CXC, XC, and CX3C). Chemokines interact with seven-transmembrane receptors which are typically coupled to G protein for signaling. Currently, there are ten known receptors for CC chemokines, seven for CXC chemokines, and single receptors for the XC and CX3C chemokines. 276 matched cddid_all.tbl CDD cd15188 cd15188 320316 7tmA_ACKR2_D6 atypical chemokine receptor 2, member of the class A family of seven-transmembrane G protein-coupled receptors. ACKR2 (also known as D6) binds non-selectively to all inflammatory CC-chemokines, but not to homeostatic CC-chemokines involved in controlling the migration of cells. Unlike the classical chemokine receptors that contain a conserved DRYLAIV motif in the second intracellular loop, which is required for G-protein coupling, the ACKRs lack this conserved motif and fail to couple to G-proteins and induce classical GPCR signaling. Five receptors have been identified for the ACKR family, including CC-chemokine receptors like 1 and 2 (CCRL1 and CCRL2), CXCR7, Duffy antigen receptor for chemokine (DARC), and D6. Both ACKR1 (DARC) and ACKR3 (CXCR7) show low sequence homology to the classic chemokine receptors. 278 matched cddid_all.tbl CDD cd15189 cd15189 320317 7tmA_Bradykinin_R bradykinin receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. The bradykinin receptor family is a group of the seven transmembrane G-protein coupled receptors, whose endogenous ligand is the pro-inflammatory nonapeptide bradykinin that mediates various vascular and pain responses. Two major bradykinin receptor subtypes, B1 and B2, have been identified based on their pharmacological properties. The B1 receptor is rapidly induced by tissue injury and inflammation, whereas the B2 receptor is ubiquitously expressed on many tissue types. Both receptors contain three consensus sites for N-linked glycosylation in extracellular domains and couple to G(q) protein to activate phospholipase C, leading to phosphoinositide hydrolysis and intracellular calcium mobilization. They can also interact with G(i) protein to inhibit adenylate cyclase and activate the MAPK (mitogen-activated protein kinase) pathways. 284 matched cddid_all.tbl CDD cd15190 cd15190 341340 7tmA_Apelin_R apelin receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. Apelin (APJ) receptor is a G protein-coupled receptor that binds the endogenous peptide ligands, apelin and Toddler/Elabela. APJ is an adipocyte-derived hormone that is ubiquitously expressed throughout the human body and Toddler/Elabela is a short secretory peptide that is required for normal cardiac development in zebrafish. Activation of APJ receptor plays key roles in diverse physiological processes including vasoconstriction and vasodilation, cardiac muscle contractility, angiogenesis, and regulation of water balance and food intake. 304 matched cddid_all.tbl CDD cd15191 cd15191 341341 7tmA_AT2R type 2 angiotensin II receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. Angiotensin II (Ang II), the main effector in the renin-angiotensin system, plays a crucial role in the regulation of cardiovascular homeostasis through its type 1 (AT1) and type 2 (AT2) receptors. Ang II contributes to cardiovascular diseases such as hypertension and atherosclerosis via AT1R activation. Ang II increases blood pressure through Gq-mediated activation of phospholipase C, resulting in phosphoinositide (PI) hydrolysis and increased intracellular calcium levels. Through the AT2R, Ang II counteracts the vasoconstrictor action of AT1R and thereby induces vasodilation, sodium excretion, and reduction of blood pressure. Moreover, AT1R promotes cell proliferation, whereas AT2R inhibits proliferation and stimulates cell differentiation. The AT2R is highly expressed during fetal development, however it is scarcely present in adult tissues and is induced in pathological conditions. Generally, the AT1R mediates many actions of Ang II, while the AT2R is involved in the regulation of blood pressure and renal function. 285 matched cddid_all.tbl CDD cd15192 cd15192 320320 7tmA_AT1R type 1 angiotensin II receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. Angiotensin II (Ang II), the main effector in the renin-angiotensin system, plays a crucial role in the regulation of cardiovascular homeostasis through its type 1 (AT1) and type 2 (AT2) receptors. Ang II contributes to cardiovascular diseases such as hypertension and atherosclerosis via AT1R activation. Ang II increases blood pressure through Gq-mediated activation of phospholipase C, resulting in phosphoinositide (PI) hydrolysis and increased intracellular calcium levels. Through the AT2R, Ang II counteracts the vasoconstrictor action of AT1R and thereby induces vasodilation, sodium excretion, and reduction of blood pressure. Moreover, AT1R promotes cell proliferation, whereas AT2R inhibits proliferation and stimulates cell differentiation. The AT2R is highly expressed during fetal development, however it is scarcely present in adult tissues and is induced in pathological conditions. Generally, the AT1R mediates many actions of Ang II, while the AT2R is involved in the regulation of blood pressure and renal function. 285 matched cddid_all.tbl CDD cd15193 cd15193 320321 7tmA_GPR25 G protein-coupled receptor 25, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR25 is an orphan G-protein coupled receptor that shares strong sequence homology to GPR15 and the angiotensin II receptors. These closely related receptors form a group within the class A G-protein coupled receptors (GPCRs). GPR15 controls homing of T cells, especially FOXP3(+) regulatory T cells, to the large intestine mucosa and thereby mediates local immune homeostasis. Moreover, GRP15-deficient mice were shown to be prone to develop more severe large intestine inflammation. Angiotensin II (Ang II), the main effector in the renin-angiotensin system, plays a crucial role in the regulation of cardiovascular homeostasis through its type 1 (AT1) and type 2 (AT2) receptors. 279 matched cddid_all.tbl CDD cd15194 cd15194 320322 7tmA_GPR15 G protein-coupled receptor 15, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR15, also called as Brother of Bonzo (BOB), is an orphan G-protein coupled receptor that was originally identified as a co-receptor for human immunodeficiency virus. GPR15 is upregulated in patients with rheumatoid arthritis and shares high sequence homology with angiotensin II type AT1 and AT2 receptors; however, its endogenous ligand is unknown. GPR15 controls homing of T cells, especially FOXP3(+) regulatory T cells, to the large intestine mucosa and thereby mediates local immune homeostasis. Moreover, GRP15-deficient mice were shown to be prone to develop more severe large intestine inflammation. 281 matched cddid_all.tbl CDD cd15195 cd15195 320323 7tmA_GnRHR-like gonadotropin-releasing hormone and adipokinetic hormone receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Gonadotropin-releasing hormone (GnRH) and adipokinetic hormone (AKH) receptors share strong sequence homology to each other, suggesting that they have a common evolutionary origin. GnRHR, also known as luteinizing hormone releasing hormone receptor (LHRHR), plays an central role in vertebrate reproductive function; its activation by binding to GnRH leads to the release of follicle stimulating hormone (FSH) and luteinizing hormone (LH) from the pituitary gland. Adipokinetic hormone (AKH) is a lipid-mobilizing hormone that is involved in control of insect metabolism. Generally, AKH behaves as a typical stress hormone by mobilizing lipids, carbohydrates and/or certain amino acids such as proline. Thus, it utilizes the body's energy reserves to fight the immediate stress problems and subdue processes that are less important. Although AKH is known to responsible for regulating the energy metabolism during insect flying, it is also found in insects that have lost its functional wings and predominantly walk for their locomotion. Both GnRH and AKH receptors are members of the class A of the seven-transmembrane, G-protein coupled receptor (GPCR) superfamily. 293 matched cddid_all.tbl CDD cd15196 cd15196 320324 7tmA_Vasopressin_Oxytocin vasopressin and oxytocin receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Vasopressin (also known as arginine vasopressin or anti-diuretic hormone) and oxytocin are synthesized in the hypothalamus and are released from the posterior pituitary gland. The actions of vasopressin are mediated by the interaction of this hormone with three receptor subtypes: V1aR, V1bR, and V2R. These subtypes are differ in localization, function, and signaling pathways. Activation of V1aR and V1bR stimulate phospholipase C, while activation of V2R stimulates adenylate cyclase. Although vasopressin and oxytocin differ only by two amino acids and stimulate the same cAMP/PKA pathway, they have divergent physiological functions. Vasopressin is involved in regulating blood pressure and the balance of water and sodium ions, whereas oxytocin plays an important role in the uterus during childbirth and in lactation. 264 matched cddid_all.tbl CDD cd15197 cd15197 320325 7tmA_NPSR neuropeptide S receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. Neuropeptide S (NPS) promotes arousal and anxiolytic-like effects by activating its cognate receptor NPSR. NPSR is widely expressed in the brain, and its activation induces an elevation of intracellular calcium and cAMP concentrations, presumably by coupling to G(s) and G(q) proteins. Mutations in NPSR have been associated with an increased susceptibility to asthma. NPSR was originally identified as an orphan receptor GPR154 and is also known as G protein receptor for asthma susceptibility (GPRA) or vasopressin receptor-related receptor 1 (VRR1). 294 matched cddid_all.tbl CDD cd15198 cd15198 320326 7tmA_GPR150 G protein-coupled receptor 150, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR150 is an orphan receptor closely related to the oxytocin and vasopressin receptors. Its endogenous ligand is not known. These receptors share a significant amino acid sequence similarity, suggesting that they have a common evolutionary origin. 299 matched cddid_all.tbl CDD cd15199 cd15199 320327 7tmA_GPR31 G protein-coupled receptor 31, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR31, also known as 12-(S)-HETE receptor, is a high-affinity receptor for 12-(S)-hydroxy-5,8,10,14-eicosatetraenoic acid. Phylogenetic analysis showed that GPR31 and oxoeicosanoid receptor 1 (OXER1, GPR170) are the most closely related receptors to the hydroxycarboxylic acid receptor family (HCARs). GPR31, like OXER1, activates the ERK1/2 (MAPK3/MAPK1) pathway of intracellular signaling, but unlike the OXER1, does not cause increase in the cytosolic calcium level. GPR31 is also shown to activate NFkB. 12-(S)-HETE is a 12-lipoxygenase metabolite of arachidonic acid produced by mammalian platelets and tumor cells. It promotes tumor cells adhesion to endothelial cells and sub-endothelial matrix, which is a critical step for metastasis. 278 matched cddid_all.tbl CDD cd15200 cd15200 320328 7tmA_OXER1 oxoeicosanoid receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors. OXER1, also called GPR170, is a receptor for eicosanoids and polyunsaturated fatty acids such as 5-oxo-6E,8Z,11Z,14Z-eicosatetraenoic acid (5-OXO-ETE), 5(S)-hydroperoxy-6E,8Z,11Z,14Z-eicosatetraenoic acid (5(S)-HPETE) and arachidonic acid. OXER1 is a member of the class A family of seven-transmembrane G-protein coupled receptors and appears to be coupled to the G(i/o) protein. The receptor is expressed in various tissues except brain. Phylogenetic analysis showed that GPR31 and OXER1 are the most closely related receptors to the hydroxycarboxylic acid receptor family (HCARs). OXER1, like GPR31, activates the ERK1/2 (MAPK3/MAPK1) pathway of intracellular signaling, but unlike GPR31, does cause increase in the cytosolic calcium level. 276 matched cddid_all.tbl CDD cd15201 cd15201 320329 7tmA_HCAR1-3 hydroxycarboxylic acid receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Hydroxycarboxylic acid receptor (HCAR) subfamily, a member of the class A G-protein coupled receptors (GPCRs), contains three receptor subtypes: HCAR1, HCAR2, and HCAR3. The endogenous ligand of HCAR1 (also known as lactate receptor 1, GPR104, or GPR81) is L-lactic acid. The endogenous ligands of HCAR2 (also known as niacin receptor 1, GPR109A, or nicotinic acid receptor) and HCAR3 (also known as niacin receptor 2 or GPR109B) are 3-hydroxybutyric acid and 3-hydroxyoctanoic acid, respectively. Because nicotinic acid is capable of stimulating HCAR2 at higher concentrations only (in the range of sub-micromolar concentration), it is unlikely that nicotinic acts as a physiological ligand of HCAR2. All three receptors are expressed in adipocytes and mediate anti-lipolytic effects in fat cells through G(i) type G protein-dependent inhibition of adenylate cyclase. 281 matched cddid_all.tbl CDD cd15202 cd15202 320330 7tmA_TACR-like tachykinin receptors and related receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes the neurokinin/tachykinin receptors and its closely related receptors such as orphan GPR83 and leucokinin-like peptide receptor. The tachykinins are widely distributed throughout the mammalian central and peripheral nervous systems and act as excitatory transmitters on neurons and cells in the gastrointestinal tract. The TKs are characterized by a common five-amino acid C-terminal sequence, Phe-X-Gly-Leu-Met-NH2, where X is a hydrophobic residue. The three major mammalian tachykinins are substance P (SP), neurokinin A (NKA), and neurokinin B (NKB). The physiological actions of tachykinins are mediated through three types of receptors: neurokinin receptor type 1 (NK1R), NK2R, and NK3R. SP is a high-affinity endogenous ligand for NK1R, which interacts with the Gq protein and activates phospholipase C, leading to elevation of intracellular calcium. NK2R is a high-affinity receptor for NKA, the tachykinin neuropeptide substance K. SP and NKA are found in the enteric nervous system and mediate in the regulation of gastrointestinal motility, secretion, vascular permeability, and pain perception. NK3R is activated by its high-affinity ligand, NKB, which is primarily involved in the central nervous system and plays a critical role in the regulation of gonadotropin hormone release and the onset of puberty. 288 matched cddid_all.tbl CDD cd15203 cd15203 320331 7tmA_NPYR-like neuropeptide Y receptors and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. NPY is a 36-amino acid peptide neurotransmitter with a C-terminal tyrosine amide residue that is widely distributed in the brain and the autonomic nervous system of many mammalian species. NPY exerts its functions through five, G-protein coupled receptor subtypes including NPY1R, NPY2R, NPY4R, NPY5R, and NPY6R; however, NPY6R is not functional in humans. NYP receptors are also activated by its two other family members, peptide YY (PYY) and pancreatic polypeptide (PP). They typically couple to Gi or Go proteins, which leads to a decrease in adenylate cyclase activity, thereby decreasing intracellular cAMP levels, and are involved in diverse physiological roles including appetite regulation, circadian rhythm, and anxiety. Also included in this subgroup is prolactin-releasing peptide (PrRP) receptor (previously known as GPR10), which is activated by its endogenous ligand PrRP, a neuropeptide possessing C-terminal Arg-Phe-amide motif. There are two active isoforms of PrRP in mammals: one consists of 20 amino acid residues (PrRP-20) and the other consists of 31 amino acid residues (PrRP-31). PrRP receptor shows significant sequence homology to the NPY receptors, and a micromolar level of NPY can bind and completely inhibit the PrRP-evoked intracellular calcium response in PrRP receptor-expressing cells, suggesting that the PrRP receptor shares a common ancestor with the NPY receptors. 293 matched cddid_all.tbl CDD cd15204 cd15204 320332 7tmA_prokineticin-R prokineticin receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Prokineticins 1 (PROK1) and 2 (PROK2), also known as endocrine gland vascular endothelial factor and Bombina varigata 8, respectively, are multifunctional chemokine-like peptides that are highly conserved across species. Prokineticins can bind with similar affinities to two closely homologous 7-transmembrane G protein coupled receptors, PROKR1 and PROKR2, which are phylogenetically related to the tachykinin receptors. Prokineticins and their GPCRs are widely distributed in human tissues and are involved in numerous physiological roles, including gastrointestinal motility, generation of circadian rhythms, neuron migration and survival, pain sensation, angiogenesis, inflammation, and reproduction. Moreover, different point mutations in genes encoding PROK2 or its receptor (PROKR2) can lead to Kallmann syndrome, a disease characterized by delayed or absent puberty and impaired olfactory function. 288 matched cddid_all.tbl CDD cd15205 cd15205 320333 7tmA_QRFPR pyroglutamylated RFamide peptide receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. 26RFa, also known as QRFP (Pyroglutamylated RFamide peptide), is a 26-amino acid residue peptide that belongs to a family of neuropeptides containing an Arg-Phe-NH2 (RFamide) motif at its C-terminus. 26Rfa/QRFP exerts similar orexigenic activity including the regulation of feeding behavior in mammals. It is the ligand for G-protein coupled receptor 103 (GPR103), which is predominantly expressed in paraventricular (PVN) and ventromedial (VMH) nuclei of the hypothalamus. GPR103 shares significant protein sequence homology with orexin receptors (OX1R and OX2R), which have recently shown to produce a neuroprotective effect in Alzheimer's disease by forming a functional heterodimer with GPR103. 298 matched cddid_all.tbl CDD cd15206 cd15206 320334 7tmA_CCK_R cholecystokinin receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Cholecystokinin receptors (CCK-AR and CCK-BR) are a group of G-protein coupled receptors which bind the peptide hormones cholecystokinin (CCK) or gastrin. CCK, which facilitates digestion in the small intestine, and gastrin, a major regulator of gastric acid secretion, are highly similar peptides. Like gastrin, CCK is a naturally-occurring linear peptide that is synthesized as a preprohormone, then proteolytically cleaved to form a family of peptides with the common C-terminal sequence (Gly-Trp-Met-Asp-Phe-NH2), which is required for full biological activity. CCK-AR (type A, alimentary; also known as CCK1R) is found abundantly on pancreatic acinar cells and binds only sulfated CCK-peptides with very high affinity, whereas CCK-BR (type B, brain; also known as CCK2R), the predominant form in the brain and stomach, binds CCK or gastrin and discriminates poorly between sulfated and non-sulfated peptides. CCK is implicated in regulation of digestion, appetite control, and body weight, and is involved in neurogenesis via CCK-AR. There is some evidence to support that CCK and gastrin, via their receptors, are involved in promoting cancer development and progression, acting as growth and invasion factors. 269 matched cddid_all.tbl CDD cd15207 cd15207 320335 7tmA_NPFFR neuropeptide FF receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Neuropeptide FF (NPFF) is a mammalian octapeptide that belongs to a family of neuropeptides containing an RF-amide motif at their C-terminus that have been implicated in a wide range of physiological functions in the brain including pain sensitivity, insulin release, food intake, memory, blood pressure, and opioid-induced tolerance and hyperalgesia. The effects of these peptides are mediated through neuropeptide FF1 and FF2 receptors (NPFF1-R and NPFF2-R) which are predominantly expressed in the brain. NPFF induces pro-nociceptive effects, mainly through the NPFF1-R, and anti-nociceptive effects, mainly through the NPFF2-R. NPFF has been shown to inhibit adenylate cyclase via the Gi protein coupled to NPFF1-R. 291 matched cddid_all.tbl CDD cd15208 cd15208 320336 7tmA_OXR orexin receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Orexins (OXs, also referred to as hypocretins) are neuropeptide hormones that regulate the sleep-wake cycle and potently influence homeostatic systems regulating appetite and feeding behavior or modulating emotional responses such as anxiety or panic. OXs are synthesized as prepro-orexin (PPO) in the hypothalamus and then proteolytically cleaved into two forms of isoforms: orexin-A (OX-A) and orexin-B (OX-B). OXA is a 33 amino-acid peptide with N-terminal pyroglutamyl residue and two intramolecular disulfide bonds, whereas OXB is a 28 amino-acid linear peptide with no disulfide bonds. OX-A binds orexin receptor 1 (OX1R) with high-affinity, but also binds with somewhat low-affinity to OX2R, and signals primarily to Gq coupling, whereas OX-B shows a strong preference for the orexin receptor 2 (OX2R) and signals through Gq or Gi/o coupling. Thus, activation of OX1R or OX2R will activate phospholipase activity and the phosphatidylinositol and calcium signaling pathways. Additionally, OX2R activation can also lead to inhibition of adenylate cyclase. 303 matched cddid_all.tbl CDD cd15209 cd15209 320337 7tmA_Mel1 melatonin receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors. Melatonin (N-acetyl-5-methoxytryptamine) is a naturally occurring sleep-promoting chemical found in vertebrates, invertebrates, bacteria, fungi, and plants. In mammals, melatonin is secreted by the pineal gland and is involved in regulation of circadian rhythms. Its production peaks during the nighttime, and is suppressed by light. Melatonin is shown to be synthesized in other organs and cells of many vertebrates, including the Harderian gland, leukocytes, skin, and the gastrointestinal (GI) tract, which contains several hundred times more melatonin than the pineal gland and is involved in the regulation of GI motility, inflammation, and sensation. Melatonin exerts its pleiotropic physiological effects through specific membrane receptors, named MT1A, MT1B, and MT1C, which belong to the class A rhodopsin-like G-protein coupled receptor family. MT1A and MT1B subtypes are present in mammals, whereas MT1C subtype has been found in amphibians and birds. The melatonin receptors couple to G proteins of the G(i/o) class, leading to the inhibition of adenylate cyclase. 279 matched cddid_all.tbl CDD cd15210 cd15210 320338 7tmA_GPR84-like G protein-coupled receptor 84 and similar proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR84, also known as the inflammation-related G-Protein coupled receptor EX33, is a receptor for medium-chain free fatty acid (FFA) with carbon chain lengths of C9 to C14. Among these medium-chain FFAs, capric acid (C10:0), undecanoic acid (C11:0), and lauric acid (C12:0) are the most potent endogenous agonists of GPR84, whereas short-chain and long-chain saturated and unsaturated FFAs do not activate this receptor. GPR84 contains a [G/N]RY-motif instead of the highly conserved Asp-Arg-Tyr (DRY) motif found in the third transmembrane helix (TM3) of the rhodopsin-like class A receptors and important for efficient G protein-coupled signal transduction. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, which then activate the heterotrimeric G proteins. In the case of GPR84, activation of the receptor couples to a pertussis toxin sensitive G(i/o)-protein pathway. GPR84 knockout mice showed increased Th2 cytokine production including IL-4, IL-5, and IL-13 compared to wild-type mice. It has been also shown that activation of GPR84 augments lipopolysaccharide-stimulated IL-8 production in polymorphonuclear leukocytes and TNF-alpha production in macrophages, suggesting that GPR84 may function as a proinflammatory receptor. 254 matched cddid_all.tbl CDD cd15211 cd15211 320339 7tmA_GPR88-like G protein-coupled receptor 88, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR88, an orphan G protein-coupled receptor, is predominantly and almost exclusively expressed within medium spiny neurons (MSNs) of the brain's striatum in both human and rodents; thus it is also called Striatum-specific GPCR (STRG). The striatum is known to involve in motor coordination, reward-based decision making, and response learning. GPR88 is shown to co-localize with both dopamine D1 and D2 receptors and displays the highest sequence similarity to receptors for biogenic amines such as dopamine and serotonin. GPR88 knockout mice showed abnormal behaviors observed in schizophrenia, such as disrupted sensorimotor gating, increased stereotypic behavior and locomotor activity in response to treatment with dopaminergic compounds such as apomorphine and amphetamine, respectively, suggesting a role for GPR88 in dopaminergic signaling. Furthermore, the transcriptional profiling studies showed that GPR88 expression is altered in a number of psychiatric disorders such as depression, drug addiction, bipolar and schizophrenia, providing further evidence that GPR88 plays an important role in CNS signaling pathways related to psychiatric disorder. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 283 matched cddid_all.tbl CDD cd15212 cd15212 320340 7tmA_GPR135 G protein-coupled receptor 135, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR135, also known as the somatostatin- and angiotensin-like peptide receptor (SALPR), is found in various tissues including eye, brain, cervix, stomach, and testis. Pharmacological studies have shown that relaxin-3 (R3) is a high-affinity endogenous ligand for GPR135. R3 has recently been identified as a new member of the insulin/relaxin family of peptide hormones and is exclusively expressed in the brain neurons. In addition to GPR135, R3 also acts as an agonist for GPR142, a pseudogene in the rat, and can activate LGR7 (leucine repeat-containing G-protein receptor-7), which is the main receptor for relaxin-1 (R1) and relaxin-2 (R2). While R1 and R2 are hormones primarily associated with reproduction and pregnancy, R3 is involved in neuroendocrine and sensory processing. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 285 matched cddid_all.tbl CDD cd15213 cd15213 320341 7tmA_PSP24-like G protein-coupled receptor PSP24 and similar proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes two human orphan receptors, GPR45 and GPR65, and their closely related proteins found in vertebrates and invertebrates. GPR45 and GPR 65 are also called PSP24-alpha (or PSP24-1) and PSP24-beta (or PSP24-2) in other vertebrates, respectively. These receptors exhibit the highest sequence homology to each other. PSP24 was originally identified as a novel, high-affinity lysophosphatidic acid (LPA) receptor in Xenopus laevis oocytes; however, PSP24 receptors (GPR45 and GPR63) have not been shown to be activated by LPA. Instead, sphingosine 1-phosphate and dioleoylphosphatidic acid have been shown to act as low affinity agonists for GPR63. PSP24 receptors are highly expressed in neuronal cells of cerebellum and their expression level remains constant from the early embryonic stages to adulthood, suggesting the important role of PSP24s in brain neuronal functions. Members of this subgroup contain the highly conserved Asp-Arg-Tyr/Phe (DRY/F) motif found in the third transmembrane helix (TM3) of the rhodopsin-like class A receptors which is important for efficient G protein-coupled signal transduction. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 262 matched cddid_all.tbl CDD cd15214 cd15214 320342 7tmA_GPR161 orphan G protein-coupled receptor 161, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR161, an orphan GPCR, is a negative regulator of Sonic hedgehog (Shh) signaling, which promotes the processing of zinc finger protein GLI3 into its transcriptional repressor form (GLI3R) during neural tube development. In the absence of Shh, this proteolytic processing is normally mediated by cAMP-dependent protein kinase A (PKA). GPR161 is recruited to primary cilia by a mechanism depends on TULP3 (tubby-related protein 3) and the intraflagellar complex A (IFT-A). Moreover, Gpr161 knockout mice show phenotypes observed in Tulp3/IFT-A mutants, and cause increased Shh signaling in the neural tube. Taken together, GPR161 negatively regulates the PKA-dependent GLI3 processing in the absence of Shh signal by coupling to G(s) protein, which causes activation of adenylate cyclase, elevated cAMP levels, and activation of PKA. Conversely, in the presence of Shh, GPR161 is removed from the cilia by internalization into the endosomal recycling compartment, leading to downregulation of its activity and thereby allowing Shh signaling to proceed. In addition, GPR161 is over-expressed in triple-negative breast cancer (lacking estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 (HER2) expression) and correlates with poor prognosis. Mutations of GPR161 have also been implicated as a novel cause for pituitary stalk interruption syndrome (PSIS), a rare congenital disease of the pituitary gland. GPR161 is a member of the class A family of GPCRs, which contains receptors for hormones, neurotransmitters, sensory stimuli, and a variety of other ligands. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 261 matched cddid_all.tbl CDD cd15215 cd15215 320343 7tmA_GPR101 orphan G protein-coupled receptor 101, member of the class A family of seven-transmembrane G protein-coupled receptors. Gpr101, an orphan GPCR, is predominantly expressed in the brain within discrete nuclei and is predicted to couple to the stimulatory G(s) protein, a potent activator of adenylate cyclase. GPR101 has been implicated in mediating the actions of GnRH-(1-5), a pentapeptide formed by metallopeptidase cleavage of the decapeptide gonadotropin-releasing hormone (GnRH), which plays a critical role in the regulation of the hypothalamic-pituitary-gonadal axis. GnRH-(1-5) acts on GPR101 to stimulate epidermal growth factor (EFG) release and EFG-receptor (EGFR) phosphorylation, leading to enhanced cell migration and invasion in the Ishikawa endometrial cancer cell line. Furthermore, these effects of GnRH-(1-5) are also dependent on enzymatic activation of matrix metallopeptidase-9 (MMP-9). GPR101 is a member of the class A family of GPCRs, which includes receptors for hormones, neurotransmitters, sensory stimuli, and a variety of other ligands. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 261 matched cddid_all.tbl CDD cd15216 cd15216 320344 7tmA_SREB1_GPR27 super conserved receptor expressed in brain 1 (or GPR27), member of the class A family of seven-transmembrane G protein-coupled receptors. The SREB (super conserved receptor expressed in brain) subfamily consists of at least three members, named SREB1 (GPR27), SREB2 (GPR85), and SREB3 (GPR173). They are very highly conserved G protein-coupled receptors throughout vertebrate evolution, however no endogenous ligands have yet been identified. SREB2 is greatly expressed in brain regions involved in psychiatric disorders and cognition, such as the hippocampal dentate gyrus. Genetic studies in both humans and mice have shown that SREB2 influences brain size and negatively regulates hippocampal adult neurogenesis and neurogenesis-dependent cognitive function, all of which are suggesting a potential link between SREB2 and schizophrenia. All three SREB genes are highly expressed in differentiated hippocampal neural stem cells. Furthermore, all GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 332 matched cddid_all.tbl CDD cd15217 cd15217 320345 7tmA_SREB3_GPR173 super conserved receptor expressed in brain 3 (or GPR173), member of the class A family of seven-transmembrane G protein-coupled receptors. The SREB (super conserved receptor expressed in brain) subfamily consists of at least three members, named SREB1 (GPR27), SREB2 (GPR85), and SREB3 (GPR173). They are very highly conserved G protein-coupled receptors throughout vertebrate evolution, however no endogenous ligands have yet been identified. SREB2 is greatly expressed in brain regions involved in psychiatric disorders and cognition, such as the hippocampal dentate gyrus. Genetic studies in both humans and mice have shown that SREB2 influences brain size and negatively regulates hippocampal adult neurogenesis and neurogenesis-dependent cognitive function, all of which are suggesting a potential link between SREB2 and schizophrenia. All three SREB genes are highly expressed in differentiated hippocampal neural stem cells. Furthermore, all GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 329 matched cddid_all.tbl CDD cd15218 cd15218 320346 7tmA_SREB2_GPR85 super conserved receptor expressed in brain 2 (or GPR85), member of the class A family of seven-transmembrane G protein-coupled receptors. The SREB (super conserved receptor expressed in brain) subfamily consists of at least three members, named SREB1 (GPR27), SREB2 (GPR85), and SREB3 (GPR173). They are very highly conserved G protein-coupled receptors throughout vertebrate evolution, however no endogenous ligands have yet been identified. SREB2 is greatly expressed in brain regions involved in psychiatric disorders and cognition, such as the hippocampal dentate gyrus. Genetic studies in both humans and mice have shown that SREB2 influences brain size and negatively regulates hippocampal adult neurogenesis and neurogenesis-dependent cognitive function, all of which are suggesting a potential link between SREB2 and schizophrenia. All three SREB genes are highly expressed in differentiated hippocampal neural stem cells. Furthermore, all GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 330 matched cddid_all.tbl CDD cd15219 cd15219 320347 7tmA_GPR26_GPR78-like G protein-coupled receptors 26 and 78, member of the class A family of seven-transmembrane G protein-coupled receptors. Orphan G-protein coupled receptor 26 (GPR26) and GPR78 are constitutively active and coupled to increased cAMP formation. They are closely related based on sequence homology and comprise a conserved subgroup within the class A G-protein coupled receptor (GPCR) superfamily. Both receptors are widely expressed in selected tissues of the brain but their endogenous ligands are unknown. GPR26 knockout mice showed increased levels of anxiety- and depression-like behaviors, whereas GPR78 has been implicated in susceptibility to bipolar affective disorder and schizophrenia. Members of this subgroup contain the highly conserved Asp-Arg-Tyr/Phe (DRY/F) motif found in the third transmembrane helix (TM3) of the rhodopsin-like class A receptors which is important for efficient G protein-coupled signal transduction. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 264 matched cddid_all.tbl CDD cd15220 cd15220 410633 7tmA_GPR61_GPR62-like G protein-coupled receptors 61 and 62, member of the class A family of seven-transmembrane G protein-coupled receptors. This subgroup includes the orphan receptors GPR61 and GPR62, which are both constitutively active and predominantly expressed in the brain. While GPR61 couples to G(s) subtype of G proteins, the signaling pathway and function of GPR 62 are unknown. GPR61-deficient mice displayed significant hyperphagia and heavier body weight compared to wild-type mice, suggesting that GPR61 is involved in the regulation of food intake and body weight. GPR61 transcript expression was found in the caudate, putamen, and thalamus of human brain, whereas GPR62 transcript expression was found in the basal forebrain, frontal cortex, caudate, putamen, thalamus, and hippocampus. Both receptors share the highest sequence homology with each other and comprise a conserved subgroup within the class A family of GPCRs, which includes receptors for hormones, neurotransmitters, sensory stimuli, and a variety of other ligands. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, which then activate the heterotrimeric G proteins. Members of this subgroup contain [A/E]RY motif, a variant of the highly conserved Asp-Arg-Tyr (DRY) motif found in the third transmembrane helix (TM3) of the class A GPCRs and important for efficient G protein-coupled signal transduction. 264 matched cddid_all.tbl CDD cd15221 cd15221 320349 7tmA_OR52B-like olfactory receptor subfamily 52B and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor (OR) subfamilies 52B, 52D, 52H and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 275 matched cddid_all.tbl CDD cd15222 cd15222 320350 7tmA_OR51-like olfactory receptor family 51 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor family 51 and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 275 matched cddid_all.tbl CDD cd15223 cd15223 320351 7tmA_OR56-like olfactory receptor family 56 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor family 56 and related proteins in other mammals, sauropsids, and fishes. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 279 matched cddid_all.tbl CDD cd15224 cd15224 320352 7tmA_OR6B-like olfactory receptor subfamily 6B and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor 6B, 6A, 6Y, 6P, and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 270 matched cddid_all.tbl CDD cd15225 cd15225 320353 7tmA_OR10A-like olfactory receptor subfamily 10A and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor 10A, 10C, 10H, 10J, 10V, 10R, 10J, 10W, among others, and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 277 matched cddid_all.tbl CDD cd15226 cd15226 320354 7tmA_OR4-like olfactory receptor family 4 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor family 4 and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 267 matched cddid_all.tbl CDD cd15227 cd15227 320355 7tmA_OR14-like olfactory receptor family 14 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor family 14 and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 270 matched cddid_all.tbl CDD cd15228 cd15228 320356 7tmA_OR10D-like olfactory receptor subfamily 10D and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 10D and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 275 matched cddid_all.tbl CDD cd15229 cd15229 320357 7tmA_OR8S1-like olfactory receptor subfamily 8S1 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor 8S1 and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 277 matched cddid_all.tbl CDD cd15230 cd15230 320358 7tmA_OR5-like olfactory receptor family 5 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor family 5, some subfamilies from families 8 and 9, and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 270 matched cddid_all.tbl CDD cd15231 cd15231 320359 7tmA_OR5V1-like olfactory receptor subfamily 5V1 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 5V1 and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 277 matched cddid_all.tbl CDD cd15232 cd15232 320360 7tmA_OR13-like olfactory receptor family 13 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor family 13 (subfamilies 13A1 and 13G1) and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 270 matched cddid_all.tbl CDD cd15233 cd15233 320361 7tmA_OR3A-like olfactory receptor subfamily 3A3 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 3A3 and 3A4, and related proteins in other mammals. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 277 matched cddid_all.tbl CDD cd15234 cd15234 320362 7tmA_OR7-like olfactory receptor family 7 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor family 7 and related proteins in other mammals. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 277 matched cddid_all.tbl CDD cd15235 cd15235 320363 7tmA_OR1A-like olfactory receptor subfamily 1A and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 1A, 1B, 1K, 1L, 1Q and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 278 matched cddid_all.tbl CDD cd15236 cd15236 320364 7tmA_OR1E-like olfactory receptor subfamily 1E and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 1E, 1J, and related proteins in other mammals. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 277 matched cddid_all.tbl CDD cd15237 cd15237 320365 7tmA_OR2-like olfactory receptor family 2 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor families 2 and 13, and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 270 matched cddid_all.tbl CDD cd15238 cd15238 320366 7tm_ARII-like Acetabularia rhodopsin II and similar proteins, member of the seven-transmembrane GPCR superfamily. This subgroup includes the eukaryotic light-driven proton-pumping Acetabularia rhodopsin II from the giant unicellular marine alga Acetabularis acetabulum, as well as its closely related proteins. They belong to the microbial rhodopsin family, also known as type I rhodopsins, comprising the light-driven inward chloride pump halorhodopsin (HR), the outward proton pump bacteriorhodopsin (BR), the light-gated cation channel channelrhodopsin (ChR), the light-sensor activating transmembrane transducer protein sensory rhodopsin II (SRII), and the other light-driven proton pumps such as blue-light absorbing and green-light absorbing proteorhodopsins, among others. Microbial rhodopsins have been found in various single-celled microorganisms from all three domains of life, including halophile archaea, gamma-proteobacteria, cyanobacteria, fungi, and green algae. While microbial (type 1) and animal (type 2) rhodopsins have no sequence similarity with each other, they share a common architecture consisting of seven-transmembrane alpha-helices (TM) connected by extracellular loops and intracellular loops. Both types of rhodopsins consist of opsin and a covalently attached retinal (the aldehyde of vitamin A), a photoreactive chromophore, via a protonated Schiff base linkage to an amino group of lysine in the middle of the seventh transmembrane helix (TM7). Upon the absorption of light, microbial rhodopsins undergo light-induced photoisomerization of all-trans retinal into the 13-cis isomer, whereas the photoisomerization of 11-cis retinal to all-trans isomer occurs in the animal rhodopsins. While animal visual rhodopsins are activated by light to catalyze GDP/GTP exchange in the alpha subunit of the retinal G protein transducin (Gt), microbial rhodopsins do not activate G proteins, but instead can function as light-dependent ion pumps, cation channels, and sensors. 219 matched cddid_all.tbl CDD cd15239 cd15239 320367 7tm_YRO2_fungal-like fungal YRO2 and related proteins, member of the seven-transmembrane GPCR superfamily. This subgroup includes the yeast YRO2 protein and it closely related proteins. Although the exact function of these proteins is unknown, they show strong sequence homology to the family of microbial rhodopsins, also known as type I rhodopsins, comprising the light-driven inward chloride pump halorhodopsin (HR), the outward proton pump bacteriorhodopsin (BR), the light-gated cation channel channelrhodopsin (ChR), the light-sensor activating transmembrane transducer protein sensory rhodopsin II (SRII), and the other light-driven proton pumps such as blue-light absorbing and green-light absorbing proteorhodopsins, among others. Microbial rhodopsins have been found in various single-celled microorganisms from all three domains of life, including halophile archaea, gamma-proteobacteria, cyanobacteria, fungi, and green algae. While microbial (type 1) and animal (type 2) rhodopsins have no sequence similarity with each other, they share a common architecture consisting of seven-transmembrane alpha-helices (TM) connected by extracellular loops and intracellular loops. Both types of rhodopsins consist of opsin and a covalently attached retinal (the aldehyde of vitamin A), a photoreactive chromophore, via a protonated Schiff base linkage to an amino group of lysine in the middle of the seventh transmembrane helix (TM7). Upon the absorption of light, microbial rhodopsins undergo light-induced photoisomerization of all-trans retinal into the 13-cis isomer, whereas the photoisomerization of 11-cis retinal to all-trans isomer occurs in the animal rhodopsins. While animal visual rhodopsins are activated by light to catalyze GDP/GTP exchange in the alpha subunit of the retinal G protein transducin (Gt), microbial rhodopsins do not activate G proteins, but instead can function as light-dependent ion pumps, cation channels, and sensors. 227 matched cddid_all.tbl CDD cd15240 cd15240 320368 7tm_ASR-like Anabaena sensory rhodopsin and similar proteins, member of the seven-transmembrane GPCR superfamily. This subgroup includes eubacterial sensory rhodopsin from the freshwater cyanobacterium Anabaena and its closely related proteins. Unlike other sensory rhodopsins (SRI and SRII), the Anabaena sensory rhodopsin (ASR) activates a soluble transducer protein (ASRT), which may leading to transcriptional control of several genes. Although ASRT was shown to interact with DNA in vitro, the exact mechanism of photosensory transduction is not clearly understood. Moreover, the regulation of CRP (cAMP receptor protein) expression by ASR has been reported demonstrating a direct interaction of the C-terminal region of ASR with DNA, suggesting that ASR itself may also work as a transcription factor. ASR belongs to the microbial rhodopsin family, also known as type I rhodopsins, comprising the light-driven inward chloride pump halorhodopsin (HR), the outward proton pump bacteriorhodopsin (BR), the light-gated cation channel channelrhodopsin (ChR), the light-sensor activating transmembrane transducer protein sensory rhodopsin II (SRII), and the other light-driven proton pumps such as blue-light absorbing and green-light absorbing proteorhodopsins, among others. Microbial rhodopsins have been found in various single-celled microorganisms from all three domains of life, including halophile archaea, gamma-proteobacteria, cyanobacteria, fungi, and green algae. While microbial (type 1) and animal (type 2) rhodopsins have no sequence similarity with each other, they share a common architecture consisting of seven-transmembrane alpha-helices (TM) connected by extracellular loops and intracellular loops. Both types of rhodopsins consist of opsin and a covalently attached retinal (the aldehyde of vitamin A), a photoreactive chromophore, via a protonated Schiff base linkage to an amino group of lysine in the middle of the seventh transmembrane helix (TM7). Upon the absorption of light, microbial rhodopsins undergo light-induced photoisomerization of all-trans retinal into the 13-cis isomer, whereas the photoisomerization of 11-cis retinal to all-trans isomer occurs in the animal rhodopsins. While animal visual rhodopsins are activated by light to catalyze GDP/GTP exchange in the alpha subunit of the retinal G protein transducin (Gt), microbial rhodopsins do not activate G proteins, but instead can function as light-dependent ion pumps, cation channels, and sensors. 221 matched cddid_all.tbl CDD cd15241 cd15241 320369 7tm_ChRs channelrhodopsins, member of the seven-transmembrane GPCR superfamily. Channelrhodopsins (ChRs) are light-gated ion channels acting as sensory photoreceptors in unicellular green algae, controlling phototaxis (directional movement toward or away from light). ChRs are large seven-transmembrane proteins with large C-terminal extensions, which have been implicated in localizing the channel to the algal eyespot, a single layer of pigmented granules, overlaying part of the plasma membrane but are not required for ion channel function. ChRs are belongs to the microbial rhodopsin family, also known as type I rhodopsins, comprising the light-driven inward chloride pump halorhodopsin (HR), the outward proton pump bacteriorhodopsin (BR), the light-sensor activating transmembrane transducer protein sensory rhodopsin II (SRII), the light-sensor activating soluble transducer protein Anabaena sensory rhodopsin (ASR), and the other light-driven proton pumps such as blue-light absorbing and green-light absorbing proteorhodopsins, among others. Microbial rhodopsins have been found in various single-celled microorganisms from all three domains of life, including halophile archaea, gamma-proteobacteria, cyanobacteria, fungi, and green algae. While microbial (type 1) and animal (type 2) rhodopsins have no sequence similarity with each other, they share a common architecture consisting of seven-transmembrane alpha-helices (TM) connected by extracellular loops and intracellular loops. Both types of rhodopsins consist of opsin and a covalently attached retinal (the aldehyde of vitamin A), a photoreactive chromophore, via a protonated Schiff base linkage to an amino group of lysine in the middle of the seventh transmembrane helix (TM7). Upon the absorption of light, microbial rhodopsins undergo light-induced photoisomerization of all-trans retinal into the 13-cis isomer, whereas the photoisomerization of 11-cis retinal to all-trans isomer occurs in the animal rhodopsins. While animal visual rhodopsins are activated by light to catalyze GDP/GTP exchange in the alpha subunit of the retinal G protein transducin (Gt), microbial rhodopsins do not activate G proteins, but instead can function as light-dependent ion pumps, cation channels, and sensors. 219 matched cddid_all.tbl CDD cd15242 cd15242 320370 7tm_Proteorhodopsin green- and blue-light absorbing proteorhodopsins, member of the seven-transmembrane GPCR superfamily. This subgroup represents blue-light absorbing and green-light absorbing proteorhodopsins (PRs), which act as a light-driven proton pump that plays a major role in supplying light energy for phototropic marine microorganisms, by a mechanism similar to that of bacteriorhodopsin. PRs are found in most marine bacteria in surface waters, as well as in archaea and eukaryotes. They belong to the microbial rhodopsin family, also known as type 1 rhodopsins, comprising the light-driven inward chloride pump halorhodopsin (HR), the light-gated cation channel channelrhodopsin (ChR), the light-sensor activating transmembrane transducer protein sensory rhodopsin II (SRII), the light-sensor activating soluble transducer protein Anabaena sensory rhodopsin (ASR), and the other light-driven proton pumps such as bacteriorhodopsin (BR). They have been found in various single-celled microorganisms from all three domains of life, including halophile archaea, gamma-proteobacteria, cyanobacteria, fungi, and green algae. While microbial (type 1) and animal (type 2) rhodopsins have no sequence similarity with each other, they share a common architecture consisting of seven-transmembrane alpha-helices (TM) connected by extracellular loops and intracellular loops. Both types of rhodopsins consist of opsin and a covalently attached retinal (the aldehyde of vitamin A), a photoreactive chromophore, via a protonated Schiff base linkage to an amino group of lysine in the middle of the seventh transmembrane helix (TM7). Upon the absorption of light, microbial rhodopsins undergo light-induced photoisomerization of all-trans retinal into the 13-cis isomer, whereas the photoisomerization of 11-cis retinal to all-trans isomer occurs in the animal rhodopsins. While animal visual rhodopsins are activated by light to catalyze GDP/GTP exchange in the alpha subunit of the retinal G protein transducin (Gt), microbial rhodopsins do not activate G proteins, but instead can function as light-dependent ion pumps, cation channels, and sensors. 229 matched cddid_all.tbl CDD cd15243 cd15243 320371 7tm_Halorhodopsin light-driven inward chloride pump halorhodopsin, member of the seven-transmembrane GPCR superfamily. Halorhodopsin (HR) acts as a light-driven inward-directed chloride pump. When activated by yellow light, HR pumps chloride ions into the cell cytoplasm, generating a negative-inside membrane potential which drives proton uptake. The resulting electrochemical ion gradient provides an energy source to the cell and contributes to pH homeostasis. HR is found in phylogenetically ancient archaea, known as halobacteria which live in high salty environments. HR belongs to the microbial rhodopsin family, also known as type I rhodopsins, comprising light-driven retinal-binding outward pump bacteriorhodopsin (BR), light-gated cation channel channelrhodopsin (ChR), light-sensor activating transmembrane transducer protein sensory rhodopsin II (SRII), light-sensor activating soluble transducer protein Anabaena sensory rhodopsin (ASR), and other light-driven proton pumps such as blue-light absorbing and green-light absorbing proteorhodopsins, among others. They have been found in various single-celled microorganisms from all three domains of life, including halophile archaea, gamma-proteobacteria, cyanobacteria, fungi, and green algae. While microbial (type 1) and animal (type 2) rhodopsins have no sequence similarity with each other, they share a common architecture consisting of seven-transmembrane alpha-helices (TM) connected by extracellular loops and intracellular loops. Both types of rhodopsins consist of opsin and a covalently attached retinal (the aldehyde of vitamin A), a photoreactive chromophore, via a protonated Schiff base linkage to an amino group of lysine in the middle of the seventh transmembrane helix (TM7). Upon the absorption of light, microbial rhodopsins undergo light-induced photoisomerization of all-trans retinal into the 13-cis isomer, whereas the photoisomerization of 11-cis retinal to all-trans isomer occurs in the animal rhodopsins. While animal visual rhodopsins are activated by light to catalyze GDP/GTP exchange in the alpha subunit of the retinal G protein transducin (Gt), microbial rhodopsins do not activate G proteins, but instead can function as light-dependent ion pumps, cation channels, and sensors. 226 matched cddid_all.tbl CDD cd15244 cd15244 320372 7tm_bacteriorhodopsin light-driven outward proton pump bacteriorhodopsin, member of the seven-transmembrane GPCR superfamily. Bacteriorhodopsin (BR) serves as a light-driven retinal-binding outward proton pump, generating an outside positive membrane potential and thus creating an inwardly directed proton motive force (PMF) necessary for ATP synthesis. BR belongs to the microbial rhodopsin family, also known as type I rhodopsins, comprising light-driven inward chloride pump halorhodopsin (HR), light-gated cation channel channelrhodopsin (ChR), light-sensor activating transmembrane transducer protein sensory rhodopsin II (SRII), light-sensor activating soluble transducer protein Anabaena sensory rhodopsin (ASR), and other light-driven proton pumps such as blue-light absorbing and green-light absorbing proteorhodopsins, among others. They have been found in various single-celled microorganisms from all three domains of life, including halophile archaea, gamma-proteobacteria, cyanobacteria, fungi, and green algae. While microbial (type 1) and animal (type 2) rhodopsins have no sequence similarity with each other, they share a common architecture consisting of seven-transmembrane alpha-helices (TM) connected by extracellular loops and intracellular loops. Both types of rhodopsins consist of opsin and a covalently attached retinal (the aldehyde of vitamin A), a photoreactive chromophore, via a protonated Schiff base linkage to an amino group of lysine in the middle of the seventh transmembrane helix (TM7). Upon the absorption of light, microbial rhodopsins undergo light-induced photoisomerization of all-trans retinal into the 13-cis isomer, whereas the photoisomerization of 11-cis retinal to all-trans isomer occurs in the animal rhodopsins. While animal visual rhodopsins are activated by light to catalyze GDP/GTP exchange in the alpha subunit of the retinal G protein transducin (Gt), microbial rhodopsins do not activate G proteins, but instead can function as light-dependent ion pumps, cation channels, and sensors. 221 matched cddid_all.tbl CDD cd15245 cd15245 320373 7tmF_FZD2 class F frizzled subfamily 2, member of 7-transmembrane G protein-coupled receptors. This group includes subfamily 2 of the frizzled (FZD) family of seven transmembrane-spanning proteins, which constitute a novel and separate class of G-protein coupled receptors. This class F protein family consists of 10 isoforms (FZD1-10) in mammals. The FZDs are activated by the wingless/int-1 (WNT) family of secreted lipoglycoproteins and preferentially couple to stimulatory G proteins of the Gs family, which activate adenylate cyclase, but can also couple to G proteins of the Gi/Gq families. In the WNT/beta-catenin signaling pathway, the WNT ligand binds to FZD and a lipoprotein receptor-related protein (LRP) co-receptor. This leads to the stabilization and translocation of beta-catenin to the nucleus, where it induces the activation of TCF/LEF family transcription factors. The conserved cytoplasmic motif of FZD, Lys-Thr-X-X-X-Trp, is required for activation of the WNT/beta-catenin pathway, and for membrane localization and phosphorylation of Dsh (dishevelled) protein, a key component of the WNT pathway that relays the WNT signals from the activated receptor to downstream effector proteins. The WNT pathway plays a critical role in many developmental processes, such as cell-fate determination, cell proliferation, neural patterning, stem cell renewal, tissue homeostasis and repair, and tumorigenesis, among many others. 330 matched cddid_all.tbl CDD cd15246 cd15246 320374 7tmF_FZD7 class F frizzled subfamily 7, member of 7-transmembrane G protein-coupled receptors. This group includes subfamily 7 of the frizzled (FZD) family of seven transmembrane-spanning proteins, which constitute a novel and separate class of G-protein coupled receptors. This class F protein family consists of 10 isoforms (FZD1-10) in mammals. The FZDs are activated by the wingless/int-1 (WNT) family of secreted lipoglycoproteins and preferentially couple to stimulatory G proteins of the Gs family, which activate adenylate cyclase, but can also couple to G proteins of the Gi/Gq families. In the WNT/beta-catenin signaling pathway, the WNT ligand binds to FZD and a lipoprotein receptor-related protein (LRP) co-receptor. This leads to the stabilization and translocation of beta-catenin to the nucleus, where it induces the activation of TCF/LEF family transcription factors. The conserved cytoplasmic motif of FZD, Lys-Thr-X-X-X-Trp, is required for activation of the WNT/beta-catenin pathway, and for membrane localization and phosphorylation of Dsh (dishevelled) protein, a key component of the WNT pathway that relays the WNT signals from the activated receptor to downstream effector proteins. The WNT pathway plays a critical role in many developmental processes, such as cell-fate determination, cell proliferation, neural patterning, stem cell renewal, tissue homeostasis and repair, and tumorigenesis, among many others 331 matched cddid_all.tbl CDD cd15247 cd15247 320375 7tmF_FZD1 class F mammalian frizzled subfamily 1, member of 7-transmembrane G protein-coupled receptors. This group includes subfamily 1 of the frizzled (FZD) family of seven transmembrane-spanning proteins, which constitute a novel and separate class of G-protein coupled receptors. This class F protein family consists of 10 isoforms (FZD1-10) in mammals. The FZDs are activated by the wingless/int-1 (WNT) family of secreted lipoglycoproteins and preferentially couple to stimulatory G proteins of the Gs family, which activate adenylate cyclase, but can also couple to G proteins of the Gi/Gq families. In the WNT/beta-catenin signaling pathway, the WNT ligand binds to FZD and a lipoprotein receptor-related protein (LRP) co-receptor. This leads to the stabilization and translocation of beta-catenin to the nucleus, where it induces the activation of TCF/LEF family transcription factors. The conserved cytoplasmic motif of FZD, Lys-Thr-X-X-X-Trp, is required for activation of the WNT/beta-catenin pathway, and for membrane localization and phosphorylation of Dsh (dishevelled) protein, a key component of the WNT pathway that relays the WNT signals from the activated receptor to downstream effector proteins. The WNT pathway plays a critical role in many developmental processes, such as cell-fate determination, cell proliferation, neural patterning, stem cell renewal, tissue homeostasis and repair, and tumorigenesis, among many others. 341 matched cddid_all.tbl CDD cd15248 cd15248 320376 7tmF_FZD1_insect class F insect frizzled subfamily 1, member of 7-transmembrane G protein-coupled receptors. This group includes subfamily 1 of the frizzled (FZD) family of seven transmembrane-spanning proteins, which constitute a novel and separate class of G-protein coupled receptors, found in insects such as Drosophila melanogaster. This class F protein family consists of 10 isoforms (FZD1-10) in mammals. The FZDs are activated by the wingless/int-1 (WNT) family of secreted lipoglycoproteins and preferentially couple to stimulatory G proteins of the Gs family, which activate adenylate cyclase, but can also couple to G proteins of the Gi/Gq families. In the WNT/beta-catenin signaling pathway, the WNT ligand binds to FZD and a lipoprotein receptor-related protein (LRP) co-receptor. This leads to the stabilization and translocation of beta-catenin to the nucleus, where it induces the activation of TCF/LEF family transcription factors. The conserved cytoplasmic motif of FZD, Lys-Thr-X-X-X-Trp, is required for activation of the WNT/beta-catenin pathway, and for membrane localization and phosphorylation of Dsh (dishevelled) protein, a key component of the WNT pathway that relays the WNT signals from the activated receptor to downstream effector proteins. The WNT pathway plays a critical role in many developmental processes, such as cell-fate determination, cell proliferation, neural patterning, stem cell renewal, tissue homeostasis and repair, and tumorigenesis, among many others. 332 matched cddid_all.tbl CDD cd15249 cd15249 320377 7tmF_FZD5 class F frizzled subfamily 5, member of 7-transmembrane G protein-coupled receptors. This group includes subfamily 5 of the frizzled (FZD) family of seven transmembrane-spanning proteins, which constitute a novel and separate class of GPCRs, and its closely related proteins. This class F protein family consists of 10 isoforms (FZD1-10) in mammals. The FZDs are activated by the wingless/int-1 (WNT) family of secreted lipoglycoproteins and preferentially couple to stimulatory G proteins of the Gs family, which activate adenylate cyclase, but can also couple to G proteins of the Gi/Gq families. In the WNT/beta-catenin signaling pathway, the WNT ligand binds to FZD and a lipoprotein receptor-related protein (LRP) co-receptor. This leads to the stabilization and translocation of beta-catenin to the nucleus, where it induces the activation of TCF/LEF family transcription factors. The conserved cytoplasmic motif of FZD, Lys-Thr-X-X-X-Trp, is required for activation of the WNT/beta-catenin pathway, and for membrane localization and phosphorylation of Dsh (dishevelled) protein, a key component of the WNT pathway that relays the WNT signals from the activated receptor to downstream effector proteins. The WNT pathway plays a critical role in many developmental processes, such as cell-fate determination, cell proliferation, neural patterning, stem cell renewal, tissue homeostasis and repair, and tumorigenesis, among many others. 310 matched cddid_all.tbl CDD cd15250 cd15250 320378 7tmF_FZD8 class F frizzled subfamily 8, member of 7-transmembrane G protein-coupled receptors. This group includes subfamily 8 of the frizzled (FZD) family of seven transmembrane-spanning proteins, which constitute a novel and separate class of GPCRs, and its closely related proteins. This class F protein family consists of 10 isoforms (FZD1-10) in mammals. The FZDs are activated by the wingless/int-1 (WNT) family of secreted lipoglycoproteins and preferentially couple to stimulatory G proteins of the Gs family, which activate adenylate cyclase, but can also couple to G proteins of the Gi/Gq families. In the WNT/beta-catenin signaling pathway, the WNT ligand binds to FZD and a lipoprotein receptor-related protein (LRP) co-receptor. This leads to the stabilization and translocation of beta-catenin to the nucleus, where it induces the activation of TCF/LEF family transcription factors. The conserved cytoplasmic motif of FZD, Lys-Thr-X-X-X-Trp, is required for activation of the WNT/beta-catenin pathway, and for membrane localization and phosphorylation of Dsh (dishevelled) protein, a key component of the WNT pathway that relays the WNT signals from the activated receptor to downstream effector proteins. The WNT pathway plays a critical role in many developmental processes, such as cell-fate determination, cell proliferation, neural patterning, stem cell renewal, tissue homeostasis and repair, and tumorigenesis, among many others. 314 matched cddid_all.tbl CDD cd15251 cd15251 320379 7tmB2_BAI_Adhesion_VII brain-specific angiogenesis inhibitors, group VII adhesion GPCRs, member of the class B2 family of seven-transmembrane G protein-coupled receptors. Brain-specific angiogenesis inhibitors (BAI1-3) constitute the group VII of cell-adhesion receptors that have been implicated in vascularization of glioblastomas. They belong to the B2 subfamily of class B GPCRs, are predominantly expressed in the brain, and are only present in vertebrates. Three BAIs, like all adhesion receptors, are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. For example, BAI1 N-terminus contain an integrin-binding RGD (Arg-Gly-Asp) motif in addition to five thrombospondin type 1 repeats (TSRs), which are known to regulate the anti-angiogenic activity of thrombospondin-1, whereas BAI2 and BAI3 have four TSRs, but do not possess RGD motifs. The TSRs are functionally involved in cell attachment, activation of latent TGF-beta, inhibition of angiogenesis and endothelial cell migration. The TSRs of BAI1 mediate direct binding to phosphatidylserine, which enables both recognition and internalization of apoptotic cells by phagocytes. Thus, BAI1 functions as a phosphatidylserine receptor that forms a trimeric complex with ELMO and Dock180, leading to activation of Rac-GTPase which promotes the binding and phagocytosis of apoptotic cells. BAI3 can also interact with the ELMO-Dock180 complex to activate the Rac pathway and can also bind to secreted C1ql proteins of the C1Q complement family via its N-terminal TSRs. BAI3 and its ligands C1QL1 are highly expressed during synaptogenesis and are involved in synapse specificity. Moreover, BAI2 acts as a transcription repressor to regulate vascular endothelial growth factor (VEGF) expression through interaction with GA-binding protein gamma (GABP). The N-terminal extracellular domains of all three BAIs also contain an evolutionarily conserved GPCR-autoproteolysis inducing (GAIN) domain, which undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif to generate N- and C-terminal fragments (NTF and CTF), a putative hormone-binding domain (HBD), and multiple N-glycosylation sites. The C-terminus of each BAI subtype ends with a conserved Gln-Thr-Glu-Val (QTEV) motif known to interact with PDZ domain-containing proteins, but only BAI1 possesses a proline-rich region, which may be involved in protein-protein interactions. 253 matched cddid_all.tbl CDD cd15252 cd15252 320380 7tmB2_Latrophilin_Adhesion_I Latrophilins and similar receptors, group I adhesion GPCRs, member of class B2 family of seven-transmembrane G protein-coupled receptors. Group I adhesion GPCRs consist of latrophilins (also called lectomedins or latrotoxin receptors) and ETL (EGF-TM7-latrophilin-related protein. These receptors are a member of the adhesion family (subclass B2) that belongs to the class B GPCRs. Three subtypes of latrophilins have been identified: LPH1 (latrophilin-1), LPH2, and LPH3. The latrophilin-1 is a brain-specific calcium-independent receptor of alpha-latrotoxin, a potent presynaptic neurotoxin from the venom of the black widow spider that induces massive neurotransmitter release from sensory and motor neurons as well as endocrine cells, leading to nerve-terminal degeneration. Latrophilin-2 and -3, although sharing strong sequence homology to latrophilin-1, do not bind alpha-latrotoxin. While latrophilin-3 is also brain specific, latrophilin-2 is ubiquitously distributed. The endogenous ligands for these two receptors are unknown. ETL, a seven transmembrane receptor containing EGF-like repeats is highly expressed in heart, where developmentally regulated, as well as in normal smooth cells. The function of the ETL is unknown. All adhesion GPCRs possess large N-terminal extracellular domains containing multiple structural motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, coupled to a seven-transmembrane domain. In addition, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR-autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 257 matched cddid_all.tbl CDD cd15253 cd15253 320381 7tmB2_GPR113 orphan adhesion receptor GPR113, member of the class B2 family of seven-transmembrane G protein-coupled receptors. GPR113 is an orphan receptor that belongs to group VI adhesion-GPCRs along with GPR110, GPR111, GPR115, and GPR116. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in ligand recognition as well as cell-cell adhesion and cell-matrix interactions, linked by a stalk region to a class B seven-transmembrane domain. GPR113 contains a hormone binding domain and one EGF (epidermal grown factor) domain, and is primarily expressed in a subset of taste receptor cells. In addition, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR-autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. However, several adhesion GPCRs, including GPR 111, GPR115, and CELSR1, are predicted to be non-cleavable at the GAIN domain because of the lack of a consensus catalytic triad sequence (His-Leu-Ser/Thr) within their GPS. 271 matched cddid_all.tbl CDD cd15254 cd15254 320382 7tmB2_GPR116_Ig-Hepta The immunoglobulin-repeat-containing receptor Ig-hepta/GPR116, member of the class B2 family of seven-transmembrane G protein-coupled receptors. GPR116 (also known as Ig-hepta) is an orphan receptor that belongs to group VI adhesion-GPCRs along with GPR110, GPR111, GPR113, and GPR115. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in ligand recognition as well as cell-cell adhesion and cell-matrix interactions, linked by a stalk region to a class B seven-transmembrane domain. GPR116 has four I-set immunoglobulin-like repeats, which is found in the members of the immunoglobulin superfamily of cell surface proteins, and a SEA (sea urchin sperm protein, enterokinase, and a grin)-box, which is present in the extracellular domain of the transmembrane mucin (MUC) family and known to enhance O-glycosylation. GPR116 is highly expressed in fetal and adult lung, and it has been shown to regulate lung surfactant levels as well as to stimulate breast cancer metastasis through a G(q)-p63-RhoGEF-Rho GTPase signaling pathway. In addition, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR-autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. However, several adhesion GPCRs, including GPR 111, GPR115, and CELSR1, are predicted to be non-cleavable at the GAIN domain because of the lack of a consensus catalytic triad sequence (His-Leu-Ser/Thr) within their GPS. 275 matched cddid_all.tbl CDD cd15255 cd15255 320383 7tmB2_GPR144 orphan adhesion receptor GPR114, member of the class B2 family of seven-transmembrane G protein-coupled receptors. GPR144 is an orphan receptor that belongs to the group V adhesion-GPCRs together with GPR133. The function of GPR144 has not yet been characterized, whereas GPR133 is highly expressed in the pituitary gland and is coupled to the Gs protein, leading to activation of adenylyl cyclase pathway. Moreover, genetic variations in the GPR133 have been reported to be associated with adult height and heart rate. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in ligand recognition as well as cell-cell adhesion and cell-matrix interactions, linked by a stalk region to a class B seven-transmembrane domain. In addition, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR-autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. However, several adhesion GPCRs, including GPR 111, GPR115, and CELSR1, are predicted to be non-cleavable at the GAIN domain because of the lack of a consensus catalytic triad sequence (His-Leu-Ser/Thr) within their GPS. 263 matched cddid_all.tbl CDD cd15256 cd15256 320384 7tmB2_GPR133 orphan adhesion receptor GPR133, member of the class B2 family of seven-transmembrane G protein-coupled receptors. GPR133 is an orphan receptor that belongs to the group V adhesion-GPCRs together with GPR144. The function of GPR144 has not yet been characterized, whereas GPR133 is highly expressed in the pituitary gland and is coupled to the Gs protein, leading to activation of adenylyl cyclase pathway. Moreover, genetic variations in the GPR133 have been reported to be associated with adult height and heart rate. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in ligand recognition as well as cell-cell adhesion and cell-matrix interactions, linked by a stalk region to a class B seven-transmembrane domain. In addition, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR-autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. However, several adhesion GPCRs, including GPR 111, GPR115, and CELSR1, are predicted to be non-cleavable at the GAIN domain because of the lack of a consensus catalytic triad sequence (His-Leu-Ser/Thr) within their GPS. 260 matched cddid_all.tbl CDD cd15257 cd15257 320385 7tmB2_GPR128 orphan adhesion receptor GPR128, member of the class B2 family of seven-transmembrane G protein-coupled receptors. GPR128 is an orphan receptor of the adhesion family (subclass B2) that belongs to the class B GPCRs. Expression of GPR128 was detected in the mouse intestinal mucosa and is thought to be involved in energy balance, as its knockout mice showed a decrease in body weight gain and an increase in intestinal contraction frequency compared to wild-type controls. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. These include, for example, EGF (epidermal growth factor)-like domains in CD97, Celsr1 (cadherin family member), Celsr2, Celsr3, EMR1 (EGF-module-containing mucin-like hormone receptor-like 1), EMR2, EMR3, and Flamingo; two laminin A G-type repeats and nine cadherin domains in Flamingo and its human orthologs Celsr1, Celsr2 and Celsr3; olfactomedin-like domains in the latrotoxin receptors; and five or four thrombospondin type 1 repeats in BAI1 (brain-specific angiogenesis inhibitor 1), BAI2 and BAI3. Furthermore, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 303 matched cddid_all.tbl CDD cd15258 cd15258 320386 7tmB2_GPR126-like_Adhesion_VIII orphan GPR126 and related proteins, group VIII adhesion GPCRs, member of the class B2 family of seven-transmembrane G protein-coupled receptors. Group VIII adhesion GPCRs include orphan GPCRs such as GPR56, GPR64, GPR97, GPR112, GPR114, and GPR126. GPR56 is involved in the regulation of oligodendrocyte development and myelination in the central nervous system via coupling to G(12/13) proteins, which leads to the activation of RhoA GTPase. GPR126, on the other hand, is required for Schwann cells, but not oligodendrocyte myelination in the peripheral nervous system. Gpr64 is mainly expressed in the epididymis of male reproductive tract, and targeted deletion of GPR64 causes sperm stasis and efferent duct blockage due to abnormal fluid reabsorption, resulting in male infertility. GPR64 is also over-expressed in Ewing's sarcoma (ES), as well as upregulated in other carcinomas from kidney, prostate or lung, and promotes invasiveness and metastasis in ES via the upregulation of placental growth factor (PGF) and matrix metalloproteinase (MMP) 1. GPR97 is identified as a lymphatic adhesion receptor that is specifically expressed in lymphatic endothelium, but not in blood vascular endothelium, and is shown to regulate migration of lymphatic endothelial cells via the small GTPases RhoA and cdc42. GPR112 is specifically expressed in normal enterochromatin cells and gastrointestinal neuroendocrine carcinoma cells, but its biological function is unknown. GPR114 is mainly found in granulocytes (polymorphonuclear leukocytes), and GPR114-transfected cells induced an increase in cAMP levels via coupling to G(s) protein. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. Furthermore, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 267 matched cddid_all.tbl CDD cd15259 cd15259 320387 7tmB2_GPR124-like_Adhesion_III orphan GPR124 and related proteins, group III adhesion GPCRs, member of class B2 family of seven-transmembrane G protein-coupled receptors. group III adhesion GPCRs include orphan GPR123, GPR124, GPR125, and their closely related proteins. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. Furthermore, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. GPR123 is predominantly expressed in the CNS including thalamus, brain stem and regions containing large pyramidal cells. GPR124, also known as tumor endothelial marker 5 (TEM5), is highly expressed in tumor vessels and in the vasculature of the developing embryo. GPR124 is essentially required for proper angiogenic sprouting into neural tissue, CNS-specific vascularization, and formation of the blood-brain barrier. GPR124 also interacts with the PDZ domain of DLG1 (discs large homolog 1) through its PDZ-binding motif. Recently, studies of double-knockout mice showed that GPR124 functions as a co-activator of Wnt7a/Wnt7b-dependent beta-catenin signaling in brain endothelium. Furthermore, WNT7-stimulated beta-catenin signaling is regulated by GPR124's intracellular PDZ binding motif and leucine-rich repeats (LRR) in its N-terminal extracellular domain. GPR125 directly interacts with dishevelled (Dvl) via its intracellular C-terminus, and together, GPR125 and Dvl recruit a subset of planar cell polarity (PCP) components into membrane subdomains, a prerequisite for activation of Wnt/PCP signaling. Thus, GPR125 influences the noncanonical WNT/PCP pathway, which does not involve beta-catenin, through interacting with and modulating the distribution of Dvl. 260 matched cddid_all.tbl CDD cd15260 cd15260 320388 7tmB1_NPR_B4_insect-like insect neuropeptide receptor subgroup B4 and related proteins, member of the class B family of seven-transmembrane G protein-coupled receptors. This subgroup includes a neuropeptide receptor found in Nilaparvata lugens (brown planthopper) and its closely related proteins from mollusks and annelid worms. They belong to the B1 subfamily of class B GPCRs, also referred to as secretin-like receptor family, which includes receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, glucagon, glucagon-like peptide (GLP), calcitonin gene-related peptide, parathyroid hormone (PTH), and corticotropin-releasing factor. These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. All members of the B1 subfamily preferentially couple to G proteins of G(s) family, which positively stimulate adenylate cyclase, leading to increased intracellular cAMP formation and calcium influx. The class B GPCRs have been identified in all the vertebrates, from fishes to mammals, as well as invertebrates including Caenorhabditis elegans and Drosophila melanogaster, but are not present in plants, fungi, or prokaryotes. 267 matched cddid_all.tbl CDD cd15261 cd15261 320389 7tmB1_PDFR The pigment dispersing factor receptor, member of the class B seven-transmembrane G protein-coupled receptors. The pigment dispersing factor receptor (PDFR) is a G protein-coupled receptor that binds the circadian clock neuropeptide PDF, a functional ortholog of the mammalian vasoactive intestinal peptide (VIP), on the pacemaker neurons. The PDFR is implicated in regulating flight circuit development and in modulating acute flight In Drosophila melanogaster. The PDFR activation stimulates adenylate cyclase, thereby increasing cAMP levels in many different pacemakers, and the receptor signaling has been shown to regulate behavioral circadian rhythms and geotaxis in Drosophila. The PDFR belongs to the B1 subfamily of class B GPCRs, also referred to as secretin-like receptor family, which includes receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, glucagon, glucagon-like peptide (GLP), calcitonin gene-related peptide, parathyroid hormone (PTH), and corticotropin-releasing factor. . These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. All members of the B1 subfamily preferentially couple to G proteins of G(s) family, which positively stimulate adenylate cyclase, leading to increased intracellular cAMP formation and calcium influx. They play key roles in hormone homeostasis in mammals and are promising drug targets in various human diseases including diabetes, osteoporosis, obesity, neurodegenerative conditions (Alzheimer###s and Parkinson's), cardiovascular disease, migraine, and psychiatric disorders (anxiety, depression). 282 matched cddid_all.tbl CDD cd15262 cd15262 320390 7tmB1_NPR_B3_insect-like insect neuropeptide receptor subgroup B3 and related proteins belong to subfamily B1 of hormone receptors; member of the class B secretin-like seven-transmembrane G protein-coupled receptors. This subgroup includes a neuropeptide receptor found in Bombyx mori (silk worm) and its closely related proteins from arthropods. They belong to the B1 subfamily of class B GPCRs, also referred to as secretin-like receptor family, which includes receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, glucagon, glucagon-like peptide (GLP), calcitonin gene-related peptide, parathyroid hormone (PTH), and corticotropin-releasing factor. These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. All members of the B1 subfamily preferentially couple to G proteins of G(s) family, which positively stimulate adenylate cyclase, leading to increased intracellular cAMP formation and calcium influx. The class B GPCRs have been identified in all the vertebrates, from fishes to mammals, as well as invertebrates including Caenorhabditis elegans and Drosophila melanogaster, but are not present in plants, fungi, or prokaryotes. 270 matched cddid_all.tbl CDD cd15263 cd15263 320391 7tmB1_DH_R insect diuretic hormone receptors, member of the class B family of seven-transmembrane G protein-coupled receptors. This group includes G protein-coupled receptors that specifically bind to insect diuretic hormones found in Manduca sexta (moth) and Acheta domesticus (the house cricket), among others. Insect diuretic hormone and their GPCRs play critical roles in the regulation of water and ion balance. Thus they are attractive targets for developing new insecticides. Activation of the diuretic hormone receptors stimulate adenylate cyclase, thereby increasing cAMP levels in Malpighian tube. They belong to the B1 subfamily of class B GPCRs, also referred to as secretin-like receptor family, which includes receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, glucagon, glucagon-like peptide (GLP), calcitonin gene-related peptide, parathyroid hormone (PTH), and corticotropin-releasing factor. These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. All members of the B1 subfamily preferentially couple to G proteins of Gs family, which positively stimulate adenylate cyclase, leading to increased intracellular cAMP formation and calcium influx. 272 matched cddid_all.tbl CDD cd15264 cd15264 320392 7tmB1_CRF-R corticotropin-releasing factor receptors, member of the class B family of seven-transmembrane G protein-coupled receptors. The vertebrate corticotropin-releasing factor (CRF) receptors are predominantly expressed in central nervous system with high levels in cortex tissue, brain stem, and pituitary. They have two isoforms as a result of alternative splicing of the same receptor gene: CRF-R1 and CRF-R2, which differ in tissue distribution and ligand binding affinities. Recently, a third CRF receptor (CRF-R3) has been identified in catfish pituitary. The catfish CRF-R1 is highly homologous to CRF-R3. CRF is a 41-amino acid neuropeptide that plays a central role in coordinating neuroendocrine, behavioral, and autonomic responses to stress by acting as the primary neuroregulator of the hypothalamic-pituitary-adrenal axis, which controls the levels of cortisol and other stress related hormones. In addition, the CRF family of neuropeptides also includes structurally related peptides such as mammalian urocortin, fish urotensin I, and frog sauvagine. The actions of CRF and CRF-related peptides are mediated through specific binding to CRF-R1 and CRF-R2. CRF and urocortin 1 bind and activate mammalian CRF-R1 with similar high affinities. By contrast, urocortin 2 and urocortin 3 do not bind to CRF-R1 or stimulate CRF-R1-mediated cAMP formation. Urocortin 1 also shows high affinity for mammalian CRF-R2, whereas CRF has significantly lower affinity for this receptor. These evidence suggest that urocortin 1 is an endogenous ligand for CRF-R1 and CRF-R2. The CRF receptors are members of the B1 subfamily of class B GPCRs, also referred to as secretin-like receptor family, which includes receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, glucagon, glucagon-like peptide (GLP), calcitonin gene-related peptide, and parathyroid hormone (PTH). These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. All members of the B1 subfamily preferentially couple to G proteins of G(s) family, which positively stimulate adenylate cyclase, leading to increased intracellular cAMP formation and calcium influx. However, depending on its cellular location and function, CRF receptors can activate multiple G proteins, which can in turn stimulate different second messenger pathways. 265 matched cddid_all.tbl CDD cd15265 cd15265 320393 7tmB1_PTHR parathyroid hormone receptors, member of the class B family of seven-transmembrane G protein-coupled receptors. The parathyroid hormone (PTH) receptor family has three subtypes: PTH1R, PTH2R and PTH3R. PTH1R is expressed in bone and kidney and is activated by two polypeptide ligands: PTH, an endocrine hormone that regulates calcium homoeostasis and bone maintenance, and PTH-related peptide (PTHrP), a paracrine factor that regulates endochondral bone development. PTH1R couples predominantly to a G(s)-protein that in turn activates adenylate cyclase thereby producing cAMP, but it can also couple to several G protein subtypes, including G(q/11), G(i/o), and G(12/13), resulting in activation of multiple intracellular signaling pathways. PTH2R is potently activated by tuberoinfundibular peptide-39 (TIP-39), but not by PTHrP. PTH also strongly activates human PTH2R, but only weakly activates rat and zebrafish PTH2Rs, suggesting that TIP-39 is a natural ligand for PTH2R. On the other hand, PTH3R binds and responds to both PTH and PTHrP, but not the TIP-39. Moreover, the PTH3R is more closely related to the PTH1R than PTH2R. PTH1R is found in all vertebrate species, whereas PTH2R is found in mammals and fish, but not in chicken or frog. The PTH3R is found in chicken and fish, but it is absent in mammals. The PTH receptors are members of the B1 (or secretin-like) subfamily of class B GPCRs, which include receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, glucagon, glucagon-like peptide (GLP), and calcitonin gene-related peptide. These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. 289 matched cddid_all.tbl CDD cd15266 cd15266 320394 7tmB1_GLP2R glucagon-like peptide-2 receptor, member of the class B family of seven-transmembrane G protein-coupled receptors. Glucagon-like peptide-2 receptor (GLP2R) is a member of the glucagon receptor family of G protein-coupled receptors, which also includes glucagon receptor (GCGR) and GLP1R. GLP2R is activated by glucagon-like peptide 2, which is derived from the large proglucagon precursor. Activation of GLP1R stimulates glucose-dependent insulin secretion from pancreatic beta cells, whereas activation of GLP2R stimulates intestinal epithelial proliferation and increases villus height in the small intestine. GCGR regulates blood glucose levels by control of hepatic glycogenolysis and gluconeogenesis and by regulation of insulin secretion from the pancreatic beta-cells. GLP2R belongs to the B1 (or secretin-like) subfamily of class B GPCRs, which includes receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, calcitonin gene-related peptide, parathyroid hormone (PTH), and corticotropin-releasing factor. These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. All members of the B1 subfamily preferentially couple to G proteins of G(s) family, which positively stimulate adenylate cyclase, leading to increased intracellular cAMP formation and calcium influx. However, depending on their cellular location, GCGR and GLP receptors can activate multiple G proteins, which can in turn stimulate different second messenger pathways. 280 matched cddid_all.tbl CDD cd15267 cd15267 320395 7tmB1_GCGR glucagon receptor, member of the class B family of seven-transmembrane G protein-coupled receptors. Glucagon receptor (GCGR) is a member of the glucagon receptor family of G protein-coupled receptors, which also includes glucagon-like peptide-1 receptor (GLP1R) and GLP2R. GCGR is activated by glucagon, which is derived from the large proglucagon precursor. GCGR regulates blood glucose levels by control of hepatic glycogenolysis and gluconeogenesis and by regulation of insulin secretion from the pancreatic beta-cells. Activation of GLP1R stimulates glucose-dependent insulin secretion from pancreatic beta cells, whereas activation of GLP2R stimulates intestinal epithelial proliferation and increases villus height in the small intestine. GCGR belongs to the B1 (or secretin-like) subfamily of class B GPCRs, which includes receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, calcitonin gene-related peptide, parathyroid hormone (PTH), and corticotropin-releasing factor. These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. All members of the B1 subfamily preferentially couple to G proteins of G(s) family, which positively stimulate adenylate cyclase, leading to increased intracellular cAMP formation and calcium influx. However, depending on their cellular location, GCGR and GLP receptors can activate multiple G proteins, which can in turn stimulate different second messenger pathways. 281 matched cddid_all.tbl CDD cd15268 cd15268 341342 7tmB1_GLP1R glucagon-like peptide-1 receptor, member of the class B family of seven-transmembrane G protein-coupled receptors. Glucagon-like peptide-1 receptor (GLP1R) is a member of the glucagon receptor family of G protein-coupled receptors, which also includes glucagon receptor and GLP2R. GLP1R is activated by glucagon-like peptide 1 (GLP1), which is derived from the large proglucagon precursor. Activation of GLP1R stimulates glucose-dependent insulin secretion from pancreatic beta cells, whereas activation of GLP2R stimulates intestinal epithelial proliferation and increases villus height in the small intestine. GCGR regulates blood glucose levels by control of hepatic glycogenolysis and gluconeogenesis and by regulation of insulin secretion from the pancreatic beta-cells. Receptors in this group belong to the B1 (or secretin-like) subfamily of class B GPCRs, which includes receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, calcitonin gene-related peptide, parathyroid hormone (PTH), and corticotropin-releasing factor. These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. All members of the B1 subfamily preferentially couple to G proteins of G(s) family, which positively stimulate adenylate cyclase, leading to increased intracellular cAMP formation and calcium influx. However, depending on their cellular location, GCGR and GLP receptors can activate multiple G proteins, which can in turn stimulate different second messenger pathways. 279 matched cddid_all.tbl CDD cd15269 cd15269 320397 7tmB1_VIP-R1 vasoactive intestinal polypeptide (VIP) receptor 1, member of the class B family of seven-transmembrane G protein-coupled receptors. Vasoactive intestinal peptide (VIP) receptor 1 is a member of the group of G protein-coupled receptors for structurally similar peptide hormones that also include secretin, growth-hormone-releasing hormone (GHRH), and pituitary adenylate cyclase activating polypeptide (PACAP). These receptors are classified into the subfamily B1 of class B GRCRs that consists of the classical hormone receptors and have been identified in all the vertebrates, from fishes to mammals, but are not present in plants, fungi, or prokaryotes. For all class B receptors, the large N-terminal extracellular domain plays a critical role in peptide hormone recognition. VIP and PACAP exert their effects through three G protein-coupled receptors, PACAP-R1, VIP-R1 (vasoactive intestinal receptor type 1, also known as VPAC1) and VIP-R2 (or VPAC2). PACAP-R1 binds only PACAP with high affinity, whereas VIP-R1 and -R2 specifically bind and respond to both VIP and PACAP. VIP and PACAP and their receptors are widely expressed in the brain and periphery. They are upregulated in neurons and immune cells in responses to CNS injury and/or inflammation and exert potent anti-inflammatory effects, as well as play important roles in the control of circadian rhythms and stress responses, among many others. VIP-R1 is preferentially coupled to a stimulatory G(s) protein, which leads to the activation of adenylate cyclase and thereby increases in intracellular cAMP level. However, depending on its cellular location, VIP-R1 is also capable of coupling to additional G proteins such as G(q) protein, thus leading to the activation of phospholipase C and intracellular calcium influx. 268 matched cddid_all.tbl CDD cd15270 cd15270 320398 7tmB1_GHRHR growth-hormone-releasing hormone receptor, member of the class B family of seven-transmembrane G protein-coupled receptors. Growth hormone-releasing hormone receptor (GHRHR) is a member of the group of G protein-coupled receptors for structurally similar peptide hormones that also include secretin, pituitary adenylate cyclase activating polypeptide (PACAP), and vasoactive intestinal peptide. These receptors are classified into the subfamily B1 of class B GRCRs that consists of the classical hormone receptors and have been identified in all the vertebrates, from fishes to mammals, but are not present in plants, fungi, or prokaryotes. For all class B receptors, the large N-terminal extracellular domain plays a critical role in peptide hormone recognition. GHRHR is a specific receptor for the growth hormone-releasing hormone (GHRH) that controls the synthesis and release of growth hormone (GH) from the anterior pituitary somatotrophs. Mutations in the gene encoding GHRHR have been connected to isolated growth hormone deficiency (IGHD), a short-stature condition caused by deficient production of GH or lack of GH action. GHRH is preferentially coupled to a stimulatory G(s) protein, which leads to the activation of adenylate cyclase and thereby increases in intracellular cAMP level. GHRHR is found in mammals as well as zebrafish and chicken, whereas the GHRHR type 2, an ortholog of the GHRHR, has only been identified in ray-finned fish, chicken and Xenopus. Xenopus laevis GHRHR2 has been shown to interact with both endogenous GHRH and PACAP-related peptide (PRP). 268 matched cddid_all.tbl CDD cd15271 cd15271 320399 7tmB1_GHRHR2 growth-hormone-releasing hormone receptor type 2, member of the class B family of seven-transmembrane G protein-coupled receptors. Growth hormone-releasing hormone receptor type 2 (GHRHR2) is found in non-mammalian vertebrates such as chicken and frog. It is a member of the group of G protein-coupled receptors for structurally similar peptide hormones that also include secretin, pituitary adenylate cyclase activating polypeptide (PACAP), vasoactive intestinal peptide, and mammalian growth hormone-releasing hormone. These receptors are classified into the subfamily B1 of class B GRCRs that consists of the classical hormone receptors and have been identified in all the vertebrates, from fishes to mammals, but are not present in plants, fungi, or prokaryotes. For all class B receptors, the large N-terminal extracellular domain plays a critical role in peptide hormone recognition. Mammalian GHRHR is a specific receptor for the growth hormone-releasing hormone (GHRH) that controls the synthesis and release of growth hormone (GH) from the anterior pituitary somatotrophs. Mutations in the gene encoding GHRHR have been connected to isolated growth hormone deficiency (IGHD), a short-stature condition caused by deficient production of GH or lack of GH action. Mammalian GHRH is preferentially coupled to a stimulatory G(s) protein, which leads to the activation of adenylate cyclase and thereby increases in intracellular cAMP level. GHRHR is found in mammals as well as zebrafish and chicken, whereas the GHRHR type 2, an ortholog of the GHRHR, has only been identified in ray-finned fish, chicken and Xenopus. Xenopus laevis GHRHR2 has been shown to interact with both endogenous GHRH and PACAP-related peptide (PRP). 267 matched cddid_all.tbl CDD cd15272 cd15272 320400 7tmB1_PTH-R_related invertebrate parathyroid hormone-related receptors, member of the class B family of seven-transmembrane G protein-coupled receptors. This group includes parathyroid hormone (PTH)-related receptors found in invertebrates such as mollusks and annelid worms. The PTH family receptors are members of the B1 subfamily of class B GPCRs, which includes receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, glucagon, glucagon-like peptide (GLP), and calcitonin gene-related peptide. These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. The parathyroid hormone type 1 receptor (PTH1R) is found in all vertebrate species and is activated by two polypeptide ligands: parathyroid hormone (PTH), an endocrine hormone that regulates calcium homoeostasis and bone maintenance, and PTH-related peptide (PTHrP), a paracrine factor that regulates endochondral bone development. PTH1R couples predominantly to G(s)- protein that in turn activates adenylyl cyclase thereby producing cAMP, but it can also couple to several G protein subtypes, including G(q/11), G(i/o), and G(12/13), resulting in activation of multiple signaling pathways. 285 matched cddid_all.tbl CDD cd15273 cd15273 320401 7tmB1_NPR_B7_insect-like insect neuropeptide receptor subgroup B7 and related proteins, member of the class B family of seven-transmembrane G protein-coupled receptors. This subgroup includes a neuropeptide receptor found in Nilaparvata lugens (brown planthopper) and its closely related proteins from invertebrates. They belong to the B1 subfamily of class B GPCRs, also referred to as secretin-like receptor family, which includes receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, glucagon, glucagon-like peptide (GLP), calcitonin gene-related peptide, parathyroid hormone (PTH), and corticotropin-releasing factor. These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. All members of the B1 subfamily preferentially couple to G proteins of G(s) family, which positively stimulate adenylate cyclase, leading to increased intracellular cAMP formation and calcium influx. The class B GPCRs have been identified in all the vertebrates, from fishes to mammals, as well as invertebrates including Caenorhabditis elegans and Drosophila melanogaster, but are not present in plants, fungi, or prokaryotes. 285 matched cddid_all.tbl CDD cd15274 cd15274 341343 7tmB1_calcitonin_R calcitonin receptor, member of the class B family of seven-transmembrane G protein-coupled receptors. This group includes G protein-coupled receptors for calcitonin (CT) and calcitonin gene-related peptides (CGRPs). Calcitonin, a 32-amino acid peptide hormone, is involved in calcium metabolism in many mammalian species and acts to reduce blood calcium levels and directly inhibits bone resorption by acting on osteoclast. Thus, CT acts as an antagonist to parathyroid hormone and is commonly used in the treatment of bone disorders. The CT receptor is predominantly found in osteoclasts, kidney, and brain, and is primarily coupled to stimulatory G(s) protein, which leads to activation of adenylate cyclase, thereby increasing cAMP production. CGRP, a member of the calcitonin family of peptides, is a potent vasodilator and may contribute to migraine. It is expressed in the peripheral and central nervous system and exists in two forms in humans (alpha-CGRP and beta-CGRP). CGRP meditates its physiological effects through calcitonin receptor-like receptor (CRLR) and receptor activity-modifying protein 1 (RAMP1), a single transmembrane domain protein. Thus, the CRLR/RAMP1 complex serves as a functional CGRP receptor. On the other hand, the CRLR/RAMP2 and CRLR/RAMP3 complexes function as adrenomedullin-specific receptors. The CT and CGRP receptors belong to the B1 subfamily of class B GPCRs, also referred to as secretin-like receptor family, which includes receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, glucagon, glucagon-like peptide (GLP), parathyroid hormone (PTH), and corticotropin-releasing factor. These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. 274 matched cddid_all.tbl CDD cd15275 cd15275 320403 7tmB1_secretin secretin receptor, member of the class B family of seven-transmembrane G protein-coupled receptors. Secretin receptor is a member of the group of G protein-coupled receptors for structurally similar peptide hormones that also include vasoactive intestinal peptide (VIP), growth-hormone-releasing hormone (GHRH), and pituitary adenylate cyclase activating polypeptide (PACAP). These receptors are classified into the subfamily B1 of class B GRCRs that consists of the classical hormone receptors, and have been identified in all the vertebrates, from fishes to mammals, but are not present in plants, fungi, or prokaryotes. For all class B receptors, the large N-terminal extracellular domain plays a critical role in peptide hormone recognition. Secretin, a polypeptide secreted by entero-endocrine S cells in the small intestine, is involved in maintaining body fluid balance. This polypeptide regulates the secretion of bile and bicarbonate into the duodenum from the pancreatic and biliary ducts, as well as regulates the duodenal pH by the control of gastric acid secretion. Studies with secretin receptor-null mice indicate that secretin plays a role in regulating renal water reabsorption. Secretin mediates its biological actions by elevating intracellular cAMP via G protein-coupled secretin receptor, which is expressed in the brain, pancreas, stomach, kidney, and liver. 271 matched cddid_all.tbl CDD cd15277 cd15277 320404 7tmC_RAIG3_GPRC5C retinoic acid-inducible orphan G-protein-coupled receptor 3; class C family of seven-transmembrane G protein-coupled receptors, group 5, member C. Retinoic acid-inducible G-protein-coupled receptors (RAIGs), also referred to as GPCR class C group 5, are a group consisting of four orphan receptors RAIG1 (GPRC5A), RAIG2 (GPRC5B), RAIG3 (GPRC5C), and RAIG4 (GPRC5D). Unlike other members of the class C GPCRs which contain a large N-terminal extracellular domain, RAIGs have a shorter N-terminus. Thus, it is unlikely that RAIGs bind an agonist at its N-terminus domain. Instead, the agonists may bind to the seven-transmembrane domain of these receptors. In addition, RAIG2 and RAIG3 contain a cleavable signal peptide whereas RAIG1 and RAIG4 do not. Although their expression is induced by retinoic acid (vitamin A analog), their biological function is not clearly understood. To date, no ligand is known for the members of RAIG family. Three receptor types (RAIG1-3) are found in vertebrates, while RAIG4 is only present in mammals. They show distinct tissue distribution with RAIG1 being primarily expressed in the lung, RAIG2 in the brain and placenta, RAIG3 in the brain, kidney and liver, and RAIG4 in the skin. The specific function of RAIG3 is unknown; however, this protein may play a role in mediating the effects of retinoic acid on embryogenesis, differentiation, and tumorigenesis through interaction with a G-protein signaling cascade. 250 matched cddid_all.tbl CDD cd15278 cd15278 320405 7tmC_RAIG2_GPRC5B retinoic acid-inducible orphan G-protein-coupled receptor 2; class C family of seven-transmembrane G protein-coupled receptors, group 5, member B. Retinoic acid-inducible G-protein-coupled receptors (RAIGs), also referred to as GPCR class C group 5, are a group consisting of four orphan receptors RAIG1 (GPRC5A), RAIG2 (GPRC5B), RAIG3 (GPRC5C), and RAIG4 (GPRC5D). Unlike other members of the class C GPCRs which contain a large N-terminal extracellular domain, RAIGs have a shorter N-terminus. Thus, it is unlikely that RAIGs bind an agonist at its N-terminus domain. Instead, the agonists may bind to the seven-transmembrane domain of these receptors. In addition, RAIG2 and RAIG3 contain a cleavable signal peptide whereas RAIG1 and RAIG4 do not. Although their expression is induced by retinoic acid (vitamin A analog), their biological function is not clearly understood. To date, no ligand is known for the members of RAIG family. Three receptor types (RAIG1-3) are found in vertebrates, while RAIG4 is only present in mammals. They show distinct tissue distribution with RAIG1 being primarily expressed in the lung, RAIG2 in the brain and placenta, RAIG3 in the brain, kidney and liver, and RAIG4 in the skin. RAIG2 (GPRC5B), a mammalian Boss (Bride of sevenless) homolog, has been shown to activate obesity-associated inflammatory signaling in adipocytes, and that the GPRC5B knockout mice have been shown to be resistance to high-fat diet-induced obesity and insulin resistance. 244 matched cddid_all.tbl CDD cd15279 cd15279 320406 7tmC_RAIG1_4_GPRC5A_D retinoic acid-inducible orphan G-protein-coupled receptors 1 and 4; class C family of seven-transmembrane G protein-coupled receptors, group 5, member A and D. Retinoic acid-inducible G-protein-coupled receptors (RAIGs), also referred to as GPCR class C group 5, are a group consisting of four orphan receptors RAIG1 (GPRC5A), RAIG2 (GPRC5B), RAIG3 (GPRC5C), and RAIG4 (GPRC5D). Unlike other members of the class C GPCRs which contain a large N-terminal extracellular domain, RAIGs have a shorter N-terminus. Thus, it is unlikely that RAIGs bind an agonist at its N-terminus domain. Instead, the agonists may bind to the seven-transmembrane domain of these receptors. In addition, RAIG2 and RAIG3 contain a cleavable signal peptide whereas RAIG1 and RAIG4 do not. Although their expression is induced by retinoic acid (vitamin A analog), their biological function is not clearly understood. To date, no ligand is known for the members of RAIG family. Three receptor types (RAIG1-3) are found in vertebrates, while RAIG4 is only present in mammals. They show distinct tissue distribution with RAIG1 being primarily expressed in the lung, RAIG2 in the brain and placenta, RAIG3 in the brain, kidney and liver, and RAIG4 in the skin. RAIG1 is evolutionarily conserved from mammals to fish. RAIG1 has been to shown to act as a tumor suppressor in non-small cell lung carcinoma as well as oral squamous cell carcinoma, but it could also act as an oncogene in breast cancer, colorectal cancer, and pancreatic cancer. Studies have shown that overexpression of RAIG1 decreases intracellular cAMP levels. Moreover, knocking out RAIG1 induces the activation of the NF-kB and STAT3 signaling pathways leading to cell proliferation and resistance to apoptosis. The specific function of RAIG4 is unknown; however, this protein may play a role in mediating the effects of retinoic acid on embryogenesis, differentiation, and tumorigenesis through interaction with a G-protein signaling cascade. 248 matched cddid_all.tbl CDD cd15280 cd15280 320407 7tmC_V2R-like vomeronasal type-2 receptor-like proteins, member of the class C family of seven-transmembrane G protein-coupled receptors. This group represents vomeronasal type-2 receptor-like proteins that are closely related to the V2R family of vomeronasal GPCRs. Members of the V2R family of vomeronasal GPCRs are involved in detecting protein pheromones for social and sexual cues between the same species. V2Rs and G-alpha(o) protein are coexpressed in the basal layer of the vomeronasal organ (VNO), which is the sensory organ of the accessory olfactory system present in amphibians, reptiles, and non-primate mammals such as mice and rodents, but it is non-functional or absent in humans, apes, and monkeys. On the other hand, members of the V1R receptor family and G-alpha(i2) protein are co-expressed in the apical neurons of the VNO. Activation of V1R or V2R causes activation of phospholipase pathway, generating the secondary messengers diacylglycerol (DAG) and IP3. However, in contrast to V1Rs, V2Rs contain the long N-terminal extracellular domain, which is believed to bind pheromones. Human V2R1-like protein, also known as putative calcium-sensing receptor-like 1 (CASRL1), is not included here because it is a nonfunctional pseudogene. 253 matched cddid_all.tbl CDD cd15281 cd15281 320408 7tmC_GPRC6A class C of seven-transmembrane G protein-coupled receptors, subtype 6A. GRPC6A (GPCR, class C, group 6, subtype A) is a widely expressed amino acid-sensing GPCR that is most closely related to CaSR. GPRC6A is most potently activated by the basic amino acids L-arginine, L-lysine, and L-ornithine and less potently by small aliphatic amino acids. Moreover, the receptor can be either activated or modulated by divalent cations such as Ca2+ and Mg2+. GPRC6A is expressed in the testis, but not the ovary and specifically also binds to the osteoblast-derived hormone osteocalcin (OCN), which regulates testosterone production by the testis and male fertility independently of the hypothalamic-pituitary axis. Furthermore, GPRC6A knockout studies suggest that GRPC6A is involved in regulation of bone metabolism, male reproduction, energy homeostasis, glucose metabolism, and in activation of inflammation response, as well as prostate cancer growth and progression, among others. GPRC6A has been suggested to couple to the Gq subtype of G proteins, leading to IP3 production and intracellular calcium mobilization. GPRC6A contains a large extracellular Venus flytrap-like domain in the N-terminus, cysteine-rich domain (CRD), and seven-transmembrane (7TM) domain, which are characteristics of the class C GPCRs. The Venus flytrap-like domain shares strong sequence homology to bacterial periplasmic binding proteins and possess the orthosteric amino acid and calcium binding sites for members of the class C, including CaSR, GABA-B, GPRC6A, mGlu, and TAS1R receptors. 249 matched cddid_all.tbl CDD cd15282 cd15282 320409 7tmC_CaSR calcium-sensing receptor, member of the class C of seven-transmembrane G protein-coupled receptors. CaSR is a widely expressed GPCR that is involved in sensing small changes in extracellular levels of calcium ion to maintain a constant level of the extracellular calcium via modulating the synthesis and secretion of calcium regulating hormones, such as parathyroid hormone (PTH), in order to regulate Ca(2+)transport into or out of the extracellular fluid via kidney, intestine, and/or bone. For instance, when Ca2+ is high, CaSR downregulates PTH synthesis and secretion, leading to an increase in renal Ca2+ excretion, a decrease in intestinal Ca2+ absorption, and a reduction in release of skeletal Ca2+. CaSR is coupled to both G(q/11)-dependent activation of phospholipase and, subsequently, intracellular calcium mobilization and protein kinase C activation as well as G(i/o)-dependent inhibition of adenylate cyclase leading to inhibition of cAMP formation. CaSR is closely related to GRPC6A (GPCR, class C, group 6, subtype A), which is an amino acid-sensing GPCR that is most potently activated by the basic amino acids L-arginine, L-lysine, and L-ornithine. These receptors contain a large extracellular Venus flytrap-like domain in the N-terminus, cysteine-rich domain (CRD), and seven-transmembrane (7TM) domain, which are characteristics of the class C GPCRs. The Venus flytrap-like domain shares strong sequence homology to bacterial periplasmic binding proteins and possess the orthosteric amino acid and calcium binding sites for members of the class C, including CaSR, GABA-B1, GPRC6A, mGlu, and TASR1 receptors. 252 matched cddid_all.tbl CDD cd15283 cd15283 320410 7tmC_V2R_pheromone vomeronasal type-2 pheromone receptors, member of the class C family of seven-transmembrane G protein-coupled receptors. This group represents vomeronasal type-2 pheromone receptors (V2Rs). Members of the V2R family of vomeronasal GPCRs are involved in detecting protein pheromones for social and sexual cues between the same species. V2Rs and G-alpha(o) protein are coexpressed in the basal layer of the vomeronasal organ (VNO), which is the sensory organ of the accessory olfactory system present in amphibians, reptiles, and non-primate mammals such as mice and rodents, but it is non-functional or absent in humans, apes, and monkeys. On the other hand, members of the V1R receptor family and G-alpha(i2) protein are coexpressed in the apical neurons of the VNO. Activation of V1R or V2R causes activation of phospholipase pathway, producing the second messengers diacylglycerol (DAG) and IP3. However, in contrast to V1Rs, V2Rs contain the long N-terminal extracellular domain, which is believed to bind pheromones. 252 matched cddid_all.tbl CDD cd15284 cd15284 320411 7tmC_mGluR_group2 metabotropic glutamate receptors in group 2, member of the class C family of seven-transmembrane G protein-coupled receptors. The metabotropic glutamate receptors (mGluRs) in group 2 include mGluR 2 and 3. They are homodimeric class C G-protein coupled receptors which are activated by glutamate, the major excitatory neurotransmitter of the CNS. mGluRs are involved in regulating neuronal excitability and synaptic transmission via intracellular activation of second messenger signaling pathways. While the ionotropic glutamate receptor subtypes (AMPA, NMDA, and kainite) mediate fast excitatory postsynaptic transmission, mGluRs are known to mediate slower excitatory postsynaptic responses and to be involved in synaptic plasticity in the mammalian brain. In addition to seven-transmembrane helices, the class C GPCRs are characterized by a large N-terminal extracellular Venus flytrap-like domain, which is composed of two adjacent lobes separated by a cleft which binds an endogenous ligand. Moreover, they exist as either homo- or heterodimers, which are essential for their function. For instance, mGluRs form homodimers via interactions between the N-terminal Venus flytrap domains and the intermolecular disulphide bonds between cysteine residues located in the cysteine-rich domain (CRD). At least eight different subtypes of metabotropic receptors (mGluR1-8) have been identified and further classified into three groups based on their sequence homology, pharmacological properties, and signaling pathways. Group 1 (mGluR1 and mGluR5) receptors are predominantly located postsynaptically on neurons and are involved in long-term synaptic plasticity in the brain, including long-term potentiation (LTP) in the hippocampus and long-term depression (LTD) in the cerebellum. They are coupled to G(q/11) proteins, thereby activating phospholipase C to generate inositol-1,4,5-triphosphate (IP3) and diacyglycerol (DAG), which in turn lead to Ca2+ release and protein kinase C activation, respectively. Group 1 mGluR expression is shown to be strongly upregulated in animal models of epilepsy, brain injury, inflammatory, and neuropathic pain, as well as in patients with amyotrophic lateral sclerosis or multiple sclerosis. Group 2 (mGluR2 and mGluR3) and 3 (mGluR4, mGluR6, mGluR7, and mGluR8) receptors are predominantly localized presynaptically in the active region of neurotransmitter release. They are coupled to G(i/o) proteins, which leads to inhibition of adenylate cyclase activity and cAMP formation, and consequently to a decrease in protein kinase A (PKA) activity. Ultimately, activation of these receptors leads to inhibition of neurotransmitter release such as glutamate and GABA via inhibition of Ca2+ channels and activation of K+ channels. Furthermore, while activation of Group 1 mGluRs increases NMDA (N-methyl-D-aspartate) receptor activity and risk of neurotoxicity, Group 2 and 3 mGluRs decrease NMDA receptor activity and prevent neurotoxicity. 254 matched cddid_all.tbl CDD cd15285 cd15285 320412 7tmC_mGluR_group1 metabotropic glutamate receptors in group 1, member of the class C family of seven-transmembrane G protein-coupled receptors. Group 1 mGluRs includes mGluR1 and mGluR5, as well as their closely related invertebrate receptors. They are homodimeric class C G-protein coupled receptors which are activated by glutamate, the major excitatory neurotransmitter of the CNS. mGluRs are involved in regulating neuronal excitability and synaptic transmission via intracellular activation of second messenger signaling pathways. While the ionotropic glutamate receptor subtypes (AMPA, NMDA, and kainite) mediate fast excitatory postsynaptic transmission, mGluRs are known to mediate slower excitatory postsynaptic responses and to be involved in synaptic plasticity in the mammalian brain. In addition to seven-transmembrane helices, the class C GPCRs are characterized by a large N-terminal extracellular Venus flytrap-like domain, which is composed of two adjacent lobes separated by a cleft which binds an endogenous ligand. Moreover, they exist as either homo- or heterodimers, which are essential for their function. For instance, mGluRs form homodimers via interactions between the N-terminal Venus flytrap domains and the intermolecular disulphide bonds between cysteine residues located in the cysteine-rich domain (CRD). At least eight different subtypes of metabotropic receptors (mGluR1-8) have been identified and further classified into three groups based on their sequence homology, pharmacological properties, and signaling pathways. Group 1 (mGluR1 and mGluR5) receptors are predominantly located postsynaptically on neurons and are involved in long-term synaptic plasticity in the brain, including long-term potentiation (LTP) in the hippocampus and long-term depression (LTD) in the cerebellum. They are coupled to G(q/11) proteins, thereby activating phospholipase C to generate inositol-1,4,5-triphosphate (IP3) and diacyglycerol (DAG), which in turn lead to Ca2+ release and protein kinase C activation, respectively. Group 1 mGluR expression is shown to be strongly upregulated in animal models of epilepsy, brain injury, inflammatory, and neuropathic pain, as well as in patients with amyotrophic lateral sclerosis or multiple sclerosis. Group 2 (mGluR2 and mGluR3) and 3 (mGluR4, mGluR6, mGluR7, and mGluR8) receptors are predominantly localized presynaptically in the active region of neurotransmitter release. They are coupled to G(i/o) proteins, which leads to inhibition of adenylate cyclase activity and cAMP formation, and consequently to a decrease in protein kinase A (PKA) activity. Ultimately, activation of these receptors leads to inhibition of neurotransmitter release such as glutamate and GABA via inhibition of Ca2+ channels and activation of K+ channels. Furthermore, while activation of Group 1 mGluRs increases NMDA (N-methyl-D-aspartate) receptor activity and risk of neurotoxicity, Group 2 and 3 mGluRs decrease NMDA receptor activity and prevent neurotoxicity. 250 matched cddid_all.tbl CDD cd15286 cd15286 320413 7tmC_mGluR_group3 metabotropic glutamate receptors in group 3, member of the class C family of seven-transmembrane G protein-coupled receptors. The metabotropic glutamate receptors (mGluRs) in group 3 include mGluRs 4, 6, 7, and 8. They are homodimeric class C G-protein coupled receptors which are activated by glutamate, the major excitatory neurotransmitter of the CNS. mGluRs are involved in regulating neuronal excitability and synaptic transmission via intracellular activation of second messenger signaling pathways. While the ionotropic glutamate receptor subtypes (AMPA, NMDA, and kainite) mediate fast excitatory postsynaptic transmission, mGluRs are known to mediate slower excitatory postsynaptic responses and to be involved in synaptic plasticity in the mammalian brain. In addition to seven-transmembrane helices, the class C GPCRs are characterized by a large N-terminal extracellular Venus flytrap-like domain, which is composed of two adjacent lobes separated by a cleft which binds an endogenous ligand. Moreover, they exist as either homo- or heterodimers, which are essential for their function. For instance, mGluRs form homodimers via interactions between the N-terminal Venus flytrap domains and the intermolecular disulphide bonds between cysteine residues located in the cysteine-rich domain (CRD). At least eight different subtypes of metabotropic receptors (mGluR1-8) have been identified and further classified into three groups based on their sequence homology, pharmacological properties, and signaling pathways. Group 1 (mGluR1 and mGluR5) receptors are predominantly located postsynaptically on neurons and are involved in long-term synaptic plasticity in the brain, including long-term potentiation (LTP) in the hippocampus and long-term depression (LTD) in the cerebellum. They are coupled to G(q/11) proteins, thereby activating phospholipase C to generate inositol-1,4,5-triphosphate (IP3) and diacyglycerol (DAG), which in turn lead to Ca2+ release and protein kinase C activation, respectively. Group 1 mGluR expression is shown to be strongly upregulated in animal models of epilepsy, brain injury, inflammatory, and neuropathic pain, as well as in patients with amyotrophic lateral sclerosis or multiple sclerosis. Group 2 (mGluR2 and mGluR3) and 3 (mGluR4, mGluR6, mGluR7, and mGluR8) receptors are predominantly localized presynaptically in the active region of neurotransmitter release. They are coupled to G(i/o) proteins, which leads to inhibition of adenylate cyclase activity and cAMP formation, and consequently to a decrease in protein kinase A (PKA) activity. Ultimately, activation of these receptors leads to inhibition of neurotransmitter release such as glutamate and GABA via inhibition of Ca2+ channels and activation of K+ channels. Furthermore, while activation of Group 1 mGluRs increases NMDA (N-methyl-D-aspartate) receptor activity and risk of neurotoxicity, Group 2 and 3 mGluRs decrease NMDA receptor activity and prevent neurotoxicity. 271 matched cddid_all.tbl CDD cd15287 cd15287 320414 7tmC_TAS1R2a-like type 1 taste receptor subtype 2a and similar proteins, member of the class C of seven-transmembrane G protein-coupled receptors. This group includes TAS1R2a and its similar proteins found in fish. They are members of the type I taste receptor (TAS1R) family that belongs to the class C of G protein-coupled receptors. The functional TAS1Rs are obligatory heterodimers built from three known members, TAS1R1-3. TAS1R1 combines with TAS1R3 to form an umami taste receptor, which is responsible for the perception of savory taste, such as the food additive mono-sodium glutamate (MSG); whereas the combination of TAS1R2-TAS1R3 forms a sweet-taste receptor for sugars and D-amino acids. On the other hand, the type II taste receptors (TAS2Rs), which belong to the class A family of GPCRs, recognize bitter tasting compounds. In the case of sweet, for example, the TAS1R2-TAS1R3 heterodimer activates phospholipase C (PLC) via alpha-gustducin, a heterodimeric G protein that is involved in perception of sweet and bitter tastes. This activation leads to generation of inositol (1, 4, 5)-trisphosphate (IP3) and diacylglycerol (DAG), and consequently increases intracellular Ca2+ mobilization and activates a cation channel, TRPM5. In contrast to the TAS1R2-TAS1R3 heterodimer, TAS1R3 alone could activate adenylate cyclase leading to cAMP formation in the absence of alpha-gustducin. Each TAS1R contains a large extracellular Venus flytrap-like domain in the N-terminus, cysteine-rich domain (CRD) and seven-transmembrane (7TM) domain, which are characteristics of the class C GPCRs. The Venus flytrap-like domain shares strong sequence homology to bacterial periplasmic binding proteins and possess the orthosteric amino acid and calcium binding sites for members of the class C, including CaSR, GABA-B1, GPRC6A, mGlu, and TAS1R receptors. 252 matched cddid_all.tbl CDD cd15288 cd15288 320415 7tmC_TAS1R2 type 1 taste receptor subtype 2, member of the class C of seven-transmembrane G protein-coupled receptors. This group represents TAS1R2, which is a member of the type I taste receptor (TAS1R) family that belongs to the class C of G protein-coupled receptors. The functional TAS1Rs are obligatory heterodimers built from three known members, TAS1R1-3. TAS1R1 combines with TAS1R3 to form an umami taste receptor, which is responsible for the perception of savory taste, such as the food additive mono-sodium glutamate (MSG); whereas the combination of TAS1R2-TAS1R3 forms a sweet-taste receptor for sugars and D-amino acids. On the other hand, the type II taste receptors (TAS2Rs), which belong to the class A family of GPCRs, recognize bitter tasting compounds. In the case of sweet, for example, the TAS1R2-TAS1R3 heterodimer activates phospholipase C (PLC) via alpha-gustducin, a heterodimeric G protein that is involved in perception of sweet and bitter tastes. This activation leads to generation of inositol (1, 4, 5)-trisphosphate (IP3) and diacylglycerol (DAG), and consequently increases intracellular Ca2+ mobilization and activates a cation channel, TRPM5. In contrast to the TAS1R2-TAS1R3 heterodimer, TAS1R3 alone could activate adenylate cyclase leading to cAMP formation in the absence of alpha-gustducin. Each TAS1R contains a large extracellular Venus flytrap-like domain in the N-terminus, cysteine-rich domain (CRD) and seven-transmembrane (7TM) domain, which are characteristics of the class C GPCRs. The Venus flytrap-like domain shares strong sequence homology to bacterial periplasmic binding proteins and possess the orthosteric amino acid and calcium binding sites for members of the class C, including CaSR, GABA-B1, GPRC6A, mGlu, and TAS1R receptors. 254 matched cddid_all.tbl CDD cd15289 cd15289 320416 7tmC_TAS1R1 type 1 taste receptor subtype 1, member of the class C of seven-transmembrane G protein-coupled receptors. This group represents TAS1R1, which is a member of the type I taste receptor (TAS1R) family that belongs to the class C of G protein-coupled receptors. The functional TAS1Rs are obligatory heterodimers built from three known members, TAS1R1-3. TAS1R1 combines with TAS1R3 to form an umami taste receptor, which is responsible for the perception of savory taste, such as the food additive mono-sodium glutamate (MSG); whereas the combination of TAS1R2-TAS1R3 forms a sweet-taste receptor for sugars and D-amino acids. On the other hand, the type II taste receptors (TAS2Rs), which belong to the class A family of GPCRs, recognize bitter tasting compounds. In the case of sweet, for example, the TAS1R2-TAS1R3 heterodimer activates phospholipase C (PLC) via alpha-gustducin, a heterodimeric G protein that is involved in perception of sweet and bitter tastes. This activation leads to generation of inositol (1, 4, 5)-trisphosphate (IP3) and diacylglycerol (DAG), and consequently increases intracellular Ca2+ mobilization and activates a cation channel, TRPM5. In contrast to the TAS1R2-TAS1R3 heterodimer, TAS1R3 alone could activate adenylate cyclase leading to cAMP formation in the absence of alpha-gustducin. Each TAS1R contains a large extracellular Venus flytrap-like domain in the N-terminus, cysteine-rich domain (CRD) and seven-transmembrane (7TM) domain, which are characteristics of the class C GPCRs. The Venus flytrap-like domain shares strong sequence homology to bacterial periplasmic binding proteins and possess the orthosteric amino acid and calcium binding sites for members of the class C, including CaSR, GABA-B1, GPRC6A, mGlu, and TAS1R receptors. 253 matched cddid_all.tbl CDD cd15290 cd15290 320417 7tmC_TAS1R3 type 1 taste receptor subtype 3, member of the class C of seven-transmembrane G protein-coupled receptors. This group represents TAS1R3, which is a member of the type I taste receptor (TAS1R) family that belongs to the class C of G protein-coupled receptors. The functional TAS1Rs are obligatory heterodimers built from three known members, TAS1R1-3. TAS1R1 combines with TAS1R3 to form an umami taste receptor, which is responsible for the perception of savory taste, such as the food additive mono-sodium glutamate (MSG); whereas the combination of TAS1R2-TAS1R3 forms a sweet-taste receptor for sugars and D-amino acids. On the other hand, the type II taste receptors (TAS2Rs), which belong to the class A family of GPCRs, recognize bitter tasting compounds. In the case of sweet, for example, the TAS1R2-TAS1R3 heterodimer activates phospholipase C (PLC) via alpha-gustducin, a heterodimeric G protein that is involved in perception of sweet and bitter tastes. This activation leads to generation of inositol (1, 4, 5)-trisphosphate (IP3) and diacylglycerol (DAG), and consequently increases intracellular Ca2+ mobilization and activates a cation channel, TRPM5. In contrast to the TAS1R2-TAS1R3 heterodimer, TAS1R3 alone could activate adenylate cyclase leading to cAMP formation in the absence of alpha-gustducin. Each TAS1R contains a large extracellular Venus flytrap-like domain in the N-terminus, cysteine-rich domain (CRD) and seven-transmembrane (7TM) domain, which are characteristics of the class C GPCRs. The Venus flytrap-like domain shares strong sequence homology to bacterial periplasmic binding proteins and possess the orthosteric amino acid and calcium binding sites for members of the class C, including CaSR, GABA-B1, GPRC6A, mGlu, and TAS1R receptors. 253 matched cddid_all.tbl CDD cd15291 cd15291 320418 7tmC_GABA-B-R1 gamma-aminobutyric acid type B receptor subunit 1, member of the class C family of seven-transmembrane G protein-coupled receptors. The type B receptor for gamma-aminobutyric acid, GABA-B, is activated by its endogenous ligand GABA, the principal inhibitory neurotransmitter. The functional GABA-B receptor is an obligatory heterodimer composed of two related subunits, GABA-B1, which is primarily involved in GABA ligand binding, and GABA-B2, which is responsible for both G-protein coupling and trafficking of the heterodimer to the plasma membrane. Activation of GABA-B couples to G(i/o)-type G proteins, which in turn modulate three major downstream effectors: adenylate cyclase, voltage-sensitive Ca2+ channels, and inwardly-rectifying K+ channels. Consequently, GABA-B receptor produces slow and sustained inhibitory responses by decreased neurotransmitter release via inhibition of Ca2+ channels and by postsynaptic hyperpolarization via the activation of K+ channels through the G-protein beta-gamma dimer. The GABA-B is expressed in both pre- and postsynaptic sites of glutamatergic and GABAergic neurons in the brain where it regulates synaptic activity. Thus, the GABA-B receptor agonist, baclofen, is used to treat muscle tightness and cramping caused by spasticity in multiple sclerosis patients. Moreover, GABA-B antagonists improves cognitive performance in mammals, while GABA-B agonists suppress cognitive behavior. In most of the class C family members, the extracellular Venus-flytrap domain in the N-terminus is connected to the seven-transmembrane (7TM) via a cysteine-rich domain (CRD). However, in the GABA-B receptor, the CRD is absent in both subunits and the Venus-flytrap ligand-binding domain is directly connected to the 7TM via a 10-15 amino acids linker, suggesting that GABA-B receptor may utilize a different activation mechanism. 274 matched cddid_all.tbl CDD cd15292 cd15292 320419 7tmC_GPR156 orphan GPR156, member of the class C family of seven-transmembrane G protein-coupled receptors. This subgroup represents orphan GPR156 that is closely related to the type B receptor for gamma-aminobutyric acid (GABA-B), which is activated by its endogenous ligand GABA, the principal inhibitory neurotransmitter. The functional GABA-B receptor is an obligatory heterodimer composed of two related subunits, GABA-B1, which is primarily involved in GABA ligand binding, and GABA-B2, which is responsible for both G-protein coupling and trafficking of the heterodimer to the plasma membrane. Activation of GABA-B couples to G(i/o)-type G proteins, which in turn modulate three major downstream effectors: adenylate cyclase, voltage-sensitive Ca2+ channels, and inwardly-rectifying K+ channels. Consequently, GABA-B receptor produces slow and sustained inhibitory responses by decreased neurotransmitter release via inhibition of Ca2+ channels and by postsynaptic hyperpolarization via the activation of K+ channels through the G-protein beta-gamma dimer. The GABA-B is expressed in both pre- and postsynaptic sites of glutamatergic and GABAergic neurons in the brain where it regulates synaptic activity. Thus, the GABA-B receptor agonist, baclofen, is used to treat muscle tightness and cramping caused by spasticity in multiple sclerosis patients. Moreover, GABA-B antagonists improves cognitive performance in mammals, while GABA-B agonists suppress cognitive behavior. In most of the class C family members, the extracellular Venus-flytrap domain in the N-terminus is connected to the seven-transmembrane (7TM) via a cysteine-rich domain (CRD). However, in the GABA-B receptor, the CRD is absent in both subunits and the Venus-flytrap ligand-binding domain is directly connected to the 7TM via a 10-15 amino acids linker, suggesting that GABA-B receptor may utilize a different activation mechanism. 268 matched cddid_all.tbl CDD cd15293 cd15293 320420 7tmC_GPR158-like orphan GPR158 and similar proteins, member of the class C family of seven-transmembrane G protein-coupled receptors. This group includes orphan receptors GPR158, GPR158-like (also called GPR179) and similar proteins. These orphan receptors are closely related to the type B receptor for gamma-aminobutyric acid (GABA-B), which is activated by its endogenous ligand GABA, the principal inhibitory neurotransmitter. The functional GABA-B receptor is an obligatory heterodimer composed of two related subunits, GABA-B1, which is primarily involved in GABA ligand binding, and GABA-B2, which is responsible for both G-protein coupling and trafficking of the heterodimer to the plasma membrane. Activation of GABA-B couples to G(i/o)-type G proteins, which in turn modulate three major downstream effectors: adenylate cyclase, voltage-sensitive Ca2+ channels, and inwardly-rectifying K+ channels. Consequently, GABA-B receptor produces slow and sustained inhibitory responses by decreased neurotransmitter release via inhibition of Ca2+ channels and by postsynaptic hyperpolarization via the activation of K+ channels through the G-protein beta-gamma dimer. The GABA-B is expressed in both pre- and postsynaptic sites of glutamatergic and GABAergic neurons in the brain where it regulates synaptic activity. Thus, the GABA-B receptor agonist, baclofen, is used to treat muscle tightness and cramping caused by spasticity in multiple sclerosis patients. Moreover, GABA-B antagonists improves cognitive performance in mammals, while GABA-B agonists suppress cognitive behavior. In most of the class C family members, the extracellular Venus-flytrap domain in the N-terminus is connected to the seven-transmembrane (7TM) via a cysteine-rich domain (CRD). However, in the GABA-B receptor, the CRD is absent in both subunits and the Venus-flytrap ligand-binding domain is directly connected to the 7TM via a 10-15 amino acids linker, suggesting that GABA-B receptor may utilize a different activation mechanism. 252 matched cddid_all.tbl CDD cd15294 cd15294 320421 7tmC_GABA-B-R2 gamma-aminobutyric acid type B receptor subunit 2, member of the class C family of seven-transmembrane G protein-coupled receptors. The type B receptor for gamma-aminobutyric acid, GABA-B, is activated by its endogenous ligand GABA, the principal inhibitory neurotransmitter. The functional GABA-B receptor is an obligatory heterodimer composed of two related subunits, GABA-B1, which is primarily involved in GABA ligand binding, and GABA-B2, which is responsible for both G-protein coupling and trafficking of the heterodimer to the plasma membrane. Activation of GABA-B couples to G(i/o)-type G proteins, which in turn modulate three major downstream effectors: adenylate cyclase, voltage-sensitive Ca2+ channels, and inwardly-rectifying K+ channels. Consequently, GABA-B receptor produces slow and sustained inhibitory responses by decreased neurotransmitter release via inhibition of Ca2+ channels and by postsynaptic hyperpolarization via the activation of K+ channels through the G-protein beta-gamma dimer. The GABA-B is expressed in both pre- and postsynaptic sites of glutamatergic and GABAergic neurons in the brain where it regulates synaptic activity. Thus, the GABA-B receptor agonist, baclofen, is used to treat muscle tightness and cramping caused by spasticity in multiple sclerosis patients. Moreover, GABA-B antagonists improves cognitive performance in mammals, while GABA-B agonists suppress cognitive behavior. In most of the class C family members, the extracellular Venus-flytrap domain in the N-terminus is connected to the seven-transmembrane (7TM) via a cysteine-rich domain (CRD). However, in the GABA-B receptor, the CRD is absent in both subunits and the Venus-flytrap ligand-binding domain is directly connected to the 7TM via a 10-15 amino acids linker, suggesting that GABA-B receptor may utilize a different activation mechanism. 270 matched cddid_all.tbl CDD cd15295 cd15295 320422 7tmA_Histamine_H4R histamine receptor subtype H4R, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes histamine subtype H4R, a member of the histamine receptor family, which belong to the class A of GPCRs. Histamine plays a key role as chemical mediator and neurotransmitter in various physiological and pathophysiological processes in the central and peripheral nervous system. Histamine exerts its functions by binding to four different G protein-coupled receptors (H1-H4). The H3 and H4 receptors couple to the G(i)-proteins, which leading to the inhibition of cAMP formation. The H3R receptor functions as a presynaptic autoreceptors controlling histamine release and synthesis. The H4R plays an important role in histamine-mediated chemotaxis in mast cells and eosinophils. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 267 matched cddid_all.tbl CDD cd15296 cd15296 320423 7tmA_Histamine_H3R histamine receptor subtypes H3R and H3R-like, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes histamine subtypes H3R and H3R-like, members of the histamine receptor family, which belong to the class A of GPCRs. Histamine plays a key role as chemical mediator and neurotransmitter in various physiological and pathophysiological processes in the central and peripheral nervous system. Histamine exerts its functions by binding to four different G protein-coupled receptors (H1-H4). The H3 and H4 receptors couple to the G(i)-proteins, which leading to the inhibition of cAMP formation. The H3R receptor functions as a presynaptic autoreceptors controlling histamine release and synthesis. The H4R plays an important role in histamine-mediated chemotaxis in mast cells and eosinophils. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 271 matched cddid_all.tbl CDD cd15297 cd15297 320424 7tmA_mAChR_M2 muscarinic acetylcholine receptor subtype M2, member of the class A family of seven-transmembrane G protein-coupled receptors. Muscarinic acetylcholine receptors (mAChRs) regulate the activity of many fundamental central and peripheral functions. The mAChR family consists of 5 subtypes M1-M5, which can be further divided into two major groups according to their G-protein coupling preference. The M1, M3 and M5 receptors selectively interact with G proteins of the G(q/11) family, whereas the M2 and M4 receptors preferentially link to the G(i/o) types of G proteins. Activation of M2 receptor causes a decrease in cAMP production, generally leading to inhibitory-type effects. This causes an outward current of potassium in the heart, resulting in a decreased heart rate. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 262 matched cddid_all.tbl CDD cd15298 cd15298 341344 7tmA_mAChR_M4 muscarinic acetylcholine receptor subtype M4, member of the class A family of seven-transmembrane G protein-coupled receptors. Muscarinic acetylcholine receptors (mAChRs) regulate the activity of many fundamental central and peripheral functions. The mAChR family consists of 5 subtypes M1-M5, which can be further divided into two major groups according to their G-protein coupling preference. The M1, M3 and M5 receptors selectively interact with G proteins of the G(q/11) family, whereas the M2 and M4 receptors preferentially link to G(i/o) types of G proteins. The M4 receptor is mainly found in the CNS and function as an inhibitory autoreceptor regulating acetycholine release. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 262 matched cddid_all.tbl CDD cd15299 cd15299 320426 7tmA_mAChR_M3 muscarinic acetylcholine receptor subtype M3, member of the class A family of seven-transmembrane G protein-coupled receptors. Muscarinic acetylcholine receptors (mAChRs) regulate the activity of many fundamental central and peripheral functions. The mAChR family consists of 5 subtypes M1-M5, which can be further divided into two major groups according to their G-protein coupling preference. The M1, M3 and M5 receptors selectively interact with G proteins of the G(q/11) family, whereas the M2 and M4 receptors preferentially link to the G(i/o) types of G proteins. The M3 receptor is mainly located in smooth muscle, exocrine glands and vascular endothelium. It induces vomiting in the central nervous system and is a critical regulator of glucose homeostasis by modulating insulin secretion. Generally, M3 receptor causes contraction of smooth muscle resulting in vasoconstriction and increased glandular secretion. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 274 matched cddid_all.tbl CDD cd15300 cd15300 320427 7tmA_mAChR_M5 muscarinic acetylcholine receptor subtype M5, member of the class A family of seven-transmembrane G protein-coupled receptors. Muscarinic acetylcholine receptors (mAChRs) regulate the activity of many fundamental central and peripheral functions. The mAChR family consists of 5 subtypes M1-M5, which can be further divided into two major groups according to their G-protein coupling preference. The M1, M3 and M5 receptors selectively interact with G proteins of the G(q/11) family, whereas the M2 and M4 receptors preferentially link to the G(i/o) types of G proteins. M5 mAChR is primarily found in the central nervous system and mediates acetylcholine-induced dilation of cerebral blood vessels. Activation of M5 receptor triggers a variety of cellular responses, including inhibition of adenylate cyclase, breakdown of phosphoinositides, and modulation of potassium channels. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 262 matched cddid_all.tbl CDD cd15301 cd15301 320428 7tmA_mAChR_DM1-like muscarinic acetylcholine receptor DM1, member of the class A family of seven-transmembrane G protein-coupled receptors. This subgroup includes muscarinic acetylcholine receptor DM1-like from invertebrates. Muscarinic acetylcholine receptors (mAChRs) regulate the activity of many fundamental central and peripheral functions. The mAChR family consists of 5 subtypes M1-M5, which can be further divided into two major groups according to their G-protein coupling preference. The M1, M3 and M5 receptors selectively interact with G proteins of the G(q/11) family, whereas the M2 and M4 receptors preferentially link to the G(i/o) types of G proteins. Activation of mAChRs by agonist (acetylcholine) leads to a variety of biochemical and electrophysiological responses. In general, the exact nature of these responses and the subsequent physiological effects mainly depend on the molecular and pharmacological identity of the activated receptor subtype(s). All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 270 matched cddid_all.tbl CDD cd15302 cd15302 320429 7tmA_mAChR_GAR-2-like muscarinic acetylcholine receptor GAR-2 and similar proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. Muscarinic acetylcholine receptors (mAChRs) regulate the activity of many fundamental central and peripheral functions. The mAChR family consists of 5 subtypes M1-M5, which can be further divided into two major groups according to their G-protein coupling preference. The M1, M3 and M5 receptors selectively interact with G proteins of the G(q/11) family, whereas the M2 and M4 receptors preferentially link to the G(i/o) types of G proteins. Activation of mAChRs by agonist (acetylcholine) leads to a variety of biochemical and electrophysiological responses. In general, the exact nature of these responses and the subsequent physiological effects mainly depend on the molecular and pharmacological identity of the activated receptor subtype(s). All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 266 matched cddid_all.tbl CDD cd15304 cd15304 341345 7tmA_5-HT2A serotonin receptor subtype 2A, member of the class A family of seven-transmembrane G protein-coupled receptors. The 5-HT2 receptors are a subfamily of serotonin receptors that bind the neurotransmitter serotonin (5HT; 5-hydroxytryptamine) in the central nervous system (CNS). The 5-HT2 subfamily is composed of three subtypes that mediate excitatory neurotransmission: 5-HT2A, 5-HT2B, and 5-HT2C. They are selectively linked to G proteins of the G(q/11) family and activate phospholipase C, which leads to activation of protein kinase C and calcium release. In the CNS, serotonin is involved in the regulation of appetite, mood, sleep, cognition, learning and memory, as well as implicated in diseases such as migraine, schizophrenia, and depression. Indeed, 5-HT2 receptors are attractive targets for a variety of psychoactive drugs, ranging from atypical antipsychotic drugs, antidepressants, and anxiolytics, which have an antagonistic action on 5-HT2 receptors, to hallucinogens, which act as agonists at postsynaptic 5-HT2 receptors. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 267 matched cddid_all.tbl CDD cd15305 cd15305 341346 7tmA_5-HT2C serotonin receptor subtype 2C, member of the class A family of seven-transmembrane G protein-coupled receptors. The 5-HT2 receptors are a subfamily of serotonin receptors that bind the neurotransmitter serotonin (5HT; 5-hydroxytryptamine) in the central nervous system (CNS). The 5-HT2 subfamily is composed of three subtypes that mediate excitatory neurotransmission: 5-HT2A, 5-HT2B, and 5-HT2C. They are selectively linked to G proteins of the G(q/11) family and activate phospholipase C, which leads to activation of protein kinase C and calcium release. In the CNS, serotonin is involved in the regulation of appetite, mood, sleep, cognition, learning and memory, as well as implicated in diseases such as migraine, schizophrenia, and depression. Indeed, 5-HT2 receptors are attractive targets for a variety of psychoactive drugs, ranging from atypical antipsychotic drugs, antidepressants, and anxiolytics, which have an antagonistic action on 5-HT2 receptors, to hallucinogens, which act as agonists at postsynaptic 5-HT2 receptors. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 275 matched cddid_all.tbl CDD cd15306 cd15306 341347 7tmA_5-HT2B serotonin receptor subtype 2B, member of the class A family of seven-transmembrane G protein-coupled receptors. The 5-HT2 receptors are a subfamily of serotonin receptors that bind the neurotransmitter serotonin (5HT; 5-hydroxytryptamine) in the central nervous system (CNS). The 5-HT2 subfamily is composed of three subtypes that mediate excitatory neurotransmission: 5-HT2A, 5-HT2B, and 5-HT2C. They are selectively linked to G proteins of the G(q/11) family and activate phospholipase C, which leads to activation of protein kinase C and calcium release. In the CNS, serotonin is involved in the regulation of appetite, mood, sleep, cognition, learning and memory, as well as implicated in diseases such as migraine, schizophrenia, and depression. Indeed, 5-HT2 receptors are attractive targets for a variety of psychoactive drugs, ranging from atypical antipsychotic drugs, antidepressants, and anxiolytics, which have an antagonistic action on 5-HT2 receptors, to hallucinogens, which act as agonists at postsynaptic 5-HT2 receptors. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 277 matched cddid_all.tbl CDD cd15307 cd15307 320433 7tmA_5-HT2_insect-like serotonin receptor subtype 2 from insects, member of the class A family of seven-transmembrane G protein-coupled receptors. The 5-HT2 receptors are a subfamily of serotonin receptors that bind the neurotransmitter serotonin (5HT; 5-hydroxytryptamine) in the central nervous system (CNS). The 5-HT2 subfamily is composed of three subtypes that mediate excitatory neurotransmission: 5-HT2A, 5-HT2B, and 5-HT2C. They are selectively linked to G proteins of the G(q/11) family and activate phospholipase C, which leads to activation of protein kinase C and calcium release. In the CNS, serotonin is involved in the regulation of appetite, mood, sleep, cognition, learning and memory, as well as implicated in diseases such as migraine, schizophrenia, and depression. Indeed, 5-HT2 receptors are attractive targets for a variety of psychoactive drugs, ranging from atypical antipsychotic drugs, antidepressants, and anxiolytics, which have an antagonistic action on 5-HT2 receptors, to hallucinogens, which act as agonists at postsynaptic 5-HT2 receptors. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 279 matched cddid_all.tbl CDD cd15308 cd15308 320434 7tmA_D4_dopamine_R D4 dopamine receptor of the D2-like family, member of the class A family of seven-transmembrane G protein-coupled receptors. Dopamine receptors are members of the class A G protein-coupled receptors that are involved in many neurological processes in the central nervous system (CNS). The neurotransmitter dopamine is the primary endogenous agonist for dopamine receptors. Dopamine receptors consist of at least five subtypes: D1, D2, D3, D4, and D5. The D1 and D5 subtypes are members of the D1-like family of dopamine receptors, whereas the D2, D3 and D4 subtypes are members of the D2-like family. Activation of D2-like family receptors is linked to G proteins of the G(i) family. This leads to a decrease in adenylate cyclase activity, thereby decreasing cAMP levels. Dopamine receptors are major therapeutic targets for neurological and psychiatric disorders such as drug abuse, depression, schizophrenia, or Parkinson's disease. 258 matched cddid_all.tbl CDD cd15309 cd15309 320435 7tmA_D2_dopamine_R D2 subtype of the D2-like family of dopamine receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Dopamine receptors are members of the class A G protein-coupled receptors that are involved in many neurological processes in the central nervous system (CNS). The neurotransmitter dopamine is the primary endogenous agonist for dopamine receptors. Dopamine receptors consist of at least five subtypes: D1, D2, D3, D4, and D5. The D1 and D5 subtypes are members of the D1-like family of dopamine receptors, whereas the D2, D3 and D4 subtypes are members of the D2-like family. Activation of D2-like family receptors is linked to G proteins of the G(i) family. This leads to a decrease in adenylate cyclase activity, thereby decreasing cAMP levels. Dopamine receptors are major therapeutic targets for neurological and psychiatric disorders such as drug abuse, depression, schizophrenia, or Parkinson's disease. 254 matched cddid_all.tbl CDD cd15310 cd15310 320436 7tmA_D3_dopamine_R D3 subtype of the D2-like family of dopamine receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Dopamine receptors are members of the class A G protein-coupled receptors that are involved in many neurological processes in the central nervous system (CNS). The neurotransmitter dopamine is the primary endogenous agonist for dopamine receptors. Dopamine receptors consist of at least five subtypes: D1, D2, D3, D4, and D5. The D1 and D5 subtypes are members of the D1-like family of dopamine receptors, whereas the D2, D3 and D4 subtypes are members of the D2-like family. Activation of D2-like family receptors is linked to G proteins of the G(i) family. This leads to a decrease in adenylate cyclase activity, thereby decreasing cAMP levels. Dopamine receptors are major therapeutic targets for neurological and psychiatric disorders such as drug abuse, depression, schizophrenia, or Parkinson's disease. 259 matched cddid_all.tbl CDD cd15312 cd15312 320437 7tmA_TAAR2_3_4 trace amine-associated receptors 2, 3, 4, and similar receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. TAAR2, TAAR3, and TAAR4 are among the 15 identified trace amine-associated receptor subtypes, which form a distinct subfamily within the class A G protein-coupled receptor family. Trace amines are endogenous amines of unknown function that have strong structural and metabolic similarity to classical monoamine neurotransmitters (serotonin, noradrenaline, adrenaline, dopamine, and histamine), which play critical roles in human and animal physiological activities such as cognition, consciousness, mood, motivation, perception, and autonomic responses. However, trace amines are found in the mammalian brain at very low concentrations compared to classical monoamines. Trace amines, including p-tyramine, beta-phenylethylamine, and tryptamine, are also thought to act as chemical messengers to exert their biological effects in vertebrates. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 289 matched cddid_all.tbl CDD cd15314 cd15314 320438 7tmA_TAAR1 trace amine-associated receptor 1 and similar receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. The trace amine-associated receptor 1 (TAAR1) is one of the 15 identified trace amine-associated receptor subtypes, which form a distinct subfamily within the class A G protein-coupled receptor family. Trace amines are endogenous amines of unknown function that have strong structural and metabolic similarity to classical monoamine neurotransmitters (serotonin, noradrenaline, adrenaline, dopamine, and histamine), which play critical roles in human and animal physiological activities such as cognition, consciousness, mood, motivation, perception, and autonomic responses. However, trace amines are found in the mammalian brain at very low concentrations compared to classical monoamines. TAAR1 is coupled to the Gs protein, which leads to activation of adenylate cyclase, and is thought to play functional role in the regulation of brain monoamines. TAAR1 is also shown to be activated by psychoactive compounds such as Ecstasy (MDMA), amphetamine and LSD. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 282 matched cddid_all.tbl CDD cd15316 cd15316 320439 7tmA_TAAR6_8_9 trace amine-associated receptors 6, 8, and 9, member of the class A family of seven-transmembrane G protein-coupled receptors. Included in this group are mammalian TAAR6, TAAR8, TAAR9, and similar proteins. They are among the 15 identified amine-associated receptors (TAARs), a distinct subfamily within the class A G protein-coupled receptors. Trace amines are endogenous amines of unknown function that have strong structural and metabolic similarity to classical monoamine neurotransmitters (serotonin, noradrenaline, adrenaline, dopamine, and histamine), which play critical roles in human and animal physiological activities such as cognition, consciousness, mood, motivation, perception, and autonomic responses. However, trace amines are found in the mammalian brain at very low concentrations compared to classical monoamines. Trace amines, including p-tyramine, beta-phenylethylamine, and tryptamine, are also thought to act as chemical messengers to exert their biological effects in vertebrates. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 290 matched cddid_all.tbl CDD cd15317 cd15317 320440 7tmA_TAAR5-like trace amine-associated receptor 5 and similar receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Included in this group are mammalian TAAR5, TAAR6, TAAR8, TAAR9, and similar proteins. They are among the 15 identified trace amine-associated receptors (TAARs), a distinct subfamily within the class A G protein-coupled receptors. Trace amines are endogenous amines of unknown function that have strong structural and metabolic similarity to classical monoamine neurotransmitters (serotonin, noradrenaline, adrenaline, dopamine, and histamine), which play critical roles in human and animal physiological activities such as cognition, consciousness, mood, motivation, perception, and autonomic responses. However, trace amines are found in the mammalian brain at very low concentrations compared to classical monoamines. Trace amines, including p-tyramine, beta-phenylethylamine, and tryptamine, are also thought to act as chemical messengers to exert their biological effects in vertebrates. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 290 matched cddid_all.tbl CDD cd15318 cd15318 320441 7tmA_TAAR5 trace amine-associated receptor 5, member of the class A family of seven-transmembrane G protein-coupled receptors. The trace amine-associated receptor 5 is one of the 15 identified amine-activated G protein-coupled receptors (TAARs), a distinct subfamily within the class A G protein-coupled receptors. Trace amines are endogenous amines of unknown function that have strong structural and metabolic similarity to classical monoamine neurotransmitters (serotonin, noradrenaline, adrenaline, dopamine, and histamine), which play critical roles in human and animal physiological activities such as cognition, consciousness, mood, motivation, perception, and autonomic responses. However, trace amines are found in the mammalian brain at very low concentrations compared to classical monoamines. Trace amines, including p-tyramine, beta-phenylethylamine, and tryptamine, are also thought to act as chemical messengers to exert their biological effects in vertebrates. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 282 matched cddid_all.tbl CDD cd15319 cd15319 320442 7tmA_D1B_dopamine_R D1B (or D5) subtype dopamine receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. Dopamine receptors are members of the class A G protein-coupled receptors that are involved in many neurological processes in the central nervous system (CNS). The neurotransmitter dopamine is the primary endogenous agonist for dopamine receptors. Dopamine receptors consist of at least five subtypes: D1, D2, D3, D4, and D5. The D1 and D5 subtypes are members of the D1-like family of dopamine receptors, whereas the D2, D3 and D4 subtypes are members of the D2-like family. The D1-like family receptors are coupled to G proteins of the G(s) family, which activate adenylate cyclase, causing cAMP formation and activation of protein kinase A. Dopamine receptors are major therapeutic targets for neurological and psychiatric disorders such as drug abuse, depression, schizophrenia, or Parkinson's disease. 317 matched cddid_all.tbl CDD cd15320 cd15320 320443 7tmA_D1A_dopamine_R D1A (or D1) subtype dopamine receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. Dopamine receptors are members of the class A G protein-coupled receptors that are involved in many neurological processes in the central nervous system (CNS). The neurotransmitter dopamine is the primary endogenous agonist for dopamine receptors. Dopamine receptors consist of at least five subtypes: D1, D2, D3, D4, and D5. The D1 and D5 subtypes are members of the D1-like family of dopamine receptors, whereas the D2, D3 and D4 subtypes are members of the D2-like family. The D1-like family receptors are coupled to G proteins of the G(s) family, which activate adenylate cyclase, causing cAMP formation and activation of protein kinase A. Dopamine receptors are major therapeutic targets for neurological and psychiatric disorders such as drug abuse, depression, schizophrenia, or Parkinson's disease. 319 matched cddid_all.tbl CDD cd15321 cd15321 320444 7tmA_alpha2B_AR alpha-2 adrenergic receptors subtype B, member of the class A family of seven-transmembrane G protein-coupled receptors. The alpha-2 adrenergic receptors (or adrenoceptors) are a subfamily of the class A rhodopsin-like GPCRs that share a common architecture of seven transmembrane helices. This subfamily consists of three highly homologous receptor subtypes that have a key role in neurotransmitter release: alpha-2A, alpha-2B, and alpha-2C. In addition, a fourth subtype, alpha-2D is present in ray-finned fishes and amphibians, but is not found in humans. The alpha-2 receptors are found in both central and peripheral nervous system and serve to produce inhibitory functions through the G(i) proteins. Thus, the alpha-2 receptors inhibit adenylate cyclase, which decreases cAMP production and thereby decreases calcium influx during the action potential. Consequently, lowered levels of calcium will lead to a decrease in neurotransmitter release by negative feedback. 268 matched cddid_all.tbl CDD cd15322 cd15322 320445 7tmA_alpha2A_AR alpha-2 adrenergic receptors subtype A, member of the class A family of seven-transmembrane G protein-coupled receptors. The alpha-2 adrenergic receptors (or adrenoceptors) are a subfamily of the class A rhodopsin-like GPCRs that share a common architecture of seven transmembrane helices. This subfamily consists of three highly homologous receptor subtypes that have a key role in neurotransmitter release: alpha-2A, alpha-2B, and alpha-2C. In addition, a fourth subtype, alpha-2D is present in ray-finned fishes and amphibians, but is not found in humans. The alpha-2 receptors are found in both central and peripheral nervous system and serve to produce inhibitory functions through the G(i) proteins. Thus, the alpha-2 receptors inhibit adenylate cyclase, which decreases cAMP production and thereby decreases calcium influx during the action potential. Consequently, lowered levels of calcium will lead to a decrease in neurotransmitter release by negative feedback. 259 matched cddid_all.tbl CDD cd15323 cd15323 320446 7tmA_alpha2C_AR alpha-2 adrenergic receptors subtype C, member of the class A family of seven-transmembrane G protein-coupled receptors. The alpha-2 adrenergic receptors (or adrenoceptors) are a subfamily of the class A rhodopsin-like GPCRs that share a common architecture of seven transmembrane helices. This subfamily consists of three highly homologous receptor subtypes that have a key role in neurotransmitter release: alpha-2A, alpha-2B, and alpha-2C. In addition, a fourth subtype, alpha-2D is present in ray-finned fishes and amphibians, but is not found in humans. The alpha-2 receptors are found in both central and peripheral nervous system and serve to produce inhibitory functions through the G(i) proteins. Thus, the alpha-2 receptors inhibit adenylate cyclase, which decreases cAMP production and thereby decreases calcium influx during the action potential. Consequently, lowered levels of calcium will lead to a decrease in neurotransmitter release by negative feedback. 261 matched cddid_all.tbl CDD cd15324 cd15324 320447 7tmA_alpha-2D_AR alpha-2 adrenergic receptors subtype D, member of the class A family of seven-transmembrane G protein-coupled receptors. The alpha-2 adrenergic receptors (or adrenoceptors) are a subfamily of the class A rhodopsin-like GPCRs that share a common architecture of seven transmembrane helices. This subfamily consists of three highly homologous receptor subtypes that have a key role in neurotransmitter release: alpha-2A, alpha-2B, and alpha-2C. In addition, a fourth subtype, alpha-2D is present in ray-finned fishes and amphibians, but is not found in humans. The alpha-2 receptors are found in both central and peripheral nervous system and serve to produce inhibitory functions through the G(i) proteins. Thus, the alpha-2 receptors inhibit adenylate cyclase, which decreases cAMP production and thereby decreases calcium influx during the action potential. Consequently, lowered levels of calcium will lead to a decrease in neurotransmitter release by negative feedback. 256 matched cddid_all.tbl CDD cd15325 cd15325 320448 7tmA_alpha1A_AR alpha-1 adrenergic receptors subtype A, member of the class A family of seven-transmembrane G protein-coupled receptors. The alpha-1 adrenergic receptors (or adrenoceptors) are a subfamily of the class A rhodopsin-like GPCRs that share a common architecture of seven transmembrane helices. This subfamily consists of three highly homologous receptor subtypes that primarily mediate smooth muscle contraction: alpha-1A, alpha-1B, and alpha-1D. Activation of alpha-1 receptors by catecholamines such as norepinephrine and epinephrine couples to the G(q) protein, which then activates the phospholipase C pathway, leading to an increase in IP3 and calcium. Consequently, the elevation of intracellular calcium concentration leads to vasoconstriction in smooth muscle of blood vessels. In addition, activation of alpha-1 receptors by phenylpropanolamine (PPA) produces anorexia and may induce appetite suppression in rats. 261 matched cddid_all.tbl CDD cd15326 cd15326 320449 7tmA_alpha1B_AR alpha-1 adrenergic receptors subtype B, member of the class A family of seven-transmembrane G protein-coupled receptors. The alpha-1 adrenergic receptors (or adrenoceptors) are a subfamily of the class A rhodopsin-like GPCRs that share a common architecture of seven transmembrane helices. This subfamily consists of three highly homologous receptor subtypes that primarily mediate smooth muscle contraction: alpha-1A, alpha-1B, and alpha-1D. Activation of alpha-1 receptors by catecholamines such as norepinephrine and epinephrine couples to the G(q) protein, which then activates the phospholipase C pathway, leading to an increase in IP3 and calcium. Consequently, the elevation of intracellular calcium concentration leads to vasoconstriction in smooth muscle of blood vessels. In addition, activation of alpha-1 receptors by phenylpropanolamine (PPA) produces anorexia and may induce appetite suppression in rats. 261 matched cddid_all.tbl CDD cd15327 cd15327 320450 7tmA_alpha1D_AR alpha-1 adrenergic receptors subtype D, member of the class A family of seven-transmembrane G protein-coupled receptors. The alpha-1 adrenergic receptors (or adrenoceptors) are a subfamily of the class A rhodopsin-like GPCRs that share a common architecture of seven transmembrane helices. This subfamily consists of three highly homologous receptor subtypes that primarily mediate smooth muscle contraction: alpha-1A, alpha-1B, and alpha-1D. Activation of alpha-1 receptors by catecholamines such as norepinephrine and epinephrine couples to the G(q) protein, which then activates the phospholipase C pathway, leading to an increase in IP3 and calcium. Consequently, the elevation of intracellular calcium concentration leads to vasoconstriction in smooth muscle of blood vessels. In addition, activation of alpha-1 receptors by phenylpropanolamine (PPA) produces anorexia and may induce appetite suppression in rats. 261 matched cddid_all.tbl CDD cd15328 cd15328 320451 7tmA_5-HT5 serotonin receptor subtype 5, member of the class A family of seven-transmembrane G protein-coupled receptors. 5-HT5 receptor, one of 14 mammalian 5-HT receptors, is activated by the neurotransmitter and peripheral signal mediator serotonin (also known as 5-hydroxytryptamine or 5-HT). The 5-HT5A and 5-HT5B receptors have been cloned from rat and mouse, but only the 5-HT5A isoform has been identified in human because of the presence of premature stop codons in the human 5-HT5B gene, which prevents a functional receptor from being expressed. 5-HT5 receptors mediate inhibitory neurotransmission by coupling to G proteins of the G(i/0) family, which lead to a decrease in adenylate cyclase activity, thereby decreasing intracellular cAMP levels and calcium influx. In the CNS, serotonin is involved in the regulation of appetite, mood, sleep, cognition, learning and memory, as well as implicated in neurologic disorders such as migraine, schizophrenia, and depression. 259 matched cddid_all.tbl CDD cd15329 cd15329 320452 7tmA_5-HT7 serotonin receptor subtype 7, member of the class A family of seven-transmembrane G protein-coupled receptors. The 5-HT7 receptor, one of 14 mammalian serotonin receptors, is a member of the class A of GPCRs and is activated by the neurotransmitter serotonin (5-hydroxytryptamine, 5-HT). 5-HT7 receptor mainly couples to Gs protein, which positively stimulates adenylate cyclase, leading to increased intracellular cAMP formation and calcium influx. 5-HT7 receptor is expressed in various human tissues, mainly in the brain, the lower gastrointestinal tract and in vital blood vessels including the coronary artery. In the CNS, serotonin is involved in the regulation of appetite, mood, sleep, cognition, learning and memory, as well as implicated in neurologic disorders such as migraine, schizophrenia, and depression. 260 matched cddid_all.tbl CDD cd15330 cd15330 320453 7tmA_5-HT1A_vertebrates serotonin receptor subtype 1A from vertebrates, member of the class A family of seven-transmembrane G protein-coupled receptors. The 5-HT1 receptors, one of 14 mammalian 5-HT receptors, is a member of the class A of GPCRs and is activated by the endogenous neurotransmitter and peripheral signal mediator serotonin (5-hydroxytryptamine, 5-HT). The 5-HT1 receptors mediate inhibitory neurotransmission by coupling to G proteins of the G(i/o) family, which lead to a decrease in adenylate cyclase activity, thereby decreasing intracellular cAMP levels and calcium influx. The 5-HT1 receptor subfamily includes 5 subtypes: 5-HT1A, 5-HT1B, 5-HT1D, 5-HT1E, and 5-HT1F. There is no 5-HT1C receptor subtype, as it has been reclassified as the 5-HT2C receptor. In the CNS, serotonin is involved in the regulation of appetite, mood, sleep, cognition, learning and memory, as well as implicated in neurologic disorders such as migraine, schizophrenia, and depression. 260 matched cddid_all.tbl CDD cd15331 cd15331 320454 7tmA_5-HT1A_invertebrates serotonin receptor subtype 1A from invertebrates, member of the class A family of seven-transmembrane G protein-coupled receptors. The 5-HT1 receptors, one of 14 mammalian 5-HT receptors, is a member of the class A of GPCRs and is activated by the endogenous neurotransmitter and peripheral signal mediator serotonin (5-hydroxytryptamine, 5-HT). The 5-HT1 receptors mediate inhibitory neurotransmission by coupling to G proteins of the G(i/o) family, which lead to a decrease in adenylate cyclase activity, thereby decreasing intracellular cAMP levels and calcium influx. The 5-HT1 receptor subfamily includes 5 subtypes: 5-HT1A, 5-HT1B, 5-HT1D, 5-HT1E, and 5-HT1F. There is no 5-HT1C receptor subtype, as it has been reclassified as the 5-HT2C receptor. In the CNS, serotonin is involved in the regulation of appetite, mood, sleep, cognition, learning and memory, as well as implicated in neurologic disorders such as migraine, schizophrenia, and depression. 261 matched cddid_all.tbl CDD cd15333 cd15333 320455 7tmA_5-HT1B_1D serotonin receptor subtypes 1B and 1D, member of the class A family of seven-transmembrane G protein-coupled receptors. The 5-HT1 receptors, one of 14 mammalian 5-HT receptors, is a member of the class A of GPCRs and is activated by the endogenous neurotransmitter and peripheral signal mediator serotonin (5-hydroxytryptamine, 5-HT). The 5-HT1 receptors mediate inhibitory neurotransmission by coupling to G proteins of the G(i/o) family, which lead to a decrease in adenylate cyclase activity, thereby decreasing intracellular cAMP levels and calcium influx. The 5-HT1 receptor subfamily includes 5 subtypes: 5-HT1A, 5-HT1B, 5-HT1D, 5-HT1E, and 5-HT1F. There is no 5-HT1C receptor subtype, as it has been reclassified as the 5-HT2C receptor. In the CNS, serotonin is involved in the regulation of appetite, mood, sleep, cognition, learning and memory, as well as implicated in neurologic disorders such as migraine, schizophrenia, and depression. 265 matched cddid_all.tbl CDD cd15334 cd15334 320456 7tmA_5-HT1F serotonin receptor subtype 1F, member of the class A family of seven-transmembrane G protein-coupled receptors. The 5-HT1 receptors, one of 14 mammalian 5-HT receptors, is a member of the class A of GPCRs and is activated by the endogenous neurotransmitter and peripheral signal mediator serotonin (5-hydroxytryptamine, 5-HT). The 5-HT1 receptors mediate inhibitory neurotransmission by coupling to G proteins of the G(i/o) family, which lead to a decrease in adenylate cyclase activity, thereby decreasing intracellular cAMP levels and calcium influx. The 5-HT1 receptor subfamily includes 5 subtypes: 5-HT1A, 5-HT1B, 5-HT1D, 5-HT1E, and 5-HT1F. There is no 5-HT1C receptor subtype, as it has been reclassified as the 5-HT2C receptor. In the CNS, serotonin is involved in the regulation of appetite, mood, sleep, cognition, learning and memory, as well as implicated in neurologic disorders such as migraine, schizophrenia, and depression. 259 matched cddid_all.tbl CDD cd15335 cd15335 320457 7tmA_5-HT1E serotonin receptor subtype 1E, member of the class A family of seven-transmembrane G protein-coupled receptors. The 5-HT1 receptors, one of 14 mammalian 5-HT receptors, is a member of the class A of GPCRs and is activated by the endogenous neurotransmitter and peripheral signal mediator serotonin (5-hydroxytryptamine, 5-HT). The 5-HT1 receptors mediate inhibitory neurotransmission by coupling to G proteins of the G(i/o) family, which lead to a decrease in adenylate cyclase activity, thereby decreasing intracellular cAMP levels and calcium influx. The 5-HT1 receptor subfamily includes 5 subtypes: 5-HT1A, 5-HT1B, 5-HT1D, 5-HT1E, and 5-HT1F. There is no 5-HT1C receptor subtype, as it has been reclassified as the 5-HT2C receptor. In the CNS, serotonin is involved in the regulation of appetite, mood, sleep, cognition, learning and memory, as well as implicated in neurologic disorders such as migraine, schizophrenia, and depression. 258 matched cddid_all.tbl CDD cd15336 cd15336 320458 7tmA_Melanopsin vertebrate melanopsins (Opsin-4), member of the class A family of seven-transmembrane G protein-coupled receptors. Melanopsin (also called Opsin-4) is the G protein-coupled photopigment that mediates non-visual responses to light. In mammals, these photoresponses include the photo-entrainment of circadian rhythm, pupillary constriction, and acute nocturnal melatonin suppression. Mammalian melanopsins are expressed only in the inner retina, whereas non-mammalian vertebrate melanopsins are localized in various extra-retinal tissues such as iris, brain, pineal gland, and skin. Melanopsins belong the class A of the G protein-coupled receptors and possess seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. 290 matched cddid_all.tbl CDD cd15337 cd15337 320459 7tmA_Opsin_Gq_invertebrates invertebrate Gq opsins, member of the class A family of seven-transmembrane G protein-coupled receptors. The invertebrate Gq-coupled opsin subfamily includes the arthropod and mollusc visual opsins. Like the vertebrate visual opsins, arthropods possess color vision by the use of multiple opsins sensitive to different light wavelengths. The invertebrate Gq opsins are closely related to the vertebrate melanopsins, the primary photoreceptor molecules for non-visual responses to light, and the R1-R6 photoreceptors, which are the fly equivalent to the vertebrate rods. The Gq opsins belong the class A of the G protein-coupled receptors and possess seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. 292 matched cddid_all.tbl CDD cd15338 cd15338 320460 7tmA_MCHR1 melanin concentrating hormone receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors. Melanin-concentrating hormone receptor (MCHR) binds melanin concentrating hormone and is presumably involved in the neuronal regulation of food intake and energy homeostasis. Despite strong homology with somatostatin receptors, MCHR does not appear to bind somatostatin. Two MCHRs have been characterized in vertebrates, MCHR1 and MCHR2. MCHR1 is expressed in all mammals, whereas MCHR2 is only expressed in the higher order mammals, such as humans, primates, and dogs, and is not found in rodents. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 282 matched cddid_all.tbl CDD cd15339 cd15339 320461 7tmA_MCHR2 melanin concentrating hormone receptor 2, member of the class A family of seven-transmembrane G protein-coupled receptors. Melanin-concentrating hormone receptor (MCHR) binds melanin concentrating hormone and is presumably involved in the neuronal regulation of food intake and energy homeostasis. Despite strong homology with somatostatin receptors, MCHR does not appear to bind somatostatin. Two MCHRs have been characterized in vertebrates, MCHR1 and MCHR2. MCHR1 is expressed in all mammals, whereas MCHR2 is only expressed in the higher order mammals, such as humans, primates, and dogs, and is not found in rodents. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 283 matched cddid_all.tbl CDD cd15340 cd15340 320462 7tmA_CB1 cannabinoid receptor subtype 1, member of the class A family of seven-transmembrane G protein-coupled receptors. Cannabinoid receptors belong to the class A G-protein coupled receptor superfamily. Two types of cannabinoid receptors, CB1 and CB2, have been identified so far. They are activated by naturally occurring endocannabinoids, cannabis plant-derived cannabinoids such as tetrahydrocannabinol, or synthetic cannabinoids. The CB receptors are involved in the various physiological processes such as appetite, mood, memory, and pain sensation. CB1 receptor is expressed predominantly in central and peripheral neurons, while CB2 receptor is found mainly in the immune system. 292 matched cddid_all.tbl CDD cd15341 cd15341 320463 7tmA_CB2 cannabinoid receptor subtype 2, member of the class A family of seven-transmembrane G protein-coupled receptors. Cannabinoid receptors belong to the class A G-protein coupled receptor superfamily. Two types of cannabinoid receptors, CB1 and CB2, have been identified so far. They are activated by naturally occurring endocannabinoids, cannabis plant-derived cannabinoids such as tetrahydrocannabinol, or synthetic cannabinoids. The CB receptors are involved in the various physiological processes such as appetite, mood, memory, and pain sensation. CB1 receptor is expressed predominantly in central and peripheral neurons, while CB2 receptor is found mainly in the immune system. 279 matched cddid_all.tbl CDD cd15342 cd15342 320464 7tmA_LPAR2_Edg4 lysophosphatidic acid receptor subtype 2 (LPAR2 or LPA2), also called Endothelial differentiation gene 4 (Edg4), member of the class A family of seven-transmembrane G protein-coupled receptors. The endothelial differentiation gene (Edg) family of G-protein coupled receptors binds blood borne lysophospholipids including sphingosine-1-phosphate (S1P) and lysophosphatidic acid (LPA), which are involved in the regulation of cell proliferation, survival, migration, invasion, endothelial cell shape change and cytoskeletal remodeling. The Edg receptors are classified into two subfamilies: the lysophosphatidic acid subfamily that includes LPA1 (Edg2), LPA2 (Edg4), and LPA3 (Edg7); and the S1P subfamily that includes S1P1 (Edg1), S1P2 (Edg5), S1P3 (Edg3), S1P4 (Edg6), and S1P5 (Edg8). The Edg receptors couple and activate at least three different G protein subtypes including G(i/o), G(q/11), and G(12/13). 274 matched cddid_all.tbl CDD cd15343 cd15343 320465 7tmA_LPAR3_Edg7 lysophosphatidic acid receptor subtype 3 (LPAR3 or LPA3), also called endothelial differentiation gene 7 (Edg7), member of the class A family of seven-transmembrane G protein-coupled receptors. The endothelial differentiation gene (Edg) family of G-protein coupled receptors binds blood borne lysophospholipids including sphingosine-1-phosphate (S1P) and lysophosphatidic acid (LPA), which are involved in the regulation of cell proliferation, survival, migration, invasion, endothelial cell shape change and cytoskeletal remodeling. The Edg receptors are classified into two subfamilies: the lysophosphatidic acid subfamily that includes LPA1 (Edg2), LPA2 (Edg4), and LPA3 (Edg7); and the S1P subfamily that includes S1P1 (Edg1), S1P2 (Edg5), S1P3 (Edg3), S1P4 (Edg6), and S1P5 (Edg8). The Edg receptors couple and activate at least three different G protein subtypes including G(i/o), G(q/11), and G(12/13). 274 matched cddid_all.tbl CDD cd15344 cd15344 341348 7tmA_LPAR1_Edg2 lysophosphatidic acid receptor subtype 1 (LPAR1 or LPA1), also called endothelial differentiation gene 2 (Edg2), member of the class A family of seven-transmembrane G protein-coupled receptors. The endothelial differentiation gene (Edg) family of G-protein coupled receptors binds blood borne lysophospholipids including sphingosine-1-phosphate (S1P) and lysophosphatidic acid (LPA), which are involved in the regulation of cell proliferation, survival, migration, invasion, endothelial cell shape change and cytoskeletal remodeling. The Edg receptors are classified into two subfamilies: the lysophosphatidic acid subfamily that includes LPA1 (Edg2), LPA2 (Edg4), and LPA3 (Edg7); and the S1P subfamily that includes S1P1 (Edg1), S1P2 (Edg5), S1P3 (Edg3), S1P4 (Edg6), and S1P5 (Edg8). The Edg receptors couple and activate at least three different G protein subtypes including G(i/o), G(q/11), and G(12/13). 273 matched cddid_all.tbl CDD cd15345 cd15345 320467 7tmA_S1PR3_Edg3 sphingosine-1-phosphate receptor subtype 3 (S1PR3 or S1P3), also called endothelial differentiation gene 3 (Edg3), member of the class A family of seven-transmembrane G protein-coupled receptors. The endothelial differentiation gene (Edg) family of G-protein coupled receptors binds blood borne lysophospholipids including sphingosine-1-phosphate (S1P) and lysophosphatidic acid (LPA), which are involved in the regulation of cell proliferation, survival, migration, invasion, endothelial cell shape change and cytoskeletal remodeling. The Edg receptors are classified into two subfamilies: the lysophosphatidic acid subfamily that includes LPA1 (Edg2), LPA2 (Edg4), and LPA3 (Edg7); and the S1P subfamily that includes S1P1 (Edg1), S1P2 (Edg5), S1P3 (Edg3), S1P4 (Edg6), and S1P5 (Edg8). The Edg receptors couple and activate at least three different G protein subtypes including G(i/o), G(q/11), and G(12/13). 270 matched cddid_all.tbl CDD cd15346 cd15346 320468 7tmA_S1PR1_Edg1 sphingosine-1-phosphate receptor subtype 1 (S1PR1 or S1P1), also called endothelial differentiation gene 1 (Edg1), member of the class A family of seven-transmembrane G protein-coupled receptors. The endothelial differentiation gene (Edg) family of G-protein coupled receptors binds blood borne lysophospholipids including sphingosine-1-phosphate (S1P) and lysophosphatidic acid (LPA), which are involved in the regulation of cell proliferation, survival, migration, invasion, endothelial cell shape change and cytoskeletal remodeling. The Edg receptors are classified into two subfamilies: the lysophosphatidic acid subfamily that includes LPA1 (Edg2), LPA2 (Edg4), and LPA3 (Edg7); and the S1P subfamily that includes S1P1 (Edg1), S1P2 (Edg5), S1P3 (Edg3), S1P4 (Edg6), and S1P5 (Edg8). The Edg receptors couple and activate at least three different G protein subtypes including G(i/o), G(q/11), and G(12/13). 277 matched cddid_all.tbl CDD cd15347 cd15347 320469 7tmA_S1PR2_Edg5 sphingosine-1-phosphate receptor subtype 2 (S1PR2 or S1P2), also called endothelial differentiation gene 5 (Edg5), member of the class A family of seven-transmembrane G protein-coupled receptors. The endothelial differentiation gene (Edg) family of G-protein coupled receptors binds blood borne lysophospholipids including sphingosine-1-phosphate (S1P) and lysophosphatidic acid (LPA), which are involved in the regulation of cell proliferation, survival, migration, invasion, endothelial cell shape change and cytoskeletal remodeling. The Edg receptors are classified into two subfamilies: the lysophosphatidic acid subfamily that includes LPA1 (Edg2), LPA2 (Edg4), and LPA3 (Edg7); and the S1P subfamily that includes S1P1 (Edg1), S1P2 (Edg5), S1P3 (Edg3), S1P4 (Edg6), and S1P5 (Edg8). The Edg receptors couple and activate at least three different G protein subtypes including G(i/o), G(q/11), and G(12/13). 266 matched cddid_all.tbl CDD cd15348 cd15348 320470 7tmA_S1PR5_Edg8 sphingosine-1-phosphate receptor subtype 5 (S1PR5 or S1P5), also called endothelial differentiation gene 8 (Edg8), member of the class A family of seven-transmembrane G protein-coupled receptors. The endothelial differentiation gene (Edg) family of G-protein coupled receptors binds blood borne lysophospholipids including sphingosine-1-phosphate (S1P) and lysophosphatidic acid (LPA), which are involved in the regulation of cell proliferation, survival, migration, invasion, endothelial cell shape change and cytoskeletal remodeling. The Edg receptors are classified into two subfamilies: the lysophosphatidic acid subfamily that includes LPA1 (Edg2), LPA2 (Edg4), and LPA3 (Edg7); and the S1P subfamily that includes S1P1 (Edg1), S1P2 (Edg5), S1P3 (Edg3), S1P4 (Edg6), and S1P5 (Edg8). The Edg receptors couple and activate at least three different G protein subtypes including G(i/o), G(q/11), and G(12/13). 277 matched cddid_all.tbl CDD cd15349 cd15349 320471 7tmA_S1PR4_Edg6 sphingosine-1-phosphate receptor subtype 4 (S1PR4 or S1P4), also called endothelial differentiation gene 6 (Edg6), member of the class A family of seven-transmembrane G protein-coupled receptors. The endothelial differentiation gene (Edg) family of G-protein coupled receptors binds blood borne lysophospholipids including sphingosine-1-phosphate (S1P) and lysophosphatidic acid (LPA), which are involved in the regulation of cell proliferation, survival, migration, invasion, endothelial cell shape change and cytoskeletal remodeling. The Edg receptors are classified into two subfamilies: the lysophosphatidic acid subfamily that includes LPA1 (Edg2), LPA2 (Edg4), and LPA3 (Edg7); and the S1P subfamily that includes S1P1 (Edg1), S1P2 (Edg5), S1P3 (Edg3), S1P4 (Edg6), and S1P5 (Edg8). The Edg receptors couple and activate at least three different G protein subtypes including G(i/o), G(q/11), and G(12/13). 271 matched cddid_all.tbl CDD cd15350 cd15350 320472 7tmA_MC2R_ACTH_R melanocortin receptor subtype 2, also called adrenocorticotropic hormone receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. The melanocortin receptor (MCR) subfamily is a member of the class A family of seven-transmembrane G-protein coupled receptors. MCRs bind a group of pituitary peptide hormones known as melanocortins, which include adrenocorticotropic hormone (ACTH) and the different isoforms of melanocyte-stimulating hormones. There are five known subtypes of the MCR subfamily. MC1R is involved in regulating skin pigmentation and hair color. ACTH (adrenocorticotropic hormone) is the only endogenous ligand for MC2R, which shows low sequence similarity with other melanocortin receptors. Mutations in MC2R cause familial glucocorticoid deficiency type 1, in which patients have elevated plasma ACTH and low cortisol levels. MC3R is expressed in many parts of the brain and peripheral tissues and involved in the regulation of energy homeostasis. MC4R is expressed primarily in the central nervous system and involved in both eating behavior and sexual function. MC5R is widely expressed in peripheral tissues and is mainly involved in the regulation of exocrine gland function. 270 matched cddid_all.tbl CDD cd15351 cd15351 320473 7tmA_MC1R melanocortin receptor subtype 1, member of the class A family of seven-transmembrane G protein-coupled receptors. The melanocortin receptor (MCR) subfamily is a member of the class A family of seven-transmembrane G-protein coupled receptors. MCRs bind a group of pituitary peptide hormones known as melanocortins, which include adrenocorticotropic hormone (ACTH) and the different isoforms of melanocyte-stimulating hormones. There are five known subtypes of the MCR subfamily. MC1R is involved in regulating skin pigmentation and hair color. ACTH (adrenocorticotropic hormone) is the only endogenous ligand for MC2R, which shows low sequence similarity with other melanocortin receptors. Mutations in MC2R cause familial glucocorticoid deficiency type 1, in which patients have elevated plasma ACTH and low cortisol levels. MC3R is expressed in many parts of the brain and peripheral tissues and involved in the regulation of energy homeostasis. MC4R is expressed primarily in the central nervous system and involved in both eating behavior and sexual function. MC5R is widely expressed in peripheral tissues and is mainly involved in the regulation of exocrine gland function. 271 matched cddid_all.tbl CDD cd15352 cd15352 320474 7tmA_MC3R melanocortin receptor subtype 3, member of the class A family of seven-transmembrane G protein-coupled receptors. The melanocortin receptor (MCR) subfamily is a member of the class A family of seven-transmembrane G-protein coupled receptors. MCRs bind a group of pituitary peptide hormones known as melanocortins, which include adrenocorticotropic hormone (ACTH) and the different isoforms of melanocyte-stimulating hormones. There are five known subtypes of the MCR subfamily. MC1R is involved in regulating skin pigmentation and hair color. ACTH (adrenocorticotropic hormone) is the only endogenous ligand for MC2R, which shows low sequence similarity with other melanocortin receptors. Mutations in MC2R cause familial glucocorticoid deficiency type 1, in which patients have elevated plasma ACTH and low cortisol levels. MC3R is expressed in many parts of the brain and peripheral tissues and involved in the regulation of energy homeostasis. MC4R is expressed primarily in the central nervous system and involved in both eating behavior and sexual function. MC5R is widely expressed in peripheral tissues and is mainly involved in the regulation of exocrine gland function. 272 matched cddid_all.tbl CDD cd15353 cd15353 320475 7tmA_MC4R melanocortin receptor subtype 4, member of the class A family of seven-transmembrane G protein-coupled receptors. The melanocortin receptor (MCR) subfamily is a member of the class A family of seven-transmembrane G-protein coupled receptors. MCRs bind a group of pituitary peptide hormones known as melanocortins, which include adrenocorticotropic hormone (ACTH) and the different isoforms of melanocyte-stimulating hormones. There are five known subtypes of the MCR subfamily. MC1R is involved in regulating skin pigmentation and hair color. ACTH (adrenocorticotropic hormone) is the only endogenous ligand for MC2R, which shows low sequence similarity with other melanocortin receptors. Mutations in MC2R cause familial glucocorticoid deficiency type 1, in which patients have elevated plasma ACTH and low cortisol levels. MC3R is expressed in many parts of the brain and peripheral tissues and involved in the regulation of energy homeostasis. MC4R is expressed primarily in the central nervous system and involved in both eating behavior and sexual function. MC5R is widely expressed in peripheral tissues and is mainly involved in the regulation of exocrine gland function. 269 matched cddid_all.tbl CDD cd15354 cd15354 320476 7tmA_MC5R melanocortin receptor subtype 5, member of the class A family of seven-transmembrane G protein-coupled receptors. The melanocortin receptor (MCR) subfamily is a member of the class A family of seven-transmembrane G-protein coupled receptors. MCRs bind a group of pituitary peptide hormones known as melanocortins, which include adrenocorticotropic hormone (ACTH) and the different isoforms of melanocyte-stimulating hormones. There are five known subtypes of the MCR subfamily. MC1R is involved in regulating skin pigmentation and hair color. ACTH (adrenocorticotropic hormone) is the only endogenous ligand for MC2R, which shows low sequence similarity with other melanocortin receptors. Mutations in MC2R cause familial glucocorticoid deficiency type 1, in which patients have elevated plasma ACTH and low cortisol levels. MC3R is expressed in many parts of the brain and peripheral tissues and involved in the regulation of energy homeostasis. MC4R is expressed primarily in the central nervous system and involved in both eating behavior and sexual function. MC5R is widely expressed in peripheral tissues and is mainly involved in the regulation of exocrine gland function. 270 matched cddid_all.tbl CDD cd15355 cd15355 320477 7tmA_NTSR1 neurotensin receptor subtype 1, member of the class A family of seven-transmembrane G protein-coupled receptors. Neurotensin (NTS) is a 13 amino-acid neuropeptide that functions as both a neurotransmitter and a hormone in the nervous system and peripheral tissues, respectively. NTS exerts various biological activities through activation of the G protein-coupled neurotensin receptors, NTSR1 and NTSR2. In the brain, NTS is involved in the modulation of dopamine neurotransmission, opioid-independent analgesia, hypothermia, and the inhibition of food intake, while in the periphery NTS promotes the growth of various normal and cancer cells and acts as a paracrine and endocrine modulator of the digestive tract. The third neurotensin receptor, NTSR3 or also called sortilin, is not a G protein-coupled receptor. 310 matched cddid_all.tbl CDD cd15356 cd15356 320478 7tmA_NTSR2 neurotensin receptor subtype 2, member of the class A family of seven-transmembrane G protein-coupled receptors. Neurotensin (NTS) is a 13 amino-acid neuropeptide that functions as both a neurotransmitter and a hormone in the nervous system and peripheral tissues, respectively. NTS exerts various biological activities through activation of the G protein-coupled neurotensin receptors, NTSR1 and NTSR2. In the brain, NTS is involved in the modulation of dopamine neurotransmission, opioid-independent analgesia, hypothermia, and the inhibition of food intake, while in the periphery NTS promotes the growth of various normal and cancer cells and acts as a paracrine and endocrine modulator of the digestive tract. The third neurotensin receptor, NTSR3 or also called sortilin, is not a G protein-coupled receptor. 285 matched cddid_all.tbl CDD cd15357 cd15357 320479 7tmA_NMU-R2 neuromedin U receptor subtype 2, member of the class A family of seven-transmembrane G protein-coupled receptors. Neuromedin U (NMU) is a highly conserved neuropeptide with a common C-terminal heptapeptide sequence (FLFRPRN-amide) found at the highest levels in the gastrointestinal tract and pituitary gland of mammals. Disruption or replacement of residues in the conserved heptapeptide region can result in the reduced ability of NMU to stimulate smooth-muscle contraction. Two G-protein coupled receptor subtypes, NMU-R1 and NMU-R2, with a distinct expression pattern, have been identified to bind NMU. NMU-R1 is expressed primarily in the peripheral nervous system, while NMU-R2 is mainly found in the central nervous system. Neuromedin S, a 36 amino-acid neuropeptide that shares a conserved C-terminal heptapeptide sequence with NMU, is a highly potent and selective NMU-R2 agonist. Pharmacological studies have shown that both NMU and NMS inhibit food intake and reduce body weight, and that NMU increases energy expenditure. 293 matched cddid_all.tbl CDD cd15358 cd15358 320480 7tmA_NMU-R1 neuromedin U receptor subtype 1, member of the class A family of seven-transmembrane G protein-coupled receptors. Neuromedin U (NMU) is a highly conserved neuropeptide with a common C-terminal heptapeptide sequence (FLFRPRN-amide) found at the highest levels in the gastrointestinal tract and pituitary gland of mammals. Disruption or replacement of residues in the conserved heptapeptide region can result in the reduced ability of NMU to stimulate smooth-muscle contraction. Two G-protein coupled receptor subtypes, NMU-R1 and NMU-R2, with a distinct expression pattern, have been identified to bind NMU. NMU-R1 is expressed primarily in the peripheral nervous system, while NMU-R2 is mainly found in the central nervous system. Neuromedin S, a 36 amino-acid neuropeptide that shares a conserved C-terminal heptapeptide sequence with NMU, is a highly potent and selective NMU-R2 agonist. Pharmacological studies have shown that both NMU and NMS inhibit food intake and reduce body weight, and that NMU increases energy expenditure. 305 matched cddid_all.tbl CDD cd15359 cd15359 320481 7tmA_LHCGR luteinizing hormone-choriogonadotropin receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. The glycoprotein hormone receptors are seven transmembrane domain receptors with a very large extracellular N-terminal domain containing many leucine-rich repeats responsible for hormone recognition and binding. The glycoprotein hormone family includes the three gonadotropins: luteinizing hormone (LH), follicle-stimulating hormone (FSH), chorionic gonadotropin (CG), and a pituitary thyroid-stimulating hormone (TSH). The glycoprotein hormones exert their biological functions by interacting with their cognate GPCRs. Both LH and CG bind to the same receptor, the luteinizing hormone-choriogonadotropin receptor (LHCGR); FSH binds to FSH-R and TSH to TSH-R. LHCGR is expressed predominantly in the ovary and testis, and plays an essential role in sexual development and reproductive processes. LHCGR couples primarily to the G(s)-protein and activates adenylate cyclase, thereby promoting cAMP production. 275 matched cddid_all.tbl CDD cd15360 cd15360 320482 7tmA_FSH-R follicle-stimulating hormone receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. The glycoprotein hormone receptors are seven transmembrane domain receptors with a very large extracellular N-terminal domain containing many leucine-rich repeats responsible for hormone recognition and binding. The glycoprotein hormone family includes the three gonadotropins: luteinizing hormone (LH), follicle-stimulating hormone (FSH), chorionic gonadotropin (CG), and a pituitary thyroid-stimulating hormone (TSH). The glycoprotein hormones exert their biological functions by interacting with their cognate GPCRs. Both LH and CG bind to the same receptor, the luteinizing hormone-choriogonadotropin receptor (LHCGR); FSH binds to FSH-R and TSH to TSH-R. FSH-R functions in gonad development and is found in the ovary, testis, and uterus. Defects in this receptor cause ovarian dysgenesis type 1, and also ovarian hyperstimulation syndrome. The FSH-R activation couples to the G(s)-protein and stimulates adenylate cyclase, thereby promoting cAMP production. 275 matched cddid_all.tbl CDD cd15361 cd15361 320483 7tmA_LGR4 leucine-rich repeats-containing G protein-coupled receptor 4, member of the class A family of seven-transmembrane G protein-coupled receptors. The leucine-rich repeat containing G-protein coupled receptor Lgr4 (formerly known as Gpr48), together with its close family members LGR5 and LGR6, is structurally related to the glycoprotein hormone receptor family, which includes the luteinizing hormone (LH) receptor, the follicle-stimulating hormone (FSH) receptor, and the pituitary thyroid-stimulating hormone (TSH) receptor. LGR4-6 are receptors for the R-spondin (Rspo) family of secreted proteins containing two N-terminal furin-like repeats and a thrombospondin domain. The Rspo proteins are involved in regulating proliferation and differentiation of adult stem cells by potently enhancing the WNT-stimulated beta-catenin signaling. LGR4 is broadly expressed in proliferating cells, and its deficient mice display development defects in multiple organs. LGR5 acts as a marker for resident stem cell in numerous epithelial cell layers, including small intestine, colon, stomach, and kidney. LGR6 also serves as a marker of multipotent stem cells in the hair follicle that generate all skin cell lineages. Members of this group are characterized by a very large extracellular N-terminal domain containing 17 leucine-rich repeats (LRRs), flanked by cysteine-rich N- and C-terminal capping domains, and the extracellular domain is responsible for high-affinity binding with the Rspo proteins. 274 matched cddid_all.tbl CDD cd15362 cd15362 320484 7tmA_LGR6 leucine-rich repeats-containing G protein-coupled receptor 6, the class A of 7-transmembrane GPCRs. The leucine-rich repeat containing G-protein coupled receptor LGR5, together with its family members LGR4 and LGR6, is structurally related to the glycoprotein hormone receptor family, which includes the luteinizing hormone (LH) receptor, the follicle-stimulating hormone (FSH) receptor, and the pituitary thyroid-stimulating hormone (TSH) receptor. LGR4-6 are receptors for the R-spondin (Rspo) family of secreted proteins containing two N-terminal furin-like repeats and a thrombospondin domain. The Rspo proteins are involved in regulating proliferation and differentiation of adult stem cells by potently enhancing the WNT-stimulated beta-catenin signaling. LGR5 serves as a marker for resident stem cell in numerous epithelial cell layers, including small intestine, colon, stomach, and kidney. LGR6 is a marker for multipotent stem cells in the hair follicle that generate all skin cell lineages. In addition, LGR4 is broadly expressed in proliferating cells, and its deficient mice display development defects in multiple organs. Members of this group are characterized by a very large extracellular N-terminal domain containing 17 leucine-rich repeats (LRRs), flanked by cysteine-rich N- and C-terminal capping domains, and the extracellular domain is responsible for high-affinity binding with the Rspo proteins. 276 matched cddid_all.tbl CDD cd15363 cd15363 320485 7tmA_LGR5 leucine-rich repeats-containing G protein-coupled receptor 5, member of the class A family of seven-transmembrane G protein-coupled receptors. The leucine-rich repeat containing G-protein coupled receptor LGR6, together with its family members LGR4 and LGR5, is structurally related to the glycoprotein hormone receptor family, which includes the luteinizing hormone (LH) receptor, the follicle-stimulating hormone (FSH) receptor, and the pituitary thyroid-stimulating hormone (TSH) receptor. LGR4-6 are receptors for the R-spondin (Rspo) family of secreted proteins containing two N-terminal furin-like repeats and a thrombospondin domain. The Rspo proteins are involved in regulating proliferation and differentiation of adult stem cells by potently enhancing the WNT-stimulated beta-catenin signaling. LGR6 serves as a marker of multipotent stem cells in the hair follicle that generate all skin cell lineages, whereas LGR5 is a marker for resident stem cell in numerous epithelial cell layers, including small intestine, colon, stomach, and kidney. In addition, LGR4 is broadly expressed in proliferating cells, and its deficient mice display development defects in multiple organs. Members of this group are characterized by a very large extracellular N-terminal domain containing 17 leucine-rich repeats (LRRs), flanked by cysteine-rich N- and C-terminal capping domains, and the extracellular domain is responsible for high-affinity binding with the Rspo proteins. 274 matched cddid_all.tbl CDD cd15364 cd15364 320486 7tmA_GPR132_G2A proton-sensing G protein-coupled receptor 132, member of the class A family of seven-transmembrane G protein-coupled receptors. The G2 accumulation receptor (G2A, also known as GPR132) is a member of the proton-sensing G-protein-coupled receptor (GPCR) family which also includes the T cell death associated gene-8 (TDAG8, GPR65) receptor, ovarian cancer G-protein receptor 1 (OGR-1, GPR68), and G-protein-coupled receptor 4 (GPR4). Proton-sensing G-protein coupled receptors sense pH of 7.6 to 6.0 and mediates a variety of biological activities in neutral and mildly acidic pH conditions, whereas the acid-sensing ionotropic ion channels typically sense strong acidic pH. G2A was originally identified as a stress-inducible receptor that causes the cell cycle arrest at G2/M phase when serum is deprived. Lysophosphatidylcholine was identified as a ligand for G2A, and whose overexpression was shown to induce cell proliferation, oncogenic transformation, and apoptosis. 279 matched cddid_all.tbl CDD cd15365 cd15365 320487 7tmA_GPR65_TDAG8 proton-sensing G protein-coupled receptor 65, member of the class A family of seven-transmembrane G protein-coupled receptors. The T cell death associated gene-8 receptor (TDAG8, also known as GPR65) is a member of the proton-sensing G-protein-coupled receptor (GPCR) family which also includes the G2 accumulation receptor (G2A, also known as GPR132), ovarian cancer G-protein receptor 1 (OGR-1, GPR68), and G-protein-coupled receptor 4 (GPR4). Proton-sensing G-protein coupled receptors sense pH of 7.6 to 6.0 and mediates a variety of biological activities in neutral and mildly acidic pH conditions, whereas the acid-sensing ionotropic ion channels typically sense strong acidic pH. Activation of TDAG8 by extracellular acidosis increases the cAMP production, stimulates Rho, and induces stress fiber formation. TDAG8 has also been shown to regulate the extracellular acidosis-induced inhibition of pro-inflammatory cytokine production in peritoneal macrophages. 277 matched cddid_all.tbl CDD cd15366 cd15366 320488 7tmA_GPR4 proton-sensing G protein-coupled receptor 4, member of the class A family of seven-transmembrane G protein-coupled receptors. G-protein-coupled receptor 4 (GPR4) is a member of the proton-sensing G-protein-coupled receptor (GPCR) family which also includes the G2 accumulation receptor (G2A, also known as GPR132), the T cell death associated gene-8 receptor (TDAG8, GPR65), ovarian cancer G-protein receptor 1 (OGR-1, GPR68), and G-protein-coupled receptor 4 (GPR4). Proton-sensing G-protein coupled receptors sense pH of 7.6 to 6.0 and mediates a variety of biological activities in neutral and mildly acidic pH conditions, whereas the acid-sensing ionotropic ion channels typically sense strong acidic pH. GPR4 overexpression in melanoma cells was shown to reduce cell migration, membrane ruffling, and cell spreading under acidic pH conditions. Activation of GPR4 via extracellular acidosis is coupled to the G(s), G(q), and G(12/13) pathways. 280 matched cddid_all.tbl CDD cd15367 cd15367 320489 7tmA_GPR68_OGR1 G protein-coupled receptor 68, member of the class A family of seven-transmembrane G protein-coupled receptors. The ovarian cancer G-protein receptor 1 (OGR1, also known as GPR68) is a member of the proton-sensing G-protein-coupled receptor (GPCR) family which also includes the G2 accumulation receptor (G2A, also known as GPR132), the T cell death associated gene-8 receptor (TDAG8, GPR65), and the G-protein-coupled receptor 4 (GPR4). Proton-sensing G-protein coupled receptors sense pH of 7.6 to 6.0 and mediates a variety of biological activities in neutral and mildly acidic pH conditions, whereas the acid-sensing ionotropic ion channels typically sense strong acidic pH. Knock-out mice studies have suggested that OGR1 plays a role in the regulation of insulin secretion and glucose metabolism. OGR1 couples to G(q/11) proteins and activates phospholipase C and Ca2+ signaling pathways. 276 matched cddid_all.tbl CDD cd15368 cd15368 320490 7tmA_P2Y8 purinergic receptor P2Y8, member of the class A family of seven-transmembrane G protein-coupled receptors. P2Y8 (or P2RY8) expression is often increased in leukemia patients, and it plays a role in the pathogenesis of acute leukemia. P2Y8 is phylogenetically closely related to the protease-activated receptors (PARs), which are activated by serine proteases such as thrombin, trypsin, and tryptase. These proteases cleave the extracellular domain of the receptor to form a new N-terminus, which in turn functions as a tethered ligand. The newly-formed tethered ligand binds intramolecularly to activate the receptor and triggers G-protein binding and intracellular signaling. Four different types of the protease-activated receptors have been identified (PAR1-4) and are predominantly expressed in platelets. PAR1, PA3, and PAR4 are activated by thrombin, whereas PAR2 is activated by trypsin. The PARs are known to couple with several G-proteins including Gi (cAMP inhibitory), G12/13 (Rho and Ras activation), and Gq (calcium signaling) to activate downstream signaling messengers which induces numerous cellular and physiological effects. 281 matched cddid_all.tbl CDD cd15369 cd15369 320491 7tmA_PAR1 protease-activated receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors. Protease-acted receptors (PARs) are seven-transmembrane proteins that belong to the class A G-protein coupled receptor (GPCR) family. Four different types of the protease-activated receptors have been identified: PAR1, PAR2, PAR3, and PAR4. PARs are predominantly expressed in platelets and are activated by serine proteases such as thrombin, trypsin, and tryptase. These proteases cleave the extracellular domain of the receptor to form a new N-terminus, which in turn functions as a tethered ligand. The newly-formed tethered ligand binds intramolecularly to activate the receptor and triggers G-protein binding and intracellular signaling. PAR1, PA3, and PAR4 are activated by thrombin, whereas PAR2 is activated by trypsin. The PARs are known to couple with several G-proteins including Gi (cAMP inhibitory), G12/13 (Rho and Ras activation), and Gq (calcium signaling) to activate downstream signaling messengers which induces numerous cellular and physiological effects. 281 matched cddid_all.tbl CDD cd15370 cd15370 341349 7tmA_PAR2 protease-activated receptor 2, member of the class A family of seven-transmembrane G protein-coupled receptors. Protease-acted receptors (PARs) are seven-transmembrane proteins that belong to the class A G-protein coupled receptor (GPCR) family. Four different types of the protease-activated receptors have been identified: PAR1, PAR2, PAR3, and PAR4. PARs are predominantly expressed in platelets and are activated by serine proteases such as thrombin, trypsin, and tryptase. These proteases cleave the extracellular domain of the receptor to form a new N-terminus, which in turn functions as a tethered ligand. The newly-formed tethered ligand binds intramolecularly to activate the receptor and triggers G-protein binding and intracellular signaling. PAR1, PA3, and PAR4 are activated by thrombin, whereas PAR2 is activated by trypsin. The PARs are known to couple with several G-proteins including Gi (cAMP inhibitory), G12/13 (Rho and Ras activation), and Gq (calcium signaling) to activate downstream signaling messengers which induces numerous cellular and physiological effects. 280 matched cddid_all.tbl CDD cd15371 cd15371 320493 7tmA_PAR3 protease-activated receptor 3, member of the class A family of seven-transmembrane G protein-coupled receptors. Protease-acted receptors (PARs) are seven-transmembrane proteins that belong to the class A G-protein coupled receptor (GPCR) family. Four different types of the protease-activated receptors have been identified: PAR1, PAR2, PAR3, and PAR4. PARs are predominantly expressed in platelets and are activated by serine proteases such as thrombin, trypsin, and tryptase. These proteases cleave the extracellular domain of the receptor to form a new N-terminus, which in turn functions as a tethered ligand. The newly-formed tethered ligand binds intramolecularly to activate the receptor and triggers G-protein binding and intracellular signaling. PAR1, PA3, and PAR4 are activated by thrombin, whereas PAR2 is activated by trypsin. The PARs are known to couple with several G-proteins including Gi (cAMP inhibitory), G12/13 (Rho and Ras activation), and Gq (calcium signaling) to activate downstream signaling messengers which induces numerous cellular and physiological effects. 274 matched cddid_all.tbl CDD cd15372 cd15372 320494 7tmA_PAR4 protease-activated receptor 4, member of the class A family of seven-transmembrane G protein-coupled receptors. Protease-acted receptors (PARs) are seven-transmembrane proteins that belong to the class A G-protein coupled receptor (GPCR) family. Four different types of the protease-activated receptors have been identified: PAR1, PAR2, PAR3, and PAR4. PARs are predominantly expressed in platelets and are activated by serine proteases such as thrombin, trypsin, and tryptase. These proteases cleave the extracellular domain of the receptor to form a new N-terminus, which in turn functions as a tethered ligand. The newly-formed tethered ligand binds intramolecularly to activate the receptor and triggers G-protein binding and intracellular signaling. PAR1, PA3, and PAR4 are activated by thrombin, whereas PAR2 is activated by trypsin. The PARs are known to couple with several G-proteins including Gi (cAMP inhibitory), G12/13 (Rho and Ras activation), and Gq (calcium signaling) to activate downstream signaling messengers which induces numerous cellular and physiological effects. 274 matched cddid_all.tbl CDD cd15373 cd15373 320495 7tmA_P2Y2 P2Y purinoceptor 2, member of the class A family of seven-transmembrane G protein-coupled receptors. P2Y2 belongs to the P2Y receptor family of purinergic G-protein coupled receptors and is implicated to play a role in the control of the cell cycle of endometrial carcinoma cells. The P2Y receptor family is composed of eight subtypes, which are activated by naturally occurring extracellular nucleotides such as ATP, ADP, UTP, UDP, and UDP-glucose. These eight receptors are ubiquitous in human tissues and can be further classified into two subfamilies based on sequence homology and second messenger coupling: a subfamily of five P2Y1-like receptors (P2Y1, P2Y2, P2Y4, P2Y6, and P2Y11Rs) that are coupled to G(q) protein to activate phospholipase C (PLC) and a second subfamily of three P2Y12-like receptors (P2Y12, P2YR13, and P2Y14Rs) that are coupled to G(i) protein to inhibit adenylate cyclase. Several cloned subtypes, such as P2Y3, P2Y5, and P2Y7-10, are not functional mammalian nucleotide receptors. The native agonists for P2Y receptors are: ATP (P2Y2, P2Y12), ADP (P2Y1, P2Y12, and P2Y13), UTP (P2Y2, P2Y4), UDP (P2Y6, P2Y14), and UDP-glucose (P2Y14). 283 matched cddid_all.tbl CDD cd15374 cd15374 320496 7tmA_P2Y4 P2Y purinoceptor 4, member of the class A family of seven-transmembrane G protein-coupled receptors. P2Y4 belongs to the P2Y receptor family of purinergic G-protein coupled receptors. This family is composed of eight subtypes, which are activated by naturally occurring extracellular nucleotides such as ATP, ADP, UTP, UDP, and UDP-glucose. These eight receptors are ubiquitous in human tissues and can be further classified into two subfamilies based on sequence homology and second messenger coupling: a subfamily of five P2Y1-like receptors (P2Y1, P2Y2, P2Y4, P2Y6, and P2Y11Rs) that are coupled to G(q) protein to activate phospholipase C (PLC) and a second subfamily of three P2Y12-like receptors (P2Y12, P2YR13, and P2Y14Rs) that are coupled to G(i) protein to inhibit adenylate cyclase. Several cloned subtypes, such as P2Y3, P2Y5, and P2Y7-10, are not functional mammalian nucleotide receptors. The native agonists for P2Y receptors are: ATP (P2Y2, P2Y12), ADP (P2Y1, P2Y12, and P2Y13), UTP (P2Y2, P2Y4), UDP (P2Y6, P2Y14), and UDP-glucose (P2Y14). 285 matched cddid_all.tbl CDD cd15375 cd15375 320497 7tmA_OXGR1 2-oxoglutarate receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors. 2-oxoglutarate receptor 1 (OXGR1) is also known as GPR80, GPR99, or P2Y15. OXGR1 functions as a receptor for alpha-ketoglutarate, a citric acid cycle intermediate, and acts exclusively through a G(q)-dependent pathway. OXGR1 belongs to the class A GPCR superfamily and is phylogenetically related to the purinergic P2Y1-like receptor subfamily, whose members are coupled to G(q) protein to activate phospholipase C (PLC). OXGR1 has also been reported as a potential third cysteinyl leukotriene receptor with specificity for leukotriene E4. 280 matched cddid_all.tbl CDD cd15376 cd15376 320498 7tmA_P2Y11 P2Y purinoceptor 11, member of the class A family of seven-transmembrane G protein-coupled receptors. P2Y11 belongs to the P2Y receptor family of purinergic G-protein coupled receptors. The activation of P2Y11 is a major pathway of macrophage activation that leads to the release of cytokines. The P2Y receptor family is composed of eight subtypes, which are activated by naturally occurring extracellular nucleotides such as ATP, ADP, UTP, UDP, and UDP-glucose. These eight receptors are ubiquitous in human tissues and can be further classified into two subfamilies based on sequence homology and second messenger coupling: a subfamily of five P2Y1-like receptors (P2Y1, P2Y2, P2Y4, P2Y6, and P2Y11Rs) that are coupled to G(q) protein to activate phospholipase C (PLC) and a second subfamily of three P2Y12-like receptors (P2Y12, P2YR13, and P2Y14Rs) that are coupled to G(i) protein to inhibit adenylate cyclase. Several cloned subtypes, such as P2Y3, P2Y5, and P2Y7-10, are not functional mammalian nucleotide receptors. The native agonists for P2Y receptors are: ATP (P2Y2, P2Y12), ADP (P2Y1, P2Y12, and P2Y13), UTP (P2Y2, P2Y4), UDP (P2Y6, P2Y14), and UDP-glucose (P2Y14). 284 matched cddid_all.tbl CDD cd15377 cd15377 341350 7tmA_P2Y1 P2Y purinoceptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors. P2Y1 belongs to the P2Y receptor family of purinergic G-protein coupled receptors. This family is composed of eight subtypes, which are activated by naturally occurring extracellular nucleotides such as ATP, ADP, UTP, UDP, and UDP-glucose. These eight receptors are ubiquitous in human tissues and can be further classified into two subfamilies based on sequence homology and second messenger coupling: a subfamily of five P2Y1-like receptors (P2Y1, P2Y2, P2Y4, P2Y6, and P2Y11Rs) that are coupled to G(q) protein to activate phospholipase C (PLC) and a second subfamily of three P2Y12-like receptors (P2Y12, P2YR13, and P2Y14Rs) that are coupled to G(i) protein to inhibit adenylate cyclase. Several cloned subtypes, such as P2Y3, P2Y5, and P2Y7-10, are not functional mammalian nucleotide receptors. The native agonists for P2Y receptors are: ATP (P2Y2, P2Y12), ADP (P2Y1, P2Y12, and P2Y13), UTP (P2Y2, P2Y4), UDP (P2Y6, P2Y14), and UDP-glucose (P2Y14). 289 matched cddid_all.tbl CDD cd15378 cd15378 320500 7tmA_SUCNR1_GPR91 succinate receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors. Succinate receptor (SUCNR1) GPR91 exclusively couples to G(i) protein to inhibit cAMP production and also activates PLC-beta to increase intracellular calcium concentrations in an inositol phosphate dependent mechanism. Succinate, an intermediate molecule of the citric cycle, is shown to cause cardiac hypertrophy via GPR91 activation. Furthermore, succinate-induced GPR91 activation is involved in the regulation of renin-angiotensin system and is suggested to play an important role in the development of renovascular hypertension and diabetic nephropathy. SUCNR1 belongs to the class A GPCR superfamily and is phylogenetically related to the purinergic P2Y1-like receptor subfamily, whose members are coupled to G(q) protein to activate phospholipase C (PLC). 283 matched cddid_all.tbl CDD cd15379 cd15379 320501 7tmA_P2Y6 P2Y purinoceptor 6, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes mammalian P2Y6, avian P2Y3, and similar proteins. P2Y3 is the avian homolog of mammalian P2Y6. They belong to the G(i) class of a family of purinergic G-protein coupled receptors. The P2Y receptor family is composed of eight subtypes, which are activated by naturally occurring extracellular nucleotides such as ATP, ADP, UTP, UDP, and UDP-glucose. These eight receptors are ubiquitous in human tissues and can be further classified into two subfamilies based on sequence homology and second messenger coupling: a subfamily of five P2Y1-like receptors (P2Y1, P2Y2, P2Y4, P2Y6, and P2Y11Rs) that are coupled to G(q) protein to activate phospholipase C (PLC) and a second subfamily of three P2Y12-like receptors (P2Y12, P2YR13, and P2Y14Rs) that are coupled to G(i) protein to inhibit adenylate cyclase. Several cloned subtypes, such as P2Y3, P2Y5, and P2Y7-10, are not functional mammalian nucleotide receptors. The native agonists for P2Y receptors are: ATP (P2Y2, P2Y12), ADP (P2Y1, P2Y12, and P2Y13), UTP (P2Y2, P2Y4), UDP (P2Y6, P2Y14), and UDP-glucose (P2Y14). 288 matched cddid_all.tbl CDD cd15380 cd15380 320502 7tmA_BK-1 bradykinin receptor B1, member of the class A family of seven-transmembrane G protein-coupled receptors. The bradykinin receptor family is a group of the seven transmembrane G-protein coupled receptors, whose endogenous ligand is the pro-inflammatory nonapeptide bradykinin that mediates various vascular and pain responses. Two major bradykinin receptor subtypes, B1 and B2, have been identified based on their pharmacological properties. The B1 receptor is rapidly induced by tissue injury and inflammation, whereas the B2 receptor is ubiquitously expressed on many tissue types. Both receptors contain three consensus sites for N-linked glycosylation in extracellular domains and couple to G(q) protein to activate phospholipase C, leading to phosphoinositide hydrolysis and intracellular calcium mobilization. They can also interact with G(i) protein to inhibit adenylate cyclase and activate the MAPK (mitogen-activated protein kinase) pathways. 286 matched cddid_all.tbl CDD cd15381 cd15381 320503 7tmA_BK-2 bradykinin receptor B2, member of the class A family of seven-transmembrane G protein-coupled receptors. The bradykinin receptor family is a group of the seven transmembrane G-protein coupled receptors, whose endogenous ligand is the pro-inflammatory nonapeptide bradykinin that mediates various vascular and pain responses. Two major bradykinin receptor subtypes, B1 and B2, have been identified based on their pharmacological properties. The B1 receptor is rapidly induced by tissue injury and inflammation, whereas the B2 receptor is ubiquitously expressed on many tissue types. Both receptors contain three consensus sites for N-linked glycosylation in extracellular domains and couple to G(q) protein to activate phospholipase C, leading to phosphoinositide hydrolysis and intracellular calcium mobilization. They can also interact with G(i) protein to inhibit adenylate cyclase and activate the MAPK (mitogen-activated protein kinase) pathways. 284 matched cddid_all.tbl CDD cd15382 cd15382 320504 7tmA_AKHR adipokinetic hormone receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. Adipokinetic hormone (AKH) is a lipid-mobilizing hormone that is involved in control of insect metabolism. Generally, AKH behaves as a typical stress hormone by mobilizing lipids, carbohydrates and/or certain amino acids such as proline. Thus, it utilizes the body's energy reserves to fight the immediate stress problems and subdue processes that are less important. Although AKH is known to responsible for regulating the energy metabolism during insect flight, it is also found in insects that have lost its functional wings and predominantly walk for their locomotion. AKH is structurally related to the mammalian gonadotropin-releasing hormone (GnRH) and they share a common ancestor. Both GnRH and AKH receptors are members of the class A of the seven-transmembrane, G-protein coupled receptor (GPCR) superfamily. 298 matched cddid_all.tbl CDD cd15383 cd15383 320505 7tmA_GnRHR_vertebrate vertebrate gonadotropin-releasing hormone receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. GnRHR, also known as luteinizing hormone releasing hormone receptor (LHRHR), plays an central role in vertebrate reproductive function; its activation by binding to GnRH leads to the release of follicle stimulating hormone (FSH) and luteinizing hormone (LH) from the pituitary gland. GnRHR is expressed predominantly in the gonadotrope membrane of the anterior pituitary as well as found in numerous extrapituitary tissues including lymphocytes, breast, ovary, prostate, and cancer cell lines. There are at least two types of GnRH receptors, GnRHR1 and GnRHR2, which couple primarily to G proteins of the Gq/11 family. GnRHR is closely related to the adipokinetic hormone receptor (AKH), which binds to a lipid-mobilizing hormone that is involved in control of insect metabolism. They share a common ancestor and are members of the class A of the seven-transmembrane, G-protein coupled receptor (GPCR) superfamily. 295 matched cddid_all.tbl CDD cd15384 cd15384 320506 7tmA_GnRHR_invertebrate invertebrate gonadotropin-releasing hormone receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. GnRHR, also known as luteinizing hormone releasing hormone receptor (LHRHR), plays an central role in vertebrate reproductive function; its activation by binding to GnRH leads to the release of follicle stimulating hormone (FSH) and luteinizing hormone (LH) from the pituitary gland. GnRHR is expressed predominantly in the gonadotrope membrane of the anterior pituitary as well as found in numerous extrapituitary tissues including lymphocytes, breast, ovary, prostate, and cancer cell lines. There are at least two types of GnRH receptors, GnRHR1 and GnRHR2, which couple primarily to G proteins of the Gq/11 family. GnRHR is closely related to the adipokinetic hormone receptor (AKH), which binds to a lipid-mobilizing hormone that is involved in control of insect metabolism. They share a common ancestor and are members of the class A of the seven-transmembrane, G-protein coupled receptor (GPCR) superfamily. 293 matched cddid_all.tbl CDD cd15385 cd15385 320507 7tmA_V1aR vasopressin receptor subtype 1A, member of the class A family of seven-transmembrane G protein-coupled receptors. V1a-type receptor is a G(q/11)-coupled receptor that mediates blood vessel constriction. Vasopressin (also known as arginine vasopressin or anti-diuretic hormone) is synthesized in the hypothalamus and is released from the posterior pituitary gland. The actions of vasopressin are mediated by the interaction of this hormone with three receptor subtypes: V1aR, V1bR, and V2R. These subtypes are differ in localization, function, and signaling pathways. Activation of V1aR and V1bR stimulate phospholipase C, while activation of V2R stimulates adenylate cyclase. Although vasopressin and oxytocin differ only by two amino acids and stimulate the same cAMP/PKA pathway, they have divergent physiological functions. Vasopressin is involved in regulating blood pressure and the balance of water and sodium ions, whereas oxytocin plays an important role in the uterus during childbirth and in lactation. 301 matched cddid_all.tbl CDD cd15386 cd15386 320508 7tmA_V1bR vasopressin receptor subtype 1B, member of the class A family of seven-transmembrane G protein-coupled receptors. The V1b receptor is specifically expressed in corticotropes of the anterior pituitary and plays a critical role in regulating the activity of hypothalamic-pituitary-adrenal axis, a key part of the neuroendocrine system that controls reactions to stress, by maintaining adrenocorticotropic hormone (ACTH) and corticosterone levels. Vasopressin (also known as arginine vasopressin or anti-diuretic hormone) is synthesized in the hypothalamus and is released from the posterior pituitary gland. The actions of vasopressin are mediated by the interaction of this hormone with three receptor subtypes: V1aR, V1bR, and V2R. These subtypes are differ in localization, function, and signaling pathways. Activation of V1aR and V1bR stimulate phospholipase C, while activation of V2R stimulates adenylate cyclase. Although vasopressin and oxytocin differ only by two amino acids and stimulate the same cAMP/PKA pathway, they have divergent physiological functions. Vasopressin is involved in regulating blood pressure and the balance of water and sodium ions, whereas oxytocin plays an important role in the uterus during childbirth and in lactation. 302 matched cddid_all.tbl CDD cd15387 cd15387 320509 7tmA_OT_R oxytocin receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. Oxytocin is a peptide of nine amino acids synthesized in the hypothalamus and is released from the posterior pituitary gland. Oxytocin plays an important role in sexual reproduction of both sexes and is structurally very similar to vasopressin. Although vasopressin and oxytocin differ only by two amino acids and stimulate the same cAMP/PKA pathway, they have divergent physiological functions. Vasopressin is involved in regulating blood pressure and the balance of water and sodium ions, whereas oxytocin plays an important role in the uterus during childbirth and in lactation. 297 matched cddid_all.tbl CDD cd15388 cd15388 320510 7tmA_V2R vasopressin receptor 2, member of the class A family of seven-transmembrane G protein-coupled receptors. The vasopressin type 2 receptor (V2R) is a G(s)-coupled receptor that controls balance of water and sodium ion by regulating their reabsorption in the renal collecting duct. Mutations of V2R is responsible for nephrogenic diabetes insipidus. Vasopressin (also known as arginine vasopressin or anti-diuretic hormone) is synthesized in the hypothalamus and is released from the posterior pituitary gland. The actions of vasopressin are mediated by the interaction of this hormone with three receptor subtypes: V1aR, V1bR, and V2R. These subtypes are differ in localization, function, and signaling pathways. Activation of V1aR and V1bR stimulate phospholipase C, while activation of V2R stimulates adenylate cyclase. Although vasopressin and oxytocin differ only by two amino acids and stimulate the same cAMP/PKA pathway, they have divergent physiological functions. Vasopressin is involved in regulating blood pressure and the balance of water and sodium ions, whereas oxytocin plays an important role in the uterus during childbirth and in lactation. 295 matched cddid_all.tbl CDD cd15389 cd15389 320511 7tmA_GPR83 G protein-coupled receptor 83, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR83, also known as GPR72, is widely expressed in the brain, including hypothalamic nuclei which is involved in regulating energy balance and food intake. The hypothalamic expression of GPR83 is tightly regulated in response to nutrient availability and is decreased in obese mice. A recent study suggests that GPR83 has a critical role in the regulation of systemic energy metabolism via ghrelin-dependent and ghrelin-independent mechanisms. GPR83 shares a significant amino acid sequence identity with the tachykinin receptors, however its endogenous ligand is unknown. 285 matched cddid_all.tbl CDD cd15390 cd15390 320512 7tmA_TACR neurokinin receptors (or tachykinin receptors), member of the class A family of seven-transmembrane G protein-coupled receptors. This group represents G-protein coupled receptors for a variety of neuropeptides of the tachykinin (TK) family. The tachykinins are widely distributed throughout the mammalian central and peripheral nervous systems and act as excitatory transmitters on neurons and cells in the gastrointestinal tract. The TKs are characterized by a common five-amino acid C-terminal sequence, Phe-X-Gly-Leu-Met-NH2, where X is a hydrophobic residue. The three major mammalian tachykinins are substance P (SP), neurokinin A (NKA), and neurokinin B (NKB). The physiological actions of tachykinins are mediated through three types of receptors: neurokinin receptor type 1 (NK1R), NK2R, and NK3R. SP is a high-affinity endogenous ligand for NK1R, which interacts with the Gq protein and activates phospholipase C, leading to elevation of intracellular calcium. NK2R is a high-affinity receptor for NKA, the tachykinin neuropeptide substance K. SP and NKA are found in the enteric nervous system and mediate in the regulation of gastrointestinal motility, secretion, vascular permeability, and pain perception. NK3R is activated by its high-affinity ligand, NKB, which is primarily involved in the central nervous system and plays a critical role in the regulation of gonadotropin hormone release and the onset of puberty. 289 matched cddid_all.tbl CDD cd15391 cd15391 320513 7tmA_NPR-like_invertebrate invertebrate neuropeptide receptor-like, member of the class A family of seven-transmembrane G protein-coupled receptors. This subgroup includes putative neuropeptide receptor found in invertebrates, which is a member of class A of 7-transmembrane G protein-coupled receptors. This orphan receptor shares a significant amino acid sequence identity with the neurokinin 1 receptor (NK1R). The endogenous ligand for NK1R is substance P, an 11-amino acid peptide that functions as a vasodilator and neurotransmitter and is released from the autonomic sensory nerve fibers. 289 matched cddid_all.tbl CDD cd15392 cd15392 320514 7tmA_PR4-like neuropeptide Y receptor-like found in insect and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This subgroup includes a novel G protein-coupled receptor (also known as PR4 receptor) from Drosophila melanogaster, which can be activated by the members of the neuropeptide Y (NPY) family, including NPY, peptide YY (PYY) and pancreatic polypeptide (PP), when expressed in Xenopus oocytes. These homologous peptides of 36-amino acids in length contain a hairpin-like structural motif, which referred to as the pancreatic polypeptide fold, and function as gastrointestinal hormones and neurotransmitters. The PR4 receptor also shares strong sequence homology to the mammalian tachykinin receptors (NK1R, NK2R, and NK3R), whose endogenous ligands are substance P (SP), neurokinin A (NKA), and neurokinin B (NKB), respectively. The tachykinins function as excitatory transmitters on neurons and cells in the gastrointestinal tract. 287 matched cddid_all.tbl CDD cd15393 cd15393 320515 7tmA_leucokinin-like leucokinin-like peptide receptor from tick and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This subgroup includes a leucokinin-like peptide receptor from the Southern cattle tick, Boophilus microplus, a pest of cattle world-wide. Leucokinins are invertebrate neuropeptides that exhibit myotropic and diuretic activity. This receptor is the first neuropeptide receptor known from the Acari and the second known in the subfamily of leucokinin-like peptide G-protein-coupled receptors. The other known leucokinin-like peptide receptor is a lymnokinin receptor from the mollusc Lymnaea stagnalis. 288 matched cddid_all.tbl CDD cd15394 cd15394 320516 7tmA_PrRP_R prolactin-releasing peptide receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. Prolactin-releasing peptide (PrRP) receptor (previously known as GPR10) is expressed in the central nervous system with the highest levels located in the anterior pituitary and is activated by its endogenous ligand PrRP, a neuropeptide possessing a C-terminal Arg-Phe-amide motif. There are two active isoforms of PrRP in mammals: one consists of 20 amino acids (PrRP-20) and the other consists of 31 amino acids (PrRP-31), where PrRP-20 is a C-terminal fragment of PrRP-31. Binding of PrRP to the receptor coupled to G(i/o) proteins activates the extracellular signal-related kinase (ERK) and it can also couple to G(q) protein leading to an increase in intracellular calcium and activation of c-Jun N-terminal protein kinase (JNK). The PrRP receptor shares significant sequence homology with the neuropeptide Y (NPY) receptor, and micromolar levels of NPY can bind and completely inhibit the PrRP-evoked intracellular calcium response in PrRP receptor-expressing cells, suggesting that the PrRP receptor shares a common ancestor with the NPY receptors. PrRP has been shown to reduce food intake and body weight and modify body temperature when administered in rats. It also has been shown to decrease circulating growth hormone levels by activating somatostatin-secreting neurons in the hypothalamic periventricular nucleus. 286 matched cddid_all.tbl CDD cd15395 cd15395 320517 7tmA_NPY1R neuropeptide Y receptor type 1, member of the class A family of seven-transmembrane G protein-coupled receptors. NPY is a 36-amino acid peptide neurotransmitter with a C-terminal tyrosine amide residue that is widely distributed in the brain and the autonomic nervous system of many mammalian species. NPY exerts its functions through five, G-protein coupled receptor subtypes including NPY1R, NPY2R, NPY4R, NPY5R, and NPY6R; however, NPY6R is not functional in humans. NYP receptors are also activated by its two other family members, peptide YY (PYY) and pancreatic polypeptide (PP). They typically couple to G(i) or G(o) proteins, which leads to a decrease in adenylate cyclase activity, thereby decreasing intracellular cAMP levels, and are involved in diverse physiological roles including appetite regulation, circadian rhythm, and anxiety. When NPY signals through NPY2R in concert with NPY5R, it induces angiogenesis and consequently plays an important role in revascularization and wound healing. On the other hand, when NPY acts through NPY1R and NPYR5, it acts as a vascular mitogen, leading to restenosis and atherosclerosis. 293 matched cddid_all.tbl CDD cd15396 cd15396 320518 7tmA_NPY6R neuropeptide Y receptor type 6, member of the class A family of seven-transmembrane G protein-coupled receptors. NPY is a 36-amino acid peptide neurotransmitter with a C-terminal tyrosine amide residue that is widely distributed in the brain and the autonomic nervous system of many mammalian species. NPY exerts its functions through five, G-protein coupled receptor subtypes including NPY1R, NPY2R, NPY4R, NPY5R, and NPY6R; however, NPY6R is not functional in humans. NYP receptors are also activated by its two other family members, peptide YY (PYY) and pancreatic polypeptide (PP). They typically couple to G(i) or G(o) proteins, which leads to a decrease in adenylate cyclase activity, thereby decreasing intracellular cAMP levels, and are involved in diverse physiological roles including appetite regulation, circadian rhythm, and anxiety. 293 matched cddid_all.tbl CDD cd15397 cd15397 320519 7tmA_NPY4R neuropeptide Y receptor type 4, member of the class A family of seven-transmembrane G protein-coupled receptors. NPY is a 36-amino acid peptide neurotransmitter with a C-terminal tyrosine amide residue that is widely distributed in the brain and the autonomic nervous system of many mammalian species. NPY exerts its functions through five, G-protein coupled receptor subtypes including NPY1R, NPY2R, NPY4R, NPY5R, and NPY6R; however, NPY6R is not functional in humans. NYP receptors are also activated by its two other family members, peptide YY (PYY) and pancreatic polypeptide (PP). They typically couple to G(i) or G(o) proteins, which leads to a decrease in adenylate cyclase activity, thereby decreasing intracellular cAMP levels, and are involved in diverse physiological roles including appetite regulation, circadian rhythm, and anxiety. 293 matched cddid_all.tbl CDD cd15398 cd15398 320520 7tmA_NPY5R neuropeptide Y receptor type 5, member of the class A family of seven-transmembrane G protein-coupled receptors. NPY is a 36-amino acid peptide neurotransmitter with a C-terminal tyrosine amide residue that is widely distributed in the brain and the autonomic nervous system of many mammalian species. NPY exerts its functions through five, G-protein coupled receptor subtypes including NPY1R, NPY2R, NPY4R, NPY5R, and NPY6R; however, NPY6R is not functional in humans. NYP receptors are also activated by its two other family members, peptide YY (PYY) and pancreatic polypeptide (PP). They typically couple to G(i) or G(o) proteins, which leads to a decrease in adenylate cyclase activity, thereby decreasing intracellular cAMP levels, and are involved in diverse physiological roles including appetite regulation, circadian rhythm, and anxiety. When NPY signals through NPY2R in concert with NPY5R, it induces angiogenesis and consequently plays an important role in revascularization and wound healing. On the other hand, when NPY acts through NPY1R and NPYR5, it acts as a vascular mitogen, leading to restenosis and atherosclerosis. 273 matched cddid_all.tbl CDD cd15399 cd15399 320521 7tmA_NPY2R neuropeptide Y receptor type 2, member of the class A family of seven-transmembrane G protein-coupled receptors. NPY is a 36-amino acid peptide neurotransmitter with a C-terminal tyrosine amide residue that is widely distributed in the brain and the autonomic nervous system of many mammalian species. NPY exerts its functions through five, G-protein coupled receptor subtypes including NPY1R, NPY2R, NPY4R, NPY5R, and NPY6R; however, NPY6R is not functional in humans. NYP receptors are also activated by its two other family members, peptide YY (PYY) and pancreatic polypeptide (PP). They typically couple to G(i) or G(o) proteins, which leads to a decrease in adenylate cyclase activity, thereby decreasing intracellular cAMP levels, and are involved in diverse physiological roles including appetite regulation, circadian rhythm, and anxiety. When NPY signals through NPY2R in concert with NPY5R, it induces angiogenesis and consequently plays an important role in revascularization and wound healing. On the other hand, when NPY acts through NPY1R and NPYR5, it acts as a vascular mitogen, leading to restenosis and atherosclerosis. 285 matched cddid_all.tbl CDD cd15400 cd15400 320522 7tmA_Mel1B melatonin receptor subtype 1B, member of the class A family of seven-transmembrane G protein-coupled receptors. Melatonin (N-acetyl-5-methoxytryptamine) is a naturally occurring sleep-promoting chemical found in vertebrates, invertebrates, bacteria, fungi, and plants. In mammals, melatonin is secreted by the pineal gland and is involved in regulation of circadian rhythms. Its production peaks during the nighttime, and is suppressed by light. Melatonin is shown to be synthesized in other organs and cells of many vertebrates, including the Harderian gland, leukocytes, skin, and the gastrointestinal (GI) tract, which contains several hundred times more melatonin than the pineal gland and is involved in the regulation of GI motility, inflammation, and sensation. Melatonin exerts its pleiotropic physiological effects through specific membrane receptors, named MT1A, MT1B, and MT1C, which belong to the class A rhodopsin-like G-protein coupled receptor family. MT1A and MT1B subtypes are present in mammals, whereas MT1C subtype has been found in amphibians and birds. The melatonin receptors couple to G proteins of the G(i/o) class, leading to the inhibition of adenylate cyclase. 279 matched cddid_all.tbl CDD cd15401 cd15401 320523 7tmA_Mel1C melatonin receptor subtype 1C, member of the class A family of seven-transmembrane G protein-coupled receptors. Melatonin (N-acetyl-5-methoxytryptamine) is a naturally occurring sleep-promoting chemical found in vertebrates, invertebrates, bacteria, fungi, and plants. In mammals, melatonin is secreted by the pineal gland and is involved in regulation of circadian rhythms. Its production peaks during the nighttime, and is suppressed by light. Melatonin is shown to be synthesized in other organs and cells of many vertebrates, including the Harderian gland, leukocytes, skin, and the gastrointestinal (GI) tract, which contains several hundred times more melatonin than the pineal gland and is involved in the regulation of GI motility, inflammation, and sensation. Melatonin exerts its pleiotropic physiological effects through specific membrane receptors, named MT1A, MT1B, and MT1C, which belong to the class A rhodopsin-like G-protein coupled receptor family. MT1A and MT1B subtypes are present in mammals, whereas MT1C subtype has been found in amphibians and birds. The melatonin receptors couple to G proteins of the G(i/o) class, leading to the inhibition of adenylate cyclase. 279 matched cddid_all.tbl CDD cd15402 cd15402 320524 7tmA_Mel1A melatonin receptor subtype 1A, member of the class A family of seven-transmembrane G protein-coupled receptors. Melatonin (N-acetyl-5-methoxytryptamine) is a naturally occurring sleep-promoting chemical found in vertebrates, invertebrates, bacteria, fungi, and plants. In mammals, melatonin is secreted by the pineal gland and is involved in regulation of circadian rhythms. Its production peaks during the nighttime, and is suppressed by light. Melatonin is shown to be synthesized in other organs and cells of many vertebrates, including the Harderian gland, leukocytes, skin, and the gastrointestinal (GI) tract, which contains several hundred times more melatonin than the pineal gland and is involved in the regulation of GI motility, inflammation, and sensation. Melatonin exerts its pleiotropic physiological effects through specific membrane receptors, named MT1A, MT1B, and MT1C, which belong to the class A rhodopsin-like G-protein coupled receptor family. MT1A and MT1B subtypes are present in mammals, whereas MT1C subtype has been found in amphibians and birds. The melatonin receptors couple to G proteins of the G(i/o) class, leading to the inhibition of adenylate cyclase. 279 matched cddid_all.tbl CDD cd15403 cd15403 320525 7tmA_GPR45 G protein-coupled receptor 45, member of the class A family of seven-transmembrane G protein-coupled receptors. This subgroup includes the human orphan receptor GPR45 and closely related proteins found in vertebrates. GPR45 is also called PSP24 in Xenopus and PSP24-alpha (or PSP24-1) in mammals. GPR45 shows the highest sequence homology with GPR63 (PSP24-beta, or PSP24-2). PSP24 was originally identified as a novel, high-affinity lysophosphatidic acid (LPA) receptor in Xenopus laevis oocytes; however, PSP24 receptors (GPR45 and GPR63) have not been shown to be activated by LPA. Mammalian PSP24 receptors are highly expressed in neuronal cells of cerebellum and their expression level remains constant from the early embryonic stages to adulthood, suggesting the important role of PSP24s in brain neuronal functions. Members of this subgroup contain the highly conserved Asp-Arg-Tyr/Phe (DRY/F) motif found in the third transmembrane helix (TM3) of the rhodopsin-like class A receptors which is important for efficient G protein-coupled signal transduction. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 301 matched cddid_all.tbl CDD cd15404 cd15404 320526 7tmA_GPR63 G protein-coupled receptor 63, member of the class A family of seven-transmembrane G protein-coupled receptors. This subgroup includes the human orphan receptor GPR63, which is also called PSP24-beta or PSP24-2, and its closely related proteins found in vertebrates. GPR63 shares the highest sequence homology with GPR45 (Xenopus PSP24, mammalian PSP24-alpha or PSP24-1). PSP24 was originally identified as a novel, high-affinity lysophosphatidic acid (LPA) receptor in Xenopus laevis oocytes; however, PSP24 receptors (GPR45 and GPR63) have not been shown to be activated by LPA. Mammalian PSP24 receptors are highly expressed in neuronal cells of cerebellum and their expression level remains constant from the early embryonic stages to adulthood, suggesting the important role of PSP24s in brain neuronal functions. Members of this subgroup contain the highly conserved Asp-Arg-Tyr/Phe (DRY/F) motif found in the third transmembrane helix (TM3) of the rhodopsin-like class A receptors which is important for efficient G protein-coupled signal transduction. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 265 matched cddid_all.tbl CDD cd15405 cd15405 320527 7tmA_OR8B-like olfactory receptor subfamily 8B and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 8B and related proteins in other mammals. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 277 matched cddid_all.tbl CDD cd15406 cd15406 320528 7tmA_OR8D-like olfactory receptor subfamily 8D and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 8D and related proteins in other mammals. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 290 matched cddid_all.tbl CDD cd15407 cd15407 320529 7tmA_OR5B-like olfactory receptor subfamily 5B and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 5B and related proteins in other mammals. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 279 matched cddid_all.tbl CDD cd15408 cd15408 320530 7tmA_OR5AK3-like olfactory receptor subfamily 5AK3, 5AU1, and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 5AK3, 5AU1, and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 287 matched cddid_all.tbl CDD cd15409 cd15409 320531 7tmA_OR5H-like olfactory receptor subfamily 5H and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 5H, 5K, 5AC, 5T and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 279 matched cddid_all.tbl CDD cd15410 cd15410 320532 7tmA_OR5D-like olfactory receptor subfamily 5D and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 5D, 5L, 5W, and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 294 matched cddid_all.tbl CDD cd15411 cd15411 320533 7tmA_OR8H-like olfactory receptor subfamily 8H and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 8H, 8I, 5F and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 279 matched cddid_all.tbl CDD cd15412 cd15412 320534 7tmA_OR5M-like olfactory receptor subfamily 5M and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 5M and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 279 matched cddid_all.tbl CDD cd15413 cd15413 320535 7tmA_OR8K-like olfactory receptor subfamily 8K and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 8K, 8U, 8J, 5R, 5AL and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 279 matched cddid_all.tbl CDD cd15414 cd15414 320536 7tmA_OR5G-like olfactory receptor subfamily 5G and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 5G and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 285 matched cddid_all.tbl CDD cd15415 cd15415 320537 7tmA_OR5J-like olfactory receptor subfamily 5J and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 5J and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 279 matched cddid_all.tbl CDD cd15416 cd15416 320538 7tmA_OR5P-like olfactory receptor subfamily 5P and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 5P and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 279 matched cddid_all.tbl CDD cd15417 cd15417 320539 7tmA_OR5A1-like olfactory receptor subfamily 5A1 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 5A1, 5A2, 5AN1, and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 279 matched cddid_all.tbl CDD cd15418 cd15418 320540 7tmA_OR9G-like olfactory receptor subfamily 9G and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 9G and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 281 matched cddid_all.tbl CDD cd15419 cd15419 320541 7tmA_OR9K2-like olfactory receptor subfamily 9K2 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes transmembrane olfactory receptor subfamily 9K2 and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 279 matched cddid_all.tbl CDD cd15420 cd15420 320542 7tmA_OR2A-like olfactory receptor subfamily 2A and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 2A and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 277 matched cddid_all.tbl CDD cd15421 cd15421 320543 7tmA_OR2T-like olfactory receptor subfamily 2T and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamilies 2T, 2M, 2L, 2V, 2Z, 2AE, 2AG, 2AK, 2AJ, and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 277 matched cddid_all.tbl CDD cd15424 cd15424 320544 7tmA_OR2_unk olfactory receptor family 2, unknown subfamily, member of the class A family of seven-transmembrane G protein-coupled receptors. This group represents an unknown subfamily, conserved in some mammalia and sauropsids, in family 2 of olfactory receptors. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 277 matched cddid_all.tbl CDD cd15428 cd15428 320545 7tmA_OR2D-like olfactory receptor subfamily 2D and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 2D and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 277 matched cddid_all.tbl CDD cd15429 cd15429 320546 7tmA_OR2F-like olfactory receptor subfamily 2F and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 2F and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 277 matched cddid_all.tbl CDD cd15430 cd15430 320547 7tmA_OR13-like olfactory receptor family 13 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor family 13 (subfamilies 13C, 13D, 13F, and 13J), some subfamilies from OR family 2 (2K and 2S), and related proteins in other mammals. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 270 matched cddid_all.tbl CDD cd15431 cd15431 320548 7tmA_OR13H-like olfactory receptor subfamily 13H and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 13H and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 269 matched cddid_all.tbl CDD cd15432 cd15432 320549 7tmA_OR2B2-like olfactory receptor subfamily 2B2 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes transmembrane olfactory receptor subfamily 2B2 and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 277 matched cddid_all.tbl CDD cd15433 cd15433 320550 7tmA_OR2Y-like olfactory receptor subfamily 2Y and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 2Y, 2I, and related protein in other mammals. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 277 matched cddid_all.tbl CDD cd15434 cd15434 320551 7tmA_OR2W-like olfactory receptor subfamily 2W and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 2W and related proteins in other mammals. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 277 matched cddid_all.tbl CDD cd15436 cd15436 320552 7tmB2_Latrophilin Latrophilins, member of the class B2 family of seven-transmembrane G protein-coupled receptors. Latrophilins (also called lectomedins or latrotoxin receptors) belong to Group I adhesion GPCRs, which also include ETL (EGF-TM7-latrophilin-related protein). These receptors are a member of the adhesion family (subclass B2) that belongs to the class B GPCRs. Three subtypes of latrophilins have been identified: LPH1 (latrophilin-1), LPH2, and LPH3. The latrophilin-1 is a brain-specific calcium-independent receptor of alpha-latrotoxin, a potent presynaptic neurotoxin from the venom of the black widow spider that induces massive neurotransmitter release from sensory and motor neurons as well as endocrine cells, leading to nerve-terminal degeneration. Latrophilin-2 and -3, although sharing strong sequence homology to latrophilin-1, do not bind alpha-latrotoxin. While latrophilin-3 is also brain specific, latrophilin-2 is ubiquitously distributed. The endogenous ligands for these two receptors are unknown. ETL, a seven transmembrane receptor containing EGF-like repeats is highly expressed in heart, where developmentally regulated, as well as in normal smooth cells. The function of the ETL is unknown. All adhesion GPCRs possess large N-terminal extracellular domains containing multiple structural motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, coupled to a seven-transmembrane domain. In addition, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR-autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 258 matched cddid_all.tbl CDD cd15437 cd15437 320553 7tmB2_ETL Epidermal Growth Factor, latrophilin and seven transmembrane domain-containing protein 1; member of the class B2 family of seven-transmembrane G protein-coupled receptors. ETL (EGF-TM7-latrophilin-related protein) belongs to Group I adhesion GPCRs, which also include latrophilins (also called lectomedins or latrotoxin receptors). All adhesion GPCRs possess large N-terminal extracellular domains containing multiple structural motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, coupled to a seven-transmembrane domain. ETL, for instance, contains EGF-like repeats, which also present in other EGF-TM7 adhesion GPCRs, such as Cadherin EGF LAG seven-pass G-type receptors (CELSR1-3), EGF-like module receptors (EMR1-3), CD97, and Flamingo. ETL is highly expressed in heart, where developmentally regulated, as well as in normal smooth cells. Furthermore, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR-autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 258 matched cddid_all.tbl CDD cd15438 cd15438 320554 7tmB2_CD97 CD97 antigen, member of the class B2 family of seven-transmembrane G protein-coupled receptors. group II adhesion GPCRs, including the leukocyte cell-surface antigen CD97 and the epidermal growth factor (EGF)-module-containing, mucin-like hormone receptor (EMR1-4), are primarily expressed in cells of the immune system. All EGF-TM7 receptors, which belong to the B2 subfamily B2 of adhesion GPCRs, are members of group II, except for ETL (EGF-TM7-latrophilin related protein), which is classified into group I. Members of the EGF-TM7 receptors are characterized by the presence of varying numbers of N-terminal EGF-like domains, which play critical roles in ligand recognition and cell adhesion, linked by a stalk region to a class B seven-transmembrane domain. In the case of CD97, alternative splicing results in three isoforms possessing either three (EGF1,2,5), four (EGF1,2,3,5) or five (EGF1,2,3,4,5) EGF-like domains. Moreover, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. For example, CD97, which is involved in angiogenesis and the migration and invasion of tumor cells, has been shown to promote cell aggregation in a GPS proteolysis-dependent manner. CD97 is widely expressed on lymphocytes, monocytes, macrophages, dendritic cells, granulocytes and smooth muscle cells as well as in a variety of human tumors including colorectal, gastric, esophageal pancreatic, and thyroid carcinoma. EMR2 shares strong sequence homology with CD97, differing by only six amino acids. However, unlike CD97, EMR2 is not found in those of CD97-positive tumor cells and is not expressed on lymphocytes but instead on monocytes, macrophages and granulocytes. CD97 has three known ligands: CD55, decay-accelerating factor for regulation of complement system; chondroitin sulfate, a glycosaminoglycan found in the extracellular matrix; and the integrin alpha5beta1, which play a role in angiogenesis. Although EMR2 does not effectively interact with CD55, the fourth EGF-like domain of this receptor binds to chondroitin sulfate to mediate cell attachment. 261 matched cddid_all.tbl CDD cd15439 cd15439 320555 7tmB2_EMR epidermal growth factor-like module-containing mucin-like hormone receptors, member of the class B2 family of seven-transmembrane G protein-coupled receptors. group II adhesion GPCRs, including the epidermal growth factor (EGF)-module-containing, mucin-like hormone receptor (EMR1-4) and the leukocyte cell-surface antigen CD97, are primarily expressed in cells of the immune system. All EGF-TM7 receptors, which belong to the B2 subfamily of adhesion GPCRs, are members of group II, except for ETL (EGF-TM7-latrophilin related protein), which is classified into group I. Members of the EGF-TM7 receptors are characterized by the presence of varying number of N-terminal EGF-like domains, which play critical roles in ligand recognition and cell adhesion, linked by a stalk region to a class B seven-transmembrane domain. In the case of EMR2, alternative splicing results in four isoforms possessing either two (EGF1,2), three (EGF1,2,5), four (EGF1,2,3,5) or five (EGF1,2,3,4,5) EGF-like domains. Moreover, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR-autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. EMR2 shares strong sequence homology with CD97, differing by only six amino acids. CD97 is widely expressed on lymphocytes, monocytes, macrophages, dendritic cells, granulocytes and smooth muscle cells as well as in a variety of human tumors including colorectal, gastric, esophageal pancreatic, and thyroid carcinoma. However, unlike CD97, EMR2 is not found in those of CD97-positive tumor cells and is not expressed on lymphocytes but instead on monocytes, macrophages and granulocytes. CD97 has three known ligands: CD55, decay-accelerating factor for regulation of complement system; chondroitin sulfate, a glycosaminoglycan found in the extracellular matrix; and the integrin alpha5beta1, which play a role in angiogenesis. Although EMR2 does not effectively interact with CD55, the fourth EGF-like domain of this receptor binds to chondroitin sulfate to mediate cell attachment. 263 matched cddid_all.tbl CDD cd15440 cd15440 320556 7tmB2_latrophilin-like_invertebrate invertebrate latrophilin-like receptors, member of the class B2 family of seven-transmembrane G protein-coupled receptors. This subgroup includes latrophilin-like proteins that are found in invertebrates such as insects and worms. Latrophilins (also called lectomedins or latrotoxin receptors) belong to Group I adhesion GPCRs, which also include ETL (EGF-TM7-latrophilin-related protein). These receptors are a member of the adhesion family (subclass B2) that belongs to the class B GPCRs. Three subtypes of vertebrate latrophilins have been identified: LPH1 (latrophilin-1), LPH2, and LPH3. The latrophilin-1 is a brain-specific calcium-independent receptor of alpha-latrotoxin, a potent presynaptic neurotoxin from the venom of the black widow spider that induces massive neurotransmitter release from sensory and motor neurons as well as endocrine cells, leading to nerve-terminal degeneration. Latrophilin-2 and -3, although sharing strong sequence homology to latrophilin-1, do not bind alpha-latrotoxin. While latrophilin-3 is also brain specific, latrophilin-2 is ubiquitously distributed. The endogenous ligands for these two receptors are unknown. ETL, a seven transmembrane receptor containing EGF-like repeats is highly expressed in heart, where developmentally regulated, as well as in normal smooth cells. The function of the ETL is unknown. All adhesion GPCRs possess large N-terminal extracellular domains containing multiple structural motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, coupled to a seven-transmembrane domain. In addition, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR-autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 259 matched cddid_all.tbl CDD cd15441 cd15441 320557 7tmB2_CELSR_Adhesion_IV cadherin EGF LAG seven-pass G-type receptors, group IV adhesion GPCRs, member of the class B2 family of seven-transmembrane G protein-coupled receptors. The group IV adhesion GPCRs include the cadherin EGF LAG seven-pass G-type receptors (CELSRs) and their Drosophila homolog Flamingo (also known as Starry night). These receptors are also classified as that belongs to the EGF-TM7 group of subfamily B2 adhesion GPCRs, because they contain EGF-like domains. Functionally, the group IV receptors act as key regulators of many physiological processes such as endocrine cell differentiation, neuronal migration, dendrite growth, axon, guidance, lymphatic vessel and valve formation, and planar cell polarity (PCP) during embryonic development. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. In the case of CELSR/Flamingo/Starry night, their extracellular domains comprise nine cadherin repeats linked to a series of epidermal growth factor (EGF)-like and laminin globular (G)-like domains. The cadherin repeats contain sequence motifs that mediate calcium-dependent cell-cell adhesion by homophilic interactions. Moreover, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. Three mammalian orthologs of Flamingo, Celsr1-3, are widely expressed in the nervous system from embryonic development until the adult stage. Each Celsr exhibits different expression patterns in the developing brain, suggesting that they serve distinct functions. Mutations of CELSR1 cause neural tube defects in the nervous system, while mutations of CELSR2 are associated with coronary heart disease. Moreover, CELSR1 and several other PCP signaling molecules, such as dishevelled, prickle, frizzled, have been shown to be upregulated in B lymphocytes of chronic lymphocytic leukemia patients. Celsr3 is expressed in both the developing and adult mouse brain. It has been functionally implicated in proper neuron migration and axon guidance in the CNS. 254 matched cddid_all.tbl CDD cd15442 cd15442 320558 7tmB2_GPR97 orphan adhesion receptor GPR97, member of the class B2 family of seven-transmembrane G protein-coupled receptors. GPR97 is an orphan receptor that has been classified into the group VIII of adhesion GPCRs. Other members of the Group VII include GPR56, GPR64, GPR112, GPR114, and GPR126. GPR97 is identified as a lymphatic adhesion receptor that is specifically expressed in lymphatic endothelium, but not in blood vascular endothelium, and is shown to regulate migration of lymphatic endothelial cells via the small GTPases RhoA and cdc42. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. Furthermore, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 277 matched cddid_all.tbl CDD cd15443 cd15443 320559 7tmB2_GPR114 orphan adhesion receptor GPR114, member of the class B2 family of seven-transmembrane G protein-coupled receptors. GPR114 is an orphan receptor that has been classified as that belongs to the Group VIII of adhesion GPCRs. Other members of the Group VII include GPR56, GPR64, GPR97, GPR112, and GPR126. GPR114 is mainly found in granulocytes (polymorphonuclear leukocytes), and GPR114-transfected cells induced an increase in cAMP levels via coupling to G(s) protein. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. Furthermore, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 268 matched cddid_all.tbl CDD cd15444 cd15444 320560 7tmB2_GPR64 orphan adhesion receptor GPR64 and related proteins, member of subfamily B2 of the class B secretin-like receptors of seven-transmembrane G protein-coupled receptors. GPR64 is an orphan receptor that has been classified as that belongs to the Group VIII of adhesion GPCRs. Other members of the Group VII include orphan GPCRs such as GPR56, GPR97, GPR112, GPR114, and GPR126. GPR64 is mainly expressed in the epididymis of male reproductive tract, and targeted deletion of GPR64 causes sperm stasis and efferent duct blockage due to abnormal fluid reabsorption, resulting in male infertility. GPR64 is also over-expressed in Ewing's sarcoma (ES), as well as upregulated in other carcinomas from kidney, prostate or lung, and promotes invasiveness and metastasis in ES via the upregulation of placental growth factor (PGF) and matrix metalloproteinase (MMP) 1. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. Furthermore, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 271 matched cddid_all.tbl CDD cd15445 cd15445 320561 7tmB1_CRF-R1 corticotropin-releasing factor receptor 1, member of the class B family of seven-transmembrane G protein-coupled receptors. The vertebrate corticotropin-releasing factor (CRF) receptors are predominantly expressed in central nervous system with high levels in cortex tissue, brain stem, and pituitary. They have two isoforms as a result of alternative splicing of the same receptor gene: CRF-R1 and CRF-R2, which differ in tissue distribution and ligand binding affinities. Recently, a third CRF receptor (CRF-R3) has been identified in catfish pituitary. The catfish CRF-R1 is highly homologous to CRF-R3. CRF is a 41-amino acid neuropeptide that plays a central role in coordinating neuroendocrine, behavioral, and autonomic responses to stress by acting as the primary neuroregulator of the hypothalamic-pituitary-adrenal axis, which controls the levels of cortisol and other stress related hormones. In addition, the CRF family of neuropeptides also includes structurally related peptides such as mammalian urocortin, fish urotensin I, and frog sauvagine. The actions of CRF and CRF-related peptides are mediated through specific binding to CRF-R1 and CRF-R2. CRF and urocortin 1 bind and activate mammalian CRF-R1 with similar high affinities. By contrast, urocortin 2 and urocortin 3 do not bind to CRF-R1 or stimulate CRF-R1-mediated cAMP formation. Urocortin 1 also shows high affinity for mammalian CRF-R2, whereas CRF has significantly lower affinity for this receptor. These evidence suggest that urocortin 1 is an endogenous ligand for CRF-R1 and CRF-R2. The CRF receptors are members of the B1 subfamily of class B GPCRs, also referred to as secretin-like receptor family, which includes receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, glucagon, glucagon-like peptide (GLP), calcitonin gene-related peptide, and parathyroid hormone (PTH). These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. All members of the B1 subfamily preferentially couple to G proteins of G(s) family, which positively stimulate adenylate cyclase, leading to increased intracellular cAMP formation and calcium influx. However, depending on its cellular location and function, CRF receptors can activate multiple G proteins, which can in turn stimulate different second messenger pathways. 265 matched cddid_all.tbl CDD cd15446 cd15446 320562 7tmB1_CRF-R2 corticotropin-releasing factor receptor 2, member of the class B family of seven-transmembrane G protein-coupled receptors. The vertebrate corticotropin-releasing factor (CRF) receptors are predominantly expressed in central nervous system with high levels in cortex tissue, brain stem, and pituitary. They have two isoforms as a result of alternative splicing of the same receptor gene: CRF-R1 and CRF-R2, which differ in tissue distribution and ligand binding affinities. Recently, a third CRF receptor (CRF-R3) has been identified in catfish pituitary. The catfish CRF-R1 is highly homologous to CRF-R3. CRF is a 41-amino acid neuropeptide that plays a central role in coordinating neuroendocrine, behavioral, and autonomic responses to stress by acting as the primary neuroregulator of the hypothalamic-pituitary-adrenal axis, which controls the levels of cortisol and other stress related hormones. In addition, the CRF family of neuropeptides also includes structurally related peptides such as mammalian urocortin, fish urotensin I, and frog sauvagine. The actions of CRF and CRF-related peptides are mediated through specific binding to CRF-R1 and CRF-R2. CRF and urocortin 1 bind and activate mammalian CRF-R1 with similar high affinities. By contrast, urocortin 2 and urocortin 3 do not bind to CRF-R1 or stimulate CRF-R1-mediated cAMP formation. Urocortin 1 also shows high affinity for mammalian CRF-R2, whereas CRF has significantly lower affinity for this receptor. These evidence suggest that urocortin 1 is an endogenous ligand for CRF-R1 and CRF-R2. The CRF receptors are members of the B1 subfamily of class B GPCRs, also referred to as secretin-like receptor family, which includes receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, glucagon, glucagon-like peptide (GLP), calcitonin gene-related peptide, and parathyroid hormone (PTH). These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. All members of the B1 subfamily preferentially couple to G proteins of G(s) family, which positively stimulate adenylate cyclase, leading to increased intracellular cAMP formation and calcium influx. However, depending on its cellular location and function, CRF receptors can activate multiple G proteins, which can in turn stimulate different second messenger pathways. 264 matched cddid_all.tbl CDD cd15447 cd15447 320563 7tmC_mGluR2 metabotropic glutamate receptor 2 in group 2, member of the class C family of seven-transmembrane G protein-coupled receptors. The metabotropic glutamate receptors (mGluRs) in group 2 include mGluR 2 and 3. They are homodimeric class C G-protein coupled receptors which are activated by glutamate, the major excitatory neurotransmitter of the CNS. mGluRs are involved in regulating neuronal excitability and synaptic transmission via intracellular activation of second messenger signaling pathways. While the ionotropic glutamate receptor subtypes (AMPA, NMDA, and kainite) mediate fast excitatory postsynaptic transmission, mGluRs are known to mediate slower excitatory postsynaptic responses and to be involved in synaptic plasticity in the mammalian brain. In addition to seven-transmembrane helices, the class C GPCRs are characterized by a large N-terminal extracellular Venus flytrap-like domain, which is composed of two adjacent lobes separated by a cleft which binds an endogenous ligand. Moreover, they exist as either homo- or heterodimers, which are essential for their function. For instance, mGluRs form homodimers via interactions between the N-terminal Venus flytrap domains and the intermolecular disulphide bonds between cysteine residues located in the cysteine-rich domain (CRD). At least eight different subtypes of metabotropic receptors (mGluR1-8) have been identified and further classified into three groups based on their sequence homology, pharmacological properties, and signaling pathways. Group 1 (mGluR1 and mGluR5) receptors are predominantly located postsynaptically on neurons and are involved in long-term synaptic plasticity in the brain, including long-term potentiation (LTP) in the hippocampus and long-term depression (LTD) in the cerebellum. They are coupled to G(q/11) proteins, thereby activating phospholipase C to generate inositol-1,4,5-triphosphate (IP3) and diacyglycerol (DAG), which in turn lead to Ca2+ release and protein kinase C activation, respectively. Group 1 mGluR expression is shown to be strongly upregulated in animal models of epilepsy, brain injury, inflammatory, and neuropathic pain, as well as in patients with amyotrophic lateral sclerosis or multiple sclerosis. Group 2 (mGluR2 and mGluR3) and 3 (mGluR4, mGluR6, mGluR7, and mGluR8) receptors are predominantly localized presynaptically in the active region of neurotransmitter release. They are coupled to G(i/o) proteins, which leads to inhibition of adenylate cyclase activity and cAMP formation, and consequently to a decrease in protein kinase A (PKA) activity. Ultimately, activation of these receptors leads to inhibition of neurotransmitter release such as glutamate and GABA via inhibition of Ca2+ channels and activation of K+ channels. Furthermore, while activation of Group 1 mGluRs increases NMDA (N-methyl-D-aspartate) receptor activity and risk of neurotoxicity, Group 2 and 3 mGluRs decrease NMDA receptor activity and prevent neurotoxicity. 254 matched cddid_all.tbl CDD cd15448 cd15448 320564 7tmC_mGluR3 metabotropic glutamate receptor 3 in group 2, member of the class C family of seven-transmembrane G protein-coupled receptors. The metabotropic glutamate receptors (mGluRs) in group 2 include mGluR 2 and 3. They are homodimeric class C G-protein coupled receptors which are activated by glutamate, the major excitatory neurotransmitter of the CNS. mGluRs are involved in regulating neuronal excitability and synaptic transmission via intracellular activation of second messenger signaling pathways. While the ionotropic glutamate receptor subtypes (AMPA, NMDA, and kainite) mediate fast excitatory postsynaptic transmission, mGluRs are known to mediate slower excitatory postsynaptic responses and to be involved in synaptic plasticity in the mammalian brain. In addition to seven-transmembrane helices, the class C GPCRs are characterized by a large N-terminal extracellular Venus flytrap-like domain, which is composed of two adjacent lobes separated by a cleft which binds an endogenous ligand. Moreover, they exist as either homo- or heterodimers, which are essential for their function. For instance, mGluRs form homodimers via interactions between the N-terminal Venus flytrap domains and the intermolecular disulphide bonds between cysteine residues located in the cysteine-rich domain (CRD). At least eight different subtypes of metabotropic receptors (mGluR1-8) have been identified and further classified into three groups based on their sequence homology, pharmacological properties, and signaling pathways. Group 1 (mGluR1 and mGluR5) receptors are predominantly located postsynaptically on neurons and are involved in long-term synaptic plasticity in the brain, including long-term potentiation (LTP) in the hippocampus and long-term depression (LTD) in the cerebellum. They are coupled to G(q/11) proteins, thereby activating phospholipase C to generate inositol-1,4,5-triphosphate (IP3) and diacyglycerol (DAG), which in turn lead to Ca2+ release and protein kinase C activation, respectively. Group 1 mGluR expression is shown to be strongly upregulated in animal models of epilepsy, brain injury, inflammatory, and neuropathic pain, as well as in patients with amyotrophic lateral sclerosis or multiple sclerosis. Group 2 (mGluR2 and mGluR3) and 3 (mGluR4, mGluR6, mGluR7, and mGluR8) receptors are predominantly localized presynaptically in the active region of neurotransmitter release. They are coupled to G(i/o) proteins, which leads to inhibition of adenylate cyclase activity and cAMP formation, and consequently to a decrease in protein kinase A (PKA) activity. Ultimately, activation of these receptors leads to inhibition of neurotransmitter release such as glutamate and GABA via inhibition of Ca2+ channels and activation of K+ channels. Furthermore, while activation of Group 1 mGluRs increases NMDA (N-methyl-D-aspartate) receptor activity and risk of neurotoxicity, Group 2 and 3 mGluRs decrease NMDA receptor activity and prevent neurotoxicity. 254 matched cddid_all.tbl CDD cd15449 cd15449 320565 7tmC_mGluR1 metabotropic glutamate receptor 1 in group 1, member of the class C family of seven-transmembrane G protein-coupled receptors. Group 1 mGluRs includes mGluR1 and mGluR5, as well as their closely related invertebrate receptors. They are homodimeric class C G-protein coupled receptors which are activated by glutamate, the major excitatory neurotransmitter of the CNS. mGluRs are involved in regulating neuronal excitability and synaptic transmission via intracellular activation of second messenger signaling pathways. While the ionotropic glutamate receptor subtypes (AMPA, NMDA, and kainite) mediate fast excitatory postsynaptic transmission, mGluRs are known to mediate slower excitatory postsynaptic responses and to be involved in synaptic plasticity in the mammalian brain. In addition to seven-transmembrane helices, the class C GPCRs are characterized by a large N-terminal extracellular Venus flytrap-like domain, which is composed of two adjacent lobes separated by a cleft which binds an endogenous ligand. Moreover, they exist as either homo- or heterodimers, which are essential for their function. For instance, mGluRs form homodimers via interactions between the N-terminal Venus flytrap domains and the intermolecular disulphide bonds between cysteine residues located in the cysteine-rich domain (CRD). At least eight different subtypes of metabotropic receptors (mGluR1-8) have been identified and further classified into three groups based on their sequence homology, pharmacological properties, and signaling pathways. Group 1 (mGluR1 and mGluR5) receptors are predominantly located postsynaptically on neurons and are involved in long-term synaptic plasticity in the brain, including long-term potentiation (LTP) in the hippocampus and long-term depression (LTD) in the cerebellum. They are coupled to G(q/11) proteins, thereby activating phospholipase C to generate inositol-1,4,5-triphosphate (IP3) and diacyglycerol (DAG), which in turn lead to Ca2+ release and protein kinase C activation, respectively. Group 1 mGluR expression is shown to be strongly upregulated in animal models of epilepsy, brain injury, inflammatory, and neuropathic pain, as well as in patients with amyotrophic lateral sclerosis or multiple sclerosis. Group 2 (mGluR2 and mGluR3) and 3 (mGluR4, mGluR6, mGluR7, and mGluR8) receptors are predominantly localized presynaptically in the active region of neurotransmitter release. They are coupled to G(i/o) proteins, which leads to inhibition of adenylate cyclase activity and cAMP formation, and consequently to a decrease in protein kinase A (PKA) activity. Ultimately, activation of these receptors leads to inhibition of neurotransmitter release such as glutamate and GABA via inhibition of Ca2+ channels and activation of K+ channels. Furthermore, while activation of Group 1 mGluRs increases NMDA (N-methyl-D-aspartate) receptor activity and risk of neurotoxicity, Group 2 and 3 mGluRs decrease NMDA receptor activity and prevent neurotoxicity. 250 matched cddid_all.tbl CDD cd15450 cd15450 320566 7tmC_mGluR5 metabotropic glutamate receptor 5 in group 1, member of the class C family of seven-transmembrane G protein-coupled receptors. Group 1 mGluRs includes mGluR1 and mGluR5, as well as their closely related invertebrate receptors. They are homodimeric class C G-protein coupled receptors which are activated by glutamate, the major excitatory neurotransmitter of the CNS. mGluRs are involved in regulating neuronal excitability and synaptic transmission via intracellular activation of second messenger signaling pathways. While the ionotropic glutamate receptor subtypes (AMPA, NMDA, and kainite) mediate fast excitatory postsynaptic transmission, mGluRs are known to mediate slower excitatory postsynaptic responses and to be involved in synaptic plasticity in the mammalian brain. In addition to seven-transmembrane helices, the class C GPCRs are characterized by a large N-terminal extracellular Venus flytrap-like domain, which is composed of two adjacent lobes separated by a cleft which binds an endogenous ligand. Moreover, they exist as either homo- or heterodimers, which are essential for their function. For instance, mGluRs form homodimers via interactions between the N-terminal Venus flytrap domains and the intermolecular disulphide bonds between cysteine residues located in the cysteine-rich domain (CRD). At least eight different subtypes of metabotropic receptors (mGluR1-8) have been identified and further classified into three groups based on their sequence homology, pharmacological properties, and signaling pathways. Group 1 (mGluR1 and mGluR5) receptors are predominantly located postsynaptically on neurons and are involved in long-term synaptic plasticity in the brain, including long-term potentiation (LTP) in the hippocampus and long-term depression (LTD) in the cerebellum. They are coupled to G(q/11) proteins, thereby activating phospholipase C to generate inositol-1,4,5-triphosphate (IP3) and diacyglycerol (DAG), which in turn lead to Ca2+ release and protein kinase C activation, respectively. Group 1 mGluR expression is shown to be strongly upregulated in animal models of epilepsy, brain injury, inflammatory, and neuropathic pain, as well as in patients with amyotrophic lateral sclerosis or multiple sclerosis. Group 2 (mGluR2 and mGluR3) and 3 (mGluR4, mGluR6, mGluR7, and mGluR8) receptors are predominantly localized presynaptically in the active region of neurotransmitter release. They are coupled to G(i/o) proteins, which leads to inhibition of adenylate cyclase activity and cAMP formation, and consequently to a decrease in protein kinase A (PKA) activity. Ultimately, activation of these receptors leads to inhibition of neurotransmitter release such as glutamate and GABA via inhibition of Ca2+ channels and activation of K+ channels. Furthermore, while activation of Group 1 mGluRs increases NMDA (N-methyl-D-aspartate) receptor activity and risk of neurotoxicity, Group 2 and 3 mGluRs decrease NMDA receptor activity and prevent neurotoxicity. 250 matched cddid_all.tbl CDD cd15451 cd15451 320567 7tmC_mGluR7 metabotropic glutamate receptor 7 in group 3, member of the class C family of seven-transmembrane G protein-coupled receptors. The receptors in group 3 include mGluRs 4, 6, 7, and 8. They are homodimeric class C G-protein coupled receptors which are activated by glutamate, the major excitatory neurotransmitter of the CNS. mGluRs are involved in regulating neuronal excitability and synaptic transmission via intracellular activation of second messenger signaling pathways. While the ionotropic glutamate receptor subtypes (AMPA, NMDA, and kainite) mediate fast excitatory postsynaptic transmission, mGluRs are known to mediate slower excitatory postsynaptic responses and to be involved in synaptic plasticity in the mammalian brain. In addition to seven-transmembrane helices, the class C GPCRs are characterized by a large N-terminal extracellular Venus flytrap-like domain, which is composed of two adjacent lobes separated by a cleft which binds an endogenous ligand. Moreover, they exist as either homo- or heterodimers, which are essential for their function. For instance, mGluRs form homodimers via interactions between the N-terminal Venus flytrap domains and the intermolecular disulphide bonds between cysteine residues located in the cysteine-rich domain (CRD). At least eight different subtypes of metabotropic receptors (mGluR1-8) have been identified and further classified into three groups based on their sequence homology, pharmacological properties, and signaling pathways. Group 1 (mGluR1 and mGluR5) receptors are predominantly located postsynaptically on neurons and are involved in long-term synaptic plasticity in the brain, including long-term potentiation (LTP) in the hippocampus and long-term depression (LTD) in the cerebellum. They are coupled to G(q/11) proteins, thereby activating phospholipase C to generate inositol-1,4,5-triphosphate (IP3) and diacyglycerol (DAG), which in turn lead to Ca2+ release and protein kinase C activation, respectively. Group 1 mGluR expression is shown to be strongly upregulated in animal models of epilepsy, brain injury, inflammatory, and neuropathic pain, as well as in patients with amyotrophic lateral sclerosis or multiple sclerosis. Group 2 (mGluR2 and mGluR3) and 3 (mGluR4, mGluR6, mGluR7, and mGluR8) receptors are predominantly localized presynaptically in the active region of neurotransmitter release. They are coupled to G(i/o) proteins, which leads to inhibition of adenylate cyclase activity and cAMP formation, and consequently to a decrease in protein kinase A (PKA) activity. Ultimately, activation of these receptors leads to inhibition of neurotransmitter release such as glutamate and GABA via inhibition of Ca2+ channels and activation of K+ channels. Furthermore, while activation of Group 1 mGluRs increases NMDA (N-methyl-D-aspartate) receptor activity and risk of neurotoxicity, Group 2 and 3 mGluRs decrease NMDA receptor activity and prevent neurotoxicity. 307 matched cddid_all.tbl CDD cd15452 cd15452 320568 7tmC_mGluR4 metabotropic glutamate receptor 4 in group 3, member of the class C family of seven-transmembrane G protein-coupled receptors. The receptors in group 3 include mGluRs 4, 6, 7, and 8. They are homodimeric class C G-protein coupled receptors which are activated by glutamate, the major excitatory neurotransmitter of the CNS. mGluRs are involved in regulating neuronal excitability and synaptic transmission via intracellular activation of second messenger signaling pathways. While the ionotropic glutamate receptor subtypes (AMPA, NMDA, and kainite) mediate fast excitatory postsynaptic transmission, mGluRs are known to mediate slower excitatory postsynaptic responses and to be involved in synaptic plasticity in the mammalian brain. In addition to seven-transmembrane helices, the class C GPCRs are characterized by a large N-terminal extracellular Venus flytrap-like domain, which is composed of two adjacent lobes separated by a cleft which binds an endogenous ligand. Moreover, they exist as either homo- or heterodimers, which are essential for their function. For instance, mGluRs form homodimers via interactions between the N-terminal Venus flytrap domains and the intermolecular disulphide bonds between cysteine residues located in the cysteine-rich domain (CRD). At least eight different subtypes of metabotropic receptors (mGluR1-8) have been identified and further classified into three groups based on their sequence homology, pharmacological properties, and signaling pathways. Group 1 (mGluR1 and mGluR5) receptors are predominantly located postsynaptically on neurons and are involved in long-term synaptic plasticity in the brain, including long-term potentiation (LTP) in the hippocampus and long-term depression (LTD) in the cerebellum. They are coupled to G(q/11) proteins, thereby activating phospholipase C to generate inositol-1,4,5-triphosphate (IP3) and diacyglycerol (DAG), which in turn lead to Ca2+ release and protein kinase C activation, respectively. Group 1 mGluR expression is shown to be strongly upregulated in animal models of epilepsy, brain injury, inflammatory, and neuropathic pain, as well as in patients with amyotrophic lateral sclerosis or multiple sclerosis. Group 2 (mGluR2 and mGluR3) and 3 (mGluR4, mGluR6, mGluR7, and mGluR8) receptors are predominantly localized presynaptically in the active region of neurotransmitter release. They are coupled to G(i/o) proteins, which leads to inhibition of adenylate cyclase activity and cAMP formation, and consequently to a decrease in protein kinase A (PKA) activity. Ultimately, activation of these receptors leads to inhibition of neurotransmitter release such as glutamate and GABA via inhibition of Ca2+ channels and activation of K+ channels. Furthermore, while activation of Group 1 mGluRs increases NMDA (N-methyl-D-aspartate) receptor activity and risk of neurotoxicity, Group 2 and 3 mGluRs decrease NMDA receptor activity and prevent neurotoxicity. 327 matched cddid_all.tbl CDD cd15453 cd15453 320569 7tmC_mGluR6 metabotropic glutamate receptor 6 in group 3, member of the class C family of seven-transmembrane G protein-coupled receptors. The receptors in group 3 include mGluRs 4, 6, 7, and 8. They are homodimeric class C G-protein coupled receptors which are activated by glutamate, the major excitatory neurotransmitter of the CNS. mGluRs are involved in regulating neuronal excitability and synaptic transmission via intracellular activation of second messenger signaling pathways. While the ionotropic glutamate receptor subtypes (AMPA, NMDA, and kainite) mediate fast excitatory postsynaptic transmission, mGluRs are known to mediate slower excitatory postsynaptic responses and to be involved in synaptic plasticity in the mammalian brain. In addition to seven-transmembrane helices, the class C GPCRs are characterized by a large N-terminal extracellular Venus flytrap-like domain, which is composed of two adjacent lobes separated by a cleft which binds an endogenous ligand. Moreover, they exist as either homo- or heterodimers, which are essential for their function. For instance, mGluRs form homodimers via interactions between the N-terminal Venus flytrap domains and the intermolecular disulphide bonds between cysteine residues located in the cysteine-rich domain (CRD). At least eight different subtypes of metabotropic receptors (mGluR1-8) have been identified and further classified into three groups based on their sequence homology, pharmacological properties, and signaling pathways. Group 1 (mGluR1 and mGluR5) receptors are predominantly located postsynaptically on neurons and are involved in long-term synaptic plasticity in the brain, including long-term potentiation (LTP) in the hippocampus and long-term depression (LTD) in the cerebellum. They are coupled to G(q/11) proteins, thereby activating phospholipase C to generate inositol-1,4,5-triphosphate (IP3) and diacyglycerol (DAG), which in turn lead to Ca2+ release and protein kinase C activation, respectively. Group 1 mGluR expression is shown to be strongly upregulated in animal models of epilepsy, brain injury, inflammatory, and neuropathic pain, as well as in patients with amyotrophic lateral sclerosis or multiple sclerosis. Group 2 (mGluR2 and mGluR3) and 3 (mGluR4, mGluR6, mGluR7, and mGluR8) receptors are predominantly localized presynaptically in the active region of neurotransmitter release. They are coupled to G(i/o) proteins, which leads to inhibition of adenylate cyclase activity and cAMP formation, and consequently to a decrease in protein kinase A (PKA) activity. Ultimately, activation of these receptors leads to inhibition of neurotransmitter release such as glutamate and GABA via inhibition of Ca2+ channels and activation of K+ channels. Furthermore, while activation of Group 1 mGluRs increases NMDA (N-methyl-D-aspartate) receptor activity and risk of neurotoxicity, Group 2 and 3 mGluRs decrease NMDA receptor activity and prevent neurotoxicity. 273 matched cddid_all.tbl CDD cd15454 cd15454 320570 7tmC_mGluR8 metabotropic glutamate receptor 8 in group 3, member of the class C family of seven-transmembrane G protein-coupled receptors. The receptors in group 3 include mGluRs 4, 6, 7, and 8. They are homodimeric class C G-protein coupled receptors which are activated by glutamate, the major excitatory neurotransmitter of the CNS. mGluRs are involved in regulating neuronal excitability and synaptic transmission via intracellular activation of second messenger signaling pathways. While the ionotropic glutamate receptor subtypes (AMPA, NMDA, and kainite) mediate fast excitatory postsynaptic transmission, mGluRs are known to mediate slower excitatory postsynaptic responses and to be involved in synaptic plasticity in the mammalian brain. In addition to seven-transmembrane helices, the class C GPCRs are characterized by a large N-terminal extracellular Venus flytrap-like domain, which is composed of two adjacent lobes separated by a cleft which binds an endogenous ligand. Moreover, they exist as either homo- or heterodimers, which are essential for their function. For instance, mGluRs form homodimers via interactions between the N-terminal Venus flytrap domains and the intermolecular disulphide bonds between cysteine residues located in the cysteine-rich domain (CRD). At least eight different subtypes of metabotropic receptors (mGluR1-8) have been identified and further classified into three groups based on their sequence homology, pharmacological properties, and signaling pathways. Group 1 (mGluR1 and mGluR5) receptors are predominantly located postsynaptically on neurons and are involved in long-term synaptic plasticity in the brain, including long-term potentiation (LTP) in the hippocampus and long-term depression (LTD) in the cerebellum. They are coupled to G(q/11) proteins, thereby activating phospholipase C to generate inositol-1,4,5-triphosphate (IP3) and diacyglycerol (DAG), which in turn lead to Ca2+ release and protein kinase C activation, respectively. Group 1 mGluR expression is shown to be strongly upregulated in animal models of epilepsy, brain injury, inflammatory, and neuropathic pain, as well as in patients with amyotrophic lateral sclerosis or multiple sclerosis. Group 2 (mGluR2 and mGluR3) and 3 (mGluR4, mGluR6, mGluR7, and mGluR8) receptors are predominantly localized presynaptically in the active region of neurotransmitter release. They are coupled to G(i/o) proteins, which leads to inhibition of adenylate cyclase activity and cAMP formation, and consequently to a decrease in protein kinase A (PKA) activity. Ultimately, activation of these receptors leads to inhibition of neurotransmitter release such as glutamate and GABA via inhibition of Ca2+ channels and activation of K+ channels. Furthermore, while activation of Group 1 mGluRs increases NMDA (N-methyl-D-aspartate) receptor activity and risk of neurotoxicity, Group 2 and 3 mGluRs decrease NMDA receptor activity and prevent neurotoxicity. 311 matched cddid_all.tbl CDD cd15457 cd15457 271319 NADAR Escherichia coli swarming motility protein YbiA and related proteins. This family of uncharacterized domains was initially classified as Domain of Unknown Function (DUF1768). It contains members such as the E. coli swarming motility protein YbiA. Mutations in YbiA cause defects in Escherichia coli swarming, but not necessarily in motility. More recently, this family has been predicted to be involved in NAD-utilizing pathways, likely to act on ADP-ribose derivatives, and has been named the NADAR (NAD and ADP-ribose) superfamily. 148 matched cddid_all.tbl CDD cd15464 cd15464 271230 HN_like Haemagglutinin-neuraminidase (HN) of paramyxoviridae and similar proteins. Most paramyxoviridae have two membrane-anchored glycoproteins that mediate entry of the virus into the host cell. The protein characterized by this model is called hemagglutinin-neuraminidase (HN), hemagglutinin glycoprotein (H), or glycoprotein (G). Typically it has a variety of functions during viral infection; it participates in virus attachment to host cells, may cleave sialic acid off host oligosaccharides, and has a stimulating effect on membrane fusion during the entry of the virus into the host cell. 391 matched cddid_all.tbl CDD cd15465 cd15465 275386 bS6_mito Mitochondrial Ribosomal Protein (MRP) S6. bS6_MRPS6 is one of the proteins of the small subunit of the mitochondrial ribosome. Mitochondrial and chloroplastic ribosomes are similar to bacterial ribosomes. The ribosome is a ribonucleoprotein organelle that decodes the genetic information in messenger RNA and forms peptide bonds to synthesize the corresponding polypeptide. Ribosomes consist of a large and a small subunit, which assemble during the initiation stage of protein synthesis. Prokaryotic ribosomes consist of three molecules of RNA and more than 50 proteins. The small subunits of bacterial and eukaryotic ribosomes have the same overall shapes (with structural elements described as head, body, platform, beak and shoulder). Mitochondrial and chloroplastic ribosomes synthesize proteins that are involved in oxidative phosphorylation (ATP generation) and photosynthesis. bS6_MRPS6 is one of the fourteen mitochondrial ribosomal proteins that is known to have significant sequence homology with their bacterial counterpart. 95 matched cddid_all.tbl CDD cd15466 cd15466 271318 CLU-central An uncharacterized central domain of CLU mitochondrial proteins. Mutations in the mitochondrial CLU proteins have been shown to result in clustered mitochondria. CLU proteins include Saccharomyces cerevisiae clustered mitochondria protein (Clu1p, alias translation initiation factor 31/TIF31p), Dictyostelium discoideum clustered mitochondria protein homolog (CluA), Caenorhabditis elegans clustered mitochondria protein homolog (CLUH/ Protein KIAA0664), Drosophila clueless (alias clustered mitochondria protein homolog), Arabidopsis clustered mitochondria protein (CLU, alias friendly mitochondria protein/FMT), and human clustered mitochondria protein homolog (CLUH). Dictyostelium CluA is involved in mitochondrial dynamics and is necessary for both, mitochondrial fission and fusion. Drosophila clueless is essential for cytoplasmic localization and function of cellular mitochondria. The Drosophila clu gene interacts genetically with parkin (park, the Drosophila ortholog of a human gene responsible for many familial cases of Parkinson's disease). Arabidopsis CLU/FMT is required for correct mitochondrial distribution and morphology. The specific role CLU proteins play in mitochondrial processes in not yet known. In an early study, S. cerevisiae Clu1/TIF31p was reported as sometimes being associated with the elF3 translation initiation factor. The authors noted, however, that its tentative assignment as a subunit of elf3 was uncertain, and to date there has been no direct evidence for a role of this protein in translation. 159 matched cddid_all.tbl CDD cd15467 cd15467 271231 MV-h Measles virus hemagglutinin. The hemagglutinin (H) of measles virus plays several roles during viral infection; it participates in virus attachment to host cells via binding to a proteinaceous receptor and it has a stimulating effect on membrane fusion during the entry of the virus into the host cell by interacting with the fusion protein F. This model characterizes the globular ectodomain of measles hemagglutinin, minus the stalk region. Receptors for measles virus have been identified as the signaling lymphocyte activation molecule (SLAM, in particular its distal ectodomain), CD46, and nectin-4 in epithelial cells. 415 matched cddid_all.tbl CDD cd15468 cd15468 271232 HeV-G Glycoprotein G, or hemagglutinin-neuraminidase of Hendravirus and Nipah virus. The glycoprotein (G) of Nendravirus and Nipah virus has a variety of functions during viral infection; it participates in virus attachment to host cells and has a stimulating effect on membrane fusion during the entry of the virus into the host cell. This models characterizes the globular ectodomain of glycoprotein G. The receptors for Hendravirus and Nipah virus have been identified as ephrin B2 (EFNB2) and ephrin B3 (EFNB3). 413 matched cddid_all.tbl CDD cd15469 cd15469 271233 HN Hemagglutinin-neuraminidase (HN) of parainfluenza virus 5, Newcastle disease virus, and related paramyxoviridiae. The hemagglutinin-neuraminidase (HN) found in this family of viruses has a variety of functions during viral infection; it participates in virus attachment to host cells, cleaves sialic acid off host oligosaccharides, and has a stimulating effect on membrane fusion during the entry of the virus into the host cell. This model characterizes the global ectodomain of HN. Hemagglutinin-neuraminidase ectodomains of these viruses attaches the virion to sialic acid receptors on host cells; the neuraminidase cleaves sialic acid moieties from host cell molecules as well as virus particles, this removal may happen in the trans Golgi network. 408 matched cddid_all.tbl CDD cd15470 cd15470 271254 Myo5_CBD Cargo binding domain of myosin 5. Class V myosins are well studied unconventional myosins, represented by three paralogs (Myo5a,b,c) in vertebrates. Their C-terminal cargo binding domains (CBDs) are important for the binding of a diverse set of cargos, including membrane vesicles, organelles, proteins and mRNA. The MyoV-CBDs directly interact with several adaptor proteins, in case of Myo5a, melanophilin (MLPH), Rab interacting lysosomal protein-like 2 (RILPL2), and granuphilin, and in case of Myo5b, Rab11-family interacting protein 2. 332 matched cddid_all.tbl CDD cd15471 cd15471 271255 Myo5p-like_CBD_afadin cargo binding domain of myosin 5-like of afadin. Afadin is an actin filament (F-actin) and Rap1 small G protein-binding protein, found in cadherin-based adherens junctions in epithelial cells, endothelial cells, and fibroblasts. It interacts with cell adhesion molecules and signaling molecules and plays a role in the formation of cell junctions, cell polarization, migration, survival, proliferation, and differentiation. Afadin is a multi domain protein, that contains beside a myosin5-like CBD, two Ras-associated domains, a forkhead-associated domain, a PDZ domain, three proline-rich domains, and an F-actin-binding domain. 322 matched cddid_all.tbl CDD cd15472 cd15472 271256 Myo5p-like_CBD_Rasip1 cargo binding domain of myosin 5-like of Ras-interacting protein 1. Ras-interacting protein 1 (Rasip1 or RAIN) is an effector of the small G protein Rap1 and plays an important role in endothelial junction stabilization. Rasip1, like afadin, is a multi domain protein, that contains beside a myosin5-like CBD, a Ras-associated domain and a PDZ domain. 366 matched cddid_all.tbl CDD cd15473 cd15473 271257 Myo5p-like_CBD_DIL_ANK cargo binding domain of myosin 5-like of dil and ankyrin domain containing protein. DIL and ankyrin domain-containing protein are a group of fungal proteins that contain a domain homologous to the cargo binding domain of class V myosins and ankyrin repeats. Their function is unknown. 316 matched cddid_all.tbl CDD cd15474 cd15474 271258 Myo5p-like_CBD_fungal cargo binding domain of fungal myosin V -like proteins. Yeast myosin V travels along actin cables, actin filaments that are bundled by fimbrin, in the presence of tropomyosin. This is in contrast to the other vertebrate class V myosins. Like other class V myosins, fungal myosin 2 and 4 contain a C-terminal cargo binding domain. In case of Myo4 it has been shown to bind to the adapter protein She3p (Swi5p-dependent HO expression 3), which in turn anchors myosin 4 to its cargos, zip-coded mRNP (messenger ribonucleoprotein particles) and tER (tubular endoplasmic reticulum). Myo 2 binds to Vac17, vacuole-specific cargo adaptor, and Mmr1, mitochondria-specific cargo adaptor. Both adaptors bind competitivly at the same site. 352 matched cddid_all.tbl CDD cd15475 cd15475 271259 MyosinXI_CBD cargo binding domain of myosin XI. Class XI myosins are a plant specific group, homologous to class V myosins. C-terminal domain of Arabidopsis myosin XI has been shown to be homologous to the cargo-binding domain of yeast myosin V myo2p, which targets myosin to vacuole- and mitochondria, as well as secretory vesicle. 326 matched cddid_all.tbl CDD cd15476 cd15476 271260 Myo5c_CBD Cargo binding domain of myosin 5C. Class V myosins are well studied unconventional myosins, represented by three paralogs (Myo5a,b,c) in vertebrates. Their C-terminal cargo binding domains (CBDs) are important for the binding of a diverse set of cargos, including membrane vesicles, organelles, proteins and mRNA. The MyoV-CBDs directly interact with several adaptor proteins.MyoVb and myoVc areprimarily expressed in epithelial cells, and have been implicated as motors involved in recycling endosomes. 332 matched cddid_all.tbl CDD cd15477 cd15477 271261 Myo5b_CBD Cargo binding domain of myosin 5b. Class V myosins are well studied unconventional myosins, represented by three paralogs (Myo5a,b,c) in vertebrates. Their C-terminal cargo binding domains (CBDs) are important for the binding of a diverse set of cargos, including membrane vesicles, organelles, proteins and mRNA. They interact with several adaptor proteins, in case of Myo5b-CBD, Rab11-family interacting protein 2. 372 matched cddid_all.tbl CDD cd15478 cd15478 271262 Myo5a_CBD Cargo binding domain of myosin 5a. Class V myosins are well studied unconventional myosins, represented by three paralogs (Myo5a,b,c) in vertebrates. Their C-terminal cargo binding domains (CBDs) are important for the binding of a diverse set of cargos, including membrane vesicles, organelles, proteins and mRNA. They interact with several adaptor proteins, in case of Myo5a-CBD, melanophilin (MLPH), Rab interacting lysosomal protein-like 2 (RILPL2), and granuphilin. Mutations in human Myo5a (many of which map to the cargo binding domain) lead to Griscelli syndrome, a severe neurological disease. 375 matched cddid_all.tbl CDD cd15479 cd15479 271263 fMyo4p_CBD cargo binding domain of fungal myosin 4. Yeast myosin V travels along actin cables, actin filaments that are bundled by fimbrin, in the presence of tropomyosin. This is in contrast to the other vertebrate class V myosins. Like other class V myosins, fungal myosin 2 and 4 contain a C-terminal cargo binding domain. In case of Myo4 it has been shown to bind to the adapter protein She3p (Swi5p-dependent HO expression 3), which in turn anchors myosin 4 to its cargos, zip-coded mRNP (messenger ribonucleoprotein particles) and tER (tubular endoplasmic reticulum). 329 matched cddid_all.tbl CDD cd15480 cd15480 271264 fMyo2p_CBD cargo binding domain of fungal myosin 2. Yeast myosin V travels along actin cables, actin filaments that are bundled by fimbrin, in the presence of tropomyosin. This is in contrast to the other vertebrate class V myosins. Like other class V myosins, fungal myosin 2 and 4 contain a C-terminal cargo binding domain. Myo 2 binds to Vac17, vacuole-specific cargo adaptor, and Mmr1, mitochondria-specific cargo adaptor. Both adaptors bind competitivly at the same site. 363 matched cddid_all.tbl CDD cd15481 cd15481 271252 SRP68-RBD RNA-binding domain of signal recognition particle subunit 68. Signal recognition particles (SRPs) are ribonucleoprotein complexes that target particular nascent pre-secretory proteins to the endoplasmic reticulum. SRP68 is one of the two largest proteins found in SRPs (the other being SRP72), and it forms a heterodimer with SRP72. Heterodimer formation is essential for SRP function. This model characterizes the N-terminal RNA-binding domain SRP68-RBD, a tetratricopeptide-like module. Interactions between SRP68-RBD and SRP RNA (7SL RNA) are thought to facilitate a conformation of SRP RNA that is required for interactions with ribosomal RNA. 195 matched cddid_all.tbl CDD cd15482 cd15482 271234 Sialidase_non-viral Non-viral sialidases. Sialidases or neuraminidases function to bind and hydrolyze terminal sialic acid residues from various glycoconjugates, they play vital roles in pathogenesis, bacterial nutrition and cellular interactions. They have a six-bladed, beta-propeller fold with the non-viral sialidases containing 2-5 Asp-box motifs (most commonly Ser/Thr-X-Asp-[X]-Gly-X-Thr- Trp/Phe). This CD includes eubacterial and eukaryotic sialidases. 339 matched cddid_all.tbl CDD cd15483 cd15483 271235 Influenza_NA Sialidase or neuraminidase (EC 3.2.1.18) of Influenza viruses A and B. Sialidases or neuraminidases function to bind and hydrolyze terminal sialic acid residues from various glycoconjugates. Viral neuraminidases, such as this family from Influenza viruses A and B, play a vital role in pathogenesis. Influenza neuraminidase cleaves an alpha-ketosidic linkage between sialic acid and a neighboring sugar residue. During budding of virus particles from the infected cell, the sialidase helps to prevent the newly formed viral particles from aggregating. The viral sialidase cleaves terminal sialic acid from glycan structures on the infected cell surface, promoting virus release and the spread of virus to neighboring cells that are not yet infected. Also, sialidase modifies mucins in the respiratory tract and may improve access of the viral particle to its target cells. Sialidases have a six-bladed beta-propeller fold. 386 matched cddid_all.tbl CDD cd15484 cd15484 271251 uS7_plant plant ribosomal protein S7. uS7, also known as Ribosomal protein (RP)S7, is an important part of the translation process which is universally present in the small subunit of prokaryotic and eukaryotic ribosomes. The ribosome small subunit is one of the two subunits of ribosome organelles that use mRNA as a template for protein synthesis in a process called translation. The small subunits of bacteria and eukaryotes have the same shape of head, body, platform, beak, and shoulder. RPS7 is located at the head of the small subunit. RPS7 is a primary ribosomal RNA (rRNA) binding protein that assists in rRNA folding and the binding of other proteins during small subunit assembly in all species. RPS7 is also involved in the formation of the mRNA exit channel at the interface of the large and small subunits. Some ribosomal proteins have extra ribosomal functions in cell differentiation and apoptosis. 147 matched cddid_all.tbl CDD cd15485 cd15485 271243 ZIP_Cat8 Leucine zipper Dimerization domain of transcription factor Cat8 and similar proteins. Cat8p binds to carbon source-responsive element (CSRE) motifs and activates target genes under conditions of glucose deprivation. It mediates the transcriptional control of at least nine genes (ACS1, FBP1, ICL1, IDP2, JEN1, MLS1, PCK1, SFC1, and SIP4) under non-fermentative growth conditions in yeast. Studies show another 25 genes or open reading frames whose expression at the transition between the fermentative and the oxidative metabolism (diauxic shift) is altered in the absence of Cat8p. This Cat8p-dependent control results in a parallel alteration in mRNA and protein synthesis. The biochemical functions of proteins encoded by Cat8p-dependent genes are essentially related to the first steps of ethanol utilization, the glyoxylate cycle, and gluconeogenesis. Cat8p is a member of the Gal4p family of transcriptional activators which contain an N-terminal DNA-binding domain with a Zn2Cys6 binuclear cluster that interact with CCG triplets and a leucine zipper-like heptad repeat that dimerizes. Dimerization allows binding of targets which contain two CCG motifs oriented in an inverted (CGG-CCG), direct (CCG-CCG), or everted (CCG-CGG) manner. 27 matched cddid_all.tbl CDD cd15486 cd15486 271244 ZIP_Sip4 Leucine zipper Dimerization domain transcription factor Sip4p and similar fungal proteins. Sip4p binds to carbon source-responsive element (CSRE) motifs and activates transcription of target genes under conditions of glucose deprivation. Its function is modulated through phosphorylation by SNF1 protein kinase, a protein essential for expression of glucose-repressed genes in response to glucose deprivation. Sip4p is a member of the Gal4p family of transcriptional activators which contain an N-terminal DNA-binding domain with a Zn2Cys6 binuclear cluster that interact with CCG triplets and a leucine zipper-like heptad repeat that dimerizes. Dimerization allows binding of targets which contain two CCG motifs oriented in an inverted (CGG-CCG), direct (CCG-CCG), or everted (CCG-CGG) manner. 27 matched cddid_all.tbl CDD cd15487 cd15487 275387 bS6_chloro_cyano 30S ribosomal protein S6 of chloroplasts and cyanobacteria. bS6 is one of the components of the small subunit of the prokaryotic ribosome, a ribonucleoprotein organelle that decodes the genetic information in messenger RNA and forms peptide bonds to synthesize the corresponding polypeptides. Mitochondrial and chloroplastic ribosomes are similar to bacterial ribosomes. Ribosomes consist of a large and a small subunit, which assemble during the initiation stage of protein synthesis. Prokaryotic ribosomes consist of three molecules of RNA and more than 50 proteins. The small subunits of bacterial and eukaryotic ribosomes have the same overall shapes (with structural elements described as head, body, platform, beak and shoulder). The bacterial ribosomal protein S6 is important for the assembly of the central domain of the small subunit via heterodimerization with ribosomal protein S18. 94 matched cddid_all.tbl CDD cd15488 cd15488 350626 Tm-1-like ATP-binding domain found in plant Tm-1-like (Tm-1L) and similar proteins. Members of this family have been annotated as UPF0261-domain containing proteins. They are found in plants, fungi, bacteria, and archaea. A three-dimensional structure of a complex between the tomato resistance gene product Tm-1 and tomato mosaic virus helicase reveals an organization encompassing two distinct structurally similar domains and an ATP-binding site present in the N-terminal subdomain. The Tm-1-like domain is found co-occurring with a C-terminal TIM-barrel signal transduction (TBST) domain in some plant proteins like Tm-1, and with an N-terminal ABC-transporter ATP-binding domain in a few bacterial proteins. 399 matched cddid_all.tbl CDD cd15489 cd15489 276966 PHD_SF PHD finger superfamily. The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies. 48 matched cddid_all.tbl CDD cd15490 cd15490 294011 eIF2_gamma_III Domain III of eukaryotic initiation factor eIF2 gamma. This family represents the C-terminal domain of the gamma subunit of eukaryotic translation initiation factor 2 (eIF2-gamma) found in eukaryotes and archaea. eIF2 is a G protein that delivers the methionyl initiator tRNA to the small ribosomal subunit and releases it upon GTP hydrolysis after the recognition of the initiation codon. eIF2 is composed three subunits, alpha, beta and gamma. Subunit gamma shows strongest conservation, and it confers both tRNA binding and GTP/GDP binding. 90 matched cddid_all.tbl CDD cd15491 cd15491 294012 selB_III Domain III of selenocysteine-specific translation elongation factor. This family represents domain III of bacterial selenocysteine (Sec)-specific elongation factor (EFSec), homologous to domain III of EF-Tu. SelB is a specialized translation elongation factor responsible for the co-translational incorporation of selenocysteine into proteins by recoding of a UGA stop codon in the presence of a downstream mRNA hairpin loop, called Sec insertion sequence (SECIS) element. 87 matched cddid_all.tbl CDD cd15492 cd15492 276967 PHD_BRPF_JADE_like PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins. The family includes BRPF proteins, Jade proteins, protein AF-10 and AF-17. BRPF proteins are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. Jade proteins are required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6, to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor that has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is a putative transcription factor that may play a role in multiple signaling pathways. All Jade proteins, AF-10, and AF-17 contain a canonical PHD finger followed by a non-canonical ePHD finger. This model corresponds to the canonical PHD finger. 46 matched cddid_all.tbl CDD cd15493 cd15493 276968 PHD_JMJD2 PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases. JMJD2 proteins, also termed lysine-specific demethylase 4 histone demethylases (KDM4), have been implicated in various cellular processes including DNA damage response, transcription, cell cycle regulation, cellular differentiation, senescence, and carcinogenesis. They selectively catalyze the demethylation of di- and trimethylated H3K9 and H3K36. This model contains only three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a Cys4HisCys3 canonical PHD finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. JMJD2D is not included in this family, since it lacks both PHD and Tudor domains and has a different substrate specificity. JMJD2A-C are required for efficient cancer cell growth. This model corresponds to the Cys4HisCys3 canonical PHD finger. 42 matched cddid_all.tbl CDD cd15494 cd15494 276969 PHD_ATX1_2_like PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like protein ATX1, ATX2, and similar proteins. The family includes A. thaliana ATX1 and ATX2, both of which are sister paralogs originating from a segmental chromosomal duplication. They are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1, also termed protein SET domain group 27, or trithorax-homolog protein 1 (TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2, also termed protein SET domain group 30, or trithorax-homolog protein 2 (TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). Both ATX1 and ATX2 are multi-domain containing proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a C-terminal SET domain; this model corresponds to the Cys4HisCys3 canonical PHD finger. 47 matched cddid_all.tbl CDD cd15495 cd15495 276970 PHD_ATX3_4_5_like PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like protein ATX3, ATX4, ATX5, and similar proteins. The family includes A. thaliana ATX3 (also termed protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also termed protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also termed protein SET domain group 29, or trithorax-homolog protein 5), which belong to the histone-lysine methyltransferase family. They show distinct phylogenetic origins from the ATX1 and ATX2 family. They are multi-domain containing proteins that consist of an N-terminal PWWP domain, a canonical Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a C-terminal SET domain; this model corresponds to the Cys4HisCys3 canonical PHD finger. 47 matched cddid_all.tbl CDD cd15496 cd15496 276971 PHD_PHF7_G2E3_like PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3). PHF7, also termed testis development protein NYD-SP6, is a testis-specific plant homeodomain (PHD) finger-containing protein that associates with chromatin and binds histone H3 N-terminal tails with a preference for dimethyl lysine 4 (H3K4me2). It may play an important role in stimulating transcription involved in testicular development and/or spermatogenesis. PHF7 contains a canonical Cys4HisCys3 PHD finger and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which may be involved in activating transcriptional regulation. G2E3 is a dual function ubiquitin ligase (E3) that may play a possible role in cell cycle regulation and the cellular response to DNA damage. It is essential for prevention of apoptosis in early embryogenesis. It is also a nucleo-cytoplasmic shuttling protein with DNA damage responsive localization. G2E3 contains two distinct RING-like ubiquitin ligase domains that catalyze lysine 48-linked polyubiquitination, and a C-terminal catalytic HECT domain that plays an important role in ubiquitin ligase activity and in the dynamic subcellular localization of the protein. The RING-like ubiquitin ligase domains consist of a PHD finger and an ePHD finger. This model corresponds to the Cys4HisCys3 canonical PHD finger. 54 matched cddid_all.tbl CDD cd15497 cd15497 276972 PHD1_Snt2p_like PHD finger 1 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins. Snt2p is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical Cys4HisCys3 plant homeodomain (PHD) fingers, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain; this model corresponds to the first canonical Cys4HisCys3 PHD finger. 48 matched cddid_all.tbl CDD cd15498 cd15498 276973 PHD2_Snt2p_like PHD finger 2 found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins. This group corresponds to Snt2p and similar proteins. Snt2p is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical Cys4HisCys3 plant homeodomain (PHD) fingers, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain; this model corresponds to the second canonical Cys4HisCys3 PHD finger. 55 matched cddid_all.tbl CDD cd15499 cd15499 276974 PHD1_MTF2_PHF19_like PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins. The family includes two PCL family proteins, metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are homologs of PHD finger protein1 (PHF1). PCL family proteins are accessory components of the polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. They specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD finger-containing proteins, the first PHD fingers of PCL proteins do not display histone H3K4 binding affinity and they do not affect the Tudor domain binding to histones. This model corresponds to the first PHD finger. 53 matched cddid_all.tbl CDD cd15500 cd15500 276975 PHD1_PHF1 PHD finger 1 found in PHD finger protein1 (PHF1). PHF1, also termed polycomb-like protein 1 (PCL1), together with JARID2 and AEBP2, associates with the polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF1 is essential in epigenetic regulation and genome maintenance. It acts as a dual reader of Lysine trimethylation at Lysine 36 of Histone H3 and Lysine 27 of Histone variant H3t. PHF1 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. Its Tudor domain selectively binds to histone H3K36me3. Moreover, PHF1 is required for efficient H3K27me3 and Hox gene silencing. It can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response. This model corresponds to the first PHD finger. 51 matched cddid_all.tbl CDD cd15501 cd15501 276976 PHD_Int12 PHD finger found in integrator complex subunit 12 (Int12) and similar proteins. Int12, also termed IntS12, or PHD finger protein 22, is a component of integrator, a multi-protein mediator of small nuclear RNA processing. The integrator complex directly interacts with the C-terminal domain of RNA polymerase II (RNAPII) largest subunit and mediates the 3' end processing of small nuclear RNAs (snRNAs) U1 and U2. Different from other components of integrator, Int12 contains a PHD finger, which is not required for snRNA 3' end cleavage. Instead, Int12 harbors a small microdomain at its N-terminus which is necessary and sufficient for Int12 function; this microdomain facilitates Int12 binding to Int1 and promotes snRNA 3' end formation. 52 matched cddid_all.tbl CDD cd15502 cd15502 276977 PHD_Phf1p_Phf2p_like PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 (Phf1p) and Phf2 (Phf2p). Phf1p and Phf2p are components of the SWM histone demethylase complex that specifically demethylates histone H3 at lysine 9 (H3K9me2), a specific tag for epigenetic transcriptional activation. They function as corepressors and play roles in regulating heterochromatin propagation and euchromatic transcription. Both Phf1p and Phf2p contain a plant homeodomain (PHD) finger. 52 matched cddid_all.tbl CDD cd15503 cd15503 276978 PHD2_MTF2_PHF19_like PHD finger 2 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins. The PCL family includes PHD finger protein1 (PHF1) and its homologs metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are accessory components of the Polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two plant homeodomain (PHD) fingers, and a C-terminal MTF2 domain. PCL proteins specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD finger-containing proteins, the first PHD finger of PCL proteins do not display histone H3K4 binding affinity and they do not affect the Tudor domain binding to histones. This model corresponds to the second PHD finger. 52 matched cddid_all.tbl CDD cd15504 cd15504 276979 PHD_PRHA_like PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins. PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain. 53 matched cddid_all.tbl CDD cd15505 cd15505 276980 PHD_ING PHD finger found in the inhibitor of growth (ING) protein family. The ING family includes a group of tumor suppressors, ING1-5, which act as readers and writers of the histone epigenetic code, affecting DNA damage response, chromatin remodeling, cellular senescence, differentiation, cell cycle regulation and apoptosis. They may have a general role in mediating the cellular response to genotoxic stress through binding to and regulating the activities of histone acetyltransferase (HAT) and histone deacetylase (HDAC) chromatin remodeling complexes. All ING proteins contain an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger. 45 matched cddid_all.tbl CDD cd15506 cd15506 276981 PHD1_KMT2A_like PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B). This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger. 47 matched cddid_all.tbl CDD cd15507 cd15507 276982 PHD2_KMT2A_like PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B). This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger. 50 matched cddid_all.tbl CDD cd15508 cd15508 276983 PHD3_KMT2A_like PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B). This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger. 57 matched cddid_all.tbl CDD cd15509 cd15509 276984 PHD1_KMT2C_like PHD finger 1 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D). KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the first PHD finger. 48 matched cddid_all.tbl CDD cd15510 cd15510 276985 PHD2_KMT2C_like PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D). KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger. 46 matched cddid_all.tbl CDD cd15511 cd15511 276986 PHD3_KMT2C PHD finger 3 found in Histone-lysine N-methyltransferase 2C (KMT2C). KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the third PHD finger. 52 matched cddid_all.tbl CDD cd15512 cd15512 276987 PHD4_KMT2C_like PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD domain 3 found in KMT2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, two extended PHD (ePHD) fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fourth PHD finger of KMT2C and the third domain of KMT2D. 49 matched cddid_all.tbl CDD cd15513 cd15513 276988 PHD5_KMT2C_like PHD finger 5 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 4 found in KMT2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger of KMT2C and the fourth PHD finger of KMT2D. 47 matched cddid_all.tbl CDD cd15514 cd15514 276989 PHD6_KMT2C_like PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C) and PHD finger 5 found in KMT2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the sixth PHD finger of KMT2C and the fifth PHD finger of KMT2D. 51 matched cddid_all.tbl CDD cd15515 cd15515 276990 PHD1_KDM5A_like PHD finger 1 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and similar proteins. The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me2 and H3K4me3), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. This family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent H3K4me3 demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger. 46 matched cddid_all.tbl CDD cd15516 cd15516 276991 PHD2_KDM5A_like PHD finger 2 found in Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D, and similar proteins. The JARID subfamily within the JmjC proteins includes Lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog protein, little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 and H3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. The family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger. 53 matched cddid_all.tbl CDD cd15517 cd15517 276992 PHD_TCF19_like PHD finger found in Transcription factor 19 (TCF-19), Lysine-specific demethylase KDM5A and KDM5B, and other similar proteins. TCF-19 was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interaction with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. This family also includes Caenorhabditis elegans Lysine-specific demethylase 7 homolog (ceKDM7A). ceKDM7A (also termed JmjC domain-containing protein 1.2, PHD finger protein 8 homolog, or PHF8 homolog) is a plant homeodomain (PHD)- and JmjC domain-containing protein that functions as a histone demethylase specific for H3K9me2 and H3K27me2. The binding of the PHD finger to H3K4me3 guides H3K9me2- and H3K27me2-specific demethylation by its catalytic JmjC domain in a trans-histone regulation mechanism. In addition, this family includes plant protein OBERON 1 and OBERON 2, Alfin1-like (AL) proteins, histone acetyltransferases (HATs) HAC, and AT-rich interactive domain-containing protein 4 (ARID4). 49 matched cddid_all.tbl CDD cd15518 cd15518 276993 PHD_Ecm5p_Lid2p_like PHD finger found in Saccharomyces cerevisiae extracellular matrix protein 5 (Ecm5p), Schizosaccharomyces pombe Lid2 complex component Lid2p, and similar proteins. The family includes Saccharomyces cerevisiae Ecm5p, Schizosaccharomyces pombe Lid2 complex component Lid2p, and similar proteins. Ecm5p is a JmjC domain-containing protein that directly removes histone lysine methylation via a hydroxylation reaction. It associates with the yeast Snt2p and Rpd3 deacetylase, which may play a role in regulating transcription in response to oxidative stress. Ecm5p promotes oxidative stress tolerance, while Snt2p ultimately decreases tolerance. Ecm5p contains an N-terminal ARID domain, a JmjC domain, and a C-terminal plant homeodomain (PHD) finger. Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model includes the second PHD finger of Lid2p. 45 matched cddid_all.tbl CDD cd15519 cd15519 276994 PHD1_Lid2p_like PHD finger 1 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins. Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1 and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. This model corresponds to the first PHD finger. 46 matched cddid_all.tbl CDD cd15520 cd15520 276995 PHD3_Lid2p_like PHD finger 3 found in Schizosaccharomyces pombe Lid2 complex component Lid2p and similar proteins. Lid2p is a trimethyl H3K4 (H3K4me3) demethylase responsible for H3K4 hypomethylation in heterochromatin. It interacts with the histone lysine-9 methyltransferase, Clr4, through the Dos1/Clr8-Rik1 complex, and mediates H3K9 methylation and small RNA production. It also acts cooperatively with the histone modification enzymes Set1 and Lsd1, and plays an essential role in cross-talk between H3K4 and H3K9 methylation in euchromatin. Lid2p contains a JmjC domain, three PHD fingers and a JmjN domain. The family corresponds to the third PHD finger. 47 matched cddid_all.tbl CDD cd15521 cd15521 276996 PHD_VIN3_plant PHD finger found in Arabidopsis thaliana protein Vernalization Insensitive 3 (VIN3) and similar proteins. The lineage specific VIN3 family of proteins includes VIN3, VIN3-like1 (VIL1, or Vernalization5 (VRN5)), VIN3-like2 (VIL2, or Vernalization5/VIN3-like protein 1 (VEL1)), VIN3-like3 (VIL3 or Vernalization5/VIN3-like protein 2 (VEL2)), and similar proteins. They contain a plant homeodomain (PHD) finger, and collectively repress different sets of members of the Flowering LOCUS C (FLC) gene family during the course of vernalization. Both VIN3 and VIL1 are required for modifying the histone architecture of the MADS box floral repressor FLC in response to prolonged cold exposure in Arabidopsis. VIN3 is required for both Histone H3 Lys 9 (H3K9) and Histone H3 Lys 27 (H3K27) methylation at FLC chromatin, ultimately leading to its repression. It is regulated by the components of Polycomb Response Complex2 (PRC2), which trimethylates histone H3 Lys 27 (H3K27me3). VIL1 appears to play a prominent role in regulating FLC by vernalization. VIL2 acts together with PRC2 to repress the floral repressor MAF5, an FLC clade member, in a photoperiod-dependent manner to accelerate flowering under non-inductive photoperiods. 64 matched cddid_all.tbl CDD cd15522 cd15522 276997 PHD_TAF3 PHD finger found in transcription initiation factor TFIID subunit 3 (TAF3). TAF3 (also termed 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, transcription initiation factor TFIID 140 kDa subunit (TAF140), or TAFII-140, is an integral component of TFIID) is a general initiation factor (GTF) that plays a key role in preinitiation complex (PIC) assembly through core promoter recognition. The interaction of H3K4me3 with TAF3 directs global TFIID recruitment to active genes, which regulates gene-selective functions of p53 in response to genotoxic stress. TAF3 is highly enriched in embryonic stem cells and is required for endoderm lineage differentiation and prevents premature specification of neuroectoderm and mesoderm. Moreover, TAF3, along with TRF3, forms a complex that is essential for myogenic differentiation. TAF3 contains a plant homeodomain (PHD) finger. This family also includes Drosophila melanogaster BIP2 (Bric-a-brac interacting protein 2) protein, which functions as an interacting partner of D. melanogaster p53 (Dmp53). 46 matched cddid_all.tbl CDD cd15523 cd15523 276998 PHD_PHF21A PHD finger found in PHD finger protein 21A (PHF21A). PHF21A (also termed BHC80a or BRAF35-HDAC complex protein BHC80) along with HDAC1/2, CtBP1, CoREST, and BRAF35, is associated with LSD1, a lysine (K)-specific histone demethylase. It inhibits LSD1-mediated histone demethylation in vitro. PHF21A is predominantly present in the central nervous system and spermatogenic cells and is one of the six components of BRAF-HDAC complex (BHC) involved in REST-dependent transcriptional repression of neuron-specific genes in non-neuronal cells. It acts as a scaffold protein in BHC in neuronal as well as non-neuronal cells and also plays a role in spermatogenesis. PHF21A contains a C-terminal plant homeodomain (PHD) finger that is responsible for the binding directly to each of five other components of BHC, and of organizing BHC mediating transcriptional repression. 43 matched cddid_all.tbl CDD cd15524 cd15524 276999 PHD_PHF21B PHD finger found in PHD finger protein 21B (PHF21B). PHF21B is a plant homeodomain (PHD) finger-containing protein whose biological function remains unclear. It shows high sequence similarity with PHF21A, which is associated with LSD1, a lysine (K)-specific histone demethylase and inhibits LSD1-mediated histone demethylation in vitro. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. 43 matched cddid_all.tbl CDD cd15525 cd15525 277000 PHD_UHRF1_2 PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein UHRF1 and UHRF2. UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger. 47 matched cddid_all.tbl CDD cd15526 cd15526 277001 PHD1_MOZ_d4 PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ), its factor (MORF), and d4 gene family proteins. MOZ is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity and to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF) is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphoma genesis and bone development, and its homologs. This family also includes three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes via changing the condensed/decondensed state of chromatin in nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro specific gene clusters. All family members contain two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger. 56 matched cddid_all.tbl CDD cd15527 cd15527 277002 PHD2_KAT6A_6B PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF). MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger. 46 matched cddid_all.tbl CDD cd15528 cd15528 277003 PHD1_PHF10 PHD finger 1 found in PHD finger protein 10 (PHF10) and similar proteins. PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger. 54 matched cddid_all.tbl CDD cd15529 cd15529 277004 PHD2_PHF10 PHD finger 2 found in PHD finger protein 10 (PHF10) and similar proteins. PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is a ubiquitously expressed transcriptional regulator that is required for maintaining the undifferentiated status of neuroblasts. It contains a SAY (supporter of activation of yellow) domain and two adjacent plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger. 44 matched cddid_all.tbl CDD cd15530 cd15530 277005 PHD2_d4 PHD finger 2 found in d4 gene family proteins. The family includes proteins coded by three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes by changing the condensed/decondensed state of chromatin in the nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro-specific gene clusters. The d4 family proteins show distinct domain organization with domain 2/3 in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc finger in the central part and two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the second PHD finger. 46 matched cddid_all.tbl CDD cd15531 cd15531 277006 PHD1_CHD_II PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins. Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the first PHD finger. 43 matched cddid_all.tbl CDD cd15532 cd15532 277007 PHD2_CHD_II PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins. Class II CHD proteins includes chromodomain-helicase-DNA-binding protein CHD3, CHD4, and CHD5, which are nuclear and ubiquitously expressed chromatin remodelling ATPases generally associated with histone deacetylases (HDACs). They are involved in DNA Double Strand Break (DSB) signaling, DSB repair and/or p53-dependent pathways such as apoptosis and senescence, as well as in the maintenance of genomic stability, and/or cancer prevention. They function as subunits of the Nucleosome Remodelling and Deacetylase (NuRD) complex, which is generally associated with gene repression, heterochromatin formation, and overall chromatin compaction. In contrast to the class I CHD enzymes (CHD1 and CHD2), class II CHD proteins lack identifiable DNA-binding domains, but possess a C-terminal coiled-coil region. Moreover, in addition to the tandem chromodomains and a helicase domain, they all harbor tandem plant homeodomain (PHD) zinc fingers involved in the recognition of methylated histone tails. This model corresponds to the second PHD finger. 43 matched cddid_all.tbl CDD cd15533 cd15533 277008 PHD1_PHF12 PHD finger 1 found in PHD finger protein 12 (PHF12). PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant-homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This model corresponds to the first PHD finger. 45 matched cddid_all.tbl CDD cd15534 cd15534 277009 PHD2_PHF12_Rco1 PHD finger 2 found in PHD finger protein 12 (PHF12), yeast Rco1, and similar proteins. PHF12, also termed PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. PHF12 contains two plant homeodomain (PHD) zinc fingers followed by a polybasic region. The PHD fingers function downstream of phosphoinositide signaling triggered by the interaction between polybasic regions and phosphoinositides. This subfamily also includes yeast transcriptional regulatory protein Rco1 and similar proteins. Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two PHD fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the second PHD finger. 47 matched cddid_all.tbl CDD cd15535 cd15535 277010 PHD1_Rco1 PHD finger 1 found in Saccharomyces cerevisiae transcriptional regulatory protein Rco1 and similar proteins. Rco1 is a component of the Rpd3S histone deacetylase complex that plays an important role at actively transcribed genes. Rco1 contains two plant homeodomain (PHD) fingers, which are required for the methylation of histone H3 lysine 36 (H3K36) nucleosome recognition by Rpd3S. This model corresponds to the first PHD finger. 45 matched cddid_all.tbl CDD cd15536 cd15536 277011 PHD_PHRF1 PHD finger found in PHD and RING finger domain-containing protein 1 (PHRF1). PHRF1, also termed KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase that induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a RING finger. 46 matched cddid_all.tbl CDD cd15537 cd15537 277012 PHD_BS69 PHD finger found in protein BS69. Protein BS69, also termed zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. It also mediates repression, at least in part, through interaction with the co-repressor N-CoR. Moreover, it interacts with Toll-interleukin 1 receptor domain (TIR)-containing adaptor molecule-1 (TICAM-1, also named TRIF) to facilitate NF-kappaB activation and type I IFN induction. It associates with PIAS1, a SUMO E3 enzyme, and Ubc9, a SUMO E2 enzyme, and plays an inhibitory role in muscle and neuronal differentiation. Moreover, BS69 regulates Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1)/C-terminal activation region 2 (CTAR2)-mediated NF-kappaB activation by interfering with the complex formation between TNFR-associated death domain protein (TRADD) and LMP1/CTAR2. It also cooperates with tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) in the regulation of EBV-derived LMP1/CTAR1-induced NF-kappaB activation. Furthermore, BS69 is involved in the p53-p21Cip1-mediated senescence pathway. BS69 contains a plant homeodomain (PHD) finger, a bromodomain, a proline-tryptophan-tryptophan-proline (PWWP) domain, and a Myeloid translocation protein 8, Nervy and DEAF-1 (MYND) domain. 43 matched cddid_all.tbl CDD cd15538 cd15538 277013 PHD_PRKCBP1 PHD finger found in protein kinase C-binding protein 1 (PRKCBP1). PRKCBP1, also termed cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), or Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor; the RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. 41 matched cddid_all.tbl CDD cd15539 cd15539 277014 PHD1_AIRE PHD finger 1 found in autoimmune regulator (AIRE). AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the first PHD finger that recognizes the unmethylated tail of histone H3 and targets AIRE-dependent genes. 43 matched cddid_all.tbl CDD cd15540 cd15540 277015 PHD2_AIRE PHD finger 2 found in autoimmune regulator (AIRE). AIRE, also termed autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED) protein, functions as a regulator of gene transcription in the thymus. It is essential for prevention of autoimmunity. AIRE plays a critical role in the induction of central tolerance. It promotes self-tolerance through tissue-specific antigen (TSA) expression. It also acts as an active regulator of chondrocyte differentiation. AIRE contains a homogeneously-staining region (HSR) or caspase-recruitment domain (CARD), a nuclear localization signal (NLS), a SAND (for Sp100, AIRE, nuclear phosphoprotein 41/75 or NucP41/75, and deformed epidermal auto regulatory factor 1 or Deaf1) domain, two plant homeodomain (PHD) fingers, and four LXXLL (where L stands for leucine) motifs. This model corresponds to the second PHD finger that may play a critical role in the activation of gene transcription. 42 matched cddid_all.tbl CDD cd15541 cd15541 277016 PHD_TIF1_like PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins. The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. Sp110 is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. SP140 is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD). 43 matched cddid_all.tbl CDD cd15542 cd15542 277017 PHD_UBR7 PHD finger found in putative E3 ubiquitin-protein ligase UBR7. UBR7, also termed N-recognin-7, is a UBR box-containing protein that belongs to the E3 ubiquitin ligase family that recognizes N-degrons or structurally related molecules for ubiquitin-dependent proteolysis or related processes through the UBR box motif. In addition to the UBR box, UBR7 also harbors a plant homeodomain (PHD) finger. The biochemical properties of UBR7 remain unclear. 54 matched cddid_all.tbl CDD cd15543 cd15543 277018 PHD_RSF1 PHD finger found in Remodeling and spacing factor 1 (Rsf-1). Rsf-1, also termed HBV pX-associated protein 8, or Hepatitis B virus X-associated protein alpha (HBxAPalpha), or p325 subunit of RSF chromatin-remodeling complex, is a novel nuclear protein with histone chaperon function. It is a subunit of an ISWI chromatin remodeling complex, remodeling and spacing factor (RSF), and plays a role in mediating ATPase-dependent chromatin remodeling and conferring tumor aggressiveness in common carcinomas. As an ataxia-telangiectasia mutated (ATM)-dependent chromatin remodeler, Rsf-1 facilitates DNA damage checkpoints and homologous recombination repair. It regulates the mitotic spindle checkpoint and chromosome instability through the association with serine/threonine kinase BubR1 (BubR1) and Hepatitis B virus (HBV) X protein (HBx) in the chromatin fraction during mitosis. It also interacts with cyclin E1 and promotes tumor development. Rsf-1 contains a plant homeodomain (PHD) finger. 46 matched cddid_all.tbl CDD cd15544 cd15544 277019 PHD_BAZ1A_like PHD finger found in bromodomain adjacent to zinc finger domain protein BAZ1A and BAZ1B. BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. Both BAZ1A and BAZ1B contain a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. 46 matched cddid_all.tbl CDD cd15545 cd15545 277020 PHD_BAZ2A_like PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A) and 2B (BAZ2B). BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A. Both BAZ2A and BAZ2B contain a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. BAZ2B also harbors an extra Apolipophorin-III like domain in its N-terminal region. 46 matched cddid_all.tbl CDD cd15546 cd15546 277021 PHD_PHF13_like PHD finger found in PHD finger proteins PHF13 and PHF23. PHF13, also termed survival time-associated PHD finger protein in ovarian cancer 1 (SPOC1), is a novel plant homeodomain (PHD) finger-containing protein that shows strong expression in spermatogonia and ovarian cancer cells, modulates chromatin structure and mitotic chromosome condensation, and is important for proper cell division. It is also required for spermatogonial stem cell differentiation and sustained spermatogenesis. The overexpression of PHF13 associates with unresectable carcinomas and shorter survival in ovarian cancer. PHF23, also termed PHD-containing protein JUNE-1, is a hypothetical protein with a PHD finger. It is encoded by gene PHF23 that acts as a candidate fusion partner for the nucleoporin gene NUP98. The NUP98-PHF23 fusion results from a cryptic translocation t(11;17)(p15;p13) in acute myeloid leukemia (AML). 44 matched cddid_all.tbl CDD cd15547 cd15547 277022 PHD_SHPRH PHD finger found in E3 ubiquitin-protein ligase SHPRH. SHPRH, also termed SNF2, histone-linker, PHD and RING finger domain-containing helicase, belongs to the SWI2/SNF2 family of ATP-dependent chromatin remodeling enzymes, containing the Cys3HisCys4 RING-finger characteristic of E3 ubiquitin ligases. It plays a key role in the error-free branch of DNA damage tolerance. As functional homologs of Saccharomyces cerevisiae Rad5, SHPRH and its closely-related protein, helicase like transcription factor (HLTF), act as ubiquitin ligases that cooperatively mediate Ubc13-Mms2-dependent polyubiquitination of proliferating cell nuclear antigen (PCNA) and maintain genomic stability. SHPRH contains a SNF2 domain, a H1.5 (linker histone H1 and H5) domain, a plant homeodomain (PHD) finger, a Cys3HisCys4 RING-finger, and a C-terminal helicase domain. 47 matched cddid_all.tbl CDD cd15548 cd15548 277023 PHD_ASH1L PHD finger found in histone-lysine N-methyltransferase ASH1L. ASH1L, also termed ASH1-like protein, or absent small and homeotic disks protein 1 homolog, or lysine N-methyltransferase 2H, is a protein belonging to the Trithorax family. It methylates Lys36 of histone H3 independently of transcriptional elongation to promote the establishment of Hox gene expression by counteracting Polycomb silencing. It can suppress interleukin-6 (IL-6), and tumor necrosis factor (TNF) production in Toll-like receptor (TLR)-triggered macrophages, and inflammatory autoimmune diseases by inducing the ubiquitin-editing enzyme A20. ASH1L contains an associated with SET domain (AWS), a SET domain, a post-SET domain, a bromodomain, a bromo-adjacent homology domain (BAH), and a plant homeodomain (PHD) finger. 43 matched cddid_all.tbl CDD cd15549 cd15549 277024 PHD_PHF20_like PHD finger found in PHD finger protein 20 (PHF20) and PHD finger protein 20-like protein 1 (P20L1). PHF20, also termed Glioma-expressed antigen 2, or hepatocellular carcinoma-associated antigen 58, or novel zinc finger protein, or transcription factor TZP (referring to Tudor and zinc finger domain containing protein), is a regulator of NF-kappaB activation by disrupting recruitment of PP2A to p65. It also functions as a transcription factor that binds Akt and plays a role in Akt cell survival/growth signaling. Moreover, it transcriptionally regulates p53. The phosphorylation of PHF20 on Ser291 mediated by protein kinase B (PKB) is essential in tumorigenesis via the regulation of p53 mediated signaling. P20L1 is an active malignant brain tumor (MBT) domain-containing protein that binds to monomethylated lysine 142 on DNA (Cytosine-5) Methyltransferase 1 (DNMT1) (DNMT1K142me1) and colocalizes at the perinucleolar space in a SET7-dependent manner. Its MBT domain reads and controls enzyme levels of methylated DNMT1 in cells, thus representing a novel antagonist of DNMT1 proteasomal degradation. Both PHF20 and PHF20L1 contain an N-terminal MBT domain, two Tudor domains, a plant homeodomain (PHD) finger and the putative DNA-binding domains, AT hook and Cys2His2-type zinc finger. 45 matched cddid_all.tbl CDD cd15550 cd15550 277025 PHD_MLL5 PHD finger found in mixed lineage leukemia 5 (MLL5). MLL5 is a histone methyltransferase that plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. It contains a single plant homeodomain (PHD) finger followed by a catalytic SET domain. MLL5 can be recruited to E2F1-responsive promoters to stimulate H3K4 trimethylation and transcriptional activation by binding to the cell cycle regulator host cell factor (HCF-1), thereby facilitating the cell cycle G1 to S phase transition. It is also involved in mitotic fidelity and genomic integrity by modulating the stability of the chromosomal passenger complex (CPC) via the interaction with Borealin. Moreover, MLL5 is a component of a complex associated with retinoic acid receptor that requires GlcN Acylation of its SET domain in order to activate its histone lysine methyltransferase activity. It also participates in the camptothecin (CPT)-induced p53 activation. Furthermore, MLL5 indirectly regulates H3K4 methylation, represses cyclin A2 (CycA) expression, and promotes myogenic differentiation. 44 matched cddid_all.tbl CDD cd15551 cd15551 277026 PHD_PYGO PHD finger found in PYGO proteins. The family includes Drosophila melanogaster protein pygopus (dPYGO) and its two homologs, PYGO1 and PYGO2. dPYGO is a fundamental Wnt signaling transcriptional component in Drosophila. PYGO1 is essential for the association with Legless (Lgs)/Bcl9 that acts an adaptor between Pygopus (Pygo) and Arm/beta-catenin. dPYGO and PYGO2 function as context-dependent beta-catenin coactivators, and they bind di- and trimethylated lysine 4 of histone H3 (H3K4me2/3). Moreover, PYGO2 acts as a histone methylation reader, and a chromatin remodeler in a testis-specific and Wnt-unrelated manner. It also mediates chromatin regulation and links Wnt signaling and Notch signaling to suppress the luminal/alveolar differentiation competence of mammary stem and basal cells. PYGO2 also plays a new role in rRNA transcription during cancer cell growth. It regulates mammary tumor initiation and heterogeneity in MMTV-Wnt1 mice. All family members contain a plant homeodomain (PHD) finger. 54 matched cddid_all.tbl CDD cd15552 cd15552 277027 PHD_PHF3_like PHD finger found in PHD finger protein 3 (PHF3), and death-inducer obliterator variants Dido1, Dido2, and Dido3. PHF3 is a human homolog of yeast protein bypass of Ess1 (Bye1), a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. PHF3 contains an N-terminal plant homeodomain (PHD) finger, a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. This family also includes Dido gene encoding three alternative splicing variants (Dido1, 2, and 3), which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1 is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved PHD finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine4 (H3K4me3). Gene Dido1 is a Bone morphogenetic protein (BMP) target gene and promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform and is ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but is involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, a SPOC module, and a long C-terminal region (CT) of unknown homology. 50 matched cddid_all.tbl CDD cd15553 cd15553 277028 PHD_Cfp1 PHD finger found in CXXC-type zinc finger protein 1 (Cfp1). Cfp1, also termed CpG-binding protein, or PHD finger and CXXC domain-containing protein 1 (PCCX1), is a specificity factor that binds to unmethylated CpGs and links H3K4me3 with CpG islands (CGIs). It integrates both promoter CpG content and gene activity for accurate trimethylation of histone H3 Lys 4 (H3K4me3) deposition in embryonic stem cells. Moreover, Cfp1 is an essential component of the SETD1 histone H3K4 methyltransferase complex and functions as a critical regulator of histone methylation, cytosine methylation, cellular differentiation, and vertebrate development. Cfp1 contains a plant homeodomain (PHD) finger, a CXXC domain, and a CpG binding protein zinc finger C-terminal domain. Its CXXC domain selectively binds to non-methylated CpG islands, following by a preference for a guanosine nucleotide. 46 matched cddid_all.tbl CDD cd15554 cd15554 277029 PHD_PHF2_like PHD finger found in PHF2, PHF8 and KDM7. This family includes PHF2, PHF8, KDM7, and similar proteins. PHF2, also termed GRC5, or PHD finger protein 2, is a histone lysine demethylase ubiquitously expressed in various tissues. PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20(H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. All family members contain a plant homeodomain (PHD) finger and a JmjC domain. 47 matched cddid_all.tbl CDD cd15555 cd15555 277030 PHD_KDM2A_2B PHD finger found in Lysine-specific demethylase KDM2A, KDM2B, and similar proteins. This family includes KDM2A, KDM2B, and F-box and leucine-rich repeat protein 19 (FBXL19). KDM2A is a ubiquitously expressed histone H3 lysine 36 (H3K36) demethylase that has been implicated in gene silencing, cell cycle, cell growth, and cancer development. KDM2B is a ubiquitously expressed histone H3 lysine 4 (H3K4me2) or histone H3 lysine 36 (H3K36me2) demethylase that functions as a regulator of chemokine expression, cellular morphology, and the metabolome of fibroblasts. Both KDM2A and KDM2B belong to the JmjC-domain-containing histone demethylase family. They consist of two Jumonji C (JmjC) domains, and FBXHA and FBXHB domains. A CXXC zinc-finger domain, followed by a plant homeodomain (PHD) finger, is located within the FBXHA domain, and an F-box domain, followed by an antagonist of mitotic exit network protein 1 (AMN1) domain, is located within the FBXHB domain. FBXL19 belongs to the Skp1-Cullin-F-box (SCF) family of E3 ubiquitin ligases. It mediates ubiquitination and interleukin 33 (IL-33)-induced degradation of ST2L receptor in lung epithelia, blocks IL-33-mediated apoptosis, and prevents endotoxin-induced acute lung injury. FBXL19 consists of FBXHA and FBXHB domains, similar to KDM2A and KDM2B. 55 matched cddid_all.tbl CDD cd15556 cd15556 277031 PHD_MMD1_like PHD finger found in Arabidopsis thaliana PHD finger protein MALE MEIOCYTE DEATH 1 (MMD1), PHD finger protein MALE STERILITY 1 (MS1), and similar proteins. MMD1 is a plant homeodomain (PHD) finger protein expressed in male meiocytes. It is encoded by the gene DUET, which is required for male meiotic chromosome organization and progression. MMD1 has been implicated in the regulation of gene expression during meiosis. The mmd1 mutation triggers cell death in male meiocytes. MS1 is a nuclear transcriptional activator that is important for tapetal development and pollen wall biosynthesis. It contains a Leu zipper-like domain and a PHD finger motif, both of which are essential for its function. 46 matched cddid_all.tbl CDD cd15557 cd15557 277032 PHD_CBP_p300 PHD finger found in CREB-binding protein (CBP) and histone acetyltransferase p300. This p300/CBP family includes two highly homologous histone acetyltransferases (HATs), CREB-binding protein (CBP) and p300. CBP is also known as KAT3A or CREBBP. It specifically interacts with the phosphorylated form of cyclic adenosine monophosphate-responsive element-binding protein (CREB). p300, also termed as KAT3B, or E1A-associated protein p300 (EP300), is a paralog of CBP. and is involved in E1A function in cell cycle progression and cellular differentiation. Both CBP and p300 are co-activator proteins that have been implicated in cell cycle regulation, apoptosis, embryonic development, cellular differentiation and cancer. They associate with a number of DNA-binding transcription activators as well as general transcription factors (GTFs), thus mediating recruitment of basal transcription machinery to the promoter. They contain a cysteine-histidine rich region, KIX (CREB interaction) domain, a plant homeodomain (PHD) finger, a HAT domain, followed by a SRC interaction domain. 37 matched cddid_all.tbl CDD cd15558 cd15558 277033 PHD_Hop1p_like PHD finger found in Schizosaccharomyces pombe meiosis-specific protein hop1 (Hop1p) and similar proteins. Fission yeast Hop1p, also termed linear element-associated protein hop1, is an S. pombe homolog of the synaptonemal complex (SC)-associated protein Hop1 in Saccharomyces cerevisiae. In contrast to S. cerevisiae, S. pombe forms thin threads, known as linear elements (LinEs), in meiotic nuclei, instead of a canonical synaptonemal complex. LinEs contain Rec10 protein and are evolutionary relics of SC axial elements. Fission yeast Hop1p is a linear element (LinE)-associated protein. It also associates with Rec10, which plays a role in recruiting the recombination machinery to chromatin. Hop1p contains an N-terminal HORMA (for Hop1p, Rev7p, and MAD2) domain and a C-terminal plant homeodomain (PHD) finger. 47 matched cddid_all.tbl CDD cd15559 cd15559 277034 PHD1_BPTF PHD finger 1 found in bromodomain and PHD finger-containing transcription factor (BPTF). BPTF, also termed nucleosome-remodeling factor subunit BPTF, or fetal Alz-50 clone 1 protein (FAC1), or fetal Alzheimer antigen, functions as a transcriptional regulator that exhibits altered expression and subcellular localization during neuronal development and neurodegenerative diseases such as Alzheimer's disease. It interacts with the human orthologue of the Kelch-like Ech-associated protein (Keap1). Its function and subcellular localization can be regulated by Keap1. Moreover, BPTF is a novel DNA-binding protein that recognizes the DNA sequence CACAACAC and represses transcription through this site in a phosphorylation-dependent manner. Furthermore, BPTF interacts with the Myc-associated zinc finger protein (ZF87/MAZ) and alters its transcriptional activity, which has been implicated in gene regulation in neurodegeneration. Some family members contain two or three plant homeodomain (PHD) fingers, which may be involved in complex formation with histone H3 trimethylated at K4 (H3K4me3). This family corresponds to the first PHD finger. 43 matched cddid_all.tbl CDD cd15560 cd15560 277035 PHD2_3_BPTF PHD finger 2 and 3 found in bromodomain and PHD finger-containing transcription factor (BPTF). BPTF, also termed nucleosome-remodeling factor subunit BPTF, or fetal Alz-50 clone 1 protein (FAC1), or fetal Alzheimer antigen, functions as a transcriptional regulator that exhibits altered expression and subcellular localization during neuronal development and neurodegenerative diseases such as Alzheimer's disease. It interacts with the human orthologue of the Kelch-like Ech-associated protein (Keap1). Its function and subcellular localization can be regulated by Keap1. Moreover, BPTF is a novel DNA-binding protein that recognizes the DNA sequence CACAACAC and represses transcription through this site in a phosphorylation-dependent manner. Furthermore, BPTF interacts with the Myc-associated zinc finger protein (ZF87/MAZ) and alters its transcriptional activity, which has been implicated in gene regulation in neurodegeneration. Some family members contain two or three plant homeodomain (PHD) fingers, which may be involved in complex formation with histone H3 trimethylated at K4 (H3K4me3). This family corresponds to the second and third PHD fingers. 47 matched cddid_all.tbl CDD cd15561 cd15561 277036 PHD1_PHF14 PHD finger 1 found in PHD finger protein 14 (PHF14) and similar proteins. PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the first PHD finger. 56 matched cddid_all.tbl CDD cd15562 cd15562 277037 PHD2_PHF14 PHD finger 2 found in PHD finger protein 14 (PHF14) and similar proteins. PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the second PHD finger. 50 matched cddid_all.tbl CDD cd15563 cd15563 277038 PHD3_PHF14 PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins. PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the third PHD finger. 49 matched cddid_all.tbl CDD cd15564 cd15564 277039 PHD1_NSD PHD finger 1 found in nuclear receptor-binding SET domain-containing (NSD) proteins. The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the first PHD finger. 43 matched cddid_all.tbl CDD cd15565 cd15565 277040 PHD2_NSD PHD finger 2 found in nuclear receptor-binding SET domain-containing (NSD) proteins. The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the second PHD finger. 51 matched cddid_all.tbl CDD cd15566 cd15566 277041 PHD3_NSD PHD finger 3 found in nuclear receptor-binding SET domain-containing (NSD) proteins. The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the third PHD finger. 48 matched cddid_all.tbl CDD cd15567 cd15567 277042 PHD4_NSD PHD finger 4 found in nuclear receptor-binding SET domain-containing (NSD) proteins. The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fourth PHD finger. 41 matched cddid_all.tbl CDD cd15568 cd15568 277043 PHD5_NSD PHD finger 5 found in nuclear receptor-binding SET domain-containing (NSD) proteins. The nuclear receptor binding SET domain (NSD) protein is a family of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1, that are critical in maintaining chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising to help suppress cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and they play non-redundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). This model corresponds to the fifth PHD finger. 43 matched cddid_all.tbl CDD cd15569 cd15569 277044 PHD_RAG2 PHD finger found in V(D)J recombination-activating protein 2 (RAG-2) and similar proteins. RAG-2 is an essential component of the lymphoid-specific recombination activating gene RAG1/2 V(D)J recombinase mediating antigen-receptor gene assembly. It contains an acidic hinge region implicated in histone-binding, a non-canonical plant homeodomain (PHD) finger followed by a C-terminal extension of 40 amino acids that is essential for phosphoinositide (PtdIns)-binding. The PHD finger is a chromatin-binding module that specifically recognizes histone H3 trimethylated at lysine 4 (H3K4me3) and influences V(D)J recombination. 67 matched cddid_all.tbl CDD cd15570 cd15570 277045 PHD_Bye1p_SIZ1_like PHD domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p), the E3 Sumo Ligase SIZ1, and similar proteins. Yeast Bye1p is a nuclear transcription factor with a domain resembling the central domain in the transcription elongation factor TFIIS and plays an inhibitory role during transcription elongation. It functions as a multicopy suppressor of Ess1, a peptidyl-prolyl cis-trans isomerase involved in proline isomerization of the C-terminal domain (CTD) of RNA polymerase II (Pol II). Bye1p contains an N-terminal plant homeodomain (PHD) finger, a central Pol II-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. The PHD domain binds to a histone H3 tail peptide containing trimethylated lysine 4 (H3K4me3). The TLD domain is responsible for the association with chromatin. Plant SIZ1 protein is a SUMO (small ubiquitin-related modifier) E3 ligase that facilitates conjugation of SUMO to substrate target proteins (sumoylation) and belongs to the protein inhibitor of activated STAT (PIAS) protein family. It negatively regulates abscisic acid (ABA) signaling, which is dependent on the bZIP transcripton factor ABI5. It also modulates plant growth and plays a role in drought stress response likely through the regulation of gene expression. SIZ1 functions as a floral repressor that not only represses the salicylic acid (SA)-dependent pathway, but also promotes FLOWERING LOCUS C (FLC) expression by repressing FLOWERING LOCUS D (FLD) activity through sumoylation. SIZ1 contains a PHD finger, which specifically binds methylated histone H3 at lysine 4 and arginine 2. 50 matched cddid_all.tbl CDD cd15571 cd15571 277046 ePHD Extended plant homeodomain (PHD) finger, characterized by Cys2HisCys5HisCys2His. PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. The extended PHD finger is characterized as Cys2HisCys5HisCys2His, which has been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. 112 matched cddid_all.tbl CDD cd15572 cd15572 277047 PHD_BRPF PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins. The family of BRPF proteins includes BRPF1, BRD1/BRPF2, and BRPF3. They are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. This model corresponds to the canonical Cys4HisCys3 PHD finger. 54 matched cddid_all.tbl CDD cd15573 cd15573 277048 PHD_JADE PHD finger found in proteins Jade-1, Jade-2, Jade-3, and similar proteins. This family includes proteins Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16), each of which is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger. 46 matched cddid_all.tbl CDD cd15574 cd15574 277049 PHD_AF10_AF17 PHD finger found in protein AF-10 and AF-17. This family includes protein AF-10 and AF-17. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor encoded by gene AF10, a translocation partner of the MLL (mixed-lineage leukemia) oncogene in leukemia. AF-10 has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. It plays a key role in the survival of uncommitted hematopoietic cells. Moreover, AF-10 functions as a follistatin-related gene (FLRG)-interacting protein. The interaction with FLRG enhances AF10-dependent transcription. It interacts with the human counterpart of the yeast Dot1, hDOT1L, and may act as a bridge for the recruitment of hDOT1L to the genes targeted by MLL-AF10. It also interacts with the synovial sarcoma associated SYT protein and may play a role in synovial sarcomas and acute leukemias. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is encoded by gene AF17 that has been identified in hematological malignancies as translocation partners of the mixed lineage leukemia gene MLL. It is a putative transcription factor that may play a role in multiple signaling pathways. It is involved in chromatin-mediated gene regulation mechanisms. It functions as a component of the multi-subunit Dot1 complex (Dotcom) and plays a role in the Wnt/Wingless signaling pathway. It also seems to be a downstream target of the beta-catenin/T-cell factor pathway, and participates in G2-M progression. Moreover, it may function as an important regulator of ENaC-mediated Na+ transport and thus blood pressure. Both AF-10 and AF-17 contain an N-terminal canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. The PHD finger is involved in their homo-oligomerization. In the C-terminal region, they possess a leucine zipper domain and a glutamine-rich region. This family also includes ZFP-1, the Caenorhabditis elegans AF10 homolog. It was originally identified as a factor promoting RNAi interference in C. elegans. It also acts as a Dot1-interacting protein that opposes H2B ubiquitination to reduce polymerase II (Pol II) transcription. This model corresponds to the canonical Cys4HisCys3 PHD finger. 48 matched cddid_all.tbl CDD cd15575 cd15575 277050 PHD_JMJD2A PHD finger found in Jumonji domain-containing protein 2A (JMJD2A). JMJD2A, also termed lysine-specific demethylase 4A (KDM4A), or JmjC domain-containing histone demethylation protein 3A (JHDM3A), catalyzes the demethylation of di- and trimethylated H3K9 and H3K36. It is involved in carcinogenesis and functions as a transcription regulator that may either stimulate or repress gene transcription. It associates with nuclear receptor co-repressor complex or histone deacetylases. Moreover, JMJD2A forms complexes with both the androgen and estrogen receptor (ER) and plays an essential role in growth of both ER-positive and -negative breast tumors. It is also involved in prostate, colon, and lung cancer progression. JMJD2A contains jmjN and jmjC domains in the N-terminal region, followed by a canonical Cys4HisCys3 PHD finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. This model corresponds to the canonical Cys4HisCys3 PHD finger. 100 matched cddid_all.tbl CDD cd15576 cd15576 277051 PHD_JMJD2B PHD finger found in Jumonji domain-containing protein 2B (JMJD2B). JMJD2B, also termed lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the trimethyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical Cys4HisCys3 PHD finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. This model corresponds to the canonical Cys4HisCys3 PHD finger. 99 matched cddid_all.tbl CDD cd15577 cd15577 277052 PHD_JMJD2C PHD finger found in Jumonji domain-containing protein 2C (JMJD2C). JMJD2C, also termed lysine-specific demethylase 4C (KDM4C), or gene amplified in squamous cell carcinoma 1 protein (GASC-1 protein), or JmjC domain-containing histone demethylation protein 3C (JHDM3C), is an epigenetic factor that catalyzes the demethylation of di- and trimethylated H3K9 and H3K36, and may be involved in the development and/or progression of various types of cancer including esophageal squamous cell carcinoma (ESC) and breast cancer. It selectively interacts with hypoxia-inducible factor 1alpha (HIF1alpha) and plays a role in breast cancer progression. Moreover, JMJD2C may play an important role in the treatment of obesity and its complications through modulating the regulation of adipogenesis by nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma). JMJD2C contains jmjN and jmjC domains in the N-terminal region, followed by a canonical Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a Tudor domain. This model corresponds to the canonical Cys4HisCys3 PHD finger. 104 matched cddid_all.tbl CDD cd15578 cd15578 277053 PHD1_MTF2 PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2). MTF2, also termed metal regulatory transcription factor 2, or metal-response element DNA-binding protein M96, or polycomb-like protein 2 (PCL2), complexes with the polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. This model corresponds to the first PHD finger. 53 matched cddid_all.tbl CDD cd15579 cd15579 277054 PHD1_PHF19 PHD finger 1 found in PHD finger protein 19 (PHF19). PHF19, also termed Polycomb-like protein 3 (PCL3), is a component of the polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF19 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. It binds trimethylated histone H3 Lys36 (H3K36me3) through its Tudor domain and recruits the PRC2 complex and the H3K36me3 demethylase NO66 to embryonic stem cell genes during differentiation. Moreover, PHF19 and its upstream regulator, Akt, play roles in the phenotype switch of melanoma cells from proliferative to invasive states. This model corresponds to the first PHD finger. 53 matched cddid_all.tbl CDD cd15580 cd15580 277055 PHD2_MTF2 PHD finger 2 found in metal-response element-binding transcription factor 2 (MTF2). MTF2, also termed metal regulatory transcription factor 2, or metal-response element DNA-binding protein M96, or Polycomb-like protein 2 (PCL2), complexes with the Polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2 consists of an N-terminal Tudor domain followed by two plant homeodomain (PHD) fingers, and a C-terminal MTF2 domain. This model corresponds to the second PHD finger. 52 matched cddid_all.tbl CDD cd15581 cd15581 277056 PHD2_PHF19 PHD finger 2 found in PHD finger protein 19 (PHF19). PHF19, also termed Polycomb-like protein 3 (PCL3), is a component of the Polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF19 consists of an N-terminal Tudor domain followed by two plant homeodomain (PHD) fingers, and a C-terminal MTF2 domain. It binds H3K36me3 through its Tudor domain and recruits the PRC2 complex and the H3K36me3 demethylase NO66 to embryonic stem cell genes during differentiation. Moreover, PHF19 and its upstream regulator, Akt, play roles in the phenotype switch of melanoma cells from proliferative to invasive states. This model corresponds to the second PHD finger. 52 matched cddid_all.tbl CDD cd15582 cd15582 277057 PHD2_PHF1 PHD finger 2 found in PHD finger protein1 (PHF1). PHF1, also termed Polycomb-like protein 1 (PCL1), together with JARID2 and AEBP2, associates with the Polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF1 is essential in epigenetic regulation and genome maintenance. It acts as a dual reader of Lysine trimethylation at Lysine 36 of Histone H3 and Lysine 27 of Histone variant H3t. PHF1 consists of an N-terminal Tudor domain followed by two plant homeodomain (PHD) fingers, and a C-terminal MTF2 domain. Its Tudor domain selectively binds to histone H3K36me3. Moreover, PHF1 is required for efficient H3K27me3 and Hox gene silencing. It can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response. This model corresponds to the second PHD finger. 52 matched cddid_all.tbl CDD cd15583 cd15583 277058 PHD_ash2p_like PHD finger found in Schizosaccharomyces pombe Set1 complex component ash2 (spAsh2p) and similar proteins. spAsh2p, also termed Set1C component ash2, or COMPASS component ash2, or complex proteins associated with set1 protein ash2, or Lid2 complex component ash2, or Lid2C component ash2, is orthologous to Drosophila melanogaster Ash2 protein. Both spAsh2p and D. melanogaster Ash2 contain a plant homeodomain (PHD) finger and a SPRY domain. In contrast, its counterpart in Saccharomyces cerevisiae, Bre2p, has no PHD finger and is not included in this family. spAsh2p shows histone H3 Lys4 (H3K4) methyltransferase activity through its PHD finger. It also interacts with Lid2p in S. pombe. Human Ash2L contains an atypical PHD finger that lacks part of the Cys4HisCys3 signature characteristic of PHD fingers, it binds to only one zinc ion through the second half of the motif and does not have histone tail binding activity. 50 matched cddid_all.tbl CDD cd15584 cd15584 277059 PHD_ING1_2 PHD finger found in inhibitor of growth protein 1 (ING1) and 2 (ING2). ING1 is an epigenetic regulator and a type II tumor suppressor that impacts cell growth, aging, apoptosis, and DNA repair, by affecting chromatin conformation and gene expression. It acts as a reader of the active chromatin mark, the trimethylation of histone H3 lysine 4 (H3K4me3). It binds and directs Growth arrest and DNA damage inducible protein 45 a (Gadd45a) to target sites, thus linking the histone code with DNA demethylation. It interacts with the proliferating cell nuclear antigen (PCNA) via the PCNA-interacting protein (PIP) domain in a UV-inducible manner. It also interacts with a PCNA-interacting protein, p15 (PAF). Moreover, ING1 associates with members of the 14-3-3 family, which is necessary for cytoplasmic relocalization. Endogenous ING1 protein specifically interacts with the pro-apoptotic BCL2 family member BAX and colocalizes with BAX in a UV-inducible manner. It stabilizes the p53 tumor suppressor by inhibiting polyubiquitination of multi-monoubiquitinated forms via interaction with and colocalization of the herpesvirus-associated ubiquitin-specific protease (HAUSP)-deubiquitinase with p53. It is also involved in trichostatin A-induced apoptosis and caspase 3 signaling in p53-deficient glioblastoma cells. In addition, tyrosine kinase Src can bind and phosphorylate ING1 and further regulates its activity. ING2, also termed inhibitor of growth 1-like protein (ING1Lp), or p32, or p33ING2, belongs to the inhibitor of growth (ING) family of type II tumor suppressors. It is a core component of a multi-factor chromatin-modifying complex containing the transcriptional co-repressor SIN3A and histone deacetylase 1 (HDAC1). It has been implicated in the control of cell cycle, in genome stability, and in muscle differentiation. ING2 independently interacts with H3K4me3 (Histone H3 trimethylated on lysine 4) and PtdIns(5)P, and modulates crosstalk between lysine methylation and lysine acetylation on histone proteins through association with chromatin in the presence of DNA damage. It collaborates with SnoN to mediate transforming growth factor (TGF)-beta-induced Smad-dependent transcription and cellular responses. It is upregulated in colon cancer and increases invasion by enhanced MMP13 expression. It also acts as a cofactor of p300 for p53 acetylation and plays a positive regulatory role during p53-mediated replicative senescence. Both ING1 and ING2 contain an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger. 45 matched cddid_all.tbl CDD cd15585 cd15585 277060 PHD_ING3 PHD finger found in inhibitor of growth protein 3 (ING3) and similar proteins. ING3, also termed p47ING3, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It is ubiquitously expressed and has been implicated in transcription modulation, cell cycle control, and the induction of apoptosis. It is an important subunit of human NuA4 histone acetyltransferase complex, which regulates the acetylation of histones H2A and H4. Moreover, ING3 promotes ultraviolet (UV)-induced apoptosis through the Fas/caspase-8-dependent pathway in melanoma cells. It physically interacts with subunits of E3 ligase Skp1-Cullin-F-boxprotein complex (SCF complex) and is degraded by the SCF (F-box protein S-phase kinase-associated protein 2, Skp2)-mediated ubiquitin-proteasome system. It also acts as a suppression factor during tumorigenesis and progression of hepatocellular carcinoma (HCC). ING3 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger. 45 matched cddid_all.tbl CDD cd15586 cd15586 277061 PHD_ING4_5 PHD finger found in inhibitor of growth protein 4 (ING4) and 5 (ING5). ING4, also termed p29ING4, and ING5, also termed p28ING5, belong to the inhibitor of growth (ING) family of type II tumor suppressors. ING4 acts as an E3 ubiquitin ligase to induce ubiquitination of the p65 subunit of NF-kappaB and inhibit the transactivation of NF-kappaB target genes. It also induces apoptosis through a p53 dependent pathway, including increasing p53 acetylation, inhibiting Mdm2-mediated degradation of p53 and enhancing the expression of p53 responsive genes both at the transcriptional and post-translational levels. Moreover, ING4 can inhibit the translation of proto-oncogene MYC by interacting with AUF1. It also regulates other transcription factors, such as hypoxia-inducible factor (HIF). ING5 is a Tip60 cofactor that acetylates p53 at K120 and subsequently activates the expression of p53-dependent apoptotic genes in response to DNA damage. Aberrant ING5 expression may contribute to pathogenesis, growth, and invasion of gastric carcinomas and colorectal cancer. ING5 can physically interact with p300 and p53 in vivo, and its overexpression induces apoptosis in colorectal cancer cells. It also associates with cyclin A1 (INCA1) and functions as a growth suppressor with suppressed expression in Acute Myeloid Leukemia (AML). Moreover, ING5 translocation from the nucleus to the cytoplasm might be a critical event for carcinogenesis and tumor progression in human head and neck squamous cell carcinoma. Both ING4 and ING5 contain an N-terminal ING histone-binding domain and a C-terminal plant homeodomain (PHD) finger. They associate with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further direct the MOZ/MORF and HBO1 complexes to chromatin. 45 matched cddid_all.tbl CDD cd15587 cd15587 277062 PHD_Yng1p_like PHD finger found in yeast orthologs of ING tumor suppressor family. The yeast orthologs of the plant homeodomain (PHD) finger-containing ING tumor suppressor family consists of chromatin modification-related protein YNG1 (Yng1p), YNG2 (Yng2p), and transcriptional regulatory protein PHO23 (Pho23p). Yng1p, also termed ING1 homolog 1, is one of the components of the NuA3 histone acetyltransferase (HAT) complex. Its PHD finger binding to H3 Trimethylated at K4 (H3K4me3) promotes NuA3 H3 HAT activity at K14 of H3 on chromatin. Yng2p, also termed ESA1-associated factor 4, or ING1 homolog 2, is a subunit of the NuA4 HAT complex. It plays a critical role in intra-S-phase DNA damage response. Pho23p is part of the Rpd3/Sin3 histone deacetylase (HDAC) complex. It is required for the normal function of Rpd3 in the silencing of rDNA, telomeric, and mating-type loci. Yng1p and Pho23p inhibit p53-dependent transcription. In contrast, Yng2p has the opposite effect. All family members contain an N-terminal ING histone-binding domain and a C-terminal PHD finger. 47 matched cddid_all.tbl CDD cd15588 cd15588 277063 PHD1_KMT2A PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A). KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (Htrx), or zinc finger protein HRX) is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger. 47 matched cddid_all.tbl CDD cd15589 cd15589 277064 PHD1_KMT2B PHD finger 1 found in Histone-lysine N-methyltransferase 2B (KMT2B). KMT2B, also termed trithorax homolog 2 or WW domain-binding protein 7 (WBP-7), is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger. 47 matched cddid_all.tbl CDD cd15590 cd15590 277065 PHD2_KMT2A PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A). KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (Htrx), or zinc finger protein HRX) is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger. 50 matched cddid_all.tbl CDD cd15591 cd15591 277066 PHD2_KMT2B PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B). KMT2B, also termed trithorax homolog 2 or WW domain-binding protein 7 (WBP-7), is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD), an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger. 50 matched cddid_all.tbl CDD cd15592 cd15592 277067 PHD3_KMT2A PHD finger 3 found in histone-lysine N-methyltransferase 2A (KMT2A). KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (Htrx), or zinc finger protein HRX) is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger. 57 matched cddid_all.tbl CDD cd15593 cd15593 277068 PHD3_KMT2B PHD finger 3 found in Histone-lysine N-methyltransferase 2B (KMT2B). KMT2B, also termed trithorax homolog 2 or WW domain-binding protein 7 (WBP-7), is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the third PHD finger. 57 matched cddid_all.tbl CDD cd15594 cd15594 277069 PHD2_KMT2C PHD finger 2 found in Histone-lysine N-methyltransferase 2C (KMT2C). KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the second PHD finger. 46 matched cddid_all.tbl CDD cd15595 cd15595 277070 PHD2_KMT2D PHD finger 2 found in Histone-lysine N-methyltransferase 2D (KMT2D). KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the second PHD finger. 46 matched cddid_all.tbl CDD cd15596 cd15596 277071 PHD4_KMT2C PHD finger 4 found in Histone-lysine N-methyltransferase 2C (KMT2C). KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the fourth PHD finger. 57 matched cddid_all.tbl CDD cd15597 cd15597 277072 PHD3_KMT2D PHD finger 3 found in Histone-lysine N-methyltransferase 2D (KMT2D). KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the third PHD finger. 51 matched cddid_all.tbl CDD cd15600 cd15600 277073 PHD6_KMT2C PHD finger 6 found in Histone-lysine N-methyltransferase 2C (KMT2C). KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. This model corresponds to the sixth PHD finger. 51 matched cddid_all.tbl CDD cd15601 cd15601 277074 PHD5_KMT2D PHD finger 5 found in Histone-lysine N-methyltransferase 2D (KMT2D). KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such asHOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is downregulated in cholestasis. KMT2D contains the catalytic domain SET, five plant homeodomain (PHD) fingers, two extended PHD (ePHD) fingers, Cys2HisCys5HisCys2His, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. This model corresponds to the fifth PHD finger. 51 matched cddid_all.tbl CDD cd15602 cd15602 277075 PHD1_KDM5A PHD finger 1 found in Lysine-specific demethylase 5A (KDM5A). KDM5A (also termed Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2)) was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger. 49 matched cddid_all.tbl CDD cd15603 cd15603 277076 PHD1_KDM5B PHD finger 1 found in lysine-specific demethylase 5B (KDM5B). KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A)) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of pregnant females and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger. 46 matched cddid_all.tbl CDD cd15604 cd15604 277077 PHD1_KDM5C_5D PHD finger 1 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D). The family includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C (also termed Histone demethylase JARID1C, Jumonji/ARID domain-containing protein 1C, SmcX, or Xe169) is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D (also termed Histocompatibility Y antigen (H-Y), Histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or SmcY) is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 andH3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. Both KDM5C and KDM5D contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger. 46 matched cddid_all.tbl CDD cd15605 cd15605 277078 PHD1_Lid_like PHD finger 1 found in Drosophila melanogaster protein little imaginal discs (Lid) and similar proteins. Drosophila melanogaster Lid, also termed Retinoblastoma-binding protein 2 homolog, is identified genetically as a trithorax group (trxG) protein that is a Drosophila homolog of the human protein JARID1A/kdm5A, a member of the JARID subfamily within the JmjC proteins. Lid functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Lid contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the first PHD finger of Lid. 46 matched cddid_all.tbl CDD cd15606 cd15606 277079 PHD2_KDM5A PHD finger 2 found in Lysine-specific demethylase 5A (KDM5A). KDM5A (also termed Histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2)) was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK, and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger. 56 matched cddid_all.tbl CDD cd15607 cd15607 277080 PHD2_KDM5B PHD finger 2 found in lysine-specific demethylase 5B (KDM5B). KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), or PLU-1) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger. 44 matched cddid_all.tbl CDD cd15608 cd15608 277081 PHD2_KDM5C_5D PHD finger 2 found in Lysine-specific demethylase 5C (KDM5C) and 5D (KDM5D). The family includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C (also termed Histone demethylase JARID1C, Jumonji/ARIDdomain-containing protein 1C, SmcX, or Xe169) is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D (also termed Histocompatibility Y antigen (H-Y), Histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or SmcY) is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 and H3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. Both KDM5C and KDM5D contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as two plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger. 58 matched cddid_all.tbl CDD cd15609 cd15609 277082 PHD_TCF19 PHD finger found in Transcription factor 19 (TCF-19) and similar proteins. TCF-19, also termed transcription factor SC1, was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It also functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. TCF-19 contains an N-terminal fork head association domain (FHA), a proline rich region, and a C-terminal plant homeodomain (PHD) finger. The FHA domain may serve as a nuclear signaling domain or as a phosphoprotein binding domain. The proline rich region is a common characteristic of trans-activating factors. The PHD finger may allow TCF-19 to interact with chromatin via methylated histone H3. 50 matched cddid_all.tbl CDD cd15610 cd15610 277083 PHD3_KDM5A_like PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A), 5B (KDM5B), and similar proteins. The family includes KDM5A and KDM5B, both of which belong to the JARID subfamily within the JmjC proteins. KDM5A, also termed Histone demethylase JARID1A, or Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2), was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as the trimethylated histone H3 lysine 4 (H3K4me3) demethylase. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5B, also termed Cancer/testis antigen 31 (CT31), or Histone demethylase JARID1B, or Jumonji/ARID domain-containing protein 1B (JARID1B), or PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well asTIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. The family also includes the Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members in this family contain the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the third PHD finger. 50 matched cddid_all.tbl CDD cd15612 cd15612 277084 PHD_OBE1_like PHD finger found in Arabidopsis thaliana protein OBERON 1, OBERON 2, and similar proteins mainly found in plants. Included in this family are OBERON 1 (OBE1, or potyvirus VPg-interacting protein 2) and OBERON 2 (OBE2, or potyvirus VPg-interacting protein 1), which have been involved in the maintenance and/or establishment of the meristems in Arabidopsis. They interact with potyvirus VPg-interacting proteins (PVIP1 and 2) and act as central regulators in auxin-mediated control of development. Both OBE1and OBE2 contain a plant homeodomain (PHD) finger. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. 60 matched cddid_all.tbl CDD cd15613 cd15613 277085 PHD_AL_plant PHD finger found in plant Alfin1-like (AL) proteins. AL proteins are ubiquitously expressed nuclear proteins existing only in plants. They are involved in chromatin regulation by binding to tri- and dimethylated histone H3 at lysine 4 (H3K4me3/2), the active histone markers, through their plant homeodomain (PHD) fingers. 51 matched cddid_all.tbl CDD cd15614 cd15614 277086 PHD_HAC_like PHD finger found in Arabidopsis thaliana histone acetyltransferases (HATs) HAC and similar proteins. This family includes A. thaliana HACs (HAC1/2/4/5/12), which are histone acetyltransferases of the p300/CREB-binding protein (CBP) co-activator family. CBP-type HAT proteins are also found in animals, but absent in fungi. The domain architecture of CBP-type HAT proteins differs between plants and animals. Members in this family contain an N-terminal partially conserved KIX domain, a Zf-TAZ domain, a Cysteine rich CBP-type HAT domain that harbors a plant homeodomain (PHD) finger, a Zf-ZZ domain, and a Zf-TAZ domain. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. 73 matched cddid_all.tbl CDD cd15615 cd15615 277087 PHD_ARID4_like PHD finger found in Arabidopsis thaliana AT-rich interactive domain-containing protein 4 (ARID4) and similar proteins. This family includes A. thaliana ARID4 (ARID domain-containing protein 4) and similar proteins. Their biological roles remain unclear, but they all contain an AT-rich interactive domain (ARID) and a plant homeodomain (PHD) finger at the C-terminus. ARID is a helix-turn-helix motif-based DNA-binding domain conserved in all eukaryotes. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. 57 matched cddid_all.tbl CDD cd15616 cd15616 277088 PHD_UHRF1 PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1). UHRF1 (also termed inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1) is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintaining DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1. 47 matched cddid_all.tbl CDD cd15617 cd15617 277089 PHD_UHRF2 PHD finger found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2). UHRF2 (also termed Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2) was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs,p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger. 47 matched cddid_all.tbl CDD cd15618 cd15618 277090 PHD1_MOZ_MORF PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF). MOZ (also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60protein 3 (MYST-3), runt-related transcription factor-binding protein 2, or zinc finger protein 220) is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The model corresponds to the first PHD finger. 58 matched cddid_all.tbl CDD cd15619 cd15619 277091 PHD1_d4 PHD finger 1 found in d4 gene family proteins. The family includes proteins coded by three members of the d4 gene family, DPF1 (neuro-d4), DPF2 (ubi-d4/Requiem), and DPF3 (cer-d4), which function as transcription factors and are involved in transcriptional regulation of genes by changing the condensed/decondensed state of chromatin in the nucleus. DPF2 is ubiquitously expressed and it acts as a transcription factor that may participate in developmentally programmed cell death. DPF1 and DPF3 are expressed predominantly in neural tissues, and they may be involved in the transcription regulation of neuro-specific gene clusters. The d4 family proteins show distinct domain organization with domain 2/3 in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc finger in the central part and two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the first PHD finger. 56 matched cddid_all.tbl CDD cd15622 cd15622 277092 PHD_TIF1alpha PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha). TIF1-alpha, also termed tripartite motif-containing protein 24 (TRIM24), or E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the TRIM/RBCC protein family. It interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoid X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta) and MOD2 (HP1gamma), as well as vertebrate Kruppel-type (C2H2) zinc finger proteins that contain transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif, and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53 and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal plant homeodomain (PHD)-Bromodomain (Bromo) region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development. TIF1-alpha contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region. 43 matched cddid_all.tbl CDD cd15623 cd15623 277093 PHD_TIF1beta PHD finger found in transcription intermediary factor 1-beta (TIF1-beta). TIF1-beta, also termed Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), or KRAB-interacting protein 1 (KRIP-1), or nuclear co-repressor KAP-1, or RING finger protein 96, or tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, acts as a nuclear co-repressor that plays a role in transcription and in DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. In addition, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. TIF1-beta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), which can interact with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and mediates homo- and heterodimerization, a plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region, which interact with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity. 43 matched cddid_all.tbl CDD cd15624 cd15624 277094 PHD_TIF1gamma PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma). TIF1gamma, also termed tripartite motif-containing 33 (trim33), or ectodermin, or RFG7, or PTC7, is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling; it inhibits the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1gamma is an important regulator of transcription during hematopoiesis, as well as a key factor of tumorigenesis. Like other TIF1 family members, TIF1gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis. TIF1gamma contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region. 46 matched cddid_all.tbl CDD cd15625 cd15625 277095 PHD_TIF1delta PHD finger found in transcriptional intermediary factor 1 delta (TIF1delta). TIF1delta, also termed tripartite motif-containing protein 66 (TRIM66), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor1 (TIF1) family expressed by elongating spermatids. Like other TIF1 proteins, TIF1delta displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TIF1delta plays an important role in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. It functions as a negative regulator of postmeiotic genes acting through HP1 isotype gamma (HP1gamma) complex formation and centromere association. TIF1delta contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region. 49 matched cddid_all.tbl CDD cd15626 cd15626 277096 PHD_SP110_140 PHD finger found in the Sp100/Sp140 family of nuclear body components. The Sp100/Sp140 family includes nuclear body proteins SP100, SP140, and similar proteins. Sp110, also termed interferon-induced protein 41/75, or speckled 110 kDa, or transcriptional coactivator Sp110, is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. Sp110 gene polymorphisms may be associated with susceptibility to tuberculosis in Chinese population. Sp110 contains a Sp100-like domain, a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD). SP140, also termed lymphoid-restricted homolog of Sp100 (LYSp100), or nuclear autoantigen Sp-140, or speckled 140 kDa, is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus's viral infectivity factor (Vif) protein. Sp140 contains a nuclear localization signal, a dimerization domain (HSR or CARD domain), a SAND domain, a PHD finger, and a BRD. 42 matched cddid_all.tbl CDD cd15627 cd15627 277097 PHD_BAZ1A PHD finger found in bromodomain adjacent to zinc finger domain protein 1A (BAZ1A). BAZ1A, also termed ATP-dependent chromatin-remodeling protein, or ATP-utilizing chromatin assembly and remodeling factor 1 (ACF1), or CHRAC subunit ACF1, or Williams syndrome transcription factor-related chromatin-remodeling factor 180 (WCRF180), or WALp1, is a subunit of the conserved imitation switch (ISWI)-family ATP-dependent chromatin assembly and remodeling factor (ACF)/chromatin accessibility complex (CHRAC) chromatin remodeling complex, which is required for DNA replication through heterochromatin. It alters the remodeling properties of the ATPase motor protein sucrose nonfermenting-2 homolog (SNF2H). Moreover, BAZ1A and its complexes play important roles in DNA double-strand break (DSB) repair. It is essential for averting improper gene expression during spermatogenesis. It also regulates transcriptional repression of vitamin D3 receptor-regulated genes. BAZ1A contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. 46 matched cddid_all.tbl CDD cd15628 cd15628 277098 PHD_BAZ1B PHD finger found in bromodomain adjacent to zinc finger domain protein 1B (BAZ1B). BAZ1B, also termed Tyrosine-protein kinase BAZ1B, or Williams syndrome transcription factor (WSTF), or Williams-Beuren syndrome chromosomal region 10 protein, Williams-Beuren syndrome chromosomal region 9 protein, or WALp2, is a multifunctional protein implicated in several nuclear processes, including replication, transcription, and the DNA damage response. BAZ1B/WSTF, together with the imitation switch (ISWI) ATPase, forms a WSTF-ISWI chromatin remodeling complex (WICH), which transiently associates with the human inactive X chromosome (Xi) during late S-phase prior to BRCA1 and gamma-H2AX. Moreover, BAZ1B/WSTF, SNF2h, and nuclear myosin 1 (NM1) forms the chromatin remodeling complex B-WICH that is involved in regulating rDNA transcription. BAZ1B contains a WAC motif, a DDT domain, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. 46 matched cddid_all.tbl CDD cd15629 cd15629 277099 PHD_BAZ2A PHD finger found in bromodomain adjacent to zinc finger domain protein 2A (BAZ2A). BAZ2A, also termed transcription termination factor I-interacting protein 5 (TTF-I-interacting protein 5, or Tip5), or WALp3, is an epigenetic regulator. It has been implicated in epigenetic rRNA gene silencing, as the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP- and histone H4 tail-dependent fashion. BAZ2A has also been shown to be broadly overexpressed in prostate cancer, to regulate numerous protein-coding genes and to cooperate with EZH2 (enhancer of zeste homolog 2) to maintain epigenetic silencing at genes repressed in prostate cancer metastasis. Its overexpression is tightly associated with a prostate cancer subtype displaying CpG island methylator phenotype (CIMP) in tumors and with prostate cancer recurrence in patients. It contains a TAM (TIP5/ARBP/MBD) domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. 47 matched cddid_all.tbl CDD cd15630 cd15630 277100 PHD_BAZ2B PHD finger found in bromodomain adjacent to zinc finger domain protein 2B (BAZ2B). BAZ2B, also termed WALp4, is a bromodomain-containing protein whose biological role is still elusive. It shows high sequence similarly with BAZ2A, which is the large subunit of the SNF2h-containing chromatin-remodeling complex NoRC that induces nucleosome sliding in an ATP-and histone H4 tail-dependent fashion. BAZ2B contains a TAM (TIP5/ARBP/MBD) domain, an Apolipophorin-III like domain, a DDT domain, four AT-hooks, BAZ 1 and BAZ 2 motifs, a WAKZ (WSTF/Acf1/KIAA0314/ZK783.4) motif, a plant homeodomain (PHD) finger, and a bromodomain. 49 matched cddid_all.tbl CDD cd15631 cd15631 277101 PHD_PHF23 PHD finger found in PHD finger protein 23 (PHF23). PHF23, also termed PHD-containing protein JUNE-1, is a hypothetical protein with a plant homeodomain (PHD) finger. It is encoded by gene PHF23 that acts as a candidate fusion partner for the nucleoporin gene NUP98. The NUP98-PHF23 fusion results from a cryptic translocation t(11;17)(p15;p13) in acute myeloid leukemia (AML). 44 matched cddid_all.tbl CDD cd15632 cd15632 277102 PHD_PHF13 PHD finger found in PHD finger protein 13 (PHF13). PHF13, also termed survival time-associated PHD finger protein in ovarian cancer 1 (SPOC1), is a novel plant homeodomain (PHD) finger-containing protein that shows strong expression in spermatogonia and ovarian cancer cells, modulates chromatin structure and mitotic chromosome condensation, and is important for proper cell division. It is also required for spermatogonial stem cell differentiation and sustained spermatogenesis. The overexpression of PHF13 associates with unresectable carcinomas and shorter survival in ovarian cancer. 47 matched cddid_all.tbl CDD cd15633 cd15633 277103 PHD_PHF20L1 PHD finger found in PHD finger protein 20-like protein 1 (P20L1). P20L1 is an active malignant brain tumor (MBT) domain-containing protein that binds to monomethylated lysine 142 on DNA (Cytosine-5) Methyltransferase 1 (DNMT1) (DNMT1K142me1) and colocalizes at the perinucleolar space in a SET7-dependent manner. Its MBT domain reads and controls enzyme levels of methylated DNMT1 in cells, thus representing a novel antagonist of DNMT1 proteasomal degradation. In addition to the MBT domain, PHF20L1 also contains two Tudor domains, a plant homeodomain (PHD) finger and the putative DNA-binding domains, AT hook and Cys2His2-type zinc finger. 46 matched cddid_all.tbl CDD cd15634 cd15634 277104 PHD_PHF20 PHD finger found in PHD finger protein 20 (PHF20). PHF20, also termed Glioma-expressed antigen 2, or hepatocellular carcinoma-associated antigen 58, or novel zinc finger protein, or transcription factor TZP (referring to Tudor and zinc finger domain containing protein), is a regulator of NF-kappaB activation by disrupting recruitment of PP2A to p65. It also functions as a transcription factor that binds Akt and plays a role in Akt cell survival/growth signaling. Moreover, it transcriptionally regulates p53. The phosphorylation of PHF20 on Ser291 mediated by protein kinase B (PKB) is essential in tumorigenesis via the regulation of p53 mediated signaling. PHF20 contains an N-terminal malignant brain tumor (MBT) domain, two Tudor domains, a plant homeodomain (PHD) finger and the putative DNA-binding domains, AT hook and Cys2His2-type zinc finger. 44 matched cddid_all.tbl CDD cd15635 cd15635 277105 PHD_PYGO1 PHD finger found in pygopus homolog 1 (PYGO1). PYGO1 is a homolog of Drosophila melanogaster protein pygopus (dPYGO), which is a fundamental Wnt signaling transcriptional component in Drosophila. It functions as a context-dependent beta-catenin coactivator, and binds di- and trimethylated lysine 4 of histone H3 (H3K4me2/3). PYGO1 is essential for the association with Legless (Lgs)/Bcl9 that acts as an adaptor between Pygopus (Pygo) and Arm/beta-catenin. PYGO1 contains a plant homeodomain (PHD) finger, which is important for Lgs/Bcl9 recognition as well as for the regulation of the Wnt/beta-catenin signaling pathway. 57 matched cddid_all.tbl CDD cd15636 cd15636 277106 PHD_PYGO2 PHD finger found in pygopus homolog 2 (PYGO2). PYGO2 is a homolog of Drosophila melanogaster protein pygopus (dPYGO), which is a fundamental Wnt signaling transcriptional component in Drosophila. It functions as a context-dependent beta-catenin coactivator, as well as a histone methylation reader that binds di-and trimethylated lysine 4 of histone H3 (H3K4me2/3). Moreover, PYGO2 acts as a chromatin remodeler in a testis-specific and Wnt-unrelated manner. It also mediates chromatin regulation and links Wnt signaling and Notch signaling to suppress the luminal/alveolar differentiation competence of mammary stem and basal cells. Furthermore, PYGO2 plays a new role in rRNA transcription during cancer cell growth. It regulates mammary tumor initiation and heterogeneity in MMTV-Wnt1 mice. PYGO2 contains a plant homeodomain (PHD) finger, which is important for Lgs/Bcl9 recognition as well as for the regulation of the Wnt/beta-catenin signaling pathway. 54 matched cddid_all.tbl CDD cd15637 cd15637 277107 PHD_dPYGO PHD finger found in Drosophila melanogaster protein pygopus (dPYGO) and similar proteins. dPYGO, also termed protein gammy legs, is a nuclear adapter protein encoded by pygopus (pygo). It is a fundamental Wnt signaling transcriptional component in Drosophila, and has both Wnt-related and Wnt-independent functions. It plays a critical role in aging-related cardiac dysfunction that is canonical Wnt signaling independent. dPYGO contains a plant homeodomain (PHD) finger, which is important for Lgs/Bcl9 recognition as well as for the regulation of the Wnt/beta-catenin signaling pathway. 54 matched cddid_all.tbl CDD cd15638 cd15638 277108 PHD_PHF3 PHD finger found in PHD finger protein 3 (PHF3). PHF3 is a human homolog of yeast protein bypass of Ess1 (Bye1), a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. PHF3 contains an N-terminal plant homeodomain (PHD) finger, a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal Spen paralogue and orthologue C-terminal (SPOC) domain. 51 matched cddid_all.tbl CDD cd15639 cd15639 277109 PHD_DIDO1_like PHD finger found in death-inducer obliterator variants Dido1, Dido2, and Dido3. This family includes three alternative splicing variants (Dido1, 2, and 3) encoded by the Dido gene, which have been implicated in a number of cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. Dido1, also termed DIO-1, or death-associated transcription factor 1 (DATF-1), is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved plant homeodomain (PHD) finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine 4 (H3K4me3). Gene Dido is a Bonemorphogenetic protein (BMP) target gene, which promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, aspen paralog and ortholog (SPOC) module, and a long C-terminal region (CT) of unknown homology. Its PHD finger interacts with H3K4me3. 54 matched cddid_all.tbl CDD cd15640 cd15640 277110 PHD_KDM7 PHD finger found in lysine-specific demethylase 7 (KDM7). KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. KDM7 contains a plant homeodomain (PHD) that binds Lys4-trimethylated histone 3 (H3K4me3) and a jumonji domain that demethylates either H3K9me2 or H3K27me2. 50 matched cddid_all.tbl CDD cd15641 cd15641 277111 PHD_PHF2 PHD finger found in lysine-specific demethylase PHF2. PHF2, also termed GRC5, or PHD finger protein 2, is a histone lysine demethylase ubiquitously expressed in various tissues. It contains a plant homeodomain (PHD) finger and a JmjC domain and plays an important role in adipogenesis. The PHD finger domain can recognize trimethylated histone H3 lysine 4 (H3K4me3). PHF2 also has dimethylated histone H3 lysine 9(H3K9me2) demethylase activity and acts as a coactivator of several metabolism-related transcription factors. Moreover, it can demethylate ARID5B and further forms a complex with demethylated ARD5B to bind the promoter regions of target genes. The overexpression of PHF2 is involved in the progression of esophageal squamous cell carcinoma (ESCC). 50 matched cddid_all.tbl CDD cd15642 cd15642 277112 PHD_PHF8 PHD finger found in histone lysine demethylase PHF8. PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20 (H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. PHF8 contains an N-terminal plant homeodomain (PHD) finger followed by a JmjC domain. The PHD finger mediates binding to nucleosomes at active gene promoters and the JmjC domain catalyzes the demethylation of mono- or dimethyl-lysines. 52 matched cddid_all.tbl CDD cd15643 cd15643 277113 PHD_KDM2A PHD finger found in Lysine-specific demethylase 2A (KDM2A). KDM2A, also termed CXXC-type zinc finger protein 8, or F-box and leucine-rich repeat protein 11 (FBXL11), or F-box protein FBL7, or F-box protein Lilina, or F-box/LRR-repeat protein 11, or JmjC domain-containing histone demethylation protein 1A (Jhdm1a), or [Histone-H3]-lysine-36 demethylase 1A, is a ubiquitously expressed histone H3 lysine 36 (H3K36) demethylase that has been implicated in gene silencing, cell cycle, cell growth, and cancer development. It acts as a key negative regulator of gluconeogenic gene expression and plays a critical role in the invasiveness, proliferation, and anchorage-independent growth of non-small cell lung cancer (NSCLC) cells, as well as in the osteo/dentinogenic differentiation of Mesenchymal stem cells (MSCs). It regulates rRNA transcription in response to starvation. Meanwhile, it is a negative regulator of NFkappaB. Moreover, KDM2A is a heterochromatin-associated and HP1-interacting protein that promotes HP1 localization to chromatin. It is specifically recruited to CpG islands to define a unique chromatin architecture, which requires direct and specific interaction with linker DNA. It also functions as a H3K4 demethylase that regulates cell proliferation through p15 (INK4B) and p27 (Kip1) in stem cells from apical papilla (SCAPs). KDM2A belongs to the JmjC-domain-containing histone demethylase family. KDM2A consists of two Jumonji C (JmjC) domains, and FBXHA and FBXHB domains. A CXXC zinc-finger domain, followed by a plant homeodomain (PHD) finger, is located within the FBXHA domain, and an F-box domain, followed by an antagonist of mitotic exit network protein 1 (AMN1) domain, is located within the FBXHB domain. 57 matched cddid_all.tbl CDD cd15644 cd15644 277114 PHD_KDM2B PHD finger found in Lysine-specific demethylase 2B (KDM2B). KDM2B, also termed Ndy1, or CXXC-type zinc finger protein 2, or F-box and leucine-rich (LRR) repeat protein 10 (FBXL10), or F-box protein FBL10, or JmjC domain-containing histone demethylation protein 1B (Jhdm1b), or Jumonji domain-containing EMSY-interactor methyltransferase motif protein (Protein JEMMA), or [Histone-H3]-lysine-36 demethylase 1B, is a ubiquitously expressed histone H3 lysine 4 (H3K4me2) or histone H3 lysine 36 (H3K36me2) demethylase that functions as a regulator of chemokine expression, cellular morphology, and the metabolome of fibroblasts. It regulates the differentiation of Mesenchymal Stem Cells (MSCs) and has been implicated in cell cycle regulation by de-repressing cyclin-dependent kinase inhibitor 2B (CDKN2B or p15INK4B). It also plays a role in recruiting polycomb repressive complex 1 (PRC1) to CpG islands (CGIs) of developmental genes and regulates lysine 119 monoubiquitylation on H2A (H2AK119ub1) in embryonic stem cells (ESCs). Moreover, it acts as an oncogene that plays a critical role in leukemia development and maintenance. KDM2B consists of two Jumonji C (JmjC) domains, and FBXHA and FBXHB domains. A CXXC zinc-finger domain, followed by a plant homeodomain (PHD) finger, is located within the FBXHA domain, and an F-box domain, followed by an antagonist of mitotic exit network protein 1 (AMN1) domain, is located within the FBXHB domain. 62 matched cddid_all.tbl CDD cd15645 cd15645 277115 PHD_FXL19 PHD finger found in F-box and leucine-rich repeat protein 19 (FBXL19). FBXL19, also termed F-box/LRR-repeat protein 19, is a novel homolog of KDM2A and KDM2B. It belongs to the Skp1-Cullin-F-box (SCF) family of E3 ubiquitin ligases. FBXL19 mediates ubiquitination and interleukin 33 (IL-33)-induced degradation of ST2L receptor in lung epithelia, blocks IL-33-mediated apoptosis, and prevents endotoxin-induced acute lung injury. It also functions as a RhoA antagonist during cell proliferation and cytoskeleton rearrangement, and regulates RhoA ubiquitination and degradation in lung epithelial cells. Moreover, FBXL19 regulates cell migration by targeting Rac1 for its polyubiquitination and proteasomal degradation. It plays an essential role in regulating TGFbeta1-induced E-cadherin down-regulation by mediating Rac3 site-specific ubiquitination and stability. FBXL19 consists of FBXHA and FBXHB domains. A CXXC zinc-finger domain, followed by a plant homeodomain (PHD) finger, is located within the FBXHA domain, and an F-box domain, followed by an antagonist of mitotic exit network protein 1 (AMN1) domain, is located within the FBXHB domain. 62 matched cddid_all.tbl CDD cd15646 cd15646 277116 PHD_p300 PHD finger found in histone acetyltransferase p300. p300, also termed KAT3B, or E1A-associated protein p300 (EP300), is a paralog of CREB-binding protein (CBP). It is involved in E1A function in cell cycle progression and cellular differentiation. It functions as an intrinsic HAT, as well as a factor acetyltransferase (FAT) for many transcription regulators. And thus, p300 serves as a scaffold or bridge for transcription factors and other components of the basal transcription machinery to facilitate chromatin remodeling and to activate gene transcription. p300 contains a cysteine-histidine rich region, KIX (CREB interaction) domain, a plant homeodomain (PHD) finger, a HAT domain, followed by a SRC interaction domain. 40 matched cddid_all.tbl CDD cd15647 cd15647 277117 PHD_CBP PHD finger found in CREB-binding protein (CBP). CBP, also termed as KAT3A, is an acetyltransferase acting on histone, which gives a specific tag for transcriptional activation and also acetylates non-histone proteins. CBP is also known as CREBBP, since it specifically interacts with the phosphorylated form of cyclic adenosine monophosphate-responsive element-binding protein (CREB). It augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes. CBP contains a cysteine-histidine rich region, a KIX (CREB interaction) domain, a plant homeodomain (PHD) finger, a HAT domain, followed by a SRC interaction domain. 40 matched cddid_all.tbl CDD cd15648 cd15648 277118 PHD1_NSD1_2 PHD finger 1 found in nuclear receptor-binding SET domain-containing protein NSD1 and NSD2. NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). Both NSD1 and NSD2 contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). In addition, NSD2 harbors a high mobility group (HMG) box. The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the first PHD finger. 43 matched cddid_all.tbl CDD cd15649 cd15649 277119 PHD1_NSD3 PHD finger 1 found in nuclear SET domain-containing protein 3 (NSD3). NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the first PHD finger. 44 matched cddid_all.tbl CDD cd15650 cd15650 277120 PHD2_NSD1 PHD finger 2 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1). NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or LysineN-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD1 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (C5HCH). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the second PHD finger. 47 matched cddid_all.tbl CDD cd15651 cd15651 277121 PHD2_NSD2 PHD finger 2 found in nuclear SET domain-containing protein 2 (NSD2). NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). NSD2 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, a high mobility group (HMG) box, five PHD (plant homeodomain) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the second PHD finger. 47 matched cddid_all.tbl CDD cd15652 cd15652 277122 PHD2_NSD3 PHD finger 2 found in nuclear SET domain-containing protein 3 (NSD3). NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the second PHD finger. 47 matched cddid_all.tbl CDD cd15653 cd15653 277123 PHD3_NSD1 PHD finger 3 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1). NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD1 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the third PHD finger. 54 matched cddid_all.tbl CDD cd15654 cd15654 277124 PHD3_NSD2 PHD finger 3 found in nuclear SET domain-containing protein 2 (NSD2). NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). NSD2 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, a high mobility group (HMG) box, five PHD (plant homeodomain) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the third PHD finger. 54 matched cddid_all.tbl CDD cd15655 cd15655 277125 PHD3_NSD3 PHD finger 3 found in nuclear SET domain-containing protein 3 (NSD3). NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the third PHD finger. 53 matched cddid_all.tbl CDD cd15656 cd15656 277126 PHD4_NSD1 PHD finger 4 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1). NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD1 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fourth PHD finger. 40 matched cddid_all.tbl CDD cd15657 cd15657 277127 PHD4_NSD2 PHD finger 4 found in nuclear SET domain-containing protein 2 (NSD2). NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). NSD2 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, a high mobility group (HMG) box, five PHD (plant-homeodomain) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the fourth PHD finger. 41 matched cddid_all.tbl CDD cd15658 cd15658 277128 PHD4_NSD3 PHD finger 4 found in nuclear SET domain-containing protein 3 (NSD3). NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fourth PHD finger. 40 matched cddid_all.tbl CDD cd15659 cd15659 277129 PHD5_NSD1 PHD finger 5 found in nuclear receptor-binding SET domain-containing protein 1 (NSD1). NSD1, also termed H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, or androgen receptor coactivator 267 kDa protein, or androgen receptor-associated protein of 267 kDa, or H3-K36-HMTase H4-K20-HMTase, or Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD1 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fifth PHD finger. 43 matched cddid_all.tbl CDD cd15660 cd15660 277130 PHD5_NSD2 PHD finger 5 found in nuclear SET domain-containing protein 2 (NSD2). NSD2, also termed histone-lysine N-methyltransferase NSD2, or multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, by mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). NSD2 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, a high mobility group (HMG) box, five PHD (plant-homeodomain) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD fingers mediate chromatin interaction and recognition of histone marks. This model corresponds to the fifth PHD finger. 43 matched cddid_all.tbl CDD cd15661 cd15661 277131 PHD5_NSD3 PHD finger 5 found in nuclear SET domain-containing protein 3 (NSD3). NSD3, also termed histone-lysine N-methyltransferase NSD3, or protein whistle, or WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc fingers, and an NSD-specific Cys-His rich domain (Cys5HisCysHis). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD fingers are involved in protein-protein interactions. This model corresponds to the fifth PHD finger. 43 matched cddid_all.tbl CDD cd15662 cd15662 277132 ePHD_ATX1_2_like Extended PHD finger found in Arabidopsis thaliana ATX1, -2, and similar proteins. The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of A. thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like proteins ATX1, -2, and similar proteins. ATX1 and -2 are sister paralogs originating from a segmental chromosomal duplication; they are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1 (also known as protein SET domain group 27, or trithorax-homolog protein 1/TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1 regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2 (also known as protein SET domain group 30, or trithorax-homolog protein 2/TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). ATX1 and ATX2 are multi-domain proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical PHD finger, this non-canonical ePHD finger, and a C-terminal SET domain. 115 matched cddid_all.tbl CDD cd15663 cd15663 277133 ePHD_ATX3_4_5_like Extended PHD finger found in Arabidopsis thaliana ATX3, -4, -5, and similar proteins. The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of A. thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like proteins ATX3 (also termed protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also termed protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also termed protein SET domain group 29, or trithorax-homolog protein 5), which belong to the histone-lysine methyltransferase family. These proteins show distinct phylogenetic origins from the family of ATX1 and ATX2. They are multi-domain proteins that consist of an N-terminal PWWP domain, a canonical PHD finger, this non-canonical extended PHD finger, and a C-terminal SET domain. 112 matched cddid_all.tbl CDD cd15664 cd15664 277134 ePHD_KMT2A_like Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B). The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A/MLL1 and KMT2B/MLL2. KMT2A and KMT2B comprise the mammalian Trx branch of COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation by mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three PHD fingers, this extended PHD (ePHD) finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. 105 matched cddid_all.tbl CDD cd15665 cd15665 277135 ePHD1_KMT2C_like Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D). The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMTC2C and KMTC2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five plant PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. 90 matched cddid_all.tbl CDD cd15666 cd15666 277136 ePHD2_KMT2C_like Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C) and 2D (KMT2D). The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C, and KMT2D. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 Lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. Both KMT2C and KMT2D contain the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobilitygroup)-binding motif, and two FY-rich regions. 105 matched cddid_all.tbl CDD cd15667 cd15667 277137 ePHD_Snt2p_like Extended PHD finger found in Saccharomyces cerevisiae SANT domain-containing protein 2 (Snt2p) and similar proteins. The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Snt2p. Sntp2 is a yeast protein that may function in multiple stress pathways. It coordinates the transcriptional response to hydrogen peroxide-mediated oxidative stress through interaction with Ecm5 and the Rpd3 deacetylase. Snt2p contains a bromo adjacent homology (BAH) domain, two canonical PHD fingers, a non-canonical ePHD finger, and a SANT (SWI3, ADA2, N-CoR and TFIIIB) DNA-binding domain. 141 matched cddid_all.tbl CDD cd15668 cd15668 277138 ePHD_RAI1_like Extended PHD finger found in retinoic acid-induced protein 1 (RAI1), transcription factor 20 (TCF-20) and similar proteins. The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1 and TCF-20. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. TCF-20 is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). Both RAI1 and TCF-20 are strongly enriched in chromatin in interphase HeLa cells, and display low nuclear mobility, and have been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome. 103 matched cddid_all.tbl CDD cd15669 cd15669 277139 ePHD_PHF7_G2E3_like Extended PHD finger found in PHD finger protein 7 (PHF7) and G2/M phase-specific E3 ubiquitin-protein ligase (G2E3). The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF7 and G2E3. PHF7, also termed testis development protein NYD-SP6, is a testis-specific PHD finger-containing protein that associates with chromatin and binds histone H3 N-terminal tails with a preference for dimethyl lysine 4 (H3K4me2). It may play an important role in stimulating transcription involved in testicular development and/or spermatogenesis. PHF7 contains a PHD finger and a non-canonical ePHD finger, both of which may be involved in activating transcriptional regulation. G2E3 is a dual function ubiquitin ligase (E3) that may play a possible role in cell cycle regulation and the cellular response to DNA damage. It is essential for prevention of apoptosis in early embryogenesis. It is also a nucleo-cytoplasmic shuttling protein with DNA damage responsive localization. G2E3 contains two distinct RING-like ubiquitin ligase domains that catalyze lysine 48-linked polyubiquitination, and a C-terminal catalytic HECT domain that plays an important role in ubiquitin ligase activity and in the dynamic subcellular localization of the protein. The RING-like ubiquitin ligase domains consist of a PHD finger and an ePHD finger. 112 matched cddid_all.tbl CDD cd15670 cd15670 277140 ePHD_BRPF Extended PHD finger found in BRPF proteins. The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the ePHD finger of the family of BRPF proteins, which includes BRPF1, BRD1/BRPF2, and BRPF3. These are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a plant homeodomain (PHD) zinc finger followed by a non-canonical ePHD finger, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. This PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties. 116 matched cddid_all.tbl CDD cd15671 cd15671 277141 ePHD_JADE Extended PHD finger found in protein Jade-1, Jade-2, Jade-3 and similar proteins. The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16); each of these proteins is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, has reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs. 112 matched cddid_all.tbl CDD cd15672 cd15672 277142 ePHD_AF10_like Extended PHD finger found in protein AF-10 and AF-17. The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-10 and AF-17. AF-10, also termed ALL1 (acute lymphoblastic leukaemia)-fused gene from chromosome 10 protein, is a transcription factor encoded by gene AF10, a translocation partner of the MLL (mixed-lineage leukaemia) oncogene in leukaemia. AF-10 has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. It plays a key role in the survival of uncommitted hematopoietic cells. Moreover, AF-10 functions as a follistatin-related gene (FLRG)-interacting protein. The interaction with FLRG enhances AF10-dependent transcription. It interacts with the human counterpart of yeast Dot1, hDOT1L, and may act as a bridge for the recruitment of hDOT1L to the genes targeted by MLL-AF10. It also interacts with the synovial sarcoma associated protein SYT protein and may play a role in synovial sarcomas and acute leukemias. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is encoded by gene AF17 that has been identified in hematological malignancies as translocation partners of the mixed lineage leukemia gene MLL. It is a putative transcription factor that may play a role in multiple signaling pathways. It is involved in chromatin-mediated gene regulation mechanisms. It functions as a component of the multi-subunit Dot1 complex (Dotcom) and plays a role in the Wnt/Wingless signaling pathway. It also seems to be a downstream target of the beta-catenin/T-cell factor pathway, and participates in G2-M progression. Moreover, it may function as an important regulator of ENaC-mediated Na+ transport and thus blood pressure. Both AF-10 and AF-17 contain an N-terminal plant homeodomain (PHD) finger followed by this non-canonical ePHD finger. The PHD finger is involved in their homo-oligomerization. In the C-terminal region, they possess a leucine zipper domain and a glutamine-rich region. This family also includes ZFP-1, the Caenorhabditis elegans AF10 homolog. It was originally identified as a factor promoting RNAi interference in C. elegans. It also acts as Dot1-interacting protein that opposes H2B ubiquitination to reduce polymerase II (Pol II) transcription. 116 matched cddid_all.tbl CDD cd15673 cd15673 277143 ePHD_PHF6_like Extended PHD finger found in PHD finger protein 6 (PHF6) and PHD finger protein 11 (PHF11). The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the two ePHD fingers of PFH6 and the single ePHD finger of PFH11. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. PHF6 contains two non-canonical ePHD fingers. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema. 116 matched cddid_all.tbl CDD cd15674 cd15674 277144 ePHD_PHF14 Extended PHD finger found in PHD finger protein 14 (PHF14) and similar proteins. The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF14. PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and this non-canonical ePHD finger. It can interact with histones through its PHD fingers. 114 matched cddid_all.tbl CDD cd15675 cd15675 277145 ePHD_JMJD2 Extended PHD finger found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases. The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2 proteins. JMJD2 proteins, also termed lysine-specific demethylase 4 histone demethylases (KDM4), have been implicated in various cellular processes including DNA damage response, transcription, cell cycle regulation, cellular differentiation, senescence, and carcinogenesis. They selectively catalyze the demethylation of di- and trimethylated H3K9 and H3K36. This model contains three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain. JMJD2D is not included in this family, since it lacks both PHD and Tudor domains and has a different substrate specificity. JMJD2A-C are required for efficient cancer cell growth. 112 matched cddid_all.tbl CDD cd15676 cd15676 277146 PHD_BRPF1 PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins. BRPF1, also termed peregrin or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ)-dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It contains a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. BRPF1 may be involved in chromatin remodeling. This model corresponds to the canonical Cys4HisCys3 PHD finger. 62 matched cddid_all.tbl CDD cd15677 cd15677 277147 PHD_BRPF2 PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins. BRPF2, also termed bromodomain-containing protein 1 (BRD1), or BR140-like protein, is encoded by BRL (BR140 Like gene). It is responsible for the bulk of the acetylation of H3K14 and forms a novel monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with HBO1 and ING4. The complex is required for full transcriptional activation of the erythroid-specific regulator genes essential for terminal differentiation and survival of erythroblasts in fetal liver. BRPF2 shows widespread expression and localizes to the nucleus within spermatocytes. It contains a cysteine rich region harboring a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. This model corresponds to the canonical Cys4HisCys3 PHD finger. 54 matched cddid_all.tbl CDD cd15678 cd15678 277148 PHD_BRPF3 PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar proteins. BRPF3 is a homolog of BRPF1 and BRPF2. It is a scaffold protein that forms a novel monocytic leukemic zinc finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with other regulatory subunits. BRPF3 contains a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. This model corresponds to the canonical Cys4HisCys3 PHD finger. 55 matched cddid_all.tbl CDD cd15679 cd15679 277149 PHD_JADE1 PHD finger found in protein Jade-1 and similar proteins. Jade-1, also termed PHD finger protein 17 (PHF17), is a novel binding partner of von Hippel-Lindau (VHL) tumor suppressor Pvhl, a key regulator of the cellular oxygen sensing pathway. It is highly expressed in renal proximal tubules. Jade-1 functions as an essential regulator of multiple cell signaling pathways. It may be involved in the serine/threonine kinase AKT/AKT1 pathway during renal cancer pathogenesis and normally prevents renal epithelial cell proliferation and transformation. It also acts as a pro-apoptotic and growth suppressive ubiquitin ligase to inhibit canonical Wnt downstream effector beta-catenin for proteasomal degradation, and as a transcription factor associated with histone acetyltransferase activity and with increased abundance of cyclin-dependent kinase inhibitor p21. Moreover, Jade-1 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex, and plays a role in epithelial cell regeneration. It has also been identified as a novel component of the nephrocystin protein (NPHP) complex and interacts with the ciliary protein nephrocystin-4 (NPHP4). Jade-1 contains a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger. 46 matched cddid_all.tbl CDD cd15680 cd15680 277150 PHD_JADE2 PHD finger found in protein Jade-2 and similar proteins. Jade-2, also termed PHD finger protein 15 (PHF15), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-2 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-2 contains a canonical Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger. 46 matched cddid_all.tbl CDD cd15681 cd15681 277151 PHD_JADE3 PHD finger found in protein Jade-3 and similar proteins. Jade-3, also termed PHD finger protein 16 (PHF16), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-3 is required for ING4 and ING5 to associate with histone acetyl transferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-3 contains a canonical Cys4HisCys3 PHD domain followed by a non-canonical extended PHD (ePHD) domain, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger. 50 matched cddid_all.tbl CDD cd15682 cd15682 277152 PHD_ING1 PHD finger found in inhibitor of growth protein 1 (ING1). ING1 is an epigenetic regulator and a type II tumor suppressor that impacts cell growth, aging, apoptosis, and DNA repair, by affecting chromatin conformation and gene expression. It acts as a reader of the active chromatin mark, the trimethylation of histone H3 lysine 4 (H3K4me3). It binds and directs Growth arrest and DNA damage inducible protein 45 a (Gadd45a) to target sites, thus linking the histone code with DNA demethylation. It interacts with the proliferating cell nuclear antigen (PCNA) via the PCNA-interacting protein (PIP) domain in a UV-inducible manner. It also interacts with a PCNA-interacting protein, p15 (PAF). Moreover, ING1 associates with members of the 14-3-3 family, which is necessary for the cytoplasmic relocalization. Endogenous ING1 protein specifically interacts with the pro-apoptotic BCL2 family member BAX and colocalizes with BAX in a UV-inducible manner. It stabilizes the p53 tumor suppressor by inhibiting polyubiquitination of multi-monoubiquitinated forms via interaction with and colocalization of the herpesvirus-associated ubiquitin-specific protease (HAUSP)-deubiquitinase with p53. It is also involved in trichostatin A-induced apoptosis and caspase 3 signaling in p53-deficient glioblastoma cells. In addition, tyrosine kinase Src can bind phosphorylate ING1 and further regulates its activity. ING1 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger. 49 matched cddid_all.tbl CDD cd15683 cd15683 277153 PHD_ING2 PHD finger found in inhibitor of growth protein 2 (ING2). ING2, also termed inhibitor of growth 1-like protein (ING1Lp), or p32, or p33ING2, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It is a core component of a multi-factor chromatin-modifying complex containing the transcriptional co-repressor SIN3A and histone deacetylase 1 (HDAC1). It has been implicated in the control of cell cycle, in genome stability, and in muscle differentiation. ING2 independently interacts with H3K4me3 (Histone H3 trimethylated on lysine 4) and PtdIns(5)P, and modulates crosstalk between lysine methylation and lysine acetylation on histone proteins through association with chromatin in the presence of DNA damage. It collaborates with SnoN to mediate transforming growth factor (TGF)-beta-induced Smad-dependent transcription and cellular responses. It is upregulated in colon cancer and increases invasion by enhanced MMP13 expression. It also acts as a cofactor of p300 for p53 acetylation and plays a positive regulatory role during p53-mediated replicative senescence. ING2 contains an N-terminal ING domain and a C-terminal plant homeodomain (PHD) finger. 49 matched cddid_all.tbl CDD cd15684 cd15684 277154 PHD_ING4 PHD finger found in inhibitor of growth protein 4 (ING4). ING4, also termed p29ING4, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It acts as an E3 ubiquitin ligase to induce ubiquitination of the p65 subunit of NF-kappaB and inhibit the transactivation of NF-kappaB target genes. It also induces apoptosis through a p53 dependent pathway, including increasing p53 acetylation, inhibiting Mdm2-mediated degradation of p53 and enhancing the expression of p53 responsive genes both at the transcriptional and post-translational levels. Moreover, ING4 can inhibit the translation of proto-oncogene MYC by interacting with AUF1. It also regulates other transcription factors, such as hypoxia-inducible factor (HIF). In addition, ING4 associates with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further directs the MOZ/MORF and HBO1 complexes to chromatin. ING4 contains an N-terminal ING histone-binding domain and a C-terminal plant homeodomain (PHD) finger. 48 matched cddid_all.tbl CDD cd15685 cd15685 277155 PHD_ING5 PHD finger found in inhibitor of growth protein 5 (ING5). ING5, also termed p28ING5, is one member of the inhibitor of growth (ING) family of type II tumor suppressors. It acts as a Tip60 cofactor that acetylates p53 at K120 and subsequently activates the expression of p53-dependent apoptotic genes in response to DNA damage. Aberrant ING5 expression may contribute to pathogenesis, growth, and invasion of gastric carcinomas and colorectal cancer. ING5 can physically interact with p300 and p53 in vivo, and its overexpression induces apoptosis in colorectal cancer cells. It also associates with cyclin A1 (INCA1) and functions as a growth suppressor with suppressed expression in Acute Myeloid Leukemia (AML). Moreover, ING5 translocation from the nucleus to the cytoplasm might be a critical event for carcinogenesis and tumor progression in human head and neck squamous cell carcinoma. In addition, ING5 associates with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further directs the MOZ/MORF and HBO1 complexes to chromatin. ING5 contains an N-terminal ING histone-binding domain and a C-terminal plant homeodomain (PHD) finger. 49 matched cddid_all.tbl CDD cd15686 cd15686 277156 PHD3_KDM5A PHD finger 3 found in Lysine-specific demethylase 5A (KDM5A). KDM5A, also termed Histone demethylase JARID1A, or Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2), was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as a trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the third PHD finger. 52 matched cddid_all.tbl CDD cd15687 cd15687 277157 PHD3_KDM5B PHD finger 3 found in lysine-specific demethylase 5B (KDM5B). KDM5B, also termed Cancer/testis antigen 31 (CT31), or Histone demethylase JARID1B, or Jumonji/ARID domain-containing protein 1B (JARID1B), or PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the third PHD finger. 50 matched cddid_all.tbl CDD cd15688 cd15688 277158 PHD1_MOZ PHD finger 1 found in monocytic leukemia zinc-finger protein (MOZ). MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ and MOZ-related factor (MORF) are catalytic subunits of histone acetyltransferase (HAT) complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and implicated in human leukemias. It is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. The model corresponds to the first PHD finger. 59 matched cddid_all.tbl CDD cd15689 cd15689 277159 PHD1_MORF PHD finger 1 found in monocytic leukemia zinc finger protein-related factor (MORF). MORF, also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic histone acetyltransferase (HAT) activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. MORF and monocytic leukemia zinc-finger protein (MOZ) are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MORF contains an N-terminal region containing two plant homeodomain (PHD) fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The model corresponds to the first PHD finger. 59 matched cddid_all.tbl CDD cd15690 cd15690 277160 PHD1_DPF1 PHD finger 1 found in D4, zinc and double PHD fingers family 1 (DPF1). DPF1, also termed zinc finger protein neuro-d4, or BRG1-associated factor 45B (BAF45B), is encoded by a neuro specific gene, neuro-d4. It may be involved in the transcription regulation of neuro specific gene clusters. DPF1 contains a nuclear localization signal in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc-finger and a sequence of negatively charged amino acids in the central, and a cysteine/histidine-rich region that is composed of two adjacent plant homeodomain (PHD)-fingers (d4-domain) in the C-terminal part of the molecule. The family corresponds to the first PHD finger. 58 matched cddid_all.tbl CDD cd15691 cd15691 277161 PHD1_DPF2_like PHD finger 1 found in D4, zinc and double PHD fingers family 2 (DPF2). DPF2 (also termed zinc finger protein ubi-d4, apoptosis response zinc finger protein, BRG1-associated factor 45D (BAF45D), or protein requiem) is a transcription factor that is encoded by the ubiquitously expressed gene, ubi-d4, and may be involved in leukemia or other cancers with other genes connected with cancer. It recognizes acetylated histone H3 and suppresses the function of estrogen-related receptor alpha (ERRalpha) through histone deacetylase 1 (HDAC1). Moreover, DPF2 functions as a linker protein between the SWI/SNF complex and RelB/p52 NF-kappaB heterodimer and plays important roles in NF-kappaB transactivation via its non-canonical pathway. It is also required as a transcriptional coactivator in SWI/SNF complex-dependent activation of NF-kappaB RelA/p50 heterodimer. DPF2 contains a nuclear localization signal in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc-finger and a sequence of negatively charged amino acids in the central region, and a cysteine/histidine-rich region that is composed of two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This subfamily also includes DPF3 from zebrafish. This model describes the first PHD finger. 56 matched cddid_all.tbl CDD cd15692 cd15692 277162 PHD1_DPF3 PHD finger 1 found in D4, zinc and double PHD fingers family 3 (DPF3). DPF3, also termed BRG1-associated factor 45C (BAF45C), or zinc finger protein cer-d4, is encoded by a neuro-specific gene, cer-d4. It functions as a new epigenetic key factor for heart and muscle development and may be involved in the transcription regulation of neuro-specific gene clusters. It interacts with the BAF chromatin remodeling complex and binds methylated and acetylated lysine residues of histone 3 and 4. DPF3 contains a nuclear localization signal in the N-terminal region, a Cys2His2 (C2H2) zinc finger or Kruppel-type zinc-finger and a sequence of negatively charged amino acids in the central region, and a cysteine/histidine-rich region that is composed of two adjacent plant homeodomain (PHD) fingers (d4-domain) in the C-terminal part of the molecule. This model corresponds to the first PHD finger. 57 matched cddid_all.tbl CDD cd15693 cd15693 277163 ePHD_KMT2A Extended PHD finger found in histone-lysine N-methyltransferase 2A (KMT2A). The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2A. KMT2A also termed ALL-1, or CXXC-type zinc finger protein 7, or myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), or trithorax-like protein (Htrx), or zinc finger protein HRX, is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, a Bromodomain domain, this extended PHD finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. 113 matched cddid_all.tbl CDD cd15694 cd15694 277164 ePHD_KMT2B Extended PHD finger found in histone-lysine N-methyltransferase 2B (KMT2B). The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This subfamily includes the ePHD finger of KMT2B. KMT2B is also called trithorax homolog 2 or WW domain-binding protein 7 (WBP-7). KMT2B is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3 lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation by mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three PHD fingers, this ePHD finger, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. 105 matched cddid_all.tbl CDD cd15695 cd15695 277165 ePHD1_KMT2D Extended PHD finger 1 found in histone-lysine N-methyltransferase 2D (KMT2D). The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 at Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. 90 matched cddid_all.tbl CDD cd15696 cd15696 277166 ePHD1_KMT2C Extended PHD finger 1 found in histone-lysine N-methyltransferase 2C (KMT2C). The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the first ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains several PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. 90 matched cddid_all.tbl CDD cd15697 cd15697 277167 ePHD2_KMT2C Extended PHD finger 2 found in histone-lysine N-methyltransferase 2C (KMT2C). The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2C. KMT2C, also termed myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3), or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2C contains PHD fingers, two ePHD fingers, an ATPase alpha beta signature, a high mobility group (HMG)-1 box, a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain and two FY (phenylalanine tyrosine)-rich domains. 105 matched cddid_all.tbl CDD cd15698 cd15698 277168 ePHD2_KMT2D Extended PHD finger 2 found in histone-lysine N-methyltransferase 2D (KMT2D). The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the second ePHD finger of KMT2D. KMT2D, also termed ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D contains the catalytic domain SET, five PHD fingers, two ePHD fingers, a RING finger, an HMG (high-mobility group)-binding motif, and two FY-rich regions. 107 matched cddid_all.tbl CDD cd15699 cd15699 277169 ePHD_TCF20 Extended PHD finger (ePHD) found in transcription factor 20 (TCF-20). The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of TCF-20. TCF-20, also termed nuclear factor SPBP, or protein AR1, or stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPRE-binding protein), is involved in transcriptional activation of the MMP3 (matrix metalloprotease 3) promoter. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome and Potocki-Lupski syndrome. As a chromatin-binding protein, TCF-20 plays a role in the regulation of gene expression. It also functions as a transcriptional co-regulator that enhances or represses the transcriptional activity of certain transcription factors/cofactors, such as specificity protein 1 (Sp1), E twenty-six 1 (Ets1), paired box protein 6 (Pax6), small nuclear RING-finger (SNURF)/RNF4, c-Jun, androgen receptor (AR) and estrogen receptor alpha (ERalpha). TCF-20 contains an N-terminal transactivation domain, a novel DNA-binding domain with an AT-hook motif, three nuclear localization signals (NLSs) and a C-terminal ePHD/ADD domain. 103 matched cddid_all.tbl CDD cd15700 cd15700 277170 ePHD_RAI1 Extended PHD finger (ePHD) found in retinoic acid-induced protein 1 (RAI1). The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model corresponds to the C-terminal ePHD/ADD (ATRX-DNMT3-DNMT3L) domain of RAI1. RAI1, a homolog of stromelysin-1 PDGF (platelet-derived growth factor)-responsive element-binding protein (SPBP, also termed TCF-20), is a chromatin-binding protein implicated in the regulation of gene expression. It is strongly enriched on chromatin in interphase HeLa cells, and displays low nuclear mobility, and has been implicated in Smith-Magenis syndrome, Potocki-Lupski syndrome, and non-syndromic autism. RAI1 contains a region with homology to the novel nucleosome-binding region SPBP and an ePHD/ADD domain with ability to bind nucleosomes. 104 matched cddid_all.tbl CDD cd15701 cd15701 277171 ePHD_BRPF1 Extended PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins. The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF1. BRPF1, also termed peregrin, or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ) -dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It contains a plant homeodomain (PHD) zinc finger followed by a non-canonical ePHD finger, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. This PHD finger binds to methylated lysine 4 of histone H3 (H3K4me), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties. BRPF1 may be involved in chromatin remodeling. 121 matched cddid_all.tbl CDD cd15702 cd15702 277172 ePHD_BRPF2 Extended PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins. The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF2. BRPF2 also termed bromodomain-containing protein 1 (BRD1), or BR140-likeprotein, is encoded by BRL (BR140 Like gene). It is responsible for the bulk of the acetylation of H3K14 and forms a novel monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with HBO1 and ING4. The complex is required for full transcriptional activation of the erythroid-specific regulator genes essential for terminal differentiation and survival of erythroblasts in fetal liver. BRPF2 shows widespread expression and localizes to the nucleus within spermatocytes. It contains a cysteine rich region harboring a plant homeodomain (PHD) finger followed by a non-canonical ePHD finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. 118 matched cddid_all.tbl CDD cd15703 cd15703 277173 ePHD_BRPF3 Extended PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar proteins. The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of BRPF3. BRF3 is a homolog of BRPF1 and BRPF2. It is a scaffold protein that forms a novel monocytic leukemic zinc finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with other regulatory subunits. BRPF3 contains a plant homeodomain (PHD) finger followed by this non-canonical ePHD finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. 118 matched cddid_all.tbl CDD cd15704 cd15704 277174 ePHD_JADE1 Extended PHD finger found in protein Jade-1 and similar proteins. The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-1. Jade-1, also termed PHD finger protein 17 (PHF17), is a novel binding partner of von Hippel-Lindau (VHL) tumor suppressor Pvhl, a key regulator of cellular oxygen sensing pathway. It is highly expressed in renal proximal tubules. Jade-1 functions as an essential regulator of multiple cell signaling pathways. It may be involved in the Serine/threonine kinase AKT/AKT1 pathway during renal cancer pathogenesis and normally prevents renal epithelial cell proliferation and transformation. It also acts as a pro-apoptotic and growth suppressive ubiquitin ligase to inhibit canonical Wnt downstream effector beta-catenin for proteasomal degradation and ASA transcription factor associated with histone acetyltransferase activity and with increased abundance of cyclin-dependent kinase inhibitor p21. Moreover, Jade-1 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex, and plays a role in epithelial cell regeneration. It has also been identified as a novel component of the nephrocystin protein (NPHP) complex and interacts with the ciliary protein nephrocystin-4 (NPHP4). Jade-1 contains a canonical plant homeodomain (PHD) finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs. 118 matched cddid_all.tbl CDD cd15705 cd15705 277175 ePHD_JADE2 Extended PHD finger found in protein Jade-2 and similar proteins. The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-2. Jade-2, also termed PHD finger protein 15 (PHF15), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-2 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-2 contains a canonical PHD finger followed by this non-canonical ePHD finger, both of which are zinc-binding motifs. 111 matched cddid_all.tbl CDD cd15706 cd15706 277176 ePHD_JADE3 Extended PHD finger found in protein Jade-3 and similar proteins. The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Jade-3. Jade-3, also termed PHD finger protein 16 (PHF16), is a plant homeodomain (PHD) zinc finger protein that is close related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-3 is required for ING4 and ING5 to associate with histone acetyl transferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-3 contains a canonical PHD domain followed by this non-canonical ePHD domain, both of which are zinc-binding motifs. 111 matched cddid_all.tbl CDD cd15707 cd15707 277177 ePHD_RNO Extended PHD finger found in Drosophila melanogaster PHD finger protein rhinoceros (RNO) and similar proteins. The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of Drosophila melanogaster RNO. RNO is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating the transcription of key EGFR/Ras pathway regulators in the Drosophila eye. RNO contains a canonical PHD domain followed by this non-canonical ePHD domain, both of which are zinc-binding motifs. 113 matched cddid_all.tbl CDD cd15708 cd15708 277178 ePHD_AF10 Extended PHD finger found in protein AF-10 and similar proteins. The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-10. AF-10, also termed ALL1 (acute lymphoblastic leukaemia)-fused gene from chromosome 10 protein, is a transcription factor encoded by gene AF10, a translocation partner of the MLL (mixed-lineage leukaemia) oncogene in leukaemia. AF-10 has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. It plays a key role in the survival of uncommitted hematopoietic cells. Moreover, AF-10 functions as a follistatin-related gene (FLRG)-interacting protein. The interaction with FLRG enhances AF10-dependent transcription. It interacts with human counterpart of the yeast Dot1, hDOT1L, and may act as a bridge for the recruitment of hDOT1L to the genes targeted by MLL-AF10. It also interacts with the synovial sarcoma associated protein SYT protein and may play a role in synovial sarcomas and acute leukemias. AF-10 contains an N-terminal plant homeodomain (PHD) finger followed by this non-canonical ePHD finger. 129 matched cddid_all.tbl CDD cd15709 cd15709 277179 ePHD_AF17 Extended PHD finger found in protein AF-17 and similar proteins. The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of AF-17. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is encoded by gene AF17 that has been identified in hematological malignancies as a translocation partner of the mixed lineage leukemia gene MLL. It is a putative transcription factor that may play a role in multiple signaling pathways. It is involved in chromatin-mediated gene regulation mechanisms. It functions as a component of the multi-subunit Dot1 complex (Dotcom) and plays a role in the Wnt/Wingless signaling pathway. It also seems to be a downstream target of the beta-catenin/T-cell factor pathway, and participates in G2-M progression. Moreover, it may function as an important regulator of ENaC-mediated Na+ transport and thus blood pressure. AF-17 contains an N-terminal plant homeodomain (PHD) finger followed by a non-canonical ePHD finger. 125 matched cddid_all.tbl CDD cd15710 cd15710 277180 ePHD1_PHF6 Extended PHD finger 1 found in PHD finger protein 6 (PHF6). The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the first ePHD finger. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. . 115 matched cddid_all.tbl CDD cd15711 cd15711 277181 ePHD2_PHF6 Extended PHD finger 2 found in PHD finger protein 6 (PHF6). The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. PHF6 contains two non-canonical ePHD fingers, this model corresponds to the second ePHD finger. PHF6, also termed the X-linked mental retardation disorder Borjeson-Forssman-Lehmann syndrome-associated protein, is a nucleolus, ribosomal RNA promoter-associated protein that regulates cell cycle progression by suppressing ribosomal RNA synthesis. It has been implicated in cell cycle control, genomic maintenance, and tumor suppression. PHF6 shows transcriptional repression activity through directly interacting with the nucleosome remodeling and deacetylation complex component RBBP4. 118 matched cddid_all.tbl CDD cd15712 cd15712 277182 ePHD_PHF11 Extended PHD finger found in PHD finger protein 11 (PHF11). The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of PHF11. PHF11, also termed BRCA1 C-terminus-associated protein, or renal carcinoma antigen NY-REN-34, is a transcriptional co-activator of the Th1 effector cytokine genes, interleukin-2 (IL2) and interferon-gamma (IFNG), co-operating with nuclear factor kappa B (NF-kappaB). It is involved in T-cell activation and viability. Polymorphisms within PHF11 are associated with total IgE, allergic asthma and eczema. 115 matched cddid_all.tbl CDD cd15713 cd15713 277183 ePHD_JMJD2A Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A). The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2A. JMJD2A, also termed lysine-specific demethylase 4A (KDM4A), or JmjC domain-containing histone demethylation protein 3A (JHDM3A), catalyzes the demethylation of di- and trimethylated H3K9 and H3K36. It is involved in carcinogenesis and functions as a transcription regulator that may either stimulate or repress gene transcription. It associates with nuclear receptor co-repressor complex or histone deacetylases. Moreover, JMJD2A forms complexes with both the androgen and estrogen receptor (ER) and plays an essential role in growth of both ER-positive and -negative breast tumors. It is also involved in prostate, colon, and lung cancer progression. JMJD2A contains jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain. 110 matched cddid_all.tbl CDD cd15714 cd15714 277184 ePHD_JMJD2B Extended PHD finger found in Jumonji domain-containing protein 2B (JMJD2B). The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2B. JMJD2B, also termed lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the trimethyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD finger, this non-canonical ePHD finger, and a Tudor domain. 110 matched cddid_all.tbl CDD cd15715 cd15715 277185 ePHD_JMJD2C Extended PHD finger found in Jumonji domain-containing protein 2C (JMJD2C). The extended plant homeodomain (ePHD) zinc finger is characterized as Cys2HisCys5HisCys2His. This model includes the ePHD finger of JMJD2C. JMJD2C, also termed lysine-specific demethylase 4C (KDM4C), or gene amplified in squamous cell carcinoma 1 protein (GASC-1 protein), or JmjC domain-containing histone demethylation protein 3C (JHDM3C), is an epigenetic factor that catalyzes the demethylation of di- and trimethylated H3K9 and H3K36, and may be involved in the development and/or progression of various types of cancer including esophageal squamous cell carcinoma (ESC) and breast cancer. It selectively interacts with hypoxia-inducible factor 1alpha (HIF1alpha) and plays a role in breast cancer progression. Moreover, JMJD2C may play an important role in the treatment of obesity and its complications by modulating the regulation of adipogenesis by nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma). JMJD2C contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) finger, this non-canonical ePHD finger, and a Tudor domain. 110 matched cddid_all.tbl CDD cd15716 cd15716 277256 FYVE_RBNS5 FYVE domain found in FYVE finger-containing Rab5 effector protein rabenosyn-5 (Rbsn-5) and similar proteins. Rbsn-5, also termed zinc finger FYVE domain-containing protein 20, is a novel Rab5 effector that is complexed to the Sec1-like protein VPS45 and recruited in a phosphatidylinositol-3-kinase-dependent fashion to early endosomes. It also binds to Rab4 and EHD1/RME-1, two regulators of the recycling route, and is involved in cargo recycling to the plasma membrane. Moreover, Rbsn-5 regulates endocytosis at the apical side of the wing epithelium and plays a role of the apical endocytic trafficking of Fmi in the establishment of planar cell polarity (PCP). 61 matched cddid_all.tbl CDD cd15717 cd15717 277257 FYVE_PKHF FYVE domain found in protein containing both PH and FYVE domains 1 (phafin-1), 2 (phafin-2), and similar proteins. This family includes protein containing both PH and FYVE domains 1 (phafin-1) and 2 (phafin-2). Phafin-1 is a representative of a novel family of PH and FYVE domain-containing proteins called phafins. It is a ubiquitously expressed pro-apoptotic protein via translocating to lysosomes, facilitating apoptosis induction through a lysosomal-mitochondrial apoptotic pathway. Phafin-2 is a ubiquitously expressed endoplasmic reticulum-associated protein that facilitates tumor necrosis factor alpha (TNF-alpha)-triggered cellular apoptosis through endoplasmic reticulum (ER)-mitochondrial apoptotic pathway. It is an endosomal phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) effector, as well as an interactor of the endosomal-tethering protein EEA1. It regulates endosome fusion upstream of Rab5. Phafin-2 also functions as a novel regulator of endocytic epidermal growth factor receptor (EGFR) degradation through a role in endosomal fusion. 61 matched cddid_all.tbl CDD cd15718 cd15718 277258 FYVE_WDFY1_like FYVE domain found in WD40 repeat and FYVE domain-containing protein WDFY1 and WDFY2, and similar proteins. This family includes WD40 repeat and FYVE domain-containing protein WDFY1 and WDFY2. WDFY1, also termed FYVE domain containing protein localized to endosomes-1 (FENS-1), or phosphoinositide-binding protein 1, or zinc finger FYVE domain-containing protein 17, is a novel single FYVE domain containing protein that binds phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) with high specificity over other phosphoinositides. WDFY1 to early endosomes requires an intact FYVE domain and is inhibited by wortmannin, a PI3-kinase inhibitor. WDFY2, also termed zinc finger FYVE domain-containing protein 22, or ProF (propeller-FYVE protein), is a phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) binding protein that is localized to a distinct subset of early endosomes close to the plasma membrane. It interacts preferentially with endogenous serine/threonine kinase Akt2, but not Akt1, and plays a specific role in modulating signaling through Akt downstream of the interaction of this kinase with the endosomal proteins APPL (adaptor protein containing PH domain, PTB domain, and leucine zipper motif). In addition to Akt, WDFY2 serves as a binding partner for protein kinase C, zeta (PRKCZ), and its substrate vesicle-associated membrane protein 2 (VAMP2), and is involved in vesicle cycling in various secretory pathways. Moreover, Silencing of WDFY2 by siRNA produces a strong inhibition of endocytosis. Both WDFY1 and WDFY2 contain a FYVE domain and multiple WD-40 repeats. 70 matched cddid_all.tbl CDD cd15719 cd15719 277259 FYVE_WDFY3 FYVE domain found in WD40 repeat and FYVE domain-containing protein 3 (WDFY3) and similar proteins. WDFY3, also termed autophagy-linked FYVE protein (Alfy), is a ubiquitously expressed phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) binding protein required for selective macroautophagic degradation of aggregated proteins. It regulates the protein degradation through the direct interaction with the autophagy protein Atg5. Moreover, WDFY3 acts as a scaffold that bridges its cargo to the macroautophagic machinery via the creation of a greater complex with Atg12, Atg16L, and LC3. It also functionally associates with sequestosome-1/p62 (SQSTM1) in osteoclasts. WDFY3 shuttles between the nucleus and cytoplasm. It predominantly localizes to the nucleus and nuclear membrane under basal conditions, but is recruited to cytoplasmic ubiquitin-positive protein aggregates under stress conditions. WDFY3 contains a PH-BEACH domain assemblage, five WD40 repeats and a PtdIns3P-binding FYVE domain. 65 matched cddid_all.tbl CDD cd15720 cd15720 277260 FYVE_Hrs FYVE domain found in hepatocyte growth factor (HGF)-regulated tyrosine kinase substrate (Hrs) and similar proteins. Hrs, also termed protein pp110, is a tyrosine phosphorylated protein that plays an important role in the signaling pathway of HGF. It is localized to early endosomes and an essential component of the endosomal sorting and trafficking machinery. Hrs interacts with hypertonia-associated protein Trak1, a novel regulator of endosome-to-lysosome trafficking. It can also forms an Hrs/actinin-4/BERP/myosin V protein complex that is required for efficient transferrin receptor (TfR) recycling but not for epidermal growth factor receptor (EGFR) degradation. Moreover, Hrs, together with STAM proteins, STAM1 and STAM2, and EPs15, forms a multivalent ubiquitin-binding complex that sorts ubiquitinated proteins into the multivesicular body pathway, and plays a regulatory role in endocytosis/exocytosis. Furthermore, Hrs functions as an interactor of the neurofibromatosis 2 tumor suppressor protein schwannomin/merlin. It is also involved in the inhibition of citron kinase-mediated HIV-1 budding. Hrs contains a single ubiquitin-interacting motif (UIM) that is crucial for its function in receptor sorting, and a FYVE domain that harbors double Zn2+ binding sites. 61 matched cddid_all.tbl CDD cd15721 cd15721 277261 FYVE_RUFY1_like FYVE domain found in RUN and FYVE domain-containing protein RUFY1, RUFY2 and similar proteins. This family includes RUN and FYVE domain-containing protein RUFY1 and RUFY2. RUFY1, also termed FYVE-finger protein EIP1, or La-binding protein 1, or Rab4-interacting protein (Rabip4), or Zinc finger FYVE domain-containing protein 12 (ZFY12), a human homologue of mouse Rabip4, an effector of Rab4 GTPase that regulates recycling of endocytosed cargo. RUFY1 is an endosomal protein that functions as a dual effector of Rab4 and Rab14 and is involved in efficient recycling of transferrin (Tfn). It is a downstream effector of Etk, a downstream tyrosine kinase of PI3-kinase that is involved in regulation of vesicle trafficking. RUFY2, also termed Rab4-interacting protein related, is a novel embryonic factor that is present in the nucleus at early stages of embryonic development. It may have both endosomal functions in the cytoplasm and nuclear functions. Both RUFY1 and RUFY2 contain an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between. 58 matched cddid_all.tbl CDD cd15723 cd15723 277262 FYVE_protrudin FYVE-related domain found in protrudin and similar proteins. Protrudin, also termed zinc finger FYVE domain-containing protein 27 (ZFY27 or ZFYVE27), is a FYVE domain-containing protein involved in transport of neuronal cargoes and implicated in the onset of hereditary spastic paraplegia (HSP). It is involved in neurite outgrowth through binding to spastin. Moreover, it functions as a key regulator of the Rab11-dependent membrane trafficking during neurite extension. It serves as an adaptor molecule that links its associated proteins, such as Rab11-GDP, VAP-A and -B, Surf4, and RTN3, to KIF5, a motor protein that mediates anterograde vesicular transport in neurons, and thus plays a key role in the maintenance of neuronal function. The FYVE domain of protrudin resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif. In addition, unlike canonical FYVE domains that is located to early endosomes and specifically binds to phosphatidylinositol 3-phosphate (PtdIns3P or PI3P), the FYVE domain of protrudin is located to plasma membrane and preferentially binds phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2), phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4)P2), and phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3). In addition to FYVE-related domain, protrudin also contains a Rab11-binding domain (RBD11), two hydrophobic domains, HP-1 and HP-2, an FFAT motif, and a coiled-coil domain. 62 matched cddid_all.tbl CDD cd15724 cd15724 277263 FYVE_ZFY26 FYVE domain found in FYVE domain-containing protein 26 (ZFY26 or ZFYVE26). ZFY26, also termed FYVE domain-containing centrosomal protein (FYVE-CENT), or spastizin, is a phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) binding protein that localizes to the centrosome and midbody. ZFY26 and its interacting partners TTC19 and KIF13A are required for cytokinesis. It also interacts with Beclin 1, a subunit of class III phosphatidylinositol 3-kinase complex, and may have potential implications for carcinogenesis. In addition, it has been considered as the causal agent of a rare form of hereditary spastic paraplegia. ZFY26 contains a FYVE domain that is important for targeting of FYVE-CENT to the midbody. 61 matched cddid_all.tbl CDD cd15725 cd15725 277264 FYVE_PIKfyve_Fab1 FYVE domain found in metazoan PIKfyve, fungal and plant Fab1, and similar proteins. PIKfyve, also termed FYVE finger-containing phosphoinositide kinase, or 1-phosphatidylinositol 3-phosphate 5-kinase, or phosphatidylinositol 3-phosphate 5-kinase (PIP5K3), or phosphatidylinositol 3-phosphate 5-kinase type III (PIPkin-III or type III PIP kinase), is a phosphoinositide 5-kinase that forms a complex with its regulators, the scaffolding protein Vac14 and the lipid phosphatase Fig4. The complex is responsible for synthesizing phosphatidylinositol 3,5-bisphosphate [PtdIns(3,5)P2] from phosphatidylinositol 3-phosphate (PtdIns3P or PI3P). Then phosphatidylinositol-5-phosphate (PtdIns5P) is generated directly from PtdIns(3,5)P2. PtdIns(3,5)P2 and PtdIns5P regulate endosomal trafficking and responses to extracellular stimuli. At this point, PIKfyve is vital in early embryonic development. Moreover, PIKfyve forms a complex with ArPIKfyve (associated regulator of PIKfyve) and SAC3 at the endomembranes, which plays a role in receptor tyrosine kinase (RTK) degradation. The phosphorylation of PIKfyve by AKT can facilitate Epidermal growth factor receptor (EGFR) degradation. In addition, PIKfyve may participate in the regulation of the glutamate transporters EAAT2, EAAT3 and EAAT4, and the cystic fibrosis transmembrane conductance regulator (CFTR). It is also essential for systemic glucose homeostasis and insulin-regulated glucose uptake/GLUT4 translocation in skeletal muscle. It can be activated by protein kinase B (PKB/Akt) and further up-regulates human ether-a-go-go (hERG) channels. This family also includes the yeast and plant orthologs of human PIKfyve, Fab1. PIKfyve and its orthologs share a similar architecture. They contain an N-terminal FYVE domain, a middle region related to the CCT/TCP-1/Cpn60 chaperonins that are involved in productive folding of actin and tubulin, a second middle domain that contains a number of conserved cysteine residues (CCR) unique to this family, and a C-terminal lipid kinase domain related to PtdInsP kinases. 62 matched cddid_all.tbl CDD cd15726 cd15726 277265 FYVE_FYCO1 FYVE domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins. FYCO1, also termed zinc finger FYVE domain-containing protein 7, is a phosphatidylinositol 3-phosphate (PtdIns3P or PI3P)-binding protein that is associated with the exterior of autophagosomes and mediates microtubule plus-end-directed vesicle transport. It acts as an effector of GTP-bound Rab7, a GTPase that recruits FYCO1 to autophagosomes and has been implicated in autophagosome-lysosomal fusion. FYCO1 also interacts with two microtubule motor proteins, kinesin (KIF) 5B and KIF23, and thus functions as a platform for assembly of vesicle fusion and trafficking factors. FYCO1 contains an N-terminal alpha-helical RUN domain followed by a long central coiled-coil region, a FYVE domain and a GOLD (Golgi dynamics) domain in C-terminus. 58 matched cddid_all.tbl CDD cd15727 cd15727 277266 FYVE_ZF21 FYVE domain found in zinc finger FYVE domain-containing protein 21 (ZF21) and similar proteins. ZF21 is phosphoinositide-binding protein that functions as a regulator of focal adhesions and cell movement through interaction with focal adhesion kinase. It can also bind to the cytoplasmic tail of membrane type 1 matrix metalloproteinase, a potent invasion-promoting protease, and play a key role in regulating multiple aspects of cancer cell migration and invasion. ZF21 contains a FYVE domain, which corresponds to this model. 64 matched cddid_all.tbl CDD cd15728 cd15728 277267 FYVE_ANFY1 FYVE domain found in ankyrin repeat and FYVE domain-containing protein 1 (ANFY1) and similar proteins. ANFY1, also termed ankyrin repeats hooked to a zinc finger motif (Ankhzn), is a novel cytoplasmic protein that belongs to a new group of double zinc finger proteins involved in vesicle or protein transport. It is ubiquitously expressed in a spatiotemporal-specific manner and is located on endosomes. ANFY1 contains an N-terminal coiled-coil region and a BTB/POZ domain, ankyrin repeats in the middle, and a C-terminal FYVE domain. 63 matched cddid_all.tbl CDD cd15729 cd15729 277268 FYVE_endofin FYVE domain found in endofin and similar proteins. Endofin, also termed zinc finger FYVE domain-containing protein 16 (ZFY16), or endosome-associated FYVE domain protein, is a FYVE domain-containing protein that is localized to EEA1-containing endosomes. It is regulated by phosphoinositol lipid and engaged in endosome-mediated receptor modulation. Endofin is involved in Bone morphogenetic protein (BMP) signaling through interacting with Smad1 preferentially and enhancing Smad1 phosphorylation and nuclear localization upon BMP stimulation. It also functions as a scaffold protein that brings Smad4 to the proximity of the receptor complex in Transforming growth factor (TGF)-beta signaling. Moreover, endofin is a novel tyrosine phosphorylation target downstream of epidermal growth factor receptor (EGFR) in EGF-signaling. In addition, endofin plays a role in endosomal trafficking by recruiting cytosolic TOM1, an important molecule for membrane recruitment of clathrin, onto endosomal membranes. 68 matched cddid_all.tbl CDD cd15730 cd15730 277269 FYVE_EEA1 FYVE domain found in early endosome antigen 1 (EEA1) and similar proteins. EEA1, also termed endosome-associated protein p162, or zinc finger FYVE domain-containing protein 2, is an essential component of the endosomal fusion machinery and required for the fusion and maturation of early endosomes in endocytosis. It forms a parallel coiled-coil homodimer in cells. EEA1 serves as the p97 ATPase substrate and the p97 ATPase may regulate the size of early endosomes by governing the oligomeric state of EEA1. It can interact with the GTP-bound form of Rab22a and be involved in endosomal membrane trafficking. EEA1 also functions as an obligate scaffold for angiotensin II-induced Akt activation in early endosomes. It can be phosphorylated by p38 mitogen-activated protein kinase (MAPK) and further regulate mu opioid receptor endocytosis. EEA1 consists of an N-terminal C2H2 Zn2+ finger, four long heptad repeats, and a C-terminal region containing a calmodulin binding (IQ) motif, a Rab5 interaction site, and a FYVE domain. This model corresponds to the FYVE domain that is responsible for binding phosphatidyl inositol-3-phosphate (PtdIns3P or PI3P) on the membrane. 63 matched cddid_all.tbl CDD cd15731 cd15731 277270 FYVE_LST2 FYVE domain found in lateral signaling target protein 2 homolog (Lst2) and similar proteins. Lst2, also termed zinc finger FYVE domain-containing protein 28, is a monoubiquitinylated phosphoprotein that functions as a negative regulator of epidermal growth factor receptor (EGFR) signaling. Unlike other FYVE domain-containing proteins, Lst2 displays primarily non-endosomal localization. Its endosomal localization is regulated by monoubiquitinylation. Lst2 physically binds Trim3, also known as BERP or RNF22, which is a coordinator of endosomal trafficking and interacts with Hrs and a complex that biases cargo recycling. 65 matched cddid_all.tbl CDD cd15732 cd15732 277271 FYVE_MTMR3 FYVE domain found in myotubularin-related protein 3 (MTMR3) and similar proteins. MTMR3, also termed Myotubularin-related phosphatase 3, or FYVE domain-containing dual specificity protein phosphatase 1 (FYVE-DSP1), or zinc finger FYVE domain-containing protein 10, is a ubiquitously expressed phosphoinositide 3-phosphatase specific for phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) and phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2) and PIKfyve, which produces PtdIns(3,5)P2 from PtdIns3P. It regulates cell migration through modulating phosphatidylinositol 5-phosphate (PtdIns5P) levels. MTMR3 contains an N-terminal PH-GRAM (PH-G) domain, a MTM phosphatase domain, a coiled-coil region, and a C-terminal FYVE domain. Unlike conventional FYVE domains, the FYVE domain of MTMR3 neither confers endosomal localization nor binds to PtdIns3P. It is also not required for the enzyme activity of MTMR3. In contrast, the PH-G domain binds phosphoinositides. 61 matched cddid_all.tbl CDD cd15733 cd15733 277272 FYVE_MTMR4 FYVE domain found in myotubularin-related protein 4 (MTMR4) and similar proteins. MTMR4, also termed FYVE domain-containing dual specificity protein phosphatase 2 (FYVE-DSP2), or zinc finger FYVE domain-containing protein 11, is an dual specificity protein phosphatase that specifically dephosphorylates phosphatidylinositol 3-phosphate (PtdIns3P or PI3P). It is localizes to early endosomes, as well as to Rab11- and Sec15-positive recycling endosomes, and regulates sorting from early endosomes. Moreover, MTMR4 is preferentially associated with and dephosphorylated the activated regulatory Smad proteins (R-Smads) in cytoplasm to keep transforming growth factor (TGF) beta signaling in homeostasis. It also functions as an essential negative modulator for the homeostasis of bone morphogenetic protein (BMP)/decapentaplegic (Dpp) signaling. In addition, MTMR4 acts as a novel interactor of the ubiquitin ligase Nedd4 (neural-precursor-cell-expressed developmentally down-regulated 4) and may play a role in the biological process of muscle breakdown. MTMR4 contains an N-terminal PH-GRAM (PH-G) domain, a MTM phosphatase domain, a coiled-coil region, and a C-terminal FYVE domain. 60 matched cddid_all.tbl CDD cd15734 cd15734 277273 FYVE_ZFYV1 FYVE domains found in zinc finger FYVE domain-containing protein 1 (ZFYV1) and similar proteins. ZFYV1, also termed double FYVE-containing protein 1 (DFCP1), or SR3, or tandem FYVE fingers-1, is a novel tandem FYVE domain containing protein that binds phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) with high specificity over other phosphoinositides. The subcellular distribution of exogenously-expressed ZFYV1 to Golgi, endoplasmic reticulum (ER) and vesicular is governed in part by its FYVE domains but unaffected by wortmannin, a PI3-kinase inhibitor. In addition to C-terminal tandem FYVE domain, ZFYV1 contains an N-terminal putative C2H2 type zinc finger and a possible nucleotide binding P-loop. 61 matched cddid_all.tbl CDD cd15735 cd15735 277274 FYVE_spVPS27p_like FYVE domain found in Schizosaccharomyces pombe vacuolar protein sorting-associated protein 27 (spVps27p) and similar proteins. spVps27p, also termed suppressor of ste12 deletion protein 4 (Sst4p), is a conserved homolog of budding Saccharomyces cerevisiae Vps27 and of mammalian Hrs. It functions as a downstream factor for phosphatidylinositol 3-kinase (PtdIns 3-kinase) in forespore membrane formation with normal morphology. It colocalizes and interacts with Hse1p, a homolog of Saccharomyces cerevisiae Hse1p and of mammalian STAM, to form a complex whose ubiquitin-interacting motifs (UIMs) are important for sporulation. spVps27p contains a VHS (Vps27p/Hrs/Stam) domain, a FYVE domain, and two UIMs. 59 matched cddid_all.tbl CDD cd15736 cd15736 277275 FYVE_scVPS27p_Vac1p_like FYVE domain found in Saccharomyces cerevisiae vacuolar protein sorting-associated protein 27 (scVps27p) and FYVE-related domain 1 found in yeast protein VAC1 (Vac1p) and similar proteins. The family includes Saccharomyces cerevisiae vacuolar protein sorting-associated protein 27 (scVps27p) and protein VAC1 (Vac1p). scVps27p, also termed Golgi retention defective protein 11, is the putative yeast counterpart of the mammalian protein Hrs and is involved in endosome maturation. It is a mono-ubiquitin-binding protein that interacts with ubiquitinated cargoes, such as Hse1p, and is required for protein sorting into the multivesicular body. Vps27p forms a complex with Hse1p. The complex binds ubiquitin and mediates endosomal protein sorting. At the endosome, Vps27p and a trimeric protein complex, ESCRT-1, bind ubiquitin and are important for multivesicular body (MVB) sorting. Vps27p contains an N-terminal VHS (Vps27/Hrs/STAM) domain, a FYVE domain that binds PtdIns3P, followed by two ubiquitin-interacting motifs (UIMs), and a C-terminal clathrin-binding motif. Vac1p, also termed vacuolar segregation protein Pep7p, or carboxypeptidase Y-deficient protein 7, or vacuolar protein sorting-associated protein 19 (Vps19p), or vacuolar protein-targeting protein 19, is a phosphatidylinositol 3-phosphate (PtdIns3P or PI3P)-binding protein that interacts with a Rab GTPase, GTP-bound form of Vps21p, and a Sec1p homologue, Vps45p, to facilitate Vps45p-dependent vesicle-mediated vacuolar protein sorting. It also acts as a novel regulator of vesicle docking and/or fusion at the endosome and functions in vesicle-mediated transport of Golgi precursor carboxypeptidase Y (CPY), protease A (PrA), protease B (PrB), but not alkaline phosphatase (ALP) from the trans-Golgi network-like compartment (TGN) to the endosome. Vac1p contains an N-terminal classical TFIIIA-like zinc finger, two putative zinc-binding FYVE fingers, and a C-terminal coiled coil region. The FYVE domain in both Vps27p and Vac1p harbors a zinc-binding site composed of seven Cysteines and one Histidine, which is different from that of other FYVE domain containing proteins. 56 matched cddid_all.tbl CDD cd15737 cd15737 277276 FYVE2_Vac1p_like FYVE domain 2 found in yeast protein VAC1 (Vac1p) and similar proteins. Vac1p, also termed vacuolar segregation protein Pep7p, or carboxypeptidase Y-deficient protein 7, or vacuolar protein sorting-associated protein 19 (Vps19p), or vacuolar protein-targeting protein 19, is a phosphatidylinositol 3-phosphate (PtdIns3P or PI3P)-binding protein that interacts with a Rab GTPase, GTP-bound form of Vps21p, and a Sec1p homologue, Vps45p, to facilitate Vps45p-dependent vesicle-mediated vacuolar protein sorting. It also acts as a novel regulator of vesicle docking and/or fusion at the endosome and functions in vesicle-mediated transport of Golgi precursor carboxypeptidase Y (CPY), protease A (PrA), protease B (PrB), but not alkaline phosphatase (ALP) from the trans-Golgi network-like compartment (TGN) to the endosome. Vac1p contains an N-terminal classical TFIIIA-like zinc finger, two putative zinc-binding FYVE fingers, and a C-terminal coiled coil region. The family corresponds to the second FYVE domain that is responsible for the ability of Pep7p to efficiently interact with Vac1p and Vps45p. 83 matched cddid_all.tbl CDD cd15738 cd15738 277277 FYVE_MTMR_unchar FYVE-related domain found in uncharacterized myotubularin-related proteins mainly from eumetazoa. This family includes a group of uncharacterized myotubularin-related proteins mainly found in eumetazoa. Although their biological functions remain unclear, they share similar domain architecture that consists of an N-terminal pleckstrin homology (PH) domain, a highly conserved region related to myotubularin proteins, a C-terminal FYVE domain. The model corresponds to the FYVE domain, which resembles the FYVE-related domain as it has an altered sequence in the basic ligand binding patch. 61 matched cddid_all.tbl CDD cd15739 cd15739 277278 FYVE_RABE_unchar FYVE domain found in uncharacterized rab GTPase-binding effector proteins from bilateria. This family includes a group of uncharacterized rab GTPase-binding effector proteins found in bilateria. Although their biological functions remain unclear, they all contain a FYVE domain that harbors a putative phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) binding site. 73 matched cddid_all.tbl CDD cd15740 cd15740 277279 FYVE_FGD3 FYVE-like domain found in FYVE, RhoGEF and PH domain-containing protein 3 (FGD3) and similar proteins. FGD3, also termed zinc finger FYVE domain-containing protein 5, is a putative Cdc42-specific guanine nucleotide exchange factor (GEF) that undergoes the ubiquitin ligase SCFFWD1/beta-TrCP-mediated proteasomal degradation. It is a homologue of FGD1 and contains a DBL homology (DH) domain and pleckstrin homology (PH) domain in the middle region, a FYVE domain, and another PH domain in the C-terminus, but lacks the N-terminal proline-rich domain (PRD) found in FGD1. Due to this difference, FGD3 may play different roles from that of FGD1 to regulate cell morphology or motility. The FYVE domain of FGD3 resembles a FYVE-like domain that is different from the canonical FYVE domains, since it lacks one of the three conserved signature motifs (the WxxD motif) that are involved in phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) binding and exhibits altered lipid binding specificities. 54 matched cddid_all.tbl CDD cd15741 cd15741 277280 FYVE_FGD1_2_4 FYVE domain found in FYVE, RhoGEF and PH domain-containing protein facio-genital dysplasia FGD1, FGD2, FGD4. This family represents a group of Rho GTPase cell division cycle 42 (Cdc42)-specific guanine nucleotide exchange factors (GEFs), including FYVE, RhoGEF and PH domain-containing protein FGD1, FGD2 and FGD4. FGD1, also termed faciogenital dysplasia 1 protein, or Rho/Rac guanine nucleotide exchange factor FGD1 (Rho/Rac GEF), or zinc finger FYVE domain-containing protein 3, is a central regulator of extracellular matrix remodeling and belongs to the DBL family of GEFs that regulate the activation of the Rho GTPases. FGD1 is encoded by gene FGD1. Disabling mutations in the FGD1 gene cause the human X-linked developmental disorder faciogenital dysplasia (FGDY, also known as Aarskog-Scott syndrome). FGD2, also termed zinc finger FYVE domain-containing protein 4, is expressed in antigen-presenting cells, including B lymphocytes, macrophages, and dendritic cells. It localizes to early endosomes and active membrane ruffles. It plays a role in leukocyte signaling and vesicle trafficking in cells specialized to present antigen in the immune system. FGD4, also termed actin filament-binding protein frabin, or FGD1-related F-actin-binding protein, or zinc finger FYVE domain-containing protein 6, functions as an F-actin-binding (FAB) protein showing significant homology to FGD1. It induces the formation of filopodia through the activation of Cdc42 in fibroblasts. Those FGD proteins possess a similar domain organization that contains a DBL homology (DH) domain, a pleckstrin homology (PH) domain, a FYVE domain, and another PH domain in the C-terminus. However, each FGD has a unique N-terminal region that may directly or indirectly interact with F-actin. FGD1 and FGD4 have an N-terminal proline-rich domain (PRD) and an N-terminal F-actin binding (FAB) domain, respectively. This model corresponds to the FYVE domain, which has been found in many proteins involved in membrane trafficking and phosphoinositide metabolism, and has been defined by three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCR patch, and a C-terminal RVC motif, which form a compact phosphatidylinositol 3-phosphate (PtdIns3P or PI3P)-binding site. FGD1 possesses a FYVE-like domain that lack the N-terminal WxxD motif. Moreover, FGD2 is the only known RhoGEF family member shown to have a functional FYVE domain and endosomal binding activity. 65 matched cddid_all.tbl CDD cd15742 cd15742 277281 FYVE_FGD5 FYVE-like domain found in FYVE, RhoGEF and PH domain-containing protein 5 (FGD5) and similar proteins. FGD5, also termed zinc finger FYVE domain-containing protein 23, is an endothelial cell (EC)-specific guanine nucleotide exchange factor (GEF) that regulates endothelial adhesion, survival, and angiogenesis by modulating phosphatidylinositol 3-kinase signaling. It functions as a novel genetic regulator of vascular pruning by activation of endothelial cell-targeted apoptosis. FGD5 is a homologue of FGD1 and contains a DBL homology (DH) domain, a pleckstrin homology (PH) domain, a FYVE domain, and another PH domain in the C-terminus, but lacks the N-terminal proline-rich domain (PRD) found in FGD1. The FYVE domain of FGD5 resembles a FYVE-like domain that is different from the canonical FYVE domains, since it lacks one of the three conserved signature motifs (the WxxD motif) that are involved in phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) binding and exhibits altered lipid binding specificities. 67 matched cddid_all.tbl CDD cd15743 cd15743 277282 FYVE_FGD6 FYVE domain found in FYVE, RhoGEF and PH domain-containing protein 6 (FGD6) and similar proteins. FGD6, also termed zinc finger FYVE domain-containing protein 24 is a putative Cdc42-specific guanine nucleotide exchange factor (GEF) whose biological function remains unclear. It is a homologue of FGD1 and contains a DBL homology (DH) domain and pleckstrin homology (PH) domain in the middle region, a FYVE domain, and another PH domain in the C-terminus, but lacks the N-terminal proline-rich domain (PRD) found in FGD1. Moreover, the FYVE domain of FGD6 is a canonical FYVE domain, which has been found in many proteins involved in membrane trafficking and phosphoinositide metabolism, and has been defined by three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCR patch, and a C-terminal RVC motif, which form a compact phosphatidylinositol 3-phosphate (PtdIns3P or PI3P)-binding site. 61 matched cddid_all.tbl CDD cd15744 cd15744 277283 FYVE_RUFY3 FYVE-related domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins. RUFY3, also termed Rap2-interacting protein x (RIPx or RPIPx), or single axon-regulated protein (singar), is an N-terminal RUN domain and a C-terminal FYVE domain containing protein predominantly expressed in the brain. It suppresses formation of surplus axons for neuronal polarity. Unlike other RUFY proteins, RUFY3 can associate with the GTP-bound active form of Rab5. Moreover, the FYVE domain of RUFY3 resembles the FYVE-related domain as it lacks the WxxD motif (x for any residue). 52 matched cddid_all.tbl CDD cd15745 cd15745 277284 FYVE_RUFY4 FYVE-related domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins. RUFY4 belongs to the FUFY protein family which is characterized by the presence of an N-terminal RUN domain and a C-terminal FYVE domain. The FYVE domain of RUFY4 resembles the FYVE-related domain as it lacks the WxxD motif (x for any residue). The biological function of RUFY4 still remains unclear. 52 matched cddid_all.tbl CDD cd15746 cd15746 277285 FYVE_RP3A_like FYVE-related domain found in rabphilin-3A, Rab effector Noc2, and similar proteins. This family includes rabphilin-3A and Rab effector Noc2. Rabphilin-3A, also termed exophilin-1, is an effector protein that binds to the GTP-bound form of Rab3A, which is one of the most abundant Rab proteins in neurons and predominantly localized to synaptic vesicles. Rabphilin-3A is homologous to alpha-Rab3-interacting molecules (RIMs). It is a multi-domain protein containing an N-terminal Rab3A effector domain, a proline-rich linker region, and two tandem C2 domains. The effector domain binds specifically to the activated GTP-bound state of Rab3A and harbors a conserved FYVE zinc finger. The C2 domains are responsible for the binding of phosphatidylinositol-4,5-bisphosphate (PIP2) , a key player in the neurotransmitter release process. Thus, Rabphilin-3A has also been implicated in vesicle trafficking. Rab effector Noc2, also termed No C2 domains protein, or rabphilin-3A-like protein (RPH3AL), is a Rab3 effector that mediates the regulation of secretory vesicle exocytosis in neurons and certain endocrine cells. It also functions as a Rab27 effector and is involved in isoproterenol (IPR)-stimulated amylase release from acinar cells. Noc2 contains an N-terminal Rab3A effector domain which only harbors a conserved FYVE zinc finger. The FYVE domains of Rabphilin-3A and Noc2 resemble a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif. 55 matched cddid_all.tbl CDD cd15747 cd15747 277286 FYVE_Slp3_4_5 FYVE-related domain found in the synaptotagmin-like proteins 3, 4, 5. The synaptotagmin-like proteins 1-5 (Slp1-5) family belongs to the carboxyl-terminal-type (C-type) tandem C2 proteins superfamily, which also contains the synaptotagmin and the Doc2 families. Slp proteins are putative membrane trafficking proteins that are characterized by the presence of a unique N-terminal Slp homology domain (SHD), and C-terminal tandem C2 domains (known as the C2A domain and C2B domain). The SHD consists of two conserved regions, designated SHD1 (Slp homology domain 1) and SHD2. The SHD1 and SHD2 of Slp3, Slp4 and Slp5 are separated by a putative FYVE zinc finger. By contrast, Slp1 and Slp2 lack such zinc finger and their SHD1 and SHD2 are linked together. This model corresponds to the FYVE zinc finger. At this point, Slp1 and Slp2 are not included in this model. Moreover, the FYVE domains of Slp3, Slp4 and Slp5 resemble a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif. 48 matched cddid_all.tbl CDD cd15748 cd15748 277287 FYVE_SPIR FYVE-related domain found in Spir proteins, Spire1 and Spire2. Spir proteins were originally discovered as the protein products of the Drosophila spire gene. They are Jun N-terminal kinase (JNK)-interacting proteins that have exclusively been identified in metazoans. They may play roles in membrane trafficking and cortical filament crosslinking. This family includes Spire1 and Spire2, which function as new essential factors in asymmetric division of oocytes. They mediate asymmetric spindle positioning by assembling a cytoplasmic actin network. They are also required for polar body extrusion by promoting assembly of the cleavage furrow. Moreover, they cooperate synergistically with Fmn2 to assemble F-actin in oocytes. Both Spire1 and Spire2 contain an N-terminal protein-interaction KIND domain, WH2 actin-binding domains, a Rab GTPase-interaction Spir-box, and a C-terminal FYVE membrane-binding domain. Their FYVE domains resemble FYVE-related domains that are structurally similar to the canonical FYVE domains but lack the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif, which form a binding pocket that specifically bind the phospholipid phosphatidylinositol 3-phosphate (PtdIns3P or PI3P). 42 matched cddid_all.tbl CDD cd15749 cd15749 277288 FYVE_ZFY19 FYVE-related domain found in FYVE domain-containing protein 19 (ZFY19) and similar proteins. ZFY19, also termed mixed lineage leukemia (MLL) partner containing FYVE domain, is encoded by a novel gene, MLL partner containing FYVE domain (MPFYVE). The FYVE domain of ZFY19 resembles FYVE-related domains that are structurally similar to the canonical FYVE domains but lack the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif. The biological function of ZFY19 remains unclear. 51 matched cddid_all.tbl CDD cd15750 cd15750 277289 FYVE_CARP FYVE-like domain found in caspase-associated ring proteins, CARP1 and CARP2. CARP1 and CARP2 are a novel group of caspase regulators by the presence of a FYVE-type zinc finger domain. They do not localize to membranes in the cell and are involved in the negative regulation of apoptosis, specifically targeting two initiator caspases, caspase 8 and caspase 10, which are distinguished from other FYVE-type proteins. Moreover, these proteins have an altered sequence in the basic ligand binding patch and lack the WxxD (x for any residue) motif that is conserved only in phosphoinositide binding FYVE domains. Thus they constitute a family of unique FYVE-type domains called FYVE-like domains. 47 matched cddid_all.tbl CDD cd15751 cd15751 277290 FYVE_BSN_PCLO FYVE-related domain found in protein bassoon and piccolo. This family includes protein bassoon and piccolo. Protein bassoon, also termed zinc finger protein 231, is a core component of the presynaptic cytomatrix. It is a vertebrate-specific active zone scaffolding protein that plays a key role in structural organization and functional regulation of presynaptic release sites. Bassoon may modulate synaptic transmission efficiency by binding to presynaptic P/Q-type voltage-dependent calcium channel (VDCC) complexes and modify the channel function. As one of the most highly phosphorylated synaptic proteins, bassoon can interact with the small ubiquitous adaptor protein 14-3-3 in a phosphorylation-dependent manner, which modulates its anchoring to the presynaptic cytomatrix. Protein piccolo, also termed aczonin, is a neuron-specific presynaptic active zone scaffolding protein that mainly interacts with a detergent-resistant cytoskeletal-like subcellular fraction and is involved in the organization of the interplay between neurotransmitter vesicles, the cytoskeleton, and the plasma membrane at synaptic active zones. It binds profilin, an actin-binding protein implicated in actin cytoskeletal dynamics. It also functions as a presynaptic low-affinity Ca2+ sensor and has been implicated in Ca2+ regulation of neurotransmitter release. Both bassoon and piccolo contain two N-terminal FYVE zinc fingers, a PDZ domain and two C-terminal C2 domains. Their FYVE domain resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif. 62 matched cddid_all.tbl CDD cd15752 cd15752 277291 FYVE_SlaC2-a FYVE-related domain found in Slp homolog lacking C2 domains a (SlaC2-a) and similar proteins. SlaC2-a, also termed melanophilin, or exophilin-3, is a GTP-bound form of Rab27A-, myosin Va-, and actin-binding protein present on melanosomes. It is involved in the control of transferring of melanosomes from microtubules to actin filaments. It also functions as a melanocyte type myosin Va (McM5) binding partner and directly activates the actin-activated ATPase activity of McM5 through forming a tripartite protein complex with Rab27A and an actin-based motor myosin Va. SlaC2-a belongs to the Slp homolog lacking C2 domains (Slac2) family. It contains an N-terminal Slp homology domain (SHD), but lacks tandem C2 domains. The SHD consists of two conserved regions, designated SHD1 (Slp homology domain 1) and SHD2, which may function as protein interaction sites. The SHD1 and SHD2 of SlaC2-a are separated by a putative FYVE zinc finger, which resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif. Moreover, Slac2-a has a middle myosin-binding domain and a C-terminal actin-binding domain. 76 matched cddid_all.tbl CDD cd15753 cd15753 277292 FYVE_SlaC2-c FYVE-related domain found in Slp homolog lacking C2 domains c (SlaC2-c) and similar proteins. SlaC2-c, also termed Rab effector MyRIP, or exophilin-8, or myosin-VIIa- and Rab-interacting protein, or synaptotagmin-like protein lacking C2 domains c, is a GTP-bound form of Rab27A-, myosin Va/VIIa-, and actin-binding protein mainly present on retinal melanosomes and secretory granules. It may play a role in insulin granule exocytosis. It is also involved in the control of isoproterenol (IPR)-induced amylase release from parotid acinar cells. SlaC2-c belongs to the Slp homolog lacking C2 domains (Slac2) family. It contains an N-terminal Slp homology domain (SHD), but lacks tandem C2 domains. The SHD consists of two conserved regions, designated SHD1 (Slp homology domain 1) and SHD2, which may function as protein interaction sites. The SHD1 and SHD2 of SlaC2-c are separated by a putative FYVE zinc finger, which resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif. Moreover, Slac2-c has a middle myosin-binding domain and a C-terminal actin-binding domain. 49 matched cddid_all.tbl CDD cd15754 cd15754 277293 FYVE_PKHF1 FYVE domain found in protein containing both PH and FYVE domains 1 (phafin-1) and similar proteins. Phafin-1, also termed lysosome-associated apoptosis-inducing protein containing PH (pleckstrin homology) and FYVE domains (LAPF), or pleckstrin homology domain-containing family F member 1 (PKHF1), or PH domain-containing family F member 1, or apoptosis-inducing protein, or PH and FYVE domain-containing protein 1, or zinc finger FYVE domain-containing protein 15, is a representative of a novel family of PH and FYVE domain-containing proteins called phafins. It is a ubiquitously expressed pro-apoptotic protein via translocating to lysosomes, facilitating apoptosis induction through a lysosomal-mitochondrial apoptotic pathway. 64 matched cddid_all.tbl CDD cd15755 cd15755 277294 FYVE_PKHF2 FYVE domain found in protein containing both PH and FYVE domains 2 (phafin-2) and similar proteins. Phafin-2, also termed endoplasmic reticulum-associated apoptosis-involved protein containing PH and FYVE domains (EAPF), or pleckstrin homology domain-containing family F member 2 (PKHF2), or PH domain-containing family F member 2, or PH and FYVE domain-containing protein 2, or zinc finger FYVE domain-containing protein 18, is a ubiquitously expressed endoplasmic reticulum-associated protein that facilitates tumor necrosis factor alpha (TNF-alpha)-triggered cellular apoptosis through endoplasmic reticulum (ER)-mitochondrial apoptotic pathway. It is an endosomal phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) effector, as well as an interactor of the endosomal-tethering protein EEA1. It regulates endosome fusion upstream of Rab5. Phafin-2 also functions as a novel regulator of endocytic epidermal growth factor receptor (EGFR) degradation through a role in endosomal fusion. 64 matched cddid_all.tbl CDD cd15756 cd15756 277295 FYVE_WDFY1 FYVE domain found in WD40 repeat and FYVE domain-containing protein 1 (WDFY1) and similar proteins. WDFY1, also termed FYVE domain containing protein localized to endosomes-1 (FENS-1), or phosphoinositide-binding protein 1, or zinc finger FYVE domain-containing protein 17, is a novel single FYVE domain containing protein that binds phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) with high specificity over other phosphoinositides. WDFY1 to early endosomes requires an intact FYVE domain and is inhibited by wortmannin, a PI3-kinase inhibitor. In addition to FYVE domain, WDFY1 harbors multiple WD-40 repeats. 76 matched cddid_all.tbl CDD cd15757 cd15757 277296 FYVE_WDFY2 FYVE domain found in WD40 repeat and FYVE domain-containing protein 2 (WDFY2). WDFY2, also termed zinc finger FYVE domain-containing protein 22, or ProF (propeller-FYVE protein), is a phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) binding protein that is localized to a distinct subset of early endosomes close to the plasma membrane. It interacts preferentially with endogenous serine/threonine kinase Akt2, but not Akt1, and plays a specific role in modulating signaling through Akt downstream of the interaction of this kinase with the endosomal proteins APPL (adaptor protein containing PH domain, PTB domain, and leucine zipper motif). In addition to Akt, WDFY2 serves as a binding partner for protein kinase C, zeta (PRKCZ), and its substrate vesicle-associated membrane protein 2 (VAMP2), and is involved in vesicle cycling in various secretory pathways. Moreover, Silencing of WDFY2 by siRNA produces a strong inhibition of endocytosis. WDFY2 contains WD40 motifs and a FYVE domain. 70 matched cddid_all.tbl CDD cd15758 cd15758 277297 FYVE_RUFY1 FYVE domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins. RUFY1, also termed FYVE-finger protein EIP1, or La-binding protein 1, or Rab4-interacting protein (Rabip4), or Zinc finger FYVE domain-containing protein 12 (ZFY12), a human homologue of mouse Rabip4, an effector of Rab4 GTPase that regulates recycling of endocytosed cargo. RUFY1 is an endosomal protein that functions as a dual effector of Rab4 and Rab14 and is involved in efficient recycling of transferrin (Tfn). It is a downstream effector of Etk, a downstream tyrosine kinase of PI3-kinase that is involved in regulation of vesicle trafficking. RUFY1 contains an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between. 71 matched cddid_all.tbl CDD cd15759 cd15759 277298 FYVE_RUFY2 FYVE domain found in RUN and FYVE domain-containing protein 2 (RUFY2) and similar proteins. RUFY2, also termed Rab4-interacting protein related, is a novel embryonic factor that contains an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between. It is present in the nucleus at early stages of embryonic development. It may have both endosomal functions in the cytoplasm and nuclear functions. 71 matched cddid_all.tbl CDD cd15760 cd15760 277299 FYVE_scVPS27p_like FYVE domain found in Saccharomyces cerevisiae vacuolar protein sorting-associated protein 27 (scVps27p) and similar proteins. scVps27p, also termed Golgi retention defective protein 11, is the putative yeast counterpart of the mammalian protein Hrs and is involved in endosome maturation. It is a mono-ubiquitin-binding protein that interacts with ubiquitinated cargoes, such as Hse1p, and is required for protein sorting into the multivesicular body. Vps27p forms a complex with Hse1p. The complex binds ubiquitin and mediates endosomal protein sorting. At the endosome, Vps27p and a trimeric protein complex, ESCRT-1, bind ubiquitin and are important for multivesicular body (MVB) sorting. Vps27p contains an N-terminal VHS (Vps27/Hrs/STAM) domain, a FYVE domain that binds PtdIns3P, followed by two ubiquitin-interacting motifs (UIMs), and a C-terminal clathrin-binding motif. 59 matched cddid_all.tbl CDD cd15761 cd15761 277300 FYVE1_Vac1p_like FYVE-related domain 1 found in yeast protein VAC1 (Vac1p) and similar proteins. Vac1p, also termed vacuolar segregation protein Pep7p, or carboxypeptidase Y-deficient protein 7, or vacuolar protein sorting-associated protein 19 (Vps19p), or vacuolar protein-targeting protein 19, is a phosphatidylinositol 3-phosphate (PtdIns3P or PI3P)-binding protein that interacts with a Rab GTPase, GTP-bound form of Vps21p, and a Sec1p homologue, Vps45p, to facilitate Vps45p-dependent vesicle-mediated vacuolar protein sorting. It also acts as a novel regulator of vesicle docking and/or fusion at the endosome and functions in vesicle-mediated transport of Golgi precursor carboxypeptidase Y (CPY), protease A (PrA), protease B (PrB), but not alkaline phosphatase (ALP) from the trans-Golgi network-like compartment (TGN) to the endosome. Vac1p contains an N-terminal classical TFIIIA-like zinc finger, two putative zinc-binding FYVE fingers, and a C-terminal coiled coil region. The family corresponds to the first FYVE domain, which resembles the FYVE-related domain as it has an altered sequence in the basic ligand binding patch. 76 matched cddid_all.tbl CDD cd15762 cd15762 277301 FYVE_RP3A FYVE-related domain found in rabphilin-3A and similar proteins. Rabphilin-3A, also termed exophilin-1, is an effector protein that binds to the GTP-bound form of Rab3A, which is one of the most abundant Rab proteins in neurons and predominantly localized to synaptic vesicles. Rabphilin-3A is homologous to alpha-Rab3-interacting molecules (RIMs). It is a multi-domain protein containing an N-terminal Rab3A effector domain, a proline-rich linker region, and two tandem C2 domains. The effector domain binds specifically to the activated GTP-bound state of Rab3A and harbors a conserved FYVE zinc finger. The C2 domains are responsible for the binding of phosphatidylinositol-4,5-bisphosphate (PIP2) , a key player in the neurotransmitter release process. Thus, Rabphilin-3A has also been implicated in vesicle trafficking. The FYVE domain of Rabphilin-3A resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif. 80 matched cddid_all.tbl CDD cd15763 cd15763 277302 FYVE_RPH3L FYVE-related domain found in Rab effector Noc2 and similar proteins. Rab effector Noc2, also termed No C2 domains protein, or rabphilin-3A-like protein (RPH3AL), is a Rab3 effector that mediates the regulation of secretory vesicle exocytosis in neurons and certain endocrine cells. It also functions as a Rab27 effector and is involved in isoproterenol (IPR)-stimulated amylase release from acinar cells. Noc2 contains an N-terminal Rab3A effector domain which harbors a conserved zinc finger, but lacks tandem C2 domains. The FYVE domain of Noc2 resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif. 64 matched cddid_all.tbl CDD cd15764 cd15764 277303 FYVE_Slp4 FYVE-related domain found in synaptotagmin-like protein 4 (Slp4) and similar proteins. Slp4, also termed exophilin-2, or granuphilin, has been characterized as a regulator of the release of insulin granules from pancreatic beta-cells and dense core granules from PC12 neuronal cells by binding to Rab27A , and amylase granules from parotid gland acinar cells through interaction with syntaxin-2/3 in a Munc18-2-dependent manner on the apical plasma membrane. It can binds to syntaxin 2 in parotid acinar cells. It is also involved in granule transport by recruitment of the motor protein myosin Va. Moreover, it requires Rab8 to increase granule release in platelets. Slp4 contains an N-terminal Slp homology domain (SHD) and C-terminal tandem C2 domains. The Slp homology domain (SHD) consists of two conserved regions, designated SHD1 (Slp homology domain 1) and SHD2, which may function as protein interaction sites. The SHD1 and SHD2 of Slp4 are separated by a putative FYVE zinc finger, which resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif. 50 matched cddid_all.tbl CDD cd15765 cd15765 277304 FYVE_Slp3 FYVE-related domain found in synaptotagmin-like protein 3 (Slp3) and similar proteins. Slp3, also termed exophilin-6, functions as a Rab27A-specific effector in cytotoxic T lymphocytes. It binds to kinesin-1 motor through interaction with the tetratricopeptide repeat of the kinesin-1 light chain (KLC1). The kinesin-1/Slp3/Rab27a complex plays a role in mediating the terminal transport of lytic granules to the immune synapse. Slp3 contains an N-terminal Slp homology domain (SHD) and C-terminal tandem C2 domains. The Slp homology domain (SHD) consists of two conserved regions, designated SHD1 (Slp homology domain 1) and SHD2, which may function as protein interaction sites. The SHD1 and SHD2 of Slp3 are separated by a putative FYVE zinc finger, which resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif. In addition, the Slp3 C2A domain showed Ca2+-dependent phospholipid binding activity. At this point, Slp3 is a Ca2+-dependent isoform in Slp proteins family. 48 matched cddid_all.tbl CDD cd15766 cd15766 277305 FYVE_Slp5 FYVE-related domain found in synaptotagmin-like protein 5 (Slp5) and similar proteins. Slp5 is a novel Rab27A-specific effector that is highly expressed in placenta and liver. Slp5 specifically interacted with the GTP-bound form of Rab27A and is involved in Rab27A-dependent membrane trafficking in specific tissues. Slp5 contains an N-terminal Slp homology domain (SHD) and C-terminal tandem C2 domains. The Slp homology domain (SHD) consists of two conserved regions, designated SHD1 (Slp homology domain 1) and SHD2, which may function as protein interaction sites. The SHD1 and SHD2 of Slp5 are separated by a putative FYVE zinc finger, which resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif. 47 matched cddid_all.tbl CDD cd15767 cd15767 277306 FYVE_SPIR1 FYVE-related domain found in protein spire homolog 1 (Spire1) and similar proteins. Spire1 is encoded by gene spir-1, which is primarily found to be expressed in the developing nervous system and in neuronal cells of the adult brain, as well as in the fetal liver and in the adult spleen. It functions as a new essential factor in asymmetric division of oocytes. It mediates asymmetric spindle positioning by assembling a cytoplasmic actin network. It is also required for polar body extrusion by promoting assembly of the cleavage furrow. Moreover, it cooperates synergistically with Fmn2 to assemble F-actin in oocytes. Spire1 contains an N-terminal protein-interaction KIND domain, WH2 actin-binding domains, a Rab GTPase-interaction Spir-box, and a C-terminal FYVE membrane-binding domain. The FYVE domain resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lack the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif, which form a binding pocket that specifically binds the phospholipid phosphatidylinositol 3-phosphate (PtdIns3P or PI3P). 79 matched cddid_all.tbl CDD cd15768 cd15768 277307 FYVE_SPIR2 FYVE-related domain found in protein spire homolog 2 (Spire2) and similar proteins. Spire2 is encoded by gene spir-2, which is expressed in the nervous system and highly expressed in the colonic epithelium. It functions as a new essential factor in asymmetric division of oocytes. It mediates asymmetric spindle positioning by assembling a cytoplasmic actin network. It is also required for polar body extrusion by promoting assembly of the cleavage furrow. Moreover, it cooperates synergistically with Fmn2 to assemble F-actin in oocytes. Spire2 contains an N-terminal protein-interaction KIND domain, WH2 actin-binding domains, a Rab GTPase-interaction Spir-box, and a C-terminal FYVE membrane-binding domain. The FYVE domain resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif, which form a binding pocket that specifically binds the phospholipid phosphatidylinositol 3-phosphate (PtdIns3P or PI3P). 112 matched cddid_all.tbl CDD cd15769 cd15769 277308 FYVE_CARP1 FYVE-like domain found in caspase regulator CARP1 and similar proteins. CARP1, also termed E3 ubiquitin-protein ligase RNF34, or caspases-8 and -10-associated RING finger protein 1, or FYVE-RING finger protein Momo, or RING finger homologous to inhibitor of apoptosis protein (RFI), or RING finger protein 34, or RING finger protein RIFF, is a nuclear protein that functions as a specific E3 ubiquitin ligase for the transcriptional coactivator PGC-1alpha, a master regulator of energy metabolism and adaptive thermogenesis in the brown fat cell, and negatively regulates brown fat cell metabolism. It is preferentially expressed in esophageal, gastric and colorectal cancers, suggesting a possible association with the development of the digestive tract cancers. It regulates the p53 signaling pathway through degrading 14-3-3 sigma and stabilizing MDM2. CARP1 does not localize to membranes in the cell and is involved in the negative regulation of apoptosis, specifically targeting two initiator caspases, caspase 8 and caspase 10, which are distinguished from other FYVE-type proteins. Moreover, CARP1 has an altered sequence in the basic ligand binding patch and lack the WxxD (x for any residue) motif that is conserved only in phosphoinositide binding FYVE domains. Thus it belongs to a family of unique FYVE-type domains called FYVE-like domains. In addition to the N-terminal FYVE-like domain, CARP1 harbors a C-terminal RING domain. 47 matched cddid_all.tbl CDD cd15770 cd15770 277309 FYVE_CARP2 FYVE-like domain found in caspase regulator CARP2 and similar proteins. CARP2, also termed E3 ubiquitin-protein ligase rififylin, or caspases-8 and -10-associated RING finger protein 2, or FYVE-RING finger protein Sakura (Fring), or RING finger and FYVE-like domain-containing protein 1, or RING finger protein 189, or RING finger protein 34-like, is a novel caspase regulator containing a FYVE-type zinc finger domain. It regulates the p53 signaling pathway through degrading 14-3-3 sigma and stabilizing MDM2. CARP2 does not localize to membranes in the cell and is involved in the negative regulation of apoptosis, specifically targeting two initiator caspases, caspase 8 and caspase 10, which are distinguished from other FYVE-type proteins. Moreover, CARP2 has an altered sequence in the basic ligand binding patch and lack the WxxD (x for any residue) motif that is conserved only in phosphoinositide binding FYVE domains. Thus it belongs to a family of unique FYVE-type domains called FYVE-like domains. In addition to the N-terminal FYVE-like domain, CARP2 harbors a C-terminal RING domain. 49 matched cddid_all.tbl CDD cd15771 cd15771 277310 FYVE1_BSN_PCLO FYVE-related domain 1 found in protein bassoon and piccolo. This family includes protein bassoon and piccolo. Protein bassoon, also termed zinc finger protein 231, is a core component of the presynaptic cytomatrix. It is a vertebrate-specific active zone scaffolding protein that plays a key role in structural organization and functional regulation of presynaptic release sites. Bassoon may modulate synaptic transmission efficiency by binding to presynaptic P/Q-type voltage-dependent calcium channel (VDCC) complexes and modify the channel function. As one of the most highly phosphorylated synaptic proteins, bassoon can interact with the small ubiquitous adaptor protein 14-3-3 in a phosphorylation-dependent manner, which modulates its anchoring to the presynaptic cytomatrix. Protein piccolo, also termed aczonin, is a neuron-specific presynaptic active zone scaffolding protein that mainly interacts with a detergent-resistant cytoskeletal-like subcellular fraction and is involved in the organization of the interplay between neurotransmitter vesicles, the cytoskeleton, and the plasma membrane at synaptic active zones. It binds profilin, an actin-binding protein implicated in actin cytoskeletal dynamics. It also functions as a presynaptic low-affinity Ca2+ sensor and has been implicated in Ca2+ regulation of neurotransmitter release. Both bassoon and piccolo contain two N-terminal FYVE zinc fingers, a PDZ domain and two C-terminal C2 domains. Their FYVE domain resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif. This model corresponds to the first FYVE-related domain. 61 matched cddid_all.tbl CDD cd15772 cd15772 277311 FYVE2_BSN_PCLO FYVE-related domain 2 found in protein bassoon and piccolo. This family includes protein bassoon and piccolo. Protein bassoon, also termed zinc finger protein 231, is a core component of the presynaptic cytomatrix. It is a vertebrate-specific active zone scaffolding protein that plays a key role in structural organization and functional regulation of presynaptic release sites. Bassoon may modulate synaptic transmission efficiency by binding to presynaptic P/Q-type voltage-dependent calcium channel (VDCC) complexes and modify the channel function. As one of the most highly phosphorylated synaptic proteins, bassoon can interact with the small ubiquitous adaptor protein 14-3-3 in a phosphorylation-dependent manner, which modulates its anchoring to the presynaptic cytomatrix. Protein piccolo, also termed aczonin, is a neuron-specific presynaptic active zone scaffolding protein that mainly interacts with a detergent-resistant cytoskeletal-like subcellular fraction and is involved in the organization of the interplay between neurotransmitter vesicles, the cytoskeleton, and the plasma membrane at synaptic active zones. It binds profilin, an actin-binding protein implicated in actin cytoskeletal dynamics. It also functions as a presynaptic low-affinity Ca2+ sensor and has been implicated in Ca2+ regulation of neurotransmitter release. Both bassoon and piccolo contain two N-terminal FYVE zinc fingers, a PDZ domain and two C-terminal C2 domains. Their FYVE domain resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif. This model corresponds to the second FYVE-related domain. 64 matched cddid_all.tbl CDD cd15773 cd15773 277312 FYVE1_BSN FYVE-related domain 1 found in protein bassoon. Protein bassoon, also termed zinc finger protein 231, is a core component of the presynaptic cytomatrix. It is a vertebrate-specific active zone scaffolding protein that plays a key role in structural organization and functional regulation of presynaptic release sites. Bassoon may modulate synaptic transmission efficiency by binding to presynaptic P/Q-type voltage-dependent calcium channel (VDCC) complexes and modify the channel function. As one of the most highly phosphorylated synaptic proteins, bassoon can interact with the small ubiquitous adaptor protein 14-3-3 in a phosphorylation-dependent manner, which modulates its anchoring to the presynaptic cytomatrix. Bassoon contains two N-terminal FYVE zinc fingers, a PDZ domain and two C-terminal C2 domains. This family corresponds to the first FYVE domain, which resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif. 64 matched cddid_all.tbl CDD cd15774 cd15774 277313 FYVE1_PCLO FYVE-related domain 1 found in protein piccolo. Protein piccolo, also termed aczonin, is a neuron-specific presynaptic active zone scaffolding protein that mainly interacts with a detergent-resistant cytoskeletal-like subcellular fraction and is involved in the organization of the interplay between neurotransmitter vesicles, the cytoskeleton, and the plasma membrane at synaptic active zones. It binds profilin, an actin-binding protein implicated in actin cytoskeletal dynamics. It also functions as a presynaptic low-affinity Ca2+ sensor and has been implicated in Ca2+ regulation of neurotransmitter release. Piccolo is a multi-domain protein containing two N-terminal FYVE zinc fingers, a polyproline tract, and a PDZ domain and two C-terminal C2 domains. This family corresponds to the first FYVE domain, which resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif. 62 matched cddid_all.tbl CDD cd15775 cd15775 277314 FYVE2_BSN FYVE-related domain 2 found in protein bassoon. Protein bassoon, also termed zinc finger protein 231, is a core component of the presynaptic cytomatrix. It is a vertebrate-specific active zone scaffolding protein that plays a key role in structural organization and functional regulation of presynaptic release sites. Bassoon may modulate synaptic transmission efficiency by binding to presynaptic P/Q-type voltage-dependent calcium channel (VDCC) complexes and modify the channel function. As one of the most highly phosphorylated synaptic proteins, bassoon can interact with the small ubiquitous adaptor protein 14-3-3 in a phosphorylation-dependent manner, which modulates its anchoring to the presynaptic cytomatrix. Bassoon contains two N-terminal FYVE zinc fingers, a PDZ domain and two C-terminal C2 domains. This family corresponds to the second FYVE domain, which resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif. 65 matched cddid_all.tbl CDD cd15776 cd15776 277315 FYVE2_PCLO FYVE-related domain 2 found in protein piccolo. Protein piccolo, also termed aczonin, is a neuron-specific presynaptic active zone scaffolding protein that mainly interacts with a detergent-resistant cytoskeletal-like subcellular fraction and is involved in the organization of the interplay between neurotransmitter vesicles, the cytoskeleton, and the plasma membrane at synaptic active zones. It binds profilin, an actin-binding protein implicated in actin cytoskeletal dynamics. It also functions as a presynaptic low-affinity Ca2+ sensor and has been implicated in Ca2+ regulation of neurotransmitter release. Piccolo is a multi-domain protein containing two N-terminal FYVE zinc fingers, a polyproline tract, and a PDZ domain and two C-terminal C2 domains. This family corresponds to the second FYVE domain, which resembles a FYVE-related domain that is structurally similar to the canonical FYVE domains but lacks the three signature sequences: an N-terminal WxxD motif (x for any residue), the central basic R(R/K)HHCRxCG patch, and a C-terminal RVC motif. 64 matched cddid_all.tbl CDD cd15777 cd15777 276940 CRBN_C_like Thalidomide-binding C-terminal domain of cereblon (CRBN) and similar protein domains. Cereblon is part of an E3 ubiquitin ligase complex, together with damaged DNA-binding protein 1 (DDB1), CUL4A and ROC1. Cereblon interacts directly with DDB1, although the C-terminal domain characterized here does not contribute to that interaction. Ubiquination of cellular targets by this complex increases levels of FGF8 and FGF10, which was shown to affect the development of limbs and auditory vesicles in embryogenesis. The C-terminal domain of Cereblon was shown to contain the binding site for thalidomide and its analogs, a class of teratogenic drugs that exhibit an antiproliferative effect on myelomas. Mutations in CRBN, some of which map onto the C-terminal domain, were associated with autosomal recessive mental retardation, which may have to do with interactions between CRBN and ion channels in the brain. 101 matched cddid_all.tbl CDD cd15778 cd15778 275446 Lreu_0056_like Proteins similar to Lactobacillus reuteri ORF 0056. This family of Lactobacillus proteins has not been characterized. The 3D structure has been solved for a hypothetical protein with a predicted signal peptide, as part of a wider examination of the structural biology of commensal human gut flora and pathogens. 112 matched cddid_all.tbl CDD cd15783 cd15783 294014 SA1633_like Uncharacterized protein family conserved in Staphylococci. Some proteins in this family have been described as putative beta-lactamases. They are structurally similar to the C-terminal beta-grasp domains of Staphylococcal and Streptococcal superantigens. 143 matched cddid_all.tbl CDD cd15784 cd15784 275431 PH_RUTBC Rab-binding Pleckstrin homology domain (PH) of small G-protein signaling modulator 1 and similar proteins. Small G-protein signaling modulator 1, or RUN and TBC1 domain containing 2 (RUTBC2), as well as RUTBC1, bind to Rab9A via their Pleckstrin homology (PH) domain. They do not seem to act as GAP proteins that stimulate GTP hydrolysis by Rab9A, and RUTBC2 has been shown to also interact with Rab9B, most likely in a similar manner. RUTBC1 does stimulate GTP hydrolysis by Rab32 and Rab33B, however, while RUTBC2 appears to be a GAP for Rab36. Rab9A and associated proteins control the recycling of mannose-6-phosphate receptors from late endosomes to the trans-Golgi. 176 matched cddid_all.tbl CDD cd15785 cd15785 276946 YycH_N_like N-terminal domain of YycH and structurally similar proteins conserved in Firmicutes. These protein domains appear to be members of a somewhat larger structural family conserved in Firmicutes, including the N-terminal domain of YycH. YycH plays a role in signal transduction and is found immediately downstream of the essential histidine kinase YycG. YycG forms a two-component system together with its cognate response regulator YycF. YycH functions as a modulator of YycG activity, possibly by interacting with YchI. All three molecules (YchG, YchH, and YchI) have been characterized as membrane proteins, and they may be able to form homodimers. 113 matched cddid_all.tbl CDD cd15786 cd15786 276947 CPF_1278_like Uncharacterized protein conserved in Clostridia. This protein appears to be a member of a somewhat larger structural family conserved in Firmicutes. The 3D structure is available for one protein, CPF_1278, which has been labelled a putative lipoprotein. CPF_1278 displays structural similarity to the N-terminal domain of YycH, which plays a role in signal transduction and is found immediately downstream of the essential histidine kinase YycG. YycG forms a two-component system together with its cognate response regulator YycF. YycH functions as a modulator of YycG activity, possibly by interacting with YchI. All three molecules (YchG, YchH, and YchI) have been characterized as membrane proteins, and they may be able to form homodimers. 124 matched cddid_all.tbl CDD cd15787 cd15787 276948 YycH_N N-terminal domain of YycH and similar proteins. This protein appears to be a member of a somewhat larger structural family conserved in Firmicutes. YycH plays a role in signal transduction and is found immediately downstream of the essential histidine kinase YycG. YycG forms a two-component system together with its cognate response regulator YycF. YycH functions as a modulator of YycG activity, possibly by interacting with YchI. All three molecules (YchG, YchH, and YchI) have been characterized as membrane proteins, and they may be able to form homodimers. This model describes the N-terminal domain of YycH. 143 matched cddid_all.tbl CDD cd15788 cd15788 276949 Clospo_01618_like Uncharacterized protein conserved in Clostridia. This protein appears to be a member of a somewhat larger structural family conserved in Firmicutes. It displays structural similarity to the N-terminal domain of YycH, which plays a role in signal transduction and is found immediately downstream of the essential histidine kinase YycG. YycG forms a two-component system together with its cognate response regulator YycF. YycH functions as a modulator of YycG activity, possibly by interacting with YchI. All three molecules (YchG, YchH, and YchI) have been characterized as membrane proteins, and they may be able to form homodimers. 129 matched cddid_all.tbl CDD cd15789 cd15789 275432 PH_ARHGEF2_18_like rho guanine nucleotide exchange factor. RhoGEFs belongs to regulator of G-protein signaling (RGS) domain-containing RhoGEFs that are RhoA-selective and directly activated by the Galpha12/13 family of heterotrimeric G proteins. The members here all contain Dbl homology (DH)-PH domains. In addition some members contain N-terminal C1 (Protein kinase C conserved region 1) domains, PDZ (also called DHR/Dlg homologous regions) domains, ANK (ankyrin) domains, and RGS (Regulator of G-protein signalling) domains or C-terminal ATP-synthase B subunit. The DH-PH domains bind and catalyze the exchange of GDP for GTP on RhoA. RhoGEF2/Rho guanine nucleotide exchange factor 2, p114RhoGEF/p114 Rho guanine nucleotide exchange factor, p115RhoGEF, p190RhoGEF, PRG/PDZ Rho guanine nucleotide exchange factor, RhoGEF 11, RhoGEF 12, RhoGEF 18, AKAP13/A-kinase anchoring protein 13, and LARG/Leukemia-associated Rho guanine nucleotide exchange factor are included in this CD. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 102 matched cddid_all.tbl CDD cd15790 cd15790 275433 PH-GRAM_MTMR11 Myotubularian (MTM) related 11 protein (MTMR11) Pleckstrin Homology-Glucosyltransferases, Rab-like GTPase activators and Myotubularins (PH-GRAM) domain. MTMR10, MTMR11, and MTMR12 are catalytically inactive phosphatases that play a role as an adapter for the phosphatase myotubularin to regulate myotubularintracellular location. They contains a Glu residue instead of a conserved Cys residue in the dsPTPase catalytic loop which renders it catalytically inactive as a phosphatase. They contains an N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, an inactive PTP domain, a SET interaction domain, and a C-terminal coiled-coil domain. Myotubularin-related proteins are a subfamily of protein tyrosine phosphatases (PTPs) that dephosphorylate D3-phosphorylated inositol lipids. Mutations in this family cause the human neuromuscular disorders myotubular myopathy and type 4B Charcot-Marie-Tooth syndrome. 6 of the 13 MTMRs (MTMRs 5, 9-13) contain naturally occurring substitutions of residues required for catalysis by PTP family enzymes. Although these proteins are predicted to be enzymatically inactive, they are thought to function as antagonists of endogenous phosphatase activity or interaction modules. Most MTMRs contain a N-terminal PH-GRAM domain, a Rac-induced recruitment domain (RID) domain, a PTP domain (which may be active or inactive), a SET-interaction domain, and a C-terminal coiled-coil region. In addition some members contain DENN domain N-terminal to the PH-GRAM domain and FYVE, PDZ, and PH domains C-terminal to the coiled-coil region. The GRAM domain, found in myotubularins, glucosyltransferases, and other putative membrane-associated proteins, is part of a larger motif with a pleckstrin homology (PH) domain fold. 123 matched cddid_all.tbl CDD cd15791 cd15791 275434 PH1_FDG4 FYVE, RhoGEF and PH domain containing/faciogenital dysplasia proteins 4, N-terminal Pleckstrin homology (PH) domain. In general, FGDs have a RhoGEF (DH) domain, followed by an N-terminal PH domain, a FYVE domain and a C-terminal PH domain. All FGDs are guanine nucleotide exchange factors that activates the Rho GTPase Cdc42, an important regulator of membrane trafficking. The RhoGEF domain is responsible for GEF catalytic activity, while the N-terminal PH domain is involved in intracellular targeting of the DH domain. FGD4 is one of the genes associated with Charcot-Marie-Tooth neuropathy type 4 (CMT4), a group of progressive motor and sensory axonal and demyelinating neuropathies that are distinguished from other forms of CMT by autosomal recessive inheritance. Those affected have distal muscle weakness and atrophy associated with sensory loss and, frequently, pes cavus foot deformity. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 94 matched cddid_all.tbl CDD cd15792 cd15792 275435 PH1_FGD5 FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 5, N-terminal Pleckstrin Homology (PH) domain. FGD5 regulates promotes angiogenesis of vascular endothelial growth factor (VEGF) in vascular endothelial cells, including network formation, permeability, directional movement, and proliferation. In general, FGDs have a RhoGEF (DH) domain, followed by a PH domain, a FYVE domain and a C-terminal PH domain. All FGDs are guanine nucleotide exchange factors that activate the Rho GTPase Cdc42, an important regulator of membrane trafficking. The RhoGEF domain is responsible for GEF catalytic activity, while the PH domain is involved in intracellular targeting of the DH domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 123 matched cddid_all.tbl CDD cd15793 cd15793 275436 PH1_FGD6 FYVE, RhoGEF and PH domain containing/faciogenital dysplasia protein 6, N-terminal Pleckstrin Homology (PH) domain. FGD5 regulates promotes angiogenesis of vascular endothelial growth factor (VEGF) in vascular endothelial cells, including network formation, permeability, directional movement, and proliferation. The specific function of FGD6 is unknown. In general, FGDs have a RhoGEF (DH) domain, followed by a PH domain, a FYVE domain and a C-terminal PH domain. All FGDs are guanine nucleotide exchange factors that activate the Rho GTPase Cdc42, an important regulator of membrane trafficking. The RhoGEF domain is responsible for GEF catalytic activity, while the PH domain is involved in intracellular targeting of the DH domain. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 123 matched cddid_all.tbl CDD cd15794 cd15794 275437 PH_ARHGEF18 Rho guanine nucleotide exchange factor 18 Pleckstrin homology (PH) domain. ARHGEF18, also called p114RhoGEF, is a key regulator of RhoA-Rock2 signaling that is crucial for maintenance of polarity in the vertebrate retinal epithelium, and consequently is essential for cellular differentiation, morphology and eventually organ function. ARHGEF18 contains Dbl-homology (DH) and pleckstrin-homology (PH) domains which bind and catalyze the exchange of GDP for GTP on RhoA. PH domains have diverse functions, but in general are involved in targeting proteins to the appropriate cellular location or in the interaction with a binding partner. They share little sequence conservation, but all have a common fold, which is electrostatically polarized. Less than 10% of PH domains bind phosphoinositide phosphates (PIPs) with high affinity and specificity. PH domains are distinguished from other PIP-binding domains by their specific high-affinity binding to PIPs with two vicinal phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or PtdIns(3,4,5)P3 which results in targeting some PH domain proteins to the plasma membrane. A few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains. PH domains are found in cellular signaling proteins such as serine/threonine kinase, tyrosine kinases, regulators of G-proteins, endocytotic GTPases, adaptors, as well as cytoskeletal associated molecules and in lipid associated enzymes. 119 matched cddid_all.tbl CDD cd15795 cd15795 275439 PMEI-Pla_a_1_like Pollen allergen Pla a 1 and similar plant proteins. The major Platanus acerifolia pollen allergen Pla a 1 belongs to a class of allergens related to proteinaceous invertase and pectin methylesterase inhibitors. Platanus acerifolia is an important cause of pollinosis; Pla a 1 has a prevalence of about 80% among plane tree pollen-allergic patients. Recombinant Pla a 1 binds IgE in vitro, similar to its natural counterpart, rendering it suitable for specific diagnosis and structural studies. Invertase inhibitors are structurally similar to those of pectin methylesterase (PMEIs), an enzyme that is involved in the control of pectin metabolism and is structurally unrelated to invertases. All inhibitors share a size of about 18 kDa, two strictly conserved disulfide bridges and only moderate sequence homology (about 20% sequence identity). 148 matched cddid_all.tbl CDD cd15796 cd15796 275440 CIF_like Cell-wall inhibitor of beta fructosidase and similar proteins. Cell-wall invertases (CWIs) are secreted apoplastic enzymes belonging to the glycoside hydrolase family 32 (EC 3.2.1.26) that catalyze the hydrolytic cleavage of the disaccharide sucrose into glucose and fructose. Their activity is tightly regulated by compartment-specific inhibitor proteins at transcriptional and post-transcriptional levels. Invertase inhibitors are structurally similar to those of pectin methylesterase (PMEIs), an enzyme that is involved in the control of pectin metabolism and is structurally unrelated to invertases. All inhibitors share a size of about 18 kDa, two strictly conserved disulfide bridges and only moderate sequence homology (about 20% sequence identity). Interaction of invertase inhibitor Nt-CIF (Nicotiana tabacum cell-wall inhibitor of beta-fructosidase) with CWI is strictly pH-dependent, modulated between pH 4 and 6, with rapid dissociation at neutral pH mediated by structure rearrangement or surface charge pattern in the binding interface. Comparison of the CIF/INV1 structure with the complex between the structurally CIF-related pectin methylesterase inhibitor (PMEI) and pectin methylesterase indicates a common targeting mechanism in PMEI and CIF. 148 matched cddid_all.tbl CDD cd15797 cd15797 275441 PMEI Pectin methylesterase inhibitor. Pectin methylesterase (PME; Pectinesterase; EC 3.1.1.11; CAZy class 8 of carbohydrate esterases) catalyzes the demethylesterification of homogalacturonans in the cell wall. Its activity is regulated by the proteinaceous PME inhibitor (PMEI) which inhibits PME and invertase through formation of a non-covalent 1:1 complex. Depending on the mode of demethylesterification, PMEI activity results in either loosening or rigidification of the cell wall. PMEI has been implicated in the regulation of fruit development, carbohydrate metabolism and cell wall extension. It may also be involved in inhibiting microbial pathogen PMEs. Thus, PMEI probably plays an important physiological role in PME regulation in plants, possessing several potential applications in a food-technological context. 149 matched cddid_all.tbl CDD cd15798 cd15798 275442 PMEI-like_3 Uncharacterized subfamily of plant invertase/pectin methylesterase inhibitor domains. This subfamily contains inhibitors similar to those of pectin methylesterase (PME; Pectinesterase; EC 3.1.1.11; CAZy class 8 of carbohydrate esterases) that catalyzes the demethylesterification of homogalacturonans in the cell wall. The proteinaceous PME inhibitor (PMEI) inhibits PME and invertase through formation of a non-covalent 1:1 complex. Depending on the mode of demethylesterification, PMEI activity results in either loosening or rigidification of the cell wall. PMEI has been implicated in the regulation of fruit development, carbohydrate metabolism and cell wall extension. It may also be involved in inhibiting microbial pathogen PMEs. Thus, PMEI probably plays an important physiological role in PME regulation in plants, possessing several potential applications in a food-technological context. 154 matched cddid_all.tbl CDD cd15799 cd15799 275443 PMEI-like_4 plant invertase/pectin methylesterase inhibitor domain-containing protein. This subfamily contains inhibitors similar to those of pectin methylesterase (PME; Pectinesterase; EC 3.1.1.11; CAZy class 8 of carbohydrate esterases) that catalyzes the demethylesterification of homogalacturonans in the cell wall, and cell-wall invertases (CWIs) that catalyze the hydrolytic cleavage of the disaccharide sucrose into glucose and fructose. The proteinaceous PME inhibitor (PMEI) inhibits PME and invertase through formation of a non-covalent 1:1 complex. Cell-wall inhibitor of beta-fructosidase from tobacco (CIF) interacts with CWI in a strictly pH-dependent manner, modulated between pH 4 and 6, with rapid dissociation at neutral pH mediated by structure rearrangement or surface charge pattern in the binding interface. Comparison of the CIF/INV1 structure with the complex between the structurally CIF-related pectin methylesterase inhibitor (PMEI) and pectin methylesterase indicates a common targeting mechanism in PMEI and CIF. 151 matched cddid_all.tbl CDD cd15800 cd15800 275444 PMEI-like_2 Uncharacterized subfamily of plant invertase/pectin methylesterase inhibitors. This subfamily contains inhibitors similar to those of pectin methylesterase (PME; Pectinesterase; EC 3.1.1.11; CAZy class 8 of carbohydrate esterases) that catalyzes the demethylesterification of homogalacturonans in the cell wall, and cell-wall invertases (CWIs) that catalyze the hydrolytic cleavage of the disaccharide sucrose into glucose and fructose. The proteinaceous PME inhibitor (PMEI) inhibits PME and invertase through formation of a non-covalent 1:1 complex. Cell-wall inhibitor of beta-fructosidase from tobacco (CIF) interacts with CWI in a strictly pH-dependent manner, modulated between pH 4 and 6, with rapid dissociation at neutral pH mediated by structure rearrangement or surface charge pattern in the binding interface. Comparison of the CIF/INV1 structure with the complex between the structurally CIF-related pectin methylesterase inhibitor (PMEI) and pectin methylesterase indicates a common targeting mechanism in PMEI and CIF. 148 matched cddid_all.tbl CDD cd15801 cd15801 275445 PMEI-like_1 Uncharacterized subfamily of plant invertase/pectin methylesterase inhibitors. This subfamily contains inhibitors similar to those of pectin methylesterase (PME; Pectinesterase; EC 3.1.1.11; CAZy class 8 of carbohydrate esterases) that catalyzes the demethylesterification of homogalacturonans in the cell wall, and cell-wall invertases (CWIs) that catalyze the hydrolytic cleavage of the disaccharide sucrose into glucose and fructose. The proteinaceous PME inhibitor (PMEI) inhibits PME and invertase through formation of a non-covalent 1:1 complex. Cell-wall inhibitor of beta-fructosidase from tobacco (CIF) interacts with CWI in a strictly pH-dependent manner, modulated between pH 4 and 6, with rapid dissociation at neutral pH mediated by structure rearrangement or surface charge pattern in the binding interface. Comparison of the CIF/INV1 structure with the complex between the structurally CIF-related pectin methylesterase inhibitor (PMEI) and pectin methylesterase indicates a common targeting mechanism in PMEI and CIF. 146 matched cddid_all.tbl CDD cd15802 cd15802 276805 RING_CBP-p300 atypical RING domain found in CREB-binding protein and p300 histone acetyltransferases. CBP and p300 (also known as CREBBP or KAT3A and EP300 or KAT3B, respectively) are two histone acetyltransferases (HATs) that associate with and acetylate transcriptional regulators and chromatin. The catalytic core of animal CBP-p300 contains a bromodomain, a CH2 region containing a discontinuous PHD domain interrupted by this RING domain, and a HAT domain. Bromodomain-RING-PHD forms a compact module in which the RING domain is juxtaposed with the HAT substrate-binding site. This ring domain contains only a single zinc ion-binding cluster instead of two; instead of a second zinc atom, a network of hydrophobic interactions stabilizes the domain. The RING domain has an inhibitory role. Disease mutations that disrupt RING attachment lead to upregulation of HAT activity. HAT regulation may require repositioning of the RING domain to facilitate access to an otherwise partially occluded HAT active site. Plant CBP-p300 type HATs lack a bromodomain whose role in the animal animal CBP-p300's is to bind acetylated histones; it has been suggested that these plant proteins may utilize a different domain or another bromodomain protein to perform this function. This RING domain has also been referred to as DUF902. 73 matched cddid_all.tbl CDD cd15803 cd15803 276941 RLR_C_like C-terminal domain of Retinoic acid-inducible gene (RIG)-I-like Receptors, Cereblon (CRBN), and similar protein domains. Retinoic acid-inducible gene (RIG)-I-like Receptors (RLRs) are cytoplasmic RNA receptors that recognize non-self RNA and act as molecular sensors to detect viral pathogens. They play crucial roles in innate antiviral responses, including the production of proinflammatory cytokines and type I interferon. There are three RLRs in vertebrates, RIG-I, LGP2, and MDA5. They are characterized by a central DExD/H-box helicase domain and a C-terminal domain, both of which are responsible for binding viral RNA. Cereblon is part of an E3 ubiquitin ligase complex, together with damaged DNA binding protein 1 (DDB1), CUL4A and ROC1. Cereblon interacts directly with DDB1, although the C-terminal domain characterized here does not contribute to that interaction. The C-terminal domain of Cereblon was shown to contain the binding site for thalidomide and its analogs, a class of teratogenic drugs that exhibit an antiproliferative effect on myelomas. Mutations in CRBN, some of which map onto the C-terminal domain, were associated with autosomal recessive mental retardation, which may have to do with interactions between CRBN and ion channels in the brain. RLRs and Cereblon contain a common conserved zinc binding site in their C-terminal domains. 84 matched cddid_all.tbl CDD cd15804 cd15804 276942 RLR_C C-terminal domain of Retinoic acid-inducible gene (RIG)-I-like Receptors. Retinoic acid-inducible gene (RIG)-I-like Receptors (RLRs) are cytoplasmic RNA receptors that recognize non-self RNA and act as molecular sensors to detect viral pathogens. They play crucial roles in innate antiviral responses, including the production of proinflammatory cytokines and type I interferon. There are three RLRs in vertebrates, RIG-I, LGP2, and MDA5. They are characterized by a central DExD/H-box helicase domain and a C-terminal domain, both of which are responsible for binding viral RNA. The helicase domain catalyzes the unwinding of double stranded RNA in an ATP-dependent manner. RIG-I and MDA5 also contain two N-terminal caspase activation and recruitment domains (CARDs), which initiate downstream signaling upon viral RNA sensing. They may detect partially overlapping viral substrates, including dengue virus, West Nile virus (WNV), reoviruses, and several paramyxoviruses (such as measles virus and Sendai virus). LGP2 lacks CARD and may play a regulatory role in RLR signaling. It may cooperate with either RIG-I or MDA5 to sense viral RNA. 111 matched cddid_all.tbl CDD cd15805 cd15805 276943 RIG-I_C C-terminal domain of Retinoic acid-inducible gene (RIG)-I protein, a cytoplasmic viral RNA receptor. Retinoic acid-inducible gene (RIG)-I protein, also called DEAD box protein 58 (DDX58), is one of three members of the RIG-I-like Receptor (RLR) family. RLRs are cytoplasmic RNA receptors that recognize non-self RNA and act as molecular sensors to detect viral pathogens. RIG-I is activated by blunt-ended double-stranded RNA with or without a 5'-triphosphate (ppp), by single-stranded RNA marked by a 5'-ppp and by polyuridine sequences. It has been found to confer resistance to many negative-sense RNA viruses, including orthomyxoviruses, rhabdoviruses, bunyaviruses, and paramyxoviruses, as well as the positive-strand hepatitis C virus. RLRs are characterized by a central DExD/H-box helicase domain and a C-terminal domain, both of which are responsible for binding viral RNA. The helicase domain catalyzes the unwinding of double stranded RNA in an ATP-dependent manner. RIG-I and MDA5 also contain two N-terminal caspase activation and recruitment domains (CARDs), which initiate downstream signaling upon viral RNA sensing. 112 matched cddid_all.tbl CDD cd15806 cd15806 276944 LGP2_C C-terminal domain of Laboratory of Genetics and Physiology 2 (LGP2), a cytoplasmic viral RNA receptor. Laboratory of Genetics and Physiology 2 (LGP2) is one of three members of the RIG-I-like Receptor (RLR) family. RLRs are cytoplasmic RNA receptors that recognize non-self RNA and act as molecular sensors to detect viral pathogens. They are characterized by a central DExD/H-box helicase domain and a C-terminal domain, both of which are responsible for binding viral RNA. LGP2 lacks the caspase activation and recruitment domains (CARDs) that are present in other RLRs, which initiate downstream signaling upon viral RNA sensing. LGP2 may play a regulatory role in RLR signaling, and may cooperate with either RIG-I or MDA5 to sense viral RNA. 112 matched cddid_all.tbl CDD cd15807 cd15807 276945 MDA5_C C-terminal domain of Melanoma differentiation-associated protein 5, a cytoplasmic viral RNA receptor. Melanoma differentiation-associated protein 5 (MDA5) is also called Interferon-induced helicase C domain-containing protein 1 (IFIH1) or RIG-I-like receptor 2 (RLR-2). It is one of three members of the RLR family. RLRs are cytoplasmic RNA receptors that recognize non-self RNA and act as molecular sensors to detect viral pathogens. It has been shown to detect viruses from the Picornaviridae and Caliciviridae families. RLRs are characterized by a central DExD/H-box helicase domain and a C-terminal domain, both of which are responsible for binding viral RNA. The helicase domain catalyzes the unwinding of double stranded RNA in an ATP-dependent manner. RIG-I and MDA5 also contain two N-terminal caspase activation and recruitment domains (CARDs), which initiate downstream signaling upon viral RNA sensing. 117 matched cddid_all.tbl CDD cd15808 cd15808 293980 SPRY_PRY_TRIM47 PRY/SPRY domain in tripartite motif-containing protein 47 (TRIM47), also known as RING finger protein 100 (RNF100) or Gene overexpressed in astrocytoma protein (GOA). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM47, also known as GOA (Gene overexpressed in astrocytoma protein) or RNF100 (RING finger protein 100). TRIM47 domains are composed of RING/B-box/coiled-coil core and also known as RBCC proteins. It is highly expressed in kidney tubular cells, but lowly expressed in most tissue. It is overexpressed in astrocytoma tumor cells and plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis; astrocytoma, also known as cerebral astrocytoma, is a malignant glioma that arises from astrocytes. Genome wide studies on white matter lesions have identified a novel locus on chromosome 17q25 harboring several genes such as TRIM47 and TRIM65 which pinpoints to possible novel mechanisms leading to these lesions. 206 matched cddid_all.tbl CDD cd15809 cd15809 293981 SPRY_PRY_TRIM4 PRY/SPRY domain in tripartite motif-binding protein 4 (TRIM4), also known as RING finger protein 87 (RNF87). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM4 which is also known as RING finger protein 87 (RNF87). TRIM4 domain is composed of RING/B-box/coiled-coil core and also known as RBCC protein. It is a positive regulator of RIG-I-mediated interferon (IFN) induction. It regulates virus-induced IFN induction and cellular antiviral innate immunity by targeting RIG-I for K63-linked poly-ubiquitination. Over-expression of TRIM4 enhances virus-triggered activation of transcription factors IRF3 and NF-kappaB, as well as IFN-beta induction. Expression of TRIM4 differs significantly in Huntington's Disease (HD) neural cells when compared with wild-type controls, possibly impacting down-regulation of the Huntingtin (HTT) gene, which is involved in the regulation of diverse cellular activities that are impaired in Huntington's Disease (HD) cells. 191 matched cddid_all.tbl CDD cd15810 cd15810 293982 SPRY_PRY_TRIM5_6_22_34 PRY/SPRY domain of tripartite motif-binding protein 5, 6, 22 and 34 (TRIM5, TRIM6, TRIM22 and TRIM34). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of very close paralogs, TRIM5, TRIM6, TRIM22 and TRIM34. These domains are composed of RING/B-box/coiled-coil core and are also known as RBCC proteins. They form a locus of four closely related TRIM genes within an olfactory receptor-rich region on chromosome 11 of the human genome. Genetic analysis of this locus indicates that these four genes have evolved by gene duplication from a common ancestral gene. All genes in the TRIM6/TRIM34/TRIM5/TRIM22 locus are type I interferon inducible, with TRIM5 and TRIM22 possessing antiviral properties. TRIM5 promotes innate immune signaling by activating the TAK1 kinase complex by cooperating with the heterodimeric E2, UBC13/UEV1A. It also stimulates NFkB and AP-1 signaling, and the transcription of inflammatory cytokines and chemokines, amplifying these activities upon retroviral infection. Interaction of its PRY-SPRY or cyclophilin domains with the retroviral capsid lattice stimulates the formation of a complementary lattice by TRIM5, with greatly increased TRIM5 E3 activity, and host cell signal transduction. TRIM6 is selectively expressed in embryonic stem (ES) cells and interacts with the proto-oncogene product Myc, maintaining the pluripotency of the ES cells. TRIM6, together with E2 Ubiquitin conjugase (UbE2K) and K48-linked poly-Ub chains, is critical for the IkappaB kinase epsilon (IKKepsilon) branch of type I interferon (IFN-I) signaling pathway and subsequent establishment of a protective antiviral response. TRIM22 plays an integral role in the host innate immune response to viruses; it has been shown to inhibit the replication of a number of viruses, including HIV-1, hepatitis B, and influenza A. Altered TRIM22 expression has also been associated with multiple sclerosis, cancer, and autoimmune disease. While the PRY-SPRY domain of TRIM5a provides specificity and the capsid recognition motif to retroviral restriction, TRIM34 binds HIV-1 capsid but does not restrict HIV-1 infection. 189 matched cddid_all.tbl CDD cd15811 cd15811 293983 SPRY_PRY_TRIM11 PRY/SPRY domain of tripartite motif-binding protein 11 (TRIM11), also known as RING finger protein 92 (RNF92). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM11, also known as RING finger protein 92 (RNF92) or BIA1. TRIM11 domains are composed of RING/B-box/coiled-coil core and also known as RBCC proteins. It localizes to the nucleus and the cytoplasm; it is overexpressed in high-grade gliomas and promotes proliferation, invasion, migration and glial tumor growth. TRIM11 increases expression of dopamine beta-hydroxylase gene by interacting with the homeodomain transcription factor, PHOX2B, via the B30.2/SPRY domain, thus playing a potential role in the specification of noradrenergic (NA) neuron phenotype. It has also been shown that TRIM11 plays a critical role in the clearance of mutant PHOX2B, which causes congenital central hypoventilation syndrome, via the proteasome. TRIM11 binds a key component of the activator-mediated cofactor complex (ARC105), and destabilizes it, through the ubiquitin-proteasome system; ARC105 mediates chromatin-directed transcription activation and is a key regulatory factor for transforming growth factor beta (TGFbeta) signaling. 169 matched cddid_all.tbl CDD cd15812 cd15812 293984 SPRY_PRY_TRIM17 PRY/SPRY domain of tripartite motif-binding protein 17 (TRIM17), also known as testis RING finger protein (terf). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM17, also known as RING finger protein 16 (RNF16) or testis RING finger protein (terf). TRIM17 domain is composed of RING/B-box/coiled-coil core and also known as RBCC protein, expressed almost exclusively in the testis. It exhibits E3 ligase activity, causing protein degradation of ZW10 interacting protein (ZWINT), a known component of the kinetochore complex required for the mitotic spindle checkpoint, and negatively regulates proliferation of breast cancer cells. TRIM17 undergoes ubiquitination in COS7 fibroblast-like cells but is inhibited and stabilized by TRIM44. 176 matched cddid_all.tbl CDD cd15813 cd15813 293985 SPRY_PRY_TRIM20 PRY/SPRY domain in tripartite motif-binding protein 20 (TRIM20), also known as pyrin. This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM20, which is also known as pyrin or marenostrin. Unlike TRIM domains that are composed of RING/B-box/coiled-coil core, the N-terminal RING domain in TRIM20 is exchanged by a PYRIN domain (PYD), a prime mediator of protein interactions necessary for apoptosis, inflammation and innate immune signaling pathway, and it also harbors a C-terminal B30.2 domain. Mutations in pyrin (TRIM20) are associated with familial Mediterranean fever (FMF), a recessively hereditary periodic fever syndrome, characterized by episodes of inflammation and fever. These mutations cluster in the C-terminal B30.2 domain and therefore it is assumed that pyrin plays a role in the innate immune system by possibly effecting caspase-1-dependent IL-1beta maturation. 184 matched cddid_all.tbl CDD cd15814 cd15814 293986 SPRY_PRY_TRIM27 PRY/SPRY domain in tripartite motif-containing protein 27 (TRIM27), also known as RING finger protein 76 (RNF76). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM27, also known as RING finger protein 76 (RNF76) or RET finger protein (RFP). TRIM27 domain is composed of RING/B-box/coiled-coil core and also known as RBCC proteins. It is highly expressed in the spleen, thymus and in cells of the hematopoietic compartment. TRIM27 exhibits either nuclear or cytosolic localization depending on the cell type. TRIM27 negatively regulates nucleotide-binding oligomerization domain containing 2 (NOD2)-mediated signaling by proteasomal degradation of NOD2, suggesting that TRIM27 could be a new target for therapeutic intervention in NOD2-associated diseases such as Crohn's. High expression of TRIM27 is observed in several human cancers, including breast and endometrial cancer, where elevated TRIM27 expression predicts poor prognosis. Also, TRIM27 forms an oncogenic fusion protein with Ret proto-oncogene. It is involved in different stages of spermatogenesis and its significant expression in male germ cells and seminomas, suggests that TRIM27 may be associated with the regulation of testicular germ cell proliferation and histological-type of germ cell tumors. TRIM27 could also be a predictive marker for chemoresistance in ovarian cancer patients. In the neurotoxin model of Parkinson's disease (PD), deficiency of TRIM27 decreases apoptosis and protects dopaminergic neurons, making TRIM27 an effective potential target during the treatment of PD. 177 matched cddid_all.tbl CDD cd15815 cd15815 293987 SPRY_PRY_TRIM38 PRY/SPRY domain of tripartite motif-binding protein 38 (TRIM38), also known as Ring finger protein 15 (RNF15). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM38, which is also known as RING finger protein 15 (RNF15) or RORET. TRIM38 domains are composed of RING/B-box/coiled-coil core and also known as RBCC proteins. TRIM38 has been shown to act as a suppressor in TOLL-like receptor (TLR)-mediated interferon (IFN)-beta induction by promoting degradation of TRAF6 and NAP1 through the ubiquitin-proteasome system. Another study has shown that TRIM38 may act as a novel negative regulator for TLR3-mediated IFN-beta signaling by targeting TRIF for degradation. TRIM38 has been identified as a critical negative regulator in TNFalpha- and IL-1beta-triggered activation of NF-kappaB and MAP Kinases (MAPKs); it causes degradation of two essential cellular components, TGFbeta-associated kinase 1 (TAK1)-associating chaperones 2 and 3 (TAB2/3). The degradation is promoted through a lysosomal-dependent pathway, which requires the C-terminal PRY-SPRY of TRIM38. Enterovirus 71 infection induces degradation of TRIM38, suggesting that TRIM38 may play a role in viral infections. 182 matched cddid_all.tbl CDD cd15816 cd15816 293988 SPRY_PRY_TRIM58 PRY/SPRY domain in tripartite motif-binding protein 58 (TRIM58), also known as BIA2. This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM58, also known as BIA2. TRIM58 domains are composed of RING/B-box/coiled-coil core and also known as RBCC proteins.It is implicated by genome-wide association studies (GWAS) to regulate erythrocyte traits, including cell size and number. Trim58 facilitates erythroblast enucleation by inducing proteolytic degradation of the microtubule motor dynein. 168 matched cddid_all.tbl CDD cd15817 cd15817 293989 SPRY_PRY_TRIM60_75 PRY/SPRY domain of tripartite motif-binding protein 60 and 75 (TRIM60 and TRIM75). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM60 and TRIM75, both composed of RING/B-box/coiled-coil core and also known as RBCC proteins. TRIM60 domain is also known as RING finger protein 33 (RNF33) or 129 (RNF129). Based on its expression profile, RNF33 likely plays an important role in the spermatogenesis process, the development of the pre-implantation embryo, and in testicular functions; Rnf33 is temporally transcribed in the unfertilized egg and the pre-implantation embryo, and is permanently silenced before the blastocyst stage. Mice experiments have shown that RNF33 associates with the cytoplasmic motor proteins, kinesin-2 family members 3A (KIF3A) and 3B (KIF3B), suggesting possible contribution to cargo movement along the microtubule in the expressed sites. TRIM75, also known as Gm794, has a single site of positive selection in its RING domain associated with E3 ubiquitin ligase activity. It has not been detectably expressed experimentally due to their constant turnover by the proteasome, and therefore not been characterized. 168 matched cddid_all.tbl CDD cd15818 cd15818 293990 SPRY_PRY_TRIM69 PRY/SPRY domain in tripartite motif-binding protein 69 (TRIM69), also known as RING finger protein 36 (RNF36). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM69, which is also known as RING finger protein 36 (RNF36) or testis-specific ring finger (Trif). TRIM69 domains are composed of RING/B-box/coiled-coil core and also known as RBCC proteins. It is a novel testis E3 ubiquitin ligase that may function to ubiquitinate its particular substrates during spermatogenesis. In humans, TRIM69 localizes in the cytoplasm and nucleus, and requires an intact RING finger domain to function. The mouse ortholog of this gene is specifically expressed in germ cells at the round spermatid stages during spermatogenesis and, when overexpressed, induces apoptosis. TRIM69 has been shown to be a novel regulator of mitotic spindle assembly in tumor cells; it associates with spindle poles and promotes centrosomal clustering, and is therefore essential for formation of a bipolar spindle. 187 matched cddid_all.tbl CDD cd15819 cd15819 293991 SPRY_PRY_BTN1_2 butyrophilin subfamily member A1 and A2 (BTN1A and BTN2A). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of butyrophilin family 1A and 2A (BTN1A and BTN2A). BTNs belong to receptor glycoproteins of immunoglobulin (Ig) superfamily, characterized by the presence of extracellular Ig-like domains (IgV and/or IgC). BTN1A plays a role in the secretion, formation and stabilization of milk fat globules. The B30.2 domain of BTN1A1 binds the enzyme xanthine oxidoreductase (XOR) in order to participate in milk fat globule secretion; this interaction may lead to the production of reactive oxygen species, which have immunomodulatory and antimicrobial functions. Duplication events have led to three paralogs of BTN2A in primates: BTN2A1, BTN2A2, and BTN2A3. In humans, only BTN2A1 has been functionally characterized; it has been detected on epithelial cells and leukocytes, and identified as a novel ligand of dendritic cell-specific ICAM-3 grabbing nonintegrin (DCSIGN), a C-type lectin receptor that acts as an internalization receptor for HIV-1, HCV, and other pathogens. BTN2A2 mRNA has been shown to be expressed in circulating human immune cells. 172 matched cddid_all.tbl CDD cd15820 cd15820 293992 SPRY_PRY_BTN3 PRY/SPRY domain of butyrophilin 3 (BTN3), includes BTN3A1, BTN3A2, BTN3A3 as well as BTN-like 3 (BTNL3); BTN3A also known as CD277. This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of butyrophilin family 3A (BTN3A); duplication events have led to three paralogs in primates: BTN3A1, BTN3A2, and BTN3A3. BTNs belong to receptor glycoproteins of immunoglobulin (Ig) superfamily, characterized by the presence of extracellular Ig-like domains (IgV and/or IgC). BTN3 transcripts are ubiquitously present in all immune cells (T cells, B cells, NK cells, monocytes, dendritic cells, and hematopoietic precursors) with different expression levels; BTN3A1 and BTN3A2 are expressed mainly by CD4+ and CD8+ T cells, BTN3A2 is the major form expressed in NK cells, and BTN3A3 is poorly expressed in these immune cells. The PRY/SPRY domain of the BTN3A1 isoform mediates phosphoantigen (pAg)-induced activation by binding directly to the pAg. 176 matched cddid_all.tbl CDD cd15821 cd15821 293993 SPRY_PRY_RFPL Ret finger protein-like (RFPL), includes RFP1, 2, 3, 4. This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of RFPL protein family, which includes RFPL1, RFPL2, RFPL3 and RFPL4. In humans, RFPL transcripts can be detected at the onset of neurogenesis in differentiating human embryonic stem cells, and in the developing human neocortex. The human RFPL1, 2, 3 genes have a role in neocortex development. RFPL1 is a primate-specific target gene of Pax6, a key transcription factor for pancreas, eye and neocortex development; human RFPL1 decreases cell number through its RFPL-defining motif (RDM) and SPRY domains. The RFPL4 (also known as RFPL4A) gene encodes a putative E3 ubiquitin-protein ligase expressed in adult germ cells and interacts with oocyte proteins of the ubiquitin-proteasome degradation pathway. 178 matched cddid_all.tbl CDD cd15822 cd15822 293994 SPRY_PRY_TRIM5 PRY/SPRY domain in tripartite motif-binding protein 5 (TRIM5), also known as RING finger protein 88 (RNF88). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM5 which is also known as RING finger protein 88 (RNF88) or TRIM5alpha (TRIM5a), an antiretroviral restriction factor and a retrovirus capsid sensor in immune signaling. TRIM5 domain is composed of RING/B-box/coiled-coil core and also known as RBCC protein. It blocks retrovirus infection soon after the virion core enters the cell cytoplasm by recognizing the capsid protein lattice that encases the viral genomic RNA; the SPRY domain provides the capsid recognition motif that dictates specificity to retroviral restriction. TRIM5a, an E3 ubiquitin ligase, promotes innate immune signaling by activating the TAK1 kinase complex by cooperating with the heterodimeric E2, UBC13/UEV1A. It also stimulates NFkB and AP-1 signaling, and the transcription of inflammatory cytokines and chemokines, and amplifies these activities upon retroviral infection. Interaction of its PRY-SPRY or cyclophilin domains with the retroviral capsid lattice stimulates the formation of a complementary lattice by TRIM5, with greatly increased TRIM5 E3 activity, and host cell signal transduction. 200 matched cddid_all.tbl CDD cd15823 cd15823 293995 SPRY_PRY_TRIM6 PRY/SPRY domain in tripartite motif-binding protein 6 (TRIM6), also known as RING finger protein 89 (RNF89). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM6, also known as RING finger protein 89 (RNF89). TRIM6 domain is composed of RING/B-box/coiled-coil core and also known as RBCC protein. It is selectively expressed in embryonic stem (ES) cells and interacts with the proto-oncogene product Myc, maintaining the pluripotency of the ES cells. TRIM6, together with E2 Ubiquitin conjugase (UbE2K) and K48-linked poly-Ub chains, is critical for the IkappaB kinase epsilon (IKKepsilon) branch of type I interferon (IFN-I) signaling pathway and subsequent establishment of a protective antiviral response. 188 matched cddid_all.tbl CDD cd15824 cd15824 293996 SPRY_PRY_TRIM22 PRY/SPRY domain in tripartite motif-containing protein 22 (TRIM22), also known as RING finger protein 94 (RNF94) or Stimulated trans-acting factor of 50 kDa (STAF50). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM22, also known as RING finger protein 94 (RNF94) or STAF50 (Stimulated trans-acting factor of 50 kDa). TRIM6 domain is composed of RING/B-box/coiled-coil core and also known as RBCC protein. TRIM22 is an interferon-induced protein, predominantly expressed in peripheral blood leukocytes, in lymphoid tissue such as spleen and thymus, and in the ovary.TRIM22 plays an integral role in the host innate immune response to viruses; it has been shown to inhibit the replication of a number of viruses, including HIV-1, hepatitis B, and influenza A. TRIM22 inhibits influenza A virus (IAV) infection by targeting the viral nucleoprotein for degradation; it represents a novel restriction factor up-regulated upon IAV infection that curtails its replicative capacity in epithelial cells. Altered TRIM22 expression has also been associated with multiple sclerosis, cancer, and autoimmune disease. A large number of high-risk non-synonymous (ns)SNPs have been identified in the highly polymorphic TRIM22 gene, most of which are located in the SPRY domain and could possibly alter critical regions of the SPRY structural and functional residues, including several sites that undergo post-translational modification. TRIM22 is a direct p53 target gene and inhibits the clonogenic growth of leukemic cells. Its expression in Wilms tumors is negatively associated with disease relapse. It is greatly under-expressed in breast cancer cells as compared to non-malignant cell lines; p53 dysfunction may be one of the mechanisms for its down-regulation. 198 matched cddid_all.tbl CDD cd15825 cd15825 293997 SPRY_PRY_TRIM34 PRY/SPRY domain in tripartite motif-containing protein 34 (TRIM34), also known as RING finger protein 21 (RNF21) or interferon-responsive finger protein (IFP1). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM34, also known as RING finger protein 21 (RNF21) or interferon-responsive finger protein (IFP1). TRIM34 domain is composed of RING/B-box/coiled-coil core and also known as RBCC protein. The TRIM21 cDNA possesses at least three kinds of isoforms, due to alternative splicing, of which only the long and medium forms contain the SPRY domain. It is an interferon-induced protein, predominantly expressed in the testis, kidney, and ovary. The SPRY domain provides the capsid recognition motif that dictates specificity to retroviral restriction. While the PRY-SPRY domain provides specificity and the capsid recognition motif to retroviral restriction, TRIM34 binds HIV-1 capsid but does not restrict HIV-1 infection. 185 matched cddid_all.tbl CDD cd15826 cd15826 293998 SPRY_PRY_TRIM15 PRY/SPRY domain in tripartite motif-binding protein 15 (TRIM15). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of tripartite motif-containing protein 15 (TRIM15), also referred to as RING finger protein 93 (RNF93) or Zinc finger protein B7 or 178 (ZNFB7 or ZNF178). TRIM15 domains are composed of RING/B-box/coiled-coil core and also known as RBCC proteins. The PRY and SPRY/B30.2 domains can function as immune defense components and in pathogen sensing. TRIM15 has been shown to regulate inflammatory and innate immune signaling, in addition to displaying antiviral activities. Down-regulation of TRIM15, as well as TRIM11, enhances virus release, suggesting that these proteins contribute to the endogenous restriction of retroviruses in cells. TRIM15 is also a regulatory component of focal adhesion turnover and cell migration. 170 matched cddid_all.tbl CDD cd15827 cd15827 293999 SPRY_PRY_TRIM10 PRY/SPRY domain of tripartite motif-binding protein 10 (TRIM10) also known as hematopoietic RING finger 1 (HERF1). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM10, also known as RING finger protein 9 (RNF9) or hematopoietic RING finger 1 (HERF1). TRIM10 domain is composed of RING/B-box/coiled-coil core and also known as RBCC protein. TRIM10/HERF1 is predominantly expressed during definitive erythropoiesis and in embryonic liver, and minimally expressed in adult liver, kidney, and colon. It is critical for erythroid cell differentiation and its down-regulation leads to cell death; inhibition of TRIM10 expression blocks terminal erythroid differentiation, while its over-expression in erythroid cells induces beta-major globin expression and erythroid differentiation. 172 matched cddid_all.tbl CDD cd15828 cd15828 294000 SPRY_PRY_TRIM60 PRY/SPRY domain of tripartite motif-binding protein 60 (TRIM60) also known as RING finger protein 33 (RNF33). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM60, which is also known as RING finger protein 33 (RNF33) or 129 (RNF129). TRIM60 domains are composed of RING/B-box/coiled-coil core and also known as RBCC proteins. Based on its expression profile, RNF33 likely plays an important role in the spermatogenesis process, the development of the pre-implantation embryo, and in testicular functions; Rnf33 is temporally transcribed in the unfertilized egg and the pre-implantation embryo, and is permanently silenced before the blastocyst stage. Mice experiments have shown that RNF33 associates with the cytoplasmic motor proteins, kinesin-2 family members 3A (KIF3A) and 3B (KIF3B), suggesting possible contribution to cargo movement along the microtubule in the expressed sites. 180 matched cddid_all.tbl CDD cd15829 cd15829 294001 SPRY_PRY_TRIM75 PRY/SPRY domain of tripartite motif-binding protein 75 (TRIM75). This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of TRIM75, also known as Gm794. TRIM75 domains are composed of RING/B-box/coiled-coil core and also known as RBCC proteins. TRIM75 has a single site of positive selection in its RING domain associated with E3 ubiquitin ligase activity. It has not been detectably expressed experimentally due to their constant turnover by the proteasome, and therefore not been characterized. 187 matched cddid_all.tbl CDD cd15830 cd15830 276939 BamD BamD lipoprotein, a component of the beta-barrel assembly machinery. BamD, also called YfiO, is part of the beta-barrel assembly machinery (BAM), which is essential for the folding and insertion of outer membrane proteins (OMPs) in the OM of Gram-negative bacteria. Transmembrane OMPs carry out important functions including nutrient and waste management, cell adhesion, and structural roles. The BAM complex is composed of the beta-barrel OMP BamA (also called Omp85/YaeT) and four lipoproteins BamBCDE. BamD is the only BAM lipoprotein required for viability. Both BamA and BamD are broadly distributed in Gram-negative bacteria, and may constitute the core of the BAM complex. BamD contains five Tetratricopeptide repeats (TPRs). The three TPRs at the N-terminus may participate in interaction with substrates, while the two TPRs in the C-terminus may be involved in binding with other BAM components. 213 matched cddid_all.tbl CDD cd15831 cd15831 276938 BTAD Bacterial Transcriptional Activation (BTA) domain. The Bacterial Transcriptional Activation (BTA) domain is present in the putative transcriptional regulator Mycobacterium EmbR and the related Streptomyces antibiotic regulatory protein (SARP) family of transcription factors, which includes DnrI and AfsR, among others. Members of this family contain an N-terminal DNA-binding domain, followed by the BTA domain, and many have diverse domains at the C-terminus. EmbR contains an C-terminal forkhead-associated (FHA) domain, which mediates binding to threonine-phosphorylated sites in a sequence-specific manner. The BTA domain of EmbR contains three Tetratricopeptide repeats (TPRs) and two C-terminal helices. The TPR motif typically contains 34 amino acids, and 5 or 6 tandem repeats of the motif generate a right-handed helical structure with an amphipathic channel that is thought to accommodate an alpha-helix of a target protein. 146 matched cddid_all.tbl CDD cd15832 cd15832 276937 SNAP Soluble N-ethylmaleimide-sensitive factor (NSF) Attachment Protein family. Members of the soluble NSF attachment protein (SNAP) family are involved in intracellular membrane trafficking, including vesicular transport between the endoplasmic reticulum and Golgi apparatus. Higher eukaryotes contain three isoforms of SNAPs: alpha, beta, and gamma. Alpha-SNAP is universally present in eukaryotes and acts as an adaptor protein between SNARE (integral membrane SNAP receptor) and NSF for recruitment to the 20S complex. Beta-SNAP is brain-specific and shares high sequence identity (about 85%) with alpha-SNAP. Gamma-SNAP is weakly related (about 20-25% identity) to the two other isoforms, and is ubiquitous. It may help regulate the activity of the 20S complex. The X-ray structures of vertebrate gamma-SNAP and yeast Sec17, a SNAP family member, show similar all-helical structures consisting of an N-terminal extended twisted sheet of four Tetratricopeptide repeat (TPR)-like helical hairpins and a C-terminal helical bundle. 278 matched cddid_all.tbl CDD cd15834 cd15834 276930 TNFRSF1A_teleost Tumor necrosis factor receptor superfamily member 1A (TNFRSF1A) in teleosts; also known as TNFR1. This subfamily of TNFRSF1 ((also known as type I TNFR, TNFR1, DR1, TNFRSF1A, CD120a, p55) is found in teleosts. It binds TNF-alpha, through the death domain (DD), and activates NF-kappaB, mediates apoptosis and activates signaling pathways controlling inflammatory, immune, and stress responses. It mediates signal transduction by interacting with antiapoptotic protein BCL2-associated athanogene 4 (BAG4/SODD) and adaptor proteins TRAF2 and TRADD that play regulatory roles. The human genetic disorder called tumor necrosis factor associated periodic syndrome (TRAPS), or periodic fever syndrome, is associated with germline mutations of the extracellular domains of this receptor, possibly due to impaired receptor clearance. Serum levels of TNFRSF1A are elevated in schizophrenia and bipolar disorder, and high levels are also associated with cognitive impairment and dementia. Knockout studies in zebrafish embryos have shown that a signaling balance between TNFRSF1A and TNFRSF1B is required for endothelial cell integrity. TNFRSF1A signals apoptosis through caspase-8, whereas TNFRSF1B signals survival via NF-kappaB in endothelial cells. Thus, this apoptotic pathway seems to be evolutionarily conserved, as TNFalpha promotes apoptosis of human endothelial cells and triggers caspase-2 and P53 activation in these cells via TNFRSF1A. 150 matched cddid_all.tbl CDD cd15835 cd15835 276931 TNFRSF1B_teleost Tumor necrosis factor receptor superfamily member 1B (TNFRSF1B) in teleost; also known as TNFR2. This subfamily of TNFRSF1B (also known as TNFR2, type 2 TNFR, TNFBR, TNFR80, TNF-R75, TNF-R-II, p75, CD120b) is found in teleosts. It binds TNF-alpha, but lacks the death domain (DD) that is associated with the cytoplasmic domain of TNFRSF1A (TNFR1). It is inducible and expressed exclusively by oligodendrocytes, astrocytes, T cells, thymocytes, myocytes, endothelial cells, and in human mesenchymal stem cells. TNFRSF1B protects oligodendrocyte progenitor cells (OLGs) against oxidative stress, and induces the up-regulation of cell survival genes. While pro-inflammatory and pathogen-clearing activities of TNF are mediated mainly through activation of TNFRSF1A, a strong activator of NF-kappaB, TNFRSF1B is more responsible for suppression of inflammation. Although the affinities of both receptors for soluble TNF are similar, TNFRSF1B is sometimes more abundantly expressed and thought to associate with TNF, thereby increasing its concentration near TNFRSF1A receptors, and making TNF available to activate TNFRSF1A (a ligand-passing mechanism). Knockout studies in zebrafish embryos have shown that a signaling balance between TNFRSF1A and TNFRSF1B is required for endothelial cell integrity. TNFRSF1A signals apoptosis through caspase-8, whereas TNFRSF1B signals survival via NF-kB in endothelial cells. In goldfish (Carassius aurutus L.), TNFRSF1B expression is substantially higher than that of TNFRSF1 in tissues and various immune cell types. Both receptors are most robustly expressed in monocytes; mRNA levels of TNFRSF1B are lowest in peripheral blood leukocytes. 130 matched cddid_all.tbl CDD cd15836 cd15836 276932 TNFRSF11A_teleost Tumor necrosis factor receptor superfamily member 11A (TNFRSF11A) in teleost; also known as RANK. TNFRSF11A (also known as RANK, FEO, OFE, ODFR, OSTS, PDB2, CD26, OPTB7, TRANCER, LOH18CR1) induces the activation of NF-kappa B and MAPK8/JNK through interactions with various TRAF adaptor proteins. This receptor and its ligand are important regulators of the interaction between T cells and dendritic cells. This receptor is also an essential mediator for osteoclast and lymph node development. Mutations at this locus have been associated with familial expansile osteolysis, autosomal recessive osteopetrosis, and Juvenile Paget's disease (JPD) of bone. Alternatively spliced transcript variants have been described for this locus. Mutation analysis may improve diagnosis, prognostication, recurrence risk assessment, and perhaps treatment selection among the monogenic disorders of RANKL/OPG/RANK activation. 122 matched cddid_all.tbl CDD cd15837 cd15837 276933 TNFRSF26 Tumor necrosis factor receptor superfamily member 26 (TNFRSF26), also known as tumor necrosis factor receptor homolog 3 (TNFRH3). TNFRSF26 (also known as tumor necrosis factor receptor homolog 3 (TNFRH3) or TNFRSF24) is predominantly expressed in embryos and lymphoid cell types, along with its closely related TNFRSF22 and TNFRSF23 orthologs, and is developmentally regulated. Unlike TNFRSF22/23, TNFRSF26 does not serve as a TRAIL decoy receptor; it remains an orphan receptor. 118 matched cddid_all.tbl CDD cd15838 cd15838 276934 TNFRSF27 Tumor necrosis factor receptor superfamily member 27 (TNFRSF27), also known as ectodysplasin A2 receptor (EDA2R) or X-linked ectodermal dysplasia receptor (XEDAR). TNFRSF27 (also known as ectodysplasin A2 receptor (EDA2R), X-linked ectodermal dysplasia receptor (XEDAR), EDAA2R, EDA-A2R) has two isoforms, EDA-A1 and EDA-A2, that are encoded by the anhidrotic ectodermal dysplasia (EDA) gene. It is highly expressed during embryonic development and binds to ectodysplasin-A2 (EDA-A2), playing a crucial role in the p53-signaling pathway. EDA2R is a direct p53 target that is frequently down-regulated in colorectal cancer tissues due to its epigenetic alterations or through the p53 gene mutations. Mutations in the EDA-A2/XEDAR signaling give rise to ectodermal dysplasia, characterized by loss of hair, sweat glands, and teeth. A non-synonymous SNP on EDA2R, along with genetic variants in human androgen receptor is associated with androgenetic alopecia (AGA). 116 matched cddid_all.tbl CDD cd15839 cd15839 276935 TNFRSF_viral "Tumor necrosis factor receptor superfamily members, virus-encoded. This family contains viral TNFR homologs that include vaccinia virus (VACV) cytokine response modifier E (CrmE), an encoded TNFR that shares significant sequence similarity with mammalian type 2 TNF receptors (TNFSFR1B, p75, TNFR type 2), a cowpox virus encoded cytokine-response modifier B (crmB), which is a secreted form of TNF receptor that can contribute to the modification of TNF-mediated antiviral processes, and a myxoma virus (MYXV) T2 (M-T2) protein that binds and inhibits rabbit TNF-alpha. The CrmE structure confirms that the canonical TNFR fold is adopted, but only one of the two ""ligand-binding"" loops of TNFRSF1A is conserved, suggesting a mechanism for the higher affinity of poxvirus TNFRs for TNFalpha over lymphotoxin-alpha. CrmB protein specifically binds TNF-alpha and TNF-beta indicating that cowpox virus seeks to invade antiviral processes mediated by TNF. Intracellular M-T2 blocks virus-induced lymphocyte apoptosis via a highly conserved viral preligand assembly domain (vPLAD), which controls receptor signaling competency prior to ligand binding." 125 matched cddid_all.tbl CDD cd15840 cd15840 277193 SNARE_Qa SNARE motif, subgroup Qa. SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Examples for members of the Qa SNAREs are syntaxin 18, syntaxin 5, syntaxin 16, and syntaxin 1. 59 matched cddid_all.tbl CDD cd15841 cd15841 277194 SNARE_Qc SNARE motif, subgroup Qc. SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qc-, as well as Qa- and Qb-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Examples for members of the Qc SNAREs are C-terminal domains of SNAP23 and SNAP25, syntaxin 8, syntaxin 6, and Bet1. 59 matched cddid_all.tbl CDD cd15842 cd15842 277195 SNARE_Qb SNARE motif, subgroup Qb. SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Examples for members of the Qb SNAREs are N-terminal domains of SNAP23 and SNAP25, Vti1, Sec20 and GS27. 62 matched cddid_all.tbl CDD cd15843 cd15843 277196 R-SNARE SNARE motif, subgroup R-SNARE. SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). In contrast to Qa-, Qb- and Qc-SNAREs that are localized to target organelle membranes, R-SNAREs are localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Examples for members of the Qa SNAREs are syntaxin 18, syntaxin 5, syntaxin 16, and syntaxin 1. 60 matched cddid_all.tbl CDD cd15844 cd15844 277197 SNARE_syntaxin5 SNARE motif of syntaxin 5. Syntaxin 5 (Syn5) regulates the transport from the ER to the Golgi, as well as the early/recycling endosomes to the trans-Golgi network and participates in the assembly of transitional ER and the Golgi, lipid droplet fusion, and cytokinesis. Syn5 exists in 2 isoforms, long (42 kDa) and short (35 kDa). The short form is localized in the Golgi complex, whereas the long form is additionally found in the endoplasmic reticulum (ER). The syntaxin-5 SNARE complexes, which also contain Bet1 (Qc) and either GS27 (Qb) and Sec22B (R-SNARE) or GS28 (Qb) and Ykt6 (R-SNARE), regulate the early secretory pathway of eukaryotic cells at the level of endoplasmic reticulum (ER) to Golgi transport. The syntaxin-5 SNARE complex, which also contains GS15 (Qc), GS28 (Qb) and Ykt6 (R-SNAREs) is involved in the transport from the trans-Golgi network to the cis-Golgi. Syn5 is member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 86 matched cddid_all.tbl CDD cd15845 cd15845 277198 SNARE_syntaxin16 SNARE motif of syntaxin 16. Syntaxin 16 is located in trans-Golgi network (TGN) and regulated by the SM protein Vps45p. It forms a complex with syntaxin 6 (Qc), Vti1a (Qb) and VAMP4 (R-SNARE) and is involved in the regulation of recycling of early endosomes to the trans-Golgi network (TGN). Syntaxin 16 is a member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 59 matched cddid_all.tbl CDD cd15846 cd15846 277199 SNARE_syntaxin17 SNARE motif of syntaxin 17. Synthaxin 17 (STX17) belongs to the Qa subgroup of SNAREs and interacts with SNAP29 (Qb/Qc) and the lysosomal R-SNARE VAMP8. The complex plays a role in autophagosome-lysosome fusion. Autophagosome transports cytoplasmic materials, including cytoplasmic proteins, glycogen, lipids, organelles, and invading bacteria to the lysosome for degradation. SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 62 matched cddid_all.tbl CDD cd15847 cd15847 277200 SNARE_syntaxin7_like SNARE motif of syntaxin 7, 12 and related sequences. SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. This subgroup of the Qa SNAREs includes syntaxin 7, syntaxin 12, TSNARE1 and related proteins. 60 matched cddid_all.tbl CDD cd15848 cd15848 277201 SNARE_syntaxin1-like SNARE motif of syntaxin 1 and related proteins. SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. This subgroup of the Qa SNAREs includes syntaxin 1, syntaxin 11, syntaxin 19, syntaxin 2, syntaxin 3, syntaxin 4 and related proteins. 63 matched cddid_all.tbl CDD cd15849 cd15849 277202 SNARE_Sso1 SNARE motif of Sso1. Saccharomyces cerevisiae SNARE protein Sso1p forms a complex with synaptobrevin homolog Snc1p (R-SNARE) and the SNAP-25 homolog Sec9p (Qb/c) which is involved in exocytosis. Sso1 is member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 64 matched cddid_all.tbl CDD cd15850 cd15850 277203 SNARE_syntaxin18 SNARE motif, subgroup Qa. Syntaxin18 (also known as Ufe1p) is involved in retrograde transport of CopI coatomer coated vesicles from the Golgi to the ER. It forms a complex with USE1 (SLT1, Qc), Bnip1 (Sec20p, Qb) and Sec22b (R-SNARE). Syntaxin18 is a member of the Qa subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein family. SNARE proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qc-, as well as Qa- and Qb-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. 59 matched cddid_all.tbl CDD cd15851 cd15851 277204 SNARE_Syntaxin6 SNARE motif of syntaxin 6. Syntaxin 6 forms a complex with syntaxin 16 (Qa), Vti1a (Qb) and VAMP4 (R-SNARE) and is involved in the regulation of recycling of early endosomes to the trans-Golgi network (TGN). Syntaxin 6 and its yeast homolog TLG1 are members of the Qc subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 66 matched cddid_all.tbl CDD cd15852 cd15852 277205 SNARE_Syntaxin8 SNARE motif of syntaxin 8. Syntaxin 8 forms a complex with syntaxin 7 (Qa), Vti1b (Qb) and either VAMP7 or VAMP8 (R-SNARE) and is involved in the transport from early endosomes to the lysosome. Syntaxin 8 is a member of the Qc subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 59 matched cddid_all.tbl CDD cd15853 cd15853 277206 SNARE_Bet1 SNARE motif of Bet1. Bet1 forms a complexes with GS27 (Qb), syntaxin-5 (Qa) and Sec22B (R-SNARE) or GS28 (Qb), syntaxin-5 (Qa) and Ykt6 (R-SNARE). These complexes regulates the early secretory pathway of eukaryotic cells at the level of the transport from endoplasmic reticulum (ER) to the ER-Golgi intermediate compartment (ERGIC) and from ERGIC to the cis-Golgi, respectively. Bet1 is a member of the Qc subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 59 matched cddid_all.tbl CDD cd15854 cd15854 277207 SNARE_SNAP47C C-terminal SNARE motif of SNAP47. C-terminal SNARE motif of SNAP47, a member of the Qb/Qc subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins. The exact funtion of SNAP47 is unknown. Qb/Qc SNAREs consist of 2 coiled-coil helices (called SNARE motifs, one belonging to the Qb subgroup and one belonging to the Qc subgroup), which mediate the interactions with other SNARE proteins, and a transmembrane domain. In general, the SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Other members of the Qb/Qc SNAREs are SNAP23, SNAP25, SNAP29 and SEC9. 59 matched cddid_all.tbl CDD cd15855 cd15855 277208 SNARE_SNAP25C_23C C-terminal SNARE motif of SNAP25 and SNAP23. C-terminal SNARE motifs of SNAP25 and SNAP23, members of the Qb/Qc subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins. SNAP23 interacts with STX4 (Qa) and the lysosomal R-SNARE VAMP8. The complex plays a role in transport of secretory granule from trans-Golgi network to the plasma membrane. SNAP25 interacts with Syntaxin-1 (Qa) and the R-SNARE VAMP2 (also called synaptobrevin-2). The complex plays a role in transport of secretory granule from trans-Golgi network to the plasma membrane. Qb/Qc SNAREs consist of 2 coiled-coil helices (called SNARE motifs, one belonging to the Qb subgroup and one belonging to the Qc subgroup), which mediate the interactions with other SNARE proteins, and a transmembrane domain. In general, the SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Other members of the Qb/Qc SNAREs are SNAP29, SNAP47 and SEC9. 59 matched cddid_all.tbl CDD cd15856 cd15856 277209 SNARE_SNAP29C C-terminal SNARE motif of SNAP29. C-terminal SNARE motif of SNAP29, a member of the Qb/Qc subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins. SNAP29 interacts with STX17 (Qa) and the lysosomal R-SNARE VAMP8. The complex plays a role in autophagosome-lysosome fusion. Autophagosome transports cytoplasmic materials including cytoplasmic proteins, glycogen, lipids, organelles, and invading bacteria to the lysosome for degradation. Qb/Qc SNAREs consist of 2 coiled-coil helices (called SNARE motifs, one belonging to the Qb subgroup and one belonging to the Qc subgroup), which mediate the interactions with other SNARE proteins, and a transmembrane domain. In general, the SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Other members of the Qb/Qc SNAREs are SNAP23, SNAP25, SNAP47 and SEC9. 59 matched cddid_all.tbl CDD cd15857 cd15857 277210 SNARE_SEC9C C-terminal SNARE motif of SEC9. C-terminal SNARE motif of fungal SEC9, a member of the Qb/Qc subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins. SEC9 interacts with Sso1(Qa) and the lysosomal R-SNARE Snc1. The complex plays a role in post-Golgi transport. Qb/Qc SNAREs consist of 2 coiled-coil helices (called SNARE motifs, one belonging to the Qb subgroup and one belonging to the Qc subgroup), which mediate the interactions with other SNARE proteins, and a transmembrane domain. In general, the SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Other members of the Qb/Qc SNAREs are SNAP23, SNAP25, SNAP47 and SNAP29. 59 matched cddid_all.tbl CDD cd15858 cd15858 277211 SNARE_VAM7 SNARE motif of VAM7. Fungal VAM7 (vacuolar morphogenesis protein 7) is a member of the Qc subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein family involved in vacuolar protein transport and membrane fusion. SNARE proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qc-, as well as Qa- and Qb-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. 59 matched cddid_all.tbl CDD cd15859 cd15859 277212 SNARE_SYN8 SNARE motif of SYN8. Fungal SYN8 is a member of the Qc subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein family presetn in the endosomes. SNARE proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qc-, as well as Qa- and Qb-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. 68 matched cddid_all.tbl CDD cd15860 cd15860 277213 SNARE_USE1 SNARE motif of USE1. USE1 (unconventional SNARE in the ER 1 homolog, also known as SNARE-like tail-anchored protein 1 or SLT1) is involved in retrograde transport of CopI coatomer coated vesicles from the Golgi to the ER. It forms a complex with syntaxin18 (Ufe1p, Qa), Bnip1 (Sec20p, Qb) and Sec22b (R-SNARE). USE1 is a member of the Qc subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein family. SNARE proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qc-, as well as Qa- and Qb-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. 60 matched cddid_all.tbl CDD cd15861 cd15861 277214 SNARE_SNAP25N_23N_29N_SEC9N N-terminal SNARE motif of SNAP25, SNAP23, SNAP29, and SEC9. N-terminal SNARE motif of members of the Qb/Qc subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins. Qb/Qc SNAREs consist of 2 coiled-coil helices (called SNARE motifs, one belonging to the Qb subgroup and one belonging to the Qc subgroup), which mediate the interactions with other SNARE proteins, and a transmembrane domain. In general, the SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Examples for members of the Qb/Qc SNAREs are SNAP23, SNAP25, SNAP29, SNAP47 and SEC9. 65 matched cddid_all.tbl CDD cd15862 cd15862 277215 SNARE_Vti1 SNARE motif of Vti1. Vti1 (vesicle transport through interaction with t-SNAREs homolog 1) belongs to the Qb subgroup of SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptor). Vti1b interacts with syntaxin 7 (Qa), syntaxin 8 (Qc), and the lysosomal R-SNARE VAMP8 or VAMP7 to form the endosomal SNARE core complex that mediates transport from the early endosomes and the MVBs (multivesicular bodies), and from the MVBs to the lysosomes, respectively. Vti1a interacts with syntaxin 16 (Qa), syntaxin 6 (Qc), and the lysosomal R-SNARE VAMP4 to form an endosomal SNARE core complex that mediates transport from the early endosomes to the TGN (trans-Golgi network). SNARE proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Examples for members of the Qb SNAREs are N-terminal domains of SNAP23 and SNAP25, Vti1, Sec20 and GS27. 62 matched cddid_all.tbl CDD cd15863 cd15863 277216 SNARE_GS27 SNARE motif of GS27. GS27 (also known as Bos1, EPM6, golgi SNAP receptor complex member 2 or GOSR2) is a member of the Qb subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins. GS27 forms a complex together with Bet1 (Qc), syntaxin-5 (Qa) and Sec22B (R-SNARE). This complex regulates the early secretory pathway of eukaryotic cells at the level of the transport from endoplasmic reticulum (ER) to the ER-Golgi intermediate compartment (ERGIC). SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 66 matched cddid_all.tbl CDD cd15864 cd15864 277217 SNARE_GS28 SNARE motif of GS28. GS28 (also known as golgi SNAP receptor complex member 1 or GOSR1) forms complexes with syntaxin-5 (Qa), Ykt6 (R-SNARE) and either Bet1 (Qc) or GS15 (Qc). These complexes regulate the early secretory pathway of eukaryotic cells at the level of the transport from the ER-Golgi intermediate compartment (ERGIC) to the cis-Golgi and transport from the trans-Golgi network to the cis-Golgi, respectively. GS28 is a member of the Qb subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins which contain coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. 66 matched cddid_all.tbl CDD cd15865 cd15865 277218 SNARE_SEC20 SNARE motif of SEC20. SEC20 (also known as BNIP1, NIP1, or TRG-8) forms a complex with syntaxin 18 (Qa), SEC22 (R-SNARE)and USE1 (Qc), and is involved in the transport from cis-Golgi to the endoplasmic reticulum (ER). SEC20 is a member of the Qb subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins which contain coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. 93 matched cddid_all.tbl CDD cd15866 cd15866 277219 R-SNARE_SEC22 SNARE motif of SEC22. SEC22 forms complexes with syntaxin 18 (Qa), Sec20 (Qb) and USE1 (Qc), and with syntaxin 5 (Qa), GS27 (Qb) and Bet1 (Qc). These complexes are involved in the transport from cis-Golgi to the endoplasmic reticulum (ER) and in the transport from endoplasmic reticulum (ER) to the ER-Golgi intermediate compartment (ERGIC), respectively. SEC22 is a member of the R-SNARE subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins which contain coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. 64 matched cddid_all.tbl CDD cd15867 cd15867 277220 R-SNARE_YKT6 SNARE motif of YKT6. Ykt6 forms complexes with syntaxin-5 (Qa), GS28 (Qb) and either Bet1 (Qc) or GS15 (Qc). This complex regulates the early secretory pathway of eukaryotic cells at the level of the transport from the ER-Golgi intermediate compartment (ERGIC) to the cis-Golgi and transport from the trans-Golgi network to the cis-Golgi, respectively. Ykt6 is a member of the R-SNARE subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins which contain coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. 61 matched cddid_all.tbl CDD cd15868 cd15868 277221 R-SNARE_VAMP8 SNARE motif of VAMP8. The lysosomal VAMP8 (vesicle-associated membrane protein 8, also called endobrevin) protein belongs to the R-SNARE subgroup of SNAREs and interacts with STX17 (Qa) and SNAP29 (Qb/Qc). The complex plays a role in autophagosome-lysosome fusion via regulating the transport from early endosomes to multivesicular bodies. Autophagosome transports cytoplasmic materials including cytoplasmic proteins, glycogen, lipids, organelles, and invading bacteria to the lysosome for degradation. SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins contain coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. 68 matched cddid_all.tbl CDD cd15869 cd15869 277222 R-SNARE_VAMP4 SNARE motif of VAMP4. The VAMP-4 (vesicle-associated membrane protein 4) protein belongs to the R-SNARE subgroup of SNAREs and interacts with syntaxin 16 (Qa), Vti1a (Qb) and syntaxin 6 (Qc). This complex plays a role in maintenance of Golgi ribbon structure and normal retrograde trafficking from the early endosome to the trans-Golgi network (TGN). SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins contain coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. 67 matched cddid_all.tbl CDD cd15870 cd15870 277223 R-SNARE_VAMP2 SNARE motif of VAMP2. The VAMP-2 (vesicle-associated membrane protein 2, also called synaptobrevin-2) protein belongs to the R-SNARE subgroup of SNAREs and interacts with Syntaxin-1 (Qa) and SNAP-25(Qb/Qc), as well as syntaxin 12 (Qa) and SNAP23 (Qb/Qc). The complexes play a role in transport of secretory granule from trans-Golgi network to the plasma membrane, and in the transport from early endosomes to and from the plasma membrane, respectively. SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins contain coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. 63 matched cddid_all.tbl CDD cd15871 cd15871 277224 R-SNARE_VAMP7 SNARE motif of VAMP7. The VAMP-7 (vesicle-associated membrane protein 7, also called synaptobrevin-like protein 1) protein belongs to the R-SNARE subgroup of SNAREs and interacts with syntaxin 7(Qa), syntaxin 8 (Qc) and Vti1b (Qb). The complex is involved in the transport from early endosomes to the lysosome via regulating the transport from multivesicular bodies to the lysosomes. SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins contain coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. 65 matched cddid_all.tbl CDD cd15872 cd15872 277225 R-SNARE_VAMP5 SNARE motif of VAMP5. The VAMP-5 (vesicle-associated membrane protein 5) protein belongs to the R-SNARE subgroup of SNAREs. Its function is unknown. SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins contain coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. 68 matched cddid_all.tbl CDD cd15873 cd15873 277226 R-SNARE_STXBP5_6 SNARE domain of STXBP5, STXBP6 and related proteins. Syntaxin binding protein 5 (STXBP5, also called Tomosyn), as well as its relative Syntaxin binding protein 6 (STXBP6, also called Amisyn) contains a C-terminal R-SNARE-like domain, which allows it to assemble into SNARE complexes, which in turn makes the complexes inactive and inhibits exocytosis. In general, SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qc-, as well as Qa- and Qb-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 61 matched cddid_all.tbl CDD cd15874 cd15874 277227 R-SNARE_Snc1 SNARE motif of Snc1. Saccharomyces cerevisiae SNARE protein Snc1p forms a complex with synaptobrevin homolog Sso1p (Qa) and the SNAP-25 homolog Sec9p (Qb/c) which is involved in exocytosis. Snc1 is a member of the R-SNARE subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 60 matched cddid_all.tbl CDD cd15875 cd15875 277228 SNARE_syntaxin7 SNARE motif of syntaxin 7. Syntaxin 7 forms a complex with syntaxin 8 (Qc), Vti1b (Qb) and either VAMP7 or VAMP8 (R-SNARE) and is involved in the transport from early endosomes to the lysosome. Syntaxin 7 is member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 60 matched cddid_all.tbl CDD cd15876 cd15876 277229 SNARE_syntaxin12 SNARE motif of syntaxin 12. Syntaxin 12 (STX12, also known as STX13 and STX14) forms a complex with SNAP25 (Qb/Qc) or SNAP29 (Qb/Qc) and VAMP2 or VAMP3 (R-SNARE) and plays a role in plasma membrane to early endosome transport. Syntaxin 12 is a member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 67 matched cddid_all.tbl CDD cd15877 cd15877 277230 SNARE_TSNARE1 SNARE motif of TSNARE1. TSNARE1 is member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. Its function is unknown, but polymorphisms in human TSNARE1 have been associated with schizophrenia susceptibility. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. TSNARE1 is part of a subgroup of the Qa SNAREs that also includes syntaxin 7, syntaxin 12 and related proteins. 64 matched cddid_all.tbl CDD cd15878 cd15878 277231 SNARE_syntaxin11 SNARE motif of syntaxin 11. Syntaxin 11 (also known as STX11, FHL4, HLH4, HPLH4) is present on endosomal membranes, including late endosomes and lysosomes in macrophages, and has been shown to bind Vti1b and regulate the availability of Vti1b to form other SNARE-complexes. Mutations in human STX11 has been linked to familial hemophagocytic lymphohistiocytosis type-4 (FHL-4), an autosomal recessive disorder of immune dysregulation. Syntaxin 11 is a member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 63 matched cddid_all.tbl CDD cd15879 cd15879 277232 SNARE_syntaxin19 SNARE motif of syntaxin 19. Syntaxin 19 has been shown to have the potential to form SNARE complexes with SNAP-23, 25 and 29 (Qb/Qc) and VAMP3 and VAMP8 (R-SNARE), indicating a role in post-Golgi trafficking or plasma membrane fusion. Syntaxin 19 is member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 63 matched cddid_all.tbl CDD cd15880 cd15880 277233 SNARE_syntaxin1 SNARE motif of syntaxin 1. Syntaxin-1 belongs to the Qa subgroup of SNAREs and interacts with SNAP-25 (Qb/Qc) and the R-SNARE VAMP2 (also called synaptobrevin-2). The complex plays a role in exocytosis of synaptic vesicles. SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 69 matched cddid_all.tbl CDD cd15881 cd15881 277234 SNARE_syntaxin3 SNARE motif of syntaxin 3. Syntaxin 3 (STX3) has been shown to form a complex with VAMP8 (R-SNARE) and SNAP-23 (Qb/c) in mast cells. Mutations have been implicated in human microvillus inclusion disease (MVID), a disorder of the differentiation of intestinal epithelium. Syntaxin 3 is a member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 69 matched cddid_all.tbl CDD cd15882 cd15882 277235 SNARE_syntaxin2 SNARE motif of syntaxin 2. Syntaxin 2 (STX2), also known as epimorphin (EPM or EPIM), may interact with SNAP-23 (Qb/c) and genetic varioations are associated with type 1 von Willebrand disease (VWD). Syntaxin 2 is a member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 69 matched cddid_all.tbl CDD cd15883 cd15883 277236 SNARE_syntaxin4 SNARE motif of syntaxin 4. Syntaxin-4 forms a complex with SNAP-23 (Qb/Qc) and R-SNAREs VAMP8, VAMP2 and VAMP7 which plays a role in exocytosis of secetory granule. Syntaxin 4 is member of the Qa subgroup of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, which consist of coiled-coil helices (called SNARE motifs) that mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complexes mediate membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 63 matched cddid_all.tbl CDD cd15884 cd15884 277237 SNARE_SNAP23C C-terminal SNARE motif of SNAP23. C-terminal SNARE motifs of SNAP23, a member of the Qb/Qc subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins. SNAP23 interacts with Syntaxin-4 (Qa) and the R-SNARE VAMP8. The complex plays a role in exocytosis of secretory granule. Qb/Qc SNAREs consist of 2 coiled-coil helices (called SNARE motifs, one belonging to the Qb subgroup and one belonging to the Qc subgroup), which mediate the interactions with other SNARE proteins, and a transmembrane domain. In general, the SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Other members of the Qb/Qc SNAREs are SNAP25, SNAP29, SNAP47 and SEC9. 59 matched cddid_all.tbl CDD cd15885 cd15885 277238 SNARE_SNAP25C C-terminal SNARE motif of SNAP25. C-terminal SNARE motifs of SNAP25, a member of the Qb/Qc subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins. SNAP25 interacts with Syntaxin-1 (Qa) and the R-SNARE VAMP2 (also called synaptobrevin-2). The complex plays a role in transport of secretory granule from trans-Golgi network to the plasma membrane. Qb/Qc SNAREs consist of 2 coiled-coil helices (called SNARE motifs, one belonging to the Qb subgroup and one belonging to the Qc subgroup), which mediate the interactions with other SNARE proteins, and a transmembrane domain. In general, the SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Other members of the Qb/Qc SNAREs are SNAP23, SNAP29, SNAP47 and SEC9. 59 matched cddid_all.tbl CDD cd15886 cd15886 277239 SNARE_SEC9N N-terminal SNARE motif of SEC9. N-terminal SNARE motif of fungal SEC9, a member of the Qb/Qc subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins. SEC9 interacts with Sso1(Qa) and the lysosomal R-SNARE Snc1. The complex plays a role in post-Golgi transport. Qb/Qc SNAREs consist of 2 coiled-coil helices (called SNARE motifs, one belonging to the Qb subgroup and one belonging to the Qc subgroup), which mediate the interactions with other SNARE proteins, and a transmembrane domain. In general, the SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Other members of the Qb/Qc SNAREs are SNAP23, SNAP25, SNAP47 and SNAP29. 70 matched cddid_all.tbl CDD cd15887 cd15887 277240 SNARE_SNAP29N N-terminal SNARE motif of SNAP29. N-terminal SNARE motif of SNAP29, a member of the Qb/Qc subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins. SNAP29 interacts with STX17 (Qa) and the lysosomal R-SNARE VAMP8. The complex plays a role in autophagosome-lysosome fusion. Autophagosome transports cytoplasmic materials including cytoplasmic proteins, glycogen, lipids, organelles, and invading bacteria to the lysosome for degradation. Qb/Qc SNAREs consist of 2 coiled-coil helices (called SNARE motifs, one belonging to the Qb subgroup and one belonging to the Qc subgroup), which mediate the interactions with other SNARE proteins, and a transmembrane domain. In general, the SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Other members of the Qb/Qc SNAREs are SNAP23, SNAP25, SNAP47 and SEC9. 65 matched cddid_all.tbl CDD cd15888 cd15888 277241 SNARE_SNAP47N N-terminal SNARE motif of SNAP47. N-terminal SNARE motif of SNAP47, a member of the Qb/Qc subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins. The exact funtion of SNAP47 is unknown. Qb/Qc SNAREs consist of 2 coiled-coil helices (called SNARE motifs, one belonging to the Qb subgroup and one belonging to the Qc subgroup), which mediate the interactions with other SNARE proteins, and a transmembrane domain. In general, the SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Other members of the Qb/Qc SNAREs are SNAP23, SNAP25, SNAP29 and SEC9. 65 matched cddid_all.tbl CDD cd15889 cd15889 277242 SNARE_SNAP25N_23N N-terminal SNARE motif of SNAP25 and SNAP23. N-terminal SNARE motifs of SNAP25 and SNAP23, members of the Qb/Qc subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins. SNAP23 interacts with STX4 (Qa) and the lysosomal R-SNARE VAMP8. The complex plays a role in transport of secretory granule from trans-Golgi network to the plasma membrane. SNAP25 interacts with Syntaxin-1 (Qa) and the R-SNARE VAMP2 (also called synaptobrevin-2). The complex plays a role in transport of secretory granule from trans-Golgi network to the plasma membrane. Qb/Qc SNAREs consist of 2 coiled-coil helices (called SNARE motifs, one belonging to the Qb subgroup and one belonging to the Qc subgroup), which mediate the interactions with other SNARE proteins, and a transmembrane domain. In general, the SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Other members of the Qb/Qc SNAREs are SNAP29, SNAP47 and SEC9. 65 matched cddid_all.tbl CDD cd15890 cd15890 277243 SNARE_Vti1b SNARE motif of Vti1b-like. Vti1b (vesicle transport through interaction with t-SNAREs homolog 1B) belongs to the Qb subgroup of SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptor). Vti1b interacts with syntaxin 7 (Qa), syntaxin 8 (Qc), and the lysosomal R-SNARE VAMP8 or VAMP7 to form the endosomal SNARE core complexes that mediate transport from the early endosomes and the MVBs (multivesicular bodies), and from the MVBs to the lysosomes, respectively. SNARE proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Examples for members of the Qb SNAREs are N-terminal domains of SNAP23 and SNAP25, Vti1, Sec20 and GS27. 62 matched cddid_all.tbl CDD cd15891 cd15891 277244 SNARE_Vti1a SNARE motif of Vti1b-like. Vti1a (vesicle transport through interaction with t-SNAREs homolog 1A) belongs to the Qb subgroup of SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptor). Vti1a interacts with syntaxin 16 (Qa), syntaxin 6 (Qc), and the lysosomal R-SNARE VAMP4 to form an endosomal SNARE core complex that mediates transport from the early endosomes to the TGN (trans-Golgi network). SNARE proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Examples for members of the Qb SNAREs are N-terminal domains of SNAP23 and SNAP25, Vti1, Sec20 and GS27. 62 matched cddid_all.tbl CDD cd15892 cd15892 277245 R-SNARE_STXBP6 SNARE domain of STXBP6. Syntaxin binding protein 6 (STXBP6, also called Amisyn), as well as its relative Syntaxin binding protein 5 (STXBP5, also called Tomosyn), contains a C-terminal R-SNARE-like domain, which allows it to assemble into SNARE complexes, which in turn makes the complexes inactive and inhibits exocytosis. In general, SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qc-, as well as Qa- and Qb-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 62 matched cddid_all.tbl CDD cd15893 cd15893 277246 R-SNARE_STXBP5 SNARE domain of STXBP5. Syntaxin binding protein 5 (STXBP5, also called Tomosyn), as well as its relative Syntaxin binding protein 6 (STXBP6, also called Amisyn) contains a C-terminal R-SNARE-like domain, which allows it to assemble into SNARE complexes, which in turn makes the complexes inactive and inhibits exocytosis. Tomosyn contains an N-terminal WD40 repeat region and has been shown to form complexes with SNAP-25 and syntaxin 1a, as well as SNAP-23 and syntaxin 4. In general, SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins consist of coiled-coil helices (called SNARE motifs) which mediate the interactions between SNARE proteins, and a transmembrane domain. The SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qc-, as well as Qa- and Qb-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. 61 matched cddid_all.tbl CDD cd15894 cd15894 277247 SNARE_SNAP25N N-terminal SNARE motif of SNAP25. N-terminal SNARE motifs of SNAP25, a member of the Qb/Qc subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins. SNAP25 interacts with Syntaxin-1 (Qa) and the R-SNARE VAMP2 (also called synaptobrevin-2). The complex plays a role in transport of secretory granule from trans-Golgi network to the plasma membrane. Qb/Qc SNAREs consist of 2 coiled-coil helices (called SNARE motifs, one belonging to the Qb subgroup and one belonging to the Qc subgroup), which mediate the interactions with other SNARE proteins, and a transmembrane domain. In general, the SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Other members of the Qb/Qc SNAREs are SNAP23, SNAP29, SNAP47 and SEC9. 73 matched cddid_all.tbl CDD cd15895 cd15895 277248 SNARE_SNAP23N N-terminal SNARE motif of SNAP23. N-terminal SNARE motifs of SNAP23, a member of the Qb/Qc subfamily of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins. SNAP23 interacts with Syntaxin-4 (Qa) and the R-SNARE VAMP8. The complex plays a role in exocytosis of secretory granule. Qb/Qc SNAREs consist of 2 coiled-coil helices (called SNARE motifs, one belonging to the Qb subgroup and one belonging to the Qc subgroup), which mediate the interactions with other SNARE proteins, and a transmembrane domain. In general, the SNARE complex mediates membrane fusion, important for trafficking of newly synthesized proteins, recycling of pre-existing proteins and organelle formation. SNARE proteins are classified into four groups, Qa-, Qb-, Qc- and R-SNAREs, depending on whether the residue in the hydrophilic center layer of the four-helical bundle is a glutamine (Q) or arginine (R). Qa-, as well as Qb- and Qc-SNAREs, are localized to target organelle membranes, while R-SNARE is localized to vesicle membranes. They form unique complexes consisting of one member of each subgroup, that mediate fusion between a specific type of vesicles and their target organelle. Their SNARE motifs form twisted and parallel heterotetrameric helix bundles. Other members of the Qb/Qc SNAREs are SNAP25, SNAP29, SNAP47 and SEC9. 67 matched cddid_all.tbl CDD cd15896 cd15896 276899 MYSc_Myh19 "class II myosin heavy chain19, motor domain. Myosin motor domain of muscle myosin heavy chain 19. Class II myosins, also called conventional myosins, are the myosin type responsible for producing actomyosin contraction in metazoan muscle and non-muscle cells. Myosin II contains two heavy chains made up of the head (N-terminal) and tail (C-terminal) domains with a coiled-coil morphology that holds the two heavy chains together. The intermediate neck domain is the region creating the angle between the head and tail. It also contains 4 light chains which bind the heavy chains in the ""neck"" region between the head and tail. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. Class-II myosins are regulated by phosphorylation of the myosin light chain or by binding of Ca2+. A cyclical interaction between myosin and actin provides the driving force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the filament (power stroke). Release of ADP completes the cycle. CyMoBase classifications were used to confirm and identify the myosins in this hierarchy." 675 matched cddid_all.tbl CDD cd15897 cd15897 320054 EFh_PEF The penta-EF hand (PEF) family. The penta-EF hand (PEF) family contains a group of five EF-hand calcium-binding proteins, including several classical calpain large catalytic subunits (CAPN1, 2, 3, 8, 9, 11, 12, 13, 14), two calpain small subunits (CAPNS1 and CAPNS2), as well as non-calpain PEF proteins, ALG-2 (apoptosis-linked gene 2, also termed programmed cell death protein 6, PDCD6), peflin, sorcin, and grancalcin. Based on the sequence similarity of EF1 hand, ALG-2 and peflin have been classified into group I PEF proteins. Calcium-dependent protease calpain subfamily members, sorcin and grancalcin, are group II PEF proteins. Calpains (EC 3.4.22.17) are calcium-activated intracellular cysteine proteases that play important roles in the degradation or functional modulation in a variety of substrates. They have been implicated in a number of physiological processes such as cell cycle progression, remodeling of cytoskeletal-cell membrane attachments, signal transduction, gene expression and apoptosis. ALG-2 is a pro-apoptotic factor that forms a homodimer in the cell or a heterodimer with its closest paralog peflin through their EF5s. Peflin is a 30-kD PEF protein with a longer N-terminal hydrophobic domain than any other member of the PEF family, and it contains nine nonapeptide (A/PPGGPYGGP) repeats. It exists only as a heterodimer with ALG-2. The dissociation of heterodimer occurs in the presence of Ca2+. ALG-2 interacts with various proteins in a Ca2+-dependent manner. Sorcin (for soluble resistance-related calcium binding protein) is a soluble resistance-related calcium-binding protein that participates in the regulation of calcium homeostasis in cells. Grancalcin is a cytosolic Ca2+-binding protein specifically expressed in neutrophils and monocytes/macrophages. It plays a key role in leukocyte-specific functions that are responsible for host defense. Grancalcin can form a heterodimer together with sorcin. Members in this family contain five EF-hand motifs attached to an N-terminal region of variable length containing one or more short Gly/Pro-rich sequences. These proteins form homodimers or heterodimers through pairing between the 5th EF-hands from the two molecules. Unlike calmodulin, the PEF domains do not undergo major conformational changes upon binding Ca2+. 165 matched cddid_all.tbl CDD cd15898 cd15898 320029 EFh_PI-PLC EF-hand motif found in eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) isozymes. PI-PLC isozymes are signaling enzymes that hydrolyze the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which goes on to phosphorylate other molecules, leading to altered cellular activity. Calcium is required for the catalysis. This family corresponds to the four EF-hand motifs containing PI-PLC isozymes, including PI-PLC-beta (1-4), -gamma (1-2), -delta (1,3,4), -epsilon (1), -zeta (1), eta (1-2). Lower eukaryotes such as yeast and slime molds contain only delta-type isozymes. In contrast, other types of isoforms present in higher eukaryotes. This family also includes 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase 1 (PLC1) from fungi. Some homologs from plants contain only two atypical EF-hand motifs and they are not included. All PI-PLC isozymes except sperm-specific PI-PLC-zeta share a core set of domains, including an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core, and a single C2 domain. PI-PLC-zeta lacks the PH domain. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. Most of EF-hand motifs found in PI-PLCs consist of a helix-loop-helix structure, but lack residues critical to metal binding. Moreover, the EF-hand region of most of PI-PLCs may have an important regulatory function, but it has yet to be identified. However, PI-PLC-zeta is a key exception. It is responsible for Ca2+ oscillations in fertilized oocytes and exhibits a high sensitivity to Ca2+ mediated through its EF-hand domain. In addition, PI-PLC-eta2 shows a canonical EF-loop directing Ca2+-sensitivity and thus can amplify transient Ca2+ signals. Also it appears that PI-PLC-delta1 can regulate the binding of PH domain to PIP2 in a Ca2+-dependent manner through its functionally important EF-hand domains. PI-PLCs can be activated by a variety of extracellular ligands, such as growth factors, hormones, cytokines and lipids. Their activation has been implicated in tumorigenesis and/or metastasis linked to migration, proliferation, growth, inflammation, angiogenesis and actin cytoskeleton reorganization. PI-PLC-beta isozymes are activated by G-protein coupled receptor (GPCR) through different mechanisms. However, PI-PLC-gamma isozymes are activated by receptor tyrosine kinase (RTK), such as Rho and Ras GTPases. In contrast, PI-PLC-epsilon are activated by both GPCR and RTK. PI-PLC-delta1 and PLC-eta 1 are activated by GPCR-mediated calcium mobilization. The activation mechanism for PI-PLC-zeta remains unclear. 137 matched cddid_all.tbl CDD cd15899 cd15899 320021 EFh_CREC EF-hand, calcium binding motif, found in CREC-EF hand family. The CREC (Cab45/reticulocalbin/ERC45/calumenin)-EF hand family contains a group of six EF-hand, low-affinity Ca2+-binding proteins, including reticulocalbin (RCN-1), ER Ca2+-binding protein of 55 kDa (ERC-55, also known as TCBP-49 or E6BP), reticulocalbin-3 (RCN-3), Ca2+-binding protein of 45 kDa (Cab45 and its splice variant Cab45b), and calumenin ( also known as crocalbin or CBP-50). The proteins are not only localized in various parts of the secretory pathway, but also found in the cytosolic compartment and at the cell surface. They interact with different ligands or proteins and have been implicated in the secretory process, chaperone activity, signal transduction as well as in a large variety of disease processes. 267 matched cddid_all.tbl CDD cd15900 cd15900 320080 EFh_MICU EF-hand, calcium binding motif, found in mitochondrial calcium uptake proteins MICU1, MICU2, MICU3, and similar proteins. This family includes mitochondrial calcium uptake protein MICU1 and its two additional paralogs, MICU2 and MICU3. MICU1 localizes to the inner mitochondrial membrane (IMM). It functions as a gatekeeper of the mitochondrial calcium uniporter (MCU) and regulates MCU-mediated mitochondrial Ca2+ uptake, which is essential for maintaining mitochondrial homoeostasis. MICU1 and MICU2 are physically associated within the uniporter complex and are co-expressed across all tissues. They may play non-redundant roles in the regulation of the mitochondrial calcium uniporter. At present, the precise molecular function of MICU2 and MICU3 remain unclear. MICU2 may play possible roles in Ca2+ sensing and regulation of MCU, calcium buffering with a secondary impact on transport or assembly and stabilization of MCU. MICU3 likely has a role in mitochondrial calcium handling. All members in this family contains an N-terminal mitochondrial targeting sequence (MTS) as well as two evolutionarily conserved canonical Ca2+-binding EF-hands separated by a long stretch of residues predicted to form alpha-helices. 152 matched cddid_all.tbl CDD cd15901 cd15901 319999 EFh_DMD_DYTN_DTN EF-hand-like motif found in the dystrophin/dystrobrevin/dystrotelin family. The dystrophin/dystrobrevin/dystrotelin family has been characterized by a compact cluster of domains comprising four EF-hand-like motifs and a ZZ-domain, followed by a looser region with two coiled-coils. Dystrophin is the founder member of this family. It is a sub-membrane cytoskeletal protein associated with the inner surface membrane. Dystrophin and its close paralog utrophin have a large N-terminal extension of actin-binding CH domains, up to 24 spectrin repeats, and a WW domain. Its further paralog, dystrophin-related protein 2 (DRP-2), retains only two of the spectrin repeats. Dystrophin, utrophin or DRP2 can form the core of a membrane-bound complex consisting of dystroglycan, sarcoglycans and syntrophins, known as the dystrophin-glycoprotein complex (DGC) that plays an important role in brain development and disease, as well as in the prevention of muscle damage. Dystrobrevins, including alpha- and beta-dystrobrevin, lack the large N-terminal extension found in dystrophin, but alpha-dystrobrevin has a characteristic C-terminal extension. Dystrobrevins are part of the DGC. They physically associate with members of the dystrophin family and with the syntrophins through their homologous C-terminal coiled coil motifs. In contrast, dystrotelins lack both the large N-terminal extension found in dystrophin and the obvious syntrophin-binding sites (SBSs). Dystrotelins are not critical for mammalian development. They may be involved in other forms of cytokinesis. Moreover, dystrotelin is unable to heterodimerize with members of the dystrophin or dystrobrevin families, or to homodimerize. 163 matched cddid_all.tbl CDD cd15902 cd15902 320075 EFh_HEF EF-hand, calcium binding motif, found in the hexa-EF hand proteins family. The hexa-EF hand proteins family, also named the calbindin sub-family, contains a group of six EF-hand Ca2+-binding proteins, including calretinin (CR, also termed 29 kDa calbindin), calbindin D28K (CB, also termed vitamin D-dependent calcium-binding protein, avian-type), and secretagogin (SCGN). CR is a cytosolic hexa-EF-hand calcium-binding protein predominantly expressed in a variety of normal and tumorigenic t-specific neurons of the central and peripheral nervous system. It is a multifunctional protein implicated in many biological processes, including cell proliferation, differentiation, and cell death. CB is highly expressed in brain tissue. It is a strong calcium-binding and buffering protein responsible for preventing a neuronal death as well as maintaining and controlling calcium homeostasis. SCGN is a six EF-hand calcium-binding protein expressed in neuroendocrine, pancreatic endocrine and retinal cells. It plays a crucial role in cell apoptosis, receptor signaling and differentiation. It is also involved in vesicle secretion through binding to various proteins, including interacts with SNAP25, SNAP23, DOC2alpha, ARFGAP2, rootletin, KIF5B, beta-tubulin, DDAH-2, ATP-synthase and myeloid leukemia factor 2. SCGN functions as a Ca2+ sensor/coincidence detector modulating vesicular exocytosis of neurotransmitters, neuropeptides or hormones. Although the family members share a significant amount of secondary sequence homology, they display altered structural and biochemical characteristics, and operate in distinct fashions. CB contains six EF-hand motifs in a single globular domain, where EF-hands 1, 3, 4, 5 bind four calcium ions. CR contains six EF-hand motifs within two independent domains, CR I-II and CR III-VI. They harbor two and four EF-hand motifs, respectively. The first 5 EF-hand motifs are capable of binding calcium ions, while the EF-hand 6 is inactive. SCGN consists of the three globular domains each of which contains a pair of EF-hand motifs. Human SCGN simultaneously binds four calcium ions through its EF-hands 3, 4, 5 and 6 in one high affinity and three low affinity calcium-binding sites. In contrast, SCGNs in other lower eukaryotes, such as D. rerio, X. laevis, M. domestica, G. gallus, O. anatinus, are fully competent in terms of six calcium-binding. 254 matched cddid_all.tbl CDD cd15903 cd15903 277191 Dicer_PBD Partner-binding domain of the endoribonuclease Dicer. The endoribonuclease Dicer plays a central role in RNA interference by breaking down RNA molecules into fragments of about 22 nucleotides (miRNAs and siRNAs). Loading of RNA onto Dicer and the enzymatic cleavage are supported by dsRNA-binding proteins, including trans-activation response (TAR) RNA-binding protein (TRBP) or protein activator of PKR (PACT). Together with Argonaute, this constitutes the RNA-induced silencing complex (RISC) which functions to load the small RNA fragments onto Argonaute. The Partner-binding domain of Dicer is responsible for interactions with the dsRNA-binding proteins. This helical domain can be found inserted in a subset of SF2-type DEAD-box related helicases. 104 matched cddid_all.tbl CDD cd15904 cd15904 320706 TSPO_MBR Translocator protein (TSPO)/peripheral-type benzodiazepine receptor (MBR) family. This family contains tryptophan-rich translocator protein (TSPO), an integral membrane protein that is highly conserved from bacteria to mammals. In eukaryotes, it is mainly found in the outer mitochondrial membranes of steroid-synthesizing cells of the nervous system where it transports cholesterol into mitochondria. It is known to be highly expressed in metastatic cancer, steriodogenic tissues, as well as inflammatory and neurological diseases such as Alzheimer's and Parkinson's. TSPO is also known as the peripheral benzodiazepine receptor (MBR) and its ligands include benzodiazepine drugs, implicated in regulating apoptosis. In human, a single polymorphism A147T is associated with psychiatric disorders; the mutation causes structural changes in a region implicated in cholesterol binding. TSPO is homologous to bacterial tryptophan-rich sensory proteins, and their tryptophan residues are believed to be functionally important. In bacteria, TSPO acts as a negative regulator of expression of specific photosynthesis genes in response to oxygen/light; it catalyzes a photooxidative degradation of Proto porphyrine (PpIX). R. sphaeroides TSPO (RsTSPO) is involved in porphyrin transport, similar to human, while Arabidopsis translocator protein (AtTSPO) is regulated at multiple levels in response to salt stress and perturbations in tetrapyrrole metabolism. 142 matched cddid_all.tbl CDD cd15905 cd15905 320571 7tmA_GPBAR1 G protein-coupled bile acid receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors. The G-protein coupled bile acid receptor GPBAR1 is also known as BG37, TGR5 (Takeda G-protein-coupled receptor 5), M-BAR (membrane-type receptor for bile acids), and GPR131. GPBAR1 is highly expressed in the gastrointestinal tract, but also found at many other tissues including liver, colon, heart, skeletal muscle, and brown adipose tissue. GPBAR1 functions as a membrane-bound receptor specific for bile acids, which are the end products of cholesterol metabolism that facilitate digestion and absorption of lipids or fat-soluble vitamins. Bile acids act as liver-specific metabolic signaling molecules and stimulate liver regeneration by activating GPBAR1 and nuclear receptors such as the farnesoid X receptor (FXR). Upon bile acids binding, GPBAR1 activation causes release of the G-alpha(s) subunit and activation of adenylate cyclase. The increase in intracellular cAMP level then stimulates the expression of many genes via the PKA-mediated phosphorylation of cAMP-response element binding protein (CREB). Thus, GPAR1-signalling exerts various biological effects in immune cells, liver, and metabolic tissues. For example, GPBAR1 activation leads to enhanced energy expenditure in brown adipose tissue and skeletal muscle; stimulation of glucagon-like peptide-1 (GLP-1) production in enteroendocrine L-cells; and inhibition of pro-inflammatory cytokine production in macrophages and attenuation of atherosclerosis development. GPBAR1 is a member of the class A rhodopsin-like family of GPCRs, which comprises receptors for hormones, neurotransmitters, sensory stimuli, and a variety of other ligands. 272 matched cddid_all.tbl CDD cd15906 cd15906 320572 7tmA_GPR162 G protein-coupled receptor 162, member of the class A family of seven-transmembrane G protein-coupled receptors. This subgroup represents the orphan G-protein coupled receptor 162 (GPR162), also called A-2 or GRCA, with unknown endogenous ligand and function. Phylogenetic analysis indicates that GPR162 and GPR153 share a common evolutionary ancestor due to a gene duplication event. Although categorized as members of the rhodopsin-like class A GPCRs, both GPR162 and GPR153 contain HRM-motif instead of the highly conserved Asp-Arg-Tyr (DRY) motif found in the third transmembrane helix (TM3) of class A receptors and important for efficient G protein-coupled signal transduction. Moreover, the LPxF motif, a variant of NPxxY motif that plays a crucial role during receptor activation, is found at the end of TM7 in GPR162 and GPR153. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 315 matched cddid_all.tbl CDD cd15907 cd15907 320573 7tmA_GPR153 orphan G protein-coupled receptor 153, member of the class A family of seven-transmembrane G protein-coupled receptors. This subgroup represents the G-protein coupled receptor 153 (GPR153) with unknown endogenous ligand and function. GPR153 shares a common evolutionary origin with GPR162 and is highly expressed in central nervous system (CNS) including the thalamus, cerebellum, and the arcuate nucleus. Although categorized as a member of the rhodopsin-like class A GPCRs, GPR153 contains HRM-motif instead of the highly conserved Asp-Arg-Tyr (DRY) motif found in the third transmembrane helix (TM3) of class A receptors and important for efficient G protein-coupled signal transduction. Moreover, the LPxFL motif, a variant of NPxxY motif that plays a crucial role during receptor activation, is found at the end of TM7 in GPR153. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 301 matched cddid_all.tbl CDD cd15908 cd15908 320574 7tm_TAS2R40-like taste receptor 2, subtypes 39 and 40, and similar receptors, member of the seven-transmembrane G protein-coupled receptor superfamily. This group includes the mammalian taste receptor 2 (TAS2R) subtypes 39 and 40, which function as bitter taste receptors. The human TAS2R family contains about 25 functional members, which are glycoproteins and have the ability to form both homomeric and heteromeric receptor complexes. Five basic tastes are perceived by animals: bitter, sweet, sour, salty, and umami (taste of glutamate MSG). Among these, sour and salty are mediated by ion channels, while the perception of umami and sweet tastes is mediated by the TAS1R taste receptors, which belong to the class C GPCR family. The TAS2Rs in humans have a short extracellular N-terminus and the ligand binds within the transmembrane domain, whereas the TAS1Rs have a large N-terminal extracellular domain composed of the Venus flytrap module that forms the orthosteric (primary) ligand binding site. Signal transduction of bitter taste involves binding of bitter compounds to TAS2Rs linked to the alpha-subunit of gustducin, a heterotrimeric G protein expressed in taste receptor cells. This G-alpha subunit stimulates phosphodiesterase and decreases cAMP and cGMP levels. Further steps in the signaling cascade is still unknown. The beta-gamma-subunit of gustducin also mediates bitter taste transduction by activating phospholipase C, which leads to an increased formation of IP3 (inositol triphosphate) and DAG (diacylglycerol), thereby causing release of Ca2+ from intracellular stores and enhanced neurotransmitter release. 289 matched cddid_all.tbl CDD cd15909 cd15909 320575 7tmF_FZD4_9_10-like class F frizzled subfamilies 4, 9, 10, and related proteins; member of 7-transmembrane G protein-coupled receptors. This group includes subfamilies 4, 9 and 10 of the frizzled (FZD) family of seven transmembrane-spanning proteins, which constitute a novel and separate class of GPCRs, and their closely related proteins. This class F protein family consists of 10 isoforms (FZD1-10) in mammals. The FZDs are activated by the wingless/int-1 (WNT) family of secreted lipoglycoproteins and preferentially couple to stimulatory G proteins of the Gs family, which activate adenylate cyclase, but can also couple to G proteins of the Gi/Gq families. In the WNT/beta-catenin signaling pathway, the WNT ligand binds to FZD and a lipoprotein receptor-related protein (LRP) co-receptor. This leads to the stabilization and translocation of beta-catenin to the nucleus, where it induces the activation of TCF/LEF family transcription factors. The conserved cytoplasmic motif of FZD, Lys-Thr-X-X-X-Trp, is required for activation of the WNT/beta-catenin pathway, and for membrane localization and phosphorylation of Dsh (dishevelled) protein, a key component of the WNT pathway that relays the WNT signals from the activated receptor to downstream effector proteins. The WNT pathway plays a critical role in many developmental processes, such as cell-fate determination, cell proliferation, neural patterning, stem cell renewal, tissue homeostasis and repair, and tumorigenesis, among many others. 320 matched cddid_all.tbl CDD cd15910 cd15910 320576 7tmF_FZD3_FZD6-like class F frizzled subfamilies 3, 6 and related proteins; member of 7-transmembrane G protein-coupled receptors. This group includes subfamilies 3 and 6 of the frizzled (FZD) family of seven transmembrane-spanning proteins, which constitute a novel and separate class of GPCRs, and their closely related proteins. This class F protein family consists of 10 isoforms (FZD1-10) in mammals. The FZDs are activated by the wingless/int-1 (WNT) family of secreted lipoglycoproteins and preferentially couple to stimulatory G proteins of the Gs family, which activate adenylate cyclase, but can also couple to G proteins of the Gi/Gq families. In the WNT/beta-catenin signaling pathway, the WNT ligand binds to FZD and a lipoprotein receptor-related protein (LRP) co-receptor. This leads to the stabilization and translocation of beta-catenin to the nucleus, where it induces the activation of TCF/LEF family transcription factors. The conserved cytoplasmic motif of FZD, Lys-Thr-X-X-X-Trp, is required for activation of the WNT/beta-catenin pathway, and for membrane localization and phosphorylation of Dsh (dishevelled) protein, a key component of the WNT pathway that relays the WNT signals from the activated receptor to downstream effector proteins. The WNT pathway plays a critical role in many developmental processes, such as cell-fate determination, cell proliferation, neural patterning, stem cell renewal, tissue homeostasis and repair, and tumorigenesis, among many others. 321 matched cddid_all.tbl CDD cd15911 cd15911 320577 7tmA_OR11A-like olfactory receptor subfamily 11A and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor 11A and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 270 matched cddid_all.tbl CDD cd15912 cd15912 320578 7tmA_OR6C-like olfactory receptor subfamily 6C and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor 6C, 6X, 6J, 6T, 6V, 6M, 9A, and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 270 matched cddid_all.tbl CDD cd15913 cd15913 320579 7tmA_OR11G-like olfactory receptor OR11G and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor 11G, 11H, and related proteins in other mammals, and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 270 matched cddid_all.tbl CDD cd15914 cd15914 320580 7tmA_OR6N-like olfactory receptor OR6N and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor 6N, 6K, and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 270 matched cddid_all.tbl CDD cd15915 cd15915 320581 7tmA_OR12D-like olfactory receptor subfamily 12D and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 12D and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 271 matched cddid_all.tbl CDD cd15916 cd15916 320582 7tmA_OR10G-like olfactory receptor subfamily 10G and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 10G, 10S, and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 276 matched cddid_all.tbl CDD cd15917 cd15917 341351 7tmA_OR51_52-like olfactory receptor family 51, 52, 56 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor families 51, 52, 56, and related proteins in other mammals, sauropsids, amphibians, and fishes. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 275 matched cddid_all.tbl CDD cd15918 cd15918 320584 7tmA_OR1_7-like olfactory receptor families 1, 7, and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor families 1 and 7, and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 270 matched cddid_all.tbl CDD cd15919 cd15919 320585 7tmA_GPR139 G-protein-coupled receptor GPR139, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR139, a vertebrate orphan receptor, is very closely related to GPR142, but they have different expression patterns in the brain and in other tissues. These receptors couple to inhibitory G proteins and activate phospholipase C. Studies suggested that dimer formation may be required for their proper function. GPR142 is predominantly expressed in pancreatic beta-cells and plays an important role in mediating insulin secretion and maintaining glucose homeostasis, whereas GPR139 is expressed almost exclusively in the brain and is suggested to play a role in the control of locomotor activity. Tryptophan and phenylalanine have been identified as putative endogenous ligands of GPR139. These orphan receptors are phylogenetically clustered with invertebrate FMRFamide receptors such as Drosophila melanogaster DrmFMRFa-R. 270 matched cddid_all.tbl CDD cd15920 cd15920 320586 7tmA_GPR34-like P2Y-like receptor and similar proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR34 is phylogenetically related to the P2Y family of purinergic G protein-coupled receptors. The P2Y receptor family is composed of eight subtypes, which are activated by naturally occurring extracellular nucleotides such as ATP, ADP, UTP, UDP, and UDP-glucose. GPR34 is shown to couple to G(i/o) protein and is highly expressed in microglia. Recently, lysophosphatidylserine has been identified as a ligand for GPR34. This group belongs to the class A G protein-coupled receptor superfamily, which all have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, which then activate the heterotrimeric G proteins. G-proteins regulate a variety of cellular functions including metabolic enzymes, ion channels, and transporters, among many others. 278 matched cddid_all.tbl CDD cd15921 cd15921 320587 7tmA_CysLTR cysteinyl leukotriene receptors, member of the class A family of seven-transmembrane G protein-coupled receptors. Cysteinyl leukotrienes (LTC4, LTD4, and LTE4) are the most potent inflammatory lipid mediators that play an important role in human asthma. They are synthesized in the leucocytes (cells of immune system) from arachidonic acid by the actions of 5-lipoxygenase and induce bronchial constriction through G protein-coupled receptors, CysLTR1 and CysLTR2. Activation of CysLTR1 by LTD4 induces airway smooth muscle contraction and proliferation, eosinophil migration, and damage to the lung tissue. They belong to the class A GPCR superfamily, which all have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 283 matched cddid_all.tbl CDD cd15922 cd15922 320588 7tmA_P2Y-like P2Y purinoceptor-like proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. P2Y-like proteins are an uncharacterized group that is phylogenetically related to a family of purinergic G protein-coupled receptors. The P2Y receptor family is composed of eight subtypes, which are activated by naturally occurring extracellular nucleotides such as ATP, ADP, UTP, UDP, and UDP-glucose. These eight receptors are ubiquitous in human tissues and can be further classified into two subfamilies based on sequence homology and second messenger coupling: a subfamily of five P2Y1-like receptors (P2Y1, P2Y2, P2Y4, P2Y6, and P2Y11Rs) that are coupled to G(q) protein to activate phospholipase C (PLC) and a second subfamily of three P2Y12-like receptors (P2Y12, P2YR13, and P2Y14Rs) that are coupled to G(i) protein to inhibit adenylate cyclase. Several cloned subtypes, such as P2Y3, P2Y5 and P2Y7-10, are not functional mammalian nucleotide receptors. The native agonists for P2Y receptors are: ATP (P2Y2, P2Y12), ADP (P2Y1, P2Y12 and P2Y13), UTP (P2Y2, P2Y4), UDP (P2Y6, P2Y14), and UDP-glucose (P2Y14). 284 matched cddid_all.tbl CDD cd15923 cd15923 320589 7tmA_GPR35_55-like G protein-coupled receptor 35, GPR55, and similar proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This subfamily is composed of GPR35, GPR55, and similar proteins. GPR35 shares closest homology with GPR55, and they belong to the class A G protein-coupled receptor superfamily, which all have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A number of studies have suggested that GPR35 may play important physiological roles in hypertension, atherosclerosis, nociception, asthma, glucose homeostasis and diabetes, and inflammatory bowel disease. GPR35 is thought to be responsible for brachydactyly mental retardation syndrome, which is associated with a deletion comprising chromosome 2q37 in human, and is also implicated as a potential oncogene in stomach cancer. GPR35 couples to G(13) and G(i/o) proteins, whereas GPR55 has been reported to couple to G(13), G(12), or G(q) proteins. Activation of GPR55 leads to activation of phospholipase C, RhoA, ROCK, ERK, p38MAPK, and calcium release. Recently, lysophosphatidylinositol (LPI) has been identified as an endogenous ligand for GPR55, while several endogenous ligands for GPR35 have been identified including kynurenic acid, 2-oleoyl lysophosphatidic acid, and zaprinast. 273 matched cddid_all.tbl CDD cd15924 cd15924 341352 7tmA_P2Y12-like P2Y purinoceptors 12, 13, 14, and similar proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. The P2Y receptor family is composed of eight subtypes, which are activated by naturally occurring extracellular nucleotides such as ATP, ADP, UTP, UDP, and UDP-glucose. These eight receptors are ubiquitous in human tissues and can be further classified into two subfamilies based on sequence homology and second messenger coupling: a subfamily of five P2Y1-like receptors (P2Y1, P2Y2, P2Y4, P2Y6, and P2Y11Rs) that are coupled to G(q) protein to activate phospholipase C (PLC) and a second subfamily of three P2Y12-like receptors (P2Y12, P2YR13, and P2Y14Rs) that are coupled to G(i) protein to inhibit adenylate cyclase. Several cloned subtypes, such as P2Y3, P2Y5 and P2Y7-10, are not functional mammalian nucleotide receptors. The native agonists for P2Y receptors are: ATP (P2Y2, P2Y12), ADP (P2Y1, P2Y12 and P2Y13), UTP (P2Y2, P2Y4), UDP (P2Y6, P2Y14), and UDP-glucose (P2Y14). This cluster only includes P2Y12-like receptors as well as closely related orphan receptor, GPR87. 284 matched cddid_all.tbl CDD cd15925 cd15925 320591 7tmA_RNL3R2 relaxin-3 receptor 2 (RNL3R2), member of the class A family of seven-transmembrane G protein-coupled receptors. The G protein-coupled receptor RNL3R2 is also known as GPR100, GPR142, and relaxin family peptide receptor 4 (RXFP4). Insulin-like peptide 5 (INSL5) is an endogenous ligand for RNL3R2 and plays a role in fat and glucose metabolism. INSL5 is highly expressed in human rectal and colon tissues. RNL3R2 signals through G(i) protein and inhibit adenylate cyclase, thereby inhibit cAMP accumulation. 283 matched cddid_all.tbl CDD cd15926 cd15926 320592 7tmA_RNL3R1 relaxin 3 receptor 1 (RNL3R1), member of the class A family of seven-transmembrane G protein-coupled receptors. The G protein-coupled receptor RNL3R1 is also known as GPCR135, relaxin family peptide receptor 3 (RXFP3), and somatostatin- and angiotensin-like peptide receptor (SALPR). RNL3/relaxin-3, a member of the insulin superfamily, is an endogenous neuropeptide ligand for RNL3R1. RNL3R1 is predominantly expressed in brain regions and implicated in stress, anxiety, and feeding, and metabolism. RNL3R1 signals through G(i) protein and inhibit adenylate cyclase, thereby inhibit cAMP accumulation, and also activates Erk1/2 signaling pathway. 288 matched cddid_all.tbl CDD cd15927 cd15927 320593 7tmA_Bombesin_R-like bombesin receptor subfamily, member of the class A family of seven-transmembrane G protein-coupled receptors. This bombesin subfamily of G-protein coupled receptors consists of neuromedin B receptor (NMBR), gastrin-releasing peptide receptor (GRPR), and bombesin receptor subtype 3 (BRS-3). Bombesin is a tetradecapeptide, originally isolated from frog skin. Mammalian bombesin-related peptides are widely distributed in the gastrointestinal and central nervous systems. The bombesin family receptors couple mainly to the G proteins of G(q/11) family. NMBR functions as the receptor for the neuropeptide neuromedin B, a potent mitogen and growth factor for normal and cancerous lung and for gastrointestinal epithelial tissues. Gastrin-releasing peptide is an endogenous ligand for GRPR and shares high sequence homology with NMB in the C-terminal region. Both NMB and GRP possess bombesin-like biochemical properties. BRS-3 is classified as an orphan receptor and suggested to play a role in sperm cell division and maturation. BRS-3 interacts with known naturally-occurring bombesin-related peptides with low affinity; however, no endogenous high-affinity ligand to the receptor has been identified. The bombesin receptor family belongs to the seven transmembrane rhodopsin-like G-protein coupled receptors (class A GPCRs), which perceive extracellular signals and transduce them to guanine nucleotide-binding (G) proteins. 294 matched cddid_all.tbl CDD cd15928 cd15928 320594 7tmA_GHSR-like growth hormone secretagogue receptor, motilin receptor, and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This subfamily includes growth hormone secretagogue receptor (GHSR or ghrelin receptor), motilin receptor (also called GPR38), and related proteins. Both GHSR and GPR38 bind peptide hormones. Ghrelin, the endogenous ligand for GHSR, is an acylated 28-amino acid peptide hormone produced by ghrelin cells in the gastrointestinal tract. Ghrelin is also called the hunger hormone and is involved in the regulation of growth hormone release, appetite and feeding, gut motility, lipid and glucose metabolism, and energy balance. Motilin, the ligand for GPR38, is a 22 amino acid peptide hormone expressed throughout the gastrointestinal tract and stimulates contraction of gut smooth muscle. It is involved in the regulation of digestive tract motility. 288 matched cddid_all.tbl CDD cd15929 cd15929 341353 7tmB1_GlucagonR-like glucagon receptor-like subfamily, member of the class B family of seven-transmembrane G protein-coupled receptors. This group represents the glucagon receptor family of G protein-coupled receptors, which includes glucagon receptor (GCGR), glucagon-like peptide-1 receptor (GLP1R), GLP2R, and closely related receptors. These receptors are activated by the members of the glucagon (GCG) peptide family including GCG, glucagon-like peptide 1 (GLP1), and GLP2, which are derived from the large proglucagon precursor. GCGR regulates blood glucose levels by control of hepatic glycogenolysis and gluconeogenesis and by regulation of insulin secretion from the pancreatic beta-cells. Activation of GLP1R stimulates glucose-dependent insulin secretion from pancreatic beta cells, whereas activation of GLP2R stimulates intestinal epithelial proliferation and increases villus height in the small intestine. Receptors in this group belong to the B1 (or secretin-like) subfamily of class B GPCRs, which includes receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, calcitonin gene-related peptide, parathyroid hormone (PTH), and corticotropin-releasing factor. These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. All members of the B1 subfamily preferentially couple to G proteins of G(s) family, which positively stimulate adenylate cyclase, leading to increased intracellular cAMP formation and calcium influx. However, depending on their cellular location, GCGR and GLP receptors can activate multiple G proteins, which can in turn stimulate different second messenger pathways. 279 matched cddid_all.tbl CDD cd15930 cd15930 320596 7tmB1_Secretin_R-like secretin receptor-like group of hormone receptors, member of the class B family of seven-transmembrane G protein-coupled receptors. This group represents G protein-coupled receptors for structurally similar peptide hormones that include secretin, growth-hormone-releasing hormone (GHRH), pituitary adenylate cyclase activating polypeptide (PACAP), and vasoactive intestinal peptide (VIP). These receptors are classified into the subfamily B1 of class B GRCRs that consists of the classical hormone receptors and have been identified in all the vertebrates, from fishes to mammals, but are not present in plants, fungi, or prokaryotes. For all class B receptors, the large N-terminal extracellular domain plays a critical role in peptide hormone recognition. Secretin, a polypeptide secreted by entero-endocrine S cells in the small intestine, is involved in maintaining body fluid balance. This polypeptide regulates the secretion of bile and bicarbonate into the duodenum from the pancreatic and biliary ducts, as well as regulates the duodenal pH by the control of gastric acid secretion. Studies with secretin receptor-null mice indicate that secretin plays a role in regulating renal water reabsorption. Secretin mediates its biological actions by elevating intracellular cAMP via G protein-coupled secretin receptors, which are expressed in the brain, pancreas, stomach, kidney, and liver. GHRHR is a specific receptor for the growth hormone-releasing hormone (GHRH) that controls the synthesis and release of growth hormone (GH) from the anterior pituitary somatotrophs. Mutations in the gene encoding GHRHR have been connected to isolated growth hormone deficiency (IGHD), a short-stature condition caused by deficient production of GH or lack of GH action. VIP and PACAP exert their effects through three G protein-coupled receptors, PACAP-R1, VIP-R1 (vasoactive intestinal receptor type 1, also known as VPAC1) and VIP-R2 (or VPAC2). PACAP-R1 binds only PACAP with high affinity, whereas VIP-R1 and -R2 specifically bind and respond to both VIP and PACAP. VIP and PACAP and their receptors are widely expressed in the brain and periphery. They are upregulated in neurons and immune cells in responses to CNS injury and/or inflammation and exert potent anti-inflammatory effects, as well as play important roles in the control of circadian rhythms and stress responses, among many others. All B1 subfamily GPCRs are able to increase intracellular cAMP levels by coupling to adenylate cyclase via a stimulatory Gs protein. However, depending on its cellular location, some members of subfamily B1 are also capable of coupling to additional G proteins such as G(i/o) and/or G(q) proteins, thereby leading to activation of phospholipase C and intracellular calcium influx. 268 matched cddid_all.tbl CDD cd15931 cd15931 320597 7tmB2_EMR_Adhesion_II EGF-like module receptors, group II adhesion GPCRs, member of class B2 family of seven-transmembrane G protein-coupled receptors. group II adhesion GPCRs, including the leukocyte cell-surface antigen CD97 and the epidermal growth factor (EGF)-module-containing, mucin-like hormone receptor (EMR1-4), are primarily expressed in cells of the immune system. All EGF-TM7 receptors, which belong to the B2 subfamily B2 of adhesion GPCRs, are members of group II, except for ETL (EGF-TM7-latrophilin related protein), which is classified into group I. Members of the EGF-TM7 receptors are characterized by the presence of varying numbers of N-terminal EGF-like domains, which play critical roles in ligand recognition and cell adhesion, linked by a stalk region to a class B seven-transmembrane domain. In the case of CD97, alternative splicing results in three isoforms possessing either three (EGF1,2,5), four (EGF1,2,3,5) or five (EGF1,2,3,4,5) EGF-like domains. On the other hand, EMR2 generates four isoforms possessing either two (EGF1,2), three (EGF1,2,5), four (EGF1,2,3,5) or five (EGF1,2,3,4,5) EGF-like domains. Moreover, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. For example, CD97, which is involved in angiogenesis and the migration and invasion of tumor cells, has been shown to promote cell aggregation in a GPS proteolysis-dependent manner. CD97 is widely expressed on lymphocytes, monocytes, macrophages, dendritic cells, granulocytes and smooth muscle cells as well as in a variety of human tumors including colorectal, gastric, esophageal pancreatic, and thyroid carcinoma. EMR2 shares strong sequence homology with CD97, differing by only six amino acids. However, unlike CD97, EMR2 is not found in those of CD97-positive tumor cells and is not expressed on lymphocytes but instead on monocytes, macrophages and granulocytes. CD97 has three known ligands: CD55, decay-accelerating factor for regulation of complement system; chondroitin sulfate, a glycosaminoglycan found in the extracellular matrix; and the integrin alpha5beta1, which play a role in angiogenesis. Although EMR2 does not effectively interact with CD55, the fourth EGF-like domain of this receptor binds to chondroitin sulfate to mediate cell attachment. 262 matched cddid_all.tbl CDD cd15932 cd15932 320598 7tmB2_GPR116-like_Adhesion_VI orphan GPR116 and related proteins, group IV adhesion GPCRs, member of the class B2 family of seven-transmembrane G protein-coupled receptors. group VI adhesion GPCRs consist of orphan receptors GPR110, GPR111, GPR113, GPR115, GPR116, and closely related proteins. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in ligand recognition as well as cell-cell adhesion and cell-matrix interactions, linked by a stalk region to a class B seven-transmembrane domain. GPR110 possesses a SEA box in the N-terminal has been identified as an oncogene over-expressed in lung and prostate cancer. GPR113 contains a hormone binding domain and one EGF (epidermal grown factor) domain. GPR112 has extremely long N-terminus (about 2,400 amino acids) containing a number of Ser/Thr-rich glycosylation sites and a pentraxin (PTX) domain. GPR116 has two C2-set immunoglobulin-like repeats, which is found in the members of the immunoglobulin superfamily of cell surface proteins, and a SEA (sea urchin sperm protein, enterokinase, and a grin)-box, which is present in the extracellular domain of the transmembrane mucin (MUC) family and known to enhance O-glycosylation. In addition, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR-autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. However, several adhesion GPCRs, including GPR 111, GPR115, and CELSR1, are predicted to be non-cleavable at the GAIN domain because of the lack of a consensus catalytic triad sequence (His-Leu-Ser/Thr) within their GPS. 268 matched cddid_all.tbl CDD cd15933 cd15933 320599 7tmB2_GPR133-like_Adhesion_V orphan GPR133 and related proteins, group V adhesion GPCRs, member of class B2 family of seven-transmembrane G protein-coupled receptors. group V adhesion GPCRs include orphan receptors GPR133, GPR144, and closely related proteins. The function of GPR144 has not yet been characterized, whereas GPR133 is highly expressed in the pituitary gland and is coupled to the G(s) protein, leading to activation of adenylate cyclase pathway. Moreover, genetic variations in the GPR133 have been reported to be associated with adult height and heart rate. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in ligand recognition as well as cell-cell adhesion and cell-matrix interactions, linked by a stalk region to a class B seven-transmembrane domain. In addition, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR-autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. However, several adhesion GPCRs, including GPR 111, GPR115, and CELSR1, are predicted to be non-cleavable at the GAIN domain because of the lack of a consensus catalytic triad sequence (His-Leu-Ser/Thr) within their GPS. 252 matched cddid_all.tbl CDD cd15934 cd15934 320600 7tmC_mGluRs_group2_3 metabotropic glutamate receptors in group 2 and 3, member of the class C family of seven-transmembrane G protein-coupled receptors. The metabotropic glutamate receptors (mGluRs) are homodimeric class C G-protein coupled receptors which are activated by glutamate, the major excitatory neurotransmitter of the CNS. The mGluRs are involved in regulating neuronal excitability and synaptic transmission via intracellular activation of second messenger signaling pathways. While the ionotropic glutamate receptor subtypes (AMPA, NMDA, and kainite) mediate fast excitatory postsynaptic transmission, mGluRs are known to mediate slower excitatory postsynaptic responses and to be involved in synaptic plasticity in the mammalian brain. In addition to seven-transmembrane helices, the class C GPCRs are characterized by a large N-terminal extracellular Venus flytrap-like domain, which is composed of two adjacent lobes separated by a cleft which binds an endogenous ligand. Moreover, they exist as either homo- or heterodimers, which are essential for their function. For instance, mGluRs form homodimers via interactions between the N-terminal Venus flytrap domains and the intermolecular disulphide bonds between cysteine residues located in the cysteine-rich domain (CRD). At least eight different subtypes of metabotropic receptors (mGluR1-8) have been identified and further classified into three groups based on their sequence homology, pharmacological properties, and signaling pathways. Group 1 (mGluR1 and mGluR5) receptors are predominantly located postsynaptically on neurons and are involved in long-term synaptic plasticity in the brain, including long-term potentiation (LTP) in the hippocampus and long-term depression (LTD) in the cerebellum. They are coupled to G(q/11) proteins, thereby activating phospholipase C to generate inositol-1,4,5-triphosphate (IP3) and diacyglycerol (DAG), which in turn lead to Ca2+ release and protein kinase C activation, respectively. Group I mGluR expression is shown to be strongly upregulated in animal models of epilepsy, brain injury, inflammatory, and neuropathic pain, as well as in patients with amyotrophic lateral sclerosis or multiple sclerosis. Group 2 (mGluR2 and mGluR3) and 3 (mGluR4, mGluR6, mGluR7, and mGluR8) receptors are predominantly localized presynaptically in the active region of neurotransmitter release. They are coupled to (Gi/o) proteins, which leads to inhibition of adenylate cyclase activity and cAMP formation, and consequently to a decrease in protein kinase A (PKA) activity. Ultimately, activation of these receptors leads to inhibition of neurotransmitter release such as glutamate and GABA via inhibition of Ca2+ channels and activation of K+ channels. Furthermore, while activation of Group 1 mGluRs increases NMDA (N-methyl-D-aspartate) receptor activity and risk of neurotoxicity, Group 2 and 3 mGluRs decrease NMDA receptor activity and prevent neurotoxicity. 252 matched cddid_all.tbl CDD cd15935 cd15935 320601 7tmA_OR4Q3-like olfactory receptor 4Q3 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor 4Q3 and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 268 matched cddid_all.tbl CDD cd15936 cd15936 320602 7tmA_OR4D-like olfactory receptor 4D and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 4D and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 267 matched cddid_all.tbl CDD cd15937 cd15937 320603 7tmA_OR4N-like olfactory receptor 4N, 4M, and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 4N, 4M, and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 267 matched cddid_all.tbl CDD cd15938 cd15938 320604 7tmA_OR4Q2-like olfactory receptor 4Q2 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor 4Q2 and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 265 matched cddid_all.tbl CDD cd15939 cd15939 320605 7tmA_OR4A-like olfactory receptor 4A and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 4A, 4C, 4P, 4S, 4X and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 267 matched cddid_all.tbl CDD cd15940 cd15940 320606 7tmA_OR4E-like olfactory receptor 4E and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 4E and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 267 matched cddid_all.tbl CDD cd15941 cd15941 320607 7tmA_OR10S1-like olfactory receptor subfamily 10S1 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor 10S1 and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 277 matched cddid_all.tbl CDD cd15942 cd15942 320608 7tmA_OR10G6-like olfactory receptor subfamily 10G6 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor 10G6 and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 275 matched cddid_all.tbl CDD cd15943 cd15943 320609 7tmA_OR5AP2-like olfactory receptor subfamily 5AP2 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 5AP2 and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 295 matched cddid_all.tbl CDD cd15944 cd15944 320610 7tmA_OR5AR1-like olfactory receptor subfamily 5AR1 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 5AR1 and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 294 matched cddid_all.tbl CDD cd15945 cd15945 320611 7tmA_OR5C1-like olfactory receptor subfamily 5C1 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 5C1 and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 292 matched cddid_all.tbl CDD cd15946 cd15946 320612 7tmA_OR1330-like olfactory receptor 1330 and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes olfactory receptors 1330 from mouse, Olr859 from rat, and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 270 matched cddid_all.tbl CDD cd15947 cd15947 320613 7tmA_OR2B-like olfactory receptor subfamily 2B and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor family 2 (subfamilies 2B, 2C, 2G, 2H, 2I, 2J, 2W, 2Y) and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 270 matched cddid_all.tbl CDD cd15948 cd15948 320614 7tmA_OR52K-like olfactory receptor subfamily 52K and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 52K and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 277 matched cddid_all.tbl CDD cd15949 cd15949 320615 7tmA_OR52M-like olfactory receptor subfamily 52M and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 52M and related proteins in other mammals, sauropsids, and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 292 matched cddid_all.tbl CDD cd15950 cd15950 320616 7tmA_OR52I-like olfactory receptor subfamily 52I and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 52I and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 275 matched cddid_all.tbl CDD cd15951 cd15951 320617 7tmA_OR52R_52L-like olfactory receptor subfamily 52R, 52L, and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamilies 52R, 52L and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 275 matched cddid_all.tbl CDD cd15952 cd15952 320618 7tmA_OR52E-like olfactory receptor subfamily 52E and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 52E and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 274 matched cddid_all.tbl CDD cd15953 cd15953 341354 7tmA_OR52P-like olfactory receptor subfamily 52P and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 52P and related proteins in other mammals, sauropsids and amphibians. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 275 matched cddid_all.tbl CDD cd15954 cd15954 320620 7tmA_OR52N-like olfactory receptor subfamily 52N and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 52N and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 276 matched cddid_all.tbl CDD cd15955 cd15955 320621 7tmA_OR52A-like olfactory receptor subfamily 52A and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 52A and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 276 matched cddid_all.tbl CDD cd15956 cd15956 320622 7tmA_OR52W-like olfactory receptor subfamily 52W and related proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes human olfactory receptor subfamily 52W and related proteins in other mammals and sauropsids. Olfactory receptors (ORs) play a central role in olfaction, the sense of smell. ORs belong to the class A rhodopsin-like family of G protein-coupled receptors and constitute the largest multigene family in mammals of approximately 1,000 genes. More than 60% of human ORs are non-functional pseudogenes compared to only about 20% in mouse. Each OR can recognize structurally similar odorants, and a single odorant can be detected by several ORs. Binding of an odorant to the olfactory receptor induces a conformational change that leads to the activation of the olfactory-specific G protein (Golf). The G protein (Golf and/or Gs) in turn stimulates adenylate cyclase to make cAMP. The cAMP opens cyclic nucleotide-gated ion channels, which allow the influx of calcium and sodium ions, resulting in depolarization of the olfactory receptor neuron and triggering an action potential which transmits this information to the brain. A consensus nomenclature system based on evolutionary divergence is used here to classify the olfactory receptor family. The nomenclature begins with the root name OR, followed by an integer representing a family, a letter denoting a subfamily, and an integer representing the individual gene within the subfamily. 275 matched cddid_all.tbl CDD cd15957 cd15957 341355 7tmA_Beta2_AR beta-2 adrenergic receptors (adrenoceptors), member of the class A family of seven-transmembrane G protein-coupled receptors. Beta-2 AR is activated by adrenaline that plays important roles in cardiac function and pulmonary physiology. While beta-1 AR and beta-2 AR are the major subtypes involved in modulating cardiac contractility and heart rate by positively stimulating the G(s) protein-adenylate cyclase-cAMP-PKA signaling pathway, beta-2 AR can couple to both G(s) and G(i) proteins in the heart. Moreover, beta-2 AR activation leads to smooth muscle relaxation and bronchodilation in the lung. The beta adrenergic receptors are a subfamily of the class A rhodopsin-like G protein-coupled receptors. 301 matched cddid_all.tbl CDD cd15958 cd15958 320624 7tmA_Beta1_AR beta-1 adrenergic receptors (adrenoceptors), member of the class A family of seven-transmembrane G protein-coupled receptors. The beta-1 adrenergic receptor (beta-1 adrenoceptor), also known as beta-1 AR, is activated by adrenaline (epinephrine) and plays important roles in regulating cardiac function and heart rate. The human heart contains three subtypes of the beta AR: beta-1 AR, beta-2 AR, and beta-3 AR. Beta-1 AR and beta-2 AR, which expressed at about a ratio of 70:30, are the major subtypes involved in modulating cardiac contractility and heart rate by positively stimulating the G(s) protein-adenylate cyclase-cAMP-PKA signaling pathway. In contrast, beta-3 AR produces negative inotropic effects by activating inhibitory G(i) proteins. The aberrant expression of betrayers can lead to cardiac dysfunction such as arrhythmias or heart failure. 298 matched cddid_all.tbl CDD cd15959 cd15959 320625 7tmA_Beta3_AR beta-3 adrenergic receptors (adrenoceptors), member of the class A family of seven-transmembrane G protein-coupled receptors. The beta-3 adrenergic receptor (beta-3 adrenoceptor), also known as beta-3 AR, is activated by adrenaline and plays important roles in regulating cardiac function and heart rate. The human heart contains three subtypes of the beta AR: beta-1 AR, beta-2 AR, and beta-3 AR. Beta-1 AR and beta-2 AR, which expressed at about a ratio of 70:30, are the major subtypes involved in modulating cardiac contractility and heart rate by positively stimulating the G(s) protein-adenylate cyclase-cAMP-PKA signaling pathway. In contrast, beta-3 AR produces negative inotropic effects by activating inhibitory G(i) proteins. The aberrant expression of betrayers can lead to cardiac dysfunction such as arrhythmias or heart failure. 302 matched cddid_all.tbl CDD cd15960 cd15960 320626 7tmA_GPR185-like G protein-coupled receptor 185 and similar proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR185, also called GPRx, is a member of the constitutively active GPR3/6/12 subfamily of G protein-coupled receptors. It plays a role in the maintenance of meiotic arrest in Xenopus laevis oocytes through G(s) protein, which leads to increased cAMP levels. In Xenopus laevis, GPR185 is primarily expressed in brain, ovary, and testis; however, its ortholog has not been identified in other vertebrate genomes. GPR3, GPR6, and GPR12 form a subfamily of constitutively active G-protein coupled receptors with dual coupling to G(s) and G(i) proteins. These three orphan receptors are involved in the regulation of cell proliferation and survival, neurite outgrowth, cell clustering, and maintenance of meiotic prophase arrest. 268 matched cddid_all.tbl CDD cd15961 cd15961 320627 7tmA_GPR12 G protein-coupled receptor 12, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR3, GPR6, and GPR12 form a subfamily of constitutively active G-protein coupled receptors with dual coupling to G(s) and G(i) proteins. These three orphan receptors are involved in the regulation of cell proliferation and survival, neurite outgrowth, cell clustering, and maintenance of meiotic prophase arrest. They constitutively activate adenylate cyclase to a similar degree as that seen with fully activated G(s)-coupled receptors, and are also able to constitutively activate inhibitory G(i/o) proteins. Lysophospholipids such as sphingosine 1-phosphate (S1P) and sphingosylphosphorylcholine have been detected as the high-affinity ligands for Gpr6 and Gpr12, respectively, which show high sequence homology with GPR3. 268 matched cddid_all.tbl CDD cd15962 cd15962 320628 7tmA_GPR6 G protein-coupled receptor 6, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR3, GPR6, and GPR12 form a subfamily of constitutively active G-protein coupled receptors with dual coupling to G(s) and G(i) proteins. These three orphan receptors are involved in the regulation of cell proliferation and survival, neurite outgrowth, cell clustering, and maintenance of meiotic prophase arrest. They constitutively activate adenylate cyclase to a similar degree as that seen with fully activated G(s)-coupled receptors, and are also able to constitutively activate inhibitory G(i/o) proteins. Lysophospholipids such as sphingosine 1-phosphate (S1P) and sphingosylphosphorylcholine have been detected as the high-affinity ligands for Gpr6 and Gpr12, respectively, which show high sequence homology with GPR3. 268 matched cddid_all.tbl CDD cd15963 cd15963 320629 7tmA_GPR3 G protein-coupled receptor 3, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR3, GPR6, and GPR12 form a subfamily of constitutively active G-protein coupled receptors with dual coupling to G(s) and G(i) proteins. These three orphan receptors are involved in the regulation of cell proliferation and survival, neurite outgrowth, cell clustering, and maintenance of meiotic prophase arrest. They constitutively activate adenylate cyclase to a similar degree as that seen with fully activated G(s)-coupled receptors, and are also able to constitutively activate inhibitory G(i/o) proteins. Lysophospholipids such as sphingosine 1-phosphate (S1P) and sphingosylphosphorylcholine have been detected as the high-affinity ligands for Gpr6 and Gpr12, respectively, which show high sequence homology with GPR3. 268 matched cddid_all.tbl CDD cd15964 cd15964 320630 7tmA_TSH-R thyroid-stimulating hormone receptor (or thyrotropin receptor), member of the class A family of seven-transmembrane G protein-coupled receptors. The glycoprotein hormone receptors are seven transmembrane domain receptors with a very large extracellular N-terminal domain containing many leucine-rich repeats responsible for hormone recognition and binding. The glycoprotein hormone family includes the three gonadotropins: luteinizing hormone (LH), follicle-stimulating hormone (FSH), chorionic gonadotropin (CG), and a pituitary thyroid-stimulating hormone (TSH). The glycoprotein hormones exert their biological functions by interacting with their cognate GPCRs. Both LH and CG bind to the same receptor, the luteinizing hormone-choriogonadotropin receptor (LHCGR); FSH binds to FSH-R and TSH to TSH-R. TSH-R plays an important role thyroid physiology, and its activation stimulates the production of thyroxine (T4) and triiodothyronine (T3). Defects in TSH-R are a cause of several types of hyperthyroidism. The receptor is predominantly found on the surface of the thyroid epithelial cells and couples to the G(s)-protein and activates adenylate cyclase, thereby promoting cAMP production. TSH and cAMP stimulate thyroid cell proliferation, differentiation, and function. 275 matched cddid_all.tbl CDD cd15965 cd15965 320631 7tmA_RXFP1_LGR7 relaxin receptor 1 (or LGR7), member of the class A family of seven-transmembrane G protein-coupled receptors. Relaxin is a member of the insulin superfamily that has diverse actions in both reproductive and non-reproductive tissues. The relaxin-like peptide family includes relaxin-1, relaxin-2, and the insulin-like (INSL) peptides such as INSL3, INSL4, INSL5 and INSL6. The relaxin family peptides share high structural but low sequence similarity, and exert their physiological functions by activating a group of four G protein-coupled receptors, RXFP1-4. Relaxin is the endogenous ligand for RXFP1, which has a large extracellular N-terminal domain containing 10 leucine-rich repeats and a unique low-density lipoprotein type A (LDLa) module which is necessary for receptor activation. Upon receptor binding, relaxin activates a variety of signaling pathways to produce second messengers such as cAMP and nitric oxide. RXFP1 is expressed in various tissues including uterus, ovary, placenta, cerebral cortex, heart, lung and kidney, among others. 287 matched cddid_all.tbl CDD cd15966 cd15966 320632 7tmA_RXFP2_LGR8 relaxin receptor 2 (or LGR8), member of the class A family of seven-transmembrane G protein-coupled receptors. Relaxin is a member of the insulin superfamily that has diverse actions in both reproductive and non-reproductive tissues. The relaxin-like peptide family includes relaxin-1, relaxin-2, and the insulin-like (INSL) peptides such as INSL3, INSL4, INSL5 and INSL6. The relaxin family peptides share high structural similarity, but low sequence similarity, and exert their physiological functions by activating a group of four G protein-coupled receptors, RXFP1-4. INSL3 is the endogenous ligand for RXFP2, which couples to the G(s) protein to increase intracellular cAMP levels, but also to the GoB protein to decrease cAMP formation. RXFP2 (or LGR8) is expressed in various tissues including the brain, kidney, muscle, testis, thyroid, uterus, and peripheral blood cells, among others. 287 matched cddid_all.tbl CDD cd15967 cd15967 320633 7tmA_P2Y1-like P2Y purinoceptor 1-like. P2Y1-like is an uncharacterized group that is phylogenetically related to a family of purinergic G protein-coupled receptors. The P2Y receptor family is composed of eight subtypes, which are activated by naturally occurring extracellular nucleotides such as ATP, ADP, UTP, UDP, and UDP-glucose. These eight receptors are ubiquitous in human tissues and can be further classified into two subfamilies based on sequence homology and second messenger coupling: a subfamily of five P2Y1-like receptors (P2Y1, P2Y2, P2Y4, P2Y6, and P2Y11Rs) that are coupled to G(q) protein to activate phospholipase C (PLC) and a second subfamily of three P2Y12-like receptors (P2Y12, P2YR13, and P2Y14Rs) that are coupled to G(i) protein to inhibit adenylate cyclase. Several cloned subtypes, such as P2Y3, P2Y5, and P2Y7-10, are not functional mammalian nucleotide receptors. The native agonists for P2Y receptors are: ATP (P2Y2, P2Y12), ADP (P2Y1, P2Y12, and P2Y13), UTP (P2Y2, P2Y4), UDP (P2Y6, P2Y14), and UDP-glucose (P2Y14). 281 matched cddid_all.tbl CDD cd15968 cd15968 320634 7tmA_P2Y6_P2Y3-like P2Y purinoceptors 6 and 3, and similar proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. This group includes P2Y receptor 6 (P2Y6), P2Y3, and P2Y3-like proteins. These receptors belong to the G(i) class of a family of purinergic G-protein coupled receptors. In the CNS, P2Y6 plays a role in microglia activation and phagocytosis, and is involved in the secretion of interleukin from monocytes and macrophages in the immune system. The P2Y receptor family is composed of eight subtypes, which are activated by naturally occurring extracellular nucleotides such as ATP, ADP, UTP, UDP, and UDP-glucose. These eight receptors are ubiquitous in human tissues and can be further classified into two subfamilies based on sequence homology and second messenger coupling: a subfamily of five P2Y1-like receptors (P2Y1, P2Y2, P2Y4, P2Y6, and P2Y11Rs) that are coupled to G(q) protein to activate phospholipase C (PLC) and a second subfamily of three P2Y12-like receptors (P2Y12, P2YR13, and P2Y14Rs) that are coupled to G(i) protein to inhibit adenylate cyclase. Several cloned subtypes, such as P2Y3, P2Y5, and P2Y7-10, are not functional mammalian nucleotide receptors. The native agonists for P2Y receptors are: ATP (P2Y2, P2Y12), ADP (P2Y1, P2Y12, and P2Y13), UTP (P2Y2, P2Y4), UDP (P2Y6, P2Y14), and UDP-glucose (P2Y14). 285 matched cddid_all.tbl CDD cd15969 cd15969 320635 7tmA_GPR87 G protein-coupled receptor 87, member of the class A family of seven-transmembrane G protein-coupled receptors. GPR87 acts as one of multiple receptors for lysophosphatidic acid (LPA). This orphan receptor has been shown to be over-expressed in several malignant tumors including lung squamous cell carcinoma and regulated by p53. GPR87 is phylogenetically closely related to the G(i) class of the P2Y family of purinergic G protein-coupled receptors. P2Y receptor family is composed of eight subtypes, which are activated by naturally occurring extracellular nucleotides such as ATP, ADP, UTP, UDP, and UDP-sugars. These eight receptors are ubiquitous in human tissues and can be further classified into two subfamilies based on sequence homology and second messenger coupling: a subfamily of five P2Y1-like receptors (P2Y1, P2Y2, P2Y4, P2Y6, and P2Y11Rs) that are coupled to G(q) protein to activate phospholipase C (PLC) and a second subfamily of three P2Y12-like receptors (P2Y12, P2YR13, and P2Y14Rs) that are coupled to G(i) protein to inhibit adenylate cyclase. 283 matched cddid_all.tbl CDD cd15970 cd15970 320636 7tmA_SSTR1 somatostatin receptor type 1, member of the class A family of seven-transmembrane G protein-coupled receptors. G protein-coupled somatostatin receptors (SSTRs) are composed of five distinct subtypes (SSTR1-5) that display strong sequence similarity with opioid receptors. All five receptor subtypes bind the natural somatostatin (somatotropin release inhibiting factor), a polypeptide hormone that regulates a wide variety of physiological functions such as neurotransmission, cell proliferation, contractility of smooth muscle cells, and endocrine signaling as well as inhibition of the release of many secondary hormones. SSTR1 is coupled to a Na/H exchanger, voltage-dependent calcium channels, and AMPA/kainate glutamate channels. SSTR1 is expressed in the normal human pituitary and in nearly half of all pituitary adenoma subtypes. 276 matched cddid_all.tbl CDD cd15971 cd15971 320637 7tmA_SSTR2 somatostatin receptor type 2, member of the class A family of seven-transmembrane G protein-coupled receptors. G protein-coupled somatostatin receptors (SSTRs), which display strong sequence similarity with opioid receptors, binds somatostatin, a polypeptide hormone that regulates a wide variety of physiological such as neurotransmission, endocrine secretion, cell proliferation, and smooth muscle contractility. SSTRs are composed of five distinct subtypes (SSTR1-5) which are encoded by separate genes on different chromosomes. SSTR2 plays critical roles in growth hormone secretion, glucagon secretion, and immune responses. SSTR2 is expressed in the normal human pituitary and in nearly all pituitary growth hormone adenomas. 279 matched cddid_all.tbl CDD cd15972 cd15972 320638 7tmA_SSTR3 somatostatin receptor type 3, member of the class A family of seven-transmembrane G protein-coupled receptors. G protein-coupled somatostatin receptors (SSTRs) are composed of five distinct subtypes (SSTR1-5) that display strong sequence similarity with opioid receptors. All five receptor subtypes bind the natural somatostatin (somatotropin release inhibiting factor), a polypeptide hormone that regulates a wide variety of physiological functions such as neurotransmission, cell proliferation, contractility of smooth muscle cells, and endocrine signaling as well as inhibition of the release of many secondary hormones. SSTR3 is coupled to inward rectifying potassium channels. SSTR3 plays critical roles in growth hormone secretion, endothelial cell cycle arrest and apoptosis. Furthermore, SSTR3 is expressed in the normal human pituitary and in nearly half of pituitary growth hormone adenomas. 279 matched cddid_all.tbl CDD cd15973 cd15973 320639 7tmA_SSTR4 somatostatin receptor type 4, member of the class A family of seven-transmembrane G protein-coupled receptors. G protein-coupled somatostatin receptors (SSTRs) are composed of five distinct subtypes (SSTR1-5) that display strong sequence similarity with opioid receptors. All five receptor subtypes bind the natural somatostatin (somatotropin release inhibiting factor), a polypeptide hormone that regulates a wide variety of physiological functions such as neurotransmission, cell proliferation, contractility of smooth muscle cells, and endocrine signaling as well as inhibition of the release of many secondary hormones. SSTR4 plays a critical role in mediating inflammation. Unlike other SSTRs, SSTR4 subtype is not detected in all pituitary adenomas while it is expressed in the normal human pituitary. 274 matched cddid_all.tbl CDD cd15974 cd15974 320640 7tmA_SSTR5 somatostatin receptor type 5, member of the class A family of seven-transmembrane G protein-coupled receptors. G protein-coupled somatostatin receptors (SSTRs) are composed of five distinct subtypes (SSTR1-5) that display strong sequence similarity with opioid receptors. All five receptor subtypes bind the natural somatostatin (somatotropin release inhibiting factor), a polypeptide hormone that regulates a wide variety of physiological functions such as neurotransmission, cell proliferation, contractility of smooth muscle cells, and endocrine signaling as well as inhibition of the release of many secondary hormones. SSTR5 is coupled to inward rectifying K channels and phospholipase C, and plays critical roles in growth hormone and insulin secretion. SSTR5 acts as a negative regulator of PDX-1 (pancreatic and duodenal homeobox-1) expression, which is a conserved homeodomain-containing beta cell-specific transcription factor essentially involved in pancreatic development, among many other functions. 277 matched cddid_all.tbl CDD cd15975 cd15975 320641 7tmA_ET-AR endothelin A (or endothelin-1) receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. Endothelins are able to activate a number of signal transduction processes including phospholipase A2, phospholipase C, and phospholipase D, as well as cytosolic protein kinase activation. They play an important role in the regulation of the cardiovascular system and are the most potent vasoconstrictors identified, stimulating cardiac contraction, regulating the release of vasoactive substances, and stimulating mitogenesis in blood vessels. Two endothelin receptor subtypes have been isolated and identified in vertebrates, endothelin A receptor (ET-A) and endothelin B receptor (ET-B), and are members of the seven transmembrane class A G-protein coupled receptor family which activate multiple effectors via different types of G protein. Some vertebrates contain a third subtype, endothelin A receptor (ET-C). ET-A receptors are mainly located on vascular smooth muscle cells, whereas ET-B receptors are present on endothelial cells lining the vessel wall. Endothelin receptors have also been found in the brain. 300 matched cddid_all.tbl CDD cd15976 cd15976 320642 7tmA_ET-BR endothelin B receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. Endothelins are able to activate a number of signal transduction processes including phospholipase A2, phospholipase C, and phospholipase D, as well as cytosolic protein kinase activation. They play an important role in the regulation of the cardiovascular system and are the most potent vasoconstrictors identified, stimulating cardiac contraction, regulating the release of vasoactive substances, and stimulating mitogenesis in blood vessels. Two endothelin receptor subtypes have been isolated and identified in vertebrates, endothelin A receptor (ET-A) and endothelin B receptor (ET-B), and are members of the seven transmembrane class A G-protein coupled receptor family which activate multiple effectors via different types of G protein. Some vertebrates contain a third subtype, endothelin A receptor (ET-C). ET-A receptors are mainly located on vascular smooth muscle cells, whereas ET-B receptors are present on endothelial cells lining the vessel wall. Endothelin receptors have also been found in the brain. 296 matched cddid_all.tbl CDD cd15977 cd15977 320643 7tmA_ET-CR endothelin C receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. Endothelins are able to activate a number of signal transduction processes including phospholipase A2, phospholipase C, and phospholipase D, as well as cytosolic protein kinase activation. They play an important role in the regulation of the cardiovascular system and are the most potent vasoconstrictors identified, stimulating cardiac contraction, regulating the release of vasoactive substances, and stimulating mitogenesis in blood vessels. Two endothelin receptor subtypes have been isolated and identified in vertebrates, endothelin A receptor (ET-A) and endothelin B receptor (ET-B), and are members of the seven transmembrane class A G-protein coupled receptor family which activate multiple effectors via different types of G protein. Some vertebrates contain a third subtype, endothelin A receptor (ET-C). ET-A receptors are mainly located on vascular smooth muscle cells, whereas ET-B receptors are present on endothelial cells lining the vessel wall. Endothelin receptors have also been found in the brain. The ET-C receptor is specific for endothelin-3 on frog dermal melanophores; its activation causes dispersion of pigment granules. 296 matched cddid_all.tbl CDD cd15978 cd15978 320644 7tmA_CCK-AR cholecystokinin receptor type A, member of the class A family of seven-transmembrane G protein-coupled receptors. Cholecystokinin receptors (CCK-AR and CCK-BR) are a group of G-protein coupled receptors which bind the peptide hormones cholecystokinin (CCK) or gastrin. CCK, which facilitates digestion in the small intestine, and gastrin, a major regulator of gastric acid secretion, are highly similar peptides. Like gastrin, CCK is a naturally-occurring linear peptide that is synthesized as a preprohormone, then proteolytically cleaved to form a family of peptides with the common C-terminal sequence (Gly-Trp-Met-Asp-Phe-NH2), which is required for full biological activity. CCK-AR (type A, alimentary; also known as CCK1R) is found abundantly on pancreatic acinar cells and binds only sulfated CCK-peptides with very high affinity, whereas CCK-BR (type B, brain; also known as CCK2R), the predominant form in the brain and stomach, binds CCK or gastrin and discriminates poorly between sulfated and non-sulfated peptides. CCK is implicated in regulation of digestion, appetite control, and body weight, and is involved in neurogenesis via CCK-AR. There is some evidence to support that CCK and gastrin, via their receptors, are involved in promoting cancer development and progression, acting as growth and invasion factors. 278 matched cddid_all.tbl CDD cd15979 cd15979 320645 7tmA_CCK-BR cholecystokinin receptor type B, member of the class A family of seven-transmembrane G protein-coupled receptors. Cholecystokinin receptors (CCK-AR and CCK-BR) are a group of G-protein coupled receptors which bind the peptide hormones cholecystokinin (CCK) or gastrin. CCK, which facilitates digestion in the small intestine, and gastrin, a major regulator of gastric acid secretion, are highly similar peptides. Like gastrin, CCK is a naturally-occurring linear peptide that is synthesized as a preprohormone, then proteolytically cleaved to form a family of peptides with the common C-terminal sequence (Gly-Trp-Met-Asp-Phe-NH2), which is required for full biological activity. CCK-AR (type A, alimentary; also known as CCK1R) is found abundantly on pancreatic acinar cells and binds only sulfated CCK-peptides with very high affinity, whereas CCK-BR (type B, brain; also known as CCK2R), the predominant form in the brain and stomach, binds CCK or gastrin and discriminates poorly between sulfated and non-sulfated peptides. CCK is implicated in regulation of digestion, appetite control, and body weight, and is involved in neurogenesis via CCK-AR. There is some evidence to support that CCK and gastrin, via their receptors, are involved in promoting cancer development and progression, acting as growth and invasion factors. 275 matched cddid_all.tbl CDD cd15980 cd15980 320646 7tmA_NPFFR2 neuropeptide FF receptor 2, member of the class A family of seven-transmembrane G protein-coupled receptors. Neuropeptide FF (NPFF) is a mammalian octapeptide that belongs to a family of neuropeptides containing an RF-amide motif at their C-terminus that have been implicated in a wide range of physiological functions in the brain including pain sensitivity, insulin release, food intake, memory, blood pressure, and opioid-induced tolerance and hyperalgesia. The effects of these peptides are mediated through neuropeptide FF1 and FF2 receptors (NPFF1-R and NPFF2-R) which are predominantly expressed in the brain. NPFF induces pro-nociceptive effects, mainly through the NPFF1-R, and anti-nociceptive effects, mainly through the NPFF2-R. NPFF has been shown to inhibit adenylate cyclase via the Gi protein coupled to NPFF1-R. 299 matched cddid_all.tbl CDD cd15981 cd15981 320647 7tmA_NPFFR1 neuropeptide FF receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors. Neuropeptide FF (NPFF) is a mammalian octapeptide that belongs to a family of neuropeptides containing an RF-amide motif at their C-terminus that have been implicated in a wide range of physiological functions in the brain including pain sensitivity, insulin release, food intake, memory, blood pressure, and opioid-induced tolerance and hyperalgesia. The effects of these peptides are mediated through neuropeptide FF1 and FF2 receptors (NPFF1-R and NPFF2-R) which are predominantly expressed in the brain. NPFF induces pro-nociceptive effects, mainly through the NPFF1-R, and anti-nociceptive effects, mainly through the NPFF2-R. NPFF has been shown to inhibit adenylate cyclase via the Gi protein coupled to NPFF1-R. 299 matched cddid_all.tbl CDD cd15982 cd15982 320648 7tmB1_PTH2R parathyroid hormone 2 receptor, member of the class B family of seven-transmembrane G protein-coupled receptors. The parathyroid hormone 2 receptor (PTH2R), one of the three subtypes of PTH receptor family, is found in mammals and fish, but not in chicken or frog. PTH2R is potently activated by tuberoinfundibular peptide-39 (TIP-39) but not by PTH-related peptide (PTHrP), a paracrine factor that regulates endochondral bone development. PTH, an endocrine hormone that regulates calcium homoeostasis and bone maintenance, strongly activates human PTH2R, but only weakly activates rat and zebrafish PTH2Rs. These results suggest that TIP-39 is a natural ligand for PTH2R. Conversely, PTH1R is activated by PTH and PTHrP, but not by TIP-39. The PTH family receptors are members of the B1 (or secretin-like) subfamily of class B GPCRs, which include receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, glucagon, glucagon-like peptide (GLP), and calcitonin gene-related peptide. These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. 289 matched cddid_all.tbl CDD cd15983 cd15983 320649 7tmB1_PTH3R parathyroid hormone 3 receptor, member of the class B family of seven-transmembrane G protein-coupled receptors. The parathyroid hormone 3 receptor (PTH3R), one of the three subtypes of PTH receptor family, is found in chicken and fish, but it is absent in mammals. On the other hand, the PTH1R is found in all vertebrate species, whereas PTH2R is found in mammals and fish, but not in chicken or frog. PTH1R is activated by two polypeptide ligands: PTH, an endocrine hormone that regulates calcium homoeostasis and bone maintenance, and PTH-related peptide (PTHrP), a paracrine factor that regulates endochondral bone development. PTH2R is potently activated by tuberoinfundibular peptide-39 (TIP-39), but not by PTHrP. PTH also strongly activates human PTH2R, but only weakly activates rat and zebrafish PTH2Rs, suggesting that TIP-39 is a natural ligand for PTH2R. Conversely, PTH3R binds and responds to both PTH and PTHrP, but not the TIP-39. The PTH family receptors are members of the B1 (or secretin-like) subfamily of class B GPCRs, which include receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, glucagon, glucagon-like peptide (GLP), and calcitonin gene-related peptide. These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. 285 matched cddid_all.tbl CDD cd15984 cd15984 320650 7tmB1_PTH1R parathyroid hormone 1 receptor, member of the class B family of seven-transmembrane G protein-coupled receptors. The parathyroid hormone (PTH) receptor family has three subtypes: PTH1R, PTH2R and PTH3R. PTH1R is expressed in bone and kidney and is activated by two polypeptide ligands: PTH, an endocrine hormone that regulates calcium homoeostasis and bone maintenance, and PTH-related peptide (PTHrP), a paracrine factor that regulates endochondral bone development. PTH1R couples predominantly to G(s)-protein that in turn activates adenylate cyclase thereby producing cAMP, but it can also couple to several G protein subtypes, including G(q/11), G(i/o), and G(12/13), resulting in activation of multiple intracellular signaling pathways. PTH1R is found in all vertebrate species, whereas PTH2R is found in mammals and fish, but not in chicken or frog. PTH3R is found in chicken and fish, but it is absent in mammals. The PTH receptors are members of the B1 (or secretin-like) subfamily of class B GPCRs, which include receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, glucagon, glucagon-like peptide (GLP), and calcitonin gene-related peptide. These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. 290 matched cddid_all.tbl CDD cd15985 cd15985 320651 7tmB1_GlucagonR-like_1 uncharacterized group of glucagon receptor-like proteins, member of the class B family of seven-transmembrane G protein-coupled receptors. This group consists of uncharacterized proteins with similarity to members of the glucagon receptor family of G protein-coupled receptors, which include glucagon receptor (GCGR), and glucagon-like peptide-1 receptor (GLP1R), and GLP2R. The glucagon receptors are activated by the members of the glucagon (GCG) peptide family including GCG, glucagon-like peptide 1 (GLP1), and GLP2, which are derived from the large proglucagon precursor. GCGR regulates blood glucose levels by control of hepatic glycogenolysis and gluconeogenesis and by regulation of insulin secretion from the pancreatic beta-cells. Activation of GLP1R stimulates glucose-dependent insulin secretion from pancreatic beta cells, whereas activation of GLP2R stimulates intestinal epithelial proliferation and increases villus height in the small intestine. Receptors in this group belong to the B1 (or secretin-like) subfamily of class B GPCRs, which includes receptors for polypeptide hormones of 27-141 amino-acid residues such as secretin, calcitonin gene-related peptide, parathyroid hormone (PTH), and corticotropin-releasing factor. These receptors contain the large N-terminal extracellular domain (ECD), which plays a critical role in hormone recognition by binding to the C-terminal portion of the peptide. On the other hand, the N-terminal segment of the hormone induces receptor activation by interacting with the receptor transmembrane domains and connecting extracellular loops, triggering intracellular signaling pathways. All members of the B1 subfamily preferentially couple to G proteins of G(s) family, which positively stimulate adenylate cyclase, leading to increased intracellular cAMP formation and calcium influx. However, depending on their cellular location, GCGR and GLP receptors can activate multiple G proteins, which can in turn stimulate different second messenger pathways. 280 matched cddid_all.tbl CDD cd15986 cd15986 320652 7tmB1_VIP-R2 vasoactive intestinal polypeptide (VIP) receptor 2, member of the class B family of seven-transmembrane G protein-coupled receptors. Vasoactive intestinal peptide (VIP) receptor 2 is a member of the group of G protein-coupled receptors for structurally similar peptide hormones that also include secretin, growth-hormone-releasing hormone (GHRH), and pituitary adenylate cyclase activating polypeptide (PACAP). These receptors are classified into the subfamily B1 of class B GRCRs that consists of the classical hormone receptors and have been identified in all the vertebrates, from fishes to mammals, but are not present in plants, fungi, or prokaryotes. For all class B receptors, the large N-terminal extracellular domain plays a critical role in peptide hormone recognition. VIP and PACAP exert their effects through three G protein-coupled receptors, PACAP-R1, VIP-R1 (vasoactive intestinal receptor type 1, also known as VPAC1) and VIP-R2 (or VPAC2). PACAP-R1 binds only PACAP with high affinity, whereas VIP-R1 and -R2 specifically bind and respond to both VIP and PACAP. VIP and PACAP and their receptors are widely expressed in the brain and periphery. They are upregulated in neurons and immune cells in responses to CNS injury and/or inflammation and exert potent anti-inflammatory effects, as well as play important roles in the control of circadian rhythms and stress responses, among many others. VIP-R1 is preferentially coupled to a stimulatory G(s) protein, which leads to the activation of adenylate cyclase and thereby increases in intracellular cAMP level. However, depending on its cellular location, VIP-R1 is also capable of coupling to additional G proteins such as G(q) protein, thus leading to the activation of phospholipase C and intracellular calcium influx. 269 matched cddid_all.tbl CDD cd15987 cd15987 320653 7tmB1_PACAP-R1 pituitary adenylate cyclase-activating polypeptide type 1 receptor, member of the class B family of seven-transmembrane G protein-coupled receptors. Pituitary adenylate cyclase-activating polypeptide type 1 receptor (PACAP-R1) is a member of the group of G protein-coupled receptors for structurally similar peptide hormones that also include secretin, growth-hormone-releasing hormone (GHRH), and vasoactive intestinal peptide (VIP). These receptors are classified into the subfamily B1 of class B GRCRs that consists of the classical hormone receptors and have been identified in all the vertebrates, from fishes to mammals, but are not present in plants, fungi, or prokaryotes. For all class B receptors, the large N-terminal extracellular domain plays a critical role in peptide hormone recognition. VIP and PACAP exert their effects through three G protein-coupled receptors, PACAP-R1, VIP-R1 (vasoactive intestinal receptor type 1, also known as VPAC1) and VIP-R2 (or VPAC2). PACAP-R1 binds only PACAP with high affinity, whereas VIP-R1 and -R2 specifically bind and respond to both VIP and PACAP. VIP and PACAP and their receptors are widely expressed in the brain and periphery. They are upregulated in neurons and immune cells in responses to CNS injury and/or inflammation and exert potent anti-inflammatory effects, as well as play important roles in the control of circadian rhythms and stress responses, among many others. PACAP-R1 is preferentially coupled to a stimulatory G(s) protein, which leads to the activation of adenylate cyclase and thereby increases in intracellular cAMP level. 268 matched cddid_all.tbl CDD cd15988 cd15988 320654 7tmB2_BAI2 brain-specific angiogenesis inhibitor 2, a group VII adhesion GPCR, member of the class B2 family of seven-transmembrane G protein-coupled receptors. Brain-specific angiogenesis inhibitors (BAI1-3) constitute the group VII of cell-adhesion receptors that have been implicated in vascularization of glioblastomas. They belong to the B2 subfamily of class B GPCRs, are predominantly expressed in the brain, and are only present in vertebrates. Three BAIs, like all adhesion receptors, are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. For example, BAI1 N-terminus contain an integrin-binding RGD (Arg-Gly-Asp) motif in addition to five thrombospondin type 1 repeats (TSRs), which are known to regulate the anti-angiogenic activity of thrombospondin-1, whereas BAI2 and BAI3 have four TSRs, but do not possess RGD motifs. The TSRs are functionally involved in cell attachment, activation of latent TGF-beta, inhibition of angiogenesis and endothelial cell migration. The TSRs of BAI1 mediates direct binding to phosphatidylserine, which enables both recognition and internalization of apoptotic cells by phagocytes. Thus, BAI1 functions as a phosphatidylserine receptor that forms a trimeric complex with ELMO and Dock180, leading to activation of Rac-GTPase which promotes the binding and phagocytosis of apoptotic cells. BAI3 can also interact with the ELMO-Dock180 complex to activate the Rac pathway and can also bind to secreted C1ql proteins of the C1Q complement family via its N-terminal TSRs. BAI3 and its ligands C1QL1 are highly expressed during synaptogenesis and are involved in synapse specificity. Moreover, BAI2 acts as a transcription repressor to regulate vascular endothelial growth factor (VEGF) expression through interaction with GA-binding protein gamma (GABP). The N-terminal extracellular domains of all three BAIs also contain an evolutionarily conserved GPCR-autoproteolysis inducing (GAIN) domain, which undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif to generate N- and C-terminal fragments (NTF and CTF), a putative hormone-binding domain (HBD), and multiple N-glycosylation sites. The C-terminus of each BAI subtype ends with a conserved Gln-Thr-Glu-Val (QTEV) motif known to interact with PDZ domain-containing proteins, but only BAI1 possesses a proline-rich region, which may be involved in protein-protein interactions. 291 matched cddid_all.tbl CDD cd15989 cd15989 320655 7tmB2_BAI3 brain-specific angiogenesis inhibitor 3, a group VII adhesion GPCR, member of the class B2 family of seven-transmembrane G protein-coupled receptors. Brain-specific angiogenesis inhibitors (BAI1-3) constitute the group VII of cell-adhesion receptors that have been implicated in vascularization of glioblastomas. They belong to the B2 subfamily of class B GPCRs, are predominantly expressed in the brain, and are only present in vertebrates. Three BAIs, like all adhesion receptors, are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. For example, BAI1 N-terminus contain an integrin-binding RGD (Arg-Gly-Asp) motif in addition to five thrombospondin type 1 repeats (TSRs), which are known to regulate the anti-angiogenic activity of thrombospondin-1, whereas BAI2 and BAI3 have four TSRs, but do not possess RGD motifs. The TSRs are functionally involved in cell attachment, activation of latent TGF-beta, inhibition of angiogenesis and endothelial cell migration. The TSRs of BAI1 mediates direct binding to phosphatidylserine, which enables both recognition and internalization of apoptotic cells by phagocytes. Thus, BAI1 functions as a phosphatidylserine receptor that forms a trimeric complex with ELMO and Dock180, leading to activation of Rac-GTPase which promotes the binding and phagocytosis of apoptotic cells. BAI3 can also interact with the ELMO-Dock180 complex to activate the Rac pathway and can also bind to secreted C1ql proteins of the C1Q complement family via its N-terminal TSRs. BAI3 and its ligands C1QL1 are highly expressed during synaptogenesis and are involved in synapse specificity. Moreover, BAI2 acts as a transcription repressor to regulate vascular endothelial growth factor (VEGF) expression through interaction with GA-binding protein gamma (GABP). The N-terminal extracellular domains of all three BAIs also contain an evolutionarily conserved GPCR-autoproteolysis inducing (GAIN) domain, which undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif to generate N- and C-terminal fragments (NTF and CTF), a putative hormone-binding domain (HBD), and multiple N-glycosylation sites. The C-terminus of each BAI subtype ends with a conserved Gln-Thr-Glu-Val (QTEV) motif known to interact with PDZ domain-containing proteins, but only BAI1 possesses a proline-rich region, which may be involved in protein-protein interactions. 293 matched cddid_all.tbl CDD cd15990 cd15990 320656 7tmB2_BAI1 brain-specific angiogenesis inhibitor 1, a group VII adhesion GPCR, member of the class B2 family of seven-transmembrane G protein-coupled receptors. Brain-specific angiogenesis inhibitors (BAI1-3) constitute the group VII of cell-adhesion receptors that have been implicated in vascularization of glioblastomas. They belong to the B2 subfamily of class B GPCRs, are predominantly expressed in the brain, and are only present in vertebrates. Three BAIs, like all adhesion receptors, are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. For example, BAI1 N-terminus contain an integrin-binding RGD (Arg-Gly-Asp) motif in addition to five thrombospondin type 1 repeats (TSRs), which are known to regulate the anti-angiogenic activity of thrombospondin-1, whereas BAI2 and BAI3 have four TSRs, but do not possess RGD motifs. The TSRs are functionally involved in cell attachment, activation of latent TGF-beta, inhibition of angiogenesis and endothelial cell migration. The TSRs of BAI1 mediates direct binding to phosphatidylserine, which enables both recognition and internalization of apoptotic cells by phagocytes. Thus, BAI1 functions as a phosphatidylserine receptor that forms a trimeric complex with ELMO and Dock180, leading to activation of Rac-GTPase which promotes the binding and phagocytosis of apoptotic cells. BAI3 can also interact with the ELMO-Dock180 complex to activate the Rac pathway and can also bind to secreted C1ql proteins of the C1Q complement family via its N-terminal TSRs. BAI3 and its ligands C1QL1 are highly expressed during synaptogenesis and are involved in synapse specificity. Moreover, BAI2 acts as a transcription repressor to regulate vascular endothelial growth factor (VEGF) expression through interaction with GA-binding protein gamma (GABP). The N-terminal extracellular domains of all three BAIs also contain an evolutionarily conserved GPCR-autoproteolysis inducing (GAIN) domain, which undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif to generate N- and C-terminal fragments (NTF and CTF), a putative hormone-binding domain (HBD), and multiple N-glycosylation sites. The C-terminus of each BAI subtype ends with a conserved Gln-Thr-Glu-Val (QTEV) motif known to interact with PDZ domain-containing proteins, but only BAI1 possesses a proline-rich region, which may be involved in protein-protein interactions. 267 matched cddid_all.tbl CDD cd15991 cd15991 320657 7tmB2_CELSR1 Cadherin EGF LAG seven-pass G-type receptor 1, member of the class B2 family of seven-transmembrane G protein-coupled receptors. The group IV adhesion GPCRs include the cadherin EGF LAG seven-pass G-type receptors (CELSRs) and their Drosophila homolog Flamingo (also known as Starry night). These receptors are also classified as that belongs to the EGF-TM7 group of subfamily B2 adhesion GPCRs, because they contain EGF-like domains. Functionally, the group IV receptors act as key regulators of many physiological processes such as endocrine cell differentiation, neuronal migration, dendrite growth, axon, guidance, lymphatic vessel and valve formation, and planar cell polarity (PCP) during embryonic development. Three mammalian orthologs of Flamingo, Celsr1-3, are widely expressed in the nervous system from embryonic development until the adult stage. Each Celsr exhibits different expression patterns in the developing brain, suggesting that they serve distinct functions. Mutations of CELSR1 cause neural tube defects in the nervous system, while mutations of CELSR2 are associated with coronary heart disease. Moreover, CELSR1 and several other PCP signaling molecules, such as dishevelled, prickle, frizzled, have been shown to be upregulated in B lymphocytes of chronic lymphocytic leukemia patients. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. In the case of CELSR/Flamingo/Starry night, their extracellular domains comprise nine cadherin repeats linked to a series of epidermal growth factor (EGF)-like and laminin globular (G)-like domains. The cadherin repeats contain sequence motifs that mediate calcium-dependent cell-cell adhesion by homophilic interactions. Moreover, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 254 matched cddid_all.tbl CDD cd15992 cd15992 320658 7tmB2_CELSR2 Cadherin EGF LAG seven-pass G-type receptor 2, member of the class B2 family of seven-transmembrane G protein-coupled receptors. The group IV adhesion GPCRs include the cadherin EGF LAG seven-pass G-type receptors (CELSRs) and their Drosophila homolog Flamingo (also known as Starry night). These receptors are also classified as that belongs to the EGF-TM7 group of subfamily B2 adhesion GPCRs, because they contain EGF-like domains. Functionally, the group IV receptors act as key regulators of many physiological processes such as endocrine cell differentiation, neuronal migration, dendrite growth, axon, guidance, lymphatic vessel and valve formation, and planar cell polarity (PCP) during embryonic development. Three mammalian orthologs of Flamingo, Celsr1-3, are widely expressed in the nervous system from embryonic development until the adult stage. Each Celsr exhibits different expression patterns in the developing brain, suggesting that they serve distinct functions. Mutations of CELSR1 cause neural tube defects in the nervous system, while mutations of CELSR2 are associated with coronary heart disease. Moreover, CELSR1 and several other PCP signaling molecules, such as dishevelled, prickle, frizzled, have been shown to be upregulated in B lymphocytes of chronic lymphocytic leukemia patients. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. In the case of CELSR/Flamingo/Starry night, their extracellular domains comprise nine cadherin repeats linked to a series of epidermal growth factor (EGF)-like and laminin globular (G)-like domains. The cadherin repeats contain sequence motifs that mediate calcium-dependent cell-cell adhesion by homophilic interactions. Moreover, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 255 matched cddid_all.tbl CDD cd15993 cd15993 320659 7tmB2_CELSR3 Cadherin EGF LAG seven-pass G-type receptor 3, member of the class B2 family of seven-transmembrane G protein-coupled receptors. The group IV adhesion GPCRs include the cadherin EGF LAG seven-pass G-type receptors (CELSRs) and their Drosophila homolog Flamingo (also known as Starry night). These receptors are also classified as that belongs to the EGF-TM7 group of subfamily B2 adhesion GPCRs, because they contain EGF-like domains. Functionally, the group IV receptors act as key regulators of many physiological processes such as endocrine cell differentiation, neuronal migration, dendrite growth, axon, guidance, lymphatic vessel and valve formation, and planar cell polarity (PCP) during embryonic development. Three mammalian orthologs of Flamingo, Celsr1-3, are widely expressed in the nervous system from embryonic development until the adult stage. Each Celsr exhibits different expression patterns in the developing brain, suggesting that they serve distinct functions. Mutations of CELSR1 cause neural tube defects in the nervous system, while mutations of CELSR2 are associated with coronary heart disease. Moreover, CELSR1 and several other PCP signaling molecules, such as dishevelled, prickle, frizzled, have been shown to be upregulated in B lymphocytes of chronic lymphocytic leukemia patients. Celsr3 is expressed in both the developing and adult mouse brain. It has been functionally implicated in proper neuronal migration and axon guidance in the CNS. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. In the case of CELSR/Flamingo/Starry night, their extracellular domains comprise nine cadherin repeats linked to a series of epidermal growth factor (EGF)-like and laminin globular (G)-like domains. The cadherin repeats contain sequence motifs that mediate calcium-dependent cell-cell adhesion by homophilic interactions. Moreover, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 254 matched cddid_all.tbl CDD cd15994 cd15994 320660 7tmB2_GPR111_115 orphan adhesion receptors GPR111 and GPR115, member of the class B2 family of seven-transmembrane G protein-coupled receptors. GPR111 and GPR115 are highly homologous orphan receptors that belong to group VI adhesion-GPCRs along with GPR110, GPR113, and GPR116. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in ligand recognition as well as cell-cell adhesion and cell-matrix interactions, linked by a stalk region to a class B seven-transmembrane domain. In addition, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR-autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. However, several adhesion GPCRs, including GPR 111, GPR115, and CELSR1, are predicted to be non-cleavable at the GAIN domain because of the lack of a consensus catalytic triad sequence (His-Leu-Ser/Thr) within their GPS. Both GPR111 and GPR5 are present only in land-living animals and are predominantly expressed in the developing skin. 267 matched cddid_all.tbl CDD cd15995 cd15995 320661 7tmB2_GPR56 orphan adhesion receptor GPR56, member of the class B2 family of seven-transmembrane G protein-coupled receptors. GPR56 is an orphan receptor that has been classified as that belongs to the Group VIII of adhesion GPCRs. Other members of the Group VII include orphan GPCRs such as GPR64, GPR97, GPR112, GPR114, and GPR126. GPR56 is involved in the regulation of oligodendrocyte development and myelination in the central nervous system via coupling to G(12/13) proteins, which leads to the activation of RhoA GTPase. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. Furthermore, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 269 matched cddid_all.tbl CDD cd15996 cd15996 320662 7tmB2_GPR126 orphan adhesion receptor GPR126, member of the class B2 family of seven-transmembrane G protein-coupled receptors. GPR126 is an orphan receptor that has been classified as that belongs to the Group VIII of adhesion GPCRs. Other members of the Group VII include orphan GPCRs such as GPR56, GPR64, GPR97, GPR112, and GPR114. GPR126 is required in Schwann cells for proper differentiation and myelination via G-Protein Activation. GPR126 is believed to couple to G(s)-protein, which leads to activation of adenylate cyclase for cAMP production. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. Furthermore, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 271 matched cddid_all.tbl CDD cd15997 cd15997 320663 7tmB2_GPR112 Probable G protein-coupled receptor 112, member of the class B2 family of seven-transmembrane G protein-coupled receptors. GPR112 is an orphan receptor that has been classified as that belongs to the Group VIII of adhesion GPCRs. Other members of the Group VII include orphan GPCRs such as GPR56, GPR64, GPR97, GPR114, and GPR126. GPR112 is specifically expressed in normal enterochromatin cells and gastrointestinal neuroendocrine carcinoma cells, but its biological function is unknown. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. Furthermore, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 269 matched cddid_all.tbl CDD cd15998 cd15998 320664 7tmB2_GPR124 G protein-coupled receptor 124, member of the class B2 family of seven-transmembrane G protein-coupled receptors. GPR124 is an orphan receptor that has been classified as that belongs to the group III of adhesion GPCRs, which also includes orphan GPR123 and GPR125. GPR124, also known as tumor endothelial marker 5 (TEM5), is highly expressed in tumor vessels and in the vasculature of the developing embryo. GPR124 is essentially required for proper angiogenic sprouting into neural tissue, CNS-specific vascularization, and formation of the blood-brain barrier. GPR124 interacts with the PDZ domain of DLG1 (discs large homolog 1) through its PDZ-binding motif. Recently, studies of double-knockout mice showed that GPR124 functions as a co-activator of Wnt7a/Wnt7b-dependent beta-catenin signaling in brain endothelium. Moreover, WNT7-stimulated beta-catenin signaling is regulated by GPR124's intracellular PDZ binding motif and leucine-rich repeats (LRR) in its N-terminal extracellular domain. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. Furthermore, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 268 matched cddid_all.tbl CDD cd15999 cd15999 320665 7tmB2_GPR125 G protein-coupled receptor 125, member of the class B2 family of seven-transmembrane G protein-coupled receptors. GPR125 is an orphan receptor that has been classified as that belongs to the group III of adhesion GPCRs, which also includes orphan receptors GPR123 and GPR124. GPR125 directly interacts with dishevelled (Dvl) via its intracellular C-terminus, and together, GPR125 and Dvl recruit a subset of planar cell polarity (PCP) components into membrane subdomains, a prerequisite for activation of Wnt/PCP signaling. Thus, GPR125 influences the noncanonical WNT/PCP pathway, which does not involve beta-catenin, through interacting with and modulating the distribution of Dvl. The adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. Furthermore, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 312 matched cddid_all.tbl CDD cd16000 cd16000 320666 7tmB2_GPR123 G protein-coupled receptor 123, member of the class B2 family of seven-transmembrane G protein-coupled receptors. GPR123 is an orphan receptor that has been classified as that belongs to the group III of adhesion GPCRs, and also includes orphan receptors GPR124 and GPR125. GPR123 is predominantly expressed in the CNS including thalamus, brain stem and regions containing large pyramidal cells, yet its biological function remains to be determined. Adhesion receptors are characterized by the presence of large N-terminal extracellular domains containing multiple adhesion motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, that are coupled to a class B seven-transmembrane domain. Furthermore, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR- autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 275 matched cddid_all.tbl CDD cd16001 cd16001 320667 7tmA_P2Y3-like P2Y purinoceptor 3-like proteins, member of the class A family of seven-transmembrane G protein-coupled receptors. P2Y3-like proteins are an uncharacterized group that belongs to the G(i) class of a family of purinergic G-protein coupled receptors. The P2Y receptor family is composed of eight subtypes, which are activated by naturally occurring extracellular nucleotides such as ATP, ADP, UTP, UDP, and UDP-glucose. These eight receptors are ubiquitous in human tissues and can be further classified into two subfamilies based on sequence homology and second messenger coupling: a subfamily of five P2Y1-like receptors (P2Y1, P2Y2, P2Y4, P2Y6, and P2Y11Rs) that are coupled to G(q) protein to activate phospholipase C (PLC) and a second subfamily of three P2Y12-like receptors (P2Y12, P2YR13, and P2Y14Rs) that are coupled to G(i) protein to inhibit adenylate cyclase. Several cloned subtypes, such as P2Y3, P2Y5, and P2Y7-10, are not functional mammalian nucleotide receptors. The native agonists for P2Y receptors are: ATP (P2Y2, P2Y12), ADP (P2Y1, P2Y12, and P2Y13), UTP (P2Y2, P2Y4), UDP (P2Y6, P2Y14), and UDP-glucose (P2Y14). 284 matched cddid_all.tbl CDD cd16002 cd16002 320668 7tmA_NK1R neurokinin 1 receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. The neurokinin 1 receptor (NK1R), also known as tachykinin receptor 1 (TACR1) or substance P receptor (SPR), is a G-protein coupled receptor found in the mammalian central nervous and peripheral nervous systems. The tachykinins act as excitatory transmitters on neurons and cells in the gastrointestinal tract. The TKs are characterized by a common five-amino acid C-terminal sequence, Phe-X-Gly-Leu-Met-NH2, where X is a hydrophobic residue. The three major mammalian tachykinins are substance P (SP), neurokinin A (NKA), and neurokinin B (NKB). The physiological actions of tachykinins are mediated through three types of receptors: neurokinin receptor type 1 (NK1R), NK2R, and NK3R. SP is a high-affinity endogenous ligand for NK1R, which interacts with the Gq protein and activates phospholipase C, leading to elevation of intracellular calcium. SP is an extremely potent vasodilator through endothelium dependent mechanism and is released from the autonomic sensory nerves. NK2R is a high-affinity receptor for NKA, the tachykinin neuropeptide substance K. SP and NKA are found in the enteric nervous system and mediate in the regulation of gastrointestinal motility, secretion, vascular permeability, and pain perception. 284 matched cddid_all.tbl CDD cd16003 cd16003 320669 7tmA_NKR_NK3R neuromedin-K receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. The neuromedin-K receptor (NKR), also known as tachykinin receptor 3 (TACR3) or neurokinin B receptor or NK3R, is a G-protein coupled receptor that specifically binds to neurokinin B. The tachykinins (TKs) act as excitatory transmitters on neurons and cells in the gastrointestinal tract. The TKs are characterized by a common five-amino acid C-terminal sequence, Phe-X-Gly-Leu-Met-NH2, where X is a hydrophobic residue. The three major mammalian tachykinins are substance P (SP), neurokinin A (NKA), and neurokinin B (NKB). The physiological actions of tachykinins are mediated through three types of receptors: neurokinin receptor type 1 (NK1R), NK2R, and NK3R. NK3R is activated by its high-affinity ligand, NKB, which is primarily involved in the central nervous system and plays a critical role in the regulation of gonadotropin hormone release and the onset of puberty. 282 matched cddid_all.tbl CDD cd16004 cd16004 320670 7tmA_SKR_NK2R substance-K receptor, member of the class A family of seven-transmembrane G protein-coupled receptors. The substance-K receptor (SKR), also known as tachykinin receptor 2 (TACR2) or neurokinin A receptor or NK2R, is a G-protein coupled receptor that specifically binds to neurokinin A. The tachykinins are widely distributed throughout the mammalian central and peripheral nervous systems and act as excitatory transmitters on neurons and cells in the gastrointestinal tract. The TKs are characterized by a common five-amino acid C-terminal sequence, Phe-X-Gly-Leu-Met-NH2, where X is a hydrophobic residue. The three major mammalian tachykinins are substance P (SP), neurokinin A (NKA), and neurokinin B (NKB). The physiological actions of tachykinins are mediated through three types of receptors: neurokinin receptor type 1 (NK1R), NK2R, and NK3R. SP is a high-affinity endogenous ligand for NK1R, which interacts with the Gq protein and activates phospholipase C, leading to elevation of intracellular calcium. NK2R is a high-affinity receptor for NKA, the tachykinin neuropeptide substance K. SP and NKA are found in the enteric nervous system and mediate the regulation of gastrointestinal motility, secretion, vascular permeability, and pain perception. 285 matched cddid_all.tbl CDD cd16005 cd16005 320671 7tmB2_Latrophilin-3 Latrophilin-3, member of the class B2 family of seven-transmembrane G protein-coupled receptors. Latrophilins (also called lectomedins or latrotoxin receptors) belong to Group I adhesion GPCRs, which also include ETL (EGF-TM7-latrophilin-related protein). These receptors are a member of the adhesion family (subclass B2) that belongs to the class B GPCRs. Three subtypes of latrophilins have been identified: LPH1 (latrophilin-1), LPH2, and LPH3. The latrophilin-1 is a brain-specific calcium-independent receptor of alpha-latrotoxin, a potent presynaptic neurotoxin from the venom of the black widow spider that induces massive neurotransmitter release from sensory and motor neurons as well as endocrine cells, leading to nerve-terminal degeneration. Latrophilin-2 and -3, although sharing strong sequence homology to latrophilin-1, do not bind alpha-latrotoxin. While latrophilin-3 is also brain specific, latrophilin-2 is ubiquitously distributed. The endogenous ligands for these two receptors are unknown. ETL, a seven transmembrane receptor containing EGF-like repeats is highly expressed in heart, where developmentally regulated, as well as in normal smooth cells. The function of the ETL is unknown. All adhesion GPCRs possess large N-terminal extracellular domains containing multiple structural motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, coupled to a seven-transmembrane domain. In addition, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR-autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 258 matched cddid_all.tbl CDD cd16006 cd16006 320672 7tmB2_Latrophilin-2 Latrophilin-2, member of the class B2 family of seven-transmembrane G protein-coupled receptors. Latrophilins (also called lectomedins or latrotoxin receptors) belong to Group I adhesion GPCRs, which also include ETL (EGF-TM7-latrophilin-related protein). These receptors are a member of the adhesion family (subclass B2) that belongs to the class B GPCRs. Three subtypes of latrophilins have been identified: LPH1 (latrophilin-1), LPH2, and LPH3. The latrophilin-1 is a brain-specific calcium-independent receptor of alpha-latrotoxin, a potent presynaptic neurotoxin from the venom of the black widow spider that induces massive neurotransmitter release from sensory and motor neurons as well as endocrine cells, leading to nerve-terminal degeneration. Latrophilin-2 and -3, although sharing strong sequence homology to latrophilin-1, do not bind alpha-latrotoxin. While latrophilin-3 is also brain specific, latrophilin-2 is ubiquitously distributed. The endogenous ligands for these two receptors are unknown. ETL, a seven transmembrane receptor containing EGF-like repeats is highly expressed in heart, where developmentally regulated, as well as in normal smooth cells. The function of the ETL is unknown. All adhesion GPCRs possess large N-terminal extracellular domains containing multiple structural motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, coupled to a seven-transmembrane domain. In addition, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR-autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 258 matched cddid_all.tbl CDD cd16007 cd16007 320673 7tmB2_Latrophilin-1 Latrophilin-1, member of the class B2 family of seven-transmembrane G protein-coupled receptors. Latrophilins (also called lectomedins or latrotoxin receptors) belong to Group I adhesion GPCRs, which also include ETL (EGF-TM7-latrophilin-related protein). These receptors are a member of the adhesion family (subclass B2) that belongs to the class B GPCRs. Three subtypes of latrophilins have been identified: LPH1 (latrophilin-1), LPH2, and LPH3. The latrophilin-1 is a brain-specific calcium-independent receptor of alpha-latrotoxin, a potent presynaptic neurotoxin from the venom of the black widow spider that induces massive neurotransmitter release from sensory and motor neurons as well as endocrine cells, leading to nerve-terminal degeneration. Latrophilin-2 and -3, although sharing strong sequence homology to latrophilin-1, do not bind alpha-latrotoxin. While latrophilin-3 is also brain specific, latrophilin-2 is ubiquitously distributed. The endogenous ligands for these two receptors are unknown. ETL, a seven transmembrane receptor containing EGF-like repeats is highly expressed in heart, where developmentally regulated, as well as in normal smooth cells. The function of the ETL is unknown. All adhesion GPCRs possess large N-terminal extracellular domains containing multiple structural motifs, which play critical roles in cell-cell adhesion and cell-matrix interactions, coupled to a seven-transmembrane domain. In addition, almost all adhesion receptors, except GPR123, contain an evolutionarily conserved GPCR-autoproteolysis inducing (GAIN) domain that undergoes autoproteolytic processing at the GPCR proteolysis site (GPS) motif located immediately N-terminal to the first transmembrane region, to generate N- and C-terminal fragments (NTF and CTF), which may serve important biological functions. 258 matched cddid_all.tbl CDD cd16009 cd16009 293733 PPM Bacterial phosphopentomutase. Bacterial phosphopentomutases (PPMs) are alkaline phosphatase superfamily members that interconvert alpha-D-ribose 5-phosphate (ribose 5-phosphate) and alpha-D-ribose 1-phosphate (ribose 1-phosphate). This reaction bridges glucose metabolism and RNA biosynthesis. PPM is a Mn(2+)-dependent enzyme and protein phosphorylation activates the enzyme. 382 matched cddid_all.tbl CDD cd16010 cd16010 293734 iPGM 2 3 bisphosphoglycerate independent phosphoglycerate mutase iPGM. The 2,3-diphosphoglycerate- independent phosphoglycerate mutase (iPGM) catalyzes the interconversion of 3-phosphoglycerate (3PGA) and 2-phosphoglycerate (2PGA). They are the predominant PGM in plants and some other bacteria, including endospore forming Gram-positive bacteria and their close relatives. The two steps catalysis is a phosphatase reaction removing the phosphate from 2- or 3-phosphoglycerate, generating an enzyme-bound phosphoserine intermediate, followed by a phosphotransferase reaction as the phosphate is transferred from the enzyme back to the glycerate moiety. The iPGM exists as a dimer, each monomer binding 2 magnesium atoms, which are essential for enzymatic activity. 503 matched cddid_all.tbl CDD cd16011 cd16011 293735 iPGM_like uncharacterized subfamily of alkaline phosphatase, homologous to 2 3 bisphosphoglycerate independent phosphoglycerate mutase (iPGM) and bacterial phosphopentomutases. The proteins in this subfamily of alkaline phosphatase are not characterized. Their sequences show similarity to 2 3 bisphosphoglycerate independent phosphoglycerate mutase (iPGM) which catalyzes the interconversion of 3-phosphoglycerate to 2-phosphoglycerate, and to bacterial phosphopentomutases (PPMs) which interconvert alpha-D-ribose 5-phosphate (ribose 5-phosphate) and alpha-D-ribose 1-phosphate (ribose 1-phosphate). 368 matched cddid_all.tbl CDD cd16012 cd16012 293736 ALP Alkaline Phosphatase. Alkaline phosphatases are non-specific membrane-bound phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH. Alkaline phosphatase exists as a dimer, each monomer binding 2 zinc atoms and one magnesium atom, which are essential for enzymatic activity. Mammalian alkaline phosphatase is divided into four isozymes depending upon the site of tissue expression. They are Intestinal ALP, Placental ALP, Germ cell ALP and tissue nonspecific alkaline phosphatase or liver/bone/kidney (L/B/K) ALP. 283 matched cddid_all.tbl CDD cd16013 cd16013 293737 AcpA acid phosphatase A. Acid phosphatase A catalyzes the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at low pH. AcpA hydrolyzes a variety of substrates, including p-nitrophenylphosphate (pNPP), p-nitrophenylphosphorylcholine (pNPPC), peptides containing phosphotyrosine, inositol phosphates, AMP, ATP, fructose 1,6-bisphosphate, glucose and fructose 6-phosphates, NADP, and ribose 5-phosphate. AcpA is distinct from histidine ACPs and purple ACPs, as well as class A, B, and C bacterial nonspecific ACPs. 370 matched cddid_all.tbl CDD cd16014 cd16014 293738 PLC non-hemolytic phospholipase C. Nonhemolytic Phospholipases C is produced by pathogenic bacterial. The toxic phospholipases C can interact with eukaryotic cell membranes and hydrolyze phosphatidylcholine and sphingomyelin, leading to cell lysis. 287 matched cddid_all.tbl CDD cd16015 cd16015 293739 LTA_synthase Lipoteichoic acid synthase like. Lipoteichoic acid (LTA) is an important cell wall polymer found in Gram-positive bacteria. It may contain long chains of ribitol or glycerol phosphate. LTA synthase catalyzes the reaction to extend the polymer by the repeated addition of glycerolphosphate (GroP) subunits to the end of the growing chain. 283 matched cddid_all.tbl CDD cd16016 cd16016 293740 AP-SPAP SPAP is a subclass of alkaline phosphatase (AP). Alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH. Alkaline phosphatase exists as a dimer, each monomer binding 2 zinc atoms and one magnesium atom, which are essential for enzymatic activity. Although SPAP is a subclass of alkaline phosphatase, SPAP has many differences from other APs: 1) the catalytic residue is a threonine instead of serine, 2) there is no binding pocket for the third metal ion, and 3) the arginine residue forming bidentate hydrogen bonding is deleted in SPAP. A lysine and an asparagine residue, recruited together for the first time into the active site, bind the substrate phosphoryl group in a manner not observed before in any other AP. 457 matched cddid_all.tbl CDD cd16017 cd16017 293741 LptA Lipooligosaccharide Phosphoethanolamine Transferase A (LptA) or Lipid A Phosphoethanolamine Transferase. Lipooligosaccharide Phosphoethanolamine Transferase A (LptA) or Lipid A Phosphoethanolamine Transferase catalyzes the modification of the lipid A headgroups by phosphoethanolamine (PEA) or 4-amino-arabinose residues. Lipopolysaccharides, also called endotoxins, protect bacterial pathogens from antimicrobial peptides and have roles in virulence. The PEA modified lipid A increases resistance to the cationic cyclic polypeptide antibiotic, polymyxin. Lipid A PEA transferases usually consist of a transmembrane domain anchoring the enzyme to the periplasmic face of the cytoplasmic membrane. 288 matched cddid_all.tbl CDD cd16018 cd16018 293742 Enpp Ectonucleotide pyrophosphatase/phosphodiesterase, also called autotaxin. Ecto-nucleotide pyrophosphatases/phosphodiesterases (ENPPs) hydrolyze 5'-phosphodiester bonds in nucleotides and their derivatives, resulting in the release of 5'-nucleotide monophosphates. ENPPs have multiple physiological roles, including nucleotide recycling, modulation of purinergic receptor signaling, regulation of extracellular pyrophosphate levels, stimulation of cell motility, and possible roles in regulation of insulin receptor (IR) signaling and activity of ecto-kinases. The eukaryotic ENPP family contains at least five members that have different tissue distribution and physiological roles. 267 matched cddid_all.tbl CDD cd16019 cd16019 293743 GPI_EPT GPI ethanolamine phosphate transferase. Ethanolamine phosphate transferase is involved in glycosylphosphatidylinositol-anchor biosynthesis. It catalyzes the transfer of ethanolamine phosphate to the first alpha-1,4-linked mannose of the glycosylphosphatidylinositol precursor of GPI-anchor. It may act as suppressor of replication stress and chromosome missegregation. 292 matched cddid_all.tbl CDD cd16020 cd16020 293744 GPI_EPT_1 GPI ethanolamine phosphate transferase 1; PIG-N. Ethanolamine phosphate transferase is involved in glycosylphosphatidylinositol-anchor biosynthesis. It catalyzes the transfer of ethanolamine phosphate to the first alpha-1,4-linked mannose of the glycosylphosphatidylinositol precursor of GPI-anchor. It may act as suppressor of replication stress and chromosome missegregation. 294 matched cddid_all.tbl CDD cd16021 cd16021 293745 ALP_like uncharacterized Alkaline phosphatase subfamily. Alkaline phosphatases are non-specific phosphomonoesterases that catalyze the hydrolysis reaction via a phosphoseryl intermediate to produce inorganic phosphate and the corresponding alcohol, optimally at high pH. Alkaline phosphatase exists as a dimer, each monomer binding 2 zinc atoms and one magnesium atom, which are essential for enzymatic activity. 278 matched cddid_all.tbl CDD cd16022 cd16022 293746 sulfatase_like sulfatase. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 236 matched cddid_all.tbl CDD cd16023 cd16023 293747 GPI_EPT_3 GPI ethanolamine phosphate transferase 3, PIG-O. Ethanolamine phosphate transferase is involved in glycosylphosphatidylinositol-anchor biosynthesis. It catalyzes the transfer of ethanolamine phosphate to the first alpha-1,4-linked mannose of the glycosylphosphatidylinositol precursor of GPI-anchor. It may act as suppressor of replication stress and chromosome missegregation. 289 matched cddid_all.tbl CDD cd16024 cd16024 293748 GPI_EPT_2 GPI ethanolamine phosphate transferase 2; PIG-G. Ethanolamine phosphate transferase is involved in glycosylphosphatidylinositol-anchor biosynthesis. It catalyzes the transfer of ethanolamine phosphate to the first alpha-1,4-linked mannose of the glycosylphosphatidylinositol precursor of GPI-anchor. It may act as suppressor of replication stress and chromosome missegregation. 274 matched cddid_all.tbl CDD cd16025 cd16025 293749 PAS_like Bacterial Arylsulfatase of Pseudomonas aeruginosa and related proteins. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 402 matched cddid_all.tbl CDD cd16026 cd16026 293750 GALNS_like galactosamine-6-sulfatase; also known as N-acetylgalactosamine-6-sulfatase (GALNS). Lysosomal galactosamine-6-sulfatase removes sulfate groups from a terminal N-acetylgalactosamine-6-sulfate (or galactose-6-sulfate) in mucopolysaccharides such as keratan sulfate and chondroitin-6-sulfate. Defects in GALNS lead to accumulation of substrates, resulting in the development of the lysosomal storage disease mucopolysaccharidosis IV A. 399 matched cddid_all.tbl CDD cd16027 cd16027 293751 SGSH N-sulfoglucosamine sulfohydrolase (SGSH; sulfamidase). N-sulfoglucosamine sulfohydrolase (SGSH) belongs to the sulfatase family and catalyses the cleavage of N-linked sulfate groups from the GAGs heparin sulfate and heparin. The active site is characterized by the amino-acid sequence motif C(X)PSR that is highly conserved among most sulfatases. The cysteine residue is post-translationally converted to a formylglycine (FGly) residue, which is crucial for the catalytic process. Loss of function of SGSH results a disease called mucopolysaccharidosis type IIIA (Sanfilippo A syndrome), a fatal childhood-onset neurodegenerative disease with mild facial, visceral and skeletal abnormalities. 373 matched cddid_all.tbl CDD cd16028 cd16028 293752 PMH Phosphonate monoester hydrolase/phosphodiesterase. Phosphonate monoester hydrolase/phosphodiesterase hydrolyses phosphonate monoesters or phosphate diesters using a posttranslationally formed formylglycine as the catalytic nucleophile. PMH is the member of the alkaline phosphatase superfamily. The structure of PMH is more homologous to arylsulfatase than alkaline phosphatase. Sulfatases also use formylglycine as catalytic nucleophile. 449 matched cddid_all.tbl CDD cd16029 cd16029 293753 4-S N-acetylgalactosamine 4-sulfatase, also called arylsulftase B. Sulfatases catalyze the hydrolysis of sulfuric acid esters from a wide variety of substrates. N-acetylgalactosamine 4-sulfatase catalyzes the removal of the sulfate ester group from position 4 of an N-acetylgalactosamine sugar at the non-reducing terminus of the polysaccharide in the degradative pathways of the glycosaminoglycans dermatan sulfate and chondroitin-4-sulfate. N-acetylgalactosamine 4-sulfatase is a lysosomal enzyme. 393 matched cddid_all.tbl CDD cd16030 cd16030 293754 iduronate-2-sulfatase iduronate-2-sulfatase. Iduronate 2-sulfatase is a sulfatase enzyme that catalyze the hydrolysis of sulfate ester bonds from a wide variety of substrates, including steroids, carbohydrates and proteins. Iduronate 2-sulfatase is required for the lysosomal degradation of heparan sulfate and dermatan sulfate. Mutations in the iduronate 2-sulfatase gene that result in enzymatic deficiency lead to the sex-linked mucopolysaccharidosis type II, also known as Hunter syndrome. 435 matched cddid_all.tbl CDD cd16031 cd16031 293755 G6S_like unchracterized sulfatase homologous to glucosamine (N-acetyl)-6-sulfatase(G6S, GNS). N-acetylglucosamine-6-sulfatase also known as glucosamine (N-acetyl)-6-sulfatase hydrolyzes of the 6-sulfate groups of the N-acetyl-D-glucosamine 6-sulfate units of heparan sulfate and keratan sulfate. Deficiency of N-acetylglucosamine-6-sulfatase results in the disease of Sanfilippo Syndrome type IIId or Mucopolysaccharidosis III (MPS-III), a rare autosomal recessive lysosomal storage disease. 429 matched cddid_all.tbl CDD cd16032 cd16032 293756 choline-sulfatase choline-sulfatase. Choline-sulphatase is involved in the synthesis of glycine betaine from choline. The symbiotic soil bacterium Rhizobium meliloti can synthesize glycine betaine from choline-O-sulphate and choline to protect itself from osmotic stress. This biosynthetic pathway is encoded by the betICBA locus, which comprises a regulatory gene, betI, and three structural genes, betC (choline sulfatase), betB (betaine aldehyde dehydrogenase), and betA (choline dehydrogenase). betICBA genes constitute a single operon. 327 matched cddid_all.tbl CDD cd16033 cd16033 293757 sulfatase_like uncharacterized sulfatase subfamily. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 411 matched cddid_all.tbl CDD cd16034 cd16034 293758 sulfatase_like uncharacterized sulfatase subfamily. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 399 matched cddid_all.tbl CDD cd16035 cd16035 293759 sulfatase_like uncharacterized sulfatase subfamily. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 311 matched cddid_all.tbl CDD cd16037 cd16037 293760 sulfatase_like uncharacterized sulfatase subfamily. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 321 matched cddid_all.tbl CDD cd16039 cd16039 277186 PHD_SPP1 PHD finger found in Set1 complex component SPP1. Set1C component SPP1, also called COMPASS component Spp1, or Complex proteins associated with set1 protein Spp1, or Suppressor of PRP protein 1, is a component of the COMPASS complex that links histone methylation to initiation of meiotic recombination. It induces double-strand break (DSB) formation by tethering to recombinationally cold regions. SPP1 interacts with H3K4me3 and Mer2, a protein required for DSB formation, to promote recruitment of potential meiotic DSB sites to the chromosomal axis. SPP1 contains a PHD finger, a zinc binding motif. 46 matched cddid_all.tbl CDD cd16040 cd16040 294002 SPRY_PRY_SNTX Stonustoxin subunit alpha or SNTX subunit alpha. This domain, consisting of the distinct N-terminal PRY subdomain followed by the SPRY subdomain, is found at the C-terminus of Stonustoxin alpha proteins. Stonustoxin (SNTX) is a multifunctional lethal protein isolated from venom elaborated by the stonefish. It comprises two subunits, termed alpha and beta. SNTX elicits an array of biological responses, particularly a potent hypotension and respiratory difficulties. 180 matched cddid_all.tbl CDD cd16074 cd16074 293880 OCRE OCRE domain. The OCRE (OCtamer REpeat) domain contains 5 repeats of an 8-residue motif, which were shown to form beta-strands. Based on the architectures of proteins containing OCRE domains, a role in RNA metabolism and/or signalling has been proposed. 54 matched cddid_all.tbl CDD cd16075 cd16075 293922 ORC6_CTD C-terminal domain of the eukaryotic origin recognition complex subunit ORC6. In eukaryotes, a complex consisting of six subunits promotes the onset of DNA replication. The 6th subunit, ORC6, does not belong to the wider AAA+ family of nucleotide hydrolases, but contains a tandemly repeated domain resembling the transcription factor TFIIB, as well as this C-terminal domain which harbors a helical segment that is responsible for interactions with the complex by binding to ORC3. Mutations in this C-terminal helix interfere with the formation of the ORC and have been linked to Meier-Gorlin syndrome, a dwarfism disorder. 53 matched cddid_all.tbl CDD cd16076 cd16076 293923 TSPcc Coiled coil region of thrombospondin. This domain family contains coiled coil region of subgroup B of thrombospondins, comprising TSP-3, TSP-4, and TSP-5, that assemble as pentamers. This region is located adjacent to the N-terminal domain (NTD) of thrombospondin (TSP), that mediates co-translational oligomerization via formation of a left-handed super-helix which binds hydrophilic signaling molecules such as vitamin D3 and vitamin A. Pentameric TSPs are stabilized by inter-subunit disulfide bonds formed between cysteine residues adjacent to the C-terminal end. TSP-5 is also known as cartilage oligomeric matrix protein (COMP). TSPs comprise a conserved family of extracellular, oligomeric, multidomain, calcium-binding glycoproteins. In mammals, they have several complex tissue-specific roles, including activities in wound healing and angiogenesis, connective tissue organization, vessel wall biology, and synaptogenesis, all mechanistically derived from interactions with cell surfaces, cytokines, growth factors, or components of the extracellular matrix (ECM) that together regulate many aspects of cell phenotype. In invertebrates, TSPs may have ancient functions such as bridging activities in cell-cell and cell-ECM interactions. Most protostomes and inferred basal metazoa encode a single TSP with the general domain organization of subgroup B TSPs and with a pentamerizing coiled coil. 40 matched cddid_all.tbl CDD cd16077 cd16077 293924 TSP-5cc Coiled coil region of thrombospondin-5 (TSP-5). This family contains the N-terminal coiled coil region of TSP-5, also known as cartilage oligomeric matrix protein (COMP). It forms a pentameric left-handed coiled coil (COMPcc) with a channel that is a unique carrier for lipophilic compounds. It is known to bind hydrophilic signaling molecules such as vitamin D3 and vitamin A, making it a possible targeted drug delivery system. TSP-5/COMP is expressed in all types of cartilage as well as in the vitreous of the eye, tendons, vascular smooth muscle cells, and heart. The pentamer is stabilized by inter-subunit disulfide bonds formed between cysteine residues adjacent to the C-terminal end of the coiled coil region. TSP-5 is essential for modulating the phenotypic transition of vascular smooth muscle cells and vascular remodeling. Mutations in TSP-5 result in two different inherited chondrodysplasias and osteoarthritic phenotypes: pseudoachondroplasia and multiple epithelial dysplasia. Deficiency of TSP-5 causes dilated cardiomyopathy (DCM), a common cause of congestive heart failure. Early increase in serum TSP-5 is associated with joint damage progression in patients with rheumatoid arthritis, thus representing a novel indicator of an activated destructive process in the joint. 43 matched cddid_all.tbl CDD cd16079 cd16079 293925 TSP-3cc Coiled coil region of thrombospondin-3 (TSP-3). This family contains the N-terminal coiled coil region of TSP-3, which is highly expressed in osteosarcomas and associated with metastasis. TSP-3, along with TSP-5 and type IX collagen, is also expressed in the growth plate and all operate in concert and participate in growth plate organization that directly modulates linear growth. It forms a pentameric left-handed coiled coil with a channel that is a unique carrier for lipophilic compounds. The pentamer is stabilized by inter-subunit disulfide bonds formed between cysteine residues adjacent to the C-terminal end of the coiled coil region. TSP-3 knockout mice have been shown to display accelerated endochondral ossification and increased trabecular bone in the femoral head. 43 matched cddid_all.tbl CDD cd16080 cd16080 293926 TSP-4cc Coiled coil region of thrombospondin-4 (TSP-4). This family contains the N-terminal coiled coil region of TSP-4, which is abundantly expressed in tendon and muscle, as well as in neural and osteogenic tissues, and has also been detected in brain capillaries. It forms a pentameric left-handed coiled coil with a channel that is a unique carrier for lipophilic compounds. The pentamer is stabilized by inter-subunit disulfide bonds formed between cysteine residues adjacent to the C-terminal end of the coiled coil region. TSP-4 regulates the composition of the deposition of extracellular matrix (ECM) in tendon and skeletal muscle. The absence of TSP-4 alters the organization, composition and physiological functions of these tissues. TSP-4 deficiency causes incorrect modification of heparan-sulfate (HS), resulting in decreased activity of lipoprotein lipase (LpL) and loss of beta-glycan; HS is involved in a wide variety of cellular functions, LpL is an endothelial enzyme responsible for the uptake and hydrolysis of lipoproteins, and beta-glycan has inhibiting effect on TGF-beta signaling in skeletal muscle. The human gene THBS4 that encodes for TSP-4 contains a single nucleotide polymorphism (SNP), which is expressed at high frequency in Caucasians and associated with a significantly increased risk of premature myocardial infarction. TSP-4 also binds stromal interaction molecule 1 (STIM1), a transmembrane protein that functions in the endoplasmic reticulum (ER), and regulates calcium channel activity. Studies show that TSP-4 may act as an organizer of adhesive and axon outgrowth-promoting molecules in the ECM to optimize retinal ganglion cell responses. TSP-4 is also involved in the post-translational modification of collagen and may assist in collagen fibril assembly. 44 matched cddid_all.tbl CDD cd16081 cd16081 293927 TSPcc_insect Coiled coil region of thrombospondin in protostomes. This family contains the N-terminal coiled coil region of thrombospondin (TSP) in some protostomes, which suggest ancient functions that include bridging activities in cell-cell and cell-ECM interactions. It appears that most protostomes and inferred basal metazoa encode a single TSP with the general domain organization of subgroup B TSPs and with a pentamerizing coiled coil. This region has heparin-binding activity and is a component of extracellular matrix (ECM), showing that the pentameric TSPs are of earlier origin and that the trimeric TSP subfamily A form is associated with higher chordates. The left-handed coiled coil pentamer forms a channel that is a unique carrier for lipophilic compounds, and is stabilized by inter-subunit disulfide bonds formed between cysteine residues adjacent to the C-terminal end of the coiled coil region. Several heparan sulphate (HS) proteoglycans are known in D. melanogaster, including both transmembrane and matrix forms, which could contribute to its retention in pericellular matrix. 42 matched cddid_all.tbl CDD cd16082 cd16082 409504 IgC_CRIg Immunoglobulin (Ig) constant domain of the complement receptor of the immunoglobulin superfamily (CRIg). The members here are composed of the Immunoglobulin (Ig) constant domain of the complement receptor of the immunoglobulin superfamily (CRIg). The N-terminal domain of CRIg (also referred to as Z39Ig and V-set and Ig domain-containing 4 (VSIG4)) belongs to the IgV family of immunoglobulin-like domains while the C-terminal domain of CRIg belongs to the IgC family of immunoglobulin-like domains. CRIg plays a role in the complement system, an inhibitor of the alternative pathway convertases, and a negative regulator of T cell activation. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins such as T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins such as butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. 86 matched cddid_all.tbl CDD cd16083 cd16083 409505 IgC1_CD80 Immunoglobulin constant (IgC)-like domain of antigen receptor Cluster of Differentiation (CD) 80; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin constant (IgC)-like domain of the antigen receptor Cluster of Differentiation (CD) 80. CD80 (also known as glycoprotein B7-1) and CD86 (also known as glycoprotein B7-2) are expressed on antigen-presenting cells and deliver the co-stimulatory signal through CD28 and CTLA-4 (CD152) on T cells. signaling through CD28 augments the T-cell response, whereas CTLA-4 signaling attenuates it. CD80 contains two Ig-like domains, an amino-terminal immunoglobulin variable (IgV)-like domain characteristic of adhesion molecules, and a membrane proximal immunoglobulin constant (IgC)-like domain similar to the constant domains of antigen receptors. Members of the Ig family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, and the IgC domain is involved in oligomerization and molecular interactions. 91 matched cddid_all.tbl CDD cd16084 cd16084 409506 IgC1_CH2_IgD CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin delta chain; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin constant domain (IgC) in delta heavy chains. The IgC family includes immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, and the IgC domain is involved in oligomerization and molecular interactions. 97 matched cddid_all.tbl CDD cd16085 cd16085 409507 IgC1_SIRP_domain_3 "Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin (Ig)-like domain in Signal-Regulatory Protein (SIRP), domain 3 (C1 repeat 2). The SIRPs belong to the ""paired receptors"" class of membrane proteins that comprise several genes coding for proteins with similar extracellular regions but very different transmembrane/cytoplasmic regions with different (activating or inhibitory) signaling potentials. They are commonly on NK cells, but are also on many myeloid cells. Their extracellular region contains three Immunoglobulin superfamily domains a single V-set and two C1-set IgSF domains. Their cytoplasmic tails that contain either ITIMs or transmembrane regions that have positively charged residues that allow an association with adaptor proteins, such as DAP12/KARAP, containing ITAMs. There are 3 distinct SIRP members: alpha, beta, and gamma. SIRP alpha (also known as CD172a or SRC homology 2 domain-containing protein tyrosine phosphatase substrate 1/Shps-1) is a membrane receptor that interacts with a ligand CD47 expressed on many cells and gives an inhibitory signal through immunoreceptor tyrosine-based inhibition motifs in the cytoplasmic region that interact with phosphatases SHP-1 and SHP-2. SIRP beta has a short cytoplasmic region and associates with a transmembrane adapter protein DAP12 containing immunoreceptor tyrosine-based activation motifs to give an activating signal. SIRP gamma contains a very short cytoplasmic region lacking obvious signaling motifs but also binds CD47, but with much less affinity." 96 matched cddid_all.tbl CDD cd16086 cd16086 319335 IgV_CD80 Immunoglobulin variable domain (IgV) in Cluster of Differentiation (CD) 80. The members here are composed of the immunoglobulin variable region (IgV) in the Cluster of Differentiation (CD) 80). Glycoproteins B7-1 (also known as cluster of differentiation (CD) 80) and B7-2 (also known as CD86) are expressed on antigen-presenting cells and deliver the co-stimulatory signal through CD28 and CTLA-4 (also known as cluster of differentiation 152/CD152) on T cells. signaling through CD28 augments the T-cell response, whereas CTLA-4 signaling attenuates it. CD80 contains two Ig-like domains, an amino-terminal immunoglobulin variable (IgV)-like domain characteristic of adhesion molecules and a membrane proximal immunoglobulin constant (IgC)-like domain similar to the constant domains of antigen receptors. Members of the Ig family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and Major Histocompatibility Complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, and the IgC domain is involved in oligomerization and molecular interactions. 105 matched cddid_all.tbl CDD cd16087 cd16087 409508 IgV_CD86 "Immunoglobulin variable domain (IgV) in Cluster of Differentiation (CD) 86. The members here are composed of the immunoglobulin variable region (IgV) in the Cluster of Differentiation (CD) 86). Glycoproteins B7-1 (also known as cluster of differentiation (CD) 80) and B7-2 (also known as CD86) are expressed on antigen-presenting cells and deliver the co-stimulatory signal through CD28 and CTLA-4 (also known as CD152) on T cells. signaling through CD28 augments the T-cell response, whereas CTLA-4 signaling attenuates it. The CTLA-4 and B7-2 monomers are both two-layer beta-sandwiches that display the chain topology characteristic of the immunoglobulin variable (V-type) domains present in antigen receptors. The front and back sheets of B7-2 are composed of AGFCC'C"" and BED strands, respectively. Members of the IgV family are components of immunoglobulin (Ig) and T cell receptors. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. Within the variable domain, there are regions of even more variability called the hypervariable or complementarity-determining regions (CDRs) which are responsible for antigen binding. A predominant feature of most Ig domains is the disulfide bridge connecting 2 beta-sheets with a tryptophan residue packed against the disulfide bond." 108 matched cddid_all.tbl CDD cd16088 cd16088 409509 IgV_PD1 "Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1). The members here are composed of the immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1; also known as CD279/cluster of differentiation 279). PD1 is a cell surface receptor that is expressed on T cells and pro-B cells. The protein's structure includes an extracellular IgV domain followed by a transmembrane region and an intracellular tail. Activation of CD4+ T cells, CD8+ T cells, NKT cells, B cells, and monocytes induces PD-1 expression, immediately after which it binds two distinct ligands, PD-L1 (also known as B7-H1 or CD274/cluster of differentiation 274) and PD-L2, also known as B7-DC. PD-1 plays an important role in down regulating the immune system by preventing the activation of T-cells, reducing autoimmunity and promoting self-tolerance. The inhibitory effect of PD-1 is accomplished by promoting apoptosis in antigen specific T-cells in lymph nodes while simultaneously reducing apoptosis in regulatory T cells. A class of drugs that target PD-1, known as the PD-1 inhibitors, activate the immune system to attack tumors and treat cancer. Comparisons between the mouse PD-1 (mPD-1) and human PD-1 (hPD-1) reveals that unlike the mPD-1 which has a conventional IgSF V-set domain, hPD-1 lacks a C"" strand, and instead the C' and D strands are connected by a long and flexible loop. In addition, the BC loop is not stabilized by disulfide bonding to the F strand of the ligand binding beta sheet. These differences result in different binding affinities of human and mouse PD-1 for their ligands." 112 matched cddid_all.tbl CDD cd16089 cd16089 409510 IgV_CRIg "Immunoglobulin variable (IgV)-like domain in complement receptor of the immunoglobulin superfamily (CRIg). The members here are composed of the immunoglobulin variable (IgV) region of the complement receptor of the immunoglobulin superfamily (CRIg). The N-terminal domain of CRIg (also known as Z39Ig and V-set and Ig domain-containing 4 (VSIG4) belongs to the IgV family of immunoglobulin-like domains while the C-terminal domain of CRIg belongs to the IgC family of immunoglobulin-like domains. Like all members of this family, the CRIg domain contains two beta-sheets: one composed of strands A', G, F, C, C' and C"", and the other of strands B, E and D. The complement system is an important part of the innate immune system and is required for removal of pathogens from the bloodstream. After exposure to pathogens, the third component of the complement system, C3, is cleaved to C3b which, after recruitment of factor B, initiates formation of the alternative pathway convertases. CRIg, a complement receptor expressed on macrophages, binds to C3b and iC3b mediating phagocytosis of the particles. It is also a potent inhibitor of the alternative pathway convertases and a negative regulator of T cell activation. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond." 117 matched cddid_all.tbl CDD cd16090 cd16090 409511 IgV_CD47 Immunoglobulin variable region (IgV) in Cluster of Differentiation (CD) 47. The members here are composed of immunoglobulin variable (IgV) region in the Cluster of Differentiation (CD) 47 (also known as integrin associated protein/IAP). CD47 partners with membrane integrins and binds thrombospondin-1 (TSP-1) and signal-regulatory protein alpha (SIRP alpha). It is involved in apoptosis, proliferation, adhesion, migration, and immune and angiogenic responses. Members of the IgV family are components of immunoglobulin (Ig) and T cell receptors. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. Within the variable domain, there are regions of even more variability called the hypervariable or complementarity-determining regions (CDRs) which are responsible for antigen binding. A predominant feature of most Ig domains is the disulfide bridge connecting 2 beta-sheets with a tryptophan residue packed against the disulfide bond. 112 matched cddid_all.tbl CDD cd16091 cd16091 409512 IgV_HHLA2 Immunoglobulin Variable (IgV) domain in HERV-H LTR-associating 2 (HHLA2). The members here are composed of the immunoglobulin variable (IgV) region in HERV-H LTR-associating 2 (HHLA2; also known as B7-H7/B7 homolog 7). HHLA2 is a member of the B7 family of immune regulatory proteins. Mature human HHLA2 consists of an extracellular domain (ECD) with three immunoglobulin-like domains, a transmembrane segment, and a cytoplasmic domain. HHLA2 is widely expressed in human cancers including non-small cell lung carcinoma (NSCLS), triple negative breast cancer (TNBC), and melanoma, but has limited expression on normal tissues. Interestingly, unlike other members of B7 family, HHLA2 is not expressed in mice or rats. HHLA2 functions as a T cell coinhibitory molecules as it inhibits the proliferation of activated CD4(+) and CD8(+) T cells and their cytokine production. Furthermore, HHLA2 is constitutively expressed on the surface of human monocytes and is induced on B cells after stimulation, however it is not inducible on T cells. 107 matched cddid_all.tbl CDD cd16092 cd16092 319341 IgC1_CH1_IgD CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin delta chain; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the first immunoglobulin constant-1 set domain of delta chains. It belongs to a family composed of the first immunoglobulin constant-1 set domain of alpha, delta, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors. 96 matched cddid_all.tbl CDD cd16093 cd16093 409513 IgC1_CH2_Mu CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the second immunoglobulin constant domain (IgC) of mu heavy chains. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. 99 matched cddid_all.tbl CDD cd16094 cd16094 319343 IgC1_CH3_IgD CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin delta chain; member of the C1-set of Ig superfamily domains. The members here are composed of the third immunoglobulin constant domain (IgC) of delta heavy chains. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. C1-set Ig domains have one beta sheet that is formed by strands A, B, E, and D and the other strands by G, F, C, and C'. 100 matched cddid_all.tbl CDD cd16095 cd16095 409514 IgV_H_TCR_mu "T-cell receptor Mu, Heavy chain, variable (V) domain. The members here are composed of the immunoglobulin (Ig) heavy chain (H), variable (V) domain of the T-cell receptor Mu. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains. Members of this group contain standard Ig superfamily V-set AGFCC'C""/DEB domain topology." 115 matched cddid_all.tbl CDD cd16096 cd16096 409515 IgV_CD79b_beta "Immunoglobulin variable domain (IgV) Cluster of Differentiation (CD) 79B. The members here are composed of the immunoglobulin variable domain (IgV) of the Cluster of Differentiation (CD) 79B (also known as CD79b molecule, immunoglobulin-associated beta (Ig-beta), and B29). The B lymphocyte antigen receptor is a multimeric complex that includes the antigen-specific component, surface immunoglobulin (Ig). Surface Ig non-covalently associates with two other proteins, Ig-alpha and Ig-beta, which are necessary for expression and function of the B-cell antigen receptor. This gene encodes the Ig-beta protein of the B-cell antigen component. Alternatively spliced transcript variants encoding different isoforms have been described. Members of the IgV family are components of immunoglobulin (Ig) and T cell receptors. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. Within the variable domain, there are regions of even more variability called the hypervariable or complementarity-determining regions (CDRs) which are responsible for antigen binding. A predominant feature of most Ig domains is the disulfide bridge connecting 2 beta-sheets with a tryptophan residue packed against the disulfide bond. Members of this group contain standard Ig superfamily V-set AGFCC'C""/DEB domain topology." 96 matched cddid_all.tbl CDD cd16097 cd16097 409516 IgV_SIRP "Immunoglobulin (Ig)-like variable (V) domain of the Signal-Regulatory Protein (SIRP). The members here are composed of the immunoglobulin (Ig)-like domain of the Signal-Regulatory Protein (SIRP). The SIRPs belong to the ""paired receptors"" class of membrane proteins that comprise several genes coding for proteins with similar extracellular regions, but very different transmembrane/cytoplasmic regions with different (activating or inhibitory) signaling potentials. They are commonly on NK cells, but are also on many myeloid cells. Their extracellular region contains three immunoglobulin superfamily domains, a single V-set, and two C1-set IgSF domains. Their cytoplasmic tails that contain either ITIMs or transmembrane regions have positively charged residues that allow an association with adaptor proteins, such as DAP12/KARAP, containing ITAMs. There are 3 distinct SIRP members: alpha, beta, and gamma. SIRP alpha (also known as CD172a or SRC homology 2 domain-containing protein tyrosine phosphatase substrate 1/Shps-1) is a membrane receptor that interacts with a ligand CD47 expressed on many cells and gives an inhibitory signal through immunoreceptor tyrosine-based inhibition motifs in the cytoplasmic region that interact with phosphatases SHP-1 and SHP-2. SIRP beta has a short cytoplasmic region and associates with a transmembrane adapter protein DAP12 containing immunoreceptor tyrosine-based activation motifs to give an activating signal. SIRP gamma contains a very short cytoplasmic region lacking obvious signaling motifs, but also binds CD47 with much less affinity. Members of this group contain standard Ig superfamily V-set AGFCC'C""/DEB domain topology." 111 matched cddid_all.tbl CDD cd16098 cd16098 294015 FliS flagellar export chaperone FliS. This family contains flagellar export chaperone FliS, a protein critical for flagellar assembly and bacterial colonization. FliS prevents premature polymerization of flagellins, the major protein of the filament, by regulating interactions between structural components of the bacterial flagellum in the cytosol. It binds specifically to FliC (flagellin) which is sequentially secreted in large numbers through the central channel of the flagellum and polymerized to form the tail filament. FliS protects FliC from degradation and aggregation by binding to the FliC C-terminal helical domain, which contributes to stabilization of flagellin subunit interactions during polymerization. FliS has been shown to interact specifically with FlgM, whose role is to inhibit FliA, a flagellum-specific RNA polymerase responsible for flagellin transcription; FliA competes with FliS for FlgM binding. 102 matched cddid_all.tbl CDD cd16099 cd16099 381691 TenA_PqqC-like TenA-like proteins including TenA_C and TenA_E proteins, as well as pyrroloquinoline quinone (PQQ) synthesis protein C. TenA proteins participate in thiamin metabolism and can be classified into two classes: TenA_C which has an active site Cys, and TenA_E which does not; TenA_E proteins often have a pair of structurally conserved Glu residues in the active site. TenA_C proteins (EC 3.5.99.2) catalyze the hydrolysis of the thiamin breakdown product amino-HMP (4-amino-5-amino-methyl-2-methylpyrimidine) to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) in a thiamin salvage pathway; the role of TenA_E proteins is less clear. Arabidopsis thaliana TenA_E hydrolyzes amino-HMP to AMP, and the N-formyl derivative of amino-HMP to amino-HMP, but does not hydrolyze thiamin. Bacillus subtilis TenA_C can hydrolyze amino-HMP to AMP and can catalyze the hydrolysis of thiamin. Saccharomyces cerevisiae THI20 includes a C-terminal tetrameric TenA-like domain fused to an N-terminal ThiD domain, and participates in thiamin biosynthesis, degradation and salvage; the TenA-like domain catalyzes the production of HMP from thiamin degradation products (salvage). Bacillus halodurans TenA_C participates in a salvage pathway where the thiamine degradation product 2-methyl-4-formylamino-5-aminomethylpyrimidine (formylamino-HMP) is hydrolyzed first to amino-HMP by the YlmB protein, and the amino-HMP is then hydrolyzed by TenA to produce HMP. Helicobacter pylori TenA_C is also thought to catalyze a salvage reaction but the pyrimidine substrate has not yet been identified. It has also been suggested that TenA proteins act as transcriptional regulators based on changes in gene-expression patterns when TenA is overexpressed in Bacillus subtilis, however this effect may be indirect; Pyrococcus furiosus TenA_E lacks appropriate surface charges for DNA interactions. This family also includes bacterial coenzyme pyrroloquinoline quinone (PQQ) synthesis protein C (PQQC), an oxidase involved in the final step of PQQ biosynthesis, and CADD, a Chlamydia protein that interacts with death receptors. 196 matched cddid_all.tbl CDD cd16100 cd16100 350627 ARID ARID/BRIGHT DNA binding domain family. The AT-rich interaction domain (ARID) family of transcription factors, found in a broad array of organisms from fungi to mammals, is characterized by a highly conserved, helix-turn-helix DNA binding domain that binds to the major groove of DNA. The ARID domain, also called BRIGHT, was first identified in the mouse B-cell-specific transcription factor Bright and in the product of the dead ringer (dri) gene of Drosophila melanogaster. ARID family members are implicated in normal development, differentiation, cell cycle regulation, transcriptional activation and chromatin remodeling. Different family members exhibit different DNA-binding properties. Drosophila Dri, mammalian ARID3A/3B/3C and ARID5A/5B, selectively bind AT-rich sites. However, ARID1A/1B, Drosophila Osa, yeast SWI1, ARID2, ARID4A/4B, JARID1A/1B/1C/1D, and JARID2, bind DNA without sequence specificity. 87 matched cddid_all.tbl CDD cd16101 cd16101 341089 ING Inhibitor of growth (ING) domain family. The Inhibitor of growth (ING) family includes a group of tumor suppressors, ING1-5, which act as readers and writers of the histone epigenetic code, affecting DNA damage response, chromatin remodeling, cellular senescence, differentiation, cell cycle regulation, and apoptosis. They may have a general role in mediating the cellular response to genotoxic stress through binding to and regulating the activities of histone acetyltransferase (HAT) and histone deacetylase (HDAC) chromatin remodeling complexes. All ING proteins contain an N-terminal leucine zipper-like (LZL) motif-containing ING domain that binds unmodified H3 tails, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain, which binds lysine 4-tri-methylated histone H3 (H3K4me3). Although these two regions can bind histones independently, together they increase the apparent association of the ING domain for the H3 tail. The ING family also includes three yeast orthologs, chromatin modification-related protein YNG1 (Yng1p), YNG2 (Yng2p), and transcriptional regulatory protein PHO23 (Pho23p). Yng1p, also termed ING1 homolog 1, is one of the components of the NuA3 histone acetyltransferase (HAT) complex. Yng2p, also termed ESA1-associated factor 4, or ING1 homolog 2, is a subunit of the NuA4 HAT complex. It plays a critical role in intra-S-phase DNA damage response. Pho23p is part of Rpd3/Sin3 histone deacetylase (HDAC) complex. It is required for the normal function of Rpd3 in the silencing of rDNA, telomeric, and mating-type loci. Yng1p and Pho23p inhibit p53-dependent transcription. In contrast, Yng2p has the opposite effect. 88 matched cddid_all.tbl CDD cd16102 cd16102 340519 RAWUL_PCGF_like RRING finger- and WD40-associated ubiquitin-like (RAWUL) domain found in PCGF1-6, RING1 and -2, DRIP and similar proteins; structurally similar to a beta-grasp ubiquitin-like fold. The family includes six Polycomb Group (PcG) RING finger homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) that use epigenetic mechanisms to maintain or repress expression of their target genes. They were first discovered in fruit flies that can remodel chromatin such that epigenetic silencing of genes takes place, and are well known for silencing Hox genes through modulation of chromatin structure during embryonic development in fruit flies. PCGF homologs play important roles in cell proliferation, differentiation, and tumorigenesis. They all have been found to associate with ring finger protein 2 (RNF2). The RNF2-PCGF heterodimer is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. Moreover, PCGF homologs are critical components in the assembly of distinct Polycomb Repression Complex 1 (PRC1) related complexes which are involved in the maintenance of gene repression and target different genes through distinct mechanisms. The Drosophila PRC1 core complex is formed by the Polycomb (Pc), Polyhomeotic (Ph), Posterior sex combs (Psc), and Sex combs extra (Sce, also known as Ring) subunits. In mammals, the composition of PRC1 is much more diverse and varies depending on the cellular context. All PRC1 complexes contain homologs of the Drosophila Ring protein. Ring1A/RNF1 and Ring1B/RNF2 are E3 ubiquitin ligases that mark lysine 119 of histone H2A with a single ubiquitin group (H2AK119ub). Mammalian homologs of the Drosophila Psc protein, such as PCGF2/Mel-18 or PCGF4/BMI1, regulate PRC1 enzymatic activity. PRC1 complexes can be divided into at least two classes according to the presence or absence of CBX proteins, which are homologs of Drosophila Pc. Canonical PRC1 complexes contain CBX proteins that recognize and bind H3K27me3, the mark deposited by PRC2. Therefore, canonical PRC1 complexes and PRC2 can act together to repress gene transcription and maintain this repression through cell division. Non-canonical PRC1 complexes, containing RYBP (together with additional proteins, such as L3mbtl2 or Kdm2b) rather than the CBX proteins, have recently been described in mammals. PCGF homologs contain a C3HC4-type RING-HC finger, and a RAWUL domain that might be responsible for interaction with Cbx members of the Polycomb repression complexes. 87 matched cddid_all.tbl CDD cd16103 cd16103 340520 Ubl2_OASL ubiquitin-like (Ubl) domain 2 found in 2'-5'-oligoadenylate synthase-like protein (OASL) and similar proteins. OASL, also termed 2'-5'-OAS-related protein (2'-5'-OAS-RP), or 59 kDa 2'-5'-oligoadenylate synthase-like protein, or thyroid receptor-interacting protein 14, or TR-interacting protein 14 (TRIP-14), or p59 OASL (p59OASL), is an interferon (IFN)-induced antiviral protein that plays an important role in the IFNs-mediated antiviral signaling pathway. It inhibits respiratory syncytial virus replication and is targeted by the viral nonstructural protein 1 (NS1). It also displays antiviral activity against encephalomyocarditis virus (EMCV) and hepatitis C virus (HCV) via an alternative antiviral pathway independent of RNase L. Moreover, OASL does not have 2'-5'-OAS activity, but can bind double-stranded RNA (dsRNA) to enhance RIG-I signaling. OASL belongs to the 2'-5' oligoadenylate synthase (OAS) family. While each member of this family has a conserved N-terminal OAS catalytic domain, only OASL has two tandem C-terminal ubiquitin-like (Ubl) repeats, which are required for its antiviral activity. This family corresponds to the second Ubl domain. 72 matched cddid_all.tbl CDD cd16104 cd16104 340521 Ubl_USP14_like ubiquitin-like (Ubl) domain found in ubiquitin carboxyl-terminal hydrolase 14 (USP14) and similar proteins. USP14 (EC 3.4.19.12), also termed deubiquitinating enzyme 14, or ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, or ubiquitin carboxyl-terminal hydrolase 14, is a component of proteasome regulatory subunit 19S that regulates deubiquitinated proteins entering inside the proteasome core 20S, which plays an inhibitory role in protein degradation. USP14 is also associated with various signal transduction pathways and tumorigenesis, and thus plays an essential role in the development of various types of cancer. Moreover, USP14 mediates the development of cardiac hypertrophy by promoting GSK-3beta phosphorylation, suggesting a role in cardiac hypertrophy treatment. USP14 contains an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, and a C-terminal ubiquitin-specific protease (USP) domain. 75 matched cddid_all.tbl CDD cd16105 cd16105 340522 Ubl_ASPSCR1_like Ubiquitin-like (Ubl) domain found at the N-terminus of mammalian ASPSCR1 (alveolar soft part sarcoma chromosomal region candidate gene 1 protein), Saccharomyces cerevisie Ubx4p, and similar proteins. ASPSCR1 (alveolar soft part sarcoma chromosomal region candidate gene 1 protein) is also known as alveolar soft part sarcoma locus protein (ASPL), tether containing UBX domain for GLUT4, TUG, UBX domain protein 9, UBXD9, UBXN9 or renal papillary cell carcinoma protein 17 (RCC17). The majority of members of this family contain two beta-grasp ubiquitin-like fold domains: the N-terminal UBL domain (described in this CD), and a C-terminal UBX domain. This UBL domain lacks the characteristic C-terminal double glycine motif. ASPSCR1 functions as a cofactor of the hexameric AAA (ATPase associated with various activities) ATPase complex, known as p97 or VCP in mammals and Cdc48p in yeast. In mammalian cells, ASPSCR1 is involved in insulin-stimulated redistribution of the glucose transporter GLUT4 and assembly of the Golgi apparatus; ASPSCR1 also plays a role in controlling vesicle translocation by interacting with insulin-regulated aminopeptidase (IRAP), a transmembrane aminopeptidase. Ubx4p and ASPSCR1 have only partially overlapping functions: both interact with p97/Cdc48p; however, Ubx4p is important for the ERAD (endoplasmic reticulum-associated protein degradation) pathway while ASPSCR1 appears not to be. 71 matched cddid_all.tbl CDD cd16106 cd16106 340523 Ubl_Dsk2p_like ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein Dsk2p and similar proteins. The family contains several fungal multiubiquitin receptors, including Saccharomyces cerevisiae Dsk2p and Schizosaccharomyces pombe Dph1p, both of which have been characterized as shuttle proteins transporting ubiquitinated substrates destined for degradation from the E3 ligase to the 26S proteasome. They interact with the proteasome through their N-terminal ubiquitin-like domain (Ubl) and with ubiquitin (Ub) through their C-terminal Ub-associated domain (UBA). S. cerevisiae Dsk2p is a nuclear-enriched protein that may involve in the ubiquitin-proteasome proteolytic pathway through interacting with K48-linked polyubiquitin and the proteasome. Moreover, it has been implicated in spindle pole duplication through assisting in Cdc31 assembly into the new spindle pole body (SPB). S. pombe Dph1p is an ubiquitin (Ub0 receptor working in concert with the class V myosin, Myo52, to target the degradation of the S. pombe CLIP-170 homolog, Tip1. It also can protect Ub chains against disassembly by deubiquitinating enzymes. 73 matched cddid_all.tbl CDD cd16107 cd16107 340524 Ubl_AtUPL5_like ubiquitin-like (Ubl) domain found in Arabidopsis thaliana ubiquitin-protein ligase 5 (AtUPL5) and similar proteins. Arabidopsis thaliana AtUPL5, also termed HECT-type E3 ubiquitin transferase UPL5, is an E3 ubiquitin-protein ligase that contains a ubiquitin-like domain (Ubl), a C-type lectin-binding domain, a leucine zipper and a HECT domain. HECT domain containing-ubiquitin-protein ligases have more than one member in different genomes, these proteins have been classified into four sub-families (UPL1/2, UPL3/4, UPL5 and UPL6/7). AtUPL5 fUPL5 regulates leaf senescence in Arabidopsis through degradation of the transcription factor WRKY53. 70 matched cddid_all.tbl CDD cd16108 cd16108 340525 Ubl_ATG8_like ubiquitin-like (Ubl) domain found in autophagy-related 8 (ATG8) and similar proteins. The ATG8 family of proteins constitute a single member in Saccharomyces cerevisiae, Atg8p, and multiple homologs in higher eukaryotes, they are multifunctional ubiquitin-like (Ubl) key regulators of autophagy. The ATG8 system is a Ubl conjugation system that is essential for autophagosome formation. In the ATG8 system, a cysteine protease (ATG4) cleaves a C-terminal arginine from ATG8, and then the exposed C-terminal glycine is conjugated to phosphatidylethanolamine (PE) by ATG7, an E1-like enzyme, and ATG3, an E2-like enzyme. The mammalian ATG8 family is classified into three subfamilies: i) MAP1LC3 (microtubule associated protein 1 light chain 3) which includes MAP1LC3A, MAP1LC3B, MAP1LC3B2, and MAP1LC3C, ii) GABARAP (GABA type A receptor associated protein) which includes GABARAP, GABARAPL1, and GABARAPL3, and iii) GABARAPL2 (GABA type A receptor associated protein like 2), also known as GATE-16 (golgi-associated adenosine triphosphatase enhancer of 16 kDa). 85 matched cddid_all.tbl CDD cd16109 cd16109 340526 DCX1 Dublecortin-like domain 1. Members of the doublecortin (DCX) gene family are microtubule-associated proteins (MAPs). Microtubules are key components of cytoskeleton that are involved in cell movement, shape determination, division and transport. The DCX gene family consists of eleven paralogs in human and mouse, and its protein domains can occur in double tandem or single repeats. The family represents the first repeat of the DCX domain which has a stable ubiquitin-like tertiary fold. Proteins with DCX double tandem domains in general have roles in microtubule (MT) regulation and signal transduction such as X-linked doublecortin (DCX), retinitis pigmentosa-1 (RP1) and doublecortin-like kinase (DCLK). 85 matched cddid_all.tbl CDD cd16110 cd16110 340527 DCX1_RP_like Doublecortin-like domain 1 found in retinitis pigmentosa (RP)-like protein. RP-like protein family is part of doublecortin (DCX) family. It has double tandem DCX repeats that are associated with retinitis pigmentosa. DCX is a microtubule-associated protein (MAP) with a stable ubiquitin-like tertiary fold. Microtubules are key components of cytoskeleton that are involved in cell movement, shape determination, division and transport. RP-like proteins are colocalized to the photoreceptor and share a function in outer segment disc morphogenesis. 75 matched cddid_all.tbl CDD cd16111 cd16111 340528 DCX_DCLK3 Doublecortin-like domain found in doublecortin-like kinase 3 (DCLK3). DCLK3 is a member of doublecortin (DCX) protein family. It functions as a microtubule-associated protein (MAP). DCLK3 contains only one N-terminal doublecortin domain (DCX), unlike DCLK1 and DCLK2 which each have two conserved DCX domains. The DCX domain has a stable ubiquitin-like tertiary fold. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. In addition to microtubule binding domains, DCLK3 has a serine/threonine kinase domain that is similar to Ca/calmodulin-dependent (Cam) protein kinases. 85 matched cddid_all.tbl CDD cd16112 cd16112 340529 DCX1_DCX Dublecortin-like domain 1 found in neuronal migration protein doublecortin (DCX). DCX, also termed doublin or lissencephalin-X (Lis-XDCX), is a microtubule-associated protein (MAP). It belongs to the doublecortin (DCX) family, has double tandem DCX repeats, and is expressed in migrating neurons. Structure studies show that the N-terminal DCX domain has a stable ubiquitin-like fold. DCX is not only a unique MAP in terms of structure, it also interacts with multiple additional proteins. Mutations in the human DCX genes are associated with abnormal neuronal migration, epilepsy, and mental retardation. 89 matched cddid_all.tbl CDD cd16113 cd16113 340530 DCX2_DCDC2_like Doublecortin-like domain 2 found in doublecortin domain-containing protein 2 (DCDC2). DCDC2 is a member of the doublecortin (DCX) family. It is a microtubule-associated protein (MAP) with stable double tandem DCX repeats of a ubiquitin-like tertiary fold. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. Microtubules are key components of cytoskeleton that are involved in cell movement, shape determination, division and transport. DCDC2 genetic variation in humans is associated with reading disability, attention deficit hyperactivity disorder (ADHD), and difficulties in mathematics. A genetic variant of DCDC2 associates with dyslexia, a common neurobehavioral disorder of reading. DCDC2 protein interacts with many of the same cytoskeleton related proteins that other members of the DCX family interact with. 74 matched cddid_all.tbl CDD cd16114 cd16114 340531 Ubl_SUMO1 "ubiquitin-like (Ubl) domain found in small ubiquitin-related modifier 1 (SUMO-1) and similar proteins. SUMO (also known as ""Smt3"" and ""sentrin"" in other organisms) resembles ubiquitin (Ub) in structure, ligation to other proteins and the mechanism of ligation. Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of Ub and the epsilon-amino group of a substrate lysine. SUMOs, like Ub, are covalently conjugated to lysine residues in a wide variety of target proteins in eukaryotic cells and regulate numerous cellular processes, such as transcription, epigenetic gene control, genomic instability, and protein degradation. Four SUMO paralogs exist in mammals, SUMO1 through SUMO4. SUMO2-SUMO4 are more closely related to each other than they are to SUMO1. SUMO1 is a binding partner of the RAD51/52 nucleoprotein filament proteins, which mediate DNA strand exchange. SUMO1 conjugation to cellular proteins has been implicated in multiple important cellular processes, such as nuclear transport, cell cycle control, oncogenesis, inflammation, and the response to virus infection." 76 matched cddid_all.tbl CDD cd16115 cd16115 340532 Ubl_SUMO2_3_4 "ubiquitin-like (Ubl) domain found in small ubiquitin-related modifier SUMO-2, SUMO-3, SUMO-4, and similar proteins. SUMO (also known as ""Smt3"" and ""sentrin"" in other organisms) resembles ubiquitin (Ub) in structure, ligation to other proteins and the mechanism of ligation. Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of Ub and the epsilon-amino group of a substrate lysine. SUMOs, like Ub, are covalently conjugated to lysine residues in a wide variety of target proteins in eukaryotic cells and regulate numerous cellular processes, such as transcription, epigenetic gene control, genomic instability, and protein degradation. The mammalian SUMOs have four paralogs, SUMO1 through SUMO4. SUMO2 and SUMO3 are more closely related to each other than they are to SUMO1. SUMO2/3 are capable of forming chains on substrate proteins through internal lysine residues. The basic biology of SUMO4 remains unclear. A M55V polymorphism in SUMO4 has been associated with susceptibility to type I diabetes in some genetic studies." 72 matched cddid_all.tbl CDD cd16116 cd16116 340533 Ubl_Smt3_like ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae ubiquitin-like protein Smt3p and similar proteins. Smt3 (Suppressor of Mif Two 3) was originally isolated as a high-copy suppressor of a mutation in MIF2, the gene of a centromere binding protein in S. cerevisiae. Smt3p is the yeast homolog of small ubiquitin-related modifier (SUMO) proteins that are involved in post-translational protein modification called SUMOylation, covalently attaching to and detaching from other proteins in cells to modify their function. SUMO resembles ubiquitin (Ub) in its structure, its ability to be ligated to other proteins, as well as in the mechanism of ligation. Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of Ub and the epsilon-amino group of a substrate lysine. Smt3p plays essential roles in cell-cycle regulation and chromosome segregation in budding yeast. It interacts with different modification enzymes, and regulates their functions through linking covalently to its targets. 74 matched cddid_all.tbl CDD cd16117 cd16117 340534 UBX_UBXN4 Ubiquitin regulatory domain X (UBX) found in UBX domain protein 4 (UBXN4) and similar proteins. UBXN4, also termed ERAD (endoplasmic-reticulum-associated protein degradation) substrate erasing protein (erasin), or UBX domain-containing protein 2 (UBXD2), or UBXDC1, belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. UBXN4 is an endoplasmic reticulum (ER) localized protein that interacts with p97 (also known as VCP or Cdc48) via its UBX domain. Erasin exists in a complex with other p97/VCP-associated factors involved in endoplasmic-reticulum-associated protein degradation (ERAD). p97 is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. The overexpression of UBXN4 increases degradation of a classical ERAD substrate and UBXN4 levels are increased in ER stressed cells. Anti-UBXN4 staining is increased in neuropathological lesions in brains of patients with Alzheimer's disease. 77 matched cddid_all.tbl CDD cd16118 cd16118 340535 UBX2_UBXN9 Ubiquitin regulatory domain X (UBX) 2 found in UBX domain protein 9 (UBXN9, UBXD9, or ASPSCR1) and similar proteins. UBXN9, also termed tether containing UBX domain for GLUT4 (TUG), or alveolar soft part sarcoma chromosomal region candidate gene 1 protein (ASPSCR1), or alveolar soft part sarcoma locus (ASPL), or renal papillary cell carcinoma protein 17 (RCC17), belongs to the UBXD family of proteins that contains two ubiquitin regulatory domains X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. In addition, UBXN9 contains an N-terminal ubiquitin-like (Ubl) domain. UBXN9 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. However, high-affinity interacting protein ASPL efficiently promotes p97 hexamer disassembly, resulting in the formation of stable p97:ASPL heterotetramers; the extended UBX domain (eUBX) in ASPL is critical for p97 hexamer disassembly and facilitates the assembly of p97:ASPL heterotetramers.UBXN9 is involved in insulin-stimulated redistribution of the glucose transporter GLUT4, assembly of the Golgi apparatus. In addition to GLUT4, UBXN9 also controls vesicle translocation by interacting with insulin-regulated aminopeptidase (IRAP), a transmembrane aminopeptidase. UBXN9 and its budding yeast ortholog, Ubx4p, are multifunctional proteins that share some, but not all functions. Yeast Ubx4p is important for endoplasmic reticulum-associated protein degradation (ERAD) but UBXN9 appears not to share this function. 74 matched cddid_all.tbl CDD cd16119 cd16119 340536 UBX_UBXN6 Ubiquitin regulatory domain X (UBX) found in UBX domain protein 6 (UBXN6) and similar proteins. UBXN6, also termed UBX domain-containing protein 1 (UBXD1), and UBXDC2, belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. UBXN6 acts as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. Unlike other p97 cofactors that binds the N-domain of p97 through their UBX domain, UBXN6 binds p97 in two regions, at the p97 C terminus via a PUB domain and at the p97 N-domain with a short linear interaction motif termed VIM. Its UBX domain is not functional for the binding of p97. The UBXN6-p97 complex regulates the endolysosomal sorting of ubiquitylated plasma membrane protein caveolin-1 (CAV1), as well as the trafficking of ERGIC-53-containing vesicles by controlling the interaction of transport factors with the cytoplasmic tail of ERGIC-53. In addition, UBXN6 is a regulatory component of endoplasmic reticulum-associated degradation (ERAD) that may modulate the adaptor binding to p97. 73 matched cddid_all.tbl CDD cd16120 cd16120 340537 UBX_UBXN3B Ubiquitin regulatory domain X (UBX) found in FAS associated factor 2 (FAF2, also known as UBXN3B) and similar proteins. UBX domain-containing protein 3B (UBXN3B), also termed protein ETEA, or FAF2, or UBX domain-containing protein 8 (UBXD8), belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. FAF2 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. The p97-UBXD8 complex destabilizes mRNA by promoting release of ubiquitinated the RNA-binding protein HuR from messenger ribonucleoprotein (mRNP). Moreover, FAF2 is the translation product of a highly expressed gene in the T-cells and eosinophils of atopic dermatitis patients compared with those of normal individuals. A yeast two-hybrid assay showed that FAF2 can interact with Fas. 80 matched cddid_all.tbl CDD cd16121 cd16121 340538 FERM_F1_SNX17 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in sorting nexin protein 17 (SNX17). SNX17 is a member of the family of cytoplasmic sorting nexin adaptor proteins that regulate endosomal trafficking of cell surface proteins. It localizes to early endosomes, and plays an important role in mediating endocytic internalization, recycling, and/or protection from lysosomal degradation of NPxY-motif containing cell surface proteins including amyloid precursor protein (APP), P-selectin, beta1-integrin, low density lipoprotein receptor (LDLR), LDLR related protein (Lrp1), ApoER2, and FEEL1. SNX17 also affects T cell activation by regulating T cell receptor and integrin recycling. SNX17 contains a PX (Phox homology) domain and a FERM (Band 4.1, ezrin, radixin, moesin) domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 93 matched cddid_all.tbl CDD cd16122 cd16122 340539 FERM_F1_SNX31 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in sorting nexin protein 31 (SNX31). SNX31 is a member of the family of cytoplasmic sorting nexin adaptor proteins that regulate endosomal trafficking of cell surface proteins. It is a novel sorting nexin associated with the uroplakin-degrading multivesicular bodies in terminally differentiated urothelial cells. SNX31 binds multiple beta integrin cytoplasmic domains and regulates beta1 integrin surface levels and stability. SNX31 contains a PX (Phox homology) domain and a FERM (Band 4.1, ezrin, radixin, moesin) domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 98 matched cddid_all.tbl CDD cd16123 cd16123 340540 RA_RASSF7_like Ras-associating (RA) domain found in Ras-association domain family members, RASSF7, RASSF8, RASSF9, and RASSF10. The RASSF family of proteins shares a conserved RalGDS/AF6 Ras association (RA) domain either in the C-terminus (RASSF1-6) or N-terminus (RASSF7-10). RASSF7-10 lacks a conserved SARAH (Salvador/RASSF/Hpo) motif adjacent to the RA domain that is found in members of the RASSF1-6 family. The structural differences between the C-terminus and N-terminus RASSF subgroups have led to the suggestion that they are two distinct families. RA domain has the beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin (Ub). Ras proteins are small GTPases that are involved in cellular signal transduction. The N-terminus RASSF proteins are potential Ras effectors that have been linked to key biological processes, including cell death, proliferation, microtubule stability, promoter methylation, vesicle trafficking and response to hypoxia. 81 matched cddid_all.tbl CDD cd16124 cd16124 340541 RA_GRB7_10_14 Ras-associating (RA) domain found in growth factor receptor-bound (Grb) protein 7/10/14. The RA domain is highly conserved among the members of the Grb proteins family which includes Grb7, Grb10 and Grb14. Grb7/10/14 are multi-domain cytoplasmic adaptor proteins that are recruited to activated receptor tyrosine kinases. RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin (Ub). Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. Grb7 and its related family members Grb10 and Grb14 share a conserved domain architecture that includes an amino-terminal proline-rich region, a central segment termed the GM region (for Grb and Mig) which includes the RA, PIR, and pleckstrin homology (PH) domains, and a carboxyl-terminal SH2 domain. The tandem RA and PH domains of Grb7/10/14 are also found in a second adaptor family, Rap1-interacting adaptor molecule (RIAM) and lamellipodin, which is involved in actin-cytoskeleton rearrangement. Grb7/10/14 family proteins are phosphorylated on serine/threonine as well as tyrosine residues and are mainly localized to the cytoplasm. 85 matched cddid_all.tbl CDD cd16125 cd16125 340542 RA_ASPP1_2 Ras-associating (RA) domain found in apoptosis-stimulating protein of p53 (ASPP) 1 and 2. The ASPP protein (apoptosis-stimulating protein of p53; also called ankyrin repeat-, Src homology 3 domain- and Pro-rich region-containing protein) plays a critical role in regulating apoptosis. The ASPP family consists of three members, ASPP1, ASPP2 and iASPP, all of which bind to p53 and regulate p53-mediated apoptosis. ASPP1 and ASPP2, have a RA domain at their N-terminus and have pro-apoptotic functions, while iASPP is involved in anti-apoptotic responses. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and are involved in several different functions ranging from tumor suppression to being oncoproteins. Ras proteins are small GTPases that are involved in cellular signal transduction. The RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. 80 matched cddid_all.tbl CDD cd16126 cd16126 340543 Ubl_HR23B ubiquitin-like (Ubl) domain found in UV excision repair protein RAD23 homolog B (HR23B). HR23B, also termed xeroderma pigmentosum group C (XPC) repair-complementing complex 58 kDa protein (p58), is tightly complexed with XPC protein to form the XPC-HR23B complex. Although it displays a high affinity for both single- and double-stranded DNA, the XPC-HR23B complex functions as a global genome repair (GGR)-specific repair factor that is specifically involved in global genome but not transcription-coupled nucleotide excision repair (NER). HR23B also interacts specifically with S5a subunit of the human 26S proteasome, and plays an important role in shuttling ubiquitinated cargo proteins to the proteasome. HR23B contains an N-terminal ubiquitin-like (Ubl) domain that binds proteasomes and two C-terminal ubiquitin-associated (UBA) domains that bind ubiquitin or multi-ubiquitinated substrates. In addition, it has a XPC protein-binding domain that might be necessary for its efficient NER function. 78 matched cddid_all.tbl CDD cd16127 cd16127 340544 Ubl_ATG8_GABARAP_like ubiquitin-like (Ubl) domain found in gamma-aminobutyric acid receptor-associated protein (GABARAP) and similar proteins; sub-family of the autophagy-related 8 (ATG8) protein family. GABARAP (also termed GABA(A) receptor-associated protein, ATG8A, or MM46) has been implicated in intracellular protein trafficking. It is a cytosolic protein, localized to transport vesicles, the Golgi network and the endoplasmic reticulum. It interacts with the intracellular domain of the gamma2 subunit of GABA(A) receptors, and thus, functions as a trafficking modulator implicated in the intracellular trafficking of GABA(A) receptor. GABARAP also acts as a Ubl modifier belonging to the ATG8 (autophagy-related 8) protein family which is essential for autophagosome biogenesis and maturation. GABARAP recruits phosphatidylinositol 4-kinase II alpha (PI4KIIalpha) as a specific downstream effector, and regulates phosphatidylinositol 4-phosphate (PI4P)-dependent autophagosome lysosome fusion. This sub-family also includes GABARAPL1 (also termed GABA(A) receptor-associated protein-like, or GEC1), GABARAPL2/GATE-16, and GABARAPL3. GABARAPL1 has been involved in the intracellular transport of receptors via interactions with tubulin and GABA(A) or kappa opioid receptors. GABARAPL1 is also a Ubl modifier that functions as a mediator involved in androgen-regulated autophagy process. It is transcriptionally modulated by androgen receptor (AR) and has a repressive role in autophagy. In addition, GABARAPL1 is required for increased membrane expression of epidermal growth factor receptor (EGFR) during hypoxia, suggesting a possible role in the trafficking of these membrane proteins. GABARAPL1 may also play a key role in several important biological processes such as cancer or neurodegenerative diseases. Low expression of GABARAPL1 is associated with poor prognosis of patients with hepatocellular carcinoma. 107 matched cddid_all.tbl CDD cd16128 cd16128 340545 Ubl_ATG8 ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae Atg8p and related proteins; sub-family of the autophagy-related 8 (ATG8) family. The ATG8 family of proteins constitutes a single member in Saccharomyces cerevisiae, Atg8p, and multiple homologs in higher eukaryotes. These proteins are multifunctional ubiquitin-like (Ubl) key regulators of autophagy. ATG8 is characterized by a C-terminal ubiquitin-like (Ubl) domain with a short N-terminal extension. The covalent attachment of ATG8 to phosphatidylethanolamine (PtdEth) at the autophagosomal membrane places it at a crucial juncture during autophagosome formation. ATG Ubl proteins such as Saccharomyces cerevisiae Atg8p undergo a unique Ubl conjugation, a process essential for autophagosome formation. 103 matched cddid_all.tbl CDD cd16129 cd16129 340546 Ubl_ATG8_MAP1LC3 ubiquitin-like (Ubl) domain found in microtubule associate protein 1 light chain 3 (MAP1LC3). Autophagy is an essential intracellular process that targets large protein complexes, bacterial pathogens, and organelles for degradation. MAP1LC3 (also known as LC3) has a ubiquitin-like (Ubl) fold and belongs to the ATG8 autophagy protein family. A Ubl conjugation of MAP1LC3 by the phospholipid phosphatidylethanolamine (PE) is an essential process for the formation of autophagosomes. MAP1LC3 is cleaved by the cysteine protease ATG4 and is then conjugated with PE by E1-like enzyme ATG7 and ATG3, an E2-like enzyme. The Ubl conversion of MAP1LC3 is known as a marker of autophagy-induction. This sub-family includes MAP1LC3A, MAP1LC3B, and MAP1LC3C, each encoded by a different MAP1LC3 gene. 105 matched cddid_all.tbl CDD cd16130 cd16130 340547 RA_Rin3 Ras-associating (RA) domain found in Ras and Rab interactor 3 (Rin3). Rin3, also termed Ras interaction/interference protein 3, is a RAS effector and a RAB5-activating guanine nucleotide exchange factor (GEF) specifically for GTPase Rab31. It functions as a negative regulator of mast cell responses to Stem Cell Factor (SCF). Rin3 contains the Vps9p-like guanine nucleotide exchange factor and Ras-association (RA) domains. 88 matched cddid_all.tbl CDD cd16131 cd16131 340548 RA_Rin2 Ras-associating (RA) domain found in Ras and Rab interactor 2 (Rin2). Rin2, also termed Ras association domain family 4, or Ras inhibitor JC265, or Ras interaction/interference protein 2, is a Rab5 GDP/GTP exchange factor with the Vps9p-like guanine nucleotide exchange factor and Ras-association (RA) domains. Rin2 connects three GTPases, R-Ras, Rab5 and Rac1, to promote endothelial cell adhesion through the regulation of integrin internalization and Rac1 activation. Rin2 is involved in the regulation of Rab5-mediated early endocytosis. The deficiency of Rin2 can cause the RIN2 syndrome, an autosomal recessive connective tissue disorder. 91 matched cddid_all.tbl CDD cd16132 cd16132 340549 RA_RASSF10 Ras-associating (RA) domain found in N-terminal Ras-association domain family 10 (RASSF10). RASSF10 is a member of a family of N-terminus RASSF7-10 proteins. RASSF7-10 has an RA domain at the N-terminus and lacks a conserved SARAH (Salvador/RASSF/Hpo) motif adjacent to the RA domain that is found in members of the RASSF1-6 family. RA domain of N-terminal RASSF protein family has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. RASSF10 is expressed in a wide variety of tissues and its expression in human thyroid, pancreas, placenta, heart, lung and kidney has been observed. RASSF10 is the most frequently methylated of the N-terminal RASSFs in some cancers such as in childhood acute lymphoblastic leukemia and both, thyroid cancer cell lines and primary thyroid carcinomas. 102 matched cddid_all.tbl CDD cd16133 cd16133 340550 RA_RASSF9 Ras-associating (RA) domain of N-terminal Ras-association domain family 9 (RASSF9). RASSF9, also termed PAM COOH-terminal interactor protein 1 (P-CIP1), or peptidylglycine alpha-amidating monooxygenase COOH-terminal interactor, is a member of N-terminus RASSF7-10 protein family. RASSF7-10 has an RA domain at the N-terminus and lacks a conserved SARAH (Salvador/RASSF/Hpo) motif adjacent to the RA domain that is found in members of the RASSF1-6 family. The RA domain of the N-terminal RASSF proteins family has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. RASSF9 was formerly known as PAM COOH-terminal interactor-1 (P-CIP1) because of its interaction with peptidylglycine alpha-amidating mono-oxygenase (PAM) and possibility of its role in regulating the trafficking of integral membrane PAM. RASSF9 is widely expressed in multiple organs such as testis, kidney, skeletal muscle, liver, lung, brain, and heart. Cloned RASSF9 showed preferential binding to N-Ras and K-Ras. 93 matched cddid_all.tbl CDD cd16134 cd16134 340551 RA_RASSF8 Ras-associating (RA) domain found in N-terminal Ras-association domain family 8 (RASSF8). RASSF8, also termed carcinoma-associated protein HOJ-1, is a member of the N-terminus RASSF7-10 protein family. RASSF7-10 has an RA-domain at the N-terminus and lacks a conserved SARAH (Salvador/RASSF/Hpo) motif adjacent to the RA domain that is found in members of the RASSF1-6 family. The RA domain of N-terminal RASSF proteins family has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. RASSF8 has been described as a potential tumor suppressor. RASSF8 might have a role in the regulation of cell-cell adhesion and cell growth. 82 matched cddid_all.tbl CDD cd16135 cd16135 340552 RA_RASSF7 Ras-associating (RA) domain found in N-terminal Ras-association domain family 7 (RASSF7). RASSF7, also termed HRAS1-related cluster protein 1, is a member of the N-terminus RASSF7-10 protein family. RASSF7-10 has an RA-domain at the N-terminus and lacks a conserved SARAH (Salvador/RASSF/Hpo) motif adjacent to the RA domain that is found in members of the RASSF1-6 family. The RA domain of N-terminal RASSF protein family has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. RASSF7 is a potential Ras effector as its function has been linked to some key biological processes including the regulation of cell death and proliferation; for example, RASSF7 is up-regulated in pancreatic cancer. 83 matched cddid_all.tbl CDD cd16136 cd16136 340553 RA_MRL_Lpd Ras-associating (RA) domain found in the adapter protein lamellipodin (Lpd). Lpd, also termed Ras-associated and pleckstrin homology domains-containing protein 1 (RAPH1), or amyotrophic lateral sclerosis 2 chromosomal region candidate gene 18 protein, or amyotrophic lateral sclerosis 2 chromosomal region candidate gene 9 protein, or proline-rich EVH1 ligand 2 (PREL-2), or protein RMO1, is a member of MRL (Mig10/RIAM/Lpd) family proteins that regulates cell migration and promote lamellipodia protrusion in fibroblast by interacting with Ena/VASP proteins. MRL proteins share a common structural architecture, including a central structural unit consisting of an RA domain and a pleckstrin homology (PH) domain, an upstream coiled-coil region, and a number of polyproline motifs. Lpd also contains a helical region at the amino terminus for talin binding. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and are involved in several different functions ranging from tumor suppression to being oncoproteins. RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin (Ub). Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. RA and PH domain in Lpd form a tandem domain pair (RA-PH), and serve tightly coordinated functions in both Ras GTPase signaling via the RA domain and membrane translocalization via the PH domain. Lpd also exhibits other unique enzymatic functions including its catalytic activity of butyrylcholinesterase, a potent therapeutic treatment targeting cocaine abuse. 90 matched cddid_all.tbl CDD cd16137 cd16137 340554 RA_MRL_RIAM Ras-associating (RA) domain found in Rap1-GTP-interacting adapter molecule (RIAM). RIAM, also termed amyloid beta A4 precursor protein-binding family B member 1-interacting protein, or APBB1-interacting protein 1, or proline-rich EVH1 ligand 1 (PREL-1), or proline-rich protein 73, or retinoic acid-responsive proline-rich protein 1 (RARP-1), is a member of MRL (Mig10/RIAM/Lpd) family proteins that regulates cell migration and promote lamellipodia protrusion in fibroblast by interacting with Ena/VASP proteins. RIAM regulates cell migration and mediates Rap1-induced cell adhesion. MRL proteins share a common structural architecture, including a central structural unit consisting of an RA domain and a pleckstrin homology (PH) domain, an upstream coiled-coil region, and a number of polyproline motifs. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and are involved in several different functions ranging from tumor suppression to being oncoproteins. RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin (Ub). Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. RIAM also contains a helical region at the amino terminus for talin binding. RA and PH form a tandem domain pair (RA-PH), and serve tightly coordinated functions in both Ras GTPase signaling via the RA domain and membrane translocalization via the PH domain. 89 matched cddid_all.tbl CDD cd16138 cd16138 340555 RA_MRL_MIG10 Ras-associating (RA) domain found in Caenorhabditis elegans abnormal cell migration protein 10 (MIG-10) and similar proteins. MIG-10 is lamellipodin (Lpd) found in C. elegans. It stabilizes invading cell adhesion to basement membrane and is a negative transcriptional target of Evi-1 proto-oncogene, EGL-43, in C. elegans. It also shows netrin-independent functions and is a transcriptional target of FOS-1A, a transcription factor that promotes basement membrane breaching, during anchor cell invasion in C. elegans. MIG-10 is a member of MRL (Mig10/RIAM/Lpd) family of proteins that is involved in antero-posterior migration of embryonic neurons CAN (canalassociated neurons), ALM (anterior lateral microtubule cells) and HSN (hermaphrodite-specific neurons). MRL proteins share a common structural architecture, including a central structural unit consisting of an RA domain and a pleckstrin homology (PH) domain, an upstream coiled-coil region, and a number of polyproline motifs. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and are involved in several different functions ranging from tumor suppression to being oncoproteins. RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin (Ub). Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. RA and PH form a tandem domain pair (RA-PH), and serve tightly coordinated functions in both Ras GTPase signaling via the RA domain and membrane translocalization via the PH domain. 86 matched cddid_all.tbl CDD cd16139 cd16139 340556 RA_GRB14 Ras-associating (RA) domain found in growth factor receptor-bound (Grb) protein 14. Grb14, a member of cytoplasmic adaptor proteins, is a tissue-specific negative regulator of insulin signaling. RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin (Ub). Ubi is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. A novel function of Grb14 RA domain is to interact with the nucleotide binding pocket of a cyclic nucleotide gated channel alpha subunit (CNGA1) and inhibits its activity. Grb7 and its related family members Grb10 and Grb14 share a conserved domain architecture that includes an amino-terminal proline-rich region, a central segment termed the GM region (for Grb and Mig) which includes the RA, PIR, and PH domains, and a carboxyl-terminal SH2 domain. Grb7/10/14 family proteins are phosphorylated on serine/threonine as well as tyrosine residues and are mainly localized to the cytoplasm. 85 matched cddid_all.tbl CDD cd16140 cd16140 340557 RA_GRB7 Ras-associating (RA) domain found in growth factor receptor-bound (Grb) protein 7. GRB7, also termed B47, or epidermal growth factor receptor GRB-7, or GRB7 adapter protein, is a signal-transducing cytoplasmic adaptor protein that is co-opted by numerous tyrosine kinases involved in various cellular signaling and functions. Grb7 and its related family members Grb10 and Grb14 share a conserved domain architecture that includes an amino-terminal proline-rich region, a central segment termed the GM region (for Grb and Mig) which includes the RA, PIR, and pleckstrin homology (PH) domains, and a carboxyl-terminal SH2 domain. The tandem RA and PH domains of Grb7/10/14 are also found in a second adaptor family, Rap1-interacting adaptor molecule (RIAM) and lamellipodin, which is involved in actin-cytoskeleton rearrangement. Grb7/10/14 family proteins are phosphorylated on serine/threonine as well as tyrosine residues and are mainly localized to the cytoplasm. Grb7 could interact with activated N-Ras in transfected cells. 88 matched cddid_all.tbl CDD cd16141 cd16141 340558 RA_GRB10 Ras-associating (RA) domain found in growth factor receptor-bound (Grb) protein 10. GRB10, also termed insulin receptor-binding protein Grb-IR, is a multi-domain cytoplasmic adaptor protein that binds to the insulin-like growth factor 1 receptor (IGF-1R) and inhibits insulin signaling. Grb10 and its related family members Grb7 and Grb14 share a conserved domain architecture that includes an amino-terminal proline-rich region, a central segment termed the GM region (for Grb and Mig) which includes the RA, PIR, and pleckstrin homology (PH) domains, and a carboxyl-terminal SH2 domain. The tandem RA and PH domains of Grb7/10/14 are also found in a second adaptor family, Rap1-interacting adaptor molecule (RIAM) and lamellipodin, which is involved in actin-cytoskeleton rearrangement. Grb7/10/14 family proteins are phosphorylated on serine/threonine as well as tyrosine residues and are mainly localized to the cytoplasm. Grb14 binds to both GTPase-defective mutant Rab5 as well as CNGA1, whereas Grb10 binds only to GTP-bound form of active Rab5. 92 matched cddid_all.tbl CDD cd16142 cd16142 293761 ARS_like uncharacterized arylsulfatase subfamily. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 372 matched cddid_all.tbl CDD cd16143 cd16143 293762 ARS_like uncharacterized arylsulfatase subfamily. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 395 matched cddid_all.tbl CDD cd16144 cd16144 293763 ARS_like uncharacterized arylsulfatase subfamily. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 421 matched cddid_all.tbl CDD cd16145 cd16145 293764 ARS_like uncharacterized arylsulfatase subfamily. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 415 matched cddid_all.tbl CDD cd16146 cd16146 293765 ARS_like uncharacterized arylsulfatase. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 409 matched cddid_all.tbl CDD cd16147 cd16147 293766 G6S glucosamine (N-acetyl)-6-sulfatase(G6S, GNS) AND sulfatase 1(SULF1). N-acetylglucosamine-6-sulfatase also known as glucosamine (N-acetyl)-6-sulfatase hydrolyzes of the 6-sulfate groups of the N-acetyl-D-glucosamine 6-sulfate units of heparan sulfate and keratan sulfate. Deficient of N-acetylglucosamine-6-sulfatase results in disease of Sanfilippo Syndrome type IIId or Mucopolysaccharidosis III (MPS-III), a rare autosomal recessive lysosomal storage disease. SULF1 encodes an extracellular heparan sulfate endosulfatase, that removes 6-O-sulfate groups from heparan sulfate chains of heparan sulfate proteoglycans (HSPGs). 396 matched cddid_all.tbl CDD cd16148 cd16148 293767 sulfatase_like uncharacterized sulfatase subfamily. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 271 matched cddid_all.tbl CDD cd16149 cd16149 293768 sulfatase_like uncharacterized sulfatase subfamily. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 257 matched cddid_all.tbl CDD cd16150 cd16150 293769 sulfatase_like uncharacterized sulfatase subfamily. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 423 matched cddid_all.tbl CDD cd16151 cd16151 293770 sulfatase_like uncharacterized sulfatase subfamily. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 377 matched cddid_all.tbl CDD cd16152 cd16152 293771 sulfatase_like uncharacterized sulfatase subfamily. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 373 matched cddid_all.tbl CDD cd16153 cd16153 293772 sulfatase_like uncharacterized sulfatase subfamily. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 282 matched cddid_all.tbl CDD cd16154 cd16154 293773 sulfatase_like uncharacterized sulfatase subfamily. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 372 matched cddid_all.tbl CDD cd16155 cd16155 293774 sulfatase_like uncharacterized sulfatase subfamily. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 372 matched cddid_all.tbl CDD cd16156 cd16156 293775 sulfatase_like uncharacterized sulfatase subfamily; includes Escherichia coli YidJ. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 468 matched cddid_all.tbl CDD cd16157 cd16157 293776 GALNS galactosamine-6-sulfatase; also known as N-acetylgalactosamine-6-sulfatase (GALNS). Lysosomal galactosamine-6-sulfatase removes sulfate groups from a terminal N-acetylgalactosamine-6-sulfate (or galactose-6-sulfate) in mucopolysaccharides such as keratan sulfate and chondroitin-6-sulfate. Defects in GALNS lead to accumulation of substrates, resulting in the development of the lysosomal storage disease mucopolysaccharidosis IV A. 466 matched cddid_all.tbl CDD cd16158 cd16158 293777 ARSA Arylsulfatase A or cerebroside-sulfatase. Arylsulfatase A breaks down sulfatides, namely cerebroside 3-sulfate into cerebroside and sulfate. It is a member of the sulfatase family. The arylsulfatase A was located in lysosome-like structures and transported to dense lysosomes in a mannose 6-phosphate receptor-dependent manner. Deficiency of arylsulfatase A leads to the accumulation of cerebroside sulfate, which causes a lethal progressive demyelination. Arylsulfatase A requires the posttranslational oxidation of the -CH2SH group of a conserved cysteine to an aldehyde, yielding a formylglycine to be in an active form. 479 matched cddid_all.tbl CDD cd16159 cd16159 293778 ES Estrone sulfatase. Human estrone sulfatase (ES) is responsible for maintaining high levels of the active estrogen in tumor cells. ES catalyzes the hydrolysis of E1 sulfate, which is a component of the three-enzyme system that has been implicated in intracrine biosynthesis of estradiol. It is associated with the membrane of the endoplasmic reticulum (ER). The structure of ES consisting of two antiparallel alpha helices that protrude from the roughly spherical molecule. These highly hydrophobic helices anchor the functional domain on the membrane surface facing the ER lumen. 521 matched cddid_all.tbl CDD cd16160 cd16160 293779 spARS_like sea urchin arylsulfatase-like. This family includes sea urchin arylsulfatase and its homologous proteins. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 445 matched cddid_all.tbl CDD cd16161 cd16161 293780 ARSG arylsulfatase G. Arylsulfatase G is a subfamily of sulfatases which specifically hydrolyze sulfate esters in a wide variety of substrates such as glycosaminoglycans, steroid sulfates, or sulfolipids. ARSG has arylsulfatase activity toward different pseudosubstrates like p-nitrocatechol sulfate and 4-methylumbelliferyl sulfate. An active site Cys is post-translationally converted to the critical active site C(alpha)-formylglycine. ARSG mRNA expression was found to be tissue-specific with highest expression in liver, kidney, and pancreas, suggesting a metabolic role of ARSG that might be associated with a non-classified lysosomal storage disorder. 383 matched cddid_all.tbl CDD cd16162 cd16162 293881 OCRE_RBM5_like OCRE domain found in RNA-binding protein RBM5, RBM10, and similar proteins. RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing, and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain. 56 matched cddid_all.tbl CDD cd16163 cd16163 293882 OCRE_RBM6 OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins. RBM6, also called lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both specifically binds poly(G) RNA. RBM6 contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has an additional unique domain, the POZ (poxvirus and zinc finger) domain, which may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers. 57 matched cddid_all.tbl CDD cd16164 cd16164 293883 OCRE_VG5Q OCRE domain found in angiogenic factor VG5Q and similar proteins. VG5Q, also called angiogenic factor with G patch and FHA domains 1 (AGGF1), or G patch domain-containing protein 7, or vasculogenesis gene on 5q protein, functions as a potent angiogenic factor in promoting angiogenesis through interacting with TWEAK (also known as TNFSF12), which is a member of the tumor necrosis factor (TNF) superfamily that induces angiogenesis in vivo. VG5Q can bind to the surface of endothelial cells and promote cell proliferation, suggesting that it may act in an autocrine fashion. The chromosomal translocation t(5;11) and the E133K variant in VG5Q are associated with Klippel-Trenaunay syndrome (KTS), a disorder characterized by diverse effects in the vascular system. In addition to a forkhead-associated (FHA) domain and a G-patch motif, VG5Q contains an N-terminal OCtamer REpeat (OCRE) domain that is characterized by a 5-fold, imperfectly repeated octameric sequence. 54 matched cddid_all.tbl CDD cd16165 cd16165 293884 OCRE_ZOP1_plant OCRE domain found in Zinc-finger and OCRE domain-containing Protein 1 (ZOP1) and similar proteins found in plant. ZOP1 is a novel plant-specific nucleic acid-binding protein required for both RNA-directed DNA methylation (RdDM) and pre-mRNA splicing. It promotes RNA polymerase IV (Pol IV)-dependent siRNA accumulation, DNA methylation, and transcriptional silencing. As a pre-mRNA splicing factor, ZOP1 associates with several typical splicing proteins as well as with RNA polymerase II (RNAP II and Pol II). It also shows both RdDM-dependent and -independent roles in transcriptional silencing. ZOP1 contains an N-terminal C2H2-type ZnF domain and an OCtamer REpeat (OCRE) domain that is usually related to RNA processing. 55 matched cddid_all.tbl CDD cd16166 cd16166 293885 OCRE_SUA_like OCRE domain found in Suppressor of ABI3-5 (SUA) and similar proteins. SUA is an RNA-binding protein located in the nucleus and expressed in all plant tissues. It functions as a splicing factor that influences seed maturation by controlling alternative splicing of ABI3. The suppression of the cryptic ABI3 intron indicates a role of SUA in mRNA processing. SUA also interacts with the prespliceosomal component U2AF65, the larger subunit of the conserved pre-mRNA splicing factor U2AF. SUA contains two RNA recognition motifs surrounding a zinc finger domain, an OCtamer REpeat (OCRE) domain, and a Gly-rich domain close to the C-terminus. 54 matched cddid_all.tbl CDD cd16167 cd16167 293886 OCRE_RBM10 OCRE domain found in RNA-binding protein 10 (RBM10) and similar proteins. RBM10, also called G patch domain-containing protein 9, or RNA-binding protein S1-1 (S1-1), is a paralogue of putative tumor suppressor RNA-binding protein 5 (RBM5 or LUCA15 or H37). It may play an important role in mRNA generation, processing and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. RBM10 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain. 64 matched cddid_all.tbl CDD cd16168 cd16168 293887 OCRE_RBM5 OCRE domain found in RNA-binding protein 5 (RBM5) and similar proteins. RBM5 is also called protein G15, H37, putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9. It is a known modulator of apoptosis. It acts as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both of them specifically binds poly(G) RNA. RBM5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. 56 matched cddid_all.tbl CDD cd16169 cd16169 320085 Tau138_eWH extended winged-helix domain of tau138 and related proteins. Tau138 is one of three subunits of the tauB subcomplex of yeast transcription factor IIIC. This extended winged-helix domain of tau138 appears to interact with the TPR (tetratricopeptide repeat) array of tauA subunit tau131, and may therefore play a role in linking tauA, tauB, and TFIIIB to regulate the formation of the RNA polymerase III pre-initiation complex. 97 matched cddid_all.tbl CDD cd16170 cd16170 320084 MvaT_DBD DNA-binding domain of the bacterial xenogeneic silencer MvaT. MvaT is a xenogeneic silencer conserved in Pseudomonas which assists in distinguishing foreign from self DNA. It prefers binding to flexible DNA segments with multiple TpA steps, and forms nucleoprotein filaments through cooperative polymerization. 42 matched cddid_all.tbl CDD cd16171 cd16171 293781 ARSK arylsulfatase family, member K ....arylsulfatase k short ask flags precursor. ARSK is a lysosomal sulfatase which exhibits an acidic pH optimum for catalytic activity against arylsulfate substrates. Other names for ARSK include arylsulfatase K and TSULF. Sulfatases catalyze the hydrolysis of sulfate esters from wide range of substrates, including steroids, carbohydrates and proteins. Sulfate esters may be formed from various alcohols and amines. The biological roles of sulfatase includes the cycling of sulfur in the environment, in the degradation of sulfated glycosaminoglycans and glycolipids in the lysosome, and in remodeling sulfated glycosaminoglycans in the extracellular space. The sulfatases are essential for human metabolism. At least eight human monogenic diseases are caused by the deficiency of individual sulfatases. 366 matched cddid_all.tbl CDD cd16172 cd16172 293930 TorS_sensor_domain sensor domain of the sensor histidine kinase TorS. TorS is part of the trimethylamine-N-oxide (TMAO) reductase (Tor) pathway, which consists TorT, a periplasmic binding protein that binds TMAO; TorS, a sensor histidine kinase that forms a complex with TorT, and TorR, the response regulator. The Tor pathway is involved in regulating a cellular response to trimethylamine-N-oxide (TMAO), a terminal electron receptor in anaerobic respiration. TorS consists of a periplasmic sensor domain, as well as a HAMP domain, a histidine kinase domain, and a receiver domain. 261 matched cddid_all.tbl CDD cd16173 cd16173 320081 EFh_MICU1 EF-hand, calcium binding motif, found in calcium uptake protein 1, mitochondrial (MICU1) and similar proteins. MICU1, also termed atopy-related autoantigen CALC (ara CALC), or calcium-binding atopy-related autoantigen 1 (CBARA1), or Hom s 4, or EFHA3, localizes to the inner mitochondrial membrane (IMM). It functions as a gatekeeper of the mitochondrial calcium uniporter (MCU) and regulates MCU-mediated mitochondrial Ca2+ uptake, which is essential for maintaining mitochondrial homoeostasis. MICU1 and its paralog, MICU2, are physically associated within the uniporter complex and are co-expressed across all tissues. They may operate together with MCU to regulate the channel. The mutations in MICU1 are associated with neuromuscular abnormalities in children. MICU1 contains an N-terminal mitochondrial targeting sequence (MTS) as well as two evolutionarily conserved canonical Ca2+-binding EF-hands separated by a long stretch of residues predicted to form alpha-helices. 153 matched cddid_all.tbl CDD cd16174 cd16174 320082 EFh_MICU2 EF-hand, calcium binding motif, found in calcium uptake protein 2, mitochondrial (MICU2) and similar proteins. MICU2, also termed EF-hand domain-containing family member A1 (EFHA1), is a mitochondrial-localized paralog of MICU1. MICU2 and its paralog, MICU1, are physically associated within the mitochondrial calcium uniporter (MCU) complex and are co-expressed across all tissues. They may operate together with MCU to regulate the channel. At present, the precise molecular function of MICU2 remains unclear. It may play possible roles in Ca2+ sensing and regulation of MCU, calcium buffering with a secondary impact on transport or assembly and stabilization of MCU. MICU2 contains an N-terminal mitochondrial targeting sequence (MTS) as well as two evolutionarily conserved canonical Ca2+-binding EF-hands separated by a long stretch of residues predicted to form alpha-helices. 154 matched cddid_all.tbl CDD cd16175 cd16175 320083 EFh_MICU3 EF-hand, calcium binding motif, found in calcium uptake protein 3, mitochondrial (MICU3) and similar proteins. MICU3, also termed EF-hand domain-containing family member A2 (EFHA2), is a paralog of MICU1 and notably found in the central nervous system (CNS) and skeletal muscle. At present, the precise molecular function of MICU3 remains unclear. It likely has a role in mitochondrial calcium handling. MICU3 contains an N-terminal mitochondrial targeting sequence (MTS) as well as two evolutionarily conserved canonical Ca2+-binding EF-hands separated by a long stretch of residues predicted to form alpha-helices. 128 matched cddid_all.tbl CDD cd16176 cd16176 320076 EFh_HEF_CB EF-hand, calcium binding motif, found in calbindin (CB). CB, also termed calbindin D28, or D-28K, or avian-type vitamin D-dependent calcium-binding protein, is a unique intracellular calcium binding protein that functions as both a calcium sensor and buffer in eukaryotic cells, which undergoes a conformational change upon calcium binding and protects cells against insults of high intracellular calcium concentration. CB is highly expressed in brain and sensory neurons. It plays essential roles in neural functioning, altering synaptic interactions in the hippocampus, modulating calcium channel activity, calcium transients, and intrinsic neuronal firing activity. It prevents a neuronal death, as well as maintains and controls calcium homeostasis. CB also modulates the activity of proteins participating in the development of neurodegenerative disorders such as Alzheimer's disease, Huntington's disease, and bipolar disorder. Moreover, CB interacts with Ran-binding protein M, a protein known to involve in microtubule function. It also interacts with alkaline phosphatase and myo-inositol monophosphatase, as well as caspase 3, an enzyme that plays an important role in the regulation of apoptosis. CB contains six EF-hand motifs in a single globular domain, where EF-hands 1, 3, 4, 5 bind four calcium ions with high affinity. 243 matched cddid_all.tbl CDD cd16177 cd16177 320077 EFh_HEF_CR EF-hand, calcium binding motif, found in calretinin (CR). CR, also termed 29 kDa calbindin, is a cytosolic hexa-EF-hand calcium-binding protein predominantly expressed in a variety of normal and tumorigenic t specific neurons of the central and peripheral nervous system. It possibly functions as a calcium buffer, calcium sensor, and apoptosis regulator, which may be implicated in many biological processes, including cell proliferation, differentiation, and cell death. CR contains six EF-hand motifs within two independent domains, CR I-II and CR III-VI. CR I-II consists of EF-hand motifs 1 and 2, and CR III-VI consists of EF-hand motifs 3-6. The first 5 EF-hand motifs are capable of binding calcium ions, while the EF-hand 6 is inactive. Thus, CR has two pairs of cooperative binding sites (I-II and III-IV), which display high affinity calcium-binding sites, and one independent calcium ion-binding site (V), which displays lower affinity binding. 248 matched cddid_all.tbl CDD cd16178 cd16178 320078 EFh_HEF_SCGN EF-hand, calcium binding motif, found in secretagogin (SCGN). SCGN is a six EF-hand calcium-binding protein expressed in neuroendocrine, pancreatic endocrine and retinal cells. It plays a crucial role in cell apoptosis, receptor signaling and differentiation. It is also involved in vesicle secretion through binding to various proteins, including interacts with SNAP25, SNAP23, DOC2alpha, ARFGAP2, rootletin, KIF5B, beta-tubulin, DDAH-2, ATP-synthase and myeloid leukemia factor 2. SCGN functions as a calcium sensor/coincidence detector modulating vesicular exocytosis of neurotransmitters, neuropeptides or hormones. It also serves as a calcium buffer in neurons. Thus, SCGN may be linked to the pathogenesis of neurological diseases such as Alzheimer's, and also acts as a serum marker of neuronal damage, or as a tumor biomarker. SCGN consists of the three globular domains each of which contains a pair of EF-hand motifs. All six EF hand motifs of SCGN in some eukaryotes, including D. rerio, X. laevis, M. domestica, G. gallus, O. anatinus, could potentially bind six calcium ions. In contrast, SCGNs from higher eukaryotes have at least one non-functional EF-hand motif due to the mutation(s) or deletions. For instance, the EF1 loop does not coordinate calcium ion due to the key residue asparagine replaced by lysine in SCGNs of many mammalian species. Moreover, the EF2 loop seems to be competent for calcium-binding in most mammalian SCGNs except for human and chimpanzee orthologs. 257 matched cddid_all.tbl CDD cd16179 cd16179 320079 EFh_HEF_CBN EF-hand, calcium binding motif, found in Drosophila melanogaster calbindin-32 (CBN) and similar proteins. CBN, the product of the cbn gene, is a Drosophila homolog to vertebrate neuronal six EF-hand calcium binding proteins. It is expressed through most of ontogenesis with a selective distribution in the nervous system and in a few small adult thoracic muscles. Its precise biological role remains unclear. CBN contains six EF-hand motifs, but some of them may not bind calcium ions due to the lack of key residues. 261 matched cddid_all.tbl CDD cd16180 cd16180 320055 EFh_PEF_Group_I Penta-EF hand, calcium binding motifs, found in Group I PEF proteins. The family corresponds to Group I PEF proteins that have been found not only in higher animals but also in lower animals, plants, fungi and protists. Group I PEF proteins include apoptosis-linked gene 2 protein (ALG-2), peflin and similar proteins. ALG-2, also termed programmed cell death protein 6 (PDCD6), is a widely expressed calcium-binding modulator protein associated with cell proliferation and death, as well as cell survival. It forms a homodimer in the cell or a heterodimer with its closest paralog peflin. Among the PEF proteins, ALG-2 can bind three Ca2+ ions through its EF1, EF3, and EF5 hands, where it is unique in that its EF5 hand binds Ca2+ ion in a canonical coordination. Peflin is a ubiquitously expressed 30-kD PEF protein containing five EF-hand motifs in its C-terminal domain and a longer N-terminal hydrophobic domain (NHB domain) than any other member of the PEF family. The NHB domain harbors nine repeats of a nonapeptide (A/PPGGPYGGP). Peflin may modulate the function of ALG-2 in Ca2+ signaling. It exists only as a heterodimer with ALG-2, and binds two Ca2+ ions through its EF1 and EF3 hands. Its additional EF5 hand is unpaired and does not bind Ca2+ ion but mediates the heterodimerization with ALG-2. The dissociation of heterodimer occurs in the presence of Ca2+. 164 matched cddid_all.tbl CDD cd16181 cd16181 320056 EFh_PEF_Group_II_sorcin_like Penta-EF hand, calcium binding motifs, found in sorcin, grancalcin, and similar proteins. The family corresponds to the second group of penta-EF hand (PEF) proteins that includes sorcin, grancalcin, and similar proteins. Sorcin, also termed 22 kDa Ca2+-binding protein, CP-22, or V19, is a soluble resistance-related calcium-binding protein that is expressed in normal mammalian tissues, such as the liver, lungs and heart. It contains a flexible glycine and proline-rich N-terminal extension and five EF-hand motifs that associate with membranes in a calcium-dependent manner. It may harbor three potential Ca2+ binding sites through its EF1, EF2 and EF3 hands. However, binding of only two Ca2+/monomer suffices to trigger the conformational change that exposes hydrophobic regions and leads to interaction with the respective targets. Sorcin forms homodimers through the association of the unpaired EF5 hand. Among the PEF proteins, sorcin is unique in that it contains potential phosphorylation sites by cAMP-dependent protein kinase (PKA), and it can form a tetramer at slightly acid pH values although remaining a stable dimer at neutral pH. Grancalcin (GCA) is a cytosolic Ca2+-binding protein specifically expressed in neutrophils and monocytes/macrophages. It can strongly interact with sorcin to form a heterodimer and further modulate the function of sorcin. GCA exists as homodimers in solution. It contains five EF-hand motifs attached to an N-terminal region of an approximately 50 residue-long segment rich in glycines and prolines. In contrast with sorcin, GCA binds two Ca2+ ions through its EF1 and EF3 hands. 165 matched cddid_all.tbl CDD cd16182 cd16182 320057 EFh_PEF_Group_II_CAPN_like Penta-EF hand, calcium binding motifs, found in PEF calpain family. The PEF calpain family belongs to the second group of penta-EF hand (PEF) proteins. It includes classical (also called conventional or typical) calpain (referring to a calcium-dependent papain-like enzymes, EC 3.4.22.17) large catalytic subunits (CAPN1, 2, 3, 8, 9, 11, 12, 13, 14) and two calpain small subunits (CAPNS1 and CAPNS2), which are largely confined to animals (metazoans). These PEF-containing are nonlysosomal intracellular calcium-activated intracellular cysteine proteases that play important roles in the degradation or functional modulation in a variety of substrates in response to calcium signalling. The classical mu- and m-calpains are heterodimers consisting of homologous but a distinct (large) L-subunit/chain (CAPN1 or CAPN2) and a common (small) S-subunit/chain (CAPNS1 or CAPNS2). These L-subunits (CAPN1 and CAPN2) and S-subunit CAPNS1 are ubiquitously found in all tissues. Other calpains likely consist of an isolated L-subunit/chain alone. Many of them, such as CAPNS2, CAPN3 (in skeletal muscle, or lens), CAPN8 (in stomach), CAPN9 (in digestive tracts), CAPN11 (in testis), CAPN12 (in follicles), are tissue-specific and have specific functions in distinct organs. The L-subunits of similar structure (called CALPA and B) also have been found in Drosophila melanogaster. The S-subunit seems to have a chaperone-like function for proper folding of the L-subunit. The catalytic L-subunits contain a short N-terminal anchor helix, followed by a calpain cysteine protease (CysPc) domain, a C2-domain-like (C2L) domain, and a C-terminal Ca2+-binding penta-EF-hand (PEF) domain. The S-subunits only have the PEF domain following an N-terminal Gly-rich hydrophobic domain. The calpains undergo a rearrangement of the protein backbone upon Ca2+-binding. 167 matched cddid_all.tbl CDD cd16183 cd16183 320058 EFh_PEF_ALG-2 EF-hand, calcium binding motif, found in apoptosis-linked gene 2 protein (ALG-2) and similar proteins. ALG-2, also termed programmed cell death protein 6 (PDCD6), or probable calcium-binding protein ALG-2, is one of the prototypic members of the penta EF-hand protein family. It is a widely expressed calcium-binding modulator protein associated with cell proliferation and death, as well as cell survival. ALG-2 acts as a pro-apoptotic factor participating in T cell receptor-, Fas-, and glucocorticoid-induced programmed cell death, and also serves as a useful molecular marker for the prognosis of cancers. Moreover, ALG-2 functions as a calcium ion sensor at endoplasmic reticulum (ER) exit sites, and modulates ER-stress-stimulated cell death and neuronal apoptosis during organ formation. Furthermore, ALG-2 can mediate the pro-apoptotic activity of cisplatin or tumor necrosis factor alpha (TNFalpha) through the down-regulation of nuclear factor-kappaB (NF-kappaB) expression. It also inhibits angiogenesis through PI3K/mTOR/p70S6K pathway by interacting of vascular endothelial growth factor receptor-2 (VEGFR-2). In addition, nuclear ALG-2 may participate in the post-transcriptional regulation of Inositol Trisphosphate Receptor Type 1 (IP3R1) pre-mRNA at least in part by interacting with CHERP (Ca2+ homeostasis endoplasmic reticulum protein) calcium-dependently. ALG-2 contains five serially repeated EF-hand motifs and interacts with various proteins, including ALG-2-interacting protein X (Alix), Fas, annexin XI, death-associated protein kinase 1 (DAPk1), Tumor susceptibility gene 101 (TSG101), Sec31A, phospholipid scramblase 3 (PLSCR3), the P-body component PATL1, and endosomal sorting complex required for transport (ESCRT)-III-related protein IST1, in a calcium-dependent manner. It forms a homodimer in the cell or a heterodimer with its closest paralog peflin. Among the PEF proteins, ALG-2 can bind three Ca2+ ions through its EF1, EF3, and EF5 hands, where it is unique in that its EF5 hand binds Ca2+ ion in a canonical coordination. 165 matched cddid_all.tbl CDD cd16184 cd16184 320059 EFh_PEF_peflin EF-hand, calcium binding motif, found in peflin and similar proteins. Peflin, also termed penta-EF hand (PEF) protein with a long N-terminal hydrophobic domain, or penta-EF hand domain-containing protein 1, is a ubiquitously expressed 30-kD PEF protein containing five EF-hand motifs in its C-terminal domain and a longer N-terminal hydrophobic domain (NHB domain) than any other member of the PEF family. The NHB domain harbors nine repeats of a nonapeptide (A/PPGGPYGGP). Peflin may modulate the function of ALG-2 in Ca2+ signaling. It exists only as a heterodimer with ALG-2, and binds two Ca2+ ions through its EF1 and EF3 hands. Its additional EF5 hand is unpaired and does not bind Ca2+ ion but mediates the heterodimerization with ALG-2. The dissociation of heterodimer occurs in the presence of Ca2+. In lower vertebrates, peflin may interact with transient receptor potential N (TRPN1), suggesting a potential role of peflin in fast transducer channel adaptation. 165 matched cddid_all.tbl CDD cd16185 cd16185 320060 EFh_PEF_ALG-2_like EF-hand, calcium binding motif, found in homologs of mammalian apoptosis-linked gene 2 protein (ALG-2). The family includes some homologs of mammalian apoptosis-linked gene 2 protein (ALG-2) mainly found in lower eukaryotes, such as a parasitic protist Leishmarua major and a cellular slime mold Dictyostelium discoideum. These homologs contains five EF-hand motifs. Due to the presence of unfavorable residues at the Ca2+-coordinating positions, their non-canonical EF4 and EF5 hands may not bind Ca2+. Two Dictyostelium PEF proteins are the prototypes of this family. They may bind to cytoskeletal proteins and/or signal-transducing proteins localized to detergent-resistant membranes named lipid rafts, and occur as monomers or weak homo- or heterodimers like ALG-2. They can serve as a mediator for Ca2+ signaling-related Dictyostehum programmed cell death (PCD). 163 matched cddid_all.tbl CDD cd16186 cd16186 320061 EFh_PEF_grancalcin Penta-EF hand, calcium binding motifs, found in grancalcin. Grancalcin (GCA) is a cytosolic Ca2+-binding protein specifically expressed in neutrophils and monocytes/macrophages. It displays a Ca2+-dependent translocation to granules and plasma membrane upon neutrophil activation, suggesting roles in granule-membrane fusion and degranulation of neutrophils. It may also play a role in the regulation of vesicle/granule exocytosis through the reversible binding of secretory vesicles and plasma membranes upon the presence of calcium. Moreover, GCA is involved in inflammation, as well as in the process of adhesion of neutrophils to fibronectin. It plays a key role in leukocyte-specific functions that are responsible for host defense, and affects the function of integrin receptors on immune cells through binding to L-plastin in the absence of calcium. Furthermore, GCA can strongly interact with sorcin to form a heterodimer, and further modulate the function of sorcin. GCA exists as homodimers in solution. It contains five EF-hand motifs attached to an N-terminal region of an approximately 50 residue-long segment rich in glycines and prolines. GCA binds two Ca2+ ions through its EF1 and EF3 hands. 165 matched cddid_all.tbl CDD cd16187 cd16187 320062 EFh_PEF_sorcin Penta-EF hand, calcium binding motifs, found in sorcin. Sorcin, also termed 22 kDa Ca2+-binding protein, CP-22, or V19, is a soluble resistance-related calcium-binding protein that is expressed in normal mammalian tissues, such as the liver, lungs and heart. The up-regulation of sorcin is correlated with a number of cancer types, including colorectal, gastric and breast cancer. It may represent a therapeutic target for reversing tumor multidrug resistance (MDR). Sorcin participates in the regulation of calcium homeostasis in cells and is necessary for the activation of mitosis and cytokinesis. It enhances metastasis and promotes epithelial-to-mesenchymal transition of colorectal cancer. Moreover, sorcin has been implicated in the regulation of intracellular Ca2+ cycling and cardiac excitation-contraction coupling. It displays the anti-apoptotic properties via the modulation of mitochondrial Ca2+ handling in cardiac myocytes. It can target and activate the sarcolemmal Na+/Ca2+ exchanger (NCX1) in cardiac muscle. Meanwhile, sorcin modulates cardiac L-type Ca2+ current by functional interaction with the alpha1C subunit. It also associates with calcium/calmodulin-dependent protein kinase IIdeltaC (CaMKIIdelta(C)) and further modulates ryanodine receptor (RyR) function in cardiac myocytes. Furthermore, sorcin may act as a Ca2+ sensor for glucose-induced nuclear translocation and the activation of carbohydrate-responsive element-binding protein (ChREBP)-dependent genes. As a mitochondrial chaperone TRAP1 interactor, sorcin involves in mitochondrial metabolism through the TRAP1 pathway. In addition, sorcin may regulate the inhibition of type I interferon response in cells through interacting with foot-and-mouth disease virus (FMDV) VP1. Sorcin contains a flexible glycine and proline-rich N-terminal extension and five EF-hand motifs that associate with membranes in a calcium-dependent manner. It may harbor three potential Ca2+ binding sites through its EF1, EF2 and EF3 hands. However, binding of only two Ca2+/monomer suffices to trigger the conformational change that exposes hydrophobic regions and leads to interaction with the respective targets. Sorcin forms homodimers through the association of the unpaired EF5 hand. Among the PEF proteins, sorcin is unique in that it contains potential phosphorylation sites by cAMP-dependent protein kinase (PKA), and it can form a tetramer at slightly acid pH values although remaining a stable dimer at neutral pH. 165 matched cddid_all.tbl CDD cd16188 cd16188 320063 EFh_PEF_CPNS1_2 Penta-EF hand, calcium binding motifs, found in calcium-dependent protease small subunit CAPNS1 and CAPNS2. CAPNS1, also termed calpain small subunit 1 (CSS1), or calcium-activated neutral proteinase small subunit (CANP small subunit), or calcium-dependent protease small subunit (CDPS), or calpain regulatory subunit, is a common 28-kDa regulatory calpain subunit encoded by the calpain small 1 (Capns1, also known as Capn4) gene. It acts as a binding partner to form a heterodimer with the 80 kDa calpain large catalytic subunit and is required in maintaining the activity of calpain. CAPNS1 plays a significant role in tumor progression of human cancer, and functions as a potential therapeutic target in human hepatocellular carcinoma (HCC), nasopharyngeal carcinoma (NPC), glioma, and clear cell renal cell carcinoma (ccRCC). It may be involved in regulating migration and cell survival through binding to the SH3 domain of Ras GTPase-activating protein (RasGAP). It may also modulate Akt/FoxO3A signaling and apoptosis through PP2A. CAPNS1 contains an N-terminal glycine rich domain and a C-terminal PEF-hand domain. CAPNS2, also termed calpain small subunit 2 (CSS2), is a novel tissue-specific 30 kDa calpain small subunit that lacks two oligo-Gly stretches characteristic of the N-terminal Gly-rich domain of CAPNS1. CAPNS2 acts as a chaperone for the calpain large subunit, and appears to be the functional equivalent of CAPNS1. However, CAPNS2 binds the large subunit much more weakly than CAPNS1 and it does not undergo the autolytic conversion typical of CAPNS1. 169 matched cddid_all.tbl CDD cd16189 cd16189 320064 EFh_PEF_CAPN1_like Penta-EF hand, calcium binding motifs, found in mu-type calpain (CAPN1), m-type calpain (CAPN2), and similar proteins. The family includes mu-type calpain (CAPN1) and m-type calpain (CAPN2), both of which are ubiquitously expressed 80-kDa Ca2+-dependent intracellular cysteine proteases that contain a short N-terminal anchor helix, followed by a calpain cysteine protease (CysPc) domain, a C2-domain-like (C2L) domain, and a C-terminal Ca2+-binding penta-EF-hand (PEF) domain. The catalytic subunit CAPN1 or CAPN2 in complex with a regulatory subunit encoded by CAPNS1 forms a mu- or m-calpain heterodimer, respectively. 168 matched cddid_all.tbl CDD cd16190 cd16190 320065 EFh_PEF_CAPN3 Calcium-activated neutral. CAPN3, also termed calcium-activated neutral proteinase 3 (CANP 3), or calpain L3, or calpain p94, or muscle-specific calcium-activated neutral protease 3, or new calpain 1 (nCL-1), is a calpain large subunit that is mainly expressed in skeletal muscle, or lens. The skeletal muscle-specific CAPN3 are pathologically associated with limb girdle muscular dystrophy type 2A (LGMD2A). Its autolytic activity can be positively regulated by calmodulin (CaM), a known transducer of the calcium signal. CAPN3 is also involved in human melanoma tumorigenesis and progression. It impairs cell proliferation and stimulates oxidative stress-mediated cell death in melanoma cells. Moreover, it plays an important role in sarcomere remodeling and mitochondrial protein turnover. Furthermore, the phosphorylated skeletal muscle-specific CAPN3 acts as a myofibril structural component and may participate in myofibril-based signaling pathways. In the eye, the lens-specific CAPN3, together with CAPN2, is responsible for proteolytic cleavages of alpha and beta-crystallin. Overactivated alpha and beta-crystallin can lead to cataract formation. CAPN3 exists as a homodimer, rather than a heterodimer with the calpain small subunit. It may also form heterodimers with other calpain large subunits. CAPN3 contains a long N-terminal region, followed by a calpain cysteine protease (CysPc) domain, a C2-domain-like (C2L) domain, and a C-terminal Ca2+-binding penta-EF-hand (PEF) domain. Ca2+ binding at EF5 of the CAPN3 PEF domain is a distinct feature not observed in other calpain isoforms. 169 matched cddid_all.tbl CDD cd16191 cd16191 320066 EFh_PEF_CAPN8 Penta-EF hand, calcium binding motifs, found in calpain-8 (CAPN8). CAPN8, also termed new calpain 2 (nCL-2), or stomach-specific M-type calpain, is a calpain large subunit predominantly expressed in the stomach. It appears to be involved in membrane trafficking in the gastric surface mucus cells (pit cells), via its location at the Golgi and interaction with the beta-subunit of coatomer complex (beta-COP) of vesicles derived from the Golgi. Moreover, CAPN8, together with CAPN9, forms an active protease complex, G-calpain, in which both proteins are essential for stability and activity. The G-Calpain has been implicated in gastric mucosal defense. CAPN8 exists as both a monomer and homo-oligomer, but not as a heterodimer with the conventional calpain regulatory subunit (30K). The monomer and homodimer forms predominate. CAPN8 contains a short N-terminal anchor helix, followed by a calpain cysteine protease (CysPc) domain, a C2-domain-like (C2L) domain, and a C-terminal Ca2+-binding penta-EF-hand (PEF) domain. 168 matched cddid_all.tbl CDD cd16192 cd16192 320067 EFh_PEF_CAPN9 Penta-EF hand, calcium binding motifs, found in calpain-9 (CAPN9). CAPN9, also termed digestive tract-specific calpain, or new calpain 4 (nCL-4), or protein CG36, is a calpain large subunit predominantly expressed in gastrointestinal tract. It plays a physiological role in the suppression of tumorigenesis. It acts as an important biomolecule link for the regression of colorectal cancer via intracellular calcium homeostasis. CAPN9 may also play a critical role in lumen formation. Moreover, CAPN9, together with CAPN8, forms an active protease complex, G-calpain, in which both proteins are essential for stability and activity. The G-Calpain has been implicated in gastric mucosal defense. Furthermore, down-regulation of calpain 9 has been linked to hypertensive heart and kidney disease in salt-sensitive Dahl rats. CAPN9 contains a short N-terminal anchor helix, followed by a calpain cysteine protease (CysPc) domain, a C2-domain-like (C2L) domain, and a C-terminal Ca2+-binding penta-EF-hand (PEF) domain. 169 matched cddid_all.tbl CDD cd16193 cd16193 320068 EFh_PEF_CAPN11 Penta-EF hand, calcium binding motifs, found in calpain-11 (CAPN11). CAPN11, also termed calcium-activated neutral proteinase 11 (CANP 11), is a mammalian orthologue of micro/m calpain. It is one of the calpain large subunits that appears to be exclusively expressed in certain cells of the testis. It may be involved in regulating calcium-dependent signal transduction events during meiosis and sperm functional processes. CAPN11 contains a short N-terminal anchor helix, followed by a calpain cysteine protease (CysPc) domain, a C2-domain-like (C2L) domain, and a C-terminal Ca2+-binding penta-EF-hand (PEF) domain. 169 matched cddid_all.tbl CDD cd16194 cd16194 320069 EFh_PEF_CAPN12 Penta-EF hand, calcium binding motifs, found in calpain-12 (CAPN12). CAPN12, also termed calcium-activated neutral proteinase 12 (CANP 12), is a calpain large subunit mainly expressed in the cortex of the hair follicle. It may affect apoptosis regulation. CAPN12 contains a short N-terminal anchor helix, followed by a calpain cysteine protease (CysPc) domain, a C2-domain-like (C2L) domain, and a C-terminal Ca2+-binding penta-EF-hand (PEF) domain. 169 matched cddid_all.tbl CDD cd16195 cd16195 320070 EFh_PEF_CAPN13_14 Penta-EF hand, calcium binding motifs, found in calpain-13 (CAPN13), calpain-14 (CAPN14), and similar proteins. CAPN13, also termed calcium-activated neutral proteinase 13 (CANP 13), a 63.6 kDa calpain large subunit that exhibits a restricted tissue distribution with low levels of expression detected only in human testis and lung. In calpain family, CAPN13 is most closely related to calpain-14 (CAPN14). CAPN14, also termed calcium-activated neutral proteinase 14 (CANP 14), is a 76.7 kDa calpain large subunit that is most highly expressed in the oesophagus. Its expression and calpain activity can be induced by IL-13. Both CAPN13 and CAPN14 contain a calpain cysteine protease (CysPc) domain, a C2-domain-like (C2L) domain, and a C-terminal Ca2+-binding penta-EF-hand (PEF) domain. 168 matched cddid_all.tbl CDD cd16196 cd16196 320071 EFh_PEF_CalpA_B Penta-EF hand, calcium binding motifs, found in Drosophila melanogaster calpain-A (CalpA), calpain-B (CalpB), and similar proteins. The family contains two calpains that have been found in Drosophila, CalpA and CalpB. CalpA, also termed calcium-activated neutral proteinase A (CANP A), or calpain-A catalytic subunit, is a Drosophila calpain homolog specifically expressed in a few neurons in the central nervous system, in scattered endocrine cells in the midgut, and in blood cells. CalpB, also termed calcium-activated neutral proteinase B (CANP B), contains calpain-B catalytic subunit 1 and calpain-B catalytic subunit 2. Both CalpA and CalpB are closely related to that of vertebrate calpains, and they share similar domain architecture, which consists of four domains: the N-terminal domain I, the catalytic domain II carrying the three active site residues, Cys, His and Asn, the Ca2+-regulated phospholipid-binding domain III, and penta-EF-hand Ca2+-binding domain IV. Besides, CalpA and CalpB display some distinguishing structural features that are not found in mammalian typical calpains. CalpA harbors a 76 amino acid long hydrophobic stretch inserted in domain IV, which may be involved in membrane attachment of this enzyme. CalpB has an unusually long N-terminal tail of 224 amino acids, which belongs to the class of intrinsically unstructured proteins (IUP) and may become ordered upon binding to target protein(s). Moreover, they do not need small regulatory subunits for their catalytic activity, and their proteolytic function is not regulated by an intrinsic inhibitor as the Drosophila genome contains neither regulatory subunit nor calpastatin orthologs. As a result, they may exist as a monomer or perhaps as a homo- or heterodimer together with a second large subunit. Furthermore, both CalpA and CalpB are dispensable for viability and fertility and do not share vital functions during Drosophila development. Phosphatidylinositol 4,5-diphosphate, phosphatidylinositol 4-monophosphate, phosphatidylinositol, and phosphatidic acid can stimulate the activity and the rate of activation of CalpA, but not CalpB. Calpain A modulates Toll responses by limited Cactus/IkappaB proteolysis. CalpB directly interacts with talin, an important component of the focal adhesion complex, and functions as an important modulator in border cell migration within egg chambers, which may act via the digestion of talin. CalpB can be phosphorylated by cAMP-dependent protein kinase (protein kinase A, PKA; EC 2.7.11.11) at Ser240 and Ser845, as well as by mitogen-activated protein kinase (ERK1 and ERK2; EC 2.7.11.24) at Thr747. The activation of the ERK pathway by extracellular signals results in the phosphorylation and activation of calpain B. In Schneider cells (S2), calpain B was mainly in the cytoplasm and upon a rise in Ca2+ the enzyme adhered to intracellular membranes. 167 matched cddid_all.tbl CDD cd16197 cd16197 320072 EFh_PEF_CalpC Penta-EF hand, calcium binding motifs, found in Drosophila melanogaster calpain-C (CalpC) and similar proteins. CalpC, also termed calcium-activated neutral proteinase homolog C (CANP C), is a catalytically inactive homolog of CalpA and CalpB found in Drosophila. It is strongly expressed in the salivary glands. In contrast with CalpA and CalpB, both of which are closely related to that of vertebrate calpains, and they share similar domain architecture, which consists of four domains: the N-terminal domain I, the catalytic domain II carrying the three active site residues, Cys, His and Asn, the Ca2+-regulated phospholipid-binding domain III, and penta-EF-hand Ca2+-binding domain IV. CalpC is a truncated calpain form missing domain I and about 20 residues from domain II. Moreover, due to all three mutated active site residues (Cys to Arg, His to Val and Asn to Ser), it may not have proteolytic activity. 166 matched cddid_all.tbl CDD cd16198 cd16198 320073 EFh_PEF_CAPN1 Penta-EF hand, calcium binding motifs, found in mu-type calpain (CAPN1). CAPN1, also termed calpain-1 80-kDa catalytic subunit, or calpain-1 large subunit, or micromolar-calpain (muCANP), or calcium-activated neutral proteinase 1 (CANP 1), or cell proliferation-inducing gene 30 protein, is a ubiquitously expressed 80-kDa Ca2+-dependent intracellular cysteine protease that contains a short N-terminal anchor helix, followed by a calpain cysteine protease (CysPc) domain, a C2-domain-like (C2L) domain, and a C-terminal Ca2+-binding penta-EF-hand (PEF) domain. The catalytic subunit CAPN1 in complex with a regulatory subunit encoded by CAPNS1 forms a mu-calpain heterodimer. CAPN1 plays a central role in postmortem proteolysis and meat tenderization processes, as well as in regulation of proliferation and survival of skeletal satellite cells. It also acts as a novel regulator in IgE-mediated mast cell activation and could serve as a potential therapeutic target for the management of allergic inflammation. Moreover, CAPN1 is involved in neutrophil motility and functions as a potential target for intervention in inflammatory disease. It also facilitates age-associated aortic wall calcification and fibrosis through the regulation of matrix metalloproteinase 2 activity in vascular smooth muscle cells, and thus plays a role in hypertension and atherosclerosis. The proteolytic cleavage of beta-amyloid precursor protein and tau protein by CAPN1 may be involved in plaque formation. Furthermore, CAPN1 is activated in the brains of individuals with Alzheimer's disease. It is involved in the maintenance of a proliferative neural stem cell pool. The activation and macrophage inflammation of CAPN1 in hypercholesterolemic nephropathy is promoted by nicotinic acetylcholine receptor alpha1 (nAChRalpha1). In addition, CAPN1 displays a functional role in hemostasis, as well as in sickle cell disease. 169 matched cddid_all.tbl CDD cd16199 cd16199 320074 EFh_PEF_CAPN2 Penta-EF hand, calcium binding motifs, found in m-type calpain (CAPN2). CAPN2, also termed millimolar-calpain (m-calpain), or calpain-2 catalytic subunit, or calcium-activated neutral proteinase 2 (CANP 2), or calpain large polypeptide L2, or calpain-2 large subunit, is a ubiquitously expressed 80-kDa Ca2+-dependent intracellular cysteine protease that contains a short N-terminal anchor helix, followed by a calpain cysteine protease (CysPc) domain, a C2-domain-like (C2L) domain, and a C-terminal Ca2+-binding penta-EF-hand (PEF) domain. The catalytic subunit CAPN2 in complex with a regulatory subunit encoded by CAPNS1 forms an m-calpain heterodimer. CAPN2 acts as the key protease responsible for N-methyl-d-aspartic acid (NMDA)-induced cytoplasmic polyadenylation element-binding protein 3 (CPEB3) degradation in neurons. It cleaves several components of the focal adhesion complex, such as FAK and talin, triggering disassembly of the complex at the rear of the cell. The stimulation of CAPN2 activity is required for Golgi antiapoptotic proteins (GAAPs) to promote cleavage of FA kinase (FAK), cell spreading, and enhanced migration. calpain 2 is also involved in the onset of glial differentiation. It regulates proliferation, survival, migration, and tumorigenesis of breast cancer cells through a PP2A-Akt-FoxO-p27(Kip1) signaling cascade. Its expression is associated with response to platinum based chemotherapy, progression-free and overall survival in ovarian cancer. Moreover, CAPN2 may play a role in fundamental mitotic functions, such as the maintenance of sister chromatid cohesion. The activation of CAPN2 plays an essential role in hippocampal synaptic plasticity and in learning and memory. In the eye, CAPN2, together with a lens-specific variant of CAPN3, is responsible for proteolytic cleavages of alpha and beta-crystallin. Overactivated alpha and beta-crystallin can lead to cataract formation. Sometimes, CAPN2 compensates for loss of CAPN1, and both calpain isoforms are involved in AngII-induced aortic aneurysm formation. The main phosphorylation sites in m-calpain are Ser50 and Ser369/Thr370. 168 matched cddid_all.tbl CDD cd16200 cd16200 320030 EFh_PI-PLCbeta EF-hand motif found in metazoan phosphoinositide-specific phospholipase C (PI-PLC)-beta isozymes. PI-PLC-beta isozymes represent a class of metazoan PI-PLCs that hydrolyze the membrane lipid phosphatidylinositol 4,5-bisphosphate (PIP2) to propagate diverse intracellular responses that underlie the physiological action of many hormones, neurotransmitters, and growth factors (EC 3.1.4.11). They have been implicated in numerous processes relevant to central nervous system (CNS), including chemotaxis, cardiovascular function, neuronal signaling, and opioid sensitivity. Like other PI-PLC isozymes, PI-PLC-beta isozymes contain a core set of domains, including an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core, and a single C2 domain. Besides, they have a unique C-terminal coiled-coil (CT) domain necessary for homodimerization. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. There are four PI-PLC-beta isozymes (1-4). PI-PLC-beta1 and PI-PLC-beta3 are expressed in a wide range of tissues and cell types, whereas PI-PLC-beta2 and PI-PLC-beta4 have been found only in hematopoietic and neuronal tissues, respectively. All PI-PLC-beta isozymes are activated by the heterotrimeric G protein alpha subunits of the Gq class through their C2 domain and long C-terminal extension. They are GTPase-activating proteins (GAPs) for these G alpha(q) proteins. PI-PLC-beta2 and PI-PLC-beta3 can also be activated by beta-gamma subunits of the G alpha(i/o) family of heterotrimeric G proteins and the small GTPases such as Rac and Cdc42. This family also includes two invertebrate homologs of PI-PLC-beta, PLC21 from cephalopod retina and No receptor potential A protein (NorpA) from Drosophila melanogaster. 153 matched cddid_all.tbl CDD cd16201 cd16201 320031 EFh_PI-PLCgamma EF-hand motif found in phosphoinositide phospholipase C gamma isozymes (PI-PLC-gamma). PI-PLC-gamma isozymes represent a class of metazoan PI-PLCs that hydrolyze the membrane lipid phosphatidylinositol 4,5-bisphosphate (PIP2) to propagate diverse intracellular responses that underlie the physiological action of many hormones, neurotransmitters, and growth factors. They can form a complex with the phosphorylated cytoplasmic domains of the immunoglobulin Ig-alpha and Ig-beta subunits of the B cell receptor (BCR), the membrane-tethered Src family kinase Lyn, phosphorylated spleen tyrosine kinase (Syk), the phosphorylated adaptor protein B-cell linker (BLNK), and activated Bruton's tyrosine kinase (Btk). Like other PI-PLC isozymes, PI-PLC-gamma isozymes contain a core set of domains, including an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core, and a single C2 domain. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. Unique to PI-PLC-gamma, a second PH domain, which is split by two SH2 (Src homology 2) domains, and one SH3 (Src homology 3) domain, are present within this linker. The SH2 and SH3 domains are responsible for the binding of phosphotyrosine-containing sequences and proline-rich sequences, respectively. There are two PI-PLC-gamma isozymes (1-2), both of which are activated by receptor and non-receptor tyrosine kinases due to the presence of SH2 and SH3 domains. 145 matched cddid_all.tbl CDD cd16202 cd16202 320032 EFh_PI-PLCdelta EF-hand motif found in phosphoinositide phospholipase C delta (PI-PLC-delta). PI-PLC-delta isozymes represent a class of metazoan PI-PLCs that are some of the most sensitive to calcium among all PLCs. Their activation is modulated by intracellular calcium ion concentration, phospholipids, polyamines, and other proteins, such as RhoAGAP. Like other PI-PLC isozymes, PI-PLC-delta isozymes contain a core set of domains, including an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core, and a single C-terminal C2 domain. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. There are three PI-PLC-delta isozymes (1, 3 and 4). PI-PLC-delta1 is relatively well characterized. It is activated by high calcium levels generated by other PI-PLC family members, and therefore functions as a calcium amplifier within the cell. Different PI-PLC-delta isozymes have different tissue distribution and different subcellular locations. PI-PLC-delta1 is mostly a cytoplasmic protein, PI-PLC-delta3 is located in the membrane, and PI-PLC-delta4 is predominantly detected in the cell nucleus. PI-PLC-delta isozymes is evolutionarily conserved even in non-mammalian species, such as yeast, slime molds and plants. 140 matched cddid_all.tbl CDD cd16203 cd16203 320033 EFh_PI-PLCepsilon EF-hand motif found in phosphoinositide phospholipase C epsilon 1 (PI-PLC-epsilon1). PI-PLC-epsilon1, also termed 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1, or pancreas-enriched phospholipase C, or phospholipase C-epsilon-1 (PLC-epsilon-1), is dominant in connective tissues and brain. It has been implicated in carcinogenesis, such as in bladder and intestinal tumor, oesophageal squamous cell carcinoma, gastric adenocarcinoma, murine skin cancer, head and neck cancer. PI-PLC-epsilon1 contains an N-terminal CDC25 homology domain with a guanyl-nucleotide exchange factor (GFF) activity, a pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core domain, a C2 domain, and at least one and perhaps two C-terminal predicted RA (Ras association) domains that are implicated in the binding of small GTPases, such as Ras or Rap, from the Ras family. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. There is only one PI-PLC-epsilon isozyme. It is directly activated by G alpha(12/13), G beta gamma, and activated members of Ras and Rho small GTPases. 174 matched cddid_all.tbl CDD cd16204 cd16204 320034 EFh_PI-PLCzeta EF-hand motif found in phosphoinositide phospholipase C zeta 1 (PI-PLC-zeta1). PI-PLC-zeta1, also termed 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase zeta-1, or phospholipase C-zeta-1 (PLC-zeta-1), or testis-development protein NYD-SP27, is only found in the testis. The sperm-specific PI-PLC plays a fundamental role in vertebrate fertilization by initiating intracellular calcium oscillations that trigger the embryo development. However, the mechanism of its activation still remains unclear. PI-PLC-zeta1 contains an N-terminal four atypical EF-hand motifs, a PLC catalytic core domain, and a C-terminal C2 domain. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. Unlike other PI-PLCs, PI-PLC-zeta is responsible for Ca2+ oscillations in fertilized oocytes and exhibits a high sensitivity to Ca2+ mediated through its EF-hand domain. There is only one PLC-zeta isozyme. Aside from PI-PLC-zeta identified in mammals, its eukaryotic homologs have been classified with this family. 142 matched cddid_all.tbl CDD cd16205 cd16205 320035 EFh_PI-PLCeta EF-hand motif found in phosphoinositide phospholipase C eta (PI-PLC-eta). PI-PLC-eta isozymes represent a class of neuron-specific metazoan PI-PLCs that are most abundant in the brain, particularly in the hippocampus, habenula, olfactory bulb, cerebellum, and throughout the cerebral cortex. They are phosphatidylinositol 4,5-bisphosphate-hydrolyzing enzymes that are more sensitive to Ca2+ than other PI-PLC isozymes. They function as calcium sensors activated by small increases in intracellular calcium concentrations. They are also activated through G-protein-coupled receptor (GPCR) stimulation, and further mediate GPCR signalling pathways. PI-PLC-eta isozymes contain an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core domain, a C2 domain, and a unique C-terminal tail that terminates with a PDZ-binding motif, a potential interaction site for other signaling proteins. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. The C-terminal tail harbors a number of proline-rich motifs which may interact with SH3 (Src homology 3) domain-containing proteins, as well as many serine/threonine residues, suggesting possible regulation of interactions by protein kinases/phosphatases. There are two PI-PLC-eta isozymes (1-2). Aside from the PI-PLC-eta isozymes identified in mammals, their eukaryotic homologs are also present in this family. 141 matched cddid_all.tbl CDD cd16206 cd16206 320036 EFh_PRIP EF-hand motif found in phospholipase C-related but catalytically inactive proteins (PRIP). This family represents a class of metazoan phospholipase C related, but catalytically inactive proteins (PRIP), which belong to a group of novel inositol 1,4,5-trisphosphate (InsP3) binding protein. PRIP has a primary structure and domain architecture, incorporating a pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core domain with highly conserved X- and Y-regions split by a linker sequence, and a C-terminal C2 domain, similar to phosphoinositide-specific phospholipases C (PI-PLC, EC 3.1.4.11)-delta isoforms. Due to replacement of critical catalytic residues, PRIP do not have PLC enzymatic activity. PRIP consists of two subfamilies, PRIP-1(also known as p130 or PLC-L1), which is predominantly expressed in the brain, and PRIP-2 (also known as PLC-L2), which exhibits a relatively ubiquitous expression. Experiments show both, PRIP-1 and PRIP-2, are involved in InsP3-mediated calcium signaling pathway and GABA(A)receptor-mediated signaling pathway. In addition, PRIP-2 acts as a negative regulator of B-cell receptor signaling and immune responses. 143 matched cddid_all.tbl CDD cd16207 cd16207 320037 EFh_ScPlc1p_like EF-hand motif found in Saccharomyces cerevisiae phospholipase C-1 (ScPlc1p) and similar proteins. This family represents a group of putative phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11) encoded by PLC1 genes from yeasts, which are homologs of the delta isoforms of mammalian PI-PLC in terms of overall sequence similarity and domain organization. Mammalian PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which then phosphorylates other molecules, leading to altered cellular activity. Calcium is required for the catalysis. The prototype of this family is protein Plc1p (also termed 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase 1) encoded by PLC1 genes from Saccharomyces cerevisiae. ScPlc1p contains both highly conserved X- and Y- regions of PLC catalytic core domain, as well as a presumptive EF-hand like calcium binding motif. Experiments show that ScPlc1p displays calcium dependent catalytic properties with high similarity to those of the mammalian PLCs, and plays multiple roles in modulating the membrane/protein interactions in filamentation control. CaPlc1p encoded by CAPLC1 from the closely related yeast Candida albicans, an orthologue of S. cerevisiae Plc1p, is also included in this group. Like SCPlc1p, CaPlc1p has conserved presumptive catalytic domain, shows PLC activity when expressed in E. coli, and is involved in multiple cellular processes. There are two other gene copies of CAPLC1 in C. albicans, CAPLC2 (also named as PIPLC) and CAPLC3. Experiments show CaPlc1p is the only enzyme in C. albicans which functions as PLC. The biological functions of CAPLC2 and CAPLC3 gene products must be clearly different from CaPlc1p, but their exact roles remain unclear. Moreover, CAPLC2 and CAPLC3 gene products are more similar to extracellular bacterial PI-PLC than to the eukaryotic PI-PLC, and they are not included in this subfamily. 142 matched cddid_all.tbl CDD cd16208 cd16208 320038 EFh_PI-PLCbeta1 EF-hand motif found in phosphoinositide phospholipase C beta 1 (PI-PLC-beta1). PI-PLC-beta1, also termed 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1, or PLC-154, or phospholipase C-I (PLC-I), or phospholipase C-beta-1 (PLC-beta1), is expressed at highest levels in specific regions of the brain, as well as in the cardiovascular system. It has two splice variants, PI-PLC-beta1a and PI-PLC-beta1b, both of which are present within the nucleus. Nuclear PI-PLC-beta1 is a key molecule for nuclear inositide signaling, where it plays a role in cell cycle progression, proliferation and differentiation. It also contributes to generate cell-specific Ca2+ signals evoked by G protein-coupled receptor stimulation. PI-PLC-beta1 acts as an effector and a GTPase activating protein (GAP) specifically activated by the heterotrimeric G protein alpha q subunits through their C2 domain and long C-terminal extension. It regulates neuronal activity in the cerebral cortex and hippocampus, and has been implicated for participations in diverse critical functions related to forebrain diseases such as schizophrenia. It may play an important role in maintenance of the status epilepticus, and in osteosarcoma-related signal transduction pathways. PI-PLC-beta1 also functions as a regulator of erythropoiesis in kinamycin F, a potent inducer of gamma-globin production in K562 cells. The G protein activation and the degradation of PI-PLC-beta1 can be regulated by the interaction of alpha-synuclein. As a result, it may reduce cell damage under oxidative stress. Moreover, PI-PLC-beta1 works as a new intermediate in the HIV-1 gp120-triggered phosphatidylcholine-specific phospholipase C (PC-PLC)-driven signal transduction pathway leading to cytoplasmic CCL2 secretion in macrophages. PI-PLC-beta1 contains a core set of domains, including an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core, and a single C2 domain. Besides, it has a unique C-terminal coiled-coil (CT) domain necessary for homodimerization. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. 151 matched cddid_all.tbl CDD cd16209 cd16209 320039 EFh_PI-PLCbeta2 EF-hand motif found in phosphoinositide phospholipase C beta 2 (PI-PLC-beta2). PI-PLC-beta2, also termed 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-2, or phospholipase C-beta-2 (PLC-beta2), is expressed at highest levels in cells of hematopoietic origin. It is activated by the heterotrimeric G protein alpha q subunits (G alpha(q)) through their C2 domain and long C-terminal extension. It is also activated by the beta-gamma subunits of heterotrimeric G proteins. PI-PLC-beta2 has two cellular binding partners, alpha- and gamma-synuclein. The binding of either alpha- and gamma-synuclein inhibits PI-PLC-beta2 activity through preventing the binding of its activator G alpha(q). However, the binding of gamma-synuclein to PI-PLC-beta2 does not affect its binding to G beta(gamma) subunits or small G proteins, but enhances these signals. Meanwhile, gamma-synuclein may protect PI-PLC-beta2 from protease degradation and contribute to its over-expression in breast cancer. In leukocytes, the G beta(gamma)-mediated activation of PI-PLC-beta2 can be promoted by a scaffolding protein WDR26, which is also required for the translocation of PI-PLC-beta2 from the cytosol to the membrane in polarized leukocytes. PI-PLC-beta2 contains a core set of domains, including an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core, and a single C2 domain. Besides, it has a unique C-terminal coiled-coil (CT) domain necessary for homodimerization. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. 151 matched cddid_all.tbl CDD cd16210 cd16210 320040 EFh_PI-PLCbeta3 EF-hand motif found in phosphoinositide phospholipase C beta 3 (PI-PLC-beta3). PI-PLC-beta3, also termed 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3, or phospholipase C-beta-3 (PLC-beta3), is widely expressed at highest levels in brain, liver, and parotid gland. It is activated by the heterotrimeric G protein alpha q subunits through their C2 domain and long C-terminal extension. It is also activated by the beta-gamma subunits of heterotrimeric G proteins. PI-PLC-beta3 associates with CXC chemokine receptor 2 (CXCR2) and Na+/H+ exchanger regulatory factor-1 (NHERF1) to form macromolecular complexes at the plasma membrane of pancreatic cancer cells, which functionally couple chemokine signaling to PI-PLC-beta3-mediated signaling cascade. Moreover, PI-PLC-beta3 directly interacts with the M3 muscarinic receptor (M3R), a prototypical G alpha-q-coupled receptor that promotes PI-PLC-beta3 localization to the plasma membrane. This binding can alter G alpha-q-dependent PLC activation. Furthermore, PI-PLC-beta3 inhibits the proliferation of hematopoietic stem cells (HSCs) and myeloid cells through the interaction of SH2-domain-containing protein phosphatase 1 (SHP-1) and signal transducer and activator of transcription 5 (Stat5), and the augment of the dephosphorylating activity of SHP-1 toward Stat5, leading to the inactivation of Stat5. It is also involved in atopic dermatitis (AD) pathogenesis via regulating the expression of periostin in fibroblasts and thymic stromal lymphopoietin (TSLP) in keratinocytes. In addition, PI-PLC-beta3 mediates the thrombin-induced Ca2+ response in glial cells. PI-PLC-beta3 contains a core set of domains, including an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core, and a single C2 domain. Besides, it has a unique C-terminal coiled-coil (CT) domain necessary for homodimerization. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. 151 matched cddid_all.tbl CDD cd16211 cd16211 320041 EFh_PI-PLCbeta4 EF-hand motif found in phosphoinositide phospholipase C beta 4 (PI-PLC-beta4). PI-PLC-beta4, also termed 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-4, or phospholipase C-beta-4 (PLC-beta4), is expressed in high concentrations in cerebellar Purkinje and granule cells, the median geniculate body, and the lateral geniculate nucleus. It may play a critical role in linking anxiety behaviors and theta rhythm heterogeneity. PI-PLC-beta4 is activated by the heterotrimeric G protein alpha q subunits through their C2 domain and long C-terminal extension. It contributes to generate cell-specific Ca2+ signals evoked by G protein-coupled receptor stimulation. PI-PLC-beta4 functions as a downstream signaling molecule of type 1 metabotropic glutamate receptors (mGluR1s). The thalamic mGluR1-PI-PLC-beta4 cascade is essential for formalin-induced inflammatory pain by regulating the response of ventral posterolateral thalamic nucleus (VPL) neurons. Moreover, PI-PLC-beta4 is essential for long-term depression (LTD) in the rostral cerebellum, which may be required for the acquisition of the conditioned eyeblink response. Besides, PI-PLC-beta4 may play an important role in maintenance of the status epilepticus. The mutations of PI-PLC-beta4 has been identified as the major cause of autosomal dominant auriculocondylar syndrome (ACS). PI-PLC-beta4 contains a core set of domains, including an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core, and a single C2 domain. Besides, it has a unique C-terminal coiled-coil (CT) domain necessary for homodimerization. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. 153 matched cddid_all.tbl CDD cd16212 cd16212 320042 EFh_NorpA_like EF-hand motif found in Drosophila melanogaster No receptor potential A protein (NorpA) and similar proteins. NorpA, also termed 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase, is an eye-specific phosphoinositide phospholipase C (PI-PLC) encoded by norpA gene in Drosophila. It is expressed predominantly in photoreceptors and plays an essential role in the phototransduction pathway of Drosophila. A mutation within the norpA gene can render the fly blind without affecting any of the obvious structures of the eye. Like beta-class of vertebrate PI-PLCs, NorpA contains an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core, and a single C2 domain. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. 153 matched cddid_all.tbl CDD cd16213 cd16213 320043 EFh_PI-PLC21 EF-hand motif found in phosphoinositide phospholipase PLC21 and similar proteins. The family includes invertebrate homologs of phosphoinositide phospholipase C beta (PI-PLC-beta) named PLC21 from cephalopod retina. It also includes PLC21 encoded by plc-21 gene, which is expressed in the central nervous system of Drosophila. Like beta-class of vertebrate PI-PLCs, PLC21 contains an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core, and a single C2 domain. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. 154 matched cddid_all.tbl CDD cd16214 cd16214 320044 EFh_PI-PLCgamma1 EF-hand motif found in phosphoinositide phospholipase C gamma 1 (PI-PLC-gamma1). PI-PLC-gamma1, also termed 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1, or PLC-148, or phospholipase C-II (PLC-II), or phospholipase C-gamma-1 (PLC-gamma-1), is abundantly expressed in embryonal cortical structures, neurons, oligodendrocytes and astrocytes, and is involved in various cellular events, including proliferation, differentiation, migration, survival, and cell death. It also associates with many diseases, including epilepsy, Huntington's disease (HD), depression, Alzheimer's disease (AD) and bipolar disorder. PI-PLC-gamma1 plays a critical role in cell migration and tumor cell invasiveness and metastasis. It can mediate the cell motility effects of growth factors, including platelet-derived growth factor (PDGF), epidermal growth factor (EGF), insulin-like growth factor (IGF) and hepatocyte growth factor (HGF), as well as adhesion receptors. Moreover, PI-PLC-gamma1 can modulate neurite outgrowth, neuronal cell migration and synaptic plasticity through the Trk receptor. PI-PLC-gamma1 contains an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, and a C2 domain. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. Besides, PI-PLC-gamma1 has a second PH domain, two SH2 (Src homology 2) regions, and one SH3 (Src homology 3) region, which are present within this linker. PI-PLC-gamma1 is activated by receptor and non-receptor tyrosine kinases via its two SH2 and a single SH3 domain. 146 matched cddid_all.tbl CDD cd16215 cd16215 320045 EFh_PI-PLCgamma2 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2. PI-PLC-gamma2, also termed 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2, or phospholipase C-IV (PLC-IV), or phospholipase C-gamma-2 (PLC-gamma-2), is highly expressed in cells of hematopoietic origin. It has been implicated in cell motility important to invasion and dissemination of tumor cells. As an important component of the B cell receptor (BCR) signaling pathway, PI-PLC-gamma2 is required for efficient formation of germinal center (GC) and memory B cells. It works as a critical effector stimulating the increase of intracellular Ca2+ and activates various signaling pathways downstream of the BCR. Moreover, PI-PLC-gamma2 has been implicated in Fc receptor-mediated degranulation of mast cells, integrin signaling in platelets, as well as integrin and Fc receptor-mediated neutrophil functions. It also acts as a crucial signaling mediator modifying DC gene expression program to activate DC responses to beta-glucan-containing pathogens. PI-PLC-gamma2 contains an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, and a C2 domain. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. Besides, PI-PLC-gamma2 has a second PH domain, two SH2 (Src homology 2) regions, and one SH3 (Src homology 3) region, which are present within this linker. PI-PLC-gamma2 is activated by receptor and non-receptor tyrosine kinases via its two SH2 and a single SH3 domain. Unlike PI-PLC-gamma1, the activation of PI-PLC-gamma2 may require concurrent stimulation of PI 3-kinase. 154 matched cddid_all.tbl CDD cd16216 cd16216 320046 EFh_PI-PLCgamma1_like EF-hand motif found in 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1-like proteins. This family corresponds to a small group of uncharacterized 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-1-like (PI-PLC-gamma1-like) proteins. Although their biological function remains unclear, they shows high sequence similarity with other phosphoinositide phospholipase C gamma proteins. They contain a core set of domains, including an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core, and a single C2 domain. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. A second PH domain, which is split by two SH2 (Src homology 2) domains, and one SH3 (Src homology 3) domain, are present within this linker. 150 matched cddid_all.tbl CDD cd16217 cd16217 320047 EFh_PI-PLCdelta1 EF-hand motif found in phosphoinositide phospholipase C delta 1 (PI-PLC-delta1). PI-PLC-delta1, also termed 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1 (PLCD1), or phospholipase C-III (PLC-III), or phospholipase C-delta-1 (PLC-delta-1), is present in high abundancy in the brain, heart, lung, skeletal muscle and testis. It is activated by high calcium levels generated by other PI-PLC family members, and therefore functions as a calcium amplifier within the cell. PI-PLC-delta1 is required for maintenance of homeostasis in skin and metabolic tissues. Moreover, it is essential in trophoblasts for placental development. Simultaneous loss of PI-PLC-delta1 may cause placental vascular defects, leading to embryonic lethality. PI-PLC-delta1 can be positively or negatively regulated by several binding partners, including p122/Rho GTPase activating protein (RhoGAP), Gha/Transglutaminase II, RalA, and calmodulin. It is involved in Alzheimer's disease and hypertension. Furthermore, PI-PLC-delta1 regulates cell proliferation and cell-cycle progression from G1- to S-phase by control of cyclin E-CDK2 activity and p27 levels. It can be activated by alpha1-adrenoreceptors (AR) in a calcium-dependent manner and may be important for G protein-coupled receptors (GPCR) responses in vascular smooth muscle (VSM). PI-PLC-delta1 may also be involved in noradrenaline (NA)-induced phosphatidylinositol-4,5-bisphosphate (PIP2) hydrolysis and modulate sustained contraction of mesenteric small arteries. In addition, it inhibits thermogenesis and induces lipid accumulation, and therefore contributes to the development of obesity. PI-PLC-delta1 contains a core set of domains, including an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core, and a single C-terminal C2 domain. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. PI-PLC-delta1 can regulate the binding of PH domain to PIP2 in a Ca2+-dependent manner through its functionally important EF-hand domains. In addition, PI-PLC-delta1 possesses a classical leucine-rich nuclear export sequence (NES) located in the EF hand motifs, as well as a nuclear localization signal within its linker region, both of which may be responsible for translocating PI-PLC-delta1 into and out of the cell nucleus. 139 matched cddid_all.tbl CDD cd16218 cd16218 320048 EFh_PI-PLCdelta3 EF-hand motif found in phosphoinositide phospholipase C delta 3 (PI-PLC-delta3). PI-PLC-delta3, also termed 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-3 (PLCD3), phospholipase C-delta-3 (PLC-delta-3), is expressed abundantly in brain, skeletal muscle and heart. PI-PLC-delta3 gene expression is down-regulation by cAMP and calcium. PI-PLC-delta3 acts as anchoring of myosin VI on plasma membrane, and further modulates Myosin IV expression and microvilli formation in enterocytes. It negatively regulates RhoA expression, inhibits RhoA/Rho kinase signaling, and plays an essential role in normal neuronal migration by promoting neuronal outgrowth in the developing brain. Moreover, PI-PLC-delta3 is essential in trophoblasts for placental development. Simultaneous loss of PI-PLC-delta3 may cause placental vascular defects, leading to embryonic lethality. PI-PLC-delta3 contains a core set of domains, including an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core, and a single C-terminal C2 domain. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. In addition, PI-PLC-delta3 possesses a classical leucine-rich nuclear export sequence (NES) located in the EF hand motifs, which may be responsible transporting PI-PLC-delta3 from the cell nucleus. 138 matched cddid_all.tbl CDD cd16219 cd16219 320049 EFh_PI-PLCdelta4 EF-hand motif found in phosphoinositide phospholipase C delta 4 (PI-PLC-delta4). PI-PLC-delta4, also termed 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-4 (PLCD4), or phospholipase C-delta-4 (PLC-delta-4), is expressed in various tissues with the highest levels detected selectively in the brain, skeletal muscle, testis and kidney. It plays a significant role in cell growth, cell proliferation, tumorigenesis, and in an early stage of fertilization. PI-PLC-delta4 may function as a key enzyme in the regulation of PtdIns(4,5)P2 levels and Ca2+ metabolism in nuclei in response to growth factors, and its expression may be partially regulated by an increase in cytoplasmic Ca2+. Moreover, PI-PLC-delta4 binds glutamate receptor-interacting protein1 (GRIP1) in testis and is required for calcium mobilization essential for the zona pellucida-induced acrosome reaction in sperm. Overexpression or dysregulated expression of PLCdelta4 may initiate oncogenesis in certain tissues through upregulating erbB1/2 expression, extracellular signal-regulated kinase (ERK) signaling pathway, and proliferation in MCF-7 cells. PI-PLC-delta4 contains an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core domain, and a C-terminal C2 domain. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. Unlike PI-PLC-delta 1 and 3, a putative nuclear export sequence (NES) located in the EF-hand domain, which may be responsible transporting PI-PLC-delta1 and 3 from the cell nucleus, is not present in PI-PLC-delta4. 140 matched cddid_all.tbl CDD cd16220 cd16220 320050 EFh_PI-PLCeta1 EF-hand motif found in phosphoinositide phospholipase C eta 1 (PI-PLC-eta1). PI-PLC-eta1, also termed 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-1, or phospholipase C-eta-1 (PLC-eta-1), or phospholipase C-like protein 3 (PLC-L3), is a neuron-specific PI-PLC that is most abundant in the brain, particularly in the hippocampus, habenula, olfactory bulb, cerebellum, and throughout the cerebral cortex. It is also expressed in the zona incerta and in the spinal cord. PI-PLC-eta1 may perform a fundamental role in the brain. It may also act in synergy with other PLC subtypes. For instance, it is activated via intracellular Ca2+ mobilization and then plays a role in the amplification of GPCR (G-protein-coupled receptor)-mediated PLC-beta signals. In addition, its activity can be stimulated by ionomycin. PI-PLC-eta1 contains an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core domain, a C2 domain, and a unique C-terminal tail that terminates with a PDZ-binding motif, a potential interaction site for other signaling proteins. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. The C-terminal tail harbors a number of proline-rich motifs which may interact with SH3 (Src homology 3) domain-containing proteins, as well as many serine/threonine residues, suggesting possible regulation of interactions by protein kinases/phosphatases. 141 matched cddid_all.tbl CDD cd16221 cd16221 320051 EFh_PI-PLCeta2 EF-hand motif found in phosphoinositide phospholipase C eta 2 (PI-PLC-eta2). PI-PLC-eta2, also termed 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase eta-2, or phosphoinositide phospholipase C-like 4, or phospholipase C-like protein 4 (PLC-L4), or phospholipase C-eta-2 (PLC-eta2), is a neuron-specific PI-PLC that is most abundant in the brain, particularly in the hippocampus, habenula, olfactory bulb, cerebellum, and throughout the cerebral cortex. It is also expressed in the pituitary gland, pineal gland, retina, and lung, as well as in neuroendocrine cells. PI-PLC-eta2 has been implicated in the regulation of neuronal differentiation/maturation. It is required for retinoic acid-stimulated neurite growth. It may also in part function downstream of G-protein-coupled receptors and play an important role in the formation and maintenance of the neuronal network in the postnatal brain. Moreover, PI-PLC-eta2 acts as a Ca2+ sensor that shows a canonical EF-loop directing Ca2+-sensitivity and thus can amplify transient Ca2+ signals. Its activation can be triggered either by intracellular calcium mobilization or by G beta-gamma signaling. PI-PLC-eta2 contains an N-terminal pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core domain, a C2 domain, and a unique C-terminal tail that terminates with a PDZ-binding motif, a potential interaction site for other signaling proteins. The PLC catalytic core domain is a TIM barrel with two highly conserved regions (X and Y) split by a highly degenerate linker sequence. The C-terminal tail harbors a number of proline-rich motifs which may interact with SH3 (Src homology 3) domain-containing proteins, as well as many serine/threonine residues, suggesting possible regulation of interactions by protein kinases/phosphatases. 141 matched cddid_all.tbl CDD cd16222 cd16222 320052 EFh_PRIP1 EF-hand motif found in phospholipase C-related but catalytically inactive protein 1 (PRIP-1). PRIP-1, also termed phospholipase C-deleted in lung carcinoma, or inactive phospholipase C-like protein 1 (PLC-L1), or p130, is a novel inositol 1,4,5-trisphosphate (InsP3) binding protein that is predominantly expressed in the brain. It is involved in InsP3-mediated calcium signaling pathway and GABA(A)receptor-mediated signaling pathway. It interacts with the catalytic subunits of protein phosphatase 1 (PP1) and protein phosphatase 2A (PP2A), and functions as a scaffold to regulate the activities and subcellular localizations of both PP1 and PP2A in phospho-dependent cellular signaling. It also promotes the translocation of phosphatases to lipid droplets to trigger the dephosphorylation of hormone-sensitive lipase (HSL) and perilipin A, thus reducing protein kinase A (PKA)-mediated lipolysis. Moreover, PRIP-1 plays an important role in insulin granule exocytosis through the association with GABAA-receptor-associated protein (GABARAP) to form a complex to regulate KIF5B-mediated insulin secretion. It also inhibits regulated exocytosis through direct interactions with syntaxin 1 and synaptosomal-associated protein 25 (SNAP-25) via its C2 domain. Furthermore, PRIP-1 has been implicated in the negative regulation of bone formation. PRIP-1 has a primary structure and domain architecture, incorporating a pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core domain with highly conserved X- and Y-regions split by a linker sequence, and a C-terminal C2 domain, similar to phosphoinositide-specific phospholipases C (PI-PLC, EC 3.1.4.11)-delta isoforms. Due to replacement of critical catalytic residues, PRIP-1 does not have PLC enzymatic activity. 143 matched cddid_all.tbl CDD cd16223 cd16223 320053 EFh_PRIP2 EF-hand motif found in phospholipase C-related but catalytically inactive protein 2 (PRIP-2). PRIP-2, also termed phospholipase C-L2, or phospholipase C-epsilon-2 (PLC-epsilon-2), or inactive phospholipase C-like protein 2 (PLC-L2), is a novel inositol 1,4,5-trisphosphate (InsP3) binding protein that exhibits a relatively ubiquitous expression. It functions as a novel negative regulator of B-cell receptor (BCR) signaling and immune responses. PRIP-2 has a primary structure and domain architecture, incorporating a pleckstrin homology (PH) domain, four atypical EF-hand motifs, a PLC catalytic core domain with highly conserved X- and Y-regions split by a linker sequence, and a C-terminal C2 domain, similar to phosphoinositide-specific phospholipases C (PI-PLC, EC 3.1.4.11)-delta isoforms. Due to replacement of critical catalytic residues, PRIP-2 does not have PLC enzymatic activity. 144 matched cddid_all.tbl CDD cd16224 cd16224 320022 EFh_CREC_RCN2 EF-hand, calcium binding motif, found in reticulocalbin-2 (RCN2). RCN2, also termed calcium-binding protein ERC-55, or E6-binding protein (E6BP), or TCBP-49, is an endoplasmic reticulum resident low-affinity Ca2+-binding protein that has been implicated in immunity, redox homeostasis, cell cycle regulation and coagulation. It is associated with tumorigenesis, in particular with transformation of cells of the cervix induced by human papillomavirus (HPV), through binding to human papillomavirus (HPV) E6 oncogenic protein. It specifically interacts with vitamin D receptor among nuclear receptors. RCN2 contains an N-terminal signal sequence followed by six copies of the EF-hand Ca2+-binding motif, and a C-terminal His-Asp-Glu-Leu (HDEL) tetrapeptide that is required for retention of RCN2 in the endoplasmic reticulum (ER). 268 matched cddid_all.tbl CDD cd16225 cd16225 320023 EFh_CREC_cab45 EF-hand, calcium binding motif, found in 45 kDa calcium-binding protein (Cab45). Cab45, also termed stromal cell-derived factor 4 (SDF-4), is a soluble, lumenal Golgi resident low-affinity Ca2+-binding protein that contains six copies of the EF-hand Ca2+-binding motif. It is required for secretory pathway calcium ATPase1 (SPCA1)-dependent Ca2+ import into the trans-Golgi network (TGN) and plays an essential role in Ca2+-dependent secretory cargo sorting at the TGN. 278 matched cddid_all.tbl CDD cd16226 cd16226 320024 EFh_CREC_Calumenin_like EF-hand, calcium binding motif, found in calumenin, reticulocalbin-1 (RCN-1), reticulocalbin-3 (RCN-3), and similar proteins. The family corresponds to a group of six EF-hand Ca2+-binding proteins, including calumenin (also known as crocalbin or CBP-50), reticulocalbin-1 (RCN-1), reticulocalbin-3 (RCN-3), and similar proteins. Calumenin is an endo/sarcoplasmic reticulum (ER/SR) resident low-affinity Ca2+-binding protein that contains six EF-hand domains and a C-terminal SR retention signal His-Asp-Glu-Phe (HDEF) tetrapeptide. It functions as a novel regulator of SERCA2, and its expressional changes are tightly coupled with Ca2+-cycling of cardiomyocytes. It is also broadly involved in haemostasis and in the pathophysiology of thrombosis. Moreover, the extracellular calumenin acts as a suppressor of cell migration and tumor metastasis. RCN-1 is an endoplasmic reticulum resident Ca2+-binding protein with a carboxyl-terminal His-Asp-Glu-Leu (HDEL) tetrapeptide signal. It acts as a potential negative regulator of B-RAF activation and can negatively modulate cardiomyocyte hypertrophy by inhibition of the mitogen-activated protein kinase signalling cascade. It also plays a key role in the development of doxorubicin-associated resistance. RCN-3 is a putative six EF-hand Ca2+-binding protein that contains five RXXR (X is any amino acid) motifs and a C-terminal ER retrieval signal HDEL tetrapeptide. The RXXR motif represents the target sequence of subtilisin-like proprotein convertases (SPCs). RCN-3 is specifically bound to the paired basic amino-acid-cleaving enzyme-4 (PACE4) precursor protein and plays an important role in the biosynthesis of PACE4. 264 matched cddid_all.tbl CDD cd16227 cd16227 320025 EFh_CREC_RCN2_like EF-hand, calcium binding motif, found in reticulocalbin-2 (RCN2) mainly from protostomes. This family corresponds to a group of uncharacterized RCN2-like proteins, which are mainly found in protostomes. Although their biological function remains unclear, they show high sequence similarity with RCN2 (also known as E6BP or TCBP-49), which is an endoplasmic reticulum resident low-affinity Ca2+-binding protein that has been implicated in immunity, redox homeostasis, cell cycle regulation and coagulation. Members in this family contain six copies of the EF-hand Ca2+-binding motif, but may lack a C-terminal His-Asp-Glu-Leu (HDEL) tetrapeptide that is required for retention of RCN2 in the endoplasmic reticulum (ER). 263 matched cddid_all.tbl CDD cd16228 cd16228 320026 EFh_CREC_Calumenin EF-hand, calcium binding motif, found in calumenin. Calumenin, also termed crocalbin, or IEF SSP 9302, is an endo/sarcoplasmic reticulum (ER/SR) resident low-affinity Ca2+-binding protein that contains six EF-hand domains and a C-terminal SR retention signal His-Asp-Glu-Phe (HDEF) tetrapeptide. It is highly expressed in various brain regions. Thus it plays an important role in migration and differentiation of neurons, and/or in Ca2+ signaling between glial cells and neurons. Calumenin is involved in Ca2+ homeostasis through interacting with ryanodine receptor RyR2 and SERCA2. It acts as a novel regulator of SERCA2, and its expressional changes are tightly coupled with Ca2+-cycling of cardiomyocytes. Calumenin also forms a Ca2+-dependent complex with thrombospondin-1, which is broadly involved in haemostasis and thrombosis. Moreover, calumenin is a molecular chaperone that endogenously regulates the vitamin K-dependent gamma-carboxylation of several proteins, including blood coagulation factors (such as FII, FVII, FIX, FX, and proteins C, S and Z), cell survival factors (Gas6) and bone metabolism proteins (such as matrix Gla protein or MGP, osteocalcin and periostin), through targeting the gamma-glutamyl carboxylase. It also functions as a charged F508del-cystic fibrosis transmembrane regulator (CFTR) folding modulator, as well as a G551D-CFTR associated protein. Furthermore, the extracellular calumenin acts as a suppressor of cell migration and tumor metastasis. It binds to and stabilizes fibulin-1, and further inactivates extracellular signal-regulated kinases 1 and 2 (ERK1/2) signaling. 263 matched cddid_all.tbl CDD cd16229 cd16229 320027 EFh_CREC_RCN1 EF-hand, calcium binding motif, found in reticulocalbin-1 (RCN-1). RCN-1 is an endoplasmic reticulum resident low-affinity Ca2+-binding protein with six EF-hand motifs and a carboxyl-terminal His-Asp-Glu-Leu (HDEL) tetrapeptide signal. It is expressed at the cell surface. RCN-1 acts as a potential negative regulator of B-RAF activation and can negatively modulate cardiomyocyte hypertrophy by inhibition of the mitogen-activated protein kinase signaling cascade. It also plays a key role in the development of doxorubicin-associated resistance. 267 matched cddid_all.tbl CDD cd16230 cd16230 320028 EFh_CREC_RCN3 EF-hand, calcium binding motif, found in reticulocalbin-3 (RCN-3). RCN-3, also termed EF-hand calcium-binding protein RLP49, is a putative six EF-hand Ca2+-binding protein that contains five RXXR (X is any amino acid) motifs and a C-terminal ER retrieval signal His-Asp-Glu-Leu (HDEL) tetrapeptide. The RXXR motif represents the target sequence of subtilisin-like proprotein convertases (SPCs). RCN-3 is specifically bound to the paired basic amino-acid-cleaving enzyme-4 (PACE4) precursor protein and plays an important role in the biosynthesis of PACE4. 268 matched cddid_all.tbl CDD cd16231 cd16231 320010 EFh_SPARC_like EF-hand, extracellular calcium-binding (EC) motif, found in secreted protein acidic and rich in cysteine (SPARC) and similar proteins. This family includes secreted protein acidic and rich in cysteine (SPARC), secreted protein, acidic and rich in cysteine-like 1 (SPARCL1), and similar proteins. SPARC is a prototypic collagen-binding matricellular protein that is involved in extracellular matrix (ECM) assembly and fibrosis through binding both fibrillar collagen and basal lamina collagen IV. It regulates the activity of matrix metalloproteinases (MMPs), as well as the growth factor signaling mediated by cell surface receptors including vascular endothelial growth factor (VEGF) receptor, basic fibroblast growth factor (bFGF), and transforming growth factor (TGF) beta1. It also shows survival activity in tumor progression. SPARC contains an N-terminal acidic 52-residue segment followed by a follistatin-like (FS) domain, and an alpha-helical EC domain with 2 unusual calcium-binding EF-hands and the collagen-binding site. SPARCL1 is the closest family member to SPARC. It shares the three primary domains contained within SPARC with an expanded N-terminal domain. SPARCL1 may function as both a tumor suppressor and as a regulator of angiogenesis. It can bind to collagens and be counter-adhesive to wild-type dermal fibroblasts, but do not influence rates of cell proliferation. Moreover, SPARCL1 can influence central nervous system (CNS) development and synaptic rearrangement. 116 matched cddid_all.tbl CDD cd16232 cd16232 320011 EFh_SPARC_TICN EF-hand, extracellular calcium-binding (EC) motif, found in testicans. Testicans are nervous system-expressed proteoglycans that play important roles in the regulation of protease activity, as well as in the determination of age at menarche. Testican-1 (TICN1, also termed protein SPOCK) is a secreted chimeric proteoglycan that is highly expressed in brain and carries both chondroitin and heparan sulfate glycosaminoglycan side chains. It has been implicated in autoimmune disease. It also acts as a regulator of bone morphogenetic protein (BMP) signaling and show critical functions in the nervous system. Testican-2 (TICN2, also termed protein SPOCK2) is an extracellular heparan sulphate proteoglycan highly expressed in brain. It may play regulatory roles in the development of the central nervous system. It also participates in diverse steps of neurogenesis. TICN1, but not TICN2, inhibits cathepsin L. TICN1 also inhibits attachment and neurite outgrowth in cultures of N2A neuroblastoma cells, While TICN2 is able to inhibit neurite outgrowth from primary cerebellar cells. Testicans contain an N-terminal signal peptide, a testican-specific domain followed by a follistatin-like (FS) domain, an extracellular calcium-binding (EC) domain including a pair of EF hands, a thyroglobulin-like domain (TY), and a C-terminal region with two putative glycosaminoglycan attachment sites. The substitution of a ligating Asp residue by Tyr orTyr in the +Y position of EF hand 2 in testican-2 could prevent Ca2+ binding to this site and also cause EF-hand 1 to bind one Ca2+ with low affinity. The substitution of a ligating Asp residue by Phe or Tyr in the +Y position of EF-hand 2 in testicans could prevent Ca2+ binding to this site and also cause EF-hand 1 to bind one Ca2+ ion with low affinity. 108 matched cddid_all.tbl CDD cd16233 cd16233 320012 EFh_SPARC_FSTL1 EF-hand, extracellular calcium-binding (EC) motif, found in follistatin-related protein 1 (FRP-1). FRP-1, also termed follistatin-like protein 1 (fstl-1), TGF-beta-stimulated clone 36 (TSC-36/Flik), or TGF-beta inducible protein, is a secreted glycoprotein that is overexpressed in certain inflammatory diseases and has been implicated in many autoimmune diseases. FRP-1 functions as an important proinflammatory factor in the pathogenesis of osteoarthritis (OA) by activating the canonical NF-kappaB-mediated inflammatory cytokines, including tumor necrosis factor alpha (TNF-alpha), interleukin-1beta (IL-1beta) and interleukin-6 (IL-6), and enhancing fibroblast like synoviocytes proliferation. It also acts as a critical mediator of collagen-induced arthritis (CIA), juvenile rheumatoid arthritis (JRA), as well as Lyme arthritis observed after Borrelia burgdorferi infection. Meanwhile, it enhances nod-like receptor family, pyrin domain containing 3 (NLRP3) inflammasome-mediated IL-1beta secretion from monocytes and macrophages. Moreover, FRP-1 shows critical functions in the nervous system. It differentially regulates transforming growth factor beta (TGF-beta) and bone morphogenetic protein (BMP) signaling, leading to epithelial injury and fibroblast activation. Furthermore, FRP-1 functions as a cardiokine with cardioprotective properties. It may play a potential role in ischemic stroke through decreasing neuronal apoptosis and improving neurological deficits via disco-interacting protein 2 homolog A (DIP2A)/Akt pathway after middle cerebral artery occlusion (MCAO). Plasma FRP-1 is elevated in Kawasaki disease (KD) and thus may play a possible role in the formation of coronary artery aneurysm (CAA). FRP-1 contains a follistatin-like (FS) domain, an extracellular calcium-binding (EC) domain including a pair of EF hands, and a von Willebrand factor type C (VWC) domain. The EC domain does not undergo characteristic structural changes upon calcium addition or depletion and therefore is not a functional calcium binding domain. 114 matched cddid_all.tbl CDD cd16234 cd16234 320013 EFh_SPARC_SMOC EF-hand, extracellular calcium-binding (EC) motif, found in secreted modular calcium-binding protein SMOC-1, SMOC-2, and similar proteins. SMOC proteins corresponds to a group matricellular proteins that are involved in direct or indirect modulation of growth factor signaling pathways and play diverse roles in physiological processes involving extensive tissue remodeling, migration, proliferation, and angiogenesis. They may mediate intercellular signaling and cell type-specific differentiation during gonad and reproductive tract development. SMOC-1 is localized in basement membranes. Its mutations have been found to be associated with individuals with Warrdenburg Anopthalmia Syndrome. SMOC-2 is ubiquitously expressed and is involved in angiogenesis and the regulation of cell cycle progression. It enhances the angiogenic effect of basic fibroblast growth factor (bFGF) and vascular endothelial growth factor (VEGF). It has also been implicated in generalized vitiligo. SMOC proteins consist of a follistatin-like (FS) domain, two thyroglobulin-like (TY) domains, a novel domain conserved only in SMOC proteins, and an extracellular calcium-binding (EC) domain with two EF-hand calcium-binding motifs. 104 matched cddid_all.tbl CDD cd16235 cd16235 320014 EFh_SPARC_SPARC EF-hand, extracellular calcium-binding (EC) motif, found in secreted protein acidic and rich in cysteine (SPARC). SPARC, also termed basement-membrane protein 40 (BM-40), or osteonectin (ON), is a prototypic collagen-binding matricellular protein that is essential for embryo development in invertebrates and highly expressed in bone. It participates in normal tissue remodeling as it regulates the deposition of extracellular matrix, as well as in neoplastic transformation. It is involved in extracellular matrix (ECM) assembly and fibrosis through binding both fibrillar collagen and basal lamina collagen IV. It regulates the activity of matrix metalloproteinases (MMPs), as well as the growth factor signaling mediated by cell surface receptors including vascular endothelial growth factor (VEGF) receptor, basic fibroblast growth factor (bFGF), and transforming growth factor (TGF) beta1. SPARC shows survival activity in tumor progression. It plays a role in metastatic process to the lung during melanoma progression. It can suppress prostate cancer cell growth and survival. Moreover, SPARC is a bone- associated protein that has a major role in bone development and mineralisationis. It is involved in the initiation and progression of vascular calcification and upregulated by adiponectin. Furthermore, SPARC may be one of the molecules that govern the uptake and delivery of proteins from blood to the cerebrospinal fluid (CSF) during brain development. SPARC contains an N-terminal acidic 52-residue segment followed by a follistatin-like (FS) domain, and an alpha-helical EC domain with 2 unusual calcium-binding EF-hands and the collagen-binding site. Platelet-derived growth factor (PDGF) also interacts with its EC domain, but in a calcium-independent manner, whereas collagen binding is calcium-dependent. 96 matched cddid_all.tbl CDD cd16236 cd16236 320015 EFh_SPARC_SPARCL1 EF-hand, extracellular calcium-binding (EC) motif, found in secreted protein, acidic and rich in cysteine-like 1 (SPARCL1). SPARCL1, also termed SPARC-like protein 1, or high endothelial venule protein (Hevin), or MAST 9, or SC-1, or RAGS-1, or QR1, or ECM 2, is a diversely expressed and developmentally regulated extracellular matrix glycoprotein involved in tissue repair and remodeling via interaction with the surrounding extracellular matrix (ECM) proteins. It plays a pivotal role in the corneal wound healing. SPARCL1 may function as both a tumor suppressor and as a regulator of angiogenesis. It regulates cell migration/invasion and suppresses metastasis in many cancers, including prostate cancer, colorectal cancer, gastric cancer, and breast cancer. It can bind to collagens and be counter-adhesive to wild-type dermal fibroblasts, but do not influence rates of cell proliferation. Moreover, SPARCL1 contributes to neural development and participates in remodeling events associated with neuronal degeneration following neural injury. It can influence central nervous system (CNS) development and synaptic rearrangement. SPARCL1 is the closest family member to secreted protein acidic and rich in cysteine (SPARC), but does not compensate for the absence of SPARC in the CNS. SPARC contains an N-terminal acidic 52-residue segment followed by a follistatin-like (FS) domain, and an alpha-helical EC domain with 2 unusual calcium-binding EF-hands and the collagen-binding site. SPARCL1 shares the three primary domains contained within SPARC with an expanded N-terminal domain. 93 matched cddid_all.tbl CDD cd16237 cd16237 320016 EFh_SPARC_TICN1 EF-hand, extracellular calcium-binding (EC) motif, found in testican-1 (TICN1). TICN1, also termed protein SPOCK, or SPARC/osteonectin, CWCV, and Kazal-like domains proteoglycan 1 (Spock1), is a secreted chimeric proteoglycan that is highly expressed in brain and carries both chondroitin and heparan sulfate glycosaminoglycan side chains. It promotes resistance against Pseudomonas aeruginosa-induced keratitis through regulation of matrix metalloproteinase (MMP)-2 expression and activation. It also acts as a potential cancer prognostic marker that promotes the proliferation and metastasis of gallbladder cancer cells by activating the PI3K/Akt pathway. Moreover, TICN1 corresponding gene SPOCK1 is a novel transforming growth factor-beta target gene that regulates lung cancer cell epithelial-mesenchymal transition. It is also up-regulated by chromodomain helicase/adenosine triphosphatase DNA binding protein 1-like (CHD1L), and promotes human hepatocellular carcinoma (HCC) cell invasiveness and metastasis. Furthermore, TICN1 inhibits the lysosomal cysteine protease cathepsin L in intracellular vesicles and in the extracellular milieu. TICN1 contains an N-terminal signal sequence known to direct nascent polypeptides to the extracellular space, an unique region to the testicans, a follistatin (FS)-like domain generally involving five disulfide bridges, an extracellular calcium-binding (EC) domain including a pair of EF hands, and a thyroglobulin type-1 (TY) domain followed by a C-terminal acidic region with high density of negatively charged amino acids. The substitution of a ligating Asp residue by Phe291 in the +Y position of EF-hand 2 in TICN1 could prevent Ca2+ binding to this site and also cause EF-hand 1 to bind one Ca2+ ion with low affinity. 112 matched cddid_all.tbl CDD cd16238 cd16238 320017 EFh_SPARC_TICN2 EF-hand, extracellular calcium-binding (EC) motif, found in testican-2 (TICN2). TICN2, also termed SPARC/osteonectin, CWCV, and Kazal-like domains proteoglycan 2 (Spock2), is an extracellular heparan sulphate proteoglycan expressed in brain, lung, and testis. It inhibits neurite extension from cultured primary cerebellar neurons and may play regulatory roles in the development of the central nervous system. It also participates in diverse steps of neurogenesis. Moreover, TICN2 may contribute to ECM remodeling by regulating function(s) of other testican family members, which possess membrane-type matrix metalloproteinases (MT-MMPs) inhibitory function. Furthermore, TICN2 corresponding gene SPOCK2 acts as a susceptibility gene for bronchopulmonary dysplasia. TICN2 contains an N-terminal signal peptide, a testican-specific domain followed by a follistatin-like (FS) domain, an extracellular calcium-binding (EC) domain including a pair of EF hands, a thyroglobulin-like domain (TY), and a C-terminal region with two putative glycosaminoglycan attachment sites. The substitution of a ligating Asp residue by Tyr292 in the +Y position of EF-hand 2 in TICN2 could prevent Ca2+ binding to this site and also cause EF-hand 1 to bind one Ca2+ ion with low affinity. 112 matched cddid_all.tbl CDD cd16239 cd16239 320018 EFh_SPARC_TICN3 EF-hand, extracellular calcium-binding (EC) motif, found in testican-3 (TICN3). TICN3, also termed SPARC/osteonectin, CWCV, and Kazal-like domains proteoglycan 3 (Spock3), is a brain-specific heparan sulfate proteoglycan that shows a widespread distribution within the extracellular matrix of the brain. It plays an important role in the formation or maintenance of major neuronal structures in the brain. It also functions as a novel regulator to reduce the activity of matrix metalloproteinase (MMP) in adult T-cell leukemia (ATL). It suppresses membrane-type 1 MMP-mediated MMP-2 activation and tumor invasion. Moreover, TICN3 corresponding gene SPOCK3 acts as a risk gene for adult attention-deficit/hyperactivity disorder (ADHD) and personality disorders. TICN3 contains an N-terminal signal peptide, a testican-specific domain followed by the follistatin-like (FS) and extracellular calcium-binding (EC) domains characteristic of the BM-40 family. Towards the C-terminus they contain a thyroglobulin-like domain (TY) and a novel sequence (domain V), which includes two potential glycosaminoglycan attachment sites. The substitution of a ligating Asp residue by Tyr295 in the +Y position of EF-hand 2 in testican-3 could prevent Ca2+ binding to this site and also cause EF-hand 1 to bind one Ca2+ ion with low affinity. 113 matched cddid_all.tbl CDD cd16240 cd16240 320019 EFh_SPARC_SMOC1 EF-hand, extracellular calcium-binding (EC) motif, found in secreted modular calcium-binding protein 1 (SMOC-1). SMOC-1, also termed SPARC-related modular calcium-binding protein 1, or smooth muscle-associated protein 1 (SMAP-1), is an Arf6 GTPase-activating protein (GAP) that directly interacts with clathrin and regulates the clathrin-dependent endocytosis of transferrin receptors from the plasma membrane. It is predominantly localized in basement membranes. SMOC-1 acts as a regulator of osteoblast differentiation and is involved in inhibition of transforming growth factor-beta (TGF-beta) signaling through production of nitric oxide. It also plays an essential role in ocular and limb development and functions as a regulator of bone morphogenic protein (BMP) signaling. It interacts with a matricellular protein, tenascin C in addition to the serum proteins, fibulin-1 and C-reactive protein, but not collagens. Two point mutations in the SMOC1 gene may cause Waardenburg Anophtalmia Syndrome. Moreover, SMOC-1 is involved in direct or indirect modulation of growth factor signaling pathways and plays a role in physiological processes involving extensive tissue remodeling. SMOC-1 contains a follistatin-like (FS) domain, two thyroglobulin-like (TY) domains, a novel domain, which is found only in the homologous SMOC-2, and an extracellular calcium-binding (EC) domain with two EF-hand calcium-binding motifs. 115 matched cddid_all.tbl CDD cd16241 cd16241 320020 EFh_SPARC_SMOC2 EF-hand, extracellular calcium-binding (EC) motif, found in secreted modular calcium-binding protein 2 (SMOC-2). SMOC-2, also termed SPARC-related modular calcium-binding protein 2, or smooth muscle-associated protein 2 (SMAP-2), is a ubiquitously expressed matricellular protein that enhances the response to angiogenic growth factors, mediate cell adhesion, keratinocyte migration, and metastasis. It is also associated with vitiligo and craniofacial and dental defects. Moreover, SMOC-2 acts as an Arf1 GTPase-activating protein (GAP) that interacts with clathrin heavy chain (CHC) and clathrin assembly protein CALM and functions in the retrograde, early endosome/trans-Golgi network (TGN) pathway in a clathrin- and AP-1-dependent manner. It also contributes to mitogenesis via activation of integrin-linked kinase (ILK). SMOC-2 contains a follistatin-like (FS) domain, two thyroglobulin-like (TY) domains, a novel domain, which is found only in the homologous SMOC-1, and an extracellular calcium-binding (EC) domain with two EF-hand calcium-binding motifs. 114 matched cddid_all.tbl CDD cd16242 cd16242 320000 EFh_DMD_like EF-hand-like motif found in the dystrophins subfamily. This dystrophins subfamily includes dystrophin and its two paralogs, utrophin and DRP-2. Dystrophin is a large, submembrane cytoskeletal protein that is the main component of the dystrophin-glycoprotein complex (DGC) in skeletal muscle. It links the transmembrane DGC to the actin cytoskeleton through binding strongly to the cytoplasmic tail of beta-dystroglycan, the transmembrane subunit of a highly O-glycosylated cell-surface protein. Dystrophin also involves in maintaining the structural integrity of cells, as well as in the formation of the blood-brain barrier (BBB). Utrophin, also termed dystrophin-related protein 1 (DRP-1), is an autosomal dystrophin homologue that increases dystrophic muscle function and reduces pathology. It is broadly expressed at both the mRNA and protein levels, and occurs in the cerebrovascular endothelium. Utrophin forms the utrophin-glycoprotein complex (UGC) by interacting with the dystroglycans (DGs) and the sarcoglycan-dystroglycans, sarcoglycans and sarcospan (SG-SSPN) subcomplex. It may act as a scaffolding protein that stabilizes lipid microdomains and clusters mechanosensitive channel subunits, and link the F-actin cytoskeleton to the cell membrane via the associated glycoprotein complex. DRP-2 is mainly expressed in the vertebrate central nervous system (CNS). It is associated with brain membrane fractions and highly enriched in the postsynaptic density. DRP-2 plays a role in the organization of central cholinergic synapses. It interacts with dystroglycan and L-Periaxin to form a transmembrane complex, which plays a role in Schwann cell-basal lamina interactions and in the regulation of the terminal stages of myelination. The dystrophins subfamily has been characterized by a compact cluster of domains comprising a WW domain, four EF-hand-like motifs and a ZZ-domain, followed by two syntrophin binding sites (SBSs) and a looser region with two coiled-coils. 163 matched cddid_all.tbl CDD cd16243 cd16243 320001 EFh_DYTN EF-hand-like motif found in dystrotelin and similar proteins. Dystrotelin is the vertebrate orthologue of Drosophila DAH, which is involved in the synchronised cellularization of thousands of nuclei in the syncytial early fly embryo (a specialised form of cytokinesis). Dystrotelin is mainly expressed in the developing central nervous system (CNS) and adult nervous and muscular tissues. Heterologously expressed dystrotelin protein localizes spontaneously to the cytoplasmic membrane, and possibly to the endoplasmic reticulum (ER). Dystrotelin is not critical for mammalian development. It may be involved in other forms of cytokinesis. Its N-terminal region contains a compact cluster of domains comprising four EF-hand-like motifs and a ZZ-domain, followed by a looser region with two coiled-coils. These domains are believed to be involved in protein-protein interactions. The C-terminal region is extremely divergent. Unlike other superfamily members, dystrophin or dystrobrevin, the residues directly involved in beta-dystroglycan binding are not conserved in dystrotelin, which makes it unlikely that dystrotelin interacts with this ligand. Moreover, dystrotelin is unable to heterodimerize with members of the dystrophin or dystrobrevin families, or to homodimerize. 163 matched cddid_all.tbl CDD cd16244 cd16244 320002 EFh_DTN EF-hand-like motif found in dystrobrevins and similar proteins. Dystrobrevins are part of the dystrophin-glycoprotein complex (DGC). They physically associate with members of the dystrophin family and with the syntrophins through their homologous C-terminal coiled coil motifs. The family includes two paralogs dystrobrevins, alpha- and beta-dystrobrevin, both of which are cytoplasmic components of the dystrophin-associated protein complex that function as scaffold proteins in signal transduction and intracellular transport. Absence of alpha- and beta-dystrobrevin causes cerebellar synaptic defects and abnormal motor behavior. The dystrobrevins subfamily has been characterized by a compact cluster of domains comprising four EF-hand-like motifs and a ZZ-domain, followed by a looser region with two coiled-coils. These domains are believed to be involved in protein-protein interactions. In addition, dystrobrevins contain one or two syntrophin binding sites (SBSs). 161 matched cddid_all.tbl CDD cd16245 cd16245 320003 EFh_DAH EF-hand-like motif found in Drosophila melanogaster discontinuous actin hexagon (DAH) and similar proteins. DAH, the product of the dah (discontinuous actin hexagon) gene, is a Drosophila homolog to vertebrate dystrotelin. It is tightly membrane-associated and highly phosphorylated in a time-dependent fashion. DAH plays an essential role in the process of cellularization, and is associated with vesicles that convene at the cleavage furrow. The absence of DAH leads the severe disruption of the cleavage furrows around the nuclei and development stalls. DAH contains a compact cluster of domains comprising four EF-hand-like motifs and a ZZ-domain, followed by a looser region with two coiled-coils. 164 matched cddid_all.tbl CDD cd16246 cd16246 320004 EFh_DMD EF-hand-like motif found in dystrophin. Dystrophin is a large, submembrane cytoskeletal protein that is the main component of the dystrophin-glycoprotein complex (DGC) in skeletal muscle. It links the transmembrane DGC to the actin cytoskeleton through binding strongly to the cytoplasmic tail of beta-dystroglycan, the transmembrane subunit of a highly O-glycosylated cell-surface protein. It involves in maintaining the structural integrity of cells, as well as in the formation of the blood-brain barrier (BBB). The dystrophin subfamily has been characterized by a compact cluster of domains comprising four EF-hand-like motifs and a ZZ-domain, followed by a looser region with two coiled-coils. These domains are believed to be involved in protein-protein interactions. In addition, dystrophin contains two syntrophin binding sites (SBSs) and a long N-terminal extension that comprises two actin-binding calponin homology (CH) domains, approximately 24 spectrin repeats (SRs) and a WW domain. Mutations in dystrophin lead to Duchenne muscular dystrophy (DMD). Moreover, dystrophin deficiency is associated abnormal cerebral diffusion and perfusion, acute Trypanosoma cruzi infection. 162 matched cddid_all.tbl CDD cd16247 cd16247 320005 EFh_UTRO EF-hand-like motif found in utrophin. Utrophin, also termed dystrophin-related protein 1 (DRP-1), is an autosomal dystrophin homologue that increases dystrophic muscle function and reduces pathology. It is broadly expressed at both the mRNA and protein levels, and occurs in the cerebrovascular endothelium. Utrophin forms the utrophin-glycoprotein complex (UGC) by interacting with the dystroglycans (DGs) and the sarcoglycan-dystroglycans, sarcoglycans and sarcospan (SG-SSPN) subcomplex. It may act as a scaffolding protein that stabilizes lipid microdomains and clusters mechanosensitive channel subunits, and link the F-actin cytoskeleton to the cell membrane via the associated glycoprotein complex. Like dystrophin, Utrophin has a compact cluster of domains comprising four EF-hand-like motifs and a ZZ-domain, followed by a looser region with two coiled-coils. These domains are believed to be involved in protein-protein interactions. In addition, it contains two syntrophin binding sites (SBSs) and a long N-terminal extension that comprises two actin-binding calponin homology (CH) domains, up to 24 spectrin repeats (SRs) and a WW domain. However, utrophin lacks the intrinsic microtubule binding activity of dystrophin SRs. 162 matched cddid_all.tbl CDD cd16248 cd16248 320006 EFh_DRP-2 EF-hand-like motif found in dystrophin-related protein 2 (DRP-2). DRP-2 is a dystrophin homologue mainly expressed in the vertebrate central nervous system (CNS). It is associated with brain membrane fractions and highly enriched in the postsynaptic density. DRP-2 plays a role in the organization of central cholinergic synapses. It interacts with dystroglycan and L-Periaxin to form a transmembrane complex, which plays a role in Schwann cell-basal lamina interactions and in the regulation of the terminal stages of myelination. Like dystrophin, DRP-2 has a compact cluster of domains comprising four EF-hand-like motifs and a ZZ-domain, followed by a looser region with two coiled-coils. These domains are believed to be involved in protein-protein interactions. In addition, it contains two syntrophin binding sites (SBSs) and a long N-terminal extension that comprises only two spectrin repeats (SRs) and a WW domain. 162 matched cddid_all.tbl CDD cd16249 cd16249 320007 EFh_DTNA EF-hand-like motif found in alpha-dystrobrevin. Alpha-dystrobrevin, also termed dystrobrevin alpha (DTN-A), or dystrophin-related protein 3 (DRP-3), is the mammalian ortholog of the Torpedo 87 kDa postsynaptic protein that tightly associates with dystrophin. It is a cytoplasmic protein expressed predominantly in skeletal muscle, heart, lung, and brain. Alpha-dystrobrevin has been implicated in the regulation of acetylcholine receptor (AChR) aggregate density and patterning. It is also essential in the pathogenesis of dystrophin-dependent muscular dystrophies. It plays a critical role in the full functionality of dystrophin through increasing dystrophin's binding to the dystrophin-glycoprotein complex (DGC), and provides protection during cardiac stress. Alpha-dystrobrevin binds to the intermediate filament proteins syncoilin and beta-synemin, thereby linking the dystrophin-associated protein complex (DAPC) to the intermediate filament network. Moreover, alpha-dystrobrevin involves in cell signaling via interaction with other proteins such as syntrophin, a modular adaptor protein that coordinates the assembly of the signaling proteins nitric oxide synthase, stress-activated protein kinase-3, and Grb2 to the DAPC. Furthermore, alpha-dystrobrevin plays an important role in muscle function, as well as in nuclear morphology maintenance through specific interaction with the nuclear lamina component lamin B1. In addition, alpha-dystrobrevin is required in dystrophin-associated protein scaffolding in brain. Absence of glial alpha-dystrobrevin causes abnormalities of the blood-brain barrier and progressive brain edema. Alpha-dystrobrevin has a compact cluster of domains comprising four EF-hand-like motifs and a ZZ-domain, followed by a looser region with two coiled-coils. These domains are believed to be involved in protein-protein interactions. In addition, alpha-dystrobrevin contain two syntrophin binding sites (SBSs). 161 matched cddid_all.tbl CDD cd16250 cd16250 320008 EFh_DTNB EF-hand-like motif found in beta-dystrobrevin. Beta-dystrobrevin, also termed dystrobrevin beta (DTN-B), is a dystrophin-related protein that is restricted to non-muscle tissues and is abundantly expressed in brain, lung, kidney, and liver. It may be involved in regulating chromatin dynamics, possibly playing a role in neuronal differentiation, through the interactions with the high mobility group HMG20 proteins iBRAF/HMG20a and BRAF35 /HMG20b. It also binds to and represses the promoter of synapsin I, a neuronal differentiation gene. Moreover, beta-dystrobrevin functions as a kinesin-binding receptor involved in brain development via the association with the extracellular matrix components pancortins. Furthermore, beta-dystrobrevin binds directly to dystrophin and is a cytoplasmic component of the dystrophin-associated glycoprotein complex, a multimeric protein complex that links the extracellular matrix to the cortical actin cytoskeleton and acts as a scaffold for signaling proteins such as protein kinase A. Absence of alpha- and beta-dystrobrevin causes cerebellar synaptic defects and abnormal motor behavior. Beta-dystrobrevin has a compact cluster of domains comprising four EF-hand-like motifs and a ZZ-domain, followed by a looser region with two coiled-coils. These domains are believed to be involved in protein-protein interactions. In addition, beta-dystrobrevin contain two syntrophin binding sites (SBSs). 161 matched cddid_all.tbl CDD cd16251 cd16251 319994 EFh_parvalbumin_like EF-hand, calcium binding motif, found in parvalbumin-like EF-hand family. The family includes alpha- and beta-parvalbumins, and a group of uncharacterized calglandulin-like proteins. Parvalbumins are small, acidic, cytosolic EF-hand-containing Ca2+-buffer and Ca2+ transporter/shuttle proteins belonging to EF-hand superfamily. They are expressed by vertebrates in fast-twitch muscle cells, specific neurons of the central and peripheral nervous system, sensory cells of the mammalian auditory organ (Corti's cell), and some other cells, and characterized by the presence of three consecutive EF-hand motifs (helix-loop-helix) called AB, CD, and EF, but only CD and EF can chelate metal ions, such as Ca2+ and Mg2+. Thus, they may play an additional role in Mg2+ handling. Moreover, parvalbumins represent one of the major animal allergens. In metal-bound states, parvalbumins possess a rigid and stable tertiary structure and display strong allergenicity. In contrast, the metal-free parvalbumins are intrinsically disordered, and the loss of metal ions results in a conformational change that decreases their IgE binding capacity. Furthermore, parvalbumins have been widely used as a neuronal marker for a variety of functional brain systems. They also function as a Ca2+ shuttle transporting Ca2+ from troponin-C (TnC) to the sarcoplasmic reticulum (SR) Ca2+ pump during muscle relaxation. Thus they may facilitate myocardial relaxation and play important roles in cardiac diastolic dysfunction. Parvalbumins consists of alpha- and beta- sublineages, which can be distinguished on the basis of isoelectric point (pI > 5 for alpha; pI 101 matched cddid_all.tbl CDD cd16252 cd16252 319995 EFh_calglandulin_like EF-hand, calcium binding motif, found in uncharacterized calglandulin-like proteins. The family corresponds to a group of uncharacterized calglandulin-like proteins. Although their biological function remain unclear, they show high sequence similarity with human calglandulin-like protein GAGLP, which is an ortholog of calglandulin from the venom glands of Bothrops insularis snake. Both GAGLP and calglandulin are putative Ca2+-binding proteins with four EF-hand motifs. However, members in this family contain only three EF-hand motifs. In this point, they may belong to the parvalbumin-like EF-hand family, which is characterized by the presence of three consecutive EF-hand motifs (helix-loop-helix). 106 matched cddid_all.tbl CDD cd16253 cd16253 319996 EFh_parvalbumins EF-hand, calcium binding motif, found in parvalbumins. Parvalbumins are small, acidic, cytosolic EF-hand-containing Ca2+-buffer and Ca2+ transporter/shuttle proteins belonging to EF-hand superfamily. They are expressed by vertebrates in fast-twitch muscle cells, specific neurons of the central and peripheral nervous system, sensory cells of the mammalian auditory organ (Corti's cell), and some other cells, and characterized by the presence of three consecutive EF-hand motifs (helix-loop-helix) called AB, CD, and EF, but only CD and EF can chelate metal ions, such as Ca2+ and Mg2+. Thus, they may play an additional role in Mg2+ handling. Moreover, parvalbumins represent one of the major animal allergens. In metal-bound states, parvalbumins possess a rigid and stable tertiary structure and display strong allergenicity. In contrast, the metal-free parvalbumins are intrinsically disordered, and the loss of metal ions results in a conformational change that decreases their IgE binding capacity. Furthermore, parvalbumins have been widely used as a neuronal marker for a variety of functional brain systems. They also function as a Ca2+ shuttle transporting Ca2+ from troponin-C (TnC) to the sarcoplasmic reticulum (SR) Ca2+ pump during muscle relaxation. Thus they may facilitate myocardial relaxation and play important roles in cardiac diastolic dysfunction. Parvalbumins consists of alpha- and beta- sublineages, which can be distinguished on the basis of isoelectric point (pI > 5 for alpha; pI 101 matched cddid_all.tbl CDD cd16254 cd16254 319997 EFh_parvalbumin_alpha EF-hand, calcium binding motif, found in alpha-parvalbumin. Alpha-parvalbumin is cytosolic Ca2+/Mg2+-binding protein expressed mainly in fast-twitch skeletal myofibrils, where it may act as a soluble relaxing factor facilitating the Ca2+-mediated relaxation phase. It is also expressed in rapidly firing neurons, particularly GABA-ergic neurons, and thus may confer protection against Ca2+ toxicity. The major role of alpha-parvalbumin is metal buffering and transport of Ca2+. It binds different metal cations, and exhibits very high affinity for Ca2+ and physiologically significant affinity for Mg2+. Alpha-parvalbumin is characterized by the presence of three consecutive EF-hand motifs (helix-loop-helix) called AB, CD, and EF, but only CD and EF can chelate metal ions, such as Ca2+ and Mg2+. Both metal ion-binding sites in alpha-parvalbumin are high-affinity sites. Additionally, in contrast to beta-parvalbumin, alpha-parvalbumin is less acidic and has an additional residue in the C-terminal helix. 101 matched cddid_all.tbl CDD cd16255 cd16255 319998 EFh_parvalbumin_beta EF-hand, calcium binding motif, found in beta-parvalbumin. Beta-parvalbumin, also termed Oncomodulin-1 (OM), is a small calcium-binding protein that is expressed in hepatomas, as well as in the blastocyst and the cytotrophoblasts of the placenta. It is also found to be expressed in the cochlear outer hair cells of the organ of Corti and frequently expressed in neoplasms. Mammalian beta-parvalbumin is secreted by activated macrophages and neutrophils. It may function as a tissue-specific Ca2+-dependent regulatory protein, and may also serve as a specialized cytosolic Ca2+ buffer. Beta-parvalbumin acts as a potent growth-promoting signal between the innate immune system and neurons in vivo. It has high and specific affinity for its receptor on retinal ganglion cells (RGC) and functions as the principal mediator of optic nerve regeneration. It exerts its effects in a cyclic adenosine monophosphate (cAMP)-dependent manner and can further elevate intracellular cAMP levels. Moreover, beta-parvalbumin is associated with efferent function and outer hair cell electromotility, and can identify different hair cell types in the mammalian inner ear. Beta-parvalbumin is characterized by the presence of three consecutive EF-hand motifs (helix-loop-helix) called AB, CD, and EF, but only CD and EF can chelate metal ions, such as Ca2+ and Mg2+. The EF site displays a high-affinity for Ca2+/Mg2+, and the CD site is a low-affinity Ca2+-specific site. In addition, beta-parvalbumin is distinguished from other parvalbumins by its unusually low isoelectric point (pI = 3.1) and sequence eccentricities (e.g., Y57-L58-D59 instead of F57-I58-E59). 101 matched cddid_all.tbl CDD cd16256 cd16256 293929 LumP lumazine protein. Lumazine protein (LumP) is involved in the bioluminescence of certain marine bacteria. It serves as an optical transponder in bioluminescence emission. The intense fluorescence of LumP is caused by non-covalently bound 6,7- dimethyl-8-ribityllumazine. Though its amino acid sequence is very similar to riboflavin synthase it functions as a monomer, unlike the riboflavin synthases from eubacteria, yeasts and plants which act as trimers. 186 matched cddid_all.tbl CDD cd16257 cd16257 293914 EFG_III-like Domain III of Elongation factor G (EF-G) and related proteins. Bacterial Elongation factor G (EF-G) and related proteins play a role in translation and share a similar domain architecture. Elongation factor EFG participates in the elongation phase during protein biosynthesis on the ribosome by stimulating translocation. Its functional cycles depend on GTP binding and its hydrolysis. Domain III is involved in the activation of GTP hydrolysis. This domain III, which is different from domain III in EF-TU and related elongation factors, is found in several translation factors, like bacterial release factors RF3, elongation factor 4, elongation factor 2, GTP-binding protein BipA and tetracycline resistance protein Tet. 71 matched cddid_all.tbl CDD cd16258 cd16258 293915 Tet_III Domain III of Tetracycline resistance protein Tet. Tetracycline resistance proteins, including TetM and TetO, catalyze the release of tetracycline (Tc) from the ribosome in a GTP-dependent manner thereby mediating Tc resistance. Tcs are broad-spectrum antibiotics. Typical Tcs bind to the ribosome and inhibit the elongation phase of protein synthesis, by inhibiting the occupation of site A by aminoacyl-tRNA. 71 matched cddid_all.tbl CDD cd16259 cd16259 293916 RF3_III Domain III of bacterial Release Factor 3 (RF3). The class II RF3 is a member of one of two release factor (RF) classes required for the termination of protein synthesis by the ribosome. RF3 is a GTPase that removes class I RFs (RF1 or RF2) from the ribosome after release of the nascent polypeptide. RF3 in the GDP state binds to the ribosomal class I RF complex, followed by an exchange of GDP for GTP and release of the class I RF. Sequence comparison of class II release factors with elongation factors shows that prokaryotic RF3 is more similar to EF-G whereas eukaryotic eRF3 is more similar to eEF1A, implying that their precise function may differ. 70 matched cddid_all.tbl CDD cd16260 cd16260 293917 EF4_III Domain III of Elongation Factor 4 (EF4). Elongation factor 4 (EF4 or LepA) is a highly conserved guanosine triphosphatase found in bacteria and eukaryotic mitochondria and chloroplasts. EF4 functions as a translation factor, which promotes back-translocation of tRNAs on posttranslocational ribosome complexes and competes with elongation factor G for interaction with pretranslocational ribosomes, inhibiting the elongation phase of protein synthesis. 76 matched cddid_all.tbl CDD cd16261 cd16261 293918 EF2_snRNP_III Domain III of Elongation Factor 2 (EF2). This model represents domain III of Elongation factor 2 (EF2) found in eukaryotes and archaea, and the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and its yeast counterpart Snu114p. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. This translocation step is catalyzed by EF-2_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis are important for the function of the U5-116 kD/Snu114p. 72 matched cddid_all.tbl CDD cd16262 cd16262 293919 EFG_III Domain III of Elongation Factor G (EFG). This model represents domain III of bacterial Elongation factor G (EF-G), and mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2), which play an important role during peptide synthesis and tRNA site changes. In bacteria, this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. mtEFG1 and mtEFG2 show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects, and a tendency to lose mitochondrial DNA. No clear phenotype has been found for mutants of the yeast homolog of mtEFG2, MEF2. 76 matched cddid_all.tbl CDD cd16263 cd16263 293920 BipA_III Domain III of GTP-binding protein BipA (TypA). BipA (also called TypA) is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios. It is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion. 79 matched cddid_all.tbl CDD cd16264 cd16264 293921 snRNP_III Domain III of the spliceosomal 116kD U5 small nuclear ribonucleoprotein (snRNP) component. Domain III of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and its yeast counterpart Snu114p is homologous to domain III of the eukaryotic translational elongation factor EF-2. U5-116 kD is a GTPase component of the spliceosome complex which functions in the processing of precursor mRNAs to produce mature mRNAs. 72 matched cddid_all.tbl CDD cd16265 cd16265 293910 Translation_Factor_II Proteins related to domain II of EF-Tu and related translation factors. Elongation factor Tu consists of three structural domains; this family represents single domain proteins that are related to the second domain of EF-Tu. Domain II of EF-Tu adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is also found in other proteins such as elongation factor G and translation initiation factor IF-2. 80 matched cddid_all.tbl CDD cd16266 cd16266 293911 IF2_aeIF5B_IV Domain IV of prokaryotic Initiation Factor 2 and archaeal and eukaryotic Initiation Factor 5. This family represents the domain IV of prokaryotic Initiation Factor 2 (IF2) and its archaeal and eukaryotic homologs IF5B. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of the 60S ribosomal subunit. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains in EF1A, eEF1A and aeIF2gamma. 87 matched cddid_all.tbl CDD cd16267 cd16267 293912 HBS1-like_II Domain II of Hbs1-like proteins. S. cerevisiae Hbs1 is closely related to the eukaryotic class II release factor (eRF3). Hbs1, together with Dom34 (pelota), plays an important role in termination and recycling, but in contrast to eRF3/eRF1, Hbs1, together with Dom34 (pelota), functions on mRNA-bound ribosomes in a codon-independent manner and promotes subunit splitting on completely empty ribosomes. 84 matched cddid_all.tbl CDD cd16268 cd16268 293913 EF2_II Domain II of Elongation Factor 2. This subfamily represents domain II of elongation factor 2 (EF-2) found in eukaryotes and archaea. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. This translocation step is catalyzed by EF-2_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. 96 matched cddid_all.tbl CDD cd16269 cd16269 293879 GBP_C Guanylate-binding protein, C-terminal domain. Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines. 291 matched cddid_all.tbl CDD cd16270 cd16270 293878 Apc5_N N-terminal domain of the anaphase-promoting complex subunit Apc5 (or Anapc5). The N-terminal domain of Apc5 interacts with subunits Apc4, Apc15, and CDC23. Apc5 is a subunit of the eukaryotic anaphase-promoting complex/cyclosome (APC/C) which is a multi-subunit ubiquitin ligase that mediates the proteolysis of cell cycle proteins in mitosis and G1. Although Apc5 does not contain a classical RNA binding domain, it binds the poly(A) binding protein (PABP), which directly binds the internal ribosome entry site (IRES) of growth factor 2 mRNA. PABP was found to enhance IRES-mediated translation, whereas Apc5 over-expression counteracted this effect. In addition to its association with the APC/C complex, Apc5 binds much heavier complexes and co-sediments with the ribosomal fraction. The N-terminus of Afi1 serves to stabilize the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC. 143 matched cddid_all.tbl CDD cd16272 cd16272 293830 RNaseZ_MBL-fold Ribonuclease Z; MBL-fold metallo-hydrolase domain. The tRNA maturase RNase Z (also known as tRNase Z or 3' tRNase) catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors. Two forms of RNase Z exist in eukaryotes, one long (ELAC2) and one short form (ELAC1), the former may have resulted from a duplication of the shorter enzyme. Only the short form exists in bacteria. It includes the C-terminus of human ELAC2 and Escherichia coli zinc phosphodiesterase (ZiPD, also known as ecoZ, tRNase Z, or RNase BN) is a 3' tRNA-processing endonuclease, encoded by the elaC gene. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 180 matched cddid_all.tbl CDD cd16273 cd16273 293831 SNM1A-1C-like_MBL-fold SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain. Includes human SNM1A (SNM1 homolog A, also known as DNA cross-link repair 1A protein) and Saccharomyces cerevisiae Pso2 protein (PSOralen derivative sensitive 2, also known as SNM1, sensitive to nitrogen mustard 1), both proteins are 5'-exonucleases and function in interstrand cross-links (ICL) repair. Also includes the nuclease artemis (also known as SNM1C, SNM1 homolog C, SNM1-like protein, and DNA cross-link repair 1C protein) which plays a role in V(D)J recombination/DNA repair. Purified artemis protein possesses single-strand-specific 5' to 3' exonuclease activity. Upon complex formation with, and phosphorylation by, DNA-dependent protein kinase, artemis gains endonucleolytic activity on hairpins and 5' and 3' overhangs. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 160 matched cddid_all.tbl CDD cd16274 cd16274 293832 PQQB-like_MBL-fold Coenzyme pyrroloquinoline quinone (PQQ) synthesis protein B and related proteins; MBL-fold metallo hydrolase domainhydrolase domain. PQQB is essential for the synthesis of the cofactor pyrroloquinoline quinone (PQQ) in Klebsiella pneumonia. PqqB is not directly involved in the PQQ biosynthesis but may serve as a carrier for PQQ when PQQ is released from PqqC. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 220 matched cddid_all.tbl CDD cd16275 cd16275 293833 BaeB-like_MBL-fold Bacillus amyloliquefaciens BaeB and related proteins; MBL-fold metallo hydrolase domain. Bacillus amyloliquefaciens BaeB may play a role in the synthesis of the antibiotic polyketide bacillaene. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 174 matched cddid_all.tbl CDD cd16276 cd16276 293834 metallo-hydrolase-like_MBL-fold uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain. Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily.Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. 188 matched cddid_all.tbl CDD cd16277 cd16277 293835 metallo-hydrolase-like_MBL-fold uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain. Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily.Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. 222 matched cddid_all.tbl CDD cd16278 cd16278 293836 metallo-hydrolase-like_MBL-fold uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain. Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily.Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. 185 matched cddid_all.tbl CDD cd16279 cd16279 293837 metallo-hydrolase-like_MBL-fold uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo. Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily.Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. Some members of this subgroup are named as octanoyltransferase (also known as lipoate-protein ligase B). 193 matched cddid_all.tbl CDD cd16280 cd16280 293838 metallo-hydrolase-like_MBL-fold uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain. Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily.Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. 251 matched cddid_all.tbl CDD cd16281 cd16281 293839 metallo-hydrolase-like_MBL-fold uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain. Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily.Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. 252 matched cddid_all.tbl CDD cd16282 cd16282 293840 metallo-hydrolase-like_MBL-fold uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain. Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily.Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. 209 matched cddid_all.tbl CDD cd16283 cd16283 293841 RomA-like_MBL-fold Enterobacter cloacae RomA and related proteins; MBL-fold metallo hydrolase domain. Derepression of the romA-ramA locus results in a multidrug-resistance phenotype. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) from which this fold was named are only a small fraction of the activities which are included in this superfamily. Activities carried out by superfamily members include class B beta-lactamases, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry. 181 matched cddid_all.tbl CDD cd16284 cd16284 293842 UlaG-like_MBL-fold UlaG a putative l-ascorbate-6-P lactonase and related proteins; MBL-fold metallo hydrolase domain. UlaG is essential for L-ascorbate utilization under anaerobic conditions; it is a putative l-ascorbate-6-P lactonase thought to catalyze the hydrolysis of L-ascorbate-6-phosphate to 3-keto-L-gulonate-6-phosphate. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 178 matched cddid_all.tbl CDD cd16285 cd16285 293843 MBL-B1 metallo-beta-lactamases, subclass B1; MBL-fold metallo-hydrolase domain. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. Subclass B1 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. Includes chromosomally-encoded MBLs such as Bacillus cereus BcII, Bacteroides fragilis CcrA, and Elizabethkingia meningoseptica (Chryseobacterium meningosepticum) BlaB and acquired MBLs including IMP-1, VIM-1, VIM-2, GIM-1, NDM-1 and FIM-1. 210 matched cddid_all.tbl CDD cd16286 cd16286 293844 SPM-1-like_MBL-B1-B2-like Pseudomonas areoginosa SPM-1 and related metallo-beta-lactamases, subclasses B1 and B2 like; MBL-fold metallo-hydrolase domain. SPM-1 was first identified in a Pseudomonas aeruginosa strain from a paediatric leukaemia patient and is a major clinical problem. MBLs (class B of the Ambler beta-lactamase classification) have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs are most closely related to each other. SPM-1 appears to be a hybrid B1/B2 MBL. 236 matched cddid_all.tbl CDD cd16287 cd16287 293845 CphS_ImiS-like_MBL-B2 metallo-beta-lactamases, subclass B2; MBL-fold metallo-hydrolase domain. Includes Aeromonas hydrophyla CphA, Aeromonas veronii ImiS, and Serratia fonticola Sfh-I. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. B2 MBLs have a narrow substrate profile relative to subclass B1 MBLs that includes carbapenems, and they are active with one zinc ion bound in the Asp-Cys-His site, binding of a second zinc ion in the modified 3H site (Asn-His-His) inhibits catalysis. 226 matched cddid_all.tbl CDD cd16288 cd16288 293846 BJP-1_FEZ-1-like_MBL-B3 BJP-1, FEZ-1, GOB-1, Mbl1b and related metallo-beta-lactamases, subclass B3; MBL-fold metallo-hydrolase domain. This subgroup of B3 subclass MBLs includes Bradyrhizobium diazoefficiens BJP-1, Fluoribacter gormanii FEZ-1, Elizabethkingia meningoseptica (Chryseobacterium meningosepticum) GOB-1, Caulobacter crescentus Mbl1b. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. Subclass B3 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. These B3 enzymes have a modified Zn2/DCH site (Asp-His-His). 254 matched cddid_all.tbl CDD cd16289 cd16289 293847 L1_POM-1-like_MBL-B3 Stenotrophomonas maltophilia L1, Pseudomonas otitidis POM-1 and related metallo-beta-lactamases, subclass B3; MBL-fold metallo-hydrolase domain. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. This subgroup of L1- and Pom-1-like MBLs belongs to the B3 subclass. Subclass B3 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. These B3 enzymes have a modified Zn2/DCH site (Asp-His-His). 239 matched cddid_all.tbl CDD cd16290 cd16290 293848 AIM-1_SMB-1-like_MBL-B3 AIM-1, SMB-1, EVM-1, THIN-B and related metallo-beta-lactamases, subclass B3; MBL-fold metallo-hydrolase domain. This subgroup of B3 subclass MBLs includes Pseudomonas Aeruginosa AIM-1, Serratia marcescens SMB-1, Erythrobacter vulgaris EVM-1, and Janthinobacterium lividum THIN-B. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. This subgroup of AIM-1-,SMB-1-, EVM-1-, THIN-B-like MBLs belongs to the B3 subclass. Subclass B3 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. These B3 enzymes have a modified Zn2/DCH site (Asp-His-His). 256 matched cddid_all.tbl CDD cd16291 cd16291 293849 INTS11-like_MBL-fold Integrator complex subunit 11, and related proteins; MBL-fold metallo-hydrolase domain. Integrator is a metazoan-specific multisubunit, multifunctional protein complex composed of 14 subunits named Int1-Int14 (Integrator subunits). This subgroup includes Int11 (also known as cleavage and polyadenylation-specific factor (CPSF) 3-like protein, and protein related to CPSF subunits of 68 kDa (RC-68)). Integrator complex has been implicated in a variety of Pol II transcription events including 3' end processing of snRNA, transcription initiation, promoter-proximal pausing, termination of protein-coding transcripts, and in HVS pre-miRNA 3' end processing. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 199 matched cddid_all.tbl CDD cd16292 cd16292 293850 CPSF3-like_MBL-fold cleavage and polyadenylation specificity factor (CPSF) subunit 3 and related proteins; MBL-fold metallo-hydrolase domain. CPSF3 (also known as cleavage and polyadenylation specificity factor 73 kDa subunit/CPSF-73) functions as a 3' endonuclease in 3' end processing of pre-mRNAs during cleavage/polyadenylation, and in 3' end processing of metazoan histone pre-mRNAs. This subgroup also contains the yeast homolog of CPSF-73, Ysh1/Brr5 which has roles in mRNA and snoRNA synthesis. In addition to this MBL-fold metallo-hydrolase domain, members of this subgroup contain a beta-CASP (named for metallo-beta-lactamase, CPSF, Artemis, Snm1, Pso2) domain, and a RMMBL domain (RNA-metabolizing metallo-beta-lactamase). Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 194 matched cddid_all.tbl CDD cd16293 cd16293 293851 CPSF2-like_MBL-fold cleavage and polyadenylation specificity factor (CPSF) subunit 2 and related proteins; MBL-fold metallo-hydrolase domain. CPSF2, also known as cleavage and polyadenylation specificity factor 100 kDa subunit (CPSF-100), is a component of the CPSF complex, which plays a role in 3' end processing of pre-mRNAs during cleavage/polyadenylation, and during processing of metazoan histone pre-mRNAs. This subgroup includes Ydh1p, the yeast homolog of CPSF2. In addition to this MBL-fold metallo-hydrolase domain, members of this subgroup contain a beta-CASP (named for metallo-beta-lactamase, CPSF, Artemis, Snm1, Pso2) domain. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 199 matched cddid_all.tbl CDD cd16294 cd16294 293852 Int9-like_MBL-fold integrator subunit 9, and related proteins; MBL-fold metallo-hydrolase domain. Integrator is a metazoan-specific multisubunit, multifunctional protein complex composed of 14 subunits named Int1-Int14 (Integrator subunits). This subgroup includes Int9, also known as protein related to CPSF subunits of 74 kDa (RC-74). Integrator complex has been implicated in a variety of Pol II transcription events including 3' end processing of snRNA, transcription initiation, promoter-proximal pausing, termination of protein-coding transcripts, and in HVS pre-miRNA 3' end processing. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 166 matched cddid_all.tbl CDD cd16295 cd16295 293853 TTHA0252-CPSF-like_MBL-fold Thermus thermophilus TTHA0252 and related cleavage and polyadenylation specificity factors; MBL-fold metallo-hydrolase domain. Includes the archaeal cleavage and polyadenylation specificity factors (CPSFs) such as Methanothermobacter thermautotrophicus MTH1203, and Pyrococcus horikoshii PH1404. In addition to the MBL-fold metallo-hydrolase nuclease and the beta-CASP domains, members of this subgroup contain two contiguous KH domains. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 197 matched cddid_all.tbl CDD cd16296 cd16296 293854 RNaseZ_ELAC2-N-term-like_MBL-fold Ribonuclease Z, N-terminus of human ELAC2 and related proteins; MBL-fold metallo-hydrolase domain. The tRNA maturase RNase Z (also known as tRNase Z or 3' tRNase) catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors. Two forms of RNase Z exist in eukaryotes, one long (ELAC2) and one short form (ELAC1), the former may have resulted from a duplication of the shorter enzyme. This eukaryotic subgroup includes the N-terminus of human ELAC2 and related proteins. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 175 matched cddid_all.tbl CDD cd16297 cd16297 293855 artemis-SNM1C-like_MBL-fold artemis-SNM1C and related proteins; MBL-fold metallo-hydrolase domain. Includes the nuclease artemis (also known as SNM1C, SNM1 homolog C, SNM1-like protein and DNA cross-link repair 1C protein) which plays a role in V(D)J recombination/DNA repair. Purified artemis protein possesses single-strand-specific 5' to 3' exonuclease activity. Upon complex formation with, and phosphorylation by, DNA-dependent protein kinase, artemis gains endonucleolytic activity on hairpins and 5' and 3' overhangs. Inactivation of Artemis causes severe combined immunodeficiency (SCID). Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 171 matched cddid_all.tbl CDD cd16298 cd16298 293856 SNM1A-like_MBL-fold 5'-exonucleases human SNM1A and related proteins; MBL-fold metallo-hydrolase domain. Includes human SNM1A (SNM1 homolog A, also known as DNA cross-link repair 1A protein) which is a 5'-exonuclease and functions in interstrand cross-links (ICL) repair. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. 157 matched cddid_all.tbl CDD cd16299 cd16299 293857 IND_BlaB-like_MBL-B1 IND1, IND2, BlaB-1 and related metallo-beta-lactamases, subclass B1; MBL-fold metallo-hydrolase domain. Includes the chromosome-encoded metallo-beta-lactamases Chryseobacterium indologenes IND-1, IND-2, and IND-7, Elizabethkingia meningoseptica (Chryseobacterium meningosepticum) BlaB, Chryseobacterium gleum CGB-1, and Empedobacter brevis EBR-1. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. This subgroup of MBLs belongs to the B1 subclass. B1 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. 212 matched cddid_all.tbl CDD cd16300 cd16300 293858 NDM_FIM-like_MBL-B1 NDM-1, FIM-1 and related metallo-beta-lactamases, subclass B1; MBL-fold metallo-hydrolase domain. Includes the ISCR-mediated MBLs NDM-1 (NDM (New Delhi metallo-beta-lactamase) and FIM-1 (Florence imipenemase). MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. This subgroup of MBLs belongs to the B1 subclass. B1 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. 214 matched cddid_all.tbl CDD cd16301 cd16301 293859 IMP_DIM-like_MBL-B1 IMP-1, DIM-1, GIM-1, SIM-1, TMB-1 and related metallo-beta-lactamases, subclass B1; MBL-fold metallo-hydrolase domain. Includes the acquired MBLs IMP-1(a beta-lactamase that is active on imipenem), DIM-1 (Dutch imipenemase), GIM-1 (German imipenemase), KHM-1 (Kyorin Health Science MBL 1), SIM-1 (Seoul imipenemase), and TMB-1 (Tripoli metallo-beta-lactamase). IMP-1, DIM-1, GIM-1, SIM-1, and TMB-1 are Class 1 integron-mediated MBLs, KMH-1 is plasmid-mediated. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. This subgroup of acquired MBLs belongs to the B1 subclass. B1 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. 215 matched cddid_all.tbl CDD cd16302 cd16302 293860 CcrA-like_MBL-B1 Bacteroides fragilis CcrA and related metallo-beta-lactamases, subclass B1; MBL-fold metallo-hydrolase domain. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. This subgroup of MBLs belongs to the B1 subclass. B1 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. 212 matched cddid_all.tbl CDD cd16303 cd16303 293861 VIM_type_MBL-B1 VIM-type metallo-beta-lactamases, subclass B1; MBL-fold metallo-hydrolase domain. VIM (Verona integron-encoded metallo-beta-lactamase)-type MBLs are integron-associated and are widely distributed acquired MBLs. MBLs (class B of the Ambler beta-lactamase classification) have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. This subgroup of VIM-type MBLs belongs to the B1 subclass. B1 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. 218 matched cddid_all.tbl CDD cd16304 cd16304 293862 BcII-like_MBL-B1 Bacillus cereus Beta-lactamase 2 and related metallo-beta-lactamases, subclass B1; MBL-fold metallo-hydrolase domain. Bacillus cereus Beta-lactamase 2, also called BcII. MBLs (class B of the Ambler beta-lactamase classification) have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. BcII is a chromosome-encoded B1 MBL. B1 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. 212 matched cddid_all.tbl CDD cd16305 cd16305 293863 Sfh-1-like_MBL-B2 Serratia fonticola Sfh-I and related metallo-beta-lactamases, subclass B2; MBL-fold metallo-hydrolase domain. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. B2 MBLs have a narrow substrate profile relative to subclass B1 MBLs that includes carbapenems, and they are active with one zinc ion bound in the Asp-Cys-His site, binding of a second zinc ion in the modified 3H site (Asn-His-His) inhibits catalysis. 226 matched cddid_all.tbl CDD cd16306 cd16306 293864 CphA_ImiS-like_MBL-B2 Aeromonas hydrophyla CphA, Aeromonas veronii ImiS, and related metallo-beta-lactamases, subclass B2; MBL-fold metallo-hydrolase domain. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. B2 MBLs have a narrow substrate profile relative to subclass B1 MBLs that includes carbapenems, and they are active with one zinc ion bound in the Asp-Cys-His site, binding of a second zinc ion in the modified 3H site (Asn-His-His) inhibits catalysis. 222 matched cddid_all.tbl CDD cd16307 cd16307 293865 FEZ-1-like_MBL-B3 Fluoribacter gormanii FEZ-1 and related metallo-beta-lactamases, subclass B3; MBL-fold metallo-hydrolase domain. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. This subgroup of FEZ-1-like MBLs belongs to the B3 subclass. Subclass B3 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. These B3 enzymes have a modified Zn2/DCH site (Asp-His-His). 255 matched cddid_all.tbl CDD cd16308 cd16308 293866 GOB1-like_MBL-B3 Elizabethkingia meningoseptica GOB-1 and related metallo-beta-lactamases, subclass B3; MBL-fold metallo-hydrolase domain. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. This subgroup of GOB-1-like MBLs belongs to the B3 subclass. Subclass B3 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. These B3 enzymes have a modified Zn2/DCH site (Asp-His-His). 254 matched cddid_all.tbl CDD cd16309 cd16309 293867 BJP-1-like_MBL-B3 Bradyrhizobium diazoefficiens BJP-1 and related metallo-beta-lactamases, subclass B3; MBL-fold metallo-hydrolase domain. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. This subgroup of BJP-1-like MBLs belongs to the B3 subclass. Subclass B3 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. These B3 enzymes have a modified Zn2/DCH site (Asp-His-His). 252 matched cddid_all.tbl CDD cd16310 cd16310 293868 Mbl1b-like_MBL-B3 Caulobacter crescentus Mbl1b and related metallo-beta-lactamases, subclass B3; MBL-fold metallo-hydrolase domain. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. This subgroup of Mbl1b-like MBLs belongs to the B3 subclass. Subclass B3 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. These B3 enzymes have a modified Zn2/DCH site (Asp-His-His). 252 matched cddid_all.tbl CDD cd16311 cd16311 293869 THIN-B2-like_MBL-B3 Janthinobacterium lividum THIN-B2 and related metallo-beta-lactamases, subclass B3; MBL-fold metallo-hydrolase domain. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. This subgroup of THIN-B2-like MBLs belongs to the B3 subclass. Subclass B3 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. These B3 enzymes have a modified Zn2/DCH site (Asp-His-His). 257 matched cddid_all.tbl CDD cd16312 cd16312 293870 THIN-B-like_MBL-B3 Janthinobacterium lividum THIN-B and related metallo-beta-lactamases, subclass B3; MBL-fold metallo-hydrolase domain. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. This subgroup of THIN-B-like MBLs belongs to the B3 subclass. Subclass B3 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. These B3 enzymes have a modified Zn2/DCH site (Asp-His-His). 258 matched cddid_all.tbl CDD cd16313 cd16313 293871 SMB-1-like_MBL-B3 SMB-1, THIN-B and related metallo-beta-lactamases, subclass B3; MBL-fold metallo-hydrolase domain. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. This subgroup of SMB-1- and THIN-B-like MBLs belongs to the B3 subclass. Subclass B3 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. These B3 enzymes have a modified Zn2/DCH site (Asp-His-His). 254 matched cddid_all.tbl CDD cd16314 cd16314 293872 AIM-1-like_MBL-B3 Pseudomonas Aeruginosa AIM-1 and related metallo-beta-lactamases, subclass B3; MBL-fold metallo-hydrolase domain. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. This subgroup AIM-1-like MBLs belongs to the B3 subclass. Subclass B3 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. These B3 enzymes have a modified Zn2/DCH site (Asp-His-His). 255 matched cddid_all.tbl CDD cd16315 cd16315 293873 EVM-1-like_MBL-B3 Erythrobacter vulgaris EVM-1 and related metallo-beta-lactamases, subclass B3; MBL-fold metallo-hydrolase domain. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. This subgroup EVM-1-like MBLs belongs to the B3 subclass. Subclass B3 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. These B3 enzymes have a modified Zn2/DCH site (Asp-His-His). 248 matched cddid_all.tbl CDD cd16316 cd16316 293874 BlaB-like_MBL-B1 Elizabethkingia meningoseptica (Chryseobacterium meningosepticum) BlaB and related metallo-beta-lactamases, subclass B1; MBL-fold metallo-hydrolase domain. Includes the chromosome-encoded MBL Elizabethkingia meningoseptica (Chryseobacterium meningosepticum) BlaB and related MBLs. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. This subgroup of MBLs belongs to the B1 subclass. B1 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. 214 matched cddid_all.tbl CDD cd16317 cd16317 293875 IND_MBL-B1 Chryseobacterium indologenes IND-1, IND-2, IND-7and related metallo-beta-lactamases, subclass B1; MBL-fold metallo-hydrolase domain. Includes the chromosome-encoded MBLs Chryseobacterium indologenes IND-1, IND-2, and IND-7 and related MBLs. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. This subgroup of MBLs belongs to the B1 subclass. B1 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. 215 matched cddid_all.tbl CDD cd16318 cd16318 293876 MUS_TUS_MBL-B1 Myroides odoratimimus MUS-1, MUS-2, TUS-1 and related metallo-beta-lactamases, subclass B1; MBL-fold metallo-hydrolase domain. Includes the chromosome-encoded MBLs Myroides odoratimimus MUS-1 and related MBLs. MBLs (class B of the Ambler beta-lactamase classification) are a diverse group of metallo-enzymes that are capable of catalyzing the hydrolysis of a wide range of beta-lactam antibiotics. MBLs have been divided into three subclasses B1, B2 and B3, based on sequence/structural relationships and substrates, with the B1 and B2 MBLs being most closely related to each other. This subgroup of MBLs belongs to the B1 subclass. B1 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile. 214 matched cddid_all.tbl CDD cd16319 cd16319 293782 MraZ protein domain of unknown function (UPF0040) includes MraZ. This family contains proteins of unknown function (UPF0040), implicated in a cellular function of bacterial cell division. It includes protein MraZ which is present in almost all bacteria and appears to be essential for survival. It is found in gene clusters associated with the cellular function of cell division and cell wall biosynthesis. Members of this family contain two tandem copies of the domain; the crystal structure of a member of this family (MPN314) reveals that the two subdomains are related by a pseudo two-fold axis, with each subdomain containing a highly conserved DXXXR sequence motif in close proximity to each other, suggested to form the functional site. 53 matched cddid_all.tbl CDD cd16320 cd16320 293783 MraZ_N N-terminal subdomain of transcriptional regulator MraZ. This family contains the N-terminal domain of proteins of unknown function (UPF0040), implicated in a cellular function of bacterial cell division. It includes protein MraZ which is present in almost all bacteria and appears to be essential for survival. It is found in gene clusters associated with the cellular function of cell division and cell wall biosynthesis, including mraW, ftsI, murE, murF, ftsW and murG. Members of this family contain two tandem copies of the domain; the crystal structure of a member of this family (MPN314) reveals that the two subdomains are related by a pseudo two-fold axis, with each subdomain containing a highly conserved DXXXR sequence motif in close proximity to each other, suggested to form the functional site. 60 matched cddid_all.tbl CDD cd16321 cd16321 293784 MraZ_C C-terminal subdomain of transcriptional regulator MraZ. This family contains the C-terminal domain of proteins of unknown function (UPF0040), implicated in a cellular function of bacterial cell division. It includes protein MraZ which is present in almost all bacteria and appears to be essential for survival. It is found in gene clusters associated with the cellular function of cell division and cell wall biosynthesis, including mraW, ftsI, murE, murF, ftsW and murG. Members of this family contain two tandem copies of the domain; the crystal structure of a member of this family (MPN314) reveals that the two subdomains are related by a pseudo two-fold axis, with each subdomain containing a highly conserved DXXXR sequence motif in close proximity to each other, suggested to form the functional site. 62 matched cddid_all.tbl CDD cd16322 cd16322 293877 TTHA1623-like_MBL-fold uncharacterized Thermus thermophilus TTHA1623 and related proteins; MBL-fold metallo hydrolase domain. Includes the MBL-fold metallo hydrolase domain of uncharacterized Thermus thermophilus TTHA1623 and related proteins. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions. This family includes homologs present in a wide range of bacteria and archaea and some eukaryota. Members of the MBL-fold metallo-hydrolase superfamily exhibit a variety of active site metallo-chemistry, TTHA1623 exhibiting a uniquely shaped putative substrate-binding pocket with a glyoxalase II-type metal-coordination mode. 204 matched cddid_all.tbl CDD cd16323 cd16323 319993 Syd Syd, a SecY-interacting protein. This family contains the Syd protein that has been implicated in the Sec-dependent transport of polypeptides across the inner membrane in bacteria. Syd has been shown to bind the SecY subunit of membrane-embedded SecYEG heterotrimer (also known as core translocon or SecY complex) which is a conserved protein-conducting channel essential for the biogenesis of most of the secretory and integral membrane proteins. The SecY-binding site of Syd is a conserved concave and electronegative groove that forms interactions with the electropositive loops of the SecY subunit. Syd is also known to verify the proper assembly of the SecY complex in the membrane by interfering with protein translocation only when the channel displays abnormal SecY-SecE associations. Operon analysis has shown that Syd protein may function as immunity protein in bacterial toxin systems. 173 matched cddid_all.tbl CDD cd16324 cd16324 319982 LolA_fold-like family containing periplasmic molecular chaperone LolA, the outer membrane lipoprotein receptor LolB and the periplasmic protein RseB. This family contains the periplasmic molecular chaperone LolA, the outer membrane lipoprotein receptor LolB and the N-terminal domain of periplasmic protein RseB, all of which have similar unclosed beta-barrel structures that resemble a baseball glove-like scaffold consisting of an 11-stranded antiparallel sheet. There are five Lol proteins (LolA, LolB, LolC, LolD, and LolE) involved in the sorting and membrane localization of lipoprotein and are highly conserved in Gram-negative bacteria. LolA accepts outer membrane (OM)-specific lipoproteins that are released from the inner membrane by the LolCDE complex and transfers them to the OM receptor LolB. It is proposed that the LolA/LolB complex forms a tunnel-like structure, where the hydrophobic insides of LolA and LolB are connected, which enables lipoproteins to transfer from LolA to LolB. RseB exerts a crucial role in modulating the stability of RseA, the transmembrane anti-sigma-factor that is degraded during sigma-E-dependent transcription caused by bacterial envelope stress. Its structural similarity to LolA and LolB suggests that RseA may act as a sensor of periplasmic stress with a dual functionality, detecting mislocalized lipoproteins as well as propagating the signal to induce the sigma-E-response. 162 matched cddid_all.tbl CDD cd16325 cd16325 319983 LolA LolA, a periplasmic chaperone. This family contains periplasmic molecular chaperone LolA which binds to outer-membrane specific lipoproteins and transports them from inner membrane to outer membrane (OM) through LolB, a lipoprotein anchored to outer membranes. There are five Lol proteins (LolA, LolB, LolC, LolD, and LolE) involved in the sorting and membrane localization of lipoprotein and are highly conserved in Gram-negative bacteria. LolA accepts OM-specific lipoproteins that are released from the inner membrane by the LolCDE complex and transfers them to the OM receptor LolB. Studies have shown that hydrophobic surface patches large enough to accommodate acyl chains of the OM lipoproteins and the structural flexibility of LolA are important factors for its role as a periplasmic chaperone. 166 matched cddid_all.tbl CDD cd16326 cd16326 319984 LolB LolB, an outer membrane lipoprotein receptor. This family contains the outer membrane lipoprotein receptor, LolB, which catalyzes the last step of lipoprotein transfer from the inner to the outer membrane. There are five Lol proteins (LolA, LolB, LolC, LolD, and LolE) involved in the sorting and membrane localization of lipoprotein and are highly conserved in Gram-negative bacteria. LolA transports lipoproteins through the periplasm to LolB, which then localizes them to outer membranes; the protruding loop of LolB has been shown to be essential for the localization of lipoproteins in the anchoring of bacterial triacylated proteins to the outer membrane. 163 matched cddid_all.tbl CDD cd16327 cd16327 319985 RseB RseB, a sensor in periplasmic stress. This family contains the periplasmic protein RseB (also known as MucB or Mucb/RseB) which exerts a crucial role in modulating the stability of RseA, the transmembrane anti-sigma-factor that is degraded during sigma-E-dependent transcription caused by bacterial envelope stress. RseB binds to RseA and inhibits its sequential cleavage, thereby functioning as a negative modulator of this response. The protein is composed of two domains, the larger N-terminal domain resembling an unclosed beta-barrel that is remarkably similar structurally to LolA and LolB, proteins capable of binding the lipid anchor of lipoproteins, suggesting that RseA acts as a sensor of periplasmic stress with a dual functionality, detecting mislocalized lipoproteins as well as propagating the signal to induce the sigma-E-response. 166 matched cddid_all.tbl CDD cd16328 cd16328 319992 RseA_N N-terminal domain of RseA. This family contains the cytoplasmic (N-terminal) domain of RseA, the transmembrane anti-sigma-E factor. RseA is degraded during sigma-E-dependent transcription caused by bacterial envelope stress such as heat shock. It is an inner membrane protein with an N-terminal cytoplasmic domain that binds sigma-E and blocks its transcriptional activity, and a C-terminal periplasmic domain that binds RseB, an auxiliary negative regulator. Under inducing conditions, RseA is rapidly degraded and sigma-E is released into the cytoplasm, where it can bind core RNAP and induce its regulon. It has been shown that just the N-terminal domain is sufficient to bind and inhibit sigma-E. The C-terminal domain may interact with other proteins that signal periplasmic stress. 65 matched cddid_all.tbl CDD cd16329 cd16329 319986 LolA_like proteins similar to periplasmic molecular chaperone LolA, the outer membrane lipoprotein receptor LolB and the periplasmic protein RseB. This family contains uncharacterized proteins similar to the periplasmic molecular chaperone LolA, the outer membrane lipoprotein receptor LolB and the periplasmic protein RseB, all of which have similar unclosed beta-barrel structures that resemble a baseball glove-like scaffold consisting of an 11-stranded antiparallel sheet. There are five Lol proteins (LolA, LolB, LolC, LolD, and LolE) involved in the sorting and membrane localization of lipoprotein and are highly conserved in Gram-negative bacteria. LolA accepts outer membrane (OM)-specific lipoproteins that are released from the inner membrane by the LolCDE complex and transfers them to the OM receptor LolB. It is proposed that the LolA/LolB complex forms a tunnel-like structure, where the hydrophobic insides of LolA and LolB are connected, which enables lipoproteins to transfer from LolA to LolB. RseB exerts a crucial role in modulating the stability of RseA, the transmembrane anti-sigma-factor that is degraded during sigma-E-dependent transcription caused by bacterial envelope stress. Its structural similarity to LolA and LolB suggests that RseA may act as a sensor of periplasmic stress with a dual functionality, detecting mislocalized lipoproteins as well as propagating the signal to induce the sigma-E-response. 225 matched cddid_all.tbl CDD cd16330 cd16330 319987 LolA_VioE Proteins similar to violacein biosynthetic enzyme VioE that shares fold with periplasmic molecular chaperone LolA. This family includes the violacein biosynthetic enzyme VioE which shares a core fold with lipoprotein transporter proteins that include lipoprotein transporter proteins LolA and LolB. VioE is an enzyme with no characterized homologs that plays a key role in the biosynthesis of violacein, a naturally occurring bisindole product with various biological activities, including antitumor activity as well as antibacterial and cytotoxic properties. In Chromobacterium violaceum, VioE catalyzes the third step in violacein biosynthesis from a pair of Trp residues (i.e. mediates a 1,2 shift of an indole ring and oxidative chemistry) to generate prodeoxyviolacein, a precursor to violacein. Structural and mutagenesis studies suggest that VioE acts as a catalytic chaperone, using this fold associated with lipoprotein transporters to catalyze the production of its prodeoxyviolacein product. 175 matched cddid_all.tbl CDD cd16331 cd16331 319991 YjgA-like uncharacterized proteins similar to Escherichia coli YjgA. Family of conserved uncharacterized proteins similar to Escherichia coli YjgA, which has been identified as comigrating with the 50S ribosome 153 matched cddid_all.tbl CDD cd16332 cd16332 381747 Prp-like ribosomal-processing cysteine protease Prp and similar proteins. This model represents a family of cysteine proteases that include members found to cleave the N-terminus extension of ribosomal subunit L27 in eubacteria. Proteins in this family are distinguished by a pair of invariant histidine and cysteine residues with conserved spacing that form the classic catalytic dyad of a cysteine protease. Dependence of Staphylococcus aureus on L27 cleavage by Prp makes the enzyme a target for antibiotic development. 102 matched cddid_all.tbl CDD cd16333 cd16333 319989 RELM resistin-like molecule (RELM) hormone family. RELMs, secreted proteins with roles including insulin resistance and the activation of inflammatory processes, are also known as found in inflammatory zone (FIZZ), and include four members in mouse (RELM-alpha/FIZZ1/HIMF, RELM-beta/FIZZ2, Resistin/FIZZ3, and RELM-gamma/FIZZ4) and two members in human (resistin and RELM-beta). Little is yet known about the differences and similarities in function of the different isoforms. RELMs are potentially implicated in a wide range of physiological and pathological processes including obesity-associated diabetes, cardiovascular system function, cancer development and metastasis. There are significant differences between human and rodent RELMs with respect to gene and protein structure, differential gene regulation, different tissue distribution profiles, and insulin resistance induction. Resistin appears to convey insulin resistance in rodents, and to instigate inflammatory processes in humans. In the pathophysiology of obesity-associated diabetes, mouse resistin is secreted by adipocytes and increases hepatic gluconeogenesis, thereby promoting insulin resistance, human resistin is secreted by macrophages and may play a role through inflammatory contributions. Elevated levels of human resistin have been reported in various cancers including colorectal, endometrial, and postmenopausal breast cancers, and may initiate the production of further inflammatory cytokines, to promote tumor cell progression; contrary to this, in vitro overexpression of human RELM-beta abolishes invasion, metastasis and angiogenesis of gastric cancer cells. Resistin circulates as hexamers and trimers; structural similarity has been noted between the resistin homotrimer and the proprotein convertase subtilisin/kexin type 9, C-terminal cysteine-rich domain. 86 matched cddid_all.tbl CDD cd16334 cd16334 319988 LppX-like family includes lipoproteins LppX, LprA, LprF and LprG from Mycobacterium tuberculosis. This family includes the homologous lipoproteins LppX, LprA, LprF and LprG from Mycobacterium tuberculosis (Mtb), all of which share a core fold with lipoprotein transporter proteins LolA and LolB. Mtb contains components such as glycolipids, lipoglycans and lipoproteins that play critical roles in regulating host responses and promoting survival of the pathogen. Mtb LprA is a lipoprotein agonist of Toll-like receptor 2 (TLR2) that regulates innate immunity and APC function. LprF, which is also found in Mycobacterium bovis but not in the nonpathogenic Mycobacterium smegmatis, has a central hydrophobic cavity that binds a diacylated glycolipid that it transfers from the plasma membrane to the cell wall, which might be related to the pathogenesis of the bacteria. Similarly, LprG functions as a carrier of glycolipids and lipoglycans, such as lipoarabinomannan (LAM), during their trafficking and delivery to the mycobacterial cell wall, contributing to virulence; LAM inhibits fusion of phagosomes with lysosomes as a means for mycobacteria to evade host defense. In addition, LprG has potent TLR2 agonist activity that modulates antigen processing of dendritic cells and macrophages. LppX is required for the translocation of the key virulence factors, the phthiocerol dimycocerosates (PDIMs), to the surface of Mtb. 196 matched cddid_all.tbl CDD cd16335 cd16335 319981 MukF_N bacterial condensin complex subunit MukF, N-terminal domain. MukF is part of the MukBEF condensin complex that is mainly found in proteobacteria and is involved in chromosome organization and condensation. The complex is believed to serve as a part of the chromosome scaffold rather than a bulk DNA packing protein. MukE and MukF form a stable complex with each other and dynamically associate with MukB, a member of the SMC protein family. MukEF does not bind DNA on its own but modulates MukB-DNA activity. The stoichiometry of the MukEF complex is MukE4F2. 315 matched cddid_all.tbl CDD cd16336 cd16336 319980 MukE bacterial condensin complex subunit MukE. MukE is part of the MukBEF condensin complex that is mainly found in proteobacteria and is involved in chromosome organization and condensation. The complex is believed to serve as a part of the chromosome scaffold rather than a bulk DNA packing protein. MukE and MukF form a stable complex with each other and dynamically associate with MukB, a member of the SMC protein family. MukEF does not bind DNA on its own but modulates MukB-DNA activity. The stoichiometry of the MukEF complex is MukE4F2. 204 matched cddid_all.tbl CDD cd16337 cd16337 319979 MukF_C bacterial condensin complex subunit MukF, C-terminal domain. MukF is part of the MukBEF condensin complex that is mainly found in proteobacteria and is involved in chromosome organization and condensation. The complex is believed to serve as a part of the chromosome scaffold rather than a bulk DNA packing protein. MukE and MukF form a stable complex with each other and dynamically associate with MukB, a member of the SMC protein family. MukEF does not bind DNA on its own but modulates MukB-DNA activity. The stoichiometry of the MukEF complex is MukE4F2. 97 matched cddid_all.tbl CDD cd16338 cd16338 319976 CpcT T-type phycobiliprotein (PBP) lyase. This family contains the T-type phycobiliprotein (PBP) lyase (includes CpcT/CpeT, also known as CpcT bilin lyase). PBP lyases are employed by cyanobacteria, red algae, cryptophytes and glaucophytes for light-harvesting. Pigmentation of light-harvesting phycobiliproteins of cyanobacteria and cryptophytes requires covalent attachment of open-chain tetrapyrrole chromophores, the phycobilins, to the apoproteins. PBP lyases mediate this covalent attachment of phycobilin chromophores to apo-PBPs and also ensure the correct binding of the chromophore with regard to the specific attachment site and stereospecificity. The T-type lyase is distantly related to CpcS and is responsible for covalent attachment of phycocyanobilin (PCB) or phycoerythrobilin to a specific cysteine residue in the beta-subunit of phycocyanin (CpcB) and the beta-subunit of phycoerythrocyanin (PecB), and with a different stereochemistry than CpcS. In CpcT (All5339) from Nostoc (Anabaena) sp. PCC7120, sequential binding studies indicate that beta-subunit chromophorylation with PCB at a specific C- terminal cysteine residue in cyanobacterial phycocyanin and phycoerythrocyanin is hindered by a preceding chromophorylation at a specific N-terminal cysteine residue by CpcS. T-type PBP lyases adopt a beta-barrel structure with a modified lipocalin fold, similar to S-type PBP lyases. 180 matched cddid_all.tbl CDD cd16339 cd16339 319977 CpcS "S-type phycobiliprotein (PBP) lyase. This family contains the S-type phycobiliprotein (PBP) lyase (denoted CpcS/CpcU or CpeS/CpeU). PBP lyases are employed by cyanobacteria, red algae, cryptophytes and glaucophytes for light-harvesting. Pigmentation of light-harvesting phycobiliproteins of cyanobacteria and cryptophytes requires covalent attachment of open-chain tetrapyrrole chromophores, the phycobilins, to the apoproteins. PBP lyases mediate this covalent attachment of phycobilin chromophores to apo-PBPs and also ensure the correct binding of the chromophore with regard to the specific attachment site and stereospecificity. The S-type lyase is distantly related to CpcT and similarly adopts a beta-barrel structure with a modified lipocalin fold. Many members of the CpcS/CpcU family ligate phycocyanobilin (PCB) to a specific cysteine residue in the beta-subunits of phycocyanin (CpcB) or phycoerythrocyanin (PecB) and to a related cysteine residue in the alpha and beta subunits of allophycocyanin (AP); they are typically given the designation of ""CpcS"" or ""CpcU"". Other members which attach phycoerythrobilin (PEB) to the beta-subunit of phycoerythrin (PE) are given the designation ""CpeS"" or ""CpeU"". In Guillardia theta, a Cryptophyte, which has adopted phycoerythrobilin (PEB) biosynthesis from cyanobacteria, phycobiliprotein lyase has been shown to provide structural requirements for the transfer of this chromophore to the specific cysteine residue of the apophycobiliprotein." 166 matched cddid_all.tbl CDD cd16340 cd16340 319978 CpcS_T S- and T-type phycobiliprotein (PBP) lyases. This family contains the S- and T-type phycobiliprotein (PBP) lyases. PBP lyases are employed by cyanobacteria, red algae, cryptophytes and glaucophytes for light-harvesting. Pigmentation of light-harvesting phycobiliproteins of cyanobacteria and cryptophytes requires covalent attachment of open-chain tetrapyrrole chromophores, the phycobilins, to the apoproteins. PBP lyases mediate this covalent attachment of phycobilin chromophores to apo-PBPs. These lyases are distinguishable in the clades of E/F-, S/U-, and T-type lyases; T-type lyases (which include CpcT) are distantly related to S-type lyases (which include CpcS and CpcU). S- and T-type PBP lyases differ in mechanistic details; the conformation and protonation state in which the chromophore is presented account for their differences in stereochemistry of the chromophore selectivity as well as corresponding binding sites. On the other hand, both lyases carry out the main functions of assisting site selectivity in the apo-PBP, protecting the chromophore and ensuring the regio- and stereoselectivity of the addition. The S- and T-type PBP lyases adopt a beta-barrel structure with a modified lipocalin fold. 166 matched cddid_all.tbl CDD cd16341 cd16341 319975 FdhE formate dehydrogenase accessory protein FdhE and similar proteins. This family contains formate dehydrogenase accessory protein FdhE and FdhE-like protein, found largely in gamma- and some beta-Proteobacteria, where the fdhE genes are almost always genetically-linked to the structural genes for formate dehydrogenases. FdhE is required for the assembly of formate dehydrogenase although not present in the final complex. In E. coli, FdhE interacts with the catalytic subunits of the respiratory formate dehydrogenases. Purification of recombinant FdhE demonstrates the protein is an iron-binding rubredoxin that can adopt monomeric and homodimeric forms. E. coli FdhE interacts with the catalytic subunits, FdnG and FdoG, of the Tat- dependent respiratory formate dehydrogenases. Site-directed mutagenesis has shown that conserved cysteine motifs are essential for the physiological activity of the FdhE protein and are also involved in Fe(III) ligation. The iron likely is redox active, suggesting that the switch from aerobic to anaerobic conditions may be important in modulating FdhE function. Alternatively, FdhE may be involved in an electron transfer reaction, similar to other rubredoxins. 257 matched cddid_all.tbl CDD cd16342 cd16342 319974 FusC_FusB Fusidic acid resistance protein (FusC/FusB). The fusidic acid resistance protein FusC (FusB) mediates resistance to the antibiotic fusidic acid. Its C-terminal domain, which contains a zinc-binding site, interacts with EF-G with high affinity, promoting the dissociation of stalled ribosome#EF-G#GDP complexes that form in the presence of fusidic acid, thus allowing the ribosomes to resume translation. 204 matched cddid_all.tbl CDD cd16343 cd16343 319971 LMWPTP Low molecular weight protein tyrosine phosphatase. Low molecular weight protein tyrosine phosphatases (LMW-PTP) are a family of small soluble single-domain enzymes that are characterized by a highly conserved active site motif (V/I)CXGNXCRS and share no sequence similarity with other types of protein tyrosine phosphatases (PTPs). LMW-PTPs play important roles in many biological processes and are widely distributed in prokaryotes and eukaryotes. 147 matched cddid_all.tbl CDD cd16344 cd16344 319972 LMWPAP low molecular weight protein arginine phosphatase. Low molecular weight protein arginine phosphatases are part of the low molecular weight phosphatase (LMWP) family. They share a highly conserved active site motif (V/I)CXGNTCRS. It has been shown that the conserved threonine, which in many LMWPTPs is an isoleucine, confers specificity to phosphoarginine over phosphotyrosine. 142 matched cddid_all.tbl CDD cd16345 cd16345 319973 LMWP_ArsC Arsenate reductase of the LMWP family. Arsenate reductase plays an important role in the reduction of intracellular arsenate to arsenite, an important step in arsenic detoxification. The reduction involves three different thiolate nucleophiles. In arsenate reductases of the LMWP family, reduction can be coupled with thioredoxin (Trx)/thioredoxin reductase (TrxR) or glutathione (GSH)/glutaredoxin (Grx). 132 matched cddid_all.tbl CDD cd16347 cd16347 319957 VOC_like uncharacterized subfamily of the vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 221 matched cddid_all.tbl CDD cd16348 cd16348 319958 VOC_YdcJ_like uncharacterized metal-dependent enzyme similar to Shigella flexneri YdcJ. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 310 matched cddid_all.tbl CDD cd16349 cd16349 319959 VOC_like uncharacterized subfamily of the vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 301 matched cddid_all.tbl CDD cd16350 cd16350 319960 VOC_like uncharacterized subfamily of the vicinal oxygen chelate (VOC) family. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 254 matched cddid_all.tbl CDD cd16351 cd16351 319750 CheB_like methylesterase CheB domain family. This family contains the methylesterase CheB (EC 3.1.1.61; also known as CheB methylesterase, chemotaxis-specific methylesterase, methyl-accepting chemotaxis protein methyl-esterase, or protein methyl-esterase) domain, a phosphorylation-activated response regulator involved in reversible modification of bacterial chemotaxis receptors. Signaling output of the chemotaxis receptors is modulated by CheB and methyltransferase CheR by controlling the level of receptor methylation. CheB family members may also contain an N-terminal regulatory (REC) domain, which blocks the active site of the C-terminal domain until it is phosphorylated, or a CheR domain; typically cheB and cheR occur in the same operon. Reversible methylation of transmembrane chemoreceptors plays an important role in ligand-dependent signaling and cellular adaptation in bacterial chemotaxis. Phosphorylated CheB catalyzes deamidation of specific glutamine residues in the cytoplasmic region of the chemoreceptors and demethylation of specific methyl glutamate residues introduced into the chemoreceptors by CheR. 184 matched cddid_all.tbl CDD cd16352 cd16352 319352 CheD chemotaxis protein CheD stimulates methylation of methyl-accepting chemotaxis proteins. This family contains bacterial chemotaxis protein CheD that stimulates methylation of methyl-accepting chemotaxis proteins (MCPs). The CheD chemotaxis gene is not found in the Escherichia coli genome, but is present in many other organisms, including B. subtilis, where CheD appears to have two separate roles; it binds to chemoreceptors to activate them as part of the CheC/CheD/CheYp adaptation system, and it deamidates selected residues to activate chemoreceptors, enabling them to mediate amino acid chemotaxis. CheD has been shown to catalyze amide hydrolysis of specific glutaminyl side chains of the B. subtilis chemoreceptors McpA, McpB and McpC; deamination by CheD is required for the chemoreceptors to effectively transduce signals to the CheA kinase. CheD's ability to bind the receptors is controlled by CheC via a competitive binding mechanism; substituting Gln into the receptor motif of the signal-terminating phosphatase, CheC, turns the inhibitor into a receptor-modifying deamidase CheD substrate. Also, CheYp increases the affinity of CheD for CheC, controlling CheD binding to the receptors through its interactions with CheC. Thus, high levels of CheYp means CheC is a better binding target for CheD than the receptors, resulting in decreased CheA activity. The CheD structure reveals a distant homology with a class of bacterial toxins represented by the cytotoxic necrotizing factor 1 (CNF1) as well as a class of proteins of unknown function represented by B. subtilis YfiH. An invariant Cys-His pair forming a catalytic dyad is observed, and is required by the toxins for deamidation activity. 146 matched cddid_all.tbl CDD cd16353 cd16353 381732 CheC_CheX_FliY CheC/CheX/FliY (CXY) family phosphatases. The CXY family includes CheY-P-hydrolyzing proteins that function in bacterial chemotaxis, which involves cellular processes that control the movement of organisms toward favorable environments via rotating flagella, which in turn determines the sense of rotation by the intracellular response regulator CheY. When phosphorylated, CheY-P interacts directly with the flagellar motor, and this signal is terminated by the CXY family of phosphatases (Escherichia coli uses CheZ). CheC acts as a weak CheY-P phosphatase but increases activity in the presence of CheD. Bacillus subtilis has only CheC and FliY while many systems also have CheX. CheC and CheX appear to be primarily involved in restoring normal CheY-P levels, whereas FliY seems to act on CheY-P constitutively. Unlike CheC and CheX, FliY is localized in the flagellar switch complex, which also contains the stator-coupling protein FliG and the target of CheY-P, FliM. CheC, CheX, and FliY phosphatases share a consensus sequence ([DS]xxxExxNx(22)P) with four conserved residues thought to form the phosphatase active site. CheC class I and FliY each have two active sites, while CheC class II and III, and CheX have only one. This family also includes FliM, a component of the flagellar switch complex and a target of CheY, which lacks the phosphatase active site consensus sequence, and is not a CheY phosphatase. 162 matched cddid_all.tbl CDD cd16354 cd16354 319961 BAT Bleomycin N-Acetyltransferase and similar proteins. BlmB, encodes a bleomycin N-acetyltransferase, designated BAT, which inactivates Bm using acetyl-coenzyme A (AcCoA). BAT forms a dimer structure via interaction of its C-terminal domains in the monomers. The N-terminal domain of BAT has a tunnel with two entrances: a wide entrance that accommodates the metal-binding domain of Bm and a narrow entrance that accommodates acetyl-CoA (AcCoA). A groove formed on the dimer interface of two BAT C-terminal domains forms the DNA-binding domain of Bm. In a ternary complex of BAT, BmA(2), and CoA, a thiol group of CoA is positioned near the primary amine of Bm at the midpoint of the tunnel and ensures efficient transfer of an acetyl group from AcCoA to the primary amine of Bm. BAT belongs to vicinal oxygen chelate (VOC) superfamily that is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including thiocoraline, bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 114 matched cddid_all.tbl CDD cd16355 cd16355 319962 VOC_like uncharacterized subfamily of vicinal oxygen chelate (VOC) superfamily. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 121 matched cddid_all.tbl CDD cd16356 cd16356 319963 PsjN_like Burkholderia Phytofirmans glyoxalase/bleomycin resistance protein/dioxygenase family enzyme and similar proteins. Burkholderia Phytofirmans glyoxalase/bleomycin resistance protein/dioxygenase family enzyme and similar proteins. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 119 matched cddid_all.tbl CDD cd16357 cd16357 319964 GLOD4_C C-terminal domain of human glyoxalase domain-containing protein 4 and similar proteins. Uncharacterized subfamily of the vicinal oxygen chelate (VOC) superfamily contains human glyoxalase domain-containing protein 4 and similar proteins. VOC is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 114 matched cddid_all.tbl CDD cd16358 cd16358 319965 GlxI_Ni Glyoxalase I that uses Ni(++) as cofactor. This family includes Escherichia coil and other prokaryotic glyoxalase I that uses nickel as cofactor. Glyoxalase I (also known as lactoylglutathione lyase; EC 4.4.1.5) is part of the glyoxalase system, a two-step system for detoxifying methylglyoxal, a side product of glycolysis. This system is responsible for the conversion of reactive, acyclic alpha-oxoaldehydes into the corresponding alpha-hydroxyacids and involves 2 enzymes, glyoxalase I and II. Glyoxalase I catalyses an intramolecular redox reaction of the hemithioacetal (formed from methylglyoxal and glutathione) to form the thioester, S-D-lactoylglutathione. This reaction involves the transfer of two hydrogen atoms from C1 to C2 of the methylglyoxal, and proceeds via an ene-diol intermediate. Glyoxalase I has a requirement for bound metal ions for catalysis. Eukaryotic glyoxalase I prefers the divalent cation zinc as cofactor, whereas Escherichia coil and other prokaryotic glyoxalase I uses nickel. However, eukaryotic Trypanosomatid parasites also use nickel as a cofactor, which could possibly be explained by acquiring their GLOI gene by horizontal gene transfer. Human glyoxalase I is a two-domain enzyme and it has the structure of a domain-swapped dimer with two active sites located at the dimer interface. In yeast, in various plants, insects and Plasmodia, glyoxalase I is four-domain, possibly the result of a further gene duplication and an additional gene fusing event. 122 matched cddid_all.tbl CDD cd16359 cd16359 319966 VOC_BsCatE_like_C C-terminal of Bacillus subtilis CatE like protein, a vicinal oxygen chelate subfamily. Uncharacterized subfamily of vicinal oxygen chelate (VOC) superfamily contains Bacillus subtilis CatE and similar proteins. CatE is proposed to function as Catechol-2,3-dioxygenase. VOC is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 110 matched cddid_all.tbl CDD cd16360 cd16360 319967 ED_TypeI_classII_N N-terminal domain of type I, class II extradiol dioxygenases. This family contains the N-terminal non-catalytic domain of type I, class II extradiol dioxygenases. Dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. Two major groups of dioxygenases have been identified according to the cleavage site; extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon, whereas intradiol enzymes cleave the aromatic ring between two hydroxyl groups. Extradiol dioxygenases are classified into type I and type II enzymes. Type I extradiol dioxygenases include class I and class II enzymes. These two classes of enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. The extradiol dioxygenases represented in this family are type I, class II enzymes, and are composed of the N- and C-terminal domains of similar structure fold, resulting from an ancient gene duplication. The active site is located in a funnel-shaped space of the C-terminal domain. A catalytically essential metal, Fe(II) or Mn(II), presents in all the enzymes in this family. 111 matched cddid_all.tbl CDD cd16361 cd16361 319968 VOC_ShValD_like vicinal oxygen chelate (VOC) family protein similar to Streptomyces hygroscopicus ValD protein. This subfamily of vicinal oxygen chelate (VOC) family protein includes Streptomyces hygroscopicus ValD protein and similar proteins. ValD protein functions in validamycin biosynthetic pathway. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. 150 matched cddid_all.tbl CDD cd16362 cd16362 319969 TflA Toxoflavin Lyase. Toxoflavin lyase (TflA) is metalloenzyme degrading toxoflavin at the presence of oxygen, Mn(II), and dithiothreitol. TflA is structurally homologous to proteins of the vicinal oxygen chelate superfamily. The structure of TflA contains fold that displays a rare rearrangement of the structural modules indicative of domain permutation. Moreover, unlike the 2-His-1-carboxylate facial triad commonly utilized by vicinal oxygen chelate dioxygenases and other dioxygen-activating non-heme Fe(II) enzymes, the metal center in TflA consists of a 1-His-2-carboxylate facial triad. Toxoflavin is an azapteridine that is toxic to various plants, fungi, animals, and bacteria. 110 matched cddid_all.tbl CDD cd16363 cd16363 319897 Col_Im_like inhibitory immunity (Im) protein of colicin (Col) deoxyribonuclease (DNase) and pyocins. This family contains inhibitory immunity (Im) proteins that bind to colicin endonucleases (DNases) or pyocins with very high affinity and specificity; this is critical for the neutralization of endogenous DNase catalytic activity and for protection against exogenous DNase bacteriocins. The DNase colicin family (ColE2, ColE7, ColE8 and ColE9) in E. coli, and pyocin family (S1, S2, S3 and AP41) in P. aeruginosa, are potent bacteriocins where the immunity proteins (Ims) protect the colicin/pyocin producing (i.e. colicinogenic) bacteria by binding and inactivating colicin nucleases. The binding affinities between cognate and non-cognate nucleases by Im proteins can vary up to 10 orders of magnitude. 81 matched cddid_all.tbl CDD cd16364 cd16364 409301 T3SC_I-like "class I type III secretion system (T3SS) chaperones and similar proteins. This family contains class I type III secretion system (T3SS) chaperones mainly found in Gram-negative bacteria such as Pseudomonas, Yersinia, Salmonella, Escherichia and Erwinia, among others. A wide variety of these bacterial pathogens and symbionts require a T3SS to inject eukaryotic host cells with effector proteins important for suppressing host defenses and establishing infection. Many of these effector proteins interact with specific type III secretion chaperones prior to secretion. These T3SS chaperones have been classified as class I type III secretion chaperones (T3SC), which are small structurally conserved dimers that interact specifically with T3SS effector proteins. Class I T3SC consists of two subclasses: IA and IB. Class IA T3SC binds a single effector, whereas class IB T3SC binds to several effectors. Class IA and Class IB T3SCs typically exhibit little sequence similarities, but share a common overall heart-shaped structure fold (alpha-beta-beta-beta-alpha-beta-beta-alpha) and features, such as a small size, an acidic pI and an amphipathic C-terminal alpha-helix. Chaperone protein CesT serves a chaperone function for the enteropathogenic Escherichia coli (EPEC) translocated intimin receptor (Tir) protein, which confers upon EPEC the ability to alter host cell morphology following intimate bacterial attachment. In Pseudomonas aeruginosa, chaperone ExsC binds small secreted protein ExsE as well as the non-secreted anti-activator protein ExsD; it relieves repression of the transcriptional activator ExsA (which activates expression of T3SS genes) by ExsD. P. aeruginosa SpcU binds the cytotoxin ExoU, which is a broad-specificity phospholipase A2 (PLA2) and lysophospholipase, and maintains the N-terminus of ExoU in an unfolded state which is required for secretion. Salmonella enterica chaperone SicP forms a complex with effector protein SptP at an early stage of its secretion process in order to avoid premature degradation, while chaperone SigE binds to effector SigD, which, upon translocation into the host cell, preferentially dephosphorylates specific inositol phospholipids that are thought to be crucial for subsequent activation of the host cell Ser-Thr kinase Akt. This family also includes Yersinia chaperone/escortee pairs SycE/YopE, SycH/YopH, SycT/YopT and SycN+YscB/YopN, all of which bind to specific Yersinia outer proteins (Yops). Also included are several DspF and related sequences from several plant pathogenic bacteria. The ""disease-specific"" (dsp) region next to the hrp gene cluster of Erwinia amylovora is required for pathogenicity but not for elicitation of the hypersensitive reaction. In addition, a group of proteins including Escherichia coli YbjN, Erwinia amylovora AmyR, and their homologs, are included in this family. They share a class I T3SC-like fold with T3SS chaperone proteins but appear to function independently of the T3SS." 117 matched cddid_all.tbl CDD cd16365 cd16365 319887 NarH_like beta FeS subunits DMSOR NarH-like family. This subfamily contains beta FeS subunits of several DMSO reductase superfamily, including nitrate reductase A, ethylbenzene dehydrogenase and selenate reductase. DMSO Reductase (DMSOR) family members have a large, periplasmic molybdenum-containing alpha subunit as well as a small beta FeS subunit, and may also have a small gamma subunit. . The beta subunits of DMSOR contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system. Nitrate reductase A contains three subunits (the catalytic subunit NarG, the catalytic subunit NarH with four [Fe-S] clusters, and integral membrane subunit NarI) and often forms a respiratory chain with the formate dehydrogenase via the lipid soluble quinol pool. Ethylbenzene dehydrogenase oxidizes the hydrocarbon ethylbenzene to (S)-1-phenylethanol. Selenate reductase catalyzes reduction of selenate to selenite in bacterial species that can obtain energy by respiring anaerobically with selenate as the terminal electron acceptor. 201 matched cddid_all.tbl CDD cd16366 cd16366 319888 FDH_beta_like beta FeS subunits of formate dehydrogenase N (FDH-N) and similar proteins. This family contains beta FeS subunits of several dehydrogenases in the DMSO reductase superfamily, including formate dehydrogenase N (FDH-N), tungsten-containing formate dehydrogenase (W-FDH) and other similar proteins. FDH-N is a major component of nitrate respiration of Escherichia coli; it catalyzes the oxidation of formate to carbon dioxide, donating the electrons to a second substrate to a cytochrome. W-FDH contains a tungsten instead of molybdenum at the catalytic center and seems to be exclusively found in organisms such as hyperthermophilic archaea that live in extreme environments. It catalyzes the oxidation of formate to carbon dioxide, donating the electrons to a second substrate. 156 matched cddid_all.tbl CDD cd16367 cd16367 319889 DMSOR_beta_like uncharacterized subfamily of DMSO Reductase beta subunit family. This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system. 138 matched cddid_all.tbl CDD cd16368 cd16368 319890 DMSOR_beta_like uncharacterized subfamily of DMSO Reductase beta subunit family. This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system. 200 matched cddid_all.tbl CDD cd16369 cd16369 319891 DMSOR_beta_like uncharacterized subfamily of DMSO Reductase beta subunit family. This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system. 172 matched cddid_all.tbl CDD cd16370 cd16370 319892 DMSOR_beta_like uncharacterized subfamily of DMSO Reductase beta subunit family. This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system. 131 matched cddid_all.tbl CDD cd16371 cd16371 319893 DMSOR_beta_like uncharacterized subfamily of DMSO Reductase beta subunit family. This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system. 140 matched cddid_all.tbl CDD cd16372 cd16372 319894 DMSOR_beta_like uncharacterized subfamily of DMSO Reductase beta subunit family. This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system. 125 matched cddid_all.tbl CDD cd16373 cd16373 319895 DMSOR_beta_like uncharacterized subfamily of DMSO Reductase beta subunit family. This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system. 154 matched cddid_all.tbl CDD cd16374 cd16374 319896 DMSOR_beta_like uncharacterized subfamily of DMSO Reductase beta subunit family. This family consists of the small beta iron-sulfur (FeS) subunit of the DMSO Reductase (DMSOR) family. Members of this family also contain a large, periplasmic molybdenum-containing alpha subunit and may have a small gamma subunit as well. Examples of heterodimeric members with alpha and beta subunits include arsenite oxidase, and tungsten-containing formate dehydrogenase (FDH-T) while heterotrimeric members containing alpha, beta, and gamma subunits include formate dehydrogenase-N (FDH-N), and nitrate reductase (NarGHI). The beta subunit contains four Fe4/S4 and/or Fe3/S4 clusters which transfer the electrons from the alpha subunit to a hydrophobic integral membrane protein, presumably a cytochrome containing two b-type heme groups. The reducing equivalents are then transferred to menaquinone, which finally reduces the electron-accepting enzyme system. 139 matched cddid_all.tbl CDD cd16375 cd16375 319867 Avd_IVP_like proteins similar to the diversity-generating retroelement protein bAvd. A superfamily of four-helix bundles that form homopentamers, including the bacterial accessory variability determinant (bAvd) protein and a family of functionally uncharacterized bacterial proteins, some of which are encoded by an atypically large intervening sequence present within some 23S rRNA genes. 103 matched cddid_all.tbl CDD cd16376 cd16376 319868 Avd_like diversity-generating retroelement protein bAvd and similar proteins. The bacterial accessory variability determinant (bAvd) protein, together with a reverse transcriptase, is involved in retrohoming processes as part of a diversity-generating retroelement (DGR), a type of system that is involved in generating sequence variation in bacterial proteins by inserting coding information from a template region into a variable region of a protein coding gene. bAvd forms homopentamers and interacts with the reverse transcriptase as well as with DNA and/or RNA. 106 matched cddid_all.tbl CDD cd16377 cd16377 319869 23S_rRNA_IVP_like 23S rRNA-intervening sequence protein and similar proteins. A family of functionally uncharacterized bacterial proteins, some of which are encoded by an atypically large intervening sequence present within some 23S rRNA genes. The distantly related bAvd protein, which also forms a homopentamer of four-helix bundles, has been suggested to interact with nucleic acids and a reverse transcriptase. 108 matched cddid_all.tbl CDD cd16378 cd16378 319866 CcmH_N N-terminal domain of cytochrome c-type biogenesis protein CcmH and related proteins. Cytochrome c-type biogenesis protein CcmH is a membrane-anchored thiol-oxidoreductase that is essential in the maturation of c-type cytochromes. CcmH consists of an N-terminal catalytic domain with the active site CXXC motif and a C-terminal domain of unknown function which is predicted to contain TPR-like repeats. Other members of this family include NrfF, CycL, and Ccl2. 67 matched cddid_all.tbl CDD cd16379 cd16379 319863 YitT_C_like C-terminal domain of Bacillus subtilis YitT and similar protein domains. This domain, found in various bacterial proteins, has no known function. It has been given the designation DUF2179 and occurs at the C-terminus of the Bacillus subtilis membrane protein YitT as well as in single-domain proteins. 80 matched cddid_all.tbl CDD cd16380 cd16380 319864 YitT_C C-terminal domain of Bacillus subtilis YitT and similar protein domains. This domain, found in various bacterial proteins, has no known function. It has been given the designation DUF2179 and occurs at the C-terminus of the Bacillus subtilis membrane protein YitT. 85 matched cddid_all.tbl CDD cd16381 cd16381 319865 YitT_C_like_1 Proteins similar to the C-terminal domain of Bacillus subtilis YitT. This domain, characteristic of various bacterial proteins, has no known function. It has been given the designation DUF2179 and is similar to the C-terminus of the Bacillus subtilis membrane protein. 80 matched cddid_all.tbl CDD cd16382 cd16382 341357 XisI-like XisI is FdxN element excision controlling factor protein. This family contains XisI proteins, also known as FdxN element excision controlling factors, and similar proteins. FdxN element is excised from the chromosome during heterocyst differentiation in cyanobacteria. This is accomplished by the large serine recombinase XisF (fdxN element site-specific recombinase). The xisH as well as the xisF and xisI genes are required. XisI may function as recombination directionality factor (RDF), and needs XisH which may function as an endonuclease. 107 matched cddid_all.tbl CDD cd16383 cd16383 319862 GUN4 porphyrin-binding protein domain GUN4. GUN4 is a porphyrin-binding protein involved in chlorophyll biosynthesis regulation and intracellular signaling, found in aerobic photosynthetic organisms. It has been implicated in retrograde signalling between the chloroplast and nucleus. GUN4 can bind protoporphyrin IX (PIX) and magnesium protoporphyrin IX (MgPIX), substrate and product of the Mg-chelatase, as well as heme and cobalt protoporphyrin IX (CoPIX). It may play a role in protecting plants from reactive oxygen species (ROS)-mediated damage. 142 matched cddid_all.tbl CDD cd16384 cd16384 319760 VirB8_like virulence protein VirB8. This family contains bacterial virulence protein VirB8 and similar proteins which consist of cytoplasmic, transmembrane, and periplasmic regions. VirB8 is an essential assembly factor of type IV secretion system (T4SS) channel proteins that are highly diverse in function relative to other bacterial secretion systems. T4SS proteins are important virulence factors for many Gram-negative pathogens, such as Agrobacterium, Brucella, Legionella, and Helicobacter. This family also includes the conjugal transfer protein family TrbF, a family of proteins known to be involved in conjugal transfer. The TrbF protein is thought to compose part of the pilus required for transfer. This domain has a similar fold to the nuclear transport factor-2 (NTF2) protein. 133 matched cddid_all.tbl CDD cd16385 cd16385 319861 IcmL inner membrane protein IcmL/DotI. This family contains the periplasmic domain of the inner membrane protein DotI of the Dot/Icm (defect in organelle trafficking/intracellular multiplication) type IVB secretion system, including its ortholog in the conjugation system of plasmid R64, TraM, and similar proteins. These domains share striking structural similarity to the type IV secretion system (T4ASS) component VirB8 suggesting DotI/TraM to be its functional counterpart. DotI is essential for intracellular growth of Legionella pneumophila (causing agent of Legionnaires' disease) within mammalian and protozoan cells; it translocates numerous effector proteins into its eukaryotic host. 132 matched cddid_all.tbl CDD cd16386 cd16386 319860 TcpC_N N-terminal domain of conjugative transposon protein TcpC. This family contains the N-terminal domain of conjugation protein TcpC and similar proteins. TcpC is required for efficient conjugative transfer, localizing to the cell membrane independently of other conjugation proteins, where membrane localization is important for its function, oligomerization and interaction with the conjugation proteins TcpA, TcpH, and TcpG. N-terminal region (sometimes referred to as central domain) of TcpC is required for efficient conjugation, oligomerization and protein-protein interactions. TcpC has low level sequence identity to proteins encoded by the conjugative transposon Tn916, which is responsible for a large proportion of the tetracycline resistance in different pathogens. 123 matched cddid_all.tbl CDD cd16387 cd16387 319246 ParB_N_Srx ParB N-terminal domain and sulfiredoxin protein-related families. The ParB N-terminal domain/Sulfiredoxin (Srx) superfamily contains proteins with diverse activities. Many of the families are involved in segregation and competition between plasmids and chromosomes. Several families share similar activities with the N-terminal domain of ParB (Spo0J in Bacillus subtilis), a DNA-binding component of the prokaryotic parABS partitioning system. Also within this superfamily is sulfiredoxin (Srx; reactivator of oxidatively inactivated 2-cys peroxiredoxins), RepB N-terminal domain (plasmid segregation replication protein B like protein), nucleoid occlusion protein, KorB N-terminal domain partition protein of low copy number plasmid RK2, irbB (immunoglobulin-binding regulator that activates eib genes), N-terminal domain of sopB protein (promotes proper partitioning of F1 plasmid), fertility inhibition factors OSA and FiwA,DNA sulfur modification protein DndB, and a ParB-like toxin domain. Other activities includes a StrR (regulator in the streptomycin biosynthetic gene cluster), and a family containing a Pyrococcus furiosus nuclease and putative transcriptional regulators sbnI (Staphylococcus aureus siderophore biosynthetic gene cluster ). Nuclease activity has also been reported in Arabidopsis Srx. 54 matched cddid_all.tbl CDD cd16388 cd16388 319247 SbnI_like_N N-terminal domain of transcriptional regulators similar to SbnI. Siderophore staphylobactin biosynthesis protein SbnI of Staphylococcus aureus is a ParB/Spo0J like protein required for the expression of genes in the sbn operon, which is responsible for staphyloferrin B (SB) biosynthesis. SnbI forms dimers and binds DNA upstream of sdnD. SbnI binds heme, which inhibits DNA binding of SbnI, leading to a suppression of sbn operon expression. 77 matched cddid_all.tbl CDD cd16389 cd16389 319248 FIN fertility inhibition factors, including OSA and FiwA, related to the ParB/Srx superfamily. Osa and FiwA are fertility inhibition factors (FIN), which are employed by plasmids to block import of rival plasmids. Osa (oncogenic suppressive activity) of IncW group plasmid pSa gene inhibits the oncogenic properties of Agrobacterium tumefaciens. Osa is structurally similar to the ParB N-terminal domain/Srx superfamily of proteins: ParB acts in the bacterial and plasmid parABS partitioning systems. Osa has been shown to have ATPase and DNAse activities, an can block T-DNA transfer into plants. FiwA is encoded by plasmid RP1 and blocks the transfer of plasmid R388. The gene product of Haemophilus influenzae p1056.10c also blocks T-DNA transfer. 124 matched cddid_all.tbl CDD cd16390 cd16390 319249 ParB_N_Srx_like uncharacterized family distantly related to the N-terminal domain of the ParB/Srx superfamily. Uncharacterized proteins distantly related to the N-terminal domain of the ParB superfamily, primarily involved in bacterial and plasmid parABS-related partitioning systems. A small minority of proteins in this family include a C-terminal inorganic pyrophosphatase domain. Also within the ParB superfamily is sulfiredoxin (Srx), which is a reactivator of oxidatively inactivated 2-cys peroxiredoxins. Other families includes a putative regulator in the biosynthetic gene cluster and a family containing a Pyrococcus furiosus nuclease and putative transcriptional regulators SbnI (Staphylococcus aureus siderophore biosynthetic gene cluster ) and EdeB (Brevibacillus brevis antimicrobial peptide edeine biosynthetic cluster). Nuclease activity has also been reported in Arabidopsis Srx. 162 matched cddid_all.tbl CDD cd16392 cd16392 319250 toxin-ParB toxin domain of the ParB/Srx superfamily. toxin domain with similarity to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system and related proteins. Toxin found, for example, at the C-terminus of polymorphic toxin system members. 72 matched cddid_all.tbl CDD cd16393 cd16393 319251 SPO0J_N "Thermus thermophilus stage 0 sporulation protein J-like N-terminal domain, ParB family member. Spo0J (stage 0 sporulation protein J) is a ParB family member, a critical component of the ParABS-type bacterial chromosome segregation system. The Spo0J N-terminal region acts in protein-protein interaction and is adjacent to the DNA-binding domain that binds to parS sites. Two Spo0J bind per parS site, and Spo0J interacts with neighbors via the N-terminal domain to form oligomers via an Arginine-rich patch (RRXR). This superfamily represents the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA (""spreading"", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci." 97 matched cddid_all.tbl CDD cd16394 cd16394 319252 sopB_N N-terminal domain of sopB protein, which promotes proper partitioning of F1 plasmid. Escherichia coli SopB acts in the equitable partitioning of the F plasmid in the SopABC system. SopA binds to the sopAB promoter, while SopB binds SopC and helps stimulate polymerization of SopA in the presence of ATP and Mg(II). Mutation of SopA inhibits proper plasmid segregation. This N-terminal domain is related to the ParB N-terminal domain of bacterial and plasmid parABS partitioning systems, which binds parA. 67 matched cddid_all.tbl CDD cd16395 cd16395 319253 Srx Sulfiredoxin reactivates peroxiredoxins after oxidative inactivation. Sulfiredoxin reduces and thereby re-activates 2-cys peroxiredoxins. Peroxiredoxins act as molecular switches, inactivating in response to hyperoxidation from hydrogen peroxide and other free radicals. Sulfiredoxin reactivates Prx-SO(2)(-) via ATP-Mg(2+)-dependent reduction. Arabidopsis sulfiredoxin has been described as a dual function enzyme, having nuclease activity in addition to the sulfiredoxin activity. This protein is similar to ParB N-terminal-like domain of bacterial and plasmid parABS partitioning systems. 90 matched cddid_all.tbl CDD cd16396 cd16396 319254 Noc_N nucleoid occlusion protein, N-terminal domain, and related domains of the ParB partitioning protein family. Nucleoid occlusion protein has been shown in Bacillus subtilis to bind to specific DNA sequences on the chromosome (Noc-binding DNA sequences, NBS), inhibiting cell division near the nucleoid and thereby protecting the chromosome. This N-terminal domain is related to the N-terminal domain of ParB/repB partitioning system proteins. 95 matched cddid_all.tbl CDD cd16397 cd16397 319255 IbrB_like immunoglobulin-binding regulator IbrB activates eib genes. IbrB (along with IbrA) activates immunoglobulin-binding eib genes in Escherichia coli. IbrB is related to the ParB N-terminal domain family, which includes DNA-binding proteins involved in chromosomal/plasmid segregation and transcriptional regulation, consistent with a possible mechanism for IbrB in DNA binding-related regulation of eib expression. The ParB like family is a diverse domain superfamily with structural and sequence similarity to ParB of bacterial chromosomes/plasmid parABS partitioning system and Sulfiredoxin (Srx), which is a reactivator of oxidatively inactivated 2-cys peroxiredoxins. Other families includes proteins related to StrR, a putative regulator in the biosynthetic gene cluster and a family containing a Pyrococcus furiosus nuclease and putative transcriptional regulators SbnI (Staphylococcus aureus siderophore biosynthetic gene cluster ) and EdeB (Brevibacillus brevis antimicrobial peptide edeine biosynthetic cluster). Nuclease activity has also been reported in arabidopsis Srx. 100 matched cddid_all.tbl CDD cd16398 cd16398 319256 KorB_N_like "ParB-like partition protein of low copy number plasmid RK2, N-terminal domain and related domains. KorB, a member of the ParB like family, is present on the low copy number, broad host range plasmid RK2. KorB encodes a gene product involved in segregation of RK2 and acts as a transcriptional regulator, down-regulating at least 6 RK2 operons. KorB binds RNA polymerase and acts cooperatively with several co-repressors in modulating transcription. KorB is comprised of 3 domains, including a beta-strand C-terminal domain similar to SH3 domains and an alpha helical central domain that interacts with operator DNA. In ParB of P1 and SopB of F, the N-terminal region is responsible for interaction with the parA component. However, korB interaction with the RK2 parA-equivalent IncC has been mapped to the central HTH motif. This family is related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA (""spreading"", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci." 91 matched cddid_all.tbl CDD cd16400 cd16400 319257 ParB_Srx_like_nuclease ParB/Srx_like nuclease and putative transcriptional regulators related to SbnI. This family contains a Pyrococcus Furiosus enzyme reported to have DNA nuclease activity and resembles the N-terminal domain of ParB proteins of the parABS bacterial chromosome partitioning system. This sub-family also includes siderophore staphylobactin biosynthesis protein SbnI. 60% of the P. furiosus nuclease activity was retained at 90 degree C, suggesting a physiological role in the organism, which can grow in temperatures as high as 100 degrees Celsius. The protein has endo- and exo-nuclease activity vs. single- and double-stranded DNA, and nuclease activity was lost in methylated proteins prepared for structure solution. This family has a fairly well-conserved DGHHR motif that corresponds to the same structural position as the phosphorylation site (a portion of the ATP-Mg-binding site) of sulfiredoxin and the arginine-rich ParB BoxII of ParB. 72 matched cddid_all.tbl CDD cd16401 cd16401 319258 ParB_N_like_MT "ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase domain. This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA (""spreading"", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci." 85 matched cddid_all.tbl CDD cd16402 cd16402 319259 ParB_N_like_MT "ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase domain. This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains and DUF4417. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA (""spreading"", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci." 87 matched cddid_all.tbl CDD cd16403 cd16403 319260 ParB_N_like_MT "ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase. This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA (""spreading"", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci." 88 matched cddid_all.tbl CDD cd16404 cd16404 319261 pNOB8_ParB_N_like pNOB8 ParB-like N-terminal domain, plasmid partitioning system protein domain. archaeal pNOB8 ParB acts in a plasmid partitioning system made up of 3 parts: AspA, ParA motor protein, and ParB, which links ParA to the protein-DNA superhelix. As demonstrated in Sulfolobus, AspA spreads along DNA, which allows ParB binding, and links to the Walker-motif containing ParA motor protein. The Sulfolobus ParB C-terminal domain resembles eukaryotic segregation protein CenpA, and other histones. This family is related to the N-terminal domain of ParB (Spo0J in Bacillus subtilis), a DNA-binding component of the prokaryotic parABS partitioning system and related proteins. 69 matched cddid_all.tbl CDD cd16405 cd16405 319262 RepB_like_N plasmid segregation replication protein B like protein, N-terminal domain. RepB, found on plasmids and secondary chromosomes, works along with repA in directing plasmid segregation, and has been shown in Rhizobium etli to require the parS centromere-like sequence for full transcriptional repression of the repABC operon, inducing plasmid incompatibility. RepA is a Walker-type ATPase that complexes with RepB to form DNA-protein complexes in the presence of ATP/ADP. RepC is an initiator protein for the plasmid. repA and repB are homologous to the parA and ParB genes of the parABS partitioning system found on primary chromosomes. 91 matched cddid_all.tbl CDD cd16406 cd16406 319263 ParB_N_like "ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning systems. This family represents the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA (""spreading"", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci." 82 matched cddid_all.tbl CDD cd16407 cd16407 319264 ParB_N_like "ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning systems. This family represents the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA (""spreading"", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci." 86 matched cddid_all.tbl CDD cd16408 cd16408 319265 ParB_N_like "ParB N-terminal, parA -binding, -like domain of bacterial and plasmid parABS partitioning systems. This family represents the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA (""spreading"", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci." 84 matched cddid_all.tbl CDD cd16409 cd16409 319266 ParB_N_like "ParB N-terminal-like domain of bacterial and plasmid parABS partitioning systems. This family represents the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA (""spreading"", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci." 74 matched cddid_all.tbl CDD cd16410 cd16410 319267 ParB_N_like "ParB N-terminal, parA-binding, -like domain of bacterial and plasmid parABS partitioning systems. This family represents the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA (""spreading"", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci." 80 matched cddid_all.tbl CDD cd16411 cd16411 319268 ParB_N_like "ParB N-terminal, parA -binding, domain of bacterial and plasmid parABS partitioning systems. This family represents the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA (""spreading"", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci." 90 matched cddid_all.tbl CDD cd16412 cd16412 319269 dndB DNA sulfur modification protein DndB. dndB acts in the regulation of DNA modifications, including DNA phosphorothioation. DndB may act by binding near the phosphorothioate modification site and regulating access of the Dnd modification machinery to DNA. These proteins show similarity to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, and other members of the ParB/Srx superfamily. 333 matched cddid_all.tbl CDD cd16413 cd16413 319270 DGQHR_domain DGQHR motif containing domain. Uncharacterized diverse domain family with conserved DGQHR motif, in addition to QR and FXXXN motifs. Some proteins have been identified as parts of DNA phosphorothioation systems. Related to dndB, which acts in the regulation of DNA modifications, including DNA phosphorothioation. These proteins show similarity to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, and other members of the ParB/Srx superfamily. 229 matched cddid_all.tbl CDD cd16414 cd16414 319271 dndB_like DNA-sulfur modification-associated domain. Family of proteins related to dndB. dndB acts in the regulation of DNA modifications, including DNA phosphorothioation. Both have a conserved DGQHR sequence motif. These proteins show similarity to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, and other members of the ParB/Srx superfamily 238 matched cddid_all.tbl CDD cd16415 cd16415 319852 HAD_dREG-2_like uncharacterized family of the haloacid dehalogenase-like superfamily, similar to uncharacterized Drosophila melanogaster rhythmically expressed gene 2 protein and human haloacid dehalogenase-like hydrolase domain-containing protein 3. The haloacid dehalogenase-like (HAD) hydrolases are a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. Members are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 128 matched cddid_all.tbl CDD cd16416 cd16416 319853 HAD_BsYqeG-like Uncharacterized family of the the haloacid dehalogenase-like superfamily, similar to the uncharacterized protein Bacillus subtilis YqeG. The haloacid dehalogenase-like (HAD) hydrolases are a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. Members are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 108 matched cddid_all.tbl CDD cd16417 cd16417 319854 HAD_PGPase Escherichia coli Gph phosphoglycolate phosphatase and related proteins; belongs to the haloacid dehalogenase-like superfamily. Phosphoglycolate phosphatase (PGP; EC 3.1.3.18) catalyzes the conversion of 2-phosphoglycolate into glycolate and phosphate. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 212 matched cddid_all.tbl CDD cd16418 cd16418 319855 HAD_Pase phosphatases, similar to human PHOSPHO1 and PHOSPHO2 phosphatases; belongs to the haloacid dehalogenase-like superfamily. This family includes phosphatases with different substrate specificities. Human PHOSPHO1 is a phosphoethanolamine/phosphocholine phosphatase associated with high levels of expression at mineralizing regions of bone and cartilage and is thought to be involved in the generation of inorganic phosphate for bone mineralization. Human PHOSPHO2 is a putative phosphatase which shows high specific activity toward pyridoxal-5-phosphate; PHODPHO2 is not specific to bone but is expressed in a wide range of soft tissues. These belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 130 matched cddid_all.tbl CDD cd16419 cd16419 319856 HAD_SPS sucrose-phosphate synthase; belongs to the haloalcanoic acid dehalogenase (HAD) superfamily. Sucrose phosphate synthase (SPS; EC 2.4.1.14) also known as UDP-glucose-fructose-phosphate glucosyltransferase, catalyzes the transfer of a hexosyl group from UDP-glucose to D-fructose 6-phosphate to form UDP and D-sucrose-6-phosphate, this is the rate limiting step of sucrose synthesis. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 174 matched cddid_all.tbl CDD cd16421 cd16421 319857 HAD_PGPase Rhodobacter capsulatus Cbbz phosphoglycolate phosphatase and related proteins; ; belongs to the haloacid dehalogenase-like superfamily. Phosphoglycolate phosphatase (PGPase; EC 3.1.3.18) catalyzes the conversion of 2-phosphoglycolate into glycolate and phosphate. Members of this family belong to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase (C-Cl bond hydrolysis), azetidine hydrolase (C-N bond hydrolysis); phosphonoacetaldehyde hydrolase (C-P bond hydrolysis), phosphoserine phosphatase and phosphomannomutase (CO-P bond hydrolysis), P-type ATPases (PO-P bond hydrolysis) and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 105 matched cddid_all.tbl CDD cd16422 cd16422 319858 HAD_Pase_UmpH-like uncharacterized subfamily of the UmpH/NagD phosphatase family, belongs to the haloacid dehalogenase-like superfamily. This uncharacterized subfamily belongs to the UmpH/NagD phosphatase family and to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 247 matched cddid_all.tbl CDD cd16423 cd16423 319859 HAD_BPGM-like uncharacterized subfamily of beta-phosphoglucomutase-like family, similar to uncharacterized Bacillus subtilis YhcW. This subfamily includes the uncharacterized Bacillus subtilis YhcW. It belongs to the beta-phosphoglucomutase-like family whose other members include Lactococcus lactis beta-PGM, a mutase which catalyzes the interconversion of beta-D-glucose 1-phosphate (G1P) and D-glucose 6-phosphate (G6P), Saccharomyces cerevisiae phosphatases GPP1 and GPP2 that dephosphorylate DL-glycerol-3-phosphate and DOG1 and DOG2 that dephosphorylate 2-deoxyglucose-6-phosphate, and Escherichia coli 6-phosphogluconate phosphatase YieH. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases. 169 matched cddid_all.tbl CDD cd16424 cd16424 319761 VirB8 periplasmic domain of VirB8 protein. This family contains the periplasmic domain of VirB8 protein which is an essential assembly factor of type IV secretion system (T4SS) channel proteins that are highly diverse in function relative to other bacterial secretion systems. T4SS proteins are important virulence factors for many Gram-negative pathogens, such as Agrobacterium, Brucella, Legionella, and Helicobacter. VirB8 is a bacterial virulence protein with cytoplasmic, transmembrane, and periplasmic regions. It is thought that VirB8 is a primary constituent of a DNA transporter. It is a crucial structural and functional component of the T4SS, with interactions between VirB8 and many other T4SS proteins, including VirB10, VirB9, VirB1, VirB4, and VirB11, as well as with itself. 137 matched cddid_all.tbl CDD cd16425 cd16425 319762 TrbF conjugal transfer protein TrbF. This family includes the conjugal transfer protein family TrbF, a family of proteins known to be involved in conjugal transfer. The TrbF protein is thought to compose part of the pilus required for transfer. This domain is similar to the type IV secretion system (T4ASS) component VirB8 and possibly has a similar fold to the nuclear transport factor-2 (NTF-2)-like superfamily. 133 matched cddid_all.tbl CDD cd16426 cd16426 319754 VirB10_like VirB10 and similar proteins form part of core complex in Type IV secretion system (T4SS). This family contains VirB10, a component of the type IV secretion system (T4SS) and its homologs, including TraB, TraF, IcmE, and similar proteins. T4S system is employed by pathogenic bacteria to export virulence DNAs and/or proteins directly from the bacterial cytoplasm into the host cell. It forms a large multiprotein complex consisting of 12 proteins termed VirB1-11 and VirD4. VirB10 interacts with VirB7 and VirB9, forming the membrane-spanning 'core complex' (CC), around which all other components assemble. The CC is inserted in both the outer and inner membranes, playing a fundamental role as a scaffold for the rest of the T4SS components and actively participating in T4S substrate transfer through the bacterial envelope via conformational changes regulating channel opening and closing. In Gram-negative bacterial pathogen Helicobacter pylori, an important aetiological agent of gastroduodenal disease in humans, the comB3 gene encodes protein with best homologies to TraS/TraB from the Pseudomonas aeruginosa conjugative plasmid RP1 and TrbI of plasmid RP4 and VirB10 from the Ti plasmid of Agrobacterium tumefaciens, as well as DotG/IcmE of Legionella pneumophila. 151 matched cddid_all.tbl CDD cd16427 cd16427 319758 TraM-like C-terminal domain of transfer protein TraM. This family contains the C-terminal domain of transfer protein TraM of the G+ broad host range Enterococcus conjugative plasmid pIP501 and similar proteins. The protein localizes to the cell envelope and is part of the plasmid transfer system that is accessible from outside of the cell. TraM displays a fold similar to the type IV secretion system (T4SS) VirB8 proteins from A. tumefaciens and B. suis (G-) and to the transfer protein TcpC from C. perfringens plasmid pCW3 (G+), reinforcing the prediction that TraM performs a key role in the secretion process, which is underlined by its surface accessibility. It is also structurally related to members of the nuclear transport factor-2 (NTF-2)-like superfamily with a high similarity to the NTF-2 protein from Rattus norvegicus. TraM (categorized as T4SS VirB8-like class GAMMA) does not possess the binding pocket of classic VirB8 class ALPHA proteins, recognized by VirB8 interaction inhibitors. 108 matched cddid_all.tbl CDD cd16428 cd16428 319759 TcpC_C C-terminal domain of conjugative transposon protein TcpC. This family contains the C-terminal domain of conjugation protein TcpC and similar proteins. TcpC is required for efficient conjugative transfer, localizing to the cell membrane independently of other conjugation proteins, where membrane localization is important for its function, oligomerization and interaction with the conjugation proteins TcpA, TcpH, and TcpG. C-terminal domain is critical for interactions with these other conjugation proteins. TcpC has low level sequence identity to proteins encoded by the conjugative transposon Tn916, which is responsible for a large proportion of the tetracycline resistance in different pathogens. 97 matched cddid_all.tbl CDD cd16429 cd16429 319755 VirB10 VirB10 forms part of core complex in Type IV secretion system (T4SS). This family contains VirB10, a component of the type IV secretion system (T4SS), including homologs TrbI, TraF, TrwE and TraL. T4S system is employed by pathogenic bacteria to export virulence DNAs and/or proteins directly from the bacterial cytoplasm into the host cell. It forms a large multiprotein complex consisting of 12 proteins termed VirB1-11 and VirD4. VirB10, interacts with VirB7 and VirB9, forming the membrane-spanning 'core complex' (CC), around which all other components assemble. The CC is inserted in both, the outer and inner membranes, playing a fundamental role as a scaffold for the rest of the T4SS components and actively participating in T4S substrate transfer through the bacterial envelope via conformational changes regulating channel opening and closing. TrwE in R33 plasmid has been shown to be anchored to the inner membrane and its C-terminal is necessary for conjugation; the transmembrane domains of TrwB and TrwE are involved in TrwB-TrwE interactions. TraF protein of the RP4 plasmid is involved in circularization of pilin subunits of P-type pili. In gonococcal genetic island (GGI) of Neisseria gonorrhoeae, T4SS encodes TrbI and circularization occurs via a covalent intermediate between the C terminus of putative pilin protein TraA and TrbI. 180 matched cddid_all.tbl CDD cd16430 cd16430 319756 TraB TraB is a homolog of VirB10 which forms part of core complex in Type IV secretion system (T4SS). This family contains TraB (VirB10 homolog) and a component of the type IV secretion system (T4SS), and similar proteins. T4S system is employed by pathogenic bacteria to export virulence DNAs and/or proteins directly from the bacterial cytoplasm into the host cell. It forms a large multiprotein complex consisting of 12 proteins termed VirB1-11 and VirD4. VirB10, interacts with VirB7 and VirB9, forming the membrane-spanning 'core complex' (CC), around which all other components assemble. The CC is inserted in both the outer and inner membranes, playing a fundamental role as a scaffold for the rest of the T4SS components and actively participating in T4S substrate transfer through the bacterial envelope via conformational changes regulating channel opening and closing. TraB is localized similarly to related proteins in other systems, but unlike in other systems, Neisseria gonorrhoeae TraB does not require the presence of other T4SS components for proper localization. It has been shown to be expressed with TraK (VirB9 homolog) at low levels in wild-type cells, suggesting that gonococcal T4SS may be present in single copy per cell and the small amounts of these proteins are sufficient for DNA secretion. 203 matched cddid_all.tbl CDD cd16431 cd16431 319757 IcmE DotG/IcmE is a homolog of VirB10 which forms part of core complex in Type IV secretion system. This family contains DotG/IcmE (VirB10 homolog) and a component of the type IV secretion system (T4SS), and similar proteins. The Dot/Icm system is a T4SS found in the pathogens Legionella and Coxiella and the conjugative apparatus of IncI plasmids; T4SS is employed by pathogenic bacteria to export virulence DNAs and/or proteins directly from the bacterial cytoplasm into the host cell. Similar to T4SS VirB/D components, the Legionella Dot/Icm secretion apparatus contains a critical five-protein sub-assembly that forms the membrane-spanning 'core-complex' (CC), around which all other components assemble. This transmembrane connection is mediated by protein dimer pairs consisting of two inner membrane proteins, DotF and DotG, each independently associating with DotH/DotC/DotD in the outer membrane. 179 matched cddid_all.tbl CDD cd16432 cd16432 319751 CheB_Rec Chemotaxis response regulator protein-glutamate methylesterase, CheB, with N-terminal REC domain. This family contains the methylesterase CheB (EC 3.1.1.61; also known as CheB methylesterase, chemotaxis-specific methylesterase, methyl-accepting chemotaxis protein methyl-esterase, or protein methyl-esterase) domain with a REC domain at the N-terminus. CheB is a phosphorylation-activated response regulator involved in reversible modification of bacterial chemotaxis receptors. Signaling output of the chemotaxis receptors is modulated by CheB and methyltransferase CheR by controlling the level of receptor methylation. The N-terminal regulatory (REC) domain blocks the active site of the C-terminal domain until it is phosphorylated. Reversible methylation of transmembrane chemoreceptors plays an important role in ligand-dependent signaling and cellular adaptation in bacterial chemotaxis. Phosphorylated CheB catalyzes deamidation of specific glutamine residues in the cytoplasmic region of the chemoreceptors and demethylation of specific methyl glutamate residues introduced into the chemoreceptors by CheR. 184 matched cddid_all.tbl CDD cd16433 cd16433 319752 CheB Chemotaxis response regulator protein-glutamate methylesterase, CheB. This family contains the methylesterase CheB (EC 3.1.1.61; also known as CheB methylesterase, chemotaxis-specific methylesterase, methyl-accepting chemotaxis protein methyl-esterase, or protein methyl-esterase) domain, a phosphorylation-activated response regulator involved in reversible modification of bacterial chemotaxis receptors. Signaling output of the chemotaxis receptors is modulated by CheB and methyltransferase CheR by controlling the level of receptor methylation. cheR and cheB have a strong preference to occur in the same operon, and a subgroup contains multidomain proteins with CheB-CheR fusions. Reversible methylation of transmembrane chemoreceptors plays an important role in ligand-dependent signaling and cellular adaptation in bacterial chemotaxis. Phosphorylated CheB catalyzes deamidation of specific glutamine residues in the cytoplasmic region of the chemoreceptors and demethylation of specific methyl glutamate residues introduced into the chemoreceptors by CheR. 181 matched cddid_all.tbl CDD cd16434 cd16434 319753 CheB-CheR_fusion Chemotaxis response regulator protein-glutamate methylesterase, CheB, fused with CheR domain. This family contains the methylesterase CheB (EC 3.1.1.61; also known as CheB methylesterase, chemotaxis-specific methylesterase, methyl-accepting chemotaxis protein methyl-esterase, or protein methyl-esterase) domain, a phosphorylation-activated response regulator involved in reversible modification of bacterial chemotaxis receptors, fused with a CheR domain as well as other domains. Signaling output of the chemotaxis receptors is modulated by CheB and methyltransferase CheR by controlling the level of receptor methylation. cheB and cheR are typically found in the same operon. However, CheB and CheR are fused in multi-domain proteins in this subgroup. The CheR protein/domain includes an all-alpha N-terminal domain and an S-adenosylmethionine-dependent methyltransferase C-terminal domain. Reversible methylation of transmembrane chemoreceptors plays an important role in ligand-dependent signaling and cellular adaptation in bacterial chemotaxis. Phosphorylated CheB catalyzes deamidation of specific glutamine residues in the cytoplasmic region of the chemoreceptors and demethylation of specific methyl glutamate residues introduced into the chemoreceptors by CheR. 180 matched cddid_all.tbl CDD cd16435 cd16435 319740 BPL_LplA_LipB biotin-lipoate ligase family. This family includes biotin protein ligase (BPL), lipoate-protein ligase A (LplA) and octanoyl-[acyl carrier protein]-protein acyltransferase (LipB). Biotin is covalently attached at the active site of certain enzymes that transfer carbon dioxide from bicarbonate to organic acids to form cellular metabolites. Biotin protein ligase (BPL) is the enzyme responsible for attaching biotin to a specific lysine at the active site of biotin enzymes. Biotin attachment is a two step reaction that results in the formation of an amide linkage between the carboxyl group of biotin and the epsilon-amino group of the modified lysine. Lipoate-protein ligase A (LplA) catalyses the formation of an amide linkage between lipoic acid and a specific lysine residue in lipoate dependent enzymes. 198 matched cddid_all.tbl CDD cd16436 cd16436 319744 beta_Kdo_transferase beta-3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)-transferase. KpsC and KpsS are retaining beta-3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)-transferases. They are part of the ATP-binding cassette transporter dependent capsular polysaccharides (CPSs) synthesis pathway, one of two CPS synthesis pathways present in Escherichia coli. The poly-Kdo linker is thought to be the common feature of CPSs synthesized via this pathway. CPSs are high-molecular-mass cell-surface polysaccharides that are important virulence factors for many pathogenic bacteria. 222 matched cddid_all.tbl CDD cd16437 cd16437 319745 beta_Kdo_transferase_KpsC beta-3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)-transferase KpsC. KpsC is a beta-3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)-transferase. It is part of the ATP-binding cassette transporter dependent capsular polysaccharides (CPSs) synthesis pathway, one of two CPS synthesis pathways present in Escherichia coli. The poly-Kdo linker is thought to be the common feature of CPSs synthesized via this pathway. CPSs are high-molecular-mass cell-surface polysaccharides, that are important virulence factors for many pathogenic bacteria. KpsC contains a domain duplication. 256 matched cddid_all.tbl CDD cd16438 cd16438 319746 beta_Kdo_transferase_KpsS_like beta-3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)-transferase KpsS like. KpsS is a beta-3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)-transferase. It is part of the ATP-binding cassette transporter dependent capsular polysaccharides (CPSs) synthesis pathway, one of two CPS synthesis pathways present in Escherichia coli. The poly-Kdo linker is thought to be the common feature of CPSs synthesized via this pathway. CPSs are high-molecular-mass cell-surface polysaccharides that are important virulence factors for many pathogenic bacteria. 254 matched cddid_all.tbl CDD cd16439 cd16439 319747 beta_Kdo_transferase_KpsC_2 beta-3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)-transferase KpsC, repeat 2. KpsC is a beta-3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)-transferase. It is part of the ATP-binding cassette transporter dependent capsular polysaccharides (CPSs) synthesis pathway, one of two CPS synthesis pathways present in Escherichia coli. The poly-Kdo linker is thought to be the common feature of CPSs synthesized via this pathway. CPSs are high-molecular-mass cell-surface polysaccharides that are important virulence factors for many pathogenic bacteria. KpsC contains a domain duplication. 259 matched cddid_all.tbl CDD cd16440 cd16440 319748 beta_Kdo_transferase_KpsC_1 beta-3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)-transferase KpsC, repeat1. KpsC is a beta-3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)-transferase. It is part of the ATP-binding cassette transporter dependent capsular polysaccharides (CPSs) synthesis pathway, one of two CPS synthesis pathways present in Escherichia coli. The poly-Kdo linker is thought to be the common feature of CPSs synthesized via this pathway. CPSs are high-molecular-mass cell-surface polysaccharides that are important virulence factors for many pathogenic bacteria. KpsC contains a domain duplication. 262 matched cddid_all.tbl CDD cd16441 cd16441 319749 beta_Kdo_transferase_KpsS beta-3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)-transferase KpsS. KpsS is a beta-3-deoxy-D-manno-oct-2-ulosonic acid (Kdo)-transferase. It is part of the ATP-binding cassette transporter dependent capsular polysaccharides (CPSs) synthesis pathway, one of two CPS synthesis pathways present in Escherichia coli. The poly-Kdo linker is thought to be the common feature of CPSs synthesized via this pathway. CPSs are high-molecular-mass cell-surface polysaccharides that are important virulence factors for many pathogenic bacteria. 307 matched cddid_all.tbl CDD cd16442 cd16442 319741 BPL biotin protein ligase. Biotin protein ligase (EC 6.3.4.15) catalyzes the synthesis of an activated form of biotin, biotinyl-5'-AMP, from substrates biotin and ATP followed by biotinylation of the biotin carboxyl carrier protein subunit of acetyl-CoA carboxylase. Biotin protein ligase (BPL) is the enzyme responsible for attaching biotin to a specific lysine at the active site of biotin enzymes. Biotin attachment is a two step reaction that results in the formation of an amide linkage between the carboxyl group of biotin and the epsilon-amino group of the modified lysine. 173 matched cddid_all.tbl CDD cd16443 cd16443 319742 LplA lipoate-protein ligase. Lipoate-protein ligase A (LplA) catalyzes the formation of an amide linkage between free lipoic acid and a specific lysine residue of the lipoyl domain in lipoate dependent enzymes, similar to the biotinylation reaction mediated by biotinyl protein ligase (BPL). The two step reaction includes activation of exogenously supplied lipoic acid at the expense of ATP to lipoyl-AMP and then transfer to the epsilon-amino group of a specific lysine residue of the lipoyl domain of the target protein. 209 matched cddid_all.tbl CDD cd16444 cd16444 319743 LipB lipoyl/octanoyl transferase. Lipoate-protein ligase B is a octanoyl-[acyl carrier protein]-protein acyltransferase the catalyzes the first step of lipoic acid synthesis. It transfers endogenous octanoic acid attached via a thioester bond to acyl carrier protein (ACP) onto lipoyl domains, which is later converted by lipoate synthase LipA into lipoylated derivatives. 199 matched cddid_all.tbl CDD cd16448 cd16448 438112 RING-H2 "H2 subclass of RING (RING-H2) fingers and its variants. The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the ""cross-brace"" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers: some have different Cys/His patterns while some lack a single Cys or His residue at typical Zn ligand positions (the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can indeed chelate Zn in a RING finger as well). This family corresponds to the H2 subclass of RING (RING-H2) finger proteins that are characterized by containing C3H2C3-type canonical RING-H2 fingers or noncanonical RING-H2 finger variants, including C4HC3- (RING-CH alias RINGv), C3H3C2-, C3H2C2D-, C3DHC3-, and C4HC2H-type modified RING-H2 fingers. The canonical RING-H2 finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-H-X2-C-X(4-48)-C-X2-C, X is any amino acid and the number of X residues varies in different fingers. It binds two Zn ions in a unique ""cross-brace"" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-H2 finger can be found in a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serves as a scaffold for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enables efficient transfer of ubiquitin from E2 to the substrates." 43 matched cddid_all.tbl CDD cd16449 cd16449 438113 RING-HC "HC subclass of RING (RING-HC) finger and its variants. The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the ""cross-brace"" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers. Some have a different Cys/His pattern. Some lack a single Cys or His residue at typical Zn ligand positions, especially, the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can chelate Zn in a RING finger as well. This family corresponds to the HC subclass of RING (RING-HC) fingers that are characterized by containing C3HC4-type canonical RING-HC fingers or noncanonical RING-HC finger variants, including C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type modified RING-HC fingers. The canonical RING-HC finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C. It binds two Zn ions in a unique ""cross-brace"" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-HC fingers can be found in a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle, and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enables efficient transfer of ubiquitin from E2 to the substrates." 41 matched cddid_all.tbl CDD cd16450 cd16450 438114 mRING-C3HGC3_RFWD3 Modified RING finger, C3HGC3-type, found in RING finger and WD repeat domain-containing protein 3 (RFWD3) and similar proteins. RFWD3, also known as RING finger protein 201 (RNF201) or FLJ10520, is an E3 ubiquitin-protein ligase that forms a complex with Mdm2 and p53 to synergistically ubiquitinate p53 and acts as a positive regulator of p53 stability in response to DNA damage. It is phosphorylated by checkpoint kinase ATM/ATR and the phosphorylation mutant fails to stimulate p53 ubiquitination. RFWD3 also functions as a novel replication protein A (RPA)-associated protein involved in DNA replication checkpoint control. RFWD3 contains an N-terminal SQ-rich region followed by a RING finger domain that exhibits robust E3 ubiquitin ligase activity toward p53, a coiled-coil domain and three WD40 repeats in the C-terminus, the latter two of which may be responsible for protein-protein interaction. The RING finger in this family is a modified C3HGC3-type RING finger, but not a canonical C3H2C3-type RING-H2 finger or C3HC4-type RING-HC finger. 61 matched cddid_all.tbl CDD cd16451 cd16451 438115 mRING_PEX12 Modified RING finger found in peroxin-12 (PEX12) and similar proteins. PEX12, also known as peroxisome assembly protein 12 or peroxisome assembly factor 3 (PAF-3), is a RING finger domain-containing integral membrane peroxin required for protein import into peroxisomes. Mutations in human PEX12 result in the peroxisome deficiency Zellweger syndrome of complementation group III (CG-III), a lethal neurological disorder. PEX12 also functions as an E3-ubiquitin ligase that facilitates the PEX4-dependent monoubiquitination of PEX5, a key player in peroxisomal matrix protein import, to control PEX5 receptor recycling or degradation. PEX12 contains a modified RING finger that lacks the third, fourth, and eighth zinc-binding residues of the consensus RING finger motif, suggesting PEX12 may only bind one zinc ion. 54 matched cddid_all.tbl CDD cd16452 cd16452 438116 SP-RING-like SP-RING finger and SPL-RING finger, variants of RING fingers. This family corresponds to a group of proteins with variants of RING fingers that are characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues compared with the classic C3H2C3-/C3HC4-type RING fingers. They include SP-RING finger found in the Siz/PIAS RING (SP-RING) family of SUMO E3 ligases and SPL-RING finger found in E3 SUMO-protein ligase NSE2. The SP-RING family includes PIAS (protein inhibitor of activated STAT) proteins, Zmiz proteins, and Siz proteins from plants and fungi. The PIAS (protein inhibitor of activated STAT) protein family modulates the activity of several transcription factors and acts as an E3 ubiquitin ligase in the sumoylation pathway. NSE2, also known as MMS21 homolog (MMS21) or non-structural maintenance of chromosomes element 2 homolog (Non-SMC element 2 homolog, NSMCE2), is an autosumoylating small ubiquitin-like modifier (SUMO) ligase required for the response to DNA damage. It regulates sumoylation and nuclear-to-cytoplasmic translocation of skeletal and heart muscle-specific variant of the alpha subunit of nascent polypeptide associated complex (skNAC)-Smyd1 in myogenesis. It is also required for resisting extrinsically induced genotoxic stress. 45 matched cddid_all.tbl CDD cd16453 cd16453 438117 RING-Ubox U-box domain, a modified RING finger. The U-box protein family is a family of E3 enzymes that also includes the HECT family and the RING finger family. The E3 enzyme is ubiquitin-protein ligase that cooperates with a ubiquitin-activating enzyme (E1) and a ubiquitin-conjugating enzyme (E2), and plays a central role in determining the specificity of the ubiquitination system. It removes the ubiquitin molecule from the E2 enzyme and attaches it to the target substrate, forming a covalent bond between ubiquitin and the target. U-box proteins are characterized by the presence of a U-box domain of approximately 70 amino acids. The U-box is a modified form of the RING finger domain that lacks metal chelating cysteines and histidines. It resembles the cross-brace RING structure consisting of three beta-sheets and a single alpha-helix, which would be stabilized by salt bridges instead of chelated metal ions. U-box proteins are widely distributed among eukaryotic organisms and show a higher prevalence in plants than in other organisms. 44 matched cddid_all.tbl CDD cd16454 cd16454 438118 RING-H2_PA-TM-RING RING finger, H2 subclass, found in the PA-TM-RING ubiquitin ligase family. The PA-TM-RING family represents a group of transmembrane-type E3 ubiquitin ligases, which has been characterized by an N-terminal transient signal peptide, a PA (protease-associated) domain, a TM (transmembrane) domain, as well as a C-terminal C3H2C3-type RING-H2 finger domain. It includes RNF13, RNF167, ZNRF4 (zinc and RING finger 4), GRAIL (gene related to anergy in lymphocytes)/RNF128, RNF130, RNF133, RNF148, RNF149 and RNF150 (which are more closely related), as well as RNF43 and ZNRF3, which have substantially longer C-terminal tail extensions compared with the others. PA-TM-RING proteins are expressed at low levels in all mammalian tissues and species, but they are not present in yeast. They play a common regulatory role in intracellular trafficking/sorting, suggesting that abrogation of their function may result in dysregulation of cellular signaling events in cancer. 43 matched cddid_all.tbl CDD cd16455 cd16455 438119 RING-H2_AMFR RING finger, H2 subclass, found in autocrine motility factor receptor (AMFR) and similar proteins. AMFR, also known as AMF receptor, or RING finger protein 45, or ER-protein gp78, is an internalizing cell surface glycoprotein localized in both plasma membrane caveolae and the endoplasmic reticulum (ER). It is involved in the regulation of cellular adhesion, proliferation, motility and apoptosis, as well as in the process of learning and memory. AMFR also functions as a RING finger-dependent ubiquitin protein ligase (E3) implicated in the degradation from the ER. AMFR contains an N-terminal RING-H2 finger and a C-terminal ubiquitin-associated (UBA)-like CUE domain. 44 matched cddid_all.tbl CDD cd16456 cd16456 438120 RING-H2_APC11 RING finger, H2 subclass, found in anaphase-promoting complex subunit 11 (APC11) and similar proteins. APC11, also known as cyclosome subunit 11, or hepatocellular carcinoma-associated RING finger protein, is a C3H2C3-type RING-H2 protein that facilitates ubiquitin chain formation by recruiting ubiquitin-charged ubiquitin conjugating enzymes (E2) through its RING-H2 domain. APC11 and its partner, the cullin-like subunit APC2, form the dynamic catalytic core of the gigantic, multisubunit 1.2-MDa anaphase-promoting complex/cyclosome (APC), also known as the cyclosome, which is a ubiquitin-protein ligase (E3) composed of at least 12 subunits and controls cell division by ubiquitinating cell cycle regulators, such as cyclin B and securin, to drive their timely degradation. APC11 can be inhibited by hydrogen peroxide, which may contribute to the delay in cell cycle progression through mitosis that is characteristic of cells subjected to oxidative stress. APC11 contains a canonical RING-H2-finger that coordinate two Zn2+ ions. In addition, it contains a third Zn2+-binding site that is not essential for its ligase activity. 63 matched cddid_all.tbl CDD cd16457 cd16457 438121 RING-H2_BRAP2 RING finger, H2 subclass, found in BRCA1-associated protein (BRAP2) and similar proteins. BRAP2, also known as impedes mitogenic signal propagation (IMP), RING finger protein 52, or renal carcinoma antigen NY-REN-63, is a novel cytoplasmic protein interacting with the two functional nuclear localization signal (NLS) motifs of BRCA1, a nuclear protein linked to breast cancer. It also binds to the SV40 large T antigen NLS motif and the bipartite NLS motif found in mitosin. BRAP2 serves as a cytoplasmic retention protein and plays a role in the regulation of nuclear protein transport. It contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C3H2C3-type RING-H2 finger and a UBP-type zinc finger. 44 matched cddid_all.tbl CDD cd16458 cd16458 319372 RING-H2_Dmap-like RING finger, H2 subclass, found in defective in mitotic arrest proteins (Dmap) and similar proteins. This subfamily includes Schizosaccharomyces pombe protein Dma1 (SpDma1p), Saccharomyces cerevisiae proteins Dma1 (ScDma1p) and Dma2 (ScDma2p), and their homologs from fungi. SpDma1p was originally isolated as a multicopy suppressor of the temperature-sensitive growth phenotype caused by cdc16 mutations. It functions to prevent mitotic exit and cytokinesis during spindle checkpoint arrest by inhibiting septation initiation network (SIN) signaling. ScDma1p and ScDma2p, also known as checkpoint forkhead associated with RING domains-containing protein 1 and 2 respectively, seem to be functionally redundant. They are involved in proper septin ring positioning and cytokinesis. The simultaneous lack of Dma1 and Dma2 leads to spindle mispositioning and defects in the spindle position checkpoint. All members of this family contain a forkhead-associated (FHA) domain and a C3H2C3-type RING-H2 finger, the latter suggesting they may possess E3 ubiquitin-ligase activities. 47 matched cddid_all.tbl CDD cd16459 cd16459 438122 RING-H2_DTX1-like RING finger, H2 subclass, found in E3 ubiquitin-protein ligase Deltex1 (DTX1), Deltex2 (DTX2), Deltex4 (DTX4), and similar proteins. This subfamily contains the vertebrate homologs of Drosophila melanogaster Deltex, specifically DTX1, DTX2, and DTX4, and other similar proteins mainly from eumetazoa. The vertebrate homologs of Deltex are involved in Notch signaling and neurogenesis. Mammalian DTX1 is most closely related to the Drosophila Deltex. Both of them bind to SH3-domain containing protein Grb2 and further inhibit E2A. DTX1 functions as a Notch downstream transcription regulator. It interacts with the transcription coactivator p300 and inhibits transcription activation mediated by the neural specific transcription factor MASH1. It is also a transcription target of nuclear factor of activated T cells (NFAT) and participates in T cell anergy and Foxp3 protein level maintenance in vivo. Moreover, DTX1 promotes protein kinase C theta degradation and sustains Casitas B-lineage lymphoma expression. DTX4, also known as RING finger protein 155, shares the highest degree of sequence similarity with DTX1. So it likely interacts with the intracellular domain of Notch as well. Like DTX1 and DTX4, DTX2 is expressed in thymocytes. It interacts with the intracellular domain of Notch receptors and acts as a negative regulator of Notch signals in T cells. However, the endogenous levels of DTX1 and DTX2 is not important for regulating Notch signals during thymocyte development. In contrast to other DTXs, DTX3 does not contain two Notch-binding WWE domains at the N-terminus, but rather a short unique N-terminal domain. It does not interact with the intracellular domain of Notch. In addition, it has a different class of RING finger (C3HC4 type or RING-HC subclass), compared with the other DTXs which harbor a C3H2C3-type RING-H2 finger. Thus DTX3 is not included in this subfamily. Drosophila melanogaster Deltex also does not belong to this subfamily. 64 matched cddid_all.tbl CDD cd16460 cd16460 438123 RING-H2_DZIP3 RING finger, H2 subclass, found in DAZ (deleted in azoospermia)-interacting protein 3 (DZIP3) and similar proteins. DZIP3, also known as RNA-binding ubiquitin ligase of 138 kDa (RUL138) or 2A-HUB protein, is an RNA-binding E3 ubiquitin-protein ligase that interacts with coactivator-associated arginine methyltransferase 1 (CARM1) and acts as a transcriptional coactivator of estrogen receptor (ER) alpha. It is also a histone H2A ubiquitin ligase that catalyzes monoubiquitination of H2A at lysine 119, functioning as a combinatorial component of the repression machinery required for repressing a specific chemokine gene expression program, critically modulating migratory responses to Toll-like receptors (TLR) activation. DZIP3 contains a C3H2C3-type RING-H2 finger at the C-terminus. 47 matched cddid_all.tbl CDD cd16461 cd16461 438124 RING-H2_EL5-like RING finger, H2 subclass, found in rice E3 ubiquitin-protein ligase EL5 and similar proteins. EL5, also known as protein ELICITOR 5, is an E3 ubiquitin-protein ligase containing an N-terminal transmembrane domain and a C3H2C3-type RING-H2 finger that is a binding site for ubiquitin-conjugating enzyme (E2). It can be rapidly induced by N-acetylchitooligosaccharide elicitor. EL5 catalyzes polyubiquitination via the Lys48 residue of ubiquitin, and thus plays a crucial role as a membrane-anchored E3 in the maintenance of cell viability after the initiation of root primordial formation in rice. It also acts as an anti-cell death enzyme that might be responsible for mediating the degradation of cytotoxic proteins produced in root cells after the actions of phytohormones. Moreover, EL5 interacts with UBC5b, a rice ubiquitin carrier protein, through its RING-H2 finger. EL5 is an unstable protein, and its degradation is regulated by the C3H2C3-type RING-H2 finger in a proteasome-independent manner. 44 matched cddid_all.tbl CDD cd16462 cd16462 438125 RING-H2_Pep3p-like RING finger, H2 subclass, found in Saccharomyces cerevisiae vacuolar membrane protein PEP3 (Pep3p) and similar proteins. Pep3p, also known as carboxypeptidase Y-deficient protein 3, vacuolar morphogenesis protein 8, vacuolar protein sorting-associated protein 18 (Vps18p), or vacuolar protein-targeting protein 18, is a vacuolar membrane protein that affects late Golgi functions required for vacuolar protein sorting and efficient alpha-factor prohormone maturation. It is required for vacuolar biogenesis and for trafficking of hydrolase precursors to the vacuole. The disruption of PEP3 may cause hypersensitivity to heat shock and ethanol stresses, probably due to disappearance of normal vacuoles. As a component of the homotypic fusion and vacuole protein sorting (HOPS) and class C core vacuole/endosome tethering (CORVET) complexes, its overexpression shortens lag phase but does not alter growth rate in Saccharomyces cerevisiae exposed to acetic acid stress. Moreover, Pep3p forms the Class C Vps protein complex (C-Vps complex) with Pep5p (also known as Vps11), Vps16, and Vps33, and is necessary for trafficking of hydrolase precursors to the vacuole by promoting vesicular docking reactions with SNARE proteins. Pep3p contains a C3H2C3-type RING-H2 finger at the C-terminus. 50 matched cddid_all.tbl CDD cd16463 cd16463 438126 RING-H2_PHR RING finger, H2 subclass, found in the PHR (Pam/Highwire/RPM-1) protein family. The PHR protein family represents an evolutionally conserved family of large proteins including human E3 ubiquitin ligase protein associated with Myc (Pam) and its homologs, Phr1 in mouse, Highwire (HIW) in Drosophila, RPM-1 (regulator of presynaptic morphology 1) in Caenorhabditis elegans, and Esrom in zebrafish. Those proteins are large E3 ubiquitin ligases containing regulator of chromosome condensation (RCC) homology domains (RHD-1 and RHD-2) with inferred guanine exchange factor (GEF) activity, a Myc-binding domain, a B-box zinc finger, and a C-terminal C3H2C3-type RING-H2 finger with E3 ubiquitin (Ub) ligase activity. They play an important role in axon guidance and synaptogenesis. They regulate synapse formation and growth in mammals, zebrafish, Drosophila, and Caenorhabditis elegans, and may control a variety of signaling pathways, including cAMP signaling in mammalian cells, JNK/p38 MAPK signaling in Drosophila and C. elegans, and bone morphogenetic protein signaling in Drosophila. Pam also known as Myc-binding protein 2 (MYCBP2), or Pam/highwire/rpm-1 protein (PHR1), negatively regulates neuronal growth, synaptogenesis and synaptic plasticity by modulating several signaling pathways including the p38 MAPK signaling cascade. It also participates in receptor and ion channel internalization, such as regulating internalization of transient receptor potential vanilloid receptor 1 (TRPV1) in peripheral sensory neurons, as well as duration of thermal hyperalgesia through p38 MAPK. It interacts with neuron-specific electroneutral potassium (K+) and chloride (Cl-) cotransporter KCC2 and modulates its function. Moreover, Pam genetically interacts with Robo2 to modulate axon guidance in the olfactory system. It also associates with tuberous sclerosis complex (TSC) proteins, ubiquitinating TSC2 and regulating mammalian/mechanistic target of rapamycin (mTOR) signaling. Furthermore, Pam is the longest lasting nontranscriptional regulator of adenylyl cyclase activity, and can mediate sustained inhibition of cAMP signaling by sphingosine-1-phosphate. It is also involved in spinal nociceptive processing. Phr1 is an essential regulator of retinal ganglion cell projection during both dorsal lateral geniculate nucleus (dLGN) and superior colliculus (SC) topographic map development. RPM-1 positively regulates a Rab GTPase pathway to promote vesicular trafficking via late endosomes, thereby regulating synapse formation and axon termination. Esrom has E3 ligase activity and modulates the amount of phosphorylated Tuberin, a tumor suppressor, in growth cones. It is required for the formation of the retinotectal projection. 55 matched cddid_all.tbl CDD cd16464 cd16464 438127 RING-H2_Pirh2-like RING finger, H2 subclass, found in p53-induced RING-H2 protein (Pirh2) and similar proteins. Pirh2, also known as RING finger and CHY zinc finger domain-containing protein 1 (Rchy1), androgen receptor N-terminal-interacting protein, CH-rich-interacting match with PLAG1, RING finger protein 199 (RNF199), or zinc finger protein 363 (ZNF363), is a p53 inducible E3 ubiquitin-protein ligase that functions as a negative regulator of p53. It preferably ubiquitylates the tetrameric form of p53 in vitro and in vivo, suggesting a role of Pirh2 in downregulating the transcriptionally active form of p53 in the cell. Moreover, Pirh2 inhibits the transcriptional activity of p73, a homolog of the tumor suppressor p53, by promoting its ubiquitination. It also monoubiquitinates DNA polymerase eta (PolH) to suppress translesion DNA synthesis. Furthermore, Pirh2 functions as a negative regulator of the cyclin-dependent kinase inhibitor p27(Kip1) function by promoting ubiquitin-dependent proteasomal degradation. Pirh2 enhances androgen receptor (AR) signaling through inhibition of histone deacetylase 1 (HDAC1) and is overexpressed in prostate cancer. It interacts with TIP60 and this association may regulate Pirh2 stability. In addition, the oncoprotein pleomorphic adenoma gene like 2 (PLAGL2) can bind to the Pirh2 dimer and therefore control the stability of Pirh2. Pirh2 contains a total of nine zinc-binding sites with six located at the N-terminal region, two in the C3H2C3-type RING-H2 domain, and one in the C-terminal region. Nine zinc binding sites comprise three different zinc coordination schemes, including RING type cross-brace zinc coordination, C4 zinc finger, and a novel left-handed beta-spiral zinc-binding motif formed by three recurrent CCHC sequence motifs. This subfamily also includes Drosophila melanogaster Deltex, a ubiquitously expressed cytoplasmic ubiquitin E3 ligase that mediates Notch activation in Drosophila. It selectively suppresses T-cell activation through degradation of a key signaling molecule, MAP kinase kinase kinase 1 (MEKK1). It also inhibits Jun-mediated transcription at the stage of Ras-dependent Jun N-terminal protein kinase (JNK) activation. Deltex contains N-terminal two Notch-binding WWE domains that physically interact with the Notch ankyrin domains, a proline-rich motif that shares homology with SH3-binding domains, and a RING finger at the C-terminus. 45 matched cddid_all.tbl CDD cd16465 cd16465 438128 RING-H2_PJA1_2 RING finger, H2 subclass, found in protein E3 ubiquitin-protein ligase Praja-1, Praja-2, and similar proteins. This family includes two highly similar E3 ubiquitin-protein ligases, Praja-1 and Praja-2. Praja-1, also known as RING finger protein 70, is a RING-H2 finger ubiquitin ligase encoded by gene PJA1, a novel human X chromosome gene abundantly expressed in the brain. It has been implicated in bone and liver development, as well as memory formation and X-linked mental retardation (MRX). Praja-1 interacts with and activates the ubiquitin-conjugating enzyme UbcH5B, and shows E2-dependent E3 ubiquitin ligase activity. It is a 3-deazaneplanocin A (DZNep)-induced ubiquitin ligase that directly ubiquitinates individual polycomb repressive complex 2 (PRC2) subunits in a cell free system, which leads to their proteasomal degradation. It also plays an important role in neuronal plasticity, which is the basis for learning and memory. Moreover, Praja-1 ubiquitinates embryonic liver fodrin (ELF) and Smad3, but not Smad4, in a transforming growth factor-beta (TGF-beta)-dependent manner. It controls ELF abundance through ubiquitin-mediated degradation, and further regulates TGF-beta signaling, which plays a key role in the suppression of gastric carcinoma. Praja-1 also regulates the transcription function of the homeodomain protein Dlx5 by controlling the stability of Dlxin-1, via a ubiquitin-dependent degradation pathway. Praja-2, also known as RING finger protein 131, NEURODAP1, or KIAA0438, is an E2-dependent E3 ubiquitin ligase that interacts with and activates the ubiquitin-conjugating enzyme UbcH5B. It functions as an A-kinase anchoring protein (AKAP)-like E3 ubiquitin ligase that plays a critical role in controlling cyclic AMP (cAMP)-dependent PKA activity and pro-survival signaling, and further promotes cell proliferation and growth. Praja-2 is also involved in protein sorting at the postsynaptic density region of axosomatic synapses and possibly plays a role in synaptic communication and plasticity. Together with the AMPK-related kinase SIK2 and the CDK5 activator CDK5R1/p35, it forms a SIK2-p35-PJA2 complex that plays an essential role for glucose homeostasis in pancreatic beta cell functional compensation. Praja-2 ubiquitylates and degrades Mob, a core component of NDR/LATS kinase and a positive regulator of the tumor-suppressor Hippo signaling. Both Praja-1 and Praja-2 contain a potential nuclear localization signal (NLS) and a C-terminal C3H2C3-type RING-H2 motif. 46 matched cddid_all.tbl CDD cd16466 cd16466 438129 RING-H2_RBX2 RING finger, H2 subclass, found in RING-box protein 2 (RBX2) and similar proteins. RBX2, also known as CKII beta-binding protein 1 (CKBBP1), RING finger protein 7 (RNF7), regulator of cullins 2 (ROC2), or sensitive to apoptosis gene protein (SAG), is an E3 ubiquitin-protein ligase that protects cells from apoptosis, confers radioresistance, and plays an essential and non-redundant role in embryogenesis and vasculogenesis. It promotes ubiquitination and degradation of a number of protein substrates, including c-JUN, DEPTOR, HIF-1alpha, IkappaBalpha, NF1, NOXA, p27, and procaspase-3, thus regulating various signaling pathways and biological processes. RBX2 is necessary for ubiquitin ligation activity of the multimeric cullin (Cul)-RING E3 ligases (CRLs). RBX2-containing CRLs are involved in the NEDD8 pathway and RBX2 specifically regulates NEDD8ylation of Cul5. It can bind and activate the HIV-1 Vif-Cullin5 E3 ligase complex in vitro. It is also a substrate of NEDD4-1 E3 ubiquitin ligase and mediates NEDD4-1 induced chemosensitization. The inactivation of RBX2 E3 ubiquitin ligase activity triggers senescence and inhibits Kras-induced immortalization. Endothelial deletion of RBX2 causes embryonic lethality and blocks tumor angiogenesis, and may have potential use in anti-angiogenesis therapy of human cancers. Moreover, as a component of the Cullin 5-RING E3 ubiquitin ligase (CRL5) complex, RBX2 regulates neuronal migration through different CRL5 adaptors, such as SOCS7. RBX2 also functions as a redox inducible antioxidant protein that scavenges oxygen radicals by forming inter- and intra-molecular disulfide bonds when acting alone. It contains a C-terminal C3H2C3-type RING-H2 finger that is essential for its ligase activity. 60 matched cddid_all.tbl CDD cd16467 cd16467 438130 RING-H2_RNF6-like RING finger, H2 subclass, found in E3 ubiquitin-protein ligase RNF6, RNF12, and similar proteins. RNF6 is an androgen receptor (AR)-associated protein that induces AR ubiquitination and promotes AR transcriptional activity. RNF6-induced ubiquitination may regulate AR transcriptional activity and specificity by modulating cofactor recruitment. RNF6 is overexpressed in hormone-refractory human prostate cancer tissues and required for prostate cancer cell growth under androgen-depleted conditions. RNF6 also regulates local serine/threonine kinase LIM kinase 1 (LIMK1) levels in axonal growth cones. RNF6-induced LIMK1 polyubiquitination is mediated via K48 of ubiquitin and leads to proteasomal degradation of the kinase. RNF6 binds and upregulates the Inha promoter, and functions as a transcription regulatory protein in the mouse sertoli cell. It acts as a potential tumor suppressor gene involved in the pathogenesis of esophageal squamous cell carcinoma (ESCC). RNF12, also known as LIM domain-interacting RING finger protein, or RING finger LIM domain-binding protein (R-LIM), is an E3 ubiquitin-protein ligase encoded by gene RLIM that is crucial for normal embryonic development in some species and for normal X inactivation in mice. It thus functions as a major sex-specific epigenetic regulator of female mouse nurturing tissues. RNF12 is widely expressed during embryogenesis, and mainly localizes to the cell nucleus, where it regulates the levels of many proteins, including CLIM, LMO, HDAC2, TRF1, SMAD7, and REX1, by proteasomal degradation. Both RNF6 and RNF12 contain a well conserved C3H2C3-type RING-H2 finger. 43 matched cddid_all.tbl CDD cd16468 cd16468 438131 RING-H2_RNF11 RING finger, H2 subclass, found in RING finger protein 11 (RNF11) and similar proteins. RNF11 is an E3 ubiquitin-protein ligase that acts both as an adaptor and a modulator of itch-mediated control of ubiquitination events underlying membrane traffic. It acts downstream of an enzymatic cascade for the ubiquitination of specific substrates. It is also a molecular adaptor of homologous to E6-associated protein C-terminus (HECT)-type ligases. RNF11 has been implicated in the regulation of several signaling pathways. It enhances transforming growth factor receptor (TGFR) signaling by both abrogating Smurf2-mediated receptor ubiquitination and by promoting the Smurf2-mediated degradation of AMSH (associated molecule with the SH3 domain of STAM), a de-ubiquitinating enzyme that enhances TGF-beta signaling and epidermal growth factor receptor (EGFR) endosomal recycling. It also acts directly on Smad4 to enhance Smad4 function, and plays a role in prolonged TGF-beta signaling. RNF11 also functions as a critical component of the A20 ubiquitin-editing protein complex that negatively regulates tumor necrosis factor (TNF)-mediated nuclear factor (NF)-kappaB activation. It interacts with Smad anchor for receptor activation (SARA) and the endosomal sorting complex required for transport (ESCRT)-0 complex, thus participating in the regulation of lysosomal degradation of EGFR. RNF11 acts as a novel GGA cargo actively participating in regulating the ubiquitination of the GGA protein family. RNF11 functions together with TAX1BP1 to target TANK-binding kinase 1 (TBK1)/IkappaB kinase IKKi, and further restricts antiviral signaling and type I interferon (IFN)-beta production. RNF11 contains an N-terminal PPPY motif that binds WW domain-containing proteins such as AIP4/itch, Nedd4 and Smurf1/2 (SMAD-specific E3 ubiquitin-protein ligase 1/2), and a C-terminal C3H2C3-type RING-H2 finger that functions as a scaffold for the coordinated transfer of ubiquitin to substrate proteins together with the E2 enzymes UbcH527 and Ubc13. 43 matched cddid_all.tbl CDD cd16469 cd16469 438132 RING-H2_RNF24-like RING finger, H2 subclass, found in RING finger proteins RNF24, RNF122, and similar proteins. This subfamily includes RNF24, RNF122, and similar proteins. RNF24 is an intrinsic membrane protein localized in the Golgi apparatus. It specifically interacts with the ankyrin-repeats domains (ARDs) of TRPC1, -3, -4, -5, -6, and -7, and affects TRPC intracellular trafficking without affecting their activity. RNF122 is a RING finger protein associated with HEK 293T cell viability. It is localized to the endoplasmic reticulum (ER) and the Golgi apparatus, and overexpressed in anaplastic thyroid cancer cells. RNF122 functions as an E3 ubiquitin ligase that can ubiquitinate itself and undergo degradation through its RING finger in a proteasome-dependent manner. Both RNF24 and RNF122 contain an N-terminal transmembrane domain and a C-terminal C3H2C3-type RING-H2 finger. 47 matched cddid_all.tbl CDD cd16470 cd16470 438133 RING-H2_RNF25 RING finger, H2 subclass, found in RING finger protein 25 (RNF25) and similar proteins. RNF25, also known as AO7, is a putative E3 ubiquitin-protein ligase that was initially identified as an interacting protein of the E2 ubiquitin-conjugating enzyme, Ubc5B. It is ubiquitously expressed in various tissues and predominantly localized in the nucleus. RNF25 activates the nuclear factor (NF)-kappaB-dependent gene expression upon stimulation with Interleukin-1 beta (IL-1beta), or tumor necrosis factor (TNF), or overexpression of NF-kappaB-inducing kinase. It interacts with the p65 transactivation domain (TAD) and modulates its transcriptional activity. RNF25 contains an N-terminal RWD domain, a C3H2C3-type RING-H2 finger, and a C-terminal Pro-rich region. Both the RING-H2 finger and the C-terminal regions of RNF25 are necessary for transcriptional activation. 74 matched cddid_all.tbl CDD cd16471 cd16471 438134 RING-H2_RNF32 RING finger, H2 subclass, found in RING finger protein 32 (RNF32) and similar proteins. RNF32 is mainly expressed in testis spermatogenesis, most likely in spermatocytes and/or in spermatids, suggesting a possible role in sperm formation. RNF32 contains two C3H2C3-type RING-H2 fingers separated by an IQ domain of unknown function. Although the biological function of RNF32 remains unclear, proteins with double RING-H2 fingers may act as scaffolds for binding several proteins that function in the same pathway. 46 matched cddid_all.tbl CDD cd16472 cd16472 438135 RING-H2_RNF38-like RING finger, H2 subclass, found in RING finger proteins RNF38, RNF44, and similar proteins. This subfamily includes RING finger proteins RNF38, RNF44, and similar proteins. RNF38 is a nuclear E3 ubiquitin protein ligase that plays a role in regulating p53. RNF44 is an uncharacterized RING finger protein that shows high sequence similarity to RNF38. Both RNF38 and RNF44 contain a coiled-coil motif, a KIL motif (Lys-X2-Ile/Leu-X2-Ile/Leu, X can be any amino acid), and a C3H2C3-type RING-H2 finger. In addition, RNF38 harbors two potential nuclear localization signals. 46 matched cddid_all.tbl CDD cd16473 cd16473 438136 RING-H2_RNF103 RING finger, H2 subclass, found in RING finger protein 103 (RNF103) and similar proteins. RNF103, also known as KF-1 or zinc finger protein 103 homolog (Zfp-103), is an endoplasmic reticulum (ER)-resident E3 ubiquitin-protein ligase that is widely expressed in many different organs, including brain, heart, kidney, spleen, and lung. It is involved in the ER-associated degradation (ERAD) pathway by interacting with components of the ERAD pathway, including Derlin-1 and VCP. RNF103 contains several hydrophobic regions at its N-terminal and middle regions, as well as a C-terminal C3H2C3-type RING-H2 finger. 55 matched cddid_all.tbl CDD cd16474 cd16474 438137 RING-H2_RNF111-like RING finger, H2 subclass, found in RING finger proteins RNF111, RNF165, and similar proteins. The family includes RING finger proteins RNF111, RNF165, and similar proteins. RNF111, also known as Arkadia, is a nuclear E3 ubiquitin-protein ligase that targets intracellular effectors and modulators of transforming growth factor beta (TGF-beta)/Nodal-related signaling for polyubiquitination and proteasome-dependent degradation. It also interacts with the clathrin-adaptor 2 (AP2) complex and regulates endocytosis of certain cell surface receptors, leading to modulation of epidermal growth factor (EGF) and possibly other signaling pathways. The N-terminal half of RNF111 harbors three SUMO-interacting motifs (SIMs). It thus functions as a SUMO-targeted ubiquitin ligase (STUbL) that directly links nonproteolytic ubiquitylation and SUMOylation in the DNA damage response, as well as triggers degradation of signal-induced polysumoylated proteins, such as the promyelocytic leukemia protein (PML). RNF165, also known as Arkadia-like 2, Arkadia2, or Ark2C, is an E3 ubiquitin ligase with homology to the C-terminal half of RNF111. It is expressed specifically in the nervous system, and can serve to amplify neuronal responses to specific signals. It acts as a positive regulator of bone morphogenetic protein (BMP)-Smad signaling that is involved in motor neuron (MN) axon elongation. Both RNF165 and RNF111 contain a C-terminal C3H2C3-type RING-H2 finger. 46 matched cddid_all.tbl CDD cd16475 cd16475 438138 RING-H2_RNF121-like RING finger, H2 subclass, found in RING finger proteins RNF121, RNF175 and similar proteins. This subfamily includes RNF121, RNF175 and similar proteins. RNF121 is an E3-ubiquitin ligase present in the endoplasmic reticulum (ER) and cis-Golgi compartments. It is a novel regulator of apoptosis. It also facilitates the degradation and membrane localization of voltage-gated sodium (NaV) channels, and thus plays a role in the quality control of NaV channels during their synthesis and subsequent transport to the membrane. Moreover, RNF121 acts as a broad regulator of nuclear factor kappaB (NF-kappaB) signaling since its silencing also dampens NF-kappaB activation following stimulation of toll-like receptors (TLRs), nod-like receptors (NLRs), RIG-I-like Receptors (RLRs) or after DNA damage. RNF121 contains five conserved transmembrane (TM) domains and a C3H2C2-type RING-H2 finger. RNF175 is an uncharacterized RING finger protein that shows high sequence similarity with RNF121. This family also includes Arabidopsis RING finger E3 ligase RHA2A, RHA2B, and their homologs. RHA2A is a positive regulator of abscisic acid (ABA) signaling during seed germination and early seedling development. RHA2B may play a role in the ubiquitin-dependent proteolysis pathway that respond to proteasome inhibition. All subfamily members contain a C3H2C3-type RING-H2 finger, which is responsible for E3-ubiquitin ligase activity. 55 matched cddid_all.tbl CDD cd16476 cd16476 438139 RING-H2_RNF139-like RING finger, H2 subclass, found in RING finger proteins RNF139, RNF145, and similar proteins. RNF139, also known as translocation in renal carcinoma on chromosome 8 protein (TRC8), is an endoplasmic reticulum (ER)-resident multi-transmembrane protein that functions as a potent growth suppressor in mammalian cells, inducing G2/M arrest, decreased DNA synthesis and increased apoptosis. It is a tumor suppressor that has been implicated in a novel regulatory relationship linking the cholesterol/lipid biosynthetic pathway with cellular growth control. A mutation in RNF139 has been identified in families with hereditary renal (RCC) and thyroid cancers. RNF145 is an uncharacterized RING finger protein encoded by the RNF145 gene, which is expressed in T lymphocytes, and its expression is altered in acute myelomonocytic and acute promyelocytic leukemias. Although its biological function remains unclear, RNF145 shows high sequence similarity with RNF139. Both RNF139 and RNF145 contain a C3H2C3-type RING-H2 finger with possible E3-ubiquitin ligase activity. 41 matched cddid_all.tbl CDD cd16477 cd16477 438140 RING-H2_RNF214 RING finger, H2 subclass, found in RING finger protein 214 (RNF214) and similar proteins. RNF214 is an uncharacterized RING finger protein containing a C3H2C3-type RING-H2 finger, suggesting it may have E3-ubiquitin ligase activity. 45 matched cddid_all.tbl CDD cd16478 cd16478 438141 RING-H2_Rapsyn RING finger, H2 subclass, found in 43 kDa receptor-associated protein of the synapse (Rapsyn) and similar proteins. Rapsyn, also known as acetylcholine receptor (AChR)-associated 43 kDa protein or RING finger protein 205 (RNF205), is a 43 kDa postsynaptic protein that plays an essential role in the clustering and maintenance of AChR in the postsynaptic membrane of the motor endplate. AChRs enable the transport of rapsyn from the Golgi complex to the plasma membrane through a molecule-specific interaction. Rapsyn also mediates subsynaptic anchoring of protein kinase A (PKA) type I in close proximity to the postsynaptic membrane, which is essential for synapse maintenance. Its mutations in humans cause endplate AChR deficiency and myasthenic syndrome. Rapsyn contains an N-terminal myristoylation signal required for membrane association, seven tetratricopeptide repeats (TPRs) that subserve rapsyn self-association, a coiled-coil domain responsible for the binding of determinants within the long cytoplasmic loop of each AChR subunit, a C3H2C3-type RING-H2 finger that binds to the cytoplasmic domain of beta-dystroglycan and to S-NRAP and links rapsyn to the subsynaptic cytoskeleton, and a serine phosphorylation site. 48 matched cddid_all.tbl CDD cd16479 cd16479 438142 RING-H2_synoviolin RING finger, H2 subclass, found in synoviolin and similar proteins. Synoviolin, also known as synovial apoptosis inhibitor 1 (Syvn1), Hrd1, or Der3, is an endoplasmic reticulum (ER)-anchoring E3 ubiquitin ligase that functions as a suppressor of ER stress-induced apoptosis and plays a role in homeostasis maintenance. It also targets tumor suppressor gene p53 for proteasomal degradation, suggesting crosstalk between ER associated degradation (ERAD) and p53 mediated apoptotic pathway under ER stress. Moreover, synoviolin controls body weight and mitochondrial biogenesis through negative regulation of the thermogenic coactivator peroxisome proliferator-activated receptor coactivator (PGC)-1beta. It upregulates amyloid beta production by targeting a negative regulator of gamma-secretase, Retention in endoplasmic reticulum 1 (Rer1), for degradation. It is also involved in the degradation of endogenous immature nicastrin, and affects amyloid beta-protein generation. Moreover, synoviolin is highly expressed in rheumatoid synovial cells and may be involved in the pathogenesis of rheumatoid arthritis (RA). It functions as an anti-apoptotic factor that is responsible for the outgrowth of synovial cells during the development of RA. It promotes inositol-requiring enzyme 1 (IRE1) ubiquitination and degradation in synovial fibroblasts with collagen-induced arthritis. Furthermore, the upregulation of synoviolin may represent a protective response against neurodegeneration in Parkinson's disease (PD). In addition, synoviolin is involved in liver fibrogenesis. Synoviolin contains a C3H2C2-type RING-H2 finger. 43 matched cddid_all.tbl CDD cd16480 cd16480 438143 RING-H2_TRAIP RING finger, H2 subclass, found in TRAF-interacting protein (TRAIP) and similar proteins. TRAIP, also known as RING finger protein 206 (RNF206) or TRIP, is a ubiquitously expressed nucleolar E3 ubiquitin ligase important for cellular proliferation and differentiation. It is found near mitotic chromosomes and functions as a regulator of the spindle assembly checkpoint. TRAIP interacts with tumor necrosis factor (TNF)-receptor-associated factor (TRAF) proteins and inhibits TNF-alpha-mediated nuclear factor (NF)-kappaB activation. It also interacts with two tumor suppressors CYLD and spleen tyrosine kinase (Syk), and DNA polymerase eta, which facilitates translesional synthesis after DNA damage. TRAIP contains an N-terminal C3H2C2-type RING-H2 finger and an extended coiled-coil domain. 43 matched cddid_all.tbl CDD cd16481 cd16481 438144 RING-H2_TTC3 RING finger, H2 subclass, found in Tetratricopeptide repeat protein 3 (TTC3) and similar proteins. TTC3, also known as protein DCRR1, TPR repeat protein D, TPR repeat protein 3, or RING finger protein 105 (RNF105), is an E3 ubiquitin-protein ligase encoded by a gene within the Down syndrome (DS) critical region on chromosome 21. It affects differentiation and Golgi compactness in neurons through specific actin-regulating pathways. It inhibits the neuronal-like differentiation of pheocromocytoma cells by activating RhoA and by binding to Citron proteins. TTC3 is an Akt-specific E3 ligase that binds to phosphorylated Akt and facilitates its ubiquitination and degradation within the nucleus. It contains four N-terminal TPR motifs, a potential coiled-coil region and a Citron binding region in the central part, and a C-terminal C3H2C2-type RING-H2 finger. 45 matched cddid_all.tbl CDD cd16482 cd16482 438145 RING-H2_UBR1-like RING finger, H2 subclass, found in ubiquitin-protein ligase E3-alpha-1 (UBR1), E3-alpha-2 (UBR2), and similar proteins. Two UBR family members, UBR1 and UBR2, are major N-recognin ubiquitin ligases that both function in the N-end rule degradation pathway. They can recognize substrate proteins with type-1 (basic) and type-2 (bulky hydrophobic) N-terminal residues as part of N-degrons and an internal lysine residue for ubiquitin conjugation. They also function in a quality control pathway for degradation of unfolded cytosolic proteins. Their action is stimulated by Hsp70. Moreover, UBR1 and UBR2 are negative regulators of the leucine-mTOR signaling pathway. Leucine might activate this pathway in part through inhibition of their ubiquitin ligase activity. In yeast, only one E3, encoded by UBR1, mediates the recognition of substrates by the N-end rule pathway. Saccharomyces cerevisiae UBR1 also functions as an additional E3 ligase in the endoplasmic reticulum-associated protein degradation (ERAD). It can provide ubiquitin ligation activity for the ERAD substrate mutated Ste6 (sterile). Schizosaccharomyces pombe UBR1 is a critical regulator that influences the oxidative stress response via degradation of active Pap1 basic leucine zipper (bZIP) transcription factor in the nucleus. Both UBR1 and UBR2 contain an N-terminal ubiquitin-recognin (UBR) box involved in binding type-1 (basic) N-end rule substrate, an N-domain (also known as ClpS domain) required for type-2 (bulky hydrophobic) N-end rule substrate recognition, a C3H2C3-type RING-H2 finger, and a C-terminal UBR-specific autoinhibitory (UAIN) domain. 67 matched cddid_all.tbl CDD cd16483 cd16483 438146 RING-H2_UBR3 RING finger, H2 subclass, found in ubiquitin-protein ligase E3-alpha-3 (UBR3) and similar proteins. UBR3, also known as N-recognin-3, E3alpha-III, or zinc finger protein 650, is an E3 ubiquitin-protein ligase targeting the essential DNA repair protein APE1, also known as Ref-1, for ubiquitylation. It regulates cellular levels of APE1 and is required for genome stability. It also plays a regulatory role in sensory pathways, including olfaction. In Drosophila, UBR3 also regulates apoptosis by controlling the activity of Drosophila inhibitor of apoptosis protein 1 (DIAP1), which is required to prevent caspase activation. UBR3 contains an N-terminal ubiquitin-recognin (UBR) box, a C3H2C3-type RING-H2 finger, and a C-terminal UBR-specific autoinhibitory (UAIN) domain. 63 matched cddid_all.tbl CDD cd16484 cd16484 438147 RING-H2_Vps RING finger, H2 subclass, found in vacuolar protein sorting-associated proteins Vps8, Vps11, Vps18, Vps41, and similar proteins. This subfamily corresponds to a group of vacuolar protein sorting-associated proteins containing a C-terminal C3H2C3-type RING-H2 finger, which includes Vps8, Vps11, Vps18, and Vps41. Vps11 and Vps18 associate with Vps16 and Vps33 to form a Class C Vps core complex that is required for soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE)-mediated membrane fusion at the lysosome-like yeast vacuole. The core complex, together with two additional compartment-specific subunits, forms the tethering complexes HOPS (homotypic vacuole fusion and protein sorting) and CORVET (class C core vacuole/endosome transport). CORVET contains the additional Vps3 and Vps8 subunits. It operates at endosomes, controls traffic into late endosomes and interacts with the Rab5/Vps21-GTP form. HOPS contains the additional Vps39 and Vps41 subunits. It operates at the lysosomal vacuole, controls all traffic from late endosomes into the vacuole and interacts with the Rab7/Ypt7-GTP form. 48 matched cddid_all.tbl CDD cd16485 cd16485 438148 mRING-H2-C3H2C2D_RBX1 modified RING finger, H2 subclass (C3H2C2D-type), found in RING-box protein 1 (RBX1) and similar proteins. RBX1, also known as Hrt1, protein ZYP, RING finger protein 75 (RNF75), or regulator of cullins 1 (ROC1), is an E3 ubiquitin-protein ligase necessary for ubiquitin ligation activity of multimeric cullin (Cul)-RING E3 ligases (CRLs). RBX1-containing CRLs are involved in the NEDD8 pathway; RBX1 specifically regulates NEDD8ylation of Cul1-4. It can also bind and activate HIV-1 Vif-Cullin5 E3 ligase complex in vitro. Moreover, RBX1 is an essential element of Skp1/Cullin/F-box (SCF) E3-ubiquitin ligase complexes that target diverse proteins for proteasome-mediated degradation. It is a direct functional target of miR-194 and plays an important role in proliferation and migration of gastric cancer (GC) cells. RBX1 is also an essential component of KEAP1/CUL3/RBX1 E3-ubiquitin ligase complex that functions as a regulator of NFE2-related factor 2 (NRF2) and plays a key role in NRF2 pathway deregulation in multiple tumor types, including ovarian carcinomas (OVCA) and papillary thyroid carcinoma (PTC). Furthermore, RBX1 associates with DDB1, Cul4A, and Fbxw5 to form the Fbxw5-DDB1-Cul4A-Rbx1 complex that may function as a dual SUMO/ubiquitin ligase suppressing c-Myb activity through sumoylation or ubiquitination. RBX1 contains a C-terminal modified RING-H2 finger that is of C3H2C2D-type, rather than the canonical C3H2C3-type. The modified RING-H2 finger is essential for its ligase activity. 62 matched cddid_all.tbl CDD cd16486 cd16486 438149 mRING-H2-C3H2C2D_ZSWM2 Modified RING finger, H2 subclass (C3H2C2D-type), found in zinc finger SWIM domain-containing protein 2 (ZSWIM2) and similar proteins. ZSWIM2, also known as MEKK1-related protein X (MEX) or ZZ-type zinc finger-containing protein 2, is a testis-specific E3 ubiquitin ligase that promotes death receptor-induced apoptosis through Fas, death receptor (DR) 3 and DR4 signaling. ZSWIM2 is self-ubiquitinated and targeted for degradation through the proteasome pathway. It acts as an E3 ubiquitin ligase, through the E2, Ub-conjugating enzymes UbcH5a, UbcH5c, or UbcH6. ZSWIM2 contains four putative zinc-binding domains including an N-terminal SWIM (SWI2/SNF2 and MuDR) domain critical for its ubiquitination, and two modified RING-H2 fingers separated by a ZZ zinc finger domain, which was required for interaction with UbcH5a and its self-association. This model corresponds to the second RING-H2 finger, which is not a canonical C3H2C3-type, but a modified C3H2C2D-type. 49 matched cddid_all.tbl CDD cd16487 cd16487 438150 mRING-H2-C3DHC3_ZFPL1 Modified RING finger, H2 subclass (C3DHC3-type), found in zinc finger protein-like 1 (ZFPL1) and similar proteins. ZFPL1, also known as zinc finger protein MCG4, is a novel mitotic Golgi phosphoprotein required for cis-Golgi integrity and efficient endoplasmic reticulum (ER)-to-Golgi transport via directly interacting with the cis-Golgi matrix protein GM130. ZFPL1 is a widely expressed integral membrane protein with two predicted zinc fingers at its N-terminus. One is a novel type of zinc finger, and the other is a modified RING-H2 finger that lacks the fourth zinc-binding residue of the consensus C3H2C3-type RING-H2 finger. It also contains a bipartite nuclear localization signal (NLS), and a leucine zipper at the C-terminus. 57 matched cddid_all.tbl CDD cd16488 cd16488 438151 mRING-H2-C3H3C2_Mio-like Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein mio and its homologs. This subfamily contains Mio, WDR24, WDR59, and their counterparts Sea4, Sea2, and Sea3 from yeast, respectively. Mio/Sea4, Sea2/WDR24, and Sea3/WDR59 are components of the GATOR2 complex, which also includes another two subunits, Seh1and Sec13. GATOR2 and GATOR1, which is composed of three subunits, DEPDC5, Nprl2, and Nprl3, form the Rag-interacting complex GATOR (GAP Activity Towards Rags). Inhibition of GATOR1 subunits makes mTORC1 signaling resistant to amino acid deprivation. In contrast, inhibition of GATOR2 subunits suppresses mTORC1 signaling and GATOR2 negatively regulates DEPDC5. All subfamily members contain an N-terminal WD40 domain and a C-terminal RING-H2 finger with an unusual arrangement of zinc-coordinating residues. The cysteines and histidines in the RING-H2 finger are arranged as a modified C3H3C2-type, rather than the canonical C3H2C3-type. 44 matched cddid_all.tbl CDD cd16489 cd16489 438152 mRING-CH-C4HC2H_ZNRF Modified RING-CH finger, H2 subclass (C4HC2H-type), found in the ZNRF family. The ZNRF family includes zinc/RING finger proteins ZNRF1, ZNRF2, and similar proteins. It has been characterized by containing a unique combination of zinc finger-RING finger motifs in the C-terminal region, which is evolutionarily conserved in a wide range of species, including Caenorhabditis elegans and Drosophila. ZNRF proteins function as E3 ubiquitin ligases and are highly expressed in central nervous system (CNS) and peripheral nervous system (PNS) neurons, particularly during development and in adulthood. ZNRF1 and ZNRF2 are differentially localized within the synaptic region. ZNRF1 is associated with synaptic vesicle membranes, whereas ZNRF2 is present in presynaptic plasma membranes. They are N-myrisotoylated and also located in the endosome-lysosome compartment in fibroblasts. ZNRF proteins may play a role in the establishment and maintenance of neuronal transmission and plasticity via their ubiquitin ligase activity, as well as in regulating Ca2+-dependent exocytosis. The RING fingers found in ZNRF proteins are modified as C4HC2H-type RING-CH finger, rather than the typical C4HC3-type RING-CH finger, which is a variant of the RING-H2 finger. 43 matched cddid_all.tbl CDD cd16490 cd16490 438153 RING-CH-C4HC3_FANCL RING-CH finger, H2 subclass (C4HC3-type), found in Fanconi anemia group L protein (FANCL) and similar proteins. FANCL, also known as fanconi anemia-associated polypeptide of 43 kDa (FAAP43) or PHF9, is a monomeric RING E3 ubiquitin-protein ligase that monoubiquitinates FANCD2 and FANCI. The monoubiquitinated FANCD2-FANCI heterodimer complex in turn recruits key proteins involved in homologous recombination and DNA repair. FANCL is also one of seven components in Fanconi anemia (FA) nuclear core complex, which provides the essential E3 ligase function for spatially defined FANCD2 ubiquitination and FA pathway activation. In the FA core complex, FANCL associates with FANCB and FAAP100 to constitute a catalytic subcomplex that functions as the monoubiquitination module. FANCL specifically interacts with the E2 ubiquitin-conjugating (UBC) enzyme Ube2T to make an E3-E2 pair, which is the catalytic center of the Fanconi Anemia (FA) pathway required for DNA interstrand crosslink repair. Moreover, FANCL has a noncanonical function to regulate the Wnt/beta-catenin signaling, a pathway involved in hematopoietic stem cell self-renewal. It functionally enhances beta-catenin activity by ubiquitinating beta-catenin, with atypical ubiquitin chains (K11 linked). FANCL contains an N-terminal E2-like fold (ELF) domain, a novel double-RWD (DRWD) domain with a clear hydrophobic core, and a C-terminal C4HC3-type RING-CH finger. The DRWD domain is required for substrate binding. The RING-CH finger, also known as vRING or RINGv, is predicted to facilitate E2 binding. It has an unusual arrangement of zinc-coordinating residues. Its cysteines and histidines are arranged in the sequence as C4HC3-type, rather than the C3H2C3-type in canonical RING-H2 finger. 58 matched cddid_all.tbl CDD cd16491 cd16491 438154 RING-CH-C4HC3_LTN1 RING-CH finger, H2 subclass (C4HC3-type), found in E3 ubiquitin-protein ligase listerin and similar proteins. Listerin, also known as RING finger protein 160 or zinc finger protein 294, is the mammalian homolog of yeast Ltn1. It is widely expressed in all tissues, but motor and sensory neurons and neuronal processes in the brainstem and spinal cord are primarily affected in the mutant. Listerin is required for embryonic development and plays an important role in neurodegeneration. It also functions as a critical E3 ligase involving quality control of nonstop proteins. It mediates ubiquitylation of aberrant proteins that become stalled on ribosomes during translation. Ltn1 works with several cofactors to form a large ribosomal subunit-associated quality control complex (RQC), which mediates the ubiquitylation and extraction of ribosome-stalled nascent polypeptide chains for proteasomal degradation. It appears to first associate with nascent chain-stalled 60S subunits together with two proteins of unknown function, Tae2 and Rqc1. Listerin contains a long stretch of HEAT (Huntingtin, Elongation factor 3, PR65/A subunit of protein phosphatase 2A, and TOR) or ARM (Armadillo) repeats in the N terminus and middle region, and a catalytic RING-CH finger, also known as vRING or RINGv, with an unusual arrangement of zinc-coordinating residues in the C-terminus . Its cysteines and histidines are arranged in the sequence as C4HC3-type, rather than the C3H2C3-type in canonical RING-H2 finger. 50 matched cddid_all.tbl CDD cd16492 cd16492 438155 RING-CH-C4HC3_NFX1-like RING-CH finger, H2 subclass (C4HC3-type), found in transcriptional repressor NF-X1, NF-X1-type zinc finger protein NFXL1, and similar proteins. NF-X1, also known as nuclear transcription factor, X box-binding protein 1, is a novel cysteine-rich sequence-specific DNA-binding protein that interacts with the conserved X-box motif of the human major histocompatibility complex (MHC) class II genes via a repeated Cys-His domain. It functions as a cytokine-inducible transcriptional repressor that plays an important role in regulating the duration of an inflammatory response by limiting the period in which class II MHC molecules are induced by interferon gamma (IFN- gamma). NFXL1, also known as NF-X1-type zinc finger protein NFXL1 or ovarian zinc finger protein (OZFP), is encoded by a novel human cytoplasm-distribution zinc finger protein (CDZFP) gene. This subfamily also includes NF-X1 homologs from insects, plants, and fungi. Drosophila melanogaster shuttle craft (STC) is a DNA- or RNA-binding protein required for proper axon guidance in the central nervous system. It functions as a putative transcription factor and plays an essential role in the completion of embryonic development. In contrast to NF-X1, STC contains an RD domain. The Arabidopsis genome encodes two NF-X1 homologs, AtNFXL1 and AtNFXL2, both of which function as regulators of salt stress responses. The AtNFXL1 protein is a nuclear factor that positively affects adaptation to salt stress. It also functions as a negative regulator of the type A trichothecene phytotoxin-induced defense response. AtNFXL2 controls abscisic acid (ABA) levels and suppresses ABA responses. It may also prevent unnecessary and costly stress adaptation under favorable conditions. FKBP12-associated protein 1 (FAP1) is a dosage suppressor of rapamycin toxicity in budding yeast. It is localized in the cytoplasm, but upon rapamycin treatment translocates to the nucleus. FAP1 interacts with FKBP12 in a rapamycin-sensitive manner. It is a proline-rich protein containing a novel cysteine-rich DNA-binding motif. Unique structural features of the NFX1 and NFXL proteins are the Cys-rich region and a specific RING-CH finger motif with an unusual arrangement of zinc-coordinating residues. The Cys-rich region is required for binding to specific promoter elements. It frequently comprises more than 500 amino acids and harbors several NFX1-type zinc finger domains, characterized by the pattern C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C. The RING-CH finger, also known as vRING or RINGv, may have E3 ligase activity. It is characterized by a C4HC3-type Zn ligand signature and additional conserved amino acids, rather than the C3H2C3-type cysteines and histidines arrangement in canonical RING-H2 finger. In addition to the Cys-rich region and RING-CH finger, NFX1 contains a PAM2 motif in the N-terminus and a R3H domain in the C-terminus. 58 matched cddid_all.tbl CDD cd16493 cd16493 438156 RING-CH-C4HC3_NSE1 RING-CH finger, H2 subclass (C4HC3-type), found in non-structural maintenance of chromosomes (SMC) element 1 homolog (NSE1) and similar proteins. NSE1, also known as non-SMC element 1 homolog (NSMCE1), is an E3 ubiquitin ligase that contains a C4HC3-type RING-CH finger, also known as vRING or RINGv, a variant of C3H2C3-type RING-H2 finger. Together with its partner proteins NSE3 and NSE4, it forms a tight subcomplex of the SMC5-6 complex, which includes another two subcomplexes, SMC6-SMC5-NSE2 and NSE5-NSE6. The vRING finger is essential for normal NSE1-NSE3-NSE4 trimer formation in vitro and for damage-induced recruitment of NSE4 and SMC5 to subnuclear foci in vivo. Thus it functions as a protein-protein interaction domain required for SMC5-6 holocomplex integrity and recruitment to, or retention at, DNA lesions. The C-terminal half of NSE1, including the vRING finger, is required for DNA damage resistance and mitotic fidelity of SMC5-6 complex in the fission yeast Schizosaccharomyces pombe. The RING-CH finger may play an important role in Rad52-dependent post-replication repair of UV-damaged DNA in Saccharomyces cerevisiae. 49 matched cddid_all.tbl CDD cd16494 cd16494 438157 RING-CH-C4HC3_ZSWM2 RING-CH finger, H2 subclass (C4HC3-type), found in zinc finger SWIM domain-containing protein 2 (ZSWIM2) and similar proteins. ZSWIM2, also known as MEKK1-related protein X (MEX) or ZZ-type zinc finger-containing protein 2, is a testis-specific E3 ubiquitin ligase that promotes death receptor-induced apoptosis through Fas, death receptor (DR) 3, and DR4 signaling. ZSWIM2 is self-ubiquitinated and targeted for degradation through the proteasome pathway. It also acts as an E3 ubiquitin ligase, through the E2, Ub-conjugating enzymes UbcH5a, UbcH5c, or UbcH6. ZSWIM2 contains four putative zinc-binding domains including an N-terminal SWIM (SWI2/SNF2 and MuDR) domain critical for its ubiquitination and two RING fingers separated by a ZZ zinc finger domain, which was required for interaction with UbcH5a and its self-association. This model corresponds to the first RING finger, which is a C4HC3-type RING-CH finger, also known as vRING or RINGv, rather than the canonical C3H2C3-type RING-H2 finger. 57 matched cddid_all.tbl CDD cd16495 cd16495 438158 RING_CH-C4HC3_MARCH RING-CH finger, H2 subclass (C4HC3-type), found in membrane-associated RING-CH proteins (MARCH). This family of membrane-associated E3 ubiquitin ligases consists of 11 members in mammals (MARCH1-11), which are characterized by containing an N-terminal C4HC3-type RING-CH finger, also known as vRING or RINGv, a variant of the C3H2C3-type RING-H2 finger). Most family members have hydrophobic transmembrane regions and are localized to the plasma membrane and intracellular organelle membrane. Only MARCH7 and MARCH10 are predicted to have no transmembrane spanning region. MARCH proteins have been implicated in mediating the ubiquitination and subsequent down-regulation of cell-surface immune regulatory molecules, such as major histocompatibility complex class II and CD86, as well as in endoplasmic reticulum-associated degradation, endosomal protein trafficking, mitochondrial dynamics, and spermatogenesis. 51 matched cddid_all.tbl CDD cd16496 cd16496 438159 RING-HC_BARD1 RING finger, HC subclass, found in BRCA1-associated RING domain protein 1 (BARD-1) and similar proteins. BARD-1 is a critical factor in BRCA1-mediated tumor suppression and may also serve as a target for tumorigenic lesions in some human cancers. It associates with BRCA1 (breast cancer-1) to form a heterodimeric BRCA1/BARD1 complex that is responsible for maintaining genomic stability through nuclear functions involving DNA damage signaling and repair, transcriptional regulation, and cell cycle control. The BRCA1/BARD1 complex catalyzes autoubiquitination of BRCA1 and trans ubiquitination of other protein substrates. Its E3 ligase activity is dramatically reduced in the presence of UBX domain protein 1 (UBXN1). BARD-1 contains an C3HC4-type RING-HC finger that binds BRCA1 at its N-terminus and three tandem ankyrin repeats and tandem BRCT repeat domains at its C-terminus. The BRCT repeats bind CstF-50 (cleavage stimulation factor) to modulate mRNA processing and RNAP II stability in response to DNA damage. 86 matched cddid_all.tbl CDD cd16497 cd16497 438160 RING-HC_BAR RING finger, HC subclass, found in bifunctional apoptosis regulator (BAR). BAR, also known as RING finger protein 47, was originally identified as an inhibitor of Bax-induced apoptosis. It participates in the block of apoptosis induced by TNF-family death receptors (extrinsic pathway) and mitochondria-dependent apoptosis (intrinsic pathway). BAR is predominantly expressed by neurons in the central nervous system and is involved in the regulation of neuronal survival. It is an endoplasmic reticulum (ER)-associated RING-type E3 ubiquitin ligase that interacts with BI-1 protein and post-translationally regulates its stability, as well as functioning in ER stress. BAR contains an N-terminal C3HC4-type RING-HC finger, a SAM domain, a coiled-coil domain, and a C-terminal transmembrane (TM) domain. This model corresponds to the RING-HC finger responsible for the binding of ubiquitin conjugating enzymes (E2s). 52 matched cddid_all.tbl CDD cd16498 cd16498 438161 RING-HC_BRCA1 RING finger, HC subclass, found in breast cancer type 1 susceptibility protein (BRCA1) and similar proteins. BRCA1, also known as RING finger protein 53 (RNF53), is a RING finger protein encoded by the tumor suppressor gene BRCA1 that regulates all DNA double-strand break (DSB) repair pathways. BRCA1 is frequently mutated in patients with hereditary breast and ovarian cancer (HBOC). Its mutation is also associated with an increased risk of pancreatic, stomach, laryngeal, fallopian tube, and prostate cancer. It plays an important role in the DNA damage response signaling and has been implicated in various cellular processes such as cell cycle regulation, transcriptional regulation, chromatin remodeling, DNA DSBs, and apoptosis. BRCA1 contains an N-terminal C3HC4-type RING-HC finger, and two BRCT (BRCA1 C-terminus domain) repeats at the C-terminus. 94 matched cddid_all.tbl CDD cd16499 cd16499 438162 RING-HC_Bre1-like RING finger, HC subclass, found in yeast Bre1 and its homologs from eukaryotes. Bre1 is an E3 ubiquitin-protein ligase that catalyzes monoubiquitination of histone H2B in concert with the E2 ubiquitin-conjugating enzyme, Rad6. The Rad6-Bre1-mediated histone H2B ubiquitylation modulates the formation of double-strand breaks (DSBs) during meiosis in yeast. it is also required, indirectly, for the methylation of histone 3 on lysine 4 (H3K4) and 79. RNF20, also known as BRE1A and RNF40, also known as BRE1B, are the mammalian homologs of Bre1. They work together to form a heterodimeric Bre1 complex that facilitate the K120 monoubiquitination of histone H2B (H2Bub1), a DNA damage-induced histone modification that is crucial for recruitment of the chromatin remodeler SNF2h to DNA double-strand break (DSB) damage sites. Moreover, the Bre1 complex acts as a tumor suppressor, augmenting expression of select tumor suppressor genes and suppressing select oncogenes. Deficiency in the mammalian histone H2B ubiquitin ligase Bre1 leads to replication stress and chromosomal instability. All subfamily members contain a C3HC4-type RING-HC finger at its C-terminus. 59 matched cddid_all.tbl CDD cd16500 cd16500 438163 RING-HC_CARP RING finger, HC subclass, found in caspases-8 and -10-associated RING finger protein CARP-1, CARP-2 and similar proteins. The CARP subfamily includes CARP-1 and CARP-2 proteins, both of which are E3 ubiquitin ligases that ubiquitinate apical caspases and target them for proteasome-mediated degradation. As a novel group of caspase regulators with a FYVE-type zinc finger domain, they do not localize to membranes in the cell and are involved in the negative regulation of apoptosis, specifically targeting two initiator caspases, caspase 8, and caspase 10. Moreover, they stabilize MDM2 by inhibiting MDM2 self-ubiquitination, as well as by targeting 14-3-3sigma for degradation. They work together with MDM2 to enhance p53 degradation, thereby inhibiting p53-mediated cell death. CARPs contain an N-terminal FYVE-like domain that can serve as a membrane-targeting or endosome localizing signal and a C-terminal C3HC4-type RING-HC finger domain. 48 matched cddid_all.tbl CDD cd16501 cd16501 438164 RING-HC_CblA-like RING finger, HC subclass, found in Dictyostelium discoideum Cbl-like protein A (CblA) and similar proteins. CblA is a Dictyostelium homolog of the Cbl proteins which are multi-domain proteins acting as key negative regulators of various receptor and non-receptor tyrosine kinase signaling. CblA upregulates STATc tyrosine phosphorylation by downregulating PTP3, the protein tyrosine phosphatase responsible for dephosphorylating STATc. STATc is a signal transducer and activator of transcription protein. Like other Cbl proteins, CblA contains a tyrosine-kinase-binding domain (TKB), a proline-rich domain, a C3HC4-type RING-HC finger, and an ubiquitin-associated (UBA) domain. TKB, also known as a phosphotyrosine binding PTB domain, is composed of a four helix-bundle, a Ca2+ binding EF-hand and a highly variant SH2 domain. This family also includes Drosophila melanogaster defense repressor 1 (Dnr1) that was identified as an inhibitor of Dredd activity in the absence of a microbial insult in Drosophila S2 cells. It inhibits the Drosophila initiator caspases Dredd and Dronc. Moreover, Dnr1 acts as a negative regulator of the Imd (immune deficiency) innate immune-response pathway. Its mutations cause neurodegeneration in Drosophila by activating the innate immune response in the brain. Dnr1 contains a FERM N-terminal domain followed by a region rich in glutamine and serine residues, a central FERM domain, and a C-terminal C3HC4-type RING-HC finger. 53 matched cddid_all.tbl CDD cd16502 cd16502 438165 RING-HC_Cbl-like RING finger, HC subclass, found in Casitas B-lineage lymphoma (Cbl) proteins. The Cbl adaptor protein family contains a small class of RING-type E3 ubiquitin ligases with oncogenic activity, which is represented by three mammalian members, c-Cbl, Cbl-b and Cbl-c, as well as two invertebrate Cbl-family proteins, D-Cbl in Drosophila and Sli-1 in C. elegans. Cbl proteins function as potent negative regulators of various signaling cascades in a wide range of cell types. They play roles in ubiquitinating activated tyrosine kinases and targeting them for degradation. D-Cbl associates with the Drosophila epidermal growth factor receptor (EGFR) and overexpression of D-Cbl in the eye of Drosophila embryos inhibits EGFR-dependent photoreceptor cell development. Sli-1 is a negative regulator of the Let-23 receptor tyrosine kinase, an EGFR homolog, in vulva development. Cbl proteins in this subfamily consist of a highly conserved N-terminal half that includes a tyrosine-kinase-binding domain (TKB, also known as the phosphotyrosine binding PTB domain, composed of a four helix-bundle, a Ca2+ binding EF-hand and a highly variant SH2 domain) and a C3HC4-type RING-HC finger, both of which are required for Cbl-mediated downregulation of RTKs, and a divergent C-terminal region. 43 matched cddid_all.tbl CDD cd16503 cd16503 438166 RING-HC_CHFR RING finger, HC subclass, found in checkpoint with forkhead and RING finger domains protein (CHFR). CHFR, also known as RING finger protein 196 (RNF196), is a checkpoint protein that delays entry into mitosis in response to stress. It functions as an E3 ubiquitin ligase that ubiquitinates and degrades its target proteins, such as Aurora-A, Plk1, Kif22, and PARP-1, which are critical for proper mitotic transitions. It also plays an important role in cell cycle progression and tumor suppression, and is negatively regulated by SUMOylation-mediated proteasomal ubiquitylation. Moreover, CHFR is involved in the early stage of the DNA damage response, which mediates the crosstalk between ubiquitination and poly-ADP-ribosylation. CHFR contains a fork head associated (FHA) domain and a C3HC4-type RING-HC finger. 55 matched cddid_all.tbl CDD cd16504 cd16504 438167 RING-HC_COP1 RING finger, HC subclass, found in constitutive photomorphogenesis protein 1 (COP1) and similar proteins. COP1, also known as RING finger and WD repeat domain protein 2 (RFWD2) or RING finger protein 200 (RNF200), is a central regulator of photomorphogenic development in plants, which targets key transcription factors for proteasome-dependent degradation. It is localized predominantly in the nucleus, but may also be present in the cytosol. Mammalian COP1 functions as an E3 ubiquitin-protein ligase that interacts with Jun transcription factors and modulates their transcriptional activity. It also interacts with and negatively regulates the tumor-suppressor protein p53. Moreover, COP1 associates with COP9 signalosome subunit 6 (CSN6), and is involved in 14-3-3sigma ubiquitin-mediated degradation. The CSN6-COP1 link enhances ubiquitin-mediated degradation of p27(Kip1), a critical CDK inhibitor involved in cell cycle regulation, to promote cancer cell growth. Furthermore, COP1 functions as the negative regulator of ETV1 and influences prognosis in triple-negative breast cancer. COP1 contains an N-terminal extension, a C3HC4-type RING-HC finger, a coiled coil domain, and seven WD40 repeats. In human COP1, a classic leucine-rich NES, and a novel bipartite NLS is bridged by the RING-HC finger. 47 matched cddid_all.tbl CDD cd16505 cd16505 438168 RING-HC_CYHR1 RING finger, HC subclass, found in cysteine and histidine-rich protein 1 (CYHR1) and similar proteins. CYHR1, also known as cysteine/histidine-rich protein (Chrp), shows sequence similarity with the Drosophila RING finger protein Seven-in-Absentia (sina) and its murine and human siah homologs. It is a novel prognostic marker that may work as a therapeutic target in patients with esophageal squamous cell carcinoma. It is also a biomarker of the response to erythropoietin in hemodialysis patients. CYHR1 contains an N-terminal C3HC4-type RING-HC finger and a C-terminal tumor necrosis factor (TNF) receptor associated factor (TRAF)-like substrate-binding domain (SBD). 62 matched cddid_all.tbl CDD cd16506 cd16506 438169 RING-HC_DTX3-like RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3), Deltex-3-like (DTX3L) and similar proteins. This subfamily contains Deltex3 (DTX3) and Deltex-3-like (DTX3L), both of which are E3 ubiquitin-protein ligases belonging to the Deltex (DTX) family. DTX3, also known as RING finger protein 154 (RNF154), has a biological function that remains unclear. DTX3L, also known as B-lymphoma- and BAL-associated protein (BBAP) or Rhysin-2 (Rhysin2), regulates endosomal sorting of the G protein-coupled receptor CXCR4 from endosomes to lysosomes. It also regulates subcellular localization of its partner protein, B aggressive lymphoma (BAL), by a dynamic nucleocytoplasmic trafficking mechanism. In contrast to other DTXs, both DTX3 and DTX3L contain a C3HC4-type RING-HC finger, and a previously unidentified C-terminal domain. DTX3L can associate with DTX1 through its unique N termini and further enhance self-ubiquitination. 45 matched cddid_all.tbl CDD cd16507 cd16507 438170 RING-HC_GEFO-like RING finger, HC subclass, found in Dictyostelium discoideum Ras guanine nucleotide exchange factor O (RasGEFO) and similar proteins. RasGEFO, also known as RasGEF domain-containing protein O, functions as a Ras guanine-nucleotide exchange factor (RasGEFs), activating Ras by catalyzing the replacement of GDP with GTP. RasGEFs are particularly important for signaling in development and chemotaxis in many organisms, including Dictyostelium. RasGEFO contains a C3HC4-type RING-HC finger that may be responsible for E3 ubiquitin ligase activity. 58 matched cddid_all.tbl CDD cd16508 cd16508 438171 RING-HC_HAKAI-like RING finger, HC subclass, found in E3 ubiquitin-protein ligase Hakai, zinc finger protein 645 (ZNF645), and similar proteins. Hakai, also known as Casitas B-lineage lymphoma-transforming sequence-like protein 1, RING finger protein 188 (RNF188), or c-Cbl-like protein 1 (CBLL1), is an E3 ubiquitin ligase that disrupts cell-cell contacts in epithelial cells and is upregulated in human colon and gastric adenocarcinomas. It was identified to mediate the posttranslational downregulation of E-cadherin (CDH1), a major component of adherens junctions in epithelial cells and a potent tumor suppressor. It also promotes ubiquitination of several other tyrosine-phosphorylated Src substrates, including cortactin (CTTN) and DOK1. Hakai acts as a homodimer arranged in an anti-parallel configuration with a novel HYB (Hakai pTyr-binding) domain that forms a phosphotyrosine-binding pocket. Each monomer contains a C3HC4-type RING-HC finger and a short pTyr-B domain that incorporates a novel, atypical C2H2-type Zn-finger coordination motif. Both domains are important for dimerization. ZNF645 is a novel testis-specific E3 ubiquitin-protein ligase that plays a role in sperm production and quality control. It has a structure similar to that of the c-Cbl-like protein Hakai. In contrast to Hakai, its HYB domain demonstrates different target specificities. It interacts with v-Src-phosphorylated E-cadherin, but not to cortactin. 51 matched cddid_all.tbl CDD cd16509 cd16509 438172 RING-HC_HLTF RING finger, HC subclass, found in helicase-like transcription factor (HLTF) and similar proteins. HLTF, also known as DNA-binding protein/plasminogen activator inhibitor 1 regulator, HIP116, RING finger protein 80, SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3, or sucrose nonfermenting protein 2-like 3, is a yeast RAD5 homolog found in mammals. It has both E3 ubiquitin ligase and DNA helicase activities, and plays a pivotal role in the template-switching pathway of DNA damage tolerance. It is involved in Lys-63-linked poly-ubiquitination of proliferating cell nuclear antigen (PCNA) at Lys-164 and in the regulation of DNA damage tolerance. It shows double-stranded DNA translocase activity with 3'-5' polarity, thereby facilitating regression of the replication fork. HLTF contains an N-terminal HIRAN (HIP116 and RAD5 N-terminal) domain, a SWI/SNF helicase domain that is divided into N- and C-terminal parts by an insertion of a C3HC4-type RING-HC finger involved in the poly-ubiquitination of PCNA. 53 matched cddid_all.tbl CDD cd16510 cd16510 438173 RING-HC_IAPs RING finger, HC subclass, found in inhibitor of apoptosis proteins (IAPs). IAPs are frequently overexpressed in cancer and associated with tumor cell survival, chemoresistance, disease progression, and poor prognosis. They function primarily as negative regulators of cell death. They regulate caspases and apoptosis through the inhibition of specific members of the caspase family of cysteine proteases. In addition, IAPs has been implicated in a multitude of other cellular processes, including inflammatory signalling and immunity, mitogenic kinase signalling, proliferation and mitosis, as well as cell invasion and metastasis. IAPs in this family includes cellular inhibitor of apoptosis protein c-IAP1 (BIRC2) and c-IAP2 (BIRC3), XIAP (BIRC4), BIRC7, and BIRC8, all of which contain three N-terminal baculoviral IAP repeat (BIR) domains that enable interactions with proteins, a ubiquitin-association (UBA) domain that is responsible for the binding of polyubiquitin (polyUb), and a C3HC4-type RING-HC finger at the carboxyl terminus that is required for ubiquitin ligase activity. The UBA domain is only absent in mammalian homologs of BIRC7. Moreover, c-IAPs contains an additional caspase activation and recruitment domain (CARD) between the UBA and C3HC4-type RING-HC domains. The CARD domain may serve as a protein interaction surface. 40 matched cddid_all.tbl CDD cd16511 cd16511 438174 vRING-HC_IRF2BP1-like variant of RING finger, HC subclass, found in interferon regulatory factor 2-binding protein IRF-2BP1, IRF-2BP2, and similar proteins. This subfamily includes IRF-2BP1, IRF-2BP2, and their homolog, IRF-2BP-like, also known as IRF-2BPL or C14orf4. IRF-2BP1 and IRF-2BP2 are nuclear proteins that bind to the C-terminal repression domain of IRF-2 and act as IRF-2-dependent transcriptional corepressors, both enhancer-activated and basal transcription. IRF-2BPL is expressed in the mediobasal hypothalamus and plays a critical function in regulating the female reproductive neuroendocrine axis. All subfamily members contain a C-terminal variant C3HC4-type RING-HC finger. 56 matched cddid_all.tbl CDD cd16512 cd16512 438175 RING-HC_LNX3-like RING finger, HC subclass, found in ligand of Numb protein LNX3, LNX4, and similar proteins. The ligand of Numb protein X (LNX) family, also known as PDZ and RING (PDZRN) family, includes LNX1-5, which can interact with Numb, a key regulator of neurogenesis and neuronal differentiation. LNX5 (also known as PDZK4, or PDZRN4L) shows high sequence homology to LNX3 and LNX4, but it lacks the RING domain. LNX1-4 proteins function as E3 ubiquitin ligases and have a unique domain architecture consisting of an N-terminal RING-HC finger for E3 ubiquitin ligase activity and either two or four PDZ domains necessary for the substrate-binding. This family corresponds to LNX3/LNX4-like proteins, which contains a C3HC4-type RING-HC finger and two PDZ domains. 43 matched cddid_all.tbl CDD cd16513 cd16513 438176 RING-HC_LONFs_rpt1 first RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger protein family. The LON peptidase N-terminal domain and RING finger protein family includes LONRF1 (also known as RING finger protein 191 or RNF191), LONRF2 (also known as RING finger protein 192, RNF192, or neuroblastoma apoptosis-related protease), LONRF3 (also known as RING finger protein 127 or RNF127), which are characterized by containing two C3HC4-type RING-HC fingers, four tetratricopeptide (TPR) repeats, and an ATP-dependent protease La (LON) substrate-binding domain at the C-terminus. Their biological functions remain unclear. This model corresponds to the first RING-HC finger. 47 matched cddid_all.tbl CDD cd16514 cd16514 438177 RING-HC_LONFs_rpt2 second RING finger, HC subclass, found in the LON peptidase N-terminal domain and RING finger protein family. The LON peptidase N-terminal domain and RING finger protein family includes LONRF1 (also known as RING finger protein 191 or RNF191), LONRF2 (also known as RING finger protein 192, RNF192, or neuroblastoma apoptosis-related protease), LONRF3 (also known as RING finger protein 127 or RNF127), which are characterized by containing two C3HC4-type RING-HC fingers, four tetratricopeptide (TPR) repeats, and an ATP-dependent protease La (LON) substrate-binding domain at the C-terminus. Their biological functions remain unclear. This model corresponds to the second RING-HC finger. 45 matched cddid_all.tbl CDD cd16515 cd16515 438178 RING-HC_LRSAM1 RING finger, HC subclass, found in leucine-rich repeat and sterile alpha motif-containing protein 1 (LRSAM1) and similar proteins. LRSAM1, also known as Tsg101-associated ligase (TAL), or RIFLE, is an E3 ubiquitin-protein ligase that physically associates with, and selectively ubiquitylates, Tsg101, an E2-like molecule that regulates vesicular trafficking processes in yeast and mammals. It regulates a Tsg101-associated complex responsible for the sorting of cargo into cytoplasm-containing vesicles that bud at the multivesicular body and at the plasma membrane. LRSAM1 is a multidomain protein containing an N-terminal leucine-rich repeat (LRR), followed by several recognizable motifs, including an ezrin-radixin-moezin (ERM) domain, a coiled-coil (CC) region, a SAM domain, and a C-terminal C3HC4-type RING-HC finger domain. 48 matched cddid_all.tbl CDD cd16516 cd16516 438179 RING-HC_malin "RING finger, HC subclass, found in malin and similar proteins. Malin (""mal"" for seizure in French), also known as NHL repeat-containing protein 1 (NHLRC1), or EPM2B, is a nuclear E3 ubiquitin-protein ligase that ubiquitinates and promotes the degradation of laforin (EPM2A encoding protein phosphatase). Malin and laforin operate as a functional complex that play key roles in regulating cellular functions such as glycogen metabolism, unfolded cellular stress response, and proteolytic processes. They act as pro-survival factors that negatively regulate the Hipk2-p53 cell death pathway. They also negatively regulate cellular glucose uptake by preventing plasma membrane targeting of glucose transporters. Moreover, they degrade polyglucosan bodies in concert with glycogen debranching enzyme and brain isoform glycogen phosphorylase. Furthermore, they, together with Hsp70, form a new functional complex that suppress the cellular toxicity of misfolded proteins by promoting their degradation through the ubiquitin-proteasome system. Defects in either malin or laforin may cause Lafora disease (LD), a fatal form of teenage-onset autosomal recessive progressive myoclonus epilepsy. In addition, malin may have function, independent of laforin, in lysosomal biogenesis and/or lysosomal glycogen disposal. Malin contains six NHL-repeat protein-protein interaction domains and a C3HC4-type RING-HC finger." 52 matched cddid_all.tbl CDD cd16517 cd16517 438180 RING-HC_MAT1 RING finger, HC subclass, found in RING finger protein MAT1. MAT1, also known as CDK-activating kinase assembly factor MAT1, CDK7/cyclin-H assembly factor, cyclin-G1-interacting protein, menage a trois, RING finger protein 66 (RNF66), p35, or p36, is involved in cell cycle control and in RNA transcription by RNA polymerase II. It associates primarily with the catalytic subunit cyclin-dependent kinase 7 (CDK7) and the regulatory subunit cyclin H to form the CDK-activating kinase (CAK) complex that can further associate with the core-TFIIH to form the transcription factor IIH (TFIIH) basal transcription/DNA repair factor, which activates RNA polymerase II by serine phosphorylation of the repetitive C-terminal domain (CTD) of its large subunit (POLR2A), allowing its escape from the promoter, and elongation of the transcripts. MAT1 contains an N-terminal C3HC4-type RING-HC finger, a central coiled coil domain, and a C-terminal domain rich in hydrophobic residues. 55 matched cddid_all.tbl CDD cd16518 cd16518 438181 RING-HC_MEX3 RING finger, HC subclass, found in RNA-binding proteins of the evolutionarily-conserved MEX-3 family. MEX-3 phosphoproteins are found in vertebrates. They are mediators of post-transcriptional regulation in different organisms, and have been implicated in many core biological processes, including embryonic development, epithelial homeostasis, immune responses, metabolism, and cancer. They contain two K homology (KH) domains that provide RNA-binding capacity, and a C-terminal C3HC4-type RING-HC finger. They shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway. The RNA-binding protein MEX-3 from nematode Caenorhabditis elegans is the founding member of the MEX-3 family. Due to the lack of a RING-HC finger, it is not included here. 53 matched cddid_all.tbl CDD cd16519 cd16519 438182 RING-HC_MIBs RING finger, HC subclass, found in mind bomb MIB1, MIB2, and similar proteins. MIBs are large, multi-domain E3 ubiquitin-protein ligases that promote ubiquitination of the cytoplasmic tails of Notch ligands. They are also responsible for TBK1 K63-linked ubiquitination and activation, promoting interferon production and controlling antiviral immunity. Moreover, MIBs selectively control responses to cytosolic RNA and regulate type I interferon transcription. Both MIB1 and MIB2 have similar domain architectures, which consist of two Mib-Herc2 domains flanking a ZZ zinc finger, a REP region including two tandem Mib repeats, an ANK region that spans ankyrin repeats, and a RNG region, where MIB1 and MIB2 contain three and two C3HC4-type RING-HC fingers, respectively. This model corresponds to the first RING-HC finger of MIB1 and MIB2, as well as the second RING-HC finger of MIB1. 38 matched cddid_all.tbl CDD cd16520 cd16520 438183 RING-HC_MIBs-like RING finger, HC subclass, found in mind bomb MIB1, MIB2, RGLG1, RGLG2, and similar proteins. MIBs are large, multi-domain E3 ubiquitin-protein ligases that promote ubiquitination of the cytoplasmic tails of Notch ligands. They are also responsible for TBK1 K63-linked ubiquitination and activation, promoting interferon production and controlling antiviral immunity. Moreover, MIBs selectively control responses to cytosolic RNA and regulate type I interferon transcription. Both MIB1 and MIB2 have similar domain architectures, which consist of two Mib-Herc2 domains flanking a ZZ zinc finger, a REP region including two tandem Mib repeats, an ANK region that spans ankyrin repeats, and a RNG region, where MIB1 and MIB2 contain three and two C3HC4-type RING-HC fingers, respectively. This model corresponds to the third RING-HC finger of MIB1, as well as the second RING-HC finger of MIB2. In addition to MIB1 and MIB2, the RING-HC fingers of RING domain ligase RGLG1, RGLG2 and similar proteins from plant are also included in this model. RGLG1 is a ubiquitously expressed E3 ubiquitin-protein ligase that interacts with UBC13 and, together with UBC13, catalyzes the formation of K63-linked polyubiquitin chains, which is involved in DNA damage repair. RGLG1 mediates the formation of canonical, K48-linked polyubiquitin chains that target proteins for degradation. It also regulates apical dominance by acting on the auxin transport proteins abundance. RGLG1 has overlapping functions with its closest sequelog, RGLG2. They both function as RING E3 ligases that interact with ethylene response factor 53 (ERF53) in the nucleus and negatively regulate the plant drought stress response. All RGLG proteins contain a Von Willebrand factor type A (vWA) domain and a C3HC4-type RING-HC finger. 39 matched cddid_all.tbl CDD cd16521 cd16521 438184 RING-HC_MKRN RING finger, HC subclass, found in the makorin (MKRN) proteins. The MKRN protein subfamily includes ribonucleoproteins that are characterized by a variety of zinc-finger motifs, including typical arrays of one to four C3H1-type zinc fingers and a C3HC4-type RING-HC finger. Another motif rich in Cys and His residues (CH), with so far unknown function, is also generally present in MKRN proteins. MKRN proteins may have E3 ubiquitin ligase activity. 53 matched cddid_all.tbl CDD cd16522 cd16522 438185 RING-HC_MSL2 RING finger found in Drosophila melanogaster male-specific lethal-2 (MSL2) and similar proteins. MSL2, also known as RING finger protein 184 (RNF184), is a putative DNA-binding protein required for X chromosome dosage compensation in Drosophila males. Its expression is sex specifically regulated by Sex-lethal. Drosophila dosage compensation proteins MOF, MSL1, MSL2, and MSL3 are essential for elevating transcription of the single X chromosome in the male (X chromosome dosage compensation). MSL2 plays a critical role in translation and/or stability of MSL1 in males. In complex with MSL1, it acts as an E3 ubiquitin ligase that promotes ubiquitination of histone H2B. MSL2 contains a C3HC4-type RING-HC finger and a metallothionein-like domain with eight conserved and two non-conserved cysteines, as well as a positively and a negatively charged amino acid residue cluster and a coiled coil domain that may be involved in protein-protein interactions. This subfamily also includes many male-specific lethal-2 homologs from bilaterians. 60 matched cddid_all.tbl CDD cd16523 cd16523 438186 RING-HC_MYLIP RING finger, HC subclass, found in myosin regulatory light chain interacting protein (MYLIP) and similar proteins. MYLIP, also known as inducible degrader of the low-density lipoprotein (LDL)-receptor (IDOL), or MIR, is an E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of myosin regulatory light chain (MRLC), LDLR, VLDLR, and LRP8. Its activity depends on E2 ubiquitin-conjugating enzymes of the UBE2D family. MYLIP stimulates clathrin-independent endocytosis and acts as a sterol-dependent inhibitor of cellular cholesterol uptake by binding directly to the cytoplasmic tail of the LDLR and promoting its ubiquitination via the UBE2D1/E1 complex. The ubiquitinated LDLR then enters the multivesicular body (MVB) protein-sorting pathway and is shuttled to the lysosome for degradation. Moreover, MYLIP has been identified as a novel ERM-like protein that affects cytoskeleton interactions regulating cell motility, such as neurite outgrowth. The ERM proteins includes ezrin, radixin, and moesin, which are cytoskeletal effector proteins linking actin to membrane-bound proteins at the cell surface. MYLIP contains an ERM-homology domain and a C-terminal C3HC4-type RING-HC finger. 52 matched cddid_all.tbl CDD cd16524 cd16524 438187 RING-HC_NHL-1-like RING finger, HC subclass, found in Caenorhabditis elegans RING finger protein NHL-1 and similar proteins. NHL-1 functions as an E3 ubiquitin-protein ligase in the presence of both UBC-13 and UBC-1 within the ubiquitin pathway of Caenorhabditis elegans. It acts in chemosensory neurons to promote stress resistance in distal tissues by the transcription factor DAF-16 activation but is dispensable for the activation of heat shock factor 1 (HSF-1). NHL-1 belongs to the TRIM (tripartite motif)-NHL family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as an NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. 53 matched cddid_all.tbl CDD cd16525 cd16525 438188 RING-HC_PCGF RING finger, HC subclass, found in Polycomb Group RING finger homologs (PCGF1, 2, 3, 4, 5 and 6), and similar proteins. This subfamily includes six Polycomb Group (PcG) RING finger homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) that use epigenetic mechanisms to maintain or repress expression of their target genes. They were first discovered in fruit flies and are well known for silencing Hox genes through modulation of chromatin structure during embryonic development. PCGF homologs play important roles in cell proliferation, differentiation, and tumorigenesis. They all have been found to associate with ring finger protein 2 (RNF2). The RNF2-PCGF heterodimer is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. Moreover, PCGF homologs are critical components in the assembly of distinct Polycomb Repression Complex 1 (PRC1) related complexes which is involved in the maintenance of gene repression and which target different genes through distinct mechanisms. The Drosophila PRC1 core complex is formed by the Polycomb (Pc), Polyhomeotic (Ph), Posterior sex combs (Psc), and Sex combs extra (Sce, also known as Ring) subunits. In mammals, the composition of PRC1 is much more diverse and varies depending on the cellular context. All PRC1 complexes contain homologs of the Drosophila Ring protein. Ring1A/RNF1 and Ring1B/RNF2 are E3 ubiquitin ligases that mark lysine 119 of histone H2A with a single ubiquitin group (H2AK119ub). Mammalian homologs of the Drosophila Psc protein, such as PCGF2/Mel-18 or PCGF4/BMI1, regulate PRC1 enzymatic activity. PRC1 complexes can be divided into at least two classes according to the presence or absence of CBX proteins, which are homologs of Drosophila Pc. Canonical PRC1 complexes contain CBX proteins that recognize and bind H3K27me3, the mark deposited by PRC2. Therefore, canonical PRC1 complexes and PRC2 can act together to repress gene transcription and maintain this repression through cell division. Non-canonical PRC1 complexes, containing RYBP (together with additional proteins, such as L3mbtl2 or Kdm2b) rather than the CBX proteins have recently been described in mammals. PCGF homologs contain a C3HC4-type RING-HC finger. 42 matched cddid_all.tbl CDD cd16526 cd16526 438189 RING-HC_PEX2 RING finger, HC subclass, found in peroxin-2 (PEX2) and similar proteins. PEX2, also known as peroxisome biogenesis factor 2, 35 kDa peroxisomal membrane protein, peroxisomal membrane protein 3, peroxisome assembly factor 1 (PAF-1), or RING finger protein 72 (RNF72), is an integral peroxisomal membrane protein with two transmembrane regions and a C3HC4-type RING-HC finger within its cytoplasmically exposed C-terminus. It may be involved in the biogenesis of peroxisomes, as well as in peroxisomal matrix protein import. Mutations in the PEX2 gene are the primary defect in a subset of patients with Zellweger syndrome and related peroxisome biogenesis disorders. Moreover, PEX2 functions as an E3-ubiquitin ligase that mediates the UBC4-dependent polyubiquitination of PEX5, a key player in peroxisomal matrix protein import, to control PEX5 receptor recycling or degradation. 49 matched cddid_all.tbl CDD cd16527 cd16527 438190 RING-HC_PEX10 RING finger, HC subclass, found in peroxin-10 (PEX10) and similar proteins. PEX10, also known as peroxisome biogenesis factor 10, peroxisomal biogenesis factor 10, peroxisome assembly protein 10, or RING finger protein 69 (RNF69), is an integral peroxisomal membrane protein with two transmembrane regions and a C3HC4-type RING-HC finger within its cytoplasmically exposed C-terminus. It plays an essential role in peroxisome assembly, import of target substrates, and recycling or degradation of protein complexes and amino acids. It is an essential component of the spinal locomotor circuit, and thus its mutations may be involved in peroxisomal biogenesis disorders (PBD). Mutations in human PEX10 also result in autosomal recessive ataxia. Moreover, PEX10 functions as an E3-ubiquitin ligase with an E2, UBCH5C. It mono- or poly-ubiquitinates PEX5, a key player in peroxisomal matrix protein import, in a UBC4-dependent manner, to control PEX5 receptor recycling or degradation. It also links the E2 ubiquitin conjugating enzyme PEX4 to the protein import machinery of the peroxisome. 52 matched cddid_all.tbl CDD cd16528 cd16528 438191 RING-HC_prokRING RING finger, HC subclass, found in prokaryotic RING finger family proteins. The family corresponds to a group of uncharacterized prokaryotic C3HC4-type RING-HC finger containing proteins. The RING finger is fused to an N-terminal alpha-helical domain, ROT/Trove-like repeats, and a C-terminal TerD domain, suggesting a possible role in an RNA-processing complex. 42 matched cddid_all.tbl CDD cd16529 cd16529 438192 RING-HC_RAD18 RING finger, HC subclass, found in postreplication repair protein RAD18 and similar proteins. RAD18, also known as HR18 or RING finger protein 73 (RNF73), is an E3 ubiquitin-protein ligase involved in post replication repair of UV-damaged DNA via its recruitment to stalled replication forks. It associates to the E2 ubiquitin conjugating enzyme UBE2B to form the UBE2B-RAD18 ubiquitin ligase complex involved in mono-ubiquitination of DNA-associated PCNA on K164. It also interacts with another E2 ubiquitin conjugating enzyme RAD6 to form a complex that monoubiquitinates proliferating cell nuclear antigen at stalled replication forks in DNA translesion synthesis. Moreover, Rad18 is a key factor in double-strand break DNA damage response (DDR) pathways via its association with K63-linked polyubiquitylated chromatin proteins. It can function as a mediator for DNA damage response signals to activate the G2/M checkpoint in order to maintain genome integrity and cell survival after ionizing radiation (IR) exposure. RAD18 contains a C3HC4-type RING-HC finger, a ubiquitin-binding zinc finger domain (UBZ), a SAP (SAF-A/B, Acinus and PIAS) domain, and a RAD6-binding domain (R6BD). 54 matched cddid_all.tbl CDD cd16530 cd16530 319444 RING-HC_RAG1 RING finger, HC subclass, found in recombination activating gene-1 (RAG-1) and similar proteins. RAG-1, also known as V(D)J recombination-activating protein 1, RING finger protein 74 (RNF74), or endonuclease RAG1, is the catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination. RAG1 is a lymphoid-specific factor that mediates DNA-binding to conserved recombination signal sequences (RSS) and catalyzes DNA cleavage activities by introducing a double-strand break between the RSS and the adjacent coding segment. It also functions as an E3 ubiquitin-protein ligase that mediates monoubiquitination of histone H3, which is required for the joining step of V(D)J recombination. RAG-1 contains an N-terminal C3HC4-type RING-HC finger that mediates monoubiquitylation of histone H3, an adjacent C2H2-type zinc finger, and a nonamer binding (NBD) DNA-binding domain. 46 matched cddid_all.tbl CDD cd16531 cd16531 438193 RING-HC_RING1-like RING finger, HC subclass, found in really interesting new gene proteins RING1, RING2 and similar proteins. RING1, also known as polycomb complex protein RING1, RING finger protein 1 (RNF1), or RING finger protein 1A (RING1A), is a transcriptional repressor that is associated with the Polycomb group (PcG) protein complex involved in stable repression of gene activity. RING2, also known as huntingtin-interacting protein 2-interacting protein 3, HIP2-interacting protein 3, protein DinG, RING finger protein 1B (RING1B), RING finger protein 2 (RNF2), or RING finger protein BAP-1, is an E3 ubiquitin-protein ligase that interacts with both nucleosomal DNA and an acidic patch on histone H4 to achieve the specific monoubiquitination of K119 on histone H2A (H2AK119ub), thereby playing a central role in histone code and gene regulation. Both RING1 and RING2 are core components of polycomb repressive complex 1 (PRC1) that functions as an E3-ubuiquitin ligase transferring the mono-ubuiquitin mark to the C-terminal tail of Histone H2A at K118/K119. PRC1 is also capable of chromatin compaction, a function not requiring histone tails, and this activity appears important in gene silencing. RING2 acts as the main E3 ubiquitin ligase on histone H2A of the PRC1 complex, while RING1 may rather act as a modulator of RNF2/RING2 activity. Members of this family contain a C3HC4-type RING-HC finger. 66 matched cddid_all.tbl CDD cd16532 cd16532 438194 RING-HC_RNFT1-like RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein RNFT1, RNFT2, and similar proteins. Both RNFT1 and RNFT2 are multi-pass membrane proteins containing a C3HC4-type RING-HC finger. Their biological roles remain unclear. 41 matched cddid_all.tbl CDD cd16533 cd16533 438195 RING-HC_RNF4 RING finger, HC subclass, found in RING finger protein 4 (RNF4) and similar proteins. RNF4, also known as small nuclear ring finger protein (SNURF), is a SUMO-targeted E3 ubiquitin-protein ligase with a pivotal function in the DNA damage response (DDR) by interacting with the deubiquitinating enzyme ubiquitin-specific protease 11 (USP11), a known DDR-component, and further facilitating DNA repair. It plays a novel role in preventing the loss of intact chromosomes and ensures the maintenance of chromosome integrity. Moreover, RNF4 is responsible for the UbcH5A-catalyzed formation of K48 chains that target SUMO-modified promyelocytic leukemia (PML) protein for proteasomal degradation in response to arsenic treatment. It also interacts with telomeric repeat binding factor 2 (TRF2) in a small ubiquitin-like modifier (SUMO)-dependent manner and preferentially targets SUMO-conjugated TRF2 for ubiquitination through SUMO-interacting motifs (SIMs). Furthermore, RNF4 can form a complex with a Ubc13-ubiquitin conjugate and Ube2V2. It catalyzes K63-linked polyubiquitination by the Ube2V2-Ubc13 (ubiquitin-loaded) complex. Meanwhile, RNF4 negatively regulates nuclear factor kappa B (NF-kappaB) signaling by down-regulating transforming growth factor beta (TGF-beta)-activated kinase 1 (TAK1)-TAK1-binding protein2 (TAB2). RNF4 contains four SIMs followed by a C3HC4-type RING-HC finger at the C-terminus. 57 matched cddid_all.tbl CDD cd16534 cd16534 438196 RING-HC_RNF5-like RING finger, HC subclass, found in RING finger protein RNF5, RNF185 and similar proteins. RNF5 and RNF185 are E3 ubiquitin-protein ligases that are anchored to the outer membrane of the endoplasmic reticulum (ER). RNF5 acts at early stages of cystic fibrosis (CF) transmembrane conductance regulator (CFTR) biosynthesis, and functions as a target for therapeutic modalities to antagonize mutant CFTR proteins in CF patients carrying the F508del allele. RNF185 controls the degradation of CFTR and CFTR F508del allele in a RING- and proteasome-dependent manner, but does not control that of other classical endoplasmic reticulum-associated degradation (ERAD) model substrates. Moreover, both RNF5 and RNF185 play important roles in cell adhesion and migration through the modulation of cell migration by ubiquitinating paxillin. Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) are also included in this family. They possess E3 ubiquitin-protein ligase activity and may play a role in the growth and development of Arabidopsis. All members of this family contain a C3HC4-type RING-HC finger. 44 matched cddid_all.tbl CDD cd16535 cd16535 438197 RING-HC_RNF8 RING finger, HC subclass, found in RING finger protein 8 (RNF8) and similar proteins. RNF8 is a telomere-associated E3 ubiquitin-protein ligase that plays an important role in DNA double-strand break (DSB) repair via histone ubiquitination. It is localized in the nucleus and interacts with class III E2s (UBE2E2, UbcH6, and UBE2E3), but not with other E2s (UbcH5, UbcH7, UbcH10, hCdc34, and hBendless). It recruits UBC13 for lysine 63-based self polyubiquitylation. Its deficiency causes neuronal pathology and cognitive decline, and its loss results in neuron degeneration. RNF8, together with RNF168, catalyzes a series of ubiquitylation events on substrates such as H2A and H2AX, with the H2AK13/15 ubiquitylation being particularly important for recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of DSBs. RNF8 mediates the ubiquitination of gammaH2AX, and recruits 53BP1 and BRCA1 to DNA damage sites which promotes DNA damage response (DDR) and inhibits chromosomal instability. Moreover, RNF8 interacts with retinoid X receptor alpha (RXR alpha) and enhances its transcription-stimulating activity. It also regulates the rate of exit from mitosis and cytokinesis. RNF8 contains an N-terminal forkhead-associated (FHA) domain and a C-terminal C3HC4-type RING-HC finger. 64 matched cddid_all.tbl CDD cd16536 cd16536 438198 RING-HC_RNF10 RING finger, HC subclass, found in RING finger protein 10 (RNF10) and similar proteins. RNF10 is an E3 ubiquitin-protein ligase that interacts with mesenchyme Homeobox 2 (MEOX2) transcription factor, a regulator of the proliferation, differentiation and migration of vascular smooth muscle cells and cardiomyocytes; it enhances Meox2 activation of the p21 promoter. It also regulates the expression of myelin-associated glycoprotein (MAG) genes and is required for myelin production in Schwann cells of the peripheral nervous system. Moreover, RNF10 regulates retinoic acid-induced neuronal differentiation and the cell cycle exit of P19 embryonic carcinoma cells. RNF10 contains a C3HC4-type RING-HC finger and three putative nuclear localization signals. 54 matched cddid_all.tbl CDD cd16537 cd16537 438199 RING-HC_RNF37 RING finger, HC subclass, found in RING finger protein 37 (RNF37). RNF37, also known as KIAA0860, U-box domain-containing protein 5 (UBOX5), UbcM4-interacting protein 5 (UIP5), or ubiquitin-conjugating enzyme 7-interacting protein 5, is an E3 ubiquitin-protein ligase found exclusively in the nucleus as part of a nuclear dot-like structure. It interacts with the molecular chaperone VCP/p97 protein. RNF37 contains a U-box domain followed by a potential nuclear location signal (NLS) and a C-terminal C3HC4-type RING-HC finger. The U-box domain is a modified RING finger domain that lacks the hallmark metal-chelating cysteines and histidines of the latter, and is likely to adopt a RING finger-like conformation. The presence of the U-box, but not of the RING finger, is required for the E3 activity. The U-box domain can directly interact with several E2 enzymes, including UbcM2, UbcM3, UbcM4, UbcH5, and UbcH8, suggesting a similar function as the RING finger in the ubiquitination pathway. This model corresponds to the RING-HC finger. 52 matched cddid_all.tbl CDD cd16538 cd16538 438200 RING-HC_RNF112 RING finger, HC subclass, found in RING finger protein 112 (RNF112) and similar proteins. RNF112, also known as brain finger protein (BFP), zinc finger protein 179 (ZNF179), or neurolastin, is a peripheral membrane protein that is predominantly expressed in the central nervous system and localizes to endosomes. It contains functional GTPase and C3HC4-type RING-HC finger domains and has been identified as a brain-specific dynamin family GTPase that affects endosome size and spine density. Moreover, RNF112 acts as a downstream target of sigma-1 receptor (Sig-1R) regulation and may play a novel role in neuroprotection by mediating the neuroprotective effects of dehydroepiandrosterone (DHEA) and its sulfated analog (DHEAS). 52 matched cddid_all.tbl CDD cd16539 cd16539 438201 RING-HC_RNF113A_B RING finger, HC subclass, found in RING finger proteins RNF113A, RNF113B, and similar proteins. RNF113A, also known as zinc finger protein 183 (ZNF183), is an E3 ubiquitin-protein ligase that physically interacts with the E2 protein, UBE2U. A nonsense mutation in RNF113A is associated with an X-linked trichothiodystrophy (TTD). Its yeast ortholog Cwc24p is predicted to have a spliceosome function and acts in a complex with Cef1p to participate in pre-U3 snoRNA splicing, indirectly affecting pre-rRNA processing. It is also important for the U2 snRNP binding to primary transcripts and co-migrates with spliceosomes. Moreover, the ortholog of RNF113A in fruit flies may also act as a spliceosome and is hypothesized to be involved in splicing, namely within the central nervous system. The ortholog in Caenorhabditis elegans is involved in DNA repair of inter-strand crosslinks. RNF113B, also known as zinc finger protein 183-like 1, shows high sequence similarity with RNF113A. Both RNF113A and RNF113B contain a CCCH-type zinc finger, which is commonly found in RNA-binding proteins involved in splicing, and a C3HC4-type RING-HC finger, which is frequently found in E3 ubiquitin ligases. 54 matched cddid_all.tbl CDD cd16540 cd16540 438202 RING-HC_RNF114 RING finger, HC subclass, found in RING finger protein 114 (RNF114) and similar proteins. RNF114, also known as zinc finger protein 228 (ZNF228) or zinc finger protein 313 (ZNF313), is a p21(WAF1)-targeting ubiquitin E3 ligase that interacts with X-linked inhibitor of apoptosis (XIAP)-associated factor 1 (XAF1) and may play a role in p53-mediated cell-fate decisions. It is involved in the immune response to double-stranded RNA in disease pathogenesis. Moreover, RNF114 interacts with A20 and modulates its ubiquitylation. It negatively regulates nuclear factor-kappaB (NF-kappaB)-dependent transcription and positively regulates T-cell activation. RNF114 may play a putative role in the regulation of immune responses, since it corresponds to a novel psoriasis susceptibility gene, ZNF313. RNF114, together with three closely related proteins: RNF125, RNF138 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM). 46 matched cddid_all.tbl CDD cd16541 cd16541 438203 RING-HC_RNF123 RING finger, HC subclass, found in RING finger protein 123 (RNF123) and similar proteins. RNF123, also known as Kip1 ubiquitination-promoting complex protein 1 (KPC1), is an E3 ubiquitin-protein ligase that mediates ubiquitination and proteasomal processing of the nuclear factor-kappaB 1 (NF-kappaB1) precursor p105 to the p50 active subunit that restricts tumor growth. It also regulates degradation of heterochromatin protein 1alpha (HP1alpha) and 1beta (HP1beta) in lamin A/C knock-down cells. Moreover, RNF123, together with Kip1 ubiquitylation-promoting complex 2 (KPC2), forms the Kip1 ubiquitination-promoting complex (KPC), acting as a cytoplasmic ubiquitin ligase that regulates degradation of the cyclin-dependent kinase inhibitor p27 (Kip1) at the G1 phase of the cell cycle. RNF123 may also function as a clinically relevant, peripheral state marker of depression. RNF123 contains a C3HC4-type RING-HC finger at the C-terminus. 44 matched cddid_all.tbl CDD cd16542 cd16542 438204 RING-HC_RNF125 RING finger, HC subclass, found in RING finger protein 125 (RNF125). RNF125, also known as T-cell RING activation protein 1 (TRAC-1), is an E3 ubiquitin-protein ligase that is predominantly expressed in lymphoid cells, and functions as a positive regulator of T cell activation. It also down-modulates HIV replication and inhibits pathogen-induced cytokine production. It negatively regulates type I interferon signaling, which conjugates Lys(48)-linked ubiquitination to retinoic acid-inducible gene-I (RIG-I) and subsequently leads to the proteasome-dependent degradation of RIG-I. Further, RNF125 conjugates ubiquitin to melanoma differentiation-associated gene 5 (MDA5), a family protein of RIG-I. It thus acts as a negative regulator of RIG-I signaling, and is a direct target of miR-15b in the context of Japanese encephalitis virus (JEV) infection. Moreover, RNF125 binds to and ubiquitinates JAK1, prompting its degradation and inhibition of receptor tyrosine kinase (RTK) expression. It also negatively regulates p53 function through physical interaction and ubiquitin-mediated proteasome degradation. Mutations in RNF125 may lead to overgrowth syndromes (OGS). RNF125, together with three closely related proteins: RNF114, RNF138 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM). The UIM of RNF125 binds K48-linked poly-ubiquitin chains and is, together with the RING domain, required for auto-ubiquitination. 50 matched cddid_all.tbl CDD cd16543 cd16543 438205 RING-HC_TRIM77_C-IV RING finger, HC subclass, found in tripartite motif-containing protein 77 (TRIM77) and similar proteins. TRIM77 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including two consecutive zinc-binding domains, a C3HC4-type RING-HC finger and Bbox2, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. 54 matched cddid_all.tbl CDD cd16544 cd16544 438206 RING-HC_RNF138 RING finger, HC subclass, found in RING finger protein 138 (RNF138) and similar proteins. RNF138, also known as Nemo-like kinase-associated RING finger protein (NARF) or NLK-associated RING finger protein, is an E3 ubiquitin-protein ligase that plays an important role in glioma cell proliferation, apoptosis, and cell cycle. It specifically cooperates with the E2 conjugating enzyme E2-25K (Hip-2/UbcH1), regulates the ubiquitylation and degradation of T cell factor/lymphoid enhancer factor (TCF/LEF), and further suppresses Wnt-beta-catenin signaling. RNF138, together with three closely related proteins: RNF114, RNF125 and RNF166, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM). 53 matched cddid_all.tbl CDD cd16545 cd16545 438207 RING-HC_RNF141 RING finger, HC subclass, found in RING finger protein 141 (RNF141) and similar proteins. RNF141, also known as zinc finger protein 230 (ZNF230), is a RING finger protein present primarily in the nuclei of spermatogonia, the acrosome, and the tail of spermatozoa. It may have a broad function during early development of vertebrates. It plays an important role in spermatogenesis, including spermatogenic cell proliferation and sperm maturation, as well as motility and fertilization. It also exhibits DNA binding activity. RNF141/ZNF230 gene mutations may be associated with azoospermia. RNF141 contains a C3HC4-type RING finger domain that may function as an activator module in transcription. 40 matched cddid_all.tbl CDD cd16546 cd16546 438208 RING-HC_RNF146 RING finger, HC subclass, found in RING finger protein 146 (RNF146) and similar proteins. RNF146, also known as dactylidin, or iduna, is a cytoplasmic E3 ubiquitin-protein ligase that is responsible for PARylation-dependent ubiquitination (PARdU). It displays neuroprotective property due to its inhibition of Parthanatos, a PAR dependent cell death, via binding with Poly(ADP-ribose) (PAR). It also modulates PAR polymerase-1 (PARP-1)-mediated oxidative cell injury in cardiac myocytes. Moreover, RNF146 mediates tankyrase-dependent degradation of axin, thereby positively regulating Wnt signaling. It also facilitates DNA repair and protects against cell death induced by DNA damaging agents or gamma-irradiation by translocating to the nucleus after cellular injury and promoting the ubiquitination and degradation of various nuclear proteins involved in DNA damage repair. Furthermore, RNF146 is implicated in neurodegenerative disease and cancer development. It regulates the development and progression of non-small cell lung cancer (NSCLC) by enhancing cell growth, invasion, and survival. RNF146 contains an N-terminal C3HC4-type RING-HC finger followed by a WWE domain with a poly(ADP-ribose) (PAR) binding motif at the tail. 50 matched cddid_all.tbl CDD cd16547 cd16547 438209 RING-HC_RNF151 RING finger, HC subclass, found in RING finger protein 151 (RNF151) and similar proteins. RNF151 is a testis-specific RING finger protein that interacts with dysbindin, a synaptic and microtubular protein that binds brain snapin, a SNARE-binding protein that mediates intracellular membrane fusion in both neuronal and non-neuronal cells. Thus, it may be involved in acrosome formation of spermatids by interacting with multiple proteins participating in membrane biogenesis and microtubule organization. RNF151 contains a C3HC4-type RING finger domain, a putative nuclear localization signal (NLS), and a TNF receptor associated factor (TRAF)-type zinc finger domain. 49 matched cddid_all.tbl CDD cd16548 cd16548 438210 RING-HC_RNF152 RING finger, HC subclass, found in RING finger protein 152 (RNF152) and similar proteins. RNF152 is a lysosome-anchored E3 ubiquitin-protein ligase involved in apoptosis. It is polyubiquitinated through K48 linkage. It negatively regulates the activation of the mTORC1 pathway by targeting RagA GTPase for K63-linked ubiquitination. It interacts with and ubiquitinates RagA in an amino-acid-sensitive manner. The ubiquitination of RagA recruits its inhibitor GATOR1, a GAP complex for Rag GTPases, to the Rag complex, thereby inactivating mTORC1 signaling. RNF152 contains an N-terminal C3HC4-type RING-HC finger and a C-terminal transmembrane domain, both of which are responsible for its E3 ligase activity. 46 matched cddid_all.tbl CDD cd16549 cd16549 438211 RING-HC_RNF166 RING finger, HC subclass, found in RING finger protein 166 (RNF166) and similar proteins. RNF166 is encoded by the gene RNF166 targeted by thyroid hormone receptor alpha1 (TRalpha1), which is important in brain development. It plays an important role in RNA virus-induced interferon-beta production by enhancing the ubiquitination of TRAF3 and TRAF6. RNF166, together with three closely related proteins: RNF114, RNF125 and RNF138, forms a novel family of ubiquitin ligases with a C3HC4-type RING-HC finger, a C2HC-, and two C2H2-type zinc fingers, as well as a ubiquitin interacting motif (UIM). 47 matched cddid_all.tbl CDD cd16550 cd16550 438212 RING-HC_RNF168 RING finger, HC subclass, found in RING finger protein 168 (RNF168) and similar proteins. RNF168 is an E3 ubiquitin-protein ligase that promotes noncanonical K27 ubiquitination to signal DNA damage. It, together with RNF8, functions as a DNA damage response (DDR) factor that promotes a series of ubiquitylation events on substrates, such as H2A and H2AX with H2AK13/15 ubiquitylation, facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. Moreover, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. RNF168 contains an N-terminal C3HC4-type RING-HC finger that catalyzes H2A-K15ub and interacts with H2A, and two MIU (motif interacting with ubiquitin) domains responsible for the interaction with K63 linked poly-ubiquitin. 48 matched cddid_all.tbl CDD cd16551 cd16551 438213 RING-HC_RNF169 RING finger, HC subclass, found in RING finger protein 169 (RNF169) and similar proteins. RNF169 is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. RNF169 recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to regulation of the DSB repair pathway utilization via functionally competing with recruiting repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin independent of its catalytic activity, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. RNF169 contains an N-terminal C3HC4-type RING-HC finger and a C-terminal MIU (motif interacting with ubiquitin) domain. 55 matched cddid_all.tbl CDD cd16552 cd16552 438214 RING-HC_NEURL3 RING finger, HC subclass, found in neuralized-like protein 3 (NEURL3) and similar proteins. NEURL3, also known as lung-inducible neuralized-related C3HC4 RING domain protein (LINCR), is a novel inflammation-induced E3 ubiquitin-protein ligase encoded by LINCR, a glucocorticoid-attenuated response gene induced in the lung during endotoxemia. It is expressed in alveolar epithelial type II cells, preferentially interacts with the ubiquitin-conjugating enzyme UbcH6, and generates polyubiquitin chains linked via non-canonical lysine residues. Overexpression of NEURL3 in the developing lung epithelium inhibits distal differentiation and induces cystic changes in the Notch signaling pathway. NEURL3 contains an N-terminal neuralized homology repeat (NHR) domain similar to the SPRY (SPla and the RYanodine receptor) domain and a C-terminal C3HC4-type RING-HC finger. 50 matched cddid_all.tbl CDD cd16553 cd16553 438215 RING-HC_RNF170 RING finger, HC subclass, found in RING finger protein 170 (RNF170) and similar proteins. RNF170, also known as putative LAG1-interacting protein, is an endoplasmic reticulum (ER) membrane-bound E3 ubiquitin-protein ligase that mediates ubiquitination-dependent degradation of type-I inositol 1,4,5-trisphosphate (IP3) receptors (ITPR1) via the endoplasmic-reticulum-associated protein degradation (ERAD) pathway. A point mutation (arginine to cysteine at position 199) in the RNF170 gene is linked with autosomal-dominant sensory ataxia (ADSA), a disease characterized by neurodegeneration in the posterior columns of the spinal cord. RNF170 contains a C3HC4-type RING-HC finger. 57 matched cddid_all.tbl CDD cd16554 cd16554 438216 RING-HC_RNF180 RING finger, HC subclass, found in RING finger protein 180 (RNF180) and similar proteins. RNF180, also known as Rines, is a membrane-bound E3 ubiquitin-protein ligase well conserved among vertebrates. It is a critical regulator of the monoaminergic system, as well as emotional and social behavior. It interacts with brain monoamine oxidase A (MAO-A) and targets it for ubiquitination and degradation. It also functions as a novel tumor suppressor in gastric carcinogenesis. The hypermethylated CpG site count of the RNF180 DNA promoter can be used to predict survival of gastric cancer. RNF180 contains a novel conserved dual specificity protein phosphatase Rines conserved (DSPRC) domain, a basic coiled-coil domain, a C3HC4-type RING-HC finger, and a C-terminal hydrophobic region that is predicted to be a transmembrane domain. 59 matched cddid_all.tbl CDD cd16555 cd16555 438217 RING-HC_RNF182 "RING finger, HC subclass, found in RING finger protein 182 (RNF182) and similar proteins. RNF182 is a brain-enriched E3 ubiquitin-protein ligase that stimulates E2-dependent polyubiquitination in vitro. It is upregulated in Alzheimer""s disease (AD) brains and neuronal cells exposed to injurious insults. It interacts with ATP6V0C and promotes its degradation by the ubiquitin-proteosome pathway, suggesting a very specific role in controlling the turnover of an essential component of the neurotransmitter release machinery. RNF182 contains an N-terminal C3HC4-type RING-HC finger, and a C-terminal transmembrane domain." 55 matched cddid_all.tbl CDD cd16556 cd16556 438218 RING-HC_RNF183-like RING finger, HC subclass, found in RING finger protein RNF183, RNF223, RNF225 and similar proteins. RNF183 is an E3 ubiquitin-protein ligase that is upregulated during intestinal inflammation and is negatively regulated by miR-7. It promotes intestinal inflammation by increasing the ubiquitination and degradation of inhibitor of kappa B, thereby resulting in secondary activation of the Nuclear factor-kappaB (NF-kB) pathway. The interaction between RNF183-mediated ubiquitination and miRNA may be an important novel epigenetic mechanism in the pathogenesis of inflammatory bowel disease (IBD). The biological function of RNF223 and RNF225 remains unclear. Members of this family contain an N-terminal C3HC4-type RING-HC finger. 57 matched cddid_all.tbl CDD cd16557 cd16557 438219 RING-HC_RNF186 RING finger, HC subclass, found in RING finger protein 186 (RNF186) and similar proteins. RNF186 is an E3 ubiquitin-protein ligase with an N-terminal C3HC4-type RING-HC finger and two putative C-terminal transmembrane domains which enable it to localize in a certain organelle. It regulates RING-dependent self-ubiquitination, as well as endoplasmic reticulum (ER) stress-mediated apoptosis through interaction with the Bcl-2 family protein BNip1. 52 matched cddid_all.tbl CDD cd16558 cd16558 438220 RING-HC_RNF207 RING finger, HC subclass, found in RING finger protein 207 (RNF207) and similar proteins. RNF207 is a cardiac-specific E3 ubiquitin-protein ligase that plays an important role in the regulation of cardiac repolarization. It regulates action potential duration, likely via effects on human ether-a-go-go-related gene (HERG) trafficking and localization in a heat shock protein-dependent manner. RNF207 contains a C3HC4-type RING-HC finger, Bbox 1 and Bbox C-terminal (BBC) domain, as well as a C-terminal non-homologous region (CNHR). 43 matched cddid_all.tbl CDD cd16559 cd16559 438221 RING-HC_RNF208 RING finger, HC subclass, found in RING finger protein 208 (RNF208) and similar proteins. RNF208 is an E3 ubiquitin-protein ligase whose activity can be modulated by S-nitrosylation. It contains a C3HC4-type RING-HC finger. 56 matched cddid_all.tbl CDD cd16560 cd16560 438222 RING-HC_RNF212-like RING finger, HC subclass, found in RING finger proteins RNF212, RNF212B and similar proteins. This subfamily includes RING finger protein RNF212, RNF212B, and their homologs. RNF212 is a dosage-sensitive regulator of crossing-over during mammalian meiosis. It plays a central role in designating crossover sites and coupling chromosome synapsis to the formation of crossover-specific recombination complexes. It also functions as an E3 ligase for small ubiquitin-related modifier (SUMO) modification. RNF212B shows high sequence similarity with RNF212, but its biological function remains unclear. Members of this subfamily contain an N-terminal C3HC4-type RING-HC finger. Also included are two homologs of RNF212, meiotic procrossover factors Zip3 and ZHP-3, which have been identified in Saccharomyces cerevisiae and Caenorhabditis elegans, respectively. Budding yeast Zip3 is a small ubiquitin-related modifier (SUMO) E3 ligase implicated in the SUMO pathway of post-translational modification. It sumoylates chromosome axis proteins, thus promoting synaptonemal complex polymerization. It also acts as an Smt3 E3 ligase. Zip3 includes a SUMO Interacting Motif (SIM) and a modified C3HCHC2-type RING-HC finger that are important for Zip3 in vitro E3 ligase activity and necessary for SC polymerization and correct sporulation. ZHP-3 acts at crossovers to couple meiotic recombination with synaptonemal complex disassembly and chiasma formation in Caenorhabditis elegans. It possesses a C3HC4-type RING-HC finger. 42 matched cddid_all.tbl CDD cd16561 cd16561 438223 RING-HC_RNF213 RING finger, HC subclass, found in RING finger protein 213 (RNF213) and similar proteins. RNF213, also known as ALK lymphoma oligomerization partner on chromosome 17 or Moyamoya steno-occlusive disease-associated AAA+ and RING finger protein (mysterin), is an intracellular soluble protein that functions as an E3 ubiquitin-protein ligase and AAA+ ATPase, which possibly contributes to vascular development through mechanical processes in the cell. It plays a unique role in endothelial cells for proper gene expression in response to inflammatory signals from the environment. Mutations in RNF213 may be associated with Moyamoya disease (MMD), an idiopathic cerebrovascular occlusive disorder prevalent in East Asia. It also acts as a nuclear marker for acanthomorph phylogeny. RNF213 contains two tandem enzymatically active AAA+ ATPase modules and a C3HC4-type RING-HC finger. It can form a huge ring-shaped oligomeric complex. 50 matched cddid_all.tbl CDD cd16562 cd16562 438224 RING-HC_RNF219 RING finger, HC subclass, found in RING finger protein 219 (RNF219) and similar proteins. RNF219 may function as a modulator of late-onset Alzheimer's disease (LOAD) associated amyloid beta A4 precursor protein (APP) endocytosis and metabolism. It genetically interacts with apolipoprotein E epsilon4 allele (APOE4). Thus, a genetic variant of RNF219 was found to affect amyloid deposition in human brain and LOAD age-of-onset. Moreover, common genetic variants at the RNF219 locus had been associated with alternations in lipid metabolism, cognitive performance and central nervous system ventricle volume. RNF219 contains a C3HC4-type RING-HC finger. 45 matched cddid_all.tbl CDD cd16563 cd16563 438225 RING-HC_RNF220 RING finger, HC subclass, found in RING finger protein 220 (RNF220) and similar proteins. RNF220 is an E3 ubiquitin-protein ligase that promotes the ubiquitination and proteasomal degradation of Sin3B, a scaffold protein of the Sin3/HDAC (histone deacetylase) corepressor complex. It can also bind E2 and mediate auto-ubiquitination of itself. Moreover, RNF220 specifically interacts with beta-catenin, and enhances canonical Wnt signaling through ubiquitin-specific protease 7 (USP7)-mediated deubiquitination and stabilization of beta-catenin, which is independent of its E3 ligase activity. RNF220 contains a characteristic C3HC4-type RING-HC finger at its C-terminus. 52 matched cddid_all.tbl CDD cd16564 cd16564 438226 RING-HC_RNF222 RING finger, HC subclass, found in RING finger protein 222 (RNF222) and similar proteins. RNF222 is an uncharacterized C3HC4-type RING-HC finger-containing protein. It may function as an E3 ubiquitin-protein ligase. 50 matched cddid_all.tbl CDD cd16565 cd16565 438227 RING-HC_RNF224 RING finger, HC subclass, found in RING finger protein RNF224 and similar proteins. RNF224 is uncharacterized C3HC4-type RING-HC finger-containing proteins. It may function as an E3 ubiquitin-protein ligase. 59 matched cddid_all.tbl CDD cd16566 cd16566 438228 RING-HC_RSPRY1 RING finger, HC subclass, found in RING finger and SPRY domain-containing protein 1 (RSPRY1) and similar proteins. RSPRY1 is a hypothetical RING and SPRY domain-containing protein of unknown physiological function. Mutations in its corresponding gene RSPRY1 may associate with a distinct skeletal dysplasia syndrome. RSPRY1 contains a B30.2/SPRY domain and a C3HC4-type RING-HC finger. 43 matched cddid_all.tbl CDD cd16567 cd16567 438229 RING-HC_RAD16-like RING finger, HC subclass, found in Saccharomyces cerevisiae DNA repair protein RAD16, Schizosaccharomyces pombe rhp16, and similar proteins. Budding yeast RAD16, also known as ATP-dependent helicase RAD16, is encoded by a yeast excision repair gene homologous to the recombinational repair gene RAD54 and to the SNF2 gene involved in transcriptional activation. It is a component of the global genome repair (GGR) complex that promotes global genome nucleotide excision repair (GG-NER) by removing DNA damage from non-transcribing DNA. RAD16 is involved in differential repair of DNA after UV damage, and repairs preferentially the MAT-alpha locus compared with the HML-alpha locus. Fission yeast rhp16, also known as ATP-dependent helicase rhp16, is a RAD16 homolog. It is involved in GGR via nucleotide excision repair (NER), in conjunction with rhp7, after UV irradiation. Both RAD16 and rhp16 contain a C3HC4-type RING-HC finger, as well as a DEAD-like helicase domain and a helicase superfamily C-terminal domain. 48 matched cddid_all.tbl CDD cd16568 cd16568 438230 RING-HC_ScPSH1-like RING finger, HC subclass, found in Saccharomyces cerevisiae POB3/SPT16 histone-associated protein 1 (ScPSH1) and similar proteins. ScPSH1 is a Cse4-specific E3 ubiquitin ligase that interacts with the kinetochore protein Pat1 and targets the degradation of budding yeast centromeric histone H3 variant, CENP-ACse4, which is essential for faithful chromosome segregation. ScPSH1 contains a C3HC4-type RING-HC finger and a DNA directed RNA polymerase domain. 54 matched cddid_all.tbl CDD cd16569 cd16569 438231 RING-HC_SHPRH-like RING finger, HC subclass, found in SNF2 histone-linker PHD finger RING finger helicase (SHPRH) and similar proteins. SHPRH is a yeast RAD5 homolog found in mammals. It functions as an E3 ubiquitin-protein ligase that associates with proliferating cell nuclear antigen (PCNA), RAD18, and the ubiquitin-conjugating enzyme UBC13 (E2), and suppresses genomic instability by proliferating methyl methanesulfonate (MMS)-induced PCNA polyubiquitination. SHPRH contains a SWI/SNF helicase domain that is divided into N- and C-terminal parts by an insertion of a linker histone domain (H15), a PHD-finger, and a C3HC4-type RING-HC finger involved in the poly-ubiquitination of PCNA. This subfamily also includes tripartite motif-containing protein 15 (TRIM15). TRIM15, also known as RING finger protein 93 (RNF93), zinc finger protein 178 (ZNF178), or zinc finger protein B7 (ZNFB7), is a focal adhesion protein that regulates focal adhesion disassembly. It localizes to focal contacts in a myosin-II-independent manner by an interaction between its coiled-coil domain and the LD2 motif of paxillin. TRIM15 can also associate with coronin 1B, cortactin, filamin binding LIM protein1, and vasodilator-stimulated phosphoprotein, which are involved in actin cytoskeleton dynamics. As an additional component of the integrin adhesome, it regulates focal adhesion turnover and cell migration. TRIM15 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. 53 matched cddid_all.tbl CDD cd16570 cd16570 438232 RING-HC_SH3RFs RING finger, HC subclass, found in SH3 domain-containing RING finger proteins SH3RF1, SH3RF2, SH3RF3, and similar proteins. SH3RF1, also known as plenty of SH3s (POSH), RING finger protein 142 (RNF142), or SH3 multiple domains protein 2 (SH3MD2), is a trans-Golgi network-associated pro-apoptotic scaffold protein with E3 ubiquitin-protein ligase activity. SH3RF2, also known as heart protein phosphatase 1-binding protein (HEPP1), plenty of SH3s (POSH)-eliminating RING protein (POSHER), protein phosphatase 1 regulatory subunit 39, or RING finger protein 158 (RNF158), is a putative E3 ubiquitin-protein ligase that acts as an anti-apoptotic regulator for the c-Jun N-terminal kinase (JNK) pathway by binding to and promoting the proteasomal degradation of SH3RF1 (or POSH) that is required for pro-apoptotic JNK activation. SH3RF3, also known as plenty of SH3s 2 (POSH2) or SH3 multiple domains protein 4 (SH3MD4), is a scaffold protein with E3 ubiquitin-protein ligase activity. It was identified in the screen for interacting partners of p21-activated kinase 2 (PAK2) and may play a role in regulating c-Jun N-terminal kinase (JNK) mediated apoptosis in certain conditions. Members of this subfamily contain an N-terminal C3HC4-type RING-HC finger responsible for the E3 ligase activity and four Src Homology 3 (SH3) domains, which are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. 44 matched cddid_all.tbl CDD cd16571 cd16571 438233 RING-HC_SIAHs RING finger, HC subclass, found in Drosophila melanogaster protein Seven-in-Absentia (sina) and its homologs. This subfamily includes the Drosophila melanogaster protein Seven-in-Absentia (sina), its mammalian orthologs, SIAH1 and SIAH2, plant SINA-related proteins, and similar proteins. Sina plays an important role in the phyllopod-dependent degradation of the transcriptional repressor tramtrack to allow the formation of the R7 photoreceptor in the developing eye of Drosophila melanogaster. Both SIAH1 and SIAH2 are E3 ubiquitin-protein ligases, mediating the ubiquitinylation and subsequent proteasomal degradation of biologically important target proteins that regulate general functions, such as cell cycle control, apoptosis, and DNA repair. They are inducible by the tumor suppressor and transcription factor p53. SIAH2 can also be regulated by sex hormones and cytokine signaling. Moreover, they share high sequence similarity, but possess contrary roles in cancer, with SIAH1 more often acting as a tumor suppressor while SIAH2 functions as a proto-oncogene. Plant SINAT1-5 are putative E3 ubiquitin ligases involved in the regulation of stress responses. All subfamily members possess two characteristic domains, an N-terminal C3HC4-type RING-HC finger and a C-terminal tumor necrosis factor (TNF) receptor associated factor (TRAF)-like substrate-binding domain (SBD). 39 matched cddid_all.tbl CDD cd16572 cd16572 438234 RING-HC_SpRad8-like RING finger, HC subclass, found in Schizosaccharomyces pombe DNA repair protein Rad8 (SpRad8) and similar proteins. SpRad8 is a conserved protein homologous to Saccharomyces cerevisiae DNA repair protein Rad5 and human helicase-like transcription factor (HLTF) that is required for error-free postreplication repair by contributing to polyubiquitylation of PCNA. SpRad8 contains a C3HC4-type RING-HC finger responsible for the E3 ubiquitin ligase activity, a SNF2-family helicase domain including an ATP binding site, and a family-specific HIRAN domain (HIP116, Rad5p N-terminal domain) that contributes to nuclear localization. 61 matched cddid_all.tbl CDD cd16573 cd16573 438235 RING-HC_TFB3-like RING finger, HC subclass, found in RNA polymerase II transcription factor B subunit 3 (TFB3) from fungi. TFB3, also known as RNA polymerase II transcription factor B 38 kDa subunit, RNA polymerase II transcription factor B p38 subunit, or Rig2, is a component of the general transcription and DNA repair factor IIH (TFIIH or factor B), which is essential for both basal and activated transcription and is involved in nucleotide excision repair (NER) of damaged DNA. TFIIH has CTD kinase and DNA-dependent ATPase activities, and is essential for polymerase II transcription in vitro. TFB3 is a homolog of MAT1 of higher eukaryotes which forms a ternary complex with MO15 (cdk7) and cyclin H. It physically interacts with Ubc4 and the Nedd8-conjugating enzyme Ubc12 as well as the Hrt1/Rtt101 complex. It targets the yeast Cul4-type cullin Rtt101 for its neddylation and ubiquitylation, and regulates neddylation and activity of cullin-3, but not Cdc53. TFB3 contains an N-terminal C3HC4-type RING-HC finger and a C-terminal MAT1 domain responsible for the interaction with the transcription factor TFIIH. 56 matched cddid_all.tbl CDD cd16574 cd16574 438236 RING-HC_Topors RING finger, HC subclass, found in topoisomerase I-binding arginine/serine-rich protein (Topors) and similar proteins. Topors, also known as topoisomerase I-binding RING finger protein, tumor suppressor p53- binding protein 3, or p53-binding protein 3 (p53BP3), is a ubiquitously expressed nuclear E3 ubiquitin-protein ligase that can ligate both ubiquitin and small ubiquitin-like modifier (SUMO) to substrate proteins in the nucleus. It contains an N-terminal C3HC4-type RING-HC finger which ligates ubiquitin to its target proteins including DNA topoisomerase I, p53, NKX3.1, H2AX, and the AAV-2 Rep78/68 proteins. As a RING-dependent E3 ubiquitin ligase, Topors works with the E2 enzymes UbcH5a, UbcH5c, and UbcH6, but not with UbcH7, CDC34, or UbcH2b. Topors acts as a tumor suppressor in various malignancies. It regulates p53 modification, suggesting it may be responsible for astrocyte elevated gene-1 (AEG-1, also known as metadherin, or LYRIC) ubiquitin modification. Plk1-mediated phosphorylation of Topors inhibits Topors-mediated sumoylation of p53, whereas p53 ubiquitination is enhanced, leading to p53 degradation. It also functions as a negative regulator of the prostate tumor suppressor NKX3.1. Moreover, Topors is associated with promyelocytic leukemia nuclear bodies, and may be involved in the cellular response to camptothecin. It also plays a key role in the turnover of H2AX protein, discriminating the type of DNA damaging stress. Furthermore, Topors is a cilia-centrosomal protein associated with autosomal dominant retinal degeneration. Mutations in TOPORS cause autosomal dominant retinitis pigmentosa (adRP). 47 matched cddid_all.tbl CDD cd16575 cd16575 438237 RING-HC_MID_C-I RING finger, HC subclass, found in midline-1 (MID1), midline-2 (MID2) and similar proteins. MID1, also known as midin, midline 1 RING finger protein, putative transcription factor XPRF, RING finger protein 59 (RNF59), or tripartite motif-containing protein 18 (TRIM18), is a microtubule-associated E3 ubiquitin-protein ligase implicated in epithelial-mesenchymal differentiation, cell migration and adhesion, and programmed cell death along specific regions of the ventral midline during embryogenesis. MID2, also known as midin-2, midline defect 2, RING finger protein 60 (RNF60), or tripartite motif-containing protein 1 (TRIM1), associates with the microtubule network and may at least partially compensate for the loss of MID1. Both MID1 and MID2 interacts with Alpha 4, which is a regulatory subunit of PP2-type phosphatases, such as PP2A, and an integral component of the rapamycin-sensitive signaling pathway. They also play a central role in the regulation of granule exocytosis. Functional redundancy exists between MID1 and MID2 in cytotoxic lymphocytes (CTL). Both MID1 and MID2 belong to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. 54 matched cddid_all.tbl CDD cd16576 cd16576 438238 RING-HC_TRIM9-like_C-I RING finger, HC subclass, found in tripartite motif-containing proteins TRIM9, TRIM67, and similar proteins. Tripartite motif-containing proteins TRIM9 and TRIM67 belong to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, consisting of three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. TRIM9 (the human ortholog of rat Spring), also known as RING finger protein 91 (RNF91), is a brain-specific E3 ubiquitin-protein ligase collaborating with an E2 ubiquitin conjugating enzyme UBCH5b. TRIM9 plays an important role in the regulation of neuronal functions and participates in neurodegenerative disorders through its ligase activity. TRIM67, also known as TRIM9-like protein (TNL), is a protein selectively expressed in the cerebellum. It interacts with PRG-1, an important molecule in the control of hippocampal excitability dependent on presynaptic LPA2 receptor signaling, and 80K-H, also known as glucosidase II beta, a protein kinase C substrate. 42 matched cddid_all.tbl CDD cd16577 cd16577 438239 RING-HC_MuRF_C-II RING finger, HC subclass, found in muscle-specific RING finger proteins TRIM63/MuRF-1, TRIM55/MuRF-2 and TRIM54/MuRF-3. This subfamily corresponds to a group of striated muscle-specific tripartite motif (TRIM) proteins, including TRIM63/MuRF-1, TRIM55/MuRF-2, and TRIM54/MuRF-3, which function as E3 ubiquitin ligases in ubiquitin-mediated muscle protein turnover. They are tightly developmentally regulated in skeletal muscle and associate with different cytoskeleton components, such as microtubules, Z-disks and M-bands, as well as with metabolic enzymes and nuclear proteins. They also cooperate with diverse proteins implicated in selective protein degradation by the proteasome and autophagosome, and target proteins of metabolic regulation, sarcomere assembly and transcriptional regulation. Moreover, MURFs display variable fibre-type preferences. TRIM63/MuRF-1 is predominantly fast (type II) fibre-associated in skeletal muscle. TRIM55/MuRF-2 is predominantly slow-fibre associated. TRIM54/MuRF-3 is ubiquitously present. They play an active role in microtubule-mediated sarcomere assembly. MuRFs belong to the C-II subclass of the TRIM family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, and an acidic residue-rich (AR) domain positioned C-terminal to the RBCC domain. They also harbor a MURF family-specific conserved box (MFC) between its RING-HC finger and Bbox domains. 56 matched cddid_all.tbl CDD cd16578 cd16578 438240 RING-HC_TRIM42_C-III RING finger, HC subclass, found in tripartite motif-containing protein 42 (TRIM42) and similar proteins. TRIM42 belongs to the C-III subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain. It also has a novel cysteine-rich motif N-terminal to the RBCC domain, as well as a COS (carboxyl-terminal subgroup one signature) box and a fibronectin type-III (FN3) domain positioned C-terminal to the RBCC domain. TRIM42 can interact with TRIM27, a known cancer-associated protein. Its precise biological function remains unclear. 58 matched cddid_all.tbl CDD cd16579 cd16579 438241 RING-HC_PML_C-V RING finger, HC subclass, found in promyelocytic leukemia protein (PML) and similar proteins. Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cell processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. 52 matched cddid_all.tbl CDD cd16580 cd16580 438242 RING-HC_TRIM8_C-V RING finger, HC subclass, found in tripartite motif-containing protein 8 (TRIM8) and similar proteins. TRIM8, also known as glioblastoma-expressed RING finger protein (GERP) or RING finger protein 27 (RNF27), is a probable E3 ubiquitin-protein ligase that may promote proteasomal degradation of suppressor of cytokine signaling 1 (SOCS1) and further regulate interferon-gamma signaling. It functions as a new p53 modulator that stabilizes p53 impairing its association with MDM2 and inducing the reduction of cell proliferation. TRIM8 deficit dramatically impairs p53 stabilization and activation in response to chemotherapeutic drugs. TRIM8 also modulates tumor necrosis factor-alpha (TNFalpha) and interleukin-1beta (IL-1beta)-triggered nuclear factor-kappaB (NF- kappa B) activation by targeting transforming growth factor beta (TGFbeta) activated kinase 1 (TAK1) for K63-linked polyubiquitination. Moreover, TRIM8 modulates translocation of phosphorylated STAT3 into the nucleus through interaction with Hsp90beta and consequently regulates transcription of Nanog in embryonic stem cells. It also interacts with protein inhibitor of activated STAT3 (PIAS3), which inhibits IL-6-dependent activation of STAT3. TRIM8 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The coiled coil domain is required for homodimerization and the region immediately C-terminal to the RING motif is sufficient to mediate the interaction with SOCS1. 67 matched cddid_all.tbl CDD cd16581 cd16581 438243 RING-HC_TRIM13_like_C-V RING finger, HC subclass, found in tripartite motif-containing proteins TRIM13, TRIM59 and similar proteins. TRIM13 and TRIM59, two closely related tripartite motif-containing proteins, belong to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, followed by a C-terminal transmembrane domain. TRIM13, also known as B-cell chronic lymphocytic leukemia tumor suppressor Leu5, leukemia-associated protein 5, putative tumor suppressor RFP2, RING finger protein 77 (RNF77), or Ret finger protein 2, is an endoplasmic reticulum (ER) membrane anchored E3 ubiquitin-protein ligase that interacts with proteins localized to the ER, including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). TRIM59, also known as RING finger protein 104 (RNF104) or tumor suppressor TSBF-1, is a putative E3 ubiquitin-protein ligase that functions as a novel multiple cancer biomarker for immunohistochemical detection of early tumorigenesis. 50 matched cddid_all.tbl CDD cd16582 cd16582 438244 RING-HC_TRIM31_C-V RING finger, HC subclass, found in tripartite motif-containing protein 31 (TRIM31) and similar proteins. TRIM31 is an E3 ubiquitin-protein ligase that primarily localizes to the cytoplasm, but is also associated with the mitochondria. It can negatively regulate cell proliferation and may be a potential biomarker of gastric cancer as it is overexpressed from the early stage of gastric carcinogenesis. TRIM31 is downregulated in non-small cell lung cancer and serves as a potential tumor suppressor. It interacts with p52 (Shc) and inhibits Src-induced anchorage-independent growth. TRIM31 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. 44 matched cddid_all.tbl CDD cd16583 cd16583 438245 RING-HC_TRIM40-C-V RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins. TRIM40, also known as probable E3 NEDD8-protein ligase or RING finger protein 35 (RNF35), is highly expressed in the gastrointestinal tract including the stomach, small intestine, and large intestine. It enhances neddylation of inhibitor of nuclear factor kappaB kinase subunit gamma (IKKgamma), inhibits the activity of nuclear factor-kappaB (NF-kappaB)-mediated transcription, and thus prevents inflammation-associated carcinogenesis in the gastrointestinal tract. TRIM40 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. 63 matched cddid_all.tbl CDD cd16584 cd16584 438246 RING-HC_TRIM56_C-V RING finger, HC subclass, found in tripartite motif-containing protein 56 (TRIM56) and similar proteins. TRIM56, also known as RING finger protein 109 (RNF109), is a virus-inducible E3 ubiquitin ligase that restricts pestivirus infection. It positively regulates the Toll-like receptor 3 (TLR3) antiviral signaling pathway, and possesses antiviral activity against bovine viral diarrhea virus (BVDV), a ruminant pestivirus classified within the family Flaviviridae shared by tick-borne encephalitis virus (TBEV). It also possesses antiviral activity against two classical flaviviruses, yellow fever virus (YFV) and dengue virus (DENV), as well as a human coronavirus, HCoV-OC43, which is responsible for a significant share of common cold cases. It may not act on positive-strand RNA viruses indiscriminately. Moreover, TRIM56 is an interferon-inducible E3 ubiquitin ligase that modulates STING to confer double-stranded DNA-mediated innate immune responses. TRIM56 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. 56 matched cddid_all.tbl CDD cd16585 cd16585 438247 RING-HC_TIF1_C-VI RING finger, HC subclass, found in the transcriptional inknown asiary factor 1 (TIF1) subfamily and similar proteins. The TIF1 subfamily of transcriptional cofactors containing RING-HC fingers includes TIF1alpha (TRIM24), TIF1beta (TRIM28), and TIF1gamma (TRIM33), which belong to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha and TIF1beta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. They bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatin proteins HP1alpha, beta and gamma. It cannot bind to nuclear receptors (NRs). TIF1delta (TRIM66) doesn't have a RING-HC finger and is not included in this model. 62 matched cddid_all.tbl CDD cd16586 cd16586 438248 RING-HC_TRIM2_like_C-VII RING finger, HC subclass, found in tripartite motif-containing protein TRIM2, TRIM3, and similar proteins. TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It also plays an important role in the central nervous system (CNS). In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. Both TRIM2 and TRIM3 belong to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. 45 matched cddid_all.tbl CDD cd16587 cd16587 438249 RING-HC_TRIM32_C-VII RING finger, HC subclass, found in tripartite motif-containing protein 32 (TRIM32) and similar proteins. TRIM32, also known as 72 kDa Tat-interacting protein, zinc finger protein HT2A, or BBS11, is an E3 ubiquitin-protein ligase that promotes degradation of several targets, including actin, PIASgamma, Abl interactor 2, dysbindin, X-linked inhibitor of apoptosis (XIAP), p73 transcription factor, thin filaments and Z-bands during fasting. It plays important roles in neuronal differentiation of neural progenitor cells, as well as in controlling cell fate in skeletal muscle progenitor cells. It reduces PI3K-Akt-FoxO signaling in muscle atrophy by promoting plakoglobin-PI3K dissociation. It also functions as a pluripotency-reprogramming roadblock that facilitates cellular transition towards differentiation by modulating the levels of Oct4 and cMyc. Moreover, TRIM32 is an intrinsic influenza A virus (IAV) restriction factor which senses and targets the polymerase basic protein 1 (PB1) for ubiquitination and protein degradation. It also plays a significant role in mediating the biological activity of the HIV-1 Tat protein in vivo, binds specifically to the activation domain of HIV-1 Tat, and can also interact with the HIV-2 and EIAV Tat proteins in vivo. Furthermore, TRIM32 regulates myoblast proliferation by controlling turnover of NDRG2 (N-myc downstream-regulated gene). It negatively regulates tumor suppressor p53 to promote tumorigenesis. It also facilitates degradation of MYCN on spindle poles and induces asymmetric cell division in human neuroblastoma cells. In addition, TRIM32 plays important roles in regulation of hyperactivities and positively regulates the development of anxiety and depression disorders induced by chronic stress. It also plays a role in regeneration by affecting satellite cell cycle progression via modulation of the SUMO ligase PIASy (PIAS4). Defects in TRIM32 leads to limb-girdle muscular dystrophy type 2H (LGMD2H), sarcotubular myopathies (STM) and Bardet-Biedl syndrome. TRIM32 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The NHL domain mediates the interaction with Argonaute proteins and consequently allows TRIM32 to modulate the activity of certain miRNAs. 51 matched cddid_all.tbl CDD cd16588 cd16588 438250 RING-HC_TRIM45_C-VII RING finger, HC subclass, found in tripartite motif-containing protein 45 (TRIM45) and similar proteins. TRIM45, also known as RING finger protein 99 (RNF99), is a novel receptor for activated C-kinase (RACK1)-interacting protein that suppresses transcriptional activities of Elk-1 and AP-1 and downregulates mitogen-activated protein kinase (MAPK) signal transduction through inhibiting RACK1/PKC (protein kinase C) complex formation. It also negatively regulates tumor necrosis factor alpha (TNFalpha)-induced nuclear factor-kappaB (NF-kappa B)-mediated transcription and suppresses cell proliferation. TRIM45 belongs to the C-VII subclass of the TRIM (tripartite motif) family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a filamin-type immunoglobulin (IG-FLMN) domain and NHL repeats positioned C-terminal to the RBCC domain. 59 matched cddid_all.tbl CDD cd16589 cd16589 438251 RING-HC_TRIM71_C-VII RING finger, HC subclass, found in tripartite motif-containing protein 71 (TRIM71) and similar proteins. TRIM71, also known as protein lineage variant 41 (lin-41), is an E3 ubiquitin-protein ligase that may play essential roles in embryonic stem cells, cellular reprogramming and the timing of embryonic neurogenesis. It was first identified in the nematode Caenorhabditis elegans as a target of the differentiation-associated microRNA (miRNA) let-7 (lethal 7) and is therefore part of a heterochronic gene network that controls larval development. In humans, it regulates let-7 microRNA biogenesis via modulation of Lin28B protein polyubiquitination. TRIM71 localizes to cytoplasmic P-bodies and directly interacts with the miRNA pathway proteins Argonaute 2 (AGO2) and DICER. It represses miRNA activity by promoting degradative ubiquitination of AGO2. Moreover, TRIM71 associates with SHCBP1, a novel component of the fibroblast growth factor (FGF) signaling pathway, and regulates its non-degradative polyubiquitination. It is also involved in the post-transcriptional regulation of the CDKN1A, RBL1 and RBL2 or EGR1 mRNAs by mediating RNA-binding in embryonic stem cells. TRIM71 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. 91 matched cddid_all.tbl CDD cd16590 cd16590 438252 RING-HC_TRIM4_C-IV RING finger, HC subclass, found in tripartite motif-containing protein TRIM4 and similar proteins. TRIM4 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. TRIM4, also known as RING finger protein 87 (RNF87), is a cytoplasmic E3 ubiquitin-protein ligase that has recently evolved and is present only in higher mammals. It transiently interacts with mitochondria, induces mitochondrial aggregation and sensitizes the cells to hydrogen peroxide (H2O2) induced death. Its interaction with peroxiredoxin 1 (PRX1) is critical for the regulation of H2O2 induced cell death. Moreover, TRIM4 functions as a positive regulator of RIG-I-mediated type I interferon induction. It regulates the K63-linked ubiquitination of RIG-1 and assembly of antiviral signaling complex at the mitochondria. 61 matched cddid_all.tbl CDD cd16591 cd16591 438253 RING-HC_TRIM5-like_C-IV RING finger, HC subclass, found in tripartite motif-containing proteins TRIM5, TRIM6, TRIM22, TRIM34 and similar proteins. TRIM5, TRIM6, TRIM22, and TRIM34, four closely related tripartite motif-containing proteins, belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. TRIM5, also known as RING finger protein 88 (RNF88), is a capsid-specific restriction factor that prevents infection from non-host-adapted retroviruses in a species-specific manner by binding to and destabilizing the retroviral capsid lattice before reverse transcription is completed. Its retroviral restriction activity correlates with the ability to activate TAK1-dependent innate immune signaling. TRIM5 also acts as a pattern recognition receptor that activates innate immune signaling in response to the retroviral capsid lattice. Moreover, TRIM5 plays a role in regulating autophagy through activation of autophagy regulator BECN1 by causing its dissociation from its inhibitors BCL2 and TAB2. It also plays a role in autophagy by acting as a selective autophagy receptor which recognizes and targets HIV-1 capsid protein p24 for autophagic destruction. TRIM6, also known as RING finger protein 89 (RNF89), is an E3-ubiquitin ligase that cooperates with the E2-ubiquitin conjugase UbE2K to catalyze the synthesis of unanchored K48-linked polyubiquitin chains, and further stimulates the interferon-I kappa B kinase epsilon (IKKepsilon) kinase-mediated antiviral response. It also regulates the transcriptional activity of Myc during the maintenance of embryonic stem (ES) cell pluripotency, and may act as a novel regulator for Myc-mediated transcription in ES cells. TRIM22, also known as 50 kDa-stimulated trans-acting factor (Staf-50) or RING finger protein 94 (RNF94), is an E3 ubiquitin-protein ligase that plays an integral role in the host innate immune response to viruses. It has been shown to inhibit the replication of a number of viruses, including HIV-1, hepatitis B, and influenza A. TRIM22 acts as a suppressor of basal HIV-1 long terminal repeat (LTR)-driven transcription by preventing the transcription factor specificity protein 1 (Sp1) binding to the HIV-1 promoter. It also controls FoxO4 activity and cell survival by directing Toll-like receptor 3 (TLR3)-stimulated cells toward type I interferon (IFN) type I gene induction or apoptosis. Moreover, TRIM22 can activate the noncanonical nuclear factor-kappaB (NF-kappaB) pathway by activating I kappa B kinase alpha (IKKalpha). It also regulates nucleotide binding oligomerization domain containing 2 (NOD2)-dependent activation of interferon-beta signaling and nuclear factor-kappaB. TRIM34, also known as interferon-responsive finger protein 1 or RING finger protein 21 (RNF21), may function as antiviral protein that contribute to the defense against retroviral infections. 72 matched cddid_all.tbl CDD cd16592 cd16592 438254 RING-HC_RNF39 RING finger, HC subclass, found in RING finger protein 39 (RNF39) and similar proteins. RNF39, also called protein HZFw, may play a role in prolonged long term-potentiation (LTP) maintenance. It is involved in the etiology of Behcet's disease (BD). It may also be involved in HIV-1 replication. RNF39 acts as an E3 ubiquitin ligase that inhibits retinoic acid-inducible gene-I (RIG-I)-like receptor (RLR) pathways by mediating K48-linked ubiquitination and proteasomal degradation of DDX3X (DEAD-box RNA helicase 3, X-linked). RNF39 contains a typical C3HC4-type RING-HC finger. 58 matched cddid_all.tbl CDD cd16593 cd16593 438255 RING-HC_TRIM10_C-IV RING finger, HC subclass, found in tripartite motif-containing protein 10 (TRIM10) and similar proteins. TRIM10, also known as B30-RING finger protein (RFB30), RING finger protein 9 (RNF9), or hematopoietic RING finger 1 (HERF1), is a novel hematopoiesis-specific RING finger protein required for terminal differentiation of erythroid cells. TRIM10 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. 61 matched cddid_all.tbl CDD cd16594 cd16594 438256 RING-HC_TRIM7-like_C-IV RING finger, HC subclass, found in tripartite motif-containing proteins, TRIM7, TRIM11 and TRIM27, and similar proteins. TRIM7, TRIM11 and TRIM27, closely related tripartite motif-containing proteins, belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. TRIM7, also known as glycogenin-interacting protein (GNIP) or RING finger protein 90 (RNF90), is an E3 ubiquitin-protein ligase that mediates c-Jun/AP-1 activation by Ras signalling. Its phosphorylation and activation by MSK1 in response to direct activation by the Ras-Raf-MEK-ERK pathway can stimulate TRIM7 E3 ubiquitin ligase activity in mediating Lys63-linked ubiquitination of the AP-1 coactivator RACO-1, leading to RACO-1 protein stabilization. Moreover, TRIM7 binds and activates glycogenin, the self-glucosylating initiator of glycogen biosynthesis. TRIM11, also known as protein BIA1, or RING finger protein 92 (RNF92), is an E3 ubiquitin-protein ligase involved in the development of the central nervous system. It is overexpressed in high-grade gliomas and promotes proliferation, invasion, migration and glial tumor growth. TRIM11 acts as a potential therapeutic target for congenital central hypoventilation syndrome (CCHS) by mediating the degradation of CCHS-associated polyalanine-expanded Phox2b. TRIM11 modulates the function of neurogenic transcription factor Pax6 through the ubiquitin-proteosome system, and thus plays an essential role for Pax6-dependent neurogenesis. It also binds to and destabilizes a key component of the activator-mediated cofactor complex (ARC105), humanin, a neuroprotective peptide against Alzheimer's disease-relevant insults, and further regulates ARC105 function in transforming growth factor beta (TGFbeta) signaling. Moreover, TRIM11 negatively regulates retinoic acid-inducible gene-I (RIG-I)-mediated interferon-beta (IFNbeta) production and antiviral activity by targeting TANK-binding kinase-1 (TBK1). It may contribute to the endogenous restriction of retroviruses in cells. It enhances N-tropic murine leukemia virus (N-MLV) entry by interfering with Ref1 restriction. It also suppresses the early steps of human immunodeficiency virus HIV-1 transduction, resulting in decreased reverse transcripts. TRIM27, also known as RING finger protein 76 (RNF76), RET finger protein (RFP), or zinc finger protein RFP, is a nuclear E3 ubiquitin-protein ligase that is highly expressed in testis and in various tumor cell lines. Expression of TRIM27 is associated with prognosis of colon and endometrial cancers. TRIM27 was first identified as a fusion partner of the RET receptor tyrosine kinase. It functions as a transcriptional repressor and associates with several proteins involved in transcriptional activity, such as enhancer of polycomb 1 (Epc1), a member of the Polycomb group proteins, and Mi-2beta, a main component of the nucleosome remodeling and deacetylase (NuRD) complex, and the cell cycle regulator retinoblastoma protein (RB1). It also interacts with HDAC1, leading to downregulation of thioredoxin binding protein 2 (TBP-2), which inhibits the function of thioredoxin. Moreover, TRIM27 mediates Pax7-induced ubiquitination of MyoD in skeletal muscle atrophy. In addition, it inhibits muscle differentiation by modulating serum response factor (SRF) and Epc1. TRIM27 promotes a non-canonical polyubiquitination of PTEN, a lipid phosphatase that catalyzes PtdIns(3,4,5)P3 (PIP3) to PtdIns(4,5)P2 (PIP2). It is an IKKepsilon-interacting protein that regulates IkappaB kinase (IKK) function and negatively regulates signaling involved in the antiviral response and inflammation. TRIM27 also forms a protein complex with MBD4 or MBD2 or MBD3, and thus plays an important role in the enhancement of transcriptional repression through MBD proteins in tumorigenesis, spermatogenesis, and embryogenesis. It is a component of an estrogen receptor 1 (ESR1) regulatory complex that is involved in estrogen receptor-mediated transcription in MCF-7 cells. 61 matched cddid_all.tbl CDD cd16595 cd16595 438257 RING-HC_TRIM17_C-IV RING finger, HC subclass, found in tripartite motif-containing protein TRIM17 and similar proteins. TRIM17, also known as RING finger protein 16 (RNF16) or testis RING finger protein (Terf), is a crucial E3 ubiquitin ligase that is necessary and sufficient for neuronal apoptosis and contributes to Mcl-1 ubiquitination in cerebellar granule neurons (CGNs). It interacts in a SUMO-dependent manner with nuclear factor of activated T cell NFATc3 transcription factor, and thus inhibits the activity of NFATc3 by preventing its nuclear localization. In contrast, it binds to and inhibits NFATc4 transcription factor in a SUMO-independent manner. Moreover, TRIM17 stimulates degradation of kinetochore protein ZW10 interacting protein (ZWINT), a known component of the kinetochore complex required for the mitotic spindle checkpoint, and negatively regulates cell proliferation. TRIM17 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. 70 matched cddid_all.tbl CDD cd16596 cd16596 438258 RING-HC_TRIM21_C-IV RING finger, HC subclass, found in tripartite motif-containing protein TRIM21 and similar proteins. TRIM21, also known as 52 kDa Ro protein, 52 kDa ribonucleoprotein autoantigen Ro/SS-A, Ro(SS-A), RING finger protein 81 (RNF81), or Sjoegren syndrome type A antigen (SS-A), is a ubiquitously expressed E3 ubiquitin-protein ligase and a high affinity antibody receptor uniquely expressed in the cytosol of mammalian cells. As a cytosolic Fc receptor, TRIM21 binds the Fc of virus-associated antibodies and targets the complex in the cytosol for proteasomal degradation in a process known as antibody-dependent intracellular neutralization (ADIN), and provides an intracellular immune response to protect host defense against pathogen infection. It shows remarkably broad isotype specificity as it does not only bind IgG, but also IgM and IgA. Moreover, TRIM21 promotes the cytosolic DNA sensor cGAS and the cytosolic RNA sensor RIG-I sensing of viral genomes during infection by antibody-opsonized virus. It stimulates inflammatory signaling and activates innate transcription factors, such as nuclear factor-kappaB (NF-kappaB). TRIM21 also plays an essential role in p62-regulated redox homeostasis, suggesting it may be a viable target for treating pathological conditions resulting from oxidative damage. Furthermore, TRIM21 may have implications for various autoimmune diseases associated with uncontrolled antiviral signaling through the regulation of Nmi-IFI35 complex-mediated inhibition of innate antiviral response. TRIM21 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. 77 matched cddid_all.tbl CDD cd16597 cd16597 438259 RING-HC_TRIM25_C-IV RING finger, HC subclass, found in tripartite motif-containing protein TRIM25 and similar proteins. TRIM25, also known as estrogen-responsive finger protein (EFP), RING finger protein 147 (RNF147), or RING-type E3 ubiquitin transferase, is an E3 ubiquitin/ISG15 ligase that is induced by estrogen and is therefore particularly abundant in placenta and uterus. TRIM25 regulates various cellular processes through E3 ubiquitin ligase activity, transferring ubiquitin and ISG15 to target proteins. It mediates K63-linked polyubiquitination of retinoic acid inducible gene I (RIG-I) that is crucial for downstream antiviral interferon signaling. It is also required for melanoma differentiation-associated gene 5 (MDA5) and mitochondrial antiviral signaling (MAVS, also known as IPS-1, VISA, Cardiff) mediated activation of nuclear factor-kappaB (NF-kappaB) and interferon production. Upon UV irradiation, TRIM25 interacts with mono-ubiquitinated PCNA and promotes its ISG15 modification (ISGylation), suggesting a crucial role in termination of error-prone translesion DNA synthesis. TRIM25 also functions as a novel regulator of p53 and Mdm2. It enhances p53 and Mdm2 abundance by inhibiting their ubiquitination and degradation in 26S proteasomes. Meanwhile, it inhibits p53's transcriptional activity and dampens the response to DNA damage, and is essential for medaka development and this dependence is rescued by silencing of p53. Moreover, TRIM25 is involved in the host cellular innate immune response against retroviral infection. It interferes with the late stage of feline leukemia virus (FeLV) replication. Furthermore, TRIM25 acts as an oncogene in gastric cancer. Its blockade by RNA interference inhibits migration and invasion of gastric cancer cells through transforming growth factor-beta (TGF-beta) signaling, suggesting it presents a novel target for the detection and treatment of gastric cancer. In addition, TRIM25 acts as an RNA-specific activator for Lin28a/TuT4-mediated uridylation. TRIM25 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. 71 matched cddid_all.tbl CDD cd16598 cd16598 438260 RING-HC_TRIM26_C-IV RING finger, HC subclass, found in tripartite motif-containing protein 26 (TRIM26) and similar proteins. TRIM26, also known as acid finger protein (AFP), RING finger protein 95 (RNF95), or zinc finger protein 173 (ZNF173), is an E3 ubiquitin-protein ligase that negatively regulates interferon-beta production and antiviral response through polyubiquitination and degradation of nuclear transcription factor IRF3. It functions as an important regulator for RNA virus-triggered innate immune response by bridging TBK1 to NEMO (NF-kappaB essential modulator, also known as IKKgamma) and mediating TBK1 activation. It also acts as a novel tumor suppressor of hepatocellular carcinoma by regulating cancer cell proliferation, colony forming ability, migration, and invasion. TRIM26 belongs the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. 64 matched cddid_all.tbl CDD cd16599 cd16599 438261 RING-HC_TRIM35_C-IV RING finger, HC subclass, found in tripartite motif-containing protein 35 (TRIM35) and similar proteins. TRIM35, also known as hemopoietic lineage switch protein 5 (HLS5), is a putative hepatocellular carcinoma (HCC) suppressor that inhibits phosphorylation of pyruvate kinase isoform M2 (PKM2), which is involved in aerobic glycolysis of cancer cells and further suppresses the Warburg effect and tumorigenicity in HCC. It also negatively regulates Toll-like receptor 7 (TLR7)- and TLR9-mediated type I interferon production by suppressing the stability of interferon regulatory factor 7 (IRF7). Moreover, TRIM35 regulates erythroid differentiation by modulating globin transcription factor 1 (GATA-1) activity. TRIM35 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. 66 matched cddid_all.tbl CDD cd16600 cd16600 438262 RING-HC_TRIM38_C-IV RING finger, HC subclass, found in tripartite motif-containing protein 38 (TRIM38) and similar proteins. TRIM38, also known as RING finger protein 15 (RNF15) or zinc finger protein RoRet, is an E3 ubiquitin-protein ligase that promotes K63- and K48-linked ubiquitination of cellular proteins and also catalyzes self-ubiquitination. It negatively regulates Tumor necrosis factor alpha (TNF-alpha)- and interleukin-1beta-triggered Nuclear factor-kappaB (NF-kappaB) activation by mediating lysosomal-dependent degradation of transforming growth factor beta (TGFbeta)-activated kinase 1 (TAK1)-binding protein (TAB)2/3, two critical components of the TAK1 kinase complex. It also inhibits TLR3/4-mediated activation of NF-kappaB and interferon regulatory factor 3 (IRF3) by mediating ubiquitin-proteasomal degradation of TNF receptor-associated factor 6 (Traf6) and NAK-associated protein 1 (Nap1), respectively. Moreover, TRIM38 negatively regulates TLR3-mediated interferon beta (IFN-beta) signaling by targeting ubiquitin-proteasomal degradation of TIR domain-containing adaptor inducing IFN-beta (TRIF). It functions as a valid target for autoantibodies in primary Sjogren's Syndrome. TRIM38 belongs the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. 58 matched cddid_all.tbl CDD cd16601 cd16601 438263 RING-HC_TRIM39_C-IV RING finger, HC subclass, found in tripartite motif-containing protein 39 (TRIM39) and similar proteins. TRIM39, also known as RING finger protein 23 (RNF23) or testis-abundant finger protein, is an E3 ubiquitin-protein ligase that plays a role in controlling DNA damage-induced apoptosis through inhibition of the anaphase promoting complex (APC/C), a multiprotein ubiquitin ligase that controls multiple cell cycle regulators, including cyclins, geminin, and others. TRIM39 also functions as a regulator of several key processes in the proliferative cycle. It directly regulates p53 stability. It modulates cell cycle progression and DNA damage responses via stabilizing p21. Moreover, TRIM39 negatively regulates the nuclear factor kappaB (NFkappaB)-mediated signaling pathway through stabilization of Cactin, an inhibitor of NFkappaB- and Toll-like receptor (TLR)-mediated transcription, which is induced by inflammatory stimulants such as tumor necrosis factor alpha. Furthermore, TRIM39 is a MOAP-1-binding protein that can promote apoptosis signaling through stabilization of MOAP-1 via the inhibition of its poly-ubiquitination process. TRIM39 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. 44 matched cddid_all.tbl CDD cd16602 cd16602 438264 RING-HC_TRIM41-like_C-IV RING finger, HC subclass, found in tripartite motif-containing proteins TRIM41, TRIM52 and similar proteins. TRIM41 and TRIM52, two closely related tripartite motif-containing proteins, have dramatically expanded RING domains compared with the rest of the TRIM family proteins. TRIM41 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. In contrast, TRIM52 lacks the putative viral recognition SPRY/B30.2 domain, and thus has been classified to the C-V subclass of the TRIM family that contains only RBCC domains. TRIM41, also known as RING finger-interacting protein with C kinase (RINCK), is an E3 ubiquitin-protein ligase that promotes the ubiquitination of protein kinase C (PKC) isozymes in cells. It specifically recognizes the C1 domain of PKC isozymes. It controls the amplitude of PKC signaling by controlling the amount of PKC in the cell. TRIM52, also known as RING finger protein 102 (RNF102), is encoded by a novel, noncanonical antiviral TRIM52 gene in primate genomes with unique specificity determined by the rapidly evolving RING domain. 53 matched cddid_all.tbl CDD cd16603 cd16603 438265 RING-HC_TRIM43-like_C-IV RING finger, HC subclass, found in tripartite motif-containing proteins TRIM43, TRIM48, TRIM49, TRIM51, TRIM64 and similar proteins. The family includes a group of closely related uncharacterized tripartite motif-containing proteins, TRIM43, TRIM43B, TRIM48/RNF101, TRIM49/RNF18, TRIM49B, TRIM49C/TRIM49L2, TRIM49D/TRIM49L, TRIM51/SPRYD5, TRIM64, TRIM64B, and TRIM64C, whose biological function remain unclear. TRIM49, also known as testis-specific RING-finger protein, has moderate similarity with SS-A/Ro52 antigen, suggesting it may be one of the target proteins of autoantibodies in the sera of patients with these autoimmune disorders. All family members belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. In RBCC region, they all have a C3HC4-type RING-HC finger. 59 matched cddid_all.tbl CDD cd16604 cd16604 438266 RING-HC_TRIM47-like_C-IV RING finger, HC subclass, found in tripartite motif-containing protein 47 (TRIM47) and similar proteins. TRIM47, also known as gene overexpressed in astrocytoma protein (GOA) or RING finger protein 100 (RNF100), belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. It plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. This subfamily also includes RING finger protein 135 (RNF135). RNF135, also known as RIG-I E3 ubiquitin ligase (REUL) or Riplet, is a widely expressed E3 ubiquitin-protein ligase that consists of an N-terminal C3HC4-type RING-HC finger and C-terminal B30.2/SPRY and PRY motifs, but lacks the B-box and coiled-coil domains that are also typically present in TRIM proteins. RNF135 serves as a specific retinoic acid-inducible gene-I (RIG-I)-interacting protein that ubiquitinates RIG-I and specifically stimulates RIG-I-mediated innate antiviral activity to produce antiviral type-I interferon (IFN) during the early phase of viral infection. It also has been identified as a bio-marker and therapy target of glioblastoma. It associates with the ERK signal transduction pathway and plays a role in glioblastoma cell proliferation, migration and cell cycle. 49 matched cddid_all.tbl CDD cd16605 cd16605 438267 RING-HC_TRIM50_like_C-IV RING finger, HC subclass, found in tripartite motif-containing protein TRIM50, TRIM73, TRIM74 and similar proteins. TRIM50 is a stomach-specific E3 ubiquitin-protein ligase, encoded by the Williams-Beuren syndrome (WBS) TRIM50 gene, which regulates vesicular trafficking for acid secretion in gastric parietal cells. It colocalizes, interacts with, and increases the level of p62/SQSTM1, a multifunctional adaptor protein implicated in various cellular processes including the autophagy clearance of polyubiquitinated protein aggregates. It also promotes the formation and clearance of aggresome-associated polyubiquitinated proteins through the interaction with histone deacetylase 6 (HDAC6), a tubulin specific deacetylase that regulates microtubule-dependent aggresome formation. TRIM50 can be acetylated by PCAF and p300. TRIM50 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. This subfamily also includes two paralogs of TRIM50, tripartite motif-containing protein 73 (TRIM73), also known as tripartite motif-containing protein 50B (TRIM50B), and tripartite motif-containing protein 74 (TRIM74), also known as tripartite motif-containing protein 50C (TRIM50C), both of which are WBS-related genes encoding proteins that may also act as E3 ligases. In contrast with TRIM50, TRIM73 and TRIM74 belong to the C-V subclass of TRIM family of proteins that are defined by N-terminal RBCC domains only. 45 matched cddid_all.tbl CDD cd16606 cd16606 438268 RING-HC_TRIM58_C-IV RING finger, HC subclass, found in tripartite motif-containing protein TRIM58 and similar proteins. TRIM58, also known as protein BIA2, is an erythroid E3 ubiquitin-protein ligase induced during late erythropoiesis. It binds and ubiquitinates the intermediate chain of the microtubule motor dynein (DYNC1LI1/DYNC1LI2), stimulating the degradation of the dynein holoprotein complex. It may participate in the erythroblast enucleation process through regulation of nuclear polarization. TRIM58 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. 53 matched cddid_all.tbl CDD cd16607 cd16607 438269 RING-HC_TRIM60-like_C-IV RING finger, HC subclass, found in tripartite motif-containing proteins TRIM60, TRIM61, TRIM75 and similar proteins. TRIM60, also known as RING finger protein 129 (RNF129) or RING finger protein 33 (RNF33), is a cytoplasmic protein expressed in the testis. It may play an important role in the spermatogenesis process, the development of the preimplantation embryo, and in testicular functions. RNF33 interacts with the cytoplasmic kinesin motor proteins KIF3A and KIF3B suggesting possible contribution to cargo movement along the microtubule in the expressed sites. It is also involved in spermatogenesis in Sertoli cells under the regulation of nuclear factor-kappaB (NF-kappaB). TRIM75 mainly localizes within spindles, suggesting it may function in spindle organization and thereby affect meiosis. Both TRIM60 and TRIM75 belong the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B2-box, and two coiled coil domains, as well as a PRY domain and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. In contrast, TRIM61 belongs to the C-V subclass of the TRIM family that contains RBCC domains only. Its biological function remains unclear. 48 matched cddid_all.tbl CDD cd16608 cd16608 438270 RING-HC_TRIM62_C-IV RING finger, HC subclass, found in tripartite motif-containing protein 62 (TRIM62) and similar proteins. TRIM62, also known as Ductal Epithelium Associated Ring Chromosome 1 (DEAR1), is a cytoplasmic E3 ubiquitin-protein ligase that was identified as a dominant regulator of acinar morphogenesis in the mammary gland. It is implicated in the inflammatory response of immune cells by regulating the Toll-like receptor 4 (TLR4) signaling pathway, leading to increased activity of the activator protein 1 (AP-1) transcription factor in primary macrophages. It is also involved in muscular protein homeostasis, especially during inflammation-induced atrophy, and may play a role in the pathogenesis of ICU-acquired weakness (ICUAW) by activating and maintaining inflammation in myocytes. Moreover, TRIM62 facilitates K27-linked poly-ubiquitination of CARD9 and also regulates CARD9-mediated anti-fungal immunity and intestinal inflammation. It also functions as a chromosome 1p35 tumor suppressor and negatively regulates transforming growth factor beta (TGFbeta)-driven epithelial-mesenchymal transition (EMT) by binding to and promoting the ubiquitination of SMAD3, a major effector of TGFbeta-mediated EMT. TRIM62 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. 52 matched cddid_all.tbl CDD cd16609 cd16609 438271 RING-HC_TRIM65_C-IV RING finger, HC subclass, found in tripartite motif-containing protein TRIM65 and similar proteins. TRIM65 is an E3 ubiquitin-protein ligase that interacts with the innate immune receptor MDA5, enhancing its ability to stimulate interferon-beta signaling. It functions as a potential oncogenic protein that negatively regulates p53 through ubiquitination, providing insight into the development of novel approaches targeting TRIM65 for non-small cell lung carcinoma (NSCLC) treatment, and also overcoming chemotherapy resistance. Moreover, TRIM65 negatively regulates microRNA-driven suppression of mRNA translation by targeting TNRC6 proteins for ubiquitination and degradation. TRIM65 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. 58 matched cddid_all.tbl CDD cd16610 cd16610 438272 RING-HC_TRIM68_C-IV RING finger, HC subclass, found in tripartite motif-containing protein 68 (TRIM68) and similar proteins. TRIM68, also known as RING finger protein 137 (RNF137) or SSA protein SS-56 (SS-56), is an E3 ubiquitin-protein ligase that negatively regulates Toll-like receptor (TLR)- and RIG-I-like receptor (RLR)-driven type I interferon production by degrading TRK fused gene (TFG), a novel driver of IFN-beta downstream of anti-viral detection systems. It also functions as a cofactor for androgen receptor-mediated transcription by regulating ligand-dependent transcription of androgen receptor in prostate cancer cells. Moreover, TRIM68 is a cellular target of autoantibody responses in Sjogre's syndrome (SS), as well as systemic lupus erythematosus (SLE). It is also an auto-antigen for T cells in SS and SLE. TRIM68 belongs the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, a B-box, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. 49 matched cddid_all.tbl CDD cd16611 cd16611 438273 RING-HC_TRIM69_C-IV RING finger, HC subclass, found in tripartite motif-containing protein 69 (TRIM69) and similar proteins. TRIM69, also known as RFP-like domain-containing protein trimless or RING finger protein 36 (RNF36), is a testis E3 ubiquitin-protein ligase that plays a specific role in apoptosis and may also play an important role in germ cell homeostasis during spermatogenesis. TRIM69 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. 59 matched cddid_all.tbl CDD cd16612 cd16612 438274 RING-HC_TRIM72_C-IV RING finger, HC subclass, found in tripartite motif-containing protein 72 (TRIM72) and similar proteins. TRIM72, also known as Mitsugumin-53 (MG53), is a muscle-specific protein that plays a central role in cell membrane repair by nucleating the assembly of the repair machinery at muscle injury sites. It is required in repair of alveolar epithelial cells under plasma membrane stress failure. It interacts with dysferlin to regulate sarcolemmal repair. Upregulation of TRIM72 develops obesity, systemic insulin resistance, dyslipidemia, and hyperglycemia, as well as induces diabetic cardiomyopathy through transcriptional activation of the peroxisome proliferation-activated receptor alpha (PPAR-alpha) signaling pathway. Compensation for the absence of AKT signaling by ERK signaling during TRIM72 overexpression leads to pathological hypertrophy. Moreover, TRIM72 functions as a novel negative feedback regulator of myogenesis by targeting insulin receptor substrate-1 (IRS-1). It is transcriptionally activated by the synergism of myogenin (MyoD) and myocyte enhancer factor 2 (MEF2). TRIM72 belongs to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. 60 matched cddid_all.tbl CDD cd16613 cd16613 438275 RING-HC_UHRF RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing proteins, UHRF1 and UHRF2, and similar proteins. UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumor suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of transcription factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation, but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) by interacting with the HBV core protein and promoting its degradation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal C3HC4-type RING-HC finger. 46 matched cddid_all.tbl CDD cd16614 cd16614 438276 RING-HC_UNK-like RING finger, HC subclass, found in RING finger protein unkempt (UNK), unkempt-like (UNKL), and similar proteins. UNK, also known as zinc finger CCCH domain-containing protein 5, is a metazoan-specific zinc finger protein enriched in embryonic brains. It may play a broad regulatory role during the formation of the central nervous system (CNS). It is a sequence-specific RNA-binding protein required for early neuronal morphology. UNK is a neurogenic component of the mTOR pathway, and functions as a negative regulator of the timing of photoreceptor differentiation. It also specifically binds to Brg/Brm-associated factor BAF60b and promotes its ubiquitination in a Rac1-dependent manner. UNKL, also known as zinc finger CCCH domain-containing protein 5-like, is a putative E3 ubiquitin-protein ligase that may participate in a protein complex showing an E3 ligase activity regulated by RAC1. Both UNK and UNKL contain several tandem CCCH-type zinc fingers at the N-terminus, and a C3HC4-type RING-HC finger at its C-terminus. 38 matched cddid_all.tbl CDD cd16615 cd16615 438277 RING-HC_ZNF598 RING finger, HC subclass, found in zinc finger protein 598 (ZNF598) and similar proteins. ZNF598 associates with eukaryotic initiation factor 4E (eIF4E) homologous protein from mammals (m4EHP) by binding to Grb10-interacting GYF protein 2 (GIGYF2). The m4EHP-GIGYF2 complex functions as a translational repressor and is essential for normal embryonic development of mammalian. ZNF598 harbors a C3HC4-type RING-HC finger at its N-terminus. 51 matched cddid_all.tbl CDD cd16616 cd16616 438278 mRING-HC-C4C4_Asi1p-like Modified RING finger, HC subclass (C4C4-type), found in Saccharomyces cerevisiae amino acid sensor-independent protein Asi1p, Asi3p and similar proteins. Asi1p and Asi3p are inner nuclear membrane proteins that act as negative regulators of SPS (Ssy1-Ptr3-Ssy5)-sensor signaling in yeast. Together with Asi2p, they assemble into an Asi complex that functions in the SPS amino acid sensing pathway involved in degradation of Stp1 and Stp2 transcription factors. Both Asi1p and Asi3p contain five membrane-spanning domains, as well as highly conserved RING fingers at their extreme C termini, which are C4C4-type RING finger motifs whose overall folding is similar to that of the C3HC4-type RING-HC finger. 53 matched cddid_all.tbl CDD cd16617 cd16617 438279 mRING-HC-C4C4_CesA "Modified RING finger, HC subclass (C4C4-type), found in Arabidopsis thaliana cellulose synthase A (CesA) catalytic subunits 1-10, and similar proteins from plants. This subfamily includes plant catalytic subunits of cellulose synthase terminal complexes (""rosettes"") required for beta-1,4-glucan microfibril crystallization, a major mechanism of cell wall formation. CesA1, also known as protein RADIALLY SWOLLEN 1 (RSW1), is required during embryogenesis for cell elongation, orientation of cell expansion and complex cell wall formations, such as interdigitated pattern of epidermal pavement cells, stomatal guard cells, and trichomes. It plays a role in lateral roots formation, but seems unnecessary for the development of tip-growing cells such as root hairs. CesA2, also known as Ath-A, is involved in the primary cell wall formation. It forms a homodimer. CesA3, also known as constitutive expression of VSP1 protein 1, isoxaben-resistant protein 1, Ath-B, protein ECTOPIC LIGNIN 1, or protein RADIALLY SWOLLEN 5 (RSW5), is involved in primary cell wall formation, especially in roots. CesA4, also known as protein IRREGULAR XYLEM 5 (IRX5), is involved in the secondary cell wall formation, and required for xylem cell wall thickening. CesA5 may be partially redundant with CesA6. CesA6, also known as AraxCelA, isoxaben-resistant protein 2, protein PROCUSTE 1, or protein QUILL, is involved in primary cell wall formation. Like CesA1, CesA6 is critical for cell expansion. CESA6-dependent cell elongation seems to be independent of gibberellic acid, auxin, and ethylene. CesA6 interacts with and moves along cortical microtubules for the process of cellulose deposition. CesA7, also known as protein FRAGILE FIBER 5, or protein IRREGULAR XYLEM 3 (IRX3), and CesA8, also known as protein IRREGULAR XYLEM 1 (IRX1) or protein LEAF WILTING 2, are both involved in secondary cell wall formation and also required for xylem cell wall thickening. The biological function of CesA9 and CesA10 remain unclear. CesA1, CesA3, and CesA6 form a functional complex essential for primary cell wall cellulose synthesis, while CesA4, CesA7, and CesA8 form a functional complex located in secondary cell wall deposition sites. All family members contain an N-terminal C4C4-type RING-HC finger and a C-terminal glycosyltransferase family A (GT-A) domain." 51 matched cddid_all.tbl CDD cd16618 cd16618 438280 mRING-HC-C4C4_CNOT4 Modified RING finger, HC subclass (C4C4-type), found in CCR4-NOT transcription complex subunit 4 (NOT4) and similar proteins. NOT4, also known as CCR4-associated factor 4, E3 ubiquitin-protein ligase CNOT4, or potential transcriptional repressor NOT4, is a component of the multifunctional CCR4-NOT complex, a global regulator of RNA polymerase II transcription. It associates with polysomes and contributes to the negative regulation of protein synthesis. NOT4 functions as an E3 ubiquitin-protein ligase that interacts with a specific E2, Ubc4/5 in yeast, and the ortholog UbcH5B in humans, and ubiquitylates a wide range of substrates, including ribosome-associated factors. Thus, it plays a role in cotranslational quality control (QC) through ribosome-associated ubiquitination and degradation of aberrant peptides. NOT4 contains a C4C4-type RING finger motif, whose overall folding is similar to that of the C3HC4-type RING-HC finger, a central RNA recognition motif (RRM), and a C-terminal domain predicted to be unstructured. 47 matched cddid_all.tbl CDD cd16619 cd16619 438281 mRING-HC-C4C4_TRIM37_C-VIII Modified RING finger, HC subclass (C4C4-type), found in tripartite motif-containing protein 37 (TRIM37) and similar proteins. TRIM37, also known as mulibrey nanism protein, or MUL, is a peroxisomal E3 ubiquitin-protein ligase that is involved in the tumorigenesis of several cancer types, including pancreatic ductal adenocarcinoma (PDAC), hepatocellular carcinoma (HCC), breast cancer, and sporadic fibrothecoma. It mono-ubiquitinates histone H2A, a chromatin modification associated with transcriptional repression. Moreover, TRIM37 possesses anti-HIV-1 activity, and interferes with viral DNA synthesis. Mutations in the human TRIM37 gene (also known as MUL) cause Mulibrey (muscle-liver-brain-eye) nanism, a rare growth disorder of prenatal onset characterized by dysmorphic features, pericardial constriction, and hepatomegaly. TRIM37 belongs to the C-VIII subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C4C4-type RING finger, whose overall folding is similar to that of the typical C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a MATH (meprin and TRAF-C homology) domain positioned C-terminal to the RBCC domain. Its MATH domain has been shown to interact with the TRAF (TNF-Receptor-Associated Factor) domain of six known TRAFs in vitro. 43 matched cddid_all.tbl CDD cd16620 cd16620 438282 vRING-HC-C4C4_RBBP6 Variant RING finger, HC subclass (C4C4-type), found in retinoblastoma-binding protein 6 (RBBP6) and similar proteins. RBBP6, also known as proliferation potential-related protein, protein P2P-R, retinoblastoma-binding Q protein 1 (RBQ-1), or p53-associated cellular protein of testis (PACT), is a nuclear E3 ubiquitin-protein ligase involved in multiple processes, such as the control of gene expression, mitosis, cell differentiation, and cell apoptosis. It plays a role in both promoting and inhibiting apoptosis in many human cancers, including esophageal, lung, hepatocellular, and colon cancers, familial myeloproliferative neoplasms, as well as in human immunodeficiency virus-associated nephropathy (HIVAN). It functions as an Rb- and p53-binding protein that plays an important role in chaperone-mediated ubiquitination and possibly in protein quality control. It acts as a scaffold protein to promote the assembly of the p53/TP53-MDM2 complex, resulting in an increase of MDM2-mediated ubiquitination and degradation of p53/TP53, and leading to both apoptosis and cell growth. It is also a double-stranded RNA-binding protein that plays a role in mRNA processing by regulating the human polyadenylation machinery and modulating expression of mRNAs with AU-rich 3' untranslated regions (UTRs). Moreover, RBBP6 ubiquitinates and destabilizes the transcriptional repressor ZBTB38 that negatively regulates transcription and levels of the MCM10 replication factor on chromatin. Furthermore, RBBP6 is involved in tunicamycin-induced apoptosis by mediating protein kinase (PKR) activation. RBBP6 contains an N-terminal ubiquitin-like domain and a C4C4-type RING finger, whose overall folding is similar to that of the typical C3HC4-type RING-HC finger. RBBP6 interacts with chaperones Hsp70 and Hsp40 through its N-terminal ubiquitin-like domain. It promotes the ubiquitination of p53 by Hdm2 in an E4-like manner through its RING finger. It also interacts directly with the pro-proliferative transcription factor Y-box-binding protein-1 (YB-1) via its RING finger. 55 matched cddid_all.tbl CDD cd16621 cd16621 438283 vRING-HC-C4C4_RFPL Variant RING finger, HC subclass (C4C4-type), found in Ret finger protein-like (RFPL) family. The RFPL family, also known as the RING-B30 family, represents a group of RFPL gene products, RFPL1, RFPL2, RFPL3, and RFPL4A, which are characterized by containing an N-terminal RFPL1, 2, 3-specifying helix (RSH), a C4C4- or a variant C4C4-type RING finger, whose overall folding is similar to that of the typical C3HC4-type RING-HC finger, an RFPL-defining motif (RDM), and C-terminal PRY/SPRY-forming B30.2 domain. RFPL1, also known as RING finger protein 78 (RNF78), is expressed during cell differentiation. RFPL2, also known as RING finger protein 79 (RNF79), shows high sequence similarity with other RFPL gene products. Its biological role remains unclear. RFPL3 interacts directly with CREB binding protein (CBP) in the nucleus of lung cancer cells. RFPL3 and CBP synergistically upregulate TERT activity and promote lung cancer growth. Moreover, RFPL3 acts as a novel E3 ubiquitin ligase modulating the integration activity of human immunodeficiency virus, type 1 (HIV-1) preintegration complex. RFPL4A, also known as RING finger protein 210 (RNF210), is a novel factor that increases the G1 population and decreases sensitivity to chemotherapy in human colorectal cancer cells. This model corresponds to the C4C4-type RING finger. RFPL4A lacks the fourth conserved zinc-binding residue, cysteine, and the eighth zinc-binding residue, cysteine; in RFPL2, it is replaced by serine. 48 matched cddid_all.tbl CDD cd16622 cd16622 438284 vRING-HC-C4C4_RBR_RNF217 Variant RING finger, HC subclass (C4C4-type), found in RING finger protein 217 (RNF217) and similar proteins. RNF217, also known as IBR domain-containing protein 1 (IBRDC1), is a transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligase mainly expressed in testis and skeletal muscle, as different splice variants. It interacts with the anti-apoptotic protein HAX1, and is adjacent to a translocation breakpoint involving ETV6 in childhood acute lymphoblastic leukemia (ALL). RNF217 contains a RBR domain followed by TMs. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a variant C4C4-type RING finger whose overall folding is similar to that of the C3HC4-type RING-HC finger. It is required for RBR-mediated ubiquitination. 49 matched cddid_all.tbl CDD cd16623 cd16623 438285 RING-HC_RFPL4B RING finger, HC subclass, found in Ret finger protein-like 4B (RFPL4B) and similar proteins. RFPL4B, also called RING finger protein 211 (RNF211), is an uncharacterized RING finger protein containing a typical C3HC4-type RING-HC finger. 63 matched cddid_all.tbl CDD cd16624 cd16624 438286 RING-HC_RBR_CUL9 RING finger, HC subclass, found in cullin-9 (CUL-9) and similar proteins. CUL-9, also known as UbcH7-associated protein 1 (H7-AP1), p53-associated parkin-like cytoplasmic protein, or PARC, is a cytoplasmic RBR-type E3 ubiquitin-protein ligase that is a tumor suppressor and promotes p53-dependent apoptosis. It mediates the ubiquitination and degradation of cytosolic cytochrome c to promote survival in neurons and cancer cells. It is also a critical downstream effector of the 3M complex in the maintenance of microtubules and genome integrity. Moreover, CUL-9, together with CUL-7, forms homodimers and heterodimers, as well as some atypical cullin RING ligase complexes, which may exhibit ubiquitin ligase activity. CUL-9 contains a CPH domain (Cul7, PARC, and HERC2), a DOC (DOC1/APC10) domain, cullin homology (CH) domains linked with E3 ligase function, and a C-terminal RBR domain previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C3HC4-type RING-HC finger required for RBR-mediated ubiquitination. 53 matched cddid_all.tbl CDD cd16625 cd16625 438287 RING-HC_RBR_HEL2-like RING finger, HC subclass, found in Saccharomyces cerevisiae histone E3 ligase 2 (HEL2) and similar proteins. HEL2 is an E3 ubiquitin-protein ligase that interacts with the E2 ubiquitin-conjugating enzyme UBC4 and histones H3 and H4. It plays an important role in regulating histone protein levels and also likely to contribute to the maintenance of genomic stability in the budding yeast. HEL2 can be phosphorylated by the DNA damage checkpoint kinase and histone protein regulator Rad53. This subfamily also includes Schizosaccharomyces pombe histone E3 ligase 1 (HEL1), also known as DNA-break-localizing protein 4 (dbl4), and Dictyostelium discoideum Ariadne-like ubiquitin ligase (RbrA). RbrA may act as an E3 ubiquitin-protein ligase that appears to be required for normal cell-type proportioning and cell sorting during multicellular development, and is also necessary for spore cell viability. Members of this subfamily contain an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C3HC4-type RING-HC finger required for RBR-mediated ubiquitination. 57 matched cddid_all.tbl CDD cd16626 cd16626 438288 RING-HC_RBR_HHARI RING finger, HC subclass, found in human homolog of Drosophila ariadne (HHARI) and similar proteins. This subfamily includes Drosophila melanogaster protein ariadne-1 (ARI-1), and its eukaryotic homologs, such as HHARI. ARI-1 is a widely expressed Drosophila RING-finger protein that localizes mainly in the cytoplasm and is required for neural development. It interacts with a novel ubiquitin-conjugating enzyme, UbcD10. HHARI, also known as H7-AP2, monocyte protein 6 (MOP-6), protein ariadne-1 homolog, Ariadne RBR E3 ubiquitin protein ligase 1 (ARIH1), ariadne-1 (ARI-1), UbcH7-binding protein, UbcM4-interacting protein, or ubiquitin-conjugating enzyme E2-binding protein 1, is an RBR-type E3 ubiquitin-protein ligase highly expressed in nuclei, where it is co-localized with nuclear bodies including Cajal, PML, and Lewy bodies. It interacts with the E2 conjugating enzymes UbcH7, UbcH8, UbcM4, and UbcD10 in human, mouse, and fly, and modulates the ubiquitylation of substrate proteins including single-minded 2 (SIM2) and translation initiation factor 4E homologous protein (4EHP). It functions as a potent mediator of DNA damage-induced translation arrest, which protects stem and cancer cells against genotoxic stress by initiating a 4EHP-mediated mRNA translation arrest. HHARI contains an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C3HC4-type RING-HC finger required for RBR-mediated ubiquitination. 59 matched cddid_all.tbl CDD cd16627 cd16627 438289 RING-HC_RBR_parkin "RING finger, HC subclass, found in parkin and similar proteins. Parkin, also known as Parkinson juvenile disease protein 2, is an RBR-type E3 ubiquitin-protein ligase that is associated with recessive early onset Parkinson""s disease (PD), and exerts a protective effect against dopamine-induced alpha-synuclein-dependent cell toxicity. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Parkin functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, RHOT1/MIRO1, MFN1, MFN2, STUB1, SNCAIP, SEPT5, TOMM20, USP30, ZNF746, and AIMP2. It mediates monoubiquitination, as well as Lys-6-, Lys-11-, Lys-48- and Lys-63-linked polyubiquitination of substrates depending on the context. Parkin may enhance cell viability and protect dopaminergic neurons from oxidative stress-mediated death by regulating mitochondrial function. It also limits the production of reactive oxygen species (ROS) and regulates cyclin-E during neuronal apoptosis. Moreover, parkin displays a ubiquitin ligase-independent function in transcriptional repression of p53. Parkin contains an N-terminal ubiquitin-like domain and a C-terminal RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C3HC4-type RING-HC finger required for RBR-mediated ubiquitination." 59 matched cddid_all.tbl CDD cd16628 cd16628 438290 RING-HC_RBR_RNF14 RING finger, HC subclass, found in RING finger protein 14 (RNF14) and similar proteins. RNF14, also known as androgen receptor-associated protein 54 (ARA54), HFB30, or Triad2 protein, is an RBR-type E3 ubiquitin-protein ligase that is highly expressed in the testis and interacts with class III E2s (UBE2E2, UbcH6, and UBE2E3). Its differential localization may play an important role in testicular development and spermatogenesis in humans. RNF14 functions as a transcriptional regulator of mitochondrial and immune function in muscle. It is a ligand-dependent androgen receptor (AR) co-activator and may also may participate in enhancing cell cycle progression and cell proliferation via induction of cyclin D1. Moreover, RNF14 is crucial for colon cancer cell survival. It acts as a new enhancer of the Wnt-dependent transcriptional outputs that acts at the level of the T-cell factor/lymphoid enhancer factor (TCF/LEF)-beta-catenin complex. RNF14 contains an N-terminal RWD domain and a C-terminal RBR domain. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C3HC4-type RING-HC finger required for RBR-mediated ubiquitination. 59 matched cddid_all.tbl CDD cd16629 cd16629 438291 RING-HC_RBR_RNF19 RING finger, HC subclass, found in the family of RING finger proteins RNF19A, RNF19B and similar proteins. The family includes RING finger protein RNF19A and RNF19B, both of which are transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligases. RNF19A, also known as double ring-finger protein (Dorfin) or p38, localizes to the ubiquitylated inclusions in Parkinson's disease (PD), dementia with Lewy bodies, multiple system atrophy, and amyotrophic lateral sclerosis (ALS). It interacts with Psmc3, a protein component of the 19S regulatory cap of the 26S proteasome, and further participates in the ubiquitin-proteasome system in acrosome biogenesis, spermatid head shaping, and development of the head-tail coupling apparatus and tail. It modulates the ubiquitination and degradation of calcium-sensing receptor (CaR), which may contribute to a general mechanism for CaR quality control during biosynthesis. Moreover, RNF19A can also ubiquitylate mutant superoxide dismutase 1 (SOD1), the causative gene of familial ALS. It may associate with endoplasmic reticulum-associated degradation (ERAD) pathway, which is related to the pathogenesis of neurodegenerative disorders, such as PD or Alzheimer's disease. RNF19B, also known as IBR domain-containing protein 3 or natural killer lytic-associated molecule (NKLAM), plays a role in controlling tumor dissemination and metastasis. It is involved in the cytolytic function of natural killer (NK) cells and cytotoxic T lymphocytes (CTLs). It interacts with ubiquitin conjugates UbcH7 and UbcH8, and ubiquitinates uridine kinase like-1 (URKL-1) protein, targeting it for degradation. Moreover, RNF19B is a novel component of macrophage phagosomes and plays a role in macrophage anti-bacterial activity. It functions as a novel modulator of macrophage inducible nitric oxide synthase (iNOS) expression. Both RNF19A and RNF19B contain an RBR domain followed by three TMs. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C3HC4-type RING-HC finger required for RBR-mediated ubiquitination. 56 matched cddid_all.tbl CDD cd16630 cd16630 438292 RING-HC_RBR_RNF216 RING finger, HC subclass, found in RING finger protein 216 (RNF216) and similar proteins. RNF216, also known as Triad domain-containing protein 3 (Triad3A), ubiquitin-conjugating enzyme 7-interacting protein 1, or zinc finger protein inhibiting NF-kappa-B (ZIN), is a RBR-type E3 ubiquitin-protein ligase that interacts with several components of Toll-like receptor (TLR) signaling and promotes their proteolytic degradation. It negatively regulates the RIG-I RNA sensing pathway through Lys48-linked, ubiquitin-mediated degradation of the tumor necrosis factor receptor-associated factor 3 (TRAF3) adapter following RNA virus infection. It also controls ubiquitination and proteasomal degradation of receptor-interacting protein 1 (RIP1), a serine/threonine protein kinase that is critically involved in tumor necrosis factor receptor-1 (TNF-R1)-induced NF-kappa B activation, following disruption of Hsp90 binding. Moreover, RNF216 is involved in inflammatory diseases through strongly inhibiting autophagy in macrophages. It interacts with and ubiquitinates BECN1, a key regulator in autophagy, thereby contributing to BECN1 degradation. It regulates synaptic strength by ubiquitination of Arc, resulting in its rapid proteasomal degradation. It is also a key negative regulator of sustained Killer cell Ig-like receptor (KIR) with two Ig-like domains and a long cytoplasmic domain 4 (2DL4)-mediated NF-kappaB signaling from internalized 2DL4, which functions by promoting ubiquitylation and degradation of endocytosed receptor from early endosomes. Furthermore, RNF216 interacts with human immunodeficiency virus type 1 (HIV-1) Virion infectivity factor (Vif) protein, which is essential for the productive infection of primary human CD4 T lymphocytes and macrophages. Mutations in RNF216 may result in Gordon Holmes syndrome, a condition defined by hypogonadotropic hypogonadism and cerebellar ataxia, as well as in autosomal recessive Huntington-like disorder. RNF216 contains a RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain use an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This family corresponds to the RING domain, a C3HC4-type RING-HC finger motif required for RBR-mediated ubiquitination. 58 matched cddid_all.tbl CDD cd16631 cd16631 438293 mRING-HC-C4C4_RBR_HOIP Modified RING finger, HC subclass (C4C4-type), found in HOIL-1-interacting protein (HOIP) and similar proteins. HOIP, also known as RING finger protein 31 (RNF31) or zinc in-between-RING-finger ubiquitin-associated domain protein, together with HOIL-1 and SHARPIN, forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis. It also interacts with the atypical mammalian orphan receptor DAX-1, trigger DAX-1 ubiquitination and stabilization, and participate in repressing steroidogenic gene expression. HOIP contains three Npl4 zinc fingers, a central ubiquitin-associated (UBA) domain responsible for the interaction with the N-terminal ubiquitin-like domain (UBL) of HOIL-1L, an RBR domain, and a C-terminal linear chain determining domain (LDD). The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C4C4-type RING finger motif whose overall folding is similar to that of the C3HC4-type RING-HC finger. It is required for RBR-mediated ubiquitination. 54 matched cddid_all.tbl CDD cd16632 cd16632 438294 mRING-HC-C4C4_RBR_RNF144 Modified RING finger, HC subclass (C4C4-type), found in RNF144 proteins. This group includes RNF144A and RNF144B, both of which are transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligases. RNF144A, also known as UbcM4-interacting protein 4 (UIP4) or ubiquitin-conjugating enzyme 7-interacting protein 4, targets DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and thus promote DNA damage-induced cell apoptosis. It is transcriptionally repressed by metastasis-associated protein 1 (MTA1) and inhibits MTA1-driven cancer cell migration and invasion. RNF144B, also known as PIR2, IBR domain-containing protein 2 (IBRDC2), or p53-inducible RING finger protein (p53RFP), induces p53-dependent but caspase-independent apoptosis. It interacts with E2 ubiquitin-conjugating enzymes UbcH7 and UbcH8, but not with UbcH5. It is involved in ubiquitination and degradation of p21, a p53 downstream protein promoting growth arrest and antagonizing apoptosis, suggesting a role in switching a cell from p53-mediated growth arrest to apoptosis. Moreover, RNF144B regulates the levels of Bax, a pro-apoptotic protein from the Bcl-2 family, and protects cells from unprompted Bax activation and cell death. It also regulates epithelial homeostasis by mediating degradation of p21WAF1 and p63. Both RNF144A and RNF144B contain an RBR domain followed by a potential single-TM domain. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C4C4-type RING finger whose overall folding is similar to that of the C3HC4-type RING-HC finger. It is required for RBR-mediated ubiquitination. 53 matched cddid_all.tbl CDD cd16633 cd16633 438295 mRING-HC-C3HC3D_RBR_HOIL1 Modified RING finger, HC subclass (C3HC3D-type), found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins. HOIL-1, also known as RBCK1, HOIL-1L, RanBP-type and C3HC4-type zinc finger-containing protein 1, HBV-associated factor 4, Hepatitis B virus X-associated protein 4, RING finger protein 54 (RNF54), ubiquitin-conjugating enzyme 7-interacting protein 3, or UbcM4-interacting protein 28 (UIP28), together with E3 ubiquitin-protein ligase RNF31 (also known as HOIP) and SHANK-associated RH domain interacting protein (SHARPIN), form the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis through conjugation of linear polyubiquitin chains to NF-kappaB essential modulator (also known as NEMO or IKBKG). HOIL-1 plays a crucial role in TNF-alpha-mediated NF-kappaB activation. It also functions as an ubiquitin-protein ligase E3 that interacts with not only PKCbeta, but also PKCzeta. It can recognize heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. HOIL-1 contains an N-terminal ubiqutin-like (UBL) domain and an Npl4 zinc-finger (NZF) domain, which regulate the interaction with the LUBAC subunit RNF31 and ubiquitin, respectively. The NZF domain belongs to the RanBP2-type zinc finger (zf-RanBP2) domain superfamily. In addition, HOIL-1 has an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a modified C3HC3D-type RING-HC finger required for RBR-mediated ubiquitination. 56 matched cddid_all.tbl CDD cd16634 cd16634 438296 mRING-HC-C3HC3D_Nrdp1 Modified RING finger, HC subclass (C3HC3D-type), found in neuregulin receptor degradation protein-1 (Nrdp1) and similar proteins. Nrdp1 (referred to as FLRF in mice), also known as RING finger protein 41 (RNF41), is an E3 ubiquitin-protein ligase that plays a critical role in the regulation of cell growth and apoptosis, inflammation and production of reactive oxygen species (ROS), as well as in doxorubicin (DOX)-induced cardiac injury. It promotes the degradation of the epidermal growth factor receptor (EGFR/ErbB) family member, ErbB3, which is independent of growth factor stimulation. It also promotes M2 macrophage polarization by ubiquitinating and activating transcription factor CCAAT/enhancer-binding protein beta (C/EBPbeta) via Lys-63-linked ubiquitination. Moreover, Nrdp1 interacts with and modulates the activity of Parkin, a causative protein for early onset recessive juvenile parkinsonism (AR-JP). It also interacts with ubiquitin-specific protease 8 (USP8), which is involved in trafficking of various transmembrane proteins. Furthermore, Nrdp1 inhibits basal lysosomal degradation and enhances ectodomain shedding of JAK2-associated cytokine receptors. Its phosphorylation by the kinase Par-1b (also known as MARK2) is required for epithelial cell polarity. Nrdp1 contains an N-terminal modified C3HC3D-type RING-HC finger required for enhancing ErbB3 degradation, a B-box, a coiled-coil domain responsible for Nrdp1 oligomerization, and a C-terminal ErbB3-binding domain. 43 matched cddid_all.tbl CDD cd16635 cd16635 438297 mRING-HC-C3HC3D_PHRF1 Modified RING finger, HC subclass (C3HC3D-type), found in PHD and RING finger domain-containing protein 1 (PHRF1) and similar proteins. PHRF1, also known as KIAA1542, or CTD-binding SR-like protein rA9, is a ubiquitin ligase which induces the ubiquitination of TGIF (TG-interacting factor) at lysine 130. It acts as a tumor suppressor that promotes the transforming growth factor (TGF)-beta cytostatic program through selective release of TGIF-driven promyelocytic leukemia protein (PML) inactivation. PHRF1 contains a plant homeodomain (PHD) finger and a modified C3HC3D-type RING-HC finger. 51 matched cddid_all.tbl CDD cd16636 cd16636 438298 mRING-HC-C3HC3D_SCAF11 Modified RING finger, HC subclass (C3HC3D-type), found in SR-related and CTD-associated factor 11 (SCAF11) and similar proteins. SCAF11, also known as CTD-associated SR protein 11 (CASP11), renal carcinoma antigen NY-REN-40, SC35-interacting protein 1 (Sip1), Serine/arginine-rich splicing factor 2 (SRSF2)-interacting protein, or splicing regulatory protein 129 (SRrp129), is a novel arginine-serine-rich (RS) domain-containing protein essential for pre-mRNA splicing. It functions as an auxiliary splice factor interacting with the spliceosomal component SC35, promoting RNAPII elongation. In addition to SR proteins, such as SC35, ASF/SF2, SRp75, and SRp20, SCAF11 also associates with U1-70K and U2AF65, proteins associated with 5' and 3' splice sites, respectively. SCAF11 contains an N-terminal modified C3HC3D-type RING-HC finger, an internal serine-arginine rich domain (SR domain), and a C-terminal SRI domain. 52 matched cddid_all.tbl CDD cd16637 cd16637 438299 mRING-HC-C3HC3D_LNX1-like Modified RING finger, HC subclass (C3HC3D-type), found in ligand of Numb protein LNX1, LNX2, and similar proteins. The ligand of Numb protein X (LNX) family, also known as PDZ and RING (PDZRN) family, includes LNX1-5, which can interact with Numb, a key regulator of neurogenesis and neuronal differentiation. LNX5 (also known as PDZK4 or PDZRN4L) shows high sequence homology to LNX3 and LNX4, but it lacks the RING domain. LNX1-4 proteins function as E3 ubiquitin ligases and have a unique domain architecture consisting of an N-terminal RING-HC finger for E3 ubiquitin ligase activity and either two or four PDZ domains necessary for substrate-binding. LNX1/LNX2-like proteins contain a modified C3HC3D-type RING-HC finger and four PDZ domains. This model corresponds to the RING finger. 42 matched cddid_all.tbl CDD cd16638 cd16638 438300 mRING-HC-C3HC3D_Roquin Modified RING finger, HC subclass (C3HC3D-type), found in Roquin-1, Roquin-2, and similar proteins. The ROQUIN family includes Roquin-1, Roquin-2, and similar proteins, which localize to the cytoplasm and upon stress, are concentrated in stress granules. They may play essential roles in preventing T-cell-mediated autoimmune disease and in microRNA-mediated repression of inducible costimulator (Icos) mRNA. They function as E3 ubiquitin ligases consisting of an N-terminal modified C3HC3D-type RING-HC finger with a potential E3 activity, a highly conserved ROQ domain required for RNA binding and localization to stress granules, and a CCCH-type zinc finger involved in RNA recognition. 44 matched cddid_all.tbl CDD cd16639 cd16639 438301 RING-HC_TRAF2 RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 2 (TRAF2) and similar proteins. TRAF2, also known as tumor necrosis factor type 2 receptor-associated protein 3, is an E3 ubiquitin-protein ligase that was identified as a 75 kDa tumor necrosis factor receptor (TNF-R2)-associated signaling protein. It interacts with members of the TNF receptor superfamily and connects the receptors to downstream signaling proteins. It also mediates K63-linked polyubiquitination of RIP1, a kinase pivotal in TNFalpha-induced NF-kappaB activation. Moreover, TRAF2 regulates peripheral CD8(+) T-cell and NKT-cell homeostasis by modulating sensitivity to IL-15. It also acts as an important biological suppressor of necroptosis. It inhibits TNF-related apoptosis inducing ligand (TRAIL)- and CD95L-induced apoptosis and necroptosis. TRAF2 contains an N-terminal domain with a typical C3HC4-type RING-HC finger and several zinc fingers, and a C-terminal TRAF domain that comprises a coiled coil domain and a conserved TRAF-C domain. 43 matched cddid_all.tbl CDD cd16640 cd16640 438302 RING-HC_TRAF3 RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 3 (TRAF3) and similar proteins. TRAF3, also known as CAP-1, CD40 receptor-associated factor 1 (CRAF1), CD40-binding protein (CD40BP), or LMP1-associated protein 1 (LAP1), is a member of the TRAF protein family, which mainly functions in the immune system, where it mediates signaling through tumor necrosis factor receptors (TNFRs) and interleukin-1/Toll-like receptors (IL-1/TLRs). It also plays a unique cell type-specific and critical role in the restraint of B-cell homeostatic survival, a role with important implications for both B-cell differentiation and the pathogenesis of B-cell malignancies. TRAF3 differentially regulates differentiation of specific T cell subsets. It is required for iNKT cell development, restrains Treg cell development in the thymus, and plays an essential role in the homeostasis of central memory CD8+ T cells. TRAF3 contains an N-terminal domain with a typical C3HC4-type RING-HC finger and several zinc fingers, and a C-terminal TRAF domain that comprises a coiled coil domain, and a conserved TRAF-C domain. 42 matched cddid_all.tbl CDD cd16641 cd16641 438303 mRING-HC-C3HC3D_TRAF4 Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 4 (TRAF4) and similar proteins. TRAF4, also known as cysteine-rich domain associated with RING and Traf domains protein 1, metastatic lymph node gene 62 protein (MLN 62), or RING finger protein 83 (RNF83), is a member of the TRAF protein family, which mainly function in the immune system, where they mediate signaling through tumor necrosis factor receptors (TNFRs) and interleukin-1/Toll-like receptors (IL-1/TLRs). It also plays a critical role in nervous system, as well as in carcinogenesis. TRAF4 promotes the growth and invasion of colon cancer through the Wnt/beta-catenin pathway. It contributes to the TNFalpha-induced activation of the 70 kDa ribosomal protein S6 kinase (p70s6k) signaling pathway, and activation of transforming growth factor beta (TGF-beta)-induced SMAD-dependent signaling and non-SMAD signaling in breast cancer. It also enhances osteosarcoma cell proliferation and invasion by the Akt signaling pathway. Moreover, TRAF4 is a novel phosphoinositide-binding protein modulating tight junctions and favoring cell migration. TRAF4 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and several zinc fingers, and a C-terminal TRAF domain that comprises a coiled coil domain and a conserved TRAF-C domain. 45 matched cddid_all.tbl CDD cd16642 cd16642 438304 mRING-HC-C3HC3D_TRAF5 Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 5 (TRAF5) and similar proteins. TRAF5, also known as RING finger protein 84 (RNF84), is an important signal transducer for a wide range of TNF receptor superfamily members, including tumor necrosis factor receptor 1 (TNFR1), TNFR2, CD40, and other lymphocyte costimulatory receptors, RANK/TRANCE-R, ectodysplasin-A Receptor (EDAR), lymphotoxin-beta receptor (LT-betaR), latent membrane protein 1 (LMP1), and IRE1. It functions as an activator of NF-kappaB, MAPK, and JNK, and is involved in both RANKL- and TNFalpha-induced osteoclastogenesis. It mediates CD40 signaling by associating with the cytoplasmic tail of CD40. It also negatively regulates Toll-like receptor (TLR) signaling and functions as a negative regulator of the interleukin 6 (IL-6) receptor signaling pathway that limits the differentiation of inflammatory CD4(+) T cells. TRAF5 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and several zinc fingers, and a C-terminal TRAF domain that comprises a coiled coil domain and a conserved TRAF-C domain. 56 matched cddid_all.tbl CDD cd16643 cd16643 438305 mRING-HC-C3HC3D_TRAF6 Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6) and similar proteins. TRAF6, also known as interleukin-1 signal transducer or RING finger protein 85 (RNF85), is a cytoplasmic adapter protein that mediates signals induced by the tumor necrosis factor receptor (TNFR) superfamily and Toll-like receptor (TLR)/interleukin-1 receptor (IL-1R) family. It functions as a mediator involved in the activation of mitogen-activated protein kinase (MAPK), phosphoinositide 3-kinase (PI3K), and interferon regulatory factor pathways, as well as in IL-1R-mediated activation of NF-kappaB. TRAF6 is also an oncogene that plays a vital role in K-RAS-mediated oncogenesis. TRAF6 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and several zinc fingers, and a C-terminal TRAF domain that comprises a coiled coil domain and a conserved TRAF-C domain. 58 matched cddid_all.tbl CDD cd16644 cd16644 438306 mRING-HC-C3HC3D_TRAF7 Modified RING finger, HC subclass (C3HC3D-type), found in tumor necrosis factor (TNF) receptor-associated factor 7 (TRAF7) and similar proteins. TRAF7, also known as RING finger and WD repeat-containing protein 1 or RING finger protein 119 (RNF119), is an E3 ubiquitin-protein ligase involved in signal transduction pathways that lead either to activation or repression of NF-kappaB transcription factor by promoting K29-linked ubiquitination of several cellular targets, including the NF-kappaB essential modulator (NEMO) and the p65 subunit of NF-kappaB transcription factor. It is also involved in K29-linked polyubiquitination that has been implicated in lysosomal degradation of proteins. Moreover, TRAF7 is required for K48-linked ubiquitination of p53, a key tumor suppressor and a master regulator of various signaling pathways, such as those related to apoptosis, cell cycle and DNA repair. It is also required for tumor necrosis factor alpha (TNFalpha)-induced Jun N-terminal kinase activation and promotes cell death by regulating polyubiquitination and lysosomal degradation of c-FLIP protein. Furthermore, TRAF7 functions as small ubiquitin-like modifier (SUMO) E3 ligase involved in other post-translational modification, such as sumoylation. It binds to and stimulates sumoylation of the proto-oncogene product c-Myb, a transcription factor regulating proliferation and differentiation of hematopoietic cells. It potentiates MEKK3-induced AP1 and CHOP activation and induces apoptosis. Meanwhile, TRAF7 mediates MyoD1 regulation of the pathway and cell-cycle progression in myoblasts. It also plays a role in Toll-like receptors (TLR) signaling. TRAF7 contains an N-terminal domain with a modified C3HC3D-type RING-HC finger and an adjacent zinc finger, and a unique C-terminal domain that comprises a coiled coil domain and seven WD40 repeats. 47 matched cddid_all.tbl CDD cd16645 cd16645 438307 mRING-HC-C3HC3D_TRIM23_C-IX Modified RING finger, HC subclass (C3HC3D-type), found in tripartite motif-containing protein 23 (TRIM23) and similar proteins. TRIM23, also known as ADP-ribosylation factor domain-containing protein 1, GTP-binding protein ARD-1, or RING finger protein 46 (RNF46), is an E3 ubiquitin-protein ligase belonging to the C-IX subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a modified C3HC3D-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as C-terminal ADP ribosylation factor (ARF) domains. TRIM23 is involved in nuclear factor (NF)-kappaB activation. It mediates atypical lysine 27 (K27)-linked polyubiquitin conjugation to NF-kappaB essential modulator NEMO, also known as IKKgamma, which plays an important role in the NF-kappaB pathway, and this conjugation is essential for TLR3- and RIG-I/MDA5-mediated antiviral innate and inflammatory responses. It also regulates adipocyte differentiation via stabilization of the adipogenic activator peroxisome proliferator-activated receptor gamma (PPARgamma) through atypical ubiquitin conjugation to PPARgamma. Moreover, TRIM23 interacts with and polyubiquitinates yellow fever virus (YFV) NS5 to promote its binding to STAT2 and trigger type I interferon (IFN-I) signaling inhibition. 50 matched cddid_all.tbl CDD cd16646 cd16646 438308 mRING-HC-C2H2C4_MDM2-like Modified RING finger, HC subclass (C2H2C4-type), found in E3 ubiquitin-protein ligase MDM2, protein MDM4 and similar proteins. MDM2 (also known as HDM2) and MDM4 (also known as MDMX or HDMX) are the primary p53 tumor suppressor negative regulators. They have non-redundant roles in the regulation of p53. MDM2 mainly functions to control p53 stability, while MDM4 controls p53 transcriptional activity. Both MDM2 and MDM4 contain an N-terminal p53-binding domain, a RanBP2-type zinc finger (zf-RanBP2) domain near the central acidic region, and a C-terminal modified C2H2C4-type RING-HC finger. Mdm2 can form homo-oligomers through its RING domain and displays E3 ubiquitin ligase activity that catalyzes the attachment of ubiquitin to p53 as an essential step in the regulation of its levels in cells. Despite its RING domain and structural similarity with MDM2, MDM4 does not homo-oligomerize and lacks ubiquitin-ligase function, but inhibits the transcriptional activity of p53. In addition, both their RING domains are responsible for the hetero-oligomerization, which is crucial for the suppression of P53 activity during embryonic development and the recruitment of E2 ubiquitin-conjugating enzymes. Moreover, MDM2 and MDM4 can be phosphorylated and destabilized in response to DNA damage stress. In response to ribosomal stress, MDM2-mediated p53 ubiquitination and degradation can be inhibited through the interaction with ribosomal proteins L5, L11, and L23. However, MDM4 is not bound to ribosomal proteins, suggesting its different response to regulation by small basic proteins such as ribosomal proteins and ARF. 52 matched cddid_all.tbl CDD cd16647 cd16647 438309 mRING-HC-C3HC5_NEU1 Modified RING finger, HC subclass (C3HC5-type), found in neuralized-like protein NEURL1A, NEURL1B, and similar proteins. This subfamily includes Drosophila neuralized (D-neu) protein, and its two mammalian homologs, NEURL1A and NEURL1B. D-neu is a regulator of the developmentally important Notch signaling pathway. NEURL1A, also known as NEURL1, NEU, neuralized 1, or RING finger protein 67 (RNF67), is a mammalian homolog of D-neu. It functions as an E3 ubiquitin-protein ligase that directly interacts with and monoubiquitinates cytoplasmic polyadenylation element-binding protein 3 (CPEB3), an RNA binding protein and a translational regulator of local protein synthesis, which facilitates hippocampal plasticity and hippocampal-dependent memory storage. It also acts as a potential tumor suppressor that causes apoptosis and downregulates Notch target genes in medulloblastoma. NEURL1B, also known as neuralized-2 (NEUR2) or neuralized-like protein 3, is another mammalian homolog of D-neu protein. It functions as an E3 ubiquitin-protein ligase that interacts with and ubiquitinates Delta. Thus, it plays a role in the endocytic pathways for Notch signaling by working cooperatively with another E3 ligase, Mind bomb-1 (Mib1), in Delta endocytosis to hepatocyte growth factor-regulated tyrosine kinase substrate (Hrs)-positive vesicles. Members of this subfamily contain two neuralized homology regions (NHRs) responsible for Neural-ligand interactions and a modified C3HC5-type RING-HC finger required for ubiquitin ligase activity. The C3HC5-type RING-HC finger is distinguished from typical C3HC4-type RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain. 53 matched cddid_all.tbl CDD cd16648 cd16648 438310 mRING-HC-C3HC5_MAPL Modified RING finger, HC subclass (C3HC5-type), found in mitochondrial-anchored protein ligase (MAPL) and similar proteins. MAPL, also known as MULAN, mitochondrial ubiquitin ligase activator of NFKB 1, E3 SUMO-protein ligase MUL1, E3 ubiquitin-protein ligase MUL1, growth inhibition and death E3 ligase (GIDE), putative NF-kappa-B-activating protein 266, or RING finger protein 218 (RNF218), is a multifunctional mitochondrial outer membrane protein involved in several processes specific to metazoan (multicellular animal) cells, such as NF-kappaB activation, innate immunity and antiviral signaling, suppression of PINK1/parkin defects, mitophagy in skeletal muscle, and caspase-dependent apoptosis. MAPL contains a unique BAM (beside a membrane)/GIDE (growth inhibition death E3 ligase) domain and a C-terminal modified cytosolic C3HC5-type RING-HC finger which is distinguished from typical C3HC4-type RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain. 52 matched cddid_all.tbl CDD cd16649 cd16649 438311 mRING-HC-C3HC5_CGRF1-like Modified RING finger, HC subclass (C3HC5-type), found in RING finger proteins, RNF26, RNF197 (CGRRF1), RNF156 (MGRN1), RNF157 and similar proteins. This subfamily corresponds to a group of RING finger proteins containing a modified C3HC5-type RING-HC finger, which is distinguished from typical C3HC4 RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain. Cell growth regulator with RING finger domain protein 1 (CGRRF1), also known as cell growth regulatory gene 19 protein (CGR19) or RING finger protein 197 (RNF197), functions as a novel biomarker to monitor endometrial sensitivity and response to insulin-sensitizing drugs, such as metformin, in the context of obesity. RNF26 is an E3 ubiquitin ligase that temporally regulates virus-triggered type I interferon induction by increasing the stability of Mediator of IRF3 activation, MITA, also known as STING, through K11-linked polyubiquitination after viral infection and promoting degradation of IRF3, another important component required for virus-triggered interferon induction. Mahogunin ring finger-1 (MGRN1), also known as RING finger protein 156 (RNF156), is a cytosolic E3 ubiquitin-protein ligase that inhibits signaling through the G protein-coupled melanocortin receptors-1 (MC1R), -2 (MC2R) and -4 (MC4R) via ubiquitylation-dependent and -independent processes. It suppresses chaperone-associated misfolded protein aggregation and toxicity. RNF157 is a cytoplasmic E3 ubiquitin ligase predominantly expressed in the brain. It is a homolog of the E3 ligase MGRN1. In cultured neurons, it promotes neuronal survival in an E3 ligase-dependent manner. In contrast, it supports growth and maintenance of dendrites independent of its E3 ligase activity. RNF157 interacts with and ubiquitinates the adaptor protein APBB1 (amyloid beta precursor protein-binding, family B, member 1 or Fe65), which regulates neuronal survival, but not dendritic growth downstream of RNF157. The nuclear localization of APBB1 together with its interaction partner RNA-binding protein SART3 (squamous cell carcinoma antigen recognized by T cells 3 or Tip110) is crucial to trigger apoptosis. 40 matched cddid_all.tbl CDD cd16650 cd16650 438312 SP-RING_PIAS-like SP-RING finger found in the Siz/PIAS RING (SP-RING) family of SUMO E3 ligases. The SP-RING family includes PIAS (protein inhibitor of activated STAT) proteins, Zmiz proteins, and Siz proteins from plants and fungi. PIAS proteins modulate the activity of several transcription factors and act as E3 ubiquitin ligases in the sumoylation pathway. There are four members: PIAS1, PIAS2 (also known as PIASx), PIAS3, and PIAS4 (also known as PIASy). PIAS proteins were initially identified as inhibitors of activated STAT only, but are now known to interact with and modulate several other proteins, including androgen receptor (AR), tumor suppressor p53, and the transforming growth factor-beta (TGF-beta) signaling protein SMAD. They interact with STATs in a cytokine-dependent manner. PIAS proteins have SUMO E3-ligase activity and interaction of PIAS proteins with transcription factors often results in sumoylation of that protein. Zmiz1 (Zimp10) and its homolog Zmiz2 (Zimp7) were initially identified in humans as androgen receptor (AR) interacting proteins that function as transcriptional co-activators. They interact with BRG1, the catalytic subunit of the SWI-SNF remodeling complex. They also associate with other hormone nuclear receptors and transcription factors such as p53 and Smad3/Smad4, and regulate transcription of specific target genes by altering their chromatin structure. SIZ1 proteins from plants and fungi are also founding members of this family. SIZ1-mediated conjugation of SUMO1 and SUMO2 to other intracellular proteins is essential in Arabidopsis. Yeast SIZ proteins are SUMO E3 ligases involved in a novel pathway of chromosome maintenance. They enhance SUMO modification to many substrates in vivo, but also exhibit unique substrate specificity. PIAS proteins contain a specific RING finger known as Siz/PIAS (protein inhibitor of activated signal transducer and activator of transcription) RING (SP-RING) finger, which is essential for SUMO ligase activity. The SP-RING finger is a variant of the RING finger, which lacks the second, fifth, and sixth zinc-binding residues of the consensus C3H2C3-/C3HC4-type RING fingers. It binds a single Zn ion, instead of two ions bound by typical RING fingers. 48 matched cddid_all.tbl CDD cd16651 cd16651 438313 SPL-RING_NSE2 SPL-RING finger found in E3 SUMO-protein ligase NSE2 and similar proteins. NSE2, also known as MMS21 homolog (MMS21) or non-structural maintenance of chromosomes element 2 homolog (Non-SMC element 2 homolog, NSMCE2), is an autosumoylating small ubiquitin-like modifier (SUMO) ligase required for the response to DNA damage. It regulates sumoylation and nuclear-to-cytoplasmic translocation of skeletal and heart muscle-specific variant of the alpha subunit of nascent polypeptide associated complex (skNAC)-Smyd1 in myogenesis. It is also required for resisting extrinsically induced genotoxic stress. Moreover, NSE2 together with its partner proteins SMC6 and SMC5 form a tight subcomplex of the structural maintenance of chromosomes SMC5-6 complex, which includes another two subcomplexes, NSE1-NSE3-NSE4 and NSE5-NSE6. SMC6 and NSE3 are sumoylated in an NSE2-dependent manner, but SMC5 and NSE1 are not. NSE2-dependent E3 SUMO ligase activity is required for efficient DNA repair, but not for SMC5-6 complex stability. NSE2 contains a RING variant known as a Siz/PIAS (protein inhibitor of activated signal transducer and activator of transcription)-like RING (SPL-RING) finger that is likely shared by the SP-RING type SUMO E3 ligases, such as PIAS family proteins. The SPL-RING finger is a variant of the RING finger, which lacks the second, fifth, and sixth zinc-binding residues of the consensus C3H2C3-/C3HC4-type RING fingers. It harbors only one Zn binding site and is required for the sumoylating activity. 67 matched cddid_all.tbl CDD cd16652 cd16652 438314 dRING_Rmd5p-like Degenerated RING (dRING) finger found in Saccharomyces cerevisiae required for meiotic nuclear division protein 5 (Rmd5p) and similar proteins. Rmd5p, also known as glucose-induced degradation protein 2 (Gid2) or sporulation protein RMD5, is an E3 ubiquitin ligase containing a Lissencephaly type-1-like homology motif (LisH), a C-terminal to LisH motif (CTLH) domain, and a degenerated RING finger that is characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues compared with the classic C3H2C3-/C3HC4-type RING fingers. It forms the heterodimeric E3 ligase unit of the glucose induced degradation deficient (GID) complex with Gid9 (also known as Fyv10), which has a degenerated RING finger as well. The GID complex triggers polyubiquitylation and subsequent proteasomal degradation of the gluconeogenic enzymes fructose-1, 6-bisphosphate by fructose-1, 6-bisphosphatase (FBPase), phosphoenolpyruvate carboxykinase (PEPCK), and cytoplasmic malate dehydrogenase (c-MDH). Moreover, Rmd5p can form the GID complex with the other six Gid proteins, including Gid1/Vid30, Gid4/Vid24, Gid5/Vid28, Gid7, Gid8, and Gid9/Fyv10. The GID complex in which the seven Gid proteins reside functions as a novel ubiquitin ligase (E3) involved in the regulation of carbohydrate metabolism. 49 matched cddid_all.tbl CDD cd16653 cd16653 438315 RING-like_Rtf2 RING-like Rtf2 domain, C2HC2-type, found in the replication termination factor 2 (Rtf2) protein family. The Rtf2 protein family includes a group of conserved proteins found in eukaryotes ranging from fission yeast to humans. The defining member of the family is Schizosaccharomyces pombe Rtf2 (SpRtf2), which is a proliferating cell nuclear antigen-interacting protein that functions as a key requirement for efficient replication termination at the site-specific replication barrier RTS1. It promotes termination at RTS1 by preventing replication restart. SpRtf2 contains a RING-like Rtf2 domain that is characterized by a C2HC2 motif similar to C3HC4 RING-HC finger motif known to bind two Zn2+ ions and mediate protein-protein interactions. The C2HC2 motif lacks three of the seven conserved cysteines of the C3HC4 motif, and forms only one functional Zn2+ ion-binding site. The RING-like Rtf2 domain in fission yeast is required to stabilize a paused DNA replication fork during imprinting at the mating type locus, possibly by facilitating sumoylation of PCNA. The family also includes Arabidopsis RTF2 (AtRTF2), an essential nuclear protein required for both normal embryo development and for proper expression of the GFP reporter gene. It plays a critical role in splicing the GFP pre-mRNA, and may also have a more transient regulatory role during the spliceosome cycle. The biological function of Rtf2 homologs found in eumetazoa remains unclear. They contain a variant C2HC2 motif where the middle conserved histidine has been replaced by cysteine. 47 matched cddid_all.tbl CDD cd16654 cd16654 438316 RING-Ubox_CHIP U-box domain, a modified RING finger, found in carboxyl terminus of HSP70-interacting protein (CHIP) and similar proteins. CHIP, also known as STIP1 homology and U box-containing protein 1 (STUB1), CLL-associated antigen KW-8, or Antigen NY-CO-7, is a multifunctional protein that functions both as a co-chaperone and an E3 ubiquitin-protein ligase. It couples protein folding and proteasome mediated degradation by interacting with heat shock proteins (e.g. HSC70) and ubiquitinating their misfolded client proteins, thereby targeting them for proteasomal degradation. It is also important for cellular differentiation and survival (or apoptosis), as well as susceptibility to stress. It targets a wide range of proteins, such as expanded ataxin-1, ataxin-3, huntingtin, and androgen receptor, which play roles in glucocorticoid response, tau degradation, and both p53 and cAMP signaling. CHIP contains an N-terminal tetratricopeptide repeat (TPR) domain responsible for protein-protein interaction, a highly charged middle coiled-coil (CC), and a C-terminal RING-like U-box domain acting as an ubiquitin ligase. 71 matched cddid_all.tbl CDD cd16655 cd16655 438317 RING-Ubox_WDSUB1-like U-box domain, a modified RING finger, found in WD repeat, SAM and U-box domain-containing protein 1 (WDSUB1) and similar proteins. WDSUB1 is an uncharacterized protein containing seven WD40 repeats and a SAM domain in addition to the U-box. Its biological role remains unclear. This subfamily also includes many uncharacterized kinase domain-containing U-box (AtPUB) proteins and several MIF4G motif-containing AtPUB proteins from Arabidopsis. 55 matched cddid_all.tbl CDD cd16656 cd16656 438318 RING-Ubox_PRP19 U-box domain, a modified RING finger, found in pre-mRNA-processing factor 19 (Prp19) and similar proteins. Prp19, also known as nuclear matrix protein 200 (NMP200), senescence evasion factor (SNEV), or DNA repair protein Pso4 (psoralen-sensitive mutant 4), is a ubiquitously expressed multifunctional E3 ubiquitin ligase with pleiotropic activities in DNA damage signaling, repair, and replicative senescence. It functions as a critical component of DNA repair and DNA damage checkpoint complexes. It senses DNA damage, binds double-stranded DNA in a sequence-independent manner, facilitates processing of damaged DNA, promotes DNA end joining, regulates replication protein A (RPA2) phosphorylation and ubiquitination at damaged DNA, and regulates RNA splicing and mitotic spindle formation in its integral capacity as a scaffold for a multimeric core complex. Prp19 contains an N-terminal E3 ubiquitin ligase U-box domain with E2 recruitment function that facilitates dimerization and is essential for its auto-ubiquitination activity in vitro or when overexpressed, a coiled-coil Prp19 homology region that mediates its tetramerization and interaction with CDC5L and SPF27, and a C-terminal seven-bladed WD40 beta-propeller type of leucine-rich architectural repeats that form an asymmetrical barrel-shaped structure important for substrate recognition and recruitment. 54 matched cddid_all.tbl CDD cd16657 cd16657 438319 RING-Ubox_UBE4A U-box domain, a modified RING finger, found in ubiquitin conjugation factor E4 A (UBE4A) and similar proteins. This subfamily includes yeast ubiquitin fusion degradation protein 2 (UFD2p) and its mammalian homolog, UBE4A. Yeast UFD2p, also known as ubiquitin conjugation factor E4 or UB fusion protein 2, is a polyubiquitin chain conjugation factor (E4) in the ubiquitin fusion degradation (UFD) pathway which catalyzes elongation of the ubiquitin chain through Lys48 linkage. It binds to substrates conjugated with one to three ubiquitin molecules and catalyzes the addition of further ubiquitin moieties in the presence of ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2) and ubiquitin ligase (E3), yielding multiubiquitylated substrates that are targets for the 26S proteasome. UFD2p is implicated in cell survival under stress conditions and is essential for homoeostasis of unsaturated fatty acids. It interacts with UBL-UBA proteins Rad23 and Dsk2, which are involved in the endoplasmic reticulum-associated degradation, ubiquitin fusion degradation, and OLE-1 gene induction pathways. UBE4A is a U-box-type ubiquitin-protein ligase that is located in common neuroblastoma deletion regions and may be subject to mutations in tumors. It may have a specific role in different biochemical processes other than ubiquitination, including growth or differentiation. Members of this family contain an N-terminal ubiquitin elongating factor core and a RING-like U-box domain at the C-terminus. 70 matched cddid_all.tbl CDD cd16658 cd16658 438320 RING-Ubox_UBE4B U-box domain, a modified RING finger, found in ubiquitin conjugation factor E4 B (UBE4B) and similar proteins. UBE4B, also known as UFD2a, is a U-box-type ubiquitin-protein ligase that functions as an E3 ubiquitin ligase and an E4 polyubiquitin chain elongation factor, which catalyzes formation of Lys27- and Lys33-linked polyubiquitin chains rather than the Lys48-linked chain. It is a mammalian homolog of yeast UFD2 ubiquitination factor and it participates in the proteasomal degradation of misfolded or damaged proteins through association with chaperones. It is located in common neuroblastoma deletion regions and may be subject to mutations in tumors. UBE4B has contradictory functions upon tumorigenesis as an oncogene or tumor suppressor in different types of cancers. It is essential for Hdm2 (also known as Mdm2)-mediated p53 degradation. It mediates p53 polyubiquitination and degradation, as well as inhibits p53-dependent transactivation and apoptosis, and thus plays an important role in regulating phosphorylated p53 following DNA damage. UBE4B is also associated with other pathways independent of the p53 family, such as polyglutamine aggregation and Wallerian degeneration, both of which are critical in neurodegenerative diseases. Moreover, UBE4B acts as a regulator of epidermal growth factor receptor (EGFR) degradation. It is recruited to endosomes in response to EGFR activation by binding to Hrs, a key component of endosomal sorting complex required for transport (ESCRT) 0, and then regulates endosomal sorting, affecting cellular levels of the EGFR and its downstream signaling. UBE4B contains a ubiquitin elongating factor core and a RING-like U-box domain at the C-terminus. 74 matched cddid_all.tbl CDD cd16659 cd16659 438321 RING-Ubox_Emp U-box domain, a modified RING finger, found in erythroblast macrophage protein (Emp) and similar proteins. Emp, also known as cell proliferation-inducing gene 5 protein or macrophage erythroblast attacher (MAEA), is a key protein which functions in normal differentiation of erythroid cells and macrophages. It is a potential biomarker for hematopoietic evaluation of Hematopoietic stem cell transplantation (HSCT) patients. Emp was initially identified as a heparin-binding protein involved in the association of erythroblasts with macrophages. It promotes erythroid proliferation and maturation. It also plays an important role in erythroblastic island formation. Absence of Emp leads to failure of erythroblast nuclear extrusion. It is required in definitive erythropoiesis and plays a cell intrinsic role in the erythroid lineage. Emp contains a Lissencephaly type-1-like homology (LisH) motif, a C-terminal to LisH (CTLH) domain, and a RING-like U-box domain at the C-terminus. 52 matched cddid_all.tbl CDD cd16660 cd16660 438322 RING-Ubox_RNF37 U-box domain, a modified RING finger, found in RING finger protein 37 (RNF37). RNF37, also known as KIAA0860, U-box domain-containing protein 5 (UBOX5), UbcM4-interacting protein 5 (UIP5), or ubiquitin-conjugating enzyme 7-interacting protein 5, is an E3 ubiquitin-protein ligase found exclusively in the nucleus as part of a nuclear dot-like structure. It interacts with the molecular chaperone VCP/p97 protein. RNF37 contains a U-box domain followed by a potential nuclear location signal (NLS), and a C-terminal C3HC4-type RING-HC finger. The U-box domain is a modified RING finger domain that lacks the hallmark metal-chelating cysteines and histidines of the latter, but is likely to adopt a RING finger-like conformation. The presence of the U-box, but not of the RING finger, is required for the E3 activity. The U-box domain can directly interact with several E2 enzymes, including UbcM2, UbcM3, UbcM4, UbcH5, and UbcH8, suggesting a similar function as the RING finger in the ubiquitination pathway. This model corresponds to the U-box domain. 53 matched cddid_all.tbl CDD cd16661 cd16661 438323 RING-Ubox1_NOSIP U-box domain 1, a modified RING finger, found in nitric oxide synthase-interacting protein (NOSIP) and similar proteins. NOSIP, also known as endothelial NO synthase (eNOS)-interacting protein, p33RUL, is an E3 ubiquitin-protein ligase implicated in the control of airway and vascular diameter, mucosal secretion, NO synthesis in ciliated epithelium, and, therefore, of mucociliary and bronchial function. The loss of NOSIP may cause holoprosencephaly and facial anomalies, including cleft lip/palate, cyclopia, and facial midline clefting. NOSIP interacts with neuronal nitric oxide synthase (nNOS) and eNOS by inhibiting the nitric oxide (NO) production. It acts as a novel type of modulator that promotes translocation of eNOS from the plasma membrane to intracellular sites, thereby uncoupling eNOS from plasma membrane caveolae and inhibiting NO synthesis. NOSIP also interacts with protein phosphatase PP2A and mediates the monoubiquitination of the PP2A catalytic subunit. Thus, it is a critical modulator of brain and craniofacial development in mice and a candidate gene for holoprosencephaly in humans. Moreover, NOSIP associates with the erythropoietin (Epo) receptor (EpoR), mediates ubiquitination of EpoR, and plays an essential role in erythropoietin-induced proliferation. NOSIP contains an atypical N-terminal RING-like U-box domain that is split into two parts by an interjacent stretch of 104 amino acid residues, as well as a C-terminal RING-like U-box domain. This model corresponds to the first U-box domain. 46 matched cddid_all.tbl CDD cd16662 cd16662 438324 RING-Ubox2_NOSIP U-box domain 2, a modified RING finger, found in nitric oxide synthase-interacting protein (NOSIP) and similar proteins. NOSIP, also known as endothelial NO synthase (eNOS)-interacting protein, p33RUL, is an E3 ubiquitin-protein ligase implicated in the control of airway and vascular diameter, mucosal secretion, NO synthesis in ciliated epithelium, and, therefore, of mucociliary and bronchial function. The loss of NOSIP may cause holoprosencephaly and facial anomalies including cleft lip/palate, cyclopia and facial midline clefting. NOSIP interacts with neuronal nitric oxide synthase (nNOS) and eNOS by inhibiting nitric oxide (NO) production. It acts as a novel type of modulator that promotes translocation of eNOS from the plasma membrane to intracellular sites, thereby uncoupling eNOS from plasma membrane caveolae and inhibiting NO synthesis. NOSIP also interacts with protein phosphatase PP2A and mediates the monoubiquitination of the PP2A catalytic subunit. Thus, it is a critical modulator of brain and craniofacial development in mice and a candidate gene for holoprosencephaly in humans. Moreover, NOSIP associates with the erythropoietin (Epo) receptor (EpoR), mediates ubiquitination of EpoR, and plays an essential role in erythropoietin-induced proliferation. NOSIP contains an atypical N-terminal RING-like U-box domain that is split into two parts by an interjacent stretch of 104 amino acid residues, as well as a C-terminal RING-like U-box domain. This model corresponds to the second U-box domain. 68 matched cddid_all.tbl CDD cd16663 cd16663 438325 RING-Ubox_PPIL2 U-box domain, a modified RING finger, found in peptidyl-prolyl cis-trans isomerase-like 2 (PPIL2) and similar proteins. PPIL2 (EC 5.2.1.8), also known as PPIase, CYC4, cyclophilin-60 (Cyp60), cyclophilin-like protein Cyp-60, or Rotamase PPIL2, is a nuclear-specific cyclophilin which interacts with the proteinase inhibitor eglin c and regulates gene expression. PPIL2 belongs to the cyclophilin family of peptidylprolyl isomerases and catalyzes cis-trans isomerization of proline-peptide bonds, which is often a rate-limiting step in protein folding. It positively regulates beta-site amyloid precursor protein cleaving enzyme (BACE1) expression and beta-secretase activity. Moreover, PPIL2 plays an important role in the translocation of CD147 to the cell surface, and thus may present a novel target for therapeutic interventions in diseases where CD147 functions as a pathogenic factor in cancer, human immunodeficiency virus infection, or rheumatoid arthritis. PPIL2 contains an N-terminal RING-like U-box domain and a C-terminal cyclophilin (Cyp)-like chaperone domain. 73 matched cddid_all.tbl CDD cd16664 cd16664 438326 RING-Ubox_PUB U-box domain, a modified RING finger, found in Arabidopsis plant U-box proteins (AtPUB) and similar proteins. The plant PUB proteins, also known as U-box domain-containing proteins, are much more numerous in Arabidopsis which has 62 in comparison with the typical 6 in most animals. The majority of AtPUBs in this subfamily are known as ARM domain-containing PUB proteins, containing a C-terminally-located, tandem ARM (armadillo) repeat protein-interaction region in addition to the U-box domain. They have been implicated in the regulation of cell death and defense. They also play important roles in other plant-specific pathways, such as controlling both self-incompatibility and pseudo-self-incompatibility, as well as acting in abiotic stress. A subgroup of ARM domain-containing PUB proteins harbors a plant-specific U-box N-terminal domain. 53 matched cddid_all.tbl CDD cd16665 cd16665 438327 RING-H2_RNF13-like RING finger, H2 subclass, found in RING finger protein 13 (RNF13), RING finger protein 167 (RNF167), and similar proteins. This subfamily includes RING finger protein 13 (RNF13), RING finger protein 167 (RNF167), Zinc/RING finger protein 4 (ZNRF4), and similar proteins, which belong to a larger PA-TM-RING ubiquitin ligase family that has been characterized by containing an N-terminal signal peptide, a protease-associated (PA) domain, a transmembrane domain (TM), and a C-terminal C3H2C3-type RING-H2 finger followed by a putative PEST sequence. RNF13 is a widely expressed membrane-associated E3 ubiquitin-protein ligase that functions in the regulation of cancer development, muscle cell growth, and neuronal development. Its expression is developmentally regulated during myogenesis and is upregulated in various tumors. RNF13 negatively regulates cell proliferation through its E3 ligase activity. RNF167, also known as RING105, is an endosomal/lysosomal E3 ubiquitin-protein ligase involved in the ubiquitination of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR). It acts as an endosomal membrane protein which ubiquitylates vesicle-associated membrane protein 3 (VAMP3) and regulates endosomal trafficking. Moreover, RNF167 plays a role in the regulation of TSSC5 (tumor-suppressing subchromosomal transferable fragment cDNA, also known as ORCTL2/IMPT1/BWR1A/SLC22A1L), which can function in concert with the ubiquitin-conjugating enzyme UbcH6. ZNRF4, also known as RING finger protein 204 (RNF204), or Nixin, is an endoplasmic reticulum (ER) membrane-anchored ubiquitin ligase that physically interacts with the ER-localized chaperone calnexin in a glycosylation-independent manner, inducing calnexin ubiquitination, and p97-dependent degradation. The murine protein sperizin (spermatid-specific ring zinc finger) is a homolog of human ZNRF4. It is specifically expressed in Haploid germ cells and is involved in spermatogenesis. 46 matched cddid_all.tbl CDD cd16666 cd16666 438328 RING-H2_RNF43-like RING finger, H2 subclass, found in RING finger proteins RNF43, ZNRF3, and similar proteins. RNF43 and ZNRF3 (also known as RNF203) are transmembrane E3 ubiquitin-protein ligases that belong to the PA-TM-RING ubiquitin ligase family, characterized by containing an N-terminal signal peptide, a protease-associated (PA) domain, a transmembrane (TM) domain and a C3H2C3-type RING-H2 finger followed by a long C-terminal region. Both RNF43 and RNF203 function as tumor suppressors involved in the regulation of Wnt/beta-catenin signaling. They negatively regulate Wnt signaling by interacting with complexes of frizzled (FZD) receptors and low-density lipoprotein receptor-related protein (LRP) 5/6, which leads to ubiquitination of FZD and endocytosis of the Wnt receptor. Dishevelled (DVL), a positive Wnt regulator, is required for ZNRF3/RNF43-mediated ubiquitination and degradation of FZD. They also associate with R-spondin 1 (RSPO1). This interaction may block FZD ubiquitination and enhances Wnt signaling. 45 matched cddid_all.tbl CDD cd16667 cd16667 438329 RING-H2_RNF126-like RING finger, H2 subclass, found in RING finger proteins RNF126, RNF115, and similar proteins. This subfamily includes RING finger proteins RNF126, RNF115, and similar proteins. RNF126 is a Bag6-dependent E3 ubiquitin ligase that is involved in the mislocalized protein (MLP) pathway of quality control. It regulates the retrograde sorting of the cation-independent mannose 6-phosphate receptor (CI-MPR). RNF126 promotes cancer cell proliferation by targeting the tumor suppressor p21 for ubiquitin-mediated degradation, and could be a novel therapeutic target in breast and prostate cancers. It is also able to ubiquitylate cytidine deaminase (AID), a poorly soluble protein that is essential for antibody diversification. RNF115, also known as Rab7-interacting ring finger protein (Rabring 7), or zinc finger protein 364 (ZNF364), or breast cancer-associated gene 2 (BCA2), is an E3 ubiquitin-protein ligase that is an endogenous inhibitor of adenosine monophosphate-activated protein kinase (AMPK) activation; this inhibition increases the efficacy of metformin in breast cancer cells. It also functions as a cofactor in the restriction imposed by tetherin on HIV-1, and targets HIV-1 Gag for lysosomal degradation, impairing virus assembly and release, in a tetherin-independent manner. Moreover, RNF115 is a Rab7-binding protein that stimulates c-Myc degradation through mono-ubiquitination of MM-1. It also plays crucial roles as a Rab7 target protein in vesicle traffic to late endosome/lysosome and lysosome biogenesis. RNF115 and RNF126 associate with the epidermal growth factor receptor (EGFR) and promote ubiquitylation of EGFR, suggesting they play a role in the ubiquitin-dependent sorting and downregulation of membrane receptors. Both of them contain an N-terminal BCA2 Zinc-finger domain (BZF), AKT-phosphorylation sites, and a C-terminal C3H2C3-type RING-H2 finger. 43 matched cddid_all.tbl CDD cd16668 cd16668 438330 RING-H2_RNF130-like RING finger, H2 subclass, found in RING finger proteins, RNF130, RNF149, RNF150 and similar proteins. This subfamily includes RING finger proteins, RNF130, RNF149 and RNF150, which belong to a larger PA-TM-RING ubiquitin ligase family that has been characterized by an N-terminal signal peptide, a protease-associated (PA) domain, a transmembrane (TM) domain and a C-terminal C3H2C3-type RING-H2 finger domain followed by a putative PEST sequence. RNF130, also known as Goliath homolog (H-Goliath), is a paralog of RNF128. It is a transmembrane E3 ubiquitin-protein ligase expressed in leukocytes. It has a self-ubiquitination property and controls the development of T cell clonal anergy by ubiquitination. RNF133 is a testis-specific endoplasmic reticulum-associated E3 ubiquitin ligase that may play a role in sperm maturation through an ER-associated degradation (ERAD) pathway. RNF149, also known as DNA polymerase-transactivated protein 2, is an E3 ubiquitin-protein ligase that induces the ubiquitination of wild-type v-Raf murine sarcoma viral oncogene homolog B1 (BRAF) and promotes its proteasome-dependent degradation. RNF150 polymorphisms may be associated with chronic obstructive pulmonary disease (COPD) risk in the Chinese population. This subfamily also includes Drosophila melanogaster protein goliath (d-goliath), also known as protein g1, which is one of the founding members of the group. It was originally identified as a transcription factor involved in the embryo mesoderm formation. 46 matched cddid_all.tbl CDD cd16669 cd16669 438331 RING-H2_RNF181 RING finger, H2 subclass, found in RING finger protein 181 (RNF181) and similar proteins. RNF181, also known as HSPC238, is a platelet E3 ubiquitin-protein ligase containing a C3H2C3-type RING-H2 finger. It interacts with the KVGFFKR motif of platelet integrin alpha(IIb)beta3, suggesting a role for RNF181-mediated ubiquitination in integrin and platelet signaling. It also suppresses the tumorigenesis of hepatocellular carcinoma (HCC) through the inhibition of extracellular signal-regulated kinase/mitogen-activated protein kinase (ERK/MAPK) signaling in the liver. 46 matched cddid_all.tbl CDD cd16670 cd16670 438332 RING-H2_RNF215 RING finger, H2 subclass, found in RING finger protein 215 (RNF215) and similar proteins. This family includes uncharacterized protein RNF215 and similar proteins. Although its biological function remains unclear, RNF215 shares high sequence similarity with PA-TM-RING ubiquitin ligases, which have been characterized by containing an N-terminal signal peptide, a protease-associated (PA) domain, a transmembrane (TM) domain and a C-terminal C3H2C3-type RING-H2 finger. 50 matched cddid_all.tbl CDD cd16671 cd16671 438333 RING-H2_DTX1_4 RING finger, H2 subclass, found in E3 ubiquitin-protein ligase deltex1 (DTX1), deltex4 (DTX4), and similar proteins. DTX1 functions as a Notch downstream transcription regulator that mediates a Notch signal to block differentiation of neural progenitor cells. It interacts with the transcription coactivator p300 and inhibits transcription activation mediated by the neural specific transcription factor MASH1. It is also a transcription target of nuclear factor of activated T cells (NFAT) and participates in T cell anergy and Foxp3 protein level maintenance in vivo. Moreover, DTX1 appears to promote B-cell development at the expense of T-cell development. It also promotes protein kinase C theta degradation and sustains Casitas B-lineage lymphoma expression. DTX4, also known as RING finger protein 155, shares the highest degree of sequence similarity with DTX1 and likely interacts with the intracellular domain of Notch as well. Both DTX1 and DTX4 contain two Notch-binding WWE domains at the N-terminus that physically interact with the Notch ankyrin domains, a proline-rich motif that shares homology with SH3-binding domains, and a C3H2C3-type RING-H2 finger at the C-terminus. They also harbor two nuclear localization signals. 69 matched cddid_all.tbl CDD cd16672 cd16672 438334 RING-H2_DTX2 RING finger, H2 subclass, found in E3 ubiquitin-protein ligase Deltex2 (DTX2) and similar proteins. DTX2, also known as RING finger protein 58, together with DTX1 and DTX4, forms a family of related proteins that are the mammalian homologs of Drosophila Deltex, a known regulator of Notch signals. Like DTX1 and DTX4, DTX2 is expressed in thymocytes. It interacts with the intracellular domain of Notch receptors and acts as a negative regulator of Notch signals in T cells. However, the endogenous levels of DTX1 and DTX2 is not important for regulating Notch signals during thymocyte development. DTX2 contains two Notch-binding WWE domains at the N-terminus that physically interact with the Notch ankyrin domains, a proline-rich motif that shares homology with SH3-binding domains, and a C3H2C3-type RING-H2 finger at the C-terminus. It also harbors two nuclear localization signals. 72 matched cddid_all.tbl CDD cd16673 cd16673 438335 RING-H2_RNF6 RING finger, H2 subclass, found in E3 ubiquitin-protein ligase RNF6 and similar proteins. RNF6 is an androgen receptor (AR)-associated protein that induces AR ubiquitination and promotes AR transcriptional activity. RNF6-induced ubiquitination may regulate AR transcriptional activity and specificity by modulating cofactor recruitment. RNF6 is overexpressed in hormone-refractory human prostate cancer tissues and required for prostate cancer cell growth under androgen-depleted conditions. Moreover, RNF6 regulates local serine/threonine kinase LIM kinase 1 (LIMK1) levels in axonal growth cones. RNF6-induced LIMK1 polyubiquitination is mediated via K48 of ubiquitin and leads to proteasomal degradation of the kinase. RNF6 also binds and upregulates the Inha promoter, and functions as a transcription regulatory protein in the mouse sertoli cell. RNF6 also acts as a potential tumor suppressor gene involved in the pathogenesis of esophageal squamous cell carcinoma (ESCC). RNF6 contains an N-terminal coiled-coil domain, a Lys-X-X-Leu/Ile-X-X-Leu/Ile (KIL) motif, and a C-terminal C3H2C3-type RING-H2 finger which is responsible for its ubiquitin ligase activity. The KIL motif is present in a subset of RING-H2 proteins from organisms as evolutionarily diverse as human, mouse, chicken, Drosophila, Caenorhabditis elegans, and Arabidopsis thaliana. 52 matched cddid_all.tbl CDD cd16674 cd16674 438336 RING-H2_RNF12 RING finger, H2 subclass, found in RING finger protein 12 (RNF12) and similar proteins. RNF12, also known as LIM domain-interacting RING finger protein or RING finger LIM domain-binding protein (R-LIM), is an E3 ubiquitin-protein ligase encoded by gene RLIM that is crucial for normal embryonic development in some species and for normal X inactivation in mice. It thus functions as a major sex-specific epigenetic regulator of female mouse nurturing tissues. RNF12 is widely expressed during embryogenesis, and mainly localizes to the cell nucleus, where it regulates the levels of many proteins, including CLIM, LMO, HDAC2, TRF1, SMAD7, and REX1, by proteasomal degradation. Its functional activity is regulated by phosphorylation-dependent nucleocytoplasmic shuttling. It is negatively regulated by pluripotency factors in embryonic stem cells. p53 represses its transcription through Sp1. RNF12 is the primary factor responsible for X chromosome inactivation (XCI) in female placental mammals. It is an indispensable factor in up-regulation of Xist transcription, thereby leading to initiation of random XCI. It also targets REX1, an inhibitor of XCI, for proteasomal degradation. RNF12 also acts as a co-regulator for a range of transcription factors, particularly those containing a LIM homeodomain, and modulates the formation of transcriptional multiprotein complexes. It is a negative regulator of Smad7, which in turn negatively regulates the signaling of type I receptors from the transforming growth factor beta (TGF-beta) superfamily. In addition, paternal RNF12 is a critical survival factor for milk-producing alveolar cells. RNF12 contains an nuclear localization signal (NLS) and a C3H2C3-type RING-H2 finger. 51 matched cddid_all.tbl CDD cd16675 cd16675 438337 RING-H2_RNF24 RING finger, H2 subclass, found in RING finger protein 24 (RNF24) and similar proteins. RNF24 is an intrinsic membrane protein localized in the Golgi apparatus. It specifically interacts with the ankyrin-repeats domains (ARDs) of TRPC1, -3, -4, -5, -6, and -7, and affects TRPC intracellular trafficking without affecting their activity. RNF24 contains an N-terminal transmembrane domain and a C-terminal C3H2C3-type RING-H2 finger. 54 matched cddid_all.tbl CDD cd16676 cd16676 438338 RING-H2_RNF122 RING finger, H2 subclass, found in RING finger protein 122 (RNF122) and similar proteins. RNF122 is a RING finger protein associated with HEK 293T cell viability. It is localized to the endoplasmic reticulum (ER) and the Golgi apparatus, and overexpressed in anaplastic thyroid cancer cells. RNF122 functions as an E3 ubiquitin ligase that can ubiquitinate itself and undergo degradation through its RING finger in a proteasome-dependent manner. It interacts with calcium-modulating cyclophilin ligand (CAML), which is not a substrate, but a stabilizer of RNF122. RNF122 contains an N-terminal transmembrane domain and a C-terminal C3H2C3-type RING-H2 finger. 47 matched cddid_all.tbl CDD cd16677 cd16677 438339 RING-H2_RNF32_rpt1 first RING finger, H2 subclass, found in RING finger protein 32 (RNF32) and similar proteins. RNF32 is mainly expressed in testis spermatogenesis, most likely in spermatocytes and/or in spermatids, suggesting a possible role in sperm formation. RNF32 contains two C3H2C3-type RING-H2 fingers separated by an IQ domain of unknown function. Although the biological function of RNF32 remains unclear, proteins with double RING-H2 fingers may act as scaffolds for binding several proteins that function in the same pathway. This model corresponds to the first RING-H2 finger. 49 matched cddid_all.tbl CDD cd16678 cd16678 438340 RING-H2_RNF32_rpt2 second RING finger, H2 subclass, found in RING finger protein 32 (RNF32) and similar proteins. RNF32 is mainly expressed in testis spermatogenesis, most likely in spermatocytes and/or in spermatids, suggesting a possible role in sperm formation. RNF32 contains two C3H2C3-type RING-H2 fingers separated by an IQ domain of unknown function. Although the biological function of RNF32 remains unclear, proteins with double RING-H2 fingers may act as scaffolds for binding several proteins that function in the same pathway. This model corresponds to the second RING-H2 finger. 61 matched cddid_all.tbl CDD cd16679 cd16679 438341 RING-H2_RNF38 RING finger, H2 subclass, found in RING finger protein 38 (RNF38) and similar proteins. RNF38 is a nuclear E3 ubiquitin protein ligase that is widely expressed throughout the human body, and is especially highly expressed in the heart, brain, placenta and the testis. It recognizes p53 as a substrate for ubiquitination, and thus plays a role in regulating p53. The overexpression of RNF38 increases p53 ubiquitination and alters p53 localization. It is also capable of autoubiquitination. RNF38 expression is negatively regulated by the serotonergic system. Induction of RNF38 may be involved in the anxiety-like behavior or non-cell autonomy in Oryzias latipes by the decline of serotonin (5-HT) levels. RNF38 contains a coiled-coil motif, a KIL motif (Lys-X2-Ile/Leu-X2-Ile/Leu, X can be any amino acid), a C3H2C3-type RING-H2 finger, as well as two potential nuclear localization signals. 67 matched cddid_all.tbl CDD cd16680 cd16680 438342 RING-H2_RNF44 RING finger, H2 subclass, found in RING finger protein 44 (RNF44) and similar proteins. RNF44 is an uncharacterized RING finger protein that shows high sequence similarity with RNF38, which is a nuclear E3 ubiquitin protein ligase that plays a role in regulating p53. RNF44 contains a coiled-coil motif, a KIL motif (Lys-X2-Ile/Leu-X2-Ile/Leu, X can be any amino acid), and a C3H2C2-type RING-H2 finger. 62 matched cddid_all.tbl CDD cd16681 cd16681 438343 RING-H2_RNF111 RING finger, H2 subclass, found in RING finger protein 111 (RNF111) and similar proteins. RNF111, also known as Arkadia, is a nuclear E3 ubiquitin-protein ligase that targets intracellular effectors and modulators of transforming growth factor beta (TGF-beta)/Nodal-related signaling for polyubiquitination and proteasome-dependent degradation. It acts as an amplifier of Nodal signals, and enhances the dorsalizing activity of limiting amounts of Xnr1, a Nodal homolog, and requires Nodal signaling for its function. The loss of RNF111 results in early embryonic lethality, with defects attributed to compromised Nodal signaling. RNF111 also regulates tumor metastasis by modulation of the TGF-beta pathway. Its ubiquitination can be modulated by the four and a half LIM-only protein 2 (FHL2) that activates TGF-beta signal transduction. Furthermore, RNF111 interacts with the clathrin-adaptor 2 (AP2) complex and regulates endocytosis of certain cell surface receptors, leading to modulation of epidermal growth factor (EGF) and possibly other signaling pathways. In addition, RNF111 has been identified as a small ubiquitin-like modifier (SUMO)-binding protein with clustered SUMO-interacting motifs (SIMs) that together form a SUMO-binding domain (SBD). It thus functions as a SUMO-targeted ubiquitin ligase (STUbL) that directly links nonproteolytic ubiquitylation and SUMOylation in the DNA damage response, as well as triggers degradation of signal-induced polysumoylated proteins, such as the promyelocytic leukemia protein (PML). The N-terminal half of RNF111 harbors three SIMs. Its C-terminal half show high sequence similarity with RING finger protein 165 (RNF165), where it contains two serine rich domains, two nuclear localization signals, an NRG-TIER domain, and a C-terminal C3H2C3-type RING-H2 finger that is required for polyubiqutination and proteasome-dependent degradation of phosphorylated forms of Smad2/3 and three major negative regulators of TGF-beta signaling, Smad7, SnoN and c-Ski. 61 matched cddid_all.tbl CDD cd16682 cd16682 438344 RING-H2_RNF165 RING finger, H2 subclass, found in RING finger protein 165 (RNF165) and similar proteins. RNF165, also known as Arkadia-like 2, Arkadia2, or Ark2C, is an E3 ubiquitin ligase with homology to the C-terminal half of RNF111. It is expressed specifically in the nervous system, and can serve to amplify neuronal responses to specific signals. It acts as a positive regulator of bone morphogenetic protein (BMP)-Smad signaling that is involved in motor neuron (MN) axon elongation. RNF165 contains two serine rich domains, a nuclear localization signal, an NRG-TIER domain, and a C-terminal C3H2C3-type RING-H2 finger that is responsible for the enhancement of BMP-Smad1/5/8 signaling in the spinal cord. 59 matched cddid_all.tbl CDD cd16683 cd16683 438345 RING-H2_RNF139 "RING finger, H2 subclass, found in RING finger protein 139 (RNF139) and similar proteins. RNF139, also known as translocation in renal carcinoma on chromosome 8 protein (TRC8), is an endoplasmic reticulum (ER)-resident multi-transmembrane protein that functions as a potent growth suppressor in mammalian cells, inducing G2/M arrest, decreased DNA synthesis and increased apoptosis. It is a tumor suppressor that has been implicated in a novel regulatory relationship linking the cholesterol/lipid biosynthetic pathway with cellular growth control. A mutation in RNF139 has been identified in families with hereditary renal (RCC) and thyroid cancers. RNF139 physically and functionally interacts with von Hippel-Lindau (VHL), which is part of an SCF related E3-ubiquitin ligase complex with ""gatekeeper"" function in renal carcinoma and is defective in most sporadic clear-cell renal cell carcinomas (ccRCC). It suppresses growth and functions with VHL in a common pathway. RNF139 also suppresses tumorigenesis by targeting heme oxygenase-1 for ubiquitination and degradation. Moreover, RNF139 is a target of Translin (TSN), a posttranscriptional regulator of genes transcribed by the transcription factor CREM-tau in postmeiotic male germ cells, suggesting a role of RNF139 in dysgerminoma. In addition, RNF139 forms an integral part of a novel multi-protein ER complex, containing MHC I, US2, and signal peptide peptidase, which is associated with the ER-associated degradation (ERAD) pathway. It is required for the ubiquitination of MHC class I molecules before dislocation from the ER. As a novel sterol-sensing ER membrane protein, RNF139 hinders sterol regulatory element-binding protein-2 (SREBP-2) processing through interaction with SREBP-2 and SREBP cleavage-activated protein (SCAP), regulating its own turnover rate via its E3 ubiquitin ligase activity. RNF139 shows two regions of similarity with the receptor for sonic hedgehog (SHH), Patched. The first region corresponds to the second extracellular domain of Patched, which is involved in binding SHH. The second region is a putative sterol-sensing domain (SSD). The C-terminal half of RNF139 contains a C3H2C3-type RING-H2 finger with E3-ubiquitin ligase activity in vitro." 54 matched cddid_all.tbl CDD cd16684 cd16684 319598 RING-H2_RNF145 RING finger, H2 subclass, found in RING finger protein 145 (RNF145) and similar proteins. RNF145 is an uncharacterized RING finger protein encoded by the RNF145 gene, which is expressed in T lymphocytes, and its expression is altered in acute myelomonocytic and acute promyelocytic leukemias. Although its biological function remains unclear, RNF145 shows high sequence similarity with RNF139, an endoplasmic reticulum (ER)-resident multi-transmembrane protein that functions as a potent growth suppressor in mammalian cells, inducing G2/M arrest, decreased DNA synthesis and increased apoptosis. Like RNF139, RNF145 contains a C3H2C3-type RING-H2 finger with possible E3-ubiquitin ligase activity. 43 matched cddid_all.tbl CDD cd16685 cd16685 438346 RING-H2_UBR1 RING finger, H2 subclass, found in ubiquitin-protein ligase E3-alpha-1 (UBR1) and similar proteins. UBR1, also known as N-recognin-1 or E3alpha-I, is an E3 ubiquitin-protein ligase component of the N-end rule pathway. It also promotes degradation of proteins via distinct mechanism that detects a misfolded conformation. UBR1 associates with the RAD6-encoded E2 enzyme to form an E2-E3 complex that catalyzes the synthesis of a substrate-linked multi-ubiquitin chain and may also mediate the delivery of substrates to the 26S proteasome. Moreover, UBR1 promotes the degradation of misfolded proteins in the cytosol. It promotes protein kinase quality control and sensitizes cells to heat shock protein 90 (Hsp90) inhibition. Furthermore, UBR1 functions as a polyubiquitylation-enhancing component of the UBR1-UFD4 complex in its targeting of ubiquitin-fusion degradation (UFD) substrates. UBR1 harbors at least three distinct substrate-binding sites and functions in association with Ubc2/Rad6 and also Ubc4. It contains an N-terminal ubiquitin-recognin (UBR) box involved in binding type-1 (basic) N-end rule substrate, an N-domain (also known as ClpS domain) required for type-2 (bulky hydrophobic) N-end rule substrate recognition, a C3H2C3-type RING-H2 finger, and a C-terminal UBR-specific autoinhibitory (UAIN) domain. A missense mutation in UBR1 is responsible for Johanson-Blizzard syndrome leads to UBR box unfolding and loss of function. 120 matched cddid_all.tbl CDD cd16686 cd16686 438347 RING-H2_UBR2 RING finger, H2 subclass, found in ubiquitin-protein ligase E3-alpha-2 (UBR2) and similar proteins. UBR2, also known as N-recognin-2 or E3alpha-II, is an E3 ubiquitin-protein ligase that plays an important role in maintaining genome integrity and in homologous recombination repair. It regulates the level of the transcription factor Rpn4 (also known as Son1 and Ufd5) through ubiquitylation. The ubiquitin-conjugating enzyme Rad6, another binding partner of URB2, and an additional factor Mub1, are required for the ubiquitin-dependent degradation of Rpn4. UBR2 associates with Mub1 to form a Mub1/Ubr2 complex that regulates the conserved Dsn1 kinetochore protein levels, which is a part of a quality control system that monitors kinetochore integrity, thus ensuring genomic stability. As the recognition component of a major cellular proteolytic system, UBR2 is associated with chromatin and controls chromatin dynamics and gene expression in both spermatocytes and somatic cells. UBR2 also mediates transcriptional silencing during spermatogenesis via histone ubiquitination. It functions as a scaffold E3 promoting HR6B/UbcH2-dependent ubiquitylation of H2A and H2B, but not H3 and H4. It also binds to Tex19.1, also known as Tex19, a germ cell-specific protein, and metabolically stabilizes it during spermatogenesis. Furthermore, UBR2 is involved in skeletal muscle (SKM) atrophy. Its expression can be modulated by the mouse ether-a-gogo-related gene 1a (MERG1a) potassium channel. In addition, UBR2 up-regulation in cachectic muscle is mediated by the p38beta-CCAAT/enhancer binding protein (C/EBP)-beta signaling pathway responsible for the bulk of tumor-induced muscle proteolysis. UBR2 contains an N-terminal ubiquitin-recognin (UBR) box involved in binding type-1 (basic) N-end rule substrate, an N-domain (also known as ClpS domain) required for type-2 (bulky hydrophobic) N-end rule substrate recognition, a C3H2C3-type RING-H2 finger, and a C-terminal UBR-specific autoinhibitory (UAIN) domain. 116 matched cddid_all.tbl CDD cd16687 cd16687 438348 RING-H2_Vps8 RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 8 (Vps8) and similar proteins. Vps8 is the Rab-specific subunit of the endosomal tethering complex CORVET (class C core vacuole/endosome transport) that also includes Vps3 and a Class C Vps core complex composed of Vps11, Vps16, Vps18, and Vps33. CORVET operates at endosomes, controls traffic into late endosomes, and interacts with the Rab5/Vps21-GTP form. The CORVET-specific Vps3 and Vps8 subunits belong to the class D Vps. They form a subcomplex that interact with Rab5/Vps21, and is critical for localization and function of the CORVET tethering complex on endosomes. Vps8 contains an N-terminal WD40 repeat and a C-terminal C3H2C3-type RING-H2 finger. 54 matched cddid_all.tbl CDD cd16688 cd16688 438349 RING-H2_Vps11 RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins. Vps11, also known as RING finger protein 108 (RNF108), is a soluble protein involved in regulation of glycolipid degradation and retrograde toxin transport. It is highly expressed in heart and pancreas. Vps11 associates with Vps16, Vps18, and Vps33 to form a Class C Vps core complex that is required for soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE)-mediated membrane fusion at the lysosome-like yeast vacuole. The core complex, together with two additional compartment-specific subunits, forms the tethering complexes HOPS (homotypic vacuole fusion and protein sorting) and CORVET (class C core vacuole/endosome transport). CORVET contains the additional Vps3 and Vps8 subunits. It operates at endosomes, controls traffic into late endosomes and interacts with the Rab5/Vps21-GTP form. HOPS contains the additional Vps39 and Vps41 subunits. It operates at the lysosomal vacuole, controls all traffic from late endosomes into the vacuole and interacts with the Rab7/Ypt7-GTP form. Vps11 is a central scaffold protein upon which both HOPS and CORVET assemble. The HOPS and CORVET complexes disassemble in the absence of Vps11, resulting in massive fragmentation of vacuoles. Vps11 contains a clathrin repeat domain and a C-terminal C3H2C3-type RING-H2 finger. This subfamily also includes Vps11 homologs found in fungi, such as Saccharomyces cerevisiae vacuolar membrane protein Pep5p, also known as carboxypeptidase Y-deficient protein 5, vacuolar morphogenesis protein 1, or vacuolar biogenesis protein END1. Pep5p is essential for vacuolar biogenesis. It associates with Pep3p to form a core Pep3p/Pep5p complex that promotes vesicular docking/fusion reactions in conjunction with SNARE proteins at multiple steps in transport routes to the vacuole. 44 matched cddid_all.tbl CDD cd16689 cd16689 438350 RING-H2_Vps18 RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 18 (Vps18) and similar proteins. Vps18 is an ubiquitin ligase E3 that is highly expressed in heart. It induces the ubiquitylation and degradation of serum-inducible kinase. Vps18 associates with Vps11, Vps16, and Vps33 to form a Class C Vps core complex that is required for soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNARE)-mediated membrane fusion at the lysosome-like yeast vacuole. The core complex, together with two additional compartment-specific subunits, forms the tethering complexes HOPS (homotypic vacuole fusion and protein sorting) and CORVET (class C core vacuole/endosome transport). CORVET contains the additional Vps3 and Vps8 subunits. It operates at endosomes, controls traffic into late endosomes and interacts with the Rab5/Vps21-GTP form. HOPS contains the additional Vps39 and Vps41 subunits. It operates at the lysosomal vacuole, controls all traffic from late endosomes into the vacuole and interacts with the Rab7/Ypt7-GTP form. Vps18 deficiency inhibits dendritogenesis in Purkinje cells by blocking the lysosomal degradation of lysyl oxidase. Vps18 contains a clathrin heavy chain repeat, a coiled-coil domain, and a C3H2C3-type RING-H2 finger domain close to its C-terminus. This subfamily also includes Vps18 homologs found in insects and fungi, such as Drosophila melanogaster protein Dor (encoded by deep orange (dor) gene), and Saccharomyces cerevisiae vacuolar membrane protein Pep3p, also known as carboxypeptidase Y-deficient protein 3, or vacuolar morphogenesis protein 8. Drosophila Dor is part of a protein complex, that also includes the Sep1p homolog carnation (car), which localizes to endosomal compartments and is required not only for the biogenesis of pigment granules but also for the normal delivery of proteins to lysosomes. Pep3p is a vacuolar peripheral membrane protein that is required for vacuolar biogenesis in Saccharomyces cerevisiae. Pep3p associates with Pep5p to form a core Pep3p/Pep5p complex that promotes vesicular docking/fusion reactions in conjunction with SNARE proteins at multiple steps in transport routes to the vacuole. 45 matched cddid_all.tbl CDD cd16690 cd16690 438351 RING-H2_Vps41 RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 41 (Vps41) and similar proteins. Vps41, also known as S53, is a protein involved in trafficking of proteins from the late Golgi to the vacuole. It interacts with caspase-8, suggesting a potential role of Vps41 beyond lysosomal trafficking. It has been identified as a potential therapeutic target for human Parkinson's disease (PD). Vps41 and the soluble N-ethylmaleimide-sensitive factor attachment protein receptors protein VAMP7 are specifically involved in the fusion of the trans-Golgi network-derived lysosome-associated membrane protein carriers with late endosomes. Vps41 is a specific subunit of the lysosomal tethering complex HOPS (homotypic vacuole fusion and protein sorting) that also includes Vps39 and a Class C Vps core complex composed of Vps11, Vps16, Vps18, and Vps33. HOPS operates at the lysosomal vacuole, controls all traffic from late endosomes into the vacuole and interacts with the Rab7/Ypt7-GTP form. The HOPS-specific Vps39 and Vps41 subunits belong to the class B Vps. They form a subcomplex that interacts with Rab7/Ypt7 and is are required for homotypic and heterotypic late endosome fusion. Vps41 contains an N-terminal WD40 repeat, one or two clathrin repeats and a C3H2C3-type RING-H2 finger domain close to its C-terminus. 51 matched cddid_all.tbl CDD cd16691 cd16691 438352 mRING-H2-C3H3C2_Mio Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein mio and simialr proteins. This family contains Mio,its counterpart Sea4 from yeast, and other homologs. Mio/Sea4 is a component of the GATOR2 complex, which also includes another four subunits, Seh1, Sec13, Sea2/WDR24, and Sea3/WDR59. GATOR2 and GATOR1, which is composed of three subunits, DEPDC5, Nprl2, and Nprl3, form the Rag-interacting complex GATOR (GAP Activity Towards Rags). Inhibition of GATOR1 subunits makes mTORC1 signaling resistant to amino acid deprivation. In contrast, inhibition of GATOR2 subunits suppresses mTORC1 signaling and GATOR2 negatively regulates DEPDC5. Mio interacts with endogenous RagA and RagC, and plays an essential role in the activation of mTOR Complex 1 (mTORC1) by amino acids. In GATOR2, Mio and Seh1 localize to lysosomes and autolysosomes, and form a heterodimer that is required to oppose the TORC1 inhibitory activity of the Iml1/GATOR1 complex to prevent the constitutive down-regulation of TORC1 activity in later stages of oogenesis. A tissue-specific requirement is necessary for Mio to be involved in cell growth in the female germ line. Mio contains an N-terminal WD40 domain and a C-terminal RING-H2 finger with an unusual arrangement of zinc-coordinating residues. The cysteines and histidines in the RING-H2 finger are arranged as a modified C3H3C2-type, rather than the canonical C3H2C3-type. 75 matched cddid_all.tbl CDD cd16692 cd16692 438353 mRING-H2-C3H3C2_WDR59 Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein 59 (WDR59) and similar proteins. WDR59 is a component of the GATOR2 complex, which also includes another four subunits, Seh1, Sec13, Sea2/WDR24, and Mio/Sea4. GATOR2 and GATOR1, which is composed of three subunits, DEPDC5, Nprl2, and Nprl3, form the Rag-interacting complex GATOR (GAP Activity Towards Rags). Inhibition of GATOR1 subunits makes mTORC1 signaling resistant to amino acid deprivation. In contrast, inhibition of GATOR2 subunits suppresses mTORC1 signaling and GATOR2 negatively regulates DEPDC5. WDR59 contains an N-terminal WD40 domain followed by a RWD domain, and a C-terminal RING-H2 finger with an unusual arrangement of zinc-coordinating residues. The cysteines and histidines in the RING-H2 finger are arranged as a modified C3H3C2-type, rather than the canonical C3H2C3-type. Sea3 is the yeast counterpart of WDR59. It is not included in this subfamily. 47 matched cddid_all.tbl CDD cd16693 cd16693 438354 mRING-H2-C3H3C2_WDR24 Modified RING finger, H2 subclass (C3H3C2-type), found in WD repeat-containing protein 24 (WDR24) and similar proteins. WDR24 is a component of the GATOR2 complex, which also includes another four subunits, Seh1, Sec13, Sea3/WDR59, and Mio/Sea4. GATOR2 and GATOR1, which is composed of three subunits, DEPDC5, Nprl2, and Nprl3, form the Rag-interacting complex GATOR (GAP Activity Towards Rags). Inhibition of GATOR1 subunits makes mTORC1 signaling resistant to amino acid deprivation. In contrast, inhibition of GATOR2 subunits suppresses mTORC1 signaling and GATOR2 negatively regulates DEPDC5. WDR24 contains an N-terminal WD40 domain and a C-terminal RING-H2 finger with an unusual arrangement of zinc-coordinating residues. The cysteines and histidines in the RING-H2 finger are arranged as a modified C3H3C2-type, rather than the canonical C3H2C3-type. Sea2 is the yeast counterpart of WDR24. It is not included in this subfamily. 46 matched cddid_all.tbl CDD cd16694 cd16694 438355 mRING-CH-C4HC2H_ZNRF1 Modified RING-CH finger, H2 subclass (C4HC2H-type), found in zinc/RING finger protein 1 (ZNRF1) and similar proteins. ZNRF1, also known as Nerve injury-induced gene 283 protein (nin283), or peripheral nerve injury protein (PNIP), is an E3 ubiquitin-protein ligase that is highly expressed in the nervous system during development and is associated with synaptic vesicle membranes. It is N-myrisotoylated and is also located in the endosome-lysosome compartment in fibroblasts, suggesting it may participate in ubiquitin-mediated protein modification. It contains an N-terminal MAGE domain, and a special C-terminal domain that combines a zinc finger and a modified C4HC2H-type RING-CH finger, rather than the typical C4HC3-type RING-CH finger, which is a variant of the RING-H2 finger. Only the RING finger of the zinc finger-RING finger motif is required for its E3 ubiquitin ligase activity. ZNRF1 regulates Schwann cell differentiation by proteasomal degradation of glutamine synthetase (GS). It also mediates regulation of neuritogenesis via interaction with beta-tubulin type 2 (Tubb2). Moreover, ZNRF1 promotes Wallerian degeneration by degrading AKT to induce glycogen synthase kinase-3beta (GSK3B)-dependent CRMP2 phosphorylation. Furthermore, ZNRF1 and its sister protein ZNRF2 regulate the ubiquitous Na+/K+ pump (Na+/K+ATPase). In addition, ZNRF1 may be associated with leukemogenesis of acute lymphoblastic leukemia (ALL) with paired box domain gene 5 (PAX5) alteration. 45 matched cddid_all.tbl CDD cd16695 cd16695 438356 mRING-CH-C4HC2H_ZNRF2 Modified RING-CH finger, H2 subclass (C4HC2H-type), found in zinc/RING finger protein 2 (ZNRF2) and similar proteins. ZNRF2, also known as protein Ells2 or RING finger protein 202 (RNF202), is an E3 ubiquitin-protein ligase that is highly expressed in the nervous system during development and is present in presynaptic plasma membranes. It is N-myrisotoylated and is also located in the endosome-lysosome compartment in fibroblasts. It contains an N-terminal MAGE domain, and a special C-terminal domain that combines a zinc finger and a modified C4HC2H-type RING-CH finger, rather than the typical C4HC3-type RING-CH finger, which is a variant of RING-H2 finger. Only the RING finger of the zinc finger-RING finger motif is required for its E3 ubiquitin ligase activity. Together with its sister protein ZNRF1, ZNRF2 regulates the ubiquitous Na+/K+ pump (Na+/K+ATPase). 56 matched cddid_all.tbl CDD cd16696 cd16696 438357 RING-CH-C4HC3_NFX1 RING-CH finger, H2 subclass (C4HC3-type), found in transcriptional repressor NF-X1 and similar proteins. NF-X1, also known as nuclear transcription factor, X box-binding protein 1, is a novel cysteine-rich sequence-specific DNA-binding protein that interacts with the conserved X-box motif of the human major histocompatibility complex (MHC) class II genes via a repeated Cys-His domain. It functions as a cytokine-inducible transcriptional repressor that plays an important role in regulating the duration of an inflammatory response by limiting the period in which class II MHC molecules are induced by interferon gamma (IFN- gamma). NFX1 contains an N-terminal PAM2 motif, a C4HC3-type RING-CH finger, a Cys-rich region that harbors several NFX1-type zinc fingers, and a C-terminal R3H domain. 55 matched cddid_all.tbl CDD cd16697 cd16697 438358 RING-CH-C4HC3_NFXL1 RING-CH finger, H2 subclass (C4HC3-type), found in nuclear transcription factor, X-box binding-like 1 (NFXL1) and similar proteins. NFXL1, also known as NF-X1-type zinc finger protein NFXL1, or ovarian zinc finger protein (OZFP), is encoded by the novel human cytoplasm-distribution zinc finger protein (CDZFP) gene. It is a putative zinc finger protein with a C4HC3-type RING-CH finger and a Cys-rich region that harbors several NFX1-type zinc fingers. 63 matched cddid_all.tbl CDD cd16698 cd16698 438359 RING_CH-C4HC3_MARCH1-like RING-CH finger, H2 subclass (C4HC3-type), found in membrane-associated RING finger protein MARCH1, MARCH8, and similar proteins. This subfamily includes the closely related MARCH1 and MARCH8, both of which are located on endosomes and the plasma membrane and are implicated in regulating cell surface expression of their substrates. They ubiquitylate and downregulate many targets, including major histocompatibility complex class II (MHCII), CD86, transferrin receptor, HLA-DM, and Fas from the cell surface. MARCH1 is mainly expressed in cells of the immune system, while MARCH8 is more broadly expressed. Both of them contain an N-terminal C4HC3-type RING-CH finger, also known as vRING or RINGv, a variant of C3H2C3-type RING-H2 finger, and two transmembrane domains. The cytoplasmic RING-CH finger participates in the ubiquitin transfer from the E2 to its substrate. The transmembrane domains are implicated in target recognition and dimer formation. 52 matched cddid_all.tbl CDD cd16699 cd16699 438360 RING_CH-C4HC3_MARCH2-like RING-CH finger, H2 subclass (C4HC3-type), found in membrane-associated RING finger proteins MARCH2, MARCH3, and similar proteins. MARCH2 and MARCH3 contain a C4HC3-type RING-CH finger, also known as vRING or RINGv, a variant of C3H2C3-type RING-H2 finger, in the N-terminal cytoplasmic region, two transmembrane domains in the middle region, and a PDZ-binding motif at the C-terminus. MARCH2 is a Golgi-localized, membrane-associated E3 ubiquitin-protein ligase that is involved in endosomal trafficking through the binding of syntaxin 6 (STX6). It is involved in the cystic fibrosis transmembrane conductance regulator (CFTR)-associated ligand (CAL)-mediated ubiquitination and lysosomal degradation of mature CFTR through the association with adaptor proteins CAL and STX6. It also reduces the surface expression of CD86 and the transferrin receptor TFRC and regulates cell surface carvedilol-bound beta2-adrenergic receptor (beta2ARs) expression. Moreover, MARCH2 interacts with and ubiquitinates PDZ domains polarity determining scaffold protein DLG1 through its PDZ-binding motif, suggesting it may function as a molecular bridge with ubiquitin ligase activity connecting endocytic tumor suppressor proteins such as syntaxins to DLG1. MARCH3 is an E3 ubiquitin-protein ligase that is broadly expressed at relatively high levels in spleen, colon, and lung. It is localized to early endosomes, binds to MARCH2 and syntaxin 6, and is involved in the regulation of vesicular trafficking and fusion of the transport vesicles in endosomes. Its E2 specificity significantly overlaps that of MARCH2. 51 matched cddid_all.tbl CDD cd16700 cd16700 319614 RING_CH-C4HC3_MARCH4-like RING-CH finger, H2 subclass (C4HC3-type), found in membrane-associated RING finger proteins MARCH4, MARCH9, MARCH11, and similar proteins. MARCH4 and MARCH9 are closely related to each other. They downregulate major histocompatibility complex-I (MHC-I). Moreover, MARCH4 and MARCH9, but not other MARCH proteins, can associate with Mult1 and prevent Mult1 expression at the cell surface in a lysine-dependent manner that can be reversed by heat shocking the cells. MARCH11 is a transmembrane RING-finger ubiquitin ligase that is predominantly expressed in developing spermatids in a stage-specific manner and is localized to trans-Golgi network (TGN) vesicles and multivesicular bodies (MVBs). It mediates selective protein sorting via the TGN-MVB transport pathway through its ubiquitin ligase activity. SAMT family proteins have been identified as substrates of MARCH11 in mouse spermatids, suggesting that MARCH11 plays a role in mammalian spermiogenesis. Moreover, MARCH11 targets CD4 for ubiquitination. It also forms complexes with the adaptor protein complex-1 and with fucose-containing glycoproteins including ubiquitinated forms. All subfamily members contain an N-terminal C4HC3-type RING-CH finger, also known as vRING or RINGv, a variant of C3H2C3-type RING-H2 finger, followed by two transmembrane regions. 51 matched cddid_all.tbl CDD cd16701 cd16701 438361 RING_CH-C4HC3_MARCH5 RING-CH finger, H2 subclass (C4HC3-type), found in membrane-associated RING-CH5 (MARCH5). MARCH5, also known as membrane-associated RING finger protein 5, membrane-associated RING-CH protein V (MARCH-V), RING finger protein 153 (RNF153), or mitochondrial ubiquitin ligase (MITOL), is a mitochondrial outer membrane-associated E3 ubiquitin-protein ligase that regulates mitochondrial dynamics including mitochondrial morphology, transport, and interaction with endoplasmic reticulum (ER), at least in part, through the ubiquitination of mitochondrial fission factor Drp1, microtubule-associated protein 1B (MAP1B) and mitofusin 2 (Mfn2), respectively. MARCH5 also mediates the cell cycle-dependent degradation of Mitofusin 1 (Mfn1) in G2/M phase, and thus serves as an upstream quality controller of Mitofusin 1 (Mfn1), preventing excessive accumulation of Mfn1 protein under stress conditions, which is crucial for mitochondrial homeostasis and cell viability. Moreover, MARCH5 is involved in maintaining mouse-embryonic stem cell (mESC) pluripotency via suppression of ERK signalling. It is also a positive regulator of Toll-like receptor 7 (TLR7)-mediated NF-kappaB activation in mammals. MARCH5 contains an N-terminal C4HC3-type RING-CH finger, also known as vRING or RINGv, a variant of C3H2C3-type RING-H2 finger, and four C-terminal transmembrane spans. 61 matched cddid_all.tbl CDD cd16702 cd16702 438362 RING_CH-C4HC3_MARCH6 RING-CH finger, H2 subclass (C4HC3-type), found in membrane-associated RING-CH6 (MARCH6). MARCH6, also known as membrane-associated RING finger protein 6, membrane-associated RING-CH protein VI (MARCH-VI), RING finger protein 176 (RNF176), protein TEB-4, or Doa10 homolog, is an endoplasmic reticulum (ER)-localized E3 ubiquitin ligase that ubiquitinates ER-associated proteins with a cytoplasmic domain in a ubiquitin-conjugating enzyme 7 (UBC7)-dependent manner), such as Mps2, UBC6, and Ste6. It also regulates its own UBC7-mediated degradation. MARCH6 interacts with ubiquitin-specific protease USP19, which deubiquitinates and stabilizes MARCH6 and inhibits p97-dependent proteasomal degradation. It is also involved in the cholesterol synthesis pathway by controlling the degradation of squalene monooxygenase (SM), and affects 3-hydroxy-3-methyl-glutaryl coenzyme A reductase (HMGCR). Furthermore, it may be a key regulator of thyroid hormone activation in a number of tissues, since it mediates the proteasomal degradation of type 2 iodothyronine deiodinase (D2). MARCH6 contains 14 transmembrane helices and a conserved N-terminal C4HC3-type RING-CH finger, also known as vRING or RINGv, a variant of C3H2C3-type RING-H2 finger, that catalyzes ubiquitin Lys48-specific ligation. 50 matched cddid_all.tbl CDD cd16703 cd16703 438363 RING_CH-C4HC3_MARCH7-like RING-CH finger, H2 subclass (C4HC3-type), found in membrane-associated MARCH7, MARCH10, and similar proteins. This subfamily includes two closely related membrane-associated RING-CH proteins, MARCH7 and MARCH10, both of which are predicted to have no transmembrane spanning region, but do harbor a C4HC3-type RING-CH finger, also known as vRING or RINGv, a variant of C3H2C3-type RING-H2 finger, that is responsible for E3 activity. MARCH7, also known as MARCH-VII, RNF177, or axotrophin, is a ubiquitin E3 ligase expressed in multiple types of cells and tissues, including stem cells and precursor cells, and is predominantly localized on the plasma membrane, and cytoplasm. MARCH7 is involved in T cell proliferation and neuronal development. It also participates in the regulation of cytoskeleton re-organization, cellular migration and invasion, cell proliferation, and tumorigenesis in ovarian carcinoma cells. Moreover, MARCH7 modulates nuclear factor kappaB (NF-kappaB) and Wnt/beta-catenin pathways. It has been identified as an authentic target of miR-101. It ubiquitinates tau protein in vitro, impairing microtubule binding. MARCH10, also known as MARCH-X or RNF190, is a microtubule-associated E3 ubiquitin ligase of developing spermatids and is involved in spermiogenesis by regulating the formation and maintenance of the flagella. It is localized to the principal piece of elongating spermatids. in developing spermatids. 61 matched cddid_all.tbl CDD cd16704 cd16704 438364 RING-HC_RNF20-like RING finger, HC subclass, found in RING finger protein RNF20, RNF40, and similar proteins. RNF20, also known as BRE1A, and RNF40, also known as BRE1B, are E3 ubiquitin-protein ligases that work together to form a heterodimeric complex that facilitate the K120 monoubiquitination of histone H2B (H2Bub1), a DNA damage-induced histone modification that is crucial for recruitment of the chromatin remodeler SNF2h to DNA double-strand break (DSB) damage sites. RNF20 regulates the cell cycle and differentiation of neural precursor cells (NPCs) and links histone H2B ubiquitylation with inflammation and inflammation-associated cancer. RNF40, also known as 95 kDa retinoblastoma-associated protein (RBP95), was identified as a novel leucine zipper retinoblastoma protein (pRb)-associated protein that may function as a regulation factor in RNA polymerase II-mediated transcription and/or transcriptional processing. All subfamily members contain a C3HC4-type RING-HC finger at its C-terminus. 65 matched cddid_all.tbl CDD cd16705 cd16705 438365 RING-HC_dBre1-like RING finger, HC subclass, found in Drosophila melanogaster Bre1 (dBre1) and similar proteins. dBre1 is the functional homolog of yeast Bre1, an E3 ubiquitin ligase required for the monoubiquitination of histone H2B and, indirectly, for H3K4 methylation. dBre1 acts as a nuclear component required for the expression of Notch target genes in Drosophila development. dBre1 contains a C3HC4-type RING-HC finger at its C-terminus. 69 matched cddid_all.tbl CDD cd16706 cd16706 438366 RING-HC_CARP1 RING finger, HC subclass, found in caspases-8 and -10-associated RING finger protein 1 (CARP1) and similar proteins. CARP1, also known as caspase regulator CARP1, FYVE-RING finger protein Momo, RING finger homologous to inhibitor of apoptosis protein (RFI), RING finger protein 34 (RNF34), or RING finger protein RIFF, is a nuclear protein that functions as a specific E3 ubiquitin ligase for the transcriptional coactivator PGC-1alpha, a master regulator of energy metabolism and adaptive thermogenesis in the brown fat cell which negatively regulates brown fat cell metabolism. It is preferentially expressed in esophageal, gastric, and colorectal cancers, suggesting a possible association with the development of digestive tract cancers. It regulates the p53 signaling pathway by degrading 14-3-3 sigma and stabilizing MDM2. CARP1 does not localize to membranes in the cell and is involved in the negative regulation of apoptosis, specifically targeting two initiator caspases, caspase 8 and caspase 10. CARP1 contains an N-terminal FYVE-like domain and a C-terminal C3HC4-type RING-HC finger domain. 54 matched cddid_all.tbl CDD cd16707 cd16707 438367 RING-HC_CARP2 RING finger, HC subclass, found in caspases-8 and -10-associated RING finger protein 2 (CARP-2) and similar proteins. CARP-2, also known as rififylin, caspase regulator CARP2, FYVE-RING finger protein Sakura (Fring), RING finger and FYVE-like domain-containing protein 1, RING finger protein 189 (RNF189), or RING finger protein 34-like, is an endosome-associated E3 ubiquitin-protein ligase that targets internalized receptor interacting kinase (RIP) for proteasome-mediated degradation. It acts as a negative regulator of tumor necrosis factor (TNF)-induced nuclear factor (NF)-kappaB activation. It also regulates the p53 signaling pathway by degrading 14-3-3sigma and stabilizing MDM2. As a caspase regulator, CARP2 does not localize to membranes in the cell and is involved in the negative regulation of apoptosis, specifically targeting two initiator caspases, caspase 8 and caspase 10. CARP2 contains an N-terminal FYVE-like domain and a C-terminal C3HC4-type RING-HC finger domain. 50 matched cddid_all.tbl CDD cd16708 cd16708 438368 RING-HC_Cbl RING finger, HC subclass, found in E3 ubiquitin-protein ligase Cbl and similar proteins. Cbl, also known as Casitas B-lineage lymphoma proto-oncogene, proto-oncogene c-Cbl, RING finger protein 55 (RNF55), or signal transduction protein Cbl, is a multi-domain protein that acts as a key negative regulator of various receptor and non-receptor tyrosine kinase signaling. It contains a tyrosine kinase-binding domain (TKB, also known as the phosphotyrosine binding PTB domain, composed of a four helix-bundle, a Ca2+ binding EF-hand and a highly variant SH2 domain), a proline-rich domain, a C3HC4-type RING-HC finger, and an ubiquitin-associated (UBA) domain. TKB is responsible for the interactions with many tyrosine kinases, such as the colony-stimulating factor-1 (CSF-1) receptor, Syk/ZAP-70, and Src-family of protein tyrosine kinases. The proline-rich domain can recruit proteins with a SH3 domain. Moreover, Cbl functions as an E3 ubiquitin ligase that can bind ubiquitin-conjugating enzymes (E2s) through the RING-HC finger. 77 matched cddid_all.tbl CDD cd16709 cd16709 438369 RING-HC_Cbl-b RING finger, HC subclass, found in E3 ubiquitin-protein ligase Cbl-b and similar proteins. Cbl-b, also known as Casitas B-lineage lymphoma proto-oncogene b, RING finger protein 56 (RNF56), SH3-binding protein Cbl-b, or signal transduction protein Cbl-b, has been identified as a regulator of antigen-specific, T cell-intrinsic, peripheral immune tolerance, a state also known as clonal anergy. It may inhibit activation of the p85 subunit of phosphoinositide 3-kinase (PI3K), protein kinase C-theta (PKC-theta), and phospholipase C-gamma1 (PLC-gamma1) and negatively regulates T-cell receptor-induced transcription factor nuclear factor kappaB (NF-kappaB) activation. In addition, Cbl-b may target multiple signaling molecules involved in transforming growth factor (TGF)-beta-mediated transactivation pathways. Cbl-b contains a tyrosine-kinase-binding domain (TKB, also known as the phosphotyrosine binding PTB domain, is composed of a four helix-bundle, a Ca2+ binding EF-hand and a highly variant SH2 domain), a proline rich domain, a nuclear localization signal, a C3HC4-type RING-HC finger and an ubiquitin-associated (UBA) domain. 76 matched cddid_all.tbl CDD cd16710 cd16710 438370 RING-HC_Cbl-c RING finger, HC subclass, found in E3 ubiquitin-protein ligase Cbl-c and similar proteins. Cbl-c, also known as RING finger protein 57 (RNF57), SH3-binding protein Cbl-3, SH3-binding protein Cbl-c, or signal transduction protein Cbl-c, is an E3 ubiquitin-protein ligase expressed exclusively in epithelial cells. It contains a tyrosine-kinase-binding domain (TKB, also known as the phosphotyrosine binding PTB domain, composed of a four helix-bundle, a Ca2+ binding EF-hand and a highly variant SH2 domain), a C3HC4-type RING-HC finger, and a short proline-rich region, but lacks the ubiquitin-associated (UBA) leucine zipper motif that are present in Cbl and Cbl-b. Cbl-c acts as a regulator of epidermal growth factor receptor (EGFR)-mediated signal transduction. It also suppresses v-Src-induced transformation through ubiquitin-dependent protein degradation. Moreover, Cbl-c ubiquitinates and downregulates RETMEN2A and implicates Enigma (PDLIM7) as a positive regulator of RETMEN2A by blocking Cbl-mediated ubiquitination and degradation. The ubiquitin ligase activity of Cbl-c is increased via the interaction of its RING-HC finger domain with a LIM domain of the paxillin homolog, hydrogen peroxide induced construct 5 (Hic-5). 65 matched cddid_all.tbl CDD cd16711 cd16711 438371 RING-HC_DTX3 RING finger, HC subclass, found in E3 ubiquitin-protein ligase Deltex3 (DTX3) and similar proteins. DTX3, also known as RING finger protein 154 (RNF154), is an E3 ubiquitin-protein ligase that belongs to the Deltex (DTX) family. In contrast to other DTXs, DTX3 does not contain two N-terminal Notch-binding WWE domains, but a short unique N-terminal domain, suggesting it does not interact with the intracellular domain of Notch. Its C-terminal region includes a C3HC4-type RING-HC finger, and a previously unidentified C-terminal domain. 54 matched cddid_all.tbl CDD cd16712 cd16712 438372 RING-HC_DTX3L RING finger, HC subclass, found in protein Deltex-3-like (DTX3L) and similar proteins. DTX3L, also known as B-lymphoma- and BAL-associated protein (BBAP) or Rhysin-2 (Rhysin2), is a RING-domain E3 ubiquitin-protein ligase that regulates endosomal sorting of the G protein-coupled receptor CXCR4 from endosomes to lysosomes. It also regulates subcellular localization of its partner protein, B aggressive lymphoma (BAL), by a dynamic nucleocytoplasmic trafficking mechanism. DTX3L has a unique N-terminus, but lacks the highly basic N-terminal motif and the central proline-rich motif present in other Deltex (DTX) family members, such as DTX1, DTX2, and DTX4. Moreover, its C-terminal region is highly homologous to DTX3. It includes a C3HC4-type RING-HC finger, and a previously unidentified C-terminal domain. DTX3L can associate with DTX1 through its unique N-terminus and further enhance self-ubiquitination. 56 matched cddid_all.tbl CDD cd16713 cd16713 438373 RING-HC_BIRC2_3_7 RING finger, HC subclass, found in apoptosis protein c-IAP1, c-IAP2, livin, and similar proteins. The cellular inhibitor of apoptosis protein c-IAPs function as ubiquitin E3 ligases that mediate the ubiquitination of substrates involved in apoptosis, nuclear factor-kappaB (NF-kappaB) signaling, and oncogenesis. Unlike other IAPs, such as XIAP, c-IAPs exhibit minimal binding to caspases and may not play an important role in the inhibition of these proteases. c-IAP1, also known as baculoviral IAP repeat-containing protein BIRC2, IAP-2, RING finger protein 48, or TNFR2-TRAF-signaling complex protein 2, is a potent regulator of the tumor necrosis factor (TNF) receptor family and NF-kappaB signaling pathways in the cytoplasm. It can also regulate E2F1 transcription factor-mediated control of cyclin transcription in the nucleus. c-IAP2, also known as BIRC3, IAP-1, apoptosis inhibitor 2 (API2), or IAP homolog C, also influences ubiquitin-dependent pathways that modulate innate immune signalling by activation of NF-kappaB. c-IAPs contain three N-terminal baculoviral IAP repeat (BIR) domains that enable interactions with proteins, a ubiquitin-association (UBA) domain that is responsible for the binding of polyubiquitin (polyUb), a caspase activation and recruitment domain (CARD) that serves as a protein interaction surface, and a C3HC4-type RING-HC finger at the carboxyl terminus that is required for ubiquitin ligase activity. Livin, also known as baculoviral IAP repeat-containing protein 7 (BIRC7), kidney inhibitor of apoptosis protein (KIAP), melanoma inhibitor of apoptosis protein (ML-IAP), or RING finger protein 50, was identified as the melanoma IAP. It plays crucial roles in apoptosis, cell proliferation, and cell cycle control. Its anti-apoptotic activity is regulated by the inhibition of caspase-3, -7, and -9. Its E3 ubiquitin-ligase-like activity promotes degradation of Smac/DIABLO, a critical endogenous regulator of all IAPs. Unlike other family members, mammalian livin contains a single BIR domain and a C3HC4-type RING-HC finger. The UBA domain can be detected in non-mammalian homologs of livin. 57 matched cddid_all.tbl CDD cd16714 cd16714 438374 RING-HC_BIRC4_8 RING finger, HC subclass, found in E3 ubiquitin-protein ligase XIAP, baculoviral IAP repeat-containing protein 8 (BIRC8) and similar proteins. XIAP, also known as baculoviral IAP repeat-containing protein 4 (BIRC4), IAP-like protein (ILP), inhibitor of apoptosis protein 3 (IAP-3), or X-linked inhibitor of apoptosis protein (X-linked IAP), is a potent suppressor of apoptosis that directly inhibits specific members of the caspase family of cysteine proteases, including caspase-3, -7, and -9. It promotes proteasomal degradation of caspase-3 and enhances its anti-apoptotic effect in Fas-induced cell death. The ubiquitin-protein ligase (E3) activity of XIAP also exhibits in the ubiquitination of second mitochondria-derived activator of caspases (Smac). The mitochondrial proteins, Smac/DIABLO and Omi/HtrA2, can inhibit the antiapoptotic activity of XIAP. XIAP has also been implicated in several intracellular signaling cascades involved in the cellular response to stress, such as the c-Jun N-terminal kinase (JNK), the nuclear factor-kappaB (NF-kappaB), and the transforming growth factor-beta (TGF-beta) pathways. Moreover, XIAP can regulate copper homeostasis by interacting with MURR1. BIRC8, also known as inhibitor of apoptosis-like protein 2, IAP-like protein 2, ILP-2, or testis-specific inhibitor of apoptosis, is a tissue-specific homolog of E3 ubiquitin-protein ligase XIAP. It has been implicated in the control of apoptosis in the testis by direct inhibition of caspase 9. Both XIAP and BIRC8 contain three N-terminal baculoviral IAP repeat (BIR) domains, a ubiquitin-association (UBA) domain and a C3HC4-type RING-HC finger at the carboxyl terminus. 64 matched cddid_all.tbl CDD cd16715 cd16715 438375 vRING-HC_IRF2BP1 variant of RING finger, HC subclass, found in interferon regulatory factor 2-binding protein 1 (IRF-2BP1). IRF-2BP1, also known as IRF-2-binding protein 1, is a nuclear protein that binds to the C-terminal repression domain of IRF-2 and acts as an IRF-2-dependent transcriptional corepressor, both enhancer-activated and basal transcription. It binds to Jun-dimerization protein 2 (JDP2), a member of the activating protein-1 (AP-1) family of transcription factors, and enhances the polyubiquitination of JDP2. It also represses activating transcription factor-2 (ATF2)-mediated transcriptional activation from a cyclic AMP-responsive element (CRE)-containing promoter. IRF-2BP1 contains an N-terminal C4-type zinc finger and a C-terminal variant C3HC4-type RING-HC finger. 62 matched cddid_all.tbl CDD cd16716 cd16716 438376 vRING-HC_IRF2BP2 variant of RING finger, HC subclass, found in interferon regulatory factor 2 (IRF2)-binding protein 2 (IRF-2BP2). IRF-2BP2, also known as IRF-2-binding protein 2 or DIF-1, is a nuclear protein that binds to the C-terminal repression domain of IRF-2 and acts as an IRF-2-dependent transcriptional corepressor, both enhancer-activated and basal transcription. IRF-2BP2 also specifically interacts with the C-terminal domain of the nuclear factor of activated T cells NFAT1 transcription factor, and negatively regulates the NFAT1-dependent transactivation of NFAT-responsive promoters. Moreover, IRF2BP2 suppresses the transactivation activity of p53 on both Bax and p21 promoters. It also shows anti-apoptotic activity through the modulation of the death domain in NRIF3. In addition, IRF2BP2 functions as a cofactor of VGLL4 and plays a critical role controlling gene expression in skeletal, cardiac, and smooth muscle cells. It is a muscle-enriched transcription factor required to activate vascular endothelial growth factor-A (VEGF-A) expression. IRF-2BP2 contains an N-terminal C4-type zinc finger and a C-terminal variant C3HC4-type RING-HC finger. The zinc finger is responsible for the homo- and hetero-dimerization between different members of the IRF-2BP2 family. The RING-HC finger interacts with IRF2 and also with nuclear receptor interacting factor 3 (NRIF3). 67 matched cddid_all.tbl CDD cd16717 cd16717 438377 vRING-HC_IRF2BPL variant of RING finger, HC subclass, found in interferon regulatory factor 2-binding protein-like (IRF-2BPL). IRF-2BPL, also known as C14orf4 or enhanced at puberty protein 1(EAP1), is a homolog of interferon regulatory factor 2-binding proteins, IRF-2BP1 and IRF-2BP2. It is expressed in the mediobasal hypothalamus and plays a critical function in regulating the female reproductive neuroendocrine axis. IRF-2BPL is a proline-rich protein with polyglutamine and polyalanine tracks at the N-terminus and a C3HC4-type RING-HC finger domain with a partially new pattern at the C-terminus. 66 matched cddid_all.tbl CDD cd16718 cd16718 438378 RING-HC_LNX3 RING finger, HC subclass, found in ligand of numb protein X 3 (LNX3). LNX3, also known as PDZ domain-containing RING finger protein 3 (PDZRN3), or Semaphorin cytoplasmic domain-associated protein 3 (SEMACAP3), is an E3 ubiquitin-protein ligase that was first identified as a Semaphorin-binding partner. It is also responsible for the ubiquitination and degradation of Numb, a component of the Notch signaling pathway that functions in the specification of cell fates during development and is known to control cell numbers during neurogenesis in vertebrates. LNX3 acts as a negative regulator of osteoblast differentiation by inhibiting Wnt-beta-catenin signaling. LNX3 also plays an important role in neuromuscular junction formation. It interacts with and ubiquitinates the muscle specific tyrosine kinase (MuSK), thus promoting its endocytosis and negatively regulating the cell surface expression of this key regulator of postsynaptic assembly. LNX3 contains an N-terminal C3HC4-type RING-HC finger, two PDZ domains, and a C-terminal LNX3 homology (LNX3H) domain. 47 matched cddid_all.tbl CDD cd16719 cd16719 438379 RING-HC_LNX4 RING finger, HC subclass, found in ligand of numb protein X 4 (LNX4). LNX4, also known as PDZ domain-containing RING finger protein 4 (PDZRN4), or SEMACAP3-like protein (SEMCAP3L), is an E3 ubiquitin-protein ligase responsible for the ubiquitination and degradation of Numb, a component of the Notch signaling pathway that functions in the specification of cell fates during development and is known to control cell numbers during neurogenesis in vertebrates. LNX4 contains an N-terminal C3HC4-type RING-HC finger, two PDZ domains, and a C-terminal LNX3 homology (LNX3H) domain. 53 matched cddid_all.tbl CDD cd16720 cd16720 438380 RING-HC_MEX3A RING finger, HC subclass, found in RNA-binding protein MEX3A. MEX3A, also known as RING finger and KH domain-containing protein 4 (RKHD4), is an RNA-binding phosphoprotein that localizes in P-bodies and stress granules, which are two structures involved in the storage and turnover of mRNAs. It has been implicated in the regulation of tumorigenesis. It controls the polarity and stemness of intestinal epithelial cells through the post-transcriptional regulation of the homeobox transcription factor CDX2, which plays a crucial role in intestinal cell fate specification, both during normal development and in tumorigenic processes involving intestinal reprogramming. Moreover, it exhibits a transforming activity when overexpressed in gastric epithelial cells. MEX3A contains two K homology (KH) domains that provide RNA-binding capacity, and a C-terminal C3HC4-type RING-HC finger. Like other MEX-3 family proteins, MEX3A shuttles between the nucleus and the cytoplasm via the CRM1-dependent export pathway. 56 matched cddid_all.tbl CDD cd16721 cd16721 438381 RING-HC_MEX3B RING finger, HC subclass, found in RNA-binding protein MEX3B. MEX3B, also known as RING finger and KH domain-containing protein 3 (RKHD3), or RING finger protein 195 (RNF195), is an RNA-binding phosphoprotein that localizes in P-bodies and stress granules, which are two structures involved in the storage and turnover of mRNAs. It regulates the spatial organization of the Rap1 pathway that orchestrates Sertoli cell functions. It has a 3' long conserved untranslated region (3'LCU)-mediated fine-tuning system for mRNA regulation in early vertebrate development such as anteroposterior (AP) patterning and signal transduction. MEX3B contains two K homology (KH) domains that provide RNA-binding capacity, and a C-terminal C3HC4-type RING-HC finger. Like other MEX-3 family proteins, MEX3B shuttles between the nucleus and the cytoplasm via the CRM1-dependent export pathway. 58 matched cddid_all.tbl CDD cd16722 cd16722 438382 RING-HC_MEX3C RING finger, HC subclass, found in RNA-binding protein MEX3C. MEX3C, also known as RING finger and KH domain-containing protein 2 (RKHD2), or RING finger protein 194 (RNF194), is an RNA-binding phosphoprotein that acts as a suppressor of chromosomal instability. It functions as an ubiquitin E3 ligase responsible for the post-transcriptional, HLA-A allotype-specific regulation of MHC class I molecules (MHC-I). It also modifies retinoic acid inducible gene-1 (RIG-I) in stress granules and plays a critical role in eliciting antiviral immune responses. Moreover, MEX3C plays an essential role in normal postnatal growth via enhancing the local expression of insulin-like growth factor 1 (IGF1) in bone. It may also be involved in metabolic regulation of energy balance. MEX3C contains two K homology (KH) domains that provide RNA-binding capacity, and a C-terminal C3HC4-type RING-HC finger. Like other MEX-3 family proteins, MEX3C shuttles between the nucleus and the cytoplasm via the CRM1-dependent export pathway. 55 matched cddid_all.tbl CDD cd16723 cd16723 438383 RING-HC_MEX3D RING finger, HC subclass, found in RNA-binding protein MEX3D. MEX3D, also known as RING finger and KH domain-containing protein 1 (RKHD1), RING finger protein 193 (RNF193), or TINO, is an RNA-binding phosphoprotein that controls the stability of the transcripts coding for the anti-apoptotic protein BCL-2, and negatively regulates BCL-2 in HeLa cells. MEX3D contains two K homology (KH) domains that provide RNA-binding capacity, and a C-terminal C3HC4-type RING-HC finger. Like other MEX-3 family proteins, MEX3D shuttles between the nucleus and the cytoplasm via the CRM1-dependent export pathway. 64 matched cddid_all.tbl CDD cd16724 cd16724 438384 RING-HC_MIB1_rpt1 first RING finger, HC subclass, found in mind bomb 1 (MIB1) and similar proteins. MIB1, also known as DAPK-interacting protein 1 (DIP-1) or zinc finger ZZ type with ankyrin repeat domain protein 2, is a large, multi-domain E3 ubiquitin-protein ligase that promotes ubiquitination of the cytoplasmic tails of Notch ligands, and thus plays an essential role in controlling metazoan development by Notch signaling. It is also involved in Wnt/beta-catenin signaling and nuclear factor (NF)-kappaB signaling, and has been implicated in innate immunity, neuronal function, genomic stability, and cell death. MIB1 contains an MZM region with two Mib-Herc2 domains flanking a ZZ zinc finger, a REP region including two tandem Mib repeats, an ANK region that spans ankyrin repeats, and a RNG region consisting of three C3HC4-type RING-HC fingers. This model corresponds to the first RING-HC finger. 38 matched cddid_all.tbl CDD cd16725 cd16725 438385 RING-HC_MIB1_rpt2 second RING finger, HC subclass, found in mind bomb 1 (MIB1) and similar proteins. MIB1, also known as DAPK-interacting protein 1 (DIP-1) or zinc finger ZZ type with ankyrin repeat domain protein 2, is a large, multi-domain E3 ubiquitin-protein ligase that promotes ubiquitination of the cytoplasmic tails of Notch ligands, and thus plays an essential role in controlling metazoan development by Notch signaling. It is also involved in Wnt/beta-catenin signaling and nuclear factor (NF)-kappaB signaling, and has been implicated in innate immunity, neuronal function, genomic stability, and cell death. MIB1 contains an MZM region with two Mib-Herc2 domains flanking a ZZ zinc finger, a REP region including two tandem Mib repeats, an ANK region that spans ankyrin repeats, and a RNG region consisting of three C3HC4-type RING-HC fingers. This model corresponds to the second RING-HC finger. 38 matched cddid_all.tbl CDD cd16726 cd16726 438386 RING-HC_MIB2_rpt1 first RING finger, HC subclass, found in mind bomb 2 (MIB2) and similar proteins. MIB2, also known as novel zinc finger protein (Novelzin), putative NF-kappa-B-activating protein 002N, skeletrophin, or zinc finger ZZ type with ankyrin repeat domain protein 1, is a large, multi-domain E3 ubiquitin-protein ligase that promotes ubiquitination of the cytoplasmic tails of Notch ligands. It promotes Delta ubiquitylation and endocytosis in Notch activation. Overexpression of MIB2 activates NF-kappaB and interferon-stimulated response element (ISRE) reporter activity. Moreover, MIB2 acts as a novel component of the activated B-cell CLL/lymphoma 10 (BCL10) complex and controls BCL10-dependent NF-kappaB activation. It also functions as a founder myoblast-specific protein that regulates myoblast fusion and muscle stability. MIB2 contains an MZM region with two Mib-Herc2 domains flanking a ZZ zinc finger, a REP region including two tandem Mib repeats, an ANK region that spans ankyrin repeats, and a RNG region consisting of two C3HC4-type RING-HC fingers. This model corresponds to the first RING-HC finger. 38 matched cddid_all.tbl CDD cd16727 cd16727 438387 RING-HC_MIB1_rpt3 third RING finger, HC subclass, found in mind bomb 1 (MIB1) and similar proteins. MIB1, also known as DAPK-interacting protein 1 (DIP-1) or zinc finger ZZ type with ankyrin repeat domain protein 2, is a large, multi-domain E3 ubiquitin-protein ligase that promotes ubiquitination of the cytoplasmic tails of Notch ligands, and thus plays an essential role in controlling metazoan development by Notch signaling. It is also involved in Wnt/beta-catenin signaling and nuclear factor (NF)-kappaB signaling, and has been implicated in innate immunity, neuronal function, genomic stability, and cell death. MIB1 contains an MZM region with two Mib-Herc2 domains flanking a ZZ zinc finger, a REP region including two tandem Mib repeats, an ANK region that spans ankyrin repeats, and a RNG region consisting of three C3HC4-type RING-HC fingers. This model corresponds to the third RING-HC finger. 46 matched cddid_all.tbl CDD cd16728 cd16728 438388 RING-HC_MIB2_rpt2 second RING finger, HC subclass, found in mind bomb 2 (MIB2) and similar proteins. MIB2, also known as novel zinc finger protein (Novelzin), putative NF-kappa-B-activating protein 002N, skeletrophin, or zinc finger ZZ type with ankyrin repeat domain protein 1, is a large, multi-domain E3 ubiquitin-protein ligase that promotes ubiquitination of the cytoplasmic tails of Notch ligands. Especially, it promotes Delta ubiquitylation and endocytosis in Notch activation. Overexpression of MIB2, activates NF-kappaB and interferon-stimulated response element (ISRE) reporter activity. Moreover, MIB2 acts as a novel component of the activated B-cell CLL/lymphoma 10 (BCL10) complex and controls BCL10-dependent NF-kappaB activation. It also functions as a founder myoblast-specific protein that regulates myoblast fusion and muscle stability. MIB2 contains an MZM region with two Mib-Herc2 domains flanking a ZZ zinc finger, a REP region including two tandem Mib repeats, an ANK region that spans ankyrin repeats, and a RNG region consisting of two C3HC4-type RING-HC fingers. This model corresponds to the second RING-HC finger. 51 matched cddid_all.tbl CDD cd16729 cd16729 438389 RING-HC_RGLG_plant RING finger, HC subclass, found in RING domain ligase RGLG1, RGLG2 and similar proteins from plant. RGLG1 is a ubiquitously expressed E3 ubiquitin-protein ligase that interacts with UBC13 and, together with UBC13, catalyzes the formation of K63-linked polyubiquitin chains, which is involved in DNA damage repair. RGLG1 mediates the formation of canonical, K48-linked polyubiquitin chains that target proteins for degradation. It also regulates apical dominance by acting on the auxin transport proteins abundance. RGLG1 has overlapping functions with its closest sequelog, RGLG2. They both function as RING E3 ligases that interact with ethylene response factor 53 (ERF53) in the nucleus and negatively regulate the plant drought stress response. Members of this subfamily contain a Von Willebrand factor type A (vWA) domain and a C3HC4-type RING-HC finger. 48 matched cddid_all.tbl CDD cd16730 cd16730 319644 RING-HC_MKRN1_3 RING finger, HC subclass, found in makorin-1 (MKRN1), makorin-3 (MKRN3), and similar proteins. MKRN1, also known as makorin RING finger protein 1 or RING finger protein 61 (RNF61), is an E3 ubiquitin-protein ligase targeting the telomerase catalytic subunit (TERT) for proteasome processing. It regulates the ubiquitination and degradation of peroxisome-proliferator-activated receptor gamma (PPARgamma), a nuclear receptor that is linked to obesity and metabolic diseases. It also mediates the posttranslational regulation of p14ARF, and thus potentially regulates cellular senescence and tumorigenesis in gastric cancer. Moreover, MKRN1 functions as a differentially negative regulator of p53 and p21, and controls cell cycle arrest and apoptosis. It induces degradation of West Nile virus (WNV) capsid protein to protect cells from WNV. It is a RNA-binding protein involved in the modulation of cellular stress and apoptosis. It predominantly associates with proteins involved in mRNA metabolism including regulators of mRNA turnover, transport, and/or translation, and acts as a component of a ribonucleoprotein complex in embryonic stem cells (ESCs) that is recruited to stress granules upon exposure to environmental stress. MKRN1 interacts with poly(A)-binding protein (PABP), a key component of different ribonucleoprotein complexes, in an RNA-independent manner, and stimulates translation in nerve cells. In addition, MKRN1 is a novel SEREX (serological identification of antigens by recombinant cDNA expression cloning) antigen of esophageal squamous cell carcinoma (SCC). It may be involved in carcinogenesis of the well-differentiated type of tumors possibly via ubiquitination of filamin A interacting protein 1 (L-FILIP). Human MKRN1 contains three N-terminal C3H1-type zinc fingers, a motif rich in Cys and His residues (CH), a C3HC4-type RING-HC finger, and another C3H1-type zinc finger at the C-terminus. MKRN3, also known as makorin RING finger protein 3, RING finger protein 63 (RNF63), or zinc finger protein 127 (ZNF127), is a therian mammal-specific retrocopy of MKRN1. It acts as a putative E3 ubiquitin-protein ligase involved in ubiquitination and cell signaling. MKRN3 shows a potential inhibitory effect on hypothalamic gonadotropin-releasing hormone (GnRH) secretion. Its defects represent the most frequent known genetic cause of familial central precocious puberty (CPP). In contrast to human MKRN1, human MKRN3 lacks the second C3H1-type zinc finger at the N-terminal region. The RING-HC finger of mammalian MKRN4 shows high sequence similarity with that of MKRN3, and is also included in this model. 61 matched cddid_all.tbl CDD cd16731 cd16731 319645 RING-HC_MKRN2 RING finger, HC subclass, found in makorin-2 (MKRN2) and similar proteins. MKRN2, also known as makorin RING finger protein 2, RING finger protein 62 (RNF62), or HSPC070, is a putative ribonucleoprotein that acts as a neurogenesis inhibitor acting upstream of glycogen synthase kinase-3beta (GSK-3beta) in the phosphatidylinositol 3-kinase (PI3K)/Akt pathway. It also functions in promoting cell proliferation of primary CD34+ progenitor cells and K562 cells, indicating its possible involvement in normal and malignant hematopoiesis. Mammalian MKRN2 contains three N-terminal C3H1-type zinc fingers, a motif rich in Cys and His residues (CH), a C3HC4-type RING-HC finger, and another C3H1-type zinc finger at the C-terminus. The third C3H1-type zinc finger, the CH motif, as well as the RING zinc finger are necessary for its anti-neurogenic activity. 58 matched cddid_all.tbl CDD cd16732 cd16732 438390 RING-HC_MKRN4 RING finger, HC subclass, found in makorin-4 (MKRN4) and similar proteins. MKRN4, also known as makorin RING finger protein pseudogene 4, makorin RING finger protein pseudogene 5, RING finger protein 64 (RNF64), zinc finger protein 127-Xp (ZNF127-Xp), or zinc finger protein 127-like 1, is a new divergent member of the makorin protein family in vertebrates. It may have an ancestral gonad-specific function and maternal embryonic expression before duplication in vertebrates. MKRN4 contains typical arrays of one to four C3H1-type zinc fingers, a motif rich in Cys and His residues (CH) and a C3HC4-type RING-HC finger. The RING-HC finger of mammalian MKRN4 shows high sequence similarity with that of MKRN3, and is not included in this model. 61 matched cddid_all.tbl CDD cd16733 cd16733 438391 RING-HC_PCGF1 RING finger, HC subclass, found in polycomb group RING finger protein 1 (PCGF1) and similar proteins. PCGF1, also known as nervous system Polycomb-1 (NSPc1) or RING finger protein 68 (RNF68), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR). It serves as the core component of a noncanonical Polycomb repressive complex 1 (PRC1)-like BCOR complex that also contains RING1, RNF2, RYBP, SKP1, as well as the BCL6 co-repressor BCOR and the histone demethylase KDM2B, and is required to maintain the transcriptionally repressive state of some genes, such as Hox genes, BCL6 and the cyclin-dependent kinase inhibitor, CDKN1A. PCGF1 promotes cell cycle progression and enhances cell proliferation as well. It is a cell growth regulator that acts as a transcriptional repressor of p21Waf1/Cip1 via the retinoid acid response element (RARE element). Moreover, PCGF1 functions as an epigenetic regulator involved in hematopoietic cell differentiation. It cooperates with the transcription factor runt-related transcription factor 1 (Runx1) in regulating differentiation and self-renewal of hematopoietic cells. Furthermore, PCGF1 represents a physical and functional link between Polycomb function and pluripotency. PCGF1 contains a C3HC4-type RING-HC finger. 71 matched cddid_all.tbl CDD cd16734 cd16734 438392 RING-HC_PCGF2 RING finger found in polycomb group RING finger protein 2 (PCGF2) and similar proteins. PCGF2, also known as DNA-binding protein Mel-18, RING finger protein 110 (RNF110), or zinc finger protein 144 (ZNF144), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR). It serves as the core component of a canonical Polycomb repressive complex 1 (PRC1), which is composed of a chromodomain-containing protein (CBX2, CBX4, CBX6, CBX7 or CBX8) and a Polyhomeotic protein (PHC1, PHC2, or PHC3). Like other PCGF homologs, PCGF2 associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. Moreover, PCGF2 uniquely regulates PRC1 to specify mesoderm cell fate in embryonic stem cells. It is required for PRC1 stability and maintenance of gene repression in embryonic stem cells (ESCs) and essential for ESC differentiation into early cardiac-mesoderm precursors. PCGF2 also plays a significant role in the angiogenic function of endothelial cells (ECs) by regulating endothelial gene expression. Furthermore, PCGF2 is a SUMO-dependent regulator of hormone receptors. It facilitates the deSUMOylation process by inhibiting PCGF4/BMI1-mediated ubiquitin-proteasomal degradation of SUMO1/sentrin-specific protease 1 (SENP1). It is also a novel negative regulator of breast cancer stem cells (CSCs) that inhibits the stem cell population and in vitro and in vivo self-renewal through the inactivation of Wnt-mediated Notch signaling. PCGF2 contains a C3HC4-type RING-HC finger. 80 matched cddid_all.tbl CDD cd16735 cd16735 438393 RING-HC_PCGF3 RING finger found in polycomb group RING finger protein 3 (PCGF3) and similar proteins. PCGF3, also known as RING finger protein 3A (RNF3A), is one of six PcG RING finger (PCGF) homologs (PCGF1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6) and serves as the core component of a Polycomb repressive complex 1 (PRC1). Like other PCGF homologs, PCGF3 associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. PCGF3 contains a C3HC4-type RING-HC finger. 66 matched cddid_all.tbl CDD cd16736 cd16736 438394 RING-HC_PCGF4 RING finger found in polycomb group RING finger protein 4 (PCGF4) and similar proteins. PCGF4, also known as polycomb complex protein BMI-1 (B cell-specific Moloney murine leukemia virus integration site 1) or RING finger protein 51 (RNF51), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR). It serves as the core component of a canonical Polycomb repressive complex 1 (PRC1), which is composed of a chromodomain-containing protein (CBX2, CBX4, CBX6, CBX7 or CBX8) and a Polyhomeotic protein (PHC1, PHC2, or PHC3), and plays important roles in chromatin compaction and H2AK119 monoubiquitination. PCGF4 associates with the Runx1/CBFbeta transcription factor complex to silence target genes in a PRC2-independent manner. Moreover, PCGF4 is expressed in the hair cells and supporting cells. It can regulate cell survival by controlling mitochondrial function and reactive oxygen species (ROS) level in thymocytes and neurons, thus having an important role in the survival and sensitivity to ototoxic drug of auditory hair cells. Furthermore, PCGF4 controls memory CD4 T-cell survival through direct repression of Noxa gene in an Ink4a- and Arf-independent manner. It is required in neurons to suppress p53-induced apoptosis via regulating the antioxidant defensive response, and also involved in the tumorigenesis of various cancer types. PCGF4 contains a C3HC4-type RING-HC finger. 97 matched cddid_all.tbl CDD cd16737 cd16737 438395 RING-HC_PCGF5 RING finger found in polycomb group RING finger protein 5 (PCGF5) and similar proteins. PCGF5, also known as RING finger protein 159 (RNF159), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) and serves as the core component of a Polycomb repressive complex 1 (PRC1). Like other PCGF homologs, PCGF5 associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. PCGF5 contains a C3HC4-type RING-HC finger. 95 matched cddid_all.tbl CDD cd16738 cd16738 438396 RING-HC_PCGF6 RING finger found in polycomb group RING finger protein 6 (PCGF6) and similar proteins. PCGF6, also known as Mel18 and Bmi1-like RING finger (MBLR), or RING finger protein 134 (RNF134), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR). It serves as the core component of a noncanonical Polycomb repressive complex 1 (PRC1)-like L3MBTL2 complex, which is composed of some canonical components, such as RNF2, CBX3, CXB4, CXB6, CXB7, and CXB8, as well as some noncanonical components, such as L3MBTL2, E2F6, WDR5, HDAC1, and RYBP, and plays a critical role in epigenetic transcriptional silencing in higher eukaryotes. Like other PCGF homologs, PCGF6 possesses the transcriptional repression activity, and also associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. Moreover, PCGF6 can regulate the enzymatic activity of JARID1d/KDM5D, a trimethyl H3K4 demethylase, through direct interaction. Furthermore, PCGF6 is expressed predominantly in meiotic and post-meiotic male germ cells and may play important roles in mammalian male germ cell development. It also regulates mesodermal lineage differentiation in mammalian embryonic stem cells (ESCs) and functions in induced pluripotent stem (iPS) reprogramming. The activity of PCGF6 is found to be regulated by cell cycle dependent phosphorylation. PCGF6 contains a C3HC4-type RING-HC finger. 59 matched cddid_all.tbl CDD cd16739 cd16739 438397 RING-HC_RING1 RING finger, HC subclass, found in really interesting new gene 1 protein (RING1) and similar proteins. RING1, also known as polycomb complex protein RING1, RING finger protein 1 (RNF1), or RING finger protein 1A (RING1A), was identified as a transcriptional repressor that is associated with the Polycomb group (PcG) protein complex involved in stable repression of gene activity. It is a core component of polycomb repressive complex 1 (PRC1) that functions as an E3-ubuiquitin ligase that transferring the mono-ubuiquitin mark to the C-terminal tail of Histone H2A at K118/K119. PRC1 is also capable of chromatin compaction, a function not requiring histone tails, and this activity appears important in gene silencing. RING1 interacts with multiple PcG proteins and displays tumorigenic activity. It also shows zinc-dependent DNA binding activity. Moreover, RING1 inhibits transactivation of the DNA-binding protein recombination signal binding protein-Jkappa (RBP-J) by Notch through interaction with the LIM domains of KyoT2. RING1 contains a C3HC4-type RING-HC finger. 70 matched cddid_all.tbl CDD cd16740 cd16740 438398 RING-HC_RING2 RING finger, HC subclass, found in really interesting new gene 2 protein (RING2) and similar proteins. RING2, also known as huntingtin-interacting protein 2-interacting protein 3, HIP2-interacting protein 3, protein DinG, RING finger protein 1B (RING1B), RING finger protein 2 (RNF2), or RING finger protein BAP-1, is an E3 ubiquitin-protein ligase that interacts with both nucleosomal DNA and an acidic patch on histone H4 to achieve the specific monoubiquitination of K119 on histone H2A (H2AK119ub), thereby playing a central role in histone code and gene regulation. RING2 is a core component of polycomb repressive complex 1 (PRC1) that functions as an E3-ubuiquitin ligase transferring the mono-ubuiquitin mark to the C-terminal tail of Histone H2A at K118/K119. PRC1 is also capable of chromatin compaction, a function not requiring histone tails, and this activity appears important in gene silencing. The enzymatic activity of RING2 is enhanced by the interaction with BMI1/PCGF4, and it is dispensable for early embryonic development and much of the gene repression activity of PRC1. Moreover, RING2 plays a key role in terminating neural precursor cell (NPC)-mediated production of subcerebral projection neurons (SCPNs) during neocortical development. It also plays a critical role in nonhomologous end-joining (NHEJ)-mediated end-to-end chromosome fusions. Furthermore, RING2 is essential for expansion of hepatic stem/progenitor cells. It promotes hepatic stem/progenitor cell expansion through simultaneous suppression of cyclin-dependent kinase inhibitors (CDKIs) Cdkn1a and Cdkn2a, known negative regulators of cell proliferation. RING2 also negatively regulates p53 expression through directly binding with both p53 and MDM2 and promoting MDM2-mediated p53 ubiquitination in selective cancer cell types to stimulate tumor development. RING2 contains a C3HC4-type RING-HC finger. 77 matched cddid_all.tbl CDD cd16741 cd16741 438399 RING-HC_RNFT1 RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 1 (RNFT1). RNFT1, also known as protein PTD016, is a multi-pass membrane protein containing a C3HC4-type RING-HC finger. Its biological role remains unclear. 58 matched cddid_all.tbl CDD cd16742 cd16742 438400 RING-HC_RNFT2 RING finger, HC subclass, found in RING finger and transmembrane domain-containing protein 2(RNFT2). RNFT2, also known as transmembrane protein 118 (TMEM118), is a multi-pass membrane protein containing a C3HC4-type RING-HC finger. Its biological role remains unclear. 67 matched cddid_all.tbl CDD cd16743 cd16743 438401 RING-HC_RNF5 RING finger, HC subclass, found in RING finger protein 5 (RNF5) and similar proteins. RNF5, also known as protein G16 or Ram1, is an E3 ubiquitin-protein ligase anchored to the outer membrane of the endoplasmic reticulum (ER). It acts at early stages of cystic fibrosis (CF) transmembrane conductance regulator (CFTR) biosynthesis and functions as a target for therapeutic modalities to antagonize mutant CFTR proteins in CF patients carrying the F508del allele. It also regulates the turnover of specific G protein-coupled receptors by ubiquitinating JNK-associated membrane protein (JAMP) and preventing proteasome recruitment. RNF5 limits basal levels of autophagy and influences susceptibility to bacterial infection through the regulation of ATG4B stability. It is also involved in the degradation of Pendrin, a transmembrane chloride/anion exchanger highly expressed in thyroid, kidney, and inner ear. RNF5 plays an important role in cell adhesion and migration. It can modulate cell migration by ubiquitinating paxillin. Furthermore, RNF5 interacts with virus-induced signaling adaptor (VISA) at mitochondria in a viral infection-dependent manner, and further targets VISA at K362 and K461 for K48-linked ubiquitination and degradation after viral infection. It also negatively regulates virus-triggered signaling by targeting MITA, also known as STING, for ubiquitination and degradation at the mitochondria. In addition, RNF5 determines breast cancer response to ER stress-inducing chemotherapies through the regulation of the L-glutamine carrier proteins SLC1A5 and SLC38A2 (SLC1A5/38A2). It also has been implicated in muscle organization and in recognition and processing of misfolded proteins. RNF5 contains a C3HC4-type RING-HC finger. 54 matched cddid_all.tbl CDD cd16744 cd16744 438402 RING-HC_RNF185 RING finger, HC subclass, found in RING finger protein 185 (RNF185) and similar proteins. RNF185 is an E3 ubiquitin-protein ligase of endoplasmic reticulum-associated degradation (ERAD) that targets cystic fibrosis transmembrane conductance regulator (CFTR). It controls the degradation of CFTR and CFTR F508del allele in a RING- and proteasome-dependent manner, but does not control that of other classical ERAD model substrates. It also negatively regulates osteogenic differentiation by targeting dishevelled2 (Dvl2), a key mediator of the Wnt signaling pathway, for degradation. Moreover, RNF185 regulates selective mitochondrial autophagy through interaction with the Bcl-2 family protein BNIP1. It also plays an important role in cell adhesion and migration through the modulation of cell migration by ubiquitinating paxillin. RNF185 contains a C3HC4-type RING-HC finger. 57 matched cddid_all.tbl CDD cd16745 cd16745 438403 RING-HC_AtRMA-like RING finger, HC subclass, found in Arabidopsis thaliana RING membrane-anchor proteins (AtRMAs) and similar proteins. AtRMAs, including AtRma1, AtRma2, and AtRma3, are endoplasmic reticulum (ER)-localized Arabidopsis homologs of human outer membrane of the ER-anchor E3 ubiquitin-protein ligase, RING finger protein 5 (RNF5). AtRMAs possess E3 ubiquitin ligase activity, and may play a role in the growth and development of Arabidopsis. The AtRMA1 and AtRMA3 genes are predominantly expressed in major tissues, such as cotyledons, leaves, shoot-root junction, roots, and anthers, while AtRMA2 expression is restricted to the root tips and leaf hydathodes. AtRma1 probably functions with the Ubc4/5 subfamily of E2. AtRma2 is likely involved in the cellular regulation of ABP1 expression levels through interacting with auxin binding protein 1 (ABP1). AtRMA proteins contain an N-terminal C3HC4-type RING-HC finger and a trans-membrane-anchoring domain in their extreme C-terminal region. 45 matched cddid_all.tbl CDD cd16746 cd16746 438404 RING-HC_RNF212 RING finger, HC subclass, found in RING finger protein 212 (RNF212) and similar proteins. RNF212 is a dosage-sensitive regulator of crossing-over during mammalian meiosis. It plays a central role in designating crossover sites and coupling chromosome synapsis to the formation of crossover-specific recombination complexes. It also functions as an E3 ligase for SUMO modification. RNF212 contains an N-terminal C3HC4-type RING-HC finger. 48 matched cddid_all.tbl CDD cd16747 cd16747 438405 RING-HC_RNF212B RING finger, HC subclass, found in RING finger protein 212B (RNF212B) and similar proteins. RNF212B is an uncharacterized protein with high sequence similarity with RNF212, a dosage-sensitive regulator of crossing-over during mammalian meiosis. RNF212B contains an N-terminal C3HC4-type RING-HC finger. 37 matched cddid_all.tbl CDD cd16748 cd16748 438406 RING-HC_SH3RF1 RING finger, HC subclass, found in SH3 domain-containing RING finger protein 1 (SH3RF1) and similar proteins. SH3RF1, also known as plenty of SH3s (POSH), RING finger protein 142 (RNF142), or SH3 multiple domains protein 2 (SH3MD2), is a trans-Golgi network-associated pro-apoptotic scaffold protein with E3 ubiquitin-protein ligase activity. It also plays a role in calcium homeostasis through the control of the ubiquitin domain protein Herp. It may also have a role in regulating death receptor mediated and c-Jun N-terminal kinase (JNK) mediated apoptosis, linking Rac1 to downstream components. SH3RF1 also enhances the ubiquitination of ROMK1 potassium channel resulting in its increased endocytosis. Moreover, SH3RF1 assembles an inhibitory complex with the actomyosin regulatory protein Shroom3, which links to the actin-myosin network to regulate neuronal process outgrowth. It also forms a complex with apoptosis-linked gene-2 (ALG-2) and ALG-2-interacting protein (ALIX/AIP1) in a calcium-dependent manner to play a role in the regulation of the JNK pathway. Furthermore, direct interaction of SH3RF1 and another molecular scaffold JNK-interacting protein (JIP) is required for apoptotic activation of JNKs. Interaction of SH3RF1 and E3 ubiquitin-protein isopeptide ligases, Siah proteins, further promotes JNK activation and apoptosis. In addition, SH3RF1 binds to and degrades TAK1, a crucial activator of both the JNK and the Relish signaling pathways. SH3RF1 contains an N-terminal C3HC4-type RING-HC finger responsible for the E3 ligase activity and four Src Homology 3 (SH3) domains, which are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. 48 matched cddid_all.tbl CDD cd16749 cd16749 438407 RING-HC_SH3RF2 RING finger, HC subclass, found in SH3 domain-containing RING finger protein 2 (SH3RF2) and similar proteins. SH3RF2, also known as heart protein phosphatase 1-binding protein (HEPP1), plenty of SH3s (POSH)-eliminating RING protein (POSHER), protein phosphatase 1 regulatory subunit 39, or RING finger protein 158 (RNF158), is a putative E3 ubiquitin-protein ligase that acts as an anti-apoptotic regulator for the c-Jun N-terminal kinase (JNK) pathway by binding to and promoting the proteasomal degradation of SH3RF1 (or POSH), a scaffold protein that is required for pro-apoptotic JNK activation. It may also play a role in cardiac functions together with protein phosphatase 1. SH3RF2 contains an N-terminal C3HC4-type RING-HC finger responsible for the E3 ligase activity and four Src Homology 3 (SH3) domains, which are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. 46 matched cddid_all.tbl CDD cd16750 cd16750 438408 RING-HC_SH3RF3 RING finger, HC subclass, found in SH3 domain-containing RING finger protein 3 (SH3RF3) and similar proteins. SH3RF3, also known as plenty of SH3s 2 (POSH2) or SH3 multiple domains protein 4 (SH3MD4), is a scaffold protein with E3 ubiquitin-protein ligase activity. It was identified in a screen for interacting partners of p21-activated kinase 2 (PAK2). It may play a role in regulating c-Jun N-terminal kinase (JNK) mediated apoptosis in certain conditions. It also interacts with GTP-loaded Rac1. SH3RF3 is highly homologous to SH3RF1. Both contain an N-terminal C3HC4-type RING-HC finger responsible for the E3 ligase activity and four Src Homology 3 (SH3) domains, which are protein interaction domains that bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. 46 matched cddid_all.tbl CDD cd16751 cd16751 438409 RING-HC_SIAH1 RING finger, HC subclass, found in seven in absentia homolog 1 (SIAH1) and similar proteins. SIAH1, also known as Siah-1a, is an inducible E3 ubiquitin-protein ligase that contributes to proteasome-mediated degradation of multiple targets in numerous cellular processes including apoptosis, tumor suppression, cell cycle, axon guidance, transcription regulation, and tumor necrosis factor signaling. SIAH1 functions as a scaffolding protein and interacts with a variety of different substrates for ubiquitination and subsequent degradation. It regulates the oncoprotein p34SEI-1 polyubiquitination and its subsequent degradation in a p53-dependent manner, which mediates p53 preferential vitamin C cytotoxicity. It targets the nonreceptor tyrosine kinase activated Cdc42-associated kinase 1 (ACK1), a valid target in cancer therapy, for ubiquitinylation and proteasomal degradation. It also interacts with KLF10 and targets it for degradation. The CDK2 phosphorylation-mediated KLF10 dissociation from SIAH1 is linked to cell cycle progression. Moreover, SIAH1 is downregulated and associated with apoptosis and invasion in human breast cancer. It targets TAp73, a homolog of the tumor suppressor p53, for degradation. It is suppressed by hypoxia-inducible factor 1-alpha (HIF-1alpha) under hypoxic conditions to regulate TAp73 levels. It also promotes the migration and invasion of human glioma cells by regulating HIF-1alpha signaling under hypoxia. Furthermore, SIAH1 forms a protein complex with glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The apoptosis signal-regulating kinase 1 (ASK1) functions as an activator of the GAPDH-Siah1 stress-signaling cascade. It also plays an important role in ethanol-induced apoptosis in neural crest cells (NCCs). SIAH1 contains an N-terminal C3HC4-type RING-HC finger, two zinc-finger subdomains, and a C-terminal tumor necrosis factor (TNF) receptor associated factor (TRAF)-like substrate-binding domain (SBD) responsible for dimer formation. 45 matched cddid_all.tbl CDD cd16752 cd16752 438410 RING-HC_SIAH2 RING finger, HC subclass, found in seven in absentia homolog 2 (SIAH2) and similar proteins. SIAH2 is an E3 ubiquitin-protein ligase that contributes to proteasome-mediated degradation of multiple targets in numerous cellular processes. It targets the ubiquitylation and degradation of tumor necrosis factor receptor-associated factor 2 (TRAF2) under stress conditions, which is required for the cell to commit to undergoing apoptosis. It is, therefore, a key regulator of TRAF2-dependent signaling in response to tumor necrosis factor-alpha (TNF-alpha) treatment and UV irradiation. SIAH2 modulates the polyubiquitination of G protein pathway suppressor 2 (GPS2), and targets it for proteasomal degradation. It is also a regulator of NF-E2-related factor 2 (Nrf2), a key regulator of cellular oxidative response, and contributes to the degradation of Nrf2 irrespective of its phosphorylation status. Moreover, SIAH2 contributes to castration-resistant prostate cancer (CRPC) by regulation of androgen receptor (AR) transcriptional activity. It enhances AR transcriptional activity and prostate cancer cell growth. Its stability can be regulated by AKR1C3. SIAH2 also inhibits tyrosine kinase-2 (TYK2)-STAT3 signaling in lung carcinoma cells. Furthermore, SIAH2 regulates obesity-induced adipose tissue inflammation by altering peroxisome proliferator-activated receptor gamma (PPAR gamma) protein levels and selectively regulating PPAR gamma activity. It also functions as a regulator of the nuclear hormone receptor RevErbalpha (Nr1d1) stability and rhythmicity, and overall circadian oscillator function. In addition, SIAH2 is an essential component of the hypoxia response Hippo signaling pathway and has been implicated in normal development and tumorigenesis. It modulates the hypoxia pathway upstream of hypoxia-induced transcription factor subunit HIF-1alpha, and therefore may play an important role in angiogenesis in response to hypoxic stress in endothelial cells. It also stimulates transcriptional coactivator YAP1 by destabilizing serine/threonine-protein kinase LATS2, a critical component of the Hippo pathway, in response to hypoxia. Meanwhile, SIAH2 is involved in regulation of tight junction integrity and cell polarity under hypoxia, through its regulation of apoptosis-stimulating proteins of p53 subunit 2 (ASPP2) stability. SIAH2 contains an N-terminal C3HC4-type RING-HC finger, two zinc-finger subdomains, and a C-terminal tumor necrosis factor (TNF) receptor associated factor (TRAF)-like substrate-binding domain (SBD) responsible for dimer formation. 51 matched cddid_all.tbl CDD cd16753 cd16753 438411 RING-HC_MID1 RING finger, HC subclass, found in midline-1 (MID1) and similar proteins. MID1, also known as midin, midline 1 RING finger protein, putative transcription factor XPRF, RING finger protein 59 (RNF59), or tripartite motif-containing protein 18 (TRIM18), is a microtubule-associated E3 ubiquitin-protein ligase implicated in epithelial-mesenchymal differentiation, cell migration and adhesion, and programmed cell death along specific regions of the ventral midline during embryogenesis. It monoubiquinates the alpha4 subunit of protein phosphatase 2A (PP2A), promoting proteosomal degradation of the catalytic subunit of PP2A (PP2Ac) and preventing the A and B subunits from forming an active complex. It promotes allergen and rhinovirus-induced asthma through the inhibition of PP2A activity. It is strongly upregulated in cytotoxic lymphocytes (CTLs) and directs lytic granule exocytosis and cytotoxicity of killer T cells. Loss-of-function mutations in MID1 lead to the human X-linked Opitz G/BBB (XLOS) syndrome characterized by defective midline development during embryogenesis. MID1 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. MID1 hetero-dimerizes in vitro with its paralog MID2. 72 matched cddid_all.tbl CDD cd16754 cd16754 438412 RING-HC_MID2 RING finger, HC subclass, found in midline-2 (MID2) and similar proteins. MID2, also known as midin-2, midline defect 2, RING finger protein 60 (RNF60), or tripartite motif-containing protein 1 (TRIM1), is a probable E3 ubiquitin-protein ligase and is highly related to MID1 that associates with cytoplasmic microtubules along their length and throughout the cell cycle. Like MID1, MID2 associates with the microtubule network and may at least partially compensate for the loss of MID1. Both MID1 and MID2 interacts with Alpha 4, which is a regulatory subunit of PP2-type phosphatases, such as PP2A, and an integral component of the rapamycin-sensitive signaling pathway. MID2 can also substitute for MID1 to control exocytosis of lytic granules in cytotoxic T cells. Loss-of-function mutations in MID2 lead to the human X-linked intellectual disability (XLID). MID2 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxy-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. MID2 hetero-dimerizes in vitro with its paralog MID1. 70 matched cddid_all.tbl CDD cd16755 cd16755 438413 RING-HC_TRIM9 RING finger, HC subclass, found in tripartite motif-containing protein 9 (TRIM9) and similar proteins. TRIM9, human ortholog of rat Spring, also known as RING finger protein 91 (RNF91), is a brain-specific E3 ubiquitin-protein ligase collaborating with an E2 ubiquitin conjugating enzyme UBCH5b. TRIM9 plays an important role in the regulation of neuronal functions and participates in the neurodegenerative disorders through its ligase activity. It interacts with the WD repeat region of beta-transducin repeat-containing protein (beta-TrCP) through its N-terminal degron motif depending on the phosphorylation status, and thus negatively regulates nuclear factor-kappaB (NF-kappaB) activation in the NF-kappaB pro-inflammatory signaling pathway. Moreover, TRIM9 acts as a critical catalytic link between Netrin-1 and the exocytic soluble NSF attachment receptor protein (SNARE) machinery in murine cortical neurons. It promotes SNARE-mediated vesicle fusion and axon branching in a Netrin-dependent manner. TRIM9 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. 55 matched cddid_all.tbl CDD cd16756 cd16756 438414 RING-HC_TRIM36_C-I RING finger, HC subclass, found in tripartite motif-containing protein 36 (TRIM36) and similar proteins. TRIM36, the human ortholog of mouse Haprin, also known as RING finger protein 98 (RNF98) or zinc-binding protein Rbcc728, is an E3 ubiquitin-protein ligase expressed in the germ plasm. It has been implicated in acrosome reaction, fertilization, and embryogenesis, as well as in carcinogenesis. TRIM36 functions upstream of Wnt/beta-catenin activation, and plays a role in controlling the stability of proteins regulating microtubule polymerization during cortical rotation, and subsequently dorsal axis formation. It is also potentially associated with chromosome segregation by interacting with the kinetochore protein centromere protein-H (CENP-H), and colocalizing with the microtubule protein alpha-tubulin. Its overexpression may cause chromosomal instability and carcinogenesis. It is, thus, a novel regulator affecting cell cycle progression. Moreover, TRIM36 plays a critical role in the arrangement of somites during embryogenesis. TRIM36 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, a PRY domain and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. 49 matched cddid_all.tbl CDD cd16757 cd16757 438415 RING-HC_TRIM46_C-I RING finger, HC subclass, found in tripartite motif-containing protein 46 (TRIM46) and similar proteins. TRIM46, also known as gene Y protein (GeneY) or tripartite, fibronectin type-III and C-terminal SPRY motif protein (TRIFIC), is a microtubule-associated protein that specifically localizes to the proximal axon, partly overlaps with the axon initial segment (AIS) at later stages, and organizes uniform microtubule orientation in axons. It controls neuronal polarity and axon specification by driving the formation of parallel microtubule arrays. TRIM46 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins, which are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, a PRY domain and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. 43 matched cddid_all.tbl CDD cd16758 cd16758 438416 RING-HC_TRIM67 RING finger, HC subclass, found in tripartite motif-containing protein 67 (TRIM67) and similar proteins. TRIM67, also known as TRIM9-like protein (TNL), is selectively expressed in the cerebellum. It interacts with PRG-1, an important molecule in the control of hippocampal excitability dependent on presynaptic LPA2 receptor signaling, and 80K-H (also known as glucosidase II beta), a protein kinase C substrate. It negatively regulates Ras signaling in cell proliferation via degradation of 80K-H, leading to neural differentiation including neuritogenesis. TRIM67 belongs to the C-I subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. 57 matched cddid_all.tbl CDD cd16759 cd16759 319673 RING-HC_MuRF1 RING finger, HC subclass, found in muscle-specific RING finger protein 1 (MuRF-1) and similar proteins. MuRF-1, also known as tripartite motif-containing protein 63 (TRIM63), RING finger protein 28 (RNF28), iris RING finger protein, or striated muscle RING zinc finger, is an E3 ubiquitin-protein ligase in ubiquitin-mediated muscle protein turnover. It is predominantly fast (type II) fibre-associated in skeletal muscle and can bind to many myofibrillar proteins, including titin, nebulin, the nebulin-related protein NRAP, troponin-I (TnI), troponin-T (TnT), myosin light chain 2 (MLC-2), myotilin, and T-cap. The early and robust upregulation of MuRF-1 is triggered by disuse, denervation, starvation, sepsis, or steroid administration resulting in skeletal muscle atrophy. It also plays a role in maintaining titin M-line integrity. It associates with the periphery of the M-line lattice and may be involved in the regulation of the titin kinase domain. It also participates in muscle stress response pathways and gene expression. MuRF-1 belongs to the C-II subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, and an acidic residue-rich (AR) domain. It also harbors a MURF family-specific conserved box (MFC) between its RING-HC finger and Bbox domains. 63 matched cddid_all.tbl CDD cd16760 cd16760 438417 RING-HC_MuRF2 RING finger, HC subclass, found in muscle-specific RING finger protein 2 (MuRF-2) and similar proteins. MuRF-2, also known as tripartite motif-containing protein 55 (TRIM55) or RING finger protein 29 (RNF29), is a muscle-specific E3 ubiquitin-protein ligase in ubiquitin-mediated muscle protein turnover and is also a ligand of the transactivation domain of the serum response transcription factor (SRF). It is predominantly slow-fibre associated and highly expressed in embryonic skeletal muscle. MuRF-2 associates transiently with microtubules, myosin, and titin during sarcomere assembly. It has been implicated in microtubule, intermediate filament, and sarcomeric M-line maintenance in striated muscle development, as well as in signaling from the sarcomere to the nucleus. It plays an important role in the earliest stages of skeletal muscle differentiation and myofibrillogenesis. It is developmentally downregulated and is assembled at the M-line region of the sarcomere and with microtubules. MuRF-2 belongs to the C-II subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, and an acidic residue-rich (AR) domain. It also harbors a MURF family-specific conserved box (MFC) between its RING-HC finger and Bbox domains. 64 matched cddid_all.tbl CDD cd16761 cd16761 319675 RING-HC_MuRF3 RING finger, HC subclass, found in muscle-specific RING finger protein 3 (MuRF-3) and similar proteins. MuRF-3, also known as tripartite motif-containing protein 54 (TRIM54), or RING finger protein 30 (RNF30), is an E3 ubiquitin-protein ligase in ubiquitin-mediated muscle protein turnover. It is ubiquitously detected in all fibre types, is developmentally upregulated, associates with microtubules, the sarcomeric M-line and Z-line, and is required for microtubule stability and myogenesis. It associates with glutamylated microtubules during skeletal muscle development, and is required for skeletal myoblast differentiation and development of cellular microtubular networks. MuRF-3 controls the degradation of four-and-a-half LIM domain (FHL2) and gamma-filamin and is required for maintenance of ventricular integrity after myocardial infarction (MI). MuRF-3 belongs to the C-II subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, and an acidic residue-rich (AR) domain. It also harbors a MURF family-specific conserved box (MFC) between its RING-HC finger and Bbox domains. 59 matched cddid_all.tbl CDD cd16762 cd16762 438418 RING-HC_TRIM13_C-V RING finger, HC subclass, found in tripartite motif-containing protein 13 (TRIM13) and similar proteins. TRIM13, also known as B-cell chronic lymphocytic leukemia tumor suppressor Leu5, leukemia-associated protein 5, putative tumor suppressor RFP2, RING finger protein 77 (RNF77), or Ret finger protein 2, is an endoplasmic reticulum (ER) membrane anchored E3 ubiquitin-protein ligase that interacts with proteins localized to the ER, including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). It also targets the known ER proteolytic substrate CD3-delta, but not the N-end rule substrate Ub-R-YFP (yellow fluorescent protein) for degradation. Moreover, TRIM13 regulates ubiquitination and degradation of NEMO to suppress tumor necrosis factor (TNF) induced nuclear factor-kappaB (NF- kappa B) activation. It is also involved in NF-kappaB p65 activation and nuclear factor of activated T-cells (NFAT)-dependent activation of c-Rel upon T-cell receptor engagement. Furthermore, TRIM13 negatively regulates melanoma differentiation-associated gene 5 (MDA5)-mediated type I interferon production. It also regulates caspase-8 ubiquitination, translocation to autophagosomes, and activation during ER stress induced cell death. Meanwhile, TRIM13 enhances ionizing radiation-induced apoptosis by increasing p53 stability and decreasing AKT kinase activity through MDM2 and AKT degradation. TRIM13 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region. In addition, TRIM13 contains a C-terminal transmembrane domain. 56 matched cddid_all.tbl CDD cd16763 cd16763 438419 RING-HC_TRIM59_C-V RING finger, HC subclass, found in tripartite motif-containing protein 59 (TRIM59) and similar proteins. TRIM59, also known as RING finger protein 104 (RNF104) or tumor suppressor TSBF-1, is a putative E3 ubiquitin-protein ligase that functions as a novel multiple cancer biomarker for immunohistochemical detection of early tumorigenesis. It is upregulated in gastric cancer and promotes gastric carcinogenesis by interacting with and targeting the P53 tumor suppressor for its ubiquitination and degradation. It also acts as a novel accessory molecule involved in cytotoxicity of BCG-activated macrophages (BAM). Moreover, TRIM59 may serve as a multifunctional regulator for innate immune signaling pathways. It interacts with ECSIT and negatively regulates nuclear factor-kappaB (NF- kappa B) and interferon regulatory factor (IRF)-3/7-mediated signal pathways. TRIM59 belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domain, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region. In addition, TRIM59 contains a C-terminal transmembrane domain. 56 matched cddid_all.tbl CDD cd16764 cd16764 438420 RING-HC_TIF1alpha RING finger, HC subclass, found in transcription inknown asiary factor 1-alpha (TIF1-alpha). TIF1-alpha, also known as tripartite motif-containing protein 24 (TRIM24), E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. It interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoid X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta), and MOD2 (HP1gamma), as well as the vertebrate Kruppel-type (C2H2) zinc finger proteins that contain the transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of RAR that interacts with multiple nuclear receptors in vitro via an LXXLL motif and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53, and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal PHD-Bromo region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development. 71 matched cddid_all.tbl CDD cd16765 cd16765 438421 RING-HC_TIF1beta RING finger, HC subclass, found in transcription inknown asiary factor 1-beta (TIF1-beta). TIF1-beta, also known as Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), KRAB-interacting protein 1 (KRIP-1), nuclear co-repressor KAP-1, RING finger protein 96, tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, belongs to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. It acts as a nuclear co-repressor that plays a role in transcription and in the DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during the DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. Moreover, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. The N-terminal RBCC domain of TIF1-beta is responsible for the interaction with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and the regulation of homo- and heterodimerization. The C-terminal PHD/Bromo domains are involved in interacting with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity. 63 matched cddid_all.tbl CDD cd16766 cd16766 438422 RING-HC_TIF1gamma RING finger, HC subclass, found in transcriptional inknown asiary factor 1 gamma (TIF1gamma). TIF1gamma, also known as tripartite motif-containing 33 (TRIM33), ectodermin, RFG7, or PTC7, belongs to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. It is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling, inhibiting the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1gamma is an important regulator of transcription during hematopoiesis, as well as a key actor of tumorigenesis. Like other TIF1 proteins, TIF1gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis. 67 matched cddid_all.tbl CDD cd16767 cd16767 438423 RING-HC_TRIM2 RING finger, HC subclass, found in tripartite motif-containing protein 2 (TRIM2). TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM2 also plays a role in mediating the p42/p44 MAPK-dependent ubiquitination of the cell death-promoting protein Bcl-2-interacting mediator of cell death (Bim) in rapid ischemic tolerance. TRIM2 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. 51 matched cddid_all.tbl CDD cd16768 cd16768 438424 RING-HC_TRIM3 RING finger, HC subclass, found in tripartite motif-containing protein 3 (TRIM3). TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It functions as a tumor suppressor that regulates asymmetric cell division in glioblastoma. It binds to the cdk inhibitor p21(WAF1/CIP1) and regulates its availability that promotes cyclin D1-cdk4 nuclear accumulation. Moreover, TRIM3 plays an important role in the central nervous system (CNS). It is encoded by the gene BERP (brain-expressed RING finger protein), a unique p53-regulated gene that modulates seizure susceptibility and GABAAR cell surface expression. Furthermore, TRIM3 mediates activity-dependent turnover of postsynaptic density (PSD) scaffold proteins GKAP/SAPAP1 and is a negative regulator of dendritic spine morphology. In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. It also regulates the motility of the kinesin superfamily protein KIF21B. TRIM3 belongs to the C-VII subclass of the TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a C3HC4-type RING-HC finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. 48 matched cddid_all.tbl CDD cd16769 cd16769 438425 RING-HC_UHRF1 RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1). UHRF1, also known as inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1, is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 can acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumor suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also a N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET and RING finger associated (SRA) domain, and a C-terminal C3HC4-type RING-HC finger. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintenance DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD domain targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-HC finger exhibits both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1. 84 matched cddid_all.tbl CDD cd16770 cd16770 438426 RING-HC_UHRF2 RING finger, HC subclass, found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2). UHRF2, also known as Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2, was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation, but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET- and RING-associated (SRA) domain, and a C-terminal C3HC4-type RING-HC finger. 65 matched cddid_all.tbl CDD cd16771 cd16771 438427 RING-HC_UNK RING finger, HC subclass, found in RING finger protein unkempt (UNK) and similar proteins. UNK, also known as zinc finger CCCH domain-containing protein 5, is a metazoan-specific zinc finger protein enriched in embryonic brains. It may play a broad regulatory role during the formation of the central nervous system (CNS). It is a sequence-specific RNA-binding protein required for early neuronal morphology. UNK is a neurogenic component of the mTOR pathway, and functions as a negative regulator of the timing of photoreceptor differentiation. It also specifically binds to Brg/Brm-associated factor BAF60b and promotes its ubiquitination in a Rac1-dependent manner. UNK contains six tandem CCCH-type zinc fingers at the N-terminus, and a C3HC4-type RING-HC finger at its C-terminus. 42 matched cddid_all.tbl CDD cd16772 cd16772 438428 RING-HC_UNKL RING finger, HC subclass, found in RING finger protein unkempt-like (UNKL) and similar proteins. UNKL, also known as zinc finger CCCH domain-containing protein 5-like, is a putative E3 ubiquitin-protein ligase that may participate in a protein complex showing an E3 ligase activity regulated by RAC1. It shows high sequence similarity with RING finger protein unkempt (UNK), which is a metazoan-specific zinc finger protein enriched in embryonic brains, and may play a broad regulatory role during the formation of the central nervous system (CNS). UNKL contains several CCCH-type zinc fingers at the N-terminus, and a C3HC4-type RING-HC finger at its C-terminus. 44 matched cddid_all.tbl CDD cd16773 cd16773 438429 RING-HC_RBR_TRIAD1 RING finger, HC subclass, found in two RING fingers and DRIL [double RING finger linked] 1 (TRIAD1). TRIAD1, also known as ariadne-2 (ARI-2), protein ariadne-2 homolog, Ariadne RBR E3 ubiquitin protein ligase 2 (ARIH2), or UbcM4-interacting protein 48, is an RBR-type E3 ubiquitin-protein ligase that catalyzes the formation of polyubiquitin chains linked via lysine-48, as well as lysine-63 residues. Its auto-ubiquitylation can be catalyzed by the E2 conjugating enzyme UBCH7. TRIAD1 has been implicated in hematopoiesis, specifically in myelopoiesis, as well as in embryogenesis. It functions as a regulator of endosomal transport and is required for the proper function of multivesicular bodies. It also acts as a novel ubiquitination target for proteasome-dependent degradation by murine double minute 2 (MDM2). As a proapoptotic protein, TRIAD1 promotes p53 activation, and inhibits MDM2-mediated p53 ubiquitination and degradation. Furthermore, TRIAD1 can inhibit the ubiquitination and proteasomal degradation of growth factor independence 1 (Gfi1), a transcriptional repressor essential for the function and development of many different hematopoietic lineages. TRIAD1 contains an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C3HC4-type RING-HC finger required for RBR-mediated ubiquitination. 54 matched cddid_all.tbl CDD cd16774 cd16774 438430 RING-HC_RBR_ANKIB1 RING finger, HC subclass, found in ankyrin repeat and IBR domain-containing protein 1 (ANKIB1) and similar proteins. ANKIB1 is an RBR-type E3 ubiquitin-protein ligase that may function as part of an E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates. It contains an N-terminal ankyrin repeat domain and an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C3HC4-type RING-HC finger required for RBR-mediated ubiquitination. 58 matched cddid_all.tbl CDD cd16775 cd16775 438431 RING-HC_RBR_RNF19A RING finger, HC subclass, found in RING finger protein 19A (RNF19A) and similar proteins. RNF19A, also known as double ring-finger protein (Dorfin) or p38, is a transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligase that localizes to the ubiquitylated inclusions in Parkinson's disease (PD), dementia with Lewy bodies, multiple system atrophy, and amyotrophic lateral sclerosis (ALS). It interacts with Psmc3, a protein component of the 19S regulatory cap of the 26S proteasome, and further participates in the ubiquitin-proteasome system in acrosome biogenesis, spermatid head shaping, and development of the head-tail coupling apparatus and tail. It modulates the ubiquitination and degradation of calcium-sensing receptor (CaR), which may contribute to a general mechanism for CaR quality control during biosynthesis. Moreover, RNF19A can also ubiquitylate mutant superoxide dismutase 1 (SOD1), the causative gene of familial ALS. It may associate with endoplasmic reticulum-associated degradation (ERAD) pathway, which is related to the pathogenesis of neurodegenerative disorders, such as PD or Alzheimer's disease. RNF19A contains an RBR domain followed by three TMs. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C3HC4-type RING-HC finger required for RBR-mediated ubiquitination. 56 matched cddid_all.tbl CDD cd16776 cd16776 438432 RING-HC_RBR_RNF19B RING finger, HC subclass, found in RING finger protein 19B (RNF19B) and similar proteins. RNF19B, also known as IBR domain-containing protein 3 or natural killer lytic-associated molecule (NKLAM), is a transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligase that plays a role in controlling tumor dissemination and metastasis. It is involved in the cytolytic function of natural killer (NK) cells and cytotoxic T lymphocytes (CTLs). It interacts with ubiquitin conjugates UbcH7 and UbcH8, and ubiquitinates uridine kinase like-1 (URKL-1) protein, targeting it for degradation. Moreover, RNF19B is a novel component of macrophage phagosomes and plays a role in macrophage anti-bacterial activity. It functions as a novel modulator of macrophage inducible nitric oxide synthase (iNOS) expression. RNF19B contains an RBR domain followed by three TMs. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C3HC4-type RING-HC finger required for RBR-mediated ubiquitination. 64 matched cddid_all.tbl CDD cd16777 cd16777 438433 mRING-HC-C4C4_RBR_RNF144A Modified RING finger, HC subclass (C4C4-type), found in RING finger protein 144A (RNF144A). RNF144A, also known as UbcM4-interacting protein 4 (UIP4) or ubiquitin-conjugating enzyme 7-interacting protein 4, is a transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligase that targets DNA-dependent protein kinase catalytic subunit (DNA-PKcs) and thus promotes DNA damage-induced cell apoptosis. It is transcriptionally repressed by metastasis-associated protein 1 (MTA1) and inhibits MTA1-driven cancer cell migration and invasion. RNF144A contains an RBR domain followed by a potential single-TM domain. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C4C4-type RING finger whose overall folding is similar to that of the C3HC4-type RING-HC finger. It is responsible for the interaction of E2-conjugating enzymes UbcH7 and UbcH8. 55 matched cddid_all.tbl CDD cd16778 cd16778 438434 mRING-HC-C4C4_RBR_RNF144B Modified RING finger, HC subclass (C4C4-type), found in RING finger protein 144B (RNF144B). RNF144B, also known as PIR2, IBR domain-containing protein 2 (IBRDC2), or p53-inducible RING finger protein (p53RFP), is a transmembrane (TM) domain-containing RBR (RING1-IBR-RING2) E3 ubiquitin-protein ligase that induces p53-dependent, but caspase-independent apoptosis. It interacts with E2 ubiquitin-conjugating enzymes UbcH7 and UbcH8, but not with UbcH5. It is involved in ubiquitination and degradation of p21, a p53 downstream protein promoting growth arrest and antagonizing apoptosis, suggesting a role in switching a cell from p53-mediated growth arrest to apoptosis. Moreover, RNF144B regulates the levels of Bax, a pro-apoptotic protein from the Bcl-2 family, and protects cells from unprompted Bax activation and cell death. It also regulates epithelial homeostasis by mediating degradation of p21WAF1 and p63. RNF144B contains an RBR domain followed by a potential single-TM domain. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the RING domain, a C4C4-type RING finger whose overall folding is similar to that of the C3HC4-type RING-HC finger. It is required for RBR-mediated ubiquitination. 57 matched cddid_all.tbl CDD cd16779 cd16779 438435 mRING-HC-C3HC3D_LNX1 Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 1 (LNX1). LNX1, also known as numb-binding protein 1 or PDZ domain-containing RING finger protein 2, is a PDZ domain-containing RING-type E3 ubiquitin ligase responsible for the ubiquitination and degradation of Numb, a component of the Notch signaling pathway that functions in the specification of cell fates during development and is known to control cell numbers during neurogenesis in vertebrates. LNX1 contains an N-terminal modified C3HC3D-type RING-HC finger, a NPAY motif for Numb-LNX interaction, and four PDZ domains necessary for the binding of substrates, including CAR, ErbB2, SKIP, JAM4, CAST, c-Src, Claudins, RhoC, KCNA4, PAK6, PLEKHG5, PKC-alpha1, TYK2, PDZ-binding kinase (PBK), LNX2, and itself. 42 matched cddid_all.tbl CDD cd16780 cd16780 319694 mRING-HC-C3HC3D_LNX2 Modified RING finger, HC subclass (C3HC3D-type), found in ligand of numb protein X 2 (LNX2). LNX2, also known as numb-binding protein 2, or PDZ domain-containing RING finger protein 1 (PDZRN1), is a PDZ domain-containing RING-type E3 ubiquitin ligase responsible for the ubiquitination and degradation of Numb, a component of the Notch signaling pathway that functions in the specification of cell fates during development and is known to control cell numbers during neurogenesis in vertebrates. It interacts with contactin-associated protein 4 (Caspr4, also known as CNTNAP4) in a PDZ domain-dependent manner, which modulates the proliferation and neuronal differentiation of neural progenitor cells (NPCs). LNX2 contains an N-terminal modified C3HC3D-type RING-HC finger, a NPAF motif for Numb/ Numblike-LNX interaction, and four PDZ domains necessary for the binding of substrates, including ErbB2, RhoC, the presynaptic protein CAST, the melanoma/cancer-testis antigen MAGEB18 and several proteins associated with cell junctions, such as JAM4 and the Coxsackievirus and adenovirus receptor (CAR). 45 matched cddid_all.tbl CDD cd16781 cd16781 438436 mRING-HC-C3HC3D_Roquin1 Modified RING finger, HC subclass (C3HC3D-type), found in Roquin-1. Roquin-1, also known as RING finger and C3H zinc finger protein 1 (RC3H1), or RING finger protein 198 (RNF198), is a ubiquitously expressed RNA-binding protein essential for degradation of inflammation-related mRNAs and maintenance of immune homeostasis. It is localized in cytoplasmic granules and binds to the 3' untranslated region (3'UTR) of inducible costimulator (Icos) mRNA to post-transcriptionally repress its expression. Roquin-1 interacts with the 3'UTR of tumor necrosis factor receptor superfamily member 4 (TNFRSF4) and tumor-necrosis factor-alpha (TNFalpha), and post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-kappaB pathway. Moreover, Roquin-1 shares functions with its paralog Roquin-2 in the repression of mRNAs controlling T follicular helper cells and systemic inflammation. Roquin-1 contains an N-terminal modified C3HC3D-type RING-HC finger with a potential E3 ubiquitin-ligase function, a highly conserved ROQ domain required for RNA binding and localization to stress granules, and a CCCH-type zinc finger that is involved in RNA recognition, typically contacting AU-rich elements. In addition, both N- and C-terminal to the ROQ domain are combined to form a HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain that is highly likely to function as an RNA-binding domain. 49 matched cddid_all.tbl CDD cd16782 cd16782 438437 mRING-HC-C3HC3D_Roquin2 Modified RING finger, HC subclass (C3HC3D-type), found in Roquin-2. Roquin-2, also known as membrane-associated nucleic acid-binding protein (MNAB), RING finger and CCCH-type zinc finger domain-containing protein 2 (RC3H2), or RING finger protein 164 (RNF164), is an E3 ubiquitin ligase that is localized to the cytoplasm and upon stress, is concentrated in stress granules. It is required for reactive oxygen species (ROS)-induced ubiquitination and degradation of apoptosis signal-regulating kinase 1 (ASK1, also known as MAP3K5). Roquin-2 interacts with the 3'UTR of tumor necrosis factor receptor superfamily member 4 (TNFRSF4) and tumor-necrosis factor-alpha (TNFalpha), and modulates immune responses. Moreover, Roquin-2 shares functions with its paralog Roquin-1 in the repression of mRNAs controlling T follicular helper cells and systemic inflammation. Roquin-2 contains an N-terminal modified C3HC3D-type RING-HC finger with a potential E3 ubiquitin-ligase function, a highly conserved ROQ domain required for RNA binding and localization to stress granules, a coiled-coil (CC1), and a CCCH-type zinc finger that is involved in RNA recognition. 49 matched cddid_all.tbl CDD cd16783 cd16783 438438 mRING-HC-C2H2C4_MDM2 Modified RING finger, HC subclass (C2H2C4-type), found in E3 ubiquitin-protein ligase MDM2 and similar proteins. MDM2, also known as double minute 2 protein (Hdm2), oncoprotein MDM2, or p53-binding protein, exerts its oncogenic activity predominantly by binding p53 tumor suppressor and blocking its transcriptional activity. It forms homo-oligomers and displays E3 ubiquitin ligase activity that catalyzes the attachment of ubiquitin to p53 as an essential step in the regulation of its levels in cells. Moreover, in response to ribosomal stress, MDM2-mediated p53 ubiquitination and degradation can be inhibited through its interaction with ribosomal proteins L5, L11, and L23. MDM2 can be phosphorylated in the DNA damage. Meanwhile, MDM2 has a p53-independent role in tumorigenesis and cell growth regulation. In addition, it binds interferon (IFN) regulatory factor-2 (IRF-2), an IFN-regulated transcription factor, and mediates its ubiquitination. MDM2 contains an N-terminal p53-binding domain, and a C-terminal modified C2H2C4-type RING-HC finger conferring E3 ligase activity that is required for ubiquitination and nuclear export of p53. It is also responsible for the hetero-oligomerization of MDM2, which is crucial for the suppression of P53 activity during embryonic development, and the recruitment of E2 ubiquitin-conjugating enzymes. MDM2 also harbors a RanBP2-type zinc finger (zf-RanBP2) domain, as well as a nuclear localization signal (NLS) and a nuclear export signal (NES), near the central acidic region. The zf-RanBP2 domain plays an important role in mediating MDM2 binding to ribosomal proteins and thus is involved in MDM2-mediated p53 suppression. 57 matched cddid_all.tbl CDD cd16784 cd16784 319698 mRING-HC-C2H2C4_MDM4 Modified RING finger, HC subclass (C2H2C4-type), found in protein MDM4 and similar proteins. MDM4, also known as double minute 4 protein (Hdm4), MDM2-like p53-binding protein, protein MDMX, HDMX, or p53-binding protein MDM4, exerts its oncogenic activity predominantly by binding p53 tumor suppressor and blocking its transcriptional activity. MDM4 is phosphorylated and destabilized in response to DNA damage stress. It can also be specifically dephosphorylated by directly interacting with protein phosphatase 1 (PP1), which may increase its stability and thus inhibit p53 activity. Meanwhile, MDM4 has a p53-independent role in tumorigenesis and cell growth regulation. MDM4 contains an N-terminal p53-binding domain and a C-terminal modified C2H2C4-type RING-HC finger responsible for its hetero-oligomerization, which is crucial for the suppression of P53 activity during embryonic development and the recruitment of E2 ubiquitin-conjugating enzymes. MDM4 also harbors a RanBP2-type zinc finger (zf-RanBP2) domain near the central acidic region. 59 matched cddid_all.tbl CDD cd16785 cd16785 438439 mRING-HC-C3HC5_NEU1A Modified RING finger, HC subclass (C3HC5-type), found in neuralized-like protein 1A (NEURL1A) and similar proteins. NEURL1A, also known as NEURL1, NEU, neuralized 1, or RING finger protein 67 (RNF67), is a mammalian homolog of the Drosophila neuralized (D-neu) protein. It functions as an E3 ubiquitin-protein ligase that directly interacts with and monoubiquitinates cytoplasmic polyadenylation element-binding protein 3 (CPEB3), an RNA binding protein and a translational regulator of local protein synthesis, which facilitates hippocampal plasticity and hippocampal-dependent memory storage. It also acts as a potential tumor suppressor that causes apoptosis and downregulates Notch target genes in the medulloblastoma. NEURL1A contains two neuralized homology regions (NHRs) responsible for Neural-ligand interactions and a modified C3HC5-type RING-HC finger required for ubiquitin ligase activity. The C3HC5-type RING-HC finger is distinguished from typical C3HC4-type RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain. 59 matched cddid_all.tbl CDD cd16786 cd16786 438440 mRING-HC-C3HC5_NEU1B Modified RING finger, HC subclass (C3HC5-type), found in neuralized-like protein 1B (NEURL1B). NEURL1B, also known as neuralized-2 (NEUR2) or neuralized-like protein 3, is a mammalian homolog of the Drosophila neuralized (D-neu) protein. It functions as an E3 ubiquitin-protein ligase that interacts with and ubiquitinates Delta. Thus, it plays a role in the endocytic pathways for Notch signaling through working cooperatively with another E3 ligase, Mind bomb-1 (Mib1), in Delta endocytosis to hepatocyte growth factor-regulated tyrosine kinase substrate (Hrs)-positive vesicles. NEURL1B contains two neuralized homology regions (NHRs) responsible for Neural-ligand interactions and a modified C3HC5-type RING-HC finger required for ubiquitin ligase activity. The C3HC5-type RING-HC finger is distinguished from typical C3HC4-type RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain. 57 matched cddid_all.tbl CDD cd16787 cd16787 438441 mRING-HC-C3HC5_CGRF1 Modified RING finger, HC subclass (C3HC5-type), found in cell growth regulator with RING finger domain protein 1 (CGRRF1) and similar proteins. CGRRF1, also known as cell growth regulatory gene 19 protein (CGR19) or RING finger protein 197 (RNF197), functions as a novel biomarker to monitor endometrial sensitivity and response to insulin-sensitizing drugs, such as metformin, in the context of obesity. CGRRF1 contains a C-terminal modified C3HC5-type RING-HC finger, which is distinguished from typical C3HC4 RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain. 38 matched cddid_all.tbl CDD cd16788 cd16788 438442 mRING-HC-C3HC5_RNF26 Modified RING finger, HC subclass (C3HC5-type), found in RING finger protein 26 (RNF26) and similar proteins. RNF26 is an E3 ubiquitin ligase that temporally regulates virus-triggered type I interferon induction by increasing the stability of Mediator of IRF3 activation, MITA, also known as STING, through K11-linked polyubiquitination of MITA after viral infection, and promoting the degradation of IRF3, another important component required for virus-triggered interferon induction. Although RNF26 substrates of ubiquitination remain unclear at present, RNF26 upregulation in gastric cancer might be implicated in carcinogenesis through dysregulation of growth regulators. RNF26 contains an N-terminal leucine zipper domain and a C-terminal modified C3HC5-type RING-HC finger, which is distinguished from typical C3HC4 RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain. 60 matched cddid_all.tbl CDD cd16789 cd16789 438443 mRING-HC-C3HC5_MGRN1-like Modified RING finger, HC subclass (C3HC5-type), found in mahogunin RING finger protein 1 (MGRN1), RING finger protein 157 (RNF157) and similar proteins. MGRN1, also known as RING finger protein 156 (RNF156), is a cytosolic E3 ubiquitin-protein ligase that inhibits signaling through the G protein-coupled melanocortin receptors-1 (MC1R), -2 (MC2R) and -4 (MC4R) via ubiquitylation-dependent and -independent processes. It suppresses chaperone-associated misfolded protein aggregation and toxicity. MGRN1 interacts with cytosolic prion proteins (PrPs) that are linked with neurodegeneration. It also interacts with expanded polyglutamine proteins, and suppresses misfolded polyglutamine aggregation and cytotoxicity. Moreover, MGRN1 inhibits melanocortin receptor signaling by competition with Galphas, suggesting a novel pathway for melanocortin signaling from the cell surface to the nucleus. MGRN1 also interacts with and ubiquitylates TSG101, a key component of the endosomal sorting complex required for transport (ESCRT)-I, and regulates endosomal trafficking. A null mutation in the gene encoding MGRN1 causes spongiform neurodegeneration, suggesting a link between dysregulation of endosomal trafficking and spongiform neurodegeneration. RNF157 is a cytoplasmic E3 ubiquitin ligase predominantly expressed in the brain. It is a homolog of the E3 ligase mahogunin ring finger-1 (MGRN1). In cultured neurons, it promotes neuronal survival in an E3 ligase-dependent manner. In contrast, it supports growth and maintenance of dendrites independent of its E3 ligase activity. RNF157 interacts with and ubiquitinates the adaptor protein APBB1 (amyloid beta precursor protein-binding, family B, member 1 or Fe65), which regulates neuronal survival, but not dendritic growth downstream of RNF157. The nuclear localization of APBB1 together with its interaction partner RNA-binding protein SART3 (squamous cell carcinoma antigen recognized by T cells 3 or Tip110) is crucial to trigger apoptosis. Both MGRN1 and RNF157 contain a modified C3HC5-type RING-HC finger, and a functionally uncharacterized region, known as domain associated with RING2 (DAR2), N-terminal to the RING finger. The C3HC5-type RING-HC finger is distinguished from typical C3HC4 RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain. 42 matched cddid_all.tbl CDD cd16790 cd16790 438444 SP-RING_PIAS SP-RING finger found in protein inhibitor of activated signal transducer and activator of transcription (PIAS) proteins. The PIAS (protein inhibitor of activated STAT) protein family modulates the activity of several transcription factors and acts as an E3 ubiquitin ligase in the sumoylation pathway. It consists of four members: PIAS1, PIAS2 (also known as PIASx), PIAS3, and PIAS4 (also known as PIASy). PIAS proteins were initially identified as inhibitors of activated STAT only, but are now known to interact with and modulate several other proteins, including androgen receptor (AR), tumor suppressor p53, and the transforming growth factor-beta (TGF-beta) signaling protein SMAD. They interact with STATs in a cytokine-dependent manner. PIAS1, PIAS2, and PIAS3 interact with STAT1, STAT3, and STAT4, respectively. In addition, PIAS4 is associated with STAT1. PIAS proteins have SUMO E3-ligase activity and interaction of PIAS proteins with transcription factors often results in sumoylation of that protein. PIAS proteins contain an N-terminal SAP (scaffold attachment factor A/B (SAF-A/B), acinus and PIAS) box with the LXXLL signature, which is required for the trans-repression of STAT1 activity by PIAS2, a PINT motif, which is essential for nuclear retention of PIAS3L (the long form of PIAS3), a specific RING finger known as Siz/PIAS (protein inhibitor of activated signal transducer and activator of transcription) RING (SP-RING) finger, which is essential for SUMO ligase activity, and the acidic C-terminal domain, which is involved in binding of PIAS3 to the nuclear coactivator TIF2. The SP-RING finger is a variant of RING finger, which lacks the second, fifth, and sixth zinc-binding residues of the consensus C3H2C3-/C3HC4-type RING fingers. It binds a single Zn ion, instead of two ions bound by typical RING fingers. 48 matched cddid_all.tbl CDD cd16791 cd16791 438445 SP-RING_ZMIZ SP-RING finger found in zinc finger MIZ domain-containing protein Zmiz1, Zmiz2, and similar proteins. This subfamily includes Zmiz1 (Zimp10) and its homolog Zmiz2 (Zimp7), both initially identified in humans as androgen receptor (AR) interacting proteins which function as transcriptional co-activators. They interact with BRG1, the catalytic subunit of the SWI-SNF remodeling complex. They also associate with other hormone nuclear receptors and transcription factors, such as p53 and Smad3/Smad4, and regulate transcription of specific target genes by altering their chromatin structure. This subfamily also includes tonalli (Tna), an ortholog identified in Drosophila. It genetically interacts with the ATP-dependent SWI/SNF and Mediator complexes, suggesting a potential role for the Zmiz proteins in chromatin remodeling. Zmiz proteins contain a highly conserved Siz/PIAS (protein inhibitor of activated signal transducer and activator of transcription) RING (SP-RING) finger, also known as msx-interacting zinc finger (Miz domain), and a strong transactivation domain within the C-terminus. The SP-RING/Miz domain is highly conserved in members of the PIAS family and confers SUMO-conjugating activity. It is a variant of the RING finger, and lacks the second, fifth, and sixth zinc-binding residues of the consensus C3H2C3-/C3HC4-type RING fingers. It binds a single Zn ion, instead of two ions bound by typical RING fingers. The strong intrinsic transactivation domain facilitates Zmiz proteins to augment the transcriptional activity of nuclear hormone receptors and other transcriptional factors. They may act as transcriptional co-regulators. 48 matched cddid_all.tbl CDD cd16792 cd16792 438446 SP-RING_Siz-like SP-RING finger found in Arabidopsis thaliana E3 SUMO-protein ligase SIZ1 (AtSIZ1) and similar proteins. SIZ1-mediated conjugation of SUMO1 and SUMO2 to other intracellular proteins is essential in Arabidopsis. AtSIZ1 negatively regulates abscisic acid (ABA) signaling through the sumoylation of bZIP transcripton factor ABI5. It also mediates sumoylation of bromodomain GTE proteins. Moreover, AtSIZ1 regulates flowering by controlling a salicylic acid-mediated floral promotion pathway and through affecting on FLOWERING LOCUS C (FLC) chromatin structure. It also plays a role in drought stress response likely through the regulation of gene expression. Members of this subfamily contain an N-terminal SAP (scaffold attachment factor A/B (SAF-A/B), acinus and PIAS) box, a plant homeodomain (PHD) finger, and a specific RING finger known as Siz/PIAS (protein inhibitor of activated signal transducer and activator of transcription) RING (SP-RING) finger. The SP-RING finger is a variant of RING finger, which lacks the second, fifth, and sixth zinc-binding residues of the consensus C3H2C3-/C3HC4-type RING fingers. It binds a single Zn ion, instead of two ions bound by typical RING fingers. 50 matched cddid_all.tbl CDD cd16793 cd16793 438447 SP-RING_ScSiz-like SP-RING finger found in Saccharomyces cerevisiae E3 SUMO-protein ligase SIZ1, SIZ2, and similar proteins. Saccharomyces cerevisiae SIZ proteins, also known as SAP and Miz-finger domain-containing proteins, are Siz/PIAS RING (SP-RING) family SUMO E3 ligases, and may be involved in a novel pathway of chromosome maintenance. They enhance SUMO modification with many substrates in vivo, but also exhibit unique substrate specificity. SIZ1, also known as ubiquitin-like protein ligase 1 (Ull1), modifies both cytoplasmic and nuclear proteins. It functions as an E3 factor specific for septin components. SIZ1-dependent substrates include Cdc3 and Cdc11 (septin subunits), Prp45 (a splicing factor), and the proliferating cell nuclear antigen (PCNA). SIZ2, also known as NFI1, interacts with Smt3, SUMO/Smt3 conjugating enzyme Ubc9, and a septin component Cdc3. Members of this subfamily contain an N-terminal SAP (scaffold attachment factor A/B (SAF-A/B), acinus and PIAS) box with the LXXLL signature, a PINT motif, a specific RING finger known as Siz/PIAS (protein inhibitor of activated signal transducer and activator of transcription) RING (SP-RING) finger, and an acidic C-terminal domain. The SP-RING finger is a variant of RING finger, which lacks the second, fifth, and sixth zinc-binding residues of the consensus C3H2C3-/C3HC4-type RING fingers. It binds a single Zn ion, instead of two ions bound by typical RING fingers. 56 matched cddid_all.tbl CDD cd16794 cd16794 438448 dRING_RMD5A Degenerated RING finger found in protein RMD5 homolog A (RMD5A). RMD5A is one of the vertebrate homologs of yeast Rmd5p. The biological function of RMD5A remains unclear. RMD5A contains a Lissencephaly type-1-like homology motif (LisH), a C-terminal to LisH motif (CTLH) domain, and a degenerated RING finger that is characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues compared with the classic C3H2C3-/C3HC4-type RING fingers. 60 matched cddid_all.tbl CDD cd16795 cd16795 438449 dRING_RMD5B Degenerated RING finger found in protein RMD5 homolog B (RMD5B). RMD5B is one of the vertebrate homologs of yeast Rmd5p. The biological function of RMD5B remains unclear. RMD5B contains a Lissencephaly type-1-like homology motif (LisH), a C-terminal to LisH motif (CTLH) domain, and a degenerated RING finger that is characterized by lacking the second, fifth, and sixth Zn2+ ion-coordinating residues compared with the classic C3H2C3-/C3HC4-type RING fingers. 59 matched cddid_all.tbl CDD cd16796 cd16796 438450 RING-H2_RNF13 RING finger, H2 subclass, found in RING finger protein 13 (RNF13) and similar proteins. RNF13 is a widely expressed membrane-associated E3 ubiquitin-protein ligase that is functionally significant in the regulation of cancer development, muscle cell growth, and neuronal development. Its expression is developmentally regulated during myogenesis and is upregulated in various tumors. RNF13 negatively regulates cell proliferation through its E3 ligase activity. It functions as an important regulator of inositol-requiring transmembrane kinase/endonuclease IRE1alpha, mediating endoplasmic reticulum (ER) stress-induced apoptosis through the activation of the IRE1alpha-TRAF2-JNK signaling pathway. Moreover, RNF13 is involved in the regulation of the soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor (SNARE) complex via the ubiquitination of snapin, a SNAP25-interacting protein, which thereby controls synaptic function. In addition, RNF13 participates in regulating the function of satellite cells by modulating cytokine composition. RNF13 is evolutionarily conserved among many metazoans and contains an N-terminal signal peptide, a protease-associated (PA) domain, a transmembrane (TM) domain and a C-terminal C3H2C3-type RING-H2 finger domain followed by a putative PEST sequence. 59 matched cddid_all.tbl CDD cd16797 cd16797 319711 RING-H2_RNF167 RING finger, H2 subclass, found in RING finger protein 167 (RNF167) and similar proteins. RNF167, also known as RING105, is an endosomal/lysosomal E3 ubiquitin-protein ligase involved in alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) ubiquitination. It ubiquitinates AMPA-type glutamate receptor subunit GluA2 and regulates its surface expression, and thus acts as a selective regulator of AMPAR-mediated neurotransmission. It acts as an endosomal membrane protein which ubiquitylates vesicle-associated membrane protein 3 (VAMP3) and regulates endosomal trafficking. Moreover, RNF167 plays a role in the regulation of TSSC5 (tumor-suppressing subchromosomal transferable fragment cDNA, also known as ORCTL2/IMPT1/BWR1A/SLC22A1L), which can function in concert with the ubiquitin-conjugating enzyme UbcH6. RNF167 is widely conserved in metazoans and contains an N-terminal signal peptide, a protease-associated (PA) domain, two transmembrane domains (TM1 and TM2), and a C-terminal C3H2C3-type RING-H2 finger domain followed by a putative PEST sequence. 46 matched cddid_all.tbl CDD cd16798 cd16798 438451 RING-H2_RNF43 RING finger, H2 subclass, found in RING finger protein 43 (RNF43) and similar proteins. RNF43 is a transmembrane E3 ubiquitin-protein ligase that plays an important role in frizzled (FZD)-dependent regulation of the Wnt/beta-catenin pathway. It functions as a tumor suppressor that inhibits Wnt/beta-catenin signaling by ubiquitinating FZD receptor and targeting it to the lysosomal pathway for degradation. miR-550a-5p directly targeted the 3'-UTR of gene RNF43 and regulated its expression. Moreover, RNF43 interacts with NEDD-4-like ubiquitin-protein ligase-1 (NEDL1) and regulates p53-mediated transcription. It may also be involved in cell growth control through the interaction with HAP95, a chromatin-associated protein interfacing the nuclear envelope. Mutations of RNF43 have been identified in various tumors, including colorectal cancer (CRC), endometrial cancer, mucinous ovarian tumors, gastric adenocarcinoma, pancreatic ductal adenocarcinoma, liver fluke-associated cholangiocarcinoma, hepatocellular carcinoma, and glioma. RNF43 contains an N-terminal signal peptide, a protease-associated (PA) domain, a transmembrane (TM) domain and a C3H2C3-type RING-H2 finger followed by a long C-terminal region. 53 matched cddid_all.tbl CDD cd16799 cd16799 319713 RING-H2_ZNRF3 RING finger, H2 subclass, found in zinc/RING finger protein 3 (ZNRF3) and similar proteins. ZNRF3, also known as RING finger protein 203 (RNF203), is a homolog of Ring finger protein 43 (RNF43). It is a transmembrane E3 ubiquitin-protein ligase that is associated with the Wnt receptor complex, and negatively regulates Wnt signaling by promoting the turnover of frizzled and lipoprotein receptor-related protein LRP6 in an R-spondin-sensitive manner. It inhibits gastric cancer cell growth and promotes cell apoptosis by affecting the Wnt/beta-catenin/TCF signaling pathway. ZNRF3 contains an N-terminal signal peptide, a protease-associated (PA) domain, a transmembrane (TM) domain and a C3H2C3-type RING-H2 finger followed by a long C-terminal region. 45 matched cddid_all.tbl CDD cd16800 cd16800 438452 RING-H2_RNF115 RING finger, H2 subclass, found in RING finger protein 115 (RNF115) and similar proteins. RNF115, also known as Rab7-interacting ring finger protein (Rabring 7), or zinc finger protein 364 (ZNF364), or breast cancer-associated gene 2 (BCA2), is an E3 ubiquitin-protein ligase that is an endogenous inhibitor of adenosine monophosphate-activated protein kinase (AMPK) activation and its inhibition increases the efficacy of metformin in breast cancer cells. It also functions as a co-factor in the restriction imposed by tetherin on HIV-1, and targets HIV-1 Gag for lysosomal degradation, impairing virus assembly and release, in a tetherin-independent manner. Moreover, RNF115 is a Rab7-binding protein that stimulates c-Myc degradation through mono-ubiquitination of MM-1. It also plays crucial roles as a Rab7 target protein in vesicle traffic to late endosome/lysosome and lysosome biogenesis. Furthermore, RNF115 and the related protein, RNF126 associate with the epidermal growth factor receptor (EGFR) and promote ubiquitylation of EGFR, suggesting they play a role in the ubiquitin-dependent sorting and downregulation of membrane receptors. RNF115 contains an N-terminal BCA2 Zinc-finger domain (BZF), the AKT-phosphorylation sites, and the C-terminal C3H2C3-type RING-H2 finger. 50 matched cddid_all.tbl CDD cd16801 cd16801 438453 RING-H2_RNF126 RING finger, H2 subclass, found in RING finger protein 126 (RNF126) and similar proteins. RNF126 is a Bag6-dependent E3 ubiquitin ligase that is involved in the mislocalized protein (MLP) pathway of quality control. It regulates the retrograde sorting of the cation-independent mannose 6-phosphate receptor (CI-MPR). Moreover, RNF126 promotes cancer cell proliferation by targeting the tumor suppressor p21 for ubiquitin-mediated degradation, and could be a novel therapeutic target in breast and prostate cancers. It is also able to ubiquitylate cytidine deaminase (AID), a poorly soluble protein that is essential for antibody diversification. In addition, RNF126 and the related protein, RNF115 associate with the epidermal growth factor receptor (EGFR) and promote ubiquitylation of EGFR, suggesting they play a role in the ubiquitin-dependent sorting and downregulation of membrane receptors. RNF126 contains an N-terminal BCA2 Zinc-finger domain (BZF), the AKT-phosphorylation sites, and the C-terminal C3H2C3-type RING-H2 finger. 44 matched cddid_all.tbl CDD cd16802 cd16802 438454 RING-H2_RNF128-like RING finger, H2 subclass, found in RING finger protein 128 (RNF128) and similar proteins. This subfamily includes RING finger proteins RNF128, RNF133, RNF148, and similar proteins, which belong to a larger PA-TM-RING ubiquitin ligase family that has been characterized by containing an N-terminal signal peptide, a protease-associated (PA) domain, a transmembrane (TM) domain and a C-terminal C3H2C3-type RING-H2 finger followed by a putative PEST sequence. RNF128, also known as gene related to anergy in lymphocytes protein (GRAIL), is a type 1 transmembrane E3 ubiquitin-protein ligase that is a critical regulator of adaptive immunity and development. It inhibits cytokine gene transcription, is expressed in anergic CD4+ T cells, and has been implicated in primary T cell activation, survival, and differentiation, as well as in T cell anergy and oral tolerance. It induces T cell anergy through the ubiquitination activity of its cytosolic RING finger. It regulates expression of the costimulatory molecule CD40L on CD4 T cells, and ubiquitinates the costimulatory molecule CD40 ligand (CD40L) during the induction of T cell anergy. Moreover, RNF128 interacts with the luminal/extracellular portion of both CD151 and the related tetraspanin CD81 via its PA domain, which promoted ubiquitination of cytosolic lysine residues. It also down-modulates the expression of CD83 (previously described as a cell surface marker for mature dendritic cells) on CD4 T cells. Furthermore, Rho guanine dissociation inhibitor (RhoGDI) has been identified as a potential substrate of RNF128, suggesting a role for Rho effector molecules in T cell anergy. In addition, RNF128 plays a role in environmental stress responses. It promotes environmental salinity tolerance in euryhaline tilapia. RNF133 is a testis-specific endoplasmic reticulum-associated E3 ubiquitin ligase that is mainly present in the cytoplasm of elongated spermatids. It may play a role in sperm maturation through an ER-associated degradation (ERAD) pathway. RNF148 is a testis-specific E3 ubiquitin ligase that is abundantly expressed in testes and slightly expressed in pancreas. Its expression is regulated by histone deacetylases. 49 matched cddid_all.tbl CDD cd16803 cd16803 319717 RING-H2_RNF130 RING finger, H2 subclass, found in RING finger protein 130 (RNF130) and similar proteins. RNF130, also known as Goliath homolog (H-Goliath), is a paralog of RNF128, also known as gene related to anergy in lymphocytes protein (GRAIL). It is a transmembrane E3 ubiquitin-protein ligase expressed in leukocytes. It has a self-ubiquitination property, and controls the development of T cell clonal anergy by ubiquitination. RNF130 contains an N-terminal signal peptide, a protease-associated (PA) domain, a transmembrane (TM) domain and a C-terminal C3H2C3-type RING-H2 finger domain followed by a putative PEST sequence. 49 matched cddid_all.tbl CDD cd16804 cd16804 438455 RING-H2_RNF149 RING finger, H2 subclass, found in RING finger protein 149 (RNF149) and similar proteins. RNF149, also known as DNA polymerase-transactivated protein 2, is an E3 ubiquitin-protein ligase that interacts with wild-type v-Raf murine sarcoma viral oncogene homolog B1 (BRAF), a RING domain-containing E3 ubiquitin ligase involved in control of gene transcription, translation, cytoskeletal organization, cell adhesion, and epithelial development. RNF149 induces the ubiquitination of wild-type BRAF and promotes its proteasome-dependent degradation. Mutated RNF149 has been found in some human breast, ovarian, and colorectal cancers. RNF149 contains an N-terminal signal peptide, a protease-associated (PA) domain, a transmembrane (TM) domain and a C-terminal C3H2C3-type RING-H2 finger domain followed by a putative PEST sequence. 48 matched cddid_all.tbl CDD cd16805 cd16805 438456 RING-H2_RNF150 RING finger, H2 subclass, found in RING finger protein 150 (RNF150) and similar proteins. RNF150 is a RING finger protein and its polymorphisms may be associated with chronic obstructive pulmonary disease (COPD) risk in the Chinese population. Further studies with larger numbers of participants worldwide are needed for validation of the relationships between RNF150 genetic variants and the pathogenesis of COPD. RNF150 contains an N-terminal signal peptide, a protease-associated (PA) domain, a transmembrane (TM) domain and a C-terminal C3H2C3-type RING-H2 finger domain followed by a putative PEST sequence. 55 matched cddid_all.tbl CDD cd16806 cd16806 438457 RING_CH-C4HC3_MARCH1 RING-CH finger, H2 subclass (C4HC3-type), found in membrane-associated RING-CH1 (MARCH1). MARCH1, also known as membrane-associated RING finger protein 1, membrane-associated RING-CH protein I (MARCH-I), or RING finger protein 171 (RNF171), is a membrane-anchored E3 ubiquitin ligase that is mainly expressed in cells of the immune system. It regulates antigen presentation and T-cell costimulatory functions of dendritic cells by down-regulating the cell surface expression of major histocompatibility complex class II (MHCII) and CD86 molecules. It mediates ubiquitination of MHCII and CD86 in dendritic cells (DCs). This ubiquitination induces MHCII and CD86 endocytosis, lysosomal transport, and degradation. MARCH1 also plays a regulatory role in T cell activation during immune responses, as well as in splenic DC homeostasis. Moreover, MARCH1 may regulate its own expression through dimerization and autoubiquitination. MARCH1 contains an N-terminal cytoplasmic C4HC3-type RING-CH finger, also known as vRING or RINGv, a variant of C3H2C3-type RING-H2 finger and two transmembrane domains. 70 matched cddid_all.tbl CDD cd16807 cd16807 438458 RING_CH-C4HC3_MARCH8 "RING-CH finger, H2 subclass (C4HC3-type), found in membrane-associated RING-CH8 (MARCH8). MARCH8, also known as membrane-associated RING finger protein 8, membrane-associated RING-CH protein VIII (MARCH-VIII), RING finger protein 178 (RNF178), or cellular modulator of immune recognition (c-MIR), is a membrane-anchored E3 ubiquitin ligase that is broadly expressed. It is a functional homolog of Kaposi""s sarcoma associated-herpes virus encoded proteins, modulator of immune recognition (MIR) 1 and 2, which are involved in the evasion of host immunity. MARCH8 mediates the ubiquitination and down-regulation of immune regulatory cell surface molecules, including major histocompatibility complex class II (MHCII), CD86, transferrin receptor, HLA-DM, and Fas in immune cells. Moreover, MARCH8 controls cell surface expression of some additional proteins. It regulates the ubiquitination and lysosomal degradation of the transferrin receptor (TfR). Tumor necrosis factor-related apoptosis inducing ligand receptor 1 (TRAIL-R1) is also a physiological substrate of the endogenous MARCH8, which regulates the steady-state cell surface expression of TRAIL-R1. Meanwhile, it negatively regulates interleukin-1 (IL-1) beta-induced NF-kappaB activation by targeting the IL-1 receptor accessory protein (IL1RAP) coreceptor for ubiquitination and degradation. Furthermore, MARCH8 functions in the embryo to modulate the strength of cell adhesion by regulating the localization of E-cadherin. In addition, MARCH8 plays a role in the inhibition of inflammatory cytokine production, suggesting a new therapeutic approach to the treatment of rheumatoid arthritis (RA). MARCH8 contains an N-terminal cytoplasmic C4HC3-type RING-CH finger, also known as vRING or RINGv, a variant of C3H2C3-type RING-H2 finger and two transmembrane domains." 64 matched cddid_all.tbl CDD cd16808 cd16808 319722 RING_CH-C4HC3_MARCH2 RING-CH finger, H2 subclass (C4HC3-type), found in membrane-associated RING-CH2 (MARCH2). MARCH2, also known as membrane-associated RING finger protein 2, membrane-associated RING-CH protein II (MARCH-II), or RING finger protein 172 (RNF172), is a Golgi-localized, membrane-associated E3 ubiquitin-protein ligase that is involved in endosomal trafficking through the binding of syntaxin 6 (STX6). It is involved in the cystic fibrosis transmembrane conductance regulator (CFTR)-associated ligand (CAL)-mediated ubiquitination and lysosomal degradation of mature CFTR through the association with adaptor proteins CAL and STX6. It also reduces the surface expression of CD86 and the transferrin receptor TFRC and regulates cell surface carvedilol-bound beta2-adrenergic receptor (beta2AR) expression. Moreover, MARCH2 interacts with and ubiquitinates PDZ domains polarity determining scaffold protein DLG1 through its PDZ-binding motif, suggesting it may function as a molecular bridge with ubiquitin ligase activity connecting endocytic tumor suppressor proteins such as syntaxins to DLG1. MARCH2 contains a C4HC3-type RING-CH finger, also known as vRING or RINGv, a variant of C3H2C3-type RING-H2 finger, in the N-terminal cytoplasmic region, two transmembrane domains in the middle region, and a PDZ-binding motif at the C-terminus. 52 matched cddid_all.tbl CDD cd16809 cd16809 438459 RING_CH-C4HC3_MARCH3 RING-CH finger, H2 subclass (C4HC3-type), found in membrane-associated RING-CH3 (MARCH3). MARCH3, also known as membrane-associated RING finger protein 3, or membrane-associated RING-CH protein III (MARCH-III), or RING finger protein 173 (RNF173), is an E3 ubiquitin-protein ligase that is broadly expressed and is found at relatively high levels in spleen, colon, and lung. It is localized to early endosomes, binds to MARCH2 and syntaxin 6, and is involved in the regulation of vesicular trafficking and fusion of the transport vesicles in endosomes. MARCH3 is the closest homolog of MARCH2 and it is also a functional homolog of K3 and K5 viral ubiquitin E3 ligases related to immune-evasion strategies used by Kaposi's sarcoma-associated herpesvirus (KSHV). Its E2 specificity significantly overlaps that of MARCH2. MARCH3 contains a C4HC3-type RING-CH finger, also known as vRING or RINGv, a variant of C3H2C3-type RING-H2 finger, in the N-terminal cytoplasmic region, two transmembrane domains in the middle region, and a PDZ-binding motif at the C-terminus. The RING-CH finger and PDZ-binding motif are essential for the subcellular localization of MARCH3 and the inhibitory effect on transferrin uptake. 56 matched cddid_all.tbl CDD cd16810 cd16810 438460 RING_CH-C4HC3_MARCH11 RING-CH finger, H2 subclass (C4HC3-type), found in membrane-associated RING-CH11 (MARCH11). MARCH11, also known as membrane-associated RING finger protein 11, or membrane-associated RING-CH protein XI (MARCH-XI), is a transmembrane RING-finger ubiquitin ligase that is predominantly expressed in developing spermatids in a stage-specific manner and is localized to trans-Golgi network (TGN) vesicles and multivesicular bodies (MVBs). It mediates selective protein sorting via the TGN-MVB transport pathway through its ubiquitin ligase activity. SAMT family proteins have been identified as substrates of MARCH11 in mouse spermatids, suggesting that MARCH11 plays a role in mammalian spermiogenesis. Moreover, MARCH11 targets CD4 for ubiquitination. It also forms complexes with the adaptor protein complex-1 and with fucose-containing glycoproteins including ubiquitinated forms. MARCH11 contains an N-terminal C4HC3-type RING-CH finger, also known as vRING or RINGv, a variant of C3H2C3-type RING-H2 finger, and two transmembrane domains. In addition, it harbors a proline-rich region, a tyrosine-based motif, and a PDZ binding motif. 60 matched cddid_all.tbl CDD cd16811 cd16811 319725 RING_CH-C4HC3_MARCH4_9 RING-CH finger, H2 subclass (C4HC3-type), found in membrane-associated RING finger protein MARCH4, MARCH9, and similar proteins. This subfamily includes the closely related MARCH4 and MARCH9, both belonging to the family of MARCH E3 ligases. They downregulate major histocompatibility complex-I (MHC-I). In the presence of MARCH4 or MARCH9, MHC-I can be ubiquitinated and rapidly internalized by endocytosis, whereas MHC-I molecules lacking lysines in their cytoplasmic tail are resistant to downregulation. Moreover, MARCH4 and MARCH9, but not other MARCH proteins, can associate with Mult1 and prevent Mult1 expression at the cell surface in a lysine-dependent manner that can be reversed by heat shocking the cells. Both MARCH4 and MARCH9 contain an N-terminal C4HC3-type RING-CH finger, also known as vRING or RINGv, a variant of C3H2C3-type RING-H2 finger, followed by two transmembrane regions. 51 matched cddid_all.tbl CDD cd16812 cd16812 438461 RING_CH-C4HC3_MARCH7 RING-CH finger, H2 subclass (C4HC3-type), found in membrane-associated RING-CH7 (MARCH7). MARCH7, also known as membrane-associated RING finger protein 7, membrane-associated RING-CH protein VII (MARCH-VII), RING finger protein 177 (RNF177), or axotrophin, is a ubiquitin E3 ligase expressed in multiple types of cells and tissues, including stem cells and precursor cells, and is predominantly localized on the plasma membrane and cytoplasm. MARCH7 is involved in T cell proliferation and neuronal development. It also participates in the regulation of cytoskeleton re-organization, cellular migration and invasion, cell proliferation, and tumorigenesis in ovarian carcinoma cells. Moreover, MARCH7 modulates nuclear factor kappaB (NF-kappaB) and Wnt/beta-catenin pathways. It has been identified as an authentic target of miR-101. Furthermore, it ubiquitinates tau protein in vitro, impairing microtubule binding. Unlike other MARCH proteins, MARCH7 is predicted to have no transmembrane spanning region. It harbors a C4HC3-type RING-CH finger, also known as vRING or RINGv, a variant of C3H2C3-type RING-H2 finger, that is responsible for its E3 activity. 65 matched cddid_all.tbl CDD cd16813 cd16813 438462 RING_CH-C4HC3_MARCH10 RING-CH finger, H2 subclass (C4HC3-type), found in membrane-associated RING-CH10 (MARCH10). MARCH10, also known as membrane-associated RING finger protein 10, membrane-associated RING-CH protein X (MARCH-X), or RING finger protein 190 (RNF190), is a microtubule-associated E3 ubiquitin ligase in developing spermatids and is involved in spermiogenesis by regulating the formation and maintenance of the flagella. It is localized to the principal piece of elongating spermatids. Unlike other MARCH proteins, MARCH10 is predicted to have no transmembrane spanning region. It harbors a C4HC3-type RING-CH finger, also known as vRING or RINGv, a variant of C3H2C3-type RING-H2 finger, that is responsible for its E3 activity. 76 matched cddid_all.tbl CDD cd16814 cd16814 438463 RING-HC_RNF20 RING finger, HC subclass, found in RING finger protein 20 (RNF20). RNF20, also known as BRE1A or BRE1, is an E3 ubiquitin-protein ligase that forms a heterodimeric complex together with BRE1B, also known as RNF40, to facilitate the K120 monoubiquitination of histone H2B (H2Bub1), a DNA damage-induced histone modification that is crucial for recruitment of the chromatin remodeler SNF2h to DNA double-strand break (DSB) damage sites. It regulates the cell cycle and differentiation of neural precursor cells (NPCs), and links histone H2B ubiquitylation with inflammation and inflammation-associated cancer. Moreover, RNF20 promotes the polyubiquitination and proteasome-dependent degradation of transcription factor activator protein 2alpha (AP-2alpha), a negative regulator of adipogenesis by repressing the transcription of CCAAT/enhancer binding protein (C/EBPalpha) gene. Furthermore, RNF20 functions as an additional chromatin regulator that is necessary for mixed-lineage leukemia (MLL)-fusion-mediated leukemogenesis. It also inhibits TFIIS-facilitated transcriptional elongation to suppress pro-oncogenic gene expression. TFIIS is a factor capable of relieving stalled RNA polymerase II. RNF20 contains a C3HC4-type RING-HC finger at its C-terminus. 75 matched cddid_all.tbl CDD cd16815 cd16815 438464 RING-HC_RNF40 RING finger, HC subclass, found in RING finger protein 40 (RNF40). RNF40, also known as BRE1B or 95 kDa retinoblastoma-associated protein (RBP95), was identified as a novel leucine zipper retinoblastoma protein (pRb)-associated protein that may function as a regulation factor in RNA polymerase II-mediated transcription and/or transcriptional processing. RNF40 also functions as an E3 ubiquitin-protein ligase that forms a heterodimeric complex with BRE1B, also known as RNF40, to facilitate the K120 monoubiquitination of histone H2B (H2Bub1), a DNA damage-induced histone modification that is crucial for recruitment of the chromatin remodeler SNF2h to DNA double-strand break (DSB) damage sites. It cooperates with SUPT16H to induce dynamic changes in chromatin structure during DSB repair. RNF40 contains a C3HC4-type RING-HC finger at the C-terminus. 78 matched cddid_all.tbl CDD cd16816 cd16816 438465 mRING-HC-C3HC5_MGRN1 Modified RING finger, HC subclass (C3HC5-type), found in mahogunin RING finger protein 1 (MGRN1) and similar proteins. MGRN1, also known as RING finger protein 156 (RNF156), is a cytosolic E3 ubiquitin-protein ligase that inhibits signaling through the G protein-coupled melanocortin receptors-1 (MC1R), -2 (MC2R) and -4 (MC4R) via ubiquitylation-dependent and -independent processes. It suppresses chaperone-associated misfolded protein aggregation and toxicity. MGRN1 interacts with cytosolic prion proteins (PrPs) that are linked with neurodegeneration. It also interacts with expanded polyglutamine proteins, and suppresses misfolded polyglutamine aggregation and cytotoxicity. Moreover, MGRN1 inhibits melanocortin receptor signaling by competition with Galphas, suggesting a novel pathway for melanocortin signaling from the cell surface to the nucleus. Furthermore, MGRN1 interacts with and ubiquitylates TSG101, a key component of the endosomal sorting complex required for transport (ESCRT)-I, and regulates endosomal trafficking. A null mutation in the gene encoding MGRN1 causes spongiform neurodegeneration, suggesting a link between dysregulation of endosomal trafficking and spongiform neurodegeneration. MGRN1 contains a modified C3HC5-type RING-HC finger, a conserved PSAP motif necessary for interaction between MGRN1 and TSG101. In addition, MGRN1 harbors a functionally uncharacterized region, as known as the domain associated with RING2 (DAR2), N-terminal to the RING finger. The C3HC5-type RING-HC finger is distinguished from typical C3HC4 RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain. 58 matched cddid_all.tbl CDD cd16817 cd16817 438466 mRING-HC-C3HC5_RNF157 Modified RING finger, HC subclass (C3HC5-type), found in RING finger protein 157 (RNF157) and similar proteins. RNF157 is a cytoplasmic E3 ubiquitin ligase predominantly expressed in brain. It is a homolog of the E3 ligase mahogunin ring finger-1 (MGRN1). In cultured neurons, it promotes neuronal survival in an E3 ligase-dependent manner. In contrast, it supports growth and maintenance of dendrites independent of its E3 ligase activity. RNF157 interacts with and ubiquitinates the adaptor protein APBB1 (amyloid beta precursor protein-binding, family B, member 1 or Fe65), which regulates neuronal survival, but not dendritic growth downstream of RNF157. The nuclear localization of APBB1 together with its interaction partner RNA-binding protein SART3 (squamous cell carcinoma antigen recognized by T cells 3 or Tip110) is crucial to trigger apoptosis. RNF157 contains a modified C3HC5-type RING-HC finger, and a functionally uncharacterized region, known as domain associated with RING2 (DAR2), N-terminal to the RING finger. The C3HC5-type RING-HC finger is distinguished from typical C3HC4 RING-HC finger due to the existence of the additional cysteine residue in the middle portion of the RING finger domain. 60 matched cddid_all.tbl CDD cd16818 cd16818 438467 SP-RING_PIAS1 SP-RING finger found in protein inhibitor of activated STAT protein 1 (PIAS1) and similar proteins. PIAS1, also known as DEAD/H box-binding protein 1, Gu-binding protein (GBP), or RNA helicase II-binding protein, was initially identified as an inhibitor of STAT1 that blocks the DNA-binding activity of STAT1 and specifically inhibits STAT1-mediated gene transcription in response to cytokine stimulation. It selectively inhibits interferon-inducible gene expression and plays an important role in the IFN-gamma- or IFN-beta-mediated innate immune response through negative regulation of STAT1. It also regulates the activity of other transcription factors to regulate immune response, such as NF-kappaB and Smad4. Moreover, PIAS1 functions as an E3 small ubiquitin-like modifier (SUMO)-protein ligase specifying target proteins for SUMO conjugation by Ubc9. The sumoylation activity of PIAS1 can suppress cytokine transforming growth factor beta (TGFbeta)-induced epithelial mesenchymal transition (EMT) in non-transformed epithelial cells to promote activation of the matrix metalloproteinase 2 (MMP2). It thus regulates TGFbeta-induced cancer cell invasion and metastasis. PIAS1 may also be involved in spatial learning and memory formation through its SUMOylation of cAMP-responsive element binding protein (CREB). In addition, PIAS1 is the E3 ligase responsible for SUMOylation of High mobility group nucleosomal binding domain 2 (HMGN2), which is a small and unique non-histone protein that has many functions in a variety of cellular processes, including regulation of chromatin structure, transcription, and DNA repair, as well as antimicrobial activity, cell homing, and regulating cytokine release. Furthermore, PIAS1 is a genuine chromatin-bound androgen receptor (AR) co-regulator that functions in a target gene selective fashion to regulate prostate cancer cell growth. It also mediates the SUMOylation of c-Myc, which is the most frequently overexpressed oncogene in tumors, including breast cancer, colon cancer, and lung cancer. Necdin, a pleiotropic protein that promotes differentiation and survival of mammalian neurons, can suppress PIAS1 both by inhibiting SUMO E3 ligase activity and by promoting ubiquitin-dependent degradation. PIAS1 contains an N-terminal SAP (scaffold attachment factor A/B (SAF-A/B), acinus and PIAS) box with the LXXLL signature, a PINT motif, a specific RING finger known as Siz/PIAS (protein inhibitor of activated signal transducer and activator of transcription) RING (SP-RING) finger, and the acidic C-terminal domain. The SP-RING finger mediates the interaction of PIAS1 with the SUMO E2 conjugating enzyme Ubc9. It binds a single Zn ion, instead of two ions bound by typical RING fingers. 60 matched cddid_all.tbl CDD cd16819 cd16819 438468 SP-RING_PIAS2 SP-RING finger found in protein inhibitor of activated STAT protein 2 (PIAS2) and similar proteins. PIAS2, also known as androgen receptor-interacting protein 3 (ARIP3), DAB2-interacting protein (DIP), Msx-interacting zinc finger protein (Miz1), PIAS-NY protein, protein inhibitor of activated STAT x, protein inhibitor of activated STAT2, is an E3 SUMO-protein ligase highly expressed in the testis. It functions as a transcriptional activator of BCL2 and is essential for blocking c-MYC-induced apoptosis. It also acts as a negative regulator of cell proliferation, induces expression of the cell-cycle inhibitors p15(Ink4b) and p21(Cip1), and activates transcription of the p21(Cip1) gene in response to UV irradiation. Moreover, PIAS2 associates with topoisomerase II binding protein 1 (TopBP1), an essential activator of the Atr kinase. It thus affects the activity of the Atr checkpoint. Receptor of activated C kinase 1 (RACK1), glucocorticoid receptor (GR)-interacting protein 1 (GRIP1), friend leukemia integration-I (FLI-1), and ubiquitously expressed transcript (UXT) are binding partners of PIAS2. The interaction between UXT and PIAS2 may be important for the transcriptional activation of androgen receptor (AR). PIAS2 contains an N-terminal SAP (scaffold attachment factor A/B (SAF-A/B), acinus, and PIAS) box with the LXXLL signature, a PINT motif, a specific RING finger known as Siz/PIAS (protein inhibitor of activated signal transducer and activator of transcription) RING (SP-RING) finger, and an acidic C-terminal domain. The SP-RING finger is a variant of RING finger, which lacks the second, fifth, and sixth zinc-binding residues of the consensus C3H2C3-/C3HC4-type RING fingers. It binds a single Zn ion, instead of two ions bound by typical RING fingers. 60 matched cddid_all.tbl CDD cd16820 cd16820 438469 SP-RING_PIAS3 SP-RING finger found in protein inhibitor of activated STAT protein 3 (PIAS3) and similar proteins. PIAS3 is an E3 SUMO-protein ligase that was initially identified as an interleukin-6 (IL-6)-dependent repressor of signal transducer and activator of transcription 3 (STAT3) and has anti-proliferative properties. It binds specifically to phosphorylated STAT3 and inhibits its transcriptional activity by blocking its binding to DNA. It regulates STAT3-mediated induction of Snail expression, as well as suppresses acute graft-versus-host disease (GVHD) by modulating effector T and B cell subsets through inhibition of STAT3 activation. It activates the intrinsic apoptotic pathway in non-small cell lung cancer cells independent of p53 status. When overexpressed, it can interact with STAT5 to regulate prolactin-induced STAT5-mediated gene expression. Moreover, PIAS3 binds to and activates Smad3 transcriptional activity, resulting in the enhancement of transforming growth factor-beta (TGF-beta) signaling. It functions as a transcriptional corepressor of Erythroid Kruppel-like factor (EKLF or KLF1) and thus plays an important role in erythropoiesis. It also plays a significant role in the DNA damage response (DDR) pathway by promoting homologous recombination (HR)- and non-homologous end joining (NHEJ)-mediated DNA double-strand break (DSB) repair. Furthermore, PIAS3 preferentially interacts with and enhances the SUMOylation of TAK1-binding protein 2 (TAB2), an upstream adaptor protein in the IL-1 signaling pathway. It also promotes SUMOylation and nuclear sequestration of ErbB4 receptor tyrosine kinase. In addition, PIAS3 may form a complex with microphthalmia-associated transcription factor, nuclear factor-kappaB, Smad, and estrogen receptor. Its other transcription factor binding partners include: ETS, EGR1, NR1I2, and GATA1. PIAS3 contains an N-terminal SAP (scaffold attachment factor A/B (SAF-A/B), acinus and PIAS) box with the LXXLL signature, a PINT motif, a specific RING finger known as Siz/PIAS (protein inhibitor of activated signal transducer and activator of transcription) RING (SP-RING) finger, and an acidic C-terminal domain. The SP-RING finger is a variant of RING finger, which lacks the second, fifth, and sixth zinc-binding residues of the consensus C3H2C3-/C3HC4-type RING fingers. It binds a single Zn ion, instead of two ions bound by typical RING fingers. 62 matched cddid_all.tbl CDD cd16821 cd16821 438470 SP-RING_PIAS4 SP-RING finger found in protein inhibitor of activated STAT protein 4 (PIAS4) and similar proteins. PIAS4, also known as PIASy or protein inhibitor of activated STAT protein gamma (PIAS-gamma), is an E3 SUMO-protein ligase that interacts with the androgen receptor (AR) and is involved in ubiquitin signaling pathways. It is associated with macro/microcephaly in the novel interstitial 19p13.3 microdeletion/microduplication syndrome. It also regulates the hypoxia signalling pathway by interacting with the tumor suppressor von Hippel-Lindau (VHL), which leads to VHL sumoylation, oligomerization, and impaired function during growth of pancreatic cancer cells. Moreover, PIAS4 acts as a direct binding partner for vitamin D receptor (VDR) and facilitates its modification with SUMO2. The process of SUMOylation modulates VDR-mediated signaling. As components of the DNA-damage response (DDR), PIAS4 together with PIAS1 promote responses to DNA double-strand breaks (DSBs). They are required for effective ubiquitin-adduct formation mediated by RNF8, RNF168, and BRCA1 at sites of DNA damage. PIAS4 contains an N-terminal SAP (scaffold attachment factor A/B (SAF-A/B), acinus and PIAS) box with the LXXLL signature, a PINT motif, a specific RING finger known as Siz/PIAS (protein inhibitor of activated signal transducer and activator of transcription) RING (SP-RING) finger, and an acidic C-terminal domain. The SP-RING finger is a variant of RING finger, which lacks the second, fifth, and sixth zinc-binding residues of the consensus C3H2C3-/C3HC4-type RING fingers. It binds a single Zn ion, instead of two ions bound by typical RING fingers. 58 matched cddid_all.tbl CDD cd16822 cd16822 438471 SP-RING_ZMIZ1 SP-RING finger found in zinc finger MIZ domain-containing protein 1 (Zmiz1) and similar proteins. Zmiz1, also known as PIAS-like protein Zimp10 (zinc finger-containing, Miz1, PIAS-like protein on chromosome 10) or retinoic acid-induced protein 17, is a novel PIAS-like protein that was initially identified as an androgen receptor (AR) interacting protein and functions as a transcriptional co-activator. It co-localizes with AR and small ubiquitin-like modifier SUMO-1, forms a protein complex at replication foci in the nucleus, and augments AR-mediated transcription. It also functions as a transcriptional co-activator of the p53 tumor suppressor that plays a critical role in cell cycle progression, DNA repair, and apoptosis. Moreover, Zmiz1 dysfunction may be associated with multiple autoimmune diseases and it has been implicated in the development, function, and survival of melanocytes. Zmiz1 also interacts with Smad3/4 proteins and augments Smad-mediated transcription, suggesting it is important in the regulation of the transforming growth factor beta (TGF-beta)/Smad signaling pathway and may have an inhibitory effect on the immune system. Zmiz1 is overexpressed in a significant percentage of human cutaneous squamous cell carcinoma (SCC), breast, ovarian, and colon cancers, suggesting it may play a broader role in epithelial cancers. It functionally interacts with NOTCH1 to promote C-MYC transcription and activity, and thus is involved in a variety of C-MYC-driven cancers. Zmiz1 contains a PAT domain, a highly conserved Siz/PIAS (protein inhibitor of activated signal transducer and activator of transcription) RING (SP-RING) finger, also known as msx-interacting zinc finger (Miz domain), and a putative nuclear localization sequence (NLS), as well as a strong intrinsic transactivation domain within the C-terminus. The SP-RING finger is a variant of RING finger, which lacks the second, fifth, and sixth zinc-binding residues of the consensus C3H2C3-/C3HC4-type RING fingers. It binds a single Zn ion, instead of two ions bound by typical RING fingers. 64 matched cddid_all.tbl CDD cd16823 cd16823 438472 SP-RING_ZMIZ2 SP-RING finger found in zinc finger MIZ domain-containing protein 2 (Zmiz2) and similar proteins. Zmiz2, also known as PIAS-like protein Zimp7 (zinc finger-containing, Miz1, PIAS-like protein on chromosome 7), is a novel PIAS-like protein that was initially identified as an androgen receptor (AR) interacting protein and functions as a transcriptional co-activator. It interacts with beta-catenin and enhances Wnt/beta-catenin-mediated transcription. It also associates with BRG1 and BAF57, components of the ATP-dependent mammalian SWI/SNF-like BAF chromatin-remodeling complexes, and thus plays a potential role in modulation of AR and/or other nuclear receptor-mediated transcription. For instance, it can increase the effects of BRG1 on AR-mediated transcriptional activity. Moreover, Zmiz2 physically interacts with PIAS proteins, especially PIAS3. Through this interaction, PIAS3 augments Zmiz2-mediated transcription, suggesting PIAS proteins may play a regulatory role in Zmiz-mediated transcription. Furthermore, Zmiz2 is involved in transcriptional regulation of factors essential for patterning in the dorsoventral axis. It is required for the restriction of the zebrafish organizer and mesoderm development. Zmiz2 contains a PAT domain, a highly conserved Siz/PIAS (protein inhibitor of activated signal transducer and activator of transcription) RING (SP-RING) finger, also known as msx-interacting zinc finger (Miz domain), and a strong intrinsic transactivation domain within the C-terminus. The SP-RING finger is a variant of RING finger, which lacks the second, fifth, and sixth zinc-binding residues of the consensus C3H2C3-/C3HC4-type RING fingers. It binds a single Zn ion, instead of two ions bound by typical RING fingers. 61 matched cddid_all.tbl CDD cd16824 cd16824 438473 RING_CH-C4HC3_MARCH4 RING-CH finger, H2 subclass (C4HC3-type), found in membrane-associated RING-CH4 (MARCH4). MARCH4, also known as membrane-associated RING finger protein 4, membrane-associated RING-CH protein IV (MARCH-IV), or RING finger protein 174 (RNF174), is a transmembrane E3 ubiquitin-protein ligase that down-regulates the tetraspanin CD81 and major histocompatibility complex-I (MHC). It also associates with Mult1, suppressing Mult1 expression at the cell surface in a lysine-dependent manner that can be reversed by heat shocking the cells. MARCH4 contains an N-terminal C4HC3-type RING-CH finger, also known as vRING or RINGv, a variant of C3H2C3-type RING-H2 finger, followed by two transmembrane regions. 56 matched cddid_all.tbl CDD cd16825 cd16825 438474 RING_CH-C4HC3_MARCH9 RING-CH finger, H2 subclass (C4HC3-type), found in membrane-associated RING-CH9 (MARCH9). MARCH9, also known as membrane-associated RING finger protein 9, membrane-associated RING-CH protein IX (MARCH-IX), or RING finger protein 179 (RNF179), is a transmembrane E3 ubiquitin-protein ligase that down-regulates Mult1, CD4, major histocompatibility complex-I (MHC), and intercellular adhesion molecule (ICAM-1). It may also interact with receptor-type protein-tyrosine phosphatases (e.g. PTPRJ/CD148) as well as Fc gamma receptor IIB (CD32B), HLA-DQ, signaling lymphocytic activation molecule (CD150), and polio virus receptor (CD155). MARCH9 contains an N-terminal C4HC3-type RING-CH finger, also known as vRING or RINGv, a variant of C3H2C3-type RING-H2 finger, followed by two transmembrane regions. 54 matched cddid_all.tbl CDD cd16827 cd16827 319356 ChuX-like heme utilization protein ChuX and similar proteins. This family contains ChuX, a member of the conserved heme utilization operon from pathogenic E. coli, and similar proteins, which include ChuS, HutX, HuvX, HugX, and ShuX in proteobacteria, among others. It forms a dimer which displays a very similar fold and organization to the monomeric structure of other heme utilization proteins such as HemS, ChuS, HmuS, PhuS; these latter occurring as duplicated domains. They all bind heme via a key conserved histidine. The genes encoded within these heme utilization operons enable the effective uptake and utilization of heme as an iron source in pathogenic microorganisms to enable multiplication and survival within hosts they invade. 141 matched cddid_all.tbl CDD cd16828 cd16828 319357 HemS-like N- and C-terminal domains of heme degrading enzyme HemS, and similar proteins. This family contains the N- and C-terminal domains of heme degrading enzyme HemS, and similar proteins, including PhuS, ChuS, ShuS, and HmuS in proteobacteria. Despite low sequence identity between the N- and C-terminal halves, these segments represent a structural duplication, with each terminal half having similar fold to single domains of ChuX. HemS shares homology with both heme degrading enzymes and heme trafficking enzymes. Heme is an iron source for pathogenic microorganisms to enable multiplication and survival within hosts they invade and therefore heme degrading enzyme activity is required for the release of iron from heme after its transportation into the cytoplasm. N- and C-terminal halves of ChuS are each a functional heme oxygenase (HO). The mode of heme coordination by ChuS has been shown to be distinct, whereby the heme is stabilized mostly by residues from the C-terminal domain, assisted by a distant arginine from the N-terminal domain. ChuS can use ascorbic acid or cytochrome P450 reductase-NADPH as electron sources for heme oxygenation. Shigella dysenteriae ShuS promotes utilization of heme as an iron source and protects against heme toxicity by physically sequestering DNA. PhuS in Pseudomonas aeruginosa has been reported as a heme chaperone and as a heme degrading enzyme, and is unique among this family since it contains three histidines in the heme-binding pocket, compared with only one in ChuX. Heme transporter protein PhuS in Pseudomonas aeruginosa is unique among this family since it contains three histidines in the heme-binding pocket, compared with only one in ChuX. 152 matched cddid_all.tbl CDD cd16829 cd16829 319358 ChuX_HutX-like heme iron utilization protein ChuX and similar proteins. This family contains proteins similar to ChuX, a member of the conserved heme utilization operon from pathogenic E. coli, and includes ChuS, HutX, HuvX, HugX, and ShuX in proteobacteria, among others. It forms a dimer which displays a very similar fold and organization to the monomeric structure of other heme utilization proteins such as HemS, ChuS, HmuS, PhuS; these latter occurring as duplicated domains. They all bind heme via a key conserved histidine. The genes encoded within these heme utilization operons enable the effective uptake and utilization of heme as an iron source in pathogenic microorganisms to enable multiplication and survival within hosts they invade. ChuX, a member of the conserved heme utilization operon from pathogenic E. coli O157:H7, forms a dimer with a very similar fold to the monomer structure of two other heme utilization proteins, ChuS and HemS, despite low sequence homology. ChuX has been shown to bind heme in a 1:1 manner, inferring that the ChuX homodimer could coordinate two heme molecules in contrast to only one heme molecule bound in ChuS and HemS. Similarly, cytoplasmic heme-binding protein HutX in Vibrio cholera, an intracellular heme transport protein for the heme-degrading enzyme HutZ, forms a dimer, each domain binding heme that is transferred from HutX to HutZ via a specific protein-protein interaction. This family also includes AGR_C_4470p from Agrobacterium tumefaciens and found to be a dimer, with each subunit having strong structural homology and organization to the heme utilization protein ChuS from Escherichia coli and HemS from Yersinia enterocolitica. However, the heme binding site is not conserved in AGR_C_4470p, suggesting a possible different function. 143 matched cddid_all.tbl CDD cd16830 cd16830 319359 HemS-like_N N-terminal domain of heme degrading enzyme HemS, and similar proteins. This family contains the N-terminal domain of heme degrading enzyme HemS, and similar proteins, including PhuS, ChuS, ShuS, and HmuS in proteobacteria. Despite low sequence identity between the N- and C-terminal halves, these segments represent a structural duplication, with each terminal half having similar fold to single domains of ChuX. HemS shares homology with both heme degrading enzymes and heme trafficking enzymes. Heme is an iron source for pathogenic microorganisms to enable multiplication and survival within hosts they invade and therefore heme degrading enzyme activity is required for the release of iron from heme after its transportation into the cytoplasm. N- and C-terminal halves of ChuS are each a functional heme oxygenase (HO). The mode of heme coordination by ChuS has been shown to be distinct, whereby the heme is stabilized mostly by residues from the C-terminal domain, assisted by a distant arginine from the N-terminal domain. ChuS can use ascorbic acid or cytochrome P450 reductase-NADPH as electron sources for heme oxygenation. Shigella dysenteriae ShuS promotes utilization of heme as an iron source and protects against heme toxicity by physically sequestering DNA. Heme transporter protein PhuS in Pseudomonas aeruginosa is unique among this family since it contains three histidines in the heme-binding pocket, compared with only one in ChuX. 152 matched cddid_all.tbl CDD cd16831 cd16831 319360 HemS-like_C C-terminal domain of heme degrading enzyme HemS, and similar proteins. This family contains the C-terminal domain of heme degrading enzyme HemS, and similar proteins, including PhuS, ChuS, ShuS, and HmuS in proteobacteria. Despite low sequence identity between the N- and C-terminal halves, these segments represent a structural duplication, with each terminal half having similar fold to single domains of ChuX. HemS shares homology with both, heme degrading enzymes and heme trafficking enzymes. Heme is an iron source for pathogenic microorganisms to enable multiplication and survival within hosts they invade and therefore heme degrading enzyme activity is required for the release of iron from heme after its transportation into the cytoplasm. N- and C-terminal halves of ChuS are each a functional heme oxygenase (HO). The mode of heme coordination by ChuS has been shown to be distinct, whereby the heme is stabilized mostly by residues from the C-terminal domain, assisted by a distant arginine from the N-terminal domain. ChuS can use ascorbic acid or cytochrome P450 reductase-NADPH as electron sources for heme oxygenation. Shigella dysenteriae ShuS promotes utilization of heme as an iron source and protects against heme toxicity by physically sequestering DNA. Heme transporter protein PhuS in Pseudomonas aeruginosa is unique among this family since it contains three histidines in the heme-binding pocket, compared with only one in ChuX. 155 matched cddid_all.tbl CDD cd16832 cd16832 319353 CNF1_CheD_YfiH-like cytotoxic necrotizing factor 1 (CNF1), chemotaxis protein CheD and YfiH (DUF152) are distant homologs. This family contains distant homologs that include cytotoxic necrotizing factor 1 (CNF1), chemotaxis protein CheD and a protein of unknown function YfiH. CNF-1 along with dermonecrotic toxin (DNT) from Bordetella species, and Burkholderia Lethal Factor 1 (BLF1, also known as BPSL1549) are Rho-activating toxins. The bacterial chemotaxis protein CheD stimulates methylation of methyl-accepting chemotaxis proteins (MCPs). YfiH, a domain of unknown function, also included in this family reveals a structure with a distant homology between to the CNF1, and CheD, all having an invariant Cys-His pair forming a catalytic dyad that is required by the CNF-1 toxins for deamidation activity. 145 matched cddid_all.tbl CDD cd16833 cd16833 319354 YfiH protein of unknown function YfiH. This subfamily contains YfiH, a protein of unknown function from Shigella flexneri, E. coli, and many similar proteins which collectively are often called DUF152. The structure of YfiH reveals a distant homology to Rho-activating toxins cytotoxic necrotizing factor 1 (CNF1) as well as chemotaxis protein CheD that stimulates methylation of methyl-accepting chemotaxis proteins (MCPs), all having an invariant Cys-His pair forming a catalytic dyad, and is required by the CNF-1 toxins for deamidation activity. 185 matched cddid_all.tbl CDD cd16834 cd16834 319355 CNF1-like cytotoxic necrotizing factor 1 (CNF1) and similar proteins. This subfamily contains Rho-activating toxins cytotoxic necrotizing factor 1 (CNF1) and dermonecrotic toxin (DNT) from Bordetella species, as well as Burkholderia Lethal Factor 1 (BLF1, also known as BPSL1549), and similar proteins. CNF1 causes alteration of the host cell actin cytoskeleton and promotes bacterial invasion of blood-brain barrier endothelial cells. E. coli CNF1 constitutively activates host small G proteins such as RhoA and Cdc42 by deamidating a glutamine residue essential for GTP hydrolysis. DNT stimulates the assembly of actin stress fibers and focal adhesions by deamidation/polyamination of a specific glutamine of the small GTPase Rho. CNF1 and DNT are A-B toxins composed of an N-terminal receptor-binding (B) domain and a C-terminal enzymatically active (A) domain; their homology is restricted to the catalytic domains at the C termini of the toxins, suggesting that they share a similar molecular mechanism. BLF1, a toxin that inhibits helicase activity of translation factor eIF4A, is similar to the catalytic domain of Escherichia coli CNF1 (CNF1-C); although CNF1-C and BLF1 show little sequence identity, the active sites have the conserved LSGC (Leu, Ser, Gly, Cys) motif. 168 matched cddid_all.tbl CDD cd16837 cd16837 319351 BldD_C_like C-terminal domain of BldD and similar transcription factors. The Streptomyces transcription factor BldD dimerizes via an unusual mechanism that inolves a tetrameric c-di-GMP assembly. BdlD is involved in controlling multicellular differentiation in sporulating actinomycetes. 73 matched cddid_all.tbl CDD cd16839 cd16839 319350 PCSK9_C-CRD proprotein convertase subtilisin/kexin type 9, C-terminal cysteine-rich domain (CRD). PCSK9 post-translationally regulates hepatic low-density lipoprotein receptors (LDLRs) by binding to LDLRs on the cell surface, leading to their degradation. Other known PSCK9 targets include very-low-density lipoprotein receptor (VLDLR), apoE receptor2, lipoprotein receptor-related protein 1, etc. This PCSK9 C-terminal CRD may play an analogous role to the P (processing) domains of Furin and Kex2 (i.e. be required for the correct functioning/folding of the protein). Structural similarity has been noted between PCSK9 C-terminal CRD and the resistin homotrimer. This alignment model represents a three-fold repeat. 225 matched cddid_all.tbl CDD cd16840 cd16840 411037 toxin_MLD toxin effector region membrane localization domain. This MLD domain functions as a membrane-targeting domain for toxin effectors such as the Rho-inactivation domain of Vibrio MARTX, Pasteurella mitogenic toxin (PMT), where it has been termed PMT C1 domain, and clostridial glycosylating cytotoxins including Clostridium difficile toxins A (TcdA) and B (TcdB), Clostridium novyi alpha-toxin (TcnA), and Clostridium sordellii lethal toxin (TcsL). During infection, the C. difficile homologous exotoxins, TcdA and TcdB, target and disrupt the colonic epithelium, leading to diarrhea and colitis. They disrupt host cell function through a multistep process involving receptor binding, endocytosis, low pH-induced pore formation, and the translocation and delivery of a C-terminal glucosyltransferase domain (GTD) that inactivates host GTPases. Their N-terminal MLD domains confer membrane localization of adjacent effector domains via the 4-helix-bundle motif. 78 matched cddid_all.tbl CDD cd16841 cd16841 319245 RraA_family ribonuclease activity regulator RraA family. RraA protein family is named after the regulator of ribonuclease activity A (RraA), a protein that binds to RNase E and inhibits RNase E endonucleolytic cleavages. Members also include proteins with other functions, like a 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate (HMG/CHA) aldolase from Pseudomonas putida, which catalyzes the last step of the bacterial protocatechuate 4,5-cleavage pathway and the uncharacterized YER010Cp protein from yeast, an organism lacking RNAse E. 150 matched cddid_all.tbl CDD cd16842 cd16842 409517 Ig_SLAM-like_N N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family. The members here are composed of the N-terminal immunoglobulin (Ig)-like domain of the signaling lymphocyte activation molecule (SLAM) family and similar proteins. The SLAM family is a group of immune-cell specific receptors that can regulate both adaptive and innate immune responses. Members of this group include proteins such as CD84, SLAM (CD150), Ly-9 (CD229), NTB-A (ly-108, SLAM6), 19A (CRACC), and SLAMF9. The genes coding for the SLAM family are nested on chromosome 1, in humans at 1q23, and in mice at 1H2. The SLAM family is a subset of the CD2 family, which also includes CD2 and CD58 located on chromosome 1 at 1p13 in humans. In mice, CD2 is located on chromosome 3, and there is no CD58 homolog. The SLAM family proteins are organized as an extracellular domain with either two or four Ig-like domains, a single transmembrane segment, and a cytoplasmic region having Tyr-based motifs. The extracellular domain is organized as a membrane-distal Ig variable (IgV) domain that is responsible for ligand recognition and a membrane-proximal truncated Ig constant-2 (IgC2) domain. 102 matched cddid_all.tbl CDD cd16843 cd16843 409518 IgC2_D1_D2_LILR_KIR_like Immunoglobulin (Ig)-like domain found in Leukocyte Ig-like receptors, Natural killer inhibitory receptors (KIRs) and similar domains; member of Immunoglobulin Constant-2 set of IgSF domains. The members here are composed of the first and second immunoglobulin (Ig)-like domains found in Leukocyte Ig-like receptors (LILRs), Natural killer inhibitory receptors (KIRs, also known as also known as cluster of differentiation (CD) 158), and similar proteins. This group includes LILRB1 (also known as LIR-1), LILRA5 (also known as LIR9), an activating natural cytotoxicity receptor NKp46, the immune-type receptor glycoprotein VI (GPVI), and the IgA-specific receptor Fc-alphaRI (also known as cluster of differentiation (CD) 89). LILRs are a family of immunoreceptors expressed on expressed on T and B cells, on monocytes, dendritic cells, and subgroups of natural killer (NK) cells. The human LILR family contains nine proteins (LILRA1-3, and 5, and LILRB1-5). From functional assays, and as the cytoplasmic domains of various LILRs, for example LILRB1, LILRB2 (also known as LIR-2), and LILRB3 (also known as LIR-3) contain immunoreceptor tyrosine-based inhibitory motifs (ITIMs), it is thought that LIR proteins are inhibitory receptors. Of the eight LIR family proteins, only LILRB1, and LILRB2, show detectable binding to class I MHC molecules; ligands for the other members have yet to be determined. The extracellular portions of the different LIR proteins contain different numbers of Ig-like domains for example, four in the case of LILRB1, and LILRB2, and two in the case of LILRB4 (also known as LIR-5). The activating natural cytotoxicity receptor NKp46 is expressed in natural killer cells, and is organized as an extracellular portion having two Ig-like extracellular domains, a transmembrane domain, and a small cytoplasmic portion. GPVI, which also contains two Ig-like domains, participates in the processes of collagen-mediated platelet activation and arterial thrombus formation. Fc-alphaRI is expressed on monocytes, eosinophils, neutrophils, and macrophages; it mediates IgA-induced immune effector responses such as phagocytosis, antibody-dependent cell-mediated cytotoxicity and respiratory burst. Killer cell immunoglobulin-like receptors (KIRs; also known as CD158 for human KIR) are transmembrane glycoproteins expressed by natural killer cells and subsets of T cells. KIRs are a family of highly polymorphic activating and inhibitory receptors that serve as key regulators of human NK cell function. The KIR proteins are classified by the number of extracellular immunoglobulin domains (2D or 3D) and by whether they have a long (L) or short (S) cytoplasmic domain. KIR proteins with the long cytoplasmic domain transduce inhibitory signals upon ligand binding via an immune tyrosine-based inhibitory motif (ITIM), while KIR proteins with the short cytoplasmic domain lack the ITIM motif and instead associate with the TYRO protein tyrosine kinase binding protein to transduce activating signals. The major ligands for KIR are MHC class I (HLA-A, -B or -C) molecules. 90 matched cddid_all.tbl CDD cd16844 cd16844 319272 ParB_N_like_MT "ParB N-terminal-like domain, some attached to C-terminal S-adenosylmethionine-dependent methyltransferase domain. This family represents domains related to the N-terminal domain of ParB, a DNA-binding component of the prokaryotic parABS partitioning system, fused to a variety of C-terminal domains, including S-adenosylmethionine-dependent methyltransferase-like domains and DUF4417. parABS contributes to the efficient segregation of chromosomes and low-copy number plasmids to daughter cells during prokaryotic cell division. The process includes the parA (Walker box) ATPase, the ParB DNA-binding protein and a parS cis-acting DNA sites. Binding of ParB to centromere-like parS sites is followed by non-specific binding to DNA (""spreading"", which has been implicated in gene silencing in plasmid P1) and oligomerization of additional ParB molecules near the parS sites. It has been proposed that ParB-ParB cross-linking compacts the DNA, binds to parA via the N-terminal region, and leads to parA separating the ParB-parS complexes and the recruitment of the SMC (structural maintenance of chromosomes) complexes. The ParB N-terminal domain of Bacillus subtilis and other species contains a Arginine-rich ParB Box II with residues essential for bridging of the ParB-parS complexes. The arginine-rich ParB Box II consensus (I[VIL]AGERR[FYW]RA[AS] identified in several species is partially conserved with this family and related families. Mutations within the basic columns particularly debilitate spreading from the parS sites and impair SMC recruitment. The C-terminal domain contains a HTH DNA-binding motif and is the primary homo-dimerization domain, and binds to parS DNA sites. Additional homo-dimerization contacts are found along the N-terminal domain, but dimerization of the N-terminus may only occur after concentration at ParB-parS foci." 54 matched cddid_all.tbl CDD cd16845 cd16845 341083 STAT1_DBD DNA-binding domain of Signal Transducer and Activator of Transcription 1 (STAT1). This family consists of the DNA-binding domain (DBD) of the STAT1 proteins (Signal Transducer and Activator of Transcription 1, or Signal Transduction And Transcription 1). The DNA binding domain has an Ig-like fold. STAT1 plays an essential role in mediating responses to all types of interferons (IFN), transducing signals from cytoplasmic domains of transmembrane receptors into the nucleus where it regulates gene expression. Thus STAT1 is involved in modulating diverse cellular processes, such as antimicrobial activities, cell proliferation and cell death. STAT1 function is crucial in the innate and adaptive arm of immunity and protects from pathogen infections; phosphorylation of a critical tyrosine by Janus kinases (JAKs) leads to its activation and nuclear translocation, while phosphorylation of a critical serine is required for full transcriptional activation upon IFN stimulation and in response to cellular stress. Transcription of protein-encoding genes (including Stat1 itself) as well as expression of microRNAs (miRNAs) is regulated by activated STAT1. Animal studies have shown that STAT1 is generally considered a tumor suppressor but it can also act as a tumor promoter; its functions are not restricted to tumor cells, but extend to parts of the tumor microenvironment such as immune cells, endothelial cells. STAT1 abundance is a reliable marker for good prognosis in selected tumor types, but it can also correlate with disease progression. In head and neck cancer (HNC) patients, upregulation of STAT1-induced HLA class I enhances immunogenicity and clinical response to anti-EGFR mAb cetuximab therapy. In systemic juvenile idiopathic arthritis (sJIA) characterized by systemic inflammation and arthritis, STAT1 phosphorylation downstream of IFNs is impaired. It exerts anti-oncogenic activities through interferon-gamma and interferon-alpha. STAT1 may inhibit hepatocellular carcinoma cell growth by regulating p53-related cell cycling and apoptosis. Studies also show a significant correlation of high STAT1 activity with longer colorectal cancer patient overall survival. Recent studies have shown that STAT1 suppresses mouse mammary gland tumorigenesis by immune regulatory as well as tumor cell-specific functions of STAT1. 161 matched cddid_all.tbl CDD cd16846 cd16846 341084 STAT2_DBD DNA-binding domain of Signal Transducer and Activator of Transcription 2 (STAT2). This family consists of the DNA-binding domain (DBD) of the STAT2 proteins (Signal Transducer and Activator of Transcription 2, or Signal Transduction And Transcription 2). The DNA binding domain has an Ig-like fold. STAT2 activation is driven predominantly by only two classes of cell surface receptors: Type I and III interferon receptors, making it a unique STAT family of transcription factors. Thus, STAT2 plays a critical role in host defenses against viral infections since type I interferon (IFN-I) response inhibits viral replication, and sets the stage for the development of adaptive immunity; viruses target STAT2 by either inhibiting its expression, blocking its activity, or by targeting it for degradation, thus triggering remarkable divergence in the STAT2 gene across species compared to other STAT family members. STAT2 function is regulated by tyrosine phosphorylation which enables STAT dimerization, and subsequent nuclear translocation and transcriptional activation of IFN stimulated genes. Dengue virus (DENV)-mediated degradation of STAT2 has emerged as an important determinant of DENV pathogenesis and host tropism. This vector-borne flavivirus suppresses IFN1 signaling to replicate and cause disease in vertebrates via proteasome-dependent STAT2 degradation mediated by the nonstructural protein NS5 and its interaction partner UBR4, an E3 ubiquitin ligase. The mechanism of Zika virus (ZIKV) NS5 resembles DENV NS5 but through different mechanism - ZIKV does not require the UBR4 to induce STAT2 degradation. It has also been shown that the STAT2 and STAT4 genes are direct targets for transcription factor Oct-1 protein which is involved in the regulation of expression of genes of the JAK-STAT signaling pathway in the Namalwa Burkitt's lymphoma cell line. 160 matched cddid_all.tbl CDD cd16847 cd16847 341085 STAT3_DBD DNA-binding domain of Signal Transducer and Activator of Transcription 3 (STAT3). This family consists of the DNA-binding domain (DBD) of the STAT3 proteins (Signal Transducer and Activator of Transcription 3, or Signal Transduction And Transcription 3). The DNA binding domain has an Ig-like fold. STAT3 plays key roles in vertebrate development and mature tissue function including control of inflammation and immunity. Mutations in human STAT3, especially in the DNA-binding and SH2 domains, are associated with diseases such as autoimmunity, immunodeficiency and cancer. STAT3 regulation is tightly controlled since either inactivation or hyperactivation results in disease. STAT3 activation is stimulated by several cytokines and growth factors, via diverse receptors. For example, IL-6 receptors depend on the tyrosine kinases JAK1 or JAK2, which associate with the cytoplasmic tail of gp130, and results in STAT3 phosphorylation, dimerization, and translocation to the nucleus; this leads to further IL-6 production and up-regulation of anti-apoptotic genes, thus promoting various cellular processes required for cancer progression. Other activators of STAT3 include IL-10, IL-23, and LPS activation of Toll-like receptors TLR4 and TLR9. STAT3 is constitutively activated in numerous cancer types, including over 40% of breast cancers. It has been shown to play a significant role in promoting acute myeloid leukemia (AML) through three mechanisms: promoting proliferation and survival, preventing AML differentiation to functional dendritic cells (DCs), and blocking T-cell function through other pathways. STAT3 also regulates mitochondrion functions, as well as gene expression through epigenetic mechanisms; its activation is induced by overexpression of Bcl-2 via an increase in mitochondrial superoxide. Thus, many of the regulators and functions of JAK-STAT3 in tumors are important therapeutic targets for cancer treatment. 164 matched cddid_all.tbl CDD cd16848 cd16848 341086 STAT4_DBD DNA-binding domain of Signal Transducer and Activator of Transcription 4 (STAT4). This family consists of the DNA-binding domain (DBD) of the STAT4 proteins (Signal Transducer and Activator of Transcription 4, or Signal Transduction And Transcription 4). The DNA binding domain has an Ig-like fold. STAT4 acts as the major signaling transducing STATs in response to interleukin-12 (IL-12) by inducing interferon-gamma (IFNg) , and is a central mediator in generating inflammation during protective immune responses and immune-mediated diseases. STAT4 is a critical regulator of Th1 differentiation and inflammatory disease. It is essential for the differentiation and function of many immune cells, including natural killer cells, dendritic cells, mast cells and T helper cells. STAT4-mediated signaling promotes the production of autoimmune-associated components, which are implicated in the pathogenesis of autoimmune diseases, such as rheumatoid arthritis, systemic lupus erythematosus, systemic sclerosis and psoriasis, making STAT4 a promising therapeutic target for autoimmune diseases. Variations in STAT4 gene are linked to the development of systemic lupus erythematosus (SLE) in humans. STAT4 activation is detected in chronic liver diseases; polymorphism in STAT4 gene has been shown to be associated with the antiviral response in primary biliary cirrhosis (PBC), HCV-associated liver fibrosis, hepatocellular carcinoma (HCC), chronic hepatitis C and in drug-induced liver injury (DILI). STAT4 may inhibit HCC development by modulating HCC cell proliferation. Studies show that increased expression of STAT4 is positively correlated with the depth of invasion in colorectal cancer (CRC) patients, and the growth and invasion of CRC cells are repressed by inhibition of STAT4 expression, making STAT4 a promising therapeutic target for the treatment of CRC. 152 matched cddid_all.tbl CDD cd16849 cd16849 341087 STAT5_DBD DNA-binding domain of Signal Transducer and Activator of Transcription 5 (STAT5). This family consists of the DNA-binding domain (DBD) of the STAT5 proteins (Signal Transducer and Activator of Transcription 5, or Signal Transduction And Transcription 4), which include STAT5A and STAT5B, both of which are >90% identical despite being encoded by separate genes. The DNA binding domain has an Ig-like fold. STAT5A and STAT5B regulate erythropoiesis, lymphopoiesis, and the maintenance of the hematopoietic stem cell population. STAT5A and STAT5B have overlapping and redundant functions; both isoforms can be activated by the same set of cytokines, but some cytokines preferentially activate either STAT5A or STAT5B, e.g. during pregnancy and lactation, STAT5A rather than STAT5B is required for the production of luminal progenitor cells from mammary stem cells and is essential for the differentiation of milk producing alveolar cells during pregnancy. STAT5 has been found to be constitutively phosphorylated in cancer cells, and therefore constantly activated, either by aberrant cell signaling expression or by mutations. It differentially regulates cellular behavior in human mammary carcinoma. Prolactin (PRL) in the prostate gland can induce growth and survival of prostate cancer cells and tissues through the activation of STAT5, its downstream target; PRL expression and STAT5 activation correlates with disease severity. STAT5A and STAT5B are central signaling molecules in leukemias driven by Abelson fusion tyrosine kinases, displaying unique nuclear shuttling mechanisms and having a key role in resistance of leukemic cells against treatment with tyrosine kinase inhibitors (TKI). In addition, STAT5A and STAT5B promote survival of leukemic stem cells. STAT5 is a key transcription factor for IL-3-mediated inhibition of RANKL-induced osteoclastogenesis via the induction of the expression of Id genes. Autosomal recessive STAT5B mutations are associated with severe growth failure, insulin-like growth factor (IGF) deficiency and growth hormone insensitivity (GHI) syndrome. STAT5B deficiency can lead to potentially fatal primary immunodeficiency. 159 matched cddid_all.tbl CDD cd16850 cd16850 341088 STAT6_DBD DNA-binding domain of Signal Transducer and Activator of Transcription 6 (STAT6). This family consists of the DNA-binding domain (DBD) of the STAT6 proteins (Signal Transducer and Activator of Transcription 6, or Signal Transduction And Transcription 6). The DNA binding domain has an Ig-like fold. STAT6 is essential for the functional responses of T helper 2 (Th2) lymphocyte mediated by interleukins IL-4 and IL-13. STAT6 almost exclusively mediates the expression of genes activated by these cytokines; IL-4 signaling regulates the expression of genes involved in immune and anti-inflammatory responses. Abnormal production of IL-4 and IL-13 play important roles in the pathogenesis of asthma where upregulation of the Th2 response mediated by IL-4/IL-13 is a main characteristic. STAT6 has a unique extended transactivation domain, not found in other STATs, through which it recruits p300/CBP and NCoA-1, two coactivators needed for transcriptional activation by IL-4. STAT6 activation is linked to Kaposi's sarcoma-associated herpesvirus (KSHV)-associated cancers such as primary effusion lymphoma, a cancerous proliferation of B cells. Studies show that Meningeal solitary fibrous tumor (SFT) and hemangiopericytoma (HPC) represent a histopathologic spectrum linked by STAT6 nuclear expression and recurrent somatic fusions of the two genes, NGFI-A-binding protein 2 (NAB2) and STAT6 (NAB2-STAT6), similar to their soft tissue counterparts. It is associated with local recurrence and late distance metastasis of brain tumors to extracranial sites. 160 matched cddid_all.tbl CDD cd16851 cd16851 341076 STAT1_CCD Coiled-coil domain of Signal Transducer and Activator of Transcription 1 (STAT1). This family consists of the coiled-coil (alpha) domain of the STAT1 proteins (Signal Transducer and Activator of Transcription 1, or Signal Transduction And Transcription 1). STAT1 plays an essential role in mediating responses to all types of interferons (IFN), transducing signals from cytoplasmic domains of transmembrane receptors into the nucleus where it regulates gene expression. Thus STAT1 is involved in modulating diverse cellular processes, such as antimicrobial activities, cell proliferation and cell death. STAT1 function is crucial in the innate and adaptive arm of immunity and protects from pathogen infections; phosphorylation of a critical tyrosine by Janus kinases (JAKs) leads to its activation and nuclear translocation, while phosphorylation of a critical serine is required for full transcriptional activation upon IFN stimulation and in response to cellular stress. Transcription of protein-encoding genes (including Stat1 itself) as well as expression of microRNAs (miRNAs) is regulated by activated STAT1. Animal studies have shown that STAT1 is generally considered a tumor suppressor but it can also act as a tumor promoter; its functions are not restricted to tumor cells, but extend to parts of the tumor microenvironment such as immune cells, endothelial cells. STAT1 abundance is a reliable marker for good prognosis in selected tumor types, but it can also correlate with disease progression. In head and neck cancer (HNC) patients, upregulation of STAT1-induced HLA class I enhances immunogenicity and clinical response to anti-EGFR mAb cetuximab therapy. In systemic juvenile idiopathic arthritis (sJIA) characterized by systemic inflammation and arthritis, STAT1 phosphorylation downstream of IFNs is impaired. It exerts anti-oncogenic activities through interferon-gamma and interferon-alpha. STAT1 may inhibit hepatocellular carcinoma cell growth by regulating p53-related cell cycling and apoptosis. Studies also show a significant correlation of high STAT1 activity with longer colorectal cancer patient overall survival. Recent studies have shown that STAT1 suppresses mouse mammary gland tumorigenesis by immune regulatory as well as tumor cell-specific functions of STAT1. 176 matched cddid_all.tbl CDD cd16852 cd16852 341077 STAT2_CCD Coiled-coil domain of Signal Transducer and Activator of Transcription 2 (STAT2). This family consists of the coiled-coil (alpha) domain of the STAT2 proteins (Signal Transducer and Activator of Transcription 2, or Signal Transduction And Transcription 2). STAT2 activation is driven predominantly by only two classes of cell surface receptors: Type I and III interferon receptors, making it a unique STAT family of transcription factors. It differs from other STAT family members in that it associates constitutively with a non-STAT protein, the interferon regulatory factor 9 (IRF9). The coiled-coil domain of STAT2 is necessary for binding the carboxyl terminus of IRF9, an association required for the constitutive nuclear import of unphosphorylated STAT2. STAT2 plays a critical role in host defenses against viral infections since type I interferon (IFN-I) response inhibits viral replication, and sets the stage for the development of adaptive immunity; viruses target STAT2 by either inhibiting its expression, blocking its activity, or by targeting it for degradation, thus triggering remarkable divergence in the STAT2 gene across species compared to other STAT family members. STAT2 function is regulated by tyrosine phosphorylation which enables STAT dimerization, and subsequent nuclear translocation and transcriptional activation of IFN stimulated genes. Dengue virus (DENV)-mediated degradation of STAT2 has emerged as an important determinant of DENV pathogenesis and host tropism. This vector-borne flavivirus suppresses IFN1 signaling to replicate and cause disease in vertebrates via proteasome-dependent STAT2 degradation mediated by the nonstructural protein NS5 and its interaction partner UBR4, an E3 ubiquitin ligase. The mechanism of Zika virus (ZIKV) NS5 resembles DENV NS5 but through different mechanism - ZIKV does not require the UBR4 to induce STAT2 degradation. It has also been shown that the STAT2 and STAT4 genes are direct targets for transcription factor Oct-1 protein which is involved in the regulation of expression of genes of the JAK-STAT signaling pathway in the Namalwa Burkitt's lymphoma cell line. 172 matched cddid_all.tbl CDD cd16853 cd16853 341078 STAT3_CCD Coiled-coil domain of Signal Transducer and Activator of Transcription 3 (STAT3). This family consists of the coiled-coil (alpha) domain of the STAT3 proteins (Signal Transducer and Activator of Transcription 3, or Signal Transduction And Transcription 3). STAT3 continuously shuttles between nuclear and cytoplasmic compartments. The coiled-coil domain (CCD) of STAT3 appears to be required for constitutive nuclear localization signals (NLS) function; small deletions within the STAT3 CCD can abrogate nuclear import. Studies show that the CCD binds to the importin-alpha3 in the testis, and importin-alpha6 NLS adapters in most cells. STAT3 plays key roles in vertebrate development and mature tissue function including control of inflammation and immunity. Mutations in human STAT3, especially in the DNA-binding and SH2 domains, are associated with diseases such as autoimmunity, immunodeficiency and cancer. STAT3 regulation is tightly controlled since either inactivation or hyperactivation results in disease. STAT3 activation is stimulated by several cytokines and growth factors, via diverse receptors. For example, IL-6 receptors depend on the tyrosine kinases JAK1 or JAK2, which associate with the cytoplasmic tail of gp130, and results in STAT3 phosphorylation, dimerization, and translocation to the nucleus; this leads to further IL-6 production and up-regulation of anti-apoptotic genes, thus promoting various cellular processes required for cancer progression. Other activators of STAT3 include IL-10, IL-23, and LPS activation of Toll-like receptors TLR4 and TLR9. STAT3 is constitutively activated in numerous cancer types, including over 40% of breast cancers. It has been shown to play a significant role in promoting acute myeloid leukemia (AML) through three mechanisms: promoting proliferation and survival, preventing AML differentiation to functional dendritic cells (DCs), and blocking T-cell function through other pathways. STAT3 also regulates mitochondrion functions, as well as gene expression through epigenetic mechanisms; its activation is induced by overexpression of Bcl-2 via an increase in mitochondrial superoxide. Thus, many of the regulators and functions of JAK-STAT3 in tumors are important therapeutic targets for cancer treatment. 180 matched cddid_all.tbl CDD cd16854 cd16854 341079 STAT4_CCD Coiled-coil domain of Signal Transducer and Activator of Transcription 4 (STAT4). This family consists of the coiled-coil (alpha) domain of the STAT4 proteins (Signal Transducer and Activator of Transcription 4, or Signal Transduction And Transcription 4). STAT4 expression is restricted to spermatozoa, myeloid cells, and T lymphocytes, making it distinct from other STATs. It acts as the major signaling transducing STATs in response to interleukin-12 (IL-12) by inducing interferon-gamma (IFNgamma), and is a central mediator in generating inflammation during protective immune responses and immune-mediated diseases. STAT4 is a critical regulator of Th1 differentiation and inflammatory disease. It is essential for the differentiation and function of many immune cells, including natural killer cells, dendritic cells, mast cells and T helper cells. STAT4-mediated signaling promotes the production of autoimmune-associated components, which are implicated in the pathogenesis of autoimmune diseases, such as rheumatoid arthritis, systemic lupus erythematosus, systemic sclerosis and psoriasis, making STAT4 a promising therapeutic target for autoimmune diseases. Variations in STAT4 gene are linked to the development of systemic lupus erythematosus (SLE) in humans. STAT4 activation is detected in chronic liver diseases; polymorphism in STAT4 gene has been shown to be associated with the antiviral response in primary biliary cirrhosis (PBC), HCV-associated liver fibrosis, hepatocellular carcinoma (HCC), chronic hepatitis C and in drug-induced liver injury (DILI). STAT4 may inhibit HCC development by modulating HCC cell proliferation. Studies show that increased expression of STAT4 is positively correlated with the depth of invasion in colorectal cancer (CRC) patients, and the growth and invasion of CRC cells are repressed by inhibition of STAT4 expression, making STAT4 a promising therapeutic target for the treatment of CRC. 173 matched cddid_all.tbl CDD cd16855 cd16855 341080 STAT5_CCD Coiled-coil domain of Signal Transducer and Activator of Transcription 5 (STAT5). This family consists of the coiled-coil (alpha) domain of the STAT5 proteins (Signal Transducer and Activator of Transcription 5, or Signal Transduction And Transcription 5) which include STAT5A and STAT5B, both of which are >90% identical despite being encoded by separate genes. The coiled-coil domain (CCD) of STAT5A and STAT5B appears to be required for constitutive nuclear localization signals (NLS) function; small deletions within the CCD can abrogate nuclear import. Studies show that the CCD binds to the importin-alpha3 NLS adapter in most cells. STAT5A and STAT5B regulate erythropoiesis, lymphopoiesis, and the maintenance of the hematopoietic stem cell population. STAT5A and STAT5B have overlapping and redundant functions; both isoforms can be activated by the same set of cytokines, but some cytokines preferentially activate either STAT5A or STAT5B, e.g. during pregnancy and lactation, STAT5A rather than STAT5B is required for the production of luminal progenitor cells from mammary stem cells and is essential for the differentiation of milk producing alveolar cells during pregnancy. STAT5 has been found to be constitutively phosphorylated in cancer cells, and therefore constantly activated, either by aberrant cell signaling expression or by mutations. It differentially regulates cellular behavior in human mammary carcinoma. Prolactin (PRL) in the prostate gland can induce growth and survival of prostate cancer cells and tissues through the activation of STAT5, its downstream target; PRL expression and STAT5 activation correlates with disease severity. STAT5A and STAT5B are central signaling molecules in leukemias driven by Abelson fusion tyrosine kinases, displaying unique nuclear shuttling mechanisms and having a key role in resistance of leukemic cells against treatment with tyrosine kinase inhibitors (TKI). In addition, STAT5A and STAT5B promote survival of leukemic stem cells. STAT5 is a key transcription factor for IL-3-mediated inhibition of RANKL-induced osteoclastogenesis via the induction of the expression of Id genes. Autosomal recessive STAT5B mutations are associated with severe growth failure, insulin-like growth factor (IGF) deficiency and growth hormone insensitivity (GHI) syndrome. STAT5B deficiency can lead to potentially fatal primary immunodeficiency. 194 matched cddid_all.tbl CDD cd16856 cd16856 341081 STAT6_CCD Coiled-coil domain of Signal Transducer and Activator of Transcription 6 (STAT6). This family consists of the coiled-coil (alpha) domain of the STAT6 proteins (Signal Transducer and Activator of Transcription 6, or Signal Transduction And Transcription 6). SImilar to STAT3 and STAT5. the coiled-coil domain (CCD) of STAT6 is required for constitutive nuclear localization signals (NLS) function; small deletions within the CCD can abrogate nuclear import. Studies show that the CCD binds to the importin-alpha3 NLS adapter in most cells.STAT6 is essential for the functional responses of T helper 2 (Th2) lymphocyte mediated by interleukins IL-4 and IL-13. STAT6 almost exclusively mediates the expression of genes activated by these cytokines; IL-4 signaling regulates the expression of genes involved in immune and anti-inflammatory responses. Abnormal production of IL-4 and IL-13 play important roles in the pathogenesis of asthma where upregulation of the Th2 response mediated by IL-4/IL-13 is a main characteristic. STAT6 has a unique extended transactivation domain, not found in other STATs, through which it recruits p300/CBP and NCoA-1, two coactivators needed for transcriptional activation by IL-4. STAT6 activation is linked to Kaposi's sarcoma-associated herpesvirus (KSHV)-associated cancers such as primary effusion lymphoma, a cancerous proliferation of B cells. Studies show that Meningeal solitary fibrous tumor (SFT) and hemangiopericytoma (HPC) represent a histopathologic spectrum linked by STAT6 nuclear expression and recurrent somatic fusions of the two genes, NGFI-A-binding protein 2 (NAB2) and STAT6 (NAB2-STAT6), similar to their soft tissue counterparts. It is associated with local recurrence and late distance metastasis of brain tumors to extracranial sites. 167 matched cddid_all.tbl CDD cd16857 cd16857 341090 ING_ING1_2 Inhibitor of growth (ING) domain of inhibitor of growth protein ING1, ING2, and similar proteins. ING1 is an epigenetic regulator and a type II tumor suppressor that impacts cell growth, aging, apoptosis, and DNA repair, by affecting chromatin conformation and gene expression. It acts as a reader of the active chromatin mark, the trimethylation of histone H3 lysine 4 (H3K4me3). It binds and directs growth arrest and DNA damage inducible protein 45 a (Gadd45a) to target sites, thus linking the histone code with DNA demethylation. It interacts with the proliferating cell nuclear antigen (PCNA) via the PCNA-interacting protein (PIP) domain in a UV-inducible manner. It also interacts with a PCNA-interacting protein, p15 (PAF). Moreover, ING1 associates with members of the 14-3-3 family, which is necessary for cytoplasmic relocalization. Endogenous ING1 protein specifically interacts with the pro-apoptotic BCL2 family member BAX and colocalizes with BAX in a UV-inducible manner. It stabilizes the p53 tumor suppressor by inhibiting polyubiquitination of multi-monoubiquitinated forms via interaction with and colocalization of the herpesvirus-associated ubiquitin-specific protease (HAUSP)-deubiquitinase with p53. It is also involved in trichostatin A-induced apoptosis and caspase 3 signaling in p53-deficient glioblastoma cells. In addition, tyrosine kinase Src can bind and phosphorylate ING1 and further regulates its activity. ING2, also termed inhibitor of growth 1-like protein (ING1Lp), or p32, or p33ING2, is a core component of a multi-factor chromatin-modifying complex containing the transcriptional co-repressor SIN3A and histone deacetylase 1 (HDAC1). It has been implicated in the control of cell cycle, in genome stability, and in muscle differentiation. ING2 independently interacts with H3K4me3 (Histone H3 trimethylated on lysine 4) and PtdIns(5)P, and modulates crosstalk between lysine methylation and lysine acetylation on histone proteins through association with chromatin in the presence of DNA damage. It collaborates with SnoN to mediate transforming growth factor (TGF)-beta-induced Smad-dependent transcription and cellular responses. It is upregulated in colon cancer and increases invasion by enhanced MMP13 expression. It also acts as a cofactor of p300 for p53 acetylation and plays a positive regulatory role during p53-mediated replicative senescence. Both ING1 and ING2 contain an N-terminal leucine zipper-like (LZL) motif-containing ING domain, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain. 89 matched cddid_all.tbl CDD cd16858 cd16858 341091 ING_ING3_Yng2p Inhibitor of growth (ING) domain of inhibitor of growth protein 3 (ING3), Yng2p and similar proteins. ING3, also termed p47ING3, is a member of the inhibitor of growth (ING) family of type II tumor suppressors. It is ubiquitously expressed and has been implicated in transcription modulation, cell cycle control, and the induction of apoptosis. It is an important subunit of human NuA4 histone acetyltransferase complex, which regulates the acetylation of histones H2A and H4. Moreover, ING3 promotes ultraviolet (UV)-induced apoptosis through the Fas/caspase-8-dependent pathway in melanoma cells. It physically interacts with subunits of E3 ligase Skp1-Cullin-F-boxprotein complex (SCF complex) and is degraded by the SCF (F-box protein S-phase kinase-associated protein 2, Skp2)-mediated ubiquitin-proteasome system. It also acts as a suppression factor during tumorigenesis and progression of hepatocellular carcinoma (HCC). Yeast chromatin modification-related protein Yng2p, also termed ESA1-associated factor 4 or ING1 homolog 2, is a subunit of the NuA4 histone acetyltransferase (HAT) complex. It plays a critical role in intra-S-phase DNA damage response. Members of this family contain an N-terminal leucine zipper-like (LZL) motif-containing ING domain, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain. 92 matched cddid_all.tbl CDD cd16859 cd16859 341092 ING_ING4_5 Inhibitor of growth (ING) domain of inhibitor of growth protein ING4, ING5, and similar proteins. ING4, also termed p29ING4, and ING5, also termed p28ING5, belong to the inhibitor of growth (ING) family of type II tumor suppressors. ING4 acts as an E3 ubiquitin ligase to induce ubiquitination of the p65 subunit of NF-kappaB and inhibit the transactivation of NF-kappaB target genes. It also induces apoptosis through a p53 dependent pathway, including increasing p53 acetylation, inhibiting Mdm2-mediated degradation of p53, and enhancing the expression of p53 responsive genes both at the transcriptional and post-translational levels. Moreover, ING4 can inhibit the translation of proto-oncogene MYC by interacting with AUF1. It also regulates other transcription factors, such as hypoxia-inducible factor (HIF). ING5 is a Tip60 cofactor that acetylates p53 at K120 and subsequently activates the expression of p53-dependent apoptotic genes in response to DNA damage. Aberrant ING5 expression may contribute to pathogenesis, growth, and invasion of gastric carcinomas and colorectal cancer. ING5 can physically interact with p300 and p53 in vivo, and its overexpression induces apoptosis in colorectal cancer cells. It also associates with Inhibitor of cyclin A1 (INCA1) and functions as a growth suppressor with suppressed expression in Acute Myeloid Leukemia (AML). Moreover, ING5 translocation from the nucleus to the cytoplasm might be a critical event for carcinogenesis and tumor progression in human head and neck squamous cell carcinoma. Both ING4 and ING5 contain an N-terminal leucine zipper-like (LZL) motif-containing ING domain, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain. They associate with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further direct the MOZ/MORF and HBO1 complexes to chromatin. 91 matched cddid_all.tbl CDD cd16860 cd16860 341093 ING_ING1 Inhibitor of growth (ING) domain of inhibitor of growth protein 1 (ING1). ING1 is an epigenetic regulator and a type II tumor suppressor that impacts cell growth, aging, apoptosis, and DNA repair, by affecting chromatin conformation and gene expression. It acts as a reader of the active chromatin mark, the trimethylation of histone H3 lysine 4 (H3K4me3). It binds and directs growth arrest and DNA damage inducible protein 45 a (Gadd45a) to target sites, thus linking the histone code with DNA demethylation. It interacts with the proliferating cell nuclear antigen (PCNA) via the PCNA-interacting protein (PIP) domain in a UV-inducible manner. It also interacts with a PCNA-interacting protein, p15 (PAF). Moreover, ING1 associates with members of the 14-3-3 family, which is necessary for the cytoplasmic relocalization. Endogenous ING1 protein specifically interacts with the pro-apoptotic BCL2 family member BAX and colocalizes with BAX in a UV-inducible manner. It stabilizes the p53 tumor suppressor by inhibiting polyubiquitination of multi-monoubiquitinated forms via interaction with and colocalization of the herpesvirus-associated ubiquitin-specific protease (HAUSP)-deubiquitinase with p53. It is also involved in trichostatin A-induced apoptosis and caspase 3 signaling in p53-deficient glioblastoma cells. In addition, tyrosine kinase Src can bind phosphorylate ING1 and further regulates its activity. ING1 contains an N-terminal leucine zipper-like (LZL) motif-containing ING domain, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain. 88 matched cddid_all.tbl CDD cd16861 cd16861 341094 ING_ING2 Inhibitor of growth (ING) domain of inhibitor of growth protein 2 (ING2). ING2, also termed inhibitor of growth 1-like protein (ING1Lp), or p32, or p33ING2, is a core component of a multi-factor chromatin-modifying complex containing the transcriptional co-repressor SIN3A and histone deacetylase 1 (HDAC1). It has been implicated in the control of cell cycle, in genome stability, and in muscle differentiation. ING2 independently interacts with H3K4me3 (Histone H3 trimethylated on lysine 4) and PtdIns(5)P, and modulates crosstalk between lysine methylation and lysine acetylation on histone proteins through association with chromatin in the presence of DNA damage. It collaborates with SnoN to mediate transforming growth factor (TGF)-beta-induced Smad-dependent transcription and cellular responses. It is upregulated in colon cancer and increases invasion by enhanced MMP13 expression. It also acts as a cofactor of p300 for p53 acetylation and plays a positive regulatory role during p53-mediated replicative senescence. ING2 contains an N-terminal leucine zipper-like (LZL) motif-containing ING domain, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain. 88 matched cddid_all.tbl CDD cd16862 cd16862 341095 ING_ING4 Inhibitor of growth (ING) domain of inhibitor of growth protein 4 (ING4). ING4, also termed p29ING4, is a member of the inhibitor of growth (ING) family of type II tumor suppressors. It acts as an E3 ubiquitin ligase to induce ubiquitination of the p65 subunit of NF-kappaB and inhibit the transactivation of NF-kappaB target genes. It also induces apoptosis through a p53 dependent pathway, including increasing p53 acetylation, inhibiting Mdm2-mediated degradation of p53 and enhancing the expression of p53 responsive genes both at the transcriptional and post-translational levels. Moreover, ING4 can inhibit the translation of proto-oncogene MYC by interacting with AUF1. It also regulates other transcription factors, such as hypoxia-inducible factor (HIF). In addition, ING4 associates with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further directs the MOZ/MORF and HBO1 complexes to chromatin. ING4 contains an N-terminal leucine zipper-like (LZL) motif-containing ING domain, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain. 94 matched cddid_all.tbl CDD cd16863 cd16863 341096 ING_ING5 Inhibitor of growth (ING) domain of inhibitor of growth protein 5 (ING5). ING5, also termed p28ING5, is a member of the inhibitor of growth (ING) family of type II tumor suppressors. It acts as a Tip60 cofactor that acetylates p53 at K120 and subsequently activates the expression of p53-dependent apoptotic genes in response to DNA damage. Aberrant ING5 expression may contribute to pathogenesis, growth, and invasion of gastric carcinomas and colorectal cancer. ING5 can physically interact with p300 and p53 in vivo, and its overexpression induces apoptosis in colorectal cancer cells. It also associates with Inhibitor of cyclin A1 (INCA1) and functions as a growth suppressor with suppressed expression in Acute Myeloid Leukemia (AML). Moreover, ING5 translocation from the nucleus to the cytoplasm might be a critical event for carcinogenesis and tumor progression in human head and neck squamous cell carcinoma. In addition, ING5 associates with histone acetyltransferase (HAT) complexes containing MOZ (monocytic leukemia zinc finger protein)/MORF (MOZ-related factor) and HBO1, and further directs the MOZ/MORF and HBO1 complexes to chromatin. ING5 contains an N-terminal leucine zipper-like (LZL) motif-containing ING domain, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain. 93 matched cddid_all.tbl CDD cd16864 cd16864 350628 ARID_JARID ARID/BRIGHT DNA binding domain of JARID proteins. The JARID subfamily within the JmjC protein family includes lysine-specific demethylase KDM5A, KDM5B, KDM5C, KDM5D and a Drosophila homolog, protein little imaginal discs (Lid). KDM5A was originally identified as a retinoblastoma protein (Rb)-binding partner and its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5B has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. Both KDM5A and KDM5B function as trimethylated histone H3 lysine 4 (H3K4me3) demethylases. KDM5C is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 and H3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. The family also includes Drosophila melanogaster protein little imaginal discs (Lid) that functions as a JmjC-dependent trimethyl histone H3K4 (H3K4me3) demethylase, which is required for dMyc-induced cell growth. It positively regulates Hox gene expression in S2 cells. Members of this subfamily contain the catalytic JmjC domain, JmjN, the AT-rich domain interacting domain (ARID)/BRIGHT domain, a C5HC2 zinc finger, as well as two or three plant homeodomain (PHD) fingers. 87 matched cddid_all.tbl CDD cd16865 cd16865 350629 ARID_ARID1A-like ARID/BRIGHT DNA binding domain found in AT-rich interactive domain-containing proteins ARID1A, ARID1B and similar proteins. This subfamily contains ARID1A and its paralog ARID1B. They are mutually exclusive components of human SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling protein complexes, but display different functions in development and cell-cycle control. SWI/SNF complexes containing ARID1A have an antiproliferative function, whereas the one harboring ARID1B shows a pro-proliferative function. ARID1A functions as an important tumor suppressor in various tumor types. It has been implicated in cell-cycle arrest, as well as in the interactions with p53 and BRG1/BRM and with topoisomerase II alpha. ARID1B may be considered as a potential therapeutic target for ARID1A-mutant cancers. Moreover, mutations in the ARID1B gene cause Coffin-Siris syndrome, exhibiting developmental defects, and haplo-insufficiency of ARID1B is a frequent cause of intellectual disability. Mutations in the ARID1B gene also have been found in many cancers. Both ARID1A and ARID1B contain an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which binds DNA in a non-sequence-specific manner. 93 matched cddid_all.tbl CDD cd16866 cd16866 350630 ARID_ARID2 ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 2 (ARID2) and similar proteins. ARID2, also called BRG1-associated factor 200 (BAF200) or zinc finger protein with activation potential (Zipzap/p200), is a novel serum response factor (SRF)-binding protein with multiple conserved domains, including an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), RFX DNA-binding domain, a glutamine-rich domain, and two C2H2 zinc fingers. It binds DNA without sequence specificity. ARID2 is an intrinsic subunit of PBAF (SWI/SNF-B) remodeling complex, which needs ARID2 to play an essential role in promoting osteoblast differentiation, maintaining cellular identity and activating tissue-specific gene expression. Moreover, ARID2 may function as a tumor suppressor in many cancers. It may also serve as a transcription co-activator for the regulation of cardiac gene expression, and is required for heart morphogenesis and coronary artery development. 88 matched cddid_all.tbl CDD cd16867 cd16867 350631 ARID_ARID3 "ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID3A, ARID3B, ARID3C, dead ringer (Dri) from Drosophila melanogaster, and similar proteins. The ARID3 subfamily includes AT-rich interactive domain (ARID, also known as BRIGHT)-containing proteins ARID3A, ARID3B and ARID3C, which are the most direct mammalian counterparts of the Drosophila ""dead ringer"" protein Dri. They consist of an acidic N-terminal region of unknown function, the central ARID matrix association (or attachment) region (MAR)-DNA binding domain, a SUMO-I conjugation (SUMO) motif, and a multifunctional homomerization/nuclear export REKLES domain in the C-terminal third of the molecule. The ARID domain in this subfamily has been described as the ""extended"" or e-ARID due to additional conserved sequences at both the N and C termini of the core ARID region. The REKLES domain is found only in the ARID3 subfamily. It has co-evolved with and regulates functional properties of the ARID DNA-binding domain." 118 matched cddid_all.tbl CDD cd16868 cd16868 350632 ARID_ARID4 ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID4A, ARID4B and similar proteins. This subfamily contains ARID4A and its paralog ARID4B, both of which are retinoblastoma (Rb)-binding proteins that function as coactivators to enhance the androgen receptor (AR) and Rb transcriptional activity, and play important roles in the AR and Rb pathways to control male fertility. They also act as the leukemia and tumor suppressors involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndrome. Moreover, they associate with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through the interaction with each other, as well as with the breast cancer associated tumor suppressor ING1 and the breast cancer metastasis suppressor BRMS1. Both ARID4A and ARID4B contain a Tudor domain, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. 87 matched cddid_all.tbl CDD cd16869 cd16869 350633 ARID_ARID5 ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing proteins ARID5A, ARID5B, and similar proteins. This subfamily contains ARID5A and its paralog ARID5B. ARID5A, also called modulator recognition factor 1 (MRF-1), is an estrogen receptor alpha (ER alpha)-interacting protein that is expressed abundantly in cardiovascular tissues and suppresses ER alpha-induced transactivation. It also plays an important role in the promotion of inflammatory processes and autoimmune diseases. ARID5B, also called MRF1-like protein or modulator recognition factor 2 (MRF-2), is a DNA-binding protein that directly interacts with plant homeodomain (PHD) finger 2 (PHF2) to form a protein kinase A (PKA)-dependent PHF2-ARID5B histone H3K9Me2 demethylase complex. It also functions as a transcriptional co-regulator for the transcription factor sex determining region Y (SRY)-box protein 9 (Sox9) and promotes chondrogenesis through histone modification. Moreover, ARID5B is highly expressed in the cardiovascular system and may play essential roles in the phenotypic change of smooth muscle cells (SMCs) through its regulation of SMC differentiation. Both ARID5A and ARID5B contain an AT-rich DNA-interacting domain (ARID, also known as BRIGHT). 87 matched cddid_all.tbl CDD cd16870 cd16870 350634 ARID_JARD2 ARID/BRIGHT DNA binding domain of Jumonji/ARID domain-containing protein 2 (JARID2) and similar proteins. JARID2, also called protein Jumonji, is a DNA-binding protein that contains both the Jumonji C (JmjC) domain and AT-rich DNA-interacting domain (ARID, also known as BRIGHT). It is an interacting component of Polycomb repressive complex-2 (PRC2) that catalyzes methylation of lysine 27 of histone H3 (H3K27) and regulates important gene expression patterns during development. It exhibits nucleosome-binding activity that contributes to PRC2 stimulation. However, unlike other JmjC domain-containing proteins, JARID2 is catalytically inactive due to the lack of conserved residues essential for histone demethylase activity. JARID2 is also involved in transforming growth factor-beta (TGF-beta)-induced epithelial-mesenchymal transition (EMT) of lung and colon cancer cell lines through the modulation of histone H3K27 methylation. Moreover, JARID2 is a part of GLP- and G9a-containing protein complex that promotes lysine 9 on histone H3 (H3K9) methylation on the cyclin D1 promoter and silences the expression of cyclin D1 and other cell cycle genes. It functions as a transcriptional repressor that plays critical roles in embryonic development including heart development in mice, and regulates cardiomyocyte proliferation via interaction with retinoblastoma protein (Rb), one of the master regulatory genes of the cell cycle. Furthermore, JARID2 acts as a transcriptional repressor of target genes, including Notch1. It directly binds to SETDB1 (SET domain, bifurcated 1) to form a complex that plays an important role in a novel process involving the modification of H3K9 methylation during heart development. Meanwhile, JARID2 is a key transcriptional repressor that plays a role in invariant natural killer T (iNKT) cell maturation. It regulates promyelocytic leukemia zinc finger (PLZF) expression by linking T-cell receptor (TCR) signaling to H3K9me3. JARID2 polymorphisms are associated with non-syndromic orofacial clefts (NSOC) susceptibility. 112 matched cddid_all.tbl CDD cd16871 cd16871 350635 ARID_Swi1p-like ARID/BRIGHT DNA binding domain of yeast SWI/SNF chromatin-remodeling complex subunit Swi1p and similar proteins. Saccharomyces cerevisiae Swi1p, also called SWI/SNF chromatin-remodeling complex subunit SWI1, regulatory protein GAM3, or transcription regulatory protein ADR6, is a transcription regulatory protein that is a subunit of the SWI/SNF complex, which plays critical roles in the regulation of gene transcription and expression. It can exist as a prion, [SWI(+)], which demonstrates a link between prionogenesis and global transcriptional regulation. Swi1p contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT) that binds DNA nonspecifically. This subfamily also includes Schizosaccharomyces pombe SWI/SNF chromatin-remodeling complex subunit sol1 (sol1p, also known as switch one-like protein). sol1p is a homolog of S. cerevisiae Swi1p and is also a part of SWI/SNF chromatin-remodeling complex. 90 matched cddid_all.tbl CDD cd16872 cd16872 350636 ARID_HMGB9-like ARID/BRIGHT DNA binding domain of Arabidopsis thaliana high mobility group B proteins HMGB9, HMGB10, HMGB11, HMGB15 and similar proteins. This subfamily includes a group of conserved plant DNA-binding proteins, including HMGB9 (or ARID-HMG1), HMGB10 (or ARID-HMG2), HMGB11, and HMGB15. They have been termed ARID-HMG proteins, due to containing two DNA-binding domains, an N-terminal AT-rich DNA-interacting domain (ARID, also known as BRIGHT), and a C-terminal high mobility group (HMG)-box domain. They are widely expressed in Arabidopsis and localize primarily to the nucleus. HMGB9/ARID-HMG1 binds specifically to A/T-rich DNA. HMGB15 is a transcription factor predominantly expressed in mature pollen grains and pollen tubes. It may work in the form of a homodimer, or interact with HMGB9, HMGB10 and HMGB11 to form heteromultimers in plant cells. HMGB15 is required for pollen tube growth in Arabidopsis and is involved in transcriptional regulation through the interaction with AGL66 and AGL104. 86 matched cddid_all.tbl CDD cd16873 cd16873 350637 ARID_KDM5A ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5A (KDM5A). KDM5A, also called histone demethylase JARID1A, Jumonji/ARID domain-containing protein 1A, or Retinoblastoma-binding protein 2 (RBBP-2 or RBP2), was originally identified as a retinoblastoma protein (Rb)-binding partner; its inactivation may be important for Rb to promote differentiation. It is involved in transcription through interacting with TBP, p107, nuclear receptors, Myc, Sin3/HDAC, Mad1, RBP-J, CLOCK and BMAL1. KDM5A functions as the trimethylated histone H3 lysine 4 (H3K4me3) demethylase that belongs to the JARID subfamily within the JmjC proteins. It also displays DNA-binding activities that can recognize the specific DNA sequence CCGCCC. KDM5A contains the catalytic JmjC domain, a JmjN domain, an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a C5HC2 zinc finger, as well as three plant homeodomain (PHD) fingers. 92 matched cddid_all.tbl CDD cd16874 cd16874 350638 ARID_KDM5B ARID/BRIGHT DNA binding domain of lysine-specific demethylase 5B (KDM5B). KDM5B, also called cancer/testis antigen 31 (CT31), histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), PLU-1, or retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible earlygene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, a JmjN domain, an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a C5HC2 zinc finger, as well as three plant homeodomain (PHD) fingers. 90 matched cddid_all.tbl CDD cd16875 cd16875 350639 ARID_KDM5C_5D ARID/BRIGHT DNA binding domain of lysine-specific demethylase KDM5C and KDM5D. This group includes KDM5C and KDM5D, both of which belong to the JARID subfamily within the JmjC proteins. KDM5C, also called histone demethylase JARID1C, Jumonji/ARID domain-containing protein 1C, protein SmcX, or protein Xe169, is a H3K4 trimethyl-histone demethylase that catalyzes demethylation of H3K4me3 and H3K4me2 to H3K4me1. It plays a role in neuronal survival and dendrite development. KDM5C defects are associated with X-linked mental retardation (XLMR). KDM5D, also called histocompatibility Y antigen (H-Y), histone demethylase JARID1D, Jumonji/ARID domain-containing protein 1D, or protein SmcY, is a male-specific antigen that shows a demethylase activity specific for di- and tri-methylated histone H3K4 (H3K4me3 and H3K4me2), and has a male-specific function as a histone H3K4 demethylase by recruiting a meiosis-regulatory protein, MSH5, to condensed DNA. KDM5D directly interacts with a polycomb-like protein Ring6a/MBLR, and plays a role in regulation of transcriptional initiation through H3K4 demethylation. Both KDM5C and KDM5D contain the catalytic JmjC domain, a JmjN domain, an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a C5HC2 zinc finger, as well as two plant homeodomain (PHD) fingers. 92 matched cddid_all.tbl CDD cd16876 cd16876 350640 ARID_ARID1A ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1A (ARID1A) and similar proteins. ARID1A, also called B120, BRG1-associated factor 250a (BAF250A), Osa homolog 1(OSA1), SWI-like protein, SWI/SNF complex protein p270, or SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily F member 1 (SWI1), has been identified as a novel tumor suppressor in various tumor types. It interacts with BRG1 adenosine triphosphatase to form a SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeling protein complex, which plays a critical role in transcriptional control and gene expression. ARID1A contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), and Eld/Osa homology domains (EHD) 1 and 2 within the C-terminus. The ARID in ARID1A binds nonspecific DNA in general and plays an important role in targeting SWI/SNF to chromatin. The EHD1 may be capable of mediating an intramolecular association with EHD2, and/or an intermolecular association resulting in homo- or hetero-dimerization. The EHD2 binds Swi2/Brahma homologue Brahma-related gene 1 (BRG1, also known as Snf2b), a human homologue of yeast Swi2. 93 matched cddid_all.tbl CDD cd16877 cd16877 350641 ARID_ARID1B ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1B (ARID1B) and similar proteins. ARID1B, also called BRG1-associated factor 250b (BAF250B), BRG1-binding protein ELD/OSA1, Osa homolog 2 (Osa2), or p250R, is the largest subunit of ATP-dependent SWItch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex, which plays a critical role in transcriptional control and gene expression. ARID1B exhibits tumour-suppressor activities in pancreatic cancer cell lines. Mutations in the ARID1B gene cause Coffin-Siris syndrome, exhibiting developmental defects, and haplo-insufficiency of ARID1B is a frequent cause of intellectual disability. Moreover, mutations in the ARID1B gene have been found in many cancers. ARID1B contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which binds DNA in a non-sequence-specific manner similar to ARID1A. 93 matched cddid_all.tbl CDD cd16878 cd16878 350642 ARID_ARID3A ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3A (ARID3A) and similar proteins. ARID3A, also called B-cell regulator of IgH transcription (Bright), dead ringer-like protein 1 (Dril1), or E2F-binding protein 1 (E2FBP1), is an ubiquitously expressed DNA-binding protein that has been implicated in embryonic patterning, cell lineage gene regulation, and cell cycle control, chromatin remodeling and transcriptional regulation. It was originally identified as a B cell-specific trans-activator of immunoglobulin heavy-chain (IgH) transcription, which increases immunoglobulin transcription in antigen-activated B cells and plays regulatory roles in hematopoiesis. It also functions as an E2F transcription regulator, inducing promyelocytic leukemia protein (PML) reduction and suppressing the formation of PML-nuclear bodies. It antagonizes the p16(INK4A)-Rb tumor suppressor machinery by regulating PML stability. ARID3A transcriptional activity can be modulated by SUMO (Small Ubiquitin-related Modifier) modification through the interaction with the SUMO-conjugating enzyme Ubc9. ARID3A also plays an important role in marginal zone B lymphocyte development and autoantibody production. Furthermore, ARID3A is a direct p53 target gene. It controls cell growth in a p53-dependent manner. ARID3A contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a SUMO-I conjugation (SUMO) motif and a multifunctional homomerization/nuclear export REKLES domain, which consists of two subdomains: a modestly conserved N-terminal REKLES alpha and a highly conserved (among ARID3 orthologous proteins) C-terminal REKLES beta. 133 matched cddid_all.tbl CDD cd16879 cd16879 350643 ARID_ARID3B ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3B (ARID3B) and similar proteins. ARID3B, also called Bright and dead ringer protein, or Bright-Dri-like protein (Bdp), is a DNA binding protein involved in cellular immortalization, epithelial-mesenchymal transition (EMT), and tumorigenesis. Its expression is differentially regulated in normal and malignant tissues. It is required for heart development by regulating the motility and differentiation of heart progenitors. ARID3B is overexpressed in neuroblastoma and ovarian cancer. It acts as a novel target with roles in cell motility in breast cancer cells, promotes migration of mouse embryo fibroblasts (MEFs) and breast cancer cells, and induces tumor necrosis factor alpha (TNFalpha)-mediated apoptosis. ARID3B contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a SUMO-I conjugation (SUMO) motif and a multifunctional homomerization/nuclear export REKLES domain, which consists of two subdomains: a modestly conserved N-terminal REKLES alpha and a highly conserved (among ARID3 orthologous proteins) C-terminal REKLES beta. 126 matched cddid_all.tbl CDD cd16880 cd16880 350644 ARID_ARID3C ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 3C (ARID3C) and similar proteins. ARID3C, also called Brightlike, is a new ARID3 family transcription factor that co-activates ARID3A-mediated immunoglobulin gene transcription. It also functions as a potential regulator of early events in B cell antigen receptor (BCR) signaling. ARID3C contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a SUMO-I conjugation (SUMO) motif and a multifunctional homomerization/nuclear export REKLES domain, which consists of two subdomains: a modestly conserved N-terminal REKLES alpha and a highly conserved (among ARID3 orthologous proteins) C-terminal REKLES beta. 127 matched cddid_all.tbl CDD cd16881 cd16881 350645 ARID_Dri-like "ARID/BRIGHT DNA binding domain of dead ringer (Dri) from Drosophila melanogaster and similar proteins. Dri, also termed retained (retn), is a nuclear protein with a sequence-specific DNA-binding domain termed AT-rich DNA-interacting domain (ARID, also known as BRIGHT). It is a founding member of the ARID family. Sequence comparison shows that DRI belongs to the ""extended"" or e-ARID subfamily, which exhibits an extended region of similarity either side of the ARID. Dri plays an important role in embryogenesis. It functions as an essential transcription factor involved in aspects of dorsal/ventral and anterior/posterior axis patterning, as well as myogenesis and hindgut development." 125 matched cddid_all.tbl CDD cd16882 cd16882 350646 ARID_ARID4A ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins. ARID4A, also called retinoblastoma-binding protein 1 (RBBP1, or RBP1), is a leukemia and tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndrome. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through the interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4B (also known as RBP1L1). ARID4A specifically interacts with retinoblastoma protein (pRb) and shows both HDAC-dependent and -independent repression activities. It is also involved in the pocket domain of pRb-mediated repression of E2F-dependent transcription and cellular proliferation. Moreover, it acts as a Runx2 coactivator and is involved in the regulation of osteoblastic differentiation in Runx2-osterix transcriptional cascade. ARID4A contains a Tudor domain, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The ARID and R2 domains are responsible for the repression activities. The Tudor, PWWP, and chromobarrel domains are all Royal Family domains, but only chromobarrel domain of ARID4A is responsible for recognizing both dsDNA and methylated histone tails, particularly H4K20me3, in chromatin remodeling and epigenetic regulation. 87 matched cddid_all.tbl CDD cd16883 cd16883 350647 ARID_ARID4B ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins. ARID4B, also called 180 kDa Sin3-associated polypeptide (p180), breast cancer-associated antigen BRCAA1, histone deacetylase complex subunit SAP180, or retinoblastoma-binding protein 1-like 1 (RBP1L1, or RBBP1L1), is a tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndrome. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through the interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4A ( also known as RBP1). ARID4B plays a causative role in metastatic progression of breast cancer. It may also be associated with regulating cell cycle. ARID4B contains a Tudor domain, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. 92 matched cddid_all.tbl CDD cd16884 cd16884 350648 ARID_ARID5A ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5A (ARID5A) and similar proteins. ARID5A, also called modulator recognition factor 1 (MRF-1), is an estrogen receptor alpha (ER alpha)-interacting protein that is expressed abundantly in cardiovascular tissues and suppresses ER alpha-induced transactivation. It also associates with thyroid receptor alpha (TR alpha) and retinoid X receptor alpha (RXR alpha) in a ligand-dependent manner, and with ER beta, androgen receptor (AR), and the retinoic acid receptor (RAR) in a ligand-independent manner. ARID5A functions as a negative regulator of RORgamma-induced Th17 cell differentiation and may be involved in the pathogenesis of rheumatoid arthritis (RA). Moreover, it is an important transcriptional partner of the transcription factor sex determining region Y (SRY)-box protein 9 (Sox9) in stimulation of chondrocyte-specific transcription. Meanwhile, ARID5A plays an important role in promotion of inflammatory processes and autoimmune diseases. It works as a unique RNA binding protein, which stabilizes interleukin-6 (IL-6) but not tumor necrosis factor-alpha (TNF-alpha) mRNA through binding to the 3' untranslated region (UTR) of IL-6 mRNA, and inhibits the destabilizing effect of regnase-1 on IL-6 mRNA. ARID5A contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT). 87 matched cddid_all.tbl CDD cd16885 cd16885 350649 ARID_ARID5B ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5B (ARID5B) and similar proteins. ARID5B, also called MRF1-like protein or modulator recognition factor 2 (MRF-2), is a DNA-binding protein that directly interacts with plant homeodomain (PHD) finger 2 (PHF2) to form a protein kinase A (PKA)-dependent PHF2-ARID5B histone H3K9Me2 demethylase complex, which is a signal-sensing modulator of histone methylation and gene transcription. It also functions as a transcriptional co-regulator for the transcription factor sex determining region Y (SRY)-box protein 9 (Sox9) and promotes chondrogenesis through histone modification. Moreover, ARID5B is highly expressed in the cardiovascular system and may play essential roles in the phenotypic change of smooth muscle cells (SMCs) through its regulation of SMC differentiation. Its polymorphism has been associated with risk for pediatric acute lymphoblastic leukemia (ALL). ARID5B contains an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), which can bind both the major and minor grooves of its target sequences. 95 matched cddid_all.tbl CDD cd16887 cd16887 341123 YEATS YEATS domain family, chromatin reader proteins. The YEATS family is named for several family members: 'YNK7', 'ENL', 'AF-9', and 'TFIIF small subunit', and also contains the GAS41 protein, YEATS2, Drosophila D12, and others. DNA regulation by chromatin through histone post-translational modification and other mechanisms involves complexes with write, eraser and reader functions. YEATS domains act as readers of the chromatin state and stimulates transcriptional activity through preferential interactions with crotonylated lysines on histones. 120 matched cddid_all.tbl CDD cd16888 cd16888 381609 lyz_G-like_1 lysozyme G-like protein 1. Eukaryotic goose-type or G-type lysozymes (goose egg-white lysozyme; GEWL) catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc). Mammals have two lysozyme G-like proteins, and this family corresponds to human and mouse lysozyme G-like protein 1. In humans and some other species, the canonical catalytic glutamate residue is absent, suggesting a loss of muramidase activity. 160 matched cddid_all.tbl CDD cd16889 cd16889 381610 chitinase-like chitinase-like domain. This family includes proteins such as chitinases, chitosanase, pesticin, and endolysin, which are involved in the degradation of 1,4-N-acetyl D-glucosamine linkages in chitin polymers and related activities. Chitinases are enzymes that catalyze the hydrolysis of the beta-1,4-N-acetyl-D-glucosamine linkages in chitin polymers. Chitosanase enzymes hydrolyze chitosan, a biopolymer of beta (1,4)-linked-D-glucosamine (GlcN) residues produced by partial or full deacetylation of chitin. Pesticin (Pst) is a anti-bacterial toxin produced by Yersinia pestis that acts through uptake by the target related bacteria and the hydrolysis of peptidoglycan in the periplasm. The dsDNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell walls. Similarly, bacteria produce autolysins to facilitate the biosynthesis of its cell wall heteropolymer peptidoglycan and cell division. 105 matched cddid_all.tbl CDD cd16890 cd16890 381611 lyz_i I-type lysozyme. Invertebrate type (I-type) lysozyme, initially identified in starfish and marine bivalves, are found in various invertebrate phyla and are apparently ubiquitous in insects. Lysozymes cleave the beta-(1,4)-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine in peptidoglycan, the major bacterial cell wall polymer. I-type enzymes share structural similarity and the conserved glutamate catalytic residue of the lysozyme family. 117 matched cddid_all.tbl CDD cd16891 cd16891 381612 CwlT-like "CwlT-like N-terminal lysozyme domain and similar domains. CwlT is a bifunctional cell wall hydrolase containing an N-terminal lysozyme domain and a C-terminal NlpC/P60 endopeptidase domain (gamma-d-D-glutamyl-L-diamino acid endopeptidase), and has been implicated in the spread of transposons. Proteins similar to this family include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as the eukaryotic ""goose-type"" lysozymes (goose egg-white lysozyme; GEWL)." 151 matched cddid_all.tbl CDD cd16892 cd16892 381613 LT_VirB1-like "VirB1-like subfamily. This subfamily includes VirB1 protein, one of twelve proteins making up type IV secretion systems (T4SS). T4SS are macromolecular assemblies generally composed of VirB1-11 and VirD4 proteins, and are used by bacteria to transport material across their membranes. VirB1 acts as a lytic transglycosylase (LT), and is important with respect to piercing the peptidoglycan layer in the periplasm. LTs catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc) as do ""goose-type"" lysozymes. However, in addition to this, they also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue. Proteins similar to this family include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as the eukaryotic ""goose-type"" lysozymes (goose egg-white lysozyme; GEWL)." 143 matched cddid_all.tbl CDD cd16893 cd16893 381614 LT_MltC_MltE membrane-bound lytic murein transglycosylases MltC and MltE, and similar proteins. MltC and MltE are periplasmic, outer membrane attached lytic transglycosylases (LTs), which cleave beta-1,4-glycosidic bonds joining N-acetylmuramic acid and N-acetylglucosamine in the cell wall peptidoglycan, yielding 1,6-anhydromuropeptides. Proteins similar to this family include the soluble and insoluble membrane-bound LTs in bacteria and the LTs in bacteriophage lambda 162 matched cddid_all.tbl CDD cd16894 cd16894 381615 MltD-like "Membrane-bound lytic murein transglycosylase D and similar proteins. Lytic transglycosylases (LT) catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc). Membrane-bound lytic murein transglycosylase D protein (MltD) family members may have one or more small LysM domains, which may contribute to peptidoglycan binding. Unlike the similar ""goose-type"" lysozymes, LTs also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue. Proteins similar to this family include the soluble and insoluble membrane-bound LTs in bacteria, the LTs in bacteriophage lambda, as well as the eukaryotic ""goose-type"" lysozymes (goose egg-white lysozyme; GEWL)." 129 matched cddid_all.tbl CDD cd16895 cd16895 381616 TraH-like conjugal transfer protein H and similar proteins. This subfamily consists of several TraH proteins, putative conjugal transfer proteins of uncharacterized function, apparently found only in alphaproteobacteria. They have similarity to lysozyme and preserve the critical glutamate residue which has catalytic activity in lysozyme-like proteins. 198 matched cddid_all.tbl CDD cd16896 cd16896 381617 LT_Slt70-like "uncharacterized lytic transglycosylase subfamily with similarity to Slt70. Uncharacterized lytic transglycosylase (LT) with a conserved sequence pattern suggesting similarity to the Slt70, a 70kda soluble lytic transglycosylase which also has an N-terminal U-shaped U-domain and a linker L-domain. LTs catalyze the cleavage of the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), as do ""goose-type"" lysozymes. However, in addition to this, they also make a new glycosidic bond with the C6 hydroxyl group of the same muramic acid residue." 146 matched cddid_all.tbl CDD cd16897 cd16897 340383 LYZ_C C-type lysozyme. C-type lysozyme (chicken or conventional type; 1, 4-beta-N-acetylmuramidase). In humans, lysozyme is found in a wide variety of tissue types and body fluids. It has bacteriolytic properties through the hydolysis of beta-1,4, glyocosidic linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan, as well as between N-acetyl-D-glucosamine residues in chitodextrins. This family also includes digestive stomach lysozyme, which allow ruminants to digest bacteria in the foregut. The mammalian enzyme is related to lysozyme found hen egg-whites and related species. 126 matched cddid_all.tbl CDD cd16898 cd16898 340384 LYZ_LA alpha lactalbumin. alpha-lactalbumin (lactose synthase B protein, LA) is a calcium-binding metalloprotein that is expressed exclusively in the mammary gland during lactation. LA is the regulatory subunit of the enzyme lactose synthase. The association of LA with the catalytic component of lactose synthase, galactosyltransferase, alters the acceptor substrate specificity of this glycosyltransferase, facilitating biosynthesis of lactose. 123 matched cddid_all.tbl CDD cd16899 cd16899 381618 LYZ_C_invert C-type invertebrate lysozyme. C-type lysozyme proteins of invertebrates, including digestive lysozymes 1 and 2 from Musca domestica, which aid in the use of bacteria as a food source. These lysozymes have high expression in the gut and optimal lytic activity at a lower pH. Other lysozymes in this subfamily have immunological roles. e.g. Anopheles gambiae has eight lysozymes, most of which seem to have immunological roles, those some may function as digestive enzymes in larvae. C-type lysozyme (chicken or conventional type; 1, 4-beta-N-acetylmuramidase) has bacteriolytic properties through the hydolysis of beta-1,4, glyocosidic linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan, as well as between N-acetyl-D-glucosamine residues in chitodextrins. 121 matched cddid_all.tbl CDD cd16900 cd16900 381619 endolysin_R21-like endolysin R21-like proteins. Unlike T4 E phage lysozyme, the endolysin R21 from Enterobacteria phage P21 has an N-terminal SAR (signal-arrest-release) domain that anchors the endolysin to the membrane in an inactive form, which act to prevent premature lysis of the infected bacterium. The dsDNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell walls. Similarly, bacteria produce autolysins to facilitate the biosynthesis of its cell wall heteropolymer peptidoglycan and cell division. Endolysins and autolysins are found in viruses and bacteria, respectively. Both endolysin and autolysin enzymes cleave the glycosidic beta 1,4-bonds between the N-acetylmuramic acid and the N-acetylglucosamine of the peptidoglycan. 142 matched cddid_all.tbl CDD cd16901 cd16901 381620 lyz_P1 P1 lysozyme Lyz-like proteins. Enterobacteria phage P1 lysozyme Lyz is secreted to the Escherichia coli periplasm where it is membrane bound and inactive. Activation involves the release from the membrane, an intramolecular thiol-disulfide isomerization and extensive structural rearrangement of the N-terminal region. The dsDNA phages of eubacteria use endolysins or muralytic enzymes in conjunction with hollin, a small membrane protein, to degrade the peptidoglycan found in bacterial cell walls. Similarly, bacteria produce autolysins to facilitate the biosynthesis of its cell wall heteropolymer peptidoglycan and cell division. Endolysins and autolysins are found in viruses and bacteria, respectively. Both endolysin and autolysin enzymes cleave the glycosidic beta 1,4-bonds between the N-acetylmuramic acid and the N-acetylglucosamine of the peptidoglycan. 140 matched cddid_all.tbl CDD cd16902 cd16902 381621 pesticin_lyz lysozyme-like C-terminal domain of pesticin. Pesticin (Pst) is an anti-bacterial toxin produced by Yersinia pestis that acts through uptake by the target related bacteria and the hydrolysis of peptidoglycan in the periplasm. Pst contains an N-terminal translocation domain, an intermediate receptor binding domain, and a phage-lysozyme like C-terminal activity domain. Bacteriocins such as pesticin are produced by gram-negative bacteria to attack related bacterial stains. Pst is transported to the periplasm via FyuA, an outer-membrane receptor of Y. pestis and E. coli, where it hydrolyzes peptidoglycan via the cleavage of N-acetylmuramic acid and C4 of N-acetylglucosamine. Disruption of the peptidoglycan layer renders the bacteria vulnerable to lysis via osmotic pressure. The pesticin C-terminal domain resembles the lysozyme-like family, which includes soluble lytic transglycosylases (SLT), goose egg-white lysozymes (GEWL), hen egg-white lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases. All the members are involved in the hydrolysis of beta-1,4- linked polysaccharides. 178 matched cddid_all.tbl CDD cd16903 cd16903 340389 pesticin_lyz-like pesticin C-terminal-like domain of uncharacterized proteins. This subfamily is composed of uncharacterized proteins containing a lysozyme-like domain similar to the C-terminal domain of pesticin. Some members also contain an EF hand domain. Pesticin (Pst) is an anti-bacterial toxin produced by Yersinia pestis that acts through uptake by the target related bacteria and the hydrolysis of peptidoglycan in the periplasm. Pst contains an N-terminal translocation domain, an intermediate receptor binding domain, and a phage-lysozyme like C-terminal activity domain. Bacteriocins such as pesticin are produced by gram-negative bacteria to attack related bacterial stains. Pst is transported to the periplasm via FyuA, an outer-membrane receptor of Y. pestis and E. coli, where it hydrolyzes peptidoglycan via the cleavage of N-acetylmuramic acid and C4 of N-acetylglucosamine. Disruption of the peptidoglycan layer renders the bacteria vulnerable to lysis via osmotic pressure. The pesticin C-terminal domain resembles the lysozyme-like family, which includes soluble lytic transglycosylases (SLT), goose egg-white lysozymes (GEWL), hen egg-white lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases. All the members are involved in the hydrolysis of beta-1,4- linked polysaccharides. 150 matched cddid_all.tbl CDD cd16904 cd16904 340390 pesticin_lyz-like pesticin C-terminal-like domain of uncharacterized proteins. This subfamily is composed of uncharacterized proteins containing a lysozyme-like domain similar to the C-terminal domain of pesticin. Pesticin (Pst) is an anti-bacterial toxin produced by Yersinia pestis that acts through uptake by the target related bacteria and the hydrolysis of peptidoglycan in the periplasm. Pst contains an N-terminal translocation domain, an intermediate receptor binding domain, and a phage-lysozyme like C-terminal activity domain. Bacteriocins such as pesticin are produced by gram-negative bacteria to attack related bacterial stains. Pst is transported to the periplasm via FyuA, an outer-membrane receptor of Y. pestis and E. coli, where it hydrolyzes peptidoglycan via the cleavage of N-acetylmuramic acid and C4 of N-acetylglucosamine. Disruption of the peptidoglycan layer renders the bacteria vulnerable to lysis via osmotic pressure. The pesticin C-terminal domain resembles the lysozyme-like family, which includes soluble lytic transglycosylases (SLT), goose egg-white lysozymes (GEWL), hen egg-white lysozymes (HEWL), chitinases, bacteriophage lambda lysozymes, endolysins, autolysins, and chitosanases. All the members are involved in the hydrolysis of beta-1,4- linked polysaccharides. 138 matched cddid_all.tbl CDD cd16905 cd16905 341124 YEATS_Taf14_like YEATS domain found in Taf14 and similar proteins. Taf14 has been identified as a component of TFIIF and TFIID transcription factor complexes, various chromatin-remodeling complexes (such as SWI/SNF, INO80, and RSC) and the NuA3 histone acetyltransferase complex. DNA regulation by chromatin thru histone post-translational modification and other mechanism involves complexes with write, eraser and reader functions. YEATS domains act as readers of the chromatin state, and stimulate transcriptional activity, thru preferential interactions with crotonylated lysines on histones. Specifically, Taf14 has been show to be a reader of lysine crotonylation, associated with active gene promoters and enhancers and binding acetyllysine on in histone H3. The YEATS family is named for several family members: 'YNK7', 'ENL', 'AF-9', and 'TFIIF small subunit', and also contains the GAS41 protein. 118 matched cddid_all.tbl CDD cd16906 cd16906 341125 YEATS_AF-9_like YEATS domain found in ENL and AF-9-like proteins. Yeast AFF9 is a YEATS domain protein that binds to modified histones, with a preference for crotonyllysine over acetyllysine. Histone crotonylation upregulates gene expression in an AF9-dependent manner. Sub-family also includes eleven-nineteen-leukemia protein ENL, which binds histones H3 and H1. DNA regulation by chromatin through histone post-translational modification and other mechanisms involves complexes with write, eraser and reader functions. YEATS domains act as readers of the chromatin state and stimulates transcriptional activity through preferential interactions with crotonylated lysines on histones. The YEATS family is named for several family members: 'YNK7', 'ENL', 'AF-9', and 'TFIIF small subunit', and also contains the GAS41 protein. 127 matched cddid_all.tbl CDD cd16907 cd16907 341126 YEATS_YEATS2_like YEATS domain found in YEATS2 and Drosophila D12. YEATS2 is a YEATS domain reader protein with a preference for recognition of histone H3 crotonylation on lysine 27 (H3K27crHistone crotonylation upregulates gene expression in an AF9-dependent manner. DNA regulation by chromatin thru histone post-translational modification and other mechanism involves complexes with write, eraser and reader functions. YEATS domains act as readers of the chromatin state, and stimulate transcriptional activity, thru preferential interactions with crotonylated lysines on histones. The YEATS family is named for several family members: 'YNK7', 'ENL', 'AF-9', and 'TFIIF small subunit', and also contains the GAS41 protein. 123 matched cddid_all.tbl CDD cd16908 cd16908 341127 YEATS_Yaf9_like YEATS domain found in Yaf9 and similar proteins. Yaf9 is a YEATS domain family protein essential in the function the NuA4 histone acetyltransferase complex and the SWR1-C ATP-dependent chromatin remodeling complex. Yaf9 shares structural similarity with histone chaperone Asf1, both exhibit histone H3 and H4 binding in vitro, and evidence supports both play a role in the same histone acetylation mechanism. DNA regulation by chromatin thru histone post-translational modification and other mechanism involves complexes with write, eraser and reader functions. YEATS domains act as readers of the chromatin state, and stimulate transcriptional activity, thru preferential interactions with crotonylated lysines on histones. The YEATS family is named for several family members: `YNK7', `ENL', `AF-9', and `TFIIF small subunit', and also contains the GAS41 protein. 145 matched cddid_all.tbl CDD cd16909 cd16909 341128 YEATS_GAS41_like YEATS domain found in YEATS domain-containing protein 4 and similar proteins. glioma amplified sequence 41 (GAS41, also known as, YEATS domain-containing protein 4, NuMA-binding protein 1 ) is a YEATS domain family protein that is amplified and acts as an oncogene in human glioma. GAS41 is a YEATS domain family protein and has been shown to interact with the general transcription factor TFIIF via the YEATS domain. DNA regulation by chromatin thru histone post-translational modification and other mechanism involves complexes with write, eraser and reader functions. YEATS domains act as readers of the chromatin state, and stimulate transcriptional activity, thru preferential interactions with crotonylated lysines on histones. The YEATS family is named for several family members: 'YNK7', 'ENL', 'AF-9', and 'TFIIF small subunit', and also contains the GAS41 protein. 137 matched cddid_all.tbl CDD cd16910 cd16910 341129 YEATS_TFIID14_like YEATS domain found in transcription initiation factor TFIID subunit 14 and similar proteins. YEATS domain containing proteins, which include Transcription initiation factor TFIID subunits 14 and 14b of Arabidopsis, shown to be part of the TFIID general transcriptional regulator complex in a two-hybrid screen. DNA regulation by chromatin thru histone post-translational modification and other mechanism involves complexes with write, eraser and reader functions. YEATS domains act as readers of the chromatin state, and stimulate transcriptional activity, thru preferential interactions with crotonylated lysines on histones. The YEATS family is named for several family members: 'YNK7', 'ENL', 'AF-9', and 'TFIIF small subunit', and also contains the GAS41 protein. 131 matched cddid_all.tbl CDD cd16911 cd16911 350650 AfaD_SafA-like AfaD-like family of invasins. This family consists of Escherichia coli AfaD, Salmonella SafA and SafD, Yersinia pestis PsaA, Yersinia enterocolitica MyfA, and similar proteins. The afa gene clusters encode an afimbrial adhesive sheath produced by Escherichia coli. The adhesive sheath is composed of two proteins, AfaD and AfaE, which are independently exposed at the bacterial cell surface. AfaE is required for bacterial adhesion to HeLa cells and AfaD for the uptake of adherent bacteria into these cells. Saf-pilin pilus formation proteins SafA and SafD are the major and minor subunits, respectively, of Saf pili, which are often found in clinical isolates of Salmonella and are assembled by the chaperone-usher secretion pathway. PsaA and MyfA are the major subunits of pH 6 antigen (Psa) and Myf fimbrial homopolymers. Also included is the enteroaggregative Escherichia coli AAF/IV pilus tip protein, which is implicated in adhesion as well. During fimbria/pili assembly, polymerization occurs when the N-terminal extension (NTE) of one AfaD-like family monomer is inserted into an adjacent monomer, providing the final beta strand or G-strand, to complete the Ig-like fold, in a mechanism called the donor-strand complementation (DSC) or donor-strand exchange (DSE). 120 matched cddid_all.tbl CDD cd16913 cd16913 341130 YkuD_like L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD. Members of the YkuD-like family of proteins are found in a range of bacteria. The best studied member Bacillus YkuD has been shown to act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. Another member Helicobacter pylori Csd6 functions as an L,D-carboxypeptidase and regulates helical cell shape and motility. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue. 121 matched cddid_all.tbl CDD cd16914 cd16914 410987 EcfT T component of ECF-type transporters. The transmembrane component (T component) of the energy coupling-factor (ECF)-type transporter is a transmembrane protein important for vitamin uptake in prokaryotes. In addition to the T component, energy-coupling factor (ECF) transporters contain an energy-coupling module that consists of two ATP-binding proteins (known as the A and A' components) and a substrate-binding (S) component. ECF transporters comprise a subgroup of ATP-binding cassette (ABC) transporters that do not make use of water-soluble substrate binding proteins or domains, but instead employ integral membrane proteins for substrate binding, the S component, in contrast to classical ABC importers. The T component links the S component to the ATP-binding subcomplex that is composed of the A and A' components. 233 matched cddid_all.tbl CDD cd16915 cd16915 340392 HATPase_DpiB-CitA-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli K-12 DpiB, DcuS, and Bacillus subtilis CitS, DctS, and YufL. This family includes histidine kinase-like ATPase domains of Escherichia coli K-12 DpiB and DcuS, and Bacillus subtilis CitS, DctS and MalK histidine kinases (HKs) all of which are two component transduction systems (TCSs). E. coli K-12 DpiB (also known as CitA) is the histidine kinase (HK) of DpiA-DpiB, a two-component signal transduction system (TCS) required for the expression of citrate-specific fermentation genes and genes involved in plasmid inheritance. E. coli K-12 DcuS (also known as YjdH) is the HK of DcuS-DcuR, a TCS that in the presence of the extracellular C4-dicarboxlates, activates the expression of the genes of anaerobic fumarate respiration and of aerobic C4-dicarboxylate uptake. CitS is the HK of Bacillus subtilis CitS-CitT, a TCS which regulates expression of CitM, the Mg-citrate transporter. Bacillus subtilis DctS forms a tripartite sensor unit (DctS/DctA/DctB) for sensing C4 dicarboxylates. Bacillus subtilis MalK (also known as YfuL) is the HK of MalK-MalR (YufL-YufM) a TCS which regulates the expression of the malate transporters MaeN (YufR) and YflS, and is essential for utilization of malate in minimal medium. Proteins having this DpiB-CitA-like HATPase domain generally have sensor domains such as Cache and PAS, and a histidine kinase A (HisKA)-like SpoOB-type, alpha-helical domain. 104 matched cddid_all.tbl CDD cd16916 cd16916 340393 HATPase_CheA-like Histidine kinase-like ATPase domain of the chemotaxis protein histidine kinase CheA, and some hybrid sensor histidine kinases. This family includes the cytoplasmic histidine kinase (HK) CheA, a transmembrane receptor which, together with cytoplasmic adaptor protein (CheW), forms the lattice at the core of the chemosensory array that controls the cellular chemotaxis of motile bacteria and archaea. CheA forms a two-component signal transduction system (TCS) with the response regulator CheY. Proteins having this CheA-like HATPase domain generally also have a histidine-phosphotransfer domain, a histidine kinase homodimeric domain, and a regulatory domain; some are hybrid sensor histidine kinases as they contain a REC signal receiver domain. 178 matched cddid_all.tbl CDD cd16917 cd16917 340394 HATPase_UhpB-NarQ-NarX-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli UhpB, NarQ and NarX, and Bacillus subtilis YdfH, YhcY and YfiJ. This family includes the histidine kinase-like ATPase (HATPase) domains of various histidine kinases (HKs) of two-component signal transduction systems (TCSs) such as Escherichia coli UhpB, a HK of the UhpB-UhpA TCS, NarQ and NarX, HKs of the NarQ-NarP and NarX-NarL TCSs, respectively, and Bacillus YdfH, YhcY and YfiJ HKs, of the YdfH-YdfI, YhcY-YhcZ and YfiJ-YfiK TCSs, respectively. In addition, it includes Bacillus YxjM, ComP, LiaS and DesK, HKs of the YxjM-YxjML, ComP-ComA, LiaS-LiaR, DesR-DesK TCSs, respectively. Proteins having this HATPase domain have a histidine kinase dimerization and phosphoacceptor domain; some have accessory domains such as GAF, HAMP, PAS and MASE sensor domains. 87 matched cddid_all.tbl CDD cd16918 cd16918 340395 HATPase_Glnl-NtrB-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli GlnL (synonyms NtrB and NRII). This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs), similar to Escherichia coli GlnL/NtrB/NRII HK of the two-component regulatory system (TCS) GlnL/GlnG (NtrB-NtrC, or NRII-NRI), which regulates the transcription of genes encoding metabolic enzymes and permeases in response to carbon and nitrogen status in E. coli and related bacteria. Also included in this family are Rhodobacter capsulatus NtrB, Azospirillum brasilense NtrB, Vibrio alginolyticus NtrB, Rhizobium leguminosarum biovar phaseoli NtrB, and Herbaspirillum seropedicae NtrB. Escherichia coli GlnL/NtrB/NRII is both a kinase and a phosphatase, catalyzing the phosphorylation and dephosphorylation of GlnG/NtrC/NRI. The kinase and phosphatase activities of GlnL/NtrB/NRII are regulated by the PII signal transduction protein, which on binding to GlnL/NtrB/NRII, inhibits the kinase activity of GlnL/NtrB/NRII and activates the GlnL/NtrB/NRII phosphatase activity. Proteins having this HATPase domain also have a histidine kinase dimerization and phosphoacceptor domain (HisKA); some also contain PAS sensor domain(s). 109 matched cddid_all.tbl CDD cd16919 cd16919 340396 HATPase_CckA-like Histidine kinase-like ATPase domain of two-component sensor hybrid histidine kinases, similar to Brucella abortus 2308 CckA. This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component hybrid sensor histidine kinase (HKs) similar to Brucella abortus 2308 CckA, which is a component of an essential protein phosphorelay that regulates expression of genes required for growth, division, and intracellular survival; phosphoryl transfer initiates from the sensor kinase CckA and proceeds via the ChpT phosphotransferase to two regulatory substrates: the DNA-binding response regulator CtrA and the phospho-receiver protein CpdR. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA), a REC signal receiver domain, and some contain PAS or PAS and GAF sensor domain(s). 116 matched cddid_all.tbl CDD cd16920 cd16920 340397 HATPase_TmoS-FixL-DctS-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Rhizobium meliloti FixL, and Rhodobacter capsulatus DctS; includes hybrid sensor histidine kinase similar to Pseudomonas mendocina TmoS. This family includes the histidine kinase-like ATPase (HATPase) domains of various histidine kinases (HKs) of two-component signal transduction systems (TCSs), such as Pseudomonas mendocina TmoS HK of the TmoS-TmoT TCS, which controls the expression of the toluene-4-monooxygenase pathway, Rhizobium meliloti FixL HK of the FixL-FixJ TCS, which regulates the expression of the genes related to nitrogen fixation in the root nodule in response to O(2) levels, and Rhodobacter capsulatus DctS of the DctS-DctR TCS, which controls synthesis of the high-affinity C4-dicarboxylate transport system. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA) and PAS sensor domain(s); many are hybrid sensor histidine kinases as they also contain a REC signal receiver domain. 104 matched cddid_all.tbl CDD cd16921 cd16921 340398 HATPase_FilI-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Methanosaeta harundinacea FilI and some hybrid sensor histidine kinases. This family includes FilI, the histidine kinase (HK) component of FilI-FilRs, a two-component signal transduction system (TCS) of the methanogenic archaeon, Methanosaeta harundinacea, which is involved in regulating methanogenesis. The cytoplasmic HK core consists of a C-terminal HK-like ATPase domain (represented here) and a histidine kinase dimerization and phosphoacceptor domain (HisKA) domain, which, in FilI, are coupled to CHASE, HAMP, PAS, and GAF sensor domains. FilI-FilRs catalyzes the phosphotransfer between FilI (HK) and FilRs (FilR1 and FilR2, response regulators) of the TCS. TCSs are predicted to be of bacterial origin, and acquired by archaea by horizontal gene transfer. This model also includes related HATPase domains such as that of Synechocystis sp. PCC6803 phytochrome-like protein Cph1. Proteins having this HATPase domain and HisKA domain also have accessory sensor domains such as CHASE, GAF, HAMP and PAS; some are hybrid sensor histidine kinases as they also contain a REC signal receiver domain. 105 matched cddid_all.tbl CDD cd16922 cd16922 340399 HATPase_EvgS-ArcB-TorS-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases, many are hybrid sensor histidine kinases, similar to Escherichia coli EvgS, ArcB, TorS, BarA, RcsC. This family contains the histidine kinase-like ATPase (HATPase) domains of various two-component hybrid sensor histidine kinases (HKs), including the following Escherichia coli HKs: EvgS, a HK of the EvgS-EvgA two-component system (TCS) that confers acid resistance; ArcB, a HK of the ArcB-ArcA TCS that modulates the expression of numerous genes in response to respiratory growth conditions; TorS, a HK of the TorS-TorR TCS which is involved in the anaerobic utilization of trimethylamine-N-oxide; BarA, a HK of the BarA-UvrY TCS involved in the regulation of carbon metabolism; and RcsC, a HK of the RcsB-RcsC TCS which regulates the expression of the capsule operon and of the cell division gene ftsZ. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA), with most having accessory sensor domain(s) such as GAF, PAS and CHASE; many are hybrid sensor histidine kinases as they also contain a REC signal receiver domain. 110 matched cddid_all.tbl CDD cd16923 cd16923 340400 HATPase_VanS-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Enterococcus faecium VanS. This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Enterococcus faecium VanS HK of the VanS-VanR two-component regulatory system (TCS) which activates the transcription of vanH, vanA and vanX vancomycin resistance genes. It also contains Ecoli YedV and PcoS, probable members of YedW-YedV TCS and PcoS-PcoR TCS, repectively. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA); most also have a HAMP sensor domain. 102 matched cddid_all.tbl CDD cd16924 cd16924 340401 HATPase_YpdA-YehU-LytS-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli YpdA, YehU, Bacillus subtilis LytS, and some hybrid sensor histidine kinases. This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Bacillus subtilis LytS, a HK of the two-component system (TCS) LytS-LytR needed for growth on pyruvate, and Staphylococcus aureus LytS-LytR TCS involved in the adaptation of S. aureus to cationic antimicrobial peptides. It also includes the HATPase domains of Escherichia coli YpdA and YehU, HKs of YpdA-YpdB and YehU-YehTCSs, which are involved together in a nutrient sensing regulatory network. Proteins having this HATPase domain also contain a histidine kinase domain (His-kinase), some having accessory sensor domain(s) such as Cache, HAMP or GAF; some are hybrid sensor histidine kinases as they also contain a REC signal receiver domain. 103 matched cddid_all.tbl CDD cd16925 cd16925 340402 HATPase_TutC-TodS-like Histidine kinase-like ATPase domain of hybrid sensor histidine kinases similar to Pseudomonas putida TodS and Thauera aromatica TutC. This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component hybrid sensor histidine kinase (HKs) such Pseudomonas putida TodS HK of the TodS-TodT two-component regulatory system (TCS) which controls the expression of a toluene degradation pathway. Thauera aromatica TutC may be part of a TCS that is involved in anaerobic toluene metabolism. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA), PAS sensor domain(s) and a REC domain. 110 matched cddid_all.tbl CDD cd16926 cd16926 340403 HATPase_MutL-MLH-PMS-like Histidine kinase-like ATPase domain of DNA mismatch repair proteins Escherichia coli MutL, human MutL homologs (MLH/ PMS), and related domains. This family includes the histidine kinase-like ATPase (HATPase) domains of Escherichia coli MutL, human MLH1 (mutL homolog 1), human PMS1 (PMS1 homolog 1, mismatch repair system component), human MLH3 (mutL homolog 3), and human PMS2 (PMS1 homolog 2, mismatch repair system component). MutL homologs (MLH/PMS) participate in MMR (DNA mismatch repair), and in addition have role(s) in DNA damage signaling and suppression of homologous recombination (recombination between partially homologous parental DNAs). The primary role of MutL in MMR is to mediate protein-protein interactions during mismatch recognition and strand removal; a ternary complex is formed between MutS, MutL, and the mismatched DNA, which activates the MutH endonuclease. 188 matched cddid_all.tbl CDD cd16927 cd16927 340404 HATPase_Hsp90-like Histidine kinase-like ATPase domain of human cytosolic Hsp90 and its homologs including Escherichia coli HtpG, and related domains. This family includes the histidine kinase-like ATPase (HATPase) domains of 90 kilodalton heat-shock protein (Hsp90) eukaryotic homologs including cytosolic Hsp90, mitochondrial TRAP1 (tumor necrosis factor receptor-associated protein 1), GRP94 (94 kDa glucose-regulated protein) of the endoplasmic reticulum (ER), and chloroplast Hsp90C. It also includes the bacterial homologs of Hsp90, known as HtpG (High temperature protein G). Hsp90 family of chaperones assist other proteins to fold correctly, stabilizes them against heat stress, and aids in protein degradation. 189 matched cddid_all.tbl CDD cd16928 cd16928 340405 HATPase_GyrB-like Histidine kinase-like ATPase domain of the B subunit of DNA gyrase. This family includes histidine kinase-like ATPase domain of the B subunit of DNA gyrase. Bacterial DNA gyrase is a type II topoisomerase (type II as it transiently cleaves both strands of DNA) which catalyzes the introduction of negative supercoils into DNA, possibly by a mechanism in which one segment of the double-stranded DNA substrate is passed through a transient break in a second segment. It consists of GyrA and GyrB subunits in an A2B2 stoichiometry; GyrA subunits catalyze strand-breakage and reunion reactions, and GyrB subunits hydrolyze ATP. DNA gyrase is found in bacteria, plants and archaea, but as it is absent in humans it is a possible drug target for the treatment of bacterial and parasite infections. 180 matched cddid_all.tbl CDD cd16929 cd16929 340406 HATPase_PDK-like Histidine kinase-like ATPase domain of pyruvate dehydrogenase kinase, branched-chain alpha-ketoacid dehydrogenase kinase and related domains. This family includes the histidine kinase-like ATPase (HATPase) domains of all four PDK isoforms (pyruvate dehydrogenase kinases 1-4) that have been described in mammals, and other PDKs including Saccharomyces Pkp1p and Pkp2p. PDKs and phosphatases tightly regulate the mitochondrial pyruvate dehydrogenase complex (PDC) by reversible phosphorylation. PDC catalyzes the oxidative decarboxylation of pyruvate to acetyl-CoA, connecting glycolysis and the TCA acid cycle. Also included in this family is mammalian branched-chain alpha-ketoacid dehydrogenase kinase (BDK), a mitochondrial protein kinase that phosphorylates a subunit of the branched-chain a-ketoacid dehydrogenase (BCKD) complex, which catalyzes the oxidative decarboxylation of branched-chain alpha-ketoacids derived from leucine, isoleucine, and valine, a rate-limiting step in the oxidative degradation of these branched-chain amino acids. 169 matched cddid_all.tbl CDD cd16930 cd16930 340407 HATPase_TopII-like Histidine kinase-like ATPase domain of eukaryotic topoisomerase II. This family includes the histidine kinase-like ATPase (HATpase) domains of human topoisomerase IIA (TopIIA) and TopIIB, Saccharomyces cerevisae TOP2p, and related proteins. These proteins catalyze the passage of DNA double strands through a transient double-strand break in the presence of ATP. 147 matched cddid_all.tbl CDD cd16931 cd16931 340408 HATPase_MORC-like Histidine kinase-like ATPase domain of human microrchidia (MORC) family CW-type zinc finger proteins MORC1-4, and related domains. This family includes the histidine kinase-like ATPase (HATPase) domain of human microrchidia (MORC) family CW-type zinc finger proteins MORC1-4, and related domains. In addition to the HATPase domain, MORC family proteins have a CW-type zinc finger domain containing four conserved cysteines and two conserved tryptophans, and coiled-coil domains at the carboxy-terminus. MORC1 has cross-species differential methylation in association with early life stress, and genome-wide association with major depressive disorder (MDD). MORC2 is involved in several nuclear processes, including transcription modulation and DNA damage repair, and exhibits a cytosolic function in lipogenesis, adipogenic differentiation, and lipid homeostasis by increasing the activity of ACLY. MORC3 regulates p53, and is an antiviral factor which plays an important role during HSV-1 and HCMV infection, and is a positive regulator of influenza virus transcription. MORC4 is highly expressed in a subset of diffuse large B-cell lymphomas and has potential as a lymphoma biomarker. 118 matched cddid_all.tbl CDD cd16932 cd16932 340409 HATPase_Phy-like Histidine kinase-like ATPase domain of plant phytochromes similar to Arabidopsis thaliana Phytochrome A, B, C, D and E. This family includes the histidine kinase-like ATPase (HATPase) domains of plant red/far-red photoreceptors, the phytochromes, and includes the Arabidopsis thaliana phytochrome family phyA-phyE. Following red light absorption, biologically inactive forms of phytochromes convert to active forms, which rapidly convert back to inactive forms upon far-red light irradiation. Phytochromes can be considered as having an N-terminal photosensory region to which a bilin chromophore is bound, and a C-terminal output region, which includes the HATPase domain represented here, and is involved in dimerization and presumably contributes to relaying the light signal to downstream signaling events. 113 matched cddid_all.tbl CDD cd16933 cd16933 340410 HATPase_TopVIB-like Histidine kinase-like ATPase domain of type IIB topoisomerase, Topo VI, subunit B. This family includes the histidine kinase-like ATPase (HATPase) domain of the B subunit of topoisomerase VI (Topo VIB). Topo VI is a heterotetrameric complex composed of two TopVIA and two TopVIB subunits and is categorized as a type II B DNA topoisomerase. It is found in archaea and also in plants. Type II enzymes cleave both strands of a DNA duplex and pass a second duplex through the resulting break in an ATP-dependent mechanism. DNA cleavage by Topo VI generates two-nucleotide 5'-protruding ends. 203 matched cddid_all.tbl CDD cd16934 cd16934 340411 HATPase_RsbT-like Histidine kinase-like ATPase domain of the anti sigma-B factor Bacillus subtilis serine/threonine-protein kinase RsbT, and related domains. This family includes the histidine kinase-like ATPase (HATPase) domain of Bacillus subtilis serine/threonine-protein kinase RsbT, a component of the stressosome signaling complex of Bacillus subtilis. The stressosome is formed from multiple copies of three proteins, a sensor protein RsbR, a scaffold protein RsbS, and RsbT, and responds to environmental changes by initiating a protein partner switching cascade. Stress perception increases the phosphorylation of RsbR and RsbS, by RsbT. Subsequent dissociation of RsbT from the stressosome activates the sigma-B cascade, leading to the release of the alternative sigma factor, sigma-B. 117 matched cddid_all.tbl CDD cd16935 cd16935 340412 HATPase_AgrC-ComD-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Staphylococcus aureus AgrC and Streptococcus pneumoniae ComD which are involved in quorum sensing. This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) including Staphylococcus aureus AgrC which is an HK of the accessory gene regulator (agr) quorum sensing two-component regulatory system (TCS) AgrC-AgrA. The agr system plays a part in the transition from persistent to virulent phenotype. This family also includes Streptococcus pneumoniae ComD HK of the ComD-ComE TCS, involved in quorum sensing and genetic competence. 134 matched cddid_all.tbl CDD cd16936 cd16936 340413 HATPase_RsbW-like Histidine kinase-like ATPase domain of RsbW, an anti sigma-B factor and serine-protein kinase involved in regulating sigma-B during stress in Bacilli, and related domains. This family includes histidine kinase-like ATPase (HATPase) domain of RsbW, an anti sigma-B factor as well as a serine-protein kinase involved in regulating sigma-B during stress in Bacilli. The alternative sigma factor sigma-B is an important regulator of the general stress response of Bacillus cereus and B. subtilis. RsbW is an anti-sigma factor while RsbV is an anti-sigma factor antagonist (anti-anti-sigma factor). RsbW can also act as a kinase on RsbV. In a partner-switching mechanism, RsbW, RsbV, and sigma-B participate as follows: in non-stressed cells, sigma-B is present in an inactive form complexed with RsbW; in this form, sigma-B is unable to bind to RNA polymerase. Under stress, RsbV binds to RsbW, forming an RsbV-RsbW complex, and sigma-B is released to bind to RNA polymerase. RsbW may then act as a kinase on RsbV, phosphorylating a serine residue; RsbW is then released to bind to sigma-B, hence blocking its ability to bind RNA polymerase. A phosphatase then dephosphorylates RsbV so that it can again form a complex with RsbW, leading to the release of sigma-B. 91 matched cddid_all.tbl CDD cd16937 cd16937 340414 HATPase_SMCHD1-like Histidine kinase-like ATPase domain of structural maintenance of chromosomes flexible hinge domain containing 1 (SMCHD1) protein. This family includes histidine kinase-like ATPase (HATPase) domain of structural maintenance of chromosomes flexible hinge domain containing 1 (SMCHD1) protein, which is involved in gene silencing and in DNA damage. It has critical roles in X-chromosome inactivation and is also an important regulator of autosomal gene clusters. Upon DNA damage, SMCHD1 promotes non-homologous end joining and inhibits homologous recombination repair. SMCHD1 is implicated in the pathogenesis of facioscapulohumeral muscular dystrophy. 119 matched cddid_all.tbl CDD cd16938 cd16938 340415 HATPase_ETR2_ERS2-EIN4-like Histidine kinase-like ATPase domain of Arabidopsis thaliana ETR2, ERS2, and EIN4, and related domains. This family includes the histidine kinase-like ATPase domains (HATPase) of three out of the five receptors that recognize the plant hormone ethylene in Arabidopsis thaliana. These three proteins have been classified as belonging to subfamily 2: ETR2, ERS2, and EIN4. They lack most of the motifs characteristic of histidine kinases, and EIN4 is the only one in this group containing the conserved histidine that is phosphorylated in two-component and phosphorelay systems. This family also includes the HATPase domains of Escherichia coli RcsD phosphotransferase which is a component of the Rcs-signaling system, a complex multistep phosphorelay involving five proteins, and is involved in many transcriptional networks such as cell division, biofilm formation, and virulence, among others. Also included is Schizosaccharomyces pombe Mak3 (Phk1) which participates in a multi-step two-component related system which regulates H2O2-induced activation of the Sty1 stress-activated protein kinase pathway. Most proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA), and a GAF sensor domain; most are hybrid sensor histidine kinases as they also contain a REC signal receiver domain. 133 matched cddid_all.tbl CDD cd16939 cd16939 340416 HATPase_RstB-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Salmonella typhimurium RstB. This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Salmonella typhimurium RstB HK of the RstA-RstB two-component regulatory system (TCS), which regulates expression of the constituents participating in pyrimidine metabolism and iron acquisition, and may be required for regulation of Salmonella motility and invasion. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA), and a HAMP sensor domain. 104 matched cddid_all.tbl CDD cd16940 cd16940 340417 HATPase_BasS-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli BasS. This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) similar to Escherichia coli BasS HK of the BasS-BasR two-component regulatory system (TCS). Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA); some contain a HAMP sensory domain, while some an N-terminal two-component sensor kinase domain. 113 matched cddid_all.tbl CDD cd16942 cd16942 340418 HATPase_SpoIIAB-like Histidine kinase-like ATPase domain of SpoIIAB, an anti sigma-F factor and serine-protein kinase involved in regulating sigma-F during sporulation in Bacilli, and related domains. This family includes histidine kinase-like ATPase (HATPase) domain of SpoIIAB, an anti sigma-F factor and a serine-protein kinase involved in regulating sigma-F during sporulation in Bacilli where, early in sporulation, the cell divides into two unequal compartments: a larger mother cell and a smaller forespore. Sigma-F transcription factor is activated in the forespore directly after the asymmetric septum forms, and its spatial and temporal activation is required for sporulation. Free sigma-F can associate with the RNA polymerase core and activate transcription of the sigma-F regulon, its regulation may comprise a partner-switching mechanism involving SpoIIAB, SpoIIAA, and sigma-F as follows: SpoIIAB can form alternative complexes with either: i) sigma-F, holding it in an inactive form and preventing its association with RNA polymerase, or ii) unphosphorylated SpoIIAA and a nucleotide, either ATP or ADP. In the presence of ATP, SpoIIAB acts as a kinase to specifically phosphorylate a serine residue of SpoIIAA; this phosphorylated form has low affinity for SpoIIAB and dissociates, making SpoIIAB available to capture sigma-F. SpoIIAA may then be dephosphorylated by a SpoIIE serine phosphatase and be free to attack the SpoIIAB sigma-F complex to induce the release of sigma-F. 135 matched cddid_all.tbl CDD cd16943 cd16943 340419 HATPase_AtoS-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli K-12 AtoS. This family includes the histidine kinase-like ATPase (HATPase) domains of various histidine kinases (HKs) of two-component signal transduction systems (TCSs) such as Escherichia coli AtoS, an HK of the AtoS-AtoC TCS. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA); some have accessory domains such as HAMP or PAS sensor domains or CBS-pair domains. 105 matched cddid_all.tbl CDD cd16944 cd16944 340420 HATPase_NtrY-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Azorhizobium caulinodans NtrY. This family includes the histidine kinase-like ATPase (HATPase) domains of various histidine kinases (HKs) of two-component signal transduction systems (TCSs) such as Azorhizobium caulinodans ORS571 NtrY of the NtrY-NtrX TCS, which is involved in nitrogen fixation and metabolism. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA) and a HAMP sensor domain; some also have PAS sensor domains. 108 matched cddid_all.tbl CDD cd16945 cd16945 340421 HATPase_CreC-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli CreC. This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Escherichia coli CreC of the CreC-CreB two-component regulatory system (TCS) involved in catabolic regulation. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA), and accessory sensory domain(s) such as HAMP, CACHE or PAS. 106 matched cddid_all.tbl CDD cd16946 cd16946 340422 HATPase_BaeS-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli BasS. This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) similar to Escherichia coli BaeS HK of the BaeS/BaeR two-component regulatory system (TCS), which responds to envelope stress. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA), and a HAMP sensory domain. 109 matched cddid_all.tbl CDD cd16947 cd16947 340423 HATPase_YcbM-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Bacillus subtilis YcbM. This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Bacillus subtilis YcbM, a HK of the two-component system YcbM-YcbL. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA). 125 matched cddid_all.tbl CDD cd16948 cd16948 340424 HATPase_BceS-YxdK-YvcQ-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Bacillus subtilis BceS, YxdK, and Bacillus thuringiensis YvcQ. This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Bacillus subtilis BceS and Bacillus thuringiensis YvcQ, the HKs of the two-component regulatory system (TCSs) BceS-BceR and YvcQ-YvcP, repsectively, which are both involved in regulating bacitracin resistance. It also includes the HATPase domain of YxdK, the HK of YxdK-YxdJ TCS involved in sensing antimicrobial compounds. 109 matched cddid_all.tbl CDD cd16949 cd16949 340425 HATPase_CpxA-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli CpxA. This family includes the histidine kinase-like ATPase (HATPase) domains of two-component sensor histidine kinase (HKs) similar to Escherichia coli CpxA, HK of the CpxA-CpxR two-component regulatory system (TCS) which may function in acid stress and in cell wall stability. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA) and a HAMP sensor domain; some also contain a CpxA family periplasmic domain. 104 matched cddid_all.tbl CDD cd16950 cd16950 340426 HATPase_EnvZ-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli EnvZ and Pseudomonas aeruginosa BfmS. This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Escherichia coli EnvZ of the EnvZ-OmpR two-component regulatory system (TCS), which functions in osmoregulation. It also contains the HATPase domain of Pseudomonas aeruginosa BfmS, the HK of the BfmSR TCS, which functions in the regulation of the rhl quorum-sensing system and bacterial virulence in P. aeruginosa. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA) and a HAMP sensor domain; some also contain a periplasmic domain. 101 matched cddid_all.tbl CDD cd16951 cd16951 340427 HATPase_EL346-LOV-HK-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Erythrobacter litoralis blue light-activated histidine kinase 2. This domain family includes the histidine kinase-like ATPase (HATPase) domain of blue light-activated histidine kinase 2 of Erythrobacter litoralis (EL346). Signaling commonly occurs within HK dimers, however EL346 functions as a monomer. Also included in this family are the HATPase domains of ethanolamine utilization sensory transduction histidine kinase (EutW), whereby regulation of ethanolamine, a carbon and nitrogen source for gut bacteria, results in autophosphorylation and subsequent phosphoryl transfer to a response regulator (EutV) containing an RNA-binding domain. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA); some have an accessory PAS sensor domain, while some have an N-terminal histidine kinase domain. 131 matched cddid_all.tbl CDD cd16952 cd16952 340428 HATPase_EcPhoR-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli PhoR. This family includes histidine kinase-like ATPase (HATPase) domain of two-component sensor histidine kinases similar to Escherichia coli or Vibrio cholera PhoR, the histidine kinase (HK) of PhoB-PhoR a two-component signal transduction system (TCS) involved in phosphate regulation. PhoR monitors extracellular inorganic phosphate (Pi) availability and PhoB, the response regulator, regulates transcription of genes of the phosphate regulon. PhoR is a bifunctional histidine autokinase/phospho-PhoB phosphatase; in phosphate deficiency, it autophosphorylates and Pi is transferred to PhoB, and when environmental Pi is abundant, it removes the phosphoryl group from phosphorylated PhoB. Other roles of PhoB-PhoR TCS have been described, including motility, biofilm formation, intestinal colonization, and virulence in V. cholera. E.coli PhoR and Bacillus subtilis PhoR (whose HATPase domain belongs to a different family) sense very different signals in each bacterium. In E. coli the PhoR signal comes from phosphate transport mediated by the PstSCAB2 phosphate transporter and the PhoU chaperone-like protein while in B. subtilis, the PhoR activation signal comes from wall teichoic acid (WTA) metabolism. 108 matched cddid_all.tbl CDD cd16953 cd16953 340429 HATPase_BvrS-ChvG-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Brucella abortus BvrS and Sinorhizobium meliloti ChvG. This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Brucella abortus BvrS of the BvrR-BvrS two-component regulatory system (TCS), which controls cell invasion and intracellular survival, as well as Sinorhizobium meliloti and Agrobacterium tumefaciens ChvG of the ChvI-ChvG TCS necessary for endosymbiosis and pathogenicity in plants. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA), an accessory HAMP sensor domain, a periplasmic stimulus-sensing domain, and some also have a sensor N-terminal transmembrane domain. 110 matched cddid_all.tbl CDD cd16954 cd16954 340430 HATPase_PhoQ-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli PhoQ and Providencia stuartii AarG. This family includes histidine kinase-like ATPase (HATPase) domain of two-component sensor histidine kinases similar to Escherichia coli PhoQ and Providencia stuartii AarG. PhoQ is the histidine kinase (HK) of the PhoP-PhoQ two-component regulatory system (TCS), which responds to the levels of Mg2+ and Ca2+, controls virulence, mediates the adaptation to Mg2+-limiting environments, and regulates numerous cellular activities. Providencia stuartii AarG is a putative sensor kinase which controls the expression of the 2'-N-acetyltransferase and an intrinsic multiple antibiotic resistance (Mar) response in Providencia stuartii. The AarG product is similar to PhoQ in that it is able to restore wild-type levels of resistance to a Salmonella typhimurium phoQ mutant. However, the expression of the 2'-N-acetyltransferase gene and of aarP (a gene encoding a transcriptional activator of 2'-N-acetyltransferase) are not significantly affected by the levels of Mg2+ or Ca2+. Most proteins in this group contain a histidine kinase dimerization and phosphoacceptor domain (HisKA); some have an accessory HAMP sensor domain, and some have an intracellular membrane -interaction PhoQ sensor domain. 135 matched cddid_all.tbl CDD cd16955 cd16955 340431 HATPase_YpdA-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli YpdA. This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Escherichia coli YpdA, a HK of the two-component system (TCS) YpdA-YpdB which is involved in a nutrient sensing regulatory network with YehU-YehT. Proteins having this HATPase domain also contain a histidine kinase domain (His-kinase), and some have a GAF sensor domain; some contain a DUF3816 domain; some are hybrid sensor histidine kinases as they also contain a REC signal receiver domain. 102 matched cddid_all.tbl CDD cd16956 cd16956 340432 HATPase_YehU-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Escherichia coli YehU. This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) including Escherichia coli YehU, a HK of the two-component system (TCS) YehU-YehT which is involved in a nutrient sensing regulatory network. Proteins having this HATPase domain also contain a histidine kinase domain (His-kinase); some have a GAF sensor domain while some have a cupin domain. 101 matched cddid_all.tbl CDD cd16957 cd16957 340433 HATPase_LytS-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Bacillus subtilis LytS and Staphylococcus aureus LytS. This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Bacillus subtilis LytS, a HK of the two-component system (TCS) LytS-LytR needed for growth on pyruvate, and Staphylococcus aureus LytS-LytR TCS involved in the adaptation of S. aureus to cationic antimicrobial peptides. Proteins having this HATPase domain also contain a histidine kinase domain (His-kinase), and a GAF sensor domain; most contain a DUF3816 domain. 106 matched cddid_all.tbl CDD cd16961 cd16961 341131 RMtype1_S_TRD-CR_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR) and similar domains. The restriction-modification (RM) system S subunit generally consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This superfamily represents a single TRD-CR unit; in addition to type I TRD-CR units, it includes RMtype1_S_TRD-CR_like domains of various putative Helicobacter type II restriction enzymes and methyltransferases, such as Hci611ORFHP and HfeORF12890P, as well as TRD-CR-like sequence-recognition domains of the M subunit of putative type I DNA methyltransferase such as M2.CinURNWORF2828P and M.Mae7806ORF3969P. 178 matched cddid_all.tbl CDD cd16962 cd16962 438562 RuvC Crossover junction endodeoxyribonuclease RuvC. Crossover junction endodeoxyribonuclease RuvC is also called Holliday junction resolvase RuvC. It is part of the RuvABC pathway in Escherichia coli and other Gram-negative bacteria that is involved in processing Holliday junctions, which are formed by the reciprocal exchange of strands between two DNA duplexes. Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. RuvC is thought to bind either on the open, DNA exposed face of a single RuvA tetramer, or to replace one of the two tetramers. Binding is proposed to be mediated by an unstructured loop on RuvC, which becomes structured on binding RuvA. RuvC can be bound to the complex in either orientation, therefore resolving Holliday junctions in either a horizontal or vertical manner. HJRs occur in archaea, bacteria, and in the mitochondria of certain fungi. These are referred to as the RuvC family of Holliday junction resolvases, RuvC being the Escherichia coli HJR. RuvC and its orthologs are homodimers and display structural similarity to RNase H and Hsp70. 152 matched cddid_all.tbl CDD cd16963 cd16963 438563 CCE1 fungal mitochondrial Holliday junction resolvases similar to Saccharomyces cerevisiae CCE1. Saccharomyces cerevisiae Cruciform cutting endonuclease 1 (CCE1) is a Holliday junction resolvase specific for 4-way junctions. CCE1 is involved in the maintenance of mitochondrial DNA. Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. Holliday junctions are formed by the reciprocal exchange of strands between two DNA duplexes. HJRs occur in archaea, bacteria, and in the mitochondria of certain fungi; they may form homodimers and display structural similarity to RNase H and Hsp70. 288 matched cddid_all.tbl CDD cd16964 cd16964 438564 YqgF putative pre-16S rRNA nuclease YqgF and RuvX family. Escherichia coli YqgF has been shown to act as a pre-16S rRNA nuclease, presumably as a monomer. It is involved in the processing of pre-16S rRNA during ribosome maturation. The RuvX gene product from Mycobacterium tuberculosis was shown to act, in a dimeric form, as a Holliday junction resolvase (HJR). HJRs endonucleases specifically resolve Holliday junction DNA intermediates during homologous recombination. Holliday junctions are formed by the reciprocal exchange of strands between two DNA duplexes. HJRs occur in archaea, bacteria, and in the mitochondria of certain fungi; they may form homodimers and display structural similarity to RNase H and Hsp70. 132 matched cddid_all.tbl CDD cd16965 cd16965 341215 Alpha_kinase_ChaK Alpha-kinase domain of channel kinases. This group is composed of channel kinases 1 (ChaK1) and 2 (ChaK2), and similar proteins. ChaK1 and ChaK2 are also called transient receptor potential cation channel subfamily M members 7 (TRMP7) and 6 (TRMP6), respectively. They are fusion proteins containing a transmembrane ion pore or channel and a C-terminal alpha-kinase domain, both of which are functional. They are both cation-selective channels that preferentially permeate Zn2+, Mg2+, and Ca2+ ions. They are central regulators of Mg2+ and Ca2+ homeostasis. TRMP7 is ubiquitously expressed while TRMP6 is highly expressed in specific tissues such as the kidney and intestine. Alpha-kinase is an atypical protein kinase catalytic domain with no detectable similarity to conventional protein serine/threonine kinases. The alpha-kinase family was named after the unique mode of substrate recognition by its initial members, the Dictyostelium heavy chain kinases, which targeted protein sequences that adopt an alpha-helical conformation. More recently, alpha-kinases were found to also target residues in non-helical regions. 239 matched cddid_all.tbl CDD cd16966 cd16966 341216 Alpha_kinase_ALPK2_3 Alpha-kinase domain of alpha-protein kinases 2 and 3. Alpha-protein kinases 2 (ALPK2) and 3 (ALPK3) are also called heart alpha-protein kinase (HAK) and muscle alpha-protein kinase (MAK), respectively. They both contain a C-terminal alpha-kinase domain and two immunoglobulin (Ig)-like domains. Loss of function mutations in ALPK3 can cause early-onset and familial cardiomyopathy in humans. The ALPK2 gene may also be a novel candidate gene for inherited hypertension in Dahl rats. Alpha-kinase is an atypical protein kinase catalytic domain with no detectable similarity to conventional protein serine/threonine kinases. The alpha-kinase family was named after the unique mode of substrate recognition by its initial members, the Dictyostelium heavy chain kinases, which targeted protein sequences that adopt an alpha-helical conformation. More recently, alpha-kinases were found to also target residues in non-helical regions. 239 matched cddid_all.tbl CDD cd16967 cd16967 341217 Alpha_kinase_eEF2K Alpha-kinase domain of eukaryotic elongation factor-2 kinase. Eukaryotic elongation factor-2 kinase (eEF2K) is also called calcium/calmodulin (CaM)-dependent eEF2K. It phosphorylates eukaryotic elongation factor-2 (EEF2) at a single site, leading to its inactivation and inability to bind ribosomes, and slowing down the elongation stage of protein synthesis. It has been linked to many human diseases including cardiovascular conditions (atherosclerosis) and pulmonary arterial hypertension, as well as solid tumors and neurological disorders. eEF2K is an atypical protein kinase containing a CaM binding region, an alpha-kinase catalytic domain, and TPR-like Sel1 repeats at the C-terminus. Alpha-kinase is an atypical protein kinase catalytic domain with no detectable similarity to conventional protein serine/threonine kinases. The alpha-kinase family was named after the unique mode of substrate recognition by its initial members, the Dictyostelium heavy chain kinases, which targeted protein sequences that adopt an alpha-helical conformation. More recently, alpha-kinases were found to also target residues in non-helical regions. 216 matched cddid_all.tbl CDD cd16968 cd16968 341218 Alpha_kinase_MHCK_like Alpha-kinase domain of myosin heavy chain kinase and similar domains. This group is composed of alpha-kinase domains of Dictyostelium discoideum myosin heavy chain kinases A-D (MHCKA, MHCKB, MHCKC, MHCKD), alpha-protein kinase 1 (AK1), and similar proteins. The myosin heavy chain kinases are involved in regulating myosin II filament assembly in Dictyostelium discoideum. They phosphorylate target threonine residues located in the carboxyl-terminal portion of the myosin II heavy chain (MHC) tail, resulting in filament disassembly. The different MHCK isoforms display different spatial regulation, indicating specific roles for each isoform in fine tuning the Dictyostelium actomyosin cytoskeleton. They all contain an alpha-kinase domain as well as WD40 repeats at the C-terminus. AK1 contains an N-terminal Arf-GAP domain and a central alpha-kinase domain. Alpha-kinase is an atypical protein kinase catalytic domain with no detectable similarity to conventional protein serine/threonine kinases. The alpha-kinase family was named after the unique mode of substrate recognition by its initial members, the Dictyostelium heavy chain kinases, which targeted protein sequences that adopt an alpha-helical conformation. More recently, alpha-kinases were found to also target residues in non-helical regions. 202 matched cddid_all.tbl CDD cd16969 cd16969 341219 Alpha_kinase_ALPK1 Alpha-kinase domain of alpha-protein kinase 1. Alpha-protein kinase 1 is also called chromosome 4 kinase or lymphocyte alpha-protein kinase (LAK). ALPK1 is implicated in epithelial cell polarity and exocytic vesicular transport towards the apical plasma membrane. It resides on Golgi-derived vesicles where it phosphorylates myosin IA, a motor protein that regulates the delivery of vesicles to the plasma-membrane. It may be associated with inflammation-related diseases such as gout and type 2 diabetes mellitus. ALPK1 contains a C-terminal alpha-kinase domain, an atypical protein kinase catalytic domain with no detectable similarity to conventional protein serine/threonine kinases. The alpha-kinase family was named after the unique mode of substrate recognition by its initial members, the Dictyostelium heavy chain kinases, which targeted protein sequences that adopt an alpha-helical conformation. More recently, alpha-kinases were found to also target residues in non-helical regions. 227 matched cddid_all.tbl CDD cd16970 cd16970 341220 Alpha_kinase_VwkA_like Alpha-kinase domain of Dictyostelium discoideum VwkA and similar domains. Dictyostelium discoideum alpha-protein kinase VwkA is also called von Willebrand factor A alpha-kinase or vWF kinase. It influences myosin II abundance and assembly behavior as vWKA gene disruption leads to significant myosin II overassembly. VwkA also serves a critical conserved role in the periodic contractions of the contractile vacuole through its regulation of the myosin II cortical cytoskeleton. It contains a vWFa domain (named after its homology to von Willebrand factor A, a plasma glycoprotein essential for proper blood clotting) and a C-terminal alpha-kinase domain. Alpha-kinase is an atypical protein kinase catalytic domain with no detectable similarity to conventional protein serine/threonine kinases. The alpha-kinase family was named after the unique mode of substrate recognition by its initial members, the Dictyostelium heavy chain kinases, which targeted protein sequences that adopt an alpha-helical conformation. More recently, alpha-kinases were found to also target residues in non-helical regions. 227 matched cddid_all.tbl CDD cd16971 cd16971 341221 Alpha_kinase_ChaK1_TRMP7 Alpha-kinase domain of channel kinase 1, also called transient receptor potential cation channel subfamily M member 7. Channel kinase 1 (ChaK1), also called transient receptor potential cation channel subfamily M member 7 (TRMP7) or long transient receptor potential channel 7 (LTrpC7), is a fusion protein containing a transmembrane ion pore or channel and a C-terminal alpha-kinase domain, both of which are functional. It is ubiquitously expressed and is a cation-selective channel that preferentially permeates Zn2+, Mg2+, and Ca2+ ions. It is a central regulator of Mg2+ and Ca2+ homeostasis. TRPM7 plays a role in cancer proliferation, stroke, hydrogen peroxide dependent neurodegeneration, and heavy metal toxicity. Alpha-kinase is an atypical protein kinase catalytic domain with no detectable similarity to conventional protein serine/threonine kinases. The alpha-kinase family was named after the unique mode of substrate recognition by its initial members, the Dictyostelium heavy chain kinases, which targeted protein sequences that adopt an alpha-helical conformation. More recently, alpha-kinases were found to also target residues in non-helical regions. 239 matched cddid_all.tbl CDD cd16972 cd16972 341222 Alpha_kinase_ChaK2_TRPM6 Alpha-kinase domain of channel kinase 2, also called transient receptor potential cation channel subfamily M member 6. Channel kinase 2 (ChaK2), also called transient receptor potential cation channel subfamily M member 6 (TRMP6) or melastatin-related TRP cation channel 6, is a fusion protein containing a transmembrane ion pore or channel and a C-terminal alpha-kinase domain, both of which are functional. It is highly expressed in the kidney and instestine. It is a cation-selective channel that preferentially permeates Zn2+, Mg2+, and Ca2+ ions. It is a central regulator of Mg2+ and Ca2+ homeostasis. TRPM6 is considered to be the Mg2+ entry pathway in the distal convoluted tubule of the kidney, where it functions as a gatekeeper for controlling the body's Mg2+ balance. Mutations in the TRPM6 gene cause the autosomal recessive disorder hypomagnesemia with secondary hypocalcemia, which often results in severe muscular and neurologic complications from early infancy that can lead to neurologic damage or cardiac arrest if left untreated. Alpha-kinase is an atypical protein kinase catalytic domain with no detectable similarity to conventional protein serine/threonine kinases. The alpha-kinase family was named after the unique mode of substrate recognition by its initial members, the Dictyostelium heavy chain kinases, which targeted protein sequences that adopt an alpha-helical conformation. More recently, alpha-kinases were found to also target residues in non-helical regions. 239 matched cddid_all.tbl CDD cd16973 cd16973 341223 Alpha_kinase_ALPK3 Alpha-kinase domain of alpha-protein kinase 3. Alpha-protein kinase 3 (ALPK3) is also called muscle alpha-protein kinase (MAK) or myocytic induction/differentiation originator (Midori). Its expression is restricted to fetal and adult heart and adult skeletal muscle, and is localized in the nucleus. It is thought to act as a transcriptional regulator implicated in early cardiac development. Loss of function mutations in ALPK3 can cause early-onset and familial cardiomyopathy in humans. ALPK3 contains a C-terminal alpha-kinase domain and two immunoglobulin (Ig)-like domains. Alpha-kinase is an atypical protein kinase catalytic domain with no detectable similarity to conventional protein serine/threonine kinases. The alpha-kinase family was named after the unique mode of substrate recognition by its initial members, the Dictyostelium heavy chain kinases, which targeted protein sequences that adopt an alpha-helical conformation. More recently, alpha-kinases were found to also target residues in non-helical regions. 239 matched cddid_all.tbl CDD cd16974 cd16974 341224 Alpha_kinase_ALPK2 Alpha-kinase domain of alpha-protein kinase 2. Alpha-protein kinase 2 (ALPK2) is also called heart alpha-protein kinase (HAK). Little functional information is known about ALPK2. In a three-dimensional colonic-crypt model, it has been identified as crucial for luminal apoptosis and expression of DNA repair-related genes, possibly in the transition of normal colonic crypt to adenoma. The ALPK2 gene may also be a novel candidate gene for inherited hypertension in Dahl rats. ALPK2 contains a C-terminal alpha-kinase domain and two immunoglobulin (Ig)-like domains. Alpha-kinase is an atypical protein kinase catalytic domain with no detectable similarity to conventional protein serine/threonine kinases. The alpha-kinase family was named after the unique mode of substrate recognition by its initial members, the Dictyostelium heavy chain kinases, which targeted protein sequences that adopt an alpha-helical conformation. More recently, alpha-kinases were found to also target residues in non-helical regions. 239 matched cddid_all.tbl CDD cd16975 cd16975 340434 HATPase_SpaK_NisK-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Bacillus subtilis SpaK and Lactococcus lactis NisK. This family includes histidine kinase-like ATPase (HATPase) domain of two-component sensor histidine kinases similar to Bacillus subtilis SpaK and Lactococcus lactis NisK. SpaK is the histidine kinase (HK) of the SpaK-SpaR two-component regulatory system (TCS), which is involved in the regulation of the biosynthesis of lantibiotic subtilin. NisK is the HK of the NisK-NisR TCS, which is involved in the regulation of the biosynthesis of lantibiotic nisin. SpaK and NisK may function as membrane-associated protein kinases that phosphorylate SpaR and NisR, respectively, in response to environmental signals. 107 matched cddid_all.tbl CDD cd16976 cd16976 340435 HATPase_HupT_MifS-like Histidine kinase-like ATPase domain of two-component sensor histidine kinases similar to Rhodobacter capsulatus HupT and Pseudomonas aeruginosa MifS. This family includes the histidine kinase-like ATPase (HATPase) domains of various two-component sensor histidine kinase (HKs) such as Rhodobacter capsulatus HupT of the HupT-HupR two-component regulatory system (TCS), which regulates the synthesis of HupSL, a membrane bound [NiFe]hydrogenase. It also contains the HATPase domain of Pseudomonas aeruginosa MifS, the HK of the MifS-MifR TCS, which may be involved in sensing alpha-ketoglutarate and regulating its transport and subsequent metabolism. Proteins having this HATPase domain also contain a histidine kinase dimerization and phosphoacceptor domain (HisKA); some also have a C-terminal PAS sensor domain. 102 matched cddid_all.tbl CDD cd16977 cd16977 340774 VHS_GGA VHS (Vps27/Hrs/STAM) domain of GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) subfamily. GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprises a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins involved in membrane trafficking between the Trans-Golgi Network (TGN) and endosomes. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (Gamma-Adaptin Ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the Trans-Golgi Network and the endosomal system. 133 matched cddid_all.tbl CDD cd16978 cd16978 340775 VHS_HSE1 VHS (Vps27/Hrs/STAM) domain of Class E vacuolar protein-sorting machinery protein HSE1. Class E vacuolar protein-sorting machinery protein HSE1, together with Vps27, comprise the ESCRT-0 complex, the sorting receptor for ubiquitinated cargo proteins at the multivesicular body (MVB). The complex directly binds to ubiquitinated transmembrane proteins and recruits both ubiquitin ligases and deubiquitinating enzymes. It is also required the efficient recycling of late Golgi proteins including the carboxypeptidase Y (CPY) sorting receptor, Vps10. Similar to metazoan STAMs, HSE1 contain: an N-terminal VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats; a Ubiquitin-Interacting Motif (UIM); a SH3 (Src Homology 3) domain, a well-established protein-protein interaction domain; and a GAT (GGA and TOM) domain, which is essential for the normal sorting function of HSE1. 134 matched cddid_all.tbl CDD cd16979 cd16979 340776 VHS_Vps27 VHS (Vps27/Hrs/STAM) domain of Vacuolar protein sorting-associated protein 27. Vacuolar protein sorting-associated protein 27 (Vps27 or Vps27p) is also called Golgi retention defective protein 11, and is the yeast homolog of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate). Together with class E vacuolar protein-sorting machinery protein HSE1, it comprises the ESCRT-0 complex, the sorting receptor for ubiquitinated cargo proteins at the multivesicular body (MVB). The complex directly binds to ubiquitinated transmembrane proteins and recruits both ubiquitin ligases and deubiquitinating enzymes. It is also required the efficient recycling of late Golgi proteins including the carboxypeptidase Y (CPY) sorting receptor, Vps10. Vps27 contain similar domains and motifs to Hrs; it contains an N-terminal VHS domain, which has a superhelical structure similar to the structure of ARM (Armadillo) repeats, a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain, two Ubiquitin-Interacting Motifs (UIMs), a GAT (GGA and TOM) domain, two a P(S/T)XP motifs that recruit ESCRT-I, and a short peptide motif near the C-terminus that recruits clathrin. 141 matched cddid_all.tbl CDD cd16980 cd16980 340777 VHS_Lsb5 VHS (Vps27/Hrs/STAM) domain of LAS seventeen-binding protein 5. LAS seventeen-binding protein 5 (LAS17-binding protein 5, Lsb5, or Lsb5p) localizes to the plasma membrane and plays a role in endocytosis in yeast. It interacts with actin regulators Sla1p and Las17p, ubiquitin, and Arf3p, coupling actin dynamics to membrane trafficking processes. Lsb5p contains an N-terminal VHS domain and a GAT (GGA and TOM) domain. The VHS domain has a superhelical structure similar to the structure of ARM (Armadillo) repeats. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. 132 matched cddid_all.tbl CDD cd16981 cd16981 340778 CID_RPRD_like CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing proteins. This family is composed of Regulation of nuclear pre-mRNA domain-containing proteins 1A (RPRD1A), 1B (RPRD1B), 2 (RPRD2), yeast Rtt103, and similar proteins. RPRD1A, RPRD1B, and RPRD2 are CID (CTD-Interacting Domain) containing proteins that co-purify with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. Yeast transcription termination factor Rtt103 is a CID containing protein that functions in DNA damage response. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices. 125 matched cddid_all.tbl CDD cd16982 cd16982 340779 CID_Pcf11 CID (CTD-Interacting Domain) of Pcf11. Pcf11 is conserved across eukaryotes. The best studied protein is Saccharomyces cerevisiae Pcf11, also called protein 1 of CF I, an essential subunit of the cleavage factor IA (CFIA) complex which is required for polyadenylation-dependent pre-mRNA 3'-end processing and RNA polymerase (Pol) II (RNAP II) transcription termination. Human Pcf11, also referred to as pre-mRNA cleavage complex 2 protein Pcf11, has been shown to enhance degradation of RNAP II-associated nascent RNA and transcriptional termination. The family also includes plant PCFS4 (Pcf11-similar-4 protein or Polyadenylation and cleavage factor homolog 4) and Caenorhabditis elegans Polyadenylation and cleavage factor homolog 11. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. Pcf11 CID preferentially interacts with CTD phosphorylated at Ser2. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices. 127 matched cddid_all.tbl CDD cd16983 cd16983 340780 CID_SCAF8_like CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8 and similar proteins. This subfamily includes SR-related and CTD-associated factors 8 (SCAF8) and 4 (SCAF4), and similar proteins. SCAF4 is also called Splicing factor arginine serine rich 15 (SFRS15). Members may play roles in mRNA processing. Both SCAF4 and SCAF8 contains a CTD-interacting domain (CID) at the amino terminus and a Ser/Arg-rich domain followed by an RNA recognition motif. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices. 131 matched cddid_all.tbl CDD cd16984 cd16984 340781 CID_Nrd1_like CID (CTD-Interacting Domain) of Nrd1 and similar proteins. This subfamily includes Saccharomyces cerevisiae protein Nrd1, Schizosaccharomyces pombe Rpb7-binding protein Seb1, and similar proteins. Nrd1 cooperates with Nab3 and Sen1, also called the Nrd1-Nab3-Sen1 (NNS) complex, to terminate the transcription by RNA polymerase (Pol) II (RNAPII) of many noncoding RNAs (ncRNAs), including small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), and cryptic unstable transcripts (CUTs). Schizosaccharomyces pombe Seb1 does not function in an NNS-like termination pathway but promotes polyadenylation site selection of coding and noncoding genes. It cotranscriptionally controls alternative polyadenylation. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. Nrd1 CID preferentially interacts with CTD phosphorylated at Ser5. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices. 145 matched cddid_all.tbl CDD cd16985 cd16985 340782 ANTH_N_AP180 ANTH (AP180 N-Terminal Homology) domain, N-terminal region, of adaptor protein 180 (AP180) subfamily. The Adaptor Protein 180 (AP180) subfamily members are phosphatidylinositol-binding clathrin assembly proteins, including mammalian clathrin coat assembly protein AP180 and Clathrin Assembly Lymphoid Myeloid Leukemia protein (CALM), Drosophila LAP (also called Like-AP180 or AP180), and Caenorhabditis elegans Uncoordinated protein 11 (unc-11, also called AP180-like adaptor protein). They are components of the adaptor complexes which link clathrin to receptors in coated vesicles. AP180 and CALM play important roles in clathrin-mediated endocytosis. AP180, also called 91 kDa synaptosomal-associated protein (SNAP91) or phosphoprotein F1-20, is a brain-specific clathrin-binding protein which stimulates clathrin assembly during the recycling of synaptic vesicles. CALM, also called phosphatidylinositol binding clathrin assembly protein (PICALM), is ubiquitously expressed. Members of this subfamily contain ANTH domains, which bind both inositol phospholipids and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. The ANTH domain is a unique module whose N-terminal half is structurally similar to the Epsin N-Terminal Homology (ENTH) and Vps27/Hrs/STAM (VHS) domains, containing a superhelix of eight alpha helices. In addition, it contains a coiled-coil C-terminal half with strutural similarity to spectrin repeats. It binds phosphoinositide PtdIns(4,5)P2 at a short conserved motif K[X]9[K/R][H/Y] between helices 1 and 2. This model describes the N-terminal region of ANTH domains of the Adaptor Protein 180 (AP180) subfamily. 117 matched cddid_all.tbl CDD cd16986 cd16986 340783 ANTH_N_Sla2p_HIP1_like ANTH (AP180 N-Terminal Homology) domain, N-terminal region, of Sla2p/HIP1/HIP1R subfamily. Members of the Sla2p/HIP1/HIP1R subfamily share a common domain architecture, containing an N-terminal ANTH, a central clathrin-binding colied-coil, and a C-terminal actin-binding talin-like (also called I/LWEQ) domains. HIP1 was identified in 1997 as an interactor of huntingtin; when mutated, it is involved in the neurodegenerative disorder Huntington's disease. Both HIP1 and HIP1R promote clathrin assembly in vitro. Yeast Sla2p, is a regulator of membrane cytoskeleton assembly. ANTH domains bind both inositol phospholipids and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. The ANTH domain is a unique module whose N-terminal half is structurally similar to the Epsin N-Terminal Homology (ENTH) and Vps27/Hrs/STAM (VHS) domains, containing a superhelix of eight alpha helices. In addition, it contains a coiled-coil C-terminal half with strutural similarity to spectrin repeats. It binds phosphoinositide PtdIns(4,5)P2 at a short conserved motif K[X]9[K/R][H/Y] between helices 1 and 2. While the ANTH domain of Sla2p preferentially binds PtdIns(4,5)P2, which is considered to be an interaction hub in the clathrin interactome, mammalian HIP1 and HIP1R were found to preferentially bind PtdIns(3,4)P2 and PtdIns(3,5)P2, respectively. This model describes the N-terminal region of ANTH domains of the Sla2p/HIP1/HIP1R subfamily. 117 matched cddid_all.tbl CDD cd16987 cd16987 340784 ANTH_N_AP180_plant ANTH (AP180 N-Terminal Homology) domain, N-terminal region, of plant Clathrin coat assembly protein AP180 and similar proteins. This subfamily is composed of plant clathrin coat assembly protein AP180 and other ANTH domain containing proteins that are yet to be characterized. Arabidopsis thaliana AP180 (At-AP180) is a binding partner of plant alphaC-adaptin; it functions as a clathrin assembly protein that promotes the formation of cages with an almost uniform size distribution. In addition to At-AP180, Arabidopsis thaliana contains many ANTH domain containing proteins labelled as putative clathrin assembly proteins included in this subfamily such as At4g02650, At5g10410, At2g25430, and At1g33340, among others. ANTH domains bind both inositol phospholipids and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. The ANTH domain is a unique module whose N-terminal half is structurally similar to the Epsin N-Terminal Homology (ENTH) and Vps27/Hrs/STAM (VHS) domains, containing a superhelix of eight alpha helices. In addition, it contains a coiled-coil C-terminal half with strutural similarity to spectrin repeats. It binds phosphoinositide PtdIns(4,5)P2 at a short conserved motif K[X]9[K/R][H/Y] between helices 1 and 2. This model describes the N-terminal region of ANTH domains of plant clathrin coat assembly protein AP180 and similar proteins. 122 matched cddid_all.tbl CDD cd16988 cd16988 340785 ANTH_N_YAP180 ANTH (AP180 N-Terminal Homology) domain, N-terminal region, of yeast clathrin coat assembly protein AP180 (YAP180) and similar proteins. This subfamily includes yeast clathrin coat assembly protein AP180 (YAP180) and similar proteins. There are two YAP180 proteins in Saccharomyces cerevisiae, AP180A (yAP180A or YAP1801) and AP180B (yAP180B or YAP1802). They are involved in endocytosis and clathrin cage assembly. ANTH domains bind both inositol phospholipids and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. The ANTH domain is a unique module whose N-terminal half is structurally similar to the Epsin N-Terminal Homology (ENTH) and Vps27/Hrs/STAM (VHS) domains, containing a superhelix of eight alpha helices. In addition, it contains a coiled-coil C-terminal half with strutural similarity to spectrin repeats. It binds phosphoinositide PtdIns(4,5)P2 at a short conserved motif K[X]9[K/R][H/Y] between helices 1 and 2. This model describes the N-terminal region of ANTH domains of plant clathrin coat assembly protein AP180 and similar proteins. 117 matched cddid_all.tbl CDD cd16989 cd16989 340786 ENTH_EpsinR Epsin N-Terminal Homology (ENTH) domain of Epsin-related protein. Epsin-related protein (EpsinR) is also called clathrin interactor 1 (Clint), enthoprotin, or epsin-4. It is a clathrin-coated vesicle (CCV) protein that binds to membranes enriched in phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2), clathrin, and the gamma appendage domain of the adaptor protein complex 1 (AP1). It contains an Epsin N-Terminal Homology (ENTH) domain, an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. The ENTH domain is highly similar to the N-terminal region of the AP180 N-Terminal Homology (ANTH_N) domain. ENTH and ANTH_N domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. ENTH domains bind both, inositol phospholipids with preference for PtdIns(4,5)P2, and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. The ENTH domain of human epsinR binds directly to the helical bundle domain of the mouse SNARE Vti1b; soluble NSF attachment protein receptors (SNAREs) are type II transmembrane proteins that have critical roles in providing the specificity and energy for transport-vesicle fusion. Specific ENTH domains may also function as protein cargo selection/recognition modules. ENTH and ANTH (E/ANTH)-containing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the Trans-Golgi Network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding. 130 matched cddid_all.tbl CDD cd16990 cd16990 340787 ENTH_Epsin Epsin N-Terminal Homology (ENTH) domain of Epsin family. Members of the epsin family play an important role as accessory proteins in clathrin-mediated endocytosis. They are important factors in clathrin-coated vesicle (CCV) generation. They contribute to membrane deformation and play a key function as adaptor proteins, coupling various components of clathrin-mediated uptake. They also have an important role in selecting and recognizing cargo. Three isoforms have been identified in mammals, epsin-1 to -3, and these are conserved in vertebrates. Epsin-1 is highly enriched and represents the dominant isoform in the brain. It is required for proper synaptic vesicle retrieval and modulates the endocytic capacity of synaptic vesicles. Epsins contain an Epsin N-Terminal Homology (ENTH) domain, an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. The ENTH domain is highly similar to the N-terminal region of the AP180 N-Terminal Homology (ANTH_N) domain. ENTH and ANTH_N domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. ENTH domains bind both, inositol phospholipids with preference for PtdIns(4,5)P2, and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of CCVs. ENTH and ANTH (E/ANTH)-containing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the Trans-Golgi Network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding. 124 matched cddid_all.tbl CDD cd16991 cd16991 340788 ENTH_Ent1_Ent2 Epsin N-Terminal Homology (ENTH) domain of Yeast Ent1, Ent2, and similar proteins. This subfamily is composed of the two orthologs of epsin in Saccharomyces cerevisiae, Epsin-1 (Ent1 or Ent1p) and Epsin-2 (Ent2 or Ent2p), and similar proteins. Yeast single epsin knockouts, either Ent1 and Ent2, are viable while the double knockout is not. Yeast epsins are required for endocytosis and localization of actin. Ent2 also plays a signaling role during cell division. The ENTH domain of Ent2 interacts with the septin organizing, Cdc42 GTPase activating protein, Bem3, leading to increased cytokinesis failure when overexpressed. Yeast epsins contain an Epsin N-Terminal Homology (ENTH) domain, an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. ENTH domain is highly similar to the N-terminal region of the AP180 N-Terminal Homology (ANTH_N) domain. ENTH and ANTH_N domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. ENTH domains bind both, inositol phospholipids with preference for PtdIns(4,5)P2, and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. ENTH and ANTH (E/ANTH)-containing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the Trans-Golgi Network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding. 132 matched cddid_all.tbl CDD cd16992 cd16992 340789 ENTH_Ent3 Epsin N-Terminal Homology (ENTH) domain of Yeast Ent3 and similar proteins. This subfamily is composed of one of two epsinR orthologs present in Saccharomyces cerevisiae, Epsin-3 (Ent3 or Ent3p), and similar proteins. Ent3 is an adaptor proteins at the Trans-Golgi Network (TGN); it cooperates with yeast SNARE Vti1p to regulate transport from the TGN to the prevacuolar endosome. Ent3 facilitates the interaction between Gga2p with both the endosomal syntaxin Pep12p and clathrin in the GGA-dependent transport to the late endosome. Yeast epsins contain an Epsin N-Terminal Homology (ENTH) domain, an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. ENTH domain is highly similar to the N-terminal region of the AP180 N-Terminal Homology (ANTH_N) domain. ENTH and ANTH_N domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. ENTH domains bind both, inositol phospholipids with preference for PtdIns(4,5)P2, and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. Similar to mammalian epsinR, The ENTH domain of Ent3 binds to the yeast SNARE Vti1p; soluble NSF attachment protein receptors (SNAREs) are type II transmembrane proteins that have critical roles in providing the specificity and energy for transport-vesicle fusion. Specific ENTH domains may also function as protein cargo selection/recognition modules. ENTH and ANTH (E/ANTH)-containing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the Trans-Golgi Network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding. 121 matched cddid_all.tbl CDD cd16993 cd16993 340790 ENTH_Ent5 Epsin N-Terminal Homology (ENTH) domain of Yeast Ent5 and similar proteins. This subfamily is composed of one of two epsinR orthologs present in Saccharomyces cerevisiae, Epsin-5 (Ent5 or Ent5p), and similar proteins. Ent5 is required, together with Ent3 and Vps27p for ubiquitin-dependent protein sorting into the multivesicular body. It is also required for protein transport from the Trans-Golgi Network (TGN) to the vacuole. Yeast epsins contain an Epsin N-Terminal Homology (ENTH) domain, an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. ENTH domain is highly similar to the N-terminal region of the AP180 N-Terminal Homology (ANTH_N) domain. ENTH and ANTH_N domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. ENTH domains bind both, inositol phospholipids with preference for PtdIns(4,5)P2, and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. ENTH and ANTH (E/ANTH)-containing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the Trans-Golgi Network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding. 158 matched cddid_all.tbl CDD cd16994 cd16994 340791 ENTH_Ent4 Epsin N-Terminal Homology (ENTH) domain of Yeast Ent4 and similar proteins. Yeast Epsin-4 (Ent4 or Ent4p) has been reported to be involved in the Trans-Golgi Network (TGN)-to-vacuole sorting of Arn1p, a transporter for the uptake of ferrichrome, an important nutritional source of iron. Yeast epsins contain an Epsin N-Terminal Homology (ENTH) domain, an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. ENTH domain is highly similar to the N-terminal region of the AP180 N-Terminal Homology (ANTH_N) domain. ENTH and ANTH_N domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. ENTH domains bind both, inositol phospholipids with preference for PtdIns(4,5)P2, and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. ENTH and ANTH (E/ANTH)-containing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the Trans-Golgi Network, which suggests that E/ANTH domains are universal components of the machinery for clathrin-mediated membrane budding. 126 matched cddid_all.tbl CDD cd16995 cd16995 340792 VHS_Tom1 VHS (Vps27/Hrs/STAM) domain of Target of Myb protein 1. Tom1 (Target of myb1 - retroviral oncogene) is a novel negative regulator of interleukin-1 and tumor necrosis factor-induced signaling pathways. It also plays important roles in protein-degradation systems in Alzheimer's disease pathogenesis. Tom1 contains VHS and GAT domains in the N-terminal and central region, respectively. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of Tom1 is essential for its function as a negative regulator. 137 matched cddid_all.tbl CDD cd16996 cd16996 340793 VHS_Tom1L2 VHS (Vps27/Hrs/STAM) domain of TOM1-like protein 2. TOM1-like protein 2 (Tom1L2) is a member of the Tom1 (Target of myb1) subfamily, characterized by the presence of a VHS (Vps27p/Hrs/Stam) domain in the N-terminal portion followed by a GAT (GGA and Tom) domain. They are novel regulators for post-Golgi trafficking and signaling. Studies in Tom1L2 hypomorphic mice suggest that Tom1L2 may play roles in immune responses and tumor suppression. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. 137 matched cddid_all.tbl CDD cd16997 cd16997 340794 VHS_Tom1L1 VHS (Vps27/Hrs/STAM) domain of TOM1-like protein 1. TOM1-like protein 1 (Tom1L1) is also called Src-activating and signaling molecule protein (Srcasm). It is a member of the Tom1 (Target of myb1) subfamily, characterized by the presence of a VHS (Vps27p/Hrs/Stam) domain in the N-terminal portion followed by a GAT (GGA and Tom) domain. They are novel regulators for post-Golgi trafficking and signaling. Tom1L1 has been implicated in multivesicular body (MVB) formation, viral egress from the cell, and cytokinesis. Its amplification enhances the metastatic progression of ERBB2-positive breast cancers. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. 137 matched cddid_all.tbl CDD cd16998 cd16998 340795 VHS_GGA_fungi VHS (Vps27/Hrs/STAM) domain of fungal GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) proteins. GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprises a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins involved in membrane trafficking between the Trans-Golgi Network (TGN) and endosomes. Yeast GGAs facilitate the specific and direct delivery of vacuolar sorting receptor Vps10p and the processing protease Kex2p from the TGN to the late endosome/prevacuolar compartment (PVC). The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (Gamma-Adaptin Ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the Trans-Golgi Network and the endosomal system. 139 matched cddid_all.tbl CDD cd16999 cd16999 340796 VHS_STAM2 VHS (Vps27/Hrs/STAM) domain of Signal Transducing Adapter Molecule 2. Signal Transducing Adapter Molecule 2 (STAM2) is also called EAST (EGFR-Associated protein with SH3 and TAM domain) and Hbp (Hrs-binding protein). It is highly expressed in neurons, where it is localized in the nucleus. STAM (Signal Transducing Adaptor Molecule) subfamily members have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a Ubiquitin-Interacting Motif (UIM) and a SH3 (Src Homology 3) domain, which is a well-established protein-protein interaction domain, and a GAT (GGA and TOM) domain. At the C-termini of most vertebrate STAMS, an Immunoreceptor Tyrosine-based Activation Motif (ITAM) is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries. STAM is a component of the ESCRT (Endosomal Sorting Complex Required for Transport)-0 machinery and together with Hrs, functions to bind and sequester cargoes for downstream sorting into intralumenal vesicles. 139 matched cddid_all.tbl CDD cd17000 cd17000 340797 VHS_STAM1 VHS (Vps27/Hrs/STAM) domain of Signal Transducing Adapter Molecule 1. Signal Transducing Adapter Molecule 1 (STAM1) is part of a crucial regulatory axis for the ventral axonal trajectory of developing spinal motor neurons. It forms a complex with beta-arrestin, which regulates lysosomal trafficking of the chemokine receptor CXCR4 and also mediates CXCR4-dependent chemotaxis. STAM (Signal Transducing Adaptor Molecule) subfamily members have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a Ubiquitin-Interacting Motif (UIM) and a SH3 (Src Homology 3) domain, which is a well-established protein-protein interaction domain, and a GAT (GGA and TOM) domain. At the C-termini of most vertebrate STAMS, an Immunoreceptor Tyrosine-based Activation Motif (ITAM) is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries. STAM is a component of the ESCRT (Endosomal Sorting Complex Required for Transport)-0 machinery and together with Hrs, functions to bind and sequester cargoes for downstream sorting into intralumenal vesicles. 131 matched cddid_all.tbl CDD cd17001 cd17001 340798 CID_RPRD2 CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 2. Regulation of nuclear pre-mRNA domain-containing protein 2 (RPRD2) is a CID (CTD-Interacting Domain) domain containing protein that co-purifies with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices. 125 matched cddid_all.tbl CDD cd17002 cd17002 340799 CID_RPRD1 CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1 and similar proteins. This subfamily contains Regulation of nuclear pre-mRNA domain-containing proteins 1A (RPRD1A) and 1B (RPRD1B) from jawed vertebrates, CID domain-containing protein 1 (CIDS1 or cids-1) from Caenorhabditis elegans, and similar proteins. RPRD1A and RPRD1B are CID (CTD-Interacting Domain) containing proteins that co-purify with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. RPRD1A and RPRD1B form homodimers and heterodimers through their coiled-coil domains. Both associate directly with RPAP2 phosphatase and serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2. The function of CIDS1 is not yet known. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices. 128 matched cddid_all.tbl CDD cd17003 cd17003 340800 CID_Rtt103 CID (CTD-Interacting Domain) of yeast transcription termination factor Rtt103 and similar proteins. Yeast transcription termination factor Rtt103 is a CID (CTD-Interacting Domain) containing protein that functions in DNA damage response. It associates with sites of DNA breaks and is essential for recovery from DNA double strand breaks in the chromosome. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). Rtt103 CID preferentially interacts with CTD phosphorylated at Ser2. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices. 127 matched cddid_all.tbl CDD cd17004 cd17004 340801 CID_SCAF8 CID (CTD-Interacting Domain) of SR-related and CTD-associated factor 8. SR-related and CTD-associated factor 8 (SCAF8) is also called CDC5L complex-associated protein 7 (CCAP7) or RNA-binding motif protein 16 (RBM16). It may play a role in mRNA processing. SCAF8 contains a CTD-interacting domain (CID) at the amino terminus and a Ser/Arg-rich domain followed by an RNA recognition motif. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices. 131 matched cddid_all.tbl CDD cd17005 cd17005 340802 CID_SFRS15_SCAF4 CID (CTD-Interacting Domain) of Splicing factor arginine serine rich 15. Splicing factor arginine serine rich 15 (SFRS15) is also called CTD-binding SR-like protein RA4 or SR-related and CTD-associated factor 4 (SCAF4). It may act to physically and functionally link transcription and pre-mRNA processing. SFRS15/SCAF4 contains a CTD-interacting domain (CID) at the amino terminus and a Ser/Arg-rich domain followed by an RNA recognition motif. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II (RNAP II). During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices. 131 matched cddid_all.tbl CDD cd17006 cd17006 340803 ANTH_N_HIP1_like ANTH (AP180 N-Terminal Homology) domain, N-terminal region, of Huntingtin-interacting protein 1 and related proteins. This subfamily includes Huntingtin-interacting protein 1 (HIP1), HIP1-related protein (HIP1R), and similar proteins. Mammalian HIP1 was identified in 1997 as an interactor of huntingtin; when mutated, it is involved in the neurodegenerative disorder Huntington's disease. HIP1 is expressed only in neurons while HIP1R is ubiquitously expressed. Together with its interacting partner HIPPI, HIP1 regulates apoptosis and gene expression. Both HIP1 and HIP1R promote clathrin assembly in vitro, and they share a common domain architecture, containing an N-terminal ANTH, a central clathrin-binding colied-coil, and a C-terminal actin-binding talin-like (also called I/LWEQ) domains. ANTH domains bind both inositol phospholipids and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. The ANTH domain is a unique module whose N-terminal half is structurally similar to the Epsin N-Terminal Homology (ENTH) and Vps27/Hrs/STAM (VHS) domains, containing a superhelix of eight alpha helices. In addition, it contains a coiled-coil C-terminal half with strutural similarity to spectrin repeats. It binds phosphoinositide PtdIns(4,5)P2 at a short conserved motif K[X]9[K/R][H/Y] between helices 1 and 2. Mammalian HIP1 and HIP1R were found to preferentially bind PtdIns(3,4)P2 and PtdIns(3,5)P2, respectively, instead of PtdIns(4,5)P2, which is considered to be an interaction hub in the clathrin interactome. This model describes the N-terminal region of the ANTH domain of Huntingtin-interacting protein 1 and related proteins. 114 matched cddid_all.tbl CDD cd17007 cd17007 340804 ANTH_N_Sla2p ANTH (AP180 N-Terminal Homology) domain, N-terminal region, of Sla2p and similar proteins. This subfamily is composed of Saccharomyces cerevisiae Sla2 protein (Sla2p, also called transmembrane protein MOP2), Schizosaccharomyces pombe endocytosis protein End4 (End4p, also called Sla2 protein homolog), and similar proteins. In yeast, cells lacking Sla2p have severe defects in actin organization, cell morphology, and endocytosis, suggesting roles in these processes. Sla2p regulates the Eps15-like Arp2/3 complex activator, Pan1p, controlling actin polymerization during endocytosis. In fission yeast, End4p has been implicated in cellular morphogenesis. Sla2p contains an N-terminal ANTH, a central colied-coil, and a C-terminal actin-binding talin-like (also called I/LWEQ) domains. ANTH domains bind both inositol phospholipids and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. The ANTH domain is a unique module whose N-terminal half is structurally similar to the Epsin N-Terminal Homology (ENTH) and Vps27/Hrs/STAM (VHS) domains, containing a superhelix of eight alpha helices. In addition, it contains a coiled-coil C-terminal half with strutural similarity to spectrin repeats. It binds phosphoinositide PtdIns(4,5)P2 at a short conserved motif K[X]9[K/R][H/Y] between helices 1 and 2. The ANTH domain of Sla2p preferentially binds PtdIns(4,5)P2, which is considered to be an interaction hub in the clathrin interactome. This model describes the N-terminal region of ANTH domains f Sla2p and similar proteins. 115 matched cddid_all.tbl CDD cd17008 cd17008 340805 VHS_GGA3 VHS (Vps27/Hrs/STAM) domain of ADP-ribosylation factor-binding protein GGA3. ADP-ribosylation factor-binding protein GGA3 (Golgi-localized, Gamma-ear-containing, Arf-binding 3) regulates the trafficking and is required for the lysosomal degradation of BACE (beta-site APP-cleaving enzyme), the protease that initiates the production of beta-amyloid, which causes Alzheimer's disease. It also plays a key role in GABA (+) transmission, which is important in the regulation of anxiety-like behaviors. GGA3 is a member of the GGA subfamily, which is comprised of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins involved in membrane trafficking between the Trans-Golgi Network (TGN) and endosomes. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (Gamma-Adaptin Ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the Trans-Golgi Network and the endosomal system. 141 matched cddid_all.tbl CDD cd17009 cd17009 340806 VHS_GGA1 VHS (Vps27/Hrs/STAM) domain of ADP-ribosylation factor-binding protein GGA1. ADP-ribosylation factor-binding protein GGA1 (Golgi-localized, Gamma-ear-containing, Arf-binding 1) is also called Gamma-adaptin-related protein 1. It is expressed in human brain and affects the generation of amyloid beta-peptide, and may be involved in the pathogenesis of Alzheimer disease. It is a member of the GGA subfamily, which is comprised of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins involved in membrane trafficking between the Trans-Golgi Network (TGN) and endosomes. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (Gamma-Adaptin Ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the Trans-Golgi Network and the endosomal system. 139 matched cddid_all.tbl CDD cd17010 cd17010 340807 VHS_GGA2 VHS (Vps27/Hrs/STAM) domain of ADP-ribosylation factor-binding protein GGA2. ADP-ribosylation factor-binding protein GGA2 (Golgi-localized, Gamma-ear-containing, Arf-binding 2) is also called Gamma-adaptin-related protein 2 and VHS domain and ear domain of gamma-adaptin (Vear). It is a member of the GGA subfamily, which is comprised of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins involved in membrane trafficking between the Trans-Golgi Network (TGN) and endosomes. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (Gamma-Adaptin Ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the Trans-Golgi Network and the endosomal system. 139 matched cddid_all.tbl CDD cd17011 cd17011 340808 CID_RPRD1A CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1A. Regulation of nuclear pre-mRNA domain-containing protein 1A (RPRD1A) is also called Cyclin-dependent kinase inhibitor 2B-related protein or p15INK4B-related protein (P15RS). RPRD1A is a CID (CTD-Interacting Domain) containing protein that co-purifies with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. RPRD1A form homodimers and heterodimers with RPRD1B through their coiled-coil domains. Both RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices. 128 matched cddid_all.tbl CDD cd17012 cd17012 340809 CID_RPRD1B CID (CTD-Interacting Domain) of Regulation of nuclear pre-mRNA domain-containing protein 1B. Regulation of nuclear pre-mRNA domain-containing protein 1B (RPRD1B) is also called Cell cycle-related and expression-elevated protein in tumor (CREPT). RPRD1B is a CID (CTD-Interacting Domain) containing protein that co-purifies with RNA polymerase (Pol) II (RNAP II) and three other RNAP II-associated proteins, RPAP2, GRINL1A and RECQL5, but not with the Mediator complex. CID binds tightly to the carboxy-terminal domain (CTD) of RNAP II. During transcription, RNAP II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7. RPRD1B form homodimers and heterodimers with RPRD1A through their coiled-coil domains. Both RPRD1A and RPRD1B associate directly with RPAP2 phosphatase and serve as CTD scaffolds to coordinate the dephosphorylation of phospho-S5 by RPAP2. RPRD1B is highly expressed during tumorigenesis and in endometrial cancer, has been shown to promote tumor growth by accelerating the cell cycle. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices. 129 matched cddid_all.tbl CDD cd17013 cd17013 340810 ANTH_N_HIP1 ANTH (AP180 N-Terminal Homology) domain, N-terminal region, of Huntingtin-interacting protein 1. Huntingtin-interacting protein 1 (HIP1) was identified in 1997 as an interactor of huntingtin; when mutated, it is involved in the neurodegenerative disorder Huntington's disease. HIP1 promotes clathrin assembly in vitro. Together with its interacting partner HIPPI, it regulates apoptosis and gene expression. HIP1 contains an N-terminal ANTH, a central clathrin-binding colied-coil, and a C-terminal actin-binding talin-like (also called I/LWEQ) domain. ANTH domains bind both inositol phospholipids and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. The ANTH domain is a unique module whose N-terminal half is structurally similar to the Epsin N-Terminal Homology (ENTH) and Vps27/Hrs/STAM (VHS) domains, containing a superhelix of eight alpha helices. In addition, it contains a coiled-coil C-terminal half with strutural similarity to spectrin repeats. It binds phosphoinositide PtdIns(4,5)P2 at a short conserved motif K[X]9[K/R][H/Y] between helices 1 and 2. The ANTH domain of mammalian HIP1 was found to preferentially bind PtdIns(3,4)P2 instead of PtdIns(4,5)P2, which is considered to be an interaction hub in the clathrin interactome. This model describes the N-terminal region of ANTH domain of Huntingtin-interacting protein 1. 114 matched cddid_all.tbl CDD cd17014 cd17014 340811 ANTH_N_HIP1R ANTH (AP180 N-Terminal Homology) domain, N-terminal region, of Huntingtin-interacting protein 1-related protein. Huntingtin-interacting protein 1-related protein (HIP1R), also called HIP12, promotes clathrin assembly in vitro. It is an endocytic protein involved in receptor trafficking, including regulating cell surface expression of receptor tyrosine kinases. Low HIP1R protein expression is associated with worse survival in diffuse large B-cell lymphoma (DLBCL) patients; it is preferentially expressed in germinal center B-cell (GCB)-like DLBCL, and may be potentially useful in subtyping DLBCL cases. HIP1R contains an N-terminal ANTH, a central clathrin-binding colied-coil, and a C-terminal actin-binding talin-like (also called I/LWEQ) domain. ANTH domains bind both inositol phospholipids and proteins, and contribute to the nucleation and formation of clathrin coats on membranes. The ANTH domain is a unique module whose N-terminal half is structurally similar to the Epsin N-Terminal Homology (ENTH) and Vps27/Hrs/STAM (VHS) domains, containing a superhelix of eight alpha helices. In addition, it contains a coiled-coil C-terminal half with strutural similarity to spectrin repeats. It binds phosphoinositide PtdIns(4,5)P2 at a short conserved motif K[X]9[K/R][H/Y] between helices 1 and 2. The ANTH domain of mammalian HIP1R was found to preferentially bind PtdIns(3,5)P2 instead of PtdIns(4,5)P2, which is considered to be an interaction hub in the clathrin interactome. This model describes the N-terminal region of ANTH domain of Huntingtin-interacting protein 1-related protein. 114 matched cddid_all.tbl CDD cd17015 cd17015 341097 ING_plant Inhibitor of growth (ING) domain of plant inhibitor of growth proteins. This subfamily is composed of mainly plant inhibitor of growth proteins such as Arabidopsis thaliana ING1 (AtING1 or PHD finger protein ING1) and ING2 (AtING2 or PHD finger protein ING2). They are histone-binding components that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which mark transcription start sites of virtually all active genes. The related mammalian ING proteins act as readers and writers of the histone epigenetic code, affecting DNA damage response, chromatin remodeling, cellular senescence, differentiation, cell cycle regulation, and apoptosis. They may have a general role in mediating the cellular response to genotoxic stress through binding to and regulating the activities of histone acetyltransferase (HAT) and histone deacetylase (HDAC) chromatin remodeling complexes. All ING proteins contain an N-terminal leucine zipper-like (LZL) motif-containing ING domain that binds unmodified H3 tails, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain, which binds lysine 4-tri-methylated histone H3 (H3K4me3). Although these two regions can bind histones independently, together they increase the apparent association of the ING domain for the H3 tail. 98 matched cddid_all.tbl CDD cd17016 cd17016 341098 ING_Pho23p_like Inhibitor of growth (ING) domain of yeast Pho23p and similar proteins. This family is composed of Saccharomyces cerevisiae transcriptional regulatory protein PHO23 (Pho23p), Schizosaccharomyces pombe chromatin modification-related protein png2 (also called ING1 homolog 2), and similar proteins. Pho23p is part of Rpd3/Sin3 histone deacetylase (HDAC) complex. It is required for the normal function of Rpd3 in the silencing of rDNA, telomeric, and mating-type loci. Pho23p inhibits p53-dependent transcription. The related mammalian ING proteins act as readers and writers of the histone epigenetic code, affecting DNA damage response, chromatin remodeling, cellular senescence, differentiation, cell cycle regulation and apoptosis. They may have a general role in mediating the cellular response to genotoxic stress through binding to and regulating the activities of histone acetyltransferase (HAT) and histone deacetylase (HDAC) chromatin remodeling complexes. All ING proteins contain an N-terminal leucine zipper-like (LZL) motif-containing ING domain that binds unmodified H3 tails, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3). Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail. 89 matched cddid_all.tbl CDD cd17017 cd17017 341099 ING_Yng1p Inhibitor of growth (ING) domain of yeast Yng1p and similar proteins. The ING family includes three yeast orthologs, chromatin modification-related protein YNG1 (Yng1p), YNG2 (Yng2p), and transcriptional regulatory protein PHO23 (Pho23p). Yng1p, also termed ING1 homolog 1, is one of the components of the NuA3 histone acetyltransferase (HAT) complex. Yng2p, also termed ESA1-associated factor 4, or ING1 homolog 2, is a subunit of the NuA4 HAT complex. It plays acritical role in intra-S-phase DNA damage response. Pho23p is part of Rpd3/Sin3 histone deacetylase (HDAC) complex. It is required for the normal function of Rpd3 in the silencing of rDNA, telomeric, and mating-type loci. Yng1p and Pho23p inhibit p53-dependent transcription. In contrast, Yng2p has the opposite effect. The related mammalian ING proteins act as readers and writers of the histone epigenetic code, affecting DNA damage response, chromatin remodeling, cellular senescence, differentiation, cell cycle regulation and apoptosis. They may have a general role in mediating the cellular response to genotoxic stress through binding to and regulating the activities of histone acetyltransferase (HAT) and histone deacetylase (HDAC) chromatin remodeling complexes. All ING proteins contain an N-terminal leucine zipper-like (LZL) motif-containing ING domain that binds unmodified H3 tails, and a well-characterized C-terminal plant homeodomain (PHD)-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3). Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail. 100 matched cddid_all.tbl CDD cd17018 cd17018 409302 T3SC_IA_ExsC-like Class IA type III secretion system chaperone protein, similar to Pseudomonas aeruginosa exoenzyme S synthesis protein C (ExsC). This family includes type III secretion system (T3SS) chaperone proteins similar to Pseudomonas aeruginosa and Aeromonas hydrophila ExsC (also known as exoenzyme S synthesis protein C). P. aeruginosa ExsC, a member of the type IA family of T3SS chaperones, is unique because, as part of the signaling process, it binds small secreted protein ExsE as well as the non-secreted anti-activator protein ExsD; it relieves repression of the transcriptional activator ExsA (which activates expression of T3SS genes) by ExsD. However, in Aeromonas, although ExsA is likely the master regulator of the T3SS, there is little evidence of ExsC and ExsE involvement in the regulation of the T3SS. 127 matched cddid_all.tbl CDD cd17019 cd17019 409303 T3SC_IA_ShcA-like Class IA type III secretion system chaperone protein, similar to Pseudomonas syringae chaperone protein ShcA. This family includes type III secretion system (T3SS) chaperone proteins similar to Pseudomonas syringae ShcA and similar proteins. In P. syringae, which is a plant pathogen that can infect a wide range of species, the T3SS allows injection of the effector HopA1 (previously known as HopPsyA or HrmA), a protein that has unknown functions in the host cell but possesses close homologs that trigger the plant hypersensitive response in resistant strains. Chaperone ShcA binding to Hop1A shows that interactions in animal pathogens are preserved in the Gram-negative pathogens of plants. 122 matched cddid_all.tbl CDD cd17020 cd17020 409304 T3SC_IA_ShcM-like Class IA type III secretion system chaperone protein, similar to Pseudomonas syringae chaperone protein ShcM. This family includes type III secretion system (T3SS) chaperone proteins similar to Pseudomonas syringae ShcM and similar proteins. In P. syringae, which is a plant pathogen that can infect a wide range of species, the T3SS allows injection of the effector protein HopPtoM (previously known as CEL ORF3), among known plant pathogen effectors, that makes a major contribution to the elicitation of lesion symptoms but not growth in host tomato leaves. Chaperone ShcM is required for efficient translocation and function of HopPtoM in the plant cell, consistent with the presence of customized chaperones in plant pathogenic bacteria. 122 matched cddid_all.tbl CDD cd17021 cd17021 409305 T3SC_IA_SicP-like Class IA type III secretion system chaperone protein, similar to Salmonella enterica chaperone protein SicP. This family includes type III secretion system (T3SS) chaperone proteins similar to Salmonella enterica SicP and similar proteins. In S. enterica, many of its serovars being serious human pathogens, the T3SS allows injection of the effector SptP, a virulence protein that is involved in bacterial invasion into a host cell. Chaperone SicP forms a complex with SptP at an early stage of the effector protein secretion process in order to avoid premature degradation; also, the complex is dissociated at a late stage to secrete only SptP with the help of the ATPase InvC which is part of the related T3SS injectisome. 121 matched cddid_all.tbl CDD cd17022 cd17022 409306 T3SC_IA_SigE-like Class IA type III secretion system chaperone protein, similar to Salmonella enterica SigE. This family includes type III secretion system (T3SS) chaperone proteins similar to Salmonella enterica chaperone SigE and similar proteins. In S. enterica, many of its serovars being serious human pathogens, the T3SS allows injection of the effector SigD (also known as SopB) which is an inositol phosphatase. Chaperone SigE binds to SigD, which, upon translocation into the host cell, preferentially dephosphorylates specific inositol phospholipids that are thought to be crucial for subsequent activation of the host cell Ser-Thr kinase Akt. 113 matched cddid_all.tbl CDD cd17023 cd17023 409307 T3SC_IA_CesT-like Class IA type III secretion system chaperone protein, similar to Escherichia coli CesT. This family includes type III secretion system (T3SS) chaperone proteins similar to Escherichia coli CesT and also contains Stm2138, a novel virulence chaperone in Salmonella enterica subsp. enterica serovar Typhimurium. In E. coli, the T3SS allows injection of the effector Tir (translocated intimin receptor), which plays a key role in enterohemorrhagic Escherichia coli (EHEC) infection, attaching and effacing (A/E) lesions, and intracellular signal transduction. CesT binds to Tir, which interacts with intimin and anchors the infected cell membrane inside the host cytoplasm for signaling. 133 matched cddid_all.tbl CDD cd17024 cd17024 409308 T3SC_IA_DspF-like Class IA type III secretion system chaperone protein, similar to Erwinia amylovora DspF (DspF/AvrF family protein). This family includes type III secretion system (T3SS) chaperone proteins similar to Erwinia amylovora DspF, Pantoea stewartii WtsE, Pseudomonas viridiflava AvrF, and similar proteins, all of which bind AvrE family type III effector proteins. In E. amylovora, a gram-negative enterobacterium that causes a devastating blight disease of apple and pear trees, the T3SS allows injection of effector DspE via the chaperone DspF. DspE has been shown to interact with several apple proteins, suppress salicylic acid-mediated host defenses and cause necrotic cell death in host and non-host plants. In Pectobacterium carotovorum, DspE is required early in solanum tuberosum leaf infection to cause cell death. Effector WtsE in P. stewartii causes disease-associated cell death in corn and requires the chaperone protein WtsF for stability. 121 matched cddid_all.tbl CDD cd17025 cd17025 409309 T3SC_IA_ShcF-like Class IA type III secretion system chaperone protein, similar to Pseudomonas syringae ShcF. This family includes type III secretion system (T3SS) chaperone proteins similar to Pseudomonas syringae ShcF and similar proteins. In P. syringae, which is a plant pathogen that can infect a wide range of species, the T3SS allows injection of the effector protein AvrPphF into genetically susceptible host cells. Chaperone ShcF (originally known as AvrPphF ORD1) binds AvrPphF in a similar manner to type III chaperones from bacterial pathogens of animals, indicating structural conservation of these specialized chaperones, despite high sequence divergence. 124 matched cddid_all.tbl CDD cd17026 cd17026 409310 T3SC_IA_SpcU-like Class IA type III secretion system chaperone protein, similar to Pseudomonas aeruginosa SpcU. This family includes type III secretion system (T3SS) chaperone proteins similar to Pseudomonas aeruginosa SpcU and similar proteins. In P. aeruginosa, a multidrug resistant pathogen associated with serious illnesses such as ventilator-associated pneumonia and various sepsis syndromes, the T3SS allows injection of effector protein ExoU, one of the most aggressive toxins injected by a T3SS, into the cytosol of target eukaryotic cells, leading to rapid cell necrosis. Chaperone SpcU binds the cytotoxin ExoU, which is a broad-specificity phospholipase A2 (PLA2) and lysophospholipase, and maintains the N-terminus of ExoU in an unfolded state which is required for secretion. 120 matched cddid_all.tbl CDD cd17027 cd17027 409311 T3SC_IA_YscB_AscB-like Class IA type III secretion system chaperone protein, similar to Yersinia pestis YscB. This family includes type III secretion system (T3SS) chaperone proteins similar to Yersinia pestis YscB and its homologs, Aeromonas hydrophila AscB and Photorhabdus luminescens LscB. In Yersinia pestis, which causes the deadly bubonic plague, the T3SS allows injection of effector proteins, termed Yersinia outer proteins (Yops) into macrophages and other immune cells, forming pores in the host cell membrane. The secretion of Yops is regulated by the activity of the YopN/SycN/YscB/TyeA complex. YscB acts, along with SycN, as a chaperone for YopN, a key part of a complex that regulates type III secretion so that it responds to contact with the eukaryotic target cell. 127 matched cddid_all.tbl CDD cd17028 cd17028 409312 T3SC_IA_SycE_Scc1-like Class IA type III secretion system chaperone protein, similar to Chlamydia SycE/Scc1. This family includes type III secretion system (T3SS) chaperone proteins similar to Chlamydia SycE (also known as Scc1) and similar proteins. Chlamydia SycE is homologous to that of the SycE chaperone protein of Yersinia, which is involved in promoting translocation of Yersinia outer protein E (YopE). In Chlamydia, two T3SS chaperones, Scc1 and Scc4, work together to promote secretion of the important effector and plug protein, CopN, whereas, the Scc3 chaperone represses its secretion. 134 matched cddid_all.tbl CDD cd17029 cd17029 409313 T3SC_IA_SycE_SpcS-like Class IA type III secretion system chaperone protein, similar to Yersinia SycE. This family includes type III secretion system (T3SS) chaperone proteins similar to Yersinia SycE and its homolog Pseudomonas aeruginosa SpcS. Involvement of Yersinia chaperone SycE (also known as YerA) in promoting translocation of Yersinia outer protein E (YopE), a selective activator of mammalian Rho-family GTPases, into host macrophages is essential to Yersinia pathogenesis. In P. aeruginosa, which is an opportunistic pathogen that harbors multiple virulence factors that widely manipulate host cell signaling and immune response, the effector toxin proteins of T3SS are ExoT, ExoS, ExoU and ExoY. Chaperone SpcS (formerly known as Orf1) binds to ExoT as well as its homolog, ExoS, both known to be the actual virulence determinants due to the presence of bifunctional GTPase-activating (GAP) and ADP-ribosyltransferase (ADPRT) domains which are essential for inhibition of bacterial internalization and epithelial cell migration by altering the actin cytoskeleton. 115 matched cddid_all.tbl CDD cd17030 cd17030 409314 T3SC_IA_SycH-like Class IA type III secretion system chaperone protein, similar to Yersinia pestis SycH. This family includes type III secretion system (T3SS) chaperone proteins similar to Yersinia pestis SycH and similar proteins. In Yersinia pestis, the causative agent of bubonic and pneumonic plague, the T3SS allows injection of effector proteins, termed Yersinia outer proteins (Yops) into macrophages and other immune cells, forming pores in the host cell membrane and have been linked to cytolysis. The secretion of Yops is regulated by the activity of the YopN/SycN/YscB/TyeA complex. SycH is the chaperone for YopH, a potent eukaryotic-like protein tyrosine phosphatase that is essential for virulence. SycH also binds two negative regulators of type III secretion, YscM1 and YscM2, both sharing significant sequence homology with the chaperone-binding domain of YopH. 120 matched cddid_all.tbl CDD cd17031 cd17031 409315 T3SC_IA_SycN-like Class IA type III secretion system chaperone protein, similar to Yersinia pestis SycN. This family includes type III secretion system (T3SS) chaperone proteins similar to Yersinia pestis SycN and similar proteins. In Yersinia pestis, the causative agent of bubonic and pneumonic plague, the T3SS allows injection of effector proteins, termed Yersinia outer proteins (Yops) into macrophages and other immune cells, forming pores in the host cell membrane and have been linked to cytolysis. The secretion of Yops is regulated by the activity of the YopN/SycN/YscB/TyeA complex; SycN-YscB forms a heterodimeric secretion chaperone and binds YopN, a key part of a complex that regulates type III secretion, in response to calcium levels, so that secretion occurs only after contact with the targeted eukaryotic cell. Negative regulation is mediated by the complex by blocking the entrance to the secretion apparatus prior to contact with mammalian cells. 118 matched cddid_all.tbl CDD cd17032 cd17032 409316 T3SC_IA_SycT-like Class IA type III secretion system chaperone protein, similar to Yersinia enterocolitica SycT. This family includes type III secretion system (T3SS) chaperone proteins similar to Yersinia enterocolitica SycT and similar proteins. In Y. enterocolitica, a food-borne pathogen causing gastroenteritis and mesenteric lymphadenitis, chaperone SycT promotes translocation of effector YopT (Yersinia outer protein T), a cysteine protease that inactivates the small GTPase RhoA of targeted host cells by cleaving its C-terminal, prenylated cysteine, thereby releasing the GTPase into the host cytosol. 121 matched cddid_all.tbl CDD cd17033 cd17033 409317 DR1245-like possible type III secretion system (T3SS) chaperone protein DR1245 found in Deinococcus radiodurans. This family includes a possible type III secretion system (T3SS) chaperone protein DR1245 found in Deinococcus radiodurans, a bacterium that is exceptionally resistant to the lethal effects of ionizing radiation (IR), ultraviolet light and other DNA-damaging agents. DR1245, a protein of unknown function conserved only in the Deinococcaceae, and with strong structural homology to YbjN proteins and T3SS chaperones, may display some chaperone activity towards DdrB, a protein found to be highly up-regulated following irradiation; DR1245 may also bind to other substrates. 138 matched cddid_all.tbl CDD cd17034 cd17034 409318 T3SC_IA_ShcO1-like Class IA type III secretion system chaperone proteins, similar to Pseudomonas syringae ShcO1, ShcS1, and ShcS2. This family includes type III secretion system (T3SS) chaperone proteins similar to Pseudomonas syringae ShcO1 and similar proteins. In P. syringae, which is a plant pathogen that can infect a wide range of species, the T3SS allows injection of effector Hrp-dependent outer proteins (HOPs) HopO1-1, HopS1, and HopS2. Three homologous chaperones ShcO1, ShcS1, and ShcS2 facilitate the translocation of their cognate effectors HopO1-1, HopS1, and HopS2, respectively. Interestingly, ShcS1 and ShcS2 are capable of substituting for ShcO1 in facilitating HopO1-1 secretion and translocation. ShcS1 and ShcO1 are exceptional class IA T3SS chaperones because they can bind more than one target effector. 123 matched cddid_all.tbl CDD cd17035 cd17035 409319 T3SC_IB_Spa15-like Class IB type III secretion system chaperone protein, similar to Shigella flexneri Spa15. This family includes type III secretion system (T3SS) chaperone proteins similar to Shigella flexneri Spa15, Salmonella enterica InvB, and similar proteins. In S. flexineri, which is a facultative intracellular pathogen that invades the colonic epithelium and causes bacillary dysentery, the T3SS allows injection of a number of effectors to ensure their stabilization prior to secretion. Spa15 is the chaperone for several TTS effectors, including IpaA, IpgB1, OspC3, OspB and OspD1. Effector IpgB that chaperone Spa15 is a mimic of the human Ras-like Rho guanosine triphosphatase RhoG, thus activating Rac1 guanosine triphosphatase and setting off membrane ruffling of the cell, assisting the internalization of Shigella. Also, Spa15 is a chaperone for secreted anti-activator OspD1 which is involved in the control of transcription by the type III secretion apparatus (T3SA) activity in Shigella flexneri. 129 matched cddid_all.tbl CDD cd17036 cd17036 409320 T3SC_YbjN-like_1 T110839 is structurally similar to type III secretion system chaperones and YbjN family proteins. This family includes protein T110839 from Synechococcus elongatus that is structurally similar to type III secretion system (T3SS) chaperones (T3SC) that bind effector proteins, and is homologous to YbjN, a putative sensory transduction regulator protein found in Proteobacteria. 125 matched cddid_all.tbl CDD cd17037 cd17037 409321 T3SC_IA_ShcV-like Class IA type III secretion system chaperone protein, similar to Pseudomonas syringae ShcV. This family includes type III secretion system (T3SS) chaperone protein similar to Pseudomonas syringae ShcV. In P. syringae, which is a plant pathogen that can infect a wide range of species, the T3SS allows injection of effector HopPtoV which may play a subtle role in pathogenesis. Chaperone ShcV facilitates secretion of HopProV into plant cells via the amino-terminal third of the effector. 131 matched cddid_all.tbl CDD cd17038 cd17038 341208 Flavi_M Flavivirus envelope glycoprotein M. Flaviviruses are small enveloped viruses with a membrane-anchored envelope comprised of 3 proteins called C, M and E. The envelope glycoprotein M is translated as a precursor, called prM. The precursor portion of the protein is the signal peptide for the protein's entry into the membrane. prM is cleaved to form M by the proprotein convertase furin in a late-stage cleavage event. Associated with this cleavage is a change in the infectivity and fusion activity of the virus. 75 matched cddid_all.tbl CDD cd17039 cd17039 340559 Ubl_ubiquitin_like ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins. Ubiquitin-like (Ubl) proteins have a similar ubiquitin (Ub) beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ub and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some Ubl domains have adaptor roles in Ub-signaling by mediating protein-protein interaction. Prokaryotic sulfur carrier proteins are Ub-related proteins that can be activated in an ATP-dependent manner. Polyubiquitination signals for a diverse set of cellular events via different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the epsilon-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. One of these seven lysine residues (K27, Ub numbering) is conserved in this Ubl_ubiquitin_like family. K27-linked Ub chains are versatile and can be recognized by several downstream receptor proteins. K27 has roles beyond chain linkage, such as in Ubl NEDD8 (which contains many of the same lysines (K6, K11, K27, K33, K48) as Ub) where K27 has a role (other than conjugation) in the mechanism of protein neddylation. 68 matched cddid_all.tbl CDD cd17040 cd17040 340560 Ubl_MoaD_like ubiquitin-like (Ubl) domain found in a group of small sulfide carrier proteins. Ubiquitin-like (Ubl) domain found in a group of small sulfide carrier proteins This family includes ThiS, MoaD, CysO, QbsE, and their homologs, which are structurally homologous to ubiquitin (Ub) and may function as the sulfide donor for the biosynthesis of thiamin, molybdopterin, cysteine, thioquinolobactin, and other sulfur-containing natural products. Ub is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of Ub and the epsilon-amino group of a substrate lysine. Like Ub, small sulfide carrier proteins in this family are adenylated at a diglycyl C-terminus by specific activating proteins. The adenylated C-terminus is subsequently converted to a thiocarboxylate, serving as the sulfide source. Those activating proteins are diverse and show little sequence similarity. This family also includes the small archaeal modifier protein (SAMP), including SAMP1, SAMP2 and SAMP3, which are Ub-like proteins that function as protein modifiers and are required for the production of sulfur-containing biomolecules in the archaeon Haloferax volcanii. SAMP1 and SAMP2 are involved in sulfur transfer during molybdenum cofactor biosynthesis and tRNA thiolation much like MoaD and Urm1, respectively. They can form covalent conjugates with their protein targets through an isopeptide linkage via their C-terminal diglycine motif in a streamlined archaeal E1-dependent pathway. SAMP2 also forms homo-conjugates through the intermolecular isopeptide bond between the C-terminal Gly and the Lys58 side chain, a feature that likely resembles polyubiquitination. SAMP3 conjugates are dependent on the Ub-activating E1 enzyme homolog of archaea (UbaA) for synthesis and are cleaved by the JAMM/MPN+ domain metalloprotease HvJAMM1. 88 matched cddid_all.tbl CDD cd17041 cd17041 340561 Ubl_WDR48 Ubiquitin-like (Ubl) domain found in WD repeat-containing protein 48 (WDR48) and similar proteins. WDR48, also termed USP1-associated factor 1 (UAF1), or WD repeat endosomal protein, or p80, is required for the histone deubiquitination activity. It stimulates activity of ubiquitin-specific proteases USP1, USP12, and USP46.As potential tumor suppressor, WDR48 in complex with deubiquitinase USP12 suppresses Akt-dependent cell survival signaling by stabilizing PH domain leucine-rich repeat protein phosphatase 1 (PHLPP1). WDR48 also functions as a novel interaction partner of E1 helicase from anogenital human papillomavirus (HPV) types, and plays an essential role in anogenital HPV DNA replication. WDR48 contains a WD40 domain and a ubiquitin-like domain that shows high sequence and structural similarity with RING finger- and WD40-associated ubiquitin-like (RAWUL) domain. 97 matched cddid_all.tbl CDD cd17042 cd17042 340562 Ubl_TmoB Ubiquitin-like (Ubl) domain found in toluene-4-monooxygenase system protein B (TmoB). TmoB is a component of the multicomponent toluene-4-monooxygenase (T4MO) system that metabolizes toluene as a carbon source. The T4MO complex is composed of a diiron hydroxylase (T4MOH), a Rieske-type ferredoxin (T4MOC), an effector protein (T4MOD), and an NADH oxidoreductase (T4MOF). The T4MOH component consists of TmoA, TmoB, and TmoE. TmoB adopts a beta-grasp ubiquitin-like fold but its precise role remains unclear. 79 matched cddid_all.tbl CDD cd17043 cd17043 340563 RA Ras-associating (RA) domain, structurally similar to a beta-grasp ubiquitin-like fold. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and are involved in various functions ranging from tumor suppression to being oncoproteins. Ras proteins are small GTPases that are involved in cellular signal transduction. The RA domain has the beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin (Ub); Ub is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. RA-containing proteins include RalGDS, AF6, RIN, RASSF1, SNX27, CYR1, STE50, and phospholipase C epsilon. 87 matched cddid_all.tbl CDD cd17044 cd17044 340564 Ubl_TBCE ubiquitin-like (Ubl) domain found in tubulin-folding cofactor E (TBCE) and similar proteins. TBCE, also termed tubulin-specific chaperone E, is a tubulin polymerizing protein involved in the second step of the tubulin folding pathway through cooperating in tubulin heterodimer dissociation both in vivo and in vitro. It may also be implicated in the maintenance of the neuronal microtubule network. Mutations in TBCE gene cause hypoparathyroidism, mental retardation and facial dysmorphism. TBCE contains an N-terminal cytoskeleton-associated protein with glycine-rich segment (CAP-Gly) domain, a leucine-rich repeat protein-protein interaction domain followed by leucine-rich repeat (LRR) domains, and a C-terminal ubiquitin-like (Ubl) domain. Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes. 83 matched cddid_all.tbl CDD cd17045 cd17045 340565 Ubl_TBCEL ubiquitin-like (Ubl) domain found in tubulin-specific chaperone cofactor E-like protein (TBCEL) and similar proteins. TBCEL, also termed leucine-rich repeat-containing protein 35 (LRRC35), or E-like (EL), is a novel regulator of tubulin stability, suggesting a link between tubulin turnover and vesicle transport. TBCEL is abundantly expressed in testis, but is also present in several tissues at a much lower level. It is required for the synchronous movement of the investment cones and is important for normal male fertility. TBCEL shows high sequence similarity to tubulin-specific chaperone cofactor E (TBCE), a component of the multimolecular complex required for tubulin heterodimer formation in all eukaryotic cells. It contains a leucine-rich repeat protein-protein interaction domain and a C-terminal ubiquitin-like (Ubl) domain, but does not harbor the cytoskeleton-associated protein with glycine-rich segment (CAP-Gly) domain found in TBCE. 87 matched cddid_all.tbl CDD cd17046 cd17046 340566 Ubl_IKKA_like ubiquitin-like (Ubl) domain found in inhibitor of nuclear factor kappa-B kinases, IKK-alpha and IKK-beta, and similar proteins. IKK, also termed IkappaB kinase, is an enzyme complex involved in propagating the cellular response to inflammation. It is part of the upstream nuclear factor kappa-B kinase (NF-kappaB) signal transduction cascade, and plays an important role in regulating the NF-kappaB transcription factor. IKK is composed of three subunits, IKK-alpha/CHUK, IKK-beta/IKBKB, and IKK-gamma/NEMO. The IKK-alpha and IKK-beta subunits together are catalytically active whereas the IKK-gamma subunit serves a regulatory function. IKK-alpha and IKK-beta phosphorylate the IkappaB proteins, marking them for degradation via ubiquitination and allowing NF-kappaB transcription factors to go into the nucleus. IKK-alpha, also known as IKK-A, or IkappaB kinase A (IkBKA), or conserved helix-loop-helix ubiquitous kinase (CHUK), or I-kappa-B kinase 1 (IKK1), or nuclear factor NF-kappa-B inhibitor kinase alpha (NFKBIKA), or transcription factor 16 (TCF-16), belongs to the serine/threonine protein kinase family. In addition to NF-kappaB response, it has many additional cellular targets in an NF-kappaB-independent manner. For instance, it plays a role in epidermal differentiation, as well as in the regulation of the cell cycle protein cyclin D1. IKK-beta, also known as IKK-B, or IkappaB kinase B (IkBKB), or I-kappa-B kinase 2 (IKK2), or nuclear factor NF-kappa-B inhibitor kinase beta (NFKBIKB), belongs to the serine/threonine protein kinase family as well. It interacts with many different protein partners and has been implicated in the treatment of many inflammatory diseases and cancers. Both IKK-alpha and IKK-beta contain an N-terminal catalytic domain followed by a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. 75 matched cddid_all.tbl CDD cd17047 cd17047 340567 Ubl_UBFD1 ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein UBFD1 and similar proteins. UBFD1, also termed ubiquitin-binding protein homolog (UBPH), is a polyubiquitin binding protein containing a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. It may play a role as nuclear factor-kappaB (NF-kappaB) regulator. 70 matched cddid_all.tbl CDD cd17048 cd17048 340568 Ubl_UBL3 ubiquitin-like (Ubl) domain found in ubiquitin-like protein 3 (UBL3) and similar proteins. UBL3, also termed membrane-anchored ubiquitin-fold protein (MUB), or protein HCG-1, belongs to a newly described MUB protein family with structural homology with ubiquitin. MUB proteins have a beta-grasp ubiquitin-like (Ubl) domain with longer N- and C-termini and extended loops. The Ubl domain contains a C-terminal CAAX-box, a canonical motif for protein prenylation, which is modified through protein lipidation with a hydrophobic membrane anchor. The lipidation and membrane localization inhibit attachment of MUBs to target proteins. 82 matched cddid_all.tbl CDD cd17049 cd17049 340569 Ubl_Sacsin ubiquitin-like (Ubl) domain found in Sacsin and similar proteins. Sacsin, also termed DnaJ homolog subfamily C member 29 (DNAJC29), is encoded by SACS gene that is highly expressed in the brain. Mutations in SACS can cause the neurodegenerative disease autosomal recessive spastic ataxia of Charlevoix Saguenay (ARSACS) which is characterized by early-onset spastic ataxia. Sacsin is a modular protein that is localized on the mitochondrial surface and possibaly required for normal mitochondrial network organization. Sacsin knockdown resulted in a reduction in cells expressing plyglutamine-expanded ataxin-1, which correlated with a loss of cells with large nuclear ataxin-1 incusions. At the N-terminus, sacsin contains a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, which can interact with the proteasome. At the C-terminus, sacsin harbors a protein-protein interaction J-domain followed by an higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domain. The J-domain is typically associated with DnaJ-like co-chaperones involved in regulation of the Hsp70 heat shock system. 73 matched cddid_all.tbl CDD cd17050 cd17050 340570 Ubl1_ANKUB1 ubiquitin-like (Ubl) domain 1 found in Ankyrin repeat and ubiquitin domain-containing 1 (ANKUB1) and similar proteins. ANKUB1 is an uncharacterized protein with two tandem ubiquitin-like (Ubl) domains located at the N-terminal of Ankyrin repeats (ANK). The Ubl domain may have an adaptor role in ubiquitin (Ub)-signaling by mediating protein-protein interaction. Ubl proteins have a beta-grasp Ubl fold and attach to other proteins in a Ubl manner with biochemically distinct roles. The ankyrin repeats have been identified in numerous proteins with diverse functions. The family corresponds to the first Ubl domain. 79 matched cddid_all.tbl CDD cd17051 cd17051 340571 Ubl2_ANKUB1 ubiquitin-like (Ubl) domain 2 found in Ankyrin repeat and ubiquitin domain-containing 1 (ANKUB1) and similar proteins. ANKUB1 is an uncharacterized protein with two tandem ubiquitin-like (Ubl) domains located at the N-terminal of Ankyrin repeats (ANK). The Ubl domain may have an adaptor role in ubiquitin(Ub)-signaling by mediating protein-protein interaction. Ubl proteins have a beta-grasp Ubl fold and attach to other proteins in a Ubl manner with biochemically distinct roles. The ankyrin repeats have been identified in numerous proteins with diverse functions. The family corresponds to the second Ubl domain. 83 matched cddid_all.tbl CDD cd17052 cd17052 340572 Ubl1_FAT10 ubiquitin-like (Ubl) domain 1 found in leukocyte antigen F (HLA-F) adjacent transcript 10 (FAT10) and similar proteins. FAT10, also termed ubiquitin D (UBD), or diubiquitin, is a cytokine-inducible ubiquitin-like (Ubl) modifer that is highly expressed in the thymus, and targets substrates covalently for 26S proteasomal degradation. It is also associated with cancer development, antigen processing and antimicrobial defense, chromosomal stability and cell cycle regulation. FAT10 is presented on immune cells and under the inflammatory conditions, is synergistically induced by interferon gamma (IFNgamma) and tumor necrosis factor (TNFalpha) in the non-immune (liver parenchymal) cells. FAT10 contains two Ubl domains. The family corresponds to the first Ubl domain of FAT10. Some family members contain only one Ubl domain. 74 matched cddid_all.tbl CDD cd17053 cd17053 340573 Ubl2_FAT10 ubiquitin-like (Ubl) domain 2 found in leukocyte antigen F (HLA-F) adjacent transcript 10 (FAT10) and similar proteins. FAT10, also termed ubiquitin D (UBD), or diubiquitin, is a cytokine-inducible ubiquitin-like (Ubl) modifer that is highly expressed in the thymus, and targets substrates covalently for 26S proteasomal degradation. It is also associated with cancer development, antigen processing and antimicrobial defense, chromosomal stability and cell cycle regulation. FAT10 is presented on immune cells and under the inflammatory conditions, is synergistically induced by interferon gamma (IFNgamma) and tumor necrosis factor (TNFalpha) in the non-immune (liver parenchymal) cells. FAT10 contains two Ubl domains. The family corresponds to the second Ubl domain of FAT10. Some family members contain only one Ubl domain. 71 matched cddid_all.tbl CDD cd17054 cd17054 340574 Ubl_AtBAG1_like ubiquitin-like (Ubl) domain found in Arabidopsis thaliana Bcl-2-associated athanogenes AtBAG1, AtBAG2, AtBAG3, AtBAG4, and similar proteins. The family includes four Arabidopsis BAG family proteins (AtBAG1, AtBAG2, AtBAG3, AtBAG4) that have very similar domain organizations with a ubiquitin-like (Ubl) domain in the N-terminus and a BAG domain in the C-terminus. They may function as co-chaperones that regulate diverse cellular pathways, such as programmed cell death and stress responses. AtBAG1, AtBAG3, and AtBAG4 are predicted to localize in the cytoplasm, but the localization of AtBAG2 is the microbody. AtBAG4 can interact with Hsc70. The overexpression of AtBAG4 in tobacco plants confers tolerance to a wide range of abiotic stresses such as UV light, cold, oxidants, and salt treatments. 70 matched cddid_all.tbl CDD cd17055 cd17055 340575 Ubl_AtNPL4_like ubiquitin-like (Ubl) domain found in Arabidopsis thaliana NPL4-like proteins NPL4-1, NPL4-2, and similar proteins. The family includes a group of uncharacterized plant ubiquitin-like (Ubl) domain-containing proteins, including Arabidopsis thaliana NPL4-like protein 1 and NPL4-like protein 2. 73 matched cddid_all.tbl CDD cd17056 cd17056 340576 Ubl_FAF1 ubiquitin-like (Ubl) domain found in FAS-associated factor 1 (FAF1) and similar proteins. FAF1, also termed UBX domain-containing protein 12 (UBXD12), or UBX domain-containing protein 3A (UBXN3A), belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like (Ubl) fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. In addition, FAF1 contains two tandem Ubl domains, which show high structural similarity with UBX domain. FAF1 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. The FAF1-p97 complex inhibits the proteasomal protein degradation in which p97 acts as a co-chaperone. Moreover, FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF1 is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kappaB (NF-kappaB) by interfering with the nuclear translocation of the p65 subunit. Although the precise role of FAF1 in the ubiquitination pathway remains unclear, FAF1 interacts with valosin-containing protein (VCP), which is involved in the ubiquitin-proteosome pathway. This family corresponds to Ubl domains. 71 matched cddid_all.tbl CDD cd17057 cd17057 340577 Ubl_TMUB1_like ubiquitin-like (Ubl) domain found in transmembrane and ubiquitin-like domain-containing proteins TMUB1, TMUB2, and similar proteins. TMUB1, also termed dendritic cell-derived ubiquitin-like protein (DULP), or hepatocyte odd protein shuttling protein, or ubiquitin-like protein SB144, or HOPS, is highly expressed in the nervous system. It is involved in the termination of liver regeneration and plays a negative role in interleukin-6-induced hepatocyte proliferation. The overexpression of Tmub1 has been shown to play a role in the inhibition of cell proliferation. TMUB1 has been implicated in the regulation of locomotor activity and wakefulness in mice, perhaps acting through its interaction with CAMLG. It also facilitates the recycling of AMPA receptors into synaptic membrane in cultured primary neurons. TMUB1 contains transmembrane domains and a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. TMUB2 is an uncharacterized transmembrane domain and Ubl domain-containing protein that shows high sequence similarity to TMUB1. 74 matched cddid_all.tbl CDD cd17058 cd17058 340578 Ubl_SNRNP25 ubiquitin-like (Ubl) domain found in small nuclear ribonucleoprotein U11/U12 subunit 25 (SNRNP25) and similar proteins. SNRNP25, also termed U11/U12 small nuclear ribonucleoprotein 25 kDa protein, U11/U12 snRNP 25 kDa protein (U11/U12-25K), or minus-99 protein, is a component of the U11/U12 snRNPs that are part of the U12-type spliceosome. It contains a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. 89 matched cddid_all.tbl CDD cd17059 cd17059 340579 Ubl_OTU1 ubiquitin-like (Ubl) domain found in ubiquitin thioesterase OTU1 and similar proteins. OTU1 (EC 3.4.19.12), also termed YOD1, or DUBA-8, or HIV-1-induced protease 7 (HIN-7), or OTU domain-containing protein 2 (OTUD2), is a p97-associated deubiquitinylase that functions as a key player in endoplasmic reticulum-associated degradation (ERAD). Its deubiquitinylase activity is also required for negatively regulating cholera toxin A1 (CTA1) retro-translocation. OTU1 contains a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a C2H2-type zinc finger, and an OTU domain. 75 matched cddid_all.tbl CDD cd17060 cd17060 340580 Ubl_RB1CC1 ubiquitin-like (Ubl) domain found in retinoblastoma 1-inducible coiled-coil protein 1 (RB1CC1) and similar proteins. RB1CC1, also termed FAK family kinase-interacting protein of 200 kDa (FIP200), is the mammalian counterpart of the yeast Atg17 gene and functions as a component of the ULK1/Atg13/RB1CC1/Atg101 complex essential for induction of autophagy. RB1CC1 is a key signaling node to regulate cellular proliferation and differentiation. As a DNA-binding transcription factor, RB1CC1 has been implicated in the regulation of retinoblastoma 1 (RB1) expression. RB1CC1 contains a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, as well as a nuclear localization signal (KPRK), a leucine zipper motif and a coiled-coil structure. 75 matched cddid_all.tbl CDD cd17061 cd17061 340581 Ubl_IQUB ubiquitin-like (Ubl) domain found in IQ and ubiquitin-like domain-containing protein (IQUB) and similar proteins. IQUB is an IQ motif and ubiquitin domain-containing protein that may play roles in cilia formation and/or maintenance. It contains a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. 79 matched cddid_all.tbl CDD cd17062 cd17062 340582 Ubl_NUB1 ubiquitin-like (Ubl) domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins. NUB1, also termed negative regulator of ubiquitin-like proteins 1, or renal carcinoma antigen NY-REN-18, or protein BS4, is a NEDD8-interacting protein that can be induced by interferon. It functions as a strong post-transcriptional down-regulator of the NEDD8 expression and plays critical roles in regulating many biological events, such as cell growth, NF-kappaB signaling, and biological responses to hypoxia. NUB1 can also interact with aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1), which may function in the regulation of cell cycle progression. NUB1 contains a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, three ubiquitin-associated domains (UBA), a bipartite nuclear localization signal (NLS) and a PEST motif. 78 matched cddid_all.tbl CDD cd17063 cd17063 340583 Ubl_ANKRD60 ubiquitin-like (Ubl) domain found in ankyrin repeat domain-containing protein 60 (ANKRD60) and similar proteins. ANKRD60 is an uncharacterized ankyrin repeat domain-containing protein which also harbors a conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. 77 matched cddid_all.tbl CDD cd17064 cd17064 340584 Ubl_TAFs_like ubiquitin-like (Ubl) domain found in plant TBP-associated factors (TAFs) and similar proteins. TAFs, also termed transcription initiation factor TFIID subunits, or TAFII250 subunits, are components of the TFIID complex, a multisubunit protein complex involved in promoter recognition and essential for mediating regulation of RNA polymerase transcription. TAFs is the core scaffold of the TFIID complex, which is comprised of the TATA binding protein (TBP) and 12-15 TAFs. TAFs contain a ubiquitin-like (Ubl) domain and a Bromo domain. 72 matched cddid_all.tbl CDD cd17065 cd17065 340585 Ubl_UBP24 ubiquitin-like (Ubl) domain found in ubiquitin carboxyl-terminal hydrolase 24 (UBP24) and similar proteins. UBP24 (EC 3.4.19.12), also termed deubiquitinating enzyme 24, or ubiquitin thioesterase 24, or ubiquitin-specific-processing protease 24 (USP24), is a deubiquitinating protein that interacts with damage-specific DNA-binding protein 2 (DDB2) and regulates DDB2 stability. It may also play a role in the pathogenesis of Parkinson's disease (PD). UBP24 proteins contain an N-terminal ubiquitin-associated (UBA) domain, a ubiquitin-like (Ubl) domain, and a C-terminal peptidase C19 domain. 79 matched cddid_all.tbl CDD cd17066 cd17066 340586 Ubl_KPC2 ubiquitin-like (Ubl) domain found in Kip1 ubiquitination-promoting complex protein 2 (KPC2) and similar proteins. KPC2, also termed ubiquitin-associated domain-containing protein 1 or UBA domain containing 1 (UBAC1), or glialblastoma cell differentiation-related protein 1 (GBDR1), is one of two subunits of Kip1 ubiquitination-promoting complex (KPC), a novel E3 ubiquitin-protein ligase that also contains KPC1 subunit and regulates the ubiquitin-dependent degradation of the cyclin-dependent kinase (CDK) inhibitor p27 at G1 phase. KPC2 contains an ubiquitin-like (Ubl) domain and two ubiquitin-associated (UBA) domains. 87 matched cddid_all.tbl CDD cd17067 cd17067 340587 RBD2_RGS12_like Ras-binding domain (RBD) 2 of regulator of G protein signaling 12 (RGS12) and similar proteins. Regulator of G-protein signaling (RGS) proteins belong to a large family of GTPase-accelerating proteins (GAPs) which act as key inhibitors of G-protein-mediated cell responses in eukaryotes. The RGS12-like subfamily is composed of RGS12 and RGS14, with multidomain architectures including a RGS domain, two tandem Ras-binding domains (RBDs), and a second Galpha interacting domain, the GoLoco motif. The RBD is structurally similar to the beta-grasp fold of ubiquitin, a common structure involved in protein-protein interactions. Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. 72 matched cddid_all.tbl CDD cd17068 cd17068 340588 RBD_PLEKHG5 Ras-binding domain (RBD) found in pleckstrin homology (PH) and RhoGEF domain containing G5 (PLEKHG5) and similar proteins. PLEKHG5, is also termed PH domain-containing family G member 5, or guanine nucleotide exchange factor 720 (GEF720), Syx, or Tech, is a novel Dbl-like protein related to p115Rho-GEF. It functions as a Rho guanine nucleotide exchange factor directly activating RhoA in vivo and potentially involved in the control of neuronal cell differentiation. It also regulates the balance of the RhoA downstream effector Dia and ROCK activities to promote polarized-cancer-cell migration. Moreover, PLEKHG5 activates the nuclear factor kappaB (NFkappaB) signaling pathway. Mutations in the PLEKHG5 gene are relevant with autosomal recessive intermediate Charcot-Marie-Tooth disease (CMT) and lower motor neuron disease (LMND). 75 matched cddid_all.tbl CDD cd17069 cd17069 340589 DCX2 Dublecortin-like domain 2. Members in doublecortin (DCX) gene family are microtubule-associated proteins (MAPs). Microtubules are key components of cytoskeleton that are involved in cell movement, shape determination, division and transport. The DCX gene family consists of eleven paralogs in human and mouse, and its protein domains can occur in double tandem or as a single repeat. The first repeat of DCX domain has a stable ubiquitin-like tertiary fold. Proteins with DCX double tandem domains in general have roles in microtubule (MT) regulation and signal transduction such as X-linked doublecortin (DCX), retinitis pigmentosa-1 (RP1) and doublecortin-like kinase (DCLK). 84 matched cddid_all.tbl CDD cd17070 cd17070 340590 DCX2_RP_like Dublecortin-like domain 2 found in retinitis pigmentosa (RP)-like protein. RP-like protein family is part of doublecortin (DCX) superfamily with double tandem DCX repeats that are associated with retinitis pigmentosa. DCX is a microtubule-associated protein (MAP) with a stable ubiquitin-like tertiary fold. Microtubules are key components of cytoskeleton that are involved in cell movement, shape determination, division and transport. RP-like proteins are colocalized to the photoreceptor and share a function in outer segment disc morphogenesis. 69 matched cddid_all.tbl CDD cd17071 cd17071 340591 DCX1_DCDC2_like Dublecortin-like domain 1 found in doublecortin domain-containing protein 2 (DCDC2) and similar proteins. DCDC2 is a member of the doublecortin (DCX) family. It is a microtubule-associated protein (MAP) with stable double tandem DCX repeats of ubiquitin-like tertiary fold. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Microtubules are key components of the cytoskeleton that are involved in cell movement, shape determination, division and transport. DCDC2 genetic variation in humans is associated with reading disability, attention deficit hyperactivity disorder (ADHD), and difficulties in mathematics. A genetic variant of DCDC2 associates with dyslexia, a common neurobehavioral disorder of reading. DCDC2 protein interacts with many of the same cytoskeleton related proteins that other members of the DCX family interact with. 80 matched cddid_all.tbl CDD cd17072 cd17072 340592 DCX_DCDC5_like Doublecortin-like domain found in doublecortin domain-containing protein 5 (DCDC5) and similar proteins. DCDC5 is a member of doublecortin (DCX) family. It is a microtubule-associated protein (MAP) with stable double tandem DCX repeats of ubiquitin-like tertiary fold. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Microtubules are key components of the cytoskeleton that are involved in cell movement, shape determination, division and transport. DCDC5 is expressed during mitosis and involved in coordinating late cytokinesis. DCDC5 interacts with cytoplasmic dynein and Rab8 as well as with the Rab8 nucleotide exchange factor Rabin8. This family also includes DCDC1, which is a hydrophilic intracellular protein that contains only one DCX repeat. Therefore, DCDC1 might only bind to microtubules without microtubule polymerization properties. DCDC1 is mainly expressed in adult testis. 71 matched cddid_all.tbl CDD cd17073 cd17073 340593 KHA KHA, dimerization domain of potassium ion channel, similar to doublecortin-like domain, found in potassium channel tetramerization domain containing 9 (KCTD9) and similar proteins. This family corresponds to KHA, the tetramerization domain of eukaryotic voltage-dependent potassium ion-channel proteins, mainly found in vertebrates KCTD9 and plants AKT proteins. In plants the domain lies at the C-terminus whereas in many chordates it lies at the N-terminus. KHA shows high sequence similarity with doublecortin-like domain, which has a stable ubiquitin-like tertiary fold. KCTD9, also termed BTB/POZ domain-containing protein 9, belongs to the KCTD protein family, which corresponds to potassium channel tetramerization domain proteins, a class of BTB-domain-containing proteins. It is involved in potassium channel formation. Moreover, KCTD9 contributes to liver injury through NK cell activation during hepatitis B virus (HBV)-induced acute-on-chronic liver failure. AKT proteins play crucial roles in K+ uptake and translocation in plant cells. 65 matched cddid_all.tbl CDD cd17074 cd17074 340594 Ubl_CysO_like ubiquitin-like (Ubl) domain found in Mycobacterium tuberculosis CysO and similar proteins. CysO, also termed 9.5 kDa culture filtrate antigen cfp10A, together with CysM (Cysteine synthase M), forms a protein complex CysM-CysO that represents a new cysteine biosynthetic pathway in Mycobacterium tuberculosis. The replacement of the acetyl group of O-acetylserine by CysO thiocarboxylate to generate a protein-bound cysteine is catalyzed by CysM in a pyridoxal 5?-phosphate (PLP)-dependent manner. The family also includes QbsE that functions as the sulfide donor for the biosynthesis of thioquinolobactin in Pseudomonas fluorescens. A JAMM motif protein QbsD catalyzes removal of the carboxy-terminal dipeptide from QbsE. Both CysO and QbsE are similar to prokaryotic sulfur carrier proteins such as ThiS and MoaD, containing the beta-grasp ubiquitin-like fold. 89 matched cddid_all.tbl CDD cd17075 cd17075 340595 UBX1_UBXN9 Ubiquitin regulatory domain X (UBX) 1 found in UBX domain protein 9 (UBXN9, UBXD9, or ASPSCR1) and similar proteins. UBXN9, also termed tether containing UBX domain for GLUT4 (TUG), or alveolar soft part sarcoma chromosomal region candidate gene 1 protein (ASPSCR1), or alveolar soft part sarcoma locus (ASPL), or renal papillary cell carcinoma protein 17 (RCC17), belongs to the UBXD family of proteins that contains two ubiquitin regulatory domains X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. In addition, UBXN9 contains an N-terminal ubiquitin-like (Ubl) domain. UBXN9 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. UBXN9 is involved in insulin-stimulated redistribution of the glucose transporter GLUT4, assembly of the Golgi apparatus. In addition to GLUT4, UBXN9 also controls vesicle translocation by interacting with insulin-regulated aminopeptidase (IRAP), a transmembrane aminopeptidase. UBXN9 and its budding yeast ortholog, Ubx4p, are multifunctional proteins that share some, but not all functions. Yeast Ubx4p is important for endoplasmic reticulum-associated protein degradation (ERAD) but UBXN9 appears not to share this function. 85 matched cddid_all.tbl CDD cd17076 cd17076 340596 UBX_UBXN10 Ubiquitin regulatory domain X (UBX) found in UBX domain protein 10 (UBXN10) and similar proteins. UBXN10, also termed UBX domain-containing protein 3 (UBXD3), belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. UBXN10 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. UBXN10 localizes to cilia in a p97-dependent manner, and both p97 and UBXN10 are required for ciliogenesis. Additionally, UBXN10 interacts with the intraflagellar transport B (IFT-B) and regulates anterograde transport into cilia. 76 matched cddid_all.tbl CDD cd17077 cd17077 340597 UBX_UBXN11 Ubiquitin regulatory domain X (UBX) found in UBX domain protein 11 (UBXN11) and similar proteins. UBXN11, also termed colorectal tumor-associated antigen COA-1, or socius, or UBX domain-containing protein 5 (UBXD5), belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. UBXN11 may function as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. UBXN11 also acts as a novel interacting partner of Rnd proteins (Rnd1, Rnd2, and Rnd3/RhoE), new members of Rho family of small GTPases. It directly binds to Rnd GTPases through its C-terminal region, and further participates in disassembly of actin stress fibers. UBXN11 also binds directly to Galpha12 and Galpha13 through its N-terminal region. As a novel activator of the Galpha12 family, UBXN11 promotes the Galpha12-induced RhoA activation. 76 matched cddid_all.tbl CDD cd17078 cd17078 340598 Ubl_SLD1_NFATC2ip SUMO-like domain 1 (SLD1), structurally similar to a beta-grasp ubiquitin-like fold, found in nuclear factor of activated T-cells 2 interacting protein (NFATC2ip) and similar proteins. NFATC2ip, also termed nuclear factor of activated T cells (NFAT), cytoplasmic, calcineurin dependent 2 interacting protein, or 45 kDa NF-AT-interacting protein, or 45 kDa NFAT-interacting protein (Nip45), or nuclear factor of activated T-cells, or cytoplasmic 2-interacting protein, belongs to the eukaryotic-specific Rad60-Esc2-Nip45 (RENi) protein family. The family members may act as factors in transcriptional regulation, chromatin silencing and genomic stability, and typically contain an N-terminal polar/charged low-complexity segment and two C-terminal consecutive unique small ubiquitin-related modifier (SUMO)-like domains (SLD1 and SLD2) with beta-grasp fold. NFATC2ip was firstly identified as a co-regulator with NFAT and the T helper 2 (Th2)-specific transcription factor, c-Maf, to induce IL-4 production. NFATC2ip has also been involved in cellular differentiation and coordination of the immune response in humans and mice. 74 matched cddid_all.tbl CDD cd17079 cd17079 340599 Ubl_SLD2_NFATC2ip SUMO-like domain 2 (SLD2), structurally similar to a beta-grasp ubiquitin-like fold, found in nuclear factor of activated T-cells 2 interacting protein (NFATC2ip) and similar proteins. NFATC2ip, also termed nuclear factor of activated T cells (NFAT), cytoplasmic, calcineurin dependent 2 interacting protein, or 45 kDa NF-AT-interacting protein, or 45 kDa NFAT-interacting protein (Nip45), or nuclear factor of activated T-cells, or cytoplasmic 2-interacting protein, belongs to the eukaryotic-specific Rad60-Esc2-Nip45 (RENi) protein family. The family members may act as factors in transcriptional regulation, chromatin silencing and genomic stability, and typically contain an N-terminal polar/charged low-complexity segment and two C-terminal consecutive unique small ubiquitin-related modifier (SUMO)-like domains (SLD1 and SLD2) with beta-grasp fold. NFATC2ip was firstly identified as a co-regulator with NFAT and the T helper 2 (Th2)-specific transcription factor, c-Maf, to induce IL-4 production. NFATC2ip has also been involved in cellular differentiation and coordination of the immune response in humans and mice. NFATC2ip SLD2 domain binds to E2 SUMOylation enzyme, Ubc9, in an almost identical manner to that of SUMO and thereby inhibits elongation of poly-SUMO chains. 73 matched cddid_all.tbl CDD cd17080 cd17080 340600 Ubl_SLD2_Esc2_like SUMO-like domain 2 (SLD2), structurally similar to a beta-grasp ubiquitin-like fold, found in Saccharomyces cerevisiae establishes silent chromatin protein 2 (Esc2p) and similar proteins. Protein Esc2p belongs to the eukaryotic-specific Rad60-Esc2-Nip45 (RENi) protein family, whose members may act as factors in transcriptional regulation, chromatin silencing and genomic stability, and typically contain an N-terminal polar/charged low-complexity segment and two C-terminal consecutive unique small ubiquitin-related modifier (SUMO)-like domains (SLD1 and SLD2) with beta-grasp fold. Yeast Esc2p was identified as a factor promoting gene silencing. It is also required for genome integrity during DNA replication and sister chromatid cohesion in Saccharomyces cerevisiae. Esc2p promotes Mus81p complex-activity via its SUMO-like and DNA binding domains. It also acts as a novel structure-specific DNA-binding factor implicated in the local regulation of the Srs2p helicase through promoting recombination at sites of stalled replication. In addition, Esc2p specifically promotes the accumulation of SUMOylated Mms21-specific substrates and functions with Mms21p to suppress gross chromosomal rearrangements (GCRs). This family also includes DNA repair protein Rad60p from Schizosaccharomyces pombe. It is a SUMO mimetic and SUMO-targeted ubiquitin ligase (STUbL)-interacting protein that is required for the repair of DNA double strand breaks, recovery from S phase replication arrest, and plays an essential role in cell viability. Like other RENi family members, Rad60p has two SLD domains. 74 matched cddid_all.tbl CDD cd17081 cd17081 340601 RAWUL_PCGF1 RING finger- and WD40-associated ubiquitin-like (RAWUL) domain found in polycomb group RING finger protein 1 (PCGF1) and similar proteins. PCGF1, also termed nervous system Polycomb-1 (NSPc1), or RING finger protein 68 (RNF68), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) and serves as the core component of a noncanonical Polycomb repressive complex 1 (PRC1)-like BCOR complex that also contains RING1, RNF2, RYBP, SKP1, as well as the BCL6 co-repressor BCOR and the histone demethylase KDM2B, and is required to maintain the transcriptionally repressive state of some genes, such as Hox genes, BCL6 and the cyclin-dependent kinase inhibitor, CDKN1A. PCGF1 promotes cell cycle progression and enhances cell proliferation as well. It is a cell growth regulator that acts as a transcriptional repressor of p21Waf1/Cip1 via the retinoid acid response element (RARE element). Moreover, PCGF1 functions as an epigenetic regulator involved in hematopoietic cell differentiation. It cooperates with the transcription factor runt-related transcription factor 1 (Runx1) in regulating differentiation and self-renewal of hematopoietic cells. Furthermore, PCGF1 represents a physical and functional link between Polycomb function and pluripotency. PCGF1 contains a C3HC4-type RING-HC finger and a RAWUL domain. 92 matched cddid_all.tbl CDD cd17082 cd17082 340602 RAWUL_PCGF2_like RING finger- and WD40-associated ubiquitin-like (RAWUL) domain found in polycomb group RING finger proteins PCGF2, PCGF4, and similar proteins. This family includes polycomb group RING finger proteins, PCGF2 (also known as Mel-18, or RNF110, or ZNF144) and PCGF4 (also known as BMI-1, or RNF51), both serving as the core component of a canonical polycomb repressive complex 1 (PRC1). PRC1 is composed of a chromodomain-containing protein (CBX2, CBX4, CBX6, CBX7 or CBX8) and a polyhomeotic protein (PHC1, PHC2, or PHC3). Like other PCGF homologs, PCGF2 associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. PCGF4 associates with the Runx1/CBFbeta transcription factor complex to silence the target gene in a PRC2-independent manner. Both, PCGF2 and PCGF4, contain a C3HC4-type RING-HC finger and a RAWUL domain. 108 matched cddid_all.tbl CDD cd17083 cd17083 340603 RAWUL_PCGF3 RING finger- and WD40-associated ubiquitin-like (RAWUL) domain found in polycomb group RING finger protein 3 (PCGF3) and similar proteins. PCGF3, also termed RING finger protein 3A (RNF3A), is one of six PcG RING finger (PCGF) homologs (PCGF1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6) and serves as the core component of a Polycomb repressive complex 1 (PRC1). Like other PCGF homologs, PCGF3 associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. PCGF3 contains a C3HC4-type RING-HC finger, and a RAWUL domain. 85 matched cddid_all.tbl CDD cd17084 cd17084 340604 RAWUL_PCGF5 RING finger- and WD40-associated ubiquitin-like (RAWUL) domain found in polycomb group RING finger protein 5 (PCGF5) and similar proteins. PCGF5, also termed RING finger protein 159 (RNF159), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) and serves as the core component of a Polycomb repressive complex 1 (PRC1). Like other PCGF homologs, PCGF5 associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. PCGF5 contains a C3HC4-type RING-HC finger, and a RAWUL domain. 101 matched cddid_all.tbl CDD cd17085 cd17085 340605 RAWUL_PCGF6 RING finger- and WD40-associated ubiquitin-like (RAWUL) domain found in polycomb group RING finger protein 6 (PCGF6) and similar proteins. PCGF6, also termed Mel18 and Bmi1-like RING finger (MBLR), or RING finger protein 134 (RNF134), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5 and PCGF6/MBLR), and serves as the core component of a noncanonical Polycomb repressive complex 1 (PRC1)-like L3MBTL2 complex, which is composed of some canonical components, such as RNF2, CBX3, CXB4, CXB6, CXB7 and CXB8, as well as some noncanonical components, such as L3MBTL2, E2F6, WDR5, HDAC1 and RYBP, and plays critical roles in epigenetic transcriptional silencing in higher eukaryotes. Like other PCGF homologs, PCGF6 possesses the transcriptional repression activity, and also associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. Moreover, PCGF6 can regulate the enzymatic activity of JARID1d/KDM5D, a trimethyl H3K4 demethylase, through the direct interaction with it. Furthermore, PCGF6 is expressed predominantly in meiotic and post-meiotic male germ cells and may play important roles in mammalian male germ cell development. It also regulates mesodermal lineage differentiation in mammalian embryonic stem cells (ESCs) and functions in induced pluripotent stem (iPS) reprogramming. The activity of PCGF6 is found to be regulated by cell cycle dependent phosphorylation. PCGF6 contains a C3HC4-type RING-HC finger, and a RAWUL domain. 89 matched cddid_all.tbl CDD cd17086 cd17086 340606 RAWUL_RING1_like RING finger- and WD40-associated ubiquitin-like (RAWUL) domain found in really interesting new gene proteins RING1, RING2 and similar proteins. RING1, also termed polycomb complex protein RING1, or RING finger protein 1 (RNF1), or RING finger protein 1A (RING1A), has been identified as a transcriptional repressor that is associated with the Polycomb group (PcG) protein complex involved in stable repression of gene activity. RING2, also termed huntingtin-interacting protein 2-interacting protein 3, or HIP2-interacting protein 3, or protein DinG, or RING finger protein 1B (RING1B), or RING finger protein 2 (RNF2), or RING finger protein BAP-1, is an E3 ubiquitin-protein ligase that interacts with both nucleosomal DNA and an acidic patch on histone H4 to achieve the specific monoubiquitination of K119 on histone H2A (H2AK119ub), thereby playing a central role in histone code and gene regulation. Both, RING1 and RING2, are core components of polycomb repressive complex 1 (PRC1) that functions as an E3-ubuiquitin ligase transferring the mono-ubuiquitin mark to the C-terminal tail of Histone H2A at K118/K119. PRC1 is also capable of chromatin compaction, a function not requiring histone tails, and this activity appears important in gene silencing. RING2 acts as the main E3 ubiquitin ligase on histone H2A of the PRC1 complex, while RING1 may rather act as a modulator of RNF2/RING2 activity. Members in this family contain a C3HC4-type RING-HC finger, and a RAWUL domain. 106 matched cddid_all.tbl CDD cd17087 cd17087 340607 RAWUL_DRIP_like RING finger- and WD40-associated ubiquitin-like (RAWUL) domain found in DREB2A-interacting protein (DRIP) and similar proteins. Dehydration-Responsive Element-Binding Protein 2A (DREB2A) regulates the expression of stress-inducible genes via the dehydration-responsive elements and requires posttranslational modification for its activation. DREB2A-Interacting Protein (DRIP) contains a RING finger, and a RING finger- and WD40-associated ubiquitin-like (RAWUL) domain. DRIP interacts with DREB2A and functions as a E3 ubiquitin ligases that negatively regulates DREB2A expression. 104 matched cddid_all.tbl CDD cd17088 cd17088 340608 FERM_F1_FRMPD1_like FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in FERM and PDZ domain-containing proteins FRMPD1, FRMPD3, FRMPD4, and similar proteins. This family includes FERM and PDZ domain-containing proteins FRMPD1, FRMPD3, and FRMPD4, which all contain a PDZ domain and a FERM domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain of the FERM domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). FRMPD1, also termed FERM domain-containing protein 2, is an activator of G-protein signaling 3 (AGS3)-binding protein that regulates the subcellular location of AGS3 and its interaction with G-proteins. FRMPD4, also termed PDZ domain-containing protein 10, or PSD-95-interacting regulator of spine morphogenesis (Preso), is a multiscaffolding protein that modulates both Homer1 and post-synaptic density protein 95 activity. Both FRMPD1 and FRMPD4 can associate with the tetratricopeptide repeat (TPR) motif-containing adaptor protein LGN. The biological role of FRMPD3 remains unclear. 90 matched cddid_all.tbl CDD cd17089 cd17089 340609 FERM_F0_TLN FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F0 sub-domain, found in Talin and similar proteins. Talin is a cytoskeletal protein that activates integrins and couples them to cytoskeletal actin. Talin consists of an N-terminal head and a C-terminal rod. The talin head harbors a FERM (Band 4.1, ezrin, radixin, moesin) domain made up of F1, F2 and F3 domains, as well as an N-terminal region that precedes the FERM domain and has been referred to as the F0 domain. Both F0 and F1 domains have similar ubiquitin-like folds. This family corresponds to the F0 domain that is joined to the F1 domain in a novel fixed orientation by an extensive charged interface. It is required for maximal integrin-activation, by interacting with other FA components; no binding partner has yet been found for it. 84 matched cddid_all.tbl CDD cd17090 cd17090 340610 FERM_F1_TLN FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in Talin and similar proteins. Talin is a cytoskeletal protein that activates integrins and couples them to cytoskeletal actin. Talin consists of an N-terminal head and a C-terminal rod. The talin head harbors a FERM (Band 4.1, ezrin, radixin, moesin) domain made up of F1, F2 and F3 domains, as well as an N-terminal region that precedes the FERM domain and has been referred to as the F0 domain. Both F0 and F1 domains have similar ubiquitin-like folds. This family corresponds to the F0 domain that is joined to the F1 domain in a novel fixed orientation by an extensive charged interface. It is required for maximal integrin-activation, by interacting with other FA components; no binding partner has yet been found for it. 111 matched cddid_all.tbl CDD cd17091 cd17091 340611 FERM_F0_SHANK FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F0 sub-domain, found in SH3 and multiple ankyrin repeat domains proteins, SHANK1, SHANK2, and SHANK3. SHANK proteins (SHANK1, SHANK2, and SHANK3) are core components of the postsynaptic density (PSD) of excitatory synapses. They act as scaffolding molecules that cluster neurotransmitter receptors as well as cell adhesion molecules attaching them to the actin cytoskeleton. They play important roles in proper excitatory synapse and circuit function. Mutations in SHANK genes, especially in SHANK3 and SHANK2, may lead to neuropsychiatric disorders, such as autism spectrum disorder (ASD). SHANK proteins contain an N-terminal F0 domain of FERM (Band 4.1, ezrin, radixin, moesin), six ankyrin (ANK) repeats, one SH3 (Src homology 3) domain, one PDZ (PSD-95, Dlg, and ZO-1/2, also termed DHR or GLGF) domain, and a C-terminal SAM (sterile alpha motif) domain. This family corresponds to the F0 domain that adopts a ubiquitin-like fold. 84 matched cddid_all.tbl CDD cd17092 cd17092 340612 FERM1_F1_Myosin-VII FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain 1, F1 sub-domain, found in Myosin-VIIa, Myosin-VIIb, and similar proteins. This family includes two nontraditional members of the myosin superfamily, myosin-VIIa and myosin-VIIb. Myosin-VIIa, also termed myosin-7a (Myo7a), has been implicated in the structural organization of hair bundles at the apex of sensory hair cells (SHCs) where it serves mechanotransduction in the process of hearing and balance. Mutations in the MYO7A gene may be associated with Usher Syndrome type 1B (USH1B) and nonsyndromic hearing loss (DFNB2, DFNA11). Myosin-VIIb, also termed myosin-7b (Myo7b), is a high duty ratio motor adapted for generating and maintaining tension. It associates with harmonin and ANKS4B to form a stable ternary complex for anchoring microvilli tip-link cadherins. Like other unconventional myosins, myosin-VII is composed of a conserved motor head, a neck region and a tail region containing two MyTH4 domains, a SH3 domain, and two FERM domains. The FERM domain is made up of three sub-domains, F1, F2, and F3. The family corresponds to the F1 sub-domain of the first FERM domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 99 matched cddid_all.tbl CDD cd17093 cd17093 340613 FERM2_F1_Myosin-VII FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain 2, F1 sub-domain, found in Myosin-VIIa, Myosin-VIIb, and similar proteins. This family includes two nontraditional members of myosin superfamily, myosin-VIIa and myosin-VIIb. Myosin-VIIa, also termed myosin-7a (Myo7a), has been implicated in the structural organization of hair bundles at the apex of sensory hair cells (SHCs) where it serves mechanotransduction in the process of hearing and balance. Mutations in MYO7A gene may be associated with Usher Syndrome type 1B (USH1B) and nonsyndromic hearing loss (DFNB2, DFNA11). Myosin-VIIb, also termed myosin-7b (Myo7b), is a high duty ratio motor adapted for generating and maintaining tension. It associates with harmonin and ANKS4B to form a stable ternary complex for anchoring microvilli tip-link cadherins. Like other unconventional myosins, myosin-VII is composed of a conserved motor head, a neck region and a tail region containing two MyTH4 domains, a SH3 domain, and two FERM domains. The FERM domain is made up of three sub-domains, F1, F2, and F3. The family corresponds to the F1 sub-domain of the second FERM domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 98 matched cddid_all.tbl CDD cd17094 cd17094 340614 FERM_F1_Max1_like FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in Caenorhabditis elegans max-1 and its homologs PLEKHH1 and PLEKHH2. Caenorhabditis elegans max-1 is expressed and functions in motor neurons. MAX-1 protein plays a possible role in netrin-induced axon repulsion by modulating the UNC-5 receptor signaling pathway. PLEKHH1 is critically required in vascular patterning in vertebrate species through acting upstream of the ephrin pathway. PLEKHH2 is highly enriched in renal glomerular podocytes, and acts as a novel, important component of the podocyte foot processes. It is involved in matrix adhesion and actin dynamics. Members in this family all contain two Pleckstrin homology (PH) domains, a MyTH4 domain, and a FERM (Band 4.1, ezrin, radixin, moesin) domain within the C-terminal half. The FERM domain is made up of three sub-domains, F1, F2, and F3. The family corresponds to F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 102 matched cddid_all.tbl CDD cd17095 cd17095 340615 FERM_F0_kindlins FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F0 sub-domain, found in the kindlin family. The kindlin family is composed of kindlin-1, 2 and 3, which are FERM domain-containing adaptor molecules that interact with the cytoplasmic component of integrins and regulate cell-matrix connections. Kindlins belong to the 4.1- ezrin-ridixin-moesin (FERM) domain containing protein family. They contain F1, F2 and F3 subdomains that typify FERM family members, and these subdomains are preceded by an N-terminal F0 subdomain. Both F0 and F1 domains have similar ubiquitin-like folds. This family corresponds to the F0 domain. In addition, a distinctive feature of kindlins is the insertion of a pleckstrin homology (PH) subdomain into the F2 subdomain. 80 matched cddid_all.tbl CDD cd17096 cd17096 340616 FERM_F1_kindlins FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in the kindlin family. The kindlin family is composed of Kindlin-1, 2 and 3, which are FERM domain-containing adaptor molecules that interact with the cytoplasmic component of integrins and regulate cell-matrix connections. Kindlins belong to the 4.1- ezrin-ridixin-moesin (FERM) domain containing protein family. They contain F1, F2 and F3 subdomains that typify FERM family members, and these subdomains are preceded by an N-terminal F0 subdomain. Both F0 and F1 domains have similar ubiquitin-like folds. This family corresponds to the F1 domain. In addition, a distinctive feature of kindlins is the insertion of a pleckstrin homology (PH) subdomain into the F2 subdomain. 90 matched cddid_all.tbl CDD cd17097 cd17097 340617 FERM_F1_ERM_like FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in the ERM family proteins. The ezrin-radixin-moesin (ERM) family includes a group of closely related cytoskeletal proteins that play an essential role in microvilli formation, T-cell activation, and tumor metastasis through providing a regulated linkage between F-actin and membrane-associated proteins. These proteins may also function in signaling cascades that regulate the assembly of actin stress fibers. The ERM proteins consist of an N-terminal FERM domain, a coiled-coil (CC) domain and a C-terminal tail segment (C-tail) containing a well-defined actin-binding motif. They exist in two states, a dormant state in which the FERM domain binds to its own C-terminal tail and thereby precludes binding of some partner proteins, and an activated state, in which the FERM domain binds to one of many membrane binding proteins and the C-terminal tail binds to F-actin. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). Merlin, which is highly related to the members of the ezrin, radixin, and moesin (ERM) protein family that are directly attached to and functionally linked with NHE1, is included in this family. 83 matched cddid_all.tbl CDD cd17098 cd17098 340618 FERM_F1_FARP1_like FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in FERM, RhoGEF and pleckstrin domain-containing protein 1 (FARP1) and similar proteins. This family includes the F1 sub-domain of FERM, RhoGEF and pleckstrin domain-containing proteins FARP1, FARP2, and FERM domain-containing protein 7 (FRMD7). FARP1, also termed chondrocyte-derived ezrin-like protein (CDEP), or pleckstrin homology (PH) domain-containing family C member 2 (PLEKHC2), is a neuronal activator of the RhoA GTPase. It promotes outgrowth of developing motor neuron dendrites. It also regulates excitatory synapse formation and morphology, as well as activates the GTPase Rac1 to promote F-actin assembly. FARP2, also termed FERM domain including RhoGEF (FIR), or Pleckstrin homology (PH) domain-containing family C member 3, is a Dbl-family guanine nucleotide exchange factor (GEF) that activates Rac1 or Cdc42 in response to upstream signals, suggesting roles in regulating processes such as neuronal axon guidance and bone homeostasis. It is also a key molecule involved in the response of neuronal growth cones to class-3 semaphorins. FRMD7 plays an important role in neuronal development and is involved in the regulation of F-actin, neurofilament, and microtubule dynamics. All family members contain a FERM domain that is made up of three sub-domains, F1, F2, and F3. This family corresponds to F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 85 matched cddid_all.tbl CDD cd17099 cd17099 340619 FERM_F1_PTPN14_like FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in tyrosine-protein phosphatase non-receptors PTPN14, PTPN21, and similar proteins. This family includes tyrosine-protein phosphatase non-receptors PTPN14 and PTPN21, both of which are protein-tyrosine phosphatase (PTP). They belong to the FERM family of PTPs characterized by a conserved N-terminal FERM domain and a C-terminal PTP catalytic domain with an intervening sequence containing an acidic region and a putative SH3 domain-binding sequence. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). PTPN14 plays a role in the nucleus during cell proliferation. PTPN21 interacts with a Tec tyrosine kinase family member, the epithelial and endothelial tyrosine kinase (Etk, also known as Bmx), modulates Stat3 activation, and plays a role in the regulation of cell growth and differentiation. 85 matched cddid_all.tbl CDD cd17100 cd17100 340620 FERM_F1_PTPN3_like FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in tyrosine-protein phosphatase non-receptor type 3 (PTPN3) and similar proteins. This family includes two tyrosine-protein phosphatase non-receptors, PTPN3 and PTPN4, both of which belong to the non-transmembrane FERM-containing protein-tyrosine phosphatase (PTP) subfamily characterized by a conserved N-terminal FERM domain, a PDZ domain, and a C-terminal PTP catalytic domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 86 matched cddid_all.tbl CDD cd17101 cd17101 340621 FERM_F1_PTPN13_like FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in tyrosine-protein phosphatase non-receptor type 13 (PTPN13) and similar proteins. This family includes tyrosine-protein phosphatase non-receptor type 13 (PTPN13), FERM and PDZ domain-containing protein 2 (FRMPD2), and FERM domain-containing proteins FRMD1 and FRMD6. All family members contain a FERM domain that is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 97 matched cddid_all.tbl CDD cd17102 cd17102 340622 FERM_F1_FRMD3 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in FERM domain-containing protein 3 (FRMD3) and similar proteins. FRMD3, also termed band 4.1-like protein 4O, or ovary type protein 4.1 (4.1O), belongs to the 4.1 protein superfamily, which share the highly conserved membrane-association FERM domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). FRMD3 is involved in maintaining cell shape and integrity. It also functions as a tumour suppressor in non-small cell lung carcinoma (NSCLC). Some single nucleotide polymorphisms (SNPs) located in FRMD3 have been associated with diabetic kidney disease (DKD) in different ethnicities. 82 matched cddid_all.tbl CDD cd17103 cd17103 340623 FERM_F1_FRMD4 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in FERM domain-containing proteins FRMD4A, FRMD4B, and similar proteins. This family includes FERM domain-containing proteins FRMD4A and FRMD4B, both of which contain a FERM domain that is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). FRMD4A is a cytohesin adaptor involved in cell structure, transport and signaling. It promotes the growth of cancer cells in tongue, head and neck squamous cell carcinomas. FRMD4B, also termed GRP1-binding protein GRSP1, interacts with the coil-coil domain of ARF exchange factor GRP1 to form the Grsp1-Grp1 complex that co-localizes with cortical actin rich regions in response to stimulation of CHO-T cells with insulin or epidermal growth factor (EGF). 91 matched cddid_all.tbl CDD cd17104 cd17104 340624 FERM_F1_MYLIP FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in E3 ubiquitin-protein ligase MYLIP and similar proteins. MYLIP, also termed inducible degrader of the LDL-receptor (Idol), or myosin regulatory light chain interacting protein (MIR), is an E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of myosin regulatory light chain (MRLC), LDLR, VLDLR and LRP8. Its activity depends on E2 ubiquitin-conjugating enzymes of the UBE2D family, including UBE2D1, UBE2D2, UBE2D3, and UBE2D4. MYLIP stimulates clathrin-independent endocytosis and acts as a sterol-dependent inhibitor of cellular cholesterol uptake by binding directly to the cytoplasmic tail of the LDLR and promoting its ubiquitination via the UBE2D1/E1 complex. The ubiquitinated LDLR then enters the multivesicular body (MVB) protein-sorting pathway and is shuttled to the lysosome for degradation. Moreover, MYLIP has been identified as a novel ERM-like protein that affects cytoskeleton interactions regulating cell motility, such as neurite outgrowth. The ERM proteins includes ezrin, radixin, and moesin, which are cytoskeletal effector proteins linking actin to membrane-bound proteins at the cell surface. MYLIP contains a FERM-domain and a C-terminal C3HC4-type RING-HC finger. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 81 matched cddid_all.tbl CDD cd17105 cd17105 340625 FERM_F1_EPB41 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in erythrocyte membrane protein band 4.1 (EPB41) and similar proteins. EPB41, also termed protein 4.1 (P4.1), or 4.1R, or Band 4.1, or EPB4.1, belongs to the skeletal protein 4.1 family that is involved in cellular processes such as cell adhesion, migration and signaling. EPB41 is a widely expressed cytoskeletal phosphoprotein that stabilizes the spectrin-actin cytoskeleton and anchors the cytoskeleton to the cell membrane. EPB41 contains a FERM domain, a spectrin and actin binding (SAB) domain, and a C-terminal domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 83 matched cddid_all.tbl CDD cd17106 cd17106 340626 FERM_F1_EPB41L FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in erythrocyte membrane protein band 4.1-like proteins. The family includes erythrocyte membrane protein band 4.1-like proteins EPB41L1/4.1N, EPB41L2/4.1G, and EPB41L3/4.1B. They belong to the skeletal protein 4.1 family that is involved in cellular processes such as cell adhesion, migration and signaling. EPB41L1 is a cytoskeleton-associated protein that may serve as a tumor suppressor in solid tumors. EPB41L2 is involved in cellular processes such as cell adhesion, migration and signaling. EPB41L3 also acts as a tumor suppressor implicated in a variety of meningiomas and carcinomas. Members in this family contain a FERM domain, a spectrin and actin binding (SAB) domain, and a C-terminal domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 84 matched cddid_all.tbl CDD cd17107 cd17107 340627 FERM_F1_EPB41L4A FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in erythrocyte band 4.1-like protein 4A (EPB41L4A) and similar proteins. EPB41L4A, also termed protein NBL4, is a member of the band 4.1/Nbl4 (novel band 4.1-like protein 4) group of the FERM protein superfamily. It contains a FERM domain that is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). EPB41L4A is an important component of the beta-catenin/Tcf pathway. It may be related to determination of cell polarity or proliferation. 91 matched cddid_all.tbl CDD cd17108 cd17108 340628 FERM_F1_EPB41L5_like FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in erythrocyte membrane protein band 4.1-like 5 (EPB41L5) and similar proteins. This family includes FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in erythrocyte membrane protein band 4.1-like proteins, EPB41L5 and EPB41L4B. EPB41L5 is a mesenchymal-specific protein that is an integral component of the ARF6-based pathway. EPB41L4B is a positive regulator of keratinocyte adhesion and motility, suggesting a role in wound healing. It also promotes cancer metastasis in melanoma, prostate cancer and breast cancer. Both EPB41L5 and EPB41L4B contain a FERM domain that is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 81 matched cddid_all.tbl CDD cd17109 cd17109 340629 FERM_F1_SNX17_like FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in PX-FERM family sorting nexin proteins. This family includes three endosome-associated PX (Phox homology) and FERM (Band 4.1, ezrin, radixin, moesin) domain-containing proteins called sorting nexin (SNX) 17, SNX27, and SNX31, which are modular peripheral membrane proteins acting as central scaffolds mediating protein-lipid interactions, cargo binding, and regulatory protein recruitment. They are key regulators of endosomal recycling and bind conserved NPX(Y/F) peptide sorting motifs in transmembrane cargos via an atypical FERM domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 93 matched cddid_all.tbl CDD cd17110 cd17110 340630 FERM_F1_Myo10_like FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in unconventional myosin-X and similar proteins. Myosin-X, also termed myosin-10 (Myo10), is an untraditional member of myosin superfamily. It is an actin-based motor protein that plays a critical role in diverse cellular motile events, such as filopodia formation/extension, phagocytosis, cell migration, and mitotic spindle maintenance, as well as a number of disease states including cancer metastasis and pathogen infection. Myosin-X functions as an important regulator of cytoskeleton that modulates cell motilities in many different cellular contexts. It regulates neuronal radial migration through interacting with N-cadherin. Like other unconventional myosins, Myosin-X is composed of a conserved motor head, a neck region and a variable tail. The neck region consists of three IQ motifs (light chain-binding sites), and a predicted stalk of coiled coil. The tail contains three PEST regions, three PH domains, a MyTH4 domain, and a FERM domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). Amoebozoan Dictyostelium discoideum myosin VII (DdMyo7) and uncharacterized pleckstrin homology domain-containing family H member 3 (PLEKHH3) are also included in this family. Like metazoan Myo10, DdMyo7 is essential for the extension of filopodia, plasma membrane protrusions filled with parallel bundles of F-actin. 97 matched cddid_all.tbl CDD cd17111 cd17111 340631 RA1_DAGK-theta Ras-associating (RA) domain 1 found in diacylgylcerol kinase theta (DAGK-theta) and similar proteins. DAGK phosphorylates the second messenger diacylglycerol to phosphatidic acid as part of a protein kinase C pathway. DAGK-theta is characterized as a type V DAGK that has three cysteine-rich domains (all other isoforms have two), a proline/glycine-rich domain at its N-terminal, and a proposed Ras-associating (RA) domain. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and are involved in several different functions ranging from tumor suppression to being oncoproteins. Ras proteins are small GTPases that are involved in cellular signal transduction. The RA domain has a beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin (Ub). Ub is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. Ten mammalian isoforms of DAGK have been identified to date which are organized into five categories based on the domain architecture. DAGK-theta also contains a pleckstrin homology (PH) domain. The subcellular localization and the activity of DAGK-theta are regulated in a complex (stimulation- and cell type-dependent) manner. This family corresponds to the first RA domain of DAGK-theta. 91 matched cddid_all.tbl CDD cd17112 cd17112 340632 RA_MRL_like Ras-associating (RA) domain found in Mig10/RIAM/Lpd (MRL) family and growth factor receptor-bound (Grb) protein 7/10/14. MRL proteins share a common structural architecture, including a central structural unit consisting of a Ras-associating (RA) domain and a pleckstrin homology (PH) domain, an upstream coiled-coil region, and a number of polyproline motifs. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and are involved in several different functions ranging from tumor suppression to being oncoproteins. Ras proteins are small GTPases that are involved in cellular signal transduction. RA domain has the beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin (Ub). Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. RA and PH form a tandem domain pair (RA-PH), and serve tightly coordinated functions in both Ras GTPase signaling via the RA domain and membrane translocalization via the PH domain. MRL proteins have distinct functions in cell migration and adhesion, signaling, and in cell growth. Grb7/10/14 are multi-domain cytoplasmic adaptor proteins that are recruited to activated receptor tyrosine kinases. Grb7 and its related family members Grb10 and Grb14 share a conserved domain architecture that includes an amino-terminal proline-rich region, a central segment termed the GM region (for Grb and Mig) which includes the RA, PIR, and pleckstrin homology (PH) domains, and a carboxyl-terminal SH2 domain. The tandem RA and PH domains of Grb7/10/14 are also found in a second adaptor family, Rap1-interacting adaptor molecule (RIAM) and lamellipodin, which is involved in actin-cytoskeleton rearrangement. Grb7/10/14 family proteins are phosphorylated on serine/threonine as well as tyrosine residues and are mainly localized to the cytoplasm. 81 matched cddid_all.tbl CDD cd17113 cd17113 340633 RA_ARAPs Ras-associating (RA) domain found in Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing proteins ARAP1, ARAP2, ARAP3, and similar proteins. ARAPs are phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P(3))-dependent Arf Rap-activated guanosine triphosphatase (GTPase)-activating proteins (GAPs). They contain multiple functional domains, including ArfGAP and RhoGAP domains, as well as a sterile alpha motif (Sam) domain, five PH domains, and a RA domain. The RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin (Ub); Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. 95 matched cddid_all.tbl CDD cd17114 cd17114 340634 RA_PLC-epsilon Ras-associating (RA) domain found in Phosphatidylinositide-specific phospholipase C (PLC)-epsilon. PLC is a signaling enzyme that hydrolyzes membrane phospholipids to generate inositol triphosphate. PLC-epsilon represents a novel forth class of PLC that has a PLC catalytic core domain, a CDC25 guanine nucleotide exchange factor domain and two RA (Ras-association) domains. RA domain has the beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin (Ub). Although PLC RA1 and RA2 have homologous ubiquitin-like folds only RA2 can bind Ras and activate it. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and are involved in several different functions ranging from tumor suppression to being oncoproteins. Ras proteins are small GTPases that are involved in cellular signal transduction. 97 matched cddid_all.tbl CDD cd17115 cd17115 340635 RA_RHG20 Ras-associating (RA) domain found in Rho GTPase-activating protein 20 (RHG20) and similar proteins. RHG20, also termed ARHGAP20, is one of GTPase activating proteins for Rho family proteins (RhoGAPs). It contains a PH-like domain, an RA domain, a RhoGap domain, and two Annexin-like (ANXL) repeats. RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin that is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. 117 matched cddid_all.tbl CDD cd17116 cd17116 340636 RA_Radil_like Ras-associating (RA) domain found in ras-associating and dilute domain-containing protein (Radil) and similar proteins. Radil acts as an important small GTPase Rap1 effector required for cell spreading and migration. It regulates neutrophil adhesion and motility through linking Rap1 to beta2-integrin activation.This family also includes Ras-interacting protein 1 (Rain, also termed Rasip1), which is a novel Ras-interacting protein with a unique subcellular localization. It interacts with Ras in a GTP-dependent manner, and may serve as an effector for endomembrane-associated Ras. Radil contains RA, DIL, and PDZ domains. In contrast, Rain contains a myosin5-like cargo binding domain, a RA domain and a PDZ domain. RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin (Ub). Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. 121 matched cddid_all.tbl CDD cd17117 cd17117 340637 RA_ANKFN1_like Ras-associating (RA) domain found in Ankyrin repeat and fibronectin type-III domain-containing protein 1 (ANKFN1) and similar proteins. ANKFN1 is a multi-domain protein, with unknown function, that contains two ankyrin repeats and one fibronectin type-III domain. Except for the mammalian homologs, most metazon ANKFN1 harbor a RA domain at the C-terminus. The RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. 97 matched cddid_all.tbl CDD cd17118 cd17118 340638 Ubl_HERP1 ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress protein HERP1 and similar proteins. HERP1, also termed homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (HERPUD1), or methyl methanesulfonate (MMF)-inducible fragment protein 1 (MIF1), is an endoplasmic reticulum (ER) integral membrane protein containing an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. HERP1 is a component of the ER quality control (ERQC) system, also called ER-associated degradation (ERAD), which is involved in ubiquitin-dependent degradation of misfolded ER proteins. It promotes the degradation of ER-resident Ca2+ channels. It is also involved in ubiquitin ligase HRD1-dependent protein degradation at the ER. Moreover, HERP1 plays a role in regulating the cell cycle, apoptosis and steroid hormone biosynthesis in mouse granulosa cells. 78 matched cddid_all.tbl CDD cd17119 cd17119 340639 Ubl_HERP2 ubiquitin-like (Ubl) domain found in homocysteine-inducible endoplasmic reticulum stress protein HERP2 and similar proteins. HERP2, also termed homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 2 protein (HERPUD2), is an endoplasmic reticulum (ER) integral membrane protein containing an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. It is homologous to HERP1, and could be involved in the unfolded protein response (UPR) pathway. It regulates the ubiquitin ligase HRD1-dependent protein degradation at the ER. 77 matched cddid_all.tbl CDD cd17120 cd17120 340640 Ubl_UBTD1 ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein 1 (UBTD1). UBTD1 is the mammalian homolog of the mitochondrial Dc-UbP/UBTD2 protein, both of which contain an N-terminal ubiquitin binding domain (UBD) and a C-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. UBTD1 stably interacts with the UBE2D family of E2 ubiquitin conjugating enzymes. As a tumor suppressor, UBTD1 plays a pivotal role in in regulating cellular senescence that mediates p53 function. It is also involved in MDM2 ubiquitination and degradation. 69 matched cddid_all.tbl CDD cd17121 cd17121 340641 Ubl_UBTD2 ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein 2 (UBTD2). UBTD2, also termed dendritic cell-derived ubiquitin-like protein (DC-UbP), or ubiquitin-like protein SB72, is a potential ubiquitin shuttle protein firstly identified in dendritic cells and implicated in apoptosis. It binds proteins involved in the ubiquitination pathway and may play an important role in regulating protein ubiquitination and delivery of ubiquitinated substrates in eukaryotic cells. UBTD2 is expressed in tumor cells but not in normal human adult tissue suggesting a role in tumorogenesis. It can potentially regulate the stability of proteins involved in various physiological processes relevant to many disease phenotypes, such as ageing and cancer. UBTD2 reconciles protein ubiquitination and deubiquitination via linking UbE1 and USP5 enzymes. 75 matched cddid_all.tbl CDD cd17122 cd17122 340642 Ubl_UHRF1 ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing protein 1(UHRF1). UHRF1, also termed inverted CCAAT box-binding protein of 90 kDa, or nuclear protein 95, or nuclear zinc finger protein Np95 (Np95), or RING finger protein 106, or transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1, is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma, gastric cancer, esophageal squamous cell carcinoma, colorectal cancer, prostate cancer, and breast cancer. UHRF1 can acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumor suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21.Moreover, UHRF1-dependent repression of factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination ofTIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (Ubl), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitination has an essential role in maintenance DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibits both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1. 74 matched cddid_all.tbl CDD cd17123 cd17123 340643 Ubl_UHRF2 ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2). UHRF2, also termed Np95/ICBP90-like RING finger protein (NIRF), or Np95-likeRING finger protein, or nuclear protein 97, or nuclear zinc finger protein Np97, or RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2, was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131(ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (Ubl), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a set- and ring-associated (SRA) domain, and a C-terminal RING finger. 74 matched cddid_all.tbl CDD cd17124 cd17124 340644 Ubl_TECR ubiquitin-like (Ubl) domain found in trans-2,3-enoyl-CoA reductase (TECR). TECR, also termed very-long-chain enoyl-CoA reductase, or synaptic glycoprotein SC2, or TER, or GPSN2, is a synaptic glycoprotein that catalyzes the fourth reaction in the synthesis of very long-chain fatty acids (VLCFA) which is the reduction step of the microsomal fatty acyl-elongation process. Diseases involving perturbations to normal synthesis and degradation of VLCFA (e.g. adrenoleukodystrophy and Zellweger syndrome) have significant neurological consequences. The mammalian TECR P182L mutation causes nonsyndromic mental retardation. Deletion of the yeast TECR homolog (TSC13p) is lethal. TECR contains an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions, as well as a C-terminal catalytic domain. 79 matched cddid_all.tbl CDD cd17125 cd17125 340645 Ubl_TECRL ubiquitin-like (Ubl) domain found in trans-2,3-enoyl-CoA reductase-like (TECRL). TECRL, also termed steroid 5-alpha-reductase 2-like 2 protein (SRD5A2L2), is associated with life?threatening inherited arrhythmias displaying features of both long QT syndrome (LQTS) and catecholaminergic polymorphic ventricular tachycardia (CPVT). TECRL contains an N-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions, as well as a C-terminal catalytic domain. 78 matched cddid_all.tbl CDD cd17126 cd17126 340646 Ubl_HR23A ubiquitin-like (Ubl) domain found in UV excision repair protein RAD23 homolog A (HR23A). HR23A, also termed RAD23A, is a DNA repair protein that binds to 19S subunit of the 26S proteasome and shuttles ubiquitinated proteins to the proteasome for degradation, which is required for efficient nucleotide excision repair (NER), a primary mechanism for removing UV-induced DNA lesions. HR23A also plays a critical role in the interaction of HIV-1 viral protein R (Vpr) with the proteasome, especially facilitating Vpr to promote protein poly-ubiquitination. HR23A contains an N-terminal ubiquitin-like (Ubl) domain that binds proteasomes and two C-terminal ubiquitin-associated (UBA) domains that bind ubiquitin or multi-ubiquitinated substrates. In addition, it has a XPC protein-binding domain that might be necessary for its efficient NER function. 76 matched cddid_all.tbl CDD cd17127 cd17127 340647 Ubl_TBK1 ubiquitin-like (Ubl) domain found in TRAF family member-associated NF-kappaB activator (TANK)-binding kinase 1 (TBK1). TBK1, also termed NF-kappa-B-activating kinase, or T2K, or TANK-binding kinase 1, is an interferon regulatory factor-activating kinase that is a non-canonical member of IKK family. It plays a role in regulating innate immunity, inflammation and oncogenic signaling. TBK1 is involved in the regulation of type I interferons and of nuclear factor-kappaB (NF-kappaB) signal transduction. It regulates factors such as IRF3 and IRF7, promoting antiviral activity in the interferon signaling pathways. It modulates inflammatory hyperalgesia by regulating MAP kinases and NF-kappaB dependent genes. Moreover, TBK1 acts as a central player in the intracellular nucleic acid-sensing pathways involved in antiviral signaling. Dysregulation of TBK1 activity is often associated with autoimmune diseases and cancer. TBK1 contains an N-terminal protein kinase domain followed a ubiquitin-like (Ubl) domain, and a C-terminal elongated helical domain. The Ubl domain acts as a protein-protein interaction domain, and has been implicated in regulating kinase activity, which modulates interactions in the interferon pathway. 78 matched cddid_all.tbl CDD cd17128 cd17128 340648 Ubl_IKKE ubiquitin-like (Ubl) domain found in inhibitor of nuclear factor kappa-B kinase subunit epsilon (IKK-E). IKK-E (EC 2.7.11.10), also termed I-kappa-B kinase epsilon (IKKepsilon), or IKK-epsilon, or IkBKE, or inducible I kappa-B kinase (IKK-i), is an interferon regulatory factor-activating kinase that is a non-canonical member of IKK family. It is involved in the cellular innate immunity by inducing type I interferons. It is induced by the activation of nuclear factor-kappaB (NF-kappaB). IKK-E has also been implicated in antiviral immune response in higher vertebrates. It acts as a crucial pro-survival factor in human T cell leukemia virus type 1 (HTLV-1)-transformed T lymphocytes. Moreover, IKK-E plays an essential role in tumor initiation and progression. It inhibits protein kinase C (PKC) to promote Fascin-dependent actin bundling. IKK-E contains an N-terminal protein kinase domain followed a ubiquitin-like (Ubl) domain, and a C-terminal elongated helical domain. The Ubl domain acts as a protein-protein interaction domain, and has been implicated in regulating kinase activity, which modulates interactions in the interferon pathway. 78 matched cddid_all.tbl CDD cd17129 cd17129 340649 Ubl1_FAF1 ubiquitin-like (Ubl) domain 1 found in FAS-associated factor 1 (FAF1) and similar proteins. FAF1, also termed UBX domain-containing protein 12 (UBXD12), or UBX domain-containing protein 3A (UBXN3A), belongs to the UBXD family of proteins that contains the ubiquitin (Ub) regulatory domain X (UBX) with a beta-grasp ubiquitin-like (Ubl) fold, but without the C-terminal double glycine motif. The UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. In addition, FAF1 contains two tandem Ubl domains, which show high structural similarity with the UBX domain. FAF1 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. The FAF1-p97 complex inhibits the proteasomal protein degradation in which p97 acts as a co-chaperone. Moreover, FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF1 is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kappaB (NF-kappaB) by interfering with the nuclear translocation of the p65 subunit. Although the precise role of FAF1 in the ubiquitination pathway remains unclear, FAF1 interacts with valosin-containing protein (VCP), which is involved in the ubiquitin-proteosome pathway. The family corresponds to the first Ubl domain. 73 matched cddid_all.tbl CDD cd17130 cd17130 340650 Ubl2_FAF1 ubiquitin-like (Ubl) domain 2 found in FAS-associated factor 1 (FAF1) and similar proteins. FAF1, also termed UBX domain-containing protein 12 (UBXD12), or UBX domain-containing protein 3A (UBXN3A), belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like (Ubl) fold, but without the C-terminal double glycine motif. The UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. In addition, FAF1 contains two tandem Ubl domains, which show high structural similarity with the UBX domain. FAF1 functions as a cofactor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. The FAF1-p97 complex inhibits the proteasomal protein degradation in which p97 acts as a co-chaperone. Moreover, FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF1 is widely expressed in adult and embryonic tissues, and in tumor cell lines, and is localized not only in the cytoplasm where it interacts with Fas, but also in the nucleus. FAF1 contains phosphorylation sites for protein kinase CK2 within the nuclear targeting domain. Phosphorylation influences nuclear localization of FAF1 but does not affect its potentiation of Fas-induced apoptosis. Other functions have also been attributed to FAF1. It inhibits nuclear factor-kappaB (NF-kappaB) by interfering with the nuclear translocation of the p65 subunit. Although the precise role of FAF1 in the ubiquitination pathway remains unclear, FAF1 interacts with valosin-containing protein (VCP), which is involved in the ubiquitin-proteosome pathway. The family corresponds to the second Ubl domain. 75 matched cddid_all.tbl CDD cd17131 cd17131 340651 Ubl_TMUB1 ubiquitin-like (Ubl) domain found in transmembrane and ubiquitin-like domain-containing protein 1 (TMUB1). TMUB1, also termed dendritic cell-derived ubiquitin-like protein (DULP), or hepatocyte odd protein shuttling protein, or ubiquitin-like protein SB144, or HOPS, is highly expressed in the nervous system. It is involved in the termination of liver regeneration and plays a negative role in interleukin-6-induced hepatocyte proliferation. The overexpression of Tmub1 has been shown to play a role in the inhibition of cell proliferation. TMUB1 has also been implicated in the regulation of locomotor activity and wakefulness in mice, perhaps acting through its interaction with CAMLG. It also facilitates the recycling of AMPA receptors into synaptic membrane in cultured primary neurons. TMUB1 contains transmembrane domains and a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold. 71 matched cddid_all.tbl CDD cd17132 cd17132 340652 Ubl_TMUB2 ubiquitin-like (Ubl) domain found in transmembrane and ubiquitin-like domain-containing protein 2 (TMUB2). TMUB2 is composed of an uncharacterized transmembrane domain and a ubiquitin-like (Ubl) domain-containing protein that shows high sequence similarity to TMUB1; the latter is highly expressed in the nervous system and is involved in the termination of liver regeneration. 71 matched cddid_all.tbl CDD cd17133 cd17133 340653 RBD_ARAF Ras-binding domain (RBD) found in serine/threonine-protein kinase ARAF. ARAF, also termed proto-oncogene ARAF, or proto-oncogene ARAF1, or proto-oncogene PKS2, belongs to the RAF protein family. The RAF family includes three RAF kinases ARAF, BRAF, and RAF1/CRAF, encoded by proto-oncogenes, which activate the mitogen-activated protein kinase/extracellular-signal-regulated kinase (MAPK/ERK) cascade downstream of RAS. They share a common structure consisting of an N-terminal regulatory domain and a C-terminal kinase domain. There are three conserved regions (CR1-3) in the regulatory domain, CR1 contains a Ras-binding domain (RBD) and a cysteine-rich domain (CRD), CR2 is a serine/threonine-rich domain, and CR3 encodes the kinase domain required for RAF. The RBD of RAF has a beta-grasp ubiquitin-like fold, a common structure involved in protein-protein interactions. ARAF is predominantly found in urogenital tissue with a low basal kinase activity. It directly cross-talks with NODAL/SMAD2 signaling in a MAPK-independent manner. It also promotes MAPK pathway activation and cell migration in a cell type-dependent manner. Moreover, ARAF acts as a scaffold to stabilize BRAF-CRAF heterodimers. Mice deleted for ARAF are viable but die perinatally. 73 matched cddid_all.tbl CDD cd17134 cd17134 340654 RBD_BRAF Ras-binding domain (RBD) found in serine/threonine-protein kinase BRAF. BRAF, also termed proto-oncogene B-Raf, or p94, or v-Raf murine sarcoma viral oncogene homolog B1, belongs to the RAF family. The RAF family includes three RAF kinases ARAF, BRAF, and RAF1/CRAF, encoded by proto-oncogenes, which activate the mitogen-activated protein kinase/extracellular-signal-regulated kinase (MAPK/ERK) cascade downstream of RAS. They share a common structure consisting of an N-terminal regulatory domain and a C-terminal kinase domain. There are three conserved regions (CR1-3) in the regulatory domain, CR1 contains a Ras-binding domain (RBD) and a cysteine-rich domain (CRD), CR2 is a serine/threonine-rich domain, and CR3 encodes the kinase domain required for RAF. The RBD of RAF has a beta-grasp ubiquitin-like fold, a common structure involved in protein-protein interactions. BRAF is the most effective RAF kinase in terms of induction of MEK/ERK activity. It is somatically mutated in a number of human cancers. 79 matched cddid_all.tbl CDD cd17135 cd17135 340655 RBD_CRAF Ras-binding domain (RBD) found in RAF proto-oncogene serine/threonine-protein kinase RAF1/CRAF. RAF1/CRAF, also termed proto-oncogene c-RAF (cRaf), or Raf-1, belongs to the RAF family. The RAF family includes three RAF kinases ARAF, BRAF, and RAF1/CRAF, encoded by proto-oncogenes, which activate the mitogen-activated protein kinase/extracellular-signal-regulated kinase (MAPK/ERK) cascade downstream of RAS. They share a common structure consisting of an N-terminal regulatory domain and a C-terminal kinase domain. There are three conserved regions (CR1-3) in the regulatory domain, CR1 contains a Ras-binding domain (RBD) and a cysteine-rich domain (CRD), CR2 is a serine/threonine-rich domain, and CR3 encodes the kinase domain required for RAF. The RBD of RAF has a beta-grasp ubiquitin-like fold, a common structure involved in protein-protein interactions. RAF1/CRAF is an important effector of Ras-mediated signaling and is a critical regulator of the MAPK/ERK pathway. 77 matched cddid_all.tbl CDD cd17136 cd17136 340656 RBD1_RGS12 Ras-binding domain (RBD) 1 of regulator of G protein signaling 12 (RGS12). RGS12 (regulator of G protein signaling 12) is a multidomain RGS protein with numerous signaling regulatory elements. In addition to a central RGS domain which is responsible for GAP activity, the long RGS12 splice variant contains a PDZ (PSD-95/Discs-large/ZO-1 homology) domain capable of binding the interleukin-8 receptor B (CXCR2) or its own C-terminal, a phosphotyrosine-binding (PTB) domain that associates with tyrosine-phosphorylated N-type calcium channel, two tandem Ras-binding domains (RBDs) that may integrate signaling pathways involving both heterotrimeric and monomeric G-proteins, and a GoLoco (G-alpha-i/o-Loco) interaction motif which has guanine nucleotide dissociation inhibitor (GDI) activity toward G-alpha-i subunits. RBD is structurally similar to the beta-grasp fold of ubiquitin, a common structure involved in protein-protein interactions. RGS proteins belong to a large family of GTpase-accelerating proteins (GAPs) which act as key inhibitors of G-protein-mediated cell responses in eukaryotes. 70 matched cddid_all.tbl CDD cd17137 cd17137 340657 RBD1_RGS14 Ras-binding domain (RBD) 1 of regulator of G protein signaling 14 (RGS14). RGS12 (regulator of G protein signaling 14) is a RGS protein with a multidomain structure that allows it to interact with binding partners from multiple signaling pathways. RGS proteins belong to a large family of GTPase-accelerating proteins (GAPs) which act as key inhibitors of G-protein-mediated cell responses in eukaryotes. RGS14 contains an N-terminal RGS domain, two tandem Ras-binding domains (RBDs) and a G protein regulatory (GPR, also referred to as a GoLoco) motif. RGS14 binds activated H-Ras-GTP through its first RBD and interacts with Rap2-GTP and RAF kinases by the second tandem RBD. RBD is structurally similar to the beta-grasp fold of ubiquitin, a common structure involved in protein-protein interactions. RGS14 modulates neuronal physiology and all of its binding partners have roles in synaptic plasticity. 71 matched cddid_all.tbl CDD cd17138 cd17138 340658 RBD2_RGS12 Ras-binding domain (RBD) 2 of regulator of G protein signaling 12 (RGS12). RGS12 (regulator of G-protein signaling 12) is a multidomain RGS protein with numerous signaling regulatory elements. In addition to a central RGS domain which is responsible for GAP activity, the long RGS12 splice variant contains a PDZ (PSD-95/Discs-large/ZO-1 homology) domain capable of binding the interleukin-8 receptor B (CXCR2) or its own C-terminal, a phosphotyrosine-binding (PTB) domain that associates with tyrosine-phosphorylated N-type calcium channel, two tandem Ras-binding domains (RBDs) that may integrate signaling pathways involving both heterotrimeric and monomeric G-proteins, and a GoLoco (G-alpha-i/o-Loco) interaction motif which has guanine nucleotide dissociation inhibitor (GDI) activity toward G-alpha-i subunits. RBD is structurally similar to the beta-grasp fold of ubiquitin, a common structure involved in protein-protein interactions. RGS proteins belong to a large family of GTpase-accelerating proteins (GAPs) which act as key inhibitors of G-protein-mediated cell responses in eukaryotes. 73 matched cddid_all.tbl CDD cd17139 cd17139 340659 RBD2_RGS14 Ras-binding domain (RBD) 2 of regulator of G protein signaling 14 (RGS14). RGS14 (regulator of G protein signaling 14) is a RGS protein with a multidomain structure that allows it to interact with binding partners from multiple signaling pathways. RGS proteins belong to a large family of GTPase-accelerating proteins (GAPs) which act as key inhibitors of G-protein-mediated cell responses in eukaryotes. RGS14 contains an N-terminal RGS domain, two tandem Ras-binding domains (RBDs) and a G protein regulatory (GPR, also referred to as a GoLoco) motif. RGS14 binds activated H-Ras-GTP through its first RBD and interacts with RAP2-GTP and RAF kinases by the second tandem RBD. RBD is structurally similar to the beta-grasp fold of ubiquitin, a common structure involved in protein-protein interactions. RGS14 modulates neuronal physiology and all of its binding partners have roles in synaptic plasticity. 73 matched cddid_all.tbl CDD cd17140 cd17140 340660 DCX1_DCLK1 Dublecortin-like domain 1 found in doublecortin-like kinase 1 (DCLK1). DCLK1 is a member of doublecortin (DCX) protein superfamily that functions as a microtubule-associated protein (MAP), and contains two conserved tubulin binding domains. The DCX domain has a stable ubiquitin-like tertiary fold. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. In addition to microtubule-binding domains, DCLK encodes a serine/threonine kinase domain that is similar to Ca/calmodulin-dependent (Cam) protein kinases. DCLK1 appears to regulate cyclic AMP signaling and is involved in neuronal migration, retrograde transport, neuronal apoptosis and neurogenesis. Unlike DCX, this DCLK has varying levels of expression throughout embryonic and adult life. 89 matched cddid_all.tbl CDD cd17141 cd17141 340661 DCX1_DCLK2 Dublecortin-like domain 1 found in doublecortin-like kinase 2 (DCLK2). DCLK2 is a member of doublecortin (DCX) protein superfamily that functions as a microtubule-associated protein (MAP), and contains two conserved tubulin binding domains, which typically occur in tandem. The DCX domain has a stable ubiquitin-like tertiary fold. Ubiquitin (Ub) is a protein modifier (Ubiquitination) in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. In addition to microtubule binding domains, DCLK encodes a serine/threonine kinase-domain that is similar to Ca/calmodulin-dependent (Cam) protein kinases. Molecular actions of DCX members are less well characterized and it shows that DCLK2 members regulate cyclic AMP signaling. Unlike DCX, this DCLK has varying levels of expression throughout embryonic and adult life. 85 matched cddid_all.tbl CDD cd17142 cd17142 340662 DCX2_DCX Dublecortin-like domain 2 found in neuronal migration protein doublecortin (DCX). DCX, also termed doublin or lissencephalin-X (Lis-XDCX), is a microtubule-associated protein (MAP). It belongs to the doublecortin (DCX) family, has double tandem DCX repeats, and is expressed in migrating neurons. Structure studies show that the N-terminal DCX domain has a stable ubiquitin-like fold. DCX is not only a unique MAP in terms of its structure, but also interacts with multiple additional proteins. Mutations in the human DCX genes are associated with abnormal neuronal migration, epilepsy, and mental retardation. 84 matched cddid_all.tbl CDD cd17143 cd17143 340663 DCX2_DCLK1 Dublecortin-like domain 2 found in doublecortin-like kinase 1 (DCLK1). DCLK1 is a member of doublecortin (DCX) protein family that functions as a microtubule-associated protein (MAP), and contains two conserved tubulin binding domains. The DCX domain has a stable ubiquitin-like tertiary fold. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. In addition to microtubule binding domains, DCLK encodes a serine/threonine kinase-domain that is similar to Ca/calmodulin-dependent (Cam) protein kinases. DCLK1 appears to regulate cyclic AMP signaling and is involved in neuronal migration, retrograde transport, neuronal apoptosis and neurogenesis. Unlike DCX, the DCLK has varying levels of expression throughout embryonic and adult life. 84 matched cddid_all.tbl CDD cd17144 cd17144 340664 DCX2_DCLK2 Dublecortin-like domain 2 found in doublecortin-like kinase 2 (DCLK2). DCLK2 is a member of doublecortin (DCX) protein family that functions as a microtubule-associated protein (MAP), and contains two conserved tubulin binding domains, which typically occur in double tandem. The DCX domain has a stable ubiquitin-like tertiary fold. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. In addition to microtubule binding domains, DCLK encodes a serine/threonine kinase-domain that is similar to Ca/calmodulin-dependent (Cam) protein kinases. DCLK2 members regulate cyclic AMP signaling. Unlike DCX, the DCLK has varying levels of expression throughout embryonic and adult life. 84 matched cddid_all.tbl CDD cd17145 cd17145 340665 DCX1_RP1 Doublecortin-like domain 1 found in retinitis pigmentosa 1 (RP1)-like protein. RP1, also termed oxygen-regulated protein 1, is a member of the doublecortin (DCX) family. Its DCX domains occur in double tandem repeats. RP1 is associated with retinitis pigmentosa, which is a type of inherited blindness. DCX is a microtubule-associated protein (MAP) with a stable ubiquitin-like tertiary fold. Microtubules are key components of cytoskeleton that are involved in cell movement, shape determination, division and transport. The RP1 protein is expressed in photoreceptors and is required for correct stacking of outer segment discs. It interacts with many of the same cytoskeleton related proteins that other members of the DCX family interact with. 79 matched cddid_all.tbl CDD cd17146 cd17146 340666 DCX1_RP1L1 Doublecortin-like domain 1 found in retinitis pigmentosa 1-like 1 (RP1L1) protein. RP1L1 is a member of the doublecortin (DCX) family. Its DCX domains occur in double tandem repeats. DCX is a microtubule-associated protein (MAP) with a stable ubiquitin-like tertiary fold. Microtubules are key components of cytoskeleton that are involved in cell movement, shape determination, division and transport. The DCX-domain of RP1L1 localizes to the photoreceptor and is genetically associated with retinitis pigmentosa. 79 matched cddid_all.tbl CDD cd17147 cd17147 340667 DCX2_RP1 Dublecortin-like domain 2 found in retinitis pigmentosa 1 (RP1)-like protein. RP1, also termed oxygen-regulated protein 1, is a member of doublecortin (DCX) superfamily that contains double tandem repeats of the DCX domains. RP1 is associated with retinitis pigmentosa, which is a type of inherited blindness. DCX is a microtubule-associated protein (MAP) with a stable ubiquitin-like tertiary fold. Microtubules are key components of cytoskeleton that are involved in cell movement, shape determination, division and transport. The RP1 protein is expressed in photoreceptors that is required for correct stacking of outer segment discs. RP1 protein interacts with many of the same cytoskeleton related proteins that other members of the DCX family interact with. 76 matched cddid_all.tbl CDD cd17148 cd17148 340668 DCX2_RP1L1 Dublecortin-like domain 2 found in retinitis pigmentosa 1-like 1 (RP1L1) protein. RP1L1 is a member of doublecortin (DCX) family. Its protein domains occur in tandem repeats. DCX is a microtubule-associated protein (MAP) with a stable ubiquitin-like tertiary fold. Microtubules are key components of cytoskeleton that are involved in cell movement, shape determination, division and transport. The DCX-domain of RP1L1 localizes to the photoreceptor and is genetically associated with retinitis pigmentosa. 76 matched cddid_all.tbl CDD cd17149 cd17149 340669 DCX1_DCDC2 Dublecortin-like domain 1 found in doublecortin domain-containing protein 2 (DCDC2). DCDC2 is a member of doublecortin (DCX) family. It is a microtubule-associated protein (MAP) with a stable ubiquitin-like tertiary fold. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Microtubules are key components of the cytoskeleton that are involved in cell movement, shape determination, division and transport. DCDC2 genetic variation in humans is associated with reading disability, attention deficit hyperactivity disorder (ADHD), and difficulties in mathematics. A genetic variant of DCDC2 associates with dyslexia, a common neurobehavioral disorder of reading. DCDC2 protein interacts with many of the same cytoskeleton related proteins that other members of the DCX family interact with. 80 matched cddid_all.tbl CDD cd17150 cd17150 340670 DCX1_DCDC2B Dublecortin-like domain 1 found in doublecortin domain-containing protein 2B (DCDC2B). DCDC2 is a member of doublecortin (DCX) family. It is a microtubule-associated protein (MAP) with stable double tandem DCX repeats of ubiquitin-like tertiary fold. Microtubules are key components of the cytoskeleton that are involved in cell movement, shape determination, division and transport. DCDC2 genetic variation in humans is associated with reading disability, attention deficit hyperactivity disorder (ADHD), and difficulties in mathematics. A genetic variant of DCDC2 associates with dyslexia, a common neurobehavioral disorder of reading. DCDC2 protein interacts with many of the same cytoskeleton related proteins that other members of the DCX family interact with. 79 matched cddid_all.tbl CDD cd17151 cd17151 340671 DCX1_DCDC2C Dublecortin-like domain 1 found in doublecortin domain-containing protein 2C (DCDC2C). DCDC2 is a member of doublecortin (DCX) family. It is a microtubule-associated protein (MAP) with stable double tandem DCX repeats of ubiquitin-like tertiary fold. Microtubules are key components of the cytoskeleton that are involved in cell movement, shape determination, division and transport. DCDC2 genetic variation in humans is associated with reading disability, attention deficit hyperactivity disorder (ADHD), and difficulties in mathematics. A genetic variant of DCDC2 associates with dyslexia, a common neurobehavioral disorder of reading. DCDC2 protein interacts with many of the same cytoskeleton related proteins that other members of the DCX family interact with. 79 matched cddid_all.tbl CDD cd17152 cd17152 340672 DCX2_DCDC2 Doublecortin-like domain 2 found in doublecortin domain-containing protein 2 (DCDC2). DCDC2 is a member of the doublecortin (DCX) family. It is a microtubule-associated protein (MAP) with a stable ubiquitin-like tertiary fold. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Microtubules are key components of cytoskeleton that are involved in cell movement, shape determination, division and transport. DCDC2 genetic variation in humans is associated with reading disability, attention deficit hyperactivity disorder (ADHD), and difficulties in mathematics. A genetic variant of DCDC2 associates with dyslexia, a common neurobehavioral disorder of reading. DCDC2 protein interacts with many of the same cytoskeleton related proteins that other members of the DCX family interact with. 80 matched cddid_all.tbl CDD cd17153 cd17153 340673 DCX2_DCDC2B Doublecortin-like domain 2 found in doublecortin domain-containing protein 2B (DCDC2B). DCDC2 is a member of the doublecortin (DCX) family. It is a microtubule-associated protein (MAP) with stable double tandem DCX repeats of a ubiquitin-like tertiary fold. Microtubules are key components of cytoskeleton that are involved in cell movement, shape determination, division and transport. DCDC2 genetic variation in humans is associated with reading disability, attention deficit hyperactivity disorder (ADHD), and difficulties in mathematics. A genetic variant of DCDC2 associates with dyslexia, a common neurobehavioral disorder of reading. DCDC2 protein interacts with many of the same cytoskeleton related proteins that other members of the DCX family interact with. 80 matched cddid_all.tbl CDD cd17154 cd17154 340674 DCX2_DCDC2C Doublecortin-like domain 2 found in doublecortin domain-containing protein 2C (DCDC2C). DCDC2 is a member of the doublecortin (DCX) family. It is a microtubule-associated protein (MAP) with stable double tandem DCX repeats of a ubiquitin-like tertiary fold. Microtubules are key components of cytoskeleton that are involved in cell movement, shape determination, division and transport. DCDC2 genetic variation in humans is associated with reading disability, attention deficit hyperactivity disorder (ADHD), and difficulties in mathematics. A genetic variant of DCDC2 associates with dyslexia, a common neurobehavioral disorder of reading. DCDC2 protein interacts with many of the same cytoskeleton related proteins that other members of the DCX family interact with. 80 matched cddid_all.tbl CDD cd17155 cd17155 340675 DCX_DCDC1 Doublecortin-like domain found in doublecortin domain-containing protein 1 (DCDC1). Doublecortin (DCX) is a microtubule-associated protein (MAP) with a stable ubiquitin-like tertiary fold. Microtubules are key components of the cytoskeleton that are involved in cell movement, shape determination, division and transport. DCX gene family consists of eleven paralogs in human and mouse, such that its protein domains can occur in tandem or single repeats. Proteins with DCX tandem domains in general have roles in microtubule (MT) regulation and signal transduction while single DCX repeat proteins are normally localized to actin-rich subcellular structures or to the nucleus. DCDC1 is a hydrophilic intracellular protein that contains only one DCX repeat. Therefore, DCDC1 might only bind to microtubules without microtubule polymerization properties. DCDC1 is mainly expressed in adult testis. 72 matched cddid_all.tbl CDD cd17156 cd17156 340676 DCX1_DCDC5 Doublecortin-like domain 1 found in doublecortin domain-containing protein 5 (DCDC5). DCDC5 is a member of doublecortin (DCX) family. It is a microtubule-associated protein (MAP) with stable double tandem DCX repeats of ubiquitin-like tertiary fold. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Microtubules are key components of the cytoskeleton that are involved in cell movement, shape determination, division and transport. DCDC5 is expressed during mitosis and is involved in coordinating late cytokinesis. DCDC5 interacts with cytoplasmic dynein and Rab8, as well as with the Rab8 nucleotide exchange factor Rabin8. 76 matched cddid_all.tbl CDD cd17157 cd17157 340677 DCX2_DCDC5 Doublecortin-like domain 2 found in doublecortin domain-containing protein 5 (DCDC5). DCDC5 is a member of doublecortin (DCX) family. It is a microtubule-associated protein (MAP) with stable double tandem DCX repeats of ubiquitin-like tertiary fold. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Microtubules are key components of the cytoskeleton that are involved in cell movement, shape determination, division and transport. DCDC5 is expressed during mitosis and involved in coordinating late cytokinesis. DCDC5 interacts with cytoplasmic dynein and Rab8, as well as with the Rab8 nucleotide exchange factor Rabin8. 86 matched cddid_all.tbl CDD cd17158 cd17158 340678 DCX3_DCDC5 Doublecortin-like domain 3 found in doublecortin domain-containing protein 5 (DCDC5). DCDC5 is a member of doublecortin (DCX) family. It is a microtubule-associated protein (MAP) with stable double tandem DCX repeats of ubiquitin-like tertiary fold. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Microtubules are key components of the cytoskeleton that are involved in cell movement, shape determination, division and transport. DCDC5 is expressed during mitosis and involved in coordinating late cytokinesis. DCDC5 interacts with cytoplasmic dynein and Rab8, as well as with the Rab8 nucleotide exchange factor Rabin8. 73 matched cddid_all.tbl CDD cd17159 cd17159 340679 DCX4_DCDC5 Doublecortin-like domain 4 found in doublecortin domain-containing protein 5 (DCDC5). DCDC5 is a member of doublecortin (DCX) family. It is a microtubule-associated protein (MAP) with stable double tandem DCX repeats of ubiquitin-like tertiary fold. Ubiquitin (Ub) is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Microtubules are key components of the cytoskeleton that are involved in cell movement, shape determination, division and transport. DCDC5 is expressed during mitosis and involved in coordinating late cytokinesis. DCDC5 interacts with cytoplasmic dynein and Rab8, as well as with the Rab8 nucleotide exchange factor Rabin8. 73 matched cddid_all.tbl CDD cd17160 cd17160 340680 UBX_UBXN2A Ubiquitin regulatory domain X (UBX) found in UBX domain protein 2A (UBXN2A) and similar proteins. UBXN2A, also termed UBX domain-containing protein 4 (UBXD4), belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. UBXN2A functions as a p97 (also known as VCP or Cdc48) adaptor protein facilitating the regulation of the cell surface number and stability of alpha3-containing neuronal nicotinic acetylcholine receptors (nAChRs). It also regulates nicotinic receptor degradation by modulating the E3 ligase activity of carboxyl terminus of Hsc70 interacting protein (CHIP) that is involved in the degradation of several disease-related proteins. In addition, UBXN2A is an important anticancer factor that contributes to p53 localization and activation as a host defense mechanism against cancerous growth. It acts as a potential mortalin inhibitor, as well as a potential chemotherapy sensitizer for clinical application. It binds to the oncoprotein mortalin-2 (mot-2), and further unsequesters p53 from mot-2 in the cytoplasm, resulting in translocation of p53 to the nucleus where p53 proteins activate their downstream biological effects, including apoptosis. 84 matched cddid_all.tbl CDD cd17161 cd17161 340681 UBX_UBXN2B Ubiquitin regulatory domain X (UBX) found in UBX domain protein 2B (UBXN2B) and similar proteins. UBXN2B, also termed NSFL1 cofactor p37, or p97 cofactor p37, belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. UBXN2B is an adaptor protein of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. UBXN2B forms a tight complex with p97 in the cytosol and localizes to the Golgi and endoplasmic reticulum (ER). 82 matched cddid_all.tbl CDD cd17162 cd17162 340682 UBX_UBXN2C Ubiquitin regulatory domain X (UBX) found in NSFL1 cofactor (also known as UBX domain-containing protein 2C (UBXN2C) and similar proteins. UBXN2C, also termed NSFL1C, or NSFL1 cofactor p47, or p97 cofactor p47, UBX1, or UBXD10, belongs to the UBXD family of proteins that contains the ubiquitin regulatory domain X (UBX) with a beta-grasp ubiquitin-like fold, but without the C-terminal double glycine motif. UBX domain is typically located at the carboxyl terminus of proteins, and participates broadly in the regulation of protein degradation. UBXN2C is a major adaptor of p97 (also known as VCP or Cdc48), which is a homohexameric AAA ATPase (ATPase associated with a variety of activities) involved in a variety of functions ranging from cell-cycle regulation to membrane fusion and protein degradation. The main role of the UBXN2C/p97 complex is in regulation of membrane fusion events. It plays an essential role in the reassembly of Golgi stacks at the end of mitosis. UBXN2C also functions as an essential factor for Golgi membrane fusion, which associates with the nuclear factor-kappaB essential modulator (NEMO) subunit of the IkappaB kinase (IKK) complex upon tumor necrosis factor (TNF)-alpha or interleukin (IL)-1 stimulation, induces the lysosome-dependent degradation of polyubiquitinated NEMO without p97, and thus inhibits IKK activation. Moreover, UBXN2C regulates a membrane fusion process, which is required by the maintenance of the endoplasmic reticulum (ER) network, through phosphorylation by Cdc2 kinase. 82 matched cddid_all.tbl CDD cd17163 cd17163 340683 Ubl_ATG8_GABARAPL2 ubiquitin-like (Ubl) domain found in GABA type A receptor associated protein like 2 (GABARAPL2, also known as GATE16). Autophagy is an essential intracellular process that targets large protein complexes, bacterial pathogens, and organelles for degradation. GABARAPL2 (GABA type A receptor associated protein like 2), also known as GATE-16 (golgi-associated adenosine triphosphatase enhancer of 16 kDa), has a ubiquitin-like (Ubl) domain and is a sub-family of the autophagy-related 8 (ATG8) protein family. GABARAPL2 participates to the autophagosome maturation, and seems to be involved in constitutive transport under normal conditions and in autophagic processes during stress. GABARAPL2 is characterized as a membrane transport modulator that controls intra-Golgi transport by interacting with NSF and Golgi v-SNARE GOS-28. 112 matched cddid_all.tbl CDD cd17164 cd17164 340684 RAWUL_PCGF2 RING finger- and WD40-associated ubiquitin-like (RAWUL) domain found in polycomb group RING finger protein 2 (PCGF2). PCGF2, also termed DNA-binding protein Mel-18, or RING finger protein 110 (RNF110), or zinc finger protein 144 (ZNF144), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) and serves as the core component of a canonical polycomb repressive complex 1 (PRC1), which is composed of a chromodomain-containing protein (CBX2, CBX4, CBX6, CBX7 or CBX8) and a polyhomeotic protein (PHC1, PHC2, or PHC3). Like other PCGF homologs, PCGF2 associates with ring finger protein 2 (RNF2) to form a RNF2-PCGF heterodimer, which is catalytically competent as an E3 ubiquitin transferase and is the scaffold for the assembly of additional components. Moreover, PCGF2 uniquely regulates PRC1 to specify mesoderm cell fate in embryonic stem cells. It is required for PRC1 stability and maintenance of gene repression in embryonic stem cells (ESCs) and essential for ESC differentiation into early cardiac-mesoderm precursors. PCGF2 also plays a significant role in the angiogenic function of endothelial cells (ECs) by regulating endothelial gene expression. Furthermore, PCGF2 is a SUMO-dependent regulator of hormone receptors. It facilitates the deSUMOylation process by inhibiting PCGF4/BMI1-mediated ubiquitin-proteasomal degradation of SUMO1/sentrin-specific protease 1 (SENP1). It is also a novel negative regulator of breast cancer stem cells (CSCs) that inhibits the stem cell population, and in vitro and in vivo self-renewal through the inactivation of Wnt-mediated Notch signaling. PCGF2 contains a C3HC4-type RING-HC finger, and a RAWUL domain. 99 matched cddid_all.tbl CDD cd17165 cd17165 340685 RAWUL_PCGF4 RING finger- and WD40-associated ubiquitin-like (RAWUL) domain found in polycomb group RING finger protein 4 (PCGF4). PCGF4, also termed polycomb complex protein BMI-1 (B cell-specific Moloney murine leukemia virus integration site 1), or RING finger protein 51 (RNF51), is one of six PcG RING finger (PCGF) homologs (PCGF1/NSPc1, PCGF2/Mel-18, PCGF3, PCGF4/BMI1, PCGF5, and PCGF6/MBLR) and serves as the core component of a canonical Polycomb repressive complex 1 (PRC1), which is composed of a chromodomain-containing protein (CBX2, CBX4, CBX6, CBX7 or CBX8) and a Polyhomeotic protein (PHC1, PHC2, or PHC3), and plays important roles in chromatin compaction and H2AK119 monoubiquitination. PCGF4 associates with the Runx1/CBFbeta transcription factor complex to silence target gene in a PRC2-independent manner. Moreover, PCGF4 is expressed in the hair cells and supporting cells. It can regulate cell survival by controlling mitochondrial function and reactive oxygen species (ROS) level in thymocytes and neurons, thus having an important role in the survival and sensitivity to ototoxic drug of auditory hair cells. Furthermore, PCGF4 controls memory CD4 T-cell survival through direct repression of Noxa gene in an Ink4a- and Arf-independent manner. It is required in neurons to suppress p53-induced apoptosis via regulating the antioxidant defensive response, and also involved in the tumorigenesis of various cancer types. PCGF4 contains a C3HC4-type RING-HC finger, and a RAWUL domain. 97 matched cddid_all.tbl CDD cd17166 cd17166 340686 RAWUL_RING1 RING finger- and WD40-associated ubiquitin-like (RAWUL) domain found in really interesting new gene 1 protein (RING1). RING1, also termed polycomb complex protein RING1, or RING finger protein 1 (RNF1), or RING finger protein 1A (RING1A), has been identified as a transcriptional repressor that is associated with the Polycomb group (PcG) protein complex involved in stable repression of gene activity. It is a core component of polycomb repressive complex 1 (PRC1) that functions as an E3-ubuiquitin ligase that transferring the mono-ubuiquitin mark to the C-terminal tail of Histone H2A at K118/K119. PRC1 is also capable of chromatin compaction, a function not requiring histone tails, and this activity appears important in gene silencing. RING1 interacts with multiple PcG proteins and displays tumorigenic activity. It also shows zinc-dependent DNA binding activity. Moreover, RING1 inhibits transactivation of the DNA-binding protein recombination signal binding protein-Jkappa (RBP-J) by Notch through interaction with the LIM domains of KyoT2. RING1 contains a C3HC4-type RING-HC finger, and a RAWUL domain. 124 matched cddid_all.tbl CDD cd17167 cd17167 340687 RAWUL_RING2 RING finger- and WD40-associated ubiquitin-like (RAWUL) domain found in really interesting new gene 2 protein (RING2). RING2, also termed huntingtin-interacting protein 2-interacting protein 3, or HIP2-interacting protein 3, or protein DinG, or RING finger protein 1B (RING1B), or RING finger protein 2 (RNF2), or RING finger protein BAP-1, is an E3 ubiquitin-protein ligase that interacts with both nucleosomal DNA and an acidic patch on histone H4 to achieve the specific monoubiquitination of K119 on histone H2A (H2AK119ub), thereby playing a central role in histone code and gene regulation. RING2 is a core component of polycomb repressive complex 1 (PRC1) that functions as an E3-ubuiquitin ligase transferring the mono-ubuiquitin mark to the C-terminal tail of Histone H2A at K118/K119. PRC1 is also capable of chromatin compaction, a function not requiring histone tails, and this activity appears important in gene silencing. The enzymatic activity of RING2 is enhanced by the interaction with BMI1/PCGF4, and it is dispensable for early embryonic development and much of the gene repression activity of PRC1. Moreover, RING2 plays a key role in terminating neural precursor cell (NPC)-mediated production of subcerebral projection neurons (SCPNs) during neocortical development. It also plays a critical role in nonhomologous end-joining (NHEJ)-mediated end-to-end chromosome fusions. Furthermore, RING2 is essential for expansion of hepatic stem/progenitor cells. It promotes hepatic stem/progenitor cell expansion through simultaneous suppression of cyclin-dependent kinase inhibitors (CDKIs) Cdkn1a and Cdkn2a, known negative regulators of cell proliferation. RING2 also negatively regulates p53 expression through directly binding with both p53 and MDM2 and promoting MDM2-mediated p53 ubiquitination in selective cancer cell types to stimulate tumor development. RING2 contains a C3HC4-type RING-HC finger, and a RAWUL domain. 106 matched cddid_all.tbl CDD cd17168 cd17168 340688 FERM_F1_FRMPD1 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in FERM and PDZ domain-containing protein 1 (FRMPD1). FRMPD1, also termed FERM domain-containing protein 2, is an activator of G-protein signaling 3 (AGS3)-binding protein that regulates the subcellular location of AGS3 and its interaction with G-proteins. It also binds to the tetratricopeptide repeat (TPR) motif-containing adaptor protein LGN. FRMPD1 contains a PDZ domain and a FERM domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. The family corresponds to the F1 sub-domain of the FERM domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 90 matched cddid_all.tbl CDD cd17169 cd17169 340689 FERM_F1_FRMPD3 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in FERM and PDZ domain-containing protein 3 (FRMPD3). FRMPD3 is an uncharacterized FERM and PDZ domain-containing protein. The FERM domain is made up of three sub-domains, F1, F2, and F3. The family corresponds to the F1 sub-domain of the FERM domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 93 matched cddid_all.tbl CDD cd17170 cd17170 340690 FERM_F1_FRMPD4 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in FERM and PDZ domain-containing protein 4 (FRMPD4). FRMPD4, also termed PDZ domain-containing protein 10, or PSD-95-interacting regulator of spine morphogenesis (Preso), is a multiscaffolding protein that modulates both Homer1 and postsynaptic density protein 95 activity. It can associate with the tetratricopeptide repeat (TPR) motif-containing adaptor protein LGN. Moreover, FRMPD4 is asymmetrically distributed in the cytosol and nuclei of neural stem/progenitor cells in the adult brain, suggesting a significant role in cell differentiation via association with cell polarity machinery. FRMPD4 contains a WW domain, a PDZ domain, and a FERM domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain of the FERM domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 94 matched cddid_all.tbl CDD cd17171 cd17171 340691 FERM_F0_TLN1 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F0 sub-domain, found in Talin-1 (TLN1). TLN1 is a cytoskeletal protein that plays a pivotal role in regulating the activity of the integrin family of cell adhesion proteins by coupling them to F-actin. It functions as a focal adhesion protein involved in the attachment of the bacterium. It binds to multiple adhesion molecules, including integrins, vinculin, focal adhesion kinase (FAK), and actin. TLN1 also plays an essential role in integrin activation. TLN1 interacts with the hepatitis B virus (HBV) accessory protein X (HBx), which induces the degradation of TLN1. It also acts as an adaptor protein that regulates leukocyte function-associated antigen-1 (LFA-1) affinity. In addition, TLN1 is required for myoblast fusion, sarcomere assembly and the maintenance of myotendinous junctions. TLN1 consists of an N-terminal head and a C-terminal rod. The talin head harbors a FERM (Band 4.1, ezrin, radixin, moesin) domain made up of F1, F2 and F3 domains, as well as an N-terminal region that precedes the FERM domain and has been referred to as the F0 domain. Both F0 and F1 domains have similar ubiquitin-like folds. This family corresponds to the F0 domain. 84 matched cddid_all.tbl CDD cd17172 cd17172 340692 FERM_F0_TLN2 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F0 sub-domain, found in Talin-2 (TLN2). TLN2 is a cytoskeletal protein that plays an important role in cell adhesion and recycling of synaptic vesicles. TLN2 is required for myoblast fusion, sarcomere assembly and the maintenance of myotendinous junctions. TLN2 consists of an N-terminal head and a C-terminal rod. The talin head harbors a FERM (Band 4.1, ezrin, radixin, moesin) domain made up of F1, F2 and F3 domains, as well as an N-terminal region that precedes the FERM domain and has been referred to as the F0 domain. Both F0 and F1 domains have similar ubiquitin-like folds. This family corresponds to the F0 domain. 84 matched cddid_all.tbl CDD cd17173 cd17173 340693 FERM_F1_TLN1 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in Talin-1 (TLN1). TLN1 is a cytoskeletal protein that plays a pivotal role in regulating the activity of the integrin family of cell adhesion proteins by coupling them to F-actin. It functions as a focal adhesion protein involved in the attachment of the bacterium. It binds to multiple adhesion molecules, including integrins, vinculin, focal adhesion kinase (FAK), and actin. TLN1 also plays an essential role in integrin activation. TLN1 interacts with the hepatitis B virus (HBV) accessory protein X (HBx), which induces the degradation of TLN1. It also acts as an adaptor protein that regulates leukocyte function-associated antigen-1 (LFA-1) affinity. In addition, TLN1 is required for myoblast fusion, sarcomere assembly and the maintenance of myotendinous junctions. TLN1 consists of an N-terminal head and a C-terminal rod. The talin head harbors a FERM (Band 4.1, ezrin, radixin, moesin) domain made up of F1, F2 and F3 domains, as well as an N-terminal region that precedes the FERM domain and has been referred to as the F0 domain. Both F0 and F1 domains have similar ubiquitin-like folds. This family corresponds to the F1 domain. 112 matched cddid_all.tbl CDD cd17174 cd17174 340694 FERM_F1_TLN2 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in Talin-2 (TLN2). TLN2 is a cytoskeletal protein that plays an important role in cell adhesion and recycling of synaptic vesicles. TLN2 is required for myoblast fusion, sarcomere assembly and the maintenance of myotendinous junctions. TLN2 consists of an N-terminal head and a C-terminal rod. The talin head harbors a FERM (Band 4.1, ezrin, radixin, moesin) domain made up of F1, F2 and F3 domains, as well as an N-terminal region that precedes the FERM domain and has been referred to as the F0 domain. Both F0 and F1 domains have similar ubiquitin-like folds. This family corresponds to the F1 domain. 112 matched cddid_all.tbl CDD cd17175 cd17175 340695 FERM_F0_SHANK1 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F0 sub-domain, found in SH3 and multiple ankyrin repeat domains protein 1 (SHANK1). SHANK1, also termed somatostatin receptor-interacting protein, or SSTR-interacting protein (SSTRIP), is a postsynaptic density (PSD)-associated scaffolding proteins at the excitatory synapse that interconnects neurotransmitter receptors and cell adhesion molecules by direct and indirect interactions with numerous other PSD-associated proteins. Mutations in the SHANK1 synaptic scaffolding gene may lead to autism spectrum disorder and mental retardation. SHANK1 contains an N-terminal F0 domain of FERM (Band 4.1, ezrin, radixin, moesin), six ankyrin (ANK) repeats, one SH3 (Src homology 3) domain, one PDZ (PSD-95, Dlg, and ZO-1/2, also termed DHR or GLGF) domain, and a C-terminal SAM (sterile alpha motif) domain. This family corresponds to the F0 domain that adopts a ubiquitin-like fold. 89 matched cddid_all.tbl CDD cd17176 cd17176 340696 FERM_F0_SHANK2 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F0 sub-domain, found in SH3 and multiple ankyrin repeat domains protein 2 (SHANK2). SHANK2, also termed cortactin-binding protein 1 (CortBP1), or proline-rich synapse-associated protein 1, is a postsynaptic density (PSD)-associated scaffolding proteins at the excitatory synapse that interconnects neurotransmitter receptors and cell adhesion molecules by direct and indirect interactions with numerous other PSD-associated proteins. It is strongly expressed in the cerebellum. Moreover, SHANK2 acts as a component of the albumin endocytic pathway in podocytes, and regulates renal albumin endocytosis. It also associates with and regulates Na+/H+ exchanger 3 (NHE3) and is involved in the fine regulation of transepithelial salt and water transport through affecting NHE3 expression and activity. Mutations in the SHANK2 synaptic scaffolding gene may lead to autism spectrum disorder and mental retardation. SHANK2 contains an N-terminal F0 domain of FERM (Band 4.1, ezrin, radixin, moesin), six ankyrin (ANK) repeats, one SH3 (Src homology 3) domain, one PDZ (PSD-95, Dlg, and ZO-1/2, also termed DHR or GLGF) domain, and a C-terminal SAM (sterile alpha motif) domain. This family corresponds to the F0 domain that adopts a ubiquitin-like fold. 88 matched cddid_all.tbl CDD cd17177 cd17177 340697 FERM_F0_SHANK3 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F0 sub-domain, found in SH3 and multiple ankyrin repeat domains protein 3 (SHANK3). SHANK3, also termed proline-rich synapse-associated protein 2 (ProSAP2), is a postsynaptic density (PSD)-associated scaffolding protein at the excitatory synapse that interconnects neurotransmitter receptors and cell adhesion molecules by direct and indirect interactions with numerous other PSD-associated proteins. It is critical for synaptic plasticity and the trans-synaptic coupling between the reliability of presynaptic neurotransmitter release and postsynaptic responsiveness. It is a key component of a zinc-sensitive signaling system that regulates excitatory synaptic strength. Mutations in the SHANK3 synaptic scaffolding gene may lead to autism spectrum disorder and mental retardation, and the cause of human Phelan-McDermid syndrome (22q13.3 deletion syndrome) has been isolated to loss of function of one copy of the SHANK3 gene. SHANK3 contains an N-terminal F0 domain of FERM (Band 4.1, ezrin, radixin, moesin), six ankyrin (ANK) repeats, one SH3 (Src homology 3) domain, one PDZ (PSD-95, Dlg, and ZO-1/2, also known as DHR or GLGF) domain, and a C-terminal SAM (sterile alpha motif) domain. This family corresponds to the F0 domain that adopts a ubiquitin-like fold. 87 matched cddid_all.tbl CDD cd17178 cd17178 340698 FERM_F1_PLEKHH1 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in pleckstrin homology domain-containing family H member 1 (PLEKHH1). PLEKHH1 is a homolog of Caenorhabditis elegans MAX-1 that has been implicated in motor neuron axon guidance. PLEKHH1 is critical in vascular patterning in vertebrate species through acting upstream of the ephrin pathway. PLEKHH1 contains a putative alpha-helical coiled-coil segment within the N-terminal half, and two Pleckstrin homology (PH) domains, a MyTH4 domain, and a FERM (Band 4.1, ezrin, radixin, moesin) domain within the C-terminal half. The FERM domain is made up of three sub-domains, F1, F2, and F3. The family corresponds to F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 106 matched cddid_all.tbl CDD cd17179 cd17179 340699 FERM_F1_PLEKHH2 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in pleckstrin homology domain-containing family H member 2 (PLEKHH2). PLEKHH2 is a novel podocyte protein downregulated in human focal segmental glomerulosclerosis. It is highly enriched in renal glomerular podocytes, and acts as a novel, important component of the podocyte foot processes. PLEKHH2 contains a putative alpha-helical coiled-coil segment within the N-terminal half, and two Pleckstrin homology (PH) domains, a MyTH4 domain, and a FERM (Band 4.1, ezrin, radixin, moesin) domain within the C-terminal half. The FERM domain is made up of three sub-domains, F1, F2, and F3. The family corresponds to F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). PLEKHH2 is involved in matrix adhesion and actin dynamics. It directly interacts through its FERM domain with the focal adhesion protein Hic-5 and actin. 103 matched cddid_all.tbl CDD cd17180 cd17180 340700 FERM_F0_KIND1 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F0 sub-domain, found in kindlin-1 (KIND1). KIND1, also termed Kindlerin, or Kindler syndrome protein, or fermitin family homolog 1 (FERMT1), or Unc-112-related protein 1 (URP1), is an integrin-interacting protein that has been implicated in cell adhesion, proliferation, polarity, and motility. It is essential for maintaining the structure of cell-matrix adhesion, such as focal adhesions and podosomes. KIND1 is expressed primarily in epithelial cells. Loss or mutations of KIND1 gene may cause the Kindler syndrome (KS), an autosomal recessive skin disorder with an intriguing progressive phenotype comprising skin blistering, photosensitivity, progressive poikiloderma with extensive skin atrophy, and propensity to skin cancer. KIND1 forms a molecular complex with the key transforming growth factor (TGF)-beta/Smad3 signaling components including type I TGFbeta receptor (TbetaRI), Smad3 and Smad anchor for receptor activation (SARA) to control the activation of TGF-beta/Smad3 signaling pathway. KIND1 consists of an atypical FERM domain that is made up of F1, F2 and F3 domains, as well as an N-terminal region, which precedes the FERM domain and has been referred to as the F0 domain. This family corresponds to the F0 domain. 84 matched cddid_all.tbl CDD cd17181 cd17181 340701 FERM_F0_KIND2 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F0 sub-domain, found in kindlin-2 (KIND2). KIND2, also termed fermitin family homolog 2 (FERMT2), or mitogen-inducible gene 2 protein (MIG-2), or Pleckstrin homology (PH) domain-containing family C member 1, is an adaptor protein that is widely distributed and is particularly abundant in adherent cells. It binds to the integrin beta cytoplasmic tail to promote integrin activation. It promotes carcinogenesis through regulation of cell-cell and cell-extracellular matrix adhesion. In additon, KIND2 plays an important role in cardiac development. KIND2 consists of an atypical FERM domain that is made up of F1, F2 and F3 domains, as well as an N-terminal region, which precedes the FERM domain and has been referred to as the F0 domain. This family corresponds to the F0 domain. 80 matched cddid_all.tbl CDD cd17182 cd17182 340702 FERM_F0_KIND3 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F0 sub-domain, found in kindlin-3 (KIND3). KIND3, also termed fermitin family homolog 3 (FERMT3), or MIG2-like protein, or Unc-112-related protein 2, is an adaptor protein that expressed primarily in hematopoietic cells. It plays a central role in cell adhesion in hematopoietic cells, and also promotes integrin activation, clustering and outside-in signaling. KIND3, together with talin-1, contributes essentially to the activation of beta2-integrins in neutrophils. In addition, KIND3 interacts with the ribosome and regulates c-Myc expression required for proliferation of chronic myeloid leukemia cells. Mutations in the KIND3 gene cause leukocyte adhesion deficiency type III (LAD III), which is characterized by high susceptibility to infections, spontaneous and episodic bleedings, and osteopetrosis. KIND3 consists of an atypical FERM domain that is made up of F1, F2 and F3 domains, as well as an N-terminal region, which precedes the FERM domain and has been referred to as the F0 domain. This family corresponds to the F0 domain. 83 matched cddid_all.tbl CDD cd17183 cd17183 340703 FERM_F1_KIND1 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in kindlin-1 (KIND1). KIND1, also termed Kindlerin, or Kindler syndrome protein, or fermitin family homolog 1 (FERMT1), or Unc-112-related protein 1 (URP1), is an integrin-interacting protein that has been implicated in cell adhesion, proliferation, polarity, and motility. It is essential for maintaining the structure of cell-matrix adhesion, such as focal adhesions and podosomes. KIND1 is expressed primarily in epithelial cells. Loss or mutations of KIND1 gene may cause the Kindler syndrome (KS), an autosomal recessive skin disorder with an intriguing progressive phenotype comprising skin blistering, photosensitivity, progressive poikiloderma with extensive skin atrophy, and propensity to skin cancer. KIND1 forms a molecular complex with the key transforming growth factor (TGF)-beta/Smad3 signaling components including type I TGFbeta receptor (TbetaRI), Smad3 and Smad anchor for receptor activation (SARA) to control the activation of TGF-beta/Smad3 signaling pathway. KIND1 consists of an atypical FERM domain that is made up of F1, F2 and F3 domains, as well as an N-terminal region, which precedes the FERM domain and has been referred to as the F0 domain. This family corresponds to the F1 domain. 93 matched cddid_all.tbl CDD cd17184 cd17184 340704 FERM_F1_KIND2 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in kindlin-2 (KIND2). KIND2, also termed fermitin family homolog 2 (FERMT2), or mitogen-inducible gene 2 protein (MIG-2), or Pleckstrin homology (PH) domain-containing family C member 1, is an adaptor protein that is widely distributed and is particularly abundant in adherent cells. It binds to the integrin beta cytoplasmic tail to promote integrin activation. It promotes carcinogenesis through regulation of cell-cell and cell-extracellular matrix adhesion. KIND2 also plays an important role in cardiac development. KIND2 consists of an atypical FERM domain that is made up of F1, F2 and F3 domains, as well as an N-terminal region, which precedes the FERM domain and has been referred to as the F0 domain. This family corresponds to the F1 domain. 101 matched cddid_all.tbl CDD cd17185 cd17185 340705 FERM_F1_KIND3 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in kindlin-3 (KIND3). KIND3, also termed fermitin family homolog 3 (FERMT3), or MIG2-like protein, or Unc-112-related protein 2, is an adaptor protein that expressed primarily in hematopoietic cells. It plays a central role in cell adhesion in hematopoietic cells, and also promotes integrin activation, clustering and outside-in signaling. KIND3, together with talin-1, contributes essentially to the activation of beta2-integrins in neutrophils. In addition, KIND3 interacts with the ribosome and regulates c-Myc expression required for proliferation of chronic myeloid leukemia cells. Mutations in the KIND3 gene cause leukocyte adhesion deficiency type III (LAD III), which is characterized by high susceptibility to infections, spontaneous and episodic bleedings, and osteopetrosis. KIND3 consists of an atypical FERM domain that is made up of F1, F2 and F3 domains, as well as an N-terminal region, which precedes the FERM domain and has been referred to as the F0 domain. This family corresponds to the F1 domain. 91 matched cddid_all.tbl CDD cd17186 cd17186 340706 FERM_F1_Merlin FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in merlin and similar proteins. Merlin, also termed moesin-ezrin-radixin-like protein, or neurofibromin-2 (NF2), or Schwannomerlin, or Schwannomin, is a member of the ezrin/radixin/moesin (ERM) family of cytoskeletal proteins that plays an essential role in microvilli formation, T-cell activation, and tumor metastasis through providing a regulated linkage between F-actin and membrane-associated proteins. These proteins may also function in signaling cascades that regulate the assembly of actin stress fibers. The ERM proteins consist of an N-terminal FERM domain, a coiled-coil (CC) domain and a C-terminal tail segment (C-tail) containing a well-defined actin-binding motif, merlin however lacks the typical actin-binding motif in the C-tail. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). Merlin plays vital roles in controlling proper development of organ sizes by specifically binding to a large number of target proteins localized both in cytoplasm and nuclei. Merlin may function as a tumor suppressor that functions upstream of the core Hippo pathway kinases Lats1/2 (Wts in Drosophila) and Mst1/2 (Hpo in Drosophila), as well as the nuclear E3 ubiquitin ligase DDB1-and-Cullin 4-associated Factor 1 (DCAF1)-associated cullin 4-Roc1 ligase, CRL4(DCAF1). Merlin may also has a tumor suppressor function in melanoma cells, the inhibition of the proto-oncogenic Na(+)/H(+) exchanger isoform 1 (NHE1) activity. 85 matched cddid_all.tbl CDD cd17187 cd17187 340707 FERM_F1_ERM FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in the ERM family proteins, Ezrin, Radixin, and Moesin. The ezrin-radixin-moesin (ERM) family includes a group of closely related cytoskeletal proteins that plays an essential role in microvilli formation, T-cell activation, and tumor metastasis through providing a regulated linkage between F-actin and membrane-associated proteins. These proteins may also function in signaling cascades that regulate the assembly of actin stress fibers. The ERM proteins consist of an N-terminal FERM domain, a coiled-coil (CC) domain and a C-terminal tail segment (C-tail) containing a well-defined actin-binding motif. They exist in two states, a dormant state in which the FERM domain binds to its own C-terminal tail and thereby precludes binding of some partner proteins, and an activated state, in which the FERM domain binds to one of many membrane binding proteins and the C-terminal tail binds to F-actin. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 83 matched cddid_all.tbl CDD cd17188 cd17188 340708 FERM_F1_FRMD7 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in FERM domain-containing protein 7 (FRMD7). FRMD7 plays an important role in neuronal development and is involved in the regulation of F-actin, neurofilament, and microtubule dynamics. It interacts with the Rho GTPase regulator, RhoGDIalpha, and activates the Rho subfamily member Rac1, which regulates reorganization of actin filaments and controls neuronal outgrowth. Mutations in the FRMD7 gene are responsible for the X-linked idiopathic congenital nystagmus (ICN), a disease which affects ocular motor control. FRMD7 contains a FERM domain, and a pleckstrin homology (PH) domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 86 matched cddid_all.tbl CDD cd17189 cd17189 340709 FERM_F1_FARP1 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in FERM, ARH/RhoGEF and pleckstrin domain-containing protein 1 (FARP1). FARP1, also termed chondrocyte-derived ezrin-like protein (CDEP), or pleckstrin homology (PH) domain-containing family C member 2 (PLEKHC2), is a neuronal activator of the RhoA GTPase. It promotes outgrowth of developing motor neuron dendrites. It also regulates excitatory synapse formation and morphology, as well as activates the GTPase Rac1 to promote F-actin assembly. As a novel downstream signaling partner of Rif, FARP1 is involved in the regulation of semaphorin signaling in neurons. FARP1 contains a FERM domain, a Dbl-homology (DH) domain and two pleckstrin homology (PH) domains. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 85 matched cddid_all.tbl CDD cd17190 cd17190 340710 FERM_F1_FARP2 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in FERM, ARH/RhoGEF and pleckstrin domain-containing protein 2 (FARP2) and similar proteins. FARP2, also termed FERM domain including RhoGEF (FIR), or Pleckstrin homology (PH) domain-containing family C member 3, is a Dbl-family guanine nucleotide exchange factor (GEF) that activates Rac1 or Cdc42 in response to upstream signals, suggesting roles in regulating processes such as neuronal axon guidance and bone homeostasis. It is also a key molecule involved in the response of neuronal growth cones to class-3 semaphorins. FARP2 contains a FERM domain, a Dbl-homology (DH) domain and two pleckstrin homology (PH) domains. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 85 matched cddid_all.tbl CDD cd17191 cd17191 340711 FERM_F1_PTPN14 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in tyrosine-protein phosphatase non-receptor type 14 (PTPN14) and similar proteins. PTPN14, also termed protein-tyrosine phosphatase pez, or PTPD2, or PTP36, is a widely expressed non-transmembrane cytosolic protein tyrosine phosphatase (PTP). It belongs to the FERM family of PTPs characterized by a conserved N-terminal FERM domain and a C-terminal PTP catalytic domain with an intervening sequence containing an acidic region and a putative SH3 domain-binding sequence. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). PTPN14 plays a role in the nucleus during cell proliferation. It forms a complex with Kibra and LATS1 proteins and negatively regulates the key Hippo pathway protein Yes-associated protein (YAP) oncogenic function by controlling its localization. It specifically regulates p130 Crk-associated substrate (p130Cas) phosphorylation at tyrosine residue 128 (Y128) in colorectal cancer (CRC) cells. Moreover, PTPN14 may be a critical enzyme in regulating endothelial cell function. It plays a crucial role in organogenesis by inducing transforming growth factor beta (TGFbeta) and epithelial-mesenchymal transition (EMT). It also acts as a modifier of angiogenesis and hereditary haemorrhagic telangiectasia. It regulates the lymphatic function and choanal development through the interaction with the vascular endothelial growth factor receptor 3 (VEGFR3), a receptor tyrosine kinase essential for lymphangiogenesis. Furthermore, PTPN14 functions as a regulator of cell motility through its action on cell-cell adhesion. Beta-Catenin, a central component of adherens junctions, has been identified as a PTPN14 substrate. PTPN14 works as a novel sperm-motility biomarker and a potential mitochondrial protein. 87 matched cddid_all.tbl CDD cd17192 cd17192 340712 FERM_F1_PTPN21 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in tyrosine-protein phosphatase non-receptor type 21 (PTPN21) and similar proteins. PTPN21, also termed protein-tyrosine phosphatase D1 (PTPD1), is a cytosolic non-receptor protein-tyrosine phosphatase (PTP) that belongs to the FERM family of PTPs characterized by a conserved N-terminal FERM domain and a C-terminal PTP catalytic domain with an intervening sequence containing an acidic region and a putative SH3 domain-binding sequence. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). PTPN21 interacts with a Tec tyrosine kinase family member, the epithelial and endothelial tyrosine kinase (Etk, also known as Bmx), modulates Stat3 activation, and plays a role in the regulation of cell growth and differentiation. It also associates with and activates Src tyrosine kinase, and directs epidermal growth factor (EGF)/Src signaling to the nucleus through activating ERK1/2- and Elk1-dependent gene transcription. PTPD1-Src complex interacts a protein kinase A-anchoring protein AKAP121 to forms a PTPD1-Src-AKAP121 complex, which is required for efficient maintenance of mitochondrial membrane potential and ATP oxidative synthesis. As a novel component of the endocytic pathway, PTPN21 supports EGF receptor stability and mitogenic signaling in bladder cancer cells. Moreover, PTPD1 regulates focal adhesion kinase (FAK) autophosphorylation and cell migration through modulating Src-FAK signaling at adhesion sites. 87 matched cddid_all.tbl CDD cd17193 cd17193 340713 FERM_F1_PTPN3 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in tyrosine-protein phosphatase non-receptor type 3 (PTPN3). PTPN3, also termed protein-tyrosine phosphatase H1 (PTP-H1), belongs to the non-transmembrane FERM-containing protein-tyrosine phosphatase (PTP) subfamily characterized by a conserved N-terminal FERM domain, a PDZ domain, and a C-terminal PTP catalytic domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). PTPN3 associates with the mitogen-activated protein kinase p38gamma (also known as MAPK12) to form a PTPN3-p38gamma complex that promotes Ras-induced oncogenesis. It may also act as a tumor suppressor in lung cancer through its modulation of epidermal growth factor receptor (EGFR) signaling. Moreover, PTPN3 shows sensitizing effect to anti-estrogens. It dephosphorylates the tyrosine kinase EGFR, disrupts its interaction with the nuclear estrogen receptor, and increases breast cancer sensitivity to small molecule tyrosine kinase inhibitors (TKIs). It also cooperates with vitamin D receptor to stimulate breast cancer growth through their mutual stabilization. 84 matched cddid_all.tbl CDD cd17194 cd17194 340714 FERM_F1_PTPN4 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in tyrosine-protein phosphatase non-receptor type 4 (PTPN4). PTPN4, also termed protein-tyrosine phosphatase MEG1 (MEG) or PTPase-MEG1, belongs to the non-transmembrane FERM-containing protein-tyrosine phosphatase (PTP) subfamily characterized by a conserved N-terminal FERM domain, a PDZ domain, and a C-terminal PTP catalytic domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). PTPN4 protects cells against apoptosis. It associates with the mitogen-activated protein kinase p38gamma (also known as MAPK12) to form a PTPN4-p38gamma complex that promotes cellular signaling, preventing cell death induction. It also inhibits tyrosine phosphorylation and subsequent cytoplasm translocation of TRIF-related adaptor molecule (TRAM, also known as TICAM2), resulting in the disturbance of TRAM-TRIF interaction. Moreover, PTPN4 negatively regulates cell proliferation and motility through dephosphorylation of CrkI. 84 matched cddid_all.tbl CDD cd17195 cd17195 340715 FERM_F1_PTPN13 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in tyrosine-protein phosphatase non-receptor type 13 (PTPN13). PTPN13, also termed Fas-associated protein-tyrosine phosphatase 1 (FAP-1), or PTP-BAS, or protein-tyrosine phosphatase 1E (PTP-E1 or PTPE1), or protein-tyrosine phosphatase PTPL1, belongs to the non-transmembrane FERM-containing protein-tyrosine phosphatase (PTP) subfamily characterized by a KIND domain, a FERM domain, five PDZ domains, and a C-terminal PTP catalytic domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). PTPN13 interacts with a variety of ligands, suggests an important role as a scaffolding protein. It is also involved in the regulation of apoptosis, cytokinesis and cell cycle progression. 96 matched cddid_all.tbl CDD cd17196 cd17196 340716 FERM_F1_FRMPD2 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in FERM and PDZ domain-containing protein 2 (FRMPD2). FRMPD2, also termed PDZ domain-containing protein 4 (PDZK4), or PDZ domain-containing protein 5C (PDZD5C), is a potential scaffold protein involved in basolateral membrane targeting in epithelial cells. It interacts with nucleotide-binding oligomerization domain-2 (NOD2) through leucine-rich repeats and forms a complex with the membrane-associated protein ERBB2IP. FRMPD2 contains an N-terminal KIND domain, a FERM domain and three PDZ domains. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 95 matched cddid_all.tbl CDD cd17197 cd17197 340717 FERM_F1_FRMD1 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in FERM domain-containing protein 1 (FRMD1). FRMD1 is an uncharacterized FERM domain-containing protein. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 98 matched cddid_all.tbl CDD cd17198 cd17198 340718 FERM_F1_FRMD6 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in FERM domain-containing protein 6 (FRMD6). FRMD6, also termed willin, expanded or expanded homolog, is a FERM domain-containing protein that plays a critical role in regulating both cell proliferation and apoptosis. It acts as a tumor suppressor of human breast cancer cells independently of the Hippo pathway. It also inhibits human glioblastoma growth and progression by negatively regulating activity of receptor tyrosine kinases. As an upstream component of the hippo signaling pathway, FRMD6 orchestrates mammalian peripheral nerve fibroblasts. FRMD6 contains a FERM domain that is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 98 matched cddid_all.tbl CDD cd17199 cd17199 340719 FERM_F1_FRMD4A FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in FERM domain-containing protein 4A (FRMD4A). FRMD4A is a cytohesin adaptor involved in cell structure, transport and signaling. It promotes the growth of cancer cells in tongue, head and neck squamous cell carcinomas. It also regulates tau secretion by activating cytohesin-Arf6 signaling through connecting cytohesin family Arf6-specific guanine-nucleotide exchange factors (GEFs) and Par-3 at primordial adherens junctions during epithelial polarization. As a genetic risk factor for late-onset Alzheimer's disease (AD), FRMD4A may play a role in amyloidogenic and tau-related pathways in AD. FRMD4A contains a FERM domain that is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 89 matched cddid_all.tbl CDD cd17200 cd17200 340720 FERM_F1_FRMD4B FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in FERM domain-containing protein 4B (FRMD4B). FRMD4B, also termed GRP1-binding protein GRSP1, interacts with the coil-coil domain of ARF exchange factor GRP1 to form the Grsp1-Grp1 complex that co-localizes with cortical actin rich regions in response to stimulation of CHO-T cells with insulin or epidermal growth factor (EGF). FRMD4B contains a FERM protein interaction domain as well as two coiled coil domains and may therefore function as a scaffolding protein. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 89 matched cddid_all.tbl CDD cd17201 cd17201 340721 FERM_F1_EPB41L1 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in erythrocyte membrane protein band 4.1-like protein 1 (EPB41L1) and similar proteins. EPB41L1, also termed neuronal protein 4.1 (4.1N), belongs to the skeletal protein 4.1 family that is involved in cellular processes such as cell adhesion, migration and signaling. It is a cytoskeleton-associated protein that may serve as a tumor suppressor in solid tumors. It suppresses hypoxia-induced epithelial-mesenchymal transition in epithelial ovarian cancer (EOC) cells. The down-regulation of EPB41L1 expression is a critical step for non-small cell lung cancer (NSCLC) development. Moreover, EPB41L1 functions as a linker protein between inositol 1,4,5-trisphosphate receptor type1 (IP3R1) and actin filaments in neurons. EPB41L1 contains a FERM domain, a spectrin and actin binding (SAB) domain, and a C-terminal domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 84 matched cddid_all.tbl CDD cd17202 cd17202 340722 FERM_F1_EPB41L2 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in erythrocyte membrane protein band 4.1-like protein 2 (EPB41L2) and similar proteins. EPB41L2, also termed generally expressed protein 4.1 (4.1G), belongs to the skeletal protein 4.1 family that is involved in cellular processes such as cell adhesion, migration and signaling. EPB41L2 contains a FERM domain, a spectrin and actin binding (SAB) domain, and a C-terminal domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 84 matched cddid_all.tbl CDD cd17203 cd17203 340723 FERM_F1_EPB41L3 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in erythrocyte membrane protein band 4.1-like protein 3 (EPB41L3) and similar proteins. EPB41L3, also termed 4.1B, or differentially expressed in adenocarcinoma of the lung protein 1 (DAL-1), belongs to the skeletal protein 4.1 family that is involved in cellular processes such as cell adhesion, migration and signaling. EPB41L3 is a tumor suppressor that has been implicated in a variety of meningiomas and carcinomas. EPB41L3 contains a FERM domain, a spectrin and actin binding (SAB) domain, and a C-terminal domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 84 matched cddid_all.tbl CDD cd17204 cd17204 340724 FERM_F1_EPB41L4B FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in erythrocyte band 4.1-like protein 4B (EPB41L4B). EPB41L4B, also termed FERM-containing protein CG1, or expressed in high metastatic cells (Ehm2), or Lulu2, is a member of the band 4.1/Nbl4 (novel band 4.1-like protein 4) group of the FERM protein superfamily. It contains a FERM domain that is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). EPB41L4B is a positive regulator of keratinocyte adhesion and motility, suggesting a role in wound healing. It also promotes cancer metastasis in melanoma, prostate cancer and breast cancer. 84 matched cddid_all.tbl CDD cd17205 cd17205 340725 FERM_F1_EPB41L5 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in erythrocyte membrane protein band 4.1-like 5 (EPB41L5). EPB41L5 is a mesenchymal-specific protein that is an integral component of the ARF6-based pathway. It is normally induced during epithelial-mesenchymal transition (EMT) by an EMT-related transcriptional factor, ZEB1, which drives ARF6-based invasion, metastasis and drug resistance. EPB41L5 also binds to paxillin to enhance integrin/paxillin association, and thus promotes focal adhesion dynamics. Moreover, EPB41L5 acts as a substrate for the E3 ubiquitin ligase Mind bomb 1 (Mib1), which is essential for activation of Notch signaling. EPB41L5 is a member of the band 4.1/Nbl4 (novel band 4.1-like protein 4) group of the FERM protein superfamily. It contains a FERM domain that is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 86 matched cddid_all.tbl CDD cd17206 cd17206 340726 FERM_F1_Myosin-X FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in unconventional myosin-X. Myosin-X, also termed myosin-10 (Myo10), is an untraditional member of myosin superfamily. It is an actin-based motor protein that plays a critical role in diverse cellular motile events, such as filopodia formation/extension, phagocytosis, cell migration, and mitotic spindle maintenance, as well as a number of disease states including cancer metastasis and pathogen infection. Myosin-X functions as an important regulator of cytoskeleton that modulates cell motilities in many different cellular contexts. It regulates neuronal radial migration through interacting with N-cadherin. Like other unconventional myosins, Myosin-X is composed of a conserved motor head, a neck region and a variable tail. The neck region consists of three IQ motifs (light chain-binding sites), and a predicted stalk of coiled coil. The tail contains three PEST regions, three PH domains, a MyTH4 domain, and a FERM domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 97 matched cddid_all.tbl CDD cd17207 cd17207 340727 FERM_F1_PLEKHH3 FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in pleckstrin homology domain-containing family H member 3 (PLEKHH3). PLEKHH3 is an uncharacterized Pleckstrin homology (PH) domain-containing protein that shows high sequence similarity with unconventional myosin-X, an actin-based motor protein that plays a critical role in diverse cellular motile events, such as filopodia formation/extension, phagocytosis, cell migration, and mitotic spindle maintenance, as well as a number of disease states including cancer metastasis and pathogen infection. In addition to two PH domains, PLEKHH3 harbors a MyTH4 domain, and a FERM (Band 4.1, ezrin, radixin, moesin) domain. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 96 matched cddid_all.tbl CDD cd17208 cd17208 340728 FERM_F1_DdMyo7_like FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in Dictyostelium discoideum Myosin-VIIa (DdMyo7) and similar proteins. DdMyo7, also termed Myosin-I heavy chain, or class VII unconventional myosin, or M7, plays a role in adhesion in Dictyostelium where it is a component of a complex of proteins that serve to link membrane receptors to the underlying actin cytoskeleton. It interacts with talinA, an actin-binding protein with a known role in cell-substrate adhesion. DdMyo7 is required for phagocytosis. It is also essential for the extension of filopodia, plasma membrane protrusions filled with parallel bundles of F-actin. Members in this family contain a myosin motor domain, two MyTH4 domains, two FERM (Band 4.1, ezrin, radixin, moesin) domains, and two Pleckstrin homology (PH) domains. Some family members contain an extra SH3 domain. Each FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). 98 matched cddid_all.tbl CDD cd17209 cd17209 340729 RA_RalGDS Ras-associating (RA) domain found in Ral guanine nucleotide dissociation stimulator (RalGDS) and similar proteins. RalGDS, also termed Ral guanine nucleotide exchange factor (RalGEF), is a guanine exchange factor (GEF) for the Ral family of small GTPases. It is the prototype of RalGDS family proteins that are involved in Ras and Ral signaling pathways as downstream effector proteins. RalGDS stimulates the dissociation of GDP from the Ras-related RalA and RalB GTPases which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-Ras, H-Ras, K-Ras, and Rap. Moreover, RalGDS functions as a novel interacting partner for Rab7-interacting lysosomal protein (RILP), a key regulator for late endosomal/lysosomal trafficking. RILP suppresses invasion of breast cancer cells by inhibiting the GEF activity for RalA of RalGDS. RalGDS also plays a vital role in the regulation of Ral-dependent Weibel-Palade bodies (WPB) exocytosis from endothelial cells. In addition, RalGDS couples growth factor signaling to Akt activation by promoting PDK1-induced Akt phosphorylation. Members in this family have similar domain structure: a central CDC25 homology domain with an upstream Ras Exchange motif (REM), and a C-terminal Ras-associating (RA) domain. The RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin; ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. 86 matched cddid_all.tbl CDD cd17210 cd17210 340730 RA_RGL Ras-associating (RA) domain found in Ral guanine nucleotide dissociation stimulator-like 1 (RalGDS-like 1) and similar proteins. RalGDS-like 1 (RGL) is a Ral-specific guanine nucleotide exchange factor that belongs to RalGDS family, whose members are involved in Ras and Ral signaling pathways as downstream effector proteins. RGL has been identified as a possible effector protein of Ras. It also regulates c-fos promoter and the GDP/GTP exchange of Ral. Members in this family have similar structure: a central CDC25 homology domain with an upstream Ras Exchange motif (REM), and a C-terminal Ras-associating (RA) domain. The RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin; ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. 87 matched cddid_all.tbl CDD cd17211 cd17211 340731 RA_RGL2 Ras-associating (RA) domain found in Ral guanine nucleotide dissociation stimulator-like 2 (RalGDS-like 2) and similar proteins. RalGDS-like 2 (RGL2), also termed RalGDS-like factor (RLF), or Ras-associated protein RAB2L, is a novel Ras and Rap 1A-associating protein that belongs to RalGDS family, whose members are involved in Ras and Ral signaling pathways as downstream effector proteins. RGL2 exhibits guanine nucleotide exchange activity towards the small GTPase Ral. Members in this family have similar domain structure: a central CDC25 homology domain with an upstream Ras Exchange motif (REM), and a C-terminal Ras-associating (RA) domain. The RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin; ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. The RA domain of RGL2 is phosphorylated by protein kinase A and the phosphorylation affects the ability of RGL2 to bind both Ras and Rap1. 86 matched cddid_all.tbl CDD cd17212 cd17212 340732 RA_RGL3 Ras-associating (RA) domain found in Ral guanine nucleotide dissociation stimulator-like 3 (RalGDS-like 3) and similar proteins. RalGDS-like 3 (RGL3), also termed Ras pathway modulator (RPM), interacts in a GTP- and effector loop-dependent manner with Rit and Ras. As a novel potential effector of both p21 Ras and M-Ras, RGL3 negatively regulates Elk-1-dependent gene induction downstream of p21 Ras or mitogen activated protein/extracellular signal regulated kinase Kinase 1 (MEKK1). It also functions as a potential binding partner for Rap-family small G-proteins and profilin II. RGL3 belongs to RalGDS family, whose members are involved in Ras and Ral signaling pathways as downstream effector proteins. Members in this family have similar domain structure: a central CDC25 homology domain with an upstream Ras Exchange motif (REM), and a C-terminal Ras-associating (RA) domain. The RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin; ubiquitin is a protein modifier (Ubiquitination) in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. 87 matched cddid_all.tbl CDD cd17213 cd17213 340733 RA_PHLPP Ras-associating (RA) domain found in PH domain leucine-rich repeat-containing protein phosphatase PHLPP1, PHLPP2, and similar proteins. PHLPP represents a novel family of Ser/Thr protein phosphatases, which is involved in two key signaling pathways, the phosphatidylinositol 3-kinase and diacylglycerol signaling pathways, by directly dephosphorylating and inactivating Akt serine-threonine kinases (Akt1, Akt2, Akt3) and protein kinase C (PKC) isoforms. PHLPP targets oncogenic kinases and may act as a tumor suppressor in several types of cancers. Two PHLPP isoforms are included in this family, PHLPP1 and PHLPP2. They regulate Akt activation together when both phosphatases are expressed. PHLPP1 is also termed pleckstrin homology domain-containing family E member 1, or PH domain-containing family E member 1, or suprachiasmatic nucleus circadian oscillatory protein (SCOP). It plays a suppression role in inflammatory response of glioma. Its loss contributes to gliomas development and progression. Loss of PHLPP1 also protects against colitis by inhibiting intestinal epithelial cell apoptosis. The overexpression of PHLPP1 impairs hippocampus-dependent learning, suggesting a role for PHLPP1 in learning and memory. PHLPP2 is also termed PH domain leucine-rich repeat-containing protein phosphatase-like (PHLPP-like). Both PHLPP1 and PHLPP2 contain a putative Ras-associating (RA) domain followed by a pleckstrin homology (PH) domain, a series of leucine-rich repeats and a protein phosphatase 2C (PP2C) domain. 97 matched cddid_all.tbl CDD cd17214 cd17214 340734 RA_CYR1_like Ras-associating (RA) domain found in Saccharomyces cerevisiae adenylate cyclase and similar proteins. CYR1, also termed ATP pyrophosphate-lyase, or adenylyl cyclase, is a fungal adenylate cyclase that regulates developmental processes such as hyphal growth, biofilm formation, and phenotypic switching. CYR1 plays essential roles in regulation of cellular metabolism by catalyzing the synthesis of a second messenger, cAMP. It acts as a scaffold protein keeping Ras2 available for its regulatory factors, the Ira proteins. CYR1 has at least four domains, including an N-terminal adenylate cyclase G-alpha binding domain, a Ras-associating (RA) domain, a middle leucine-rich repeat region, and a catalytic domain. The RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin; ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. The RA domain of CYR1 post-translationally modifies a small GTPase called Ras, which is involved in cellular signal transduction. CYR1 activity is stimulated directly by regulatory proteins (Ras1 and Gpa2), peptidoglycan fragments and carbon dioxide. 99 matched cddid_all.tbl CDD cd17215 cd17215 340735 RA_Rin1 Ras-associating (RA) domain found in Ras and Rab interactor 1 (Rin1). Rin1, also termed Ras inhibitor JC99, or Ras interaction/interference protein 1, is a downstream Ras effector that represents a unique class of Ras effector connected to two independent signaling pathways. The first effector pathway is the direct activation of RAB5-mediated endocytosis and the second pathway involves direct activation of ABL tyrosine kinase activity. Rin1 functions as a guanine nucleotide exchange factor (GEF) for RAB5 GTPases. The RAB5 GEF activity of Rin1 promotes early endosome fusion, an early event in transit to the lysosome. Rin1 binds the SH3 and SH2 domains of ABL proteins, ABL1 and ABL2, and activates their tyrosine kinase activity. Rin1 contains SH2 and proline-rich domains in the N-terminal region, and RH, VPS9, and RA domains in the C-terminal region. The RA domain has the beta-grasp ubiquitin-like (Ubl) fold with low sequence similarity to ubiquitin; ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair. 88 matched cddid_all.tbl CDD cd17216 cd17216 340736 RA_Myosin-IXa Ras-associating (RA) domain found in Myosin-IXa. Myosin-IXa, also termed myosin-9a (Myo9a), is a single-headed, actin-dependent motor protein of the unconventional myosin IX class. It is expressed in several tissues and is enriched in the brain and testes. Myosin-IXa contains a Ras-associating (RA) domain, a motor domain, a protein kinase C conserved region 1 (C1), and a Rho GTPase activating domain (RhoGAP). Its RA domain is located at its head domain and has the beta-grasp ubiquitin-like fold with unknown function. Myosin-IXa binds the alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor (AMPAR) GluA2 subunit, and plays a key role in controlling the molecular structure and function of hippocampal synapses. Moreover, Myosin-IXa functions in epithelial cell morphology and differentiation such that its knockout mice develop hydrocephalus and kidney dysfunction. Myosin-IXa regulates collective epithelial cell migration by targeting RhoGAP activity to cell-cell junctions. Myosin-IXa negatively regulates Rho GTPase signaling, and functions as a regulator of kidney tubule function. 96 matched cddid_all.tbl CDD cd17217 cd17217 340737 RA_Myosin-IXb Ras-associating (RA) domain found in Myosin-IXb. Myosin-IXb, also termed myosin-9b (Myo9b), is a motor protein with a Rho GTPase activating domain (RhoGAP); it is an actin-dependent motor protein of the unconventional myosin IX class. It is expressed abundantly in tissues of the immune system, like lymph nodes, thymus, and spleen and in several immune cells including dendritic cells, macrophages and CD4+ T. Myosin-IXb contains a Ras-associating (RA) domain, a motor domain, a protein kinase C conserved region 1 (C1), and a RhoGAP domain. Its RA domain is located at its head domain and has the beta-grasp ubiquitin-like fold with unknown function. Myosin-IXb acts as a motorized signaling molecule that links Rho signaling to the dynamic actin cytoskeleton. It regulates leukocyte migration by controlling RhoA signaling. Myosin-IXb is also involved in the development of autoimmune diseases, including rheumatoid arthritis, systemic lupus erythematosus and type 1 diabetes. Moreover, Myosin-IXb is a ROBO-interacting protein that suppresses RhoA activity in lung cancer cells. 96 matched cddid_all.tbl CDD cd17218 cd17218 340738 RA_RASSF1 Ras-associating (RA) domain found in Ras-association domain-containing protein 1 (RASSF1). RASSF1 is a member of a family of six related RASSF1-6 proteins (the classical RASSF proteins). RASSF1 has eight transcripts (A-H) arising from alternative splicing and differential promoter usage. With the exception of some minor splice variants (RASSF1F and RASSF1G), RASSF1 contains an RA domain and a C-terminal SARAH protein-protein interaction motif. The RA domain of the classical RASSF proteins has a beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. The RA domain mediates interactions with Ras and other small GTPases, and the SARAH domain mediates protein-protein interactions crucial in the pathways that induce cell cycle arrest and apoptosis. RASSF1A and 1C are the most extensively studied RASSF1 with both localized to microtubules and involved in regulation of growth and migration. 157 matched cddid_all.tbl CDD cd17219 cd17219 340739 RA_RASSF3 Ras-associating (RA) domain found in Ras-association domain-containing protein 3 (RASSF3). RASSF3 is a member of a family of six related classical RASSF1-6 proteins (the classical RASSF proteins). RASSF3 has three transcripts (A-C) due to alternative splicing of the exons. The RASSF3B and 3C isoforms are shorter than RASSF3A, and unlike RASSF3A do not contain the RA or SARAH domains. The RA domain of the classical RASSF proteins has a beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. The RA domain mediates interactions with Ras and other small GTPases, and the SARAH domain mediates protein-protein interactions crucial in the pathways that induce cell cycle arrest and apoptosis. RASSF3A regulates apoptosis and cell cycle via p53 stabilization and possibly is involved in DNA repair. 141 matched cddid_all.tbl CDD cd17220 cd17220 340740 RA_RASSF5 Ras-associating (RA) domain of Ras-association domain family 5 (RASSF5). RASSF5, also called New ras effector 1 (NORE1), or regulator for cell adhesion and polarization enriched in lymphoid tissues (RAPL), is a member of a family of six related RASSF1-6 proteins (the classical RASSF proteins) and is expressed as three transcripts (A-C) via differential promoter usage and alternative splicing. All transcripts variants of RASSF5 contain the RA or SARAH domains. The RA domain of the classical RASSF proteins has a beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. The RA domain mediates interactions with Ras and other small GTPases, and the SARAH domain mediates protein-protein interactions crucial in the pathways that induce cell cycle arrest and apoptosis. RASSF5A is a pro-apoptotic Ras effector and functions as a Ras regulated tumor suppressor. RASSF5C is regulated by Ras related protein and modulates cellular adhesion. 152 matched cddid_all.tbl CDD cd17221 cd17221 340741 RA_RASSF2 Ras-associating (RA) domain found in Ras-association domain-containing protein 2 (RASSF2). RASSF2 is a member of a family of six related classical RASSF1-6 proteins. The RASSF2 gene is transcribed into two major isoforms (A and C). RASSF2 is structurally related to RASSF1A but unlike RASSF1A It is primarily a nuclear protein. RASSF2 contains the RA and SARAH domains. The RA domain of the classical RASSF protein family has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. RA domains mediate interactions with Ras and other small GTPases, and SARAH domains mediate protein-protein interactions crucial in the pathways that induce cell cycle arrest and apoptosis. RASSF2 is inactivated in different cancers and cancer cell lines by promoter methylation and loss of expression, implicating the correlation and significance of RASSF2 in tumorigenesis. In addition to regulating apoptosis and proliferation RASSF2 may have other functions as RASSF2 knockout mice develop normally for the first two weeks but then develop growth retardation and die 4 weeks after birth. 87 matched cddid_all.tbl CDD cd17222 cd17222 340742 RA_RASSF4 Ras-associating (RA) domain found in Ras-association domain-containing protein 4 (RASSF4). RASSF4 is a member of a family of six related classical RASSF1-6 proteins and is broadly expressed in normal tissues. RASSF4 expression is reduced in tumor cell lines and primary tumors by promoter specific hypermethylation. RASSF4 contains the RA and SARAH domains. The RA domain of the classical RASSF protein family has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. RA domains mediate interactions with Ras and other small GTPases, and SARAH domains mediate protein-protein interactions crucial in the pathways that induce cell cycle arrest and apoptosis. RASSF4 inhibits lung cancer cell proliferation and invasion. 87 matched cddid_all.tbl CDD cd17223 cd17223 340743 RA_RASSF6 Ras-associating (RA) domain found in Ras-association domain-containing protein 6 (RASSF6). RASSF6 is a member of a family of six related classical RASSF1-6 proteins and is expressed as four transcripts via alternative splicing. All transcripts variant of RASSF6 contain the RA and SARAH domains. The RA domain of the classical RASSF protein family has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. RA domains mediate interactions with Ras and other small GTPases, SARAH domains mediate protein-protein interactions crucial in the pathways that induce cell cycle arrest and apoptosis. RASSF6 is ubiquitiated and degraded by interacting with MDM2 to stabilize P53 and regulates apoptosis and cell cycle. RASSF6 is a tumor suppressor protein and is epigenetically silenced in childhood leukemia and neuroblastomas. Overexpression of RASSF6 causes apoptosis in HeLa cells. 87 matched cddid_all.tbl CDD cd17224 cd17224 340744 RA_ASPP1 Ras-associating (RA) domain found in apoptosis-stimulating protein of p53 protein 1 (ASPP1). ASPP1 is a member of the ASPP protein family (Apoptosi-Stimulating Protein of p53) that activates the p53-mediated apoptotic response. ASSP1 functions as a tumor suppressor and coordinates with p53 to protect hematopoietic stem cell (HSC) pool integrity, guarding against hematological malignancies. ASSP1 contains a RA domain at the N-terminus. The RA domain is a ubiquitin-like domain and RA domain-containing proteins are involved in several different functions ranging from tumor suppression to being oncoproteins. 85 matched cddid_all.tbl CDD cd17225 cd17225 340745 RA_ASPP2 Ras-associating (RA) domain found in apoptosis-stimulating protein of p53 protein 2 (ASPP2). ASPP2, also termed Bcl2-binding protein (Bbp), or renal carcinoma antigen NY-REN-51, or tumor suppressor p53-binding protein 2 (53BP2), or p53-binding protein 2 (p53BP2), is a member of ASPP protein family and it functions as a tumor suppressor. ASPP2 binds to p53 and enhances p53-mediated transcription of proapoptotic genes. ASSP2 contains a RA domain at the N-terminus. The RA domain is a ubiquitin-like domain and RA domain-containing proteins are involved in several different functions ranging from tumor suppression to being oncoproteins. All p53 amino acids that are important for ASPP2 binding are mutated in human cancer, and ASPP2 is frequently downregulated in these tumor cells. 80 matched cddid_all.tbl CDD cd17226 cd17226 340746 RA_ARAP1 Ras-associating (RA) domain found in Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1 (ARAP1). ARAP1, also termed Centaurin-delta-2 (Cnt-d2), is a phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P(3))-dependent Arf Rap-activated guanosine triphosphatase (GTPase)-activating protein (GAP) that inhibits the trafficking of epidermal growth factor receptor (EGFR) to the early endosome. It associates with the Cbl-interacting protein of 85 kDa (CIN85), regulates endocytic trafficking of the EGFR, and thus affects ubiquitination of EGFR. It also regulates the ring size of circular dorsal ruffles through Arf1 and Arf5. ARAP1 contains multiple functional domains, including ArfGAP and RhoGAP domains, as well as a sterile alpha motif (Sam) domain, five PH domains, and a RA domain. The RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin (Ub); Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. 93 matched cddid_all.tbl CDD cd17227 cd17227 340747 RA_ARAP2 Ras-associating (RA) domain found in Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 2 (ARAP2). ARAP2, also termed Centaurin-delta-1 (Cnt-d1), or Protein PARX, is a phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P(3))-dependent Arf Rap-activated guanosine triphosphatase (GTPase)-activating protein (GAP), which promotes GLUT1-mediated basal glucose uptake by modifying sphingolipid metabolism through glucosylceramide synthase (GCS). ARAP2 signals through Arf6 and Rac1 to control focal adhesion morphology. ARAP2 contains multiple functional domains, including ArfGAP and RhoGAP domains, as well as a sterile alpha motif (Sam) domain, five PH domains, and a RA domain. The RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin (Ub); Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. 98 matched cddid_all.tbl CDD cd17228 cd17228 340748 RA_ARAP3 Ras-associating (RA) domain found in Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3 (ARAP3). ARAP3, also termed Centaurin-delta-3 (Cnt-d3), is a phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P(3))-dependent Arf Rap-activated guanosine triphosphatase (GTPase)-activating protein (GAP) that modulates actin cytoskeleton remodeling by regulating ARF and RHO family members, ADP-ribosylation factor 6 (Arf6) and Ras homolog gene family member A (RhoA). It is regulated by phosphatidylinositol 3,4,5-trisphosphate and a small GTPase Rap1-GTP, and has been implicated in the regulation of cell shape and adhesion. ARAP3 contains multiple functional domains, including ArfGAP and RhoGAP domains, as well as a sterile alpha motif (Sam) domain, five PH domains, and a RA domain. The RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin (Ub); Ub is a protein modifier in eukaryotes that is involved in various cellular processes including transcriptional regulation, cell cycle control, and DNA repair in eukaryotes. 99 matched cddid_all.tbl CDD cd17229 cd17229 340749 RA1_PLC-epsilon Ras-associating (RA) domain 1 found in Phosphatidylinositide-specific phospholipase C (PLC)-epsilon. PLC is a signaling enzyme that hydrolyzes membrane phospholipids to generate inositol triphosphate. PLC-epsilon represents a novel forth class of PLC that has a PLC catalytic core domain, a CDC25 guanine nucleotide exchange factor domain and two RA (Ras-association) domains. RA domain has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. Although PLC RA1 and RA2 have homologous ubiquitin-like folds only RA2 can bind Ras and activate it. RA domain-containing proteins function by interacting with Ras proteins directly or indirectly and involve in several different functions ranging from tumor suppression to being oncoproteins. Ras proteins are small GTPases that are involved in cellular signal transduction. This family corresponds to the first RA domain of PLC-epsilon. 108 matched cddid_all.tbl CDD cd17230 cd17230 340750 TGS_DRG1 TGS (ThrRS, GTPase and SpoT) domain found in developmentally regulated GTP binding protein 1 (DRG-1). DRG-1 is a potassium-dependent GTPase that belongs to the DRG family GTP-binding proteins. It plays an important role in regulating cell growth. It functions as a potential oncogene in lung adenocarcinoma and promotes tumor progression via spindle checkpoint signaling regulation. It also plays an important role in melanoma cell growth and transformation, indicating a novel role in CD4(+) T cell-mediated immunotherapy in melanoma. In addition, DRG-1 is regulated by ZC3H15 (zinc finger CCCH-type containing 15, also known as Lerepo4), and displays a high temperature optimum of activity at 42C, suggesting the ability of being active under possible heat stress conditions. DRG-1 contains a domain of characteristic Obg-type G-motifs that may be the core of GTPase activity, as well as this C-terminal TGS (ThrRS, GTPase and SpoT) domain that has a predominantly beta-grasp ubiquitin-like fold and may be related to RNA binding. 80 matched cddid_all.tbl CDD cd17231 cd17231 340751 TGS_DRG2 TGS (ThrRS, GTPase and SpoT) domain found in developmentally regulated GTP binding protein 2 (DRG-2). DRG-2 is a member of the DRG family GTP-binding proteins. It has been implicated in cell growth, differentiation and death. DRG-2 plays a critical role in control of the cell cycle and apoptosis in Jurkat T cells. It regulates G2/M progression via the cyclin B1-Cdk1 complex. Moreover, DRG-2 is an endosomal protein and a key regulator of the small GTPase Rab5 deactivation and transferrin recycling. It enhances experimental autoimmune encephalomyelitis (EAE) by suppressing the development of TH17 cells. It is also associated with survival and cytoskeleton organization of osteoclasts under influence of macrophage colony-stimulating factor, and its overexpression leads to elevated bone resorptive activity of osteoclasts, resulting in bone loss. DRG-2 contains a domain of characteristic Obg-type G-motifs that may be the core of GTPase activity, as well as this C-terminal TGS (ThrRS, GTPase and SpoT) domain that has a predominantly beta-grasp ubiquitin-like fold and may be involved in RNA binding. 79 matched cddid_all.tbl CDD cd17232 cd17232 340752 Ubl_ATG8_GABARAP ubiquitin-like (Ubl) domain found in gamma-aminobutyric acid receptor-associated protein (GABARAP). GABARAP (also termed GABA(A) receptor-associated protein, ATG8A, or MM46) has been implicated in intracellular protein trafficking. It is a cytosolic protein that is localized to transport vesicles, the Golgi network and the endoplasmic reticulum. It interacts with the intracellular domain of the gamma2 subunit of GABA(A) receptors, and thus functions as a trafficking modulator implicated in the intracellular trafficking of GABA(A) receptor. GABARAP also acts as a Ubl modifier belonging to the ATG8 (autophagy-related 8) protein family, which is essential for autophagosome biogenesis and maturation. GABARAP recruits phosphatidylinositol 4-kinase II alpha (PI4KIIalpha) as a specific downstream effector, and regulates phosphatidylinositol 4-phosphate (PI4P)-dependent autophagosome lysosome fusion. 115 matched cddid_all.tbl CDD cd17233 cd17233 340753 Ubl_ATG8_GABARAPL1_like ubiquitin-like (Ubl) domain found in gamma-aminobutyric acid receptor-associated protein-like 1 (GABARAPL1) and similar proteins. GABARAPL1, also termed GEC1, or GABA(A) receptor-associated protein-like, belongs to the small family of GABARAP proteins which includes GABARAP, GABARAPL1, GABARAPL2/GATE-16, and GABARAPL3. GABARAPL1 has been involved in the intracellular transport of receptors via interactions with tubulin and GABA(A) or kappa opioid receptors. It is also a Ubl modifier that functions as a mediator involved in androgen-regulated autophagy process. It is transcriptionally modulated by androgen receptor (AR) and has a repressive role in autophagy. In addition, GABARAPL1 is required for increased membrane expression of epidermal growth factor receptor (EGFR) during hypoxia, suggesting a possible role in the trafficking of these membrane proteins. GABARAPL1 may also play a key role in several important biological processes such as cancer or neurodegenerative diseases. Low expression of GABARAPL1 is associated with poor prognosis of patients with hepatocellular carcinoma. This family also includes GABARAPL3, a paralog of GABARAPL1. 107 matched cddid_all.tbl CDD cd17234 cd17234 340754 Ubl_ATG8_MAP1LC3A ubiquitin-like (Ubl) domain found in microtubule associate protein 1 light chain 3A (MAP1LC3A). Autophagy is an essential intracellular process that targets large protein complexes, bacterial pathogens, and organelles for degradation. MAP1LC3A is belong to MAP1LC3 (short name LC3) family proteins. MAP1LC3 has a ubiquitin-like fold (Ubl) that belongs to the autophagy-related 8 (ATG8) protein family. A Ubl conjugation of MAP1LC3 by the phospholipid phosphatidylethanolamine (PE) is an essential process for the formation of autophagosomes. MAP1LC3 is cleaved by cysteine protease ATG4 and then conjugated with PE by E1-like enzyme ATG7 and ATG3, an E2-like enzyme. The Ubl conversion of MAPLC3 is known as a marker of autophagy-induction. MAP1LC3A staining patterns are used for different cancer diagnostic. 117 matched cddid_all.tbl CDD cd17235 cd17235 340755 Ubl_ATG8_MAP1LC3B ubiquitin-like (Ubl) domain found in microtubule associate protein 1 light chain 3B (MAP1LC3B). Autophagy is an essential intracellular process that targets large protein complexes, bacterial pathogens, and organelles for degradation. MAPLC3B belongs to the MAP1LC3 (short name LC3) family proteins. MAP1LC3 has a ubiquitin-like (Ubl) fold and belongs to the autophagy-related 8 (ATG8) protein family. A Ubl conjugation of MAPLC3 by the phospholipid phosphatidylethanolamine (PE) is an essential process for the formation of autophagosomes. MAP1LC3 is cleaved by cysteine protease ATG4 and then conjugated with PE by E1-like enzyme ATG7 and ATG3, an E2-like enzyme. The Ubl conversion of MAP1LC3 is known as a marker of autophagy-induction. All MAP1LC3 proteins are dispensable for basal autophagy; however, it has been shown that MAP1LC3B is responsible for selective degradation of p62 through autophagy. 115 matched cddid_all.tbl CDD cd17236 cd17236 340756 Ubl_ATG8_MAP1LC3C ubiquitin-like (Ubl) domain found in microtubule associate protein 1 light chain 3C (MAPLC3C). Autophagy is an essential intracellular process that targets large protein complexes, bacterial pathogens, and organelles for degradation. MAP1LC3C belongs to the MAP1LC3 (short name LC3) family proteins. MAP1LC3 has a ubiquitin-like (Ubl) fold that belongs to the autophagy-related 8 (ATG8) protein family. A Ubl conjugation of MAP1LC3 by the phospholipid phosphatidylethanolamine (PE) is an essential process for the formation of autophagosomes. MAP1LC3 is cleaved by cysteine protease ATG4 and then conjugated with PE by E1-like enzyme ATG7 and ATG3, a E2-like enzyme. The Ubl conversion of MAP1LC3 is known as a marker of autophagy-induction. ATG8 proteins are ubiquitously expressed, although some subfamily members are expressed at increased levels in certain tissues, e.g. MAP1LC3C is transcribed at lower levels than other members of MAP1LC3 subfamily and expressed predominantly in the lung. 113 matched cddid_all.tbl CDD cd17237 cd17237 340757 FERM_F1_Moesin FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in moesin and similar proteins. Moesin, also termed membrane-organizing extension spike protein, is a member of the ezrin/radixin/moesin (ERM) family of cytoskeletal proteins that plays an essential role in microvilli formation, T-cell activation, and tumor metastasis through providing a regulated linkage between F-actin and membrane-associated proteins. These proteins may also function in signaling cascades that regulate the assembly of actin stress fibers. The ERM proteins consist of an N-terminal FERM domain, a coiled-coil (CC) domain and a C-terminal tail segment (C-tail) containing a well-defined actin-binding motif. The C-terminal domain can fold back to bind to the FERM domain forming an autoinhibited conformation. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). Moesin is involved in mitotic spindle function through stabilizing cell shape and microtubules at the cell cortex. It is required for the formation of F-actin networks that mediate endosome biogenesis or maturation and transport through the degradative pathway. 84 matched cddid_all.tbl CDD cd17238 cd17238 340758 FERM_F1_Radixin FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in radixin and similar proteins. Radixin is a member of the ezrin/radixin/moesin (ERM) family of cytoskeletal proteins that plays an essential role in microvilli formation, T-cell activation, and tumor metastasis through providing a regulated linkage between F-actin and membrane-associated proteins. These proteins may also function in signaling cascades that regulate the assembly of actin stress fibers. The ERM proteins consist of an N-terminal FERM domain, a coiled-coil (CC) domain and a C-terminal tail segment (C-tail) containing a well-defined actin-binding motif. The C-terminal domain can fold back to bind to the FERM domain forming an autoinhibited conformation. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to the F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). Radixin plays important roles in cell polarity, cell motility, invasion and tumor progression. It mediates the binding of F-actin to the plasma membrane after a conformational activation through Akt2-dependent phosphorylation at Thr564. It is also involved in reversal learning and short-term memory by regulating synaptic GABAA receptor density. 83 matched cddid_all.tbl CDD cd17239 cd17239 340759 FERM_F1_Ezrin FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in Ezrin and similar proteins. Ezrin, also termed cytovillin, or villin-2, or p81, is a member of the ezrin/radixin/moesin (ERM) family of cytoskeletal proteins that plays an essential role in microvilli formation, T-cell activation, and tumor metastasis through providing a regulated linkage between F-actin and membrane-associated proteins. These proteins may also function in signaling cascades that regulate the assembly of actin stress fibers. The ERM proteins consist of an N-terminal FERM domain, a coiled-coil (CC) domain and a C-terminal tail segment (C-tail) containing a well-defined actin-binding motif. The C-terminal domain can fold back to bind to the FERM domain forming an autoinhibited conformation. The FERM domain is made up of three sub-domains, F1, F2, and F3. This family corresponds to F1 sub-domain, which is also called the N-terminal ubiquitin-like structural domain of the FERM domain (FERM_N). Ezrin is a tyrosine kinase substrate that functions as a cross-linker between actin cytoskeleton and plasma membrane. It has been implicated in the regulation of the proliferation, apoptosis, adhesion, invasion, metastasis and angiogenesis of cancer cells. 85 matched cddid_all.tbl CDD cd17240 cd17240 340760 RA_PHLPP1 Ras-associating (RA) domain found in PH domain leucine-rich repeat-containing protein phosphatase 1 (PHLPP1). PHLPP1, also termed pleckstrin homology domain-containing family E member 1, or PH domain-containing family E member 1, or suprachiasmatic nucleus circadian oscillatory protein (SCOP), is involved in two key signaling pathways, the phosphatidylinositol 3-kinase and diacylglycerol signaling pathways, by directly dephosphorylating and inactivating Akt serine-threonine kinases (Akt1, Akt2, Akt3) and protein kinase C (PKC) isoforms. PHLPP1 also plays critical roles in many cancers, such as gastric cancer, sacral chordoma, gallbladder cancer, hypopharyngeal squamous cell carcinomas, and non-small cell lung cancer. It plays a suppression role in inflammatory response of glioma. Its loss contributes to gliomas development and progression. Loss of PHLPP1 also protects against colitis by inhibiting intestinal epithelial cell apoptosis. The overexpression of PHLPP1 impairs hippocampus-dependent learning, suggesting a role in learning and memory. PHLPP1 contains a Ras-associating (RA) domain followed by a pleckstrin homology (PH) domain, a series of leucine-rich repeats and a protein phosphatase 2C (PP2C) domain. 90 matched cddid_all.tbl CDD cd17241 cd17241 340761 RA_PHLPP2 Ras-associating (RA) domain found in PH domain leucine-rich repeat-containing protein phosphatase 2 (PHLPP2). PHLPP2, also termed PH domain leucine-rich repeat-containing protein phosphatase-like (PHLPP-like), is involved in two key signaling pathways, the phosphatidylinositol 3-kinase and diacylglycerol signaling pathways, by directly dephosphorylating and inactivating Akt serine-threonine kinases (Akt1, Akt2, Akt3) and protein kinase C (PKC) isoforms. PHLPP2 also plays critical roles in many cancers, such as glioma, hypopharyngeal squamous cell carcinomas, and non-small cell lung cancer. PHLPP2 contains a Ras-associating (RA) domain followed by a PH domain, leucine-rich repeats and protein phosphatase 2C (PP2C) domain. 108 matched cddid_all.tbl CDD cd17242 cd17242 410988 MobM_relaxase relaxase domain of MobM and similar proteins. With some plasmids, recombination can occur in a site-specific manner that is independent of RecA. In such cases, the recombination event requires another protein called Pre (plasmid recombination enzyme), also known as Mob (conjugative mobilization). The best characterized member of this family is encoded by the streptococcal plasmid pMV158 that recognizes the plasmid origin of transfer. MobM converts supercoiled plasmid DNA into relaxed DNA by cleaving a phosphodiester bond of a specific dinucleotide and remains bound to the 5'-end of the nick site. 196 matched cddid_all.tbl CDD cd17243 cd17243 341132 RMtype1_S_AchA6I-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Arthrobacter chlorophenolicus A6 S subunit (S.AchA6I) TRD2-CR2. The S.AchA6I S subunit recognizes 5'... TGAANNNNNTCG ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.AchA6I-TRD1 recognizes TGAA/TTCA, and TRD2 recognizes CGA/TCG. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 182 matched cddid_all.tbl CDD cd17244 cd17244 341133 RMtype1_S_Apa101655I-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Acetobacter pasteurianus S subunit (S.Apa101655I) TRD2-CR2. The S. Apa101655I S subunit recognizes 5'... TTAGNNNNNNTTC... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 180 matched cddid_all.tbl CDD cd17245 cd17245 341134 RMtype1_S_TteMORF1547P-TRD2-CR2_Aco12261I-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Thermoanaerobacter tengcongensis S subunit (S.TteMORF1547P) TRD2-CR2 and Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I) TRD1-CR1. The S.Aco12261I S subunit recognizes 5'... GCANNNNNNTGT ... 3', while the recognition sequence is undetermined for S.TteMORF1547P TRD2-CR2. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. S.TteMORF1547P TRD1-CR1 and S.Aco12261I TRD2-CR2 do not belong to this family. This family may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 174 matched cddid_all.tbl CDD cd17246 cd17246 341135 RMtype1_S_SonII-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Shewanella oneidensis MR-1 S subunit (S.SonII) TRD2-CR2. This model contains Shewanella oneidensis MR-1 S subunit (S.SonII) TRD2-CR2 and similar TRD-CR's. S.SonII recognizes 5'... GTCANNNNNNRTCA ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. S.SonII TRD1-CR1 does not belong to this subfamily. 189 matched cddid_all.tbl CDD cd17247 cd17247 341136 RMtype1_S_Eco2747I-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli ST2747 S subunit (S.Eco2747I) TRD2-CR2. The S. Eco2747I S subunit recognizes 5'... CACNNNNNNNGTTG ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This CD contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 190 matched cddid_all.tbl CDD cd17248 cd17248 341137 RMtype1_S_AmiI-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Actinosynnema mirum DSM 43827 S subunit (S. AmiI) TRD2-CR2. The S. AmiI S subunit recognizes 5'... CAGNNNNNNNTCGA ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S. AmiI -TRD1 recognizes CAG/CTG, and TRD2 recognizes TCGA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 196 matched cddid_all.tbl CDD cd17249 cd17249 341138 RMtype1_S_EcoR124I-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoR124I TRD2-CR2, S.Eco540I TRD2-CR2, S.Eco540AI TRD2-CR2, and S.Eco540ANI TRD2-CR2. Escherichia coli (R124) S subunit (S.EcoR124I), E. coli ST540 S subunit (S.Eco540I), E. coli ST540A S subunit (S.Eco540AI), and Escherichia coli ST540AN S subunit (S.Eco540ANI) recognize the sequence 5'... GAANNNNNNRTCG ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoR124I -TRD1 recognizes GAA/TTC, and -TRD2 recognizes CGAY/RTCG. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 185 matched cddid_all.tbl CDD cd17250 cd17250 341139 RMtype1_S_Eco4255II_TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255II) TRD2-CR2 and Shewanella oneidensis MR-1 S subunit (S.SonIV) TRD1-CR1. Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255II) recognizes 5'... TACNNNNNNNRTRTC ... 3 while Shewanella oneidensis MR-1 S subunit (S.SonIV) recognizes 5'... TACNNNNNNGTNGT ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.SonIV-TRD1 recognizes TAC/GTA and S.SonIV-TRD2 recognizes ACNAC/GTNGT. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 185 matched cddid_all.tbl CDD cd17251 cd17251 341140 RMtype1_S_HinAWORF1578P-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S.HinAWORF1578P TRD2-CR2. Haemophilus influenzae RdAW S subunit (S.HinAWORF1578P) recognizes 5'... CTANNNNNGTTY ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains mostly TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 185 matched cddid_all.tbl CDD cd17252 cd17252 341141 RMtype1_S_EcoKI-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoKI TRD1-CR1, S.StySPI TRD1-CR1, S.Ara36733II TRD1-CR1, and S.Eco3722I TRD1-CR1. Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) and Escherichia coli NCM3722 S subunit (S.Eco3722I) recognize 5'... AACNNNNNNGTGC ... 3', Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) recognizes 5'... AACNNNNNNGTRC ... 3', and Actinomyces radicidentis S subunit (S.Ara36733II) recognizes 5'... CATCNNNNNNCTC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoKI-TRD1 and S.StySPI-TRD1 recognize AAC/GTT, S.EcoKI-TRD2 recognizes GCAC/GTGC, and S.StySPI-TRD2 recognizes GYAC/GTRC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases such as Treponema pedis T A4 putative Type IIG restriction enzyme/N6-adenine DNA methyltransferase RM.TpeTA4ORF2695P. It may also include type I DNA methyltransferases. 189 matched cddid_all.tbl CDD cd17253 cd17253 341142 RMtype1_S_Eco933I-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli O157:H7 EDL933 S subunit (S.Eco933I), Escherichia coli O104:H4 2009EL-2071 S subunit (S.Eco2071ORF3585P) TRD2-CR2, and Streptomyces species SirexAA-E S subunit (S.SspAAEORF2129P) TRD1-CR1 and TRD2-CR2. Escherichia coli O157:H7 EDL933 S subunit (S.Eco933I) recognizes 5'... CACNNNNNNNCTGG ... 3' and Escherichia coli O104:H4 2009EL-2071 S subunit (S.Eco2071ORF3585P) recognizes 5'... RTCANNNNNNNNGTGG ... 3'. The recognition sequence of Streptomyces species SirexAA-E S subunit (S.SspAAEORF2129P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.Eco2071ORF3585P TRD1 recognizes RTCA/TGAY and S.Eco2071ORF3585P TRD2 recognizes CCAC/GTGG. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 193 matched cddid_all.tbl CDD cd17254 cd17254 341143 RMtype1_S_FclI-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.FclI TRD1-CR1. The recognition sequence of Flavobacterium columnare G4 S subunit (S.FclI) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also contains TRD-CR-like sequence-recognition domains of type I DNA methyltransferases, such as putative Type I N6-adenine DNA methyltransferases from Microbacterium ketosireducens (M.Msp12510ORF408P) and Treponema primitia ZAS-2 (M.TprZAS2ORF3630P). It may also include various type II restriction enzymes and methyltransferases. 173 matched cddid_all.tbl CDD cd17255 cd17255 341144 RMtype1_S_Fco49512ORF2615P-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Flavobacterium columnare S subunit (S.Fco49512ORF2615P) TRD2-CR2. The recognition sequence of Flavobacterium columnare S subunit (S.Fco49512ORF2615P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 166 matched cddid_all.tbl CDD cd17256 cd17256 341145 RMtype1_S_EcoJA65PI-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoJA65PI TRD1-CR1, S.Fco49512ORF2615P TRD1-CR1, and S.SonIV TRD2-CR2. Escherichia coli UCD_JA65_pb S subunit (S.EcoJA65PI) recognizes 5'... AGCANNNNNNTGA ... 3' while Shewanella oneidensis MR-1 S subunit (S.SonIV) recognizes 5'... TACNNNNNNGTNGT ... 3'. The recognition sequence of Flavobacterium columnare S subunit (S.Fco49512ORF2615P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoJA65PI TRD1 recognizes AGCA/TGCT and S.EcoJA65PI TRD2 recognizes TCA/TGA; S.SonIV TRD1 recognizes TAC/GTA and S.SonIV TRD2 recognizes ACNAC/GTNGT. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 182 matched cddid_all.tbl CDD cd17257 cd17257 341146 RMtype1_S_EcoBI-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoBI TRD1-CR1, S.EcoSanI TRD1-CR1, and S.EcoVR50I TRD1-CR1. Escherichia coli B S subunit (S.EcoBI) and Escherichia coli VR50 S subunit (S.EcoVR50I) recognize 5'... TGANNNNNNNNTGCT ... 3', while Escherichia coli Sanji S subunit (S.EcoSanI) recognizes 5'... TGANNNNNNCTTC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 176 matched cddid_all.tbl CDD cd17258 cd17258 341147 RMtype1_S_Sau13435ORF2165P-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.Sau13435ORF2165P TRD1-CR1 and S.SauL3067ORFAP TRD1-CR1. Staphylococcus aureus NCTC 13435 S subunit (S.Sau13435ORF2165P) recognizes 5'... TCTANNNNNNRTTC ... 3'; the recognition sequence of Staphylococcus aureus 3067 S.Sau3067ORFAP S subunit is as yet undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.Sau13435ORF2165P TRD1 recognizes TCTA/TAGA, and S.Sau13435ORF2165P TRD2 recognizes GAAY/RTTC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains mostly TRD1-CR1. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 173 matched cddid_all.tbl CDD cd17259 cd17259 341148 RMtype1_S_StySKI-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to TRD2-CR2's of StySKI, S.EcoAI, S.EcoJA17PI, and S.EcoJA23PI. Salmonella kaduna CDC-388 S subunit (StySKI) recognizes 5'... CGATNNNNNNNGTTA ... 3' while Escherichia coli Type-1 restriction enzyme EcoAI specificity protein (S.EcoAI), Escherichia coli UCD_JA17_pb S subunit (S.EcoJA17PI) and Escherichia coli UCD_JA23_pb S subunit (S.EcoJA23PI) recognize 5'... GAGNNNNNNNGTCA ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 189 matched cddid_all.tbl CDD cd17260 cd17260 341149 RMtype1_S_EcoEI-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoEI TRD1-CR1, S.EcoJA17PI TRD1-CR1, S.EcoJA23PI TRD1-CR1, and S.StyLTIII TRD1-CR1. Escherichia coli A58 S subunit (S.EcoEI) recognizes 5'... GAGNNNNNNNATGC ... 3', Escherichia coli UCD_JA17_pb S subunit (S.EcoJA17PI) and Escherichia coli UCD_JA23_pb S subunit (S.EcoJA23PI) recognize 5'... GAGNNNNNNNGTCA ... 3', and Salmonella typhimurium LT7 S subunit (S.StyLTIII) recognizes 5'... GAGNNNNNNRTAYG ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example: S.EcoEI TRD1 and S.StyLTIII TRD1 recognize GAG/CTC, S.EcoEI TRD2 recognizes GCAT/ATGC, and S.StyLTIII TRD2 recognizes CRTAY/RTAYG. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Pseudomonas putida Jo 4-731 Type IIG restriction enzyme/N6-adenine DNA methyltransferas RM.PpiI and Porphyromonas macacae COT-192 OH2631 RM.Pma2631ORF8845P, as well as type I DNA methyltransferases such as Chlorobium limicola M.Cli245ORF128P. RM.PpiI recognizes the sequence 5' ... GAACNNNNNCTC ... 3'. 165 matched cddid_all.tbl CDD cd17261 cd17261 341150 RMtype1_S_EcoKI-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) TRD2-CR2, Escherichia coli A58 S subunit (S.EcoEI) TRD2-CR2, and Aminomonas paucivorans S subunit (S.Apa12260I) TRD2-CR2. Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) recognizes 5'... AACNNNNNNGTGC ... 3', Escherichia coli A58 S subunit (S.EcoEI) recognizes 5'... GAGNNNNNNNATGC ... 3', and Aminomonas paucivorans S subunit (S.Apa12260I) recognizes 5'... GCCNNNNNCTCC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoKI-TRD1 recognizes AAC/GTT and S.EcoKI-TRD2 recognizes GCAC/GTGC, S.EcoEI TRD1 recognizes GAG/CTC and S.EcoEI TRD2 recognizes GCAT/ATGC, and S.Apa12260I TRD1 recognizes GCC/GGC and S.Apa12260I TRD2 recognizes GGAG/CTCC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 191 matched cddid_all.tbl CDD cd17262 cd17262 341151 RMtype1_S_Aco12261I-TRD2-CR2 Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I) TRD2-CR2 and Moraxella catarrhalis S subunit (S.Mca353ORF290P) TRD2-CR2. Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I) recognizes 5'... GCANNNNNNTGT ... 3', and Moraxella catarrhalis S subunit (S.Mca353ORF290P) recognizes 5'... CAAGNNNNNNTGT ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 172 matched cddid_all.tbl CDD cd17263 cd17263 341152 RMtype1_S_AbaB8300I-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Acinetobacter baumannii B8300 S subunit (S.AbaB8300I) TRD1-CR1. Acinetobacter baumannii B8300 S subunit (S.AbaB8300I) recognizes 5'... GAYNNNNNNNTCYC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 177 matched cddid_all.tbl CDD cd17264 cd17264 341153 RMtype1_S_Eco3763I-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli O69:H11 07-3763 S subunit (S.Eco3763I) TRD2-CR2. Escherichia coli O69:H11 07-3763 S subunit (S.Eco3763I) recognizes 5'... TACNNNNNNNRTRTC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 184 matched cddid_all.tbl CDD cd17265 cd17265 341154 RMtype1_S_Eco4255III-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255III) TRD2-CR2 and Escherichia coli ECONIH1 S subunit (S.EcoNIH1II) TRD2-CR2. Escherichia coli O118:H16 07-4255 S subunit (S.Eco4255III) recognizes 5'... GAGNNNNNGTTY ... 3', and Escherichia coli ECONIH1 S subunit (S.EcoNIH1II) recognizes 5'... YTCANNNNNNGTTY ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.Eco4255III-TRD1 recognizes GAG/CTC and S.EcoNIH1II-TRD1 recognizes YTCA/TGAR, while both S.EcoNIH1II-TRD2 and S.Eco4255III-TRD2 recognize RAAC/GTTY. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 181 matched cddid_all.tbl CDD cd17266 cd17266 341155 RMtype1_S_Sau1132ORF3780P-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Staphylococcus aureus subsp. aureus MSHR1132 S subunit (S.Sau1132ORF3780P) TRD2-CR2. Staphylococcus aureus subsp. aureus MSHR1132 S subunit (S.Sau1132ORF3780P) recognizes 5'... CAAGNNNNNRTC ... 3'. The RM system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example S.Sau1132ORF3780P-TRD1 recognizes CAAG/CTTG and S.Sau1132ORF3780P-TRD2 recognizes GAY/RTC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 159 matched cddid_all.tbl CDD cd17267 cd17267 341156 RMtype1_S_EcoAO83I-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoAO83I TRD1-CR1 and S.AbaB8342I TRD2-CR2. Escherichia coli strain A0 34/86 S subunit (S.EcoAO83I) recognizes 5'... GGANNNNNNNNATGC ... 3, and Acinetobacter baumannii B8342 S subunit (S.AbaB8342I) recognizes 5'... TTCANNNNNNTCC ... 3. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example S.AbaB8342I-TRD1 recognizes TTCA/TGAA and S.AbaB8342I-TRD2 recognizes GGA/TCC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases such as Type IIG restriction enzyme/N6-adenine DNA methyltransferases from Thermus scotoductus RFL1 (RM.TstI) and Acinetobacter lwoffi Ks 4-8 (RM.AloI), as well as type I DNA methyltransferases such as Sideroxydans lithotrophicus ES-1 Type I N6-adenine DNA methyltransferase (M.SliESORF1090P). RM.TstI recognizes 5' ... CACNNNNNNTCC ... 3' and RM.AloI recognizes 5' ... GAACNNNNNNTCC ... 3'. 158 matched cddid_all.tbl CDD cd17268 cd17268 341157 RMtype1_S_Ara36733I_TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.Ara36733I TRD1-CR1 AND S.Ara36733I TRD2-CR2. Actinomyces radicidentis S subunit (S.Ara36733I) recognizes 5'... CGAGNNNNNCTG ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 185 matched cddid_all.tbl CDD cd17269 cd17269 341158 RMtype1_S_PluTORF4319P-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Photorhabdus luminescens S subunit (S.PluTORF4319P) TRD2-CR2. The recognition sequence of Photorhabdus luminescens S subunit (S.PluTORF4319P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 168 matched cddid_all.tbl CDD cd17270 cd17270 341159 RMtype1_S_Sba223ORF3470P-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.Sba223ORF3470P TRD1-CR1. The recognition sequence of Shewanella baltica OS223 S subunit (S.Sba223ORF3470P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 183 matched cddid_all.tbl CDD cd17271 cd17271 341160 RMtype1_S_NmaSCMORF606P_TRD2-CR2_like Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Nitrosopumilus maritimus SCM1 S subunit (S2.NmaSCMORF606P) TRD2-CR2, Corynebacterium jeikeium K411 S subunit (S.CjeKORF1254P) TRD2-CR2 and Porphyromonas canoris COT-108 OH2762 S subunit (S2.Pca2762ORF8685P) TRD1-CR1. The recognition sequences of Nitrosopumilus maritimus SCM1 S subunit (S2.NmaSCMORF606P), Corynebacterium jeikeium K411 S subunit (S.CjeKORF1254P), and Porphyromonas canoris COT-108 OH2762 S subunit (S2.Pca2762ORF8685P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 186 matched cddid_all.tbl CDD cd17272 cd17272 341161 RMtype1_S_Eco2747II-TRD2-CR2-like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.Eco2747II TRD2-CR2 and S.Eco2747AII TRD2-CR2. Escherichia coli ST2747 S subunit (S.Eco2747II) and Escherichia coli ST2747A s SUBUNIT (S.Eco2747AII) recognize 5'... GAANNNNNNNTAAA ... 3'. Generally The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains mainly TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 189 matched cddid_all.tbl CDD cd17273 cd17273 341162 RMtype1_S_EcoJA69PI-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.EcoJA69PI TRD1-CR1, MjaXIP/S.MjaORF132P TRD2-CR2, and S.HspDL1ORF16625P TRD2-CR2. Escherichia coli UCD_JA69_pb S subunit (S.EcoJA69PI) recognizes 5'... CCANNNNNNNCTTC ... 3'. The recognition sequences of Methanococcus jannaschii MjaXIP/S.MjaORF132P TRD2-CR2 and Halobacterium species DL1 S subunit (S.HspDL1ORF16625P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various putative type II restriction enzymes and methyltransferases and may also include type I DNA methyltransferases. 186 matched cddid_all.tbl CDD cd17274 cd17274 341163 RMtype1_S_Eco540ANI-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.Eco540ANI TRD1-CR1, S.Eco2747AII TRD1-CR1, S.Eco540AI TRD1-CR1, S.Eco2747II TRD1-CR1, and S.Eco540I TRD1-CR1. Escherichia coli ST540AN S subunit (S.Eco540ANI ), Escherichia coli ST540A S subunit (S.Eco540AI), and Escherichia coli ST540 S subunit (S.Eco540I) recognize 5'... GAANNNNNNRTCG ... 3'. Escherichia coli ST2747A S subunit (S.Eco2747AII) and Escherichia coli ST2747 S subunit (S.Eco2747II) recognize 5'... GAANNNNNNNTAAA ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 171 matched cddid_all.tbl CDD cd17275 cd17275 341164 RMtype1_S_MjaORF132P-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit TRD-CR, similar to MjaXIP/S.MjaORF132P TRD1-CR1. The recognition sequence of Methanococcus jannaschii S subunit (MjaXIP/S.MjaORF132P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 186 matched cddid_all.tbl CDD cd17276 cd17276 341165 RMtype1_S_Sau1132ORF3780P-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit TRD-CR, similar to S.Sau1132ORF3780P TRD1-CR1, and S.Mca353ORF290P TRD1-CR1. The Staphylococcus aureus subsp. aureus MSHR1132 S subunit (S.Sau1132ORF3780P) recognizes 5'... CAAGNNNNNRTC ... 3', and Moraxella catarrhalis S subunit (S.Mca353ORF290P) recognizes 5'... CAAGNNNNNNTGT ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.Sau1132ORF3780P-TRD1 recognizes CAAG/CTTG, and S.Sau1132ORF3780P-TRD2 recognizes GAY/RTC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 187 matched cddid_all.tbl CDD cd17277 cd17277 341166 RMtype1_M_Cni19672ORF1405P_RMtype11G_Hci611ORFHP_TRD1-CR1_like Restriction modification N6-adenine DNA methyltransferase TRD-CR, similar to RMtype1 Calditerrivibrio nitroreducens M.Cni19672ORF1405P TRD1-CR1 and RMtype11G Helicobacter cinaedi PAGU611 RM.Hci611ORFHP TRD1-CR1. The recognition sequence of Calditerrivibrio nitroreducens M.Cni19672ORF1405P is undetermined, and the predicted recognition sequence of RM.Hci611ORFHP is 5'... GAGNNNNNGT ... 3'. M.Cni19672ORF1405P is a putative type I N6-adenine DNA methyltransferase. RM.Hci611ORFHP is a type II subtype gamma (also called type IIG and type IIC) N6-adenine DNA methyltransferase. Both are DNA methyltransferase-specificity subunit fusion proteins, they each have a domain corresponding to a HsdM methylation (M) subunit followed by a C-terminal, TRD-CR-like domain for sequence-recognition, which corresponds to the HsdS specificty (S) subunit. The latter consists of two variable TRDs, and two CRs which separate the TRDs; the TRDs each bind to different specific sequences in the DNA. RM.Hci611ORFHP has an additional N-terminal HSDR_N domain. Restriction-modification (RM) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit, two modification (M) subunits, and two restriction (R) subunits. 184 matched cddid_all.tbl CDD cd17278 cd17278 341167 RMtype1_S_LdeBORF1052P-TRD2-CR2 Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Lactobacillus delbrueckii subsp. bulgaricus S subunit (S2.LdeBORF1052P) TRD2-CR2. The recognition sequence of Lactobacillus delbrueckii subsp. bulgaricus S subunit (S2.LdeBORF1052P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 189 matched cddid_all.tbl CDD cd17279 cd17279 341168 RMtype1_S_BmuCF2ORF3362P_TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Burkholderia multivorans CF2 S subunit (S.BmuCF2ORF3362P) TRD1-CR1 and and Halomonas campaniensis LS21 S subunit (S.HcaLS21ORF9970P) TRD1-CR1. The recognition sequences of Burkholderia multivorans CF2 S subunit (S.BmuCF2ORF3362P) and Halomonas campaniensis LS21 S subunit (S.HcaLS21ORF9970P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 184 matched cddid_all.tbl CDD cd17280 cd17280 341169 RMtype1_S_MspEN3ORF6650P_TRD2-CR2_like Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Marinobacter species EN3 S subunit (S.MspEN3ORF6650P) TRD1-CR1, Methanothermobacter marburgensis str. Marburg S subunit (S.Mma2133ORF14720P) TRD2-CR2 and Nostoc species NIES-3756 S subunit (S.Nsp3756ORF27100P) TRD1-CR1. The recognition sequences of Marinobacter species EN3 S subunit (S.MspEN3ORF6650P), Methanothermobacter marburgensis str. Marburg S subunit (S.Mma2133ORF14720P), and Nostoc species NIES-3756 S subunit (S.Nsp3756ORF27100P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 187 matched cddid_all.tbl CDD cd17281 cd17281 341170 RMtype1_S_HpyAXIII_TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Helicobacter pylori 26695 S subunit (S.HpyAXIII/Prototype S.Hpy26695ORF4050P) TRD1-CR1, Neisseria meningitidis 510612 S subunit (S.Nme510612ORF1157P) TRD1-CR1 and Streptococcus mitis SVGS_061 S subunit (S2.Smi61ORF7905P) TRD1-CR1. Helicobacter pylori 26695 S subunit (S.HpyAXIII/Prototype S.Hpy26695ORF4050P) recognizes 5'... CTANNNNNNNNTGT ... 3', and the recognition sequences of Neisseria meningitidis 510612 S subunit (S.Nme510612ORF1157P) and Streptococcus mitis SVGS_061 S subunit (S2.Smi61ORF7905P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, Helicobacter pylori 26695 S subunit (S.HpyAXIII/Prototype S.Hpy26695ORF4050P) TRD1 recognizes CTA/TAG, and TRD2 recognizes ACA/TGT. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 196 matched cddid_all.tbl CDD cd17282 cd17282 341171 RMtype1_S_Eco16444ORF1681_TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli G4/9 S subunit (S.Eco16444ORF1681P) TRD1-CR1 and Zobellia galactanivorans DsiJT S subunit (S.ZgaJTORF2697P)TRD2-CR2. The recognition sequences of Escherichia coli G4/9 S subunit (S.Eco16444ORF1681P) and Zobellia galactanivorans DsiJT S subunit (S.ZgaJTORF2697P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various putative type II restriction enzymes and methyltransferases and may also include type I DNA methyltransferases. 186 matched cddid_all.tbl CDD cd17283 cd17283 341172 RMtype1_S_Hpy180ORF7835P_TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Helicobacter pylori SJM180 S subunit (S.Hpy180ORF7835P) TRD2-CR2 and Haemophilus influenzae PittGG S subunit (S.HinGGORF3080P) TRD2-CR2. The recognition sequences of Helicobacter pylori SJM180 S subunit (S.Hpy180ORF7835P) and Haemophilus influenzae PittGG S subunit (S.HinGGORF3080P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 181 matched cddid_all.tbl CDD cd17284 cd17284 341173 RMtype1_S_Cbo7060ORF11580P_TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Clostridium botulinum CFSAN024410 S subunit (S.Cbo7060ORF11580P) TRD2-CR2 and Shewanella xiamenensis BC01 S subunit (S.SxiBC01ORF77P) TRD1-CR1. The recognition sequences of Clostridium botulinum CFSAN024410 S subunit (S.Cbo7060ORF11580P) and Shewanella xiamenensis BC01 S subunit (S.SxiBC01ORF77P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 185 matched cddid_all.tbl CDD cd17285 cd17285 341174 RMtype1_S_Csp16704I_TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Campylobacter species RM1670 S subunit (S.Csp16704I) TRD2-CR2, Aeromonas media WS S subunit (S.AmeWSORF2351P) TRD1-CR1, and Clostridium carboxidivorans P7 S subunit (S.CcaPORF573P) TRD2-CR2. Campylobacter species RM16704 S subunit (S.Csp16704I ) recognizes 5'... ACANNNNNNNNTCG ... 3', and the recognition sequences of Aeromonas media WS TRD1-CR1 S subunit (S.AmeWSORF2351P) and Clostridium carboxidivorans P7 S subunit (S.CcaPORF573P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 181 matched cddid_all.tbl CDD cd17286 cd17286 341175 RMtype1_S_Lla161ORF747P_TRD1-CR1_like Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Lactococcus lactis subsp. lactis Dephy 1 S subunit (S.Lla161ORF747P) TRD1-CR1, and Lactococcus lactis IO-1 S subunit (S2.LlaIO1ORF1141P) TRD2-CR2. The recognition sequences of Lactococcus lactis subsp. lactis Dephy 1 S subunit (S.Lla161ORF747P) and Lactococcus lactis IO-1 S subunit (S2.LlaIO1ORF1141P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 179 matched cddid_all.tbl CDD cd17287 cd17287 341176 RMtype1_S_EcoN10ORF171P_TRD2-CR2_like Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli N10-0505 S subunit (S.EcoN10ORF171P) TRD2-CR2, and Herpetosiphon aurantiacus S subunit (S.HauORF5277P) TRD2-CR2. The recognition sequences of Escherichia coli N10-0505 S subunit (S.EcoN10ORF171P) and Herpetosiphon aurantiacus S subunit (S.HauORF5277P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 184 matched cddid_all.tbl CDD cd17288 cd17288 341177 RMtype1_S_LlaAI06ORF1089P_TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Lactococcus lactis S subunit (S.LlaAI06ORF1089P) TRD1-CR1 and Bacillus subtilis B4071 S subunit (S2.BsuCC16ORF609P) TRD2-CR2. The recognition sequences of Lactococcus lactis S subunit (S.LlaAI06ORF1089P) and Bacillus subtilis B4071 S subunit (S2.BsuCC16ORF609P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 163 matched cddid_all.tbl CDD cd17289 cd17289 341178 RMtype1_S_BamJRS5ORF1993P-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Bacillus amyloliquefaciens JRS5 S subunit (S.BamJRS5ORF1993P) TRD1-CR1 and Bacillus pumilus Jo2 S subunit (S.BpuJo2I) TRD1-CR1. The recognition sequences of Bacillus amyloliquefaciens JRS5 S subunit (S.BamJRS5ORF1993P) and Bacillus pumilus Jo2 S subunit (S.BpuJo2I) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 191 matched cddid_all.tbl CDD cd17290 cd17290 341179 RMtype1_S_AleSS8ORF2795P_TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Algibacter lectus S subunit (S.AleSS8ORF2795P) TRD1-CR1 and Vibrio parahaemolyticus O1:K33 CDC_K4557 S subunit (S.Vpa4557ORF22590P) TRD2-CR2. The recognition sequences of Algibacter lectus S subunit (S.AleSS8ORF2795P) and Vibrio parahaemolyticus O1:K33 CDC_K4557 S subunit (S.Vpa4557ORF22590P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 184 matched cddid_all.tbl CDD cd17291 cd17291 341180 RMtype1_S_MgeORF438P-TRD-CR_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.MgeORF438P TRD1-CR1 and TRD2-CR2, and to Escherichia coli G5 S subunit (S.Eco16445ORF5013P ) TRD2-CR2 and Acetobacter pasteurianus IFO 3283-01 S subunit (S2.Apa3283ORF14230P) TRD1-CR1. The recognition sequences of Mycoplasma genitalium G-37 S subunit (S.MgeORF438P), Escherichia coli G5 S subunit (S.Eco16445ORF5013P), and Acetobacter pasteurianus IFO 3283-01 S subunit (S2.Apa3283ORF14230P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 161 matched cddid_all.tbl CDD cd17292 cd17292 341181 RMtype1_S_LlaA17I_TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to the S subunit TRD2-CR2 regions of Lactococcus lactis subsp. cremoris A17 (S.LlaA17I), Haemophilus influenzae Rd (S.HindORF215P) and Clostridium species ASF502 (S.Csp502ORF478P). Lactococcus lactis subsp. cremoris A17 S subunit (S.LlaA17I) recognizes 5'... CAANNNNNNNNTAYG... 3', while the recognition sequences of Clostridium species ASF502 S subunit (S.Csp502ORF478P) and Haemophilus influenzae Rd S subunit (S.HindORF215P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Porphyromonas species COT-108 OH1349 Type IIG restriction enzyme/N6-adenine DNA methyltransferase (RM.Psp1349ORF730P) of unknown recognition sequence. It may also include type I DNA methyltransferases. 149 matched cddid_all.tbl CDD cd17293 cd17293 341182 RMtype1_S_Ppo21ORF8840P_TRD1-CR1_like Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Paenibacillus polymyxa SQR-21 SQR21 S subunit (S.Ppo21ORF8840P) TRD1-CR1, Nitrosococcus halophilus Nc4 S subunit (S.NhaNc4ORF3964P) TRD1-CR1. The recognition sequences of Paenibacillus polymyxa SQR-21 SQR21 S subunit (S.Ppo21ORF8840P) and Nitrosococcus halophilus Nc4 S subunit (S.NhaNc4ORF3964P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This superfamily contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 180 matched cddid_all.tbl CDD cd17294 cd17294 341183 RMtype1_S_MmaC7ORF19P_TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) TRD1-CR1 and Mycoplasma gallinaceum S subunit (S3.Mme68BORF1125P) TRD2-CR2. The recognition sequences of Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) and Mycoplasma gallinaceum S subunit (S3.Mme68BORF1125P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 188 matched cddid_all.tbl CDD cd17296 cd17296 341184 RMtype1_S_MmaC5ORF1169P_TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Methanococcus maripaludis C5 S subunit (S.MmaC5ORF1169P) TRD1-CR1, and Methanobacterium formicicum S subunit (S.Mfo3637ORF3708P) TRD2-CR2. The recognition sequences of Methanococcus maripaludis C5 S subunit (S.MmaC5ORF1169P) and Methanobacterium formicicum S subunit (S.Mfo3637ORF3708P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 182 matched cddid_all.tbl CDD cd17297 cd17297 341209 AldB-like proteins similar to alpha-acetolactate dehydrogenase. The structure of this domain displays an alpha-beta-beta-alpha four layer topology, with an H(x)H(x)nH motif (x could be any residue, n could be 9 or 10) that coordinates a zinc ion. The proteins are homologous to bacterial alpha-acetolactate decarboxylase (AldB, E.C. 4.1.1.5), which converts acetolactate into acetoin. 209 matched cddid_all.tbl CDD cd17298 cd17298 341210 DUF1907 proteins similar to putative ester hydrolase C11orf54/PTD012. The structure of this domain displays an alpha-beta-beta-alpha four layer topology, with an HxHxxxxxxxxxH motif (x could be any residue) that coordinates a zinc ion, and an acetate anion at a site that may support the enzymatic activity of a ester. In vitro hydrolytic activity towards para-nitrophenylacetate for the human enzyme was reported. The proteins are homologous to bacterial alpha-acetolactate decarboxylase (AldB, E.C. 4.1.1.5), which converts acetolactate into acetoin. 287 matched cddid_all.tbl CDD cd17299 cd17299 341211 acetolactate_decarboxylase alpha-acetolactate decarboxylase. alpha-acetolactate decarboxylase (AldB, E.C. 4.1.1.5) converts acetolactate ((2S)-2-hydroxy-2-methyl-3-oxobutanoate) into acetoin ((3R)-3-hydroxybutan-2-one) and CO(2). Acetoin may be secreted by the cells, perhaps in order to control the internal pH. AldB may function as a regulator in valine and leucine biosynthesis and in catalyzing the second step of the 2,3-butanediol pathway. The structure of this domain displays an alpha-beta-beta-alpha four layer topology, with an HxHxxxxxxxxxxH motif (x could be any residue) that coordinates a zinc ion. 232 matched cddid_all.tbl CDD cd17300 cd17300 340437 PIPKc_PIKfyve Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in 1-phosphatidylinositol-3-phosphate 5-kinase and similar proteins. 1-phosphatidylinositol-3-phosphate 5-kinase (EC 2.7.1.150) is also called FYVE finger-containing phosphoinositide kinase, PIKfyve, phosphatidylinositol 3-phosphate 5-kinase (PIP5K3), or phosphatidylinositol 3-phosphate 5-kinase type III (PIPkin-III or type III PIP kinase). It forms a complex with its regulators, the scaffolding protein Vac14 and the lipid phosphatase Fig4. The complex is responsible for synthesizing phosphatidylinositol 3,5-bisphosphate [PtdIns(3,5)P2] by catalyzing the phosphorylation of phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) on the fifth hydroxyl of the myo-inositol ring. Then phosphatidylinositol-5-phosphate (PtdIns5P) is generated directly from PtdIns(3,5)P2. PtdIns(3,5)P2 and PtdIns5P regulate endosomal trafficking and responses to extracellular stimuli. PIKfyve is vital in early embryonic development. It forms a complex with ArPIKfyve (associated regulator of PIKfyve) and SAC3 at the endomembranes, playing a role in receptor tyrosine kinase (RTK) degradation. The phosphorylation of PIKfyve by AKT can facilitate epidermal growth factor receptor (EGFR) degradation. In addition, PIKfyve may participate in the regulation of the glutamate transporters EAAT2, EAAT3 and EAAT4, and the cystic fibrosis transmembrane conductance regulator (CFTR). It is also essential for systemic glucose homeostasis and insulin-regulated glucose uptake/GLUT4 translocation in skeletal muscle. It can be activated by protein kinase B (PKB/Akt) and further up-regulates human Ether-a-go-go-Related Gene (hERG) channels. This family also includes the yeast ortholog of human PIKfyve, Fab1. PIKfyve and its orthologs share a similar architecture. They contain an N-terminal FYVE domain, a middle region related to the CCT/TCP-1/Cpn60 chaperonins that are involved in productive folding of actin and tubulin, a second middle domain that contains a number of conserved cysteine residues (CCR) unique to this family, and a C-terminal catalytic lipid kinase domain related to PtdInsP kinases (or the PIPKc domain). 262 matched cddid_all.tbl CDD cd17301 cd17301 340438 PIPKc_PIP5KI Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in type I phosphatidylinositol 4-phosphate (PtdIns(4)P) 5-kinases (PIP5KI) and similar proteins. PIP5KIs, also known as PIPKIs, or PI4P5KIs, phosphorylate the head group of phosphatidylinositol 4-phosphate (PtdIns4P) to generate phosphatidylinositol 4,5-bisphosphate (PtdIns4,5P2), an essential lipid molecule in various cellular processes. Three distinct PIP5KIs have been characterized in erythrocytes, PIP5K1alpha, PIP5K1beta, and PIP5K1gamma isoforms. 320 matched cddid_all.tbl CDD cd17302 cd17302 340439 PIPKc_AtPIP5K_like Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in Arabidopsis thaliana phosphatidylinositol 4-phosphate 5-kinases (PIP5Ks) and similar proteins. PIP5K (EC 2.7.1.68), also known as PtdIns(4)P-5-kinase, or diphosphoinositide kinase, phosphorylates phosphatidylinositol-4-phosphate to produce phosphatidylinositol-4,5-bisphosphate as a precursor of two second messengers, inositol-1,4,5-triphosphate and diacylglycerol, and as a regulator of many cellular proteins involved in signal transduction and cytoskeletal organization. The family includes several PIP5Ks from Arabidopsis thaliana. AtPIP5K1 is involved in water-stress signal transduction. AtPIP5K2 acts as an interactor of all five Arabidopsis RAB-E proteins but not with other Rab subclasses residing at the Golgi or trans-Golgi network. AtPIP5K3 is a key regulator of root hair tip growth. AtPIP5K4 and AtPIP5K5 are type B PI4P 5-kinases expressed in pollen and have important functions in pollen germination and in pollen tube growth. AtPIP5K6 regulates clathrin-dependent endocytosis in pollen tubes. AtPIP5K9 interacts with a cytosolic invertase to negatively regulate sugar-mediated root growth. 314 matched cddid_all.tbl CDD cd17303 cd17303 340440 PIPKc_PIP5K_yeast_like Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in yeast phosphatidylinositol 4-phosphate 5-kinases (PIP5Ks) and similar proteins. PIP5K (EC 2.7.1.68), also known as PtdIns(4)P-5-kinase, or diphosphoinositide kinase, phosphorylates phosphatidylinositol-4-phosphate to produce phosphatidylinositol-4,5-bisphosphate as a precursor of two second messengers, inositol-1,4,5-triphosphate and diacylglycerol, and as a regulator of many cellular proteins involved in signal transduction and cytoskeletal organization. The family includes Saccharomyces cerevisiae PIP5K MSS4, Schizosaccharomyces pombe PIP5K Its3. MSS4 is required for organization of the actin cytoskeleton in budding yeast. Its3 is involved, together with the calcineurin ppb1, in cytokinesis of fission yeast. 318 matched cddid_all.tbl CDD cd17304 cd17304 340441 PIPKc_PIP5KL1 Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in phosphatidylinositol 4-phosphate 5-kinase-like protein 1 (PIP5KL1) and similar proteins. PIP5KL1 (EC 2.7.1.68), also known as PI(4)P 5-kinase-like protein 1, or PtdIns(4)P-5-kinase-like protein 1, may act as a scaffold to localize and regulate type I PI(4)P 5-kinases to specific compartments within the cell, where they generate PI(4,5)P2 for actin nucleation, signaling and scaffold protein recruitment, and conversion to PI(3,4,5)P3. 319 matched cddid_all.tbl CDD cd17305 cd17305 340442 PIPKc_PIP5KII Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in type II phosphatidylinositol 5-phosphate 4-kinase (PIP5KII) and similar proteins. PIP5KIIs, also known as PIPKIIs, or PI4P5KIIs, are responsible for the synthesis of phosphatidylinositol-4,5-bisphosphate (PtdIns4,5P2), an essential lipid molecule in various cellular processes, from phosphatidylinositol-5-phosphate (PtdIns5P). Three distinct PIP5KIs have been characterized in erythrocytes, PIP5K2A, PIP5K2B, and PIP5K2C isoforms. 300 matched cddid_all.tbl CDD cd17306 cd17306 340443 PIPKc_PIP5K1A_like Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in phosphatidylinositol 4-phosphate 5-kinase type-1 alpha (PIP5K1alpha) and similar proteins. PIP5K1alpha (EC 2.7.1.68), also termed PIP5K1A, or PtdIns(4)P-5-kinase 1 alpha, or 68 kDa type I phosphatidylinositol 4-phosphate 5-kinase alpha, or PIPKI-alpha, catalyzes the phosphorylation of phosphatidylinositol 4-phosphate (PtdIns4P) to form phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2). It mediates extracellular calcium-induced keratinocyte differentiation. Unlike other type I phosphatidylinositol-4-phosphate 5-kinase (PIPKI) isoforms, PIP5K1alpha regulates directed cell migration by modulating Rac1 plasma membrane targeting and activation. This function is independent of its catalytic activity, and requires physical interaction of PIP5K1alpha with the Rac1 polybasic domain. The family also includes testis-specific PIP5K1A and PSMD4-like protein, also known as PIP5K1A-PSMD4 or PIPSL. It has negligeable PIP5 kinase activity and binds to ubiquitinated proteins. 339 matched cddid_all.tbl CDD cd17307 cd17307 340444 PIPKc_PIP5K1B Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in phosphatidylinositol 4-phosphate 5-kinase type-1 beta (PIP5K1beta) and similar proteins. PIP5K1beta (EC 2.7.1.68), also known as PtdIns(4)P-5-kinase 1 beta, or protein STM-7, or PIP5K1B, is encoded by the Friedreich's ataxia (FRDA) gene, STM7. FRDA is a progressive neurodegenerative disease characterized by ataxia, variously associating heart disease, diabetes mellitus, and/or glucose intolerance. PIP5K1beta is an enzyme functionally linked to actin cytoskeleton dynamics and it phosphorylates phosphatidylinositol 4-phosphate (PtdIns4P) to generate phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2). 321 matched cddid_all.tbl CDD cd17308 cd17308 340445 PIPKc_PIP5K1C Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in phosphatidylinositol 4-phosphate 5-kinase type-1 gamma (PIP5K1gamma) and similar proteins. PIP5K1gamma(EC 2.7.1.68), also known as PtdIns(4)P-5-kinase 1 gamma, or PIP5K1gamma, or PIPKIgamma, or PtdInsPKI gamma, is a phosphatidylinositol-4-phosphate 5-kinase that catalyzes the phosphorylation of phosphatidylinositol 4-phosphate (PtdIns4P) to form phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2), which is involved in a variety of cellular processes and is the substrate to form phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3), another second messenger. PIP5K1gamma is required for epidermal growth factor (EGF)-stimulated directional cell migration. It also modulates adherens junction and E-cadherin trafficking via a direct interaction with mu 1B adaptin. 323 matched cddid_all.tbl CDD cd17309 cd17309 340446 PIPKc_PIP5K2A Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in Phosphatidylinositol 5-phosphate 4-kinase type-2 alpha (PIP5K2A) and similar proteins. PIP5K2A (EC 2.7.1.149), also known as PIP4K2A, or 1-phosphatidylinositol 5-phosphate 4-kinase 2-alpha, or diphosphoinositide kinase 2-alpha, or PIP5KIII, or phosphatidylinositol 5-phosphate 4-kinase type II alpha, or PI(5)P 4-kinase type II alpha, or PIP4KII-alpha, or PtdIns(4)P-5-kinase C isoform, or PtdIns(5)P-4-kinase isoform 2-alpha, catalyzes the phosphorylation of phosphatidylinositol 5-phosphate (PtdIns5P) on the fourth hydroxyl of the myo-inositol ring, to form phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2), one of the key metabolic crossroads in phosphoinositide signaling. It is possibly involved in a mechanism protecting against tardive dyskinesia-inducing neurotoxicity. PIP5K2A is associated with schizophrenia. It controls the function of KCNQ channels via phosphatidylinositol-4,5-bisphosphate (PIP2) synthesis, and plays a potential role in the regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptors. 309 matched cddid_all.tbl CDD cd17310 cd17310 340447 PIPKc_PIP5K2B Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in Phosphatidylinositol 5-phosphate 4-kinase type-2 beta (PIP5K2B) and similar proteins. PIP5K2B (EC 2.7.1.149), also known as 1-phosphatidylinositol 5-phosphate 4-kinase 2-beta, or diphosphoinositide kinase 2-beta, or phosphatidylinositol 5-phosphate 4-kinase type II beta, or PI(5)P 4-kinase type II beta, or PIP4KII-beta, or PtdIns(5)P-4-kinase isoform 2-beta, or PIP5KIIbeta, or PIP4K2B, participates in the biosynthesis of phosphatidylinositol 4,5-bisphosphate. It directly regulates the levels of two important phosphoinositide second messengers, PtdIns5P and phosphatidylinositol-(4,5)-bisphosphate (PtdIns(4,5)P2), one of the key metabolic crossroads in phosphoinositide signaling. It regulates the levels of nuclear PtdIns5P, which in turn modulates the acetylation of the tumour suppressor p53. It also interacts with and modulates nuclear localization of the high-activity PtdIns5P-4-kinase isoform PIP4Kalpha. Moreover, PIP5K2B is a molecular sensor that transduces changes in GTP into changes in the levels of the phosphoinositide PtdIns5P to modulate tumour cell growth. 311 matched cddid_all.tbl CDD cd17311 cd17311 340448 PIPKc_PIP5K2C Phosphatidylinositol phosphate kinase (PIPK) catalytic domain found in Phosphatidylinositol 5-phosphate 4-kinase type-2 gamma (PIP5K2C) and similar proteins. PIP5K2C (EC 2.7.1.149), also known as 1-phosphatidylinositol 5-phosphate 4-kinase 2-gamma, or PI5P4Kgamma, or diphosphoinositide kinase 2-gamma, or phosphatidylinositol 5-phosphate 4-kinase type II gamma, or PI(5)P 4-kinase type II gamma, or PIP4KII-gamma, or PIP4K2C, may play an important role in the production of phosphatidylinositol bisphosphate (PIP2) in the endoplasmic reticulum. It contributes to the development and maintenance of epithelial cell functional polarity. It also plays a role in the regulation of the immune system via mTORC1 signaling. Moreover, PIP5K2C is involved in arsenic trioxide (ATO) cytotoxicity. It mediates PIP2 generation required for positioning and assembly of bipolar spindles and alteration of PIP5K2C function by ATO may thus lead to spindle abnormalities. 298 matched cddid_all.tbl CDD cd17312 cd17312 340870 MFS_OPA_SLC37 Organophosphate:Pi antiporter/Solute Carrier family 37 of the Major Facilitator Superfamily of transporters. Organophosphate:Pi antiporters (OPA) are integral membrane proteins responsible for the transport of specific organophosphates or sugar phosphates across biological membranes with the simultaneous translocation of inorganic phosphate into the opposite direction. The OPA family is also called solute carrier family 37 (SLC37) in vertebrates. Members include glucose-6-phosphate (Glc6P) transporter (also called translocase or exchanger), glycerol-3-phosphate permease, 2-phosphonopropionate transporter, phosphoglycerate transporter, as well as membrane sensor protein UhpC from Escherichia coli. UhpC is both a sensor and a transport protein; it recognizes external Glc6P and induces transport by UhpT, and it can also transport Glc6P. Vertebrates contain four SLC37 or sugar-phosphate exchange (SPX) proteins: SLC37A1 (SPX1), SLC37A2 (SPX2), SLC37A3 (SPX3), and SLC37AA4 (SPX4). The OPA/SLC37 family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 364 matched cddid_all.tbl CDD cd17313 cd17313 340871 MFS_SLC45_SUC Solute carrier family 45 and similar sugar transporters of the Major Facilitator Superfamily of transporters. This group includes the solute carrier 45 (SLC45) family as well as plant sucrose transporters (SUCs or SUTs) and similar proteins such as Schizosaccharomyces pombe general alpha-glucoside permease. the SLC45 family is composed of four (A1-A4) vertebrate proteins as well as related insect proteins such as Drosophila sucrose transporter SCRT or Slc45-1. Members of this group transport sucrose and other sugars like maltose into the cell, with the concomitant uptake of protons (symport system). Plant sucrose transporters are crucial to carbon partitioning, playing a key role in phloem loading/unloading. They play a key role in loading and unloading of sucrose into the phloem and as a result, they control sucrose distribution throughout the whole plant and drive the osmotic flow system in the phloem. They also play a role in the exchange of sucrose between beneficial symbionts (mycorrhiza and Rhizobium) as well as pathogens such as nematodes and parasitic fungi. There are nine sucrose transporter genes in Arabidopsis and five in rice. Vertebrate SLC45 family proteins have been implicated in the regulation of glucose homoeostasis in the brain (SLC45A1), with skin and hair pigmentation (SLC45A2), and with prostate cancer and myelination (SLC45A3). Mutations in SLC45A2, also called MATP (membrane-associated transporter protein) or melanoma antigen AIM1, cause oculocutaneous albinism type 4 (OCA4), an autosomal recessive disorder of melanin biosynthesis that results in congenital hypopigmentation of ocular and cutaneous tissues. The SLC45 family and related sugar transporters belong to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 421 matched cddid_all.tbl CDD cd17314 cd17314 340872 MFS_MCT_like Monocarboxylate transporter (MCT) family and similar transporters of the Major Facilitator Superfamily. The group is composed of the Monocarboxylate transporter (MCT) family in animals and similar transporters from fungi, plants, archaea, and bacteria. MCT is also called Solute carrier family 16 (SLC16 or SLC16A). It is composed of 14 members, MCT1-14. MCTs play an integral role in cellular metabolism via lactate transport and have been implicated in metabolic synergy in tumors. MCTs have been found to facilitate the transport across the plasma membrane not only of monocarboxylates (MCT1-4), but also thyroid hormones (MCT8/10), and aromatic acids (MCT10). Yeast MCT homologous (Mch) proteins are not involved in the uptake of monocarboxylates; their substrates are not known. The MCT-like family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 385 matched cddid_all.tbl CDD cd17315 cd17315 340873 MFS_GLUT_like Glucose transporters (GLUTs) and other similar sugar transporters of the Major Facilitator Superfamily. This family is composed of glucose transporters (GLUTs) and other sugar transporters including fungal hexose transporters (HXT), bacterial xylose transporter (XylE), plant sugar transport proteins (STP) and polyol transporters (PLT), H(+)-myo-inositol cotransporter (HMIT), and similar proteins. GLUTs, also called Solute carrier family 2, facilitated glucose transporters (SLC2A), are a family of proteins that facilitate the transport of hexoses such as glucose and fructose. There are fourteen GLUTs found in humans; they display different substrate specificities and tissue expression. They have been categorized into three classes based on sequence similarity: Class 1 (GLUTs 1-4, 14); Class 2 (GLUTs 5, 7, 9, and 11); and Class 3 (GLUTs 6, 8, 10, 12, and HMIT). GLUT proteins are comprised of about 500 amino acid residues, possess a single N-linked oligosaccharide, and have 12 transmembrane segments. The GLUT-like family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 365 matched cddid_all.tbl CDD cd17316 cd17316 340874 MFS_SV2_like Metazoan Synaptic vesicle glycoprotein 2 (SV2) and related small molecule transporters of the Major Facilitator Superfamily. This family is composed of metazoan synaptic vesicle glycoprotein 2 (SV2) and related small molecule transporters including those that transport inorganic phosphate (Pht), aromatic compounds (PcaK and related proteins), proline/betaine (ProP), alpha-ketoglutarate (KgtP), citrate (CitA), shikimate (ShiA), and cis,cis-muconate (MucK), among others. SV2 is a transporter-like protein that serves as the receptor for botulinum neurotoxin A (BoNT/A), one of seven neurotoxins produced by the bacterium Clostridium botulinum. BoNT/A blocks neurotransmitter release by cleaving synaptosome-associated protein of 25 kD (SNAP-25) within presynaptic nerve terminals. Also included in this family is synaptic vesicle 2 (SV2)-related protein (SVOP) and similar proteins. SVOP is a transporter-like nucleotide binding protein that localizes to neurotransmitter-containing vesicles. The SV2-like family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 353 matched cddid_all.tbl CDD cd17317 cd17317 340875 MFS_SLC22 Solute carrier 22 (SLC22) family of organic cation/anion/zwitterion transporters of the Major Facilitator Superfamily. The Solute carrier 22 (SLC22) family of organic cation/anion/zwitterion transporters includes organic cation transporters (OCTs), organic zwitterion/cation transporters (OCTNs), and organic anion transporters (OATs). SLC22 transporters interact with a variety of compounds that include drugs of abuse, environmental toxins, opioid analgesics, antidepressant and anxiolytic agents, and neurotransmitters and their metabolites. The SLC22 family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 331 matched cddid_all.tbl CDD cd17318 cd17318 340876 MFS_SLC17 Solute carrier 17 (SLC17) family of the Major Facilitator Superfamily of transporters. The Solute carrier 17 (SLC17) family is primarily involved in the transport of organic anions. There are nime human proteins belonging to this family including: the type I phosphate transporters (SLC17A1-4) that were initially identified as sodium-dependent inorganic phosphate (Pi) transporters but are now known to be involved in tha transport of organic anions; lysosomal acidic sugar transporter (SLC17A5 or sialin), vesicular glutamate transporters (VGluT1#3 or SLC17A7, SLC17A6, and SLC17A8, respectively), and a vesicular nucleotide transporter (VNUT or SLC17A9). SLC17A1 and SLC17A3 have roles in the transport of urate and para-aminohippurate, respectively. The SLC17 family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 389 matched cddid_all.tbl CDD cd17319 cd17319 340877 MFS_ExuT_GudP_like Hexuronate transporter, Glucarate transporter, and similar transporters of the Major Facilitator Superfamily. This family is composed of predominantly bacterial transporters for hexuronate (ExuT), glucarate (GudP), galactarate (GarP), and galactonate (DgoT). They mediate the uptake of these compounds into the cell. They belong to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 358 matched cddid_all.tbl CDD cd17320 cd17320 340878 MFS_MdfA_MDR_like Multidrug transporter MdfA and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily. This family is composed of bacterial multidrug resistance (MDR) transporters including several proteins from Escherichia coli such as MdfA (also called chloramphenicol resistance pump Cmr), EmrD, MdtM, MdtL, bicyclomycin resistance protein (also called sulfonamide resistance protein), and the uncharacterized inner membrane transport protein YdhC. EmrD is a proton-dependent secondary transporter, first identified as an efflux pump for uncouplers of oxidative phosphorylation. It expels a range of drug molecules and amphipathic compounds across the inner membrane of E. coli. Similarly, MdfA is a secondary multidrug transporter that exports a broad spectrum of structurally and electrically dissimilar toxic compounds. These MDR transporters are drug/H+ antiporters (DHA) belonging to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 379 matched cddid_all.tbl CDD cd17321 cd17321 340879 MFS_MMR_MDR_like Methylenomycin A resistance protein (also called MMR peptide) and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily. This family is composed of bacterial, fungal, and archaeal multidrug resistance (MDR) transporters including several proteins from Bacilli such as methylenomycin A resistance protein (also called MMR peptide), tetracycline resistance protein (TetB), and lincomycin resistance protein LmrB, as well as fungal proteins such as vacuolar basic amino acid transporters, which are involved in the transport into vacuoles of the basic amino acids histidine, lysine, and arginine in Saccharomyces cerevisiae, and aminotriazole/azole resistance proteins. MDR transporters are drug/H+ antiporters (DHA) that mediate the efflux of a variety of drugs and toxic compounds, and confer resistance to these compounds. For example, MMR confers resistance to the epoxide antibiotic methylenomycin while TetB resistance to tetracycline by an active tetracycline efflux. MMR-like MDR transporters belong to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 370 matched cddid_all.tbl CDD cd17322 cd17322 340880 MFS_ARN_like Yeast ARN family of Siderophore iron transporters and similar proteins of the Major Facilitator Superfamily. The ARN family of siderophore iron transporters includes ARN1 (or ferrichrome permease), ARN2 (or triacetylfusarinine C transporter 1 or TAF1), ARN3 (or siderophore iron transporter 1 or SIT1 or ferrioxamine B permease) and ARN4 (or Enterobactin permease or ENB1). They specifically recognize siderophore-iron chelates are expressed under conditions of iron deprivation. They facilitate the uptake of both hydroxamate- and catecholate-type siderophores. This group also includes glutathione exchanger 1 (Gex1p) and Gex2p, which are proton/glutathione antiporters that import glutathione from the vacuole and exports it through the plasma membrane. The ARN family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 514 matched cddid_all.tbl CDD cd17323 cd17323 340881 MFS_Tpo1_MDR_like Yeast Polyamine transporter 1 (Tpo1) and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily. This family is composed of fungal multidrug resistance (MDR) transporters including several proteins from Saccharomyces cerevisiae such as polyamine transporters 1-4 (Tpo1-4), quinidine resistance proteins 1-3 (Qdr1-3), dityrosine transporter 1 (Dtr1), fluconazole resistance protein 1 (Flr1), and protein HOL1. MDR transporters are drug/H+ antiporters (DHA) that mediate the efflux of a variety of drugs and toxic compounds, and confer resistance to these compounds. For example, Flr1 confers resistance to the azole derivative fluconazole while Tpo1 confers resistance and adaptation to quinidine and ketoconazole. The polyamine transporters are involved in the detoxification of excess polyamines in the cytoplasm. Tpo1-like MDR transporters belong to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 376 matched cddid_all.tbl CDD cd17324 cd17324 340882 MFS_NepI_like Purine ribonucleoside efflux pump NepI and similar transporters of the Major Facilitator Superfamily. This family is composed of purine efflux pumps such as Escherichia coli NepI and Bacillus subtilis PbuE, sugar efflux transporters such as Corynebacterium glutamicum arabinose efflux permease, multidrug resistance (MDR) transporters such as Streptomyces lividans chloramphenicol resistance protein (CmlR), and similar proteins. NepI and PbuE are involved in the efflux of purine ribonucleosides such as guanosine, adenosine and inosine, as well as purine bases like guanine, adenine, and hypoxanthine, and purine base analogs. They play a role in the maintenance of cellular purine base pools, as well as in protecting the cells and conferring resistance against toxic purine base analogs such as 6-mercaptopurine. MDR transporters are drug/H+ antiporters (DHA) that mediate the efflux of a variety of drugs and toxic compounds, and confer resistance to these compounds. The NepI-like family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 370 matched cddid_all.tbl CDD cd17325 cd17325 340883 MFS_MdtG_SLC18_like bacterial MdtG-like and eukaryotic solute carrier 18 (SLC18) family of the Major Facilitator Superfamily of transporters. This family is composed of eukaryotic solute carrier 18 (SLC18) family transporters and related bacterial multidrug resistance (MDR) transporters including several proteins from Escherichia coli such as multidrug resistance protein MdtG, from Bacillus subtilis such as multidrug resistance proteins 1 (Bmr1) and 2 (Bmr2), and from Staphylococcus aureus such as quinolone resistance protein NorA. The family also includes Escherichia coli arabinose efflux transporters YfcJ and YhhS. MDR transporters are drug/H+ antiporters (DHA) that mediate the efflux of a variety of drugs and toxic compounds, and confer resistance to these compounds. The SLC18 transporter family includes vesicular monoamine transporters (VAT1 and VAT2), vesicular acetylcholine transporter (VAChT), and SLC18B1, which is proposed to be a vesicular polyamine transporter (VPAT). The MdtG/SLC18 family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 375 matched cddid_all.tbl CDD cd17326 cd17326 340884 MFS_MFSD8 Major facilitator superfamily domain-containing protein 8. Major facilitator superfamily (MFS) domain-containing protein 8 (MFSD8) is also called ceroid-lipofuscinosis neuronal protein 7 (CLN7). It is a polytopic lysosomal membrane protein that may transport small solutes by using chemiosmotic ion gradients. Mutations in MFSD8/CLN7 cause a variant of late-infantile neuronal ceroid lipofuscinoses (vLINCL), a neurodegenerative lysosomal storage disorder. Some variants are associated with nonsyndromic autosomal recessive macular dystrophy. MFSD8/CLN7 belongs to the Eukaryotic Solute carrier 46 (SLC46)/Bacterial Tetracycline resistance -like (SLC46/TetA-like) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 374 matched cddid_all.tbl CDD cd17327 cd17327 340885 MFS_FEN2_like Pantothenate transporter FEN2 and similar transporters of the Major Facilitator Superfamily. This family is composed of Saccharomyces cerevisiae pantothenate transporter FEN2 (or fenpropimorph resistance protein 2) and similar proteins from fungi and bacteria including fungal vitamin H transporter, allantoate permease, and high-affinity nicotinic acid transporter, as well as Pseudomonas putida phthalate transporter and nicotinate degradation protein T (nicT). These proteins are involved in the uptake into the cell of specific substrates such as pathothenate, biotin, allantoate, and nicotinic acid, among others. The FEN2-like family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 406 matched cddid_all.tbl CDD cd17328 cd17328 340886 MFS_spinster_like Protein spinster and spinster homologs of the Major Facilitator Superfamily of transporters. The protein spinster family includes Drosophila protein spinster, its vertebrate homologs, and similar proteins. Humans contain three homologs called protein spinster homologs 1 (SPNS1), 2 (SPNS2), and 3 (SPNS3). Protein spinster and its homologs may be sphingolipid transporters that play central roles in endosomes and/or lysosomes storage. SPNS2 is also called sphingosine 1-phosphate (S1P) transporter and is required for migration of myocardial precursors. S1P is a secreted lipid mediator that plays critical roles in cardiovascular, immunological, and neural development and function. The spinster-like family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 405 matched cddid_all.tbl CDD cd17329 cd17329 340887 MFS_MdtH_MDR_like Multidrug resistance protein MdtH and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily. This family is composed of Escherichia coli MdtH and similar multidrug resistance (MDR) transporters from bacteria and archaea, many of which remain uncharacterized. MDR transporters are drug/H+ antiporters (DHA) that mediate the efflux of a variety of drugs and toxic compounds, and confer resistance to these compounds. MdtH confers resistance to norfloxacin and enoxacin. MdtH-like MDR transporters belong to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 376 matched cddid_all.tbl CDD cd17330 cd17330 340888 MFS_SLC46_TetA_like Eukaryotic Solute carrier 46 (SLC46) family, Bacterial Tetracycline resistance proteins, and similar proteins of the Major Facilitator Superfamily of transporters. This family is composed of the eukaryotic proteins MFSD9, MFSD10, MFSD14, and SLC46 family proteins, as well as bacterial multidrug resistance (MDR) transporters such as tetracycline resistance protein TetA and multidrug resistance protein MdtG. MDR transporters are drug/H+ antiporters (DHA) that mediate the efflux of a variety of drugs and toxic compounds, and confer resistance to these compounds. TetA proteins confer resistance to tetracycline while MdtG confers resistance to fosfomycin and deoxycholate. The Solute carrier 46 (SLC46) family is composed of three vertebrate members (SLC46A1, SLC46A2, and SLC46A3), the best-studied of which is SLC46A1, which functions both as an intestinal proton-coupled high-affinity folate transporter involved in the absorption of folates and as an intestinal heme transporter which mediates heme uptake. MFSD10 facilitates the uptake of organic anions such as some non-steroidal anti-inflammatory drugs (NSAIDs) and confers resistance to such NSAIDs. The SLC46/TetA-like family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 349 matched cddid_all.tbl CDD cd17331 cd17331 340889 MFS_SLC22A18 Solute carrier family 22 member 18 of the Major Facilitator Superfamily of transporters. Solute carrier family 22 member 18 (SLC22A18) is also called Beckwith-Wiedemann syndrome chromosomal region 1 candidate gene A protein (BWR1A or BWSCR1A), efflux transporter-like protein, imprinted multi-membrane-spanning polyspecific transporter-related protein 1 (IMPT1), organic cation transporter-like protein 2 (ORCTL2), or tumor-suppressing subchromosomal transferable fragment candidate gene 5 protein (TSSC5). It is localized at the apical membrane surface of renal proximal tubules and may act as an organic cation/proton antiporter. It functions as a tumor suppressor in several cancer types including glioblastoma and colorectal cancer. SLC22A18 belongs to the Eukaryotic Solute carrier 46 (SLC46)/Bacterial Tetracycline resistance (TetA) -like (SLC46/TetA-like) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 382 matched cddid_all.tbl CDD cd17332 cd17332 340890 MFS_MelB_like Salmonella enterica Na+/melibiose symporter MelB and similar transporters of the Major Facilitator Superfamily. This family is composed of Salmonella enterica Na+/melibiose symporter MelB, Major Facilitator Superfamily domain-containing proteins, MFSD2 and MFSD12, and other sugar transporters. MelB catalyzes the electrogenic symport of galactosides with Na+, Li+ or H+. The MFSD2 subfamily is composed of two vertebrate members, MFSD2A and MFSD2B. MFSD2A is more commonly called sodium-dependent lysophosphatidylcholine symporter 1 (NLS1). It is an LPC symporter that plays an essential role for blood-brain barrier formation and function. Inactivating mutations in MFSD2A cause a lethal microcephaly syndrome. MFSD2B is a potential risk or protect factor in the prognosis of lung adenocarcinoma. MelB-like family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 424 matched cddid_all.tbl CDD cd17333 cd17333 340891 MFS_FucP_MFSD4_like Bacterial fucose permease, eukaryotic Major facilitator superfamily domain-containing protein 4, and similar proteins. This family is composed of bacterial L-fucose permease (FucP), eukaryotic Major facilitator superfamily domain-containing protein 4 (MFSD4) proteins, and similar proteins. L-fucose permease facilitates the uptake of L-fucose across the boundary membrane with the concomitant transport of protons into the cell; it can also transport L-galactose and D-arabinose. The MFSD4 subfamily consists of two vertebrate members: MFSD4A and MFSD4B. The function of MFSD4A is unknown. MFSD4B is more commonly know as Sodium-dependent glucose transporter 1 (NaGLT1), a primary fructose transporter in rat renal brush-border membranes that also facilitates sodium-independent urea uptake. The FucP/MFSD4 family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 372 matched cddid_all.tbl CDD cd17334 cd17334 340892 MFS_SLC49 Solute carrier 49 (SLC49) family of the Major Facilitator Superfamily of transporters. The Solute carrier 49 (SLC49) family is composed of four members: feline leukemia virus subgroup C receptor 1 (FLVCR1, SLC49A1); FLVCR2 (SLC49A2); major facilitator superfamily domain-containing protein 7 (MFSD7, SLC49A3); and disrupted in renal carcinoma protein 2 (DIRC2, SLC49A4). FLVCR1 and FLVCR2 are heme transporters. In addition, FLVCR2 also functions as a transporter for a calcium-chelator complex that is important for growth and calcium metabolism. The function of MFSD7 is unknown. DIRC2 is an electrogenic lysosomal metabolite transporter that is regulated by limited proteolytic processing by cathepsin L. The SLC49 family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 407 matched cddid_all.tbl CDD cd17335 cd17335 340893 MFS_MFSD6 Major facilitator superfamily domain-containing protein 6. Human Major facilitator superfamily domain-containing protein 6 (MFSD6) is also called macrophage MHC class I receptor 2 homolog (MMR2). It has been postulated as a possible receptor for human leukocyte antigen (HLA)-B62. MFSD6 is conserved through evolution and appeared before bilateral animals. It belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 375 matched cddid_all.tbl CDD cd17336 cd17336 340894 MFS_SLCO_OATP Solute carrier organic anion transporters of the Major Facilitator Superfamily of transporters. Solute carrier organic anion transporters (SLCOs) are also called organic anion transporting polypeptides (OATPs) or SLC21 (Solute carrier family 21) proteins. They are sodium-independent transporters that mediate the transport of a broad range of endo- as well as xenobiotics. Their substrates are mainly amphipathic organic anions with a molecular weight of more than 300Da, although there are a few known neutral or positively charged substrates. These include drugs including statins, angiotensin-converting enzyme inhibitors, angiotensin receptor blockers, antibiotics, antihistaminics, antihypertensives, and anticancer drugs. SLCOs/OATPs can be classified into 6 families (SLCO1-6 or OATP1-6) and each family may have subfamilies (e.g. OATP1A, OATP1B, OATP1C). Within the subfamilies, individual members are numbered according to the chronology of their identification and if there is already an ortholog known, they are given the same number. For example, the first SLCO identified, is rat OATP1A1 (encoded by the Slco1a1 gene). The second SLCO identified is the first human SLCO from the same subfamily and is called OATP1A2 (encoded by the SLCO1A2 gene). There are 11 human SLCOs/OATPs. SLCOs belong to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 411 matched cddid_all.tbl CDD cd17337 cd17337 340895 MFS_CsbX CsbX family of the Major Facilitator Superfamily of transporters. The CsbX family is composed of Bacillus subtilis CsbX protein (also named alpha-ketoglutarate permease), Klebsiella pneumoniae D-arabinitol transporter (DalT), and similar proteins. The csbX gene is a sigmaB-controlled gene that is expressed during the stationary phase of cell growth. DalT is a pentose-specific ion symporter for D-arabinitol uptake. Most members of this family remain uncharacterized. The CsbX family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 388 matched cddid_all.tbl CDD cd17338 cd17338 340896 MFS_unc93_like Unc-93 family of the Major Facilitator Superfamily of transporters. The Unc-93 family is composed of Caenorhabditis elegans uncoordinated protein 93 (also called putative potassium channel regulatory protein unc-93) and similar proteins including three vertebrate members: protein unc-93 homolog A (UNC93A), protein unc-93 homolog B1 (UNC93B1), and UNC93-like protein MFSD11 (also called major facilitator superfamily domain-containing protein 11 or protein ET). Unc-93 acts as a regulatory subunit of a multi-subunit potassium channel complex that may function in coordinating muscle contraction in C. elegans. The human UNC93A gene is located in a region of the genome that is frequently associated with ovarian cancer, however, there is no evidence that UNC93A has a tumor suppressor function. UNC93B1 controls intracellular trafficking and transport of a subset of Toll-like receptors (TLRs), including TLR3, TLR7 and TLR9, from the endoplasmic reticulum to endolysosomes where they can engage pathogen nucleotides and activate signaling cascades. MFSD11 is ubiquitously expressed in the periphery and the central nervous system of mice, where it is expressed in excitatory and inhibitory mouse brain neurons. The unc93-like family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 388 matched cddid_all.tbl CDD cd17339 cd17339 340897 MFS_NIMT_CynX_like 2-nitroimidazole and cyanate transporters and similar proteins of the Major Facilitator Superfamily of transporters. This family is composed of Escherichia coli 2-nitroimidazole transporter (NIMT) and cyanate transport protein CynX, and similar proteins. NIMT, also called YeaN, confers resistance to 2-nitroimidazole, the antibacterial and antifungal antibiotic, by mediating the active efflux of this compound. CynX is part of an active transport system that transports exogenous cyanate into E. coli cells. The NIMT/CynX-like family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 374 matched cddid_all.tbl CDD cd17340 cd17340 340898 MFS_MFSD1 Major facilitator superfamily domain-containing protein 1. Human major facilitator superfamily domain-containing protein 1 (MFSD1) is also called smooth muscle cell-associated protein 4 (SMAP-4). The function of MFSD1 is still unknown. Its expression is affected by altered nutrient intake. During starvation, expression of MFSD1 is downregulated in anterior brain sections in mice while it is upregulated in the brainstem. In mice raised on high-fat diet, MFSD1 is specifically downregulated in brainstem and hypothalamus. MFSD1 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 394 matched cddid_all.tbl CDD cd17341 cd17341 340899 MFS_NRT2_like Plant Nitrate transporter NRT2 family and Bacterial Nitrate/Nitrite transporters of the Major Facilitator Superfamily. This family is composed of plant NRT2 family high-affinity nitrate transporters as well as nitrate and nitrite transporters from bacteria including Bacillus subtilis nitrate transporter NasA and nitrite extrusion protein NarK, Staphylococcus aureus NarT, Synechococcus sp. nitrate permease NapA, Mycobacterium tuberculosis NarK2 and nitrite extrusion protein NarU. NRT2 family proteins are involved in the uptake of nitrate by plant roots from the soil through the high-affinity transport system (HATS). There are seven Arabidopsis thaliana NRT2 proteins, called AtNRT2:1 to AtNRT2:7. The NRT2-like family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 384 matched cddid_all.tbl CDD cd17342 cd17342 340900 MFS_SLC37A3 Solute carrier family 37 member 3 of the Major Facilitator Superfamily of transporters. Solute carrier family 37 member 3 (SLC37A3) is also called sugar phosphate exchanger 3 (SPX3), and is one of four SLC37 family proteins in vertebrates. It's function and activity is unknown. The best characterized SLC37 family member is SLC37A4, also called the glucose-6-phosphate transporter (G6PT), a phosphate (Pi)-linked G6P antiporter. SLC37A3 is a member of the Organophosphate:Pi antiporter (OPA)/SLC37 family, whose members are integral membrane proteins responsible for the transport of specific organophosphates or sugar phosphates across biological membranes with the simultaneous translocation of inorganic phosphate into the opposite direction. The OPA/SLC37 family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 399 matched cddid_all.tbl CDD cd17343 cd17343 340901 MFS_SLC37A4 Solute carrier family 37 member 4 of the Major Facilitator Superfamily of transporters. Solute carrier family 37 member 4 (SLC37A4), one of four SLC37 family proteins in vertebrates, is better known as glucose-6-phosphate transporter (G6PT). It is also called sugar phosphate exchanger 4 (SPX4), G6P translocase, or transformation-related gene 19 protein (TRG-19). G6PT is a phosphate (Pi)-linked G6P antiporter, catalyzing G6P:Pi and Pi:Pi exchanges. Deficiencies in human G6PT lead to glycogen storage disease type Ib (GSD-Ib), which is a metabolic and immune disorder. G6PT is a member of the Organophosphate:Pi antiporter (OPA)/SLC37 family, whose members are integral membrane proteins responsible for the transport of specific organophosphates or sugar phosphates across biological membranes with the simultaneous translocation of inorganic phosphate into the opposite direction. The OPA/SLC37 family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 409 matched cddid_all.tbl CDD cd17344 cd17344 340902 MFS_SLC37A1_2 Solute carrier family 37 members 1 and 2 of the Major Facilitator Superfamily of transporters. Solute carrier family 37 members 1 (SLC37A1) and 2 (SLC37A2) are also called sugar phosphate exchangers 1 (SPX1) and 2 (SPX2). SLC37A1 and SLC37A2 are ER-associated, Pi-linked antiporters that can transport glucose-6-phosphate (G6P) but are insensitive to chlorogenic acid, a competitive inhibitor of physiological ER G6P transport, unlike SLC37A4, the best characterized SLC37 family member and is the physiological G6P transporter (G6PT). SLC37A1 and SLC37A2 belong to the Organophosphate:Pi antiporter (OPA)/SLC37 family, whose members are integral membrane proteins responsible for the transport of specific organophosphates or sugar phosphates across biological membranes with the simultaneous translocation of inorganic phosphate into the opposite direction. The OPA/SLC37 family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 400 matched cddid_all.tbl CDD cd17345 cd17345 340903 MFS_GlpT Glycerol-3-Phosphate Transporter of the Major Facilitator Superfamily of transporters. Glycerol-3-Phosphate Transporter (also called GlpT or G-3-P permease) is responsible for glycerol-3-phosphate uptake. It is part of the Organophosphate:Pi antiporter (OPA) family of integral membrane proteins responsible for the transport of specific organophosphates or sugar phosphates across biological membranes with the simultaneous translocation of inorganic phosphate into the opposite direction. The GlpT group belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 411 matched cddid_all.tbl CDD cd17346 cd17346 340904 MFS_DtpA_like Dipeptide and tripeptide permease A (DtpA)-like subfamily of the Major Facilitator Superfamily of transporters. The DtpA-like subfamily includes four Escherichia coli proteins: dipeptide and tripeptide permeases A (DtpA, TppB or YdgR), B (DtpB or YhiP), C (DtpC or YjdL), and D (DtpD or YbgH). They are proton-dependent permeases that transport di- and tripeptides. DtpA and DtpB display a preference for di- and tripeptides composed of L-amino acids. DtpC shows higher specificity for dipeptides compared to tripeptides, and prefers dipeptides containing a C-terminal lysine residue. The DtpA-like subfamily belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 399 matched cddid_all.tbl CDD cd17347 cd17347 340905 MFS_SLC15A1_2_like Solute carrier family 15 members 1 and 2, and similar Major Facilitator Superfamily transporters. Solute carrier family 15 member 1 (SLC15A1) and SLC15A2 are members of the proton-coupled oligopeptide transporter (POT) family of integral membrane proteins that mediate the cellular uptake of di/tripeptides and peptide-like drugs. They mediate the proton-coupled active transport of a broad range of dipeptides and tripeptides, including zwitterionic, anionic and cationic peptides, as well as a variety of peptide-like drugs such as cefadroxil, enalapril, and valacyclovir. SLC15A1, or peptide transporter 1 (PepT1), is primarily expressed in the brush border membranes of enterocytes of the small intestine and is also known as the intestinal isoform. SLC15A2, or peptide transporter 2 (PepT2), is abundantly expressed in the apical membrane of kidney proximal tubules and is also referred to as the renal isoform. Both proteins transport di/tripeptides, but not tetrapeptides or free amino acids, using the energy generated by an inwardly directed transmembrane proton gradient. The SLC15A1/SLC15A2-like group belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 427 matched cddid_all.tbl CDD cd17348 cd17348 340906 MFS_SLC15A3_4 Solute Carrier family 15 members 3 and 4 of the Major Facilitator Superfamily of transporters. Solute carrier family 15 members 3 (SLC15A3) and 4 (SLC15A4) are members of the proton-coupled oligopeptide transporter (POT) family of integral membrane proteins that mediate the cellular uptake of di/tripeptides and peptide-like drugs. They are peptide/histidine transporters (PHTs) that transport free histidine in addition to di/tripeptides. SLC15A4, also called peptide transporter 4 or peptide/histidine transporter 1 (PHT1), is expressed in the human brain, retina, placenta, and immune cells. It is required for Toll-like receptor 7 (TLR7)- and TLR9-mediated type I interferon production in plasmacytoid dendritic cells (pDCs) and is involved in the pathogenesis of lupus-like autoimmunity. SLC15A3, also called osteoclast transporter, peptide transporter 3, or peptide/histidine transporter 2 (PHT2), is expressed in immune tissues including the spleen and thymus. The SLC15A3/SLC15A4 group belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 435 matched cddid_all.tbl CDD cd17349 cd17349 340907 MFS_SLC15A5 Solute Carrier family 15 member 5 of the Major Facilitator Superfamily of transporters. Solute carrier family 15 member 5 (SLC15A5) is a member of the proton-coupled oligopeptide transporter (POT) family of integral membrane proteins that mediate the cellular uptake of di/tripeptides and peptide-like drugs. The specific function of SLC15A5 is unknown. SLC15A5 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 437 matched cddid_all.tbl CDD cd17350 cd17350 340908 MFS_PTR2 Peptide transporter PTR2 of the Major Facilitator Superfamily of transporters. Fungal peptide transporter or permease PTR2 is a member of the proton-coupled oligopeptide transporter (POT) family of integral membrane proteins that mediate the cellular uptake of di/tripeptides and peptide-like drugs. It is a 12-transmembrane domain (TMD) integral membrane protein that translocates di-/tripeptides. As with other POT family proteins, it displays characteristic substrate multispecificity. PTR2 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 438 matched cddid_all.tbl CDD cd17351 cd17351 340909 MFS_NPF Plant NRT1/PTR family (NPF) of the Major Facilitator Superfamily of transporters. The plant Nitrate transporter/Peptide transporter (NRT1/PTR) family (NPF) is related to the POT (proton-coupled oligopeptide transporter), Peptide transporter (PepT/PTR), or Solute Carrier 15 (SLC15) family in animals. In contrast to related animal and bacterial counterparts, the plant proteins transport a wide variety of substrates including nitrate, peptides, amino acids, dicarboxylates, glucosinolates, as well as the plant hormones indole-3-acetic acid (IAA) and abscisic acid (ABA). A recent study identified eight subfamilies within this family, named NPF1-NPF8. NPF belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 445 matched cddid_all.tbl CDD cd17352 cd17352 340910 MFS_MCT_SLC16 Monocarboxylate transporter (MCT) family of the Major Facilitator Superfamily of transporters. The animal Monocarboxylate transporter (MCT) family is also called Solute carrier family 16 (SLC16 or SLC16A). It is composed of 14 members, MCT1-14. MCTs play an integral role in cellular metabolism via lactate transport and have been implicated in metabolic synergy in tumors. MCT1-4 are proton-coupled transporters that facilitate the transport across the plasma membrane of monocarboxylates such as lactate, pyruvate, branched-chain oxo acids derived from leucine, valine and isoleucine, and ketone bodies such as acetoacetate, beta-hydroxybutyrate and acetate. MCT8 and MCT10 are transporters which stimulate the cellular uptake of thyroid hormones such as thyroxine (T4), triiodothyronine (T3), reverse triiodothyronine (rT3) and diidothyronine (T2). MCT10 also functions as a sodium-independent transporter that mediates the uptake or efflux of aromatic acids. Many members are orphan transporters whose substrates are yet to be determined. The MCT family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 361 matched cddid_all.tbl CDD cd17353 cd17353 340911 MFS_OFA_like Oxalate:formate antiporter (OFA) and similar proteins of the Major Facilitator Superfamily of transporters. This subfamily is composed of Oxalobacter formigenes oxalate:formate antiporter (OFA or OxlT) and similar proteins. O. formigenes, a commensal found in the gut of animals and humans, plays an important role in clearing dietary oxalate from the intestinal tract, which is carried out by OFA/OxlT, an anion transporter that facilitates the exchange of divalent oxalate with monovalent formate, the product of oxalate decarboxylation. This exchange generates an electrochemical proton gradient and is the source of energy for ATP synthesis in this cell. The OFA-like subfamily belongs to the Monocarboxylate transporter -like (MCT-like) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 389 matched cddid_all.tbl CDD cd17354 cd17354 340912 MFS_Mch1p_like Monocarboxylate transporter-homologous (Mch) 1 protein and similar transporters of the Major Facilitator Superfamily of transporters. Yeast monocarboxylate transporter-homologous (Mch) proteins are putative transporters that do not transport monocarboxylic acids across the plasma membrane, and may play roles distinct from their mammalian counterparts. Their function has not been determined. The Mch1p-like group belongs to the Monocarboxylate transporter -like (MCT-like) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 385 matched cddid_all.tbl CDD cd17355 cd17355 340913 MFS_YcxA_like MFS-type transporter YcxA and similar proteins of the Major Facilitator Superfamily of transporters. This group is composed of uncharacterized bacterial MFS-type transporters including Bacillus subtilis YcxA and YbfB. YcxA has been shown to facilitate the export of surfactin in B. subtilis. The YcxA-like group belongs to the Monocarboxylate transporter -like (MCT-like) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 386 matched cddid_all.tbl CDD cd17356 cd17356 340914 MFS_HXT Fungal Hexose transporter subfamily of the Major Facilitator Superfamily of transporters and similar proteins. The fungal hexose transporter (HXT) subfamily is comprised of functionally redundant proteins that function mainly in the transport of glucose, as well as other sugars such as galactose and fructose. Saccharomyces cerevisiae has 20 genes that encode proteins in this family (HXT1 to HXT17, GAL2, SNF3, and RGT2). Seven of these (HXT1-7) encode functional glucose transporters. Gal2p is a galactose transporter, while Rgt2p and Snf3p act as cell surface glucose receptors that initiate signal transduction in response to glucose, functioning in an induction pathway responsible for glucose uptake. Rgt2p is activated by high levels of glucose and stimulates expression of low affinity glucose transporters such as Hxt1p and Hxt3p, while Snf3p generates a glucose signal in response to low levels of glucose, stimulating the expression of high affinity glucose transporters such as Hxt2p and Hxt4p. Schizosaccharomyces pombe contains eight GHT genes (GHT1-8) belonging to this family. Ght1, Ght2, and Ght5 are high-affinity glucose transporters; Ght3 is a high-affinity gluconate transporter; and Ght6 high-affinity fructose transporter. The substrate specificities for Ght4, Ght7, and Ght8 remain undetermined. The HXT subfamily belongs to the Glucose transporter -like (GLUT-like) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 403 matched cddid_all.tbl CDD cd17357 cd17357 340915 MFS_GLUT_Class1_2_like Class 1 and Class 2 Glucose transporters (GLUTs) of the Major Facilitator Superfamily. This subfamily includes Class 1 and Class 2 glucose transporters (GLUTs) including Solute carrier family 2, facilitated glucose transporter member 1 (SLC2A1, also called glucose transporter type 1 or GLUT1), SLC2A2-5 (GLUT2-5), SLC2A7 (GLUT7), SLC2A9 (GLUT9), SLC2A11 (GLUT11), SLC2A14 (GLUT14), and similar proteins. GLUTs are a family of proteins that facilitate the transport of hexoses such as glucose and fructose. There are fourteen GLUTs found in humans; they display different substrate specificities and tissue expression. They have been categorized into three classes based on sequence similarity: Class 1 (GLUTs 1-4, 14); Class 2 (GLUTs 5, 7, 9, and 11); and Class 3 (GLUTs 6, 8, 10, 12, and HMIT). GLUTs 1-5 are the most thoroughly studied and are well-established as glucose and/or fructose transporters in various tissues and cell types. GLUT proteins are comprised of about 500 amino acid residues, possess a single N-linked oligosaccharide, and have 12 transmembrane segments. They belong to the Glucose transporter -like (GLUT-like) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 447 matched cddid_all.tbl CDD cd17358 cd17358 340916 MFS_GLUT6_8_Class3_like Glucose transporter (GLUT) types 6 and 8, Class 3 GLUTs, and similar transporters of the Major Facilitator Superfamily. This subfamily is composed of glucose transporter type 6 (GLUT6), GLUT8, plant early dehydration-induced gene ERD6-like proteins, and similar insect proteins including facilitated trehalose transporter Tret1-1. GLUTs, also called Solute carrier family 2, facilitated glucose transporters (SLC2A), are a family of proteins that facilitate the transport of hexoses such as glucose and fructose. There are fourteen GLUTs found in humans; they display different substrate specificities and tissue expression. They have been categorized into three classes based on sequence similarity: Class 1 (GLUTs 1-4, 14); Class 2 (GLUTs 5, 7, 9, and 11); and Class 3 (GLUTs 6, 8, 10, 12, and HMIT). Insect Tret1-1 is a low-capacity facilitative transporter for trehalose that mediates the transport of trehalose synthesized in the fat body and the incorporation of trehalose into other tissues that require a carbon source. GLUT proteins are comprised of about 500 amino acid residues, possess a single N-linked oligosaccharide, and have 12 transmembrane segments. They belong to the Glucose transporter -like (GLUT-like) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 436 matched cddid_all.tbl CDD cd17359 cd17359 340917 MFS_XylE_like D-xylose-proton symporter and similar transporters of the Major Facilitator Superfamily. This subfamily includes bacterial transporters such as D-xylose-proton symporter (XylE or XylT), arabinose-proton symporter (AraE), galactose-proton symporter (GalP), major myo-inositol transporter IolT, glucose transport protein, putative metabolite transport proteins YfiG, YncC, and YwtG, and similar proteins. The symporters XylE, AraE, and GalP facilitate the uptake of D-xylose, arabinose, and galactose, respectively, across the boundary membrane with the concomitant transport of protons into the cell. IolT is involved in polyol metabolism and myo-inositol degradation into acetyl-CoA. The XylE-like subfamily belongs to the Glucose transporter -like (GLUT-like) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 383 matched cddid_all.tbl CDD cd17360 cd17360 340918 MFS_HMIT_like H(+)-myo-inositol cotransporter and similar transporters of the Major Facilitator Superfamily. This subfamily is composed of myo-inositol/inositol transporters and similar transporters from vertebrates, plant, and fungi. The human protein is called H(+)-myo-inositol cotransporter/Proton myo-inositol cotransporter (HMIT), or H(+)-myo-inositol symporter, or Solute carrier family 2 member 13 (SLC2A13). HMIT is classified as a Class 3 GLUT (glucose transporter) based on sequence similarity with GLUTs, but it does not transport glucose. It specifically transports myo-inositol and is expressed predominantly in the brain, with high expression in the hippocampus, hypothalamus, cerebellum and brainstem. HMIT may be involved in regulating processes that require high levels of myo-inositol or its phosphorylated derivatives, such as membrane recycling, growth cone dynamics, and synaptic vesicle exocytosis. Arabidopsis Inositol transporter 4 (AtINT4) mediates high-affinity H+ symport of myo-inositol across the plasma membrane. The HMIT-like subfamily belongs to the Glucose transporter -like (GLUT-like) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 362 matched cddid_all.tbl CDD cd17361 cd17361 340919 MFS_STP Plant Sugar transport protein subfamily of the Major Facilitator Superfamily of transporters. The plant Sugar transport protein (STP) subfamily includes STP1-STP14; they are also called hexose transporters. They mediate the active uptake of hexoses such as glucose, 3-O-methylglucose, fructose, xylose, mannose, galactose, fucose, 2-deoxyglucose and arabinose, by sugar/hydrogen symport. Several STP family transporters are expressed in a tissue-specific manner, or at specific developmental stages. STP1 is the member with the highest expression level of all members and high expression is detected in photosynthetic tissues, such as leaves and stems, while roots, siliques, and flowers show lower expression levels. It plays a major role in the uptake and response of Arabidopsis seeds and seedlings to sugars. The STP subfamily belongs to the Glucose transporter -like (GLUT-like) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 390 matched cddid_all.tbl CDD cd17362 cd17362 340920 MFS_GLUT10_12_Class3_like Glucose transporter (GLUT) types 10 and 12, Class 3 GLUTs, and similar transporters of the Major Facilitator Superfamily. This subfamily is composed of glucose transporter type 10, GLUT12, plant polyol transporters (PLTs), and similar proteins. GLUTs, also called Solute carrier family 2, facilitated glucose transporters (SLC2A), are a family of proteins that facilitate the transport of hexoses such as glucose and fructose. There are fourteen GLUTs found in humans; they display different substrate specificities and tissue expression. They have been categorized into three classes based on sequence similarity: Class 1 (GLUTs 1-4, 14); Class 2 (GLUTs 5, 7, 9, and 11); and Class 3 (GLUTs 6, 8, 10, 12, and HMIT). GLUT proteins are comprised of about 500 amino acid residues, possess a single N-linked oligosaccharide, and have 12 transmembrane segments. They belong to the Glucose transporter -like (GLUT-like) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 389 matched cddid_all.tbl CDD cd17363 cd17363 340921 MFS_SV2 Synaptic vesicle glycoprotein 2 of the Major Facilitator Superfamily of transporters. Synaptic vesicle glycoprotein 2 (SV2) is a transporter-like integral membrane glycoprotein, with 12 transmembrane regions, expressed in vertebrates and is localized to synaptic and endocrine secretory vesicles. Three isoforms have been identified, SV2A, SV2B, and SV2C. SV2A and SV2B are widely expressed in the brain, while SV2C is more restricted to evolutionarily older brain. SV2 isoforms have been shown to be critical for the proper function of the central nervous system. SV2 serves as the receptor for botulinum neurotoxin A (BoNT/A), one of seven neurotoxins produced by the bacterium Clostridium botulinum. BoNT/A blocks neurotransmitter release by cleaving synaptosome-associated protein of 25 kD (SNAP-25) within presynaptic nerve terminals. The SV2 family belongs to the Metazoan Synaptic Vesicle Glycoprotein 2 (SV2) and related small molecule transporter family (SV2-like) of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 474 matched cddid_all.tbl CDD cd17364 cd17364 340922 MFS_PhT Inorganic Phosphate Transporter of the Major Facilitator Superfamily of transporters. This subfamily is composed of predominantly fungal and plant high-affinity inorganic phosphate transporters (PhT or PiPT), which are involved in the uptake, translocation, and internal transport of inorganic phosphate. They also function in sensing external phosphate levels as transceptors. Phosphate is crucial for structural and metabolic needs, including nucleotide and lipid synthesis, signalling and chemical energy storage. The Pht subfamily belongs to the Metazoan Synaptic Vesicle Glycoprotein 2 (SV2) and related small molecule transporter family (SV2-like) of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 389 matched cddid_all.tbl CDD cd17365 cd17365 340923 MFS_PcaK_like 4-hydroxybenzoate transporter PcaK and similar transporters of the Major Facilitator Superfamily. This aromatic acid:H(+) symporter subfamily includes Acinetobacter sp. 4-hydroxybenzoate transporter PcaK, Pseudomonas putida gallate transporter (GalT), Corynebacterium glutamicum gentisate transporter (GenK), Nocardioides sp. 1-hydroxy-2-naphthoate transporter (PhdT), Escherichia coli 3-(3-hydroxy-phenyl)propionate (3HPP) transporter (MhpT), and similar proteins. These transporters are involved in the uptake across the cytoplasmic membrane of specific aromatic compounds such as 4-hydroxybenzoate, gallate, gentisate (2,5-dihydroxybenzoate), 1-hydroxy-2-naphthoate, and 3HPP, respectively. The PcaK-like aromatic acid:H(+) symporter subfamily belongs to the Metazoan Synaptic Vesicle Glycoprotein 2 (SV2) and related small molecule transporter family (SV2-like) of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 351 matched cddid_all.tbl CDD cd17366 cd17366 340924 MFS_ProP Proline/betaine transporter of the Major Facilitator Superfamily of transporters. This subfamily is composed of Escherichia coli proline/betaine transporter, also called proline porter II (PPII), and similar proteins. ProP is a proton symporter that senses osmotic shifts and responds by importing osmolytes such as proline, glycine betaine, stachydrine, pipecolic acid, ectoine and taurine. It is both an osmosensor and an osmoregulator which is available to participate early in the bacterial osmoregulatory response. The ProP subfamily belongs to the Metazoan Synaptic Vesicle Glycoprotein 2 (SV2) and related small molecule transporter family (SV2-like) of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 377 matched cddid_all.tbl CDD cd17367 cd17367 340925 MFS_KgtP Alpha-ketoglutarate permease of the Major Facilitator Superfamily of transporters. This subfamily includes Escherichia coli alpha-ketoglutarate permease (KgtP) and similar proteins. KgtP is a constitutively expressed proton symporter that functions in the uptake of alpha-ketoglutarate across the boundary membrane. Also included is a putative transporter from Pseudomonas aeruginosa named dicarboxylic acid transporter PcaT. The KgtP subfamily belongs to the Metazoan Synaptic Vesicle Glycoprotein 2 (SV2) and related small molecule transporter family (SV2-like) of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 407 matched cddid_all.tbl CDD cd17368 cd17368 340926 MFS_CitA Citrate-proton symporter of the Major Facilitator Superfamily of transporters. Citrate-proton symporter, also called citrate carrier protein or citrate transporter or citrate utilization protein A (CitA), is a proton symporter that functions in the uptake of citrate across the boundary membrane. It allows the utilization of citrate as a sole source of carbon and energy. In Klebsiella pneumoniae, the gene encoding this protein is called citH, instead of citA, which is the case for Escherichia coli and other organisms. CitA belongs to the Metazoan Synaptic Vesicle Glycoprotein 2 (SV2) and related small molecule transporter family (SV2-like) of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 407 matched cddid_all.tbl CDD cd17369 cd17369 340927 MFS_ShiA_like Shikimate transporter and similar proteins of the Major Facilitator Superfamily. This subfamily is composed of Escherichia coli shikimate transporter (ShiA), inner membrane metabolite transport protein YhjE, and other putative metabolite transporters. ShiA is involved in the uptake of shikimate, an aromatic compound involved in siderophore biosynthesis. It has been suggested that YhjE may mediate the uptake of osmoprotectants. The ShiA-like subfamily belongs to the Metazoan Synaptic Vesicle Glycoprotein 2 (SV2) and related small molecule transporter family (SV2-like) of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 408 matched cddid_all.tbl CDD cd17370 cd17370 340928 MFS_MJ1317_like MJ1317 and similar transporters of the Major Facilitator Superfamily. This family is composed of Methanocaldococcus jannaschii MFS-type transporter MJ1317, Mycobacterium bovis protein Mb2288, and similar proteins. They are uncharacterized transporters belonging to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 371 matched cddid_all.tbl CDD cd17371 cd17371 340929 MFS_MucK Cis,cis-muconate transport protein and similar proteins of the Major Facilitator Superfamily. This subfamily is composed of Acinetobacter sp. Cis,cis-muconate transport protein (MucK), Escherichia coli putative sialic acid transporter 1, and similar proteins. MucK functions in the uptake of muconate and allows Acinetobacter calcoaceticus ADP1 (BD413) to grow on exogenous cis,cis-muconate as the sole carbon source. The MucK subfamily belongs to the Metazoan Synaptic Vesicle Glycoprotein 2 (SV2) and related small molecule transporter family (SV2-like) of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 389 matched cddid_all.tbl CDD cd17372 cd17372 340930 MFS_SVOP_like Synaptic vesicle 2-related protein (SVOP) and related proteins of the Major Facilitator Superfamily. This subfamily is composed of synaptic vesicle 2 (SV2)-related protein (SVOP), SVOP-like protein (SVOPL), and similar proteins. SVOP is a transporter-like nucleotide binding protein that localizes to neurotransmitter-containing vesicles. Like SV2, SVOP is expressed in all brain regions, with highest levels in cerebellum, hindbrain and pineal gland. Studies with knockout mice suggets that SVOP may perform a subtle function that is not necessary for survival under normal conditions, since mice lacking SVOP are viable, fertile, and phenotypically normal. SVOP and SVOPL share structural similarity to the solute carrier family 22 (SLC22), a large family of organic cation and anion transporters. The SVOP-like subfamily belongs to the Metazoan Synaptic Vesicle Glycoprotein 2 (SV2) and related small molecule transporter family (SV2-like) of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 367 matched cddid_all.tbl CDD cd17373 cd17373 340931 MFS_SLC22A17_like Solute carrier family 22, member 17 and similar proteins of the Major Facilitator Superfamily. This group is composed of Solute carrier family 22, members 17, 23, and 31. They are members of the SLC22 family of organic cation/anion/zwitterion transporters, which includes organic cation transporters (OCTs/OCTNs) and organic anion transporters (OATs). SLC22A17 functions as a cell surface receptor for lipocalin-2 (LCN2), also called NGAL or 24p3, which plays a key role in iron homeostasis and transport. SLC22A23 and SLC22A31 are orphan members of the SLC22 family. SLC22 transporters interact with a variety of compounds that include drugs of abuse, environmental toxins, opioid analgesics, antidepressant and anxiolytic agents, and neurotransmitters and their metabolites. The SLC22A17-like group belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 348 matched cddid_all.tbl CDD cd17374 cd17374 340932 MFS_OAT Organic anion transporters of the Major Facilitator Superfamily of transporters. Organic anion transporters (OATs) generally display broad substrate specificity and they facilitate the exchange of extracellular with intracellular organic anions (OAs). Several OATs have been characterized including OAT1-10 and urate anion exchanger 1 (URAT1, also called SLC22A12). Many OATs occur in renal proximal tubules, the site of active drug secretion. OATs mediate the absorption, distribution, and excretion of a diverse array of environmental toxins, and clinically important drugs, including anti-HIV therapeutics, anti-tumor drugs, antibiotics, anti-hypertensives, and anti-inflammatories, and therefore is critical for the survival of the mammalian species. OAT falls into the SLC22 (solute carrier 22) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 341 matched cddid_all.tbl CDD cd17375 cd17375 340933 MFS_SLC22A16_CT2 Solute carrier family 22 member 16 (also called Carnitine transporter 2) of the Major Facilitator Superfamily of transporters. Solute carrier family 22 member 16 (SLC22A16) is also called carnitine transporter 2 (CT2), fly-like putative transporter 2 (FLIPT2), organic cation transporter OKB1, or organic cation/carnitine transporter 6 (OCT6). It is a partially sodium-ion dependent high affinity carnitine transporter. It also transports organic cations such as tetraethylammonium (TEA) and doxorubicin. It is one of several organic cation transporters (OCTs) that falls into the SLC22 (solute carrier 22) family. OCTs are broad-specificity transporters that play a critical role in the excretion and distribution of endogeneous organic cations and for the uptake, elimination and distribution of cationic drugs, toxins, and environmental waste products. SLC22A16 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 341 matched cddid_all.tbl CDD cd17376 cd17376 340934 MFS_SLC22A4_5_OCTN1_2 Solute carrier family 22 members 4 and 5 (also called Organic cation/carnitine transporters 1 and 2) of the Major Facilitator Superfamily of transporters. This subfamily is composed of solute carrier family 22 members 4 (SLC22A4) and 5 (SLC22A5), and similar proteins. SLC22A4 is also called ergothioneine transporter (ETT) or organic cation/carnitine transporter 1 (OCTN1). It is a sodium-ion dependent, low affinity carnitine transporter, and a highly specific transporter for the uptake of ergothioneine (ET), a thiolated derivative of histidine with antioxidant properties. ET is a natural compound produced only by certain fungi and bacteria and must be absorbed from the diet by humans and other vetebrates. SLC22A5, also called organic cation/carnitine transporter 2 (OCTN2), is a sodium-ion dependent, high affinity carnitine transporter involved in the active cellular uptake of carnitine. SLC22A4/5 belongs to the Solute carrier 22 (SLC22) family of organic cation/anion/zwitterion transporters of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 342 matched cddid_all.tbl CDD cd17377 cd17377 340935 MFS_SLC22A15 Solute carrier family 22 member 15 of the Major Facilitator Superfamily of transporters. Solute carrier family 22 member 15 (SLC22A15) is also called fly-like putative transporter 1 (FLIPT1). It is expressed at the highest levels in the kidney and brain. It is a member of the SLC22 family of transporters, which includes organic cation transporters (OCTs), organic zwitterion/cation transporters (OCTNs), and organic anion transporters (OATs). SLC22 transporters interact with a variety of compounds that include drugs of abuse, environmental toxins, opioid analgesics, antidepressant and anxiolytic agents, and neurotransmitters and their metabolites. SLC22A15 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 353 matched cddid_all.tbl CDD cd17378 cd17378 340936 MFS_OCT_plant Plant organic cation/carnitine transporters of the Major Facilitator Superfamily of transporters. Plant organic cation/carnitine transporters (OCTs) are sequence-similar to their animal counterparts, which are broad-specificity transporters that play a critical role in the excretion and distribution of endogeneous organic cations and for the uptake, elimination and distribution of cationic drugs, toxins, and environmental waste products. Little is know about plant OCTs. In Arabidopsis, there are six genes belonging to this family that show distinct, organ-specific expression pattern of the individual genes. AtOCT1 has been found to affect root development and carnitine-related responses in Arabidopsis. AtOCT4, 5 and 6 are up-regulated during drought stress, AtOCT3 and 5 during cold stress and AtOCT5 and 6 during salt stress treatments. Plant OCTs belongs to the Solute carrier 22 (SLC22) family of organic cation/anion/zwitterion transporters of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 342 matched cddid_all.tbl CDD cd17379 cd17379 340937 MFS_SLC22A1_2_3 Solute carrier family 22 members 1, 2, and 3 (also called Organic cation transporters 1, 2, and 3) of the Major Facilitator Superfamily of transporters. This sufamily includes solute carrier family 22 member 1 (SLC22A1, also called organic cation transporter 1 or OCT1), SLC22A2 (or OCT2), SLC22A3 (or OCT3), and similar proteins. OCT1-3 have similar basic functional properties: they are able to translocate a variety of structurally different organic cations in both directions across the plasma membrane; to translocate organic cations independently from sodium, chloride or proton gradients; and to function as electrogenic uniporters for cations or as electroneutral cation exchangers. They show overlapping but distinct substrate and inhibitor specificities, and different tissue expression pattern. In humans, OCT1 is strongly expressed in the liver, OCT2 is highly expressed in the kidney where it is localized at the basolateral membrane of renal proximal tubules, and OCT3 is most strongly expressed in skeletal muscle. OCTs are broad-specificity transporters that play a critical role in the excretion and distribution of endogeneous organic cations and for the uptake, elimination and distribution of cationic drugs, toxins, and environmental waste products. The SLC22A1-3 subfamily belongs to the Solute carrier 22 (SLC22) family of organic cation/anion/zwitterion transporters of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 340 matched cddid_all.tbl CDD cd17380 cd17380 340938 MFS_SLC17A9_like Solute carrier family 17 member 9 and similar proteins of the Major Facilitator Superfamily of transporters. This subfamily includes solute carrier family 17 member 9 (SLC17A9) and similar proteins including plant inorganic phosphate transporters (PHT4) that are also probably anion transporters. SLC17A9, also called vesicular nucleotide transporter (VNUT), is involved in vesicular storage and exocytosis of ATP. It facilitates the accumulation of ATP and other nucleotides in secretory vesicles such as adrenal chromaffin granules and synaptic vesicles. It also functions as a lysosomal ATP transporter and regulates cell viability. Plant PHT4 family transporters mediate the transport of inorganic phosphate and may also transport organic anions. The Arabidopsis protein AtPHT4;4 is a chloroplast-localized ascorbate transporter. PHT4 proteins show differential expression that suggests specialized functions. The SLC17A9-like subfamily belongs to the Solute carrier 17 (SLC17) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 361 matched cddid_all.tbl CDD cd17381 cd17381 340939 MFS_SLC17A5 Solute carrier family 17 member 5 (also called sialin) of the Major Facilitator Superfamily of transporters. Solute carrier family 17 member 5 (SLC17A5) is also called sialin, H(+)/nitrate cotransporter, H(+)/sialic acid cotransporter (AST), membrane glycoprotein HP59, or vesicular H(+)/aspartate-glutamate cotransporter. It transports glucuronic acid and free sialic acid out of the lysosome after its cleavage from sialoglycoconjugates, which is required for normal CNS myelination. It also mediates the membrane potential-dependent uptake of aspartate and glutamate into synaptic vesicles and synaptic-like microvesicles. In the plasma membrane, it functions as a nitrate transporter. Recessive mutations in the SLC17A5 gene cause the allelic disorders, Infantile sialic acid storage disease (ISSD) and Salla disease (a predominantly neurological disorder). SLC17A5 belongs to the Solute carrier 17 (SLC17) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 397 matched cddid_all.tbl CDD cd17382 cd17382 340940 MFS_SLC17A6_7_8_VGluT Solute carrier family 17 members 6, 7, and 8 (also called Vesicular glutamate transporters) of the Major Facilitator Superfamily of transporters. This subfamily is composed of solute carrier family 17 member 6 (SLC17A6), SLC17A7, SLC17A8, and similar proteins. SLC17A6 is also called vesicular glutamate transporter 2 (VGluT2), differentiation-associated BNPI, or differentiation-associated Na(+)-dependent inorganic phosphate cotransporter. SLC17A7 is also called VGluT1 or brain-specific Na(+)-dependent inorganic phosphate cotransporter. SLC17A8 is also called VGluT3. They mediate the uptake of glutamate into synaptic vesicles at presynaptic nerve terminals of excitatory neural cells, and may also mediate the transport of inorganic phosphate. VGluTs are also expressed and localized in various secretory vesicles in non-neuronal peripheral organelles such as hormone-containing secretory granules in endocrine cells, and thus, also act as metabolic regulators. The VGluT subfamily belongs to the Solute carrier 17 (SLC17) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 380 matched cddid_all.tbl CDD cd17383 cd17383 340941 MFS_SLC18A3_VAChT Vesicular acetylcholine transporter (VAChT) and similar transporters of the Major Facilitator Superfamily. Vesicular acetylcholine transporter (VAChT) is also called solute carrier family 18 member 3 (SLC18A3) in vertebrates and uncoordinated protein 17 (unc-17) in Caenorhabditis elegans. It is a glycoprotein involved in acetylcholine transport into synaptic vesicles and is responsible for the accumulation of acetylcholine into pre-synaptic vesicules of cholinergic neurons. Variants in SLC18A3 are associated with congenital myasthenic syndrome in humans. VAChT belongs to the bacterial MdtG-like and eukaryotic solute carrier 18 (SLC18) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 378 matched cddid_all.tbl CDD cd17384 cd17384 340942 MFS_SLC18A1_2_VAT1_2 Vesicular amine transporters 1 (VAT1) and 2 (VAT2), and similar transporters of the Major Facilitator Superfamily. Vesicular amine transporter 1 (VAT1 or VMAT1) is also called solute carrier family 18 member 1 (SLC18A1) or chromaffin granule amine transporter, while VAT2 (or VMAT2) is also called SLC18A2, synaptic vesicular amine transporter, or monoamine transporter. VATs (or VMATs) are responsible for the uptake of cytosolic monoamines into synaptic vesicles in monoaminergic neurons. VAT1 and VAT2 distinct pharmacological properties and tissue distributions. VAT1 is preferentially expressed in neuroendocrine cells and endocrine cells, where it transports biogenic monoamines, such as serotonin, from the cytoplasm into the secretory vesicles. VAT2 is primarily expressed in the CNS and is involved in the ATP-dependent vesicular transport of biogenic amine neurotransmitters including dopamine, norepinephrine, serotonin, and histamine into synaptic vesicles. VATs belong to the bacterial MdtG-like and eukaryotic solute carrier 18 (SLC18) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 373 matched cddid_all.tbl CDD cd17385 cd17385 340943 MFS_SLC18B1 Solute carrier family 18 member B1 of the Major Facilitator Superfamily of transporters. Solute carrier family 18 member B1 (SLC18B1) is the fourth member of the SLC18 transporter family, which includes vesicular monoamine transporters and vesicular acetylcholine transporter. It is predominantly expressed in the hippocampus and is associated with vesicles in astrocytes. It actively transports spermine and spermidine by exchange of H(+), and has been suggested to be a vesicular polyamine transporter (VPAT). SLC18B1 belongs to the bacterial MdtG-like and eukaryotic solute carrier 18 (SLC18) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 390 matched cddid_all.tbl CDD cd17386 cd17386 340944 MFS_SLC46 Solute carrier 46 (SLC46) family of the Major Facilitator Superfamily of transporters. The solute carrier 46 (SLC46) family is composed of three vertebrate members (SLC46A1, SLC46A2, and SLC46A3) and similar proteins from insects and nematodes. The best-studied member is SLC46A1, also called proton-coupled folate transporter (PCFT), which functions both as an intestinal proton-coupled high-affinity folate transporter involved in the absorption of folates and as an intestinal heme transporter which mediates heme uptake. SLC46A2, also called thymic stromal cotransporter protein (TSCOT), is a putative 12-transmembrane protein mainly expressed in the thymic cortex in a specific thymic epithelial cell (TEC) subpopulation. SLC46A3 is a lysosomal membrane protein that functions as a direct transporter of noncleavable antibody maytansine-based catabolites from the lysosome to the cytoplasm. The SLC46 family belongs to the Eukaryotic Solute carrier 46 (SLC46)/Bacterial Tetracycline resistance (TetA) -like (SLC46/TetA-like) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 360 matched cddid_all.tbl CDD cd17387 cd17387 340945 MFS_MFSD14 Major facilitator superfamily domain-containing 14A and 14B. This subfamily is composed of major facilitator superfamily domain-containing 14A (MFSD14A) and MFSD14B, and similar proteins. MFSD14A and MFSD14B are also called hippocampus abundant transcript 1 protein (HIAT1) and hippocampus abundant transcript-like protein 1 (HIATL1), respectively. They are both ubiquitously expressed with HIAT1 highly expressed intestis and HIATL1 most abundantly expressed in skeletal muscle. Gene disruption of MFSD14A causes globozoospermia and infertility in male mice. It has bee suggested that MFSD14A may transport a solute from the bloodstream that is required for spermiogenesis. The function of MFSD14B is unknown. The MFSD14 subfamily belongs to the Eukaryotic Solute carrier 46 (SLC46)/Bacterial Tetracycline resistance (TetA) -like (SLC46/TetA-like) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 410 matched cddid_all.tbl CDD cd17388 cd17388 340946 MFS_TetA Tetracycline resistance protein TetA and related proteins of the Major Facilitator Superfamily of transporters. This subfamily is composed of tetracycline resistance proteins similar to Escherichia coli TetA(A), TetA(B), and TetA(E), which are metal-tetracycline/H(+) antiporters that confer resistance to tetracycline by an active tetracycline efflux, which is an energy-dependent process that decreases the accumulation of the antibiotic in cells. TetA-like tetracycline resistance proteins belongs to the Eukaryotic Solute carrier 46 (SLC46)/Bacterial Tetracycline resistance (TetA) -like (SLC46/TetA-like) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 385 matched cddid_all.tbl CDD cd17389 cd17389 340947 MFS_MFSD10 Major facilitator superfamily domain-containing protein 10. Major facilitator superfamily domain-containing protein 10 (MFSD10) is also called tetracycline transporter-like protein (TETRAN). It is expressed in various human tissues, including the kidney. In cultured cells, its overexpression facilitated the uptake of organic anions such as some non-steroidal anti-inflammatory drugs (NSAIDs). MFSD10/TETRAN overexpression cause resistance to some NSAIDs, suggesting that it may be an organic anion transporter that serves as an efflux pump for some NSAIDs and various other organic anions at the final excretion step. MFSD10 belongs to the Eukaryotic Solute carrier 46 (SLC46)/Bacterial Tetracycline resistance (TetA) -like (SLC46/TetA-like) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 391 matched cddid_all.tbl CDD cd17390 cd17390 340948 MFS_MFSD9 Major facilitator superfamily domain-containing protein 9. Major facilitator superfamily domain-containing protein 9 (MFSD9) is expressed in the central nervous system (CNS) and in most peripheral tissues but at very low expression levels. The function of MFSD9 is unknown. MFSD9 belongs to the Eukaryotic Solute carrier 46 (SLC46)/Bacterial Tetracycline resistance (TetA) -like (SLC46/TetA-like) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 350 matched cddid_all.tbl CDD cd17391 cd17391 340949 MFS_MdtG_MDR_like Multidrug resistance protein MdtG and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily. This subfamily is composed of Escherichia coli multidrug resistance protein MdtG, Streptococcus pneumoniae multidrug resistance efflux pump PmrA, and similar multidrug resistance (MDR) transporters from bacteria. MDR transporters are drug/H+ antiporters (DHA) that mediate the efflux of a variety of drugs and toxic compounds, and confer resistance to these compounds. MdtG confers resistance to fosfomycin and deoxycholate. PmrA serves as an efflux pump for various substrates and is associated with fluoroquinolone resistance. MdtG-like MDR transporters belong to the bacterial MdtG-like and eukaryotic solute carrier 18 (SLC18) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 380 matched cddid_all.tbl CDD cd17392 cd17392 340950 MFS_MFSD2 Major facilitator superfamily domain-containing protein 2 subfamily. The major facilitator superfamily domain-containing protein 2 (MFSD2) subfamily is composed of two vertebrate members, MFSD2A amd MFSD2B. MFSD2A is more commonly called sodium-dependent lysophosphatidylcholine symporter 1 (NLS1). It is an LPC symporter that plays an essential role for blood-brain barrier formation and function. Inactivating mutations in MFSD2A cause a lethal microcephaly syndrome. MFSD2B is a potential risk or protect factor in the prognosis of lung adenocarcinoma. The MFSD2 subfamily belongs to the Salmonella enterica Na+/melibiose symporter like (MelB-like) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 446 matched cddid_all.tbl CDD cd17393 cd17393 340951 MFS_MosC_like Membrane protein MosC and similar proteins of the Major Facilitator Superfamily of transporters. The gene encoding Sinorhizobium meliloti membrane protein MosC is part of the mos locus, which encodes the biosynthesis of the rhizopine 3-O-methyl-scyllo-inosamine. MosC belongs to the bacterial fucose permease, eukaryotic Major facilitator superfamily domain-containing protein 4 (FucP/MFSD4) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 373 matched cddid_all.tbl CDD cd17394 cd17394 340952 MFS_FucP_like Fucose permease and similar proteins of the Major Facilitator Superfamily of transporters. This subfamily is composed of L-fucose permease (also called L-fucose-proton symporter) and similar proteins such as glucose/galactose transporter and N-acetyl glucosamine transporter NagP. L-fucose permease facilitates the uptake of L-fucose across the boundary membrane with the concomitant transport of protons into the cell; it can also transport L-galactose and D-arabinose. Glucose/galactose transporter functions in the uptake of of glucose and galactose. The FucP-like subfamily belongs to the bacterial fucose permease, eukaryotic Major facilitator superfamily domain-containing protein 4 (FucP/MFSD4) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 401 matched cddid_all.tbl CDD cd17395 cd17395 340953 MFS_MFSD4 Major facilitator superfamily domain-containing protein 4. The Major facilitator superfamily domain-containing protein 4 (MFSD4) subfamily consists of two vertebrate members: MFSD4A and MFSD4B. The function of MFSD4A is unknown. MFSD4B is more commonly know as sodium-dependent glucose transporter 1 (NaGLT1), a primary fructose transporter in rat renal brush-border membranes that also facilitates sodium-independent urea uptake. The MFSD4 subfamily belongs to the bacterial fucose permease, eukaryotic Major facilitator superfamily domain-containing protein 4 (FucP/MFSD4) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 367 matched cddid_all.tbl CDD cd17396 cd17396 340954 MFS_YdiM_like Inner membrane transport protein YdiM and similar proteins of the Major Facilitator Superfamily of transporters. This subfamily contains Escherichia coli inner membrane transport proteins YdiM and YdiN, which belong to the bacterial fucose permease, eukaryotic Major facilitator superfamily domain-containing protein 4 (FucP/MFSD4) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 384 matched cddid_all.tbl CDD cd17397 cd17397 340955 MFS_DIRC2 Disrupted in renal carcinoma protein 2 of the Major Facilitator Superfamily of transporters. Disrupted in renal carcinoma protein 2 or disrupted in renal cancer protein 2 (DIRC2), encoded by the SLC49A4 gene, was initially identified as a breakpoint-spanning gene in a chromosomal translocation associated with the development of renal cancer. It is an electrogenic lysosomal metabolite transporter that is regulated by limited proteolytic processing by cathepsin L. DIRC2 belongs to the Solute carrier 49 (SLC49) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 381 matched cddid_all.tbl CDD cd17398 cd17398 340956 MFS_FLVCR_like Feline leukemia virus subgroup C receptor subfamily of the Major Facilitator Superfamily of transporters. The Feline leukemia virus subgroup C receptor (FLVCR) subfamily is conserved in metazoans and is composed of two vertebrate members, FLVCR1 and FLVCR2. FLVCR1 is a heme transporter and it has two isoforms: 1 (or FLVCR1a), which exports cytoplasmic heme as well as coproporphyrin and protoporphyrin IX; and 2 (FLVCR1b), which promotes heme efflux from the mitochondrion to the cytoplasm. FLVCR2 functions as a heme importer as well as a transporter for a calcium-chelator complex that is important for growth and calcium metabolism. The FLVCR subfamily belongs to the Solute carrier 49 (SLC49) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 406 matched cddid_all.tbl CDD cd17399 cd17399 340957 MFS_MFSD7 Major facilitator superfamily domain-containing protein 7. Major facilitator superfamily domain-containing protein 7 (MFSD7) is also called myosin light polypeptide 5 regulatory protein (MYL5). It's function is unknown. It is encoded by the a SLC49A3 gene and is a member of the Solute carrier 49 (SLC49) family, which also includes feline leukemia virus subgroup C receptor 1 (FLVCR1, SLC49A1), FLVCR2 (SLC49A2), as well as disrupted in renal carcinoma protein 2 (DIRC2, SLC49A4). FLVCR1 and FLVCR2 are heme transporters. DIRC2 is an electrogenic lysosomal metabolite transporter that is regulated by limited proteolytic processing by cathepsin L. MFSD7 belongs to the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 419 matched cddid_all.tbl CDD cd17400 cd17400 340958 MFS_SLCO1_OATP1 Solute carrier organic anion transporter 1 family of the Major Facilitator Superfamily of transporters. The Solute carrier organic anion transporter 1 (SLCO1) or Organic anion transporting polypeptide 1 (OATP1) family contains three subfamilies: OATP1A, OATP1B, and OATP1C. OATP1A contains one human member, OATP1A2, which shows a broad spectrum of substrates including endogenous compounds (such as bile acids, steroid hormones and their conjugates, thyroid hormones) and various drugs (such as fexofenadine, ouabain and the cyanobacterial toxin microcystin). OATP1B contains two human proteins, OATP1B1 and OATP1B3, which can both accept a wide variety of structurally-unrelated compounds as substrates including clinically-important drugs such as hydroxymethylglutaryl (HMG)-CoA reductase inhibitors (statins), angiotensin II receptor blockers (sartans), angiotensin converting enzyme (ACE) inhibitors, and anti-diabetes drugs (glinides). OATP1C contains one mammalian member, OATP1C1, which is also called thyroxine transporter. It mediates the high affinity transport of the thyroid hormones, T4 (3,5,3',5'tetraiodo-L-thyronine or thyroxine), rT3 (3,3'5'-triiodo-L-thyronine), and T3 (3,5,3'tri-iodo-L-thyronine or triiodothyronine). The SLCO1/OATP1 family belongs to the Solute carrier organic anion transporter [SLCO, also called organic anion transporting polypeptides (OATPs) or Solute carrier family 21] family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 436 matched cddid_all.tbl CDD cd17401 cd17401 340959 MFS_SLCO2_OATP2 Solute carrier organic anion transporter 2 family of the Major Facilitator Superfamily of transporters. The Solute carrier organic anion transporter 2 (SLCO2) or Organic anion transporting polypeptide 2 (OATP2) family contains two subfamilies: OATP2A and OATP2B, each containing one mammalian member, OATP2A1 and OATP2B1, respectively. OATP2A1 (encoded by SLCO2A1) is a lactate/prostaglandin anion exchanger that mediates the release of newly synthesized prostaglandins (PGD2, PGE1, PGE2, PGF2A and PGI2) from cells, the transepithelial transport of prostaglandins, and the clearance of prostaglandins from the circulation. OATP2B1 (encoded by SLCO2B1) mediates the Na(+)-independent transport of various organic anions such as taurocholate, the prostaglandins PGD2, PGE1, PGE2, leukotriene C4, thromboxane B2 and iloprost, as well as endogenous sex steroid conjugates such as dehydroepiandrosterone sulfate (DHEAS). The SLCO2/OATP2 family belongs to the Solute carrier organic anion transporter [SLCO, also called organic anion transporting polypeptides (OATPs) or Solute carrier family 21] family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 440 matched cddid_all.tbl CDD cd17402 cd17402 340960 MFS_SLCO3_OATP3 Solute carrier organic anion transporter 3 family of the Major Facilitator Superfamily of transporters. The Solute carrier organic anion transporter 3 (SLCO3) or Organic anion transporting polypeptide 3 (OATP3) family contains only one subfamily, OATP3A, which contains only one mammalian member OATP3A1 (encoded by SLCO3A1). It mediates the Na(+)-independent transport of organic anions such as estrone-3-sulfate, prostaglandins (PG) E1 and E2, thyroxine (T4), deltorphin II, BQ-123, and vasopressin. SLCO3A1 has been identified as a Crohn's disease (CD)-associated gene, which mediates inflammatory processes in intestinal epithelial cells through NF-kappaB transcription activation, resulting in a higher incidence of bowel perforation in CD patients. The SLCO3/OATP3 family belongs to the Solute carrier organic anion transporter [SLCO, also called organic anion transporting polypeptides (OATPs) or Solute carrier family 21] family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 444 matched cddid_all.tbl CDD cd17403 cd17403 340961 MFS_SLCO4_OATP4 Solute carrier organic anion transporter 4 family of the Major Facilitator Superfamily of transporters. The Solute carrier organic anion transporter 4 (SLCO4) or Organic anion transporting polypeptide 4 (OATP4) family contains two families: OATP4A and OATP4C, each containing one mammalian member, OATP4A1 and OATP4C1, respectively. OATP4A1 (encoded by SLCO4A1), is ubiquitously expressed and mediates the Na(+)-independent transport of the thyroid hormones T3 (triiodo-L-thyronine), T4 (thyroxine) and rT3, and other organic anions such as estrone sulfate and taurocholate. OATP4C1 (encoded by SLCO4C1) is capable of transporting pharmacological substances such as digoxin, ouabain, thyroxine, methotrexate, cAMP, and uremic toxins, which accumulate in patients with chronic kidney diseases (CKDs). The SLCO4/OATP4 family belongs to the Solute carrier organic anion transporter [SLCO, also called organic anion transporting polypeptides (OATPs) or Solute carrier family 21] family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 420 matched cddid_all.tbl CDD cd17404 cd17404 340962 MFS_SLCO5_OATP5 Solute carrier organic anion transporter 5 family of the Major Facilitator Superfamily of transporters. The Solute carrier organic anion transporter 5 (SLCO5) or Organic anion transporting polypeptide 5 (OATP5) family contains only one subfamily, OATP5A, which contains only one mammalian member OATP5A1 (encoded by SLCO5A1). Deletion of the SLCO5A1 gene has been implicated in the pathogenesis of Mesomelia-synostoses syndrome (MSS), a rare autosomal-dominant disorder characterized by mesomelic limb shortening, acral synostoses, and multiple congenital malformations. OATP5A1 may be a non-classical OATP which is involved in biological processes that require the reorganization of the cell shape, such as differentiation and migration. It seems to affect intracellular transport of drugs and may participate in chemoresistance of small cell lung cancer (SCLC by sequestration), rather than mediating cellular uptake. The SLCO5/OATP5 family belongs to the Solute carrier organic anion transporter [SLCO, also called organic anion transporting polypeptides (OATPs) or Solute carrier family 21] family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 425 matched cddid_all.tbl CDD cd17405 cd17405 340963 MFS_SLCO6_OATP6 Solute carrier organic anion transporter 6 family of the Major Facilitator Superfamily of transporters. The Solute carrier organic anion transporter 6 (SLCO6) or Organic anion transporting polypeptide 6 (OATP6) family contains only one subfamily, OATP6A, which contains only one human member OATP6A1 (encoded by SLCO6A1). The OATP6 family is the most diverged of the OATPs. OATP6A1 is also called cancer/testis antigen 48 (CT48) or gonad-specific transporter. It is strongly expressed only in normal testis, and weakly in spleen, brain, fetal brain, and placenta. It is found in tumor samples (lung, bladder, and esophageal) and cancer cell lines (lung), and may be of potential use as a target for therapy for a variety of tumor types. The SLCO6/OATP6 family belongs to the Solute carrier organic anion transporter [SLCO, also called organic anion transporting polypeptides (OATPs) or Solute carrier family 21] family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 428 matched cddid_all.tbl CDD cd17406 cd17406 340964 MFS_unc93A_like Protein unc-93 homolog A and similar proteins of the Major Facilitator Superfamily of transporters. This subfamily is composed of Caenorhabditis elegans Uncoordinated protein 93 (also called putative potassium channel regulatory protein unc-93), human protein unc-93 homolog A (HmUnc-93A or UNC93A), and similar proteins. Unc-93 acts as a regulatory subunit of a multi-subunit potassium channel complex that may function in coordinating muscle contraction in C. elegans. The human UNC93A gene is located in a region of the genome that is frequently associated with ovarian cancer, however, there is no evidence that UNC93A has a tumor suppressor function. This unc93A-like subfamily belongs to the Unc-93 family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 390 matched cddid_all.tbl CDD cd17407 cd17407 340965 MFS_MFSD11 UNC93-like Major facilitator superfamily domain-containing protein 11. This group is composed of UNC93-like protein MFSD11 (also called major facilitator superfamily domain-containing protein 11 or protein ET) and similar proteins, most of which are uncharacterized. MFSD11 is ubiquitously expressed in the periphery and the central nervous system of mice, where it is expressed in excitatory and inhibitory mouse brain neurons. Its expression is affected by altered energy homeostasis, suggesting plausible involvement in the energy regulation. MFSD11 belongs to the Unc-93 family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 387 matched cddid_all.tbl CDD cd17408 cd17408 340966 MFS_unc93B1 Protein unc-93 homolog B1 of the Major Facilitator Superfamily of transporters. Protein unc-93 homolog B1 (UNC93B1) controls intracellular trafficking and transport of a subset of Toll-like receptors (TLRs), including TLR3, TLR7 and TLR9, from the endoplasmic reticulum to endolysosomes where they can engage pathogen nucleotides and activate signaling cascades. It regulates differential transport of TLR7 and TLR9 into signaling endosomes to prevent autoimmunity. UNC93B1 belongs to the Unc-93 family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 456 matched cddid_all.tbl CDD cd17409 cd17409 340967 MFS_NIMT_like 2-nitroimidazole transporter and similar proteins of the Major Facilitator Superfamily of transporters. This subfamily is composed of Escherichia coli 2-nitroimidazole transporter (NIMT), also called YeaN, and similar proteins. NIMT confers resistance to 2-nitroimidazole, the antibacterial and antifungal antibiotic, by mediating the active efflux of this compound. The NIMT-like subfamily belongs to the 2-nitroimidazole and cyanate transporters like (NIMT/CynX-like) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 374 matched cddid_all.tbl CDD cd17410 cd17410 340968 MFS_CynX_like Cyanate transport protein CynX and similar proteins of the Major Facilitator Superfamily of transporters. This subfamily is composed of Escherichia coli cyanate transport protein CynX and similar proteins. CynX is part of an active transport system that transports exogenous cyanate into E. coli cells. The gene encoding CynX is part of the cyn operon that also includes cynS, encoding cynase, which catalyzes the reaction of cyanate with bicarbonate to give ammonia and carbon dioxide, and cynT, which encodes a carbonic anhydrase. The CynX-like subfamily belongs to the 2-nitroimidazole and cyanate transporters like (NIMT/CynX-like) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 372 matched cddid_all.tbl CDD cd17411 cd17411 340969 MFS_SLC15A2 Solute carrier family 15 member 2 of the Major Facilitator Superfamily of transporters. Solute carrier family 15 member 2 (SLC15A2), also called peptide transporter 2 (PepT2), is a member of the proton-coupled oligopeptide transporter (POT) family of integral membrane proteins that mediate the cellular uptake of di/tripeptides and peptide-like drugs. SLC15A2, as well as SLC15A1, mediate the proton-coupled active transport of a broad range of dipeptides and tripeptides, including zwitterionic, anionic and cationic peptides, as well as a variety of peptide-like drugs such as cefadroxil, enalapril, and valacyclovir. SLC15A2 is a high-affinity transporter and is abundantly expressed in the apical membrane of kidney proximal tubules and choroid plexus epithelial cells. It is the major transporter involved in the reclamation of peptide-bound amino acids and peptide-like drugs in the kidney, and is also called the renal isoform. In choroid plexus and the brain, it acts as an efflux transporter and plays a role in regulating peptide/neuropeptide homeostasis. SLC15A2/PepT2 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 403 matched cddid_all.tbl CDD cd17412 cd17412 340970 MFS_SLC15A1 Solute Carrier family 15 member 1 of the Major Facilitator Superfamily of transporters. Solute carrier family 15 member 1 (SLC15A1), also called peptide transporter 1 (PepT1), is a member of the proton-coupled oligopeptide transporter (POT) family of integral membrane proteins that mediate the cellular uptake of di/tripeptides and peptide-like drugs. SLC15A1, as well as SLC15A2, mediate the proton-coupled active transport of a broad range of dipeptides and tripeptides, including zwitterionic, anionic and cationic peptides, as well as a variety of peptide-like drugs such as cefadroxil, enalapril, and valacyclovir. SLC15A1 is primarily expressed in the brush border membranes of enterocytes of the small intestine and is also known as the intestinal isoform. It is a high-capacity/low-affinity transporter that drives the transport of di-and tripeptides for metabolic purposes. It's expression is upregulated in the colon during chronic inflammation associated with inflammatory bowel disease. SLC15A1/PepT1 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 415 matched cddid_all.tbl CDD cd17413 cd17413 340971 MFS_NPF6 NRT1/PTR family (NPF), subfamily 6 of the Major Facilitator Superfamily of transporters. The plant Nitrate transporter 1/Peptide transporter (NRT1/PTR) family (NPF) is related to the POT (proton-coupled oligopeptide transporter), Peptide transporter (PepT/PTR), or Solute Carrier 15 (SLC15) family in animals. In contrast to related animal and bacterial counterparts, the plant proteins transport a wide variety of substrates including nitrate, peptides, amino acids, dicarboxylates, glucosinolates, as well as the plant hormones indole-3-acetic acid (IAA) and abscisic acid (ABA). A recent study identified eight subfamilies within this family, named NPF1-NPF8. NPF6 includes the first identified member of the NRT1/PTR family: Arabidopsis thaliana NRT1.1, now called AtNPF6.3. It is a dual affinity nitrate influx transporter and a nitrate sensor. It also transports auxin and has nitrate efflux activity. NPF6 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 457 matched cddid_all.tbl CDD cd17414 cd17414 340972 MFS_NPF4 NRT1/PTR family (NPF), subfamily 4 of the Major Facilitator Superfamily of transporters. The plant Nitrate transporter/Peptide transporter (NRT1/PTR) family (NPF) is related to the POT (proton-coupled oligopeptide transporter), Peptide transporter (PepT/PTR), or Solute Carrier 15 (SLC15) family in animals. In contrast to related animal and bacterial counterparts, the plant proteins transport a wide variety of substrates including nitrate, peptides, amino acids, dicarboxylates, glucosinolates, as well as the plant hormones indole-3-acetic acid (IAA) and abscisic acid (ABA). A recent study identified eight subfamilies within this family, named NPF1-NPF8. Members of the NPF4 subfamily have been shown to transport ABA. NPF4 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 456 matched cddid_all.tbl CDD cd17415 cd17415 340973 MFS_NPF3 NRT1/PTR family (NPF), subfamily 3 of the Major Facilitator Superfamily of transporters. The plant Nitrate transporter/Peptide transporter (NRT1/PTR) family (NPF) is related to the POT (proton-coupled oligopeptide transporter), Peptide transporter (PepT/PTR), or Solute Carrier 15 (SLC15) family in animals. In contrast to related animal and bacterial counterparts, the plant proteins transport a wide variety of substrates including nitrate, peptides, amino acids, dicarboxylates, glucosinolates, as well as the plant hormones indole-3-acetic acid (IAA) and abscisic acid (ABA). A recent study identified eight subfamilies within this family, named NPF1-NPF8. NPF3 is the smallest NPF subfamily and it includes Cucumis sativus nitrite transporter (CsNitr1), now named CsNPF3.2. It functions as a chloroplast nitrite uptake transporter to remove toxic nitrite from the cytosol. NPF3 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 448 matched cddid_all.tbl CDD cd17416 cd17416 340974 MFS_NPF1_2 NRT1/PTR family (NPF), subfamily 1 and 2 of the Major Facilitator Superfamily of transporters. The plant Nitrate transporter/Peptide transporter (NRT1/PTR) family (NPF) is related to the POT (proton-coupled oligopeptide transporter), Peptide transporter (PepT/PTR), or Solute Carrier 15 (SLC15) family in animals. In contrast to related animal and bacterial counterparts, the plant proteins transport a wide variety of substrates including nitrate, peptides, amino acids, dicarboxylates, glucosinolates, as well as the plant hormones indole-3-acetic acid (IAA) and abscisic acid (ABA). A recent study identified eight subfamilies within this family, named NPF1-NPF8. NPF1 includes Medicago truncatula LATD/NIP, now named MtNPF1.7, which is a high-affinity nitrate transporter and is involved in nodulation and root architecture. NPF2 members are well-established nitrate and glucosinolate transporters, including Arabidopsis nitrate influx and efflux transporters with varied tissue and developmental specificity. Examples are AtNPF2.7, which is expressed in the cortex of mature roots, and AtNPF2.9, which is expressed in root companion cells where it is involved in phloem loading. NPF1/2 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 444 matched cddid_all.tbl CDD cd17417 cd17417 340975 MFS_NPF5 NRT1/PTR family (NPF), subfamily 5 of the Major Facilitator Superfamily of transporters. The plant Nitrate transporter/Peptide transporter (NRT1/PTR) family (NPF) is related to the POT (proton-coupled oligopeptide transporter), Peptide transporter (PepT/PTR), or Solute Carrier 15 (SLC15) family in animals. In contrast to related animal and bacterial counterparts, the plant proteins transport a wide variety of substrates including nitrate, peptides, amino acids, dicarboxylates, glucosinolates, as well as the plant hormones indole-3-acetic acid (IAA) and abscisic acid (ABA). A recent study identified eight subfamilies within this family, named NPF1-NPF8. NPF5 includes Arabidopsis thaliana PTR3 (AtPTR3, now named AtNPF5.2), which is a wound-induced peptide transporter that is necessary for defense against virulent bacterial pathogens. NPF5 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 452 matched cddid_all.tbl CDD cd17418 cd17418 340976 MFS_NPF8 NRT1/PTR family (NPF), subfamily 8 of the Major Facilitator Superfamily of transporters. The plant Nitrate transporter/Peptide transporter (NRT1/PTR) family (NPF) is related to the POT (proton-coupled oligopeptide transporter), Peptide transporter (PepT/PTR), or Solute Carrier 15 (SLC15) family in animals. In contrast to related animal and bacterial counterparts, the plant proteins transport a wide variety of substrates including nitrate, peptides, amino acids, dicarboxylates, glucosinolates, as well as the plant hormones indole-3-acetic acid (IAA) and abscisic acid (ABA). A recent study identified eight subfamilies within this family, named NPF1-NPF8. NPF8 contains the Arabidopsis dipeptide transporters AtNPF8.1 (PTR1), AtNPF8.2 (PTR5), and AtNPF8.3 (PTR2), as well as tonoplast-localized transporters AtNPF8.4 (PTR4) and AtNPF8.5 (PTR6). Oryza sativa NRT1 (now called OsNPF8.9) is a low-affinity nitrate transporter. NPF8 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 447 matched cddid_all.tbl CDD cd17419 cd17419 340977 MFS_NPF7 NRT1/PTR family (NPF), subfamily 7 of the Major Facilitator Superfamily of transporters. The plant Nitrate transporter/Peptide transporter (NRT1/PTR) family (NPF) is related to the POT (proton-coupled oligopeptide transporter), Peptide transporter (PepT/PTR), or Solute Carrier 15 (SLC15) family in animals. In contrast to related animal and bacterial counterparts, the plant proteins transport a wide variety of substrates including nitrate, peptides, amino acids, dicarboxylates, glucosinolates, as well as the plant hormones indole-3-acetic acid (IAA) and abscisic acid (ABA). A recent study identified eight subfamilies within this family, named NPF1-NPF8. NPF7 includes the nitrate transporters AtNPF7.2 and AtNPF7.3, as well as the dipeptide transporter OsNPF7.3. AtNPF7.3 is a bidirectional transporter involved in nitrate influx and efflux. NPF7 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 447 matched cddid_all.tbl CDD cd17420 cd17420 340978 MFS_MCT8_10 Monocarboxylate transporters 8 and 10, and similar proteins of the Major Facilitator Superfamily of transporters. Monocarboxylate transporters 8 (MCT8) and 10 (MCT10) are transporters which stimulate the cellular uptake of thyroid hormones such as thyroxine (T4), triiodothyronine (T3), reverse triiodothyronine (rT3) and diidothyronine (T2). MCT has a preference for T3 and is also a sodium-independent transporter that mediates the uptake or efflux of aromatic acids such as Phe, Tyr, and Trp, as well as L-3,4-di-hydroxy-phenylalanine. MCT8/10 and similar proteins belong to the Monocarboxylate transporter (MCT) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 400 matched cddid_all.tbl CDD cd17421 cd17421 340979 MFS_MCT5 Monocarboxylate transporter 5 of the Major Facilitator Superfamily of transporters. Monocarboxylate transporter 5 (MCT5) is also called Solute carrier family 16 member 4 (SLC16A4). It is an orphan transporter expressed in the brain, muscle, liver, kidney, lung, ovary, placenta, and heart. It is a member of the monocarboxylate transporter (MCT) family, whose members include MCT1-4, which are proton-coupled transporters that facilitate the transport across the plasma membrane of monocarboxylates such as lactate, pyruvate, branched-chain oxo acids derived from leucine, valine and isoleucine, and ketone bodies such as acetoacetate, beta-hydroxybutyrate and acetate. MCT5 belongs to the Monocarboxylate transporter (MCT) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 369 matched cddid_all.tbl CDD cd17422 cd17422 340980 MFS_MCT7 Monocarboxylate transporter 7 of the Major Facilitator Superfamily of transporters. Monocarboxylate transporter 7 (MCT7) is also called Solute carrier family 16 member 6 (SLC16A6). Zebrafish MCT7 is required for hepatocyte secretion of ketone bodies during fasting; it has been shown to be a selective transporter of the major ketone body beta-hydroxybutyrate, whose abundance is increased during fasting. MCT7 is expressed in the brain, pancreas, muscle, and prostate. It belongs to the Monocarboxylate transporter (MCT) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 363 matched cddid_all.tbl CDD cd17423 cd17423 340981 MFS_MCT11_13 Monocarboxylate transporters 11 and 13 of the Major Facilitator Superfamily of transporters. Monocarboxylate transporters 11 (MCT11) and 13 (MCT13) are also called Solute carrier family 16 members 11 (SLC16A11) and 13 (SLC16A13), respectively. They are orphan transporters whose substrates are yet to be determined. MCT11 is expressed in skin, lung, ovary, breast, lung, pancreas, retinal pigment epithelium, and choroid plexus. Genetic variants in SLC16A11, the gene encoding MCT11, are associated with type 2 diabetes in Mexican and other Latin American populations. MCT13 is expressed in breast and bone marrow stem cells. MCT11/13 belongs to the Monocarboxylate transporter (MCT) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 383 matched cddid_all.tbl CDD cd17424 cd17424 340982 MFS_MCT12 Monocarboxylate transporter 12 of the of the Major Facilitator Superfamily of transporters. Monocarboxylate transporter 12 (MCT12) is also called Solute carrier family 16 member 12 (SLC16A12). It is a creatine transporter encoded by the cataract and glucosuria associated gene SLC16A12. A heterozygous mutation of the gene causes a syndrome with juvenile cataracts, microcornea, and glucosuria. MCT12 may function in a basolateral exit pathway for creatine in the proximal tubule. It belongs to the Monocarboxylate transporter (MCT) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 363 matched cddid_all.tbl CDD cd17425 cd17425 340983 MFS_MCT6 Monocarboxylate transporter 6 of the Major Facilitator Superfamily of transporters. Monocarboxylate transporter 6 (MCT6) is also called Solute carrier family 16 member 5 (SLC16A5). MCT6 has been shown to transport bumetanide, nateglinide, probenecid, and prostaglandin F2a, but not L-lactic acid, in a pH- and membrane potential-dependent manner. It may be involved in the disposition and absorption of various drugs. MCT6 is expressed in the kidney, muscle, brain, heart, pancreas, prostate, lung, and placenta. It belongs to the Monocarboxylate transporter (MCT) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 364 matched cddid_all.tbl CDD cd17426 cd17426 340984 MFS_MCT1 Monocarboxylate transporter 1 of the Major Facilitator Superfamily of transporters. Monocarboxylate transporter 1 (MCT1) is also called Solute carrier family 16 member 1 (SLC16A1). It is a proton-coupled transporter that facilitates the transport across the plasma membrane of monocarboxylates such as lactate, pyruvate, branched-chain oxo acids derived from leucine, valine and isoleucine, and ketone bodies such as acetoacetate, beta-hydroxybutyrate and acetate. It is widely expressed in many tissues its main function is to transport lactate into the cell. MCT1 deficiency has been identified as a cause of profound ketoacidosis, a potentially lethal condition caused by the imbalance between hepatic production and extrahepatic utilization of ketone bodies. This suggests that MCT1-mediated ketone-body transport is crucial in maintaining acid-base balance. MCT1 belongs to the Monocarboxylate transporter (MCT) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 374 matched cddid_all.tbl CDD cd17427 cd17427 340985 MFS_MCT2 Monocarboxylate transporter 2 of the Major Facilitator Superfamily of transporters. Monocarboxylate transporter 2 (MCT2) is also called Solute carrier family 16 member 7 (SLC16A7). It is a proton-coupled transporter that facilitates the transport across the plasma membrane of monocarboxylates such as lactate, pyruvate, branched-chain oxo acids derived from leucine, valine and isoleucine, and ketone bodies such as acetoacetate, beta-hydroxybutyrate and acetate. It transports pyruvate and lactate outside and inside of sperm and plays roles in the regulation of spermatogenesis. Genetic variation in MCT2 has functional and clinical relevance with male infertility. MCT2 is consistently overexpressed in prostate cancer (PCa) cells and its location at peroxisomes is associated with malignant transformation. MCT2 belongs to the Monocarboxylate transporter (MCT) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 367 matched cddid_all.tbl CDD cd17428 cd17428 340986 MFS_MCT9 Monocarboxylate transporter 9 of the Major Facilitator Superfamily of transporters. Monocarboxylate transporter 9 (MCT9) is also called Solute carrier family 16 member 9 (SLC16A9). It is an orphan transporter that is expressed in a number of tissues including intestine and kidney. A missense variant of MCT9 (K258T) is associated with significant increase in susceptibility to renal overload (ROL) gout with intestinal urate underexcretion. This suggests that MCT9 may have a role in intestinal urate excretion; it is possible that it transports urate. MCT9 belongs to the Monocarboxylate transporter (MCT) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 361 matched cddid_all.tbl CDD cd17429 cd17429 340987 MFS_MCT14 Monocarboxylate transporter 14 of the Major Facilitator Superfamily of transporters. Monocarboxylate transporter 14 (MCT14) is also called Solute carrier family 16 member 14 (SLC16A14). It is an orphan transporter expressed in the brain, heart, muscle, ovary, prostate, breast, lung, pancreas, liver, spleen, and thymus. It may function as a neuronal aromatic-amino-acid transporter. MCT14 belongs to the Monocarboxylate transporter (MCT) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 361 matched cddid_all.tbl CDD cd17430 cd17430 340988 MFS_MCT3_4 Monocarboxylate transporters 9 and 14, and similar proteins of the Major Facilitator Superfamily of transporters. Monocarboxylate transporters 3 (MCT3) and 4 (MCT4) are also called Solute carrier family 16 members 8 (SLC16A8) and 3 (SLC16A3), respectively. They are proton-coupled transporters that facilitate the transport across the plasma membrane of monocarboxylates such as lactate, pyruvate, branched-chain oxo acids derived from leucine, valine and isoleucine, and ketone bodies such as acetoacetate, beta-hydroxybutyrate and acetate. MCT3 is preferentially expressed in the basolateral membrane of the retinal pigment epithelium and plays a role in pH and ion homeostasis of the outer retina by facilitating the transport of lactate and H(+) out of the retina. Mice deficient with MCT3 display altered visual function. MCT4 is highly expressed in tissues dependent on glycolysis, and it plays an important role in lactate efflux from cells. MCT4 is expressed in neurons and astrocytes; it has been found to play a role in neuroprotective mechanism of ischemic preconditioning in animals (in the gerbil) with transient cerebral ischemia. Increased MCT4 expression has also been correlated with worse prognosis across many cancer types. MCT3/4 belongs to the Monocarboxylate transporter (MCT) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 368 matched cddid_all.tbl CDD cd17431 cd17431 340989 MFS_GLUT_Class1 Class 1 Glucose transporters (GLUTs) of the Major Facilitator Superfamily. GLUTs, also called Solute carrier family 2, facilitated glucose transporters (SLC2A), are a family of proteins that facilitate the transport of hexoses such as glucose and fructose. There are fourteen GLUTs found in humans; they display different substrate specificities and tissue expression. They have been categorized into three classes based on sequence similarity: Class 1 (GLUTs 1-4, 14); Class 2 (GLUTs 5, 7, 9, and 11); and Class 3 (GLUTs 6, 8, 10, 12, and HMIT). GLUTs 1-4 are well-established as glucose and/or fructose transporters in various tissues and cell types. GLUT1, also called solute carrier family 2, facilitated glucose transporter member 1 (SLC2A1), displays broad substrate specificity and can transport a wide range of pentoses and hexoses including glucose, galactose, mannose, and glucosamine. It is found in the brain, erythrocytes, and in many fetal tissues. GLUT2 (or SLC2A2) is found in the liver, islet of Langerhans, intestine, and kidney, and is the isoform that likely mediates the bidirectional transfer of glucose across the plasma membrane of hepatocytes and is responsible for uptake of glucose by beta cells. GLUT3 (or SLC2A3) is found in the brain and can mediates the uptake of glucose, 2-deoxyglucose, galactose, mannose, xylose and fucose, and dehydroascorbate. GLUT4 (or SLC2A4) is an insulin-regulated facilitative glucose transporter found in adipose tissues, and in skeletal and cardiac muscle. GLUT14 (or SLC2A14) is an orphan transporter expressed mainly in the testis. GLUT proteins are comprised of about 500 amino acid residues, possess a single N-linked oligosaccharide, and have 12 transmembrane segments. They belong to the Glucose transporter -like (GLUT-like) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 445 matched cddid_all.tbl CDD cd17432 cd17432 340990 MFS_GLUT_Class2 Class 2 Glucose transporters (GLUTs) of the Major Facilitator Superfamily. GLUTs, also called Solute carrier family 2, facilitated glucose transporters (SLC2A), are a family of proteins that facilitate the transport of hexoses such as glucose and fructose. There are fourteen GLUTs found in humans; they display different substrate specificities and tissue expression. They have been categorized into three classes based on sequence similarity: Class 1 (GLUTs 1-4, 14); Class 2 (GLUTs 5, 7, 9, and 11); and Class 3 (GLUTs 6, 8, 10, 12, and HMIT). GLUT5, also called Solute carrier family 2, facilitated glucose transporter member 5 (SLC2A5), is a well-established fructose transporter found in the small intestine. GLUT7 (or SLC2A7) is a high-affinity glucose and fructose transporter expressed in the small intestine and colon. GLUT9 (or SLC2A9) transports urate and fructose, and is most strongly expressed in the basolateral membranes of proximal renal tubular cells, liver and placenta. It may play a role in urate reabsorption by proximal tubules. GLUT11 (or SLC2A11) is a facilitative glucose transporter expressed in heart and skeletal muscle. GLUT proteins are comprised of about 500 amino acid residues, possess a single N-linked oligosaccharide, and have 12 transmembrane segments. They belong to the Glucose transporter -like (GLUT-like) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 452 matched cddid_all.tbl CDD cd17433 cd17433 340991 MFS_GLUT8_Class3 Glucose transporter type 8, a Class 3 GLUT, of the Major Facilitator Superfamily of transporters. Glucose transporter type 8 (GLUT8) is also called Solute carrier family 2, facilitated glucose transporter member 8 (SLC2A8) or glucose transporter type X1 (GLUTX1). It is classified as a Class 3 GLUT protein and is an insulin-regulated facilitative glucose transporter predominantly expressed in testis and brain. It can also transport fructose and galactose. SLC2A8 knockout mice were viable, developed normally, and display only a very mild phenotype, including mild alterations in the brain (increased proliferation of hippocampal neurons), heart (impaired transmission of electrical wave through the atrium), and sperm cells (reduced number of motile sperm cells). GLUT proteins are comprised of about 500 amino acid residues, possess a single N-linked oligosaccharide, and have 12 transmembrane segments. They belong to the Glucose transporter -like (GLUT-like) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 416 matched cddid_all.tbl CDD cd17434 cd17434 340992 MFS_GLUT6_Class3 Glucose transporter type 6, a Class 3 GLUT, of the Major Facilitator Superfamily of transporters. Glucose transporter type 6 (GLUT6) is also called Solute carrier family 2, facilitated glucose transporter member 6 (SLC2A6). It is classified as a Class 3 GLUT protein, and is a facilitative glucose transporter that binds cytochalasin B with low affinity. It is found in the brain, spleen, and leucocytes. GLUT6 may function in oxalate secretion. SLC2A6 has been identified as an oxalate nephrolithiasis gene in mice; its deletion causes spontaneous calcium oxalate nephrolithiasis in the setting of hyperoxalaemia, hyperoxaluria, and nephrocalcinosis. GLUT proteins are comprised of about 500 amino acid residues, possess a single N-linked oligosaccharide, and have 12 transmembrane segments. They belong to the Glucose transporter -like (GLUT-like) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 417 matched cddid_all.tbl CDD cd17435 cd17435 340993 MFS_GLUT12_Class3 Glucose transporter type 12 (GLUT12), a Class 3 GLUT, of the Major Facilitator Superfamily of transporters. Glucose transporter type 12 (GLUT12) is also called Solute carrier family 2, facilitated glucose transporter member 12 (SLC2A12). It is a facilitative glucose transporter, classified as a Class 3 GLUT, and is expressed in the heart, skeletal muscle, prostate, and small intestine, and is highly upregulated in breast ductal cell carcinoma. It plays a role as a secondary insulin-sensitive glucose transporter in insulin-dependent tissues. The GLUT12 subfamily belongs to the Glucose transporter -like (GLUT-like) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 376 matched cddid_all.tbl CDD cd17436 cd17436 340994 MFS_GLUT10_Class3 Glucose transporter type 10 (GLUT10), a Class 3 GLUT, of the Major Facilitator Superfamily of transporters. Glucose transporter type 10 (GLUT10) is also called Solute carrier family 2, facilitated glucose transporter member 10 (SLC2A10). It is classified as a Class 3 GLUT and is a facilitative glucose transporter that exhibits a wide tissue distribution. It is expressed in pancreas, placenta, heart, lung, liver, brain, fat, muscle, and kidney. GLUT10 facilitates the transport of dehydroascorbic acid (DHA), the oxidized form of vitamin C, into mitochondria, and also increases cellular uptake of DHA, which in turn protects cells against oxidative stress. Loss-of-function mutations in SLC2A10 cause arterial tortuosity syndrome (ATS), an autosomal recessive connective tissue disorder characterized by twisting and lengthening of the major arteries, hypermobility of the joints, and laxity of skin. The GLUT10 subfamily belongs to the Glucose transporter -like (GLUT-like) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 376 matched cddid_all.tbl CDD cd17437 cd17437 340995 MFS_PLT Plant Polyol transporter family of the Major Facilitator Superfamily of transporters. The plant Polyol transporter (PLT) subfamily includes PLT1-6 from Arabidopsis thaliana and similar transporters. The best characterized member of the group is Polyol transporter 5, also called Sugar-proton symporter PLT5, which mediates the H+-symport of numerous substrates including linear polyols (such as sorbitol, xylitol, erythritol or glycerol), cyclic polyol myo-inositol, and different hexoses, pentoses (including ribose), tetroses, and sugar alcohols. It functions to transport a wide range of substrates into specific sink tissues in the plant. The PLT subfamily belongs to the Glucose transporter -like (GLUT-like) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 387 matched cddid_all.tbl CDD cd17438 cd17438 340996 MFS_SV2B Synaptic vesicle glycoprotein 2B of the Major Facilitator Superfamily of transporters. Synaptic vesicle glycoprotein 2 (SV2) is a transporter-like integral membrane glycoprotein, with 12 transmembrane regions, expressed in vertebrates and is localized to synaptic and endocrine secretory vesicles. Three isoforms have been identified, SV2A, SV2B, and SV2C. SV2A and SV2B are widely expressed in the brain, while SV2C is more restricted to evolutionarily older brain. SV2 isoforms have been shown to be critical for the proper function of the central nervous system. SV2 serves as the receptor for botulinum neurotoxin A (BoNT/A), one of seven neurotoxins produced by the bacterium Clostridium botulinum. BoNT/A blocks neurotransmitter release by cleaving synaptosome-associated protein of 25 kD (SNAP-25) within presynaptic nerve terminals. SV2B is a key modulator of amyloid toxicity at the synaptic site and also has an essential role in the formation and maintenance of the glomerular capillary wall. SV2B belongs to the Metazoan Synaptic Vesicle Glycoprotein 2 (SV2) and related small molecule transporter family (SV2-like) of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 477 matched cddid_all.tbl CDD cd17439 cd17439 340997 MFS_SV2A Synaptic vesicle glycoprotein 2A of the Major Facilitator Superfamily of transporters. Synaptic vesicle glycoprotein 2 (SV2) is a transporter-like integral membrane glycoprotein, with 12 transmembrane regions, expressed in vertebrates and is localized to synaptic and endocrine secretory vesicles. Three isoforms have been identified, SV2A, SV2B, and SV2C. SV2A and SV2B are widely expressed in the brain, while SV2C is more restricted to evolutionarily older brain. SV2 isoforms have been shown to be critical for the proper function of the central nervous system. SV2 serves as the receptor for botulinum neurotoxin A (BoNT/A), one of seven neurotoxins produced by the bacterium Clostridium botulinum. BoNT/A blocks neurotransmitter release by cleaving synaptosome-associated protein of 25 kD (SNAP-25) within presynaptic nerve terminals. It is unclear how SV2A is involved in correct SV function, but it has been suggested to either act as a transporter or a regulator of exocytosis by mediating Ca2+ dynamics. SV2A has been identified as the molecular target of the antiepileptic drug levetiracetam (LEV). Its expression is decreased in patients with epilepsy and in epileptic animal models. SV2A belongs to the Metazoan Synaptic Vesicle Glycoprotein 2 (SV2) and related small molecule transporter family (SV2-like) of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 478 matched cddid_all.tbl CDD cd17440 cd17440 340998 MFS_SV2C Synaptic vesicle glycoprotein 2C of the Major Facilitator Superfamily of transporters. Synaptic vesicle glycoprotein 2 (SV2) is a transporter-like integral membrane glycoprotein, with 12 transmembrane regions, expressed in vertebrates and is localized to synaptic and endocrine secretory vesicles. Three isoforms have been identified, SV2A, SV2B, and SV2C. SV2A and SV2B are widely expressed in the brain, while SV2C is more restricted to evolutionarily older brain. SV2 isoforms have been shown to be critical for the proper function of the central nervous system. SV2 serves as the receptor for botulinum neurotoxin A (BoNT/A), one of seven neurotoxins produced by the bacterium Clostridium botulinum. BoNT/A blocks neurotransmitter release by cleaving synaptosome-associated protein of 25 kD (SNAP-25) within presynaptic nerve terminals. SV2C exhibits enriched expression in several basal ganglia nuclei, and has been found to be involved in normal operation of the basal ganglia network and could be also be involved in system adaptation in basal ganglia pathological conditions. SV2C belongs to the Metazoan Synaptic Vesicle Glycoprotein 2 (SV2) and related small molecule transporter family (SV2-like) of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 479 matched cddid_all.tbl CDD cd17441 cd17441 340999 MFS_SVOP Synaptic vesicle 2-related protein (SVOP) of the Major Facilitator Superfamily. Synaptic vesicle 2 (SV2)-related protein (SVOP) is a transporter-like nucleotide binding protein that localizes to neurotransmitter-containing vesicles. Like SV2, SVOP is expressed in all brain regions, with highest levels in cerebellum, hindbrain and pineal gland. Studies with knockout mice suggets that SVOP may perform a subtle function that is not necessary for survival under normal conditions, since mice lacking SVOP are viable, fertile, and phenotypically normal. SVOP shares structural similarity to the solute carrier family 22 (SLC22), a large family of organic cation and anion transporters. This SVOP subfamily belongs to the Metazoan Synaptic Vesicle Glycoprotein 2 (SV2) and related small molecule transporter family (SV2-like) of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 372 matched cddid_all.tbl CDD cd17442 cd17442 341000 MFS_SVOPL Synaptic vesicle 2 (SV2)-related protein-like (SVOPL) of the Major Facilitator Superfamily. Synaptic vesicle 2 (SV2)-related protein-like (SVOPL) or SVOP-like protein is a transporter-like protein that shares structural similarity to the solute carrier family 22 (SLC22), a large family of organic cation and anion transporters. It belongs to the Metazoan Synaptic Vesicle Glycoprotein 2 (SV2) and related small molecule transporter family (SV2-like) of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 375 matched cddid_all.tbl CDD cd17443 cd17443 341001 MFS_SLC22A31 Solute carrier family 22, member 31 of the Major Facilitator Superfamily. Solute carrier family 22, member 31 (SLC22A31) is an uncharacterized member of the SLC22 family of transporters, which includes organic cation transporters (OCTs), organic zwitterion/cation transporters (OCTNs), and organic anion transporters (OATs). SLC22 transporters interact with a variety of compounds that include drugs of abuse, environmental toxins, opioid analgesics, antidepressant and anxiolytic agents, and neurotransmitters and their metabolites. SLC22A31 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 343 matched cddid_all.tbl CDD cd17444 cd17444 341002 MFS_SLC22A23 Solute carrier family 22, member 23 of the Major Facilitator Superfamily. Solute carrier family 22, member 23 (SLC22A23) is an orphan member of the SLC22 family of organic cation/anion/zwitterion transporters, which includes organic cation transporters (OCTs/OCTNs) and organic anion transporters (OATs). It is abundantly expressed in brain and is also found in liver. Single-nucleotide polymorphisms in SLC22A23 are associated with inflammatory bowel disease (IBD) in a Canadian white population. SLC22 transporters interact with a variety of compounds that include drugs of abuse, environmental toxins, opioid analgesics, antidepressant and anxiolytic agents, and neurotransmitters and their metabolites. SLC22A23 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 364 matched cddid_all.tbl CDD cd17445 cd17445 341003 MFS_SLC22A17 Solute carrier family 22, member 17 of the Major Facilitator Superfamily. Solute carrier family 22, member 17 (SLC22A17) is also called 24p3 receptor (24p3R), lipocalin-2 receptor, or neutrophil gelatinase-associated lipocalin (NGAL) receptor (NGALR). It functions as a cell surface receptor for lipocalin-2 (LCN2), also called NGAL or 24p3, which plays a key role in iron homeostasis and transport. LCN2 is a secreted protein of the lipocalin family that induces apoptosis in some types of cells and inhibits bacterial growth by sequestration of the iron-laden bacterial siderophore. Over-expressions of NGAL and NGALR have been found to be correlated with unfavorable clinicopathologic features and poor prognosis of patients with hepatocellular carcinoma. SLC22A17 is a member of the SLC22 family of organic cation/anion/zwitterion transporters, which includes organic cation transporters (OCTs/OCTNs) and organic anion transporters (OATs). It belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 346 matched cddid_all.tbl CDD cd17446 cd17446 341004 MFS_SLC22A6_OAT1_like Solute carrier family 22 member 6 (also called Organic anion transporter 1) and similar transporters of the Major Facilitator Superfamily. This subfamily includes solute carrier family 22 member 6 (SLC22A6, also called organic anion transporter 1 or OAT1 or para-aminohippurate (PAH) transporter), SLC22A8 (or OAT3), and SLC22A20 (or OAT6). OAT1 and OAT3 are involved in the renal elimination of endogenous and exogenous organic anions (OAs). They function as OA exchangers, coupling the uptake of OAs against an electrochemical gradient with the efflux of intracellular dicarboxylates. SLC22A20 is an OA transporter that mediates the uptake of estrone sulfate. The OAT1-like subfamily belongs to the Solute carrier 22 (SLC22) family of organic cation/anion/zwitterion transporters of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 339 matched cddid_all.tbl CDD cd17447 cd17447 341005 MFS_SLC22A7_OAT2 Solute carrier family 22 member 7 (also called Organic anion transporter 2) of the Major Facilitator Superfamily of transporters. Solute carrier family 22 member 7 (SLC22A7), also called organic anion transporter 2 (OAT2) mediates sodium-independent transport of a variety of organic anions including prostaglandin E2, prostaglandin F2, tetracycline, bumetanide, estrone sulfate, glutarate, dehydroepiandrosterone sulfate, allopurinol, 5-fluorouracil, paclitaxel, L-ascorbic acid, salicylate, ethotrexate, and alpha-ketoglutarate. It also plays a role in renal uric acid uptake from blood as a first step of tubular secretion. OAT2 belongs to the Solute carrier 22 (SLC22) family of organic cation/anion/zwitterion transporters of the Major Facilitator Superfamily (MFS)of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 341 matched cddid_all.tbl CDD cd17448 cd17448 341006 MFS_SLC46A3 Solute carrier family 46 member 3 of the Major Facilitator Superfamily of transporters. Solute carrier family 46 member 3 (SLC46A3) is a lysosomal membrane protein that functions as a direct transporter of noncleavable antibody maytansine-based catabolites from the lysosome to the cytoplasm. SLC46A3 belongs to the Eukaryotic Solute carrier 46 (SLC46)/Bacterial Tetracycline resistance (TetA) -like (SLC46/TetA-like) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 396 matched cddid_all.tbl CDD cd17449 cd17449 341007 MFS_SLC46A1_PCFT "Solute carrier family 46 member 1, also called Proton-coupled folate transporter, of the Major Facilitator Superfamily of transporters. Solute carrier family 46 member 1 (SLC46A1) is also called proton-coupled folate transporter (PCFT), G21, or heme carrier protein 1 (HCP1). It functions in two ways: as an intestinal proton-coupled high-affinity folate transporter that facilitates the absorption of folates across the brush-border membrane of the small intestine; and as an intestinal heme transporter which mediates heme uptake from the gut lumen into duodenal epithelial cells. It displays a higher affinity for folate than heme. It is also expressed in the choroid plexus and is required for transport of folates into the cerebrospinal fluid. Loss of function mutations in the SLC46A1 gene results in the autosomal recessive disorder ""hereditary folate malabsorption"" (HFM), characterized by severe systemic and cerebral folate deficiency. SLC46A1 belongs to the Eukaryotic Solute carrier 46 (SLC46)/Bacterial Tetracycline resistance (TetA) -like (SLC46/TetA-like) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement." 425 matched cddid_all.tbl CDD cd17450 cd17450 341008 MFS_SLC46A2_TSCOT Solute carrier family 46 member 2, also called Thymic stromal cotransporter protein, of the Major Facilitator Superfamily of transporters. Solute carrier family 46 member 2 (SLC46A2) is also called thymic stromal cotransporter protein (TSCOT). It is a putative 12-transmembrane protein mainly expressed in the thymic cortex in a specific thymic epithelial cell (TEC) subpopulation. Polymorphisms in TSCOT are linked to cervical cancer in affected sib-pairs with high mean age at diagnosis. TSCOT belongs to the Eukaryotic Solute carrier 46 (SLC46)/Bacterial Tetracycline resistance (TetA) -like (SLC46/TetA-like) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 383 matched cddid_all.tbl CDD cd17451 cd17451 341009 MFS_NLS1_MFSD2A Sodium-dependent lysophosphatidylcholine symporter 1 of the Major Facilitator Superfamily of transporters. Sodium-dependent lysophosphatidylcholine (LPC) symporter 1 (NLS1) is also called major facilitator superfamily domain-containing protein 2A (MFSD2A). NLS1/MFSD2A is an LPC symporter that plays an essential role for blood-brain barrier formation and function. It also transports the essential omega-3 fatty acid docosahexaenoic acid (DHA), which is essential for normal brain growth and cognitive function, in the form of LPC into the brain across the blood-brain barrier. Inactivating mutations in MFSD2A cause a lethal microcephaly syndrome. NLS1/MFSD2A belongs to the Salmonella enterica Na+/melibiose symporter like (MelB-like) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 419 matched cddid_all.tbl CDD cd17452 cd17452 341010 MFS_MFSD2B Major facilitator superfamily domain-containing protein 2B. Major facilitator superfamily domain-containing protein 2B (MFSD2B) is closely related to MFSD2A, and their conserved genomic structure suggests that they are derived from the duplication of an ancestral gene. Variations of chromosome 2 gene expressions among patients with lung cancer or non-cancer identified MFSD2B as a potential risk or protect factor in the prognosis of lung adenocarcinoma. MFSD2B belongs to the Salmonella enterica Na+/melibiose symporter like (MelB-like) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 416 matched cddid_all.tbl CDD cd17453 cd17453 341011 MFS_MFSD4A Major facilitator superfamily domain-containing protein 4A. Major facilitator superfamily domain-containing protein 4A (MFSD4A) belongs to the bacterial fucose permease, eukaryotic Major facilitator superfamily domain-containing protein 4 (FucP/MFSD4) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 415 matched cddid_all.tbl CDD cd17454 cd17454 341012 MFS_NaGLT1_MFSD4B Sodium-dependent glucose transporter 1, also called Major facilitator superfamily domain-containing protein 4B. Sodium-dependent glucose transporter 1 (NaGLT1) is also called major facilitator superfamily domain-containing protein 4B (MFSD4B). NaGLT1 is a primary fructose transporter in rat renal brush-border membranes. It also facilitates sodium-independent urea uptake in assays performed on Xenopus oocytes. NaGLT1/MFSD4B belongs to the bacterial fucose permease, eukaryotic Major facilitator superfamily domain-containing protein 4 (FucP/MFSD4) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 369 matched cddid_all.tbl CDD cd17455 cd17455 341013 MFS_FLVCR1 Feline leukemia virus subgroup C receptor-related protein 1 of the Major Facilitator Superfamily of transporters. Feline leukemia virus subgroup C receptor-related protein 1 (FLVCR1) is also called feline leukemia virus subgroup C receptor (FLVCR). FLVCR1 is a heme transporter and it has two isoforms: 1 (or FLVCR1a), which exports cytoplasmic heme as well as coproporphyrin and protoporphyrin IX; and 2 (FLVCR1b), which promotes heme efflux from the mitochondrion to the cytoplasm. Mutations in the FLVCR1 gene have been linked to vision impairment, posterior column ataxia, and sensory neurodegeneration with loss of pain perception. FLVCR1 belongs to the Solute carrier 49 (SLC49) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 407 matched cddid_all.tbl CDD cd17456 cd17456 341014 MFS_FLVCR2 Feline leukemia virus subgroup C receptor-related protein 2 of the Major Facilitator Superfamily of transporters. Feline leukemia virus subgroup C receptor-related protein 2 (FLVCR2) is also called calcium-chelate transporter (CCT). It functions as a heme importer as well as a transporter for a calcium-chelator complex that is important for growth and calcium metabolism. Mutations in the FLVCR2 gene cause Proliferative vasculopathy and hydranencephaly-hydrocephaly syndrome (PVHH), also known as Fowler syndrome, a rare autosomal recessive disorder characterized by glomerular vasculopathy in the central nervous system, severe hydrocephaly, hypokinesia and arthrogryphosis. FLVCR2 belongs to the Solute carrier 49 (SLC49) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 406 matched cddid_all.tbl CDD cd17457 cd17457 341015 MFS_SLCO1B_OATP1B Solute carrier organic anion transporter 1B subfamily of the Major Facilitator Superfamily of transporters. The Solute carrier organic anion transporter 1B (SLCO1B), also called organic anion-transporting polypeptide 1B (OATP1B), subfamily is composed of two human proteins, OATP1B1 (encoded by SLCO1B1) and OATP1B3 (encoded by SLCO1B3), and one rodent member, OATP1B2 (encoded by Slco1b2). OATP1B1 and OATP1B3 are almost exclusively expressed on the basal side of hepatocytes in normal human organs. They both can accept a wide variety of structurally-unrelated compounds as substrates including clinically-important drugs such as hydroxymethylglutaryl (HMG)-CoA reductase inhibitors (statins), angiotensin II receptor blockers (sartans), angiotensin converting enzyme (ACE) inhibitors, and anti-diabetes drugs (glinides). Loss-of-function mutations in both SLCO1B1 and SLCO1B3 genes result in the Rotor syndrome, a hereditary hyperbilirubinemia. The SLCO1B/OATP1B subfamily belongs to the Solute carrier organic anion transporter [SLCO, also called organic anion transporting polypeptides (OATPs) or Solute carrier family 21] family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 455 matched cddid_all.tbl CDD cd17458 cd17458 341016 MFS_SLCO1A_OATP1A Solute carrier organic anion transporter 1A subfamily of the Major Facilitator Superfamily of transporters. The Solute carrier organic anion transporter 1A (SLCO1A), also called Organic anion-transporting polypeptide 1A (OATP1A), subfamily is composed of one human member OATP1A2 (encoded by SLCO1A2) and several rodent proteins encoded by the Slco1a1, Slco1a3, Slco1a4, Slco1a5, and Slco1a6 genes. OATP1A2, also known as human OATP-A or OATP1, shows a broad spectrum of substrates including endogenous compounds (such as bile acids, steroid hormones and their conjugates, thyroid hormones) and various drugs (such as fexofenadine, ouabain and the cyanobacterial toxin microcystin). It is expressed in the brain, kidney, intestine, liver, lung, testes, and the eye (ciliary body). The SLCO1A/OATP1A subfamily belongs to the Solute carrier organic anion transporter [SLCO, also called organic anion transporting polypeptides (OATPs) or Solute carrier family 21] family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 527 matched cddid_all.tbl CDD cd17459 cd17459 341017 MFS_SLCO1C_OATP1C Solute carrier organic anion transporter 1C subfamily of the Major Facilitator Superfamily of transporters. The Solute carrier organic anion transporter 1C (SLCO1C), also called Organic anion-transporting polypeptide 1C (OATP1C), subfamily contains one mammalian member, OATP1C1 (encoded by SLCO1C1), which is also called thyroxine transporter. It mediates the high affinity transport of the thyroid hormones, T4 (3,5,3',5'tetraiodo-L-thyronine or thyroxine), rT3 (3,3'5'-triiodo-L-thyronine), and T3 (3,5,3'tri-iodo-L-thyronine or triiodothyronine), as well as organic anions such as 17-beta-glucuronosyl estradiol, estrone-3-sulfate, and sulfobromophthalein (BSP), which are transported with much lower efficiency. The SLCO1C/OATP1C subfamily belongs to the Solute carrier organic anion transporter [SLCO, also called organic anion transporting polypeptides (OATPs) or Solute carrier family 21] family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 498 matched cddid_all.tbl CDD cd17460 cd17460 341018 MFS_SLCO2B_OATP2B Solute carrier organic anion transporter 2B subfamily of the Major Facilitator Superfamily of transporters. The Solute carrier organic anion transporter 2B (SLCO2B), also called Organic anion-transporting polypeptide 2B (OATP2B), subfamily has one mammalian member, OATP2B1 (encoded by SLCO2B1). It mediates the Na(+)-independent transport of various organic anions such as taurocholate, the prostaglandins PGD2, PGE1, PGE2, leukotriene C4, thromboxane B2 and iloprost. It also mediates the transport of endogenous sex steroid conjugates such as dehydroepiandrosterone sulfate (DHEAS). SLCO2B1 variations result in differential expression and uptake of DHEAS, which impacts subsequent resistance to androgen-deprivation therapy (ADT), the primary treatment of metastatic prostate cancer. The SLCO2B/OATP2B subfamily belongs to the Solute carrier organic anion transporter [SLCO, also called organic anion transporting polypeptides (OATPs) or Solute carrier family 21] family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 479 matched cddid_all.tbl CDD cd17461 cd17461 341019 MFS_SLCO2A_OATP2A Solute carrier organic anion transporter 2A subfamily of the Major Facilitator Superfamily of transporters. The Solute carrier organic anion transporter 2A (SLCO2A), also called Organic anion-transporting polypeptide 2A (OATP2A), subfamily has one mammalian member, OATP2A1 (encoded by SLCO2A1), which is also called prostaglandin transporter. It is a lactate/prostaglandin anion exchanger that mediates the release of newly synthesized prostaglandins (PGD2, PGE1, PGE2, PGF2A and PGI2) from cells, the transepithelial transport of prostaglandins, and the clearance of prostaglandins from the circulation. Mutations in SLCO2A1 can cause primary hypertrophic osteoarthropathy (PHO), a rare multi-organic disease characterized by digital clubbing, pachydermia and periosteal reaction. The SLCO2A/OATP2A subfamily belongs to the Solute carrier organic anion transporter [SLCO, also called organic anion transporting polypeptides (OATPs) or Solute carrier family 21] family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 474 matched cddid_all.tbl CDD cd17462 cd17462 341020 MFS_SLCO4A_OATP4A Solute carrier organic anion transporter 4A subfamily of the Major Facilitator Superfamily of transporters. The Solute carrier organic anion transporter 4A (SLCO4A), also called Organic anion-transporting polypeptide 4A (OATP4A), subfamily has one mammalian member, OATP4A1 (encoded by SLCO4A1). It is ubiquitously expressed and it mediates the Na(+)-independent transport of the thyroid hormones T3 (triiodo-L-thyronine), T4 (thyroxine) and rT3, and other organic anions such as estrone sulfate and taurocholate. OATP4A1 is the most abundantly expressed transporter colorectal cancer (CRC) and its role in the transport of estrone sulfate, which is used in hormone replacement therapy (HRT), affects the outcome of the treatment. The SLCO4A/OATP4A subfamily belongs to the Solute carrier organic anion transporter [SLCO, also called organic anion transporting polypeptides (OATPs) or Solute carrier family 21] family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 427 matched cddid_all.tbl CDD cd17463 cd17463 341021 MFS_SLCO4C_OATP4C Solute carrier organic anion transporter 4C subfamily of the Major Facilitator Superfamily of transporters. The Solute carrier organic anion transporter 4C (SLCO4C), also called Organic anion-transporting polypeptide 4C (OATP4C), subfamily has one mammalian member, OATP4C1 (encoded by SLCO4C1). It is capable of transporting pharmacological substances such as digoxin, ouabain, thyroxine, methotrexate and cAMP. It is the only OATP expressed at the basolateral side of proximal tubular cells in human kidney and it mediates the excretion of uremic toxins, which accumulate in patients with chronic kidney diseases (CKDs) and cause further progression of renal damage and cardiovascular diseases. Overexpression of human SLCO4C1 in rat kidney promotes the renal excretion of uremic toxins and reduces hypertension, cardiomegaly, and renal inflammation in renal failure. The SLCO4C/OATP4C subfamily belongs to the Solute carrier organic anion transporter [SLCO, also called organic anion transporting polypeptides (OATPs) or Solute carrier family 21] family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 429 matched cddid_all.tbl CDD cd17464 cd17464 341022 MFS_MCT10 Monocarboxylate transporter 10 of the Major Facilitator Superfamily of transporters. Monocarboxylate transporter 10 (MCT10) is also called Solute carrier family 16 member 10 (SLC16A10). In addition, human MCT10 is also called T-type amino acid transporter 1 (TAT1). MCT10 is a sodium-independent transporter that mediates the uptake or efflux of aromatic acids such as Phe, Tyr, and Trp, as well as L-3,4-di-hydroxy-phenylalanine. It is also a thyroid hormone transporter with preference for triiodothyronine (T3). MCT10 is expressed in intestine, kidney, liver, muscle, and placenta, and appears predominantly localized in the basolateral membrane. It belongs to the Monocarboxylate transporter (MCT) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 395 matched cddid_all.tbl CDD cd17465 cd17465 341023 MFS_MCT8 Monocarboxylate transporter 8 of the Major Facilitator Superfamily of transporters. Monocarboxylate transporter 8 (MCT8) is also called Solute carrier family 16 member 2 (SLC16A2) or X-linked PEST-containing transporter. MCT8 is a very active and specific thyroid hormone transporter which stimulates the cellular uptake of thyroxine (T4), triiodothyronine (T3), reverse triiodothyronine (rT3) and diidothyronine (T2). Inactivating mutations in SLC16A2, the gene that encodes MCT8, lead to an X-linked syndrome with severe neurological impairment known as Allan-Herndon-Dudley syndrome (AHDS). AHDS is characterized by congenital hypotonia that progresses to spasticity with severe psychomotor delays, spastic paraplegia and dystonic movements, global developmental delay, and profound intellectual disability. MCT8 belongs to the Monocarboxylate transporter (MCT) family of the Major Facilitator Superfamily (MFS) of membrane transport proteins. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 367 matched cddid_all.tbl CDD cd17466 cd17466 350654 T3SS_Flik_C_like C-terminal domain of type III secretion proteins FliK, HrpP, YscP, and similar domains. Type III secretion systems (T3SS) are essential components of two complex bacterial machineries: the flagellum, which drives cell motility, and the non-flagellar T3SS, which delivers effectors into eukaryotic cells. This model represents the C-terminal domain of T3SS proteins such as the flagellar hook-length control protein FliK, and non-flagellar Yop proteins translocation protein P (YscP) and HrpP. FliK is responsible for switching secretion from the hook protein to that of the filament protein, by interacting with FlhB, the switchable secretion gate. HrpP is a type III secretion system substrate specificity switch-domain protein that is required for the export of pathogenicity factors into plant cells by pathogens. YscP is a needle-length sensing protein that controls the needle length of the injectisome, which is used by pathogenic bacteria to inject effector proteins across eukaryotic cell membranes. FliK, YscP, and HrpP contain a C-terminal globular domain that is necessary for the hierarchical switching of substrates during T3SS assembly and subsequent virulence effector secretion and is also referred to as the substrate-switching (SS) domain or the type III secretion substrate specificity switch (T3S4) domain. 87 matched cddid_all.tbl CDD cd17467 cd17467 350655 T3SS_YscP_C C-terminal substrate-switching domain of ruler proteins from the Ysc family, such as YscP and PscP. This subfamily includes needle-length sensing proteins, also called ruler proteins, in type 3 secretion systems (T3SS), such as Yersinia pestis Yop proteins translocation protein P (YscP) and Pseudomonas aeruginosa PscP. T3SS ruler proteins contain an N-terminal helical region that dictates needle length and is referred to as the length-sensing (LS) domain, and a C-terminal globular domain that is necessary for the hierarchical switching of substrates during T3SS assembly and subsequent virulence effector secretion and is also referred to as the substrate-switching (SS) domain or the type III secretion substrate specificity switch (T3S4) domain. The C-terminal SS domain is highly stable and sits on the extracellular side prior to needle assembly. 111 matched cddid_all.tbl CDD cd17468 cd17468 350656 T3SS_HrpP_C C-terminal domain of type III secretion protein HrpP and similar domains. This subfamily contains Pseudomonas syringae HrpP, a type III secretion system (T3SS) substrate specificity switch-domain protein that has has an atypical T3SS translocation signal. HrpP is required for the export of pathogenicity factors into plant cells. HrpP contains a C-terminal domain similar to the globular C-terminal substrate-switching (SS) domain, also called the type III secretion substrate specificity switch (T3S4) domain, of Yersinia pestis YscP. 89 matched cddid_all.tbl CDD cd17470 cd17470 350657 T3SS_Flik_C C-terminal domain of flagellar hook-length control protein FliK and similar domains. The flagellar hook-length control protein FliK is a soluble cytoplasmic protein that is secreted during flagellar formation. It controls hook elongation by two successive events: by determining hook length and by stopping the supply of hook protein. It contains an N-terminal domain that determines hook length and a C-terminal domain that is responsible for switching secretion from the hook protein to that of the filament protein, by interacting with FlhB, the switchable secretion gate. 86 matched cddid_all.tbl CDD cd17471 cd17471 341024 MFS_Set Sugar efflux transporter (Set) family of the Major Facilitator Superfamily of transporters. This family is composed of sugar transporters such as Escherichia coli Sugar efflux transporter SetA, SetB, SetC and other sugar transporters. SetA, SetB, and SetC are involved in the efflux of sugars such as lactose, glucose, IPTG, and substituted glucosides or galactosides. They may be involved in the detoxification of non-metabolizable sugar analogs. The Set family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 371 matched cddid_all.tbl CDD cd17472 cd17472 341025 MFS_YajR_like Escherichia coli inner membrane transport protein YajR and similar multidrug-efflux transporters of the Major Facilitator Superfamily. This family is composed of Escherichia coli inner membrane transport protein YajR and some uncharacterized multidrug-efflux transporters. YajR is a putative proton-driven major facilitator superfamily (MFS) transporter found in many gram-negative bacteria. Unlike most MFS transporters, YajR contains a C-terminal, cytosolic YAM domain, which may play an essential role for the proper functioning of the transporter. YajR-like transporters belong to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 371 matched cddid_all.tbl CDD cd17473 cd17473 341026 MFS_arabinose_efflux_permease_like Putative arabinose efflux permease family transporters of the Major Facilitator Superfamily. This family includes a group of putative arabinose efflux permease family transporters, such as alpha proteobacterium quinolone resistance protein NorA (characterized Staphylococcus aureus Quinolone resistance protein NorA belongs to a different group), Desulfovibrio dechloracetivorans bacillibactin exporter, Vibrio aerogenes antiseptic resistance protein. The biological function of those transporters remain unclear. They belong to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 374 matched cddid_all.tbl CDD cd17474 cd17474 341027 MFS_YfmO_like Bacillus subtilis multidrug efflux protein YfmO and similar transporters of the Major Facilitator Superfamily. This family is composed of Bacillus subtilis multidrug efflux protein YfmO, bacillibactin exporter YmfD/YmfE, uncharacterized MFS-type transporter YvmA, and similar proteins. YfmO acts to efflux copper or a copper complex, and could contribute to copper resistance. YmfD/YmfE is involved in secretion of bacillibactin. The YfmO-like family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 374 matched cddid_all.tbl CDD cd17475 cd17475 341028 MFS_MT3072_like Mycobacterium tuberculosis uncharacterized MFS-type transporter MT3072 and similar transporters of the Major Facilitator Superfamily. This family includes the Mycobacterium tuberculosis uncharacterized MFS-type transporter MT3072. It belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 378 matched cddid_all.tbl CDD cd17476 cd17476 341029 MFS_Amf1_MDR_like Saccharomyces cerevisiae low affinity ammonium transporter Amf1p/YOR378W, aminotriazole resistance protein Atr1p, and similar transporters of the Major Facilitator Superfamily. Saccharomyces cerevisiae Amf1p/Ammonium Facilitator 1/YOR378W functions as a low affinity NH4+ transporter. S. cerevisiae aminotriazole resistance protein (Atr1p) is required for controlling sensitivity to aminotriazole; it is a putative component of the machinery responsible for pumping aminotriazole (and possibly other toxic compounds) out of the cell. This subfamily also includes S. cerevisiae YMR279C, a putative boron transporter involved in boron efflux and resistance, and Kluyveromyces lactis Knq1p which is involved in oxidative stress response and iron homeostasis. Amf1p, Atr1p, and YMR279C have been classified as group 1 members of the DHA2 (Drug:H+ Antiporter family 2) family, K. lactis Knq1 as group 2. This subfamily also includes two Aspergillus terreus terrein biosynthesis cluster proteins, efflux pump TerG and TerJ which may be required for efficient secretion of terrein or other secondary metabolites produced by the terrein gene cluster. The Amf1p-like subfamily belongs to the Methylenomycin A resistance protein (also called MMR peptide) and similar multidrug resistance (MDR) transporters (MMR-like MDR transporter) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 362 matched cddid_all.tbl CDD cd17477 cd17477 341030 MFS_YcaD_like YcaD and similar transporters of the Major Facilitator Superfamily. This family is composed of Escherichia coli MFS-type transporter YcaD, Bacillus subtilis MFS-type transporter YfkF, and similar proteins. They are uncharacterized transporters belonging to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 360 matched cddid_all.tbl CDD cd17478 cd17478 341031 MFS_FsR Fosmidomycin resistance protein of the Major Facilitator Superfamily of transporters. Fosmidomycin resistance protein (FsR) confers resistance against fosmidomycin. It shows sequence similarity with the bacterial drug-export proteins that mediate resistance to tetracycline and chloramphenicol. This FsR family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 365 matched cddid_all.tbl CDD cd17479 cd17479 341032 MFS_MFSD6L Major facilitator superfamily domain-containing protein 6-like and similar transporters of the Major Facilitator Superfamily. Major facilitator superfamily domain-containing protein 6-like (MFSD6L) protein family includes a group uncharacterized proteins similar to human major facilitator superfamily domain-containing protein 6 (MFSD6). MFSD6 is also called Macrophage MHC class I receptor 2 homolog (MMR2). It has been postulated as a possible receptor for human leukocyte antigen (HLA)-B62. The MFSD6L family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 376 matched cddid_all.tbl CDD cd17480 cd17480 341033 MFS_SLC40A1_like Solute carrier family 40 member 1 of the Major Facilitator Superfamily of transporters. Solute carrier family 40 member 1 (SLC40A1 or SLC11A3) is also called ferroportin-1 (FPN1) or iron-regulated transporter 1 (IREG1). In the presence of a ferroxidase (hephaestin and/or ceruloplasmin), SLC40A1 acts as an iron exporter ferroportin releases Fe(2+) from cells into plasma, thereby maintaining iron homeostasis. Specially, it is involved in iron export from duodenal epithelial cell and also in the transfer of iron between maternal and fetal circulation. The transport activity of SLC40A1 is suppressed by the peptide hormone hepcidin. This family also includes a bacterial homologue of SLC40A1 (Bdellovibrio bacteriovorus ferroportin). It adopts the major facilitator superfamily fold, but undergoes an intra-domain conformational rearrangement during the transport cycle. SLC40A1 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 386 matched cddid_all.tbl CDD cd17481 cd17481 341034 MFS_MFSD13A Major facilitator superfamily domain containing 13A. Human major facilitator superfamily domain containing 13A (MFSD1A) protein is also called transmembrane protein 180. Its function is still unknown. MFSD13A belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement 429 matched cddid_all.tbl CDD cd17482 cd17482 341035 MFS_YxiO_like Bacillus subtilis YxiO, Listeria monocytogenes BtlA, and similar transporters of the Major Facilitator Superfamily. This family is composed of Bacillus subtilis MFS-type transporter YxiO, and similar proteins including Listeria monocytogenes BtlA. The function of B. subtilis YxiO is still unknown, and L. monocytogenes BtlA is a putative secondary transporter involved in bile tolerance and general stress resistance. This family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 362 matched cddid_all.tbl CDD cd17483 cd17483 341036 MFS_Atg22_like Autophagy-related protein 22 and similar proteins; member of the Major Facilitator Superfamily of transporters. Atg22 (also known as Aut4) protein functions as a vacuolar effluxer which mediates the efflux of amino acids resulting from autophagic degradation. The release of autophagic amino acids allows the maintenance of protein synthesis and viability during nitrogen starvation. Members of this family belong to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 467 matched cddid_all.tbl CDD cd17484 cd17484 341037 MFS_FBT Folate-biopterin transporter of the Major Facilitator Superfamily of transporters. The Folate-biopterin transporter (FBT) family includes folate carriers related to those of trypanosomatids in higher plant plastids and cyanobacteria. FBT mediates folate monoglutamate transport involved in tetrahydrofolate biosynthesis. It also mediates transport of antifolates, such as methotrexate and aminopterin. The FBT family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 399 matched cddid_all.tbl CDD cd17485 cd17485 341038 MFS_MFSD3 Major facilitator superfamily domain containing 3 protein. Major facilitator superfamily domain containing 3 protein (MFSD3) is a predicted acetyl-CoA transporter. As an atypical putative membrane-bound solute carrier (SLC), MFSD3 is most likely to be functionally active in the plasma membrane and not in any intracellular organelles. MFSD3 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 386 matched cddid_all.tbl CDD cd17486 cd17486 341039 MFS_AmpG_like AmpG and similar transporters of the Major Facilitator Superfamily. AmpG acts as an inner membrane permease in the beta-lactamase induction system and in peptidoglycan recycling. It transports meuropeptide from the periplasm into the cytosol in gram-negative bacteria, which is essential for the induction of the ampC encoding beta-lactamase. The AmpG family belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 387 matched cddid_all.tbl CDD cd17487 cd17487 341040 MFS_MFSD5_like Major facilitator superfamily domain containing 5 protein. Human major facilitator superfamily domain containing 5 protein (MFSD5) is also called molybdate-anion transporter, or molybdate transporter 2 homolog (MOT2). It acts as an atypical solute carrier (SLC) that mediates high-affinity intracellular uptake of the rare oligo-element molybdenum. It may also play a role in maintaining the glucose homeostasis and pancreatic beta-cell proliferation, as well as in altered energy homeostasis. MFSD5 belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 385 matched cddid_all.tbl CDD cd17488 cd17488 341041 MFS_UhpC Membrane sensor protein UhpC of the Major Facilitator Superfamily of transporters. Membrane sensor protein UhpC acts as both a sensor and a transport protein. It is part of the UhpABC signaling cascade that controls the expression of the hexose phosphate transporter UhpT. UhpC recognizes external glucose-6-phosphate (Glc6P) and induces transport by UhpT. It can also transport and sense Glc6P, and interacts with the histidine kinase UhpB, leading to the stimulation of the autokinase activity of UhpB. This group also includes the hexose phosphate transport protein UhpT from Chlamydia pneumoniae; it is a transport protein for sugar phosphate uptake. It is part of the Organophosphate:Pi antiporter (OPA) family of integral membrane proteins responsible for the transport of specific organophosphates or sugar phosphates across biological membranes with the simultaneous translocation of inorganic phosphate into the opposite direction. The UhpC group belongs to the Major Facilitator Superfamily (MFS) of membrane transport proteins, which are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 364 matched cddid_all.tbl CDD cd17489 cd17489 341042 MFS_YfcJ_like Escherichia coli YfcJ, YhhS, and similar transporters of the Major Facilitator Superfamily. This subfamily is composed of Escherichia coli membrane proteins, YfcJ and YhhS, Bacillus subtilis uncharacterized MFS-type transporter YwoG, and similar proteins. YfcJ and YhhS are putative arabinose efflux transporters. YhhS has been implicated glyphosate resistance. YfcJ-like arabinose efflux transporters belong to the bacterial MdtG-like and eukaryotic solute carrier 18 (SLC18) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 367 matched cddid_all.tbl CDD cd17490 cd17490 341043 MFS_YxlH_like Bacillus subtilis YxlH and similar transporters of the Major Facilitator Superfamily. This subfamily is composed of Bacillus subtilis YxlH uncharacterized MFS-type transporter YxlH and similar proteins. The biological function of YxlH remains unclear. The YxlH-like subfamily belongs to the bacterial MdtG-like and eukaryotic solute carrier 18 (SLC18) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 371 matched cddid_all.tbl CDD cd17491 cd17491 341044 MFS_MFSD12 Major facilitator superfamily domain-containing protein 12. Major facilitator superfamily domain-containing protein 12 (MFSD12) protein subfamily includes a group of uncharacterized proteins similar to human MFSD2. MFSD2 is composed of two vertebrate members, MFSD2A and MFSD2B. MFSD2A is an LPC symporter that plays an essential role for blood-brain barrier formation and function. MFSD2B is a potential risk or protect factor in the prognosis of lung adenocarcinoma. The MFSD12 subfamily belongs to the Salmonella enterica Na+/melibiose symporter like (MelB-like) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 438 matched cddid_all.tbl CDD cd17492 cd17492 341212 toxin_CptN type III toxin-antitoxin system toxin CptN and similar proteins. CptN-like toxin component of a type III toxin-antitoxin (TA) system, which consists of a ribonuclease (RNase) toxin that processes its structured and specific cognate RNA antitoxin, which in turn then directly inhibits the toxin. TA systems have been associated with many important phenotypes, like phage resistance, maintenance of genomic islands, and formation of bacterial persister cells. 149 matched cddid_all.tbl CDD cd17493 cd17493 341213 toxin_TenpN type III toxin-antitoxin system toxin TenpN and similar proteins. TenpN-like toxin component of a type III toxin-antitoxin (TA) system, which consists of a ribonuclease (RNase) toxin that processes its structured and specific cognate RNA antitoxin, which in turn then directly inhibits the toxin. TA systems have been associated with many important phenotypes, like phage resistance, maintenance of genomic islands, and formation of bacterial persister cells. 121 matched cddid_all.tbl CDD cd17494 cd17494 341185 RMtype1_S_Sma198ORF994P-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Streptococcus macedonicus ACA-DC 198 S subunit (S1.Sma198ORF994P) TRD2-CR2 and Lactobacillus amylovorus GRL 1112 S subunit (S1.LamGRLORF5415P) TRD2-CR2. The recognition sequences of Streptococcus macedonicus ACA-DC 198 S subunit (S1.Sma198ORF994P) and Lactobacillus amylovorus GRL 1112 S subunit (S1.LamGRLORF5415P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 171 matched cddid_all.tbl CDD cd17495 cd17495 341186 RMtype1_S_Cep9333ORF4827P-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Crinalium epipsammum S subunit (S.Cep9333ORF4827P) TRD2-CR2 and Corynebacterium genitalium sp. nov. S subunit (S.CgeORF10704P) TRD2-CR2. The recognition sequences for Crinalium epipsammum S subunit (S.Cep9333ORF4827P) and Corynebacterium genitalium sp. nov. S subunit (S.CgeORF10704P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 174 matched cddid_all.tbl CDD cd17496 cd17496 341187 RMtype1_S_BliBORF2384P-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Bacillus licheniformis S subunit (S1.BliBORF2384P) TRD1-CR1 and Chlorobium tepidum TLS S subunit (S.CteTORF675P) TRD1-CR1. The recognition sequences for Bacillus licheniformis S subunit (S1.BliBORF2384P) and Chlorobium tepidum TLS S subunit (S.CteTORF675P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 175 matched cddid_all.tbl CDD cd17497 cd17497 341188 RMtype1_S_TteMORF1547P-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Thermoanaerobacter tengcongensis S subunit (S.TteMORF1547P) TRD2-CR2. The recognition sequence is undetermined for Thermoanaerobacter tengcongensis S subunit (S.TteMORF1547P). The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This CD contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. S.TteMORF1547P TRD1-CR1 does not belong to this subfamily. 174 matched cddid_all.tbl CDD cd17498 cd17498 341189 RMtype1_S_Aco12261I-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I) TRD1-CR1. The S.Aco12261I S subunit recognizes 5'... GCANNNNNNTGT ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. This subfamily may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. S.Aco12261I TRD2-CR2 does not belong to this subfamily. 173 matched cddid_all.tbl CDD cd17499 cd17499 341190 RMtype1_S_CloLW9ORF3270P-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Cecembia lonarensis LW9 S subunit (S.CloLW9ORF3270P) TRD1-CR1 and Bacillus licheniformis 9945A S subunit (S.Bli9945ORF10320P) TRD1-CR1. The recognition sequences for Cecembia lonarensis LW9 S subunit (S.CloLW9ORF3270P) and Bacillus licheniformis 9945A S subunit (S.Bli9945ORF10320P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. This subfamily of TRD-CR's shows similarity to TRD1-CR1 of Aminobacterium colombiense DSM 12261 S subunit (S.Aco12261I), which recognizes 5'... GCANNNNNNTGT ... 3'. This subfamily also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases such as Helicobacter bizzozeronii CIII-1 putative Type IIG restriction enzyme/N6-adenine DNA methyltransferase RM.HbiCORF8670P, and may also contain type I DNA methyltransferases. 175 matched cddid_all.tbl CDD cd17500 cd17500 341191 RMtype1_S_MmaGORF2198P_TRD1-CR1_like Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Methanosarcina mazei Goe1 S subunit (S.MmaGORF2198P) TRD1-CR1, and Flavobacterium psychrophilum FPG3 S subunit (S.FpsFPG3ORF6820P) TRD1-CR1. The recognition sequences of Methanosarcina mazei Goe1 S subunit (S.MmaGORF2198P) and Flavobacterium psychrophilum FPG3 S subunit (S.FpsFPG3ORF6820P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains TRD1-CR1. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 186 matched cddid_all.tbl CDD cd17501 cd17501 341192 RMtype1_S_Vch69ORF1407P_TRD2-CR2_like Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Vibrio cholerae 1311-69 S subunit (S.Vch69ORF1407P) TRD2-CR2, and Methanococcoides methylutens MM1 S subunit (S.MmeMM1ORF456P) TRD2-CR2. The recognition sequences of Vibrio cholerae 1311-69 S subunit (S.Vch69ORF1407P) and Methanococcoides methylutens MM1 S subunit (S.MmeMM1ORF456P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 191 matched cddid_all.tbl CDD cd17502 cd17502 341045 MFS_Azr1_MDR_like Saccharomyces cerevisiae Azole resistance protein 1 (Azr1p), and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily. This subfamily is composed of multidrug resistance (MDR) transporters including various Saccharomyces cerevisiae proteins such as azole resistance protein 1 (Azr1p), vacuolar basic amino acid transporter 1 (Vba1p), vacuolar basic amino acid transporter 5 (Vba5p), and Sge1p (also known as Nor1p, 10-N-nonyl acridine orange resistance protein, and crystal violet resistance protein). MDR transporters are drug/H+ antiporters (DHA) that mediate the efflux of a variety of drugs and toxic compounds, and confer resistance to these compounds. This subfamily belongs to the Methylenomycin A resistance protein (also called MMR peptide) and similar multidrug resistance (MDR) transporters (MMR-like MDR transporter) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 337 matched cddid_all.tbl CDD cd17503 cd17503 341046 MFS_LmrB_MDR_like Bacillus subtilis lincomycin resistance protein (LmrB) and similar multidrug resistance (MDR) transporters of the Major Facilitator Superfamily. This subfamily is composed of multidrug resistance (MDR) transporters including Bacillus subtilis lincomycin resistance protein LmrB, and several proteins from Escherichia coli such as the putative MDR transporters EmrB, MdtD, and YieQ. MDR transporters are drug/H+ antiporters (DHA) that mediate the efflux of a variety of drugs and toxic compounds, and confer resistance to these compounds. For example, MMR confers resistance to the epoxide antibiotic methylenomycin. This subfamily belongs to the Methylenomycin A resistance protein (also called MMR peptide) and similar multidrug resistance (MDR) transporters (MMR-like MDR transporter) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 380 matched cddid_all.tbl CDD cd17504 cd17504 341047 MFS_MMR_MDR_like Methylenomycin A resistance protein (also called MMR peptide)-like multidrug resistance (MDR) transporters of the Major Facilitator Superfamily. This subfamily is composed of putative multidrug resistance (MDR) transporters including Chlamydia trachomatis antiseptic resistance protein QacA_2, and Serratia sp. DD3 Bmr3. MDR transporters are drug/H+ antiporters (DHA) that mediate the efflux of a variety of drugs and toxic compounds, and confer resistance to these compounds. This subfamily belongs to the Methylenomycin A resistance protein (also called MMR peptide) and similar multidrug resistance (MDR) transporters (MMR-like MDR transporter) family of the Major Facilitator Superfamily (MFS) of transporters. MFS proteins are thought to function through a single substrate binding site, alternating-access mechanism involving a rocker-switch type of movement. 371 matched cddid_all.tbl CDD cd17505 cd17505 340762 Ubl_SAMP1_like ubiquitin-like (Ubl) domain found in small archaeal modifier protein 1 (SAMP1). Ubiquitin-like small archaeal modifier protein 1 (SAMP1) shows a beta-grasp fold of Ub, suggesting that this archaeal Ubl molecule is more closely related to eukaryotic Ub and Ubls than to its prokaryotic counterpart. Several Ub-like structural features such as an N-terminal single lysine residue and di-glycine motif at the C-terminus, spatially isolated, implicate formation of a poly-SAMPylated chainpoly-SAMPylation. SAMP1 can form covalent conjugates with its protein targets through an isopeptide linkage via their C-terminal diglycine motif in a streamlined archaeal E1-dependent pathway. It is involved in sulfur transfer during molybdenum cofactor biosynthesis much like MoaD. This family also includes proteins such as Thermoplasma acidophilum TA0895 and others, all closely related to proteins MoaD. 90 matched cddid_all.tbl CDD cd17506 cd17506 340763 Ubl_SAMP2_like ubiquitin-like (Ubl) domain found in small archaeal modifier protein (SAMP2). Ubiquitin-like small archaeal modifier protein 2 (SAMP2) shows a beta-grasp fold of Ub, suggesting that this archaeal Ubl molecule is more closely related to eukaryotic Ub and Ubls than to its prokaryotic counterpart. Several Ub-like structural features such as an N-terminal single lysine residue and di-glycine motif at the C-terminus, spatially isolated, implicate formation of a poly-SAMPylated chainpoly-SAMPylation. SAMP2 can form covalent conjugates with its protein targets through an isopeptide linkage via their C-terminal diglycine motif in a streamlined archaeal E1-dependent pathway. It also forms homo-conjugates through the intermolecular isopeptide bond between the C-terminal Gly and the Lys58 side chain, a feature that likely resembles polyubiquitination. SAMP2 is involved in sulfur transfer during tRNA thiolation much like Urm1. This family also includes uncharacterized proteins such as Methanothermococcus thermolithotrophicus Mth1743, Pyrococcus furiosus PF1061 and others, all closely related to proteins MoaD. 67 matched cddid_all.tbl CDD cd17507 cd17507 340861 GT28_Beta-DGS-like beta-diglucosyldiacylglycerol synthase and similar proteins. beta-diglucosyldiacylglycerol synthase (processive diacylglycerol beta-glucosyltransferase EC 2.4.1.315) is involved in the biosynthesis of both the bilayer- and non-bilayer-forming membrane glucolipids. This family of glycosyltransferases also contains plant major galactolipid synthase (chloroplastic monogalactosyldiacylglycerol synthase 1 EC 2.4.1.46). Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. The structures of the formed glycoconjugates are extremely diverse, reflecting a wide range of biological functions. The members of this family share a common GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homology. The large cleft that separates the two domains includes the catalytic center and permits a high degree of flexibility. 364 matched cddid_all.tbl CDD cd17508 cd17508 341225 Alpha_kinase Alpha kinase family; uncharacterized subgroup. The alpha kinase family is a novel family of eukaryotic protein kinase catalytic domains, which have no detectable similarity to conventional serine/threonine protein kinases. The family contains myosin heavy chain kinases, elongation factor-2 kinases, and bifunctional ion channel kinases. These kinases are implicated in a large variety of cellular processes such as protein translation, Mg2+/Ca2+ homeostasis, intracellular transport, cell migration, adhesion, and proliferation. The alpha-kinase family was named after the unique mode of substrate recognition by its initial members, the Dictyostelium heavy chain kinases, which targeted protein sequences that adopt an alpha-helical conformation. More recently, alpha-kinases were found to also target residues in non-helical regions. 243 matched cddid_all.tbl CDD cd17509 cd17509 341226 Alpha_kinase Alpha kinase family; uncharacterized subgroup. The alpha kinase family is a novel family of eukaryotic protein kinase catalytic domains, which have no detectable similarity to conventional serine/threonine protein kinases. The family contains myosin heavy chain kinases, elongation factor-2 kinases, and bifunctional ion channel kinases. These kinases are implicated in a large variety of cellular processes such as protein translation, Mg2+/Ca2+ homeostasis, intracellular transport, cell migration, adhesion, and proliferation. The alpha-kinase family was named after the unique mode of substrate recognition by its initial members, the Dictyostelium heavy chain kinases, which targeted protein sequences that adopt an alpha-helical conformation. More recently, alpha-kinases were found to also target residues in non-helical regions. 221 matched cddid_all.tbl CDD cd17510 cd17510 409322 T3SC_YbjN-like_2 Uncharacterized protein is structurally similar to type III secretion system chaperones and YbjN family proteins. This family includes an uncharacterized protein from Methanothermobacter Thermautotrophicus that is structurally similar to type III secretion system (T3SS) chaperones (T3SC) that bind effector proteins, and is homologous to YbjN, a putative sensory transduction regulator protein found in Proteobacteria. 142 matched cddid_all.tbl CDD cd17511 cd17511 409323 YbjN_AmyR-like YbjN protein family is structurally similar to type III secretion system chaperones. This YbjN protein family includes Escherichia coli YbjN, Erwinia amylovora AmyR, and similar proteins. YbjN proteins share a class I type III secretion chaperone (T3SC)-like fold with type III secretion system (T3SS) chaperone proteins but appear to function independently of the T3SS. YbjN is an enterobacteria-specific protein. In E. coli, it acts as a sensory transduction regulator that may play important roles in regulating bacterial multicellular behavior, metabolism, and survival under stress conditions. E. amylovora AmyR, a functionally conserved ortholog of E. coli YbjN, is a stress and virulence associated protein that regulates the ams operon. Ams proteins are required for amylovoran biosynthesis. AmyR may also regulate the Rcs phosphorelay system, an atypical two-component signal transduction (TCST) system present only in Enterobacteriaceae and positively regulates amylovoran biosynthesis by activating the ams operon transcription. 122 matched cddid_all.tbl CDD cd17512 cd17512 341193 RMtype1_S_BceB55ORF5615P-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Bacillus cereus HuB5-5 S subunit (S.BceB55ORF5615P) TRD2-CR2. The recognition sequence of Bacillus cereus HuB5-5 S subunit (S.BceB55ORF5615P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 195 matched cddid_all.tbl CDD cd17513 cd17513 341194 RMtype1_S_AveSPN6ORF1907P_TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Archaeoglobus veneficus SNP6 S subunit (S.AveSPN6ORF1907P) TRD2-CR2 and Bacillus subtilis JRS2 S subunit (S.BsuJRS7ORF3308P) TRD1-CR1. The recognition sequences of Archaeoglobus veneficus SNP6 S subunit (S.AveSPN6ORF1907P) and Bacillus subtilis JRS2 S subunit (S.BsuJRS7ORF3308P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 182 matched cddid_all.tbl CDD cd17514 cd17514 341195 RMtype1_S_Eco2747I_MmaC7ORF19P-TRD-CR_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Escherichia coli ST2747 S subunit (S.Eco2747I) TRD2-CR2, Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) TRD1-CR1, and related domains. The S. Eco2747I S subunit recognizes 5'... CACNNNNNNNGTTG ... 3'. The recognition sequence of Methanococcus maripaludis C7 S subunit (S.MmaC7ORF19P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This CD contains both TRD1-CR1 and TRD2-CR2. It also includes the TRD-CR-like domains of putative type II restriction enzymes and methyltransferases, such as Helicobacter cinaedi PAGU611 Hci611ORFHP which may recognize 5'... GAGNNNNNGT ... 3', and type I N6-adenine DNA methyltransferases, such as Calditerrivibrio nitroreducens M.Cni19672ORF1405P whose recognition sequence is undetermined. 183 matched cddid_all.tbl CDD cd17515 cd17515 341196 RMtype1_S_MjaORF132P_Sau1132ORF3780P-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to MjaXIP/S.MjaORF132P TRD1-CR1, S.Sau1132ORF3780P TRD1-CR1, S.Mca353ORF290P TRD1-CR1, and other TRD-CR's. The Staphylococcus aureus subsp. aureus MSHR1132 S subunit (S.Sau1132ORF3780P) recognizes 5'... CAAGNNNNNRTC ... 3', and Moraxella catarrhalis S subunit (S.Mca353ORF290P) recognizes 5'... CAAGNNNNNNTGT ... 3'. The recognition sequence of Methanococcus jannaschii S subunit (MjaXIP/S.MjaORF132P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.Sau1132ORF3780P-TRD1 recognizes CAAG/CTTG, and S.Sau1132ORF3780P-TRD2 recognizes GAY/RTC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 181 matched cddid_all.tbl CDD cd17516 cd17516 341197 RMtype1_S_HinAWORF1578P-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to S.HinAWORF1578P TRD2-CR2. Haemophilus influenzae RdAW S subunit (S.HinAWORF1578P) recognizes 5'... CTANNNNNGTTY ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 184 matched cddid_all.tbl CDD cd17517 cd17517 341198 RMtype1_S_EcoKI_StySPI-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR),similar to Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) TRD2-CR2, Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) TRD2-CR2, and other TRD-CR's. Escherichia coli str. K-12 substr. MG1655 S subunit (S.EcoKI) recognizes 5'... AACNNNNNNGTGC ... 3' and Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) recognizes 5'... AACNNNNNNGTRC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.EcoKI-TRD1 and S.StySPI-TRD1 both recognize AAC/GTT, S.EcoKI-TRD2 recognizes GCAC/GTGC and S.StySPI-TRD2 recognizes GYAC/GTRC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2.It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Pseudomonas putida Jo 4-731 Type IIG restriction enzyme/N6-adenine DNA methyltransferase (RM.PpiI), and type I DNA methyltransferases such as Bacillus cereus BDRD-ST24 M subunit of Type I N6-adenine DNA methyltransferase (M.Bce24ORF51270P). RM.PpiI recognizes 5' ... GAACNNNNNCTC ... 3'. 192 matched cddid_all.tbl CDD cd17518 cd17518 341199 RMtype1_S_Asp27244ORF1181P-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Acinetobacter sp. S subunit (S.Asp27244ORF1181P) TRD1-CR1. The recognition sequence of Acinetobacter sp. S subunit (S.Asp27244ORF1181P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 180 matched cddid_all.tbl CDD cd17519 cd17519 341200 RMtype1_S_HpyCR35ORFAP-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Helicobacter pylori CR35 S subunit (S.HpyCR35ORFAP) TRD1-CR1 and Mycoplasma haemofelis str. Langford 1 S subunit (S2.Mha1ORF7190P) TRD1-CR1. The recognition sequences of Helicobacter pylori CR35 S subunit (S.HpyCR35ORFAP) and Mycoplasma haemofelis str. Langford 1 S subunit (S2.Mha1ORF7190P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 183 matched cddid_all.tbl CDD cd17520 cd17520 341201 RMtype1_S_HmoORF3075P-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit Target Recognition Domain-ConseRved domain (TRD-CR), similar to Heliobacterium modesticaldum Ice1 S subunit (S1.HmoORF3075P) TRD1-CR1. The recognition sequence of Heliobacterium modesticaldum Ice1 S subunit (S1.HmoORF3075P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This subfamily also includes the TRD-CR-like sequence-recognition domain of type I N6-adenine DNA methyltransferase (M) subunit of Clostridium intestinale URNW (M2.CinURNWORF2828P). The recognition sequence of M2.CinURNWORF2828P is undetermined. Type I methyltransferases included in this group include two domains: one for methylation, and another (TRD-CR-like) for sequence-recognition. 180 matched cddid_all.tbl CDD cd17521 cd17521 341202 RMtype1_S_Sau13435ORF2165P_TRD2-CR2_like Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Staphylococcus aureus NCTC 13435 S subunit (S.Sau13435ORF2165P) TRD2-CR2, Escherichia coli E24377A S subunit (S.EcoE24377ORF286P) TRD1-CR1 and Pseudoalteromonas species P1-13-1a S. subunit (S.Psp1bORF2093P) TRD2-CR2. Staphylococcus aureus NCTC 13435 S subunit (S.Sau13435ORF2165P) recognizes 5'... TCTANNNNNNRTTC ... 3', and the recognition sequences of Escherichia coli E24377A S subunit (S.EcoE24377ORF286P) and Pseudoalteromonas species P1-13-1a S subunit (S.Psp1bORF2093P) are undetermined. The restriction-modification (RM) system S subunit generally consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, Staphylococcus aureus NCTC 13435 S subunit (S.Sau13435ORF2165P) TRD1 recognizes TCTA/TAGA, and -TRD2 recognizes GAAY/RTTC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. In addition, this family includes RMtype1_S_TRD-CR_like domains of various putative Helicobacter type II restriction enzymes and methyltransferases, such as Hci611ORFHP and HfeORF12890P. 187 matched cddid_all.tbl CDD cd17522 cd17522 341203 RMtype1_S_MjaORF1531P-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Methanocaldococcus jannaschii DSM 2661 S subunit (S.MjaORF1531P/MjaXIIP) TRD1-CR1. The recognition sequence of Methanocaldococcus jannaschii DSM 2661 S subunit (S.MjaORF1531P, also called MjaXIIP) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 190 matched cddid_all.tbl CDD cd17523 cd17523 341204 RMtype1_S_StySPI-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) TRD2-CR2. Salmonella enterica subsp. enterica serovar Potsdam S subunit (S.StySPI) recognizes 5'... AACNNNNNNGTRC ... 3'. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. For example, S.StySPI-TRD1 recognizes AAC/GTT and S.StySPI-TRD2 recognizes GYAC/GTRC. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 190 matched cddid_all.tbl CDD cd17524 cd17524 341205 RMtype1_S_EcoUTORF5051P-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli UTI89 S subunit (S.EcoUTORF5051P) TRD2-CR2 and Archaeoglobus fulgidus VC-16 S subunit (S.AfuORF1715P) TRD2-CR2. Escherichia coli UTI89 S subunit (S.EcoUTORF5051P) recognizes 5'... CCANNNNNNNCTTC ... 3' and the recognition sequence of Archaeoglobus fulgidus VC-16 S subunit (S.AfuORF1715P) is undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It also includes TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases, such as Pseudomonas putida Jo 4-731 Type IIG restriction enzyme/N6-adenine DNA methyltransferase (RM.PpiI), and type I DNA methyltransferases such as Bacillus cereus BDRD-ST24 M subunit of Type I N6-adenine DNA methyltransferase (M.Bce24ORF51270P). RM.PpiI recognizes 5' ... GAACNNNNNCTC ... 3'. 189 matched cddid_all.tbl CDD cd17525 cd17525 341206 RMtype1_S_Eco15ORF14057P-TRD1-CR1_like Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Escherichia coli 541-15 S subunit (S.Eco15ORF14057P) TRD1-CR1 and Desulfotignum phosphitoxidans S subunit (S.Dph13687ORF2110P) TRD2-CR2. The recognition sequences of Escherichia coli 541-15 S subunit (S.Eco15ORF14057P) and Desulfotignum phosphitoxidans S subunit (S.Dph13687ORF2110P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. It may also include TRD-CR-like sequence-recognition domains of various type II restriction enzymes and methyltransferases and type I DNA methyltransferases. 190 matched cddid_all.tbl CDD cd17526 cd17526 341207 RMtype1_S_Cje2232P-TRD2-CR2_like Type I restriction-modification system specificity (S) subunit TRD-CR, similar to Campylobacter jejuni RM 2232 S subunit (S.Cje2232P) TRD2-CR2 and Shewanella baltica OS223 S subunit (S.Sba223ORF389P) TRD1-CR1. The recognition sequences of Campylobacter jejuni RM 2232 S subunit (S.Cje2232P) and Shewanella baltica OS223 S subunit (S.Sba223ORF389P) are undetermined. The restriction-modification (RM) system S subunit consists of two variable target recognition domains (TRD1 and 2) and two conserved regions (CR1 and CR2) which separate the TRDs. The TRDs each bind to different specific sequences in the DNA. RM systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one enzyme complex composed of one DNA specificity (S) subunit (this family), two modification (M) subunits and two restriction (R) subunits. This model contains both TRD1-CR1 and TRD2-CR2. Also included in this subfamily is the C-terminal TRD-CR-like sequence-recognition domain of Microcystis aeruginosa putative type I N6-adenine DNA methyltransferase M subunit (M.Mae7806ORF3969P). The recognition sequence of M.Mae7806ORF3969P is undetermined. 192 matched cddid_all.tbl CDD cd17527 cd17527 381744 HAMP_II second HAMP domain of aerotaxis transducer Aer2 and similar domains. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The structure of the Af1503 HAMP dimer from Archaeoglobus fulgidus has been solved using nuclear magnetic resonance, revealing a parallel four-helix bundle; this structure has been confirmed by cross-linking analysis of HAMP domains from the Escherichia coli aerotaxis receptor Aer. It has been suggested that the four-helix arrangement can rotate between the unusually packed conformation observed in the NMR structure and a canonical coiled-coil arrangement. Such rotation may coincide with signal transduction, but a common mechanism by which HAMP domains relay a variety of input signals has yet to be established. 46 matched cddid_all.tbl CDD cd17528 cd17528 381745 HAMP_III third HAMP domain of aerotaxis transducer Aer2 and similar domains. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The structure of the Af1503 HAMP dimer from Archaeoglobus fulgidus has been solved using nuclear magnetic resonance, revealing a parallel four-helix bundle; this structure has been confirmed by cross-linking analysis of HAMP domains from the Escherichia coli aerotaxis receptor Aer. It has been suggested that the four-helix arrangement can rotate between the unusually packed conformation observed in the NMR structure and a canonical coiled-coil arrangement. Such rotation may coincide with signal transduction, but a common mechanism by which HAMP domains relay a variety of input signals has yet to be established. 44 matched cddid_all.tbl CDD cd17529 cd17529 381746 HAMP_I first HAMP domain of aerotaxis transducer Aer2 and similar domains. HAMP is a signaling domain which occurs in a wide variety of signaling proteins, many of which are bacterial. The HAMP domain consists of two alpha helices connected by an extended linker. The structure of the Af1503 HAMP dimer from Archaeoglobus fulgidus has been solved using nuclear magnetic resonance, revealing a parallel four-helix bundle; this structure has been confirmed by cross-linking analysis of HAMP domains from the Escherichia coli aerotaxis receptor Aer. It has been suggested that the four-helix arrangement can rotate between the unusually packed conformation observed in the NMR structure and a canonical coiled-coil arrangement. Such rotation may coincide with signal transduction, but a common mechanism by which HAMP domains relay a variety of input signals has yet to be established. 44 matched cddid_all.tbl CDD cd17530 cd17530 381086 REC_RocR phosphoacceptor receiver (REC) domain of response regulator RocR. The response regulator RocR from some pathogens contains an N-terminal phosphoreceiver (REC) domain and a C-terminal EAL domain that possesses c-di-GMP specific phosphodiesterase activity. The RocR REC domain is phosphorylated and modulates its EAL domain enzymatic activity, regulating the local level of c-di-GMP. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 123 matched cddid_all.tbl CDD cd17532 cd17532 381087 REC_LytTR_AlgR-like phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AlgR. Members of the LytTR/AlgR family of response regulators contain a REC domain and a unique LytTR DNA-binding output domain that lacks the helix-turn-helix motif and consists mostly of beta-strands. Transcriptional regulators with the LytTR-type output domains are involved in biosynthesis of extracellular polysaccharides, fimbriation, expression of exoproteins, including toxins, and quorum sensing. Included in this AlgR-like group of LytTR/AlgR family response regulators are Streptococcus agalactiae sensory transduction protein LytR, Pseudomonas aeruginosa positive alginate biosynthesis regulatory protein AlgR, Bacillus subtilis sensory transduction protein LytT, and Escherichia coli transcriptional regulatory protein BtsR, which are members of two-component regulatory systems. LytR and LytT are components of regulatory systems that regulate genes involved in cell wall metabolism. AlgR positively regulates the algD gene, which codes for a GDP-mannose dehydrogenase, a key enzyme in the alginate biosynthesis pathway. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 118 matched cddid_all.tbl CDD cd17533 cd17533 381088 REC_LytTR_AgrA-like phosphoacceptor receiver (REC) domain of LytTR/AlgR family response regulators similar to AgrA. Members of the LytTR/AlgR family of response regulators contain a REC domain and a unique LytTR DNA-binding output domain that lacks the helix-turn-helix motif and consists mostly of beta-strands. Transcriptional regulators with the LytTR-type output domains are involved in biosynthesis of extracellular polysaccharides, fimbriation, expression of exoproteins, including toxins, and quorum sensing. Included in this AgrA-like group of LytTR/AlgR family response regulators are Staphylococcus aureus accessory gene regulator protein A (AgrA) and Streptococcus pneumoniae response regulator ComE, which are members of two-component regulatory systems. AgrA is a global regulator that controls the synthesis of virulence factors and other exoproteins. ComE is part of the ComD-ComE system that is part of a quorum-sensing signaling pathway that controls the development of competence, a physiological state required for genetic transformation. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 131 matched cddid_all.tbl CDD cd17534 cd17534 381089 REC_DC-like phosphoacceptor receiver (REC) domain of modulated diguanylate cyclase and similar domains. This groups includes a modulated diguanylate cyclase containing a PAS sensor domain from Desulfovibrio desulfuricans G20. Members of this group contain N-terminal REC domains and various output domains including the GGDEF, histidine kinase, and helix-turn-helix (HTH) DNA binding domains. Also included in this family is Mycobacterium tuberculosis PdtaR, a transcriptional antiterminator that contains a REC domain and an ANTAR RNA-binding output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 117 matched cddid_all.tbl CDD cd17535 cd17535 381090 REC_NarL-like phosphoacceptor receiver (REC) domain of NarL (Nitrate/Nitrite response regulator L) family response regulators. The NarL family is one of the more abundant families of DNA-binding response regulators (RRs). Members of the NarL family contain a REC domain and a helix-turn-helix (HTH) DNA-binding output domain, with a majority of members containing a LuxR-type HTH domain. They function as transcriptional regulators. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 117 matched cddid_all.tbl CDD cd17536 cd17536 381091 REC_YesN-like phosphoacceptor receiver (REC) domain of YesN and related helix-turn-helix containing response regulators. This family is composed of uncharacterized response regulators that contain a REC domain and a AraC family helix-turn-helix (HTH) DNA-binding output domain, including Bacillus subtilis uncharacterized transcriptional regulatory protein YesN and Staphylococcus aureus uncharacterized response regulatory protein SAR0214. YesN is a member of the two-component regulatory system YesM/YesN and SAR0214 is a member of the probable two-component regulatory system SAR0215/SAR0214. Also included in this family is the AlgR-like group of LytTR/AlgR family response, which includes Pseudomonas aeruginosa positive alginate biosynthesis regulatory protein AlgR and Bacillus subtilis sensory transduction protein LytT, among others. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 121 matched cddid_all.tbl CDD cd17537 cd17537 381092 REC_FixJ phosphoacceptor receiver (REC) domain of FixJ family response regulators. FixJ family response regulators contain an N-terminal receiver domain (REC) and a C-terminal LuxR family helix-turn-helix (HTH) DNA-binding output domain. The Sinorhizobium meliloti two-component system FixL/FixJ regulates nitrogen fixation in response to oxygen during symbiosis. Under microaerobic conditions, the kinase FixL phosphorylates the response regulator FixJ resulting in the regulation of nitrogen fixation genes such as nifA and fixK. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 116 matched cddid_all.tbl CDD cd17538 cd17538 381093 REC_D1_PleD-like first (D1) phosphoacceptor receiver (REC) domain of response regulator PleD and similar domains. PleD contains a REC domain (D1) with the phosphorylatable aspartate, a REC-like adaptor domain (D2), and the enzymatic diguanylate cyclase (DGC) domain, also called the GGDEF domain according to a conserved sequence motif, as its output domain. The GGDEF-containing PleD response regulators are global regulators of cell metabolism in some important human pathogens. This model describes D1 of PleD and similar domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 104 matched cddid_all.tbl CDD cd17539 cd17539 381094 psREC-like_D2_PleD REC-like adaptor domain (D2) of response regulator PleD. PleD contains a REC domain (D1) with the phosphorylatable aspartate, a pseudo receiver (psREC)-like adaptor domain (D2), and the enzymatic diguanylate cyclase (DGC) domain, also called the GGDEF domain according to a conserved sequence motif, as its output domain. The GGDEF-containing PleD response regulators are global regulators of cell metabolism in some important human pathogens. This model describes the REC-like adaptor domain D2 of PleD, which is an inactive domain. 124 matched cddid_all.tbl CDD cd17540 cd17540 381095 REC_PhyR phosphoacceptor receiver (REC) domain of response regulator PhyR and similar proteins. PhyR is a hybrid stress regulator that contains an N-terminal sigma-like (SL) domain and a C-terminal REC domain. Phosphorylation of the REC domain is known to promote binding of the SL domain to an anti-sigma factor. PhyR thus functions as an anti-anti-sigma factor in its phosphorylated state. It is involved in the general stress response. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 117 matched cddid_all.tbl CDD cd17541 cd17541 381096 REC_CheB-like phosphoacceptor receiver (REC) domain of chemotaxis response regulator protein-glutamate methylesterase CheB and similar chemotaxis proteins. Methylesterase CheB is a chemotaxis response regulator with an N-terminal REC domain and a C-terminal methylesterase domain. Chemotaxis is a behavior known in motile bacteria that directs their movement in response to chemical gradients. CheB is a phosphorylation-activated response regulator involved in the reversible modification of bacterial chemotaxis receptors. It catalyzes the demethylation of specific methylglutamate residues introduced into the chemoreceptors (methyl-accepting chemotaxis proteins) by CheR. The CheB REC domain packs against the active site of the C-terminal domain and inhibits methylesterase activity by directly restricting access to the active site. Also included in this family is chemotaxis response regulator CheY, which contains a stand-alone REC domain, and an uncharacterized subfamily composed of proteins containing an N-terminal REC domain and a C-terminal CheY-P phosphatase (CheC) domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 125 matched cddid_all.tbl CDD cd17542 cd17542 381097 REC_CheY phosphoacceptor receiver (REC) domain of chemotaxis protein CheY. The chemotaxis response regulator CheY contains a stand-alone REC domain. Chemotaxis is a behavior known for motile bacteria that directs their movement in response to chemical gradients. CheY is involved in transmitting sensory signals from chemoreceptors to the flagellar motors. Phosphorylated CheY interacts with the flagella switch components FliM and FliY, which causes counterclockwise rotation of the flagella, resulting in smooth swimming. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 117 matched cddid_all.tbl CDD cd17544 cd17544 381098 REC_2_GGDEF second phosphoacceptor receiver (REC) domain of uncharacterized GGDEF domain proteins. This family is composed of uncharacterized PleD-like response regulators that contain two N-terminal REC domains and a C-terminal diguanylate cyclase output domain with the characteristic GGDEF motif at the active site. Unlike PleD which contains a REC-like adaptor domain, the second REC domain of these uncharacterized GGDEF domain proteins, described in this model, contains characteristic metal-binding and active site residues. PleD response regulators are global regulators of cell metabolism in some important human pathogens. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 122 matched cddid_all.tbl CDD cd17546 cd17546 381099 REC_hyHK_CKI1_RcsC-like phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinases/response regulators similar to Arabidopsis thaliana CKI1 and Escherichia coli RcsC. This family is composed of hybrid sensor histidine kinases/response regulators that are sensor histidine kinases (HKs) fused with a REC domain, similar to the sensor histidine kinase CKI1 from Arabidopsis thaliana, which is involved in multi-step phosphorelay (MSP) signaling that mediates responses to a variety of important stimuli in plants. MSP involves a signal being transferred from HKs via histidine phosphotransfer proteins (AHP1-AHP5) to nuclear response regulators. The CKI1 REC domain specifically interacts with the downstream signaling protein AHP2, AHP3 and AHP5. The plant MSP system has evolved from the prokaryotic two-component system (TCS), which allows organisms to sense and respond to changes in environmental conditions. This family also includes bacterial hybrid sensor HKs such as Escherichia coli RcsC, which is a component of the Rcs signalling pathway that controls a variety of physiological functions like capsule synthesis, cell division, and motility. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 113 matched cddid_all.tbl CDD cd17548 cd17548 381100 REC_DivK-like phosphoacceptor receiver (REC) domain of DivK and similar proteins. Caulobacter crescentus DivK is an essential response regulator that is involved in the complex phosphorelay pathways controlling both cell division and motility. It localizes cell cycle regulators to specific poles of the cell during division. DivK contains a stand-alone REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 115 matched cddid_all.tbl CDD cd17549 cd17549 381101 REC_DctD-like phosphoacceptor receiver (REC) domain of C4-dicarboxylic acid transport protein D (DctD) and similar proteins. C4-dicarboxylic acid transport protein D (DctD) is part of the two-component regulatory system DctB/DctD, which regulates C4-dicarboxylate transport via regulation of expression of the dctPQM operon and dctA. It is an activator of sigma(54)-RNA polymerase holoenzyme that uses the energy released from ATP hydrolysis to stimulate the isomerization of a closed promoter complex to an open complex capable of initiating transcription. DctD is a member of the NtrC family, characterized by a domain architecture containing an N-terminal REC domain, followed by a central sigma-54 interaction/ATPase domain, and a C-terminal DNA binding domain. The ability of the central domain to hydrolyze ATP and thus to interact effectively with a complex of RNA polymerase, sigma54, and promoter, is controlled by the phosphorylation status of the REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 130 matched cddid_all.tbl CDD cd17550 cd17550 381102 REC_NtrX-like phosphoacceptor receiver (REC) domain of nitrogen assimilation regulatory protein NtrX and similar proteins. NtrX is part of the two-component regulatory system NtrY/NtrX that is involved in the activation of nitrogen assimilatory genes such as Gln. It is phosphorylated by the histidine kinase NtrY and interacts with sigma-54. NtrX is a member of the NtrC family, characterized by a domain architecture containing an N-terminal REC domain, followed by a central sigma-54 interaction/ATPase domain, and a C-terminal DNA binding domain. NtrC family response regulators are sigma54-dependent transcriptional activators. Also included in this subfamily is Aquifex aeolicus NtrC4. The ability of the central domain to hydrolyze ATP and thus to interact effectively with a complex of RNA polymerase, sigma54, and promoter, is controlled by the phosphorylation status of the REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 115 matched cddid_all.tbl CDD cd17551 cd17551 381103 REC_RpfG-like phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase response regulator RpfG and similar proteins. Cyclic di-GMP phosphodiesterase response regulator RpfG, together with sensory/regulatory protein RpfC, constitute a two-component system implicated in sensing and responding to the diffusible signal factor (DSF) that is essential for cell-cell signaling. RpfC is a hybrid sensor/histidine kinase that phosphorylates and activates RpfG, which degrades cyclic di-GMP to GMP, leading to the activation of Clp, a global transcriptional regulator that regulates a large set of genes in the DSF pathway. RpfG contains a CheY-like receiver domain attached to a histidine-aspartic acid-glycine-tyrosine-proline (HD-GYP) cyclic di-GMP phosphodiesterase domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 118 matched cddid_all.tbl CDD cd17552 cd17552 381104 REC_RR468-like phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator RR468 and similar domains. Thermotoga maritima RR468 (encoded by gene TM0468) is the cognate response regulator (RR) of the class I histidine kinase HK853 (product of gene TM0853). HK853/RR468 comprise a two-component system (TCS) that couples environmental stimuli to adaptive responses. This subfamily also includes Fremyella diplosiphon complementary adaptation response regulator homolog RcaF, a small RR that is involved in four-step phosphorelays of the complementary chromatic adaptation (CCA) system that occurs in many cyanobacteria. Both RR468 and RcaF are stand-alone RRs containing only a REC domain with no output/effector domain. The REC domain itself functions as an effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 121 matched cddid_all.tbl CDD cd17553 cd17553 381105 REC_Spo0F-like phosphoacceptor receiver (REC) domain of Spo0F and similar domains. Spo0F, a stand-alone response regulator containing only a REC domain with no output/effector domain, controls sporulation in Bacillus subtilis through the exchange of a phosphoryl group. Bacillus subtilis forms spores when conditions for growth become unfavorable. The initiation of sporulation is controlled by a phosphorelay (an expanded version of the two-component system) that consists of four main components: a histidine kinase (KinA), a secondary messenger (Spo0F), a phosphotransferase (Spo0B), and a transcription factor (Spo0A). REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 117 matched cddid_all.tbl CDD cd17554 cd17554 381106 REC_TrrA-like phosphoacceptor receiver (REC) domain of Thermotoga maritima response regulator TrrA and similar domains. Thermotoga maritima contains a two-component signal transduction system (TCS) composed of the ThkA sensory histidine kinase (HK) and its cognate response regulator (RR) TrrA; the specific function of the system is unknown. TCSs couple environmental stimuli to adaptive responses. TrrA is a stand-alone RR containing only a REC domain with no output/effector domain. The REC domain itself functions as an effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 113 matched cddid_all.tbl CDD cd17555 cd17555 381107 REC_RssB-like phosphoacceptor receiver (REC) domain of Pseudomonas aeruginosa RssB and similar domains. Pseudomonas aeruginosa RssB is an orphan atypical response regulator containing a REC domain and a PP2C-type protein phosphatase output domain. Its function is still unknown. Escherichia RssB, which is not included in this subfamily, is a ClpX adaptor protein which alters ClpX specificity by mediating a specific interaction between ClpX and the substrates such as RpoS, an RNA polymerase sigma factor. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 116 matched cddid_all.tbl CDD cd17557 cd17557 381108 REC_Rcp-like phosphoacceptor receiver (REC) domain of cyanobacterial phytochrome response regulator Rcp and similar domains. This family is composed of response regulators (RRs) that are members of phytochrome-associated, light-sensing two-component signal transduction pathways such as Synechocystis sp. Rcp1, Tolypothrix sp. RcpA, and Agrobacterium tumefaciens bacteriophytochrome response regulator AtBRR. They are stand-alone RRs containing only a REC domain with no output/effector domain. The REC domain itself functions as an effector domain. Also included in this family us Methanosaeta harundinacea methanogenesis regulatory protein FilR2, also a stand-alone RR. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 129 matched cddid_all.tbl CDD cd17561 cd17561 381109 REC_Spo0A phosphoacceptor receiver (REC) domain of Spo0A. Spo0A is a response regulator of the phosphorelay system in the early stage of spore formation. It may be an element of the effector pathway responsible for the activation of sporulation genes in response to nutritional stress and may act in the with sigma factor spo0H to control the expression of some genes that are critical to the sporulation process. Spo0A contains a regulatory N-terminal REC domain and a C-terminal DNA-binding transcription activation domain as its effector/output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 108 matched cddid_all.tbl CDD cd17562 cd17562 381110 REC_CheY4-like phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY4 and similar CheY family proteins. CheY family chemotaxis response regulators (RRs) comprise about 17% of bacterial RRs and almost half of all RRs in archaea. This subfamily contains Vibrio cholerae CheY4 and similar CheY family RRs. CheY proteins control bacterial motility and participate in signaling phosphorelays and in protein-protein interactions. CheY RRs contain only the REC domain with no output/effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 118 matched cddid_all.tbl CDD cd17563 cd17563 381111 REC_RegA-like phosphoacceptor receiver (REC) domain of photosynthetic apparatus regulatory protein RegA. Rhodobacter sphaeroides RegA, also called response regulator PrrA, is the DNA binding regulatory protein of a redox-responsive two-component regulatory system RegB/RegA that is involved in transactivating anaerobic expression of the photosynthetic apparatus. It contains a REC domain and a DNA-binding helix-turn-helix output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 112 matched cddid_all.tbl CDD cd17565 cd17565 381112 REC_GlnL-like phosphoacceptor receiver (REC) domain of transcriptional regulatory protein GlnL and similar proteins. Bacillus subtilis GlnL is part of the GlnK-GlnL (formerly YcbA-YcbB) two-component system that positively regulates the expression of the glsA-glnT (formerly ybgJ-ybgH) operon in response to glutamine. It contains a REC domain and a DNA-binding output domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 103 matched cddid_all.tbl CDD cd17569 cd17569 381113 REC_HupR-like phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR) and similar domains. This family is composed of mostly uncharacterized response regulators with similarity to the REC domains of response regulator components of two-component systems that regulates hydrogenase activity, including HupR and HoxA. HupR is part of the HupT/HupR system that controls the synthesis of the membrane-bound [NiFe]hydrogenase, HupSL, of the photosynthetic bacterium Rhodobacter capsulatus. It contains an N-terminal REC domain, a central sigma-54 interaction domain that lacks ATPase activity, and a C-terminal DNA-binding domain. Members of this family contain a REC domain and various output domains including the cyclase homology domain (CHD) and the c-di-GMP phosphodiesterase domains, HD-GYP and EAL. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 118 matched cddid_all.tbl CDD cd17572 cd17572 381114 REC_NtrC1-like phosphoacceptor receiver (REC) domain of nitrogen regulatory protein C 1 (NtrC1) from Aquifex aeolicus and similar NtrC family response regulators. NtrC family proteins are transcriptional regulators that have REC, AAA+ ATPase/sigma-54 interaction, and DNA-binding output domains. This subfamily of NtrC proteins include Aquifex aeolicus NtrC1 and Vibrio quorum-sensing signal integrator LuxO. The N-terminal REC domain of NtrC proteins regulate the activity of the protein and its phosphorylation controls the AAA+ domain oligomerization, while the central AAA+ domain participates in nucleotide binding, hydrolysis, oligomerization, and sigma54 interaction. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 121 matched cddid_all.tbl CDD cd17573 cd17573 381115 REC_HP-RR-like phosphoacceptor receiver (REC) domain of orphan response regulator HP-RR and similar proteins. Helicobacter pylori response regulator hp1043 (HP-RR) is an orphan response regulator which is phosphorylation-independent and is essential for growth. HP-RR functions as a cell growth-associated regulator in the absence of post-translational modification. Members of this subfamily contain REC and DNA-binding output domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 110 matched cddid_all.tbl CDD cd17574 cd17574 381116 REC_OmpR phosphoacceptor receiver (REC) domain of OmpR family response regulators. OmpR-like proteins are one of the most widespread transcriptional regulators. OmpR family members contain REC and winged helix-turn-helix (wHTH) DNA-binding output effector domain. They are involved in the control of environmental stress tolerance (such as the oxidative, osmotic and acid stress response), motility, virulence, outer membrane biogenesis and other processes. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 99 matched cddid_all.tbl CDD cd17575 cd17575 381117 REC_WspR-like phosphoacceptor receiver (REC) domain of WspR response regulator and similar proteins. The GGDEF response regulator WspR is part of the Wsp system that is homologous to chemotaxis systems and also includes the membrane-bound receptor protein WspA. In response to growth on surfaces, WspR is phosphorylated by the Wsp signal transduction complex and is activated, functioning as a diguanylate cyclase (DGC) that catalyzes c-di-GMP synthesis. WspR is a hybrid response regulator-diguanylate cyclase, containing an N-terminal REC domain and a C-terminal GGDEF domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 128 matched cddid_all.tbl CDD cd17580 cd17580 381118 REC_2_DhkD-like second phosphoacceptor receiver (REC) domain of Dictyostelium discoideum hybrid signal transduction histidine kinase D and similar domains. Dictyostelium discoideum hybrid signal transduction histidine kinase D (DhkD) is a large protein that contains two histidine kinase (HK) and two REC domains on the intracellular side of a single pass transmembrane domain, and extracellular PAS and PAC domains that likely are involved in ligand binding. This model represents the second REC domain and similar domains. DhkD activates the cAMP phosphodiesterase RegA to ensure proper prestalk and prespore patterning, tip formation, and the vertical elongation of the mound into a finger, in Dictyostelium discoideum. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 112 matched cddid_all.tbl CDD cd17581 cd17581 381119 REC_typeA_ARR phosphoacceptor receiver (REC) domain of type A Arabidopsis response regulators (ARRs) and similar proteins. Type-A response regulators of Arabidopsis (ARRs) are involved in cytokinin signaling, which involves a phosphorelay cascade by histidine kinase receptors (AHKs), histidine phosphotransfer proteins (AHPs) and downstream ARRs. Cytokinin is a plant hormone implicated in many growth and development processes including shoot organogenesis, leaf senescence, sink/source relationships, vascular development, lateral bud release, and photomorphogenic development. Type-A ARRs function downstream of and are regulated by type-B ARRs, which are a class of MYB-type transcription factors. As primary cytokinin response genes, type-A ARRs act as redundant negative feedback regulators of cytokinin signaling by inactivating the phosphorelay. ARRs are divided into two groups, type-A and -B, according to their sequence and domain structure. Type-A ARRs are similar in domain structure to CheY, in that they lack a typical output domain and only contain a stand-alone receiver (REC) domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 122 matched cddid_all.tbl CDD cd17582 cd17582 381120 psREC_PRR pseudo receiver domain of pseudo-response regulators. In Arabidopsis, five pseudo-response regulators (PRRs), also called APRRs, comprise a core group of clock components that controls the pace of the central oscillator of the circadian clock, an endogenous time-keeping mechanism that enables organisms to adapt to external daily cycles. The coordinated sequential expression of PRR9 (APRR9), PRR7 (APRR7), PRR5 (APRR5), PRR3 (APRR3), and PRR1 (APRR1) results in circadian waves that may be at the basis of the endogenous circadian clock. PRRs contain an N-terminal pseudo receiver (psREC) domain that resembles the receiver domain of a two-component response regulator, but lacks an aspartate residue that accepts a phosphoryl group from the sensor kinase, and a CCT motif at the C-terminus that contains a putative nuclear localization signal. The psREC domain is involved in protein-protein interactions. 104 matched cddid_all.tbl CDD cd17584 cd17584 381121 REC_typeB_ARR-like phosphoacceptor receiver (REC) domain of type B Arabidopsis response regulators (ARRs) and similar domains. Type-B ARRs (Arabidopsis response regulators) are a class of MYB-type transcription factors that act as major players in the transcriptional activation of cytokinin-responsive genes. They directly regulate the expression of type-A ARR genes and other downstream target genes. Cytokinin is a plant hormone implicated in many growth and development processes including shoot organogenesis, leaf senescence, sink/source relationships, vascular development, lateral bud release, and photomorphogenic development. Cytokinin signaling involves a phosphorelay cascade by histidine kinase receptors (AHKs), histidine phosphotransfer proteins (AHPs) and downstream ARRs. ARRs are divided into two groups, type-A and -B, according to their sequence and domain structure. Type-B ARRs contain a receiver (REC) domain and a large C-terminal extension that has characteristics of an effector or output domain, with a Myb-like DNA binding domain referred to as the GARP domain. The GARP domain is a motif specific to plant transcription factors. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 115 matched cddid_all.tbl CDD cd17586 cd17586 381122 REC_PFxFATGY phosphoacceptor receiver (REC) domain of PFxFATGY motif single-domain (stand-alone) response regulators. This subfamily is composed of stand-alone response regulators (RRs) containing the PFxFATG[G/Y] motif; RRs with such a motif are also called ''FAT GUY'' response regulators. Included in this subfamily are Sphingomonas melonis SdrG, Sinorhizobium meliloti Sma0114, and Erythrobacter litoralis EL_LovR. SdrG is involved in the control of the general stress response. Sma0114 is part of the Sma0113/Sma0114 two-component system (TCS) that is involved in catabolite repression and polyhydroxy butyrate synthesis. EL_LovR is involved in a light-regulated TCS. PFxFATG[G/Y] RRs are typically associated with histidine-tryptophan-glutamate (HWE) histidine kinases that constitute a subclass of the larger histidine kinase superfamily characterized by an altered ATP binding site, which lacks the F-box that is normally an integral component of the ATP lid. The PFxFATG[G/Y] motif is involved in conformational changes after phosphorylation that results in the activation of the RR. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 111 matched cddid_all.tbl CDD cd17589 cd17589 381123 REC_TPR phosphoacceptor receiver (REC) domain of uncharacterized tetratricopeptide repeat (TPR)-containing response regulators. Response regulators share the common phosphoacceptor REC domain and different output domains. This subfamily contains uncharacterized response regulators with TPR repeats as the effector or output domain, which might contain between 3 to 16 TPR repeats (each about 34 amino acids). TPR-containing proteins occur in all domains of life and the abundance of TPR-containing proteins in a bacterial proteome is not indicative of virulence. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Some members in this subfamily may contain inactive REC domains lacking canonical metal-binding and active site residues. 115 matched cddid_all.tbl CDD cd17593 cd17593 381124 REC_CheC-like phosphoacceptor receiver (REC) domain of uncharacterized response regulators containing a CheC domain. This subfamily is composed of uncharacterized proteins containing an N-terminal REC domain and a C-terminal CheC domain that may function as the output/effector domain of a response regulator. CheC is a CheY-P phosphatase, affecting the level of phosphorylated CheY which controls the sense of flagella rotation and determine swimming behavior of chemotactic bacteria. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 117 matched cddid_all.tbl CDD cd17594 cd17594 381125 REC_OmpR_VirG phosphoacceptor receiver (REC) domain of VirG-like OmpR family response regulators. VirG is part of the VirA/VirG two-component system that regulates the expression of virulence (vir) genes. The histidine kinase VirA senses a phenolic wound response signal, undergoes autophosphorylation, and phosphorelays to the VirG response regulator, which induces transcription of the vir regulon. VirG belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 113 matched cddid_all.tbl CDD cd17595 cd17595 381126 REC_TrxB phosphoacceptor receiver (REC) domain a fused response regulator with a thioredoxin reductase output domain. This family is composed of uncharacterized fusion proteins containing a REC domain and a thioredoxin reductase domain. Thioredoxin reductase catalyzes the reduction of thioredoxin and is thus a central component in the thioredoxin system. Fusion proteins containing REC and thioredoxin reductase domains could play an important role in the environmental regulation of the cellular dithiol-disulfide ratio. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 135 matched cddid_all.tbl CDD cd17596 cd17596 381127 REC_HupR phosphoacceptor receiver (REC) domain of hydrogen uptake protein regulator (HupR). Members of this subfamily are response regulator components of two-component systems that regulates hydrogenase activity, including HupR and HoxA. HupR is part of the HupT/HupR system that controls the synthesis of the membrane-bound [NiFe]hydrogenase, HupSL, of the photosynthetic bacterium Rhodobacter capsulatus. It belongs to the nitrogen regulatory protein C (NtrC) family of response regulators, which activate transcription by RNA polymerase (RNAP) in response to a change in the environment. HupR is an unusual member of this family as it activates transcription when unphosphorylated, and transcription is inhibited by phosphorylation. Proteins in this subfamily contain an N-terminal REC domain, a central sigma-54 interaction domain that lacks ATPase activity, and a C-terminal DNA-binding domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 133 matched cddid_all.tbl CDD cd17598 cd17598 381128 REC_hyHK phosphoacceptor receiver (REC) domain of uncharacterized hybrid sensor histidine kinase/response regulators. Typically, two-component regulatory systems (TCSs) consist of a sensor (histidine kinase) that responds to specific input(s) by modifying the output of a cognate response regulator (RR). TCSs allow organisms to sense and respond to changes in environmental conditions. Hybrid sensor histidine kinase/response regulators contain all the elements of a classical TCS in a single polypeptide chain. RRs share the common phosphoacceptor REC domain and different effector/output domains such as DNA, RNA, ligand-binding, protein-binding, or enzymatic domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 118 matched cddid_all.tbl CDD cd17602 cd17602 381129 REC_PatA-like phosphoacceptor receiver (REC) domain of PatA and similar domains. Nostoc sp. (or Anabaena sp.) PatA is necessary for proper patterning of heterocysts along filaments. PatA contains phosphoacceptor REC domain at its C-terminus and an N-terminal PATAN (PatA N-terminus) domain, which was proposed in a bioinformatics study to mediate protein-protein interactions. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. Some members of this group may have an inactive REC domain, lacking canonical metal-binding and active site residues. 102 matched cddid_all.tbl CDD cd17614 cd17614 381130 REC_OmpR_YycF-like phosphoacceptor receiver (REC) domain of YrcF-like OmpR family response regulators. YycF appears to play an important role in cell wall integrity in a wide range of gram-positive bacteria, and may also modulate cell membrane integrity. It functions as part of a phosphotransfer system that ultimately controls the levels of competence within the bacteria. YycF belongs to the OmpR family of response regulators, which are characterized by a REC domain and a winged helix-turn-helix effector domain involved in DNA binding. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 115 matched cddid_all.tbl CDD cd17615 cd17615 381131 REC_OmpR_MtPhoP-like phosphoacceptor receiver (REC) domain of MtPhoP-like OmpR family response regulators. Mycobacterium tuberculosis PhoP (MtPhoP) is part of the PhoP/PhoR two-component system that is involved in phosphate control by stimulating expression of genes involved in scavenging, transport and mobilization of phosphate, and repressing the utilization of nitrogen sources. Also included in this subfamily is Mycobacterium tuberculosis transcriptional regulatory protein TcrX, part of the two-component regulatory system TcrY/TcrX that may be involved in virulence. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 118 matched cddid_all.tbl CDD cd17616 cd17616 381132 REC_OmpR_CtrA phosphoacceptor receiver (REC) domain of CtrA-like OmpR family response regulators. CtrA is part of the CckA-ChpT-CtrA phosphorelay that is conserved in alphaproteobacteria and is important in orchestrating the cell cycle, polar development, and flagellar biogenesis. CtrA is the master regulator of flagella synthesis genes and also regulates genes involved in the cell cycle, exopolysaccharide synthesis, and cyclic-di-GMP signaling. CtrA is active as a transcription factor when phosphorylated. It is a member of the OmpR family of DNA-binding response regulators, characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 114 matched cddid_all.tbl CDD cd17618 cd17618 381133 REC_OmpR_PhoB phosphoacceptor receiver (REC) domain of PhoB response regulator from the OmpR family. The transcription factor PhoB is a component of the PhoR/PhoB two-component system, a key regulatory protein network that facilitates response to inorganic phosphate (Pi) starvation conditions by turning on the phosphate (pho) regulon whose products are involved in phosphorus uptake and metabolism. PhoB is a member of the OmpR family of DNA-binding response regulators that contains REC and winged helix-turn-helix (wHTH) DNA-binding output effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 118 matched cddid_all.tbl CDD cd17619 cd17619 381134 REC_OmpR_ArcA_TorR-like phosphoacceptor receiver (REC) domain of ArcA- and TorR-like OmpR family response regulators. This subfamily includes Escherichia coli TorR and ArcA, both OmpR family response regulators that mediate adaptation to changes in various respiratory growth conditions. The TorS-TorR two-component system (TCS) is responsible for the tight regulation of the torCAD operon, which encodes the trimethylamine N-oxide (TMAO) reductase respiratory system in response to anaerobic conditions and the presence of TMAO. The ArcA-ArcB TCS is involved in cell growth during anaerobiosis. ArcA is a global regulator that controls more than 30 operons involved in redox regulation (the Arc modulon). OmpR family DNA-binding response regulators are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 113 matched cddid_all.tbl CDD cd17620 cd17620 381135 REC_OmpR_KdpE-like phosphoacceptor receiver (REC) domain of KdpE-like OmpR family response regulators. KdpE is a component of the KdpD/KdpE two-component system (TCS) and is activated when histidine kinase KdpD senses a drop in external K+ concentration or upshift in ionic osmolarity, resulting in the expression of a heterooligomeric transporter KdpFABC. In addition, the KdpD/KdpE TCS is also an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. KdpE is a member of the OmpR family of DNA-binding response regulators that contain REC and winged helix-turn-helix (wHTH) DNA-binding output effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 99 matched cddid_all.tbl CDD cd17621 cd17621 381136 REC_OmpR_RegX3-like phosphoacceptor receiver (REC) domain of RegX3-like OmpR family response regulators. RegX3 is a member of the SenX3-RegX3 two-component system that is involved in phosphate-sensing signal transduction. Phosphorylated RegX3 functions as a transcriptional activator of phoA. It induces transcription in phosphate limiting environment and also controls expression of several critical metabolic enzymes in aerobic condition. RegX3 belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 99 matched cddid_all.tbl CDD cd17622 cd17622 381137 REC_OmpR_kpRstA-like phosphoacceptor receiver (REC) domain of kpRstA-like OmpR family response regulators. Klebsiella pneumoniae RstA (kpRstA) is part of the RstA/RstB two-component regulatory system that may play a regulatory role in virulence. It belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 116 matched cddid_all.tbl CDD cd17623 cd17623 381138 REC_OmpR_CpxR phosphoacceptor receiver (REC) domain of CpxR-like OmpR family response regulators. CpxR is part of the CpxA/CpxR two-component regulatory system that mediates envelope stress responses that is key for virulence and antibiotic resistance in several Gram negative pathogens. CpxR is a transcription factor/response regulator that controls the expression of numerous genes, including those of the classical porins OmpF and OmpC. It belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 115 matched cddid_all.tbl CDD cd17624 cd17624 381139 REC_OmpR_PmrA-like phosphoacceptor receiver (REC) domain of PmrA-like OmpR family response regulators. This subfamily contains various OmpR family response regulators including PmrA, BasR, QseB, tctD, and RssB, which are components of two-component regulatory systems (TCSs). The PmrA/PmrB TCS controls transcription of genes that are involved in lipopolysaccharide modification in the outer membrane of bacteria, increasing bacterial resistance to host-derived antimicrobial peptides. The BasS/BasR TCS functions as an iron- and zinc-sensing transcription regulator. The QseB/QseC TCS activates the flagella regulon by activating transcription of FlhDC. The RssA/RssB TCS regulates swarming behavior in Serratia marcescens. OmpR family DNA-binding response regulators contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 115 matched cddid_all.tbl CDD cd17625 cd17625 381140 REC_OmpR_DrrD-like phosphoacceptor receiver (REC) domain of DrrD-like OmpR family response regulators. DrrD is a OmpR/PhoB homolog from Thermotoga maritima whose function is not yet known. This subfamily also includes Streptococcus agalactiae transcriptional regulatory protein DltR, part of the DltS/DltR two-component system (TCS), and Pseudomonas aeruginosa transcriptional activator protein PfeR, part of the PfeR/PfeS TCS, which activates expression of the ferric enterobactin receptor. The DltS/DltR TCS regulates the expression of the dlt operon, which comprises four genes (dltA, dltB, dltC, and dltD) that catalyze the incorporation of D-alanine residues into the lipoteichoic acids. Members of this subfamily belong to the OmpR/PhoB family, which comprises of two domains, an N-terminal receiver domain and a C-terminal DNA-binding winged helix-turn-helix effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 115 matched cddid_all.tbl CDD cd17626 cd17626 381141 REC_OmpR_MtrA-like phosphoacceptor receiver (REC) domain of MtrA-like OmpR family response regulators. MtrA is part of MtrA/MtrB (or MtrAB), a highly conserved two-component system (TCS) implicated in the regulation of cell division in the actinobacteria. In unicellular Mycobacterium tuberculosis, MtrAB coordinates DNA replication with cell division and regulates the transcription of resuscitation-promoting factor B. In filamentous Streptomyces venezuelae, it links antibiotic production to sporulation. MtrA belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 115 matched cddid_all.tbl CDD cd17627 cd17627 381142 REC_OmpR_PrrA-like phosphoacceptor receiver (REC) domain of PrrA-like OmpR family response regulators. The Mycobacterium tuberculosis PrrA is part of the PrrA/PrrB two-component system (TCS) that has been implicated in early intracellular multiplication and is essential for viability. Also included in this subfamily is Mycobacterium tuberculosis MprA, part of the MprAB TCS that regulates EspR, a key regulator of the ESX-1 secretion system, and is required for establishment and maintenance of persistent infection in a tissue- and stage-specific fashion. PrrA and MprA belong to the OmpR family of DNA-binding response regulators, which contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 116 matched cddid_all.tbl CDD cd17630 cd17630 341285 OSB_MenE-like O-succinylbenzoic acid-CoA ligase. This family contains O-succinylbenzoyl-CoA (OSB-CoA) synthetase (also known as O-succinylbenzoic acid CoA ligase) that belongs to the ANL superfamily and catalyzes the ligation of CoA to o-succinylbenzoate (OSB). It includes MenE in the bacterial menaquinone biosynthesis pathway which is a promising target for the development of novel antibacterial agents. MenE catalyzes CoA ligation via an acyl-adenylate intermediate; tight-binding inhibitors of MenE based on stable acyl-sulfonyladenosine analogs of this intermediate provide a pathway toward the development of optimized MenE inhibitors. 325 matched cddid_all.tbl CDD cd17631 cd17631 341286 FACL_FadD13-like fatty acyl-CoA synthetase, including FadD13. This family contains fatty acyl-CoA synthetases, including Mycobacterium tuberculosis acid-induced operon MymA encoding the fatty acyl-CoA synthetase FadD13 which is essential for virulence and intracellular growth of the pathogen. The fatty acyl-CoA synthetase activates lipids before entering into the metabolic pathways and is also involved in transmembrane lipid transport. However, unlike soluble fatty acyl-CoA synthetases, but like the mammalian integral-membrane very-long-chain acyl-CoA synthetases, FadD13 accepts lipid substrates up to the maximum length of C26, and this is facilitated by an extensive hydrophobic tunnel from the active site to a positively charged patch. Also included is feruloyl-CoA synthetase (Fcs) in Rhodococcus strains where it is involved in biotechnological vanillin production from eugenol and ferulic acid via a non-beta-oxidative pathway. 435 matched cddid_all.tbl CDD cd17632 cd17632 341287 AFD_CAR-like adenylation domain of carboxylic acid reductase (CAR). This family contains the adenylation domain of carboxylic acid reductase enzymes (CARs), and performs an equivalent function to that of the ANL superfamily of adenylating enzymes. It takes a carboxylic acid substrate and ATP, and produces an AMP-acyl phosphoester intermediate, releasing pyrophosphate. Kinetic analysis using various substrates shows that this enzyme has a broad but similar substrate specificity, preferring electron-rich acids. This suggests that attack by the carboxylate on the alpha-phosphate of adenosine triphosphate (ATP) is the step that determines the substrate specificity and reaction kinetics. CAR is an important enzyme for use as a biocatalyst providing regiospecific route to aldehydes from their respective carboxylic acids. 588 matched cddid_all.tbl CDD cd17633 cd17633 341288 AFD_YhfT-like fatty acid-CoA ligase VraA. This family of acyl-CoA ligases includes Bacillus subtilis YhfT, as well as long-chain fatty acid-CoA ligase VraA, all of which are as yet to be characterized. These proteins belong to the adenylate-forming enzymes which catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain 320 matched cddid_all.tbl CDD cd17634 cd17634 341289 ACS-like acetate-CoA ligase. This family includes acyl- and aryl-CoA ligases, as well as the adenylation domain of nonribosomal peptide synthetases and firefly luciferases. The adenylate-forming enzymes catalyze an ATP-dependent two-step reaction to first activate a carboxylate substrate as an adenylate and then transfer the carboxylate to the pantetheine group of either coenzyme A or an acyl-carrier protein. The active site of the domain is located at the interface of a large N-terminal subdomain and a smaller C-terminal subdomain. 587 matched cddid_all.tbl CDD cd17635 cd17635 341290 FADD10 adenylate forming domain, fatty acid CoA ligase (FadD10). This family contains long chain fatty acid CoA ligases, including FadD10 which is involved in the synthesis of a virulence-related lipopeptide. FadD10 is a fatty acyl-AMP ligase (FAAL) that transfers fatty acids to an acyl carrier protein. Structures of FadD10 in apo- and complexed form with dodecanoyl-AMP, show a novel open conformation, facilitated by its unique inter-domain and intermolecular interactions, which is critical for the enzyme to carry out the acyl transfer onto the acyl carrier protein (Rv0100) rather than coenzyme A. 340 matched cddid_all.tbl CDD cd17636 cd17636 341291 PtmA long-chain fatty acid CoA ligase (FadD). This family contains fatty acid CoA ligases, including acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II, most of which are yet to be characterized. Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. 331 matched cddid_all.tbl CDD cd17637 cd17637 341292 ACLS-CaiC acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II. This family contains fatty acid CoA ligases, including acyl-CoA synthetase (AMP-forming)/AMP-acid ligase II, most of which are yet to be characterized, but may be similar to Carnitine-CoA ligase (CaiC) which catalyzes the transfer of CoA to carnitine. Fatty acyl-CoA ligases catalyze the ATP-dependent activation of fatty acids in a two-step reaction. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. 333 matched cddid_all.tbl CDD cd17638 cd17638 341293 FadD3 acyl-CoA synthetase FadD3 and similar proteins. This family contains long chain fatty acid CoA ligases, including FadD3 which is an acyl-CoA synthetase that initiates catabolism of cholesterol rings C and D in actinobacteria. The cholesterol catabolic pathway occurs in most mycolic acid-containing actinobacteria, such as Rhodococcus jostii RHA1, and is critical for Mycobacterium tuberculosis (Mtb) during infection. FadD3 catalyzes the ATP-dependent CoA thioesterification of 3a-alpha-H-4alpha(3'-propanoate)-7a-beta-methylhexahydro-1,5-indanedione (HIP) to yield HIP-CoA. Hydroxylated analogs of HIP, 5alpha-OH HIP and 1beta-OH HIP, can also be used. 330 matched cddid_all.tbl CDD cd17639 cd17639 341294 LC_FACS_euk1 Eukaryotic long-chain fatty acid CoA synthetase (LC-FACS), including fungal proteins. The members of this family are eukaryotic fatty acid CoA synthetases (EC 6.2.1.3) that activate fatty acids with chain lengths of 12 to 20 and includes fungal proteins. They act on a wide range of long-chain saturated and unsaturated fatty acids, but the enzymes from different tissues show some variation in specificity. LC-FACS catalyzes the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, and the formation of a fatty acyl-CoA. This is a required step before free fatty acids can participate in most catabolic and anabolic reactions. Organisms tend to have multiple isoforms of LC-FACS genes with multiple splice variants. For example, nine genes are found in Arabidopsis and six genes are expressed in mammalian cells. In Schizosaccharomyces pombe, lcf1 gene encodes a new fatty acyl-CoA synthetase that preferentially recognizes myristic acid as a substrate. 507 matched cddid_all.tbl CDD cd17640 cd17640 341295 LC_FACS_like "Long-chain fatty acid CoA synthetase. This family includes long-chain fatty acid (C12-C20) CoA synthetases, including an Arabidopsis gene At4g14070 that plays a role in activation and elongation of exogenous fatty acids. FACS catalyzes the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, and the formation of a fatty acyl-CoA. Eukaryotes generally have multiple isoforms of LC-FACS genes with multiple splice variants. For example, nine genes are found in Arabidopsis and six genes are expressed in mammalian cells. Free fatty acids must be ""activated"" to their CoA thioesters before participating in most catabolic and anabolic reactions." 468 matched cddid_all.tbl CDD cd17641 cd17641 341296 LC_FACS_bac1 "bacterial long-chain fatty acid CoA synthetase. The members of this family are bacterial long-chain fatty acid CoA synthetase, most of which are as yet uncharacterized. LC-FACS catalyzes the formation of fatty acyl-CoA in a two-step reaction: the formation of a fatty acyl-AMP molecule as an intermediate, and the formation of a fatty acyl-CoA. Free fatty acids must be ""activated"" to their CoA thioesters before participating in most catabolic and anabolic reactions." 569 matched cddid_all.tbl CDD cd17642 cd17642 341297 Firefly_Luc insect luciferase, similar to plant 4-coumarate: CoA ligases. This family contains insect firefly luciferases that share significant sequence similarity to plant 4-coumarate:coenzyme A ligases, despite their functional diversity. Luciferase catalyzes the production of light in the presence of MgATP, molecular oxygen, and luciferin. In the first step, luciferin is activated by acylation of its carboxylate group with ATP, resulting in an enzyme-bound luciferyl adenylate. In the second step, luciferyl adenylate reacts with molecular oxygen, producing an enzyme-bound excited state product (Luc=O*) and releasing AMP. This excited-state product then decays to the ground state (Luc=O), emitting a quantum of visible light. 532 matched cddid_all.tbl CDD cd17643 cd17643 341298 A_NRPS_Cytc1-like similar to adenylation domain of cytotrienin synthetase CytC1. This family of the adenylation (A) domain of nonribosomal peptide synthases (NRPS) includes Streptomyces sp. cytotrienin synthetase (CytC1), a relatively promiscuous adenylation enzyme that installs the aminoacyl moieties on the phosphopantetheinyl arm of the holo carrier protein CytC2. Also included are Streptomyces sp Thr1, involved in the biosynthesis of 4-chlorothreonine, Pseudomonas aeruginosa pyoverdine synthetase D (PvdD), involved in the biosynthesis of the siderophore pyoverdine and Pseudomonas syringae syringopeptin synthetase, where syringpeptin is a necrosis-inducing phytotoxin that functions as a virulence determinant in the plant-pathogen interaction. The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester bond to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. 450 matched cddid_all.tbl CDD cd17644 cd17644 341299 A_NRPS_ApnA-like similar to adenylation domain of anabaenopeptin synthetase (ApnA). This family of the adenylation (A) domain of nonribosomal peptide synthases (NRPS) includes Planktothrix agardhii anabaenopeptin synthetase (ApnA A1), which is capable of activating two chemically distinct amino acids (Arg and Tyr). Structural studies show that the architecture of the active site forces Arg to adopt a Tyr-like conformation, thus explaining the bispecificity. The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester bond to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. 465 matched cddid_all.tbl CDD cd17645 cd17645 341300 A_NRPS_LgrA-like adenylation (A) domain of linear gramicidin synthetase (LgrA) and similar proteins. This family of the adenylation (A) domain of nonribosomal peptide synthases (NRPS) includes linear gramicidin synthetase (LgrA) in Brevibacillus brevis. LgrA has a formylation domain fused to the N-terminal end that formylates its substrate for linear gramicidin synthesis to proceed. This formyl group is essential for the clinically important antibacterial activity of gramicidin by enabling head-to-head gramicidin dimers to make a beta-helical pore in gram-positive bacterial membranes, allowing free passage of monovalent cations, destroying the ion gradient and killing bacteria. This family also includes bacitracin synthetase 1 (known as ATP-dependent cysteine adenylase or BA1); it activates cysteine, incorporates two D-amino acids, releases and cyclizes the mature bacitracin, an antibiotic that is a mixture of related cyclic peptides that disrupt gram positive bacteria by interfering with cell wall and peptidoglycan synthesis. Also included is surfactin synthetase which activates and polymerizes the amino acids Leu, Glu, Asp, and Val to form the antibiotic surfactin. 440 matched cddid_all.tbl CDD cd17646 cd17646 341301 A_NRPS_AB3403-like Peptide Synthetase. The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester bond to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. 488 matched cddid_all.tbl CDD cd17647 cd17647 341302 A_NRPS_alphaAR Alpha-aminoadipate reductase. This family contains L-2-aminoadipate reductase, also known as alpha-aminoadipate reductase (EC 1.2.1.95) or alpha-AR or L-aminoadipate-semialdehyde dehydrogenase (EC 1.2.1.31), which catalyzes the activation of alpha-aminoadipate by ATP-dependent adenylation and the reduction of activated alpha-aminoadipate by NADPH. The activated alpha-aminoadipate is bound to the phosphopantheinyl group of the enzyme itself before it is reduced to (S)-2-amino-6-oxohexanoate. 520 matched cddid_all.tbl CDD cd17648 cd17648 341303 A_NRPS_ACVS-like N-(5-amino-5-carboxypentanoyl)-L-cysteinyl-D-valine synthase. This family contains ACV synthetase (ACVS, EC 6.3.2.26; also known as N-(5-amino-5-carboxypentanoyl)-L-cysteinyl-D-valine synthase or delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetase) is involved in medically important antibiotic biosynthesis. ACV synthetase is active in an early step in the penicillin G biosynthesis pathway which involves the formation of the tripeptide 6-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine (ACV); each of the constituent amino acids of the tripeptide ACV are activated as aminoacyl-adenylates with peptide bonds formed through the participation of amino acid thioester intermediates. ACV is then cyclized by the action of isopenicillin N synthase. 453 matched cddid_all.tbl CDD cd17649 cd17649 341304 A_NRPS_PvdJ-like non-ribosomal peptide synthetase. This family of the adenylation (A) domain of nonribosomal peptide synthases (NRPS) includes pyoverdine biosynthesis protein PvdJ involved in the synthesis of pyoverdine, which consists of a chromophore group attached to a variable peptide chain and comprises around 6-12 amino acids that are specific for each Pseudomonas species, and for which the peptide might be first synthesized before the chromophore assembly. Also included is ornibactin biosynthesis protein OrbI; ornibactin is a tetrapeptide siderophore with an l-ornithine-d-hydroxyaspartate-l-serine-l-ornithine backbone. The adenylation domain at the N-terminal of OrbI possibly initiates the ornibactin with the binding of N5-hydroxyornithine. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. 450 matched cddid_all.tbl CDD cd17650 cd17650 341305 A_NRPS_PpsD_like similar to adenylation domain of plipastatin synthase (PpsD). This family of the adenylation (A) domain of nonribosomal peptide synthases (NRPS) includes bacitracin synthetase 1 (BacA) in Bacillus licheniformis, tyrocidine synthetase in Brevibacillus brevis, plipastatin synthase (PpsD, an important antifungal protein) in Bacillus subtilis and mannopeptimycin peptide synthetase (MppB) in Streptomyces hygroscopicus. Plipastatin has strong fungitoxic activity and is involved in inhibition of phospholipase A2 and biofilm formation. Bacitracin, a mixture of related cyclic peptides, is used as a polypeptide antibiotic while function of tyrocidine is thought to be regulation of sporulation. MppB is involved in biosynthetic pathway of mannopeptimycin, a novel class of mannosylated lipoglycopeptides. The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester bond to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. 447 matched cddid_all.tbl CDD cd17651 cd17651 341306 A_NRPS_VisG_like similar to adenylation domain of virginiamycin S synthetase. This family of the adenylation (A) domain of nonribosomal peptide synthases (NRPS) includes virginiamycin S synthetase (VisG) in Streptomyces virginiae; VisG is involved in virginiamycin S (VS) biosynthesis as the provider of an L-pheGly molecule, a highly specific substrate for the last condensation step by VisF. This family also includes linear gramicidin synthetase B (LgrB) in Brevibacillus brevis. Substrate specificity analysis using residues of the substrate-binding pockets of all 16 adenylation domains has shown good agreement of the substrate amino acids predicted with the sequence of linear gramicidin. The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester bond to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. 491 matched cddid_all.tbl CDD cd17652 cd17652 341307 A_NRPS_CmdD_like similar to adenylation domain of chondramide synthase cmdD. This family of the adenylation (A) domain of nonribosomal peptide synthases (NRPS) includes phosphinothricin tripeptide (PTT, phosphinothricylalanylalanine) synthetase, where PTT is a natural-product antibiotic and potent herbicide that is produced by Streptomyces hygroscopicus. This adenylation domain has been confirmed to directly activate beta-tyrosine, and fluorinated chondramides are produced through precursor-directed biosynthesis. Also included in this family is chondramide synthase D (also known as ATP-dependent phenylalanine adenylase or phenylalanine activase or tyrosine activase). Chondramides A-D are depsipeptide antitumor and antifungal antibiotics produced by C. crocatus, are a class of mixed peptide/polyketide depsipeptides comprised of three amino acids (alanine, N-methyltryptophan, plus the unusual amino acid beta-tyrosine or alpha-methoxy-beta-tyrosine) and a polyketide chain ([E]-7-hydroxy-2,4,6-trimethyloct-4-enoic acid). 436 matched cddid_all.tbl CDD cd17653 cd17653 341308 A_NRPS_GliP_like nonribosomal peptide synthase GliP-like. This family includes the adenylation (A) domain of nonribosomal peptide synthases (NRPS) gliotoxin biosynthesis protein P (GliP), thioclapurine biosynthesis protein P (tcpP) and Sirodesmin biosynthesis protein P (SirP). In the filamentous fungus Aspergillus fumigatus, NRPS GliP is involved in the biosynthesis of gliotoxin, which is initiated by the condensation of serine and phenylalanine. Studies show that GliP is not required for invasive aspergillosis, suggesting that the principal targets of gliotoxin are neutrophils or other phagocytes. SirP is a phytotoxin produced by the fungus Leptosphaeria maculans, which causes blackleg disease of canola (Brassica napus). In the fungus Claviceps purpurea, NRPS tcpP catalyzes condensation of tyrosine and glycine, part of biosynthesis of an unusual class of epipolythiodioxopiperazines (ETPs) that lacks the reactive thiol group for toxicity. The adenylation (A) domain of NRPS recognizes a specific amino acid or hydroxy acid and activates it as an (amino) acyl adenylate by hydrolysis of ATP. The activated acyl moiety then forms a thioester bond to the enzyme-bound cofactor phosphopantetheine of a peptidyl carrier protein domain. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. 433 matched cddid_all.tbl CDD cd17654 cd17654 341309 A_NRPS_acs4 acyl-CoA synthetase family member 4. This family of the adenylation (A) domain of nonribosomal peptide synthases (NRPS) contains acyl-CoA synthethase family member 4, also known as 2-aminoadipic 6-semialdehyde dehydrogenase or aminoadipate-semialdehyde dehydrogenase, most of which are uncharacterized. Acyl-CoA synthetase catalyzes the initial reaction in fatty acid metabolism, by forming a thioester with CoA. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. 449 matched cddid_all.tbl CDD cd17655 cd17655 341310 A_NRPS_Bac bacitracin synthetase and related proteins. This family of the adenylation (A) domain of nonribosomal peptide synthases (NRPS) includes bacitracin synthetases 1, 2, and 3 (BA1, also known as ATP-dependent cysteine adenylase or cysteine activase, BA2, also known as ATP-dependent lysine adenylase or lysine activase, and BA3, also known as ATP-dependent isoleucine adenylase or isoleucine activase) in Bacilli. Bacitracin is a mixture of related cyclic peptides used as a polypeptide antibiotic. This family also includes gramicidin synthetase 1 involved in synthesis of the cyclic peptide antibiotic gramicidin S via activation of phenylalanine. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. 490 matched cddid_all.tbl CDD cd17656 cd17656 341311 A_NRPS_ProA gramicidin S synthase 2, also known as ATP-dependent proline adenylase. This family of the adenylation (A) domain of nonribosomal peptide synthases (NRPS) contains gramicidin S synthase 2 (also known as ATP-dependent proline adenylase or proline activase or ProA). ProA is a multifunctional enzyme involved in synthesis of the cyclic peptide antibiotic gramicidin S and able to activate and polymerize the amino acids proline, valine, ornithine and leucine. NRPSs are large multifunctional enzymes which synthesize many therapeutically useful peptides in bacteria and fungi via a template-directed, nucleic acid independent nonribosomal mechanism. These natural products include antibiotics, immunosuppressants, plant and animal toxins, and enzyme inhibitors. NRPS has a distinct modular structure in which each module is responsible for the recognition, activation, and in some cases, modification of a single amino acid residue of the final peptide product. The modules can be subdivided into domains that catalyze specific biochemical reactions. 479 matched cddid_all.tbl CDD cd17657 cd17657 350495 CDC14_N N-terminal domain pseudophosphatase domain of CDC14 family proteins. The cell division control protein 14 (CDC14) family is highly conserved in all eukaryotes, although the roles of its members seem to have diverged during evolution. Yeast Cdc14, the best characterized member of this family, is a dual-specificity phosphatase that plays key roles in cell cycle control. It preferentially dephosphorylates cyclin-dependent kinase (CDK) targets, which makes it the main antagonist of CDK in the cell. Cdc14 functions at the end of mitosis and it triggers the events that completely eliminates the activity of CDK and other mitotic kinases. It is also involved in coordinating the nuclear division cycle with cytokinesis through the cytokinesis checkpoint, and in chromosome segregation. Cdc14 phosphatases also function in DNA replication, DNA damage checkpoint, and DNA repair. Vertebrates may contain more than one Cdc14 homolog; humans have three (CDC14A, CDC14B, and CDC14C). CDC14 family proteins contain a highly conserved N-terminal pseudophosphatase domain that contributes to substrate specificity and a C-terminal catalytic dual-specificity phosphatase domain with the PTP signature motif. The N-terminal pseudophosphatase domain lacks the catalytic residues. 144 matched cddid_all.tbl CDD cd17658 cd17658 350496 PTPc_plant_PTP1 protein tyrosine phosphatase 1 from Arabidopsis thaliana and similar plant PTPs. Arabidopsis thaliana protein tyrosine phosphatase 1 (AtPTP1) belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. AtPTP1 dephosphorylates and inhibits MAP kinase 6 (MPK6) in non-oxidative stress conditions. Together with MAP kinase phosphatase 1 (MKP1) it expresses salicylic acid (SA) and camalexin biosynthesis, and therefore, modulating defense response. 206 matched cddid_all.tbl CDD cd17659 cd17659 350497 PTP_paladin_1 protein tyrosine phosphatase-like domain of paladin, repeat 1. Paladin is a putative phosphatase, which in mouse is expressed in endothelial cells during embryonic development and in arterial smooth muscle cells in adults. It has been suggested to be an antiphosphatase that regulates the activity of specific neural crest regulatory factors and thus, modulates neural crest cell formation and migration. Paladin contains two tyrosine-protein phosphatase domains. This model represents repeat 1. 220 matched cddid_all.tbl CDD cd17660 cd17660 350498 PTP_paladin_2 protein tyrosine phosphatase-like domain of paladin, repeat 2. Paladin is a putative phosphatase, which in mouse is expressed in endothelial cells during embryonic development and in arterial smooth muscle cells in adults. It has been suggested to be an antiphosphatase that regulates the activity of specific neural crest regulatory factors and thus, modulates neural crest cell formation and migration. Paladin contains two tyrosine-protein phosphatase domains. This model represents repeat 2. 216 matched cddid_all.tbl CDD cd17661 cd17661 350499 PFA-DSP_Oca2 atypical dual specificity phosphatases similar to oxidant-induced cell-cycle arrest protein 2. Oxidant-induced cell-cycle arrest protein 2 (Oca2) is an atypical dual specificity phosphatase of unknown function. It has been identified as a putative negative regulator acting on cell wall integrity and mating MAPK pathways in yeast. It belongs to a group of atypical DSPs present in plants, fungi, kinetoplastids, and slime molds called plant and fungi atypical dual-specificity phosphatases (PFA-DSPs). Oca2 may be an inactive DSP-like protein as it lacks the CxxxxxR catalytic motif. 146 matched cddid_all.tbl CDD cd17662 cd17662 350500 PFA-DSP_Oca4 atypical dual specificity phosphatases similar to oxidant-induced cell-cycle arrest protein 4. Oxidant-induced cell-cycle arrest protein 4 (Oca4) is an atypical dual specificity phosphatase of unknown function. It belongs to a group of atypical DSPs present in plants, fungi, kinetoplastids, and slime molds called plant and fungi atypical dual-specificity phosphatases (PFA-DSPs). Oca4 may be an inactive DSP-like protein as it lacks the CxxxxxR catalytic motif. 177 matched cddid_all.tbl CDD cd17663 cd17663 350501 PFA-DSP_Oca6 atypical dual specificity phosphatases similar to oxidant-induced cell-cycle arrest protein 6. Oxidant-induced cell-cycle arrest protein 6 (Oca6) is an atypical dual specificity phosphatase of unknown function. It belongs to a group of atypical DSPs present in plants, fungi, kinetoplastids, and slime molds called plant and fungi atypical dual-specificity phosphatases (PFA-DSPs). Oca6 may be an inactive DSP-like protein as it lacks the CxxxxxR catalytic motif. 162 matched cddid_all.tbl CDD cd17664 cd17664 350502 Mce1_N N-terminal triphosphatase domain of mRNA capping enzyme. mRNA capping enzyme, also known as RNA guanylyltransferase and 5'-phosphatase (RNGTT) or mammalian mRNA capping enzyme (Mce1) in mammals, is a bifunctional enzyme that catalyzes the first two steps of cap formation: (1) by removing the gamma-phosphate from the 5'-triphosphate end of nascent mRNA to yield a diphosphate end using the polynucleotide 5'-phosphatase activity (EC 3.1.3.33) of the N-terminal triphosphatase domain; and (2) by transferring the GMP moiety of GTP to the 5'-diphosphate terminus through the C-terminal mRNA guanylyltransferase domain (EC 2.7.7.50). The enzyme is also referred to as CEL-1 in Caenorhabditis elegans. 167 matched cddid_all.tbl CDD cd17665 cd17665 350503 DSP_DUSP11 dual-specificity phosphatase domain of dual specificity protein phosphatase 11 and similar proteins. dual specificity protein phosphatase 11 (DUSP11), also known as RNA/RNP complex-1-interacting phosphatase or phosphatase that interacts with RNA/RNP complex 1 (PIR1), has RNA 5'-triphosphatase and diphosphatase activity, but only poor protein-tyrosine phosphatase activity. It has activity for short RNAs but is less active toward mononucleotide triphosphates, suggesting that its primary function in vivo is to dephosphorylate RNA 5'-ends. It may play a role in nuclear mRNA metabolism. Also included in this subfamily is baculovirus RNA 5'-triphosphatase for Autographa californica nuclear polyhedrosis virus. 169 matched cddid_all.tbl CDD cd17666 cd17666 350504 PTP-MTM-like_fungal protein tyrosine phosphatase-like domain of fungal myotubularins. Myotubularins are a unique subgroup of protein tyrosine phosphatases that use inositol phospholipids, rather than phosphoproteins, as substrates. They dephosphorylate the D-3 position of phosphatidylinositol 3-phosphate [PI(3)P] and phosphatidylinositol 3,5-bisphosphate [PI(3,5)P2], generating phosphatidylinositol and phosphatidylinositol 5-phosphate [PI(5)P], respectively. Not all members are catalytically active proteins, some function as adaptors for the active members. 229 matched cddid_all.tbl CDD cd17667 cd17667 350505 R-PTPc-G-1 catalytic domain of receptor-type tyrosine-protein phosphatase G, repeat 1. Receptor-type tyrosine-protein phosphatase G (PTPRG), also called protein-tyrosine phosphatase gamma (R-PTP-gamma), belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRG is an important tumor suppressor gene in multiple human cancers such as lung, ovarian, and breast cancers. It is widely expressed in many tissues, including the central nervous system, where it plays a role during neuroinflammation processes. It can dephosphorylate platelet-derived growth factor receptor beta (PDGFRB) and may play a role in PDGFRB-related infantile myofibromatosis. PTPRG has four splicing isoforms: three transmembrane isoforms, PTPRG-A, B, and C, and one secretory isoform, PTPRG-S, which are expressed in many tissues including the brain. PTPRG is a type 1 integral membrane protein consisting of an extracellular region with a carbonic anhydrase-like (CAH) and a fibronectin type III (FN3) domains, and an intracellular region with a catalytic PTP domain (repeat 1) proximal to the membrane, and a catalytically inactive PTP-fold domain (repeat 2) distal to the membrane. This model represents the catalytic PTP domain (repeat 1). 274 matched cddid_all.tbl CDD cd17668 cd17668 350506 R-PTPc-Z-1 catalytic domain of receptor-type tyrosine-protein phosphatase Z, repeat 1. Receptor-type tyrosine-protein phosphatase Z (PTPRZ), also called receptor-type tyrosine-protein phosphatase zeta (R-PTP-zeta), belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. Three isoforms are generated by alternative splicing from a single PTPRZ gene: two transmembrane isoforms, PTPRZ-A and PTPRZ-B, and one secretory isoform, PTPRZ-S (also known as phosphacan); all are preferentially expressed in the central nervous system (CNS) as chondroitin sulfate (CS) proteoglycans. PTPRZ isoforms play important roles in maintaining oligodendrocyte precursor cells in an undifferentiated state. PTPRZ is a type 1 integral membrane protein consisting of an extracellular region with a carbonic anhydrase-like (CAH) and a fibronectin type III (FN3) domains, and an intracellular region with a catalytic PTP domain (repeat 1) proximal to the membrane, and a catalytically inactive PTP-fold domain (repeat 2) distal to the membrane. This model represents the catalytic PTP domain (repeat 1). 209 matched cddid_all.tbl CDD cd17669 cd17669 350507 R-PTP-Z-2 catalytic domain of receptor-type tyrosine-protein phosphatase Z, repeat 2. Receptor-type tyrosine-protein phosphatase Z (PTPRZ), also called receptor-type tyrosine-protein phosphatase zeta (R-PTP-zeta), belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. Three isoforms are generated by alternative splicing from a single PTPRZ gene: two transmembrane isoforms, PTPRZ-A and PTPRZ-B, and one secretory isoform, PTPRZ-S (also known as phosphacan); all are preferentially expressed in the central nervous system (CNS) as chondroitin sulfate (CS) proteoglycans. PTPRZ isoforms play important roles in maintaining oligodendrocyte precursor cells in an undifferentiated state. PTPRZ is a type 1 integral membrane protein consisting of an extracellular region with a carbonic anhydrase-like (CAH) and a fibronectin type III (FN3) domains, and an intracellular region with a catalytic PTP domain (repeat 1) proximal to the membrane, and a catalytically inactive PTP-fold domain (repeat 2) distal to the membrane. This model represents the inactive PTP-like domain (repeat 2). 204 matched cddid_all.tbl CDD cd17670 cd17670 350508 R-PTP-G-2 PTP-like domain of receptor-type tyrosine-protein phosphatase G, repeat 2. Receptor-type tyrosine-protein phosphatase G (PTPRG), also called protein-tyrosine phosphatase gamma (R-PTP-gamma), belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. PTPRG is an important tumor suppressor gene in multiple human cancers such as lung, ovarian, and breast cancers. It is widely expressed in many tissues, including the central nervous system, where it plays a role during neuroinflammation processes. It can dephosphorylate platelet-derived growth factor receptor beta (PDGFRB) and may play a role in PDGFRB-related infantile myofibromatosis. PTPRG is a type 1 integral membrane protein consisting of an extracellular region with a carbonic anhydrase-like (CAH) and a fibronectin type III (FN3) domains, and an intracellular region with a catalytic PTP domain (repeat 1) proximal to the membrane, and a catalytically inactive PTP-fold domain (repeat 2) distal to the membrane. This model represents the inactive PTP-like domain (repeat 2). 205 matched cddid_all.tbl CDD cd17671 cd17671 439038 RUN RUN domain. RUN domain, named after RPIP8 (Rap2 interacting protein 8), UNC-14 and NESCA (new molecule containing SH3 at the carboxyl-terminus), is a less conserved protein motif that comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases. RUN domains are often found in proteins linked particularly to the functions of GTPases in the Rap and Rab families, suggesting the RUN domain may be involved in Rab-mediated membrane trafficking, possibly as a Rab-binding site. RUN domain-containing proteins could hence play important roles in multiple Ras-like GTPase signalling pathways. 154 matched cddid_all.tbl CDD cd17672 cd17672 349491 MDM2 p53-binding domain found in E3 ubiquitin-protein ligase MDM2 and similar proteins. MDM2, also known as double minute 2 protein (Hdm2), or oncoprotein MDM2, or p53-binding protein, exerts its oncogenic activity predominantly by binding the p53 tumor suppressor and blocking its transcriptional activity. It forms homo-oligomers and displays E3 ubiquitin ligase activity, catalyzing the attachment of ubiquitin to p53 as an essential step in the regulation of its expression levels in cells. Moreover, in response to ribosomal stress, MDM2-mediated p53 ubiquitination and degradation can be inhibited through the interaction with ribosomal proteins L5, L11, and L23. MDM2 also has a p53-independent role in tumorigenesis and cell growth regulation. In addition, it binds interferon (IFN) regulatory factor-2 (IRF-2), an IFN-regulated transcription factor, and mediates its ubiquitination. MDM2 contains an N-terminal p53-binding domain and a C-terminal zinc RING-finger domain conferring E3 ligase activity that is required for ubiquitination and nuclear export of p53. It is also responsible for the hetero-oligomerization of MDM2, which is crucial for the suppression of P53 activity during embryonic development, and the recruitment of E2 ubiquitin-conjugating enzymes. MDM2 also harbors a RanBP2-type zinc finger (zf-RanBP2) domain, as well as a nuclear localization signal (NLS) and a nuclear export signal (NES), near the central acidic region. 83 matched cddid_all.tbl CDD cd17673 cd17673 349492 MDM4 p53-binding domain found in MDM4 and similar proteins. MDM4, also known as double minute 4 protein, MDM2-like p53-binding protein, protein MDMX, HDMX, or p53-binding protein MDM4, exerts its oncogenic activity predominantly by binding the p53 tumor suppressor and blocking its transcriptional activity. MDM4 is phosphorylated and destabilized in response to DNA damage stress. It can also be specifically dephosphorylated through directly interacting with protein phosphatase 1 (PP1), which may increase its stability and thus inhibit p53 activity. MDM4 also has a p53-independent role in tumorigenesis and cell growth regulation. MDM4 contains an N-terminal p53-binding domain and a C-terminal zinc RING-finger domain responsible for its hetero-oligomerization, which is crucial for the suppression of P53 activity during embryonic development and the recruitment of E2 ubiquitin-conjugating enzymes. MDM4 also harbors a RanBP2-type zinc finger (zf-RanBP2) domain near the central acidic region. 79 matched cddid_all.tbl CDD cd17674 cd17674 349493 SWIB_BAF60A SWIB domain found in BRG1-associated factor 60A (BAF60A) and similar proteins. BAF60A, also termed SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1 (SMARCD1), or 60 kDa BRG-1/Brm-associated factor subunit A, or SWI/SNF complex 60 kDa subunit, is a core subunit of the SWI/SNF chromatin-remodeling complex that activates the transcription of fatty acid oxidation genes during fasting. BAF60A is involved in chromatin remodeling and hepatic lipid metabolism. It mediates critical interactions between nuclear receptors and the BRG1 chromatin-remodeling complex for transactivation. It is also a key component of the transcriptional control in cardiac progenitors. Moreover, BAF60A interacts with p53 to recruit the SWI/SNF complex, suggesting that the SWI/SNF chromatin remodeling complex is involved in the suppression of tumors. 77 matched cddid_all.tbl CDD cd17675 cd17675 349494 SWIB_BAF60B SWIB domain found in BRG1-associated factor 60B (BAF60B) and similar proteins. BAF60B, also termed SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 2 (SMARCD2), or 60 kDa BRG-1/Brm-associated factor subunit B, is a component of the BAF complex. It is involved in transcriptional activation and repression of select genes by chromatin remodeling. It plays a role in the ATM-p53 pathway in sensing chromatin opening by facilitating ATM recruitment to the SWI/SNF complex, as well as ATM activation. It also regulates transcriptional networks controlling differentiation of neutrophil granulocytes. Thus, it acts as a key factor controlling myelopoiesis and is a potential tumor suppressor in leukemia. 80 matched cddid_all.tbl CDD cd17676 cd17676 349495 SWIB_BAF60C SWIB domain found in BRG1-associated factor 60C (BAF60C) and similar proteins. BAF60C, also termed SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 3 (SMARCD3), or 60 kDa BRG-1/Brm-associated factor subunit C, is a core subunit of the SWI/SNF chromatin-remodeling complex that activates the transcription of fatty acid oxidation genes during fasting. It is involved in chromatin remodeling and hepatic lipid metabolism. It is also essential for cardiomyocyte differentiation at the early heart development. Moreover, BAF60C drives glycolytic metabolism in the muscle and improves systemic glucose homeostasis through Deptor-mediated Akt activation. Furthermore, BAF60C epigenetically regulates epithelial-mesenchymal transition (EMT) by activating WNT signaling pathways. 74 matched cddid_all.tbl CDD cd17677 cd17677 439039 RUN1_DENND5 RUN1 domain found in DENN domain-containing protein 5 (DENND5) and similar proteins. DENND5 has been characterized as Rab6-interacting protein which is composed of an N-terminal DENN (Differentially Expressed in Normal and Neoplastic cells) domain followed by two RUN (RPIP8 [RaP2-interacting protein 8], UNC-14, and NESCA [new molecule containing SH3 at the carboxyl terminus]) domains flanking a PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain. It functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. DENND5 has two isoforms, DENND5A and DENND5B. This model represents the first RUN domain of DENND5. 183 matched cddid_all.tbl CDD cd17678 cd17678 439040 RUN2_DENND5 RUN2 domain found in DENN domain-containing protein 5 (DENND5) and similar proteins. DENND5 has been characterized as Rab6-interacting protein which is composed of an N-terminal DENN (Differentially Expressed in Normal and Neoplastic cells) domain followed by two RUN (RPIP8 [RaP2-interacting protein 8], UNC-14, and NESCA [new molecule containing SH3 at the carboxyl terminus]) domains flanking a PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain. It functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. DENND5 has two isoforms, DENND5A and DENND5B. This model represents the second RUN domain of DENND5. 182 matched cddid_all.tbl CDD cd17679 cd17679 439041 RUN_PLEKHM1 RUN domain found in pleckstrin homology domain-containing family M member 1 (PLEKHM1) and similar proteins. PLEKHM1, also called PH domain-containing family M member 1, or 162 kDa adapter protein (AP162), may act as a multivalent adapter protein that regulates Rab7-dependent and HOPS complex-dependent fusion events in the endolysosomal system and couples autophagic and the endocytic trafficking pathways. This model represents the RUN domain of PLEKHM1. 171 matched cddid_all.tbl CDD cd17680 cd17680 439042 RUN_PLEKHM2 RUN domain found in pleckstrin homology domain-containing family M member 2 (PLEKHM2) and similar proteins. PLEKHM2, also called PH domain-containing family M member 2, or Salmonella-induced filaments A (SifA) and Kinesin-Interacting Protein (SKIP), is the lysosome, melanosome and lytic granule cargo adaptor that controls lysosome positioning using a composite kinesin-1 heavy and light chain-binding domain. In addition to kinesin-1, it also interacts with several Rabs to affect endosomal trafficking. This model represents the RUN domain of PLEKHM2. 145 matched cddid_all.tbl CDD cd17681 cd17681 439043 RUN_RUFY1_like RUN domain found in RUN and FYVE domain-containing proteins, RUFY1, RUFY2, RUFY3 and similar proteins. This family includes RUN and FYVE domain-containing protein RUFY1, RUFY2, and RUFY3. RUFY1, also called FYVE-finger protein EIP1, or La-binding protein 1, or Rab4-interacting protein (Rabip4), or Zinc finger FYVE domain-containing protein 12 (ZFY12), a human homolog of mouse Rabip4, an effector of Rab4 GTPase that regulates recycling of endocytosed cargo. RUFY1 is an endosomal protein that functions as a dual effector of Rab4 and Rab14 and is involved in efficient recycling of transferrin (Tfn). It is a downstream effector of Etk, a downstream tyrosine kinase of PI3-kinase that is involved in regulation of vesicle trafficking. RUFY2, also called Rab4-interacting protein related, is a novel embryonic factor that is present in the nucleus at early stages of embryonic development. It may have both endosomal functions in the cytoplasm and nuclear functions. RUFY3, also called Rap2-interacting protein x (RIPx or RPIPx), or single axon-regulated protein (singar), is an N-terminal RUN domain and a C-terminal FYVE domain containing protein predominantly expressed in the brain. It suppresses formation of surplus axons for neuronal polarity. Unlike other RUFY proteins, RUFY3 can associate with the GTP-bound active form of Rab5. RUFY1, RUFY2, and RUFY3 contain an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between; this model represents the RUN domain. 155 matched cddid_all.tbl CDD cd17682 cd17682 439044 RUN_RUFY4_like RUN domain found in RUN and FYVE domain-containing protein 4 (RUFY4), FYVE and coiled-coil domain-containing protein 1 (FYCO1), and similar proteins. The family includes RUFY4 and FYCO1. RUFY4 acts as a positive regulator that enhances autophagy and lysosome tethering in response to Interleukin-4. It is expressed in a cell-specific manner or under specific immunological conditions associated with IL4 expression such as allergic asthma. FYCO1, also called zinc finger FYVE domain-containing protein 7 (ZFYVE7), is a multidomain autophagy adaptor protein that interacts with kinesin motor proteins and with the autophagosomal membrane components microtubule-associated protein 1 light chain 3 (LC3), Rab7, and phosphatidylinositol 3-phosphate (PI3P), to mediate microtubule plus-end-directed autophagosome transport. Both RUFY4 and FYCO1 contain an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between; this model represents the RUN domain. 150 matched cddid_all.tbl CDD cd17683 cd17683 439045 RUN_RUNDC1 RUN domain found in RUN domain-containing protein 1 (RUNDC1) and similar proteins. RUN domain-containing protein 1 (RUNDC1) is thought to a role as p53/TP53 inhibitor and as such may have oncogenic activity. This model contains the RUN domain. 248 matched cddid_all.tbl CDD cd17684 cd17684 439046 RUN_RUNDC3 RUN domain found in RUN domain-containing protein 3 (RUNDC3) and similar proteins. RUNDC3 contains two isoforms, RUNDC3A and RUNDC3B. RUNDC3A, also called Rap2-interacting protein 8 (RPIP8), may act as an effector of Rap2A GTPase in neuronal cells. RUNDC3B, also called Rap2-binding protein 9, or Rap2-interacting protein 9 (RPIP-9), contains a RUN domain in its N-terminal region that mediates interaction with Rap2, an important component of the Mitogen-Activated Protein Kinase (MAPK) cascade, which regulates cellular proliferation and differentiation. It also contains characteristic binding sites for MAPK intermediates. Both RUNDC3A and RUNDC3B contain a RUN domain. 150 matched cddid_all.tbl CDD cd17685 cd17685 439047 RUN_RUSC RUN domain found in RUN and SH3 domain-containing proteins, RUSC1, RUSC2 and similar proteins. RUSC1, also called new molecule containing SH3 at the carboxy-terminus (NESCA), may acts as a signaling adapter that translocates to the nuclear envelope and regulates neurotrophin-induced neurite outgrowth. RUSC2, also called iporin, or interacting protein of Rab1, is a novel interacting molecule for the active GTP-bound conformation of Rab1. It may function as a link between the targeting of endoplasmic reticulum derived vesicles, triggered by the Rab1 GTPase and a signaling pathway regulated by molecules containing SH3 and/or poly-proline regions. This model contains the RUN domain of RUSC1 and RUSC2. 178 matched cddid_all.tbl CDD cd17686 cd17686 439048 RUN_RUBCN RUN domain found in Run domain Beclin-1-interacting and cysteine-rich domain-containing protein (RUBCN) and similar proteins. RUBCN, also called rubicon, or beclin-1 associated RUN domain containing protein (Baron), is part of a Beclin-1-Vps34-containing autophagy complex. It negatively regulates endosome maturation and degradative endocytic trafficking and impairs autophagosome maturation process. It is also an important negative regulator of the innate immune response, enhances viral replication and may play a role in viral immune evasion. This model contains the RUN domain of RUBCN. 151 matched cddid_all.tbl CDD cd17687 cd17687 439049 RUN_SGSM1_like RUN domain found in small G protein signaling modulators, SGSM1, SGSM2, and similar proteins. SGSM1, also called RUN and TBC1 domain-containing protein 2 (RUTBC2), interacts with numerous Rab family members, functioning as Rab effector for some, and as GTPase activator for others. It is a Rab9A effector and GTPase-activating protein for Rab36, and links Rab9A function to Rab36 function in the endosomal system. SGSM2, also called RUN and TBC1 domain-containing protein 1 (RUTBC1), is a GTPase-activating protein for Rab32/38, and regulates melanogenic enzyme trafficking in melanocytes. It also acts as a Rab9A effector that activates GTP hydrolysis by Rab32 and Rab33B proteins. This model contains the RUN domain of SGSM1 and SGSM2. 161 matched cddid_all.tbl CDD cd17688 cd17688 439050 RUN_SGSM3 RUN domain found in small G protein signaling modulator 3 (SGSM3) and similar proteins. SGSM3, also called RUN and TBC1 domain-containing protein 3 (RUTBC3), or Merlin-Associated Protein (MAP), or Rab-GTPase-activating protein-like protein (RabGAPLP), may play a cooperative role in NF2-mediated growth suppression of cells. This model contains the RUN domain of SGSM3. 214 matched cddid_all.tbl CDD cd17689 cd17689 439051 RUN_SNX29 RUN domain found in sorting nexin-29 (SNX29) and similar proteins. SNX29, also called RUN domain-containing protein 2A (RUNDC2A), belongs to the sorting nexin family. Sorting nexins are a large group of proteins that are localized in the cytoplasm and have the potential for membrane association either through their lipid-binding PX domain, a phospholipid-binding motif, or through protein-protein interactions with membrane-associated protein complexes. Some sorting nexin family members have been shown to facilitate protein sorting. This model contains the RUN domain of SNX29. 166 matched cddid_all.tbl CDD cd17690 cd17690 439052 RUN1_DENND5A RUN1 domain found in DENN domain-containing protein 5A (DENND5A) and similar proteins. DENND5A, also called Rab6-interacting protein 1 (Rab6IP1), is present predominantly in developing neuronal tissue, and functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. It is composed of an N-terminal DENN (Differentially Expressed in Normal and Neoplastic cells) domain followed by two RUN (RPIP8 [RaP2-interacting protein 8], UNC-14, and NESCA [new molecule containing SH3 at the carboxyl terminus]) domains flanking a PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain. This model represents the first RUN domain of DENND5A. 209 matched cddid_all.tbl CDD cd17691 cd17691 439053 RUN1_DENND5B RUN1 domain found in DENN domain-containing protein 5B (DENND5B) and similar proteins. DENND5B, also called Rab6-interacting protein 1 (Rab6IP1)-like protein, functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. It is composed of an N-terminal DENN (Differentially Expressed in Normal and Neoplastic cells) domain followed by two RUN (RPIP8 [RaP2-interacting protein 8], UNC-14, and NESCA [new molecule containing SH3 at the carboxyl terminus]) domains flanking a PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain. This model represents the first RUN domain of DENND5B. 206 matched cddid_all.tbl CDD cd17692 cd17692 439054 RUN2_DENND5A RUN2 domain found in DENN domain-containing protein 5A (DENND5A) and similar proteins. DENND5A, also called Rab6-interacting protein 1 (Rab6IP1), is present predominantly in developing neuronal tissue, and functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. It is composed of an N-terminal DENN (Differentially Expressed in Normal and Neoplastic cells) domain followed by two RUN (RPIP8 [RaP2-interacting protein 8], UNC-14, and NESCA [new molecule containing SH3 at the carboxyl terminus]) domains flanking a PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain. This model represents the second RUN domain of DENND5A. 176 matched cddid_all.tbl CDD cd17693 cd17693 439055 RUN2_DENND5B RUN2 domain found in DENN domain-containing protein 5B (DENND5B) and similar proteins. DENND5B, also called Rab6-interacting protein 1 (Rab6IP1)-like protein, functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. It is composed of an N-terminal DENN (Differentially Expressed in Normal and Neoplastic cells) domain followed by two RUN (RPIP8 [RaP2-interacting protein 8], UNC-14, and NESCA [new molecule containing SH3 at the carboxyl terminus]) domains flanking a PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain. This model represents the second RUN domain of DENND5B. 179 matched cddid_all.tbl CDD cd17694 cd17694 439056 RUN_RUFY1 RUN domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins. RUFY1, also called FYVE-finger protein EIP1, or La-binding protein 1, or Rab4-interacting protein (Rabip4), or Zinc finger FYVE domain-containing protein 12 (ZFY12), a human homolog of mouse Rabip4, an effector of Rab4 GTPase that regulates recycling of endocytosed cargo. RUFY1 is an endosomal protein that functions as a dual effector of Rab4 and Rab14 and is involved in efficient recycling of transferrin (Tfn). It is a downstream effector of Etk, a downstream tyrosine kinase of PI3-kinase that is involved in regulation of vesicle trafficking. RUFY1 contains an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between; this model represents the RUN domain. 156 matched cddid_all.tbl CDD cd17695 cd17695 439057 RUN_RUFY2 RUN domain found in RUN and FYVE domain-containing protein 2 (RUFY2) and similar proteins. RUFY2, also called Rab4-interacting protein related, is a novel embryonic factor that contains an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between. It is present in the nucleus at early stages of embryonic development. It may have both endosomal functions in the cytoplasm and nuclear functions. This model represents the RUN domain of RUFY2. 156 matched cddid_all.tbl CDD cd17696 cd17696 439058 RUN_RUFY3 RUN domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins. RUFY3, also called Rap2-interacting protein x (RIPx or RPIPx), or single axon-regulated protein (singar), is an N-terminal RUN domain and a C-terminal FYVE domain containing protein predominantly expressed in the brain. It suppresses formation of surplus axons for neuronal polarity. Unlike other RUFY proteins, RUFY3 can associate with the GTP-bound active form of Rab5. This model represents the RUN domain of RUFY3. 156 matched cddid_all.tbl CDD cd17697 cd17697 439059 RUN_RUFY4 RUN domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins. RUFY4 acts as a positive regulator that enhances autophagy and lysosome tethering in response to Interleukin-4. It is expressed in a cell-specific manner or under specific immunological conditions associated with IL4 expression such as allergic asthma. RUFY4 belongs to the FUFY protein family which is characterized by the presence of an N-terminal RUN domain and a C-terminal FYVE domain; this model represents the RUN domain of RUFY4. 150 matched cddid_all.tbl CDD cd17698 cd17698 439060 RUN_FYCO1 RUN domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins. FYCO1, also called zinc finger FYVE domain-containing protein 7 (ZFYVE7), is a multidomain autophagy adaptor protein that interacts with kinesin motor proteins and with the autophagosomal membrane components microtubule-associated protein 1 light chain 3 (LC3), Rab7, and Phosphatidylinositol 3-phosphate (PI3P), to mediate microtubule plus-end-directed autophagosome transport. This model represents the RUN domain of FYCO1. 158 matched cddid_all.tbl CDD cd17699 cd17699 439061 RUN_RUNDC3A RUN domain found in RUN domain-containing protein 3A (RUNDC3A) and similar proteins. RUN domain-containing protein 3A (RUNDC3A), also called Rap2-interacting protein 8 (RPIP8), may act as an effector of Rap2A GTPase in neuronal cells. It contains a RUN domain. 151 matched cddid_all.tbl CDD cd17700 cd17700 439062 RUN_RUNDC3B RUN domain found in RUN domain-containing protein 3B (RUNDC3B) and similar proteins. RUN domain-containing protein 3B (RUNDC3B), also called Rap2-binding protein 9, or Rap2-interacting protein 9 (RPIP-9), contains a RUN domain in its N-terminal region that mediates interaction with Rap2, an important component of the Mitogen-Activated Protein Kinase (MAPK) cascade, which regulates cellular proliferation and differentiation. It also contains characteristic binding sites for MAPK intermediates. RUNDC3B contains a RUN domain. 151 matched cddid_all.tbl CDD cd17701 cd17701 439063 RUN_RUSC1 RUN domain found in RUN and SH3 domain-containing protein 1 (RUSC1) and similar proteins. RUSC1, also called new molecule containing SH3 at the carboxy-terminus (NESCA), may acts as a signaling adapter that translocates to the nuclear envelope and regulates neurotrophin-induced neurite outgrowth. This model contains the RUN domain of RUSC1. 183 matched cddid_all.tbl CDD cd17702 cd17702 439064 RUN_RUSC2 RUN domain found in RUN and SH3 domain-containing protein 2 (RUSC2) and similar proteins. RUSC2, also called iporin, or interacting protein of Rab1, is a novel interacting molecule for the active GTP-bound conformation of Rab1. It may function as a link between the targeting of endoplasmic reticulum derived vesicles, triggered by the Rab1 GTPase and a signaling pathway regulated by molecules containing SH3 and/or poly-proline regions. This model contains the RUN domain of RUSC2. 183 matched cddid_all.tbl CDD cd17703 cd17703 439065 RUN_SGSM1 RUN domain found in small G protein signaling modulator 1 (SGSM1) and similar proteins. SGSM1, also called RUN and TBC1 domain-containing protein 2 (RUTBC2), interacts with numerous Rab family members, functioning as Rab effector for some, and as GTPase activator for others. It is a Rab9A effector and GTPase-activating protein for Rab36, and links Rab9A function to Rab36 function in the endosomal system. This model contains the RUN domain of SGSM1. 177 matched cddid_all.tbl CDD cd17704 cd17704 439066 RUN_SGSM2 RUN domain found in small G protein signaling modulator 2 (SGSM2) and similar proteins. SGSM2, also called RUN and TBC1 domain-containing protein 1 (RUTBC1), is a GTPase-activating protein for Rab32/38, and regulates melanogenic enzyme trafficking in melanocytes. It also acts as a Rab9A effector that activates GTP hydrolysis by Rab32 and Rab33B proteins. This model contains the RUN domain of SGSM2. 180 matched cddid_all.tbl CDD cd17706 cd17706 350658 MCM MCM helicase family. MCM helicases are a family of helicases that play an important role in replication and homologous recombination repair. The heterohexameric ring-shaped Mcm2-7 complex is part of the replicative helicase that unwinds parental double-stranded DNA at a replication fork to provide single-stranded DNA templates for the replicative polymerases. Mcm8 and Mcm9, form a complex required for homologous recombination (HR) repair induced by DNA interstrand crosslinks (ICLs). 311 matched cddid_all.tbl CDD cd17707 cd17707 349340 BRCT_XRCC1_rpt2 Second (C-terminal) BRCT domain in X-ray repair cross-complementing protein 1 (XRCC1) and similar proteins. XRCC1 is a DNA repair protein that corrects defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents. It forms homodimers and interacts with polynucleotide kinase (PNK), DNA polymerase-beta (POLB), DNA ligase III (LIG3), APTX, APLF, and APEX1. XRCC1 contains an N-terminal XRCC1-specific domain and two BRCT domains. This model corresponds to the second BRCT domain. 94 matched cddid_all.tbl CDD cd17709 cd17709 349341 BRCT_pescadillo_like BRCT domain of pescadillo and related proteins. Pescadillo has been characterized in zebrafish as a protein involved in the control of cell proliferation, specifically in the developing embryo. Mammalian homologs have been linked to ribosome biogenesis and nucleologenesis, and yeast homologs have been shown to be required for synthesis of the 60S ribosomal subunit. Pescadillo contains a BRCT domain. 86 matched cddid_all.tbl CDD cd17710 cd17710 349342 BRCT_PAXIP1_rpt2 second BRCT domain of PAX-interacting protein 1 (PAXIP1) and similar proteins. PAXIP1, also termed PAX transactivation activation domain-interacting protein (PTIP), is involved in DNA damage response and in transcriptional regulation through histone methyltransferase (HMT) complexes. It also facilitates ATM-mediated activation of p53 and promotes cellular resistance to ionizing radiation. PAXIP1 contains six BRCT repeats. This family corresponds to the second BRCT domain. 81 matched cddid_all.tbl CDD cd17711 cd17711 349343 BRCT_PAXIP1_rpt3 third BRCT domain of PAX-interacting protein 1 (PAXIP1) and similar proteins. PAXIP1, also termed PAX transactivation activation domain-interacting protein (PTIP), is involved in DNA damage response and in transcriptional regulation through histone methyltransferase (HMT) complexes. It also facilitates ATM-mediated activation of p53 and promotes cellular resistance to ionizing radiation. PAXIP1 contains six BRCT repeats. This family corresponds to the third BRCT domain. 81 matched cddid_all.tbl CDD cd17712 cd17712 349344 BRCT_PAXIP1_rpt5 fifth BRCT domain of PAX-interacting protein 1 (PAXIP1) and similar proteins. PAXIP1, also termed PAX transactivation activation domain-interacting protein (PTIP), is involved in DNA damage response and in transcriptional regulation through histone methyltransferase (HMT) complexes. It also facilitates ATM-mediated activation of p53 and promotes cellular resistance to ionizing radiation. PAXIP1 contains six BRCT repeats. This family corresponds to the fifth BRCT domain. 75 matched cddid_all.tbl CDD cd17713 cd17713 349345 BRCT_polymerase_mu_like BRCT domain of DNA-directed DNA/RNA polymerase mu (polymerase mu), DNA nucleotidylexotransferase and similar proteins. The family includes DNA-directed DNA/RNA polymerase mu (polymerase mu) and DNA nucleotidylexotransferase. Polymerase mu (EC 2.7.7.7), also termed Pol mu, or terminal transferase, is a Gap-filling polymerase involved in repair of DNA double-strand breaks by non-homologous end joining (NHEJ). It participates in immunoglobulin (Ig) light chain gene rearrangement in V(D)J recombination. DNA nucleotidylexotransferase (EC 2.7.7.31), also termed terminal addition enzyme, or terminal deoxynucleotidyltransferase, or terminal transferase, is a template-independent DNA polymerase which catalyzes the random addition of deoxynucleoside 5'-triphosphate to the 3'-end of a DNA initiator. It is the addition of nucleotides at the junction (N region) of rearranged Ig heavy chain and T-cell receptor gene segments during the maturation of B- and T-cells. All family members contains a BRCT domain. 87 matched cddid_all.tbl CDD cd17714 cd17714 349346 BRCT_PAXIP1_rpt1 first (N-terminal) BRCT domain of PAX-interacting protein 1 (PAXIP1) and similar proteins. PAXIP1, also termed PAX transactivation activation domain-interacting protein (PTIP), is involved in DNA damage response and in transcriptional regulation through histone methyltransferase (HMT) complexes. It also facilitates ATM-mediated activation of p53 and promotes cellular resistance to ionizing radiation. PAXIP1 contains six BRCT repeats. This family corresponds to the first BRCT domain. 76 matched cddid_all.tbl CDD cd17715 cd17715 349347 BRCT_polymerase_lambda BRCT domain of DNA polymerase lambda and similar proteins. DNA polymerase lambda, also termed Pol Lambda, or DNA polymerase beta-2 (Pol beta2), or DNA polymerase kappa, is involved in base excision repair (BER) and is responsible for repair of lesions that give rise to abasic (AP) sites in DNA. It also contributes to DNA double-strand break repair by non-homologous end joining and homologous recombination. DNA polymerase lambda has both template-dependent and template-independent (terminal transferase) DNA polymerase activities, as well as a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity. DNA polymerase lambda contains one BRCT domain. 80 matched cddid_all.tbl CDD cd17716 cd17716 349348 BRCT_microcephalin_rpt1 first (N-terminal) BRCT domain of microcephalin and similar proteins. Microcephalin is a DNA damage response protein involved in regulation of CHK1 and BRCA1. It has been implicated in chromosome condensation and DNA damage induced cellular responses. It may play a role in neurogenesis and regulation of the size of the cerebral cortex. Microcephalin contains three BRCT repeats. This family corresponds to the first repeat. 78 matched cddid_all.tbl CDD cd17717 cd17717 349349 BRCT_DNA_ligase_IV_rpt2 second BRCT domain of DNA ligase 4 (LIG4) and similar proteins. LIG4 (EC 6.5.1.1), also termed DNA ligase IV, or polydeoxyribonucleotide synthase [ATP] 4, is involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. It is a component of the LIG4-XRCC4 complex that is responsible for the NHEJ ligation step. LIG4 contains two BRCT domains. The family corresponds to the second one. 88 matched cddid_all.tbl CDD cd17718 cd17718 349350 BRCT_TopBP1_rpt3 third BRCT domain of DNA topoisomerase 2-binding protein 1 (TopBP1) and similar proteins. TopBP1, also termed DNA topoisomerase II-beta-binding protein 1, or DNA topoisomerase II-binding protein 1, functions in DNA replication and damage response. It binds double-stranded DNA breaks and nicks as well as single-stranded DNA. TopBP1 contains six copies of BRCT domain. The family corresponds to the third BRCT domain. 83 matched cddid_all.tbl CDD cd17719 cd17719 349351 BRCT_Rev1 BRCT domain of DNA repair protein Rev1 and similar proteins. REV1, also termed alpha integrin-binding protein 80, or AIBP80, or Rev1-like terminal deoxycytidyl transferase, is a DNA template-dependent dCMP transferase required for mutagenesis induced by UV light. 87 matched cddid_all.tbl CDD cd17720 cd17720 349352 BRCT_Bard1_rpt2 second (C-terminal) BRCT domain of BRCA1-associated RING domain protein 1 (Bard1) and similar proteins. Bard1, also termed BARD-1, or RING-type E3 ubiquitin transferase BARD1, is a critical factor in BRCA1-mediated tumor suppression and may also serve as a target for tumorigenic lesions in some human cancers. It associates with BRCA1 (breast cancer-1) to form a heterodimeric BRCA1/BARD1 complex that is responsible for maintaining genomic stability through nuclear functions involving DNA damage signaling and repair, transcriptional regulation, and cell cycle control. The BRCA1/BARD1 complex catalyzes autoubiquitination of BRCA1 and trans ubiquitination of other protein substrates. Its E3 ligase activity is dramatically reduced in the presence of UBX domain protein 1 (UBXN1). BARD-1 contains an N-terminal C3HC4-type RING-HC finger that binds BRCA1, and a C-terminal region with three ankyrin repeats and tandem BRCT domains that bind CstF-50 (cleavage stimulation factor) to modulate mRNA processing and RNAP II stability in response to DNA damage. The family corresponds to the second BRCT domain. 101 matched cddid_all.tbl CDD cd17721 cd17721 349353 BRCT_BRCA1_rpt2 second (C-terminal) BRCT domain of breast cancer type 1 susceptibility protein (BRCA1) and similar proteins. BRCA1, also termed RING finger protein 53 (RNF53), is a RING finger protein encoded by BRCA1, a tumor suppressor gene that regulates all DNA double-strand break (DSB) repair pathways. BRCA1 is frequently mutated in patients with hereditary breast and ovarian cancer (HBOC). Its mutation is also associated with an increased risk of pancreatic, stomach, laryngeal, fallopian tube, and prostate cancer. It plays an important role in the DNA damage response signaling, and has been implicated in various cellular processes such as cell cycle regulation, transcriptional regulation, chromatin remodeling, DNA DSBs, and apoptosis. BRCA1 contains an N-terminal C3HC4-type RING-HC finger, and two BRCT repeats at the C-terminus. The family corresponds to the second BRCT domain. 98 matched cddid_all.tbl CDD cd17722 cd17722 349354 BRCT_DNA_ligase_IV_rpt1 first BRCT domain of DNA ligase 4 (LIG4) and similar proteins. LIG4 (EC 6.5.1.1), also termed DNA ligase IV, or polydeoxyribonucleotide synthase [ATP] 4, is involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. It is a component of the LIG4-XRCC4 complex that is responsible for the NHEJ ligation step. LIG4 contains two BRCT domains. The family corresponds to the first one. 90 matched cddid_all.tbl CDD cd17723 cd17723 349355 BRCT_Rad4_rpt4 fourth BRCT domain of Schizosaccharomyces pombe S-M checkpoint control protein Rad4 and similar proteins. Rad4, also termed P74, or protein cut5, is an essential component for DNA replication and the checkpoint control system, which couples S and M phases. It may directly or indirectly interact with chromatin proteins to form the complex required for the initiation and/or progression of DNA synthesis. Rad4 contains four BRCT repeats. The family corresponds to the fourth one. 74 matched cddid_all.tbl CDD cd17724 cd17724 349356 BRCT_p53bp1_rpt2 Second (C-terminal) BRCT domain in p53-binding protein 1 (p53BP1) and similar proteins. p53BP1, also termed 53BP1, or TP53-binding protein 1 (TP53BP1) , is a double-strand break (DSB) repair protein involved in response to DNA damage, telomere dynamics, and class-switch recombination (CSR) during antibody genesis. TP53BP1 contains two tandem BRCT repeats. This family corresponds to the second BRCT domain. 87 matched cddid_all.tbl CDD cd17725 cd17725 349357 BRCT_XRCC1_rpt1 First (central) BRCT domain in X-ray repair cross-complementing protein 1 (XRCC1) and similar proteins. XRCC1 is a DNA repair protein that corrects defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents. It forms homodimers and interacts with polynucleotide kinase (PNK), DNA polymerase-beta (POLB), DNA ligase III (LIG3), APTX, APLF, and APEX1. XRCC1 contains an N-terminal XRCC1-specific domain and two BRCT domains. This family corresponds to the first one. 80 matched cddid_all.tbl CDD cd17726 cd17726 349358 BRCT_PARP4_like BRCT domain of poly [ADP-ribose] polymerase 4 (PARP-4) and similar proteins. PARP-4, also termed 193 kDa vault protein, or ADP-ribosyltransferase diphtheria toxin-like 4 (ARTD4), or PARP-related/IalphaI-related H5/proline-rich (PH5P), or vault poly(ADP-ribose) polymerase (VPARP), shows poly(ADP-ribosyl)ation activity that catalyzes the formation of ADP-ribose polymers in response to DNA damage. PARP-4 is a component of the vault ribonucleoprotein particle, at least composed of MVP, PARP4 and one or more vault RNAs (vRNAs). The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this group. 85 matched cddid_all.tbl CDD cd17727 cd17727 349359 BRCT_TopBP1_rpt6 sixth BRCT domain of DNA topoisomerase 2-binding protein 1 (TopBP1) and similar proteins. TopBP1, also termed DNA topoisomerase II-beta-binding protein 1, or DNA topoisomerase II-binding protein 1, functions in DNA replication and damage response. It binds double-stranded DNA breaks and nicks as well as single-stranded DNA. TopBP1 contains six copies of BRCT domain. The family corresponds to the sixth BRCT domain. 75 matched cddid_all.tbl CDD cd17728 cd17728 349360 BRCT_TopBP1_rpt8 eighth (C-terminal) BRCT domain of DNA topoisomerase 2-binding protein 1. TopBP1, also termed DNA topoisomerase II-beta-binding protein 1, or DNA topoisomerase II-binding protein 1, functions in DNA replication and damage response. It binds double-stranded DNA breaks and nicks as well as single-stranded DNA. TopBP1 contains six copies of BRCT domain. The family corresponds to the eighth BRCT domain. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this group. 80 matched cddid_all.tbl CDD cd17729 cd17729 349361 BRCT_CTDP1 BRCT domain of RNA polymerase II subunit A C-terminal domain phosphatase (CTDP1) and similar proteins. CTDP1 (EC 3.1.3.16), also termed TFIIF-associating CTD phosphatase, or TFIIF- associating RNA polymerase C-terminal domain phosphatase (FCP1), promotes the activity of RNA polymerase II through processively dephosphorylating 'Ser-2' and 'Ser-5' of the heptad repeats YSPTSPS in the C-terminal domain of the largest RNA polymerase II subunit. It plays a role in the exit from mitosis by dephosphorylating crucial mitotic substrates (USP44, CDC20 and WEE1) that are required for M-phase-promoting factor (MPF)/CDK1 inactivation. 97 matched cddid_all.tbl CDD cd17730 cd17730 349362 BRCT_PAXIP1_rpt4 fourth BRCT domain of PAX-interacting protein 1 (PAXIP1) and similar proteins. PAXIP1, also termed PAX transactivation activation domain-interacting protein (PTIP), is involved in DNA damage response and in transcriptional regulation through histone methyltransferase (HMT) complexes. It also facilitates ATM-mediated activation of p53 and promotes cellular resistance to ionizing radiation. PAXIP1 contains six BRCT repeats. This family corresponds to the fourth BRCT domain. 73 matched cddid_all.tbl CDD cd17731 cd17731 349363 BRCT_TopBP1_rpt2_like second BRCT domain of DNA topoisomerase 2-binding protein 1 (TopBP1) and similar proteins. TopBP1, also termed DNA topoisomerase II-beta-binding protein 1, or DNA topoisomerase II-binding protein 1, functions in DNA replication and damage response. It binds double-stranded DNA breaks and nicks as well as single-stranded DNA. TopBP1 contains six copies of BRCT domain. The family corresponds to the second BRCT domain. 77 matched cddid_all.tbl CDD cd17732 cd17732 349364 BRCT_Ect2_rpt2 second BRCT domain of epithelial cell-transforming sequence 2 protein (ECT2) and similar proteins. ECT2 is a guanine nucleotide exchange factor (GEF) for Rho GTPases, phosphorylated in G2/M phases, and is involved in the regulation of cytokinesis. It contains two tandem BRCT domains. The family corresponds to the second BRCT domain. 80 matched cddid_all.tbl CDD cd17733 cd17733 349365 BRCT_Ect2_rpt1 first BRCT domain of epithelial cell-transforming sequence 2 protein (ECT2) and similar proteins. ECT2 is a guanine nucleotide exchange factor (GEF) for Rho GTPases, phosphorylated in G2/M phases, and is involved in the regulation of cytokinesis. It contains two tandem BRCT domains. The family corresponds to the first BRCT domain. 76 matched cddid_all.tbl CDD cd17734 cd17734 349366 BRCT_Bard1_rpt1 first BRCT domain of BRCA1-associated RING domain protein 1 (Bard1) and similar proteins. Bard1, also termed BARD-1, or RING-type E3 ubiquitin transferase BARD1, is a critical factor in BRCA1-mediated tumor suppression and may also serve as a target for tumorigenic lesions in some human cancers. It associates with BRCA1 (breast cancer-1) to form a heterodimeric BRCA1/BARD1 complex that is responsible for maintaining genomic stability through nuclear functions involving DNA damage signaling and repair, transcriptional regulation, and cell cycle control. The BRCA1/BARD1 complex catalyzes autoubiquitination of BRCA1 and trans ubiquitination of other protein substrates. Its E3 ligase activity is dramatically reduced in the presence of UBX domain protein 1 (UBXN1). BARD-1 contains an N-terminal C3HC4-type RING-HC finger that binds BRCA1, and a C-terminal region with three ankyrin repeats and tandem BRCT domains that bind CstF-50 (cleavage stimulation factor) to modulate mRNA processing and RNAP II stability in response to DNA damage. The family corresponds to the first BRCT domain. 80 matched cddid_all.tbl CDD cd17735 cd17735 349367 BRCT_BRCA1_rpt1 first BRCT domain of breast cancer type 1 susceptibility protein (BRCA1) and similar proteins. BRCA1, also termed RING finger protein 53 (RNF53), is a RING finger protein encoded by BRCA1, a tumor suppressor gene that regulates all DNA double-strand break (DSB) repair pathways. BRCA1 is frequently mutated in patients with hereditary breast and ovarian cancer (HBOC). Its mutation is also associated with an increased risk of pancreatic, stomach, laryngeal, fallopian tube, and prostate cancer. It plays an important role in the DNA damage response signaling, and has been implicated in various cellular processes such as cell cycle regulation, transcriptional regulation, chromatin remodeling, DNA DSBs, and apoptosis. BRCA1 contains an N-terminal C3HC4-type RING-HC finger, and two BRCT (BRCA1 C-terminus domain) repeats at the C-terminus. The family corresponds to the first BRCT domain. 97 matched cddid_all.tbl CDD cd17736 cd17736 349368 BRCT_microcephalin_rpt2 second BRCT domain of microcephalin and similar proteins. Microcephalin is a DNA damage response protein involved in regulation of CHK1 and BRCA1. It has been implicated in chromosome condensation and DNA damage induced cellular responses. It may play a role in neurogenesis and regulation of the size of the cerebral cortex. Microcephalin contains three BRCT repeats. This family corresponds to the second repeat. 76 matched cddid_all.tbl CDD cd17737 cd17737 349369 BRCT_TopBP1_rpt1 first BRCT domain of DNA topoisomerase 2-binding protein 1 (TopBP1) and similar proteins. TopBP1, also termed DNA topoisomerase II-beta-binding protein 1, or DNA topoisomerase II-binding protein 1, functions in DNA replication and damage response. It binds double-stranded DNA breaks and nicks as well as single-stranded DNA. TopBP1 contains six copies of BRCT domain. The family corresponds to the first BRCT domain. 72 matched cddid_all.tbl CDD cd17738 cd17738 349370 BRCT_TopBP1_rpt7 seventh BRCT domain of DNA topoisomerase 2-binding protein 1. TopBP1, also termed DNA topoisomerase II-beta-binding protein 1, or DNA topoisomerase II-binding protein 1, functions in DNA replication and damage response. It binds double-stranded DNA breaks and nicks as well as single-stranded DNA. TopBP1 contains six copies of BRCT domain. The family corresponds to the seventh BRCT domain. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is missing in this group. 75 matched cddid_all.tbl CDD cd17740 cd17740 349371 BRCT_Rad4_rpt1 first BRCT domain of Schizosaccharomyces pombe S-M checkpoint control protein Rad4 and similar proteins. Rad4, also termed P74, or protein cut5, is an essential component for DNA replication and the checkpoint control system which couples the S and M phases. It may directly or indirectly interact with chromatin proteins to form the complex required for the initiation and/or progression of DNA synthesis. Rad4 contains four BRCT repeats. The family corresponds to the first one. 82 matched cddid_all.tbl CDD cd17741 cd17741 349372 BRCT_nibrin BRCT domain of nibrin and similar proteins. Nibrin (NBN), also termed Nijmegen breakage syndrome protein 1 (NBS1), or cell cycle regulatory protein p95, is a novel DNA double-strand break repair protein that is mutated in Nijmegen breakage syndrome. It is a component of the MRE11-RAD50-NBN (MRN complex) which plays a critical role in the cellular response to DNA damage and the maintenance of chromosome integrity. The BRCT (Breast Cancer Suppressor Protein BRCA1, carboxy-terminal) domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is absent in this group. 74 matched cddid_all.tbl CDD cd17742 cd17742 349373 BRCT_CHS5_like BRCT domain of yeast chitin biosynthesis protein CHS5 and similar proteins. CHS5, also termed protein CAL3, is a component of the CHS5/6 complex which mediates export of specific cargo proteins, including chitin synthase CHS3. It is also involved in targeting FUS1 to sites of polarized growth. 77 matched cddid_all.tbl CDD cd17743 cd17743 349374 BRCT_BRC1_like_rpt5 fifth BRCT domain of Schizosaccharomyces pombe BRCT-containing protein 1 (BRC1) and similar proteins. Schizosaccharomyces pombe BRC1 is required for mitotic fidelity, specifically in the G2 phase of the cell cycle. It plays a role in chromatin organization. The family also includes Cryptococcus neoformans DNA ligase 4 (LIG4, also known as DNA ligase IV or polydeoxyribonucleotide synthase [ATP] 4), which is involved in dsDNA break repair, and plays a role in non-homologous integration (NHI) pathways where it is required in the final step of non-homologus end-joining. Members in this family contain six BRCT domains. This family corresponds to the fifth one. 70 matched cddid_all.tbl CDD cd17744 cd17744 349375 BRCT_MDC1_rpt1 first BRCT domain of mediator of DNA damage checkpoint protein 1 (MDC1) and similar proteins. MDC1, also termed nuclear factor with BRCT domains 1 (NFBD1), is a nuclear chromatin-associated protein that is required for checkpoint mediated cell cycle arrest in response to DNA damage within both the S phase and G2/M phases of the cell cycle. It directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-strand breaks. MDC1 contains a forkhead-associated (FHA) domain and two BRCT domains, as well as an internal 41-amino acid repeat sequence. The family corresponds to the first BRCT domain. 72 matched cddid_all.tbl CDD cd17745 cd17745 349376 BRCT_p53bp1_rpt1 first (central) BRCT domain in p53-binding protein 1 (p53BP1) and similar proteins. p53BP1, also termed 53BP1, or TP53-binding protein 1 (TP53BP1) , is a double-strand break (DSB) repair protein involved in response to DNA damage, telomere dynamics and class-switch recombination (CSR) during antibody genesis. TP53BP1 contains two tandem BRCT repeats. This family also includes Schizosaccharomyces pombe Crb2, which is a checkpoint mediator required for the cellular response to DNA damage. This model corresponds to the first BRCT domain. 99 matched cddid_all.tbl CDD cd17746 cd17746 349377 BRCT_Rad4_rpt2 second BRCT domain of Schizosaccharomyces pombe S-M checkpoint control protein Rad4 and similar proteins. Rad4, also termed P74, or protein cut5, is an essential component for DNA replication and the checkpoint control system which couples S and M phases. It may directly or indirectly interact with chromatin proteins to form the complex required for the initiation and/or progression of DNA synthesis. Rad4 contains four BRCT repeats. The family corresponds to the second one. 91 matched cddid_all.tbl CDD cd17747 cd17747 349378 BRCT_PARP1 BRCT domain of poly [ADP-ribose] polymerase 1 (PARP-1) and similar proteins. PARP-1 (EC 2.4.2.30), also termed ADP-ribosyltransferase diphtheria toxin-like 1 (ARTD1), or NAD(+) ADP-ribosyltransferase 1 (ADPRT 1), or poly[ADP-ribose] synthase 1, is involved in the base excision repair (BER) pathway, by catalyzing the poly(ADP-ribosyl)ation of a limited number of acceptor proteins involved in chromatin architecture and in DNA metabolism. 76 matched cddid_all.tbl CDD cd17748 cd17748 349379 BRCT_DNA_ligase_like BRCT domain of bacterial NAD-dependent DNA ligase (LigA) and similar proteins. LigA, also called NAD(+)-dependent polydeoxyribonucleotide synthase, catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction. It is essential for DNA replication and repair of damaged DNA. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family. 76 matched cddid_all.tbl CDD cd17749 cd17749 349380 BRCT_TopBP1_rpt4 fourth BRCT domain of DNA topoisomerase 2-binding protein 1 (TopBP1) and similar proteins. TopBP1, also called DNA topoisomerase II-beta-binding protein 1, or DNA topoisomerase II-binding protein 1, functions in DNA replication and damage response. It binds double-stranded DNA breaks and nicks as well as single-stranded DNA. TopBP1 contains six copies of BRCT domain. The family corresponds to the fourth BRCT domain. 84 matched cddid_all.tbl CDD cd17750 cd17750 349381 BRCT_SLF1 BRCT domain of SMC5-SMC6 complex localization factor protein 1 (SLF1) and similar proteins. SLF1, also termed Smc5/6 localization factor 1, or ankyrin repeat domain-containing protein 32 (ANKRD32), or BRCT domain-containing protein 1 (BRCTD1), plays a role in the DNA damage response (DDR) pathway by regulating post replication repair of UV-damaged DNA and genomic stability maintenance. It is a component of the SLF1-SLF2 complex that acts to link RAD18 with the SMC5-SMC6 complex at replication-coupled interstrand cross-links (ICL) and DNA double-strand break (DSB) sites on chromatin during DNA repair in response to stalled replication forks. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is missing in this group. 81 matched cddid_all.tbl CDD cd17751 cd17751 349382 BRCT_microcephalin_rpt3 third BRCT domain of microcephalin and similar proteins. Microcephalin is a DNA damage response protein involved in regulation of CHK1 and BRCA1. It has been implicated in chromosome condensation and DNA damage induced cellular responses. It may play a role in neurogenesis and regulation of the size of the cerebral cortex. Microcephalin contains three BRCT repeats. This family corresponds to the third repeat. 75 matched cddid_all.tbl CDD cd17752 cd17752 349383 BRCT_RFC1 BRCT domain of replication factor C subunit 1 (RFC1) and similar proteins. RFC1, also termed activator 1 140 kDa subunit, or A1 140 kDa subunit, or activator 1 large subunit, or activator 1 subunit 1, or replication factor C 140 kDa subunit, or RF-C 140 kDa subunit, or RFC140, is the large subunit of replication factor C (RFC), which is a heteropentameric protein essential for DNA replication and repair. RFC1 can bind single- or double-stranded DNA. It could play a role in DNA transcription regulation as well as DNA replication and/or repair. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family. 79 matched cddid_all.tbl CDD cd17753 cd17753 350659 MCM2 DNA replication licensing factor Mcm2. Mcm2 is a helicase that play an important role in replication. It is part of the heterohexameric ring-shaped Mcm2-7 complex, which is part of the replicative helicase that unwinds parental double-stranded DNA at a replication fork to provide single-stranded DNA templates for the replicative polymerases. 325 matched cddid_all.tbl CDD cd17754 cd17754 350660 MCM3 DNA replication licensing factor Mcm3. Mcm3 is a helicase that play an important role in replication. It is part of the heterohexameric ring-shaped Mcm2-7 complex, which is part of the replicative helicase that unwinds parental double-stranded DNA at a replication fork to provide single-stranded DNA templates for the replicative polymerases. 299 matched cddid_all.tbl CDD cd17755 cd17755 350661 MCM4 DNA replication licensing factor Mcm4. Mcm4 is a helicase that play an important role in replication. It is part of the heterohexameric ring-shaped Mcm2-7 complex, which is part of the replicative helicase that unwinds parental double-stranded DNA at a replication fork to provide single-stranded DNA templates for the replicative polymerases. 309 matched cddid_all.tbl CDD cd17756 cd17756 350662 MCM5 DNA replication licensing factor Mcm5. Mcm5 is a helicase that play an important role in replication. It is part of the heterohexameric ring-shaped Mcm2-7 complex, which is part of the replicative helicase that unwinds parental double-stranded DNA at a replication fork to provide single-stranded DNA templates for the replicative polymerases. 317 matched cddid_all.tbl CDD cd17757 cd17757 350663 MCM6 DNA replication licensing factor Mcm6. Mcm6 is a helicase that play an important role in replication. It is part of the heterohexameric ring-shaped Mcm2-7 complex, which is part of the replicative helicase that unwinds parental double-stranded DNA at a replication fork to provide single-stranded DNA templates for the replicative polymerases. 307 matched cddid_all.tbl CDD cd17758 cd17758 350664 MCM7 DNA replication licensing factor Mcm7. Mcm7 is a helicase that play an important role in replication. It is part of the heterohexameric ring-shaped Mcm2-7 complex, which is part of the replicative helicase that unwinds parental double-stranded DNA at a replication fork to provide single-stranded DNA templates for the replicative polymerases. 306 matched cddid_all.tbl CDD cd17759 cd17759 350665 MCM8 DNA helicase Mcm8. Mcm8 plays an important role homologous recombination repair. It forms a complex with Mcm9 that is required for homologous recombination (HR) repair induced by DNA interstrand crosslinks (ICLs). 289 matched cddid_all.tbl CDD cd17760 cd17760 350666 MCM9 DNA helicase Mcm9. Mcm9 plays an important role homologous recombination repair. It forms a complex with Mcm8 that is required for homologous recombination (HR) repair induced by DNA interstrand crosslinks (ICLs). 299 matched cddid_all.tbl CDD cd17761 cd17761 350667 MCM_arch archaeal MCM protein. archaeal MCM proteins form a homohexameric ring homologous to the eukaryotic Mcm2-7 helicase and also function as the replicative helicase at the replication fork 308 matched cddid_all.tbl CDD cd17762 cd17762 350162 AMN AMP nucleosidase. AMP nucleosidase (AMN) catalyzes the hydrolysis of AMP to ribose 5-phosphate and adenine. It is a prokaryotic enzyme which plays a role in purine nucleoside salvage and intracellular AMP level regulation. AMN is active as a homohexamer; each monomer is comprised of a catalytic domain and a putative regulatory domain. This model represents the catalytic domain. AMN belongs to the nucleoside phosphorylase-I (NP-I) family, whose members accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. The NP-1 family includes phosphorolytic nucleosidases, such as purine nucleoside phosphorylase (PNPs, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases, such as AMP nucleosidase (AMN, EC 3.2.2.4), and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). The NP-I family is distinct from nucleoside phosphorylase-II, which belongs to a different structural family. 242 matched cddid_all.tbl CDD cd17763 cd17763 350163 UP_hUPP-like uridine phosphorylases similar to a human UPP1 and UPP2. Uridine phosphorylase (UP) catalyzes the reversible phosphorolysis of uracil ribosides and analogous compounds to their respective nucleobases and ribose 1-phosphate. Human UPP1 has a role in the activation of pyrimidine nucleoside analogues used in chemotherapy, such as 5-fluorouracil. This subfamily belongs to the nucleoside phosphorylase-I (NP-I) family, whose members accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. The NP-1 family includes phosphorolytic nucleosidases, such as purine nucleoside phosphorylase (PNPs, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases, such as AMP nucleosidase (AMN, EC 3.2.2.4), and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). The NP-I family is distinct from nucleoside phosphorylase-II, which belongs to a different structural family. 276 matched cddid_all.tbl CDD cd17764 cd17764 350164 MTAP_SsMTAPI_like 5'-deoxy-5'-methylthioadenosine phosphorylases similar to Sulfolobus solfataricus MTAPI. 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP) catalyzes the reversible phosphorolysis of 5'-deoxy-5'-methylthioadenosine (MTA) to adenine and 5-methylthio-D-ribose-1-phosphate. Sulfolobus solfataricus MTAPI will utilize inosine, guanosine, and adenosine as substrates, in addition to MTA. Two MTAPs have been isolated from S. solfataricus: SsMTAP1 and SsMTAPII, SsMTAPII belongs to a different subfamily of the nucleoside phosphorylase-I (NP-I) family, whose members accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. The NP-I family includes phosphorolytic nucleosidases, such as purine nucleoside phosphorylase (PNPs, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases, such as AMP nucleosidase (AMN, EC 3.2.2.4), and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). The NP-I family is distinct from nucleoside phosphorylase-II, which belongs to a different structural family. 220 matched cddid_all.tbl CDD cd17765 cd17765 350165 PNP_ThPNP_like purine nucleoside phosphorylases similar to Thermus thermophiles PNP. Purine nucleoside phosphorylase (PNP) catalyzes the reversible phosphorolysis of purine nucleosides. Thermus thermophiles PNP catalyzes the phosphorolysis of guanosine but not adenosine. This subfamily belongs to the nucleoside phosphorylase-I (NP-I) family, whose members accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. The NP-1 family includes phosphorolytic nucleosidases, such as purine nucleoside phosphorylase (PNPs, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases, such as AMP nucleosidase (AMN, EC 3.2.2.4), and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). The NP-I family is distinct from nucleoside phosphorylase-II, which belongs to a different structural family. 234 matched cddid_all.tbl CDD cd17766 cd17766 350166 futalosine_nucleosidase_MqnB futalosine nucleosidase which catalyzes the hydrolysis of futalosine to dehypoxanthinylfutalosine and a hypoxanthine base; similar to Thermus thermophiles MqnB. Futalosine nucleosidase (MqnB, EC 3.2.2.26, also known as futalosine hydrolase) functions in an alternative menaquinone biosynthetic pathway (the futalosine pathway) which operates in some bacteria, including Streptomyces coelicolor and Thermus thermophiles. This domain model belongs to the PNP_UDP_1 superfamily which includes members which accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. PNP_UDP_1 includes phosphorolytic nucleosidases, such as purine nucleoside phosphorylase (PNPs, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases, such as AMP nucleosidase (AMN, EC 3.2.2.4), and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). Superfamily members have different physiologically relevant quaternary structures: hexameric such as the trimer-of-dimers arrangement of Shewanella oneidensis MR-1 UP, homotrimeric such as human PNP and Escherichia coli PNPII (XapA), homohexomeric (with some evidence for co-existence of a trimeric form) such as E. coli PNPI (DeoD), or homodimeric such as human and Trypanosoma brucei UP. The PNP_UDP_2 (nucleoside phosphorylase-II family) is a different structural family. 217 matched cddid_all.tbl CDD cd17767 cd17767 350167 UP_EcUdp-like uridine phosphorylases similar to Escherichia coli Udp and related phosphorylases. Uridine phosphorylase (UP) is specific for pyrimidines, and is involved in pyrimidine salvage and in the maintenance of uridine homeostasis. In addition to E. coli Udp, this subfamily includes Shewanella oneidensis MR-1 UP and Plasmodium falciparum purine nucleoside phosphorylase (PfPNP). PfPNP is an outlier in terms of genetic distance from the other families of PNPs. PfPNP is catalytically active for inosine and guanosine, and in addition, has a weak UP activity. This subfamily belongs to the nucleoside phosphorylase-I (NP-I) family, whose members accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. The NP-1 family includes phosphorolytic nucleosidases, such as purine nucleoside phosphorylase (PNPs, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases, such as AMP nucleosidase (AMN, EC 3.2.2.4), and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). The NP-I family is distinct from nucleoside phosphorylase-II, which belongs to a different structural family. 239 matched cddid_all.tbl CDD cd17768 cd17768 350168 adenosylhopane_nucleosidase_HpnG-like adenosylhopane nucleosidase which cleaves adenine from adenosylhopane to form ribosyl hopane; similar to Burkholderia cenocepacia HpnG. adenosylhopane nucleosidase HpnG, catalyzes the second step in hopanoid side-chain biosynthesis. Hopanoids are bacterial membrane lipids. This CD belongs to the PNP_UDP_1 superfamily which includes members which accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. PNP_UDP_1 includes phosphorolytic nucleosidases, such as purine nucleoside phosphorylase (PNPs, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases, such as AMP nucleosidase (AMN, EC 3.2.2.4), and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). Superfamily members have different physiologically relevant quaternary structures: hexameric such as the trimer-of-dimers arrangement of Shewanella oneidensis MR-1 UP, homotrimeric such as human PNP and Escherichia coli PNPII (XapA), homohexameric (with some evidence for co-existence of a trimeric form) such as E. coli PNPI (DeoD), or homodimeric such as human and Trypanosoma brucei UP. The PNP_UDP_2 (nucleoside phosphorylase-II family) is a different structural family. 188 matched cddid_all.tbl CDD cd17769 cd17769 350169 NP_TgUP-like nucleoside phosphorylases similar to Toxoplasma gondii uridine phosphorylase. This subfamily is composed of mostly uncharacterized proteins with similarity to Toxoplasma gondii uridine phosphorylase (TgUPase). Toxoplasma gondii appears to have a single non-specific uridine phosphorylase which catalyzes the reversible phosphorolysis of uridine, deoxyuridine and thymidine, rather than the two distinct enzymes of mammalian cells: uridine phosphorylase (nucleoside phosphorylase-I family) and thymidine phosphorylase (nucleoside phosphorylase-II family). TgUPase is a potential target for intervention against toxoplasmosis. It belongs to the nucleoside phosphorylase-I (NP-I) family, whose members accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. The NP-1 family includes phosphorolytic nucleosidases, such as purine nucleoside phosphorylase (PNPs, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases, such as AMP nucleosidase (AMN, EC 3.2.2.4), and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). The NP-I family is distinct from nucleoside phosphorylase-II, which belongs to a different structural family. 255 matched cddid_all.tbl CDD cd17771 cd17771 341407 CBS_pair_CAP-ED_NT_Pol-beta-like_DUF294_assoc CBS domain protein. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the bacterial CAP_ED (cAMP receptor protein effector domain) family of transcription factors, the NT_Pol-beta-like domain, and the DUF294 domain. Members of CAP_ED, include CAP which binds cAMP, FNR (fumarate and nitrate reductase) which uses an iron-sulfur cluster to sense oxygen, and CooA a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. The NT_Pol-beta-like domain includes the Nucleotidyltransferase (NT) domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of class I and class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. DUF294 is a putative nucleotidyltransferase with a conserved DxD motif. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 115 matched cddid_all.tbl CDD cd17772 cd17772 341408 CBS_pair_DHH_polyA_Pol_assoc Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the DHH and nucleotidyltransferase (NT) domains. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with an upstream DHH domain which performs a phosphoesterase function and a downstream nucleotidyltransferase (NT) domain of family X DNA polymerases. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 112 matched cddid_all.tbl CDD cd17773 cd17773 341409 CBS_pair_NeuB Two tandem repeats of the cystathionine beta-synthase (CBS pair) domain present in N-acylneuraminate-9-phosphate synthase. This CD contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain present in N-acylneuraminate-9-phosphate synthase NeuB. NeuB catalyzes the condensation of phosphoenolpyruvate (PEP) and N-acetylmannosamine, directly forming N-acetylneuraminic acid (or sialic acid). The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 118 matched cddid_all.tbl CDD cd17774 cd17774 341410 CBS_two-component_sensor_histidine_kinase_repeat2 2 tandem repeats of the CBS domain in the two-component sensor histidine kinase and related-proteins, repeat 2. This cd contains 2 tandem repeats of the CBS domain in the two-component sensor histidine kinase and related-proteins. Two-component regulation is the predominant form of signal recognition and response coupling mechanism used by bacteria to sense and respond to diverse environmental stresses and cues ranging from common environmental stimuli to host signals recognized by pathogens and bacterial cell-cell communication signals. The structures of both sensors and regulators are modular, and numerous variations in domain architecture and composition have evolved to tailor to specific needs in signal perception and signal transduction. The simplest histidine kinase sensors consists of only sensing and kinase domains. The more complex hybrid sensors contain an additional REC domain typical of two-component regulators and in some cases a C-terminal histidine phosphotransferase (HPT) domain. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 137 matched cddid_all.tbl CDD cd17775 cd17775 341411 CBS_pair_bact_arch Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in bacteria and archaea. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 117 matched cddid_all.tbl CDD cd17776 cd17776 341412 CBS_pair_arch Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in archaea. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 115 matched cddid_all.tbl CDD cd17777 cd17777 341413 CBS_arch_repeat1 CBS pair domains found in archeal proteins, repeat 1. CBS pair domains found in archeal proteins that contain 2 repeats. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. 137 matched cddid_all.tbl CDD cd17778 cd17778 341414 CBS_arch_repeat2 CBS pair domains found in archeal proteins, repeat 2. CBS pair domains found in archeal proteins that contain 2 repeats. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. 131 matched cddid_all.tbl CDD cd17779 cd17779 341415 CBS_archAMPK_gamma-repeat1 signal transduction protein with CBS domains. Archeal gamma-subunit of 5'-AMP-activated protein kinase (AMPK) contains four CBS domains in tandem repeats, similar to eukaryotic homologs. AMPK is an important regulator of metabolism and of energy homeostasis. It is a heterotrimeric protein composed of a catalytic serine/threonine kinase subunit (alpha) and two regulatory subunits (beta and gamma). The gamma subunit senses the intracellular energy status by competitively binding AMP and ATP and is believed to be responsible for allosteric regulation of the whole complex. In humans mutations in gamma- subunit of AMPK are associated with hypertrophic cardiomiopathy, Wolff-Parkinson-White syndrome and glycogen storage in the skeletal muscle. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. 136 matched cddid_all.tbl CDD cd17780 cd17780 341416 CBS_pair_arch1_repeat1 Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in archaea, repeat 1. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 106 matched cddid_all.tbl CDD cd17781 cd17781 341417 CBS_pair_MUG70_1 Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains similar to MUG70 repeat1. Two tandem repeats of the cystathionine beta-synthase (CBS pair) domain, present in MUG70. The MUG70 protein, encoded by the Meiotically Up-regulated Gene 70, plays a role in meiosis and contains, beside the two CBS pairs, a PB1 domain. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 118 matched cddid_all.tbl CDD cd17782 cd17782 341418 CBS_pair_MUG70_2 Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains similar to MUG70 repeat2. Two tandem repeats of the cystathionine beta-synthase (CBS pair) domain, present in MUG70. The MUG70 protein, encoded by the Meiotically Up-regulated Gene 70, plays a role in meiosis and contains, beside the two CBS pairs, a PB1 domain. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 118 matched cddid_all.tbl CDD cd17783 cd17783 341419 CBS_pair_bac Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in bacteria. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 108 matched cddid_all.tbl CDD cd17784 cd17784 341420 CBS_pair_Euryarchaeota Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in Euryarchaeota. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 120 matched cddid_all.tbl CDD cd17785 cd17785 341421 CBS_pair_bac_arch Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in bacteria and archaea. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 136 matched cddid_all.tbl CDD cd17786 cd17786 341422 CBS_pair_Thermoplasmatales Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in Thermoplasmatales. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 114 matched cddid_all.tbl CDD cd17787 cd17787 341423 CBS_pair_ACT Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains found in Thermatoga in combination with an ACT domain. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 111 matched cddid_all.tbl CDD cd17788 cd17788 341424 CBS_pair_bac Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains present in bacteria. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 137 matched cddid_all.tbl CDD cd17789 cd17789 341425 CBS_pair_plant_CBSX Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains from plant CBSX proteins. This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains of plant single cystathionine beta-synthase (CBS) pair proteins (CBSX). CBSX1 and CBSX2 have been identified as redox regulators of the thioredoxin (Trx) system. The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic generalized epilepsy, hypercalciuric nephrolithiasis, and classic Bartter syndrome (CLC chloride channel family members), Wolff-Parkinson-White syndrome (gamma 2 subunit of AMP-activated protein kinase), retinitis pigmentosa (IMP dehydrogenase-1), and homocystinuria (cystathionine beta-synthase). 141 matched cddid_all.tbl CDD cd17790 cd17790 341356 7tmA_mAChR_M1 muscarinic acetylcholine receptor subtype M1, member of the class A family of seven-transmembrane G protein-coupled receptors. Muscarinic acetylcholine receptors (mAChRs) regulate the activity of many fundamental central and peripheral functions. The mAChR family consists of 5 subtypes M1-M5, which can be further divided into two major groups according to their G-protein coupling preference. The M1, M3 and M5 receptors selectively interact with G proteins of the G(q/11) family, whereas the M2 and M4 receptors preferentially link to the G(i/o) types of G proteins. Activation of mAChRs by agonist (acetylcholine) leads to a variety of biochemical and electrophysiological responses. M1 is the dominant mAChR subtype involved in learning and memory. It is linked to synaptic plasticity, neuronal excitability, and neuronal differentiation during early development. All GPCRs have a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 262 matched cddid_all.tbl CDD cd17791 cd17791 341490 HipA-like serine/threonine-protein kinases similar to HipA and CtkA. This family contains serine/threonine-protein kinases similar to Escherichia coli HipA, a type II toxin-antitoxin (TA) system HipA family toxin that phosphorylates Glu-tRNA-ligase (GltX), preventing it from being charged, leading to an increase in uncharged tRNA(Glu), and is the toxin component of the HipA-HipB TA module, as well as similar to the Helicobacter pylori serine/threonine-protein kinase CtkA (proinflammatory kinase), which has been shown to be secreted by the bacteria and to induce cytokines in gastric epithelial cells relevant to chronic gastric inflammation. 284 matched cddid_all.tbl CDD cd17792 cd17792 341491 CtkA serine/threonine-protein kinase CtkA and similar proteins. The Helicobacter pylori serine/threonine-protein kinase CtkA (proinflammatory kinase), encoded by the jhp940 gene, has been shown to be secreted by the bacterium and to induce cytokines in gastric epithelial cells. It may play a role in chronic gastric inflammation. CtkA autophosphorylates itself at a threonine residue near the N-terminus and it translocates into cultured human cells. It also enhances phosphorylation of the NF-kappaB p65 subunit at Ser276 in human epithelial cancer cells; phosphorylation at this position is known to activate the transcriptional activity of NF-kappaB. 281 matched cddid_all.tbl CDD cd17793 cd17793 341492 HipA type II toxin-antitoxin sytem toxin HipA and similar proteins. This family contains type II toxin-antitoxin (TA) system HipA family toxins similar to Escherichia coli and Shewanella oneidensis HipA, which is a serine/threonine-protein kinase that phosphorylates Glu-tRNA-ligase (GltX), preventing it from being charged, leading to an increase in uncharged tRNA(Glu). This induces amino acid starvation and the stringent response via RelA/SpoT and increased (p)ppGpp levels, which inhibits replication, transcription, translation and cell wall synthesis, reducing growth and leading to persistence and multidrug resistance. HipA is the toxin component of the HipA-HipB TA module that is a major factor in persistence and bioflim formation; its toxic effect is neutralized by its cognate antitoxin HipB. HipA, with HipB, acts as a a corepressor for transcription of the hipBA promoter. Structures of HipAB:DNA complexes from both Escherichia coli and Shewanella oneidensis reveal distinct complex assembly. 358 matched cddid_all.tbl CDD cd17808 cd17808 341493 HipA_Ec_like type II toxin-antitoxin sytem toxin HipA from Escherichia coli and similar proteins. This family contains type II toxin-antitoxin (TA) system HipA family toxins similar to Escherichia coli HipA, a serine/threonine-protein kinase that phosphorylates Glu-tRNA-ligase (GltX), preventing it from being charged, leading to an increase in uncharged tRNA(Glu). This induces amino acid starvation and the stringent response via RelA/SpoT and increased (p)ppGpp levels, which inhibits replication, transcription, translation and cell wall synthesis, reducing growth and leading to persistence and multidrug resistance. HipA is the toxin component of the HipA-HipB TA module that is a major factor in persistence and bioflim formation; its toxic effect is neutralized by its cognate antitoxin HipB. HipA, with HipB, acts as a a corepressor for transcription of the hipBA promoter. In the Escherichia coli HipAB:DNA promoter complex, HipA forms a dimer and each HipA monomer interacts with a HipB homodimer which binds DNA. The HipAB component of the complex is composed of two HipA and four HipB subunits. 401 matched cddid_all.tbl CDD cd17809 cd17809 341494 HipA_So_like type II toxin-antitoxin sytem toxin HipA from Shewanella oneidensis and similar proteins. This family contains type II toxin-antitoxin (TA) system HipA family toxins similar to Shewanella oneidensis HipA, a serine/threonine-protein kinase that phosphorylates Glu-tRNA-ligase (GltX), preventing it from being charged, leading to an increase in uncharged tRNA(Glu). This induces amino acid starvation and the stringent response via RelA/SpoT and increased (p)ppGpp levels, which inhibits replication, transcription, translation and cell wall synthesis, reducing growth and leading to persistence and multidrug resistance. HipA is the toxin component of the HipA-HipB TA module that is a major factor in persistence and bioflim formation; its toxic effect is neutralized by its cognate antitoxin HipB. HipA, with HipB, acts as a a corepressor for transcription of the hipBA promoter. In the Shewanella oneidensis HipAB:DNA promoter complex, HipB forms a dimer that binds the duplex operator DNA, with each HipB monomer interacting with separate HipA monomers. The HipAB component of the complex is composed of two HipA and two HipB subunits. 405 matched cddid_all.tbl CDD cd17814 cd17814 341489 Fe-ADH-like iron-containing alcohol dehydrogenases (Fe-ADH)-like. This family contains iron-containing alcohol dehydrogenase (Fe-ADH) which catalyzes the reduction of acetaldehyde to alcohol with NADP as cofactor. Its activity requires iron ions. The protein structure represents a dehydroquinate synthase-like fold and is a member of the iron-activated alcohol dehydrogenase-like family. It is distinct from other alcohol dehydrogenases which contains different protein domains. Proteins of this family have not been characterized. 374 matched cddid_all.tbl CDD cd17868 cd17868 349777 GPN GPN-loop GTPase. GPN-loop GTPases are deeply evolutionarily conserved family of three small GTPases, Gpn1, 2, and 3. They form heterodimers, interact with RNA polymerase II and may function in nuclear import of RNA polymerase II. 198 matched cddid_all.tbl CDD cd17869 cd17869 349778 TadZ-like pilus assembly protein TadZ. Pilus assembly protein TadZ is involved in the production of a variant of type IV pili. It is part of the SIMIBI superfamily which contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion. 219 matched cddid_all.tbl CDD cd17870 cd17870 349779 GPN1 GPN-loop GTPase 1. GPN-loop GTPase 1 (GPN1, also kown as MBD2-interacting protein or MBDin, RNAPII-associated protein 4, and XPA-binding protein 1) is a GTPase is required for nuclear targeting of RNA polymerase II. It forms heterodimers with GPN3. 241 matched cddid_all.tbl CDD cd17871 cd17871 349780 GPN2 GPN-loop GTPase 2. GPN-loop GTPase 2 (GPN2) is a small GTPase required for proper localization of RNA polymerase II and III (RNAPII and RNAPIII). It forms heterodimers with GPN1 or GPN3. 196 matched cddid_all.tbl CDD cd17872 cd17872 349781 GPN3 GPN-loop GTPase 3. GPN-loop GTPase 3 (GPN3) is a small GTPase that is required for nuclear targeting of RNA polymerase II. It forms heterodimers with GPN1. 196 matched cddid_all.tbl CDD cd17873 cd17873 349782 FlhF signal-recognition particle GTPase FlhF. FlhF protein is a signal-recognition particle (SRP)-type GTPase that is essential for the placement and assembly of polar flagella. It is similar to the 54 kd subunit (SRP54) of the signal recognition particle (SRP) that mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal signal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). 189 matched cddid_all.tbl CDD cd17874 cd17874 349783 FtsY signal recognition particle receptor FtsY. FtsY, the bacterial signal-recognition particle (SRP) receptor (SR), is homologous to the SRP receptor alpha-subunit (SRalpha) of the eukaryotic SR. It interacts with the signal-recognition particle (SRP) and is required for the co-translational membrane targeting of proteins. 199 matched cddid_all.tbl CDD cd17875 cd17875 349784 SRP54_G GTPase domain of the signal recognition 54 kDa subunit. The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal signal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain. 193 matched cddid_all.tbl CDD cd17876 cd17876 349785 SRalpha_C C-terminal domain of signal recognition particle receptor alpha subunit. The signal-recognition particle (SRP) receptor (SR) alpha-subunit (SRalpha) of the eukaryotic SR interacts with the signal-recognition particle (SRP) and is essential for the co-translational membrane targeting of proteins. 204 matched cddid_all.tbl CDD cd17877 cd17877 350170 NP_MTAN-like nucleoside phosphorylases similar to 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidases. This subfamily includes both bacterial and plant 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidases (MTANs), as well as futalosine nucleosidase and adenosylhopane nucleosidase. Bacterial MTANs show comparable efficiency in hydrolyzing MTA and SAH, while plant enzymes are highly specific for MTA and are unable to metabolize SAH or show significantly reduced activity towards SAH. MTAN is involved in methionine and S-adenosyl-methionine recycling, polyamine biosynthesis, and bacterial quorum sensing. This subfamily belongs to the nucleoside phosphorylase-I (NP-I) family, whose members accept a range of purine nucleosides as well as the pyrimidine nucleoside uridine. The NP-1 family includes phosphorolytic nucleosidases, such as purine nucleoside phosphorylase (PNPs, EC. 2.4.2.1), uridine phosphorylase (UP, EC 2.4.2.3), and 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP, EC 2.4.2.28), and hydrolytic nucleosidases, such as AMP nucleosidase (AMN, EC 3.2.2.4), and 5'-methylthioadenosine/S-adenosylhomocysteine (MTA/SAH) nucleosidase (MTAN, EC 3.2.2.16). The NP-I family is distinct from nucleoside phosphorylase-II, which belongs to a different structural family. 210 matched cddid_all.tbl CDD cd17880 cd17880 350625 D-Ala-D-Ala_dipeptidase D-Ala-D-Ala_dipeptidase. This family contains D-Ala-D-Ala dipeptidase enzymes which include D-alanyl-D-alanine dipeptidase vanX and Aad, among others. VanX is a Zn2+-dependent enzyme that mediates resistance to the antibiotic vancomycin in Enterococci and other bacteria (both Gram-positive and Gram-negative). It is part of a gene cluster that affects cell-wall biosynthesis. The operon triggers the termination of peptidoglycan precursors by D-Ala-(R)-lactate instead of D-Ala-D-Ala dipeptides. The enzyme is stereospecific, as L-Ala-L-Ala, D-Ala-L-Ala and L-Ala-D-Ala are not substrates. It fasmily includes Lactobacillus Aad peptidase and belongs in the MEROPS peptidase family M15, subfamily D. 110 matched cddid_all.tbl CDD cd17892 cd17892 467615 GAPDH_N_E4PDH N-terminal NAD(P)-binding domain of D-erythrose-4-phosphate dehydrogenase (E4PDH) and similar proteins. E4PDH (EC 1.2.1.72), also called E4P dehydrogenase, catalyzes the NAD-dependent conversion of D-erythrose 4-phosphate (E4P) to 4-phosphoerythronate, a precursor for the de novo synthesis of pyridoxine via 4-hydroxythreonine and D-1-deoxyxylulose. This enzyme activity appears to have evolved from glyceraldehyde-3-phosphate dehydrogenase (GADPH), whose substrate differs only in the lack of one carbon relative to E4P. E4PDH proteins contain an N-terminal Rossmann fold NAD(P) binding domain and a C-terminal GADPH-like catalytic domain and are members of the GAPDH family of proteins. 169 matched cddid_all.tbl CDD cd17894 cd17894 467520 ASADH_USG1_N N-terminal NAD(P)-binding domain of USG-1 protein and similar proteins. The family includes Escherichia coli USG-1 protein, Pseudomonas aeruginosa USG-1 homolog proteins and similar proteins. Although their biological function remains unknown, they are homologs to aspartate beta-semialdehyde dehydrogenase (ASADH) which contains an N-terminal Rossmann fold NAD(P) binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like domain. However, USG-1 proteins lack the conserved active site residues of the ASADH protein C-terminal domain. 144 matched cddid_all.tbl CDD cd17895 cd17895 467521 AGPR_1_N N-terminal NAD(P)-binding domain of N-acetyl-gamma-glutamyl-phosphate reductase (AGPR), type 1 and similar proteins. AGPR (EC 1.2.1.38), also called N-acetyl-glutamate semialdehyde dehydrogenase, or NAGSA dehydrogenase, catalyzes the NADPH-dependent reduction of N-acetyl-gamma-glutamyl-phosphate phosphate; the third step of arginine biosynthesis. N-acetyl-gamma-glutamyl-phosphate phosphate, the product of the second step catalyzed by acetylglutamate kinase, undergoes reductive dephosphorylation to give N-acetylglutamic semialdehyde, which is converted to ornithine by acetylornithine aminotransferase and acetylornithine deacetylase. AGPR proteins contain an N-terminal Rossmann fold NAD(P)-binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like catalytic domain and are members of the GAPDH superfamily of proteins. NADP(+) binds in a cleft between these domains and contacts both. There are two related families of N-acetyl-gamma-glutamyl-phosphate reductase, which differ by phylogeny, similarity clustering, and gap architecture in a multiple sequence alignment. The model corresponds to type 1 AGPR family. Bacterial members of this family tend to be found within Arg biosynthesis operons. The type 1 AGPR family also includes LysY (LysW-L-2-aminoadipate/LysW-L-glutamate phosphate reductase), which is involved in both the arginine and lysine biosynthetic pathways. 170 matched cddid_all.tbl CDD cd17896 cd17896 467522 AGPR_2_N N-terminal NAD(P)-binding domain of N-acetyl-gamma-glutamyl-phosphate reductase (AGPR), type 2 and similar proteins. AGPR (EC 1.2.1.38), also called N-acetyl-glutamate semialdehyde dehydrogenase, or NAGSA dehydrogenase, catalyzes the NADPH-dependent reduction of N-acetyl-gamma-glutamyl-phosphate phosphate; the third step of arginine biosynthesis. N-acetyl-gamma-glutamyl-phosphate phosphate, the product of the second step catalyzed by acetylglutamate kinase, undergoes reductive dephosphorylation to give N-acetylglutamic semialdehyde, which is converted to ornithine by acetylornithine aminotransferase and acetylornithine deacetylase. AGPR proteins contain an N-terminal Rossmann fold NAD(P)-binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like catalytic domain and are members of the GAPDH superfamily of proteins. NADP(+) binds in a cleft between these domains and contacts both. There are two related families of N-acetyl-gamma-glutamyl-phosphate reductase, which differ by phylogeny, similarity clustering, and gap architecture in a multiple sequence alignment. The model corresponds to type 2 AGPR family. 132 matched cddid_all.tbl CDD cd17900 cd17900 350087 ArfGap_ASAP3 ArfGAP domain of ASAP3 (ArfGAP with ANK repeat and PH domain-containing protein 3). The ArfGAPs are a family of multidomain proteins with a common catalytic domain that promotes the hydrolysis of GTP bound to Arf, thereby inactivating Arf signaling. ASAP-subfamily GAPs include three members: ASAP1, ASAP2, ASAP3. The ASAP subfamily comprises Arf GAP, SH3, ANK repeat and PH domains. From the N-terminus, each member has a BAR, PH, Arf GAP, ANK repeat, and proline rich domains. Unlike ASAP1 and ASAP2, ASAP3 do not have an SH3 domain at the C-terminus. ASAP1 and ASAP2 show strong GTPase-activating protein (GAP) activity toward Arf1 and Arf5 and weak activity toward Arf6. ASAP1 is a target of Src and FAK signaling that regulates focal adhesions, circular dorsal ruffles (CDR), invadopodia, and podosomes. ASAP1 GAP activity is synergistically stimulated by phosphatidylinositol 4,5-bisphosphate (PIP2) and phosphatidic acid. ASAP2 is believed to function as an ArfGAP that controls ARF-mediated vesicle budding when recruited to Golgi membranes. It also functions as a substrate and downstream target for protein tyrosine kinases Pyk2 and Src, a pathway that may be involved in the regulation of vesicular transport. ASAP3 is a focal adhesion-associated ArfGAP that functions in cell migration and invasion. Similar to ASAP1, the GAP activity of ASAP3 is strongly enhanced by PIP2 via PH domain. Like ASAP1, ASAP3 associates with focal adhesions and circular dorsal ruffles. However, unlike ASAP1, ASAP3 does not localize to invadopodia or podosomes. ASAP 1 and 3 have been implicated in oncogenesis, as ASAP1 is highly expressed in metastatic breast cancer and ASAP3 in hepatocellular carcinoma. 124 matched cddid_all.tbl CDD cd17901 cd17901 350088 ArfGap_ARAP1 ArfGap with Rho-Gap domain, ANK repeat and PH domain-containing protein 1. The ARAP subfamily includes three members, ARAP1-3, and belongs to the ADP-ribosylation factor GTPase-activating proteins (Arf GAPs) family of proteins that promotes the hydrolysis of GTP bound to Arf, thereby inactivating Arf signaling. The function of Arfs is dependent on GAPs and guanine nucleotide exchange factors (GEFs), which allow Arfs to cycle between the GDP-bound and GTP-bound forms. In addition to the Arf GAP domain, ARAPs contain the SAM (sterile-alpha motif) domain, 5 pleckstrin homology (PH) domains, the Rho-GAP domain, the Ras-association domain, and ANK repeats. ARAPs show phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3)-dependent GAP activity toward Arf6. ARAPs play important roles in endocytic trafficking, cytoskeleton reorganization in response to growth factors stimulation, and focal adhesion dynamics. ARAP1 localizes to the plasma membrane, the Golgi complex, and endosomal compartments. It displays PI(3,4,5)P3-dependent ArfGAP activity that regulates Arf-, RhoA-, and Cdc42-dependent cellular events. For example, ARAP1 inhibits the trafficking of epidermal growth factor receptor (EGFR) to the early endosome. 116 matched cddid_all.tbl CDD cd17902 cd17902 350089 ArfGap_ARAP3 ArfGap with Rho-Gap domain, ANK repeat and PH domain-containing protein 3. The ARAP subfamily includes three members, ARAP1-3, and belongs to the ADP-ribosylation factor GTPase-activating proteins (Arf GAPs) family of proteins that promotes the hydrolysis of GTP bound to Arf, thereby inactivating Arf signaling. The function of Arfs is dependent on GAPs and guanine nucleotide exchange factors (GEFs), which allow Arfs to cycle between the GDP-bound and GTP-bound forms. In addition to the Arf GAP domain, ARAPs contain the SAM (sterile-alpha motif) domain, 5 pleckstrin homology (PH) domains, the Rho-GAP domain, the Ras-association domain, and ANK repeats. ARAPs show phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3)-dependent GAP activity toward Arf6. ARAPs play important roles in endocytic trafficking, cytoskeleton reorganization in response to growth factors stimulation, and focal adhesion dynamics. ARAP3 possesses a unique dual-specificity GAP activity for Arf6 and RhoA regulated by PI(3,4,5)P3 and a small GTPase Rap1-GTP. The RhoGAP activity of ARAP3 is enhanced by direct binding of Rap1-GTP to the Ras-association (RA) domain. ARAP3 is involved in regulation of cell shape and adhesion. 116 matched cddid_all.tbl CDD cd17903 cd17903 350090 ArfGap_AGFG2 ArfGAP domain of AGFG2 (ArfGAP domain and FG repeat-containing protein 2). The ArfGAP domain and FG repeat-containing proteins (AFGF) subfamily of Arf GTPase-activating proteins consists of the two structurally-related members: AGFG1 and AGFG2. AGFG2 is a member of the HIV-1 Rev binding protein (HRB) family and contains one Arf-GAP zinc finger domain, several Phe-Gly (FG) motifs, and four Asn-Pro-Phe (NPF) motifs. AGFG2 interacts with Eps15 homology (EH) domains and plays a role in the Rev export pathway, which mediates the nucleocytoplasmic transfer of proteins and RNAs. In humans, the presence of the FG repeat motifs (11 in AGFG1 and 7 in AGFG2) are thought to be required for these proteins to act as HIV-1 Rev cofactors. Hence, AGFG promotes movement of Rev-responsive element-containing RNAs from the nuclear periphery to the cytoplasm, which is an essential step for HIV-1 replication. 116 matched cddid_all.tbl CDD cd17904 cd17904 380783 PFM_monalysin-like pore-forming module of Pseudomonas entomophila monalysin and similar aerolysin-type beta-barrel pore-forming proteins. Monalysin plays a role in Pseudomonas entomophila virulence against Drosophila, contributing to host intestinal damage and lethality. Members of this group belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 206 matched cddid_all.tbl CDD cd17905 cd17905 381733 CheC-like chemotaxis protein CheC; includes CheC classes I, II, and III. This family contains chemotaxis protein CheC that acts as a weak CheY-P phosphatase but shows increased activity in the presence of CheD. This CheC family includes three classes: class I containing Bacillus subtilis CheC which might function as a regulator of CheD; class II CheCs that likely function as phosphatases in systems other than chemotaxis; and class III CheCs that are found chiefly in the archaeal class Halobacteria and might function similarly as class I CheCs. Class I CheCs contain two active sites with the consensus sequence ([DS]xxxExxNx(22)P), with four conserved residues thought to form the phosphatase active site; class II and class III CheCs have only one actve site. 173 matched cddid_all.tbl CDD cd17906 cd17906 381734 CheX chemotaxis phosphatase CheX. This family contains CheX CheY-P phosphatase which is very closely related to CheC chemotaxis phosphatase; both dephosphorylate CheY, although CheC requires binding of CheD to achieve the level of activity of CheX. CheX has been shown to be the most powerful CheY-P phosphatase of the CheC-FliY-CheX (CXY) family. Structural and functional data of CheX and its CheY3 substrate in Borrelia burgdorferi (the causative agent of Lyme disease) bound to the phosphoryl analog BeF3(-) and Mg2+ reveal a unique mode of binding, but a catalytic mechanism which is virtually identical to that used by the structurally unrelated CheZ, providing a striking example of convergent evolution. Thus, CheX is quite divergent from the rest of the CXY family; it forms a dimer and some may function outside chemotaxis. The data also suggest a possible CheX regulatory mechanism through dissociation of the CheX homodimer. 148 matched cddid_all.tbl CDD cd17907 cd17907 381735 FliY_FliN-Y flagellar motor switch protein FliY. This family contains the flagellar rotor protein FliY, a highly conserved and essential member of the CheC phosphatase family, that distinguishes flagellar architecture and function in different types of bacteria. Unlike CheC and CheX, FliY is localized in the flagellar switch complex, which also contains the stator-coupling protein FliG and the target of CheY-P, FliM, all present in many copies, and together corresponding structurally to the C-ring of the flagellar basal body. FliY structure resembles that of the rotor protein FliM but contains two active centers for CheY dephosphorylation. In bacteria such as Thermotogae and Bacilli, FliY is fused to FliN. It incorporates properties of the FliM/FliN rotor proteins and the CheC/CheX phosphatases to serve multiple functions in the flagellar switch. FliY seems to act on CheY-P constitutively, as compared to CheC and CheX that appear to be primarily involved in restoring normal CheY-P levels. 191 matched cddid_all.tbl CDD cd17908 cd17908 381736 FliM flagellar protein FliM. This family contains bacterial flagellar protein FliM which is localized in the flagellar switch complex along with FliG and FliY; all are present in many copies, and together they correspond structurally to the C-ring of the flagellar basal body. FliM does not contain the CheC consensus sequence of the phosphatase active site ([DS]xxxExxNx(22)P) and is not a CheY-P phosphatase. FliM sits in the center of the rotor with the N-terminal region interacting with the signaling protein, phosphorylated CheY (CheY-P). The activated form of CheY destabilizes the parallel arrangement of FliM molecules, and perturbs FliG alignment in a process that may reflect the onset of rotation switching. This suggests a model of C-ring assembly in which intermolecular contacts among FliG domains provide a template for FliM assembly. Recent data show that binding of FliM to spermine synthase, SpeE, contributes to flagellar motility, an association that is unique to Helicobacter species. 181 matched cddid_all.tbl CDD cd17909 cd17909 381737 CheC_ClassI chemotaxis protein CheC, Class I. This subfamily contains Class I CheC proteins with phosphatase activity. The Class I cheC genes are generally found in firmicute and archaeal chemotaxis operons with cheD, usually translationally coupled. Class I CheCs interact with the CheD protein which is responsible for deamidation of certain glutamine residues to glutamates on the chemotaxis receptor proteins. This family contains two active sites with the consensus sequence ([DS]xxxExxNx(22)P), with four conserved residues thought to form the phosphatase active site. The C-terminal helix of CheC acts as a mimic of the natural enzymatic target of CheD, the alpha-helical receptors, and serves as the binding site for CheD. The CheC/CheD heterodimerization increases CheY-P phosphatase activity five-fold. Class I CheCs are involved in adaptation of the chemotaxis system. 189 matched cddid_all.tbl CDD cd17910 cd17910 381738 CheC_ClassII chemotaxis protein CheC, Class II. This family contains class II CheC proteins found in proteobacteria, which diverge from class I CheCs in sequence conservation and lack critical well-conserved residues for CheD binding. These proteins are likely to be dedicated phosphatases. The class II cheC genes are not found in chemotaxis operons, but in operons containing more archetypical two-component signaling components, non-signaling operons, or as orphans. Thus, class II CheCs appear to be involved in non-chemotactic two component systems. Class II CheCs lack the first of the two phosphatase active sites of class I CheCs, and retain the second active site of class I CheCs. 187 matched cddid_all.tbl CDD cd17911 cd17911 381739 CheC_ClassIII chemotactic protein CheC, Class III. This family contains class III CheC proteins, present chiefly in the archaeal class Halobacteria. Sequence analysis shows that class III CheC proteins are structurally and functionally similar to class I CheCs, and not to CheX, despite the fact that both class III CheCs and CheX lack the first of the two phosphatase active sites of class I CheCs, and retain the second active site. Mutation analysis shows that the second active site is more important for function that the first one, suggesting that class III proteins arose by loss of the unnecessary first active site through mutational shift. All chemotactic archaea have a CheC homologue. 187 matched cddid_all.tbl CDD cd17912 cd17912 350670 DEAD-like_helicase_N N-terminal helicase domain of the DEAD-box helicase superfamily. The DEAD-like helicase superfamily is a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. The N-terminal domain contains the ATP-binding region. 81 matched cddid_all.tbl CDD cd17913 cd17913 350671 DEXQc_Suv3 DEXQ-box helicase domain of Suv3. Suppressor of var1 3-like protein (Suv3) is a DNA/RNA unwinding enzyme belonging to the class of DexH-box helicases. It localizes predominantly in the mitochondria, where it forms an RNA-degrading complex called mitochondrial degradosome (mtEXO) with exonuclease PNP (polynucleotide phosphorylase), that degrades 3' overhang double-stranded RNA with a 3'-to-5' directionality in an ATP-dependent manner. Suv3 plays a role in the RNA surveillance system in mitochondria; it regulates the stability of mature mRNAs, the removal of aberrantly formed mRNAs and the rapid degradation of non coding processing intermediates. It also confers salinity and drought stress tolerance by maintaining both photosynthesis and antioxidant machinery, probably via an increase in plant hormone levels such as gibberellic acid (GA3), the cytokinin zeatin (Z), and indole-3-acetic acid (IAA). Suv3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 142 matched cddid_all.tbl CDD cd17914 cd17914 438706 DExxQc_SF1-N DEXQ-box helicase domain of superfamily 1 helicase. The superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Like SF2, they do not form toroidal, predominantly hexameric structures like SF3-6. Their helicase core is surrounded by C and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains or domains engaged in protein-protein interactions. SF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 121 matched cddid_all.tbl CDD cd17915 cd17915 350673 DEAHc_XPD-like DEAH-box helicase domain of XPD family DEAD-like helicases. The xeroderma pigmentosum group D (XPD)-like family members are DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 138 matched cddid_all.tbl CDD cd17916 cd17916 350674 DEXHc_UvrB DEXH-box helicase domain of excinuclease ABC subunit B. Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II) and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA, but its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a member of the DEAD-like helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 299 matched cddid_all.tbl CDD cd17917 cd17917 438707 DEXHc_RHA-like DEXH-box helicase domain of DEAD-like helicase RHA family proteins. The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 159 matched cddid_all.tbl CDD cd17918 cd17918 350676 DEXHc_RecG DEXH/Q-box helicase domain of DEAD-like helicase RecG family proteins. The DEAD-like helicase RecG family is part of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 180 matched cddid_all.tbl CDD cd17919 cd17919 350677 DEXHc_Snf DEXH/Q-box helicase domain of DEAD-like helicase Snf family proteins. Sucrose Non-Fermenting (SNF) proteins DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 182 matched cddid_all.tbl CDD cd17920 cd17920 350678 DEXHc_RecQ DEXH-box helicase domain of RecQ family proteins. The RecQ family of the type II DEAD box helicase superfamily is a family of highly conserved DNA repair helicases. This domain contains the ATP-binding region. 200 matched cddid_all.tbl CDD cd17921 cd17921 350679 DEXHc_Ski2 DEXH-box helicase domain of DEAD-like helicase Ski2 family proteins. Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 181 matched cddid_all.tbl CDD cd17922 cd17922 350680 DEXHc_LHR-like DEXH-box helicase domain of LHR. Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases from the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 166 matched cddid_all.tbl CDD cd17923 cd17923 350681 DEXHc_Hrq1-like DEAH-box helicase domain of Hrq1 and similar proteins. Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. Hrq1 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 182 matched cddid_all.tbl CDD cd17924 cd17924 350682 DDXDc_reverse_gyrase DDXD-box helicase domain of reverse gyrase. Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 189 matched cddid_all.tbl CDD cd17925 cd17925 350683 DEXDc_ComFA DEXD-box helicase domain of ComFA. ATP-dependent helicase ComFA (also called ComF operon protein 1) is part of the complex mediating the binding and uptake of single-stranded DNA. ComFA is required for DNA uptake but not for binding. It belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 143 matched cddid_all.tbl CDD cd17926 cd17926 350684 DEXHc_RE DEXH-box helicase domain of DEAD-like helicase restriction enzyme family proteins. This family is composed of helicase restriction enzymes and similar proteins such as TFIIH basal transcription factor complex helicase XPB subunit. These proteins are part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 146 matched cddid_all.tbl CDD cd17927 cd17927 350685 DEXHc_RIG-I DEXH-box helicase domain of DEAD-like helicase RIG-I family proteins. Members of the RIG-I family include FANCM, dicer, Hef, and the RIG-I-like receptors. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). Hef (helicase-associated endonuclease fork-structure) is involved in stalled replication fork repair. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprises RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). The RIG-I family is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 201 matched cddid_all.tbl CDD cd17928 cd17928 350686 DEXDc_SecA DEXD-box helicase domain of SecA. SecA is a part of the Sec translocase that transports the vast majority of bacterial and ER-exported proteins. SecA binds both the signal sequence and the mature domain of the preprotein emerging from the ribosome. SecA belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 230 matched cddid_all.tbl CDD cd17929 cd17929 350687 DEXHc_priA DEXH-box helicase domain of PriA. PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' superfamily 2 DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 178 matched cddid_all.tbl CDD cd17930 cd17930 350688 DEXHc_cas3 DEXH/Q-box helicase domain of Cas3. CRISPR-associated (Cas) 3 is a nuclease-helicase responsible for degradation of dsDNA. The two enzymatic units of Cas3, a histidine-aspartate (HD) nuclease and a Superfamily 2 (SF2) helicase, may be expressed from separate genes as Cas3' (SF2 helicase) and Cas3'' (HD nuclease) or may be fused as a single HD-SF2 polypeptide. The nucleolytic activity of most Cas3 enzymes is transition metal ion-dependent. Cas3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 186 matched cddid_all.tbl CDD cd17931 cd17931 350689 DEXHc_viral_Ns3 DEXH-box helicase domain of NS3 protease-helicase. NS3 is a nonstructural multifunctional protein found in pestiviruses that contains an N-terminal protease and a C-terminal helicase. The N-terminal domain is a chymotrypsin-like serine protease, which is responsible for most of the maturation cleavages of the polyprotein precursor in the cytosolic side of the endoplasmic reticulum membrane. The C-terminal domain, about two-thirds of NS3, is a helicase belonging to superfamily 2 (SF2) thought to be important for unwinding highly structured regions of the RNA genome during replication. NS3 plays an essential role in viral polyprotein processing and genome replication. NS3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 151 matched cddid_all.tbl CDD cd17932 cd17932 350690 DEXQc_UvrD DEXQD-box helicase domain of UvrD. UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. UvrD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 189 matched cddid_all.tbl CDD cd17933 cd17933 350691 DEXSc_RecD-like DEXS-box helicase domain of RecD and similar proteins. RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 155 matched cddid_all.tbl CDD cd17934 cd17934 438708 DEXXQc_Upf1-like DEXXQ-box helicase domain of Upf1-like helicase. The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 121 matched cddid_all.tbl CDD cd17935 cd17935 350693 EEXXQc_AQR EEXXQ-box helicase domain of AQR. Aquarius (AQR) is a multifunctional RNA helicase that binds precursor-mRNA introns at a defined position and is part of a pentameric intron-binding complex (IBC). It is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 207 matched cddid_all.tbl CDD cd17936 cd17936 350694 EEXXEc_NFX1 EEXXE-box helicase domain of NFX1. Human NFX1 protein was identified as a protein that represses class II MHC (major histocompatibility complex) gene expression. NFX1 binds a conserved cis-acting element, termed the X-box, in promoters of human class II MHC genes. The Cys-rich region contains several NFX1-type zinc finger domains. Frequently, a R3H domain is present in the C-terminus, and a RING finger domain and a PAM2 motif are present in the N-terminus. The lack of R3H and PAM2 motifs in the plant proteins indicates functional differences. Plant NFX1-like proteins are proposed to modulate growth and survival by coordinating reactive oxygen species, salicylic acid, further biotic stress and abscisic acid responses. A common feature of all members may be E3 ubiquitin ligase, due to the presence of a RING finger domain, as well as DNA binding. NFX1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 178 matched cddid_all.tbl CDD cd17937 cd17937 350695 DEXXYc_viral_SF1-N DEXXY-box helicase domain of viral superfamily 1 helicase. Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. The members here contain arterivirus equine arteritis virus (EAV) non-structural protein (nsp)10. Nsp10 is composed of two domains, ZBD (ATPase) and HEL1 (helicase) along with 2 additional non-enzymatic domains that are thought to regulate HEL1 function. The helicase activity depends on the extensive relay of interactions between the ZBD and HEL1 domains. The arterivirus helicase structurally resembles the cellular Upf1 helicase, suggesting that nidoviruses may also use their helicases for post-transcriptional quality control of their large RNA genomes. The proteins here are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 137 matched cddid_all.tbl CDD cd17938 cd17938 350696 DEADc_DDX1 DEAD-box helicase domain of DEAD box protein 1. DEAD box protein 1 (DDX1) acts as an ATP-dependent RNA helicase, able to unwind both RNA-RNA and RNA-DNA duplexes. It possesses 5' single-stranded RNA overhang nuclease activity as well as ATPase activity on various RNA, but not DNA polynucleotides. DDX1 may play a role in RNA clearance at DNA double-strand breaks (DSBs), thereby facilitating the template-guided repair of transcriptionally active regions of the genome. It may also be involved in 3'-end cleavage and polyadenylation of pre-mRNAs. DDX1 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 204 matched cddid_all.tbl CDD cd17939 cd17939 350697 DEADc_EIF4A DEAD-box helicase domain of eukaryotic initiation factor 4A. The eukaryotic initiation factor-4A (eIF4A) family consists of 3 proteins EIF4A1, EIF4A2, and EIF4A3. These factors are required for the binding of mRNA to 40S ribosomal subunits. In addition these proteins are helicases that function to unwind double-stranded RNA. EIF4A proteins are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 199 matched cddid_all.tbl CDD cd17940 cd17940 350698 DEADc_DDX6 DEAD-box helicase domain of DEAD box protein 6. DEAD box protein 6 (DDX6, also known as Rck or p54) participates in mRNA regulation mediated by miRNA-mediated silencing. It also plays a role in global and transcript-specific messenger RNA (mRNA) storage, translational repression, and decay. It is a member of the DEAD-box helicase family, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 201 matched cddid_all.tbl CDD cd17941 cd17941 350699 DEADc_DDX10 DEAD-box helicase domain of DEAD box protein 10. Fusion of the DDX10 gene and the nucleoporin gene, NUP98, by inversion 11 (p15q22) chromosome translocation is found in the patients with de novo or therapy-related myeloid malignancies. Diseases associated with DDX10 (also known as DDX10-NUP98 Fusion Protein Type 2) include myelodysplastic syndrome and leukemia, acute myeloid. DDX10 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 198 matched cddid_all.tbl CDD cd17942 cd17942 350700 DEADc_DDX18 DEAD-box helicase domain of DEAD box protein 18. This DDX18 gene encodes a DEAD box protein and is activated by Myc protein. DDX18 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 198 matched cddid_all.tbl CDD cd17943 cd17943 350701 DEADc_DDX20 DEAD-box helicase domain of DEAD box protein 20. DDX20 (also called DEAD Box Protein DP 103, Component Of Gems 3, Gemin-3, and SMN-Interacting Protein) interacts directly with SMN (survival of motor neurons), the spinal muscular atrophy gene product, and may play a catalytic role in the function of the SMN complex on ribonucleoproteins. Diseases associated with DDX20 include spinal muscular atrophy and muscular atrophy. DDX20 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 192 matched cddid_all.tbl CDD cd17944 cd17944 350702 DEADc_DDX21_DDX50 DEAD-box helicase domain of DEAD box proteins 21 and 50. DDX21 (also called Gu-Alpha and nucleolar RNA helicase 2) is an RNA helicase that acts as a sensor of the transcriptional status of both RNA polymerase (Pol) I and II. It promotes ribosomal RNA (rRNA) processing and transcription from polymerase II (Pol II) and binds various RNAs, such as rRNAs, snoRNAs, 7SK and, at lower extent, mRNAs. DDX50 (also called Gu-Beta, Nucleolar Protein Gu2, and malignant cell derived RNA helicase). DDX21 and DDX50 have similar genomic structures and are in tandem orientation on chromosome 10, suggesting that the two genes arose by gene duplication in evolution. Diseases associated with DDX21 include stomach disease and cerebral creatine deficiency syndrome 3. Diseases associated with DDX50 include rectal disease. Both are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. Their name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region. 202 matched cddid_all.tbl CDD cd17945 cd17945 350703 DEADc_DDX23 DEAD-box helicase domain of DEAD box protein 23. DDX23 (also called U5 snRNP 100kD protein and PRP28 homolog) is involved in pre-mRNA splicing and its phosphorylated form (by SRPK2) is required for spliceosomal B complex formation. Diseases associated with DDX23 include distal hereditary motor neuropathy, type II. DDX23 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 220 matched cddid_all.tbl CDD cd17946 cd17946 350704 DEADc_DDX24 DEAD-box helicase domain of DEAD box protein 24. The human DDX24 gene encodes a DEAD box protein, which shows little similarity to any of the other known human DEAD box proteins, but shows a high similarity to mouse Ddx24 at the amino acid level. MDM2 mediates nonproteolytic polyubiquitylation of the DEAD-Box RNA helicase DDX24. DDX24 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP- binding region. 235 matched cddid_all.tbl CDD cd17947 cd17947 350705 DEADc_DDX27 DEAD-box helicase domain of DEAD box protein 27. DDX27 (also called RHLP, deficiency of ribosomal subunits protein 1 homolog, and probable ATP-dependent RNA helicase DDX27) is involved in the processing of 5.8S and 28S ribosomal RNAs. More specifically, the encoded protein localizes to the nucleolus, where it interacts with the PeBoW complex to ensure proper 3' end formation of 47S rRNA. DDX27 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 196 matched cddid_all.tbl CDD cd17948 cd17948 350706 DEADc_DDX28 DEAD-box helicase domain of DEAD box protein 28. DDX28 (also called mitochondrial DEAD-box polypeptide 28) plays an essential role in facilitating the proper assembly of the mitochondrial large ribosomal subunit and its helicase activity is essential for this function. DDX28 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 231 matched cddid_all.tbl CDD cd17949 cd17949 350707 DEADc_DDX31 DEAD-box helicase domain of DEAD box protein 31. DDX31 (also called helicain or G2 helicase) plays a role in ribosome biogenesis and TP53/p53 regulation through its interaction with NPM1. DDX31 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 214 matched cddid_all.tbl CDD cd17950 cd17950 350708 DEADc_DDX39 DEAD-box helicase domain of DEAD box protein 39. DDX39A is involved in pre-mRNA splicing and is required for the export of mRNA out of the nucleus. DDX39B is an essential splicing factor required for association of U2 small nuclear ribonucleoprotein with pre-mRNA, and it also plays an important role in mRNA export from the nucleus to the cytoplasm. Diseases associated with DDX39A (also called UAP56-Related Helicase, 49 kDa) include gastrointestinal stromal tumor and inflammatory bowel disease 6, while diseases associated with DDX39B (also called 56 kDa U2AF65-Associated Protein) include Plasmodium vivax malaria. DDX39 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 208 matched cddid_all.tbl CDD cd17951 cd17951 350709 DEADc_DDX41 "DEAD-box helicase domain of DEAD box protein 41. DDX41 (also called ABS and MPLPF) interacts with several spliceosomal proteins and may recognize the bacterial second messengers cyclic di-GMP and cyclic di-AMP, resulting in the induction of genes involved in the innate immune response. Diseases associated with DDX41 include ""myeloproliferative/lymphoproliferative neoplasms, familial"" and ""Ddx41-related susceptibility to familial myeloproliferative/lymphoproliferative neoplasms"". DDX41 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region." 206 matched cddid_all.tbl CDD cd17952 cd17952 350710 DEADc_DDX42 DEAD-box helicase domain of DEAD box protein 42. DDX42 (also called Splicing Factor 3B-Associated 125 kDa Protein, RHELP, or RNAHP) is an NTPase with a preference for ATP, the hydrolysis of which is enhanced by various RNA substrates. It acts as a non-processive RNA helicase with protein displacement and RNA annealing activities. DDX42 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 197 matched cddid_all.tbl CDD cd17953 cd17953 350711 DEADc_DDX46 DEAD-box helicase domain of DEAD box protein 46. DDX46 (also called Prp5-like DEAD-box protein) is a component of the 17S U2 snRNP complex. It plays an important role in pre-mRNA splicing and has a role in antiviral innate immunity. DDX46 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 222 matched cddid_all.tbl CDD cd17954 cd17954 350712 DEADc_DDX47 DEAD-box helicase domain of DEAD box protein 47. DDX47 (also called E4-DEAD box protein) can shuttle between the nucleus and the cytoplasm, and has an RNA-independent ATPase activity. DX47 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 203 matched cddid_all.tbl CDD cd17955 cd17955 350713 DEADc_DDX49 DEAD-box helicase domain of DEAD box protein 49. DDX49 (also called Dbp8) is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 204 matched cddid_all.tbl CDD cd17956 cd17956 350714 DEADc_DDX51 DEAD-box helicase domain of DEAD box protein 51. DDX51 aids cell cancer proliferation by regulating multiple signalling pathways. Mammalian DEAD box protein Ddx51 acts in 3' end maturation of 28S rRNA by promoting the release of U8 snoRNA.It is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 231 matched cddid_all.tbl CDD cd17957 cd17957 350715 DEADc_DDX52 DEAD-box helicase domain of DEAD box protein 52. DDX52 (also called ROK1 and HUSSY19) is ubiquitously expressed in testis, endometrium, and other tissues in humans. DDX52 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 198 matched cddid_all.tbl CDD cd17958 cd17958 350716 DEADc_DDX43_DDX53 DEAD-box helicase domain of DEAD box proteins 43 and 53. DDX43 (also called cancer/testis antigen 13 or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 is also called cancer/testis antigen 26 or DEAD-Box Protein CAGE. Both DDX46 and DDX53 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 197 matched cddid_all.tbl CDD cd17959 cd17959 350717 DEADc_DDX54 DEAD-box helicase domain of DEAD box protein 54. DDX54 interacts in a hormone-dependent manner with nuclear receptors, and represses their transcriptional activity. DDX54 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 205 matched cddid_all.tbl CDD cd17960 cd17960 350718 DEADc_DDX55 DEAD-box helicase domain of DEAD box protein 55. DDX55 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 202 matched cddid_all.tbl CDD cd17961 cd17961 350719 DEADc_DDX56 DEAD-box helicase domain of DEAD box protein 56. DDX56 is a helicase required for assembly of infectious West Nile virus particles. New research suggests that DDX56 relocalizes to the site of virus assembly during WNV infection and that its interaction with WNV capsid in the cytoplasm may occur transiently during virion morphogenesis. DDX56 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 206 matched cddid_all.tbl CDD cd17962 cd17962 350720 DEADc_DDX59 DEAD-box helicase domain of DEAD box protein 59. DDX59 plays an important role in lung cancer development by promoting DNA replication. DDX59 knockdown mice showed reduced cell proliferation, anchorage-independent cell growth, and reduction of tumor formation. Recent work shows that EGFR and Ras regulate DDX59 during lung cancer development. Diseases associated with DDX59 (also called zinc finger HIT domain-containing protein 5) include orofaciodigital syndrome V and orofaciodigital syndrome. DDX59 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 193 matched cddid_all.tbl CDD cd17963 cd17963 350721 DEADc_DDX19_DDX25 DEAD-box helicase domain of ATP-dependent RNA helicases DDX19 and DDX25. DDX19 (also called DEAD box RNA helicase DEAD5) and DDX25 (also called gonadotropin-regulated testicular RNA helicase (GRTH)) are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 196 matched cddid_all.tbl CDD cd17964 cd17964 350722 DEADc_MSS116 DEAD-box helicase domain of DEAD-box helicase Mss116. Mss116 is an RNA chaperone important for mitochondrial group I and II intron splicing, translational activation, and RNA end processing. Mss116 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 211 matched cddid_all.tbl CDD cd17965 cd17965 350723 DEADc_MRH4 DEAD-box helicase domain of ATP-dependent RNA helicase MRH4. Mitochondrial RNA helicase 4 (MRH4) plays an essential role during the late stages of mitochondrial ribosome or mitoribosome assembly by promoting remodeling of the 21S rRNA-protein interactions. MRH4 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 251 matched cddid_all.tbl CDD cd17966 cd17966 350724 DEADc_DDX5_DDX17 DEAD-box helicase domain of ATP-dependent RNA helicases DDX5 and DDX17. DDX5 and DDX17 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 197 matched cddid_all.tbl CDD cd17967 cd17967 350725 DEADc_DDX3_DDX4 DEAD-box helicase domain of ATP-dependent RNA helicases DDX3 and DDX4. This subfamily includes Drosophila melanogaster Vasa, which is essential for development. DEAD box protein 3 (DDX3) has been reported to display a high level of RNA-independent ATPase activity stimulated by both RNA and DNA. DEAD box protein 4 (DDX4, also known as VASA homolog) is an ATP-dependent RNA helicase required during spermatogenesis and is essential for the germline integrity. DDX3 and DDX4 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 221 matched cddid_all.tbl CDD cd17968 cd17968 350726 DEAHc_DDX11_starthere DEAH-box helicase domain of ATP-dependent DNA helicase DDX11. DDX11 (also called ChlR1) encodes a protein of the conserved family of Iron-Sulfur (Fe-S) cluster DNA helicases and is thought to function in maintaining chromosome transmission fidelity and genome stability. Mutations in the Chl1 human homologs ChlR1/DDX11 and BACH1/BRIP1/FANCJ collectively result in Warsaw Breakage Syndrome, Fanconi anemia, cell aneuploidy and breast and ovarian cancers. DDX11 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 134 matched cddid_all.tbl CDD cd17969 cd17969 350727 DEAHc_XPD DEAH-box helicase domain of TFIIH basal transcription factor complex helicase XPD subunit. TFIIH can be resolved biochemically into a seven subunit core complex containing XPD/Rad3, XPB/Ssl2, p62/Tfb1, p52/Tfb2, p44/Ssl1, p34/Tfb4, and p8/Tfb5 and a three subunit Cdk Activating Kinase (CAK) complex containing CDK7/Kin28, cyclin H/Ccl1, and MAT1/Tfb3. XPD interacts directly with p44, which stimulates XPD helicase activity. XPD/Rad3 also interacts directly with the CAK via its MAT1/Tfb3 subunit inhibiting the helicase activity of XPD. XPD is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 157 matched cddid_all.tbl CDD cd17970 cd17970 350728 DEAHc_FancJ DEAH-box helicase domain of Fanconi anemia group J protein and similar proteins. Fanconi anemia group J protein (FACJ or FANCJ, also known as BRIP1) is a DNA helicase required for the maintenance of chromosomal stability. It plays a role in the repair of DNA double-strand breaks by homologous recombination dependent on its interaction with BRCA1. FANCJ belongs to the DEAD-box helicase family, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 181 matched cddid_all.tbl CDD cd17971 cd17971 350729 DEXHc_DHX8 DEXH-box helicase domain of DEAH-box helicase 8. DEAH-box helicase 8 (DHX8 ,also known as pre-mRNA-splicing factor ATP-dependent RNA helicase PRP22) acts late in the splicing of pre-mRNA and mediates the release of the spliced mRNA from spliceosomes. DHX8 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 179 matched cddid_all.tbl CDD cd17972 cd17972 350730 DEXHc_DHX9 DEXH-box helicase domain of DEAH-box helicase 9. DEAH-box helicase 9 (DHX9, also known as ATP-dependent RNA helicase A or RHA and leukophysin or LKP) plays an important role in many cellular processes, including regulation of DNA replication, transcription, translation, microRNA biogenesis, RNA processing and transport, and maintenance of genomic stability. DHX9 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 234 matched cddid_all.tbl CDD cd17973 cd17973 438709 DEXHc_DHX15 DEXH-box helicase domain of DEAH-box helicase 15. DEAH-box helicase 15 (DHX15) is a pre-mRNA processing factor involved in disassembly of spliceosomes after the release of mature mRNA. DHX15 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 187 matched cddid_all.tbl CDD cd17974 cd17974 350732 DEXHc_DHX16 DEXH-box helicase domain of DEAH-box helicase 16. DEAH-box helicase 16 (DHX16) is probably involved in pre-mRNA splicing. DHX16 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 174 matched cddid_all.tbl CDD cd17975 cd17975 350733 DEXHc_DHX29 DEXH-box helicase domain of DEAH-box helicase 29. DEAH-box helicase 29 (DHX29) is a part of the 43S pre-initiation complex involved in translation initiation of mRNAs with structured 5'-UTRs. DHX29 is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 183 matched cddid_all.tbl CDD cd17976 cd17976 350734 DEXHc_DHX30 DEXH-box helicase domain of DEAH-box helicase 30. DEAH-box helicase 30 (DHX30) plays an important role in the assembly of the mitochondrial large ribosomal subunit. DHX30 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 178 matched cddid_all.tbl CDD cd17977 cd17977 350735 DEXHc_DHX32 DEXH-box helicase domain of DEAH-box helicase 32. DEAH-box helicase 32 (DHX32) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 176 matched cddid_all.tbl CDD cd17978 cd17978 438710 DEXHc_DHX33 DEXH-box helicase domain of DEAH-box helicase 33. DEAH-box helicase 33 (DHX33) stimulates RNA polymerase I transcription of the 47S precursor rRNA. DHX33 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 178 matched cddid_all.tbl CDD cd17979 cd17979 350737 DEXHc_DHX34 DEXH-box helicase domain of DEAH-box helicase 34. DEAH-box helicase 34 (DHX34) plays a role in the nonsense-mediated decay (NMD), a surveillance mechanism that degrades aberrant mRNAs. DHX34 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 170 matched cddid_all.tbl CDD cd17980 cd17980 350738 DEXHc_DHX35 DEXH-box helicase domain of DEAH-box helicase 35. DHX35 plays a role in colorectal cancers and seems to be associated with risk to thyroid cancers. It also has been shown to positively regulate poxviruses, such as Myxoma virus. DEAH-box helicase 35 (DHX35) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 185 matched cddid_all.tbl CDD cd17981 cd17981 350739 DEXHc_DHX36 DEXH-box helicase domain of DEAH-box helicase 36. DEAH-box helicase 36 (DHX36, also known as G4-resolvase 1 or G4R1, MLE-like protein 1 and RNA helicase associated with AU-rich element or RHAU) unwinds a G4-quadruplex in human telomerase RNA. DHX36 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 180 matched cddid_all.tbl CDD cd17982 cd17982 350740 DEXHc_DHX37 DEXH-box helicase domain of DEAH-box helicase 37. DHX37 plays a role in the development of the human nervous system and has been linked to schizophrenia. It also negatively regulates poxviruses such as Myxoma virus. DEAH-box helicase 37 (DHX37) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 191 matched cddid_all.tbl CDD cd17983 cd17983 350741 DEXHc_DHX38 DEXH-box helicase domain of DEAH-box helicase 38. DEAH-box helicase 38 (DHX38, also known as PRP16) is involved in pre-mRNA splicing. DHX38 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 173 matched cddid_all.tbl CDD cd17984 cd17984 350742 DEXHc_DHX40 DEXH-box helicase domain of DEAH-box helicase 40. DEAH-box helicase 40 (DHX40) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 178 matched cddid_all.tbl CDD cd17985 cd17985 350743 DEXHc_DHX57 DEXH-box helicase domain of DEAH-box helicase 57. DEAH-box helicase 57 (DHX57) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 177 matched cddid_all.tbl CDD cd17986 cd17986 350744 DEXQc_DQX1 DEXQ-box helicase domain of DEAQ-box RNA dependent ATPase 1. DEAQ-box RNA dependent ATPase 1 (DQX1) belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 177 matched cddid_all.tbl CDD cd17987 cd17987 350745 DEXHc_YTHDC2 DEXH-box helicase domain of YTH domain containing 2. YTH domain containing 2 (YTHDC2) regulates mRNA translation and stability via binding to N6-methyladenosine, a modified RNA nucleotide enriched in the stop codons and 3' UTRs of eukaryotic messenger RNAs. YTHDC2 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 176 matched cddid_all.tbl CDD cd17988 cd17988 350746 DEXHc_TDRD9 DEXH-box helicase domain of tudor domain containing 9. Tudor domain containing 9 (TDRD9, also known as HIG-1or NET54 or C14orf75) is a part of the nuclear PIWI-interacting RNA (piRNA) pathway essential for transposon silencing and male fertility TDRD9 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 180 matched cddid_all.tbl CDD cd17989 cd17989 350747 DEXHc_HrpA DEXH-box helicase domain of ATP-dependent RNA helicase HrpA. HrpA is part of the HrpB-HrpA two-partner secretion (TPS) system, a secretion pathway important to the secretion of large virulence-associated proteins. HrpA belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 173 matched cddid_all.tbl CDD cd17990 cd17990 438711 DEXHc_HrpB DEXH-box helicase domain of ATP-dependent helicase HrpB. HrpB is part of the HrpB-HrpA two-partner secretion (TPS) system, a secretion pathway important to the secretion of large virulence-associated proteins. HrpB belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 174 matched cddid_all.tbl CDD cd17991 cd17991 350749 DEXHc_TRCF DEXH/Q-box helicase domain of the transcription-repair coupling factor. Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 193 matched cddid_all.tbl CDD cd17992 cd17992 350750 DEXHc_RecG DEXH/Q-box helicase domain of RecG. ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. It is a member of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 225 matched cddid_all.tbl CDD cd17993 cd17993 350751 DEXHc_CHD1_2 DEXH-box helicase domain of the chromodomain helicase DNA binding proteins 1 and 2, and similar proteins. Chromodomain-helicase-DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin-remodeling factor which functions as the substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. It regulates polymerase II transcription and is also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. It is not only involved in transcription-related chromatin-remodeling, but is also required to maintain a specific chromatin configuration across the genome. CHD1 is also associated with histone deacetylase (HDAC) activity. Chromodomain-helicase-DNA-binding protein 2 (CHD2) is a DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3. It is involved in myogenesis via interaction with MYOD1; it binds to myogenic gene regulatory sequences and mediates incorporation of histone H3.3 prior to the onset of myogenic gene expression, promoting their expression. Both are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 218 matched cddid_all.tbl CDD cd17994 cd17994 350752 DEXHc_CHD3_4_5 DEAH-box helicase domain of the chromodomain helicase DNA binding proteins 3, 4 and 5. Chromodomain-helicase-DNA-binding protein 3 (CHD3) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. It is required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity. Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. Chromodomain-helicase-DNA-binding protein 5 (CHD5) is a chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. It is thought to specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone H3 and plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at 'Lys-27' thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. As a tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa. CHD3, CHD4, and CHD5 are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 196 matched cddid_all.tbl CDD cd17995 cd17995 350753 DEXHc_CHD6_7_8_9 DEXH-box helicase domain of the chromodomain helicase DNA binding protein 6, 7, 8 and 9. Chromodomain-helicase-DNA-binding protein 6-9 (CHD6, CHD7, CHD8, and CHD9) are members of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 223 matched cddid_all.tbl CDD cd17996 cd17996 350754 DEXHc_SMARCA2_SMARCA4 DEXH-box helicase domain of SMARCA2 and SMARCA4. SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, members 2 and 4 (SMARCA2 and SMARCA4) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 233 matched cddid_all.tbl CDD cd17997 cd17997 350755 DEXHc_SMARCA1_SMARCA5 DEAH-box helicase domain of SMARCA1 and SMARCA5. SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 and 5 (SMARCA1 and SMARCA5) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 222 matched cddid_all.tbl CDD cd17998 cd17998 350756 DEXHc_SMARCAD1 DEXH-box helicase domain of SMARCAD1. SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 (SMARCAD1, also known as ATP-dependent helicase 1 or Hel1) possesses intrinsic ATP-dependent nucleosome-remodeling activity and is required for both DNA repair and heterochromatin organization. SMARCAD1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 187 matched cddid_all.tbl CDD cd17999 cd17999 350757 DEXHc_Mot1 DEXH-box helicase domain of Mot1. Modifier of transcription 1 (Mot1, also known as TAF172 in eukaryotes) regulates transcription in association with TATA binding protein (TBP). Mot1, Ino80C, and NC2 function coordinately to regulate pervasive transcription in yeast and mammals. Mot1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 232 matched cddid_all.tbl CDD cd18000 cd18000 350758 DEXHc_ERCC6 DEXH-box helicase domain of ERCC6. ERCC excision repair 6, chromatin remodeling factor (ERCC6, also known Cockayne syndrome group B (CSB), Rad26 in Saccharomyces cerevisiae, and Rhp26 in Schizosaccharomyces pombe) is a DNA-binding protein that is important in transcription-coupled excision repair. ERCC6 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 193 matched cddid_all.tbl CDD cd18001 cd18001 350759 DEXHc_ERCC6L DEXH-box helicase domain of ERCC6L. ERCC excision repair 6 like, spindle assembly checkpoint helicase (ERCC6L, also known as RAD26L) is an essential component of the mitotic spindle assembly checkpoint, by acting as a tension sensor that associates with catenated DNA which is stretched under tension until it is resolved during anaphase. ERCC6L is proposed to stimulate cancer cell proliferation by promoting cell cycle through a way of RAB31-MAPK-CDK2. ERCC6L is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 232 matched cddid_all.tbl CDD cd18002 cd18002 350760 DEXQc_INO80 DEAQ-box helicase domain of INO80. INO80 is the catalytic ATPase subunit of the INO80 chromatin remodeling complex. INO80 removes histone H3-containing nucleosomes from associated chromatin, promotes CENP-ACnp1 chromatin assembly at the centromere in a redundant manner with another chromatin-remodeling factor Chd1Hrp1. INO80 mutants have severe defects in oxygen consumption and promiscuous cell division that is no longer coupled with metabolic status. INO80 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 229 matched cddid_all.tbl CDD cd18003 cd18003 350761 DEXQc_SRCAP DEXH/Q-box helicase domain of SRCAP. Snf2-related CBP activator (SRCAP, also known as SWR1 or DOMO1) is the core catalytic component of the multiprotein chromatin-remodeling SRCAP complex, that is necessary for the incorporation of the histone variant H2A.Z into nucleosomes. SRCAP is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 223 matched cddid_all.tbl CDD cd18004 cd18004 350762 DEXHc_RAD54 DEXH-box helicase domain of RAD54. RAD54 proteins play a role in recombination. They are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 240 matched cddid_all.tbl CDD cd18005 cd18005 350763 DEXHc_ERCC6L2 DEXH-box helicase domain of ERCC6L2. ERCC excision repair 6 like 2 (ERCC6L2, also known as RAD26L) may play a role in DNA repair and mitochondrial function. In humans, mutations in the ERCC6L2 gene are associated with bone marrow failure syndrome 2. ERCC6L2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 245 matched cddid_all.tbl CDD cd18006 cd18006 350764 DEXHc_CHD1L DEAH/Q-box helicase domain of CHD1L. Chromodomain helicase DNA binding protein 1 like (CHD1L, also known as ALC1) is involved in DNA repair by regulating chromatin relaxation following DNA damage. CHD1L is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 216 matched cddid_all.tbl CDD cd18007 cd18007 350765 DEXHc_ATRX-like DEXH-box helicase domain of ATRX-like proteins. This family includes ATRX-like members such as transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) which is involved in transcriptional regulation and chromatin remodeling, and ARIP4 (also called androgen receptor-interacting protein 4, RAD54 like 2 or RAD54L2) which modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. They are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 239 matched cddid_all.tbl CDD cd18008 cd18008 350766 DEXDc_SHPRH-like DEXH-box helicase domain of SHPRH-like proteins. The SHPRH-like subgroup belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 241 matched cddid_all.tbl CDD cd18009 cd18009 350767 DEXHc_HELLS_SMARCA6 DEXH-box helicase domain of HELLS. HELLS (helicase, lymphoid specific, also known as Lsh or SMARCA6) is a major epigenetic regulator crucial for normal heterochromatin structure and function. HELLS is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 236 matched cddid_all.tbl CDD cd18010 cd18010 350768 DEXHc_HARP_SMARCAL1 DEXH-box helicase domain of SMARCAL1. SMARCAL1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1, also known as HARP) is recruited to stalled replication forks to promote repair and helps restart replication. It plays a role in DNA repair, telomere maintenance and replication fork stability in response to DNA replication stress. Mutations cause Schimke Immunoosseous Dysplasia. SMARCAL1 is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 213 matched cddid_all.tbl CDD cd18011 cd18011 350769 DEXDc_RapA DEXH-box helicase domain of RapA. In bacteria, RapA is an RNA polymerase (RNAP)-associated SWI2/SNF2 (switch/sucrose non-fermentable) protein that mediates RNAP recycling during transcription. The ATPase activity of RapA is stimulated by its interaction with RNAP and inhibited by its N-terminal domain. The conformational changes of RapA and its interaction with RNAP are essential for RNAP recycling. RapA is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 207 matched cddid_all.tbl CDD cd18012 cd18012 350770 DEXQc_arch_SWI2_SNF2 DEAQ-box helicase domain of archaeal and bacterial SNF2-related proteins. Proteins belonging to SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprises a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. Archaeal SWI2 and SNF2 are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 218 matched cddid_all.tbl CDD cd18013 cd18013 350771 DEXQc_bact_SNF2 DEXQ-box helicase domain of bacterial SNF2 family proteins. Proteins belonging to the SNF2 family of DNA dependent ATPases are important members of the chromatin remodeling complexes that are implicated in epigenetic control of gene expression. The Snf2 family comprise a large group of ATP-hydrolyzing proteins that are ubiquitous in eukaryotes, but also present in eubacteria and archaea. The bacterial SNF2 present in this family are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 218 matched cddid_all.tbl CDD cd18014 cd18014 350772 DEXHc_RecQ5 DEAH-box helicase domain of RecQ5. ATP-dependent DNA helicase Q5 (RecQ5) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 205 matched cddid_all.tbl CDD cd18015 cd18015 350773 DEXHc_RecQ1 DEXH-box helicase domain of RecQ1. ATP-dependent DNA helicase Q1 (RecQ1) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 209 matched cddid_all.tbl CDD cd18016 cd18016 350774 DEXHc_RecQ2_BLM DEAH-box helicase domain of RecQ2. ATP-dependent DNA helicase Q2 (RecQ2, also called Bloom syndrome protein homolog or BLM) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Mutations in RecQ2 cause Bloom syndrome. 208 matched cddid_all.tbl CDD cd18017 cd18017 350775 DEXHc_RecQ3 DEAH-box helicase domain of RecQ3. DEAD-like helicase RecQ3 (also called Werner syndrome ATP-dependent helicase or WRN) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Mutations cause Werner's syndrome. 193 matched cddid_all.tbl CDD cd18018 cd18018 350776 DEXHc_RecQ4-like DEAH-box helicase domain of RecQ4 and similar proteins. ATP-dependent DNA helicase Q4 (RecQ4) is part of the RecQ family of highly conserved DNA repair helicases that is part of the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. Mutations cause Rothmund-Thomson/RAPADILINO/Baller-Gerold syndrome. 201 matched cddid_all.tbl CDD cd18019 cd18019 350777 DEXHc_Brr2_1 N-terminal DEXH-box helicase domain of spliceosomal Brr2 RNA helicase. Brr2 is a type II DEAD box helicase that mediates spliceosome catalytic activation. It is a stable subunit of the spliceosome, required during splicing catalysis and spliceosome disassembly. Brr2 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 214 matched cddid_all.tbl CDD cd18020 cd18020 350778 DEXHc_ASCC3_1 N-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3. Activating signal cointegrator 1 complex subunit 3 (ASCC3) is a type II DEAD box helicase that plays a role in the repair of N-alkylated nucleotides. ASCC3 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 199 matched cddid_all.tbl CDD cd18021 cd18021 350779 DEXHc_Brr2_2 C-terminal D[D/E]X[H/Q]-box helicase domain of spliceosomal Brr2 RNA helicase. Brr2 is a type II DEAD box helicase that mediates spliceosome catalytic activation. It is a stable subunit of the spliceosome, required during splicing catalysis and spliceosome disassembly. Brr2 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 191 matched cddid_all.tbl CDD cd18022 cd18022 350780 DEXHc_ASCC3_2 C-terminal DEXH-box helicase domain of Activating signal cointegrator 1 complex subunit 3. Activating signal cointegrator 1 complex subunit 3 (ASCC3) is a type II DEAD box helicase that plays a role in the repair of N-alkylated nucleotides. ASCC3 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 189 matched cddid_all.tbl CDD cd18023 cd18023 350781 DEXHc_HFM1 DEXH-box helicase domain of ATP-dependent DNA helicase HFM1. HFM1 is a type II DEAD box helicase, required for crossover formation and complete synapsis of homologous chromosomes during meiosis. HFM1 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 206 matched cddid_all.tbl CDD cd18024 cd18024 350782 DEXHc_Mtr4-like DEXH-box helicase domain of ATP-dependent RNA helicase Mtr4. Mtr4 (also known as DOB1 or SKIV2L2) is a type II DEAD box helicase that plays a role in the processing of structured RNAs, including the maturation of 5.8S ribosomal RNA (rRNA)and is part of the TRAMP complex that is involved in exosome-mediated degradation of aberrant RNAs. Mtr4 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 205 matched cddid_all.tbl CDD cd18025 cd18025 350783 DEXHc_DDX60 DEXH-box helicase domain of DEAD box protein 60. DEAD box protein 60 (DDX60) is an IFN-inducible cytoplasmic helicase that plays a role in RIG-I-mediated type I interferon (IFN) nuclease-mediated viral RNA degradation. DDX60 belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 192 matched cddid_all.tbl CDD cd18026 cd18026 350784 DEXHc_POLQ-like DEXH-box helicase domain of DNA polymerase theta. DNA polymerase theta (POLQ) is important in the repair of genomic double-strand breaks (DSBs). POLQ contains an N-terminal type II DEAD box helicase domain which contains the ATP-binding region. 202 matched cddid_all.tbl CDD cd18027 cd18027 350785 DEXHc_SKIV2L DEXH-box helicase domain of SKIV2L. Superkiller viralicidic activity 2-like (SKIV2L, also called SKI2 or DHX13) plays a role in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. SKIV2L belongs to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 179 matched cddid_all.tbl CDD cd18028 cd18028 350786 DEXHc_archSki2 DEXH-box helicase domain of archaeal Ski2-type helicase. Archaeal Ski2-type RNA helicases play an important role in RNA degradation, processing and splicing pathways. They belong to the type II DEAD box helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 177 matched cddid_all.tbl CDD cd18029 cd18029 350787 DEXHc_XPB DEXH-box helicase domain of TFIIH XPB subunit and similar proteins. TFIIH basal transcription factor complex helicase XPB subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 169 matched cddid_all.tbl CDD cd18030 cd18030 350788 DEXHc_RE_I_HsdR DEXH-box helicase domain of type I restriction enzyme HdsR subunit. The HdsR motor subunit of type I restriction-modification enzymes contains the DNA cleavage and ATP-dependent DNA translocation activities of the heteromeric complex. It is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 208 matched cddid_all.tbl CDD cd18031 cd18031 350789 DEXHc_UvsW DEXH-box helicase domain of bacteriophage UvsW. Bacteriophage UvsW is part of the WXY system that repairs DNA damage by a process that involves homologous recombination. UvsW is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 161 matched cddid_all.tbl CDD cd18032 cd18032 350790 DEXHc_RE_I_III_res DEXH-box helicase domain of type III restriction enzyme res subunit. Members of this model includes both type I and type III restriction enzymes. Both are hetero-oligomeric proteins. Type I REs are encoded by three closely linked genes: a specificity subunit (HsdS or S) for recognizing a DNA sequence, a methylation subunit (HsdM or M) for methylating the recognized target bases, and a restriction subunit (HsdR or R) for the translocation and random cleavage of non-methylated DNA. They show diverse catalytic activities, including methyltransferase (MTase), ATP hydrolase (ATPase), DNA translocation and restriction activities. These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions: one containing 3-4 nucleotides, and another containing 4-5 nucleotides, separated by a non-specific spacer of about 6-8 nucleotides. Type III enzymes are composed of two subunits, Res and Mod. The Mod subunit recognizes the DNA sequence specific for the system and is a modification methyltransferase; as such, it is functionally equivalent to the M and S subunits of type I restriction endonucleases. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp-long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Both type I and type III REs are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 163 matched cddid_all.tbl CDD cd18033 cd18033 350791 DEXDc_FANCM DEAH-box helicase domain of FANCM. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. In complex with CENPS and CENPX, it binds double-stranded DNA (dsDNA), fork-structured DNA (fsDNA), and Holliday junction substrates. Its ATP-dependent DNA branch migration activity can process branched DNA structures such as a movable replication fork. This activity is strongly stimulated in the presence of CENPS and CENPX. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, it strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA. FANCM is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 182 matched cddid_all.tbl CDD cd18034 cd18034 350792 DEXHc_dicer DEXH-box helicase domain of endoribonuclease Dicer. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicers exist throughout eukaryotes, and a subset have an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 200 matched cddid_all.tbl CDD cd18035 cd18035 350793 DEXHc_Hef DEXH-box helicase domain of Hef. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. All archaea encode a protein of the XPF/MUS81/FANCM family of endonucleases. It exists in two forms: a long form, referred as Hef which consists of an N-terminal helicase fused to a C-terminal nuclease and is specific to euryarchaea and a short form, referred as XPF which lacks the helicase domain and is specific to crenarchaea and thaumarchaea. Hef has the unique feature of having both active helicase and nuclease domains. This domain configuration is highly similar with the human FANCM, a possible ortholog of archaeal Hef proteins. Hef is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 181 matched cddid_all.tbl CDD cd18036 cd18036 350794 DEXHc_RLR DEXH-box helicase domain of RIG-I-like receptors. RIG-I-like receptors (RLRs) sense cytoplasmic viral RNA and comprise RIG-I, RLR-2/MDA5 (melanoma differentiation-associated protein 5) and RLR-3/LGP2 (laboratory of genetics and physiology 2). RIG-I-like receptors (RLRs) are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 204 matched cddid_all.tbl CDD cd18037 cd18037 350795 DEXSc_Pif1_like DEAD-box helicase domain of Pif1. Pif1 and other members of this family are RecD-like helicases involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. The members of Pif1 helicase subfamily studied so far all appear to contribute to telomere maintenance. Pif1 is a member of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 183 matched cddid_all.tbl CDD cd18038 cd18038 350796 DEXXQc_Helz-like DEXXQ/H-box helicase domain of Helz-like helicase. This subfamily contains HELZ, Mov10L1, and similar proteins. Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. All are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 229 matched cddid_all.tbl CDD cd18039 cd18039 350797 DEXXQc_UPF1 DEXXQ-box helicase domain of UPF1. UPF1 (also called RNA Helicase And ATPase, Regulator Of Nonsense Transcripts, or ATP-Dependent Helicase RENT1) is an RNA-dependent helicase and ATPase required for nonsense-mediated decay (NMD) of mRNAs containing premature stop codons. It is recruited to mRNAs upon translation termination and undergoes a cycle of phosphorylation and dephosphorylation; its phosphorylation appears to be a key step in NMD. It is recruited by release factors to stalled ribosomes together with the SMG1C protein kinase complex to form the transient SURF (SMG1-UPF1-eRF1-eRF3) complex. In EJC-dependent NMD, the SURF complex associates with the exon junction complex (EJC) located downstream from the termination codon through UPF2 and allows the formation of an UPF1-UPF2-UPF3 surveillance complex which is believed to activate NMD. Diseases associated with UPF1 include juvenile amyotrophic lateral sclerosis and epidermolysis bullosa, junctional, non-Herlitz type. UPF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 234 matched cddid_all.tbl CDD cd18040 cd18040 350798 DEXXc_HELZ2-C C-terminal DEXX-box helicase domain of HELZ2. Helicase with zinc finger 2 (HELZ2, also known as PPAR-alpha-interacting complex protein 285 or PRIC285 and PPAR-gamma DBD-interacting protein 1 or PDIP1) acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB and RXRA. It belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 271 matched cddid_all.tbl CDD cd18041 cd18041 350799 DEXXQc_DNA2 DEXXQ-box helicase domain of DNA2. DNA2 (DNA Replication Helicase/Nuclease 2) possesses different enzymatic activities, such as single-stranded DNA (ssDNA)-dependent ATPase, 5-3 helicase, and endonuclease activities, and is involved in DNA replication and DNA repair in the nucleus and mitochondrion. It is involved in Okazaki fragment processing by cleaving long flaps that escape FEN1: flaps that are longer than 27 nucleotides are coated by replication protein A complex (RPA), leading to recruit DNA2 which cleaves the flap until it is too short to bind RPA and becomes a substrate for FEN1. It is also involved in 5-end resection of DNA during double-strand break (DSB) repair; it is recruited by BLM and mediates the cleavage of 5-ssDNA, while the 3-ssDNA cleavage is prevented by the presence of RPA. DNA2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 203 matched cddid_all.tbl CDD cd18042 cd18042 438712 DEXXQc_SETX DEXXQ-box helicase domain of SETX. The RNA/DNA helicase senataxin (SETX) plays a role in transcription, neurogenesis, and antiviral response. SEXT is an R-loop-associated protein that is thought to function as an RNA/DNA helicase. R-loops consist of RNA/DNA hybrids, formed during transcription when nascent RNA hybridizes to the DNA template strand, displacing the non-template DNA strand. Mutations in SETX are linked to two neurodegenerative disorders: ataxia with oculomotor apraxia type 2 (AOA2) and amyotrophic lateral sclerosis type 4 (ALS4). S. cerevisiae homolog splicing endonuclease 1 (Sen1) is an exclusively nuclear protein, important for nucleolar organization. S. cerevisiae Sen1 and its ortholog, the Schizosaccharomyces pombe Sen1, share conserved domains and belong to the family I class of helicases. Both proteins translocate 5' to 3' and unwind both DNA and RNA duplexes and also RNA/DNA hybrids in vitro. SETX is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 218 matched cddid_all.tbl CDD cd18043 cd18043 350801 DEXXQc_SF1 DEXXQ-box helicase domain of Superfamily 1 helicases. Superfamily 1 (SF1) helicases are nucleic acid motor proteins that couple ATP hydrolysis to translocation along with the concomitant unwinding of DNA or RNA. This is central to many aspects of cellular DNA and RNA metabolism and accordingly, they are implicated in a wide range of nucleic acid processing events including DNA replication, recombination, and repair as well as many aspects of RNA metabolism. Superfamily 1 helicases are members of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 127 matched cddid_all.tbl CDD cd18044 cd18044 350802 DEXXQc_SMUBP2 DEXXQ-box helicase domain of SMUBP2. SMUBP2 (also called immunoglobulin mu-binding protein 2, or IGHMBP2) is a 5' to 3' helicase that unwinds RNA and DNA duplexes in an ATP-dependent reaction. It is a DNA-binding protein specific to 5'-phosphorylated single-stranded guanine-rich sequence (5'-GGGCT-3') related to the immunoglobulin mu chain switch region. The IGHMBP2 gene is responsible for Charcot-Marie-Tooth disease (CMT) type 2S and spinal muscular atrophy with respiratory distress type 1 (SMARD1). It is also thought to play a role in frontotemporal dementia (FTD) with amyotrophic lateral sclerosis (ALS) and major depressive disorder (MDD). SMUBP2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 191 matched cddid_all.tbl CDD cd18045 cd18045 350803 DEADc_EIF4AIII_DDX48 DEAD-box helicase domain of eukaryotic initiation factor 4A-III. Eukaryotic initiation factor 4A-III (EIF4AIII, also known as DDX48) is part of the exon junction complex (EJC) that plays a major role in posttranscriptional regulation of mRNA. EJC consists of four proteins (eIF4AIII, Barentsz [Btz], Mago, and Y14), mRNA, and ATP. DDX48 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 201 matched cddid_all.tbl CDD cd18046 cd18046 350804 DEADc_EIF4AII_EIF4AI_DDX2 DEAD-box helicase domain of eukaryotic initiation factor 4A-I and 4-II. Eukaryotic initiation factor 4A-I (DDX2A) and eukaryotic initiation factor 4A-II (DDX2B) are involved in cap recognition and are required for mRNA binding to ribosome. They are DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 201 matched cddid_all.tbl CDD cd18047 cd18047 350805 DEADc_DDX19 DEAD-box helicase domain of DEAD box protein 19. DDX19 is an RNA helicase involved in both mRNA (mRNA) export from the nucleus into the cytoplasm and in mRNA translation. DDX19 functions in the nucleus in resolving RNA:DNA hybrids (R-loops). Activation of a DNA damage response pathway dependent upon the ATR kinase, a major regulator of replication fork progression, stimulates translocation of DDX19 from the cytoplasm into the nucleus. Only nuclear Ddx19 is competent to resolve R-loops. DDX19 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 205 matched cddid_all.tbl CDD cd18048 cd18048 350806 DEADc_DDX25 DEAD-box helicase domain of DEAD box protein 25. DDX25 (also called gonadotropin-regulated testicular RNA helicase (GRTH) is a testis-specific protein essential for completion of spermatogenesis. DDX25 is also a novel negative regulator of IFN pathway and facilitates RNA virus infection. Diseases associated with DDX25 include hydrolethalus syndrome, an autosomal recessive lethal malformation syndrome characterized by multiple developmental defects of fetus.. DDX25 (also called gonadotropin-regulated testicular RNA helicase) is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 229 matched cddid_all.tbl CDD cd18049 cd18049 350807 DEADc_DDX5 DEAD-box helicase domain of DEAD box protein 5. DDX5 (also called RNA helicase P68, HLR1, G17P1, or HUMP68) is involved in pathways that include the alteration of RNA structures, plays a role as a coregulator of transcription, a regulator of splicing, and in the processing of small noncoding RNAs. It synergizes with DDX17 and SRA1 RNA to activate MYOD1 transcriptional activity and is involved in skeletal muscle differentiation. Dysregulation of this gene may play a role in cancer development. DDX5 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 234 matched cddid_all.tbl CDD cd18050 cd18050 350808 DEADc_DDX17 DEAD-box helicase domain of DEAD box protein 17. DDX17 (also called DEAD Box Protein P72 or DEAD Box Protein P82) has a wide variety of functions including regulating the alternative splicing of exons exhibiting specific features such as the inclusion of AC-rich alternative exons in CD44 transcripts, playing a role in innate immunity, and promoting mRNA degradation mediated by the antiviral zinc-finger protein ZC3HAV1 in an ATPase-dependent manner. DDX17 synergizes with DDX5 and SRA1 RNA to activate MYOD1 transcriptional activity and is involved in skeletal muscle differentiation. DDX17 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 271 matched cddid_all.tbl CDD cd18051 cd18051 350809 DEADc_DDX3 DEAD-box helicase domain of DEAD box protein 3. DDX3 (also called helicase-like protein, DEAD box, X isoform, or DDX14) has been reported to display a high level of RNA-independent ATPase activity stimulated by both RNA and DNA. This protein has multiple conserved domains and is thought to play roles in both the nucleus and cytoplasm. Nuclear roles include transcriptional regulation, mRNP assembly, pre-mRNA splicing, and mRNA export. In the cytoplasm, this protein is thought to be involved in translation, cellular signaling, and viral replication. Misregulation of this gene has been implicated in tumorigenesis. Diseases associated with DDX3 include mental retardation, X-linked 102 and agenesis of the corpus callosum, with facial anomalies and robin sequence. DDX3 is a member of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 249 matched cddid_all.tbl CDD cd18052 cd18052 350810 DEADc_DDX4 DEAD-box helicase domain of DEAD box protein 4. DEAD box protein 4 (DDX4, also known as VASA homolog) is an ATP-dependent RNA helicase required during spermatogenesis and is essential for the germline integrity. DEAD-box helicases are a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif (motif II). This domain contains the ATP-binding region. 264 matched cddid_all.tbl CDD cd18053 cd18053 350811 DEXHc_CHD1 DEAH-box helicase domain of the chromodomain helicase DNA binding protein 1. Chromodomain-helicase-DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. It regulates polymerase II transcription and is also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. It is not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome. CHD1 is also associated with histone deacetylase (HDAC) activity. It is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 237 matched cddid_all.tbl CDD cd18054 cd18054 350812 DEXHc_CHD2 DEAH-box helicase domain of the chromodomain helicase DNA binding protein 2. Chromodomain-helicase-DNA-binding protein 2 (CHD2) is a DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3. It is involved in myogenesis via interaction with MYOD1; it binds to myogenic gene regulatory sequences and mediates incorporation of histone H3.3 prior to the onset of myogenic gene expression, promoting their expression. CHD2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 237 matched cddid_all.tbl CDD cd18055 cd18055 350813 DEXHc_CHD3 DEAH-box helicase domain of the chromodomain helicase DNA binding protein 3. Chromodomain-helicase-DNA-binding protein 3 (CHD3) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. It is required for anchoring centrosomal pericentrin in both interphase and mitosis, for spindle organization and centrosome integrity. CHD3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 232 matched cddid_all.tbl CDD cd18056 cd18056 350814 DEXHc_CHD4 DEAH-box helicase domain of the chromodomain helicase DNA binding protein 4. Chromodomain-helicase-DNA-binding protein 4 (CHD4) is a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin by deacetylating histones. CHD4 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 232 matched cddid_all.tbl CDD cd18057 cd18057 350815 DEXHc_CHD5 DEAH-box helicase domain of the chromodomain helicase DNA binding protein 5. Chromodomain-helicase-DNA-binding protein 5 (CHD5) is a chromatin-remodeling protein that binds DNA through histones and regulates gene transcription. It is thought to specifically recognize and bind trimethylated 'Lys-27' (H3K27me3) and non-methylated 'Lys-4' of histone H3 and plays a role in the development of the nervous system by activating the expression of genes promoting neuron terminal differentiation. In parallel, it may also positively regulate the trimethylation of histone H3 at 'Lys-27' thereby specifically repressing genes that promote the differentiation into non-neuronal cell lineages. As a tumor suppressor, it regulates the expression of genes involved in cell proliferation and differentiation. In spermatogenesis, it probably regulates histone hyperacetylation and the replacement of histones by transition proteins in chromatin, a crucial step in the condensation of spermatid chromatin and the production of functional spermatozoa. CHD5 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 232 matched cddid_all.tbl CDD cd18058 cd18058 350816 DEXHc_CHD6 DEAH-box helicase domain of the chromodomain helicase DNA binding protein 6. Chromodomain-helicase-DNA-binding protein 6 (CHD6) is a DNA-dependent ATPase that plays a role in chromatin remodeling. It regulates transcription by disrupting nucleosomes in a largely non-sliding manner which strongly increases the accessibility of chromatin. It activates transcription of specific genes in response to oxidative stress through interaction with NFE2L2.2 and acts as a transcriptional repressor of different viruses including influenza virus or papillomavirus. During influenza virus infection, the viral polymerase complex localizes CHD6 to inactive chromatin where it gets degraded in a proteasome independent-manner. CHD6 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 222 matched cddid_all.tbl CDD cd18059 cd18059 350817 DEXHc_CHD7 DEAH-box helicase domain of the chromodomain helicase DNA binding protein 7. Chromodomain-helicase-DNA-binding protein 7 (CHD7) is a probable transcription regulator. It may be involved in the 45S precursor rRNA production. CHD7 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 222 matched cddid_all.tbl CDD cd18060 cd18060 350818 DEXHc_CHD8 DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8. Chromodomain-helicase-DNA-binding protein 8 (CHD8) is a DNA helicase that acts as a chromatin remodeling factor and regulates transcription. It also acts as a transcription repressor by remodeling chromatin structure and recruiting histone H1 to target genes. It suppresses p53/TP53-mediated apoptosis by recruiting histone H1 and preventing p53/TP53 transactivation activity and of STAT3 activity by suppressing the LIF-induced STAT3 transcriptional activity. It also acts as a negative regulator of Wnt signaling pathway and CTNNB1-targeted gene expression. CHD8 is also involved in both enhancer blocking and epigenetic remodeling at chromatin boundary via its interaction with CTCF. It also acts as a transcription activator via its interaction with ZNF143 by participating in efficient U6 RNA polymerase III transcription. CHD8 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 222 matched cddid_all.tbl CDD cd18061 cd18061 350819 DEXHc_CHD9 DEAH-box helicase domain of the chromodomain helicase DNA binding protein 9. Chromodomain-helicase-DNA-binding protein 9 (CHD9) acts as a transcriptional coactivator for PPARA and possibly other nuclear receptors. It is proposed to be a ATP-dependent chromatin remodeling protein. CHD9 has DNA-dependent ATPase activity and binds to A/T-rich DNA. It also associates with A/T-rich regulatory regions in promoters of genes that participate in the differentiation of progenitors during osteogenesis. CHD9 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 222 matched cddid_all.tbl CDD cd18062 cd18062 350820 DEXHc_SMARCA4 DEXH-box helicase domain of SMARCA4. SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 (SMARCA4, also known as transcription activator BRG1) is a component of the CREST-BRG1 complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders. SMARCA4 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 251 matched cddid_all.tbl CDD cd18063 cd18063 350821 DEXHc_SMARCA2 DEXH-box helicase domain of SMARCA2. SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 (SMARCA2, also known as brahma homolog) is a component of the BAF complex. SMARCA2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 251 matched cddid_all.tbl CDD cd18064 cd18064 350822 DEXHc_SMARCA5 DEAH-box helicase domain of SMARCA5. SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5 (SMARCA5, also called SNF2H) is the catalytic subunit of the four known chromatin-remodeling complexes: CHRAC, RSF, ACF/WCRF, and WICH. SMARCA5 plays a major role organising arrays of nucleosomes adjacent to the binding sites for the architectural transcription factor CTCF sites and acts to promote CTCF binding SMARCA5 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 244 matched cddid_all.tbl CDD cd18065 cd18065 350823 DEXHc_SMARCA1 DEAH-box helicase domain of SMARCA1. SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 (SMARCA1, also called SNF2L) is a component of NURF (nucleosome-remodeling factor) and CERF (CECR2-containing-remodeling factor) complexes which promote the perturbation of chromatin structure in an ATP-dependent manner. SMARCA1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 233 matched cddid_all.tbl CDD cd18066 cd18066 350824 DEXHc_RAD54B DEXH-box helicase domain of RAD54B. DNA repair and recombination protein RAD54B, also known as RDH54, binds to double-stranded DNA, displays ATPase activity in the presence of DNA, and may have a role in meiotic and mitotic recombination. RAD54B is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 235 matched cddid_all.tbl CDD cd18067 cd18067 350825 DEXHc_RAD54A DEXH-box helicase domain of RAD54A. DNA repair and recombination protein RAD54A, also known as RAD54L or RAD54, plays a role in homologous recombination related repair of DNA double-strand breaks. RAD54A is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 243 matched cddid_all.tbl CDD cd18068 cd18068 350826 DEXHc_ATRX DEXH-box helicase domain of ATRX. Transcriptional regulator ATRX (also called alpha thalassemia/mental retardation syndrome X-linked and X-linked nuclear protein or XNP) is involved in transcriptional regulation and chromatin remodeling. Mutations in humans cause mental retardation, X-linked, syndromic, with hypotonic facies 1 (MRXSHF1) and alpha-thalassemia myelodysplasia syndrome (ATMDS). ATRX is part of the a DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 246 matched cddid_all.tbl CDD cd18069 cd18069 350827 DEXHc_ARIP4 DEXH-box helicase domain of ARIP4. Androgen receptor-interacting protein 4 (ARIP4, also called RAD54 like 2 or RAD54L2 ) modulates androgen receptor (AR)-dependent transactivation in a promoter-dependent manner. ARIP4 is part of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 227 matched cddid_all.tbl CDD cd18070 cd18070 350828 DEXQc_SHPRH DEXQ-box helicase domain of SHPRH. E3 ubiquitin-protein ligase SHPRH is a ubiquitously expressed protein that contains motifs characteristic of several DNA repair proteins, transcription factors, and helicases. SHPRH is a functional homolog of S. cerevisiae RAD5 and is involved in DNA repair. SHPRH is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 257 matched cddid_all.tbl CDD cd18071 cd18071 350829 DEXHc_HLTF1_SMARC3 DEXH-box helicase domain of HLTF1. Helicase like transcription factor (HLTF1, also known as HIP116 or SMARCA3) has both helicase and E3 ubiquitin ligase activities and ATP-dependent nucleosome-remodeling activity. HLTF1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 239 matched cddid_all.tbl CDD cd18072 cd18072 350830 DEXHc_TTF2 DEAH-box helicase domain of TTF2. Transcription termination factor 2 (TTF2 also called Forkhead-box E1/FOXE1 ) is a transcription termination factor that couples ATP hydrolysis with the removal of RNA polymerase II from the DNA template. Single nucleotide polymorphism (SNP) within the 5'-UTR of TTF2 is associated with thyroid cancer risk.TTF2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 241 matched cddid_all.tbl CDD cd18073 cd18073 350831 DEXHc_RIG-I_DDX58 DEXH-box helicase domain of RIG-I. RIG-I (Retinoic acid-inducible gene I protein), also called DEAD box protein 58 (DDX58), is a pathogen-recognition receptor that recognizes viral 5'-triphosphates carrying double-stranded RNA. Upon binding to these microbe-associated molecular patterns (MAMPs), RIG-I forms oligomers and promotes downstream processes that result in type I interferon production and induction of an antiviral state. The optimal ligand for RIG-I has been found to be base-paired or double-stranded RNA (dsRNA) molecules containing a 5' triphosphate (5'-ppp-dsRNA). RIG-I contains two N-terminal caspase activation and recruitment domains (CARDs), which are required for interaction with IPS-1, a superfamily 2 helicase/translocase/ATPase (SF2) domain and a C-terminal regulatory/repressor domain (RD). RIG-I is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 202 matched cddid_all.tbl CDD cd18074 cd18074 350832 DEXHc_RLR-2 DEXH-box helicase domain of RLR-2. RIG-I-like receptor 2 (RLR-2, also known as melanoma differentiation-associated protein 5 or Mda5 and IFIH1) is a viral double-stranded RNA (dsRNA) receptor that shares sequence similarity and signaling pathways with RIG-I, yet plays essential functions in antiviral immunity through distinct specificity for viral RNA. RLR-2 recognizes the internal duplex structure, whereas RIG-I recognizes the terminus of dsRNA. RLR-2 uses direct protein-protein contacts to stack along dsRNA in a head-to-tail arrangement. The signaling domain (tandem CARD), which decorates the outside of the core RLR-2 filament, also has an intrinsic propensity to oligomerize into an elongated structure that activates the signaling adaptor, MAVS. RLR-2 uses long dsRNA as a signaling platform to cooperatively assemble the core filament, which in turn promotes stochastic assembly of the tandem CARD oligomers for signaling. LGP2 appears to positively and negatively regulate RLR-2 and RIG-I signaling, respectively. RLR-2 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 216 matched cddid_all.tbl CDD cd18075 cd18075 350833 DEXHc_RLR-3 DEXH-box helicase domain of RLR-3. RIG-I-like receptor 3 (RLR-3, also known as laboratory of genetics and physiology 2 or LGP2 and DHX58) appears to positively and negatively regulate MDA5 and RIG-I signaling, respectively. RLR-3 resembles a chimera combining a MDA5-like helicase domain and RIG-I like CTD supporting both stem and end binding. RNA binding is required for RLR-3-mediated enhancement of MDA5 activation. RLR-3 end-binding may promote nucleation of MDA5 oligomerization on dsRNA. RLR-3 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 200 matched cddid_all.tbl CDD cd18076 cd18076 350834 DEXXQc_HELZ2-N N-terminal DEXXQ-box helicase domain of HELZ2. Helicase with zinc finger 2 (HELZ2, also known as PPAR-alpha-interacting complex protein 285 or PRIC285 and PPAR-gamma DBD-interacting protein 1 or PDIP1) acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB, and RXRA. It belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 230 matched cddid_all.tbl CDD cd18077 cd18077 350835 DEXXQc_HELZ DEXXQ-box helicase domain of HELZ. Helicase with zinc finger (HELZ) acts as a helicase that plays a role in RNA metabolism during development. HELZ is a member of the family I class of RNA helicases of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 226 matched cddid_all.tbl CDD cd18078 cd18078 350836 DEXXQc_Mov10L1 DEXXQ-box helicase domain of Mov10L1. Moloney leukemia virus 10-like protein 1 (Mov10L1) binds Piwi-interacting RNA (piRNA) precursors to initiate piRNA processing. Mov10L1 is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 230 matched cddid_all.tbl CDD cd18079 cd18079 350837 S-AdoMet_synt S-adenosylmethionine synthetase. S-adenosylmethionine synthetase (EC 2.5.1.6), also known as methionine adenosyltransferase, catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP in two steps, the formation of AdoMet and hydrolysis of the tripolyphosphate, which occurs prior to release of the product from the enzyme, which consists of three structural domains that have a similar alpha+beta fold. 371 matched cddid_all.tbl CDD cd18080 cd18080 349953 TrmD-like tRNA-M1G37-methyltransferase TrmD. The bacterial tRNA-(N(1)G37) methyltransferase (TrmD) catalyzes the transfer of a methyl group from S-adenosyl-L-methionine (AdoMet) to the N1 position of G37 in the anticodon loop of a subset of tRNA that contains a G at position 36. The presence of the modification prevents Watson-Crick base-pairing of this guanosine with cytosine in mRNA and translational frame-shifting. This family of proteins contains members of the SPOUT methyltransferases. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 219 matched cddid_all.tbl CDD cd18081 cd18081 349954 RlmH-like 23S-rRNA-pseudouridine1915-N3-methyltransferase RlmH. 23S rRNA (pseudouridine1915-N3)-methyltransferase RlmH catalyzes the addition of a methyl group at the N-3 position of pseudouridine Psi1915 in 23S rRNA to form m(3)Psi1915. This family of proteins belongs to the SPOUT methyltransferases. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 152 matched cddid_all.tbl CDD cd18082 cd18082 349955 SpoU-like_family SAM-dependent rRNA or tRNA methylase related to SpoU. RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 145 matched cddid_all.tbl CDD cd18083 cd18083 349956 aTrm56-like archaeal tRNA (cytidine(56)-2'-O)-methyltransferase Trm56. Archaeal tRNA (cytidine(56)-2'-O)-methyltransferase Trm56 catalyzes the 2'-O-ribose methylation of cytidine at position 56 in tRNAs. Trm56 is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 169 matched cddid_all.tbl CDD cd18084 cd18084 349957 RsmE-like SPOUT superfamily RNA methyltransferase RsmE-like. 16S rRNA m3U1498 methyltransferase RsmE modifies nucleotides during ribosomal RNA maturation in a site-specific manner. The Escherichia coli member is specific for U1498 methylation. RsmE is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 159 matched cddid_all.tbl CDD cd18085 cd18085 349958 TM1570-like SPOUT superfamily RNA methyltransferase TM1570-like. DUF2168; This domain, found in various hypothetical prokaryotic proteins, has no known function. It is also found in a few prokaryotic tRNA (guanine-N(1)-)-methyltransferases. Proteins of this family are members of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 178 matched cddid_all.tbl CDD cd18086 cd18086 349959 HsC9orf114-like SPOUT superfamily RNA methyltransferase HsC9orf114-like. Human C9orf114 (also known as centromere protein 32 or CENP-32) is required for association of the centrosomes with the poles of the bipolar mitotic spindle during metaphase. CENP-32 is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 187 matched cddid_all.tbl CDD cd18087 cd18087 349960 TrmY-like tRNA (pseudouridine(54)-N(1))-methyltransferase TrmY. tRNA (pseudouridine(54)-N(1))-methyltransferase TrmY catalyzes the N1-methylation of pseudouridine at position 54 (Psi54) in tRNAs. TrmY is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 193 matched cddid_all.tbl CDD cd18088 cd18088 349961 Nep1-like 18S rRNA (pseudouridine(1248)-N1)-methyltransferase Nep1. 18S rRNA (pseudouridine(1248)-N1)-methyltransferase Nep1 (also known as EMG1) methylates pseudouridine at position1248 (Psi1248) in 18S rRNA and is required for small subunit (SSU) ribosomal RNA (rRNA) maturation. Mutations on human cause in Bowen-Conradi Syndrome. Nep1 is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 204 matched cddid_all.tbl CDD cd18089 cd18089 349962 SPOUT_Trm10-like tRNA methyltransferase Trm10-like. Family of tRNA methyltransferase Trm10-like proteins catalyzes the N(1) methylation of guanine at position 9 (m(1)G9) of tRNA (eukaryotes) or N(1) methylation of guanine or adenine at position 9 (m1G9/m1A9) of tRNA (archaea), which might play a role in the stabilization of tRNA and in translation termination efficiency. Trm10 is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 171 matched cddid_all.tbl CDD cd18090 cd18090 349963 Arginine_MT_Sfm1 SAM-dependent arginine methyltransferase related to yeast Sfm1. Arginine methyltransferase Sfm1 methylates R146 of 40S ribosomal protein S3 (Rps3), which contacts 18S RNA. Sfm1 is part of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent mainly RNA MTases which are structurally characterized by a deep trefoil knot. 140 matched cddid_all.tbl CDD cd18091 cd18091 349964 SpoU-like_TRM3-like SAM-dependent tRNA methylase related to TRM3. Yeast tRNA (guanosine(18)-2'-O)-methyltransferase TRM3 catalyzes the formation of 2'-O-methylguanosine at position 18 (Gm18) in various tRNAs. TRM3 is similar to C-terminal domain of TAR (HIV-1) RNA binding protein 1 (TARBP1), a protein binding to TAR, which functions as a RNA regulatory signal by forming a stable stem-loop structure to which transactivator protein Tat binds. The role of TARBP1 is believed to be to disengage RNA polymerase II from TAR during transcriptional elongation. TRM3 and the C-terminal methyltransferase domain of TARBP1 are members of the SPOUT methyltransferase superfamily. 145 matched cddid_all.tbl CDD cd18092 cd18092 349965 SpoU-like_TrmH SAM-dependent tRNA methylase related to TrmH. TrmH catalyzes the transfer of the methyl group from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of the ribose of the universally conserved guanosine 18 (G18) position in tRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 162 matched cddid_all.tbl CDD cd18093 cd18093 349966 SpoU-like_TrmJ SAM-dependent tRNA methylase related to TrmJ. tRNA methyltransferase TrmJ catalyzes the methyl transfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH at position 32 in both tRNASer1 and tRNAGln2. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 153 matched cddid_all.tbl CDD cd18094 cd18094 349967 SpoU-like_TrmL SAM-dependent tRNA methylase related to TrmL. tRNA (Um34/Cm34) methyltransferase TrmL catalyzes the methyl transfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH at position 34 in both tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 145 matched cddid_all.tbl CDD cd18095 cd18095 349968 SpoU-like_rRNA-MTase SAM-dependent rRNA methylase related to SpoU-TrmH. RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 143 matched cddid_all.tbl CDD cd18096 cd18096 349969 SpoU-like SAM-dependent rRNA or tRNA methylase related to SpoU. RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 140 matched cddid_all.tbl CDD cd18097 cd18097 349970 SpoU-like SAM-dependent rRNA or tRNA methylase related to SpoU. RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 144 matched cddid_all.tbl CDD cd18098 cd18098 349971 SpoU-like SAM-dependent rRNA or tRNA methylase related to SpoU. RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 138 matched cddid_all.tbl CDD cd18099 cd18099 349972 Trm10arch archaeal tRNA(m1G9/m1A9)-methyltransferase Trm10. Archaeal tRNA(m1G9/m1A9)-methyltransferase Trm10 catalyzes the N(1) methylation of guanine or adenine at position 9 (m1G9/m1A9) of tRNA, which might play a role in the stabilization of tRNA and in translation termination efficiency. Trm10 is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 170 matched cddid_all.tbl CDD cd18100 cd18100 349973 Trm10euk_B eukaryotic tRNA m1G9 methyltransferase Trm10 homolog B. Eukaryotic tRNA m1G9 methyltransferase Trm10 homolog B (TM10B) catalyzes the N(1) methylation of guanine at Position 9 (m(1)G9) of tRNA, which might play a role in the stabilization of tRNA and in translation termination efficiency. Trm10 is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 182 matched cddid_all.tbl CDD cd18101 cd18101 349974 Trm10euk_A eukaryotic tRNA m1G9 methyltransferase Trm10 homolog A. Eukaryotic tRNA m1G9 methyltransferase Trm10 homolog A (TM10A) catalyzes the N(1) methylation of guanine at Position 9 (m(1)G9) of tRNA, which might play a role in the stabilization of tRNA and in translation termination efficiency. Trm10 is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 174 matched cddid_all.tbl CDD cd18102 cd18102 349975 Trm10_MRRP1 Mitochondrial ribonuclease P protein 1. Mitochondrial ribonuclease P protein 1 (or tRNA methyltransferase 10 homolog C) functions in mitochondrial tRNA maturation and is part of mitochondrial ribonuclease P, an enzyme composed of MRPP1/RG9MTD1, MRPP2/HSD17B10 and MRPP3/KIAA0391, which cleaves tRNA molecules in their 5'-ends. MRRP1 is related to Trm10, a tRNA m1G9 methyltransferase and is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 179 matched cddid_all.tbl CDD cd18103 cd18103 349976 SpoU-like_RlmB SAM-dependent rRNA methylase related to RlmB. 23S rRNA-M2G2251-MTase RlmB catalyzes the methylation of guanosine 2251, a modification conserved in the peptidyltransferase domain of 23S rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 143 matched cddid_all.tbl CDD cd18104 cd18104 349977 SpoU-like_RNA-MTase SAM-dependent RNA methylase related to SpoU-TrmH. RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 146 matched cddid_all.tbl CDD cd18105 cd18105 349978 SpoU-like_MRM1 SAM-dependent rRNA methylase related to MRM1. MRM1 catalyzes the methylation of 2'-O-ribose residues G1145 to GmG residue of the mitochondrial 16S rRNA. MRM1 is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 158 matched cddid_all.tbl CDD cd18106 cd18106 349979 SpoU-like_RNMTL1 SAM-dependent rRNA methylase related to RNMTL1. RNMTL1 (also known as HC90, MRM3 and RMTL1) catalyzes the methylation of 2'-O-ribose residues G1370 to GmG residue of the mitochondrial 16S rRNA. RNMTL1 is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 148 matched cddid_all.tbl CDD cd18107 cd18107 349980 SpoU-like_AviRb SAM-dependent rRNA methylase related to AviRb. AviRb from Streptomyces viridochromogenes methylates the 2'-O atom of U2479 of the 23S ribosomal RNA. AviRb is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 148 matched cddid_all.tbl CDD cd18108 cd18108 349981 SpoU-like_NHR Nosiheptide-resistance methyltransferase (NHR). Nosiheptide-resistance methyltransferase (NHR) confers resistance to the thiazole antibiotic nosiheptide via catalyzing 2'O-methylation of 23S rRNA at the nucleotide A1067. NHR is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 144 matched cddid_all.tbl CDD cd18109 cd18109 349982 SpoU-like_RNA-MTase SAM-dependent RNA methylase related to SpoU-TrmH. RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. 141 matched cddid_all.tbl CDD cd18110 cd18110 349745 ATP-synt_F1_beta_C F1-ATP synthase beta (B) subunit, C-terminal domain. The beta (B) subunit of the F1 complex of F0F1-ATP synthase, C-terminal domain. The F-ATP synthase (also called FoF1-ATPase) is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinsic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic. 108 matched cddid_all.tbl CDD cd18111 cd18111 349746 ATP-synt_V_A-type_alpha_C V/A-type ATP synthase catalytic subunit A (alpha), C-terminal domain. The alpha (A) subunit of the V1/A1 complex of V/A-type ATP synthases, C-terminal domain. The V- and A-type family of ATPases are composed of two linked multi-subunit complexes: the V1 and A1 complexes contain three copies each of the alpha and beta subunits that form the soluble catalytic core, which is involved in ATP synthesis/hydrolysis, and the Vo or Ao complex that forms the membrane-embedded proton pore. The A-ATP synthase (AoA1-ATPase) is found in archaea and functions like F-ATP synthase. Structurally, however, the A-ATP synthase is more closely related to the V-ATP synthase (vacuolar VoV1-ATPase), which is a proton-translocating ATPase responsible for acidification of eukaryotic intracellular compartments and for ATP synthesis in archaea and some eubacteria. Collectively, the V- and A-type synthases can function in both ATP synthesis and hydrolysis modes. 105 matched cddid_all.tbl CDD cd18112 cd18112 349747 ATP-synt_V_A-type_beta_C V/A-type ATP synthase beta (B) subunit, C-terminal domain. The beta (B) subunit of the V1/A1 complexes of V/A-type ATP synthases, C-terminal domain. The V- and A-type family of ATPases are composed of two linked multi-subunit complexes: the V1 and A1 complexes contain three copies each of the alpha and beta subunits that form the soluble catalytic core, which is involved in ATP synthesis/hydrolysis, and the Vo or Ao complex that forms the membrane-embedded proton pore. The A-ATP synthase (AoA1-ATPase) is found in archaea and functions like F-ATP synthase. Structurally, however, the A-ATP synthase is more closely related to the V-ATP synthase (vacuolar VoV1-ATPase), which is a proton-translocating ATPase responsible for acidification of eukaryotic intracellular compartments and for ATP synthesis in archaea and some eubacteria. Collectively, the V- and A-type synthases can function in both ATP synthesis and hydrolysis modes. This subfamily consists of the non-catalytic beta subunit. 95 matched cddid_all.tbl CDD cd18113 cd18113 349748 ATP-synt_F1_alpha_C F1-ATP synthase alpha (A) subunit, C-terminal domain. The alpha (A) subunit of the F1 complex of F0F1-ATP synthase, C-terminal domain. The F-ATP synthase (also called FoF1-ATPase) is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinsic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic. 126 matched cddid_all.tbl CDD cd18114 cd18114 349749 ATP-synt_flagellum-secretory_path_III_C Flagellum-specific ATP synthase, C-terminal domain. The C-terminal domain of the flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The flagellum-specific ATPase FliI is the soluble export component that drives flagellar protein export, and it shows extensive similarity to the alpha and beta subunits of FoF1-ATP synthase. Although they both are proton driven rotary molecular devices, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens such as Salmonella and Chlamydia also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway. 71 matched cddid_all.tbl CDD cd18115 cd18115 349739 ATP-synt_F1_beta_N F1-ATP synthase beta (B) subunit, N-terminal domain. The beta (B) subunit of the F1 complex of FoF1-ATP synthase, N-terminal domain. The F-ATP synthase (also called FoF1-ATPase) is found in bacterial plasma membranes, mitochondrial inner membranes and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinsic membrane domain, F1, is composed of alpha, beta, gamma, delta and epsilon subunits with a stoichiometry of 3:3:1:1:1. The beta subunit of ATP synthase is catalytic. 76 matched cddid_all.tbl CDD cd18116 cd18116 349740 ATP-synt_F1_alpha_N F1-ATP synthase alpha (A) subunit, N-terminal domain. The alpha (A) subunit of the F1 complex of FoF1-ATP synthase, N-terminal domain. The F-ATP synthase (also called FoF1-ATPase) is found in bacterial plasma membranes, in mitochondrial inner membranes, and in chloroplast thylakoid membranes. It has also been found in the archaea Methanosarcina barkeri. It uses a proton gradient to drive ATP synthesis and hydrolyzes ATP to build the proton gradient. The extrinsic membrane domain, F1, is composed of alpha, beta, gamma, delta, and epsilon subunits with a stoichiometry of 3:3:1:1:1. The alpha subunit of the F1 ATP synthase can bind nucleotides, but is non-catalytic. 67 matched cddid_all.tbl CDD cd18117 cd18117 349741 ATP-synt_flagellum-secretory_path_III_N Flagellum-specific ATP synthase, N-terminal domain. The N-terminal domain of the flagellum-specific ATPase/type III secretory pathway virulence-related protein. This group of ATPases are responsible for the export of flagellum and virulence-related proteins. The FliI ATPase is the soluble export component that drives flagellar protein export, and it shows extensive similarity to the alpha and beta subunits of F1-ATP synthase. Although they both are proton driven rotary molecular devices, the main function of the bacterial flagellar motor is to rotate the flagellar filament for cell motility. Intracellular pathogens, such as Salmonella and Chlamydia, also have proteins which are similar to the flagellar-specific ATPase, but function in the secretion of virulence-related proteins via the type III secretory pathway. 70 matched cddid_all.tbl CDD cd18118 cd18118 349742 ATP-synt_V_A-type_beta_N V/A-type ATP synthase beta (B) subunit, N-terminal domain. The beta (B) subunit of the V1/A1 complexes of V/A-type ATP synthases, N-terminal domain. The V- and A-type family of ATPases are composed of two linked multi-subunit complexes: the V1 or A1 complex which contains three copies each of the alpha and beta subunits that form the soluble catalytic core, that is involved in ATP synthesis/hydrolysis, and the Vo or Ao complex which forms the membrane-embedded proton pore. The A-ATP synthase (AoA1-ATPase) is found in archaea and functions like F-ATP synthase. Structurally, however, the A-ATP synthase is more closely related to the V-ATP synthase (vacuolar VoV1-ATPase), which is a proton-translocating ATPase responsible for acidification of eukaryotic intracellular compartments and for ATP synthesis in archaea and some eubacteria. Collectively, the V- and A-type synthases can function in both ATP synthesis and hydrolysis modes. This subfamily consists of the non-catalytic beta subunit. 72 matched cddid_all.tbl CDD cd18119 cd18119 349743 ATP-synt_V_A-type_alpha_N V/A-type ATP synthase catalytic subunit A (alpha), N-terminal domain. The alpha (A) subunit of the V1/A1 complexes of V/A-type ATP synthases, N-terminal domain. The V- and A-type family of ATPases are composed of two linked multi-subunit complexes: the V1 or A1 complex contain three copies each of the alpha and beta subunits that form the soluble catalytic core, which is involved in ATP synthesis/hydrolysis, and the Vo or Ao complex that forms the membrane-embedded proton pore. The A-ATP synthase (AoA1-ATPase) is found in archaea and functions like F-ATP synthase. Structurally, however, the A-ATP synthase is more closely related to the V-ATP synthase (vacuolar VoV1-ATPase), which is a proton-translocating ATPase responsible for acidification of eukaryotic intracellular compartments and for ATP synthesis in archaea and some eubacteria. Collectively, the V- and A-type synthases can function in both ATP synthesis and hydrolysis modes. 67 matched cddid_all.tbl CDD cd18120 cd18120 349413 ATP-synt_Vo_Ao_c Membrane-bound Vo/Ao complexes of V/A-type ATP synthases, subunit c. Vo/Ao-ATP synthase subunit c. The V- and A-type family of ATPases are composed of two linked multi-subunit complexes: the V1 and A1 complexes contain three copies each of the alpha and beta subunits that form the soluble catalytic core, which is involved in ATP synthesis/hydrolysis, and the Vo or Ao complex that forms the membrane-embedded proton pore. The A-ATP synthase (AoA1-ATPases) is exclusively found in archaea and functions like the F-ATP synthase. Structurally, however, the A-ATP synthase is more closely related to the V-ATP synthase (vacuolar VoV1-ATPase), which is a proton-translocating ATPase responsible for acidification of eukaryotic intracellular compartments and for ATP synthesis in archaea and some eubacteria. The V- and A-type synthases can function in both ATP synthesis and hydrolysis modes. The V1 complex consists of three A and three B subunits, two G subunits plus the C, D, E, F, and H subunits. The Vo complex consists of five different subunits: a, c, c', c'', and d. The Ao/A1 complexes are composed of nine subunits in a stoichiometry of A(3):B(3):C:D:E:F:H(2):a:c(x). ATP is synthesized on the A3:B3 hexamer and the energy released during that process is transferred to the Ao complex, which consists of the C-terminal segment of subunit a and subunit c. 62 matched cddid_all.tbl CDD cd18121 cd18121 349414 ATP-synt_Fo_c membrane-bound Fo complex of F-ATP synthase, subunit c. Subunit c (also called subunit 9, or proteolipid) of the Fo complex of F-ATP synthase. The F-ATP synthase (also called FoF1-ATPase) consists of two structural domains: the F1 (factor one) complex containing the soluble catalytic core, and the Fo (oligomycin sensitive factor) complex containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. F1 is composed of alpha, beta, gamma, delta, and epsilon subunits with a stoichiometry of 3:3:1:1:1, while Fo consists of the three subunits a, b, and c (1:2:10-14). An oligomeric ring of 10-14 c subunits (c-ring) make up the Fo rotor. The flux of protons though the ATPase channel (Fo) drives the rotation of the c-ring, which in turn is coupled to the rotation of the F1 complex gamma subunit rotor due to the permanent binding between the gamma and epsilon subunits of F1 and the c-ring of Fo. The F-ATP synthases are primarily found in the inner membranes of eukaryotic mitochondria, in the thylakoid membranes of chloroplasts, or in the plasma membranes of bacteria. The F-ATP synthases are the primary producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). Alternatively, under conditions of low driving force, ATP synthases function as ATPases, thus generating a transmembrane proton or Na(+) gradient at the expense of energy derived from ATP hydrolysis. This group also includes F-ATP synthase that has also been found in the archaea Methanosarcina acetivorans. 65 matched cddid_all.tbl CDD cd18122 cd18122 467672 GAPDH_like_C C-terminal catalytic domain found in glyceraldehyde-3-phosphate dehydrogenase (GAPDH) superfamily of proteins. GAPDH-like C-terminal catalytic domains are typically associated with a classic N-terminal Rossmann fold NAD(P)-binding domain. This superfamily includes the C-terminal domains of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), N-acetyl-gamma-glutamyl-phosphate reductase (AGPR), aspartate beta-semialdehyde dehydrogenase (ASADH), acetaldehyde dehydrogenase (ALDH) and USG-1 homolog proteins. 166 matched cddid_all.tbl CDD cd18123 cd18123 467673 GAPDH_C C-terminal catalytic domain of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and similar proteins. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an important role in glycolysis and gluconeogenesis by reversibly catalyzing the oxidation and phosphorylation of D-glyceraldehyde-3-phosphate to 1,3-diphospho-glycerate. It has been implicated in varied activities including regulating mRNA stability, the regulation of gene expression, induction of apoptosis, intracellular membrane trafficking, iron uptake and transport (via secreted GAPDH), heme metabolism, the maintenance of genomic integrity, and nuclear tRNA export. GAPDH proteins contains an N-terminal NAD(P)-binding domain and a C-terminal catalytic domain. The primarily N-terminal NAD(P)-binding domain contains a Rossmann fold which combines with the catalytic cysteine-containing C-terminus to form a catalytic cleft. Phosphatidyl-serine, RNA, and glutathione binding sites have been identified in the N-terminus. Different forms of GAPDH exist which utilize NAD (1.2.1.12), NADP (1.2.1.13) or either (1.2.1.59). GADPH family members include the ubiquitous NAD+ or NADP+ utilizing type I, type II NADP+ utilizing mainly from archaea, and a small clade of dehydrogenases, called erythrose-4-phosphate dehydrogenase (E4PDH) proteins, which utilize NAD+ to oxidize erythrose-4-phosphate (E4P) to 4-phospho-erythronate, a precursor for the de novo synthesis of pyridoxine via 4-hydroxythreonine and D-1-deoxyxylulose. 164 matched cddid_all.tbl CDD cd18124 cd18124 467674 ASADH_C_like C-terminal catalytic domain of aspartate beta-semialdehyde dehydrogenase (ASADH), USG-1 protein and similar proteins. The family includes aspartate beta-semialdehyde dehydrogenase (ASADH), NADP-dependent malonyl-CoA reductase (MCR), and USG-1 protein. These proteins contain an N-terminal Rossmann fold NAD(P) binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like domain and are members of the GAPDH superfamily of proteins. ASADH (EC 1.2.1.11), also called ASA dehydrogenase (ASD), or aspartate-beta-semialdehyde dehydrogenase, catalyzes the NADPH-dependent formation of L-aspartate-semialdehyde (ASA) by the reductive dephosphorylation of L-aspartyl-4-phosphate, which is the second step of the aspartate biosynthetic pathway. ASA can either be further reduced to homoserine, which leads to methionine, threonine, or isoleucine, or it can be condensed with pyruvate and cyclized into dihydrodipicolinate, and then converted into diaminopimelate, a component of bacterial cell walls, and finally decarboxylated to produce lysine. NADP-dependent MCR (EC 1.2.1.75) is mainly found in Archaea. It catalyzes the reduction of malonyl-CoA to malonate semialdehyde, a key step in the 3-hydroxypropanoate and the 3-hydroxypropanoate/4-hydroxybutyrate cycles. It can also use succinyl-CoA and succinate semialdehyde as substrates but at a lower rate than malonyl-CoA. Sequence comparison suggests that the archaeal MCR gene (mcr) has evolved from the duplication of a common ancestral ASADH gene (asd). The biological function of USG-1 protein and homologs remains unclear. They are homologs to ASADH but lack the conserved active site residues of the ASADH protein C-terminal catalytic domain. 193 matched cddid_all.tbl CDD cd18125 cd18125 467675 AGPR_C C-terminal catalytic domain of N-acetyl-gamma-glutamyl-phosphate reductase (AGPR) and similar proteins. N-acetyl-gamma-glutamyl-phosphate reductase (AGPR; EC 1.2.1.38), also called N-acetyl-glutamate semialdehyde dehydrogenase, or NAGSA dehydrogenase, catalyzes the third step in the biosynthesis of arginine from glutamate, the NADP-dependent reduction of N-acetyl-5-glutamyl phosphate into N-acetylglutamate 5-semialdehyde. In bacteria it is a monofunctional protein of 35 to 38kDa (gene argC), while in fungi it is part of a bifunctional mitochondrial enzyme (gene ARG5,6, arg11 or arg-6) which contains a N-terminal acetylglutamate kinase (EC 2.7.2.8) domain and a C-terminal AGPR domain. There are two related families (type 1 and type 2) of N-acetyl-gamma-glutamyl-phosphate reductase, which differ by phylogeny, similarity clustering, and gap architecture in a multiple sequence alignment. This family also includes LysY (LysW-L-2-aminoadipate/LysW-L-glutamate phosphate reductase, EC 1.2.1.103/EC 1.2.1.106), which is involved in both the arginine and lysine biosynthetic pathways. 166 matched cddid_all.tbl CDD cd18126 cd18126 467676 GAPDH_I_C C-terminal catalytic domain of type I glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and similar proteins. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an important role in glycolysis and gluconeogenesis by reversibly catalyzing the oxidation and phosphorylation of D-glyceraldehyde-3-phosphate to 1,3-diphospho-glycerate. It has been implicated in varied activities including regulating mRNA stability, the regulation of gene expression, induction of apoptosis, intracellular membrane trafficking, iron uptake and transport (via secreted GAPDH), heme metabolism, the maintenance of genomic integrity, and nuclear tRNA export. GAPDH proteins contains an N-terminal NAD(P)-binding domain and a C-terminal catalytic domain. The primarily N-terminal NAD(P)-binding domain contains a Rossmann fold which combines with the catalytic cysteine-containing C-terminus to form a catalytic cleft. Phosphatidyl-serine, RNA, and glutathione binding sites have been identified in the N-terminus. Different forms of GAPDH exist which utilize NAD (1.2.1.12), NADP (1.2.1.13) or either (1.2.1.59). The family corresponds to the ubiquitous NAD+ or NADP+ utilizing type I GAPDH and a small clade of dehydrogenases, called erythrose-4-phosphate dehydrogenase (E4PDH) proteins, which utilize NAD+ to oxidize erythrose-4-phosphate (E4P) to 4-phospho-erythronate, a precursor for the de novo synthesis of pyridoxine via 4-hydroxythreonine and D-1-deoxyxylulose. 165 matched cddid_all.tbl CDD cd18127 cd18127 467677 GAPDH_II_C C-terminal catalytic domain of type II glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and similar proteins. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) plays an important role in glycolysis and gluconeogenesis by reversibly catalyzing the oxidation and phosphorylation of D-glyceraldehyde-3-phosphate to 1,3-diphospho-glycerate. It has been implicated in varied activities including regulating mRNA stability, the regulation of gene expression, induction of apoptosis, intracellular membrane trafficking, iron uptake and transport (via secreted GAPDH), heme metabolism, the maintenance of genomic integrity, and nuclear tRNA export. GAPDH proteins contains an N-terminal NAD(P)-binding domain and a C-terminal catalytic domain. The primarily N-terminal NAD(P)-binding domain contains a Rossmann fold which combines with the catalytic cysteine-containing C-terminus to form a catalytic cleft. Phosphatidyl-serine, RNA, and glutathione binding sites have been identified in the N-terminus. Different forms of GAPDH exist which utilize NAD (1.2.1.12), NADP (1.2.1.13) or either (1.2.1.59). The family corresponds to type II NADP+ utilizing GAPDHs, mainly from archaea. 162 matched cddid_all.tbl CDD cd18128 cd18128 467678 ASADH_C C-terminal catalytic domain of aspartate beta-semialdehyde dehydrogenase (ASADH) and similar proteins. Aspartate beta-semialdehyde dehydrogenase (ASADH; EC 1.2.1.11), also called ASA dehydrogenase (ASD), or aspartate-beta-semialdehyde dehydrogenase, catalyzes the NADPH-dependent formation of L-aspartate-semialdehyde (ASA) by the reductive dephosphorylation of L-aspartyl-4-phosphate, which is the second step of the aspartate biosynthetic pathway. ASA can either be further reduced to homoserine, which leads to methionine, threonine, or isoleucine, or it can be condensed with pyruvate and cyclized into dihydrodipicolinate, and then converted into diaminopimelate, a component of bacterial cell walls, and finally decarboxylated to produce lysine. ASADH contains an N-terminal Rossmann fold NAD(P) binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like catalytic domain and are members of the GAPDH superfamily of proteins. 165 matched cddid_all.tbl CDD cd18129 cd18129 467679 ASADH_C_USG1_like C-terminal domain of USG-1 protein and similar proteins. The family includes Escherichia coli USG-1 protein, Pseudomonas aeruginosa USG-1 homolog proteins and similar proteins. Although its biological function remains unknown, it is found to be homologous to aspartate beta-semialdehyde dehydrogenase (ASADH) which contains an N-terminal Rossmann fold NAD(P) binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like domain. However, USG-1 proteins lack the conserved active site residues of the ASADH protein C-terminal domain. 186 matched cddid_all.tbl CDD cd18130 cd18130 467680 ASADH_C_arch_fung_like C-terminal catalytic domain of fungal/archaeal aspartate beta-semialdehyde dehydrogenase (ASADH) and similar proteins. The family corresponds to a new branch of aspartate beta-semialdehyde dehydrogenase (ASADH) enzymes that has a similar overall fold and domain organization but share very little sequence homology with the typical bacterial ASADHs. They are mainly from archaea and fungi. ASADH (EC 1.2.1.11), also called ASA dehydrogenase (ASD), or aspartate-beta-semialdehyde dehydrogenase, catalyzes the NADPH-dependent formation of L-aspartate-semialdehyde (ASA) by the reductive dephosphorylation of L-aspartyl-4-phosphate, which is the second step of the aspartate biosynthetic pathway. ASA can either be further reduced to homoserine, which leads to methionine, threonine, or isoleucine, or it can be condensed with pyruvate and cyclized into dihydrodipicolinate, and then converted into diaminopimelate, a component of bacterial cell walls, and finally decarboxylated to produce lysine. ASADH contains an N-terminal Rossmann fold NAD(P) binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like catalytic domain and are members of the GAPDH superfamily of proteins. This family also includes NADP-dependent malonyl-CoA reductase (MCR, EC 1.2.1.75), which catalyzes the reduction of malonyl-CoA to malonate semialdehyde, a key step in the 3-hydroxypropanoate and the 3-hydroxypropanoate/4-hydroxybutyrate cycles. It can also use succinyl-CoA and succinate semialdehyde as substrates but at a lower rate than malonyl-CoA. 180 matched cddid_all.tbl CDD cd18131 cd18131 467681 ASADH_C_bac_euk_like C-terminal catalytic domain of bacterial/eukaryotic aspartate beta-semialdehyde dehydrogenase (ASADH) and similar proteins. The family corresponds to a new branch of bacterial aspartate beta-semialdehyde dehydrogenase (ASADH) enzymes that has a similar overall fold and domain organization but share less sequence homology with the other bacterial ASADHs. The second isoform of ASADH in Vibrio cholerae is one of the prototypes of this family. It also includes ASADHs from Streptococcus pneumoniae, Mycobacterium tuberculosis, Thermus thermophilus, as well as from eukaryotes. ASADH (EC 1.2.1.11), also called ASA dehydrogenase (ASD), or aspartate-beta-semialdehyde dehydrogenase, catalyzes the NADPH-dependent formation of L-aspartate-semialdehyde (ASA) by the reductive dephosphorylation of L-aspartyl-4-phosphate, which is the second step of the aspartate biosynthetic pathway. ASA can either be further reduced to homoserine, which leads to methionine, threonine, or isoleucine, or it can be condensed with pyruvate and cyclized into dihydrodipicolinate, and then converted into diaminopimelate, a component of bacterial cell walls, and finally decarboxylated to produce lysine. ASADH contains an N-terminal Rossmann fold NAD(P) binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like catalytic domain and are members of the GAPDH superfamily of proteins. 188 matched cddid_all.tbl CDD cd18133 cd18133 350838 HLD_clamp helical lid domain of clamp loader-like AAA+ proteins. Clamp loader complexes are multisubunit complexes that play an important role in DNA replication. They open sliding clamps for assembly and close them around DNA, specifically targeting them to sites where DNA synthesis is initiated and orienting them correctly for replication. The subunits belong to the clamp loader clade of AAA+ superfamily. 65 matched cddid_all.tbl CDD cd18137 cd18137 350839 HLD_clamp_pol_III_gamma_tau helical lid domain of DNA polymerase III subunits gamma and tau. DNA polymerase III subunit gamma/tau is part of the DNA polymerase III holoenzyme. Gamma and tau subunits are isoforms, both containing the helical lid domain. Gamma interacts with the delta subunit to transfer the beta subunit on the DNA while tau serves as a scaffold to help in the dimerization of the core complex. Both are members of the clamp-loader clade of the AAA+ superfamily. 65 matched cddid_all.tbl CDD cd18138 cd18138 350840 HLD_clamp_pol_III_delta helical lid domain of DNA polymerase III subunits delta. DNA polymerase III subunit delta is part of the DNA polymerase III holoenzyme. the delta subunit id required for ring opening and binds the beta subunit. It is a member of the clamp-loader clade of the AAA+ superfamily. 65 matched cddid_all.tbl CDD cd18139 cd18139 350841 HLD_clamp_RarA helical lid domain of recombination factor protein RarA. Recombination factor RarA (Replication associated recombination gene/protein A, also known as MgsA (Maintenance of genome stability A) or Mgs1 in yeast and WRNIP1 in mammals) is a member of the clamp-loader clade of the AAA+ superfamily. It functions as a tetramer. RarA co-localize with the replication fork throughout the cell cycle and may play a role in the rescue of stalled replication forks. 75 matched cddid_all.tbl CDD cd18140 cd18140 350842 HLD_clamp_RFC helical lid domain of replication factor C subunit. Replication factor C (RFC) is five-protein clamp loader complex that forms a stable ATP-dependent complex with the sliding clamp, PCNA, which binds specifically to primed DNA. RFC subunits belong to the clamp loader clade of the AAA+ superfamily. 63 matched cddid_all.tbl CDD cd18159 cd18159 381143 REC_OmpR_NsrR-like phosphoacceptor receiver (REC) domain of Streptococcus agalactiae NsrR-like OmpR family response regulators. Streptococcus agalactiae NsrR is a lantibiotic resistance-associated response regulator and is part of the nisin resistance operon. It is a member of the NsrRK two-component system (TCS) that is involved in the regulation of lantibiotic resistance genes such as a membrane-associated lipoprotein of LanI, and the nsr gene cluster which encodes for the resistance protein NSR and the ABC transporter NsrFP, both conferring resistance against nisin. This subfamily also includes Staphylococcus epidermidis GraR, part of the GraR/GraS TCS involved in resistance against cationic antimicrobial peptides, and Bacillus subtilis BceR, part of the BceS/BceR TCS involved in the regulation of bacitracin resistance. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 113 matched cddid_all.tbl CDD cd18160 cd18160 381144 REC_CpdR_CckA-like phosphoacceptor receiver (REC) domain of Brucella abortus CpdR and CckA, and similar domains. Two-component systems (TCSs), consisting of a sensor and a response regulator, are used by bacteria to adapt to changing environments. Processes regulated by TCSs in bacteria include sporulation, pathogenicity, virulence, chemotaxis and membrane transport. Response regulators share the common phosphoacceptor REC domain and differ output domains such as DNA, RNA, ligand, and protein-binding, or enzymatic domain. CpdR is a stand-alone REC protein. CckA is a sensor histidine kinase containing N-terminal PAS domains and a C-terminal REC domain. CpdR and CckA are components of a regulatory phosphorelay system (composed of CckA, ChpT, CtrA and CpdR) that controls Brucella abortus cell growth, division, and intracellular survival inside mammalian host cells. CckA autophosphorylates in the presence of ATP and transfers a phosphoryl group to the conserved aspartic acid residue on its C-terminal REC domain, which is relayed to the ChpT phosphotransferase. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 103 matched cddid_all.tbl CDD cd18161 cd18161 381145 REC_hyHK_blue-like phosphoacceptor receiver (REC) domain of hybrid sensor histidine kinase/response regulators similar to Pseudomonas savastanoi blue-light-activated histidine kinase. Typically, two-component regulatory systems (TCSs) consist of a sensor (histidine kinase) that responds to specific input(s) by modifying the output of a cognate response regulator (RR). TCSs allow organisms to sense and respond to changes in environmental conditions. Hybrid sensor histidine kinase (HK)/response regulators contain all the elements of a classical TCS in a single polypeptide chain. Pseudomonas savastanoi blue-light-activated histidine kinase is a photosensitive HK and RR that is involved in increased bacterial virulence upon exposure to light. RRs share the common phosphoacceptor REC domain and different effector/output domains such as DNA, RNA, ligand-binding, protein-binding, or enzymatic domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 102 matched cddid_all.tbl CDD cd18172 cd18172 349482 M14_CP_plant Zinc carboxypeptidase, including SOL1, a carboxypeptidase D in plant. This family includes only plant members of the carboxypeptidase (CP) N/E-like subfamily of the M14 family of metallocarboxypeptidases (MCPs). It includes Arabidopsis thaliana SOL1 carboxypeptidase D which is known to possess enzymatic activity to remove the C-terminal arginine residue of CLE19 proprotein in vitro, and SOL1-dependent cleavage of the C-terminal arginine residue is necessary for CLE19 activity in vivo. The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. The N/E subfamily includes eight members, of which five (CPN, CPE, CPM, CPD, CPZ) are considered enzymatically active, while the other three are non-active (CPX1, PCX2, ACLP/AEBP1) and lack the critical active site and substrate-binding residues considered necessary for CP activity. These non-active members may function as binding proteins or display catalytic activity towards other substrates. Unlike the A/B CP subfamily, enzymes belonging to the N/E subfamily are not produced as inactive precursors that require proteolysis to produce the active form; rather, they rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavages that would otherwise damage the cell. In addition, all members of the N/E subfamily contain an extra C-terminal domain that is not present in the A/B subfamily. This domain has structural homology to transthyretin and other proteins and has been proposed to function as a folding domain. The active N/E enzymes fulfill a variety of cellular functions, including prohormone processing, regulation of peptide hormone activity, alteration of protein-protein or protein-cell interactions and transcriptional regulation. 276 matched cddid_all.tbl CDD cd18173 cd18173 349483 M14_CP_bacteria bacterial peptidase M14 carboxypeptidase, uncharacterized. This family contains only bacterial carboxypeptidase (CP) members of the M14 family of metallocarboxypeptidases (MCPs), mostly of which have yet to be characterized. The M14 family are zinc-binding CPs which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. The N/E subfamily includes eight members, of which five (CPN, CPE, CPM, CPD, CPZ) are considered enzymatically active, while the other three are non-active (CPX1, PCX2, ACLP/AEBP1) and lack the critical active site and substrate-binding residues considered necessary for CP activity. These non-active members may function as binding proteins or display catalytic activity towards other substrates. Unlike the A/B CP subfamily, enzymes belonging to the N/E subfamily are not produced as inactive precursors that require proteolysis to produce the active form; rather, they rely on their substrate specificity and subcellular compartmentalization to prevent inappropriate cleavages that would otherwise damage the cell. In addition, all members of the N/E subfamily contain an extra C-terminal domain that is not present in the A/B subfamily. This domain has structural homology to transthyretin and other proteins and has been proposed to function as a folding domain. The active N/E enzymes fulfill a variety of cellular functions, including prohormone processing, regulation of peptide hormone activity, alteration of protein-protein or protein-cell interactions and transcriptional regulation. 281 matched cddid_all.tbl CDD cd18174 cd18174 349484 M14_ASTE_ASPA_like Peptidase M14 Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA)-like; uncharacterized subgroup. A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. 187 matched cddid_all.tbl CDD cd18175 cd18175 349415 ATP-synt_Vo_c_ATP6C_rpt1 V-type proton ATPase 16 kDa proteolipid subunit (ATP6C/ATP6V0C/ATP6L/ATPL) and similar proteins. ATP6C (also called the V-ATPase 16 kDa proteolipid subunit, or vacuolar proton pump 16 kDa proteolipid subunit) is a proton-conducting pore forming subunit of the membrane integral Vo complex of vacuolar ATPase. V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells. 68 matched cddid_all.tbl CDD cd18176 cd18176 349416 ATP-synt_Vo_c_ATP6C_rpt2 V-type proton ATPase 16 kDa proteolipid subunit (ATP6C/ATP6V0C/ATP6L/ATPL) and similar proteins. ATP6C (also called V-ATPase 16 kDa proteolipid subunit, or vacuolar proton pump 16 kDa proteolipid subunit) is a proton-conducting pore forming subunit of the membrane integral Vo complex of vacuolar ATPase. V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells. 68 matched cddid_all.tbl CDD cd18177 cd18177 349417 ATP-synt_Vo_c_ATP6F_rpt1 V-type proton ATPase 21 kDa proteolipid subunit (ATP6F/ATP6V0B) and similar proteins. ATP6F (also called V-ATPase 21 kDa proteolipid subunit, or vacuolar proton pump 21 kDa proteolipid subunit) is a proton-conducting pore forming subunit of the membrane integral Vo complex of vacuolar ATPase. V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells. 63 matched cddid_all.tbl CDD cd18178 cd18178 349418 ATP-synt_Vo_c_ATP6F_rpt2 V-type proton ATPase 21 kDa proteolipid subunit (ATP6F/ATP6V0B) and similar proteins. ATP6F (also called V-ATPase 21 kDa proteolipid subunit, or vacuolar proton pump 21 kDa proteolipid subunit) is a proton-conducting pore forming subunit of the membrane integral Vo complex of vacuolar ATPase. V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells. 65 matched cddid_all.tbl CDD cd18179 cd18179 349419 ATP-synt_Vo_Ao_c_NTPK_rpt1 V-type sodium ATPase subunit K (NTPK) and similar proteins. NTPK (also called Na(+)-translocating ATPase subunit K, or sodium ATPase proteolipid component) is involved in ATP-driven sodium extrusion. 63 matched cddid_all.tbl CDD cd18180 cd18180 349420 ATP-synt_Vo_Ao_c_NTPK_rpt2 V-type sodium ATPase subunit K (NTPK) and similar proteins. NTPK (also called Na(+)-translocating ATPase subunit K, or sodium ATPase proteolipid component) is involved in ATP-driven sodium extrusion. 64 matched cddid_all.tbl CDD cd18181 cd18181 349421 ATP-synt_Vo_Ao_c_TtATPase_like Thermus thermophilus V/A-ATPase and similar proteins. This family includes a group of uncharacterized ATPase similar to Thermus thermophilus V/A-ATPase, which is homologous to the eukaryotic V-ATPase, but has a simpler subunit composition and functions in vivo to synthesize ATP rather than pump protons. 62 matched cddid_all.tbl CDD cd18182 cd18182 349422 ATP-synt_Fo_c_ATP5G3 ATP synthase F(0) complex subunit C3 (ATP5G3) and similar proteins. ATP5G3 (also called ATP synthase lipid-binding protein, ATP synthase proteolipid P3, ATP synthase proton-transporting mitochondrial F(o) complex subunit C3, ATPase protein 9, or ATPase subunit c) transports protons across the inner mitochondrial membrane to the F1-ATPase protruding on the matrix side, resulting in the generation of ATP. 65 matched cddid_all.tbl CDD cd18183 cd18183 349423 ATP-synt_Fo_c_ATPH F-type proton-translocating ATP synthase (ATPH) and similar proteins. This family includes subunit c of chloroplast F-ATP synthase (F1Fo-ATP synthase), also known as ATP synthase F(o) sector subunit c (also called ATPase subunit III, F-type ATPase subunit c, or F-ATPase subunit c)and similar proteins. It is a proton-translocating subunit of the ATP synthase encoded by gene atpH. 75 matched cddid_all.tbl CDD cd18184 cd18184 349424 ATP-synt_Fo_c_NaATPase F-type sodium ion-translocating ATP synthase and similar proteins. This family includes F-type Na(+)-coupled ATP synthase and similar proteins. 65 matched cddid_all.tbl CDD cd18185 cd18185 349425 ATP-synt_Fo_c_ATPE F-type proton-translocating ATPase subunit c (ATPE) and similar proteins. This family includes subunit c of F-ATP synthase (also called ATP synthase F(o) sector subunit c, F-type ATPase subunit c, or F-ATPase subunit c) and similar proteins. It is a proton-translocating subunit of the ATP synthase encoded by gene atpE. 65 matched cddid_all.tbl CDD cd18186 cd18186 349497 BTB_POZ_ZBTB_KLHL-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing (ZBTB) proteins, Kelch-like (KLHL) proteins, and similar proteins. This family includes a variety of BTB/POZ domain-containing proteins, such as zinc finger and BTB domain-containing (ZBTB) proteins and Kelch-like (KLHL) proteins. They have diverse functions, such as transcriptional regulation, chromatin remodeling, protein degradation and cytoskeletal regulation. Many BTB/POZ proteins contain one or two additional domains, such as kelch repeats, zinc-finger domains, FYVE (Fab1, YOTB, Vac1, and EEA1) fingers, or ankyrin repeats. These special additional domains or interaction partners provide unique characteristics and functions to BTB/POZ proteins. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 82 matched cddid_all.tbl CDD cd18187 cd18187 349498 BTB_POZ_Kv_KCTD BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in voltage-gated potassium (Kv) channels and potassium channel tetramerization domain-containing (KCTD) proteins. This family includes two protein groups: voltage-gated potassium (Kv) channels and potassium channel tetramerization domain-containing (KCTD) proteins. Kv channels are membrane proteins with fundamental physiological roles. They are responsible for a variety of electrical phenomena, such as the repolarization of the action potential, spike frequency adaptation, synaptic repolarization, and smooth muscle contraction. KCTD proteins play crucial roles in a variety of fundamental biological processes, such as protein ubiquitination and degradation, suppression of proliferation or transcription, cytoskeleton regulation, tetramerization and gating of ion channels, and others. All family members contain the BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. 83 matched cddid_all.tbl CDD cd18190 cd18190 349499 BTB_POZ_ETO1-like BTB (Broad-Complex, Tramtrack and Bric a brac) /POZ (poxvirus and zinc finger) domain found in Arabidopsis thaliana ethylene-overproduction protein 1 (ETO1) and similar proteins. ETO1, also called protein ethylene overproducer 1, is an essential regulator of the ethylene pathway, which acts by regulating the stability of 1-aminocyclopropane-1-carboxylate synthase (ACS) enzymes. It may act as a substrate-specific adaptor that connects ACS enzymes, such as ACS5, to ubiquitin ligase complexes, leading to proteasomal degradation of ACS enzymes. The family also includes ETO1-like proteins 1 (EOL1) and 2 (EOL2). ETO1, EOL1, and EOL2 contain a BTB domain and tetratricopeptide (TPR) repeats. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 83 matched cddid_all.tbl CDD cd18191 cd18191 349500 BTB_POZ_ARMC5 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in armadillo repeat-containing protein 5 (ARMC5). ARMC5 plays a role in steroidogenesis, and modulates the expression and cortisol production of steroidogenic enzymes. It negatively regulates adrenal cells survival. It contains armadillo (ARM) repeats and a BTB domain, which is a common protein-protein interaction motif of about 100 amino acids. 100 matched cddid_all.tbl CDD cd18192 cd18192 349501 BTB_POZ_ZBTB1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 1 (ZBTB1). ZBTB1 acts as a transcriptional repressor that represses cAMP-responsive element (CRE)-mediated transcriptional activation. It also has a role in translesion DNA synthesis, and is essential for lymphocyte development. ZBTB1 contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 114 matched cddid_all.tbl CDD cd18193 cd18193 349502 BTB_POZ_ZBTB2 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 2 (ZBTB2). ZBTB2 is a POZ domain Kruppel-like zinc finger (POK) family transcription factor acting as a potent repressor of the ARF-HDM2-p53-p21 pathway, which is important in cell cycle regulation. It represses transcription of the ARF, p53, and p21 genes, but activates the HDM2 gene. ZBTB2 contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 115 matched cddid_all.tbl CDD cd18194 cd18194 349503 BTB_POZ_ZBTB3-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing proteins, ZBTB3, ZBTB18, ZBTB42 and similar proteins. The family includes zinc finger and BTB domain-containing proteins, ZBTB3, ZBTB18 and ZBTB42. ZBTB3 is a transcription factor essential for cancer cell growth via the regulation of the reactive oxygen species (ROS) detoxification pathway. ZBTB18 is a sequence-specific transrepressor associated with heterochromatin. ZBTB42 is a transcriptional repressor that specifically binds DNA and probably acts by recruiting chromatin remodeling multiprotein complexes. Members of this family contain a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 128 matched cddid_all.tbl CDD cd18195 cd18195 349504 BTB_POZ_ZBTB4 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 4 (ZBTB4). ZBTB4, also called KAISO-like zinc finger protein 1 (KAISO-L1), is a transcriptional repressor with bimodal DNA-binding specificity. It binds with a higher affinity to methylated CpG dinucleotides in the consensus sequence 5'-CGCG-3' but can also bind to the non-methylated consensus sequence 5'-CTGCNA-3', also known as the consensus kaiso binding site (KBS). It can also bind specifically to a single methyl-CpG pair and can bind hemimethylated DNA but with a lower affinity compared to methylated DNA. ZBTB4 contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 124 matched cddid_all.tbl CDD cd18196 cd18196 349505 BTB_POZ_ZBTB5 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 5 (ZBTB5). ZBTB5 is a POZ domain Kruppel-like zinc finger (POK) family transcription repressor of cell cycle arrest gene p21 and a potential proto-oncogene stimulating cell proliferation. ZBTB5 contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 126 matched cddid_all.tbl CDD cd18197 cd18197 349506 BTB_POZ_ZBTB6 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 6 (ZBTB6). ZBTB6, also called zinc finger protein 482 (ZNF482) or zinc finger protein with interaction domain, may be involved in transcriptional regulation. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 116 matched cddid_all.tbl CDD cd18198 cd18198 349507 BTB_POZ_ZBTB7 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 7 (ZBTB7). There are three ZBTB7 isoforms: ZBTB7A, ZBTB7B, and ZBTB7C. ZBTB7A is a transcription repressor of key glycolytic genes, including GLUT3, PFKP, and PKM, and its downregulation in human cancer contributes to tumor metabolism. ZBTB7B is a transcriptional regulator of extracellular matrix gene expression. ZBTB7C is a transcriptional repressor with a pro-oncogenic role that relies upon binding to p53 and inhibition of its transactivation function. ZBTB7 isoforms contain a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 120 matched cddid_all.tbl CDD cd18199 cd18199 349508 BTB_POZ_ZBTB8 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 8 (ZBTB8). There are two ZBTB8 isoforms: ZBTB8A and ZBTB8B. ZBTB8A is a novel proto-oncoprotein that stimulates cell proliferation. ZBTB8B may be involved in transcriptional regulation. They both contain a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 113 matched cddid_all.tbl CDD cd18200 cd18200 349509 BTB_POZ_ZBTB9 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 9 (ZBTB9). ZBTB9 may be involved in transcriptional regulation. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 111 matched cddid_all.tbl CDD cd18201 cd18201 349510 BTB_POZ_ZBTB10 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 10 (ZBTB10). ZBTB10, also called zinc finger protein RIN ZF, is an mRNA target of miR-27a and a transcriptional repressor of Specificity protein (Sp) expression. The microRNA-27a:ZBTB10-specificity protein pathway is involved in follicle stimulating hormone-induced VEGF, Cox2, and survivin expression in ovarian epithelial cancer cells. ZBTB10 contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 122 matched cddid_all.tbl CDD cd18202 cd18202 349511 BTB_POZ_ZBTB11 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 11 (ZBTB11). ZBTB11 is a transcriptional repressor of TP53. It is critical for basal and emergency granulopoiesis. It regulates neutrophil development through its integrase-like zinc finger domain. ZBTB11 contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 118 matched cddid_all.tbl CDD cd18203 cd18203 349512 BTB_POZ_ZBTB12 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 12 (ZBTB12). ZBTB12, also called protein G10, may be involved in transcriptional regulation. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 122 matched cddid_all.tbl CDD cd18204 cd18204 349513 BTB_POZ_ZBTB14 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 14 (ZBTB14). ZBTB14 is also called zinc finger protein 161 (Zfp-161), zinc finger protein 478, zinc finger protein 5 (ZF5), or Zfp-5. It is a novel transcriptional activator of the dopamine transporter, binding it's promoter at the consensus sequence 5'-CCTGCACAGTTCACGGA-3'. It also binds to 5'-d(GCC)(n)-3' trinucleotide repeats in promoter regions and acts as a repressor of the FMR1 gene. ZBTB14 acts as a transcriptional repressor of MYC and thymidine kinase promoters. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 114 matched cddid_all.tbl CDD cd18205 cd18205 349514 BTB_POZ_ZBTB16_PLZF BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 16 (ZBTB16). ZBTB16 is also called promyelocytic leukemia zinc finger protein, zinc finger protein 145, or zinc finger protein PLZF. It is a DNA-binding transcription factor essential for undifferentiated cell maintenance. ZBTB16 also acts as a downstream transcriptional regulator of Osterix and can be useful as a late marker of osteoblastic differentiation. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 107 matched cddid_all.tbl CDD cd18206 cd18206 349515 BTB_POZ_ZBTB17_MIZ1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 17 (ZBTB17). ZBTB1 is also called c-Myc-interacting zinc finger protein 1 (Miz-1), zinc finger protein 151, or zinc finger protein 60. It is a poly-Cys2His2 zinc finger (ZF) transcription factor that can function as an activator or repressor depending on its binding partners, and by targeting negative regulators of cell cycle progression. ZBTB17 has been implicated in cardiomyopathy and is important in cardiac stress response. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 112 matched cddid_all.tbl CDD cd18207 cd18207 349516 BTB_POZ_ZBTB19_PATZ1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in POZ-, AT hook-, and zinc finger-containing protein 1 (PATZ1). PATZ1 is also called zinc finger and BTB domain-containing protein 19 (ZBTB19), BTB/POZ domain zinc finger transcription factor, protein kinase A RI subunit alpha-associated protein, zinc finger protein 278, or zinc finger sarcoma gene protein. It is an important transcriptional regulatory factor that regulates divergent pathways depending on the cellular context. For instance, it acts as a transcriptional suppressor that functions in T lymphocytes. It is also a DNA damage-responsive transcription factor that inhibits p53 function. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 128 matched cddid_all.tbl CDD cd18208 cd18208 349517 BTB_POZ_ZBTB20_DPZF BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 20 (ZBTB20). ZBTB20, also called dendritic-derived BTB/POZ zinc finger protein (DPZF) or zinc finger protein 288, may be a transcription factor involved in hematopoiesis, oncogenesis, and immune responses. It is an essential regulator of hepatic lipogenesis and may be a therapeutic target for the treatment of fatty liver disease. It also functions as a critical regulator of anterior pituitary development and lactotrope specification. Moreover, it promotes astrocytogenesis during neocortical development. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 117 matched cddid_all.tbl CDD cd18209 cd18209 349518 BTB_POZ_ZBTB21_ZNF295 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 21 (ZBTB21). ZBTB21, also called zinc finger protein 295 (ZNF295), is a transcription repressor that acts in a selective manner on different promoters. It may be involved in the bi-directional control of gene expression in concert with another transcription factor ZFP161. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 112 matched cddid_all.tbl CDD cd18210 cd18210 349519 BTB_POZ_ZBTB22_BING1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 22 (ZBTB22). ZBTB22, also called protein BING1 or zinc finger protein 297, may be involved in transcriptional regulation. Its gene, together with BING 3-5, TAPASIN, DAXX, RGL2, and HKE2, form a dense cluster at the centromeric end of the major histocompatibility complex class I region. ZBTB22 contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 112 matched cddid_all.tbl CDD cd18211 cd18211 349520 BTB_POZ_ZBTB23_GZF1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in glial cell line-derived neurotrophic factor-inducible zinc finger protein 1 (GZF1). GZF1 is also called GDNF-inducible zinc finger protein 1, zinc finger and BTB domain-containing protein 23 (ZBTB23), or zinc finger protein 336 (ZNF336). It is a sequence-specific transcriptional repressor that binds the GZF1 responsive element (GRE), with the consensus sequence of 5'-TGCGCN[TG][CA]TATA-3'. It may play a role in renal branching morphogenesis. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 128 matched cddid_all.tbl CDD cd18212 cd18212 349521 BTB_POZ_ZBTB24_ZNF450 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 24 (ZBTB24). ZBTB24, also called zinc finger protein 450, functions as a transcription factor essentially involved in B-cell functions in humans. The loss-of-function mutations in ZBTB24 can cause ICF2 (immunodeficiency, centromeric instability and facial anomalies syndrome 2) with immunological characteristics of greatly reduced serum antibodies and circulating memory B cells. ZBTB24 contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 118 matched cddid_all.tbl CDD cd18213 cd18213 349522 BTB_POZ_ZBTB25_ZNF46_KUP BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 25 (ZBTB25). ZBTB25, also called zinc finger protein 46 (ZNF46) or zinc finger protein KUP, is a transcription repressor that facilitates viral RNA transcription and replication. It interacts with viral RNA-dependent RNA polymerase (RdRp) proteins and modulates their transcription activity. It also functions as a viral RNA-binding protein, binding preferentially to the U-rich sequence within 5' UTR of vRNA. ZBTB25 contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 128 matched cddid_all.tbl CDD cd18214 cd18214 349523 BTB_POZ_ZBTB26_Bioref BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 26 (ZBTB26). ZBTB26, also called zinc finger protein 481 (ZNF481) or zinc finger protein Bioref, may be involved in transcriptional regulation. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 122 matched cddid_all.tbl CDD cd18215 cd18215 349524 BTB_POZ_ZBTB27-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in B-cell lymphoma 6 proteins, BCL-6 and BCL-6B. This family includes B-cell lymphoma 6 proteins, BCL-6 and BCL-6B. BCL-6 is a transcriptional repressor mainly required for germinal center (GC) formation and antibody affinity maturation, which have different mechanisms of action specific to the lineage and biological functions. BCL-6B is a sequence-specific transcriptional repressor in association with BCL-6. It may function in a narrow stage or be related to some events in the early B-cell development. Family members contain a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 113 matched cddid_all.tbl CDD cd18216 cd18216 349525 BTB_POZ_ZBTB29-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in hypermethylated in cancer proteins, Hic-1 and Hic-2. The family includes hypermethylated in cancer proteins, Hic-1 and Hic-2. Hic-1 is a sequence-specific transcriptional repressor that recognizes and binds to the consensus sequence '5-[CG]NG[CG]GGGCA[CA]CC-3'. Hic-2 is a homolog of tumor suppressor Hic-1 that functions as a transcriptional regulator. Family members contain a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 118 matched cddid_all.tbl CDD cd18217 cd18217 349526 BTB_POZ_ZBTB31_myoneurin BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in myoneurin. Myoneurin, also called zinc finger and BTB domain-containing protein 31 (ZBTB31), is a novel member of the BTB/POZ-zinc finger family highly expressed in the neuromuscular system and is associated with neuromuscular junctions during the late embryonic period. It may function as a synaptic gene regulator. Myoneurin contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 111 matched cddid_all.tbl CDD cd18218 cd18218 349527 BTB_POZ_ZBTB32_FAZF_TZFP BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 32 (ZBTB32). ZBTB32 is also called FANCC-interacting protein, fanconi anemia zinc finger protein (FAZF), testis zinc finger protein (TZFP), or zinc finger protein 538 (ZNF538). It is a DNA-binding transcription factor that binds to the 5'-TGTACAGTGT-3' core sequence. It acts as a transcription suppressor that controls T cell-mediated autoimmunity. ZBTB32 is essential for down-regulation of GATA3 via ZPO2; this promotes aggressive breast cancer development. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 110 matched cddid_all.tbl CDD cd18219 cd18219 349528 BTB_POZ_ZBTB33_KAISO BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kaiso. Kaiso, also called zinc finger and BTB domain-containing protein 33 (ZBTB33), is a DNA methylation-dependent transcriptional repressor that binds to methylated CpG dinucleotides in the consensus sequence 5'-CGCG-3'. It also binds to the non-methylated consensus sequence 5'-CTGCNA-3', also known as the consensus kaiso binding site (KBS). It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 106 matched cddid_all.tbl CDD cd18220 cd18220 349529 BTB_POZ_ZBTB34 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 34 (ZBTB34). ZBTB34 acts as a transcriptional regulator. It downregulates specificity protein (Sp) transcription factors Sp1, Sp3, and Sp4 in pancreatic cancer cells. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 120 matched cddid_all.tbl CDD cd18221 cd18221 349530 BTB_POZ_ZBTB35_ZNF131 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger protein 131 (ZNF131). ZNF131, also called zinc finger and BTB domain-containing protein 35 (ZBTB35), is a transcriptional activator implicated as a regulator of Kaiso-mediated biological processes. It regulates cell growth of developing and mature T cells. It inhibits estrogen signaling by suppressing estrogen receptor alpha homo-dimerization, and plays a role in breast cancer cell proliferation. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 113 matched cddid_all.tbl CDD cd18222 cd18222 349531 BTB_POZ_ZBTB37 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 37 (ZBTB37). ZBTB37 may be involved in transcriptional regulation. It is differentially expressed in aryl hydrocarbon receptor (AhR)-KO mice compared with WT mice, and may potentially contribute to the aging phenotype of AhR-KO mice. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 123 matched cddid_all.tbl CDD cd18223 cd18223 349532 BTB_POZ_ZBTB38_CIBZ BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 38 (ZBTB38). ZBTB38, also termed CIBZ, is a transcriptional regulator with bimodal DNA-binding specificity. It binds with a higher affinity to methylated CpG dinucleotides in the consensus sequence 5'-CGCG-3', as well as E-box elements (5'-CACGTG-3'). It can also bind specifically to a single methyl-CpG pair. ZBTB38 represses transcription in a methyl-CpG-dependent manner. It is a negative regulator of endoplasmic reticulum stress-associated apoptosis. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 114 matched cddid_all.tbl CDD cd18224 cd18224 349533 BTB_POZ_ZBTB39 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 39 (ZBTB39). ZBTB39 may be involved in transcriptional regulation. Its specific function is as yet unknown. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 123 matched cddid_all.tbl CDD cd18225 cd18225 349534 BTB_POZ_ZBTB40 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 40 (ZBTB40). ZBTB40 may be involved in transcriptional regulation. Single-nucleotide polymorphisms of ZBTB40 are associated with bone mineral density in European and East-Asian populations. ZBTB40 contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 116 matched cddid_all.tbl CDD cd18226 cd18226 349535 BTB_POZ_ZBTB41 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 41 (ZBTB41). ZBTB41, also called FRBZ1, may be involved in transcriptional regulation. Its specific function is as yet unknown. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 114 matched cddid_all.tbl CDD cd18227 cd18227 349536 BTB_POZ_ZBTB43 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 43 (ZBTB43). ZBTB43, also called zinc finger and BTB domain-containing protein 22B (ZBTB22b), zinc finger protein 297B (ZNF297B), or ZnF-x, may be involved in transcriptional regulation. It interacts with BDP1, a subunit of transcription factor IIIB (TFIIIB). Since BDP1 is essential in Pol III transcription, ZBTB43 may also regulate these transcriptional pathways. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 121 matched cddid_all.tbl CDD cd18228 cd18228 349537 BTB_POZ_ZBTB44 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 44 (ZBTB44). ZBTB44, also called BTB/POZ domain-containing protein 15 (BTBD15) or zinc finger protein 851 (ZNF851), may be involved in transcriptional regulation. Single-nucleotide polymorphisms of ZBTB44 showed a suggestive association with disease progression of Crohn's disease. ZBTB44 has also preferentially been recognized by sera of patients with peripheral T-cell lymphoma (PTCL). It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 126 matched cddid_all.tbl CDD cd18229 cd18229 349538 BTB_POZ_ZBTB45 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 45 (ZBTB45). ZBTB45, also called zinc finger protein 499 (ZNF499), may act as a transcriptional regulator that is essential for proper glial differentiation of neural and oligodendrocyte progenitor cells. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 112 matched cddid_all.tbl CDD cd18230 cd18230 349539 BTB_POZ_ZBTB46 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 46 (ZBTB46). ZBTB46 is also called BTB-ZF protein expressed in effector lymphocytes (BZEL), BTB/POZ domain-containing protein 4 (BTBD4), or zinc finger protein 340 (ZNF340). It is a conventional dendritic cell (cDC) lineage specific transcription factor that acts as a negative regulator required to prevent activation of classical dendritic cells in the steady state. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 125 matched cddid_all.tbl CDD cd18231 cd18231 349540 BTB_POZ_ZBTB47_ZNF651 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 47 (ZBTB47). ZBTB47, also called zinc finger protein 651 (ZNF651), is a paralog of ZNF652, a novel zinc-finger transcriptional repressor. It interacts with CBFA2T3 via its carboxy-terminal proline-rich region. CBFA2T3-ZNF651 functions as a transcriptional co-repressor complex. ZBTB47 contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 115 matched cddid_all.tbl CDD cd18232 cd18232 349541 BTB_POZ_ZBTB48_TZAP_KR3 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in telomere zinc finger-associated protein (TZAP). TZAP is also called Krueppel-related zinc finger protein 3 (KR3), zinc finger and BTB domain-containing protein 48 (ZBTB48), or zinc finger protein 855 (ZNF855). It is a vertebrate telomere-binding protein involved in telomere length control. It directly binds the telomeric double-stranded 5'-TTAGGG-3' repeat. TZAP also acts as a transcription regulator that binds to promoter regions. It is a transcriptional activator of alternate reading frame (ARF) gene. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 108 matched cddid_all.tbl CDD cd18233 cd18233 349542 BTB_POZ_ZBTB49 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 49 (ZBTB49). ZBTB49, also called zinc finger protein 509 (ZNF509), is a transcription factor that inhibits cell proliferation by activating either CDKN1A/p21 transcription or RB1 transcription. There are four ZNF509 isoforms generated by alternative splicing. Short ZNF509 (ZNF509S1, -S2 and -S3) isoforms contain one or two out of the seven zinc-fingers contained in long ZNF509 (ZNF509L). ZBTB49 contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 112 matched cddid_all.tbl CDD cd18234 cd18234 349543 BTB_POZ_KLHL1-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like proteins KLHL1, KLHL4 and KLHL5. This family contains the Kelch-like proteins: KLHL1, KLHL4 and KLHL5, all of which share high identity and similarity with the Drosophila kelch protein, a component of ring canals. KLHL1 is a neuronal actin-binding protein that modulates voltage-gated CaV2.1 (P/Q-type) and CaV3.2 (alpha1H T-type) calcium channels. Family members contain a BTB domain and kelch repeat domains, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 105 matched cddid_all.tbl CDD cd18235 cd18235 349544 BTB_POZ_KLHL2-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like proteins, KLHL2 and KLHL3. The family includes Kelch-like proteins, KLHL2 and KLHL3. KLHL2 is a novel actin-binding protein predominantly expressed in brain. It plays a role in the reorganization of the actin cytoskeleton, and promotes growth of cell projections in oligodendrocyte precursors. KLHL2 and KLHL3 each functions as a component of an E3 ubiquitin ligase complex that mediates the ubiquitination of target proteins. They contain a BTB domain and kelch repeat domains, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 121 matched cddid_all.tbl CDD cd18236 cd18236 349545 BTB_POZ_KLHL6 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 6 (KLHL6). KLHL6 is a BTB-kelch protein with a lymphoid tissue-restricted expression pattern. It is involved in B-lymphocyte antigen receptor signaling and germinal center formation. It belongs to the KLHL gene family, which is composed of an N-terminal BTB-POZ domain and four to six Kelch motifs in tandem. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 129 matched cddid_all.tbl CDD cd18237 cd18237 349546 BTB_POZ_KLHL7 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 7 (KLHL7). KLHL7 is a component of a Cul3-based E3 ubiquitin ligase complex and is involved in the ubiquitination of target proteins for proteasome-mediated degradation. Mutations in KLHL7 causes autosomal-dominant retinitis pigmentosa. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 126 matched cddid_all.tbl CDD cd18238 cd18238 349547 BTB_POZ_KLHL8 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 8 (KLHL8). KLHL8 is a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex required for the ubiquitination and degradation of rapsyn, a postsynaptic protein required for clustering of nicotinic acetylcholine receptors (nAChRs) at the neuromuscular junction. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 120 matched cddid_all.tbl CDD cd18239 cd18239 349548 BTB_POZ_KLHL9_13 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like proteins KLHL9 and KLHL13. KLHL9 and KLHL13 (also called BTB and kelch domain-containing protein 2, or BKLHD2) are substrate-specific adaptors of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex required for mitotic progression and cytokinesis. The BCR(KLHL9-KLHL13) E3 ubiquitin ligase complex mediates the ubiquitination of AURKB and controls the dynamic behavior of AURKB on mitotic chromosomes, thereby coordinating faithful mitotic progression and completion of cytokinesis. They contain a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 128 matched cddid_all.tbl CDD cd18240 cd18240 349549 BTB_POZ_KLHL10 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 10 (KLHL10). KLHL10 is a substrate-specific adaptor of a CUL3-based E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins specifically in the testis during spermatogenesis. Haploinsufficiency of Klhl10 causes infertility in male mice. KLHL10 contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 120 matched cddid_all.tbl CDD cd18241 cd18241 349550 BTB_POZ_KLHL11 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 11 (KLHL11). KLHL11 is a component of a cullin-RING-based BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex that mediates the ubiquitination of target proteins, leading most often to their proteasomal degradation. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 135 matched cddid_all.tbl CDD cd18242 cd18242 349551 BTB_POZ_KLHL12_C3IP1_DKIR BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 12 (KLHL12). KLHL12, also called CUL3-interacting protein 1 (C3IP1) or DKIR homolog, is a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex that acts as a negative regulator of the Wnt signaling pathway and ER-Golgi transport. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 124 matched cddid_all.tbl CDD cd18243 cd18243 349552 BTB_POZ_KLHL14_printor BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 14 (KLHL14). KLHL14 is also called protein interactor of Torsin-1A (TOR1A), protein interactor of torsinA, or Printor. It is a novel torsinA-interacting protein that preferentially interacts with ATP-free form of TOR1A and is implicated in dystonia pathogenesis. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 130 matched cddid_all.tbl CDD cd18244 cd18244 349553 BTB_POZ_KLHL15 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 15 (KLHL15). KLHL15 is a substrate-specific adaptor for the Cullin3 E3 ubiquitin-protein ligase complex that targets the serine/threonine-protein phosphatase 2A (PP2A) subunit PPP2R5B for ubiquitination and subsequent proteasomal degradation, thus promoting exchange with other regulatory subunits. It also plays a key role in DNA damage response, favoring DNA double-strand repair through error-prone non-homologous end joining (NHEJ) over error-free, RBBP8-mediated homologous recombination (HR), by targeting the DNA-end resection factor RBBP8/CtIP for ubiquitination and subsequent proteasomal degradation. KLHL15 contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 137 matched cddid_all.tbl CDD cd18245 cd18245 349554 BTB_POZ_KLHL16_gigaxonin BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in gigaxonin. Gigaxonin, also called Kelch-like protein 16 (KLHL16), may be a cytoskeletal component that directly or indirectly plays an important role in neurofilament architecture. It may also act as a substrate-specific adaptor of an E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins, including tubulin folding cofactor B (TBCB), microtubule-associated protein MAP1B, and glial fibrillary acidic protein (GFAP). Gigaxonin is mutated in giant axonal neuropathy. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 111 matched cddid_all.tbl CDD cd18246 cd18246 349555 BTB_POZ_KLHL17_actinfilin BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 17 (KLHL17). KLHL17, also called actinfilin, is a substrate-recognition component of some cullin-RING-based BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complexes. It acts as a Cullin 3 (Cul3) substrate adaptor that links GLUR6 to the E3 ubiquitin-ligase complex, and mediates the ubiquitination and subsequent degradation of GLUR6. It may play a role in actin-based neuronal function. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 139 matched cddid_all.tbl CDD cd18247 cd18247 349556 BTB_POZ_KLHL18 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 18 (KLHL18). KLHL18 acts as a substrate-specific adaptor for a Cullin3 E3 ubiquitin-protein ligase complex that regulates mitotic entry and ubiquitylates Aurora-A. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 116 matched cddid_all.tbl CDD cd18248 cd18248 349557 BTB_POZ_KLHL19_KEAP1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like ECH-associated protein 1 (KEAP1). KEAP1, also called cytosolic inhibitor of Nrf2 (INrf2) or Kelch-like protein 19 (KLHL19), is a redox-regulated substrate adaptor protein for a Cullin3-dependent ubiquitin ligase complex that targets NFE2L2/NRF2 for ubiquitination and degradation by the proteasome, thus resulting in the suppression of its transcriptional activity and the repression of antioxidant response element-mediated detoxifying enzyme gene expression. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 124 matched cddid_all.tbl CDD cd18249 cd18249 349558 BTB_POZ_KLHL20_KLEIP BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 20 (KLHL20). KLHL20, also called Kelch-like ECT2-interacting protein (KLEIP) or Kelch-like protein X, is a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex involved in interferon response and anterograde Golgi to endosome transport. KLHL20 plays a role in actin assembly at cell-cell contact sites of Madin-Darby canine kidney cells. It also controls endothelial migration and sprouting angiogenesis. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 128 matched cddid_all.tbl CDD cd18250 cd18250 349559 BTB_POZ_KLHL21 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 21 (KLHL21). KLHL21 is a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex required for efficient chromosome alignment and cytokinesis. The BCR(KLHL21) E3 ubiquitin ligase complex regulates localization of the chromosomal passenger complex (CPC) from chromosomes to the spindle midzone in anaphase and mediates the ubiquitination of aurora B. KLHL21 also targets IkappaB kinase-beta to regulate nuclear factor kappa-light chain enhancer of activated B cells (NF-kappaB) signaling negatively. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 124 matched cddid_all.tbl CDD cd18251 cd18251 349560 BTB_POZ_KLHL22 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 22 (KLHL22). KLHL22 is a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex required for chromosome alignment and localization of polo-like kinase 1 (PLK1) at kinetochores. The BCR(KLHL22) ubiquitin ligase complex mediates mono-ubiquitination of PLK1, leading to PLK1 dissociation from phosphoreceptor proteins and subsequent removal from kinetochores, allowing silencing of the spindle assembly checkpoint (SAC) and chromosome segregation. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 125 matched cddid_all.tbl CDD cd18252 cd18252 349561 BTB_POZ_KLHL23 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 23 (KLHL23). KLHL23 overexpression is associated with increased cell proliferation and invasion in gastric cancer. Downregulation of KLHL23 is associated with invasion, metastasis, and poor prognosis of hepatocellular carcinoma and pancreatic cancer. KLHL23 contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 127 matched cddid_all.tbl CDD cd18253 cd18253 349562 BTB_POZ_KLHL24_KRIP6 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 24 (KLHL24). KLHL24, also called kainate receptor-interacting protein for GluR6 (KRIP6) or protein DRE1, is necessary to maintain the balance between intermediate filament stability and degradation, a process that is essential for skin integrity. KLHL24 is a component of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex that mediates ubiquitination of KRT14 and controls its levels during keratinocyte differentiation. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 121 matched cddid_all.tbl CDD cd18254 cd18254 349563 BTB_POZ_KLHL25 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 25 (KLHL25). KLHL25, also called ectoderm-neural cortex protein 2 (ENC-2), is a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex that is required for translational homeostasis. The BCR(KLHL25) ubiquitin ligase complex acts by mediating ubiquitination of hypophosphorylated EIF4EBP1 (4E-BP1). Cullin3-KLHL25 ubiquitin ligase also targets ATP-citrate lyase (ACLY), a key enzyme for lipid synthesis, for degradation to inhibit lipid synthesis and tumor progression. KLHL25 contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 128 matched cddid_all.tbl CDD cd18255 cd18255 349564 BTB_POZ_KLHL26 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 26 (KLHL26). KLHL26 is encoded by the klhl26 gene, which is regulated by p53 via fuzzy tandem repeats. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 121 matched cddid_all.tbl CDD cd18256 cd18256 349565 BTB_POZ_KLHL27_IPP BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in intracisternal A particle-promoted polypeptide (IPP). IPP, also called Kelch-like protein 27 (KLHL27) or actin-binding protein IPP, is an actin-binding protein that may play a role in organizing the actin cytoskeleton. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 125 matched cddid_all.tbl CDD cd18257 cd18257 349566 BTB_POZ_KLHL28_BTBD5 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 28 (KLHL28). KLHL28, also called BTB/POZ domain-containing protein 5 (BTBD5), contains a BTB domain and kelch repeats, characteristics of a kelch family protein. Its function remains unclear. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 118 matched cddid_all.tbl CDD cd18258 cd18258 349567 BTB_POZ_KLHL29_KBTBD9 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 29 (KLHL29). KLHL29 is also called Kelch repeat and BTB domain-containing protein 9 (KBTBD9). A novel fusion transcript NR5A2-KLHL29FT, resulting from transchromosomal insertion, may influence the origin or progression of colon cancer. KLHL29 contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 125 matched cddid_all.tbl CDD cd18259 cd18259 349568 BTB_POZ_KLHL30 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 30 (KLHL30). KLHL30 contains a BTB domain and kelch repeats, characteristics of a kelch family protein. Its function remains unclear. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 137 matched cddid_all.tbl CDD cd18260 cd18260 349569 BTB_POZ_KLHL31_KBTBD1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 31 (KLHL31). KLHL31 is also called BTB and kelch domain-containing protein 6 (BKLHD6), Kelch repeat and BTB domain-containing protein 1 (KBTBD1), or Kelch-like protein KLHL. It is a transcriptional repressor in the MAPK/JNK signaling pathway to regulate cellular functions. Overexpression inhibits the transcriptional activities of both the TPA-response element (TRE) and serum response element (SRE). It is also a novel modulator of canonical Wnt signaling, which is important for vertebrate myogenesis. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. Its function remains unclear. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 120 matched cddid_all.tbl CDD cd18261 cd18261 349570 BTB_POZ_KLHL32 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 32 (KLHL32). KLHL32, also called BTB and kelch domain-containing protein 5 (BKLHD5), contains a BTB domain and kelch repeats, characteristics of a kelch family protein. Its function remains unclear. Deletion of KLHL32 may be ssociated with Tourette syndrome and obsessive-compulsive disorder. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 133 matched cddid_all.tbl CDD cd18262 cd18262 349571 BTB1_POZ_KLHL33 first BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 33 (KLHL33). KLHL33 contains BTB domains and kelch repeats, characteristics of a kelch family protein. Its function remains unclear. KLHL33 gene expression in normal and tumor tissue suggest a significant association with prostate cancer risk. KLHL33 contains two BTB domains. This model corresponds to the first BTB domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 101 matched cddid_all.tbl CDD cd18263 cd18263 349572 BTB2_POZ_KLHL33 second BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 33 (KLHL33). KLHL33 contains BTB domains and kelch repeats, characteristics of a kelch family protein. Its function remains unclear. KLHL33 gene expression in normal and tumor tissue suggest a significant association with prostate cancer risk. KLHL33 contains two BTB domains. This model corresponds to the second BTB domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 118 matched cddid_all.tbl CDD cd18264 cd18264 349573 BTB_POZ_KLHL34 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 34 (KLHL34). KLHL34 contains a BTB domain and kelch repeats, characteristics of a kelch family protein. Its function remains unclear. The methylation status of KLHL34 cg14232291 appears to be predictive of pathologic response to preoperative chemoradiation therapy in rectal cancer patients. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 136 matched cddid_all.tbl CDD cd18265 cd18265 349574 BTB_POZ_KLHL35 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 35 (KLHL35). KLHL35 contains a BTB domain and kelch repeats, characteristics of a kelch family protein. Its function remains unclear. Significant differences in DNA methylation of the KLHL35 gene in abdominal aortic aneurysm (AAA) patients compared to non-AAA controls suggest a potential role in AAA pathology. Hypermethylation of the KLHL35 gene has also been associated with the development of hepatocellular carcinoma. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 128 matched cddid_all.tbl CDD cd18266 cd18266 349575 BTB_POZ_KLHL36 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 36 (KLHL36). KLHL36 may act as a substrate-specific adaptor of an E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 135 matched cddid_all.tbl CDD cd18267 cd18267 349576 BTB_POZ_KLHL37_ENC1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Ectoderm-neural cortex protein 1 (ENC-1). ENC-1 is also called Kelch-like protein 37 (KLHL37), nuclear matrix protein NRP/B, or p53-induced gene 10 protein. It is an actin-binding nuclear matrix protein that associates with p110(RB), and is involved in the regulation of neuronal process formation and in differentiation of neural crest cells. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 147 matched cddid_all.tbl CDD cd18268 cd18268 349577 BTB_POZ_KLHL38 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 38 (KLHL38). KLHL38 contains a BTB domain and kelch repeats, characteristics of a kelch family protein. Its function remains unclear. The KLHL38 gene is significantly up-regulated during diapause, a temporary arrest of development during early ontogeny. It may also function in preadipocyte differentiation in the chicken. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 129 matched cddid_all.tbl CDD cd18269 cd18269 349578 BTB_POZ_KLHL40-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like proteins, KLHL40 and KLHL41. This family includes Kelch-like proteins, KLHL40 and KLHL41. KLHL40 is a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex that acts as a key regulator of skeletal muscle development. KLHL41 is a novel kelch related protein that is involved in pseudopod elongation in transformed cells. They both contain a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 133 matched cddid_all.tbl CDD cd18270 cd18270 349579 BTB_POZ_KBTBD2_BKLHD1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch repeat and BTB domain-containing protein 2 (KBTBD2). KBTBD2, also called BTB and kelch domain-containing protein 1 (BKLHD1), plays an essential role in the regulation of insulin-signaling pathway. It is a BTB-Kelch family substrate recognition subunit of the Cullin-3-based E3 ubiquitin ligase, which targets p85alpha, the regulatory subunit of the phosphoinositol-3-kinase (PI3K) heterodimer, causing p85alpha ubiquitination and proteasome-mediated degradation. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 133 matched cddid_all.tbl CDD cd18271 cd18271 349580 BTB_POZ_KBTBD3_BKLHD3 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch repeat and BTB domain-containing protein 3 (KBTBD3). KBTBD3, also called BTB and kelch domain-containing protein 3 (BKLHD3), contains a BTB domain and kelch repeats, characteristics of a kelch family protein. Its function remains unclear. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 130 matched cddid_all.tbl CDD cd18272 cd18272 349581 BTB_POZ_KBTBD4 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch repeat and BTB domain-containing protein 4 (KBTBD4). KBTBD4, also called BTB and kelch domain-containing protein 4 (BKLHD4), is a BTB-BACK-Kelch domain protein belonging to a large family of cullin-RING ubiquitin ligase adaptors that facilitate the ubiquitination of target substrates. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 140 matched cddid_all.tbl CDD cd18273 cd18273 349582 BTB_POZ_KBTBD6_7 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch repeat and BTB domain-containing proteins KBTBD6 and KBTBD7. KBTBD6 and KBTBD7 are substrate adaptors of a cullin-3 RING ubiquitin ligase complex that mediates ubiquitylation and proteasomal degradation of T-lymphoma and metastasis gene 1 (TIAM1), a RAC1-specific guanine exchange factor (GEF), by cooperating with gamma-aminobutyric acid receptor-associated proteins (GABARAP). KBTBD7 may also act as a new transcriptional activator in mitogen-activated protein kinase (MAPK) signaling. They both contain a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 142 matched cddid_all.tbl CDD cd18274 cd18274 349583 BTB_POZ_KBTBD8 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch repeat and BTB domain-containing protein 8 (KBTBD8). KBTBD8, also called T-cell activation kelch repeat protein (TA-KRP), is a BTB-kelch family protein that is located in the Golgi apparatus and translocates to the spindle apparatus during mitosis. It acts as a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex that acts as a regulator of neural crest specification. The BCR(KBTBD8) complex monoubiquitylates NOLC1 and its paralog TCOF1, the mutation of which underlies the neurocristopathy Treacher Collins syndrome. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 129 matched cddid_all.tbl CDD cd18275 cd18275 349584 BTB_POZ_KBTBD11 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch repeat and BTB domain-containing protein 11 (KBTBD11). KBTBD11 is also called chronic myelogenous leukemia-associated protein (CMLAP) or Kelch domain-containing protein 7B, or KLHDC7C. It is a BTB-Kelch family protein whose function remains unclear. A novel polymorphism rs11777210 in KBTBD11 is significantly associated with colorectal cancer risk. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 104 matched cddid_all.tbl CDD cd18276 cd18276 349585 BTB_POZ_KBTBD12 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch repeat and BTB domain-containing protein 12 (KBTBD12). KBTBD12, also called Kelch domain-containing protein 6 (KLHDC6), contains a BTB domain and kelch repeats, characteristics of a kelch family protein. Its function remains unclear. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 127 matched cddid_all.tbl CDD cd18277 cd18277 349586 BTB_POZ_BACH1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB and CNC homolog 1 (BACH1). BACH1, also called BTB-basic leucine zipper transcription factor 1, belongs to the cap 'n' collar (CNC) and basic leucine zipper (bZIP) factor family. It can act as repressor or activator. BACH1 is a heme-responsive transcriptional repressor of heme oxygenase (HO)-1. It represses genes involved in heme metabolism and oxidative stress response. It is also a negative regulator of nuclear factor erythroid 2-related factor 2 (Nrf2) that controls antioxidant response elements (ARE)-dependent gene expressions. BACH1 binds to NF-E2 binding sites in vitro, and plays important roles in coordinating transcription activation and repression by MafK. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 120 matched cddid_all.tbl CDD cd18278 cd18278 349587 BTB_POZ_BACH2 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB and CNC homolog 2 (BACH2). BACH2, also called BTB-basic leucine zipper transcription factor 2, belongs to the cap 'n' collar (CNC) and basic leucine zipper (bZIP) factor family. BACH2 is a lymphoid-specific transcription factor with a prominent role in B-cell development. It is transcriptionally regulated by the BCR/ABL oncogene. It represses the anti-apoptotic factor heme oxygenase-1 (HO-1). It is also a potent general repressor of effector differentiation in naive T cells. Moreover, BACH2 is required for pulmonary surfactant homeostasis and alveolar macrophage function. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 124 matched cddid_all.tbl CDD cd18279 cd18279 349588 BTB_POZ_SPOP-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in speckle-type POZ protein (SPOP) and similar proteins. This family includes speckle-type POZ protein (SPOP), speckle-type POZ protein-like (SPOPL), TD and POZ domain-containing proteins (TDPOZ), Drosophila melanogaster protein roadkill and similar proteins. Both, SPOP and SPOPL, serve as adaptors of cullin-RING-based BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complexes that mediate the ubiquitination and proteasomal degradation of target proteins. TDPOZ is a family of bipartite animal and plant proteins that contain a tumor necrosis factor receptor-associated factor (TRAF) domain (TD) and a POZ/BTB domains. TDPOZ proteins may be nuclear scaffold proteins probably involved in transcription regulation in early development and other cellular processes. Drosophila melanogaster protein roadkill, also called Hh-induced MATH and BTB domain-containing protein (HIB), is a hedgehog-induced BTB protein that modulates hedgehog signaling by degrading Ci/Gli transcription factor. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 120 matched cddid_all.tbl CDD cd18280 cd18280 349589 BTB_POZ_BPM_plant BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in plant BTB/POZ-MATH (BPM) protein family. The BPM protein family includes Arabidopsis thaliana BTB/POZ and MATH domain-containing proteins, AtBPM1-6, and similar proteins from other plants. BPM protein, also called protein BTB-POZ and MATH domain, may act as a substrate-specific adaptor of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 121 matched cddid_all.tbl CDD cd18281 cd18281 349590 BTB_POZ_BTBD1_2 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB/POZ domain-containing proteins, BTBD1 and BTBD2. This family includes BTB/POZ domain-containing proteins BTBD1 and BTBD2, both of which are BTB-domain-containing Kelch-like proteins that interact with DNA topoisomerase 1 (Topo1), a key enzyme of cell survival. BTBD1 and BTBD2 colocalize to cytoplasmic bodies with the RBCC/tripartite motif protein, TRIM5delta. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 127 matched cddid_all.tbl CDD cd18282 cd18282 349591 BTB_POZ_BTBD3_6 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB/POZ domain-containing proteins, BTBD3 and BTBD6. This family includes BTB/POZ domain-containing proteins BTBD3 and BTBD6, both of which are BTB-domain-containing Kelch-like proteins. BTBD3 controls dendrite orientation toward active axons in mammalian neocortex. BTBD6 is required for proper embryogenesis and plays an essential evolutionary conserved role during neuronal development. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 108 matched cddid_all.tbl CDD cd18283 cd18283 349592 BTB1_POZ_BTBD7 first BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB/POZ domain-containing protein 7 (BTBD7). BTBD7 is a crucial regulator that is essential for region-specific epithelial cell dynamics and branching morphogenesis. It has been implicated in various cancers. BTBD7 contains two BTB domains. This model corresponds to the first domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 92 matched cddid_all.tbl CDD cd18284 cd18284 349593 BTB2_POZ_BTBD7 second BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB/POZ domain-containing protein 7 (BTBD7). BTBD7 is a crucial regulator that is essential for region-specific epithelial cell dynamics and branching morphogenesis. It has been implicated in various cancers. BTBD7 contains two BTB domains. This model corresponds to the second domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 146 matched cddid_all.tbl CDD cd18285 cd18285 349594 BTB1_POZ_BTBD8 first BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB/POZ domain-containing protein 8 (BTBD8). BTBD8 is a BTB-domain-containing Kelch-like protein that may play a role in developmental processes. It may also act as a protein-protein adaptor in a transcription complex and thus be involved in brain development. BTBD8 contains two BTB domains. This model corresponds to the first domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 104 matched cddid_all.tbl CDD cd18286 cd18286 349595 BTB2_POZ_BTBD8 second BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB/POZ domain-containing protein 8 (BTBD8). BTBD8 is a BTB-domain-containing Kelch-like protein that may play a role in developmental processes. It may also act as a protein-protein adaptor in a transcription complex and thus be involved in brain development. BTBD8 contains two BTB domains. This model corresponds to the second domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 121 matched cddid_all.tbl CDD cd18287 cd18287 349596 BTB_POZ_BTBD9 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB/POZ domain-containing protein 9 (BTBD9). BTBD9 is a risk factor for Restless Legs Syndrome (RLS) encoding a Cullin-3 substrate adaptor. The BTBD9 gene may be associated with antipsychotic-induced RLS in schizophrenia. Mutations in BTBD9 lead to reduced dopamine, increased locomotion and sleep fragmentation. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 119 matched cddid_all.tbl CDD cd18288 cd18288 349597 BTB_POZ_BTBD12_SLX4 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Structure-specific endonuclease subunit SLX4. SLX4, also called BTB/POZ domain-containing protein 12 (BTBD12), is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases and is required for DNA repair. Mutations of the SLX4 gene are found in Fanconi anemia. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 116 matched cddid_all.tbl CDD cd18289 cd18289 349598 BTB_POZ_BTBD14A_NAC2 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in nucleus accumbens-associated protein 2 (NAC-2). NAC-2, also called BTB/POZ domain-containing protein 14A (BTBD14A) or repressor with BTB domain and BEN domain (RBB), is a novel transcription repressor through its association with the NuRD complex. It recruits the NuRD complex to the promoter of MDM2, leading to the repression of MDM2 transcription and subsequent stability of p53/TP53. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 131 matched cddid_all.tbl CDD cd18290 cd18290 349599 BTB_POZ_BTBD14B_NAC1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in nucleus accumbens-associated protein 1 (NAC-1). NAC-1, also called BTB/POZ domain-containing protein 14B (BTBD14B), is a transcriptional repressor that contributes to tumor progression, tumor cell proliferation, and survival. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 123 matched cddid_all.tbl CDD cd18291 cd18291 349600 BTB_POZ_BTBD16 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB/POZ domain-containing protein 16 (BTBD16). BTBD16 is a BTB domain-containing protein. Its function remains unclear. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 114 matched cddid_all.tbl CDD cd18292 cd18292 349601 BTB_POZ_BTBD17 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB/POZ domain-containing protein 17 (BTBD17). BTBD17, also called galectin-3-binding protein-like, is a BTB domain-containing protein. Its function remains unclear. It may be associated with hepatocellular carcinoma. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 114 matched cddid_all.tbl CDD cd18293 cd18293 349602 BTB_POZ_BTBD18 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB/POZ domain-containing protein 18 (BTBD18). BTBD18 acts as a specific controller for transcription activation through RNA polymerase II elongation at a subset of genomic PIWI-interacting RNA (piRNA) loci. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 120 matched cddid_all.tbl CDD cd18294 cd18294 349603 BTB_POZ_BTBD19 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB/POZ domain-containing protein 19 (BTBD19). BTBD19 is a BTB domain-containing protein. Its function remains unclear. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 111 matched cddid_all.tbl CDD cd18295 cd18295 349604 BTB1_POZ_ABTB1_BPOZ1 first BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Ankyrin repeat and BTB/POZ domain-containing protein 1 (ABTB1). ABTB1, also called elongation factor 1A-binding protein or bood POZ containing gene type 1 (BPOZ-1), is an anti-proliferative factor that may act as a mediator of the phosphatase and tensin homolog (PTEN) growth-suppressive signaling pathway. It may play a role in developmental processes. ABTB1 contains an ankyrin repeat and two BTB domains. This model corresponds to the first BTB domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 119 matched cddid_all.tbl CDD cd18296 cd18296 349605 BTB2_POZ_ABTB1_BPOZ1 second BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Ankyrin repeat and BTB/POZ domain-containing protein 1 (ABTB1). ABTB1, also called elongation factor 1A-binding protein or bood POZ containing gene type 1 (BPOZ-1), is an anti-proliferative factor that may act as a mediator of the phosphatase and tensin homolog (PTEN) growth-suppressive signaling pathway. It may play a role in developmental processes. ABTB1 contains an ankyrin repeat and two BTB domains. This model corresponds to the second BTB domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 121 matched cddid_all.tbl CDD cd18297 cd18297 349606 BTB_POZ_ABTB2-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Ankyrin repeat and BTB/POZ domain-containing protein 2 (ABTB2) and similar proteins. This family includes ABTB2, BTBD11, plant ARM repeat protein interacting with ABF2 (ARIA), and similar proteins. ABTB2, also called bood POZ containing gene type 2 (BPOZ-2), is a scaffold protein that controls the degradation of many biological proteins ranging from embryonic development to tumor progression. It may be involved in the initiation of hepatocyte growth. ABTB2 functions as an adaptor protein for the E3 ubiquitin ligase scaffold protein Cullin-3. It directly binds to eukaryotic elongation factor 1A1 (eEF1A1) to promote eEF1A1 ubiquitylation and degradation, and prevent translation. The BTBD11 gene has been recently identified as an all-trans retinoic acid (atRA)-responsive gene that lies downstream of atRA and its receptors in the regulation of neurite outgrowth and cell adhesion in neural as well as non-neural tissues. ARIA is an armadillo (ARM) repeat and BTB domain-containing protein that acts as a positive regulator of ABA response via the modulation of the transcriptional activity of ABF2. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 117 matched cddid_all.tbl CDD cd18298 cd18298 349607 BTB_POZ_RCBTB1_2 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in RCC1 and BTB domain-containing proteins, RCBTB1 and RCBTB2. The RCC1-related guanine nucleotide exchange factor (GEF) family includes RCC1 and BTB domain-containing proteins, RCBTB1 and RCBTB2, both of which are chromosome condensation regulator-like guanine nucleotide exchange factors. They contain an RCC1 repeat, a BTB domain, and a BACK domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 108 matched cddid_all.tbl CDD cd18299 cd18299 349608 BTB1_POZ_RhoBTB first BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Rho-related BTB domain-containing proteins (RhoBTB). RhoBTB proteins constitute a subfamily of atypical members within the Rho family of small guanosine triphosphatases (GTPases), which is characterized by containing a GTPase domain (in most cases, non-functional) followed by a proline-rich region, tandem BTB domains, and a conserved C-terminal region. In vertebrates, the RhoBTB subfamily consists of 3 isoforms: RhoBTB1, RhoBTB2, and RhoBTB3. Orthologs are present in several other eukaryotes, such as Drosophila and Dictyostelium, but have been lost in plants and fungi. This model corresponds to the first BTB domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 103 matched cddid_all.tbl CDD cd18300 cd18300 349609 BTB2_POZ_RhoBTB second BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Rho-related BTB domain-containing proteins (RhoBTB). RhoBTB proteins constitute a subfamily of atypical members within the Rho family of small guanosine triphosphatases (GTPases), which is characterized by containing a GTPase domain (in most cases, non-functional) followed by a proline-rich region, a tandem of 2 BTB domains, and a conserved C-terminal region. In humans, the RhoBTB subfamily consists of 3 isoforms: RhoBTB1, RhoBTB2, and RhoBTB3. Orthologs are present in several other eukaryotes, such as Drosophila and Dictyostelium, but have been lost in plants and fungi. This model corresponds to the second BTB domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 108 matched cddid_all.tbl CDD cd18301 cd18301 349610 BTB1_POZ_IBtk first BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in inhibitor of Bruton tyrosine kinase (IBtk). IBtk is an inhibitor or negative regulator of Bruton tyrosine kinase (Btk), which is required for B-cell differentiation and development. IBtk binds to the PH domain of Btk and down-regulates the Btk kinase activity. It contains two BTB domains. This model corresponds to the first BTB domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 99 matched cddid_all.tbl CDD cd18302 cd18302 349611 BTB2_POZ_IBtk second BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in inhibitor of Bruton tyrosine kinase (IBtk). IBtk is an inhibitor or negative regulator of Bruton tyrosine kinase (Btk), which is required for B-cell differentiation and development. IBtk binds to the PH domain of Btk and down-regulates the Btk kinase activity. It contains two BTB domains. This model corresponds to the second BTB domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 113 matched cddid_all.tbl CDD cd18303 cd18303 349612 BTB_POZ_Rank-5 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in rabankyrin-5 (Rank-5). Rank-5, also called ankyrin repeat and FYVE domain-containing protein 1 (ANKFY1) or ankyrin repeats hooked to a zinc finger motif (ANKHZN), is a Rab5 effector that regulates and coordinates different endocytic mechanisms. It contains an N-terminal BTB domain, followed by a BACK domain, several ankyrin (ANK) repeats and a C-terminal FYVE domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 120 matched cddid_all.tbl CDD cd18304 cd18304 349613 BTB_POZ_M2BP BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Mac-2-binding protein (MAC2BP/M2BP). M2BP is also called galectin-3-binding protein, basement membrane autoantigen p105, lectin galactoside-binding soluble 3-binding protein (LGALS3BP), or tumor-associated antigen 90K. It promotes integrin-mediated cell adhesion and may stimulate host defense against viruses and tumor cells. It contains a scavenger receptor cysteine-rich domain, followed by BTB and BACK domains. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 114 matched cddid_all.tbl CDD cd18305 cd18305 349614 BTB_POZ_GCL BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Drosophila melanogaster protein germ cell-less (GCL) and similar proteins. GCL proteins are nuclear envelope proteins highly conserved between the mammalian and Drosophila orthologs. Drosophila melanogaster GCL is a key regulator required for the specification of pole cells and primordial germ cell formation in embryos. Both, human germ cell-less protein-like 1 (GMCL1) and germ cell-less protein-like 2 (GMCL2), also called germ cell-less protein-like 1-like (GMCL1P1 or GMCL1L), may function in spermatogenesis. They may also be substrate-specific adaptors of E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. They contain BTB and BACK domains. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 115 matched cddid_all.tbl CDD cd18306 cd18306 349615 BTB_POZ_NS1BP BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Influenza virus NS1A-binding protein (NS1-BP). NS1-BP is also called NS1-binding protein, aryl hydrocarbon receptor-associated protein 3 (ARA3), or IVNS1ABP. It is a novel protein that interacts with the influenza A virus nonstructural NS1 protein, which is relocalized in the nuclei of infected cells. It plays a role in cell division and in the dynamic organization of the actin skeleton as a stabilizer of actin filaments by association with F-actin through its kelch repeats. It also interacts with alpha-enolase/MBP-1 and is involved in c-Myc gene transcriptional control. NS1-BP contains BTB and BACK domains at the N-terminal region and kelch repeats at the C-terminal region. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 124 matched cddid_all.tbl CDD cd18307 cd18307 349616 BTB_POZ_calicin BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in calicin. Calicin is a basic cytoskeletal protein involved in the formation and maintenance of the highly regular organization of the postacrosomal perinuclear theca, the calyx of mammalian spermatozoa. It contains BTB and BACK domains at the N-terminal region and kelch repeats at the C-terminal region. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 97 matched cddid_all.tbl CDD cd18308 cd18308 349617 BTB1_POZ_LZTR1 first BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in leucine-zipper-like transcriptional regulator 1 (LZTR-1). LZTR-1 is a golgi BTB-kelch protein that is degraded upon induction of apoptosis. It may also function as a transcriptional regulator that plays a crucial role in embryogenesis. Germline loss-of-function mutations in LZTR-1 predispose to an inherited disorder of multiple schwannomas. LZTR-1 contains two BTB domains. This model corresponds to the first domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 156 matched cddid_all.tbl CDD cd18309 cd18309 349618 BTB2_POZ_LZTR1 second BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in leucine-zipper-like transcriptional regulator 1 (LZTR-1). LZTR-1 is a golgi BTB-kelch protein that is degraded upon induction of apoptosis. It may also function as a transcriptional regulator that plays a crucial role in embryogenesis. Germline loss-of-function mutations in LZTR-1 predispose to an inherited disorder of multiple schwannomas. LZTR-1 contains two BTB domains. This model corresponds to the second domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 126 matched cddid_all.tbl CDD cd18310 cd18310 349619 BTB_POZ_NPR_plant BTB (Broad-Complex, Tramtrack and Bric a brac) /POZ (poxvirus and zinc finger) domain found in plant regulatory proteins, NPR1-4, and similar proteins. NPR1 and NPR2 are essential for pathogenicity and the utilization of many nitrogen sources. NPR1 is also called nitrogen pathogenicity regulation protein NPR1, non-inducible immunity protein 1 (Nim1), nonexpresser of PR genes 1, or salicylic acid insensitive 1 (Sai1). It acts as a transcription coactivator that plays dual roles in regulating plant immunity. NPR3 and NPR4 are involved in negative regulation of defense responses against pathogens in plant. NPR proteins contain a BTB domain, DUF3420, ankyrin (ANK) repeats, and a conserved C-terminal domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 145 matched cddid_all.tbl CDD cd18311 cd18311 349620 BTB_POZ_CP190-like BTB (Broad-Complex, Tramtrack and Bric a brac) /POZ (poxvirus and zinc finger) domain found in Drosophila melanogaster centrosomal protein 190kD (CP190) and similar proteins. CP190 is a large, multi-domain protein, first identified as a centrosome protein with oscillatory localization over the course of the cell cycle. It has an essential function in the nucleus as a chromatin insulator. It is known to associate with the nuclear matrix, components of the RNAi machinery, active promoters and borders of the repressive chromatin domains. CP190 contains an N-terminal BTB domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 110 matched cddid_all.tbl CDD cd18312 cd18312 349621 BTB_POZ_NPY3-like BTB (Broad-Complex, Tramtrack and Bric a brac) /POZ (poxvirus and zinc finger) domain found in Arabidopsis thaliana protein naked pins in YUC mutants 3 (NPY3), Root phototropism protein 3 (RPT3), and similar proteins. NPY3 may play an essential role in auxin-mediated organogenesis and in root gravitropic responses in Arabidopsis. RPT3 is a signal transducer of the phototropic response and photo-induced movements. It is necessary for root and hypocotyl phototropisms, but not for the regulation of stomata opening. Proteins in this subfamily contain an N-terminal BTB domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 105 matched cddid_all.tbl CDD cd18313 cd18313 349622 BTB_POZ_BT BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Arabidopsis thaliana BTB/POZ and TAZ domain-containing proteins, BT1-5. BT1-5 may act as substrate-specific adaptors of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. They contain a BTB domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 102 matched cddid_all.tbl CDD cd18314 cd18314 349623 BTB_POZ_trishanku-like BTB (Broad-Complex, Tramtrack and Bric a brac) /POZ (poxvirus and zinc finger) domain found in Dictyostelium discoideum trishanku and similar proteins. Trishanku is a novel regulator required for normal morphogenesis and cell-type stability in Dictyostelium discoideum. It contains a BTB domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 96 matched cddid_all.tbl CDD cd18315 cd18315 349624 BTB_POZ_BAB-like BTB (Broad-Complex, Tramtrack and Bric a brac) /POZ (poxvirus and zinc finger) domain found in Drosophila melanogaster proteins bric-a-brac 1 (BAB1), bric-a-brac 2 (BAB2), modifier of mdg4 (doom), and similar proteins. BAB1 and BAB2 probably act as transcriptional regulators that are required for specification of the tarsal segment and are involved in antenna development. Doom is a product of the Drosophila mod(mdg4) gene. It induces apoptosis and binds to baculovirus inhibitor-of-apoptosis proteins. This subfamily also includes Drosophila melanogaster sex determination protein fruitless (FRU), protein jim lovell (LOV), zinc finger protein chinmo, transcription factor GAGA, transcription factor Ken, and longitudinals lacking proteins (LOLA). FRU probably acts as a transcriptional regulator that plays a role in male courtship behavior and sexual orientation, and enhances male-specific expression of takeout in brain-associated fat body. LOV, also called tyrosine kinase-related (TKR), has a regulatory role during midline cell development. Chinmo is a functional effector of the JAK/STAT pathway that regulates eye development, tumor formation, and stem cell self-renewal in Drosophila. GAGA is a transcriptional activator that functions by regulating chromatin structure. Ken, also termed protein Ken and Barbie, is a transcription factor required for Terminalia development. LOLA proteins are putative transcription factors required for axon growth and guidance in the central and peripheral nervous systems. Proteins in this subfamily contain a BTB domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 85 matched cddid_all.tbl CDD cd18316 cd18316 349625 BTB_POZ_KCTD-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing proteins. The potassium channel tetramerization domain (KCTD) family proteins contain the BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD proteins play crucial roles in a variety of fundamental biological processes, such as protein ubiquitination and degradation, suppression of proliferation or transcription, cytoskeleton regulation, tetramerization and gating of ion channels and others. Some KCTD proteins are involved in protein ubiquitination as part of the CRL (Cullin RING Ligase) E3 ligases. Some others show Cullin-independent functions including binding and regulation of GABA (gamma-aminobutyric acid) receptors (KCTD8, KCTD12 and KCTD16) and inhibition of AP-2 function (KCTD15). KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. 83 matched cddid_all.tbl CDD cd18317 cd18317 349626 BTB_POZ_Kv BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in voltage-gated potassium (Kv) channels. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. This family includes several groups of alpha subunits such as KCNA/Kv1 family of Shaker-type Kv channels, KCNB/Kv2 family of Shab-type Kv channels, KCNC/Kv3 family of Shaw-type Kv channels, KCND/Kv4 family of Shal-type Kv channels, KCNF/Kv5 subfamily of Kv channels, KCNG/Kv6 subfamily of Kv channels, KCNV/Kv8 subfamily of Kv channels, and KCNS/Kv9 subfamily of Kv channels. Kv alpha subunits form functional homo- or hetero-tetrameric channels (typically with other alpha subunits from the same subfamily) through their BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. KCNQ/Kv7 channels are not included in this family, since they do not contain a BTB/POZ domain. 82 matched cddid_all.tbl CDD cd18318 cd18318 349627 BTB_POZ_KCTD20-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 20 (KCTD20) and BTB/POZ domain-containing protein 10 (BTBD10). KCTD20, also termed potassium channel tetramerization domain containing 20, is a positive regulator of Akt signaling. It may play an important role in regulating the death and growth of some non-nervous and nervous cells. BTBD10, also termed glucose metabolism-related protein 1 (GMRP1), plays a major role as an activator of AKT family members. It binds to Akt and protein phosphatase 2A (PP2A) and inhibits the PP2A-mediated dephosphorylation of Akt, thereby keeping Akt activated. It also plays a role in preventing motor neuronal death and accelerating the growth of pancreatic beta cells. 92 matched cddid_all.tbl CDD cd18319 cd18319 349628 BTB_POZ_KLHL42 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 42 (KLHL42). KLHL42, also called Cullin-3-binding protein 9 (Ctb9) or Kelch domain-containing protein 5, is a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex required for mitotic progression and cytokinesis. The BCR(KLHL42) E3 ubiquitin ligase complex mediates the ubiquitination and subsequent degradation of katanin (KATNA1). KLHL42 is involved in microtubule dynamics throughout mitosis. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 93 matched cddid_all.tbl CDD cd18320 cd18320 349629 BTB_POZ_KBTBD13 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch repeat and BTB domain-containing protein 13 (KBTBD13). KBTBD13 is a muscle specific protein. Its autosomal dominant mutations may cause Nemaline Myopathy (NEM). KBTBD13 may act as a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex that functions as a muscle specific ubiquitin ligase, and thereby implicating the ubiquitin proteasome pathway in the pathogenesis of KBTBD13-associated NEM. KBTBD13 contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 83 matched cddid_all.tbl CDD cd18321 cd18321 349630 BTB_POZ_EloC BTB (Broad-Complex, Tramtrack and Bric a brac) /POZ (poxvirus and zinc finger) domain found in Elongin-C (EloC) and similar proteins. Elongin-C is also called elongin 15 kDa subunit, RNA polymerase II transcription factor SIII subunit C, SIII p15, or transcription elongation factor B polypeptide 1 (TCEB1). It is a component of SIII (also known as elongin), which is a general transcription elongation factor that increases the RNA polymerase II transcription elongation past template-encoded arresting sites. It forms a regulatory complex with subunit B or elongin-B (BC) that enhances the activity of the transcriptionally active subunit A. The BC complex also functions as an adaptor protein in the proteasomal degradation of target proteins via different E3 ubiquitin ligase complexes, including the von Hippel-Lindau ubiquitination complex CBC (VHL) and the suppressors of cytokine signaling (SOCS) box ubiquitin ligase family. Elongin-C belongs to the BTB/POZ domain family; the domain is a common protein-protein interaction motif of about 100 amino acids. 95 matched cddid_all.tbl CDD cd18322 cd18322 349631 BTB_POZ_SKP1 BTB (Broad-Complex, Tramtrack and Bric a brac) /POZ (poxvirus and zinc finger) domain found in S-phase kinase-associated protein 1 (SKP1) and similar proteins. SKP1 is also called cyclin-A/CDK2-associated protein p19 (p19A), organ of Corti protein 2 (OCP-2), organ of Corti protein II (OCP-II), RNA polymerase II elongation factor-like protein, transcription elongation factor B polypeptide 1-like, or p19skp1. It is an essential component of the SCF (SKP1-CUL1-F-box protein) ubiquitin ligase complex, which mediates the ubiquitination of proteins involved in cell cycle progression, signal transduction and transcription. SKP1 serves as an adaptor protein that links the F-box protein to CUL1. SKP1 and CUL1 are invariant components of all SCF complexes, while F-box proteins are variable substrate binding modules that determine specificity. SKP1 belongs to the BTB/POZ domain family; the domain is a common protein-protein interaction motif of about 100 amino acids. 120 matched cddid_all.tbl CDD cd18323 cd18323 349632 BTB_POZ_ZBTB3 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 3 (ZBTB3). ZBTB3 is a transcription factor essential for cancer cell growth via the regulation of the reactive oxygen species (ROS) detoxification pathway. ZBTB3 contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 128 matched cddid_all.tbl CDD cd18324 cd18324 349633 BTB_POZ_ZBTB18_RP58 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 18 (ZBTB18). ZBTB18 is also called 58 kDa repressor protein (RP58), transcriptional repressor RP58, translin-associated zinc finger protein 1 (TAZ-1), zinc finger protein 238 (ZNF238), or zinc finger protein C2H2-171. It is a sequence-specific transrepressor associated with heterochromatin. It plays a role in various developmental processes such as myogenesis and brain development. It specifically binds the consensus DNA sequence 5'-[AC]ACATCTG[GT][AC]-3' which contains the E box core, and acts by recruiting chromatin remodeling multiprotein complexes. ZBTB18 contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 147 matched cddid_all.tbl CDD cd18325 cd18325 349634 BTB_POZ_ZBTB18_2-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 18.2 and similar proteins. This subfamily is composed of Xenopus laevis zinc finger and BTB domain-containing protein 18.2, encoded by the znf238.2.L gene, and similar proteins. Many proteins in this group are annotated as zinc finger and BTB domain-containing protein 42 (ZBTB42). However, characterized mammalian ZBTB42 does not belong to this subfamily. ZBTB18.2, like ZBTB18, functions as a transcriptional repressor that plays a role in various developmental processes. Members of this family contain a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 128 matched cddid_all.tbl CDD cd18326 cd18326 349635 BTB_POZ_ZBTB7A BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 7A (ZBTB7A). ZBTB7A is also called factor binding IST protein 1 (FBI-1), factor that binds to inducer of short transcripts protein 1, HIV-1 1st-binding protein 1, Leukemia/lymphoma-related factor (LRF), POZ and Krueppel erythroid myeloid ontogenic factor, POK erythroid myeloid ontogenic factor, Pokemon, TTF-I-interacting peptide 21 (TIP21), or zinc finger protein 857A (ZNF857A). It is a transcription repressor of key glycolytic genes, including GLUT3, PFKP, and PKM, and its downregulation in human cancer contributes to tumor metabolism. It has been implicated in carcinogenesis and cell differentiation and development. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 120 matched cddid_all.tbl CDD cd18327 cd18327 349636 BTB_POZ_ZBTB7B_ZBTB15 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 7B (ZBTB7B). ZBTB7B is also called Krueppel-related zinc finger protein cKrox, T-helper-inducing POZ/Krueppel-like factor, zinc finger and BTB domain-containing protein 15 (ZBTB15), zinc finger protein 67 (ZNF67), Zfp67, zinc finger protein 857B (ZNF857B), or zinc finger protein Th-POK. It is a transcriptional regulator of extracellular matrix gene expression. It plays widespread and critical roles in T-cell development, particularly as the master regulator of CD4 commitment. It also plays a role as a potent driver of brown fat development and thermogenesis, as well as cold-induced beige fat formation. ZBTB7B contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 127 matched cddid_all.tbl CDD cd18328 cd18328 349637 BTB_POZ_ZBTB7C_ZBTB36 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 7C (ZBTB7C). ZBTB7C is also called affected by papillomavirus DNA integration in ME180 cells protein 1 (APM-1), zinc finger and BTB domain-containing protein 36 (ZBTB36), zinc finger protein 857C (ZNF857C), or kidney cancer-related POZ domain and Kruppel-like protein (Kr-POK). It is a transcriptional repressor with a pro-oncogenic role that relies upon binding to p53 and inhibition of its transactivation function. It may act as an important regulator of fatty acid synthesis and may induce rapid cancer cell proliferation by increasing palmitate synthesis. The ZBTB7C gene has been identified as a susceptibility gene to ischemic injury. ZBTB7C contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 120 matched cddid_all.tbl CDD cd18329 cd18329 349638 BTB_POZ_ZBTB8A_BOZF1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 8A (ZBTB8A). ZBTB8A, also called BTB/POZ and zinc-finger domain-containing factor or BTB/POZ and zinc-finger domains factor on chromosome 1 (BOZ-F1), is a novel proto-oncoprotein that stimulates cell proliferation. It binds to all the proximal GC boxes to repress transcription, and it inhibits p53 acetylation without affecting p53 stability. It may be involved in gastric adenocarcinoma cell differentiation, cancer invasion, and metastasis. ZBTB8A contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 116 matched cddid_all.tbl CDD cd18330 cd18330 349639 BTB_POZ_ZBTB8B BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 8B (ZBTB8B). ZBTB8B may be involved in transcriptional regulation. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 113 matched cddid_all.tbl CDD cd18331 cd18331 349640 BTB_POZ_ZBTB27_BCL6 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in B-cell lymphoma 6 protein (BCL-6). BCL-6 is also called B-cell lymphoma 5 protein (BCL-5), zinc finger and BTB domain-containing protein 27 (ZBTB27), protein LAZ-3, or zinc finger protein 51 (ZNF51). It is a transcriptional repressor mainly required for germinal center (GC) formation and antibody affinity maturation, which have different mechanisms of action specific to the lineage and biological functions. It represses its target genes by binding directly to the DNA sequence 5'-TTCCTAGAA-3' or indirectly by repressing the transcriptional activity of transcription factors. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 118 matched cddid_all.tbl CDD cd18332 cd18332 349641 BTB_POZ_ZBTB28_BCL6B BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in B-cell CLL/lymphoma 6 member B protein (BCL6B). BCL6B is also called Bcl6-associated zinc finger protein, zinc finger protein 62, or zinc finger and BTB domain-containing protein 28 (ZBTB28). It is a sequence-specific transcriptional repressor in association with BCL-6. It may function in a narrow stage or be related to some events in the early B-cell development. BCL6B plays an important role as a potential tumor suppressor in gastric cancer; it is found preferentially methylated in gastric cancer. It also inhibits both colorectal cancer growth and hepatocellular carcinoma metastases. BCL6B contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 114 matched cddid_all.tbl CDD cd18333 cd18333 349642 BTB_POZ_ZBTB29_HIC1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in hypermethylated in cancer 1 protein (Hic-1). Hic-1, also called zinc finger and BTB domain-containing protein 29 (ZBTB29), is a sequence-specific transcriptional repressor that recognizes and binds to the consensus sequence '5-[CG]NG[CG]GGGCA[CA]CC-3'. It may act as a tumor suppressor, and is involved in regulatory loops modulating P53-dependent and E2F1-dependent cell survival, growth control, and stress responses. It also regulates intestinal immunity and homeostasis. Hic-1 contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 121 matched cddid_all.tbl CDD cd18334 cd18334 349643 BTB_POZ_ZBTB30_HIC2 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in hypermethylated in cancer 2 protein (Hic-2). Hic-2 is also called HIC1-related gene on chromosome 22 protein (HRG22), Hic-3, or zinc finger and BTB domain-containing protein 30 (ZBTB30). It is a homolog of tumor suppressor Hic-1. It functions as a transcriptional regulator. It is a dosage-dependent regulator of cardiac development located within the distal 22q11 deletion syndrome region. Hic-2 contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 120 matched cddid_all.tbl CDD cd18335 cd18335 349644 BTB_POZ_KLHL1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 1 (KLHL1). KLHL1 is a neuronal actin-binding protein that modulates voltage-gated CaV2.1 (P/Q-type) and CaV3.2 (alpha1H T-type) calcium channels. It may play a role in organizing the actin cytoskeleton the brain cells. KLHL1 contains a BTB domain and kelch repeat domains, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 126 matched cddid_all.tbl CDD cd18336 cd18336 349645 BTB_POZ_KLHL4 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 4 (KLHL4). KLHL4 shares high identity and similarity with the Drosophila kelch protein, a component of ring canals. It may be associated with X-linked cleft palate (CPX) and is also a candidate gene in the impairment of mullerian duct development. In addition, it has been identified as a target of insulin-like growth factor binding protein 5 (IGFBP5). KLHL4 contains a BTB domain and kelch repeat domains, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 126 matched cddid_all.tbl CDD cd18337 cd18337 349646 BTB_POZ_KLHL5 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 5 (KLHL5). KLHL5 shares high identity and similarity with the Drosophila kelch protein, a component of ring canals. It is abundantly expressed in the ovary, adrenal gland, and thymus. It contains a BTB domain and kelch repeat domains, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 130 matched cddid_all.tbl CDD cd18338 cd18338 349647 BTB_POZ_KLHL2_Mayven BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 2 (KLHL2). KLHL2, also called actin-binding protein Mayven, is a novel actin-binding protein predominantly expressed in the brain. It plays a role in the reorganization of the actin cytoskeleton, and promotes growth of cell projections in oligodendrocyte precursors. KLHL2 is a component of a cullin-RING-based BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex that mediates the ubiquitination of target proteins, such as NPTXR, leading most often to their proteasomal degradation. It contains a BTB domain and kelch repeat domains, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 121 matched cddid_all.tbl CDD cd18339 cd18339 349648 BTB_POZ_KLHL3 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 3 (KLHL3). KLHL3 is a component of an E3 ubiquitin ligase complex that regulates blood pressure by targeting With-No-Lysine (WNK) kinases for degradation. It contains a BTB domain and kelch repeat domains, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 121 matched cddid_all.tbl CDD cd18340 cd18340 349649 BTB_POZ_KLHL40_KBTBD5 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 40 (KLHL40). KLHL40, also called Kelch repeat and BTB domain-containing protein 5 (KBTBD5) or sarcosynapsin, is a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex that acts as a key regulator of skeletal muscle development. Mutations in KLHL40 may cause severe autosomal-recessive nemaline myopathy. KLHL40 contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 134 matched cddid_all.tbl CDD cd18341 cd18341 349650 BTB_POZ_KLHL41_KBTBD10 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Kelch-like protein 41 (KLHL41). KLHL41 is also called Kel-like protein 23, Kelch repeat and BTB domain-containing protein 10 (KBTBD10), Kelch-related protein 1 (Krp1), or sarcosine. It is a novel kelch-related protein that is involved in pseudopod elongation in transformed cells. It is also involved in skeletal muscle development and differentiation. It regulates proliferation and differentiation of myoblasts and plays a role in myofibril assembly by promoting lateral fusion of adjacent thin fibrils into mature, wide myofibrils. It contains a BTB domain and kelch repeats, characteristics of a kelch family protein. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 133 matched cddid_all.tbl CDD cd18342 cd18342 349651 BTB_POZ_SPOP BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in speckle-type POZ protein (SPOP). SPOP, also called HIB homolog 1 or Roadkill homolog 1, is a novel nuclear speckle-type protein which serves as an adaptor of a cullin-RING-based BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex that mediates the ubiquitination and proteasomal degradation of target proteins, such as BRMS1, DAXX, PDX1/IPF1, GLI2 and GLI3. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 125 matched cddid_all.tbl CDD cd18343 cd18343 349652 BTB_POZ_SPOPL BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in speckle-type POZ protein-like (SPOPL). SPOPL, also called HIB homolog 2 or Roadkill homolog 2, is a component of a cullin-RING-based BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complexes that mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The complexes may contain homodimeric SPOPL or the heterodimers formed by speckle-type POZ protein (SPOP) and SPOPL, which are less efficient than ubiquitin ligase complexes containing only SPOP. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 123 matched cddid_all.tbl CDD cd18344 cd18344 349653 BTB_POZ_TDPOZ "BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in TD and POZ domain-containing proteins (TDPOZ). TDPOZ is a family of bipartite animal and plant proteins that contains a tumor necrosis factor receptor-associated factor (TRAF) domain (TD) and a POZ/BTB domain. TDPOZ proteins may be nuclear scaffold proteins probably involved in transcription regulation in early development and other cellular processes. This subfamily contains only mammalian members. Plant TDPOZ proteins contain a MATH domain at the N-terminal region and are named ""BTB/POZ and MATH domain-containing proteins (BPM)"", not included in this subfamily. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids." 128 matched cddid_all.tbl CDD cd18345 cd18345 349654 BTB_POZ_roadkill-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Drosophila melanogaster protein roadkill and similar proteins. Drosophila melanogaster protein roadkill, also called Hh-induced MATH and BTB domain-containing protein (HIB), is a hedgehog-induced BTB protein that modulates hedgehog signaling by degrading Ci/Gli transcription factor. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 121 matched cddid_all.tbl CDD cd18346 cd18346 349655 BTB_POZ_BTBD1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB/POZ domain-containing protein 1 (BTBD1). BTBD1, also called Hepatitis C virus NS5A-transactivated protein 8 or HCV NS5A-transactivated protein 8, is a BTB-domain-containing Kelch-like protein that is expressed in skeletal muscle and interacts with DNA topoisomerase 1 (Topo1), a key enzyme of cell survival. BTBD1 and BTBD2 colocalize to cytoplasmic bodies with the RBCC/tripartite motif protein, TRIM5delta. BTBD1 may serve as substrate-specific adaptor of an E3 ubiquitin-protein ligase complex that mediates the ubiquitination and subsequent proteasomal degradation of target proteins. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 133 matched cddid_all.tbl CDD cd18347 cd18347 349656 BTB_POZ_BTBD2 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB/POZ domain-containing protein 2 (BTBD2). BTBD2 is a BTB-domain-containing Kelch-like protein that interacts with DNA topoisomerase 1 (Topo1), a key enzyme of cell survival. BTBD1 and BTBD2 colocalize to cytoplasmic bodies with the RBCC/tripartite motif protein, TRIM5delta. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 127 matched cddid_all.tbl CDD cd18348 cd18348 349657 BTB_POZ_BTBD3 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB/POZ domain-containing protein 3 (BTBD3). BTBD3 is a BTB-domain-containing Kelch-like protein that controls dendrite orientation toward active axons in the mammalian neocortex. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 131 matched cddid_all.tbl CDD cd18349 cd18349 349658 BTB_POZ_BTBD6 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB/POZ domain-containing protein 6 (BTBD6). BTBD6, also termed lens BTB domain protein, is a BTB-domain-containing Kelch-like protein required for proper embryogenesis and plays an essential evolutionary conserved role during neuronal development. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 109 matched cddid_all.tbl CDD cd18350 cd18350 349659 BTB_POZ_ABTB2_BPOZ2 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Ankyrin repeat and BTB/POZ domain-containing protein 2 (ABTB2). ABTB2, also called bood POZ containing gene type 2 (BPOZ-2), is a scaffold protein that controls the degradation of many biological proteins with various functions ranging from embryonic development to tumor progression. It may be involved in the initiation of hepatocyte growth. It inhibits the aggregation of alpha-synuclein, with implications for Parkinson's disease. ABTB2 functions as an adaptor protein for the E3 ubiquitin ligase scaffold protein Cullin-3. It directly binds to eukaryotic elongation factor 1A1 (eEF1A1) to promote eEF1A1 ubiquitylation and degradation, and prevent translation. It is also involved in the growth suppressive effect of the phosphatase and tensin homolog (PTEN). It contains an ankyrin repeat, BTB/POZ, and BACK domains. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 134 matched cddid_all.tbl CDD cd18351 cd18351 349660 BTB_POZ_BTBD11 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB/POZ domain-containing protein 11 (BTBD11). BTBD11, also called ankyrin repeat and BTB/POZ domain-containing protein BTBD11, is a BTB-domain-containing protein. The BTBD11 gene has been recently identified as an all-trans retinoic acid (atRA)-responsive gene that lies downstream of atRA and its receptors in the regulation of neurite outgrowth and cell adhesion in neural as well as non-neural tissues. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 131 matched cddid_all.tbl CDD cd18352 cd18352 349661 BTB_POZ_ARIA_plant BTB (Broad-Complex, Tramtrack and Bric a brac) /POZ (poxvirus and zinc finger) domain found in plant ARM repeat protein interacting with ABF2 (ARIA) and similar proteins. ARIA is an armadillo (ARM) repeat and BTB domain-containing protein that acts as a positive regulator of ABA response via the modulation of the transcriptional activity of ABF2, a transcription factor which controls ABA-dependent gene expression via the G-box-type ABA-responsive elements. ARIA is a novel abscisic acid signaling component. It negatively regulates seed germination and young seedling growth. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 116 matched cddid_all.tbl CDD cd18353 cd18353 349662 BTB_POZ_RCBTB1_CLLD7 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in RCC1 and BTB domain-containing protein 1 (RCBTB1). RCBTB1 is also called chronic lymphocytic leukemia deletion region gene 7 protein (CLLD7), CLL deletion region gene 7 protein, regulator of chromosome condensation and BTB domain-containing protein 1, or E4.5. It is a novel chromosome condensation regulator-like guanine nucleotide exchange factor that may be involved in cell cycle regulation by chromatin remodeling. It may also function as a tumor suppressor that regulates pathways of DNA damage/repair and apoptosis. RCBTB1 may also be a substrate adaptor for a cullin3 (CUL3) E3 ligase complex that mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Biallelic mutations in RCBTB1 may cause isolated and syndromic retinal dystrophy. It contains an RCC1 repeat, a BTB domain, and a BACK domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 117 matched cddid_all.tbl CDD cd18354 cd18354 349663 BTB_POZ_RCBTB2_CHC1L BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in RCC1 and BTB domain-containing protein 2 (RCBTB2). RCBTB2 is also called chromosome condensation 1-like (CHC1-L), RCC1-like G exchanging factor, or regulator of chromosome condensation and BTB domain-containing protein 2. It is a chromosome condensation regulator-like guanine nucleotide exchange factor (GEF) protein for the Ras-related GTPase Ran. It contains an RCC1 repeat, a BTB domain, and a BACK domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 117 matched cddid_all.tbl CDD cd18355 cd18355 349664 BTB1_POZ_RHOBTB1 first BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Rho-related BTB domain-containing protein 1 (RhoBTB1). RhoBTB1 is an atypical Rho family small guanosine triphosphatase (GTPase) and is a member of the RhoBTB subfamily, which is characterized by containing a GTPase domain (in most cases, non-functional) followed by a proline-rich region, tandem BTB domains, and a conserved C-terminal region. The carboxyl terminal extension that harbors two BTB domains is capable of assembling cullin 3-dependent ubiquitin ligase complexes. RhoBTB1 functions as a tumor suppressor that regulates the integrity of the Golgi complex through the methyltransferase METTL7B. It also acts an adaptor of the Cullin-3-dependent E3 ubiquitin ligase complex. This model corresponds to the first BTB domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 146 matched cddid_all.tbl CDD cd18356 cd18356 349665 BTB1_POZ_RHOBTB2 first BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Rho-related BTB domain-containing protein 2 (RhoBTB2). RhoBTB2, also called Deleted in breast cancer 2 gene protein (DBC2) or p83, is an atypical Rho family small guanosine triphosphatase (GTPase) and is a member of the RhoBTB subfamily, which is characterized by containing a GTPase domain (in most cases, non-functional) followed by a proline-rich region, tandem BTB domains, and a conserved C-terminal region. The carboxyl terminal extension that harbors two BTB domains is capable of assembling cullin 3-dependent ubiquitin ligase complexes. RhoBTB2 functions as a tumor suppressor that regulates the expression of the methyltransferase METTL7A. It also acts an adaptor of the Cullin-3-dependent E3 ubiquitin ligase complex. This model corresponds to the first BTB domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 148 matched cddid_all.tbl CDD cd18357 cd18357 349666 BTB1_POZ_RHOBTB3 first BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Rho-related BTB domain-containing protein 3 (RhoBTB3). RhoBTB3 is an atypical Rho family small guanosine triphosphatase (GTPase) and is a member of the RhoBTB subfamily, which is characterized by containing a GTPase domain (in most cases, non-functional) followed by a proline-rich region, tandem BTB domains, and a conserved C-terminal region. The carboxyl terminal extension that harbors two BTB domains is capable of assembling cullin 3-dependent ubiquitin ligase complexes. RhoBTB3 is a Golgi-associated Rho-related ATPase that regulates the S/G2 transition of the cell cycle by targeting cyclin E for ubiquitylation. It is involved in vesicle trafficking and in targeting proteins for degradation in the proteasome. It binds directly to Rab9 GTPase and functions with Rab9 in protein transport from endosomes to the trans Golgi network. It also promotes proteasomal degradation of Hypoxia-inducible factor alpha (HIFalpha) through facilitating hydroxylation and suppresses the Warburg effect. This model corresponds to the first BTB domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 159 matched cddid_all.tbl CDD cd18358 cd18358 349667 BTB2_POZ_RHOBTB1 second BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Rho-related BTB domain-containing protein 1 (RhoBTB1). RhoBTB1 is an atypical Rho family small guanosine triphosphatase (GTPase) and is a member of the RhoBTB subfamily, which is characterized by containing a GTPase domain (in most cases, non-functional) followed by a proline-rich region, tandem BTB domains, and a conserved C-terminal region. The carboxyl terminal extension that harbors two BTB domains is capable of assembling cullin 3-dependent ubiquitin ligase complexes. RhoBTB1 functions as a tumor suppressor that regulates the integrity of the Golgi complex through the methyltransferase METTL7B. It also acts an adaptor of the Cullin-3-dependent E3 ubiquitin ligase complex. This model corresponds to the second BTB domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 126 matched cddid_all.tbl CDD cd18359 cd18359 349668 BTB2_POZ_RHOBTB2 second BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Rho-related BTB domain-containing protein 2 (RhoBTB2). RhoBTB2, also called Deleted in breast cancer 2 gene protein (DBC2) or p83, is an atypical Rho family small guanosine triphosphatase (GTPase) and is a member of the RhoBTB subfamily, which is characterized by containing a GTPase domain (in most cases, non-functional) followed by a proline-rich region, tandem BTB domains, and a conserved C-terminal region. The carboxyl terminal extension that harbors two BTB domains is capable of assembling cullin 3-dependent ubiquitin ligase complexes. RhoBTB2 functions as a tumor suppressor that regulates the expression of the methyltransferase METTL7A. It also acts an adaptor of the Cullin-3-dependent E3 ubiquitin ligase complex. This model corresponds to the second BTB domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 124 matched cddid_all.tbl CDD cd18360 cd18360 349669 BTB2_POZ_RHOBTB3 second BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Rho-related BTB domain-containing protein 3 (RhoBTB3). RhoBTB3 is an atypical Rho family small guanosine triphosphatase (GTPase) and is a member of the RhoBTB subfamily, which is characterized by containing a GTPase domain (in most cases, non-functional) followed by a proline-rich region, tandem BTB domains, and a conserved C-terminal region. The carboxyl terminal extension that harbors two BTB domains is capable of assembling cullin 3-dependent ubiquitin ligase complexes. RhoBTB3 is a Golgi-associated Rho-related ATPase that regulates the S/G2 transition of the cell cycle by targeting cyclin E for ubiquitylation. It is involved in vesicle trafficking and in targeting proteins for degradation in the proteasome. It binds directly to Rab9 GTPase and functions with Rab9 in protein transport from endosomes to the trans Golgi network. It also promotes proteasomal degradation of Hypoxia-inducible factor alpha (HIFalpha) through facilitating hydroxylation and suppresses the Warburg effect. This model corresponds to the second BTB domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 110 matched cddid_all.tbl CDD cd18361 cd18361 349670 BTB_POZ_KCTD1-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing proteins, KCTD1 and KCTD15. This subfamily of KCTD proteins includes KCTD1 and KCTD15. KCTD1 is a nuclear BTB/POZ domain-containing protein that acts as a transcriptional repressor and mediates protein-protein interactions through a BTB domain. It represses the transcriptional activity of AP-2 family members, including TFAP2A, TFAP2B and TFAP2C. It also functions as a novel inhibitor of the Wnt signaling pathway. Mutations in KCTD1 cause scalp-ear-nipple (SEN) syndrome. KCTD15 is a BTB/POZ domain-containing protein that plays a role in the regulation of neural crest (NC) formation and other steps in embryonic development. It inhibits AP2 transcriptional activity by interaction with its activation domain. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. The KCTD1 BTB domains form pentamers. 94 matched cddid_all.tbl CDD cd18362 cd18362 349671 BTB_POZ_KCTD2-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing proteins KCTD2, KCTD5, and KCTD17, and similar proteins. This subfamily includes potassium channel tetramerization domain-containing proteins KCTD2, KCTD5, and KCTD17, all of which function as adaptors of Cullin3 based ubiquitin E3 ubiquitin ligases. KCTD2 suppresses gliomagenesis by destabilizing c-Myc. KCTD5 is a negative regulator of the AKT pathway, a key signaling cascade frequently deregulated in cancer. KCTD5 does not impact the operation of Kv4.2, Kv3.4, Kv2.1, or Kv1.2 channels. KCTD17 polyubiquitylates trichoplein, a protein involved in ciliogenesis down-regulation. It is a positive regulator of ciliogenesis, playing a crucial role in the initial steps of axoneme extension. A missense mutation in KCTD17 causes autosomal dominant myoclonus-dystonia (M-D). The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. KCTD5 and KCTD17 BTB domains form pentamer structures. 85 matched cddid_all.tbl CDD cd18363 cd18363 349672 BTB_POZ_KCTD3-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 3 (KCTD3) and SH3KBP1-binding protein 1 (SHKBP1). The group of KCTD proteins includes KCTD3 and SHKBP1. KCTD3, also called renal carcinoma antigen NY-REN-45, is a BTB/POZ domain-containing protein that is an accessory subunit of potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3 (HCN3), upregulating its cell-surface expression and current density without affecting its voltage dependence and kinetics. SHKBP1, also called SETA-binding protein 1, interacts with cathepsin B and participates in tumor necrosis factor (TNF)-induced apoptosis in ovarian cancer cells. It can promote epidermal growth factor receptor (EGFR) signaling by interrupting c-Cbl-CIN85 complex and inhibiting EGFR degradation. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. 86 matched cddid_all.tbl CDD cd18364 cd18364 349673 BTB_POZ_KCTD4 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 4 (KCTD4). KCTD4 is a BTB/POZ domain-containing protein with an unknown biological function. KCTD proteins play crucial roles in a variety of fundamental biological processes, such as protein ubiquitination and degradation, suppression of proliferation or transcription, cytoskeleton regulation, tetramerization and gating of ion channels and others. Some KCTD proteins are involved in protein ubiquitination as part of the CRL (Cullin RING Ligase) E3 ligases. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. 86 matched cddid_all.tbl CDD cd18365 cd18365 349674 BTB_POZ_KCTD6_like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing proteins, KCTD6, KCTD21 and similar proteins. KCTD6, also called KCASH3 (KCTD containing, Cullin3 adaptor, suppressor of Hedgehog 3), is a substrate-specific adaptor of cullin-3, effectively regulating protein levels of the muscle small ankyrin-1 isoform 5 (sAnk1.5). KCTD21, also called KCASH2, functions as a substrate-specific adaptor of cullin-3, promoting the ubiquitination and degradation of histone deacetylase HDAC1, thereby inhibiting the deacetylation-mediated transcriptional activation of the Hedgehog effectors Gli1 and Gli2. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. 94 matched cddid_all.tbl CDD cd18366 cd18366 349675 BTB_POZ_KCTD7 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 7 (KCTD7). KCTD7 is a BTB/POZ domain-containing protein that has an impact on K+ fluxes, neurotransmitter synthesis, and neuronal function. It functions as a regulator of potassium conductance in neurons, and is involved in the control of excitability of cortical neurons. Mutations in KCTD7 may cause progressive myoclonus epilepsy (PME). The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. 92 matched cddid_all.tbl CDD cd18367 cd18367 349676 BTB_POZ_KCTD8-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing proteins, KCTD8, KCTD12, KCTD16 and similar proteins. This subfamily of KCTD proteins includes KCTD8, KCTD12 (also called predominantly fetal expressed T1 domain/Pfetin), and KCTD16. They act as auxiliary subunits of GABAB receptors associated with mood disorders. KCTD8 interacts as a tetramer with GABRB1 and GABRB2. KCTD12 regulates agonist potency and kinetics of GABAB receptor signaling. It promotes tumorigenesis by facilitating CDC25B/CDK1/Aurora A-dependent G2/M transition. KCTD16 interacts with amyloid beta precursor protein (APP), a type I transmembrane protein involved in a variety of cellular processes such as cell adhesion, and axon guidance. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. 100 matched cddid_all.tbl CDD cd18368 cd18368 349677 BTB_POZ_KCTD9 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 9 (KCTD9). KCTD9 is a BTB/POZ domain-containing protein that contributes to liver injury through NK cell activation during hepatitis B virus-induced acute-on-chronic liver failure. It functions as a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex, which mediates the ubiquitination of target proteins, leading to their degradation by the proteasome. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. The KCTD9 BTB domain forms a pentameric structure. 100 matched cddid_all.tbl CDD cd18369 cd18369 349678 BTB_POZ_KCTD10-like_BACURD BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing proteins, KCTD10 (BACURD3), KCTD13 (BACURD1), and TNFAIP1 (BACURD2). This subfamily of KCTD proteins, also called the BTB/POZ domain-containing adapter for CUL3-mediated RhoA degradation protein (BACURD) subfamily, includes KCTD10 (BACURD3), KCTD13 (BACURD1), and TNFAIP1 (BACURD2). KCTD10 is a BTB/POZ domain-containing protein that interacts with proliferating cell nuclear antigen (PCNA) and polymerase delta, and participates in DNA repair, DNA replication, and cell-cycle control. Its down-regulation could inhibit cell proliferation. KCTD10 also plays crucial roles in embryonic angiogenesis and heart development in mammals by negatively regulating the Notch signaling pathway. KCTD13 is a BTB/POZ domain-containing protein that may function as a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex that mediates the ubiquitination of RhoA, leading to its degradation by the proteasome, thereby regulating the actin cytoskeleton and cell migration. TNFAIP1, also called protein B12, is a BTB/POZ domain-containing protein that is involved in DNA replication, DNA damage repair, cell apoptosis, and is implicated in human diseases including cancer, Alzheimer's disease (AD) and type 2 diabetic nephropathy. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. KCTD10 and KCTD13 BTB domains form a novel two-fold symmetric tetramer that is distinct from the tetramer formed by voltage-gated potassium (Kv) channels. 91 matched cddid_all.tbl CDD cd18370 cd18370 349679 BTB_POZ_KCTD11 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein KCTD11. KCTD11 may function as an antagonist of the Hedgehog pathway of cell proliferation and differentiation by affecting the nuclear transfer of transcription factor GLI1, thus maintaining cerebellar granule cells in the undifferentiated state. It is a probable substrate-specific adapter for a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex towards HDAC1. It contains a BTB/POZ domain; in some cases the domain may be truncated. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. Variants of the human/mouse KCTD11 appear to contain truncated BTB/POZ domains. 88 matched cddid_all.tbl CDD cd18371 cd18371 349680 BTB_POZ_KCTD14 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 14 (KCTD14). KCTD14 is a BTB/POZ domain-containing protein with unknown biological function. KCTD proteins play crucial roles in a variety of fundamental biological processes, such as protein ubiquitination and degradation, suppression of proliferation or transcription, cytoskeleton regulation, tetramerization and gating of ion channels and others. Some KCTD proteins are involved in protein ubiquitination as part of the CRL (Cullin RING Ligase) E3 ligases. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. 99 matched cddid_all.tbl CDD cd18372 cd18372 349681 BTB_POZ_KCTD18 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 18 (KCTD18). KCTD18 is a BTB/POZ domain-containing protein with with unknown biological function. A duplication of the KCTD18 gene has been found in a patient with epilepsy, developmental delay, and autistic behavior, which may contribute to the phenotype. KCTD proteins play crucial roles in a variety of fundamental biological processes, such as protein ubiquitination and degradation, suppression of proliferation or transcription, cytoskeleton regulation, tetramerization and gating of ion channels and others. Some KCTD proteins are involved in protein ubiquitination as part of the CRL (Cullin RING Ligase) E3 ligases. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. 101 matched cddid_all.tbl CDD cd18373 cd18373 349682 BTB1_POZ_KCTD19 first BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 19 (KCTD19). KCTD19 is a BTB/POZ domain-containing protein with unclear biological function. It may be a host factor involved in Nef-induced downregulation of MHC-I. Nef is a HIV-1-encoded protein that plays a key role in the development of AIDS. KCTD19 contains two BTB domains. This model corresponds to the first domain. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. 98 matched cddid_all.tbl CDD cd18374 cd18374 349683 BTB2_POZ_KCTD19 second BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 19 (KCTD19). KCTD19 is a BTB/POZ domain-containing protein with unclear biological function. It may be a host factor involved in Nef-induced downregulation of MHC-I. Nef is a HIV-1-encoded protein that plays a key role in the development of AIDS. KCTD19 contains two BTB domains. This model corresponds to the second domain. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. 99 matched cddid_all.tbl CDD cd18375 cd18375 349684 BTB_POZ_KCNRG BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel regulatory protein (KCNRG). KCNRG, also called potassium channel regulator or protein CLLD4, is an endoplasmic reticulum (ER)-associated tumor suppressor that regulates Kv1 family potassium channel proteins by retaining a fraction of the channels in endomembranes. It contains a BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. 97 matched cddid_all.tbl CDD cd18376 cd18376 349685 BTB_POZ_FIP2-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Arabidopsis thaliana FH protein interacting protein FIP2 and similar proteins. FIP2 may act as a substrate-specific adaptor of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. It contains a BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. 89 matched cddid_all.tbl CDD cd18377 cd18377 349686 BTB_POZ_Kv1_KCNA BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in KCNA/Kv1 subfamily of Shaker-type voltage-dependent potassium channels. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. The potassium voltage-gated channel subfamily Kv1, also known as subfamily A, contains eight alpha subunit members, Kv1.1 (KCNA1), Kv1.2 (KCNA2), Kv1.3 (KCNA3), Kv1.4 (KCNA4), Kv1.5 (KCNA5), Kv1.6 (KCNA6), Kv1.7 (KCNA7), and Kv1.8 (KCNA10), which are orthologs of the Shaker gene in Drosophila. They are delayed rectifiers except for Kv1.4 (KCNA4), which is an A-type potassium channel. Delayed rectifiers are slow opening and closing voltage-gated potassium channels. Because of their delayed activation kinetics, they play an important role in controlling action potential duration. A-type channels are fast/rapidly inactivating potassium channels. Kv1/KCNA subfamily alpha subunits form functional homo- or hetero-tetrameric channels (with other Kv1/KCNA alpha subunits) through their BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 85 matched cddid_all.tbl CDD cd18378 cd18378 349687 BTB_POZ_Kv2_KCNB BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in KCNB/Kv2 subfamily of Shab-type voltage-dependent potassium channels. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. The potassium voltage-gated channel subfamily Kv3, also known as subfamily C, contains two alpha subunit members, Kv2.1 (KCNB1) and Kv2.2 (KCNB2), which are orthologs of the Shab gene in Drosophila. They are delayed-rectifier potassium currents in various neurons, although their physiological roles often remain elusive. Kv2/KCNB subfamily alpha subunits form functional homo- or hetero-tetrameric channels (with other alpha subunits) through their BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 109 matched cddid_all.tbl CDD cd18379 cd18379 349688 BTB_POZ_Kv3_KCNC BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in KCNC/Kv3 subfamily of Shaw-type voltage-dependent potassium channels. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. The potassium voltage-gated channel subfamily Kv3, also known as subfamily C, contains four alpha subunit members, Kv3.1 (KCNC1), Kv3.2 (KCNC2), Kv3.3 (KCNC3), and Kv3.4 (KCNC4), which are orthologs of the Shaw gene in Drosophila. Unlike other Kv subfamilies, Kv3 channels typically open only at positive potentials and both, activation and deactivation, in response to changes in voltage are very rapid. They are uniquely associated with the ability of certain neurons to fire action potentials and to release neurotransmitter at high rates of up to 1,000 Hz. Kv3/KCNC subfamily alpha subunits form functional homo- or hetero-tetrameric channels (with other alpha subunits) through their BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 109 matched cddid_all.tbl CDD cd18380 cd18380 349689 BTB_POZ_Kv4_KCND BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in KCND/Kv4 subfamily of Shal-type voltage-dependent potassium channels. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. The potassium voltage-gated channel subfamily Kv4, also known as subfamily D, contains three alpha subunit members, Kv4.1 (KCND1), Kv4.2 (KCND2), and Kv4.3 (KCND3), which are orthologs of the Shal gene in Drosophila. They are A-type potassium channels that mediate the native, fast inactivating (A-type) K+ current (IA) described both in the nervous system (A currents) and the heart (transient outward current). Kv4/KCND subfamily alpha subunits form functional homo- or hetero-tetrameric channels through their BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. They are modulated by cytoplasmic KChIPs/KCNIPs (Kv-channel interacting proteins), which are small calcium binding proteins with EF-hand-like domains. 102 matched cddid_all.tbl CDD cd18381 cd18381 349690 BTB_POZ_Kv5_KCNF1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in KCNF/Kv5 subfamily of potassium voltage-gated channels. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. The potassium voltage-gated channel subfamily Kv5, also known as subfamily F, only contains KCNF1 (also known as Kv5.1 or kH1), which functions as a regulatory alpha-subunit of voltage-gated potassium channel that when coassembled with Kv2.1 can modulate gating in a physiologically relevant manner. It forms hetero-tetrameric channels (with other alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 116 matched cddid_all.tbl CDD cd18382 cd18382 349691 BTB_POZ_Kv6_KCNG BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in KCNG/Kv6 subfamily of potassium voltage-gated channels. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. The potassium voltage-gated channel subfamily Kv6, also known as subfamily G, includes KCNG1 (Kv6.1), KCNG2 (Kv6.2 or KCNF2), KCNG3 (Kv6.3) and KCNG4 (Kv6.4), which are regulatory alpha subunits and do not form functional channels on their own. KCNG1 can form functional heterotetrameric channels with KCNB1 (also known as Kv2.1), and further modulates the delayed rectifier voltage-gated potassium channel activation and deactivation rates of KCNB1. KCNG2, also called cardiac potassium channel subunit, can form functional heterodimeric channels with KCNB1, and further modulates channel activity by shifting the threshold and the half-maximal activation to more negative values. KCNG3, also called voltage-gated potassium channel subunit Kv10.1, is an electrically silent modulatory subunit that can form functional heterotetrameric channels with KCNB1, and further promotes a reduction in the rate of activation and inactivation of the delayed rectifier voltage-gated potassium channel KCNB1. KCNG4 is a silent voltage-gated potassium (KvS) channel subunit that can form functional heterotetrameric channels with KCNB1, and further modulates the delayed rectifier voltage-gated potassium channel activation and deactivation rates of KCNB1. 109 matched cddid_all.tbl CDD cd18384 cd18384 349692 BTB_POZ_Kv9_KCNS BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in KCNS/Kv9 subfamily of potassium voltage-gated channels. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. The potassium voltage-gated channel subfamily Kv9, also known as subfamily S, includes KCNS1 (Kv9.1), KCNS2 (Kv9.2) and KCNS3 (Kv9.3). They are regulatory alpha subunits that cannot form functional homo-tetrameric channels. Both KCNS1 and KCNS2 are delayed-rectifier K(+) channel alpha subunits that can form functional heterotetrameric channels with KCNB1 (also known as Kv2.1) and KCNB2 (also known as Kv2.2), and further modulates the delayed rectifier voltage-gated potassium channel activation and deactivation rates of KCNB1 and KCNB2. KCNS3 is a delayed-rectifier K(+) channel alpha subunit linked to tissue oxygenation responses. It can form functional heterotetrameric channels with KCNB1, and further modulates the delayed rectifier voltage-gated potassium channel activation and deactivation rates of KCNB1. 106 matched cddid_all.tbl CDD cd18385 cd18385 349693 BTB_POZ_BTBD10_GMRP1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB/POZ domain-containing protein 10 (BTBD10). BTBD10, also called glucose metabolism-related protein 1 (GMRP1), plays a major role as an activator of AKT family members. It binds to Akt and protein phosphatase 2A (PP2A) and inhibits the PP2A-mediated dephosphorylation of Akt, thereby keeping Akt activated. It also plays a role in preventing motor neuronal death and accelerating the growth of pancreatic beta cells. BTBD10 contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. 110 matched cddid_all.tbl CDD cd18386 cd18386 349694 BTB_POZ_KCTD20 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 20 (KCTD20). KCTD20, also called potassium channel tetramerization domain containing 20, is a positive regulator of Akt signaling. It may play an important role in regulating the death and growth of some non-nervous and nervous cells. It contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. 104 matched cddid_all.tbl CDD cd18387 cd18387 349695 BTB_POZ_KCTD1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 1 (KCTD1). KCTD1 is a nuclear BTB/POZ domain-containing protein that acts as a transcriptional repressor and mediates protein-protein interactions through a BTB domain. It represses the transcriptional activity of AP-2 family members, including TFAP2A, TFAP2B and TFAP2C to various extent. It also functions as a novel inhibitor of the Wnt signaling pathway. Mutations in KCTD1 cause scalp-ear-nipple (SEN) syndrome. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. The KCTD1 BTB domains form pentamers. 105 matched cddid_all.tbl CDD cd18388 cd18388 349696 BTB_POZ_KCTD15 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 15 (KCTD15). KCTD15 is a BTB/POZ domain-containing protein that plays a role in the regulation of neural crest (NC) formation and other steps in embryonic development. It inhibits AP2 transcriptional activity by interaction with its activation domain. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. The KCTD1 BTB domains, closely related to KCTD15, form pentamers. 99 matched cddid_all.tbl CDD cd18389 cd18389 349697 BTB_POZ_KCTD2 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 2 (KCTD2). KCTD2 is a BTB/POZ domain-containing protein that functions as an adaptor of Cullin3 E3 ubiquitin ligase. It suppresses gliomagenesis by destabilizing c-Myc. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. KCTD5 and KCTD17 BTB domain, highly similar to KCTD2, form pentamer structures. 105 matched cddid_all.tbl CDD cd18390 cd18390 349698 BTB_POZ_KCTD5 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 5 (KCTD5). KCTD5 is a BTB/POZ domain-containing protein that functions as a substrate adaptor for cullin3 based ubiquitin E3 ligases. It is a negative regulator of the AKT pathway, a key signaling cascade frequently deregulated in cancer. KCTD5 does not impact the operation of Kv4.2, Kv3.4, Kv2.1, or Kv1.2 channels. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. KCTD5 forms pentamers mediated by its BTB domain. 112 matched cddid_all.tbl CDD cd18391 cd18391 349699 BTB_POZ_KCTD17 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 17 (KCTD17). KCTD17 is a BTB/POZ domain-containing protein that functions as a substrate-adaptor for cullin3-RING ubiquitin ligases that polyubiquitylates trichoplein, a protein involved in ciliogenesis down-regulation. It is a positive regulator of ciliogenesis, playing a crucial role in the initial steps of axoneme extension. A missense mutation in KCTD17 causes autosomal dominant myoclonus-dystonia (M-D). The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. The KCTD17 BTB domains form pentamers. 101 matched cddid_all.tbl CDD cd18392 cd18392 349700 BTB_POZ_KCTD3 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 3 (KCTD3). KCTD3, also called renal carcinoma antigen NY-REN-45, is a BTB/POZ domain-containing protein that is an accessory subunit of potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 3 (HCN3), upregulating its cell-surface expression and current density without affecting its voltage dependence and kinetics. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. 88 matched cddid_all.tbl CDD cd18393 cd18393 349701 BTB_POZ_SHKBP1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in SH3KBP1-binding protein 1 (SHKBP1). SHKBP1, also called SETA-binding protein 1, interacts with cathepsin B and participates in tumor necrosis factor (TNF)-induced apoptosis in ovarian cancer cells. It can promote epidermal growth factor receptor (EGFR) signaling by interrupting c-Cbl-CIN85 complex and inhibiting EGFR degradation. It contains a BTB/POZ domain, also known as tetramerization (T1) domain, a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. 103 matched cddid_all.tbl CDD cd18394 cd18394 349702 BTB_POZ_KCTD6 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 6 (KCTD6). KCTD6, also called KCTD containing, Cullin3 adaptor, suppressor of Hedgehog 3 (KCASH3), is a BTB/POZ domain-containing protein that functions as a substrate-specific adaptor of cullin-3, regulating protein levels of the muscle small ankyrin-1 isoform 5 (sAnk1.5) as well as suppressing histone deacetylase and Hedgehog activity in medulloblastoma. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. 104 matched cddid_all.tbl CDD cd18395 cd18395 349703 BTB_POZ_KCTD21 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 21 (KCTD21). KCTD21, also calledz KCTD containing, Cullin3 adaptor, suppressor of Hedgehog 2 (KCASH2), is a BTB/POZ domain-containing protein that functions as a substrate-specific adaptor of cullin-3, promoting the ubiquitination and degradation of histone deacetylase HDAC1, thereby inhibiting the deacetylation-mediated transcriptional activation of the Hedgehog effectors Gli1 and Gli2. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. 98 matched cddid_all.tbl CDD cd18396 cd18396 349704 BTB_POZ_KCTD8 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein KCTD8. KCTD8, a BTB/POZ domain-containing protein, is an auxiliary subunit of GABA-B receptors that determine the pharmacology and kinetics of the receptor response. It interacts as a tetramer with GABRB1 and GABRB2. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. 103 matched cddid_all.tbl CDD cd18397 cd18397 349705 BTB_POZ_KCTD12_Pfetin BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 12 (KCTD12). KCTD12, also called predominantly fetal expressed T1 domain (Pfetin), is a BTB/POZ domain-containing protein that is an auxiliary subunit of GABAB receptors associated with mood disorders. It regulates agonist potency and kinetics of GABAB receptor signaling. It promotes tumorigenesis by facilitating CDC25B/CDK1/Aurora A-dependent G2/M transition. It also regulates colorectal cancer cell stemness through the ERK pathway. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. 100 matched cddid_all.tbl CDD cd18398 cd18398 349706 BTB_POZ_KCTD16 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 16 (KCTD16). KCTD16 is a BTB/POZ domain-containing protein that is an auxiliary subunit of GABAB receptors associated with mood disorders. It interacts with amyloid beta precursor protein (APP), a type I transmembrane protein involved in a variety of cellular processes such as cell adhesion and axon guidance. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. 103 matched cddid_all.tbl CDD cd18399 cd18399 349707 BTB_POZ_KCTD10_BACURD3 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 10 (KCTD10). KCTD10, also called BTB/POZ domain-containing adapter for CUL3-mediated RhoA degradation protein 3 (BACURD3), is a BTB/POZ domain-containing protein that interacts with proliferating cell nuclear antigen (PCNA) and polymerase delta, and participates in DNA repair, DNA replication, and cell-cycle control. Its down-regulation could inhibit cell proliferation. KCTD10 also plays crucial roles in embryonic angiogenesis and heart development in mammals by negatively regulating the Notch signaling pathway. Furthermore, KCTD10 may function as a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex, which mediates the ubiquitination of target proteins, leading to their degradation by the proteasome. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. The KCTD10 BTB domain forms a novel two-fold symmetric tetramer that is distinct from the tetramer formed by voltage-gated potassium (Kv) channels. 110 matched cddid_all.tbl CDD cd18400 cd18400 349708 BTB_POZ_KCTD13_BACURD1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium channel tetramerization domain-containing protein 13 (KCTD13). KCTD13, also called BTB/POZ domain-containing adapter for CUL3-mediated RhoA degradation protein 1 (BACURD1), or TNFAIP1-like protein, is a BTB/POZ domain-containing protein that may function as a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex that mediates the ubiquitination of RhoA, leading to its degradation by the proteasome, thereby regulating the actin cytoskeleton and cell migration. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. The KCTD13 BTB domain forms a novel two-fold symmetric tetramer that is distinct from the tetramer formed by voltage-gated potassium (Kv) channels. 103 matched cddid_all.tbl CDD cd18401 cd18401 349709 BTB_POZ_TNFAIP1_BACURD2 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in tumor necrosis factor, alpha-induced protein 1, endothelial (TNFAIP1). TNFAIP1, also called BTB/POZ domain-containing adapter for CUL3-mediated RhoA degradation protein 2 (BACURD2), or protein B12, is a BTB/POZ domain-containing protein that is involved in DNA replication, DNA damage repair and cell apoptosis, and is implicated in human diseases including cancer, Alzheimer's disease (AD) and type 2 diabetic nephropathy. The BTB/POZ domain, also known as tetramerization (T1) domain, is a versatile protein-protein interaction motif that facilitates homodimerization or heterodimerization. KCTD family BTB domains can adopt a wide range of oligomerization geometries, including homodimerization, tetramerization, and pentamerization. The BTB domains of other BACURD subfamily members, KCTD10 and KCTD13, form a novel two-fold symmetric tetramer that is distinct from the tetramer formed by voltage-gated potassium (Kv) channels. 104 matched cddid_all.tbl CDD cd18402 cd18402 349710 BTB_POZ_KCNA1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily A member 1 (KCNA1). KCNA1 is also called voltage-gated K(+) channel HuKI, voltage-gated potassium channel HBK1, or voltage-gated potassium channel subunit Kv1.1. It mediates transmembrane potassium transport in excitable membranes, primarily in the brain and the central nervous system, but also in the kidney. It is involved in the regulation of the membrane potential and nerve signaling, and prevents neuronal hyperexcitability. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a tetrameric potassium-selective channel through which potassium ions may pass in accordance with their electrochemical gradient. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCNA1 is an alpha subunit that forms functional homo- or hetero-tetrameric channels (with other Kv1/KCNA alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 98 matched cddid_all.tbl CDD cd18403 cd18403 349711 BTB_POZ_KCNA2_KCNA3 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily A members 2 (KCNA2) and 3 (KCNA3). KCNA2 is also called NGK1, voltage-gated K(+) channel HuKIV, voltage-gated potassium channel HBK5, or voltage-gated potassium channel subunit Kv1.2. KCNA3 is also called HGK5, HLK3, HPCN3, voltage-gated K(+) channel HuKIII, or voltage-gated potassium channel subunit Kv1.3. KCNA2 and KCNA3 mediate transmembrane potassium transport in excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a tetrameric potassium-selective channel through which potassium ions may pass in accordance with their electrochemical gradient. KCNA2 primarily functions in the brain and the central nervous system, but also in the cardiovascular system. It prevents aberrant action potential firing and regulates neuronal output. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCNA2 and KCNA3 are alpha subunits that form functional homo- or hetero-tetrameric channels (with other Kv1/KCNA alpha subunits) through their BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 99 matched cddid_all.tbl CDD cd18405 cd18405 349712 BTB_POZ_KCNA4 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily A member 4 (KCNA4). KCNA4 is also called HPCN2, or voltage-gated K(+) channel HuKII, voltage-gated potassium channel HBK4, voltage-gated potassium channel HK1, or voltage-gated potassium channel subunit Kv1.4. It mediates transmembrane potassium transport in excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a tetrameric potassium-selective channel through which potassium ions may pass in accordance with their electrochemical gradient. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCNA4 is an alpha subunit that forms functional homo- or hetero-tetrameric channels (with other Kv1/KCNA alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 97 matched cddid_all.tbl CDD cd18406 cd18406 349713 BTB_POZ_KCNA5 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily A member 5 (KCNA5). KCNA5, also called HPCN1, voltage-gated potassium channel HK2, or voltage-gated potassium channel subunit Kv1.5, mediates transmembrane potassium transport in excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a tetrameric potassium-selective channel through which potassium ions may pass in accordance with their electrochemical gradient. KCNA5 may play a role in regulating the secretion of insulin in normal pancreatic islets. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCNA5 is an alpha subunit that forms functional homo- or hetero-tetrameric channels (with other Kv1/KCNA alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 97 matched cddid_all.tbl CDD cd18407 cd18407 349714 BTB_POZ_KCNA6 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily A member 6 (KCNA6). KCNA6, also called voltage-gated potassium channel HBK2 or voltage-gated potassium channel subunit Kv1.6, mediates transmembrane potassium transport in excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a tetrameric potassium-selective channel through which potassium ions may pass in accordance with their electrochemical gradient. KCNA6 is distributed primarily in neurons of central and peripheral nervous systems. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCNA6 is an alpha subunit that forms functional homo- or hetero-tetrameric channels (with other Kv1/KCNA alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 127 matched cddid_all.tbl CDD cd18408 cd18408 349715 BTB_POZ_KCNA7 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily A member 7 (KCNA7). KCNA7, also called voltage-gated potassium channel subunit Kv1.7, mediates transmembrane potassium transport in excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a tetrameric potassium-selective channel through which potassium ions may pass in accordance with their electrochemical gradient. KCNA7 plays an important role in the repolarization of cell membranes. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCNA7 is an alpha subunit that forms functional homo- or hetero-tetrameric channels (with other Kv1/KCNA alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 115 matched cddid_all.tbl CDD cd18409 cd18409 349716 BTB_POZ_KCNA10 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily A member 10 (KCNA10). KCNA10, also called voltage-gated potassium channel subunit Kv1.8, is a cyclic nucleotide-gated, voltage-activated potassium channel that mediates transmembrane potassium transport in excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a tetrameric potassium-selective channel through which potassium ions may pass in accordance with their electrochemical gradient. KCNA10 is expressed in proximal tubular cells, glomerular and vascular endothelial cells, as well as in vascular smooth muscle cells. It may facilitate proximal tubular sodium absorption by stabilizing cell membrane voltage. The channel activity is up-regulated by cAMP. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCNA10 is an alpha subunit that forms functional homotetrameric channels through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 87 matched cddid_all.tbl CDD cd18410 cd18410 349717 BTB_POZ_Shaker-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Drosophila melanogaster potassium voltage-gated channel protein Shaker and similar proteins. Shaker, also termed protein minisleep, represents a family of putative potassium channel proteins in the nervous system of Drosophila. It is a voltage-gated potassium channel that mediates transmembrane potassium transport in excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a tetrameric potassium-selective channel through which potassium ions may pass in accordance with their electrochemical gradient. Shaker plays a role in the regulation of sleep need or efficiency. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. Shaker is an alpha subunit that forms functional homo- or hetero-tetrameric channels (with other alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 100 matched cddid_all.tbl CDD cd18411 cd18411 349718 BTB_POZ_KCNB1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily B member 1 (KCNB1). KCNB1, also called delayed rectifier potassium channel 1 (DRK1) or voltage-gated potassium channel subunit Kv2.1, mediates transmembrane potassium transport in excitable membranes, primarily in the brain, but also in the pancreas and cardiovascular system. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a tetrameric potassium-selective channel through which potassium ions may pass in accordance with their electrochemical gradient. KCNB1 is involved in the regulation of the action potential (AP) repolarization, duration and frequency of repetitive AP firing in neurons, muscle cells and endocrine cells and plays a role in homeostatic attenuation of electrical excitability throughout the brain. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCNB1 is an alpha subunit that forms functional homo- or hetero-tetrameric channels (with other alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 117 matched cddid_all.tbl CDD cd18412 cd18412 349719 BTB_POZ_KCNB2 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily B member 2 (KCNB2). KCNB2, also called voltage-gated potassium channel subunit Kv2.2, mediates transmembrane potassium transport in excitable membranes, primarily in the brain and smooth muscle cells. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a tetrameric potassium-selective channel through which potassium ions may pass in accordance with their electrochemical gradient. KCNB2 contributes to the delayed-rectifier voltage-gated potassium current in cortical pyramidal neurons and smooth muscle cells. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCNB2 is an alpha subunit that forms functional homo- or hetero-tetrameric channels (with other alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 127 matched cddid_all.tbl CDD cd18413 cd18413 349720 BTB_POZ_Shab-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Drosophila melanogaster potassium voltage-gated channel protein Shab and similar proteins. Shab is a slow delayed rectifier voltage-gated potassium channel in Drosophila. It mediates transmembrane potassium transport in excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a tetrameric potassium-selective channel through which potassium ions may pass in accordance with their electrochemical gradient. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. Shab is an alpha subunit that forms functional homo- or hetero-tetrameric channels (with other alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 109 matched cddid_all.tbl CDD cd18414 cd18414 349721 BTB_KCNC1_3 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily C members KCNC1 and KCNC3. KCNC1 (also called NGK2, voltage-gated potassium channel subunit Kv3.1, or voltage-gated potassium channel subunit Kv4) and KCNC3 (also called KSHIIID or voltage-gated potassium channel subunit Kv3.3) play important roles in the rapid repolarization of fast-firing brain neurons. Assuming opened or closed conformations in response to the voltage difference across the membrane, the proteins form tetrameric potassium-selective channels through which potassium ions may pass in accordance with their electrochemical gradient. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCNC1 and KCNC3 are alpha subunit that form functional homo- or hetero-tetrameric channels (with other alpha subunits) through their BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 117 matched cddid_all.tbl CDD cd18415 cd18415 349722 BTB_KCNC2_4 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily C members KCNC2 and KCNC4. KCNC2, also called Shaw-like potassium channel or voltage-gated potassium channel Kv3.2, is a delayed rectifier voltage-gated potassium channel that mediates transmembrane potassium transport in excitable membranes, primarily in the brain. It contributes to the regulation of the fast action potential repolarization and in sustained high-frequency firing in neurons of the central nervous system. KCNC4, also called KSHIIIC or voltage-gated potassium channel subunit Kv3.4, is a novel high-voltage-activating, tetraethylammonium (TEA)-sensitive, type-A potassium channel that mediates the voltage-dependent potassium ion permeability of excitable membranes. It plays a pivotal role in oxidative stress-related neural cell damage as an oxidation-sensitive channel. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCNC2 and KCNC4 are alpha subunit that form functional homo- or hetero-tetrameric channels (with other alpha subunits) through their BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 124 matched cddid_all.tbl CDD cd18416 cd18416 349723 BTB_Shaw-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel protein Shaw. Shaw, also called Shaw2, is a voltage-gated potassium channel in Drosophila. It mediates transmembrane potassium transport in excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a tetrameric potassium-selective channel through which potassium ions may pass in accordance with their electrochemical gradient. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. Shaw is an alpha subunit that forms functional homo- or hetero-tetrameric channels (with other alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 112 matched cddid_all.tbl CDD cd18417 cd18417 349724 BTB_POZ_KCND1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily D member 1 (KCND1). KCND1, also called voltage-gated potassium channel subunit Kv4.1, is a pore-forming subunit of voltage-gated rapidly inactivating A-type potassium channels. It may contribute to I (To) current in heart and I (Sa) current in neurons. Its properties are modulated by interactions with other alpha subunits and with regulatory subunits. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCND1 is an alpha subunit that forms functional homo- or hetero-tetrameric channels (with other Kv4/KCND alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. It is modulated by cytoplasmic KChIPs/KCNIPs (Kv-channel interacting proteins), which are small calcium binding proteins with EF-hand-like domains. 138 matched cddid_all.tbl CDD cd18418 cd18418 349725 BTB_POZ_KCND2 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily D member 2 (KCND2). KCND2, also called voltage-gated potassium channel subunit Kv4.2, is a major pore-forming subunit in somatodendritic subthreshold A-type potassium current I(SA) channels. It mediates transmembrane potassium transport in excitable membranes, primarily in the brain. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCND2 is an alpha subunit that forms functional homo- or hetero-tetrameric channels (with other Kv4/KCND alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. It is modulated by cytoplasmic KChIPs/KCNIPs (Kv-channel interacting proteins), which are small calcium binding proteins with EF-hand-like domains. 103 matched cddid_all.tbl CDD cd18419 cd18419 349726 BTB_POZ_KCND3 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily D member 3 (KCND3). KCND3, also called voltage-gated potassium channel subunit Kv4.3, is a pore-forming subunit of voltage-gated rapidly inactivating A-type potassium channels. Mutations in KCND3 cause spinocerebellar ataxia. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCND3 is an alpha subunit that forms functional homo- or hetero-tetrameric channels (with other Kv4/KCND alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. It is modulated by cytoplasmic KChIPs/KCNIPs (Kv-channel interacting proteins), which are small calcium binding proteins with EF-hand-like domains. 138 matched cddid_all.tbl CDD cd18420 cd18420 349727 BTB_POZ_Shal-like BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in Drosophila melanogaster potassium voltage-gated channel protein Shal and similar proteins. Drosophila melanogaster Shal, also called Shaker cognate l or Shal2, is a transient potassium current (I(A)) channel, which is required for maintaining excitability during repetitive firing and normal locomotion in Drosophila. It may play a role in the nervous system and in the regulation of beating frequency in pacemaker cells. Shal mediates the voltage-dependent potassium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a potassium-selective channel through which potassium ions may pass in accordance with their electrochemical gradient. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. Shal is an alpha subunit that forms functional homo- or hetero-tetrameric channels (with other alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 139 matched cddid_all.tbl CDD cd18421 cd18421 349728 BTB_POZ_KCNG1_2 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily G members, KCNG1 and KCNG2. KCNG1, also called voltage-gated potassium channel subunit Kv6.1 or kH2, functions as a regulatory alpha-subunit of voltage-gated potassium channel that can form functional heterotetrameric channels with KCNB1 (also known as Kv2.1), and further modulates the delayed rectifier voltage-gated potassium channel activation and deactivation rates of KCNB1. KCNG2, also called cardiac potassium channel subunit or voltage-gated potassium channel subunit Kv6.2, is a new gamma-subunit of voltage-gated potassium channels that can form functional heterodimeric channels with KCNB1, and further modulates channel activity by shifting the threshold and the half-maximal activation to more negative values. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCNG1 and KCNG2 are regulatory alpha subunits and do not form homomultimers. They form heteromultimers (with other alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 114 matched cddid_all.tbl CDD cd18422 cd18422 349729 BTB_POZ_KCNG3 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily G member 3 (KCNG3). KCNG3, also called voltage-gated potassium channel subunit Kv6.3 or voltage-gated potassium channel subunit Kv10.1, is an electrically silent modulatory subunit that can form functional heterotetrameric channels with KCNB1 (also known as Kv2.1), and further promotes a reduction in the rate of activation and inactivation of the delayed rectifier voltage-gated potassium channel KCNB1. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCNG3 is a regulatory alpha subunit that cannot form a functional homo-tetrameric channel. It forms hetero-tetrameric channels (with other functional alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 111 matched cddid_all.tbl CDD cd18423 cd18423 349730 BTB_POZ_KCNG4 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily G member 4 (KCNG4). KCNG4, also called voltage-gated potassium channel subunit Kv6.4, is a silent voltage-gated potassium (KvS) channel subunit that can form functional heterotetrameric channels with KCNB1 (also known as Kv2.1), and further modulates the delayed rectifier voltage-gated potassium channel activation and deactivation rates of KCNB1. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCNG4 is a regulatory alpha subunit that cannot form a functional homo-tetrameric channel. It forms hetero-tetrameric channels (with other functional alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 112 matched cddid_all.tbl CDD cd18424 cd18424 349731 BTB_POZ_KCNV1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily V member 1 (KCNV1). KCNV1, also called neuronal potassium channel alpha subunit HNKA or voltage-gated potassium channel subunit Kv8.1, is a new neuronal voltage-gated potassium channel alpha subunit with specific inhibitory properties towards Shab and Shaw channels. It modulates KCNB1 (also known as Kv2.1) and KCNB2 (also known as Kv2.2) channel activity by shifting the threshold for inactivation to more negative values and by slowing the rate of inactivation. It can also down-regulate the channel activity of KCNB1, KCNB2, KCNC4 (also known as Kv3.4) and KCND1 (also known as Kv4.1), possibly by trapping them in intracellular membranes. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCNV1 is a regulatory alpha subunit that cannot form a functional homo-tetrameric channel. It forms hetero-tetrameric channels (with other functional alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 109 matched cddid_all.tbl CDD cd18425 cd18425 349732 BTB_POZ_KCNV2 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily V member 2 (KCNV2). KCNV2, also called voltage-gated potassium channel subunit Kv8.2, is a modulatory voltage-gated potassium channel alpha subunit that modulates channel activity by shifting the threshold and the half-maximal activation to more negative values. KCNV2 is essential for visual function and cone survival. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCNV2 is a regulatory alpha subunit that cannot form a functional homo-tetrameric channel. It forms hetero-tetrameric channels (with other functional alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 108 matched cddid_all.tbl CDD cd18426 cd18426 349733 BTB_POZ_KCNS1 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily S member 1 (KCNS1). KCNS1, also called delayed-rectifier K(+) channel alpha subunit 1 or voltage-gated potassium channel subunit Kv9.1, is a modulatory alpha subunit of voltage-gated potassium channel that mediates neuropathic pain following nerve injury. It can form functional heterotetrameric channels with KCNB1 (also known as Kv2.1) and KCNB2 (also known as Kv2.2), and further modulates the delayed rectifier voltage-gated potassium channel activation and deactivation rates of KCNB1 and KCNB2. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCNS1 is a regulatory alpha subunit that cannot form a functional homo-tetrameric channel. It forms hetero-tetrameric channels (with other functional alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 106 matched cddid_all.tbl CDD cd18427 cd18427 349734 BTB_POZ_KCNS2 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily S member 2 (KCNS2). KCNS2, also called delayed-rectifier K(+) channel alpha subunit 2 or voltage-gated potassium channel subunit Kv9.2, is a modulatory alpha subunit of voltage-gated potassium channel that can form functional heterotetrameric channels with KCNB1 (also known as Kv2.1) and KCNB2 (also known as Kv2.2), and further modulates the delayed rectifier voltage-gated potassium channel activation and deactivation rates of KCNB1 and KCNB2. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCNS2 is a regulatory alpha subunit that cannot form a functional homo-tetrameric channel. It forms hetero-tetrameric channels (with other functional alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 107 matched cddid_all.tbl CDD cd18428 cd18428 349735 BTB_POZ_KCNS3 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in potassium voltage-gated channel subfamily S member 3 (KCNS3). KCNS3, also called delayed-rectifier K(+) channel alpha subunit 3 or voltage-gated potassium channel subunit Kv9.3, is an alpha subunit of voltage-gated potassium channel linked to tissue oxygenation responses. It can form functional heterotetrameric channels with KCNB1 (also known as Kv2.1), and further modulates the delayed rectifier voltage-gated potassium channel activation and deactivation rates of KCNB1. Voltage-gated potassium (Kv) channels are composed of alpha subunits, which form the actual conductance pore, and cytoplasmic beta subunits, which are auxiliary proteins that associate with alpha subunits to modulate the activity of the Kv channel. KCNS3 is a regulatory alpha subunit that cannot form a functional homo-tetrameric channel. It forms hetero-tetrameric channels (with other functional alpha subunits) through its BTB/POZ domain, also known as tetramerization (T1) domain, which is a versatile protein-protein interaction motif. 108 matched cddid_all.tbl CDD cd18429 cd18429 349485 M14_Nna1-like Peptidase M14-like domain of ATP/GTP binding proteins and cytosolic carboxypeptidases; uncharacterized bacterial subgroup. A bacterial subgroup of the Peptidase M14-like domain of Nna-1 (Nervous system Nuclear protein induced by Axotomy), also known as ATP/GTP binding protein (AGTPBP-1) and cytosolic carboxypeptidase (CCP),-like proteins. The Peptidase M14 family of metallocarboxypeptidases are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Nna1-like proteins are active metallopeptidases that are thought to act on cytosolic proteins (such as alpha-tubulin in eukaryotes) to remove a C-terminal tyrosine. Nna1-like proteins from the different phyla are highly diverse, but they all contain a unique N-terminal conserved domain right before the CP domain. It has been suggested that this N-terminal domain might act as a folding domain. 253 matched cddid_all.tbl CDD cd18430 cd18430 349486 M14_ASTE_ASPA_like Succinylglutamate desuccinylase/aspartoacylase; uncharacterized. A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD. 168 matched cddid_all.tbl CDD cd18431 cd18431 349384 BRCT_DNA_ligase_III BRCT domain of DNA ligase 3 (LIG3) and similar proteins. LIG3 (EC 6.5.1.1), also termed DNA ligase III, or polydeoxyribonucleotide synthase [ATP] 3, functions as heterodimer with DNA-repair protein XRCC1 in the nucleus and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents. 78 matched cddid_all.tbl CDD cd18432 cd18432 349385 BRCT_PAXIP1_rpt6_like sixth BRCT domain of PAX-interacting protein 1 (PAXIP1), second BRCT domain of mediator of DNA damage checkpoint protein 1 (MDC1) and similar proteins. PAXIP1, also termed PAX transactivation activation domain-interacting protein (PTIP), is involved in DNA damage response and in transcriptional regulation through histone methyltransferase (HMT) complexes. It also facilitates ATM-mediated activation of p53 and promotes cellular resistance to ionizing radiation. PAXIP1 contains six BRCT repeats. MDC1, also termed nuclear factor with BRCT domains 1 (NFBD1), is a nuclear chromatin-associated protein that is required for checkpoint mediated cell cycle arrest in response to DNA damage within both the S phase and G2/M phases of the cell cycle. It directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-strand breaks. MDC1 contains a forkhead-associated (FHA) domain and two BRCT domains, as well as an internal 41-amino acid repeat sequence. The family corresponds to the sixth BRCT domain of PAXIP1 and the second BRCT domain of MDC1. 85 matched cddid_all.tbl CDD cd18433 cd18433 349386 BRCT_Rad4_rpt3 third BRCT domain of Schizosaccharomyces pombe S-M checkpoint control protein Rad4 and similar proteins. Rad4, also termed P74, or protein cut5, is an essential component for DNA replication and the checkpoint control system which couples S and M phases. It may directly or indirectly interact with chromatin proteins to form the complex required for the initiation and/or progression of DNA synthesis. Rad4 contains four BRCT repeats. The family corresponds to the third repeat. 83 matched cddid_all.tbl CDD cd18434 cd18434 349387 BRCT_TopBP1_rpt5 fifth BRCT domain of DNA topoisomerase 2-binding protein 1 (TopBP1) and similar proteins. TopBP1, also termed DNA topoisomerase II-beta-binding protein 1, or DNA topoisomerase II-binding protein 1, functions in DNA replication and damage response. It binds double-stranded DNA breaks and nicks as well as single-stranded DNA. TopBP1 contains six copies of BRCT domain. The family corresponds to the fifth BRCT domain. 89 matched cddid_all.tbl CDD cd18435 cd18435 349388 BRCT_BRC1_like_rpt1 first (N-terminal) BRCT domain of Schizosaccharomyces pombe BRCT-containing protein 1 (BRC1) and similar proteins. Schizosaccharomyces pombe BRC1 is required for mitotic fidelity, specifically in the G2 phase of the cell cycle. It plays a role in chromatin organization. Members in this family contains six BRCT domains. This family corresponds to the fourth repeat. 107 matched cddid_all.tbl CDD cd18436 cd18436 349389 BRCT_BRC1_like_rpt2 second BRCT domain of Schizosaccharomyces pombe BRCT-containing protein 1 (BRC1) and similar proteins. Schizosaccharomyces pombe BRC1 is required for mitotic fidelity, specifically in the G2 phase of the cell cycle. It plays a role in chromatin organization. The family also includes Cryptococcus neoformans DNA ligase 4 (LIG4, also known as DNA ligase IV or polydeoxyribonucleotide synthase [ATP] 4), which is involved in dsDNA break repair, and plays a role in non-homologous integration (NHI) pathways where it is required in the final step of non-homologus end-joining. Members in this family contains six BRCT domains. This family corresponds to the second repeat. 75 matched cddid_all.tbl CDD cd18437 cd18437 349390 BRCT_BRC1_like_rpt3 third BRCT domain of Schizosaccharomyces pombe BRCT-containing protein 1 (BRC1) and similar proteins. Schizosaccharomyces pombe BRC1 is required for mitotic fidelity, specifically in the G2 phase of the cell cycle. It plays a role in chromatin organization. The family also includes Cryptococcus neoformans DNA ligase 4 (LIG4, also known as DNA ligase IV or polydeoxyribonucleotide synthase [ATP] 4), which is involved in dsDNA break repair, and plays a role in non-homologous integration (NHI) pathways where it is required in the final step of non-homologus end-joining. Members in this family contains six BRCT domains. This family corresponds to the third repeat. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this group; it contains a conserved Trp, but not the Cys/Ser residue. 78 matched cddid_all.tbl CDD cd18438 cd18438 349391 BRCT_BRC1_like_rpt4 fourth BRCT domain of Schizosaccharomyces pombe BRCT-containing protein 1 (BRC1) and similar proteins. Schizosaccharomyces pombe BRC1 is required for mitotic fidelity, specifically in the G2 phase of the cell cycle. It plays a role in chromatin organization. Members in this family contains six BRCT domains. This family corresponds to the fourth repeat. 68 matched cddid_all.tbl CDD cd18439 cd18439 349392 BRCT_BRC1_like_rpt6 sixth (C-terminal) BRCT domain of Schizosaccharomyces pombe BRCT-containing protein 1 (BRC1) and similar proteins. Schizosaccharomyces pombe BRC1 is required for mitotic fidelity, specifically in the G2 phase of the cell cycle. It plays a role in chromatin organization. The family also includes Cryptococcus neoformans DNA ligase 4 (LIG4, also known as DNA ligase IV or polydeoxyribonucleotide synthase [ATP] 4), which is involved in dsDNA break repair, and plays a role in non-homologous integration (NHI) pathways where it is required in the final step of non-homologus end-joining. Members in this family contains six BRCT domains. This family corresponds to the sixth repeat. 116 matched cddid_all.tbl CDD cd18440 cd18440 349393 BRCT_PAXIP1_rpt6 sixth BRCT domain of PAX-interacting protein 1 (PAXIP1) and similar proteins. PAXIP1, also termed PAX transactivation activation domain-interacting protein (PTIP), is involved in DNA damage response and in transcriptional regulation through histone methyltransferase (HMT) complexes. It also facilitates ATM-mediated activation of p53 and promotes cellular resistance to ionizing radiation. PAXIP1 contains six BRCT repeats. This family corresponds to the sixth BRCT domain. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family. 90 matched cddid_all.tbl CDD cd18441 cd18441 349394 BRCT_MDC1_rpt2 second BRCT domain of mediator of DNA damage checkpoint protein 1 (MDC1) and similar proteins. MDC1, also termed nuclear factor with BRCT domains 1 (NFBD1), is a nuclear chromatin-associated protein that is required for checkpoint mediated cell cycle arrest in response to DNA damage within both the S phase and G2/M phases of the cell cycle. It directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-strand breaks. MDC1 contains a forkhead-associated (FHA) domain and two BRCT domains, as well as an internal 41-amino acid repeat sequence. The family corresponds to the second BRCT domain. The Trp-X-X-X-Cys/Ser signature motif of the BRCT family is not conserved in this family. 81 matched cddid_all.tbl CDD cd18442 cd18442 349395 BRCT_polymerase_mu BRCT domain of DNA-directed DNA/RNA polymerase mu (polymerase mu) and similar proteins. Polymerase Mu (EC 2.7.7.7), also termed Pol mu, or terminal transferase, is a Gap-filling polymerase involved in repair of DNA double-strand breaks by non-homologous end joining (NHEJ). It participates in immunoglobulin (Ig) light chain gene rearrangement in V(D)J recombination. Polymerase Mu contains a BRCT domain. 98 matched cddid_all.tbl CDD cd18443 cd18443 349396 BRCT_DNTT BRCT domain of DNA nucleotidylexotransferase (DNTT) and similar proteins. DNTT (EC 2.7.7.31), also termed terminal addition enzyme, or terminal deoxynucleotidyltransferase, or terminal transferase, is a template-independent DNA polymerase which catalyzes the random addition of deoxynucleoside 5'-triphosphate to the 3'-end of a DNA initiator. It is the addition of nucleotides at the junction (N region) of rearranged Ig heavy chain and T-cell receptor gene segments during the maturation of B- and T-cells. DNA nucleotidylexotransferase contains a BRCT domain. 95 matched cddid_all.tbl CDD cd18444 cd18444 350519 BACK_KLHL1_like BACK (BTB and C-terminal Kelch) domain found in Kelch-like proteins KLHL1, KLHL4 and KLHL5. This subfamily contains Kelch-like proteins: KLHL1, KLHL4 and KLHL5, all of which share high identity and similarity with the Drosophila kelch protein, a component of ring canals. Members of this subfamily contain a BTB domain and kelch repeat domains, characteristics of a kelch family protein. KLHL1 is a neuronal actin-binding protein that modulates voltage-gated CaV2.1 (P/Q-type) and CaV3.2 (alpha1H T-type) calcium channels. 106 matched cddid_all.tbl CDD cd18445 cd18445 350520 BACK_KLHL2_like BACK (BTB and C-terminal Kelch) domain found in Kelch-like proteins, KLHL2 and KLHL3. This subfamily includes Kelch-like proteins, KLHL2 and KLHL3. KLHL2 is a novel actin-binding protein predominantly expressed in the brain. It plays a role in the reorganization of the actin cytoskeleton, and promotes growth of cell projections in oligodendrocyte precursors. Both KLHL2 and KLHL3 function as a component of an E3 ubiquitin ligase complex that mediates the ubiquitination of target proteins. 114 matched cddid_all.tbl CDD cd18446 cd18446 350521 BACK_KLHL6 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 6 (KLHL6). KLHL6 is a BTB-kelch protein with a lymphoid tissue-restricted expression pattern. It belongs to the KLHL gene family, which is composed of an N-terminal BTB-POZ domain and four to six Kelch motifs in tandem. It is involved in B-lymphocyte antigen receptor signaling and germinal center formation. 108 matched cddid_all.tbl CDD cd18447 cd18447 350522 BACK_KLHL7 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 7 (KLHL7). KLHL7 is a BTB-Kelch protein that constitutes a Cul3-based E3 ubiquitin ligase complex and is involved in the ubiquitination of target proteins for proteasome-mediated degradation. Mutations in KLHL7 cause autosomal-dominant retinitis pigmentosa. 98 matched cddid_all.tbl CDD cd18448 cd18448 350523 BACK_KLHL8 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 8 (KLHL8). KLHL8 is a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex. The BCR(KLHL8) ubiquitin ligase complex mediates ubiquitination and degradation of RAPSN. 97 matched cddid_all.tbl CDD cd18449 cd18449 350524 BACK_KLHL9_13 BACK (BTB and C-terminal Kelch) domain found in Kelch-like proteins, KLHL9 and KLHL13. KLHL9 and KLHL13 (also termed BTB and kelch domain-containing protein 2, or BKLHD2) are substrate-specific adaptors of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex required for mitotic progression and cytokinesis. The BCR(KLHL9-KLHL13) E3 ubiquitin ligase complex mediates the ubiquitination of AURKB and controls the dynamic behavior of AURKB on mitotic chromosomes and thereby coordinates faithful mitotic progression and completion of cytokinesis. 95 matched cddid_all.tbl CDD cd18450 cd18450 350525 BACK_KLHL10 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 10 (KLHL10). KLHL10 may be a substrate-specific adapter of a CUL3-based E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins during spermatogenesis. 80 matched cddid_all.tbl CDD cd18451 cd18451 350526 BACK_KLHL11 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 11 (KLHL11). KLHL11 is a component of a cullin-RING-based BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex that mediates the ubiquitination of target proteins, leading most often to their proteasomal degradation. 88 matched cddid_all.tbl CDD cd18452 cd18452 350527 BACK_KLHL12 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 12 (KLHL12). KLHL12, also termed CUL3-interacting protein 1 (C3IP1), or DKIR, is a substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex that acts as a negative regulator of Wnt signaling pathway and ER-Golgi transport. 136 matched cddid_all.tbl CDD cd18453 cd18453 350528 BACK_KLHL14 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 14 (KLHL14). KLHL14, also termed protein interactor of Torsin-1A, or Printor, or protein interactor of torsinA, is a novel ATP-free form of torsinA-interacting protein implicated in dystonia pathogenesis. 102 matched cddid_all.tbl CDD cd18454 cd18454 350529 BACK_KLHL15 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 15 (KLHL15). KLHL15 is a substrate-specific adaptor for Cullin3 E3 ubiquitin-protein ligase complex that target the serine/threonine-protein phosphatase 2A (PP2A) subunit PPP2R5B for ubiquitination and subsequent proteasomal degradation, thus promoting exchange with other regulatory subunits. It also plays a key role in DNA damage response, favoring DNA double-strand repair through error-prone non-homologous end joining (NHEJ) over error-free, RBBP8-mediated homologous recombination (HR), by targeting the DNA-end resection factor RBBP8/CtIP for ubiquitination and subsequent proteasomal degradation. 108 matched cddid_all.tbl CDD cd18455 cd18455 350530 BACK_KLHL16_gigaxonin BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 16 (KLHL16). Gigaxonin, also termed Kelch-like protein 16 (KLHL16), may be a cytoskeletal component that directly or indirectly plays an important role in neurofilament architecture. It may also act as a substrate-specific adaptor of an E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins, such as tubulin folding cofactor B (TBCB), microtubule-associated protein MAP1B and glial fibrillary acidic protein (GFAP). Gigaxonin is mutated in giant axonal neuropathy. 97 matched cddid_all.tbl CDD cd18456 cd18456 350531 BACK_KLHL17 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 17 (KLHL17). KLHL17, also termed actinfilin, is a substrate-recognition component of some cullin-RING-based BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complexes. It acts as a Cullin 3 (Cul3) substrate adaptor that links GluR6 to the E3 ubiquitin-ligase complex, and mediates the ubiquitination and subsequent degradation of GLUR6. It may play a role in the actin-based neuronal function. 102 matched cddid_all.tbl CDD cd18457 cd18457 350532 BACK_KLHL18 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 18 (KLHL18). KLHL18 acts as a substrate-specific adaptor for the Cullin3 E3 ubiquitin-protein ligase complex that regulates mitotic entry and ubiquitylates Aurora-A. 107 matched cddid_all.tbl CDD cd18458 cd18458 350533 BACK_KLHL19_KEAP1 BACK (BTB and C-terminal Kelch) domain found in Kelch-like ECH-associated protein 1 (KEAP1). KEAP1, also termed cytosolic inhibitor of Nrf2 (INrf2), or Kelch-like protein 19 (KLHL19), is a redox-regulated substrate adaptor protein for a Cullin3-dependent ubiquitin ligase complex that targets NFE2L2/NRF2 for ubiquitination and degradation by the proteasome, thus resulting in the suppression of its transcriptional activity and the repression of antioxidant response element-mediated detoxifying enzyme gene expression. 91 matched cddid_all.tbl CDD cd18459 cd18459 350534 BACK_KLHL20 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 20 (KLHL20). KLHL20, also termed Kelch-like ECT2-interacting protein (KLEIP), or Kelch-like protein X, is a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex involved in interferon response and anterograde Golgi to endosome transport. KLHL20 plays a role in actin assembly at cell-cell contact sites of Madin-Darby canine kidney cells. It also controls endothelial migration and sprouting angiogenesis. 100 matched cddid_all.tbl CDD cd18460 cd18460 350535 BACK_KLHL21 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 21 (KLHL21). KLHL21 is a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex required for efficient chromosome alignment and cytokinesis. The BCR(KLHL21) E3 ubiquitin ligase complex regulates localization of the chromosomal passenger complex (CPC) from chromosomes to the spindle midzone in anaphase and mediates the ubiquitination of aurora B. KLHL21 targets IkappaB kinase-beta to regulate nuclear factor kappa-light chain enhancer of activated B cells (NF-kappaB) signaling negatively. 101 matched cddid_all.tbl CDD cd18461 cd18461 350536 BACK_KLHL22 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 22 (KLHL22). KLHL22 is a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex required for chromosome alignment and localization of Polo-like kinase 1 (PLK1) at kinetochores. The BCR(KLHL22) ubiquitin ligase complex mediates monoubiquitination of PLK1, leading to PLK1 dissociation from phosphoreceptor proteins and subsequent removal from kinetochores, allowing silencing of the spindle assembly checkpoint (SAC) and chromosome segregation. 104 matched cddid_all.tbl CDD cd18462 cd18462 350537 BACK_KLHL23 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 23 (KLHL23). KLHL23 is involved in tumorigenesis and resistance to anticancer drug treatment. It also associates with cone-rod dystrophy. 102 matched cddid_all.tbl CDD cd18463 cd18463 350538 BACK_KLHL24 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 24 (KLHL24). KLHL24, also called kainate receptor-interacting protein for GluR6 (KRIP6), or protein DRE1, is necessary to maintain the balance between intermediate filament stability and degradation, a process that is essential for skin integrity. KLHL24 is a component of the BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex that mediates ubiquitination of KRT14 and controls its levels during keratinocyte differentiation. 78 matched cddid_all.tbl CDD cd18464 cd18464 350539 BACK_KLHL25_like BACK (BTB and C-terminal Kelch) domain found in Kelch-like proteins, KLHL25 and KLHL37. The family includes KLHL25 and KLHL37. KLHL25, also called ectoderm-neural cortex protein 2 (ENC-2), is a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex required for translational homeostasis. The BCR(KLHL25) ubiquitin ligase complex acts by mediating ubiquitination of hypophosphorylated EIF4EBP1 (4E-BP1). KLHL37, also called ectoderm-neural cortex protein 1 (ENC-1), or nuclear matrix protein NRP/B, or p53-induced gene 10 protein, is an actin-binding nuclear matrix protein that associates with p110(RB), and is involved in the regulation of neuronal process formation and in differentiation of neural crest cells. 98 matched cddid_all.tbl CDD cd18465 cd18465 350540 BACK_KLHL26 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 26 (KLHL26). KLHL26 is a kelch family protein encoded by gene klhl26, which is regulated by p53 via fuzzy tandem repeats. 97 matched cddid_all.tbl CDD cd18466 cd18466 350541 BACK_KLHL27_IPP BACK (BTB and C-terminal Kelch) domain found in intracisternal A particle-promoted polypeptide (IPP). IPP, also termed Kelch-like protein 27 (KLHL27), is an actin-binding protein that may play a role in organizing the actin cytoskeleton. 103 matched cddid_all.tbl CDD cd18467 cd18467 350542 BACK_KLHL28_BTBD5 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 28 (KLHL28). KLHL28, also termed BTB/POZ domain-containing protein 5 (BTBD5), belongs to the KLHL family. Its function remains unclear. 99 matched cddid_all.tbl CDD cd18468 cd18468 350543 BACK_KLHL29_KBTBD9 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 29 (KLHL29). KLHL29, also termed Kelch repeat and BTB domain-containing protein 9 (KBTBD9), belongs to the KLHL family. Its function remains unclear. A nuclear receptor subfamily 5, group A, member 2 (NR5A2)-Kelch-like family member 29 (KLHL29) fusion transcript may participate in the origin or progression of some colon cancers. 102 matched cddid_all.tbl CDD cd18469 cd18469 350544 BACK_KLHL30 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 30 (KLHL30). KLHL30 belongs to the KLHL family. Its function remains unclear. Differential expression of the KLHL30 gene has been observed in glioblastoma multiforme versus normal brain. 104 matched cddid_all.tbl CDD cd18470 cd18470 350545 BACK_KLHL31_KBTBD1 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 31 (KLHL31). KLHL31, also termed BTB and kelch domain-containing protein 6, or Kelch repeat and BTB domain-containing protein 1, or Kelch-like protein KLHL, is a transcriptional repressor in MAPK/JNK signaling pathway that regulates cellular functions. Overexpression inhibits the transcriptional activities of both the TPA-response element (TRE) and serum response element (SRE). 98 matched cddid_all.tbl CDD cd18471 cd18471 350546 BACK_KLHL32_BKLHD5 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 32 (KLHL32). KLHL32, also termed BTB and kelch domain-containing protein 5 (BKLHD5), belongs to the KLHL family. Its function remains unclear. KLHL32 SNPs may be associated with body mass index in individuals of African ancestry. 98 matched cddid_all.tbl CDD cd18472 cd18472 350547 BACK_KLHL33 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 33 (KLHL33). KLHL33 belongs to the KLHL family. Its function remains unclear. KLHL33 SNPs may be associated with prostate cancer risk. 75 matched cddid_all.tbl CDD cd18473 cd18473 350548 BACK_KLHL34 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 34 (KLHL34). KLHL34 belongs to the KLHL family. Its function remains unclear. The methylation status of KLHL34 cg14232291 may be a predictive candidate of sensitivity to preoperative chemoradiation therapy. 106 matched cddid_all.tbl CDD cd18474 cd18474 350549 BACK_KLHL35 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 35 (KLHL35). KLHL35 belongs to the KLHL family. Its function remains unclear. Hypermethylation of KLHL35 is associated with hepatocellular carcinoma and abdominal aortic aneurysm. 79 matched cddid_all.tbl CDD cd18475 cd18475 350550 BACK_KLHL36 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 36 (KLHL36). KLHL36 may act as a substrate-specific adaptor of an E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. 100 matched cddid_all.tbl CDD cd18476 cd18476 350551 BACK_KLHL38 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 38 (KLHL38). KLHL38 belongs to the KLHL family. Its function remains unclear. The klhl38 gene has recently been identified as a possible diapause (a temporary arrest of development during early ontogeny) gene, as it is significantly up-regulated during diapause. It may also be involved in chicken preadipocyte differentiation. 99 matched cddid_all.tbl CDD cd18477 cd18477 350552 BACK_KLHL40_like BACK (BTB and C-terminal Kelch) domain found in Kelch-like proteins, KLHL40 and KLHL41. The family includes Kelch-like proteins, KLHL40 and KLHL41. KLHL40 is a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex that acts as a key regulator of skeletal muscle development. KLHL41 is a novel kelch related protein that is involved in pseudopod elongation in transformed cells. 99 matched cddid_all.tbl CDD cd18478 cd18478 350553 BACK_KLHL42_KLHDC5 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 42 (KLHL42). KLHL42, also called Cullin-3-binding protein 9 (Ctb9), or Kelch domain-containing protein 5, is a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex required for mitotic progression and cytokinesis. The BCR(KLHL42) E3 ubiquitin ligase complex mediates the ubiquitination and subsequent degradation of KATNA1. KLHL42 is involved in microtubule dynamics throughout mitosis. 103 matched cddid_all.tbl CDD cd18479 cd18479 350554 BACK_KBTBD2 BACK (BTB and C-terminal Kelch) domain found in Kelch repeat and BTB domain-containing protein 2 (KBTBD2). KBTBD2, also called BTB and kelch domain-containing protein 1 (BKLHD1), plays an essential role in the regulating the insulin-signaling pathway. It is a BTB-Kelch family substrate recognition subunit of the Cullin-3-based E3 ubiquitin ligase, which targets p85alpha, the regulatory subunit of the phosphoinositol-3-kinase (PI3K) heterodimer, causing p85alpha ubiquitination and proteasome-mediated degradation. 96 matched cddid_all.tbl CDD cd18480 cd18480 350555 BACK_KBTBD3 BACK (BTB and C-terminal Kelch) domain found in Kelch repeat and BTB domain-containing protein 3 (KBTBD3). KBTBD3, also termed BTB and kelch domain-containing protein 3 (BKLHD3), is a BTB-Kelch family protein. Its function remains unclear. 82 matched cddid_all.tbl CDD cd18481 cd18481 350556 BACK_KBTBD4 BACK (BTB and C-terminal Kelch) domain found in Kelch repeat and BTB domain-containing protein 4 (KBTBD4). KBTBD4, also termed BTB and kelch domain-containing protein 4 (BKLHD4), is a BTB-BACK-Kelch domain protein belonging to a large family of cullin-RING ubiquitin ligase adaptors that facilitate the ubiquitination of target substrates. 88 matched cddid_all.tbl CDD cd18482 cd18482 350557 BACK_KBTBD6_7 BACK (BTB and C-terminal Kelch) domain found in Kelch repeat and BTB domain-containing proteins, KBTBD6 and KBTBD7. KBTBD6 and KBTBD7 are substrate adaptors of a cullin-3 RING ubiquitin ligase complex that mediates ubiquitylation and proteasomal degradation of T-lymphoma and metastasis gene 1 (TIAM1), a RAC1-specific guanine exchange factor (GEF), by cooperating with gamma-aminobutyric acid receptor-associated proteins (GABARAP). KBTBD7 may also act as a new transcriptional activator in mitogen-activated protein kinase (MAPK) signaling. 99 matched cddid_all.tbl CDD cd18483 cd18483 350558 BACK_KBTBD8 BACK (BTB and C-terminal Kelch) domain found in Kelch repeat and BTB domain-containing protein 8 (KBTBD8). KBTBD8, also called T-cell activation kelch repeat protein (TA-KRP), is a BTB-kelch family protein that is located in the Golgi apparatus and translocates to the spindle apparatus during mitosis. It acts as a substrate-specific adaptor for a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex that acts as a regulator of neural crest specification. The BCR(KBTBD8) complex monoubiquitylates NOLC1 and its paralogue TCOF1, the mutation of which underlies the neurocristopathy Treacher Collins syndrome. 97 matched cddid_all.tbl CDD cd18484 cd18484 350559 BACK_KBTBD11_CMLAP BACK (BTB and C-terminal Kelch) domain found in Kelch repeat and BTB domain-containing protein 11 (KBTBD11). KBTBD11, also termed chronic myelogenous leukemia-associated protein (CMLAP), or Kelch domain-containing protein 7B, or KLHDC7C, is a BTB-Kelch family protein. Its function remains unclear. A novel polymorphism rs11777210 in KBTBD11 is significantly associated with colorectal cancer risk; KBTBD11 may function as a tumor suppressor. KBTBD11 hypomethylation may also be a potential target for differentiating between the mostly fatal TCF3-HLF and curable TCF3-PBX1 pediatric acute lymphoblastic leukemia subtypes. 77 matched cddid_all.tbl CDD cd18485 cd18485 350560 BACK_KBTBD12 BACK (BTB and C-terminal Kelch) domain found in Kelch repeat and BTB domain-containing protein 12 (KBTBD12). KBTBD12, also termed Kelch domain-containing protein 6 (KLHDC6), is a BTB-Kelch family protein. Its function remains unclear. 100 matched cddid_all.tbl CDD cd18486 cd18486 350561 BACK_KBTBD13 BACK (BTB and C-terminal Kelch) domain found in Kelch repeat and BTB domain-containing protein 13 (KBTBD13). KBTBD13 is a muscle-specific protein. Autosomal dominant mutations may cause nemaline myopathy (NEM); these disease-associated mutations are located in conserved Kelch repeats and are predicted to disrupt the beta-propeller structure. KBTBD13 may act as a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex that functions as a muscle specific ubiquitin ligase, and thereby implicate the ubiquitin proteasome pathway in the pathogenesis of KBTBD13-associated NEM. 89 matched cddid_all.tbl CDD cd18487 cd18487 350562 BACK_BTBD1_like BACK (BTB and C-terminal Kelch) domain found in BTB/POZ domain-containing proteins, BTBD1 and BTBD2. This subfamily includes BTB/POZ domain-containing proteins BTBD1 and BTBD2, both of which are BTB-domain-containing Kelch-like proteins that interact with DNA topoisomerase 1 (Topo1), a key enzyme in cell survival. BTBD1 and BTBD2 colocalize to cytoplasmic bodies with the RBCC/tripartite motif protein, TRIM5delta. 95 matched cddid_all.tbl CDD cd18488 cd18488 350563 BACK_BTBD3_like BACK (BTB and C-terminal Kelch) domain found in BTB/POZ domain-containing proteins, BTBD3 and BTBD6. This subfamily includes BTB/POZ domain-containing proteins BTBD3 and BTBD6, both of which are BTB-domain-containing Kelch-like proteins. BTBD3 controls dendrite orientation toward active axons in mammalian neocortex. BTBD6 is required for proper embryogenesis and plays an essential evolutionarily-conserved role during neuronal development. 95 matched cddid_all.tbl CDD cd18489 cd18489 350564 BACK_BTBD7 BACK (BTB and C-terminal Kelch) domain found in BTB/POZ domain-containing protein 7 (BTBD7). BTBD7 is a crucial regulator that is essential for region-specific epithelial cell dynamics and branching morphogenesis. It has been implicated in various cancers. BTBD7 contains two BTB domains and a BACK domain. 98 matched cddid_all.tbl CDD cd18490 cd18490 350565 BACK_BTBD8 BACK (BTB and C-terminal Kelch) domain found in BTB/POZ domain-containing protein 8 (BTBD8). BTBD8 is a BTB-domain-containing Kelch-like protein that may play a role in developmental process. It may also act as a protein-protein adaptor in a transcription complex and thus may be involved in brain development. 64 matched cddid_all.tbl CDD cd18491 cd18491 350566 BACK_ABTB2_like BACK (BTB and C-terminal Kelch) domain found in ankyrin repeat and BTB/POZ domain-containing protein 2 (ABTB2) and similar proteins. ABTB2, also called Bood POZ containing gene type 2 (BPOZ-2), is a scaffold protein that controls the degradation of many biological proteins involved in a range of functions from embryonic development to tumor progression. It may be involved in the initiation of hepatocyte growth. It inhibits the aggregation of alpha-synuclein, with implications in Parkinson's disease. ABTB2 functions as an adaptor protein for the E3 ubiquitin ligase scaffold protein Cullin-3. It directly binds to eukaryotic elongation factor 1A1 (eEF1A1) to promote eEF1A1 ubiquitylation and degradation and prevent translation. It is also involved in the growth suppressive effect of the phosphatase and tensin homologue (PTEN). This subfamily also includes BTB/POZ domain-containing protein 11 (BTBD11), whose function is unclear. 72 matched cddid_all.tbl CDD cd18492 cd18492 350567 BACK_BTBD16 BACK (BTB and C-terminal Kelch) domain found in BTB/POZ domain-containing protein 16 (BTBD16). BTBD16 is a BTB-domain-containing Kelch-like protein. Its function remains unclear. BTBD16 SNPs may be bipolar disorder (BD) genetic susceptibility variants exhibiting genetic background-dependent effects. 97 matched cddid_all.tbl CDD cd18493 cd18493 350568 BACK_BTBD17 BACK (BTB and C-terminal Kelch) domain found in BTB/POZ domain-containing protein 17 (BTBD17). BTBD17, also termed galectin-3-binding protein-like, is a BTB-domain-containing Kelch-like protein. Its function remains unclear. It may be involved in hepatocellular carcinoma development and progression. 74 matched cddid_all.tbl CDD cd18494 cd18494 350569 BACK_BTBD19 BACK (BTB and C-terminal Kelch) domain found in BTB/POZ domain-containing protein 19 (BTBD19). BTBD19 is a BTB-domain-containing Kelch-like protein. Its function remains unclear. 73 matched cddid_all.tbl CDD cd18495 cd18495 350570 BACK_GCL BACK (BTB and C-terminal Kelch) domain found in Drosophila melanogaster protein germ cell-less (GCL) and similar proteins. The GCL protein is a nuclear envelope protein highly conserved between the mammalian and Drosophila orthologs. Drosophila melanogaster GCL is a key regulator required for the specification of pole cells and primordial germ cell formation in Drosophila embryos. Both human germ cell-less protein-like 1 (GMCL1) and germ cell-less protein-like 1-like (GMCL1P1 or GMCL1L) may function in spermatogenesis. They may also be substrate-specific adaptors of an E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. 78 matched cddid_all.tbl CDD cd18496 cd18496 350571 BACK_LGALS3BP BACK (BTB and C-terminal Kelch) domain found in lectin galactoside-binding soluble 3-binding protein (LGALS3BP). LGALS3BP, also called galectin-3-binding protein, or basement membrane autoantigen p105, or Mac-2-binding protein (MAC2BP/M2BP), or tumor-associated antigen 90K, promotes integrin-mediated cell adhesion. It may stimulate host defense against viruses and tumor cells. 74 matched cddid_all.tbl CDD cd18497 cd18497 350572 BACK_ABTB1_BPOZ BACK (BTB and C-terminal Kelch) domain found in ankyrin repeat and BTB/POZ domain-containing protein 1 (ABTB1). ABTB1, also called elongation factor 1A-binding protein, or Bood POZ containing gene type 1 (BPOZ-1), is an anti-proliferative factor that may act as a mediator of the phosphatase and tensin homologue (PTEN) growth-suppressive signaling pathway. It may play a role in developmental processes. 72 matched cddid_all.tbl CDD cd18498 cd18498 350573 BACK_RCBTB1_2 BACK (BTB and C-terminal Kelch) domain found in RCC1 and BTB domain-containing proteins, RCBTB1 and RCBTB2. The RCC1-related guanine nucleotide exchange factor (GEF) family includes RCC1 and BTB domain-containing proteins, RCBTB1 and RCBTB2, both of which are chromosome condensation regulator-like guanine nucleotide exchange factors. 64 matched cddid_all.tbl CDD cd18499 cd18499 350574 BACK_RHOBTB BACK (BTB and C-terminal Kelch) domain found in Rho-related BTB domain-containing proteins (RhoBTB). RhoBTB proteins constitute a subfamily of atypical members within the Rho family of small guanosine triphosphatases (GTPases), which is characterized by containing a GTPase domain (in most cases, non-functional) followed by a proline rich region, a tandem of 2 BTB domains, and a C-terminal BACK domain. In humans, the RhoBTB subfamily consists of 3 isoforms: RhoBTB1, RhoBTB2, and RhoBTB3. Orthologs are present in several other eukaryotes, such as Drosophila and Dictyostelium, but have been lost in plants and fungi. 76 matched cddid_all.tbl CDD cd18500 cd18500 350575 BACK_IBtk BACK (BTB and C-terminal Kelch) domain found in inhibitor of Bruton tyrosine kinase (IBtk). IBtk is an inhibitor of Bruton's tyrosine kinase (Btk), thereby playing a role in B-cell development. 60 matched cddid_all.tbl CDD cd18501 cd18501 350576 BACK_ANKFY1_Rank5 BACK (BTB and C-terminal Kelch) domain found in rabankyrin-5 (Rank-5). Rank-5, also called ankyrin repeat and FYVE domain-containing protein 1 (ANKFY1), or ankyrin repeats hooked to a zinc finger motif (ANKHZN), is a Rab5 effector that regulates and coordinates different endocytic mechanisms. 89 matched cddid_all.tbl CDD cd18502 cd18502 350577 BACK_NS1BP_IVNS1ABP BACK (BTB and C-terminal Kelch) domain found in influenza virus NS1A-binding protein (NS1-BP). NS1-BP, also called NS1-binding protein, or Aryl hydrocarbon receptor-associated protein 3, or IVNS1ABP, is a novel protein that interacts with the influenza A virus nonstructural NS1 protein, which is relocalized in the nuclei of infected cells. It plays a role in cell division and in the dynamic organization of the actin skeleton as a stabilizer of actin filaments by association with F-actin through Kelch repeats. It also interacts with alpha-enolase/MBP-1 and is involved in c-Myc gene transcriptional control. 99 matched cddid_all.tbl CDD cd18503 cd18503 350578 BACK_calicin BACK (BTB and C-terminal Kelch) domain found in calicin. Calicin is a basic cytoskeletal protein involved in the formation and maintenance of the highly regular organization of the postacrosomal perinuclear theca, the calyx of mammalian spermatozoa. 78 matched cddid_all.tbl CDD cd18504 cd18504 350579 BACK_ARIA_like BACK (BTB and C-terminal Kelch) domain found in plant ARM repeat protein interacting with ABF2 (ARIA) and similar proteins. ARIA is an ARM repeat protein that acts as a positive regulator of ABA response via the modulation of the transcriptional activity of ABF2, a transcription factor which controls ABA-dependent gene expression via the G-box-type ABA-responsive elements. ARIA is a novel abscisic acid signaling component. It negatively regulates seed germination and young seedling growth. 64 matched cddid_all.tbl CDD cd18505 cd18505 350580 BACK1_LZTR1 first BACK (BTB and C-terminal Kelch) domain found in leucine-zipper-like transcriptional regulator 1 (LZTR-1). LZTR-1 is a Golgi BTB-kelch protein that is degraded upon induction of apoptosis. It may also function as a transcriptional regulator that plays a crucial role in embryogenesis. Germline loss-of-function mutations in LZTR-1 predispose to an inherited disorder of multiple schwannomas. 59 matched cddid_all.tbl CDD cd18506 cd18506 350581 BACK2_LZTR1 second BACK (BTB and C-terminal Kelch) domain found in leucine-zipper-like transcriptional regulator 1 (LZTR-1). LZTR-1 is a Golgi BTB-kelch protein that is degraded upon induction of apoptosis. It may also function as a transcriptional regulator that plays a crucial role in embryogenesis. Germline loss-of-function mutations in LZTR-1 predispose to an inherited disorder of multiple schwannomas. 61 matched cddid_all.tbl CDD cd18507 cd18507 350582 BACK_GPRS_like BACK (BTB and C-terminal Kelch) domain found in Drosophila melanogaster serine-enriched protein (GPRS) and similar proteins. The family includes uncharacterized Drosophila melanogaster serine-enriched protein (GPRS) and similar proteins. 80 matched cddid_all.tbl CDD cd18508 cd18508 350583 BACK_KEL_like BACK (BTB and C-terminal Kelch) domain found in Drosophila melanogaster ring canal kelch protein (KEL) and similar proteins. KEL, also termed kelch short protein, is a component of ring canals that regulates the flow of cytoplasm between cells. It binds actin and may be involved in the regulation of cytoplasm flow from nurse cells to the oocyte during oogenesis. 77 matched cddid_all.tbl CDD cd18509 cd18509 350584 BACK_KLHL1 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 1 (KLHL1). KLHL1 is a neuronal actin-binding protein that modulates voltage-gated CaV2.1 (P/Q-type) and CaV3.2 (alpha1H T-type) calcium channels. It may play a role in organizing the actin cytoskeleton in brain cells. KLHL1 contains a BTB domain and kelch repeat domains, characteristics of a kelch family protein. 106 matched cddid_all.tbl CDD cd18510 cd18510 350585 BACK_KLHL4 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 4 (KLHL4). KLHL4 shares high identity and similarity with the Drosophila kelch protein, a component of ring canals. It contains a BTB domain and kelch repeat domains, characteristics of a kelch family protein. 106 matched cddid_all.tbl CDD cd18511 cd18511 350586 BACK_KLHL5 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 5 (KLHL5). KLHL5 shares high identity and similarity with the Drosophila kelch protein, a component of ring canals. It contains a BTB domain and kelch repeat domains, characteristics of a kelch family protein. It is abundantly expressed in ovary, adrenal gland, and thymus. 106 matched cddid_all.tbl CDD cd18512 cd18512 350587 BACK_KLHL2_Mayven BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 2 (KLHL2). KLHL2, also called actin-binding protein Mayven, is a novel actin-binding protein predominantly expressed in the brain. It plays a role in the reorganization of the actin cytoskeleton, and promotes growth of cell projections in oligodendrocyte precursors. KLHL2 is a component of a cullin-RING-based BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex that mediates the ubiquitination of target proteins, such as NPTXR, leading most often to their proteasomal degradation. 130 matched cddid_all.tbl CDD cd18513 cd18513 350588 BACK_KLHL3 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 3 (KLHL3). KLHL3 serves as a substrate adapter in Cullin3 (Cul3) E3 ubiquitin ligase complexes. It is a component of an E3 ubiquitin ligase complex that regulates blood pressure by targeting With-No-Lysine (WNK) kinases for degradation. 130 matched cddid_all.tbl CDD cd18514 cd18514 350589 BACK_KLHL25_ENC2 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 25 (KLHL25). KLHL25, also called ectoderm-neural cortex protein 2 (ENC-2), is a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex required for translational homeostasis. The BCR(KLHL25) ubiquitin ligase complex acts by mediating ubiquitination of hypophosphorylated EIF4EBP1 (4E-BP1). 99 matched cddid_all.tbl CDD cd18515 cd18515 350590 BACK_KLHL37_ENC1 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 37 (KLHL37). KLHL37, also called ectoderm-neural cortex protein 1 (ENC-1), or nuclear matrix protein NRP/B, or p53-induced gene 10 protein, is an actin-binding nuclear matrix protein that associates with p110(RB), and is involved in the regulation of neuronal process formation and in differentiation of neural crest cells. 98 matched cddid_all.tbl CDD cd18516 cd18516 350591 BACK_KLHL40_KBTBD5 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 40 (KLHL40). KLHL40, also called Kelch repeat and BTB domain-containing protein 5, or sarcosynapsin, is a substrate-specific adaptor of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex that acts as a key regulator of skeletal muscle development. Mutations in KLHL40 may cause severe autosomal-recessive nemaline myopathy. 99 matched cddid_all.tbl CDD cd18517 cd18517 350592 BACK_KLHL41_KBTBD10 BACK (BTB and C-terminal Kelch) domain found in Kelch-like protein 41 (KLHL41). KLHL41, also called Kel-like protein 23, or Kelch repeat and BTB domain-containing protein 10, or Kelch-related protein 1 (Krp1), or sarcosine, is a novel kelch related protein that is involved in pseudopod elongation in transformed cells. It is also involved in skeletal muscle development and differentiation. It regulates proliferation and differentiation of myoblasts and plays a role in myofibril assembly by promoting lateral fusion of adjacent thin fibrils into mature, wide myofibrils. 99 matched cddid_all.tbl CDD cd18518 cd18518 350593 BACK_SPOP BACK (BTB and C-terminal Kelch) domain found in speckle-type POZ protein (SPOP). SPOP, also termed HIB homolog 1, or Roadkill homolog 1, is a novel nuclear speckle-type protein which serves as an adaptor of cullin-RING-based BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex that mediates the ubiquitination and proteasomal degradation of target proteins, such as BRMS1, DAXX, PDX1/IPF1, GLI2 and GLI3. 71 matched cddid_all.tbl CDD cd18519 cd18519 350594 BACK_SPOPL BACK (BTB and C-terminal Kelch) domain found in speckle-type POZ protein-like (SPOPL). SPOPL, also termed HIB homolog 2, or Roadkill homolog 2, is a component of a cullin-RING-based BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex that mediates the ubiquitination and subsequent proteasomal degradation of target proteins. The complexes containing homodimeric SPOPL or the heterodimer formed by speckle-type POZ protein (SPOP) and SPOPL are less efficient than ubiquitin ligase complexes containing only SPOP. 96 matched cddid_all.tbl CDD cd18520 cd18520 350595 BACK_roadkill_like BACK (BTB and C-terminal Kelch) domain found in Drosophila melanogaster protein roadkill and similar proteins. Drosophila melanogaster protein roadkill, also termed Hh-induced MATH and BTB domain-containing protein (HIB), is a hedgehog-induced BTB protein that modulates hedgehog signaling by degrading Ci/Gli transcription factor. 74 matched cddid_all.tbl CDD cd18521 cd18521 350596 BACK_Tdpoz "BACK (BTB and C-terminal Kelch) domain found in TD and POZ domain-containing proteins, Tdpoz1-4. TDPOZ is a family of bipartite animal and plant proteins that contain a tumor necrosis factor receptor-associated factor (TRAF) domain (TD) and a POZ/BTB domain. TDPOZ proteins may be nuclear scaffold proteins probably involved in transcription regulation in early development and other cellular processes. This subfamily contains only mammalian members. Plant TDPOZ proteins contain a MATH domain at the N-terminal region and are named ""BTB/POZ and MATH domain-containing proteins (BPM)"", and are not inlcuded in this subfamily." 67 matched cddid_all.tbl CDD cd18522 cd18522 350597 BACK_BTBD1 BACK (BTB and C-terminal Kelch) domain found in BTB/POZ domain-containing protein 1 (BTBD1). BTBD1, also called Hepatitis C virus NS5A-transactivated protein 8 or HCV NS5A-transactivated protein 8, is a BTB-domain-containing Kelch-like protein specifically expressed in skeletal muscle. It interacts with DNA topoisomerase 1 (Topo1), a key enzyme in cell survival. BTBD1 and BTBD2 colocalize to cytoplasmic bodies with the RBCC/tripartite motif protein, TRIM5delta. It may serve as a substrate-specific adaptor of an E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. 107 matched cddid_all.tbl CDD cd18523 cd18523 350598 BACK_BTBD2 BACK (BTB and C-terminal Kelch) domain found in BTB/POZ domain-containing protein 2 (BTBD2). BTBD2 is a BTB-domain-containing Kelch-like protein that interacts with DNA topoisomerase 1 (Topo1), a key enzyme in cell survival. BTBD1 and BTBD2 colocalize to cytoplasmic bodies with the RBCC/tripartite motif protein, TRIM5delta. 106 matched cddid_all.tbl CDD cd18524 cd18524 350599 BACK_BTBD3 BACK (BTB and C-terminal Kelch) domain found in BTB/POZ domain-containing protein 3 (BTBD3). BTBD3 is a BTB-domain-containing Kelch-like protein that controls dendrite orientation toward active axons in mammalian neocortex. 95 matched cddid_all.tbl CDD cd18525 cd18525 350600 BACK_BTBD6 BACK (BTB and C-terminal Kelch) domain found in BTB/POZ domain-containing protein 6 (BTBD6). BTBD6, also called lens BTB domain protein, is a BTB-domain-containing Kelch-like protein that is required for proper embryogenesis and plays an essential evolutionarily-conserved role during neuronal development. 95 matched cddid_all.tbl CDD cd18526 cd18526 350601 BACK_ABTB2 BACK (BTB and C-terminal Kelch) domain found in ankyrin repeat and BTB/POZ domain-containing protein 2 (ABTB2). ABTB2, also called Bood POZ containing gene type 2 (BPOZ-2), is a scaffold protein that controls the degradation of many biological proteins with functions ranging from embryonic development to tumor progression. It may be involved in the initiation of hepatocyte growth. It inhibits the aggregation of alpha-synuclein, with implications in Parkinson's disease. ABTB2 functions as an adaptor protein for the E3 ubiquitin ligase scaffold protein Cullin-3. It directly binds to eukaryotic elongation factor 1A1 (eEF1A1) to promote eEF1A1 ubiquitylation and degradation and prevent translation. It is also involved in the growth suppressive effect of the phosphatase and tensin homologue (PTEN). 79 matched cddid_all.tbl CDD cd18527 cd18527 350602 BACK_BTBD11 BACK (BTB and C-terminal Kelch) domain found in BTB/POZ domain-containing protein 11 (BTBD11). BTBD11, also termed ankyrin repeat and BTB/POZ domain-containing protein BTBD11, is a BTB-domain-containing Kelch-like protein. Its function remains unclear. The BTBD11 gene has been identified as an all-trans retinoic acid-responsive gene that may play a role in neural development. 83 matched cddid_all.tbl CDD cd18528 cd18528 350603 BACK_RCBTB1 BACK (BTB and C-terminal Kelch) domain found in RCC1 and BTB domain-containing protein 1 (RCBTB1). RCBTB1, also called chronic lymphocytic leukemia deletion region gene 7 protein (CLLD7), or CLL deletion region gene 7 protein, or regulator of chromosome condensation and BTB domain-containing protein 1, or E4.5, is a novel chromosome condensation regulator-like guanine nucleotide exchange factor (GEF) that may be involved in cell cycle regulation by chromatin remodeling. It may also function as a tumor suppressor that regulates pathways of DNA damage/repair and apoptosis. Moreover, RCBTB1 acts as a putative substrate adaptor for a cullin3 (CUL3) E3 ligase complex that mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Biallelic mutations in RCBTB1 may cause isolated and syndromic retinal dystrophy. 66 matched cddid_all.tbl CDD cd18529 cd18529 350604 BACK_RCBTB2 BACK (BTB and C-terminal Kelch) domain found in RCC1 and BTB domain-containing protein 2 (RCBTB2). RCBTB2, also called chromosome condensation 1-like (CHC1-L), or RCC1-like G exchanging factor, or regulator of chromosome condensation and BTB domain-containing protein 2, is a chromosome condensation regulator-like guanine nucleotide exchange factor (GEF) protein for the Ras-related GTPase Ran. 65 matched cddid_all.tbl CDD cd18530 cd18530 350605 BACK_RHOBTB1 BACK (BTB and C-terminal Kelch) domain found in Rho-related BTB domain-containing protein 1 (RhoBTB1). RhoBTB1 is an atypical member of the Rho GTPase family of signaling proteins, which is characterized by containing a carboxyl terminal extension that harbors two BTB domains and a BACK domain and is capable of assembling cullin 3-dependent ubiquitin ligase complexes. It functions as a tumor suppressor that regulates the integrity of the Golgi complex through the methyltransferase METTL7B. RhoBTB1 also acts an adaptor of the Cullin-3-dependent E3 ubiquitin ligase complex. 100 matched cddid_all.tbl CDD cd18531 cd18531 350606 BACK_RHOBTB2 BACK (BTB and C-terminal Kelch) domain found in Rho-related BTB domain-containing protein 2 (RhoBTB2). RhoBTB2, also called Deleted in breast cancer 2 gene protein (DBC2), or p83, is an atypical member of the Rho GTPase family of signaling proteins, which is characterized by containing a carboxyl terminal extension that harbors two BTB domains and a BACK domain and is capable of assembling cullin 3-dependent ubiquitin ligase complexes. It functions as a tumor suppressor that regulates the expression of the methyltransferase METTL7A. RhoBTB2 also acts an adaptor of the Cullin-3-dependent E3 ubiquitin ligase complex. 97 matched cddid_all.tbl CDD cd18532 cd18532 350607 BACK_RHOBTB3 BACK (BTB and C-terminal Kelch) domain found in Rho-related BTB domain-containing protein 3 (RhoBTB3). RhoBTB3 is an atypical member of the Rho GTPase family of signaling proteins, which is characterized by containing a carboxyl terminal extension that harbors two BTB domains and a BACK domain and is capable of assembling cullin 3-dependent ubiquitin ligase complexes. It is a Golgi-associated Rho-related ATPase that regulates the S/G2 transition of the cell cycle by targeting cyclin E for ubiquitylation. RhoBTB3 is involved in vesicle trafficking and in targeting proteins for degradation in the proteasome. It binds directly to Rab9 GTPase and functions with Rab9 in protein transport from endosomes to the trans Golgi network. It also promotes proteasomal degradation of Hypoxia-inducible factor alpha (HIFalpha) by facilitating hydroxylation and ubiquitination. 83 matched cddid_all.tbl CDD cd18533 cd18533 350509 PTP_fungal fungal protein tyrosine phosphatases. This subfamily contains Saccharomyces cerevisiae protein-tyrosine phosphatases 1 (PTP1) and 2 (PTP2), Schizosaccharomyces pombe PTP1, PTP2, and PTP3, and similar fungal proteins. PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. PTP2, together with PTP3, is the major phosphatase that dephosphorylates and inactivates the MAP kinase HOG1 and also modulates its subcellular localization. 212 matched cddid_all.tbl CDD cd18534 cd18534 350510 DSP_plant_IBR5-like dual specificity phosphatase domain of plant IBR5-like protein phosphatases. This subfamily is composed of Arabidopsis thaliana INDOLE-3-BUTYRIC ACID (IBA) RESPONSE 5 (IBR5) and similar plant proteins. IBR5 protein is also called SKP1-interacting partner 33. The IBR5 gene encodes a dual-specificity phosphatase (DUSP) which acts as a positive regulator of plant responses to auxin and abscisic acid. DUSPs function as protein-serine/threonine phosphatases (EC 3.1.3.16) and protein-tyrosine-phosphatases (EC 3.1.3.48). Typical DUSPs, also called mitogen-activated protein kinase (MAPK) phosphatases (MKPs), deactivate MAPKs by dephosphorylating the threonine and tyrosine residues in the conserved Thr-Xaa-Tyr motif residing in their activation sites. IBR5 is an atypical DUSP; it contains the catalytic dual specificity phosphatase domain but lacks the N-terminal Cdc25/rhodanese-like domain that is present in typical DUSPs. It has been shown to target MPK12, which is a negative regulator of auxin signaling. 130 matched cddid_all.tbl CDD cd18535 cd18535 350511 PTP-IVa3 protein tyrosine phosphatase type IVA 3. Protein tyrosine phosphatase type IVA 3 (PTP-IVa3), also known as protein-tyrosine phosphatase of regenerating liver 3 (PRL-3), stimulates progression from G1 into S phase during mitosis and enhances cell proliferation, cell motility and invasive activity, and promotes cancer metastasis. It exerts its oncogenic functions through activation of PI3K/Akt, which is a key regulator of the rapamycin-sensitive mTOR complex 1. PRL-3 is a member of the PTP-IVa/PRL family of small, prenylated phosphatases that are the most oncogenic of all PTPs. PRLs associate with magnesium transporters of the cyclin M (CNNM) family, which results in increased intracellular magnesium levels that promote oncogenic transformation. 154 matched cddid_all.tbl CDD cd18536 cd18536 350512 PTP-IVa2 protein tyrosine phosphatase type IVA 2. Protein tyrosine phosphatase type IVA 2 (PTP-IVa2), also known as protein-tyrosine phosphatase of regenerating liver 2 (PRL-2), stimulates progression from G1 into S phase during mitosis and promotes tumors. It regulates tumor cell migration and invasion through an ERK-dependent signaling pathway. Its overexpression correlates with breast tumor formation and progression. PRL-2 is a member of the PTP-IVa/PRL family of small, prenylated phosphatases that are the most oncogenic of all PTPs. PRLs associate with magnesium transporters of the cyclin M (CNNM) family, which results in increased intracellular magnesium levels that promote oncogenic transformation. 155 matched cddid_all.tbl CDD cd18537 cd18537 350513 PTP-IVa1 protein tyrosine phosphatase type IVA 1. Protein tyrosine phosphatase type IVA 1 (PTP-IVa1), also known as protein-tyrosine phosphatase of regenerating liver 1 (PRL-1), stimulates progression from G1 into S phase during mitosis and enhances cell proliferation, cell motility and invasive activity, and promotes cancer metastasis. It may play a role in the development and maintenance of differentiating epithelial tissues. PRL-1 promotes cell growth and migration by activating both the ERK1/2 and RhoA pathways. It is a member of the PTP-IVa/PRL family of small, prenylated phosphatases that are the most oncogenic of all PTPs. PRLs associate with magnesium transporters of the cyclin M (CNNM) family, which results in increased intracellular magnesium levels that promote oncogenic transformation. 167 matched cddid_all.tbl CDD cd18538 cd18538 350514 PFA-DSP_unk unknown subfamily of atypical dual-specificity phosphatases from fungi. This uncharacterized subfamily belongs to the plant and fungi atypical dual-specificity phosphatases (PFA-DSPs) group of atypical DSPs that present in plants, fungi, kinetoplastids, and slime molds. They share structural similarity with atypical- and lipid phosphatase DSPs from mammals. The PFA-DSP group is composed of active as well as inactive phosphatases. This unknown subgroup contains the conserved the CxxxxxR catalytic motif present in active cysteine phosphatases. 145 matched cddid_all.tbl CDD cd18539 cd18539 349786 SRP_G GTPase domain of signal recognition particle protein. The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal signal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain. 193 matched cddid_all.tbl CDD cd18540 cd18540 349984 ABC_6TM_exporter_like Six-transmembrane helical domain (TMD) of an uncharacterized ABC exporter, and similar proteins. This group includes a subunit of six transmembrane (TM) helices typically found in the ATP-binding cassette (ABC) transporters that function as exporters, which contain 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds and a various type of lipids. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting the chemical diversity of the translocated substrates, while NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane. However, some ABC genes are organized as half-transporters, which must form either homodimers or heterodimers to form a functional transporter. The ABC exporters play a role in multidrug resistance to antibiotics and anticancer agents, and mutations in these proteins have been shown to cause severe human diseases such as cystic fibrosis. 295 matched cddid_all.tbl CDD cd18541 cd18541 349985 ABC_6TM_TmrB_like Six-transmembrane helical domain (TmrB) of the heterodimeric Thermus thermophilus multidrug resistance proteins TmrAB, and similar proteins. This group represents the six-transmembrane helical domain (6-TMD) of the heterodimeric Thermus thermophilus multidrug resistance proteins A and B (TmrAB), a homolog of the Antigen Translocation Complex Tap, and similar proteins. TmrAB has been shown to able to restore antigen processing in human TAP-deficient cells. The 6-transmembrane (TM) helices typically found in the ATP-binding cassette (ABC) transporters that function as exporters, which contain 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds and a various type of lipids. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting significant structural diversity of the translocated substrates, while NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane. However, some ABC genes are organized as half-transporters, which must form either homodimers or heterodimers to form a functional transporter. The ABC exporters play a role in multidrug resistance to antibiotics and anticancer agents, and mutations in these proteins have been shown to cause severe human diseases such as cystic fibrosis. 293 matched cddid_all.tbl CDD cd18542 cd18542 349986 ABC_6TM_YknU_like Six-transmembrane helical domain (6-TMD) of the uncharacterized ABC transporter YknU and similar proteins. This group represents the six-transmembrane helical domain (6-TMD) of the uncharacterized ABC transporter YknU and similar proteins. This TMD possesses the ATP-binding cassette (ABC) exporter fold, which is characterized by 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds and a various type of lipids. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting significant structural diversity of the translocated substrates, while NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane. However, some ABC genes are organized as half-transporters, which must form either homodimers or heterodimers to form a functional transporter. The ABC exporters play a role in multidrug resistance to antibiotics and anticancer agents, and mutations in these proteins have been shown to cause severe human diseases such as cystic fibrosis. 292 matched cddid_all.tbl CDD cd18543 cd18543 349987 ABC_6TM_Rv0194_D1_like Six-transmembrane helical domain 1 (TMD1) of the multidrug efflux ABC transporter Rv0194 and similar proteins. This group includes the six-transmembrane helical domain 1 (TMD1) of the multidrug efflux ATP-binding/permease protein Rv0194 from Mycobacterium tuberculosis and similar proteins. This TMD possesses the ATP-binding cassette (ABC) exporter fold, which is characterized by 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds and a various type of lipids. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting significant structural diversity of the translocated substrates, while NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane. However, some ABC genes are organized as half-transporters, which must form either homodimers or heterodimers to form a functional transporter. The ABC exporters play a role in multidrug resistance to antibiotics and anticancer agents, and mutations in these proteins have been shown to cause severe human diseases such as cystic fibrosis. 291 matched cddid_all.tbl CDD cd18544 cd18544 349988 ABC_6TM_TmrA_like Six-transmembrane helical domain (TmrA) of the heterodimeric Thermus thermophilus multidrug resistance proteins TmrAB, and similar proteins. This group represents the six-transmembrane helical domain (TrmA) of the heterodimeric Thermus thermophilus multidrug resistance proteins A and B (TmrAB), a homolog of the Antigen Translocation Complex Tap, and similar proteins. TmrAB has been shown to able to restore antigen processing in human TAP-deficient cells. The 6-transmembrane (TM) helices typically found in the ATP-binding cassette (ABC) transporters that function as exporters, which contain 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds and a various type of lipids. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting significant structural diversity of the translocated substrates, while NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane. However, some ABC genes are organized as half-transporters, which must form either homodimers or heterodimers to form a functional transporter. The ABC exporters play a role in multidrug resistance to antibiotics and anticancer agents, and mutations in these proteins have been shown to cause severe human diseases such as cystic fibrosis. 294 matched cddid_all.tbl CDD cd18545 cd18545 349989 ABC_6TM_YknV_like Six-transmembrane helical domain (6-TMD) of the uncharacterized ABC transporter YknV and similar proteins. This group represents the six-transmembrane helical domain (6-TMD) of the uncharacterized ABC transporter YknV and similar proteins. This TMD possesses the ATP-binding cassette (ABC) exporter fold, which is characterized by 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds and a various type of lipids. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting significant structural diversity of the translocated substrates, while NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane. However, some ABC genes are organized as half-transporters, which must form either homodimers or heterodimers to form a functional transporter. The ABC exporters play a role in multidrug resistance to antibiotics and anticancer agents, and mutations in these proteins have been shown to cause severe human diseases such as cystic fibrosis. 293 matched cddid_all.tbl CDD cd18546 cd18546 349990 ABC_6TM_Rv0194_D2_like Six-transmembrane helical domain 2 (TMD2) of the multidrug efflux ABC transporter Rv0194 and similar proteins. This group includes the six-transmembrane helical domain 2 (TMD2) of the multidrug efflux ATP-binding/permease protein Rv0194 from Mycobacterium tuberculosis and similar proteins. This TMD possesses the ATP-binding cassette (ABC) exporter fold, which is characterized by 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds and a various type of lipids. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting significant structural diversity of the translocated substrates, while NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane. However, some ABC genes are organized as half-transporters, which must form either homodimers or heterodimers to form a functional transporter. The ABC exporters play a role in multidrug resistance to antibiotics and anticancer agents, and mutations in these proteins have been shown to cause severe human diseases such as cystic fibrosis. 292 matched cddid_all.tbl CDD cd18547 cd18547 349991 ABC_6TM_Tm288_like Six-transmembrane helical domain Tm288 of a heterodimeric ABC transporter Tm287/288 from Thermotoga maritima and similar proteins. This group represents the six-transmembrane helical domain (Tm288) of a heterodimeric ABC transporter Tm287/288 from Thermotoga maritima and similar proteins. This TMD possesses the ATP-binding cassette (ABC) exporter fold, which is characterized by 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds, a various type of lipids and polypeptides. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting significant structural diversity of the translocated substrates, while NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane by alternating between inward- and outward-facing conformations. Moreover, some ABC genes are organized as half-transporters, which must form either homodimers or heterodimers to form a functional transporter. The ABC exporters play a role in multidrug resistance to antibiotics and anticancer agents, and mutations in these proteins have been shown to cause severe human diseases such as cystic fibrosis. 298 matched cddid_all.tbl CDD cd18548 cd18548 349992 ABC_6TM_Tm287_like Six-transmembrane helical domain Tm287 of a heterodimeric ABC transporter Tm287/288 from Thermotoga maritima and similar proteins. This group represents the six-transmembrane helical domain (Tm287) of a heterodimeric ABC transporter Tm287/288 from Thermotoga maritima and similar proteins. This TMD possesses the ATP-binding cassette (ABC) exporter fold, which is characterized by 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds, a various type of lipids and polypeptides. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting significant structural diversity of the translocated substrates, while NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane by alternating between inward- and outward-facing conformations. Moreover, some ABC genes are organized as half-transporters, which must form either homodimers or heterodimers to form a functional transporter. The ABC exporters play a role in multidrug resistance to antibiotics and anticancer agents, and mutations in these proteins have been shown to cause severe human diseases such as cystic fibrosis. 292 matched cddid_all.tbl CDD cd18549 cd18549 349993 ABC_6TM_YwjA_like Six-transmembrane helical domain of an uncharacterized ABC transporter YwjA and similar proteins. This group represents the six-transmembrane helical domain of an uncharacterized ABC transporter YwjA from Bacillus subtilis and similar proteins. This transmembrane (TM) subunit possesses the ATP-binding cassette (ABC) exporter fold, which is characterized by 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds, a various type of lipids and polypeptides. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting significant structural diversity of the translocated substrates, while NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane by alternating between inward- and outward-facing conformations. Moreover, some ABC genes are organized as half-transporters, which must form either homodimers or heterodimers to form a functional transporter. The ABC exporters play a role in multidrug resistance to antibiotics and anticancer agents, and mutations in these proteins have been shown to cause severe human diseases such as cystic fibrosis. 295 matched cddid_all.tbl CDD cd18550 cd18550 349994 ABC_6TM_exporter_like Six-transmembrane helical domain (TMD) of an uncharacterized ABC exporter, and similar proteins. This group includes a subunit of six transmembrane (TM) helices typically found in the ATP-binding cassette (ABC) transporters that function as exporters, which contain 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds and a various type of lipids. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting the chemical diversity of the translocated substrates, while NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane. However, some ABC genes are organized as half-transporters, which must form either homodimers or heterodimers to form a functional transporter. The ABC exporters play a role in multidrug resistance to antibiotics and anticancer agents, and mutations in these proteins have been shown to cause severe human diseases such as cystic fibrosis. 294 matched cddid_all.tbl CDD cd18551 cd18551 349995 ABC_6TM_LmrA_like Six-transmembrane helical domain of the multidrug resistance ABC transporter LmrA and similar proteins. This group represents the six-transmembrane helical domain of the multidrug resistance ABC transporter LmrA from Lactococcus lactis and similar proteins. This transmembrane (TM) subunit possesses the ATP-binding cassette (ABC) exporter fold, which is characterized by 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds, a various type of lipids and polypeptides. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting significant structural diversity of the translocated substrates, while NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane by alternating between inward- and outward-facing conformations. Moreover, some ABC genes are organized as half-transporters, which must form either homodimers or heterodimers to form a functional transporter. The ABC exporters play a role in multidrug resistance to antibiotics and anticancer agents, and mutations in these proteins have been shown to cause severe human diseases such as cystic fibrosis. 289 matched cddid_all.tbl CDD cd18552 cd18552 349996 ABC_6TM_MsbA_like Six-transmembrane helical domain of the bacterial ABC lipid flippase MsbA and similar proteins. The bacterial lipid flippase MsbA is found in Gram-negative bacteria and transports lipid A and lipopolysaccharide (LPS) from the cytoplasmic leaflet to the periplasmic leaflet of the inner membrane. MsbA is also a polyspecific transporter capable of transporting a broad spectrum of drug molecules. Additionally, MsbA exhibits significant sequence similarity to mammalian multidrug resistance (MDR) proteins such as human MDR protein 1 (MDR1) and LmrA from Lactococcus lactis. This subgroup also contains a putative transporter Brevibacillus brevis TycD; the location of the tycD gene within the Tyc (tyrocidine) biosynthesis operon suggests that TycD may play a role in the secretion of the cyclic decapeptide antibiotic tyrocidine. This transmembrane (TM) subunit possesses the ATP-binding cassette (ABC) exporter fold, which is characterized by 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds, a various type of lipids and polypeptides. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting significant structural diversity of the translocated substrates, while NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane by alternating between inward- and outward-facing conformations. Moreover, some ABC genes are organized as half-transporters, which must form either homodimers or heterodimers to form a functional transporter. The ABC exporters play a role in multidrug resistance to antibiotics and anticancer agents, and mutations in these proteins have been shown to cause severe human diseases such as cystic fibrosis. 292 matched cddid_all.tbl CDD cd18553 cd18553 349997 ABC_6TM_PglK_like Six-transmembrane helical domain of the ABC transporter PglK and similar proteins. This group represents the transmembrane (TM) domain of an active lipid-linked oligosaccharides flippase PglK (protein glycosylation K), which is a homodimeric ABC transporter that flips a lipid-linked oligosaccharide that serves as a glycan donor in N-linked protein glycosylation. Pglk mediates the ATP-dependent translocation of the undecaprenylpyrophosphate-linked heptasaccharide intermediate across the cell membrane; this is an essential step during the N-linked protein glycosylation pathway. This TM subunit exhibits the ATP-binding cassette (ABC) exporter fold, which is characterized by 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds, a various type of lipids and polypeptides. Bacterial ABC exporters are typically expressed as half-transporters that contain one transmembrane domain (TMD) fused to a nucleotide-binding domain (NBD), which dimerize to form the full transporter. 300 matched cddid_all.tbl CDD cd18554 cd18554 349998 ABC_6TM_Sav1866_like Six-transmembrane helical domain of the bacterial ABC multidrug exporter Sav1866 and similar proteins. This group represents the homodimeric bacterial ABC multidrug exporter Sav1866, which is homologous to the lipid flippase MsbA, and both of which are functionally related to the human P-glycoprotein multidrug transporter (ABCB1 or MDR1). This transmembrane (TM) subunit possesses the ATP-binding cassette (ABC) exporter fold, which is characterized by 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds, a various type of lipids and polypeptides. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting significant structural diversity of the translocated substrates, while NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane by alternating between inward- and outward-facing conformations. Bacterial exporters are typically formed by dimers of TMD-NBD half-transporters. Thus, most bacterial ABC transporters are formed of two identical TMDs and two identical NBDs. 299 matched cddid_all.tbl CDD cd18555 cd18555 349999 ABC_6TM_T1SS_like Six-transmembrane helical domain (6-TMD) of the ATP-binding cassette subunit in the type 1 secretion systems, and similar proteins. This group represents the six-transmembrane helical domain (6-TMD) of the ABC subunit in the type 1 secretion systems (T1SS) and similar proteins. These transporter subunits include HylB, PrtD, CyaB, CvaB, RsaD, HasD, LipB, and LapB, among many others. T1SS are found in pathogenic Gram-negative bacteria (such as Escherichia coli, Vibrio cholerae or Bordetella pertussis) to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. In the case of the Escherichia coli HlyA T1SS, these three proteins are HlyB (a dimeric ABC transporter), HlyD (MFP, oligomeric membrane fusion protein) and TolC (OMP, a trimeric oligomeric outer membrane protein). Most targeted proteins are not cleaved at the N terminus, but rather carry signals located toward the extreme C terminus to direct type I secretion. However, the 10 kDa Escherichia coli colicin V (CvaB) targets the ABC transporter using a cleaved, N-terminal signal sequence. Almost all transport substrates of the type I system have critical functions in attacking host cells either directly or by being essential for host colonization. The ABC-dependent T1SS transports various molecules, from ions, drugs, to proteins of various sizes up to 900 kDa. The molecules secreted vary in size from the small Escherichia coli peptide colicin V, (10 kDa) to the Pseudomonas fluorescens cell adhesion protein LapA of 520 kDa. The best characterized are the RTX toxins such as the adenylate cyclase (CyaA) toxin from Bordetella pertussis, the causative agent of whooping cough, and the lipases such as LipA. Type I secretion is also involved in export of non-protein substrates such as cyclic beta-glucans and polysaccharides. 294 matched cddid_all.tbl CDD cd18556 cd18556 350000 ABC_6TM_McjD_like Six-transmembrane helical domain of the antibacterial peptide ATP-binding cassette transporter McjD and similar proteins. This group represents the 6-TM subunit of the ABC transporter McjD that exports the antibacterial peptide microcin J25, which is an antimicrobial peptide produced by Enterobacteriaceae against other microorganisms for survival under nutrient starvation. Thus, the ABC exporter McjD provides self-immunity of the producing bacteria through export of the toxic peptide out of the cell. Bacterial ABC exporters are typically expressed as half-transporters that contain one transmembrane domain (TMD) fused to a nucleotide-binding domain (NBD), which dimerize to form the full transporter. 298 matched cddid_all.tbl CDD cd18557 cd18557 350001 ABC_6TM_TAP_ABCB8_10_like Six-transmembrane helical domain (6-TMD) of the ABC transporter TAP, ABCB8 and ABCB10. This group includes ABC transporter associated with antigen processing (TAP), which is essential to cellular immunity against viral infection, as well as ABCB8 and ABCB10, which are found in the inner membrane of mitochondria, with the nucleotide-binding domains (NBDs) inside the mitochondrial matrix. TAP is involved in the transport of antigens from the cytoplasm to the endoplasmic reticulum(ER) for association with MHC class I molecules, which play a central role in the adaptive immune response to viruses and cancers by presenting antigenic peptides to CD8+ cytotoxic T lymphocytes (CTLs). Mammalian ABCB10 is essential for erythropoiesis and for protection of mitochondria against oxidative stress, while ABCB8 is essential for normal cardiac function, maintenance of mitochondrial iron homeostasis and maturation of cytosolic Fe/S proteins. 289 matched cddid_all.tbl CDD cd18558 cd18558 350002 ABC_6TM_Pgp_ABCB1 Six-transmembrane helical domain of P-glycoprotein 1 (Pgp) and related proteins. P-glycoprotein 1 (permeability glycoprotein, Pgp) also known as multidrug resistance protein 1 (MDR1) or ATP-binding cassette sub-family B member 1(ABCB1) is a member of the superfamily of ATP-binding cassette (ABC) transporters. Pgp acts as an ATP-dependent efflux pump, binds drugs with diverse chemical structures and pump them out of the drug resistant cancer cells. It is responsible for decreased drug accumulation in multidrug-resistant cells and mediates the development of resistance to anticancer drugs. Pgp consists of two alpha-helical transmembrane domains (TMDs) and two cytoplasmic nucleotide-binding domains (NBDs). This protein also functions as a transporter in the blood-brain barrier. In addition to Pgp, breast cancer resistance protein (BCRP/MXR/ABC-P/ABCG2) and multidrug resistance-associated proteins (MRP1/ABCC1 and MRP2/ABCC2) function as drug efflux pumps of anticancer drugs, and overexpression of these transporters induces multidrug resistance to a broad spectrum of anticancer drugs including doxorubicin, taxol, and vinca alkaloids by actively pumping the drugs out of cells. 312 matched cddid_all.tbl CDD cd18559 cd18559 350003 ABC_6TM_ABCC Six-transmembrane helical domain of the ABC transporters, subfamily C. This group represents the 6-transmembrane (6TM) domain of the ABC transporters that belong to the ABCC subfamily, such as the sulphonylurea receptors SUR1/2 (ABCC8), the cystic fibrosis transmembrane conductance regulator (CFTR, ABCC7), Multidrug-Resistance associated Proteins (MRP1-9), VMR1 (vacuolar multidrug resistance protein 1), and YOR1 (yeast oligomycin resistance transporter protein). This TM subunit exhibits the type 3 ATP-binding cassette (ABC) exporter fold, which is characterized by 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The type 3 ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds, a various type of lipids and polypeptides. 290 matched cddid_all.tbl CDD cd18560 cd18560 350004 ABC_6TM_ATM1_ABCB7_HMT1_ABCB6 Six-transmembrane helical domain (6-TMD) of the Atm1/ABCB7/HMT1/ABCB6 subfamily. This group represents the Atm1/ABCB7/HMT1/ABCB6 subfamily of ATP Binding Cassette (ABC) transporters that are involved in transition metal homeostasis and detoxification processes. Yeast ATM1 and human ABCB7 (ABC transporter subfamily B, member 7), which are involved in the assembly of cytosolic iron-sulfur (Fe/S) cluster-containing proteins by mediating export of Fe/S cluster precursors from mitochondria. In eukaryotes, the Atm1/ABCB7 is present in the inner membrane of mitochondria and is required for the formation of cytosolic iron sulfur cluster containing proteins; mutations of ABCB7 gene result in mitochondrial iron accumulation and are responsible for X-linked sideroblastic anemia. ABCB6 is originally identified as a porphyrin transporter present in the outer membrane of mitochondria. It is highly expressed in cells resistance to arsenic and protects against arsenic cytotoxicity. Moreover, Heavy Metal Tolerance Factor-1 (HMT1) proteins are required for cadmium resistance in Caenorhabditis elegans and Drosophila melanogaster. 292 matched cddid_all.tbl CDD cd18561 cd18561 350005 ABC_6TM_AarD_CydDC_like Six-transmembrane helical domain (6-TMD) of the ABC cysteine/GSH transporter CydDC, and similar proteins. The CydD protein, together with the CydC protein, constitutes a bacterial heterodimeric ATP-binding cassette (ABC) transporter complex required for formation of the functional cytochrome bd oxidase in both gram-positive and gram-negative aerobic bacteria. In Escherichia coli, the biogenesis of both cytochrome bd-type quinol oxidases and periplasmic cytochromes requires the ABC-type cysteine/GSH transporter CydDC, which exports cysteine and glutathione from the cytoplasm to the periplasm to maintain redox homeostasis. Mutations in AarD, a homolog from Providencia stuartii, also show phenotypic characteristic consistent with a defect in the cytochrome d oxidase. The CydDC forms a heterodimeric ABC transporter with two transmembrane domains (TMDs), each predicted to comprise six TM alpha-helices and two nucleotide binding domains (NBDs). 289 matched cddid_all.tbl CDD cd18562 cd18562 350006 ABC_6TM_NdvA_beta-glucan_exporter_like Six-transmembrane helical domain of the cyclic beta-glucan ABC transporter NdvA, and similar proteins. This group represents the six-transmembrane domain of NdvA, an ATP-dependent exporter of cyclic beta glucans, and similar proteins. NdvA is required for nodulation of legume roots and is involved in beta-(1,2)-glucan export to the periplasm. NdvA mutants in Brucella abortus and Sinorhizobium meliloti have been shown to exhibit decreased virulence in mice and inhibit intracellular multiplication in HeLa cells. These results suggest that cyclic beta-(1,2)-glucan is required to transport into the periplasmatic space to function as a virulence factor. Bacterial exporters are typically formed by dimers of TMD-NBD half-transporters. Thus, most bacterial ABC transporters are formed of two identical TMDs and two identical NBDs. 289 matched cddid_all.tbl CDD cd18563 cd18563 350007 ABC_6TM_exporter_like Six-transmembrane helical domain (TMD) of an uncharacterized ABC exporter, and similar proteins. This group includes a subunit of six transmembrane (TM) helices typically found in the ATP-binding cassette (ABC) transporters that function as exporters, which contain 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds and a various type of lipids. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting the chemical diversity of the translocated substrates, while NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane. However, some ABC genes are organized as half-transporters, which must form either homodimers or heterodimers to form a functional transporter. The ABC exporters play a role in multidrug resistance to antibiotics and anticancer agents, and mutations in these proteins have been shown to cause severe human diseases such as cystic fibrosis. 296 matched cddid_all.tbl CDD cd18564 cd18564 350008 ABC_6TM_exporter_like Six-transmembrane helical domain (TMD) of an uncharacterized ABC exporter, and similar proteins. This group includes a subunit of six transmembrane (TM) helices typically found in the ATP-binding cassette (ABC) transporters that function as exporters, which contain 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds and a various type of lipids. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting the chemical diversity of the translocated substrates, while NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane. However, some ABC genes are organized as half-transporters, which must form either homodimers or heterodimers to form a functional transporter. The ABC exporters play a role in multidrug resistance to antibiotics and anticancer agents, and mutations in these proteins have been shown to cause severe human diseases such as cystic fibrosis. 307 matched cddid_all.tbl CDD cd18565 cd18565 350009 ABC_6TM_exporter_like Six-transmembrane helical domain (TMD) of an uncharacterized ABC exporter, and similar proteins. This group includes a subunit of six transmembrane (TM) helices typically found in the ATP-binding cassette (ABC) transporters that function as exporters, which contain 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds and a various type of lipids. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting the chemical diversity of the translocated substrates, while NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane. However, some ABC genes are organized as half-transporters, which must form either homodimers or heterodimers to form a functional transporter. The ABC exporters play a role in multidrug resistance to antibiotics and anticancer agents, and mutations in these proteins have been shown to cause severe human diseases such as cystic fibrosis. 313 matched cddid_all.tbl CDD cd18566 cd18566 350010 ABC_6TM_PrtD_LapB_HlyB_like Six-transmembrane helical domain (6-TMD) of the ABC subunit in the type 1 secretion systems (PrtD, LapB, HylB), and similar proteins. This group represents the six-transmembrane helical domain (6-TMD) of the ABC subunit in the type 1 secretion systems (T1SS), including PrtD, LapB, and HylB. T1SS are found in pathogenic Gram-negative bacteria (such as Escherichia coli, Vibrio cholerae or Bordetella pertussis) to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type 1 secretion apparatus. In the case of the Escherichia coli HlyA T1SS, these three proteins are HlyB (a dimeric ABC transporter), HlyD (MFP, oligomeric membrane fusion protein) and TolC (OMP, a trimeric oligomeric outer membrane protein). These three components assemble into a complex spanning both membranes and provide a channel for the translocation of unfolded polypeptides. In addition, PrtD is the integral membrane ATP-binding cassette component of the Erwinia chrysanthemi metalloprotease secretion system (PrtDEF). LabB is an inner-membrane transporter component of the LapBCE system that is required for the secretion of the LapA adhesion. 294 matched cddid_all.tbl CDD cd18567 cd18567 350011 ABC_6TM_CvaB_RaxB_like Six-transmembrane helical domain (6-TMD) of the ABC transporter subunit of the type 1 secretion systems, CvaB and RaxB, and similar proteins. This group represents the six-transmembrane helical domain (6-TMD) of the peptidase-containing ABC transporter subunit of T1SS (Type 1 secretion systems), such as Escherichia coli colicin V secretion/processing ATP-binding protein CvaB and putative ABC transporter RaxB. These ABC-transporter proteins carry a proteolytic peptidase domain in their N-termini, termed as C39, which cleaves a double glycine (GG) motif-containing signal peptide from substrates before secretion. RaxB is part of the T1SS RaxABC, which is responsible for the type 1-dependent secretion of the bacterial quorum-sensing molecule AvrXa21. Both CvaB and RaxB belong to a subgroup of T1SS ABC transporters that contain a C39 peptidase domain. T1SS are found in pathogenic Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. 294 matched cddid_all.tbl CDD cd18568 cd18568 350012 ABC_6TM_HetC_like Six-transmembrane helical domain (6-TMD) of the ABC subunit of T1SS-like HetC and similar proteins. This group represents the six-transmembrane helical domain (6-TMD) of the ABC subunit of T1SS (type 1 secretion systems), such as heterocyst differentiation protein HetC. HetC is similar to ABC protein exporters of T1SS (type 1 secretion systems) and is involved in early regulation of heterocyst differentiation in the filamentous cynobacterium Anabaena sp. T1SS are found in pathogenic Gram-negative bacteria (such as Escherichia coli, Vibrio cholerae or Bordetella pertussis) to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. ABC-transporter proteins in this group carry a proteolytic peptidase domain in their N-termini, termed as C39, which cleaves a double glycine (GG) motif-containing signal peptide from substrates before secretion. 294 matched cddid_all.tbl CDD cd18569 cd18569 350013 ABC_6TM_NHLM_bacteriocin Six-transmembrane helical domain (6-TMD) of NHLP family bacteriocin export ABC transporters. This group includes the six-transmembrane helical domain (6-TMD) of the ABC subunit of NHLM (Nitrile Hydratase Leader Microcin) bacteriocin system, which contains ABC transporter (permease/ATP-binding fused protein) with a peptidase domain. ABC-transporter proteins in this group are predicted to be a subunit of a bacteriocin processing and export system, and they carry a proteolytic peptidase domain in their N-termini, termed as C39, which cleaves a double glycine (GG) motif-containing signal peptide from substrates before secretion. 294 matched cddid_all.tbl CDD cd18570 cd18570 350014 ABC_6TM_PCAT1_LagD_like Six-transmembrane helical domain (6-TMD) of the peptidase-containing ATP-binding cassette transporters. This group includes the 6-TMD of the peptidase-containing ATP-binding cassette transporters (PCATs) such as Clostridium thermocellum PCAT1, a polypeptide processing and secretion transporter, and LagD, a bacteriocin ABC transporter from Lactococcus lactis. Bacterial exporters are typically formed by dimers of TMD-NBD half-transporters. Thus, most bacterial ABC transporters are formed of two identical TMDs and two identical NBDs. The transporters involved in protein secretion often contain additional peptidase domains essential for substrate processing. These peptidase domains belong to the cysteine protease superfamily, classified as family C39, bacteriocin-processing peptidase. LagD is highly similar to the peptidase-containing ATP-binding cassette transporters (PCATs). In Gram-positive bacteria, the PCATs are responsible for exporting quorum-sensing or antimicrobial peptides called bacteriocins. 294 matched cddid_all.tbl CDD cd18571 cd18571 350015 ABC_6TM_peptidase_like Six-transmembrane helical domain (6-TMD) of an uncharacterized peptidase ABC transporter and similar proteins. This group includes the 6-TMD of an uncharacterized peptidase-containing ABC transporter of T1SS (type 1 secretion systems), similar to heterocyst differentiation protein HetC. HetC is involved in early regulation of heterocyst differentiation in the filamentous cynobacterium Anabaena sp. T1SS are found in pathogenic Gram-negative bacteria (such as Escherichia coli, Vibrio cholerae or Bordetella pertussis) to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. ABC-transporter proteins in this group carry a proteolytic peptidase domain in their N-termini, termed as C39, which cleaves a double glycine (GG) motif-containing signal peptide from substrates before secretion. 294 matched cddid_all.tbl CDD cd18572 cd18572 350016 ABC_6TM_TAP Six-transmembrane helical domain (6-TMD) of the ABC transporter associated with antigen processing. This group represents the 6-TM subunit of the ABC transporter associated with antigen processing (TAP), which is essential to cellular immunity against viral infection. TAP is involved in the transport of antigens from the cytoplasm to the endoplasmic reticulum(ER) for association with MHC class I molecules, which play a central role in the adaptive immune response to viruses and cancers by presenting antigenic peptides to CD8+ cytotoxic T lymphocytes (CTLs). It also acts as a molecular scaffold for the assembly of the MHC I peptide-loading complex in the ER membrane. Newly synthesized MHC class I molecules associate with TAP via tapasin, which is one component of the peptide-loading complex. TAP is a heterodimer formed by two distinct subunits, TAP1 (ABCB2) and TAP2 (ABCB3), each half-transporter comprises one transmembrane domain (TMD) and one nucleotide domain (NBD). Two 6-helical core TMDs contain the peptide-binding pocket and translocation channel, while the NBDs bind and hydrolyze ATP to power peptide translocation. 289 matched cddid_all.tbl CDD cd18573 cd18573 350017 ABC_6TM_ABCB10_like Six-transmembrane helical domain (6-TMD) of the mitochondrial transporter ABCB10 (subfamily B, member 10) and similar proteins. This group includes the 6-TM subunit of the ABC10 (also known as ABC mitochondrial erythroid, ABC-me, mABC2, or ABCBA), which is one of the three ATP-binding cassette (ABC) transporters found in the inner membrane of mitochondria, with the nucleotide-binding domains (NBDs) inside the mitochondrial matrix. In mammals, ABCB10 is essential for erythropoiesis and for protection of mitochondria against oxidative stress. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting significant structural diversity of the translocated substrates, while NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane. 294 matched cddid_all.tbl CDD cd18574 cd18574 350018 ABC_6TM_ABCB8_like Six-transmembrane helical domain (6-TMD) of ATP-binding cassette transporter subfamily B member 8, mitochondrial, and similar proteins. This group includes ABCB8, which is one of the three ATP-binding cassette (ABC) transporters found in the inner membrane of mitochondria, with the nucleotide-binding domains (NBDs) inside the mitochondrial matrix. ABCB8 is essential for maintenance of normal cardiac function, involves mitochondrial iron export, and plays a role in the maturation of cytosolic Fe/S cluster-containing enzymes. ABCB8 is a half-molecule ABC protein that contains one TMD fused to a NBD, which dimerize to form a functional transporter. 295 matched cddid_all.tbl CDD cd18575 cd18575 350019 ABC_6TM_bac_exporter_ABCB8_10_like Six-transmembrane helical domain of putative bacterial ABC exporters, similar to ABCB8 and ABCB10. This group includes putative bacterial ABC transporters similar to ABCB8 and ABCB10, which are found in the inner membrane of mitochondria, with the nucleotide-binding domains (NBDs) inside the mitochondrial matrix. Mammalian ABCB10 is essential for erythropoiesis and for protection of mitochondria against oxidative stress, while ABCB8 is essential for normal cardiac function, maintenance of mitochondrial iron homeostasis and maturation of cytosolic Fe/S proteins. Bacterial exporters are typically formed by dimers of TMD-NBD half-transporters. Thus, most bacterial ABC transporters are formed of two identical TMDs and two identical NBDs. 289 matched cddid_all.tbl CDD cd18576 cd18576 350020 ABC_6TM_bac_exporter_ABCB8_10_like Six-transmembrane helical domain of putative bacterial ABC exporters, similar to ABCB8 and ABCB10. This group includes putative bacterial ABC transporters similar to ABCB8 and ABCB10, which are found in the inner membrane of mitochondria, with the nucleotide-binding domains (NBDs) inside the mitochondrial matrix. Mammalian ABCB10 is essential for erythropoiesis and for protection of mitochondria against oxidative stress, while ABCB8 is essential for normal cardiac function, maintenance of mitochondrial iron homeostasis and maturation of cytosolic Fe/S proteins. Bacterial exporters are typically formed by dimers of TMD-NBD half-transporters. Thus, most bacterial ABC transporters are formed of two identical TMDs and two identical NBDs. 289 matched cddid_all.tbl CDD cd18577 cd18577 350021 ABC_6TM_Pgp_ABCB1_D1_like Six-transmembrane helical domain 1 (TMD1) of P-glycoprotein 1 (Pgp) and related proteins. P-glycoprotein 1 (permeability glycoprotein, Pgp) also known as multidrug resistance protein 1 (MDR1) or ATP-binding cassette sub-family B member 1 (ABCB1) is a member of the superfamily of ATP-binding cassette (ABC) transporters. Pgp acts as an ATP-dependent efflux pump, binds drugs with diverse chemical structures and pump them out of the drug resistant cancer cells. It is responsible for decreased drug accumulation in multidrug-resistant cells and mediates the development of resistance to anticancer drugs. Pgp consists of two alpha-helical transmembrane domains (TMDs) and two cytoplasmic nucleotide-binding domains (NBDs). This protein also functions as a transporter in the blood-brain barrier. In addition to Pgp, breast cancer resistance protein (BCRP/MXR/ABC-P/ABCG2) and multidrug resistance-associated proteins (MRP1/ABCC1 and MRP2/ABCC2) function as drug efflux pumps of anticancer drugs, and overexpression of these transporters induces multidrug resistance to a broad spectrum of anticancer drugs including doxorubicin, taxol, and vinca alkaloids by actively pumping the drugs out of cells. 300 matched cddid_all.tbl CDD cd18578 cd18578 350022 ABC_6TM_Pgp_ABCB1_D2_like Six-transmembrane helical domain 2 (TMD2) of P-glycoprotein 1 (Pgp) and related proteins. P-glycoprotein 1 (permeability glycoprotein, Pgp) also known as multidrug resistance protein 1 (MDR1) or ATP-binding cassette sub-family B member 1 (ABCB1) is a member of the superfamily of ATP-binding cassette (ABC) transporters. Pgp acts as an ATP-dependent efflux pump, binds drugs with diverse chemical structures and pump them out of the drug resistant cancer cells. It is responsible for decreased drug accumulation in multidrug-resistant cells and mediates the development of resistance to anticancer drugs. Pgp consists of two alpha-helical transmembrane domains (TMDs) and two cytoplasmic nucleotide-binding domains (NBDs). This protein also functions as a transporter in the blood-brain barrier. In addition to Pgp, breast cancer resistance protein (BCRP/MXR/ABC-P/ABCG2) and multidrug resistance-associated proteins (MRP1/ABCC1 and MRP2/ABCC2) function as drug efflux pumps of anticancer drugs, and overexpression of these transporters induces multidrug resistance to a broad spectrum of anticancer drugs including doxorubicin, taxol, and vinca alkaloids by actively pumping the drugs out of cells. 317 matched cddid_all.tbl CDD cd18579 cd18579 350023 ABC_6TM_ABCC_D1 Six-transmembrane helical domain 1 (TMD1) of the ABC transporters, subfamily C. This group represents the six-transmembrane domain 1 (TMD1)of the ABC transporters that belong to the ABCC subfamily, such as the sulphonylurea receptors SUR1/2 (ABCC8), the cystic fibrosis transmembrane conductance regulator (CFTR, ABCC7), Multidrug-Resistance associated Proteins (MRP1-9), VMR1 (vacuolar multidrug resistance protein 1), and YOR1 (yeast oligomycin resistance transporter protein). This TM subunit exhibits the type 3 ATP-binding cassette (ABC) exporter fold, which is characterized by 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The type 3 ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds, a various type of lipids and polypeptides. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane by alternating between inward- and outward-facing conformations. By contrast, bacterial ABC exporters are typically assembled from dimers of TMD-NBD half-transporters. Thus, most bacterial ABC transporters are comprised of two identical TMDs and two identical NBDs. 289 matched cddid_all.tbl CDD cd18580 cd18580 350024 ABC_6TM_ABCC_D2 Six-transmembrane helical domain 2 (TMD2) of the ABC transporters, subfamily C. This group represents the six-transmembrane domain 2 (TMD2) of the ABC transporters that belong to the ABCC subfamily, such as the sulphonylurea receptors SUR1/2 (ABCC8), the cystic fibrosis transmembrane conductance regulator (CFTR, ABCC7), Multidrug-Resistance associated Proteins (MRP1-9), VMR1 (vacuolar multidrug resistance protein 1), and YOR1 (yeast oligomycin resistance transporter protein). This TM subunit exhibits the type 3 ATP-binding cassette (ABC) exporter fold, which is characterized by 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The type 3 ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds, a various type of lipids and polypeptides. All ABC transporters share a common architecture of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane by alternating between inward- and outward-facing conformations. By contrast, bacterial ABC exporters are typically assembled from dimers of TMD-NBD half-transporters. Thus, most bacterial ABC transporters are comprised of two identical TMDs and two identical NBDs. 294 matched cddid_all.tbl CDD cd18581 cd18581 350025 ABC_6TM_ABCB6 Six-transmembrane helical domain of the ATP-binding cassette subfamily B member 6, mitochondrial. This group represents the ABCB6 subfamily of ATP Binding Cassette (ABC) transporters that are involved in transition metal homeostasis and detoxification processes. ABCB6 is originally identified as a porphyrin transporter present in the outer membrane of mitochondria. It is highly expressed in cells resistance to arsenic and protects against arsenic cytotoxicity. Moreover, ABCB6 (ABC transporter subfamily B, member 6) is closely related to yeast ATM1 and human ABCB7, which are involved in the assembly of cytosolic iron-sulfur (Fe/S) cluster-containing proteins by mediating export of Fe/S cluster precursors from mitochondria. In eukaryotes, the Atm1/ABCB7 is present in the inner membrane of mitochondria and is required for the formation of cytosolic iron sulfur cluster containing proteins; mutations of ABCB7 gene result in mitochondrial iron accumulation and are responsible for X-linked sideroblastic anemia. 300 matched cddid_all.tbl CDD cd18582 cd18582 350026 ABC_6TM_ATM1_ABCB7 Six-transmembrane helical domain of the Atm1/ABC7 transporters. This group represents the Atm1/ABCB7 subfamily of ATP Binding Cassette (ABC) transporters that are involved in transition metal homeostasis and detoxification processes. Yeast ATM1 and human ABCB7 (ABC transporter subfamily B, member 7), which are involved in the assembly of cytosolic iron-sulfur (Fe/S) cluster-containing proteins by mediating export of Fe/S cluster precursors from mitochondria. In eukaryotes, the Atm1/ABCB7 is present in the inner membrane of mitochondria and is required for the formation of cytosolic iron sulfur cluster containing proteins; mutations of ABCB7 gene result in mitochondrial iron accumulation and are responsible for X-linked sideroblastic anemia. 292 matched cddid_all.tbl CDD cd18583 cd18583 350027 ABC_6TM_HMT1 Six-transmembrane helical domain of the heavy metal tolerance protein. This group represents the HMT1 subfamily of ATP Binding Cassette (ABC) transporters that are involved in transition metal homeostasis and detoxification processes. Heavy Metal Tolerance Factor-1 (HMT1) proteins are required for cadmium resistance in Caenorhabditis elegans and Drosophila melanogaster. HMT1 is closely related to Yeast ATM1 and human ABCB7 (ABC transporter subfamily B, member 7), which are involved in the assembly of cytosolic iron-sulfur (Fe/S) cluster-containing proteins by mediating export of Fe/S cluster precursors from mitochondria. 290 matched cddid_all.tbl CDD cd18584 cd18584 350028 ABC_6TM_AarD_CydD Six-transmembrane helical domain (6TM) of the CydD, a component of the ABC cysteine/GSH transporter, and a homolog AarD. The CydD protein, together with the CydC protein, constitutes a bacterial heterodimeric ATP-binding cassette (ABC) transporter complex required for formation of the functional cytochrome bd oxidase in both gram-positive and gram-negative aerobic bacteria. In Escherichia coli, the biogenesis of both cytochrome bd-type quinol oxidases and periplasmic cytochromes requires the ABC-type cysteine/GSH transporter CydDC, which exports cysteine and glutathione from the cytoplasm to the periplasm to maintain redox homeostasis. Mutations in AarD, a homolog from Providencia stuartii, also show phenotypic characteristic consistent with a defect in the cytochrome d oxidase. The CydDC forms a heterodimeric ABC transporter with two transmembrane domains (TMDs), each predicted to comprise six TM alpha-helices and two nucleotide binding domains (NBDs). 290 matched cddid_all.tbl CDD cd18585 cd18585 350029 ABC_6TM_CydC Six-transmembrane helical domain (6-TMD) of the CydC, a component of the ABC cysteine/GSH transporter. The CydC protein, together with the CydD protein, constitutes a bacterial heterodimeric ATP-binding cassette (ABC) transporter complex required for formation of the functional cytochrome bd oxidase in both gram-positive and gram-negative aerobic bacteria. In Escherichia coli, the biogenesis of both cytochrome bd-type quinol oxidases and periplasmic cytochromes requires the ABC-type cysteine/GSH transporter CydDC, which exports cysteine and glutathione from the cytoplasm to the periplasm to maintain redox homeostasis. The CydDC forms a heterodimeric ABC transporter with two transmembrane domains (TMDs), each predicted to comprise six TM alpha-helices and two nucleotide binding domains (NBDs). 290 matched cddid_all.tbl CDD cd18586 cd18586 350030 ABC_6TM_PrtD_like Six-transmembrane helical domain (6TM) domain of the ABC subunit (PrtD) in the T1SS metalloprotease secretion system, and similar proteins. This group represents the six-transmembrane helical domain (6-TMD) of the ABC subunit in the type 1 secretion systems (T1SS) such as PrtD, which is the integral membrane ATP-binding cassette component of the Erwinia chrysanthemi metalloprotease secretion system (PrtDEF). T1SS are found in pathogenic Gram-negative bacteria (such as Escherichia coli, Vibrio cholerae or Bordetella pertussis) to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. The Aquifex aeolicus PrtDEF of T1SS is composed of an inner-membrane ABC transporter (PrtD), a periplasmic membrane-fusion protein (PrtE), and an outer-membrane porin (PrtF). These three components assemble into complex spanning both membranes and provide a channel for the translocation of unfolded polypeptides 291 matched cddid_all.tbl CDD cd18587 cd18587 350031 ABC_6TM_LapB_like Six-transmembrane helical domain of the ABC transporter subunit LapB and similar proteins. This group represents the six-transmembrane helical domain (6-TMD) of the ABC subunit in the type 1 secretion systems (T1SS), such as LapB. LapB is an inner-membrane transporter component of the LapBCE system that is required for the secretion of the LapA adhesion, LapA is a RTX (repeats in toxin) protein found in Pseudomonas fluorescens and is required for biofilm formation in this organism. T1SS are found in pathogenic Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. In this T1SS system, LapB is a cytoplasmic membrane-localized ATPase, LapC is a membrane fusion protein, and LapE is an outer membrane protein. 293 matched cddid_all.tbl CDD cd18588 cd18588 350032 ABC_6TM_CyaB_HlyB_like Six-transmembrane helical domain of the ABC subunits of T1SS, CyaB/HylB, and similar proteins. This group represents the six-transmembrane helical domain (6-TMD) of the ABC subunits of T1SS, such as CyaG and HlyB. T1SS are found in pathogenic Gram-negative bacteria (such as Escherichia coli, Vibrio cholerae or Bordetella pertussis) to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. In the case of the Escherichia coli HlyA T1SS, these three proteins are HlyB (a dimeric ABC transporter), HlyD (MFP, oligomeric membrane fusion protein) and TolC (OMP, a trimeric oligomeric outer membrane protein). These three components assemble into a complex spanning both membranes and provide a channel for the translocation of unfolded polypeptides. Additionally, CyaB is part of the three T1SS complex proteins for adenylate cyclase toxin CyaA, which is a primary virulence factor in Bordetella pertussis: CyaB (an ABC transporter) CyaD (a membrane fusion protein), and CyaE (an outer membrane protein). 294 matched cddid_all.tbl CDD cd18589 cd18589 350033 ABC_6TM_TAP1 Six-transmembrane helical domain 1 (6-TMD1) of the ABC transporter associated with antigen processing 1 (TAP1). This group represents the 6-TM subunit of the ABC transporter associated with antigen processing (TAP), which is essential to cellular immunity against viral infection. TAP is involved in the transport of antigens from the cytoplasm to the endoplasmic reticulum(ER) for association with MHC class I molecules, which play a central role in the adaptive immune response to viruses and cancers by presenting antigenic peptides to CD8+ cytotoxic T lymphocytes (CTLs). It also acts as a molecular scaffold for the assembly of the MHC I peptide-loading complex in the ER membrane. Newly synthesized MHC class I molecules associate with TAP via tapasin, which is one component of the peptide-loading complex. TAP is a heterodimer formed by two distinct subunits, TAP1 (ABCB2) and TAP2 (ABCB3), each half-transporter comprises one transmembrane domain (TMD) and one nucleotide domain (NBD). Two 6-helical core TMDs contain the peptide-binding pocket and translocation channel, while the NBDs bind and hydrolyze ATP to power peptide translocation. 289 matched cddid_all.tbl CDD cd18590 cd18590 350034 ABC_6TM_TAP2 Six-transmembrane helical domain 2 (6-TMD2) of the ABC transporter associated with antigen processing 2 (TAP2). This group represents the 6-TM subunit of the ABC transporter associated with antigen processing (TAP), which is essential to cellular immunity against viral infection. TAP is involved in the transport of antigens from the cytoplasm to the endoplasmic reticulum(ER) for association with MHC class I molecules, which play a central role in the adaptive immune response to viruses and cancers by presenting antigenic peptides to CD8+ cytotoxic T lymphocytes (CTLs). It also acts as a molecular scaffold for the assembly of the MHC I peptide-loading complex in the ER membrane. Newly synthesized MHC class I molecules associate with TAP via tapasin, which is one component of the peptide-loading complex. TAP is a heterodimer formed by two distinct subunits, TAP1 (ABCB2) and TAP2 (ABCB3), each half-transporter comprises one transmembrane domain (TMD) and one nucleotide domain (NBD). Two 6-helical core TMDs contain the peptide-binding pocket and translocation channel, while the NBDs bind and hydrolyze ATP to power peptide translocation. 289 matched cddid_all.tbl CDD cd18591 cd18591 350035 ABC_6TM_SUR1_D1_like Six-transmembrane helical domain 1 (TMD1) of the sulphonylurea receptors SUR1/2. This group represents the six-transmembrane domain 1 (TMD1) of the sulphonylurea receptors SUR1/2 (ABCC8), which function as a modulator of ATP-sensitive potassium channels and insulin release, and they belong to the ABCC subfamily. The ATP-sensitive (K-ATP) channel is an octameric complex of four pore-forming Kir6.2 subunits and four regulatory SUR subunits. Thus, in contrast to other ABC transporters, the SUR serves as the regulatory subunit of an ion channel. Mutations and deficiencies in the SUR proteins have been observed in patients with hyperinsulinemic hypoglycemia of infancy, an autosomal recessive disorder of unregulated and high insulin secretion. Mutations have also been associated with non-insulin-dependent diabetes mellitus type 2, an autosomal dominant disease of defective insulin secretion. 309 matched cddid_all.tbl CDD cd18592 cd18592 350036 ABC_6TM_MRP5_8_9_D1 Six-transmembrane helical domain 1 (TMD1) of multidrug resistance-associated proteins (MRPs) 5, 8, and 9. This group represents the six-transmembrane domain 1 (TMD1) of multidrug resistance-associated proteins (MRPs) 5, 8, and 9, all of which are belonging to the subfamily C of the ATP-binding cassette (ABC) transporter superfamily. The MRP subfamily (ABCC subfamily) is composed of 13 members, of which MRP1 to MRP9 are the major transporters that cause multidrug resistance in tumor cells by pumping anticancer drugs out of the cell. These nine MRP members function as ATP-dependent exporters for endogenous substances and xenobiotics. MRP family can be divided into two groups, depending on their structural architecture. MRP4, MRP5, MRP8, and MRP9 (ABCC4, 5, 11 and 12, respectively) have a typical ABC transporter structure and each composed of two transmembrane domains (TMD1 and TMD2) and two nucleotide domains (NBD1 and NBD2). On the other hand, MRP1, 2, 3, 6 and 7 (ABCC1, 2, 3, 6 and 7, respectively) have an additional N-terminal five transmembrane segments in a single domain (TMD0) connected to the core (TMD-NBD) by a cytoplasmic linker (L0). 287 matched cddid_all.tbl CDD cd18593 cd18593 350037 ABC_6TM_MRP4_D1_like Six-transmembrane helical domain 1 (TMD1) of multidrug resistance-associated protein 4 (MRP4) and similar proteins. This group represents the six-transmembrane domain 1 (TMD1) of multidrug resistance-associated protein 4 (MRP4), which belongs to the subfamily C of the ATP-binding cassette (ABC) transporter superfamily. The MRP subfamily (ABCC subfamily) is composed of 13 members, of which MRP1 to MRP9 are the major transporters that cause multidrug resistance in tumor cells by pumping anticancer drugs out of the cell. These nine MRP members function as ATP-dependent exporters for endogenous substances and xenobiotics. MRP family can be divided into two groups, depending on their structural architecture. MRP4, MRP5, MRP8, and MRP9 (ABCC4, 5, 11 and 12, respectively) have a typical ABC transporter structure and each composed of two transmembrane domains (TMD1 and TMD2) and two nucleotide domains (NBD1 and NBD2). On the other hand, MRP1, 2, 3, 6 and 7 (ABCC1, 2, 3, 6 and 7, respectively) have an additional N-terminal five transmembrane segments in a single domain (TMD0) connected to the core (TMD-NBD) by a cytoplasmic linker (L0). 291 matched cddid_all.tbl CDD cd18594 cd18594 350038 ABC_6TM_CFTR_D1 Six-transmembrane helical domain 1 of Cystic Fibrosis Transmembrane Conductance Regulator. This group represents the six-transmembrane domain 1 (TMD1) of the cystic fibrosis transmembrane conductance regulator (CFTR, ABCC7), which belongs to the ABCC subfamily. CFTR functions as a chloride channel, in contrast to other ABC transporters, and controls ion and water secretion and absorption in epithelial tissues. ABC proteins are formed from two homologous halves each containing a transmembrane domain (TMD) and a cytosolic nucleotide binding domain (NBD). In CFTR, these two TMD-NBD halves are linked by the unique regulatory (R) domain, which is not present in other ABC transporters. The ion channel only opens when its R-domain is phosphorylated by cyclic AMP-dependent protein kinase (PKA) and ATP is bound at the NBDs. Mutations in CFTR cause cystic fibrosis, the most common lethal genetic disorder in populations of Northern European descent. 291 matched cddid_all.tbl CDD cd18595 cd18595 350039 ABC_6TM_MRP1_2_3_6_D1_like Six-transmembrane helical domain 1 (TMD1) of multidrug resistance-associated proteins (MRPs) 1, 2, 3 and 6. This group represents the six-transmembrane domain 1 (TMD1) of multidrug resistance-associated proteins (MRPs) 1, 2, 3 and 6, all of which are belonging to the subfamily C of the ATP-binding cassette (ABC) transporter superfamily. The MRP subfamily (ABCC subfamily) is composed of 13 members, of which MRP1 to MRP9 are the major transporters that cause multidrug resistance in tumor cells by pumping anticancer drugs out of the cell. These nine MRP members function as ATP-dependent exporters for endogenous substances and xenobiotics. MRP family can be divided into two groups, depending on their structural architecture. MRP4, MRP5, MRP8, and MRP9 (ABCC4, 5, 11 and 12, respectively) have a typical ABC transporter structure and each composed of two transmembrane domains (TMD1 and TMD2) and two nucleotide domains (NBD1 and NBD2). On the other hand, MRP1, 2, 3, 6 and 7 (ABCC1, 2, 3, 6 and 7, respectively) have an additional N-terminal five transmembrane segments in a single domain (TMD0) connected to the core (TMD-NBD) by a cytoplasmic linker (L0). 290 matched cddid_all.tbl CDD cd18596 cd18596 350040 ABC_6TM_VMR1_D1_like Six-transmembrane helical domain 1 (TMD1) of the yeast Vmr1p, Ybt1p and Nft1; ABCC subfamily. This group includes the six-transmembrane domain 1 (TMD1) of the yeast Vmr1p, Ybt1p and Nft1, all of which are ABC transporters of the MRP (multidrug resistance-associated protein) subfamily (ABCC). Yeast ABCC (also termed MRP/CFTR) subfamily includes six members (Ycf1p, Bpt1p, Ybt1p/Bat1p, Nft1p, Vmr1p, and Yor1p), of which three members (Ycf1p, Bpt1P and Yor1p) are not included here. While Yor1p, an oligomycin resistance ABC transporter, has been shown to localize to the plasma membrane, the other 4 members (Ycf1p, Bpt1p, Ybt1p/Bat1p, Nft1p and Vmr1p) have been shown to localize to the vacuolar membrane. Ybt1p is originally identified as a bile acid transporter and regulates membrane fusion through Ca2+ transport modulation. Ybt1p also plays a part in ade2 pigment transport. Moreover, Ybt1p has been recently shown to translocate phosphatidylcholine from the outer leaflet of the vacuole to the inner leaflet for degradation and choline recycling. Vmr1p, a vacuolar membrane protein, participates in the export of numerous growth inhibitors from the cell, such as cycloheximide, 2,4-dinitrophenole, cadmium and other toxic metals. Nft1p is not well-characterized, but it is proposed to be regulate Ycf1p, which is involved in heavy metal detoxification. 309 matched cddid_all.tbl CDD cd18597 cd18597 350041 ABC_6TM_YOR1_D1_like Six-transmembrane helical domain 1 (TMD1) of the yeast Yor1p and similar proteins; ABCC subfamily. This group includes the six-transmembrane domain 1 (TMD1) of the yeast Yor1p, an oligomycin resistance ABC transporter, and similar proteins. Members of this group belong to the MRP (multidrug resistance-associated protein) subfamily (ABCC). In addition to Yor1p, yeast ABCC (also termed MRP/CFTR) subfamily also comprises five other members (Ycf1p, Bpt1p, Ybt1p/Bat1p, Nft1p, and Vmr1p), which are not included in this group. Yor1p is a plasma membrane ATP-binding transporter that mediates export of many different organic anions including oligomycin. While Yor1p has been shown to localize to the plasma membrane, the other 4 members (Ycf1p, Bpt1p, Ybt1p/Bat1p, Nft1p and Vmr1p) have been shown to localize to the vacuolar membrane. 293 matched cddid_all.tbl CDD cd18598 cd18598 350042 ABC_6TM_MRP7_D1_like Six-transmembrane helical domain 1 (TMD1) of multidrug resistance-associated protein 7, and similar proteins. This group represents the six-transmembrane domain 1 (TMD1) of multidrug resistance-associated protein 7 (MRP7), which belongs to the subfamily C of the ATP-binding cassette (ABC) transporter superfamily. The MRP subfamily (ABCC subfamily) is composed of 13 members, of which MRP1 to MRP9 are the major transporters that cause multidrug resistance in tumor cells by pumping anticancer drugs out of the cell. These nine MRP members function as ATP-dependent exporters for endogenous substances and xenobiotics. MRP family can be divided into two groups, depending on their structural architecture. MRP4, MRP5, MRP8, and MRP9 (ABCC4, 5, 11 and 12, respectively) have a typical ABC transporter structure and each composed of two transmembrane domains (TMD1 and TMD2) and two nucleotide domains (NBD1 and NBD2). On the other hand, MRP1, 2, 3, 6 and 7 (ABCC1, 2, 3, 6 and 7, respectively) have an additional N-terminal five transmembrane segments in a single domain (TMD0) connected to the core (TMD-NBD) by a cytoplasmic linker (L0). 288 matched cddid_all.tbl CDD cd18599 cd18599 350043 ABC_6TM_MRP5_8_9_D2 Six-transmembrane helical domain 2 (TMD2) of multidrug resistance-associated proteins (MRPs) 5, 8, and 9. This group represents the six-transmembrane domain 2 (TMD2) of multidrug resistance-associated proteins (MRPs) 5, 8, and 9, all of which are belonging to the subfamily C of the ATP-binding cassette (ABC) transporter superfamily. The MRP subfamily (ABCC subfamily) is composed of 13 members, of which MRP1 to MRP9 are the major transporters that cause multidrug resistance in tumor cells by pumping anticancer drugs out of the cell. These nine MRP members function as ATP-dependent exporters for endogenous substances and xenobiotics. MRP family can be divided into two groups, depending on their structural architecture. MRP4, MRP5, MRP8, and MRP9 (ABCC4, 5, 11 and 12, respectively) have a typical ABC transporter structure and each composed of two transmembrane domains (TMD1 and TMD2) and two nucleotide domains (NBD1 and NBD2). On the other hand, MRP1, 2, 3, 6 and 7 (ABCC1, 2, 3, 6 and 7, respectively) have an additional N-terminal five transmembrane segments in a single domain (TMD0) connected to the core (TMD-NBD) by a cytoplasmic linker (L0). 313 matched cddid_all.tbl CDD cd18600 cd18600 350044 ABC_6TM_CFTR_D2 Six-transmembrane helical domain 2 of Cystic Fibrosis Transmembrane Conductance Regulator. This group represents the six-transmembrane domain 2 (TMD2) of the ABC transporters that belong to the ABCC subfamily, such as the sulphonylurea receptors SUR1/2 (ABCC8), the cystic fibrosis transmembrane conductance regulator (CFTR, ABCC7), Multidrug-Resistance associated Proteins (MRP1-9), VMR1 (vacuolar multidrug resistance protein 1), and YOR1 (yeast oligomycin resistance transporter protein). This TM subunit exhibits the type 3 ATP-binding cassette (ABC) exporter fold, which is characterized by 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The type 3 ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds, a various type of lipids and polypeptides. All ABC transporters share a common architecture of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane by alternating between inward- and outward-facing conformations. By contrast, bacterial ABC exporters are typically assembled from dimers of TMD-NBD half-transporters. Thus, most bacterial ABC transporters are comprised of two identical TMDs and two identical NBDs. 324 matched cddid_all.tbl CDD cd18601 cd18601 350045 ABC_6TM_MRP4_D2_like Six-transmembrane helical domain 2 (TMD2) of multidrug resistance-associated protein 4 (MRP4) and similar proteins. This group represents the six-transmembrane domain 2 (TMD2) of multidrug resistance-associated protein 4 (MRP4), which belongs to the subfamily C of the ATP-binding cassette (ABC) transporter superfamily. The MRP subfamily (ABCC subfamily) is composed of 13 members, of which MRP1 to MRP9 are the major transporters that cause multidrug resistance in tumor cells by pumping anticancer drugs out of the cell. These nine MRP members function as ATP-dependent exporters for endogenous substances and xenobiotics. MRP family can be divided into two groups, depending on their structural architecture. MRP4, MRP5, MRP8, and MRP9 (ABCC4, 5, 11 and 12, respectively) have a typical ABC transporter structure and each composed of two transmembrane domains (TMD1 and TMD2) and two nucleotide domains (NBD1 and NBD2). On the other hand, MRP1, 2, 3, 6 and 7 (ABCC1, 2, 3, 6 and 7, respectively) have an additional N-terminal five transmembrane segments in a single domain (TMD0) connected to the core (TMD-NBD) by a cytoplasmic linker (L0). 314 matched cddid_all.tbl CDD cd18602 cd18602 350046 ABC_6TM_SUR1_D2_like Six-transmembrane helical domain 2 (TMD2) of the sulphonylurea receptors SUR1/2. This group represents the six-transmembrane domain 2 (TMD2) of the sulphonylurea receptors SUR1/2 (ABCC8), which function as a modulator of ATP-sensitive potassium channels and insulin release, and belong to the ABCC subfamily. The ATP-sensitive (K-ATP) channel is an octameric complex of four pore-forming Kir6.2 subunits and four regulatory SUR subunits. Thus, in contrast to other ABC transporters, the SUR serves as the regulatory subunit of an ion channel. Mutations and deficiencies in the SUR proteins have been observed in patients with hyperinsulinemic hypoglycemia of infancy, an autosomal recessive disorder of unregulated and high insulin secretion. Mutations have also been associated with non-insulin-dependent diabetes mellitus type 2, an autosomal dominant disease of defective insulin secretion. 307 matched cddid_all.tbl CDD cd18603 cd18603 350047 ABC_6TM_MRP1_2_3_6_D2_like Six-transmembrane helical domain 2 (TMD2) of multidrug resistance-associated proteins (MRPs) 1, 2, 3 and 6. This group represents the six-transmembrane domain 2 (TMD2) of multidrug resistance-associated proteins (MRPs) 1, 2, 3 and 6, all of which are belonging to the subfamily C of the ATP-binding cassette (ABC) transporter superfamily. The MRP subfamily (ABCC subfamily) is composed of 13 members, of which MRP1 to MRP9 are the major transporters that cause multidrug resistance in tumor cells by pumping anticancer drugs out of the cell. These nine MRP members function as ATP-dependent exporters for endogenous substances and xenobiotics. MRP family can be divided into two groups, depending on their structural architecture. MRP4, MRP5, MRP8, and MRP9 (ABCC4, 5, 11 and 12, respectively) have a typical ABC transporter structure and each composed of two transmembrane domains (TMD1 and TMD2) and two nucleotide domains (NBD1 and NBD2). On the other hand, MRP1, 2, 3, 6 and 7 (ABCC1, 2, 3, 6 and 7, respectively) have an additional N-terminal five transmembrane segments in a single domain (TMD0) connected to the core (TMD-NBD) by a cytoplasmic linker (L0). 296 matched cddid_all.tbl CDD cd18604 cd18604 350048 ABC_6TM_VMR1_D2_like Six-transmembrane helical domain 2 (TMD2) of the yeast Vmr1p, Ybt1p and Nft1; ABCC subfamily. This group includes the six-transmembrane domain 2 (TMD2) of the yeast Vmr1p, Ybt1p and Nft1, all of which are ABC transporters of the MRP (multidrug resistance-associated protein) subfamily (ABCC). Yeast ABCC (also termed MRP/CFTR) subfamily includes six members (Ycf1p, Bpt1p, Ybt1p/Bat1p, Nft1p, Vmr1p, and Yor1p), of which three members (Ycf1p, Bpt1P and Yor1p) are not included here. While Yor1p, an oligomycin resistance ABC transporter, has been shown to localize to the plasma membrane, the other 4 members (Ycf1p, Bpt1p, Ybt1p/Bat1p, Nft1p and Vmr1p) have been shown to localize to the vacuolar membrane. Ybt1p is originally identified as a bile acid transporter and regulates membrane fusion through Ca2+ transport modulation. Ybt1p also plays a part in ade2 pigment transport. Moreover, Ybt1p has been recently shown to translocate phosphatidylcholine from the outer leaflet of the vacuole to the inner leaflet for degradation and choline recycling. Vmr1p, a vacuolar membrane protein, participates in the export of numerous growth inhibitors from the cell, such as cycloheximide, 2,4-dinitrophenole, cadmium and other toxic metals. Nft1p is not well-characterized, but it is proposed to be regulate Ycf1p, which is involved in heavy metal detoxification. 297 matched cddid_all.tbl CDD cd18605 cd18605 350049 ABC_6TM_MRP7_D2_like Six-transmembrane helical domain 2 (TMD2) of multidrug resistance-associated protein 7, and similar proteins. This group represents the six-transmembrane domain 2 (TMD2) of multidrug resistance-associated protein 7 (MRP7), which belongs to the subfamily C of the ATP-binding cassette (ABC) transporter superfamily. The MRP subfamily (ABCC subfamily) is composed of 13 members, of which MRP1 to MRP9 are the major transporters that cause multidrug resistance in tumor cells by pumping anticancer drugs out of the cell. These nine MRP members function as ATP-dependent exporters for endogenous substances and xenobiotics. MRP family can be divided into two groups, depending on their structural architecture. MRP4, MRP5, MRP8, and MRP9 (ABCC4, 5, 11 and 12, respectively) have a typical ABC transporter structure and each composed of two transmembrane domains (TMD1 and TMD2) and two nucleotide domains (NBD1 and NBD2). On the other hand, MRP1, 2, 3, 6 and 7 (ABCC1, 2, 3, 6 and 7, respectively) have an additional N-terminal five transmembrane segments in a single domain (TMD0) connected to the core (TMD-NBD) by a cytoplasmic linker (L0). 300 matched cddid_all.tbl CDD cd18606 cd18606 350050 ABC_6TM_YOR1_D2_like Six-transmembrane helical domain 2 (TMD2) of the yeast Yor1p and similar proteins; ABCC subfamily. This group includes the six-transmembrane domain 1 (TMD1) of the yeast Yor1p, an oligomycin resistance ABC transporter, and similar proteins. Members of this group belong to the MRP (multidrug resistance-associated protein) subfamily (ABCC). In addition to Yor1p, yeast ABCC (also termed MRP/CFTR) subfamily also comprises five other members (Ycf1p, Bpt1p, Ybt1p/Bat1p, Nft1p, and Vmr1p), which are not included in this group. Yor1p is a plasma membrane ATP-binding transporter that mediates export of many different organic anions including oligomycin. While Yor1p has been shown to localize to the plasma membrane, the other 4 members (Ycf1p, Bpt1p, Ybt1p/Bat1p, Nft1p and Vmr1p) have been shown to localize to the vacuolar membrane. 290 matched cddid_all.tbl CDD cd18607 cd18607 350119 GH130 Glycoside hydrolase family 130. Members of the glycosyl hydrolase family 130, as classified by the carbohydrate-active enzymes database (CAZY), are phosphorylases and hydrolases for beta-mannosides, and include beta-1,4-mannosylglucose phosphorylase (EC 2.4.1.281), beta-1,4-mannooligosaccharide phosphorylase (EC 2.4.1.319), beta-1,4-mannosyl-N-acetyl-glucosamine phosphorylase (EC 2.4.1.320), beta-1,2-mannobiose phosphorylase (EC 2.4.1.-), beta-1,2-oligomannan phosphorylase (EC 2.4.1.-) and beta-1,2-mannosidase (EC 3.2.1.-). They possess 5-bladed beta-propeller domains similar to families 32, 43, 62, 68, 117 (GH32, GH43, GH62, GH68, GH117). GH130 enzymes are involved in the bacterial utilization of mannans or N-linked glycans. Beta-1,4-mannosylglucose phosphorylase is involved in degradation of beta-1,4-D-mannosyl-N-acetyl-D-glucosamine linkages in the core of N-glycans; it produces alpha-mannose 1-phosphate and glucose from 4-O-beta-D-mannosyl-D-glucose and inorganic phosphate, using a critical catalytic Asp as a proton donor. 269 matched cddid_all.tbl CDD cd18608 cd18608 350120 GH43_F5-8_typeC-like Glycosyl hydrolase family 43 protein most having a F5/8 type C domain C-terminal to the GH43 domain. This glycosyl hydrolase family 43 (GH43) subgroup includes enzymes that have been annotated as having beta-xylosidase (EC 3.2.1.37), xylanase (EC 3.2.1.8), and beta-galactosidase (EC 3.2.1.145) activities, and some as F5/8 type C domain (also known as the discoidin (DS) domain)-containing proteins. Most contain a F5/8 type C domain C-terminal to the GH43 domain. It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. Characterized enzymes belonging to this subgroup include Lactobacillus brevis (LbAraf43) and Weissella sp (WAraf43) which show activity with similar catalytic efficiency on 1,5-alpha-L-arabinooligosaccharides with a degree of polymerization (DP) of 2-3; size is limited by an extended loop at the entrance to the active site. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 276 matched cddid_all.tbl CDD cd18609 cd18609 350121 GH32-like Glycosyl hydrolase family 32 family protein. The GH32 family contains glycosyl hydrolase family GH32 proteins that cleave sucrose into fructose and glucose via beta-fructofuranosidase activity, producing invert sugar that is a mixture of dextrorotatory D-glucose and levorotatory D-fructose, thus named invertase (EC 3.2.1.26). This family also contains other fructofuranosidases such as inulinase (EC 3.2.1.7), exo-inulinase (EC 3.2.1.80), levanase (EC 3.2.1.65), and transfructosidases such sucrose:sucrose 1-fructosyltransferase (EC 2.4.1.99), fructan:fructan 1-fructosyltransferase (EC 2.4.1.100), sucrose:fructan 6-fructosyltransferase (EC 2.4.1.10), fructan:fructan 6G-fructosyltransferase (EC 2.4.1.243) and levan fructosyltransferases (EC 2.4.1.-). These retaining enzymes (i.e. they retain the configuration at anomeric carbon atom of the substrate) catalyze hydrolysis in two steps involving a covalent glycosyl enzyme intermediate: an aspartate located close to the N-terminus acts as the catalytic nucleophile and a glutamate acts as the general acid/base; a conserved aspartate residue in the Arg-Asp-Pro (RDP) motif stabilizes the transition state. These enzymes are predicted to display a 5-fold beta-propeller fold as found for GH43 and CH68. The breakdown of sucrose is widely used as a carbon or energy source by bacteria, fungi, and plants. Invertase is used commercially in the confectionery industry, since fructose has a sweeter taste than sucrose and a lower tendency to crystallize. A common structural feature of all these enzymes is a 5-bladed beta-propeller domain, similar to GH43, that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 303 matched cddid_all.tbl CDD cd18610 cd18610 350122 GH130_BT3780-like Glycosyl hydrolase family 130, such as beta-mammosidase BT3780 and BACOVA_03624. This subfamily contains glycosyl hydrolase family 130, as classified by the carbohydrate-active enzymes database (CAZY), and includes Bacteroides enzymes, BT3780 and BACOVA_03624. Members of this family possess 5-bladed beta-propeller domains similar to families 32, 43, 62, 68, 117 (GH32, GH43, GH62, GH68, GH117). GH130 enzymes are involved in the bacterial utilization of mannans or N-linked glycans. GH130 enzymes have also been shown to target beta-1,2- and beta-1,4-mannosidic linkages where these phosphorylases mediate bond cleavage by a single displacement reaction in which phosphate functions as the catalytic nucleophile. However, some lack the conserved basic residues that bind the phosphate nucleophile, as observed for the Bacteroides enzymes, BT3780 and BACOVA_03624, which are indeed beta-mannosidases that hydrolyze beta-1,2-mannosidic linkages through an inverting mechanism. 301 matched cddid_all.tbl CDD cd18611 cd18611 350123 GH130 Glycosyl hydrolase family 130; uncharacterized. This subfamily contains glycosyl hydrolase family 130 (GH130) proteins, as classified by the carbohydrate-active enzymes database (CAZY), most of which are as yet uncharacterized. GH130 enzymes are phosphorylases and hydrolases for beta-mannosides, and include beta-1,4-mannosylglucose phosphorylase (EC 2.4.1.281), beta-1,4-mannooligosaccharide phosphorylase (EC 2.4.1.319), beta-1,4-mannosyl-N-acetyl-glucosamine phosphorylase (EC 2.4.1.320), beta-1,2-mannobiose phosphorylase (EC 2.4.1.-), beta-1,2-oligomannan phosphorylase (EC 2.4.1.-) and beta-1,2-mannosidase (EC 3.2.1.-). They possess 5-bladed beta-propeller domains similar to families 32, 43, 62, 68, 117 (GH32, GH43, GH62, GH68, GH117). GH130 enzymes are involved in the bacterial utilization of mannans or N-linked glycans. Beta-1,4-mannosylglucose phosphorylase is involved in degradation of beta-1,4-D-mannosyl-N-acetyl-D-glucosamine linkages in the core of N-glycans; it produces alpha-mannose 1-phosphate and glucose from 4-O-beta-D-mannosyl-D-glucose and inorganic phosphate, using a critical catalytic Asp as a proton donor. 289 matched cddid_all.tbl CDD cd18612 cd18612 350124 GH130_Lin0857-like Glycoside hydrolase family 130 such as Listeria innocua beta-1,2-mannobiose phosphorylase. This subfamily contains the glycosyl hydrolase family 130 (GH130), as classified by the carbohydrate-active enzymes database (CAZY), enzymes that are phosphorylases and hydrolases for beta-mannosides, and includes Listeria innocua beta-1,2-mannobiose phosphorylase (Lin0857). hey possess 5-bladed beta-propeller domains similar to families 32, 43, 62, 68, 117 (GH32, GH43, GH62, GH68, GH117). GH130 enzymes are involved in the bacterial utilization of mannans or N-linked glycans. Structure of Lin0857 shows beta-1,2-mannotriose bound in a U-shape, interacting with a phosphate analog at both ends. Lin0857 has a unique dimer structure connected by a loop, with a significant open-close loop displacement observed for substrate entry. A long loop, which is exclusively present in Lin0857, covers the active site to limit the pocket size. 261 matched cddid_all.tbl CDD cd18613 cd18613 350125 GH130 Glycosyl hydrolase family 130; uncharacterized. This subfamily contains glycosyl hydrolase family 130 (GH130) proteins, as classified by the carbohydrate-active enzymes database (CAZY), most of which are as yet uncharacterized. GH130 enzymes are phosphorylases and hydrolases for beta-mannosides, and include beta-1,4-mannosylglucose phosphorylase (EC 2.4.1.281), beta-1,4-mannooligosaccharide phosphorylase (EC 2.4.1.319), beta-1,4-mannosyl-N-acetyl-glucosamine phosphorylase (EC 2.4.1.320), beta-1,2-mannobiose phosphorylase (EC 2.4.1.-), beta-1,2-oligomannan phosphorylase (EC 2.4.1.-) and beta-1,2-mannosidase (EC 3.2.1.-). They possess 5-bladed beta-propeller domains similar to families 32, 43, 62, 68, 117 (GH32, GH43, GH62, GH68, GH117). GH130 enzymes are involved in the bacterial utilization of mannans or N-linked glycans. Beta-1,4-mannosylglucose phosphorylase is involved in degradation of beta-1,4-D-mannosyl-N-acetyl-D-glucosamine linkages in the core of N-glycans; it produces alpha-mannose 1-phosphate and glucose from 4-O-beta-D-mannosyl-D-glucose and inorganic phosphate, using a critical catalytic Asp as a proton donor. 302 matched cddid_all.tbl CDD cd18614 cd18614 350126 GH130 Glycosyl hydrolase family 130; uncharacterized. This subfamily contains glycosyl hydrolase family 130 (GH130) proteins, as classified by the carbohydrate-active enzymes database (CAZY), most of which are as yet uncharacterized. GH130 enzymes are phosphorylases and hydrolases for beta-mannosides, and include beta-1,4-mannosylglucose phosphorylase (EC 2.4.1.281), beta-1,4-mannooligosaccharide phosphorylase (EC 2.4.1.319), beta-1,4-mannosyl-N-acetyl-glucosamine phosphorylase (EC 2.4.1.320), beta-1,2-mannobiose phosphorylase (EC 2.4.1.-), beta-1,2-oligomannan phosphorylase (EC 2.4.1.-) and beta-1,2-mannosidase (EC 3.2.1.-). They possess 5-bladed beta-propeller domains similar to families 32, 43, 62, 68, 117 (GH32, GH43, GH62, GH68, GH117). GH130 enzymes are involved in the bacterial utilization of mannans or N-linked glycans. Beta-1,4-mannosylglucose phosphorylase is involved in degradation of beta-1,4-D-mannosyl-N-acetyl-D-glucosamine linkages in the core of N-glycans; it produces alpha-mannose 1-phosphate and glucose from 4-O-beta-D-mannosyl-D-glucose and inorganic phosphate, using a critical catalytic Asp as a proton donor. 276 matched cddid_all.tbl CDD cd18615 cd18615 350127 GH130 Glycosyl hydrolase family 130; uncharacterized. This subfamily contains glycosyl hydrolase family 130 (GH130) proteins, as classified by the carbohydrate-active enzymes database (CAZY), most of which are as yet uncharacterized. GH130 enzymes are phosphorylases and hydrolases for beta-mannosides, and include beta-1,4-mannosylglucose phosphorylase (EC 2.4.1.281), beta-1,4-mannooligosaccharide phosphorylase (EC 2.4.1.319), beta-1,4-mannosyl-N-acetyl-glucosamine phosphorylase (EC 2.4.1.320), beta-1,2-mannobiose phosphorylase (EC 2.4.1.-), beta-1,2-oligomannan phosphorylase (EC 2.4.1.-) and beta-1,2-mannosidase (EC 3.2.1.-). They possess 5-bladed beta-propeller domains similar to families 32, 43, 62, 68, 117 (GH32, GH43, GH62, GH68, GH117). GH130 enzymes are involved in the bacterial utilization of mannans or N-linked glycans. Beta-1,4-mannosylglucose phosphorylase is involved in degradation of beta-1,4-D-mannosyl-N-acetyl-D-glucosamine linkages in the core of N-glycans; it produces alpha-mannose 1-phosphate and glucose from 4-O-beta-D-mannosyl-D-glucose and inorganic phosphate, using a critical catalytic Asp as a proton donor. 277 matched cddid_all.tbl CDD cd18616 cd18616 350128 GH43_ABN-like Glycosyl hydrolase family 43 such as arabinan endo-1 5-alpha-L-arabinosidase. This glycosyl hydrolase family 43 (GH43) subgroup includes mostly enzymes with endo-alpha-L-arabinanase (ABN; EC 3.2.1.99) activity. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. The GH43 ABN enzymes hydrolyze alpha-1,5-L-arabinofuranoside linkages. These arabinan-degrading enzymes are important in the food industry for efficient production of L-arabinose from agricultural waste; L-arabinose is often used as a bioactive sweetener. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 291 matched cddid_all.tbl CDD cd18617 cd18617 350129 GH43_XynB-like Glycosyl hydrolase family 43, such as Bacteroides ovatus alpha-L-arabinofuranosidase (BoGH43, XynB). This glycosyl hydrolase family 43 (GH43) subgroup includes enzymes that have been characterized to have alpha-L-arabinofuranosidase (EC 3.2.1.55) and beta-1,4-xylosidase (beta-D-xylosidase;xylan 1,4-beta-xylosidase; EC 3.2.1.37) activities. Beta-1,4-xylosidases are part of an array of hemicellulases that are involved in the final breakdown of plant cell-wall whereby they degrade xylan. They hydrolyze beta-1,4 glycosidic bonds between two xylose units in short xylooligosaccharides. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Also included in this subfamily are Bacteroides ovatus alpha-L-arabinofuranosidases, BoGH43A and BoGH43B, both having a two-domain architecture, consisting of an N-terminal 5-bladed beta-propeller domain harboring the catalytic active site, and a C-terminal beta-sandwich domain. However, despite significant functional overlap between these two enzymes, BoGH43A and BoGH43B share just 41% sequence identity. The latter appears to be significantly less active on the same substrates, suggesting that these paralogs may play subtly different roles during the degradation of xyloglucans from different sources, or may function most optimally at different stages in the catabolism of xyloglucan oligosaccharides (XyGOs), for example before or after hydrolysis of certain side-chain moieties. It also includes Phanerochaete chrysosporium BKM-F-1767 Xyl, a bifunctional xylosidase/arabinofuranosidase. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 285 matched cddid_all.tbl CDD cd18618 cd18618 350130 GH43_Xsa43E-like Glycosyl hydrolase family 43, including Butyrivibrio proteoclasticus arabinofuranosidase Xsa43E. This glycosyl hydrolase family 43 (GH43) subgroup belongs to the GH43_AXH-like subgroup which includes enzymes that have been characterized with beta-xylosidase (EC 3.2.1.37), alpha-L-arabinofuranosidase (EC 3.2.1.55), alpha-1,2-L-arabinofuranosidase 43A (arabinan-specific; EC 3.2.1.-), endo-alpha-L-arabinanase as well as arabinoxylan arabinofuranohydrolase (AXH) activities. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. AXHs specifically hydrolyze the glycosidic bond between arabinofuranosyl substituents and xylopyranosyl backbone residues of arabinoxylan. This subgroup includes Cellvibrio japonicus arabinan-specific alpha-1,2-arabinofuranosidase, CjAbf43A, which confers its specificity by a surface cleft that is complementary to the helical backbone of the polysaccharide, and Butyrivibrio proteoclasticus GH43 enzyme Xsa43E, also an arabinofuranosidase, which has been shown to cleave arabinose side chains from short segments of xylan. Several of these enzymes also contain carbohydrate binding modules (CBMs) that bind cellulose or xylan. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 275 matched cddid_all.tbl CDD cd18619 cd18619 350131 GH43_CoXyl43_like Glycosyl hydrolase family 43 protein such as metagenomic beta-xylosidase/alpha-L-arabinofuranosidase CoXyl43. This glycosyl hydrolase family 43 (GH43) subgroup belongs to the GH43_AXH-like subgroup which includes enzymes that have been characterized with beta-xylosidase (EC 3.2.1.37), alpha-L-arabinofuranosidase (EC 3.2.1.55), alpha-1,2-L-arabinofuranosidase 43A (arabinan-specific; EC 3.2.1.-), endo-alpha-L-arabinanase as well as arabinoxylan arabinofuranohydrolase (AXH) activities. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. Included in this subfamily is the metagenomic beta-xylosidase/alpha-L-arabinofuranosidase CoXyl43, which shows synergy with Trichoderma reesei cellulases and promotes plant biomass saccharification by degrading xylo-oligosaccharides, such as xylobiose and xylotriose, into the monosaccharide xylose. Studies show that the hydrolytic activity of CoXyl43 is stimulated in the presence of calcium. Several of these enzymes also contain carbohydrate binding modules (CBMs) that bind cellulose or xylan. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 313 matched cddid_all.tbl CDD cd18620 cd18620 350132 GH43_XylA-like Glycosyl hydrolase family 43-like protein such as Clostridium stercorarium alpha-L-arabinofuranosidase XylA. This glycosyl hydrolase family 43 (GH43) subgroup belongs to the GH43_AXH-like subgroup which includes enzymes that have been characterized with beta-xylosidase (EC 3.2.1.37), alpha-L-arabinofuranosidase (EC 3.2.1.55), alpha-1,2-L-arabinofuranosidase 43A (arabinan-specific; EC 3.2.1.-), endo-alpha-L-arabinanase as well as arabinoxylan arabinofuranohydrolase (AXH) activities. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. The GH43_XylA-like subgroup includes Clostridium stercorarium alpha-L-arabinofuranosidase XylA, and enzymes that have been annotated as having beta-xylosidase (EC 3.2.1.37), alpha-L-arabinofuranosidase (EC 3.2.1.55), endo-alpha-L-arabinanase (EC 3.2.1.-) as well as arabinoxylan arabinofuranohydrolase (AXH) activities. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. AXHs specifically hydrolyze the glycosidic bond between arabinofuranosyl substituents and xylopyranosyl backbone residues of arabinoxylan. 274 matched cddid_all.tbl CDD cd18621 cd18621 350133 GH32_XdINV-like glycoside hydrolase family 32 protein such as Xanthophyllomyces dendrorhous beta-fructofuranosidase (Inv;Xd-INV;XdINV). This subfamily of glycosyl hydrolase family GH32 includes fructan:fructan 1-fructosyltransferase (FT, EC 2.4.1.100) and beta-fructofuranosidase (invertase or Inv, EC 3.2.1.26), among others. These enzymes cleave sucrose into fructose and glucose via beta-fructofuranosidase activity, producing invert sugar that is a mixture of dextrorotatory D-glucose and levorotatory D-fructose, thus named invertase (EC 3.2.1.26). These retaining enzymes (i.e. they retain the configuration at anomeric carbon atom of the substrate) catalyze hydrolysis in two steps involving a covalent glycosyl enzyme intermediate: an aspartate located close to the N-terminus acts as the catalytic nucleophile and a glutamate acts as the general acid/base; a conserved aspartate residue in the Arg-Asp-Pro (RDP) motif stabilizes the transition state. Xanthophyllomyces dendrorhous beta-fructofuranosidase (XdINV) also catalyzes the synthesis of fructooligosaccharides (FOS, a beneficial prebiotic), producing neo-FOS, making it an interesting biotechnology target. Structural studies show plasticity of its active site, having a flexible loop that is essential in binding sucrose and beta(2-1)-linked oligosaccharide, making it a valuable biocatalyst to produce novel bioconjugates. The breakdown of sucrose is widely used as a carbon or energy source by bacteria, fungi, and plants. Invertase is used commercially in the confectionery industry, since fructose has a sweeter taste than sucrose and a lower tendency to crystallize. A common structural feature of all these enzymes is a 5-bladed beta-propeller domain, similar to GH43, that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 337 matched cddid_all.tbl CDD cd18622 cd18622 350134 GH32_Inu-like glycoside hydrolase family 32 protein such as Aspergillus ficuum endo-inulinase (Inu2). This subfamily of glycosyl hydrolase family GH32 includes endo-inulinase (inu2, EC 3.2.1.7), exo-inulinase (Inu1, EC 3.2.1.80), invertase (EC 3.2.1.26), and levan fructotransferase (LftA, EC 4.2.2.16), among others. These enzymes cleave sucrose into fructose and glucose via beta-fructofuranosidase activity, producing invert sugar that is a mixture of dextrorotatory D-glucose and levorotatory D-fructose, thus named invertase (EC 3.2.1.26). These retaining enzymes (i.e. they retain the configuration at anomeric carbon atom of the substrate) catalyze hydrolysis in two steps involving a covalent glycosyl enzyme intermediate: an aspartate located close to the N-terminus acts as the catalytic nucleophile and a glutamate acts as the general acid/base; a conserved aspartate residue in the Arg-Asp-Pro (RDP) motif stabilizes the transition state. These enzymes are predicted to display a 5-fold beta-propeller fold as found for GH43 and CH68. The breakdown of sucrose is widely used as a carbon or energy source by bacteria, fungi, and plants. Invertase is used commercially in the confectionery industry, since fructose has a sweeter taste than sucrose and a lower tendency to crystallize. A common structural feature of all these enzymes is a 5-bladed beta-propeller domain, similar to GH43, that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 289 matched cddid_all.tbl CDD cd18623 cd18623 350135 GH32_ScrB-like glycoside hydrolase family 32 sucrose 6 phosphate hydrolase (sucrase). Glycosyl hydrolase family GH32 subgroup contains sucrose-6-phosphate hydrolase (sucrase, EC:3.2.1.26) among others. The enzyme cleaves sucrose into fructose and glucose via beta-fructofuranosidase activity, producing invert sugar that is a mixture of dextrorotatory D-glucose and levorotatory D-fructose. These retaining enzymes (i.e. they retain the configuration at anomeric carbon atom of the substrate) catalyze hydrolysis in two steps involving a covalent glycosyl enzyme intermediate: an aspartate located close to the N-terminus acts as the catalytic nucleophile and a glutamate acts as the general acid/base; a conserved aspartate residue in the Arg-Asp-Pro (RDP) motif stabilizes the transition state. The breakdown of sucrose is widely used as a carbon or energy source by bacteria, fungi, and plants. Invertase is used commercially in the confectionery industry, since fructose has a sweeter taste than sucrose and a lower tendency to crystallize. A common structural feature of all these enzymes is a 5-bladed beta-propeller domain, similar to GH43, that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 289 matched cddid_all.tbl CDD cd18624 cd18624 350136 GH32_Fruct1-like glycoside hydrolase family 32 protein such as Arabidopsis thaliana cell-wall invertase 1 (AtBFruct1;Fruct1;AtcwINV1;At3g13790). This subfamily of glycosyl hydrolase family GH32 includes fructan beta-(2,1)-fructosidase and fructan 1-exohydrolase IIa (1-FEH IIa, EC 3.2.1.153), cell-wall invertase 1 (EC 3.2.1.26), sucrose:fructan 6-fructosyltransferase (6-Sst/6-Dft, EC 2.4.1.10), and levan fructosyltransferases (EC 2.4.1.-) among others. This enzyme cleaves sucrose into fructose and glucose via beta-fructofuranosidase activity, producing invert sugar that is a mixture of dextrorotatory D-glucose and levorotatory D-fructose, thus named invertase. These retaining enzymes (i.e. they retain the configuration at anomeric carbon atom of the substrate) catalyze hydrolysis in two steps involving a covalent glycosyl enzyme intermediate: an aspartate located close to the N-terminus acts as the catalytic nucleophile and a glutamate acts as the general acid/base; a conserved aspartate residue in the Arg-Asp-Pro (RDP) motif stabilizes the transition state. The breakdown of sucrose is widely used as a carbon or energy source by bacteria, fungi, and plants. Invertase is used commercially in the confectionery industry, since fructose has a sweeter taste than sucrose and a lower tendency to crystallize. A common structural feature of all these enzymes is a 5-bladed beta-propeller domain, similar to GH43, that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 296 matched cddid_all.tbl CDD cd18625 cd18625 350137 GH32_BfrA-like glycoside hydrolase family 32 protein such as Thermotoga maritima invertase (BfrA or Tm1414). This subfamily of glycosyl hydrolase family GH32 includes beta-fructosidase (invertase, EC 3.2.1.26) that cleaves sucrose into fructose and glucose via beta-fructofuranosidase activity, producing invert sugar that is a mixture of dextrorotatory D-glucose and levorotatory D-fructose, thus named invertase. These retaining enzymes (i.e. they retain the configuration at anomeric carbon atom of the substrate) catalyze hydrolysis in two steps involving a covalent glycosyl enzyme intermediate: an aspartate located close to the N-terminus acts as the catalytic nucleophile and a glutamate acts as the general acid/base; a conserved aspartate residue in the Arg-Asp-Pro (RDP) motif stabilizes the transition state. The breakdown of sucrose is widely used as a carbon or energy source by bacteria, fungi, and plants. Invertase is used commercially in the confectionery industry, since fructose has a sweeter taste than sucrose and a lower tendency to crystallize. A common structural feature of all these enzymes is a 5-bladed beta-propeller domain, similar to GH43, that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 286 matched cddid_all.tbl CDD cd18626 cd18626 349276 CD_eEF3 chromodomain-like insertion in an ATPase domain of elongation factor eEF3. Eukaryotic elongation factor eEF3 (also known as EF-3, YEF3, and TEF3), a member of the ATP-binding cassette (ABC) family of proteins, is a ribosomal binding ATPase essential for fungal translation machinery. Until recently it was considered fungal-specific and therefore an attractive target for antifungal therapy; however, recent bioinformatics analysis indicates it may be more widely distributed among other unicellular eukaryotes, and translation elongation factor 3 activity has been demonstrated from a non-fungal species, Phytophthora infestans. eEF3 is a soluble factor lacking a transmembrane domain and having two ABC domains arranged in tandem, with a unique chromodomain inserted within the ABC2 domain. Chromodomain mutations in the ABC2 domain of eEF3 have been shown to reduce ATPase activity, but not ribosome binding. Thus, the chromodomain-like insertion is critical to eEF3 function. In addition to its elongation function, eEF3 has been shown to interact with mRNA in a translation independent manner, suggesting an additional, non-elongation function for this factor. 56 matched cddid_all.tbl CDD cd18627 cd18627 349277 CD_polycomb_like chromodomain of polycomb and chromobox family proteins. CHRomatin Organization Modifier (chromo) domain of Polycomb and Polycomb-group (PcG) chromobox (CBX) family proteins such as CBX2, CBX4, CBX6, CBX7, and CBX8. These CBX proteins are components of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells. 49 matched cddid_all.tbl CDD cd18628 cd18628 349278 CD3_cpSRP43_like chromodomain 3 of chloroplast signal recognition particle 43 kDa protein, and similar proteins. This subgroup includes the chromodomain 3 of chloroplast SRP43 (cpSRP43), and similar proteins. CpSRP43 is a component of the chloroplast signal recognition particle (SRP) pathway. It forms a stable complex with cpSRP54 (cpSRP complex) which is required for the efficient posttranslational transport of members of the nuclearly encoded light harvesting chlorophyll-a/b-binding proteins (LHCPs) to the thylakoid membrane. Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromodomain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followed by a related chromo shadow domain. 51 matched cddid_all.tbl CDD cd18629 cd18629 349279 CD2_cpSRP43_like chromodomain 2 of chloroplast signal recognition particle 43 kDa protein, and similar proteins. This subgroup includes the chromodomain 2 of chloroplast SRP43 (cpSRP43), and similar proteins. CpSRP43 is a component of the chloroplast signal recognition particle (SRP) pathway. It forms a stable complex with cpSRP54 (cpSRP complex) which is required for the efficient posttranslational transport of members of the nuclearly encoded light harvesting chlorophyll-a/b-binding proteins (LHCPs) to the thylakoid membrane. Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromodomain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followed by a related chromo shadow domain. 48 matched cddid_all.tbl CDD cd18630 cd18630 349280 CD_Rhino chromodomain of Drosophila melanogaster Rhino, and similar proteins. N-terminal CHRomatin Organization Modifier (chromo) domain of Drosophila melanogaster Rhino (also known as heterochromatin protein 1-like), and similar proteins. Rhino is a female-specific protein that affects chromosome structure and egg polarity that is required for germline PIWI-interacting RNA (piRNA) production. In Drosophila the RDC (rhino, deadlock, and cutoff) complex, composed of rhino, the protein deadlock (Del) and the Rai1-like transcription termination cofactor cutoff (Cuff) binds to chromatin of dual-strand piRNA clusters, special genomic regions, which encode piRNA precursors. The RDC complex is anchored to H3K9me3-marked chromatin in part via the H3K9me3-binding activity of Rhino, and is required for transcription of piRNA precursors. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 51 matched cddid_all.tbl CDD cd18631 cd18631 349281 CD_HP1_like chromodomain of heterochromatin protein 1 proteins, including HP1alpha, HP1beta, and HP1gamma. CHRomatin Organization Modifier (chromo) domain of mammalian HP1alpha (Cbx5), HP1beta (Cbx1), HP1gamma (Cbx5), and similar proteins. HP1 has diverse functions in heterochromatin formation and impacts both gene expression and gene silencing. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3). 50 matched cddid_all.tbl CDD cd18632 cd18632 349282 CD_Clr4_like N-terminal chromodomain of the fission yeast histone methyltransferase Clr4, and similar proteins. N-terminal CHRomatin Organization Modifier (chromo) domain of cryptic loci regulator 4 (Clr4), a histone H3 lysine methyltransferase which targets H3K9. Clr4 regulates silencing and switching at the mating-type loci and affects chromatin structure at centromeres. Clr4 is a catalytic component of the rik1-associated E3 ubiquitin ligase complex that shows ubiquitin ligase activity and is required for histone H3K9 methylation. H3K9me represents a specific tag for epigenetic transcriptional repression by recruiting swi6/HP1 to methylated histones which leads to transcriptional silencing within centromeric heterochromatin, telomeric regions and at the silent mating-type loci. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 55 matched cddid_all.tbl CDD cd18633 cd18633 349283 CD_MMP8 chromodomain of M-phase phosphoprotein 8. The chromodomain of M-phase phosphoprotein 8 (MPP8), a component of the RanBPM-containing large protein complex, binds methylated H3K9. This may in turn recruit the H3K9 methyltransferases GLP and ESET, and DNA methyltransferase 3A to the promoter of the E-cadherin gene, mediating the E-cadherin gene silencing and promoting tumor cell motility and invasion. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 51 matched cddid_all.tbl CDD cd18634 cd18634 349284 CD_CDY chromodomain of the Chromodomain Y-like protein family. This group includes the chromodomain found in the mammalian chromodomain Y-like (CDY) protein family, and similar proteins. The human CDY family includes 6 proteins: the genes encoding four of these: two copies of CDY1 (CDY1a, CDY1a) and two copies of CDY2(CDY2a and CDY2b), are located on chromosome Y, and the genes encoding the other two members (CDYL and CDYL2) are located on autosomes. The chromosomal genes are only present in primates, whereas the CDYL and CDYL2 genes exist in most mammalian species. The CDY family proteins contain two functional domains: a chromodomain involved in chromatin binding and a catalytic domain found in many coenzyme A (CoA)- dependent acylation enzymes. CDYL is ubiquitously expressed, whereas CDYL2 shows selective expression in tissues of testis, prostate, spleen, and leukocyte. The CDYL genes are ubiquitously expressed, the CDY genes are only expressed in the testis. Deletion of the CDY1b gene has been shown to be a risk factor for male infertility. Impairments in CDY2 expression could be implicated in the pathogenesis of maturation arrest (a failure of germ cell development). 52 matched cddid_all.tbl CDD cd18635 cd18635 349285 CD_CMT3_like chromodomain of chromomethylase 3, and similar proteins. CHRomatin Organization Modifier (chromo) domain of DNA (cytosine-5)-methyltransferase chromomethylase 3 (CMT3, EC:2.1.1.37), and similar proteins. CMT3 is primarily a CHG (where H is either A, T or C) methyltransferase and is predominantly expressed in actively replicating cells. The protein is involved in preferentially methylating transposon-related sequences, reducing their mobility. Studies suggest that in order to target DNA methylation, CMT3 associates with H3K9me2-containing nucleosomes through binding of its BAH- and chromo-domains to H3K9me2. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 57 matched cddid_all.tbl CDD cd18636 cd18636 349286 CD_Chp1_like chromodomain of chromodomain-containing protein 1, and similar proteins. CHRomatin Organization Modifier (chromo) domain of chromodomain-containing protein 1 (CHp1), and similar proteins. Chp1 is needed for RNA interference-dependent heterochromatin formation in fission yeast. Chp1 is a member of the RNA-induced transcriptional silencing (RITS) complex which maintains the heterochromatin regions. The chromodomain of the Chp1 component binds the histone H3 lysine 9 methylated tail (H3K9me) and the core of the nucleosome. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 52 matched cddid_all.tbl CDD cd18637 cd18637 349287 CD_Swi6_like chromodomain of fission yeast Swi6, and similar proteins. Fission yeast Swi6 protein is a structural and functional homolog of mammalian HP1 (heterochromatin protein 1) and is involved in the chromatin structure by binding to centromeres, telomeres, and the silent mating-type locus. Swi6 contains a N-terminal chromo (CHRromatin Organization MOdifier) domain and a C-terminal chromo shadow domain (CSD). Swi6 binds histone H3 tails methylated at Lys- and the cohesion subunit Psc3, leading to silencing the genes and sister chromatid cohesion. It is also involved in the repression of the silent mating-type loci MAT2 and MAT3. Swi6 may compact MAT2/3 into a heterochromatin-like conformation which represses the transcription of these silent cassettes. chromodomains mediate the interaction of the heterochromatin with other heterochromatin proteins, thereby affecting chromatin structure (e.g. Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2). CSDs have only been found in proteins that also possess a chromodomain. 54 matched cddid_all.tbl CDD cd18638 cd18638 349288 CD_EhHp1_like chromodomain of Entamoeba histolytica heterochromatin protein 1, and similar proteins. This subgroup includes the N-terminal CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 (HP1)-like protein from Entamoeba histolytica, and similar proteins. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 52 matched cddid_all.tbl CDD cd18639 cd18639 349289 CD_SUV39H1_like chromodomain of histone methyltransferase SUV39H1, and similar proteins. CHRomatin Organization Modifier (chromo) domain of human SUV39H1, a histone lysine methyltransferase (HMT) which catalyzes di- and tri-methylation of lysine 9 of histone H3 (H3K9me2/3), leading to heterochromatin formation and gene silencing. H3K9me2/3 represents a specific mark for epigenetic transcriptional repression by recruiting HP1 (CBX1, CBX3, and/or CBX5) proteins to methylated histones. SUV39H1 mainly functions in heterochromatin regions. The human SUV39H1/2, histone H3K9 methyltransferases, are the mammalian homologs of Drosophila Su(var)3-9 and Schizosaccharomyces pombe Clr4. SUV39H1 contains a chromodomain at its N-terminus and a SET domain at its C-terminus. Although the SET domain performs the catalytic activity, the chromodomain of SUV39H1 is essential for the catalytic activity of SUV39H1. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 49 matched cddid_all.tbl CDD cd18640 cd18640 349290 CD_Chro-like chromodomain of Drosophila melanogaster chromator chromodomain protein, and similar proteins. This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in chromodomain of Drosophila melanogaster chromator (also known as Chriz/Chro) chromodomain protein, and similar proteins. Chromator is a nuclear protein that plays a role in proper spindle dynamics during mitosis. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 52 matched cddid_all.tbl CDD cd18641 cd18641 350843 CBD_RBP1_like chromo barrel domain of retinoblastoma binding protein 1, and similar proteins. Retinoblastoma-binding protein 1 (RBP1), also termed AT-rich interaction domain 4A, is a ubiquitously expressed nuclear protein. RBP1 is a tumor and leukemia suppressor that binds both methylated histone tails and DNA, and is involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. The chromo barrel domain of RBP1 has been reported to recognize histone H4K20me3 weakly, and this binding is enhanced by the simultaneous binding of DNA. RBP1 binds directly, with several other proteins, to retinoblastoma protein (pRB) which regulates cell proliferation; pRB represses transcription by recruiting RBP1. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains, and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromodomain. 59 matched cddid_all.tbl CDD cd18642 cd18642 350844 CBD_MOF_like chromo barrel domain of Drosophila melanogaster males-absent on the first protein, and similar proteins. This subgroup includes the chromo barrel domains found in human Tat-interactive protein 60 (TIP60, (also known as KAT5 or HTATIP), Drosophila melanogaster males-absent on the first (MOF) protein, and Saccharomyces ESA1. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains, and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain. The MOF-like chromo barrels may be may be auto-inhibited, i.e. they seem to have occluded peptide binding sites. 67 matched cddid_all.tbl CDD cd18643 cd18643 350845 CBD chromo barrel domain of MOF acetyltransferase, and similar proteins. This group includes the chromo barrel domains found in human Tat-interactive protein 60 (TIP60, (also known as KAT5 or HTATIP), Drosophila melanogaster males-absent on the first (MOF) protein, human male-specific lethal (MSL) complex subunit 3 (MSL3), and retinoblastoma binding protein 1. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains, and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain. The chromobarrel domains include a MOF-like subgroup which may be may be auto-inhibited, i.e. they seem to have occluded peptide binding sites. 61 matched cddid_all.tbl CDD cd18644 cd18644 349291 CD_polycomb chromodomain of polycomb. CHRomatin Organization Modifier (chromo) domain of the PcG (polycomb-group) chromodomain protein Polycomb (Pc) from Drosophila melanogaster, anthropod, worm, and sea cucumber, and similar proteins. Pc is a component of the Polycomb-group (PcG) multiprotein PRC1 complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. The core subunits of PRC1 are polycomb (Pc), polyhomeotic (Ph), posterior sex combs (Psc), and sex comb extra (Sce, also known as dRing). Polycomb (Pc) plays a role in modulating life span in flies, it negatively regulates longevity. 54 matched cddid_all.tbl CDD cd18645 cd18645 349292 CD_Cbx4 chromodomain of chromobox homolog 4. CHRomatin Organization Modifier (chromo) domain of chromobox homolog 4 (CBX4), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells. In addition to a chromodomain with H3K27me3-binding activity, Cbx4 contains two SUMO-interacting motifs responsible for its small ubiquitin-related modifier (SUMO) E3 ligase activity. CBX proteins may act as an oncogene or tumor suppressor in a cell-type-dependent manner, for example CBX8 promotes proliferation while suppressing metastasis, in colorectal carcinoma progression. CBX4 may serve as a tumor suppressor in colorectal carcinoma, and has been shown to be an oncogene in osteosarcoma and breast cancer. 55 matched cddid_all.tbl CDD cd18646 cd18646 349293 CD_Cbx7 chromodomain of chromobox homolog 7. CHRomatin Organization Modifier (chromo) domain of chromobox homolog 7 (CBX7), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells. CBX proteins may act as an oncogene or tumor suppressor in a cell-type-dependent manner, for example CBX8 promotes proliferation while suppressing metastasis, in colorectal carcinoma progression. CBX7 has been shown to function as a tumor suppressor in lung carcinoma and an oncogene in gastric cancer and lymphoma. 56 matched cddid_all.tbl CDD cd18647 cd18647 349294 CD_Cbx2 chromodomain of chromobox homolog 2. CHRomatin Organization Modifier (chromo) domain of chromobox homolog 2 (CBX2), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells. 53 matched cddid_all.tbl CDD cd18648 cd18648 349295 CD_Cbx6 chromodomain of chromobox homolog 6. CHRomatin Organization Modifier (chromo) domain of chromobox homolog 6 (CBX6), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells. 58 matched cddid_all.tbl CDD cd18649 cd18649 349296 CD_Cbx8 chromodomain of chromobox homolog 8. CHRomatin Organization Modifier (chromo) domain of chromobox homolog 8 (CBX8), a component of the PcG repressive complex PRC1, one of the two classes of PRCs. PcG proteins form large multiprotein complexes (PcG bodies) which are involved in the stable repression of genes involved in development, signaling or cancer via chromatin-based epigenetic modifications. Mammalian PRC1 includes canonical (cPRC1) and non-canonical complexes; cPRC1, contains four core subunits including one CBX protein (CBX2, CBX4, and CBX6-CBX8) that binds H3K27me3. CBX family members have different affinity for H3K27me3, with CBX7 having the highest binding capability. The human CBX proteins show distinct nuclear localizations and contribute differently to transcriptional repression. Some CBX proteins of the PRC1 complex have been implicated in transcriptional activation as well as in PRC1-independent roles in embryonic stem cells and in somatic cells. CBX proteins may act as an oncogene or tumor suppressor in a cell-type-dependent manner, CBX8 for example promotes proliferation while suppressing metastasis, in colorectal carcinoma progression. 55 matched cddid_all.tbl CDD cd18650 cd18650 349297 CD_HP1beta_Cbx1 chromodomain of heterochromatin protein 1 homolog beta. CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog beta (also known as HP1beta, CBX1, and chromobox 1), and related proteins. HP1beta is a highly conserved non-histone protein, which is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta, and HP1gamma (also known as Cbx3). 50 matched cddid_all.tbl CDD cd18651 cd18651 349298 CD_HP1alpha_Cbx5 chromodomain of heterochromatin protein 1 homolog alpha. CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog alpha (also known as HP1alpha, Cbx5, and Chromobox 5), and related proteins. HP1alpha has diverse functions in heterochromatin formation, gene regulation, and mitotic progression, and forms complex networks of gene, RNA, and protein interactions. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha, HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3). 50 matched cddid_all.tbl CDD cd18652 cd18652 349299 CD_HP1gamma_Cbx3 chromodomain of heterochromatin protein 1 homolog gamma. CHRomatin Organization Modifier (chromo) domain of heterochromatin protein 1 homolog gamma (also known as HP1gamma, Cbx3, and Chromobox 3), and related proteins. HP1gamma is a highly conserved non-histone protein, which is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. In addition to being involved in transcriptional silencing in heterochromatin-like complexes, HP1gamma also binds lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the protein may explain the association of heterochromatin with the inner nuclear membrane. HP1gamma is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma. 50 matched cddid_all.tbl CDD cd18653 cd18653 349300 CD_HP1a_insect chromodomain of insect HP1a. CHRomatin Organization Modifier (chromo) domain of insect HP1a. HP1a is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1 has diverse functions in heterochromatin formation and impacts both gene expression and gene silencing. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. In Drosophila, there are at least five HP1 family proteins, this subgroup includes the CD of Drosophila melanogaster HP1a. 50 matched cddid_all.tbl CDD cd18654 cd18654 349301 CSD_HP1beta_Cbx1 chromo shadow domain of heterochromatin protein 1 homolog beta. heterochromatin protein 1 homolog beta (also known as HP1beta, Cbx1, chromobox 1) is a highly conserved non-histone protein, which is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1beta has a single N-terminal chromodomain which can bind to histone proteins via methylated lysine residues, and a C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1beta may play an important role in the epigenetic control of chromatin structure and gene expression. CSD domains have only been found in proteins that also possess a related chromodomain, while chromodomains can exist in isolation. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta, and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3 58 matched cddid_all.tbl CDD cd18655 cd18655 349302 CSD_HP1alpha_Cbx5 chromo shadow domain of heterochromatin protein 1 homolog alpha. Chromo shadow domain (CSD) of heterochromatin protein 1 homolog alpha (also known as HP1alpha, Cbx5, and Chromobox 5), and related proteins. HP1alpha has diverse functions in heterochromatin formation, gene regulation, and mitotic progression, and forms complex networks of gene, RNA, and protein interactions. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. CSD domains have only been found in proteins that also possess a related chromodomain, while chromodomains can exist in isolation. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha, HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3. 58 matched cddid_all.tbl CDD cd18656 cd18656 349303 CSD_HP1gamma_Cbx3 chromo shadow domain of heterochromatin protein 1 gamma homolog gamma. Chromo shadow domain (CSD) of heterochromatin protein 1 gamma homolog gamma (also known as HP1gamma, Cbx3, Chromobox 3), and related proteins. HP1gamma appears to be involved in transcriptional silencing in heterochromatin-like complexes. It binds histone H3 tails methylated at Lys-9, leading to epigenetic repression, and also binds lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the protein may explain the association of heterochromatin with the inner nuclear membrane. HP1gamma is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal CSD which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. CSD domains have only been found in proteins that also possess a related chromodomain, while chromodomains can exist in isolation. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma. The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3. 58 matched cddid_all.tbl CDD cd18657 cd18657 349304 CSD_Swi6 chromo shadow domain of chromatin-associated protein Swi6. Chromo shadow domain (CSD) of fission yeast Swi6 protein. Swi6 is a structural and functional homolog of mammalian HP1 (heterochromatin protein 1) and is involved in the chromatin structure by binding to centromere, telomere and silent mating-type locus. Swi6 contains a N-terminal chromo (CHRromatin Organization MOdifier) domain and a C-terminal chromo shadow domain (CSD). Swi6 binds histone H3 tails methylated at Lys- and the cohesion subunit Psc3, leading to silencing the genes and sister chromatid cohesion. It is also involved in the repression of the silent mating-type loci MAT2 and MAT3. Swi6 may compact MAT2/3 into a heterochromatin-like conformation which represses the transcription of these silent cassettes. The chromo shadow domain (CSD) is always found in association with a related N-terminal chromo (CHRromatin Organization MOdifier) domain. CSD domains have only been found in proteins that also possess a chromodomain, while chromodomains can exist in isolation. 55 matched cddid_all.tbl CDD cd18658 cd18658 349305 CSD_HP1a_insect chromo shadow domain of insect heterochromatin protein 1a. The chromo shadow domain (CSD) is always found in association with a related N-terminal chromo (CHRromatin Organization MOdifier) domain. CSD domains have only been found in proteins that also possess a chromodomain, while chromodomains can exist in isolation. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal CSD which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3. In Drosophila, there are at least five HP1 family proteins, this subgroup includes the CSD of Drosophila melanogaster HP1a. 53 matched cddid_all.tbl CDD cd18659 cd18659 349306 CD2_tandem repeat 2 of paired tandem chromodomains. Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 to CHD9, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 54 matched cddid_all.tbl CDD cd18660 cd18660 349307 CD1_tandem repeat 1 of paired tandem chromodomains. Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 to CHD9, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 70 matched cddid_all.tbl CDD cd18661 cd18661 349308 CD2_tandem_CHD1-2_like repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins. Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 and CHD2. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 58 matched cddid_all.tbl CDD cd18662 cd18662 349309 CD2_tandem_CHD3-4_like repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins. Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD3 and CHD4, and yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. Human CHD3 (also named Mi-2 alpha) and CHD4 (also named Mi-2 beta) are coexpressed in many cell lines and tissues and may act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). The proteins form distinct CHD3- and CHD4-NuRD complexes that repress, as well as activate gene transcription of overlapping and specific target genes. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 55 matched cddid_all.tbl CDD cd18663 cd18663 349310 CD2_tandem_CHD5-9_like repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins. Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD5, CHD6, CHD7, CHD8, and CHD9. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. CHD6, CHD7, and CHD8 enzymes have been demonstrated to have different substrate specificities and remodeling activities. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 59 matched cddid_all.tbl CDD cd18664 cd18664 349311 CD2_tandem_ScCHD1_like repeat 2 of the paired tandem chromodomains of yeast chromodomain helicase DNA-binding protein 1, and similar proteins. Repeat 2 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 59 matched cddid_all.tbl CDD cd18665 cd18665 349312 CD1_tandem_CHD1_yeast_like repeat 1 of the paired tandem chromodomains of yeast chromodomain helicase DNA-binding protein 1, and similar proteins. Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as yeast protein CHD1. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 65 matched cddid_all.tbl CDD cd18666 cd18666 349313 CD1_tandem_CHD1-2_like repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 1 and 2, and similar proteins. Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD1 and CHD2. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 85 matched cddid_all.tbl CDD cd18667 cd18667 349314 CD1_tandem_CHD3-4_like repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins. Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD3 and CHD4. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. Human CHD3 (also named Mi-2 alpha) and CHD4 (also named Mi-2 beta) are coexpressed in many cell lines and tissues and may act as the motor subunit of the NuRD complex (nucleosome remodeling and deacetylase activities). The proteins form distinct CHD3- and CHD4-NuRD complexes that repress, as well as activate gene transcription of overlapping and specific target genes. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 79 matched cddid_all.tbl CDD cd18668 cd18668 349315 CD1_tandem_CHD5-9_like repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins. Repeat 1 of tandem CHRomatin Organization Modifier (chromo) domains, found in CHD (chromodomain helicase DNA-binding) proteins such as mammalian helicase DNA-binding proteins CHD5, CHD6, CHD7, CHD8, and CHD9. The CHD proteins belong to the SNF2 superfamily of ATP-dependent chromatin remodelers and contain two signature motifs: a pair of chromodomains located in the N-terminal region, and the SNF2-like ATPase domain located in the central region of the protein. CHD chromatin remodelers are important regulators of transcription and play critical roles during developmental processes. The N-terminal chromodomains of CHD1 have been shown to guard against sliding hexasomes. Mutations in the chromodomains of mouse CHD1 result in nuclear redistribution, suggesting that the chromodomain is essential for proper association with chromatin; also, deletion of the chromodomains in the Drosophila melanogaster CHD3-4 homolog impaired nucleosome binding, mobilization, and ATPase functions. CHD6, CHD7, and CHD8 enzymes have been demonstrated to have different substrate specificities and remodeling activities. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 68 matched cddid_all.tbl CDD cd18669 cd18669 349948 M20_18_42 M20, M18 and M42 Zn-peptidases include aminopeptidases and carboxypeptidases. This family corresponds to the MEROPS MH clan families M18, M20, and M42. The peptidase M20 family contains exopeptidases, including carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase, dipeptidases such as bacterial dipeptidase, peptidase V (PepV), a eukaryotic, non-specific dipeptidase, and two Xaa-His dipeptidases (carnosinases). This family also includes the bacterial aminopeptidase peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. These peptidases generally hydrolyze the late products of protein degradation so as to complete the conversion of proteins to free amino acids. Glutamate carboxypeptidase hydrolyzes folate analogs such as methotrexate, and therefore can be used to treat methotrexate toxicity. Peptidase families M18 and M42 contain metallo-aminopeptidases. M18 (aspartyl aminopeptidase, DAP) family cleaves only unblocked N-terminal acidic amino-acid residues and is highly selective for hydrolyzing aspartate or glutamate residues. Some M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacyl-peptidase activity (i.e. hydrolysis of acylated N-terminal residues). 198 matched cddid_all.tbl CDD cd18670 cd18670 350850 PIN_Mut7-C-like PIN domain at the C-terminus of Caenorhabditis elegans exonuclease Mut-7 and related domains. The Mut7-C-like family of the PIN domain superfamily includes the C-terminal domain of Caenorhabditis elegans Mut-7 (also known as exonuclease 3'-5' domain-containing protein 3 homolog). Mut-7 is involved in RNA interference (RNAi) and transposon silencing in C. elegans. The Mut7-C PIN domain family is recognized as a genuine PIN domain, however it is not included it in the CDD PIN domain superfamily hierarchical model as it is lacks a core strand and helix (H3 and S3). The PIN (PilT N terminus) domain belongs to a large nuclease superfamily, and were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Other PIN domain families are: the FEN-like PIN domain family which includes the PIN domains of Flap endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap Endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease, 5'-3' exonucleases of DNA polymerase I and bacteriophage T4- and T5-5' nucleases; the VapC-like PIN domain family which includes toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and, rRNA-processing protein Fcf1; the LabA-like PIN domain family which includes the PIN domains of Synechococcus elongatus LabA (low-amplitude and bright); the PRORP-Zc3h12a-like PIN domain family which includes the PIN domains of of RNase P (PRORP), ribonuclease Zc3h12a; and Bacillus subtilis YacP/Rae1-like PIN domains. Matelska et al. recently classified PIN-like domains into distinct groups, this family includes some sequences belonging to two of these, PIN _10 and PIN_16. 65 matched cddid_all.tbl CDD cd18671 cd18671 350238 PIN_PRORP-Zc3h12a-like PIN domain of protein-only RNase P (PRORP), ribonuclease Zc3h12a, and related proteins. PRORPs catalyze the maturation of the 5' end of precursor tRNAs in eukaryotes. This family includes human PRORP, also known as proteinaceous RNase P and mitochondrial RNase P protein subunit 3 (MRPP3), and Arabidopsis thaliana PRORP1-3, PRORP1 localizes to the chloroplast and the mitochondria, and PRORP2 and PRORP3 localize to the nucleus. Zc3h12a (zinc finger CCCH-type containing 12A, also known as MCPIP1/MCP induced protein 1 and Regnase-1) is a critical regulator of inflammatory response, with additional roles in defense against viruses and various stresses, cellular differentiation, and apoptosis. This PIN_PRORP-Zc3h12a-like family also includes Caenorhabditis elegans REGE-1 (REGnasE-1), which also functions as a cytoplasmic endonuclease. Additionally, it includes three less-studied mammalian homologs: Zc3h12b-d/Regnase-2-4, as well as N4BP1 (NEDD4-binding partner-1), NYNRIN (NYN domain and retroviral integrase containing, also known as CGIN1/Cousin of GIN1), and KHNYN (KH and NYN domain containing) protein. N4BP1, CGIN1, and KHNYN proteins are probably of retroviral origin. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 126 matched cddid_all.tbl CDD cd18672 cd18672 350239 PIN_FAM120B-like "FEN-like PIN domains of FAM120B (family with sequence similarity 120B) and related proteins. FAM120B (also known as CCPG, ""constitutive coactivator of PPAR-gamma"", PGCC1, ""PPARgamma constitutive coactivator 1"") is a constitutive coactivator of peroxisome proliferator-activated receptor (PPARgamma) that promotes adipogenesis in a PPARgamma-dependent manner. This subfamily belongs to the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), the helical arch/clamp region is involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons." 210 matched cddid_all.tbl CDD cd18673 cd18673 350240 PIN_XRN1-2-like FEN-like PIN domains of XRN1, XRN2, and related proteins. XRN1 (5'-3' exoribonuclease 1, also known as SEP1) is a processive 5'-3' exoribonuclease that degrades the body of transcripts in the major pathway of RNA decay; XRN2 (5'-3' exoribonuclease 2) is predominantly localized in the nucleus and recognizes single-stranded RNAs with a 5'-terminal monophosphate to degrade them possessively to mononucleotides. XRN2 has a critical function to process maturation of 5.8S and 25S/28S rRNAs as well as degradation of some spacer fragments that are excised during rRNA maturation. Both XRN1 and XRN2 preferentially cleave 5'-monophosphorylated RNA. XRN2 is also known as Rat1p in yeast. This subfamily belongs to the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), the helical arch/clamp region is involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 240 matched cddid_all.tbl CDD cd18674 cd18674 350241 PIN_Pox_G5 FEN-like PIN domain of vaccinia virus G5 protein and related proteins. Poxvirus G5 nuclease is involved in DNA replication and double-strand break repair by homologous recombination. This subfamily belongs to the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), the helical arch/clamp region is involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 151 matched cddid_all.tbl CDD cd18675 cd18675 350242 PIN_SpAst1-like FEN-like PIN domain of Schizosaccharomyces pombe asteroid homolog 1 and related proteins. Schizosaccharomyces pombe Ast1 is a homologue of Drosophila Asteroid and human ASTE1. Ast1 appears to be involved in mounting a checkpoint response to endogenous damage in cells lacking Rad2 and Exo1. This subfamily belongs to the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), the helical arch/clamp region is involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 163 matched cddid_all.tbl CDD cd18676 cd18676 350243 PIN_asteroid-like FEN-like PIN domain of Drosophila melanogaster asteroid and related proteins. This subfamily includes Drosophila melanogaster asteroid protein which may function in EGF receptor signaling, and may play a role in compound eye morphogenesis. This subfamily belongs to the structure-specific, 5' nuclease family (FEN-like) that catalyzes hydrolysis of DNA duplex-containing nucleic acid structures during DNA replication, repair, and recombination. Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), the helical arch/clamp region is involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 164 matched cddid_all.tbl CDD cd18677 cd18677 350244 PIN_MjVapC2-VapC6_like VapC-like PIN domain of Methanocaldococcus jannaschii VapC2, and VapC6, and related proteins. This subfamily includes Methanocaldococcus jannaschii VapC2 and VapC6. It belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 136 matched cddid_all.tbl CDD cd18678 cd18678 350245 PIN_MtVapC25_VapC33-like VapC-like PIN domain of Mycobacterium tuberculosis VapC25, VapC33, and related proteins. This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC25, VapC29, VapC33, VapC37, and VapC39 toxins. It belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is a PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 140 matched cddid_all.tbl CDD cd18679 cd18679 350246 PIN_VapC-Af1683-like VapC-like PIN domain of VapC ribonuclease similar to Archaeoglobus fulgidus uncharacterized Af1683 protein. Uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 126 matched cddid_all.tbl CDD cd18680 cd18680 350247 PIN_MtVapC20-like VapC-like PIN domain of Mycobacterium tuberculosis VapC20 and related proteins. M. tuberculosis VapC20 inhibits translation by site-specific cleavage of the universally conserved Sarcin-Ricin loop in 23S rRNA. This subfamily belongs to the VapC (virulence-associated protein C)-like nuclease family of the PIN domain-like superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. 131 matched cddid_all.tbl CDD cd18681 cd18681 350248 PIN_MtVapC27-VapC40_like VapC-like PIN domain of Mycobacterium tuberculosis VapC27, and VapC40, and related proteins. This subfamily includes Mycobacterium tuberculosis VapC27 and VapC40. It belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 129 matched cddid_all.tbl CDD cd18682 cd18682 350249 PIN_VapC-like Uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 118 matched cddid_all.tbl CDD cd18683 cd18683 350250 PIN_VapC-like Uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 125 matched cddid_all.tbl CDD cd18684 cd18684 350251 PIN_VapC-like uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 131 matched cddid_all.tbl CDD cd18685 cd18685 350252 PIN_VapC-like uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains and included distant subgroups, this subgroup includes some sequences belonging to one of these, PIN_14. 110 matched cddid_all.tbl CDD cd18686 cd18686 350253 PIN_VapC-like uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 119 matched cddid_all.tbl CDD cd18687 cd18687 350254 PIN_VapC-like uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_3. 118 matched cddid_all.tbl CDD cd18688 cd18688 350255 PIN_VapC-like uncharacterized subfamily of the VapC-like nuclease family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 134 matched cddid_all.tbl CDD cd18689 cd18689 350256 PIN_VapC-like uncharacterized subfamily of the VapC-like nuclease family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 125 matched cddid_all.tbl CDD cd18690 cd18690 350257 PIN_VapC-like uncharacterized subfamily of the VapC-like nuclease family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_12. 134 matched cddid_all.tbl CDD cd18691 cd18691 350258 PIN_VapC-like uncharacterized subfamily of the VapC-like nuclease family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 130 matched cddid_all.tbl CDD cd18692 cd18692 350259 PIN_VapC-like uncharacterized subfamily of the VapC-like nuclease family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 129 matched cddid_all.tbl CDD cd18693 cd18693 350260 PIN_VapC-like uncharacterized subfamily of the VapC-like nuclease family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_22. 129 matched cddid_all.tbl CDD cd18694 cd18694 350261 PIN_VapC-like uncharacterized subfamily of the VapC-like nuclease family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_24. 133 matched cddid_all.tbl CDD cd18695 cd18695 350262 PIN_VapC-like uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_13. 118 matched cddid_all.tbl CDD cd18696 cd18696 350263 PIN_MtVapC26-like VapC-like PIN domain of Mycobacterium tuberculosis VapC26 and related proteins. Mycobacterium tuberculosis VapC26 cleaves 23S rRNA in the Sarcin-Ricin Loop, it is inhibited by the cognate VapB26 antitoxin. This subfamily belongs to the VapC (virulence-associated protein C)-like nuclease family of the PIN domain-like superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 132 matched cddid_all.tbl CDD cd18697 cd18697 350264 PIN_VapC_N-like VapC-like N-terminal PIN (DUF4935) domain of DUF4935 domain-containing proteins and related proteins. This subgroup the includes N-terminal PIN domain of DUF4935 domain-containing proteins, and is an uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 183 matched cddid_all.tbl CDD cd18698 cd18698 350265 PIN_VapC_C-like VapC-like C-terminus of DUF1308 domain in DUF1308 domain-containing proteins and related proteins. This subfamily includes the C-terminus of DUF1308 domain in DUF1308 domain-containing proteins, and is an uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 138 matched cddid_all.tbl CDD cd18699 cd18699 350266 PIN_VapC_like uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_15. 129 matched cddid_all.tbl CDD cd18700 cd18700 350267 PIN_GNAT-like VapC-like PIN domain of uncharacterized GNAT family proteins. This subfamily includes uncharacterized GNAT family proteins having an N-terminal GNAT family N-acetyltransferase domain. This subgroup belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_17. 137 matched cddid_all.tbl CDD cd18701 cd18701 350268 PIN_VapC_like uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_18. 144 matched cddid_all.tbl CDD cd18702 cd18702 350269 PIN_VapC_like uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_19 139 matched cddid_all.tbl CDD cd18703 cd18703 350270 PIN_VapC-like uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_20. 148 matched cddid_all.tbl CDD cd18704 cd18704 350271 PIN_VapC-like uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_21. 145 matched cddid_all.tbl CDD cd18705 cd18705 350272 PIN_VapC-like uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_23. 130 matched cddid_all.tbl CDD cd18706 cd18706 350273 PIN_STKc_like uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily; includes the PIN domains of uncharacterized serine/threonine kinases. This subfamily includes the PIN domains of some uncharacterized proteins having serine/threonine kinase catalytic domains and annotated as serine/threonine kinases. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_25. 126 matched cddid_all.tbl CDD cd18707 cd18707 350274 PIN_VapC-like uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_26. 131 matched cddid_all.tbl CDD cd18708 cd18708 350275 PIN_VapC-like uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_28. 116 matched cddid_all.tbl CDD cd18709 cd18709 350276 PIN_VapC-like uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_4-1. 196 matched cddid_all.tbl CDD cd18710 cd18710 350277 PIN_VapC-like uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_4-2. 130 matched cddid_all.tbl CDD cd18711 cd18711 350278 PIN_VapC-like_DUF411 VapC-like PIN (DUF411) domain in DUF411 domain-containing proteins and related proteins. This subfamily includes the DUF411 PIN domain in proteins annotated as DUF411 domain-containing proteins. It is an uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 146 matched cddid_all.tbl CDD cd18712 cd18712 350279 PIN_VapC-like_DUF411 CapC-like PIN (DUF411) domain in DUF411 domain-containing proteins and related proteins. This subfamily includes the DUF411 PIN domain in proteins annotated as DUF411 domain-containing proteins. It is an uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 148 matched cddid_all.tbl CDD cd18713 cd18713 350280 PIN_VapC-like uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_27. 140 matched cddid_all.tbl CDD cd18714 cd18714 350281 PIN_VapC-like uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_8. 228 matched cddid_all.tbl CDD cd18715 cd18715 350282 PIN_VapC-like uncharacterized subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 125 matched cddid_all.tbl CDD cd18716 cd18716 350283 PIN_SSO1118-like VapC-like PIN domain of Sulfolobus solfataricus SSO1118 and related proteins. This subfamily includes the functionally uncharacterized protein SSO1118 from the hyperthermophilic archaeon Sulfolobus solfataricus P2. This subfamily belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 102 matched cddid_all.tbl CDD cd18717 cd18717 350284 PIN_ScNmd4p-like VapC-like PIN domain of Saccharomyces cerevisiae Nmd4p and related proteins. Saccharomyces cerevisiae Nmd4p may be involved in nonsense-mediated mRNA decay. This subfamily belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 150 matched cddid_all.tbl CDD cd18718 cd18718 350285 PIN_PRORP PIN domain of protein-only RNase P (PRORP) and related proteins. PRORPs catalyze the maturation of the 5' end of precursor tRNAs in eukaryotes. This family includes human PRORP, also known as proteinaceous RNase P and mitochondrial RNase P protein subunit 3 (MRPP3), and Arabidopsis thaliana PRORP1-3, PRORP1 localizes to the chloroplast and the mitochondria, and PRORP2 and PRORP3 localize to the nucleus. This subfamily belongs to the PRORP-Zc3h12a-like PIN family which in addition includes Zc3h12a (also known as MCPIP1/MCP induced protein 1 and Regnase-1), Caenorhabditis elegans REGE-1 (REGnasE-1), Zc3h12b-d (also known as Regnase-2-4), N4BP1, and NYNRIN (also known as CGIN1). The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 124 matched cddid_all.tbl CDD cd18719 cd18719 350286 PIN_Zc3h12a-N4BP1-like PRORP-like PIN domain of ribonuclease Zc3h12a, NEDD4-binding partner-1, and related proteins. Zc3h12a (zinc finger CCCH-type containing 12A, also known as MCPIP1/MCP induced protein 1 and Regnase-1) is a critical regulator of inflammatory response, with additional roles in defense against viruses and various stresses, cellular differentiation, and apoptosis. This subfamily also includes Caenorhabditis elegans REGE-1 (REGnasE-1), which also functions as a cytoplasmic endonuclease. Additionally, it includes three less-studied mammalian homologs: Zc3h12b-d/Regnase-2-4, as well as N4BP1 (NEDD4-binding partner-1), NYNRIN (NYN domain and retroviral integrase containing, also known as CGIN1/Cousin of GIN1), and KHNYN (KH and NYN domain containing) protein. N4BP1, CGIN1, and KHNYN proteins are probably of retroviral origin. This subfamily belongs to the PRORP-Zc3h12a-like PIN family which in addition includes human PRORP, also known as proteinaceous RNase P and mitochondrial RNase P protein subunit 3 (MRPP3), and Arabidopsis thaliana PRORP1-3. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 127 matched cddid_all.tbl CDD cd18720 cd18720 350287 PIN_YqxD-like LabA-like PIN domain of uncharacterized Bacillus subtilis YqxD and related proteins. This subfamily includes the PIN domain of uncharacterized Bacillus subtilis YqxD (also known as YqfM) and Escherichia coli YaiI. Firmicute, such as Bacillus and Listeria, YqxD proteins are encoded within RNA polymerase major sigma43 operons, whereas E. coli YaiL is transcribed as a mono cistron. This subfamily belongs to LabA-like PIN domain family which includes Synechococcus elongatus PCC 7942 LabA, human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like PIN family. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 96 matched cddid_all.tbl CDD cd18721 cd18721 350288 PIN_ZNF451-like LabA-like PIN domain of human zinc finger protein 451 and related proteins. Human ZNF451 (also known as COASTER) functions as a transcriptional cofactor in promyelocytic leukemia bodies in the nucleus, it acts as a coactivator or corepressor, depending on the factors with which it interacts. ZNF451 interacts with p300 by the PIN-like domain and down regulates TGF-beta signaling in a p300-dependent and sumoylation-independent manner. This subfamily belongs to LabA-like PIN domain family which includes Synechococcus elongatus PCC 7942 LabA, human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like PIN family. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_11. 117 matched cddid_all.tbl CDD cd18722 cd18722 350289 PIN_NicB-like LabA-like PIN domain of Pseudomonas putida S16 NicB and related proteins. Curiously NicB from Pseudomonas putida S16 is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine. This subfamily also includes the uncharacterized CPP15 (plasmid) protein from Campylobacter jejuni. This subfamily belongs to LabA-like PIN domain family which includes Synechococcus elongatus PCC 7942 LabA, human ZNF451, uncharacterized Bacillus subtilis YqxD and Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously, a gene labeled NicB from Pseudomonas putida S16, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into the LabA-like PIN family. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 117 matched cddid_all.tbl CDD cd18723 cd18723 350290 PIN_LabA-like uncharacterized subfamily of the LabA-like PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins. The LabA-like PIN domain family includes Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing, it is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system, and appears to be necessary for KaiC-dependent repression of gene expression. It also includes the N-terminal domain of limkain b1, a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes, human ZNF451, uncharacterized Bacillus subtilis YqxD, uncharacterized Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously Pseudomonas putida S16 NicB, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into this family. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_7. 110 matched cddid_all.tbl CDD cd18724 cd18724 350291 PIN_LabA-like uncharacterized subfamily of the LabA-like PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins. The LabA-like PIN domain family includes Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing, it is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system, and appears to be necessary for KaiC-dependent repression of gene expression. It also includes the N-terminal domain of limkain b1, a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes, human ZNF451, uncharacterized Bacillus subtilis YqxD, uncharacterized Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously Pseudomonas putida S16 NicB, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into this family. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 172 matched cddid_all.tbl CDD cd18725 cd18725 350292 PIN_LabA-like uncharacterized subfamily of the LabA-like PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins. The LabA-like PIN domain family includes Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing, it is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system, and appears to be necessary for KaiC-dependent repression of gene expression. It also includes the N-terminal domain of limkain b1, a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes, human ZNF451, uncharacterized Bacillus subtilis YqxD, uncharacterized Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously Pseudomonas putida S16 NicB, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into this family. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 131 matched cddid_all.tbl CDD cd18726 cd18726 350293 PIN_LabA-like uncharacterized subfamily of the LabA-like PIN domain of Synechococcus elongatus LabA (low-amplitude and bright) and related proteins. The LabA-like PIN domain family includes Synechococcus elongatus PCC 7942 LabA which participates in cyanobacterial circadian timing, it is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system, and appears to be necessary for KaiC-dependent repression of gene expression. It also includes the N-terminal domain of limkain b1, a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes, human ZNF451, uncharacterized Bacillus subtilis YqxD, uncharacterized Escherichia coli YaiI, and the N-terminal domain of a well-conserved group of mainly bacterial proteins with no defined function, which contain a C-terminal LabA_like_C domain. Curiously Pseudomonas putida S16 NicB, which is described as a putative NADH-dependent hydroxylase involved in the microbial degradation of nicotine also falls into this family. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 113 matched cddid_all.tbl CDD cd18727 cd18727 350294 PIN_Swt1-like VapC-like PIN domain of Saccharomyces cerevisiae Swt1p, human SWT1 and related proteins. Saccharomyces cerevisiae mRNA-processing endoribonuclease Swt1p plays an important role in quality control of nuclear mRNPs in eukaryotes. Human transcriptional protein SWT1 (RNA endoribonuclease homolog, also known as HsSwt1, C1orf26, and chromosome 1 open reading frame 26) is an RNA endonuclease that participates in quality control of nuclear mRNPs and can associate with the nuclear pore complex (NPC). This subfamily belongs to the Smg5 and Smg6-like PIN domain family. Smg5 and Smg6 are essential factors in NMD, a post-transcriptional regulatory pathway that recognizes and rapidly degrades mRNAs containing premature translation termination codons. In vivo, the Smg6 PIN domain elicits degradation of bound mRNAs, as well as, metal-ion dependent, degradation of single-stranded RNA, in vitro. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases (also known as Flap endonuclease-1-like), PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Point mutation studies of the conserved aspartate residues in the catalytic center of the Smg6 PIN domain revealed that Smg6 is the endonuclease involved in human NMD. However, Smg5 lacks several of these key catalytic residues and does not degrade single-stranded RNA, in vivo. 141 matched cddid_all.tbl CDD cd18728 cd18728 350295 PIN_N4BP1-like PRORP-like PIN domain of NEDD4 binding protein 1 and related proteins. NEDD4-binding partner-1 (N4BP1) interacts with and is a substrate of NEDD4 ubiquitin ligase (neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase). It is also an inhibitor of the E3 ubiquitin-protein ligase ITCH, a NEDD4 structurally related E3. This subfamily additionally includes NYNRIN (NYN domain and retroviral integrase containing, also known as CGIN1/Cousin of GIN1), and KHNYN (KH and NYN domain containing) protein. N4BP1, CGIN1, and KHNYN proteins are probably of retroviral origin. This subfamily belongs to the Zc3h12a-N4BP1-like PIN subfamily of the PRORP-Zc3h12a-like PIN family, the latter of which additionally includes human PRORP, also known as proteinaceous RNase P and mitochondrial RNase P protein subunit 3 (MRPP3), and Arabidopsis thaliana PRORP1-3. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 127 matched cddid_all.tbl CDD cd18729 cd18729 350296 PIN_Zc3h12-like PRORP-like PIN domain of ribonuclease Zc3h12a and related proteins. Zc3h12a (zinc finger CCCH-type containing 12A, also known as MCPIP1/MCP induced protein 1 and Regnase-1) is a critical regulator of inflammatory response, with additional roles in defense against viruses and various stresses, cellular differentiation, and apoptosis. This subfamily also includes three less-studied mammalian homologs: Zc3h12b-d/Regnase-2-4. It belongs to the Zc3h12a-N4BP1-like PIN subfamily of the PRORP-Zc3h12a-like PIN family, the latter of which additionally includes human PRORP, also known as proteinaceous RNase P and mitochondrial RNase P protein subunit 3 (MRPP3), and Arabidopsis thaliana PRORP1-3. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 131 matched cddid_all.tbl CDD cd18730 cd18730 350297 PIN_PH0500-like VapC-like PIN-domain of Pyrococcus horikoshii protein PH0500 and related proteins. This subfamily includes Pyrococcus horikoshii protein PH0500, a protein with possible exonuclease activity and involvement in DNA or RNA editing. This subfamily belongs to the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 126 matched cddid_all.tbl CDD cd18731 cd18731 350298 PIN_NgFitB-like VapC-like PIN domain of Neisseria gonorrhoeae FitB and related proteins. This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Neisseria gonorrhoeae FitB toxin of the FitAB toxin/antitoxin (TA) system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. In N. gonorrhoeae, FitA and FitB form a heterodimer: FitA is the DNA binding subunit and FitB contains a ribonuclease activity that is blocked by the presence of FitA. A tetramer of FitAB heterodimers binds DNA from the fitAB upstream promoter region with high affinity. This results in both sequestration of FitAB and repression of fitAB transcription. It is thought that FitAB release from the DNA and subsequent dissociation both slows N. gonorrhoeae replication and transcytosis by an as yet undefined mechanism. The toxin M. tuberculosis VapC is a structural homolog of N. gonorrhoeae FitB, but their antitoxin partners, VapB and FitA, respectively, differ structurally. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 136 matched cddid_all.tbl CDD cd18732 cd18732 350299 PIN_MtVapC4-C5_like VapC-like PIN domain of Mycobacterium tuberculosis VapC4, VapC5, and related proteins. This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 toxin of the VapBC toxin/antitoxin (TA) system. This family belongs to the PIN_VapC4-5_FitB-like subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. M. tuberculosis VapC4 interacts with, and cleaves tRNA44Cys-GCA. M. tuberculosis VapC5 has endonucleolytic activity with RNA, this activity is low with dsRNA, and no activity has been demonstrated on dsDNA. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 124 matched cddid_all.tbl CDD cd18733 cd18733 350300 PIN_RfVapC1-like VapC-like PIN domain of Rickettsia felis VapC1 and related proteins. This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Rickettsia felis VapC1, a ribonuclease toxin of the VapBC toxin/antitoxin (TA) system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC TA systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 131 matched cddid_all.tbl CDD cd18734 cd18734 350301 PIN_RfVapC2-like VapC-like PIN domain of Rickettsia felis VapC2 and related proteins. This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Rickettsia felis VapC2, a ribonuclease toxin of the VapBC toxin/antitoxin (TA) system. Rickettsia felis VapC2 cleaves single-stranded RNA. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC TA systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 129 matched cddid_all.tbl CDD cd18735 cd18735 350302 PIN_HiVapC1-like VapC-like PIN domain of Haemophilus influenzae VapC1 and related proteins. Haemophilus influenzae VapC1 has endonucleolytic activity with RNA, it cleaves initiator tRNA between the anticodon stem and loop, but does not cleave mRNA, rRNA or tmRNA, and has no activity on ssDNA or dsDNA. This subfamily belongs to the PIN_VapC4-5_FitB-like subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC TA systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. FitB is a toxin of the FitAB TA system. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 128 matched cddid_all.tbl CDD cd18736 cd18736 350303 PIN_CcVapC1-like VapC-like PIN domain of Caulobacter Crescentus VapC1-like and related proteins. This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Caulobacter Crescentus VapC1, a ribonuclease toxin of the VapBC toxin/antitoxin (TA) system. This subfamily belongs to the PIN_VapC4-5_FitB-like subfamily of the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC TA systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. FitB is a toxin of the FitAB TA system. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 123 matched cddid_all.tbl CDD cd18737 cd18737 350304 PIN_VapC4-5_FitB-like uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily. The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 115 matched cddid_all.tbl CDD cd18738 cd18738 350305 PIN_VapC4-5_FitB-like uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily. The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 118 matched cddid_all.tbl CDD cd18739 cd18739 350306 PIN_VapC4-5_FitB-like uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily. The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 124 matched cddid_all.tbl CDD cd18740 cd18740 350307 PIN_VapC4-5_FitB-like uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily. The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 126 matched cddid_all.tbl CDD cd18741 cd18741 350308 PIN_VapC4-5_FitB-like uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily. The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 120 matched cddid_all.tbl CDD cd18742 cd18742 350309 PIN_VapC4-5_FitB-like uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily. The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 127 matched cddid_all.tbl CDD cd18743 cd18743 350310 PIN_VapC4-5_FitB-like uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily. The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 127 matched cddid_all.tbl CDD cd18744 cd18744 350311 PIN_VapC4-5_FitB-like uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily. The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 128 matched cddid_all.tbl CDD cd18745 cd18745 350312 PIN_VapC4-5_FitB-like uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily. The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 130 matched cddid_all.tbl CDD cd18746 cd18746 350313 PIN_VapC4-5_FitB-like uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily. The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 133 matched cddid_all.tbl CDD cd18747 cd18747 350314 PIN_VapC4-5_FitB-like uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily. The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 132 matched cddid_all.tbl CDD cd18748 cd18748 350315 PIN_VapC4-5_FitB-like uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily. The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 128 matched cddid_all.tbl CDD cd18749 cd18749 350316 PIN_VapC4-5_FitB-like uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily. The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 126 matched cddid_all.tbl CDD cd18750 cd18750 350317 PIN_VapC4-5_FitB-like uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily. The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 127 matched cddid_all.tbl CDD cd18751 cd18751 350318 PIN_VapC4-5_FitB-like uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily. The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 133 matched cddid_all.tbl CDD cd18752 cd18752 350319 PIN_VapC4-5_FitB-like uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily. The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 130 matched cddid_all.tbl CDD cd18753 cd18753 350320 PIN_VapC4-5_FitB-like uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily. The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 123 matched cddid_all.tbl CDD cd18754 cd18754 350321 PIN_VapC4-5_FitB-like uncharacterized subgroup of the PIN_VapC4-5_FitB-like subfamily of the PIN domain superfamily. The PIN_VapC4-5_FitB-like subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 ribonuclease toxins of the VapBC toxin/antitoxin (TA) system, and Neisseria gonorrhoeae FitB toxin of the FitAB TA system. This subfamily belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 128 matched cddid_all.tbl CDD cd18755 cd18755 350322 PIN_MtVapC3_VapC21-like VapC-like PIN domain of Mycobacterium tuberculosis VapC3, VapC21 and related proteins. This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC3 and VapC21 toxins. It belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is a PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 127 matched cddid_all.tbl CDD cd18756 cd18756 350323 PIN_MtVapC15-VapC11-like VapC-like PIN domain of Mycobacterium tuberculosis VapC11, VapC15, and related proteins. This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC11 and VapC15 toxins. M. tuberculosis VapC11 and VapC15 cleave tRNA3 Leu-CAG, VapC11 may additionally cleave tRNA13Leu-GAG and tRNA10Gln-CTG. This subgroup belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is a PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 129 matched cddid_all.tbl CDD cd18757 cd18757 350324 PIN_MtVapC3-like uncharacterized subgroup of the VapC3-like nuclease subfamily of the PIN domain superfamily. The VapC3-like nuclease subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of various Mycobacterium tuberculosis VapC toxins including VapC3, VapC11, VapC15, VapC21, VapC25, VapC28, VapC29, VapC30, VapC32, VapC33, VapC37, and VapC39. It belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is a PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 129 matched cddid_all.tbl CDD cd18758 cd18758 350325 PIN_MtVapC3-like uncharacterized subgroup of the VapC3-like nuclease subfamily of the PIN domain superfamily. The VapC3-like nuclease subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of various Mycobacterium tuberculosis VapC toxins including VapC3, VapC11, VapC15, VapC21, VapC25, VapC28, VapC29, VapC30, VapC32, VapC33, VapC37, and VapC39. It belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is a PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 127 matched cddid_all.tbl CDD cd18759 cd18759 350326 PIN_MtVapC3-like uncharacterized subgroup of the VapC3-like nuclease subfamily of the PIN domain superfamily. The VapC3-like nuclease subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of various Mycobacterium tuberculosis VapC toxins including VapC3, VapC11, VapC15, VapC21, VapC25, VapC28, VapC29, VapC30, VapC32, VapC33, VapC37, and VapC39. It belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is a PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 126 matched cddid_all.tbl CDD cd18760 cd18760 350327 PIN_MtVapC3-like uncharacterized subgroup of the VapC3-like nuclease subfamily of the PIN domain superfamily. The VapC3-like nuclease subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of various Mycobacterium tuberculosis VapC toxins including VapC3, VapC11, VapC15, VapC21, VapC25, VapC28, VapC29, VapC30, VapC32, VapC33, VapC37, and VapC39. It belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is a PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 126 matched cddid_all.tbl CDD cd18761 cd18761 350328 PIN_MtVapC3-like uncharacterized subgroup of the VapC3-like nuclease subfamily of the PIN domain superfamily. The VapC3-like nuclease subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of various Mycobacterium tuberculosis VapC toxins including VapC3, VapC11, VapC15, VapC21, VapC25, VapC28, VapC29, VapC30, VapC32, VapC33, VapC37, and VapC39. It belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is a PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 127 matched cddid_all.tbl CDD cd18762 cd18762 350329 PIN_MtVapC3-like uncharacterized subgroup of the VapC3-like nuclease subfamily of the PIN domain superfamily. The VapC3-like nuclease subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of various Mycobacterium tuberculosis VapC toxins including VapC3, VapC11, VapC15, VapC21, VapC25, VapC28, VapC29, VapC30, VapC32, VapC33, VapC37, and VapC39. It belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is a PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 130 matched cddid_all.tbl CDD cd18763 cd18763 350330 PIN_MtVapC3-like uncharacterized subgroup of the VapC3-like nuclease subfamily of the PIN domain superfamily. The VapC3-like nuclease subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of various Mycobacterium tuberculosis VapC toxins including VapC3, VapC11, VapC15, VapC21, VapC25, VapC28, VapC29, VapC30, VapC32, VapC33, VapC37, and VapC39. It belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is a PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 128 matched cddid_all.tbl CDD cd18764 cd18764 350331 PIN_MtVapC3-like uncharacterized subgroup of the VapC3-like nuclease subfamily of the PIN domain superfamily. The VapC3-like nuclease subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of various Mycobacterium tuberculosis VapC toxins including VapC3, VapC11, VapC15, VapC21, VapC25, VapC28, VapC29, VapC30, VapC32, VapC33, VapC37, and VapC39. It belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is a PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 129 matched cddid_all.tbl CDD cd18765 cd18765 350332 PIN_MtVapC3-like uncharacterized subgroup of the VapC3-like nuclease subfamily of the PIN domain superfamily. The VapC3-like nuclease subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of various Mycobacterium tuberculosis VapC toxins including VapC3, VapC11, VapC15, VapC21, VapC25, VapC28, VapC29, VapC30, VapC32, VapC33, VapC37, and VapC39. It belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is a PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 131 matched cddid_all.tbl CDD cd18766 cd18766 350333 PIN_MtVapC3-like uncharacterized subgroup of the VapC3-like nuclease subfamily of the PIN domain superfamily. The VapC3-like nuclease subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of various Mycobacterium tuberculosis VapC toxins including VapC3, VapC11, VapC15, VapC21, VapC25, VapC28, VapC29, VapC30, VapC32, VapC33, VapC37, and VapC39. It belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is a PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 130 matched cddid_all.tbl CDD cd18767 cd18767 350334 PIN_MtVapC3-like uncharacterized subgroup of the VapC3-like nuclease subfamily of the PIN domain superfamily. The VapC3-like nuclease subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of various Mycobacterium tuberculosis VapC toxins including VapC3, VapC11, VapC15, VapC21, VapC25, VapC28, VapC29, VapC30, VapC32, VapC33, VapC37, and VapC39. It belongs to the VapC-like family of the PIN domain nuclease superfamily. VapC is a PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. Other members of the VapC-like nuclease family include FitB toxin of the FitAB TA system, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and rRNA-processing protein Fcf1. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members, additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 126 matched cddid_all.tbl CDD cd18768 cd18768 350335 PIN_MtVapC4-C5-like VapC-like PIN domain of Mycobacterium tuberculosis VapC4, VapC5, and related proteins. This subfamily includes the Virulence associated protein C (VapC)-like PIN (PilT N terminus) domain of Mycobacterium tuberculosis VapC4 and VapC5 toxin of the VapBC toxin/antitoxin (TA) system. This family belongs to the PIN_VapC4-5_FitB-like subfamily of the VapC (virulence-associated protein C)-like family of the PIN domain nuclease superfamily. VapC is the PIN-domain ribonuclease toxin from prokaryotic VapBC toxin-antitoxin (TA) systems. VapB is a transcription factor-like protein antitoxin acting as an inhibitor. M. tuberculosis VapC4 interacts with, and cleaves tRNA44Cys-GCA. M. tuberculosis VapC5 has endonucleolytic activity with RNA, this activity is low with dsRNA, and no activity has been demonstrated on dsDNA. The structural properties of the PIN (PilT N terminus) domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions, in some members, additional metal coordinating residues can be found. Some members of the superfamily lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. 123 matched cddid_all.tbl CDD cd18769 cd18769 350851 PIN_Mut7-C-like uncharacterized subgroup of the Mut7-C-like family of the PIN domain superfamily. The Mut7-C-like family of the PIN domain superfamily includes the C-terminal domain of Caenorhabditis elegans Mut-7 (also known as exonuclease 3'-5' domain-containing protein 3 homolog). Mut-7 is involved in RNA interference (RNAi) and transposon silencing in C. elegans. The Mut7-C PIN domain family is recognized as a genuine PIN domain, however it not included it in the CDD PIN domain superfamily hierarchical model as it is lacks a core strand and helix (H3 and S3). The PIN (PilT N terminus) domain belongs to a large nuclease superfamily, and were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Other PIN domain families are: the FEN-like PIN domain family which includes the PIN domains of Flap endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease, 5'-3' exonucleases of DNA polymerase I and bacteriophage T4- and T5-5' nucleases; the VapC-like PIN domain family which includes toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and, rRNA-processing protein Fcf1; the LabA-like PIN domain family which includes the PIN domains of Synechococcus elongatus LabA (low-amplitude and bright); the PRORP-Zc3h12a-like PIN domain family which includes the PIN domains of of RNase P (PRORP), ribonuclease Zc3h12a; and Bacillus subtilis YacP/Rae1-like PIN domains. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_10. 85 matched cddid_all.tbl CDD cd18770 cd18770 350852 PIN_Mut7-C-like uncharacterized subgroup of the Mut7-C-like family of the PIN domain superfamily. The Mut7-C-like family of the PIN domain superfamily includes the C-terminal domain of Caenorhabditis elegans Mut-7 (also known as exonuclease 3'-5' domain-containing protein 3 homolog) Mut-7 is involved in RNA interference (RNAi) and transposon silencing in C. elegans. The Mut7-C PIN domain family is recognized as a genuine PIN domain, however it is not included it in the CDD PIN domain superfamily hierarchical model as it is lacks a core strand and helix (H3 and S3). The PIN (PilT N terminus) domain belongs to a large nuclease superfamily, and were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Other PIN domain families are: the FEN-like PIN domain family which includes the PIN domains of Flap endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease, 5'-3' exonucleases of DNA polymerase I and bacteriophage T4- and T5-5' nucleases; the VapC-like PIN domain family which includes toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and, rRNA-processing protein Fcf1; the LabA-like PIN domain family which includes the PIN domains of Synechococcus elongatus LabA (low-amplitude and bright); the PRORP-Zc3h12a-like PIN domain family which includes the PIN domains of of RNase P (PRORP), ribonuclease Zc3h12a; and Bacillus subtilis YacP/Rae1-like PIN domains. Matelska et al. recently classified PIN-like domains into distinct groups; this subgroup includes some sequences belonging to one of these, PIN_16. 80 matched cddid_all.tbl CDD cd18771 cd18771 350853 PIN_Mut7-C-like uncharacterized subgroup of the Mut7-C-like family of the PIN domain superfamily. The Mut7-C-like family of the PIN domain superfamily includes the C-terminal domain of Caenorhabditis elegans Mut-7 (also known as exonuclease 3'-5' domain-containing protein 3 homolog). Mut-7 is involved in RNA interference (RNAi) and transposon silencing in C. elegans. The Mut7-C PIN domain family is recognized as a genuine PIN domain, however it is not included it in the CDD PIN domain superfamily hierarchical model as it is lacks a core strand and helix (H3 and S3). The PIN (PilT N terminus) domain belongs to a large nuclease superfamily, and were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Other PIN domain families are: the FEN-like PIN domain family which includes the PIN domains of Flap endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease, 5'-3' exonucleases of DNA polymerase I and bacteriophage T4- and T5-5' nucleases; the VapC-like PIN domain family which includes toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and, rRNA-processing protein Fcf1; the LabA-like PIN domain family which includes the PIN domains of Synechococcus elongatus LabA (low-amplitude and bright); the PRORP-Zc3h12a-like PIN domain family which includes the PIN domains of of RNase P (PRORP), ribonuclease Zc3h12a; and Bacillus subtilis YacP/Rae1-like PIN domains. 62 matched cddid_all.tbl CDD cd18772 cd18772 350854 PIN_Mut7-C-like Mut7-C-like family of the PIN domain superfamily similar to the PIN domain found at the C-terminus of Caenorhabditis elegans exonuclease Mut-7 and related proteins. This Mut7-C-like subgroup of the PIN domain superfamily includes the C-terminal domain of Caenorhabditis elegans Mut-7 (also known as exonuclease 3'-5' domain-containing protein 3 homolog). Mut-7 is involved in RNA interference (RNAi) and transposon silencing in C. elegans. The PIN (PilT N terminus) domain belongs to a large nuclease superfamily, and were originally named for their sequence similarity to the N-terminal domain of an annotated pili biogenesis protein, PilT, a domain fusion between a PIN-domain and a PilT ATPase domain. The structural properties of the PIN domain indicate its active center, consisting of three highly conserved catalytic residues which coordinate metal ions; in some members additional metal coordinating residues can be found while some others lack several of these key catalytic residues. The PIN active site is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. Other PIN domain families are: the FEN-like PIN domain family which includes the PIN domains of Flap endonuclease-1 (FEN1), Exonuclease-1 (EXO1), Mkt1, Gap endonuclease 1 (GEN1), and Xeroderma pigmentosum complementation group G (XPG) nuclease, 5'-3' exonucleases of DNA polymerase I and bacteriophage T4- and T5-5' nucleases; the VapC-like PIN domain family which includes toxins of prokaryotic toxin/antitoxin operons FitAB and VapBC, as well as, eukaryotic ribonucleases such as Smg6, ribosome assembly factor NOB1, exosome subunit Rrp44 endoribonuclease and, rRNA-processing protein Fcf1; the LabA-like PIN domain family which includes the PIN domains of Synechococcus elongatus LabA (low-amplitude and bright); the PRORP-Zc3h12a-like PIN domain family which includes the PIN domains of of RNase P (PRORP), ribonuclease Zc3h12a; and Bacillus subtilis YacP/Rae1-like PIN domains. 81 matched cddid_all.tbl CDD cd18773 cd18773 350341 PDC1_HK_sensor first PDC (PhoQ/DcuS/CitA) domain of methyl-accepting chemotaxis proteins, diguanylate-cyclase and similar domains. Histidine kinase (HK) receptors are part of two-component systems (TCS) in bacteria that play a critical role for sensing and adapting to environmental changes. Typically, HK receptors contain an extracellular sensing domain flanked by two transmembrane helices, an intracellular dimerization histidine phosphorylation domain (DHp), and a C-terminal kinase domain, with many variations on this theme. HK receptors in this family contain double PDC (PhoQ/DcuS/CitA) sensor domains. Signals detected by the sensor domain are transmitted through DHp to the kinase domain, resulting in the phosphorylation of a conserved histidine residue in DHp; phosphotransfer to a conserved aspartate in its cognate response regulator (RR) follows, which leads to the activation of genes for downstream cellular responses. The HK family includes not just histidine kinase receptors but also sensors for chemotaxis proteins and diguanylate cyclase receptors, implying a combinatorial molecular evolution. 125 matched cddid_all.tbl CDD cd18774 cd18774 350342 PDC2_HK_sensor second PDC (PhoQ/DcuS/CitA) domain of methyl-accepting chemotaxis proteins, diguanylate-cyclase and similar domains. Histidine kinase (HK) receptors are part of two-component systems (TCS) in bacteria that play a critical role for sensing and adapting to environmental changes. Typically, HK receptors contain an extracellular sensing domain flanked by two transmembrane helices, an intracellular dimerization histidine phosphorylation domain (DHp), and a C-terminal kinase domain, with many variations on this theme. HK receptors in this family contain double PDC (PhoQ/DcuS/CitA) sensor domains. Signals detected by the sensor domain are transmitted through DHp to the kinase domain, resulting in the phosphorylation of a conserved histidine residue in DHp; phosphotransfer to a conserved aspartate in its cognate response regulator (RR) follows, which leads to the activation of genes for downstream cellular responses. The HK family includes not just histidine kinase receptors but also sensors for chemotaxis proteins and diguanylate cyclase receptors, implying a combinatorial molecular evolution. 89 matched cddid_all.tbl CDD cd18775 cd18775 350651 SafA-like Saf-pilin pilus formation protein SafA. This subfamily is composed of Saf-pilin pilus formation protein SafA from Salmonella enterica and similar proteins. SafA is the major subunit of Saf pili, which are often found in clinical isolates of Salmonella and are assembled by the chaperone-usher secretion pathway. In addition to safA, the saf operon is also composed of safB (periplasmic chaperone), safC (outer membrane usher), and safD (minor subunit). SafA and SafD subunits are transported from the cytoplasm into the periplasm via the SEC machinery, and the periplasmic chaperone SafB donates its G1 strand to complete the correct folding of SafA or SafD. In Saf pili assembly, the N-terminal extension (NTE) of an incoming SafA replaces the G1 strand (in SafB) via a zip-in-zip-out mechanism (also called donor-strand complementation or exchange) to form the polymer of SafD-(SafA)n (n > 100). 122 matched cddid_all.tbl CDD cd18776 cd18776 350652 AfaD-like AfaD and similar proteins. This subfamily consists of Escherichia coli AfaD, Salmonella SafD, and similar proteins. The afa gene clusters encode an afimbrial adhesive sheath produced by Escherichia coli. The adhesive sheath is composed of two proteins, AfaD and AfaE, which are independently exposed at the bacterial cell surface. AfaE is required for bacterial adhesion to HeLa cells and AfaD for the uptake of adherent bacteria into these cells. SafD is the minor subunit of Saf pili, which are often found in clinical isolates of Salmonella and are assembled by the chaperone-usher secretion pathway. In addition to safD, the saf operon is also composed of safA (major subunit), safB (periplasmic chaperone), and safC (outer membrane usher). Also included is the enteroaggregative Escherichia coli AAF/IV pilus tip protein, which is implicated in adhesion as well. During fimbria/pili assembly, polymerization occurs when the N-terminal extension (NTE) of one monomer is inserted into an adjacent monomer, providing the final beta strand or G-strand, to complete the Ig-like fold, in a mechanism called the donor-strand complementation (DSC) or donor-strand exchange (DSE). 118 matched cddid_all.tbl CDD cd18777 cd18777 350653 PsaA_MyfA Fimbrial subunit PsaA, MyfA, and similar proteins. This subfamily is composed of Yersinia pestis PsaA, Yersinia enterocolitica MyfA, and similar proteins. PsaA and MyfA are the major subunits of pH 6 antigen (Psa) and Myf fimbrial homopolymers. Psa and Myf specifically recognize beta1-3- or beta1-4-linked galactose in glycosphingolipids, but while Psa also binds phosphatidylcholine, Myf does not. Psa has acquired a tyrosine-rich surface that enables it to bind to phosphatidylcholine and mediate adhesion of Y. pestis/pseudotuberculosis to alveolar cells. Myf has specialized as a carbohydrate-binding adhesin, facilitating the attachment of Y. enterocolitica to intestinal cells. During fimbria/pili assembly, polymerization occurs when the N-terminal extension (NTE) of one monomer is inserted into an adjacent monomer, providing the final beta strand or G-strand, to complete the Ig-like fold, in a mechanism called the donor-strand complementation (DSC) or donor-strand exchange (DSE). 110 matched cddid_all.tbl CDD cd18778 cd18778 350051 ABC_6TM_exporter_like Six-transmembrane helical domain (TMD) of an uncharacterized ABC exporter, and similar proteins. This group includes a subunit of six transmembrane (TM) helices typically found in the ATP-binding cassette (ABC) transporters that function as exporters, which contain 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds and a various type of lipids. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting the chemical diversity of the translocated substrates, while NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane. However, some ABC genes are organized as half-transporters, which must form either homodimers or heterodimers to form a functional transporter. The ABC exporters play a role in multidrug resistance to antibiotics and anticancer agents, and mutations in these proteins have been shown to cause severe human diseases such as cystic fibrosis. 293 matched cddid_all.tbl CDD cd18779 cd18779 350052 ABC_6TM_T1SS_like uncharacterized subgroup of the six-transmembrane helical domain (6-TMD) of the ATP-binding cassette subunit in the type 1 secretion systems, and similar proteins. uncharacterized subgroup of the six-transmembrane helical domain (6-TMD) of the ABC subunit in the type 1 secretion systems (T1SS) and similar proteins. These transporter subunits include HylB, PrtD, CyaB, CvaB, RsaD, HasD, LipB, and LapB, among many others. T1SS are found in pathogenic Gram-negative bacteria (such as Escherichia coli, Vibrio cholerae or Bordetella pertussis) to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. In the case of the Escherichia coli HlyA T1SS, these three proteins are HlyB (a dimeric ABC transporter), HlyD (MFP, oligomeric membrane fusion protein) and TolC (OMP, a trimeric oligomeric outer membrane protein). Most targeted proteins are not cleaved at the N terminus, but rather carry signals located toward the extreme C terminus to direct type I secretion. However, the 10 kDa Escherichia coli colicin V (CvaB) targets the ABC transporter using a cleaved, N-terminal signal sequence. Almost all transport substrates of the type I system have critical functions in attacking host cells either directly or by being essential for host colonization. The ABC-dependent T1SS transports various molecules, from ions, drugs, to proteins of various sizes up to 900 kDa. The molecules secreted vary in size from the small Escherichia coli peptide colicin V, (10 kDa) to the Pseudomonas fluorescens cell adhesion protein LapA of 520 kDa. The best characterized are the RTX toxins such as the adenylate cyclase (CyaA) toxin from Bordetella pertussis, the causative agent of whooping cough, and the lipases such as LipA. Type I secretion is also involved in export of non-protein substrates such as cyclic beta-glucans and polysaccharides. 294 matched cddid_all.tbl CDD cd18780 cd18780 350053 ABC_6TM_AtABCB27_like Six-transmembrane helical domain (6-TMD) of the Arabidopsis ABC transporter B family member 27 and similar proteins. This group includes Arabidopsis ABC transporter B family member 27 (also known as AtABCB27, aluminum tolerance-related ATP-binding cassette transporter, transporter associated with antigen processing-like protein 2, AtTAP2, and ALS1) which may play a role in aluminum resistance. The ABC_6TM_TAP_ABCB8_10_like subgroup of the ABC_6TM exporter family includes ABC transporter associated with antigen processing (TAP), which is essential to cellular immunity against viral infection, as well as ABCB8 and ABCB10, which are found in the inner membrane of mitochondria, with the nucleotide-binding domains (NBDs) inside the mitochondrial matrix. Mammalian ABCB10 is essential for erythropoiesis and for protection of mitochondria against oxidative stress, while ABCB8 is essential for normal cardiac function, maintenance of mitochondrial iron homeostasis and maturation of cytosolic Fe/S proteins. The ABC_6TM exporter family represents the six transmembrane (TM) helices typically found in the ATP-binding cassette (ABC) transporters that function as exporters, which contain 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds and a various type of lipids. In addition to ABC exporters, ABC transporters include two classes of ABC importers, classified depending on details of their architecture and mechanism. Only the ABC exporters are included in the ABC_6TM exporter family. 295 matched cddid_all.tbl CDD cd18781 cd18781 350054 ABC_6TM_AarD_CydDC_like uncharacterized subgroup of the six-transmembrane helical domain (6-TMD) of the ABC cysteine/GSH transporter CydDC, and similar proteins. This subgroup belongs to the ABC_6TM_AarD_CydDC_like subgroup of the ABC_6TM exporter family. The CydD protein, together with the CydC protein, constitutes a bacterial heterodimeric ATP-binding cassette (ABC) transporter complex required for formation of the functional cytochrome bd oxidase in both gram-positive and gram-negative aerobic bacteria. In Escherichia coli, the biogenesis of both cytochrome bd-type quinol oxidases and periplasmic cytochromes requires the ABC-type cysteine/GSH transporter CydDC, which exports cysteine and glutathione from the cytoplasm to the periplasm to maintain redox homeostasis. Mutations in AarD, a homolog from Providencia stuartii, also show phenotypic characteristic consistent with a defect in the cytochrome d oxidase. The CydDC forms a heterodimeric ABC transporter with two transmembrane domains (TMDs), each predicted to comprise six TM alpha-helices and two nucleotide binding domains (NBDs). The ABC_6TM exporter family represents the six transmembrane (TM) helices typically found in the ATP-binding cassette (ABC) transporters that function as exporters, which contain 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds and a various type of lipids. In addition to ABC exporters, ABC transporters include two classes of ABC importers, classified depending on details of their architecture and mechanism. Only the ABC exporters are included in the ABC_6TM exporter family. 290 matched cddid_all.tbl CDD cd18782 cd18782 350055 ABC_6TM_PrtD_LapB_HlyB_like uncharacterized subgroup of the six-transmembrane helical domain (6-TMD) of the ABC subunit in the type 1 secretion systems (PrtD, LapB, HylB), and similar proteins. Uncharacterized subgroup of the six-transmembrane helical domain (6-TMD) of the ABC subunit in the type 1 secretion systems (T1SS), including PrtD, LapB, and HylB. T1SS are found in pathogenic Gram-negative bacteria (such as Escherichia coli, Vibrio cholerae or Bordetella pertussis) to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type 1 secretion apparatus. In the case of the Escherichia coli HlyA T1SS, these three proteins are HlyB (a dimeric ABC transporter), HlyD (MFP, oligomeric membrane fusion protein) and TolC (OMP, a trimeric oligomeric outer membrane protein). These three components assemble into a complex spanning both membranes and provide a channel for the translocation of unfolded polypeptides. In addition, PrtD is the integral membrane ATP-binding cassette component of the Erwinia chrysanthemi metalloprotease secretion system (PrtDEF). LabB is an inner-membrane transporter component of the LapBCE system that is required for the secretion of the LapA adhesion. 294 matched cddid_all.tbl CDD cd18783 cd18783 350056 ABC_6TM_PrtD_LapB_HlyB_like uncharacterized subgroup of the six-transmembrane helical domain (6-TMD) of the ABC subunit in the type 1 secretion systems (PrtD, LapB, HylB), and similar proteins. Uncharacterized subgroup of the six-transmembrane helical domain (6-TMD) of the ABC subunit in the type 1 secretion systems (T1SS), including PrtD, LapB, and HylB. T1SS are found in pathogenic Gram-negative bacteria (such as Escherichia coli, Vibrio cholerae or Bordetella pertussis) to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type 1 secretion apparatus. In the case of the Escherichia coli HlyA T1SS, these three proteins are HlyB (a dimeric ABC transporter), HlyD (MFP, oligomeric membrane fusion protein) and TolC (OMP, a trimeric oligomeric outer membrane protein). These three components assemble into a complex spanning both membranes and provide a channel for the translocation of unfolded polypeptides. In addition, PrtD is the integral membrane ATP-binding cassette component of the Erwinia chrysanthemi metalloprotease secretion system (PrtDEF). LabB is an inner-membrane transporter component of the LapBCE system that is required for the secretion of the LapA adhesion. 294 matched cddid_all.tbl CDD cd18784 cd18784 350057 ABC_6TM_ABCB9_like Six-transmembrane helical domain (6-TMD) of ATP-binding cassette sub-family B member 9 and similar proteins. ATP-binding cassette sub-family B member 9 is also known as transporter associated with antigen processing, TAP-like protein, TAPL, and ABCB9. It is a half transporter comprises a homodimeric lysosomal peptide transport complex. It belongs to the ABC_6TM_TAP_ABCB8_10_like subgroup of the ABC_6TM exporter family. The ABC_6TM exporter family represents the six transmembrane (TM) helices typically found in the ATP-binding cassette (ABC) transporters that function as exporters, which contain 6 TM helices per subunit (domain), or a total of 12 TM helices for the complete transporter. The ABC exporters are found in both prokaryotes and eukaryotes, where they mediate the cellular secretion of toxic compounds and a various type of lipids. In addition to ABC exporters, ABC transporters include two classes of ABC importers, classified depending on details of their architecture and mechanism. Only the ABC exporters are included in the ABC_6TM exporter family. ABC transporters typically consist of two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs. The sequences and structures of the TMDs are quite varied between the different type of transporters, suggesting chemical diversity of the translocated substrates, whereas NBDs are conserved among all ABC transporters. The two NBDs together bind and hydrolyze ATP, thereby providing the driving force for transport, while the TMDs participate in substrate recognition and translocation across the lipid membrane. However, some ABC genes are organized as half-transporters, which must form either homodimers or heterodimers to form a functional unit. 289 matched cddid_all.tbl CDD cd18785 cd18785 350172 SF2_C C-terminal helicase domain of superfamily 2 DEAD/H-box helicases. Superfamily (SF)2 helicases include DEAD-box helicases, UvrB, RecG, Ski2, Sucrose Non-Fermenting (SNF) family helicases, and dicer proteins, among others. Similar to SF1 helicases, they do not form toroidal structures like SF3-6 helicases. SF2 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 77 matched cddid_all.tbl CDD cd18786 cd18786 350173 SF1_C C-terminal helicase domain of superfamily 1 DEAD/H-box helicases. Superfamily (SF)1 family members include UvrD/Rep, Pif1-like, and Upf-1-like proteins. Similar to SF2 helicases, they do not form toroidal, predominantly hexameric structures like SF3-6. SF1 helicases are a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Their helicase core is surrounded by C- and N-terminal domains with specific functions such as nucleases, RNA or DNA binding domains, or domains engaged in protein-protein interactions. The core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 89 matched cddid_all.tbl CDD cd18787 cd18787 350174 SF2_C_DEAD C-terminal helicase domain of the DEAD box helicases. DEAD-box helicases comprise a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis, and RNA degradation. They are superfamily (SF)2 helicases that, similar to SF1, do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 131 matched cddid_all.tbl CDD cd18788 cd18788 350175 SF2_C_XPD C-terminal helicase domain of xeroderma pigmentosum group D (XPD) family DEAD-like helicases. The xeroderma pigmentosum group D (XPD)-like family members are DEAD-box helicases belonging to superfamily (SF)2. This family includes DDX11 (also called ChlR1), a protein involved in maintaining chromosome transmission fidelity and genome stability, the TFIIH basal transcription factor complex XPD subunit, and FANCJ (also known as BRIP1), a DNA helicase required for the maintenance of chromosomal stability. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 159 matched cddid_all.tbl CDD cd18789 cd18789 350176 SF2_C_XPB C-terminal helicase domain of XPB-like helicases. TFIIH basal transcription factor complex helicase XPB (xeroderma pigmentosum type B) subunit (also known as DNA excision repair protein ERCC-3 or TFIIH 89 kDa subunit) is the ATP-dependent 3'-5' DNA helicase component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. XPB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 153 matched cddid_all.tbl CDD cd18790 cd18790 350177 SF2_C_UvrB C-terminal helicase domain of the UvrB family helicases. Excinuclease ABC subunit B (or UvrB) plays a central role in nucleotide excision repair (NER). Together with other components of the NER system, like UvrA, UvrC, UvrD (helicase II), and DNA polymerase I, it recognizes and cleaves damaged DNA in a multistep ATP-dependent reaction. UvrB is critical for the second phase of damage recognition by verifying the nature of the damage and forming the pre-incision complex. Its ATPase site becomes activated in the presence of UvrA and damaged DNA. Its activity is strand destabilization via distortion of the DNA at lesion site, with very limited DNA unwinding. UvrB is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 171 matched cddid_all.tbl CDD cd18791 cd18791 350178 SF2_C_RHA C-terminal helicase domain of the RNA helicase A (RHA) family helicases. The RNA helicase A (RHA) family includes RHA, also called DEAH-box helicase 9 (DHX9), DHX8, DHX15-16, DHX32-38, and many others. The RHA family members are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 171 matched cddid_all.tbl CDD cd18792 cd18792 350179 SF2_C_RecG_TRCF C-terminal helicase domain of the RecG family helicases. The DEAD-like helicase RecG family contains recombination factor RecG and transcription-repair coupling factor TrcF. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 160 matched cddid_all.tbl CDD cd18793 cd18793 350180 SF2_C_SNF C-terminal helicase domain of the SNF family helicases. The Sucrose Non-Fermenting (SNF) family includes chromatin-remodeling factors, such as CHD proteins and SMARCA proteins, recombination proteins Rad54, and many others. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 135 matched cddid_all.tbl CDD cd18794 cd18794 350181 SF2_C_RecQ C-terminal helicase domain of the RecQ family helicases. The RecQ helicase family is an evolutionarily conserved class of enzymes, dedicated to preserving genomic integrity by operating in telomere maintenance, DNA repair, and replication. They are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 134 matched cddid_all.tbl CDD cd18795 cd18795 350182 SF2_C_Ski2 C-terminal helicase domain of the Ski2 family helicases. Ski2-like RNA helicases play an important role in RNA degradation, processing, and splicing pathways. This family includes spliceosomal Brr2 RNA helicase, ASCC3 (involved in the repair of N-alkylated nucleotides), Mtr4 (involved in processing of structured RNAs), DDX60 (involved in viral RNA degradation), and other proteins. Ski2-like RNA helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 154 matched cddid_all.tbl CDD cd18796 cd18796 350183 SF2_C_LHR C-terminal helicase domain of LHR family helicases. Large helicase-related protein (LHR) is a DNA damage-inducible helicase that uses ATP hydrolysis to drive unidirectional 3'-to-5' translocation along single-stranded DNA (ssDNA) and to unwind RNA:DNA duplexes. This group also includes related bacterial and archaeal helicases. LHR family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 150 matched cddid_all.tbl CDD cd18797 cd18797 350184 SF2_C_Hrq C-terminal helicase domain of HrQ family helicases. Yeast Hrq1, similar to RecQ4, plays a role in DNA inter-strand crosslink (ICL) repair and in telomere maintenance. Hrq1 lacks the Sld2-like domain found in RecQ4. HrQ family helicases are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 146 matched cddid_all.tbl CDD cd18798 cd18798 350185 SF2_C_reverse_gyrase C-terminal helicase domain of the reverse gyrase. Reverse gyrase modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process. Reverse gyrase is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 174 matched cddid_all.tbl CDD cd18799 cd18799 350186 SF2_C_EcoAI-like C-terminal helicase domain of EcoAI HsdR-like restriction enzyme family helicases. This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoAI R protein (R.EcoAI). The EcoAI enzyme recognizes 5'-GAGN(7)GTCA-3'. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 116 matched cddid_all.tbl CDD cd18800 cd18800 350187 SF2_C_EcoR124I-like C-terminal helicase domain of EcoR124I HsdR-like restriction enzyme family helicases. This family is composed of helicase restriction enzymes, including the HsdR subunit of restriction-modification enzymes such as Escherichia coli type I restriction enzyme EcoR124I R protein. EcoR124I recognizes the sequence, 5'-GAAN(6)RTCG-3', and cleaves at random sites. The HsdR or R subunit is required for both nuclease and ATPase activities, but not for modification. These proteins are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 82 matched cddid_all.tbl CDD cd18801 cd18801 350188 SF2_C_FANCM_Hef C-terminal helicase domain of Fanconi anemia group M family helicases. Fanconi anemia group M (FANCM) protein is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. Hef (helicase-associated endonuclease fork-structure) belongs to the XPF/MUS81/FANCM family of endonucleases and is involved in stalled replication fork repair. FANCM and Hef are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 143 matched cddid_all.tbl CDD cd18802 cd18802 350189 SF2_C_dicer C-terminal helicase domain of the endoribonuclease Dicer. Dicer ribonucleases cleave double-stranded RNA (dsRNA) precursors to generate microRNAs (miRNAs) and small interfering RNAs (siRNAs). In concert with Argonautes, these small RNAs bind complementary mRNAs to down-regulate their expression. miRNAs are processed by Dicer from small hairpins, while siRNAs are typically processed from longer dsRNA, from endogenous sources, or exogenous sources such as viral replication intermediates. Some organisms, such as Homo sapiens and Caenorhabditis elegans, encode one Dicer that generates miRNAs and siRNAs, but other organisms have multiple dicers with specialized functions. Dicer exists throughout eukaryotes, and a subset has an N-terminal helicase domain of the RIG-I-like receptor (RLR) subgroup. RLRs often function in innate immunity and Dicer helicase domains sometimes show differences in activity that correlate with roles in immunity. Dicer helicase domains are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 142 matched cddid_all.tbl CDD cd18803 cd18803 350190 SF2_C_secA C-terminal helicase domain of the protein translocase subunit secA. SecA is a component of the Sec translocase that transports the vast majority of bacterial and ER-exported proteins. SecA binds both the signal sequence and the mature domain of the preprotein emerging from the ribosome. SecA is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 141 matched cddid_all.tbl CDD cd18804 cd18804 350191 SF2_C_priA C-terminal helicase domain of ATP-dependent helicase PriA. PriA, also known as replication factor Y or primosomal protein N', is a 3'-->5' DNA helicase that acts to remodel stalled replication forks and as a specificity factor for origin-independent assembly of a new replisome at the stalled fork. PriA is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 238 matched cddid_all.tbl CDD cd18805 cd18805 350192 SF2_C_suv3 C-terminal helicase domain of ATP-dependent RNA helicase. The SUV3 (suppressor of Var 3) gene encodes a DNA and RNA helicase, which is localized in mitochondria and is a subunit of the degradosome complex involved in regulation of RNA surveillance and turnover. SUV3 exhibits DNA and RNA-dependent ATPase, DNA and RNA-binding and DNA and RNA unwinding activities. SUV3 is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 135 matched cddid_all.tbl CDD cd18806 cd18806 350193 SF2_C_viral C-terminal helicase domain of viral helicase. Viral helicases in this family here are DEAD-like helicases belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 145 matched cddid_all.tbl CDD cd18807 cd18807 350194 SF1_C_UvrD C-terminal helicase domain of UvrD family helicases. UvrD is a highly conserved helicase involved in mismatch repair, nucleotide excision repair, and recombinational repair. It plays a critical role in maintaining genomic stability and facilitating DNA lesion repair in many prokaryotic species including Helicobacter pylori and Escherichia coli. This family also includes ATP-dependent helicase/nuclease AddA and helicase/nuclease RecBCD subunit RecB, among others. UvrD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 150 matched cddid_all.tbl CDD cd18808 cd18808 350195 SF1_C_Upf1 C-terminal helicase domain of Upf1-like family helicases. The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), and similar proteins. They are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 184 matched cddid_all.tbl CDD cd18809 cd18809 350196 SF1_C_RecD C-terminal helicase domain of RecD family helicases. RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD family helicases are DEAD-like helicases belonging to superfamily (SF)1, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF2 helicases, SF1 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 80 matched cddid_all.tbl CDD cd18810 cd18810 350197 SF2_C_TRCF C-terminal helicase domain of the transcription-repair coupling factor. Transcription-repair coupling factor (TrcF) dissociates transcription elongation complexes blocked at nonpairing lesions and mediates recruitment of DNA repair proteins. TrcF is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 151 matched cddid_all.tbl CDD cd18811 cd18811 350198 SF2_C_RecG C-terminal helicase domain of DNA helicase RecG. ATP-dependent DNA helicase RecG plays a critical role in recombination and DNA repair. RecG helps process Holliday junction intermediates to mature products by catalyzing branch migration. It is a DEAD-like helicase belonging to superfamily (SF)2, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. Similar to SF1 helicases, SF2 helicases do not form toroidal structures like SF3-6 helicases. Their helicase core consists of two similar protein domains that resemble the fold of the recombination protein RecA. This model describes the C-terminal domain, also called HelicC. 159 matched cddid_all.tbl CDD cd18812 cd18812 349406 CAP_PI15-like CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain of peptidase inhibitor 15 and similar proteins. This family is composed of peptidase inhibitor 15 (PI15), peptidase inhibitor R3HDML, cysteine-rich secretory protein LCCL domain-containing 1 (CRISPLD1), and cysteine-rich secretory protein LCCL domain-containing 2 (CRISPLD2). PI15 is a serine protease inhibitor which displays weak inhibitory activity against trypsin and may play a role in facial patterning during embryonic development. The PI15 gene is a candidate gene for abdominal aortic internal elastic lamina ruptures in the rat. R3HDML is a putative serine protease inhibitor, whose gene may be associated with clinical dimensions of schizophrenia. CRISPLD1 may play a role in NSCLP (nonsyndromic cleft lip with or without cleft palate) through the interaction with CRISPLD2 and folate pathway genes. plays a role in the etiology of NSCLP and is required for neural crest cell migration and cell viability during craniofacial development. The wider family of CAP domain containing proteins includes plant pathogenesis-related protein 1 (PR-1), cysteine-rich secretory proteins (CRISPs), and allergen 5 from vespid venom, among others. 146 matched cddid_all.tbl CDD cd18813 cd18813 349407 CAP_CRISPLD1 CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain of cysteine-rich secretory protein LCCL domain-containing 1. Cysteine-rich secretory protein LCCL domain-containing 1 (CRISPLD1) is also called cysteine-rich secretory protein 10 (CRISP-10), CocoaCrisp, LCCL domain-containing cysteine-rich secretory protein 1 (LCRISP1), or CAP and LCCL domain containing protein 1 (CAPLD1). CRISPLD1 is clearly distinct from CRISPs because they do not contain the 10 absolutely conserved cysteines or the ICR (ion channel regulator) domain of the CRISPs. It may play a role in NSCLP (nonsyndromic cleft lip with or without cleft palate) through the interaction with CRISPLD2 and folate pathway genes. The wider family of CAP domain containing proteins includes plant pathogenesis-related protein 1 (PR-1), cysteine-rich secretory proteins (CRISPs), and allergen 5 from vespid venom, among others. 146 matched cddid_all.tbl CDD cd18814 cd18814 349408 CAP_PI15 CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain of peptidase inhibitor 15. Peptidase inhibitor 15 (PI15) is also called 25 kDa trypsin inhibitor (p25TI), cysteine-rich secretory protein 8 (CRISP-8), or SugarCrisp. It is a serine protease inhibitor which displays weak inhibitory activity against trypsin and may play a role in facial patterning during embryonic development. The PI15 gene is a candidate gene for abdominal aortic internal elastic lamina ruptures in the rat. PI15 may also participate in the regulation of drug resistance in ovarian cancer and serve as a potential target in targeted therapies. The wider family of CAP domain containing proteins includes plant pathogenesis-related protein 1 (PR-1), cysteine-rich secretory proteins (CRISPs), and allergen 5 from vespid venom, among others. 146 matched cddid_all.tbl CDD cd18815 cd18815 349409 CAP_R3HDML CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain of peptidase inhibitor R3HDML. Peptidase inhibitor R3HDML, also called cysteine-rich secretory protein R3HDML, is a putative serine protease inhibitor. The R3HDML gene may be associated with clinical dimensions of schizophrenia. The wider family of CAP domain containing proteins includes plant pathogenesis-related protein 1 (PR-1), cysteine-rich secretory proteins (CRISPs), and allergen 5 from vespid venom, among others. 146 matched cddid_all.tbl CDD cd18816 cd18816 349410 CAP_CRISPLD2 CAP (cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins) domain of cysteine-rich secretory protein LCCL domain-containing 2. Cysteine-rich secretory protein LCCL domain-containing 2 (CRISPLD2) is also called cysteine-rich secretory protein 11 (CRSIP-11), LCCL domain-containing cysteine-rich secretory protein 2 (LCRISP2), or CAP and LCCL domain containing protein 2 (CAPLD2). It plays a role in the etiology of NSCLP (non-syndromic cleft lip with or without cleft palate). It is required for neural crest cell migration and cell viability during craniofacial development. The CRISPLD2 gene has been identified a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells. The wider family of CAP domain containing proteins includes plant pathogenesis-related protein 1 (PR-1), cysteine-rich secretory proteins (CRISPs), and allergen 5 from vespid venom, among others. 146 matched cddid_all.tbl CDD cd18817 cd18817 350138 GH43f_LbAraf43-like Glycosyl hydrolase family 43 such as Lactobacillus brevis alpha-L-arabinofuranosidase LbAraf43. This glycosyl hydrolase family 43 (GH43) subgroup includes characterized enzymes with alpha-L-arabinofuranosidase (EC 3.2.1.55) activity. It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. Characterized enzymes belonging to this subgroup include Lactobacillus brevis (LbAraf43) and Weissella sp (WAraf43) which show activity with similar catalytic efficiency on 1,5-alpha-L-arabinooligosaccharides with a degree of polymerization (DP) of 2-3; size is limited by an extended loop at the entrance to the active site. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 262 matched cddid_all.tbl CDD cd18818 cd18818 350139 GH43_GbtXyl43B-like Glycosyl hydrolase family 43 such as Geobacillus thermoleovorans IT-08 beta-xylosidase/exo-xylanase (GbtXyl43B). This glycosyl hydrolase family 43 (GH43) subgroup includes the characterized enzymes Geobacillus thermoleovorans IT-08 beta-xylosidase (EC 3.2.1.37) / exo-xylanase (GbtXyl43B), and Paenibacillus sp. strain E18 alpha-L-arabinofuranosidase (EC 3.2.1.55) Abf43B. It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 273 matched cddid_all.tbl CDD cd18819 cd18819 350140 GH43_LbAraf43-like Glycosyl hydrolase family 43 proteins similar to Lactobacillus brevis alpha-L-arabinofuranosidase LbAraf43 and Geobacillus thermoleovorans GbtXyl43B. This uncharacterized glycosyl hydrolase family 43 (GH43) subgroup belongs to a subgroup which includes enzymes with beta-xylosidase (EC 3.2.1.37), alpha-L-arabinofuranosidase (EC 3.2.1.55) and possibly bifunctional xylosidase/arabinofuranosidase activities, similar to Lactobacillus brevis alpha-L-arabinofuranosidase LbAraf43 and Geobacillus thermoleovorans IT-08 beta-xylosidase / exo-xylanase (GbtXyl43B). It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 277 matched cddid_all.tbl CDD cd18820 cd18820 350141 GH43_LbAraf43-like Glycosyl hydrolase family 43 proteins similar to Lactobacillus brevis alpha-L-arabinofuranosidase LbAraf43 and Geobacillus thermoleovorans GbtXyl43B. This uncharacterized glycosyl hydrolase family 43 (GH43) subgroup belongs to a subgroup which includes enzymes with beta-xylosidase (EC 3.2.1.37), alpha-L-arabinofuranosidase (EC 3.2.1.55) and possibly bifunctional xylosidase/arabinofuranosidase activities, similar to Lactobacillus brevis alpha-L-arabinofuranosidase LbAraf43 and Geobacillus thermoleovorans IT-08 beta-xylosidase / exo-xylanase (GbtXyl43B). It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 258 matched cddid_all.tbl CDD cd18821 cd18821 350142 GH43_Pc3Gal43A-like Glycosyl hydrolase family 43 protein such as Phanerochaete chrysosporium exo-beta-1,3-galactanase (Pc1, 3Gal43A, 1,3Gal43A). This glycosyl hydrolase family 43 (GH43) subgroup includes characterized enzymes with exo-beta-1,3-galactanase (EC 3.2.1.145, also known as galactan 1,3-beta-galactosidase) activity such as Phanerochaete chrysosporium 1,3Gal43A (Pc1, 3Gal43A), Fusarium oxysporum 12S Fo/1 (3Gal), and Streptomyces sp. 19(2012) SGalase1 and SGalase2. It belongs to the GH43_CtGH43 subgroup of the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. GH43_CtGH43 includes proteins such as Clostridium thermocellum exo-beta-1,3-galactanase (Ct1,3Gal43A or CtGH43) which is comprised of the GH43 domain, a CBM13 domain, and a dockerin domain, exhibits an unusual ability to hydrolyze beta-1,3-galactan in the presence of a beta-1,6 linked branch, and is missing an essential acidic residue suggesting a mechanism by which it bypasses beta-1,6 linked branches in the substrate. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 262 matched cddid_all.tbl CDD cd18822 cd18822 350143 GH43_CtGH43-like Glycosyl hydrolase family 43 protein such as Clostridium thermocellum exo-beta-1,3-galactanase (Ct1,3Gal43A or CtGH43). This glycosyl hydrolase family 43 (GH43) subgroup includes characterized enzymes with exo-beta-1,3-galactanase (EC 3.2.1.145, also known as galactan 1,3-beta-galactosidase) activity such as Clostridium thermocellum exo-beta-1,3-galactanase (Ct1,3Gal43A or CtGH43), Streptomyces avermitilis MA-4680 = NBRC 14893 (Sa1,3Gal43A;SAV2109) (1,3Gal43A), and Ruminiclostridium thermocellum ATCC 27405 (Ct1,3Gal43A;CtGH43;Cthe_0661) (1,3Gal43A). It belongs to the GH43_CtGH43 subgroup of the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. GH43_CtGH43 includes proteins such as Clostridium thermocellum exo-beta-1,3-galactanase (Ct1,3Gal43A or CtGH43) which is comprised of the GH43 domain, a CBM13 domain, and a dockerin domain, exhibits an unusual ability to hydrolyze beta-1,3-galactan in the presence of a beta-1,6 linked branch, and is missing an essential acidic residue suggesting a mechanism by which it bypasses beta-1,6 linked branches in the substrate. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 266 matched cddid_all.tbl CDD cd18823 cd18823 350144 GH43_RcAra43A-like Glycosyl hydrolase family 43 such as Ruminococcus champanellensis arabinanase Ara43A. This glycosyl hydrolase family 43 (GH43) subgroup includes characterized enzymes with arabinanase (EC 3.2.1.99) activity such as Ruminococcus champanellensis arabinanase Ara43A and Fibrobacter succinogenes subsp. succinogenes S85 Fisuc_1994 / FSU_2517. It belongs to the GH43_CtGH43 subgroup of the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. GH43_CtGH43 includes proteins such as Clostridium thermocellum exo-beta-1,3-galactanase (Ct1,3Gal43A or CtGH43) (EC 3.2.1.145, also known as galactan 1,3-beta-galactosidase) which is comprised of the GH43 domain, a CBM13 domain, and a dockerin domain, exhibits an unusual ability to hydrolyze beta-1,3-galactan in the presence of a beta-1,6 linked branch, and is missing an essential acidic residue suggesting a mechanism by which it bypasses beta-1,6 linked branches in the substrate. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 289 matched cddid_all.tbl CDD cd18824 cd18824 350145 GH43_CtGH43-like Glycosyl hydrolase family 43 protein similar to Clostridium thermocellum exo-beta-1,3-galactanase CtGH43 and Ruminococcus champanellensis arabinanase Ara43A. This uncharacterized glycosyl hydrolase family 43 (GH43) subgroup belongs to a subgroup which includes characterized enzymes with exo-beta-1,3-galactanase (EC 3.2.1.145, also known as galactan 1,3-beta-galactosidase) activity such as Clostridium thermocellum (Ct1,3Gal43A or CtGH43) and Phanerochaete chrysosporium 1,3Gal43A (Pc1, 3Gal43A), and arabinanase (EC 3.2.1.99) activity such as Ruminococcus champanellensis Ara43A. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 282 matched cddid_all.tbl CDD cd18825 cd18825 350146 GH43_CtGH43-like Glycosyl hydrolase family 43 protein similar to Clostridium thermocellum exo-beta-1,3-galactanase CtGH43 and Ruminococcus champanellensis arabinanase Ara43A. This uncharacterized glycosyl hydrolase family 43 (GH43) subgroup belongs to a subgroup which includes characterized enzymes with exo-beta-1,3-galactanase (EC 3.2.1.145, also known as galactan 1,3-beta-galactosidase) activity such as Clostridium thermocellum (Ct1,3Gal43A or CtGH43) and Phanerochaete chrysosporium 1,3Gal43A (Pc1, 3Gal43A), and arabinanase (EC 3.2.1.99) activity such as Ruminococcus champanellensis Ara43A. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 285 matched cddid_all.tbl CDD cd18826 cd18826 350147 GH43_CtGH43-like Glycosyl hydrolase family 43 protein similar to Clostridium thermocellum exo-beta-1,3-galactanase CtGH43 and Ruminococcus champanellensis arabinanase Ara43A. This uncharacterized glycosyl hydrolase family 43 (GH43) subgroup belongs to a subgroup which includes characterized enzymes with exo-beta-1,3-galactanase (EC 3.2.1.145, also known as galactan 1,3-beta-galactosidase) activity such as Clostridium thermocellum (Ct1,3Gal43A or CtGH43) and Phanerochaete chrysosporium 1,3Gal43A (Pc1, 3Gal43A), and arabinanase (EC 3.2.1.99) activity such as Ruminococcus champanellensis Ara43A. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 269 matched cddid_all.tbl CDD cd18827 cd18827 350148 GH43_XlnD-like Glycosyl hydrolase family 43 protein such as Aspergillus niger DMS1957 xylanase D (XlnD); includes mostly xylanases. This glycosyl hydrolase family 43 (GH43) subgroup includes enzymes that have mostly been annotated as xylanases (endo-alpha-L-arabinanase, EC 3.2.1.8). It belongs to the GH43_bXyl-like subgroup of the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. The GH43_bXyl-like subgroup includes enzymes that have been annotated as xylan-digesting beta-xylosidases (EC 3.2.1.37) and xylanases, as well the Bacteroides thetaiotaomicron VPI-5482 alpha-L-arabinofuranosidases (EC 3.2.1.55) (BT3675;BT_3675) and (BT3662;BT_3662). GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 277 matched cddid_all.tbl CDD cd18828 cd18828 350149 GH43_BT3675-like Glycosyl hydrolase family 43 protein such as Bacteroides thetaiotaomicron VPI-5482 alpha-L-arabinofuranosidases (BT3675;BT_3675). This glycosyl hydrolase family 43 (GH43) subgroup includes the Bacteroides thetaiotaomicron VPI-5482 alpha-L-arabinofuranosidases (EC 3.2.1.55) (BT3675;BT_3675) and (BT3662;BT_3662). It belongs to the GH43_bXyl subgroup of the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. The GH43_bXyl subgroup also includes enzymes annotated as having xylan-digesting beta-xylosidase (EC 3.2.1.37) and xylanase (endo-alpha-L-arabinanase, EC 3.2.1.8) activities. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. Many GH43 enzymes display both alpha-L-arabinofuranosidase and beta-D-xylosidase activity using aryl-glycosides as substrates. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 283 matched cddid_all.tbl CDD cd18829 cd18829 350150 GH43_BsArb43A-like Glycosyl hydrolase family 43 protein such as Bacillus subtilis subsp. subtilis str. 168 endo-alpha-1,5-L-arabinanase Arb43A. This glycosyl hydrolase family 43 (GH43) subgroup includes mostly enzymes annotated as having endo-alpha-L-arabinanase (ABN; EC 3.2.1.99) activities, and includes Bacillus subtilis subsp. subtilis str. 168 endo-alpha-1,5-L-arabinanase (AbnA;BSU28810) (Arb43A). It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. The GH43 ABN enzymes hydrolyze alpha-1,5-L-arabinofuranoside linkages while the arabinofuranosidase (ABF; EC 3.2.1.55) enzymes cleave arabinose side chains so that the combined actions of these two enzymes reduce arabinan to L-arabinose and/or arabinooligosaccharides. Many of these enzymes such as the Bacillus subtilis arabinanase Abn2, that hydrolyzes sugar beet arabinan (branched), linear alpha-1,5-L-arabinan and pectin, are different from other arabinases; they are organized into two different domains with a divalent metal cluster close to the catalytic residues to guarantee the correct protonation state of the catalytic residues and consequently the enzyme activity. These arabinan-degrading enzymes are important in the food industry for efficient production of L-arabinose from agricultural waste; L-arabinose is often used as a bioactive sweetener. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 273 matched cddid_all.tbl CDD cd18830 cd18830 350151 GH43_CjArb43A-like Glycosyl hydrolase family 43 protein such as Cellvibrio japonicus Ueda107 endo-alpha-1,5-L-arabinanase / exo-alpha-1,5-L-arabinanase 43A (ArbA;CJA_0805) (Arb43A). This glycosyl hydrolase family 43 (GH43) subgroup includes mostly enzymes annotated with alpha-L-arabinofuranosidase (ABF; EC 3.2.1.55) and endo-alpha-L-arabinanase (ABN; EC 3.2.1.99) activities, and includes the bifunctional Cellvibrio japonicus Ueda107 endo-alpha-1,5-L-arabinanase / exo-alpha-1,5-L-arabinanase 43A (ArbA;CJA_0805) (Arb43A). It belongs to the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. GH43 are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. The GH43 ABN enzymes hydrolyze alpha-1,5-L-arabinofuranoside linkages while the ABF enzymes cleave arabinose side chains so that the combined actions of these two enzymes reduce arabinan to L-arabinose and/or arabinooligosaccharides. Many of these enzymes such as the Bacillus subtilis arabinanase Abn2, that hydrolyzes sugar beet arabinan (branched), linear alpha-1,5-L-arabinan and pectin, are different from other arabinases; they are organized into two different domains with a divalent metal cluster close to the catalytic residues to guarantee the correct protonation state of the catalytic residues and consequently the enzyme activity. These arabinan-degrading enzymes are important in the food industry for efficient production of L-arabinose from agricultural waste; L-arabinose is often used as a bioactive sweetener. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 291 matched cddid_all.tbl CDD cd18831 cd18831 350152 GH43_AnAbnA-like Glycosyl hydrolase family 43 protein such as Aspergillus niger endo-alpha-L-arabinanase (AbnA). This glycosyl hydrolase family 43 (GH43) subgroup includes characterized enzymes with endo-alpha-L-arabinanase (ABN; EC 3.2.1.99) activities such as Aspergillus niger AbnA, Aspergillus niveus AbnA, and Chrysosporium lucknowense Abn1. It belongs to the GH43_Arb43a subgroup of the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. GH43_Arb43a subgroup includes mostly enzymes with alpha-L-arabinofuranosidase (ABF; EC 3.2.1.55) and endo-alpha-L-arabinanase activities. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. The GH43 ABN enzymes hydrolyze alpha-1,5-L-arabinofuranoside linkages while the ABF enzymes cleave arabinose side chains so that the combined actions of these two enzymes reduce arabinan to L-arabinose and/or arabinooligosaccharides. The GH43_Arb43a subgroup includes many enzymes such as Bacillus subtilis arabinanase Abn2, that hydrolyzes sugar beet arabinan (branched), linear alpha-1,5-L-arabinan and pectin, and are different from other arabinases; they are organized into two different domains with a divalent metal cluster close to the catalytic residues to guarantee the correct protonation state of the catalytic residues and consequently the enzyme activity. These arabinan-degrading enzymes are important in the food industry for efficient production of L-arabinose from agricultural waste; L-arabinose is often used as a bioactive sweetener. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 286 matched cddid_all.tbl CDD cd18832 cd18832 350153 GH43_GsAbnA-like Glycosyl hydrolase family 43 protein such as Geobacillus stearothermophilus endo-alpha-1,5-L-arabinanase AbnA. This glycosyl hydrolase family 43 (GH43) subgroup includes mostly enzymes with alpha-L-arabinofuranosidase (ABF; EC 3.2.1.55) and endo-alpha-L-arabinanase (ABN; EC 3.2.1.99) activities. It includes Geobacillus stearothermophilus T-6 NCIMB 40222 AbnA, Bacillus subtilis subsp. subtilis str. 168 (Abn2;YxiA;J3A;BSU39330) (Arb43B), and Thermotoga petrophila RKU-1 (AbnA;TpABN;Tpet_0637). These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. The GH43 ABN enzymes hydrolyze alpha-1,5-L-arabinofuranoside linkages while the ABF enzymes cleave arabinose side chains so that the combined actions of these two enzymes reduce arabinan to L-arabinose and/or arabinooligosaccharides. Many of these enzymes are different from other arabinases; they are organized into two different domains with a divalent metal cluster close to the catalytic residues to guarantee the correct protonation state of the catalytic residues and consequently the enzyme activity. These arabinan-degrading enzymes are important in the food industry for efficient production of L-arabinose from agricultural waste; L-arabinose is often used as a bioactive sweetener. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 332 matched cddid_all.tbl CDD cd18833 cd18833 350154 GH43_PcXyl-like Glycosyl hydrolase family 43 protein such as the bifunctional Phanerochaete chrysosporium xylosidase/arabinofuranosidase (Xyl;PcXyl). This glycosyl hydrolase family 43 (GH43) subgroup includes Phanerochaete chrysosporium BKM-F-1767 Xyl, a characterized bifunctional enzyme with beta-1,4-xylosidase (beta-D-xylosidase;xylan 1,4-beta-xylosidase; EC 3.2.1.37)/ alpha-L-arabinofuranosidase (EC 3.2.1.55) activities. This subgroup belongs to the GH43_XybB subgroup of the glycosyl hydrolase clan F (according to carbohydrate-active enzymes database (CAZY)) which includes family 43 (GH43) and 62 (GH62) families. The GH43_XybB subgroup includes enzymes having beta-1,4-xylosidase and alpha-L-arabinofuranosidase activities. Beta-1,4-xylosidases are part of an array of hemicellulases that are involved in the final breakdown of plant cell-wall whereby they degrade xylan. They hydrolyze beta-1,4 glycosidic bonds between two xylose units in short xylooligosaccharides. These are inverting enzymes (i.e. they invert the stereochemistry of the anomeric carbon atom of the substrate) that have an aspartate as the catalytic general base, a glutamate as the catalytic general acid and another aspartate that is responsible for pKa modulation and orienting the catalytic acid. The GH43_XybB subgroup includes Bacteroides ovatus alpha-L-arabinofuranosidases, BoGH43A and BoGH43B, both having a two-domain architecture, consisting of an N-terminal 5-bladed beta-propeller domain harboring the catalytic active site, and a C-terminal beta-sandwich domain. However, despite significant functional overlap between these two enzymes, BoGH43A and BoGH43B share just 41% sequence identity. The latter appears to be significantly less active on the same substrates, suggesting that these paralogs may play subtly different roles during the degradation of xyloglucans from different sources, or may function most optimally at different stages in the catabolism of xyloglucan oligosaccharides (XyGOs), for example before or after hydrolysis of certain side-chain moieties. A common structural feature of GH43 enzymes is a 5-bladed beta-propeller domain that contains the catalytic acid and catalytic base. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 292 matched cddid_all.tbl CDD cd18869 cd18869 467581 NUDIX_U8_SnoRNA_DE_Nudt16 "nucleoside diphosphate-linked moiety X)) motif 16. U8 SnoRNA-decapping enzyme, also known as NUDIX (nucleoside diphosphate-linked moiety X)) motif 16/Nudt16, is encoded by the human NUDT16 gene and a RNA-binding and decapping enzyme that catalyzes the cleavage of the cap structure of snoRNAs and mRNAs in a metal-dependent manner. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & ""house-cleaning"" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required." 175 matched cddid_all.tbl CDD cd18870 cd18870 467582 NUDIX_AcylCoAdiphos_Nudt19 "Nucleoside diphosphate-linked moiety X)) motif 19. Acyl CoA diphosphohydrolase (also known as NUDIX (nucleoside diphosphate linked moiety X))-type motif 10; Nudt19; testosterone-regulated protein rp2) has activity towards CoA, oxidized CoA and a wide range of CoA esters, including choloyl-CoA and branched-chain fatty-acyl-CoA esters. CoA is the major acyl carrier in mammals and a key cofactor in energy metabolism. Dynamic regulation of CoA in different tissues and organs supports metabolic flexibility. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 159 matched cddid_all.tbl CDD cd18871 cd18871 467583 NUDIX_Cfim25_Nudt21 "25 kDa subunit of cleavage factor Im. Precursor mRNA (pre-mRNA) cleavage factor I(m) (also called NUDIX (nucleoside diphosphate linked moiety X))-type motif 21) is a oligomer composed of a small 25 kDa subunit (CF I(m)25) and a variable larger subunit of either 59, 68 or 72 kDa and plays an important role in pre-mRNA 3'-end cleavage and the selection of poly(A) sites in a 3'-untranslated region (3'-UTR) of mRNA, producing mRNAs with variable 3' ends. The small subunit also interacts with RNA, poly(A) polymerase, and the nuclear poly(A)-binding protein and belongs to the NUDIX hydrolase superfamily. NUDIX hydrolases are found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes." 184 matched cddid_all.tbl CDD cd18872 cd18872 467584 NUDIX_eIF-2B "translation initiation factor IF-2B alpha subunit. Eukaryotic translation initiation factor 2B subunit alpha (EIF2B1) is one of five subunits of eukaryotic translation initiation factor 2B (EIF2B), a GTP exchange factor for eukaryotic initiation factor 2 and an essential regulator for protein synthesis. Mutations in this gene and the genes encoding other EIF2B subunits have been associated with leukoencephalopathy with vanishing white matter. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & ""house-cleaning"" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required." 129 matched cddid_all.tbl CDD cd18873 cd18873 467585 NUDIX_NadM_like "bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase and similar proteins. Bacterial NadM-Nudix is a bifunctional enzyme containing a nicotinamide mononucleotide (NMN) adenylyltransferase (NMNAT) and an ADP-ribose pyrophosphatase (ADPRase) domain. NMNAT was initially identified as an NAD+ synthase that catalyzes the reversible conversion of NMN to NAD+ in the final step of both the de novo biosynthesis and salvage pathways in most organisms across all three kingdoms of life ADPRase is a member of the NUDIX family proteins, catalyzes the metal-induced and concerted general acid-base hydrolysis of ADP ribose (ADPR) into AMP and ribose-5'-phosphate (R5P). Additional members in this cd include bacterial transcriptional regulator, NrtR, which represses the transcription of NAD biosynthetic genes in vitro and adenosine diphosphate ribose (ADPR), as well as NadQ, a NUDIX-like ATP-responsive regulator of NAD biosynthesis. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belong to this superfamily requires a divalent cation, such as Mg2+ or Mn2+ for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, U=I, L or V) which functions as metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & ""house-cleaning"" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required." 132 matched cddid_all.tbl CDD cd18874 cd18874 467586 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 125 matched cddid_all.tbl CDD cd18875 cd18875 467587 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 144 matched cddid_all.tbl CDD cd18876 cd18876 467588 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 121 matched cddid_all.tbl CDD cd18877 cd18877 467589 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 141 matched cddid_all.tbl CDD cd18879 cd18879 467590 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 142 matched cddid_all.tbl CDD cd18880 cd18880 467591 NUDIX_ADPRase ADP-ribose pyrophosphatase and similar proteins. ADP-ribose pyrophosphatase (ADPRase; EC 3.6.1.13) catalyzes the hydrolysis of ADP-ribose to AMP and ribose-5-P. Like other members of the NUDIX hydrolase superfamily of enzymes, it is thought to require a divalent cation, such as Mg2+, for its activity. It also contains a 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the NUDIX motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. In humans, there are four distinct ADPRase activities, three putative cytosolic (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). ADPRase-m is also known as NUDT9. It can be distinugished from the cytosolic ADPRase by a N-terminal target sequence unique to mitochondrial ADPRase. NUDT9 functions as a monomer. 126 matched cddid_all.tbl CDD cd18881 cd18881 467592 NUDIX_Tm1382 "uncharacterized NUDIX hydrolase subfamily Tm1382 found in Thermotoga maritima, and similar proteins. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 187 matched cddid_all.tbl CDD cd18882 cd18882 467593 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 130 matched cddid_all.tbl CDD cd18883 cd18883 467594 NUDIX_MutT_Nudt1 MutT homolog-1 and similar proteins. MutT homolog-1 (MTH1), also known as NUDIX (nucleoside diphosphate-linked moiety X)) motif 1/Nudt1, is a member of the NUDIX hydrolase superfamily. MTH1, the mammalian counterpart of MutT, hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to monophosphates, thereby preventing the incorporation of such oxygen radicals during replication. This is an important step in the repair mechanism in genomic and mitochondrial DNA. Like other members of the NUDIX family, it requires a divalent cation, such as Mg2+ or Mn2+, for activity, and contain the NUDIX motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. MTH1 is predominantly localized in the cytoplasm and mitochondria. Structurally, this enzyme adopts a similar fold to MutT despite low sequence similarity outside the conserved NUDIX motif. The most distinctive structural difference between MutT and MTH1 is the presence of a beta-hairpin, which is absent in MutT. This results in a much deeper and narrower substrate binding pocket. Mechanistically, MTH1 contains dual specificity for nucleotides that contain 2-OH-adenine bases and those that contain 8-oxo-guanine bases. 136 matched cddid_all.tbl CDD cd18884 cd18884 467595 NUDIX_Hydrolase "uncharacterized NUDIX hydrolase subfamily. NUDIX hydrolase is a superfamily of enzymes found in all three kingdoms of life, and it catalyzes the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+ for their activity. Members of this family are recognized by a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which forms a structural motif that functions as a metal binding and catalytic site. Substrates of NUDIX hydrolase include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance and ""house-cleaning"" enzymes. Substrate specificity is used to define child families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required. This superfamily consists of at least nine families: IPP (isopentenyl diphosphate) isomerase, ADP ribose pyrophosphatase, mutT pyrophosphohydrolase, coenzyme-A pyrophosphatase, MTH1-7,8-dihydro-8-oxoguanine-triphosphatase, diadenosine tetraphosphate hydrolase, NADH pyrophosphatase, GDP-mannose hydrolase and the c-terminal portion of the mutY adenine glycosylase." 125 matched cddid_all.tbl CDD cd18886 cd18886 467596 NUDIX_MutT_Nudt1 MutT homolog-1 and similar proteins. MutT homolog-1 (MTH1), also known as NUDIX (nucleoside diphosphate-linked moiety X)) motif 1/Nudt1, is a member of the NUDIX hydrolase superfamily. MTH1, the mammalian counterpart of MutT, hydrolyzes oxidized purine nucleoside triphosphates, such as 8-oxo-dGTP and 2-hydroxy-ATP, to monophosphates, thereby preventing the incorporation of such oxygen radicals during replication. This is an important step in the repair mechanism in genomic and mitochondrial DNA. Like other members of the NUDIX family, it requires a divalent cation, such as Mg2+ or Mn2+, for activity, and contain the NUDIX motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. MTH1 is predominantly localized in the cytoplasm and mitochondria. Structurally, this enzyme adopts a similar fold to MutT despite low sequence similarity outside the conserved NUDIX motif. The most distinctive structural difference between MutT and MTH1 is the presence of a beta-hairpin, which is absent in MutT. This results in a much deeper and narrower substrate binding pocket. Mechanistically, MTH1 contains dual specificity for nucleotides that contain 2-OH-adenine bases and those that contain 8-oxo-guanine bases. 147 matched cddid_all.tbl CDD cd18887 cd18887 467597 NUDIX_UGPPase_Nudt14 UDP-glucose pyrophosphatase. UDP-glucose pyrophosphatase (UGPPase) (EC 3.6.1.45; also known as NUDIX (nucleoside diphosphate-linked moiety X)) motif 14; Nudt14) hydrolyzes the pyrophosphate of the nucleoside diphosphate sugar to generate glucose-1-P and UMP. In mammals, UDP-glucose is the glucosyl donor for the synthesis of the storage polysaccharide glycogen. UGPPase, as a regulator of UDP-glucose, could play a regulatory role, but it has been shown to prefer ADP-ribose over UDP-glucose. Like other members of the NUDIX hydrolase superfamily, it requires a divalent cation, such as Mg2+, for its activity. It also contains a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. 181 matched cddid_all.tbl CDD cd18888 cd18888 467598 NUDIX_ADPRase_Nudt5 ADP-ribose pyrophosphatase. ADP-ribose pyrophosphatase (ADPRase) (also known as NUDIX (Nucleoside diphosphate-linked moiety X)) motif 5; Nudt5) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. In humans, there are four distinct ADPRase activities, three putative cytosolic enzymes (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). Human ADPRase-II is also referred to as NUDT5. It lacks the N-terminal target sequence unique to mitochondrial ADPRase. The different cytosolic types are distinguished by their specificities for substrate and specific requirement for metal ions. NUDT5 forms a homodimer. It also contains a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the NUDIX motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. 149 matched cddid_all.tbl CDD cd18889 cd18889 467599 NUDIX_ADPRase ADP-ribose pyrophosphatase. ADP-ribose pyrophosphatase (ADPRase; EC 3.6.1.13) catalyzes the hydrolysis of ADP-ribose to AMP and ribose-5-P. Like other members of the NUDIX hydrolase superfamily of enzymes, it is thought to require a divalent cation, such as Mg2+, for its activity. It also contains a 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the NUDIX motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. In humans, there are four distinct ADPRase activities, three putative cytosolic (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). ADPRase-m is also known as NUDT9. It can be distinugished from the cytosolic ADPRase by a N-terminal target sequence unique to mitochondrial ADPRase. NUDT9 functions as a monomer. 127 matched cddid_all.tbl CDD cd18890 cd18890 467600 NUDIX_CDP-Chase "CDP-choline pyrophosphatase. CDP-choline pyrophosphatase catalyzes the hydrolysis of CDP-choline to produce CMP and phosphocholine. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & ""house-cleaning"" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required." 129 matched cddid_all.tbl CDD cd18891 cd18891 467601 NUDIX_UDP-X_diphosphatase "UDP-X diphosphatase. UDP-X diphosphatase hydrolyzes UDP-N-acetylmuramic acid and UDP-N-acetylmuramoyl-L-alanine, the last step of the Mur pathway of peptidoglycan biosynthesis. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & ""house-cleaning"" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required." 128 matched cddid_all.tbl CDD cd18892 cd18892 380671 TET oxygenase domain of ten-eleven translocation (TET)1, TET2, and TET3 methylcytosine dioxygenases and similar proteins. TET proteins are involved in DNA demethylation through iteratively oxidizing 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). TET proteins contain a C-terminal catalytic domain which consists of a cysteine-rich region and a double-stranded beta-helix (DSBH) fold. Alterations in TET protein function have been linked to cancer, and TETs influence many cell differentiation processes. TET family genes have been implicated as tumor suppressors, for example mutations/deletions of the TET2 gene frequently occur in multiple spectra of myeloid malignancies. TET3 acts as a suppressor of ovarian cancer by demethylating the miR-30d precursor gene promoter to block TGF-beta1 induced epithelial-mesenchymal transition (EMT). TET3 (and TET2) promoters are silenced in melanoma cells by mechanisms triggered by TGF-beta and mediated by DNA methyltransferase 3 alpha (DNMT3A). TET genes are downregulated in endometriosis. TET proteins belong to the TET/JBP family of dioxygenases that require Fe2+ and alpha-ketoglutarate (also known as 2-oxoglutarate) for activity. 398 matched cddid_all.tbl CDD cd18893 cd18893 380672 TET-like oxygenase domain of ten-eleven translocation (TET)-like proteins such as Naegleria gruberi Tet-like protein (NgTet1) and similar proteins. Naegleria gruberi Tet1 can catalyze the iterative oxidation of both 5-methylcytosine (5mC) and thymidine (T) on various DNA forms. Like mammalian TETs, it catalyzes the oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) in three consecutive, Fe2+ and alpha-ketoglutarate (also known as 2-oxoglutarate, 2-OG)-dependent oxidation reactions. Like JBP1 and JBP2, NgTet1 can perform T-oxidation to form 5-hydroxymethyluridine (5hmU), but in addition it can catalyze the formation of 5-formyluridine (5fU) and 5-carboxyluridine (5caU). This family belongs to the TET/JBP family of dioxygenases that require Fe2+ and alpha-ketoglutarate (also known as 2-oxoglutarate) for activity. 243 matched cddid_all.tbl CDD cd18894 cd18894 380673 JBP-like oxygenase domain of J-binding protein (JBP) 1 and JBP2 thymidine hydroxylases and similar proteins, including uncharacterized bacterial and phage proteins. J binding protein (JBP) 1 and JBP2 catalyze the first step of base J biosynthesis: the hydroxylation of thymine in DNA to form 5-hydroxymethyluracil (hmU). Base J (beta-d-glucopyranosyloxymethyluracil) is a hyper-modified DNA base found in the DNA of kinetoplastids (Trypanosoma brucei, Trypanosoma cruzi, and Leishmania). JBP1 and JBP2 each contain a J-DNA binding domain and this oxygenase domain. They belong to the TET/JBP family of dioxygenases that require Fe2+ and alpha-ketoglutarate (also known as 2-oxoglutarate) for activity. 250 matched cddid_all.tbl CDD cd18895 cd18895 380674 TET1 oxygenase domain of ten-eleven translocation (TET)1 methylcytosine dioxygenase and similar proteins. TET1 is involved in DNA demethylation through iteratively oxidizing 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Human TET1 (and TET2) are more active on 5mC-DNA than 5hmC/5fC-DNA substrates. TET proteins contain a C-terminal catalytic domain which consists of a cysteine-rich region and a double-stranded beta-helix (DSBH) fold. TET1 plays multiple roles in in tumor development and progression. TET1 serves as a tumor suppressor gene; loss of TET1 is associated with tumorigenesis and can be used as a potential biomarker for cancer therapy. In addition to its dioxygenase activity, it can induce epithelial-mesenchymal transition and act as a coactivator to regulate gene transcription. The regulation of TET1 is also correlated with microRNA in a posttranscriptional modification process. TET1 belongs to the TET/JBP family of dioxygenases that require Fe2+ and alpha-ketoglutarate (also known as 2-oxoglutarate) for activity. 410 matched cddid_all.tbl CDD cd18896 cd18896 380675 TET2 oxygenase domain of ten-eleven translocation (TET)2 methylcytosine dioxygenase and similar proteins. TET2 is involved in DNA demethylation through iteratively oxidizing 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Human TET2 (and TET1) have been shown to be more active on 5mC-DNA than 5hmC/5fC-DNA substrates. TET proteins contain a C-terminal catalytic domain which consists of a cysteine-rich region and a double-stranded beta-helix (DSBH) fold. TET2 acts as a tumor suppressor in hematopoiesis; mutations/deletions of the TET2 gene frequently occur in multiple spectra of myeloid malignancies. TET2 (and TET3) promoters are silenced in melanoma cells by mechanisms triggered by TGF-beta and mediated by DNA methyltransferase 3 alpha (DNMT3A), which play a functional role in the epithelial-mesenchymal transition process and metastasis. In addition, TET2 (and TET3) may be guardians of regulatory T cell stability and immune homeostasis. TET2 belongs to the TET/JBP family of dioxygenases that require Fe2+ and alpha-ketoglutarate (also known as 2-oxoglutarate) for activity. 434 matched cddid_all.tbl CDD cd18897 cd18897 380676 TET3 oxygenase domain of ten-eleven translocation (TET)3 methylcytosine dioxygenase and similar proteins. TET3 is involved in DNA demethylation through iteratively oxidizing 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). TET proteins contain a C-terminal catalytic domain which consists of a cysteine-rich region and a double-stranded beta-helix (DSBH) fold. TET3 serves as a tumor suppressor; it acts as a suppressor of ovarian cancer by demethylating the miR-30d precursor gene promoter to block TGF-beta1 induced epithelial-mesenchymal transition (EMT). TET3 (and TET2) promoters are silenced in melanoma cells by mechanisms triggered by TGF-beta and mediated by DNA methyltransferase 3 alpha (DNMT3A), which play a functional role in the EMT process and metastasis. In addition, TET3 (and TET2) may be guardians of regulatory T cell stability and immune homeostasis. TET3 has been shown to prevent terminal differentiation of adult neural stem cells by a mechanism involving direct binding and repression of TET3 to the imprinted gene Snrpn. TET3 has also been shown to mediate the activation of hepatic stellate cells via modulation of the long non-coding RNA HIF1A-AS1 expression. TET1 belongs to the TET/JBP family of dioxygenases that require Fe2+ and alpha-ketoglutarate (also known as 2-oxoglutarate) for activity. 452 matched cddid_all.tbl CDD cd18908 cd18908 381478 bHLH_SOHLH1_2 basic helix-loop-helix (bHLH) domain found in the spermatogenesis- and oogenesis-specific basic helix-loop-helix-containing protein (SOHLH) family. The SOHLH family includes two bHLH transcription factors, SOHLH1 and SOHLH2. They are specifically in spermatogonia and oocytes and essential for early spermatogonial and oocyte differentiation. 59 matched cddid_all.tbl CDD cd18909 cd18909 381479 bHLH_TCFL5 basic helix-loop-helix (bHLH) domain found in transcription factor-like 5 protein (TCFL5) and similar proteins. TCFL5, also termed Cha transcription factor, or HPV-16 E2-binding protein 1 (E2BP-1), is a bHLH transcription factor that plays a crucial role in spermatogenesis. It regulates cell proliferation or differentiation of cells through binding to a specific DNA sequence like other bHLH molecules. 60 matched cddid_all.tbl CDD cd18910 cd18910 381480 bHLHzip_USF3 basic Helix-Loop-Helix-zipper (bHLHzip) domain found in basic helix-loop-helix domain-containing protein USF3 and similar proteins. USF3, also termed upstream transcription factor 3, is a bHLHzip protein that is involved in the negative regulation of epithelial-mesenchymal transition, the process by which epithelial cells lose their polarity and adhesion properties to become mesenchymal cells with enhanced migration and invasive properties. 65 matched cddid_all.tbl CDD cd18911 cd18911 381481 bHLHzip_MGA basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MAX gene-associated protein (MGA) and similar proteins. MGA, also termed MAX dimerization protein 5 (MAD5), is a dual specificity T-box/ bHLHzip transcription factor that regulates the expression of both Max-network and T-box family target genes. It contains a Myc-like bHLHZip motif and requires heterodimerization with Max for binding to the preferred Myc-Max-binding site CACGTG. In addition to the bHLHZip domain, MGA harbors a second DNA-binding domain, the T-box or T-domain. It thus binds the preferred Brachyury-binding sequence and represses transcription of reporter genes containing promoter-proximal Brachyury-binding sites. 65 matched cddid_all.tbl CDD cd18912 cd18912 381482 bHLH_TS_bHLHa9 basic helix-loop-helix (bHLH) domain found in Class A basic helix-loop-helix protein 9 (bHLHa9) and similar proteins. bHLHa9, also termed Class F basic helix-loop-helix factor 42 (bHLHf42), is a bHLH transcription factor that plays an essential role in limb development. 63 matched cddid_all.tbl CDD cd18913 cd18913 381483 bHLH-O_hairy_like basic helix-loop-helix-orange (bHLH-O) domain found in Drosophila melanogaster protein hairy, protein deadpan and similar proteins. Protein hairy is a bHLH transcriptional repressor of genes that require a bHLH-O protein for their transcription. It acts as a pair-rule protein that regulates embryonic segmentation and adult bristle patterning. Protein deadpan is closely related to the product of the segmentation gene hairy. It is a direct target of Notch signaling and regulates neuroblast self-renewal in Drosophila. 67 matched cddid_all.tbl CDD cd18914 cd18914 381484 bHLH_AtORG2_like basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana OBP3-responsive gene 2 (ORG2), 3 (ORG3) and similar proteins. The family includes ORG2 (also termed AtbHLH38, or EN 8) and ORG3 (also termed AtbHLH39, or EN 9), both of which act as bHLH transcription factors. 77 matched cddid_all.tbl CDD cd18915 cd18915 381485 bHLH_AtLHW_like basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein LONESOME HIGHWAY (LHW) and similar proteins. The family includes several bHLH transcription factors from Arabidopsis thaliana, such as LHW, and EMB1444. LHW, also termed AtbHLH156, or bHLH delta, is a bHLH transcription activator that regulates root development and promotes the production of stele cells in roots. It coordinately controls the number of all vascular cell types by regulating the size of the pool of cells from which they arise. EMB1444, also termed AtbHLH169, or lonesome highway-like protein 1, or protein embryo defective 1444, may regulate root development. 71 matched cddid_all.tbl CDD cd18916 cd18916 381486 bHLH-O_ESM5_like basic helix-loop-helix-orange (bHLH-O) domain found in Drosophila melanogaster Enhancer of split proteins, E(spl)m5, E(spl)m8 and similar proteins. The family includes two bHLH-O transcriptional repressors, E(spl)m5 and E(spl)m8, which participate in the control of cell fate choice by uncommitted neuroectodermal cells in the embryo. They bind DNA on N-box motifs, 5'-CACNAG-3'. 59 matched cddid_all.tbl CDD cd18917 cd18917 381487 bHLH_AtSAC51_like basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana suppressor of acaulis 51 (SAC51) and similar proteins. SAC51, also termed AtbHLH142, or EN 128, is a bHLH transcription factor that is involved in stem elongation, probably by regulating a subset of genes involved in this process. 53 matched cddid_all.tbl CDD cd18918 cd18918 381488 bHLH_AtMYC1_like basic Helix-Loop-Helix (bHLH) domain found in Arabidopsis thaliana MYC1 and similar proteins. MYC1, also termed AtbHLH12, or EN 58, acts as a transcription activator, when associated with MYB75/PAP1 or MYB90/PAP2. 70 matched cddid_all.tbl CDD cd18919 cd18919 381489 bHLH_AtBPE_like basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana BIG PETAL (BPE) and similar proteins. The family includes several bHLH transcription factors from Arabidopsis thaliana, such as BPE, HBI1 and BEE proteins (BEE1-3). BPE, also termed AtbHLH31, or EN 88, is involved in the control of Arabidopsis petal size, by interfering with postmitotic cell expansion to limit final petal cell size. HBI1, also termed AtbHLH64, or homolog of bee2 interacting with IBH1, or EN 79, is an atypical bHLH transcription factor that acts as positive regulator of cell elongation downstream of multiple external and endogenous signals by direct binding to the promoters and activation of the two expansin genes EXPA1 and EXPA8, encoding cell wall loosening enzymes. BEEs, also termed protein Brassinosteroid enhanced expression, are positive regulators of brassinosteroid signaling. 86 matched cddid_all.tbl CDD cd18920 cd18920 381490 bHLH-O_HEY2 basic helix-loop-helix-orange (bHLH-O) domain found in hairy/enhancer-of-split related with YRPW motif protein 2 (HEY2) and similar proteins. HEY2, also termed cardiovascular helix-loop-helix factor 1 (CHF-1), or Class B basic helix-loop-helix protein 32 (bHLHb32), or HES-related repressor protein 2, or hairy and enhancer of split-related protein 2 (HESR-2), or hairy-related transcription factor 2 (HRT-2), or protein gridlock homolog, is a bHLH-O transcriptional repressor expressed preferentially in the developing and adult cardiovascular system. As a downstream effector of Notch signaling, HEY2 may be required for cardiovascular development. It also plays an important role in neurologic development, as well as in the progression of human cancers. 82 matched cddid_all.tbl CDD cd18921 cd18921 381491 bHLHzip_SREBP1 basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein 1 (SREBP1) and similar proteins. SREBP1, also termed Class D basic helix-loop-helix protein 1 (bHLHd1), or sterol regulatory element-binding transcription factor 1 (SREBF1), is a member of a family of bHLHzip transcription factors that recognize sterol regulatory element 1 (SRE-1). It acts as a transcriptional activator required for lipid homeostasis. It may control transcription of the low-density lipoprotein receptor gene as well as the fatty acid. SREBP1 has dual sequence specificity binding to both an E-box motif (5'-ATCACGTGA-3') and to SRE-1 (5'-ATCACCCCAC-3'). 75 matched cddid_all.tbl CDD cd18922 cd18922 381492 bHLHzip_SREBP2 basic Helix-Loop-Helix-zipper (bHLHzip) domain found in sterol regulatory element-binding protein 2 (SREBP2) and similar proteins. SREBP2, also termed Class D basic helix-loop-helix protein 2 (bHLHd2), or sterol regulatory element-binding transcription factor 2 (SREBF2), is a member of a family of bHLHzip transcription factors that recognize sterol regulatory element 1 (SRE-1). It acts as a transcription activator of cholesterol biosynthesis. 77 matched cddid_all.tbl CDD cd18923 cd18923 381493 bHLHzip_USF2 basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 2 (USF2) and similar proteins. USF2, also termed Class B basic helix-loop-helix protein 12 (bHLHb12), or major late transcription factor 2, or FOS-interacting protein (FIP), or upstream transcription factor 2, is a bHLHzip transcription factor that binds to a symmetrical DNA sequence (E-boxes) (5'-CACGTG-3') that is found in a variety of viral and cellular promoters. 80 matched cddid_all.tbl CDD cd18924 cd18924 381494 bHLHzip_USF1 basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins. USF1, also termed Class B basic helix-loop-helix protein 11 (bHLHb11), or major late transcription factor 1, is a bHLHzip transcription factor that binds to a symmetrical DNA sequence (E-boxes) (5'-CACGTG-3') that is found in a variety of viral and cellular promoters. It is ubiquitously expressed and involved in the transcription activation of various functional genes implicated in lipid and glucose metabolism, stress response, immune response, cell cycle control and tumour suppression. USF-1 recruits chromatin remodeling enzymes and interact with co-activators and the members of the transcription pre-initiation complex. Genetic polymorphisms of USF1 are associated with some metabolic and cardiovascular diseases, like diabetes, atherosclerosis, coronary artery calcifications and familial combined hyperlipidaemia (FCHL). 65 matched cddid_all.tbl CDD cd18925 cd18925 381495 bHLHzip_TFEC basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EC (TFEC) and similar proteins. TFEC, also termed Class E basic helix-loop-helix protein 34 (bHLHe34), or transcription factor EC-like (TFEC-L), is a bHLHzip transcriptional regulator that acts as a repressor or an activator and regulates gene expression in macrophages. It plays an important role in the niche to expand hematopoietic progenitors through the modulation of several cytokines. 85 matched cddid_all.tbl CDD cd18926 cd18926 381496 bHLHzip_MITF basic Helix-Loop-Helix-zipper (bHLHzip) domain found in microphthalmia-associated transcription factor (MITF) and similar proteins. MITF, also termed Class E basic helix-loop-helix protein 32 (bHLHe32), is a bHLHzip transcription factor that is involved in neural crest melanocytes development as well as the pigmented retinal epithelium. It regulates the expression of genes with essential roles in cell differentiation, proliferation and survival. It binds to M-boxes (5'-TCATGTG-3') and symmetrical DNA sequences (E-boxes) (5'-CACGTG-3') found in the promoters of target genes, such as BCL2 and tyrosinase (TYR). 104 matched cddid_all.tbl CDD cd18927 cd18927 381497 bHLHzip_TFEB basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor EB (TFEB) and similar proteins. TFEB, also termed Class E basic helix-loop-helix protein 35 (bHLHe35), is a bHLHzip transcription factor that is required for vascularization of the mouse placenta. It specifically recognizes and binds E-box sequences (5'-CANNTG-3'). Its efficient DNA-binding requires dimerization with itself or with another MiT/TFE family member such as TFE3 or MITF. 91 matched cddid_all.tbl CDD cd18928 cd18928 381498 bHLHzip_TFE3 basic Helix-Loop-Helix-zipper (bHLHzip) domain found in transcription factor E3 (TFE3) and similar proteins. TFE3, also termed Class E basic helix-loop-helix protein 33 (bHLHe33), is a bHLHzip transcription factor that is involved in B cell function. It specifically recognizes and binds E-box sequences (5'-CANNTG-3'). Its efficient DNA-binding requires dimerization with itself or with another MiT/TFE family member such as TFEB or MITF. 91 matched cddid_all.tbl CDD cd18929 cd18929 381499 bHLHzip_Mad4 basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-associated protein 4 (Mad4) and similar proteins. Mad4, also termed Max dimerization protein 4, or Max dimerizer 4 (MXD4), or Class C basic helix-loop-helix protein 12 (bHLHc12), or Max-interacting transcriptional repressor MAD4, is a bHLHZip Max-interacting transcriptional repressor that suppresses c-myc dependent transformation and is expressed during neural and epidermal differentiation. It is regulated by a transcriptional repressor complex that contains Miz-1 and c-Myc. 88 matched cddid_all.tbl CDD cd18930 cd18930 381500 bHLHzip_MXI1 basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-interacting protein 1 (MXI1) and similar proteins. MXI1, also termed Max interactor 1, or Class C basic helix-loop-helix protein 11 (bHLHc11), is a bHLHZip transcriptional repressor that binds with MAX to form a sequence-specific DNA-binding protein complex which recognizes the core sequence 5'-CAC[GA]TG-3'. It thus antagonizes MYC transcriptional activity by competing for MAX. It plays an important role in the regulation of cell proliferation. 80 matched cddid_all.tbl CDD cd18931 cd18931 381501 bHLHzip_Mad1 basic Helix-Loop-Helix-zipper (bHLHzip) domain found in protein Max-associated protein 1 (Mad1) and similar proteins. Mad1, also termed Max dimerization protein 1 (MXD1), or Max dimerizer 1, or protein MAD, is a bHLHZip transcriptional repressor that binds with MAX to form a sequence-specific DNA-binding protein complex which recognizes the core sequence 5'-CAC[GA]TG-3'. It thus antagonizes MYC transcriptional activity by competing for MAX. 80 matched cddid_all.tbl CDD cd18932 cd18932 381502 bHLHzip_Mad3 basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-associated protein 3 (Mad3) and similar proteins. Mad3, also termed Max dimerization protein 3, or Max dimerizer 3 (MXD3), or Class C basic helix-loop-helix protein 13 (bHLHc13), or Max-interacting transcriptional repressor MAD3, or Myx, is a bHLHZip Max-interacting transcriptional repressor that plays an important role in cellular proliferation. It suppresses c-myc dependent transformation and is expressed during neural and epidermal differentiation. 85 matched cddid_all.tbl CDD cd18933 cd18933 381503 bHLH-O_HES3 basic helix-loop-helix-orange (bHLH-O) domain found in transcription factor HES-3 and similar proteins. HES-3, also termed Class B basic helix-loop-helix protein 43 (bHLHb43), or hairy and enhancer of split 3, is a bHLH-O transcription factor expressed in neural stem and progenitor cells that is involved in tissue regeneration. It regulates gene expression, cell growth, and insulin release. HES-3 is one mammalian counterpart of the Hairy and Enhancer of split proteins that play a critical role in many physiological processes including cellular differentiation, cell cycle arrest, apoptosis and self-renewal ability. 55 matched cddid_all.tbl CDD cd18934 cd18934 381504 bHLH_TS_MRF4_Myf6 basic helix-loop-helix (bHLH) domain found in muscle-specific regulatory factor 4 (MRF4) and similar proteins. MRF4, also termed Class C basic helix-loop-helix protein 4 (bHLHc4), or myogenic factor 6 (Myf-6), is a bHLH transcription factor associated with myogenesis. It plays a role in skeletal muscle differentiation. 64 matched cddid_all.tbl CDD cd18935 cd18935 381505 bHLH_TS_MYOG_Myf4 basic helix-loop-helix (bHLH) domain found in myogenin (MYOG) and similar proteins. MYOG, also termed Class C basic helix-loop-helix protein 3 (bHLHc3), or myogenic factor 4 (Myf-4), is a bHLH transcriptional activator that promotes transcription of muscle-specific target genes and plays a role in muscle differentiation, cell cycle exit and muscle atrophy. 59 matched cddid_all.tbl CDD cd18936 cd18936 381506 bHLH_TS_MYOD1_Myf3 basic helix-loop-helix (bHLH) domain found in myoblast determination protein 1 (MYOD1) and similar proteins. MYOD1, also termed Class C basic helix-loop-helix protein 1 (bHLHc1), or myogenic factor 3 (Myf-3), is a bHLH transcriptional activator that promotes transcription of muscle-specific target genes and plays a role in muscle differentiation. Together with Myf-5 and MYOG, MYOD1 co-occupies muscle-specific gene promoter core region during myogenesis. 61 matched cddid_all.tbl CDD cd18937 cd18937 381507 bHLH_TS_Myf5 basic helix-loop-helix (bHLH) domain found in myogenic factor 5 (Myf-5) and similar proteins. Myf-5, also termed Class C basic helix-loop-helix protein 2 (bHLHc2), is a nuclear bHLH transcriptional activator that promotes transcription of muscle-specific target genes and plays a role in muscle specification and differentiation. It also acts as an RNA-binding protein which enhances Ccnd1/Cyclin D1 mRNA translation during myogenesis. 64 matched cddid_all.tbl CDD cd18938 cd18938 381508 bHLH_TS_Mesp basic helix-loop-helix (bHLH) domain found in the mesoderm posterior protein (Mesp) family. Mesp, a bHLH tissue specific transcription factor, acts as a key regulator of the cardiovascular transcriptional network by inducing directly and/or indirectly the expression of the majority of key cardiovascular transcription factors. The Mesp family includes two bHLH transcription factors, Mesp1 and Mesp2. Mesp1, also termed Class C basic helix-loop-helix protein 5 (bHLHc5), promotes cardiovascular differentiation during embryonic development and embryonic stem cell differentiation. Mesp2, also termed Class C basic helix-loop-helix protein 6 (bHLHc6), plays an important role in somitogenesis. 65 matched cddid_all.tbl CDD cd18939 cd18939 381509 bHLH_TS_Msgn1 basic helix-loop-helix (bHLH) domain found in mesogenin-1 (Msgn1) and similar proteins. Msgn1, also termed paraxial mesoderm-specific mesogenin1, or pMesogenin1 (pMsgn1), is a bHLH transcription factor required for maturation and segmentation of paraxial mesoderm. It may regulate the expression of T-box transcription factors essential for mesoderm formation and differentiation. 66 matched cddid_all.tbl CDD cd18940 cd18940 381510 bHLH_TS_OLIG2 basic helix-loop-helix (bHLH) domain found in oligodendrocyte transcription factor 2 (Oligo2) and similar proteins. Oligo2, also termed Class B basic helix-loop-helix protein 1 (bHLHb1), or Class E basic helix-loop-helix protein 19 (bHLHe19), or protein kinase C-binding protein 2, or protein kinase C-binding protein RACK17, is a bHLH transcription factor that is required for oligodendrocyte and motor neuron specification in the spinal cord, as well as for the development of somatic motor neurons in the hindbrain. It cooperates with OLIG1 to establish the MN progenitors (pMN) domain of the embryonic neural tube. 85 matched cddid_all.tbl CDD cd18941 cd18941 381511 bHLH_TS_OLIG3 basic helix-loop-helix (bHLH) domain found in oligodendrocyte transcription factor 3 (Oligo3) and similar proteins. Oligo3, also termed Class B basic helix-loop-helix protein 7 (bHLHb7), or Class E basic helix-loop-helix protein 20 (bHLHe20), is a bHLH transcription factor that is expressed in the ventricular zone of the dorsal alar plate of the hindbrain and involved in regulating the development of dorsal and ventral spinal cord. It may determine the distinct specification program of class A neurons in the dorsal part of the spinal cord and suppress specification of class B neurons. 81 matched cddid_all.tbl CDD cd18942 cd18942 381512 bHLH_TS_OLIG1 basic helix-loop-helix (bHLH) domain found in oligodendrocyte transcription factor 1 (Oligo1) and similar proteins. Oligo1, also termed Class B basic helix-loop-helix protein 6 (bHLHb6), or Class E basic helix-loop-helix protein 21 (bHLHe21), is a bHLH transcription factor that promotes formation and maturation of oligodendrocytes, especially within the brain. 75 matched cddid_all.tbl CDD cd18943 cd18943 381513 bHLH_E-protein_E47-like basic helix-loop-helix (bHLH) domain found in transcription factor E47 and similar proteins. E47 is a class I bHLH transcriptional regulator that forms heterodimers with class II bHLH proteins to regulate distinct differentiation pathways. Its homodimers regulate B lymphocytes development. 74 matched cddid_all.tbl CDD cd18944 cd18944 381514 bHLH_E-protein_E2A_TCF3 basic helix-loop-helix (bHLH) domain found in transcription factor E2-alpha (E2A) and similar proteins. E2A, also termed Class B basic helix-loop-helix protein 21 (bHLHb21), or immunoglobulin enhancer-binding factor E12/E47, or immunoglobulin transcription factor 1, or Kappa-E2-binding factor, or transcription factor 3 (TCF-3), or transcription factor ITF-1, is a bHLH transcriptional regulator involved in the initiation of neuronal differentiation. 74 matched cddid_all.tbl CDD cd18945 cd18945 381515 bHLH_E-protein_TCF4_E2-2 basic helix-loop-helix (bHLH) domain found in transcription factor 4 (TCF-4) and similar proteins. TCF-4, also termed E2-2, or Class B basic helix-loop-helix protein 19 (bHLHb19), or immunoglobulin transcription factor 2 (ITF-2), or SL3-3 enhancer factor 2 (SEF-2), is a bHLH transcription factor that binds to the immunoglobulin enhancer Mu-E5/KE5-motif. It is involved in the initiation of neuronal differentiation. 85 matched cddid_all.tbl CDD cd18946 cd18946 381516 bHLH_E-protein_TCF12_HEB basic helix-loop-helix (bHLH) domain found in transcription factor 12 (TCF-12) and similar proteins. TCF-12, also termed HEB, or Class B basic helix-loop-helix protein 20 (bHLHb20), or DNA-binding protein HTF4, or E-box-binding protein, or transcription factor HTF-4, is a bHLH transcription factor that is involved in the initiation of neuronal differentiation. 83 matched cddid_all.tbl CDD cd18947 cd18947 381517 bHLH-PAS_ARNT basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in aryl hydrocarbon receptor nuclear translocator (ARNT) and similar proteins. ARNT, also termed Class E basic helix-loop-helix protein 2 (bHLHe2), or Dioxin receptor, nuclear translocator, or hypoxia-inducible factor 1-beta (HIF1b), or HIF-1-beta, or HIF1-beta, is a member of bHLH-PAS transcription regulators that acts as the heterodimeric partner for bHLH-PAS proteins such as aryl hydrocarbon receptor (AhR), hypoxia-inducible factor (HIF), and single-minded (SIM). These bHLH-PAS transcription complexes are involved in transcriptional responses to xenobiotic, hypoxia, and developmental pathways. Heterodimerization of bHLH-PAS proteins with ARNT is mediated by contacts between both the bHLH and the tandem PAS domains. ARNT use bHLH and/or PAS domains to interact with several transcriptional coactivators. It is required for activity of the aryl hydrocarbon (dioxin) receptor. 65 matched cddid_all.tbl CDD cd18948 cd18948 381518 bHLH-PAS_NCoA1_SRC1 basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 1 (NCoA-1) and similar proteins. NCoA-1, also termed Class E basic helix-loop-helix protein 74 (bHLHe74), or protein Hin-2, or RIP160, or renal carcinoma antigen NY-REN-52, or steroid receptor coactivator 1 (SRC-1), is a bHLH-PAS nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. 61 matched cddid_all.tbl CDD cd18949 cd18949 381519 bHLH-PAS_NCoA3_SRC3 basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 3 (NCoA-3) and similar proteins. NCoA-3, also termed ACTR, or amplified in breast cancer 1 protein (AIB-1), or CBP-interacting protein (pCIP), or Class E basic helix-loop-helix protein 42 (bHLHe42), or receptor-associated coactivator 3 (RAC-3), or steroid receptor coactivator protein 3 (SRC-3), or thyroid hormone receptor activator molecule 1 (TRAM-1), is a bHLH-PAS steroid/nuclear receptor-associated coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. It also plays a central role in creating a multisubunit coactivator complex, which probably acts via remodeling of chromatin. 73 matched cddid_all.tbl CDD cd18950 cd18950 381520 bHLH-PAS_NCoA2_SRC2 basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in nuclear receptor coactivator 2 (NCoA-2) and similar proteins. NCoA-2, also termed Class E basic helix-loop-helix protein 75 (bHLHe75), or transcriptional intermediary factor 2 (TIF2), or steroid receptor coactivator 2 (SRC-2), or glucocorticoid receptor interacting protein-1 (GRIP1), is a bHLH-PAS transcriptional coactivator for steroid receptors and nuclear receptors. It is required with NCoA-1 to control energy balance between white and brown adipose tissues. 64 matched cddid_all.tbl CDD cd18951 cd18951 381521 bHLH_TS_scleraxis basic helix-loop-helix (bHLH) domain found in scleraxis and similar proteins. Scleraxis, also termed SCX, or Class A basic helix-loop-helix protein 41 (bHLHa41), or Class A basic helix-loop-helix protein 48 (bHLHa48), is a bHLH transcription factor that is expressed in sclerotome limb bud cranial and body wall mesenchyme, pericardium and heart valves, ligaments and tendons. It is required for tendon formation ligaments, connective tissue, the diaphragm, and testis development. Scleraxis plays a central role in promoting fibroblast proliferation and matrix synthesis during the embryonic development of tendons. 68 matched cddid_all.tbl CDD cd18952 cd18952 381522 bHLH_TS_HAND1 basic helix-loop-helix (bHLH) domain found in heart- and neural crest derivatives-expressed protein 1 (HAND1) and similar proteins. HAND1, also termed Class A basic helix-loop-helix protein 27 (bHLHa27), or extraembryonic tissues, heart, autonomic nervous system and neural crest derivatives-expressed protein 1 (eHAND), is a bHLH transcription factor that plays an essential role in both trophoblast-giant cells differentiation and in cardiac morphogenesis. 60 matched cddid_all.tbl CDD cd18953 cd18953 381523 bHLH_TS_bHLHe23_bHLHb4 basic helix-loop-helix (bHLH) domain found in Class E basic helix-loop-helix protein 23 (bHLHe23) and similar proteins. bHLHe23, also termed Class B basic helix-loop-helix protein 4 (bHLHb4), is an OLIG-related bHLH transcription factor that is expressed in rod bipolar cells and is required for rod bipolar cell maturation. bHLHe23 have roles in spinal interneuron differentiation by mechanisms linked to the Notch signaling pathway. It modulates the expression of genes required for the differentiation and/or maintenance of pancreatic and neuronal cell types. 81 matched cddid_all.tbl CDD cd18954 cd18954 381524 bHLH_TS_bHLHe22_bHLHb5 basic helix-loop-helix (bHLH) domain found in Class E basic helix-loop-helix protein 22 (bHLHe22) and similar proteins. bHLHe22, also termed Class B basic helix-loop-helix protein 5 (bHLHb5), or trinucleotide repeat-containing gene 20 protein, is an OLIG-related bHLH neural-specific transcriptional repressor that is expressed in both excitatory (unipolar brush cells) and inhibitory neurons (cartwheel cells) of the dorsal cochlear nucleus (DCN) during development. It is important for the proper development and/or survival of a number of neural cell types. 70 matched cddid_all.tbl CDD cd18955 cd18955 349736 BTB_POZ_BACH BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in BTB and CNC homolog (BACH) proteins. This subfamily includes BACH1 (also called BTB-basic leucine zipper transcription factor 1), BACH2 (also called BTB-basic leucine zipper transcription factor 2), and similar proteins. They belong to the cap 'n' collar (CNC) and basic leucine zipper (bZIP) factor family. BACH1 is a heme-responsive transcriptional repressor of heme oxygenase (HO)-1. It represses genes involved in heme metabolism and oxidative stress response. BACH2 is a lymphoid-specific transcription factor with a prominent role in B-cell development. It is transcriptionally regulated by the BCR/ABL oncogene. It represses the anti-apoptotic factor heme oxygenase-1 (HO-1). Subfamily members contain a BTB domain and a basic leucine zipper (bZIP) domain. The BTB/POZ domain is a common protein-protein interaction motif of about 100 amino acids. 94 matched cddid_all.tbl CDD cd18956 cd18956 349737 BTB_POZ_ZBTB42 BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain found in zinc finger and BTB domain-containing protein 42 (ZBTB42). ZBTB42 is a transcriptional repressor that specifically binds DNA and probably acts by recruiting chromatin remodeling multiprotein complexes. It is enriched in skeletal muscles, especially at the neuromuscular junction. A ZBTB42 mutation has been identified to define a novel lethal congenital contracture syndrome (LCCS6), a lethal autosomal recessive form of arthrogryposis multiplex congenita (AMC). ZBTB42 contains a BTB/POZ domain, a common protein-protein interaction motif of about 100 amino acids. 129 matched cddid_all.tbl CDD cd18960 cd18960 349316 CD_HP1_like chromodomain of heterochromatin protein 1 proteins, including HP1alpha, HP1beta, and HP1gamma; uncharacterized subgroup. CHRomatin Organization Modifier (chromo) domain of mammalian HP1alpha (Cbx5), HP1beta (Cbx1), HP1gamma (Cbx5), and similar proteins. HP1 has diverse functions in heterochromatin formation and impacts both gene expression and gene silencing. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3). 51 matched cddid_all.tbl CDD cd18961 cd18961 349317 CD_CEC-4_like chromodomain of Caenorhabditis elegans chromodomain protein 4, and similar proteins. CHRomatin Organization Modifier (chromo) domain of Caenorhabditis elegans CEC-4, and similar proteins. CEC-4 is a perinuclear heterochromatin anchor, it mediates the anchoring of H3K9 methylation-bearing chromatin at the nuclear periphery in early to mid-stage embryos. It is necessary for anchoring, but does not affect transcriptional repression. CEC-4 contributes to the efficiency with which muscle differentiation is induced following ectopic expression of the master regulator, HLH-1 (MyoD in mammals). A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 51 matched cddid_all.tbl CDD cd18962 cd18962 349318 CD_MT_like chromodomain of a putative Coemansia reversa NRRL 1564 methyltransferase, and similar proteins. This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in a Coemansia reversa NRRL 1564 SET (Su(var)3-9, enhancer-of-zeste, trithorax) domain-containing protein, and similar proteins. The SU(VAR)3-9 protein is the main chromocenter-specific histone H3-K9 methyltransferase (HMTase) in Drosophila where it plays a role in heterochromatic gene silencing. A chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 52 matched cddid_all.tbl CDD cd18963 cd18963 349319 chromodomain CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain. 57 matched cddid_all.tbl CDD cd18964 cd18964 349320 chromodomain CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain. 54 matched cddid_all.tbl CDD cd18965 cd18965 349321 chromodomain CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain. 53 matched cddid_all.tbl CDD cd18966 cd18966 349322 chromodomain CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain. 49 matched cddid_all.tbl CDD cd18967 cd18967 349323 chromodomain CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain. 55 matched cddid_all.tbl CDD cd18968 cd18968 349324 chromodomain CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain. 57 matched cddid_all.tbl CDD cd18969 cd18969 349325 chromodomain CHROMO (CHRromatin Organization Modifier) domain; uncharacterized subgroup; for most members of this subgroup, the chromodomain is followed by a chromo shadow domain. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. Chromodomains belong to the chromo-like superfamily of SH3-fold-beta-barrel domains which includes chromo shadow domains and chromo barrel domains. Chromodomains differ from these in that they lack the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain. For the majority of members of this subgroup, the chromodomain is followed by a chromo shadow domain (CSD). 56 matched cddid_all.tbl CDD cd18970 cd18970 349326 CD_POL_like chromodomain of Hypsizygus marmoreus TY3B-I_0 protein, and similar proteins. This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Hypsizygus marmoreus TY3B-I_0 protein, a putative TY3/gypsy retrotransposon polyprotein, and similar proteins. The pol gene in TY3/gypsy elements generally encodes domains in the following order: an aspartyl protease, a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 49 matched cddid_all.tbl CDD cd18971 cd18971 349327 CD_POL_like chromodomain of a Magnaporthe grisea putative retrotransposon polyprotein, and similar proteins. This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in a Magnaporthe grisea putative retrotransposon polyprotein which includes domains in the following order: an aspartyl protease, a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 50 matched cddid_all.tbl CDD cd18972 cd18972 349328 CD_POL_like "chromodomain of a Moniliophthora perniciosa FA553 putative retrotransposon polyprotein, and similar proteins. This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in a Moniliophthora perniciosa FA553 putative retrotelement polyprotein, which includes domains in the following order: a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related ""chromo shadow"" domain" 50 matched cddid_all.tbl CDD cd18973 cd18973 349329 CD_Tf2-1_POL_like chromodomain of Rhizoctonia solani AG-1 IB retrotransposable element Tf2 155 kDa protein type 1, and similar proteins. This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Rhizoctonia solani AG-1 IB retrotransposable element Tf2 155 kDa protein type 1 (Tf2-1), and similar proteins. It belongs to the Ty3/gypsy family of long terminal repeat (LTR) retrotransposons. The pol gene in TY3/gypsy elements generally encodes domains in the following order: an aspartyl protease, a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 50 matched cddid_all.tbl CDD cd18974 cd18974 349330 CD_POL_like chromodomain of Penicillium solitum protein PENSOL_c198G03123. This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Penicillium solitum protein PENSOL_c198G03123 a putative polyprotein from a Ty3/Gypsy long terminal repeat (LTR) retroelement. The pol gene in TY3/gypsy elements generally encodes domains in the following order: an aspartyl protease, a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 50 matched cddid_all.tbl CDD cd18975 cd18975 349331 CD_MarY1_POL_like chromodomain of Tricholoma matsutake polyprotein, and similar proteins. This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in the polyprotein from the MarY1 Ty3/Gypsy long terminal repeat (LTR) retroelement from the from the Ectomycorrhizal Basidiomycete Tricholoma matsutake. The pol gene in TY3/gypsy elements generally encodes domains in the following order: prt-reverse transcriptase-RNase H-integrase, in marY1 POL the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 49 matched cddid_all.tbl CDD cd18976 cd18976 349332 CD_POL_like chromodomain of uncharacterized putative retroelement polyprotein proteins. This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in uncharacterized putative retrotransposon proteins, and similar proteins. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 51 matched cddid_all.tbl CDD cd18977 cd18977 349333 CD_POL_like chromodomain of a Rhizoctonia solani AG-3 Rhs1AP polyprotein, and similar proteins. This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in a Rhizoctonia solani AG-3 Rhs1AP, a putative Ty3/Gypsy polyprotein/retrotransposon which includes a protease, a reverse transcriptase, a ribonuclease H, and an integrase domain, in that order, with a chromodomain at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 57 matched cddid_all.tbl CDD cd18978 cd18978 349334 CD_DDE_transposase_like chromodomain of Rhizopus microsporus putative DDE transposases, and similar proteins. This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Rhizopus microsporus putative DDE transposases, and similar proteins. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 52 matched cddid_all.tbl CDD cd18979 cd18979 349335 CD_POL_like chromodomain of a Zea maize putative metaviridae (gypsy-type) retrotransposon polyproteins (Z195D10.9), and similar proteins. This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Zea maize Z195D10.9 protein, and other putative TY3/gypsy retrotransposon polyproteins. The pol gene in TY3/gypsy elements generally encodes domains in the following order: an aspartyl protease, a reverse transcriptase, RNase H, and an integrase, here the chromodomain is found at the C-terminus of the integrase domain. The chromodomain, is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 48 matched cddid_all.tbl CDD cd18980 cd18980 349336 CD_NC-like chromodomain of a Tasahii var. asahii CBS 8904 retrotransposon nucleocapsid protein, and similar proteins. This subgroup includes the CHROMO (CHRromatin Organization Modifier) domain found in Trichosporon asahii var. asahii CBS 8904 retrotransposon nucleocapsid protein, and similar proteins. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. A chromodomain may occur as a single instance, in a tandem arrangement, or followed by a related chromo shadow domain. 56 matched cddid_all.tbl CDD cd18981 cd18981 349337 CSD_HP1e_insect chromo shadow domain of insect heterochromatin protein 1E. The chromo shadow domain (CSD) is always found in association with a related N-terminal chromo (CHRromatin Organization MOdifier) domain. CSD domains have only been found in proteins that also possess a chromodomain, while chromodomains can exist in isolation. CSDs are found for example in Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3. 53 matched cddid_all.tbl CDD cd18982 cd18982 349338 CSD chromo shadow domain; uncharacterized subgroup. The chromo shadow domain (CSD) is always found in association with a related N-terminal chromo (CHRromatin Organization MOdifier) domain. CSD domains have only been found in proteins that also possess a chromodomain, while chromodomains can exist in isolation. CSDs are found for example in Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3. 50 matched cddid_all.tbl CDD cd18983 cd18983 350846 CBD_MSL3_like chromo barrel domain of human male-specific lethal complex subunit 3, and similar proteins. This subgroup includes human male-specific lethal (MSL) complex subunit 3 (MSL3, also known as MSL3L1). The MSL3 chromodomain specifically recognizes the H4K20 monomethyl mark, in a DNA-dependent manner, and may be involved in chromosomal targeting of the MSL complex. Also included is MORF-related gene on chromosome 15 (MRG15, also known as MORF4L1) which specifically binds to Lys36-methylated histone H3 and plays a role in transcriptional regulation and in DNA repair. This subgroup also includes Arabidopsis thaliana Morf Related Gene 2 (MRG2) which acts as a H3K4me3/H3K36me3 reader involved in the regulation of Arabidopsis flowering. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromo domain. 57 matched cddid_all.tbl CDD cd18984 cd18984 350847 CBD_MOF_like chromo barrel domain of Drosophila melanogaster males-absent on the first protein, and similar proteins. This subgroup includes the chromo barrel domain of Drosophila melanogaster males-absent on the first (MOF) protein. The histone H4 lysine 16 (H4K16)-specific acetyltransferase MOF is part of two distinct complexes involved in X chromosome dosage compensation and autosomal transcription regulation. Its chromobarrel domain is essential for H4K16 acetylation throughout the Drosophila genome and controls spreading of the male-specific lethal (MSL) complex on the X chromosome. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains, and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromodomain. The MOF-like chromo barrels may be may be auto-inhibited, i.e. they seem to have occluded peptide binding sites. 70 matched cddid_all.tbl CDD cd18985 cd18985 350848 CBD_TIP60_like chromo barrel domain of human tat-interactive protein 60, and similar proteins. Tat-interactive protein 60 (also known as KAT5 or HTATIP) catalyzes the acetylation of lysine side chains in various histone and nonhistone proteins, and in itself. It plays roles in multiple cellular processes including remodeling, transcription, DNA double-strand break repair, apoptosis, embryonic stem cell identity, and embryonic development. The TIP60 chromo barrel domain recognizes trimethylated lysine at site 9 of histone H3 (H3K9me3) which triggers TIP60 to acetylate and activate ataxia telangiectasia-mutated kinase, thereby promoting the DSB repair pathway. In a different study, the TIP60 chromo barrel domain was shown to bind H3K4me1, which stabilizes TIP60 recruitment to a subset of estrogen receptor alpha target genes, facilitating regulation of the associated gene transcription. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains, and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromodomain. This subgroup belongs to the MOF-like chromo barrels may be may be auto-inhibited, i.e. they seem to have occluded peptide binding sites. 64 matched cddid_all.tbl CDD cd18986 cd18986 350849 CBD_ESA1_like chromo barrel domain of yeast NuA4 histone acetyltransferase complex catalytic subunit ESA1, and similar proteins. The subgroup includes the chromo barrel domain of NuA4 histone acetyltransferase (HAT) complex catalytic subunit Esa1 (also known as Tas1 and Kat5). Yeast Esa1p acetylates specific histones nonrandomly in H4, H3, and H2A. Esa1 also plays roles in cell cycle progression. In addition, its chromo barrel domain plays a role in the yeast Piccolo NuA4 complex's ability to distinguish between histones and nucleosomes; however, the chromodomain is not required for the Piccolo to bind to nucleosomes. SH3-fold-beta-barrel domains of the chromo-like superfamily include chromodomains, chromo shadow domains, and chromo barrel domains, and are implicated in the recognition of lysine-methylated histone tails and nucleic acids. The chromodomain differs, in that it lacks the first strand of the SH3-fold-beta-barrel. This first strand is altered by insertion in the chromo shadow domains, and chromo barrel domains are typical SH3-fold-beta-barrel domains with sequence similarity to the canonical chromodomain. This subgroup belongs to the MOF-like chromo barrels may be may be auto-inhibited, i.e. they seem to have occluded peptide binding sites. 65 matched cddid_all.tbl CDD cd18987 cd18987 349788 LGIC_ECD_anion extracellular domain (ECD) of anionic Cys-loop neurotransmitter-gated ion channels. This family contains the extracellular domain (ECD) of anionic Cys-loop neurotransmitter-gated ion channels which include type-A gamma-aminobutyric acid receptor (GABAAR), glycine receptor (GlyR), invertebrate glutamate-gated chloride channel (GluCl), and histimine-gated chloride channel (HisCl). These neurotransmitter receptors directly mediate chloride permeability and constitute one half of the Cys-loop receptor family. Receptors in this family are composed of five either identical or homologous subunits, which generate diversity in functional profiles and pharmacological preferences. GABAAR and GlyR, both mediate fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR receptor pore, resulting in hyperpolarization of the neuron. GluCl channels are found only in protostomia, but are closely related to mammalian glycine receptors (GlyRs). They have several roles in these invertebrates, including controlling locomotion and feeding, and mediating sensory inputs into behavior. Ligand-gated chloride channels are critical not only for maintaining appropriate neuronal activity, but have long been important therapeutic targets: benzodiazepines, barbiturates, some intravenous and volatile anaesthetics, alcohol, strychnine, picrotoxin, and ivermectin all derive their biological activity from acting on this inhibitory half of the Cys-loop receptor family. Many of the therapeutically useful compounds acting at Cys-loop receptors target an allosteric site. The sites in Cys-loop receptors at which these allosteric ligands bind and their structure-based mechanisms of action are largely unresolved. 185 matched cddid_all.tbl CDD cd18988 cd18988 349789 LGIC_ECD_bact extracellular domain of prokaryotic pentameric ligand-gated ion channels (pLGIC). This family contains extracellular domain (ECD) of bacterial pentameric ligand-gated ion channels (pLGICs), including ones from Gloebacter violaceus (GLIC) and Erwinia chrysanthemi (ELIC). These prokaryotic homologs of Cys-loop receptors have been useful in understanding their eukaryotic counterparts. The largely beta-sheet ECD in this family is similar to other pLGICs, but lacks the cysteine loop and an intracellular domain. While most pLGICs undergo desensitization on prolonged exposure to the agonist, GLIC is activated by protons, but does not desensitize, even at proton concentrations eliciting maximal electrophysiological response (pH 4.5). Studies show that GLIC activation is inhibited by most general anaesthetics at clinical concentrations, including xenon which has been used in clinical practice as a potent gaseous anesthetic for decades. Xenon binding sites have been identified in three distinct regions of the TMD: in a large intra-subunit cavity, in the pore, and at the interface between adjacent subunits. 182 matched cddid_all.tbl CDD cd18989 cd18989 349790 LGIC_ECD_cation extracellular domain (LBD) of cationic Cys-loop neurotransmitter-gated ion channels. This superfamily contains the extracellular domain (ECD) of cationic Cys-loop neurotransmitter-gated ion channels, which include nicotinic acetylcholine receptor (nAChR), serotonin 5-hydroxytryptamine receptor (5-HT3), and zinc-activated ligand-gated ion channel (ZAC) receptor. These ligand-gated ion channels (LGICs) are found across metazoans and have close homologs in bacteria. They are vital for communication throughout the nervous system. nAChR is a non-selective cation channel that is permeable to Na+ and K+, and some subunit combinations are also permeable to Ca2+. Na+ enters and K+ exits to allow net flow of positively charged ions inward. 5-HT3, a cation-selective channel, binds serotonin and is permeable to Na+, K+, and Ca2+. It mediates neuronal depolarization and excitation within the central and peripheral nervous systems. ZAC forms an ion channel gated by Zn2+, Cu2+, and H+ and is non-selectively permeable to monovalent cations. However, the role of ZAC in Zn2+, Cu2+, and H+ signaling require is as yet unknown. 180 matched cddid_all.tbl CDD cd18990 cd18990 349791 LGIC_ECD_GABAAR "gamma-aminobutyric acid receptor extracellular domain. This family contains extracellular domain (ECD) of type-A gamma-aminobutyric acid receptor (GABAAR), a member of the pentameric ""Cys-loop"" superfamily of transmitter-gated ion channels. This family includes 19 isoforms in human; six alpha, 3 beta, 3 gamma, one of delta, epsilon, pi, and theta, known to form heteropentameric GABAARs, and 3 rho subunits that only form homopentameric channels (also known as GABAA rho or GABAC receptor) or pseudoheteromeric if consisting of different rho subunits. The majority of GABAA receptor pentamers contain two alpha subunits, two beta subunits, and a gamma subunit, with different isoforms affecting potency of the neurotransmitter. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to its site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. Benzodiazepine and barbiturates each bind to their own distinct sites on the ECD. The channels have to contain the gamma subunit and alpha subunits in order to respond to benzodiazepines. Specific combinations of alpha, beta, and gamma subunits exhibit ethanol sensitivity. All these major classes of drugs favor channel-opening. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy." 184 matched cddid_all.tbl CDD cd18991 cd18991 349792 LGIC_ECD_GlyR extracellular domain of glycine receptor (GlyR). This subfamily contains extracellular domain of glycine receptor (GlyR or GLR) of the amino acid neurotransmitter glycine. GlyR has four known isoforms of the alpha-subunit (alpha1-4, encoded by GLRA1, GLRA2, GLRA3, GLRA4) that are essential to bind ligands and a single beta-subunit (encoded by GLRB), all of which have been described to have a regionally and temporally controlled expression during development and maturation of the central nervous system (CNS). Functional chloride-permeable GlyR ion channels are formed by 5 alpha subunit homopentamers or by alpha and beta subunit heteropentamers, which form complexes with either a 2alpha-3beta or 3alpha-2beta stoichiometry. The receptor can be activated by glycine as well as beta-alanine and taurine, and can be selectively blocked by the high-affinity competitive antagonist strychnine. Caffeine is also a competitive antagonist of GlyR. In human, glycine receptor alpha1 and beta subunits are the major targets of mutations that cause disruption of GlyR surface expression or reduced ability of expressed GlyRs to conduct chloride ions, leading to hyperekplexia, a rare neurological disorder characterized by neonatal hypertonia and exaggerated startle responses to unexpected stimuli. Mutations in GlyR alpha2 are known to cause cortical neuronal migration/autism spectrum disorder and in GlyR alpha3 to cause inflammatory pain sensitization/rhythmic breathing. 185 matched cddid_all.tbl CDD cd18992 cd18992 349793 LGIC_ECD_HisCl extracellular domain of histimine-gated chloride channel (HisCl or HGCC). This family contains extracellular domain (ECD) of histamine-gated chloride channel (HisCl), a member of the Cys-loop receptor superfamily of ligand-gated ion channels and is closely related to the mammalian GABAA receptor and glycine receptor (GlyR). Histamine (HA) is a neurotransmitter that activates GPCRs in vertebrates, but in arthropods, it is a photoreceptor neurotransmitter, directly gating chloride channels on large monopolar cells (LMCs), postsynaptic to photoreceptors in the lamina. It has also been reported to play important roles in mechanosensory reception, temperature preference, and sleep in insects. HA activates its receptor channels to cause an inward chloride flux in the insect nervous system. In Drosophila, HA acts on two histamine-gated chloride channel (HGCC) subunits called HisCl1 (HisClalpha2, HCLB) and HisCl2 (HisClalpha1, Ort, HCLA). HisCl1 (HCLB) and HisCl2 (HCLA) are expressed predominantly in the insect eye, sharing 60% sequence identity, and forming homomeric and heteromeric HGCCs. HCLA homomers are involved in synaptic transmission in the lamina, while HCLB homomers, localized in the glia cells, have a role in shaping the transmission. HCLB channels, but not HCLA channels, are also responsible for the activation and maintenance of wake state in D. melanogaster. In Manduca sexta, HCLB channels in the flight sensory-motor have been shown to be involved in olfactory processing circuit. Studies show that HCLB channels are more sensitive to agonists when compared with HCLA channels, but insensitive to known LGCC insecticides. 185 matched cddid_all.tbl CDD cd18993 cd18993 349794 LGIC_ECD_GluCl glutamate-gated chloride channel (GluCl) extracellular domain. This subfamily contains extracellular domain of glutamate-gated chloride channel (GluCl) found only in protostomia, but are closely related to mammalian glycine receptors. They have several roles in these invertebrates, including controlling locomotion and feeding, and mediating sensory inputs into behavior. Comparison of the GluCl gene families between organisms shows that insect gene family is relatively simple, while that found in nematodes tends to be larger and more diverse. Glutamate is an inhibitory neurotransmitter that shapes the responses of projection neurons to olfactory stimuli in the Drosophila. GluCls are targeted by the macrocyclic lactone family of anthelmintics and pesticides in arthropods and nematodes, thus making the GluCls of considerable medical and economic importance. In Drosophila melanogaster, GluCl mediates sensitivity to the antiparasitic agents ivermectin and nodulisporic acid, suggesting that their drug target is the same throughout the Ecdysozoa. 183 matched cddid_all.tbl CDD cd18994 cd18994 349795 LGIC_ECD_ZAC extracellular domain of zinc-activated ligand-gated ion channel. This family is the extracellular domain of zinc-activated ligand-gated ion channel (ZAC), a cationic ion channel belonging to the superfamily of Cys-loop receptors, which consists of pentameric ligand-gated ion channels. ZAC displays low sequence similarity to other members in the superfamily, with closest matches to the human serotonin 5-HT3 receptor (5-HT3R) subunits 5-HT3A and 5-HT3B, and nAChR alpha7 subunits that exhibit approximately 15% amino acid sequence identity to ZAC. Expression of ZAC has been detected in human fetal whole brain, spinal cord, pancreas, placenta, prostate, thyroid, trachea, and stomach, as well as in adult hippocampus, striatum, amygdala, and thalamus. ZAC forms an ion channel gated by Zn2+, Cu2+, and H+, and is non-selectively permeable to monovalent cations. However, the role of ZAC in Zn2+, Cu2+, and H+ signaling is as yet unknown. 170 matched cddid_all.tbl CDD cd18995 cd18995 349796 LGIC_AChBP acetylcholine binding protein (AChBP). This family contains acetylcholine binding protein (AChBP) which is a soluble extracellular domain homolog secreted by protostomia, and has been widely recognized as a surrogate for the ligand binding domain of nicotinic acetylcholine receptors (nAChRs). AChBP forms a pentameric structure where the interfaces between the subunits provide an acetylcholine (ACh) binding pocket homologous to the binding pocket of nAChRs. Thus far, AChBPs have been characterized only in aquatic mollusks, which have shown low sensitivity to neonicotinoids, the insecticides targeting insect nAChRs. Lymnaea stagnalis acetylcholine binding protein (Ls-AChBP) which has been found in glial cells as a water-soluble protein modulating synaptic ACh concentration has its the binding pocket show better resemblance as it contains all the five aromatic residues fully conserved in nAChR. Five AChBP subunits have been characterized in Pardosa pseudoannulata, a predator enemy against rice insect pests, and share higher sequence similarities with nAChR subunits of both insects and mammals compared with mollusk AChBP subunits. 180 matched cddid_all.tbl CDD cd18996 cd18996 349797 LGIC_ECD_5-HT3 extracellular domain of serotonin 5-HT3 receptor. This family contains extracellular domain of serotonin 5-HT3 receptor which belongs to the Cys-loop superfamily of ligand-gated ion channels (LGICs). This ion channel is cation-selective and mediates neuronal depolarization and excitation within the central and peripheral nervous systems. Like other ligand gated ion channels, the 5-HT3 receptor consists of five subunits arranged around a central ion conducting pore, which is permeable to Na+, K+, and Ca2+ ions. Binding of the neurotransmitter 5-hydroxytryptamine (serotonin) to the 5-HT3 receptor opens the channel, which then leads to an excitatory response in neurons, and the rapidly activating, desensitizing, inward current is predominantly carried by Na+ and K+ ions. This receptor is most closely related by homology to the nicotinic acetylcholine receptor (nAChR). Five subunits have been identified for this family: 5-HT3A, 5-HT3B, 5-HT3C, 5-HT3D, and 5-HT3E, encoded by HTR3A-E genes. Only 5-HT3A subunits are able to form functional homomeric receptors, whereas the 5-HT3B, C, D, and E subunits form heteromeric receptors with 5-HT3A. Different receptor subtypes are important mediators of nausea and vomiting during chemotherapy, pregnancy, and following surgery, while some contribute to neuro-gastroenterologic disorders such irritable bowel syndrome (IBS) and eating disorders as well as co-morbid psychiatric conditions. 5-HT3 receptor antagonists are established treatments for emesis and IBS, and are beneficial in the treatment of psychiatric diseases. 215 matched cddid_all.tbl CDD cd18997 cd18997 349798 LGIC_ECD_nAChR "extracellular domain of nicotinic acetylcholine receptor. This family contains the extracellular domain of nicotinic acetylcholine receptor (nAChR), a member of the pentameric ""Cys-loop"" superfamily of transmitter-gated ion channels. nAChR is found in high concentrations at the nerve-muscle synapse, where it mediates fast chemical transmission of electrical signals in response to the endogenous neurotransmitter acetylcholine (ACh) released from the nerve terminal into the synaptic cleft. Thus far, seventeen nAChR subunits have been identified, including ten alpha subunits, four beta subunits, and one gamma, delta, and epsilon subunit each, all found on the cell membrane that non-selectively conducts cations (Na+, K+, Ca++). These nAChR subunits combine in several different ways to form functional nAChR subtypes which are broadly categorized as either muscle subtype located at the neuromuscular junction or neuronal subtype that are found on neurons and on other cell types throughout the body. The muscle type of nAChRs are formed by the alpha1, beta1, gamma, delta, and epsilon subunits while the neuronal type are composed of nine alpha subunits and three beta subunits, which combine in various permutations and combinations to form functional receptors. Among various subtypes of neuronal nAChRs, the homomeric alpha7 and the heteromeric alpha4beta2 receptors are the main subtypes widely distributed in the brain and implicated in the pathophysiology of neurodevelopmental disorders such as schizophrenia and autism and neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease. Among subtypes of muscle nAChRs, the heteromeric subunits (alpha1)2, beta, gamma, and delta in fetal muscle, and the gamma subunit replaced by epsilon in adult muscle have been implicated in congenital myasthenic syndromes and multiple pterygium syndromes due to various mutations. This family also includes alpha- and beta-like nAChRs found in protostomia." 181 matched cddid_all.tbl CDD cd18998 cd18998 349799 LGIC_ECD_GABAAR_A "extracellular domain of gamma-aminobutyric acid receptor subunit alpha. This family contains extracellular domain (ECD) of type-A gamma-aminobutyric acid receptor (GABAAR), a member of the pentameric ""Cys-loop"" superfamily of transmitter-gated ion channels. This family includes 19 isoforms in human; six alpha, 3 beta, 3 gamma, one of delta, epsilon, pi, and theta, known to form heteromeric GABAARs, and 3 rho subunits that only form homomeric channels (also known as GABAA rho or GABAC receptor) or pseudoheteromeric if consisting of different rho subunits. GABAAR is assembled from a variety of different subunit subtypes which determines their pharmacology and physiology; the most abundant being 2alpha2beta1gamma stoichiometry. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to its site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. Benzodiazepine and barbiturates each bind to their own distinct sites on the ECD. The channels have to contain the gamma subunit and alpha subunits in order to respond to benzodiazepines. All these major classes of drugs favor channel-opening. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. GABRA1, GABRA3, GABRB3, GABRG2, and GABRD, encoding the alpha1-, alpha3-, beta2-, gamma3-, and delta-subunits have been directly associated with epilepsy. Specific combinations of alpha, beta, and gamma subunits exhibit ethanol sensitivity." 184 matched cddid_all.tbl CDD cd18999 cd18999 349800 LGIC_ECD_GABAAR_B extracellular domain of gamma-aminobutyric acid receptor subunit beta (GABAAR-B or GABRB). This family contains extracellular domain (ECD) of beta subunits of type-A gamma-aminobutyric acid receptor (GABAAR), which include beta1-beta4 in vertebrates. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. Benzodiazepine and barbiturates each bind to their own distinct sites on the LBD. The channels must contain the gamma subunit and alpha subunits in order to respond to benzodiazepines. Specific combinations of alpha, beta, and gamma subunits exhibit ethanol sensitivity. All these major classes of drugs favor channel-opening. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. Mutations or genetic variations of the genes encoding the GABRB2 and GABRB3 have been associated with human epilepsy, both with and without febrile seizures. Mutations in GABRB2, and GABRB3 have been associated with infantile spasms and Lennox-Gastaut syndrome. A de novo missense mutation of GABRB2 causes early myoclonic encephalopathy, a disease with a devastating prognosis, characterized by neonatal onset of seizures. Another de novo heterozygous missense variant in exon 4 of GABRB2 is associated with intellectual disability and epilepsy. Mutations in the GABRB1 gene promote alcohol consumption through increased tonic inhibition. 182 matched cddid_all.tbl CDD cd19000 cd19000 349801 LGIC_ECD_GABAAR_G extracellular domain of gamma-aminobutyric acid receptor subunit gamma. This family contains extracellular domain (ECD) of the theta subunit of type-A gamma-aminobutyric acid receptor (GABAAR). GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. GABA stimulates human hepatocellular carcinoma growth through overexpressed GABAA receptor theta subunit. Also, two autism spectrum disorder (ASD)-associated protein truncation variants have been identified in alpha 3 (GABRA3) and theta (GABRQ) genes. 182 matched cddid_all.tbl CDD cd19001 cd19001 349802 LGIC_ECD_GABAAR_delta extracellular domain of gamma-aminobutyric acid receptor subunit delta. This family contains extracellular domain of delta subunit of type-A gamma-aminobutyric acid receptor (GABAAR). GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ligand binding site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. Receptors containing the delta subunit (GABRD) are expressed exclusively extra-synaptically (in the cortex, hippocampus, thalamus, striatum, and cerebellum) and mediate tonic inhibition. Studies suggest that delta subunits form heteropentamers in similar stoichiometry and arrangement as alpha/beta/gamma receptors, with the delta subunit replacing the gamma subunit (2alpha:2beta:1delta), although other stoichiometries have also been detected. The delta subunit is flexible in its positioning in the pentameric complex, producing receptors with diverse pharmacological properties. Mutations in GABRD have been associated with susceptibility to generalized epilepsy with febrile seizures, type 5. GABRD gene may also be associated with childhood-onset mood disorders. 184 matched cddid_all.tbl CDD cd19002 cd19002 349803 LGIC_ECD_GABAAR_E extracellular domain of gamma-aminobutyric acid receptor subunit epsilon (GABRE). This family contains extracellular domain of epsilon subunit of type-A gamma-aminobutyric acid receptor (GABAAR), a protein that is encoded by the GABRE gene in humans. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ligand binding site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. The epsilon subunits form heteropentamers with other GABAAR subunits, possibly with alpha3, beta4, and theta subunits since their genes are clustered on the same human chromosome. Various combinations of alpha3-, theta-, and epsilon-subunits may be assembled at a regional and developmental level in the brain. Brainstem expression of epsilon subunit-containing GABAA receptors is upregulated during pregnancy, particularly in the ventral respiratory neurons, thus protecting breathing, despite increased neurosteroid levels during pregnancy. 182 matched cddid_all.tbl CDD cd19003 cd19003 349804 LGIC_ECD_GABAAR_theta extracellular domain of gamma-aminobutyric acid receptor subunit theta (GABRQ). This family contains extracellular domain (ECD) of the theta subunit of type-A gamma-aminobutyric acid receptor (GABAAR), and encoded by the GABRQ gene, which is mapped to chromosome Xq28 in a cluster of genes that also that encode the alpha 3 and epsilon subunits. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. GABA stimulates human hepatocellular carcinoma growth through overexpressed GABAAR theta subunit. Also, two autism spectrum disorder (ASD)-associated protein truncation variants have been identified in alpha 3 (GABRA3) and theta (GABRQ) genes. 183 matched cddid_all.tbl CDD cd19004 cd19004 349805 LGIC_ECD_GABAAR_pi extracellular domain of gamma-aminobutyric acid receptor subunit pi (GABRP). This family contains extracellular domain of pi subunit of type-A gamma-aminobutyric acid receptor (GABAAR). GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ligand binding site on ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. GABRP is expressed mainly in non-neuronal tissues such as the mammary gland, prostate gland, lung, thymus, and uterus. It is also highly expressed in certain types of cancer such as basal-like breast cancer and pancreatic ductal adenocarcinoma. GABRP is involved in inhibitory synaptic transmission in the central nervous system. Its assembly with other GABAAR subunits alters the sensitivity of recombinant receptors to modulatory agents such as pregnanolone. Studies suggest that polymorphisms in the GABRP gene may be associated with the susceptibility to systematic lupus erythematosus (SLE). 182 matched cddid_all.tbl CDD cd19005 cd19005 349806 LGIC_ECD_GABAAR_rho extracellular domain of gamma-aminobutyric acid receptor subunit rho. This family contains extracellular domain of rho subunits (rho1, rho2, and rho3, encoded by GABRR1, GABRR2, and GABRR3, respectively) of type-A gamma-aminobutyric acid receptor (GABAAR). These subunits homo-oligomerize to form GABAA-rho receptors (formerly classified as GABA-rho or GABAC receptor), but do not co-assemble with any of the classical GABAA subunits. They are especially high expression in the retina and their distinctive pharmacological properties are unique; they are not modulated by many GABAA receptor modulators such as barbiturates, benzodiazepines, and neuroactive steroids. In humans, mutations in the GABRR1 and GABRR2 genes may be responsible for some cases of autosomal recessive retinitis pigmentosa. Variation in GABRR1 is also associated with susceptibility to bipolar schizoaffective disorder while a SNP in GABRR2 has been reported to show association with autism. 186 matched cddid_all.tbl CDD cd19006 cd19006 349807 LGIC_ECD_GABAAR_LCCH3-like gamma-aminobutyric acid receptor subunit beta-like extracellular domain in protostomia, such as LCCH3 (ligand-gated chloride channel homolog 3). This family contains extracellular domain of beta-like subunits of type-A gamma-aminobutyric acid receptor (GABAAR) found in protostomia, similar to Drosophila melanogaster ligand-gated chloride channel homolog 3 (LCCH3) subunits. Drosophila melanogaster expresses three GABA-receptor subunit orthologs: (RDL, resistant to dieldrin; GRD, GABA/glycine-like receptor of Drosophila; LCCH3, ligand-gated chloride channel homolog 3), and may possibly form homo- and/or heteropentameric associations. LCCH3 has been shown to combine with subunit GRD to form cation-selective GABA-gated ion channels when coexpressed in Xenopus laevis oocytes. GABAARs are known to be the molecular targets of a class of insecticides. The resulting pentameric receptors in this family have been shown to be activated by insect GABA-receptor agonists muscimol and CACA, and blocked by antagonists fipronil, dieldrin, and picrotoxin, but not bicuculline. GABAARs are abundant in the CNS, where their physiological role is to mediate fast inhibitory neurotransmission. In insects, this inhibitory transmission plays a crucial role in olfactory information processing. 183 matched cddid_all.tbl CDD cd19007 cd19007 349808 LGIC_ECD_GABAR_GRD-like gamma-aminobutyric acid receptor subunit alpha-like extracellular domain in protostomia, such as GRD (GABA/glycine-like receptor of Drosophila). This family contains extracellular domain of alpha-like subunits of type-A gamma-aminobutyric acid receptor (GABAAR) found in protostomia, similar to Drosophila melanogaster GABA/ glycine-like receptor of Drosophila (GRD) subunits. Drosophila melanogaster expresses three GABA-receptor subunit orthologs: (RDL, resistant to dieldrin; GRD, GABA/glycine-like receptor of Drosophila; LCCH3, ligand-gated chloride channel homolog 3), and may possibly form homo- and/or heteropentameric associations. LCCH3 has been shown to combine with subunit GRD to form cation-selective GABA-gated ion channels when co-expressed in Xenopus laevis oocytes. GABAARs are known to be the molecular targets of a class of insecticides. The resulting pentameric receptors in this family have been shown to be activated by insect GABA-receptor agonists muscimol and CACA, and blocked by antagonists fipronil, dieldrin, and picrotoxin, but not bicuculline. GABAARs are abundant in the CNS, where their physiological role is to mediate fast inhibitory neurotransmission. In insects, this inhibitory transmission plays a crucial role in olfactory information processing. 183 matched cddid_all.tbl CDD cd19008 cd19008 349809 LGIC_ECD_GABAR_RDL-like gamma-aminobutyric acid receptor subunit beta-like extracellular domain in protostomia, such as RDL (resistant to dieldrin). This family contains extracellular domain of beta-like subunits of type-A gamma-aminobutyric acid receptor (GABAAR) found in protostomia, similar to Drosophila melanogaster resistant to dieldrin (RDL) subunits. Drosophila melanogaster expresses three GABA-receptor subunit orthologs: (RDL, resistant to dieldrin; GRD, GABA/glycine-like receptor of Drosophila; LCCH3, ligand-gated chloride channel homolog 3), and may possibly form homo- and/or heteropentameric associations. GABAARs are known to be the molecular targets of a class of insecticides. The resulting pentameric receptors in this family have been shown to be activated by insect GABA-receptor agonists muscimol and CACA, and blocked by antagonists fipronil, dieldrin, and picrotoxin, but not bicuculline. GABAARs are abundant in the CNS, where their physiological role is to mediate fast inhibitory neurotransmission. In insects, this inhibitory transmission plays a crucial role in olfactory information processing. Bombyx mori includes three RDL (RD1, RD2, RD3), one LCCH3, and one GRD subunits. Its RDL1 gene has RNA-editing sites, and the RDL1 and RDL3 genes possess alternative splicing, enhancing the diversity of its GABA-receptor gene family. The three RDL subunits may have arisen from two duplication events. 184 matched cddid_all.tbl CDD cd19009 cd19009 349810 LGIC_ECD_GlyR_alpha extracellular domain of glycine receptor alpha subunit. This subfamily contains extracellular domain of glycine receptor (GlyR or GLR) alpha subunits of the amino acid neurotransmitter glycine. GlyR has four known isoforms of alpha-subunit (alpha1-4, encoded by GLRA1, GLRA2, GLRA3, GLRA4) that are essential to bind ligands, and, along with the GlyR beta subunit, have been described to have a regionally and temporally controlled expression during development and maturation of the central nervous system (CNS). These alpha subunits are highly homologous, but differ in their kinetic properties, temporal and regional expression and physiological functions. They can form functional chloride-permeable GlyR ion channels by forming homopentamers with 5 alpha subunits or heteropentamers with a combination of alpha and beta subunits, either a 2alpha-3beta or 3alpha-2beta stoichiometry. In human, mutations in glycine receptor alpha subunits cause disruption of GlyR surface expression or reduced ability of expressed GlyRs to conduct chloride ions. Mutations in GlyR alpha1 subunit leads to hyperekplexia, a rare neurological disorder characterized by neonatal hypertonia and exaggerated startle responses to unexpected stimuli, while mutations in GlyR alpha2 are known to cause cortical neuronal migration/autism spectrum disorder and in GlyR alpha3 to cause inflammatory pain sensitization/rhythmic breathing. GlyR alpha1 and alpha2 subunits have an important role in regulation of the excitatory-inhibitory balance, control of motor actions, modulation of sedative ethanol effects and probably regulation ethanol preference and consumption. 184 matched cddid_all.tbl CDD cd19010 cd19010 349811 LGIC_ECD_GlyR_beta extracellular domain of glycine receptor beta subunit. This subfamily contains extracellular domain of glycine receptor (GlyR or GLR) beta subunit of the amino acid neurotransmitter glycine encoded by GLRB gene. These subunits form heteropentamers with a combination of alpha and beta subunits, either a 2alpha-3beta or 3alpha-2beta stoichiometry. While the alpha subunits contain binding sites for agonists and antagonists and are responsible for ion channel formation, the beta subunit displays structural and regulatory functions, such as GlyR clustering in synaptic locations by interaction between intracellular loop domains with the scaffolding protein gephyrin, and control of pharmacologic responses to agonist or allosteric modulators due in part to the presence of interfaces alpha/beta and beta/beta. GLRB gene mutations are associated with the neurological disorder hyperekplexia, a rare neurological disorder characterized by neonatal hypertonia and exaggerated startle responses to unexpected stimuli, as well as agoraphobic cognitions. 187 matched cddid_all.tbl CDD cd19011 cd19011 349812 LGIC_ECD_5-HT3A extracellular domain of serotonin 5-hydroxytryptamine receptor (5-HT3) receptor subunit A (5HT3A). This subfamily contains extracellular domain of subunit A of serotonin 5-HT3 receptor (5-HT3AR), encoded by the HTR3A gene. 5-HT3A subunit forms a homopentameric complex or a heterologous combination with other subunits (B-E). Heteromeric combination of A and B subunits provides the full functional features of this receptor, since either subunit alone results in receptors with very low conductance and response amplitude. 5-HT3A receptors are located in the dorsal vagal complex of the brainstem and in the gastrointestinal (GI) tract, and form a channel circuit that controls gut motility, secretion, visceral perception, and the emesis reflex. These receptors are implicated in several GI and psychiatric disorder conditions including anxiety, depression, bipolar disorder, and irritable bowel syndrome (IBS). Several 5-HT3AR antagonists, such as the isoquinoline Palonosetron, are in clinical use to control emetic reflexes associated with gastrointestinal pathologies and cancer therapies. SNPs in the 5-HT3A serotonin receptor gene are associated with psychiatric disorders. 208 matched cddid_all.tbl CDD cd19012 cd19012 349813 LGIC_ECD_5-HT3B extracellular domain of serotonin 5-hydroxytryptamine receptor (5-HT3) receptor subunit B (5HT3B). This subfamily contains extracellular domain of subunit B of serotonin 5-HT3 receptor (5-HT3BR), encoded by the HTR3B gene. 5-HT3B is not functional as a homopentameric complex and is co-expression with the 5-HT3A subunit, resulting in heteromeric 5-HT3AB receptors that are functionally distinct from homomeric 5-HT3A receptors. This receptor causes fast, depolarizing responses in neurons after activation, with affinities of competitive ligands at the two receptor subtypes extracellular domains mostly similar. HTR3B gene variants may contribute to variability in severity of and response to anti-emetic therapy for nausea and vomiting in pregnancy, as well as efficacy of ondansetron in cancer chemotherapy, radiation therapy, or surgery. 5-HT3B subunit affects high-potency inhibition of 5-HT3 receptors by morphine by reducing its affinity at its high-affinity, non-competitive site. 210 matched cddid_all.tbl CDD cd19013 cd19013 349814 LGIC_ECD_5-HT3C_E extracellular domain of serotonin 5-hydroxytryptamine receptor (5-HT3) receptor subunit E (5HT3E); may include subunits C and D (5-HT3C,D). This subfamily contains extracellular domain of subunit E of serotonin 5-HT3 receptor (5-HT3ER), encoded by the HTR3E gene, and may also contain subunits C and D, all three encoding genes forming a cluster on chromosome 3. Data show that 5-HT3C, 5-HT3D, and 5-HT3E subunits are co-expressed with 5-HT3A in cell bodies of myenteric neurons, and that 5-HT3A and 5-HT3D are expressed in submucosal plexus of the human large intestine while HTR3E is restricted to the colon, intestine, and stomach. None of these subunits can form functional homopentamers, but, upon co-expression with the 5-HT3A subunit, they give rise to functional receptors that differ in maximal responses to 5-HT, and thus modulate 5-HT3 receptor's pharmacological profile. HTR3A and HTR3E polymorphisms have been shown to remarkably up-regulate the expression of 5-HT3 receptors, which have been proved to cause the gastric functional disorders including emesis, eating disorders and IBS-D. 215 matched cddid_all.tbl CDD cd19014 cd19014 349815 LGIC_ECD_nAChR_A1 extracellular domain of nicotinic acetylcholine receptor subunit alpha 1 (CHRNA1). This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 1 (alpha1), encoded by the CHRNA1 gene. These muscle type nicotinic subunits form heteropentamers with other nAChR subunits, most broadly expressed as combination of two alpha1, beta1, delta, and epsilon subunits in mature muscles, and of two alpha1, beta1, delta, and gamma in embryonic cells. The alpha1 subunit in human nAChR is the primary target of Myasthenia gravis antibodies that disrupt communication between the nervous system and the muscle, causing chronic muscle weakness. 210 matched cddid_all.tbl CDD cd19015 cd19015 349816 LGIC_ECD_nAChR_A2 extracellular domain of nicotinic acetylcholine receptor subunit alpha 2 (CHRNA2). This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 2 (alpha2), encoded by the CHRNA2 gene. It is specifically expressed in medial subpallium-derived amygdalar nuclei from early developmental stages to adult. This subunit is incorporated in heteropentameric neuronal nAChRs mainly with beta2 or beta4 subunits and, along with the alpha4 and alpha7, is one of the main nAChR subunits expressed in primate brain. In Xenopus laevis oocytes, when alpha2 is co-expressed with the beta2 subunit, two subtypes of alpha2beta2 nAChR are formed with either low or high ACh sensitivity. Mouse mutation studies show that alpha2 subunits in the nAChRs influence hippocampus-dependent learning and memory as well as CA1 synaptic plasticity in adolescent mice. 207 matched cddid_all.tbl CDD cd19016 cd19016 349817 LGIC_ECD_nAChR_A3 extracellular domain of nicotinic acetylcholine receptor subunit alpha 3 (CHRNA3). This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 3 (alpha3), encoded by the CHRNA3 gene, and likely plays a role in neurotransmission. The alpha3 subunit is expressed in the aorta and macrophages, and may play a regulatory role in the process of vascular inflammation. One of the most broadly expressed subtype is the alpha3beta4 nAChR, also known as the ganglion-type nicotinic receptor, located in the autonomic ganglia and adrenal medulla, where activation yields post- and/or presynaptic excitation, mainly by increased Na+ and K+ permeability. The exact pentameric stochiometry of alpha3beta4 receptor is not known and functional assemblies with varying subunit stoichiometries are possible. Alpha4 plays a pivotal role in regulating the inflammatory responses in endothelial cells and macrophages, via mechanisms involving the modulations of multiple cell signaling pathways. Polymorphisms in this gene (CHRNA3) have been associated with an increased risk of smoking initiation and an increased susceptibility to lung cancer. 207 matched cddid_all.tbl CDD cd19017 cd19017 349818 LGIC_ECD_nAChR_A4 extracellular domain of neuronal acetylcholine receptor subunit alpha 4 (CHRNA4). This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 4 (alpha4), encoded by the CHRNA4 gene. Alpha4 forms a functional nAChR by interacting with either nAChR beta2 or beta4 subunits. Alpha4beta2, the major heteropentameric nAChR in the brain, exists in two isoforms, (alpha4)3(beta2)2 and (alpha4)2(beta2)3, with the latter believed to constitute the majority of alpha4beta2 nAChR in the cortex. Both isoforms contain two canonical alpha4:beta2 ACh-binding sites with either low or high ACh sensitivity. This protein is an integral membrane receptor subunit that can interact with either nAChR beta-2 or nAChR beta-4 to form a functional receptor. Mutations in this gene (CHRNA4) cause nocturnal frontal lobe epilepsy type 1. Polymorphisms in this gene may provide protection against nicotine addiction. 181 matched cddid_all.tbl CDD cd19018 cd19018 349819 LGIC_ECD_nAChR_A5 extracellular domain of nicotinic acetylcholine receptor subunit alpha 5 (CHRNA5). This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 5 (alpha5), encoded by the CHRNA5 gene, which is part of the CHRNA5/A3/B4 gene cluster. Polymorphisms in this gene cluster have been identified as risk factors for nicotine dependence, lung cancer, chronic obstructive pulmonary disease, alcoholism, and peripheral arterial disease. A loss-of-function polymorphism in CHRNA5 is strongly linked to nicotine abuse and schizophrenia; the alpha5 nAChR subunit is strategically situated in the prefrontal cortex (PFC), where a loss-of-function in this subunit may contribute to cognitive disruptions in both disorders. Alpha5 forms heteropentamers with alpha3beta2 or alpha3beta4 nAChRs which increases the calcium permeability of the resulting receptors possibly playing significant roles in the initiation of ACh-induced signaling cascades under normal and pathological condition. Acetylcholine (ACh) release and signaling via alpha4/beta2 nAChR subunits plays a central role in the control of attention, but a subset of these oligomers also contains alpha5 subunit. A strong association is seen between a CHRNA5 polymorphism and the risk of lung cancer, especially in smokers. 207 matched cddid_all.tbl CDD cd19019 cd19019 349820 LGIC_ECD_nAChR_A6 extracellular domain of nicotinic acetylcholine receptor subunit alpha 6 (CHRNA6). This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 6 (alpha6), encoded by the CHRNA6 gene. Human (alpha6beta2)(alpha4beta2)3 nicotinic acetylcholine receptors (AChRs) are essential for addiction to nicotine and a target for drug development for smoking cessation. In xenopus oocytes, data show efficient expression of (alpha6beta2)2beta3 AChR subunits with only small changes in alpha6 subunits, while not altering AChR pharmacology or channel structure. Alternatively spliced transcript variants have been observed for this gene. Single nucleotide polymorphisms in this gene have been associated with both nicotine and alcohol dependence. CHRNA6 has a cellular expression signature for retinal ganglion cells with high correlation to Thy1, a known marker, and is preferentially expressed by retinal ganglion cells (RGCs) in the young and adult mouse retina and expression is reduced in glaucoma. A genetic variant in CHRNB3#CHRNA6 cluster is associated with esophageal adenocarcinoma. 181 matched cddid_all.tbl CDD cd19020 cd19020 349821 LGIC_ECD_nAChR_A7 extracellular domain of neuronal acetylcholine receptor subunit alpha 7 (CHRNA7). This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 7 (alpha7), encoded by the CHRNA7 gene. Alpha7 subunits form a homo-pentameric channel, displays marked permeability to calcium ions and is a major component of brain nicotinic receptors that are blocked by, and highly sensitive to, alpha-bungarotoxin. This protein is ubiquitously expressed in both the central nervous system and in the periphery, in several tissues, including adrenal, small intestine, testis, and stomach. CHRNA7 is located in a region identified as a major susceptibility locus for juvenile myoclonic epilepsy and a chromosomal location involved in the genetic transmission of schizophrenia. It is also genetically linked to other disorders with cognitive deficits, including bipolar disorder, ADHD, Alzheimer's disease, and Rett syndrome. An evolutionarily recent partial duplication of CHRNA7 on chromosome 15 forms a new gene, CHRFAM7A or FAM7A, which encodes the protein dup-alpha7. This protein assembles with alpha7 subunits, results in fewer binding sites and is a dominant negative regulator of alpha7 nAChR function. 180 matched cddid_all.tbl CDD cd19021 cd19021 349822 LGIC_ECD_nAChR_A7L "extracellular domain of neuronal acetylcholine receptor subunit alpha-7-like. This family contains the extracellular domain of nicotinic acetylcholine receptor (nAChR), a member of the pentameric ""Cys-loop"" superfamily of transmitter-gated ion channels. nAChR is found in high concentrations at the nerve-muscle synapse, where it mediates fast chemical transmission of electrical signals in response to the endogenous neurotransmitter acetylcholine (ACh) released from the nerve terminal into the synaptic cleft. Thus far, seventeen nAChR subunits have been identified, including ten alpha subunits, four beta subunits and one gamma, delta, and epsilon subunit each, all found on the cell membrane that non-selectively conducts cations (Na+, K+, Ca++). These nAChR subunits combine in several different ways to form functional nAChR subtypes which are broadly categorized as either muscle subtype located at the neuromuscular junction or neuronal subtype that are found on neurons and on other cell types throughout the body. The muscle type of nAChRs are formed by the alpha1, beta1, gamma, delta, and epsilon subunits while the neuronal type are composed of nine alpha subunits and three beta subunits, which combine in various permutations and combinations to form functional receptors. Among various subtypes of neuronal nAChRs, the homomeric alpha7 and the heteromeric alpha4beta2 receptors are the main subtypes widely distributed in the brain and implicated in the pathophysiology of neurodevelopmental disorders such as schizophrenia and autism and neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease." 179 matched cddid_all.tbl CDD cd19022 cd19022 349823 LGIC_ECD_nAChR_A9 extracellular domain of neuronal acetylcholine receptor subunit alpha 9 (CHRNA9). This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 9 (alpha9), encoded by the CHRNA9 gene. This protein is involved in cochlea hair cell development and is also expressed in the outer hair cells (OHCs) of the adult cochlea as well as in keratinocytes, the pituitary gland, B-cells, and T-cells. Mammalian alpha9 subunits can form functional homomeric alpha9 receptors as well as the heteromeric alpha9alpha10 receptors, the latter being atypical since the heteromeric alpha9alpha10 receptor is composed only of alpha subunits compared to nAChRs typically assembled from alpha and beta subunits. A stoichiometry of (alpha9)2(alpha10)3 has been determined for the rat recombinant receptor. The alpha9alpha10 nAChR is an important therapeutic target for pain; selective block of alpha9alpha10 nicotinic acetylcholine receptors by the conotoxin RgIA has been shown to be analgesic in an animal model of nerve injury pain, and accelerates recovery of nerve function after injury, possibly through immune/inflammatory-mediated mechanisms. CHRNA9 polymorphisms are associated with non-small cell lung cancer, and effect of a particular SNP (rs73229797) and passive smoking exposure on risk of breast malignancy has been observed. 207 matched cddid_all.tbl CDD cd19023 cd19023 349824 LGIC_ECD_nAChR_A10 extracellular domain of neuronal acetylcholine receptor subunit alpha 10 (CHRNA10). This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha 10 (alpha10), encoded by the CHRNA10 gene. This protein is involved in cochlea hair cell development and is also expressed in the outer hair cells (OHCs) of the adult cochlea as well as in keratinocytes, the pituitary gland, B-cells, and T-cells. Unlike alpha9 nAChR subunits, alpha10 subunits do not generate functional channels when expressed heterologously, suggesting that alpha10 might serve as a structural subunit, much like a beta subunit of heteromeric receptors, providing only complementary components to the agonist binding site. Mammalian alpha10 subunits can form functional heteromeric alpha9alpha10 receptors, an atypical heteromeric receptor since it is composed only of alpha subunits compared to nAChRs typically assembled from alpha and beta subunits. A stoichiometry of (alpha9)2(alpha10)3 has been determined for the rat recombinant receptor. The alpha9alpha10 nAChR is an important therapeutic target for pain; selective block of alpha9alpha10 nicotinic acetylcholine receptors by the conotoxin RgIA has been shown to be analgesic in an animal model of nerve injury pain, and accelerates recovery of nerve function after injury, possibly through immune/inflammatory-mediated mechanisms. 181 matched cddid_all.tbl CDD cd19024 cd19024 349825 LGIC_ECD_nAChR_B1 extracellular domain of nicotinic acetylcholine receptor subunit beta 1 (CHRNB1). This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit beta 1 (beta1), encoded by the CHRNB1 gene. It is a muscle type subunit found predominantly in the neuromuscular junction (NMJ), but also in other tissues and cell lines such as adrenal glands, carcinomas, brain, and lung. Simultaneous mRNA and protein expression of beta1 nAChR subunit is present in human placenta and skeletal muscle. The beta1 nAChR subunit forms a heteropentamer with either (alpha1)2, gamma and delta subunits in embryonic type or (alpha1)2, epsilon and delta subunits in adult type receptors. nAChRs containing beta1 subunits have been attributed to efficient clustering and anchoring of the receptors to the cytoskeleton which is important for formation of synapses in the NMJ. Mutations in the transmembrane domain region of this gene are associated with slow-channel congenital myasthenic syndrome (CMS). 213 matched cddid_all.tbl CDD cd19025 cd19025 349826 LGIC_ECD_nAChR_B2 extracellular domain of nicotinic acetylcholine receptor subunit beta 2 (CHRNB2). This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit beta 2 (beta2), encoded by the CHRNB2 gene. The most abundant nicotinic subtype in the human brain is alpha4beta2 receptor which is known to assemble in two functional subunit stoichiometries, (alpha4)3(beta2)2 and (alpha4)2(beta2)3, the latter having a much higher affinity for both acetylcholine and nicotine. This subtype is implicated in the pathophysiology of neurodevelopmental disorders such as schizophrenia and autism, and neurodegenerative disorders such as Parkinson's disease and Alzheimer's disease. Thus, pharmacological ligands targeting this subtype have been researched and developed as a treatment approach implicated in these diseases. They include agonists such as varenicline and cytisine used as smoking cessation aids, as well as positive allosteric modulators (PAMs) such as desformylflustrabromine (dFBr), which are ligands that bind to nicotinic receptors at sites other than the orthosteric site where acetylcholine binds, and are not able to act as agonists on nAChR. 204 matched cddid_all.tbl CDD cd19026 cd19026 349827 LGIC_ECD_nAChR_B3 extracellular domain of nicotinic acetylcholine receptor subunit beta 3 (CHRNB3). This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit beta 3 (beta3), encoded by the CHRNB3 gene. CHRNB3 polymorphisms have been reported to potentially affect nicotine-induced upregulation of nicotinic and to be associated with disorders such as schizophrenia, autism, and cancer. Beta3 subunit is depleted in the striatum of Parkinson's disease patients. Rare variants in CHRNB3 are also implicated in risk for alcohol and cocaine dependence and independently associated with bipolar disorder. Human alpha6beta2beta3* (* indicating possible additional assembly partners) nAChRs on dopaminergic neurons are important targets for drugs to treat nicotine addiction and Parkinson's disease; (alpha6beta2)(alpha4beta2)beta3 nAChR is essential for addiction to nicotine and a target for drug development for smoking cessation. 179 matched cddid_all.tbl CDD cd19027 cd19027 349828 LGIC_ECD_nAChR_B4 extracellular domain of nicotinic acetylcholine receptor subunit beta 4 (CHRNB4). This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit beta 4 (beta4), encoded by the CHRNB4 gene and ubiquitously expressed on lung epithelial cells. The cluster of human neuronal nicotinic receptor gene CHRNA5-CHRNA3-CHRNB4 is related to drug-related behaviors and the development of lung cancer. One of the most broadly expressed subtype is the alpha-3 beta-4 nAChR, also known as the ganglion-type nicotinic receptor, located in the autonomic ganglia and adrenal medulla, where activation yields post- and/or pre-synaptic excitation, mainly by increased Na+ and K+ permeability. Beta4 forms heteromeric nAchRs to modulate receptor affinity for nicotine, but the exact pentameric stochiometry of alpha3beta4 receptor is not known; functional assemblies with varying subunit stoichiometries are possible. 178 matched cddid_all.tbl CDD cd19028 cd19028 349829 LGIC_ECD_nAChR_D extracellular domain of nicotinic acetylcholine receptor subunit delta (CHRND). This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit delta (delta), encoded by the CHRND gene and found in the muscle. Delta nAChR subunit forms a heteropentamer with either (alpha1)2, beta and gamma subunits in embryonic type or (alpha1)2, beta and epsilon subunits in adult type receptors. Defects in this gene are a cause of multiple pterygium syndrome lethal type (MUPSL), congenital myasthenic syndrome slow-channel type (SCCMS), and congenital myasthenic syndrome fast-channel type (FCCMS). The slow-channel congenital myasthenic syndromes (SCCMS) are caused by prolonged opening episodes of AChR due to dominant gain-of-function mutations in the transmembrane regions of the heteropentamer. These mutations produce an increase in the channel opening rate, a decrease in the channel closing rate, or an increase in the affinity of ACh for the AChR, resulting in the stabilization of the open state or the destabilization of the closed state of the AChR. 221 matched cddid_all.tbl CDD cd19029 cd19029 349830 LGIC_ECD_nAChR_G extracellular domain of nicotinic acetylcholine receptor subunit gamma (CHRNG). This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit gamma (gamma), encoded by the CHRNG gene expressed during early fetal development, and replaced by the epsilon subunit in the adult. The gamma subunit forms a heteropentamer with (alpha1)2, beta, and delta and plays a role in neuromuscular organogenesis and ligand binding. Disruption of gamma subunit expression prevents the correct localization of the receptor in cell membranes. Mutations in CHRNG may cause the non-lethal Escobar variant (EVMPS) and lethal form (LMPS) of multiple pterygium syndrome (MPS), a condition characterized by prenatal growth failure with pterygium and akinesia leading to muscle weakness and severe congenital contractures, as well as scoliosis. Muscle-type acetylcholine receptor is the major antigen in the autoimmune disease myasthenia gravis. 193 matched cddid_all.tbl CDD cd19030 cd19030 349831 LGIC_ECD_nAChR_E extracellular domain of nicotinic acetylcholine receptor subunit epsilon (CHRNE). This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit epsilon (epsilon), encoded by the CHRNE gene and found in adult skeletal muscle. Epsilon subunit forms a heteropentamer with (alpha1)2, beta and delta after birth, replacing the gamma subunit seen in embryonic receptors. The adult-type epsilon-AChR has a higher conductance and a shorter open time compared to embryonic gamma-AChR and the open channel is non-selectively cation permeable. Mutations of the CHRNE gene are the most common causes of congenital myasthenic syndrome (CMS), most of which are autosomal recessive loss-of-function mutations, resulting in endplate AChR deficiency. A highly fatal fast-channel syndrome is caused by AChR epsilon subunit mutation (Trp to Arg; changing environment from anionic to cationic) at the agonist binding site at the alpha/epsilon interface of the receptor, thus disrupting agonist binding affinity and gating efficiency. 191 matched cddid_all.tbl CDD cd19031 cd19031 349832 LGIC_ECD_nAChR_proto_alpha-like extracellular domain of nicotinic acetylcholine receptor subunit alpha-like found in protostomia. This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit alpha-like in organisms that include arthropods, mollusks, annelid worms, and flat worms, and have their cholinergic system limited to the central nervous system. C. elegans genome encodes 29 acetylcholine receptor subunits, of which the levamisole-sensitive receptor (L-AChR) alpha-subunits, UNC-38, UNC-63, and LEV-8, included in this subfamily, form heteromers with the two non-alpha (also known as beta-like) subunits, UNC-29 and LEV-1. This receptor functions as the main excitatory postsynaptic receptor at neuromuscular junctions, indicating that many are expressed in neurons. Also included is the nicotinic alpha subunit MARA1 (Manduca ACh Receptor Alpha 1) which is expressed in Ca2+ responding neurons and contributes to the nicotinic responses in the neurons. In insects, the receptors supply fast synaptic excitatory transmission and represent a major target for several insecticides. In Drosophila, ten exclusively neuronal nAChRs have been identified, Dalpha1-Dalpha7 and Dbeta1-Dbeta3, and various combinations of these subunits and mutations are key to nAChR function. Alpha5 subunit is involved in alpha-bungarotoxin sensitivity while the alpha6 subunit is essential for the insecticidal effect of spinosad. nAChR agonists acetylcholine, nicotine, and neonicotinoids stimulate dopamine release in Drosophila larval ventral nerve cord and mutations in nAChR subunits affect how insecticides stimulate dopamine release. 222 matched cddid_all.tbl CDD cd19032 cd19032 349833 LGIC_ECD_nAChR_proto_beta-like extracellular domain of nicotinic acetylcholine receptor subunit beta-like found in protostomia. This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit beta-like in organisms that include arthropods, mollusks, annelid worms, and flat worms, and have their cholinergic system limited to the central nervous system. C. elegans genome encodes 29 acetylcholine receptor subunits, of which the levamisole-sensitive receptor alpha-subunits (L-AChR), UNC-38, UNC-63, and LEV-8, form heteromers with the two non-alpha (also known as beta-like) subunits, UNC-29 and LEV-1 found in this subfamily. This receptor functions as the main excitatory postsynaptic receptor at neuromuscular junctions, indicating that many are expressed in neurons. In insects, the receptors supply fast synaptic excitatory transmission and represent a major target for several insecticides. In Drosophila, ten exclusively neuronal nAChR subunits have been identified, Dalpha1-Dalpha7 and Dbeta1-Dbeta3, and various combinations of these subunits and mutations are key to nAChR function. Dbeta1 subunits in dopaminergic neurons play a role in acute locomotor hyperactivity caused by nicotine in male Drosophila. Mutations of Dbeta2 or Dalpha1 nAChR subunits in Drosophila strains have significantly lower neonicotinoid-stimulated release, but no changes in nicotine-stimulated release; they are highly resistant to the neonicotinoids nitenpyram and imidacloprid. This family also includes a novel nAChR found in Aplysia bag cell neurons (neuroendocrine cells that control reproduction) which is a cholinergic ionotropic receptor that is both, nicotine insensitive and acetylcholine sensitive. 208 matched cddid_all.tbl CDD cd19033 cd19033 349834 LGIC_ECD_nAChR_proto-like nicotinic acetylcholine receptor (nAChR) subunit extracellular domain in molluscs and annelids. This subfamily contains the extracellular domain of nicotinic acetylcholine receptor subunit found in molluscs, including several Lymnaea nAChRs, and annelids that are mostly uncharacterized. To date, 12 Lymnaea nAChRs have been identified which can be subdivided in two subtypes according to the residues that may be contributing to the selectivity of ion conductance. Phylogenetic analysis of the nAChR gene sequences suggests that anionic nAChRs in molluscs probably evolved from cationic ancestors through amino acid substitutions in the ion channel pore which is a mechanism different from acetylcholine-gated channels in other invertebrates. 183 matched cddid_all.tbl CDD cd19034 cd19034 349835 LGIC_ECD_GABAAR_A1 extracellular domain of gamma-aminobutyric acid receptor subunit alpha-1 (GABAAR-A1 or GABRA1). This family contains extracellular domain of gamma-aminobutyric acid receptor subunit alpha-1 (GABAAR-A1), a protein that is encoded by the GABRA1 gene in humans. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ligand binding site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. The alpha-1 subunits form heteropentamers with other GABAAR subunits, most broadly expressed as combination of two alpha1, beta1, gamma. Alpha1, beta2, and gamma2 subunits are clustered on the same human chromosome and may be why alpha1beta2gamma2 receptors are one of the most abundant GABAA receptor isoforms in CNS neurons. Mutations in this gene cause familial juvenile myoclonic epilepsy, sporadic childhood absence epilepsy type 4, and idiopathic familial generalized epilepsy. Polymorphisms in GABRA1 are also significantly associated with schizophrenia. GABRA1 has also been associated with methamphetamine abuse. The GABRA1 receptor is the specific target of the z-drug class of nonbenzodiazepine hypnotic agents and is responsible for their hypnotic and hallucinogenic effects. 194 matched cddid_all.tbl CDD cd19035 cd19035 349836 LGIC_ECD_GABAAR_A2 extracellular domain of gamma-aminobutyric acid receptor subunit alpha-2 (GABAAR-A2 or GABRA2). This family contains extracellular domain of gamma-aminobutyric acid receptor subunit alpha-2 (GABAAR-A2), a protein that is encoded by the GABRA2 gene in humans. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ligand binding site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. The alpha-2 subunit forms heteropentamers with other GABAAR subunits, most broadly expressed as combination of alpha2beta3gamma2. The alpha-2 (GABRA2) subunit is found primarily in the forebrain and hippocampus, and is more confined to areas of the brain compared to other alpha subunits. GABRA2 increases the risk of anxiety, making it a target for treating behavioral disorders including alcohol dependence, and drug use. GABRA2 is a binding site for benzodiazepines (psychoactive drugs known to reduce anxiety), causing chloride channels to open, leading to the hyper-polarization of the membrane. Other anxiolytic drugs such as Diazepam bind this subunit to induce inhibitory effects. GABRA2 is associated with reward behavior when it activates the insula, the part of the cerebral cortex responsible for emotions. GABA alpha2 and/or alpha3 receptor subtypes are also involved in GABAergic modulation of prolactin secretion. 203 matched cddid_all.tbl CDD cd19036 cd19036 349837 LGIC_ECD_GABAAR_A3 extracellular domain of gamma-aminobutyric acid receptor subunit alpha-3 (GABAAR-A3 or GABRA3). This family contains extracellular domain of gamma-aminobutyric acid receptor subunit alpha-3 (GABAAR-A3), a protein that is encoded by the GABRA3 gene in humans. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ligand binding site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. The alpha-3 subunit forms heteropentamers with other GABAAR subunits, most broadly expressed as combination of alpha3betagamma2, typically found post-synaptically. Rare loss-of-function variants in GABRA3 have been shown to increase the risk for a varying combination of epilepsy, intellectual disability/developmental delay, and dysmorphic features. GABRA3, normally exclusively expressed in adult brain, is also expressed in breast cancer, with high expression being inversely correlated with breast cancer survival. It activates the AKT pathway to promote breast cancer cell migration, invasion, and metastasis. GABRA3 promotes lymphatic metastasis in lung adenocarcinoma by mediating upregulation of matrix metalloproteinases, MMP-2 and MMP-9, through activation of the JNK/AP-1 signaling pathway. GABRA3 is overexpressed in human hepatocellular carcinoma growth and, with GABA, promotes the proliferation of cancer cells. 200 matched cddid_all.tbl CDD cd19037 cd19037 349838 LGIC_ECD_GABAAR_A4 extracellular domain of gamma-aminobutyric acid receptor subunit alpha-4 (GABAAR-A4 or GABRA4). This family contains extracellular domain of gamma-aminobutyric acid receptor subunit alpha-4 (GABAAR-A4), a protein that is encoded by the GABRA4 gene in humans, with biased expression in the brain and heart. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ligand binding site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. The alpha-4 subunit forms heteropentamers with other GABAAR subunits, most broadly expressed as combination of alpha2alpha4beta1gamma1, all four subunits existing on the same gene cluster. Alpha-4 is involved in the etiology of autism and eventually increases autism risk through interaction with the beta-1 (GABRB1) subunit. Polymorphism in GABRA4 may trigger migraine by ethanol, while another is associated to faster reaction times and with lower ethanol effects. A rare variant in GABRA4 may have modest physiological effect in autism spectrum disorder etiology. 199 matched cddid_all.tbl CDD cd19038 cd19038 349839 LGIC_ECD_GABAAR_A5 extracellular domain of gamma-aminobutyric acid receptor subunit alpha-5 (GABAAR-A5 or GABRA5). This family contains extracellular domain of gamma-aminobutyric acid receptor subunit alpha-5 (GABAAR-A5), a protein that is encoded by the GABRA5 gene in humans, with biased expression in the brain and heart. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ligand binding site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. The alpha-5 subunit forms heteropentamers with other GABAAR subunits, most broadly expressed as alpha5-beta-gamma2, and probably alpha5-beta3-gamma2, predominantly expressed in the hippocampus and localized extrasynaptically. These receptors have been demonstrated to play an important modulatory role in learning and memory processes, thus making them suitable targets for pharmacological intervention. Studies show that alpha5-containing GABAARs play an important part in tonic inhibition in hippocampal pyramidal neurons, and that these can also contribute to synaptic inhibition. Studies strongly suggest that amnesia is primarily mediated by alpha5-beta-gamma2. Polymorphisms in GABRA5 (and GABRA3) are linked to the susceptibility to panic disorder. A genetic association also exists between GABRA5 and bipolar affective disorder. 199 matched cddid_all.tbl CDD cd19039 cd19039 349840 LGIC_ECD_GABAAR_A6 extracellular domain of gamma-aminobutyric acid receptor subunit alpha-6 (GABAAR-A6 or GABRA6). This family contains extracellular domain of gamma-aminobutyric acid receptor subunit alpha-6 (GABAAR-A6), a protein that is encoded by the GABRA6 gene in humans. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ligand binding site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. The alpha-6 subunit forms heteropentamers with other GABAAR subunits, most broadly expressed as alpha6-beta-gamma2 found extrasynaptically, alpha6-beta2/3-delta in the cerebellar granule cells and likely also forms alpha1-alpha6-beta-gamma/alpha1-alpha6-beta-delta. A GABRA6 mutation from Arg to Trp, has been identified as a susceptibility gene that may contribute to the pathogenesis of childhood absence epilepsy and cause neuronal disinhibition and increase in seizures via a reduction of alphabetagamma and alphabetadelta receptor function and expression. Polymorphism in the GABRA6 gene is associated with specific personality characteristics as well as a marked attenuation in hormonal and blood pressure responses to psychological stress. Alpha6-containing receptors lack high sensitivity to diazepam. 198 matched cddid_all.tbl CDD cd19040 cd19040 349841 LGIC_ECD_GABAAR_B1 extracellular domain of gamma-aminobutyric acid receptor subunit beta-1 (GABAAR-B1 or GABRB1). This family contains extracellular domain (ECD) of gamma-aminobutyric acid receptor beta-1 subunit, a protein that is encoded by the GABRB1 gene. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ligand binding site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. The beta-1 subunit forms heteropentamers with other GABAAR subunits, likely expressed as alpha-beta1-gamma/delta, mainly found in the brain. It is clustered on the chromosome with genes encoding alpha 4, alpha 2, and gamma 1 subunits of the GABAAR. GABRB1 expression is altered significantly in the lateral cerebellum of subjects with schizophrenia, major depression, and bipolar disorder. Mutations in the GABRB1 gene promote alcohol consumption through increased tonic inhibition. Epigenetic control of gene expression may affect the expression of GABRB1 and disrupt inhibitory synaptic transmission during embryonic development. The GABRB1 gene is also associated with thalamus volume and modulates the association between thalamus volume and intelligence. 182 matched cddid_all.tbl CDD cd19041 cd19041 349842 LGIC_ECD_GABAAR_B2 extracellular domain of gamma-aminobutyric acid receptor subunit beta-2 (GABAAR-B2 or GABRB2). This family contains extracellular domain (ECD) of gamma-aminobutyric acid receptor beta-2 subunit, a protein that is encoded by the GABRB2 gene. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ligand binding site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. The beta-2 subunit forms heteropentamers with other GABAAR subunits, with alpha1-beta2-gamma2 subtype being the most prevalent isoform (approximately 50%-60% of all GABAARs), and are expressed in almost all regions of the brain. It also assembles less abundantly as alpha4beta2/3delta and alpha6beta2/3delta. Mutations or genetic variations of the genes encoding the GABRB2 and GABRB3 have been associated with human epilepsy, both with and without febrile seizures. Mutations in GABRB2, and GABRB3 have been associated with infantile spasms and Lennox-Gastaut syndrome. A de novo missense mutation of GABRB2 causes early myoclonic encephalopathy, a disease with a devastating prognosis, characterized by neonatal onset of seizures. Another de novo heterozygous missense variant in exon 4 of GABRB2 is associated with intellectual disability and epilepsy. GABRB2 plays important tumorigenic functions and acts as a novel oncogene in papillary thyroid carcinoma (PTC). 182 matched cddid_all.tbl CDD cd19042 cd19042 349843 LGIC_ECD_GABAAR_B3 extracellular domain of gamma-aminobutyric acid receptor subunit beta-3 (GABAAR-B3 or GABRB3). This family contains extracellular domain (ECD) of gamma-aminobutyric acid receptor beta-3 subunit, a protein that is encoded by the GABRB3 gene. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ligand binding site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. The beta-3 subunit forms heteropentamers with other GABAAR subunits, with alpha2-beta3-gamma2 and alpha3-beta3-gamma2 subtypes highly enriched in hippocampal pyramidal neurons and cholinergic neurons of the basal forebrain, respectively. Other heteromers include alpha1-beta3-gamma2 and alpha5-beta3-gamma2. GABRB3 mutations are likely associated with a broad phenotypic spectrum of epilepsies and that reduced receptor function causing GABAergic disinhibition represents the relevant disease mechanism. GABRB3 might be associated with heroin dependence, and increased expression possibly contributing to the pathogenesis of heroin dependence. This gene may also be associated with the pathogenesis of other disorders such as Angelman syndrome, Prader-Willi syndrome, nonsyndromic orofacial clefts, schizophrenia, and autism. 183 matched cddid_all.tbl CDD cd19043 cd19043 349844 LGIC_ECD_GABAAR_G1 extracellular domain of gamma-aminobutyric acid receptor subunit gamma-1 (GABAAR-G1 or GABRG1). This family contains extracellular domain of gamma-aminobutyric acid receptor subunit gamma-1 (GABAAR-G1), a protein that is encoded by the GABRG1 gene in humans, clustered with the alpha2 gene GABRA2, which is associated with alcohol dependence. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ligand binding site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. The gamma-1 subunit forms heteropentamers with other GABAAR subunits, likely expressed as combination of alpha1/2-beta-gamma1 subunits. A variant in GABRG1 shows the strongest statistical evidence of association of recovery from eating disorders. Studies show that upregulating or preserving GABAA gamma1/3 and gamma2 receptors may protect neurons against neurofibrillary pathology in Alzheimer's disease. 182 matched cddid_all.tbl CDD cd19044 cd19044 349845 LGIC_ECD_GABAAR_G2 extracellular domain of gamma-aminobutyric acid receptor subunit gamma-2 (GABAAR-G2 or GABRG2). This family contains extracellular domain of gamma-aminobutyric acid receptor subunit gamma-2 (GABAAR-G2), a protein that is encoded by the GABRG2 gene in humans. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ligand binding site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. The gamma-2 subunit forms heteropentamers with other GABAAR subunits, most prevalently expressed as alpha1-beta2-gamma2. The gamma2 subunit also coassembles with other alpha and beta variants in the brain, but these receptors are found in considerably less abundance and are restricted in their regional, e.g. the alpha2-beta3-gamma2 and alpha3-beta3-gamma2 subtypes are highly enriched in hippocampal pyramidal neurons and cholinergic neurons of the basal forebrain, respectively. Pathogenic missense and truncating variants in this gene have been associated with spectrum of epilepsies, from Dravet syndrome to milder simple febrile seizures, while a recurrent GABRG2 missense variant is associated with early-onset seizures, significant motor and speech delays, intellectual disability, hypotonia, movement disorder, dysmorphic features, and vision/ocular issues. 184 matched cddid_all.tbl CDD cd19045 cd19045 349846 LGIC_ECD_GABAAR_G3 extracellular domain of gamma-aminobutyric acid receptor subunit gamma-3 (GABAAR-G3 or GABRG3). This family contains extracellular domain of gamma-aminobutyric acid receptor subunit gamma-3 (GABAAR-G3), a protein that is encoded by the GABRG3 gene in humans. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Upon gamma-aminobutyric acid (GABA) binding to the ligand binding site on the ECD, Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. The gamma-3 subunit forms heteropentamers with other GABAAR subunits, likely expressed as alpha1-beta3-gamma3. This subunit contains the benzodiazepine binding site. Polymorphisms in GABG3 show consistent evidence of alcohol dependence. 182 matched cddid_all.tbl CDD cd19046 cd19046 349847 LGIC_ECD_GABAAR_rho1 extracellular domain of gamma-aminobutyric acid receptor subunit rho-1 (GABA-rho1 or GABRR1). This family contains extracellular domain (ECD) of the rho subunit 1 of type-A gamma-aminobutyric acid receptor (GABAAR), encoded by the GABRR1 gene, expressed in many areas of the brain, but especially high in the retina. GABRR1 exists next to GABRR2 (encoding rho subunit 2) on the chromosome region thought to be associated with susceptibility for psychiatric disorders and epilepsy. Close proximity of the rho1 and rho2 subunit genes suggests that they emerged via a local duplication event. This subunit homo-oligomerizes to form GABAA-rho receptors (formerly classified as GABA-rho or GABAc receptor), but does not co-assemble with any of the classical GABAAR subunits. In humans, mutations in the GABRR1 gene may be responsible for some cases of autosomal recessive retinitis pigmentosa. Variation in GABRR1 is also associated with susceptibility to bipolar schizoaffective disorder, and may be associated with alcohol dependency. 186 matched cddid_all.tbl CDD cd19047 cd19047 349848 LGIC_ECD_GABAAR_rho2 extracellular domain of gamma-aminobutyric acid receptor subunit rho-2 (GABA-rho2 or GABRR2). This family contains extracellular domain (ECD) of the rho subunit 2 of type-A gamma-aminobutyric acid receptor (GABAAR), encoded by the GABRR2 gene which exists next to GABRR1 (encoding rho subunit 1) on the chromosome region thought to be associated with susceptibility for psychiatric disorders and epilepsy. Close proximity of the rho1 and rho2 subunit genes suggests that they emerged via a local duplication event. Rho1 is expressed in many areas of the brain, but especially high in the retina. This subunit homo-oligomerizes to form GABAA-rho receptors (formerly classified as GABA-rho or GABAc receptor), but does not co-assemble with any of the classical GABAAR subunits. In humans, mutations in the GABRR2 gene may be responsible for some cases of autosomal recessive retinitis pigmentosa. Variation in GABRR2 is also associated with susceptibility to bipolar schizoaffective disorder, as well as alcohol dependence and general cognitive ability. GABA-rho2 receptors expressed pre-synaptically in the spinal dorsal horn have been implicated in pain perception and identified as a novel target for analgesia. 186 matched cddid_all.tbl CDD cd19048 cd19048 349849 LGIC_ECD_GABAAR_rho3 extracellular domain of gamma-aminobutyric acid receptor subunit rho-3 (GABAA-rho3). This family contains extracellular domain (ECD) of the rho subunit 3 of type-A gamma-aminobutyric acid receptor (GABAAR), encoded by the GABRR3 gene which maps to a different chromosome to that of GABRR1 and GABRR2. While close proximity of the rho1 and rho2 subunit genes suggests that they emerged via a local duplication event, GABRR3 may have arisen by duplication of a GABRR1/GABRR2 progenitor. This subunit homo-oligomerizes to form GABAA-rho receptors (formerly classified as GABA-rho or GABAc receptor), but does not co-assemble with any of the classical GABAAR subunits. In humans, some individuals contain a variant that is predicted to inactivate this gene product. 186 matched cddid_all.tbl CDD cd19049 cd19049 349851 LGIC_TM_anion transmembrane domain of anionic Cys-loop neurotransmitter-gated ion channels, includes GABAAR, GlyR and GluCl. This family contains transmembrane domain of type-A gamma-aminobutyric acid receptor (GABAAR) as well as glycine receptor (GlyR) subunits. Thus far, there are 18 vertebrate receptor subunits categorized in 7 families: alpha1-6, beta1-4, gamma1-4, delta, epsilon, theta, rho, and pi. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. GlyR, with a similar structure as GABAAR, is concentrated in the brain stem and spinal cord in the CNS and can be activated by glycine, beta-alanine, or taurine. It is selectively blocked by the high-affinity competitive antagonist strychnine, which causes death by asphyxiation. An autosomal dominant R271Q mutation in GLRA1 causes hyperekplexia (Startle disease or Stiff Baby Syndrome) by decreasing glycine sensitivity. 111 matched cddid_all.tbl CDD cd19050 cd19050 349852 LGIC_TM_bact transmembrane domain of prokaryotic pentameric ligand-gated ion channels (pLGIC). This family contains transmembrane (TM) domain of bacterial pentameric ligand-gated ion channels (pLGICs) including ones from Gloeobacter violaceus (GLIC) and Erwinia chrysanthemi (ELIC). The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. Studies show that GLIC activation is inhibited by most general anaesthetics at clinical concentrations, including xenon which has been used in clinical practice as a potent gaseous anesthetic for decades. Xenon binding sites have been identified in three distinct regions of the TMD: in a large intra-subunit cavity, in the pore, and at the interface between adjacent subunits. Propofol, the drug used for induction and maintenance of general anesthesia, and desflurane, a negative allosteric modulator of GLIC bind at the entrance in the intra-subunit cavity. Alzheimer's drug memantine, which blocks ion conduction at vertebrate pLGICs by plugging the channel pore, has been shown to have similar potency in ELIC. 119 matched cddid_all.tbl CDD cd19051 cd19051 349853 LGIC_TM_cation transmembrane domain of Cys-loop neurotransmitter-gated ion channels, includes 5HT3, nAChR, and ZAC. This superfamily contains the transmembrane (TM) domain of cationic Cys-loop neurotransmitter-gated ion channels, which include nicotinic acetylcholine receptor (nAChR), serotonin 5-hydroxytryptamine receptor (5-HT3), and zinc-activated ligand-gated ion channel (ZAC) receptor. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. The ligand-gated ion channels (LGICs) in this family are found across metazoans and have close homologs in bacteria. They are vital for communication throughout the nervous system. nAChR is a non-selective cation channel that is permeable to Na+ and K+, and some subunit combinations are also permeable to Ca2+. Na+ enters and K+ exits to allow net flow of positively charged ions inward. 5-HT3, a cation-selective channel, binds serotonin and is permeable to Na+, K+, and Ca2+. It mediates neuronal depolarization and excitation within the central and peripheral nervous systems. ZAC forms an ion channel gated by Zn2+, Cu2+, and H+ and is non-selectively permeable to monovalent cations. However, the role of ZAC in Zn2+, Cu2+, and H+ signaling require is as yet unknown. 112 matched cddid_all.tbl CDD cd19052 cd19052 349854 LGIC_TM_GABAAR_alpha transmembrane domain of alpha subunits of type-A gamma-aminobutyric acid receptor (GABAAR). This family contains transmembrane domain of type-A gamma-aminobutyric acid receptor (GABAAR) as well as glycine receptor (GlyR) subunits. Thus far, there are 18 vertebrate receptor subunits categorized in 7 families: alpha1-6, beta1-4, gamma1-4, delta, epsilon, theta, rho, and pi. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. GlyR, with a similar structure as GABAAR, is concentrated in the brain stem and spinal cord in the CNS and can be activated by glycine, beta-alanine or taurine. It is selectively blocked by the high-affinity competitive antagonist strychnine, which causes death by asphyxiation. An autosomal dominant R271Q mutation in GLRA1 causes hyperekplexia (Startle disease or Stiff Baby Syndrome) by decreasing glycine sensitivity. 111 matched cddid_all.tbl CDD cd19053 cd19053 349855 LGIC_TM_GABAAR_beta transmembrane domain of beta subunits of type-A gamma-aminobutyric acid receptor (GABAAR). This family contains transmembrane (TM) domain of the beta subunit of type-A beta-aminobutyric acid receptor (GABAAR), which includes beta1-beta4 in vertebrates. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. Mutations or genetic variations of the genes encoding beta2 (GABRB2) and beta3 (GABRB3) have been associated with human epilepsy, both with and without febrile seizures. Mutations in GABRB2, and GABRB3 have been associated with infantile spasms and Lennox-Gastaut syndrome. A de novo missense mutation of GABRB2 causes early myoclonic encephalopathy, a disease with a devastating prognosis, characterized by neonatal onset of seizures. Another de novo heterozygous missense variant in exon 4 of GABRB2 is associated with intellectual disability and epilepsy. Mutations in the GABRB1 gene encoding beta1 promote alcohol consumption through increased tonic inhibition. 111 matched cddid_all.tbl CDD cd19054 cd19054 349856 LGIC_TM_GABAAR_gamma transmembrane domain of gamma subunits of type-A gamma-aminobutyric acid receptor (GABAAR). This family contains transmembrane (TM) domain of the gamma subunit of type-A beta-aminobutyric acid receptor (GABAAR), which includes gamma1-gamma3 in vertebrates. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. Studies show upregulating or preserving GABAA gamma1/3 and gamma2 receptors may protect neurons against neurofibrillary pathology in Alzheimer's disease. Pathogenic missense and truncating variants in GABRG2 have been associated with spectrum of epilepsies, from Dravet syndrome to milder simple febrile seizures. Polymorphisms in GABG3 show consistent evidence of alcohol dependence. 111 matched cddid_all.tbl CDD cd19055 cd19055 349857 LGIC_TM_GABAAR_delta transmembrane domain of delta subunits of type-A gamma-aminobutyric acid receptor (GABAAR). This family contains transmembrane (TM) domain of the delta subunit of type-A gamma-aminobutyric acid receptor (GABAAR), encoded by the gene GABRD. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. Receptors containing the delta subunit (GABRD) are expressed exclusively extra-synaptically (in the cortex, hippocampus, thalamus, striatum, and cerebellum) and mediate tonic inhibition. Studies suggest that delta subunits form heteropentamers in similar stoichiometry and arrangement as alpha/beta/gamma receptors, with the delta subunit replacing the gamma subunit (2alpha:2beta:1delta), although other stoichiometries have also been detected. The delta subunit is flexible in its positioning in the pentameric complex, producing receptors with diverse pharmacological properties. Mutations in GABRD have been associated with susceptibility to generalized epilepsy with febrile seizures, type 5. GABRD gene may also be associated with childhood-onset mood disorders. 121 matched cddid_all.tbl CDD cd19056 cd19056 349858 LGIC_TM_GABAAR_theta transmembrane domain of theta subunits of type-A gamma-aminobutyric acid receptor (GABAAR). This family contains transmembrane (TM) domain of the theta subunit of type-A gamma-aminobutyric acid receptor (GABAAR). The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. GABA stimulates human hepatocellular carcinoma growth through overexpressed GABAA receptor theta subunit. Also, two autism spectrum disorder (ASD)-associated protein truncation variants have been identified in alpha 3 (GABRA3) and theta (GABRQ) genes. 118 matched cddid_all.tbl CDD cd19057 cd19057 349859 LGIC_TM_GABAAR_epsilon transmembrane domain of epsilon subunits of type-A gamma-aminobutyric acid receptor (GABAAR). This family contains transmembrane (TM) domain of type-A gamma-aminobutyric acid receptor (GABAAR) subunits as well as glycine receptor (GlyR). Thus far, there are 18 vertebrate receptor subunits categorized in 7 families: alpha1-6, beta1-4, gamma1-4, delta, epsilon, theta, rho, and pi. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. GlyR, with a similar structure as GABAAR, is concentrated in the brain stem and spinal cord in the CNS and can be activated by glycine, beta-alanine, or taurine. It is selectively blocked by the high-affinity competitive antagonist strychnine, which causes death by asphyxiation. An autosomal dominant R271Q mutation in GLRA1 causes hyperekplexia (Startle disease or Stiff Baby Syndrome) by decreasing glycine sensitivity. 115 matched cddid_all.tbl CDD cd19058 cd19058 349860 LGIC_TM_GABAAR_pi transmembrane domain of pi subunits of type-A gamma-aminobutyric acid receptor (GABAAR). This family contains transmembrane (TM) domain of the pi subunit of type-A gamma-aminobutyric acid receptor (GABAAR), encoded my the gene GABRP. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. GABRP is expressed mainly in non-neuronal tissues such as the mammary gland, prostate gland, lung, thymus, and uterus. It is also highly expressed in certain types of cancer such as basal-like breast cancer and pancreatic ductal adenocarcinoma. GABRP is involved in inhibitory synaptic transmission in the central nervous system. Its assembly with other GABAAR subunits alters the sensitivity of recombinant receptors to modulatory agents such as pregnanolone. Studies suggest that polymorphisms in the GABRP gene may be associated with the susceptibility to systematic lupus erythematosus (SLE). 123 matched cddid_all.tbl CDD cd19059 cd19059 349861 LGIC_TM_GABAAR_rho transmembrane domain of rho subunits of type-A gamma-aminobutyric acid receptor (GABAAR). This family contains transmembrane (TM) domain of the rho subunit of type-A gamma-aminobutyric acid receptor (GABAAR), which includes rho1-3. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. GABAAR is an anionic channel, mediating fast inhibitory synaptic transmission. Cl- ions are selectively conducted through the GABAAR pore, resulting in hyperpolarization of the neuron. GABAAR is the principal mediator of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signaling triggers hyperactive neurological disorders such as insomnia, anxiety, and epilepsy. These rho subunits homo-oligomerize to form GABAA-rho receptors (formerly classified as GABA-rho or GABAC receptor) but do not co-assemble with any of the classical GABAA subunits. They are especially high expression in the retina and their distinctive pharmacological properties are unique; they are not modulated by many GABAA receptor modulators such as barbiturates, benzodiazepines, and neuroactive steroids. In humans, mutations in the rho-1 and rho genes, GABRR1 and GABRR2, may be responsible for some cases of autosomal recessive retinitis pigmentosa. Variation in GABRR1 is also associated with susceptibility to bipolar schizoaffective disorder while a SNP in GABRR2 has been reported to show association with autism. 113 matched cddid_all.tbl CDD cd19060 cd19060 349862 LGIC_TM_GlyR_alpha transmembrane domain of alpha subunits of glycine receptor (GlyR). This family contains transmembrane (TM) domain of the alpha subunit of glycine receptor (GlyR or GLR) of the amino acid neurotransmitter glycine. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. GlyR has four known isoforms of the alpha-subunit (alpha1-4, encoded by GLRA1, GLRA2, GLRA3, GLRA4) that are essential to bind ligands and, along with the GlyR beta subunit, have been described to have a regionally and temporally controlled expression during development and maturation of the central nervous system (CNS). These alpha subunits are highly homologous but differ in their kinetic properties, temporal and regional expression and physiological functions. They can form functional chloride-permeable GlyR ion channels by forming homopentamers with 5 alpha subunits or heteropentamers with a combination of alpha and beta subunits, either a 2alpha-3beta or 3alpha-2beta stoichiometry. In human, mutations in glycine receptor alpha subunits cause disruption of GlyR surface expression or reduced ability of expressed GlyRs to conduct chloride ions. Mutations in GlyR alpha1 subunit leads to hyperekplexia, a rare neurological disorder characterized by neonatal hypertonia and exaggerated startle responses to unexpected stimuli, while mutations in GlyR alpha2 are known to cause cortical neuronal migration/autism spectrum disorder and in GlyR alpha3 to cause inflammatory pain sensitization/rhythmic breathing. GlyR alpha1 and alpha2 subunits have an important role in regulation of the excitatory-inhibitory balance, control of motor actions, modulation of sedative ethanol effects and probably regulation of ethanol preference and consumption. 120 matched cddid_all.tbl CDD cd19061 cd19061 349863 LGIC_TM_GlyR_beta transmembrane domain of beta subunits of glycine receptor (GlyR). This family contains transmembrane (TM) domain of the beta subunit of glycine receptor (GlyR or GLR) of the amino acid neurotransmitter glycine, encoded by GLRB gene. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. These subunits form heteropentamers with a combination of alpha and beta subunits, either a 2alpha-3beta or 3alpha-2beta stoichiometry. While the alpha subunits contain binding sites for agonists and antagonists and are responsible for ion channel formation, the beta subunit displays structural and regulatory functions, such as GlyR clustering in synaptic locations by interaction between intracellular loop domains with the scaffolding protein gephyrin, and control of pharmacologic responses to agonist or allosteric modulators due in part to the presence of interfaces alpha/beta and beta/beta. GLRB gene mutations are associated with the neurological disorder hyperekplexia, a rare neurological disorder characterized by neonatal hypertonia and exaggerated startle responses to unexpected stimuli, as well as agoraphobic cognitions. 114 matched cddid_all.tbl CDD cd19062 cd19062 349864 LGIC_TM_GluCl transmembrane domain of glutamate gated chloride channel (GluCl). This family contains transmembrane (TM) domain of the glutamate-gated chloride channel (GluCl) found only in protostomia but are closely related to mammalian glycine receptors. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. These GluCl channels have several roles in these invertebrates, including controlling locomotion and feeding, and mediating sensory inputs into behavior. Comparison of the GluCl gene families between organisms shows that insect gene family is relatively simple, while that found in nematodes tends to be larger and more diverse. Glutamate is an inhibitory neurotransmitter that shapes the responses of projection neurons to olfactory stimuli in the Drosophila. GluCls are targeted by the macrocyclic lactone family of anthelmintics and pesticides in arthropods and nematodes, thus making the GluCls of considerable medical and economic importance. In Drosophila melanogaster, GluCl mediates sensitivity to the antiparasitic agents ivermectin and nodulisporic acid, suggesting that their drug target is the same throughout the Ecdysozoa. 116 matched cddid_all.tbl CDD cd19063 cd19063 349865 LGIC_TM_5-HT3 transmembrane domain of 5-hydroxytryptamine 3 (5-HT3) receptor. This family contains transmembrane (TM) domain of the serotonin 5-HT3 receptors. The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. The 5-HT3 channel is cation-selective and mediates neuronal depolarization and excitation within the central and peripheral nervous systems. Like other ligand gated ion channels, the 5-HT3 receptor consists of five subunits arranged around a central ion conducting pore, which is permeable to Na+, K+, and Ca2+ ions. Binding of the neurotransmitter 5-hydroxytryptamine (serotonin) to the 5-HT3 receptor opens the channel, which then leads to an excitatory response in neurons, and the rapidly activating, desensitizing, inward current is predominantly carried by Na+ and K+ ions. This receptor is most closely related by homology to the nicotinic acetylcholine receptor (nAChR). Five subunits have been identified for this family: 5-HT3A, 5-HT3B, 5-HT3C, 5-HT3D, and 5-HT3E, encoded by HTR3A-E genes. Only 5-HT3A subunits are able to form functional homomeric receptors, whereas the 5-HT3B, C, D, and E subunits form heteromeric receptors with 5-HT3A. Different receptor subtypes are important mediators of nausea and vomiting during chemotherapy, pregnancy, and following surgery, while some contribute to neuro-gastroenterologic disorders such irritable bowel syndrome (IBS) and eating disorders as well as co-morbid psychiatric conditions. 5-HT3 receptor antagonists are established treatments for emesis and IBS, and are beneficial in the treatment of psychiatric diseases. 121 matched cddid_all.tbl CDD cd19064 cd19064 349866 LGIC_TM_nAChR transmembrane domain of nicotinic acetylcholine receptor (nAChR). This family contains transmembrane (TM) domain of the nicotinic acetylcholine receptor (nAChR). The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. nAChR is found in high concentrations at the nerve-muscle synapse, where it mediates fast chemical transmission of electrical signals in response to the endogenous neurotransmitter acetylcholine (ACh) released from the nerve terminal into the synaptic cleft. Thus far, seventeen nAChR subunits have been identified, including ten alpha subunits, four beta subunits and one gamma, delta, and epsilon subunit each, all found on the cell membrane that non-selectively conducts cations (Na+, K+, Ca++). These nAChR subunits combine in several different ways to form functional nAChR subtypes which are broadly categorized as either muscle subtype located at the neuromuscular junction or neuronal subtype that are found on neurons and on other cell types throughout the body. The muscle type of nAChRs are formed by the alpha1, beta1, gamma, delta, and epsilon subunits while the neuronal type are composed of nine alpha subunits and three beta subunits, which combine in various permutations and combinations to form functional receptors. Among various subtypes of neuronal nAChRs, the homomeric alpha7 and the heteromeric alpha4beta2 receptors are the main subtypes widely distributed in the brain and implicated in the pathophysiology of neurodevelopmental disorders such as schizophrenia and autism and neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease. Among subtypes of muscle nAChRs, the heteromeric subunits (alpha1)2, beta, gamma, and delta in fetal muscle, and the gamma subunit replaced by epsilon in adult muscle have been implicated in congenital myasthenic syndromes and multiple pterygium syndromes due to various mutations. This family also includes alpha- and beta-like nAChRs found in protostomia. 113 matched cddid_all.tbl CDD cd19065 cd19065 349867 LGIC_TM_ZAC transmembrane domain of zinc-activated ligand-gated ion channel. This family contains transmembrane (TM) domain of zinc-activated ligand-gated ion channel (ZAC). The transmembrane region consists of four transmembrane-spanning alpha-helical segments (M1-M4) that are linked by loops. The intracellular loop that links M1 and M2 determines the ion selectivity of the channel. ZAC displays low sequence similarity to other members in the superfamily, with closest matches to the human serotonin 5-HT3 receptor (5-HT3R) subunits 5-HT3A and 5-HT3B, and nAChR alpha7 subunits that exhibit approximately 15% amino acid sequence identity to ZAC. Expression of ZAC has been detected in human fetal whole brain, spinal cord, pancreas, placenta, prostate, thyroid, trachea, and stomach, as well as in adult hippocampus, striatum, amygdala, and thalamus. ZAC forms an ion channel gated by Zn2+, Cu2+, and H+, and is non-selectively permeable to monovalent cations. However, the role of ZAC in Zn2+, Cu2+, and H+ signaling is as yet unknown. 176 matched cddid_all.tbl CDD cd19066 cd19066 380453 C_NRPS-like Condensation domain of nonribosomal peptide synthetases (NRPSs). Condensation (C) domains of nonribosomal peptide synthetases (NRPSs) catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long, with various activities such as antibiotic, antifungal, antitumor and immunosuppression. There are various subtypes of C-domains such as the LCL-type which catalyzes peptide bond formation between two L-amino acids, the DCL-type which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. C-domains typically have a conserved HHxxxD motif at the active site; mutations in this motif can abolish or diminish condensation activity. 427 matched cddid_all.tbl CDD cd19067 cd19067 410989 PfuEndoQ-like lesion-specific endonuclease similar to Pyrococcus furiosus EndoQ. Pyrococcus furiosus EndoQ is a lesion-specific endonuclease which is assumed to be involved in DNA repair pathways in Thermococcales. It recognizes a deaminated base and hydrolyzes the phosphodiester bond 5' to the site of the lesion. Initially identified as a hypoxanthine-specific endonuclease, it has now been shown that EndoQ also recognizes uracil, xanthine, and apurinic/apyrimidinic (AP) sites in DNA, and that a homolog in Bacillus pumilus shares functional properties of the archaeal EndoQs. 395 matched cddid_all.tbl CDD cd19071 cd19071 381297 AKR_AKR1-5-like AKR1/2/3/4/5 family of aldo-keto reductase (AKR) and similar proteins. Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. The family includes AKR1A/B/C/D/E/G/I, AKR2A/B/C/D/E, AKR3A/B/C/D/E/G, AKR4A/B/C, AKR5A/B/C/D/E/F/G/H, and similar proteins. 251 matched cddid_all.tbl CDD cd19072 cd19072 381298 AKR_AKR3F1-like Thermotoga maritime Tm1743, Escherichia coli YeaE and similar proteins. Thermotoga maritime Tm1743 is a founding member of aldo-keto reductase family 3 member F1 (AKR3F1). It is a aldo/keto reductase family oxidoreductase. Escherichia coli YeaE may act as an aldo-keto reductase (AKR) that catalyzes the reversible reduction of ketones to the respective alcohols using NAD(P)H as a hydride donor. 263 matched cddid_all.tbl CDD cd19073 cd19073 381299 AKR_AKR3F2_3 Escherichia coli 2,5-diketo-D-gluconic acid reductase B (DkgB/YafB), Sinorhizobium meliloti isatin reductase and similar proteins. Escherichia coli DkgB/YafB (EC 1.1.1.346), also called 2,5-didehydrogluconate reductase (2-dehydro-L-gulonate-forming), or 2,5-DKG reductase B, or 2,5-DKGR B, or 25DKGR-B, is a founding member of aldo-keto reductase family 3 member F2 (AKR3F2). It catalyzes the reduction of 2,5-diketo-D-gluconic acid (25DKG) to 2-keto-L-gulonic acid (2KLG). Sinorhizobium meliloti isatin reductase is a founding member of aldo-keto reductase family 3 member F3 (AKR3F3). It is a aldo/keto reductase family oxidoreductase. 243 matched cddid_all.tbl CDD cd19074 cd19074 381300 Aldo_ket_red_shaker-like Shaker potassium channel beta subunit family and similar proteins. This family includes voltage-gated potassium channel subunits, beta-1 (KCAB1B), beta-2 (KCAB2B) and beta-3 (KCAB3B). KCAB1B and KCAB2B are cytoplasmic potassium channel subunits that modulate the characteristics of the channel-forming alpha-subunits. KCAB3B is an accessory potassium channel protein which modulates the activity of the pore-forming alpha subunit. The family also includes Drosophila melanogaster Hk protein, a founding member of aldo-keto reductase family 6 member B1 (AKR6B1), as well as voltage-gated potassium channel subunit beta (KCAB) from Arabidopsis thaliana and Egeria densa, founding members of AKR6C1and AKR6C2, respectively. Hk protein, also called hyperkinetic, is a beta subunit of Shaker (Sh) K+ channels and shows high sequence homology to aldoketoreductase. KCAB, also called Shaker channel b-subunit, or K(+) channel subunit beta, or potassium voltage beta 1, or KV-beta1, or KAB1, is a probable accessory potassium channel protein which modulates the activity of the pore-forming alpha subunit. 297 matched cddid_all.tbl CDD cd19075 cd19075 381301 AKR_AKR7A1-5 AKR7A family of aldo-keto reductase (AKR). Aflatoxin B1 aldehyde reductase member 1/3 (AKR7A1/AKR7A3/AFAR) from Rattus norvegicus, aflatoxin B1 aldehyde reductase member 2 (AKR7A2/AFAR1/AFAR) and aflatoxin B1 aldehyde reductase member 3 (AKR7A3/AFAR2) from Homo sapiens, aflatoxin B1 aldehyde reductase member 2 (AKR7A2/AFAR2) from Rattus norvegicus, and aflatoxin B1 aldehyde reductase member 2 (AKR7A2/AKR7A5/AFAR) from Mus musculus, are founding members of aldo-keto reductase family 7 member A1-5 (AKR7A1-5), respectively. AKR7A2 (EC 1.1.1.n11), also called AFB1 aldehyde reductase 1, or AFB1-AR 1, or aldoketoreductase 7, or succinic semialdehyde reductase, or SSA reductase, catalyzes the NADPH-dependent reduction of succinic semialdehyde to gamma-hydroxybutyrate (GHB). It has NADPH-dependent aldehyde reductase activity towards 2-carboxybenzaldehyde, 2-nitrobenzaldehyde and pyridine-2-aldehyde (in vitro). AKR7A2, AKR7A3 (also called AFB1 aldehyde reductase 2 or AFB1-AR 2), and AKR7A4 (also called AFB1 aldehyde reductase 3, or AFB1-AR 3, or aldoketoreductase 7-like), may be involved in protection of liver against the toxic and carcinogenic effects of aflatoxin B1 (AFB1), a potent hepatocarcinogen. They can reduce the dialdehyde protein-binding form of AFB1 to the non-binding AFB1 dialcohol. 304 matched cddid_all.tbl CDD cd19076 cd19076 381302 AKR_AKR13A_13D AKR13A and AKR13D families of aldo-keto reductase (AKR). Schizosaccharomyces pombe aldo-keto reductase YakC is a founding member of aldo-keto reductase family 13 member A1 (AKR13A1). It catalyzes the reversible reduction of ketones to the respective alcohols using NADP(+) as a hydride donor. Rauvolfia serpentina PR is a founding member of aldo-keto reductase family 13 member D1 (AKR13D1). It catalyzes the NADPH-dependent reduction of the aldehyde perakine to yield the alcohol raucaffrinoline in the biosynthetic pathway of ajmaline in Rauvolfia, a key step in indole alkaloid biosynthesis. This family also includes Arabidopsis thaliana aldo-keto reductases, ALKR1-6. 303 matched cddid_all.tbl CDD cd19077 cd19077 381303 AKR_AKR8A1-2 AKR8A family of aldo-keto reductase (AKR). Schizosaccharomyces pombe PLR and PLR2 are founding members of aldo-keto reductase family 8 member A1-2 (AKR8A1-2), respectively. PLR (EC 1.1.1.65), also called PL reductase (PL-red), catalyzes the reduction of pyridoxal (PL) with NADPH and oxidation of pyridoxine (PN) with NADP(+). 302 matched cddid_all.tbl CDD cd19078 cd19078 381304 AKR_AKR13C1_2 AKR13C family of aldo-keto reductase (AKR). The AKR13C family includes Helicobacter pyroli aldehyde reductase (AKR13C1) and Thermotoga maritima aldo-keto reductase (AKR13C2). Aldehyde reductase (EC 1.1.1.21), also called aldose reductase, is a cytosolic NADPH-dependent oxidoreductase that catalyzes the reduction of a variety of aldehydes and carbonyls, including monosaccharides. 301 matched cddid_all.tbl CDD cd19079 cd19079 381305 AKR_EcYajO-like Escherichia coli YajO and similar proteins. Escherichia coli YajO is the prototype of this family. It is an uncharacterized aldo/keto reductase family oxidoreductase. 312 matched cddid_all.tbl CDD cd19080 cd19080 381306 AKR_AKR9A_9B AKR9A and AKR9B families of aldo-keto reductase (AKR). The AKR9A family includes Aspergillus nidulans sterigmatocystin biosynthesis dehydrogenase StcV, Aspergillus flavus norsolorinic acid reductase (NOR), and Phanerochaete chrysosporium aryl-alcohol dehydrogenase [NADP(+)] (AAD), are founding members of aldo-keto reductase family 9 member A1-3 (AKR9A1-3), respectively. StcV may be involved in the dehydration of 5'-hydroxyaverantin to form averufin. NOR is involved in aflatoxin biosynthesis. AAD (EC1.1.1.91) is involved in lignin degradation and reduces aromatic benzaldehydes to their respective alcohols in the presence of NADP(H). The AKR9B family includes Saccharomyces cerevisiae aryl-alcohol dehydrogenases AAD14p, AAD3p, AAD4p, and AAD10p, which are founding members of aldo-keto reductase family 9 member B1-4 (AKR9B1-4), respectively. 307 matched cddid_all.tbl CDD cd19081 cd19081 381307 AKR_AKR9C1 AKR9C family of aldo-keto reductase (AKR). Haloferax volcanii aldo-keto reductase is a founding member of aldo-keto reductase family 9 member C1 (AKR9C1). 308 matched cddid_all.tbl CDD cd19082 cd19082 381308 AKR_AKR10A1_2 AKR10A family of aldo-keto reductase (AKR). Streptomyces bluensis aldo-keto reductase (BlmT) and Streptomyces glaucescens aldo-keto reductase (StrT) are founding members of aldo-keto reductase family 10 member A1 (AKR10A1) and A2 (AKR10A2). BlmT is bluensomycin aldo-keto reductase (AKR) and StrT is streptomycin AKR. 291 matched cddid_all.tbl CDD cd19083 cd19083 381309 AKR_AKR11A1_11D1 AKR11A and AKR11D families of aldo-keto reductase (AKR). Bacillus subtilis aldo-keto reductase IolS, also called vegetative protein 147 (VEG147), is a founding member of aldo-keto reductase family 11 member A1 (AKR11A1). It is able to reduce the standard aldo-keto reductase (AKR) substrates DL-glyceraldehyde, D-erythrose, and methylglyoxal in the presence of NADPH, albeit with poor efficiency in vitro. Bacillus aryabhattai aldo keto reductase is a founding member of aldo-keto reductase family 11 member D1 (AKR11D1). 307 matched cddid_all.tbl CDD cd19084 cd19084 381310 AKR_AKR11B1-like AKR11B1/AKR11B2 subfamily of aldo-keto reductase (AKR). Bacillus subtilis YhdN, also called general stress protein 69 (GSP69), is a founding member of aldo-keto reductase family 11 member B1 (AKR11B1). It acts as an aldo-keto reductase (AKR) that catalyzes the reversible reduction of ketones to the respective alcohols using NAD(P)H as a hydride donor. Escherichia coli YdjG is a founding member of aldo-keto reductase family 11 member B2 (AKR11B2). It catalyzes the NADH-dependent reduction of methylglyoxal (2-oxopropanal) in vitro. It may play some role in intestinal colonization. 296 matched cddid_all.tbl CDD cd19085 cd19085 381311 AKR_AKR11B3 Synechococcus sp. aldo-keto reductase (SakR1) and similar proteins. Synechococcus sp. SakR1 is a founding member of aldo-keto reductase family 11 member B3(AKR11B3). It is responsible for methylglyoxal detoxification. 292 matched cddid_all.tbl CDD cd19086 cd19086 381312 AKR_AKR11C1 AKR11C family of aldo-keto reductase (AKR). Bacillus subtilis uncharacterized oxidoreductase YqkF is a founding member of aldo-keto reductase family 11 member C1 (AKR11C1). It may function as oxidoreductase. This family also includes Bacillus halodurans AKR11C1, an NADPH-dependent 4-hydroxy-2,3-trans-nonenal reductase. 238 matched cddid_all.tbl CDD cd19087 cd19087 381313 AKR_AKR12A1_B1_C1 AKR12A, AKR12B, AKR12C families of aldo-keto reductase (AKR). Streptomyces fradiae TylCII, Saccharopolyspora erythraea EryBII, and Streptomyces avermitilis aveBVIII are founding members of aldo-keto reductase family 12 member A1 (AKR12A1), B1 (AKR12B1), and C1(AKR12C1), respectively. TylCII acts as a NDP-hexose 2,3-enoyl reductase. EryBII is a mycarose/desosamine reductase involved in L-mycarose and D-desosamine production. aveBVIII functions as a dTDP-4-keto-6-deoxy-L-hexose-2,3-reductase. 310 matched cddid_all.tbl CDD cd19088 cd19088 381314 AKR_AKR13B1 AKR13B family of aldo-keto reductase (AKR). Xylella fastidiosa phenylacetaldehyde dehydrogenase is a founding member of aldo-keto reductase family 13 member B1 (AKR13B1). phenylacetaldehyde dehydrogenase (EC 1.2.1.39) catalyzes the NAD+-dependent oxidation of phenylactealdehyde to phenylacetic acid. 256 matched cddid_all.tbl CDD cd19089 cd19089 381315 AKR_AKR14A1_2 AKR14A family of aldo-keto reductase (AKR). Escherichia coli L-glyceraldehyde 3-phosphate reductase (GPR/YghZ), also called GAP reductase, is a founding member of aldo-keto reductase family 14 member A1 (AKR14A1). It catalyzes the stereospecific, NADPH-dependent reduction of L-glyceraldehyde 3-phosphate (L-GAP). It is also involved in the stress response as a methylglyoxal reductase which converts the toxic metabolite methylglyoxal to acetol in vitro and in vivo. Salmonella enterica AKR is a founding member of aldo-keto reductase family 14 member A2 (AKR14A2). It catalyzes the conversion of 3-hydroxybutanal (3-HB) to 1,3-butanediol (1,3-BDO) by using NADPH as a cofactor. 308 matched cddid_all.tbl CDD cd19090 cd19090 381316 AKR_AKR15A-like AKR15A family of aldo-keto reductase and similar proteins. The AKR15 family includes Microbacterium luteolum pyridoxal 4-dehydrogenase (PLD), Pseudomonas sp. D-threo-aldose 1-dehydrogenase (FDH) and similar proteins. PLD (EC1.1.1.107) catalyzes irreversible oxidation of pyridoxal. FDH (EC1.1.1.122), also called (2S,3R)-aldose dehydrogenase, or L-fucose dehydrogenase, catalyzes the oxidation of L-fucose to L-fuconolactone in the presence of NADP(+). It is also active against L-galactose and, to a much lesser degree, D-arabinose. FDH (EC1.1.1.122), also called (2S,3R)-aldose dehydrogenase, or L-fucose dehydrogenase, catalyzes the oxidation of L-fucose to L-fuconolactone in the presence of NADP(+). It is also active against L-galactose and, to a much lesser degree, D-arabinose. The family also includes L-galactose dehydrogenase (L-galDH) and D-arabinose 1-dehydrogenase (ARA2). L-galDH (EC 1.1.1.316), also called L-galactose 1-dehydrogenase, catalyzes the oxidation of L-galactose to L-galactono-1,4-lactone in the presence of NAD(+). It uses NAD(+) as a hydrogen acceptor much more efficiently than NADP(+). ARA2 (EC1.1.1.116), also called NAD(+)-specific D-arabinose dehydrogenase, catalyzes the the oxidation of D-arabinose to D-arabinono-1,4-lactone in the presence of NAD(+). 278 matched cddid_all.tbl CDD cd19091 cd19091 381317 AKR_PsAKR Polaromonas Sp. aldo-keto reductase and similar proteins. The prototype of this family is an uncharacterized aldo-keto reductase from Polaromonas sp. 319 matched cddid_all.tbl CDD cd19092 cd19092 381318 AKR_BsYcsN_EcYdhF-like Bacillus subtilis YcsN, Escherichia coli YdhF and similar proteins. Bacillus subtilis YcsN and Escherichia coli YdhF are prototypes of this family. They are uncharacterized aldo/keto reductase family oxidoreductases. 287 matched cddid_all.tbl CDD cd19093 cd19093 381319 AKR_AtPLR-like Arabidopsis thaliana pyridoxal reductase (PLR) and similar proteins. Arabidopsis thaliana PLR (EC 1.1.1.65) is the prototype of this family. It catalyzes the reduction of pyridoxal (PL) with NADPH and oxidation of pyridoxine (PN) with NADP(+), and is involved in the PLP salvage pathway. 293 matched cddid_all.tbl CDD cd19094 cd19094 381320 AKR_Tas-like Escherichia coli Tas protein and similar proteins. Escherichia coli Tas protein is the prototype of this family. It is an NADP(H)-dependent aldo-keto reductase that catalyzes the reversible reduction of ketones to the respective alcohols using NADP(H) as a hydride donor. 328 matched cddid_all.tbl CDD cd19095 cd19095 381321 AKR_PA4992-like Pseudomona aeruginosa PA4992 and similar proteins. Pseudomona aeruginosa PA4992 is the prototype of this family. It is a putative aldo-keto reductase that catalyzes the reversible reduction of ketones to the respective alcohols using NAD(P)H as a hydride donor. 253 matched cddid_all.tbl CDD cd19096 cd19096 381322 AKR_Fe-S_oxidoreductase Fe-S oxidoreductase and similar proteins. The family includes a group of uncharacterized Fe-S oxidoreductase that belongs to aldo-keto reductase (AKR) superfamily. Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance in both health and industrial applications. 255 matched cddid_all.tbl CDD cd19097 cd19097 381323 AKR_unchar uncharacterized aldo-keto reductase (AKR) superfamily protein. This family includes a group of uncharacterized AKR superfamily proteins. Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance in both health and industrial applications. 267 matched cddid_all.tbl CDD cd19098 cd19098 381324 AKR_unchar uncharacterized aldo-keto reductase (AKR) superfamily protein. This family includes a group of uncharacterized AKR superfamily proteins. Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance in both health and industrial applications. 318 matched cddid_all.tbl CDD cd19099 cd19099 381325 AKR_unchar uncharacterized aldo-keto reductase (AKR) superfamily protein. This family includes a group of uncharacterized AKR superfamily proteins. Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance in both health and industrial applications. 316 matched cddid_all.tbl CDD cd19100 cd19100 381326 AKR_unchar uncharacterized aldo-keto reductase (AKR) superfamily protein. This family includes a group of uncharacterized AKR superfamily proteins. Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance in both health and industrial applications. 238 matched cddid_all.tbl CDD cd19101 cd19101 381327 AKR_unchar uncharacterized aldo-keto reductase (AKR) superfamily protein. This family includes a group of uncharacterized AKR superfamily proteins. Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance in both health and industrial applications. 304 matched cddid_all.tbl CDD cd19102 cd19102 381328 AKR_unchar uncharacterized aldo-keto reductase (AKR) superfamily protein. This family includes a group of uncharacterized AKR superfamily proteins. Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance in both health and industrial applications. 302 matched cddid_all.tbl CDD cd19103 cd19103 381329 AKR_unchar uncharacterized aldo-keto reductase (AKR) superfamily protein. This family includes a group of uncharacterized AKR superfamily proteins. Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance in both health and industrial applications. 299 matched cddid_all.tbl CDD cd19104 cd19104 381330 AKR_unchar uncharacterized aldo-keto reductase (AKR) superfamily protein. This family includes a group of uncharacterized AKR superfamily proteins. Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance in both health and industrial applications. 321 matched cddid_all.tbl CDD cd19105 cd19105 381331 AKR_unchar uncharacterized aldo-keto reductase (AKR) superfamily protein. This family includes a group of uncharacterized AKR superfamily proteins. Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance in both health and industrial applications. 250 matched cddid_all.tbl CDD cd19106 cd19106 381332 AKR_AKR1A1-4 AKR1A family of aldo-keto reductase (AKR). The AKR1A family of AKR includes alcohol dehydrogenase [NADP(+)] (ALR, EC 1.1.1.2) from Homo sapiens (AKR1A1), Sus scrofa (AKR1A2), Rattus norvegicus (liver, AKR1A3), and Mus musculus (AKR1A4). ALR, also known as aldehyde reductase, or ALDR1, catalyzes the NADPH-dependent reduction of a variety of aromatic and aliphatic aldehydes to their corresponding alcohols. In vitro substrates include succinic semialdehyde, 4-nitrobenzaldehyde, 1,2-naphthoquinone, methylglyoxal, and D-glucuronic acid. 305 matched cddid_all.tbl CDD cd19107 cd19107 381333 AKR_AKR1B1-19 AKR1B family of aldo-keto reductase (AKR). The AKR1B family of AKR includes aldose reductase (AR, EC 1.1.1.21) from Homo sapiens (AKR1B1), Oryctolagus cuniculus (kidney, AKR1B2), Mus musculus (AKR1B3), Rattus norvegicus (lens, AKR1B4), Bos taurus (lens/testis, AKR1B5), and Sus scrofa (lens, AKR1B6), aldose reductase-related protein 1 (ALD1, EC1.1.1.21) from Mus musculus (AKR1B7), Rattus norvegicus (AKR1B14), and Homo sapiens (AKR1B15), Mus musculus fibroblast growth factor induced protein (FR-1 or AKR1B8, EC 1.1.1.21), Cricetulus griseus aldose reductase-related protein 2 (ALD2 or AKR1B9, EC 1.1.1.21), aldose reductase-like from Homo sapiens (ARL-1 or AKR1B10) and Rattus norvegicus (AKR1B13), aldo-keto reductase from Gallus domesticus (eye, tongue, esophagus, AKR1B12), and Oryctolagus cuniculus AR-like protein (3beta-HSD, AKR1B19). AR, also called aldehyde reductase, catalyzes the NADPH-dependent reduction of a wide variety of carbonyl-containing compounds to their corresponding alcohols with a broad range of catalytic efficiencies. ALD1 reduces a broad range of aliphatic and aromatic aldehydes to the corresponding alcohols. It may play a role in the metabolism of xenobiotic aromatic aldehydes. FR-1, also called aldose reductase-related protein 2, or fibroblast growth factor-regulated protein (FGFRP), is induced by fibroblast growth factor-1. It may play a role in the regulation of the cell cycle. FR-1 belongs to the NADPH-dependent aldo-keto reductase family. ALD2 is an inducible aldo-keto reductase with a preference for aliphatic substrates. It can also act on small aromatic aldehydes, steroid aldehydes and some ketone substrates. ARL-1, also called aldose reductase-like, or aldose reductase-related protein (ARP), or small intestine reductase, or SI reductase, acts as all-trans-retinaldehyde reductase that can efficiently reduce aliphatic and aromatic aldehydes, and is less active on hexoses (in vitro). It may be responsible for detoxification of reactive aldehydes in the digested food before the nutrients are passed on to other organs. AKR1B15, also called estradiol 17-beta-dehydrogenase AKR1B15, is a mitochondrial aldo-keto reductase that catalyzes the reduction of androgens and estrogens with high positional selectivity (shows 17-beta-hydroxysteroid dehydrogenase activity) as well as 3-keto-acyl-CoAs. It has a strong selectivity towards NADP(H). AKR1B19 is aldose reductase-like that may show 3-beta-hydroxysteroid dehydrogenase (3beta-HSD) activity. 307 matched cddid_all.tbl CDD cd19108 cd19108 381334 AKR_AKR1C1-35 AKR1C family of aldo-keto reductase (AKR). The AKR1C family of aldo-keto reductase (AKR) includes AKR1C1 (20-alpha-hydroxysteroid dehydrogenase, also known as 20alpha-HSD), AKR1C2 (3alpha-HSD type 3), AKR1C3 (17beta-HSD type 5), and AKR1C4 (3alpha-HSD type 1) from Homo sapiens; AKR1C5 (20alpha-HSD, also known as prostaglandin-E(2) 9-reductase) from Rattus norvegicus (ovary); AKR1C6 (estradiol 17beta-HSD type 5) from Mus musculus; AKR1C7 (prostaglandin F synthase 1 or PGF1) from Bos taurus (lung); AKR1C8 (20alpha-HSD) from Rattus norvegicus (ovary); AKR1C9 (3alpha-HSD) from Rattus norvegicus (liver); AKR1C10a (Rho crystallin) from Rana temporaria and AKR1C10b (Rho crystallin) from Rana catesbeina; AKR1C11 (prostaglandin F synthase 2 or PGF2) from Bos taurus (liver); AKR1C12 (aldo-keto reductase or AKR), AKR1C13 (interleukin-3-regulated AKR), and AKR1C14 (3alpha-HSD) from Mus musculus; AKR1C15 (NADPH-dependent reductase), AKR1C16 (NAD+-preferring 3alpha/17beta/20alpha-HSD), and AKR1C17 (NAD+-dependent 3alpha-HSD) from Rattus norvegicus; AKR1C18 (20alpha-HSD), AKR1C19 (3-hydroxybutyrate dehydrogenase or 3HB dehydrogenase), AKR1C20 (3alpha(17beta)-HSD), AKR1C21 (3(17)alpha-HSD), AKR1C22 (dihydrodiol dehydrogenase or DD) from Mus musculus; AKR1C23 (20alpha-HSD) from Equus caballus; AKR1C24 (NAD+-dependent 17beta-HSD) from Rattus norvegicus; AKR1C25 (3(20)alpha-HSD) from Macaca fuscata; AKR1C26 (identical to morphine 6-dehydrogenase or M6DH, acts as NAD(+)-dependent 3alpha/17beta-HSD), AKR1C27/AKR1C28 (NAD(+)-dependent 3alpha/17beta-HSDs), AKR1C29 (identical to 3-hydroxyhexobarbital dehydrogenase or 3HBD, acts as NADPH-preferring reductase with 3alpha/3beta/17beta/20alpha-HSD activity), AKR1C30 (identical to naloxone reductase type 1 and acts as 17beta-HSD), AKR1C31 (3alpha/17beta/20alpha-HSD), AKR1C32 (identical to loxoprofen reductase and acts as 3alpha/20alpha-HSD), and AKR1C33 (identical to naloxone reductase type 2 and mainly acts as 3alpha-HSD) from Oryctolagus cuniculus; AKR1C34 (NAD+-dependent morphine 6-dehydrogenase or M6DH with 3beta/17beta/20alpha-HSD activity) and AKR1C35 (NAD+-dependent dehydrogenase with 3(17)beta-HSD activity) from Mesocricetus auratus. 303 matched cddid_all.tbl CDD cd19109 cd19109 381335 AKR_AKR1D1-3 AKR1D family of aldo-keto reductase (AKR). The AKR1D family of aldo-keto reductase includes 3-oxo-5-beta-steroid 4-dehydrogenase (EC 1.3.1.3) from Homo sapiens (AKR1D1), Rattus norvegicus (liver, AKR1D2), and Oryctolagus cuniculus (AKR1D3). 3-oxo-5-beta-steroid 4-dehydrogenase, also called delta(4)-3-ketosteroid 5-beta-reductase (EC 1.3.99.6), or delta(4)-3-oxosteroid 5-beta-reductase, or 5-beta-reductase, efficiently catalyzes the reduction of progesterone, androstenedione, 17-alpha-hydroxyprogesterone and testosterone to 5-beta-reduced metabolites. 308 matched cddid_all.tbl CDD cd19110 cd19110 381336 AKR_AKR1E1-2 AKR1E family of aldo-keto reductase (AKR). The AKR1E family of AKR includes 1,5-anhydro-D-fructose reductase (EC 1.1.1.263) from Mus musculus (liver, AKR1E1) and Homo sapiens (AKR1E2). 1,5-anhydro-D-fructose reductase), also called AF reductase, or aldo-keto reductase family 1 member C-like protein 2 (AKR1CL2), catalyzes the NADPH-dependent reduction of 1,5-anhydro-D-fructose (AF) to 1,5-anhydro-D-glucitol. AKR1E2 is a testis aldo-keto reductase (tAKR), which is also known as testis-specific protein (TSP), or LoopADR. 301 matched cddid_all.tbl CDD cd19111 cd19111 381337 AKR_AKR1G1_1I Caenorhabditis elegans aldo-keto reductase (CeAKR), Coptotermes gestroi aldo-keto reductase (CgAKR-1) and similar proteins. CeAKR is a founding member of aldo-keto reductase family 1 member G1 (AKR1G1). It may catalyze the reversible reduction of ketones to the respective alcohols using NAD(P)H as a hydride donor. Coptotermes gestroi aldo-keto reductase (CgAKR-1) is a founding member of aldo-keto reductase family 1 member I (AKR1I). It is a multipurpose enzyme with potential biotechnological applications. 286 matched cddid_all.tbl CDD cd19112 cd19112 381338 AKR_AKR2A1-2 AKR2A family of aldo-keto reductase (AKR). The AKR2A family of AKR includes AKR2A1 (NADP-dependent D-sorbitol-6-phosphate dehydrogenase or NADP-S6PDH) from Malus domestica, and AKR2A2 (NADPH-dependent mannose-6-phosphate reductase or NADPH-M6PR) from Apium graveolens. NADP-S6PDH (EC 1.1.1.200), also called aldose-6-phosphate reductase [NADPH], synthesizes sorbitol-6-phosphate, a key intermediate in the synthesis of sorbitol which is a major photosynthetic product in many members of the Rosaceae family. NADPH-M6PR (EC 1.1.1.224), also called NADPH-dependent M6P reductase, is a key enzyme involved in mannitol biosynthesis. 308 matched cddid_all.tbl CDD cd19113 cd19113 381339 AKR_AKR2B1-10 AKR2B family of aldo-keto reductase (AKR). The AKR2B family of AKR includes NAD(P)H-dependent D-xylose reductase (XR) from Pichia stipites, Kluyveromyces lactis, Pachysolen tannophilus, Candida tropicalis, and Candida tenuis, Gre3p from Saccharomyces cerevisiae, XR from Candida tropicalis, Pichia guilliermondii, Debaryomyces hansenli, and Debaryomyces nepalensis, which correspond to aldo-keto reductase family 2 member B1-B10 (AKR2B1-10), respectively. XR (EC1.1.1.307) catalyzes the NAD(P)H dependent reduction of xylose to xylitol. 310 matched cddid_all.tbl CDD cd19114 cd19114 381340 AKR_AKR2C1 AKR2C family of aldo-keto reductase (AKR). Mucor mucedo NADP-dependent 4-dihydromethyl-trisporate dehydrogenase (TDH), also called 4-dihydromethyltrisporate dehydrogenase, or 4-dihydromethyl-TA dehydrogenase, is a founding member of aldo-keto reductase family 2 member C1 (AKR2C1). It is involved in the biosynthesis of trisporic acid, the sexual hormone of zygomycetes, which induces the first steps of zygophore development. TDH catalyzes the NADP-dependent oxidation of (+) mating-type specific precursor 4-dihydromethyl-trisporate to methyl-trisporate. 302 matched cddid_all.tbl CDD cd19115 cd19115 381341 AKR_AKR2D1 AKR2D family of aldo-keto reductase (AKR). Aspergillus niger NAD(P)H-dependent D-xylose reductase xyl1 (XR, EC 1.1.1.307) is a founding member of aldo-keto reductase family 2 member D1 (AKR2D1). It catalyzes the initial reaction in the xylose utilization pathway by reducing D-xylose into xylitol in a NAD(P)H dependent manner. 311 matched cddid_all.tbl CDD cd19116 cd19116 381342 AKR_AKR2E1-5 AKR2E family of aldo-keto reductase (AKR). Bombyx mori 3-dehydroecdysone reductase is a founding member of aldo-keto reductase family 2 member E4 (AKR2E4). It is a NADP-dependent oxidoreductase with high 3-dehydroecdysone reductase activity. It may play a role in the regulation of molting and has lower activity with phenylglyoxal and isatin (in vitro). This family also includes 3-dehydroecdysone 3b-reductase from Spodoptera littoralis and Trichoplusia ni, DL-glyceraldehyde reductase from Drosophila melanogaster, aldo-keto reductase from Bombyx mori, which correspond to aldo-keto reductase family 2 member E1, E2, E3 and E5 (AKR2E1/2/3/5), respectively. 292 matched cddid_all.tbl CDD cd19117 cd19117 381343 AKR_AKR3A1-2 AKR3A family of aldo-keto reductase (AKR). Saccharomyces cerevisiae Gcy1p and Ypr1p are founding members of aldo-keto reductase family 3 member A1 (AKR3A1) and A2 (AKR3A2), respectively. Gcy1p, also called galactose-inducible crystallin-like protein 1, is a glycerol dehydrogenase involved in glycerol catabolism under microaerobic conditions. It has mRNA binding activity. Ypr1p acts as a 2-methylbutyraldehyde reductase that displays high specific activity towards 2-methylbutyraldehyde, as well as other aldehydes such as hexanal. 284 matched cddid_all.tbl CDD cd19118 cd19118 381344 AKR_AKR3B1-3 AKR3B family of aldo-keto reductase (AKR). Sporidiobolus salmonicolor NADPH-dependent aldehyde reductase 1 (ARI, EC 1.1.1.2), Trichosporonoides megachilieni NADPH-dependent erthyrose reductase (ER) 1/2 and 3, are founding members of aldo-keto reductase family 3 member B1 (AKR3B1), B2 (AKR3B2), and B3 (AKR3B3), respectively. Sporidiobolus salmonicolor NADPH-ARI, also called alcohol dehydrogenase [NADP(+)], or aldehyde reductase I, or ALR 1, catalyzes the asymmetric reduction of aliphatic and aromatic aldehydes and ketones to an R-enantiomer. It reduces ethyl 4-chloro-3-oxobutanoate to ethyl (R)-4-chloro-3-hydroxybutanoate. Trichosporonoides megachilieni NADPH-ERs catalyze the reduction of D-erythrose. 283 matched cddid_all.tbl CDD cd19119 cd19119 381345 AKR_AKR3C1 Saccharomyces cerevisiae D-arabinose dehydrogenase [NAD(P)+] heavy chain (Ara1p) and similar proteins. Saccharomyces cerevisiae Ara1p (EC 1.1.1.117), also called D-arabinose 1-dehydrogenase (NAD(P)(+)), is a founding members of aldo-keto reductase family 3 member C1 (AKR3C1). It catalyzes the oxidation of D-arabinose, L-xylose, L-fucose, and L-galactose in the presence of NADP(+). 294 matched cddid_all.tbl CDD cd19120 cd19120 381346 AKR_AKR3C2-3 Saccharomyces pombe NAD/NADP-dependent indole-3-acetaldehyde reductase, Candida parapsilosis NADPH-dependent conjugated polyketone reductase C2 (CPR), and similar proteins. Saccharomyces pombe NAD/NADP-dependent indole-3-acetaldehyde reductase (EC 1.1.1.190/EC 1.1.1.191) and Candida parapsilosis NADPH-dependent CPR (EC 1.1.1.358/EC 1.1.1.168) are founding members of aldo-keto reductase family 3 member C2 (AKR3C2) and C3 (AKR3C3), respectively. Saccharomyces pombe NAD/NADP-dependent indole-3-acetaldehyde reductase catalyzes the conversion from (Indol-3-yl)ethanol to (indol-3-yl)acetaldehyde in a NAD/NADP-dependent manner. CPR, also called 2-dehydropantolactone reductase, or 2-dehydropantolactone reductase (A-specific), or ketopantoyl-lactone reductase, acts as a NADPH-dependent conjugated polyketone reductase with broad substrate specificity and strict stereospecificity. It reduces ketopantoyl lactone and isatin. 269 matched cddid_all.tbl CDD cd19121 cd19121 381347 AKR_AKR3D1 AKR3D family of aldo-keto reductase (AKR). Trichoderma reesei D-galacturonate reductase (GAR1, EC 1.1.1.365), also called D-galacturonic acid reductase, or GalUR, is a founding member of aldo-keto reductase family 3 member D1 (AKR3D1). It mediates the reduction of D-galacturonate to L-galactonate, the first step in D-galacturonate catabolic process. It also has activity with D-glucuronate and DL-glyceraldehyde. Its activity is seen only with NADPH and not with NADH. 279 matched cddid_all.tbl CDD cd19122 cd19122 381348 AKR_AKR3E1 AKR3E family of aldo-keto reductase (AKR). Trichoderma reesei NADP(+)-dependent glycerol 2-dehydrogenase (GLD2, EC 1.1.1.156), also called dihydroxyacetone reductase, is a founding member of aldo-keto reductase family 3 member E1 (AKR3E1). It acts as a glycerol oxidoreductase probably involved in glycerol synthesis. 291 matched cddid_all.tbl CDD cd19123 cd19123 381349 AKR_AKR3G1 AKR3G family of aldo-keto reductase (AKR). Synechocystis sp. aldo/keto reductase slr0942 is a founding member of aldo-keto reductase family 3 member G1 (AKR3G1). It is an aldo/keto reductase that catalyzes the NADPH-dependent reduction of aldehyde- and ketone-groups of different classes of carbonyl compounds to the corresponding alcohols. 297 matched cddid_all.tbl CDD cd19124 cd19124 381350 AKR_AKR4A_4B AKR4A and AKR4B families of aldo-keto reductase (AKR). The AKR4A family of AKR includes Glycine max NAD(P)H-dependent 6'-deoxychalcone synthase (6DCS, EC 3.1.170), chalcone reductase (CHR, EC 2.3.1.74) from Medicago sativa, Glycyrrhiza echinate, and Glycyrrhiza glabra, which are founding members of aldo-keto reductase family 4 member A1 (AKR4A1), A2 (AKR4A2), A3 (AKR4A3), and A4 (AKR4A4), respectively. NAD(P)H-6DCS co-acts with chalcone synthase in formation of 4,2',4'-trihydroxychalcone, involved in the biosynthesis of glyceollin type phytoalexins. CHR, also called chalcone polyketide reductase, is a key enzyme of the flavonoid/isoflavonoid biosynthesis pathway. The AKR4B family of AKR includes Sesbania rostrate chalcone reductase (CHR, AKR4B1), Papaver somniferum codeinone reductase (COR, AKR4B2/ AKR4B3), Fragaria x ananassa D-galacturonate reductase (GalUR, AKR4B4), deoxymugineic acid synthase 1 (DMAS1) from Zea mays (AKR4B5), Oryza sativa (AKR4B6), Hordeum vulgare (AKR4B7), Triticum aestivum (AKR4B8), and Erythroxylum coca methylecgonone reductase (MecgoR, AKR4B10). CHR, also called chalcone polyketide reductase, is a key enzyme of the flavonoid/isoflavonoid biosynthesis pathway. NADPH-dependent COR and non-functional NADPH-dependent COR from Papaver somniferum are founding members of aldo-keto reductase family 4 member B2 (AKR4B2) and B3 (AKR4B3), respectively. NADPH-dependent COR (EC 1.1.1.247) reduces codeinone to codeine in the penultimate step in morphine biosynthesis. It can use morphinone, hydrocodone, and hydromorphone as substrates during reductive reaction with NADPH as cofactor, and morphine and dihydrocodeine as substrates during oxidative reaction with NADP as cofactor. GalUR (EC 1.1.1.365), also called aldo-keto reductase 2 (AKR2), is involved in ascorbic acid (vitamin C) biosynthesis by catalyzing the conversion from L-galactonate and NADP(+) to D-galacturonate and NADPH. DMAS1 (EC 1.1.1.285) catalyzes the reduction of a 3''-keto intermediate during the biosynthesis of 2'-deoxymugineic acid (DMA) from L-Met. It is involved in the formation of phytosiderophores (MAs) belonging to the mugineic acid family and required to acquire iron. MecgoR catalyzes the stereospecific reduction of methylecgonone to methylecgonine, the penultimate step in cocaine biosynthesis. 281 matched cddid_all.tbl CDD cd19125 cd19125 381351 AKR_AKR4C1-15 AKR4C family of aldo-keto reductase (AKR). The AKR4C family of AKR includes aldose reductase (ALR) from Hordeum vulgare (AKR4C1), Bromus inermis (AKR4C2), Avena fatua (AKR4C3), and Xerophyta viscosa (AKR4C4), two aldose reductases, DpAR1 (AKR4C5) and DpAR2(AKR4C6), from Digitalis purpurea, aldehyde reductase from Zea mays (AKR4C7), four aldo-keto reductases from Arabidopsis thaliana (AKR4C8-11), and another three aldo-keto reductases from Aloe arborescens (AKR4C12) and Oryza sativa (AKR4C14/15). ALR (EC 1.1.1.21), also called AR, aldehyde reductase, or polyol dehydrogenase (NADP(+)), is a cytosolic NADPH-dependent oxidoreductase that catalyzes the reduction of a variety of aldehydes and carbonyls, including monosaccharides. Both DpAR1 and DpAR2 reduce the ketone group of steroid structures. They may be involved in plant steroid metabolism in general and in cardenolide biosynthesis in particular. Plant aldo-keto reductases of the AKR4C subfamily play key roles during stress and are attractive targets for developing stress-tolerant crops. 287 matched cddid_all.tbl CDD cd19126 cd19126 381352 AKR_AKR5A_5G AKR5A and AKR5G families of aldo-keto reductase (AKR). The AKR5A family of AKR includes prostaglandin F2-alpha synthase (PGFS) from Leishmania major (AKR5A1) and Trypanosoma brucei (AKR5A2). PGFS, also called 9,11-endoperoxide prostaglandin H2 reductase, catalyzes the NADP-dependent formation of prostaglandin F2-alpha from prostaglandin H2. It has also aldo/ketoreductase activity for synthetic substrates 9,10-phenanthrenequinone and p-nitrobenzaldehyde. The AKR5G family of AKR includes Bacillus subtilis glyoxal reductase (GR), uncharacterized oxidoreductase YtbE, and Bacillus aryabhattai aldo-keto reductase, which corresponds to aldo-keto reductase family 5 member G1-3 (AKR5G1-3), respectively. GR (YvgN, EC 1.1.1.283), also called methylglyoxal reductase, reduces glyoxal and methylglyoxal (2-oxopropanal). It is not involved in vitamin B6 biosynthesis. 254 matched cddid_all.tbl CDD cd19127 cd19127 381353 AKR_AKR5B1 AKR5B family of aldo-keto reductase (AKR). Pseudomonas putida morphine 6-dehydrogenase (M6DH) is a founding member of the aldo-keto reductase family 5 member B1 (AKR5B1). M6DH (EC 1.1.1.218), also called naloxone reductase, oxidizes the C-6 hydroxy group of morphine and codeine. 268 matched cddid_all.tbl CDD cd19128 cd19128 381354 AKR_GlAR-like Giardia lamblia aldose reductase (AR) and similar proteins. Giardia lamblia AR (EC 1.1.1.21), also called aldehyde reductase, is the prototype of this family. It catalyzes the NADPH-dependent reduction of a wide variety of carbonyl-containing compounds to their corresponding alcohols with a broad range of catalytic efficiencies. 277 matched cddid_all.tbl CDD cd19129 cd19129 381355 AKR_BaDH-like Bradyrhizobium diazoefficiens dehydrogenase (DH) and similar proteins. Bradyrhizobium diazoefficiens DH is the prototype of this family. It belongs to aldo/keto reductase family. 295 matched cddid_all.tbl CDD cd19130 cd19130 381356 AKR_AKR5C1 Corynebacterium sp. 2,5-diketo-D-gluconic acid reductase A (DkgA) and similar proteins. Corynebacterium sp. DkgA is a founding member of aldo-keto reductase family 5 member C1 (AKR5C1). DkgA (EC 1.1.1.346), also called 2,5-DKG reductase A, or 2,5-DKGR A, or 25DKGR-A, or AKR5C, catalyzes the reduction of 2,5-diketo-D-gluconic acid (25DKG) to 2-keto-L-gulonic acid (2KLG). 5-keto-D-fructose and dihydroxyacetone can also serve as substrates. 256 matched cddid_all.tbl CDD cd19131 cd19131 381357 AKR_AKR5C2 Escherichia coli 2,5-diketo-D-gluconic acid reductase A (DkgA/YqhE) and similar proteins. Escherichia coli DkgA/YqhE is a founding member of aldo-keto reductase family 5 member C2 (AKR5C2). DkgA/YqhE (EC 1.1.1.274), also called 2,5-DKG reductase A, or 2,5-DKGR A, or 25DKGR-A, or AKR5C, catalyzes the reduction of 2,5-diketo-D-gluconic acid (25DKG) to 2-keto-L-gulonic acid (2KLG). It is also capable of stereoselective -keto ester reductions on ethyl acetoacetate and other 2-substituted derivatives. 256 matched cddid_all.tbl CDD cd19132 cd19132 381358 AKR_AKR5D1_E1 AKR5D and AKR5E families of aldo-keto reductase (AKR). 2,5-diketo-D-gluconic acid reductase B (DkgB) from Corynebacterium sp. and 2,5-diketo-D-gluconic acid reductase Zymomonas mobilis are founding members of aldo-keto reductase family 5 member D1 (AKR5D1) and E1 (AKR5E1), respectively. DkgB (EC 1.1.1.274), also called 2,5-didehydrogluconate reductase (2-dehydro-D-gluconate-forming), or 2,5-DKG reductase B, or 2,5-DKGR B, or 25DKGR-B, catalyzes the reduction of 2,5-diketo-D-gluconic acid (25DKG) to 2-keto-L-gulonic acid (2KLG). 255 matched cddid_all.tbl CDD cd19133 cd19133 381359 AKR_AKR5F1 the AKR5F family of aldo-keto reductase (AKR). Klebsiella sp. 2,5-diketo-D-gluconic acid reductase (2,5-DKG reductase) is a founding member of aldo-keto reductase family 5 member F1 (AKR5F1). It catalyzes the reduction of 2,5-diketo-D-gluconic acid (25DKG) to 2-keto-L-gulonic acid (2KLG). 255 matched cddid_all.tbl CDD cd19134 cd19134 381360 AKR_AKR5H1 AKR5H family of aldo-keto reductase (AKR). Mycobacterium smegmatis MSMEG_2407 is a founding member of aldo-keto reductase family 5 member H1 (AKR5H1). It is a NADPH-dependent aldo-keto reductase that reduces methylglyoxal and phenylglyoxal. 263 matched cddid_all.tbl CDD cd19135 cd19135 381361 AKR_CeZK1290-like Caenorhabditis elegans ZK1290.5 and similar proteins. Caenorhabditis elegans ZK1290.5 is the prototype of this family. It is an uncharacterized aldo/keto reductase family oxidoreductase. 265 matched cddid_all.tbl CDD cd19136 cd19136 381362 AKR_DrGR-like Danio rerio glyoxal reductase-like (GR-like) protein and similar proteins. Danio rerio GR-like protein is the prototype of this family. It is an uncharacterized aldo/keto reductase family oxidoreductase similar to Bacillus subtilis glyoxal reductase (YvgN) that reduces glyoxal and methylglyoxal (2-oxopropanal). 262 matched cddid_all.tbl CDD cd19137 cd19137 381363 AKR_AKR3F1 Thermotoga maritime Tm1743 and similar proteins. Thermotoga maritime Tm1743 is a founding member of aldo-keto reductase family 3 member F1 (AKR3F1). It is a aldo/keto reductase family oxidoreductase. 260 matched cddid_all.tbl CDD cd19138 cd19138 381364 AKR_YeaE Escherichia coli YeaE and similar proteins. Escherichia coli YeaE is the prototype of this family. It acts as an aldo-keto reductase (AKR) that catalyzes the reversible reduction of ketones to the respective alcohols using NAD(P)H as a hydride donor. 266 matched cddid_all.tbl CDD cd19139 cd19139 381365 AKR_AKR3F2 Escherichia coli 2,5-diketo-D-gluconic acid reductase B (DkgB/YafB) and similar proteins. Escherichia coli DkgB/YafB (EC 1.1.1.346), also called 2,5-didehydrogluconate reductase (2-dehydro-L-gulonate-forming), or 2,5-DKG reductase B, or 2,5-DKGR B, or 25DKGR-B, is a founding member of aldo-keto reductase family 3 member F2 (AKR3F2). It catalyzes the reduction of 2,5-diketo-D-gluconic acid (25DKG) to 2-keto-L-gulonic acid (2KLG). 248 matched cddid_all.tbl CDD cd19140 cd19140 381366 AKR_AKR3F3 Sinorhizobium meliloti isatin reductase and similar proteins. Sinorhizobium meliloti isatin reductase is a founding member of aldo-keto reductase family 3 member F3 (AKR3F3). It is a aldo/keto reductase family oxidoreductase. 253 matched cddid_all.tbl CDD cd19141 cd19141 381367 Aldo_ket_red_shaker Shaker potassium channel beta subunit (AKR6A) family of aldo-keto reductase (AKR). This family includes voltage-gated potassium channel subunits, beta-1 (KCAB1B), beta-2 (KCAB2B) and beta-3 (KCAB3B). KCAB1B and KCAB2B are cytoplasmic potassium channel subunits that modulate the characteristics of the channel-forming alpha-subunits. KCAB3B is an accessory potassium channel protein which modulates the activity of the pore-forming alpha subunit. 310 matched cddid_all.tbl CDD cd19142 cd19142 381368 AKR_AKR6B1 AKR6B family of aldo-keto reductase (AKR). Drosophila melanogaster Hk protein is a founding member of aldo-keto reductase family 6 member B1 (AKR6B1). Hk protein, also called hyperkinetic, is a beta subunit of Shaker (Sh) K+ channels and shows high sequence homology to aldoketoreductase. 325 matched cddid_all.tbl CDD cd19143 cd19143 381369 AKR_AKR6C1_2 AKR6C family of aldo-keto reductase (AKR). Voltage-gated potassium channel subunit beta (KCAB) from Arabidopsis thaliana and Egeria densa are founding members of aldo-keto reductase family 6 member C1 (AKR6C1) and C2 (AKR6C2), respectively. KCAB, also called Shaker channel b-subunit, or K(+) channel subunit beta, or potassium voltage beta 1, or KV-beta1, or KAB1, is a probable accessory potassium channel protein which modulates the activity of the pore-forming alpha subunit. 319 matched cddid_all.tbl CDD cd19144 cd19144 381370 AKR_AKR13A1 AKR13A family of aldo-keto reductase (AKR). Schizosaccharomyces pombe aldo-keto reductase YakC is a founding member of aldo-keto reductase family 13 member A1 (AKR13A1). It catalyzes the reversible reduction of ketones to the respective alcohols using NADP(+) as a hydride donor. 323 matched cddid_all.tbl CDD cd19145 cd19145 381371 AKR_AKR13D1 AKR13D family of aldo-keto reductase (AKR). Rauvolfia serpentina PR is a founding member of aldo-keto reductase family 13 member D1 (AKR13D1). It catalyzes the NADPH-dependent reduction of the aldehyde perakine to yield the alcohol raucaffrinoline in the biosynthetic pathway of ajmaline in Rauvolfia, a key step in indole alkaloid biosynthesis. This family also includes Arabidopsis thaliana aldo-keto reductases, ALKR1-6. 304 matched cddid_all.tbl CDD cd19146 cd19146 381372 AKR_AKR9A1-2 Aspergillus nidulans sterigmatocystin biosynthesis dehydrogenase StcV, Aspergillus flavus norsolorinic acid reductase (NOR), and similar proteins. Aspergillus nidulans sterigmatocystin biosynthesis dehydrogenase StcV and Aspergillus flavus norsolorinic acid reductase (NOR), are founding members of aldo-keto reductase family 9 member A1-2 (AKR9A1-2), respectively. StcV may be involved in the dehydration of 5'-hydroxyaverantin to form averufin. NOR is involved in aflatoxin biosynthesis. 326 matched cddid_all.tbl CDD cd19147 cd19147 381373 AKR_AKR9A3_9B1-4 Phanerochaete chrysosporium aryl-alcohol dehydrogenase [NADP(+)] (AAD) and similar proteins. Phanerochaete chrysosporium ADD (EC1.1.1.91) is a founding member of aldo-keto reductase family 9 member A3. It is involved in lignin degradation and reduces aromatic benzaldehydes to their respective alcohols in the presence of NADP(H). This family also includes Saccharomyces cerevisiae aryl-alcohol dehydrogenases AAD14p, AAD3p, AAD4p, and AAD10p, which are founding members of aldo-keto reductase family 9 member B1-4 (AKR9B1-4), respectively. 319 matched cddid_all.tbl CDD cd19148 cd19148 381374 AKR_AKR11B1 Bacillus subtilis aldo-keto reductase YhdN and similar proteins. Bacillus subtilis YhdN, also called general stress protein 69 (GSP69), is a founding member of aldo-keto reductase family 11 member B1 (AKR11B1). It acts as an aldo-keto reductase (AKR) that catalyzes the reversible reduction of ketones to the respective alcohols using NAD(P)H as a hydride donor. 302 matched cddid_all.tbl CDD cd19149 cd19149 381375 AKR_AKR11B2 Escherichia coli NADH-specific methylglyoxal reductase (YdjG) and similar proteins. Escherichia coli YdjG is a founding member of aldo-keto reductase family 11 member B2 (AKR11B2). It catalyzes the NADH-dependent reduction of methylglyoxal (2-oxopropanal) in vitro. It may play some role in intestinal colonization. 315 matched cddid_all.tbl CDD cd19150 cd19150 381376 AKR_AKR14A1 Escherichia coli L-glyceraldehyde 3-phosphate reductase (GPR/YghZ/AKR14A1) and similar proteins. Escherichia coli L-glyceraldehyde 3-phosphate reductase (GPR/YghZ), also called GAP reductase, is a founding member of aldo-keto reductase family 14 member A1 (AKR14A1). It catalyzes the stereospecific, NADPH-dependent reduction of L-glyceraldehyde 3-phosphate (L-GAP). It is also involved in the stress response as a methylglyoxal reductase which converts the toxic metabolite methylglyoxal to acetol in vitro and in vivo. 309 matched cddid_all.tbl CDD cd19151 cd19151 381377 AKR_AKR14A2 Salmonella enterica aldo-keto reductase (AKR) and similar protein. Salmonella enterica AKR is a founding member of aldo-keto reductase family 14 member A2 (AKR14A2). 309 matched cddid_all.tbl CDD cd19152 cd19152 381378 AKR_AKR15A AKR15A family of aldo-keto reductase. The AKR15 family includes Microbacterium luteolum pyridoxal 4-dehydrogenase (PLD), Pseudomonas sp. D-threo-aldose 1-dehydrogenase (FDH), and similar proteins. PLD (EC1.1.1.107) catalyzes irreversible oxidation of pyridoxal. FDH(EC1.1.1.122), also called (2S,3R)-aldose dehydrogenase, or L-fucose dehydrogenase, catalyzes the oxidation of L-fucose to L-fuconolactone in the presence of NADP(+). It is also active against L-galactose, and to a much lesser degree, D-arabinose. FDH (EC1.1.1.122), also called (2S,3R)-aldose dehydrogenase, or L-fucose dehydrogenase, catalyzes the oxidation of L-fucose to L-fuconolactone in the presence of NADP(+). It is also active against L-galactose, and to a much lesser degree, D-arabinose. 308 matched cddid_all.tbl CDD cd19153 cd19153 381379 AKR_galDH-like L-galactose dehydrogenase (L-galDH), D-arabinose 1-dehydrogenase (ARA2) and similar proteins. L-galDH (EC 1.1.1.316), also called L-galactose 1-dehydrogenase, catalyzes the oxidation of L-galactose to L-galactono-1,4-lactone in the presence of NAD(+). It uses NAD(+) as a hydrogen acceptor much more efficiently than NADP(+). ARA2 (EC1.1.1.116), also called NAD(+)-specific D-arabinose dehydrogenase, catalyzes the the oxidation of D-arabinose to D-arabinono-1,4-lactone in the presence of NAD(+). 294 matched cddid_all.tbl CDD cd19154 cd19154 381380 AKR_AKR1G1_CeAKR Caenorhabditis elegans aldo-keto reductase (CeAKR) and similar proteins. CeAKR is a founding member of aldo-keto reductase family 1 member G1 (AKR1G1). It may catalyze the reversible reduction of ketones to the respective alcohols using NAD(P)H as a hydride donor. 303 matched cddid_all.tbl CDD cd19155 cd19155 381381 AKR_AKR1I_CgAKR1 Coptotermes gestroi aldo-keto reductase (CgAKR-1) and similar proteins. Coptotermes gestroi aldo-keto reductase (CgAKR-1) is a founding member of aldo-keto reductase family 1 member I (AKR1I). It is a multipurpose enzyme with potential biotechnological applications. 307 matched cddid_all.tbl CDD cd19156 cd19156 381382 AKR_AKR5A1_2 AKR5A family of aldo-keto reductase (AKR). Prostaglandin F2-alpha synthase (PGFS) from Leishmania major and Trypanosoma brucei are founding members of aldo-keto reductase family 5 member A1 (AKR5A1) and A2 (AKR5A2), respectively. PGFS, also called 9,11-endoperoxide prostaglandin H2 reductase, catalyzes the NADP-dependent formation of prostaglandin F2-alpha from prostaglandin H2. It has also aldo/ketoreductase activity toward the synthetic substrates 9,10-phenanthrenequinone and p-nitrobenzaldehyde. 266 matched cddid_all.tbl CDD cd19157 cd19157 381383 AKR_AKR5G1-3 AKR5G family of aldo-keto reductase (AKR). Bacillus subtilis glyoxal reductase (GR), uncharacterized oxidoreductase YtbE, and Bacillus aryabhattai aldo-keto reductase are founding members of aldo-keto reductase family 5 member G1-3 (AKR5G1-3), respectively. GR (YvgN, EC 1.1.1.283), also called methylglyoxal reductase, reduces glyoxal and methylglyoxal (2-oxopropanal). It is not involved in vitamin B6 biosynthesis. 265 matched cddid_all.tbl CDD cd19158 cd19158 381384 AKR_KCAB2B_AKR6A1-like voltage-gated potassium channel subunit beta-2 (KCAB2B) and similar proteins. KCAB2B from Bos taurus, Rattus norvegicus, Mus musculus, Homo sapiens, and Oryctolagus cuniculus, are founding members of aldo-keto reductase family 6 member A1 (AKR6A1), A2 (AKR6A2), A4 (AKR6A4), A5 (AKR6A5), and A6 (AKR6A6), respectively. KCAB2B, also called Shaker channel b-subunit 2 (Kvb2), or K(+) channel subunit beta-2, or Kv-beta-2, or Kvbeta2, is a cytoplasmic potassium channel subunit that modulates the characteristics of the channel-forming alpha-subunits. It may be involved in the regulation of nerve signaling, and prevents neuronal hyperexcitability. 324 matched cddid_all.tbl CDD cd19159 cd19159 381385 AKR_KCAB1B_AKR6A3-like voltage-gated potassium channel subunit beta-1 (KCAB1B) and similar proteins. KCAB1B from Homo sapiens, Mus musculus, Mustela putorius, Rattus norvegicus, and Kvb1.1, Kvb1.2 from Oryctolagus cuniculus, are founding members of aldo-keto reductase family 6 member A3 (AKR6A3), A8 (AKR6A8), A10a (AKR6A10a), A13 (AKR6A13), A7 (AKR6A7) and A10b (AKR6A10b), respectively. KCAB1B, also called Shaker channel b-subunit 1(Kvb1), K(+) channel subunit beta-1, or Kv-beta-1, is a cytoplasmic potassium channel subunit that modulates the characteristics of the channel-forming alpha-subunits. It modulates action potentials via its effect on the pore-forming alpha subunits. 323 matched cddid_all.tbl CDD cd19160 cd19160 381386 AKR_KCAB3B_AKR6A9-like voltage-gated potassium channel subunit beta-3 (KCAB3B) and similar proteins. KCAB3B from Homo sapiens, Rattus norvegicus, and Mus musculus, are founding members of aldo-keto reductase family 6 member A9 (AKR6A9), A12 (AKR6A12), A14 (AKR6A14), respectively. KCAB3B, also called Shaker channel b-subunit 3 (Kvb3), K(+) channel subunit beta-3, or Kv-beta-3, is an accessory potassium channel protein which modulates the activity of the pore-forming alpha subunit. It alters the functional properties of Kv1.5. 325 matched cddid_all.tbl CDD cd19161 cd19161 381387 AKR_AKR15A1 Microbacterium luteolum pyridoxal 4-dehydrogenase (PLD) and similar proteins. Microbacterium luteolum PLD (EC1.1.1.107) is a founding member of aldo-keto reductase family 15 member A1 (AKR15A1). It catalyzes irreversible oxidation of pyridoxal. 310 matched cddid_all.tbl CDD cd19162 cd19162 381388 AKR_FDH D-threo-aldose 1-dehydrogenase (FDH) and similar proteins. FDH (EC1.1.1.122), also called (2S,3R)-aldose dehydrogenase, or L-fucose dehydrogenase, catalyzes the oxidation of L-fucose to L-fuconolactone in the presence of NADP(+). It is also active against L-galactose, and to a much lesser degree, D-arabinose. 290 matched cddid_all.tbl CDD cd19163 cd19163 381389 AKR_galDH L-galactose dehydrogenase (L-galDH) and similar proteins. L-galDH (EC 1.1.1.316), also called L-galactose 1-dehydrogenase, catalyzes the oxidation of L-galactose to L-galactono-1,4-lactone in the presence of NAD(+). It uses NAD(+) as a hydrogen acceptor much more efficiently than NADP(+). 293 matched cddid_all.tbl CDD cd19164 cd19164 381390 AKR_ARA2 D-arabinose 1-dehydrogenase (ARA2) and similar proteins. ARA2 (EC1.1.1.116), also called NAD(+)-specific D-arabinose dehydrogenase, catalyzes the the oxidation of D-arabinose to D-arabinono-1,4-lactone in the presence of NAD(+). 298 matched cddid_all.tbl CDD cd19165 cd19165 350856 HemeO heme oxygenase in eukaryotes and some bacteria. This subfamily contains heme oxygenase (HO, EC 1.14.14.18) found in eukaryotes as well as some proteobacteria, including cyanobacteria. Heme oxygenase (HO) catalyzes the rate limiting step in the degradation of heme to biliverdin in a multi-step reaction. HO is essential for recycling of iron from heme which is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. In vertebrates, HO plays a role in heme homeostasis and oxidative stress response, and cellular signaling in mammals that include isoforms HO-1, HO-2 and HO-3. HO-1 is ubiquitously expressed after induction while HO-2 expression is constitutive, mostly limited to certain organs, such as the brain, testes, and the vascular system. HO-3 is non-functional in humans, suggesting that the Hmox3 gene is a pseudogene derived from HO-2 transcripts. In higher plants and cyanobacteria, heme oxygenase is required for the synthesis of light-harvesting pigments, which contain tetrapyrrols derived from biliverdin. Candida albicans expresses a heme oxygenase that is required for the utilization of heme as a nutritional iron source, whereas Saccharomyces cerevisiae responds to iron deprivation by increasing Hmx1p transcription, which is controlled by the major iron-dependent transcription factor, Aft1p, and promotes both the re-utilization of heme iron and the regulation of heme-dependent transcription during periods of iron scarcity. In pathogenic bacteria, HO is part of a pathway for iron acquisition from host heme. In Leptospira interrogans, a pathogenic spirochete that causes leptospirosis, HO is required for iron utilization when hemoglobin is the sole iron source, thus making HO an interesting target for novel antimicrobial agents. HO shares tertiary structure similarity to methane monooxygenase (EC 1.14.13.25), ribonucleotide reductase (EC 1.17.4.1) and thiaminase II (EC 3.5.99.2), but shares little sequence homology. 205 matched cddid_all.tbl CDD cd19166 cd19166 350857 HemeO-bac heme oxygenase found in pathogenic bacteria. This subfamily contains bacterial heme oxygenase (HO, EC 1.14.14.18), where HO is part of a pathway for iron acquisition from host heme and heme products. Most of these proteins have yet to be characterized. HO catalyzes the rate limiting step in the degradation of heme to biliverdin in a multi-step reaction. HO is essential for recycling of iron from heme which is used as a substrate and cofactor for its own degradation to biliverdin, iron, and carbon monoxide. This family includes heme oxygenase (pa-HO) from Pseudomonas aeruginosa, an opportunistic pathogen that causes a variety of systemic infections, particularly in those afflicted with cystic fibrosis, as well as cancer and AIDS patients who are immunosuppressed. Pa-HO, expressed by the PigA gene, is critical for the acquisition of host iron since there is essentially no free iron in mammals, and is unusual since it hydroxylates heme predominantly at the delta-meso heme carbon, while all other well-studied HOs hydroxylate the alpha-meso carbon. Also included in this family is Neisseria meningitidis HO which is substantially different from the human HO, with the reaction product being ferric biliverdin IXalpha rather than reduced iron and free biliverdin IXalpha. HO shares tertiary structure similarity to methane monooxygenase (EC 1.14.13.25), ribonucleotide reductase (EC 1.17.4.1) and thiaminase II (EC 3.5.99.2), but shares little sequence homology. 182 matched cddid_all.tbl CDD cd19167 cd19167 380944 SET_SMYD1_2_3-like SET domain (including post-SET domain) found in SET and MYND domain-containing proteins, SMYD1, SMYD2, SMYD3 and similar proteins. The family includes SET and MYND domain-containing proteins, SMYD1, SMYD2 and SMYD3. SMYD1 (EC 2.1.1.43; also termed BOP) is a heart and muscle specific SET-MYND domain containing protein, which functions as a histone methyltransferase and regulates downstream gene transcription. It methylates histone H3 at 'Lys-4' (H3K4me), seems able to perform both mono-, di-, and trimethylation. SMYD2 (also termed HSKM-B, or lysine N-methyltransferase 3C (KMT3C)) functions as a histone methyltransferase that methylates both histones and non-histone proteins, including p53/TP53 and RB1. It specifically methylates histone H3 'Lys-4' (H3K4me) and dimethylates histone H3 'Lys-36' (H3K36me2). SMYD3 (also termed zinc finger MYND domain-containing protein 1) functions as a histone methyltransferase that specifically methylates 'Lys-4' of histone H3, inducing di- and tri-methylation, but not monomethylation. It also methylates 'Lys-5' of histone H4. SMYD3 plays an important role in transcriptional activation as a member of an RNA polymerase complex. 205 matched cddid_all.tbl CDD cd19168 cd19168 380945 SET_EZH-like SET domain found in enhancer of zeste homolog 1 (EZH1) and zeste homolog 2 (EZH2) of polycomb repressive complex 2 (PRC2), and similar proteins. The family includes EZH1 and EZH2. EZH1 (EC 2.1.1.43; also termed ENX-2, or histone-lysine N-methyltransferase EZH1) is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. EZH2 (EC 2.1.1.43; also termed lysine N-methyltransferase 6, ENX-1, or histone-lysine N-methyltransferase EZH2) is a catalytic subunit of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. Both EZH1 and EZH2 can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. PRC2 is involved in several cancers; EZH2 is overexpressed in breast, liver and prostate cancer, while point mutations in EZH2 alter the substrate preference and product specificity of PRC2 in Non-Hodgkin lymphomas (NHLs). Thus, PRC2 is a popular target for cancer therapeutics. 124 matched cddid_all.tbl CDD cd19169 cd19169 380946 SET_SETD1 SET domain (including post-SET domain) found in SET domain-containing protein 1 (SETD1) and similar proteins. This family includes SET domain-containing protein 1A (SETD1A) and SET domain-containing protein 1B (SETD1B). These proteins are histone-lysine N-methyltransferases that specifically methylate 'Lys-4' of histone H3 (H3K4me) when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. 148 matched cddid_all.tbl CDD cd19170 cd19170 380947 SET_KMT2A_2B SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A), 2B (KMT2B) and similar proteins. This family includes KMT2A and KMT2B. Both KMT2A (also termed ALL-1 or CXXC7 or MLL or MLL1 or TRX1 or HRX) and KMT2B (also termed MLL4 or TRX2) act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me). 152 matched cddid_all.tbl CDD cd19171 cd19171 380948 SET_KMT2C_2D SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C), 2D (KMT2D) and similar proteins. This family includes KMT2C and KMT2D. Both, KMT2C (also termed HALR or MLL3) and KMT2D (also termed ALR or MLL2), act as histone methyltransferases that methylate 'Lys-4' of histone H3 (H3K4me). They are subunits of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation. 153 matched cddid_all.tbl CDD cd19172 cd19172 380949 SET_SETD2 SET domain (including post-SET domain) found in SET domain-containing protein 2 (SETD2) and similar proteins. SETD2 (also termed HIF-1, huntingtin yeast partner B, huntingtin-interacting protein 1 (HIP-1), huntingtin-interacting protein B, lysine N-methyltransferase 3A or protein-lysine N-methyltransferase SETD2) acts as histone-lysine N-methyltransferase that specifically trimethylates 'Lys-36' of histone H3 (H3K36me3) using demethylated 'Lys-36' (H3K36me2) as substrate. It has been shown that methylation is a posttranslational modification of dynamic microtubules and that SETD2 methylates alpha-tubulin at lysine 40, the same lysine that is marked by acetylation on microtubules. Methylation of microtubules occurs during mitosis and cytokinesis and can be ablated by SETD2 deletion, which causes mitotic spindle and cytokinesis defects, micronuclei, and polyploidy. 142 matched cddid_all.tbl CDD cd19173 cd19173 380950 SET_NSD SET domain (including post-SET domain) found in nuclear SET domain-containing proteins, NSD1, NSD2, NSD3 and similar proteins. The nuclear receptor-binding SET Domain (NSD) family of histone H3 lysine 36 methyltransferases is comprised of NSD1, NSD2, and NSD3, which are primarily known to be involved in chromatin integrity and gene expression through mono-, di-, or tri-methylating lysine 36 of histone H3 (H3K36), respectively. NSD1 (EC 2.1.1.43; also termed histone-lysine N-methyltransferase H3 lysine-36 and H4 lysine-20 specific, androgen receptor coactivator 267 kDa protein (ARA267), androgen receptor-associated protein of 267 kDa, H3-K36-HMTase, H4-K20-HMTase, lysine N-methyltransferase 3B (KMT3B) or NR-binding SET domain-containing protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-36' of histone H3 and 'Lys-20' of histone H4. NSD2 (EC 2.1.1.43; also termed multiple myeloma SET domain-containing protein (MMSET), protein trithorax-5 (TRX5), or wolf-Hirschhorn syndrome candidate 1 protein (WHSC1)) acts as histone-lysine N-methyltransferase with histone H3 'Lys-27' (H3K27me) methyltransferase activity. NSD3 (EC 2.1.1.43; also termed protein whistle, WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1L1), or WHSC1-like protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-4' and 'Lys-27' of histone H3. 142 matched cddid_all.tbl CDD cd19174 cd19174 380951 SET_ASH1L SET domain (including post-SET domain) found in ASH1-like protein (ASH1L) and similar proteins. ASH1L (EC 2.1.1.43; also termed absent small and homeotic disks protein 1 homolog, KMT2H, or lysine N-methyltransferase 2H) acts as histone-lysine N-methyltransferase that specifically methylates 'Lys-36' of histone H3 (H3K36me). It plays important roles in development; heterozygous mutation of ASH1L is associated with severe intellectual disability (ID) and multiple congenital anomaly (MCA). 141 matched cddid_all.tbl CDD cd19175 cd19175 380952 SET_ASHR3-like SET domain (including post-SET domain) found in Arabidopsis thaliana ASH1-related protein 3 (ASHR3) and similar proteins. This family includes Arabidopsis thaliana ASH1-related protein 3 (ASHR3, also termed protein SET DOMAIN GROUP 4 or protein stamen loss), ASH1 homolog 3 (ASHH3, also termed protein SET DOMAIN GROUP 7) and homolog 4 (ASHH4, also termed protein SET DOMAIN GROUP 24). They all function as histone-lysine N-methyltransferases (EC 2.1.1.43). 139 matched cddid_all.tbl CDD cd19176 cd19176 380953 SET_SETD3 SET domain found in SET domain-containing protein 3 (SETD3) and similar proteins. SETD3 (EC 2.1.1.43) is a histone-lysine N-methyltransferase that methylates 'Lys-4' and 'Lys-36' of histone H3 (H3K4me and H3K36me). It functions as a transcriptional activator that plays an important role in the transcriptional regulation of muscle cell differentiation via interaction with MYOD1. 251 matched cddid_all.tbl CDD cd19177 cd19177 380954 SET_SETD4 SET domain found in SET domain-containing protein 4 (SETD4) and similar proteins. SETD4 is a cytosolic and nuclear functional lysine methyltransferase that plays a crucial role in breast carcinogenesis. However, its specific substrates and modification sites remain to be disclosed. 245 matched cddid_all.tbl CDD cd19178 cd19178 380955 SET_SETD6 SET domain found in SET domain-containing protein 6 (SETD6) and similar proteins. SETD6 is a lysine N-methyltransferase that monomethylates 'Lys-310' of the RELA subunit of NF-kappa-B complex, leading to down-regulate NF-kappa-B transcription factor activity. It also monomethylates 'Lys-8' of H2AZ (H2AZK8me1). 250 matched cddid_all.tbl CDD cd19179 cd19179 380956 SET_RBCMT SET domain found in chloroplastic ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase (RBCMT) and similar proteins. RBCMT (EC 2.1.1.127; also termed [Ribulose-bisphosphate carboxylase]-lysine N-methyltransferase, RuBisCO LSMT, RuBisCO methyltransferase, or rbcMT) methylates 'Lys-14' of the large subunit of RuBisCO. 237 matched cddid_all.tbl CDD cd19180 cd19180 380957 SET_SpSET10-like SET domain found in Schizosaccharomyces pombe SET domain-containing protein 10 (SETD10) and similar proteins. Schizosaccharomyces pombe SETD10 is a ribosomal S-adenosyl-L-methionine-dependent protein-lysine N-methyltransferase that methylates ribosomal protein L23 (rpl23a and rpl23b). 252 matched cddid_all.tbl CDD cd19181 cd19181 380958 SET_SETD5 SET domain (including post-SET domain) found in SET domain-containing protein 5 (SETD5) and similar proteins. SETD5 is a probable transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. SETD5 loss-of-function mutations are a likely cause of a familial syndromic intellectual disability with variable phenotypic expression. 150 matched cddid_all.tbl CDD cd19182 cd19182 380959 SET_KMT2E SET domain found in inactive histone-lysine N-methyltransferase 2E (KMT2E) and similar proteins. KMT2E (also termed inactive lysine N-methyltransferase 2E, myeloid/lymphoid or mixed-lineage leukemia protein 5 (MLL5)) plays a key role in hematopoiesis, spermatogenesis and cell cycle progression. It associates with chromatin regions downstream of transcriptional start sites of active genes and thus regulates gene transcription. Lack of key residues in the SET domain as well as the presence of an unusually large loop in the SET-I subdomain preclude the interaction of MLL5 SET with its cofactor and substrate thus making MLL5 devoid of any in vitro methyltransferase activity on full-length histones and histone H3 peptide. 129 matched cddid_all.tbl CDD cd19183 cd19183 380960 SET_SpSET3-like SET domain (including post-SET domain) found in Schizosaccharomyces pombe SET domain-containing protein 3 (SETD3) and similar proteins. Schizosaccharomyces pombe SETD3 functions as a transcriptional regulator that acts via the formation of large multiprotein complexes that modify and/or remodel the chromatin. It is required for both, gene activation and repression. 173 matched cddid_all.tbl CDD cd19184 cd19184 380961 SET_KMT5B SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 5B (KMT5B) and similar proteins. KMT5B (also termed lysine N-methyltransferase 5B, lysine-specific methyltransferase 5B, suppressor of variegation 4-20 homolog 1, Su(var)4-20 homolog 1 or Suv4-20h1) is a histone methyltransferase that specifically trimethylates 'Lys-20' of histone H4 (H4K20me3). It plays a central role in the establishment of constitutive heterochromatin in pericentric heterochromatin regions. 144 matched cddid_all.tbl CDD cd19185 cd19185 380962 SET_KMT5C SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 5C (KMT5C) and similar proteins. KMT5C (also termed lysine N-methyltransferase 5C, lysine-specific methyltransferase 5C, suppressor of variegation 4-20 homolog 2, Su(var)4-20 homolog 2 or Suv4-20h2) is a histone methyltransferase that specifically trimethylates 'Lys-20' of histone H4 (H4K20me3). It plays a central role in the establishment of constitutive heterochromatin in pericentric heterochromatin regions. 142 matched cddid_all.tbl CDD cd19186 cd19186 380963 SET_Suv4-20 SET domain (including post-SET domain) found in Drosophila melanogaster suppressor of variegation 4-20 (Suv4-20) and similar proteins. Suv4-20 (also termed Su(var)4-20) is a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-20' of histone H4. It acts as a dominant suppressor of position-effect variegation. 142 matched cddid_all.tbl CDD cd19187 cd19187 380964 PR-SET_PRDM1 PR-SET domain found in PR domain zinc finger protein 1 (PRDM1) and similar proteins. PRDM1 (also termed BLIMP-1, beta-interferon gene positive regulatory domain I-binding factor, PR domain-containing protein 1, positive regulatory domain I-binding factor 1, PRDI-BF1, or PRDI-binding factor 1) acts as a transcription factor that mediates a transcriptional program in various innate and adaptive immune tissue-resident lymphocyte T cell types such as tissue-resident memory T (Trm), natural killer (trNK) and natural killer T (NKT) cells and negatively regulates gene expression of proteins that promote the egress of tissue-resident T-cell populations from non-lymphoid organs. 128 matched cddid_all.tbl CDD cd19188 cd19188 380965 PR-SET_PRDM2 PR-SET domain found in PR domain zinc finger protein 2 (PRDM2) and similar proteins. PRDM2 (also termed GATA-3-binding protein G3B, lysine N-methyltransferase 8, MTB-or MTE-binding protein, PR domain-containing protein 2, retinoblastoma protein-interacting zinc finger protein, or zinc finger protein RIZ) is S-adenosyl-L-methionine-dependent histone methyltransferase that specifically methylates 'Lys-9' of histone H3. It may function as a DNA-binding transcription factor. 123 matched cddid_all.tbl CDD cd19189 cd19189 380966 PR-SET_PRDM4 PR-SET domain found in PR domain zinc finger protein 4 (PRDM4) and similar proteins. PRDM4 (also termed PR domain-containing protein 4, or PFM1) may function as a transcription factor involved in cell differentiation. 133 matched cddid_all.tbl CDD cd19190 cd19190 380967 PR-SET_PRDM5 PR-SET domain found in PR domain zinc finger protein 5 (PRDM5) and similar proteins. PRDM5 (also termed PR domain-containing protein 5) is a sequence-specific DNA-binding transcription factor that represses transcription at least in part by recruitment of the histone methyltransferase EHMT2/G9A and histone deacetylases such as HDAC1. 127 matched cddid_all.tbl CDD cd19191 cd19191 380968 PR-SET_PRDM6 PR-SET domain found in PR domain zinc finger protein 6 (PRDM6) and similar proteins. PRDM6 (also termed PR domain-containing protein 6) is a putative histone-lysine N-methyltransferase that acts as a transcriptional repressor of smooth muscle gene expression. It may specifically methylate 'Lys-20' of histone H4 when associated with other proteins and in vitro. 128 matched cddid_all.tbl CDD cd19192 cd19192 380969 PR-SET_PRDM8 PR-SET domain found in PR domain zinc finger protein 8 (PRDM8) and similar proteins. PRDM8 (also termed PR domain-containing protein 8) may function as histone methyltransferase, preferentially acting on 'Lys-9' of histone H3. 131 matched cddid_all.tbl CDD cd19193 cd19193 380970 PR-SET_PRDM7_9 PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins. PRDM7 (also termed PR domain-containing protein 7) is a primate-specific histone methyltransferase that is the result of a recent gene duplication of PRDM9. It selectively catalyzes the trimethylation of H3 lysine 4 (H3K4me3). PRDM9 (also termed PR domain-containing protein 9) is a histone methyltransferase that specifically trimethylates 'Lys-4' of histone H3 (H3K4me3) during meiotic prophase and is essential for proper meiotic progression. It also efficiently mono-, di-, and trimethylates H3K36. Aberrant PRDM9 expression is assciated with with genome instability in cancer. 129 matched cddid_all.tbl CDD cd19194 cd19194 380971 PR-SET_PRDM10 PR-SET domain found in PR domain zinc finger protein 10 (PRDM10) and similar proteins. PRDM10 (also termed PR domain-containing protein 10, or tristanin) may be involved in transcriptional regulation. 128 matched cddid_all.tbl CDD cd19195 cd19195 380972 PR-SET_PRDM11 PR-SET domain found in PR domain zinc finger protein 11 (PRDM11) and similar proteins. PRDM11 (also termed PR domain-containing protein 11) may be involved in transcription regulation. 127 matched cddid_all.tbl CDD cd19196 cd19196 380973 PR-SET_PRDM12 PR-SET domain found in PR domain zinc finger protein 12 (PRDM12) and similar proteins. PRDM12 (also termed PR domain-containing protein 12) acts as a transcription factor that is involved in the positive regulation of histone H3-K9 dimethylation. 130 matched cddid_all.tbl CDD cd19197 cd19197 380974 PR-SET_PRDM13 PR-SET domain found in PR domain zinc finger protein 13 (PRDM13) and similar proteins. PRDM13 (also termed PR domain-containing protein 13) may be involved in transcriptional regulation. It mediates the balance of inhibitory and excitatory neurons in somatosensory circuits. 103 matched cddid_all.tbl CDD cd19198 cd19198 380975 PR-SET_PRDM14 PR-SET domain found in PR domain zinc finger protein 14 (PRDM14) and similar proteins. PRDM14 (also termed PR domain-containing protein 14) acts as a transcription factor that has both positive and negative roles on transcription. It acts on regulating epigenetic modifications in the cells, playing a key role in the regulation of cell pluripotency, epigenetic reprogramming, differentiation and development. Aberrant PRDM14 expression is associated with tumorigenesis, cell migration and cell chemotherapeutic drugs resistance. 133 matched cddid_all.tbl CDD cd19199 cd19199 380976 PR-SET_PRDM15 PR-SET domain found in PR domain zinc finger protein 15 (PRDM15) and similar proteins. PRDM15 (also termed PR domain-containing protein 15, or zinc finger protein 298 (ZNF298)) may be involved in transcriptional regulation. It plays an essential role as a chromatin factor that modulates the transcription of upstream regulators of WNT and MAPK-ERK signaling to safeguard naive pluripotency. 126 matched cddid_all.tbl CDD cd19200 cd19200 380977 PR-SET_PRDM16_PRDM3 PR-SET domain found in PR domain zinc finger protein 16 (PRDM16), MDS1 and EVI1 complex locus protein and similar proteins. PRDM16 (also termed PR domain-containing protein 16, transcription factor MEL1, or MDS1/EVI1-like gene 1) functions as a transcriptional regulator. PRDM16 is preferentially expressed by hematopoietic and neuronal stem cells. It is closely related to paralog of PRDM3 (also termed MDS1 and EVI1 complex locus protein, ecotropic virus integration site 1 protein, EVI-1, myelodysplasia syndrome 1 protein, myelodysplasia syndrome-associated protein 1, or MECOM) which is a nuclear transcription factor essential for the proliferation/maintenance of hematopoietic stem cells (HSCs). PRDM3 and PRDM16 are both directly linked to various aspects of oncogenic transformation. 135 matched cddid_all.tbl CDD cd19201 cd19201 380978 PR-SET_ZFPM PR-SET domain found in zinc finger protein ZFPM1, ZFPM2 and similar proteins. ZFPM1 (also termed friend of GATA protein 1, FOG-1, friend of GATA 1, zinc finger protein 89A, or zinc finger protein multitype 1) functions as a transcription regulator that plays an essential role in erythroid and megakaryocytic cell differentiation. ZFPM2 (also termed friend of GATA protein 2, FOG-2, friend of GATA 2, zinc finger protein 89B, or zinc finger protein multitype 2) functions as a transcription regulator that plays a central role in heart morphogenesis and development of coronary vessels from epicardium, by regulating genes that are essential during cardiogenesis. 122 matched cddid_all.tbl CDD cd19202 cd19202 380979 SET_SMYD2 SET domain (including post-SET domain) found in SET and MYND domain-containing protein 2 (SMYD2) and similar proteins. SMYD2 (also termed HSKM-B, lysine N-methyltransferase 3C (KMT3C)) functions as a histone methyltransferase that methylates both histones and non-histone proteins, including p53/TP53 and RB1. It specifically methylates histone H3 'Lys-4' (H3K4me) and dimethylates histone H3 'Lys-36' (H3K36me2). It plays a role in myofilament organization in both skeletal and cardiac muscles via Hsp90 methylation. SMYD2 overexpression is associated with tumor cell proliferation and a worse outcome in human papillomavirus-unrelated nonmultiple head and neck carcinomas. It regulates leukemia cell growth such that diminished SMYD2 expression upregulates SET7/9, thereby possibly shifting leukemia cells from growth to quiescence state associated with resistance to DNA damage associated with Acute Myeloid Leukemia (AML). 206 matched cddid_all.tbl CDD cd19203 cd19203 380980 SET_SMYD3 SET domain (including post-SET domain) found in SET and MYND domain-containing protein 3 (SMYD3) and similar proteins. SMYD3 (also termed zinc finger MYND domain-containing protein 1) functions as a histone methyltransferase that specifically methylates 'Lys-4' of histone H3, inducing di- and tri-methylation, but not monomethylation. It also methylates 'Lys-5' of histone H4. SMYD3 plays an important role in transcriptional activation as a member of an RNA polymerase complex. It is overexpressed in colorectal, breast, prostate, and hepatocellular tumors, and has been implicated as an oncogene in human malignancies. Methylation of MEKK2 by SMYD3 is important for regulation of the MEK/ERK pathway, suggesting the possibility of selectively targeting SMYD3 in RAS-driven cancers. 210 matched cddid_all.tbl CDD cd19204 cd19204 380981 SET_SETD1A SET domain (including post-SET domain) found in SET domain-containing protein 1A (SETD1A) and similar proteins. SETD1A (EC2.1.1.43), also termed lysine N-methyltransferase 2F, or Set1/Ash2 histone methyltransferase complex subunit SET1, is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me), when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. Human SET domain containing protein 1A (hSETD1A) expression occurs at a high rate in hepatocellular carcinoma patients and controls tumor metastasis in breast cancer by activating MMP expression. 153 matched cddid_all.tbl CDD cd19205 cd19205 380982 SET_SETD1B SET domain (including post-SET domain) found in SET domain-containing protein 1B (SETD1B) and similar proteins. SETD1B (EC2.1.1.43), also termed lysine N-methyltransferase 2G, is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me) when part of the SET1 histone methyltransferase (HMT) complex, but not if the neighboring 'Lys-9' residue is already methylated. Loss of SETD1B occurs in up to half the gastric and colorectal cancers, most commonly via SETD1B mutations, while de novo variants in SETD1B are associated with intellectual disability, epilepsy and autism. 153 matched cddid_all.tbl CDD cd19206 cd19206 380983 SET_KMT2A SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2A (KMT2A) and similar proteins. KMT2A (EC2.1.1.43; also termed lysine N-methyltransferase 2A, ALL-1, CXXC-type zinc finger protein 7 (CXXC7), myeloid/lymphoid or mixed-lineage leukemia (MLL), myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (TRX1), or zinc finger protein HRX) acts as a histone methyltransferase that plays an essential role in early development and hematopoiesis. It is a catalytic subunit of the MLL1/MLL complex, a multiprotein complex that mediates both methylation of 'Lys-4' of histone H3 (H3K4me) complex and acetylation of 'Lys-16' of histone H4 (H4K16ac). 154 matched cddid_all.tbl CDD cd19207 cd19207 380984 SET_KMT2B SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2B (KMT2B) and similar proteins. KMT2B (EC2.1.1.43; also termed lysine N-methyltransferase 2B, myeloid/lymphoid or mixed-lineage leukemia protein 4 (MLL2/MLL4), trithorax homolog 2 (TRX2), or WW domain-binding protein 7 (WBP-7)), acts as a histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me). It is required during the transcriptionally active period of oocyte growth for the establishment and/or maintenance of bulk H3K4 trimethylation (H3K4me3), global transcriptional silencing that precedes resumption of meiosis, oocyte survival and normal zygotic genome activation. 154 matched cddid_all.tbl CDD cd19208 cd19208 380985 SET_KMT2C SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2C (KMT2C) and similar proteins. KMT2C (EC2.1.1.43; also termed lysine N-methyltransferase 2C, homologous to ALR protein (HALR) myeloid/lymphoid, or mixed-lineage leukemia protein 3 (MLL3)), acts as a histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me) and may be involved in leukemogenesis and developmental disorder. KMT2C is a catalytic subunit of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation. Overexpression of KMT2C is associated with estrogen receptor-positive breast cancer; KMT2C mediates the estrogen dependence of breast cancer through regulation of estrogen receptor alpha (ERalpha) enhancer function. KMT2C is frequently mutated in certain populations with diffuse-type gastric adenocarcinomas (DGA); its loss promotes epithelial-to-mesenchymal transition (EMT) and is associated with worse overall survival. 154 matched cddid_all.tbl CDD cd19209 cd19209 380986 SET_KMT2D SET domain (including post-SET domain) found in histone-lysine N-methyltransferase 2D (KMT2D) and similar proteins. KMT2D (EC2.1.1.43; also termed lysine N-methyltransferase 2D, ALL1-related protein (ALR), or myeloid/lymphoid or mixed-lineage leukemia protein 2 (MLL2)), acts as histone methyltransferase that methylates 'Lys-4' of histone H3 (H3K4me). It is a coactivator for estrogen receptor by being recruited by ESR1, thereby activating transcription. KMT2D is a subunit of MLL2/3 complex, a coactivator complex of nuclear receptors, involved in transcriptional coactivation. 155 matched cddid_all.tbl CDD cd19210 cd19210 380987 SET_NSD1 SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing protein 1 (NSD1) and similar proteins. NSD1 (EC 2.1.1.43; also termed Histone-lysine N-methyltransferase H3 lysine-36 and H4 lysine-20 specific, androgen receptor coactivator 267 kDa protein (ARA267), androgen receptor-associated protein of 267 kDa, H3-K36-HMTase, H4-K20-HMTase, lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-36' of histone H3 and 'Lys-20' of histone H4. NSD1 is altered in approximately 10% of head and neck cancer patients with 55% decrease in risk of death in NSD1-mutated versus non-mutated patients; its disruption promotes favorable chemotherapeutic responses linked to hypomethylation. 142 matched cddid_all.tbl CDD cd19211 cd19211 380988 SET_NSD2 SET domain (including post-SET domain) found in nuclear SET domain-containing protein 2 (NSD2) and similar proteins. NSD2 (EC 2.1.1.43; also termed multiple myeloma SET domain-containing protein (MMSET), protein trithorax-5 (TRX5), or wolf-Hirschhorn syndrome candidate 1 protein (WHSC1)) acts as histone-lysine N-methyltransferase with histone H3 'Lys-36' (H3K36me) methyltransferase activity. NSD2 has been shown to mediate di- and trimethylation of H3K36 and dimethylation of H4K20 in different systems, and has been characterized as a transcriptional repressor interacting with histone deacetylase HDAC1 and histone demethylase LSD1. NSD2 mediates constitutive NF-kappaB signaling for cancer cell proliferation, survival and tumor growth. It is highly overexpressed in several types of human cancers, including small-cell lung cancers, neuroblastoma, carcinomas of stomach and colon, and bladder cancers, and its overexpression tends to be associated with tumor aggressiveness. WHSC1 is frequently deleted in Wolf-Hirschhorn syndrome (WHS). 142 matched cddid_all.tbl CDD cd19212 cd19212 380989 SET_NSD3 SET domain (including post-SET domain) found in nuclear receptor-binding SET domain-containing protein 3 (NSD3) and similar proteins. NSD3 (EC 2.1.1.43; also termed protein whistle, WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1L1), or WHSC1-like protein 1) functions as a histone-lysine N-methyltransferase that preferentially methylates 'Lys-4' and 'Lys-27' of histone H3. NSD3 is amplified and overexpressed in multiple cancer types, including acute myeloid leukemia (AML), breast, lung, pancreatic and bladder cancers, as well as squamous cell carcinoma of the head and neck (SCCHN). NSD3 contributes to tumorigenesis by interacting with bromodomain-containing protein 4 (BRD4), the bromodomain and extraterminal (BET) protein, which is a potential therapeutic target in acute myeloid leukemia (AML). NSD3 is amplified in primary tumors and cell lines from breast carcinoma, and can promote the cell viability of small-cell lung cancer and pancreatic ductal adenocarcinoma. High NSD3 expression is implicated in poor grade and heavy smoking history in SCCHN. Thus, NSD3 may serve as a potential druggable target for selective cancer therapy. 142 matched cddid_all.tbl CDD cd19213 cd19213 380990 PR-SET_PRDM16 PR-SET domain found in PR domain zinc finger protein 16 (PRDM16) and similar proteins. PRDM16, also termed PR domain-containing protein 16, or transcription factor MEL1, or MDS1/EVI1-like gene 1, functions as a transcriptional regulator. PRDM16 is preferentially expressed by hematopoietic and neuronal stem cells and is closely related to paralog of PRDM3, both of which are directly linked to various aspects of oncogenic transformation. 162 matched cddid_all.tbl CDD cd19214 cd19214 380991 PR-SET_PRDM3 PR-SET domain found in MDS1 and EVI1 complex locus protein and similar proteins. PRDM3 (also termed MDS1 and EVI1 complex locus protein, ecotropic virus integration site 1 protein, EVI-1, myelodysplasia syndrome 1 protein, myelodysplasia syndrome-associated protein 1, or MECOM) is a nuclear transcription factor, which is essential for the proliferation/maintenance of hematopoietic stem cells (HSCs). It is closely related to paralog PRDM16, both o fwhich are directly linked to various aspects of oncogenic transformation. 158 matched cddid_all.tbl CDD cd19215 cd19215 380992 PR-SET_ZFPM1 PR-SET domain found in zinc finger protein ZFPM1 and similar proteins. ZFPM1 (also termed friend of GATA protein 1, FOG-1, friend of GATA 1, zinc finger protein 89A, or zinc finger protein multitype 1) functions as a transcription regulator that plays an essential role in erythroid and megakaryocytic cell differentiation. 110 matched cddid_all.tbl CDD cd19216 cd19216 380993 PR-SET_ZFPM2 PR-SET domain found in zinc finger protein ZFPM2 and similar proteins. ZFPM2 (also termed friend of GATA protein 2, FOG-2, friend of GATA 2, zinc finger protein 89B, or zinc finger protein multitype 2) functions as a transcription regulator that plays a central role in heart morphogenesis and development of coronary vessels from epicardium, by regulating genes that are essential during cardiogenesis. 111 matched cddid_all.tbl CDD cd19217 cd19217 380994 SET_EZH1 SET domain found in enhancer of zeste homolog 1 (EZH1) and similar proteins. EZH1 (EC 2.1.1.43), also termed ENX-2, or histone-lysine N-methyltransferase EZH1, is a catalytic subunit of the PRC2/EED-EZH1 complex, which methylates 'Lys-27' of histone H3, leading to transcriptional repression of the affected target gene. It can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. 136 matched cddid_all.tbl CDD cd19218 cd19218 380995 SET_EZH2 SET domain found in enhancer of zeste homolog 2 (EZH2) and similar proteins. EZH2 (EC 2.1.1.43), also termed lysine N-methyltransferase 6, or ENX-1, or histone-lysine N-methyltransferase EZH2, is a catalytic subunit of the polycomb repressive complex 2 (PRC2)/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. It can mono-, di- and trimethylate 'Lys-27' of histone H3 to form H3K27me1, H3K27me2 and H3K27me3, respectively. PRC2 is involved in several cancers; EZH2 is overexpressed in breast, liver and prostate cancer, while point mutations in EZH2 alter the substrate preference and product specificity of PRC2 in Non-Hodgkin lymphomas (NHLs). Thus, PRC2 is a popular target for cancer therapeutics. 120 matched cddid_all.tbl CDD cd19318 cd19318 412037 Rev1_UBM2 Ubiquitin-Binding Motif 2 (UBM2) of Y-family polymerase Rev1. This model characterizes UBM2, the second ubiquitin-binding motif of Rev1, a DNA damage tolerance protein. Rev1 acts as a translesion synthesis (TLS) DNA polymerase and may also recruit other TLS polymerases to the site of DNA damage; in that process the UBMs are essential for Rev1 function, triggering TLS activation via recognition of ubiquitin moieties in PCNA, the proliferating cell nuclear antigen. 36 matched cddid_all.tbl CDD cd19333 cd19333 381707 Wnt_Wnt1 Wnt domain found in proto-oncogene Wnt-1 and similar proteins. Wnt-1, also called proto-oncogene Int-1, acts in the canonical Wnt signaling pathway by promoting beta-catenin-dependent transcriptional activation. It plays a role in osteoblast function, bone development and bone homeostasis. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 311 matched cddid_all.tbl CDD cd19334 cd19334 381708 Wnt_Wnt2_like Wnt domain found in protein Wnt-2, Wnt-2b and similar proteins. The family includes Wnt-2 and Wnt-2b. Wnt-2, also called Int-1-like protein 1 (INT1L1), or Int-1-related protein (IRP), functions in the canonical Wnt signaling pathway that results in activation of transcription factors of the TCF/LEF family. It plays an important role in embryonic lung development. Wnt-2b, also called protein Wnt-13, functions in the canonical Wnt/beta-catenin signaling pathway. It plays a redundant role in embryonic lung development. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 314 matched cddid_all.tbl CDD cd19335 cd19335 381709 Wnt_Wnt3_Wnt3a Wnt domain found in proto-oncogene Wnt-3 and similar proteins. Wnt-3, also called proto-oncogene Int-4, functions in the canonical Wnt signaling pathway that results in activation of transcription factors of the TCF/LEF family. It is required for normal embryonic development, and especially for limb development. Wnt-3a functions in the canonical Wnt signaling pathway and plays crucial roles in both proliferation and differentiation processes in several types of stem cells. Wnt3a stimulates the migration and invasion of trophoblasts and induce the survival, proliferation, and migration of human embryonic kidney (HEK) 293 cells. It also up-regulates genes implicated in melanocyte differentiation and increases the expression and nuclear localization of the transcriptional co-activator with PDZ-binding motif (TAZ), a transcriptional modulator involved in activating osteoblastic differentiation. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 314 matched cddid_all.tbl CDD cd19336 cd19336 381710 Wnt_Wnt4 Wnt domain found in protein Wnt-4 and similar proteins. Wnt-4 may function as a signaling molecule which affects the development of discrete regions of tissues. Its overexpression may be associated with abnormal proliferation in human breast tissue. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 310 matched cddid_all.tbl CDD cd19337 cd19337 381711 Wnt_Wnt5 Wnt domain found in protein Wnt-5a, Wnt-5b and similar proteins. The family includes Wnt-5a and Wnt-5b, both of which are secreted growth factors that belong to the noncanonical members of the Wingless-related MMTV-integration family. Wnt-5a can activate or inhibit canonical Wnt signaling, depending on receptor context. It specifically regulates dendritic spine formation in rodent hippocampal neurons, resulting in postsynaptic development that promotes the clustering of the postsynaptic density protein 95 (PSD-95). The overexpression of Wnt-5b is associated with cancer aggressiveness. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 313 matched cddid_all.tbl CDD cd19338 cd19338 381712 Wnt_Wnt6 Wnt domain found in protein Wnt-6 and similar proteins. Wnt-6 may function as a signaling molecule which affects the development of discrete regions of tissues. It may promote tumorigenesis in gastrointestinal cancer and cervical cancer. It can compensate for the absence of ectoderm and can induce the formation of muscle cells in the limb. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 310 matched cddid_all.tbl CDD cd19339 cd19339 381713 Wnt_Wnt7 Wnt domain found in protein Wnt-7a, Wnt-7b and similar proteins. The family includes Wnt-7a and Wnt-7b. Wnt-7a acts as a canonical Wnt ligand that modulates the synaptic vesicle cycle and synaptic transmission in hippocampal neurons. It also plays an important role in embryonic development, including dorsal versus ventral patterning during limb development, skeleton development, and urogenital tract development. Wnt-7b functions in the canonical Wnt/beta-catenin signaling pathway in vascular smooth muscle cells. It is required for normal fusion of the chorion and the allantois during placenta development. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 313 matched cddid_all.tbl CDD cd19340 cd19340 381714 Wnt_Wnt8 Wnt domain found in protein Wnt-8a, Wnt-8b and similar proteins. The family includes Wnt-8a and Wnt-8b. Wnt-8a, also called protein Wnt-8d, plays a role in embryonic patterning. Wnt-8b may play an important role in the development and differentiation of certain forebrain structures, notably the hippocampus. It acts as a suppressor of early eye and retinal progenitor formation. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 301 matched cddid_all.tbl CDD cd19341 cd19341 381715 Wnt_Wnt9 Wnt domain found in protein Wnt-9a, Wnt-9b and similar proteins. The family includes Wnt-9a and Wnt-9b, both of which function in the canonical Wnt/beta-catenin signaling pathway. Wnt-9a, also called protein Wnt-14, is required for normal timing of IHH expression during embryonic bone development, normal chondrocyte maturation and for normal bone mineralization during embryonic bone development. Wnt-9a plays a redundant role in maintaining joint integrity. It is a conserved regulator of hematopoietic stem and progenitor cell development. Wnt-9b, also called protein Wnt-14b, or protein Wnt-15, plays a central role in the regulation of mesenchymal to epithelial transitions underlying organogenesis of the mammalian urogenital system. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 299 matched cddid_all.tbl CDD cd19342 cd19342 381716 Wnt_Wnt10 Wnt domain found in protein Wnt-10a, Wnt-10b and similar proteins. The family includes protein Wnt-10a and Wnt-10b. Wnt-10a plays a role in normal ectoderm development. It is required for normal postnatal development and maintenance of tongue papillae and sweat ducts, as well as normal hair follicle function. Wnt-10b, also called protein Wnt-12, specifically activates canonical Wnt/beta-catenin signaling and thus triggers beta-catenin/LEF/TCF-mediated transcriptional programs. It is involved in signaling networks controlling stemness, pluripotency, and cell fate decisions. Wnt-10b is unique and plays an important role in differentiation of epithelial cells in the hair follicle. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 316 matched cddid_all.tbl CDD cd19343 cd19343 381717 Wnt_Wnt11 Wnt domain found in protein Wnt-11 and similar proteins. Wnt-11 may be a signaling molecule which has possible roles in the development of skeleton, kidney and lung. It is a positive regulator of the Wnt signaling pathway, which plays a crucial role in carcinogenesis. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 305 matched cddid_all.tbl CDD cd19344 cd19344 381718 Wnt_Wnt16 Wnt domain found in protein Wnt-16 and similar proteins. Wnt-16 is a mixed canonical and noncanonical Wnt ligand involved in the regulation of postnatal bone homeostasis. It promotes bone formation and inhibits bone resorption. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 306 matched cddid_all.tbl CDD cd19345 cd19345 381719 Wnt_Wnt2 Wnt domain found in protein Wnt-2 and similar proteins. Wnt-2, also called Int-1-like protein 1 (INT1L1), or Int-1-related protein (IRP), functions in the canonical Wnt signaling pathway that results in activation of transcription factors of the TCF/LEF family. It plays an important role in embryonic lung development. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 314 matched cddid_all.tbl CDD cd19346 cd19346 381720 Wnt_Wnt2b Wnt domain found in protein Wnt-2b and similar proteins. Wnt-2b, also called protein Wnt-13, functions in the canonical Wnt/beta-catenin signaling pathway. It plays a redundant role in embryonic lung development. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 314 matched cddid_all.tbl CDD cd19347 cd19347 381721 Wnt_Wnt5a Wnt domain found in protein Wnt-5a and similar proteins. Wnt-5a is a secreted growth factor that belongs to the noncanonical members of the Wingless-related MMTV-integration family. It can activate or inhibit canonical Wnt signaling, depending on receptor context. Wnt-5a specifically regulates dendritic spine formation in rodent hippocampal neurons, resulting in postsynaptic development that promotes the clustering of the postsynaptic density protein 95 (PSD-95). Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 312 matched cddid_all.tbl CDD cd19348 cd19348 381722 Wnt_Wnt5b Wnt domain found in protein Wnt-5b and similar proteins. Wnt-5b is a secreted growth factor that belongs to the noncanonical members of the Wingless-related MMTV-integration family. Its overexpression is associated with cancer aggressiveness. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 312 matched cddid_all.tbl CDD cd19349 cd19349 381723 Wnt_Wnt7a Wnt domain found in protein Wnt-7a and similar proteins. Wnt-7a acts as a canonical Wnt ligand that modulates the synaptic vesicle cycle and synaptic transmission in hippocampal neurons. It also plays an important role in embryonic development, including dorsal versus ventral patterning during limb development, skeleton development and urogenital tract development. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 318 matched cddid_all.tbl CDD cd19350 cd19350 381724 wnt_Wnt7b Wnt domain found in protein Wnt-7b and similar proteins. Wnt-7b functions in the canonical Wnt/beta-catenin signaling pathway in vascular smooth muscle cells. It is required for normal fusion of the chorion and the allantois during placenta development. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 318 matched cddid_all.tbl CDD cd19351 cd19351 381725 Wnt_Wnt8a Wnt domain found in protein Wnt-8a and similar proteins. Wnt-8a, also called protein Wnt-8d, plays a role in embryonic patterning. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 307 matched cddid_all.tbl CDD cd19352 cd19352 381726 Wnt_Wnt8b Wnt domain found in protein Wnt-8b and similar proteins. Wnt-8b may play an important role in the development and differentiation of certain forebrain structures, notably the hippocampus. It acts as a suppressor of early eye and retinal progenitor formation. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 305 matched cddid_all.tbl CDD cd19353 cd19353 381727 Wnt_Wnt9a Wnt domain found in protein Wnt-9a and similar proteins. Wnt-9a, also called protein Wnt-14, functions in the canonical Wnt/beta-catenin signaling pathway. It is required for normal timing of IHH expression during embryonic bone development, normal chondrocyte maturation and for normal bone mineralization during embryonic bone development. Wnt-9a plays a redundant role in maintaining joint integrity. It is a conserved regulator of hematopoietic stem and progenitor cell development. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 298 matched cddid_all.tbl CDD cd19354 cd19354 381728 Wnt_Wnt9b Wnt domain found in protein Wnt-9b and similar proteins. Wnt-9b, also called protein Wnt-14b or Wnt-15, functions in the canonical Wnt/beta-catenin signaling pathway. It plays a central role in the regulation of mesenchymal to epithelial transitions underlying organogenesis of the mammalian urogenital system. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 297 matched cddid_all.tbl CDD cd19355 cd19355 381729 Wnt_Wnt10a Wnt domain found in protein Wnt-10a and similar proteins. Wnt-10a plays a role in normal ectoderm development. It is required for normal postnatal development and maintenance of tongue papillae and sweat ducts, as well as normal hair follicle function. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 302 matched cddid_all.tbl CDD cd19356 cd19356 381730 Wnt_Wnt10b Wnt domain found in protein Wnt-10b and similar proteins. Wnt-10b, also called protein Wnt-12, specifically activates canonical Wnt/beta-catenin signaling and thus triggers beta-catenin/LEF/TCF-mediated transcriptional programs. It is involved in signaling networks controlling stemness, pluripotency and cell fate decisions. Wnt-10b is unique and plays an important role in differentiation of epithelial cells in the hair follicle. Wnt genes have been identified in vertebrates and invertebrates, but not in plants, unicellular eukaryotes, or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. The Wnt signaling mediated by Wnt proteins that orchestrate and influence a myriad of cellular processes, such as cell proliferation, differentiation, tumorigenesis, apoptosis, and participation in immune defense during microbe infection. 299 matched cddid_all.tbl CDD cd19357 cd19357 381692 TenA_E_At3g16990-like TenA_E proteins similar to Arabidopsis thaliana At3g16990. This family of TenA proteins belongs to the TenA_E class, and lacks the conserved active site Cys residue of the TenA_C class; most have a pair of structurally conserved Glu residues in the active site. TenA_C proteins (EC 3.5.99.2; aminopyrimidine aminohydrolase, also known as thiaminase II) catalyze the hydrolysis of the thiamin breakdown product 4-amino-5-amino-methyl-2-methylpyrimidine (amino-HMP) to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) in a thiamin salvage pathway; the role of TenA_E proteins is less clear. Members of this family include Arabidopsis thaliana At3g16990, Zea mays GRMZM2G080501, and Pyrococcus furiosus PF1337, among others. Arabidopsis thaliana TenA_E hydrolyzes amino-HMP to AMP, and the N-formyl derivative of amino-HMP to amino-HMP, but does not hydrolyze thiamin; nor does it have activity with other thiamine degradation products such as thiamine mono- or diphosphate, oxythiamine, oxothiamine, thiamine disulfide, desthiothiamine or thiochrome as substrates. Structural studies of P. furiosus PF1337 strongly support its enzymatic function in thiamine biosynthesis. It has also been suggested that TenA proteins act as transcriptional regulators based on changes in gene-expression patterns when TenA is overexpressed in Bacillus subtilis, however this effect may be indirect. 217 matched cddid_all.tbl CDD cd19358 cd19358 381693 TenA_E_Spr0628-like TenA_E proteins similar to Streptococcus pneumoniae Spr0628 and Saccharomyces cerevisiae S288C PET18. This family of TenA proteins belongs to the TenA_E class, and lacks the conserved active site Cys residue of the TenA_C class; most have a pair of structurally conserved Glu residues in the active site. TenA_C proteins (EC 3.5.99.2; aminopyrimidine aminohydrolase, also known as thiaminase II) catalyze the hydrolysis of the thiamin breakdown product 4-amino-5-amino-methyl-2-methylpyrimidine (amino-HMP) to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) in a thiamin salvage pathway; the role of TenA_E proteins is less clear. Arabidopsis thaliana TenA_E (not belonging to this family) hydrolyzes amino-HMP to AMP, and the N-formyl derivative of amino-HMP to amino-HMP. Members of this family include the putative thiaminase Streptococcus pneumoniae Spr0628, and Saccharomyces cerevisiae S288C PET18, a protein of unknown function whose expression is induced in the absence of thiamin. It has also been suggested that TenA proteins act as transcriptional regulators based on changes in gene-expression patterns when TenA is overexpressed in Bacillus subtilis, however this effect may be indirect. Many proteins in this family have yet to be characterized. 209 matched cddid_all.tbl CDD cd19359 cd19359 381694 TenA_C_Bt3146-like uncharacterized TenA_C proteins similar to Bacteroides thetaiotaomicron Bt3146. This family of TenA proteins belongs to the TenA_C class as it has a conserved active site Cys residue; only one of the double Glu residues identified in the active site of TenA_E from the archaeon Pyrococcus furiosus is conserved in this family. TenA_C proteins (EC 3.5.99.2) catalyze the hydrolysis of the thiamin breakdown product 4-amino-5-amino-methyl-2-methylpyrimidine (amino-HMP) to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) in a thiamin salvage pathway. It has also been suggested that TenA proteins act as transcriptional regulators based on changes in gene-expression patterns when TenA is overexpressed in Bacillus subtilis, however this effect may be indirect. This family includes mostly uncharacterized TenA-like proteins such as Bacteroides thetaiotaomicron Bt3146. 206 matched cddid_all.tbl CDD cd19360 cd19360 381695 TenA_C_SaTenA-like TenA_C proteins similar to Staphylococcus aureus TenA (SaTenA). This family of TenA proteins belongs to the TenA_C class as it has a conserved active site Cys residue; the double Glu residues identified in the active site of TenA_E from the archaeon Pyrococcus furiosus is conserved in this family. TenA_C proteins (EC 3.5.99.2) catalyze the hydrolysis of the thiamin breakdown product 4-amino-5-amino-methyl-2-methylpyrimidine (amino-HMP) to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) in a thiamin salvage pathway. This family includes Staphylococcus aureus TenA (SaTenA) which plays two essential roles in thiamin metabolism: in the deamination of aminopyrimidine to HMP, and in hydrolyzing thiamin into HMP and 5-(2-hydroxyethyl)4-methylthiazole (THZ). It has also been suggested that TenA proteins act as transcriptional regulators based on changes in gene-expression patterns when TenA is overexpressed in Bacillus subtilis, however this effect may be indirect. SaTenA is then also a putative transcriptional regulator controlling the secretion of extracellular proteases such as subtilisin-type proteases in bacteria. This family includes mostly uncharacterized TenA like proteins. 211 matched cddid_all.tbl CDD cd19361 cd19361 381696 TenA_C_HP1287-like TenA_C proteins similar to Helicobacter pylori TenA (HP1287. This family of TenA proteins belongs to the TenA_C class as it has a conserved active site Cys residue; the double Glu residues identified in the active site of TenA_E from the archaeon Pyrococcus furiosus is conserved in this family. TenA_C proteins (EC 3.5.99.2) catalyze the hydrolysis of the thiamin breakdown product 4-amino-5-amino-methyl-2-methylpyrimidine (amino-HMP) to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) in a thiamin salvage pathway. This family includes Helicobacter pylori TenA (HP1287) protein which is thought to catalyze a salvage reaction in thiamin metabolism, however its pyrimidine substrate has not yet been identified. It has also been suggested that TenA proteins act as transcriptional regulators based on changes in gene-expression patterns when TenA is overexpressed in Bacillus subtilis, however this effect may be indirect. HP1287 may contribute to stomach colonization and persistence. 212 matched cddid_all.tbl CDD cd19362 cd19362 381697 TenA_C_SsTenA-1-like uncharacterized TenA_C proteins similar to Sulfolobus solfataricus TenA-1 (Sso2206). This family of TenA proteins belongs to the TenA_C class as it has a conserved active site Cys residue; only one of the double Glu residues identified in the active site of TenA_E from the archaeon Pyrococcus furiosus is conserved in this family. TenA_C proteins (EC 3.5.99.2) catalyze the hydrolysis of the thiamin breakdown product 4-amino-5-amino-methyl-2-methylpyrimidine (amino-HMP) to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) in a thiamin salvage pathway. It has also been suggested that TenA proteins act as transcriptional regulators based on changes in gene-expression patterns when TenA is overexpressed in Bacillus subtilis, however this effect may be indirect. This family includes mostly uncharacterized TenA like proteins such as Sulfolobus solfataricus putative TenA-like thiaminase (Tena-1, Sso2206). 200 matched cddid_all.tbl CDD cd19363 cd19363 381698 TenA_C_PH1161-like uncharacterized TenA_C proteins similar to Pyrococcus horikoshii PH1161. This family of TenA proteins belongs to the TenA_C class as it has a conserved active site Cys residue; only one of the double Glu residues identified in the active site of TenA_E from the archaeon Pyrococcus furiosus is conserved in this family. TenA_C proteins (EC 3.5.99.2) catalyze the hydrolysis of the thiamin breakdown product 4-amino-5-amino-methyl-2-methylpyrimidine (amino-HMP) to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) in a thiamin salvage pathway. It has also been suggested that TenA proteins act as transcriptional regulators based on changes in gene-expression patterns when TenA is overexpressed in Bacillus subtilis, however this effect may be indirect. This family includes functionally uncharacterized TenA like proteins such as Pyrococcus horikoshii PH1161 protein. 210 matched cddid_all.tbl CDD cd19364 cd19364 381699 TenA_C_BsTenA-like TenA_C proteins similar to Bacillus subtilis TenA. This family of TenA proteins belongs to the TenA_C class as it has a conserved active site Cys residue; the double Glu residues identified in the active site of TenA_E from the archaeon Pyrococcus furiosus is conserved in this family. TenA_C proteins (EC 3.5.99.2) catalyze the hydrolysis of the thiamin breakdown product 4-amino-5-amino-methyl-2-methylpyrimidine (amino-HMP) to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) in a thiamin salvage pathway. This family includes Bacillus subtilis TenA which has been shown to be a thiaminase II, catalyzing the hydrolysis of thiamine into HMP and 5-(2-hydroxyethyl)-4-methylthiazole (THZ), within thiamine metabolism. It has also been suggested that TenA proteins act as transcriptional regulators based on changes in gene-expression patterns when TenA is overexpressed in Bacillus subtilis, however this effect may be indirect. 212 matched cddid_all.tbl CDD cd19365 cd19365 381700 TenA_C-like uncharacterized TenA_C proteins. This family of TenA proteins belongs to the TenA_C class as it has a conserved active site Cys residue; the double Glu residues identified in the active site of TenA_E from the archaeon Pyrococcus furiosus is conserved in this family. TenA_C proteins (EC 3.5.99.2) catalyze the hydrolysis of the thiamin breakdown product 4-amino-5-amino-methyl-2-methylpyrimidine (amino-HMP) to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) in a thiamin salvage pathway. It has also been suggested that TenA proteins act as transcriptional regulators based on changes in gene-expression patterns when TenA is overexpressed in Bacillus subtilis, however this effect may be indirect. This family includes mostly uncharacterized TenA_C- like proteins. 205 matched cddid_all.tbl CDD cd19366 cd19366 381701 TenA_C_BhTenA-like TenA_C proteins similar to Bacillus halodurans TenA. This family of TenA proteins belongs to the TenA_C class as it has a conserved active site Cys residue; the double Glu residues identified in the active site of TenA_E from the archaeon Pyrococcus furiosus is conserved in this family. TenA_C proteins (EC 3.5.99.2) catalyze the hydrolysis of the thiamin breakdown product 4-amino-5-amino-methyl-2-methylpyrimidine (amino-HMP) to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) in a thiamin salvage pathway. This family includes Bacillus halodurans TenA which participates in a salvage pathway where the thiamine degradation product 2-methyl-4-formylamino-5-aminomethylpyrimidine (formylamino-HMP) is hydrolyzed first to amino-HMP by the YlmB protein, and the amino-HMP is then hydrolyzed by TenA to produce HMP. It has also been suggested that TenA proteins act as transcriptional regulators based on changes in gene-expression patterns when TenA is overexpressed in Bacillus subtilis, however this effect may be indirect. 213 matched cddid_all.tbl CDD cd19367 cd19367 381702 TenA_C_ScTHI20-like TenA_C family similar to the C-terminal TenA_C domain of Saccharomyces cerevisiae THI20 protein. This TenA family belongs to the TenA_C class as it has a conserved active site Cys residue; the double Glu residues identified in the active site of TenA_E from the archaeon Pyrococcus furiosus is conserved in this family. TenA_C proteins (EC 3.5.99.2) catalyze the hydrolysis of the thiamin breakdown product 4-amino-5-amino-methyl-2-methylpyrimidine (amino-HMP) to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) in a thiamin salvage pathway. Saccharomyces cerevisiae THI20 includes a C-terminal tetrameric TenA-like domain fused to an N-terminal HMP kinase/HMP-P kinase (ThiD-like) domain, and participates in thiamin biosynthesis, degradation and salvage; the TenA-like domain catalyzes the production of HMP from thiamin degradation products (salvage). A majority of this family are single-domain TenA_C- like proteins; some however have additional domains such as a ThiD domain. It has also been suggested that TenA proteins act as transcriptional regulators based on changes in gene-expression patterns when TenA is overexpressed in Bacillus subtilis, however this effect may be indirect. 204 matched cddid_all.tbl CDD cd19368 cd19368 381703 TenA_C_AtTH2-like TenA_C family similar to the N-terminal TenA_C domain of Arabidopsis thaliana thiamine requiring 2. This TenA family belongs to the TenA_C class as it has a conserved active site Cys residue; the double Glu residues identified in the active site of TenA_E from the archaeon Pyrococcus furiosus is conserved in this family. TenA_C proteins (EC 3.5.99.2) catalyze the hydrolysis of the thiamin breakdown product 4-amino-5-amino-methyl-2-methylpyrimidine (amino-HMP) to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) in a thiamin salvage pathway. Arabidopsis thaliana TH2 is an orphan enzyme thiamin monophosphate phosphatase which has a haloacid dehalogenase (HAD) family domain fused to its TenA_C domain, it's TenA_C domain has thiamin salvage hydrolase activity against amino-HMP. This family includes mostly uncharacterized single-domain TenA_C- like proteins; some however have additional domains such as a HAD family domain or a kinase domain It has also been suggested that TenA proteins act as transcriptional regulators based on changes in gene-expression patterns when TenA is overexpressed in Bacillus subtilis, however this effect may be indirect. 210 matched cddid_all.tbl CDD cd19369 cd19369 381704 TenA_C-like uncharacterized TenA_C proteins. This family of TenA proteins belongs to the TenA_C class as it has a conserved active site Cys residue; the double Glu residues identified in the active site of TenA_E from the archaeon Pyrococcus furiosus is conserved in this family. TenA_C proteins (EC 3.5.99.2) catalyze the hydrolysis of the thiamin breakdown product 4-amino-5-amino-methyl-2-methylpyrimidine (amino-HMP) to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) in a thiamin salvage pathway. It has also been suggested that TenA proteins act as transcriptional regulators based on changes in gene-expression patterns when TenA is overexpressed in Bacillus subtilis, however this effect may be indirect. This family includes mostly uncharacterized TenA_C- like proteins. 202 matched cddid_all.tbl CDD cd19370 cd19370 381705 TenA_PqqC TenA_like proteins, including PqqC and CADD. This family contains proteins with similarity to TenA, and includes bacterial coenzyme pyrroloquinoline quinone (PQQ) synthesis protein C or PQQC proteins. PQQ is the prosthetic group of several bacterial enzymes, including methanol dehydrogenase of methylotrophs and the glucose dehydrogenase of a number of bacteria. PQQC catalyzes the last step of PQQ biogenesis which involves a ring closure and an eight-electron oxidation of the substrate [3a-(2-amino-2-carboxyethyl)-4,5-dioxo-4,5,6,7,8,9-hexahydroquinoline-7,9-dicarboxylic acid (AHQQ)]. The exact molecular function of members of this family is unclear. Also belonging to this family is Chlamydia protein CADD (Chlamydia protein Associating with Death Domains), a redox protein toxin unique to Chlamydia species, which modulates host cell apoptosis; its redox activity and death domain binding ability may be required for this biological activity. CADD may have a role in folate metabolism. 219 matched cddid_all.tbl CDD cd19371 cd19371 381686 UDG-F1-like Uracil DNA glycosylase family 1, includes Human uracil DNA glycosylase, Vaccinia virus protein D4, Nitratifractor salsuginis UNG and similar proteins. Uracil DNA glycosylase family 1 is the most efficient of all uracil-DNA glycosylases (UDGs, also known as UNGs) and shows a specificity for uracil in DNA. UDG catalyzes the removal of uracil from DNA to initiate the DNA base excision repair pathway. Uracil in DNA can arise as a result of misincorporation of dUMP residues by DNA polymerase or deamination of cytosine. Uracil mispaired with guanine in DNA is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. More distant members of UDG family 1 include Nitratifractor salsuginis UNG (NsaUNG) and Vaccinia virus (VAVC) protein D4 uracil-DNA glycosylase, a subunit of the VACV DNA polymerase holoenzyme. NsaUNG only exhibits robust enzymatic activity on uracil-containing DNAs, in particular double-stranded uracil-containing substrates; it does not act on hypoxanthine- and xanthine-containing substrates. NsUNG is not inhibited by Ugi protein that specifically inhibits conventional family 1 UDGs. D4, in addition to excising uracil residues from DNA, is part of a heterodimeric processivity factor which potentiates the DNA polymerase activity. 135 matched cddid_all.tbl CDD cd19372 cd19372 381687 UDG_F1_VAVC_D4-like Uracil DNA glycosylase family 1 subfamily, includes Vaccinia virus protein D4 and similar proteins. Vaccinia virus (VAVC) protein D4 uracil-DNA glycosylase, is a subunit of the VACV DNA polymerase holoenzyme, and a more distant member of uracil DNA glycosylase (UDG) family 1. D4, in addition to excising uracil residues from DNA, is part of a heterodimeric processivity factor which potentiates the DNA polymerase activity. UDG catalyzes the removal of uracil from DNA to initiate the DNA base excision repair pathway. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or deamination of cytosine. Uracil mispaired with guanine in DNA is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. 200 matched cddid_all.tbl CDD cd19373 cd19373 381688 UDG-F1_NsUNG-like Uracil DNA glycosylase family 1 subfamily, includes Nitratifractor salsuginis UNG and similar proteins. Uracil DNA glycosylase family 1 is the most efficient of all uracil-DNA glycosylases (UDGs, also known as UNGs) and shows a specificity for uracil in DNA. Nitratifractor salsuginis UNG (NsaUNG) only exhibits robust enzymatic activity on uracil-containing DNAs, in particular double-stranded uracil-containing substrates, and does not act on hypoxanthine- and xanthine-containing substrates. NsUNG is not inhibited by Ugi protein that specifically inhibits conventional family 1 UDGs. UDG catalyzes the removal of uracil from DNA to initiate the DNA base excision repair pathway. Uracil in DNA can arise as a result of misincorporation of dUMP residues by DNA polymerase or deamination of cytosine. Uracil mispaired with guanine in DNA is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. 174 matched cddid_all.tbl CDD cd19374 cd19374 381689 UDG-F3_SMUG1-like Uracil DNA glycosylase family 3 subfamily, includes single-strand-selective monofunctional uracil-DNA glycosylase 1 and similar proteins. Uracil DNA glycosylase family 3 includes Human SMUG1 that can remove uracil and its oxidized pyrimidine derivatives from both, single-stranded DNA and double-stranded DNA, with a preference for single-stranded DNA substrates. The SMUG-targeted mismatched uracil derivatives include 5-hydroxyuracil, 5-hydroxymethyluracil and 5-formyluracil. Also included in this subfamily is Geobacter metallireducens SMUG1 which has dual substrate specificities for DNA with uracil or xanthine. UDG catalyzes the removal of uracil from DNA to initiate the DNA base excision repair pathway. Uracil in DNA can arise as a result of mis-incorporation of dUMP residues by DNA polymerase or deamination of cytosine. Uracil mispaired with guanine in DNA is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. 232 matched cddid_all.tbl CDD cd19375 cd19375 381690 UDG-F3-like_SMUG2 Uracil DNA glycosylase family 3-like subfamily, includes single-strand-selective monofunctional uracil-DNA glycosylase 2 and similar proteins. Uracil DNA glycosylase family 3-like, which includes Pedobacter heparinus SMUG2, displays catalytic activities towards DNA containing uracil or hypoxanthine/xanthine. UDG catalyzes the removal of uracil from DNA to initiate the DNA base excision repair pathway. Uracil in DNA can arise as a result of misincorporation of dUMP residues by DNA polymerase or deamination of cytosine. Uracil mispaired with guanine in DNA is one of the major pro-mutagenic events, causing G:C->A:T mutations. Thus, UDG is an essential enzyme for maintaining the integrity of genetic information. UDGs have been classified into various families on the basis of their substrate specificity, conserved motifs, and structural similarities. Although these families demonstrate different substrate specificities, often the function of one enzyme can be complemented by the other. 218 matched cddid_all.tbl CDD cd19376 cd19376 381646 TGF_beta_GDF15 transforming growth factor beta (TGF-beta) like domain found in mammalian growth/differentiation factor 15 (GDF-15) and similar proteins. GDF-15, also termed macrophage inhibitory cytokine 1 (MIC-1), or NSAID-activated gene 1 protein (NAG-1), or NSAID-regulated gene 1 protein (NRG-1), or placental TGF-beta, or placental bone morphogenetic protein, or prostate differentiation factor, regulates food intake, energy expenditure and body weight in response to metabolic and toxin-induced stresses. 101 matched cddid_all.tbl CDD cd19377 cd19377 381647 TGF_beta_INHA_B_like transforming growth factor beta (TGF-beta) like domain found in inhibin alpha chain (INHA), beta chain (INHB) and similar proteins. INHA is a component of inhibins (inhibin A or inhibin B) that inhibit the secretion of follitropin by the pituitary gland. INHB includes inhibin beta A chain (INHBA), B chain (INHBB), C chain (INHBC), and E chain (INHBE). INHBA, also termed activin beta-A chain, or erythroid differentiation protein (EDF), is a component of inhibin A, activin A, or activin AB. Inhibins and activins inhibit and activate, respectively, the secretion of follitropin by the pituitary gland. INHBB, also termed activin beta-B chain, is a component of inhibin B, activin A, or activin AB. Inhibins and activins inhibit and activate, respectively, the secretion of follitropin by the pituitary gland. INHBC, also termed activin beta-C chain, might play important roles in carcinogenesis. It may function as a negative regulator of liver growth. INHBE, also termed activin beta-E chain, is a possible insulin resistance-associated hepatokine with hepatic gene expression that positively correlated with insulin resistance and body mass index in humans. It also acts as a possible new marker for drug-induced endoplasmic reticulum stress. 101 matched cddid_all.tbl CDD cd19378 cd19378 381648 TGF_beta_DAF7 transforming growth factor beta (TGF-beta) like domain found in Caenorhabditis elegans Dauer larva development regulatory growth factor DAF-7 and similar proteins. DAF-7, also termed abnormal dauer formation protein 7, may act as a negative regulator of dauer larva development by transducing chemosensory information from ASI neurons. It is involved in sensitivity to CO2 levels. 100 matched cddid_all.tbl CDD cd19379 cd19379 381649 TGF_beta_GSDF transforming growth factor beta (TGF-beta) like domain found in Danio rerio gonadal somatic cell derived factor (GSDF) and similar proteins. GSDF is a new member of transforming growth factor beta (TGF-beta) superfamily. It is a teleost- and gonad-specific growth factor that controls sex determination in some fish and plays an important role in mediating germ cell/soma signaling. 94 matched cddid_all.tbl CDD cd19380 cd19380 381650 TGF_beta_GDNF transforming growth factor beta (TGF-beta) like domain found in glial cell line-derived neurotrophic factor (GDNF) and similar proteins. GDNF, also termed astrocyte-derived trophic factor (ATF), is a member of the glial cell-line-derived neurotrophic factor (GDNF) family. It acts as a neurotrophic factor that enhances survival and morphological differentiation of dopaminergic neurons and increases their high-affinity dopamine uptake. 96 matched cddid_all.tbl CDD cd19381 cd19381 381651 TGF_beta_Artemin transforming growth factor beta (TGF-beta) like domain found in Artemin and similar proteins. Artemin, also termed Enovin, or Neublastin, is a member of the glial cell-line-derived neurotrophic factor (GDNF) family with growth promoting activity on neuronal cells. It acts as the ligand for the GFR-alpha-3-RET receptor complex but can also activate the GFR-alpha-1-RET receptor complex. It supports peripheral and central neurons and signals through the GFR-alpha-3-RET receptor complex. 98 matched cddid_all.tbl CDD cd19382 cd19382 381652 TGF_beta_Persephin transforming growth factor beta (TGF-beta) like domain found in Persephin and similar proteins. Persephin is a member of the glial cell-line-derived neurotrophic factor (GDNF) family with neurotrophic activity on mesencephalic dopaminergic and motor neurons. 99 matched cddid_all.tbl CDD cd19383 cd19383 381653 TGF_beta_Neurturin transforming growth factor beta (TGF-beta) like domain found in Neurturin and similar proteins. Neurturin is a member of the glial cell-line-derived neurotrophic factor (GDNF) family. It acts as a neurotrophic factor that supports the survival of sympathetic neurons in culture and may regulate the development and maintenance of the CNS. It might control the size of non-neuronal cell population such as haemopoietic cells. 104 matched cddid_all.tbl CDD cd19384 cd19384 381654 TGF_beta_TGFB1 transforming growth factor beta (TGF-beta) like domain found in transforming growth factor beta-1 (TGF-beta-1) and similar proteins. TGF-beta-1 is a polypeptide member of the transforming growth factor beta superfamily of cytokines. It is a secreted protein that performs many cellular functions, including the control of cell growth, cell proliferation, cell differentiation, and apoptosis. 99 matched cddid_all.tbl CDD cd19385 cd19385 381655 TGF_beta_TGFB2 transforming growth factor beta (TGF-beta) like domain found in transforming growth factor beta-2 (TGF-beta-2) and similar proteins. TGF-beta-2, also termed BSC-1 cell growth inhibitor, or cetermin, or glioblastoma-derived T-cell suppressor factor (G-TSF), or polyergin, is a polypeptide member of the transforming growth factor beta superfamily of cytokines. It is a secreted protein that performs many cellular functions and has a vital role during embryonic development. It can suppress the effects of interleukin-2 dependent T-cell growth. 97 matched cddid_all.tbl CDD cd19386 cd19386 381656 TGF_beta_TGFB3 transforming growth factor beta (TGF-beta) like domain found in transforming growth factor beta-3 (TGF-beta-3) and similar proteins. TGF-beta-3 is a polypeptide member of the transforming growth factor beta superfamily of cytokines. It is involved in embryogenesis and cell differentiation. It regulates molecules involved in cellular adhesion and extracellular matrix (ECM) formation during the process of palate development. 101 matched cddid_all.tbl CDD cd19387 cd19387 381657 TGF_beta_univin transforming growth factor beta (TGF-beta) like domain found in Strongylocentrotus purpuratus univin and similar proteins. Univin may have a critical role in early developmental decisions in the sea urchin embryo. 104 matched cddid_all.tbl CDD cd19388 cd19388 381658 TGF_beta_GDF8 transforming growth factor beta (TGF-beta) like domain found in growth/differentiation factor 8 (GDF8) and similar proteins. GDF8, also termed myostatin, acts specifically as a negative regulator of skeletal muscle growth. 108 matched cddid_all.tbl CDD cd19389 cd19389 381659 TGF_beta_GDF11 transforming growth factor beta (TGF-beta) like domain found in growth/differentiation factor 11 (GDF11) and similar proteins. GDF11, also termed bone morphogenetic protein 11 (BMP-11), is a secreted signal that acts globally to specify positional identity along the anterior/posterior axis during development. 109 matched cddid_all.tbl CDD cd19390 cd19390 381660 TGF_beta_BMP2 transforming growth factor beta (TGF-beta) like domain found in bone morphogenetic protein 2 (BMP-2) and similar proteins. BMP-2, also termed BMP-2A, induces cartilage and bone formation. It stimulates the differentiation of myoblasts into osteoblasts via the EIF2AK3-EIF2A- ATF4 pathway. 103 matched cddid_all.tbl CDD cd19391 cd19391 381661 TGF_beta_BMP4_BMP2B transforming growth factor beta (TGF-beta) like domain found in bone morphogenetic protein 4 (BMP-4) and similar proteins. BMP-4, also termed BMP-2B, induces cartilage and bone formation. It also acts in mesoderm induction, tooth development, limb formation and fracture repair. 107 matched cddid_all.tbl CDD cd19392 cd19392 381662 TGF_beta_DPP transforming growth factor beta (TGF-beta) like domain found in Drosophila melanogaster protein decapentaplegic (Dpp) and similar proteins. decapentaplegic (Dpp) and similar proteins Dpp, also termed as protein DPP-C, is required later in embryogenesis for dorsal closure and patterning of the hindgut. It also functions postembryonically as a long-range morphogen during imaginal disk development and is responsible for the progression of the morphogenetic furrow during eye development. 109 matched cddid_all.tbl CDD cd19393 cd19393 381663 TGF_beta_BMP3 transforming growth factor beta (TGF-beta) like domain found in bone morphogenetic protein 3 (BMP-3) and similar proteins. BMP-3, also termed BMP-3A, or osteogenin, negatively regulates bone density. It antagonizes the ability of certain osteogenic BMPs to induce osteoprogenitor differentitation and ossification. 110 matched cddid_all.tbl CDD cd19394 cd19394 381664 TGF_beta_GDF10 transforming growth factor beta (TGF-beta) like domain found in growth/differentiation factor 10 (GDF10) and similar proteins. GDF10, also termed bone morphogenetic protein 3B (BMP-3B), or bone-inducing protein (BIP), is a growth factor involved in osteogenesis and adipogenesis. 112 matched cddid_all.tbl CDD cd19395 cd19395 381665 TGF_beta_BMP5 transforming growth factor beta (TGF-beta) like domain found in bone morphogenetic protein 5 (BMP-5) and similar proteins. BMP-5 induces cartilage and bone formation. 113 matched cddid_all.tbl CDD cd19396 cd19396 381666 TGF_beta_BMP6 transforming growth factor beta (TGF-beta) like domain found in bone morphogenetic protein 6 (BMP-6) and similar proteins. BMP-6, also termed VG-1-related protein, or VG-1-R, or VGR-1, induces cartilage and bone formation. 103 matched cddid_all.tbl CDD cd19397 cd19397 381667 TGF_beta_BMP7 transforming growth factor beta (TGF-beta) like domain found in bone morphogenetic protein 7 (BMP-7) and similar proteins. BMP-7, also termed osteogenic protein 1 (OP-1), or eptotermin alfa, induces cartilage and bone formation. It may act as the osteoinductive factor responsible for the phenomenon of epithelial osteogenesis and play a role in calcium regulation and bone homeostasis. 107 matched cddid_all.tbl CDD cd19398 cd19398 381668 TGF_beta_BMP8 transforming growth factor beta (TGF-beta) like domain found in bone morphogenetic protein 8A (BMP-8A), 8B (BMP-8B) and similar proteins. BMP-8A plays a role in the maintenance of spermatogenesis and the integrity of the epididymis. BMP-8B, also termed BMP-8, or osteogenic protein 2 (OP-2), may act as secreted factor in cancer progression. It also plays an essential role in bone metabolism and can regulate thermogenesis and energy balance. Like BMP-8A, BMP-8B plays a role in spermatogenesis and placental development. Mutation in either of the genes encoding BMP-8A or BMP-8B causes postnatal depletion of spermatogonia in mice. 105 matched cddid_all.tbl CDD cd19399 cd19399 381669 TGF_beta_GDF5 transforming growth factor beta (TGF-beta) like domain found in growth/differentiation factor 5 (GDF5) and similar proteins. GDF5, also termed bone morphogenetic protein 14 (BMP-14), or cartilage-derived morphogenetic protein 1 (CDMP-1), or lipopolysaccharide-associated protein 4 (LAP-4), or LPS-associated protein 4, or radotermin, is a growth factor involved in bone and cartilage formation. 103 matched cddid_all.tbl CDD cd19400 cd19400 381670 TGF_beta_BMP9 transforming growth factor beta (TGF-beta) like domain found in bone morphogenetic protein 9 (BMP-9) and similar proteins. BMP-9, also termed growth/differentiation factor 2 (GDF-2), is a potent circulating inhibitor of angiogenesis. It signals through the type I activin receptor ACVRL1 but not other activin receptor-like kinases (ALKs). 105 matched cddid_all.tbl CDD cd19401 cd19401 381671 TGF_beta_BMP10 transforming growth factor beta (TGF-beta) like domain found in bone morphogenetic protein 10 (BMP-10) and similar proteins. BMP-10 is required for maintaining the proliferative activity of embryonic cardiomyocytes by preventing premature activation of the negative cell cycle regulator CDKN1C/p57KIP and maintaining the required expression levels of cardiogenic factors such as MEF2C and NKX2-5. It inhibits endothelial cell migration and growth. It may reduce cell migration and cell matrix adhesion in breast cancer cell lines. 105 matched cddid_all.tbl CDD cd19402 cd19402 381672 TGF_beta_GDF9B transforming growth factor beta (TGF-beta) like domain found in growth/differentiation factor 9B (GDF-9B) and similar proteins. GDF-9B, also termed bone morphogenetic protein 15 (BMP15), acts as oocyte-specific growth/differentiation factor that stimulates folliculogenesis and granulosa cell (GC) growth. 104 matched cddid_all.tbl CDD cd19403 cd19403 381673 TGF_beta_GDF9 transforming growth factor beta (TGF-beta) like domain found in growth/differentiation factor 9 (GDF-9) and similar proteins. GDF-9 is required for ovarian folliculogenesis. It promotes primordial follicle development and stimulates granulosa cell proliferation. 106 matched cddid_all.tbl CDD cd19404 cd19404 381674 TGF_beta_INHBA transforming growth factor beta (TGF-beta) like domain found in inhibin beta A chain (INHBA) and similar proteins. INHBA, also termed activin beta-A chain, or erythroid differentiation protein (EDF), is a component of inhibin A, activin A, or activin AB. Inhibins and activins inhibit and activate, respectively, the secretion of follitropin by the pituitary gland. 108 matched cddid_all.tbl CDD cd19405 cd19405 381675 TGF_beta_INHBB transforming growth factor beta (TGF-beta) like domain found in inhibin beta B chain (INHBB) and similar proteins. INHBB, also termed activin beta-B chain, is a component of inhibin B, activin A, or activin AB. Inhibins and activins inhibit and activate, respectively, the secretion of follitropin by the pituitary gland. 107 matched cddid_all.tbl CDD cd19406 cd19406 381676 TGF_beta_INHBC_E transforming growth factor beta (TGF-beta) like domain found in inhibin beta C chain (INHBC), inhibin beta E chain (INHBE) and similar proteins. The family includes INHBC and INHBE. INHBC, also termed activin beta-C chain, might play important roles in carcinogenesis. It may function as a negative regulator of liver growth. INHBE, also termed activin beta-E chain, is a possible insulin resistance-associated hepatokine with hepatic gene expression that positively correlated with insulin resistance and body mass index in humans. It also acts as a possible new marker for drug-induced endoplasmic reticulum stress. 104 matched cddid_all.tbl CDD cd19407 cd19407 438625 Tar_Tsr_sensor ligand binding sensor domain of Tar- and Tsr-related chemoreceptors. Escherichia coli Tar (taxis to aspartate and repellents) and Tsr (taxis to serine and repellents) are homologous transmembrane chemoreceptors that have a high specificity for aspartate and serine, respectively. Both are homodimeric receptors and contain an N-terminal periplasmic ligand binding domain, a transmembrane region, a HAMP domain and a C-terminal cytosolic signaling domain. E. coli Tar mediates bacterial chemotaxis toward attractants, including aspartate (Asp) and maltose, and away from repellents such as nickel and cobalt ions. Tsr has many roles, including sensing of external (serine, leucine) and internal (pH) environments. In Salmonella enterica serovar Typhimurium, Tsr, also called methyl-accepting chemotaxis protein (MCP), is involved in sensing host-derived nitrate in murine intestinal epithelium, thus contributing to invasion of Peyer's patches. This model represents the ligand binding domain of Tar and Tsr. 131 matched cddid_all.tbl CDD cd19408 cd19408 438626 NarX_NarQ_sensor ligand binding sensor domain of NarX and NarQ, and related chemoreceptors. The periplasmic ligand binding sensor domain of NarX and NarQ is a histidine kinase receptor that responds to nitrate and nitrite to effect regulation of anaerobic respiration in various bacteria and similar proteins. It forms a homodimer and binds to ligands such as nitrate via the dimerization interface, a feature that appears to be conserved in this domain superfamily. NarX-NarL sensor-response regulator pair, along with NarQ-NarP, control Escherichia coli gene expression in response to nitrate and nitrite. NarX has been shown to exhibit a clear kinetic preference for NarL over NarP, whereas NarQ exhibits a relatively slight kinetic preference for NarL. There is asymmetry in the Nar cross-regulation network with NarQ shown to interact similarly with both response regulators, while NarX interacts preferentially with NarL. 126 matched cddid_all.tbl CDD cd19409 cd19409 438627 KinB_sensor ligand binding sensor domain of KinB and related sensor histidine kinases. The ligand binding sensor domain of KinB and related sensor histidine kinases forms a homodimer and binds to an as yet uncharacterized ligand, most likely via the dimerization interface, a feature that appears to be conserved in this domain superfamily. In the human pathogen Pseudomonas aeruginosa, quorum sensing has been shown to repress biofilm formation and virulence by activating expression of genes encoding the KinB-AlgB two-component system. The response regulator phospho-AlgB represses biofilm and virulence genes, while histidine kinase KinB dephosphorylates and thereby inactivates AlgB; the stimulus for KinB is as yet unknown. 113 matched cddid_all.tbl CDD cd19410 cd19410 438628 HK9-like_sensor ligand binding sensor domain of Rhodopseudomonas palustris histidine kinase HK9 and similar proteins. The ligand binding sensor domain of Rhodopseudomonas palustris histidine kinase HK9 and similar proteins forms a homodimer and binds to an as yet uncharacterized ligand, most likely via the dimerization interface, a feature that appears to be conserved in this domain superfamily. This domain is similar to the extracellular sensory domain CHASE3, specifically found in histidine kinases, adenylate cyclases, methyl-accepting chemotaxis proteins and predicted diguanylate cyclases/phosphodiesterases. Environmental factors that are recognized by CHASE3 domains are not known at this time. 125 matched cddid_all.tbl CDD cd19411 cd19411 438629 MCP2201-like_sensor ligand-binding sensor domain of Comamonas testosteroni CNB-2 MCP2201 and similar chemoreceptors. This family includes the ligand-binding sensor domain of Comamonas testosteroni transmembrane chemoreceptor CNB-2 MCP2201 and similar chemoreceptors. The C. testosteroni methyl-accepting chemotaxis protein MCP2201 triggers chemotaxis towards tricarboxylic acid cycle intermediates such as citric acid and aromatic compounds. While the apo-form ligand binding domain (LBD) forms a typical four-helix bundle homodimer, similar to other chemoreceptors in the superfamily such as Escherichia coli Tar and Tsr, the citrate-bound LBD reveals a four-helix bundle homotrimer. This type of oligomerization has never been observed in other bacterial chemoreceptor LBD. Site-directed mutations of key amino acid residues have demonstrated the physiological importance of the homotrimer for chemotaxis. 138 matched cddid_all.tbl CDD cd19412 cd19412 410990 pMMO-AMO_C subunit C of particulate methane monooxygenase (pMMO, also known as membrane-bound MMO) from methanotrophic bacteria, and of ammonia monooxygenase (AMO) from ammonia-oxidizing bacteria, and related proteins. This family contains subunit C of particulate methane monooxygenase (pMMO; EC 1.14.18.3), an integral membrane metalloenzyme that catalyzes the conversion of methane to methanol. MMO is the first enzyme in the metabolic pathway of methanotrophic bacteria. It also contains subunit C of AMO (EC 1.14.99.39) from ammonia-oxidizing bacteria such as Nitrosomonas europaea (AmoC1-AmoC3). AMO catalyzes the conversion of ammonia to hydroxylamine. pMMO, along with soluble MMO (sMMO; EC 1.14.13.25), and the related enzyme AMO are the only known enzymes capable of methane hydroxylation. pMMO is composed of three subunits, PmoB (B or alpha), PmoA (A or beta), and PmoC (C or gamma), each containing membrane-spanning helices, with three copies each of the subunits forming a cylindrical A3B3C3 oligomer with a hole in the center. This subunit of pMMO has a metal-binding site that is exposed to the center of the pMMO oligomer, the metal being zinc or copper. Although biochemical and mutagenesis data indicate that the active site is located at the dicopper site in subunit B, the metal-binding site in this transmembrane subunit C may also be functionally relevant since all ligands are conserved and best enzymatic activity is obtained from intact pMMO containing all three subunits. Zinc inhibition studies of several respiratory complexes in Methylococcus capsulatus and Methylosinus trichosporium suggest that zinc might inhibit proton transfer in pMMO by either replacing active site copper ions or another copper site that is involved in reducing the active site. Nitrosomonas europaea AMO is composed of three subunits; AmoA, AmoB, and AmoC; it has two nearly identical copies of AmoC encoded by duplicate amoCAB operons and a more divergent AmoC encoded by a monocistronic amoC. The significantly shorter related C subunit of AMO from ammonia-oxidizing archaea are not included in this model. 217 matched cddid_all.tbl CDD cd19413 cd19413 381292 RsbR_N-like globin-like domain of positive regulator of sigma-B activity (RsbRA). The globin-like domain of Bacillus subtilis RsbRA is a non-heme globin presumed to channel sensory input to the C-terminal sulfate transporter/anti-sigma factor antagonist (STAT) domain. RsbRA is a component of the sigma B-activating stressosome, and a regulator of the RNA polymerase sigma factor subunit sigma (B). 132 matched cddid_all.tbl CDD cd19414 cd19414 381189 lipocalin_1_3_4_13-like lipocalin-1, -3, -4, -13 and similar proteins. Lipocalin-1 (LCN1, also known as tear lipocalin, von ebner's gland protein, or tear specific prealbumin), the main lipid carrier in human tears, is critical to functions involving lipids in protection of the ocular surface. Its large ligand pocket accommodates a range of ligands including alkyl alcohols, glycolipids, phospholipids, cholesterol, steroids, and siderophores. Lipocalin-3 (LCN3, also known as vomeronasal secretory protein 1) and lipocalin-4 (LCN4, also known as vomeronasal secretory protein 2) are involved in transport of lipophilic molecules, and are possibly pheromone-carriers. Lipocalin-13 (LCN13, also known as odorant binding protein 2A) may bind and transport small hydrophobic volatile molecules with a higher affinity for aldehydes and large fatty acids. Another member of this family is late lactation protein B (LLPB), a milk protein produced during the late phase of lactation, which may be involved in transporting a small ligand released during the hydrolysis of milk fat. This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 147 matched cddid_all.tbl CDD cd19415 cd19415 381190 lipocalin_ApoM_AGP apolipoprotein M and alpha1-acid glycoprotein family. Apolipoprotein M (ApoM) is mainly found in high-density lipoproteins (HDL) and is expressed in the liver and in the kidney; it is associated to a lesser extend with low density lipids and triglyceride rich lipoproteins. ApoM is involved in lipid transport and can bind sphingosine-1-phosphate, myristic acid, palmitic acid and stearic acid, retinol, all-trans-retinoic acid and 9-cis-retinoic acid. Alpha1-acid glycoprotein (AGP), also known as orosomucoid, has many important biological roles such as in the acute-phase reaction in response to inflammation, in immune regulation, in drug-binding and drug-transportation, in regulating sphingolipid synthesis and metabolism, and in maintaining the capillary barrier. This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 153 matched cddid_all.tbl CDD cd19416 cd19416 381191 lipocalin_beta-LG-like beta-lactoglobulin and similar proteins. Beta-Lactoglobulin (beta-LG) is the major whey protein of ruminant species and present in the milk of many other species, with a notable exception of human. It is the major allergen of bovine milk. Beta-LG has been shown to bind hydrophobic ligands such as curcumin, vitamin E or fatty acids, or hydrophilic such as vitamin B9. This group also includes human glycodelin (also known as placental protein 14, pregnancy-associated endometrial alpha-2 globulin, and progestagen-associated endometrial protein) which is involved in crucial biological processes such as reproduction and immune reaction. Four glycoforms of glycodelin have been identified in reproductive tissue that differ in glycosylation and biological activity. This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 160 matched cddid_all.tbl CDD cd19417 cd19417 381192 lipocalin_C8gamma complement protein C8 gamma. Human complement protein C8 gamma, together with C8alpha and C8beta, form one of five components of the cytolytic membrane attack complex (MAC), a pore-like structure that assembles on bacterial membranes. C8alpha and C8gamma form a disulfide-linked heterodimer that is noncovalently associated with C8beta. MAC plays an important role in the defense against gram-negative bacteria and other pathogenic organisms. C8gamma belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 162 matched cddid_all.tbl CDD cd19418 cd19418 381193 lipocalin_A1M-like lipocalin domain of alpha1-microglobulin and similar proteins. Alpha(1)-microglobulin (A1M, also known as protein AMBP, alpha-1 microglycoprotein, and protein HC), has immunosuppressive properties, such as inhibition of antigen induced lymphocyte cell-proliferation, cytokine secretion, and oxidative burst of neutrophils. A1M may participate in the reducing and scavenging of biological pro-oxidants such as heme and heme-proteins. It binds heme strongly, and a C-terminally processed form of the protein degrades the heme. It can reduce cytochrome C, nitroblue tetrazolium, methemoglobin and free iron, using NADH, NADPH or ascorbate as cofactor. Intravenous administration of recombinant A1M in animal models eliminates or significantly reduces the manifestations of preeclampsia. A1M is a useful biomarker in clinical diagnostics for monitoring pre-eclampsia, hepatitis E, renal tubular dysfunction, and renal toxicity. A1M belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 163 matched cddid_all.tbl CDD cd19419 cd19419 381194 lipocalin_L-PGDS lipocalin-type prostaglandin D synthase. Lipocalin-type prostaglandin D synthase (L-PGDS; EC:5.3.99.2) is a secreted enzyme and the second most abundant protein in human cerebrospinal fluid. L-PGDS acts as both, an enzyme and as a lipid transporter, converting prostaglandin H2 to prostaglandin D2 and serving as a carrier for hydrophobic ligands including retinoids, hemoglobin metabolites, thyroid hormones, gangliosides, and fatty acids. L-PGDS belongs to the lipocalin/cytosolic fatty-acid binding protein family which has a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 158 matched cddid_all.tbl CDD cd19420 cd19420 381195 lipocalin_VDE lipocalin domain of violaxanthin deepoxidase and similar proteins. Plant violaxanthin de-epoxidase (VDE, EC 1.23.5.1) participates in the xanthophyll cycle for controlling the concentration of zeaxanthin in chloroplasts. It catalyzes the conversion of violaxanthin to antheraxanthin and zeaxanthin in strong light, and plays a central role in adjusting photosynthetic activity to changing light conditions. In addition, maize VDE has been shown to interact with sugarcane mosaic virus helper component-proteinase, HC-(SCMV), and to attenuate the RNA silencing suppression activity of the latter. VDE belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 177 matched cddid_all.tbl CDD cd19421 cd19421 381196 lipocalin_5_8-like lipocalin similar to human epididymal-specific lipocalin-8, mouse lipocalin-5 and -8, and similar proteins. Lipocalin 5 (LCN5; also known as epididymal retinoic acid binding protein Erabp, mouse epididymal protein 10, MEP10, and E-RABP) and Lipocalin 8 (LCN8; also known as mouse epididymal protein 17, MEP17) are homologous proteins belonging to the epididymis-specific lipocalins; they may play a role in male fertility, and may act as retinoid carrier proteins within the epididymis. In mice, genes encoding the two proteins are contiguous; in humans, there is one gene LCN8 (which has been previously called LCN5). This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 150 matched cddid_all.tbl CDD cd19422 cd19422 381197 lipocalin_15-like lipocalin 15 and similar proteins, such as chicken CALbeta. This subfamily includes uncharacterized human lipocalin 15, and chicken chondrogenesis-associated lipocalin (CAL) beta which is associated with chondrogenesis and inflammation. It belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 143 matched cddid_all.tbl CDD cd19423 cd19423 381198 lipocalin_LTBP1-like Triatominae salivary lipocalins such as Rhodnius prolixus LTBP1 and Meccus pallidipennis triabin, and similar proteins. This subfamily includes various insect proteins found in the saliva of Triatominae (kissing bugs), including Rhodnius prolixus leukotriene-binding LTBP1. Rhodnius prolixus, a vector of the pathogen Trypanosoma cruzi, sequesters cysteinyl leukotrienes during feeding to inhibit immediate inflammatory responses; LTBP1 binds leukotrienes C4 (LTC4), D4 (LTD4), and E4 (LTE4). Meccus pallidipennis (syn Triatoma pallidipennis) triabin is a potent and selective thrombin inhibitor. It also includes Triatoma protracta procalin, a major salivary allergen which causes an allergic reaction in humans. It belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 132 matched cddid_all.tbl CDD cd19424 cd19424 381199 lipocalin_NPs-like nitrophorins and similar proteins. Nitrophorins (NPs) represent a group of nitric oxide (NO)-carrying heme proteins found in the saliva of Rhodnius prolixus. In its adult phase, R. prolixus expresses at least 4 nitrophorins (designated NP1-4 in order of their increasing abundance in the saliva of adult insects). Two additional nitrophorins, NP5 and NP6, have been detected mainly in the five instar nymphal stages of insect development. NP7 has not been isolated from the insects but was instead recognized in a cDNA library. Besides NO, NPs also show high affinities for histamine (Hm). This group also includes Rhodnius prolixus amine-binding protein (ABP) which plays an important role in biogenic amine binding; it binds serotonin and norepinephrine with high affinity. NPs belong to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 175 matched cddid_all.tbl CDD cd19425 cd19425 381200 lipocalin_10-like Epididymal-specific lipocalin-10 and similar proteins. Epididymal-specific lipocalin-10 (LCN10) may play a role in male fertility, and may act as a retinoid carrier protein within the epididymis. It belongs to the lipocalin/cytosolic fatty-acid binding protein family which has a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 111 matched cddid_all.tbl CDD cd19426 cd19426 381201 lipocalin_6 Epididymal-specific lipocalin-6. Epididymal-specific lipocalin-6 (LCN6) may play a role in male fertility. It belongs to the lipocalin/cytosolic fatty-acid binding protein family which has a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 144 matched cddid_all.tbl CDD cd19427 cd19427 381202 lipocalin_OBP-like Lipocalin odorant-binding protein and similar proteins. Odorant-binding proteins (OBPs) transport small hydrophobic molecules in the nasal mucosa of vertebrates. This subfamily includes mouse odorant-binding protein 1a (Obp1a), Obp1b, and probasin. Mouse Obp1a and Obp1b, which are expressed in the nasal mucosa, bind the chemical odorant 2-isobutyl-3-methoxypyrazine, and may form a OBPO1a/Opb1B heterodimer. Mouse probasin may play a role in the biology of the prostate gland. This group also includes hamster female-specific lacrimal gland protein (FLP) and aphrodisin. FLP may bind tear lipids or lipid-like pheromones found in hamster tears; aphrodisin is found in hamster vaginal discharge, carries pheromones, and stimulates copulatory behavior in males. This group also includes dog allergen Ca f4 which is expressed by tongue epithelial tissue and found in saliva and dander. Bovine OBP is believed to act as a homodimer, having the C-terminal alpha-helix of each monomer stacking against the beta-barrel of the other monomer; this is possible due to its lack of cysteines and therefore lack of disulfide bonds. This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 147 matched cddid_all.tbl CDD cd19428 cd19428 381203 lipocalin_MUP-like major urinary proteins (MUPs) and similar proteins. Mouse urine contains major urinary proteins (MUPs) which bind low molecular weight hydrophobic organic compounds such as urinary volatile pheromones such as the male-specific 2-sec-butyl-4,5-dihydrothiazole (SB2HT) which hastens puberty in female mice. The association between MUPs and these volatiles slows the release of the volatiles into the air from urine marks. MUPs may also act as pheromones themselves. MUPs, expressed in the nasal and vomeronasal mucosa, may be important for delivering urinary volatiles to receptors in the vomeronasal organ. This group includes MUPs encoded by central genes in the MUP cluster, as well as those encoded by peripheral genes such as Darcin/Mup20 which binds most of the male pheromone SB2HT in urine and was the first MUP shown to have male pheromonal activity in its own right. This group includes rat MUPs (also called alpha-2U globulins) and other lipocalins such as major horse allergen Equ c 1 and boar salivary lipocalin, a pheromone-binding protein specifically expressed in the submaxillary glands of the boar. It belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 158 matched cddid_all.tbl CDD cd19429 cd19429 381204 lipocalin_9 lipocalin 9. Lipocalin 9 (LCN9) is specifically expressed in the epididymis. It belongs to the lipocalin/cytosolic fatty-acid binding protein family. Lipocalins are typically small extracellular proteins that bind small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids and form covalent or non-covalent complexes with soluble macromolecules as well as membrane bound-receptors. They are involved in many important functions, like ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. 156 matched cddid_all.tbl CDD cd19430 cd19430 381205 lipocalin_trichosorin-like trichosurin and similar proteins. Trichosurin is a protein from the milk whey of the common brushtail possum, Trichosurus Vulpecula, and shows a preference for binding small phenolic ligands. This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 153 matched cddid_all.tbl CDD cd19431 cd19431 381206 lipocalin_Can_f_2 Minor allergen Can f 2. The minor dog lipocalin allergen Can f 2 is an important cause of allergic sensitization in humans worldwide. It is one of two major allergens present in dog dander extracts, and is produced by tongue and the parotid gland (a major salivary gland). Can f 2 belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 162 matched cddid_all.tbl CDD cd19432 cd19432 381207 lipocalin_2_12-like lipocalin 2 and 12 and similar proteins. Lipocalin-2 (LCN2, also known as siderocalin, uterocalin, neutrophil gelatinase-associated lipocalin) is expressed in renal, endothelial, liver, smooth muscle cells, cardiomyocytes, in various populations of immune cells and dendritic cells. Roles ascribed to LCN2 include chemotactic and bacteriostatic effects, and iron trafficking. LCN2 can also act as a growth factor. It plays a key role in the pathophysiology of renal and cardiovascular diseases, and is involved in various deleterious processes, such as inflammation and fibrosis. It is used as a renal injury biomarker. Lipocalin 12 (LCN12) is an epididymis-specific protein which binds all-trans retinoic acid. It may act as a retinoid carrier protein within the epididymis and play a role in male reproduction. This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 154 matched cddid_all.tbl CDD cd19433 cd19433 381208 lipocalin_CpcS-CpeS CpcS/CpeS phycobiliprotein lyase family. Phycobilin lyases covalently attach a chromophore to the Cys residue(s) of cyanobacterial phycobiliproteins. They include Synechococcus sp. PCC 7002 phycocyanobilin lyase CpcS which attaches a phycocyanobilin chromophore to C-phycocyanain beta subunit and to allophycocyanin alpha and beta subunits, Synechococcus sp. PCC 7002 phycocyanobilin lyase subunit CpcU which forms a heterodimer with CpcS-I to attach phycocyanobilin to beta-phycocyanin and to allophycocyanin subunits, and Prochlorococcus marinus phycoerythrobilin lyase CpeS which attaches 3Z-phycoerythrobilin to phycoerythrin. This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 169 matched cddid_all.tbl CDD cd19434 cd19434 381209 lipocalin_YxeF Lipocalin similar to uncharacterized Bacillus subtilis YxeF. Bacillus subtiuls YxeF lacks the alpha-helix that packs in all lipocalins with known structure against the beta-barrel. It belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 108 matched cddid_all.tbl CDD cd19435 cd19435 381210 lipocalin_Bacteroides bacteroides lipocalin. An uncharacterized Bacteroides subfamily of the lipocalin/cytosolic fatty-acid binding protein family a characterisitc of which is a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 131 matched cddid_all.tbl CDD cd19436 cd19436 381211 lipocalin_crustacyanin crustacyanin Type I CRTC and Type II CRTA subunits. Alpha crustacyanin bound with the carotenoid astaxanthisn (AXT) is the predominant cartenoprotein generating the slate-grey/blue color of the lobster carapace. Crustacyanin forms heterodimers (beta-crustacyanin) or complexes of 16 subunits (alpha-crustacyanin) assembled from beta-crustacyanin. Beta-crustacyanin is formed from one type I CRTC lipocalin subunit, and one type II CRTA lipocalin subunit (and two bound astaxanthin molecules). Homarus gammarus (European lobster) crustacyanin has of five distinct subunits evident on 6 M urea-PAGE gels: type I CRTC ( A1, C1, C2) and type II CRTA ( A2, A3). Homarus americanus crustacyanin consists of only two major subunits, namely type I CRTC (H1) and type II CRTA (H2), both of which behave like Ax subunits on a 6 M urea-PAGE gel. This family includes both type I CRTC subunit and type II CRTA subunits and belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 169 matched cddid_all.tbl CDD cd19437 cd19437 381212 lipocalin_apoD-like apolipoprotein D and similar proteins. Human apolipoprotein D (ApoD) is a small glycoprotein associated with high density lipoproteins (HDL) in plasma. It appears promiscuous since it can bind hydrophobic ligands belonging to different lipid groups, with different shapes and biochemical properties; however, it exhibits specificity between very similar lipidic species. Some ligands, such as progesterone and arachidonic acid, bind to the ligand-binding pocket with high affinity, while others may interact with ApoD via its region of surface hydrophobicity. This hydrophobic surface cluster may facilitate its association with HDL particles and facilitate its insertion into cellular lipid membranes. Drosophila NLaz and Schistocerca Laz belong to this group, and share functional properties with human ApoD, including regulation of lifespan, lipid and carbohydrate metabolism control, and protection against oxidative stress or starvation. This group also includes Sandercyanin, a blue protein secreted in the skin mucus of blue forms of walleye, Sander vitreus. Walleye is an important golden yellow commercial and sport fish; the findings of blue walleye are recent. This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 160 matched cddid_all.tbl CDD cd19438 cd19438 381213 lipocalin_Blc-like bacterial lipocalin Blc, Arabidopsis thaliana temperature-induced lipocalin-1, and similar proteins. Escherichia coli bacterial lipocalin (Blc, also known as YjeL) is an outer membrane lipoprotein involved in the storage or transport of lipids necessary for membrane maintenance under stressful conditions. Blc has a binding preference for lysophospholipids. This group includes eukaryotic lipocalins such as Arabidopsis thaliana temperature-induced lipocalin-1 (TIL) which is involved in thermotolerance, oxidative, salt, drought and high light stress tolerance, and is needed for seed longevity by ensuring polyunsaturated lipids integrity. This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 143 matched cddid_all.tbl CDD cd19439 cd19439 381214 lipocalin_Ex-FABP-like "extracellular fatty acid-binding protein. Ex-FABP (also known as siderocalin, lipocalin Q83 or protein Ch21) displays a dual ligand binding mode as it can bind siderophore and fatty acids simultaneously. ExFABP has a cavity which extends through the protein and has two separate ligand specificities, one for bacterial siderophores at one end, and other specifically binding co-purified lysophosphatidic acid (LPA), a potent cell signaling molecule, at the other end. As well as acting as an LPA ""sensor"", Ex-FABP is bacteriostatic, and tightly binds the 2,3-catechol-type ferric siderophores enterobactin, bacillibactin, and parabactin, associated with enteric bacteria and Gram-positive bacilli. This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development." 142 matched cddid_all.tbl CDD cd19440 cd19440 381215 lipocalin_Bla_g_4_Per_a_4 major allergens Bla g 4 and Per a 4. Inhalant allergens from cockroaches are an important cause of asthma. Bla g 4 and Per a 4 are male pheromone transport lipocalins, and both are major allergens. Bla g 4 is produced by Blattella germanica (German cockroach) and has been shown to bind two biogenic amines, tyramine and octopamine which may be its physiological ligands. Per a 4 is produced by Periplaneta americana (American cockroach) and may bind different ligands from Bla g 4 or have different modes for tyramine/octopamine binding. This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 148 matched cddid_all.tbl CDD cd19441 cd19441 381216 CRABP cellular retinoic acid-binding proteins (CRABP1 and CRABP2). Cellular retinoic acid-binding proteins (CRABPs) play a role in the metabolism of vitamin A and retinoic acid. They bind all trans retinoic acid, but not retinol. Retinol, the alcohol form of vitamin A, is an essential dietary nutrient. Within the cell, it gets oxidized into its biologically active acid form, retinoic acid, which interacts with the nuclear receptors (RARs and RXRs). The two CRABPs (CRABP1 AND CRABP2) differ in their pattern of expression across cells and developmental stages. Like other lipid binding proteins, CRABPs serve to solubilize and protect their ligand in the aqueous cytosol and transport retinoic acid between cellular compartments. CRABP1 (also known as CRABP, CRABP-I, CRABPI, RBP5) is thought to play an important role in retinoic acid-mediated differentiation and proliferation processes. CRABP1 has been shown to modulate stem cell proliferation to affect learning and memory. It has also been shown to regulate CaMKII, excessive and/or persistent activation of which is detrimental in acute and chronic cardiac injury. CRABP2 (also known as CRABP-II, RBP6) transports retinoic acid to the nucleus, and delivers all-trans-retinoic acid to nuclear retinoic acid receptors. CRABPs belong to the intracellular fatty acid-binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and besides CRABPS include the cellular retinol-binding protein (CRBPs) and the fatty acid-binding proteins (FABPs). 135 matched cddid_all.tbl CDD cd19442 cd19442 381217 CRBP cellular retinol-binding protein. Cellular retinol-binding proteins (CRBPs) participate in the cellular uptake of vitamin A in the form of free retinol. Retinol achieves a higher chemical stability when bound to CRBPs, and its interaction with retinol-binding proteins allows the solubilization in the aqueous medium of the hydrophobic retinol molecule. There are four human CRBP types (CRBP1, -2, -3, -4) which differ in their tissue-specific expression pattern, as well as in their different ligand affinities. CRBPs belong to the intracellular fatty acid-binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and, besides CRBPS, include the cellular retinoic acid-binding proteins (CRABPs) and the fatty acid-binding proteins (FABPs). 131 matched cddid_all.tbl CDD cd19443 cd19443 381218 FABP3-like fatty acid-binding protein 3 and similar proteins including FABP4, -5, -7, -8, -9, -11, and -12. This FABP3-like subfamily includes FABP3, -4, -5, -7, -8, -9, -11, -12, and similar proteins and belongs to the intracellular fatty acid-binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 128 matched cddid_all.tbl CDD cd19444 cd19444 381219 FABP1 fatty acid-binding protein 1. Fatty acid-binding protein 1, FABP1 (also known as fatty acid-binding protein 1, liver FABP, L-FABP) occurs at high cytosolic concentration in liver, intestine, and, in the case of humans, also in kidney. FABP1 binds to two molecules of long-chain fatty acids; the two binding sites appear to be inter-dependent. FABP1 binds to fatty acyl-CoAs, peroxisome proliferators, prostaglandins, bile acids, bilirubin, heme, hydroxyl and hydroperoxyl metabolites of fatty acids, lysophosphatidic acids, selenium, and other hydrophobic ligands. FABP1 is down-regulated in about ten percent of hepatocellular carcinoma (HCC) as well as in colorectal cancer at the adenoma stage, but can also be over-expressed in various cancers. This subgroup belongs to the intracellular fatty acid-binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 126 matched cddid_all.tbl CDD cd19445 cd19445 381220 FABP2 fatty acid-binding protein 2. FABP2 (also known as fatty acid-binding protein 2, intestinal, and I-FABP) is a small cytosolic protein abundantly present in mature enterocytes of small and large intestine and responsible for the absorption and intracellular transport of fatty acids. It is present throughout the small intestine; its highest expression is in the jejunum. It is a sensitive marker for damage to the intestinal epithelium. This subgroup belongs to the intracellular fatty acid-binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 130 matched cddid_all.tbl CDD cd19446 cd19446 381221 FABP6 "fatty acid-binding protein 6. Human fatty acid-binding protein 6 (also known as gastrotropin, I-15P, I-BABP, I-BALB, I-BAP, ILBP, ILBP3, ileal bile acid-binding protein, ILLBP, ""ileal lipid-binding protein) is an intracellular carrier of bile salts in the epithelial cells of the distal small intestine and has a key role in the enterohepatic circulation of bile salts. It recognizes a series of physiological bile salts that vary in the number and position of steroidal hydroxyl groups, and the presence and type of side-chain conjugation. This subgroup belongs to the intracellular fatty acid-binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development." 125 matched cddid_all.tbl CDD cd19447 cd19447 381222 L-BABP-like "liver bile acid-binding protein and similar proteins. Liver bile acid-binding protein (also known as ""fatty acid-binding protein, liver"", LB-FABP, L-BABP, L-FABP, FABP1) is present in the liver of the vertebrates fish, amphibians, reptiles, and birds but not in mammals. L-BABPs bind free fatty acids and their coenzyme A derivatives, bilirubin, and some other small molecules in the cytoplasm. The role of L-BABPs may be that of cellular and metabolic trafficking of bile acids; they may be involved in intracellular lipid transport. This subgroup belongs to the intracellular fatty acid-binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development." 124 matched cddid_all.tbl CDD cd19448 cd19448 381223 FABP_pancrustacea fatty acid-binding protein similar to Manduca sexta and Eriocheir sinensis fatty acid-binding protein 1. This subfamily includes fatty acid-binding protein found mainly in insects such as Manduca sexta FABP1 (also known as MFB1) and Luciola cerata FABP (LcFABP), and crustacea such as Eriocheir sinensis FABP (Es-FABP). MFB1, which is isolated from midgut cytosol, binds fatty acids in a 1:1 molar ratio. LcFABP, abundantly and specifically expressed in the cytosol as well as the nucleus of cells of the photogenic layer of firefly light organ, binds fatty acids of length C14-C18. Es-FABP plays a role in lipid transport during the period of rapid ovarian growth and is involved in lipid nutrient absorption and utilization processes in the hepatopancreas, ovary, and hemocytes. It is also expressed in gills, muscle, thoracic ganglia, heart, and intestine. This subgroup belongs to the intracellular fatty acid-binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 130 matched cddid_all.tbl CDD cd19449 cd19449 381224 ReP1-NCXSQ-like fatty acid-binding protein ReP1-NCXSQ and similar proteins. Arthropod ReP1-NCXSQ (regulatory protein of the squid nerve sodium calcium exchanger) is required for MgATP stimulation of the squid nerve Na(+)/Ca(2+) exchanger NCXSQ1. ReP1-NCXSQ acts as a carrier of fatty acids; is possible that its biological ligand is palmitic acid, which is abundant in squid axons. The mechanism for fine-tuning of the regulation of NCXSQ1 by ReP1-NCXSQ may then involve the transport of palmitic acid. This subgroup belongs to the intracellular fatty acid-binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 129 matched cddid_all.tbl CDD cd19450 cd19450 381225 lipocalin_ApoM Apolipoprotein M. Apolipoprotein M (ApoM) is mainly found in high-density lipoproteins (HDL) and is expressed in the liver and the kidney; it is associated to a lesser extend with low density lipids and triglyceride rich lipoproteins. It is involved in lipid transport and can bind sphingosine-1-phosphate, myristic acid, palmitic acid and stearic acid, retinol, all-trans-retinoic acid and 9-cis-retinoic acid. This subgroup belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 161 matched cddid_all.tbl CDD cd19451 cd19451 381226 lipocalin_AGP-like alpha1-acid glycoprotein and similar proteins. Alpha1-acid glycoprotein (AGP), also known as orosomucoid, has many important biological roles such as in the acute-phase reaction in response to inflammation, in immune regulation, in drug-binding and drug-transportation, in regulating sphingolipid synthesis and metabolism, and in maintaining the capillary barrier. This subgroup belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 173 matched cddid_all.tbl CDD cd19452 cd19452 381227 lipocalin_ABP Rhodnius prolixus amine-binding protein and similar proteins. Rhodnius prolixus amine-binding protein (ABP) plays an important role in biogenic amine binding; it binds serotonin and norepinephrine with high affinity. It is a subgroup of the lipocalin NP-like family. Nitrophorins (NPs) represent a group of nitric oxide (NO)-carrying heme proteins found in the saliva of Rhodnius prolixus. The lipocalin NP-like family belongs to the lipocalin/cytosolic fatty-acid binding protein family which has a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 189 matched cddid_all.tbl CDD cd19453 cd19453 381228 lipocalin_NP2 nitrophorin 2. Nitrophorins (NPs) represent a group of nitric oxide (NO)-carrying heme proteins found in the saliva of Rhodnius prolixus. In its adult phase R. prolixus expresses at least 4 nitrophorins (designated NP1-4 in order of their increasing abundance in the saliva of adult insects). Two additional nitrophorins, NP5 and NP6, have been detected mainly in the five instar nymphal stages of insect development. NP7 has not been isolated from the insects but was instead recognized in a cDNA library. NPs belong to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 179 matched cddid_all.tbl CDD cd19454 cd19454 381229 lipocalin_NP3 nitrophorin 3. Nitrophorins (NPs) represent a group of nitric oxide (NO)-carrying heme proteins found in the saliva of Rhodnius prolixus. In its adult phase R. prolixus expresses at least 4 nitrophorins (designated NP1-4 in order of their increasing abundance in the saliva of adult insects). Two additional nitrophorins, NP5 and NP6, have been detected mainly in the five instar nymphal stages of insect development. NP7 has not been isolated from the insects but was instead recognized in a cDNA library. NPs belong to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 189 matched cddid_all.tbl CDD cd19455 cd19455 381230 lipocalin_NP1 nitrophorin 1. Nitrophorins (NPs) represent a group of nitric oxide (NO)-carrying heme proteins found in the saliva of Rhodnius prolixus. In its adult phase R. prolixus expresses at least 4 nitrophorins (designated NP1-4 in order of their increasing abundance in the saliva of adult insects). Two additional nitrophorins, NP5 and NP6, have been detected mainly in the five instar nymphal stages of insect development. NP7 has not been isolated from the insects but was instead recognized in a cDNA library. NPs belong to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 184 matched cddid_all.tbl CDD cd19456 cd19456 381231 lipocalin_NP4 nitrophorin 4. Nitrophorins (NPs) represent a group of nitric oxide (NO)-carrying heme proteins found in the saliva of Rhodnius prolixus. In its adult phase R. prolixus expresses at least 4 nitrophorins (designated NP1-4 in order of their increasing abundance in the saliva of adult insects). Two additional nitrophorins, NP5 and NP6, have been detected mainly in the five instar nymphal stages of insect development. NP7 has not been isolated from the insects but was instead recognized in a cDNA library. NPs belong to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 184 matched cddid_all.tbl CDD cd19457 cd19457 381232 lipocalin_2-like lipocalin 2 and similar proteins. Lipocalin-2 (LCN2, also known as siderocalin, uterocalin, oncogene 24p3, and neutrophil gelatinase-associated lipocalin) is expressed in renal, endothelial, liver, smooth muscle cells, cardiomyocytes, in various populations of immune cells and dendritic cells. Roles ascribed to LCN2, include chemotactic and bacteriostatic effects, and iron trafficking. LCN2 can also act as a growth factor. It plays an key role in the pathophysiology of renal and cardiovascular diseases, and is involved in various deleterious processes, such as inflammation and fibrosis. It is used as a renal injury biomarker. This subgroup belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 173 matched cddid_all.tbl CDD cd19458 cd19458 381233 lipocalin_12 Lipocalin 12. Lipocalin 12 (LCN12) is an epididymis-specific protein which binds all-trans retinoic acid. It may act as a retinoid carrier protein within the epididymis and play a role in male reproduction. This subgroup belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 165 matched cddid_all.tbl CDD cd19459 cd19459 381234 lipocalin_C1_moubatin-like Ornithodoros moubata CI, O. moubata moubatin, and similar proteins. The soft tick Ornithodoros moubata complement inhibitor CI (OmCI, also known as coversin) specifically targets C5, a member of the C3/C4/C5 protein family that orchestrates the assembly of the terminal C multiprotein complexes. O. moubata moubatin is a specific inhibitor of collagen-induced platelet aggregation. This subgroup belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 146 matched cddid_all.tbl CDD cd19460 cd19460 381235 CRABP1 cellular retinoic acid-binding protein 1. Cellular retinoic acid-binding proteins (CRABPs) play a role in the metabolism of vitamin A and retinoic acid. They bind all trans retinoic acid, but not retinol. Retinol, the alcohol form of vitamin A, is an essential dietary nutrient. Within the cell, it gets oxidized into its biologically active acid form, retinoic acid, which interacts with the nuclear receptors (RARs and RXRs). The two CRABPs (CRABP1 AND CRABP2) differ in their pattern of expression across cells and developmental stages. Like other lipid binding proteins, CRABPs serve to solubilize and protect their ligand in the aqueous cytosol and transport retinoic acid between cellular compartments. This subgroup includes CRABP1 (also known as CRABP, CRABP-I, CRABPI, RBP5), which is thought to play an important role in retinoic acid-mediated differentiation and proliferation processes. CRABP1 has been shown to modulate stem cell proliferation to affect learning and memory. It has also been shown to regulate CaMKII, excessive and/or persistent activation of which is detrimental in acute and chronic cardiac injury. CRABPs belong to the intracellular fatty acid-binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and besides CRABPS include the cellular retinol-binding protein (CRBPs) and the fatty acid-binding proteins (FABPs). 136 matched cddid_all.tbl CDD cd19461 cd19461 381236 CRABP2 Cellular retinoic acid-binding protein 2. Cellular retinoic acid-binding proteins (CRABPs) play a role in the metabolism of vitamin A and retinoic acid. They bind all trans retinoic acid, but not retinol. Retinol, the alcohol form of vitamin A, is an essential dietary nutrient. Within the cell, it gets oxidized into its biologically active acid form, retinoic acid, which interacts with the nuclear receptors (RARs and RXRs). The two CRABPs (CRABP1 AND CRABP2) differ in their pattern of expression across cells and developmental stages. Like other lipid binding proteins, CRABPs serve to solubilize and protect their ligand in the aqueous cytosol and transport retinoic acid between cellular compartments. This subgroup includes CRABP2 (also known as CRABP-II, RBP6) which transports retinoic acid to the nucleus, and delivers all-trans-retinoic acid to nuclear retinoic acid receptors. CRABPs belong to the intracellular fatty acid-binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and besides CRABPS include the cellular retinol-binding protein (CRBPs) and the fatty acid-binding proteins (FABPs). 136 matched cddid_all.tbl CDD cd19462 cd19462 381237 CRBP1 cellular retinol-binding protein 1. Cellular retinol-binding proteins (CRBPs) participate in the cellular uptake of vitamin A in the form of free retinol. Retinol achieves a higher chemical stability when bound to CRBPs, and its interaction with retinol-binding proteins allows the solubilization in the aqueous medium of the hydrophobic retinol molecule. There are four human CRBP types (CRBP1, -2, -3, -4) which differ in their tissue-specific expression pattern, as well as in their different ligand affinities. CRBP1 (also known as Retinol-Binding Protein 1, CRBP, RBPC, CRBP1, CRBPI, CRABP-I) is widely expressed in numerous tissues: it has highest abundance in the liver, kidney, lung, and retinal pigment epithelium cells of the eye. CRBP1 has a high affinity for retinol. It accepts retinol transported from the plasma to cytosol via a cell surface receptor named STRA6, which interacts with serum retinol-binding protein. CRBP1 can bind all-trans-retinol, all trans-retinal and 13-cis-retinol, but not 9-cis-retinol. CRBPs belong to the intracellular fatty acid-binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and, besides CRBPS, include the cellular retinoic acid-binding proteins (CRABPs) and the fatty acid-binding proteins (FABPs). 131 matched cddid_all.tbl CDD cd19463 cd19463 381238 CRBP2 "cellular retinol-binding protein 2. Cellular retinol-binding proteins (CRBPs) participate in the cellular uptake of vitamin A in the form of free retinol. Retinol achieves a higher chemical stability when bound to CRBPs, and its interaction with retinol-binding proteins allows the solubilization in the aqueous medium of the hydrophobic retinol molecule. There are four human CRBP types (CRBP1, -2, -3, -4) which differ in their tissue-specific expression pattern, as well as in their different ligand affinities. CRBP2 is also known as: ""retinol-binding protein 2, cellular"", CRABP-II, CRBP2, CRBPII, and RBPC2. Expression of CRBP2 is limited to the small intestine. CRBP2 binds both retinol and retinal; rat CRBP2 appears to bind both with equal affinity, human CRBP2 showed a significantly higher affinity for retinol relative to retinal. CRBP2 can bind all-trans-retinol, all trans-retinal and 13-cis-retinol, but not 9-cis-retinol. CRBPs belong to the intracellular fatty acid-binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and, besides CRBPS, include the cellular retinoic acid-binding proteins (CRABPs) and the fatty acid-binding proteins (FABPs)." 131 matched cddid_all.tbl CDD cd19464 cd19464 381239 CRBP3 cellular retinol-binding protein 3. Cellular retinol-binding proteins (CRBPs) participate in the cellular uptake of vitamin A in the form of free retinol. Retinol achieves a higher chemical stability when bound to CRBPs, and its interaction with retinol-binding proteins allows the solubilization in the aqueous medium of the hydrophobic retinol molecule. There are four human CRBP types (CRBP1, -2, -3, -4) which differ in their tissue-specific expression pattern, as well as in their different ligand affinities. This group includes human CRBP3 (also known as retinol-binding protein 5, HRBPiso) which is expressed at highest levels in kidney and liver. CRBP3 binds retinol, and may be a human intracellular carrier of retinol in such tissues. CRBPs belong to the intracellular fatty acid-binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and, besides CRBPS, include the cellular retinoic acid-binding proteins (CRABPs) and the fatty acid-binding proteins (FABPs). 131 matched cddid_all.tbl CDD cd19465 cd19465 381240 CRBP4 cellular retinol-binding protein 4. Cellular retinol-binding proteins (CRBPs) participate in the cellular uptake of vitamin A in the form of free retinol. Retinol achieves a higher chemical stability when bound to CRBPs, and its interaction with retinol-binding proteins allows the solubilization in the aqueous medium of the hydrophobic retinol molecule. There are four human CRBP types (CRBP1, -2, -3, -4) which differ in their tissue-specific expression pattern, as well as in their different ligand affinities. This group includes human CRBP4 (also known as retinoid-binding protein 7, CRABP4, CRBP4, CRBPIV) which is expressed primarily in kidney, heart, and transverse colon, and mouse CRBP4 which is highly expressed in white adipose tissue and mammary gland. Human CRBP4 binds retinol with an affinity lower than those for CRBP1, -2, -3. CRBPs belong to the intracellular fatty acid-binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and, besides CRBPS, include the cellular retinoic acid-binding proteins (CRABPs) and the fatty acid-binding proteins (FABPs). 131 matched cddid_all.tbl CDD cd19466 cd19466 381241 FABP3 fatty acid binding protein 3. FABP3 (also known as heart-type fatty acid binding protein, H-FABP, MDGI, O-FABP) is a cytosolic protein mainly expressed in cardiac and skeletal muscle cells. In these tissues, it plays an important role in fatty acid transportation, cell growth, cell signaling, and gene transcription. This subgroup belongs to the intracellular fatty-acid binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 128 matched cddid_all.tbl CDD cd19467 cd19467 381242 FABP4 fatty acid binding protein 4. FABP4 (also known as A-FABP, adipocyte fatty acid binding protein, aP2) is highly expressed in macrophages and in adipocytes where it regulates fatty acid storage and lipolysis and is an important mediator of inflammation. It binds long chain fatty acids, retinoic acid and eicosanoids. This subgroup belongs to the intracellular fatty-acid binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 130 matched cddid_all.tbl CDD cd19468 cd19468 381243 FABP5 fatty acid binding protein 5. FABP5 (also known as epidermal FABP, E-FABP, cutaneous fatty-acid-binding protein, C-FABP, psoriasis-associated fatty-acid-binding protein, KFABP, PA-FABP) binds a wide array of ligands. It is an intracellular carrier for long-chain fatty acids and related active lipids, and also selectively delivers specific fatty acids from the cytosol to the nucleus. Its ligands include vitamin A metabolite all-trans-retinoic acid, endocannabinoid and numerous synthetic drugs and probes. It may be involved in keratinocyte differentiation. Mouse FABP5 is found only in the monomeric form; however, human FABP5 can exist as a monomer as well as a domain-swapped dimer. This subgroup belongs to the intracellular fatty-acid binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 128 matched cddid_all.tbl CDD cd19469 cd19469 381244 FABP8 fatty acid binding protein 8. FABP8 (also known as peripheral myelin protein 2, PMP2, myelin fatty acid binding protein, M-FABP, myelin P2 protein, MP2) is a fatty acid-binding structural component of the myelin sheath in the peripheral nervous system and may play a role in lipid transport and homeostasis in myelin. It may bind cholesterol which is present in myelin at high concentrations. In addition to binding momomeric ligands, P2 is able to bind membrane surfaces, and to stack lipid bilayers together. This subgroup belongs to the intracellular fatty-acid binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 129 matched cddid_all.tbl CDD cd19470 cd19470 381245 FABP7 Fatty acid binding protein 7. FABP7 (also known as brain FABP, B-FABP, BLBP, brain lipid binding protein) is highly expressed in glial cells through development of the nervous system. In the developing brain, FABP7 is required for the establishment of the radial glial fiber system, which is involved in the migration of immature neurons. This subgroup belongs to the intracellular fatty-acid binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 130 matched cddid_all.tbl CDD cd19471 cd19471 381246 FABP9 fatty acid binding protein 9 and similar proteins. FABP9 (also known as testis-FABP, T-FABP, PERF15) is a major protein found in the inner acrosomal membrane and outer face of the nuclear envelope of mammalian sperm. Its expression is increased in prostate cancer. This subgroup belongs to the intracellular fatty-acid binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 130 matched cddid_all.tbl CDD cd19473 cd19473 380996 SET_SUV39H_DIM5-like SET domain (including pre-SET domain) found in Neurospora crassa (DIM-5) and similar proteins. This subfamily contains Neurospora crassa DIM-5 (also termed H3-K9-HMTase dim-5, or HKMT) which functions as histone-lysine N-methyltransferase that specifically trimethylates histone H3 to form H3K9me3. 274 matched cddid_all.tbl CDD cd19475 cd19475 410883 FlaH flagellar accessory protein FlaH. Flagellar accessory protein FlaH is part of the motor of the archaellum membrane-anchored archaeal motility structure, together with FlaX and FlaI. FlaH forms a hexameric ring, and binds ATP which is essential for its interaction with FlaI and for archaellum assembly. 220 matched cddid_all.tbl CDD cd19476 cd19476 410884 RecA-like_ion-translocating_ATPases RecA-like domain of ion-translocating ATPases. RecA-like NTPases. This family includes the NTP-binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 270 matched cddid_all.tbl CDD cd19477 cd19477 410885 type_II_IV_secretion_ATPases type II/type IV hexameric secretion ATPases. RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 168 matched cddid_all.tbl CDD cd19478 cd19478 410886 Csm2 Shu complex subunit Csm2. Csm2, together with Shu1, Shu2, and Psy3, form the Shu complex which is thought to play a role in maintaining genome stability by linking error-free post-replication repair to homologous recombination. 206 matched cddid_all.tbl CDD cd19479 cd19479 410887 Elp456 Elongator subcomplex subunits Elp4, 5 and 6. Elongator is a highly conserved multiprotein complex involved in RNA polymerase II-mediated transcriptional elongation and many other processes, including cytoskeleton organization, exocytosis, and tRNA modification. It is composed of two subcomplexes, Elp1-3 and Elp4-6. Elp4-6 forms a heterohexameric RecA-like ring structure, although they lack the key sequence signatures of ATPases. 175 matched cddid_all.tbl CDD cd19480 cd19480 410888 Psy3 Shu complex subunit Psy3. Psy3, together with Shu1, Shu2, and Csm2, form the Shu complex which is thought to play a role in maintaining genome stability by linking error-free PRR to homologous recombination (HR). 218 matched cddid_all.tbl CDD cd19481 cd19481 410889 RecA-like_protease proteases similar to RecA. RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 158 matched cddid_all.tbl CDD cd19482 cd19482 410890 RecA-like_Thep1 RecA-like domain of the nucleoside-triphosphatase THEP1 family. This family represents the THEP1 family ATPase domain. It includes nucleoside-triphosphatase THEP 1 from Aquifex aeolicus (aaTHEP1) a nucleoside-phosphatase, with activity towards ATP, GTP, CTP, TTP and UTP; and which may hydrolyze nucleoside diphosphates with lower efficiency. The catalytic function of aaTHEP1 remains unclear, it may be a DNA/RNA modifying enzyme. Human THEP1 (hsTHEP1) may have a general function in many human tissues, as it is widely expressed in most examined tissues (such as in brain, heart, lymph node, skin, pancreas); it is especially highly expressed in embryonic and various tumor tissues. This family belongs to the RecA-like NTPase superfamily which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 164 matched cddid_all.tbl CDD cd19483 cd19483 410891 RecA-like_Gp4D_helicase RecA-like domain of Escherichia coli bacteriophage T7 Gp4D helicase. This family includes the RecA-like domain of the Gp4D fragment of the Gene4 helicase-primase (Gp4) from bacteriophage T7. Gp4D (residues 241-566) is the minimal fragment of the Gp4 that forms hexameric rings, it contains the helicase domain and the linker connecting the helicase and primase domains. Helicases are ring-shaped oligomeric enzymes that unwind DNA at the replication fork; they couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands. This family belongs to the RecA-like NTPase superfamily which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 231 matched cddid_all.tbl CDD cd19484 cd19484 410892 KaiC_C C-terminal domain of Circadian Clock Protein KaiC. KaiC is a circadian clock protein, most studied in cyanobacteria. KaiC, an autokinase, autophosphatase, and ATPase, is part of the core oscillator, composed of three proteins: KaiA, KaiB, and KaiC. The circadian oscillation is regulated via KaiC phosphorylation. 218 matched cddid_all.tbl CDD cd19485 cd19485 410893 KaiC-N N-terminal domain of Circadian Clock Protein Kaic. KaiC is a circadian clock protein, most studied in cyanobacteria. KaiC, an autokinase, autophosphatase, and ATPase, is part of the core oscillator, composed of three proteins: KaiA, KaiB, and KaiC. The circadian oscillation is regulated via KaiC phosphorylation. 226 matched cddid_all.tbl CDD cd19486 cd19486 410894 KaiC_arch KaiC family protein; uncharacterized subfamily similar to Pyrococcus horikoshii PH0284. KaiC is a circadian clock protein, most studied in cyanobacteria. KaiC, an autokinase, autophosphatase, and ATPase, is part of the core oscillator, composed of three proteins: KaiA, KaiB, and KaiC. The circadian oscillation is regulated via KaiC phosphorylation. 230 matched cddid_all.tbl CDD cd19487 cd19487 410895 KaiC-like_C C-terminal domain of KaiC family protein; uncharacterized subfamily. KaiC is a circadian clock protein, most studied in cyanobacteria. KaiC, an autokinase, autophosphatase, and ATPase, is part of the core oscillator, composed of three proteins: KaiA, KaiB, and KaiC. The circadian oscillation is regulated via KaiC phosphorylation. 219 matched cddid_all.tbl CDD cd19488 cd19488 410896 KaiC-like_N N-terminal domain of KaiC family protein; uncharacterized subfamily. KaiC is a circadian clock protein, most studied in cyanobacteria. KaiC, an autokinase, autophosphatase, and ATPase, is part of the core oscillator, composed of three proteins: KaiA, KaiB, and KaiC. The circadian oscillation is regulated via KaiC phosphorylation. 225 matched cddid_all.tbl CDD cd19489 cd19489 410897 Rad51D RAD51D recombinase. RAD51D recombinase, a RAD51 paralog, plays an important role in DNA repair by homologous recombination (HR). HR is an important error-free repair mechanism for chromosomal double-strand break (DSB) which otherwise leads to cell cycle arrest and death. RAD51D, together with the other RAD51 paralogs, RAD51B, RAD51C, XRCC3, and XRCC2, helps recruit RAD51 to the break site. 209 matched cddid_all.tbl CDD cd19490 cd19490 410898 XRCC2 XRCC2 recombinase. XRCC2 (X-ray repair complementing defective repair in Chinese hamster cells 2) recombinase, a RAD51 paralog, plays an important role in DNA repair by homologous recombination (HR). HR is an important error-free repair mechanism for chromosomal double-strand break (DSB) which otherwise leads to cell cycle arrest and death. XRCC2, together with the other RAD51 paralogs, RAD51B, RAD51C, RAD51D, and XRCC3, helps recruit RAD51 to the break site. 226 matched cddid_all.tbl CDD cd19491 cd19491 410899 XRCC3 XRCC3 recombinase. XRCC3 (X-ray repair complementing defective repair in Chinese hamster cells 3) recombinase, a RAD51 paralog, plays an important role in DNA repair by homologous recombination (HR). HR is an important error-free repair mechanism for chromosomal double-strand break (DSB) which otherwise leads to cell cycle arrest and death. XRCC3, together with the other RAD51 paralogs, RAD51B, RAD51C, RAD51D, and XRCC2, helps recruit RAD51 to the break site. 250 matched cddid_all.tbl CDD cd19492 cd19492 410900 Rad51C RAD51C recombinase. RAD51C recombinase, a RAD51 paralog, plays an important role in DNA repair by homologous recombination (HR). HR is an important error-free repair mechanism for chromosomal double-strand break (DSB) which otherwise leads to cell cycle arrest and death. RAD51C, together with the other RAD51 paralogs, RAD51B, RAD51D, XRCC3, and XRCC2, helps recruit RAD51 to the break site. Additionally, RAD51C acts as a mediator in the early steps of DNA damage signaling. 172 matched cddid_all.tbl CDD cd19493 cd19493 410901 Rad51B RAD51B recombinase. RAD51B recombinase, a RAD51 paralog, plays an important role in DNA repair by homologous recombination (HR). HR is an important error-free repair mechanism for chromosomal double-strand break (DSB) which otherwise leads to cell cycle arrest and death. RAD51B, together with the other RAD51 paralogs, RAD51C, RAD51D, XRCC3, and XRCC2, helps recruit RAD51 to the break site. 222 matched cddid_all.tbl CDD cd19494 cd19494 410902 Elp4 Elongator subcomplex subunit Elp4. Elongator is a highly conserved multiprotein complex involved in RNA polymerase II-mediated transcriptional elongation and many other processes, including cytoskeleton organization, exocytosis, and tRNA modification. It is composed of two subcomplexes, Elp1-3 and Elp4-6. Elp4-6 forms a heterohexameric RecA-like ring structure, although they lack the key sequence signatures of ATPases. 259 matched cddid_all.tbl CDD cd19495 cd19495 410903 Elp6 Elongator subcomplex subunit Elp6. Elongator is a highly conserved multiprotein complex involved in RNA polymerase II-mediated transcriptional elongation and many other processes, including cytoskeleton organization, exocytosis, and tRNA modification. It is composed of two subcomplexes, Elp1-3 and Elp4-6. Elp4-6 forms a heterohexameric RecA-like ring structure, although they lack the key sequence signatures of ATPases. 228 matched cddid_all.tbl CDD cd19496 cd19496 410904 Elp5 Elongator subcomplex subunit Elp5. Elongator is a highly conserved multiprotein complex involved in RNA polymerase II-mediated transcriptional elongation and many other processes, including cytoskeleton organization, exocytosis, and tRNA modification. It is composed of two subcomplexes, Elp1-3 and Elp4-6. Elp4-6 forms a heterohexameric RecA-like ring structure, although they lack the key sequence signatures of ATPases. 143 matched cddid_all.tbl CDD cd19497 cd19497 410905 RecA-like_ClpX ATP-dependent Clp protease ATP-binding subunit ClpX. ClpX is a component of the ATP-dependent protease ClpXP. In ClpXP, ClpX ATPase serves to specifically recognize, unfold, and translocate protein substrates into the chamber of ClpP protease for degradation. This RecA-like_ClpX domain subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 251 matched cddid_all.tbl CDD cd19498 cd19498 410906 RecA-like_HslU ATP-dependent protease ATPase subunit HslU. HslU is a component of the ATP-dependent protease HslVU. In HslVU, HslU ATPase serves to unfold and translocate protein substrate, and the HslV protease degrades the unfolded proteins. This RecA-like_HslU subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 183 matched cddid_all.tbl CDD cd19499 cd19499 410907 RecA-like_ClpB_Hsp104-like Chaperone protein ClpB/Hsp104 subfamily. Bacterial Caseinolytic peptidase B (ClpB) and eukaryotic Heat shock protein 104 (Hsp104) are ATP-dependent molecular chaperones and essential proteins of the heat-shock response. ClpB/Hsp104 ATPases, in concert with the DnaK/Hsp70 chaperone system, disaggregate and reactivate aggregated proteins. This RecA-like_ClpB_Hsp104_like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 178 matched cddid_all.tbl CDD cd19500 cd19500 410908 RecA-like_Lon lon protease homolog 2 peroxisomal. Lon protease (also known as Lon peptidase) is an evolutionarily conserved ATP-dependent serine protease, present in bacteria and eukaryotic mitochondria and peroxisomes, which mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Lon protease is both an ATP-dependent peptidase and a protein-activated ATPase. This RecA-like Lon domain subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 182 matched cddid_all.tbl CDD cd19501 cd19501 410909 RecA-like_FtsH ATP-dependent zinc metalloprotease FtsH. FtsH ATPase is a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. It is anchored to the cytoplasmic membrane such that the amino- and carboxy-termini are exposed to the cytoplasm. It presents a membrane-bound hexameric structure that is able to unfold and degrade protein substrates. It is comprised of an N-terminal transmembrane region and the larger C-terminal cytoplasmic region, which consists of an ATPase domain and a protease domain. This RecA-Like FTsH subfamily represents the ATPase domain, and belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 171 matched cddid_all.tbl CDD cd19502 cd19502 410910 RecA-like_PAN_like proteasome activating nucleotidase PAN and related proteasome subunits. This subfamily contains ATPase subunits of the eukaryotic 26S proteasome, and of the archaeal proteasome which carry out ATP-dependent degradation of substrates of the ubiquitin-proteasome pathway. The eukaryotic 26S proteasome consists of a proteolytic 20S core particle (CP), and a 19S regulatory particle (RP) which provides the ATP-dependence and the specificity for ubiquitinated proteins. In the archaea the RP is a homohexameric complex of proteasome-activating nucleotidase (PAN). This subfamily also includes various eukaryotic 26S subunits including, proteasome 26S subunit, ATPase 2 (PSMC2, also known as S7 and MSS1) which is a member of the 19S RP and has a chaperone like activity; and proteasome 20S subunit alpha 6 (PSMA6, also known as IOTA, p27K, and PROS27) which is a member of the 20S CP. This RecA-like_PAN subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 171 matched cddid_all.tbl CDD cd19503 cd19503 410911 RecA-like_CDC48_NLV2_r1-like first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains. CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. This subfamily also includes the first of the two ATPase domains of NVL (nuclear VCP-like protein) 2, an isoform of NVL mainly present in the nucleolus, which is involved in ribosome biogenesis, in telomerase assembly and the regulation of telomerase activity, and in pre-rRNA processing. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 165 matched cddid_all.tbl CDD cd19504 cd19504 410912 RecA-like_NSF-SEC18_r1-like first of two ATPase domains of NSF and SEC18, and similar ATPase domains. N-ethylmaleimide-sensitive factor (NSF) and Saccharomyces cerevisiae Vesicular-fusion protein Sec18, key factors for eukaryotic trafficking, are ATPases and SNARE disassembly chaperones. NSF/Sec18 activate or prime SNAREs, the terminal catalysts of membrane fusion. Sec18/NSF associates with SNARE complexes through binding Sec17/alpha-SNAP. Sec18 has an N-terminal cap domain and two nucleotide-binding domains (D1 and D2) which form the two rings of the hexameric complex. The hydrolysis of ATP by D1 generates most of the energy necessary to disassemble inactive SNARE bundles, while the D2 ring binds ATP to stabilize the homohexamer. This subfamily includes the first (D1) ATPase domain of NSF/Sec18, and belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 177 matched cddid_all.tbl CDD cd19505 cd19505 410913 RecA-like_Ycf2 ATPase domain of plant YCF2. Ycf2 is a chloroplast ATPase which has an essential function; however, its function remains unclear. The gene encoding YCF2 is the largest known plastid gene in angiosperms and has been used to predict phylogenetic relationships. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 161 matched cddid_all.tbl CDD cd19506 cd19506 410914 RecA-like_IQCA1 ATPase domain of IQ and AAA domain-containing protein 1 (IQCA1). IQCA1 (also known as dynein regulatory complex subunit 11, DRC11 and IQCA) is an ATPase subunit of the nexin-dynein regulatory complex (N-DRC). The 9 + 2 axoneme of most motile cilia and flagella consists of nine outer doublet microtubules arranged in a ring surrounding a central pair of two singlet microtubules. The N-DRC complex maintains alignment between outer doublet microtubules and limits microtubule sliding in motile axonemes. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 160 matched cddid_all.tbl CDD cd19507 cd19507 410915 RecA-like_Ycf46-like ATPase domain of Ycf46 and similar ATPase domains. Ycf46 may play a role in the regulation of photosynthesis in cyanobacteria, especially in CO2 uptake and utilization. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 161 matched cddid_all.tbl CDD cd19508 cd19508 410916 RecA-like_Pch2-like ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains. Pch2 (known as Thyroid hormone receptor interactor 13 (TRIP13) and 16E1BP) is a key regulator of specific chromosomal events, like the control of G2/prophase processes such as DNA break formation and recombination, checkpoint signaling, and chromosome synapsis. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion 199 matched cddid_all.tbl CDD cd19509 cd19509 410917 RecA-like_VPS4-like ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains. This subfamily includes the ATPase domains of vacuolar protein sorting-associated protein 4 (VPS4), ATPase family AAA domain-containing protein 1 (ATAD1, also known as Thorase), Katanin p60 ATPase-containing subunit A1 (KTNA1), Spastin, and Fidgetin-Like 1 (FIGL-1). This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 163 matched cddid_all.tbl CDD cd19510 cd19510 410918 RecA-like_BCS1 Mitochondrial chaperone BCS1. Mitochondrial chaperone BCS1 is necessary for the assembly of mitochondrial respiratory chain complex III and plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex. RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 153 matched cddid_all.tbl CDD cd19511 cd19511 410919 RecA-like_CDC48_r2-like second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase domains. This subfamily includes the second of two ATPase domains of the molecular chaperone CDC48 in yeast and p97 or VCP in metazoans, Peroxisomal biogenesis factor 1 (PEX1) and -6 (PEX6), Valosin-containing protein-like ATPase (VAT), and nuclear VCP-like protein (NVL). This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 159 matched cddid_all.tbl CDD cd19512 cd19512 410920 RecA-like_ATAD3-like ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase domains. ATPase AAA-domain protein 3 (ATAD3) is a ubiquitously expressed mitochondrial protein involved in mitochondrial dynamics, DNA-nucleoid structural organization, cholesterol transport and steroidogenesis. The ATAD3 gene family in human comprises three paralog genes: ATAD3A, ATAD3B and ATAD3C. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 150 matched cddid_all.tbl CDD cd19513 cd19513 410921 Rad51 RAD51D recombinase. RAD51 recombinase plays an essential role in DNA repair by homologous recombination (HR). HR is an important error-free repair mechanism for chromosomal double-strand break (DSB) which otherwise leads to cell cycle arrest and death. RAD51 is recruited to the break site with the help of its paralogs, RAD51D, RAD51B, RAD51C, XRCC3, and XRCC2, where it forms long helical polymers which wrap around the ssDNA tail at the break which leads to pairing and strand invasion. 235 matched cddid_all.tbl CDD cd19514 cd19514 410922 DMC1 homologous-pairing protein DMC1. DMC1 has a central role in homologous recombination in meiosis. It assembles at the sites of programmed DNA double-strand breaks and carries out a search for allelic DNA sequences located on homologous chromatids. It forms octameric rings. 236 matched cddid_all.tbl CDD cd19515 cd19515 410923 archRadA archaeal recombinase Rad51/RadA. This group includes the archaeal protein RadA which is a homolog of Rad51. RAD51 recombinase plays an essential role in DNA repair by homologous recombination (HR) 233 matched cddid_all.tbl CDD cd19516 cd19516 410924 DotB_TraJ dot/icm secretion system protein DotB-like. Defect in organelle trafficking (Dot)B is part of the type IVb secretion (T4bS) system, also known as the dot/icm system, and is the main energy supplier of the secretion system. It is an ATPase, similar to the VirB11 component of the T4aS systems. This family also includes Escherichia coli IncI plasmid-encoded conjugative transfer ATPase TraJ encoded on the tra (transfer) operon. 179 matched cddid_all.tbl CDD cd19517 cd19517 410925 RecA-like_Yta7-like ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains. Saccharomyces cerevisiae Yta7 is a chromatin-associated AAA-ATPase involved in regulation of chromatin dynamics. Its human ortholog ANCCA/ATAD2 transcriptionally activates pathways of malignancy in a broad range of cancers. The RecA-like_Yta7 subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 170 matched cddid_all.tbl CDD cd19518 cd19518 410926 RecA-like_NVL_r1-like first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains. NVL exists in two forms with N-terminal extensions of different lengths in mammalian cells. NVL has two alternatively spliced isoforms, a short form, NVL1, and a long form, NVL2. NVL2, the major species, is mainly present in the nucleolus, whereas NVL1 is nucleoplasmic. Each has an N-terminal domain, followed by two tandem ATPase domains; this subfamily includes the first of the two ATPase domains. NVL2 is involved in the biogenesis of the 60S ribosome subunit by associating specifically with ribosome protein L5 and modulating the function of DOB1. NVL2 is also required for telomerase assembly and the regulation of telomerase activity, and is involved in pre-rRNA processing. The role of NVL1 is unclear. This RecA-like_NVL_r1-like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 169 matched cddid_all.tbl CDD cd19519 cd19519 410927 RecA-like_CDC48_r1-like first of two ATPase domains of CDC48 and similar ATPase domains. CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. CDC48's roles include in the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis, and in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). This RecA-like_cdc48_r1-like subfamily belongs to the RecA-like family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 166 matched cddid_all.tbl CDD cd19520 cd19520 410928 RecA-like_ATAD1 ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains. ATPase family AAA domain-containing protein 1 (ATAD1, also known as Thorase) is an ATPase that plays a critical role in regulating the surface expression of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors, thereby regulating synaptic plasticity, learning and memory. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 166 matched cddid_all.tbl CDD cd19521 cd19521 410929 RecA-like_VPS4 ATPase domain of vacuolar protein sorting-associated protein 4. Vacuolar protein sorting-associated protein 4 (Vps4) is believed to be involved in intracellular protein transport out of a prevacuolar endosomal compartment. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 170 matched cddid_all.tbl CDD cd19522 cd19522 410930 RecA-like_KTNA1 Katanin p60 ATPase-containing subunit A1. Katanin p60 ATPase-containing subunit A1 (KTNA1) is the catalytic subunit of the Katanin complex which is severs microtubules in an ATP-dependent manner, and is implicated in multiple aspects of microtubule dynamics. In addition to the p60 catalytic ATPase subunit, Katanin contains an accessory subunit (p80 or p80-like). The microtubule-severing activity of the ATPase is essential for female meiotic spindle assembly, and male gamete production; and the katanin complex severing microtubules is under tight regulation during the transition from the meiotic to mitotic stage to allow proper embryogenesis. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 170 matched cddid_all.tbl CDD cd19523 cd19523 410931 RecA-like_fidgetin ATPase domain of fidgetin. Fidgetin (FIGN) is a ATP-dependent microtubule severing protein. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 163 matched cddid_all.tbl CDD cd19524 cd19524 410932 RecA-like_spastin ATPase domain of spastin. Spastin is an ATP-dependent microtubule-severing protein involved in microtubule dynamics; it specifically recognizes and cuts microtubules that are polyglutamylated. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 164 matched cddid_all.tbl CDD cd19525 cd19525 410933 RecA-like_Figl-1 ATPase domain of Fidgetin-Like 1 (FIGL-1). FIGL-1 may participate in DNA repair in the nucleus; it may be involved in DNA double-strand break repair via homologous recombination. Caenorhabditis elegans FIGL-1 is a nuclear protein and controls the mitotic progression in the germ line and mouse FIGL-1 may be involved in the control of male meiosis. human FIGL-1 has been shown to be a centrosome protein involved in ciliogenesis perhaps as a microtubule-severing protein. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 186 matched cddid_all.tbl CDD cd19526 cd19526 410934 RecA-like_PEX1_r2 second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1). PEX1(also known as Peroxin-1)/PEX6 is a protein unfoldase; PEX1 and PEX6 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. PEX-1 is required for stability of PEX5. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 158 matched cddid_all.tbl CDD cd19527 cd19527 410935 RecA-like_PEX6_r2 second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6). PEX6(also known as Peroxin61)/PEX1 is a protein unfoldase; PEX6 and PEX1 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. This subfamily represents the second ATPase domain of PEX6. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 160 matched cddid_all.tbl CDD cd19528 cd19528 410936 RecA-like_CDC48_r2-like second of two ATPase domains of CDC48 and similar ATPase domains. CDC48 in yeast and p97 or VCP in metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the second of the two ATPase domains. CDC48's roles include in the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis, and in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). This RecA-like_cdc48_r2-like subfamily belongs to the RecA-like family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 161 matched cddid_all.tbl CDD cd19529 cd19529 410937 RecA-like_VCP_r2 second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ATPase domains. The Valosin-containing protein-like ATPase of Thermoplasma acidophilum (VAT), is an archaeal homolog of the ubiquitous Cdc48/p97. It is a protein unfoldase that functions in concert with the 20S proteasome by unfolding proteasome substrates and passing them on for degradation. VAT forms a homohexamer, each monomer contains two tandem ATPase domains, referred to as D1 and D2, and an N-terminal domain. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 159 matched cddid_all.tbl CDD cd19530 cd19530 410938 RecA-like_NVL_r2-like second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains. NVL exists in two forms with N-terminal extensions of different lengths in mammalian cells. NVL has two alternatively spliced isoforms, a short form, NVL1, and a long form, NVL2. NVL2, the major species, is mainly present in the nucleolus, whereas NVL1 is nucleoplasmic. Each has an N-terminal domain, followed by two tandem ATPase domains; this subfamily includes the first of the two ATPase domains. NVL2 is involved in the biogenesis of the 60S ribosome subunit by associating specifically with ribosome protein L5 and modulating the function of DOB1. NVL2 is also required for telomerase assembly and the regulation of telomerase activity, and is involved in pre-rRNA processing. The role of NVL1 is unclear. This RecA-like_NVL_r1-like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion. 161 matched cddid_all.tbl CDD cd19531 cd19531 380454 LCL_NRPS-like LCL-type Condensation (C) domain of non-ribosomal peptide synthetases(NRPSs) and similar domains including the C-domain of SgcC5, a free-standing NRPS with both ester- and amide- bond forming activity. LCL-type Condensation (C) domains catalyze peptide bond formation between two L-amino acids, ((L)C(L)). C-domains of NRPSs catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). In addition to the LCL-type, there are various subtypes of C-domains such as the DCL-type which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. Streptomyces globisporus SgcC5 is a free-standing NRPS condensation enzyme (rather than a modular NRPS), which catalyzes the condensation between the SgcC2-tethered (S)-3-chloro-5-hydroxy-beta-tyrosine and (R)-1phenyl-1,2-ethanediol, forming an ester bond, during the synthesis of the chromoprotein enediyne antitumor antibiotic C-1027. It has some acceptor substrate promiscuity as it has been shown to also catalyze the formation of an amide bond between SgcC2-tethered (S)-3-chloro-5-hydroxy-beta-tyrosine and a mimic of the enediyne core acceptor substrate having an amine at its C-2 position. C-domains typically have a conserved HHxxxD motif at the active site; mutations in this motif can abolish or diminish condensation activity. An HHxx[SAG]DGxSx(6)[ED] motif is characteristic of LCL-type C-domains. 427 matched cddid_all.tbl CDD cd19532 cd19532 380455 C_PKS-NRPS Condensation domain of hybrid polyketide synthetase/nonribosomal peptide synthetases (PKS/NRPSs). Condensation (C) domains of nonribosomal peptide synthetases (NRPSs) catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. Hybrid PKS/NRPS create polymers containing both polyketide and amide linkages. C-domains typically have a conserved HHxxxD motif at the active site; mutations in this motif can abolish or diminish condensation activity. Most members of this subfamily have the typical C-domain HHxxxD motif, a few such as Monascus pilosus lovastatin nonaketide synthase MokA have a non-canonical HRxxxD motif in the C-domain and are unable to catalyze amide-bond formation. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). There are various subtypes of C-domains such as the LCL-type which catalyzes peptide bond formation between two L-amino acids, the DCL-type which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. 421 matched cddid_all.tbl CDD cd19533 cd19533 380456 starter-C_NRPS Starter Condensation domains, found in the first module of nonribosomal peptide synthetases (NRPSs). Condensation (C) domains of nonribosomal peptide synthetases (NRPSs) catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. While standard C-domains catalyze peptide bond formation between two amino acids, an initial, ('starter') C-domain may instead acylate an amino acid with a fatty acid. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). There are various subtypes of C-domains such as the LCL-type which catalyzes peptide bond formation between two L-amino acids, the DCL-type which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. C-domains typically have a conserved HHxxxD motif at the active site; mutations in this motif can abolish or diminish condensation activity. 419 matched cddid_all.tbl CDD cd19534 cd19534 380457 E_NRPS Epimerization domain of nonribosomal peptide synthetases (NRPSs); belongs to the Condensation-domain family. Epimerization (E) domains of nonribosomal peptide synthetases (NRPS) flip the chirality of the end amino acid of a peptide being manufactured by the NRPS. E-domains are homologous to the Condensation (C) domains. NRPSs catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. Specialized tailoring NRPS domains such as E-domains greatly increase the range of possible peptide products created by the NRPS machinery. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). There are various subtypes of C-domains such as the LCL-type which catalyzes peptide bond formation between two L-amino acids, the DCL-type which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the E-domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. C-domains typically have a conserved HHxxxD motif at the active site; mutations in this motif can abolish or diminish condensation activity. 428 matched cddid_all.tbl CDD cd19535 cd19535 380458 Cyc_NRPS Cyc (heterocyclization) domain of nonribosomal peptide synthetases (NRPSs); belongs to the Condensation-domain family. Cyc (heterocyclization) domains catalyze two separate reactions in the creation of heterocyclized peptide products in nonribosomal peptide synthesis: amide bond formation followed by intramolecular cyclodehydration between a Cys, Ser, or Thr side chain and a carbonyl carbon on the peptide backbone to form a thiazoline, oxazoline, or methyloxazoline ring. Cyc-domains are homologous to standard NRPS Condensation (C) domains. C-domains typically have a conserved HHxxxD motif at the active site; Cyc-domains have an alternative, conserved DxxxxD active site motif, mutation of the aspartate residues in this motif can abolish or diminish condensation activity. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). There are various subtypes of C-domains such as the LCL-type which catalyzes peptide bond formation between two L-amino acids, the DCL-type which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and Cyc-domains. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. 423 matched cddid_all.tbl CDD cd19536 cd19536 380459 DCL_NRPS-like DCL-type Condensation domains of nonribosomal peptide synthetases (NRPSs), such as terminal fungal CT domains and Dual Epimerization/Condensation (E/C) domains. Condensation (C) domains of nonribosomal peptide synthetases (NRPSs) catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). There are various subtypes of C-domains such as the LCL-type which catalyzes peptide bond formation between two L-amino acids, the DCL-type [D-specific for the peptidyl donor and L-specific for the aminoacyl acceptor ((D)C(L))], which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. C-domains typically have a conserved HHxxxD motif at the active site; mutations in this motif can abolish or diminish condensation activity. 419 matched cddid_all.tbl CDD cd19537 cd19537 380460 C_NRPS-like Condensation family domain with an atypical active site motif. Condensation (C) domains of nonribosomal peptide synthetases (NRPSs) catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. C-domains typically have a conserved HHxxxD motif at the active site; mutations in this motif can abolish or diminish condensation activity. Members of this subfamily typically have a non-canonical conserved SHXXXDX(14)Y motif. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). There are various subtypes of C-domains such as the LCL-type which catalyzes peptide bond formation between two L-amino acids, the DCL-type which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. 395 matched cddid_all.tbl CDD cd19538 cd19538 380461 LCL_NRPS LCL-type Condensation domain of non-ribosomal peptide synthetases (NRPSs) and similar domains. LCL-type Condensation (C) domains catalyze peptide bond formation between two L-amino acids, ((L)C(L)). C-domains of NRPSs catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). In addition to the LCL-type, there are various subtypes of C-domains such as the DCL-type which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. C-domains typically have a conserved HHxxxD motif at the active site; mutations in this motif can abolish or diminish condensation activity. An HHxx[SAG]DGxSx(6)[ED] motif is characteristic of LCL-type C-domains. 432 matched cddid_all.tbl CDD cd19539 cd19539 380462 SgcC5_NRPS-like SgcC5 is a non-ribosomal peptide synthetase (NRPS) condensation enzyme with ester- and amide- bond forming activity and similar C-domains of modular NRPSs. SgcC5 is a free-standing NRPS condensation enzyme (rather than a modular NRPS), which catalyzes the condensation between the SgcC2-tethered (S)-3-chloro-5-hydroxy-beta-tyrosine and (R)-1phenyl-1,2-ethanediol, forming an ester bond, during the synthesis of the chromoprotein enediyne antitumor antibiotic C-1027. It has some acceptor substrate promiscuity as it has been shown to also catalyze the formation of an amide bond between SgcC2-tethered (S)-3-chloro-5-hydroxy-beta-tyrosine and a mimic of the enediyne core acceptor substrate having an amine at its C-2 position. This subfamily also includes similar C-domains of modular NRPSs such as Penicillium chrysogenum N-(5-amino-5-carboxypentanoyl)-L-cysteinyl-D-valine synthase PCBAB. Condensation (C) domains of NRPSs normally catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). There are various subtypes of C-domains such as the LCL-type which catalyzes peptide bond formation between two L-amino acids, the DCL-type which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. C-domains typically have a conserved HHxxxD motif at the active site; mutations in this motif can abolish or diminish condensation activity. 427 matched cddid_all.tbl CDD cd19540 cd19540 380463 LCL_NRPS-like LCL-type Condensation domain of nonribosomal peptide synthetases (NRPSs) and similar domains. LCL-type Condensation (C) domains catalyze peptide bond formation between two L-amino acids, ((L)C(L)). C-domains of NRPSs catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). In addition to the LCL-type, there are various subtypes of C-domains such as the DCL-type which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. C-domains typically have a conserved HHxxxD motif at the active site; mutations in this motif can abolish or diminish condensation activity. An HHxx[SAG]DGxSx(6)[ED] motif is characteristic of LCL-type C-domains. 433 matched cddid_all.tbl CDD cd19542 cd19542 380464 CT_NRPS-like Terminal Condensation (CT)-like domains of nonribosomal peptide synthetases (NRPSs). Unlike bacterial NRPS, which typically have specialized terminal thioesterase (TE) domains to cyclize peptide products, many fungal NRPSs employ a terminal condensation-like (CT) domain to produce macrocyclic peptidyl products (e.g. cyclosporine and echinocandin). Domains in this subfamily (which includes both terminal and non-terminal domains) typically have a non-canonical conserved [SN]HxxxDx(14)Y motif at their active site compared to the standard Condensation (C) domain active site motif (HHxxxD). C-domains of NRPSs catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). There are various subtypes of C-domains such as the LCL-type which catalyzes peptide bond formation between two L-amino acids, the DCL-type which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. 401 matched cddid_all.tbl CDD cd19543 cd19543 380465 DCL_NRPS DCL-type Condensation domain of nonribosomal peptide synthetases (NRPSs), which catalyzes the condensation between a D-aminoacyl/peptidyl-PCP donor and a L-aminoacyl-PCP acceptor. The DCL-type Condensation (C) domain catalyzes the condensation between a D-aminoacyl/peptidyl-PCP donor and a L-aminoacyl-PCP acceptor. This domain is D-specific for the peptidyl donor and L-specific for the aminoacyl acceptor ((D)C(L)); this is in contrast with the standard LCL domains which catalyze peptide bond formation between two L-amino acids, and the restriction of ribosomes to use only L-amino acids. C domains of nonribosomal peptide synthetases (NRPSs) catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). There are various subtypes of C-domains in addition to the LCL- and DCL-types such as starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. C-domains typically have a conserved HHxxxD motif at the active site; mutations in this motif can abolish or diminish condensation activity. 423 matched cddid_all.tbl CDD cd19544 cd19544 380466 E-C_NRPS Dual Epimerization/Condensation (E/C) domains of nonribosomal peptide synthetases (NRPSs). Dual function Epimerization/Condensation (E/C) domains have both an epimerization and a DCL condensation activity. Dual E/C domains first epimerize the substrate amino acid to produce a D-configuration, then catalyze the condensation between the D-aminoacyl/peptidyl-PCP donor and a L-aminoacyl-PCP acceptor. They are D-specific for the peptidyl donor and L-specific for the aminoacyl acceptor ((D)C(L)); this is in contrast with the standard LCL domains which catalyze peptide bond formation between two L-amino acids, and the restriction of ribosomes to use only L-amino acids. These Dual E/C domains contain an extended His-motif (HHx(N)GD) near the N-terminus of the domain in addition to the standard Condensation (C) domain active site motif (HHxxxD). C domains of nonribosomal peptide synthetases (NRPSs) catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). There are various subtypes of C-domains, these include the DCL-type, LCL-type, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C domains, and the X-domain. 413 matched cddid_all.tbl CDD cd19545 cd19545 380467 FUM14_C_NRPS-like Condensation domains of nonribosomal peptide synthetases (NRPSs) similar to the ester-bond forming Fusarium verticillioides FUM14 protein. Condensation (C) domains of nonribosomal peptide synthetases (NRPSs) typically catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. However, some C-domains have ester-bond forming activity. This subfamily includes Fusarium verticillioides FUM14 (also known as NRPS8), a bi-domain protein with an ester-bond forming NRPS C-domain, which catalyzes linkages between an aminoacyl/peptidyl-PCP donor and a hydroxyl-containing acceptor. C-domains typically have a conserved HHxxxD motif at the active site; mutations in this motif can abolish or diminish condensation activity. FUM14 has an altered active site motif DHTHCD instead of the typical HHxxxD motif seen in other subfamily members. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). There are various subtypes of C-domains such as the LCL-type which catalyzes peptide bond formation between two L-amino acids, the DCL-type which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. 395 matched cddid_all.tbl CDD cd19546 cd19546 380468 X-Domain_NRPS X-domain is a catalytically inactive Condensation-like domain shown to recruit oxygenases to the non-ribosomal peptide synthetase (NRPS). The X-domain is a catalytically inactive member of the Condensation (C) domain family of non-ribosomal peptide synthetase (NRPS). It has been shown to recruit oxygenases to the NRPS to perform side-chain crosslinking in the production of glycopeptide antibiotics. C-domains of nonribosomal peptide synthetases (NRPSs) catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). There are various subtypes of C-domains such as the LCL-type which catalyzes peptide bond formation between two L-amino acids, the DCL-type which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as this X-domain, the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, and dual E/C (epimerization and condensation) domains. C-domains typically have a conserved HHxxxD motif at the active site; mutations in this motif can abolish or diminish condensation activity; members of this X-domain subfamily lack the second H of this motif. 440 matched cddid_all.tbl CDD cd19547 cd19547 380469 beta-lac_NRPS Condensation domain of nonribosomal peptide synthetases (NRPSs) similar to Nocardia uniformis NocB which exhibits an unusual cyclization to form beta-lactam rings in pro-nocardicin G synthesis. Nocardia uniformis NRPS NocB acts centrally in the biosynthesis of the nocardicin monocyclic beta-lactam antibiotics. Along with another NRPS NocA, it mediates an unusual cyclization to form beta-lactam rings in the synthesis of the beta-lactam-containing pentapeptide pro-nocardicin G. This small subfamily is related to DCL-type Condensation (C) domains, which catalyze condensation between a D-aminoacyl/peptidyl-PCP donor and a L-aminoacyl-PCP acceptor. NRPSs catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). There are various subtypes of C-domains such as the LCL-type which catalyzes peptide bond formation between two L-amino acids, the DCL-type which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. C-domains typically have a conserved HHxxxD motif at the active site; domains belonging to this subfamily have an HHHxxxD motif at the active site. 422 matched cddid_all.tbl CDD cd19548 cd19548 381016 serpinA_A1AT-like serpin family A member, alpha-1-antitrypsin and similar serpin proteins in birds and reptiles. The alpha-1-antitrypsin family has a variety of different members of sauropsida belonging to the clade A of the serpin superfamily. This branch includes members from zebra finch, green anole, king cobra, gekko, crocodile, and central bearded dragon. Alpha-1-antitrypsin (also called A1AT, A1A, AAT, alpha1-proteinase inhibitor/A1PI, alpha1-antiproteinase/A1AP, and serum trypsin inhibitor) is a protease inhibitor. Clade A includes the classical serine proteinase inhibitors, alpha-1-antitrypsin and alpha-1-antichymotrypsin, protein C inhibitor, kallistatin, and non-inhibitory serpins, like corticosteroid and thyroxin binding globulins. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 370 matched cddid_all.tbl CDD cd19549 cd19549 381017 serpinA_A1AT-like serpin family A member, alpha-1-antitrypsin and similar proteins. This group contains proteins similar to alpha-1-antitrypsin (also called A1AT, A1A, AAT, alpha1-proteinase inhibitor/A1PI, alpha1-antiproteinase/A1AP, and serum trypsin inhibitor), a protease inhibitor that belongs to the serpin superfamily. It is encoded in humans by the SERPINA1 gene. When the blood contains inadequate amounts of A1AT or functionally defective A1AT (such as in alpha-1 antitrypsin deficiency), neutrophil elastase is excessively free to break down elastin, degrading the elasticity of the lungs, which results in respiratory complications, such as chronic obstructive pulmonary disease. Normally, A1AT leaves its site of origin, the liver, and joins the systemic circulation; defective A1AT can fail to do so, building up in the liver, which results in cirrhosis. This group belongs to the clade A of the serpin superfamily, which includes the classical serine proteinase inhibitors, alpha-1-antitrypsin and alpha-1-antichymotrypsin, protein C inhibitor, kallistatin, and non-inhibitory serpins, like corticosteroid and thyroxin binding globulins. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 367 matched cddid_all.tbl CDD cd19550 cd19550 381018 serpinA2_PIL serpin family A member 2, protease inhibitor 1-like. Protease inhibitor 1-like (also called serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 2, ARGS, protease inhibitor 1 (alpha-1-antitrypsin)-like)/PIL, and alpha-1-antitrypsin-related protein/ATR) belongs to the serpin superfamily and is encoded by the SERPINA2 gene in humans. SERPINA2 was once thought to be a pseudogene, but recent evidence shows that it produces an active transcript. It is very similar in structure and function to SERPINA1. This family belongs to the clade A of the serpin superfamily, which includes the classical serine proteinase inhibitors, alpha-1-antitrypsin and alpha-1-antichymotrypsin, protein C inhibitor, kallistatin, and non-inhibitory serpins, like corticosteroid and thyroxin binding globulins. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 363 matched cddid_all.tbl CDD cd19551 cd19551 381019 serpinA3_A1AC serpin family A member 3, alpha 1-antichymotrypsin. Alpha 1-antichymotrypsin (a1AC/A1AC/a1ACT/AACT) is an alpha globulin glycoprotein that is a member of the serpin superfamily. In humans, it is encoded by the SERPINA3 gene. It inhibits the activity of proteases, such as cathepsin G that is found in neutrophils, and chymases found in mast cells, by cleaving them into a different shape or conformation. This activity protects some tissues, such as the lower respiratory tract, from damage caused by proteolytic enzymes. Deficiency of this protein has been associated with liver disease. Mutations have been identified in patients with Parkinson disease and chronic obstructive pulmonary disease. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 382 matched cddid_all.tbl CDD cd19552 cd19552 381020 serpinA4_KST serpin family A member 4, kallistatin. Kallistatin (KST, also called proteinase inhibitor 4/PI4, or kallikrein inhibitor/KAL) is a protein that in humans is encoded by the SERPINA4 gene. Kallistatin inhibits human amidolytic and kininogenase activities of tissue kallikrein. Heparin blocks kallistatin's complex formation with tissue kallikrein and abolishes its inhibitory effect on tissue kallikrein's activity. Kallistatin was found to be expressed in human liver, stomach, pancreas, kidney, aorta, testes, prostate, artery, atrium, ventricle, lung, renal proximal tubular cell, and a colonic carcinoma cell line T84. This family belongs to the clade A of the serpin superfamily, which includes the classical serine proteinase inhibitors, alpha-1-antitrypsin and alpha-1-antichymotrypsin, protein C inhibitor, kallistatin, and non-inhibitory serpins, like corticosteroid and thyroxin binding globulins. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 383 matched cddid_all.tbl CDD cd19553 cd19553 381021 serpinA5_PCI serpin family A member 5, protein C inhibitor. Protein C inhibitor (PCI/PROCI, also called PAI3, plasminogen activator inhibitor-3/PLANH3, plasma serine protease inhibitor) has many biological functions. It acts as a pro-coagulant in blood and in the seminal vesicles, it is required for spermatogenesis. It is a member of the clade A serpin family that includes the classical serine proteinase inhibitors, alpha-1-antitrypsin and alpha-1-antichymotrypsin, protein C inhibitor, kallistatin, and non-inhibitory serpins, like corticosteroid and thyroxin binding globulins. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 364 matched cddid_all.tbl CDD cd19554 cd19554 381022 serpinA6_CBG serpin family A member 6, corticosteroid-binding globulin. Corticosteroid-binding globulin (CBG, also known as transcortin) is encoded by the SERPINA6 gene in humans which encodes an alpha-globulin with corticosteroid-binding properties. It is produced in the liver. CBG binds several steroid hormones at high rates including cortisol, cortisone, deoxycorticosterone (DOC), corticosterone, aldosterone, progesterone, and 17a-hydroxyprogesterone. This family belongs to the clade A of the serpin superfamily, which includes the classical serine proteinase inhibitors, alpha-1-antitrypsin and alpha-1-antichymotrypsin, protein C inhibitor, kallistatin, and non-inhibitory serpins, like corticosteroid and thyroxin binding globulins. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 373 matched cddid_all.tbl CDD cd19555 cd19555 381023 serpinA7_TBG serpin family A member 7, thyroxine-binding globulin. Thyroxine-binding globulin (TBG, also called T4-binding globulin) is a globulin that binds thyroid hormones in circulation. It is one of three transport proteins (along with transthyretin and serum albumin) responsible for carrying the thyroid hormones thyroxine (T4) and triiodothyronine (T3) in the bloodstream. TBG is synthesized primarily in the liver and is a serpin with no inhibitory function like many other members of this class of proteins. There are two forms of inherited thyroxine-binding globulin deficiency: the complete form (TBG-CD), which results in a total loss of thyroxine-binding globulin, and the partial form (TBG-PD), which reduces the amount of this protein or alters its structure. Neither of these conditions causes any problems with thyroid function, but it can be mistaken for more serious thyroid disorders, such as hypothyroidism. This family belongs to the clade A of the serpin superfamily, which includes the classical serine proteinase inhibitors, alpha-1-antitrypsin and alpha-1-antichymotrypsin, protein C inhibitor, kallistatin, and non-inhibitory serpins, like corticosteroid and thyroxin binding globulins. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 379 matched cddid_all.tbl CDD cd19556 cd19556 381024 serpinA9_centerin serpin family A member 9, centerin. Centerin, also known as germinal center B-cell-expressed transcript 1/GCET1, is a serpin whose expression is restricted to germinal center B-cells and lymphoid malignancies with germinal center B-cell maturation. Expression of centerin, together with bcl-6 and GCET2, constitutes a germinal center B-cell signature, which is associated with a good prognosis in diffuse large B-cell lymphomas. Centerin is thought to function in vivo in the germinal centre as an efficient inhibitor of a trypsin-like protease. It also inhibits the trypsin-like serine proteases trypsin, thrombin and plasmin and is able to bind heparin and DNA. The centerin gene maps to the A clade serpin cluster on chromosome 14q32.1, which also contains a1-antitrypsin and a1-antichymotrypsin together with seven other serpins. The clade A of the serpin superfamily includes the classical serine proteinase inhibitors, alpha-1-antitrypsin and alpha-1-antichymotrypsin, protein C inhibitor, kallistatin, and non-inhibitory serpins, like corticosteroid and thyroxin binding globulins. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 388 matched cddid_all.tbl CDD cd19557 cd19557 381025 serpinA11 serpin family A member 11. Serpin A11, in rats also called liver regeneration-related protein LRRG023, is a serpin encoded by the gene SERPINA11. It maps on chromosome 14, at 14q32.13 and is strongly expressed in the human liver. The function of this protein is unknown. It belongs to the clade A of the serpin superfamily, which includes the classical serine proteinase inhibitors, alpha-1-antitrypsin and alpha-1-antichymotrypsin, protein C inhibitor, kallistatin, and non-inhibitory serpins, like corticosteroid and thyroxin binding globulins. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 373 matched cddid_all.tbl CDD cd19558 cd19558 381026 serpinA12_vaspin serpin family A member 12, visceral adipose tissue-derived serpin. Vaspin, also called visceral adipose tissue-derived serpin or serpinA12, was identified as an adipokine with insulin-sensitizing effects and has been shown to significantly reduce blood glucose concentrations in various mouse models. As such, vaspin may represent a novel treatment tool for diabetes intervention strategies. Human kallikrein 7 (hK7), which cleaves human insulin within A and B chain, was the first protease target of vaspin inhibited by classical serpin mechanism with high specificity in vitro. This family belongs to the clade A of the serpin superfamily, which includes the classical serine proteinase inhibitors, alpha-1-antitrypsin and alpha-1-antichymotrypsin, protein C inhibitor, kallistatin, and non-inhibitory serpins, like corticosteroid and thyroxin binding globulins. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 372 matched cddid_all.tbl CDD cd19559 cd19559 381027 serpinA14_UTMP_UABP-2 serpin family A member 14, uterine milk protein and uteroferrin-associated basic protein 2. The uteroferrin(Uf)-associated basic proteins-2(UABP-2/UABP/UfAP) are a group of three (Mr = 42K, 48K, and 50K) antigenically related, basic glycoproteins secreted by the porcine uterus under the influence of progesterone (P4), which exist as heterodimers (Mr = 80,000) with the iron-binding acid phosphatase, Uf. This group also contains UTMP (uterine milk protein), encoded by SERPINA14. UTMP binds noncovalently to the iron-containing glycoprotein uteroferrin, which displays phosphatase activity and is thought to be involved with iron transport to the fetus. Synthesis of these serpins is induced by progesterone in the uterus. UTMP is also an activin-binding protein and has been implicated in regulation of uterine immune function. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 386 matched cddid_all.tbl CDD cd19560 cd19560 381028 serpinB1_LEI serpin family B member 1 (serpin B1), leukocyte elastase inhibitor (LEI). Leukocyte elastase inhibitor (LEI , also known as proteinase inhibitor 2/PI2, monocyte neutrophil elastase inhibitor/MNEI, EI, or ELANH2) is a member of the clade B serpins or ov-serpins (ovalbumin related serpins) that in humans is encoded by the SERPINB1 gene. Human SERPINB1 is a potent intracellular inhibitor for granzyme H (GzmH) which is constitutively expressed in NK cells and induces target cell death. GzmH cleaves SERPINB1 at Phe343 in the RCL to mediate suicide inhibition. Equine leukocyte elastase inhibitor (HLEI) in contrast to other serpins contains no carbohydrate and has a blocked amino terminus. HLEI is a thymosin beta4-binding protein suggesting a physiological role for cytoplasmic elastase inhibitors in the thymosin B4-regulated rearrangement of the cytoskeleton of leukocytes. HLEI has been proposed to be involved with the control of intracellular protein turnover or the control of elastinolytic activity during inflammation. Ov-serpins are a family of closely related proteins, whose members can be secreted (ovalbumin), cytosolic (leukocyte elastase inhibitor, LEI), or targeted to both compartments (plasminogen activator inhibitor 2, PAI-2). It also characterized by N- and C-terminal extensions, the absence of a signal peptide, and a Ser rather than an Asn residue at the penultimate position. The ov-serpins corresponds to clade B of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants can cause blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 379 matched cddid_all.tbl CDD cd19562 cd19562 381029 serpinB2_PAI-2 serpin family B member 2, plasminogen activator inhibitor 2. Plasminogen activator inhibitor-2 (PAI-2/PLANH2, also called placental PAI, monocyte arg-serpin, or urokinase inhibitor) is a serine protease inhibitor that belongs to the ovalbumin family of serpins (ov-serpins). It is an effective inhibitor of urinary plasminogen activator (urokinase or uPA) and is involved in cell differentiation, tissue growth and regeneration. Ov-serpins are a family of closely related proteins, whose members can be secreted (ovalbumin), cytosolic (leukocyte elastase inhibitor, LEI), or targeted to both compartments (plasminogen activator inhibitor 2, PAI-2). It also characterized by N- and C-terminal extensions, the absence of a signal peptide, and a Ser rather than an Asn residue at the penultimate position. The ov-serpins corresponds to clade B of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants can cause blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 414 matched cddid_all.tbl CDD cd19563 cd19563 381030 serpinB3_B4_SCCA1_2 serpin family B members 3 and 4, squamous cell carcinoma antigens 1 and 2. Squamous cell carcinoma antigen 1 (SCCA1, also called HsT1196 or protein T4-A) and squamous cell carcinoma antigen 2 (SCCA2, also called PI11 or leupin), which are encoded by the SERPINB3 and SERPINB4 genes, respectively, are members of the serpin family of serine protease inhibitors. SCCA1 is a so called cross-class serpin, inhibiting cysteine proteinases such as cathepsin S, K, L, and papain. SCCA2 inhibits chymotrypsin-like serine proteases including chymase, cathepsin G, and Der p1. Elevated levels of SCCA1 and SCCA2 have been detected in chronic inflammatory conditions involving the skin, especially atopic dermatitis (AD)and psoriasis, as well as in respiratory inflammatory diseases such as asthma, chronic obstructive pulmonary disease (COPD), and tuberculosis. They are both normally co-expressed in squamous epithelial cells of tongue, esophagus, tonsils, epidermal hair follicles, lung and uterus, and become highly up-regulated in squamous carcinomas of these organs. Diseases associated with SERPINB3 include anal cancer and cervical squamous cell carcinoma, whereas SERPINB4 include squamous cell carcinoma and chromosome 18Q deletion syndrome. The ovalbumin family of serpins (ov-serpins) is a family of closely related proteins, whose members can be secreted (ovalbumin), cytosolic (leukocyte elastase inhibitor, LEI), or targeted to both compartments (plasminogen activator inhibitor 2, PAI-2). It also characterized by N- and C-terminal extensions, the absence of a signal peptide, and a Ser rather than an Asn residue at the penultimate position. The ov-serpins corresponds to clade B of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants can cause blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 390 matched cddid_all.tbl CDD cd19565 cd19565 381031 serpinB6_CAP serpin family B member 6, cytoplasmic antiproteinase. Cytoplasmic antiproteinase (CAP, also called proteinase inhibitor 6/PI6 or placental thrombin inhibitor/PTI) is thought to be involved in the regulation of serine proteinases present in the brain or extravasated from the blood. It may play an important role in the inner ear in the protection against leakage of lysosomal content during stress; loss of this protection results in cell death and sensorineural hearing loss. It is an inhibitor of cathepsin G, kallikrein-8 and thrombin. The ovalbumin family of serpins (ov-serpins) is a family of closely related proteins, whose members can be secreted (ovalbumin), cytosolic (leukocyte elastase inhibitor, LEI), or targeted to both compartments (plasminogen activator inhibitor 2, PAI-2). It also characterized by N- and C-terminal extensions, the absence of a signal peptide, and a Ser rather than an Asn residue at the penultimate position. The ov-serpins corresponds to clade B of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants can cause blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 378 matched cddid_all.tbl CDD cd19566 cd19566 381032 serpinB7_megsin serpin family B member 7, megsin. Megsin is named as such due to its primary expression in the mesangium, a structure associated with the capillaries in the glomerulus of the kidney. Megsin is thought to play a role in the regulation of a wide variety of processes in mesangial cells, such as matrix metabolism, cell proliferation, and apoptosis. Identification of the exact biological functions and target proteases of megsin will lead to the development of novel therapeutic approaches to glomerular diseases. Expression of this gene is upregulated in IgA nephropathy and mutations have been found to cause palmoplantar keratoderma, Nagashima type. Megsin belongs to the ovalbumin family of serpins (ov-serpins), a family of closely related proteins, whose members can be secreted (ovalbumin), cytosolic (leukocyte elastase inhibitor, LEI), or targeted to both compartments (plasminogen activator inhibitor 2, PAI-2). It also characterized by N- and C-terminal extensions, the absence of a signal peptide, and a Ser rather than an Asn residue at the penultimate position. The ov-serpins corresponds to clade B of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants can cause blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 380 matched cddid_all.tbl CDD cd19567 cd19567 381033 serpinB8_CAP-2 serpin family B member 8, cytoplasmic antiproteinase 2. Cytoplasmic antiproteinase 2 (CAP-2 or peptidase inhibitor 8/PI-8) is a member of the ovalbumin family of serpins (ov-serpins). Serpin B8 is produced by platelets and can bind to and inhibit the function of furin, a serine protease involved in platelet functions. In addition, this protein has been found to enhance the mechanical stability of cell-cell adhesion in the skin, and defects in this gene have been associated with an autosomal-recessive form of exfoliative ichthyosis. Diseases associated with SERPINB8 include Peeling Skin Syndrome 5 and Exfoliative Ichthyosis. Among its related pathways are Response to elevated platelet cytosolic Ca2+ and CFTR-dependent regulation of ion channels in Airway Epithelium (norm and CF). The ov-serpins are a family of closely related proteins, whose members can be secreted (ovalbumin), cytosolic (leukocyte elastase inhibitor, LEI), or targeted to both compartments (plasminogen activator inhibitor 2, PAI-2). It also characterized by N- and C-terminal extensions, the absence of a signal peptide, and a Ser rather than an Asn residue at the penultimate position. The ov-serpins corresponds to clade B of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants can cause blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 374 matched cddid_all.tbl CDD cd19568 cd19568 381034 serpinB9_CAP-3 serpin family B member 9, cytoplasmic antiproteinase 3. Cytoplasmic antiproteinase 3 (CAP-3; peptidase inhibitor 9/PI-9, Spi6, or testicular tissue protein Li 180) is an intracellular inhibitor of granzyme B (grB) that protects cytotoxic lymphocytes from grB-mediated death. It is also thought to be expressed in accessory immune cells, including dendritic cells (DCs), although there is some debate about this. Overexpression of serpin B9 may prevent cytotoxic T-lymphocytes from eliminating certain tumor cells. A pseudogene of this gene is found on chromosome 6. Diseases associated with serpin B9 include chronic obstructive pulmonary disease (COPD) and oral squamous cell carcinoma (OSCC). The ovalbumin family of serpins (ov-serpins) is a family of closely related proteins, whose members can be secreted (ovalbumin), cytosolic (leukocyte elastase inhibitor, LEI), or targeted to both compartments (plasminogen activator inhibitor 2, PAI-2). It also characterized by N- and C-terminal extensions, the absence of a signal peptide, and a Ser rather than an Asn residue at the penultimate position. The ov-serpins corresponds to clade B of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants can cause blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 376 matched cddid_all.tbl CDD cd19569 cd19569 381035 serpinB10_bomapin serpin family B member 10, bomapin. Bomapin (also called proteinase inhibitor 10/PI10) is a hematopoietic- and myeloid leukaemia-specific protease inhibitor which is thought to augment proliferation or apoptosis of leukemia cells, depending on growth factor availability. Bomapin is expressed only in bone marrow, leukocytes of patients with myeloid leukaemia that correspond to myeloid progenitors, and promyelocytic leukaemia cell lines (HL60, THP1, and AML-193), but it is not present in terminally differentiated leukocytes. The ovalbumin family of serpins (ov-serpins) is a family of closely related proteins, whose members can be secreted (ovalbumin), cytosolic (leukocyte elastase inhibitor, LEI), or targeted to both compartments (plasminogen activator inhibitor 2, PAI-2). It also characterized by N- and C-terminal extensions, the absence of a signal peptide, and a Ser rather than an Asn residue at the penultimate position. The ov-serpins corresponds to clade B of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants can cause blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 397 matched cddid_all.tbl CDD cd19570 cd19570 381036 serpinB11_epipin serpin family B member 11, epipin. Epipin/SERPINB11 has no serine protease inhibitory activity, probably due to mutations in the scaffold, impairing conformational changes, and may have evolved a non-inhibitory function. The ovalbumin family of serpins (ov-serpins) is a family of closely related proteins, whose members can be secreted (ovalbumin), cytosolic (leukocyte elastase inhibitor, LEI), or targeted to both compartments (plasminogen activator inhibitor 2, PAI-2). It also characterized by N- and C-terminal extensions, the absence of a signal peptide, and a Ser rather than an Asn residue at the penultimate position. The ov-serpins corresponds to clade B of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants can cause blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 392 matched cddid_all.tbl CDD cd19571 cd19571 381037 serpinB12_yukopin serpin family B member 12, yukopin. Yukopin, encoded by the SERPINB12 gene, is a member of the serpin superfamily of serine protease inhibitors. It inhibits trypsin and plasmin, but not thrombin, coagulation factor Xa, or urokinase-type plasminogen activator. An important paralog of this gene is SERPINB4. The ovalbumin family of serpins (ov-serpins) is a family of closely related proteins, whose members can be secreted (ovalbumin), cytosolic (leukocyte elastase inhibitor, LEI), or targeted to both compartments (plasminogen activator inhibitor 2, PAI-2). It also characterized by N- and C-terminal extensions, the absence of a signal peptide, and a Ser rather than an Asn residue at the penultimate position. The ov-serpins corresponds to clade B of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants can cause blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 420 matched cddid_all.tbl CDD cd19572 cd19572 381038 serpinB13_headpin serpin family B member 13, headpin. Headpin (also known as hurpin or proteinase inhibitor 13/P113) maps to chromosome 18q21.3 and is expressed in normal squamous epithelium of the oral mucosa, skin, and cervix. Inhibitory serpins are known to play an important role in tumor invasion, metastasis, tumor suppression and apoptosis. Headpin belongs to the ovalbumin family of serpins (ov-serpins), a family of closely related proteins, whose members can be secreted (ovalbumin), cytosolic (leukocyte elastase inhibitor, LEI), or targeted to both compartments (plasminogen activator inhibitor 2, PAI-2). It also characterized by N- and C-terminal extensions, the absence of a signal peptide, and a Ser rather than an Asn residue at the penultimate position. The ov-serpins corresponds to clade B of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants can cause blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 391 matched cddid_all.tbl CDD cd19573 cd19573 381039 serpinE2_GDN serpin family E member 2, glia derived nexin (GDN). Serpin glia-derived nexin (GDN; also called peptidase inhibitor 7/PI-7 or protease nexin 1/PN-1) is a specific and extremely efficient inhibitor of thrombin. Unlike other thrombin inhibitors, it is not synthesized in the liver and does not circulate in the blood. It is instead expressed by multiple cell types and is located on the surface of these cells, bound to glycosaminoglycans. GDN plays a role in thrombosis and atherosclerosis and is a clade E serpin. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 375 matched cddid_all.tbl CDD cd19574 cd19574 381040 serpinE3 serpin family E member 3. The function of serpin E3 is not known. It is a member of clade E, which also includes nexin and plasminogen activator inhibitor type 1, of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 384 matched cddid_all.tbl CDD cd19575 cd19575 381041 serpinH2 serpin family H member 2. The function of Danio rerio serpin H2 is not known. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants can cause blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 382 matched cddid_all.tbl CDD cd19576 cd19576 381042 serpinI2_pancpin serpin family I member 2, pancpin. Pancpin (also called proteinase inhibitor 14/PI14 or myoepithelium-derived serine protease inhibitor/MEPI ) is an inhibitory member of the serpin superfamily. It is downregulated in pancreatic and breast cancer, and is associated with acinar cell apoptosis and pancreatic insufficiency when absent in mice. Pancpin was found to inhibit pancreatic chymotrypsin and elastase. It is thought that pancpin protects pancreatic cells from the consequences of premature activation of their respective zymogens. This subgroup belongs to clade I of the serpin superfamily. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 371 matched cddid_all.tbl CDD cd19577 cd19577 381043 serpinJ_IRS-2-like serpin family J, Ixodes ricinus serpin-2 (IRS-2). The serpin family J clade contains serpins from the Chelicerates. This model includes serpins from the Japanese horseshoe crab, mites, ticks, and spiders. The Limulus intracellular coagulation inhibitor, designated LICI, was isolated from hemocytes of the Japanese horseshoe crab. It blocks the amidolytic activities of Limulus lipopolysaccharide-sensitive serine protease, factor C and also inhibits human alpha-thrombin, rat salivary kallikrein, bovine plasmin, and trypsin but not Limulus clotting enzyme, Limulus factor B, bovine factor Xa, human factor XIa, human tissue plasminogen activator, human urokinase, chymotrypsin, elastase, and papain. Glycosaminoglycans such as heparin and heparan sulfate had no effect on the inhibitory activity. The castor bean tick, Ixodes ricinus serpin-2 (IRS-2) whose structure has been solved, unlike that of the LICI, is found in the saliva of the tick and primarily targets 2 proinflammatory serine proteases: cathepsin G and mast cell chymase, and in higher molar excess, thrombin. It also blocks cathepsin G- and thrombin-induced platelet aggregation. Thus it has a dual role and can interfere with both inflammation and wound healing during tick feeding. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 372 matched cddid_all.tbl CDD cd19578 cd19578 381044 serpinK_insect_SRPN2-like serpin family K, insect Serpin-2 and similar proteins. Serpin-2 (SRPN2) is a negative regulator of the melanization response in the malaria vector Anopheles gambiae. SRPN2 irreversibly inhibits clip domain serine proteinase 9 (CLIPB9), which functions in a serine proteinase cascade ending in the activation of prophenoloxidase and melanization. Silencing of SRPN2 results in spontaneous melanization and decreased life span of the mosquito and is a promising target for vector control. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 376 matched cddid_all.tbl CDD cd19579 cd19579 381045 serpin1K-like Manduca sexta Serpin 1K and similar proteins. Serpin 1K is a chymotrypsin inhibitor and is 1 of 12 serpins found in the hemolymph of the hornworm moth Manduca sexta. Serpins may be involved in the immune response in insect hemolymph. All of these serpins are encoded by the same gene, and the message for each is produced by alternative splicing of the final exon. This exon encodes the RCL and two strands of sheet B. Serpin 1K has a canonical structure at the reactive center, as is observed in a1-antitrypsin, whereas hinge residues (P17-P13) adopt the position and conformation observed in ovalbumin. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 368 matched cddid_all.tbl CDD cd19580 cd19580 381046 serpin_silkworm16_18_22 silk gland serpins 16, 18, and 22 from Bombyx mori. Serpins 16, 18, and 22 of the silkworm Bombyx mori are found in the silk gland, a highly specialized organ that functions to synthesize and store silk proteins. These three serpins are mainly distributed in the middle silk gland and contain a signal peptide for secretion. They also share high sequence homology (~87%), implying that they might carry out a similar and specific function in the middle silk gland lumen. They have a canonical serpin fold, but contain a unique reactive center loop, which is shorter than that of typical serpins. It is thought that active proteases in silk glands are restricted by serpins until the wandering stage. Studies show that serpins 16 and 18 act as inhibitor of cysteine protease with serpin 18 acting specifically on fibroinase. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 365 matched cddid_all.tbl CDD cd19581 cd19581 381047 serpinL_nematode serpin family L, serpin family proteins from nematodes. The role of nematode serpins remains largely elusive. The only nematode serpin for which experimental evidence indicates an evasive function is Brugia malayi SPN-2 which specifically inhibits two human neutrophil-derived serine proteinases, cathepsin G and elastase. Less is known of Brugia malayi SPN-1, which is present at all stages of the parasite life cycle and could exist to inhibit a cognate proteinase endogenous to the parasite. Schistosoma serpins are hypothesized to play a role in both the physiological control of elastase within the schistosomes, and protection of the parasite from activated neutrophils during inflammation. Caenorhabditis elegans serpins are thought to regulate endogenous serine proteinases as well as inhibit proteinases produced by pathogenic microorganisms. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 357 matched cddid_all.tbl CDD cd19582 cd19582 381048 serpinM_ShSPI serpin family M, Schistosoma haematobium serpin. ShSPI is a serpin from the trematode Schistosoma haematobium. The protein is exposed on the surface of invading cercaria as well as of adult worms, suggesting its involvement in the parasite-host interaction. It has several distinctive features, mostly concerning the helical subdomain of the protein. It is proposed that these peculiarities are related to the unique biological properties of a small serpin subfamily which is conserved among pathogenic schistosomes. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 388 matched cddid_all.tbl CDD cd19583 cd19583 381049 serpinN_SPI-1_SPI-2 serpin family N, viral serpin-1 and serpin-2. This group of viral serpins are from the Orthopoxvirus branch (cowpox, ectromelia, vaccinia, variola, and rabbitpox) and corresponding to clade N which contains viral serpin-1 (SPI-1-like) and viral serpin-2 (SPI-2-like) serpins. The other is clade O which contains the viral serpin-3 (SPI-3-like) serpins. SPI-2, also called cytokine response modifier A (crmA), acts to inhibit inflammation and apoptosis. SPI-1, a serpin that is approximately 45% identical to SPI-2, has also been implicated in the inhibition of apoptosis, since certain cells infected with RPV SPI-1 mutants undergo apoptotic cell death. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 347 matched cddid_all.tbl CDD cd19584 cd19584 381050 serpinO_SPI-3_virus serpin family O, viral serpin-3. This group of viral serpins are from the Orthopoxvirus branch (cowpox, ectromelia, vaccinia, variola, and rabbitpox) and corresponding to clade O which contains the viral serpin-3 (SPI-3-like) serpins. The other is clade N which contains viral serpin-1 (SPI-1-like) and viral serpin-2 (SPI-2-like) serpins. SPI-3 is an N-glycosylated bifunctional protein that acts as both a proteinase inhibitor and a suppressor of infected cell-cell fusion. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 350 matched cddid_all.tbl CDD cd19585 cd19585 381051 serpin_poxvirus serpin-like proteins found in poxviruses. These are viral serpins from poxviridae that are not in the Orthopoxvirus branch (cowpox, ectromelia, vaccinia, variola, and rabbitpox) that contains clade N serpins (viral serpin-1/SPI-1-like and viral serpin-2/SPI-2-like) and clade O serpins (viral serpin-3/SPI-3-like). The members here include fowlpox virus, canarypox virus, deerpox virus, tanapox virus, an cotia virus and belong to other poxviridae branches including Leporipoxvirus, Yatapoxvirus, and Avipoxvirus. These viruses have a variety of hosts including humans, birds, and mice. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 345 matched cddid_all.tbl CDD cd19586 cd19586 381052 serpin_mimivirus serpin-like proteins found in mimiviruses. These viral serpins are from Mimiviridae (Tupanvirus, Powai, Bandra, Moumouvirus, and Megavirus) and may represent a new clade of viral serpins. Mimiviridae are thought to have a common evolutionary origin with Poxviridae whose viral serpins are classified into clades N and O. N is composed of viral serpin-1 (SPI-1-like) and viral serpin-2 (SPI-2-like) serpins and clade O is made up of viral serpin-3 (SPI-3-like) serpins. Mimiviruses have the only known viral serpins outside of the poxvirus family. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 355 matched cddid_all.tbl CDD cd19587 cd19587 381053 serpinA16_HongrES1-like serpin family A member 16, HongrES1 and similar proteins. HongrES1 is an epididymis-specific secretory protein and is encoded by the SERPINA16 gene. It is one of several potential decapacitation factors of rodents, including a 40-kDa glycoprotein, phosphatidylethanolamine-binding protein 1 (PEBP1), a cysteine-rich secretory protein 1, an acrosome-stabilizing factor, SVA, SVS2, and SPINKL. In humans, some potential decapacitation factors that have been reported are glycodelin-S, semenogelin I, a 130-kDa glycoprotein, and some mannosyl glycopeptides. Decapitation factors are removed from the sperm head surface during the capacitation process and are able to reverse sperm capacitation. The clade A of the serpin superfamily includes the classical serine proteinase inhibitors, alpha-1-antitrypsin and alpha-1-antichymotrypsin, protein C inhibitor, kallistatin, and non-inhibitory serpins, like corticosteroid and thyroxin binding globulins. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 373 matched cddid_all.tbl CDD cd19588 cd19588 381054 serpin_miropin-like serpin miropin and similar proteins. Miropin, the serpin from Tannerella forsythia, is thought to contribute to the virulence of periodontal pathogens by inhibiting neutrophil serine proteases. Miropin broadly inhibits serine endopeptidases (SEPs) including trypsin, neutrophil elastase, pancreatic elastase, subtilisin, and cathepsin G and cysteine endopeptidases (CEPs) including papain, calpain-like peptidase Tpr, and gingipain K through various reactive-site bonds. This is achieved by offering several target bonds of the RCL for cleavage within a bait region, instead of a single RSB as found in canonical serpins. In addition, promiscuous inhibition is facilitated by the capacity to insert strands deviating from the canonical length into the central sheet A, while keeping the prey peptidase bound and inactivated. The structural adaptation of miropin to provide a relaxed inhibitory specificity, which allows for formation of inhibitory complexes using different sites, is unique among serpins. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 365 matched cddid_all.tbl CDD cd19589 cd19589 381055 serpin_tengpin-like serpin tengpin and similar proteins. Tengpin is an unusual prokaryotic serpin from the extremophile Thermoanaerobacter tengcongensis. In addition to the serpin domain, tengpin contains an N-terminal region that functions to trap the serpin domain in the native metastable state and prevent the spontaneous transition to the latent conformation. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 367 matched cddid_all.tbl CDD cd19590 cd19590 381056 serpin_thermopin-like "serpin thermopin and similar proteins. Thermopin, the serpin from Thermobifida fusca, functions as an irreversible proteinase inhibitor with resistance to polymerization at high temperatures. The crystal structure of the cleaved thermopin was found to adopt the canonical serpin fold, supporting its inclusion as a classical inhibitory member of the serpin superfamily. A detailed structural comparison revealed unique features, including charge-stabilizing interactions, a deleted element of secondary structure (the G helix), and a C-terminal ""tail"" that interacts with the top of the A beta sheet and plays an important role in the folding/unfolding of the molecule. These unique features provide structural and biophysical evidence as to how this unusual serpin member has adapted to remain functional in an extreme environment. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans." 366 matched cddid_all.tbl CDD cd19591 cd19591 381057 serpin_like serpin family proteins. This group includes a variety of serpins in three domains of life eukaryotes, bacteria, and archaea. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 364 matched cddid_all.tbl CDD cd19593 cd19593 381058 serpin_bacteria_crustaceans serpin family proteins from bacteria and crustaceans. This group includes a variety of serpin family proteins from various bacteria and crustaceans including sea louse and salmon louse. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 370 matched cddid_all.tbl CDD cd19594 cd19594 381059 serpin_crustaceans_chelicerates_insects serpin family proteins from crustaceans, chelicerates, and insects. This group includes a variety of serpins from crustaceans (sea louse, Chinese mitten crab, signal crayfish, red king crab, Asian tiger shrimp), chelicerates (Atlantic horseshoe crab, common house spider), and insects (Asian tiger mosquito, caddisfly, pea aphid, bed bug, fruit fly, Australian sheep blowfly, tobacco hornworm, alfalfa leafcutting bee). SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 374 matched cddid_all.tbl CDD cd19596 cd19596 381060 serpin_fungal cellulosomal serpin precursor. A single fungal serpin has been characterized to date: celpin from Piromyces spp. strain E2. Piromyces is a genus of anaerobic fungi found in the gut of ruminants and is important for digesting plant material. Celpin is predicted to be inhibitory and contains two N-terminal dockerin domains in addition to its serpin domain. Dockerins are commonly found in proteins that localise to the fungal cellulosome, a large extracellular multiprotein complex that breaks down cellulose.[21] It is therefore suggested that celpin may protect the cellulosome against plant proteases. Certain bacterial serpins similarly localize to the cellulosome.[186] SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 361 matched cddid_all.tbl CDD cd19597 cd19597 381061 serpin28D-like_insects insect serpins similar to Drosophila melanogaster Serpin-28D. Serpins in insects function within development, wound healing and immunity. Drosophila melanogaster Serpin-28D is required for pupal viability and plays an essential role in regulating melanization. Insect serpins from mosquitoes, Mediterranean fruit fly, fruit fly, and blowfly are included in this subfamily. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 395 matched cddid_all.tbl CDD cd19598 cd19598 381062 serpin77Ba-like_insects insect serpins similar to Drosophila melanogaster Serpin 77Ba. Serpins in insects function within development, wound healing and immunity. Drosophila melanogaster Serpin 77Ba plays an essential role in regulating the tracheal melanization immune response to bacterial and fungal infection. Insect serpins from pine beetle, diamondback moth, red flour beetle, mosquito, silkworm, and fruit fly are included in this subfamily. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 376 matched cddid_all.tbl CDD cd19599 cd19599 381063 serpin18-like_insects insect serpins similar to Anopheles gambiae Serpin 18. Serpins in insects function within development, wound healing and immunity. A. gambiae serpin 18 is categorized as non-inhibitory based on the sequence of its reactive-center loop. It is expressed throughout all life stages in multiple tissues and the hemolymph, and is predicted to be secreted based on the presence of a signal peptide. Insect serpins from mosquitoes are included in this subfamily. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 354 matched cddid_all.tbl CDD cd19600 cd19600 381064 serpin11-like_insects insect serpins similar to Bombyx mori Serpin-11. Serpins in insects function within development, wound healing and immunity. The specific function of Bombyx mori serpin-11 (SPN19) is unknown. Insect serpins from sawfly, mealworm, riceborer, moth, silkworm, bollworm are included in this subfamily. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 366 matched cddid_all.tbl CDD cd19601 cd19601 381065 serpin42Da-like serpins similar to Drosophila melanogaster Serpin 42Da. This subfamily is composed mainly of insect serpins, including Drosophila melanogaster serpin 42Da. Serpins in insects function within development, wound healing and immunity. Serpin 42Da, previously serpin 4, is a serine protease inhibitor that is capable of remarkable functional diversity through the alternative splicing of four different reactive center loop exons. Insect serpins from stink bug, alfalfa leafcutting bee, red flour beetle, house fly, and brown planthopper are also included in this subfamily. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 361 matched cddid_all.tbl CDD cd19602 cd19602 381066 serpin_mollusks serpin family proteins from mollusks. This group includes a variety of serpins from mollusks (freshwater snail, sea slug, and disk abalone). SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 374 matched cddid_all.tbl CDD cd19603 cd19603 381067 serpin_platyhelminthes serpin family proteins from platyhelminthes. This group includes a variety of serpins from platyhelminthes (lung fluke, tapeworm, flatworm). SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 380 matched cddid_all.tbl CDD cd19604 cd19604 381068 serpin_protozoa serpin family proteins from protozoa. This group includes a variety of serpin clades from various protozoa including Neospora caninum that causes neosporosis, Toxoplasma gondii that causes toxoplasmosis, and Hammondia hammondi. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 439 matched cddid_all.tbl CDD cd19605 cd19605 381069 serpin_protozoa viral serpin. CrmA is a viral serpin that inhibits both cysteine and serine proteinases involved in the regulation of host inflammatory and apoptosis processes. It differs from other members of the serpin superfamily by having a shorter reactive center loop as well as possessing an additional highly charged antiparallel beta-strand of beta-sheet A, whose sequence and length are unique. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 413 matched cddid_all.tbl CDD cd19606 cd19606 381624 GH113-like Glycoside hydrolase family 113 beta-mannosidase and similar proteins. Family 113 glycoside hydrolases cleave (1->4)-beta-glycosidic linkages, such as endo-1,4-beta-mannanase. This family also includes TIM-barrel domains found in gene transfer agent proteins. 303 matched cddid_all.tbl CDD cd19607 cd19607 381625 GTA_TIM-barrel-like Putative glycoside hydrolase TIM-barrel domain in gene transfer agent and similar proteins. This domain is found in the gene transfer agent protein, such as the Rhodobacter capsulatus putative gene transfer agent protein encoded by orfg15. In the purple nonsulfur bacterium Rhodobacter capsulatus, DNA transmission is mediated via an unusual system, a small bacteriophage-like particle called the gene transfer agent (GTA) that transfers random 4.5-kb segments of the producing cell's genome to recipient cells, where allelic replacement occurs. 438 matched cddid_all.tbl CDD cd19608 cd19608 381626 GH113_mannanase-like Glycoside hydrolase family 113 beta-1,4-mannanase and similar proteins. Mannan endo-1,4-beta mannosidase (E.C 3.2.1.78) randomly cleaves (1->4)-beta-D-mannosidic linkages in mannans, galactomannans and glucomannans and is also called beta-1,4-mannanase, endo-1,4-beta-mannanase, endo-beta-1,4-mannase, beta-mannanase B, beta-1, 4-mannan 4-mannanohydrolase, endo-beta-mannanase, beta-D-mannanase, 1,4-beta-D-mannan mannanohydrolase, and 4-beta-D-mannan mannanohydrolase. (1->4)-beta-linked mannans are polysaccharides with a linear polymer backbone of (1->4)-beta-linked mannose units (in plants and fungi) or alternating mannose and glucose/galactose units (glucomannan in plants and fungi, and galactomannan and galactoglucomannan in plants), such as in the hemicellulose fraction of hard- and softwoods. Complete degradation of mannan requires a series of enzymes, including beta-1,4-mannanase. According to the CAZy database beta-1,4-mannanases are grouped into various glycoside hydrolase (GH) families; GH family 113 beta-1,4-mannanases include mostly bacterial and archaeal sequences. 310 matched cddid_all.tbl CDD cd19609 cd19609 410991 NTD_TDP-43 N-terminal domain of transactive response DNA-binding protein 43. Transactive response DNA-binding protein of 43 kDa (TDP-43) is a nuclear DNA/RNA-binding protein involved in gene transcription and mRNA processing, transport, and translational regulation. It is vital to pre-mRNA and microRNA processing and regulates stress granule activity through the differential regulation of G3BP and TIA-1. It also forms aggregates implicated in amyotrophic lateral sclerosis. The N-terminal domain of TDP-43 is required for its physiological functions and pathological aggregation. 74 matched cddid_all.tbl CDD cd19610 cd19610 381622 mannanase_GH134 glycosyl hydrolase family 134 inverting endo-beta-1,4-mannanase. glycosyl hydrolase family 134 beta-mannanase (E.C. 3.2.1.78) differs from other mannanases in as it has a hen egg white lysozyme fold and cleaves beta-1,4-mannans with inversion of sterochemistry. Beta-mannosidases are enzymes involved in seed germination and the degradation of the hemicellulose fraction of soft- and hardwoods. 162 matched cddid_all.tbl CDD cd19611 cd19611 381623 Ctf13_LRR_LRR-insertion leucine-rich-repeat (LRR) domain and LRR insertion domain of centromere DNA-binding protein complex CBF3 subunit C (Ctf13). Ctf13, is an F-box protein of the leucine-rich-repeat superfamily; it is a component of CEN binding factor 3 (CBF3), a complex that recognizes point centromeres found in budding yeast, associating specifically with the third centromere DNA element (CDEIII) DNA. CBF3 is comprised of two homodimers of Cep3 and Ndc10, and a Ctf13-Skp1 heterodimer. The Skp1-Ctf13 heterodimer interacts with Cep3, Ndc10 and CDEIII at a completely conserved G, centrally positioned between the TGC/CCG sites. The eight leucine-rich repeat (LRR) motifs of Ctf13 (LRR 1-8) form a solenoid structure. At the N-terminus of the Ctf13 LRR is an expanded F-box, and at the C-terminal end, an alpha-beta domain formed by insertions within the latter LRRs of Ctf13 (LRR insertion domain). This domain model includes the LLR domain and the LRR insertion domain. 290 matched cddid_all.tbl CDD cd19614 cd19614 381247 FABP_Der_p_13-like mite group 13 allergens similar to Dermatophagoides farinae Der p 13, and related proteins. The minor house dust mite allergen Der p 13 is a fatty acid-binding protein and an activator of a TLR2-mediated innate immune response. This group also contains other mite group 13 allergens, including Tyrophagus putrescentiae Tyr p 13 and Blomia tropicalis mite blo t 13. blo t 13 binds the natural fluorescent fatty acid cis-parinaric acid and oleic acid by competition, but not retinol, retinoic acid, cholesterol, or dansylated or anthroxylated fatty acids. This subgroup belongs to the intracellular fatty acid-binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 128 matched cddid_all.tbl CDD cd19615 cd19615 381248 lipocalin_NP7 nitrophorin 7. Nitrophorins (NPs) represent a group of nitric oxide (NO)-carrying heme proteins found in the saliva of Rhodnius prolixus. In its adult phase R. prolixus expresses at least 4 nitrophorins (designated NP1-4 in order of their increasing abundance in the saliva of adult insects). Two additional nitrophorins, NP5 and NP6, have been detected mainly in the five instar nymphal stages of insect development. NP7 has not been isolated from the insects but was instead recognized in a cDNA library. NP7 displays peculiar properties, such as an abnormally high isoelectric point, the ability to bind negatively charged membranes, and a strong pH sensitivity of NO affinity. In contrast to NP1-4, which show high affinities for histamine (Hm), Np7 does not appear to sequester Hm. NPs belong to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 174 matched cddid_all.tbl CDD cd19616 cd19616 381249 FABP11 fatty acid binding protein 11 similar to zebrafish FABP11. This group includes zebrafish FABP11a and FABP11b, Senegalese sole FABP11, and similar proteins. The two copies of the fabp11 gene in the zebrafish genome may have resulted from a fish-specific whole genome duplication event. Fabp11a transcripts have been detected in the liver, brain, heart, testis, muscle, ovary and skin of adult zebrafish while fabp11b transcripts have been found in the brain, heart, ovary and eye in adult tissues. This subgroup belongs to the intracellular fatty-acid binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 129 matched cddid_all.tbl CDD cd19617 cd19617 381250 FABP12 fatty acid-binding protein 12. FABP12 is expressed in rodent retina and testis, as well as in human retinoblastoma cell lines. This subgroup belongs to the intracellular fatty-acid binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 128 matched cddid_all.tbl CDD cd19668 cd19668 410998 TmYidC_peri periplasmic beta-super sandwich fold domain of membrane protein insertase YidC from Thermotoga maritima and similar domains. This subfamily is composed of Thermotoga maritima YidC (TmYidC) and similar proteins. Membrane protein insertase YidC, also called foldase YidC or membrane integrase YidC, facilitates proper folding, insertion, and assembly of inner membrane proteins and complexes. Depending on the nature of the substrate, YidC functions in a Sec-independent (YidC only) or a Sec-dependent manner as part of a complex containing YidC, the SecYEG channel, and SecDFYajC. YidC belongs to the YidC/Oxa1/Alb3 protein family of insertases that contain a core domain of five transmembrane (TM) segments that is essential to insertase function. In addition to this core transmembrane domain, YidC from Gram-negative bacteria contain an extra transmembrane segment (TM1) at the N-terminus and a large periplasmic domain, located between TM1 and TM2, that adopts a beta-super sandwich fold that is found in sugar-binding proteins such as galactose mutarotase. This periplasmic domain may have a role in protein assembly: a region of YidC that binds to SecF maps to one edge of the beta-super sandwich. The periplasmic domain of TmYidC shows no amino acid sequence identity with that of the prototypical Escherichia coli YidC (EcYidC), yet they adopt a similar fold. However, the periplasmic domain of TmYidC displays shorter beta strands and some differences in connectivity, compared to EcYidC. 196 matched cddid_all.tbl CDD cd19669 cd19669 439067 UBR-box UBR-box found in UBR family of E3 ubiquitin ligases (UBR1-7) and similar proteins. The UBR-box is a 70-residue zinc finger domain present in the UBR family of E3 ubiquitin ligases (UBR1-7, also called N-recognins) that directly binds N-terminal degradation signals (N-degrons) in substrate proteins to facilitate substrate ubiquitination and proteasomal degradation via the ubiquitin-proteasome system (UPS). UBR1 and UBR2 bind all type-1 and type-2 N-degrons. They mediate ubiquitination and proteolysis of short-lived regulators and misfolded proteins. UBR4 binds both type-1 and type-2 N-degrons and is involved in proteome-wide turnover of cell surface proteins. UBR5 preferentially binds type-1 N-degrons and mediates ubiquitination of short-lived proteins. UBR3, UBR6 (also called FBXO11), and UBR7 may not bind efficiently to N-degrons. UBR3 is a RING-type E3 ubiquitin ligase with a function in olfactory and other sensory systems. UBR6 is an E3 ubiquitin ligase and a type II methyltransferase, which functions as a key regulator of tumor initiation and progression. It does not bind N-terminal signals. UBR7 is a RING-type E3 ubiquitin ligase that may play an important role in spermiogenesis and fertilization. 66 matched cddid_all.tbl CDD cd19670 cd19670 439068 UBR-box_UBR1_2_3 UBR-box found in ubiquitin-protein ligase E3-alpha-1 (UBR1), E3-alpha-2 (UBR2), E3-alpha-3 (UBR3) and similar proteins. This family includes UBR1, UBR2, and UBR3 (all belonging to EC 2.3.2.27). Both UBR1 (also called E3alpha-I or N-recognin-1) and UBR2 (also called E3-alpha-II or N-recognin-2), are RING-type E3 ubiquitin ligases of the Arg/N-end rule degradation pathway. They recognize and bind to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. Deficiency of UBR1 causes Johanson-Blizzard syndrome. UBR2 is associated with chromatin and controls chromatin dynamics and gene expression in both germ cells and somatic cells. It plays an important role in spermatogenesis. UBR3, also called ubiquitin-protein ligase E3-alpha-III (E3alpha-III), or N-recognin-3, or zinc finger protein 650, is a RING-type E3 ubiquitin ligase with a function in olfactory and other sensory systems. It negatively regulates the mono-ubiquitination of non-muscle Myosin II, a protein associated with hearing loss in humans. It acts as a positive regulator of Hedgehog (Hh) signaling in Drosophila and vertebrates. It also plays an important role for genome stability by controlling cellular levels of the essential DNA repair protein APE1. 69 matched cddid_all.tbl CDD cd19671 cd19671 439069 UBR-box_UBR4_5_6_7 UBR-box found in UBR4, UBR5, UBR6/FBOX11, UBR7 and similar proteins. This family includes UBR4 (EC 2.3.2.27), UBR5 (EC 2.3.2.26), UBR6/FBOX11 and UBR7 (EC 2.3.2.27). Both UBR4 (also called 600 kDa retinoblastoma protein-associated factor, or N-recognin-4, or retinoblastoma-associated factor of 600 kDa, or RBAF600, or p600, or zinc finger UBR1-type protein 1) and UBR7 (also called N-recognin-7) are RING-type E3 ubiquitin ligases of the Arg/N-end rule degradation pathway. They recognize and bind to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. UBR5 (also called E3 ubiquitin-protein ligase, HECT domain-containing 1, E3 ligase identified by differential display (EDD), hyperplastic discs protein homolog (HYD), progestin-induced protein, or N-recognin-5) is a HECT (homologous to E6-AP C-terminus)-type E3 ubiquitin-protein ligase that acts as a key regulator of the ubiquitin proteasome system in both cancer and developmental biology. It is required for Wnt signal responses in Drosophila and human cell lines downstream of activated Armadillo/beta-catenin. It also plays a key role in ciliogenesis by regulating centriolar satellite stability and primary cilia. UBR6 (also called FBOX11, protein arginine N-methyltransferase 9 (PRMT9), or vitiligo-associated protein 1 (VIT-1)), is an E3 ubiquitin ligase and a type II methyltransferase, which functions as a key regulator of tumor initiation and progression. UBR6 is a substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins, such as DTL/CDT2, BCL6 and PRDM1/BLIMP1. UBR6 does not bind N-terminal signals. 67 matched cddid_all.tbl CDD cd19672 cd19672 439070 UBR-box_UBR1_like UBR-box found in ubiquitin-protein ligases, E3-alpha-1 (UBR1), E3-alpha-2 (UBR2), and similar proteins. This family includes UBR1 and UBR2 (both EC 2.3.2.27). Both UBR1 (also called E3alpha-I or N-recognin-1) and UBR2 (also called E3-alpha-II or N-recognin-2), are RING-type E3 ubiquitin ligases of the Arg/N-end rule degradation pathway. They recognize and bind to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. Deficiency of UBR1 causes Johanson-Blizzard syndrome. UBR2 is associated with chromatin and controls chromatin dynamics and gene expression in both germ cells and somatic cells. It plays an important role in spermatogenesis. 70 matched cddid_all.tbl CDD cd19673 cd19673 439071 UBR-box_UBR3 UBR-box found in ubiquitin-protein ligase E3-alpha-3 (UBR3) and similar proteins. UBR3 (EC 2.3.2.27), also called ubiquitin-protein ligase E3-alpha-III (E3alpha-III), or N-recognin-3, or zinc finger protein 650, is a RING-type E3 ubiquitin ligase with a function in olfactory and other sensory systems. It negatively regulates the mono-ubiquitination of non-muscle Myosin II, a protein associated with hearing loss in humans. It acts as a positive regulator of Hedgehog (Hh) signaling in Drosophila and vertebrates. It also plays an important role for genome stability by controlling cellular levels of the essential DNA repair protein APE1. 72 matched cddid_all.tbl CDD cd19674 cd19674 439072 UBR-box_UBR4_like UBR-box found in RING-type E3 ubiquitin-protein ligase UBR4 and similar proteins. UBR4 (EC 2.3.2.27; also called 600 kDa retinoblastoma protein-associated factor, N-recognin-4, retinoblastoma-associated factor of 600 kDa, RBAF600, p600, or zinc finger UBR1-type protein 1) is a RING-type E3 ubiquitin ligase of the Arg/N-end rule degradation pathway. It recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. UBR4 acts as a multifunctional protein with roles in anoikis, viral transformation, and protein degradation, as well as in neurogenesis, neuronal migration, neuronal signaling, and survival. The family also includes Arabidopsis thaliana auxin transport protein BIG (also called protein attenuated shade avoidance 1, protein corymbosa1, protein dark over-expression of cab 1, protein low phosphate-resistant root 1, protein transport inhibitor response 3, or protein umbrella 1). It is a calossin-like protein required for auxin efflux and polar auxin transport (PAT) influencing auxin-mediated developmental responses in Arabidopsis. 72 matched cddid_all.tbl CDD cd19675 cd19675 439073 UBR-box_UBR5 UBR-box found in HECT-type E3 ubiquitin-protein ligase UBR5 and similar proteins. UBR5 (EC 2.3.2.26; also called E3 ubiquitin-protein ligase, HECT domain-containing 1, E3 ligase identified by differential display (EDD), hyperplastic discs protein homolog (HYD), progestin-induced protein, or N-recognin-5) is a HECT (homologous to E6-AP C-terminus)-type E3 ubiquitin-protein ligase that acts as a key regulator of the ubiquitin proteasome system in both cancer and developmental biology. It is required for Wnt signal responses in Drosophila and human cell lines downstream of activated Armadillo/beta-catenin. It also plays a key role in ciliogenesis by regulating centriolar satellite stability and primary cilia. 76 matched cddid_all.tbl CDD cd19676 cd19676 439074 UBR-box_UBR6_FBXO11 UBR-box found in F-box only protein 11 (FBXO11) and similar proteins. FBXO11 (also called UBR6, protein arginine N-methyltransferase 9 (PRMT9), or vitiligo-associated protein 1 (VIT-1)) is an E3 ubiquitin ligase and a type II methyltransferase, which functions as a key regulator of tumor initiation and progression. FBXO11 is a substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins, such as DTL/CDT2, BCL6 and PRDM1/BLIMP1. FBXO11 does not bind N-terminal signals. 69 matched cddid_all.tbl CDD cd19677 cd19677 439075 UBR-box_UBR7 UBR-box found in RING-type E3 ubiquitin-protein ligase UBR7 and similar proteins. UBR7 (EC 2.3.2.27; also called N-recognin-7) is a RING-type E3 ubiquitin ligase of the Arg/N-end rule degradation pathway. It recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. UBR7 may play an important role in spermiogenesis and fertilization. 71 matched cddid_all.tbl CDD cd19678 cd19678 439076 UBR-box_UBR1 UBR-box found in ubiquitin-protein ligase E3-alpha-1 (UBR1) and similar proteins. UBR1 (EC 2.3.2.27), also called ubiquitin-protein ligase E3-alpha-I (E3alpha-I), or N-recognin-1, is a RING-type E3 ubiquitin ligase of the Arg/N-end rule degradation pathway. It recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. Deficiency of UBR1 causes Johanson-Blizzard syndrome. 71 matched cddid_all.tbl CDD cd19679 cd19679 439077 UBR-box_UBR2 UBR-box found in ubiquitin-protein ligase E3-alpha-2 (UBR2) and similar proteins. UBR2 (EC 2.3.2.27), also called ubiquitin-protein ligase E3-alpha-II (E3alpha-II), or N-recognin-2, is a RING-type E3 ubiquitin ligase of the Arg/N-end rule degradation pathway. It recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. UBR2 is associated with chromatin and controls chromatin dynamics and gene expression in both germ cells and somatic cells. It plays an important role in spermatogenesis. 70 matched cddid_all.tbl CDD cd19680 cd19680 439078 UBR-box_UBR4 UBR-box found in RING-type E3 ubiquitin-protein ligase UBR4 and similar proteins. UBR4 (EC 2.3.2.27; also called 600 kDa retinoblastoma protein-associated factor, N-recognin-4, retinoblastoma-associated factor of 600 kDa, RBAF600, p600, or zinc finger UBR1-type protein 1) is a RING-type E3 ubiquitin ligase of the Arg/N-end rule degradation pathway. It recognizes and binds to proteins bearing specific N-terminal residues that are destabilizing according to the N-end rule, leading to their ubiquitination and subsequent degradation. UBR4 acts as a multifunctional protein with roles in anoikis, viral transformation, and protein degradation, as well as in neurogenesis, neuronal migration, neuronal signaling, and survival. 71 matched cddid_all.tbl CDD cd19681 cd19681 439079 UBR-box_BIG_like UBR-box found in Arabidopsis thaliana auxin transport protein BIG and similar proteins. BIG (also called protein attenuated shade avoidance 1, protein corymbosa1, protein dark over-expression of cab 1, protein low phosphate-resistant root 1, protein transport inhibitor response 3, or protein umbrella 1) is a calossin-like protein required for auxin efflux and polar auxin transport (PAT) influencing auxin-mediated developmental responses in Arabidopsis. 74 matched cddid_all.tbl CDD cd19682 cd19682 381525 bHLHzip_MGA_like basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MAX gene-associated protein (MGA) family. The MGA family includes MGA, Schizosaccharomyces pombe ESC1 (spESC1) and similar proteins. MGA, also termed MAX dimerization protein 5 (MAD5), is a dual specificity T-box/ bHLHzip transcription factor that regulates the expression of both Max-network and T-box family target genes. It contains a Myc-like bHLHZip motif and requires heterodimerization with Max for binding to the preferred Myc-Max-binding site CACGTG. In addition to the bHLHZip domain, MGA harbors a second DNA-binding domain, the T-box or T-domain. It thus binds the preferred Brachyury-binding sequence and represses transcription of reporter genes containing promoter-proximal Brachyury-binding sites. spESC1 is a bHLHzip protein with homology to human MyoD and Myf-5 myogenic differentiation inducers. It is involved in the sexual differentiation process. 65 matched cddid_all.tbl CDD cd19683 cd19683 381526 bHLH_SOHLH_like basic helix-loop-helix (bHLH) domain found in the spermatogenesis- and oogenesis-specific basic helix-loop-helix-containing protein (SOHLH) family and similar proteins. The SOHLH family includes two bHLH transcription factors, SOHLH1 and SOHLH2. They are specifically in spermatogonia and oocytes and essential for early spermatogonial and oocyte differentiation. The family also includes transcription factor-like 5 protein (TCFL5) and similar proteins. TCFL5, also termed Cha transcription factor, or HPV-16 E2-binding protein 1 (E2BP-1), is a bHLH transcription factor that plays a crucial role in spermatogenesis. It regulates cell proliferation or differentiation of cells through binding to a specific DNA sequence like other bHLH molecules. 58 matched cddid_all.tbl CDD cd19684 cd19684 381527 bHLH_dnHLH_ID basic helix-loop-helix (bHLH) domain found in the DNA-binding protein inhibitor (ID) family. The ID family includes a dominant negative group of helix-loop-helix (dnHLH) proteins, ID1-4, that are negative regulators of bHLH transcription factors. They contain the HLH-dimerization domain but lack the basic domain necessary for DNA-binding. ID proteins inhibit binding to DNA and transcriptional transactivation by heterodimerization with bHLH proteins. They also interact with many non-bHLH proteins in complex networks. ID proteins have been implicated in regulating gene expression as well as cell-cycle progression. Whereas ID-1, ID-2 and ID-3, are generally considered as tumor promoters, ID4 on the contrary has emerged as a tumor suppressor. 47 matched cddid_all.tbl CDD cd19685 cd19685 381528 bHLH-O_HERP_HES basic helix-loop-helix-orange (bHLH-O) domain found in HERP/HES-like family. The HERP/HES-like family includes bHLH-O transcriptional regulators that are related to the Drosophila hairy and Enhancer-of-split (HES) proteins. The HERP (HES-related repressor protein) subfamily proteins contain a basic helix-loop-helix (bHLH) domain with an invariant glycine residue in its basic region, an orange domain in the central region and YXXW sequence motif at its C-terminal region. Hairy and enhancer of split (HES)-related repressor protein (HERP) proteins (HEY1, HEY2 and HEYL) act as downstream effectors of Notch signaling. They are involved in cardiovascular development and have roles in somitogenesis, myogenesis and gliogenesis. Hairy and enhancer of split-related protein HELT is a transcriptional repressor expressed in the developing central nervous system. It binds preferentially to the canonical E box sequence 5'-CACGCG-3' and regulates neuronal differentiation and/or identity. Differentially expressed in chondrocytes proteins, DEC1 and DEC2, are widely expressed in both embryonic and adult tissues and have been implicated in apoptosis, cell proliferation, and circadian rhythms, as well as malignancy in various cancers. Drosophila melanogaster protein clockwork orange (Cwo) is also included in this subfamily. It is involved in the regulation of Drosophila circadian rhythms. It functions as both an activator and a repressor of clock gene expression. The HES subfamily proteins contain a basic helix-loop-helix (bHLH) domain with an invariant proline residue in its basic region, an orange domain in the central region and a conserved tetrapeptide motif, WRPW, at its C-terminal region. They form heterodimers or homodimers via their HLH domain and bind DNA to repress gene transcription that play an essential role in development of both compartment and boundary cells of the central nervous system. 52 matched cddid_all.tbl CDD cd19686 cd19686 381529 bHLH_TS_FERD3L_like basic helix-loop-helix (bHLH) domain found in Fer3-like protein (FERD3L), pancreas transcription factor 1 subunit alpha (PTF1A) and similar proteins. The family corresponds to a group of bHLH transcription factors, including FERD3L and PTF1A. FERD3L, also termed basic helix-loop-helix protein N-twist, or Class A basic helix-loop-helix protein 31 (bHLHa31), or nephew of atonal 3 (NATO3), or Neuronal twist (NTWIST), is expressed in the developing central nervous system (CNS). It regulates floor plate (FP) cells development. FP is a critical organizing center located at the ventral-most midline of the neural tube. FERD3L binds to the E-box and functions as inhibitor of transcription. PTF1A, also termed Class A basic helix-loop-helix protein 29 (bHLHa29), or pancreas-specific transcription factor 1a, or bHLH transcription factor p48, or p48 DNA-binding subunit of transcription factor PTF1 (PTF1-p48), is implicated in the cell fate determination in various organs. It binds to the E-box consensus sequence 5'-CANNTG-3' and plays a role in early and late pancreas development and differentiation. 56 matched cddid_all.tbl CDD cd19687 cd19687 381530 bHLHzip_Mlx basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Max-like protein X (Mlx) and similar proteins. Mlx, also termed Class D basic helix-loop-helix protein 13 (bHLHd13), or Max-like bHLHZip protein, or protein BigMax, or transcription factor-like protein 4, is a Max-like bHLHZip transcription regulator that interacts with the Max network of transcription factors. It forms a sequence-specific DNA-binding protein complex with some member of Mad family (Mad1 and Mad4) and Mondo family but not the Myc family and bind the E-box DNA to control transcription. 76 matched cddid_all.tbl CDD cd19688 cd19688 381531 bHLHzip_MLXIP basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MLX-interacting protein (MLXIP) and similar proteins. MLXIP, also termed Class E basic helix-loop-helix protein 36 (bHLHe36), or transcriptional activator MondoA, is a bHLHZip transcriptional activator that binds DNA as a heterodimer with Mlx. It binds to the canonical E box sequence 5'-CACGTG-3' and plays a role in transcriptional activation of glycolytic target genes. MLXIP is most highly expressed in skeletal muscle and functions as an indirect glucose sensor, by sensing glucose 6-phosphate and shuttling between the nucleus and the cytoplasm. 72 matched cddid_all.tbl CDD cd19689 cd19689 381532 bHLHzip_MLXIPL basic Helix-Loop-Helix-zipper (bHLHzip) domain found in MLX-interacting protein-like (MLXIPL) and similar proteins. MLXIPL, also termed carbohydrate-responsive element-binding protein (ChREBP), or Class D basic helix-loop-helix protein 14 (bHLHd14), or MLX interactor, or WS basic-helix-loop-helix leucine zipper protein (WS-bHLH), or Williams-Beuren syndrome chromosomal region 14 protein (WBSCR14), is a bHLHZip transcriptional factor integral to the regulation of glycolysis and lipogenesis in the liver. It forms heterodimers with the bHLHZip protein Mlx to bind the DNA sequence 5'-CACGTG-3'. 76 matched cddid_all.tbl CDD cd19690 cd19690 381533 bHLHzip_spESC1_like basic Helix-Loop-Helix-zipper (bHLHzip) domain found in Schizosaccharomyces pombe ESC1 (spESC1) and similar proteins. spESC1 is a bHLHzip protein with homology to human MyoD and Myf-5 myogenic differentiation inducers. It is involved in the sexual differentiation process. 65 matched cddid_all.tbl CDD cd19691 cd19691 381534 bHLH_dnHLH_ID1 basic helix-loop-helix (bHLH) domain found in DNA-binding protein inhibitor ID1 and similar proteins. ID1, also termed Class B basic helix-loop-helix protein 24 (bHLHb24), or inhibitor of DNA binding 1, or inhibitor of differentiation 1, is a dominant negative helix-loop-helix (dnHLH) transcriptional regulator (lacking a basic DNA binding domain) which negatively regulates the bHLH transcription factors by forming heterodimers and inhibiting their DNA binding and transcriptional activity. ID1 interferes with centrosomal function. It has been implicated in the regulation of cell proliferation and differentiation in myogenesis, neurogenesis, and/or hematopoiesis. 52 matched cddid_all.tbl CDD cd19692 cd19692 381535 bHLH_dnHLH_ID2 basic helix-loop-helix (bHLH) domain found in DNA-binding protein inhibitor ID2 and similar proteins. ID2, also termed Class B basic helix-loop-helix protein 26 (bHLHb26), or inhibitor of DNA binding 2, or inhibitor of differentiation 2, is a dominant negative helix-loop-helix (dnHLH) transcriptional regulator (lacking a basic DNA binding domain) which negatively regulates the bHLH transcription factors by forming heterodimers and inhibiting their DNA binding and transcriptional activity. It has been implicated in the regulation of cell proliferation and differentiation in myogenesis, neurogenesis, and/or hematopoiesis. 66 matched cddid_all.tbl CDD cd19693 cd19693 381536 bHLH_dnHLH_ID3 basic helix-loop-helix (bHLH) domain found in DNA-binding protein inhibitor ID3 and similar proteins. ID3, also termed Class B basic helix-loop-helix protein 25 (bHLHb25), or helix-loop-helix protein HEIR-1, or ID-like protein inhibitor HLH 1R21, or inhibitor of DNA binding 3, or inhibitor of differentiation 3, is a dominant negative helix-loop-helix (dnHLH) transcriptional regulator (lacking a basic DNA binding domain) which negatively regulates the bHLH transcription factors by forming heterodimers and inhibiting their DNA binding and transcriptional activity. It negatively regulates muscle differentiation by inhibiting the DNA-binding activities of the myogenic regulatory factors. 61 matched cddid_all.tbl CDD cd19694 cd19694 381537 bHLH_dnHLH_ID4 basic helix-loop-helix (bHLH) domain found in DNA-binding protein inhibitor ID4 and similar proteins. ID4, also termed Class B basic helix-loop-helix protein 27 (bHLHb27), or inhibitor of DNA binding 4, or inhibitor of differentiation 4, is a dominant negative helix-loop-helix (dnHLH) transcriptional regulator (lacking a basic DNA binding domain) which negatively regulates the bHLH transcription factors by forming heterodimers and inhibiting their DNA binding and transcriptional activity. It plays a role in adipose cell differentiation. 60 matched cddid_all.tbl CDD cd19695 cd19695 381538 bHLH_dnHLH_EMC_like basic helix-loop-helix (bHLH) domain found in Drosophila melanogaster protein extra-macrochaetae and similar proteins. Extra-macrochaetae is a negative regulator of sensory organ development in Drosophila. It belongs to dominant negative group of helix-loop-helix (dnHLH) proteins, which lack a basic DNA-binding domain but can form heterodimers with other HLH proteins, thereby inhibiting DNA binding. 52 matched cddid_all.tbl CDD cd19696 cd19696 381539 bHLH-PAS_AhR_like basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in the aryl hydrocarbon receptor (AhR) family. The AhR family includes AhR, AhR repressor (AhRR) and Drosophila melanogaster protein spineless. AhR, also termed Ah receptor, or Dioxin receptor (DR), or Class E basic helix-loop-helix protein 76 (bHLHe76), is the only member of bHLH-PAS transcription regulators that bind and be activated by small chemical ligands. It is activated by Dioxin to control the expression of certain genes to influence biological processes such as apoptosis, proliferation, cell growth and differentiation. To form active DNA binding complexes AhR dimerizes with a bHLH-PAS factor ARNT (Aryl hydrocarbon Nuclear Receptor Translocator). AhRR, also termed Class E basic helix-loop-helix protein 77 (bHLHe77), is a member of bHLH-PAS transcription factors that acts as a negative regulator of AhR, playing key roles in development and environmental sensing. AhRR functions by competing with AhR for its partner ARNT. AhRR-ARNT complexes are transcriptionally inactive. Spineless is a bHLH-PAS transcription factor that plays an important role in fly morphogenesis. It is both necessary and sufficient for the formation of the ommatidial mosaic. 59 matched cddid_all.tbl CDD cd19697 cd19697 381540 bHLH-PAS_NPAS4_PASD10 basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 4 (NPAS4) and similar proteins. NPAS4, also termed neuronal Per-Arnt-Sim homology (PAS) factor 4, or neuronal PAS4, or Class E basic helix-loop-helix protein 79 (bHLHe79), or HLH-PAS transcription factor NXF, or PAS domain-containing protein 10 (PASD10), is a bHLH-PAS neuronal activity-dependent transcription factor which heterodimerizes with ARNT2 to regulate genes involved in inhibitory synapse formation. 57 matched cddid_all.tbl CDD cd19698 cd19698 381541 bHLH_AtMEE8_like basic helix-loop-helix (bHLH) domain found in Arabidopsis thaliana protein maternal effect embryo arrest 8 (AtMEE8) and similar proteins. AtMEE8, also termed AtbHLH108, or EN 132, is a bHLH transcription factor required during early embryo development, for the endosperm formation. 71 matched cddid_all.tbl CDD cd19699 cd19699 381542 bHLH_TS_dMYOD_like basic helix-loop-helix (bHLH) domain found in Drosophila melanogaster myogenic-determination protein (dMYOD) and similar proteins. dMYOD, also termed protein nautilus, or Myd, may play an important role in the early development of muscle in Drosophila. 56 matched cddid_all.tbl CDD cd19700 cd19700 381543 bHLH_TS_TWIST2 basic helix-loop-helix (bHLH) domain found in twist-related protein 2 (TWIST2) and similar proteins. TWIST2, also termed Class A basic helix-loop-helix protein 39 (bHLHa39), or Dermis-expressed protein 1, or Dermo-1, is a bHLH transcription factor that regulates the development of mesenchymal tissues and plays a critical role in embryogenesis. It binds to the E-box consensus sequence 5'-CANNTG-3' as a heterodimer and inhibits transcriptional activation by MYOD1, MYOG, MEF2A and MEF2C. 82 matched cddid_all.tbl CDD cd19701 cd19701 381544 bHLH_TS_HEN1 basic helix-loop-helix (bHLH) domain found in helix-loop-helix protein 1 (HEN-1) and similar proteins. HEN-1, also termed nescient helix-loop-helix 1 (Nhlh1), or Class A basic helix-loop-helix protein 35 (bHLHa35), or nescient helix loop helix 1 (NSCL-1), is a neuron-specific bHLH transcription factor that may serve as DNA-binding protein and may be involved in the control of cell-type determination, possibly within the developing nervous system. 72 matched cddid_all.tbl CDD cd19702 cd19702 381545 bHLH_TS_HEN2 basic helix-loop-helix (bHLH) domain found in helix-loop-helix protein 2 (HEN-2) and similar proteins. HEN-2, also termed nescient helix-loop-helix 2 (Nhlh2), or Class A basic helix-loop-helix protein 34 (bHLHa34), or nescient helix loop helix 2 (NSCL-2), is a neuron-specific bHLH transcription factor that may serve as DNA-binding protein and may be involved in the control of cell-type determination, possibly within the developing nervous system. 73 matched cddid_all.tbl CDD cd19703 cd19703 381546 bHLH_TS_musculin basic helix-loop-helix (bHLH) domain found in musculin and similar proteins. Musculin, also termed activated B-cell factor 1 (ABF-1), or Class A basic helix-loop-helix protein 22 (bHLHa22), is a bHLH transcription factor expressed in activated B lymphocytes. It acts as a transcription repressor capable of inhibiting the transactivation capability of TCF3/E47. Musculin may play a role in regulating antigen-dependent B-cell differentiation. The mouse homolog, musculin, is suggested to be a repressor of myogenesis that is expressed in developing muscle and in the spleen. Musculin heterodimerizes with products of the E2A gene. 66 matched cddid_all.tbl CDD cd19704 cd19704 381547 bHLH_TS_TCF21_capsulin basic helix-loop-helix (bHLH) domain found in transcription factor 21 (TCF-21) and similar proteins. TCF-21, also termed capsulin, or Class A basic helix-loop-helix protein 23 (bHLHa23), or epicardin, or podocyte-expressed 1 (Pod-1), is a bHLH transcription factor expressed specifically in mesodermally-derived cells that surround the epithelium of the developing gastrointestinal, genitourinary and respiratory systems during mouse embryogenesis. It may play a role in the specification or differentiation of one or more subsets of epicardial cell types. 64 matched cddid_all.tbl CDD cd19705 cd19705 381548 bHLH_TS_LYL1 basic helix-loop-helix (bHLH) domain found in protein lyl-1 and similar proteins. Lyl-1, also termed Class A basic helix-loop-helix protein 18 (bHLHa18), or lymphoblastic leukemia-derived sequence 1, is a proto-oncogenic bHLH transcription factor involved in T-cell acute lymphoblastic leukemia. It plays an important role in hematopoietic stem cell function and is required for the late stages of postnatal angiogenesis to limit the formation of new blood vessels, notably by regulating the activity of the small GTPase Rap1. LYL-1 deficiency induces a stress erythropoiesis. 65 matched cddid_all.tbl CDD cd19706 cd19706 381549 bHLH_TS_TAL1 basic helix-loop-helix (bHLH) domain found in T-cell acute lymphocytic leukemia protein 1 (TAL-1) and similar proteins. TAL-1, also termed Class A basic helix-loop-helix protein 17 (bHLHa17), or stem cell protein (SCL), or T-cell leukemia/lymphoma protein 5, is a hematopoietic-specific bHLH transcription factor that functions in embryonic and adult hematopoiesis in vertebrates. It is also required for embryonic vascular remodeling. It acts as a regulator of erythroid differentiation and binds to regulatory regions of a large cohort of erythroid genes as part of a complex with GATA-1, LMO2 and Ldb1. TAL-1 has been implicated in T-cell acute lymphoblastic leukemia. In common with other tissue-specific bHLH proteins, Tal heterodimerizes with ubiquitously-expressed members of the E2A family and form a DNA-binding complex with an E-box (CANNTG) to regulate transcription at its recognition site. 65 matched cddid_all.tbl CDD cd19707 cd19707 381550 bHLH_TS_TAL2 basic helix-loop-helix (bHLH) domain found in T-cell acute lymphocytic leukemia protein 2 (TAL-2) and similar proteins. TAL-2, also termed Class A basic helix-loop-helix protein 19 (bHLHa19), is a bHLH transcription factor essential for the normal brain development. It has been implicated in T-cell acute lymphoblastic leukemia. 61 matched cddid_all.tbl CDD cd19708 cd19708 381551 bHLH_TS_dHLH3B_like basic helix-loop-helix (bHLH) domain found in Drosophila melanogaster helix loop helix protein 3B (dHLH3B) and similar proteins. Drosophila HLH3B is an uncharacterized bHLH transcription factor that belongs to the T-cell acute lymphocytic leukemia protein/ lymphoblastic leukemia-derived sequence (TAL/LYL) family. 60 matched cddid_all.tbl CDD cd19709 cd19709 381552 bHLH_TS_TCF23_OUT basic helix-loop-helix (bHLH) domain found in transcription factor 23 (TCF-23) and similar proteins. TCF-23, also termed Class A basic helix-loop-helix protein 24 (bHLHa24), is a bHLH transcription factor that is essential for progesterone-dependent decidualization. The mouse homolog is also called ovary, uterus and testis protein (OUT), which is expressed predominantly in the reproductive organs such as the uterus, ovary and testis. It shows an Id-like inhibitory activity and functions as a negative regulator of bHLH factors through the formation of a functionally inactive heterodimeric complex. OUT inhibits the formation of TCF3 and MYOD1 homodimers and heterodimers, but lacks DNA binding activity. OUT is involved in the regulation or modulation of smooth muscle contraction of the uterus during pregnancy and particularly around the time of delivery. It also plays a role in the inhibition of myogenesis. Unlike typical bHLH factors, OUT proteins do not bind E-box (CANNTG) or N-box DNA sequences and inhibit DNA binding of homo- and heterodimers consisting of E12 and MyoD in gel mobility shift assays. 56 matched cddid_all.tbl CDD cd19710 cd19710 381553 bHLH_TS_TCF24 basic helix-loop-helix (bHLH) domain found in transcription factor 24 (TCF-24) and similar proteins. TCF-24 is an uncharacterized bHLH transcription factor that shows high sequence similarity with TCF-23. 56 matched cddid_all.tbl CDD cd19711 cd19711 381554 bHLH_TS_MIST1 basic helix-loop-helix (bHLH) domain found in muscle, intestine and stomach expression 1 (MIST-1) and similar proteins. MIST-1, also termed Class A basic helix-loop-helix protein 15 (bHLHa15), or Class B basic helix-loop-helix protein 8 (bHLHb8), is a bHLH transcription factor expressed in pancreatic acinar cells and other serous exocrine cells. It is essential for cytoskeletal organization and secretory activity. It also functions as a potent endoplasmic reticulum (ER) stress-inducible transcriptional regulator. MIST-1 is capable of binding to E-box (CANNTG) motifs as a homodimer or a heterodimer with E-proteins (E12 and E47) to regulate transcription. 62 matched cddid_all.tbl CDD cd19712 cd19712 381555 bHLH_TS_dimmed_like basic helix-loop-helix (bHLH) domain found in Drosophila melanogaster protein dimmed and similar proteins. Dimmed, also termed DIMM, is a bHLH transcription factor that regulates neurosecretory (NS) cell function and neuroendocrine cell fate in Drosophila. 60 matched cddid_all.tbl CDD cd19713 cd19713 381556 bHLH_TS_ATOH1 basic helix-loop-helix (bHLH) domain found in protein atonal homolog 1 (ATOH1) and similar proteins. ATOH1, also termed Class A basic helix-loop-helix protein 14 (bHLHa14), or helix-loop-helix protein hATH-1 (hATH1), or Math1, or Cath1, is a proneural bHLH transcription factor that is essential for inner ear hair cell differentiation. It dimerizes with E47 and activates E-box (CANNTG) dependent transcription. ATOH1 is a mammalian homolog of the Drosophila melanogaster gene atonal and mouse atonal homolog 1 (Math1). 64 matched cddid_all.tbl CDD cd19714 cd19714 381557 bHLH_TS_ATOH7 basic helix-loop-helix (bHLH) domain found in protein atonal homolog 7 (ATOH7) and similar proteins. ATOH7, also termed Class A basic helix-loop-helix protein 13 (bHLHa13), or helix-loop-helix protein hATH-5 (hATH5), or Math5, is a bHLH transcription factor involved in the differentiation of retinal ganglion cells. 69 matched cddid_all.tbl CDD cd19715 cd19715 381558 bHLH_TS_amos_like basic helix-loop-helix (bHLH) domain found in Drosophila melanogaster protein Amos and similar proteins. Amos, also termed absent MD neurons and olfactory sensilla protein, or reduced olfactory organs protein, or rough eye protein, is a bHLH transcription factor that promotes multiple dendritic neuron formation in the Drosophila peripheral nervous system. 64 matched cddid_all.tbl CDD cd19716 cd19716 381559 bHLH_TS_NGN1_NeuroD3 basic helix-loop-helix (bHLH) domain found in neurogenin-1 (NGN-1) and similar proteins. NGN-1, also termed Class A basic helix-loop-helix protein 6 (bHLHa6), or neurogenic basic-helix-loop-helix protein, or neurogenic differentiation factor 3 (NeuroD3), is a neural-specific bHLH transcription factor involved in the initiation of neuronal differentiation. It activates transcription by binding to the E box (5'-CANNTG-3'). 77 matched cddid_all.tbl CDD cd19717 cd19717 381560 bHLH_TS_NGN2_ATOH4 basic helix-loop-helix (bHLH) domain found in neurogenin-2 (NGN-2) and similar proteins. NGN-2, also termed Class A basic helix-loop-helix protein 8 (bHLHa8), or protein atonal homolog 4 (ATOH4), is a neural-specific bHLH transcription factor required for sensory neurogenesis. It activates transcription by binding to the E box (5'-CANNTG-3'). 69 matched cddid_all.tbl CDD cd19718 cd19718 381561 bHLH_TS_NGN3_ATOH5 basic helix-loop-helix (bHLH) domain found in neurogenin-3 (NGN-3) and similar proteins. NGN-3, also termed Class A basic helix-loop-helix protein 7 (bHLHa7), or protein atonal homolog 5 (ATOH5), is a neural-specific bHLH transcription factor expressed in the developing central nervous system and the embryonic pancreas. It is involved in neurogenesis and plays an important role in spermatogenesis. 68 matched cddid_all.tbl CDD cd19719 cd19719 381562 bHLH_TS_NeuroD1 basic helix-loop-helix (bHLH) domain found in neurogenic differentiation factor 1 (NeuroD1) and similar proteins. NeuroD1, also termed Class A basic helix-loop-helix protein 3 (bHLHa3), is a neuronal bHLH transcription factor involved in the development and maintenance of the endocrine pancreas and neuronal elements. It acts as an essential regulator of glutamatergic neuronal differentiation. Loss of NeuroD1 causes ataxia, cerebellar hypoplasia, sensorineural deafness, and severe retinal dystrophy in mice. 86 matched cddid_all.tbl CDD cd19720 cd19720 381563 bHLH_TS_NeuroD2 basic helix-loop-helix (bHLH) domain found in neurogenic differentiation factor 2 (NeuroD2) and similar proteins. NeuroD2, also termed Class A basic helix-loop-helix protein 1 (bHLHa1), or NeuroD-related factor (NDRF), is a neuronal calcium-dependent bHLH transcription factor that induces neuronal differentiation and promotes neuronal survival. It plays a central role in thalamocortical synaptic maturation. NeuroD2 mediates calcium-dependent transcription activation by binding to E box-containing promoter. 93 matched cddid_all.tbl CDD cd19721 cd19721 381564 bHLH_TS_NeuroD4_ATOH3 basic helix-loop-helix (bHLH) domain found in neurogenic differentiation factor 4 (NeuroD4) and similar proteins. NeuroD4, also termed Class A basic helix-loop-helix protein 4 (bHLHa4), or protein atonal homolog 3 (ATH-3), or Atoh3, or Math-3, is a bHLH transcriptional activator that mediates neuronal differentiation. 87 matched cddid_all.tbl CDD cd19722 cd19722 381565 bHLH_TS_NeuroD6_ATOH2 basic helix-loop-helix (bHLH) domain found in neurogenic differentiation factor 6 (NeuroD6) and similar proteins. NeuroD6, also termed Class A basic helix-loop-helix protein 2 (bHLHa2), or protein atonal homolog 2 (ATH-2), or Atoh2, or Math2, or Nex1, is a neurogenic bHLH transcription factor involved in neuronal development, differentiation, and survival in Alzheimer's disease (AD) brains of both cohorts. It plays an integrative role in coordinating increase in mitochondrial mass with cytoskeletal remodeling, suggesting that it may act as a co-regulator of neuronal differentiation and energy metabolism. 70 matched cddid_all.tbl CDD cd19723 cd19723 381566 bHLH_TS_ASCL1_like basic helix-loop-helix (bHLH) domain found in Drosophila melanogaster achaete-scute complex (AS-C) proteins, achaete-scute-like proteins, ASCL1-2, and similar proteins. This subfamily includes Drosophila melanogaster AS-C proteins and two ASCL family of transcription factors, ASCL-1 and ASCL-2. Drosophila melanogaster AS-C proteins includes lethal of scute (also known as achaete-scute complex protein T3 or AST3), scute (also known as achaete-scute complex protein T4 or AST4), achaete (also known as achaete-scute complex protein T5 or AST5), and asense (also known as achaete-scute complex protein T8 or AST8). They are involved in the determination of the neuronal precursors in the peripheral nervous system and the central nervous system, as well as in sex determination and dosage compensation. ASCL-1, also termed Class A basic helix-loop-helix protein 46 (bHLHa46), or achaete-scute homolog 1 (ASH-1), or mammalian achaete scute homolog 1 (Mash1), is expressed in subsets of neural progenitors in both the central and peripheral nervous system. It plays a key role in neuronal differentiation and specification in the nervous system. ASCL-2, also termed achaete-scute homolog 2 (ASH-2), or Class A basic helix-loop-helix protein 45 (bHLHa45), or mammalian achaete scute homolog 2 (Mash2), is involved in Schwann cell differentiation and control of proliferation in adult peripheral nerves. 56 matched cddid_all.tbl CDD cd19724 cd19724 381567 bHLH_TS_ASCL3_like basic helix-loop-helix (bHLH) domain found in achaete-scute-like proteins, ASCL3-5, and similar proteins. This subfamily includes three ASCL family of transcription factors, ASCL-3, ASCL-4 and ASCL-5. ASCL-3, also termed Class A basic helix-loop-helix protein 42 (bHLHa42), or bHLH transcriptional regulator Sgn-1, or achaete-scute homolog 3 (ASH-3), is specifically localized in the duct cells of the salivary glands. It may act as transcriptional repressor that inhibits myogenesis. ASCL-4, also termed Class A basic helix-loop-helix protein 44 (bHLHa44), or achaete-scute homolog 4 (ASH-4), or Hash4, may be involved in skin development. ASCL-5, also termed Class A basic helix-loop-helix protein 47 (bHLHa47), or achaete-scute homolog 5 (ASH-5), is an uncharacterized bHLH transcription factor that is close related to ASCL-3 and ASCL-4. 56 matched cddid_all.tbl CDD cd19725 cd19725 381568 bHLH_TS_OLIG2_like basic helix-loop-helix (bHLH) domain found in oligodendrocyte transcription factors, Oligo2, Oligo3 and similar proteins. The family includes two bHLH transcription factors, Oligo2 and Oligo3. Oligo2, also termed Class B basic helix-loop-helix protein 1 (bHLHb1), or Class E basic helix-loop-helix protein 19 (bHLHe19), or protein kinase C-binding protein 2, or protein kinase C-binding protein RACK17, is required for oligodendrocyte and motor neuron specification in the spinal cord, as well as for the development of somatic motor neurons in the hindbrain. It cooperates with OLIG1 to establish the MN progenitors (pMN) domain of the embryonic neural tube. Oligo3, also termed Class B basic helix-loop-helix protein 7 (bHLHb7), or Class E basic helix-loop-helix protein 20 (bHLHe20), is expressed in the ventricular zone of the dorsal alar plate of the hindbrain and involved in regulating the development of dorsal and ventral spinal cord. It may determine the distinct specification program of class A neurons in the dorsal part of the spinal cord and suppress specification of class B neurons. 63 matched cddid_all.tbl CDD cd19726 cd19726 381569 bHLH-PAS_cycle_like basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein cycle and similar proteins. Protein cycle, also termed brain and muscle ARNT-like 1 (BMAL1), or MOP3, is a putative bHLH-PAS transcription factor involved in the generation of biological rhythms in Drosophila. It activates cycling transcription of Period (PER) and Timeless (TIM) by binding to the E-box (5'-CACGTG-3') present in their promoters. 62 matched cddid_all.tbl CDD cd19727 cd19727 381570 bHLH-PAS_HIF1a_PASD8 basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor 1-alpha (HIF1a) and similar proteins. HIF1a, also termed HIF-1-alpha, or HIF1-alpha, or ARNT-interacting protein, or Basic-helix-loop-helix-PAS protein MOP1, or Class E basic helix-loop-helix protein 78 (bHLHe78), or Member of PAS protein 1, or PAS domain-containing protein 8 (PASD8), functions as a master transcriptional regulator of the adaptive response to hypoxia. 71 matched cddid_all.tbl CDD cd19728 cd19728 381571 bHLH-PAS_HIF2a_PASD2 basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor 2-alpha (HIF2a) and similar proteins. HIF2a, also termed HIF-2-alpha, or HIF2-alpha, or endothelial PAS domain-containing protein 1 (EPAS-1), or Basic-helix-loop-helix-PAS protein MOP2, or Class E basic helix-loop-helix protein 73 (bHLHe73), or Member of PAS protein 2, or PAS domain-containing protein 2 (PASD2), or HIF-1-alpha-like factor (HLF), is a bHLH-PAS transcription factor involved in the induction of oxygen regulated genes. 66 matched cddid_all.tbl CDD cd19729 cd19729 381572 bHLH-PAS_HIF3a_PASD7 basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in hypoxia-inducible factor 3-alpha (HIF3a) and similar proteins. HIF3a, also termed HIF-3-alpha, or HIF3-alpha, or endothelial PAS domain-containing protein 1 (EPAS-1), or Basic-helix-loop-helix-PAS protein MOP7, or Class E basic helix-loop-helix protein 17 (bHLHe17), or Member of PAS protein 7, or PAS domain-containing protein 7 (PASD7), or HIF3-alpha-1, or inhibitory PAS domain protein (IPAS), is a bHLH-PAS transcriptional regulator in adaptive response to low oxygen tension. It plays a role in the regulation of hypoxia-inducible gene expression. 63 matched cddid_all.tbl CDD cd19730 cd19730 381573 bHLH-PAS_spineless_like basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein spineless and similar proteins. Spineless is a bHLH-PAS transcription factor that plays an important role in fly morphogenesis. It is both necessary and sufficient for the formation of the ommatidial mosaic. 64 matched cddid_all.tbl CDD cd19731 cd19731 381574 bHLH-PAS_NPAS1_PASD5 basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 1 (NPAS1) and similar proteins. NPAS1, also termed neuronal PAS1, or Basic-helix-loop-helix-PAS protein MOP5, or Class E basic helix-loop-helix protein 11 (bHLHe11), or member of PAS protein 5, or PAS domain-containing protein 5 (PASD5), is a bHLH-PAS transcriptional repressor expressed in the central nervous system and involved in neuronal differentiation. It is active during late embryogenesis and postnatal development. 74 matched cddid_all.tbl CDD cd19732 cd19732 381575 bHLH-PAS_NPAS3_PASD6 basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 3 (NPAS3) and similar proteins. NPAS3, also termed neuronal PAS3, or Basic-helix-loop-helix-PAS protein MOP6, or Class E basic helix-loop-helix protein 12 (bHLHe12), or member of PAS protein 6, or PAS domain-containing protein 6 (PASD6), is a bHLH-PAS brain-enriched transcription factor that is involved in central nervous system development and neurogenesis. It is a replicated genetic risk factor for psychiatric disorders. Human chromosomal rearrangements that affect NPAS3 normal expression are associated with schizophrenia and mental retardation. 78 matched cddid_all.tbl CDD cd19733 cd19733 381576 bHLH-PAS_trachealess_like basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein trachealess and similar proteins. Protein trachealess is a bHLH-PAS transcription factor that acts as an inducer of tracheal cell fates in Drosophila. It is necessary for the development of the salivary gland duct and the posterior spiracles. 79 matched cddid_all.tbl CDD cd19734 cd19734 381577 bHLH-PAS_CLOCK basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Circadian locomotor output cycles protein kaput (CLOCK) and similar proteins. CLOCK, also termed Class E basic helix-loop-helix protein 8 (bHLHe8), is a bHLH-PAS transcriptional activator which forms a core component of the circadian clock. It forms heterodimers with another bHLH-PAS protein, Brain-Muscle-Arnt-Like (also known as BMAL or ARNT3 or mop3), which regulates circadian rhythm. BMAL1-CLOCK heterodimer complex activates transcription from E-box (CANNTG) elements found in the promoter of circadian responsive genes. 61 matched cddid_all.tbl CDD cd19735 cd19735 381578 bHLH-PAS_dCLOCK basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster Circadian locomotor output cycles protein kaput (dCLOCK) and similar proteins. dCLOCK, also termed dPAS1, is a bHLH-PAS Circadian regulator that acts as a transcription factor and generates a rhythmic output with a period of about 24 hours. 80 matched cddid_all.tbl CDD cd19736 cd19736 381579 bHLH-PAS_PASD1 basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in circadian clock protein PASD1. PASD1, also termed PAS domain-containing protein 1, is evolutionarily related to Circadian locomotor output cycles protein kaput (CLOCK)and functions as a suppressor of the biological clock that drives the daily circadian rhythms of cells throughout the body. Mammalian PASD1 doesn't harbor the bHLH-PAS domain and is not included in this family. 70 matched cddid_all.tbl CDD cd19737 cd19737 381580 bHLH-PAS_NPAS2_PASD4 basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in neuronal PAS domain-containing protein 2 (NPAS2) and similar proteins. NPAS2, also termed neuronal PAS2, or basic-helix-loop-helix-PAS protein MOP4, or Class E basic helix-loop-helix protein 9 (bHLHe9), or member of PAS protein 4, or PAS domain-containing protein 4 (PASD4), is a bHLH-PAS transcriptional activator which forms a core component of the circadian clock. 77 matched cddid_all.tbl CDD cd19738 cd19738 381581 bHLH-PAS_SIM1 basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded homolog 1 (SIM1) and similar proteins. SIM1, also termed Class E basic helix-loop-helix protein 14 (bHLHe14), is a bHLH-PAS transcription factor that may have pleiotropic effects during embryogenesis and in the adult. 71 matched cddid_all.tbl CDD cd19739 cd19739 381582 bHLH-PAS_SIM2 basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in single-minded homolog 2 (SIM2) and similar proteins. SIM2, also termed Class E basic helix-loop-helix protein 15 (bHLHe15), is a bHLH-PAS transcription factor that may be a master gene of central nervous system (CNS) development in cooperation with ARNT. It may have pleiotropic effects in the tissues expressed during development. 74 matched cddid_all.tbl CDD cd19740 cd19740 381583 bHLH-PAS_dSIM_like basic helix-loop-helix-Per-ARNT-Sim (bHLH-PAS) domain found in Drosophila melanogaster protein single-minded (SIM) and similar proteins. SIM is a nuclear bHLH-PAS transcription factor that functions as a master developmental regulator controlling midline development of the ventral nerve cord in Drosophila. 62 matched cddid_all.tbl CDD cd19741 cd19741 381584 bHLH-O_ESMB_like basic helix-loop-helix-orange (bHLH-O) domain found in Drosophila melanogaster enhancer of split mbeta protein (ESMB) and similar proteins. ESMB, also termed E(spl)mbeta, or HLH-mbeta, or split locus enhancer protein mA, is a bHLH-O transcriptional repressor of genes that require a bHLH protein for their transcription. It is involved in the neural-epidermal lineage decision during early neurogenesis. The family also includes Enhancer of split m7 protein (also known as E(spl)m7), which acts as a transcriptional repressor that participates in the control of cell fate choice by uncommitted neuroectodermal cells in the embryo. 69 matched cddid_all.tbl CDD cd19742 cd19742 381585 bHLH_TS_ASCL1_Mash1 basic helix-loop-helix (bHLH) domain found in achaete-scute-like protein 1 (ASCL-1) and similar proteins. ASCL-1, also termed Class A basic helix-loop-helix protein 46 (bHLHa46), or achaete-scute homolog 1 (ASH-1), or mammalian achaete scute homolog 1 (Mash1), is a neural-specific bHLH transcription factor that is expressed in subsets of neural progenitors in both the central and peripheral nervous system. It plays a key role in neuronal differentiation and specification in the nervous system. 71 matched cddid_all.tbl CDD cd19743 cd19743 381586 bHLH_TS_ASCL2_Mash2 basic helix-loop-helix (bHLH) domain found in achaete-scute-like protein 2 (ASCL-2) and similar proteins. ASCL-2, also termed achaete-scute homolog 2 (ASH-2), or Class A basic helix-loop-helix protein 45 (bHLHa45), or mammalian achaete scute homolog 2 (Mash2), is a bHLH transcription factor that is involved in Schwann cell differentiation and control of proliferation in adult peripheral nerves. 64 matched cddid_all.tbl CDD cd19744 cd19744 381587 bHLH_TS_dAS-C_like basic helix-loop-helix (bHLH) domain found in Drosophila melanogaster achaete-scute complex (AS-C) proteins and similar proteins. Drosophila melanogaster AS-C proteins includes lethal of scute (also known as achaete-scute complex protein T3 or AST3), scute (also known as achaete-scute complex protein T4 or AST4), achaete (also known as achaete-scute complex protein T5 or AST5), and asense (also known as achaete-scute complex protein T8 or AST8). They are involved in the determination of the neuronal precursors in the peripheral nervous system and the central nervous system, as well as in sex determination and dosage compensation. 67 matched cddid_all.tbl CDD cd19745 cd19745 381588 bHLH_TS_ASCL3 basic helix-loop-helix (bHLH) domain found in achaete-scute-like protein 3 (ASCL-3) and similar proteins. ASCL-3, also termed Class A basic helix-loop-helix protein 42 (bHLHa42), or bHLH transcriptional regulator Sgn-1, or achaete-scute homolog 3 (ASH-3), is a bHLH transcription factor specifically localized in the duct cells of the salivary glands. It may act as transcriptional repressor that inhibits myogenesis. 59 matched cddid_all.tbl CDD cd19746 cd19746 381589 bHLH_TS_ASCL4 basic helix-loop-helix (bHLH) domain found in achaete-scute-like protein 4 (ASCL-4) and similar proteins. ASCL-4, also termed Class A basic helix-loop-helix protein 44 (bHLHa44), or achaete-scute homolog 4 (ASH-4), or Hash4, is a bHLH transcriptional regulator that may be involved in skin development. 64 matched cddid_all.tbl CDD cd19747 cd19747 381590 bHLH_TS_ASCL5 basic helix-loop-helix (bHLH) domain found in achaete-scute-like protein 5 (ASCL-5) and similar proteins. ASCL-5, also termed Class A basic helix-loop-helix protein 47 (bHLHa47), or achaete-scute homolog 5 (ASH-5), is an uncharacterized bHLH transcription factor that belongs to AS-C (achaete, scute, lethal of scute, and asense) family. 61 matched cddid_all.tbl CDD cd19748 cd19748 381591 bHLH-O_HEY1 basic helix-loop-helix-orange (bHLH-O) domain found in hairy/enhancer-of-split related with YRPW motif protein 1 (HEY1) and similar proteins. HEY1, also termed cardiovascular helix-loop-helix factor 2 (CHF-2), or Class B basic helix-loop-helix protein 31 (bHLHb31), or HES-related repressor protein 1, or hairy and enhancer of split-related protein 1 (HESR-1), or hairy-related transcription factor 1 (HRT-1), is a bHLH-O transcriptional repressor that acts as an essential downstream effector of the Notch signaling pathway and may play a fundamental role in vascular development. HEY1 also participates several cancer-related pathways. It acts as a positive regulator of the tumor suppressor p53. 71 matched cddid_all.tbl CDD cd19749 cd19749 381592 bHLH-O_DEC1 basic helix-loop-helix-orange (bHLH-O) domain found in differentially expressed in chondrocytes protein 1 (DEC1) and similar proteins. DEC1, also termed Class E basic helix-loop-helix protein 40 (bHLHe40), or Class B basic helix-loop-helix protein 2 (bHLHb2), or enhancer-of-split and hairy-related protein 2 (SHARP-2), or stimulated by retinoic acid gene 13 protein (STRA13), is a bHLH-O transcriptional repressor involved in the regulation of the circadian rhythm by negatively regulating the activity of the clock genes and clock-controlled genes. 90 matched cddid_all.tbl CDD cd19750 cd19750 381593 bHLH-O_DEC2 basic helix-loop-helix-orange (bHLH-O) domain found in differentially expressed in chondrocytes protein 2 (DEC2) and similar proteins. DEC2, also termed Class E basic helix-loop-helix protein 41 (bHLHe41), or Class B basic helix-loop-helix protein 3 (bHLHb3), or enhancer-of-split and hairy-related protein 1 (SHARP-1), is a bHLH-O transcriptional repressor involved in the regulation of the circadian rhythm by negatively regulating the activity of the clock genes and clock-controlled genes. 92 matched cddid_all.tbl CDD cd19751 cd19751 410992 5TM_YidC_Oxa1_Alb3 Five transmembrane core domain of YidC/Oxa1/Alb3 protein family of insertases. The YidC/Oxa1/Alb3 protein family of insertases facilitate the insertion, folding and assembly of proteins of the inner membranes of bacteria and mitochondria, and the thylakoid membrane of plastids. Members include bacterial YidC, mitochondrial Cox18 and Oxa1, and chloroplastic Alb3 and Alb4. Membrane protein insertase YidC, also called foldase YidC or membrane integrase YidC, facilitates proper folding, insertion, and assembly of inner membrane proteins and complexes. Oxa1 and Cox18/Oxa2 mediate the insertion of both mitochondrion-encoded precursors and nuclear-encoded proteins from the matrix into the mitochondrial inner membrane. Alb3 and Alb3-like proteins, including Alb4, are required for the post-translational insertion of the light-harvesting chlorophyll-binding proteins (LHCPs) into the chloroplast thylakoid membrane. YidC/Oxa1/Alb3 family insertases contain a core domain of five transmembrane (5TM) segments that is essential to insertase function. 189 matched cddid_all.tbl CDD cd19752 cd19752 381391 AKR_unchar uncharacterized aldo-keto reductase (AKR) superfamily protein. This family includes a group of uncharacterized AKR superfamily proteins. Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance in both health and industrial applications. 291 matched cddid_all.tbl CDD cd19753 cd19753 381293 Mb-like_oxidoreductase Globin domain of uncharacterized oxidoreductases containing a FAD/NADH binding domain. This subfamily is composed of uncharacterized proteins containing an N-terminal myoglobin-like (M family globin) domain and a C-terminal oxygenase reductase FAD/NADH binding domain belonging to the ferredoxin reductase (FNR) family and is usually part of multi-component bacterial oxygenases which oxidize hydrocarbons using oxygen as the oxidant. The domain architecture of this subfamily is similar to flavohemoglobins, which function primarily as nitric oxide dioxygenases (NODs, EC 1.14.12.17), converting NO and O2 to inert NO3- (nitrate). They protect from nitrosative stress (the broad range of cellular toxicities caused by NO), and modulate NO signaling pathways. NO scavenging by flavoHb attenuates the expression of the nitrosative stress response, affects the swarming behavior of Escherichia coli, and maintains squid-Vibrio fischeri and Medicago truncatula-Sinorhizobium meliloti symbioses. 121 matched cddid_all.tbl CDD cd19754 cd19754 381294 FHb_fungal-globin Globin domain of fungal flavohemoglobin. FlavoHbs function primarily as nitric oxide dioxygenases (NODs, EC 1.14.12.17), converting NO and O2 to inert NO3- (nitrate). They have an N-terminal globin domain and a C-terminal ferredoxin reductase-like NAD- and FAD-binding domain, and use the reducing power of cellular NAD(P)H to drive regeneration of the ferrous heme. They protect from nitrosative stress (the broad range of cellular toxicities caused by NO), and modulate NO signaling pathways. NO scavenging by flavoHb attenuates the expression of the nitrosative stress response, affects the swarming behavior of Escherichia coli, and maintains squid-Vibrio fischeri and Medicago truncatula-Sinorhizobium meliloti symbioses. FlavoHb expression affects Aspergillus nidulans sexual development and mycotoxin production, and Dictyostelium discoideum development. 141 matched cddid_all.tbl CDD cd19755 cd19755 381295 TrHb2_AtGlb3-like_O nonsymbiotic haemoglobin Ahb3 (GLB3) and similar truncated hemoglobins, group 2 (O). The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. TrHbs are classified into three main groups based on their structural properties and named after Mycobacterium sp. genes glbN, glbO, and glbP: TrHb1s (N), TrHb2s (O) and TrHb3s (P). This subfamily includes the dimeric Arabidopsis thaliana TrHb2 AtGLB3. GLB3 is likely to have a function distinct from other plant globins: it exhibits a low O2 affinity, an unusual concentration-independent binding of O2 and CO, and does not respond to any of the treatments that induce plant 3-on-3 globins. 119 matched cddid_all.tbl CDD cd19756 cd19756 380814 Bbox2 B-box-type 2 zinc finger (Bbox2). The B-box-type zinc finger is a short zinc binding domain of around 40 amino acid residues in length. It has been found in transcription factors, ribonucleoproteins and proto-oncoproteins, such as in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). The B-box-type zinc finger often presents in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction. Based on different consensus sequence and the spacing of the 7-8 zinc-binding residues, B-box-type zinc fingers can be divided into two groups, type 1 (Bbox1: C6H2) and type 2 (Bbox2: CHC3H2). The family corresponds to type 2 B-box (Bbox2). 39 matched cddid_all.tbl CDD cd19757 cd19757 380815 Bbox1 B-box-type 1 zinc finger (Bbox1). The B-box-type zinc finger is a short zinc binding domain of around 40 amino acid residues in length. It has been found in transcription factors, ribonucleoproteins and proto-oncoproteins, such as in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). The B-box-type zinc finger often presents in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain, in functionally unrelated proteins, most likely mediating protein-protein interactions. Based on different consensus sequences and the spacing of the 7-8 zinc-binding residues, the B-box-type zinc fingers can be divided into two groups, type 1 (Bbox1: C6H2) and type 2 (Bbox2: CHC3H2). This family corresponds to the type 1 B-box (Bbox1). 44 matched cddid_all.tbl CDD cd19758 cd19758 380816 Bbox2_MID B-box-type 2 zinc finger found in midline (MID) family. The MID family includes MID1 and MID2. MID1, also known as midin, midline 1 RING finger protein, putative transcription factor XPRF, RING finger protein 59 (RNF59), or tripartite motif-containing protein 18 (TRIM18), is a microtubule-associated E3 ubiquitin-protein ligase implicated in epithelial-mesenchymal differentiation, cell migration and adhesion, and programmed cell death along specific regions of the ventral midline during embryogenesis. MID2, also known as midin-2, midline defect 2, RING finger protein 60 (RNF60), or tripartite motif-containing protein 1 (TRIM1), is highly related to MID1. It associates with the microtubule network and may at least partially compensate for the loss of MID1. Both MID1 and MID2 interacts with Alpha 4, which is a regulatory subunit of PP2-type phosphatases, such as PP2A, and an integral component of the rapamycin-sensitive signaling pathway. They also play a central role in the regulation of granule exocytosis, and functional redundancy exists between MID1 and MID2 in cytotoxic lymphocytes (CTL). Both MID1 and MID2 belong to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 40 matched cddid_all.tbl CDD cd19759 cd19759 380817 Bbox2_TRIM2-like B-box-type 2 zinc finger found in tripartite motif-containing protein TRIM2, TRIM3, and similar proteins. TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It also plays an important role in the central nervous system (CNS). In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. Both TRIM2 and TRIM3 belong to the C-VII subclass of TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 42 matched cddid_all.tbl CDD cd19760 cd19760 380818 Bbox2_TRIM4-like B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM4, TRIM17, TRIM41, TRIM52 and similar proteins. This family includes a group of tripartite motif-containing proteins, including TRIM4, TRIM17, TRIM41 and TRIM52. TRIM4, also known as RING finger protein 87 (RNF87), is a cytoplasmic E3 ubiquitin-protein ligase that recently evolved and is present only in higher mammals. It transiently interacts with mitochondria, induces mitochondrial aggregation and sensitizes the cells to hydrogen peroxide (H2O2) induced death. Its interaction with peroxiredoxin 1 (PRX1) is critical for the regulation of H2O2 induced cell death. Moreover, TRIM4 functions as a positive regulator of RIG-I-mediated type I interferon induction. It regulates the K63-linked ubiquitination of RIG-1 and assembly of antiviral signaling complex at mitochondria. TRIM17, also known as RING finger protein 16 (RNF16) or testis RING finger protein (Terf), is a crucial E3 ubiquitin ligase that is necessary and sufficient for neuronal apoptosis and contributes to Mcl-1 ubiquitination in cerebellar granule neurons (CGNs). It interacts in a SUMO-dependent manner with nuclear factor of activated T cell NFATc3 transcription factor, and thus inhibits the activity of NFATc3 by preventing its nuclear localization. In contrast, it binds to and inhibits NFATc4 transcription factor in a SUMO-independent manner. Moreover, TRIM17 stimulates degradation of kinetochore protein ZW10 interacting protein (ZWINT), a known component of the kinetochore complex required for mitotic spindle checkpoint, and negatively regulates cell proliferation. TRIM41, also known as RING finger-interacting protein with C kinase (RINCK), is an E3 ubiquitin-protein ligase that promotes the ubiquitination of protein kinase C (PKC) isozymes in cells. It specifically recognizes the C1 domain of PKC isozymes. It controls the amplitude of PKC signaling by controlling the amount of PKC in the cell. TRIM52, also known as RING finger protein 102 (RNF102), is encoded by a novel, noncanonical antiviral TRIM52 gene in primate genomes with unique specificity determined by the rapidly evolving RING domain. TRIM4, TRIM17 and TRIM41 belong to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. In contrast, TRIM52 lacks the putative viral recognition SPRY/B30.2 domain, and thus has been classified to the C-V subclass of TRIM family that contains only RBCC domains. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 39 matched cddid_all.tbl CDD cd19761 cd19761 380819 Bbox2_TRIM5-like B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM5, TRIM6, TRIM22, TRIM34, TRIM38 and similar proteins. The family includes TRIM5, TRIM6, TRIM22, TRIM34, and TRIM38, all of which belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TRIM5, also termed RING finger protein 88 (RNF88), is a capsid-specific restriction factor that prevents infection from non-host-adapted retroviruses in a species-specific manner by binding to and destabilizing the retroviral capsid lattice before reverse transcription is completed. Its retroviral restriction activity correlates with the ability to activate TAK1-dependent innate immune signaling. TRIM5 also acts as a pattern recognition receptor that activates innate immune signaling in response to the retroviral capsid lattice. Moreover, TRIM5 plays a role in regulating autophagy through activation of autophagy regulator BECN1 by causing its dissociation from its inhibitors BCL2 and TAB2. It also plays a role in autophagy by acting as a selective autophagy receptor which recognizes and targets HIV-1 capsid protein p24 for autophagic destruction. TRIM6, also termed RING finger protein 89 (RNF89), is an E3-ubiquitin ligase that cooperates with the E2-ubiquitin conjugase UbE2K to catalyze the synthesis of unanchored K48-linked polyubiquitin chains, and further stimulates the interferon-I kappa B kinase epsilon (IKKepsilon) kinase-mediated antiviral response. It also regulates the transcriptional activity of Myc during the maintenance of embryonic stem (ES) cell pluripotency, and may act as a novel regulator for Myc-mediated transcription in ES cells. TRIM22, also termed 50 kDa-stimulated trans-acting factor (Staf-50), or RING finger protein 94 (RNF94), is an E3 ubiquitin-protein ligase that plays an integral role in the host innate immune response to viruses. It has been shown to inhibit the replication of a number of viruses, including HIV-1, hepatitis B, and influenza A. TRIM22 acts as a suppressor of basal HIV-1 long terminal repeat (LTR)-driven transcription by preventing transcription factor specificity protein 1 (Sp1) binding to the HIV-1 promoter. It also controls FoxO4 activity and cell survival by directing Toll-like receptor 3 (TLR3)-stimulated cells toward type I interferon (IFN) type I gene induction or apoptosis. Moreover, TRIM22 can activate the noncanonical nuclear factor-kappaB (NF-kappaB) pathway by activating I kappa B kinase alpha (IKKalpha). It also regulates nucleotide binding oligomerization domain containing 2 (NOD2)-dependent activation of interferon-beta signaling and nuclear factor-kappaB. TRIM34, also termed interferon-responsive finger protein 1, or RING finger protein 21 (RNF21), may function as an antiviral protein that contributes to the defense against retroviral infections. TRIM38, also known as RING finger protein 15 (RNF15) or zinc finger protein RoRet, is an E3 ubiquitin-protein ligase that promotes K63- and K48-linked ubiquitination of cellular proteins and also catalyzes self-ubiquitination. It negatively regulates tumor necrosis factor alpha (TNF-alpha) and interleukin-1beta-triggered nuclear factor-kappaB (NF-kappaB) activation by mediating lysosomal-dependent degradation of transforming growth factor beta (TGFbeta)-activated kinase 1 (TAK1)-binding protein (TAB)2/3, two critical components of the TAK1 kinase complex. It also inhibits TLR3/4-mediated activation of NF-kappaB and interferon regulatory factor 3 (IRF3) by mediating ubiquitin-proteasomal degradation of TNF receptor-associated factor 6 (Traf6) and NAK-associated protein 1 (Nap1), respectively. Moreover, TRIM38 negatively regulates TLR3-mediated interferon beta (IFN-beta) signaling by targeting ubiquitin-proteasomal degradation of TIR domain-containing adaptor inducing IFN-beta (TRIF). It functions as a valid target for autoantibodies in primary Sjogren's Syndrome. 40 matched cddid_all.tbl CDD cd19762 cd19762 380820 Bbox2_TRIM7-like B-box-type 2 zinc finger found in tripartite motif-containing proteins TRIM7, TRIM27 and similar proteins. The family includes TRIM7 and TRIM27, both of which belong to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TRIM7, also known as glycogenin-interacting protein (GNIP) or RING finger protein 90 (RNF90), is an E3 ubiquitin-protein ligase that mediates c-Jun/AP-1 activation by Ras signalling. Its phosphorylation and activation by MSK1 in response to direct activation by the Ras-Raf-MEK-ERK pathway can stimulate TRIM7 E3 ubiquitin ligase activity in mediating Lys63-linked ubiquitination of the AP-1 coactivator RACO-1, leading to RACO-1 protein stabilization. Moreover, TRIM7 binds and activates glycogenin, the self-glucosylating initiator of glycogen biosynthesis. TRIM27, also termed RING finger protein 76 (RNF76), or RET finger protein (RFP), or zinc finger protein RFP, is a nuclear E3 ubiquitin-protein ligase that is highly expressed in testis and in various tumor cell lines. Expression of TRIM27 is associated with prognosis of colon and endometrial cancers. TRIM27 was first identified as a fusion partner of the RET receptor tyrosine kinase. It functions as a transcriptional repressor and associates with several proteins involved in transcriptional activity, such as enhancer of polycomb 1 (Epc1), a member of the Polycomb group proteins, and Mi-2beta, a main component of the nucleosome remodeling and deacetylase (NuRD) complex, and the cell cycle regulator retinoblastoma protein (RB1). It also interacts with HDAC1, leading to downregulation of thioredoxin binding protein 2 (TBP-2), which inhibits the function of thioredoxin. Moreover, TRIM27 mediates Pax7-induced ubiquitination of MyoD in skeletal muscle atrophy. It also inhibits muscle differentiation by modulating serum response factor (SRF) and Epc1. Furthermore, TRIM27 promotes non-canonical polyubiquitination of PTEN, a lipid phosphatase that catalyzes PtdIns(3,4,5)P3 (PIP3) to PtdIns(4,5)P2 (PIP2). It is an IKKepsilon-interacting protein that regulates IkappaB kinase (IKK) function and negatively regulates signaling involved in the antiviral response and inflammation. In addition, TRIM27 forms a protein complex with MBD4 or MBD2 or MBD3, and thus plays an important role in the enhancement of transcriptional repression through MBD proteins in tumorigenesis, spermatogenesis, and embryogenesis. It is also a component of an estrogen receptor 1 (ESR1) regulatory complex, and is involved in estrogen receptor-mediated transcription in MCF-7 cells. Meanwhile, TRIM27 interacts with the hinge region of chromosome 3 protein (SMC3), a component of the multimeric cohesin complex that holds sister chromatids together and prevents their premature separation during mitosis. 44 matched cddid_all.tbl CDD cd19763 cd19763 380821 Bbox2_TRIM8_C-V B-box-type 2 zinc finger found in tripartite motif-containing protein 8 (TRIM8) and similar proteins. TRIM8, also known as glioblastoma-expressed RING finger protein (GERP) or RING finger protein 27 (RNF27), is a probable E3 ubiquitin-protein ligase that may promote proteasomal degradation of suppressor of cytokine signaling 1 (SOCS1) and further regulate interferon-gamma signaling. It functions as a new p53 modulator that stabilizes p53, impairing its association with MDM2 and inducing the reduction of cell proliferation. TRIM8 deficit dramatically impairs p53 stabilization and activation in response to chemotherapeutic drugs. TRIM8 also modulates tumor necrosis factor-alpha (TNFalpha) and interleukin-1beta (IL-1beta)-triggered nuclear factor-kappaB (NF-kappa B) activation by targeting transforming growth factor beta (TGFbeta) activated kinase 1 (TAK1) for K63-linked polyubiquitination. Moreover, TRIM8 modulates translocation of phosphorylated STAT3 into the nucleus through interaction with Hsp90beta and consequently regulates transcription of Nanog in embryonic stem cells. It also interacts with protein inhibitor of activated STAT3 (PIAS3), which inhibits IL-6-dependent activation of STAT3. TRIM8 belongs to the C-V subclass of nuclear TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil domain, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The coiled coil domain is required for homodimerization and the region immediately C-terminal to the RING motif is sufficient to mediate the interaction with SOCS1. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 41 matched cddid_all.tbl CDD cd19764 cd19764 380822 Bbox2_TRIM9-like B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM9, TRIM67 and similar proteins. This family includes a group of tripartite motif-containing proteins including TRIM9 and TRIM67, both of which belong to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, consisting of three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TRIM9 (the human ortholog of rat Spring), also known as RING finger protein 91 (RNF91), is a brain-specific E3 ubiquitin-protein ligase collaborating with an E2 ubiquitin conjugating enzyme UBCH5b. It plays an important role in the regulation of neuronal functions and participates in neurodegenerative disorders through its ligase activity. TRIM67, also termed TRIM9-like protein (TNL), is a protein selectively expressed in the cerebellum. It interacts with PRG-1, an important molecule in the control of hippocampal excitability dependent on presynaptic LPA2 receptor signaling, and 80K-H (also known as glucosidase II beta), a protein kinase C substrate. It negatively regulates Ras signaling in cell proliferation via degradation of 80K-H, leading to neural differentiation including neuritogenesis. 39 matched cddid_all.tbl CDD cd19765 cd19765 380823 Bbox2_TRIM10-like B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM10, TRIM15, TRIM26, TRIM31 and similar proteins. This family includes TRIM10, TRIM15, TRIM26 and TRIM31. TRIM10, also known as B30-RING finger protein (RFB30), RING finger protein 9 (RNF9), or hematopoietic RING finger 1 (HERF1), is a novel hematopoiesis-specific RING finger protein required for terminal differentiation of erythroid cells. TRIM15, also termed RING finger protein 93 (RNF93), or zinc finger protein 178 (ZNF178), or zinc finger protein B7 (ZNFB7), is a focal adhesion protein that regulates focal adhesion disassembly. It localizes to focal contacts in a myosin-II-independent manner by an interaction between its coiled-coil domain and the LD2 motif of paxillin. TRIM15 can also associate with coronin 1B, cortactin, filamin binding LIM protein1, and vasodilator-stimulated phosphoprotein, which are involved in actin cytoskeleton dynamics. As an additional component of the integrin adhesome, it regulates focal adhesion turnover and cell migration. TRIM26, also known as acid finger protein (AFP), RING finger protein 95 (RNF95), or zinc finger protein 173 (ZNF173), is an E3 ubiquitin-protein ligase that negatively regulates interferon-beta production and antiviral response through polyubiquitination and degradation of nuclear transcription factor IRF3. It functions as an important regulator for RNA virus-triggered innate immune response by bridging TBK1 to NEMO (NF-kappaB essential modulator, also known as IKKgamma) and mediating TBK1 activation. It also acts as a novel tumor suppressor of hepatocellular carcinoma by regulating cancer cell proliferation, colony forming ability, migration, and invasion. TRIM31 is an E3 ubiquitin-protein ligase that primarily localizes to the cytoplasm, but is also associated with the mitochondria. It can negatively regulate cell proliferation and may be a potential biomarker of gastric cancer as it is overexpressed from the early stage of gastric carcinogenesis. TRIM31 is downregulated in non-small cell lung cancer and serves as a potential tumor suppressor. It interacts with p52 (Shc) and inhibits Src-induced anchorage-independent growth. TRIM10, TRIM15 and TRIM26 belong to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. TRIM31 belongs to the C-V subclass of TRIM family of proteins. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 39 matched cddid_all.tbl CDD cd19766 cd19766 380824 Bbox2_TRIM11_C-IV B-box-type 2 zinc finger found in tripartite motif-containing protein 11 (TRIM11) and similar proteins. TRIM11, also known as protein BIA1, or RING finger protein 92 (RNF92), is an E3 ubiquitin-protein ligase involved in the development of the central nervous system. It is overexpressed in high-grade gliomas and promotes proliferation, invasion, migration and glial tumor growth. TRIM11 acts as a potential therapeutic target for congenital central hypoventilation syndrome (CCHS) through mediating the degradation of CCHS-associated polyalanine-expanded Phox2b. Trim11 modulates the function of neurogenic transcription factor Pax6 through the ubiquitin-proteosome system, and thus plays an essential role for Pax6-dependent neurogenesis. It also binds to and destabilizes a key component of the activator-mediated cofactor complex (ARC105), humanin, a neuroprotective peptide against Alzheimer's disease-relevant insults, and further regulates ARC105 function in transforming growth factor beta (TGFbeta) signaling. Moreover, TRIM11 negatively regulates retinoic acid-inducible gene-I (RIG-I)-mediated interferon-beta (IFNbeta) production and antiviral activity by targeting TANK-binding kinase-1 (TBK1). It may contribute to the endogenous restriction of retroviruses in cells. It enhances N-tropic murine leukemia virus (N-MLV) entry by interfering with Ref1 restriction. It also suppresses the early steps of human immunodeficiency virus HIV-1 transduction, resulting in decreased reverse transcripts. TRIM11 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 44 matched cddid_all.tbl CDD cd19767 cd19767 380825 Bbox2_TRIM13_C-XI B-box-type 2 zinc finger found in tripartite motif-containing protein 13 (TRIM13) and similar proteins. TRIM13, also known as B-cell chronic lymphocytic leukemia tumor suppressor Leu5, leukemia-associated protein 5, putative tumor suppressor RFP2, RING finger protein 77 (RNF77), or Ret finger protein 2, is an endoplasmic reticulum (ER) membrane-anchored E3 ubiquitin-protein ligase that interacts with proteins localized to the ER, including valosin-containing protein (VCP), a protein indispensable for ER-associated degradation (ERAD). It also targets the known ER proteolytic substrate CD3-delta, but not the N-end rule substrate Ub-R-YFP (yellow fluorescent protein) for its degradation. Moreover, TRIM13 regulates ubiquitination and degradation of NEMO to suppress tumor necrosis factor (TNF) induced nuclear factor-kappaB (NF- kappa B) activation. It is also involved in NF-kappaB p65 activation and nuclear factor of activated T-cells (NFAT)-dependent activation of c-Rel upon T-cell receptor engagement. Furthermore, TRIM13 negatively regulates lanoma differentiation-associated gene 5 (MDA5)-mediated type I interferon production. It also regulates caspase-8 ubiquitination, translocation to autophagosomes, and activation during ER stress induced cell death. Meanwhile, TRIM13 enhances ionizing radiation-induced apoptosis by increasing p53 stability and decreasing AKT kinase activity through MDM2 and AKT degradation. TRIM13 belongs to the C-XI subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region. In addition, TRIM13 contains a C-terminal transmembrane domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 42 matched cddid_all.tbl CDD cd19768 cd19768 380826 Bbox2_TRIM14 B-box-type 2 zinc finger found in tripartite motif-containing protein 14 (TRIM14) and similar proteins. TRIM14 is a mitochondrial adaptor that facilitates innate immune signaling. It also plays a critical role in tumor development. TRIM14 belongs to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. It contains a Bbox2 zinc finger as well as a C-terminal SPRY/B30.2 domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 44 matched cddid_all.tbl CDD cd19769 cd19769 380827 Bbox2_TRIM16-like B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM16, TRIM29, TRIM47 and similar proteins. This family includes a group of tripartite motif-containing proteins, such as TRIM16, TRIM29 and TRIM47. TRIM16, also termed estrogen-responsive B box protein (EBBP), is a regulator that may play a role in the regulation of keratinocyte differentiation. It may also act as a tumor suppressor through affecting cell proliferation and migration or tumorigenicity in carcinogenesis. TRIM29, also termed ataxia telangiectasia group D-associated protein (ATDC), plays a crucial role in the regulation of macrophage activation in response to viral or bacterial infections within the respiratory tract. TRIM47, also known as gene overexpressed in astrocytoma protein (GOA) or RING finger protein 100 (RNF100), plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. TRIM16 and TRIM29 belong to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. TRIM47 belongs to the C-IV subclass of TRIM family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 46 matched cddid_all.tbl CDD cd19770 cd19770 380828 Bbox2_TRIM19_C-V B-box-type 2 zinc finger found in tripartite motif-containing protein 19, also called promyelocytic leukemia protein (PML), and similar proteins. Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cell processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 50 matched cddid_all.tbl CDD cd19771 cd19771 380829 Bbox2_TRIM20 B-box-type 2 zinc finger found in tripartite motif-containing protein TRIM20 and similar proteins. TRIM20, also termed Pyrin, or Marenostrin (MEFV), is involved in the regulation of innate immunity and the inflammatory response in response to IFNG/IFN-gamma. TRIM20 belongs to unclassified TRIM family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. It contains a pyrin domain, a Bbox2 zinc finger, and a C-terminal SPRY/B30.2 domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 39 matched cddid_all.tbl CDD cd19772 cd19772 380830 Bbox2_TRIM21_C-IV B-box-type 2 zinc finger found in tripartite motif-containing protein 21 (TRIM21) and similar proteins. TRIM21, also known as 52 kDa Ro protein, 52 kDa ribonucleoprotein autoantigen Ro/SS-A, Ro(SS-A), RING finger protein 81 (RNF81), or Sjoegren's syndrome type A antigen (SS-A), is a ubiquitously expressed E3 ubiquitin-protein ligase and a high affinity antibody receptor uniquely expressed in the cytosol of mammalian cells. As a cytosolic Fc receptor, TRIM21 binds the Fc of virus-associated antibodies and targets the complex in the cytosol for proteasomal degradation in a process known as antibody-dependent intracellular neutralization (ADIN), and provides an intracellular immune response to protect host defense against pathogen infection. It shows remarkably broad isotype specificity as it does not only bind IgG, but also IgM and IgA. Moreover, TRIM21 promotes the cytosolic DNA sensor cGAS and the cytosolic RNA sensor RIG-I sensing of viral genomes during infection by antibody-opsonized virus. It stimulates inflammatory signaling and activates innate transcription factors, such as nuclear factor-kappaB (NF-kappaB). TRIM21 also plays an essential role in p62-regulated redox homeostasis, suggesting a viable target for treating pathological conditions resulting from oxidative damage. Furthermore, TRIM21 may have implications for various autoimmune diseases associated uncontrolled antiviral signaling through the regulation of Nmi-IFI35 complex-mediated inhibition of innate antiviral response. TRIM21 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 40 matched cddid_all.tbl CDD cd19773 cd19773 380831 Bbox2_TRIM23_C-IX_rpt1 first B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and similar proteins. TRIM23, also known as ADP-ribosylation factor domain-containing protein 1, GTP-binding protein ARD-1, or RING finger protein 46 (RNF46), is an E3 ubiquitin-protein ligase belonging to the C-IX subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, two Bbox2, and a coiled coil region, as well as C-terminal ADP ribosylation factor (ARF) domains. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TRIM23 is involved in nuclear factor (NF)-kappaB activation. It mediates atypical lysine 27 (K27)-linked polyubiquitin conjugation to NF-kappaB essential modulator NEMO, also known as IKKgamma, which plays an important role in the NF-kappaB pathway, and this conjugation is essential for TLR3- and RIG-I/MDA5-mediated antiviral innate and inflammatory responses. It also regulates adipocyte differentiation via stabilization of the adipogenic activator peroxisome proliferator-activated receptor gamma (PPARgamma) through atypical ubiquitin conjugation to PPARgamma. Moreover, TRIM23 interacts with and polyubiquitinates yellow fever virus (YFV) NS5 to promote its binding to STAT2 and trigger type I interferon (IFN-I) signaling inhibition. 50 matched cddid_all.tbl CDD cd19774 cd19774 380832 Bbox2_TRIM23_C-IX_rpt2 second B-box-type 2 zinc finger found in tripartite motif-containing protein 23 (TRIM23) and similar proteins. TRIM23, also known as ADP-ribosylation factor domain-containing protein 1, GTP-binding protein ARD-1, or RING finger protein 46 (RNF46), is an E3 ubiquitin-protein ligase belonging to the C-IX subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, two Bbox2, and a coiled coil region, as well as C-terminal ADP ribosylation factor (ARF) domains. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TRIM23 is involved in nuclear factor (NF)-kappaB activation. It mediates atypical lysine 27 (K27)-linked polyubiquitin conjugation to NF-kappaB essential modulator NEMO, also known as IKKgamma, which plays an important role in the NF-kappaB pathway, and this conjugation is essential for TLR3- and RIG-I/MDA5-mediated antiviral innate and inflammatory responses. It also regulates adipocyte differentiation via stabilization of the adipogenic activator peroxisome proliferator-activated receptor gamma (PPARgamma) through atypical ubiquitin conjugation to PPARgamma. Moreover, TRIM23 interacts with and polyubiquitinates yellow fever virus (YFV) NS5 to promote its binding to STAT2 and trigger type I interferon (IFN-I) signaling inhibition. 50 matched cddid_all.tbl CDD cd19775 cd19775 380833 Bbox2_TIF1_C-VI B-box-type 2 zinc finger found in transcription intermediary factor 1 (TIF1) family. This family corresponds to the TIF1 family of transcriptional cofactors including TIF1-alpha (TRIM24), TIF1-beta (TRIM28), and TIF1-gamma (TRIM33), which belong to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha and TIF1beta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. They bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta and gamma. It cannot bind to nuclear receptors (NRs). 43 matched cddid_all.tbl CDD cd19776 cd19776 380834 Bbox2_TRIM25_C-IV B-box-type 2 zinc finger found in tripartite motif-containing protein 25 (TRIM25) and similar proteins. TRIM25, also termed estrogen-responsive finger protein (EFP), or ubiquitin/ISG15-conjugating enzyme TRIM25, or zinc finger protein 147 (ZNF147), or E3 ubiquitin/ISG15 ligase TRIM25, is induced by estrogen and particularly abundant in placenta and uterus. It has been implicated in cell proliferation, protein modification, and the retinoic acid inducible gene I (RIG-I)-mediated antiviral signaling pathway. It functions as an E3-ubiquitin ligase able to transfer ubiquitin and ISG15 to target proteins. It binds to mono-ubiquitinated PCNA and promotes the ISG15 modification (ISGylation) of PCNA, suggesting a crucial role in termination of error-prone translesion DNA synthesis. TRIM25 also enhances p53 and Mdm2 abundance by inhibiting their ubiquitination and degradation in 26S proteasomes. It suppresses p53's transcriptional activity and dampens the response to DNA damage. Upon deubiquitylation by ubiquitin-specific peptidase 15 (USP15), it mediates K63-linked polyubiquitination of RIG-I that is crucial for downstream antiviral interferon signaling. TRIM25 is required for melanoma differentiation-associated gene 5 (MDA5) and mitochondrial antiviral signaling (MAVS, also known as IPS-1, VISA, Cardiff) mediated activation of nuclear factor-kappaB (NF- kappa B) and interferon production. It is an RNA binding protein acting as RNA-specific activator for Lin28a/TuT4-mediated uridylation. TRIM25 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 38 matched cddid_all.tbl CDD cd19777 cd19777 380835 Bbox2_TRIM35_C-IV B-box-type 2 zinc finger found in tripartite motif-containing protein 35 (TRIM35) and similar proteins. TRIM35, also known as hemopoietic lineage switch protein 5 (HLS5), is a putative hepatocellular carcinoma (HCC) suppressor that inhibits phosphorylation of pyruvate kinase isoform M2 (PKM2), which is involved in aerobic glycolysis of cancer cells and further suppresses the Warburg effect and tumorigenicity in HCC. It also negatively regulates Toll-like receptor 7 (TLR7)- and TLR9-mediated type I interferon production by suppressing the stability of interferon regulatory factor 7 (IRF7). Moreover, TRIM35 regulates erythroid differentiation by modulating globin transcription factor 1 (GATA-1) activity. TRIM35 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 44 matched cddid_all.tbl CDD cd19778 cd19778 380836 Bbox2_TRIM36_C-I B-box-type 2 zinc finger found in tripartite motif-containing protein 36 (TRIM36) and similar proteins. TRIM36, human ortholog of mouse Haprin, also known as RING finger protein 98 (RNF98) or zinc-binding protein Rbcc728, is an E3 ubiquitin-protein ligase expressed in the germ plasm. It has been implicated in acrosome reaction, fertilization, and embryogenesis, as well as in carcinogenesis. TRIM36 functions upstream of Wnt/beta-catenin activation, and plays a role in controlling the stability of proteins regulating microtubule polymerization during cortical rotation, and subsequently dorsal axis formation. It is also potentially associated with chromosome segregation through interacting with the kinetochore protein centromere protein-H (CENP-H), and colocalizing with the microtubule protein alpha-tubulin. Its overexpression may cause chromosomal instability and carcinogenesis. It is, thus, a novel regulator affecting cell cycle progression. Moreover, TRIM36 plays a critical role in the arrangement of somites during embryogenesis. TRIM36 belongs to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 45 matched cddid_all.tbl CDD cd19779 cd19779 380837 Bbox2_TRIM37_C-VIII B-box-type 2 zinc finger found in tripartite motif-containing protein 37 (TRIM37) and similar proteins. TRIM37, also known as Mulibrey nanism protein, is a peroxisomal E3 ubiquitin-protein ligase that is involved in the tumorigenesis of several cancer types, including pancreatic ductal adenocarcinoma (PDAC), hepatocellular carcinoma (HCC), breast cancer, and sporadic fibrothecoma. It mono-ubiquitinates histone H2A, a chromatin modification associated with transcriptional repression. Moreover, TRIM37 possesses anti-HIV-1 activity, and interferes with viral DNA synthesis. Mutations in the human TRIM37 gene (also known as MUL) cause Mulibrey (muscle-liver-brain-eye) nanism, a rare growth disorder of prenatal onset characterized by dysmorphic features, pericardial constriction, and hepatomegaly. TRIM37 belongs to the C-VIII subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a MATH (meprin and TRAF-C homology) domain positioned C-terminal to the RBCC domain. Its MATH domain has been shown to interact with the TRAF (TNF-Receptor-Associated Factor) domain of six known TRAFs in vitro. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 40 matched cddid_all.tbl CDD cd19780 cd19780 380838 Bbox2_TRIM39-like B-box-type 2 zinc finger found in tripartite motif-containing proteins TRIM39, TRIM58 and similar proteins. The family includes TRIM39 and TRIM58, both of which belong to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TRIM39, also termed RING finger protein 23 (RNF23), or testis-abundant finger protein, is an E3 ubiquitin-protein ligase that plays a role in controlling DNA damage-induced apoptosis through inhibition of the anaphase promoting complex (APC/C), a multiprotein ubiquitin ligase that controls multiple cell cycle regulators, including cyclins, geminin, and others. TRIM39 also functions as a regulator of several key processes in the proliferative cycle. It directly regulates p53 stability and modulates cell cycle progression and DNA damage responses via stabilization of p21. TRIM39 also negatively regulates the nuclear factor kappaB (NFkappaB)-mediated signaling pathway through stabilization of Cactin, an inhibitor of NFkappaB- and Toll-like receptor (TLR)-mediated transcription, which is induced by inflammatory stimulants such as tumor necrosis factor alpha (TNFalpha). TRIM39 is a MOAP-1-binding protein that can promote apoptosis signaling through stabilization of MOAP-1 via the inhibition of its poly-ubiquitination process. TRIM58, also known as protein BIA2, is an erythroid E3 ubiquitin-protein ligase induced during late erythropoiesis. It binds and ubiquitinates the intermediate chain of the microtubule motor dynein (DYNC1LI1/DYNC1LI2), stimulating the degradation of the dynein holoprotein complex. It may participate in the erythroblast enucleation process through regulation of nuclear polarization. 44 matched cddid_all.tbl CDD cd19781 cd19781 380839 Bbox2_TRIM40_C-V B-box-type 2 zinc finger found in tripartite motif-containing protein 40 (TRIM40) and similar proteins. TRIM40, also termed probable E3 NEDD8-protein ligase, or RING finger protein 35, may function as an E3 ubiquitin-protein ligase of the NEDD8 conjugation pathway. It promotes neddylation of IKBKG/NEMO, stabilizing NFKBIA, and inhibiting NF-kappaB nuclear translocation and activity. TRIM40 belongs to the C-V subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 44 matched cddid_all.tbl CDD cd19782 cd19782 380840 Bbox2_TRIM42_C-III B-box-type 2 zinc finger found in tripartite motif-containing protein 42 (TRIM42) and similar proteins. TRIM42 belongs to the C-III subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil domain. It also has a novel cysteine-rich motif N-terminal to the RBCC domain, as well as a COS (carboxyl-terminal subgroup one signature) box and a fibronectin type-III (FN3) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TRIM42 can interact with TRIM27, a known cancer-associated protein. Its precise biological function remains unclear. 40 matched cddid_all.tbl CDD cd19783 cd19783 380841 Bbox2_TRIM43-like B-box-type 2 zinc finger found in tripartite motif-containing proteins TRIM43, TRIM48, TRIM49, TRIM51, TRIM64, TRIM77 and similar proteins. The family includes a group of closely related uncharacterized tripartite motif-containing proteins, TRIM43, TRIM43B, TRIM48/RNF101, TRIM49/RNF18, TRIM49B, TRIM49C/TRIM49L2, TRIM49D/TRIM49L, TRIM51/SPRYD5, TRIM64, TRIM64B, TRIM64C, and TRIM77, whose biological functions remain unclear. TRIM49, also known as testis-specific RING-finger protein, has moderate similarity with SS-A/Ro52 antigen, suggesting it may be one of target proteins of autoantibodies in the sera of patients with these autoimmune disorders. All family members (except for TRIM51) belong to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. TRIM51 belongs to unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 53 matched cddid_all.tbl CDD cd19784 cd19784 380842 Bbox2_TRIM44 B-box-type 2 zinc finger found in tripartite motif-containing protein 44 (TRIM44) and similar proteins. TRIM44, also termed protein DIPB, functions as a critical regulator in tumor metastasis and progression. TRIM44 belongs to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. It contains a Bbox2 domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 39 matched cddid_all.tbl CDD cd19785 cd19785 380843 Bbox2_TRIM45_C-X B-box-type 2 zinc finger found in tripartite motif-containing protein 45 (TRIM45) and similar proteins. TRIM45, also known as RING finger protein 99 (RNF99), is a novel receptor for activated C-kinase (RACK1)-interacting protein that suppresses transcriptional activities of Elk-1 and AP-1 and downregulates mitogen-activated protein kinase (MAPK) signal transduction by inhibiting RACK1/PKC (protein kinase C) complex formation. It also negatively regulates tumor necrosis factor alpha (TNFalpha)-induced nuclear factor-kappaB (NF-kappa B)-mediated transcription and suppresses cell proliferation. TRIM45 belongs to the C-X subclass of TRIM (tripartite motif) family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a filamin-type immunoglobulin (IG-FLMN) domain and NHL repeats positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 43 matched cddid_all.tbl CDD cd19786 cd19786 380844 Bbox2_TRIM46_C-I B-box-type 2 zinc finger found in tripartite motif-containing protein 46 (TRIM46) and similar proteins. TRIM46, also known as gene Y protein (GeneY) or tripartite, fibronectin type-III and C-terminal SPRY motif protein (TRIFIC), is a microtubule-associated protein that specifically localizes to the proximal axon, partly overlaps with the axon initial segment (AIS) at later stages, and organizes uniform microtubule orientation in axons. It controls neuronal polarity and axon specification by driving the formation of parallel microtubule arrays. TRIM46 belongs to the C-I subclass of TRIM (tripartite motif) family of proteins, which are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 46 matched cddid_all.tbl CDD cd19787 cd19787 380845 Bbox2_TRIM50-like B-box-type 2 zinc finger found in tripartite motif-containing protein TRIM50, TRIM73, TRIM74 and similar proteins. TRIM50 is a stomach-specific E3 ubiquitin-protein ligase, encoded by the Williams-Beuren syndrome (WBS) TRIM50 gene, which regulates vesicular trafficking for acid secretion in gastric parietal cells. It colocalizes, interacts with, and increases the level of p62/SQSTM1, a multifunctional adaptor protein implicated in various cellular processes including the autophagy clearance of polyubiquitinated protein aggregates. It also promotes the formation and clearance of aggresome-associated polyubiquitinated proteins through the interaction with the histone deacetylase 6 (HDAC6), a tubulin specific deacetylase that regulates microtubule-dependent aggresome formation. TRIM50 can be acetylated by PCAF and p300. TRIM50 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. The family also includes two paralogs of TRIM50, tripartite motif-containing protein 73 (TRIM73), also known as tripartite motif-containing protein 50B (TRIM50B), and tripartite motif-containing protein 74 (TRIM74), also known as tripartite motif-containing protein 50C (TRIM50C), both of which are WBS-related genes encoding proteins and may also act as E3 ligases. In contrast with TRIM50, TRIM73 and TRIM74 belong to the C-V subclass of TRIM family of proteins that are defined by the N-terminal RBCC domains only. 39 matched cddid_all.tbl CDD cd19788 cd19788 380846 Bbox2_MuRF B-box-type 2 zinc finger found in muscle-specific RING finger protein (MuRF) family. This family corresponds to a group of striated muscle-specific tripartite motif (TRIM) proteins, including TRIM63/MuRF-1, TRIM55/MuRF-2, and TRIM54/MuRF-3, which function as E3 ubiquitin ligases in ubiquitin-mediated muscle protein turnover. They are tightly developmentally regulated in skeletal muscle and associate with different cytoskeleton components, such as microtubules, Z-disks and M-bands, as well as with metabolic enzymes and nuclear proteins. They also cooperate with diverse proteins implicated in selective protein degradation by the proteasome and autophagosome, and target proteins of metabolic regulation, sarcomere assembly and transcriptional regulation. Moreover, MURFs display variable fibre-type preferences. TRIM63/MuRF-1 is predominantly fast (type II) fibre-associated in skeletal muscle. TRIM55/MuRF-2 is predominantly slow-fibre associated. TRIM54/MuRF-3 is ubiquitously present. They play an active role in microtubule-mediated sarcomere assembly. MuRFs belong to the C-II subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, and an acidic residue-rich (AR) domain positioned C-terminal to the RBCC domain. They also harbor a MURF family-specific conserved box (MFC) between its RING-HC finger and Bbox domains. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 39 matched cddid_all.tbl CDD cd19789 cd19789 380847 Bbox2_TRIM56_C-V B-box-type 2 zinc finger found in tripartite motif-containing protein 56 (TRIM56) and similar proteins. TRIM56, also known as RING finger protein 109 (RNF109), is a virus-inducible E3 ubiquitin ligase that restricts pestivirus infection. It positively regulates the Toll-like receptor 3 (TLR3) antiviral signaling pathway, and possesses antiviral activity against bovine viral diarrhea virus (BVDV), a ruminant pestivirus classified within the family Flaviviridae shared by tick-borne encephalitis virus (TBEV). It also possesses antiviral activity against two classical flaviviruses, yellow fever virus (YFV) and dengue virus (DENV), as well as a human coronavirus, HCoV-OC43, which is responsible for a significant share of common cold cases. It may not act on positive-strand RNA viruses indiscriminately. Moreover, TRIM56 is an interferon-inducible E3 ubiquitin ligase that modulates STING to confer double-stranded DNA-mediated innate immune responses. TRIM56 belongs to the C-V subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 47 matched cddid_all.tbl CDD cd19790 cd19790 380848 Bbox2_TRIM59_C-XI B-box-type 2 zinc finger found in tripartite motif-containing protein 59 (TRIM59) and similar proteins. TRIM59, also known as TRIM57, or RING finger protein 104 (RNF104) or tumor suppressor TSBF-1, is a putative E3 ubiquitin-protein ligase that functions as a novel multiple cancer biomarker for immunohistochemical detection of early tumorigenesis. It is upregulated in gastric cancer and promotes gastric carcinogenesis by interacting with and targeting the P53 tumor suppressor for its ubiquitination and degradation. It also acts as a novel accessory molecule involved in cytotoxicity of BCG-activated macrophages (BAM). Moreover, TRIM59 may serve as a multifunctional regulator for innate immune signaling pathways. It interacts with ECSIT and negatively regulates nuclear factor-kappaB (NF- kappa B) and interferon regulatory factor (IRF)-3/7-mediated signal pathways. TRIM59 belongs to the C-XI subclass of TRIM (tripartite motif) family of proteins that are defined by an N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region. In addition, TRIM59 contains a C-terminal transmembrane domain. 40 matched cddid_all.tbl CDD cd19791 cd19791 380849 Bbox2_TRIM60-like B-box-type 2 zinc finger found in tripartite motif-containing proteins, TRIM60, TRIM61, TRIM75 and similar proteins. This family includes a group of tripartite motif-containing proteins, including TRIM60, TRIM61 and TRIM75. TRIM60, also known as RING finger protein 129 (RNF129) or RING finger protein 33 (RNF33), is a cytoplasmic protein expressed in the testis. It may play an important role in the spermatogenesis process, the development of the preimplantation embryo, and in testicular functions. TRIM60 interacts with the cytoplasmic kinesin motor proteins KIF3A and KIF3B suggesting possible contribution to cargo movement along the microtubule in the expressed sites. It is also involved in spermatogenesis in Sertoli cells under the regulation of nuclear factor-kappaB (NF-kappaB). TRIM61 is closely related to TRIM60, but its biological function remains unclear. TRIM75 could be the product of a pseudogene. Its biological function remains unclear. TRIM60 and TRIM75 belong to the C-IV subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. In contrast, TRIM61 belongs to the C-V subclass of TRIM family that contains RBCC domains only. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 39 matched cddid_all.tbl CDD cd19792 cd19792 380850 Bbox2_TRIM62_C-IV B-box-type 2 zinc finger found in tripartite motif-containing protein 62 (TRIM62) and similar proteins. TRIM62, also known as Ductal Epithelium Associated Ring Chromosome 1 (DEAR1), is a cytoplasmic E3 ubiquitin-protein ligase that was identified as a dominant regulator of acinar morphogenesis in the mammary gland. It is implicated in the inflammatory response of immune cells by regulating the Toll-like receptor 4 (TLR4) signaling pathway, leading to increased activity of the activator protein 1 (AP-1) transcription factor in primary macrophages. It is also involved in muscular protein homeostasis, especially during inflammation-induced atrophy, and may play a role in the pathogenesis of ICU-acquired weakness (ICUAW) by activating and maintaining inflammation in myocytes. Moreover, TRIM62 facilitates K27-linked poly-ubiquitination of CARD9 and also regulates CARD9-mediated anti-fungal immunity and intestinal inflammation. Furthermore, TRIM62 is involved in the regulation of apical-basal polarity and acinar morphogenesis. It also functions as a chromosome 1p35 tumor suppressor and negatively regulates transforming growth factor beta (TGFbeta)-driven epithelial-mesenchymal transition (EMT) through binding to and promoting the ubiquitination of SMAD3, a major effector of TGFbeta-mediated EMT. TRIM62 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 38 matched cddid_all.tbl CDD cd19793 cd19793 380851 Bbox2_TRIM65-like B-box-type 2 zinc finger found in tripartite motif-containing protein 65 (TRIM65), B box and SPRY domain-containing protein (BSPRY) and similar proteins. The family includes TRIM65 and BSPRY. TRIM65 is an E3 ubiquitin-protein ligase that interacts with the innate immune receptor MDA5 enhancing its ability to stimulate interferon-beta signaling. It functions as a potential oncogenic protein that negatively regulates p53 through ubiquitination, providing insight into development of novel approaches targeting TRIM65 for non-small cell lung carcinoma (NSCLC) treatment, and also overcoming chemotherapy resistance. Moreover, TRIM65 negatively regulates microRNA-driven suppression of mRNA translation by targeting TNRC6 proteins for ubiquitination and degradation. BSPRY is a regulatory protein for maintaining calcium homeostasis. It may regulate epithelial calcium transport by inhibiting TRPV5 activity. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 43 matched cddid_all.tbl CDD cd19794 cd19794 380852 Bbox2_TRIM66-like B-box-type 2 zinc finger found in tripartite motif-containing protein 66 (TRIM66) and similar proteins. TRIM66, also termed transcriptional intermediary factor 1 delta (TIF1delta), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor 1 (TIF1) family expressed by elongating spermatids. Like other TIF1 proteins, TRIM66 displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TRIM66 plays an important role in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. It functions as a negative regulator of postmeiotic genes acting through HP1 isotype gamma (HP1gamma) complex formation and centromere association. TRIM66 belongs to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 43 matched cddid_all.tbl CDD cd19795 cd19795 380853 Bbox2_TRIM68_C-IV B-box-type 2 zinc finger found in tripartite motif-containing protein 68 (TRIM68) and similar proteins. TRIM68, also known as RING finger protein 137 (RNF137) or SSA protein SS-56 (SS-56), is an E3 ubiquitin-protein ligase that negatively regulates Toll-like receptor (TLR)- and RIG-I-like receptor (RLR)-driven type I interferon production by degrading TRK fused gene (TFG), a novel driver of IFN-beta downstream of anti-viral detection systems. It also functions as a cofactor for androgen receptor-mediated transcription by regulating ligand-dependent transcription of androgen receptor in prostate cancer cells. Moreover, TRIM68 is a cellular target of autoantibody responses in Sjogren's syndrome (SS), as well as systemic lupus erythematosus (SLE). It is also an auto-antigen for T cells in SS and SLE. TRIM68 belongs the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and two coiled coil domains, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 44 matched cddid_all.tbl CDD cd19796 cd19796 380854 Bbox2_TRIM71_C-VII B-box-type 2 zinc finger found in tripartite motif-containing protein 71 (TRIM71) and similar proteins. TRIM71, also known as protein lineage variant 41 (lin-41), is an E3 ubiquitin-protein ligase that may play essential roles in embryonic stem cells, cellular reprogramming, and the timing of embryonic neurogenesis. It was first identified in the nematode Caenorhabditis elegans as a target of the differentiation-associated microRNA (miRNA) let-7 (lethal 7), and therefore part of a heterochronic gene network that controls larval development. In humans, it regulates let-7 microRNA biogenesis via modulation of Lin28B protein polyubiquitination. TRIM71 localizes to cytoplasmic P-bodies and directly interacts with the miRNA pathway proteins Argonaute 2 (AGO2) and DICER. It represses miRNA activity by promoting degradative ubiquitination of AGO2. Moreover, TRIM71 associates with SHCBP1, a novel component of the fibroblast growth factor (FGF) signaling pathway, and regulates its non-degradative polyubiquitination. It is also involved in the post-transcriptional regulation of the CDKN1A, RBL1 and RBL2 or EGR1 mRNAs through mediating RNA-binding in embryonic stem cells. TRIM71 belongs to the C-VII subclass of TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 48 matched cddid_all.tbl CDD cd19797 cd19797 380855 Bbox2_TRIM72_C-IV B-box-type 2 zinc finger found in tripartite motif-containing protein 72 (TRIM72) and similar proteins. TRIM72, also known as Mitsugumin-53 (MG53), is a muscle-specific protein that plays a central role in cell membrane repair by nucleating the assembly of the repair machinery at muscle injury sites. It is required in repair of alveolar epithelial cells under plasma membrane stress failure. It interacts with dysferlin to regulate sarcolemmal repair. Upregulation of TRIM72 develops obesity, systemic insulin resistance, dyslipidemia, and hyperglycemia, as well as induces diabetic cardiomyopathy through transcriptional activation of peroxisome proliferation-activated receptor alpha (PPAR-alpha) signaling pathway. Compensation for the absence of AKT signaling by ERK signaling during TRIM72 overexpression leads to pathological hypertrophy. Moreover, TRIM72 functions as a novel negative feedback regulator of myogenesis via targeting insulin receptor substrate-1 (IRS-1). It is transcriptionally activated by the synergism of myogenin (MyoD) and myocyte enhancer factor 2 (MEF2). TRIM72 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 42 matched cddid_all.tbl CDD cd19798 cd19798 380856 Bbox2_BRAT-like B-box-type 2 zinc finger found in Drosophila melanogaster brain tumor protein (BRAT) and similar proteins. BRAT is a NHL-domain family protein that functions as a translational repressor to inhibit cell proliferation. This family also contains Caenorhabditis elegans B-box type zinc finger protein ncl-1, a C. elegans Brat homolog which functions as a translational repressor that inhibits protein synthesis. BRAT contains Bbox1 and Bbox2 zinc fingers and NHL repeats. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 44 matched cddid_all.tbl CDD cd19799 cd19799 380857 Bbox2_MYCBP2 B-box-type 2 zinc finger found in Myc-binding protein 2 (MYCBP2) and similar proteins. MYCBP2, also termed protein associated with Myc (Pam), is an atypical E3 ubiquitin-protein ligase which specifically mediates ubiquitination of threonine and serine residues on target proteins, instead of ubiquitinating lysine residues. MYCBP2 harbors a B-box motif that shows high sequence similarity with B-Box-type zinc finger 2 found in tripartite motif-containing proteins (TRIMs). The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 50 matched cddid_all.tbl CDD cd19800 cd19800 380858 Bbox2_xNF7-like B-box-type 2 zinc finger found in Xenopus laevis nuclear factor 7 (xNF7) and similar proteins. xNF7 is a maternally expressed novel zinc finger nuclear phosphoprotein. It acts as a transcription factor that determines dorsal-ventral body axis. xNF7 harbors a B-box motif that shows high sequence similarity with B-Box-type zinc finger 2 found in tripartite motif-containing proteins (TRIMs). The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 39 matched cddid_all.tbl CDD cd19801 cd19801 380859 Bbox1_MID B-box-type 1 zinc finger found in the midline (MID) family. The MID family includes MID1 and MID2. MID1, also known as midin, midline 1 RING finger protein, putative transcription factor XPRF, RING finger protein 59 (RNF59), or tripartite motif-containing protein 18 (TRIM18), is a microtubule-associated E3 ubiquitin-protein ligase implicated in epithelial-mesenchymal differentiation, cell migration and adhesion, and programmed cell death along specific regions of the ventral midline during embryogenesis. MID2, also known as midin-2, midline defect 2, RING finger protein 60 (RNF60), or tripartite motif-containing protein 1 (TRIM1), is highly related to MID1. It associates with the microtubule network and may at least partially compensate for the loss of MID1. Both MID1 and MID2 interacts with alpha4, a regulatory subunit of PP2-type phosphatases, such as PP2A, and an integral component of the rapamycin-sensitive signaling pathway. They also play a central role in the regulation of granule exocytosis, and functional redundancy exists between MID1 and MID2 in cytotoxic lymphocytes (CTL). Both MID1 and MID2 belong to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 49 matched cddid_all.tbl CDD cd19802 cd19802 380860 Bbox1_TRIM8-like B-box-type 1 zinc finger found in tripartite motif-containing proteins, TRIM8, TRIM16, TRIM25, TRIM29, TRIM44, TRIM47 and similar proteins. This family includes a group of tripartite motif-containing proteins, including TRIM8, TRIM16, TRIM25, TRIM29, TRIM44 and TRIM47. TRIM8, also known as glioblastoma-expressed RING finger protein (GERP) or RING finger protein 27 (RNF27), is a probable E3 ubiquitin-protein ligase that may promote proteasomal degradation of suppressor of cytokine signaling 1 (SOCS1) and further regulate interferon-gamma signaling. It functions as a new p53 modulator that stabilizes p53, impairing its association with MDM2 and inducing the reduction of cell proliferation. TRIM16, also termed estrogen-responsive B box protein (EBBP), may play a role in the regulation of keratinocyte differentiation. It may also act as a tumor suppressor by affecting cell proliferation and migration or tumorigenicity in carcinogenesis. TRIM25, also termed estrogen-responsive finger protein (EFP), or ubiquitin/ISG15-conjugating enzyme TRIM25, or zinc finger protein 147 (ZNF147), or E3 ubiquitin/ISG15 ligase TRIM25, is induced by estrogen and is particularly abundant in placenta and uterus. It has been implicated in cell proliferation, protein modification, and the retinoic acid inducible gene I (RIG-I)-mediated antiviral signaling pathway. It functions as an E3-ubiquitin ligase able to transfer ubiquitin and ISG15 to target proteins. TRIM29, also termed ataxia telangiectasia group D-associated protein (ATDC), plays a crucial role in the regulation of macrophage activation in response to viral or bacterial infections within the respiratory tract. TRIM44, also termed protein DIPB, functions as a critical regulator in tumor metastasis and progression. TRIM47, also known as gene overexpressed in astrocytoma protein (GOA) or RING finger protein 100 (RNF100), plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. The TRIM (tripartite motif) family of proteins are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 46 matched cddid_all.tbl CDD cd19803 cd19803 380861 Bbox1_TRIM9-like_C-I B-box-type 1 zinc finger found in tripartite motif-containing proteins, TRIM9, TRIM67 and similar proteins. This family includes a group of tripartite motif-containing proteins, including TRIM9 and TRIM67, both of which belong to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, consisting of three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TRIM9 (the human ortholog of rat Spring), also known as RING finger protein 91 (RNF91), is a brain-specific E3 ubiquitin-protein ligase collaborating with an E2 ubiquitin conjugating enzyme UBCH5b. It plays an important role in the regulation of neuronal functions and participates in the neurodegenerative disorders through its ligase activity. TRIM67, also termed TRIM9-like protein (TNL), is a protein selectively expressed in the cerebellum. It interacts with PRG-1, an important molecule in the control of hippocampal excitability dependent on presynaptic LPA2 receptor signaling, and 80K-H (also known as glucosidase II beta), a protein kinase C substrate. It negatively regulates Ras signaling in cell proliferation via degradation of 80K-H, leading to neural differentiation including neuritogenesis. 47 matched cddid_all.tbl CDD cd19804 cd19804 380862 Bbox1_TRIM19_C-V B-box-type 1 zinc finger found in promyelocytic leukemia protein (PML) and similar proteins. Protein PML, also known as RING finger protein 71 (RNF71) or tripartite motif-containing protein 19 (TRIM19), is predominantly a nuclear protein with a broad intrinsic antiviral activity. It is the eponymous component of PML nuclear bodies (PML NBs) and has been implicated in a wide variety of cellular processes, including DNA damage signaling, apoptosis, and transcription. PML interferes with the replication of many unrelated viruses, including human immunodeficiency virus 1 (HIV-1), human foamy virus (HFV), poliovirus, influenza virus, rabies virus, EMCV, adeno-associated virus (AAV), and vesicular stomatitis virus (VSV). It also selectively interacts with misfolded proteins through distinct substrate recognition sites, and conjugates these proteins with the small ubiquitin-like modifiers (SUMOs) through its SUMO ligase activity. PML belongs to the C-V subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 47 matched cddid_all.tbl CDD cd19805 cd19805 380863 Bbox1_TIF1 B-box-type 1 zinc finger found in transcription intermediary factor 1 (TIF1) family. This family corresponds to the TIF1 family of transcriptional cofactors including TIF1-alpha (TRIM24), TIF1-beta (TRIM28), and TIF1-gamma (TRIM33), which belongs to the C-VI subclass of the TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1-alpha and TIF1-beta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. They bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. TIF1-gamma is structurally closely related to TIF1-alpha and TIF1-beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta and gamma. It cannot bind to nuclear receptors (NRs). 44 matched cddid_all.tbl CDD cd19806 cd19806 380864 Bbox1_TRIM32_C-VII B-box-type 1 zinc finger found in tripartite motif-containing protein 32 (TRIM32) and similar proteins. TRIM32, also known as 72 kDa Tat-interacting protein, or zinc finger protein HT2A, or BBS11, is an E3 ubiquitin-protein ligase that promotes degradation of several targets, including actin, PIASgamma, Abl interactor 2, dysbindin, X-linked inhibitor of apoptosis (XIAP), p73 transcription factor, thin filaments and Z-bands during fasting. It plays important roles in neuronal differentiation of neural progenitor cells, as well as in controlling cell fate in skeletal muscle progenitor cells. It reduces PI3K-Akt-FoxO signaling in muscle atrophy by promoting plakoglobin-PI3K dissociation. It also functions as a pluripotency-reprogramming roadblock that facilitates cellular transition towards differentiation via modulating the levels of Oct4 and cMyc. Moreover, TRIM32 is an intrinsic influenza A virus (IAV) restriction factor which senses and targets the polymerase basic protein 1 (PB1) for ubiquitination and protein degradation. It also plays a significant role in mediating the biological activity of the HIV-1 Tat protein in vivo, binding specifically to the activation domain of HIV-1 Tat; it and can also interact with the HIV-2 and EIAV Tat proteins. Furthermore, TRIM32 regulates myoblast proliferation by controlling turnover of NDRG2 (N-myc downstream-regulated gene). It negatively regulates tumor suppressor p53 to promote tumorigenesis. It also facilitates degradation of MYCN on spindle poles and induces asymmetric cell division in human neuroblastoma cells. In addition, TRIM32 plays important roles in regulation of hyperactivities and positively regulates the development of anxiety and depression disorders induced by chronic stress. It also plays a role in regeneration by affecting satellite cell cycle progression via modulation of the SUMO ligase PIASy (PIAS4). Defects in TRIM32 leads to limb-girdle muscular dystrophy type 2H (LGMD2H), sarcotubular myopathies (STM) and Bardet-Biedl syndrome. TRIM32 belongs to the C-VII subclass of TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The NHL domain mediates the interaction with Argonaute proteins and consequently allows TRIM32 to modulate the activity of certain miRNAs. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 41 matched cddid_all.tbl CDD cd19807 cd19807 380865 Bbox1_TRIM36-like B-box-type 1 zinc finger found in tripartite motif-containing proteins, TRIM36, TRIM46 and similar proteins. The family includes tripartite motif-containing proteins, TRIM36 and TRIM46, both of which belong to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TRIM36, the human ortholog of mouse Haprin, also known as RING finger protein 98 (RNF98) or zinc-binding protein Rbcc728, is an E3 ubiquitin-protein ligase expressed in the germ plasm. It has been implicated in acrosome reaction, fertilization, and embryogenesis, as well as in carcinogenesis. TRIM36 functions upstream of Wnt/beta-catenin activation, and plays a role in controlling the stability of proteins regulating microtubule polymerization during cortical rotation, and subsequent dorsal axis formation. It is also potentially associated with chromosome segregation by interacting with the kinetochore protein centromere protein-H (CENP-H), and colocalizing with the microtubule protein alpha-tubulin. Its overexpression may cause chromosomal instability and carcinogenesis. It is, thus, a novel regulator affecting cell cycle progression. Moreover, TRIM36 plays a critical role in the arrangement of somites during embryogenesis. TRIM46, also known as gene Y protein (GeneY) or tripartite, fibronectin type-III and C-terminal SPRY motif protein (TRIFIC), is a microtubule-associated protein that specifically localizes to the proximal axon, partly overlaps with the axon initial segment (AIS) at later stages, and organizes uniform microtubule orientation in axons. It controls neuronal polarity and axon specification by driving the formation of parallel microtubule arrays. 52 matched cddid_all.tbl CDD cd19808 cd19808 380866 Bbox1_TRIM42_C-III B-box-type 1 zinc finger found in tripartite motif-containing protein 42 (TRIM42) and similar proteins. TRIM42 belongs to the C-III subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil domain. It also has a novel cysteine-rich motif N-terminal to the RBCC domain, as well as a COS (carboxyl-terminal subgroup one signature) box and a fibronectin type-III (FN3) domain positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TRIM42 can interact with TRIM27, a known cancer-associated protein. Its precise biological function remains unclear. 47 matched cddid_all.tbl CDD cd19809 cd19809 380867 Bbox1_TRIM45_C-X B-box-type 1 zinc finger found in tripartite motif-containing protein 45 (TRIM45) and similar proteins. TRIM45, also known as RING finger protein 99 (RNF99), is a novel receptor for activated C-kinase (RACK1)-interacting protein that suppresses transcriptional activities of Elk-1 and AP-1, and downregulates mitogen-activated protein kinase (MAPK) signal transduction by inhibiting RACK1/PKC (protein kinase C) complex formation. It also negatively regulates tumor necrosis factor alpha (TNFalpha)-induced nuclear factor-kappaB (NF-kappa B)-mediated transcription, and suppresses cell proliferation. TRIM45 belongs to the C-X subclass of the TRIM (tripartite motif) family of proteins that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a filamin-type immunoglobulin (IG-FLMN) domain and NHL repeats positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 46 matched cddid_all.tbl CDD cd19810 cd19810 380868 Bbox1_TRIM56_C-V B-box-type 1 zinc finger found in tripartite motif-containing protein 56 (TRIM56) and similar proteins. TRIM56, also known as RING finger protein 109 (RNF109), is a virus-inducible E3 ubiquitin ligase that restricts pestivirus infection. It positively regulates the Toll-like receptor 3 (TLR3) antiviral signaling pathway, and possesses antiviral activity against bovine viral diarrhea virus (BVDV), a ruminant pestivirus classified within the family Flaviviridae shared by tick-borne encephalitis virus (TBEV). It also possesses antiviral activity against two classical flaviviruses, yellow fever virus (YFV) and dengue virus (DENV), as well as a human coronavirus, HCoV-OC43, which is responsible for a significant share of common cold cases. It may not act on positive-strand RNA viruses indiscriminately. Moreover, TRIM56 is an interferon-inducible E3 ubiquitin ligase that modulates STING to confer double-stranded DNA-mediated innate immune responses. TRIM56 belongs to the C-V subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 49 matched cddid_all.tbl CDD cd19811 cd19811 380869 Bbox1_TRIM66 B-box-type 1 zinc finger found in tripartite motif-containing protein 66 (TRIM66) and similar proteins. TRIM66, also termed transcriptional intermediary factor 1 delta (TIF1delta), is a novel heterochromatin protein 1 (HP1)-interacting member of the transcriptional intermediary factor 1 (TIF1) family, and is expressed by elongating spermatids. Like other TIF1 proteins, TRIM66 displays a potent trichostatin A (TSA)-sensitive repression function; TSA is a specific inhibitor of histone deacetylases. Moreover, TRIM66 plays an important role in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. It functions as a negative regulator of postmeiotic genes acting through HP1 isotype gamma (HP1gamma) complex formation and centromere association. TRIM66 belongs to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 37 matched cddid_all.tbl CDD cd19812 cd19812 380870 Bbox1_TRIM71_C-VII B-box-type 1 zinc finger found in tripartite motif-containing protein 71 (TRIM71) and similar proteins. TRIM71, also known as protein lineage variant 41 (lin-41), is an E3 ubiquitin-protein ligase that may play essential roles in embryonic stem cells, cellular reprogramming, and the timing of embryonic neurogenesis. It was first identified in the nematode Caenorhabditis elegans as a target of the differentiation-associated microRNA (miRNA) let-7 (lethal 7) and therefore part of a heterochronic gene network that controls larval development. In humans, it regulates let-7 microRNA biogenesis via modulation of Lin28B protein polyubiquitination. TRIM71 localizes to cytoplasmic P-bodies and directly interacts with the miRNA pathway proteins Argonaute 2 (AGO2) and DICER. It represses miRNA activity by promoting degradative ubiquitination of AGO2. Moreover, TRIM71 associates with SHCBP1, a novel component of the fibroblast growth factor (FGF) signaling pathway, and regulates its non-degradative polyubiquitination. It is also involved in the post-transcriptional regulation of the CDKN1A, RBL1 and RBL2 or EGR1 mRNAs by mediating RNA-binding in embryonic stem cells. TRIM71 belongs to the C-VII subclass of the TRIM (tripartite motif) family of proteins that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 44 matched cddid_all.tbl CDD cd19813 cd19813 380871 Bbox1_BRAT-like B-box-type 1 zinc finger found in Drosophila melanogaster brain tumor protein (BRAT) and similar proteins. BRAT is a NHL-domain family protein that functions as a translational repressor to inhibit cell proliferation. The family also contains Caenorhabditis elegans B-box type zinc finger protein ncl-1, a C. elegans Brat homolog which functions as a translational repressor that inhibits protein synthesis. BRAT contains Bbox1 and Bbox2 zinc fingers and NHL repeats. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 44 matched cddid_all.tbl CDD cd19814 cd19814 380872 Bbox1_RNF207-like B-box-type 1 zinc finger found in RING finger protein 207 (RNF207) and similar proteins. RNF207 is a cardiac-specific E3 ubiquitin-protein ligase that plays an important role in the regulation of cardiac repolarization. It regulates action potential duration, likely via effects on human ether-a-go-go-related gene (HERG) trafficking and localization, in a heat shock protein-dependent manner. RNF207 contains a RING finger, a B-box motif and Bbox C-terminal (BBC) domain, as well as a C-terminal non-homologous region (CNHR). The B-box motif shows high sequence similarity with B-Box-type 1 zinc finger found in tripartite motif-containing proteins (TRIMs). The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 49 matched cddid_all.tbl CDD cd19815 cd19815 380873 Bbox1_HOIP B-box-type 1 zinc finger found in HOIL-1-interacting protein (HOIP) and similar proteins. HOIP, also termed RING finger protein 31 (RNF31), or zinc in-between-RING-finger ubiquitin-associated domain protein, together with HOIL-1 and SHARPIN, forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis. It also interacts with the atypical mammalian orphan receptor DAX-1, trigger DAX-1 ubiquitination and stabilization, and participate in repressing steroidogenic gene expression. HOIP contains a B-box motif that shows high sequence similarity with B-Box-type 1 zinc finger found in tripartite motif-containing proteins (TRIMs). The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 43 matched cddid_all.tbl CDD cd19816 cd19816 380874 Bbox1_CYLD B-box-type 1 zinc finger found in tumor suppressor cylindromatosis (CYLD) and similar proteins. CYLD, also termed ubiquitin carboxyl-terminal hydrolase CYLD, or deubiquitinating enzyme CYLD, or ubiquitin thioesterase CYLD, or ubiquitin-specific-processing protease CYLD, is a microtubule-associated deubiquitinase that specifically cleaves Lys-63-linked polyubiquitin chains. It plays a pivotal role in a wide range of cellular activities, including innate immunity, cell division, and ciliogenesis. CYLD antagonizes NF-kappaB and JNK signaling by disassembly of Lys63-linked ubiquitin chains synthesized in response to cytokine stimulation. Structural characterization reveals a small zinc-binding B-box inserted within the ubiquitin specific protease (USP) domain of CYLD. The B-box motif shows high sequence similarity with B-Box-type 1 zinc finger found in tripartite motif-containing proteins (TRIMs) and is responsible for its intermolecular interaction and cytoplasmic localization. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 56 matched cddid_all.tbl CDD cd19817 cd19817 380875 Bbox1_ANCHR-like B-box-type 1 zinc finger found in Abscission/NoCut checkpoint regulator (ANCHR) and similar proteins. ANCHR, also termed MLL partner containing FYVE domain, or zinc finger FYVE domain-containing protein 19, is a key regulator of the abscission step in cytokinesis: part of the cytokinesis checkpoint, a process required to delay abscission to prevent both premature resolution of intercellular chromosome bridges and accumulation of DNA damage. The family also includes zinc finger B-box domain-containing protein 1 (ZBBX), a B-box motif containing protein with unclear biological function. The B-box motif of this family shows high sequence similarity with B-Box-type 1 zinc finger found in tripartite motif-containing proteins (TRIMs). The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 45 matched cddid_all.tbl CDD cd19818 cd19818 380876 Bbox1_ZBBX B-box-type 1 zinc finger found in zinc finger B-box domain-containing protein 1 (ZBBX) and similar proteins. The family corresponds to a group of uncharacterized zinc finger B-box domain-containing proteins. The B-box motif shows high sequence similarity with B-Box-type 1 zinc finger found in tripartite motif-containing proteins (TRIMs). The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 43 matched cddid_all.tbl CDD cd19819 cd19819 380877 Bbox1_ZFYVE1_rpt1 first B-box-type 1 zinc finger found in zinc finger FYVE domain-containing protein 1 (ZFYVE1) and similar proteins. ZFYVE1 also termed double FYVE-containing protein 1 (DFCP1), or SR3, or tandem FYVE fingers-1, is a novel tandem FYVE domain containing protein that binds phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) with high specificity over other phosphoinositides. The subcellular distribution of exogenously-expressed ZFYVE1 to Golgi, endoplasmic reticulum (ER) and vesicular is governed in part by its FYVE domains but unaffected by Wortmannin, a PI3-kinase inhibitor. ZFYVE1 harbors two B-box motifs, both of which show high sequence similarity with B-Box-type 1 zinc finger found in tripartite motif-containing proteins (TRIMs). The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 48 matched cddid_all.tbl CDD cd19820 cd19820 380878 Bbox1_ZFYVE1_rpt2 second B-box-type 1 zinc finger found in zinc finger FYVE domain-containing protein 1 (ZFYVE1) and similar proteins. ZFYVE1 also termed double FYVE-containing protein 1 (DFCP1), or SR3, or tandem FYVE fingers-1, is a novel tandem FYVE domain containing protein that binds phosphatidylinositol 3-phosphate (PtdIns3P or PI3P) with high specificity over other phosphoinositides. The subcellular distribution of exogenously-expressed ZFYVE1 to Golgi, endoplasmic reticulum (ER) and vesicular is governed in part by its FYVE domains but unaffected by Wortmannin, a PI3-kinase inhibitor. ZFYVE1 harbors two B-box motifs, both of which show high sequence similarity with B-Box-type 1 zinc finger found in tripartite motif-containing proteins (TRIMs). The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 59 matched cddid_all.tbl CDD cd19821 cd19821 380879 Bbox1_BBX-like B-box-type 1 zinc finger found in B-box (BBX) family of plant transcription factors and similar proteins. The BBX family includes a group of zinc finger transcription factors that contain one or two B-box motifs, and sometimes also feature a CCT (CONSTANS, CO-like, and TOC1) domain. They play important roles in plant growth and development, including seedling photomorphogenesis, photoperiodic regulation of flowering, shade avoidance, and responses to biotic and abiotic stresses. Their B-box motifs show high sequence similarity with B-Box-type 1 zinc finger found in tripartite motif-containing proteins (TRIMs) and are involved in mediating transcriptional regulation and protein-protein interaction in plant signaling. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif; this family contains a modified motif, C3XC2H2, where X can be D, E, C or H. 44 matched cddid_all.tbl CDD cd19822 cd19822 380880 Bbox2_MID1_C-I B-box-type 2 zinc finger found in midline-1 (MID1) and similar proteins. MID1, also termed midin, or midline 1 RING finger protein, or putative transcription factor XPRF, or RING finger protein 59 (RNF59), or tripartite motif-containing protein 18 (TRI18), is a microtubule-associated E3 ubiquitin-protein ligase implicated in epithelial-mesenchymal differentiation, cell migration and adhesion, and programmed cell death along specific regions of the ventral midline during embryogenesis. It monoubiquinates the alpha4 subunit of protein phosphatase 2A (PP2A), promoting proteosomal degradation of the catalytic subunit of PP2A (PP2Ac) and preventing the A and B subunits from forming an active complex. It promotes allergen and rhinovirus-induced asthma through the inhibition of PP2A activity. It is strongly upregulated in cytotoxic lymphocytes (CTLs) and directs lytic granule exocytosis and cytotoxicity of killer T cells. Loss-of-function mutations in MID1 lead to the human X-linked Opitz G/BBB (XLOS) syndrome characterized by defective midline development during embryogenesis. It heterodimerizes in vitro with its paralog MID2. MID1 belongs to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, the fibronectin type III domain and the SPRY/B30.2 domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 47 matched cddid_all.tbl CDD cd19823 cd19823 380881 Bbox2_MID2_C-I B-box-type 2 zinc finger found in midline-2 (MID2) and similar proteins. MID2, also known as midin-2, midline defect 2, RING finger protein 60 (RNF60), or tripartite motif-containing protein 1 (TRIM1), is a probable E3 ubiquitin-protein ligase that is highly related to MID1 that associate with cytoplasmic microtubules along their length and throughout the cell cycle. Like MID1, MID2 associates with the microtubule network and may at least partially compensate for the loss of MID1. Both MID1 and MID2 interacts with Alpha 4, which is a regulatory subunit of PP2-type phosphatases, such as PP2A, and an integral component of the rapamycin-sensitive signaling pathway. MID2 can also substitute for MID1 to control exocytosis of lytic granules in cytotoxic T cells. It heterodimerizes in vitro with its paralog MID1. Loss-of-function mutations in MID2 lead to the human X-linked intellectual disability (XLID). MID2 belongs to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxy-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 40 matched cddid_all.tbl CDD cd19824 cd19824 380882 Bbox2_TRIM2_C-VII B-box-type 2 zinc finger found in tripartite motif-containing protein 2 (TRIM2) and similar proteins. TRIM2, also known as RING finger protein 86 (RNF86), is an E3 ubiquitin-protein ligase that ubiquitinates the neurofilament light chain, a component of the intermediate filament in axons. Loss of function of TRIM2 results in early-onset axonal neuropathy. TRIM2 also plays a role in mediating the p42/p44 Semi-independent ubiquitination of the cell death-promoting protein Bcl-2-interacting mediator of cell death (Aim) in rapid ischemic tolerance. TRIM2 belongs to the C-VII subclass of TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 42 matched cddid_all.tbl CDD cd19825 cd19825 380883 Bbox2_TRIM3_C-VII B-box-type 2 zinc finger found in tripartite motif-containing protein 3 (TRIM3). TRIM3, also known as brain-expressed RING finger protein (BERP), RING finger protein 97 (RNF97), or RING finger protein 22 (RNF22), is an E3 ubiquitin-protein ligase involved in the pathogenesis of various cancers. It functions as a tumor suppressor that regulates asymmetric cell division in neuroblastoma. It binds to the ck inhibitor p21(WAF1/CIP1) and regulates its availability that promotes cyclins D1-cdk4 nuclear accumulation. Moreover, TRIM3 plays an important role in the central nervous system (CNS). It corresponds to gene BERP (brain-expressed RING finger protein), a unique p53-regulated gene that modulates seizure susceptibility and GABAAR cell surface expression. Furthermore, TRIM3 mediates activity-dependent turnover of presynaptic density (PSD) scaffold proteins GKAP/SAPAP1 and is a negative regulator of dendrite spine morphology. In addition, TRIM3 may be involved in vesicular trafficking via its association with the cytoskeleton-associated-recycling or transport (CART) complex that is necessary for efficient transferrin receptor recycling, but not for epidermal growth factor receptor (EGFR) degradation. It also regulates the motility of the kinesin superfamily protein KIF21B. TRIM3 belongs to the C-VII subclass of TRIM (tripartite motif)-NHL family that is defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil domain, as well as a NHL (named after proteins NCL-1, HT2A and Lin-41 that contain repeats folded into a six-bladed beta propeller) repeat domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 47 matched cddid_all.tbl CDD cd19826 cd19826 380884 Bbox2_TRIM9_C-I B-box-type 2 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins. TRIM9 (the human ortholog of rat Spring), also termed RING finger protein 91 (RNF91), is a brain-specific E3 ubiquitin-protein ligase collaborating with an E2 ubiquitin conjugating enzyme UBCH5b. TRIM9 plays an important role in the regulation of neuronal functions and participates in the neurodegenerative disorders through its ligase activity. It interacts with the WD repeat region of beta-transducer repeat-containing protein (beta-TCP) through its N-terminal degron motif (DSGXXS) depending on the phosphorylation status, and thus negatively regulate nuclear factor-kappaB (NF-kappaB) activation in the NF-kappaB pro-inflammatory signaling pathway. Moreover, TRIM9 acts as a critical catalytic link between Netrin-1 and exocytosis soluble NSF attachment receptor protein (SNARE) machinery in murine cortical neurons. It promotes SNARE-mediated vesicle fusion and axon branching in a Netrin-dependent manner. TRIM9 belongs to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, the fibronectin type III domain and the SPRY/B30.2 domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 49 matched cddid_all.tbl CDD cd19827 cd19827 380885 Bbox2_TRIM67_C-I B-box-type 2 zinc finger found in tripartite motif-containing protein 67 (TRIM67) and similar proteins. TRIM67, also termed TRIM9-like protein (TNL), is a protein selectively expressed in the cerebellum. It interacts with PRG-1, an important molecule in the control of hippocampal excitability dependent on presynaptic LPA2 receptor signaling, and 80K-H (also known as glucosidase II beta), a protein kinase C substrate. It negatively regulates Ras signaling in cell proliferation via degradation of 80K-H, leading to neural differentiation including neuritogenesis. TRIM67 belongs to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, the fibronectin type III domain and the SPRY/B30.2 domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 45 matched cddid_all.tbl CDD cd19828 cd19828 380886 Bbox2_TIF1a_C-VI B-box-type 2 zinc finger found in transcription intermediary factor 1-alpha (TIF1-alpha). TIF1-alpha, also known as tripartite motif-containing protein 24 (TRIM24), E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1-alpha interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoid X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta), and MOD2 (HP1gamma), as well as the vertebrate Kruppel-type (C2H2) zinc finger proteins that contain the transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53, and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal PHD-Bromo region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development. 57 matched cddid_all.tbl CDD cd19829 cd19829 380887 Bbox2_TIF1b_C-VI B-box-type 2 zinc finger found in transcription intermediary factor 1-beta (TIF1-beta). TIF1-beta, also known as Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), KRAB-interacting protein 1 (KRIP-1), nuclear co-repressor KAP-1, RING finger protein 96, tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD) and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1-beta acts as a nuclear co-repressor that plays a role in transcription and in the DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during the DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. Moreover, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. The N-terminal RBCC domains of TIF1-beta are responsible for the interaction with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and the regulation of homo- and heterodimerization. The C-terminal PHD/Bromo domains are involved in interacting with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity. 44 matched cddid_all.tbl CDD cd19830 cd19830 380888 Bbox2_TIF1g_C-VI B-box-type 2 zinc finger found in transcription intermediary factor 1 gamma (TIF1-gamma). TIF1-gamma, also known as tripartite motif-containing 33 (TRIM33), ectodermin, RFG7, or PTC7, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. TIF1-gamma is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling. It inhibits the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1gamma is an important regulator of transcription during hematopoiesis, as well as a key actor of tumorigenesis. Like other TIF1 family members, TIF1-gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis. 53 matched cddid_all.tbl CDD cd19831 cd19831 380889 Bbox2_MuRF1_C-II B-box-type 2 zinc finger found in muscle-specific RING finger protein 1 (MuRF-1) and similar proteins. MuRF-1, also known as tripartite motif-containing protein 63 (TRIM63), RING finger protein 28 (RNF28), iris RING finger protein, or striated muscle RING zinc finger, is an E3 ubiquitin-protein ligase in ubiquitin-mediated muscle protein turnover. It is predominantly fast (type II) fibre-associated in skeletal muscle and can bind to many myofibrillar proteins, including titin, nebulin, the nebulin-related protein NRAP, troponin-I (TnI), troponin-T (TnT), myosin light chain 2 (MLC-2), myotilin, and T-cap. The early and robust upregulation of MuRF-1 is triggered by disuse, denervation, starvation, sepsis, or steroid administration resulting in skeletal muscle atrophy. It also plays a role in maintaining titin M-line integrity. It associates with the periphery of the M-line lattice and may be involved in the regulation of the titin kinase domain. It also participates in muscle stress response pathways and gene expression. MuRF-1 belongs to the C-II subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, and an acidic residue-rich (AR) domain. It also harbors a MURF family-specific conserved box (MFC) between its RING-HC finger and Bbox domains. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 43 matched cddid_all.tbl CDD cd19832 cd19832 380890 Bbox2_MuRF2_C-II B-box-type 2 zinc finger found in muscle-specific RING finger protein 2 (MuRF-2) and similar proteins. MuRF-2, also known as tripartite motif-containing protein 55 (TRIM55) or RING finger protein 29 (RNF29), is a muscle-specific E3 ubiquitin-protein ligase in ubiquitin-mediated muscle protein turnover and also a ligand of the transactivation domain of the serum response transcription factor (SRF). It is predominantly slow-fibre associated and highly expressed in embryonic skeletal muscle. MuRF-2 associates transiently with microtubules, myosin, and titin during sarcomere assembly. It has been implicated in microtubule, intermediate filament, and sarcomeric M-line maintenance in striated muscle development, as well as in signalling from the sarcomere to the nucleus. It plays an important role in the earliest stages of skeletal muscle differentiation and myofibrillogenesis. It is developmentally downregulated and is assembled at the M-line region of the sarcomere and with microtubules. MuRF-2 belongs to the C-II subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, and an acidic residue-rich (AR) domain. It also harbors a MURF family-specific conserved box (MFC) between its RING-HC finger and Bbox domains. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 45 matched cddid_all.tbl CDD cd19833 cd19833 380891 Bbox2_MuRF3_C-II B-box-type 2 zinc finger found in muscle-specific RING finger protein 3 (MuRF-3) and similar proteins. MuRF-3, also known as tripartite motif-containing protein 54 (TRIM54), or RING finger protein 30 (RNF30), is an E3 ubiquitin-protein ligase in ubiquitin-mediated muscle protein turnover. It is ubiquitously detected in all fibre types, and is developmentally upregulated, associates with microtubules, the sarcomeric M-line and Z-line, and is required for microtubule stability and myogenesis. It associates with glutamylated microtubules during skeletal muscle development, and is required for skeletal myoblast differentiation and development of cellular microtubular networks. MuRF-3 controls the degradation of four-and-a-half LIM domain (FHL2) and gamma-filamin and is required for maintenance of ventricular integrity after myocardial infarction (MI). MuRF-3 belongs to the C-II subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, and an acidic residue-rich (AR) domain. It also harbors a MURF family-specific conserved box (MFC) between its RING-HC finger and Bbox domains. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 43 matched cddid_all.tbl CDD cd19834 cd19834 380892 Bbox2_BSPRY B-box-type 2 zinc finger found in B box and SPRY domain-containing protein (BSPRY) and similar proteins. BSPRY is a regulatory protein for maintaining calcium homeostasis. It may regulate epithelial calcium transport by inhibiting TRPV5 activity. BSPRY is composed of a B-box, an alpha-helical coiled coil and a SPRY domain. The B-box motif shows high sequence similarity with B-Box-type zinc finger 2 found in tripartite motif-containing proteins (TRIMs). The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 43 matched cddid_all.tbl CDD cd19835 cd19835 380893 Bbox2_TRIM65_C-IV B-box-type 2 zinc finger found in tripartite motif-containing protein 65 (TRIM65) and similar proteins. TRIM65 is an E3 ubiquitin-protein ligase that interacts with the innate immune receptor MDA5 enhancing its ability to stimulate interferon-beta signaling. It functions as a potential oncogenic protein that negatively regulates p53 through ubiquitination, providing insight into development of novel approaches targeting TRIM65 for non-small cell lung carcinoma (NSCLC) treatment, and also overcoming chemotherapy resistance. Moreover, TRIM65 negatively regulates microRNA-driven suppression of mRNA translation by targeting TNRC6 proteins for ubiquitination and degradation. TRIM65 belongs to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox2, and a coiled coil region, as well as a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 42 matched cddid_all.tbl CDD cd19836 cd19836 380894 Bbox1_MID1_C-I B-box-type 1 zinc finger found in midline-1 (MID1) and similar proteins. MID1, also termed midin, or midline 1 RING finger protein, or putative transcription factor XPRF, or RING finger protein 59 (RNF59), or tripartite motif-containing protein 18 (TRI18), is a microtubule-associated E3 ubiquitin-protein ligase implicated in epithelial-mesenchymal differentiation, cell migration and adhesion, and programmed cell death along specific regions of the ventral midline during embryogenesis. It monoubiquinates the alpha4 subunit of protein phosphatase 2A (PP2A), promoting proteosomal degradation of the catalytic subunit of PP2A (PP2Ac) and preventing the A and B subunits from forming an active complex. It promotes allergen and rhinovirus-induced asthma through the inhibition of PP2A activity. It is strongly upregulated in cytotoxic lymphocytes (CTLs) and directs lytic granule exocytosis and cytotoxicity of killer T cells. Loss-of-function mutations in MID1 lead to the human X-linked Opitz G/BBB (XLOS) syndrome characterized by defective midline development during embryogenesis. MID1 belongs to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, the fibronectin type III domain and the SPRY/B30.2 domain positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. MID1 heterodimerizes in vitro with its paralog MID2. 50 matched cddid_all.tbl CDD cd19837 cd19837 380895 Bbox1_MID2_C-I B-box-type 1 zinc finger found in midline-2 (MID2) and similar proteins. MID2, also known as midin-2, midline defect 2, RING finger protein 60 (RNF60), or tripartite motif-containing protein 1 (TRIM1), is a probable E3 ubiquitin-protein ligase that is highly related to MID1, which associates with cytoplasmic microtubules along their length and throughout the cell cycle. Like MID1, MID2 associates with the microtubule network and may at least partially compensate for the loss of MID1. Both MID1 and MID2 interacts with alpha4, a regulatory subunit of PP2-type phosphatases, such as PP2A, and an integral component of the rapamycin-sensitive signaling pathway. MID2 can also substitute for MID1 to control exocytosis of lytic granules in cytotoxic T cells. Loss-of-function mutations in MID2 lead to human X-linked intellectual disability (XLID). MID2 belongs to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxy-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. MID2 heterodimerizes in vitro with its paralog MID1. 53 matched cddid_all.tbl CDD cd19838 cd19838 380896 Bbox1_TRIM8_C-V B-box-type 1 zinc finger found in tripartite motif-containing protein 8 (TRIM8) and similar proteins. TRIM8, also known as glioblastoma-expressed RING finger protein (GERP) or RING finger protein 27 (RNF27), is a probable E3 ubiquitin-protein ligase that may promote proteasomal degradation of suppressor of cytokine signaling 1 (SOCS1) and further regulate interferon-gamma signaling. It functions as a new p53 modulator that stabilizes p53, impairing its association with MDM2 and inducing the reduction of cell proliferation. TRIM8 deficit dramatically impairs p53 stabilization and activation in response to chemotherapeutic drugs. TRIM8 also modulates tumor necrosis factor-alpha (TNFalpha) and interleukin-1beta (IL-1beta)-triggered nuclear factor-kappaB (NF-kappa B) activation by targeting transforming growth factor beta (TGFbeta) activated kinase 1 (TAK1) for K63-linked polyubiquitination. Moreover, TRIM8 modulates translocation of phosphorylated STAT3 into the nucleus through interaction with Hsp90beta and consequently regulates transcription of Nanog in embryonic stem cells. It also interacts with protein inhibitor of activated STAT3 (PIAS3), which inhibits IL-6-dependent activation of STAT3. TRIM8 belongs to the C-V subclass of nuclear TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil domain, as well as an uncharacterized region positioned C-terminal to the RBCC domain. The coiled coil domain is required for homodimerization and the region immediately C-terminal to the RING motif is sufficient to mediate the interaction with SOCS1. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 48 matched cddid_all.tbl CDD cd19839 cd19839 380897 Bbox1_TRIM16 B-box-type 1 zinc finger found in tripartite motif-containing protein 16 (TRIM16) and similar proteins. TRIM16, also termed estrogen-responsive B box protein (EBBP), is a regulator that may play a role in the regulation of keratinocyte differentiation. It may also act as a tumor suppressor by affecting cell proliferation and migration or tumorigenicity in carcinogenesis. TRIM16 belongs to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 46 matched cddid_all.tbl CDD cd19840 cd19840 380898 Bbox1_TRIM29 B-box-type 1 zinc finger found in tripartite motif-containing protein 29 (TRIM29) and similar proteins. TRIM29, also termed ataxia telangiectasia group D-associated protein (ATDC), plays a crucial role in the regulation of macrophage activation in response to viral or bacterial infections within the respiratory tract. TRIM29 belongs to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 47 matched cddid_all.tbl CDD cd19841 cd19841 380899 Bbox1_TRIM44 B-box-type 1 zinc finger found in tripartite motif-containing protein 44 (TRIM44) and similar proteins. TRIM44, also termed protein DIPB, functions as a critical regulator in tumor metastasis and progression. TRIM44 belongs to an unclassified TRIM (tripartite motif) family of proteins that do not have RING fingers and thus lack the characteristic tripartite (RING (R), B-box, and coiled coil (CC)) RBCC motif. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif; this family contains a modified motif, C5H3. 46 matched cddid_all.tbl CDD cd19842 cd19842 380900 Bbox1_TRIM25-like_C-IV B-box-type 1 zinc finger found in tripartite motif-containing proteins, TRIM25, TRIM47 and similar proteins. The family includes tripartite motif-containing proteins, TRIM25 and TRIM47, both of which belong to the C-IV subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a SPRY/B30.2 domain positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TRIM25, also termed estrogen-responsive finger protein (EFP), or ubiquitin/ISG15-conjugating enzyme TRIM25, or zinc finger protein 147 (ZNF147), or E3 ubiquitin/ISG15 ligase TRIM25, is induced by estrogen and is particularly abundant in placenta and uterus. It has been implicated in cell proliferation, protein modification, and the retinoic acid inducible gene I (RIG-I)-mediated antiviral signaling pathway. It functions as an E3-ubiquitin ligase able to transfer ubiquitin and ISG15 to target proteins. TRIM47, also known as gene overexpressed in astrocytoma protein (GOA) or RING finger protein 100 (RNF100), plays an important role in the process of dedifferentiation that is associated with astrocytoma tumorigenesis. 49 matched cddid_all.tbl CDD cd19843 cd19843 380901 Bbox1_TRIM9_C-I B-box-type 1 zinc finger found in tripartite motif-containing protein 9 (TRIM9) and similar proteins. TRIM9 (the human ortholog of rat Spring), also termed RING finger protein 91 (RNF91), is a brain-specific E3 ubiquitin-protein ligase collaborating with an E2 ubiquitin conjugating enzyme UBCH5b. TRIM9 plays an important role in the regulation of neuronal functions and participates in neurodegenerative disorders through its ligase activity. It interacts with the WD repeat region of beta-transducer repeat-containing protein (beta-TCP) through its N-terminal degron motif depending on the phosphorylation status, and thus negatively regulate nuclear factor-kappaB (NF-kappaB) activation in the NF-kappaB pro-inflammatory signaling pathway. Moreover, TRIM9 acts as a critical catalytic link between Netrin-1 and exocytosis soluble NSF attachment receptor protein (SNARE) machinery in murine cortical neurons. It promotes SNARE-mediated vesicle fusion and axon branching in a Netrin-dependent manner. TRIM9 belongs to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, the fibronectin type III domain and the SPRY/B30.2 domain positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 47 matched cddid_all.tbl CDD cd19844 cd19844 380902 Bbox1_TRIM67_C-I B-box-type 1 zinc finger found in tripartite motif-containing protein 67 (TRIM67) and similar proteins. TRIM67, also termed TRIM9-like protein (TNL), is a protein selectively expressed in the cerebellum. It interacts with PRG-1, an important molecule in the control of hippocampal excitability dependent on presynaptic LPA2 receptor signaling, and 80K-H (also known as glucosidase II beta), a protein kinase C substrate. It negatively regulates Ras signaling in cell proliferation via degradation of 80K-H, leading to neural differentiation including neuritogenesis. TRIM67 belongs to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, the fibronectin type III domain and the SPRY/B30.2 domain positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 49 matched cddid_all.tbl CDD cd19845 cd19845 380903 Bbox1_TIF1a_C-VI B-box-type 1 zinc finger found in transcription intermediary factor 1-alpha (TIF1-alpha). TIF1-alpha, also known as tripartite motif-containing protein 24 (TRIM24), E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1-alpha interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoic X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta), and MOD2 (HP1gamma), as well as the vertebrate Kruppel-type (C2H2) zinc finger proteins that contain the transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53, and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal PHD-Bromo region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development. 45 matched cddid_all.tbl CDD cd19846 cd19846 380904 Bbox1_TIF1b_C-VI B-box-type 1 zinc finger found in transcription intermediary factor 1-beta (TIF1-beta). TIF1-beta, also known as Kruppel-associated Box (KRAB)-associated protein 1 (KAP-1), KRAB-interacting protein 1 (KRIP-1), nuclear co-repressor KAP-1, RING finger protein 96, tripartite motif-containing protein 28 (TRIM28), or E3 SUMO-protein ligase TRIM28, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1-beta/KAP-1 acts as a nuclear co-repressor that plays a role in transcription and in the DNA damage response. Upon DNA damage, the phosphorylation of KAP-1 on serine 824 by the ataxia telangiectasia-mutated (ATM) kinase enhances cell survival and facilitates chromatin relaxation and heterochromatic DNA repair. It also regulates CHD3 nucleosome remodeling during the DNA double-strand break (DSB) response. Meanwhile, KAP-1 can be dephosphorylated by protein phosphatase PP4C in the DNA damage response. Moreover, KAP-1 is a co-activator of the orphan nuclear receptor NGFI-B (or Nur77) and is involved in NGFI-B-dependent transcription. It is also a coiled-coil binding partner, substrate and activator of the c-Fes protein tyrosine kinase. The N-terminal RBCC domains of TIF1-beta are responsible for the interaction with KRAB zinc finger proteins (KRAB-ZFPs), MDM2, MM1, C/EBPbeta, and the regulation of homo- and heterodimerization. The C-terminal PHD/Bromo domains are involved in interacting with SETDB1, Mi-2alpha and other proteins to form complexes with histone deacetylase or methyltransferase activity. 52 matched cddid_all.tbl CDD cd19847 cd19847 380905 Bbox1_TIF1g_C-VI B-box-type 1 zinc finger found in transcriptional intermediary factor 1 gamma (TIF1-gamma). TIF1-gamma, also known as tripartite motif-containing 33 (TRIM33), ectodermin, RFG7, or PTC7, belongs to the C-VI subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a plant homeodomain (PHD), and a bromodomain (Bromo) positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. TIF1-gamma is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling. It inhibits the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1-gamma is an important regulator of transcription during hematopoiesis, as well as a key actor of tumorigenesis. Like other TIF1 family members, TIF1-gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis. 54 matched cddid_all.tbl CDD cd19848 cd19848 380906 Bbox1_TRIM36_C-I B-box-type 1 zinc finger found in tripartite motif-containing protein 36 (TRIM36) and similar proteins. TRIM36, the human ortholog of mouse Haprin, also known as RING finger protein 98 (RNF98) or zinc-binding protein Rbcc728, is an E3 ubiquitin-protein ligase expressed in the germ plasm. It has been implicated in acrosome reaction, fertilization, and embryogenesis, as well as in carcinogenesis. TRIM36 functions upstream of Wnt/beta-catenin activation, and plays a role in controlling the stability of proteins regulating microtubule polymerization during cortical rotation, and subsequent dorsal axis formation. It is also potentially associated with chromosome segregation by interacting with the kinetochore protein centromere protein-H (CENP-H), and colocalizing with the microtubule protein alpha-tubulin. Its overexpression may cause chromosomal instability and carcinogenesis. It is, thus, a novel regulator affecting cell cycle progression. Moreover, TRIM36 plays a critical role in the arrangement of somites during embryogenesis. TRIM36 belongs to the C-I subclass of TRIM (tripartite motif) family of proteins that are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 55 matched cddid_all.tbl CDD cd19849 cd19849 380907 Bbox1_TRIM46_C-I B-box-type 1 zinc finger found in tripartite motif-containing protein 46 (TRIM46) and similar proteins. TRIM46, also known as gene Y protein (GeneY) or tripartite, fibronectin type-III and C-terminal SPRY motif protein (TRIFIC), is a microtubule-associated protein that specifically localizes to the proximal axon, partly overlaps with the axon initial segment (AIS) at later stages, and organizes uniform microtubule orientation in axons. It controls neuronal polarity and axon specification by driving the formation of parallel microtubule arrays. TRIM46 belongs to the C-I subclass of TRIM (tripartite motif) family of proteins, which are defined by their N-terminal RBCC (RING, Bbox, and coiled coil) domains, including three consecutive zinc-binding domains, a RING finger, Bbox1 and Bbox2, and a coiled coil region, as well as a COS (carboxyl-terminal subgroup one signature) box, a fibronectin type III (FN3) domain, and a B30.2/SPRY (SplA and ryanodine receptor) domain positioned C-terminal to the RBCC domain. The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 52 matched cddid_all.tbl CDD cd19851 cd19851 381251 lipocalin_CHL chloroplastic lipocalin(CHL) similar to Arabidopsis CHL. Chloroplastic lipocalin (CHL) prevents thylakoidal membrane lipids peroxidation and is protective against oxidative stress, especially mediated by singlet oxygen in response to excess light and other stress (e.g. heat shocks). CHL is required for seed longevity. This group belongs to the lipocalin/cytosolic fatty-acid binding protein family which have a large beta-barrel ligand-binding cavity. Lipocalins are mainly low molecular weight extracellular proteins that bind principally small hydrophobic ligands, and form covalent or non-covalent complexes with soluble macromolecules, as well as membrane bound-receptors. They participate in processes such as ligand transport, modulation of cell growth and metabolism, regulation of immune response, smell reception, tissue development and animal behavior. Cytosolic fatty-acid binding proteins, also bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 141 matched cddid_all.tbl CDD cd19852 cd19852 381252 FABP_pancrustacea fatty acid-binding protein similar to Locusta migratoria FABP (Lm-FABP). This subfamily includes fatty acid-binding protein found mainly in insects such as the migratory locust (Locusta migratoria) FABP (Lm-FABP) and the desert locust (Schistocerca gregaria) FABP (Sg-FABP), having flight muscle tissues that contain unusually high levels FABP, similar to migratory birds. Both Sg- and Lm-FABP are closely related to the mammalian i-LBP subfamily IV, especially to the heart and adipocyte FABP forms. This subgroup belongs to the intracellular fatty-acid binding protein (FABP) family, members of which are small proteins that bind hydrophobic ligands in a non-covalent, reversible manner, and have been implicated in intracellular uptake, transport and storage of hydrophobic ligands, regulation of lipid metabolism and sequestration of excess toxic fatty acids, as well as in signaling, gene expression, inflammation, cell growth and proliferation, and cancer development. 128 matched cddid_all.tbl CDD cd19854 cd19854 380683 DSRM_DHX9_rpt1 first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins. DHX9 (EC 3.6.4.13; also known as ATP-dependent RNA helicase A, DExH-box helicase 9 (DDX9), Leukophysin (LKP), nuclear DNA helicase II (NDH II), NDH2, or RNA helicase A) is a multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation, and RNA-mediated gene silencing. It contains two double-stranded RNA binding motifs (DSRMs) at the N-terminal region. This model corresponds to the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 69 matched cddid_all.tbl CDD cd19855 cd19855 380684 DSRM_DHX9_rpt2 second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins. DHX9 (EC 3.6.4.13; also known as ATP-dependent RNA helicase A, DExH-box helicase 9 (DDX9), Leukophysin (LKP), nuclear DNA helicase II (NDH II), NDH2, or RNA helicase A) is a multifunctional ATP-dependent nucleic acid helicase that unwinds DNA and RNA in a 3' to 5' direction and plays important roles in many processes, such as DNA replication, transcriptional activation, post-transcriptional RNA regulation, mRNA translation and RNA-mediated gene silencing. It contains two double-stranded RNA binding motifs (DSRMs) at the N-terminal region. This model corresponds to the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 75 matched cddid_all.tbl CDD cd19856 cd19856 380685 DSRM_Kanadaptin double-stranded RNA binding motif of Kanadaptin and similar proteins. Kanadaptin (also known as human lung cancer oncogene 3 protein (HLC-3), kidney anion exchanger adapter protein, or solute carrier family 4 anion exchanger member 1 adapter protein (SLC4A1AP)) is a nuclear protein widely expressed in mammalian tissues. It was originally isolated as a kidney Cl-/HCO3- anion exchanger 1 (kAE1)-binding protein. It is a highly mobile nucleocytoplasmic shuttling and multilocalizing protein. Its role in mammalian cells remains unclear. The double-stranded RNA binding motif (DSRM) is not sequence specific, but highly specific for dsRNAs of various origin and structure. 86 matched cddid_all.tbl CDD cd19857 cd19857 380686 DSRM_STAU_rpt1 first double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins. Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 64 matched cddid_all.tbl CDD cd19858 cd19858 380687 DSRM_STAU_rpt2 second double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins. Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 67 matched cddid_all.tbl CDD cd19859 cd19859 380688 DSRM_STAU_rpt3 third double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins. Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 65 matched cddid_all.tbl CDD cd19860 cd19860 380689 DSRM_STAU_rpt4 fourth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins. Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 68 matched cddid_all.tbl CDD cd19861 cd19861 380690 DSRM_STAU_rpt5 fifth double-stranded RNA binding motif of Drosophila melanogaster maternal effect protein Staufen and similar proteins. Staufen is a double-stranded RNA binding protein required both for the localization of maternal determinants to the posterior pole of the egg, oskar (osk) RNA, and for correct localization to the anterior pole, anchoring bicoid (bcd) RNA. The family also includes two Staufen homologs from vertebrates, Staufen 1 and Staufen 2. They are present in distinct ribonucleoprotein complexes and associate with different mRNAs. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen proteins contain five double-stranded RNA binding motifs (DSRMs). This model describes the fifth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 68 matched cddid_all.tbl CDD cd19862 cd19862 380691 DSRM_PRKRA-like_rpt1 first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins. This family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)), participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. This family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 70 matched cddid_all.tbl CDD cd19863 cd19863 380692 DSRM_PRKRA-like_rpt2 second double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins. The family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)) participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. The family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 67 matched cddid_all.tbl CDD cd19864 cd19864 380693 DSRM_PRKRA-like_rpt3 third double-stranded RNA binding motif of PRKRA, TARBP2 and similar proteins. The family includes protein activator of the interferon-induced protein kinase (PRKRA) and the RISC-loading complex subunit TARBP2. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. TARBP2 (also called TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)) participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. The family also includes Drosophila melanogaster Loquacious and similar proteins. Loquacious (Loqs) is a double-stranded RNA-binding domain (dsRBD) protein, a homolog of human TAR RNA binding protein (TRBP) that is a protein first identified as binding the HIV trans-activator RNA (TAR). Loqs interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. PRKRA family proteins contain three double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 72 matched cddid_all.tbl CDD cd19865 cd19865 380694 DSRM_STRBP_RED-like_rpt1 first double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins. This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3), as well as two RNA-editing deaminases, RED1 and RED2. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. RED1 (EC 3.5.4.37; also called double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. RED2 (also called double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA, but also to ssRNA. RED2 lacks editing activity for currently known substrate RNAs. Members of this group contain two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 63 matched cddid_all.tbl CDD cd19866 cd19866 380695 DSRM_STRBP_RED-like_rpt2 second double-stranded RNA binding motif of STRBP, ILF3, RED1, RED2 and similar proteins. This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3), as well as two RNA-editing deaminases, RED1 and RED2. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. RED1 (EC 3.5.4.37; also called double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. RED2 (also called double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA but also to ssRNA. RED2 lacks editing activity for currently known substrate RNAs. Members of this group contain two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 63 matched cddid_all.tbl CDD cd19867 cd19867 380696 DSRM_DGCR8_rpt1 first double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and similar proteins. DGCR8 is a component of the microprocessor complex that acts as an RNA- and heme-binding protein that is involved in the initial step of microRNA (miRNA) biogenesis. Within the microprocessor complex, DGCR8 functions as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs DROSHA to cleave 11bp away from the junction to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. DGCR8 contains two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 74 matched cddid_all.tbl CDD cd19868 cd19868 380697 DSRM_DGCR8_rpt2 second double-stranded RNA binding motif of DiGeorge syndrome critical region 8 (DGCR8) and similar proteins. DGCR8 is a component of the microprocessor complex that acts as an RNA- and heme-binding protein that is involved in the initial step of microRNA (miRNA) biogenesis. Within the microprocessor complex, DGCR8 functions as a molecular anchor necessary for the recognition of pri-miRNA at dsRNA-ssRNA junction and directs DROSHA to cleave 11bp away from the junction to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. DGCR8 contains two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 69 matched cddid_all.tbl CDD cd19869 cd19869 380698 DSRM_DCL_plant double-stranded RNA binding motif of plant Dicer-like proteins. The family includes plant Dicer-like (DCL) proteins and other ribonuclease (RNase) III-like (RTL) proteins. DCLs are endoribonucleases involved in RNA-mediated post-transcriptional gene silencing (PTGS). They function in the microRNA (miRNA) biogenesis pathway by cleaving primary miRNAs (pri-miRNAs) and precursor miRNAs (pre-miRNAs). Family members contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 70 matched cddid_all.tbl CDD cd19870 cd19870 380699 DSRM_SON-like double-stranded RNA binding motif of protein SON and similar proteins. Protein SON (also known as Bax antagonist selected in saccharomyces 1 (BASS1), negative regulatory element-binding protein (NRE-binding protein), or protein DBP-5, or SON3) is an RNA-binding protein which acts as an mRNA splicing cofactor by promoting efficient splicing of transcripts that possess weak splice sites. It specifically promotes splicing of many cell-cycle and DNA-repair transcripts that possess weak splice sites, such as TUBG1, KATNB1, TUBGCP2, AURKB, PCNT, AKT1, RAD23A, and FANCG. Members of this group contain a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 75 matched cddid_all.tbl CDD cd19871 cd19871 380700 DSRM_DUS2L double-stranded RNA binding motif of tRNA-dihydrouridine(20) synthase [NAD(P)+]-like (DUS2L) and similar proteins. DUS2L (also known as dihydrouridine synthase 2 (DUS2), up-regulated in lung cancer protein 8 (URLC8), or tRNA-dihydrouridine synthase 2-like) catalyzes the synthesis of dihydrouridine, a modified base found in the D-loop of most tRNAs. It negatively regulates the activation of EIF2AK2/PKR. DUS2L contains an N-terminal FMN-binding domain and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure. 68 matched cddid_all.tbl CDD cd19872 cd19872 380701 DSRM_A1CF-like double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF), RNA-binding protein 46 (RBM46) and similar proteins. The family includes two dsRNA-binding motif-containing proteins, A1CF and RBM46. A1CF (also known as APOBEC1-stimulating protein) is an essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the posttranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. A1CF binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. RBM46 (also called cancer/testis antigen 68 (CT68), or RNA-binding motif protein 46) plays a novel role in the regulation of embryonic stem cell (ESC) differentiation by regulating the degradation of beta-catenin mRNA. It also regulates trophectoderm specification by stabilizing Cdx2 mRNA in early mouse embryos. Members of this family contain three RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure. 75 matched cddid_all.tbl CDD cd19873 cd19873 380702 DSRM_MRPL3_like double-stranded RNA binding motif of Saccharomyces cerevisiae mitochondrial 54S ribosomal protein L3 (MRPL3) and similar proteins. MRPL3 (also called mitochondrial large ribosomal subunit protein mL44) is a component of the mitochondrial ribosome (mitoribosome), a dedicated translation machinery responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. MRPL3 contains a RNase III-like domain and a double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 84 matched cddid_all.tbl CDD cd19874 cd19874 380703 DSRM_MRPL44 double-stranded RNA binding motif of mitochondrial 39S ribosomal protein L44 (MRPL44) and similar proteins. MRPL44 (also known as L44mt, MRP-L44, or mitochondrial large ribosomal subunit protein mL44) is a component of the 39S subunit of mitochondrial ribosome. It may play a role in the assembly/stability of nascent mitochondrial polypeptides exiting the ribosome. MRPL44 contains a RNase III-like domain and a double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 84 matched cddid_all.tbl CDD cd19875 cd19875 380704 DSRM_EIF2AK2-like double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins. The family includes EIF2AK2 and adenosine deaminase domain-containing proteins, ADAD1 and ADAD2. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. ADAD1 (also called testis nuclear RNA-binding protein (TENR)) and ADAD2 (also called testis nuclear RNA-binding protein-like (TENRL)) are phylogenetically related to a family of adenosine deaminases involved in RNA editing. ADAD1 plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD2 is a double-stranded RNA binding protein with unclear biological function. Members of this group contains varying numbers of double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 67 matched cddid_all.tbl CDD cd19876 cd19876 380705 DSRM_RNT1p-like double-stranded RNA binding motif of Saccharomyces cerevisiae ribonuclease 3 (RNT1p) and similar proteins. RNT1p (EC 3.1.26.3; also known as ribonuclease III (RNase III)) is a dsRNA-specific nuclease that cleaves eukaryotic pre-ribosomal RNA at the U3 snoRNP-dependent A0 site in the 5'-external transcribed spacer (ETS) and in the 3'-ETS. RNT1p contains a double-stranded RNA binding motif (DSRM) at the C-terminus. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 69 matched cddid_all.tbl CDD cd19877 cd19877 380706 DSRM_RNAse_III_meta_like double-stranded RNA binding motif of metazoan ribonuclease III (RNase III) and similar proteins. RNase III (EC 3.1.26.3; also known as Drosha, or ribonuclease 3) is a double-stranded RNA (dsRNA)-specific endoribonuclease that is involved in the initial step of microRNA (miRNA) biogenesis. It is a component of the microprocessor complex that is required to process primary miRNA transcripts (pri-miRNAs) to release precursor miRNA (pre-miRNA) in the nucleus. Within the microprocessor complex, RNase III cleaves the 3' and 5' strands of a stem-loop in pri-miRNAs (processing center 11 bp from the dsRNA-ssRNA junction) to release hairpin-shaped pre-miRNAs that are subsequently cut by the cytoplasmic DICER to generate mature miRNAs. It is also involved in pre-rRNA processing. Metazoan RNase III is a larger protein than bacterial RNase III. It contains two RNase III domains in the C-terminal half of the protein followed by a double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 75 matched cddid_all.tbl CDD cd19878 cd19878 380707 DSRM_AtDRB-like double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRBs)and similar proteins. This family includes a group of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRB1-5). They bind double-stranded RNA (dsRNA) and may be involved in RNA-mediated silencing. Members of this family contain two to three double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 67 matched cddid_all.tbl CDD cd19879 cd19879 380708 DSRM_STAU1_rpt1 first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 66 matched cddid_all.tbl CDD cd19880 cd19880 380709 DSRM_STAU2_rpt1 first double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 2 (Staufen 2) and similar proteins. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen 2 contains five double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 68 matched cddid_all.tbl CDD cd19881 cd19881 380710 DSRM_STAU1_rpt2 second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 79 matched cddid_all.tbl CDD cd19882 cd19882 380711 DSRM_STAU2_rpt2 second double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 2 (Staufen 2) and similar proteins. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen 2 contains five double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 82 matched cddid_all.tbl CDD cd19883 cd19883 380712 DSRM_STAU1_rpt3 third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 67 matched cddid_all.tbl CDD cd19884 cd19884 380713 DSRM_STAU2_rpt3 third double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 2 (Staufen 2) and similar proteins. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen 2 contains five double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 67 matched cddid_all.tbl CDD cd19885 cd19885 380714 DSRM_STAU1_rpt4 fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 86 matched cddid_all.tbl CDD cd19886 cd19886 380715 DSRM_STAU2_rpt4 fourth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 2 (Staufen 2) and similar proteins. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen 2 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fourth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 86 matched cddid_all.tbl CDD cd19887 cd19887 380716 DSRM_STAU1_rpt5 fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 1 (Staufen 1) and similar proteins. Staufen 1 may play a role in specific positioning of mRNAs at given sites in the cell by cross-linking cytoskeletal and RNA components, and in stimulating their translation at the site. It binds double-stranded RNA (regardless of the sequence) and tubulin. Staufen 1 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fifth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 70 matched cddid_all.tbl CDD cd19888 cd19888 380717 DSRM_STAU2_rpt5 fifth double-stranded RNA binding motif of double-stranded RNA-binding protein Staufen homolog 2 (Staufen 2) and similar proteins. Staufen 2 is an RNA-binding protein required for the microtubule-dependent transport of neuronal RNA from the cell body to the dendrite. Staufen 2 contains five double-stranded RNA binding motifs (DSRMs). This model describes the fifth motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 68 matched cddid_all.tbl CDD cd19889 cd19889 380718 DSRM_PRKRA_rpt1 first double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. PRKRA contains three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 71 matched cddid_all.tbl CDD cd19890 cd19890 380719 DSRM_TARBP2_rpt1 first double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar proteins. TARBP2 (also known as TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)), participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. TARBP2 contains three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 72 matched cddid_all.tbl CDD cd19891 cd19891 380720 DSRM_PRKRA_rpt2 second double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. PRKRA contains three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 67 matched cddid_all.tbl CDD cd19892 cd19892 380721 DSRM_PRKRA_rpt3 third double-stranded RNA binding motif of protein activator of the interferon-induced protein kinase (PRKRA) and similar proteins. PRKRA (also known as interferon-inducible double-stranded RNA-dependent protein kinase activator A, PKR-associated protein X (RAX), PKR-associating protein X, protein kinase, interferon-inducible double-stranded RNA-dependent activator, PACT, or HSD14) is a cellular activator for double-stranded RNA-dependent protein kinase during stress signaling. PRKRA contains three double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 72 matched cddid_all.tbl CDD cd19893 cd19893 380722 DSRM_TARBP2_rpt3 third double-stranded RNA binding motif of the RISC-loading complex subunit TARBP2 and similar proteins. TARBP2 (also known as TAR RNA-binding protein 2, or trans-activation-responsive RNA-binding protein (TRBP)) participates in the formation of the RNA-induced silencing complex (RISC). It is part of the RISC-loading complex (RLC), together with dicer1 and eif2c2/ago2, and is required to process precursor miRNAs. TARBP2 contains three double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 72 matched cddid_all.tbl CDD cd19894 cd19894 380723 DSRM_STRBP-like_rpt1 first double-stranded RNA binding motif of STRBP, ILF3 and similar proteins. This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3). STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. Members of this STRBP/ILF3 group contain an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 63 matched cddid_all.tbl CDD cd19895 cd19895 380724 DSRM_RED1_rpt1 first double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins. RED1 (EC 3.5.4.37; also known as double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. It contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the first DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 72 matched cddid_all.tbl CDD cd19896 cd19896 380725 DSRM_RED2_rpt1 first double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar proteins. RED2 (also known as double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA but also to ssRNA. RED2 contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the first DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. RED2 lacks editing activity for currently known substrate RNAs, and may have an inactive editase domain. 74 matched cddid_all.tbl CDD cd19897 cd19897 380726 DSRM_STRBP-like_rpt2 second double-stranded RNA binding motif of STRBP, ILF3 and similar proteins. This family includes spermatid perinuclear RNA-binding protein (STRBP) and interleukin enhancer-binding factor 3 (ILF3). STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. Members of this STRBP/ILF3 group contain an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 64 matched cddid_all.tbl CDD cd19898 cd19898 380727 DSRM_RED1_rpt2 second double-stranded RNA binding motif of RNA-editing deaminase 1 (RED1) and similar proteins. RED1 (EC 3.5.4.37; also known as double-stranded RNA-specific editase 1, RNA-editing enzyme 1, dsRNA adenosine deaminase, ADARB1, ADAR2, or DRADA2) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. It contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the second DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 70 matched cddid_all.tbl CDD cd19899 cd19899 380728 DSRM_RED2_rpt2 second double-stranded RNA binding motif of RNA-editing deaminase 2 (RED2) and similar proteins. RED2 (also known as double-stranded RNA-specific editase B2, RNA-dependent adenosine deaminase 3, RNA-editing enzyme 2, dsRNA adenosine deaminase B2, ADAR3, or ADARB2) prevents the binding of other ADAR enzymes to targets in vitro, and decreases the efficiency of these enzymes. It is capable of binding to dsRNA but also to ssRNA. RED2 contains two double-stranded RNA binding motifs (DSRMs) and a C-terminal RNA-specific adenosine-deaminase (editase) domain. This model describes the second DSRM. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. RED2 lacks editing activity for currently known substrate RNAs, and may have an inactive editase domain. 74 matched cddid_all.tbl CDD cd19900 cd19900 380729 DSRM_A1CF double-stranded RNA binding motif of APOBEC1 complementation factor (A1CF) and similar proteins. A1CF (also known as APOBEC1-stimulating protein) is an essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the posttranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. A1CF binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. It contains three RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure. 81 matched cddid_all.tbl CDD cd19901 cd19901 380730 DSRM_RBM46 double-stranded RNA binding motif of RNA-binding protein 46 (RBM46) and similar proteins. RBM46 (also known as cancer/testis antigen 68 (CT68), or RNA-binding motif protein 46) plays a novel role in the regulation of embryonic stem cell (ESC) differentiation by regulating the degradation of beta-catenin mRNA. It also regulates trophectoderm specification by stabilizing Cdx2 mRNA in early mouse embryos. RBM46 contains three RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure. 78 matched cddid_all.tbl CDD cd19902 cd19902 380731 DSRM_DRADA double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins. DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. DRADA family members contain at least one double-stranded RNA binding motifs (DSRM); vertebrate proteins contain three. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 71 matched cddid_all.tbl CDD cd19903 cd19903 380732 DSRM_EIF2AK2_rpt1 first double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. EIF2AK2 proteins contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 68 matched cddid_all.tbl CDD cd19904 cd19904 380733 DSRM_EIF2AK2_rpt2 second double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. EIF2AK2 proteins contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 69 matched cddid_all.tbl CDD cd19905 cd19905 380734 DSRM_ADAD1 double-stranded RNA binding motif of adenosine deaminase domain-containing protein 1 (ADAD1) and similar proteins. ADAD1 (also known as testis nuclear RNA-binding protein (TENR)) is phylogenetically related to a family of adenosine deaminases involved in RNA editing. It plays an essential function in spermatid morphogenesis. It may be involved in testis-specific nuclear post-transcriptional processes such as heterogeneous nuclear RNA (hnRNA) packaging, alternative splicing, or nuclear/cytoplasmic transport of mRNAs. ADAD1 contains a double-stranded RNA binding motif (DSRM) and a C-terminal adenosine-deaminase (editase) domain. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 69 matched cddid_all.tbl CDD cd19906 cd19906 380735 DSRM_ADAD2 double-stranded RNA binding motif of adenosine deaminase domain-containing protein 2 (ADAD2) and similar proteins. ADAD2 (also known as testis nuclear RNA-binding protein-like (TENRL)) is phylogenetically related to a family of adenosine deaminases involved in RNA editing. It is a double-stranded RNA binding protein with unclear biological function. ADAD2 contains a double-stranded RNA binding motif (DSRM) and a C-terminal adenosine-deaminase (editase) domain. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 74 matched cddid_all.tbl CDD cd19907 cd19907 380736 DSRM_AtDRB-like_rpt1 first double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRBs)and similar proteins. This family includes a group of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRB1-5). They bind double-stranded RNA (dsRNA) and may be involved in RNA-mediated silencing. Members of this family contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 69 matched cddid_all.tbl CDD cd19908 cd19908 380737 DSRM_AtDRB-like_rpt2 second double-stranded RNA binding motif of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRBs)and similar proteins. This family includes a group of Arabidopsis thaliana double-stranded RNA-binding proteins (AtDRB1-5). They bind double-stranded RNA (dsRNA) and may be involved in RNA-mediated silencing. Members of this family contain two to three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 69 matched cddid_all.tbl CDD cd19909 cd19909 380738 DSRM_STRBP_rpt1 first double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) and similar proteins. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. STRBP contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 84 matched cddid_all.tbl CDD cd19910 cd19910 380739 DSRM_ILF3_rpt1 first double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and similar proteins. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. ILF3 contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 73 matched cddid_all.tbl CDD cd19911 cd19911 380740 DSRM_STRBP_rpt2 second double-stranded RNA binding motif of spermatid perinuclear RNA-binding protein (STRBP) and similar proteins. STRBP is a double-stranded DNA and RNA binding protein that is involved in spermatogenesis and sperm function. It plays a role in regulation of cell growth. STRBP contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 64 matched cddid_all.tbl CDD cd19912 cd19912 380741 DSRM_ILF3_rpt2 second double-stranded RNA binding motif of interleukin enhancer-binding factor 3 (ILF3) and similar proteins. ILF3 (also known as double-stranded RNA-binding protein 76 (DRBP76), M-phase phosphoprotein 4 (MPP4), nuclear factor associated with dsRNA (NFAR), nuclear factor of activated T-cells 90 kDa (NF-AT-90), or translational control protein 80 (TCP80)) is an RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. ILF3 contains an N-terminal DZF domain and two double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 72 matched cddid_all.tbl CDD cd19913 cd19913 380742 DSRM_DRADA_rpt1 first double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA). DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA contains three double-stranded RNA binding motifs (DSRMs). This model describes the first motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 71 matched cddid_all.tbl CDD cd19914 cd19914 380743 DSRM_DRADA_rpt2 second double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins. DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA contains three double-stranded RNA binding motifs (DSRMs). This model describes the second motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 71 matched cddid_all.tbl CDD cd19915 cd19915 380744 DSRM_DRADA_rpt3 third double-stranded RNA binding motif of double-stranded RNA-specific adenosine deaminase (DRADA) and similar proteins. DRADA (EC 3.5.4.37; also known as 136 kDa double-stranded RNA-binding protein (p136), interferon-inducible protein 4 (IFI-4), K88DSRBP, ADAR1, G1P1, or ADAR) catalyzes the hydrolytic deamination of adenosine to inosine in double-stranded RNA (dsRNA), referred to as A-to-I RNA editing. Vertebrate DRADA contains three double-stranded RNA binding motifs (DSRMs). This model describes the third motif. DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 71 matched cddid_all.tbl CDD cd19916 cd19916 381179 OphMA_like tetrapyrrole methylase family protein similar to Omphalotus olearius omphalotin methyltransferase (OphMA) and Dendrothele bispora dbOphMA. OphMA, is the precursor protein of the fungal cyclic peptide Omphalotin A. Omphalotin A is a potent nematicide, having 9 out of 12 of its residues methylated at the backbone amide. Omphalotin A derives from the C-terminus of OphMA (also known as OphA). OphMA catalyzes the automethylation of its own C-terminus using S-adenosyl methionine (SAM); this C terminus is subsequently released and macrocyclized by the protease OphP to give Omphalotin A. 237 matched cddid_all.tbl CDD cd19917 cd19917 381180 RsmI_like tetrapyrrole methylase family protein similar to ribosomal RNA small subunit methyltransferase I (RsmI). RsmI, also known as rRNA (cytidine-2'-O-)-methyltransferase, is an S-AdoMet (S-adenosyl-L-methionine or SAM)-dependent methyltransferase responsible for the 2'-O-methylation of cytidine 1402 (C1402) at the P site of bacterial 16S rRNA. Another S-AdoMet-dependent methyltransferase, RsmH (not included in this family), is responsible for N4-methylation at C1402. These methylation reactions may occur at a late step during 30S assembly in the cell. The dimethyl modification is believed to be conserved in bacteria, may play a role in fine-tuning the shape and functions of the P-site to increase the translation fidelity, and has been shown for Staphylococcus aureus, to contribute to virulence in host animals by conferring resistance to oxidative stress. 217 matched cddid_all.tbl CDD cd19918 cd19918 381181 RsmI_like uncharacterized subfamily of the tetrapyrrole methylase family similar to Ribosomal RNA small subunit methyltransferase I (RsmI). RsmI, also known as rRNA (cytidine-2'-O-)-methyltransferase, is an S-AdoMet (S-adenosyl-L-methionine or SAM)-dependent methyltransferase responsible for the 2'-O-methylation of cytidine 1402 (C1402) at the P site of bacterial 16S rRNA. Another S-AdoMet-dependent methyltransferase, RsmH (not included in this family), is responsible for N4-methylation at C1402. These methylation reactions may occur at a late step during 30S assembly in the cell. The dimethyl modification is believed to be conserved in bacteria, may play a role in fine-tuning the shape and functions of the P-site to increase the translation fidelity, and has been shown for Staphylococcus aureus, to contribute to virulence in host animals by conferring resistance to oxidative stress. 217 matched cddid_all.tbl CDD cd19919 cd19919 381146 REC_NtrC phosphoacceptor receiver (REC) domain of DNA-binding transcriptional regulator NtrC. DNA-binding transcriptional regulator NtrC is also called nitrogen regulation protein NR(I) or nitrogen regulator I (NRI). It contains an N-terminal receiver (REC) domain, followed by a sigma-54 interaction domain, and a C-terminal helix-turn-helix DNA-binding domain. It is part of the two-component regulatory system NtrB/NtrC, which controls expression of the nitrogen-regulated (ntr) genes in response to nitrogen limitation. DNA-binding response regulator NtrC is phosphorylated by NtrB; phosphorylation of the N-terminal REC domain activates the central sigma-54 interaction domain and leads to the transcriptional activation from promoters that require sigma(54)-containing RNA polymerase. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 116 matched cddid_all.tbl CDD cd19920 cd19920 381147 REC_PA4781-like phosphoacceptor receiver (REC) domain of cyclic di-GMP phosphodiesterase PA4781 and similar domains. Pseudomonas aeruginosa cyclic di-GMP phosphodiesterase PA4781 contains an N-terminal REC domain and a C-terminal catalytic HD-GYP domain, characteristics of RpfG family response regulators. PA4781 is involved in cyclic di-3',5'-GMP (c-di-GMP) hydrolysis/degradation in a two-step reaction via the linear intermediate pGpG to produce GMP. Its unphosphorylated REC domain prevents accessibility of c-di-GMP to the active site. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 103 matched cddid_all.tbl CDD cd19921 cd19921 381148 REC_1_GGDEF first phosphoacceptor receiver (REC) domain of uncharacterized GGDEF domain proteins. This family is composed of uncharacterized PleD-like response regulators that contain two N-terminal REC domains and a C-terminal diguanylate cyclase output domain with the characteristic GGDEF motif at the active site. Unlike PleD which contains a REC-like adaptor domain, the second REC domain of these uncharacterized GGDEF domain proteins contains characteristic metal-binding and active site residues. PleD response regulators are global regulators of cell metabolism in some important human pathogens. This model describes the first REC domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 115 matched cddid_all.tbl CDD cd19922 cd19922 381149 REC_RitR-like receiver (REC) domain of orphan response regulator RitR and similar domains. Streptococcus pneumoniae RitR (Repressor of iron transport Regulator, formerly RR489) is an orphan two-component signal transduction response regulator that is required for lung pathogenicity. It acts to repress iron uptake via binding the pneumococcal iron uptake (Piu) transporter promoter. Members of this subfamily contain REC and DNA-binding output domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. However, members of this family do not contain the phosphorylatable aspartic acid residue and are phosphorylation-independent. 110 matched cddid_all.tbl CDD cd19923 cd19923 381150 REC_CheY_CheY3 phosphoacceptor receiver (REC) domain of chemotaxis response regulator CheY3 and similar CheY family proteins. CheY family chemotaxis response regulators (RRs) comprise about 17% of bacterial RRs and almost half of all RRs in archaea. This subfamily contains Vibrio cholerae CheY3, Escherichia coli CheY, and similar CheY family RRs. CheY proteins control bacterial motility and participate in signaling phosphorelays and in protein-protein interactions. CheY RRs contain only the REC domain with no output/effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 119 matched cddid_all.tbl CDD cd19924 cd19924 381151 REC_CheV-like phosphoacceptor receiver (REC) domain of chemotaxis protein CheV and similar proteins. This subfamily includes the REC domains of Bacillus subtilis chemotaxis protein CheV, Myxococcus xanthus gliding motility regulatory protein FrzE, and similar proteins. CheV is a hybrid protein with an N-terminal CheW-like domain and a C-terminal CheY-like REC domain. The CheV pathway is one of three systems employed by B. subtilis for sensory adaptation that contribute to chemotaxis. It is involved in the transmission of sensory signals from chemoreceptors to flagellar motors. Together with CheW, it is involved in the coupling of methyl-accepting chemoreceptors to the central two-component histidine kinase CheA. FrzE is a hybrid sensor histidine kinase/response regulator that is part of the Frz pathway that controls cell reversal frequency to support directional motility during swarming and fruiting body formation. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 111 matched cddid_all.tbl CDD cd19925 cd19925 381152 REC_citrate_TCS phosphoacceptor receiver (REC) domain of citrate family two-component system response regulators. This family includes Lactobacillus paracasei MaeR, Escherichia coli DcuR and DpiA, Klebsiella pneumoniae CitB, as well as Bacillus DctR, MalR, and CitT. These are all response regulators of two-component systems (TCSs) from the citrate family, and are involved in the transcriptional regulation of genes associated with L-malate catabolism (MaeRK), citrate-specific fermentation (DpiAB, CitAB), plasmid inheritance (DpiAB), anaerobic fumarate respiratory system (DcuRS), and malate transport/utilization (MalKR). REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 118 matched cddid_all.tbl CDD cd19926 cd19926 381153 REC_PilR phosphoacceptor receiver (REC) domain of type 4 fimbriae expression regulatory protein PilR and similar proteins. Pseudomonas aeruginosa PilR is the response regulator of the PilS/PilR two-component regulatory system (PilSR TCS) that acts in conjunction with sigma-54 to regulate the expression of type 4 pilus (T4P) major subunit PilA. In addition, the PilSR TCS regulates flagellum-dependent swimming motility and pilus-dependent twitching motility. PilR contains an N-terminal REC domain, a central sigma-54 interaction domain, and a C-terminal Fis-type helix-turn-helix DNA-binding domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 100 matched cddid_all.tbl CDD cd19927 cd19927 381154 REC_Ycf29 phosphoacceptor receiver (REC) domain of probable transcriptional regulator Ycf29. Ycf29 is a probable response regulator of a two-component system (TCS), typically consisting a sensor and a response regulator, that functions in adaptation to changing environments. Processes regulated by TCSs in bacteria include sporulation, pathogenicity, virulence, chemotaxis, and membrane transport. Ycf29 contains an N-terminal REC domain and a LuxR-type helix-turn-helix DNA-binding output domain. REC domains function as phosphorylation-mediated switches within RRs, but some also transfer phosphoryl groups in multistep phosphorelays. 102 matched cddid_all.tbl CDD cd19928 cd19928 381155 REC_RcNtrC-like phosphoacceptor receiver (REC) domain of Rhodobacter capsulatus nitrogen regulatory protein C (NtrC) and similar NtrC family response regulators. NtrC family proteins are transcriptional regulators that have REC, AAA+ ATPase/sigma-54 interaction, and DNA-binding output domains. This subfamily of NtrC proteins include NtrC, also called nitrogen regulator I (NRI), from Rhodobacter capsulatus, Azospirillum brasilense, and Azorhizobium caulinodans. NtrC is part of the NtrB/NtrC two-component system that controls the expression of the nitrogen-regulated (ntr) genes in response to nitrogen limitation. The N-terminal REC domain of NtrC proteins regulate the activity of the protein and its phosphorylation controls the AAA+ domain oligomerization, while the central AAA+ domain participates in nucleotide binding, hydrolysis, oligomerization, and sigma54 interaction. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 100 matched cddid_all.tbl CDD cd19929 cd19929 381156 psREC_Atg32 pseudo receiver domain of autophagy receptor Atg32. Autophagy receptor Atg32 is a single-pass outer mitochondrial membrane protein that is required for the selective autophagy of mitochondria, called mitophagy, in yeast. It mediates ubiquitin-independent mitophagy in response to nitrogen deprivation. It recruits the autophagy machinery to mitochondria, facilitating mitochondrial capture in phagophores, the precursors to autophagosomes. Whereas mammals have at least 7 different autophagy receptors, yeast only has one. Little is known about the structure of Atg32; it contains a binding region for the selective autophagy scaffolding protein Atg11 and an Atg8-interacting motif (AIM). Limited proteolysis has identified a structured domain, a pseudo receiver (psREC) domain, within the cytosolic region of Atg32 that is essential for the induction of mitophagy. psREC domains lack the metal-binding, phosphorylatable asp, and active site residues of canonical REC domains and are thought to function in protein-protein interactions. 139 matched cddid_all.tbl CDD cd19930 cd19930 381157 REC_DesR-like phosphoacceptor receiver (REC) domain of DesR and similar proteins. This group is composed of Bacillus subtilis DesR, Streptococcus pneumoniae response regulator spr1814, and similar proteins, all containing an N-terminal REC domain and a C-terminal LuxR family helix-turn-helix (HTH) DNA-binding output domain. DesR is a response regulator that, together with its cognate sensor kinase DesK, comprises a two-component regulatory system that controls membrane fluidity. Phosphorylation of the REC domain of DesR is allosterically coupled to two distinct exposed surfaces of the protein, controlling noncanonical dimerization/tetramerization, cooperative activation, and DesK binding. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 117 matched cddid_all.tbl CDD cd19931 cd19931 381158 REC_NarL phosphoacceptor receiver (REC) domain of Nitrate/Nitrite response regulator L (NarL). Nitrate/nitrite response regulator protein NarL contains an N-terminal REC domain and a C-terminal LuxR family helix-turn-helix (HTH) DNA-binding output domain. Escherichia coli NarL activates the expression of the nitrate reductase (narGHJI) and formate dehydrogenase-N (fdnGHI) operons, and represses the transcription of the fumarate reductase (frdABCD) operon in response to a nitrate/nitrite induction signal. Phosphorylation of the NarL REC domain releases the C-terminal HTH output domain that subsequently binds specific DNA promoter sites to repress or activate gene expression. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 117 matched cddid_all.tbl CDD cd19932 cd19932 381159 REC_PdtaR-like phosphoacceptor receiver (REC) domain of PdtaR and similar proteins. This subfamily includes Mycobacterium tuberculosis PdtaR, also called Rv1626, and similar proteins containing a REC domain and an ANTAR (AmiR and NasR transcription antitermination regulators) RNA-binding output domain. PdtaR is a response regulator that acts at the level of transcriptional antitermination and is a member of the PdtaR/PdtaS two-component regulatory system. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 118 matched cddid_all.tbl CDD cd19933 cd19933 381160 REC_ETR-like phosphoacceptor receiver (REC) domain of plant ethylene receptors ETR1, ETR2, and EIN4, and similar proteins. Plant ethylene receptors contain N-terminal transmembrane domains that contain an ethylene binding site and also serve in localization of the receptor to the endoplasmic reticulum or the Golgi apparatus and a C-terminal histidine kinase (HK)-like domain. There are five ethylene receptors (ETR1, ERS1, ETR2, ERS2, and EIN4) in Arabidopsis thaliana. ETR1, ETR2, and EIN4 also contain REC domains C-terminal to the HK domain. ETR1 and ERS1 belong to subfamily 1, and have functional HK domains while ETR2, ERS2, and EIN4 belong to subfamily 2, and lack the necessary residues for HK activity and may function as serine/threonine kinases. The plant hormone ethylene plays an important role in plant growth and development. It regulates seed germination, seedling growth, leaf and petal abscission, fruit ripening, organ senescence, and pathogen responses. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 117 matched cddid_all.tbl CDD cd19934 cd19934 381161 REC_OmpR_EcPhoP-like phosphoacceptor receiver (REC) domain of EcPhoP-like OmpR family response regulators. Escherichia coli PhoP (EcPhoP) is part of the PhoQ/PhoP two-component system (TCS) that regulates virulence genes and plays an essential role in the response of the bacteria to the environment of their mammalian hosts, sensing several stimuli such as extracellular magnesium limitation, low pH, the presence of cationic antimicrobial peptides, and osmotic upshift. This subfamily also includes Brucella suis FeuP, part of the FeuPQ TCS that is involved in the regulation of iron uptake, and Microchaete diplosiphon RcaC, which is required for chromatic adaptation. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 117 matched cddid_all.tbl CDD cd19935 cd19935 381162 REC_OmpR_CusR-like phosphoacceptor receiver (REC) domain of CusR-like OmpR family response regulators. Escherichia coli CusR is part of the CusS/CusR two-component system (TCS) that is involved in response to copper and silver. Other members of this subfamily include Escherichia coli PcoR, Pseudomonas syringae CopR, and Streptomyces coelicolor CutR, which are all transcriptional regulatory proteins and components of TCSs that regulate genes involved in copper resistance and/or metabolism. member of the subfamily is Escherichia coli HprR (hydrogen peroxide response regulator), previously called YdeW, which is part of the HprSR (or YedVW) TCS involved in stress response to hydrogen peroxide, as well as Cupriavidus metallidurans CzcR, which is part of the CzcS/CzcR TCS involved in the control of cobalt, zinc, and cadmium homeostasis. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 100 matched cddid_all.tbl CDD cd19936 cd19936 381163 REC_OmpR_ChvI-like phosphoacceptor receiver (REC) domain of ChvI-like OmpR family response regulators. Sinorhizobium meliloti ChvI is part of the ExoS/ChvI two-component regulatory system (TCS) that is required for nitrogen-fixing symbiosis and exopolysaccharide synthesis. ExoS/ChvI also play important roles in regulating biofilm formation, motility, nutrient utilization, and the viability of free-living bacteria. ChvI belongs to the OmpR family of DNA-binding response regulators that contain N-terminal receiver (REC) and C-terminal DNA-binding winged helix-turn-helix effector domains. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 99 matched cddid_all.tbl CDD cd19937 cd19937 381164 REC_OmpR_BsPhoP-like phosphoacceptor receiver (REC) domain of BsPhoP-like OmpR family response regulators. Bacillus subtilis PhoP (BsPhoP) is part of the PhoPR two-component system that participates in a signal transduction network that controls adaptation of the bacteria to phosphate deficiency by regulating (activating or repressing) genes of the Pho regulon upon phosphorylation by PhoR. When activated, PhoPR directs expression of phosphate scavenging enzymes, lowers synthesis of the phosphate-rich wall teichoic acid (WTA) and initiates synthesis of teichuronic acid, a non-phosphate containing replacement anionic polymer. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 116 matched cddid_all.tbl CDD cd19938 cd19938 381165 REC_OmpR_BaeR-like phosphoacceptor receiver (REC) domain of BaeR-like OmpR family response regulators. BaeR is part of the BaeSR two-component system that is involved in regulating genes that confer multidrug and metal resistance. In Salmonella, BaeSR induces AcrD and MdtABC drug efflux systems, increasing multidrug and metal resistance. In Escherichia coli, BaeR stimulates multidrug resistance via mdtABC (multidrug transporter ABC, formerly known as yegMNO) genes, which encode a resistance-nodulation-cell division (RND) drug efflux system. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 114 matched cddid_all.tbl CDD cd19939 cd19939 381166 REC_OmpR_BfmR-like phosphoacceptor receiver (REC) domain of BfmR-like OmpR family response regulators. Acinetobacter baumannii BfmR is part of the BfmR/S two-component system that functions as the master regulator of biofilm initiation. BfmR confers resistance to complement-mediated bactericidal activity, independent of capsular polysaccharide, and also increases resistance to the clinically important antimicrobials meropenem and colistin, making it a potential antimicrobial target. Its inhibition would have the dual benefit of significantly decreasing in vivo survival and increasing sensitivity to selected antimicrobials. Members of this subfamily belong to the OmpR family of DNA-binding response regulators, which are characterized by a REC domain and a winged helix-turn-helix (wHTH) DNA-binding output effector domain. REC domains function as phosphorylation-mediated switches within response regulators, but some also transfer phosphoryl groups in multistep phosphorelays. 116 matched cddid_all.tbl CDD cd19940 cd19940 410849 XPF_nuclease-like nuclease domain of XPF/MUS81 family proteins. The XPF/MUS81 family belongs to 3'-flap endonuclease that act upon 3'-flap structures and involved in DNA repair pathways that are necessary for the removal of UV-light-induced DNA lesions and cross-links between DNA strands. Family members exist either as heterodimers or as homodimers in their functionally competent states which consist of a catalytic and a noncatalytic subunit. The catalytic subunits have a DX(n)RKX(3)D motif. This motif is required for metal-dependent endonuclease activity but not for DNA junction binding. The equivalent regions of the noncatalytic subunits (ERCC1, EME1, and FAAP24) have diverged. The noncatalytic subunits have roles such as binding ssDNA or an ability to target the endonuclease to defined DNA structures or sites of DNA damage. 126 matched cddid_all.tbl CDD cd19941 cd19941 410995 TIL trypsin inhibitor-like cysteine rich domain. TIL (trypsin inhibitor-like) cysteine rich domains are found in smapins (small serine proteinase inhibitor), or Ascaris trypsin inhibitor (ATI)-like proteins, whose members include anticoagulant proteins, elastase inhibitors, trypsin inhibitors, thrombin inhibitors, and chymotrypsin inhibitors. The TIL domain is also found in some large modular glycoproteins, including the von Willebrand factor (VWF), mucin-6, mucin-19, and SCO-spondin, among others. The TIL domain is characterized by the presence of five disulfide bonds (two of which are located on either side of the reactive site) in a single small protein domain of 61-62 residues. The cysteine residues that form the disulfide bonds are linked in the pattern: cysteines 1-7, 2-6, 3-5, 4-10 and 8-9. TILs can occur as a single domain or in multiple tandem arrangements. The disulfide bonds account for the unusual resistance to proteolysis and heat denaturation of these proteins. Smapins possess an unusual fold and, with the exception of the reactive site, shows no similarity to other serine protease inhibitors. The serine protease inhibitors comprise a large family of molecules involved in inflammatory responses, blood clotting, and complement activation. 55 matched cddid_all.tbl CDD cd19942 cd19942 381075 Fer2_BFD-like [2Fe-2S]-binding domain of bacterioferritin-associated ferredoxin (BFD) and related proteins. The BFD-like [2Fe-2S]-binding domain comprises a helix-turn-helix fold, and binds an [2Fe-2S] cluster via 4 highly-conserved Cys residues, found in loops between the alpha-helices. The Cys residues are organized in a unique C-X2-C-X31-35-C-X2-9-C-arrangement. [2Fe-2S] clusters are sulfide-linked diiron centers, a primary role for which is electron transport. BFD-like [2Fe-2S]-binding domains are found in proteins such as bacterioferritin-associated ferredoxin (BFD), the large subunit of NADH-dependent nitrite reductase, Cu+ chaperone CopZ, anaerobic glycerol 3-phosphate dehydrogenase subunit A, hydrogen cyanide synthase subunit B, nitrogen fixation protein NifU, prokaryotic assimilatory nitrate reductase catalytic subunit NasA, and archaeal proline dehydrogenase PDH1. This superfamily also includes uncharacterized proteins having an N-terminal BFD-like [2Fe-2S]-binding domain and a C-terminal domain belonging to the Ni,Fe-hydrogenase I small subunit family. 49 matched cddid_all.tbl CDD cd19943 cd19943 381076 NirB_Fer2_BFD-like_1 first bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain of the large subunit of the NADH-dependent nitrite reductase. The NADH-dependent nitrite reductase (NirBD) complex comprises a large and a small subunit, and is also known as nitrite reductase (reduced nicotinamide adenine dinucleotide), NADH-nitrite oxidoreductase, and assimilatory nitrite reductase. NirBD uses NADH as electron donor, and FAD, iron-sulfur cluster, and siroheme cofactors, all embedded in the large subunit NirB to catalyze the 6-electron reduction of nitrite to ammonium. NirBD plays a role in regulating nitric oxide homeostasis in Streptomyces coelicolor. In addition to NirB, the BFD-like [2Fe-2S]-binding domain is found in a variety of proteins including bacterioferritin-associated ferredoxin (BFD) and Cu+ chaperone CopZ. It comprises a helix-turn-helix fold, and binds an [2Fe-2S] cluster via 4 highly-conserved Cys residues, found in loops between the alpha-helices. For the class of proteins having a BFD-like [2Fe-2S]-binding domain, the Cys residues are organized in a unique C-X2-C-X31-35-C-X2-9-C-arrangement. [2Fe-2S] clusters are sulfide-linked diiron centers, a primary role for which is electron transport. 53 matched cddid_all.tbl CDD cd19944 cd19944 381077 NirB_Fer2_BFD-like_2 second bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain of the large subunit of the NADH-dependent nitrite reductase. The NADH-dependent nitrite reductase (NirBD) complex comprises a large (NirB) and a small (NirD) subunit, and is also known as nitrite reductase (reduced nicotinamide adenine dinucleotide), NADH-nitrite oxidoreductase, and assimilatory nitrite reductase. NirBD uses NADH as electron donor, and FAD, iron-sulfur cluster, and siroheme cofactors, all embedded in the large subunit NirB to catalyze the 6-electron reduction of nitrite to ammonium. Some of the second [2Fe-2S]-binding domains, have one of the Cys residues replaced by a His residue, they may interact with non-Rieske NirD subunits. NirBD plays a role in regulating nitric oxide homeostasis in Streptomyces coelicolor. In addition to NirB, the BFD-like [2Fe-2S]-binding domain is found in a variety of proteins including bacterioferritin-associated ferredoxin (BFD) and Cu+ chaperone CopZ. It comprises a helix-turn-helix fold, and binds an [2Fe-2S] cluster via 4 highly-conserved Cys residues, found in loops between the alpha-helices. For the class of proteins having a BFD-like [2Fe-2S]-binding domain, the Cys residues are organized in a unique C-X2-C-X31-35-C-X2-9-C-arrangement. [2Fe-2S] clusters are sulfide-linked diiron centers, a primary role for which is electron transport. 52 matched cddid_all.tbl CDD cd19945 cd19945 381078 Fer2_BFD bacterioferritin-associated ferredoxin (BFD) [2Fe-2S]-binding domain. This family includes Escherichia coli and Pseudomonas aeruginosa bacterioferritin-associated ferredoxin BFD which binds an [2Fe-2S] cluster and appears to interact with bacterioferritin (E. coli BFR/YheA and P. aeruginosa BfrB), a dynamic regulator of intracellular iron levels. It has been suggested that BFD and bacterioferritin form an electron transfer complex which may participate in the iron storage or iron immobilization functions of bacterioferritin. For Pseudomonas aeruginosa, it has been shown that mobilization of Fe3+ stored in BfrB requires interaction with BFD, which transfers electrons to reduce Fe3+ in the internal cavity of BfrB for subsequent release of Fe2+. The stability of BFD may be aided by an anion-binding site found within this domain. In addition to BFD, the BFD-like [2Fe-2S]-binding domain is found in a variety of proteins such as the large subunit of NADH-dependent nitrite reductase and the Cu+ chaperone CopZ. It comprises a helix-turn-helix fold, and binds an [2Fe-2S] cluster via 4 highly-conserved Cys residues, found in loops between the alpha-helices. For the class of proteins having a BFD-like [2Fe-2S]-binding domain, the Cys residues are organized in a unique C-X2-C-X31-35-C-X2-9-C-arrangement. [2Fe-2S] clusters are sulfide-linked diiron centers, a primary role for which is electron transport. 54 matched cddid_all.tbl CDD cd19946 cd19946 381079 GlpA-like_Fer2_BFD-like bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain of anaerobic glycerol 3-phosphate dehydrogenase subunit A, hydrogen cyanide synthase subunit B, and similar proteins. This subgroup includes the BFD-like [2Fe-2S]-binding domains of subunits of various component dehydrogenase/oxidases, including anaerobic glycerol 3-phosphate dehydrogenase subunit A of GlpABC, hydrogen cyanide synthase subunit HcnB of HcnABC, octopine oxidase subunit A of OoxAB, and nopaline oxidase subunit A of NoxAB. GlpABC catalyzes the conversion of glycerol 3-phosphate to dihydroxyacetone, and participates in the glycerol degradation by glycerol kinase pathway in step 1 of the sub-pathway that synthesizes glycerone phosphate from sn-glycerol 3-phosphate (anaerobic route). HcnABC oxidizes glycine producing hydrogen cyanide and CO2. In Agrobacterium spp, the first enzymic step in the catabolic utilization of octopine and nopaline is the oxidative cleavage into L-arginine and pyruvate or 2-ketoglutarate, respectively; nopaline oxidase (NoxAB) accepts nopaline and octopine while octopine oxidase (OoaB) has high activity with octopine but barely detectable activity with nopaline, both subunits possibly contributing to the substrate specificity. The BFD-like [2Fe-2S]-binding domain is found in a variety of other proteins including bacterioferritin-associated ferredoxin (BFD), the large subunit of NADH-dependent nitrite reductase, and Cu+ chaperone CopZ. It comprises a helix-turn-helix fold, and binds an [2Fe-2S] cluster via 4 highly-conserved Cys residues, found in loops between the alpha-helices. For the class of proteins having a BFD-like [2Fe-2S]-binding domain, the Cys residues are organized in a unique C-X2-C-X31-35-C-X2-9-C-arrangement. [2Fe-2S] clusters are sulfide-linked diiron centers, a primary role for which is electron transport. 55 matched cddid_all.tbl CDD cd19947 cd19947 381080 NifU_Fer2_BFD-like bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain of nitrogen fixation protein NifU and similar proteins. This family includes the BFD-like [2Fe-2S]-binding domain of Azotobacter vinelandii and Klebsiella pneumoniae nitrogen fixation protein NifU. NifU binds one Fe cation per subunit and one [2Fe-2S] cluster per subunit, and is involved in the formation or repair of [Fe-S] clusters present in iron-sulfur proteins. The BFD-like [2Fe-2S]-binding domain is found in a variety of other proteins including bacterioferritin-associated ferredoxin (BFD), the large subunit of NADH-dependent nitrite reductase, and Cu+ chaperone CopZ. It comprises a helix-turn-helix fold, and binds an [2Fe-2S] cluster via 4 highly-conserved Cys residues, found in loops between the alpha-helices. For the class of proteins having a BFD-like [2Fe-2S]-binding domain, the Cys residues are organized in a unique C-X2-C-X31-35-C-X2-9-C-arrangement. [2Fe-2S] clusters are sulfide-linked diiron centers, a primary role for which is electron transport. 55 matched cddid_all.tbl CDD cd19948 cd19948 381081 NasA-like_Fer2_BFD-like bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain at the C-terminus of prokaryotic assimilatory nitrate reductase catalytic subunit NasA and similar proteins. The BFD-like [2Fe-2S]-binding domain described in this family is found at the C-terminus of prokaryotic assimilatory nitrate reductase catalytic subunit (NasA) such as Rhodobacter capsulatus E1F1 NasA. Nitrate reductase catalyzes the reduction of nitrate to nitrite, the first step of nitrate assimilation. R. capsulatus E1F1 nitrate reductase is composed of this NasA subunit and a small diaphorase subunit with FAD. Note that this [2Fe-2S]-binding domain is not always present; for example, it is absent from the characterized haloaechean Haloferax mediterranei NasA; both, however, have an [4Fe-4S] binding domain at their N-terminus. The BFD-like [2Fe-2S]-binding domain is found in a variety of other proteins including bacterioferritin-associated ferredoxin (BFD), the large subunit of NADH-dependent nitrite reductase, and Cu+ chaperone CopZ. It comprises a helix-turn-helix fold, and binds an [2Fe-2S] cluster via 4 highly-conserved Cys residues, found in loops between the alpha-helices. For the class of proteins having a BFD-like [2Fe-2S]-binding domain, the Cys residues are organized in a unique C-X2-C-X31-35-C-X2-9-C-arrangement. [2Fe-2S] clusters are sulfide-linked diiron centers, a primary role for which is electron transport. 53 matched cddid_all.tbl CDD cd19949 cd19949 381082 PDH1_Fer2_BFD-like bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain of the alpha-subunit of archaeal proline dehydrogenase PDH1. This domain family describes the alpha-subunit of archaeal dye-linked L-proline dehydrogenase PDH1. Dye-linked PDH catalyzes the oxidation of L-proline to 1-pyrroline-5-carboxylate in the presence of artificial electron acceptors. It includes the alpha subunit of Pyrococcus horikoshii PHD1 which has been shown to exist as an (alphabeta)4 heterooctamer and to contain three cofactors: FAD, FMN, and ATP; the alpha subunit contains ATP but exhibits no PDH activity, the beta subunit is the catalytic component contains FAD and exhibits PDH activity, and FMN is located between the alpha and beta subunits. The BFD-like [2Fe-2S]-binding domain is found in a variety of other proteins including bacterioferritin-associated ferredoxin (BFD), the large subunit of NADH-dependent nitrite reductase, and Cu+ chaperone CopZ. It comprises a helix-turn-helix fold, and binds an [2Fe-2S] cluster via 4 highly-conserved Cys residues, found in loops between the alpha-helices. For the class of proteins having a BFD-like [2Fe-2S]-binding domain, the Cys residues are organized in a unique C-X2-C-X31-35-C-X2-9-C-arrangement. [2Fe-2S] clusters are sulfide-linked diiron centers, a primary role for which is electron transport. 56 matched cddid_all.tbl CDD cd19950 cd19950 381083 Fer2_BFD-like [2Fe-2S]-binding domain of bacterioferritin-associated ferredoxin (BFD) and related proteins; uncharacterized subgroup. The BFD-like [2Fe-2S]-binding domain comprises a helix-turn-helix fold, and binds an [2Fe-2S] cluster via 4 highly-conserved Cys residues, found in loops between the alpha-helices. The Cys residues are organized in a unique C-X2-C-X31-35-C-X2-9-C-arrangement. [2Fe-2S] clusters are sulfide-linked diiron centers, a primary role for which is electron transport. BFD-like [2Fe-2S]-binding domains are found in proteins such as bacterioferritin-associated ferredoxin (BFD), the large subunit of NADH-dependent nitrite reductase, Cu+ chaperone CopZ, anaerobic glycerol 3-phosphate dehydrogenase subunit A, hydrogen cyanide synthase subunit B, nitrogen fixation protein NifU, prokaryotic assimilatory nitrate reductase catalytic subunit NasA, and archaeal proline dehydrogenase PDH1. 51 matched cddid_all.tbl CDD cd19951 cd19951 381084 HyaA_family_Fer2_BFD-like bacterioferritin-associated ferredoxin (BFD)-like [2Fe-2S]-binding domain of uncharacterized proteins having a C-terminal Ni,Fe-hydrogenase I small subunit (HyaA) family domain. The BFD-like [2Fe-2S]-binding domain is found in a variety of other proteins including bacterioferritin-associated ferredoxin (BFD), the large subunit of NADH-dependent nitrite reductase, and Cu+ chaperone CopZ. It comprises a helix-turn-helix fold, and binds an [2Fe-2S] cluster via 4 highly-conserved Cys residues, found in loops between the alpha-helices. For the class of proteins having a BFD-like [2Fe-2S]-binding domain, the Cys residues are organized in a unique C-X2-C-X31-35-C-X2-9-C-arrangement. [2Fe-2S] clusters are sulfide-linked diiron centers, a primary role for which is electron transport. 54 matched cddid_all.tbl CDD cd19952 cd19952 467690 GT29 glycosyltransferase family 29. Glycosyltransferase family 29 members (also called sialyltransferases) are enzymes that transfer sialic acid to oligosaccharide, each having specificity for a certain sugar substrate. 193 matched cddid_all.tbl CDD cd19953 cd19953 410996 PDS5 Sister chromatid cohesion protein PDS5. Pds5 plays a crucial role in sister chromatid cohesion. Together with WapI and Scc3, it is involved in the release of the cohesin complex from chromosomes during S phase. The core of the cohesin complex consists of a coiled-coiled heterodimer of Smc1 and Smc30, together with Scc1 (also called kleisin). Pds5 interacts with Scc1 via a conserved patch on the surface of its heat repeats. Pds5 also promotes the acetylation of Smc3 that protects cohesin from releasing activity in G2 phase. 630 matched cddid_all.tbl CDD cd19954 cd19954 381070 serpin42Dd-like_insects insect serpins similar to Drosophila melanogaster Serpin 42Dd. Serpins in insects function within development, wound healing and immunity. Drosophila melanogaster Serpin 42Dd, also called serpin 1 (Spn1), regulates Toll-mediated immune responses, functioning as a repressor of Toll activation upon fungal infection. Insect serpins from house flies, fruit flies, and stable flies are included in this subfamily. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 366 matched cddid_all.tbl CDD cd19955 cd19955 381071 serpin48-like_insects insect serpins similar to Tenebrio molitor serpin 48. Serpins in insects function within development, wound healing and immunity. Tenebrio molitor serpin 48 (SPN48) is highly specific for Spatzle-processing enzyme, an essential component in insect innate immunity. SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 361 matched cddid_all.tbl CDD cd19956 cd19956 381072 serpinB serpin B family, ov-serpins. The clade B of the serpin superfamily corresponds to the ovalbumin family of serpins (ov-serpins), a family of closely related proteins, whose members can be secreted (ovalbumin), cytosolic (leukocyte elastase inhibitor, LEI), or targeted to both compartments (plasminogen activator inhibitor 2, PAI-2). Family members are also characterized by N- and C-terminal extensions, the absence of a signal peptide, and a Ser rather than an Asn residue at the penultimate position. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants can cause blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 376 matched cddid_all.tbl CDD cd19957 cd19957 381073 serpinA serpin family A. The clade A of the serpin superfamily includes the classical serine proteinase inhibitors, alpha-1-antitrypsin and alpha-1-antichymotrypsin, protein C inhibitor, kallistatin, and non-inhibitory serpins, like corticosteroid and thyroxin binding globulins. In general, SERine Proteinase INhibitors (serpins) exhibit conformational polymorphism shifting from native to cleaved, latent, delta, or polymorphic forms. Many serpins, such as antitrypsin and antichymotrypsin, function as serine protease inhibitors which regulate blood coagulation cascades. Non-inhibitory serpins perform many diverse functions such as chaperoning proteins or transporting hormones. Serpins are of medical interest because mutants have been associated with blood clotting disorders, emphysema, cirrhosis, and dementia. A classification based on evolutionary relatedness has resulted in the assignment of serpins to 16 clades designated A-P along with some orphans. 363 matched cddid_all.tbl CDD cd19958 cd19958 410997 pyocin_knob knob domain of R1 and R2 pyocins and similar domains. The knob domain is present as a tandemly repeated structural domain in R-type pyocins, which are high-molecular weight bacteriocins produced by some strains of Pseudomonas aeruginosa to specifically kill other strains of the same species. R-type pyocins are structurally similar to simple contractile tails, such as those of phage P2 and Mu, and they punch a hole in the bacterial envelope to efficiently kill target cells. The second knob domain may contain regions responsible for determining the killing spectrum. Knob-like domains occur in host-recognition and binding proteins of, not only pyocins, but also phages, such as in phage K1F endosialidase (not represented by this model), where it may interact with sialic acid, the cell surface molecule that is recognized during infection. 80 matched cddid_all.tbl CDD cd19959 cd19959 467843 paratox Streptococcus prophage gene product paratox and similar proteins. Paratox (Prx), the product of a Streptococcus prophage gene, binds to the competence regulator ComR and prevents the ComR-XIP complex from interacting with DNA. 58 matched cddid_all.tbl CDD cd19960 cd19960 410999 YidC_peri periplasmic beta-super sandwich fold domain of membrane protein insertase YidC from Gram-negative bacteria and similar domains. Membrane protein insertase YidC, also called foldase YidC or membrane integrase YidC, facilitates proper folding, insertion, and assembly of inner membrane proteins and complexes. Depending on the nature of the substrate, YidC functions in a Sec-independent (YidC only) or a Sec-dependent manner as part of a complex containing YidC, the SecYEG channel, and SecDFYajC. YidC belongs to the YidC/Oxa1/Alb3 protein family of insertases that contains a core domain of five transmembrane (TM) segments that is essential to insertase function. In addition to this core transmembrane domain, YidC from Gram-negative bacteria contain an extra transmembrane segment (TM1) at the N-terminus and a large periplasmic domain, located between TM1 and TM2, that adopts a beta-super sandwich fold that is found in sugar-binding proteins such as galactose mutarotase. This periplasmic domain may have a role in protein assembly: a region of YidC that binds to SecF maps to one edge of the beta-super sandwich. Other members of the YidC/Oxa1/Alb3 family include YidC1/YidC2 from gram-positive bacteria as well as eukaryotic members such as mitochondrial Oxa1/Oxa2 (or Cox18) and chloroplastic Alb3/Alb4; they are not part of this hierarchy as they do not possess the periplasmic domain. 233 matched cddid_all.tbl CDD cd19961 cd19961 411000 EcYidC-like_peri periplasmic beta-super sandwich fold domain of membrane protein insertase YidC from Escherichia coli and similar domains. This subfamily is composed of Escherichia coli YidC and similar proteins. Membrane protein insertase YidC, also called foldase YidC or membrane integrase YidC, facilitates proper folding, insertion, and assembly of inner membrane proteins and complexes. Depending on the nature of the substrate, YidC functions in a Sec-independent (YidC only) or a Sec-dependent manner as part of a complex containing YidC, the SecYEG channel, and SecDFYajC. YidC belongs to the YidC/Oxa1/Alb3 protein family of insertases that contain a core domain of five transmembrane (TM) segments that is essential to insertase function. In addition to this core transmembrane domain, YidC from Gram-negative bacteria contain an extra transmembrane segment (TM1) at the N-terminus and a large periplasmic domain, located between TM1 and TM2, that adopts a beta-super sandwich fold that is found in sugar-binding proteins such as galactose mutarotase. This periplasmic domain may have a role in protein assembly: a region of YidC that binds to SecF maps to one edge of the beta-super sandwich. 255 matched cddid_all.tbl CDD cd19962 cd19962 380617 PBP1_ABC_RfuA-like periplasmic riboflavin-binding component (RfuA) of ABC transporter (RfuABCD) from Treponema pallidum and its close homologs in other bacteria. This group includes the basic membrane lipoprotein (BMP) family ABC transporter substrate-binding protein RfuA from Treponema pallidum and its close homologs in other bacteria. RfuA is the riboflavin-binding component of ABC transporter (RfuABCD) in spirochetes. The members of this group are highly similar to that of the periplasmic binding domain of basic membrane lipoprotein (BMP), PnrA. The PnrA lipoprotein, also known as Tp0319 or TmpC, represents a novel family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC) transport system (pnrABCDE). It shows a striking structural similarity to another basic membrane lipoprotein Med which regulates the competence transcription factor gene, comK, in Bacillus subtilis. PnrA-like proteins are likely to have similar nucleoside-binding functions and a similar type 1 periplasmic sugar-binding protein-like fold. 305 matched cddid_all.tbl CDD cd19963 cd19963 380618 PBP1_BMP-like periplasmic binding component of a basic membrane lipoprotein (BMP) from Brucella abortus and its close homologs in other bacteria. Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. These outer membrane proteins include Med, a cell-surface localized protein regulating the competence transcription factor gene comK in Bacillus subtilis, and PnrA, a periplasmic purine nucleoside binding protein of an ATP-binding cassette (ABC) transport system in Treponema pallidum. All contain the type 1 periplasmic sugar-binding protein-like fold. 279 matched cddid_all.tbl CDD cd19964 cd19964 380619 PBP1_BMP-like periplasmic binding component of a basic membrane lipoprotein (BMP) from Aeropyrum pernix K1 and its close homologs in other bacteria. Periplasmic binding component of a family of basic membrane lipoproteins from Aeropyrum pernix K1 and various putative lipoproteins from other bacteria. These outer membrane proteins include Med, a cell-surface localized protein regulating the competence transcription factor gene comK in Bacillus subtilis, and PnrA, a periplasmic purine nucleoside binding protein of an ATP-binding cassette (ABC) transport system in Treponema pallidum. All contain the type 1 periplasmic sugar-binding protein-like fold. 263 matched cddid_all.tbl CDD cd19965 cd19965 380620 PBP1_ABC_sugar_binding-like monosaccharide ABC transporter substrate binding protein CUT2 family and similar proteins. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 272 matched cddid_all.tbl CDD cd19966 cd19966 380621 PBP1_ABC_sugar_binding-like monosaccharide ABC transporter substrate binding protein CUT2 family and simialr proteins. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 278 matched cddid_all.tbl CDD cd19967 cd19967 380622 PBP1_TmRBP-like D-ribose ABC transporter substrate-binding protein such as Thermoanaerobacter tengcongensis ribose binding protein (ttRBP). Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type 1 periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability. 272 matched cddid_all.tbl CDD cd19968 cd19968 380623 PBP1_ABC_IbpA-like periplasmic sugar-binding protein IbpA of an ABC transporter and similar proteins. The periplasmic binding protein (PBP) IbpA mediates the uptake of myo-inositol by an ABC transporter that consists of the PBP IbpA, the transmembrane permease IatP, and the ABC IatA. IbpA shares homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. 271 matched cddid_all.tbl CDD cd19969 cd19969 380624 PBP1_ABC_sugar_binding-like monosaccharide ABC transporter substrate binding protein. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 278 matched cddid_all.tbl CDD cd19970 cd19970 380625 PBP1_ABC_sugar_binding-like monosaccharide ABC transporter substrate-binding protein. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 275 matched cddid_all.tbl CDD cd19971 cd19971 380626 PBP1_ABC_sugar_binding-like monosaccharide ABC transporter substrate-binding protein. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 267 matched cddid_all.tbl CDD cd19972 cd19972 380627 PBP1_ABC_sugar_binding-like monosaccharide ABC transporter substrate-binding protein. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 269 matched cddid_all.tbl CDD cd19973 cd19973 380628 PBP1_ABC_sugar_binding-like monosaccharide ABC transporter substrate-binding protein. Periplasmic sugar-binding domain of active transport systems that are members of the type 1 periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2) receptors such as LsrB and LuxP which are highly homologous to periplasmic pentose/hexose sugar-binding proteins. 285 matched cddid_all.tbl CDD cd19974 cd19974 380629 PBP1_LacI-like ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 270 matched cddid_all.tbl CDD cd19975 cd19975 380630 PBP1_CcpA-like ligand-binding domain of putative DNA transcription regulators highly similar to that of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation. This group includes the ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that of the catabolite control protein A (CcpA), which functions as the major transcriptional regulator of carbon catabolite repression/regulation (CCR), a process in which enzymes necessary for the metabolism of alternative sugars are inhibited in the presence of glucose. In gram-positive bacteria, CCR is controlled by HPr, a phosphoenolpyruvate:sugar phsophotrasnferase system (PTS) and a transcriptional regulator CcpA. Moreover, CcpA can regulate sporulation and antibiotic resistance as well as play a role in virulence development of certain pathogens such as the group A streptococcus. The ligand binding domain of CcpA is a member of the LacI-GalR family of bacterial transcription regulators. 269 matched cddid_all.tbl CDD cd19976 cd19976 380631 PBP1_DegA_Like ligand-binding domain of putative DNA transcription regulators highly similar to that of the transcription regulator DegA. This group includes the ligand-binding domain of uncharacterized DNA transcription repressors highly similar to that of the transcription regulator DegA, which is involved in the control of degradation of Bacillus subtilis amidophosphoribosyltransferase (purF). This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding. 268 matched cddid_all.tbl CDD cd19977 cd19977 380632 PBP1_EndR-like periplasmic ligand-binding domain of putative repressor of the endoglucanase operon and its close homologs. This group includes the ligand-binding domain of putative repressor of the endoglucanase operon from Paenibacillus polymyxa and its close homologs from other bacteria. This group belongs to the LacI-GalR family repressors and are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type 1 periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding. 264 matched cddid_all.tbl CDD cd19978 cd19978 380633 PBP1_ABC_ligand_binding-like periplasmic ligand-binding domain of uncharacterized ABC-type transport systems predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This group includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); its ligand specificity has not been determined experimentally, however. 341 matched cddid_all.tbl CDD cd19979 cd19979 380634 PBP1_ABC_ligand_binding-like amino acid amide ABC transporter substrate binding protein haat family. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine binding protein (LIVBP); however their ligand specificity has not been determined experimentally. 350 matched cddid_all.tbl CDD cd19980 cd19980 380635 PBP1_ABC_ligand_binding-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. 334 matched cddid_all.tbl CDD cd19981 cd19981 380636 PBP1_ABC_HAAT-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids or peptides. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of amino acids or peptides. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. 297 matched cddid_all.tbl CDD cd19982 cd19982 380637 PBP1_ABC_ligand_binding-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, their ligand specificity has not been determined experimentally. 302 matched cddid_all.tbl CDD cd19983 cd19983 380638 PBP1_ABC_HAAT-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of hydrophobic amino acids or peptides. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of hydrophobic amino acids or peptides. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. 303 matched cddid_all.tbl CDD cd19984 cd19984 380639 PBP1_ABC_ligand_binding-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. 296 matched cddid_all.tbl CDD cd19985 cd19985 380640 PBP1_ABC_HAAT-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of hydrophobic amino acids or peptides. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of hydrophobic amino acids or peptides. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. 321 matched cddid_all.tbl CDD cd19986 cd19986 380641 PBP1_ABC_HAAT-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids or peptides. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of amino acids or peptides. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. 297 matched cddid_all.tbl CDD cd19987 cd19987 380642 PBP1_SBP-like periplasmic substrate-binding domain of active transport proteins. Periplasmic substrate-binding domain of active transport proteins found in bacteria and Archaea. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids. 353 matched cddid_all.tbl CDD cd19988 cd19988 380643 PBP1_ABC_HAAT-like type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems predicted to be involved in uptake of amino acids or peptides. This subgroup includes the type 1 periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of amino acids or peptides. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP); however, its ligand specificity has not been determined experimentally. 302 matched cddid_all.tbl CDD cd19989 cd19989 380644 PBP1_SBP-like periplasmic substrate-binding domain of active transport proteins. Periplasmic substrate-binding domain of active transport proteins found in bacteria and Archaea. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids. 299 matched cddid_all.tbl CDD cd19990 cd19990 380645 PBP1_GABAb_receptor_plant periplasmic ligand-binding domain of Arabidopsis thaliana glutamate receptors and its close homologs in other plants. This group includes the ligand-binding domain of Arabidopsis thaliana glutamate receptors, which have sequence similarity with animal ionotropic glutamate receptor and its close homologs in other plants. The ligand-binding domain of GABAb receptors are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb receptor or GABAbR). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha-i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example. 373 matched cddid_all.tbl CDD cd19991 cd19991 380646 PBP1_ABC_xylose_binding D-xylose binding periplasmic protein. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. 284 matched cddid_all.tbl CDD cd19992 cd19992 380647 PBP1_ABC_xylose_binding-like periplasmic xylose-like sugar-binding component of the ABC-type transport systems. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. 284 matched cddid_all.tbl CDD cd19993 cd19993 380648 PBP1_ABC_xylose_binding-like periplasmic xylose-like sugar-binding component of the ABC-type transport systems. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. 287 matched cddid_all.tbl CDD cd19994 cd19994 380649 PBP1_ChvE periplasmic sugar binding protein ChvE that interacts with a bacterial two-component signaling system. Periplasmic aldose-monosaccharides binding protein ChvE that belongs to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. 304 matched cddid_all.tbl CDD cd19995 cd19995 380650 PBP1_ABC_xylose_binding-like periplasmic xylose-like sugar-binding component of the ABC-type transport systems. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. 294 matched cddid_all.tbl CDD cd19996 cd19996 380651 PBP1_ABC_sugar_binding-like monosaccharide ABC transporter substrate binding protein such as CUT2. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail. 302 matched cddid_all.tbl CDD cd19997 cd19997 380652 PBP1_ABC_sugar_binding-like monosaccharide ABC transporter substrate binding protein such as CUT2. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail. 305 matched cddid_all.tbl CDD cd19998 cd19998 380653 PBP1_ABC_sugar_binding-like monosaccharide ABC transporter substrate binding protein such as CUT2. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail. 302 matched cddid_all.tbl CDD cd19999 cd19999 380654 PBP1_ABC_sugar_binding-like monosaccharide ABC transporter substrate binding protein such as CUT2. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type 1 periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail. 313 matched cddid_all.tbl CDD cd20000 cd20000 380655 PBP1_ABC_rhamnose rhamnose ABC transporter substrate-binding protein. Rhamnose ABC transporter substrate-binding protein similar to periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type 1 periplasmic binding protein superfamily. LsrB, which is part of the ABC transporter complex LsrABCD, binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding protein in interspecies signaling. 298 matched cddid_all.tbl CDD cd20001 cd20001 380656 PBP1_LsrB_Quorum_Sensing-like ligand-binding protein LsrB-like of ABC transporter periplasmic binding protein. Ligand-binding protein LsrB-like of a transport system, similar to periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type 1 periplasmic binding protein superfamily. LsrB, which is part of the ABC transporter complex LsrABCD, binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding protein in interspecies signaling. 296 matched cddid_all.tbl CDD cd20002 cd20002 380657 PBP1_LsrB_Quorum_Sensing-like ligand-binding protein LsrB-like of ABC transporter periplasmic binding protein. Ligand-binding protein LsrB-like of a transport system, similar to periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type 1 periplasmic binding protein superfamily. LsrB, which is part of the ABC transporter complex LsrABCD, binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding protein in interspecies signaling. 295 matched cddid_all.tbl CDD cd20003 cd20003 380658 PBP1_LsrB_Quorum_Sensing ligand-binding protein LsrB of ABC transporter periplasmic binding protein. Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type 1 periplasmic binding protein superfamily. LsrB, which is part of the ABC transporter complex LsrABCD, binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding protein in interspecies signaling. 298 matched cddid_all.tbl CDD cd20004 cd20004 380659 PBP1_ABC_sugar_binding-like monosaccharide ABC transporter substrate-binding protein such as CUT2. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 273 matched cddid_all.tbl CDD cd20005 cd20005 380660 PBP1_ABC_sugar_binding-like monosaccharide ABC transporter substrate-binding protein such as CUT2. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 274 matched cddid_all.tbl CDD cd20006 cd20006 380661 PBP1_ABC_sugar_binding-like monosaccharide ABC transporter substrate-binding protein such as CUT2. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 274 matched cddid_all.tbl CDD cd20007 cd20007 380662 PBP1_ABC_sugar_binding-like monosaccharide ABC transporter substrate-binding protein such as CUT2. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 271 matched cddid_all.tbl CDD cd20008 cd20008 380663 PBP1_ABC_sugar_binding-like monosaccharide ABC transporter substrate-binding protein such as CUT2. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type 1 periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis. 277 matched cddid_all.tbl CDD cd20009 cd20009 380664 PBP1_RafR-like Ligand-binding domain of DNA transcription repressor specific for raffinose (RafR) and similar proteins. Ligand-binding domain of DNA transcription repressor specific for raffinose (RafR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 266 matched cddid_all.tbl CDD cd20010 cd20010 380665 PBP1_AglR-like Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) and similar proteins. Ligand-binding domain of DNA transcription repressor specific for alpha-glucosides (AglR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor. 269 matched cddid_all.tbl CDD cd20013 cd20013 380666 PBP1_RPA0985_benzoate-like type 1 periplasmic binding-protein component of an ABC system (RPA0985), involved in the active transport of lignin-derived benzoate derivative compounds, and its close homologs. This group includes RPA0985 from Rhodopseudomonas palustris and its close homologs in other bacteria. Rpa0985 is the periplasmic binding-protein component of an ABC system that is involved in the active transport of lignin-derived benzoate derivative compounds. Members of this group has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP). 356 matched cddid_all.tbl CDD cd20014 cd20014 380667 PBP1_RPA0668_benzoate-like type 1 periplasmic binding-protein component of an ABC system (RPA0668), involved in in the active transport of lignin-derived benzoate derivative compounds, and its close homologs. This group includes RPA0668 from Rhodopseudomonas palustris and its close homologs in other bacteria. Rpa0668 is the periplasmic binding-protein component of an ABC system that is involved in the active transport of lignin-derived benzoate derivative compounds. Members of this group has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine binding protein (LIVBP). 346 matched cddid_all.tbl CDD cd20015 cd20015 410789 FH_FOXA Forkhead (FH) domain found in the Forkhead box protein A (FOXA) subfamily. The FOXA subfamily includes three winged helix transcription factors, FOXA1 (also called hepatocyte nuclear factor 3-alpha or transcription factor 3A), FOXA2 (also called hepatocyte nuclear factor 3-beta or transcription factor 3B), and FOXA3 (also called hepatocyte nuclear factor 3-gamma or transcription factor 3G). FOXA1 is essential for epithelial lineage differentiation and has been found to be upregulated in numerous cancers. FOXA2 controls cell differentiation. It is a key transcriptional regulator that maintains airway mucus homeostasis and may also have an important role in bone metabolism. FOXA3 acts as an essential transcriptional regulator engaged in adipogenesis and energy metabolism. This subfamily also includes Xenopus tropicalis FOXA4, Drosophila melanogaster protein fork head (dFKH), and similar proteins. FOXA4 is only present in amphibians, where it is required for the correct regionalization and maintenance of the central nervous system. dFKH promotes terminal as opposed to segmental development. In the absence of dFKH, this developmental switch does not occur. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 97 matched cddid_all.tbl CDD cd20016 cd20016 410790 FH_FOXB Forkhead (FH) domain found in the Forkhead box protein B (FOXB) subfamily. The FOXB subfamily includes two winged helix transcription factors, FOXB1 (also called transcription factor FKH-5) and FOXB2 (also called transcription factor FKH-4). FOXB1 controls development of mammary glands and regions of the central nervous system (CNS) that regulate the milk-ejection reflex. It is essential for access of mammillothalamic axons to the thalamus. FOXB2 may act as a tumor suppressor; it has been found to inhibit the malignant characteristics of the pancreatic cancer cell line Panc-1 in vitro. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 79 matched cddid_all.tbl CDD cd20017 cd20017 410791 FH_FOXC Forkhead (FH) domain found in the Forkhead box protein C (FOXC) subfamily. The FOXC subfamily includes two winged helix transcription factors, FOXC1 (also called Forkhead-related protein FKHL7, or Forkhead-related transcription factor 3) and FOXC2 (also called Forkhead-related protein FKHL14, or Mesenchyme fork head protein 1). FOXC1 is a DNA-binding transcriptional factor that plays a role in a broad range of cellular and developmental processes such as the development of the eyes, bones, cardiovascular system, kidneys, and skin. FOXC2 acts as a transcriptional activator that might be involved in the formation of special mesenchymal tissues. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 77 matched cddid_all.tbl CDD cd20018 cd20018 410792 FH_FOXD Forkhead (FH) domain found in the Forkhead box protein D (FOXD) subfamily. The FOXD subfamily includes four winged helix transcription factors, FOXD1-4. FOXD1, also called Forkhead-related protein FKHL8 or Forkhead-related transcription factor 4 (FREAC-4), is involved in transcriptional activation of Placental Growth Factor (PGF) and the complement component (C3) genes. It plays an important role in early embryonic development and organogenesis, and functions as an oncogene in several cancers. FOXD2, also called Forkhead-related protein FKHL17 or Forkhead-related transcription factor 9 (FREAC-9), is a probable transcription factor involved in embryogenesis and somatogenesis. FOXD3, also called HNF3/FH transcription factor genesis, acts as a transcriptional repressor that binds to the consensus sequence 5'-A[AT]T[AG]TTTGTTT-3'. It also acts as a transcriptional activator. It promotes development of neural crest cells from neural tube progenitors and restricts neural progenitor cells to the neural crest lineage while suppressing interneuron differentiation. FOXD3 is required for maintenance of pluripotent cells in the pre-implantation and peri-implantation stages of embryogenesis. FOXD4, also called Forkhead-related protein FKHL9 or Forkhead-related transcription factor 5 (FREAC-5), is essential for establishing neural cell fate and for neuronal differentiation. The family also includes Forkhead box protein D4-like proteins, FOXD4L1-6. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 78 matched cddid_all.tbl CDD cd20019 cd20019 410793 FH_FOXE Forkhead (FH) domain found in the Forkhead box protein E (FOXE) subfamily. The FOXE subfamily includes two winged helix transcription factors, FOXE1 (also known as FOXE2) and FOXE3. FOXE1, also called Forkhead-related protein FKHL15, HFKH4, HNF-3/fork head-like protein 5 (HFKL5), or thyroid transcription factor 2 (TTF-2), is a transcription factor that binds consensus sites on a variety of gene promoters and activate their transcription. FOXE3, also called Forkhead-related protein FKHL12 or Forkhead-related transcription factor 8 (FREAC-8), is a transcription factor that controls lens epithelial cell growth through regulation of proliferation, apoptosis, and the cell cycle. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 94 matched cddid_all.tbl CDD cd20020 cd20020 410794 FH_FOXF Forkhead (FH) domain found in the Forkhead box protein F (FOXF) subfamily. The FOXF subfamily includes two winged helix transcription factors, FOXF1 and FOXF2, both of which are probable transcription activators for a number of lung-specific genes. FOXF1 mutations in sporadic and familial cases of alveolar capillary dysplasia with misaligned pulmonary veins (ACD/MPV) suggest its involvement in ACD/MPV and lung organogenesis. FOXF2 is involved in programming organogenesis and regulating epithelial-to-mesenchymal transition (EMT) and cell proliferation. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 78 matched cddid_all.tbl CDD cd20021 cd20021 410795 FH_FOXG "Forkhead (FH) domain found in the Forkhead box protein G (FOXG) subfamily. The FOXG subfamily includes a winged helix transcription factor FOXG1, which is also called brain factor 1 (BF-1), brain factor 2 (BF-2), Forkhead box protein G1A, Forkhead box protein G1B, Forkhead box protein G1C, Forkhead-related protein FKHL1, Forkhead-related protein FKHL2, or Forkhead-related protein FKHL3. FOXG1 acts as a transcription repression factor which plays an important role in the establishment of the regional subdivision of the developing brain and in the development of the telencephalon. It is repetitively used in the sequential events of telencephalic development to control multi-steps of brain circuit formation ranging from cell cycle control to neuronal differentiation in a clade- and species-specific manner. Individuals with mutations in FOXG1 harbor ""FOXG1-related encephalopathy"", characterized by two clinical phenotypes/syndromes including microcephaly, developmental delay, severe cognitive disabilities, early-onset dyskinesia and hyperkinetic movements, stereotypies, epilepsy, and cerebral malformation for those with deletions or intragenic mutations of FOXG1. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'." 79 matched cddid_all.tbl CDD cd20022 cd20022 410796 FH_FOXH Forkhead (FH) domain found in the Forkhead box protein H (FOXH) subfamily. The FOXH subfamily includes a winged helix transcription factor, FOXH1, which is also called Forkhead activin signal transducer 1 (Fast-1), or Forkhead activin signal transducer 2 (Fast-2). FOXH1 acts as a transcriptional activator that recognizes and binds to the DNA sequence 5'-TGT[GT][GT]ATT-3'. It is required for induction of the goosecoid (GSC) promoter by TGF-beta or activin signaling. FOXH1 forms a transcriptionally active complex containing FOXH1/SMAD2/SMAD4 on a site on the GSC promoter called TARE (TGF-beta/activin response element). The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 79 matched cddid_all.tbl CDD cd20023 cd20023 410797 FH_FOXJ1 Forkhead (FH) domain found in Forkhead box protein J1 (FOXJ1) and similar proteins. FOXJ1, also called Forkhead-related protein FKHL13 or hepatocyte nuclear factor 3 Forkhead homolog 4 (HFH-4), acts as a transcription factor specifically required for the formation of motile cilia. It acts by activating transcription of genes that mediate assembly of motile cilia, such as CFAP157. FOXJ1 binds the DNA consensus sequences 5'-HWDTGTTTGTTTA-3' or 5'-KTTTGTTGTTKTW-3' (where H is not G, W is A or T, D is not C, and K is G or T). It activates the transcription of a variety of ciliary proteins in the developing brain and lung. The FH domain is a winged helix DNA-binding domain. 79 matched cddid_all.tbl CDD cd20024 cd20024 410798 FH_FOXJ2-like Forkhead (FH) domain found in Forkhead box proteins, FOXJ2, FOXJ3 and similar proteins. The FOXJ2-like subfamily includes two winged helix transcription factors, FOXJ2 and FOXJ3. FOXJ2, also called Forkhead homologous X (FHX), plays an important role in tumorigenesis, progression, and metastasis of certain cancers. It acts as a transcriptional activator that can bind to two different type of DNA binding sites. FOXJ3 is a transcription factor which regulates sperm function. It transcriptionally activates Mef2c and regulates adult skeletal muscle fiber type identity. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 77 matched cddid_all.tbl CDD cd20025 cd20025 410799 FH_FOXI Forkhead (FH) domain found in the Forkhead box protein I (FOXI) subfamily. The FOXI subfamily includes three human winged helix transcription factors, FOXI1-3, Xenopus laevis FoxI1c, and similar proteins. FOXI1 acts as a transcriptional activator required for the development of normal hearing, sense of balance, and kidney function. FOXI2 may act as a transcriptional activator that plays a possible role in controlling cellular identity. Loss of function mutations in the FOXI2 gene may contribute to ectodermal dysplasia. FOXI3 plays a critical role in the development of the inner ear and jaw. It is a regulator of ectodermal development. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 77 matched cddid_all.tbl CDD cd20026 cd20026 410800 FH_FOXK Forkhead (FH) domain found in the Forkhead box protein K (FOXK) subfamily. The FOXK subfamily includes two winged helix transcription factors, FOXK1 and FOXK2. FOXK1, also called myocyte nuclear factor (MNF), acts as a transcriptional regulator that binds to the upstream enhancer region (CCAC box) of myoglobin genes. It positively regulates Wnt/beta-catenin signaling by translocating dishevelled (DVL) proteins into the nucleus. It also reduces virus replication, probably by binding the interferon stimulated response element (ISRE) to promote antiviral gene expression. In addition, FOXK1 plays important roles in multiple human cancers. FOXK2, also called cellular transcription factor ILF-1 or interleukin enhancer-binding factor 1, is a transcriptional regulator that recognizes the core sequence 5'-TAAACA-3'. It binds to NFAT-like motifs (purine-rich) in the IL2 promoter. It also binds to the HIV-1 long terminal repeat. FOXK2 may be involved in both, positive and negative regulation of important viral and cellular promoter elements. In addition, FOXK2 plays a critical role in suppressing tumorigenesis. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 78 matched cddid_all.tbl CDD cd20027 cd20027 410801 FH_FOXL1 Forkhead (FH) domain found in Forkhead box protein L1 (FOXL1) and similar proteins. FOXL1, also called Forkhead-related protein FKHL11 or Forkhead-related transcription factor 7 (FREAC-7), acts as a transcription factor required for proper proliferation and differentiation in the gastrointestinal epithelium. It may play a critical role in suppressing tumorigenesis. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 98 matched cddid_all.tbl CDD cd20028 cd20028 410802 FH_FOXL2 Forkhead (FH) domain found in Forkhead box protein L2 (FOXL2) and similar proteins. FOXL2 is a transcriptional regulator that is essential for ovary differentiation and maintenance, and repression of the genetic program for somatic testis determination. Mutations in the FOXL2 gene cause blepharophimosis-ptosis-epicanthus inversus syndrome (BPES) types I and II, a rare genetic disorder. In BPES type I, a complex eyelid malformation is associated with premature ovarian failure (POF), whereas in BPES type II, the eyelid defect occurs as an isolated entity. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 89 matched cddid_all.tbl CDD cd20029 cd20029 410803 FH_FOXM Forkhead (FH) domain found in the Forkhead box protein M (FOXM) subfamily. The FOXM subfamily includes a winged helix transcription factor, FOXM1, which is also called Forkhead-related protein FKHL16, Hepatocyte nuclear factor 3 Forkhead homolog 11 (HFH-11), HNF-3/fork-head homolog 11, M-phase phosphoprotein 2, MPM-2 reactive phosphoprotein 2, transcription factor Trident, or Winged-helix factor from INS-1 cells. FOXM1 acts as a transcriptional factor regulating the expression of cell cycle genes essential for DNA replication and mitosis. It plays a role in the control of cell proliferation. It is also involved in DNA break repair, participating in the DNA damage checkpoint response. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 77 matched cddid_all.tbl CDD cd20030 cd20030 410804 FH_FOXN1-like Forkhead (FH) domain found in Forkhead box protein N1 (FOXN1) and similar proteins. The FOXN1-like group includes two FOXN subfamily winged helix transcription factors, FOXN1 and FOXN4. FOXN1, also called winged helix transcription factor nude, acts as a transcriptional regulator which regulates the development, differentiation, and function of thymic epithelial cells (TECs), both in the prenatal and postnatal thymus. FOXN4 acts as a transcription factor essential for neural and some non-neural tissue development, such as retina and lung, respectively. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 81 matched cddid_all.tbl CDD cd20031 cd20031 410805 FH_FOXN2-like Forkhead (FH) domain found in Forkhead box protein N2 (FOXN2) and similar proteins. The FOXN2-like group includes two FOXN subfamily winged helix transcription factors, FOXN2 and FOXN3. FOXN2, also called human T-cell leukemia virus enhancer factor (HTLF), is a potential tumor suppressor that can facilitate replication fork reversal. It acts as a transcription factor that binds to the purine-rich region in human T-cell leukemia virus long terminal repeat (HTLV-I LTR). It may be a potential therapeutic and radiosensitization target for lung cancer. FOXN3, also called checkpoint suppressor 1, acts as a transcriptional repressor that may be involved in DNA damage-inducible cell cycle arrests (checkpoints). The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 76 matched cddid_all.tbl CDD cd20032 cd20032 410806 FH_FOXO Forkhead (FH) domain found in the Forkhead box protein O (FOXO) subfamily. The FOXO subfamily includes several winged helix transcription factors: FOXO1, FOXO3, FOXO4 and FOXO6. FOXO transcription factors are involved in the regulation of longevity phenomenon via insulin and insulin-like growth factor signaling. All FOXOs bind to the consensus sequence 5'-GTAAACAA-3', known as the DAF-16 family member-binding element, which includes the core sequence 5'-(A/C)AA(C/T)A-3' recognized by all FOX family members. FOXO1, also called Forkhead box protein O1A or Forkhead in rhabdomyosarcoma (FKHR), is a transcription factor that is the main target of insulin signaling and regulates metabolic homeostasis in response to oxidative stress. FOXO3, also called AF6q21 protein or Forkhead in rhabdomyosarcoma-like 1 (FKHRL1), is a transcriptional activator which triggers apoptosis in the absence of survival factors, including neuronal cell death upon oxidative stress. It recognizes and binds to the DNA sequence 5'-[AG]TAAA[TC]A-3'. FOXO4, also called Fork head domain transcription factor AFX1, is a transcription factor involved in the regulation of the insulin signaling pathway. It binds to insulin-response elements (IREs) and can activate transcription of IGFBP1. FOXO6 acts as a transcriptional activator that may play an important role on tumor invasion, metastasis, and prognosis. The FH domain is a winged helix DNA-binding domain. 80 matched cddid_all.tbl CDD cd20033 cd20033 410807 FH_FOXP Forkhead (FH) domain found in the Forkhead box protein P (FOXP) subfamily. The FOXP subfamily includes four winged helix transcription factors, FOXP1-4. They are involved in the development of the central nervous system. Mutations in FOXP1, also called Mac-1-regulated Forkhead (MFH), leads to developmental delay, intellectual disability, autism spectrum disorder, speech delay, and dysmorphic features. FOXP2, also called CAG repeat protein 44 or Trinucleotide repeat-containing gene 10 protein, is a transcriptional repressor that may play a role in the specification and differentiation of lung epithelium. It may also play a role in developing neural, gastrointestinal and cardiovascular tissues. FOXP3, also called Scurfin, is a transcriptional regulator which is crucial for the development and inhibitory function of regulatory T-cells (Treg). FOXP4, also called Forkhead-related protein-like A, is a transcriptional repressor that represses lung-specific expression. It is necessary for normal T cell cytokine recall responses to antigen following pathogenic infection. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 73 matched cddid_all.tbl CDD cd20034 cd20034 410808 FH_FOXQ1-like Forkhead (FH) domain found in Forkhead box protein Q1 (FOXQ1) and similar proteins. FOXQ1, also called HNF-3/Forkhead-like protein 1 (HFH-1), or hepatocyte nuclear factor 3 Forkhead homolog 1, plays a role in hair follicle differentiation. It has also been reported to promote epithelial differentiation, inhibit smooth muscle differentiation, activate T cells and autoimmunity, and control mucin gene expression and granule content in stomach surface mucous cells. FOXQ1 is significantly associated with the pathogenesis of various tumor types including gastric, breast, colorectal, pancreatic, bladder and ovarian cancer, and glioma. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 79 matched cddid_all.tbl CDD cd20035 cd20035 410809 FH_FOXQ2-like Forkhead (FH) domain found in Forkhead box protein Q2 (FOXQ2) and similar proteins. FOXQ2 is the neurogenic ectoderm specification transcription factor that controls aboral development in cnidarians and anterior identity in bilaterians. It plays essential roles in epidermal development and central brain patterning. The foxQ2 gene is absent in placental mammals. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 95 matched cddid_all.tbl CDD cd20036 cd20036 410810 FH_FOXR Forkhead (FH) domain found in the Forkhead box protein R (FOXR) subfamily. The FOXR subfamily includes two winged helix transcription factors, FOXR1-2. FOXR1, also called Forkhead box protein N5 (FOXN5), is required for proper cell division and survival possibly via the p21 and mTOR pathways. FOXR2, also called Forkhead box protein N6 (FOXN6), is an important player in a wide range of cellular processes such as proliferation, migration, differentiation, and apoptosis. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 87 matched cddid_all.tbl CDD cd20037 cd20037 410811 FH_FOXS1 Forkhead (FH) domain found in Forkhead box protein S1 (FOXS1). FOXS1, also called Forkhead-like 18 protein or Forkhead-related transcription factor 10 (FREAC-10), is a transcriptional repressor that suppresses transcription from the FASLG, FOXO3, and FOXO4 promoters. It may have a role in the organization of the testicular vasculature. It has also been implicated in energy turnover, motor function, and body weight. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 100 matched cddid_all.tbl CDD cd20038 cd20038 410812 FH_FOXA1 Forkhead (FH) domain found in Forkhead box protein A1 (FOXA1) and similar proteins. FOXA1, also called hepatocyte nuclear factor 3-alpha (HNF-3-alpha or HNF-3A) or transcription factor 3A (TCF-3A), acts as a transcription factor that is essential for epithelial lineage differentiation. It has been found to be upregulated in numerous cancers. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 112 matched cddid_all.tbl CDD cd20039 cd20039 410813 FH_FOXA2 Forkhead (FH) domain found in Forkhead box protein A2 (FOXA2) and similar proteins. FOXA2, also called hepatocyte nuclear factor 3-beta (HNF-3-beta or HNF-3B) or transcription factor 3B (TCF-3B), acts as a core transcription factor that controls cell differentiation. It is a key transcriptional regulator that maintains airway mucus homeostasis. It may also have an important role in bone metabolism. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 104 matched cddid_all.tbl CDD cd20040 cd20040 410814 FH_FOXA3 Forkhead (FH) domain found in Forkhead box protein A3 (FOXA3) and similar proteins. FOXA3, also called hepatocyte nuclear factor 3-gamma (HNF-3-gamma or HNF-3G), fork head-related protein FKH H3, or transcription factor 3G (TCF-3G), acts as an essential transcriptional regulator engaged in adipogenesis and energy metabolism. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 102 matched cddid_all.tbl CDD cd20041 cd20041 410815 FH_dFKH Forkhead (FH) domain found in Drosophila melanogaster protein fork head (dFKH) and similar proteins. dFKH promotes terminal as opposed to segmental development. In the absence of dFKH, this developmental switch does not occur. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 98 matched cddid_all.tbl CDD cd20042 cd20042 410816 FH_FOXB1 Forkhead (FH) domain found in Forkhead box protein B1 (FOXB1) and similar proteins. FOXB1, also called transcription factor FKH-5, is a winged helix transcription factor that controls development of mammary glands and regions of the central nervous system (CNS) that regulate the milk-ejection reflex. It is essential for access of mammillothalamic axons to the thalamus. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 92 matched cddid_all.tbl CDD cd20043 cd20043 410817 FH_FOXB2 Forkhead (FH) domain found in Forkhead box protein B2 (FOXB2) and similar proteins. FOXB2, also called transcription factor FKH-4, may act as a transcription factor. It may also act as a tumor suppressor; it has been found to inhibit the malignant characteristics of the pancreatic cancer cell line Panc-1 in vitro. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 110 matched cddid_all.tbl CDD cd20044 cd20044 410818 FH_FOXC1 Forkhead (FH) domain found in Forkhead box protein C1 (FOXC1) and similar proteins. FOXC1, also called Forkhead-related protein FKHL7, or Forkhead-related transcription factor 3 (FREAC-3), is a DNA-binding transcriptional factor that plays a role in a broad range of cellular and developmental processes such as the development of the eyes, bones, cardiovascular system, kidneys, and skin. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 93 matched cddid_all.tbl CDD cd20045 cd20045 410819 FH_FOXC2 Forkhead (FH) domain found in Forkhead box protein C2 (FOXC2) and similar proteins. FOXC2, also called Forkhead-related protein FKHL14, Mesenchyme fork head protein 1 (MFH-1 protein), or transcription factor FKH-14, acts as a transcriptional activator that might be involved in the formation of special mesenchymal tissues. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 90 matched cddid_all.tbl CDD cd20046 cd20046 410820 FH_FOXD1_D2-like Forkhead (FH) domain found in Forkhead box proteins FOXD1, FOXD2 and similar proteins. FOXD1, also called Forkhead-related protein FKHL8, or Forkhead-related transcription factor 4 (FREAC-4), is involved in transcriptional activation of Placental Growth Factor (PGF) and the complement component (C3) genes. It plays an important role in early embryonic development and organogenesis, and functions as an oncogene in several cancers. FOXD2, also called Forkhead-related protein FKHL17, or Forkhead-related transcription factor 9 (FREAC-9), is a probable transcription factor involved in embryogenesis and somatogenesis. It has been found that long noncoding RNA FOXD2 adjacent opposite strand RNA1 (lncRNA FOXD2-AS1) expression is upregulated in various human malignancies, including gastric, lung, bladder, colorectal, nasopharyngeal, esophageal, hepatocellular, thyroid and skin cancer. It is a promising candidate as a new biomarker and therapeutic target for cancer diagnosis/prognostication due to high tissue specificity and elevated efficiency. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 99 matched cddid_all.tbl CDD cd20047 cd20047 410821 FH_FOXD3 Forkhead (FH) domain found in Forkhead box protein D3 (FOXD3) and similar proteins. FOXD3, also called HNF3/FH transcription factor genesis, acts as a transcriptional repressor that binds to the consensus sequence 5'-A[AT]T[AG]TTTGTTT-3'. It also acts as a transcriptional activator. It promotes development of neural crest cells from neural tube progenitors and restricts neural progenitor cells to the neural crest lineage while suppressing interneuron differentiation. FOXD3 is required for maintenance of pluripotent cells in the pre-implantation and peri-implantation stages of embryogenesis. The FH domain is a winged helix DNA-binding domain. 97 matched cddid_all.tbl CDD cd20048 cd20048 410822 FH_FOXD4-like Forkhead (FH) domain found in Forkhead box protein D4 (FOXD4) and similar proteins. FOXD4, also called Forkhead-related protein FKHL9, Forkhead-related transcription factor 5 (FREAC-5), or myeloid factor-alpha, is essential for establishing neural cell fate and for neuronal differentiation. The family also includes Forkhead box protein D4-like proteins, FOXD4L1-6. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 96 matched cddid_all.tbl CDD cd20049 cd20049 410823 FH_FOXF1 Forkhead (FH) domain found in Forkhead box protein F1 (FOXF1) and similar proteins. FOXF1, also called Forkhead-related activator 1 (FREAC-1), Forkhead-related protein FKHL5, or Forkhead-related transcription factor 1, is a probable transcription activator for a number of lung-specific genes. FOXF1 mutations in sporadic and familial cases of alveolar capillary dysplasia with misaligned pulmonary veins (ACD/MPV) suggest its involvement in ACD/MPV and lung organogenesis. The role of FOXF1 in cancer is conflicting; its loss in some cancers suggests a tumor suppressive function, but its abundance in others is associated with protumorigenic and metastatic traits. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 99 matched cddid_all.tbl CDD cd20050 cd20050 410824 FH_FOXF2 Forkhead (FH) domain found in Forkhead box protein F2 (FOXF2) and similar proteins. FOXF2, also called Forkhead-related activator 2 (FREAC-2), Forkhead-related protein FKHL6, or Forkhead-related transcription factor 2, is a probable transcription activator for a number of lung-specific genes. It is involved in programming organogenesis and regulating epithelial-to-mesenchymal transition (EMT) and cell proliferation. FOXF2 dysregulation is critical for tumorigenesis of various tissue types. Its expression correlates with good prognosis in patients with early non-invasive stages of breast cancer, but with poor prognosis in advanced breast cancer. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 93 matched cddid_all.tbl CDD cd20051 cd20051 410825 FH_FOXJ2 Forkhead (FH) domain found in Forkhead box protein J2 (FOXJ2) and similar proteins. FOXJ2, also called Fork head homologous X (FHX), plays an important role in tumorigenesis, progression, and metastasis of certain cancers. It acts as a transcriptional activator that can bind to two different type of DNA binding sites. It is specifically expressed in meiotic spermatocytes in adult mouse testes and appears to promote meiotic progression during spermatogenesis. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 82 matched cddid_all.tbl CDD cd20052 cd20052 410826 FH_FOXJ3 Forkhead (FH) domain found in Forkhead box protein J3 (FOXJ3) and similar proteins. FOXJ3 is a transcription factor which regulates sperm function. It transcriptionally activates Mef2c and regulates adult skeletal muscle fiber type identity. Polymorphisms in the FOXJ3 gene may be associated with the development of rheumatoid arthritis. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 79 matched cddid_all.tbl CDD cd20053 cd20053 410827 FH_FOXI1 Forkhead (FH) domain found in Forkhead box protein I1 (FOXI1) and similar proteins. FOXI1 is also called Forkhead-related protein FKHL10, Forkhead-related transcription factor 6 (FREAC-6), Hepatocyte nuclear factor 3 Forkhead homolog 3 (HFH-3), or HNF-3/fork-head homolog 3. It is a master regulator of vacuolar H-ATPase proton pump subunits in the inner ear, kidney, and epididymis, and is required for the development of normal hearing, sense of balance, and kidney function. Its epididymal expression is required for male fertility. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 100 matched cddid_all.tbl CDD cd20054 cd20054 410828 FH_FOXK1 Forkhead (FH) domain found in Forkhead box protein K1 (FOXK1) and similar proteins. FOXK1, also called myocyte nuclear factor (MNF), acts as a transcriptional regulator that binds to the upstream enhancer region (CCAC box) of myoglobin genes. It positively regulates Wnt/beta-catenin signaling by translocating dishevelled (DVL) proteins into the nucleus. It also reduces virus replication, probably by binding the interferon stimulated response element (ISRE) to promote antiviral gene expression. In addition, FOXK1 plays important roles in multiple human cancers. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 101 matched cddid_all.tbl CDD cd20055 cd20055 410829 FH_FOXK2 Forkhead (FH) domain found in Forkhead box protein K2 (FOXK2) and similar proteins. FOXK2, also called cellular transcription factor ILF-1 or interleukin enhancer-binding factor 1, is a transcriptional regulator that recognizes the core sequence 5'-TAAACA-3'. It binds to NFAT-like motifs (purine-rich) in the IL2 promoter. It also binds to the HIV-1 long terminal repeat. FOXK2 may be involved in both, positive and negative regulation of important viral and cellular promoter elements. In addition, FOXK2 plays a critical role in suppressing tumorigenesis. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 98 matched cddid_all.tbl CDD cd20056 cd20056 410830 FH_FOXN1 Forkhead (FH) domain found in Forkhead box protein N1 (FOXN1). FOXN1, also called winged helix transcription factor nude, acts as a transcriptional regulator which regulates the development, differentiation, and function of thymic epithelial cells (TECs), both in the prenatal and postnatal thymus. It is also an important factor in controlling the skin wound healing process, as it actively participates in re-epithelialization and is responsible for scar formation. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 97 matched cddid_all.tbl CDD cd20057 cd20057 410831 FH_FOXN4 Forkhead (FH) domain found in Forkhead box protein N4 (FOXN4). FOXN4 acts as a transcription factor essential for neural and some non-neural tissue development, such as retina and lung, respectively. During development of the central nervous system, FOXN4 is required in specifying the amacrine and horizontal cell fates from multipotent retinal progenitors, while suppressing alternative photoreceptor cell fates. In non-neural tissues, it plays an essential role in specifying the atrioventricular canal and is indirectly required for patterning the distal airway during lung development. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 106 matched cddid_all.tbl CDD cd20058 cd20058 410832 FH_FOXN2 Forkhead (FH) domain found in Forkhead box protein N2 (FOXN2). FOXN2, also called human T-cell leukemia virus enhancer factor (HTLF), is a potential tumor suppressor that can facilitate replication fork reversal. It acts as a transcription factor that binds to the purine-rich region in human T-cell leukemia virus long terminal repeat (HTLV-I LTR). It may be a potential therapeutic and radiosensitization target for lung cancer. FOXN2 has also been found to be down-regulated in breast cancer, where it regulates migration, invasion, and epithelial-mesenchymal transition. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 82 matched cddid_all.tbl CDD cd20059 cd20059 410833 FH_FOXN3 Forkhead (FH) domain found in Forkhead box protein N3 (FOXN3). FOXN3, also called checkpoint suppressor 1 (CHES1), acts as a transcriptional repressor that may be involved in DNA damage-inducible cell cycle arrests (checkpoints). It displays transcriptional inhibitory activity, and is involved in cell cycle regulation and tumorigenesis. Alterations in FOXN3 are found in of a variety of cancers including melanoma, osteosarcoma, and hepatocellular carcinoma. FOXN3 also regulates hepatic glucose utilization/metabolism by regulating gluconeogenic substrate selection. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 90 matched cddid_all.tbl CDD cd20060 cd20060 410834 FH_FOXO1 Forkhead (FH) domain found in Forkhead box protein O1 (FOXO1). FOXO1, also called Forkhead box protein O1A or Forkhead in rhabdomyosarcoma (FKHR), is a transcription factor that is the main target of insulin signaling and regulates metabolic homeostasis in response to oxidative stress. It binds to the insulin response element (IRE) with the consensus sequence 5'-TT[G/A]TTTTG-3' and the related Daf-16 family binding element (DBE) with the consensus sequence 5'-TT[G/A]TTTAC-3'. The FH domain is a winged helix DNA-binding domain. 99 matched cddid_all.tbl CDD cd20061 cd20061 410835 FH_FOXO3 Forkhead (FH) domain found in Forkhead box protein O3 (FOXO3). FOXO3, also called AF6q21 protein or Forkhead in rhabdomyosarcoma-like 1 (FKHRL1), is a transcriptional activator which triggers apoptosis in the absence of survival factors, including neuronal cell death upon oxidative stress. It recognizes and binds to the DNA sequence 5'-[AG]TAAA[TC]A-3'. The FH domain is a winged helix DNA-binding domain. All FOXOs bind to the consensus sequence 5'-GTAAACAA-3', known as the DAF-16 family member-binding element, which includes the core sequence 5'-(A/C)AA(C/T)A-3' recognized by all FOX family members. 83 matched cddid_all.tbl CDD cd20062 cd20062 410836 FH_FOXO4 Forkhead (FH) domain found in Forkhead box protein O4 (FOXO4) and similar proteins. FOXO4, also called Fork head domain transcription factor AFX1, is a transcription factor involved in the regulation of the insulin signaling pathway. It binds to insulin-response elements (IREs) and can activate transcription of IGFBP1. The FH domain is a winged helix DNA-binding domain. All FOXOs bind to the consensus sequence 5'-GTAAACAA-3', known as the DAF-16 family member-binding element, which includes the core sequence 5'-(A/C)AA(C/T)A-3' recognized by all FOX family members. 86 matched cddid_all.tbl CDD cd20063 cd20063 410837 FH_FOXO6 Forkhead (FH) domain found in Forkhead box protein O6 (FOXO6) and similar proteins. FOXO6 acts as a transcriptional activator that may play an important role on tumor invasion, metastasis and prognosis. The FH domain is a winged helix DNA-binding domain. All FOXOs bind to the consensus sequence 5'-GTAAACAA-3', known as the DAF-16 family member-binding element, which includes the core sequence 5'-(A/C)AA(C/T)A-3' recognized by all FOX family members. 88 matched cddid_all.tbl CDD cd20064 cd20064 410838 FH_FOXP1 Forkhead (FH) domain found in Forkhead box protein P1 (FOXP1). FOXP1, also called Mac-1-regulated Forkhead (MFH), is a transcription factor that is widely expressed and has a broad range of functions. It has been shown to have a role in cardiac, lung, and lymphocyte development. Deregulation of FOXP1 is an important contributor to the pathogenesis of diffuse large B-cell lymphoma (DLBCL), suggesting it may function as an oncogene. Loss of FOXP1 expression in breast cancer is associated with a worse outcome, suggesting that FOXP1 may function as a tumor suppressor in some tissues. Haploinsufficiency of the FOXP1 gene leads to a neurodevelopmental disorder termed FOXP1 syndrome, characterized by developmental delay, intellectual disability, autism spectrum disorder, speech delay, and dysmorphic features. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 87 matched cddid_all.tbl CDD cd20065 cd20065 410839 FH_FOXP2 Forkhead (FH) domain found in Forkhead box protein P2 (FOXP2). FOXP2, also called CAG repeat protein 44, or Trinucleotide repeat-containing gene 10 protein, is a transcriptional repressor that may play a role in the specification and differentiation of lung epithelium. It may also play a role in developing neural, gastrointestinal, and cardiovascular tissues. An arginine-to-histidine missense mutation (R553H) in the FOXP2 Forkhead domain has been linked to a severe speech and language disorder. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 82 matched cddid_all.tbl CDD cd20066 cd20066 410840 FH_FOXP3 Forkhead (FH) domain found in Forkhead box protein P3 (FOXP3) and similar proteins. FOXP3, also called Scurfin, is a transcriptional regulator which is crucial for the development and inhibitory function of regulatory T-cells (Treg), which are required for maintaining self-tolerance. It may also have intrinsic regulatory function in conventional T (Tconv) cells. A deletion of the Forkhead domain arising from a frame-shift mutation in mouse FOXP3 is linked to the autoimmune disorder scurfy, and a similar congenital disease in humans is known as IPEX (immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome). The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 81 matched cddid_all.tbl CDD cd20067 cd20067 410841 FH_FOXP4 Forkhead (FH) domain found in Forkhead box protein P4 (FOXP4) and similar proteins. FOXP4, also called Forkhead-related protein-like A, is a transcriptional repressor that represses lung-specific expression. It is not required for T cell development, but is necessary for normal T cell cytokine recall responses to antigen following pathogenic infection. The FH domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. 87 matched cddid_all.tbl CDD cd20069 cd20069 410993 5TM_Oxa1-like Five transmembrane core domain of mitochondrial inner membrane protein Oxa1 and similar proteins. This group is composed mostly of the mitochondrial members of the YidC/Oxa1/Alb3 protein family of insertases, including mitochondrial inner membrane proteins Oxa1, Oxa1-like (Oxa1L), cytochrome c oxidase assembly protein 18 (Cox18, also called Oxa2), and Arabidopsis thaliana mitochondrial ALBINO3-like protein 3 (ALB33). It also includes Arabidopsis thaliana chloroplastic ALBINO3-like protein 2 (ALB32). Members of this group mediate the insertion of both mitochondrion-encoded precursors and nuclear-encoded proteins from the matrix into the mitochondrial inner membrane. Oxa1 and Cox18/Oxa2 are essential for the activity and assembly of cytochrome c oxidase, playing central roles in the translocation and export of the N-terminal and C-terminal parts, respectively, of the COX2 protein into the mitochondrial intermembrane space. ALB32 may be involved in the insertion of integral membrane proteins into the chloroplast thylakoid membranes. YidC/Oxa1/Alb3 family insertases contain a core domain of five transmembrane (5TM) segments that is essential to insertase function. 201 matched cddid_all.tbl CDD cd20070 cd20070 410994 5TM_YidC_Alb3 Five transmembrane core domain of membrane protein insertase YidC, Alb3, and similar proteins. This group is composed of the bacterial and chloroplastic members of the YidC/Oxa1/Alb3 protein family of insertases, including bacterial YidC, and chloroplastic ALBINO3 (Alb3) and Alb3-like proteins such as ALBINO3-like protein 1 (also called Alb4). Membrane protein insertase YidC, also called foldase YidC or membrane integrase YidC, facilitates proper folding, insertion, and assembly of inner membrane proteins and complexes. Depending on the nature of the substrate, YidC functions in a Sec-independent (YidC only) or a Sec-dependent manner as part of a complex containing YidC, the SecYEG channel, and SecDFYajC. YidC from Gram-negative bacteria contains an extra transmembrane segment (TM1) at the N-terminus and a large periplasmic domain, located between TM1 and TM2, that adopts a beta-super sandwich fold that is found in sugar-binding proteins such as galactose mutarotase. Alb3 and Alb3-like proteins are required for the post-translational insertion of the light-harvesting chlorophyll-binding proteins (LHCPs) into the chloroplast thylakoid membrane. Alb3 acts independently and may also function cooperatively with the thylakoid cpSecYE translocase to insert proteins co-translationally into the thylakoid membrane, similar to bacterial YidC that can function with the SecYEG translocase. YidC/Oxa1/Alb3 family insertases contain a core domain of five transmembrane (5TM) segments that is essential to insertase function. 181 matched cddid_all.tbl CDD cd20071 cd20071 380997 SET_SMYD SET domain (including SET domain and post-SET domain) found in SET and MYND domain-containing protein, and similar proteins. The family includes SET and MYND domain-containing proteins, SMYD1-SYMD5. SMYD1 (EC 2.1.1.43; also termed BOP) is a heart and muscle specific SET-MYND domain containing protein, which functions as a histone methyltransferase and regulates downstream gene transcription. It methylates histone H3 at 'Lys-4' (H3K4me), seems able to perform both mono-, di-, and trimethylation. SMYD2 (also termed HSKM-B, or lysine N-methyltransferase 3C (KMT3C)) functions as a histone methyltransferase that methylates both histones and non-histone proteins, including p53/TP53 and RB1. It specifically methylates histone H3 'Lys-4' (H3K4me) and dimethylates histone H3 'Lys-36' (H3K36me2). SMYD3 (also termed zinc finger MYND domain-containing protein 1) functions as a histone methyltransferase that specifically methylates 'Lys-4' of histone H3, inducing di- and tri-methylation, but not monomethylation. It also methylates 'Lys-5' of histone H4. SMYD3 plays an important role in transcriptional activation as a member of an RNA polymerase complex. SMYD4 functions as a potential tumor suppressor that plays a critical role in breast carcinogenesis at least partly through inhibiting the expression of PDGFR-alpha. SMYD5 (also termed protein NN8-4AG, or retinoic acid-induced protein 15) functions as histone lysine methyltransferase that mediates H4K20me3 at heterochromatin regions. 122 matched cddid_all.tbl CDD cd20072 cd20072 380998 SET_SET1 SET domain (including post-SET domain) found in catalytic component of the Saccharomyces cerevisiae COMPASS complex and similar proteins. The family contains mostly fungal SET domains, including SET1 found in the catalytic component of the Saccharomyces cerevisiae COMPASS (complex of proteins associated with Set1). SET1 is a histone-lysine N-methyltransferase that specifically methylates 'Lys-4' of histone H3 (H3K4me), when part of the SET1 histone methyltransferase (HMT) complex. The activity of this catalytic domain is established through forming a complex with a set of core proteins; it is extensively contacted by Cps60 (Bre2), Cps50 (Swd1), and Cps30 (Swd3). 148 matched cddid_all.tbl CDD cd20073 cd20073 380999 SET_SUV39H_Clr4-like SET domain (including pre-SET and post-SET domains) found in of Schizosaccharomyces pombe H3K9 methyltransferase Clr4, and similar proteins. This subfamily contains fission yeast Schizosaccharomyces pombe H3K9 methyltransferase Clr4 (also known as Suv39h), the sole homolog of the mammalian SUV39H1 and SUV39H2 enzymes, that has a critical role in preventing aberrant heterochromatin formation. It is known to di- and tri-methylate Lys-9 of histone H3, a central heterochromatic histone modification, with its specificity profile most similar to that of the human SUV39H2 homolog. 259 matched cddid_all.tbl CDD cd20074 cd20074 410850 XPF_nuclease_Mus81 XPF-like nuclease domain of Mus81. Mus81 is a crossover junction endonuclease that interacts with Eme1 and Eme2 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. The typical substrates include 3'-flap structures, replication forks and nicked Holliday junctions. Mus81 may be required in mitosis for the processing of stalled or collapsed replication forks. Mus81 consists of the active nuclease domain with the GDX(n)ERKX(3)D motif which is required for metal-dependent endonuclease activity and two helix-hairpin-helix (HhH2) domains. 150 matched cddid_all.tbl CDD cd20075 cd20075 410851 XPF_nuclease_XPF_arch nuclease domain of XPF found in archaea. XPF, also called DNA excision repair protein ERCC-4, or DNA repair protein complementing XP-F cells, or Xeroderma pigmentosum group F-complementing protein, is a 3'-flap repair endonuclease that cleaves 5' of ds/ssDNA interfaces in 3' flap structures, although it also cuts bubble, Y-DNA structures and mobile and immobile Holliday junctions. XPF cuts preferentially after pyrimidines, may continue to progressively cleave substrate upstream of the initial cleavage, at least in vitro. It may be involved in nucleotide excision repair. The nuclease domains of the catalytic subunits XPF have the GDX(n)ERKX(3)D motif which is required for metal-dependent endonuclease activity but not for DNA junction binding. XPF-ERRC1 and its yeast homolog Rad1-Rad10 play key roles in the excision of DNA lesions and are required for certain types of homologous recombination events and for the repair of DNA cross-links. 127 matched cddid_all.tbl CDD cd20076 cd20076 410852 XPF_nuclease_FAAP24 XPF-like nuclease domain of Fanconi anemia associated protein 24 kDa (FAAP24). FAAP24, also called Fanconi anemia core complex-associated protein 24, plays a role in DNA repair through recruitment of the Fanconi anemia (FA) core complex to damaged DNA. It regulates FANCD2 monoubiquitination upon DNA damage and induces chromosomal instability as well as hypersensitivity to DNA cross-linking agents, when repressed. FAAP24 may possess a high affinity toward single-stranded DNA (ssDNA). The nuclease domain of FAAP24 lacks the catalytic motif. The FANCM/FAAP24 complex is related to XPF/MUS81 endonucleases but lacks endonucleolytic activity. It binds branched DNA structures containing ssDNA regions, such as splayed-arm and 3'-flap DNA structures, and anchors the FA core complex to chromatin in repairing DNA interstrand crosslinks. 123 matched cddid_all.tbl CDD cd20077 cd20077 410853 XPF_nuclease_FANCM XPF-like nuclease domain of Fanconi anemia group M protein (FANCM). FANCM (EC 3.6.4.13), also called Fanconi anemia-associated polypeptide of 250 kDa (FAAP250), or protein Hef ortholog, or ATP-dependent RNA helicase FANCM, is a DNA-dependent ATPase component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. In complex with CENPS and CENPX, it binds double-stranded DNA (dsDNA), fork-structured DNA (fsDNA) and Holliday junction substrates. In complex with FAAP24, it efficiently binds to single-strand DNA (ssDNA), splayed-arm DNA, and 3'-flap substrates. In vitro, on its own, FANCM strongly binds ssDNA oligomers and weakly fsDNA, but does not bind to dsDNA. 139 matched cddid_all.tbl CDD cd20078 cd20078 410854 XPF_nuclease_XPF_euk nuclease domain of XPF found in eukaryotes. XPF, also called DNA excision repair protein ERCC-4, or DNA repair protein complementing XP-F cells, or Xeroderma pigmentosum group F-complementing protein, is a DNA repair endonuclease that is a catalytic component of a structure-specific DNA repair endonuclease responsible for the 5-prime incision during DNA repair. It is involved in homologous recombination that assists in removing interstrand cross-link. The nuclease domains of the catalytic subunits XPF have the GDX(n)ERKX(3)D motif which is required for metal-dependent endonuclease activity but not for DNA junction binding. XPF-ERRC1 and its yeast homolog Rad1-Rad10 play key roles in the excision of DNA lesions and are required for certain types of homologous recombination events and for the repair of DNA cross-links. 136 matched cddid_all.tbl CDD cd20079 cd20079 410855 XPF_nuclease_ERCC1 XPF-like nuclease domain of DNA excision repair protein ERCC1. ERCC1 is a non-catalytic component of a structure-specific DNA repair endonuclease responsible for the 5'-incision during DNA repair. In conjunction with SLX4, ERCC1 is responsible for the first step in the repair of interstrand cross-links (ICL), as well as for homology-directed repair (HDR) of DNA double-strand breaks. ERCC1 participates in the processing of anaphase bridge-generating DNA structures, which consist in incompletely processed DNA lesions arising during S or G2 phase, and can result in cytokinesis failure. ERCC1 also plays a critical role in targeting the XPF-ERCC1 complex to DNA. XPF-ERRC1 and its yeast homolog Rad1-Rad10 play key roles in the excision of DNA lesions and are required for certain types of homologous recombination events and for the repair of DNA cross-links. The critical motif, DX(n)ERKX(3)D, for endonuclease activity is absent in the nuclease domain of ERCC1. 115 matched cddid_all.tbl CDD cd20080 cd20080 410856 XPF_nuclease_EME-like XPF-like nuclease domain of the family of Essential Meiotic Endonucleases (EMEs) and similar proteins. The family of EMEs includes EME1 and EME2. EME1, also called MMS4 homolog (hMMS4), interacts with MUS81 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. Its typical substrates include 3'-flap structures, replication forks and nicked Holliday junctions. EME1 may be required in mitosis for the processing of stalled or collapsed replication forks. EME2 interacts with MUS81 to form a DNA structure-specific endonuclease which cleaves substrates such as 3'-flap structures. MUS81-EME2 is responsible for fork cleavage and restart in human cells. The MUS81-EME2 protein, whose actions are restricted to S phase, is also responsible for telomere maintenance in telomerase-negative ALT (Alternative Lengthening of Telomeres) cells. The nuclease domain of EMEs is a nuclease-like domain which is involved in targeting the MUS81-EME heterodimer complex to DNA. The family also includes budding yeast Mms4 (also known as Eme1 in other organisms), a putative transcriptional (co)activator that protects Saccharomyces cerevisiae cells from endogenous and environmental DNA damage. It interacts with MUS81 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. The nuclease domain of Mms4 lacks the catalytic motif. 164 matched cddid_all.tbl CDD cd20081 cd20081 410857 XPF_nuclease_EME1 XPF-like nuclease domain of crossover junction endonuclease EME1. EME1, also called MMS4 homolog (hMMS4), interacts with MUS81 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. Its typical substrates include 3'-flap structures, replication forks and nicked Holliday junctions. EME1 may be required in mitosis for the processing of stalled or collapsed replication forks. The nuclease domain of EME1 is a nuclease-like domain which is involved in targeting the MUS81-EME1 heterodimer complex to DNA. 179 matched cddid_all.tbl CDD cd20082 cd20082 410858 XPF_nuclease_EME2 XPF-like nuclease domain of crossover junction endonuclease EME2. EME2 interacts with MUS81 to form a DNA structure-specific endonuclease which cleaves substrates such as 3'-flap structures. MUS81-EME2 is responsible for fork cleavage and restart in human cells. The MUS81-EME2 protein, whose actions are restricted to S phase, is also responsible for telomere maintenance in telomerase-negative ALT (Alternative Lengthening of Telomeres) cells. The nuclease domain of EME2 is a nuclease-like domain which is involved in targeting the MUS81-EME2 heterodimer complex to DNA. 195 matched cddid_all.tbl CDD cd20083 cd20083 410859 XPF_nuclease_EME XPF-like nuclease domain of crossover junction endonucleases, EME1, EME2 and similar proteins. The Mus81-EME1 complex is a structure-selective endonuclease with a critical role in the resolution of recombination intermediates during DNA repair after interstrand cross-links, replication fork collapse, or double-strand breaks. ERCC4 domain of Eme1 is a nuclease-like domain which is involved in targeting the MUS81-EME1 heterodimer complex to DNA. 179 matched cddid_all.tbl CDD cd20085 cd20085 410860 XPF_nuclease_Mms4 XPF-like nuclease domain of Saccharomyces cerevisiae crossover junction endonuclease Mms4 and similar proteins. Budding yeast Mms4, also known as Eme1 in other organisms, is a putative transcriptional (co)activator that protects Saccharomyces cerevisiae cells from endogenous and environmental DNA damage. It interacts with MUS81 to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. Typical substrates include 3'-flap structures, D-loops, replication forks with regressed leading strands and nicked Holliday junctions. The nuclease domain of Mms4 lacks the catalytic motif. 220 matched cddid_all.tbl CDD cd20088 cd20088 439080 MBT malignant brain tumor (MBT) repeat. The MBT repeat is a protein module that recognizes methylated lysine residues on histones and are thought to affect a variety of chromatin processes, including transcription. It exists as tandem repeats and is found in a number of nuclear proteins such as Drosophila sex comb on midleg protein. In the human genome, there are at least 9 MBT repeat proteins, each containing two, three or four MBT repeats. MBT repeat proteins use a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine (monomethyllysine and/or dimethyllysine). 61 matched cddid_all.tbl CDD cd20090 cd20090 438853 F-box_FBXW4 F-box domain found in F-box/WD repeat-containing protein 4 (FBXW4) and similar proteins. FBXW4, also called dactylin, or F-box and WD-40 domain-containing protein 4, probably recognizes and binds to some phosphorylated proteins and promotes their ubiquitination and degradation. It is likely to be involved in key signaling pathways crucial for normal limb development. It may participate in Wnt signaling and act as a novel tumor suppressor that regulates important cellular processes. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 47 matched cddid_all.tbl CDD cd20091 cd20091 439081 MBT_dScm-like_rpt1 first malignant brain tumor (MBT) repeat found in the sex comb on midleg family. The sex comb on midleg (Scm) family of Polycomb proteins includes Drosophila melanogaster Scm protein, as well as two vertebrate homologs of Scm, sex comb on midleg homolog 1 (SCMH1) and sex comb on midleg-like protein 2 (SCML2). Scm is a putative zinc finger protein that functions as a transcriptional regulator which represses multiple homeotic genes during embryonic stages. It coordinates Polycomb group (PcG) complexes, PRC1 (PcG-repressive complex 1) or PRC2 (PcG-repressive complex 2), and polymerizes to produce broad domains of PcG silencing. Both SCMH1 and SCML2 are components of PRC1, which acts as an E3 ubiquitin ligase both for histone H2A to silence transcription and for geminin to regulate its stability. SCMH1 provides the complex with an interaction domain for geminin. SCML2 is a germline-specific Polycomb protein that acts as a critical regulator of heterochromatin organization in spermatogenesis. Members of this family contain two MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the first MBT repeat that does not contain a semi-aromatic cage and may not bind methylated lysine residues. 97 matched cddid_all.tbl CDD cd20092 cd20092 439082 MBT_dScm-like_rpt2 second malignant brain tumor (MBT) repeat found in the Polycomb protein sex comb on midleg family. The Sex comb on midleg (Scm) family of Polycomb proteins includes Drosophila melanogaster Scm protein, as well as two vertebrate homologs of Scm, Polycomb protein sex comb on midleg homolog 1 (SCMH1) and sex comb on midleg-like protein 2 (SCML2). Scm is a putative zinc finger protein that functions as a transcriptional regulator which represses multiple homeotic genes during embryonic stages. It coordinates Polycomb group (PcG) complexes, PRC1 (PcG-repressive complex 1) or PRC2 (PcG-repressive complex 2), and polymerizes to produce broad domains of PcG silencing. Both SCMH1 and SCML2 are components of PRC1, which acts as an E3 ubiquitin ligase both for histone H2A to silence transcription and for geminin to regulate its stability. SCMH1 provides the complex with an interaction domain for geminin. SCML2 is a germline-specific Polycomb protein that acts as a critical regulator of heterochromatin organization in spermatogenesis. Members of this family contain two MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the second MBT repeat that contains the semi-aromatic cage that binds methylated lysine residues. 75 matched cddid_all.tbl CDD cd20093 cd20093 439083 MBT_SFMBT_rpt1 first malignant brain tumor (MBT) repeat found in the Scm-like with four MBT domains protein (SFMBT) family. The SFMBT family includes SFMBT1 and SFMBT2. SFMBT1, also called renal ubiquitous protein 1, is a transcriptional repressor protein that selectively binds the N-terminal tail of histone H3 and functions as a chromatin reader in regulating epigenetic silencing and the myogenic gene program. It mediates the recruitment of corepressor complexes to target genes, followed by chromatin compaction and repression of transcription. SFMBT2, also called Scm-like with 4 MBT domains protein 2, is a transcriptional repressor of the HOXB13 gene. It is required for trophoblast maintenance and placenta development. It also negatively regulates cell migration and invasion in prostate cancer cells. Members of this family contain four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the first MBT repeat that contains a partially conserved semi-aromatic cage. 94 matched cddid_all.tbl CDD cd20094 cd20094 439084 MBT_SFMBT_rpt2 second malignant brain tumor (MBT) repeat found in the Scm-like with four MBT domains protein (SFMBT) family. The SFMBT family includes SFMBT1 and SFMBT2. SFMBT1, also called renal ubiquitous protein 1, is a transcriptional repressor protein that selectively binds the N-terminal tail of histone H3 and functions as a chromatin reader in regulating epigenetic silencing and the myogenic gene program. It mediates the recruitment of corepressor complexes to target genes, followed by chromatin compaction and repression of transcription. SFMBT2, also called Scm-like with 4 MBT domains protein 2, is a transcriptional repressor of the HOXB13 gene. It is required for trophoblast maintenance and placenta development. It also negatively regulates cell migration and invasion in prostate cancer cells. Members of this family contain four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the second MBT repeat that contains a partially conserved semi-aromatic cage. 91 matched cddid_all.tbl CDD cd20095 cd20095 439085 MBT_SFMBT_rpt3 third malignant brain tumor (MBT) repeat found in the Scm-like with four MBT domains protein (SFMBT) family. The SFMBT family includes SFMBT1 and SFMBT2. SFMBT1, also called renal ubiquitous protein 1, is a transcriptional repressor protein that selectively binds the N-terminal tail of histone H3 and functions as a chromatin reader in regulating epigenetic silencing and the myogenic gene program. It mediates the recruitment of corepressor complexes to target genes, followed by chromatin compaction and repression of transcription. SFMBT2, also called Scm-like with 4 MBT domains protein 2, is a transcriptional repressor of the HOXB13 gene. It is required for trophoblast maintenance and placenta development. It also negatively regulates cell migration and invasion in prostate cancer cells. Members of this family contain four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the third MBT repeat that does not contain a semi-aromatic cage and may not bind methylated lysine residues. 92 matched cddid_all.tbl CDD cd20096 cd20096 439086 MBT_SFMBT_rpt4 fourth malignant brain tumor (MBT) repeat found in the Scm-like with four MBT domains protein (SFMBT) family. The SFMBT family includes SFMBT1 and SFMBT2. SFMBT1, also called renal ubiquitous protein 1, is a transcriptional repressor protein that selectively binds the N-terminal tail of histone H3 and functions as a chromatin reader in regulating epigenetic silencing and the myogenic gene program. It mediates the recruitment of corepressor complexes to target genes, followed by chromatin compaction and repression of transcription. SFMBT2, also called Scm-like with 4 MBT domains protein 2, is a transcriptional repressor of the HOXB13 gene. It is required for trophoblast maintenance and placenta development. It also negatively regulates cell migration and invasion in prostate cancer cells. Members of this family contain four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the fourth MBT repeat that does not contain a semi-aromatic cage and may not bind methylated lysine residues. 73 matched cddid_all.tbl CDD cd20097 cd20097 439087 MBT_dSfmbt-like_rpt1 first malignant brain tumor (MBT) repeat found in the Drosophila melanogaster Polycomb protein Sfmbt (dSfmbt)-like family. The dSfmbt-like family includes Drosophila melanogaster Scm-like with four MBT domain-containing protein 1 (dSfmbt), as well as its two vertebrate homologs, MBT domain-containing protein 1 (MBTD1) and Lethal(3)malignant brain tumor-like protein 2 (L3MBTL2). dSfmbt is a Polycomb group (PcG) repressor involved in epigenetic regulation of gene expression. MBTD1 and L3MBTL2, also called L(3)mbt-like protein 2, are putative PcG proteins that specifically bind to monomethylated and dimethylated 'Lys-20' on histone H4. L3MBTL2 also binds histone H3 peptides which are monomethylated or dimethylated on 'Lys-4', 'Lys-9' or 'Lys-27'. Members of this family contain four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the first MBT repeat that contains a partially conserved semi-aromatic cage. 105 matched cddid_all.tbl CDD cd20098 cd20098 439088 MBT_dSfmbt-like_rpt2 second malignant brain tumor (MBT) repeat found in the Drosophila melanogaster Polycomb protein Sfmbt (dSfmbt)-like family. The dSfmbt-like family includes Drosophila melanogaster Scm-like with four MBT domain-containing protein 1 (dSfmbt), as well as its two vertebrate homologs, MBT domain-containing protein 1 (MBTD1) and Lethal(3)malignant brain tumor-like protein 2 (L3MBTL2). dSfmbt is a Polycomb group (PcG) repressor involved in epigenetic regulation of gene expression. MBTD1 and L3MBTL2, also called L(3)mbt-like protein 2, are putative PcG proteins that specifically bind to monomethylated and dimethylated 'Lys-20' on histone H4. L3MBTL2 also binds histone H3 peptides which are monomethylated or dimethylated on 'Lys-4', 'Lys-9' or 'Lys-27'. Members of this family contain four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the second MBT repeat that does not seem to contain a semi-aromatic cage and may not bind methylated lysine residues. 83 matched cddid_all.tbl CDD cd20099 cd20099 439089 MBT_dSfmbt-like_rpt3 third malignant brain tumor (MBT) repeat found in the Drosophila melanogaster Polycomb protein Sfmbt (dSfmbt)-like family. The dSfmbt-like family includes Drosophila melanogaster Scm-like with four MBT domain-containing protein 1 (dSfmbt), as well as its two vertebrate homologs, MBT domain-containing protein 1 (MBTD1) and Lethal(3)malignant brain tumor-like protein 2 (L3MBTL2). dSfmbt is a Polycomb group (PcG) repressor involved in epigenetic regulation of gene expression. MBTD1 and L3MBTL2, also called L(3)mbt-like protein 2, are putative PcG proteins that specifically bind to monomethylated and dimethylated 'Lys-20' on histone H4. L3MBTL2 also binds histone H3 peptides which are monomethylated or dimethylated on 'Lys-4', 'Lys-9' or 'Lys-27'. Members of this family contain four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the third MBT repeat that does not seem to contain a semi-aromatic cage and may not bind methylated lysine residues. 91 matched cddid_all.tbl CDD cd20100 cd20100 439090 MBT_dSfmbt-like_rpt4 fourth malignant brain tumor (MBT) repeat found in the Drosophila melanogaster Polycomb protein Sfmbt (dSfmbt)-like family. The dSfmbt-like family includes Drosophila melanogaster Scm-like with four MBT domain-containing protein 1 (dSfmbt), as well as its two vertebrate homologs, MBT domain-containing protein 1 (MBTD1) and Lethal(3)malignant brain tumor-like protein 2 (L3MBTL2). dSfmbt is a Polycomb group (PcG) repressor involved in epigenetic regulation of gene expression. MBTD1 and L3MBTL2, also called L(3)mbt-like protein 2, are putative PcG proteins that specifically bind to monomethylated and dimethylated 'Lys-20' on histone H4. L3MBTL2 also binds histone H3 peptides which are monomethylated or dimethylated on 'Lys-4', 'Lys-9' or 'Lys-27'. Members of this family contain four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the fourth MBT repeat that contains the semi-aromatic cage that binds methylated lysine residues. 71 matched cddid_all.tbl CDD cd20101 cd20101 439091 MBT_L3MBTL1-like_rpt1 first malignant brain tumor (MBT) repeat found in the Lethal(3)malignant brain tumor-like protein 1 (L3MBTL1)-like family. The L3MBTL1-like family includes L3MBTL1, L3MBTL3, and L3MBTL4. L3MBTL1, also called L(3)mbt-like, or L(3)mbt protein homolog, is a Polycomb group (PcG) protein that functions as a 'reader' of a network of post-translational modifications by specifically recognizing and binding mono- and dimethyllysine residues on target proteins. It acts as a chromatin compaction factor by binding mono- and dimethylated histone H1b/HIST1H1E at 'Lys-26' (H1bK26me1 and H1bK26me2) and histone H4 at 'Lys-20' (H4K20me1 and H4K20me2), leading to condensed chromatin and repressed transcription. L3MBTL3, also called L(3)mbt-like protein 3, or MBT-1, is a PcG protein that recognizes mono- and dimethylated lysine residues on histone tails. It also acts as a methyl-binding protein that binds the K142-methylated DNMT1 and recruits a novel CRL4(DCAF5) ubiquitin ligase to degrade DNMT1. L3MBTL4, also called L(3)mbt-like protein 4, or L3mbt-like 4, is a PcG protein that may act as a tumor suppressor. Members of this family contain three MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the first MBT repeat that contains the semi-aromatic cage and may bind methylated lysine residues. 101 matched cddid_all.tbl CDD cd20102 cd20102 439092 MBT_L3MBTL1-like_rpt2 second malignant brain tumor (MBT) repeat found in the Lethal(3)malignant brain tumor-like protein 1 (L3MBTL1)-like family. The L3MBTL1-like family includes L3MBTL1, L3MBTL3, and L3MBTL4. L3MBTL1, also called L(3)mbt-like, or L(3)mbt protein homolog, is a Polycomb group (PcG) protein that functions as a 'reader' of a network of post-translational modifications by specifically recognizing and binding mono- and dimethyllysine residues on target proteins. It acts as a chromatin compaction factor by binding mono- and dimethylated histone H1b/HIST1H1E at 'Lys-26' (H1bK26me1 and H1bK26me2) and histone H4 at 'Lys-20' (H4K20me1 and H4K20me2), leading to condensed chromatin and repressed transcription. L3MBTL3, also called L(3)mbt-like protein 3, or MBT-1, is a PcG protein that recognizes mono- and dimethylated lysine residues on histone tails. It also acts as a methyl-binding protein that binds the K142-methylated DNMT1 and recruits a novel CRL4(DCAF5) ubiquitin ligase to degrade DNMT1. L3MBTL4, also called L(3)mbt-like protein 4, or L3mbt-like 4, is a PcG protein that may act as a tumor suppressor. Members of this family contain three MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the second MBT repeat that contains the semi-aromatic cage that binds methylated lysine residues. 90 matched cddid_all.tbl CDD cd20103 cd20103 439093 MBT_L3MBTL1-like_rpt3 third malignant brain tumor (MBT) repeat found in the Lethal(3)malignant brain tumor-like protein 1 (L3MBTL1)-like family. The L3MBTL1-like family includes L3MBTL1, L3MBTL3, and L3MBTL4. L3MBTL1, also called L(3)mbt-like, or L(3)mbt protein homolog, is a Polycomb group (PcG) protein that functions as a 'reader' of a network of post-translational modifications by specifically recognizing and binding mono- and dimethyllysine residues on target proteins. It acts as a chromatin compaction factor by binding mono- and dimethylated histone H1b/HIST1H1E at 'Lys-26' (H1bK26me1 and H1bK26me2) and histone H4 at 'Lys-20' (H4K20me1 and H4K20me2), leading to condensed chromatin and repressed transcription. L3MBTL3, also called L(3)mbt-like protein 3, or MBT-1, is a PcG protein that recognizes mono- and dimethylated lysine residues on histone tails. It also acts as a methyl-binding protein that binds the K142-methylated DNMT1 and recruits a novel CRL4(DCAF5) ubiquitin ligase to degrade DNMT1. L3MBTL4, also called L(3)mbt-like protein 4, or L3mbt-like 4, is a PcG protein that may act as a tumor suppressor. Members of this family contain three MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the third MBT repeat that contains the semi-aromatic cage that may bind methylated lysine residues. 73 matched cddid_all.tbl CDD cd20104 cd20104 439094 MBT_PHF20L1-like malignant brain tumor (MBT) repeat found in PHD finger protein 20-like protein 1 (PHF20L1) and similar domains. PHF20L1 associates with SOX2, antagonizes SOX2 ubiquitination and the sequential degradation induced by MLL1/WDR5 complexes. It binds both monomethylated Lys-42 and Lys-117 in SOX2 and thereby prevents SOX2 proteolysis. PHF20L1 also reads and controls enzyme levels of methylated DNMT1 in cells, thus representing a novel antagonist of DNMT1 degradation. PHF20L1 contains one MBT (malignant brain tumor) repeat. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the MBT repeat of PHF20L1 and similar domains that contains the semi-aromatic cage that may bind methylated lysine residues. 60 matched cddid_all.tbl CDD cd20105 cd20105 439095 MBT_SCMH1_rpt1 first malignant brain tumor (MBT) repeat found in Polycomb protein sex comb on midleg homolog 1. Sex comb on midleg homolog 1 (SCMH1) is a homolog of Drosophila Sex comb on midleg (Scm). It is a component of PRC1 (Polycomb repressive complex 1), which acts as an E3 ubiquitin ligase, both for histone H2A to silence transcription and for geminin to regulate its stability. SCMH1 provides the complex with an interaction domain for geminin. It contains two MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the first MBT repeat that does not contain a semi-aromatic cage and may not bind methylated lysine residues. 131 matched cddid_all.tbl CDD cd20106 cd20106 439096 MBT_SCML2_rpt1 first malignant brain tumor (MBT) repeat found in sex comb on midleg-like protein 2. Sex comb on midleg-like protein 2 (SCML2) is a homolog of Drosophila Sex comb on midleg (Scm). It is a component of PRC1 (Polycomb repressive complex 1), which acts as an E3 ubiquitin ligase, both for histone H2A to silence transcription and for geminin to regulate its stability. SCML2 is a germline-specific Polycomb protein that acts as a critical regulator of heterochromatin organization in spermatogenesis. SCML2 contains two MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the first MBT repeat that does not contain a semi-aromatic cage and may not bind methylated lysine residues. 98 matched cddid_all.tbl CDD cd20107 cd20107 439097 MBT_dScm_rpt1 first malignant brain tumor (MBT) repeat found in Drosophila melanogaster Polycomb protein sex comb on midleg and similar proteins. Sex comb on midleg (Scm) is a putative zinc finger protein that functions as a transcriptional regulator which represses multiple homeotic genes during embryonic stages. It coordinates Polycomb group (PcG) complexes, PRC1 (PcG-repressive complex 1) or PRC2 (PcG-repressive complex 2), and polymerizes to produce broad domains of PcG silencing. Scm contains two MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the first MBT repeat that does not contain a semi-aromatic cage and may not bind methylated lysine residues. 99 matched cddid_all.tbl CDD cd20108 cd20108 439098 MBT_SCMH1_rpt2 second malignant brain tumor (MBT) repeat found in Polycomb protein sex comb on midleg homolog 1 (SCMH1) and similar proteins. SCMH1 is a homolog of Drosophila Sex comb on midleg (Scm). It is a component of PRC1 (Polycomb repressive complex 1), which acts as an E3 ubiquitin ligase, both for histone H2A to silence transcription and for geminin to regulate its stability. SCMH1 provides the complex with an interaction domain for geminin. It contains two MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the second MBT repeat that contains the semi-aromatic cage that binds methylated lysine residues. 75 matched cddid_all.tbl CDD cd20109 cd20109 439099 MBT_SCML2_rpt2 second malignant brain tumor (MBT) repeat found in sex comb on midleg-like protein 2 (SCML2) and similar proteins. SCML2 is a homolog of Drosophila Sex comb on midleg (Scm). It is a component of PRC1 (Polycomb repressive complex 1), which acts as an E3 ubiquitin ligase, both for histone H2A to silence transcription and for geminin to regulate its stability. SCML2 is a germline-specific Polycomb protein that acts as a critical regulator of heterochromatin organization in spermatogenesis. SCML2 contains two MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the second MBT repeat that contains the semi-aromatic cage that binds methylated lysine residues. 77 matched cddid_all.tbl CDD cd20110 cd20110 439100 MBT_dScm_rpt2 second malignant brain tumor (MBT) repeat found in Drosophila melanogaster Polycomb protein sex comb on midleg (Scm) and similar proteins. Scm is a putative zinc finger protein that functions as a transcriptional regulator which represses multiple homeotic genes during embryonic stages. It coordinates Polycomb group (PcG) complexes, PRC1 (PcG-repressive complex 1) or PRC2 (PcG-repressive complex 2), and polymerizes to produce broad domains of PcG silencing. Scm contains two MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the second MBT repeat that contains the semi-aromatic cage that binds methylated lysine residues. 75 matched cddid_all.tbl CDD cd20111 cd20111 439101 MBT_SFMBT1_rpt1 first malignant brain tumor (MBT) repeat found in Scm-like with four MBT domains protein 1 (SFMBT1). SFMBT1, also called renal ubiquitous protein 1, is a transcriptional repressor protein that selectively binds the N-terminal tail of histone H3 and functions as a chromatin reader in regulating epigenetic silencing and the myogenic gene program. It mediates the recruitment of corepressor complexes to target genes, followed by chromatin compaction and repression of transcription. SFMBT1 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the first MBT repeat that contains a partially conserved semi-aromatic cage. 94 matched cddid_all.tbl CDD cd20112 cd20112 439102 MBT_SFMBT2_rpt1 first malignant brain tumor (MBT) repeat found in Scm-like with four MBT domains protein 2 (SFMBT2). SFMBT2, also called Scm-like with 4 MBT domains protein 2, is a transcriptional repressor of the HOXB13 gene. It is required for trophoblast maintenance and placenta development. It also negatively regulates cell migration and invasion in prostate cancer cells. SFMBT2 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the first MBT repeat that contains a partially conserved semi-aromatic cage. 94 matched cddid_all.tbl CDD cd20113 cd20113 439103 MBT_SFMBT1_rpt2 second malignant brain tumor (MBT) repeat found in Scm-like with four MBT domains protein 1 (SFMBT1). SFMBT1, also called renal ubiquitous protein 1, is a transcriptional repressor protein that selectively binds the N-terminal tail of histone H3 and functions as a chromatin reader in regulating epigenetic silencing and the myogenic gene program. It mediates the recruitment of corepressor complexes to target genes, followed by chromatin compaction and repression of transcription. SFMBT1 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the second MBT repeat that contains a partially conserved semi-aromatic cage. 99 matched cddid_all.tbl CDD cd20114 cd20114 439104 MBT_SFMBT2_rpt2 second malignant brain tumor (MBT) repeat found in Scm-like with four MBT domains protein 2 (SFMBT2). SFMBT2, also called Scm-like with 4 MBT domains protein 2, is a transcriptional repressor of the HOXB13 gene. It is required for trophoblast maintenance and placenta development. It also negatively regulates cell migration and invasion in prostate cancer cells. SFMBT2 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the second MBT repeat that contains a partially conserved semi-aromatic cage. 98 matched cddid_all.tbl CDD cd20115 cd20115 439105 MBT_SFMBT1_rpt3 third malignant brain tumor (MBT) repeat found in Scm-like with four MBT domains protein 1 (SFMBT1). SFMBT1, also called renal ubiquitous protein 1, is a transcriptional repressor protein that selectively binds the N-terminal tail of histone H3 and functions as a chromatin reader in regulating epigenetic silencing and the myogenic gene program. It mediates the recruitment of corepressor complexes to target genes, followed by chromatin compaction and repression of transcription. SFMBT1 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the third MBT repeat that does not contain a semi-aromatic cage and may not bind methylated lysine residues. 94 matched cddid_all.tbl CDD cd20116 cd20116 439106 MBT_SFMBT2_rpt3 three malignant brain tumor (MBT) repeat found in Scm-like with four MBT domains protein 2 (SFMBT2). SFMBT2, also called Scm-like with 4 MBT domains protein 2, is a transcriptional repressor of the HOXB13 gene. It is required for trophoblast maintenance and placenta development. It also negatively regulates cell migration and invasion in prostate cancer cells. SFMBT2 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the third MBT repeat that does not contain a semi-aromatic cage and may not bind methylated lysine residues. 93 matched cddid_all.tbl CDD cd20117 cd20117 439107 MBT_SFMBT1_rpt4 fourth malignant brain tumor (MBT) repeat found in Scm-like with four MBT domains protein 1 (SFMBT1). SFMBT1, also called renal ubiquitous protein 1, is a transcriptional repressor protein that selectively binds the N-terminal tail of histone H3 and functions as a chromatin reader in regulating epigenetic silencing and the myogenic gene program. It mediates the recruitment of corepressor complexes to target genes, followed by chromatin compaction and repression of transcription. SFMBT1 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the fourth MBT repeat that does not contain a semi-aromatic cage and may not bind methylated lysine residues. 90 matched cddid_all.tbl CDD cd20118 cd20118 439108 MBT_SFMBT2_rpt4 fourth malignant brain tumor (MBT) repeat found in Scm-like with four MBT domains protein 2 (SFMBT2). SFMBT2, also called Scm-like with 4 MBT domains protein 2, is a transcriptional repressor of the HOXB13 gene. It is required for trophoblast maintenance and placenta development. It also negatively regulates cell migration and invasion in prostate cancer cells. SFMBT2 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the fourth MBT repeat that does not contain a semi-aromatic cage and may not bind methylated lysine residues. 91 matched cddid_all.tbl CDD cd20119 cd20119 439109 MBT_dSfmbt_rpt1 first malignant brain tumor (MBT) repeat found in Drosophila melanogaster Polycomb protein Sfmbt (dSfmbt) and similar proteins. dSfmbt, also called Scm-like with four MBT domain-containing protein 1, is a Polycomb group repressor involved in epigenetic regulation of gene expression. dSfmbt contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the first MBT repeat that contains a partially conserved semi-aromatic cage. 104 matched cddid_all.tbl CDD cd20120 cd20120 439110 MBT_MBTD1_rpt1 first malignant brain tumor (MBT) repeat found in MBT domain-containing protein 1 (MBTD1). MBTD1 is a putative Polycomb group (PcG) protein that specifically binds to monomethylated and dimethylated 'Lys-20' on histone H4. MBTD1 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the first MBT repeat that contains a partially conserved semi-aromatic cage. 103 matched cddid_all.tbl CDD cd20121 cd20121 439111 MBT_L3MBTL2_rpt1 first malignant brain tumor (MBT) repeat found in Lethal(3)malignant brain tumor-like protein 2 (L3MBTL2) and similar proteins. L3MBTL2, also called L(3)mbt-like protein 2, is a putative Polycomb group (PcG) protein that binds to monomethylated and dimethylated 'Lys-20' on histone H4 and also binds histone H3 peptides which are monomethylated or dimethylated on 'Lys-4', 'Lys-9' or 'Lys-27'. L3MBTL2 orchestrates ubiquitin signalling by dictating the sequential recruitment of RNF8 and RNF168 after DNA damage. It is an integral component of the polycomb repressive complex 1.6 (PRC1.6) and has been implicated in transcriptional repression and chromatin compaction. L3MBTL2 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the first MBT repeat that contains a partially conserved semi-aromatic cage. 102 matched cddid_all.tbl CDD cd20122 cd20122 439112 MBT_dSfmbt_rpt2 second malignant brain tumor (MBT) repeat found in Drosophila melanogaster Polycomb protein Sfmbt (dSfmbt) and similar proteins. dSfmbt, also called Scm-like with four MBT domain-containing protein 1, is a Polycomb group repressor involved in epigenetic regulation of gene expression. dSfmbt contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the second MBT repeat that does not seem to contain a semi-aromatic cage and may not bind methylated lysine residues. 83 matched cddid_all.tbl CDD cd20123 cd20123 439113 MBT_MBTD1_rpt2 second malignant brain tumor (MBT) repeat found in MBT domain-containing protein 1 (MBTD1). MBTD1 is a putative Polycomb group (PcG) protein that specifically binds to monomethylated and dimethylated 'Lys-20' on histone H4. MBTD1 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the second MBT repeat that does not seem to contain a semi-aromatic cage and may not bind methylated lysine residues. 85 matched cddid_all.tbl CDD cd20124 cd20124 439114 MBT_L3MBTL2_rpt2 second malignant brain tumor (MBT) repeat found in Lethal(3)malignant brain tumor-like protein 2 (L3MBTL2). L3MBTL2, also called L(3)mbt-like protein 2, is a putative Polycomb group (PcG) protein that binds to monomethylated and dimethylated 'Lys-20' on histone H4 and also binds histone H3 peptides which are monomethylated or dimethylated on 'Lys-4', 'Lys-9' or 'Lys-27'. L3MBTL2 orchestrates ubiquitin signalling by dictating the sequential recruitment of RNF8 and RNF168 after DNA damage. It is an integral component of the polycomb repressive complex 1.6 (PRC1.6) and has been implicated in transcriptional repression and chromatin compaction. L3MBTL2 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the second MBT repeat that does not seem to contain a semi-aromatic cage and may not bind methylated lysine residues. 84 matched cddid_all.tbl CDD cd20125 cd20125 439115 MBT_dSfmbt_rpt3 third malignant brain tumor (MBT) repeat found in Drosophila melanogaster Polycomb protein Sfmbt (dSfmbt) and similar proteins. dSfmbt, also called Scm-like with four MBT domain-containing protein 1, is a Polycomb group repressor involved in epigenetic regulation of gene expression. dSfmbt contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the third MBT repeat that does not seem to contain a semi-aromatic cage and may not bind methylated lysine residues. 107 matched cddid_all.tbl CDD cd20126 cd20126 439116 MBT_MBTD1_rpt3 third malignant brain tumor (MBT) repeat found in MBT domain-containing protein 1 (MBTD1). MBTD1 is a putative Polycomb group (PcG) protein that specifically binds to monomethylated and dimethylated 'Lys-20' on histone H4. MBTD1 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the third MBT repeat that does not seem to contain a semi-aromatic cage and may not bind methylated lysine residues. 90 matched cddid_all.tbl CDD cd20127 cd20127 439117 MBT_L3MBTL2_rpt3 third malignant brain tumor (MBT) repeat found in Lethal(3)malignant brain tumor-like protein 2 (L3MBTL2). L3MBTL2, also called L(3)mbt-like protein 2, is a putative Polycomb group (PcG) protein that binds to monomethylated and dimethylated 'Lys-20' on histone H4 and also binds histone H3 peptides which are monomethylated or dimethylated on 'Lys-4', 'Lys-9' or 'Lys-27'. L3MBTL2 orchestrates ubiquitin signalling by dictating the sequential recruitment of RNF8 and RNF168 after DNA damage. It is an integral component of the polycomb repressive complex 1.6 (PRC1.6) and has been implicated in transcriptional repression and chromatin compaction. L3MBTL2 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the third MBT repeat that does not seem to contain a semi-aromatic cage and may not bind methylated lysine residues. 91 matched cddid_all.tbl CDD cd20128 cd20128 439118 MBT_dSfmbt_rpt4 fourth malignant brain tumor (MBT) repeat found in Drosophila melanogaster Polycomb protein Sfmbt (dSfmbt). dSfmbt, also called Scm-like with four MBT domain-containing protein 1, is a Polycomb group repressor involved in epigenetic regulation of gene expression. dSfmbt contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the fourth MBT repeat that contains the semi-aromatic cage that binds methylated lysine residues. 72 matched cddid_all.tbl CDD cd20129 cd20129 439119 MBT_MBTD1_rpt4 fourth malignant brain tumor (MBT) repeat found in MBT domain-containing protein 1 (MBTD1). MBTD1 is a putative Polycomb group (PcG) protein that specifically binds to monomethylated and dimethylated 'Lys-20' on histone H4. MBTD1 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the fourth MBT repeat that contains the semi-aromatic cage that binds methylated lysine residues. 71 matched cddid_all.tbl CDD cd20130 cd20130 439120 MBT_L3MBTL2_rpt4 fourth malignant brain tumor (MBT) repeat found in Lethal(3)malignant brain tumor-like protein 2 (L3MBTL2). L3MBTL2, also called L(3)mbt-like protein 2, is a putative Polycomb group (PcG) protein that binds to monomethylated and dimethylated 'Lys-20' on histone H4 and also binds histone H3 peptides which are monomethylated or dimethylated on 'Lys-4', 'Lys-9' or 'Lys-27'. L3MBTL2 orchestrates ubiquitin signalling by dictating the sequential recruitment of RNF8 and RNF168 after DNA damage. It is an integral component of the polycomb repressive complex 1.6 (PRC1.6) and has been implicated in transcriptional repression and chromatin compaction. L3MBTL2 contains four MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the fourth MBT repeat that contains the semi-aromatic cage that binds methylated lysine residues. 75 matched cddid_all.tbl CDD cd20131 cd20131 439121 MBT_L3MBTL1_rpt1 first malignant brain tumor (MBT) repeat found in Lethal(3)malignant brain tumor-like protein 1 (L3MBTL1). L3MBTL1, also called L(3)mbt-like, or L(3)mbt protein homolog, is a Polycomb group (PcG) protein that functions as a 'reader' of a network of post-translational modifications by specifically recognizing and binding mono- and dimethyllysine residues on target proteins. It acts as a chromatin compaction factor by binding mono- and dimethylated histone H1b/HIST1H1E at 'Lys-26' (H1bK26me1 and H1bK26me2) and histone H4 at 'Lys-20' (H4K20me1 and H4K20me2), leading to condensed chromatin and repressed transcription. L3MBTL1 contains three MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the first MBT repeat that contains the semi-aromatic cage and may bind methylated lysine residues. 109 matched cddid_all.tbl CDD cd20132 cd20132 439122 MBT_L3MBTL3_rpt1 first malignant brain tumor (MBT) repeat found in Lethal(3)malignant brain tumor-like protein 3 (L3MBTL3). L3MBTL3, also called L(3)mbt-like protein 3, or MBT-1, is a Polycomb group (PcG) protein that recognizes mono- and dimethylated lysine residues on histone tails. It also acts as a methyl-binding protein that binds the K142-methylated DNMT1 and recruits a novel CRL4(DCAF5) ubiquitin ligase to degrade DNMT1. L3MBTL3 contains three MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the first MBT repeat that contains the semi-aromatic cage that binds methylated lysine residues. 101 matched cddid_all.tbl CDD cd20133 cd20133 439123 MBT_L3MBTL4_rpt1 first malignant brain tumor (MBT) repeat found in Lethal(3)malignant brain tumor-like protein 4 (L3MBTL4). L3MBTL4, also called L(3)mbt-like protein 4, or L3mbt-like 4, is a Polycomb group (PcG) protein that may act as a tumor suppressor. L3MBTL4 contains three MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the first MBT repeat that contains the semi-aromatic cage that binds methylated lysine residues. 101 matched cddid_all.tbl CDD cd20134 cd20134 439124 MBT_L3MBTL1_rpt2 second malignant brain tumor (MBT) repeat found in Lethal(3)malignant brain tumor-like protein 1 (L3MBTL1). L3MBTL1, also called L(3)mbt-like, or L(3)mbt protein homolog, is a Polycomb group (PcG) protein that functions as a 'reader' of a network of post-translational modifications by specifically recognizing and binding mono- and dimethyllysine residues on target proteins. It acts as a chromatin compaction factor by binding mono- and dimethylated histone H1b/HIST1H1E at 'Lys-26' (H1bK26me1 and H1bK26me2) and histone H4 at 'Lys-20' (H4K20me1 and H4K20me2), leading to condensed chromatin and repressed transcription. L3MBTL1 contains three MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the second MBT repeat that contains the semi-aromatic cage that binds methylated lysine residues. 93 matched cddid_all.tbl CDD cd20135 cd20135 439125 MBT_L3MBTL3_rpt2 second malignant brain tumor (MBT) repeat found in Lethal(3)malignant brain tumor-like protein 3 (L3MBTL3). L3MBTL3, also called L(3)mbt-like protein 3, or MBT-1, is a Polycomb group (PcG) protein that recognizes mono- and dimethylated lysine residues on histone tails. It also acts as a methyl-binding protein that binds the K142-methylated DNMT1 and recruits a novel CRL4(DCAF5) ubiquitin ligase to degrade DNMT1. L3MBTL3 contains three MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the second MBT repeat that contains the semi-aromatic cage that binds methylated lysine residues. 93 matched cddid_all.tbl CDD cd20136 cd20136 439126 MBT_L3MBTL4_rpt2 second malignant brain tumor (MBT) repeat found in Lethal(3)malignant brain tumor-like protein 4 (L3MBTL4). L3MBTL4, also called L(3)mbt-like protein 4, or L3mbt-like 4, is a Polycomb group (PcG) protein that may act as a tumor suppressor. L3MBTL4 contains three MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the second MBT repeat that contains the semi-aromatic cage that binds methylated lysine residues. 92 matched cddid_all.tbl CDD cd20137 cd20137 439127 MBT_L3MBTL1_rpt3 third malignant brain tumor (MBT) repeat found in Lethal(3)malignant brain tumor-like protein 1 (L3MBTL1). L3MBTL1, also called L(3)mbt-like, or L(3)mbt protein homolog, is a Polycomb group (PcG) protein that functions as a 'reader' of a network of post-translational modifications by specifically recognizing and binding mono- and dimethyllysine residues on target proteins. It acts as a chromatin compaction factor by binding mono- and dimethylated histone H1b/HIST1H1E at 'Lys-26' (H1bK26me1 and H1bK26me2) and histone H4 at 'Lys-20' (H4K20me1 and H4K20me2), leading to condensed chromatin and repressed transcription. L3MBTL1 contains three MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the third MBT repeat that contains the semi-aromatic cage that may bind methylated lysine residues. 75 matched cddid_all.tbl CDD cd20138 cd20138 439128 MBT_L3MBTL3_rpt3 third malignant brain tumor (MBT) repeat found in Lethal(3)malignant brain tumor-like protein 3 (L3MBTL3). L3MBTL3, also called L(3)mbt-like protein 3, or MBT-1, is a Polycomb group (PcG) protein that recognizes mono- and dimethylated lysine residues on histone tails. It also acts as a methyl-binding protein that binds the K142-methylated DNMT1 and recruits a novel CRL4(DCAF5) ubiquitin ligase to degrade DNMT1. L3MBTL3 contains three MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the third MBT repeat that contains the semi-aromatic cage that may bind methylated lysine residues. 78 matched cddid_all.tbl CDD cd20139 cd20139 439129 MBT_L3MBTL4_rpt3 fourth malignant brain tumor (MBT) repeat found in Lethal(3)malignant brain tumor-like protein 4 (L3MBTL4). L3MBTL4, also called L(3)mbt-like protein 4, or L3mbt-like 4, is a Polycomb group (PcG) protein that may act as a tumor suppressor. L3MBTL4 contains three MBT (malignant brain tumor) repeats. The MBT repeat is a protein module that recognizes methylated lysine residues on histones. MBT repeats contain a semi-aromatic cage to accommodate methyllysine and show specificity towards the lower methylation states of lysine. This model corresponds to the third MBT repeat that contains the semi-aromatic cage that may bind methylated lysine residues. 82 matched cddid_all.tbl CDD cd20140 cd20140 438968 PWWP_PWWP2 PWWP domain found in the PWWP domain-containing protein 2 (PWWP2) family. The PWWP2 family includes PWWP2A and its paralog PWWP2B. PWWP2A is a H2A.Z-specific chromatin binding protein which may play an important role in the neural crest stem cell migration and differentiation during early development. It is also required for proper mitosis progression. PWWP2A and PWWP2B form a stable complex with NuRD subunits MTA1/2/3:HDAC1/2:RBBP4/7, but not with MBD2/3, p66alpha/beta, and CHD3/4. The PWWP domain specifically recognizes DNA and histone methylated lysines. 92 matched cddid_all.tbl CDD cd20141 cd20141 438969 PWWP_MBD5 PWWP domain found in methyl-CpG-binding domain protein 5 (MBD5) and similar proteins. MBD5, is a methyl-CpG-binding protein that binds to heterochromatin. It does not interact with either methylated or unmethylated DNA. MBD5 acts as a transcriptional regulator responsible for 2q23.1 deletion syndrome. It belongs to the MBD family proteins, which play central roles in transcriptional regulation and development. The PWWP domain specifically recognizes DNA and histone methylated lysines. 92 matched cddid_all.tbl CDD cd20142 cd20142 438970 PWWP_AtATX1-like PWWP domain found in Arabidopsis thaliana histone-lysine N-methyltransferase trithorax-like proteins ATX1, ATX2, and similar proteins. This family includes A. thaliana ATX1 and ATX2, which are sister paralogs originating from a segmental chromosomal duplication. They are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1, also called protein SET domain group 27, or trithorax-homolog protein 1 (TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1 regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2, also called protein SET domain group 30, or trithorax-homolog protein 2 (TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). Both ATX1 and ATX2 are multi-domain containing proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical plant homeodomain (PHD) domain, a non-canonical extended PHD (ePHD) domain, and a C-terminal SET domain. The PWWP domain specifically recognizes DNA and histone methylated lysines. 97 matched cddid_all.tbl CDD cd20143 cd20143 438971 PWWP_AtATX3-like PWWP domain found in Arabidopsis thaliana histone-lysine N-methyltransferase trithorax-like protein ATX3, ATX4, ATX5, and similar proteins. The family includes A. thaliana ATX3 (also called protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also called protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also called protein SET domain group 29, or trithorax-homolog protein 5), which belong to the histone-lysine methyltransferase family. They show distinct phylogenetic origins from the family of ATX1 and ATX2. They are multi-domain containing protein that consists of an N-terminal PWWP domain, a canonical plant homeodomain (PHD) domain, a non-canonical extended PHD (ePHD) domain, and a C-terminal SET domain. The PWWP domain specifically recognizes DNA and histone methylated lysines. 100 matched cddid_all.tbl CDD cd20144 cd20144 438972 PWWP_NSD_rpt1 first PWWP domain found in nuclear receptor-binding SET domain-containing (NSD) proteins. The nuclear receptor binding SET domain (NSD) protein family consists of three HMTases, NSD1, NSD2/MMSET/WHSC1, and NSD3/WHSC1L1 that are critical in maintaining the chromatin integrity. Reducing NSD activity through specific lysine-HMTase inhibitors appears promising in suppressing cancer growth. NSD proteins have specific mono- and dimethylase activities for H3K36, and play nonredundant roles during development. NSD1 plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. NSD2 is involved in cancer cell proliferation, survival, and tumor growth, through mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. NSD3 is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD proteins contain a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (C5HCH). This model corresponds to the first PWWP domain. This family also includes Drosophila melanogaster maternal-effect sterile 4 (dMes4) that may act as a histone-lysine N-methyltransferase required for wing morphogenesis. The PWWP domain specifically recognizes DNA and histone methylated lysines. 114 matched cddid_all.tbl CDD cd20145 cd20145 438973 PWWP_ZCWPW1 PWWP domain found in zinc finger CW-type PWWP domain protein 1 (ZCWPW1) and similar proteins. ZCWPW1 is a histone H3K4me3 reader. It is associated with late-onset Alzheimer's disease (LOAD). In addition to the PWWP domain, ZCWPW1 contains a zinc finger CW (zf-CW) domain that is a histone modification reader for the histone H3 tail with trimethylated K4. The PWWP domain specifically recognizes DNA and histone methylated lysines. 115 matched cddid_all.tbl CDD cd20146 cd20146 438974 PWWP_ZCWPW2 PWWP domain found in zinc finger CW-type PWWP domain protein 2 (ZCWPW2) and similar proteins. ZCWPW2 is a histone H3K4me3 reader. In addition to the PWWP domain, ZCWPW2 contains a zinc finger CW (zf-CW) domain that is a histone modification reader for the histone H3 tail with trimethylated K4. The PWWP domain specifically recognizes DNA and histone methylated lysines. 113 matched cddid_all.tbl CDD cd20147 cd20147 438975 PWWP_HULK PWWP domain found in Arabidopsis thaliana protein HUA2-LIKE (HULK) family. The HULK family includes HUA2-like proteins 1-3 (HULK1-3), which are probable transcription factors that act with partial redundancy with each other. They may play diverse and essential roles in the control of plant development, physiology and flowering time. The PWWP domain specifically recognizes DNA and histone methylated lysines. 92 matched cddid_all.tbl CDD cd20148 cd20148 438976 PWWP_HDGF PWWP domain found in Hepatoma-derived growth factor (HDGF). HDGF, also called high mobility group protein 1-like 2 (HMG-1L2), is a heparin-binding protein that acts as a transcriptional repressor with mitogenic activity for fibroblasts. It contains a PWWP domain, which is necessary for DNA binding. 87 matched cddid_all.tbl CDD cd20149 cd20149 438977 PWWP_HDGFL2 PWWP domain found in Hepatoma-derived growth factor-related protein 2 (HDGFL2). HDGFL2, also called HDGF-related protein 2 (HRP-2), or Hepatoma-derived growth factor 2 (HDGF-2), is involved in cellular growth control, through the regulation of cyclin D1 expression. It contains a PWWP domain, which is necessary for DNA binding. 84 matched cddid_all.tbl CDD cd20150 cd20150 438978 PWWP_HDGFL3 PWWP domain found in Hepatoma-derived growth factor-related protein 3 (HDGFL3). HDGFL3, also called HDGF-related protein 3 (HRP-3), is the only hepatoma-derived growth factor (HDGF)-related protein (HRP) family member whose expression is almost restricted to the nervous tissue. It enhances DNA synthesis and may play a role in cell proliferation. It contains a PWWP domain, which is necessary for DNA binding. 93 matched cddid_all.tbl CDD cd20151 cd20151 438979 PWWP_PSIP PWWP domain found in PC4 and SFRS1-interacting protein (PSIP). PSIP, also called CLL-associated antigen KW-7, dense fine speckles 70 kDa protein (DFS 70), lens epithelium-derived growth factor (LEDGF), or transcriptional coactivator p75/p52, acts as a transcriptional coactivator involved in neuroepithelial stem cell differentiation and neurogenesis. It contains a PWWP domain, which is necessary for DNA binding. 88 matched cddid_all.tbl CDD cd20152 cd20152 438980 PWWP_PWWP2A PWWP domain found in PWWP domain-containing protein 2A (PWWP2A). PWWP2A is a H2A.Z-specific chromatin binding protein which may play an important role in the neural crest stem cell migration and differentiation during early development. It is also required for proper mitosis progression. PWWP2A and its paralog PWWP2B form a stable complex with NuRD subunits MTA1/2/3:HDAC1/2:RBBP4/7, but not with MBD2/3, p66alpha/beta, and CHD3/4. The PWWP domain specifically recognizes DNA and histone methylated lysines. 122 matched cddid_all.tbl CDD cd20153 cd20153 438981 PWWP_PWWP2B PWWP domain found in PWWP domain-containing protein 2B (PWWP2B). PWWP2B is a paralog of PWWP2A, a H2A.Z-specific chromatin binding protein which may play an important role in the neural crest stem cell migration and differentiation during early development. PWWP2A and PWWP2B form a stable complex with NuRD subunits MTA1/2/3:HDAC1/2:RBBP4/7, but not with MBD2/3, p66alpha/beta, and CHD3/4. The PWWP domain specifically recognizes DNA and histone methylated lysines. 116 matched cddid_all.tbl CDD cd20154 cd20154 438982 PWWP_DNMT3A PWWP domain found in DNA (cytosine-5)-methyltransferase 3A (DNMT3A). DNMT3A, also called DNA methyltransferase HsaIIIA, DNA MTase HsaIIIA, or M.HsaIIIA, is required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. It modifies DNA in a non-processive manner and also methylates non-CpG sites. It may preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. DNMT3A is recruited to trimethylated 'Lys-36' of histone H3 (H3K36me3) sites. It contains a PWWP domain that binds methylated histone. 134 matched cddid_all.tbl CDD cd20155 cd20155 438983 PWWP_DNMT3B PWWP domain found in DNA (cytosine-5)-methyltransferase 3B (DNMT3B). DNMT3B, also called DNA methyltransferase HsaIIIB, DNA MTase HsaIIIB, or M.HsaIIIB, is required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. It may preferentially methylate nucleosomal DNA within the nucleosome core region. DNMT3B may function as a transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. In tumorigenesis, DNA methylation by DNMT3B is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of DNMT3B has been identified in patients with ICF (immunodeficiency, centromeric instability, and facial anomalies) syndrome, a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA. 117 matched cddid_all.tbl CDD cd20156 cd20156 438984 PWWP_BRPF1 PWWP domain found in bromodomain and PHD finger-containing protein 1 (BRPF1). BRPF1, also called peregrin, or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ)-dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It may be involved in chromatin remodeling. It contains a plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PHD finger binds to methylated lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties. 120 matched cddid_all.tbl CDD cd20157 cd20157 438985 PWWP_BRPF2 PWWP domain found in bromodomain and PHD finger-containing protein 2 (BRPF2). BRPF2, also called bromodomain-containing protein 1 (BRD1), or BR140-likeprotein, is encoded by BRL (BR140 Like gene). It is responsible for the bulk of the acetylation of H3K14 and forms a novel monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with HBO1 and ING4. The complex is required for full transcriptional activation of the erythroid-specific regulator genes essential for terminal differentiation and survival of erythroblasts in fetal liver. BRPF2 shows widespread expression and localizes to the nucleus within spermatocytes. It contains a cysteine rich region harboring a plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties. 120 matched cddid_all.tbl CDD cd20158 cd20158 438986 PWWP_BRPF3 PWWP domain found in bromodomain and PHD finger-containing protein 3 (BRPF3). BRPF3 is a homolog of BRPF1 and BRPF2. It is a scaffold protein that forms a novel monocytic leukemic zinc finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with other regulatory subunits. BRPF3 contains a plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, C2HC5HC2H, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PHD finger binds to lysine 4 of histone H3 (K4H3), the bromodomain interacts with acetylated lysines on N-terminal tails of histones and other proteins, and the PWWP domain shows histone-binding and chromatin association properties. 118 matched cddid_all.tbl CDD cd20159 cd20159 438987 PWWP_BS69 PWWP domain found in protein BS69 and similar proteins. Protein BS69, also called zinc finger MYND domain-containing protein 11 (ZMYND11 or ZMY11), is a ubiquitously expressed nuclear protein acting as a transcriptional co-repressor in association with various transcription factors. It was originally identified as an adenovirus 5 E1A-binding protein that inhibits E1A transactivation, as well as c-Myb transcription. It also mediates repression, at least in part, through interaction with the co-repressor N-CoR. Moreover, it interacts with Toll-interleukin 1 receptor domain (TIR)-containing adaptor molecule-1 (TICAM-1, also named TRIF) to facilitate NF-kappaB activation and type I IFN induction. It associates with PIAS1, a SUMO E3 enzyme, and Ubc9, a SUMO E2 enzyme, and plays an inhibitory role in muscle and neuronal differentiation. Moreover, BS69 regulates Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1)/C-terminal activation region 2 (CTAR2)-mediated NF-kappaB activation by interfering with the complex formation between TNFR-associated death domain protein (TRADD) and LMP1/CTAR2. It also cooperates with tumor necrosis factor receptor (TNFR)-associated factor 3 (TRAF3) in the regulation of EBV-derived LMP1/CTAR1-induced NF-kappaB activation. Furthermore, BS69 is involved in the p53-p21Cip1-mediated senescence pathway. BS69 contains a plant homeodomain (PHD) finger, a bromodomain, a proline-tryptophan-tryptophan-proline (PWWP) domain, and a MYeloid translocation protein 8, Nervy and DEAF-1 (MYND) domain. The PWWP domain specifically recognizes DNA and histone methylated lysines. 85 matched cddid_all.tbl CDD cd20160 cd20160 438988 PWWP_PRKCBP1 PWWP domain found in protein kinase C-binding protein 1 (PRKCBP1) and similar proteins. PRKCBP1, also called cutaneous T-cell lymphoma-associated antigen se14-3 (CTCL-associated antigen se14-3), Rack7, or zinc finger MYND domain-containing protein 8 (ZMYND8), is a novel receptor for activated C-kinase (RACK)-like protein that may play an important role in the activation and regulation of PKC-beta I, and the PKC signaling cascade. It also has been identified as a formin homology-2-domain containing protein 1 (FHOD1)-binding protein that may be involved in FHOD1-regulated actin polymerization and transcription. Moreover, PRKCBP1 may function as a REST co-repressor 2 (RCOR2) interacting factor. They form a RCOR2/ZMYND8 complex which might be involved in the regulation of neural differentiation. PRKCBP1 contains a plant homeodomain (PHD) finger, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. The PWWP domain specifically recognizes DNA and histone methylated lysines. 91 matched cddid_all.tbl CDD cd20161 cd20161 438989 PWWP_NSD1_rpt1 first PWWP domain found in nuclear receptor-binding SET domain-containing protein 1 (NSD1) and similar proteins. NSD1, also called H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, androgen receptor coactivator 267 kDa protein, androgen receptor-associated protein of 267 kDa, H3-K36-HMTase H4-K20-HMTase, Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD1 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (C5HCH). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD domains are involved in protein-protein interactions. The model corresponds to the first PWWP domain. The PWWP domain specifically recognizes DNA and histone methylated lysines. 116 matched cddid_all.tbl CDD cd20162 cd20162 438990 PWWP_NSD2_rpt1 first PWWP domain found in nuclear SET domain-containing protein 2 (NSD2) and similar proteins. NSD2, also called histone-lysine N-methyltransferase NSD2, multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, through mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). NSD2 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, a high mobility group (HMG) box, five PHD (plant-homeodomain) zinc finger motifs, and an NSD-specific Cys-His rich domain (C5HCH). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD domains mediate chromatin interaction and recognition of histone marks. This model corresponds to the first PWWP domain. The PWWP domain specifically recognizes DNA and histone methylated lysines. 128 matched cddid_all.tbl CDD cd20163 cd20163 438991 PWWP_NSD3_rpt1 first PWWP domain found in nuclear SET domain-containing protein 3 (NSD3) and similar proteins. NSD3, also called histone-lysine N-methyltransferase NSD3, protein whistle, WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc finger motifs, and an NSD-specific Cys-His rich domain (C5HCH). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD domains are involved in protein-protein interactions. This model corresponds to the first PWWP domain. The PWWP domain specifically recognizes DNA and histone methylated lysines. 130 matched cddid_all.tbl CDD cd20164 cd20164 438992 PWWP_NSD1_rpt2 second PWWP domain found in nuclear receptor-binding SET domain-containing protein 1 (NSD1) and similar proteins. NSD1, also called H3 Lysine-36 and H4 Lysine-20 specific histone-lysine N-methyltransferase, androgen receptor coactivator 267 kDa protein, androgen receptor-associated protein of 267 kDa, H3-K36-HMTase H4-K20-HMTase, Lysine N-methyltransferase 3B (KMT3B), or NR-binding SET domain-containing protein, is a lysine methyltransferase that preferentially methylates H3 on Lysine36 (H3-K36) and H4 on Lysine20 (H4-K20), which is primarily associated with active transcription. It plays a role in several pathologies, including but not limited to Sotos and Weaver syndromes, acute myeloid leukemia, breast cancer, neuroblastoma, and glioblastoma formation. It can alter transcription by interacting with the protein NSD1-interacting zinc finger protein 1 (NIZP1). It also mitigates caspase-1 activation by listeriolysin o (LLO) in macrophages, and requires functional LLO for the regulation of IL-1beta secretion. Moreover, NSD1 regulates RNA polymerase II (RNAP II) recruitment to bone morphogenetic protein 4 (BMP4). NSD1 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-proline (PWWP) domains, five plant homeodomain (PHD) fingers, and an NSD-specific Cys-His rich domain (C5HCH). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD domains are involved in protein-protein interactions. This model corresponds to the second PWWP domain. The PWWP domain specifically recognizes DNA and histone methylated lysines. 96 matched cddid_all.tbl CDD cd20165 cd20165 438993 PWWP_NSD2_rpt2 second PWWP domain found in nuclear SET domain-containing protein 2 (NSD2) and similar proteins. NSD2, also called histone-lysine N-methyltransferase NSD2, multiple myeloma SET domain-containing protein (MMSET), or protein trithorax-5 Wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), is overexpressed frequently in the t(4;14) translocation in 15% to 20% of multiple myeloma. It plays important roles in cancer cell proliferation, survival, and tumor growth, through mediating constitutive NF-kappaB signaling via the cytokine autocrine loop. It also enhances androgen receptor (AR)-mediated transcription. The principal chromatin-regulatory activity of NSD2 is dimethylation of histone H3 at lysine 36 (H3K36me2). NSD2 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, an high mobility group (HMG) box, five PHD (plant-homeodomain) zinc finger motifs, and an NSD-specific Cys-His rich domain (C5HCH). The SET domain is responsible for histone methyltransferase activity. The PWWP, HMG, and PHD domains mediate chromatin interaction and recognition of histone marks. This model corresponds to the second PWWP domain. The PWWP domain specifically recognizes DNA and histone methylated lysines. 96 matched cddid_all.tbl CDD cd20166 cd20166 438994 PWWP_NSD3_rpt2 second PWWP domain found in nuclear SET domain-containing protein 3 (NSD3) and similar proteins. NSD3, also called histone-lysine N-methyltransferase NSD3, protein whistle, WHSC1-like 1 isoform 9 with methyltransferase activity to lysine, or Wolf-Hirschhorn syndrome candidate 1-like protein 1 (WHSC1-like protein 1, or WHSC1L1), is a lysine methyltransferase encoded by gene NSD3, which is amplified in human breast cancer cell lines. Moreover, translocation resulting in NUP98 fusion to NSD3 leads to the development of acute myeloid leukemia. NSD3 contains a catalytic suppressor of variegation, enhancer of zeste and trithorax (SET) domain, two proline-tryptophan-tryptophan-prolin motif (PWWP) domains, five plant-homeodomain (PHD) zinc finger motifs, and an NSD-specific Cys-His rich domain (C5HCH). The SET domain is responsible for histone methyltransferase activity. The PWWP and PHD domains are involved in protein-protein interactions. This model corresponds to the second PWWP domain. The PWWP domain specifically recognizes DNA and histone methylated lysines. 95 matched cddid_all.tbl CDD cd20167 cd20167 380911 Peptidase_M90-like M90 peptidase is a zinc-metallopeptidase. The M90 peptidase family includes the MtfA (Mlc Titration Factor A) peptidase from Escherichia coli, also known as the YeeI gene product, which is involved in the control of the glucose-phosphotransferase sensory and regulatory system by inactivation of the repressor Mlc (making large colonies). E. coli MtfA has been shown to have aminopeptidase activity with the presence of a single zinc ion in the active site ligated by two histidines in a HEXXH motif. This family also includes uncharacterized proteins similar to MtfA peptidase. 208 matched cddid_all.tbl CDD cd20169 cd20169 380912 Peptidase_M90_mtfA Mlc titration factor A (MtfA) is a zinc metallopeptidase (M90 peptidase). This subfamily includes the Mlc Titration Factor A (MtfA; also known as YeeI or DgsA anti-repressor MtfA) which is involved in the control of the glucose-phosphotransferase sensory and regulatory system by inactivation of the repressor Mlc (making large colonies). It can cleave synthetic substrates of both carboxypeptidases and aminopeptidases, with strongest activity towards the latter. Its biologically relevant substrate has yet to be identified. Although it interacts with the transcription repressor Mlc, it does not cleave it. However, Mlc seems to activate the peptidase activity of MtfA. MtfA is related to the catalytic domain of the anthrax lethal factor which is a zinc-dependent metalloprotease, targeting mitogen-activated protein kinase kinases (MAPKKs), and resulting in apoptosis, as well as the Mop (modulation of pathogenesis) protein involved in the virulence of Vibrio cholerae; although sequence similarity is low, conservation is observed in the overall structure as well as in the residues around the active site. 208 matched cddid_all.tbl CDD cd20170 cd20170 380913 Peptidase_M90-like uncharacterized M90 peptidase family-like proteins. This subfamily contains uncharacterized M90 peptidase-like domains, similar to the Mlc Titration Factor A (MtfA) peptidase from Escherichia coli, also known as the YeeI gene product, which is involved in the control of the glucose-phosphotransferase sensory and regulatory system by inactivation of the repressor Mlc (making large colonies). E. coli MtfA has been shown to have aminopeptidase activity with the presence of a single zinc ion in the active site ligated by two histidines in an HEXXH motif. MtfA is related to the catalytic domain of the anthrax lethal factor and the Mop protein involved in the virulence of Vibrio cholerae; although sequence similarity is low, conservation is observed in the overall structure as well as in the residues around the active site. 210 matched cddid_all.tbl CDD cd20171 cd20171 380332 M34_peptidase Peptidase family M34 includes the C-terminal catalytic domain of anthrax lethal factor (ATLF), the protective antigen-binding domains of ATLF and edema factor, and Pro-Pro endopeptidase. Peptidase family M34 (also known as the anthrax lethal factor family) includes the C-terminal catalytic domain of anthrax lethal factor (ATLF, EC 3.4.24.83), and the N-terminal protective antigen-binding domains (PABDs) of ATLF and edema factor (EF). ATLF and EF are enzyme components of anthrax toxin and are carried into the cell by a third component, the protective antigen (PA). ATLF is a highly selective protease whose major substrates are mitogen-activated protein kinase kinases (MKKs). At its N-terminus, ATLF has a PABD domain which lacks the hallmark metalloprotease motif HEXXH, and, at its C-terminus, the related catalytic domain has the HEXXH motif where the two His residues bind a single zinc atom, and the Glu has a catalytic role. EF acts as a Ca2+- and calmodulin-dependent adenylyl cyclase that can cause edema when associated with PA. EF is comprised of the PABD and an adenylyl cyclase domain. This family also includes Pro-Pro endopeptidase (PPEP-1; EC 3.4.24.89, also known as Zmp1) which is an extracellular metalloprotease that shows a unique specificity for hydrolyzing a Pro-Pro bond and is involved in bacterial adhesion. 156 matched cddid_all.tbl CDD cd20174 cd20174 380910 GH18_LinChi78-like_UFR an unknown function domain of Listeria innocua LinChi78 GH18 chitinase that is essential for its catalytic activity; found in similar chitinase-like proteins. This domain is referred to as an unknown-function region (UFR) and shown to be necessary for the hydrolytic activity of LinChi78 glycosyl hydrolase family 18 (GH18) chitinase (a product of the lin0153gene) from the nonpathogenic bacterium Listeria innocua. The catalytic domain (CatD) of GH18 chitinases folds into a TIM barrel and has a conserved DXXDXDXE motif, in which the Glu residue functions as a catalytic residue; these chitinases contain additional domains such as a chitin-binding domain (ChBD) and/or a fibronectin type III-like (FnIII) domain. LinChi78 consists of a CatD, a FnIII, and a ChBD domain, and has this UFR region located between the CatD and the FnIII domain. Its catalytic site is composed of a typical CatD and a portion of this UFR, in particular the key Gln and Ile residues which are indispensable for LinChi78 to exhibit full catalytic activity. This UFR domain is also found in proteins where it is located between a CatD domain and DUF5011 and ChBD(s) domains. LinChi78 exhibits chitinase activity towards artificial and natural substrates, including colloidal chitin and chitin oligosaccharides of various lengths, and hydrolyzes these in a processive manner. Members of this family include some uncharacterized chitinase-like proteins from pathogenic bacteria such as Listeria monocytogenes and Clostridium botulinum. 136 matched cddid_all.tbl CDD cd20175 cd20175 412038 ThyX FAD-dependent thymidylate synthase (ThyX), mechanistically and structurally unrelated to thymidylate synthase (ThyA). This family contains FAD-dependent thymidylate synthase (also known as ThyX, Thy1, FDTS or thymidylate synthase complementing protein), found in many microbial genomes including several human pathogens, but absent in humans. This protein is mechanistically and structurally unrelated to thymidylate synthase (TS or ThyA) found in mammals. ThyA and ThyX both produce de novo thymidylate or deoxythymidine 5'-monophosphate (dTMP), an essential DNA precursor. The classic ThyA catalyzes the reductive methylation of deoxyuridine 5'-monophosphate (dUMP) to form dTMP, with methylenetetrahydrofolate (CH2H4folate) serving as a one-carbon donor and as the source of reductive power. On the other hand, ThyX contains FAD, tightly bound by a novel fold, that mediates hydride transfer from NADPH during catalysis. Consequently, CH2H4folate serves only as a carbon donor and tetrahydrofolate (and not dihydrofolate as in the case of ThyA) is produced. The differences between the ThyX and ThyA is used for mechanism-based drugs to selectively inhibit FDTS and not have much effect on human and other eukaryotic TS. ThyX has been pursued for the development of new antibacterial agents against Mycobacterium tuberculosis, the causative agent of the widespread infectious disease tuberculosis (TB). It is also an attractive target for designing specific antibiotic drugs against many diseases such as ulcers, periodontal disease, and Lyme's disease, as well as biological warfare agents such as anthrax, botulism, and typhus. 186 matched cddid_all.tbl CDD cd20177 cd20177 439130 Dpy19 C-mannosyltransferase Dpy19. Dpy19 proteins are C-mannosyltransferases that mediate C-mannosylation of tryptophan residues on target proteins. C-mannosylation is the attachment of alpha-mannose to the indole C2 carbon of the first tryptophan residue in the consensus amino acid sequence Trp-Xaa-Xaa-Trp/Cys through a C-C bond. This reaction takes place in the endoplasmic reticulum (ER) lumen. Dpy19 is a transmembrane domain family whose name is derived from the Caenorhabditis elegans Dumpy mutant. 657 matched cddid_all.tbl CDD cd20178 cd20178 439131 Dpy19L1 C-mannosyltransferase Dpy-19-like protein 1 (Dpy19L1). Dpy19 proteins are C-mannosyltransferases that mediate C-mannosylation of tryptophan residues on target proteins. C-mannosylation is the attachment of alpha-mannose to the indole C2 carbon of the first tryptophan residue in the consensus amino acid sequence Trp-Xaa-Xaa-Trp/Cys through a C-C bond. This reaction takes place in the endoplasmic reticulum (ER) lumen. Dpy19 is a transmembrane domain family whose name is derived from the Caenorhabditis elegans Dumpy mutant. Dpy19L1 (also called protein Dpy-19 homolog 1) regulates neurite extension during development. 652 matched cddid_all.tbl CDD cd20179 cd20179 439132 Dpy19L2 C-mannosyltransferase Dpy-19-like protein 2 (Dpy19L2). Dpy19 proteins are C-mannosyltransferases that mediate C-mannosylation of tryptophan residues on target proteins. C-mannosylation is the attachment of alpha-mannose to the indole C2 carbon of the first tryptophan residue in the consensus amino acid sequence Trp-Xaa-Xaa-Trp/Cys through a C-C bond. This reaction takes place in the endoplasmic reticulum (ER) lumen. Dpy19 is a transmembrane domain family whose name is derived from the Caenorhabditis elegans Dumpy mutant. Dpy19L2 (also called protein Dpy-19 homolog 2) deletion is a major cause of globozoospermia. 652 matched cddid_all.tbl CDD cd20180 cd20180 439133 Dpy19L4 C-mannosyltransferase Dpy-19-like protein 4 (Dpy19L4). Dpy19 proteins are C-mannosyltransferases that mediate C-mannosylation of tryptophan residues on target proteins. C-mannosylation is the attachment of alpha-mannose to the indole C2 carbon of the first tryptophan residue in the consensus amino acid sequence Trp-Xaa-Xaa-Trp/Cys through a C-C bond. This reaction takes place in the endoplasmic reticulum (ER) lumen. Dpy19 is a transmembrane domain family whose name is derived from the Caenorhabditis elegans Dumpy mutant. The function of Dpy19L4 (also called protein Dpy-19 homolog 4) is unknown. 664 matched cddid_all.tbl CDD cd20181 cd20181 439134 Dpy19L3 C-mannosyltransferase Dpy-19-like protein 3 (Dpy19L3). Dpy19 proteins are C-mannosyltransferases that mediate C-mannosylation of tryptophan residues on target proteins. C-mannosylation is the attachment of alpha-mannose to the indole C2 carbon of the first tryptophan residue in the consensus amino acid sequence Trp-Xaa-Xaa-Trp/Cys through a C-C bond. This reaction takes place in the endoplasmic reticulum (ER) lumen. Dpy19 is a transmembrane domain family whose name is derived from the Caenorhabditis elegans Dumpy mutant. In humans Dpy19L3 (also called protein Dpy-19 homolog 3) is a C-mannosyltransferase of R-spondin. 667 matched cddid_all.tbl CDD cd20183 cd20183 380333 M34_PPEP Pro-Pro endopeptidase (PPEP) and similar proteins; belongs to peptidase family M34. This subfamily includes the enzyme Pro-Pro endopeptidase (PPEP-1, EC 3.4.24.89, also known as Zmp1 (Clostridium difficile-type)), an extracellular metalloprotease showing a unique specificity for hydrolyzing a Pro-Pro bond. It belongs to peptidase family M34 and has the hallmark metalloprotease motif HEXXH, where the two His residues bind a single zinc atom, and the Glu has a catalytic role. PPEP-1 cleaves two C. difficile cell surface proteins (CD2831 and CD3246) involved in adhesion, one of which is encoded by the gene adjacent to the ppep-1 gene. There are multiple PPEP-1 cleavage sites located just above the site of attachment to the peptidoglycan layer. PPEP-1 may play a role in switching from an adhesive to a motile phenotype. Also included in this subfamily is Paenibacillus alvei PPEP-2, a secreted Pro-Pro endopeptidase. The cleavage motif of PPEP-2, PLP PVP, is distinct from that of PPEP-1 (VNP PVP). PPEP-2 cleavage sites in a cell-surface protein, with putative extracellular matrix-binding domains, and encoded by the adjacent gene, suggests a similar role of PPEP-2 in controlling bacterial adhesion. 184 matched cddid_all.tbl CDD cd20184 cd20184 380334 M34_peptidase_like uncharacterized subfamily of peptidase family M34. Peptidase family M34 (also known as the anthrax lethal factor family) includes the C-terminal catalytic domain of anthrax lethal factor (ATLF, EC 3.4.24.83), and the N-terminal protective antigen-binding domains (PABDs) of ATLF and edema factor (EF). ATLF and EF are enzyme components of anthrax toxin and are carried into the cell by a third component, the protective antigen (PA). ATLF is a highly selective protease whose major substrates are mitogen-activated protein kinase kinases (MKKs). At its N-terminus, ATLF has a PABD domain which lacks the hallmark metalloprotease motif HEXXH, and, at its C-terminus, the related catalytic domain has the HEXXH motif where the two His residues bind a single zinc atom, and the Glu has a catalytic role. EF acts as a Ca2+- and calmodulin-dependent adenylyl cyclase that can cause edema when associated with PA; it is comprised of the PABD and an adenylyl cyclase domain. Pro-Pro endopeptidase (PPEP-1; EC 3.4.24.89, also known as Zmp1) is an extracellular metalloprotease that shows a unique specificity for hydrolyzing a Pro-Pro bond and is involved in bacterial adhesion. This uncharacterized subfamily includes proteins which have an N-terminal SLH domain, and proteins which may have an N-terminal IG-like domain; these proteins have the hallmark metalloprotease motif HEXXH motif. 131 matched cddid_all.tbl CDD cd20185 cd20185 380335 M34_PABD N-terminal protective antigen-binding domain (PABD) of Anthrax Toxin Lethal Factor (ATLF) and Edema Factor (EF), and similar domains; belongs to peptidase family M34. This subfamily includes the functional N-terminal protective antigen-binding domain (PABD) of the anthrax edema factor (EF), as well as the likely inactive N-terminal PABD of anthrax toxin lethal factor (ATLF), both secreted by Bacillus anthracis. ATLF and EF are enzyme components of anthrax toxin and are carried into the cell by a third component, the protective antigen (PA). ATLF-PABD resembles the C-terminal catalytic domain of ATLF (EC 3.4.24.83) but lacks the hallmark metalloprotease motif HEXXH. This subfamily belongs to the peptidase family M34 (also known as the anthrax lethal factor family), which also includes the C-terminal catalytic domain of ATLF, and Pro-Pro endopeptidase (PPEP-1; EC 3.4.24.89, also known as Zmp1), which is an extracellular metalloprotease that shows a unique specificity for hydrolyzing a Pro-Pro bond and is involved in bacterial adhesion. 219 matched cddid_all.tbl CDD cd20187 cd20187 410313 T-box_TBX1_10-like DNA-binding domain of T-box transcription factor 1 and 10, and related T-box proteifactors. This subfamily includes TBX1 and TBX10. TBX1 is a T-box transcription factor which plays an important role in heart development and has been implicated in DiGeorge or 22q11.2 deletion syndrome. This syndrome is associated with various types of cardiac outflow tract (OFT) and vascular defects. Wnt5a is regulated by TBX1 in the second heart field (SHF). TBX1 is required to maintain the integrity of extracellular matrix-cell interactions in the SHF and this interaction is critical for cardiac (OFT) development. TBX10 is a putative T-box transcription factor. Diseases associated with TBX10 include Isolated Cleft Lip and Cleft Lip/cleft lip with or without cleft palate. This subfamily belongs to the T-box family of transcription factors which play a multitude of diverse functions throughout development. The founding member of the T-box family is Brachyury (also known as TBXT, or T). T-box family members share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 189 matched cddid_all.tbl CDD cd20188 cd20188 410314 T-box_TBX2_3-like DNA-binding domain of T-box transcription factor 2 and 3, and related T-box proteins. This subfamily includes the T-box transcription factors TBX2 and TBX3 and similar proteins. TBX2 is an oncogenic transcription factor implicated in developmental processes, including coordinating cell fate, patterning and morphogenesis of a wide range of tissues and organs. It is overexpressed in several cancers, including melanoma and breast, and plays a key role during cardiac development. TBX2 is a negative regulator of promyelocytic leukemia protein (PML) function in cellular senescence, and it interacts with HP1 to recruit a repression complex to EGR1-responsive promoters to drive the proliferation of breast cancer cells. TBX3 has also been implicated in oncogenesis in breast cancer and melanoma. The tbx3 gene is downregulated by PML. TBX3 directly represses TBX2 under the control of the PRC2 complex in skeletal muscle and rhabdomyosarcoma. Also included in this family is the Drosophila melanogaster optomotor-blind protein (Omb, also known as lethal(1)optomotor-blind, or L(1)omb, or protein bifid) which controls many developmental processes such as wing, eye, and abdominal tergites and optic lobes, and induces epithelial cell migration and extrusion in vivo. This subfamily belongs to the T-box family of transcription factors which play a multitude of diverse functions throughout development. The founding member of the T-box family is brachyury (also known as TBXT, or T). T-box family members share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 185 matched cddid_all.tbl CDD cd20189 cd20189 410315 T-box_TBX4_5-like DNA-binding domain of T-box transcription factor 4 and 5, and related T-box proteins. This subfamily includes the T-box transcription factors TBX4 and TBX5 which play important roles in vertebrate limb and heart development, and in lung and trachea development. TBX4 is needed for normal skeletal and muscular hindlimb development and is involved in super-enhancer-driven transcriptional programs underlying features specific to lung fibroblasts. TBX5 plays a role in regulating cardiac conduction system function, and in coordinating forelimb muscle pattern. Mutations in human TBX5 and TBX4 are associated with Holt-Oram syndrome and Small Patella syndrome, respectively. Both syndromes are characterized by limb defects in addition to other abnormalities. This subfamily belongs to the T-box family of transcription factors which play a multitude of diverse functions throughout development. The founding member of the T-box family is Brachyury (also known as TBXT, or T). T-box family members share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 185 matched cddid_all.tbl CDD cd20190 cd20190 410316 T-box_TBX6_VegT-like DNA-binding domain of T-box transcription factor 6, VegT and related T-box proteins. This subfamily includes the transcriptional regulators TBX6 and VegT. TBX6 plays an essential role in the fate determination of axial stem to become either neural or mesodermal. It also plays an essential role in the regulation of left/right patterning in mouse embryos through effects on nodal cilia and perinodal signaling. VegT (also known as Antipodean, Brat and Xombi) is required in early Xenopus embryos for the formation of both the mesoderm and endoderm germ layers. This subfamily belongs to the T-box family of transcription factors which play a multitude of diverse functions throughout development. The founding member of the T-box family is Brachyury (also known as TBXT, or T). T-box family members share a conserved 1DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 183 matched cddid_all.tbl CDD cd20191 cd20191 410317 T-box_TBX15_18_22-like DNA-binding domain of T-box transcription factor 15, 18 and 22, and related T-box proteins. This subfamily includes the transcriptional regulators TBX15, TBX18 and TBX22 which are involved in various developmental processes. TBX15 (also known as TBX14) plays an important role in the development of the skeleton of the limb, vertebral column and head, possibly through its control of the number of mesenchymal precursor cells and chondrocytes; it also plays a role in the differentiation of brown and brite adipocytes. TBX18 is involved in the developmental processes of a variety of tissues and organs, including the ureter, vertebral column. epicardium and coronary vessels; it is important for the development of the head portion of the sino atrial node (SAN). Mutations in the T-box transcription factor gene TBX22 are found in X-linked Cleft Palate with or without Ankyloglossia syndrome (CPX syndrome), and associated with cleft lip and palate, and tooth agenesis. This subfamily belongs to the T-box family of transcription factors which play a multitude of diverse functions throughout development. The founding member of the T-box family is Brachyury (also known as TBXT, or T). T-box family members share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 194 matched cddid_all.tbl CDD cd20192 cd20192 410318 T-box_TBXT_TBX19-like DNA-binding domain of T-box transcription factor T, T-box transcription factor 19 and related T-box proteins. Tbx19 (also known as Tpit) is a T-box factor restricted to two pituitary (pro-opiomelanocortin) POMC-expressing lineages, the corticotrophs and melanotrophs; it controls terminal differentiation of these lineages. TBX19 activates POMC gene transcription with the cooperation of another transcription factor Pitx1. TBXT, also known as Brachyury protein, or protein T, is a transcription factor needed for posterior mesoderm formation and differentiation as well as for the notochord development during embryogenesis. It binds to a 24 base-pair (bp) palindromic site (called the T site) and activates gene transcription when bound to such a site. This subfamily belongs to the T-box family of transcription factors which play a multitude of diverse functions throughout development. TBXT is the founding member of the T-box family, members of which share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 180 matched cddid_all.tbl CDD cd20193 cd20193 410319 T-box_TBX20-like DNA-binding domain of T-box transcription factor 20 and related T-box proteins. TBX20 is a T-box transcriptional factor which functions in embryonic development and its deficiency is associated with congenital heart disease. It acts both as a transcriptional activator and a repressor required for cardiac development, and has key roles in maintaining the functional and structural phenotypes in the adult heart. The TBX20-cardiac transcription factor CASZ1 protein complex is protective against dilated cardiomyopathy and is essential for maintaining cardiac homeostasis. TBX20 has also been shown to regulate angiogenesis through the PROK2-PROKR1 (prokineticin receptor 1) pathway and is involved in both, pathological and developmental, angiogenesis. This subfamily belongs to the T-box family of transcription factors which play a multitude of diverse functions throughout development. The founding member of the T-box family is Brachyury (also known as TBXT, or T). T-box family members share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 190 matched cddid_all.tbl CDD cd20194 cd20194 410320 T-box_TBR1_2_21-like DNA-binding domain of T-box brain protein 1 and 2, T-box transcription factor 21 and related T-box proteins. TBX21 (also known as T-cell-specific T-box transcription factor T-bet or transcription factor TBLYM) is a lineage-defining transcription factor which directs T helper type 1 (Th1) cell differentiation. This subfamily includes TBR1 (also known as T-brain-1, or TES-56), which is a neuron-specific transcription factor involved in forebrain development, and TBR2 (also known as Eomesodermin, Eomes, or T-brain-2), which is associated with neurogenesis, cardiogenesis and tumor immune response. This subfamily belongs to the T-box family of transcription factors which play a multitude of diverse functions throughout development. The founding member of the T-box family is Brachyury (also known as TBXT, or T). T-box family members share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 185 matched cddid_all.tbl CDD cd20195 cd20195 410321 T-box_MGA-like DNA-binding domain of MAX gene-associated protein and related T-box proteins. MGA (also known as MGAP, MAX dimerization protein, MAD5, MXD5) is a dual-specificity transcription factor that regulates the expression of both, MAX-network and T-box family target genes. MGA functions as a repressor or an activator; it binds to 5'-AATTTCACACCTAGGTGTGAAATT-3' core sequence. Its function is activated by heterodimerization with MAX. This subfamily belongs to the T-box family of transcription factors which play a multitude of diverse functions throughout development. The founding member of the T-box family is Brachyury (also known as TBXT, or T). T-box family members share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 186 matched cddid_all.tbl CDD cd20196 cd20196 410322 T-box_TBX6 DNA-binding domain of T-box transcription factor 6, and related T-box proteins. TBX6 is a T-box transcription factor which plays an essential role in the fate determination of axial stem to become either neural or mesodermal. It also plays an essential role in the regulation of left/right patterning in mouse embryos, through effects on nodal cilia and perinodal signaling. This subfamily belongs to the T-box family of transcription factors which play a multitude of diverse functions throughout development. The founding member of the T-box family is Brachyury (also known as TBXT, or T). T-box family members share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 182 matched cddid_all.tbl CDD cd20197 cd20197 410323 T-box_VegT-like DNA-binding domain of Xenopus VegT and related T-box proteins. VegT, (also known as Antipodean, Brat and Xombi), is a T-box transcription factor required in early Xenopus embryos for the formation of both, the mesoderm and endoderm germ layers. This subfamily belongs to the T-box family of transcription factors which play a multitude of diverse functions throughout development. The founding member of the T-box family is Brachyury (also known as TBXT, or T). T-box family members share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 183 matched cddid_all.tbl CDD cd20198 cd20198 410324 T-box_TBX15-like DNA-binding domain of T-box transcription factor 15 and related T-box proteins. TBX15 (also known as TBX14) plays an important role in the development of the skeleton of the limb, vertebral column and head, possibly through its control of the number of mesenchymal precursor cells and chondrocytes. TBX15 also plays a role in the differentiation of brown and brite adipocytes. This subgroup belongs to the T-box family of transcription factors which play a multitude of diverse functions throughout development. The founding member of the T-box family is Brachyury (also known as TBXT, or T). T-box family members share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 198 matched cddid_all.tbl CDD cd20199 cd20199 410325 T-box_TBX18_like DNA-binding domain of T-box transcription factor 18 and related T-box proteins. TBX18 acts as a transcription repressor involved in the developmental processes of a variety of tissues and organs, including the ureter, vertebral column. epicardium and coronary vessels. TBX18 is important for the development of the head portion of the sino atrial node (SAN); SAN is the pacemaker region of the heart that initiates each heartbeat. This subgroup belongs to the T-box family of transcription factors which play a multitude of diverse functions throughout development. The founding member of the T-box family is Brachyury (also known as TBXT, or T). T-box family members share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 195 matched cddid_all.tbl CDD cd20200 cd20200 410326 T-box_TBX22-like DNA-binding domain of T-box transcription factor 22 and related T-box proteins. TBX22 is a transcriptional regulator involved in developmental processes. Mutations in the T-Box transcription factor gene TBX22 are found in X-linked Cleft Palate with or without Ankyloglossia syndrome (CPX syndrome). TBX22 mutation is also associated with cleft lip and palate, and tooth agenesis. This subgroup belongs to the T-box family of transcription factors which play a multitude of diverse functions throughout development. The founding member of the T-box family is Brachyury (also known as TBXT, or T). T-box family members share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 194 matched cddid_all.tbl CDD cd20201 cd20201 410327 T-box_TBX19-like DNA-binding domain of T-box transcription factor 19 and related T-box proteins. Tbx19 (also known as Tpit) is a T-box factor restricted to two pituitary (pro-opiomelanocortin) POMC-expressing lineages, the corticotrophs and melanotrophs; it controls terminal differentiation of these lineages. TBX19 activates POMC gene transcription with the cooperation of another transcription factor Pitx1. Mutations of the human TPIT gene cause early onset pituitary adrenocorticotrophic hormone (ACTH) deficiency. This subfamily belongs to the T-box family of transcription factors which play a multitude of diverse functions throughout development. The founding member of the T-box family is Brachyury (also known as TBXT, or T). T-box family members share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 183 matched cddid_all.tbl CDD cd20202 cd20202 410328 T-box_TBXT DNA-binding domain of T-box transcription factor T and related T-box proteins. TBXT, also known as Brachyury protein, or protein T, is a transcription factor needed for posterior mesoderm formation and differentiation as well as for the notochord development during embryogenesis. It binds to a 24 base-pair (bp) palindromic site (called the T site) and activates gene transcription when bound to such a site. This subfamily belongs to the T-box family of transcription factors which play a multitude of diverse functions throughout development. TBXT is the founding member of the T-box family, members of which share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 179 matched cddid_all.tbl CDD cd20203 cd20203 410329 T-box_TBX21 DNA-binding domain of T-box transcription factor 21 and related T-box proteins. TBX21 (also known as T-cell-specific T-box transcription factor T-bet or transcription factor TBLYM) is a lineage-defining transcription factor which directs T helper type 1 (Th1) cell differentiation. It initiates Th1 lineage development from naive T helper precursor cells both by initiating the Th1 genetic programs and by inhibiting the opposing Th2 and Th17 lineage-commitment programs. This subfamily belongs to the T-box family of transcription factors which play a multitude of diverse functions throughout development. The founding member of the T-box family is Brachyury (also known as TBXT, or T). T-box family members share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 191 matched cddid_all.tbl CDD cd20204 cd20204 410330 T-box_TBR1 DNA-binding domain of T-box brain protein 1 and related T-box proteins. TBR1 (also known as T-brain-1 or TES-56) is a neuron-specific transcription factor of the T-box family and involved in forebrain development. It has been recognized as a high-confidence risk gene for autism spectrum disorders (ASD); it regulates the expression of ASD-related genes that are critical for cortical development. This subfamily belongs to the T-box family of transcription factors which play a multitude of diverse functions throughout development. The founding member of the T-box family is Brachyury (also known as TBXT, or T). T-box family members share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 191 matched cddid_all.tbl CDD cd20205 cd20205 410331 T-box_TBR2 DNA-binding domain of T-box brain protein 2 and related T-box proteins. TBR2 (also known as Eomesodermin, Eomes, or T-brain-2) is a member of the T-box family of transcription factors and is associated with neurogenesis, cardiogenesis and tumor immune response. This subfamily belongs to the T-box family of transcription factors which plays a multitude of diverse functions throughout development. The founding member of the T-box family is Brachyury (also known as TBXT, or T). T-box family members share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 191 matched cddid_all.tbl CDD cd20206 cd20206 411001 YbbR YbbR domain. YbbR domains occur as tandem repeats or in architectures together with other domains. Putative roles in cell growth, cell division, and/or virulence have been suggested for this domain. 79 matched cddid_all.tbl CDD cd20207 cd20207 380908 Bbox2_GefO-like B-box-type 2 zinc finger found in Ras guanine nucleotide exchange factor O (GefO) and similar proteins. Ras guanine-nucleotide exchange factors (RasGEFs) activate Ras by catalyzing the replacement of GDP with GTP, and thus lie near the top of many signaling pathways. They are important for signaling in development and chemotaxis in many organisms. Ras guanine nucleotide exchange factor O (GefO), also known as RasGEF domain-containing protein O, is faintly expressed during development of Dictyostelium discoideum. It contains a C3HC4-type RING finger, a B-box motif that shows high sequence similarity with B-Box-type zinc finger 2 found in tripartite motif-containing proteins (TRIMs), a REM (Ras exchanger motif) domain, and a # RasGEF domain. The type 2 B-box (Bbox2) zinc finger is characterized by a CHC3H2 zinc-binding consensus motif. 40 matched cddid_all.tbl CDD cd20208 cd20208 380909 Bbox1_DUF2009 B-box-type 1 zinc finger found in DUF2009 domain-containing proteins and similar proteins. This group is composed of uncharacterized proteins containing a zinc finger B-box domain and a DUF2009 domain, and similar zinc finger B-box domain-containing proteins. The B-box motif shows high sequence similarity with B-Box-type 1 zinc finger found in tripartite motif-containing proteins (TRIMs). The type 1 B-box (Bbox1) zinc finger is characterized by a C6H2 zinc-binding consensus motif. 43 matched cddid_all.tbl CDD cd20214 cd20214 380784 PFM_CEL-III-like pore-forming module of hemolytic lectin Cucumaria echinate CEL-III and similar aerolysin-type beta-barrel pore-forming proteins. Cucumaria echinate CEL-III is a Ca(2+)-dependent and galactose-specific lectin, which is cytotoxic to some cultured cell lines, has strong hemolytic activity toward human and rabbit erythrocytes, and anti-malarial activity. Hemolysis results from ion-permeable pores formed from CEL-III oligomers in the target cell membrane. Members of this group includes CEL-III isoforms: CEL-III-L1, CEL-III-L2, CEL-III-S1, CEL-III-S2, and CEL-III-LS1. Many proteins belonging to this group have two N-terminal ricin-type carbohydrate-binding domains which adopt beta-trefoil folds. Members of this group belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). The CEL-III oligomer in the membrane may be composed of six monomers. 124 matched cddid_all.tbl CDD cd20215 cd20215 380785 PFM_LSL-like pore-forming module of Laetiporus sulphureus LSL lectin and similar aerolysin-type beta-barrel pore-forming proteins. LSL is a lectin, produced by the parasitic mushroom Laetiporus sulphureus, which exhibits hemolytic and hemagglutinating activities. Members of this family belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 164 matched cddid_all.tbl CDD cd20216 cd20216 380786 PFM_HFR-2-like pore-forming module of wheat HFR-2 toxin, FEM32, and similar aerolysin-type beta-barrel pore-forming proteins. HFR-2 is a wheat cytolytic toxin which may normally function in defense against certain insects or pathogens. The Hfr-2 gene is upregulated in virulent Hessian fly larval feedingdouble dagger. The HFR-2 protein may insert in plant cell membranes at the feeding sites and by forming pores provide water, ions and other small nutritive molecules to the developing larvae. This group also contains FEM32, a flower-specific lectin-like protein from the dioecious plant Rumex acetosa, which alters flower development and induces male sterility in transgenic tobacco. It has been suggested that the FEM32 gene activates some form of programmed cell death (PCD), a process that could be mediated by the action of its lectin domains for binding to specific glycoproteins on the cell membrane and facilitated by the formation of pore structures in the membranes and the subsequent leakage of the cytosolic content through its pore-forming aerolysin domain. Most proteins belonging to this group have N-terminal agglutatin (also known as amaranthin) lectin domains; most have two agglutatin domains, in combination with one aerolysin domain. Members of this group belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 152 matched cddid_all.tbl CDD cd20217 cd20217 380787 PFM_agglutinin-like pore-forming module (PFM) of uncharacterized proteins which have agglutatin domain(s), and similar aerolysin-type beta-barrel pore-forming proteins. Most proteins belonging to this group have an N-terminal agglutatin (also known as amaranthin) lectin domain; some have fascin-like domains which adopt a beta-trefoil topology. Members of this group belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 150 matched cddid_all.tbl CDD cd20218 cd20218 380788 PFM_aerolysin pore-forming module of aerolysin and similar aerolysin-type beta-barrel pore-forming proteins. Aerolysin is a cytosolic bacterial toxin that forms pores in the host membrane, leading to destruction of the membrane permeability barrier and host cell death. Another member of this family is alpha-toxin from Clostridium septicum, the main virulence factor of this bacterium, known for causing non-traumatic gas gangrene. Many proteins belonging to this group have an N-terminal APT domain; an APT domain is the N-terminal domain of aerolysin and pertussis toxin and has a type-C lectin-like fold. Members of this group belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 144 matched cddid_all.tbl CDD cd20219 cd20219 380789 PFM_physalysin-1-like pore-forming module of Physella acuta physalysin1 and similar aerolysin-type beta-barrel pore-forming proteins. From a comparative immunological study of the snail Physella acuta, physalysin1 was identified as one of three physalysins in the snail. Members of this family belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 125 matched cddid_all.tbl CDD cd20220 cd20220 380790 PFM_natterin-3-like pore-forming module of Thalassophryne nattereri fish venom natterins 1-4, and similar aerolysin-type beta-barrel pore-forming proteins. This group includes 4 of the 5 Thalassophryne nattereri fish venom natterins: natterin-1, -2, -3, and 4. Natterins have kininogenase activity, kallikrein activity, and are allodynic and edema inducing. They also cleave type I and type IV collagen, resulting in necrosis of the affected cells. Contradictory to their edematic activity, Natterins also have anti-inflammatory effects through inhibition of interactions between leukocytes and the endothelium, and reduction in neutrophil accumulation. Many proteins belonging to this group have an N-terminal DUF3421 domain. They belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 152 matched cddid_all.tbl CDD cd20221 cd20221 380791 PFM_Dln1-like pore-forming module of Danio rerio Dln1, and similar aerolysin-type beta-barrel pore-forming proteins. Since Danio rerio Dln1 has a specific affinity towards high-mannose glycans, which are common on the surface of virus and fungi, it has been suggested that it may play a defense role. Members of this group also include lamprey immune protein (LIP), a defense molecule derived from lamprey supraneural body tissue which has efficient cytocidal actions against tumor cells. Many proteins belonging to this group have a N-terminal Jacalin-like lectin domain. They belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 168 matched cddid_all.tbl CDD cd20222 cd20222 380792 PFM_parasporin-2-like pore-forming module of parasporin-2, hydralysin and similar aerolysin-type beta-barrel pore-forming proteins. Bacillus thuringiensis strain A1547 parasporin-2 (PS2, also named Cry46Aa1) is an anti-cancer protein which causes specific cell damage via PS2 oligomerization in the cell membrane. Glycosylphosphatidylinositol (GPI)-anchored proteins may be involved in the cytocidal action of PS2 as co-receptors for PS2's cytocidal action. This family also includes hydralysin (Hln-1) and Hln-2 produced by the green hydra Chlorohydra viridissima. Hydralysin is a paralysis-inducing protein not found in the stinging cells (nematocytes), with a cell type-selective cytolytic activity; it binds erythrocyte membranes and forms discrete pores. They belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 147 matched cddid_all.tbl CDD cd20223 cd20223 380793 PFM_epsilon-toxin-like pore-forming module of Clostridium perfringens epsilon-toxin and similar aerolysin-type beta-barrel pore-forming proteins. Clostridium perfringens epsilon-toxin is responsible for fatal enterotoxemia in ungulates. It forms a heptamer in the lipid rafts of Madin-Darby Canine Kidney (MDCK) cells, leading to cell death; its oligomer formation is induced by activation of neutral sphingomyelinase. This group also includes an insecticidal crystal protein Cry14-4 (encoded on plasmid pBMBt1 of Bacillus thuringiensis serovar darmstadiensis). Also included is pXO2-60 (a protein from the pathogenic pXO2 plasmid of Bacillus anthracis) which harbors a unique ubiquitin-like fold domain at the C-terminus of the aerolysin-like domain, and is involved in virulence. They belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 144 matched cddid_all.tbl CDD cd20224 cd20224 380794 PFM_alpha-toxin-like pore-forming module of Clostridium septicum alpha-toxin and similar aerolysin-type beta-barrel pore-forming proteins. Clostridium septicum alpha-toxin is the main virulence factor of this bacterium, known for causing non-traumatic gas gangrene. Members of this family belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 121 matched cddid_all.tbl CDD cd20225 cd20225 380795 PFM_lysenin-like pore-forming module of lysenin and similar aerolysin-type beta-barrel pore-forming proteins. Lysenin (also known as Efl1) is a sphingomyelin-binding defense protein found in the coelomic fluid of the annelid earthworm Eisenia fetida. This group also contains lysenin-related proteins LRP-1 , LRP-2 , and LRP-3 from Eisenia sp.. They belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 150 matched cddid_all.tbl CDD cd20226 cd20226 380796 PFM_Cry51Aa-like pore-forming module of Bacillus thuringiensis insecticidal Cry51A toxin, Bacillus thuringiensis cytotoxic parasporin-5 and similar aerolysin-type beta-barrel pore-forming proteins. Bacillus thuringiensis parasporin-5 has strong cytocidal activity against several types of cancer cells and may or may not have insecticidal activity. Cry51A toxin is toxic to coleopteran (beetle) larvae. Other members of this family include Bacillus thuringiensis Cry15Aa which is toxic to lepidopteran (butterflies and moth) larvae. They belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 172 matched cddid_all.tbl CDD cd20227 cd20227 380797 PFM_CPE-like CPE (Clostridium perfringens enterotoxin), HA-70 type C, and similar aerolysin-type beta-barrel pore-forming proteins. This domain is also known as the clenterotox domain (Chlostridium enterotoxin). Clostridium perfringens enterotoxin is the major virulence determinant for C. perfringens type-A food poisoning. After binding to its receptors, which include particular human claudins, the toxin forms pores in the cell membrane. This family also includes HA-70 type C, a component of the haemagglutinin complex of Clostridium botulinum type C toxin. They belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 162 matched cddid_all.tbl CDD cd20228 cd20228 380798 PFM_TDP-like pore-forming module of Flammulina velutipes transepithelial electrical resistance (TEER)-decreasing protein, and similar aerolysin-type beta-barrel pore-forming proteins. Flammulina velutipes TEER-decreasing protein (also known as flammutoxin, FTX), is a pore-forming hemolytic protein known to cause a rapid decrease in TEER and a parallel increase in paracellular permeability in the human intestinal epithelial Caco-2 cell monolayer. Members of this group belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 118 matched cddid_all.tbl CDD cd20229 cd20229 380799 PFM_tachylectin-like pore-forming module (PFM) of uncharacterized proteins having tachylectin domain(s), and similar aerolysin-type beta-barrel pore-forming proteins. Many proteins belonging to this group have tachylectin domain(s), N-terminal to this PFM; some also have an immunoglobulin (Ig) domain. Tachylectins are lectins which bind N-acetylglucosamine and N-acetylgalactosamine. Members of this group belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 148 matched cddid_all.tbl CDD cd20230 cd20230 380800 PFM_EP37-like pore-forming module of Cynops pyrrhogaster EP37, and similar aerolysin-type beta-barrel pore-forming proteins. Cynops pyrrhogaster (Japanese newt EP37) EP37 is an epidermis-specific protein which has a non-lens beta/gamma-crystallin domain in tandem and N-terminal to this pore-forming module. C. pyrrhogaster has several EP37-like proteins present in skin, gastric epithelium and fundic glands of an adult newt and in the swimming larva. This group also includes the alpha subunit of Bombina maxima betagamma-CAT (a non-lens betagamma-crystallin (alpha-subunit) and trefoil factor (beta subunit) complex) identified from skin secretions. Betagamma-CAT shows potent hemolytic activity on mammalian erythrocytes. Many proteins belonging to this group have N-terminal crystallin (beta/gamma crystallin) domain(s). Members of this group belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 146 matched cddid_all.tbl CDD cd20231 cd20231 380801 PFM_jacalin-like pore-forming module of uncharacterized proteins which have an N-terminal jacalin-like lectin domain, and similar aerolysin-type beta-barrel pore-forming proteins. Jacalin-like lectins are sugar-binding protein domains. Proteins having these lectin domains may bind mono- or oligosaccharides with high specificity. Generally, pore-forming proteins (PFPs) are secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores detrimental to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel. Many of this family are bacterial toxins. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 150 matched cddid_all.tbl CDD cd20232 cd20232 380802 PFM_crystallin-like pore-forming module (PFM) of uncharacterized proteins which have N-terminal crystallin domain(s), and similar aerolysin-type beta-barrel pore-forming proteins. Many proteins belonging to this group have N-terminal crystallin (beta/gamma crystallins) domain(s). Members of this group belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 151 matched cddid_all.tbl CDD cd20233 cd20233 380803 PFM_unzipped-like pore-forming module (PFM) of proteins having a DUF3421 domain including Drosophila unzipped, honey bee anarchy 1, and similar aerolysin-type beta-barrel pore-forming proteins. Many proteins belonging to this group have N-terminal DUF3421. Drosophila melanogaster unzipped protein is required for normal axon patterning during neurogenesis, and honey bee anarchy 1 may play a role in worker sterility in a social insect. Members of this group belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 134 matched cddid_all.tbl CDD cd20234 cd20234 380804 PFM_fascin-like pore-forming module (PFM) of uncharacterized proteins which have N-terminal fascin-like domain, and similar aerolysin-type beta-barrel pore-forming proteins. Most proteins belonging to this group have an N-terminal Fascin-like domains which adopt a beta-trefoil topology. Members of this group belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 139 matched cddid_all.tbl CDD cd20235 cd20235 380805 PFM_spherulin-2a-like pore-forming module of Physarum polycephalum spherulin-2a, Plodia interpunctella follicular epithelium yolk protein subunit YP4, and similar aerolysin-type beta-barrel pore-forming proteins. Spherulin 2a is a coat glycoprotein produced during encystment from the slime mold, Physarum polycephalum. YP4, is one of two subunits of the follicular epithelium yolk protein from Plodia interpunctella and other pyralid moths; it is produced in the follicle cells during vitellogenesis, and after secretion it is taken up into the oocyte and stored in the yolk spheres for utilization during embryogenesis. Members of this group belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 150 matched cddid_all.tbl CDD cd20236 cd20236 380806 PFM_SP17-like pore-forming module-like domain of Phlebotomus argentipes 29 kDa salivary protein SP17, and similar aerolysin-type beta-barrel pore-forming proteins. Members include two putative secreted proteins from the salivary glands of Phlebotomus argentipes: 29 kDa salivary protein SP17 and 30 kDa salivary protein SP15. They belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 117 matched cddid_all.tbl CDD cd20237 cd20237 380807 PFM_LIN24-like pore-forming module of Caenorhabditis elegans LIN-24 and similar aerolysin-type beta-barrel pore-forming proteins. The process of cytotoxic cell death occurs in Caenorhabditis elegans containing mutations in either of lin-24 and lin-33. The cytotoxicity caused by mutation of either gene requires the function of the other. Genes required for the engulfment of apoptotic corpses function in the cytotoxic cell deaths induced by mutations in lin-24 and lin-33. It has been proposed that Caenorhabditis elegans LIN-24 may function to interact with bacterial toxins having similarity with it, and inactivate these, thereby allowing C. elegans to consume or survive exposure to bacteria that produce such toxins. Members of this group belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 120 matched cddid_all.tbl CDD cd20238 cd20238 380808 PFM_ABFB-like pore-forming module (PFM) of uncharacterized proteins which have an N-terminal ABFB (alpha-L-arabinofuranosidase B) domain, and similar aerolysin-type beta-barrel pore-forming proteins. Most proteins belonging to this group have a PFM C-terminal to an ABFB domain. Alpha-L-arabinofuranosidase (Araf-ase, EC 3.2.1.55) belongs to the glycosyl hydrolase family GH54, and in Aspergillus niger exhibits both Araf-ase, (EC 3.2.1.55) and alpha-D-galactofuranose (Galf-ase) activities, with Galf-ase being less than Araf-ase. Some members have a Ricin-type carbohydrate-binding domain which adopts a beta-trefoil fold. Members of this group belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 146 matched cddid_all.tbl CDD cd20239 cd20239 380809 PFM_aerolysin-like pore-forming module of aerolysin-type beta-barrel pore-forming proteins; uncharacterized subgroup. Generally, pore-forming proteins (PFPs) are secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores detrimental to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel. Many of this family are bacterial toxins. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 145 matched cddid_all.tbl CDD cd20240 cd20240 380810 PFM_aerolysin-like pore-forming module of aerolysin-type beta-barrel pore-forming proteins; uncharacterized subgroup. Generally, pore-forming proteins (PFPs) are secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores detrimental to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel. Many of this family are bacterial toxins. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 145 matched cddid_all.tbl CDD cd20241 cd20241 380811 PFM_aerolysin-like pore-forming module of aerolysin-type beta-barrel pore-forming proteins; uncharacterized subgroup. Members of this group belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 139 matched cddid_all.tbl CDD cd20242 cd20242 380812 PFM_aerolysin-like pore-forming module of aerolysin-type beta-barrel pore-forming proteins; uncharacterized subgroup. Members of this group belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. Aerolysin-type beta-PFPs are believed to use an amphipathic beta-hairpin to form the beta-barrel, are found in all kingdoms of life and many are bacterial toxins. In addition to having a role in microbial infection, they have potential as biotechnological sensors and delivery systems. They share a similar monomeric architecture, with a variable membrane-binding domain and a structurally conserved pore-forming region. A significant portion of the monomeric subunit structure is re-organized to form the pore. Oligomers formed by members of the aerolysin family include: hepta- (aerolysin), octa- (Dln1), and nonameric oligomers (lysenin and monalysin). 144 matched cddid_all.tbl CDD cd20243 cd20243 380781 NoBody Negative regulator of P-body association. Negative regulator of P-body association, also called P-body dissociating protein or protein NoBody (non-annotated P-body dissociating polypeptide), is a microprotein that interacts with mRNA decapping proteins, which remove the 5' cap from mRNAs to promote 5'-to-3' decay. It localizes to P-bodies, which are mRNA-decay-associated RNA-protein granules. NoBody promotes dispersal of P-body components and is likely to play a role in the mRNA decapping process. Decapping proteins participate in mRNA turnover and nonsense-mediated decay (NMD). 68 matched cddid_all.tbl CDD cd20244 cd20244 380780 Toddler Apelin receptor early endogenous ligand, also called Toddler. Apelin receptor early endogenous ligand, also called protein Elabela or protein Toddler, is an endogenous peptidic ligand of the G protein-coupled receptor APJ, also called apelin receptor (APLNR). The apelin/APJ axis contributes to maintaining homeostasis in normal and pathological hearts, and is also involved in heart development, including endoderm differentiation, heart morphogenesis and coronary vascular formation. Elabela/Toddler plays crucial roles in heart development and disease conditions, presumably at time points or at areas of the heart different from apelin. It is a potential therapeutic peptide, showing beneficial effects on body fluid homeostasis, cardiovascular health, and renal insufficiency, as well as potential benefits for metabolism and diabetes. 53 matched cddid_all.tbl CDD cd20245 cd20245 380778 humanin humanin and similar peptides. Humanin (HN) is a peptide encoded in the mitochondrial genome by the 16S ribosomal RNA gene MT-RNR2. HN has neuroprotective, anti-inflammatory, anti-apoptotic, anti-aging, and anti-fibrilogenic properties through interaction with a series of targets including BAX, IGFBP-3 (insulin-like growth factor binding protein 3), and a trimeric CNTFR/WSX-1/gp130 complex. Endogenous HN is both, an intracellular and secreted protein, and has been detected in brain, retinal pigment epithelium, blood vessels, pancreatic beta cells, tumors, testes and other tissues, and is also present in serum and in human seminal plasma. Single amino acid substitutions of HN can lead to significant changes in its potency and biological functions. There are multiple nuclearly-encoded HN isoforms which may be functional genes regulated in a tissue- and factor-specific manner. HN has potential as a therapeutic target for neurodegenerative and cardiovascular diseases, diabetes, male infertility, and cancer; it may have value as a biomarker for these diseases. Humanin analogs and peptide mimetics have been developed which show promising results in preclinical models of degenerative diseases. 24 matched cddid_all.tbl CDD cd20246 cd20246 380775 CASIMO1 Cancer Associated Small Integral Membrane Open reading frame 1 (CASIMO1). The Cancer-Associated Small Integral Membrane Open reading frame 1 (CASIMO1), a small open reading frame (sORF)-encoded protein (also known as a microprotein), controls cell proliferation and interacts with squalene epoxidase (SQLE) modulating lipid droplet formation. CASIMO1 RNA is overexpressed predominantly in hormone receptor-positive breast tumors, and its knockdown has been shown to decrease proliferation in multiple breast cancer cell lines. Loss of CASIMO1 disturbs the organization of the actin cytoskeleton, leads to inhibition of cell motility, and stalls the cell cycle in the G0/G1 phase. CASIMO1 interacts with SQLE, a key enzyme in cholesterol synthesis and a known oncogene in breast cancer. This family contains two variants expressed on different chromosomes in humans, small integral membrane protein 5 (SMIM5) and small integral membrane protein 22 (SMIM22). 68 matched cddid_all.tbl CDD cd20247 cd20247 380779 DWORF DWarf Open Reading Frame (DWORF). DWarf Open Reading Frame (DWORF) is a small protein that plays a key role in heart muscle contraction. DWORF, Sarcolipin (SLN), and myoregulin (MRLN) are transmembrane regulators of the sarcoplasmic reticulum calcium transporting ATPase (SERCA). DWORF enhances SERCA activity by displacing phospholamban (PLN), a potent SERCA inhibitor. This makes DWORF an attractive candidate for a heart failure therapeutic. DWORF is also present in slow-twitch skeletal muscle fibers. 35 matched cddid_all.tbl CDD cd20248 cd20248 380749 phospholamban_like phospholamban, sarcolipin, and sarcolamban family of bioactive peptides. Vertebrate phospholamban (PLN), sarcolipin (SLN), and invertebrate sarcolamban (SCL) constitute a family of bioactive peptides. They are involved in the regulation of Ca2+ traffic, and their alteration can result in irregular muscle contractions. Invertebrate SCL (SCLA and SCLB) are encoded within a single putative noncoding transcript, pncr003:2L; vertebrate PLN and SLN are each encoded within a single exon of a spliced transcript. PLN is chiefly expressed in the cardiac muscle, while SLN expression is expressed in the atria of the heart and embryonic slow-type skeletal muscle; SCL is found in cardiac and somatic muscle of Drosophila melanogaster. PLN and SLN are each a single-pass transmembrane alpha-helix that interacts directly with the sarcoplasmic reticulum (SR) calcium pump (SERCA), lower its affinity for Ca2+, thereby decreasing the rate of Ca2+ reuptake into the SR from the sarcoplasm. In the heart, PLN and SLN inhibit the activity of SERCA2a isoform and function as important regulators of cardiac contractibility and disease. SCLA and SCLB are each predicted to form a single-pass transmembrane helix, localize to the SR with the SR calcium pump (Ca-P60A), and dampen its activity. SLN in skeletal muscle has also been shown to amplify calcineurin signaling, and is a potential therapeutic target for the management of muscular dystrophy, as it is upregulated in the skeletal muscle of the classical mouse model for Duchenne muscular dystrophy. 27 matched cddid_all.tbl CDD cd20249 cd20249 380772 Hemotin Hemotin. Hemotin is a transmembrane alpha-helical microprotein localized to early endosomes in hemocytes (Drosophila macrophages), where it regulates endosomal maturation during phagocytosis by repressing the cooperation of 14-3-3zeta with specific phosphatidylinositol enzymes. Hemocytes are professional phagocytes tasked with removing dying cells and microorganisms invading the body. Drosophila hemotin mutants accumulate undigested phagocytic material inside enlarged endolysosomes, resulting in reduced ability to fight bacteria and severely reduced life span. 86 matched cddid_all.tbl CDD cd20250 cd20250 380750 Phospholamban Phospholamban bioactive peptide and similar proteins. Vertebrate phospholamban (PLN) belongs to a family of bioactive peptides which includes vertebrate sarcolipin (SLN), and the invertebrate sarcolamban (SCLA, and SCLB). SCLA and SCLB are encoded within a single putative noncoding transcript, pncr003:2L; PLN and SLN are each encoded within a single exon of a spliced transcript. PLN is chiefly expressed in the cardiac muscle, while SLN is expressed in the atria of the heart and embryonic slow-type skeletal muscle; SCL is found in cardiac and somatic muscle of Drosophila melanogaster. PLN and SLN are each a single-pass transmembrane alpha-helix that interacts directly with the sarcoplasmic reticulum (SR) calcium pump (SERCA), lower its affinity for Ca2+, thereby decreasing the rate of Ca2+ reuptake into the SR from the sarcoplasm. In the heart, PLN and SLN inhibit the activity of SERCA2a isoform and function as important regulators of cardiac contractibility and disease. SCLA and SCLB are each predicted to form a single-pass transmembrane helix, localize to the SR with the SR calcium pump (Ca-P60A), and dampen its activity. PLN and SLN differ in their interaction with SERCA; PLN is an affinity modulator of SERCA. It is thought to form a pentamer in the membrane. 52 matched cddid_all.tbl CDD cd20251 cd20251 380755 Complex1_LYR_SF LYR (leucine-tyrosine-arginine) motif found in Complex1_LYR-like superfamily. The Complex1_LYR-like superfamily consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N-terminus. The human genome has at least ten LYR proteins that were predominantly identified as mitochondrial proteins. Some family members were also found in the cytosol or nucleus. LYR motif-containing protein 4 (LYRM4) represents the only LYR protein that is directly involved in the first steps of Fe-S cluster generation. Other LYR proteins have been identified as accessory subunits or assembly factors of mitochondrial OXPHOS (oxidative phosphorylation) complexes I, II, III and V, and they play specific roles in acetate metabolism. 57 matched cddid_all.tbl CDD cd20253 cd20253 380751 Sarcolipin Sarcolipin bioactive peptide and similar proteins. Vertebrate sarcolipin (SLN) belongs to a family of bioactive peptides which includes phospholamban (PLN), and invertebrate sarcolamban (SCL). SCLA and SCLB are encoded within a single putative noncoding transcript, pncr003:2L; PLN and SLN are each encoded within a single exon of a spliced transcript. PLN is chiefly expressed in the cardiac muscle, while SLN is expressed in the atria of the heart and embryonic slow-type skeletal muscle; SCL is found in cardiac and somatic muscle of Drosophila melanogaster. PLN and SLN are each a single-pass transmembrane alpha-helix that interacts directly with the sarcoplasmic reticulum (SR) calcium pump (SERCA), lower its affinity for Ca2+, thereby decreasing the rate of Ca2+ reuptake into the SR from the sarcoplasm. In the heart, PLN and SLN inhibit the activity of SERCA2a isoform and function as important regulators of cardiac contractibility and disease. SCLA and SCLB are each predicted to form a single-pass transmembrane helix, localize to the SR with the SR calcium pump (Ca-P60A), and dampen its activity. PLN and SLN differ in their interaction with SERCA. SLN in skeletal muscle has also been shown to amplify calcineurin signaling, and is a potential therapeutic target for the management of muscular dystrophy, as it is upregulated in the skeletal muscle of the classical mouse model for Duchenne muscular dystrophy. 30 matched cddid_all.tbl CDD cd20254 cd20254 380776 CASIMO1_SMIM5 small integral membrane protein 5 (SMIM5) of CASIMO1. This family contains the small integral membrane protein 5 (SMIM5) variant of the Cancer-Associated Small Integral Membrane Open reading frame 1 (CASIMO1), a small open reading frame (sORF)-encoded protein (also known as a microprotein). CASIMO1 controls cell proliferation and interacts with squalene epoxidase (SQLE) modulating lipid droplet formation. CASIMO1 RNA is overexpressed predominantly in hormone receptor-positive breast tumors, and its knockdown has been shown to decrease proliferation in multiple breast cancer cell lines. Loss of CASIMO1 disturbs the organization of the actin cytoskeleton, leads to inhibition of cell motility, and stalls the cell cycle in the G0/G1 phase. CASIMO1 interacts with SQLE, a key enzyme in cholesterol synthesis and a known oncogene in breast cancer. This variant is expressed on chromosome 16 in humans, mostly in the stomach, kidney, thyroid and esophagus. 71 matched cddid_all.tbl CDD cd20255 cd20255 380777 CASIMO1_SMIM22 small integral membrane protein 22 (SMIM22) of CASIMO1. This family contains the small integral membrane protein 22 (SMIM22) variant of the Cancer-Associated Small Integral Membrane Open reading frame 1 (CASIMO1), a small open reading frame (sORF)-encoded protein (also known as a microprotein). CASIMO1 controls cell proliferation and interacts with squalene epoxidase (SQLE) modulating lipid droplet formation. CASIMO1 RNA is overexpressed predominantly in hormone receptor-positive breast tumors, and its knockdown has been shown to decrease proliferation in multiple breast cancer cell lines. Loss of CASIMO1 disturbs the organization of the actin cytoskeleton, leads to inhibition of cell motility, and stalls the cell cycle in the G0/G1 phase. CASIMO1 interacts with SQLE, a key enzyme in cholesterol synthesis and a known oncogene in breast cancer. This variant is expressed on chromosome 17 in humans, mostly in the colon and stomach. 80 matched cddid_all.tbl CDD cd20256 cd20256 380773 Stannin_family Stannin family includes vertebrate Stannin and insect Hemotin. The Stannin family includes vertebrate Stannin and insect Hemotin, which are functional homologs required at the cellular level for endosomal maturation, and at the molecular level, to bind and antagonize 14-3-3zeta. Stannin is a monotopic membrane protein containing an N-terminal single transmembrane helix that transverses the lipid bilayer, an unstructured linker which includes a conserved CXC metal-binding motif and a putative 14-3-3zeta binding site, and a C-terminal distorted cytoplasmic helix. Analysis of the Hemotin sequence using a transmembrane topology prediction program revealed a very similar potential transmembrane alpha-helical domain arrangement as Stannin. 83 matched cddid_all.tbl CDD cd20257 cd20257 380774 Stannin Stannin. Stannin (SNN) is a monotopic membrane protein containing an N-terminal single transmembrane helix that transverses the lipid bilayer, an unstructured linker which includes a conserved CXC metal-binding motif and a putative 14-3-3zeta binding site, and a C-terminal distorted cytoplasmic helix. It binds and antagonizes 14-3-3zeta and is required for endosomal maturation. It has also been identified as the specific marker for neuronal cell apoptosis induced by trimethyltin (TMT) intoxication. TMT is one of the most toxic organotin compound (or alkyltin), and is known to selectively inflict injury to specific regions of the brain. 84 matched cddid_all.tbl CDD cd20258 cd20258 380771 Tal_Pri Tarsal-less (Tal), also known as polished rice (Pri), and related peptides. The tal/pri gene produces a single polycistronic transcript that encodes 4 related peptides: tal-1A, tal-2A, and tal-3A which are each 11 amino acids long, and tal-AA, which is 32 amino acids long, the shorter ones contain one conserved LDPTGXY motif, tal-AA contains two. The Tal/Pri peptides function redundantly in several developmental processes. They are required for embryonic and imaginal development in Drosophila. They control epidermal differentiation in Drosophila by triggering the amino-terminal truncation of the transcription factor Shavenbaby (Svb), converting Svb from a repressor to an activator. In addition, Tal/Pri peptides are required for denticle formation and may play a role in the developmental timing of trichome differentiation. They are essential for the development of taenidial folds in the trachea, and in the early stages of leg development, for the intercalation of the tarsal segments during the mid-third instar stage and later for tarsal joint formation. Furthermore, Tal/Pri peptides are required for correct wing and leg formation through their regulation of several genes including those in the Notch signaling pathway. The Tribolium orthologue mille-pattes (mlpt) is essential for embryo segmentation; it also encodes a polycistronic mRNA that codes for four peptides: Mlpt peptides 1-3 range in size from 11 to 15 amino acids and each contain one conserved LDPTGXY motif; Mlpt peptide 4 is 23 amino acids, is not represented here, and does not contain this motif. 32 matched cddid_all.tbl CDD cd20259 cd20259 380770 pgc polar granule component. Polar granule component (pgc) is implicated in primordial germ cell specification in Drosophila, which require transcriptional quiescence and three genes: pgc, nano (nos) and germ cell less (gcl), that act to down-regulate Pol II transcription. The microprotein pgc inhibits transcription elongation factor b (P-TEFb), which phosphorylates the C-terminal domain of the largest Pol II subunit. 66 matched cddid_all.tbl CDD cd20260 cd20260 380769 Myoregulin Myoregulin. Myoregulin (MLN) is encoded by a skeletal muscle-specific RNA Linc-RAM, which is annotated as a putative long noncoding RNA (lncRNA). It is a single-pass transmembrane alpha-helix that interacts directly with sarcoplasmic reticulum (SR) calcium transporting ATPase (SERCA) and impedes Ca(2+) uptake into the SR. SERCA is the membrane pump that controls muscle relaxation by regulating Ca(2+) uptake into the SR. MLN is the dominant regulator of SERCA1 activity in adult skeletal muscle and is a promising drug target for improving muscle performance. 45 matched cddid_all.tbl CDD cd20261 cd20261 380756 Complex1_LYR_LYRM1 LYR (leucine-tyrosine-arginine) motif found in LYR motif-containing protein 1 (LYRM1) and similar proteins. LYR motif-containing protein 1 (LYRM1) may promote cell proliferation and inhibition of apoptosis of preadipocytes. Overexpression of the human LYRM1 causes mitochondrial dysfunction and induces insulin resistance in 3T3-L1 adipocytes. LYRM1 belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N-terminus. 70 matched cddid_all.tbl CDD cd20262 cd20262 380757 Complex1_LYR_LYRM2 LYR (leucine-tyrosine-arginine) motif found in LYR motif-containing protein 2 (LYRM2) and similar proteins. LYRM2 is an uncharacterized LYR motif-containing protein that belongs to the Complex1_LYR-like superfamily which consists of proteins of diverse functions that are exclusively found in eukaryotes; these proteins contain the conserved tripeptide 'LYR' close to the N-terminus. 63 matched cddid_all.tbl CDD cd20263 cd20263 380758 Complex1_LYR_NDUFB9_LYRM3 LYR (leucine-tyrosine-arginine) motif found in NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 (NDUFB9) and similar proteins. NDUFB9, also called LYR motif-containing protein 3 (LYRM3), or Complex I-B22 (CI-B22), or NADH-ubiquinone oxidoreductase B22 subunit (UQOR22), is an accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (complex I), and is believed to be not involved in catalysis. In general, accessory subunits are integral for assembly and function of Complex I, which functions in the transfer of electrons from NADH to the respiratory chain. NDUFB9 belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N-terminus. 77 matched cddid_all.tbl CDD cd20264 cd20264 380759 Complex1_LYR_LYRM4 LYR (leucine-tyrosine-arginine) motif found in LYR motif-containing protein 4 (LYRM4) and similar proteins. LYRM4, also called ISD11, is a eukaryote-specific component of the mitochondrial biogenesis of Fe-S clusters which are essential cofactors in multiple processes, including oxidative phosphorylation. It is required for nuclear and mitochondrial iron-sulfur protein biosynthesis by forming a complex with, and stabilizing, the sulfur donor NFS1. LYRM4 belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N-terminus. 69 matched cddid_all.tbl CDD cd20265 cd20265 380760 Complex1_LYR_ETFRF1_LYRM5 LYR (leucine-tyrosine-arginine) motif found in electron transfer flavoprotein regulatory factor 1 (ETFRF1) and similar proteins. ETFRF1, also called LYR motif-containing protein 5 (LYRM5), or Ghiso (growth-factor inducible soluble) factor, acts as a regulator of the electron transfer flavoprotein by promoting the removal of flavin from the ETF holoenzyme (composed of ETFA and ETFB). It belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N-terminus. 74 matched cddid_all.tbl CDD cd20266 cd20266 380761 Complex1_LYR_NDUFA6_LYRM6 LYR (leucine-tyrosine-arginine) motif found in NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 6 (NDUFA6) and similar proteins. NDUFA6, also called LYR motif-containing protein 6 (LYRM6), or Complex I-B14 (CI-B14), or NADH-ubiquinone oxidoreductase B14 subunit, is an accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), and is believed to be not involved in catalysis. In general, accessory subunits are integral for assembly and function of Complex I, which functions in the transfer of electrons from NADH to the respiratory chain. NDUFA6 belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N-terminus. 75 matched cddid_all.tbl CDD cd20267 cd20267 380762 Complex1_LYR_LYRM7 LYR (leucine-tyrosine-arginine) motif found in LYR motif-containing protein 7 (LYRM7) and similar proteins. LYRM7 is an assembly factor required for Rieske iron sulfur (Fe-S) protein UQCRFS1 incorporation into the cytochrome b-c1 (CIII) complex. It functions as a chaperone, binding to this subunit within the mitochondrial matrix and stabilizing it prior to its translocation and insertion into the late CIII dimeric intermediate within the mitochondrial inner membrane. LYRM7 mutations cause a multifocal cavitating leukoencephalopathy with a distinct and recognizable magnetic resonance imaging (MRI) pattern. LYRM7 belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N-terminus. 72 matched cddid_all.tbl CDD cd20268 cd20268 380763 Complex1_LYR_SDHAF1_LYRM8 LYR (leucine-tyrosine-arginine) motif found in mitochondrial succinate dehydrogenase assembly factor 1 (SDHAF1) and similar proteins. SDHAF1, also called SDH assembly factor 1, or LYR motif-containing protein 8 (LYRM8), is a LYR complex-II specific assembly factor that plays an essential role in the assembly of succinate dehydrogenase (SDH), an enzyme complex (also referred to as respiratory complex II) that is a component of both the tricarboxylic acid (TCA) cycle and the mitochondrial electron transport chain, and which couples the oxidation of succinate to fumarate with the reduction of ubiquinone (coenzyme Q) to ubiquinol. It promotes maturation of the iron-sulfur protein subunit SDHB of the SDH catalytic dimer, protecting it from the deleterious effects of oxidants. SDHAF1 may act together with SDHAF3. It is mutated in SDH-defective infantile leukoencephalopathy. SDHAF1 belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N-terminus. 64 matched cddid_all.tbl CDD cd20269 cd20269 380764 Complex1_LYR_LYRM9 LYR (leucine-tyrosine-arginine) motif found in LYR motif-containing protein 9 (LYRM9) and similar proteins. LYRM9 is an uncharacterized LYR motif-containing protein that belongs to the Complex1_LYR-like superfamily which consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N-terminus. 60 matched cddid_all.tbl CDD cd20270 cd20270 380765 Complex1_LYR_SDHAF3_LYRM10 LYR (leucine-tyrosine-arginine) motif found in mitochondrial succinate dehydrogenase assembly factor 3 (SDHAF3) and similar proteins. SDHAF3, also called SDH assembly factor 3, or LYR motif-containing protein 10 (LYRM10), plays an essential role in the assembly of succinate dehydrogenase (SDH), an enzyme complex (also referred to as respiratory complex II) that is a component of both the tricarboxylic acid (TCA) cycle and the mitochondrial electron transport chain, and which couples the oxidation of succinate to fumarate with the reduction of ubiquinone (coenzyme Q) to ubiquinol. It promotes maturation of the iron-sulfur protein subunit SDHB of the SDH catalytic dimer, protecting it from the deleterious effects of oxidants. SDHAF3 may act together with SDHAF1. Its mutations may be associated with idiopathic SDH-associated diseases. SDHAF3 belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N-terminus. 56 matched cddid_all.tbl CDD cd20271 cd20271 380766 Complex1_LYR_FMC1 LYR (leucine-tyrosine-arginine) motif found in formation of mitochondrial complex V assembly factor 1 (FMC1) and similar proteins. FMC1, also known as formation of mitochondrial complexes protein 1, is an ATP synthase assembly factor that plays a role in the assembly/stability of the mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V). It belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N-terminus. 95 matched cddid_all.tbl CDD cd20272 cd20272 380767 Complex1_LYR_MIEF1-MP LYR (leucine-tyrosine-arginine) motif found in mitochondrial elongation factor 1 microprotein (MIEF1-MP) and similar proteins. MIEF1-MP, also called alternative mitochondrial elongation factor 1 (MIEF1) protein (AltMIEF1), or MIEF1 upstream open reading frame protein, is involved in the regulation of mitochondrial fission mediated by dynamin-1-like protein (DNM1L). It positively regulates mitochondrial translation. MIEF1-MP belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N-terminus. 58 matched cddid_all.tbl CDD cd20273 cd20273 380768 Complex1_LYR_unchar LYR (leucine-tyrosine-arginine) motif found in uncharacterized LYR motif-containing protein. This group contains uncharacterized LYR motif-containing proteins belonging to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N-terminus. 61 matched cddid_all.tbl CDD cd20274 cd20274 380752 Sarcolamban Sarcolamban A and B bioactive peptides and similar proteins. Invertebrate sarcolamban (SCLA and SCLB) belong to a family of bioactive peptides which includes vertebrate phospholamban (PLN) and sarcolipin (SLN). SCLA and SCLB are encoded within a single putative noncoding transcript, pncr003:2L; PLN and SLN are each encoded within a single exon of a spliced transcript. PLN is chiefly expressed in the cardiac muscle, while SLN is expressed in the atria of the heart and embryonic slow-type skeletal muscle; SCL is found in cardiac and somatic muscle of Drosophila melanogaster. PLN and SLN are each a single-pass transmembrane alpha-helix that interacts directly with the sarcoplasmic reticulum (SR) calcium pump (SERCA), lower its affinity for Ca2+, thereby decreasing the rate of Ca2+ reuptake into the SR from the sarcoplasm. In the heart, PLN and SLN inhibit the activity of SERCA2a isoform and function as important regulators of cardiac contractibility and disease. SCLA and SCLB are each predicted to form a single-pass transmembrane helix, localize to the SR with the SR calcium pump (Ca-P60A), and dampen its activity. 27 matched cddid_all.tbl CDD cd20275 cd20275 380753 Sarcolamban_B Sarcolamban B bioactive peptide and similar proteins. Invertebrate sarcolamban B (SCLB) belongs to a family of bioactive peptides which includes invertebrate sarcolamban A (SCLA), and vertebrate phospholamban (PLN) and sarcolipin (SLN). SCLA and SCLB are encoded within a single putative noncoding transcript, pncr003:2L; PLN and SLN are each encoded within a single exon of a spliced transcript. PLN is chiefly expressed in the cardiac muscle, while SLN is expressed in the atria of the heart and embryonic slow-type skeletal muscle; SCL is found in cardiac and somatic muscle of Drosophila melanogaster. PLN and SLN are each a single-pass transmembrane alpha-helix that interacts directly with the sarcoplasmic reticulum (SR) calcium pump (SERCA), lower its affinity for Ca2+, thereby decreasing the rate of Ca2+ reuptake into the SR from the sarcoplasm. In the heart, PLN and SLN inhibit the activity of SERCA2a isoform and function as important regulators of cardiac contractibility and disease. SCLA and SCLB are each predicted to form a single-pass transmembrane helix, localize to the SR with the SR calcium pump (Ca-P60A), and dampen its activity. 28 matched cddid_all.tbl CDD cd20276 cd20276 380754 Sarcolamban_A Sarcolamban A bioactive peptide. Invertebrate sarcolamban A (SCLA) belongs to a family of bioactive peptides which includes invertebrate sarcolamban B (SCLB), and vertebrate phospholamban (PLN) and sarcolipin (SLN). SCLA and SCLB are encoded within a single putative noncoding transcript, pncr003:2L; PLN and SLN are each encoded within a single exon of a spliced transcript. PLN is chiefly expressed in the cardiac muscle, while SLN is expressed in the atria of the heart and embryonic slow-type skeletal muscle; SCL is found in cardiac and somatic muscle of Drosophila melanogaster. PLN and SLN are each a single-pass transmembrane alpha-helix that interacts directly with the sarcoplasmic reticulum (SR) calcium pump (SERCA), lower its affinity for Ca2+, thereby decreasing the rate of Ca2+ reuptake into the SR from the sarcoplasm. In the heart, PLN and SLN inhibit the activity of SERCA2a isoform and function as important regulators of cardiac contractibility and disease. SCLA and SCLB are each predicted to form a single-pass transmembrane helix, localize to the SR with the SR calcium pump (Ca-P60A), and dampen its activity. 27 matched cddid_all.tbl CDD cd20277 cd20277 410555 FXYD phenylalanine-X-tyrosine-aspartate (FXYD) family. FXYDs are small single-transmembrane proteins that act as novel regulators of Na+/K+-ATPase (NKA). The transmembrane domain and the conserved Phe-X-Tyr-Asp motif of FXYD play a role in the binding of FXYD to the alpha- and beta-subunits of NKA. PFXYD (proline-phenylalanine-X-tyrosine-aspartate) at the beginning of the signature sequence is invariant in all known examples in mammals and identical except for the proline in other vertebrates; X is usually Y (tyrosine), but can also be E, T, or H (glutamate, threonine, or histidine). The FXYD protein family contains at least twelve members that have the extracellular FXYD motif, transmembrane domain, and intracellular domain. Members share a 35-amino acid signature sequence domain, beginning with PFXYD and containing 7 invariant and 6 highly conserved amino acids. In mammals, members of the FXYD family include FXYD1 (phospholemman, PLM), FXYD2 (the gamma-subunit of NKA), FXYD3 (mammary tumor marker Mat-8), FXYD4 (corticosteroid hormone-induced factor, CHIF), FXYD5 (dysadherin), FXYD6 (phosphohippolin), and FXYD7. In elasmobranchs, FXYD10 (phospholemman-like protein from shark, PLMS) was first identified in the rectal glands of Squalus acanthias. In addition, studies on sharks reported that the functions of FXYD10 via its C-terminal cysteine residue interactions were associated with negative regulation of shark NKA activity. Teleostean FXYD proteins (FXYD2, 5-9, 11, and 12) have been reported in certain teleosts such as the Tetraodon nigroviridis, Salmo salar, Danio rerio, and Oryzias dancena. Recent studies have demonstrated that several teleost FXYD isoforms are expressed in the gills and kidneys of the fish, and their expression levels are altered in response to salinity changes, suggesting that these FXYDs may regulate electrolyte homeostasis and body fluid of the fish. 30 matched cddid_all.tbl CDD cd20278 cd20278 380748 Minion Microprotein INducer of fusION (Minion). Microprotein INducer of fusION (Minion), also called protein myomixer or protein myomerger, is encoded by the MYMX gene. Along with Myomaker, it allows cells to fuse and form multinucleated fibers that are capable of contracting. A lack of Minion disables skeletal muscles, including the diaphragm, resulting in perinatal death in mice. This insight into the Minion-Myomaker system may one day be exploited for targeted drug delivery involving fusing cells in cancer or other contexts. The production of Minion peaks three to four days after injury, similar to the expression profile of Myomaker. 57 matched cddid_all.tbl CDD cd20279 cd20279 439135 adhesin_P110-like Mycoplasma genitalium adhesin P110 and similar proteins. P110 is a virulence factor essential for cytadherence in the human pathogen Mycoplasma genitalium, which binds eukaryotic cells by means of its transmembrane adhesion complex called the Nap. Nap consists of two heteromers, each consisting of proteins P110 and P140. The extracellular region of P110 binds to sialic acid receptors and interacts only with the neuraminic acid moiety of oligosaccharides. Structural and functional data suggests that Nap alternates between open and closed conformation to sustain a mechanism for motility and guarantee infectivity by attachment and release of M. genitalium to and from the host cell receptor. P110 and P140 are also immunodominant proteins and constitute the main target of host antibodies during infection. Thus, anti-adherence molecules, aimed at preventing the establishment of infection, are attractive potential antimicrobial drugs. This family also includes Mycoplasma pneumoniae Mgp-operon protein 3 (also called Mgp3 or ORF-3 protein). 873 matched cddid_all.tbl CDD cd20280 cd20280 411710 NotI-like Restriction endonuclease NotI and similar proteins. Restriction enzyme NotI is a type IIP restriction enzyme (the simplest being separate homodimeric endonucleases and methyltransferases that each recognize the same palindromic DNA target sequence) that recognize sites of 8 bp or longer in invasive DNA. NotI is commonly used for the introduction of radiolabeled landmarks in the restriction landmark genomic scanning (RLGS) method, which has become a common technique for the study of aberrant DNA methylation patterns in tumor- and tissue-specific cell lines. 357 matched cddid_all.tbl CDD cd20281 cd20281 380417 cupin_QDO_C quercetinase, C-terminal cupin domain. This family contains the C-terminal domain of quercetinase (also known as quercetin 2,3-dioxygenase, 2,3QD, QDO and YxaG; EC 1.13.11.24), a mononuclear copper-dependent dioxygenase that catalyzes the cleavage of the flavonol quercetin (5,7,3',4'-tetrahydroxyflavonol) heterocyclic ring to produce 2-protocatechuoyl-phloroglucinol carboxylic acid and carbon monoxide. This family includes Aspergillus japonicus quercetin 2,3-dioxygenase (QDO), a homodimer that shows oxygenase activity with Cu2+. The dioxygen binds to the metal ion of the Cu-QDO-quercetin complex, yielding a Cu2+-superoxo quercetin radical intermediate, which forms a Cu2+-alkylperoxo complex that evolves into an endoperoxide intermediate that decomposes to the product. Quercetinase is a bicupin with two tandem cupin beta-barrel domains, only the C-terminal domain is included in this alignment. The pirins, which also belong to the cupin domain family, have been shown to catalyze a reaction involving quercetin and may have a function similar to that of quercetinase. 114 matched cddid_all.tbl CDD cd20282 cd20282 380418 cupin_DddQ "dimethylsulfoniopropionate lyase DddQ, cupin domain. Dimethylsulfoniopropionate (DMSP) is produced worldwide in large amounts, mainly by marine phytoplankton and macroalgae. DMSP lyase catalyzes the cleavage of DMSP to generate the volatile dimethyl sulfide (DMS) and plays a major role in the biogeochemical cycling of sulfur. When released into the atmosphere from the oceans, DMS is oxidized, forming cloud condensation nuclei that may influence weather and climate. DMSP lyase belongs to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 103 matched cddid_all.tbl CDD cd20283 cd20283 380419 cupin_DddY "dimethylsulfoniopropionate lyase DddY, cupin domain. This family includes dimethylsulfoniopropionate (DMSP) lyase DddY, the only known periplasmic DMSP lyase that is present in certain proteobacteria. DddY cleaves dimethylsulfoniopropionate (DMSP), the organic osmolyte and antioxidant produced in marine environments, and yields acrylate and the climate-active gas dimethyl sulfide (DMS). The catabolism of DMSP by microbial organisms provides a major source of carbon and sulfur in the marine environment. Studies show that DddY binds a zinc ion as cofactor, and uses a key tyrosine as a general base to attack DMSP. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 294 matched cddid_all.tbl CDD cd20285 cd20285 380420 cupin_7S_11S_C "7S and 11S seed storage globulin, C-terminal cupin domain. This family contains the C-terminal cupin domains of 7S and 11S seed storage proteins. The 7S globulins include soybean allergen beta-conglycinin, peanut allergen conarachin (Ara h 1), walnut allergen Jug r 2, and lentil allergen Len c 1. Proteins in this family perform various functions, including a role in sucrose binding, desiccation, defense against microbes and oxidative stress. The 11S globulins include many common food allergens such as the peanut major allergen Ara h 3, almond allergen Pru du 6, pecan allergen Car i 4, hazelnut nut allergen Cor a 9, Brazil nut allergen Ber e 2, cashew allergen Ana o 2, pistachio allergen Pis v 2/5, and walnut allergen Jug n/r 4. These plant seed storage globulins have tandem cupin-like beta-barrel folds (referred to as a bicupin). Storage proteins are the cause of well-known allergic reactions to peanuts and cereals. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 109 matched cddid_all.tbl CDD cd20287 cd20287 380421 cupin_pirin-like_N "pirin-like, N-terminal cupin domain. This family contains the N-terminal cupin domain of pirin and pirin-like proteins, including Escherichia coli YhhW and YhaK. Pirin functions as both a transcriptional cofactor and an apoptosis-related protein in mammals and is involved in seed germination and seedling development in plants. Proteins in this family have two tandem cupin-like folds but the C-terminal cupin fold has diverged considerably and does not have a metal binding site. The exact functions of pirins are unknown but they have quercitinase activity in Escherichia coli and are thought to play important roles in transcription and apoptosis. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 81 matched cddid_all.tbl CDD cd20288 cd20288 380422 cupin_pirin-like_C "pirin-like, C-terminal cupin domain. This family contains the C-terminal cupin domain of pirin and pirin-like proteins, including Escherichia coli YhhW and YhaK. Pirin functions as both a transcriptional cofactor and an apoptosis-related protein in mammals and is involved in seed germination and seedling development in plants. Proteins in this family have two tandem cupin-like folds but the C-terminal cupin fold has diverged considerably and does not have a metal binding site. The exact functions of pirins are unknown but they have quercitinase activity in Escherichia coli and are thought to play important roles in transcription and apoptosis. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 70 matched cddid_all.tbl CDD cd20289 cd20289 380423 cupin_ADO "2-aminoethanethiol dioxygenase, cupin domain. This family contains 2-aminoethanethiol dioxygenase (also known as cysteamine dioxygenase, persulfurase or ADO; EC 1.13.11.19), which catalyzes the addition of two oxygen atoms to free cysteamine (2-aminoethanethiol) to form hypotaurine that subsequently oxidizes to taurine. These enzymes are found in prokaryotes as well as eukaryotes and belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 103 matched cddid_all.tbl CDD cd20290 cd20290 380424 cupin_Mj0764-like "uncharacterized Methanocaldococcus jannaschii Mj0764 and related proteins, cupin domain. This family includes archaeal and bacterial proteins homologous to MJ0764, a Methanocaldococcus jannaschii protein of unknown function. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 100 matched cddid_all.tbl CDD cd20291 cd20291 380425 cupin_CucA-like "soluble periplasm cuproprotein CucA and related proteins, cupin domain. This family includes bacterial proteins homologous to a soluble periplasm protein, CucA, found in the periplasm of the cyanobacterium Synechocystis where it shows some Cu2+-dependent quercetin dioxygenase activity. Studies show that a copper-trafficking pathway enables Cu2+ occupancy of CucA to accumulate in the periplasm, and this involves two copper transporters (CtaA and PacS) and a metallochaperone (Atx1). CucA belongs to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 201 matched cddid_all.tbl CDD cd20292 cd20292 380426 cupin_QdtA-like "sugar 3,4-ketoisomerase QdtA and related proteins, cupin domain. This family includes cupin domains of several bacterial proteins homologous to sugar 3,4-ketoisomerases. Thermoanaerobacterium thermosaccharolyticum QdtA catalyzes a key step in the biosynthesis of these sugars, the conversion of thymidine diphosphate (dTDP)-4-keto-6-deoxyglucose to dTDP-3-keto-6-deoxyglucose. In Aneurinibacillus thermoaerophilus, TDP-4-oxo-6-deoxy-alpha-D-glucose-3,4-oxoisomerase (also known as FdtA) is involved in the biosynthesis of dTDP-Fucp3NAc (3-acetamido-3,6-dideoxy-alpha-d-galactose), which is part of the repeating units of the glycan chain in the S-layer. Shewanella denitrificans bifunctional ketoisomerase/N-acetyltransferase (also known as FdtD) is involved in the third and fifth steps in the production of 3-acetamido-3,6-dideoxy-alpha-d-galactose or Fuc3NAc; the C-terminal cupin domain harbors the active site responsible for the isomerization reaction. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 117 matched cddid_all.tbl CDD cd20293 cd20293 380427 cupin_HutD_N "histidine utilization protein HutD and related proteins, N-terminal cupin domain. This model represents the N-terminal domain of a bicupin protein HutD, involved in histidine utilization (Hut) in Pseudomonas species. Although a metal binding site is not found in Pseudomonas fluorescens (PfluHutD), a binding pocket for ligands is located in the middle of the N-terminal cupin domain near the metal binding sites; N-formyl-l-glutamate (FG, a Hut pathway intermediate) has been identified as a potential ligand in vivo. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 92 matched cddid_all.tbl CDD cd20294 cd20294 380428 cupin_KduI_N "5-keto-4-deoxyuronate isomerase (KduI) and related proteins, N-terminal cupin domain. 5-keto-4-deoxyuronate isomerase (KduI; EC 5.3.1.17), also called 5-dehydro-4-deoxy-D-glucuronate isomerase or 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase, catalyzes the interconversion of 5-keto-4-deoxyuronate and 2,5-diketo-3-dexoygluconate in the breakdown of pectin. KduI is a bicupin; this model describes the N-terminal cupin domain. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 100 matched cddid_all.tbl CDD cd20295 cd20295 380429 cupin_Pac13-like "monomeric dehydratase Pac13 and related proteins, cupin domain. This family includes a small monomeric dehydratase Pac13 that mediates the formation of the 3'-deoxynucleotide of pacidamycins, which are uradyl peptide antibiotics (UPAs). Pac13 is involved in the formation of the unique 3'-deoxyuridine moiety found in these UPAs; it catalyzes the dehydration of uridine-5'-aldehyde. The similarity of the 3'-deoxy pacidamycin moiety with synthetic anti-retrovirals, offers a potential opportunity for the utilization of Pac13 in the biocatalytic generation of antiviral compounds. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 101 matched cddid_all.tbl CDD cd20296 cd20296 380430 cupin_PpnP-like "pyrimidine/purine nucleoside phosphorylase and related proteins, cupin domain. This family includes cupin domain proteins that are homologous to pyrimidine/purine nucleoside phosphorylase PpnP. Purine and pyrimidine nucleoside phosphorylases are key enzymes of the nucleoside salvage pathway; they catalyze the reversible phosphorolytic cleavage of the glycosidic bond of purine and pyrimidine nucleosides. Nucleoside phosphorylases are of medical interest since phosphorylases can be used in activating prodrugs; high-molecular mass purine nucleoside phosphorylases may be used in gene therapy of some solid tumors and their inhibitors could be selective immunosuppressive, anticancer, and antiparasitic agents. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 90 matched cddid_all.tbl CDD cd20297 cd20297 380431 cupin_HQDO_small "hydroquinol 1,2-dioxygenase (HQDO) small subunit, cupin domain. This model describes the small (or alpha) subunit of hydroquinone 1,2-dioxygenase (HQDO), which adopts a cupin domain fold. HQDO is a heterotetramer of two alpha and two beta subunits of 19kDa and 38kDa, respectively, and is a Fe(II) ring cleaving dioxygenase that is a key enzyme in the hydroquinone pathway of para-nitrophenol degradation, where it catalyzes the ring cleavage of hydroquinone to gamma-hydroxymuconic semialdehyde. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 160 matched cddid_all.tbl CDD cd20298 cd20298 380432 cupin_UAH "ureidoglycolate amidohydrolase (UAH) and related proteins, cupin domain. This family includes the cupin-fold protein, ureidoglycolate hydrolase (AllA; EC 3.5.3.19), which is involved in the breakdown of allantoin under aerobic conditions. Allantoin is the key intermediate of nitrogen fixation in bacteria, and its degradation occurs in several steps. AllA is involved in the third step of this pathway which consists of hydrolysis of (S)-ureidoglycolate to yield glyoxylate, ammonia, and CO2. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 92 matched cddid_all.tbl CDD cd20299 cd20299 380433 cupin_YP766765-like "Rhizobium leguminosarum YP_766765.1 and related proteins, cupin domain. This family includes mostly bacterial proteins homologous to Rhizobium leguminosarum YP_766765.1, a protein of unknown function. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 90 matched cddid_all.tbl CDD cd20300 cd20300 380434 cupin_npun_f5605-like_N "Nostoc punctiforme npun_f5605 and related proteins, N-terminal cupin domain. This family includes proteins homologous to Nostoc punctiforme putative dioxygenase npun_f5605, a protein of unknown function. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 99 matched cddid_all.tbl CDD cd20301 cd20301 380435 cupin_ChrR "anti-ECFsigma factor, ChrR , cupin domain. This family contains bacterial anti-sigma factor ChrR from the photosynthetic bacterium Rhodobacter sphaeroides (Rsp) and similar proteins. ChrR is a member of the ZAS (Zn2+ anti-sigma) subfamily of group IV anti-sigmas. It inhibits transcriptional activity by binding to the Rsp extra cytoplasmic function (ECF) sigma factor E (sigmaE), an essential factor to mount a transcriptional response to a singlet oxygen and for viability when carotenoids are limiting. ChrR comprises two structural and functional modules; the N-terminal anti-sigma domain (ASD) binds a Zn(2+) ion, contacts sigma(E), and is sufficient to inhibit sigma(E)-dependent transcription. The ChrR C-terminal domain adopts a cupin fold, can coordinate an additional Zn(2+), and is required for the transcriptional response to singlet oxygen, a potent oxidant that damages cellular biomolecules and can kill cells. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 161 matched cddid_all.tbl CDD cd20302 cd20302 380436 cupin_DAD "2,4'-Dihydroxyacetophenone dioxygenase (DAD), cupin domain. 2,4'-Dihydroxyacetophenone dioxygenase (DAD) catalyzes the oxidation of 2,4'-dihydroxyacetophenone to 4-hydroxybenzoate and formate as part of the 4-hydroxyacetophenone catabolic pathway. This enzyme is a homo-tetramer containing one iron per molecule of enzyme. This enzyme is an unusual dioxygenase in that it cleaves a C-C bond in a substituent of the aromatic ring rather than within the ring itself. As a bacterial dioxygenase, DAD plays an important environmental role in the aerobic catabolism of aromatic compounds; expression of this enzyme in appropriately engineered microorganisms has the potential to use these aromatic pollutants as a carbon source and thus remove them from the environment. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 123 matched cddid_all.tbl CDD cd20303 cd20303 380437 cupin_ChrR_1 "Marinobacter hydrocarbonoclasticus anti-ECFsigma factor ChrR, and similar proteins; 2 heterologous tandem repeats of cupin domain. This family contains bacterial anti-sigma factor such as ChrR from Marinobacter hydrocarbonoclasticus. Anti-sigma factor ChrR is a member of the ZAS (Zn2+ anti-sigma) subfamily of group IV anti-sigmas. It inhibits transcriptional activity by binding to the ECF sigma factor E (sigmaE), an essential factor to mount a transcriptional response to a singlet oxygen and for viability when carotenoids are limiting. This protein family likely contains two distinct homologous functional domains belonging to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 102 matched cddid_all.tbl CDD cd20304 cd20304 380438 cupin_OxDC_N "Oxalate decarboxylase (OxDC), N-terminal cupin domain. This model represents the N-terminal cupin domain of oxalate decarboxylase (OxDC; EC 4.1.1.2), a manganese-dependent bicupin that catalyzes the conversion of oxalate to formate and carbon dioxide, utilizing dioxygen as a cofactor. It is evolutionarily related to oxalate oxidase (OxOx or germin; EC 1.2.3.4) which, in contrast, converts oxalate and dioxygen to carbon dioxide and hydrogen peroxide. OxDC is classified as a bicupin because it contains two cupin folds with each domain containing one manganese binding site, with four manganese binding residues (three histidines and one glutamate) conserved as well as a number of hydrophobic residues. Members of this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 155 matched cddid_all.tbl CDD cd20305 cd20305 380439 cupin_OxDC_C "Oxalate decarboxylase (OxDC), C-terminal cupin domain. This model represents the C-terminal cupin domain of oxalate decarboxylase (OxDC; EC 4.1.1.2), a manganese-dependent bicupin that catalyzes the conversion of oxalate to formate and carbon dioxide, utilizing dioxygen as a cofactor. It is evolutionarily related to oxalate oxidase (OxOx or germin; EC 1.2.3.4) which, in contrast, converts oxalate and dioxygen to carbon dioxide and hydrogen peroxide. OxDC is classified as a bicupin because it contains two cupin folds with each domain containing one manganese binding site, with four manganese binding residues (three histidines and one glutamate) conserved as well as a number of hydrophobic residues. Members of this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 153 matched cddid_all.tbl CDD cd20306 cd20306 380440 cupin_OxDC-like Oxalate decarboxylase (OxDC)-like cupin domain. This subfamily contains bacterial and eukaryotic cupin domains of proteins homologous to oxalate decarboxylase (OxDC; EC 4.1.1.2) such as MSMEG_2254, a putative OxDC from Mycobacterium smegmatis. OxDC is a manganese-dependent bicupin that catalyzes the conversion of oxalate to formate and carbon dioxide, utilizing dioxygen as a cofactor. It is evolutionarily related to oxalate oxidase (OxOx or germin; EC 1.2.3.4) which, in contrast, converts oxalate and dioxygen to carbon dioxide and hydrogen peroxide. OxDC is classified as a bicupin because it contains two cupin folds with each domain containing one manganese binding site, with four manganese binding residues (three histidines and one glutamate) conserved as well as a number of hydrophobic residues. 151 matched cddid_all.tbl CDD cd20307 cd20307 380441 cupin_BacB_N "Bacillus subtilis bacilysin and related proteins, N-terminal cupin domain. This model represents the N-terminal domain of bacilysin (BacB, also known as AerE in Microcystis aeruginosa), a non-ribosomally synthesized dipeptide antibiotic that is produced and excreted by certain strains of Bacillus subtilis. Bacilysin is an oxidase that catalyzes the synthesis of 2-oxo-3-(4-oxocyclohexa-2,5-dienyl)propanoic acid, a precursor to L-anticapsin. Each bacilysin monomer has two tandem cupin domains. It is active against a wide range of bacteria and some fungi. The antimicrobial activity of bacilysin is antagonized by glucosamine and N-acetyl glucosamine, indicating that bacilysin interferes with glucosamine synthesis, and thus, with the synthesis of microbial cell walls. AerE is thought to be involved in the formation of the 2-carboxy-6-hydroxyoctahydroindole (Choi) moiety found on all aeruginosin tetrapeptides, based on gene knock-out experiments. It is encoded by the aerE gene of the aerABCDEF Aeruginosin biosynthesis gene cluster in Microcystis aeruginosa. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 100 matched cddid_all.tbl CDD cd20308 cd20308 380442 cupin_YdaE "D-lyxose isomerase YdaE, cupin domain. This family includes D-lyxose isomerase (D-LI; EC 5.3.1.15) homologous to YdaE from the sigma B regulon of Bacillus subtilis, a protein with an active site that is highly similar to the E. coli O157 z5688 D-lyxose isomerase. YdaE may have a synergistic role with ydaD, an NAD(P)-dependent alcohol dehydrogenase, in the adaptation to environment stresses; YdaD may be active against the ketose sugar produced by YdaE and function in providing resistance to oxidative stress through the production of reducing equivalents in the form of NAD(P)H. YdaE forms a cupin-type beta-barrel, with two alpha helices at the N-terminus. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 160 matched cddid_all.tbl CDD cd20309 cd20309 380443 cupin_EcSI "Escherichia coli sugar isomerase (EcSI), cupin domain. This family includes a sugar isomerase homologous to pathogenic Escherichia coli O157 z5688 D-lyxose isomerase (EcSI or Z5688) which has an active site highly similar to YdaE from the sigma B regulon of Bacillus subtilis. Extensive substrate screening has revealed that EcSI is capable of acting on D-lyxose and D-mannose. Studies show that overexpression of EcSI enables cell growth on D-lyxose as the sole carbon source. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 199 matched cddid_all.tbl CDD cd20310 cd20310 380444 cupin_L-RbI "L-ribose isomerase, cupin domain. L-ribose isomerase (RbI) catalyzes the reversible isomerization between L-ribose and L-ribulose, which are rare sugars and non-abundant in nature. RbI from Acinetobacter sp. DL-28 has been shown to have D-lyxose isomerase activity of about 47% compared to L-ribose. Cellulomonas parahominis MB426 RbI has a broad substrate specificity and can also catalyze the isomerization between D-lyxose and D-xylulose, D-talose and D-tagatose, L-allose and L-psicose, L-gulose and L-sorbose, and D-mannose and D-fructose. RbI adopts a cupin-type structure and belongs to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 235 matched cddid_all.tbl CDD cd20311 cd20311 380445 cupin_Yhhw_C "Escherichia coli YhhW and YhaK and related proteins, pirin-like bicupin, C-terminal cupin domain. This family includes the C-terminal domain of YhhW and YhaK, Escherichia coli pirin-like proteins with unknown function. YhhW is structurally similar not only to human pirin but also to quercitin 2,3-dioxygenase (quercitinase). Although the function of YhhW is not completely understood, YhhW and its human ortholog have quercitinase activity and are likely to play an important role in transcription and apoptosis. This C-terminal cupin-like domain has diverged considerably and has closer alignment with C-terminal pirin, while the N-terminal cupin domain of YhhW has a metal coordination site and is thought to have catalytic activity. YhaK is found in low abundance in the cytosol of E. coli and is strongly up-regulated by nitroso-glutathione (GSNO). There are major structural differences at the N-terminus of YhaK compared with YhhW; YhaK lacks the canonical cupin metal-binding residues of pirins and may be involved in chloride binding and/or sensing of oxidative stress in enterobacteria. YhaK showed no quercetinase and peroxidase activity; however, reduced YhaK was very sensitive to reactive oxygen species (ROS). Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold." 70 matched cddid_all.tbl CDD cd20313 cd20313 380745 DSRM_DND1 double-stranded RNA binding motif of dead end protein homolog 1 (DND1) and similar proteins. DND1 (also known as dead end protein, or RNA-binding motif single-stranded-interacting protein 4 (RBMS4)) is an RNA-binding protein that is required for the survival of primordial germ cells (PGCs) and suppresses the formation of germ-cell tumors. DND1 binds a UU(A/U) trinucleotide motif predominantly in the 3' untranslated regions of mRNA, and destabilizes target mRNAs. It also counteracts the function of several microRNAs (miRNAs), which are inhibitors of gene expression, by binding mRNAs and prohibiting miRNAs from associating with their target sites. DND1 contains two RNA recognition motifs (RRMs) and a C-terminal double-stranded RNA binding motif (DSRM) that is not sequence specific, but highly specific for dsRNAs of various origin and structure. 80 matched cddid_all.tbl CDD cd20314 cd20314 380746 DSRM_EIF2AK2 double-stranded RNA binding motif of eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2) and similar proteins. EIF2AK2 (EC 2.7.11.1/EC 2.7.10.2; also known as interferon-induced, double-stranded RNA-activated protein kinase, eIF-2A protein kinase 2, interferon-inducible RNA-dependent protein kinase, P1/eIF-2A protein kinase, protein kinase RNA-activated (PKR), protein kinase R, tyrosine-protein kinase EIF2AK2, or p68 kinase) acts as an IFN-induced dsRNA-dependent serine/threonine-protein kinase which plays a key role in the innate immune response to viral infection and is also involved in the regulation of signal transduction, apoptosis, cell proliferation and differentiation. EIF2AK2 proteins contain two to three double-stranded RNA binding motifs (DSRMs). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 68 matched cddid_all.tbl CDD cd20315 cd20315 380747 DSRM_mL44_subfamily double-stranded RNA binding motif of mL44 subfamily proteins. The mitochondrion-specific ribosomal protein mL44 subfamily is composed of mitochondrial 54S ribosomal protein L3 (MRPL3) and mitochondrial 39S ribosomal protein L44 (MRPL44). MRPL3 (also known as mitochondrial large ribosomal subunit protein mL44) is a component of the mitochondrial ribosome (mitoribosome), a dedicated translation machinery responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. MRPL44 (also called L44mt, MRP-L44, or mitochondrial large ribosomal subunit protein mL44) is a component of the 39S subunit of mitochondrial ribosome. It may play a role in the assembly/stability of nascent mitochondrial polypeptides exiting the ribosome. Members of this family contain a RNase III-like domain and a double-stranded RNA binding motif (DSRM). DSRM is not sequence specific, but highly specific for dsRNAs of various origin and structure. 71 matched cddid_all.tbl CDD cd20317 cd20317 410556 FXYD1 FXYD domain-containing ion transport regulator 1. FXYD domain-containing ion transport regulator 1 (FXYD1), also known as phospholemman (PLM), or sodium/potassium-transporting ATPase subunit FXYD1, associates with and regulates the activity of the sodium/potassium-transporting ATPase (NKA) which transports Na+ out of the cell and K+ into the cell. It is a plasma membrane substrate for several kinases, including protein kinase A, protein kinase C, NIMA kinase, and myotonic dystrophy kinase. It is thought to form an ion channel or regulate ion channel activity. Transcript variants with different 5' UTR sequences have been described in the literature. 64 matched cddid_all.tbl CDD cd20318 cd20318 410557 FXYD2 FXYD domain-containing ion transport regulator 2. FXYD domain-containing ion transport regulator 2 (FXYD2), also known as sodium/potassium-transporting ATPase subunit gamma, or Na(+)/K(+) ATPase subunit gamma, or sodium pump gamma chain, is the regulatory subunit of the sodium/potassium-transporting ATPase (Na,K-ATPase). Na+,K+-ATPase is a heteromeric complex consisting of a large alpha-subunit, which is responsible for ATP hydrolysis, ion transport, and CTS binding, and a beta-subunit, acting as a chaperone. Although the Na,K-ATPase does not depend on the gamma subunit to be functional, it is thought that the gamma subunit modulates the enzyme's activity by inducing ion channel activity. Mutations in this gene have been associated with renal hypomagnesaemia. 43 matched cddid_all.tbl CDD cd20322 cd20322 410558 FXYD4 FXYD domain-containing ion transport regulator 4. FXYD domain-containing ion transport regulator 4 (FXYD4), also known as CHIF (channel-inducing factor or corticosteroid hormone-induced factor), evokes K+ conductance in oocytes and is localized in the distal parts of the nephron and in the colon. CHIF, a putative K channel regulator, is regulated by aldosterone in the colon and by K+ intake in the kidney. 48 matched cddid_all.tbl CDD cd20323 cd20323 410559 FXYD_FXYD5 FXYD domain of FXYD domain-containing ion transport regulator 5. FXYD domain-containing ion transport regulator 5 (FXYD5) is also called dysadherin in humans or related to ion channel (RIC) in mice. Two transcript variants have been found for this gene, and they are both predicted to encode the same protein. Dysadherin is the gamma subunit the human Na,K-ATPase and is the only member that has a large extracellular sequence of 140 amino acids. Dysadherin has been observed to be over-expressed on the surface of cells that have down regulated levels of surface E-cadherin. CCL2 (bone homing cytokine) is a protein that is highly affected by silencing dysadherin expression. Dysadherin interferes with cell adhesion via beta1 subunit interactions and is a target for an extracellular antibody drug conjugate where the antibody to dysadherin is attached to a cardiac glycoside. FXYD5 expression in mouse is mainly in the kidney, intestine, spleen, and lung. Confocal immunofluorescence microscopy of mouse kidney detected FXYD5 on basolateral membranes of connecting tubules, collecting tubules, intercalated cells of collecting duct, and on apical membranes in long thin limb of Henle loop. 48 matched cddid_all.tbl CDD cd20324 cd20324 410560 FXYD6 FXYD domain-containing ion transport regulator 6. FXYD domain-containing ion transport regulator 6 (FXYD6 encodes the protein phosphohippolin and is located at the 11q23.3. It can be found in all human tissues except blood. FXYD6 in humans is primarily in the brain, with highest levels of expression found in the prefrontal cortex, amygdala, hypothalamus, and occipital lobe. FXYD6 is up-regulated in hepatocellular carcinoma (HCC) and it enhances the migration and proliferation of HCC cells. Therapy targeting FXYD6 could potentially benefit the clinical treatment toward HCC patients. FXYD6 is also associated with mental diseases. Mutations in the FXYD6 gene, or in sequences close to this gene, can predispose to schizophrenia which is known to be strongly heritable. FXYD6 was also found to be significantly downregulated in a Tg2576 mouse model of Alzheimer's disease (AD) brain and hippocampus. FXYD6 is a novel regulator of Na,K-ATPase expressed in the inner ear. 66 matched cddid_all.tbl CDD cd20325 cd20325 410561 FXYD7 FXYD domain-containing ion transport regulator 7. FXYD domain-containing ion transport regulator 7 (FXYD7) has a potential splice variant with an additional 3 residues. In rats, expression of FXYD7 was restricted to the brain, with highest levels in the cerebrum, followed by brainstem, and hippocampus, and relatively weak expression in the hypothalamus. Immunofluorescence microscopy demonstrated colocalization with synaptophysin and modest colocalization with glial fibrillary acidic protein, indicating predominant expression in neurons and lower expression in astroglial cells. The FXYD7 gene maps to chromosome 19. 51 matched cddid_all.tbl CDD cd20327 cd20327 410562 FXYD8 FXYD domain-containing ion transport regulator 8. FXYD domain-containing ion transport regulator 8 (FXYD8), also known as FXYD domain containing ion transport regulator 6 pseudogene 3 (FXYD6P3), is a member of the FXYD protein family that is involved in the modulation of NKA activity in the kidneys. The human FXYD8 gene is located on the X chromosome. However, the gene is located on chromosome 9 in the mouse and chromosome 8 in the rat. 93 matched cddid_all.tbl CDD cd20328 cd20328 410563 FXYD3-like FXYD domain-containing ion transport regulator 3 and similar proteins. This subfamily includes FXYD domain-containing ion transport regulator 3 (FXYD3), FXYD9, and FXYD10, also called PLMS/Phospholemman-like protein. FXYD3, also known as mammary tumor 8 kDa protein (MAT-8), or chloride conductance inducer protein Mat-8, or phospholemman-like (PLML), may function as a chloride channel or as a chloride channel regulator. It associates with and regulates the activity of the sodium/potassium-transporting ATPase (NKA) which transports Na+ out of the cell and K+ into the cell. Two transcript variants encode two different isoforms of the protein; in addition, transcripts utilizing alternative polyA signals have been described in the literature. Members here include mammalians and reptiles. FXYD9 is present in teleosts including: Danio rerio, Atlantic salmon, and Japanese Medaka fish. In general, the FXYD9 isoform has the highest degree of conservation among the examined teleost species, indicating that it may be involved in physiological processes that are not evolving within this group of vertebrates. FXYD10, present in shark, associates with and modifies the activity of Na,K-ATPase in vitro through interactions mediated by its transmembrane and cytoplasmic C-terminal domains. It is important in the phosphorylation and potassium deocclusion reactions, which are known to be controlled by A domain movements. It is thought that FXYD10 interacts with the A domain of the shark Na,K-ATPase alpha-subunit. 51 matched cddid_all.tbl CDD cd20329 cd20329 410564 FXYD11 FXYD domain-containing ion transport regulator 11. FXYD domain-containing ion transport regulator 11 (FXYD11) is a putative regulatory subunit of the Na(+)/K(+)-ATPase (NKA) pump. FXYD11 is expressed predominantly in the gills of euryhaline teleosts, such as the spotted scat, Scatophagus argus. It regulates NKA activity through protein-protein interactions. The regulation of NKA and FXYD11 is of critical importance for osmotic homeostasis. The expression and activity of NKA, as well as FXYD11 mRNA expression in gills have been shown to respond to different environmental salinity by dual-labeling immunohistochemistry and quantitative PCR (RT-qPCR) methods, indicating that there is an interaction between NKA and FXYD. 64 matched cddid_all.tbl CDD cd20330 cd20330 410565 FXYD12 FXYD domain-containing ion transport regulator 12. The FXYD domain-containing ion transport regulator 12 (FXYD12) mRNA is mainly distributed in kidneys and intestines of fish. In co-immunoprecipitation experiments, FXYD12 was shown to associate with the Na(+)/(K+)-ATPase (NKA) alpha-subunit in the intestines of two closely related medakas, Oryzias dancena and O. latipes. These results suggests that FXYD12 may play a role in modulating NKA activity in the intestines following salinity changes in the maintenance of internal homeostasis. 53 matched cddid_all.tbl CDD cd20331 cd20331 380677 JBP-like oxygenase domain of uncharacterized bacterial and phage proteins similar to kinetoplastid J-binding protein (JBP) 1 and JBP2. J binding protein (JBP) 1 and JBP2 catalyze the first step of base J biosynthesis: the hydroxylation of thymine in DNA to form 5-hydroxymethyluracil (hmU). Base J (beta-d-glucopyranosyloxymethyluracil) is a hyper-modified DNA base found in the DNA of kinetoplastids (Trypanosoma brucei, Trypanosoma cruzi, and Leishmania). JBP1 and JBP2 each contain a J-DNA binding domain and this oxygenase domain. They belong to the TET/JBP family of dioxygenases that require Fe2+ and alpha-ketoglutarate (also known as 2-oxoglutarate) for activity. 270 matched cddid_all.tbl CDD cd20332 cd20332 380678 JBP J-binding protein. J binding protein (JBP) 1 and JBP2 catalyze the first step of base J biosynthesis: the hydroxylation of thymine in DNA to form 5-hydroxymethyluracil (hmU). Base J (beta-d-glucopyranosyloxymethyluracil) is a hyper-modified DNA base found in the DNA of kinetoplastids (Trypanosoma brucei, Trypanosoma cruzi, and Leishmania). JBP1 and JBP2 each contain a J-DNA binding domain and this oxygenase domain. They belong to the TET/JBP family of dioxygenases that require Fe2+ and alpha-ketoglutarate (also known as 2-oxoglutarate) for activity. 250 matched cddid_all.tbl CDD cd20334 cd20334 380474 Cas13b Class 2 type VI-B CRISPR-associated RNA-guided ribonuclease Cas13b. CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins) adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. These systems are divided into two classes; class 1 systems utilize multiple Cas proteins and CRISPR RNA (crRNA) to form an effector complex while class 2 systems employ a large, single effector with crRNA to mediate interference. Class 2 type VI CRISPR-Cas13 systems use a single enzyme to target RNA using a programmable crRNA guide and are divided into four subtypes based on the identity of the Cas13 protein (Cas13a-d). The Cas13 proteins are capable of both pre-crRNA processing and target RNA cleavage, which protect the host from phage attacks. Once bound to a target RNA, their non-specific RNase activity is activated. Cas13b has many distinctive features compared to the other Cas13 proteins, including the lack of significant sequence similarity, disparate crRNA repeat region, and double-sided protospacer flanking sequence (PFS)-dependent target RNA cleavage. 759 matched cddid_all.tbl CDD cd20335 cd20335 438996 BRcat_RBR BRcat (benign-catalytic) domain, part of the RBR (RING1-BRcat-Rcat) domain. The RBR family of RING-type E3 ligases are characterized by containing an RBR domain, which was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. It is composed of an extended RING domain (RING1) followed by an in-between RING (IBR) domain and the catalytic domain, which is structurally an IBR domain but is commonly designated as RING2. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently, where the IBR and RING2 domains have been renamed as BRcat and Rcat domains, respectively. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. The BRcat domain adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. The model corresponds to the BRcat domain. 53 matched cddid_all.tbl CDD cd20336 cd20336 438997 Rcat_RBR Rcat (required-for-catalysis) domain, part of the RBR (RING1-BRcat-Rcat) domain. The RBR family of RING-type E3 ligases are characterized by containing an RBR domain, which was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. It is composed of an extended RING domain (RING1) followed by an in-between RING (IBR) domain and the catalytic domain, which is structurally an IBR domain but is commonly designated RING2. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently, where the IBR and RING2 domains have been renamed as BRcat and Rcat domains, respectively. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. The Rcat domain contains the catalytic cysteine residue and ubiquitination activity. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. This model corresponds to the Rcat domain that adopts the same fold as the BRcat domain. 38 matched cddid_all.tbl CDD cd20337 cd20337 438998 BRcat_RBR_HOIP BRcat domain found in HOIL-1-interacting protein (HOIP) and similar proteins. HOIP, also called RING finger protein 31 (RNF31) or zinc in-between-RING-finger ubiquitin-associated domain protein, together with HOIL-1 and SHARPIN, forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis. It also interacts with the atypical mammalian orphan receptor DAX-1, trigger DAX-1 ubiquitination and stabilization, and participate in repressing steroidogenic gene expression. HOIP contains three Npl4 zinc fingers, a central ubiquitin-associated (UBA) domain responsible for interaction with the N-terminal ubiquitin-like domain (UBL) of HOIL-1L, an RBR domain, and a C-terminal linear chain determining domain (LDD). The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of HOIP and similar proteins that adopt the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. 78 matched cddid_all.tbl CDD cd20338 cd20338 438999 BRcat_RBR_RNF19 BRcat domain found in the RING finger protein 19 (RNF19) subfamily. This subfamily includes RING finger protein RNF19A and RNF19B, both of which are transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligases. RNF19A, also called double ring-finger protein (Dorfin), or p38, localizes to the ubiquitylated inclusions in Parkinson's disease (PD), dementia with Lewy bodies (LBs), multiple system atrophy, and amyotrophic lateral sclerosis (ALS). It interacts with Psmc3, a protein component of the 19S regulatory cap of the 26S proteasome, and further participates in the ubiquitin-proteasome system in acrosome biogenesis, spermatid head shaping, and development of the head-tail coupling apparatus and tail. It modulates the ubiquitination and degradation of Calcium-sensing receptor (CaR), which may contribute to a general mechanism for CaR quality control during biosynthesis. Moreover, RNF19A can also ubiquitylate mutant superoxide dismutase 1 (SOD1), the causative gene of familial ALS. It may associate with the endoplasmic reticulum-associated degradation (ERAD) pathway, which is related to the pathogenesis of neurodegenerative disorders, such as PD or Alzheimer's disease. It is also involved in the pathogenic process of PD and LB formation by ubiquitylation of synphilin-1. RNF19B, also called IBR domain-containing protein 3 or natural killer (NK) lytic-associated molecule (NKLAM), plays a role in controlling tumor dissemination and metastasis. It is involved in the cytolytic function of NK cells and cytotoxic T lymphocytes (CTLs). It interacts with ubiquitin conjugates UbcH7 and UbcH8, and ubiquitinates uridine kinase like-1 (URKL-1) protein, targeting it for degradation. Moreover, RNF19B is a novel component of macrophage phagosomes and plays a role in macrophage anti-bacterial activity. It functions as a novel modulator of macrophage inducible nitric oxide synthase (iNOS) expression. Both RNF19A and RNF19B contain an RBR domain followed by three TMs. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of the RNF19 subfamily that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. 75 matched cddid_all.tbl CDD cd20339 cd20339 439000 BRcat_RBR_RNF216 BRcat domain found in RING finger protein 216 (RNF216). RNF216, also called Triad domain-containing protein 3 (Triad3A), ubiquitin-conjugating enzyme 7-interacting protein 1, or zinc finger protein inhibiting NF-kappa-B (ZIN), is an RBR-type E3 ubiquitin-protein ligase that interacts with several components of the Toll-like receptor (TLR) signaling pathway and promotes their proteolytic degradation. It negatively regulates the RIG-I RNA sensing pathway through Lys48-linked, ubiquitin-mediated degradation of the tumor necrosis factor (TNF) receptor-associated factor 3 (TRAF3) adapter following RNA virus infection. It also controls ubiquitination and proteasomal degradation of receptor-interacting protein 1 (RIP1), a serine/threonine protein kinase that is critically involved in TNF receptor-1-induced NF-kappa B activation, following disruption of Hsp90 binding. Moreover, RNF216 is involved in inflammatory diseases by strongly inhibiting autophagy in macrophages. It interacts with and ubiquitinates BECN1, a key regulator in autophagy, thereby contributing to BECN1 degradation. It regulates synaptic strength by ubiquitination of Arc, resulting in its rapid proteasomal degradation. It is also a key negative regulator of sustained 2DL4/KIR2DL4 (killer cell Ig-like receptor with two Ig-like domains and a long cytoplasmic domain 4)-mediated NF-kappaB signaling from internalized 2DL4, which functions by promoting ubiquitylation and degradation of endocytosed receptor from early endosomes. Furthermore, RNF216 interacts with human immunodeficiency virus type 1 (HIV-1) virion infectivity factor (Vif) protein, which is essential for the productive infection of primary human CD4 T lymphocytes and macrophages. Mutations in RNF216 may result in Gordon Holmes syndrome, a condition defined by hypogonadotropic hypogonadism and cerebellar ataxia, as well as in autosomal recessive Huntington-like disorder. RNF216 contains an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of RNF216 that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. 54 matched cddid_all.tbl CDD cd20340 cd20340 439001 BRcat_RBR_parkin BRcat domain found in parkin and similar proteins. Parkin, also called Parkinson juvenile disease protein 2, is an RBR-type E3 ubiquitin-protein ligase that is associated with recessive early onset Parkinson's disease (PD), and exerts a protective effect against dopamine-induced alpha-synuclein-dependent cell toxicity. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Parkin functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, RHOT1/MIRO1, MFN1, MFN2, STUB1, SNCAIP, SEPT5, TOMM20, USP30, ZNF746 and AIMP2. It mediates monoubiquitination as well as Lys6-, Lys11-, Lys48- and Lys63-linked polyubiquitination of substrates depending on the context. Parkin may enhance cell viability and protects dopaminergic neurons from oxidative stress-mediated death by regulating mitochondrial function. It also limits the production of reactive oxygen species (ROS), and regulates cyclin-E during neuronal apoptosis. Moreover, parkin displays a ubiquitin ligase-independent function in transcriptional repression of p53. Parkin contains an N-terminal ubiquitin-like domain and a C-terminal RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of parkin that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. 77 matched cddid_all.tbl CDD cd20341 cd20341 439002 BRcat_RBR_RNF14 BRcat domain found in RING finger protein 14 (RNF14). RNF14, also called androgen receptor (AR)-associated protein 54 (ARA54), HFB30, or Triad2 protein, is an RBR-type E3 ubiquitin-protein ligase that is highly expressed in the testis and interacts with class III E2s (UBE2E2, UbcH6, and UBE2E3). Its differential localization may play an important role in testicular development and spermatogenesis in humans. RNF14 functions as a transcriptional regulator of mitochondrial and immune function in muscles. It is a ligand-dependent AR co-activator that enhances AR-dependent transcriptional activation. It may also participate in enhancing cell cycle progression and cell proliferation via induction of cyclin D1. Moreover, RNF14 is crucial for colon cancer cell survival. It acts as a new enhancer of the Wnt-dependent transcriptional outputs that acts at the level of the T-cell factor/lymphoid enhancer factor (TCF/LEF)-beta-catenin complex. RNF14 contains an N-terminal RWD domain, and a C-terminal RBR domain. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of RNF14 that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. 57 matched cddid_all.tbl CDD cd20342 cd20342 439003 BRcat_RBR_RNF217 BRcat domain found in RING finger protein 217 (RNF217). RNF217, also termed IBR domain-containing protein 1 (IBRDC1), is a transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligase mainly expressed in testis and skeletal muscle with different splice variants. It interacts with the anti-apoptotic protein HAX1, and is adjacent to a translocation breakpoint involving ETV6 in childhood acute lymphoblastic leukemia (ALL). RNF217 contains a RBR domain followed by TMs. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR (RING1-BRcat-Rcat) domain use an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase function to facilitate the ubiquitination reaction. The family corresponds to the BRcat (benign-catalytic) domain that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. 74 matched cddid_all.tbl CDD cd20343 cd20343 439004 BRcat_RBR_HHARI-like BRcat domain found in human homolog of Drosophila Ariadne (HHARI) and similar proteins. This subfamily includes Drosophila melanogaster protein ariadne-1 (ARI-1), and its eukaryotic homologs, such as HHARI. ARI-1 is a widely expressed Drosophila RING-finger protein that localizes mainly in the cytoplasm, and is required for neural development. It interacts with the ubiquitin-conjugating enzyme, UbcD10. HHARI is also called H7-AP2, monocyte protein 6 (MOP-6), protein ariadne-1 homolog, Ariadne RBR E3 ubiquitin protein ligase 1 (ARIH1), ariadne-1 (ARI-1), UbcH7-binding protein, UbcM4-interacting protein, or ubiquitin-conjugating enzyme E2-binding protein 1. It is an RBR-type E3 ubiquitin-protein ligase highly expressed in nuclei, where it is co-localized with nuclear bodies including Cajal, PML, and Lewy bodies. It interacts with the E2 conjugating enzymes UbcH7, UbcH8, UbcM4, and UbcD10 in human, mouse and fly, and modulates the ubiquitylation of substrate proteins including single-minded 2 (SIM2) and translation initiation factor 4E homologous protein (4EHP). It functions as a potent mediator of DNA damage-induced translation arrest, which protects stem and cancer cells against genotoxic stress by initiating a 4EHP-mediated mRNA translation arrest. HHARI contains an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of HHARI and similar proteins that adopt the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. 82 matched cddid_all.tbl CDD cd20344 cd20344 439005 BRcat_RBR_TRIAD1 BRcat domain found in two RING fingers and DRIL [double RING finger linked] 1 (TRIAD1). TRIAD1, also called ariadne-2 (ARI-2), protein ariadne-2 homolog, Ariadne RBR E3 ubiquitin protein ligase 2 (ARIH2), or UbcM4-interacting protein 48, is an RBR-type E3 ubiquitin-protein ligase that catalyzes the formation of polyubiquitin chains linked via lysine-48 as well as lysine-63 residues. Its auto-ubiquitylation can be catalyzed by the E2 conjugating enzyme UBCH7. TRIAD1 has been implicated in hematopoiesis, specifically in myelopoiesis, as well as in embryogenesis. It functions as a regulator of endosomal transport, and is required for the proper function of multivesicular bodies. It also acts as a novel ubiquitination target for proteasome-dependent degradation by murine double minute 2 (MDM2). As a proapoptotic protein, TRIAD1 promotes p53 activation, and inhibits MDM2-mediated p53 ubiquitination and degradation. Furthermore, TRIAD1 can inhibit the ubiquitination and proteasomal degradation of growth factor independence 1 (Gfi1), a transcriptional repressor essential for the function and development of many different hematopoietic lineages. TRIAD1 contains an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of TRIAD1 that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. 72 matched cddid_all.tbl CDD cd20345 cd20345 439006 BRcat_RBR_HOIL1 BRcat domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins. HOIL-1 is also called RBCK1, HOIL-1L, RanBP-type and C3HC4-type zinc finger-containing protein 1, HBV-associated factor 4, Hepatitis B virus X-associated protein 4, RING finger protein 54 (RNF54), ubiquitin-conjugating enzyme 7-interacting protein 3, or UbcM4-interacting protein 28 (UIP28). Together with E3 ubiquitin-protein ligase RNF31 (also known as HOIP) and SHANK-associated RH domain interacting protein (SHARPIN), it forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis through conjugation of linear polyubiquitin chains to NF-kappaB essential modulator (also known as NEMO or IKBKG). HOIL-1 plays a crucial role in TNF-alpha-mediated NF-kappaB activation. It also functions as an ubiquitin-protein ligase E3 that interacts with not only PKCbeta but also PKCzeta. It can recognize heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. HOIL-1 contains an N-terminal ubiqutin-like (UBL) domain and an Npl4 zinc-finger (NZF) domain, which regulate the interaction with the LUBAC subunit RNF31 and ubiquitin, respectively. The NZF domain belongs to RanBP2-type zinc finger (zf-RanBP2) domain superfamily. In addition, HOIL-1 has an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of HOIL1 that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. 65 matched cddid_all.tbl CDD cd20346 cd20346 439007 BRcat_RBR_ANKIB1 BRcat domain found in ankyrin repeat and IBR domain-containing protein 1 (ANKIB1) and similar proteins. ANKIB1 is an RBR-type E3 ubiquitin-protein ligase that may function as part of the E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates. It contains N-terminal ankyrin repeats, and an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of ANKIB1 that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. 68 matched cddid_all.tbl CDD cd20347 cd20347 439008 BRcat_RBR_CUL9 BRcat domain found in cullin-9 (CUL-9) and similar proteins. CUL-9, also called UbcH7-associated protein 1 (H7-AP1), p53-associated parkin-like cytoplasmic protein, or PARC, is a cytoplasmic RBR-type E3 ubiquitin-protein ligase that functions as a tumor suppressor and promotes p53-dependent apoptosis. It mediates the ubiquitination and degradation of cytosolic cytochrome c to promote survival in neurons and cancer cells. It is also a critical downstream effector of the 3M complex in the maintenance of microtubules and genome integrity. Moreover, CUL-9, together with CUL-7, forms homodimers and heterodimers, as well as some atypical cullin RING ligase complexes, which may exhibit ubiquitin ligase activity. CUL-9 contains a CPH domain (conserved in Cul7, PARC, and HERC2 proteins), a DOC (DOC1/APC10) domain, cullin homology domains linked with E3 ligase function, and a C-terminal RBR domain previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of CUL-9 that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. 74 matched cddid_all.tbl CDD cd20348 cd20348 439009 BRcat_RBR_EMI BRcat domain found in early mitotic inhibitor (EMI) subfamily of F-box proteins. The EMI subfamily includes FBXO5 (EMI1) and FBXO43 (EMI2), which are anaphase-promoting-complex/cyclosome (APC/C) inhibitors that bind APC/C-CCD20 (Cell division cycle protein 20) and/or APC/C-CDH1 (CDC20 homolog 1) complexes. FBXO5, also called FBX5, or early mitotic inhibitor 1 (EMI1), acts as a regulator that inhibits the anaphase-promoting complex/cyclosome (APC/C), which controls cell cycle progression through the sequential degradation of various substrates from S phase to early mitosis. During the mitotic cell cycle, it plays a role as both substrate and inhibitor of the APC-FZR1 complex. During G1 phase, it plays a role as substrate of the APC-FZR1 complex E3 ligase. FBXO43, also called FBX43, or endogenous meiotic inhibitor 2 (EMI2), plays a key role during the meiotic cell cycle. It is required to establish and maintain the arrest of oocytes at the second meiotic metaphase until fertilization. It probably acts by inhibiting the APC/C ubiquitin ligase. It may recognize and bind to some phosphorylated proteins and promote their ubiquitination and degradation. Both FBXO5 and FBXO43 contain an F-box domain, and the first half of the RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of the EMI subfamily that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. 51 matched cddid_all.tbl CDD cd20349 cd20349 439010 BRcat_RBR_RNF144 BRcat domain found in the RNF144 protein subfamily. The RNF144 subfamily includes RNF144A and RNF144B, which are transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligases. RNF144A, also called UbcM4-interacting protein 4 (UIP4), or ubiquitin-conjugating enzyme 7-interacting protein 4, targets DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and thus promotes DNA damage-induced cell apoptosis. It is transcriptionally repressed by metastasis-associated protein 1 (MTA1) and inhibits MTA1-driven cancer cell migration and invasion. RNF144B, also called PIR2, IBR domain-containing protein 2 (IBRDC2), or p53-inducible RING finger protein (p53RFP), induces p53-dependent but caspase-independent apoptosis. It interacts with E2 ubiquitin-conjugating enzymes UbcH7 and UbcH8, but not with UbcH5. It is involved in ubiquitination and degradation of p21, a p53 downstream protein promoting growth arrest and antagonizing apoptosis, suggesting a role in switching a cell from p53-mediated growth arrest to apoptosis. Moreover, RNF144B regulates the levels of Bax, a pro-apoptotic protein from the Bcl-2 family, and protects cells from unprompted Bax activation and cell death. It also regulates epithelial homeostasis by mediating degradation of p21WAF1 and p63. Both RNF144A and RNF144B contain an RBR domain followed by a potential single-TM domain. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of the RNF144 protein subfamily that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. 64 matched cddid_all.tbl CDD cd20350 cd20350 439011 Rcat_RBR_RNF217 Rcat domain found in RING finger protein 217 (RNF217). RNF217, also called IBR domain-containing protein 1 (IBRDC1), is a transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligase, with different splice variants, that is mainly expressed in testis and skeletal muscle. It interacts with the anti-apoptotic protein HAX1, and is adjacent to a translocation breakpoint involving ETV6 in childhood acute lymphoblastic leukemia (ALL). RNF217 contains an RBR domain followed by TMs. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the Rcat domain of RNF217 that is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain. 68 matched cddid_all.tbl CDD cd20351 cd20351 439012 Rcat_RBR_HOIP Rcat domain found in HOIL-1-interacting protein (HOIP) and similar proteins. HOIP, also called RING finger protein 31 (RNF31) or zinc in-between-RING-finger ubiquitin-associated domain protein, together with HOIL-1 and SHARPIN, forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis. It also interacts with the atypical mammalian orphan receptor DAX-1, trigger DAX-1 ubiquitination and stabilization, and participate in repressing steroidogenic gene expression. HOIP contains three Npl4 zinc fingers, a central ubiquitin-associated (UBA) domain responsible for the interaction with the N-terminal ubiquitin-like domain (UBL) of HOIL-1L, an RBR domain, and a C-terminal linear chain determining domain (LDD). The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the Rcat domain of HOIP that is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain. 85 matched cddid_all.tbl CDD cd20352 cd20352 439013 Rcat_RBR_RNF144 Rcat domain found in the RNF144 protein subfamily. The RNF144 subfamily includes RNF144A and RNF144B, which are transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligases. RNF144A, also called UbcM4-interacting protein 4 (UIP4), or ubiquitin-conjugating enzyme 7-interacting protein 4, targets DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and thus promotes DNA damage-induced cell apoptosis. It is transcriptionally repressed by metastasis-associated protein 1 (MTA1) and inhibits MTA1-driven cancer cell migration and invasion. RNF144B, also called PIR2, IBR domain-containing protein 2 (IBRDC2), or p53-inducible RING finger protein (p53RFP), induces p53-dependent but caspase-independent apoptosis. It interacts with E2 ubiquitin-conjugating enzymes UbcH7 and UbcH8, but not with UbcH5. It is involved in ubiquitination and degradation of p21, a p53 downstream protein promoting growth arrest and antagonizing apoptosis, suggesting a role in switching a cell from p53-mediated growth arrest to apoptosis. Moreover, RNF144B regulates the levels of Bax, a pro-apoptotic protein from the Bcl-2 family, and protects cells from unprompted Bax activation and cell death. It also regulates epithelial homeostasis by mediating degradation of p21WAF1 and p63. Both RNF144A and RNF144B contain an RBR domain followed by a potential single-TM domain. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the Rcat domain of the RNF144 protein subfamily that is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain. 70 matched cddid_all.tbl CDD cd20353 cd20353 439014 Rcat_RBR_RNF216 Rcat domain found in RING finger protein 216 (RNF216). RNF216, also called Triad domain-containing protein 3 (Triad3A), ubiquitin-conjugating enzyme 7-interacting protein 1, or zinc finger protein inhibiting NF-kappa-B (ZIN), is an RBR-type E3 ubiquitin-protein ligase that interacts with several components of the Toll-like receptor (TLR) signaling and promotes their proteolytic degradation. It negatively regulates the RIG-I RNA sensing pathway through Lys48-linked, ubiquitin-mediated degradation of the tumor necrosis factor receptor-associated factor 3 (TRAF3) adapter following RNA virus infection. It also controls ubiquitination and proteasomal degradation of receptor-interacting protein 1 (RIP1), a serine/threonine protein kinase that is critically involved in tumor necrosis factor receptor-1 (TNF-R1)-induced NF-kappa B activation, following disruption of Hsp90 binding. Moreover, RNF216 is involved in inflammatory diseases by strongly inhibiting autophagy in macrophages. It interacts with and ubiquitinates BECN1, a key regulator in autophagy, thereby contributing to BECN1 degradation. It regulates synaptic strength by ubiquitination of Arc, resulting in its rapid proteasomal degradation. It is also a key negative regulator of sustained 2DL4/KIR2DL4 (killer cell Ig-like receptor with two Ig-like domains and a long cytoplasmic domain 4)-mediated NF-kappaB signaling from internalized 2DL4, which functions by promoting ubiquitylation and degradation of endocytosed receptor from early endosomes. Furthermore, RNF216 interacts with human immunodeficiency virus type 1 (HIV-1) virion infectivity factor (Vif) protein, which is essential for the productive infection of primary human CD4 T lymphocytes and macrophages. Mutations in RNF216 may result in Gordon Holmes syndrome, a condition defined by hypogonadotropic hypogonadism and cerebellar ataxia, as well as in autosomal recessive Huntington-like disorder. RNF216 contains an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. The family corresponds to the Rcat domain of RNF216 that is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain. 57 matched cddid_all.tbl CDD cd20354 cd20354 439015 Rcat_RBR_RNF14 Rcat domain found in RING finger protein 14 (RNF14). RNF14, also called androgen receptor (AR)-associated protein 54 (ARA54), HFB30, or Triad2 protein, is an RBR-type E3 ubiquitin-protein ligase that is highly expressed in the testis and interacts with class III E2s (UBE2E2, UbcH6, and UBE2E3). Its differential localization may play an important role in testicular development and spermatogenesis in humans. RNF14 functions as a transcriptional regulator of mitochondrial and immune function in muscles. It is a ligand-dependent AR co-activator that enhances AR-dependent transcriptional activation. It also may participate in enhancing cell cycle progression and cell proliferation via induction of cyclin D1. Moreover, RNF14 is crucial for colon cancer cell survival. It acts as a new enhancer of the Wnt-dependent transcriptional outputs that acts at the level of the T-cell factor/lymphoid enhancer factor (TCF/LEF)-beta-catenin complex. RNF14 contains an N-terminal RWD domain, and a C-terminal RBR domain. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the Rcat domain of RNF14 that is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain. 68 matched cddid_all.tbl CDD cd20355 cd20355 439016 Rcat_RBR_RNF19 Rcat domain found in the RING finger protein 19 (RNF19) subfamily. This subfamily includes RING finger protein RNF19A and RNF19B, which are transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligases. RNF19A, also called double ring-finger protein (Dorfin) or p38, localizes to the ubiquitylated inclusions in Parkinson's disease (PD), dementia with Lewy bodies (LBs), multiple system atrophy, and amyotrophic lateral sclerosis (ALS). It interacts with Psmc3, a protein component of the 19S regulatory cap of the 26S proteasome, and further participates in the ubiquitin-proteasome system in acrosome biogenesis, spermatid head shaping, and development of the head-tail coupling apparatus and tail. It modulates the ubiquitination and degradation of calcium-sensing receptor (CaR), which may contribute to a general mechanism for CaR quality control during biosynthesis. Moreover, RNF19A can also ubiquitylate mutant superoxide dismutase 1 (SOD1), the causative gene of familial ALS. It may associate with the endoplasmic reticulum-associated degradation (ERAD) pathway, which is related to the pathogenesis of neurodegenerative disorders, such as PD or Alzheimer's disease. It is also involved in the pathogenic process of PD and LB formation by ubiquitylation of synphilin-1. RNF19B, also called IBR domain-containing protein 3, or natural killer (NK) lytic-associated molecule (NKLAM), plays a role in controlling tumor dissemination and metastasis. It is involved in the cytolytic function of NK cells and cytotoxic T lymphocytes (CTLs). It interacts with ubiquitin conjugates UbcH7 and UbcH8, and ubiquitinates uridine kinase like-1 protein, targeting it for degradation. RNF19B is a novel component of macrophage phagosomes and plays a role in macrophage anti-bacterial activity. It functions as a novel modulator of macrophage inducible nitric oxide synthase (iNOS) expression. Both RNF19A and RNF19B contain an RBR domain followed by three TMs. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the Rcat domain of the RNF19 subfamily that is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain. 69 matched cddid_all.tbl CDD cd20356 cd20356 439017 Rcat_RBR_HHARI-like Rcat domain found in human homolog of Drosophila Ariadne (HHARI) and similar proteins. This subfamily includes Drosophila melanogaster protein ariadne-1 (ARI-1), and its eukaryotic homologs, such as HHARI. ARI-1 is a widely expressed Drosophila RING-finger protein that localizes mainly in the cytoplasm, and is required for neural development. It interacts with the ubiquitin-conjugating enzyme, UbcD10. HHARI is also called H7-AP2, monocyte protein 6 (MOP-6), protein ariadne-1 homolog, Ariadne RBR E3 ubiquitin protein ligase 1 (ARIH1), ariadne-1 (ARI-1), UbcH7-binding protein, UbcM4-interacting protein, or ubiquitin-conjugating enzyme E2-binding protein. It is an RBR-type E3 ubiquitin-protein ligase highly expressed in nuclei, where it is co-localized with nuclear bodies including Cajal, PML, and Lewy bodies. It interacts with the E2 conjugating enzymes UbcH7, UbcH8, UbcM4 and UbcD10 in human, mouse and fly, and modulates the ubiquitylation of substrate proteins including single-minded 2 (SIM2) and translation initiation factor 4E homologous protein (4EHP). It functions as a potent mediator of DNA damage-induced translation arrest, which protects stem and cancer cells against genotoxic stress by initiating a 4EHP-mediated mRNA translation arrest. HHARI contains an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the Rcat domain of HHARI and similar proteins that are essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain. 58 matched cddid_all.tbl CDD cd20357 cd20357 439018 Rcat_RBR_parkin Rcat domain found in parkin and similar proteins. Parkin, also called Parkinson juvenile disease protein 2, is an RBR-type E3 ubiquitin-protein ligase that is associated with recessive early onset Parkinson's disease (PD), and exerts a protective effect against dopamine-induced alpha-synuclein-dependent cell toxicity. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Parkin functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins, such as BCL2, SYT11, CCNE1, GPR37, RHOT1/MIRO1, MFN1, MFN2, STUB1, SNCAIP, SEPT5, TOMM20, USP30, ZNF746, and AIMP2. It mediates monoubiquitination as well as Lys6-, Lys11-, Lys48- and Lys63-linked polyubiquitination of substrates depending on the context. Parkin may enhance cell viability and protects dopaminergic neurons from oxidative stress-mediated death by regulating mitochondrial function. It also limits the production of reactive oxygen species (ROS), and regulates cyclin-E during neuronal apoptosis. Moreover, parkin displays a ubiquitin ligase-independent function in transcriptional repression of p53. Parkin contains an N-terminal ubiquitin-like domain and a C-terminal RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the Rcat domain of parkin that is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain. 55 matched cddid_all.tbl CDD cd20358 cd20358 439019 Rcat_RBR_HOIL1 Rcat domain found in heme-oxidized IRP2 ubiquitin ligase 1 (HOIL-1) and similar proteins. HOIL-1 is also called RBCK1, HOIL-1L, RanBP-type and C3HC4-type zinc finger-containing protein 1, HBV-associated factor 4, Hepatitis B virus X-associated protein 4, RING finger protein 54 (RNF54), ubiquitin-conjugating enzyme 7-interacting protein 3, or UbcM4-interacting protein 28 (UIP28). Together with the E3 ubiquitin-protein ligase RNF31 (also known as HOIP) and SHANK-associated RH domain interacting protein (SHARPIN), it forms the E3-ligase complex (also known as linear-ubiquitin-chain assembly complex LUBAC) that regulates NF-kappaB activity and apoptosis through conjugation of linear polyubiquitin chains to NF-kappaB essential modulator (also known as NEMO or IKBKG). HOIL-1 plays a crucial role in TNF-alpha-mediated NF-kappaB activation. It also functions as an ubiquitin-protein ligase E3 that interacts with not only PKCbeta but also PKCzeta. It can recognize heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. HOIL-1 contains an N-terminal ubiqutin-like (UBL) domain and an Npl4 zinc-finger (NZF) domain, which regulate the interaction with the LUBAC subunit RNF31 and ubiquitin, respectively. The NZF domain belongs to RanBP2-type zinc finger (zf-RanBP2) domain superfamily. In addition, HOIL-1 has an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the Rcat domain of HOIL1 that is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain. 73 matched cddid_all.tbl CDD cd20359 cd20359 439020 Rcat_RBR_CUL9 Rcat domain found in cullin-9 (CUL-9) and similar proteins. CUL-9, also called UbcH7-associated protein 1 (H7-AP1), p53-associated parkin-like cytoplasmic protein, or PARC, is a cytoplasmic RBR-type E3 ubiquitin-protein ligase that function as a tumor suppressor and promotes p53-dependent apoptosis. It mediates the ubiquitination and degradation of cytosolic cytochrome c to promote survival in neurons and cancer cells. It is also a critical downstream effector of the 3M complex in the maintenance of microtubules and genome integrity. Moreover, CUL-9, together with CUL-7, forms homodimers and heterodimers, as well as some atypical cullin RING ligase complexes, which may exhibit ubiquitin ligase activity. CUL-9 contains a CPH domain (conserved in Cul7, PARC, and HERC2 proteins), a DOC (DOC1/APC10) domain, cullin homology domains linked with E3 ligase function, and a C-terminal RBR domain previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the Rcat domain of CUL-9 that is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain. 58 matched cddid_all.tbl CDD cd20360 cd20360 439021 Rcat_RBR_TRIAD1 Rcat domain found in two RING fingers and DRIL [double RING finger linked] 1 (TRIAD1). TRIAD1, also called ariadne-2 (ARI-2), protein ariadne-2 homolog, Ariadne RBR E3 ubiquitin protein ligase 2 (ARIH2), or UbcM4-interacting protein 48, is an RBR-type E3 ubiquitin-protein ligase that catalyzes the formation of polyubiquitin chains linked via lysine-48 as well as lysine-63 residues. Its auto-ubiquitylation can be catalyzed by the E2 conjugating enzyme UBCH7. TRIAD1 has been implicated in hematopoiesis, specifically in myelopoiesis, as well as in embryogenesis. It functions as a regulator of endosomal transport, and is required for the proper function of multivesicular bodies. It also acts as a novel ubiquitination target for proteasome-dependent degradation by murine double minute 2 (MDM2). As a proapoptotic protein, TRIAD1 promotes p53 activation, and inhibits MDM2-mediated p53 ubiquitination and degradation. Furthermore, TRIAD1 can inhibit the ubiquitination and proteasomal degradation of growth factor independence 1 (Gfi1), a transcriptional repressor essential for the function and development of many different hematopoietic lineages. TRIAD1 contains an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the Rcat domain of TRIAD1 that is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain. 56 matched cddid_all.tbl CDD cd20361 cd20361 439022 Rcat_RBR_ANKIB1 Rcat domain found in ankyrin repeat and IBR domain-containing protein 1 (ANKIB1) and similar proteins. ANKIB1 is an RBR-type E3 ubiquitin-protein ligase that may function as part of an E3 complex, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfers it to substrates. It contains N-terminal ankyrin repeats, and an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the Rcat domain of ANKIB1 that is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain. 62 matched cddid_all.tbl CDD cd20362 cd20362 439023 BRcat_RBR_RNF19A BRcat domain found in RING finger protein 19A (RNF19A). RNF19A, also called double ring-finger protein (Dorfin) or p38, is a transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligase that localizes to the ubiquitylated inclusions in Parkinson's disease (PD), dementia with Lewy bodies (LBs), multiple system atrophy, and amyotrophic lateral sclerosis (ALS). It interacts with Psmc3, a protein component of the 19S regulatory cap of the 26S proteasome, and further participates in the ubiquitin-proteasome system in acrosome biogenesis, spermatid head shaping, and development of the head-tail coupling apparatus and tail. It modulates the ubiquitination and degradation of Calcium-sensing receptor (CaR), which may contribute to a general mechanism for CaR quality control during biosynthesis. Moreover, RNF19A can also ubiquitylate mutant superoxide dismutase 1 (SOD1), the causative gene of familial ALS. It may associate with the endoplasmic reticulum-associated degradation (ERAD) pathway, which is related to the pathogenesis of neurodegenerative disorders, such as PD or Alzheimer's disease. It is also involved in the pathogenic process of PD and LB formation by ubiquitylation of synphilin-1. RNF19A contains an RBR domain followed by three TMs. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of RNF19A that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. 83 matched cddid_all.tbl CDD cd20363 cd20363 439024 BRcat-RBR_RNF19B BRcat domain found in RING finger protein 19B (RNF19B). RNF19B, also called IBR domain-containing protein 3 or natural killer (NK) lytic-associated molecule (NKLAM), is a transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligase that plays a role in controlling tumor dissemination and metastasis. It is involved in the cytolytic function of NK cells and cytotoxic T lymphocytes (CTLs). It interacts with ubiquitin conjugates UbcH7 and UbcH8, and ubiquitinates uridine kinase like-1 (URKL-1) protein, targeting it for degradation. Moreover, RNF19B is a novel component of macrophage phagosomes and plays a role in macrophage anti-bacterial activity. It functions as a novel modulator of macrophage inducible nitric oxide synthase (iNOS) expression. RNF19B contains an RBR domain followed by three TMs. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of RNF19B that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. 75 matched cddid_all.tbl CDD cd20364 cd20364 439025 BRcat_RBR_FBXO5 BRcat domain found in F-box only protein 5 (FBXO5). FBXO5, also called FBX5 or early mitotic inhibitor 1 (EMI1), acts as a regulator that inhibits the anaphase-promoting complex/cyclosome (APC/C), which controls cell cycle progression through the sequential degradation of various substrates from S phase to early mitosis. During mitotic cell cycle, it plays a role as both substrate and inhibitor of the APC-FZR1 complex. During G1 phase, it plays a role as substrate of the APC-FZR1 complex E3 ligase. FBXO5 contains an F-box domain, and the first half of the RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of FBXO5 that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. 57 matched cddid_all.tbl CDD cd20365 cd20365 439026 BRcat_RBR_FBXO43 BRcat domain found in F-box only protein 43 (FBXO43). FBXO43, also called FBX43 or endogenous meiotic inhibitor 2 (EMI2), plays a key role during the meiotic cell cycle. It is required to establish and maintain the arrest of oocytes at the second meiotic metaphase until fertilization. It probably acts by inhibiting the anaphase-promoting complex/cyclosome (APC/C) ubiquitin ligase. It may recognize and bind to some phosphorylated proteins and promotes their ubiquitination and degradation. FBXO43 contains an F-box domain, and the first half of the RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat (benign-catalytic) domain that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. 51 matched cddid_all.tbl CDD cd20366 cd20366 439027 BRcat_RBR_RNF144A BRcat domain found in RING finger protein 144A (RNF144A). RNF144A, also called UbcM4-interacting protein 4 (UIP4) or ubiquitin-conjugating enzyme 7-interacting protein 4, is a transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligase that targets DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and thus promotes DNA damage-induced cell apoptosis. It is transcriptionally repressed by metastasis-associated protein 1 (MTA1) and inhibits MTA1-driven cancer cell migration and invasion. RNF144A contains an RBR domain followed by a potential single-TM domain. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of RNF144A that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. 65 matched cddid_all.tbl CDD cd20367 cd20367 439028 BRcat_RBR_RNF144B BRcat domain found in RING finger protein 144B (RNF144B). RNF144B, also called PIR2, IBR domain-containing protein 2 (IBRDC2), or p53-inducible RING finger protein (p53RFP), is a transmembrane (TM) domain-containing RBR E3 ubiquitin-protein ligase that induces p53-dependent but caspase-independent apoptosis. It interacts with E2 ubiquitin-conjugating enzymes UbcH7 and UbcH8, but not with UbcH5. It is involved in ubiquitination and degradation of p21, a p53 downstream protein promoting growth arrest and antagonizing apoptosis, suggesting a role in switching a cell from p53-mediated growth arrest to apoptosis. Moreover, RNF144B regulates the levels of Bax, a pro-apoptotic protein from the Bcl-2 family, and protects cells from unprompted Bax activation and cell death. It also regulates epithelial homeostasis by mediating degradation of p21WAF1 and p63. RNF144B contains an RBR domain followed by a potential single-TM domain. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the BRcat domain of RNF144B that adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. 64 matched cddid_all.tbl CDD cd20368 cd20368 439029 Rcat_RBR_RNF144A Rcat domain found in RING finger protein 144A (RNF144A). RNF144A, also called UbcM4-interacting protein 4 (UIP4), or ubiquitin-conjugating enzyme 7-interacting protein 4, is a transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligase that targets DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and thus promotes DNA damage-induced cell apoptosis. It is transcriptionally repressed by metastasis-associated protein 1 (MTA1) and inhibits MTA1-driven cancer cell migration and invasion. RNF144A contains an RBR domain followed by a potential single-TM domain. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the Rcat domain of RNF144A that is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain. 76 matched cddid_all.tbl CDD cd20369 cd20369 439030 Rcat_RBR_RNF144B Rcat domain found in RING finger protein 144B (RNF144B). RNF144B, also called PIR2, IBR domain-containing protein 2 (IBRDC2), or p53-inducible RING finger protein (p53RFP), is a transmembrane (TM) domain-containing RBR E3 ubiquitin-protein ligase that induces p53-dependent but caspase-independent apoptosis. It interacts with E2 ubiquitin-conjugating enzymes UbcH7 and UbcH8, but not with UbcH5. It is involved in ubiquitination and degradation of p21, a p53 downstream protein promoting growth arrest and antagonizing apoptosis, suggesting a role in switching a cell from p53-mediated growth arrest to apoptosis. Moreover, RNF144B regulates the levels of Bax, a pro-apoptotic protein from the Bcl-2 family, and protects cells from unprompted Bax activation and cell death. It also regulates epithelial homeostasis by mediating degradation of p21WAF1 and p63. RNF144B contains an RBR domain followed by a potential single-TM domain. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the Rcat domain of RNF144B that is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain. 71 matched cddid_all.tbl CDD cd20370 cd20370 439031 Rcat_RBR_RNF19A Rcat domain found in RING finger protein 19A (RNF19A). RNF19A, also called double ring-finger protein (Dorfin), or p38, is a transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligase that localizes to the ubiquitylated inclusions in Parkinson's disease (PD), dementia with Lewy bodies (LBs), multiple system atrophy, and amyotrophic lateral sclerosis (ALS). It interacts with Psmc3, a protein component of the 19S regulatory cap of the 26S proteasome, and further participates in the ubiquitin-proteasome system in acrosome biogenesis, spermatid head shaping, and development of the head-tail coupling apparatus and tail. It modulates the ubiquitination and degradation of calcium-sensing receptor (CaR), which may contribute to a general mechanism for CaR quality control during biosynthesis. Moreover, RNF19A can also ubiquitylate mutant superoxide dismutase 1 (SOD1), the causative gene of familial ALS. It may associate with endoplasmic reticulum-associated degradation (ERAD) pathway, which is related to the pathogenesis of neurodegenerative disorders, such as PD or Alzheimer's disease. It is also involved in the pathogenic process of PD and LB formation by ubiquitylation of synphilin-1. RNF19A contains an RBR domain followed by three TMs. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the Rcat domain of RNF19A that is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain. 74 matched cddid_all.tbl CDD cd20371 cd20371 439032 Rcat_RBR_RNF19B Rcat domain found in RING finger protein 19B (RNF19B). RNF19B, also called IBR domain-containing protein 3, or natural killer (NK) lytic-associated molecule (NKLAM), is a transmembrane (TM) domain-containing RBR-type E3 ubiquitin-protein ligase that plays a role in controlling tumor dissemination and metastasis. It is involved in the cytolytic function of NK cells and cytotoxic T lymphocytes (CTLs). It interacts with ubiquitin conjugates UbcH7 and UbcH8, and ubiquitinates uridine kinase like-1 protein, targeting it for degradation. Moreover, RNF19B is a novel component of macrophage phagosomes and plays a role in macrophage anti-bacterial activity. It functions as a novel modulator of macrophage inducible nitric oxide synthase (iNOS) expression. RNF19B contains an RBR domain followed by three TMs. The RBR domain was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the Rcat domain of RNF19B that is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain. 70 matched cddid_all.tbl CDD cd20374 cd20374 380669 Pot1C Protection Of Telomeres Protein 1 (POT1) C-terminal region. POT1 is part of shelterin, a hexameric nucleoprotein complex (comprising TRF1, TRF2, TIN2, RAP1, POT1 and TPP1 in humans) that protects telomeres, the physical ends of chromosomes. Shelterin protects against these ends being recognized as double-stranded DNA breaks, as well as against degradation of the telomeric overhang by endonucleases. It also helps control access of telomerase to the telomeric overhang, thereby affecting telomore length. This C-terminal region has an OB-fold domain and a holiday junction resolvase (HJR) domain which make dimer contacts with TPP1. 286 matched cddid_all.tbl CDD cd20378 cd20378 380668 PBP1_SBP-like periplasmic substrate-binding domain of active transport proteins. Periplasmic substrate-binding domain of active transport proteins found in bacteria and Archaea. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids. 357 matched cddid_all.tbl CDD cd20379 cd20379 410450 Tudor_dTUD-like Tudor domain found in Drosophila melanogaster maternal protein Tudor (dTUD) and similar proteins. dTUD is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation. It contains 11 Tudor domains. The family also includes mitochondrial A-kinase anchor protein 1 (AKAP1) and Tudor domain-containing proteins (TDRDs). AKAP1, also called A-kinase anchor protein 149 kDa (AKAP 149), or dual specificity A-kinase-anchoring protein 1 (D-AKAP-1), or protein kinase A-anchoring protein 1 (PRKA1), or Spermatid A-kinase anchor protein 84 (S-AKAP84), is found in mitochondria and in the endoplasmic reticulum-nuclear envelope where it anchors protein kinases, phosphatases, and a phosphodiesterase. It regulates multiple cellular processes governing mitochondrial homeostasis and cell viability. AKAP1 binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane. TDRDs have diverse biological functions and may contain one or more copies of the Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 50 matched cddid_all.tbl CDD cd20380 cd20380 410451 Tudor_TDRD13-like Tudor domain found in Tudor domain-containing protein 13 (TDRD13) and similar proteins. The TDRD13 family includes TDRD13 and OTU domain-containing protein 4 (OTUD4). TDRD13, also called asparagine-linked glycosylation 13 (ALG13), glycosyltransferase 28 domain-containing protein 1 (GLT28D1), or UDP-N-acetylglucosamine transferase subunit ALG13, is a putative bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase (EC 2.4.1.141/EC 3.4.19.12). It is a potential member of the Alg7p/Alg13p/Alg14p complex catalyzing the first two initial reactions in the N-glycosylation process. OTUD4, also called HIV-1-induced protein HIN-1, is a phospho-activated K63 deubiquitinase that hydrolyzes the isopeptide bond between the ubiquitin C-terminus and the lysine epsilon-amino group of the target protein. It may negatively regulate inflammatory and pathogen recognition signaling in innate immune response. Members of this family contain one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 54 matched cddid_all.tbl CDD cd20381 cd20381 410452 Tudor_LBR Tudor domain found in Lamin-B receptor (LBR) and similar proteins. LBR, also called integral nuclear envelope inner membrane (INM) protein or LMN2R, is a nuclear envelope protein that anchors the lamina and the heterochromatin to the inner nuclear membrane, in cellular senescence induced by excess thymidine. It is also important for cholesterol biosynthesis. LBR can interact with chromodomain proteins and DNA. It contains one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 51 matched cddid_all.tbl CDD cd20382 cd20382 410453 Tudor_SETDB1_rpt1 first Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins. SETDB1, also called ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E), acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. It contains two Tudor domains. This model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 82 matched cddid_all.tbl CDD cd20383 cd20383 410454 Tudor_53BP1 Tudor domain found in tumor suppressor TP53-binding protein 1 (53BP1) and similar proteins. 53BP1, also called p53-binding protein 1 (p53BP1), is a double-strand break (DSB) repair protein involved in response to DNA damage, telomere dynamics, and class-switch recombination (CSR) during antibody genesis. It plays a key role in the repair of DSBs in response to DNA damage by promoting non-homologous end joining (NHEJ)-mediated repair of DSBs and specifically counteracting the function of the homologous recombination (HR) repair protein BRCA1. It is recruited to DSB sites by recognizing and binding histone H2A monoubiquitinated at 'Lys-15' (H2AK15Ub) and histone H4 dimethylated at 'Lys-20' (H4K20me2), two histone marks that are present at DSB sites. 53BP1 contains one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 52 matched cddid_all.tbl CDD cd20384 cd20384 410455 Tudor_ZGPAT Tudor domain found in zinc finger CCCH-type with G patch domain-containing protein (ZGPAT) and similar proteins. ZGPAT, also called ZIP, G patch domain-containing protein 6 (GPATC6), GPATCH6, zinc finger CCCH domain-containing protein 9 (ZC3HDC9), ZC3H9, or zinc finger and G patch domain-containing protein, is a transcription repressor that specifically binds the 5'-GGAG[GA]A[GA]A-3' consensus sequence. It represses transcription by recruiting the chromatin multiprotein complex NuRD to target promoters. It contains one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 55 matched cddid_all.tbl CDD cd20385 cd20385 410456 Tudor_PCL Tudor domain found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins. The PCL family includes PHD finger protein1 (PHF1) and its homologs, metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are accessory components of the Polycomb repressive complex 2 (PRC2) core complex. Members contain an N-terminal Tudor domain followed by two PHD domains, and a C-terminal MTF2 domain. PCL proteins specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD domain-containing proteins, the first PHD domains of PCL proteins do not display histone H3K4 binding affinity and they do not affect the binding of the Tudor domain to histones. 54 matched cddid_all.tbl CDD cd20386 cd20386 410457 Tudor_PHF20-like Tudor domain found in PHD finger protein 20 (PHF20), PHF20-like protein 1 (PHF20L1), and similar proteins. PHF20, also called Glioma-expressed antigen 2, hepatocellular carcinoma-associated antigen 58, novel zinc finger protein, or transcription factor TZP (referring to Tudor and zinc finger domain containing protein), is a regulator of NF-kappaB activation by disrupting recruitment of PP2A to p65. It also functions as a transcription factor that binds to Akt and plays a role in Akt cell survival/growth signaling. Moreover, it transcriptionally regulates p53. The phosphorylation of PHF20 on Ser291 mediated by protein kinase B (PKB) is essential in tumorigenesis via the regulation of p53-mediated signaling. PHF20L1 is an active malignant brain tumor (MBT) domain-containing protein that binds to monomethylated lysine 142 on DNA (cytosine-5) Methyltransferase 1 (DNMT1) (DNMT1K142me1) and colocalizes at the perinucleolar space in a SET7-dependent manner. Both PHF20 and PHF20L1 contain an N-terminal malignant brain tumor (MBT) domain, a Tudor domain, a plant homeodomain (PHD) finger and putative DNA-binding domains AT hook and C2H2-type zinc finger. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 50 matched cddid_all.tbl CDD cd20387 cd20387 410458 Tudor_UHRF_rpt1 first Tudor domain found in the UHRF (ubiquitin-like PHD and RING finger domain-containing protein) family. The UHRF family includes UHRF1 and UHRF2. UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain(PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger. The model corresponds to the first Tudor domain. The tandem Tudor domain directs binding of UHRF to the heterochromatin mark histone H3K9me3. 73 matched cddid_all.tbl CDD cd20388 cd20388 410459 Tudor_UHRF_rpt2 second Tudor domain found in the UHRF (ubiquitin-like PHD and RING finger domain-containing protein) family. The UHRF family includes UHRF1 and UHRF2. UHRF1 is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF2 was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. Moreover, UHRF2 functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Both UHRF1 and UHRF2 contain an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain(PHD) finger, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger. The model corresponds to the second Tudor domain. The tandem Tudor domain directs binding of UHRF to the heterochromatin mark histone H3K9me3. 72 matched cddid_all.tbl CDD cd20389 cd20389 410460 Tudor_ARID4_rpt1 first Tudor domain found in AT-rich interactive domain-containing protein ARID4 family. The family contains ARID4A and its paralog ARID4B, both of which are retinoblastoma (RB)-binding proteins that function as coactivators to enhance the androgen receptor (AR) and RB transcriptional activity, and play important roles in the AR and RB pathways to control male fertility. They also act as the leukemia and tumor suppressors involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. Moreover, they associate with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through their interaction with each other, as well as with the breast cancer associated tumor suppressor ING1 and the breast cancer metastasis suppressor BRMS1. Both ARID4A and ARID4B contain tandem Tudor domains, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 53 matched cddid_all.tbl CDD cd20390 cd20390 410461 Tudor_ARID4_rpt2 second Tudor domain found in AT-rich interactive domain-containing protein ARID4 family. The family contains ARID4A and its paralog ARID4B, both of which are retinoblastoma (RB)-binding proteins that function as coactivators to enhance the androgen receptor (AR) and RB transcriptional activity, and play important roles in the AR and RB pathways to control male fertility. They also act as the leukemia and tumor suppressors involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. Moreover, they associate with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through their interaction with each other, as well as with the breast cancer associated tumor suppressor ING1 and the breast cancer metastasis suppressor BRMS1. Both ARID4A and ARID4B contain tandem Tudor domains, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The model corresponds to the second Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 53 matched cddid_all.tbl CDD cd20391 cd20391 410462 Tudor_JMJD2_rpt1 first Tudor domain found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases. JMJD2 proteins, also called lysine-specific demethylase 4 histone demethylases (KDM4), have been implicated in various cellular processes including DNA damage response, transcription, cell cycle regulation, cellular differentiation, senescence, and carcinogenesis. They selectively catalyze the demethylation of di- and trimethylated H3K9 and H3K36. This model contains only three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. JMJD2D is not included in this model, since it lacks both the PHD and Tudor domains and has a different substrate specificity. JMJD2A-C are required for efficient cancer cell growth. 53 matched cddid_all.tbl CDD cd20392 cd20392 410463 Tudor_JMJD2_rpt2 second Tudor domain found in Jumonji domain-containing protein 2 (JMJD2) family of histone demethylases. JMJD2 proteins, also called lysine-specific demethylase 4 histone demethylases (KDM4), have been implicated in various cellular processes including DNA damage response, transcription, cell cycle regulation, cellular differentiation, senescence, and carcinogenesis. They selectively catalyze the demethylation of di- and trimethylated H3K9 and H3K36. This model contains only three JMJD2 proteins, JMJD2A-C, which all contain jmjN and jmjC domains in the N-terminal region, followed by a canonical PHD domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the second Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. JMJD2D is not included in this model, since it lacks both the PHD and Tudor domains and has a different substrate specificity. JMJD2A-C are required for efficient cancer cell growth. 56 matched cddid_all.tbl CDD cd20393 cd20393 410464 Tudor_SGF29_rpt1 first Tudor domain found in SAGA-associated factor 29 (SGF29) and similar proteins. SGF29, also called coiled-coil domain-containing protein 101, or SAGA complex-associated factor 29, is a chromatin reader component of some histone acetyltransferase (HAT) SAGA-type complexes, like the TFTC-HAT, ATAC or STAGA complexes. It specifically recognizes and binds methylated 'Lys-4' of histone H3 (H3K4me), with a preference for the trimethylated form (H3K4me3). SGF29 contains two Tudor domains. The model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 67 matched cddid_all.tbl CDD cd20394 cd20394 410465 Tudor_SGF29_rpt2 second Tudor domain found in SAGA-associated factor 29 (SGF29) and similar proteins. SGF29, also called coiled-coil domain-containing protein 101, or SAGA complex-associated factor 29, is a chromatin reader component of some histone acetyltransferase (HAT) SAGA-type complexes, like the TFTC-HAT, ATAC or STAGA complexes. It specifically recognizes and binds methylated 'Lys-4' of histone H3 (H3K4me), with a preference for trimethylated form (H3K4me3). SGF29 contains two Tudor domains. The model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 60 matched cddid_all.tbl CDD cd20395 cd20395 410466 Tudor_SpCrb2-like_rpt1 first Tudor domain found in Schizosaccharomyces pombe Cut5-repeat binding protein 2 (Crb2) and similar proteins. Crb2, also called RAD9 protein homolog, or checkpoint mediator protein crb2, is a DNA repair protein essential for cell cycle arrest at the G1 and G2 stages following DNA damage by X-, and UV-irradiation, or inactivation of DNA ligase. Crb2 contains two Tudor domains. The model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 50 matched cddid_all.tbl CDD cd20396 cd20396 410467 Tudor_SpCrb2-like_rpt2 second Tudor domain found in Schizosaccharomyces pombe Cut5-repeat binding protein 2 (Crb2) and similar proteins. Crb2, also called RAD9 protein homolog, or checkpoint mediator protein crb2, is a DNA repair protein essential for cell cycle arrest at the G1 and G2 stages following DNA damage by X-, and UV-irradiation, or inactivation of DNA ligase. Crb2 contains two Tudor domains. The model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 73 matched cddid_all.tbl CDD cd20397 cd20397 410468 Tudor_BAHCC1-like Tudor domain found in the BAH and coiled-coil domain-containing protein 1 (BAHCC1) family. The family of BAHCC1 includes BAHCC1 and trinucleotide repeat-containing gene 18 protein (TNRC18). BAHCC1 may function as a transcriptional regulator. The biological function of TNRC18 remains unclear. Members of this family contain one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 67 matched cddid_all.tbl CDD cd20398 cd20398 410469 Tudor_SMN Tudor domain found in survival motor neuron protein (SMN) and similar proteins. SMN, also called component of gems 1, or Gemin-1, is part of a multimeric SMN complex that includes spliceosomal Sm core proteins and plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Mutations in human SMN lead to motor neuron degeneration and spinal muscular atrophy. SMN contains a central, highly conserved Tudor domain that is required for U snRNP assembly and Sm protein binding and has been shown to bind arginine-glycine-rich motifs in an methylarginine-dependent manner. 56 matched cddid_all.tbl CDD cd20399 cd20399 410470 Tudor_SPF30 Tudor domain found in survival of motor neuron-related-splicing factor 30 (SPF30) and similar proteins. SPF30, also called 30 kDa splicing factor SMNrp, SMN-related protein, or survival motor neuron domain-containing protein 1 (SMNDC1), is an essential pre-mRNA splicing factor required for assembly of the U4/U5/U6 tri-small nuclear ribonucleoprotein into the spliceosome. Overexpression of SPF30 causes apoptosis. It contains one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 55 matched cddid_all.tbl CDD cd20400 cd20400 410471 Tudor_ERCC6L2 Tudor domain found in DNA excision repair protein ERCC-6-like 2 (ERCC6L2) and similar proteins. ERCC6L2, also called DNA repair and recombination protein RAD26-like (RAD26L), may be involved in early DNA damage response. It regulates RNA Pol II-mediated transcription via its interaction with DNA-dependent protein kinase (DNA-PK) to resolve R loops and minimize transcription-associated genome instability. ERCC6L2 gene mutations have been associated with bone marrow failure that includes developmental delay and microcephaly. It contains an N-terminal Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 59 matched cddid_all.tbl CDD cd20401 cd20401 410472 Tudor_AtPTM-like Tudor domain found in Arabidopsis thaliana DDT domain-containing protein PTM (AtPTM), Dirigent protein 17 (AtDIR17), and similar proteins. This family includes AtPTM and AtDIR17. AtPTM, also called DDT domain-containing protein 1, or PHD type transcription factor with transmembrane domains, is a membrane-bound transcription factor required for plastid-to-nucleus retrograde signaling. AtDIR17 imparts stereoselectivity on the phenoxy radical-coupling reaction, yielding optically active lignans from two molecules of coniferyl alcohol in the biosynthesis of lignans, flavonolignans, and alkaloids, and thus plays a central role in plant secondary metabolism. Members of this family contain one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 50 matched cddid_all.tbl CDD cd20402 cd20402 410473 Tudor_Agenet_FMRP-like_rpt1 first Tudor-like Agenet domain found in the fragile X mental retardation protein (FMRP) family. The FMRP family includes synaptic functional regulator FMR1, fragile X mental retardation syndrome-related protein 1 (FXR1), and 2 (FXR2). FMR1, also called fragile X mental retardation protein 1 (FMRP), is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. FXR1 and FXR2 are RNA-binding proteins that shuttle between the nucleus and cytoplasm and associate with polyribosomes, predominantly with the 60S ribosomal subunit. Members of this family contain two copies of the Tudor-like Agenet domain. The model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 50 matched cddid_all.tbl CDD cd20403 cd20403 410474 Tudor_Agenet_FMRP-like_rpt2 second Tudor-like Agenet domain found in the fragile X mental retardation protein (FMRP) family. The FMRP family includes synaptic functional regulator FMR1, fragile X mental retardation syndrome-related protein 1 (FXR1) and 2 (FXR2). FMR1, also called fragile X mental retardation protein 1 (FMRP), is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. FXR1 and FXR2 are RNA-binding proteins that shuttle between the nucleus and cytoplasm and associate with polyribosomes, predominantly with the 60S ribosomal subunit. Members of this family contain two copies of the Tudor-like Agenet domain. The model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 50 matched cddid_all.tbl CDD cd20404 cd20404 410475 Tudor_Agenet_AtEML-like Tudor-like Agenet domain found in Arabidopsis thaliana proteins EMSY-LIKE 1-4 (AtEML1-4) and similar proteins. This family includes Arabidopsis thaliana proteins EMSY-LIKE 1-4 (AtEML1-4), histone-lysine N-methyltransferase trithorax-like proteins ATX1-2 (AtATX1-2), histone-lysine N-methyltransferase ASHH3, DNA mismatch repair protein MSH6, and similar proteins. EMSY-like proteins contain an EMSY N-terminal domain, a central Tudor-like Agenet domain, and a C-terminal coiled-coil motif. AtEML1, AtEML2, and likely AtEML4, contribute to RPP7-mediated immunity. Besides this, AtEML1 and AtEML2 participate in a second EDM2-dependent function and affect floral transition. ATX-like proteins are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1, also called protein SET domain group 27, or trithorax-homolog protein 1 (TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2, also called protein SET domain group 30, or trithorax-homolog protein 2 (TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). Both ATX1 and ATX2 are multi-domain proteins that consist of an N-terminal Tudor-like Agenet domain, a PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical plant homeodomain (PHD) domain, a non-canonical extended PHD (ePHD) domain, and a C-terminal SET domain. ASHR3, also called protein SET DOMAIN GROUP 7, functions as a histone-lysine N-methyltransferase (EC 2.1.1.43). It contains a SET domain and a Tudor-like Agenet domain. AtMSH6, also called MutS protein homolog 6, is a component of the post-replicative DNA mismatch repair system (MMR). It forms a heterodimer with MutS alpha (MSH2-MSH6 heterodimer) which binds to DNA mismatches thereby initiating DNA repair. AtMSH6 contains a Tudor-like Agenet domain and a MutS domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 51 matched cddid_all.tbl CDD cd20405 cd20405 410476 Tudor_Agenet_AtDUF_rpt1_3 first and third Tudor-like Agenet domains found in a family of Arabidopsis thaliana DUF724 domain-containing proteins (AtDUFs). The family includes a group of AtDUFs (AtDUF1-3 and AtDUF6-8) that may be involved in the polar growth of plant cells via transportation of RNAs. Members of this family have four Tudor-like Agenet domains, except for AtDUF8, which contains only two copies of the Tudor-like Agenet domain. AtDUF4 and AtDUF5 are not included here due to the lack of a Tudor-like Agenet domain. The model corresponds to the first and third Tudor-like Agenet domains in AtDUF1-3 and AtDUF6-7, as well as the first Tudor-like Agenet domain in AtDUF8. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 65 matched cddid_all.tbl CDD cd20406 cd20406 410477 Tudor_Agenet_AtDUF_rpt2_4 second and fourth Tudor-like Agenet domains found in the family of Arabidopsis thaliana DUF724 domain-containing proteins (AtDUFs). The family includes a group of AtDUFs (AtDUF1-3 and AtDUF6-8) that may be involved in the polar growth of plant cells via transportation of RNAs. Members of this family have four Tudor-like Agenet domains, except for AtDUF8, which contains only two copies of the Tudor-like Agenet domain. AtDUF4 and AtDUF5 are not included here due to the lack of a Tudor-like Agenet domain. The model corresponds to the second and fourth Tudor-like Agenet domains in AtDUF1-3 and AtDUF6-7, as well as the first Tudor-like Agenet domain in AtDUF8. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 47 matched cddid_all.tbl CDD cd20407 cd20407 410478 Tudor_AKAP1 Tudor domain found in mitochondrial A-kinase anchor protein 1 (AKAP1) and similar proteins. AKAP1, also called A-kinase anchor protein 149 kDa (AKAP 149), dual specificity A-kinase-anchoring protein 1 (D-AKAP-1), protein kinase A-anchoring protein 1 (PRKA1), or Spermatid A-kinase anchor protein 84 (S-AKAP84), is found in mitochondria and in the endoplasmic reticulum-nuclear envelope, where it anchors protein kinases, phosphatases, and a phosphodiesterase. It regulates multiple cellular processes governing mitochondrial homeostasis and cell viability. AKAP1 binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane. It contains a C-terminal Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 76 matched cddid_all.tbl CDD cd20408 cd20408 410479 Tudor_TDRD1_rpt1 first Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins. TDRD1, also called cancer/testis antigen 41.1 (CT41.1), plays a central role during spermatogenesis by participating in the repression transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins, and governs the methylation and subsequent repression of transposons. TDRD1 contains four Tudor domains. This model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 130 matched cddid_all.tbl CDD cd20409 cd20409 410480 Tudor_TDRD1_rpt2 second Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins. TDRD1, also called cancer/testis antigen 41.1 (CT41.1), plays a central role during spermatogenesis by participating in the repression transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins, and governs the methylation and subsequent repression of transposons. TDRD1 contains four Tudor domains. This model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 82 matched cddid_all.tbl CDD cd20410 cd20410 410481 Tudor_TDRD1_rpt3 third Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins. TDRD1, also called cancer/testis antigen 41.1 (CT41.1), plays a central role during spermatogenesis by participating in the repression transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins, and governs the methylation and subsequent repression of transposons. TDRD1 contains four Tudor domains. This model corresponds to the third one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 59 matched cddid_all.tbl CDD cd20411 cd20411 410482 Tudor_TDRD1_rpt4 fourth Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins. TDRD1, also called cancer/testis antigen 41.1 (CT41.1), plays a central role during spermatogenesis by participating in the repression transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins, and governs the methylation and subsequent repression of transposons. TDRD1 contains four Tudor domains. This model corresponds to the fourth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 116 matched cddid_all.tbl CDD cd20412 cd20412 410483 Tudor_TDRD2 Tudor domain found in Tudor domain-containing protein 2 (TDRD2) and similar proteins. TDRD2, also called Tudor and KH domain-containing protein (TDRKH), participates in the primary piwi-interacting RNA (piRNA) biogenesis pathway and is required during spermatogenesis to repress transposable elements and prevent their mobilization, which is essential for germline integrity. The family also includes the TDRD2 homolog found in Drosophila melanogaster (dTDRKH), which is also called partner of PIWIs protein, or PAPI, and is involved in Zucchini-mediated piRNA 3'-end maturation. TDRD2 contains two KH domains and one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 95 matched cddid_all.tbl CDD cd20413 cd20413 410484 Tudor_TDRD3 Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins. TDRD3 is a scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. In the nucleus, it acts as a coactivator; it recognizes and binds asymmetric dimethylation on the core histone tails associated with transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine-methylated loci. In the cytoplasm, it may play a role in the assembly and/or disassembly of mRNA stress granules and in the regulation of translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins. TDRD3 contains one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 53 matched cddid_all.tbl CDD cd20414 cd20414 410485 Tudor_TDRD4_rpt1 first Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins. TDRD4, also called RING finger protein 17 (RNF17), is a component of the mammalian germ cell nuage and is essential for spermiogenesis. It seems to be involved in the regulation of transcriptional activity of MYC. In vitro, TDRD4 inhibits the DNA-binding activity of Mad-MAX heterodimers. It can recruit Mad transcriptional repressors (MXD1, MXD3, MXD4 and MXI1) to the cytoplasm. TDRD4 also acts as a potential cancer/testis antigen in liver cancer. TDRD4 contains a RING finger and five Tudor domains. This model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 77 matched cddid_all.tbl CDD cd20415 cd20415 410486 Tudor_TDRD4_rpt2 second Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins. TDRD4, also called RING finger protein 17 (RNF17), is a component of the mammalian germ cell nuage and is essential for spermiogenesis. It seems to be involved in the regulation of transcriptional activity of MYC. In vitro, TDRD4 inhibits the DNA-binding activity of Mad-MAX heterodimers. It can recruit Mad transcriptional repressors (MXD1, MXD3, MXD4 and MXI1) to the cytoplasm. TDRD4 also acts as a potential cancer/testis antigen in liver cancer. TDRD4 contains a RING finger and five Tudor domains. This model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 96 matched cddid_all.tbl CDD cd20416 cd20416 410487 Tudor_TDRD4_rpt3 third Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins. TDRD4, also called RING finger protein 17 (RNF17), is a component of the mammalian germ cell nuage and is essential for spermiogenesis. It seems to be involved in the regulation of transcriptional activity of MYC. In vitro, TDRD4 inhibits the DNA-binding activity of Mad-MAX heterodimers. It can recruit Mad transcriptional repressors (MXD1, MXD3, MXD4 and MXI1) to the cytoplasm. TDRD4 also acts as a potential cancer/testis antigen in liver cancer. TDRD4 contains a RING finger and five Tudor domains. This model corresponds to the third one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 82 matched cddid_all.tbl CDD cd20417 cd20417 410488 Tudor_TDRD4_rpt4 fourth Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins. TDRD4, also called RING finger protein 17 (RNF17), is a component of the mammalian germ cell nuage and is essential for spermiogenesis. It seems to be involved in the regulation of transcriptional activity of MYC. In vitro, TDRD4 inhibits the DNA-binding activity of Mad-MAX heterodimers. It can recruit Mad transcriptional repressors (MXD1, MXD3, MXD4 and MXI1) to the cytoplasm. TDRD4 also acts as a potential cancer/testis antigen in liver cancer. TDRD4 contains a RING finger and five Tudor domains. This model corresponds to the fourth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 68 matched cddid_all.tbl CDD cd20418 cd20418 410489 Tudor_TDRD4_rpt5 fifth Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins. TDRD4, also called RING finger protein 17 (RNF17), is a component of the mammalian germ cell nuage and is essential for spermiogenesis. It seems to be involved in the regulation of transcriptional activity of MYC. In vitro, TDRD4 inhibits the DNA-binding activity of Mad-MAX heterodimers. It can recruit Mad transcriptional repressors (MXD1, MXD3, MXD4 and MXI1) to the cytoplasm. TDRD4 also acts as a potential cancer/testis antigen in liver cancer. TDRD4 contains a RING finger and five Tudor domains. This model corresponds to the fifth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 105 matched cddid_all.tbl CDD cd20419 cd20419 410490 Tudor_TDRD5 Tudor domain found in Tudor domain-containing protein 5 (TDRD5) and similar proteins. TDRD5 is an RNA-binding protein directly associated with piRNA precursors. It is required for retrotransposon silencing, chromatoid body assembly, and spermiogenesis. TDRD5 participates in the repression of transposable elements and prevents their mobilization, which is essential for germline integrity. TDRD5 contains three LOTUS domains and one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 118 matched cddid_all.tbl CDD cd20420 cd20420 410491 Tudor_TDRD6_rpt1 first Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins. TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 132 matched cddid_all.tbl CDD cd20421 cd20421 410492 Tudor_TDRD6_rpt2 second Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins. TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 130 matched cddid_all.tbl CDD cd20422 cd20422 410493 Tudor_TDRD6_rpt3 third Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins. TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the third one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 135 matched cddid_all.tbl CDD cd20423 cd20423 410494 Tudor_TDRD6_rpt4 fourth Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins. TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the fourth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 80 matched cddid_all.tbl CDD cd20424 cd20424 410495 Tudor_TDRD6_rpt5 fifth Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins. TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the fifth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 126 matched cddid_all.tbl CDD cd20425 cd20425 410496 Tudor_TDRD6_rpt6 sixth Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins. TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the sixth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 115 matched cddid_all.tbl CDD cd20426 cd20426 410497 Tudor_TDRD6_rpt7 seventh Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins. TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the seventh one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 140 matched cddid_all.tbl CDD cd20427 cd20427 410498 Tudor_TDRD7_rpt1 first Tudor domain found in Tudor domain-containing protein 7 (TDRD7) and similar proteins. TDRD7, also called PCTAIRE2-binding protein, or Tudor repeat associator with PCTAIRE-2 (Trap), is a component of specific cytoplasmic RNA granules involved in post-transcriptional regulation of specific genes: probably acts by binding to specific mRNAs and regulating their translation. It is required for lens transparency during lens development, by regulating translation of genes such as CRYBB3 and HSPB1 in the developing lens. It is also essential for dynamic ribonucleoprotein (RNP) remodeling of chromatoid bodies during spermatogenesis. TDRD7 contains three Tudor domains. The model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 98 matched cddid_all.tbl CDD cd20428 cd20428 410499 Tudor_TDRD7_rpt2 second Tudor domain found in Tudor domain-containing protein 7 (TDRD7) and similar proteins. TDRD7, also called PCTAIRE2-binding protein, or Tudor repeat associator with PCTAIRE-2 (Trap), is a component of specific cytoplasmic RNA granules involved in post-transcriptional regulation of specific genes: probably acts by binding to specific mRNAs and regulating their translation. It is required for lens transparency during lens development, by regulating translation of genes such as CRYBB3 and HSPB1 in the developing lens. It is also essential for dynamic ribonucleoprotein (RNP) remodeling of chromatoid bodies during spermatogenesis. TDRD7 contains three Tudor domains. The model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 140 matched cddid_all.tbl CDD cd20429 cd20429 410500 Tudor_TDRD7_rpt3 third Tudor domain found in Tudor domain-containing protein 7 (TDRD7) and similar proteins. TDRD7, also called PCTAIRE2-binding protein, or Tudor repeat associator with PCTAIRE-2 (Trap), is a component of specific cytoplasmic RNA granules involved in post-transcriptional regulation of specific genes: probably acts by binding to specific mRNAs and regulating their translation. It is required for lens transparency during lens development, by regulating translation of genes such as CRYBB3 and HSPB1 in the developing lens. It is also essential for dynamic ribonucleoprotein (RNP) remodeling of chromatoid bodies during spermatogenesis. TDRD7 contains three Tudor domains. The model corresponds to the third one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 91 matched cddid_all.tbl CDD cd20430 cd20430 410501 Tudor_TDRD8 Tudor domain found in Tudor domain-containing protein 8 (TDRD8) and similar proteins. TDRD8, also called serine/threonine-protein kinase (EC 2.7.11.1) 31 (STK31), serine/threonine-protein kinase NYD-SPK, or Sugen kinase 396 (SgK396), is a germ cell-specific factor expressed in embryonic gonocytes of both sexes, and in postnatal spermatocytes and round spermatids in males. It acts as a cell-cycle regulated protein that contributes to the tumorigenicity of epithelial cancer cells. TDRD8 contains a Tudor domain and a serine/threonine kinase domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 75 matched cddid_all.tbl CDD cd20431 cd20431 410502 Tudor_TDRD9 Tudor domain found in Tudor domain-containing protein 9 (TDRD9) and similar proteins. TDRD9 is an ATP-dependent DEAD-like RNA helicase required during spermatogenesis. It is involved in the biosynthesis of PIWI-interacting RNAs (piRNAs). A recessive deleterious mutation mutation in TDRD9 causes non-obstructive azoospermia in infertile men. TDRD9 contains an N-terminal HrpA-like RNA helicase module and a Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 101 matched cddid_all.tbl CDD cd20432 cd20432 410503 Tudor_TDRD10 Tudor domain found in Tudor domain-containing protein 10 (TDRD10) and similar proteins. TDRD10 is widely expressed and localized both to the nucleus and cytoplasm, and may play general roles like regulation of RNA metabolism. It contains a Tudor domain and an RNA recognition motif (RRM). The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 139 matched cddid_all.tbl CDD cd20433 cd20433 410504 Tudor_TDRD11 Tudor domain found in Tudor domain-containing protein 11 (TDRD11) and similar proteins. TDRD11, also called Staphylococcal nuclease domain-containing protein 1 (SND1), 100 kDa coactivator, EBNA2 coactivator p100, or p100 co-activator, is a multifunctional protein that is reportedly associated with different types of RNA molecules, including mRNA, miRNA, pre-miRNA, and dsRNA. It has been implicated in a number of biological processes in eukaryotic cells, including the cell cycle, DNA damage repair, proliferation, and apoptosis. TDRD11 is overexpressed in multiple cancers and functions as an oncogene. It contains multiple Staphylococcal nuclease (SN) domains and a C-terminal Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 84 matched cddid_all.tbl CDD cd20434 cd20434 410505 Tudor_TDRD12_rpt1 first Tudor domain found in Tudor domain-containing protein 12 (TDRD12) and similar proteins. TDRD12, also called ES cell-associated transcript 8 protein (ECAT8), is a putative ATP-dependent DEAD-like RNA helicase that is essential for germ cell development and maintenance. It acts as a unique piRNA biogenesis factor essential for secondary PIWI interacting RNA (piRNA) biogenesis. TDRD12 contains two Tudor domains, one at the N-terminus and the other at the C-terminal end. The model corresponds to the first/N-terminal one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 164 matched cddid_all.tbl CDD cd20435 cd20435 410506 Tudor_TDRD12_rpt2 second Tudor domain found in Tudor domain-containing protein 12 (TDRD12) and similar proteins. TDRD12, also called ES cell-associated transcript 8 protein (ECAT8), is a putative ATP-dependent DEAD-like RNA helicase that is essential for germ cell development and maintenance. It acts as a unique piRNA biogenesis factor essential for secondary PIWI interacting RNA (piRNA) biogenesis. TDRD12 contains two Tudor domains, one at the N-terminus and the other at the C-terminal end. The model corresponds to the second/C-terminal one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 134 matched cddid_all.tbl CDD cd20436 cd20436 410507 Tudor_TDRD15_rpt1 first Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins. TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 147 matched cddid_all.tbl CDD cd20437 cd20437 410508 Tudor_TDRD15_rpt2 second Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins. TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 120 matched cddid_all.tbl CDD cd20438 cd20438 410509 Tudor_TDRD15_rpt3 third Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins. TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the third one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 141 matched cddid_all.tbl CDD cd20439 cd20439 410510 Tudor_TDRD15_rpt4 fourth Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins. TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the fourth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 125 matched cddid_all.tbl CDD cd20440 cd20440 410511 Tudor_TDRD15_rpt5 fifth Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins. TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the fifth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 127 matched cddid_all.tbl CDD cd20441 cd20441 410512 Tudor_TDRD15_rpt6 sixth Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins. TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the sixth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 108 matched cddid_all.tbl CDD cd20442 cd20442 410513 Tudor_TDRD15_rpt7 seventh Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins. TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the seventh one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 160 matched cddid_all.tbl CDD cd20443 cd20443 410514 Tudor_AtTudor1-like Tudor domain found in Arabidopsis thaliana ribonuclease Tudor 1 (AtTudor1), ribonuclease Tudor 2 (AtTudor2), and similar proteins. The family includes AtTudor1 (also called Tudor-SN protein 1) and AtTudor2 (also called Tudor-SN protein 2 or 100 kDa coactivator-like protein). They are cytoprotective ribonucleases (RNases) required for resistance to abiotic stresses, acting as positive regulators of mRNA decapping during stress. Members of this family contain one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 117 matched cddid_all.tbl CDD cd20444 cd20444 410515 Tudor_vreteno-like_rpt1 first Tudor domain found in Drosophila melanogaster protein vreteno and similar proteins. Vreteno is a gonad-specific protein essential for germline development to repress transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process in both germline and somatic gonadal tissues by mediating the repression of transposable elements during meiosis. Vreteno contains two Tudor domains. The model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 55 matched cddid_all.tbl CDD cd20445 cd20445 410516 Tudor_vreteno-like_rpt2 second Tudor domain found in Drosophila melanogaster protein vreteno and similar proteins. Vreteno is a gonad-specific protein essential for germline development to repress transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process in both germline and somatic gonadal tissues by mediating the repression of transposable elements during meiosis. Vreteno contains two Tudor domains. The model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 56 matched cddid_all.tbl CDD cd20446 cd20446 410517 Tudor_SpSPF30-like Tudor domain found in Schizosaccharomyces pombe splicing factor spf30 (SpSPF30) and similar proteins. SpSPF30, also called survival of motor neuron-related-splicing factor 30, is necessary for spliceosome assembly. It contains one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 56 matched cddid_all.tbl CDD cd20447 cd20447 410518 Tudor_TDRD13 Tudor domain found in Tudor domain-containing protein 13 (TDRD13). TDRD13, also called asparagine-linked glycosylation 13 (ALG13), glycosyltransferase 28 domain-containing protein 1 (GLT28D1), or UDP-N-acetylglucosamine transferase subunit ALG13, is a putative bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase (EC 2.4.1.141/EC 3.4.19.12). It is a potential member of the Alg7p/Alg13p/Alg14p complex catalyzing the first two initial reactions in the N-glycosylation process. It contains one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 80 matched cddid_all.tbl CDD cd20448 cd20448 410519 Tudor_OTUD4 Tudor domain found in OTU domain-containing protein 4 (OTUD4). OTUD4, also called HIV-1-induced protein HIN-1, is a phospho-activated K63 deubiquitinase that hydrolyzes the isopeptide bond between the ubiquitin C-terminus and the lysine epsilon-amino group of the target protein. It may negatively regulate inflammatory and pathogen recognition signaling in innate immune response. It contains one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 64 matched cddid_all.tbl CDD cd20449 cd20449 410520 Tudor_PHF1 Tudor domain found in PHD finger protein1 (PHF1) and similar proteins. PHF1, also called Polycomb-like protein 1 (PCL1), together with JARID2 and AEBP2, associates with the Polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis, through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF1 is essential in epigenetic regulation and genome maintenance. It acts as a dual reader of lysine trimethylation at lysine 36 of histone H3 and lysine 27 of histone variant H3t. Moreover, PHF1 is required for efficient H3-K27 trimethylation (H3K27me3) and Hox gene silencing. It can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response. PHF1 consists of an N-terminal Tudor domain followed by two PHD domains, and a C-terminal MTF2 domain. Its Tudor domain selectively binds to histone H3K36me3. 54 matched cddid_all.tbl CDD cd20450 cd20450 410521 Tudor_MTF2 Tudor domain found in metal-response element-binding transcription factor 2 (MTF2) and similar proteins. MTF2, also called metal regulatory transcription factor 2, metal-response element DNA-binding protein M96, or Polycomb-like protein 2 (PCL2), complexes with the Polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2, like other PCL family proteins, consists of an N-terminal Tudor domain followed by two PHD domains, and a C-terminal MTF2 domain. PCL proteins specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. 54 matched cddid_all.tbl CDD cd20451 cd20451 410522 Tudor_PHF19 Tudor domain found in PHD finger protein1 (PHF19) and similar proteins. PHF19, also called Polycomb-like protein 3 (PCL3), is a component of the Polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF19 consists of an N-terminal Tudor domain followed by two PHD domains, and a C-terminal MTF2 domain. It binds trimethylated histone H3 Lys36 (H3K36me3) through its Tudor domain and recruits the PRC2 complex and the H3K36me3 demethylase NO66 to embryonic stem cell genes during differentiation. Moreover, PHF19 and its upstream regulator, Akt, play roles in the phenotype switch of melanoma cells from proliferative to invasive states. 57 matched cddid_all.tbl CDD cd20452 cd20452 410523 Tudor_dPCL-like Tudor domain found in Drosophila melanogaster Polycomb protein PCL (dPCL)and similar proteins. dPCL, also called Polycomblike protein, is a Polycomb group (PcG) protein that is specifically required during the first 6 hours of embryogenesis to establish the repressed state. dPCL is a component of the Esc/E(z) complex, which methylates 'Lys-9' and 'Lys-27' residues of histone H3, leading to transcriptional repression of the affected target gene. Like other PCL family proteins, it consists of an N-terminal Tudor domain followed by two PHD domains, and a C-terminal MTF2 domain. PCL proteins specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. 55 matched cddid_all.tbl CDD cd20453 cd20453 410524 Tudor_PHF20 Tudor domain found in PHD finger protein 20 (PHF20) and similar proteins. PHF20, also called Glioma-expressed antigen 2, hepatocellular carcinoma-associated antigen 58, novel zinc finger protein, or transcription factor TZP (referring to Tudor and zinc finger domain containing protein), is a regulator of NF-kappaB activation by disrupting recruitment of PP2A to p65. It also functions as a transcription factor that binds to Akt and plays a role in Akt cell survival/growth signaling. Moreover, it transcriptionally regulates p53. The phosphorylation of PHF20 on Ser291 mediated by protein kinase B (PKB) is essential in tumorigenesis via the regulation of p53-mediated signaling. PHF20 contains an N-terminal malignant brain tumor (MBT) domain, a Tudor domain, a plant homeodomain (PHD) finger and putative DNA-binding domains AT hook and C2H2-type zinc finger. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 53 matched cddid_all.tbl CDD cd20454 cd20454 410525 Tudor_PHF20L1 Tudor domain found in PHD finger protein 20-like protein 1 (PHF20L1) and similar proteins. PHF20L1 is an active malignant brain tumor (MBT) domain-containing protein that binds to monomethylated lysine 142 on DNA (cytosine-5) Methyltransferase 1 (DNMT1) (DNMT1K142me1) and colocalizes at the perinucleolar space in a SET7-dependent manner. Its MBT domain reads and controls enzyme levels of methylated DNMT1 in cells, thus representing a novel antagonist of DNMT1 proteasomal degradation. In addition to the MBT domain, PHF20L1 also contains a Tudor domain, a plant homeodomain (PHD) finger and putative DNA-binding domains AT hook and C2H2-type zinc finger. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 59 matched cddid_all.tbl CDD cd20455 cd20455 410526 Tudor_UHRF1_rpt1 first Tudor domain found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1) and similar proteins. UHRF1, also called inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1, is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 can act as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also a N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET- and RING- associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintenance DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD domain targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1. The model corresponds to the first Tudor domain. 79 matched cddid_all.tbl CDD cd20456 cd20456 410527 Tudor_UHRF2_rpt1 first Tudor domain found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2) and similar proteins. UHRF2, also called Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2, was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. UHRF2 also functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger domain. The model corresponds to the first Tudor domain. The tandem Tudor domain directs binding of UHRF to the heterochromatin mark histone H3K9me3. 91 matched cddid_all.tbl CDD cd20457 cd20457 410528 Tudor_UHRF1_rpt2 second Tudor domain found in ubiquitin-like PHD and RING finger domain-containing protein 1 (UHRF1) and similar proteins. UHRF1, also called inverted CCAAT box-binding protein of 90 kDa, nuclear protein 95, nuclear zinc finger protein Np95 (Np95), RING finger protein 106, transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1, is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma (LSCC), gastric cancer (GC), esophageal squamous cell carcinoma (ESCC), colorectal cancer, prostate cancer, and breast cancer. UHRF1 can act as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumour suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21. Moreover, UHRF1-dependent repression of factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination of TIP60. It is also a N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53 status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET- and RING- associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitylation has an essential role in maintenance DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD domain targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibit both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1. The model corresponds to the second Tudor domain. 72 matched cddid_all.tbl CDD cd20458 cd20458 410529 Tudor_UHRF2_rpt2 second Tudor domain found in ubiquitin-like PHD and RING finger domain-containing protein 2 (UHRF2) and similar proteins. UHRF2, also called Np95/ICBP90-like RING finger protein (NIRF), Np95-like RING finger protein, nuclear protein 97, nuclear zinc finger protein Np97, RING finger protein 107, or E3 ubiquitin-protein ligase UHRF2, was originally identified as a ubiquitin ligase acting as a small ubiquitin-like modifier (SUMO) E3 ligase that enhances zinc finger protein 131 (ZNF131) SUMOylation but does not enhance ZNF131 ubiquitination. It also ubiquitinates PCNP, a PEST-containing nuclear protein. UHRF2 also functions as a nuclear protein involved in cell-cycle regulation and has been implicated in tumorigenesis. It interacts with cyclins, CDKs, p53, pRB, PCNA, HDAC1, DNMTs, G9a, methylated histone H3 lysine 9, and methylated DNA. It interacts with the cyclin E-CDK2 complex, ubiquitinates cyclins D1 and E1, induces G1 arrest, and is involved in the G1/S transition regulation. Furthermore, UHRF2 is a direct transcriptional target of the transcription factor E2F-1 in the induction of apoptosis. It recruits HDAC1 and binds to methyl-CpG. UHRF2 also participates in the maturation of Hepatitis B virus (HBV) through interacting with HBV core protein and promoting its degradation. UHRF2 contains an N-terminal ubiquitin-like domain (UBL), a tandem Tudor domain (TTD), a plant homeodomain (PHD) domain, a SET- and RING-associated (SRA) domain, and a C-terminal RING finger domain. The model corresponds to the second Tudor domain. The tandem Tudor domain directs binding of UHRF to the heterochromatin mark histone H3K9me3. 73 matched cddid_all.tbl CDD cd20459 cd20459 410530 Tudor_ARID4A_rpt1 first Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins. ARID4A, also called retinoblastoma-binding protein 1 (RBBP1 or RBP1), is a leukemia and tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through its interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4B ( also known as RBP1L1). ARID4A specifically interacts with retinoblastoma protein (pRb) and shows both HDAC -dependent and -independent repression activities. It also acts as a Runx2 coactivator and is involved in the regulation of osteoblastic differentiation in Runx2-osterix transcriptional cascade. ARID4A contains tandem Tudor domains, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The ARID and R2 domains are responsible for the repression activities. The Tudor, PWWP, and chromobarrel domains are all Royal Family domains, but only the chromobarrel domain of ARID4A is responsible for recognizing both dsDNA and methylated histone tails, particularly H4K20me3, in chromatin remodeling and epigenetic regulation. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 58 matched cddid_all.tbl CDD cd20460 cd20460 410531 Tudor_ARID4B_rpt1 first Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins. ARID4B, also called 180 kDa Sin3-associated polypeptide (p180), breast cancer-associated antigen BRCAA1, histone deacetylase complex subunit SAP180, or retinoblastoma-binding protein 1-like 1 (RBP1L1 or RBBP1L1), is a leukemia and tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through its interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and ARID4A ( also known as RBP1). ARID4B plays a causative role in metastatic progression of breast cancer. It may also be associated with regulating the cell cycle. ARID4B contains tandem Tudor domains, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 61 matched cddid_all.tbl CDD cd20461 cd20461 410532 Tudor_ARID4A_rpt2 second Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins. ARID4A, also called retinoblastoma-binding protein 1 (RBBP1 or RBP1), is a leukemia and tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through its interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and the ARID4 family homolog ARID4B ( also known as RBP1L1). ARID4A specifically interacts with retinoblastoma protein (pRb) and shows both HDAC -dependent and -independent repression activities. It also acts as a Runx2 coactivator and is involved in the regulation of osteoblastic differentiation in Runx2-osterix transcriptional cascade. ARID4A contains tandem Tudor domains, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The ARID and R2 domains are responsible for the repression activities. The Tudor, PWWP, and chromobarrel domains are all Royal Family domains, but only the chromobarrel domain of ARID4A is responsible for recognizing both dsDNA and methylated histone tails, particularly H4K20me3, in chromatin remodeling and epigenetic regulation. The model corresponds to the second Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 60 matched cddid_all.tbl CDD cd20462 cd20462 410533 Tudor_ARID4B_rpt2 second Tudor domain found in AT-rich interactive domain-containing protein 4B (ARID4B) and similar proteins. ARID4B, also called 180 kDa Sin3-associated polypeptide (p180), breast cancer-associated antigen BRCAA1, histone deacetylase complex subunit SAP180, or retinoblastoma-binding protein 1-like 1 (RBP1L1 or RBBP1L1), is a leukemia and tumor suppressor involved in epigenetic regulation in leukemia and Prader-Willi/Angelman syndromes. It associates with the mSIN3A histone deacetylase (HDAC) chromatin remodeling complex through its interaction with the breast cancer associated tumor suppressor ING1, the breast cancer metastasis suppressor BRMS1, and ARID4A ( also known as RBP1). ARID4B plays a causative role in metastatic progression of breast cancer. It may also be associated with regulating the cell cycle. ARID4B contains tandem Tudor domains, a PWWP domain (also known as HATH domain or RBB1NT domain), an AT-rich DNA-interacting domain (ARID, also known as BRIGHT), a chromobarrel domain, and a C-terminal R2 domain. The model corresponds to the second Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 57 matched cddid_all.tbl CDD cd20463 cd20463 410534 Tudor_JMJD2A_rpt1 first Tudor domain found in Jumonji domain-containing protein 2A (JMJD2A) and similar proteins. JMJD2A, also called lysine-specific demethylase 4A (KDM4A), or JmjC domain-containing histone demethylation protein 3A (JHDM3A), catalyzes the demethylation of di- and trimethylated H3K9 and H3K36. It is involved in carcinogenesis and functions as a transcription regulator that may either stimulate or repress gene transcription. It associates with nuclear receptor corepressor complex or histone deacetylases. Moreover, JMJD2A forms complexes with both the androgen and estrogen receptor (ER), and plays an essential role in growth of both ER-positive and -negative breast tumors. It is also involved in prostate, colon, and lung cancer progression. JMJD2A contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 55 matched cddid_all.tbl CDD cd20464 cd20464 410535 Tudor_JMJD2B_rpt1 first Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins. JMJD2B, also called lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the tri-methyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 54 matched cddid_all.tbl CDD cd20465 cd20465 410536 Tudor_JMJD2C_rpt1 first Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins. JMJD2C, also called lysine-specific demethylase 4C (KDM4C), gene amplified in squamous cell carcinoma 1 protein (GASC-1 protein), or JmjC domain-containing histone demethylation protein 3C (JHDM3C), is an epigenetic factor that catalyzes the demethylation of di- and trimethylated H3K9 and H3K36, and may be involved in the development and/or progression of various types of cancer including esophageal squamous cell carcinoma (ESC) and breast cancer. It selectively interacts with hypoxia-inducible factor 1alpha (HIF1alpha) and plays a role in breast cancer progression. Moreover, JMJD2C may play an important role in the treatment of obesity and its complications by modulating the regulation of adipogenesis by nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma). JMJD2C contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the first Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 54 matched cddid_all.tbl CDD cd20466 cd20466 410537 Tudor_JMJD2A_rpt2 second Tudor domain found in Jumonji domain-containing protein 2A (JMJD2A) and similar proteins. JMJD2A, also called lysine-specific demethylase 4A (KDM4A), or JmjC domain-containing histone demethylation protein 3A (JHDM3A), catalyzes the demethylation of di- and trimethylated H3K9 and H3K36. It is involved in carcinogenesis and functions as a transcription regulator that may either stimulate or repress gene transcription. It associates with nuclear receptor corepressor complex or histone deacetylases. Moreover, JMJD2A forms complexes with both the androgen and estrogen receptor (ER), and plays an essential role in growth of both ER-positive and -negative breast tumors. It is also involved in prostate, colon, and lung cancer progression. JMJD2A contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the second Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 56 matched cddid_all.tbl CDD cd20467 cd20467 410538 Tudor_JMJD2B_rpt2 second Tudor domain found in Jumonji domain-containing protein 2B (JMJD2B) and similar proteins. JMJD2B, also called lysine-specific demethylase 4B (KDM4B), or JmjC domain-containing histone demethylation protein 3B (JHDM3B), specifically antagonizes the tri-methyl group from H3K9 in pericentric heterochromatin and reduces H3K36 methylation in mammalian cells. It plays an essential role in the growth regulation of cancer cells by modulating the G1-S transition and promotes cell-cycle progression through the regulation of cyclin-dependent kinase 6 (CDK6). It interacts with heat shock protein 90 (Hsp90) and its stability can be regulated by Hsp90. JMJD2B also functions as a direct transcriptional target of p53, which induces its expression through promoter binding. Moreover, JMJD2B expression can be controlled by hypoxia-inducible factor 1alpha (HIF1alpha) in colorectal cancer and estrogen receptor alpha (ERalpha) in breast cancer. It is also involved in bladder, lung, and gastric cancer. JMJD2B contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the second Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 56 matched cddid_all.tbl CDD cd20468 cd20468 410539 Tudor_JMJD2C_rpt2 second Tudor domain found in Jumonji domain-containing protein 2C (JMJD2C) and similar proteins. JMJD2C, also called lysine-specific demethylase 4C (KDM4C), gene amplified in squamous cell carcinoma 1 protein (GASC-1 protein), or JmjC domain-containing histone demethylation protein 3C (JHDM3C), is an epigenetic factor that catalyzes the demethylation of di- and trimethylated H3K9 and H3K36, and may be involved in the development and/or progression of various types of cancer including esophageal squamous cell carcinoma (ESC) and breast cancer. It selectively interacts with hypoxia-inducible factor 1alpha (HIF1alpha) and plays a role in breast cancer progression. Moreover, JMJD2C may play an important role in the treatment of obesity and its complications by modulating the regulation of adipogenesis by nuclear receptor peroxisome proliferator-activated receptor gamma (PPARgamma). JMJD2C contains jmjN and jmjC domains in the N-terminal region, followed by a canonical plant homeodomain (PHD) domain, a noncanonical extended PHD domain, and tandem Tudor domains. The model corresponds to the second Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 60 matched cddid_all.tbl CDD cd20469 cd20469 410540 Tudor_TNRC18 Tudor domain found in trinucleotide repeat-containing gene 18 protein (TNRC18) and similar proteins. TNRC18, also called long CAG trinucleotide repeat-containing gene 79 protein (CAGL79), is a protein that in humans is encoded by the TNRC18 gene. Its biological function remains unclear. TNRC18 contains one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 67 matched cddid_all.tbl CDD cd20470 cd20470 410541 Tudor_BAHCC1 Tudor domain found in BAH and coiled-coil domain-containing protein 1 (BAHCC1) and similar proteins. BAHCC1, also called Bromo adjacent homology domain-containing protein 2 (BAHD2), or BAH domain-containing protein 2, may function as a transcriptional regulator. BAHCC1 contains one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 70 matched cddid_all.tbl CDD cd20471 cd20471 410542 Tudor_Agenet_FMR1_rpt1 first Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar proteins. FMR1, also called fragile X mental retardation protein 1 (FMRP), is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. FMR1 contains two copies of the Tudor-like Agenet domain. The model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 55 matched cddid_all.tbl CDD cd20472 cd20472 410543 Tudor_Agenet_FXR1_rpt1 first Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins. FXR1 is an RNA binding protein that interacts with the functionally similar proteins FMR1 and FXR2. It shuttles between the nucleus and cytoplasm and associates with polyribosomes, predominantly with the 60S ribosomal subunit. FXR1 contains two copies of the Tudor-like Agenet domain. The model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 55 matched cddid_all.tbl CDD cd20473 cd20473 410544 Tudor_Agenet_FXR2_rpt1 first Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein 2 (FXR2) and similar proteins. FXR2 is an RNA-binding protein that associates with polyribosomes, predominantly with 60S large ribosomal subunits. It may have a role in the development of fragile X mental retardation syndrome. FXR2 contains two copies of the Tudor-like Agenet domain. The model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 55 matched cddid_all.tbl CDD cd20474 cd20474 410545 Tudor_Agenet_FMR1_rpt2 second Tudor-like Agenet domain found in synaptic functional regulator FMR1 and similar proteins. FMR1, also called fragile X mental retardation protein 1 (FMRP), is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. FMR1 contains two copies of the Tudor-like Agenet domain. The model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 63 matched cddid_all.tbl CDD cd20475 cd20475 410546 Tudor_Agenet_FXR1_rpt2 second Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins. FXR1 is an RNA binding protein that interacts with the functionally similar proteins FMR1 and FXR2. It shuttles between the nucleus and cytoplasm and associates with polyribosomes, predominantly with the 60S ribosomal subunit. FXR1 contains two copies of the Tudor-like Agenet domain. The model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 66 matched cddid_all.tbl CDD cd20476 cd20476 410547 Tudor_Agenet_FXR2_rpt2 second Tudor-like Agenet domain found in fragile X mental retardation syndrome-related protein 2 (FXR2) and similar proteins. FXR2 is an RNA-binding protein that associates with polyribosomes, predominantly with 60S large ribosomal subunits. It may have a role in the development of fragile X mental retardation syndrome. FXR2 contains two copies of the Tudor-like Agenet domain. The model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 68 matched cddid_all.tbl CDD cd20477 cd20477 380475 Cas13b_Pb-like Class 2 type VI-B CRISPR-associated RNA-guided ribonuclease Cas13b from Prevotella buccae and similar Cas13b proteins. CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins) adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. These systems are divided into two classes: class 1 systems utilize multiple Cas proteins and CRISPR RNA (crRNA) to form an effector complex while class 2 systems employ a large, single effector with crRNA to mediate interference. Class 2 type VI CRISPR-Cas13 systems use a single enzyme to target RNA using a programmable crRNA guide and are divided into four subtypes based on the identity of the Cas13 protein (Cas13a-d). The Cas13 proteins are capable of both pre-crRNA processing and target RNA cleavage, which protect the host from phage attacks. Once bound to a target RNA, their non-specific RNase activity is activated. Cas13b has many distinctive features compared to the other Cas13 proteins, including the lack of significant sequence similarity, disparate crRNA repeat region, and double-sided protospacer flanking sequence (PFS)-dependent target RNA cleavage. 995 matched cddid_all.tbl CDD cd20478 cd20478 380476 Cas13b_Bz-like Class 2 type VI-B CRISPR-associated RNA-guided ribonuclease Cas13b from Bergeyella zoohelcum and similar Cas13b proteins. CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins) adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. These systems are divided into two classes: class 1 systems utilize multiple Cas proteins and CRISPR RNA (crRNA) to form an effector complex while class 2 systems employ a large, single effector with crRNA to mediate interference. Class 2 type VI CRISPR-Cas13 systems use a single enzyme to target RNA using a programmable crRNA guide and are divided into four subtypes based on the identity of the Cas13 protein (Cas13a-d). The Cas13 proteins are capable of both pre-crRNA processing and target RNA cleavage, which protect the host from phage attacks. Once bound to a target RNA, their non-specific RNase activity is activated. Cas13b has many distinctive features compared to the other Cas13 proteins, including the lack of significant sequence similarity, disparate crRNA repeat region, and double-sided protospacer flanking sequence (PFS)-dependent target RNA cleavage. 1118 matched cddid_all.tbl CDD cd20480 cd20480 380470 ArgR-Cyc_NRPS-like Cyc (heterocyclization)-like domain of Vibrio anguillarum AngR and similar proteins; belongs to the Condensation-domain family. Vibrio anguillarum AngR plays a role in regulating the expression of iron transport genes as well as in the production of the siderophore anguibactin. Cyc-domains are a type of Condensation (C) domain. Cyc-domains catalyze two separate reactions in the creation of heterocyclized peptide products in nonribosomal peptide synthesis: amide bond formation followed by intramolecular cyclodehydration between a Cys, Ser, or Thr side chain and a carbonyl carbon on the peptide backbone to form a thiazoline, oxazoline, or methyloxazoline ring. C-domains typically have a conserved HHxxxD motif at the active site; Cyc-domains have a alternative, conserved DxxxxD active site motif, mutation of the aspartate residues in this motif can abolish or diminish condensation activity. Members of this subfamily have an SxxxD motif at the active site. C-domains of nonribosomal peptide synthetases (NRPSs) catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). In addition to Cyc-domains there are various other subtypes of C-domains such as the LCL-type which catalyzes peptide bond formation between two L-amino acids, the DCL-type which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. 406 matched cddid_all.tbl CDD cd20481 cd20481 380473 phage_tailspike_middle N-terminal and middle domains of tailspike protein in Acinetobacter bacteriophages. This model describes the middle beta-helical domain of Acinetobacter bacteriophage tailspike proteins, as well as a separate N-terminal domain that does not appear to be part of the beta-helical substructure. The N-terminal domain may be involved in virion binding, and the molecules form a homo-trimeric arrangement. A C-terminal domain that may be involved in receptor binding is omitted from the model. 419 matched cddid_all.tbl CDD cd20482 cd20482 467844 CC_brat-like coiled-coil (CC) domain of Drosophila brain tumor (brat) and similar proteins. This family contains the coiled-coil (CC) region of Drosophila brain tumor (Brat), a translational repressor that belongs to the tripartite motif (TRIM) protein superfamily. TRIM proteins play important roles in various cellular processes and are involved in many diseases which consists of two B-box domains and a coiled-coil (CC) domain at the N-terminal region, and an NHL domain at the C-terminus. Brat localizes at the basal cortex during asymmetric division of Drosophila neuroblasts by directly interacting with the scaffolding protein Miranda (Mira), which it does through the CC-NHL domain tandem, indicating that the function of the Brat CC domain is to assemble Brat-NHL in dimeric form which is necessary for Mira binding. Brat CC forms an elongated antiparallel dimer similar to its other TRIM protein counterparts, but the overall length of Brat CC dimer is shorter than the TRIMs. 122 matched cddid_all.tbl CDD cd20483 cd20483 380471 C_PKS-NRPS Condensation domain of hybrid polyketide synthetase/nonribosomal peptide synthetases (PKS/NRPSs). Condensation (C) domains of nonribosomal peptide synthetases (NRPSs) catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. Hybrid PKS/NRPS create polymers containing both polyketide and amide linkages. C-domains typically have a conserved HHxxxD motif at the active site; mutations in this motif can abolish or diminish condensation activity. Most members of this subfamily have the typical C-domain HHXXXD motif. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). There are various subtypes of C-domains such as the LCL-type which catalyzes peptide bond formation between two L-amino acids, the DCL-type which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. 430 matched cddid_all.tbl CDD cd20484 cd20484 380472 C_PKS-NRPS_PksJ-like Condensation domain of hybrid polyketide synthetase/nonribosomal peptide synthetases (PKS/NRPSs), similar to Bacillus subtilis PksJ. Condensation (C) domains of nonribosomal peptide synthetases (NRPSs) catalyze peptide bond formation within (usually) large multi-modular enzymatic complexes. Hybrid PKS/NRPS create polymers containing both polyketide and amide linkages. C-domains typically have a conserved HHxxxD motif at the active site; mutations in this motif can abolish or diminish condensation activity. Members of this subfamily have the typical C-domain HHxxxD motif. PksJ is involved in some intermediate steps for the synthesis of the antibiotic polyketide bacillaene which is important in secondary metabolism. NRPS can use a large variety of acyl monomers (approximately 500 different possible monomer substrates as opposed to the 20 standard amino acids in ribosomal protein synthesis) to construct bioactive secondary metabolites of 2 to 18 units long (with various activities such as antibiotic, antifungal, antitumor and immunosuppression). There are various subtypes of C-domains such as the LCL-type which catalyzes peptide bond formation between two L-amino acids, the DCL-type which links an L-amino acid to the D-amino acid at the end of a growing peptide, starter C-domains which acylate the first amino acid with a beta-hydroxy carboxylic acid, and heterocyclization (Cyc) domains which catalyze both peptide bond formation and cyclization of Cys, Ser, or Thr residues. Typically, an NRPS module consists of an adenylation domain, a peptidyl carrier protein (PCP) domain (also known as thiolation (T) domain) and a C-domain. NRPS modules may also include specialized domains such as the terminal-module thioesterase (Te) domain that releases the product via hydrolysis or macrocyclization and any of various C-domain family members such as the epimerization (E) domain, the ester-bond forming C-domain, dual E/C (epimerization and condensation) domains, and the X-domain. 430 matched cddid_all.tbl CDD cd20485 cd20485 380450 USP25_USP28_C-like carboxyl-terminal domain of ubiquitin-specific protease 25 (USP25) and 28 (USP28), and similar domains. This family contains the C-terminal domain of two deubiquitinases (DUBs), ubiquitin-specific proteases USP25 and USP28, which share high similarity but vary in their cellular functions. USP25 is a regulator of the innate immune system and may play a role in tumorigenesis, while USP28 is known for its tumor-promoting role. These two closely related DUBs contain an N-terminal domain harboring a Ub-associated domain (UBA) and two Ub-interacting motifs (UIMs), a central catalytic USP domain, and a C-terminal region of unknown function and variable size due to alternative splicing. In general, USP catalytic domains are around 350 amino acids in length; however, in USP25 and 28, the catalytic domains span around 550 amino acids due to a large, conserved insertion at a common insertion point called USP25/28 catalytic domain inserted domain (UCID). This alignment model represents the C-terminal region that has been implicated in substrate binding for both USP25 and USP28 and harbors the splicing site for isoform-specific sequences. 273 matched cddid_all.tbl CDD cd20486 cd20486 380451 USP25_C carboxyl-terminal domain of ubiquitin-specific protease 25 (USP25). This subfamily contains the C-terminal domain of ubiquitin-specific protease USP25, a deubiquitinase (DUB), which shares high similarity with USP28 but varies in cellular function; USP25 is a regulator of the innate immune system and may play a role in tumorigenesis, while USP28 is known for its tumor-promoting role. USP25 regulates inflammatory TRAF signaling and USP28 stabilizes c-MYC and other nuclear proteins. These two closely related DUBs contain an N-terminal domain harboring a Ub-associated domain (UBA) and two Ub-interacting motifs (UIMs), a central catalytic USP domain, and a C-terminal region of unknown function and variable size due to alternative splicing. In general, USP catalytic domains are around 350 amino acids in length; however, in USP25 and 28, the catalytic domains span around 550 amino acids due to a large, conserved insertion at a common insertion point called USP25/28 catalytic domain inserted domain (UCID). This C-terminal region has been implicated in substrate binding for USP25 and harbors the splicing site for isoform-specific sequences. Structure studies show that the C-terminally extended USP25 is exclusively tetrameric. 281 matched cddid_all.tbl CDD cd20487 cd20487 380452 USP28_C carboxyl-terminal domain of ubiquitin-specific protease 28 (USP28). This family contains the C-terminal domain of ubiquitin-specific protease USP28, a deubiquitinase (DUB), which shares high similarity with USP25 but varies in cellular function; USP28 is known for its tumor-promoting role while USP25 is a regulator of the innate immune system and may play a role in tumorigenesis. USP28 stabilizes c-MYC and other nuclear proteins, and USP25 regulates inflammatory TRAF signaling. These two closely related DUBs contain an N-terminal domain harboring a Ub-associated domain (UBA) and two Ub-interacting motifs (UIMs), a central catalytic USP domain, and a C-terminal region of unknown function and variable size due to alternative splicing. In general, USP catalytic domains are around 350 amino acids in length; however, in USP25 and 28, the catalytic domains span around 550 amino acids due to a large, conserved insertion at a common insertion point called USP25/28 catalytic domain inserted domain (UCID). This C-terminal region has been implicated in substrate binding for USP28 and harbors the splicing site for isoform-specific sequences. Structure studies suggest that the C-terminal domain forms an independent entity. 280 matched cddid_all.tbl CDD cd20488 cd20488 410774 peptidase_C58-like C58 peptidase domain and and similar domains. This family contains C58 peptidases and similar proteins. C58 family peptidases are endopeptidases that also act as transamidases, attaching a lipid moiety to the newly exposed N-terminus of the substrate. These include the Pseudomonas avirulence (Avr) protein AvrPphB and the homologous protein from Yersinia known as YopT; both are involved in bacterial pathogenesis. These proteins have a papain-like fold and a distinct substrate-binding site. Also included is a cysteine-protease-like domain in Photorhabdus asymbiotica toxin PaTox that enhances cytotoxic effects of the toxin, and therefore is essential for full PaTox activity. The C58 cysteine protease domain is also found in Vibrio vulnificus biotype 3 multifunctional autoprocessing RTX toxin. It usually contains the characteristic Cys, His, Asp residues in the active site. Some members may lack this cataytic triad. 143 matched cddid_all.tbl CDD cd20489 cd20489 380446 cupin_HppE-like_C "hydroxypropylphosphonic acid epoxidase (HppE) and similar proteins, C-terminal cupin domain. This family includes HppE (hydroxypropylphosphonic acid epoxidase or HPP epoxidase or 2-hydroxypropylphosphonic acid epoxidase; EC 1.11.1.23), a non-heme mononuclear iron-dependent enzyme that catalyzes a unique epoxidation reaction as part of the biosynthetic pathway of the clinically important oxirane antibiotic fosfomycin. HppE uses a facial triad with two histidine ligands and one aspartic acid or glutamic acid, His2(Glu/Asp), to catalyze a variety of different reactions, including DNA repair and antibiotic biosynthesis. The C-terminal catalytic domain of HppE has a cupin fold that binds a divalent cation, whereas the N-terminal domain carries a helix-turn-helix (HTH) motif with putative DNA-binding helices. HppE converts (S)-2-hydroxypropyl-1-phosphonate (S-HPP) to the antibiotic fosfomycin [(1R,2S)-epoxypropylphosphonate] in an unusual 1,3-dehydrogenation of a secondary alcohol to an epoxide; it uses H2O2 as a co-substrate to abstract hydrogen (Ho) from C1 of S-HPP to initiate epoxide ring closure, using an iron(IV)-oxo complex as the Ho abstractor. HppE belongs to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization and its structure serves as a model for numerous proteins of unknown function, predicted to be transcription factors, containing an HTH motif at the N-terminus and a cupin domain at the C-terminus." 97 matched cddid_all.tbl CDD cd20490 cd20490 380447 cupin_HutD_C "histidine utilization protein HutD and related proteins, C-terminal cupin domain. This model represents the C-terminal domain of a bicupin protein HutD, involved in histidine utilization (Hut) in Pseudomonas species. Although a metal binding site is not found in Pseudomonas fluorescens (PfluHutD), a binding pocket for ligands is located in the middle of the N-terminal cupin domain near the metal binding sites; N-formyl-l-glutamate (FG, a Hut pathway intermediate) has been identified as a potential ligand in vivo. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 77 matched cddid_all.tbl CDD cd20491 cd20491 380448 cupin_KduI_C "Escherichia coli 5-keto-4-deoxyuronate isomerase (KduI) and related proteins, C-terminal cupin domain. 5-keto-4-deoxyuronate isomerase (KduI; EC 5.3.1.17), also called 5-dehydro-4-deoxy-D-glucuronate isomerase or 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase, catalyzes the interconversion of 5-keto-4-deoxyuronate and 2,5-diketo-3-dexoygluconate in the breakdown of pectin. KduI is a bicupin; this model describes the C-terminal cupin domain. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 108 matched cddid_all.tbl CDD cd20492 cd20492 380449 cupin_HQDO_large_C "hydroquinol 1,2-dioxygenase (HQDO) large subunit, C-terminal cupin domain. This model describes the C-terminal cupin domain of the large (or beta) subunit of hydroquinone 1,2-dioxygenase (HQDO), a heterotetramer of two alpha and two beta subunits of 19kDa and 38kDa, respectively. HQDO is a Fe(II) ring cleaving dioxygenase that is a key enzyme in the hydroquinone pathway of para-nitrophenol degradation, where it catalyzes the ring cleavage of hydroquinone to gamma-hydroxymuconic semialdehyde. Proteins in this family belong to the cupin superfamily with a conserved ""jelly roll-like"" beta-barrel fold capable of homodimerization." 100 matched cddid_all.tbl CDD cd20493 cd20493 380336 M34_ATLF_C-like C-terminal catalytically active domain of anthrax toxin lethal factor and similar domains; belongs to peptidase family M34. This subfamily includes the C-terminal catalytic domain of anthrax toxin lethal factor (ATLF; EC 3.4.24.83). ATLF and edema factor are enzyme components of anthrax toxin and are carried into the cell by a third component, the protective antigen (PA). ATLF is secreted by Bacillus anthracis to promote disease virulence through disruption of host signaling pathways. ATLF belongs to peptidase family M34 and has the hallmark metalloprotease motif HEXXH motif where the two His residues bind a single zinc atom, and the Glu has a catalytic role. ATLF is a highly selective protease whose major substrates are mitogen-activated protein kinase kinases (MKKs). MKKs are cleaved by ATLF near their N-termini, removing the docking sequence for the downstream cognate mitogen-activated protein kinase. Preferred amino acids around the cleavage site can be denoted BBBBxHxH, in which B denotes Arg or Lys, H denotes a hydrophobic amino acid, and x is any amino acid. At its N-terminus, ATLF has a related PABD domain which lacks the hallmark metalloprotease motif HEXXH. This subfamily also includes Bacillus thuringiensis Vip2Ac-like_2 which belongs to the Vip family of proteins that are secreted during the vegetative growth phase. 208 matched cddid_all.tbl CDD cd20494 cd20494 410775 C58_RtxA peptidase C58-like domain of cytotoxin RtxA and similar proteins. This subfamily includes the C58 peptidase-like domain of Vibrio vulnificus biotype 3 multifunctional autoprocessing RTX (MARTX) toxin, the primary virulence factor of V. vulnificus. MARTX has been shown to be an essential virulence factor contributing to highly inflammatory skin wounds with severe damage affecting every tissue layer. This toxin is a large single-polypeptide composed of repeat sequences that form a pore in eukaryotic cell plasma membranes for the translocation of centrally located effector domains. This C58 family cysteine protease domain usually contains the invariant C/H/D residues that form an active site triad, however, cysteine is not fully conserved in this group. 229 matched cddid_all.tbl CDD cd20495 cd20495 410776 C58_PaToxP-like peptidase C58 domain of Photorhabdus asymbiotica toxin PaTox and LifA/Efa1-related large cytotoxin, and similar proteins. This subfamily includes the cysteine protease domain of Photorhabdus asymbiotica toxin PaTox, a large virulence-associated multifunctional protein toxin. This domain is similar to AvrPphB protease found in Pseudomonas syringae, a C58 protease. Mutation studies show that this domain enhances cytotoxic effects of the toxin, and therefore is essential for full PaTox activity. Also included in this family is the enteropathogenic Escherichia coli (EPEC) factor for adherence/lymphocyte activation inhibitor (efa1/lifA) gene which is strongly associated with diarrhea. Efa1/LifA proteins are important for A/E lesion formation efficiency in EPEC strains lacking multiple effectors. This domain contains the invariant C/H/D residues conserved in the C58/YopT family. 179 matched cddid_all.tbl CDD cd20496 cd20496 410777 C58 peptidase C58 domain. The C58 family peptidases are endopeptidases that also act as transamidases, attaching a lipid moiety to the newly exposed N-terminus of the substrate. These include the Pseudomonas avirulence (Avr) protein AvrPphB and the homologous protein from Yersinia known as YopT; both are involved in bacterial pathogenesis. These proteins have a papain-like fold and a distinct substrate-binding site. The proteolytic activity of AvrPphB is essential for autoproteolytic cleavage of an AvrPphB precursor as well as for eliciting the hypersensitive response in plants. Yersinia pestis YopT cleaves the post-translationally modified Rho GTPases near their carboxyl termini, releasing them from the membrane. This leads to the disruption of actin cytoskeleton in host cells. Also included in this family is the Pseudomonas syringae HopN1 peptidase, a type III secretion system effector that can suppress plant cell death events in both compatible and incompatible interactions. All of these proteolytic activities are dependent upon the invariant C/H/D residues conserved in the C58/YopT family peptidase domain. 149 matched cddid_all.tbl CDD cd20497 cd20497 410778 C58_YopT-like peptidase C58 domain of YopT-like proteins, including Pseudomonas avirulence AvrPphB. This subfamily includes the C58 peptidase domain of the Pseudomonas avirulence (Avr) protein AvrPphB which is homologous to Yersinia effector known as YopT; both are involved in bacterial pathogenesis. These proteins have a papain-like fold and a distinct substrate-binding site. The proteolytic activity of AvrPphB is essential for autoproteolytic cleavage of an AvrPphB precursor as well as for eliciting the hypersensitive response in plants. Also included is the Ralstonia solanacearum type III effector protein RipT, a YopT-like cysteine protease. All of these proteolytic activities are dependent upon the invariant C/H/D residues conserved in the C58/YopT family peptidase domain. 185 matched cddid_all.tbl CDD cd20498 cd20498 410779 C58_YopT peptidase C58 domain of the YopT subfamily, including Yersinia pestis YopT and related proteins. This subfamily includes the plague organism Yersinia pestis cysteine protease YopT, an outer membrane protein. Y. pestis can disarm the host immune response by interfering with cell-signaling pathways; YopT cleaves post-translationally modified Rho GTPases near their carboxyl termini, releasing them from the membrane. This leads to the disruption of the actin cytoskeleton in host cells. YopT's proteolytic activity is dependent upon the invariant C/H/D residues conserved in the C58/YopT family peptidase domain. 211 matched cddid_all.tbl CDD cd20499 cd20499 410780 HopN1-like peptidase C58 domain of Pseudomonas syringae type III effector HopN1 and related proteins. This family includes the C58 peptidase domain of Pseudomonas syringae HopN1 peptidase, a type III secretion system effector that can suppress plant cell death events in both compatible and incompatible interactions. HopN1's proteolytic activity is dependent upon the invariant C/H/D residues conserved in the C58/YopT family peptidase domain. 216 matched cddid_all.tbl CDD cd20500 cd20500 410973 Peptidase_C80 peptidase C80 family. The peptidase C80 family includes self-cleaving proteins that are precursors of bacterial toxins such as the Vibrio cholerae RTX self-cleaving toxin, as well as the major virulence factors of Clostridium difficile multidomain toxins, TcdA and TcdB. These toxins contain a cysteine protease domain (CPD) that autoproteolytically releases a cytotoxic effector domain upon binding intracellular inositol hexakisphosphate. This family also contains filamentous hemagglutinin family cysteine protease C80 domains, that are located at the C-terminus. All domains in this family contain the characteristic Cys/His residues in the active site. Site-directed mutagenesis has identified functional residues Asp/His/Cys in Clostridium toxin B and His/Cys in cholera RTX toxin. 150 matched cddid_all.tbl CDD cd20501 cd20501 410974 C80_RtxA-like peptidase C80 cysteine binding domain of RTX toxin RtxA and related proteins. This peptidase C80 family includes the autoproteolytic cysteine protease domain (CPD) of Vibrio cholerae multifunctional autoprocessing repeats-in-toxin (MARTX) toxin that causes disassembly of the actin cytoskeleton and enhances V. cholerae colonization of the small intestine, possibly by facilitating evasion of phagocytic cells. The central region of this toxin is composed of several domains, including the actin cross-linking domain (ACD) that introduces lysine-glutamate cross-links between actin protomers, the Rho-inactivating domain (RID) that disables small Rho GTPases, and an autoprocessing cysteine protease domain (CPD). Within the cell, the CPD is activated by the binding of inositol hexakisphosphate to release individual effector domains of the toxin into the cytosol. The CPD contains the characteristic Cys/His residues in the active site. 194 matched cddid_all.tbl CDD cd20502 cd20502 410975 C80_toxinA_B-like Peptidase C80 cysteine binding domain of Clostridium difficile toxins A and B, and related proteins. This peptidase C80 family includes the major virulence factors of Clostridium difficile multidomain toxins TcdA and TcdB. These large homologous toxins contain several distinct domains including a cysteine protease domain (CPD) that autoproteolytically releases a cytotoxic effector domain upon binding of intracellular inositol hexakisphosphate. C. difficile is a major cause of intestinal tissue damage and inflammation, and TcdA is generally more inflammatory whereas TcdB is more cytotoxic; studies show that the CPD is an internal regulator of the proinflammatory activity. Site-directed mutagenesis has identified functional residues Asp/His/Cys in Clostridium toxin B. 209 matched cddid_all.tbl CDD cd20503 cd20503 410976 C80_adhesin-like peptidase C80 domains found in filamentous hemagglutinin or adhesin, and other similar proteins. This peptidase C80 family includes the cysteine-binding domain (CPD) of several large, repetitive bacterial exoproteins involved in heme utilization or adhesion and many typically having CPD repeats as well as regions rich in repeats. Many members of this family have been designated adhesins or filamentous haemagglutinins. The CPD contains the characteristic Asp/Cys/His residues found in Clostridium toxin B active site. 156 matched cddid_all.tbl CDD cd20504 cd20504 410208 CYCLIN_CCNA_rpt1 first cyclin box found in cyclin-A (CCNA) family. The CCNA family includes two A-type cyclins, CCNA1 and CCNA2. CCNA1 may primarily function in the control of the germline meiotic cell cycle and additionally in the control of mitotic cell cycle in some somatic cells. CCNA2 controls both the G1/S and the G2/M transition phases of the cell cycle. Members in this family contain two cyclin boxes. The model corresponds to the first one. The cyclin box is a protein binding domain. 128 matched cddid_all.tbl CDD cd20505 cd20505 410209 CYCLIN_CCNA_rpt2 second cyclin box found in cyclin-A (CCNA) family. The CCNA family includes two A-type cyclins, CCNA1 and CCNA2. CCNA1 may primarily function in the control of the germline meiotic cell cycle and additionally in the control of mitotic cell cycle in some somatic cells. CCNA2 controls both the G1/S and the G2/M transition phases of the cell cycle. Members in this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 110 matched cddid_all.tbl CDD cd20506 cd20506 410210 CYCLIN_AtCycA-like_rpt2 second cyclin box found in Arabidopsis thaliana A-type cyclins (CycAs) and similar proteins. Plant A-type cyclins (CycAs) correspond to a group of G2/mitotic-specific cyclins that are functionally linked to S- and M-phases of the mitotic cycle, which predicts their involvement also in meiosis. CycAs associate with their partner cyclin-dependent kinases (CDKs) to trigger the kinase activity. They contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 111 matched cddid_all.tbl CDD cd20507 cd20507 410211 CYCLIN_CCNB1-like_rpt1 first cyclin box found in cyclin-B1 (CCNB1)-like family. The CCNB1-like family includes two B-type cyclins, CCNB1 and CCNB2, both of which are essential for the control of the cell cycle at the G2/M (mitosis) transition. Members in this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 130 matched cddid_all.tbl CDD cd20508 cd20508 410212 CYCLIN_CCNB3_rpt1 first cyclin box found in G2/mitotic-specific cyclin-B3 (CCNB3) and similar proteins. CCNB3 is a mitotic B-type cyclin that promotes the metaphase-anaphase transition. It controls anaphase onset independent of spindle assembly checkpoint in meiotic oocytes. CCNB3 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 142 matched cddid_all.tbl CDD cd20509 cd20509 410213 CYCLIN_CCNB1-like_rpt2 second cyclin box found in cyclin-B1 (CCNB1)-like family. The CCNB1-like family includes two B-type cyclins, CCNB1 and CCNB2, both of which are essential for the control of the cell cycle at the G2/M (mitosis) transition. Members in this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 111 matched cddid_all.tbl CDD cd20510 cd20510 410214 CYCLIN_CCNB3_rpt2 second cyclin box found in G2/mitotic-specific cyclin-B3 (CCNB3) and similar proteins. CCNB3 is a mitotic B-type cyclin that promotes the metaphase-anaphase transition. It controls anaphase onset independent of spindle assembly checkpoint in meiotic oocytes. CCNB3 contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 115 matched cddid_all.tbl CDD cd20511 cd20511 410215 CYCLIN_AtCycB-like_rpt2 second cyclin box found in Arabidopsis thaliana B-type cyclins (CycBs) and similar proteins. Plant B-type cyclins (CycBs) correspond to a group of G2/mitotic-specific cyclins that are functionally linked to S- and M-phases of the mitotic cycle, which predicts their involvement also in meiosis. CycBs associate with their partner cyclin-dependent kinases (CDKs) to trigger the kinase activity. They contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 117 matched cddid_all.tbl CDD cd20512 cd20512 410216 CYCLIN_CLBs_yeast_rpt2 second cyclin box found in yeast B-type cyclins. The family includes Saccharomyces cerevisiae G2/mitotic-specific cyclins 1-4 (ScCLB1-4), S-phase entry cyclins 5-6 (ScCLB5-6), and Schizosaccharomyces pombe G2/mitotic-specific cyclins, cig1, cig2 and cdc13. ScCLB1-4 are essential for the control of the cell cycle at the G2/M (mitosis) transition. They interact with the CDC2 protein kinase to form maturation promoting factor (MPF). ScCLB5-6 interact with CDC28 and are involved in DNA replication in Saccharomyces cerevisiae. ScCLB5 is required for efficient progression through S phase and possibly for the normal progression through meiosis. ScCLB6 is involved in G1/S and or S phase progression. Cig1 is required for efficient passage of the G1/S transition. Cig2 and cdc13 are essential for the control of the cell cycle at the G2/M and G1/S (mitosis) transition. They interact with the cdc2 protein kinase to form MPF. Members in this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 116 matched cddid_all.tbl CDD cd20513 cd20513 410217 CYCLIN_CCNC_rpt1 first cyclin box found in cyclin-C (CCNC) and similar proteins. CCNC, also termed CycC, or SRB11, is a component of the Mediator complex, a coactivator involved in regulated gene transcription of nearly all RNA polymerase II-dependent genes. It mediates stress-induced mitochondrial fission and apoptosis. CCNC contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 101 matched cddid_all.tbl CDD cd20514 cd20514 410218 CYCLIN_CCNC_rpt2 second cyclin box found in cyclin-C (CCNC) and similar proteins. CCNC, also termed CycC, or SRB11, is a component of the Mediator complex, a coactivator involved in regulated gene transcription of nearly all RNA polymerase II-dependent genes. It mediates stress-induced mitochondrial fission and apoptosis. CCNC contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 92 matched cddid_all.tbl CDD cd20515 cd20515 410219 CYCLIN_CCND_rpt1 first cyclin box found in cyclin-D (CCND) family. The CCND family includes three mitogen-induced D-type cyclins, CCND1, CCND2 and CCND3, which function as regulatory subunits of the cyclin-dependent kinases CDK4 and CDK6, that drive progression through the G1 phase of the cell cycle. Members in this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 150 matched cddid_all.tbl CDD cd20516 cd20516 410220 CYCLIN_CCND_rpt2 second cyclin box found in cyclin-D (CCND) family. The CCND family includes three mitogen-induced D-type cyclins, CCND1, CCND2 and CCND3, which function as regulatory subunits of the cyclin-dependent kinases CDK4 and CDK6, that drive progression through the G1 phase of the cell cycle. Members in this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 98 matched cddid_all.tbl CDD cd20517 cd20517 410221 CYCLIN_vCyC_rpt1 first cyclin box found in viral cyclin (v-cyclin). v-Cyclin modulates host cell cycle progression and apoptotic signaling pathways. It forms an active kinase complex with cellular CDK6, a cellular cyclin-dependent kinase known to interact with cellular type D cyclins. v-Cyclin belongs to Cyclin D subfamily. It contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 99 matched cddid_all.tbl CDD cd20518 cd20518 410222 CYCLIN_vCyC_rpt2 second cyclin box found in viral cyclin (v-cyclin). v-Cyclin modulates host cell cycle progression and apoptotic signaling pathways. It forms an active kinase complex with cellular CDK6, a cellular cyclin-dependent kinase known to interact with cellular type D cyclins. v-Cyclin belongs to Cyclin D subfamily. It contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 100 matched cddid_all.tbl CDD cd20519 cd20519 410223 CYCLIN_CCNE_rpt1 first cyclin box found in G1/S-specific cyclin-E (CCNE) family. The CCNE family includes two E-type cyclins, CCNE1 and CCNE2. CCNE1 is essential for the control of the cell cycle at the G1/S (start) transition. It interacts with CDK2 protein kinase to form a serine/threonine kinase holoenzyme complex. CCNE2 is essential for the control of the cell cycle at the late G1 and early S phase. It interacts with the CDK2 (in vivo) and CDK3 (in vitro) protein kinases to form a serine/threonine kinase holoenzyme complexes. Members of this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 131 matched cddid_all.tbl CDD cd20520 cd20520 410224 CYCLIN_CCNE_rpt2 second cyclin box found in G1/S-specific cyclin-E (CCNE) family. The CCNE family includes two E-type cyclins, CCNE1 and CCNE2. CCNE1 is essential for the control of the cell cycle at the G1/S (start) transition. It interacts with CDK2 protein kinase to form a serine/threonine kinase holoenzyme complex. CCNE2 is essential for the control of the cell cycle at the late G1 and early S phase. It interacts with the CDK2 (in vivo) and CDK3 (in vitro) protein kinases to form serine/threonine kinase holoenzyme complexes. Members in this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 105 matched cddid_all.tbl CDD cd20521 cd20521 410225 CYCLIN_CCNF_rpt1 first cyclin box found in G2/mitotic-specific cyclin-F (CCNF) and similar proteins. CCNF, also termed F-box only protein 1 (FBXO1), is a substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of CP110 during G2 phase, thereby acting as an inhibitor of centrosome reduplication. It is the largest among all cyclins and oscillates in the cell cycle like other cyclins. CCNF contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 95 matched cddid_all.tbl CDD cd20522 cd20522 410226 CYCLIN_CCNF_rpt2 second cyclin box found in G2/mitotic-specific cyclin-F (CCNF) and similar proteins. CCNF, also termed F-box only protein 1 (FBXO1), is a substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of CP110 during G2 phase, thereby acting as an inhibitor of centrosome reduplication. It is the largest among all cyclins and oscillates in the cell cycle like other cyclins. CCNF contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 112 matched cddid_all.tbl CDD cd20523 cd20523 410227 CYCLIN_CCNG cyclin box found in the cyclin-G (CCNG) family. The CCNG family includes two cyclins, CCNG1 and CCNG2. CCNG1 is the only cyclin that has either positive or negative effects on cell growth. It is associated with G2/M phase arrest in response to DNA damage. It is also involved in the development of human carcinoma. CCNG2 may play a role in growth regulation and in negative regulation of cell cycle progression. It has been identified as a tumor suppressor in several cancers. Members of this family contain one cyclin box. The cyclin box is a protein binding domain. 94 matched cddid_all.tbl CDD cd20524 cd20524 410228 CYCLIN_CCNH_rpt1 first cyclin box found in cyclin-H (CCNH) and similar proteins. CCNH, also called MO15-associated protein, p34, or p37, is normally associated with the cyclin-dependent kinase cdk7, the catalytic subunit of the CDK-activating kinase (CAK) enzymatic complex. CCNH contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 150 matched cddid_all.tbl CDD cd20525 cd20525 410229 CYCLIN_CCNH_rpt2 second cyclin box found in cyclin-H (CCNH) and similar proteins. CCNH, also called MO15-associated protein, p34, or p37, is normally associated with the cyclin-dependent kinase cdk7, the catalytic subunit of the CDK-activating kinase (CAK) enzymatic complex. CCNH contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 126 matched cddid_all.tbl CDD cd20526 cd20526 410230 CYCLIN_CCNI-like cyclin box found in cyclin-I (CCNI) and similar proteins. CCNI is an atypical cyclin because it is most abundant in post-mitotic cells. It is involved in various biological processes, such as cell survival, angiogenesis, cell differentiation, and cell cycle progression. CCNI contains a typical cyclin box near the N-terminus and a PEST sequence near the C-terminus. The cyclin box is a protein binding domain. 99 matched cddid_all.tbl CDD cd20528 cd20528 410231 CYCLIN_CCNJ-like_rpt1 first cyclin box found in cyclin-J (CCNJ) family. The CCNJ family includes two cyclins, CCNJ and CCNJ-like. CCNJ may regulate the cell cycle or transcription. Members of this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 103 matched cddid_all.tbl CDD cd20529 cd20529 410232 CYCLIN_CCNJ-like_rpt2 second cyclin box found in cyclin-J (CCNJ) family. The CCNJ family includes two cyclins, CCNJ and CCNJ-like. CCNJ may regulate the cell cycle or transcription. Members of this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 101 matched cddid_all.tbl CDD cd20530 cd20530 410233 CYCLIN_CCNK_rpt1 first cyclin box found in cyclin-K (CCNK) and similar proteins. CCNK is a novel RNA polymerase II-associated C-type cyclin possessing both carboxy-terminal domain kinase and Cdk-activating kinase activity. It is a regulatory subunit of cyclin-dependent kinases that mediates the activation of these target kinases. It plays a role in transcriptional regulation by controlling the phosphorylation of the C-terminal domain (CTD) of the large subunit of RNA polymerase II (POLR2A). CCNK contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 115 matched cddid_all.tbl CDD cd20531 cd20531 410234 CYCLIN_CCNK_rpt2 second cyclin box found in cyclin-K (CCNK) and similar proteins. CCNK is a novel RNA polymerase II-associated C-type cyclin possessing both carboxy-terminal domain kinase and Cdk-activating kinase activity. It is a regulatory subunit of cyclin-dependent kinases that mediates the activation of these target kinases. It plays a role in transcriptional regulation by controlling the phosphorylation of the C-terminal domain (CTD) of the large subunit of RNA polymerase II (POLR2A). CCNK contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 101 matched cddid_all.tbl CDD cd20532 cd20532 410235 CYCLIN_CCNL_rpt1 first cyclin box found in cyclin-L (CCNL) family. The CCNL family includes two cyclins, CCNL1 and CCNL2. CCNL1 is involved in the regulation of RNA polymerase II (pol II) transcription. It functions in association with cyclin-dependent kinases (CDKs). CCNL2 is a novel RNA polymerase II-associated cyclin involved in pre-mRNA splicing. It may induce cell death, possibly by acting on the transcription and RNA processing of apoptosis-related factors. Members of this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 127 matched cddid_all.tbl CDD cd20533 cd20533 410236 CYCLIN_CCNL_rpt2 second cyclin box found in cyclin-L (CCNL) family. The CCNL family includes two cyclins, CCNL1 and CCNL2. CCNL1 is involved in regulation of RNA polymerase II (pol II) transcription. It functions in association with cyclin-dependent kinases (CDKs). CCNL2 is a novel RNA polymerase II-associated cyclin involved in pre-mRNA splicing. It may induce cell death, possibly by acting on the transcription and RNA processing of apoptosis-related factors. Members of this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 92 matched cddid_all.tbl CDD cd20534 cd20534 410237 CYCLIN_CCNM_CCNQ_rpt1 first cyclin box found in cyclin-M (CCNM) family. The CCNM family proteins, also called ancient conserved domain proteins (ACDPs), are evolutionarily conserved Mg2+ transporters. CCNM, also called cyclin-Q (CCNQ), or CDK10-activating cyclin, or cyclin-related protein FAM58A, associates with CDK10 to promote its kinase activity. Members of this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 110 matched cddid_all.tbl CDD cd20535 cd20535 410238 CYCLIN_CCNM_CCNQ_rpt2 second cyclin box found in cyclin-M (CCNM) family. The CCNM family proteins, also called ancient conserved domain proteins (ACDPs), are evolutionarily conserved Mg2+ transporters. CCNM, also called cyclin-Q (CCNQ), or CDK10-activating cyclin, or cyclin-related protein FAM58A, associates with CDK10 to promote its kinase activity. Members of this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 104 matched cddid_all.tbl CDD cd20536 cd20536 410239 CYCLIN_CCNO_rpt1 first cyclin box found in cyclin-O (CCNO) and similar proteins. CCNO is specifically required for generation of multiciliated cells, possibly by promoting a cell cycle state compatible with centriole amplification and maturation. It acts downstream of MCIDAS (multiciliate differentiation and DNA synthesis associated cell cycle protein) to promote mother centriole amplification and maturation in preparation for apical docking. CCNO is involved in the activation of cyclin-dependent kinase 2. CCNO contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 93 matched cddid_all.tbl CDD cd20537 cd20537 410240 CYCLIN_CCNO-like_rpt2 second cyclin box found in cyclin-O (CCNO) and similar proteins. This subfamily is composed of CCNO and similar proteins including Schizosaccharomyces pombe meiosis-specific cyclin rem1, Drosophila melanogaster G2/mitotic-specific cyclin-A (CCNA), and Candida albicans G1/S-specific cyclin CCN1, among others. Rem1 is required for pre-meiotic DNA synthesis and S phase progression. CCNA is essential for the control of the cell cycle at the G2/M (mitosis) transition. CCN1 is essential for the control of the cell cycle at the G1/S (start) transition and for maintenance of filamentous growth. CCNO is specifically required for generation of multiciliated cells, possibly by promoting a cell cycle state compatible with centriole amplification and maturation. It is involved in the activation of cyclin-dependent kinase 2. Members of this subfamily contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 91 matched cddid_all.tbl CDD cd20538 cd20538 410241 CYCLIN_CCNT_rpt1 first cyclin box found in cyclin-T (CCNT) family. The CCNT family includes two C-type cyclins, cyclin-T1 (CCNT1) and cyclin-T2 (CCNT2), both of which are regulatory subunits of the cyclin-dependent kinase pair (CDK9/cyclin-T) complex, also called positive transcription elongation factor B (P-TEFb), which is proposed to facilitate the transition from abortive to productive elongation by phosphorylating the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNA Pol II). Members of this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 137 matched cddid_all.tbl CDD cd20539 cd20539 410242 CYCLIN_CCNT_rpt2 second cyclin box found in cyclin-T (CCNT) family. The CCNT family includes two C-type cyclins, cyclin-T1 (CCNT1) and cyclin-T2 (CCNT2), both of which are regulatory subunits of the cyclin-dependent kinase pair (CDK9/cyclin-T) complex, also called positive transcription elongation factor B (P-TEFb), which is proposed to facilitate the transition from abortive to productive elongation by phosphorylating the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNA Pol II). Members in this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 92 matched cddid_all.tbl CDD cd20540 cd20540 410243 CYCLIN_CCNY_like cyclin box found in cyclin-Y (CCNY) family. The CCNY family includes two cyclins, CCNY and CCNY-like protein 1 (CCNYL1). They can enhance Wnt/beta-catenin signaling in mitosis. CCNY, also called Cyc-Y, cyclin box protein 1 (CBCP1), cyclin fold protein 1 (CFP1), or cyclin-X (CCNX), is a key cell cycle regulator that acts as a growth factor sensor to integrate extracellular signals with the cell cycle machinery. It is a positive regulatory subunit of the cyclin-dependent kinases CDK14/PFTK1 and CDK16. It acts as a cell-cycle regulator of Wnt signaling pathway during G2/M phase by recruiting CDK14/PFTK1 to the plasma membrane and promoting phosphorylation of LRP6, leading to the activation of the Wnt signaling pathway. Members of this family contain one cyclin box. The cyclin box is a protein binding domain. 97 matched cddid_all.tbl CDD cd20541 cd20541 410244 CYCLIN_CNTD1 cyclin box found in Cyclin N-terminal domain-containing protein 1 (CNTD1) and similar proteins. CNTD1 is a cyclin-related protein critical for meiotic crossover maturation and deselection of excess precrossover sites. CNTD1 contains one cyclin box. The cyclin box is a protein binding domain. 127 matched cddid_all.tbl CDD cd20542 cd20542 410245 CYCLIN_CNTD2 cyclin box found in Cyclin N-terminal domain-containing protein 2 (CNTD2) and similar proteins. CNTD2 is an atypical cyclin upregulated in human cancer tissues. It promotes cell proliferation and migration, as well as increases tumor growth in vivo. It can function as a prognostic factor and drug target. CNTD2 contains one cyclin box. The cyclin box is a protein binding domain. 96 matched cddid_all.tbl CDD cd20543 cd20543 410246 CYCLIN_AtCycD-like_rpt1 first cyclin box found in plant cyclin-delta family. This subfamily is composed of plant delta family cyclins, including a group of G1/S-specific D-type cyclins from Arabidopsis thaliana which may activate the cell cycle in the root apical meristem (RAM) and promote embryonic root (radicle) protrusion. Members of this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 99 matched cddid_all.tbl CDD cd20544 cd20544 410247 CYCLIN_AtCycD-like_rpt2 second cyclin box found in plant cyclin-delta family. This subfamily is composed of plant delta family cyclins, including a group of G1/S-specific D-type cyclins from Arabidopsis thaliana which may activate the cell cycle in the root apical meristem (RAM) and promote embryonic root (radicle) protrusion. Members of this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 90 matched cddid_all.tbl CDD cd20545 cd20545 410248 CYCLIN_SpCG1C-like_rpt1 first cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1) and similar proteins. Cyclin pch1 is essential for progression through the whole cell cycle. It is a homolog of cyclin T; it forms a heterodimer with its partner kinase, cyclin-dependent kinase 9 (CDK9), that can phosphorylate both the pol II C-terminal domain (CTD) and the CTD of transcription elongation factor Spt5. Yeast Cdk9/Pch1, with mRNA capping enzyme Pct1, may also form an elongation checkpoint for mRNA quality control. Members of this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 116 matched cddid_all.tbl CDD cd20546 cd20546 410249 CYCLIN_SpCG1C_ScCTK2-like_rpt2 second cyclin box found in Schizosaccharomyces pombe cyclin C homolog 1 (pch1), Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2), and similar proteins. Cyclin pch1 is essential for progression through the whole cell cycle. It is a homolog of cyclin T; it forms a heterodimer with its partner kinase, cyclin-dependent kinase 9 (CDK9), that can phosphorylate both the pol II C-terminal domain (CTD) and the CTD of transcription elongation factor Spt5. Yeast Cdk9/Pch1, with mRNA capping enzyme Pct1, may also form an elongation checkpoint for mRNA quality control. CTK2, also called CTD kinase subunit beta, CTDK-I subunit beta, or CTD kinase 38 kDa subunit, is the cyclin subunit of the CTDK-I complex, which hyperphosphorylates the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit. This group also includes yeast RNA polymerase II holoenzyme cyclin-like subunit, a component of the SRB8-11 complex, a regulatory module of the Mediator complex which is involved in regulation of basal and activated RNA polymerase II-dependent transcription. Members of this family contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 97 matched cddid_all.tbl CDD cd20547 cd20547 410250 CYCLIN_ScCTK2-like_rpt1 first cyclin box found in Saccharomyces cerevisiae CTD kinase subunit 2 (ScCTK2) and similar proteins. CTK2, also called CTD kinase subunit beta, CTDK-I subunit beta, or CTD kinase 38 kDa subunit, is the cyclin subunit of the CTDK-I complex, which hyperphosphorylates the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit. CTK2 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 110 matched cddid_all.tbl CDD cd20548 cd20548 410251 CYCLIN_RB-like cyclin box found in retinoblastoma-associated protein (RB) family. The RB family includes retinoblastoma-associated protein (RB), and two retinoblastoma-like proteins, RBL1 and RBL2. RB, also called p105-Rb, pRb, or pp110, is a key regulator of entry into cell division, and also acts as a tumor suppressor. It promotes G0-G1 transition when phosphorylated by CDK3/cyclin-C. It also acts as a transcription repressor of E2F1 target genes. RB is directly involved in heterochromatin formation by maintaining overall chromatin structure. It recruits and targets histone methyltransferases SUV39H1, KMT5B and KMT5C, leading to epigenetic transcriptional repression. RBL1 and RBL2 are also key regulators of entry into cell division. RBL1 and RBL2 recruit and target histone methyltransferases KMT5B and KMT5C, leading to epigenetic transcriptional repression. They control histone H4 'Lys-20' trimethylation and probably act as transcription repressors by recruiting chromatin-modifying enzymes to promoters. They may also act as tumor suppressors. Members of this family contain one cyclin box. The cyclin box is a protein binding domain. 122 matched cddid_all.tbl CDD cd20549 cd20549 410252 CYCLIN_TFIIB_archaea_like_rpt1 first cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar proteins. Archaeal TFIIB stabilizes TATA-binding protein (TBP) binding to an archaeal box-A promoter. It is also responsible for recruiting RNA polymerase II to the pre-initiation complex (DNA-TBP-TFIIB). TFIIB contains two cyclin boxes. This model corresponds to the first one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB. 99 matched cddid_all.tbl CDD cd20550 cd20550 410253 CYCLIN_TFIIB_archaea_like_rpt2 second cyclin box found in archaeal transcription initiation factor IIB (TFIIB) and similar proteins. Archaeal TFIIB stabilizes TATA-binding protein (TBP) binding to an archaeal box-A promoter. It is also responsible for recruiting RNA polymerase II to the pre-initiation complex (DNA-TBP-TFIIB). TFIIB contains two cyclin boxes. This model corresponds to the second one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB. 87 matched cddid_all.tbl CDD cd20551 cd20551 410254 CYCLIN_TFIIB_rpt1 first cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins. TFIIB, also called B-related factor 2 (BRF-2) or S300-II, is a general transcription factor that plays a role in transcription initiation by RNA polymerase II (Pol II). It is involved in the pre-initiation complex (PIC) formation and Pol II recruitment at promoter DNA. TFIIB contains two cyclin boxes. This model corresponds to the first one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB. 88 matched cddid_all.tbl CDD cd20552 cd20552 410255 CYCLIN_TFIIB_rpt2 second cyclin box found in transcription initiation factor IIB (TFIIB) and similar proteins. TFIIB, also called B-related factor 2 (BRF-2) or S300-II, is a general transcription factor that plays a role in transcription initiation by RNA polymerase II (Pol II). It is involved in the pre-initiation complex (PIC) formation and Pol II recruitment at promoter DNA. TFIIB contains two cyclin boxes. This model corresponds to the second one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIB. 97 matched cddid_all.tbl CDD cd20553 cd20553 410256 CYCLIN_TFIIIB90_rpt1 first cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar proteins. TFIIIB90, also called B-related factor 1 (BRF-1), or TATA box-binding protein-associated factor, RNA polymerase III, subunit 2 (TAF3B2), is a general activator of RNA polymerase which utilizes different TFIIIB complexes at structurally distinct promoters. TFIIIB90 contains two cyclin boxes. This model corresponds to the first one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIIB90. 91 matched cddid_all.tbl CDD cd20554 cd20554 410257 CYCLIN_TFIIIB90_rpt2 second cyclin box found in transcription factor IIIB 90 kDa subunit (TFIIIB90) and similar proteins. TFIIIB90, also called B-related factor 1 (BRF-1), or TATA box-binding protein-associated factor, RNA polymerase III, subunit 2 (TAF3B2), is a general activator of RNA polymerase which utilizes different TFIIIB complexes at structurally distinct promoters. TFIIIB90 contains two cyclin boxes. This model corresponds to the second one. The cyclin box fold is generally a protein binding domain, but binds DNA in TFIIIB90. 92 matched cddid_all.tbl CDD cd20555 cd20555 410258 CYCLIN_BRF2 cyclin box found in B-related factor 2 (BRF-2) and similar proteins. BRF-2, also called transcription factor IIIB 50 kDa subunit (TFIIIB50), or BRFU, is a general activator of RNA polymerase (Pol) III transcription and is required for Pol III transcription of genes with promoter elements upstream of the initiation sites. It recruits Pol III to type III gene-external promoters, including the U6 spliceosomal RNA and selenocysteine tRNA genes. BRF-2 contains one cyclin box. The cyclin box fold is generally a protein binding domain, but binds DNA in BRF-2. 97 matched cddid_all.tbl CDD cd20556 cd20556 410259 CYCLIN_CABLES cyclin box found in CDK5 and ABL1 enzyme substrate (CABLES) family. The CABLES family includes CABLES1 and CABLES2. CABLES1, also called interactor with CDK3 1 (Ik3-1), is a cyclin-dependent kinase binding protein that enhances cyclin-dependent kinase tyrosine phosphorylation by non-receptor tyrosine kinases, such as that of CDK5 by activated ABL1, which leads to increased CDK5 activity and is critical for neuronal development, and that of CDK2 by WEE1, which leads to decreased CDK2 activity and growth inhibition. CABLES2, also called interactor with CDK3 2 (Ik3-2), acts as a proapoptotic factor involved in both p53-mediated and p53-independent apoptotic pathways. Both, CABLES1 and CABLES2, contain one cyclin box. The cyclin box is a protein binding domain. 119 matched cddid_all.tbl CDD cd20557 cd20557 410260 CYCLIN_ScPCL1-like cyclin box found in Saccharomyces cerevisiae G1/S-specific cyclin PCL1, PCL2 and similar proteins. The family includes a group of cyclin-like proteins that interact with the Pho85 cyclin-dependent kinase, such as Saccharomyces cerevisiae G1/S-specific cyclin PCL1, PCL2, PCL9 and their vertebrate counterparts, cyclin Pas1/PHO80 domain-containing protein 1 (CNPPD1). PCL1 (also called PHO85 cyclin-1, or cyclin HCS26) and PCL2 (also called PHO85 cyclin-1, or cyclin HCS26 homolog) are G1/S-specific cyclin partners of the cyclin-dependent kinase (CDK) PHO85. They are essential for the control of the cell cycle at the G1/S (start) transition. The PCL1-PHO85 cyclin-CDK holoenzyme is involved in phosphorylation of the CDK inhibitor (CKI) SIC1, which is required for its ubiquitination and degradation, releasing repression of b-type cyclins and promoting exit from mitosis. Together with cyclin PCL2, it positively controls degradation of sphingoid long chain base kinase LCB4. PCL1-PHO85 also phosphorylates HMS1, NCP1 and NPA3, which may all have a role in mitotic exit. PCL2-PHO85 also phosphorylates RVS167, linking cyclin-CDK activity with organization of the actin cytoskeleton. PCL9 is an M/G1-specific cyclin partner of the cyclin-dependent kinase (CDK) PHO85. It may have a role in bud site selection in the G1 phase. The family also includes cyclin Pas1/PHO80 domain-containing protein 1 (CNPPD1) and similar proteins. Their biological functions remain unclear. Members of this family contain one cyclin box. The cyclin box is a protein binding domain. 94 matched cddid_all.tbl CDD cd20558 cd20558 410261 CYCLIN_ScPCL7-like cyclin box found in Saccharomyces cerevisiae PHO85 cyclin-7 (ScPCL7) and similar proteins. ScPCL7, also called PHO85-associated protein 1, is a cyclin partner of the cyclin-dependent kinase (CDK) PHO85. Together with cyclin PCL6, ScPCL7 controls glycogen phosphorylase and glycogen synthase activities in response to nutrient availablility. This family also includes Schizosaccharomyces pombe PHO85 cyclin-like protein Psl1 (SpPsl1) and Arabidopsis thaliana PHO80-like proteins, P-type cyclins (CYCPs). SpPsl1 is the cyclin partner of the CDK pef1 (PHO85 homolog). CYCPs may be involved in cell division, cell differentiation, and the nutritional status of the cell in Arabidopsis thaliana. Members of this family contain one cyclin box. The cyclin box is a protein binding domain. 101 matched cddid_all.tbl CDD cd20559 cd20559 410262 CYCLIN_ScCLN_like cyclin box found in Saccharomyces cerevisiae G1/S-specific cyclins (ScCLNs) and similar proteins. ScCLNs, including ScCLN1-3, are essential for the control of the cell cycle at the G1/S (start) transition in Saccharomyces. ScCLN1 and ScCLN2 interact with the CDC28 protein kinase to form maturation promoting factor (MPF). ScCLN3 may be an upstream activator of the G1 cyclins that directly initiate G1/S transition. This family also includes Schizosaccharomyces pombe cyclin puc1, which contributes to negative regulation of the timing of sexual development in fission yeast, and functions at the transition between cycling and non-cycling cells. It interacts with protein kinase A. Members of this family contain one cyclin box. The cyclin box is a protein binding domain. 95 matched cddid_all.tbl CDD cd20560 cd20560 410263 CYCLIN_CCNA1_rpt1 first cyclin box found in cyclin-A1 (CCNA1). CCNA1 may primarily function in the control of the germline meiotic cell cycle and additionally in the control of mitotic cell cycle in some somatic cells. CCNA1 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 163 matched cddid_all.tbl CDD cd20561 cd20561 410264 CYCLIN_CCNA2_rpt1 first cyclin box found in cyclin-A2 (CCNA2) and similar proteins. CCNA2 controls both the G1/S and the G2/M transition phases of the cell cycle. It is significantly over-expressed in various cancer types, and can be used as a prognostic biomarker for estrogen receptor positive (ER+) breast cancer and tamoxifen resistance. CCNA2 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 131 matched cddid_all.tbl CDD cd20562 cd20562 410265 CYCLIN_AtCycA_like_rpt1 first cyclin box found in Arabidopsis thaliana A-type cyclins (CycAs) and similar proteins. Plant A-type cyclins (CycAs) correspond to a group of G2/mitotic-specific cyclins that are functionally linked to S- and M-phases of the mitotic cycle, which predicts their involvement also in meiosis. CycAs associate with their partner cyclin-dependent kinases (CDKs) to trigger the kinase activity. They contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 136 matched cddid_all.tbl CDD cd20563 cd20563 410266 CYCLIN_CCNA1_rpt2 second cyclin box found in cyclin-A1 (CCNA1) and similar proteins. CCNA1 may primarily function in the control of the germline meiotic cell cycle and additionally in the control of mitotic cell cycle in some somatic cells. CCNA1 contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 123 matched cddid_all.tbl CDD cd20564 cd20564 410267 CYCLIN_CCNA2_rpt2 second cyclin box found in cyclin-A2 (CCNA2) and similar proteins. CCNA2 controls both the G1/S and the G2/M transition phases of the cell cycle. It is significantly overexpressed in various cancer types, and can be used as a prognostic biomarker for estrogen receptor positive (ER+) breast cancer and tamoxifen resistance. CCNA2 contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 110 matched cddid_all.tbl CDD cd20565 cd20565 410268 CYCLIN_CCNB1_rpt1 first cyclin box found in G2/mitotic-specific cyclin-B1 (CCNB1). CCNB1 is essential for the control of the cell cycle at the G2/M (mitosis) transition. It is required for embryo development. Over-expression of human CCNB1 has been found in numerous cancers and has been associated with tumor aggressiveness. CCNB1 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 129 matched cddid_all.tbl CDD cd20566 cd20566 410269 CYCLIN_CCNB2_rpt1 first cyclin box found in G2/mitotic-specific cyclin-B2 (CCNB2) and similar proteins. CCNB2 is essential for the control of the cell cycle at the G2/M (mitosis) transition. It is required for progression through meiosis. CCNB2 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 133 matched cddid_all.tbl CDD cd20567 cd20567 410270 CYCLIN_AtCycB-like_rpt1 first cyclin box found in Arabidopsis thaliana B-type cyclins (CycBs) and similar proteins. Plant B-type cyclins (CycBs) correspond to a group of G2/mitotic-specific cyclins that are functionally linked to S- and M-phases of the mitotic cycle, which predicts their involvement also in meiosis. CycBs associate with their partner cyclin-dependent kinases (CDKs) to trigger the kinase activity. They contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 147 matched cddid_all.tbl CDD cd20568 cd20568 410271 CYCLIN_CLBs_yeast_rpt1 first cyclin box found in yeast B-type cyclins. This subfamily includes Saccharomyces cerevisiae G2/mitotic-specific cyclins 1-4 (ScCLB1-4), S-phase entry cyclins 5-6 (ScCLB5-6), and Schizosaccharomyces pombe G2/mitotic-specific cyclins, cig1, cig2 and cdc13. ScCLB1-4 are essential for the control of the cell cycle at the G2/M (mitosis) transition. They interact with the CDC2 protein kinase to form maturation promoting factor (MPF). ScCLB5-6 interact with CDC28 and are involved in DNA replication in Saccharomyces cerevisiae. ScCLB5 is required for efficient progression through S phase and possibly for the normal progression through meiosis. ScCLB6 is involved in G1/S and or S phase progression. Cig1 is required for efficient passage of the G1/S transition. Cig2 and cdc13 are essential for the control of the cell cycle at the G2/M and G1/S (mitosis) transitions. They interact with the cdc2 protein kinase to form MPF. Members in this family contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 134 matched cddid_all.tbl CDD cd20569 cd20569 410272 CYCLIN_CCNB1_rpt2 second cyclin box found in G2/mitotic-specific cyclin-B1 (CCNB1) and similar proteins. CCNB1 is essential for the control of the cell cycle at the G2/M (mitosis) transition. It is required for embryo development. Over-expression of human CCNB1 has been found in numerous cancers and has been associated with tumor aggressiveness. CCNB1 contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 121 matched cddid_all.tbl CDD cd20570 cd20570 410273 CYCLIN_CCNB2_rpt2 second cyclin box found in G2/mitotic-specific cyclin-B2 (CCNB2) and similar proteins. CCNB2 is essential for the control of the cell cycle at the G2/M (mitosis) transition. It is required for progression through meiosis. CCNB2 contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 119 matched cddid_all.tbl CDD cd20571 cd20571 410274 CYCLIN_AtCycC_rpt1 first cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins. Plant CycCs are the cognate cyclin partners of cyclin-dependent kinase CDK8. They may be involved in cell cycle control. CycCs contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 107 matched cddid_all.tbl CDD cd20572 cd20572 410275 CYCLIN_AtCycC_rpt2 second cyclin box found in Arabidopsis thaliana C-type cyclins (CycCs) and similar proteins. CycCs are the cognate cyclin partners of cyclin-dependent kinase CDK8. They may be involved in cell cycle control. CycCs contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 102 matched cddid_all.tbl CDD cd20573 cd20573 410276 CYCLIN_CCND1_rpt1 first cyclin box found in G1/S-specific cyclin-D1 (CCND1). CCND1, also called B-cell lymphoma 1 protein (BCL-1), or BCL-1 oncogene, or PRAD1 oncogene, is a regulatory component of the cyclin D1-CDK4 (DC) complex that phosphorylates and inhibits members of the retinoblastoma (RB) protein family, including RB1. The complex also regulates the cell-cycle during G(1)/S transition. It is an important cell cycle regulatory protein involved in carcinogenesis of various human cancers. CCND1 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 149 matched cddid_all.tbl CDD cd20574 cd20574 410277 CYCLIN_CCND2_rpt1 first cyclin box found in G1/S-specific cyclin-D2 (CCND2). CCND2 is a regulatory component of the cyclin D2-CDK4 (DC) complex that phosphorylates and inhibits members of the retinoblastoma (RB) protein family, including RB1, and regulates the cell-cycle during G(1)/S transition. It is a critical mediator of exercise-induced cardiac hypertrophy. It also acts as a regulator of cell cycle proteins affecting SAMHD1-mediated HIV-1 restriction in non-proliferating macrophages. CCND2 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 150 matched cddid_all.tbl CDD cd20575 cd20575 410278 CYCLIN_CCND3_rpt1 first cyclin box found in G1/S-specific cyclin-D3 (CCND3) and similar proteins. CCND3 is a regulatory component of the cyclin D3-CDK4 (DC) complex that phosphorylates and inhibits members of the retinoblastoma (RB) protein family, including RB1, and regulates the cell-cycle during G(1)/S transition. In skeletal muscle, CCND3 plays a unique function in controlling the proliferation/differentiation balance of myogenic progenitor cells. CCND3 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 150 matched cddid_all.tbl CDD cd20576 cd20576 410279 CYCLIN_CCND1_rpt2 second cyclin box found in G1/S-specific cyclin-D1 (CCND1). CCND1, also called B-cell lymphoma 1 protein (BCL-1), or BCL-1 oncogene, or PRAD1 oncogene, is a regulatory component of the cyclin D1-CDK4 (DC) complex that phosphorylates and inhibits members of the retinoblastoma (RB) protein family, including RB1, and regulates the cell-cycle during G(1)/S transition. It is an important cell cycle regulatory protein involved in carcinogenesis of various human cancers. CCND1 contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 110 matched cddid_all.tbl CDD cd20577 cd20577 410280 CYCLIN_CCND2_rpt2 second cyclin box found in G1/S-specific cyclin-D2 (CCND2). CCND2 is a regulatory component of the cyclin D2-CDK4 (DC) complex that phosphorylates and inhibits members of the retinoblastoma (RB) protein family, including RB1, and regulates the cell-cycle during G(1)/S transition. It is a critical mediator of exercise-induced cardiac hypertrophy. It also acts as a regulator of cell cycle proteins affecting SAMHD1-mediated HIV-1 restriction in non-proliferating macrophages. CCND2 contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 105 matched cddid_all.tbl CDD cd20578 cd20578 410281 CYCLIN_CCND3_rpt2 second cyclin box found in G1/S-specific cyclin-D3 (CCND3). CCND3 is a regulatory component of the cyclin D3-CDK4 (DC) complex that phosphorylates and inhibits members of the retinoblastoma (RB) protein family, including RB1, and regulates the cell-cycle during G(1)/S transition. In skeletal muscle, CCND3 plays a unique function in controlling the proliferation/differentiation balance of myogenic progenitor cells. CCND3 contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 105 matched cddid_all.tbl CDD cd20579 cd20579 410282 CYCLIN_CCNE1_rpt1 first cyclin box found in G1/S-specific cyclin-E1 (CCNE1). CCNE1 is essential for the control of the cell cycle at the G1/S (start) transition. It interacts with CDK2 protein kinase to form a serine/threonine kinase holoenzyme complex. CCNE1 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 137 matched cddid_all.tbl CDD cd20580 cd20580 410283 CYCLIN_CCNE2_rpt1 first cyclin box found in G1/S-specific cyclin-E2 (CCNE2). CCNE2 is essential for the control of the cell cycle at the late G1 and early S phase. It interacts with the CDK2 (in vivo) and CDK3 (in vitro) protein kinases to form a serine/threonine kinase holoenzyme complexes. CCNE2 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 137 matched cddid_all.tbl CDD cd20581 cd20581 410284 CYCLIN_CCNE1_rpt2 second cyclin box found in G1/S-specific cyclin-E1 (CCNE1). CCNE1 is essential for the control of the cell cycle at the G1/S (start) transition. It interacts with CDK2 protein kinase to form a serine/threonine kinase holoenzyme complex. CCNE1 contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 114 matched cddid_all.tbl CDD cd20582 cd20582 410285 CYCLIN_CCNE2_rpt2 second cyclin box found in G1/S-specific cyclin-E2 (CCNE2). CCNE2 is essential for the control of the cell cycle at the late G1 and early S phase. It interacts with the CDK2 (in vivo) and CDK3 (in vitro) protein kinases to form serine/threonine kinase holoenzyme complexes. CCNE2 contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 99 matched cddid_all.tbl CDD cd20583 cd20583 410286 CYCLIN_CCNG1 cyclin box found in cyclin-G1 (CCNG1) and similar proteins. CCNG1 is the only cyclin that has either positive or negative effects on cell growth. It is associated with G2/M phase arrest in response to DNA damage. It is also involved in the development of human carcinoma. CCNG1 contains one cyclin box. The cyclin box is a protein binding domain. 98 matched cddid_all.tbl CDD cd20584 cd20584 410287 CYCLIN_CCNG2 cyclin box found in cyclin-G2 (CCNG2) and similar proteins. CCNG2 may play a role in growth regulation and in negative regulation of cell cycle progression. It has been identified as a tumor suppressor in several cancers. CCNG2 contains one cyclin box. The cyclin box is a protein binding domain. 96 matched cddid_all.tbl CDD cd20585 cd20585 410288 CYCLIN_AcCycH_rpt1 first cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins. CycH associates with and activates the cyclin-dependent kinases, CDK-2 and CDK-3. CycH contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 170 matched cddid_all.tbl CDD cd20586 cd20586 410289 CYCLIN_AcCycH_rpt2 second cyclin box found in Arabidopsis thaliana H-type cyclin (CycH) and similar proteins. CycH associates with and activates the cyclin-dependent kinases, CDK-2 and CDK-3. CycH contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 132 matched cddid_all.tbl CDD cd20587 cd20587 410290 CYCLIN_AcCycT_rpt1 first cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins. CycTs associate with their partner cyclin-dependent kinases (CDKs) to trigger their kinase activity. CycTs show high sequence similarity with metazoan cyclin-K (CCNK). CycTs contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 124 matched cddid_all.tbl CDD cd20588 cd20588 410291 CYCLIN_AcCycT_rpt2 second cyclin box found in Arabidopsis thaliana T-type cyclins (CycTs) and similar proteins. CycTs associate with their partner cyclin-dependent kinases (CDKs) to trigger their kinase activity. CycTs show high sequence similarity with metazoan cyclin-K (CCNK). CycTs contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 93 matched cddid_all.tbl CDD cd20589 cd20589 410292 CYCLIN_CCNL1_rpt1 first cyclin box found in cyclin-L1 (CCNL1) and similar proteins. CCNL1 is an L-type cyclin involved in the regulation of RNA polymerase II (pol II) transcription. It functions in association with cyclin-dependent kinases (CDKs). CCNL1 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 124 matched cddid_all.tbl CDD cd20590 cd20590 410293 CYCLIN_CCNL2_rpt1 first cyclin box found in cyclin-2 (CCNL2) and similar proteins. CCNL2 is a novel RNA polymerase II-associated cyclin that is involved in pre-mRNA splicing. It may induce cell death, possibly by acting on the transcription and RNA processing of apoptosis-related factors. CCNL2 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 156 matched cddid_all.tbl CDD cd20591 cd20591 410294 CYCLIN_AcCycL_rpt1 first cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins. Cyclin-L1-1 (CycL1), also called arginine-rich cyclin 1 (AtRCY1), or protein MODIFIER OF SNC1 12, is the cognate cyclin for cyclin-dependent kinase G1 (CDKG1). It is involved in regulation of DNA methylation and transcriptional silencing. It is required for synapsis and male meiosis, and for the proper splicing of specific resistance (R) genes. L-type cyclins contain two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 128 matched cddid_all.tbl CDD cd20592 cd20592 410295 CYCLIN_CCNL1_rpt2 second cyclin box found in cyclin-L1 (CCNL1) and similar proteins. CCNL1 is an L-type cyclin involved in the regulation of RNA polymerase II (pol II) transcription. It functions in association with cyclin-dependent kinases (CDKs). CCNL1 contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 123 matched cddid_all.tbl CDD cd20593 cd20593 410296 CYCLIN_CCNL2_rpt2 second cyclin box found in cyclin-2 (CCNL2) and similar proteins. CCNL2 is a novel RNA polymerase II-associated cyclin that is involved in pre-mRNA splicing. It may induce cell death, possibly by acting on the transcription and RNA processing of apoptosis-related factors. CCNL2 contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 123 matched cddid_all.tbl CDD cd20594 cd20594 410297 CYCLIN_AcCycL_rpt2 second cyclin box found in Arabidopsis thaliana L-type cyclins (CycL) and similar proteins. Cyclin-L1-1 (CycL1), also called arginine-rich cyclin 1 (AtRCY1), or protein MODIFIER OF SNC1 12, is the cognate cyclin for cyclin-dependent kinase G1 (CDKG1). It is involved in regulation of DNA methylation and transcriptional silencing. It is required for synapsis and male meiosis, and for the proper splicing of specific resistance (R) genes. L-type cyclins contain two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 101 matched cddid_all.tbl CDD cd20595 cd20595 410298 CYCLIN_CCNT1_rpt1 first cyclin box found in cyclin-T1 (CCNT1). CCNT1, also termed CycT1, is a host factor essential for HIV-1 replication in CD4 T cells and macrophages. It is a regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin-T1) complex, also called positive transcription elongation factor B (P-TEFb), which is proposed to facilitate the transition from abortive to productive elongation by phosphorylating the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNA Pol II). CCNT1 contains two cyclin boxes. This model corresponds to the first one. The cyclin box is a protein binding domain. 138 matched cddid_all.tbl CDD cd20596 cd20596 410299 CYCLIN_CCNT2_rpt1 first cyclin box found in cyclin-T2 (CCNT2). CCNT2, also termed CycT2, is a regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin T) complex, also called positive transcription elongation factor B (P-TEFb), which is proposed to facilitate the transition from abortive to production elongation by phosphorylating the CTD (carboxy-terminal domain) of the large subunit of RNA polymerase II (RNAP II). CCNT2 contains two cyclin boxs. The model responds to the first one. The cyclin box is a protein binding domain. 139 matched cddid_all.tbl CDD cd20597 cd20597 410300 CYCLIN_CCNT1_rpt2 second cyclin box found in cyclin-T1 (CCNT1). CCNT1, also termed CycT1, is a host factor essential for HIV-1 replication in CD4 T cells and macrophages. It is a regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin-T1) complex, also called positive transcription elongation factor B (P-TEFb), which is proposed to facilitate the transition from abortive to productive elongation by phosphorylating the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNA Pol II). CCNT1 contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 109 matched cddid_all.tbl CDD cd20598 cd20598 410301 CYCLIN_CCNT2_rpt2 second cyclin box found in cyclin-T2 (CCNT2). CCNT2, also termed CycT2, is a regulatory subunit of the cyclin-dependent kinase pair (CDK9/cyclin T) complex, also called positive transcription elongation factor B (P-TEFb), which is proposed to facilitate the transition from abortive to production elongation by phosphorylating the CTD (carboxy-terminal domain) of the large subunit of RNA polymerase II (RNAP II). CCNT2 contains two cyclin boxs. The model responds to the second one. The cyclin box is a protein binding domain. 114 matched cddid_all.tbl CDD cd20599 cd20599 410302 CYCLIN_RB cyclin box found in retinoblastoma-associated protein (RB) and similar proteins. RB, also called p105-Rb, pRb, or pp110, is a key regulator of entry into cell division and also acts as a tumor suppressor. It promotes G0-G1 transition when phosphorylated by CDK3/cyclin-C. It also acts as a transcription repressor of E2F1 target genes. RB is directly involved in heterochromatin formation by maintaining overall chromatin structure, especially that of constitutive heterochromatin by stabilizing histone methylation. It recruits and targets histone methyltransferases SUV39H1, KMT5B and KMT5C, leading to epigenetic transcriptional repression. It controls histone H4 'Lys-20' trimethylation. RB contains one cyclin box. The cyclin box is a protein binding domain. 126 matched cddid_all.tbl CDD cd20600 cd20600 410303 CYCLIN_RBL cyclin box found in retinoblastoma-like protein (RBL) subfamily. The RBL subfamily includes two retinoblastoma-like proteins, RBL1 and RBL2. They are key regulators of entry into cell division and are directly involved in heterochromatin formation by maintaining overall chromatin structure. RBL1 and RBL2 recruit and target histone methyltransferases KMT5B and KMT5C, leading to epigenetic transcriptional repression. They control histone H4 'Lys-20' trimethylation and probably act as transcription repressors by recruiting chromatin-modifying enzymes to promoters. They may also act as tumor suppressors. Members of this family contain one cyclin box. The cyclin box is a protein binding domain. 112 matched cddid_all.tbl CDD cd20601 cd20601 410304 CYCLIN_AtRBR_like cyclin box found in Arabidopsis thaliana retinoblastoma-related protein 1 (AtRBR1) and similar proteins. AtRBR1 is a key regulator of entry into cell division. It acts as a transcription repressor of E2F target genes, whose activity is required for progress from the G1 to the S phase of the cell cycle. AtRBR1 plays a central role in the mechanism controlling meristem cell differentiation, cell fate establishment and cell fate maintenance during organogenesis and gametogenesis. AtRBR1 contains one cyclin box. The cyclin box is a protein binding domain. 129 matched cddid_all.tbl CDD cd20602 cd20602 410305 CYCLIN_CABLES1 cyclin box found in CDK5 and ABL1 enzyme substrate 1 (CABLES1). CABLES1, also called interactor with CDK3 1 (Ik3-1), is a cyclin-dependent kinase binding protein that enhances cyclin-dependent kinase tyrosine phosphorylation by non-receptor tyrosine kinases, such as that of CDK5 by activated ABL1, which leads to increased CDK5 activity and is critical for neuronal development, and that of CDK2 by WEE1, which leads to decreased CDK2 activity and growth inhibition. CABLES1 contains one cyclin box. The cyclin box is a protein binding domain. 132 matched cddid_all.tbl CDD cd20603 cd20603 410306 CYCLIN_CABLES2 cyclin box found in CDK5 and ABL1 enzyme substrate 2 (CABLES2). CABLES2, also called interactor with CDK3 2 (Ik3-2), acts as a proapoptotic factor involved in both p53-mediated and p53-independent apoptotic pathways. CABLES2 contains one cyclin box. The cyclin box is a protein binding domain. 121 matched cddid_all.tbl CDD cd20604 cd20604 410307 CYCLIN_AtCycU-like cyclin box found in Arabidopsis thaliana U-type cyclins (CycUs) and similar proteins. CycUs interact with cyclin-dependent kinase A-1 (CDKA-1) to trigger its kinase activity. CycUs contain one cyclin box. The cyclin box is a protein binding domain. 126 matched cddid_all.tbl CDD cd20605 cd20605 410308 CYCLIN_RBL1 cyclin box found in retinoblastoma-like protein 1 (RBL1) and similar proteins. RBL1, also called 107 kDa retinoblastoma-associated protein (p107), retinoblastoma-related protein 1 (RBR-1), or pRb1, is a key regulator of entry into cell division. It is directly involved in heterochromatin formation by maintaining overall chromatin structure, especially that of constitutive heterochromatin by stabilizing histone methylation. RBL1 recruits and targets histone methyltransferases KMT5B and KMT5C, leading to epigenetic transcriptional repression. It controls histone H4 'Lys-20' trimethylation. RBL1 probably acts as a transcription repressor by recruiting chromatin-modifying enzymes to promoters. It may also act as a tumor suppressor. RBL1 contains one cyclin box. The cyclin box is a protein binding domain. 130 matched cddid_all.tbl CDD cd20606 cd20606 410309 CYCLIN_RBL2 cyclin box found in retinoblastoma-like protein 2 (RBL2) and similar proteins. RBL2, also called 130 kDa retinoblastoma-associated protein (p130), retinoblastoma-related protein 2 (RBR-2), or pRb2, is a key regulator of entry into cell division. It is directly involved in heterochromatin formation by maintaining overall chromatin structure, especially that of constitutive heterochromatin by stabilizing histone methylation. RBL2 recruits and targets histone methyltransferases KMT5B and KMT5C, leading to epigenetic transcriptional repression. It controls histone H4 'Lys-20' trimethylation. It probably acts as a transcription repressor by recruiting chromatin-modifying enzymes to promoters. It may also act as a tumor suppressor. RBL2 contains one cyclin box. The cyclin box is a protein binding domain. 189 matched cddid_all.tbl CDD cd20607 cd20607 380328 FbiB_C-like nitroreductase family domain similar to the C-terminal domain of F420:gamma-glutamyl ligase FbiB. Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Mycobacterium tuberculosis FbiB, is a two-domain protein and produces F420 with predominantly 5 to 7 L-glutamate residues in the poly-gamma-glutamate tail, its C-terminal domain is homologous to FMN-dependent nitroreductases. 155 matched cddid_all.tbl CDD cd20608 cd20608 380329 nitroreductase nitroreductase family protein. Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are described as NAD(P)H:FMN oxidoreductases, oxygen-insensitive nitroreductase, flavin reductase P, dihydropteridine reductase, NADH oxidase or NADH dehydrogenase. 145 matched cddid_all.tbl CDD cd20609 cd20609 380330 nitroreductase nitroreductase family protein. A subfamily of the nitroreductase family containing uncharacterized proteins. Nitroreductase catalyzes the reduction of nitroaromatic compounds such as nitrotoluenes, nitrofurans and nitroimidazoles. This process requires NAD(P)H as electron donor in an obligatory two-electron transfer and uses FMN as cofactor. The enzyme is typically a homodimer.often found to be homodimers. 145 matched cddid_all.tbl CDD cd20610 cd20610 380331 nitroreductase nitroreductase family protein. Proteins of this family catalyze the reduction of flavin or nitrocompounds using NAD(P)H as electron donor in a obligatory two-electron transfer, utilizing FMN or FAD as cofactor. They are often found to be homodimers. Enzymes of this family are described as NAD(P)H:FMN oxidoreductases, oxygen-insensitive nitroreductase, flavin reductase P, dihydropteridine reductase, NADH oxidase or NADH dehydrogenase. 167 matched cddid_all.tbl CDD cd20612 cd20612 410705 CYP_LDS-like_C C-terminal cytochrome P450 domain of linoleate diol synthase and similar cytochrome P450s. This family contains Gaeumannomyces graminis linoleate diol synthase (LDS) and similar proteins including Ssp1 from the phytopathogenic basidiomycete Ustilago maydis. LDS, also called linoleate (8R)-dioxygenase, catalyzes the dioxygenation of linoleic acid to (8R)-hydroperoxylinoleate and the isomerization of the resulting hydroperoxide to (7S,8S)-dihydroxylinoleate. Ssp1 is expressed in mature teliospores, which are produced by U. maydis only after infection of its host plant, maize. Ssp1 is localized on lipid bodies in germinating teliospores, suggesting a role in the mobilization of storage lipids. LDS and Ssp1 contain an N-terminal dioxygenase domain related to animal heme peroxidases, and a C-terminal cytochrome P450 domain. The LDS-like subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 370 matched cddid_all.tbl CDD cd20613 cd20613 410706 CYP46A1-like cytochrome P450 family 46, subfamily A, polypeptide 1, also called cholesterol 24-hydroxylase, and similar cytochrome P450s. CYP46A1 is also called cholesterol 24-hydroxylase (EC 1.14.14.25), CH24H, cholesterol 24-monooxygenase, or cholesterol 24S-hydroxylase. It catalyzes the conversion of cholesterol into 24S-hydroxycholesterol and, to a lesser extent, 25-hydroxycholesterol. CYP46A1 is associated with high-order brain functions; increased expression improves cognition while a reduction leads to a poor cognitive performance. It also plays a role in the pathogenesis or progression of neurodegenerative disorders. CYP46A1 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 429 matched cddid_all.tbl CDD cd20614 cd20614 410707 CYPBJ-4-like cytochrome P450 BJ-4 homolog and similar cytochrome P450s. This group is composed of mostly uncharacterized proteins including Sinorhizobium fredii CYPBJ-4 homolog. It belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 406 matched cddid_all.tbl CDD cd20615 cd20615 410708 CYP_GliC-like cytochrome P450 monooxygenases similar to gliotoxin biosynthesis protein C. This subfamily is composed of cytochrome P450 monooxygenases that are part of gene clusters involved in the biosynthesis of various compounds such as mycotoxins and alkaloids, including Aspergillus fumigatus gliotoxin biosynthesis protein (GliC), Penicillium rubens roquefortine/meleagrin synthesis protein R (RoqR), Aspergillus oryzae aspirochlorine biosynthesis protein C (AclC), Aspergillus terreus bimodular acetylaranotin synthesis protein ataTC, Kluyveromyces lactis pulcherrimin biosynthesis cluster protein 2 (PUL2), and Aspergillus nidulans aspyridones biosynthesis protein B (ApdB). The GliC-like subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 409 matched cddid_all.tbl CDD cd20616 cd20616 410709 CYP19A1 cytochrome P450 family 19, subfamily A, polypeptide 1. CYP19A1, also called aromatase or estrogen synthetase (EC 1.14.14.14), catalyzes the formation of aromatic C18 estrogens from C19 androgens. The CYP19A1 subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 414 matched cddid_all.tbl CDD cd20617 cd20617 410710 CYP1_2-like cytochrome P450 families 1 and 2, and similar cytochrome P450s. This model includes cytochrome P450 families 1 (CYP1) and 2 (CYP2), CYP17A1, and CYP21 in vertebrates, as well as insect and crustacean CYPs similar to CYP15A1 and CYP306A1. CYP1 and CYP2 enzymes are involved in the metabolism of endogenous and exogenous compounds such as hormones, xenobiotics, and drugs. CYP17A1 catalyzes the conversion of pregnenolone and progesterone to their 17-alpha-hydroxylated products, while CYP21 catalyzes the 21-hydroxylation of steroids such as progesterone and 17-alpha-hydroxyprogesterone (17-alpha-OH-progesterone) to form 11-deoxycorticosterone and 11-deoxycortisol, respectively. Members of this group belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 419 matched cddid_all.tbl CDD cd20618 cd20618 410711 CYP71_clan Plant cytochrome P450s, clan CYP71. The number of cytochrome P450s (P450s, CYPs) in plants is considerably larger than in other taxa. In individual plant genomes, CYPs form the third largest family of plant genes; the two largest gene families code for F-box proteins and receptor-like kinases. CYPs have been classified into families and subfamilies based on homology and phylogenetic criteria; family membership is defined as 40% amino acid sequence identity or higher. However, there is a phenomenon called family creep, where a sequence (below 40% identity) is absorbed into a large family; this is seen in the plant CYP71 and CYP89 families. The plant CYPs have also been classified according to clans; land plants have 11 clans that form two groups: single-family clans (CYP51, CYP74, CYP97, CYP710, CYP711, CYP727, CYP746) and multi-family clans (CYP71, CYP72, CYP85, CYP86). The CYP71 clan has expanded dramatically and represents 50% of all plant CYPs; it includes several families including CYP71, CYP73, CYP76, CYP81, CYP82, CYP89, and CYP93, among others. It belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 429 matched cddid_all.tbl CDD cd20619 cd20619 410712 CYP_XplA cytochrome P450 XplA. XplA is a cytochrome P450 that was found to mediate the microbial metabolism of the military explosive, hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). XplA has an unusual structural organization comprising a heme domain that is fused to its flavodoxin redox partner. XplA, along with its partner reductase XplB, are plasmid encoded and the xplA gene has now been found in divergent genera across the globe with near sequence identity. It has only been detected at explosive-contaminated sites, suggesting rapid dissemination of this novel catabolic activity, possibly within a 50-year period since the introduction of RDX into the environment. XplA belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 358 matched cddid_all.tbl CDD cd20620 cd20620 410713 CYP132-like cytochrome P450 family 132 and similar cytochrome P450s. This subfamily is composed of Mycobacterium tuberculosis cytochrome P450 132 (CYP132) and similar proteins. The function of CYP132 is as yet unknown. CYP132 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 406 matched cddid_all.tbl CDD cd20621 cd20621 410714 CYP5011A1-like cytochrome P450 monooxygenase CYP5011A1 and similar cytochrome P450s. This subfamily is composed of CYPs from unicellular ciliates similar to Tetrahymena thermophila CYP5011A1, whose function is still unknown. It belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 427 matched cddid_all.tbl CDD cd20622 cd20622 410715 CYP_TRI13-like fungal cytochrome P450s similar to TRI13. This subfamily is composed of cytochrome P450 monooxygenase TRI13, also called core trichothecene cluster (CTC) protein 13, and similar proteins. The tri13 gene is located in the trichothecene biosynthesis gene cluster in Fusarium species, which produce a great diversity of agriculturally important trichothecene toxins that differ from each other in their pattern of oxygenation and esterification. Trichothecenes comprise a large family of chemically related bicyclic sesquiterpene compounds acting as mycotoxins, including the T2-toxin; TRI13 is required for the addition of the C-4 oxygen of T-2 toxin. The TRI13-like subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 494 matched cddid_all.tbl CDD cd20623 cd20623 410716 CYP_unk unknown subfamily of actinobacterial cytochrome P450s. This subfamily is composed of uncharacterized cytochrome P450s. Cytochrome P450 (P450, CYP) is a large superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. Their monooxygenase activity relies on the reductive scission of molecular oxygen bound to the P450 heme iron, and the delivery of two electrons to the heme iron during the catalytic cycle. 367 matched cddid_all.tbl CDD cd20624 cd20624 410717 CYP_unk unknown subfamily of actinobacterial cytochrome P450s. This subfamily is composed of uncharacterized cytochrome P450s. Cytochrome P450 (P450, CYP) is a large superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. Their monooxygenase activity relies on the reductive scission of molecular oxygen bound to the P450 heme iron, and the delivery of two electrons to the heme iron during the catalytic cycle. 376 matched cddid_all.tbl CDD cd20625 cd20625 410718 CYP164-like cytochrome P450 family 164 and similar cytochrome P450s. This group is composed mostly of bacterial cytochrome P450s from multiple families, including Mycobacterium smegmatis CYP164A2, Streptomyces sp. CYP245A1, Bacillus subtilis CYP107H1, Micromonospora echinospora P450 oxidase Calo2, and putative P450s such as Xylella fastidiosa CYP133 and Mycobacterium tuberculosis CYP140. CYP107H1, also called cytochrome P450(BioI), catalyzes the C-C bond cleavage of fatty acid linked to acyl carrier protein (ACP) to generate pimelic acid for biotin biosynthesis. CYP245A1, also called cytochrome P450 StaP, catalyzes the intramolecular C-C bond formation and oxidative decarboxylation of chromopyrrolic acid (CPA) to form the indolocarbazole core, a key step in staurosporine biosynthesis. CalO2 is involved in calicheamicin biosynthesis. The CYP164-like group belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 369 matched cddid_all.tbl CDD cd20626 cd20626 410719 CYP_Pc22g25500-like cytochrome P450 Pc22g25500 and similar cytochrome P450s. Penicillium rubens Pc22g25500 is a putative cytochrome P450 of unknown function. Cytochrome P450 (P450, CYP) is a large superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. Their monooxygenase activity relies on the reductive scission of molecular oxygen bound to the P450 heme iron, and the delivery of two electrons to the heme iron during the catalytic cycle. 381 matched cddid_all.tbl CDD cd20627 cd20627 410720 CYP20A1 cytochrome P450 family 20, subfamily A, polypeptide 1. Cytochrome P450, family 20, subfamily A, polypeptide 1 (cytochrome P450 20A1 or CYP20A1) is expressed in human hippocampus and substantia nigra. In zebrafish, maternal transcript of CYP20A1 occurs in eggs, suggesting involvement in brain and early development. CYP20A1 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 394 matched cddid_all.tbl CDD cd20628 cd20628 410721 CYP4 cytochrome P450 family 4. Cytochrome P450 family 4 (CYP4) proteins catalyze the omega-hydroxylation of the terminal carbon of fatty acids, including essential signaling molecules such as eicosanoids, prostaglandins and leukotrienes, and they are important for chemical defense. There are seven vertebrate family 4 subfamilies: CYP4A, CYP4B, CYP4F, CYP4T, CYP4V, CYP4X, and CYP4Z; three (CYP4X, CYP4A, CYP4Z) are specific to mammals. CYP4 enzymes metabolize fatty acids off various length, level of saturation, and branching. Specific subfamilies show preferences for the length of fatty acids; CYP4B, CYP4A and CYP4V, and CYP4F preferentially metabolize short (C7-C10), medium (C10-C16), and long to very long (C18-C26) fatty acid chains, respectively. CYP4 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 426 matched cddid_all.tbl CDD cd20629 cd20629 410722 P450_pinF1-like cytochrome P450-pinF1 and similar cytochrome P450s. This subfamily is composed of bacterial CYPs similar to Agrobacterium tumefaciens plant-inducible cytochrome P450-pinF1, which is not essential for virulence but may be involved in the detoxification of plant protective agents at the site of wounding. The P450-pinF1-like subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 353 matched cddid_all.tbl CDD cd20630 cd20630 410723 P450_epoK-like cytochrome P450epok and similar cytochrome P450s. Sorangium cellulosum cytochrome P450epoK is a heme-containing monooxygenase which participates in epothilone biosynthesis where it catalyzes the epoxidation of epothilones C and D into epothilones A and B, respectively. This subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 373 matched cddid_all.tbl CDD cd20631 cd20631 410724 CYP7A1 cytochrome P450 family 7, subfamily A, polypeptide 1. Cytochrome P450 7A1 (CYP7A1) is also called cholesterol 7-alpha-monooxygenase (EC 1.14.14.23) or cholesterol 7-alpha-hydroxylase. It catalyzes the hydroxylation at position 7 of cholesterol, a rate-limiting step in the classic (or neutral) pathway of cholesterol catabolism and bile acid biosynthesis. It is important for cholesterol homeostasis. CYP7A1 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 451 matched cddid_all.tbl CDD cd20632 cd20632 410725 CYP7B1 cytochrome P450 family 7, subfamily B, polypeptide 1. Cytochrome P450 7B1 (CYP7B1) is also called 25-hydroxycholesterol 7-alpha-hydroxylase (EC 1.14.14.29) or oxysterol 7-alpha-hydroxylase. It catalyzes the 7alpha-hydroxylation of both steroids and oxysterols, and is thus implicated in the metabolism of neurosteroids and bile acid synthesis, respectively. It participates in the alternative (or acidic) pathway of cholesterol catabolism and bile acid biosynthesis. It also mediates the formation of 7-alpha,25-dihydroxycholesterol (7-alpha,25-OHC) from 25-hydroxycholesterol; 7-alpha,25-OHC acts as a ligand for the G protein-coupled receptor GPR183/EBI2, a chemotactic receptor in lymphoid cells. CYP7B1 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 438 matched cddid_all.tbl CDD cd20633 cd20633 410726 Cyp8B1 cytochrome P450 family 8, subfamily B, polypeptide 1. Cytochrome P450 8B1 (CYP8B1) is also called 7-alpha-hydroxycholest-4-en-3-one 12-alpha-hydroxylase (EC 1.14.18.8) or sterol 12-alpha-hydroxylase. It is involved in the classic (or neutral) pathway of cholesterol catabolism and bile acid synthesis, and is responsible for sterol 12alpha-hydroxylation, which directs the synthesis to cholic acid (CA). It converts 7-alpha-hydroxy-4-cholesten-3-one into 7-alpha,12-alpha-dihydroxy-4-cholesten-3-one, but also displays broad substrate specificity including other 7-alpha-hydroxylated C27 steroids. CYP8B1 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 449 matched cddid_all.tbl CDD cd20634 cd20634 410727 PGIS_CYP8A1 prostacyclin Synthase, also called cytochrome P450 family 8, subfamily A, polypeptide 1. Prostacyclin synthase, also called prostaglandin I2 synthase (PGIS) or cytochrome P450 8a1 (CYP8A1), catalyzes the isomerization of prostaglandin H2 to prostacyclin (or prostaglandin I2), a potent mediator of vasodilation and anti-platelet aggregation. It belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 442 matched cddid_all.tbl CDD cd20635 cd20635 410728 CYP39A1 cytochrome P450 family 39, subfamily A, polypeptide 1. Cytochrome P450 39A1 (CYP39A1) is also called 24-hydroxycholesterol 7-alpha-hydroxylase (EC 1.14.14.26) or oxysterol 7-alpha-hydroxylase. It is involved in the metabolism of bile acids and has a preference for 24-hydroxycholesterol, converting it into the 7-alpha-hydroxylated product. It may play a role in the alternative bile acid synthesis pathway in the liver. CYP39A1 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 410 matched cddid_all.tbl CDD cd20636 cd20636 410729 CYP26C1 cytochrome P450 family 26, subfamily C, polypeptide 1. Cytochrome P450 26C1 (CYP26C1) is a retinoic acid-metabolizing cytochrome that plays key roles in retinoic acid (RA) metabolism. It effectively metabolizes all-trans retinoic acid (atRA), 9-cis-retinoic acid (9-cis-RA), 13-cis-retinoic acid, and 4-oxo-atRA with the highest intrinsic clearance toward 9-cis-RA. RA is a critical signaling molecule that regulates gene transcription and the cell cycle. Loss of function mutations in the CYP26C1 gene cause type IV focal facial dermal dysplasia (FFDD), a rare syndrome characterized by facial lesions resembling aplasia cutis. CYP26C1 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 431 matched cddid_all.tbl CDD cd20637 cd20637 410730 CYP26B1 cytochrome P450 family 26, subfamily B, polypeptide 1. Cytochrome P450 26B1 (CYP26B1) is a retinoic acid-metabolizing cytochrome that plays key roles in retinoic acid (RA) metabolism. It is an all-trans-retinoic acid (atRA) hydroxylase that catalyzes the formation of similar metabolites as CYP26A1. RA is a critical signaling molecule that regulates gene transcription and the cell cycle. In rats, CYP26B1 regulates sex-specific timing of meiotic initiation, independent of RA signaling. CYP26B1 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 430 matched cddid_all.tbl CDD cd20638 cd20638 410731 CYP26A1 cytochrome P450 family 26, subfamily A, polypeptide 1. Cytochrome P450s 26A1 (CYP26A1) is a retinoic acid-metabolizing cytochrome that plays key roles in retinoic acid (RA) metabolism. It is the main all-trans-retinoic acid (atRA) hydroxylase that catalyzes the formation of several hydroxylated forms of RA, including 4-OH-RA, 4-oxo-RA and 18-OH-RA. RA is a critical signaling molecule that regulates gene transcription and the cell cycle. CYP26A1 has been shown to upregulate fascin and promote the malignant behavior of breast carcinoma cells. It belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 432 matched cddid_all.tbl CDD cd20639 cd20639 410732 CYP734 cytochrome P450 family 734. Cytochrome P450 family 734 (CYP734) belongs to the plant CYP72 clan, which is generally associated with the metabolism of a diversity of fairly hydrophobic compounds including fatty acids and isoprenoids, with the catabolism of hormones (brassinosteroids and gibberellin, GA) and with the biosynthesis of cytokinins. CYP734As function as multisubstrate and multifunctional enzymes in brassinosteroid (BRs) catabolism and regulation of BRs homeostasis. Arabidopsis thaliana CYP734A1/BAS1 (formerly CYP72B1) inactivates bioactive brassinosteroids such as castasterone (CS) and brassinolide (BL) by C-26 hydroxylation. Rice CYP734As can catalyze C-22 hydroxylation as well as second and third oxidations to produce aldehyde and carboxylate groups at C-26. CYP734 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 428 matched cddid_all.tbl CDD cd20640 cd20640 410733 CYP714 cytochrome P450 family 714. Cytochrome P450 family 714 (CYP714) belongs to the plant CYP72 clan, which is generally associated with the metabolism of a diversity of fairly hydrophobic compounds including fatty acids and isoprenoids, with the catabolism of hormones (brassinosteroids and gibberellin, GA) and with the biosynthesis of cytokinins. CYP714 enzymes are involved in the biosynthesis of gibberellins (GAs) and the mechanism to control their bioactive endogenous levels. They contribute to the production of diverse GA compounds through various oxidations of C and D rings in both monocots and eudicots. CYP714B1 and CYP714B2 encode the enzyme GA 13-oxidase, which is required for GA1 biosynthesis, while CYP714D1 encodes GA 16a,17-epoxidase, which inactivates the non-13-hydroxy GAs in rice. Arabidopsis CYP714A1 is an inactivation enzyme that catalyzes the conversion of GA12 to 16-carboxylated GA12 (16-carboxy-16beta,17-dihydro GA12). CYP714 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 426 matched cddid_all.tbl CDD cd20641 cd20641 410734 CYP709 cytochrome P450 family 709. Cytochrome P450 family 709 (CYP709) belongs to the plant CYP72 clan, which is generally associated with the metabolism of a diversity of fairly hydrophobic compounds including fatty acids and isoprenoids, with the catabolism of hormones (brassinosteroids and gibberellin, GA) and with the biosynthesis of cytokinins. Arabidopsis thaliana CYP709B3 is involved in abscisic acid (ABA) and salt stress response. CYP709 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 431 matched cddid_all.tbl CDD cd20642 cd20642 410735 CYP72 cytochrome P450 family 72. Cytochrome P450 family 72 (CYP72) belongs to the plant CYP72 clan, which is generally associated with the metabolism of a diversity of fairly hydrophobic compounds including fatty acids and isoprenoids, with the catabolism of hormones (brassinosteroids and gibberellin, GA) and with the biosynthesis of cytokinins. Characterized members, among others, include: Catharanthus roseus cytochrome P450 72A1 (CYP72A1), also called secologanin synthase (EC 1.3.3.9), that catalyzes the conversion of loganin into secologanin, the precursor of monoterpenoid indole alkaloids and ipecac alkaloids; Medicago truncatula CYP72A67 that catalyzes a key oxidative step in hemolytic sapogenin biosynthesis; and Arabidopsis thaliana CYP72C1, an atypical CYP that acts on brassinolide precursors and functions as a brassinosteroid-inactivating enzyme. This family also includes Panax ginseng CYP716A47 that catalyzes the formation of protopanaxadiol from dammarenediol-II during ginsenoside biosynthesis. CYP72 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 431 matched cddid_all.tbl CDD cd20643 cd20643 410736 CYP11A1 cytochrome P450 family 11, subfamily A, polypeptide 1, also called cholesterol side-chain cleavage enzyme. Cytochrome P450 11A1 (CYP11A1, EC 1.14.15.6) is also called cholesterol side-chain cleavage enzyme, cholesterol desmolase, or cytochrome P450(scc). It catalyzes the side-chain cleavage reaction of cholesterol to form pregnenolone, the precursor of all steroid hormones. Missense or nonsense mutations of the CYP11A1 gene cause mild to severe early-onset adrenal failure depending on the severity of the enzyme dysfunction/deficiency. CYP11A1 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 425 matched cddid_all.tbl CDD cd20644 cd20644 410737 CYP11B cytochrome P450 family 11, subfamily B subfamily. Cytochrome P450 11B (CYP11B) enzymes catalyze the final steps in the production of glucocorticoids and mineralocorticoids that takes place in the adrenal gland. There are two human CYP11B isoforms: Cyb11B1 (11-beta-hydroxylase or P45011beta), which catalyzes the final step of cortisol synthesis by a one-step reaction from 11-deoxycortisol; and CYP11B2 (aldosterone synthase or P450aldo), which catalyzes three steps in the synthesis of aldosterone. The CYP11B subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 428 matched cddid_all.tbl CDD cd20645 cd20645 410738 CYP24A1 cytochrome P450 family 24, subfamily A, polypeptide 1, also called vitamin D(3) 24-hydroxylase. Cytochrome P450 24A1 (CYP24A1, EC 1.14.15.16) is also called 1,25-dihydroxyvitamin D(3) 24-hydroxylase (24-OHase), vitamin D(3) 24-hydroxylase, or cytochrome P450-CC24. It catalyzes the NADPH-dependent 24-hydroxylation of calcidiol (25-hydroxyvitamin D(3)) and calcitriol (1-alpha,25-dihydroxyvitamin D(3) or 1,25(OH)2D3). CYP24A1 regulates vitamin D activity through its hydroxylation of calcitriol, the physiologically active vitamin D hormone, which controls gene-expression and signal-transduction processes associated with calcium homeostasis, cellular growth, and the maintenance of heart, muscle, immune, and skin function. CYP24A1 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 419 matched cddid_all.tbl CDD cd20646 cd20646 410739 CYP27A1 cytochrome P450 family 27, subfamily A, polypeptide 1, also called vitamin D(3) 25-hydroxylase. Cytochrome P450 27A1 (CYP27A1, EC 1.14.15.15) is also called CYP27, cholestanetriol 26-monooxygenase, sterol 26-hydroxylase, 5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol 27-hydroxylase, cytochrome P-450C27/25, sterol 27-hydroxylase, or vitamin D(3) 25-hydroxylase. It catalyzes the first step in the oxidation of the side chain of sterol intermediates, the 27-hydroxylation of 5-beta-cholestane-3-alpha,7-alpha,12-alpha-triol, and the first three sterol side chain oxidations in bile acid biosynthesis via the neutral (classic) pathway. It also hydroxylates vitamin D3 at the 25-position, as well as cholesterol at positions 24 and 25. CYP27A1 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 430 matched cddid_all.tbl CDD cd20647 cd20647 410740 CYP27C1 cytochrome P450 family 27, subfamily C, polypeptide 1, also called all-trans retinol 3,4-desaturase. Cytochrome P450 27C1 (CYP27C1) is also called all-trans retinol 3,4-desaturase. It catalyzes the conversion of all-trans retinol (also called vitamin A1, the precursor of 11-cis retinal) to 3,4-didehydroretinol (also called vitamin A2, the precursor of 11-cis 3,4-didehydroretinal). CYP27C1 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 433 matched cddid_all.tbl CDD cd20648 cd20648 410741 CYP27B1 cytochrome P450 family 27, subfamily B, polypeptide 1, also called calcidiol 1-monooxygenase. Cytochrome p450 27B1 (CYP27B1) is also called calcidiol 1-monooxygenase (EC 1.14.15.18), 25-hydroxyvitamin D(3) 1-alpha-hydroxylase (VD3 1A hydroxylase), 25-hydroxyvitamin D-1 alpha hydroxylase, 25-OHD-1 alpha-hydroxylase, 25-hydroxycholecalciferol 1-hydroxylase, or 25-hydroxycholecalciferol 1-monooxygenase. It catalyzes the conversion of 25-hydroxyvitamin D3 (25(OH)D3) to 1-alpha,25-dihydroxyvitamin D3 (1,25(OH)2D3 or calcitriol), and of 24,25-dihydroxyvitamin D3 (24,25(OH)(2)D3) to 1-alpha,24,25-trihydroxyvitamin D3 (1alpha,24,25(OH)(3)D3). It is also active with 25-hydroxy-24-oxo-vitamin D3, and has an important role in normal bone growth, calcium metabolism, and tissue differentiation. CYP27B1 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 430 matched cddid_all.tbl CDD cd20649 cd20649 410742 CYP5A1 cytochrome P450 family 5, subfamily A, polypeptide 1, also called thromboxane-A synthase. Cytochrome P450 5A1 (CYP5A1), also called thromboxane-A synthase (EC 5.3.99.5) or thromboxane synthetase, converts prostaglandin H2 into thromboxane A2, a biologically active metabolite of arachidonic acid that has been implicated in stroke, asthma, and various cardiovascular diseases, due to its acute and chronic effects in promoting platelet aggregation, vasoconstriction, bronchoconstriction, and proliferation. CYP5A1 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 457 matched cddid_all.tbl CDD cd20650 cd20650 410743 CYP3A cytochrome P450 family 3, subfamily A. The cytochrome P450 3A (CYP3A) subfamily, the most abundant CYP subfamily in the liver, consists of drug-metabolizing enzymes. In humans, there are at least four isoforms: CYP3A4, 3A5, 3A7, and 3A3. CYP3A enzymes are embedded in the endoplasmic reticulum, where they can catalyze a wide variety of biochemical reactions including hydroxylation, N-demethylation, O-dealkylation, S-oxidation, deamination, or epoxidation of substrates. They oxidize a variety of structurally unrelated compounds including steroids, fatty acids, and xenobiotics. The CYP3A subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 426 matched cddid_all.tbl CDD cd20651 cd20651 410744 CYP15A1-like cytochrome P450 family 15, subfamily A, polypeptide 1, and similar cytochrome P450s. This subfamily is composed of insect and crustacean cytochrome P450s including Diploptera punctata cytochrome P450 15A1 (CYP15A1 or CYP15A1), Panulirus argus CYP2L1, and CYP303A1, CYP304A1, and CYP305A1 from Drosophila melanogaster. CYP15A1, also called methyl farnesoate epoxidase, catalyzes the conversion of methyl farnesoate to juvenile hormone III acid during juvenile hormone biosynthesis. CYP303A1, CYP304A1, and CYP305A1 may be involved in the metabolism of insect hormones and in the breakdown of synthetic insecticides. The CYP15A1-like subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 423 matched cddid_all.tbl CDD cd20652 cd20652 410745 CYP306A1-like cytochrome P450 306A1 and similar cytochrome P450s. This subfamily is composed of insect and crustacean cytochrome P450s including insect cytochrome P450 306A1 (CYP306A1 or Cyp306a1) and CYP18A1. CYP306A1 functions as a carbon 25-hydroxylase and has an essential role in ecdysteroid biosynthesis during insect development. CYP18A1 is a 26-hydroxylase and plays a key role in steroid hormone inactivation. The CYP306A1-like subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 432 matched cddid_all.tbl CDD cd20653 cd20653 410746 CYP81 cytochrome P450 family 81. The only characterized member of the cytochrome P450 family 81 (CYP81 or Cyp81) is CYP81E1, also called isoflavone 2'-hydroxylase, that catalyzes the hydroxylation of isoflavones, daidzein, and formononetin, to yield 2'-hydroxyisoflavones, 2'-hydroxydaidzein, and 2'-hydroxyformononetin, respectively. It is involved in the biosynthesis of isoflavonoid-derived antimicrobial compounds of legumes. CYP81 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 420 matched cddid_all.tbl CDD cd20654 cd20654 410747 CYP82 cytochrome P450 family 82. Cytochrome P450 family 82 (CYP82 or Cyp82) genes specifically reside in dicots and are usually induced by distinct environmental stresses. Characterized members include: Glycine max CYP82A3 that is induced by infection, salinity and drought stresses, and is involved in the jasmonic acid and ethylene signaling pathway, enhancing plant resistance; Arabidopsis thaliana CYP82G1 that catalyzes the breakdown of the C(20)-precursor (E,E)-geranyllinalool to the insect-induced C(16)-homoterpene (E,E)-4,8,12-trimethyltrideca-1,3,7,11-tetraene (TMTT); and Papaver somniferum CYP82N4, also called methyltetrahydroprotoberberine 14-monooxygenase, and CYP82Y1, also called N-methylcanadine 1-hydroxylase. CYP82N4 catalyzes the conversion of N-methylated protoberberine alkaloids N-methylstylopine and N-methylcanadine into protopine and allocryptopine, respectively, in the biosynthesis of isoquinoline alkaloid sanguinarine. CYP82Y1 catalyzes the 1-hydroxylation of N-methylcanadine to 1-hydroxy-N-methylcanadine, the first committed step in the formation of noscapine. CYP82 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 447 matched cddid_all.tbl CDD cd20655 cd20655 410748 CYP93 cytochrome P450 family 93. The cytochrome P450 family 93 (CYP93) is specifically found in flowering plants and could be classified into ten subfamilies, CYP93A-K. CYP93A appears to be the ancestor that was derived in flowering plants, and the remaining subfamiles show lineage-specific distribution: CYP93B and CYP93C are present in dicots; CYP93F is distributed only in Poaceae; CYP93G and CYP93J are monocot-specific; CYP93E is unique to legumes; CYP93H and CYP93K are only found in Aquilegia coerulea; and CYP93D is Brassicaceae-specific. Members of this family include: Glycyrrhiza echinata CYP93B1, also called licodione synthase (EC 1.14.14.140), that catalyzes the formation of licodione and 2-hydroxynaringenin from (2S)-liquiritigenin and (2S)-naringenin, respectively; and Glycine max CYP93A1, also called 3,9-dihydroxypterocarpan 6A-monooxygenase (EC 1.14.14.93), that is involved in the biosynthesis of the phytoalexin glyceollin. CYP93 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 433 matched cddid_all.tbl CDD cd20656 cd20656 410749 CYP98 cytochrome P450 family 98. Cytochrome P450 family 98 (CYP98) monooxygenases catalyze the meta-hydroxylation step in the phenylpropanoid biosynthetic pathway. CYP98A3, also called p-coumaroylshikimate/quinate 3'-hydroxylase, catalyzes 3'-hydroxylation of p-coumaric esters of shikimic/quinic acids to form lignin monomers. CYP98A8, also called p-coumarate 3-hydroxylase, acts redundantly with CYP98A9 as tricoumaroylspermidine meta-hydroxylase. CYP98 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 432 matched cddid_all.tbl CDD cd20657 cd20657 410750 CYP75 cytochrome P450 family 75. The cytochrome P450 family 75 (CYP75) play important roles in the biosynthesis of colored class of flavonoids, anthocyanins, which confer a diverse range of colors to flowers from orange to red to violet and blue. The number of hydroxyl groups on the B-ring of anthocyanidins, the chromophores and precursors of anthocyanins, impact the anthocyanin color - the more the bluer. The hydroxylation pattern is determined by CYP75 proteins: flavonoid 3'-hydroxylase (F3'H, EC 1.14.14.82) and and flavonoid 3',5'-hydroxylase (F3'5'H, EC 1.14.14.81), which belong to CYP75B and CYP75A subfamilies, respectively. Both enzymes have broad substrate specificity and catalyze the hydroxylation of flavanones, dihydroflavonols, flavonols and flavones. F3'H catalyzes the 3'-hydroxylation of the flavonoid B-ring to the 3',4'-hydroxylated state. F3'5'H catalysis leads to trihydroxylated delphinidin-based anthocyanins that tend to have violet/blue colours. CYP75 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 438 matched cddid_all.tbl CDD cd20658 cd20658 410751 CYP79 cytochrome P450 family 79. Cytochrome P450 family 79 (CYP79) enzymes catalyze the first committed step in the biosynthesis of the core structure of glucosinolates, the conversion of amino acids to the corresponding aldoximes. Glucosinolates are amino acid-derived natural plant products that function in the defense against herbivores and microorganisms. Arabidopsis thaliana contains seven family members: CYP79B2 and CYP79B3, which metabolize trytophan; CYP79F1 and CYP79F2, which metabolize chain-elongated methionine derivatives with respectively 1-6 or 5-6 additional methylene groups in the side chain; CYP79A2 that metabolizes phenylalanine; and CYP79C1 and CYP79C2, with unknown function. CYP79 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 444 matched cddid_all.tbl CDD cd20659 cd20659 410752 CYP4B_4F-like cytochrome P450 family 4, subfamilies B and F, and similar cytochrome P450s. This group is composed of family 4 cytochrome P450s from vertebrate subfamilies A (CYP4A), B (CYP4B), F (CYP4F), T (CYP4T), X (CYP4X), and Z (CYP4Z). Also included are similar proteins from lancelets, tunicates, hemichordates, echinoderms, mollusks, annelid worms, sponges, and choanoflagellates, among others. The CYP4A, CYP4X, and CYP4Z subfamilies are specific to mammals, CYP4T is present in fish, while CYP4B and CYP4F are conserved among vertebrates. CYP4Bs specialize in omega-hydroxylation of short chain fatty acids and also participates in the metabolism of exogenous compounds that are protoxic including valproic acid (C8), 3-methylindole (C9), 4-ipomeanol, 3-methoxy-4-aminoazobenzene, and several aromatic amines. CYP4F enzymes are known for known for omega-hydroxylation of very long fatty acids (VLFA; C18-C26), leukotrienes, prostaglandins, and vitamins with long alkyl side chains. The CYP4B_4F-like group belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 423 matched cddid_all.tbl CDD cd20660 cd20660 410753 CYP4V-like cytochrome P450 family 4, subfamily V, and similar cytochrome P450s. This group is composed of vertebrate cytochrome P450 family 4, subfamily V (CYP4V) enzymes and similar proteins, including invertebrate subfamily C (CYP4C). Insect CYP4C enzymes may be involved in the metabolism of insect hormones and in the breakdown of synthetic insecticides. CYP4V2, the most characterized member of the CYP4V subfamily, is a selective omega-hydroxylase of saturated, medium-chain fatty acids, such as laurate, myristate and palmitate, with high catalytic efficiency toward myristate. Polymorphisms in the CYP4V2 gene cause Bietti's crystalline corneoretinal dystrophy (BCD), a recessive degenerative retinopathy that is characterized clinically by a progressive decline in central vision, night blindness, and constriction of the visual field. The CYP4V-like group belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 429 matched cddid_all.tbl CDD cd20661 cd20661 410754 CYP2R1 cytochrome P450 2R1. CYP2R1, also called vitamin D 25-hydroxylase (EC 1.14.14.24), is a microsomal enzyme that is required for the activation of vitamin D; it catalyzes the initial step converting vitamin D into 25-hydroxyvitamin D (25(OH)D), the major circulating metabolite of vitamin D. The 1alpha-hydroxylation of 25(OH)D by CYP27B1 generates the fully active vitamin D metabolite, 1,25-dihydroxyvitamin D (1,25(OH)2D). Mutations in the CYP2R1 gene are associated with an atypical form of vitamin D-deficiency rickets, which has been classified as vitamin D dependent rickets type 1B. CYP2R1 belongs to family 2 of the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 436 matched cddid_all.tbl CDD cd20662 cd20662 410755 CYP2J cytochrome P450 family 2, subfamily J. Members of CYP2J are expressed in multiple tissues in mice and humans. They function as catalysts of arachidonic acid metabolism and are active in the metabolism of fatty acids to generate bioactive compounds. Human CYP2J2, also called arachidonic acid epoxygenase or albendazole monooxygenase (hydroxylating), is a membrane-bound cytochrome P450 primarily expressed in the heart and plays a significant role in cardiovascular diseases. The CYP2J subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 421 matched cddid_all.tbl CDD cd20663 cd20663 410756 CYP2D cytochrome P450 family 2, subfamily D. Members of CYP2D are present in mammals, birds, reptiles, and amphibians. The hominin CYP2D subfamily consists of a functional CYP2D6 and two paralogs, CYP2D7 and CYP2D8, that are often not functional in some species. Human CYP2D6 has a high affinity for alkaloids and can detoxify them. It is also responsible for metabolizing about 25% of commonly used drugs, such as antidepressants, beta-blockers, and antiarrhythmics. The CYP2D subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 428 matched cddid_all.tbl CDD cd20664 cd20664 410757 CYP2K cytochrome P450 family 2, subfamily K. Members of CYP2K are present in fish, birds, and amphibians. CYP2K6 from zebrafish has been shown to catalyze the conversion of aflatoxin B1 (AFB1) to its cytotoxic derivative AFB1 exo-8,9-epoxide, while its ortholog in rainbow trout CYP2K1 is also capable of oxidizing lauric acid. In birds, CYP2K is one of the largest CYP2 subfamilies. The CYP2K subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 424 matched cddid_all.tbl CDD cd20665 cd20665 410758 CYP2C-like cytochrome P450 family 2, subfamily C, and similar cytochrome P450s. This CYP2C-like group includes CYP2C, and similar CYPs including mammalian CYP2E1, also called 4-nitrophenol 2-hydroxylase, as well as chicken CYP2H1 and CYP2H2. The CYP2C subfamily is composed of four human members (CYP2C8, CYP2C9, CYP2C18, CYP2C19) that metabolize approximately 20% of clinically used drugs, and all four exhibit genetic polymorphisms that results in toxicity or altered efficacy of some drugs in affected individuals. CYP2E1 participates in the metabolism of endogenous substrates, including acetone and fatty acids, and exogenous compounds such as anesthetics, ethanol, nicotine, acetaminophen, aspartame, and chlorzoxazone, among others. The CYP2C-like subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 425 matched cddid_all.tbl CDD cd20666 cd20666 410759 CYP2U1 cytochrome P450 family 2, subfamily U, polypeptide 1. CYP2U1 is a thymus- and brain-specific cytochrome P450 that catalyzes omega- and (omega-1)-hydroxylation of fatty acids such as arachidonic acid, docosahexaenoic acid, and other long chain fatty acids. Mutations in CYP2U1 are associated with hereditary spastic paraplegia (HSP), a neurological disorder, and pigmentary degenerative maculopathy associated with progressive spastic paraplegia. CYP2U1 belongs to family 2 of the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 426 matched cddid_all.tbl CDD cd20667 cd20667 410760 CYP2AB1-like cytochrome P450, family 2, subfamily AB, polypeptide 1 and similar cytochrome P450s. The function of CYP2AB1 is unknown. CYP2AB1 belongs to family 2 of the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 423 matched cddid_all.tbl CDD cd20668 cd20668 410761 CYP2A cytochrome P450 family 2, subfamily A. Cytochrome P450 family 2, subfamily A (CYP2A) includes CYP2A1, 2A2, and 2A3 in rats; CYP2A4, 2A5, 2A12, 2A20p, 2A21p, 2A22, and 2A23p in mice; CYP2A6, 2A7, 2A13, 2A18P in humans; CYP2A8, 2A9, 2A14, 2A15, 2A16, and 2A17 in hamsters; CYP2A10 and 2A11 in rabbits; and CYP2A19 in pigs. CYP2A enzymes metabolize numerous xenobiotic compounds, including coumarin, aflatoxin B1, nicotine, cotinine, 1,3-butadiene, and acetaminophen, among others, as well as endogenous compounds, including testosterone, progesterone, and other steroid hormones. Human CYP2A6 is responsible for the systemic clearance of nicotine, while CYP2A13 activates the nicotine-derived procarcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) into DNA-altering compounds that cause lung cancer. The CYP2A subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 425 matched cddid_all.tbl CDD cd20669 cd20669 410762 Cyp2F cytochrome P450 family 2, subfamily F. Cytochrome P450 family 2, subfamily F (CYP2F) members are selectively expressed in lung tissues. They are responsible for the bioactivation of several pneumotoxic and carcinogenic chemicals such as benzene, styrene, naphthalene, and 1,1-dichloroethylene. CYP2F1 and CYP2F3 selectively catalyzes the 3-methyl dehydrogenation of 3-methylindole, forming toxic reactive intermediates that can form adducts with proteins and DNA. The CYP2F subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 425 matched cddid_all.tbl CDD cd20670 cd20670 410763 CYP2G cytochrome P450 family 2, subfamily G. CYP2G1 is uniquely expressed in the olfactory mucosa of rats and rabbits and may have important functions for the olfactory chemosensory system. It is involved in the metabolism of sex steroids and xenobiotic compounds. In cynomolgus monkeys, CYP2G2 is a functional drug-metabolizing enzyme in nasal mucosa. In humans, two different CYP2G genes, CYP2GP1 and CYP2GP2, are pseudogenes because of loss-of-function deletions/mutations. The CYP2G subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 425 matched cddid_all.tbl CDD cd20671 cd20671 410764 CYP2W1 cytochrome P450 family 2, subfamily W, polypeptide 1. Cytochrome P450 2W1 (CYP2W1) is expressed during development of the gastrointestinal tract, is silenced after birth in the intestine and colon by epigenetic modifications, but is activated following demethylation in colorectal cancer (CRC). Its expression levels in CRC correlate with the degree of malignancy, are higher in metastases and are predictive of survival. Thus, it is an attractive tumor-specific diagnostic and therapeutic target. CYP2W1 belongs to family 2 of the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 422 matched cddid_all.tbl CDD cd20672 cd20672 410765 CYP2B cytochrome P450 family 2, subfamily B. The human cytochrome P450 family 2, subfamily B (CYP2B) consists of only one functional member CYP2B6, which shows broad substrate specificity and plays a key role in the metabolism of many clinical drugs, environmental toxins, and endogenous compounds. Rodents have multiple functional CYP2B proteins; mouse subfamily members include CYP2B9, 2B10, 2B13, 2B19, and 2B23. CYP2B enzymes are highly inducible by chemicals that interact with the constitutive androstane receptor (CAR) and/or pregnane X receptor (PXR), such as rifampicin and phenobarbital. The CYP2B subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 425 matched cddid_all.tbl CDD cd20673 cd20673 410766 CYP17A1 cytochrome P450 family 17, subfamily A, polypeptide 1. Cytochrome P450 17A1 (CYP17A1 or Cyp17a1), also called cytochrome P450c17, steroid 17-alpha-hydroxylase (EC 1.14.14.19)/17,20 lyase (EC 1.14.14.32), or 17-alpha-hydroxyprogesterone aldolase, catalyzes the conversion of pregnenolone and progesterone to their 17-alpha-hydroxylated products and subsequently to dehydroepiandrosterone (DHEA) and androstenedione. It is a dual enzyme that catalyzes both the 17-alpha-hydroxylation and the 17,20-lyase reactions. Severe mutations on the enzyme cause combined 17-hydroxylase/17,20-lyase deficiency (17OHD); patients with 17OHD synthesize 11-deoxycorticosterone (DOC) which causes hypertension and hypokalemia. Loss of 17,20-lyase activity precludes sex steroid synthesis and leads to sexual infantilism. Included in this group is a second 17A P450 from teleost fish, CYP17A2, that is more efficient in pregnenolone 17-alpha-hydroxylation than CYP17A1, but does not catalyze the lyase reaction. CYP17A1 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 432 matched cddid_all.tbl CDD cd20674 cd20674 410767 CYP21 cytochrome P450 21, also called steroid 21-hydroxylase. Cytochrome P450 21 (CYP21 or Cyp21), also called steroid 21-hydroxylase (EC 1.14.14.16) or cytochrome P-450c21 or CYP21A2 (in humans), catalyzes the 21-hydroxylation of steroids such as progesterone and 17-alpha-hydroxyprogesterone (17-alpha-OH-progesterone) to form 11-deoxycorticosterone and 11-deoxycortisol, respectively. It is required for the adrenal synthesis of mineralocorticoids and glucocorticoids. Deficiency of this CYP is involved in ~95% of cases of human congenital adrenal hyperplasia, a disorder of adrenal steroidogenesis. There are two CYP21 genes in the human genome, CYP21A1 (a pseudogene) and CYP21A2 (the functional gene). Deficiencies in steroid 21-hydroxylase activity lead to a type of congenital adrenal hyperplasia, which has three clinical forms: a severe form with concurrent defects in both cortisol and aldosterone biosynthesis; a form with adequate aldosterone biosynthesis; and a mild, non-classic form that can be asymptomatic or associated with signs of postpubertal androgen excess without cortisol deficiency. CYP21A2 is also the major autoantigen in autoimmune Addison disease. Cyp21 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 424 matched cddid_all.tbl CDD cd20675 cd20675 410768 CYP1B1-like cytochrome P450 family 1, subfamily B, polypeptide 1 and similar cytochrome P450s. Cytochrome P450 1B1 (CYP1B1) is expressed in liver and extrahepatic tissues where it carries out the metabolism of numerous xenobiotics, including metabolic activation of polycyclic aromatic hydrocarbons. It is also important in regulating endogenous metabolic pathways, including the metabolism of steroid hormones, fatty acids, melatonin, and vitamins. CYP1B1 is overexpressed in a wide variety of tumors and is associated with angiogenesis. It is also associated with adipogenesis, obesity, hypertension, and atherosclerosis. It is therefore a target for the treatment of metabolic diseases and cancer. Also included in this subfamily are CYP1C proteins from fish, birds and amphibians. The CYP1B1-like subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 434 matched cddid_all.tbl CDD cd20676 cd20676 410769 CYP1A cytochrome P450 family 1, subfamily A. Cytochrome P450 family 1, subfamily A (CYP1A) consists of two human members, CYP1A1 and CYP1A2, which overlap in their activities. CYP1A2 is the highly expressed cytochrome enzyme in the human liver, while CYP1A1 is mostly found in extrahepatic tissues. Known common substrates include aromatic compounds such as polycyclic aromatic hydrocarbons, arachidonic acid and eicosapentoic acid, as well as melatonin and 6-hydroxylate melatonin. In addition, CYP1A1 activates procarcinogens into carcinogens via epoxides, and metabolizes heterocyclic aromatic amines of industrial origin. CYP1A2 metabolizes numerous natural products that result in toxic products, such as the transformation of methyleugenol to 1'-hydroxymethyleugenol, estragole to reactive metabolites, and oxidation of nephrotoxins. It also plays an important role in the metabolism of several clinical drugs including analgesics, antipyretics, antipsychotics, antidepressants, anti-inflammatory, and cardiovascular drugs. The CYP1A subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 437 matched cddid_all.tbl CDD cd20677 cd20677 410770 CYP1D1 cytochrome P450 family 1, subfamily D, polypeptide 1. The cytochrome P450 1D1 (CYP1D1) gene is pseudogenized in humans because of five nonsense mutations in the putative coding region. However, in other organisms including cynomolgus monkey, CYP1D1 is a functional drug-metabolizing enzyme that is highly expressed in the liver. CYP1D1 belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 435 matched cddid_all.tbl CDD cd20678 cd20678 410771 CYP4B-like cytochrome P450 family 4, subfamily B and similar cytochrome P450s, including subfamilies A, T, X, and Z. This group is composed of family 4 cytochrome P450s from subfamilies A (CYP4A), B (CYP4B), T (CYP4T), X (CYP4X), and Z (CYP4Z). The CYP4A, CYP4X, and CYP4Z subfamilies are specific to mammals, CYP4T is present in fish, while CYP4B is conserved among vertebrates. CYP4As are known for catalyzing arachidonic acid to 20-HETE (20-hydroxy-5Z,8Z,11Z,14Z-eicosatetraenoic acid), and some can also metabolize lauric and palmitic acid. CYP4Bs specialize in omega-hydroxylation of short chain fatty acids and also participates in the metabolism of exogenous compounds that are protoxic including valproic acid (C8), 3-methylindole (C9), 4-ipomeanol, 3-methoxy-4-aminoazobenzene, and several aromatic amines. CYP4X1 is expressed at high levels in the mammalian brain and may play a role in regulating fat metabolism. CYP4Z1 is a fatty acid hydroxylase that is unique among human CYPs in that it is predominantly expressed in the mammary gland. Monophyly was not found with the CYP4T and CYP4B subfamilies, and further consideration should be given to their nomenclature. The CYP4B-like group belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 436 matched cddid_all.tbl CDD cd20679 cd20679 410772 CYP4F cytochrome P450 family 4, subfamily F. Cytochrome P450 family 4, subfamily F (CYP4F) enzymes are known for known for omega-hydroxylation of very long fatty acids (VLFA; C18-C26), leukotrienes, prostaglandins, and vitamins with long alkyl side chains. The CYP4F subfamily show diverse specificities among its members: CYP4F2 and CYP4F3 metabolize pro- and anti-inflammatory leukotrienes; CYP4F8 and CYP4F12 metabolize prostaglandins, endoperoxides and arachidonic acid; CYP4F11 and CYP4F12 metabolize VLFA and are unique in the CYP4F subfamily since they also hydroxylate xenobiotics such as benzphetamine, ethylmorphine, erythromycin, and ebastine. CYP4F belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 442 matched cddid_all.tbl CDD cd20680 cd20680 410773 CYP4V cytochrome P450 family 4, subfamily V. Cytochrome P450 family 4, subfamily V, polypeptide 2 (CYP4V2) is the most characterized member of the CYP4V subfamily. It is a selective omega-hydroxylase of saturated, medium-chain fatty acids, such as laurate, myristate and palmitate, with high catalytic efficiency toward myristate. Polymorphisms in the CYP4V2 gene cause Bietti's crystalline corneoretinal dystrophy (BCD), a recessive degenerative retinopathy that is characterized clinically by a progressive decline in central vision, night blindness, and constriction of the visual field. The CYP4V subfamily belongs to the large cytochrome P450 (P450, CYP) superfamily of heme-containing proteins that catalyze a variety of oxidative reactions of a large number of structurally different endogenous and exogenous compounds in organisms from all major domains of life. CYPs bind their diverse ligands in a buried, hydrophobic active site, which is accessed through a substrate access channel formed by two flexible helices and their connecting loop. 440 matched cddid_all.tbl CDD cd20681 cd20681 410332 T-box_Drosocross-like DNA-binding domain of Drosophila Dorsocross and related T-box proteins. Drosophila Dorsocross (Doc) includes three Dorsocross paralogs, Doc1-3. These are key cardiogenic T-box transcription factors during specification and differentiation of heart cells. Drosophila Doc also functions in caudal visceral mesoderm development, and modulates Notch signaling in the developing Drosophila eye by regulating the expression of Delta in the eye imaginal discs. Doc also functions in the morphogenesis of epithelial tissues: in Drosophila, which possesses a single extraembryonic (EE) membrane, it is essential for EE epithelia tissue maintenance while in Tribolium castaneum, which has 2 EE membranes, Doc plays a major role in EE morphogenetic events throughout development without affecting EE tissue specificity or maintenance. This subfamily belongs to the T-box family of transcription factors which play a multitude of diverse functions throughout development. The founding member of the T-box family is Brachyury (also known as TBXT, or T). T-box family members share a conserved DNA-binding domain (T-box) which binds DNA in a sequence-specific manner. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development, and conserved expression patterns. 186 matched cddid_all.tbl CDD cd20682 cd20682 410333 T-box-like T-box DNA-binding domain; uncharacterized subfamily. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors. 191 matched cddid_all.tbl CDD cd20683 cd20683 410334 T-box_Fungi_incertae_sedis T-box DNA-binding domain; uncharacterized subfamily of fungi classified as Fungi incertae sedis. Fungi incertae sedis refers to a fungal taxonomic group where its broader relationships are unknown or undefined. The T-box family is an ancient group that appears to play a critical role in development in all animal species. These genes were uncovered on the basis of similarity to the DNA binding domain of murine Brachyury (T) gene product, the defining feature of the family. Common features shared by T-box family members are DNA-binding and transcriptional regulatory activity, a role in development and conserved expression patterns, most of the known genes in all species being expressed in mesoderm or mesoderm precursors. 214 matched cddid_all.tbl CDD cd20684 cd20684 411002 CdiA-CT_Yk_RNaseA-like C-terminal (CT) domain of the contact-dependent growth inhibition (CDI) system protein CdiA (CdiA-CT) of Yersinia kristensenii, and similar proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. This model represents the C-terminal (CT) toxin domain of CdiA effector protein from Yersinia kristensenii and similar proteins. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via the C-terminal domain. A wide variety of C-terminal toxin domains appear to exist; Yersinia kristensenii CdiA-CT has potent RNase activity in vivo and in vitro. Although CdiA-CT has structural homology with angiogenin and other RNase A paralogs, it does not share sequence similarity with these nucleases and lacks the characteristic disulfide bonds of the superfamily. It binds its cognate immunity protein CdiI which neutralizes toxicity by blocking access to RNA substrates. Y. kristensenii CdiA-CT is the first non-vertebrate protein found to possess the RNase A superfamily fold. Homologs of this toxin are associated with secretion systems in many Gram-negative and Gram-positive bacteria, suggesting that RNase A-like toxins are commonly deployed in inter-bacterial competition. 112 matched cddid_all.tbl CDD cd20685 cd20685 411003 CdiA-CT_Ecl_RNase-like C-terminal (CT) domain of the contact-dependent growth inhibition (CDI) system (CdiA-CT) protein CdiA of Enterobacter cloacae, and similar proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via the C-terminal domain. A wide variety of C-terminal toxin domains appear to exist; this particular model contains the C-terminal (CT) domain of Enterobacter cloacae CdiA and similar domains. This CdiA-CT toxin has structural homology to the C-terminal nuclease domain of colicin E3, which cleaves 16S ribosomal RNA to disrupt protein synthesis, and has been shown to use the same nuclease activity to inhibit bacterial growth. The CdiA-CT toxin is specifically neutralized by cognate immunity protein CdiI to protect the toxin-producing cell from autoinhibition. Despite carrying equivalent toxin domains, the corresponding immunity proteins for CdiA-CT and colicin E3 are unrelated in sequence, structure, and toxin-binding site, thus showing diversity among 16S rRNase toxins. 75 matched cddid_all.tbl CDD cd20686 cd20686 411004 CdiA-CT_Ec-like C-terminal (CT) domain of the contact-dependent growth inhibition (CDI) system (CdiA-CT) protein CdiA of Escherichia coli STEC_O31, and similar proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via the C-terminal domain. A wide variety of C-terminal toxin domains appear to exist; this particular model contains the C-terminal (CT) domain of Escherichia coli STEC_O31 CdiA and similar domains. The function of this CdiA-CT is as yet unknown, but its C-terminal end is similar to EndoU domain-containing protein which may act as a nuclease toxin that cleaves RNAs in competitor cells. CDI(+) bacteria also produce a CDI immunity protein (CdiI) to specifically neutralize the CdiA-CT toxins to prevent auto-inhibition. This CdiA-CT binds its cognate CdiI with high affinity. 135 matched cddid_all.tbl CDD cd20687 cd20687 412039 CdiI_Ykris-like inhibitor (or immunity protein) of the contact-dependent growth inhibition (CDI) system of Yersinia kristensenii, and similar proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. This model represents the inhibitor (CdiI, also called CdiI immunity protein) of the CdiA effector protein from Yersinia kristensenii (which is an RNase), and similar proteins. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via its C-terminal domain (CdiA-CT). The CdiI immunity proteins are intracellular proteins that inactivate the toxin/effector protein. They are specific for their cognate CdiA-CT and do not protect cells from the toxins of other CDI+ bacteria. The CdiI immunity protein binds the CdiA toxin via its C-terminal domain to prevent auto-inhibition. Thus, CDI systems encode a complex network of toxin-immunity protein pairs that are deployed for intercellular competition. Y. kristensenii CdiI binds directly over the putative active site of the CdiA-CT toxin and likely neutralizes toxicity by blocking access to RNA substrates. 90 matched cddid_all.tbl CDD cd20688 cd20688 412040 CdiI_Ecoli_Nm-like inhibitor (or immunity protein) of the contact-dependent growth inhibition (CDI) system of Escherichia coli STEC_O31, Neisseria meningitidis MC58, and similar proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. This model represents the inhibitor (CdiI, also called CdiI immunity protein) of the CdiA effector protein from Escherichia coli STEC_O31 Neisseria meningitidis MC58, and similar proteins. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via its C-terminal domain (CdiA-CT). The CdiI immunity proteins are intracellular proteins that inactivate the toxin/effector protein to prevent auto-inhibition. They are specific for their cognate CdiA-CT and do not protect cells from the toxins of other CDI+ bacteria. Thus, CDI systems encode a complex network of toxin-immunity protein pairs that are deployed for intercellular competition. Neisseria meningitidis MC58 immunity protein CdiI has structural homology to the Whirly family of RNA-binding proteins, but lacks the characteristic nucleic acid-binding motif of the family. It has been predicted to neutralize toxin activity by preventing access to RNA substrates. 100 matched cddid_all.tbl CDD cd20689 cd20689 412042 CDI_toxin_Bp_tRNase-like C-terminal (CT) domain of the contact-dependent growth inhibition (CDI) system (CdiA-CT) of Burkholderia pseudomallei, and similar proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. This model represents the C-terminal (CT) toxin domain of CdiA effector proteins. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via the C-terminal domain. A wide variety of C-terminal toxin domains appear to exist; this particular model includes the C-terminal (CT) toxin domains of Burkholderia pseudomallei E479 and 1026b, both appearing to be RNAses acting on tRNA. 99 matched cddid_all.tbl CDD cd20690 cd20690 412045 CdiI_BpE479-like inhibitor (or immunity protein) of the contact-dependent growth inhibition (CDI) system of Burkholderia pseudomallei E479, and similar proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. This model represents the inhibitor (CdiI, also called CdiI immunity protein) of the CdiA effector protein from Burkholderia pseudomallei E479 (which is a tRNase). CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via its C-terminal domain (CdiA-CT). The CdiI immunity proteins are intracellular proteins that inactivate the toxin/effector protein to prevent auto-inhibition. They are specific for their cognate CdiA-CT and do not protect cells from the toxins of other CDI+ bacteria. Thus, CDI systems encode a complex network of toxin-immunity protein pairs that are deployed for intercellular competition. Although related B. pseudomallei E479 CdiA-CT has structural homology to B. pseudomallei 1026B CdiA-CT (both tRNases), their cognate CdiI immunity proteins share no significant sequence or structure homology. This CdiI binds its cognate toxin CdiA-CT domain with high affinity. 100 matched cddid_all.tbl CDD cd20691 cd20691 412046 CdiI_EC536-like inhibitor (or immunity protein) of the contact-dependent growth inhibition (CDI) system of Escherichia coli 536, and similar proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. This model represents the inhibitor (CdiI, also called CdiI immunity protein) of the CdiA effector protein from Escherichia coli 536 (which is a predicted RNase), and similar proteins. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via its C-terminal domain (CdiA-CT). The CdiI immunity proteins are intracellular proteins that inactivate the toxin/effector protein to prevent auto-inhibition. They are specific for their cognate CdiA-CT and do not protect cells from the toxins of other CDI+ bacteria. Thus, CDI systems encode a complex network of toxin-immunity protein pairs that are deployed for intercellular competition. This E. coli CdiI's cognate toxin CdiA-CT domain is activated only when it is bound to the biosynthetic enzyme O-acetylserine sulfhydrylase-A (CysK), one of two isoenzymes (along with CysM) that catalyze the final reaction in cysteine synthesis. CdiA's predicted nuclease active site is occluded by immunity protein in the CysK/CdiA-CT/CdiI structure, suggesting that CdiI blocks the binding of tRNA substrates to the toxin. 120 matched cddid_all.tbl CDD cd20692 cd20692 411005 CdiA-CT_Ec-like C-terminal (CT) domain of the contact-dependent growth inhibition (CDI) system (CdiA-CT) protein CdiA of Escherichia coli A0 34/86, and similar proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via the C-terminal domain. A wide variety of C-terminal toxin domains appear to exist; this particular model contains the C-terminal (CT) domain Escherichia coli A0 34/86 CdiA. Activity of this E. coli CdiA-CT is as yet unknown. CDI(+) bacteria also produce a CDI immunity protein (CdiI) to specifically neutralize the CdiA-CT toxins to prevent auto-inhibition. This CdiA-CT binds its cognate CdiI with high affinity. 99 matched cddid_all.tbl CDD cd20693 cd20693 412047 CdiI_EcoliA0-like inhibitor (or immunity protein) of the contact-dependent growth inhibition (CDI) system of Escherichia coli A0 34/86, and similar proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. This model represents the inhibitor (CdiI, also called CdiI immunity protein) of the CdiA effector protein from Escherichia coli A0 34/86, and similar proteins. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via its C-terminal domain (CdiA-CT). The CdiI immunity proteins are intracellular proteins that inactivate the toxin/effector protein to prevent auto-inhibition. They are specific for their cognate CdiA-CT and do not protect cells from the toxins of other CDI+ bacteria. Thus, CDI systems encode a complex network of toxin-immunity protein pairs that are deployed for intercellular competition. This E. coli CdiI binds its cognate toxin CdiA-CT domain with high affinity. 124 matched cddid_all.tbl CDD cd20694 cd20694 412048 CdiI_Ct-like inhibitor (or immunity protein) of the contact-dependent growth inhibition (CDI) system of Cupriavidus taiwanensis CdiI immunity protein and similar proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. This model represents the inhibitor (CdiI, also called CdiI immunity protein) of the CdiA effector protein from Cupriavidus taiwanensis, and similar proteins. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via its C-terminal domain (CdiA-CT). The CdiI immunity proteins are intracellular proteins that inactivate the toxin/effector protein to prevent auto-inhibition. They are specific for their cognate CdiA-CT and do not protect cells from the toxins of other CDI+ bacteria. Thus, CDI systems encode a complex network of toxin-immunity protein pairs that are deployed for intercellular competition. This C. taiwanensis CdiI is alpha-helical and binds its cognate toxin CdiA-CT domain with high affinity. 96 matched cddid_all.tbl CDD cd20695 cd20695 411006 CdiA-CT_5T87E_Ct C-terminal (CT) domain of the contact-dependent growth inhibition (CDI) system protein CdiA (CdiA-CT) of Cupriavidus taiwanensis, and related proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via the C-terminal domain. A wide variety of C-terminal toxin domains appear to exist; this particular model contains the C-terminal (CT) domain of Cupriavidus taiwanensis CdiA. The exact biochemical function of this CdiA-CT cannot be predicted easily and may include RNase or DNase activity. CDI(+) bacteria also produce a CDI immunity protein (CdiI) to specifically neutralize the CdiA-CT toxins to prevent auto-inhibition. This CdiA-CT binds its cognate CdiI with high affinity. 61 matched cddid_all.tbl CDD cd20696 cd20696 412049 CdiI_Ecoli3006-like inhibitor (or immunity protein) of the contact-dependent growth inhibition (CDI) system of Escherichia coli 3006, and similar proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. This model represents the inhibitor (CdiI, also called CdiI immunity protein) of the CdiA effector protein from Escherichia coli 3006, and similar proteins. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via its C-terminal domain (CdiA-CT). The CdiI immunity proteins are intracellular proteins that inactivate the toxin/effector protein to prevent auto-inhibition. They are specific for their cognate CdiA-CT and do not protect cells from the toxins of other CDI+ bacteria. Thus, CDI systems encode a complex network of toxin-immunity protein pairs that are deployed for intercellular competition. The E. coli CdiI binds its cognate CdiA-CT with high affinity via one end of its beta-sandwich structure. 150 matched cddid_all.tbl CDD cd20697 cd20697 410969 CdiA-CT_Ec_Kp-like C-terminal (CT) domain of the contact-dependent growth inhibition (CDI) system (CdiA-CT) of Escherichia coli and Klebsiella pneumoniae CdiA, and similar proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. This model represents the C-terminal (CT) toxin domain of CdiA effector proteins. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via the C-terminal. A wide variety of C-terminal toxin domains appear to exist; this particular model contains the C-terminal domain of CdiA (CdiA-CT) from Escherichia coli, Klebsiella pneumoniae and other bacteria. The exact biochemical function of this CdiA-CT is as yet unknown. CDI(+) bacteria also produce a CDI immunity protein (CdiI) to specifically neutralize the CdiA-CT toxins to prevent auto-inhibition. This CdiA-CT binds its cognate CdiI with high affinity. 94 matched cddid_all.tbl CDD cd20698 cd20698 412050 CdiI_Kp-like inhibitor (or immunity protein) of the contact-dependent growth inhibition (CDI) system of Klebsiella pneumoniae, and similar proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. This model represents the inhibitor (CdiI, also called CdiI immunity protein) of the CdiA effector protein from Klebsiella pneumoniae, and similar proteins. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via its C-terminal domain (CdiA-CT). The CdiI immunity proteins are intracellular proteins that inactivate the toxin/effector protein to prevent auto-inhibition. They are specific for their cognate CdiA-CT and do not protect cells from the toxins of other CDI+ bacteria. Thus, CDI systems encode a complex network of toxin-immunity protein pairs that are deployed for intercellular competition. The K. pneumoniae CdiI binds its cognate CdiA-CT via one end of its beta-sandwich structure. 110 matched cddid_all.tbl CDD cd20699 cd20699 412051 CdiI_ECL-like inhibitor (or immunity protein) of the contact-dependent growth inhibition (CDI) system of Enterobacter cloacae, and similar proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. This model represents the inhibitor (CdiI, also called CdiI immunity protein) of the CdiA effector protein from Enterobacter cloacae, and similar proteins. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via its C-terminal domain (CdiA-CT). The CdiI immunity proteins are intracellular proteins that inactivate the toxin/effector protein to prevent auto-inhibition. They are specific for their cognate CdiA-CT and do not protect cells from the toxins of other CDI+ bacteria. Thus, CDI systems encode a complex network of toxin-immunity protein pairs that are deployed for intercellular competition. Although E. cloacae CdiA-CT has structural homology to the C-terminal nuclease domain of colicin E3, which cleaves 16S ribosomal RNA to disrupt protein synthesis, and has been shown to use the same nuclease activity to inhibit bacterial growth, the corresponding CdiI immunity proteins are unrelated in sequence, structure and toxin-binding sites. Structural homology searches reveal that E. cloacae CdiI is most similar to the Whirly family of single-stranded DNA-binding proteins. 141 matched cddid_all.tbl CDD cd20700 cd20700 411007 CdiA-CT_Ec_tRNase C-terminal (CT) domain of the contact-dependent growth inhibition (CDI) system protein CdiA (CdiA-CT) of Escherichia coli 563, and similar proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via the C-terminal domain. A wide variety of C-terminal toxin domains appear to exist; this particular model contains the C-terminal (CT) domain Escherichia coli 563 CdiA and similar domains. This CdiA-CT (EC536) region is composed of two domains that have distinct functions during CDI. This domain is the extreme C-terminal domain, an RNase toxin that possesses an all alpha-helical fold and conserved aspartate and glutamate residues, and K[DE] and [DN]HxxE motifs. The N-terminal domain facilitates translocation of the tethered nuclease into the cytosol of target bacteria. Although this CdiA-CT rapidly cleaves tRNA in vivo, the purified toxin has no detectable nuclease activity in vitro. Experiments show that it is activated when bound to the biosynthetic enzyme O-acetylserine sulfhydrylase-A (CysK), which is one of two isoenzymes (along with CysM) that catalyze the final reaction in cysteine synthesis. CDI(+) bacteria also produce a CDI immunity protein (CdiI) to specifically neutralize the CdiA-CT toxins to prevent auto-inhibition. This CdiA-CT binds its cognate CdiI with high affinity. 115 matched cddid_all.tbl CDD cd20701 cd20701 410945 MIX Marker for type sIX effectors domain. This family contains the MIX (Marker for type sIX effectors) domain, a marker of type VI secretion system (T6SS) effectors carrying polymorphic C-terminal toxins. MIX domains have been classified into five clans (called MIX I-V) by Dar et. al. based on sequence similarity. These domains have been further classified as either antibacterial or anti-eukaryotic, based on the presence or absence of adjacent putative immunity genes, respectively. In Vibrionaceae, antibacterial MIX-effectors carrying domains with pore-forming, phospholipase, nuclease, peptidoglycan hydrolase, and protease activities have been identified. Additionally, novel virulence MIX-effectors that employ a combination of antibacterial and anti-eukaryotic MIX-effectors have been found, suggesting that certain bacteria adapted their antibacterial T6SS to mediate interactions with eukaryotic hosts or predators. A subset of polymorphic MIX-effectors, a widespread class of effectors secreted by T6SSs, are horizontally shared between marine bacteria and used to diversify their T6SS effector repertoires, thus enhancing their environmental fitness. 128 matched cddid_all.tbl CDD cd20702 cd20702 410637 PoNe Polymorphic Nuclease effector (PoNe) domain is a deoxyribonuclease. This family contains the DNase toxin domain called PoNe (Polymorphic Nuclease effector), which belongs to a diverse superfamily of PD-(D/E)xK phosphodiesterases, and is associated with several toxin delivery systems including type V, type VI, and type VII. PoNe toxicity is antagonized by cognate immunity proteins (PoNi) containing DUF1911 and DUF1910 domains. The PoNe domain co-occurs with a variety of N-terminal domains such as filamentous hemagglutinin, nuclease, HINT, DUFs, PAAR, RHS repeat, or LXG domains. Some members of this family also co-occur with the FIX (Found in type sIX effector) domain of unknown function, as identified by Jana et al., who have also identified this PoNe domain. 77 matched cddid_all.tbl CDD cd20703 cd20703 410939 FIX-like Found in type sIX effector (FIX) domain of unknown function. This family contains the Found in type sIX effector (FIX) domain and similar proteins. FIX is found N-terminal to known toxin domains and is genetically and functionally linked to type VI secretion system (T6SS), a widespread mechanism used by Gram-negative bacteria to antagonize neighboring cells. In Vibrio parahaemolyticus, it also co-occurs with C-terminal nuclease toxin PoNe (Polymorphic Nuclease effector) which is associated with several toxin delivery systems including type V, type VI, and type VII. FIX is present in various established T6SS-secreted effectors that have an N-terminal VgrG or PAAR or PAAR-like (i.e., DUF4280) domain, suggesting that FIX may play a role in delivery of T6SS effectors, and serve as a new marker for T6SS-delivered proteins to enable the identification of novel T6SS substrates. 75 matched cddid_all.tbl CDD cd20704 cd20704 412052 Orc3 Origin recognition complex subunit 3. Origin recognition complex subunit 3 (Orc3) is a subunit of the heterohexameric origin recognition complex (ORC) that is essential for coordinating replication onset. ORC binds to the origin of replication, binds CDC6, and recruits the hexameric MCM2-7 ring to the DNA, which leads to the assembly of the pre-replicative complex (pre-RC). Five of the 6 ORC subunits (Orc 1-5) retain AAA+ (ATPases associated with a variety of cellular activities) folds, but Orc3, as well as Orc2, lost their ATP-binding signatures. 387 matched cddid_all.tbl CDD cd20705 cd20705 410946 MIX_I Marker for type sIX effectors domain, clan I. This subfamily contains the MIX (Marker for type sIX effectors) clan I (MIX I) domain. MIX is a marker of type VI secretion system (T6SS) effectors carrying polymorphic C-terminal toxins predicted to mediate antibacterial toxicity. These C-terminal toxin domains of Vibrionaceae MIX I effectors include pore-forming, nuclease and nucleotide deaminase activities. Members of the MIX I clan are similar, in both sequence and synteny, to the Vibrio parahaemolyticus MIX-effector VP1388, but their activity is unknown. Notably, many toxins identified as T6SS effectors do not contain a recognizable delivery domain or signal, suggesting that additional delivery domains may exist. 115 matched cddid_all.tbl CDD cd20706 cd20706 410947 MIX_II Marker for type sIX effectors domain, clan II. This subfamily contains the MIX (Marker for type sIX effectors) II clan (MIX II) domain. MIX is a marker of type VI secretion system (T6SS) effectors carrying polymorphic C-terminal toxins. Predicted activity of the C-terminal toxin domains of Vibrionaceae MIX II effectors is mainly pore-forming. Notably, many toxins identified as T6SS effectors do not contain a recognizable delivery domain or signal, suggesting that additional delivery domains may exist. Also, some of these MIX II effectors also contain N-terminal domains such as the T6SS-secreted tail component PAAR. 149 matched cddid_all.tbl CDD cd20707 cd20707 410948 MIX_III Marker for type sIX effectors domain, clan III. This subfamily contains the MIX (Marker for type sIX effectors) III clan (MIX III) domain. MIX is a marker of type VI secretion system (T6SS) effectors carrying polymorphic C-terminal toxins. No MIX III clan members have been detected in Vibrionaceae. Predicted activity of the C-terminal toxin domains of MIX III effectors is mainly pore-forming. Studies have shown that many members of the MIX III clan neighbor transposable elements. Notably, many toxins identified as T6SS effectors do not contain a recognizable delivery domain or signal, suggesting that additional delivery domains may exist. 137 matched cddid_all.tbl CDD cd20708 cd20708 410949 MIX_IV Marker for type sIX effectors domain, clan IV. This subfamily contains the MIX (Marker for type sIX effectors) IV clan (MIX IV) domain. MIX is a marker of type VI secretion system (T6SS) effectors carrying polymorphic C-terminal toxins. Predicted activity of the C-terminal toxin domains of Vibrionaceae MIX IV effectors is mainly pore-forming. Members of MIX IV are similar, in both sequence and synteny, to the Vibrio parahaemolyticus MIX-effector VP1388, but their activity is unknown. Notably, many toxins identified as T6SS effectors do not contain a recognizable delivery domain or signal, suggesting that additional delivery domains may exist. 133 matched cddid_all.tbl CDD cd20709 cd20709 410950 MIX_V Marker for type sIX effectors domain, clan V. This subfamily contains the MIX (Marker for type sIX effectors) V clan (MIX V) domain. MIX is a marker of type VI secretion system (T6SS) effectors carrying polymorphic C-terminal toxins. Predicted antibacterial activities of the C-terminal toxin domains of Vibrionaceae MIX V effectors include peptidase, peptidoglycan hydrolase, nuclease and pore-forming. Also included in this clan is VPR01S_11_01570, encoded by V. proteolyticus, that carries a CNF1 (cytotoxic necrotizing factor 1) toxin domain and modulates the actin cytoskeleton of eukaryotic phagocytic cells. Some members contain DUF2235, which is predicted as a phospholipase domain. Members of the MIX V clan are shared between marine bacteria via horizontal gene transfer, thereby enhancing their bacterial competitive fitness. Notably, many toxins identified as T6SS effectors do not contain a recognizable delivery domain or signal, suggesting that additional delivery domains may exist. 123 matched cddid_all.tbl CDD cd20710 cd20710 411008 NOT1_connector Connector domain of NOT1. This NOT1 connector domain is one of several catalytically inactive subunits of the multisubunit CCR4-NOT complex assembly that plays a central role in post-translational gene regulation in eukaryotes. CCR4-NOT contains the catalytic center formed by two deadenylase subunits CCR4 and CAF1, and the conserved core complex which contains a minimum of four catalytically inactive subunits, NOT1, NOT2, NOT3 and CAF40/NOT9. NOT1 is the largest subunit which functions as a central scaffold for complex assembly in human orthologs. The Chaetomium thermophilum NOT1 connector domain consists of five alpha-helical hairpin repeats of the HEAT type that structurally resemble MIF4G domains, and hence is also called the MIF4G-C domain. However, NOT1 MIF4G-C does not interact with DEAD-box helicases such as DDX6 like MIF4G does. Structural conservation of this domain suggests an important role but its function is as yet unknown. 202 matched cddid_all.tbl CDD cd20712 cd20712 411009 LNYV_P-protein-C_like C-terminal domain of lettuce necrotic yellows virus phosphoprotein and related domains. This family includes the C-terminal domain of the P protein of plant viruses belonging to the Rhabdoviridae family such as Lettuce necrotic yellows virus (LNYV). LNYV P protein acts as a weak local RNA silencing suppressor in plants to counteract RNA silencing antiviral defense. It suppresses both RNA induced silencing complex (RISC)-mediated cleavage and RNA silencing amplification. The C-terminal domain of LNYV P protein is essential for both local RNA silencing suppression and interaction with Argonaute (AGO) 1, AGO2, and AGO4 (key components of the RISC complexes), and with SGS3 and RDR6 (which function in the amplification step of RNA silencing). The family Rhabdoviridae belongs to the order Mononegavirales which are nonsegmented negative-stranded RNA viruses (NNVs). The genomes of NNVs are encapsidated by their nucleocapsid (N) proteins to form N-RNA complexes which serves as a template for transaction and replication. The C-terminus of P protein binds nucleocapsid. P protein plays multiple roles in transcription and translation, including acting as a chaperone of nascent nucleoprotein (N), and as a cofactor of the viral polymerase (L) where P forms a two-subunit polymerase with a large catalytic subunit (L) and stabilizes the polymerase on its template of N-RNA. 69 matched cddid_all.tbl CDD cd20714 cd20714 411010 NSP3_rotavirus rotavirus non-structural protein 3 (NSP3). Rotaviruses co-opt the eukaryotic translation machinery during their life cycle. Most eukaryotic mRNAs are characterized by a 5' cap structure and a 3' poly(A) tail. Eukaryotic translation initiation is facilitated by interactions between the 3' poly(A) tail and the 5' end of the message mediated by poly(A) binding protein (PABP) and eukaryotic translation initiation factor 4G (eIF4G). Rotavirus NSP3 is a functional analog of PABP that enables rotaviruses to direct eukaryotic translation machinery to viral mRNAs. It binds to the 3' consensus sequence of viral mRNA and participates in mRNA circularization by interacting with eIF4G. NSP3 closes the viral mRNA loop and facilitates translation of its own mRNAs while blocking recruitment of PABP to the eukaryotic translation initiation machinery. 127 matched cddid_all.tbl CDD cd20716 cd20716 410956 cyt_P460_fam Cytochrome P460 family. The cytochrome P460 family is composed mostly of monoheme, ~17 kDa, c-cytochromes typified by the cytochromes P460 of Nitrosomonas europaea and Methylococcus capsulatus (Bath), and the cytochrome c'-beta of M. capsulatus. Members of this family can be characterized by a predominantly beta-sheet structure as opposed to the four elongate, tightly-packed alpha-helices of the widely distributed cytochromes c' of photoheterotrophic and denitrifying bacteria. They are involved in the oxidation/reduction or ligation of N-oxides for detoxification or energy generation. Phylogenetic studies suggest that cytochrome P460 (cytL) genes evolved from ancestral cytochrome c'-beta genes (cytS) by acquisition of features including the lysine-heme cross-link. The protein-bound c-type heme cofactor, heme P460, named for its characteristic ferrous Soret peak maximum at 460 nm, has the distinction of being the only known heme in biology to withdraw electrons from an iron coordinated substrate. 124 matched cddid_all.tbl CDD cd20718 cd20718 467720 8prop_heme_binding_protein eight-bladed beta-propeller heme-binding domain in cytochrome cd1 and similar proteins. Members here contain an 8-bladed beta-propeller heme-binding domain in cytochrome cd1 (nitrite reductase) and similar proteins including NirN and NirF. During denitrification, nitrate (Nar), nitrite (Nir), nitric oxide (Nor), and nitrous oxide (Nos) reductases catalyze the reaction cascade of NO(3-)-> NO(2-)-> NO -> N2O -> N2. The integral membrane proteins NorC, NorB, and NosR form the core assembly platform that binds the nitrate reductase NarGHI and the periplasmic nitrite reductase NirS via its maturation factor NirF. NirN and NirF form a stable complex with the nitrite reductase NirS during enzyme maturation. NirF is involved in heme d1 insertion. 380 matched cddid_all.tbl CDD cd20721 cd20721 410310 CYCLIN_SDS-like_rpt2 second cyclin box found in Arabidopsis thaliana cyclin-SDS and similar proteins. Cyclin-SDS, also called protein SOLO DANCERS, is a meiosis-specific cyclin that is required for normal homolog synapsis and recombination in early to mid-prophase 1. It contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 104 matched cddid_all.tbl CDD cd20722 cd20722 410311 CYCLIN_CCNO_rpt2 second cyclin box found in cyclin-O (CCNO). CCNO is specifically required for generation of multiciliated cells, possibly by promoting a cell cycle state compatible with centriole amplification and maturation. It acts downstream of MCIDAS (multiciliate differentiation and DNA synthesis associated cell cycle protein) to promote mother centriole amplification and maturation in preparation for apical docking. CCNO is involved in the activation of cyclin-dependent kinase 2. CCNO contains two cyclin boxes. This model corresponds to the second one. The cyclin box is a protein binding domain. 97 matched cddid_all.tbl CDD cd20723 cd20723 410970 CdiA-CT_Ec-like C-terminal (CT) domain of the contact-dependent growth inhibition (CDI) system (CdiA-CT) of Escherichia coli CdiA, and similar proteins. This family includes the C-terminal (CT) domain of Escherichia coli CdiA, an effector protein involved in contact-dependent growth inhibition (CDI), a mechanism of inter-bacterial competition. The large CdiA effector protein carries a C-terminal toxin domain (CdiA-CT) which is delivered to neighboring bacteria to inhibit target-cell growth. The exact biochemical function of this E. coli CdiA is as yet unknown. CDI(+) bacteria also produce a CDI immunity protein (CdiI) to specifically neutralize the CdiA-CT toxins to prevent auto-inhibition. This CdiA-CT binds its all helical cognate CdiI with high affinity. 160 matched cddid_all.tbl CDD cd20724 cd20724 410971 CdiA-CT_Kp342-like C-terminal (CT) domain of the contact-dependent growth inhibition (CDI) system (CdiA-CT) of Klebsiella pneumoniae 342 CdiA, and similar proteins. This family includes the C-terminal (CT) domain of Klebsiella pneumoniae CdiA, an effector protein involved in contact-dependent growth inhibition (CDI), a mechanism of inter-bacterial competition. The large CdiA effector protein carries a C-terminal toxin domain (CdiA-CT) which is delivered to neighboring bacteria to inhibit target-cell growth. The exact biochemical function of this CdiA-CT is as yet unknown. CDI(+) bacteria also produce a CDI immunity protein (CdiI) to specifically neutralize the CdiA-CT toxins to prevent auto-inhibition. This CdiA-CT binds its cognate CdiI immunity protein (all beta-sheet structure) with high affinity. 107 matched cddid_all.tbl CDD cd20725 cd20725 410972 CdiA-CT_Kp-like CdiA C-terminal domain of the contact-dependent growth inhibition (CDI) system (CdiA-CT) similar to Klebsiella pneumoniae CdiA-CT. This family includes the C-terminal (CT) domain of bacterial CdiA, an effector protein involved in contact-dependent growth inhibition (CDI), a mechanism of inter-bacterial competition. The large CdiA effector protein carries a C-terminal toxin domain (CdiA-CT) which is delivered to neighboring bacteria to inhibit target-cell growth. Many of the domains in this family are associated with RHS repeats N-terminal to the domain. The exact biochemical function of this CdiA-CT is as yet unknown. CDI(+) bacteria also produce a CDI immunity protein (CdiI) to specifically neutralize the CdiA-CT toxins to prevent auto-inhibition. This CdiA-CT binds its cognate CdiI with high affinity. 99 matched cddid_all.tbl CDD cd20726 cd20726 412043 CDI_toxin_BpE479_tRNase-like C-terminal (CT) toxin domain of the contact-dependent growth inhibition (CDI) system (CdiA-CT) of Burkholderia pseudomallei, and similar proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. This model represents the C-terminal (CT) toxin domain of CdiA effector proteins. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via the C-terminal domain. A wide variety of C-terminal toxin domains appear to exist; this particular model contains the C-terminal (CT) domain of Burkholderia pseudomallei E479 CdiA. This CdiA-CT domain is a tRNAse that contains a core alpha/beta-fold that is characteristic of PD(D/E)XK superfamily nucleases. It is structurally similar to another CDI toxin domain from B. pseudomallei 1026b which is unrelated in sequence but has a similar nuclease domain, and shares similar fold and active-site architecture. The PD(D/E)XK superfamily includes most restriction endonucleases and other enzymes involved in DNA recombination and repair. 121 matched cddid_all.tbl CDD cd20727 cd20727 412044 CDI_toxin_Bp_tRNase-like C-terminal (CT) toxin domain of a contact-dependent growth inhibition (CDI) system (CdiA-CT) similar to that of Burkholderia pseudomallei, and related proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. This model represents the C-terminal (CT) toxin domain of CdiA effector proteins. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via the C-terminal domain. A wide variety of C-terminal toxin domains appear to exist; this particular model contains the C-terminal (CT) toxin domains that are similar to Burkholderia pseudomallei E479 and 1026b CdiA toxins, both of which are tRNAses. 105 matched cddid_all.tbl CDD cd20729 cd20729 410638 PoNe_LXG-like Polymorphic Nuclease effector (PoNe) co-occurring with N-terminal LXG domains. The DNase toxin domain called PoNe (Polymorphic Nuclease effector) belongs to a diverse superfamily of PD-(D/E)xK phosphodiesterases, and is associated with several toxin delivery systems including type V, type VI, and type VII. PoNe toxicity is antagonized by cognate immunity proteins (PoNi) containing DUF1911 and DUF1910 domains. This subfamily contains some members that contain LXG domains in the N-terminal region. This group of polymorphic toxin proteins in bacteria are predicted to be associated with type VII secretion pathways to mediate export of bacterial toxins. 139 matched cddid_all.tbl CDD cd20730 cd20730 410639 PoNe_FilH-like Polymorphic Nuclease effector (PoNe) co-occurring with filamentous hemagglutinin N-terminal domain repeats. The DNase toxin domain called PoNe (Polymorphic Nuclease effector) belongs to a diverse superfamily of PD-(D/E)xK phosphodiesterases, and is associated with several toxin delivery systems including type V, type VI, and type VII. PoNe toxicity is antagonized by cognate immunity proteins (PoNi) containing DUF1911 and DUF1910 domains. This subfamily contains proteins with PoNe domains that typically co-occur with N-terminal hemagglutinin repeats and/or a hemagglutination activity domain. 133 matched cddid_all.tbl CDD cd20731 cd20731 410640 PoNe_FilH_TF-like Polymorphic Nuclease effector (PoNe) co-occurring with N-terminal domains such as filamentous hemagglutinin repeats or TANFOR. The DNase toxin domain called PoNe (Polymorphic Nuclease effector) belongs to a diverse superfamily of PD-(D/E)xK phosphodiesterases, and is associated with several toxin delivery systems including type V, type VI, and type VII. PoNe toxicity is antagonized by cognate immunity proteins (PoNi) containing DUF1911 and DUF1910 domains. This subfamily contains members with PoNe domains typically co-occuring with N-terminal domains such as hemagglutinin repeats and/or hemagglutination activity domains, or a TANFOR domain, which contains uncharacterized single or repeat domains that co-occur with fibronectin type III domains. 129 matched cddid_all.tbl CDD cd20732 cd20732 410641 PoNe_FilH_DUF637_VENN-like Polymorphic Nuclease effector (PoNe) domain co-occurring with N-terminal domains such as filamentous hemagglutinin repeats, DUF637, or pre-toxin domain with VENN motif. The DNase toxin domain called PoNe (Polymorphic Nuclease effector) belongs to a diverse superfamily of PD-(D/E)xK phosphodiesterases, and is associated with several toxin delivery systems including type V, type VI, and type VII. PoNe toxicity is antagonized by cognate immunity proteins (PoNi) containing DUF1911 and DUF1910 domains. This subfamily contains proteins with a PoNe domain typically co-occuring with N-terminal domains such as filamentous hemagglutinin repeats, hemagglutination activity domains, DUF637 - predicted to be a hemagglutinin domain, or pre-toxin domains with VENN motifs, which are found in many bacterial polymorphic toxins and are located before the C-terminal toxin modules. 121 matched cddid_all.tbl CDD cd20733 cd20733 410642 PoNe_PAAR-like Polymorphic Nuclease effector (PoNe) co-occurring with an N-terminal PAAR domain. The DNase toxin domain called PoNe (Polymorphic Nuclease effector) belongs to a diverse superfamily of PD-(D/E)xK phosphodiesterases, and is associated with several toxin delivery systems including type V, type VI, and type VII. PoNe toxicity is antagonized by cognate immunity proteins (PoNi) containing DUF1911 and DUF1910 domains. This subfamily contain members with PoNe domains that typically co-occur with N-terminal domains such as proline-alanine-alanine-arginine (PAAR) repeat domains that form a sharp conical extension on VgrG spikes, which is a trimeric protein complex of the bacterial type VI secretion system (T6SS). 125 matched cddid_all.tbl CDD cd20734 cd20734 410643 PoNe_RHS-like Polymorphic Nuclease effector (PoNe) domain co-occurring with RHS repeat-associated core domain. The DNase toxin domain called PoNe (Polymorphic Nuclease effector) belongs to a diverse superfamily of PD-(D/E)xK phosphodiesterases, and is associated with several toxin delivery systems including type V, type VI, and type VII. PoNe toxicity is antagonized by cognate immunity proteins (PoNi) containing DUF1911 and DUF1910 domains. This subfamily contains proteins with PoNe domains typically co-occurring with N-terminal domains such as RHS repeat-associated core domains, which may contain FG-GAP, RHS or YD repeats, and are found in secreted bacterial insecticidal toxins. 90 matched cddid_all.tbl CDD cd20735 cd20735 410644 PoNe_RHS-like Polymorphic Nuclease effector (PoNe) domain co-occurring with N-terminal domains such as RHS repeats. The DNase toxin domain called PoNe (Polymorphic Nuclease effector) belongs to a diverse superfamily of PD-(D/E)xK phosphodiesterases, and is associated with several toxin delivery systems including type V, type VI, and type VII. PoNe toxicity is antagonized by cognate immunity proteins (PoNi) containing DUF1911 and DUF1910 domains. This subfamily contains proteins with PoNe domains that typically co-occur with uncharacterized N-terminal RHS repeat domains. 111 matched cddid_all.tbl CDD cd20736 cd20736 410645 PoNe_Nuclease Polymorphic Nuclease effector (PoNe) co-occurring with an N-terminal nuclease domain. The DNase toxin domain called PoNe (Polymorphic Nuclease effector) belongs to a diverse superfamily of PD-(D/E)xK phosphodiesterases, and is associated with several toxin delivery systems including type V, type VI, and type VII. PoNe toxicity is antagonized by cognate immunity proteins (PoNi) containing DUF1911 and DUF1910 domains. This subfamily contains proteins with PoNe domains that typically co-occur with nuclease N-terminal domains such as endonucleases involved in methyl-directed DNA mismatch repair in gram negative bacteria. 80 matched cddid_all.tbl CDD cd20737 cd20737 410646 PoNe_HINT Polymorphic Nuclease effector (PoNe) domain co-occurring with N-terminal domains such as the HINT domain. The DNase toxin domain called PoNe (Polymorphic Nuclease effector) belongs to a diverse superfamily of PD-(D/E)xK phosphodiesterases, and is associated with several toxin delivery systems including type V, type VI, and type VII. PoNe toxicity is antagonized by cognate immunity proteins (PoNi) containing DUF1911 and DUF1910 domains. This subfamily contains proteins with PoNe domains that typically co-occur with a pre-toxin HINT domain, a member of the HINT superfamily of proteases usually found N-terminal to the toxin module in polymorphic toxin systems; the HINT domain is predicted to function in releasing the toxin domain by autoproteolysis. 91 matched cddid_all.tbl CDD cd20738 cd20738 410647 PoNe_DUF4280 Polymorphic Nuclease effector (PoNe) co-occurring with an N-terminal DUF4280 domain. The DNase toxin domain called PoNe (Polymorphic Nuclease effector) belongs to a diverse superfamily of PD-(D/E)xK phosphodiesterases, and is associated with several toxin delivery systems including type V, type VI, and type VII. PoNe toxicity is antagonized by cognate immunity proteins (PoNi) containing DUF1911 and DUF1910 domains. This subfamily contains proteins with PoNe domains that typically co-occur with an N-terminal domain of unknown function (DUF4280), which has a single completely conserved residue C that may be functionally important. 127 matched cddid_all.tbl CDD cd20739 cd20739 410648 PoNe_DUF637 Polymorphic Nuclease effector (PoNe) co-occurring with an N-terminal DUF637 domain. The DNase toxin domain called PoNe (Polymorphic Nuclease effector) belongs to a diverse superfamily of PD-(D/E)xK phosphodiesterases, and is associated with several toxin delivery systems including type V, type VI, and type VII. PoNe toxicity is antagonized by cognate immunity proteins (PoNi) containing DUF1911 and DUF1910 domains. This subfamily contains proteins with PoNe domains that typically co-occur with N-terminal domains such as DUF637 predicted to be a hemagglutinin domain. 124 matched cddid_all.tbl CDD cd20740 cd20740 410649 PoNe_LXG_HINT-like Polymorphic Nuclease effector (PoNe) domain co-occurring with N-terminal LXG or pre-toxin HINT domains. The DNase toxin domain called PoNe (Polymorphic Nuclease effector) belongs to a diverse superfamily of PD-(D/E)xK phosphodiesterases, and is associated with several toxin delivery systems including type V, type VI, and type VII. PoNe toxicity is antagonized by cognate immunity proteins (PoNi) containing DUF1911 and DUF1910 domains. This subfamily contains members with PoNe domains that co-occur with N-terminal domains such as HINT or LXG domains. The pre-toxin HINT domain, a member of the HINT superfamily of proteases, is usually found N-terminal to the toxin module in polymorphic toxin systems; the HINT domain is predicted to function in releasing the toxin domain by autoproteolysis. The LXG domains that are present in the N-terminal region of a group of polymorphic toxin proteins in bacteria and predicted to use a Type VII secretion pathway to mediate export of bacterial toxins. 96 matched cddid_all.tbl CDD cd20741 cd20741 410650 PoNe_HINT_TF-like Polymorphic Nuclease effector (PoNe) domain co-occurring with N-terminal domains such as HINT or TANFOR. The DNase toxin domain called PoNe (Polymorphic Nuclease effector) belongs to a diverse superfamily of PD-(D/E)xK phosphodiesterases, and is associated with several toxin delivery systems including type V, type VI, and type VII. PoNe toxicity is antagonized by cognate immunity proteins (PoNi) containing DUF1911 and DUF1910 domains. This subfamily contains proteins with PoNe domains that typically co-occur with N-terminal domains such as a TANFOR domain which contains uncharacterized single or repeat domains that co-occur with fibronectin type III domains, or a pre-toxin HINT domain, a member of the HINT superfamily of proteases usually found N-terminal to the toxin module in polymorphic toxin systems; the HINT domain is predicted to function in releasing the toxin domain by autoproteolysis. 77 matched cddid_all.tbl CDD cd20742 cd20742 410940 FIX_vWA-like Found in type sIX effector (FIX) domain of unknown function co-occurring with von Willebrand factor type A (vWA) domain or MSCRAMM family adhesin SdrC domain. The Found in type sIX effector (FIX) domain is found N-terminal to known toxin domains and is genetically and functionally linked to type VI secretion system (T6SS), a widespread mechanism used by Gram-negative bacteria to antagonize neighboring cells. In Vibrio parahaemolyticus, it also co-occurs with C-terminal nuclease toxin PoNe (Polymorphic Nuclease effector) which is associated with several toxin delivery systems including type V, type VI, and type VII. In this subfamily, members contain a FIX domain that co-occurs with domains such as the von Willebrand factor type A (vWA) domain, which has a wide variety of important cellular functions, and the MSCRAMM (Microbial Surface Components Recognizing Adhesive Matrix Molecules) family adhesin SdrC domain, that contains a variable-length C-terminal region of Ser-Asp (SD) repeats. 80 matched cddid_all.tbl CDD cd20743 cd20743 410941 FIX_RhsA-like Found in type sIX effector (FIX) domain of unknown function co-occurring with RhsA domains with RHS repeats. The Found in type sIX effector (FIX) domain is found N-terminal to known toxin domains and is genetically and functionally linked to type VI secretion system (T6SS), a widespread mechanism used by Gram-negative bacteria to antagonize neighboring cells. In Vibrio parahaemolyticus, it also co-occurs with C-terminal nuclease toxin PoNe (Polymorphic Nuclease effector) which is associated with several toxin delivery systems including type V, type VI, and type VII. In this subfamily, members contain a FIX domain that co-occurs with C-terminal RhsA-like domain, which contains extended repeat regions and RHS repeats. Some in this family have additional C-terminal domains such as AAH, a predicted nuclease domain with conserved AHH motif that is found in bacterial polymorphic toxin systems and functions as a toxin module. 92 matched cddid_all.tbl CDD cd20744 cd20744 410942 FIX_AHH_RhsA-like Found in type sIX effector (FIX) domain of unknown function co-occurring with C-terminal AHH domain and some RhsA domains with RHS repeats. The Found in type sIX effector (FIX) domain is found N-terminal to known toxin domains and is genetically and functionally linked to type VI secretion system (T6SS), a widespread mechanism used by Gram-negative bacteria to antagonize neighboring cells. In Vibrio parahaemolyticus, it also co-occurs with C-terminal nuclease toxin PoNe (Polymorphic Nuclease effector) which is associated with several toxin delivery systems including type V, type VI, and type VII. In this subfamily, members contain a FIX domain that co-occurs with C-terminal domains such as AAH, a predicted nuclease domain with conserved AHH motif that is found in bacterial polymorphic toxin systems and functions as a toxin module. Some in this family have additional C-terminal domains such as RhsA protein which contains extended repeat regions and RHS repeats. 76 matched cddid_all.tbl CDD cd20745 cd20745 410943 FIX_RhsA_AHH_HNH-like Found in type sIX effector (FIX) domain of unknown function co-occurring with RhsA, AHH or HNH domain. The Found in type sIX effector (FIX) domain is found N-terminal to known toxin domains and is genetically and functionally linked to type VI secretion system (T6SS), a widespread mechanism used by Gram-negative bacteria to antagonize neighboring cells. In Vibrio parahaemolyticus, it also co-occurs with C-terminal nuclease toxin PoNe (Polymorphic Nuclease effector) which is associated with several toxin delivery systems including type V, type VI, and type VII. In this subfamily, members contain a FIX domain that co-occurs with C-terminal RhsA-like domain which contains extended repeat regions and RHS repeats. Some in this subfamily have additional C-terminal domains such as AAH, a predicted nuclease domain with conserved AHH motif that is found in bacterial polymorphic toxin systems and functions as a toxin module, and HNH endonuclease domain, which usually contains a conserved HNH motif in the sequence. Some members also contain additional N-terminal VgrG or PAAR or PAAR-like (i.e., DUF4280) domain. 69 matched cddid_all.tbl CDD cd20746 cd20746 410944 FIX_Ntox15_NUC_DUF4112_RhsA-like Found in type sIX effector (FIX) domain of unknown function co-occurring with Ntox15, endonuclease, or RHS repeat domain. The Found in type sIX effector (FIX) domain is found N-terminal to known toxin domains and is genetically and functionally linked to type VI secretion system (T6SS), a widespread mechanism used by Gram-negative bacteria to antagonize neighboring cells. In Vibrio parahaemolyticus, it also co-occurs with C-terminal nuclease toxin PoNe (Polymorphic Nuclease effector) which is associated with several toxin delivery systems including type V, type VI, and type VII. In this subfamily, members contain a FIX domain that generally co-occurs with the C-terminal Ntox15 (Novel toxin 15), a predicted RNase toxin that possesses a conserved HxxD motif, as well as with domains such as DNA/RNA non-specific endonuclease, RhsA domain regions with extende RHS repeats, or DUF4112. Some members also contain an N-terminal PAAR-like (i.e., DUF4280) domain. 84 matched cddid_all.tbl CDD cd20749 cd20749 439136 nigritoxin_M central or middle domain of nigritoxin, a bacterial toxin for crustaceans and insects. This family contains the central domain of nigritoxin expressed in Vibrio nigripulchritudo, a bacterial pathogen affecting shrimp. Nigritoxin is lethal for organisms within the Tetraconata and non-toxic to other animals. It shows significant sequence similarity with antifeeding prophage 18 (Afp18), a partially characterized toxin found in the entomopathogenic bacteria Serratia entomophila and in the fish pathogen Yersinia ruckeri, suggesting that nigritoxin may display toxicity against organisms beyond the known target, Litopenaeus stylirostris shrimp. Structure studies show that nigritoxin represents an entirely unique protein fold, indicating that Afp18 and nigritoxin do not possess the same biological functions. Nigritoxin is comprised of three domains: N-terminal, C-terminal and central domains. This central (or middle) domain has a unique fold that does not superimpose to any other known structure. 192 matched cddid_all.tbl CDD cd20750 cd20750 410957 cyt_c_I Uncharacterized subfamily of the cytochrome P460 family. This subfamily is composed mainly of hypothetical proteins, including Sphingopyxis alaskensis class I cytochrome C. Members of this subfamily belong to the cytochrome P460 family that is composed mostly of monoheme, ~17 kDa, c-cytochromes typified by the cytochromes P460 of Nitrosomonas europaea and Methylococcus capsulatus (Bath), and the cytochrome c'-beta of M. capsulatus. Cytochrome P460 family members can be characterized by a predominantly beta-sheet structure as opposed to the four elongate, tightly-packed alpha-helices of the widely distributed cytochromes c' of photoheterotrophic and denitrifying bacteria. They are involved in the oxidation/reduction or ligation of N-oxides for detoxification or energy generation. The protein-bound c-type heme cofactor, heme P460, named for its characteristic ferrous Soret peak maximum at 460 nm, has the distinction of being the only known heme in biology to withdraw electrons from an iron coordinated substrate. 146 matched cddid_all.tbl CDD cd20751 cd20751 410958 cyt_P460_Ne-like cytochrome P460 from Nitrosomonas europaea and similar proteins. Cytochrome (cyt) P460 is a small soluble periplasmic protein that binds the c-type heme cofactor, heme P460, named for its characteristic ferrous Soret peak maximum at 460 nm, which has the distinction of being the only known heme in biology to withdraw electrons from an iron coordinated substrate. The heme P460 in N. europea cyt P460 contains a third proteinaceous cross-link, similar to that found in hydroxylamine oxidoreductase (HAO), but in this case, the cross-link is to a conserved lysine residue, K70. The biological function of cyt P460 is yet to be determined, but it binds hydroxylamine, hydrazine, hydrogen peroxide, and cyanide in the ferric form, and CO in the ferrous form; it also possesses a weak hydroxylamine oxidation/cyt c reduction activity. It belongs to a family, called the cytochrome P460 family, of small mono-heme c-type cytochromes that are predominantly of beta-sheet structure, as opposed to the four elongate, tightly-packed alpha-helices of the widely distributed cytochromes c' of photoheterotrophic and denitrifying bacteria. 153 matched cddid_all.tbl CDD cd20752 cd20752 410959 cyt_c'_beta Cytochrome c'-beta from Methylococcus capsulatus (Bath) and similar proteins. Cytochromes (cyt) c' are defined by a pentacoordinate heme Fe with a CXXCH c-heme-binding motif located close to the C-terminus. Most cyt c' have four alpha-helix bundle structures, and are referred to as cyt c'-alpha. M. capsulatus (Bath) cytochrome c'-beta, encoded by the cytS gene, is a homodimeric heme protein with a higher molecular weight of about 16 kDa per monomer, compared to cyt c'-alpha (~12 kDa), and it adopts a beta-sheet structure. It is involved in nitric oxide scavenging and protection against nitrosoative stress. Cyt c'-beta belongs to a family, called the cytochrome P460 family, of small mono-heme c-type cytochromes that are predominantly of beta-sheet structure, as opposed to the four elongate, tightly-packed alpha-helices of the widely distributed cytochromes c' of photoheterotrophic and denitrifying bacteria. 136 matched cddid_all.tbl CDD cd20753 cd20753 410960 cyt_P460_Mc-like cytochrome P460 from Methylococcus capsulatus (Bath) and similar proteins. Cytochrome (cyt) P460 is a small soluble periplasmic protein that binds the c-type heme cofactor, heme P460, named for its characteristic ferrous Soret peak maximum at 460 nm, which has the distinction of being the only known heme in biology to withdraw electrons from an iron coordinated substrate. M. capsulatus (Bath) cytochrome P460, encoded by the cytL gene, catalyzes the oxidation of hydroxylamine (NH2OH) to form nitrous oxide (N2O) under anaerobic conditions. Similar to Nitrosomonas europaea cyt P460, it is defined by an unusual porphyrin (heme)-lysine cross link. This subfamily belongs to a family, called the cytochrome P460 family, of small mono-heme c-type cytochromes that are predominantly of beta-sheet structure, as opposed to the four elongate, tightly-packed alpha-helices of the widely distributed cytochromes c' of photoheterotrophic and denitrifying bacteria. 136 matched cddid_all.tbl CDD cd20754 cd20754 467730 capping_2-OMTase_viral viral Cap-0 specific (nucleoside-2'-O-)-methyltransferase. Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Some dsDNA and dsRNA viruses, like the bluetongue virus (BTV), a member of the Reoviridae family, and Vaccinia virus, a member of the Poxviridae family, as well as some ss(+)RNA viruses, like Flaviviridae and Nidovirales, cap their mRNAs and encode their own 2'OMTase. In BTV, all four reactions are catalyzed by a single protein, VP4. In Vaccinia, the activity is located in the processing factor of the poly(A) polymerase, VP39. 179 matched cddid_all.tbl CDD cd20756 cd20756 467731 capping_2-OMTase_Poxviridae Cap-0 specific (nucleoside-2'-O-)-methyltransferase of poxviridae. Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Poxviridae viruses, which comprise a family of dsDNA viruses, cap their mRNAs. The 2'OMTase activity is located in the processing factor of the poly(A) polymerase, VP39. 269 matched cddid_all.tbl CDD cd20757 cd20757 467732 capping_2-OMTase_Rotavirus Cap-0 specific (nucleoside-2'-O-)-methyltransferase of rotavirus. Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Rotaviruses, which comprise a family of dsRNA viruses, cap their mRNAs. The 2'OMTase activity is located in the multifunctional capping enzyme, VP3. 198 matched cddid_all.tbl CDD cd20758 cd20758 467733 capping_2-OMTase_Orbivirus Cap-0 specific (nucleoside-2'-O-)-methyltransferase of orbivirus. Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Orbiviruses, which comprise a family of dsRNA viruses, cap their mRNAs. The 2'OMTase activity is located in the multifunctional capping enzyme, VP4. 211 matched cddid_all.tbl CDD cd20759 cd20759 467734 capping_2-OMTase_Phytoreovirus Cap-0 specific (nucleoside-2'-O-)-methyltransferase of phytoreovirus. Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Phytoreoviruses, which comprise a family of dsRNA viruses, cap their mRNAs. The 2'OMTase activity is located in the mRNA capping enzyme P5. 200 matched cddid_all.tbl CDD cd20760 cd20760 467735 capping_2-OMTase_Mimiviridae Cap-0 specific (nucleoside-2'-O-)-methyltransferase of mimiviridae and pithoviridae. Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Mimiviridae and pithoviridae are part of the nucleocytoplasmic large dsDNA virus clade (NCLDV), and they cap their mRNAs. The 2'OMTase activity is located in the polyA polymerase regulatory subunit. This family also contains related proteins from a broad group of eukaryotes that include opisthokonts and protists. 237 matched cddid_all.tbl CDD cd20761 cd20761 467736 capping_2-OMTase_Flaviviridae Cap-0 specific (nucleoside-2'-O-)-methyltransferase of flaviviridae. Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Flaviviridae viruses, comprise a family of ss(+)RNA viruses, cap their mRNAs. The 2'OMTase activity is located in the non-structural protein 5 (NS5). 225 matched cddid_all.tbl CDD cd20762 cd20762 467737 capping_2-OMTase_Nidovirales Cap-0 specific (nucleoside-2'-O-)-methyltransferase of nidovirales. Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Nidovirales viruses, which comprise a family of ss(+)RNA viruses, cap their mRNAs. For one member, coronavirus, the 2'OMTase activity is located in the non-structural protein 16 (Nsp16). For others, the 2'OMTase activity may be located in replicase polyprotein 1ab. 175 matched cddid_all.tbl CDD cd20777 cd20777 467721 8prop_heme-binding_NirN eight-bladed heme d1-binding beta-propeller domain in dihydro-heme d1 dehydrogenase NirN. The monomeric dihydro-heme d1 dehydrogenase NirN is part of the denitrification process that enables biofilm formation of the opportunistic human pathogen Pseudomonas aeruginosa, making it more resilient to antibiotics and highly adaptable to different habitats. NirN, similar to the homodimeric cytochrome cd1 (nitrite reductase; NirS), consists of an eight-bladed heme d1-binding beta-propeller and a cytochrome c domain, but their relative orientation differs with respect to NirS. His147, His323 and Tyr461, but not His417 are essential for activity. All 8 blades of the propeller are included in this alignment. 405 matched cddid_all.tbl CDD cd20778 cd20778 467722 8prop_hemeD1_NirF eight-bladed heme d1-binding beta-propeller domain in cytochrome cd1 nitrate reductase NirF. Denitrification is a process that enables biofilm formation of the opportunistic human pathogen Pseudomonas aeruginosa, making it more resilient to antibiotics and highly adaptable to different habitats. During denitrification, nitrate (Nar), nitrite (Nir), nitric oxide (Nor), and nitrous oxide (Nos) reductases catalyze the reaction cascade of NO3- -> NO2- -> NO -> N2O -> N2. The integral membrane proteins NorC, NorB, and NosR form the core assembly platform that binds the nitrate reductase NarGHI and the periplasmic cytochrome cd1 (nitrite reductase) NirS via its maturation factor NirF. The nirFDLGHJE genes encode proteins required for heme d1 biosynthesis. NirS, NirF, and NirN, the monomeric dihydro-heme d1 dehydrogenase form a stable complex during nitrite reductase maturation. The nitrite reductase NirS is bound to the denitrification supercomplex via NorB, while the electron donor system NirM and the enzyme maturation machinery NirN-NirF-NirQ, interacting with NirS, are bound via NorC. 381 matched cddid_all.tbl CDD cd20779 cd20779 467723 8prop_hemeD1_NirS eight-bladed heme d1-binding beta-propeller domain in cytochrome cd1 nitrate reductase NirS. Cytochrome cd1 nitrite reductase NiR is a key denitrification enzyme that catalyzes the conversion of nitrite to nitric oxide in the nitrogen cycle. The crystal structure of the oxidized enzyme shows that the d1 heme iron of the active site is ligated by His/Tyr side chains, and the c heme iron is ligated by a His/His ligand pair. Nitrite reductase from Pseudomonas aeruginosa is a dimer of two identical subunits of 60 kDa, each containing one c and one d1 heme group. The c heme is the electron accepting pole of the molecule and is reduced in vitro by either azurin or cytochrome c551. The d1 heme is the site where nitrite, and oxygen reduction occur. The two types of heme are located in separate domains whose arrangement suggests a mechanism requiring domain movement during catalysis. 438 matched cddid_all.tbl CDD cd20780 cd20780 467724 8prop_hemeD1_NiR_delta_epsilon eight-bladed heme d1-binding beta-propeller domain in cytochrome cd1 nitrate reductase NiR delta/epsilon subdivisions. Cytochrome cd1 (nitrite reductase) catalyzes in vitro the reduction of molecular oxygen to water and the reduction of nitrite to nitric oxide. Purification and characterization of NiR from several bacterial sources have shown that there are two distinct classes of dissimilatory NiRs that yield NO as the main reaction product, containing either copper or heme as cofactor- the heme-containing enzyme occurring more frequently. It forms a homodimer with each subunit containing one C and one D1 heme group. The C heme is the electron accepting pole of the molecule and is reduced in vitro by either azurin or cytochrome c551. The D1 heme is the site where nitrite, and oxygen reduction occur. NiR is a key denitrification enzyme, which controls the rate of the production of toxic nitric oxide (NO) and ultimately regulates the release of NO into the atmosphere. The two types of heme are located in separate domains whose arrangement suggests a mechanism requiring domain movement during catalysis. The heme-binding nitrite reductase in delta and epsilon subdivisions are present here. 436 matched cddid_all.tbl CDD cd20781 cd20781 467725 8prop_hemeD1_NiR_alpha_gamma eight-bladed heme d1-binding beta-propeller domain in cytochrome cd1 nitrate reductase NiR alpha and gamma proteobacteria subdivisions. Cytochrome cd1 (nitrite reductase) catalyzes in vitro the reduction of molecular oxygen to water and the reduction of nitrite to nitric oxide. Purification and characterization of NiR from several bacterial sources have shown that there are two distinct classes of dissimilatory NiRs that yield NO as the main reaction product, containing either copper or heme as cofactor, the heme-containing enzyme occurring more frequently. It forms a homodimer each containing one C and one D1 heme group. The C heme is the electron accepting pole of the molecule and is reduced in vitro by either azurin or cytochrome c551. The D1 heme is the site where nitrite, and oxygen reduction occur. NiR is a key denitrification enzyme, which controls the rate of the production of toxic nitric oxide (NO) and ultimately regulates the release of NO into the atmosphere. The two types of heme are located in separate domains whose arrangement suggests a mechanism requiring domain movement during catalysis. Heme binding nitrite reductase from alphaproteobacteria and gammaproteobacteria are present here. 433 matched cddid_all.tbl CDD cd20782 cd20782 467726 8prop_hemeD1_cyt_cd1-like cytochrome cd1 nitrate reductase eight-bladed heme d1-binding beta-propeller domain and similar proteins. Cytochrome cd1 (cyt cd1) nitrite reductase catalyzes in vitro the reduction of molecular oxygen to water and the reduction of nitrite to nitric oxide). It is a dimer of two identical subunits of 60 kDa, each containing one c and one d1 heme group. The c heme is the electron accepting pole of the molecule and is reduced in vitro by either azurin or cytochrome c551. The d1 heme is the site where nitrite, and oxygen reduction occur. NiR is a key denitrification enzyme, which controls the rate of the production of toxic nitric oxide (NO) and ultimately regulates the release of NO into the atmosphere. The two types of heme are located in separate domains whose arrangement suggests a mechanism requiring domain movement during catalysis. 415 matched cddid_all.tbl CDD cd20783 cd20783 467727 8prop_hemeD1_cyt_cd1-like eight-bladed heme d1-binding beta-propeller domain and similar proteins. Cytochrome cd1 (cyt cd1) nitrite reductase catalyzes in vitro the reduction of molecular oxygen to water and the reduction of nitrite to nitric oxide). It is a dimer of two identical subunits of 60 kDa, each containing one c and one d1 heme group. The c heme is the electron accepting pole of the molecule and is reduced in vitro by either azurin or cytochrome c551. The d1 heme is the site where nitrite, and oxygen reduction occur. NiR is a key denitrification enzyme, which controls the rate of the production of toxic nitric oxide (NO) and ultimately regulates the release of NO into the atmosphere. The two types of heme are located in separate domains whose arrangement suggests a mechanism requiring domain movement during catalysis. 388 matched cddid_all.tbl CDD cd20784 cd20784 467728 8prop_hemeD1_cyt_cd1-like cytochrome cd1 nitrate reductase eight-bladed heme d1-binding beta-propeller domain and similar proteins. Cytochrome cd1 (cyt cd1) nitrite reductase catalyzes in vitro the reduction of molecular oxygen to water and the reduction of nitrite to nitric oxide). It is a dimer of two identical subunits of 60 kDa, each containing one c and one d1 heme group. The c heme is the electron accepting pole of the molecule and is reduced in vitro by either azurin or cytochrome c551. The d1 heme is the site where nitrite, and oxygen reduction occur. NiR is a key denitrification enzyme, which controls the rate of the production of toxic nitric oxide (NO) and ultimately regulates the release of NO into the atmosphere. The two types of heme are located in separate domains whose arrangement suggests a mechanism requiring domain movement during catalysis. 367 matched cddid_all.tbl CDD cd20785 cd20785 467729 8prop_hemeD1_cyt_cd1-like eight-bladed heme d1-binding beta-propeller domain in cytochrome cd1 nitrate reductase and similar proteins. Cytochrome cd1 (cyt cd1) nitrite reductase catalyzes in vitro the reduction of molecular oxygen to water and the reduction of nitrite to nitric oxide). It is a dimer of two identical subunits of 60 kDa, each containing one c and one d1 heme group. The c heme is the electron accepting pole of the molecule and is reduced in vitro by either azurin or cytochrome c551. The d1 heme is the site where nitrite, and oxygen reduction occur. NiR is a key denitrification enzyme, which controls the rate of the production of toxic nitric oxide (NO) and ultimately regulates the release of NO into the atmosphere. The two types of heme are located in separate domains whose arrangement suggests a mechanism requiring domain movement during catalysis. 412 matched cddid_all.tbl CDD cd20786 cd20786 411011 tapirin_C C-terminal domain of cellulose binding protein tapirin. This family contains the C-terminal domain of tapirin, a unique cellulose binding protein that is present only in the extremely thermophilic bacterial species Caldicellulosiruptor that grow on carbohydrates from lignocellulose at elevated temperatures. Tapirins appear to be specifically attached to cellulose, having similar binding affinities to cellulose as family 3 carbohydrate binding modules (CBM3). Structures of the C-terminal region indicate that aromatic and hydrophobic residues are responsible for cellulose binding, while a flexible peptide loop may protect and control access to this region. The basis for the genomic localization of the tapirins is unknown; however, these proteins are located next to type IV pili in the Caldicellulosiruptor genomes and therefore may be exposed on the cell membrane beside or as part of pili proteins. Caldicellulosiruptor hydrothermalis, which has less capability to deconstruct lignocellulose itself, may use tapirin as one of the mechanisms for its survival in extreme environments by anchoring itself to biomass that is hydrolyzed by enzymes from other species. Understanding mechanisms by which these microorganisms attach to and degrade lignocellulose may be important in finding effective approaches for conversion of plant biomass into fuels and chemicals. 343 matched cddid_all.tbl CDD cd20788 cd20788 412053 TBC1D23_C-like C-terminal domain of TBC1 domain family member 23, and similar proteins. This family contains the C-terminal domain of Tre2-Bub2-Cdc16 (TBC) family 23 (TBC1D23), which adopts a Pleckstrin homology (PH) domain fold. It selectively binds to phosphoinositides, in particular, PtdIns(4)P, through one surface while it binds FAM21 via the opposite surface. TBC1D23, which is highly conserved in many eukaryotes but missing in plants and fungi, also possesses an N-terminal domain which is a catalytically inactive TBC domain. TBC1D23 encodes a protein functioning in endosome-to-Golgi trafficking in cells; it is a specificity determinant that links the vesicle to the target membrane. Homozygous mutations of TBC1D23 have been found in patients diagnosed with pontocerebellar hypoplasia (PCH), a group of neurological disorders that affect the brain development, particularly, the pons and cerebellum. Mutation of key residues of TBC1D23 (or FAM21) selectively disrupts the endosomal vesicular trafficking toward the Trans-Golgi Network. This C-terminal domain is missing in some PCH patients. 115 matched cddid_all.tbl CDD cd20789 cd20789 411012 Cas13d Class 2 type VI-D CRISPR-associated RNA-guided ribonuclease Cas13d. CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins) adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. These systems are divided into two classes: class 1 systems utilize multiple Cas proteins and CRISPR RNA (crRNA) to form an effector complex while class 2 systems employ a large, single effector with crRNA to mediate interference. Class 2 type VI CRISPR-Cas13 systems use a single enzyme to target RNA using a programmable crRNA guide and are divided into four subtypes based on the identity of the Cas13 protein (Cas13a-d). The Cas13 proteins are capable of both, pre-crRNA processing and target RNA cleavage, which protect the host from phage attacks. Once bound to a target RNA, their non-specific RNase activity is activated. Cas13d enzymes are 20-30% smaller than other Cas13 subtypes, which enable flexible packaging into size-constrained therapeutic viral vectors such as adeno-associated virus. 875 matched cddid_all.tbl CDD cd20790 cd20790 411013 Cas13a Class 2 type VI-A CRISPR-associated RNA-guided ribonuclease Cas13a. CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins) adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. These systems are divided into two classes: class 1 systems utilize multiple Cas proteins and CRISPR RNA (crRNA) to form an effector complex while class 2 systems employ a large, single effector with crRNA to mediate interference. Class 2 type VI CRISPR-Cas13 systems use a single enzyme to target RNA using a programmable crRNA guide and are divided into four subtypes based on the identity of the Cas13 protein (Cas13a-d). The Cas13 proteins are capable of both pre-crRNA processing and target RNA cleavage, which protect the host from phage attacks. Once bound to a target RNA, their non-specific RNase activity is activated. Within the Cas13a (also called C2c2) subfamily, the active site is functionally diverse in terms of both nucleotide cleavage preference and turnover efficiency. There are two distinct types of Cas13a enzymes, based on their cleavage preference: adenosine (A) cleaving or uridine (U) cleaving. 1188 matched cddid_all.tbl CDD cd20792 cd20792 410342 C1_cPKC_nPKC_rpt1 first protein kinase C conserved region 1 (C1 domain) found in classical (or conventional) protein kinase C (cPKC), novel protein kinase C (nPKC), and similar proteins. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domains. PKCs undergo three phosphorylations in order to take mature forms. In addition, cPKCs depend on calcium, DAG (1,2-diacylglycerol), and in most cases, phosphatidylserine (PS) for activation. nPKCs are calcium-independent, but require DAG and PS for activity, while atypical PKCs (aPKCs) only require PS. PKCs phosphorylate and modify the activities of a wide variety of cellular proteins including receptors, enzymes, cytoskeletal proteins, transcription factors, and other kinases. They play a central role in signal transduction pathways that regulate cell migration and polarity, proliferation, differentiation, and apoptosis. This family includes classical PKCs (cPKCs) and novel PKCs (nPKCs). There are four cPKC isoforms (named alpha, betaI, betaII, and gamma) and four nPKC isoforms (delta, epsilon, eta, and theta). Members of this family contain two copies of the C1 domain. This model corresponds to the first one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 53 matched cddid_all.tbl CDD cd20793 cd20793 410343 C1_cPKC_nPKC_rpt2 second protein kinase C conserved region 1 (C1 domain) found in classical (or conventional) protein kinase C (cPKC), novel protein kinase C (nPKC), and similar proteins. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. PKCs undergo three phosphorylations in order to take mature forms. In addition, cPKCs depend on calcium, DAG (1,2-diacylglycerol), and in most cases, phosphatidylserine (PS) for activation. nPKCs are calcium-independent, but require DAG and PS for activity, while atypical PKCs (aPKCs) only require PS. PKCs phosphorylate and modify the activities of a wide variety of cellular proteins including receptors, enzymes, cytoskeletal proteins, transcription factors, and other kinases. They play a central role in signal transduction pathways that regulate cell migration and polarity, proliferation, differentiation, and apoptosis. This family includes classical PKCs (cPKCs) and novel PKCs (nPKCs). There are four cPKC isoforms (named alpha, betaI, betaII, and gamma) and four nPKC isoforms (delta, epsilon, eta, and theta). Members of this family contain two copies of C1 domain. This model corresponds to the second one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 50 matched cddid_all.tbl CDD cd20794 cd20794 410344 C1_aPKC protein kinase C conserved region 1 (C1 domain) found in the atypical protein kinase C (aPKC) family. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. aPKCs only require phosphatidylserine (PS) for activation. They contain a C2-like region, instead of a calcium-binding (C2) region found in classical PKCs, in their regulatory domain. There are two aPKC isoforms, zeta and iota. aPKCs are involved in many cellular functions including proliferation, migration, apoptosis, polarity maintenance and cytoskeletal regulation. They also play a critical role in the regulation of glucose metabolism and in the pathogenesis of type 2 diabetes. PKC-zeta plays a critical role in activating the glucose transport response. It is activated by glucose, insulin, and exercise through diverse pathways. PKC-zeta also plays a central role in maintaining cell polarity in yeast and mammalian cells. In addition, it affects actin remodeling in muscle cells. PKC-iota is directly implicated in carcinogenesis. It is critical to oncogenic signaling mediated by Ras and Bcr-Abl. The PKC-iota gene is the target of tumor-specific gene amplification in many human cancers, and has been identified as a human oncogene. In addition to its role in transformed growth, PKC-iota also promotes invasion, chemoresistance, and tumor cell survival. Expression profiling of PKC-iota is a prognostic marker of poor clinical outcome in several human cancers. PKC-iota also plays a role in establishing cell polarity, and has critical embryonic functions. Members of this family contain one C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 55 matched cddid_all.tbl CDD cd20795 cd20795 410345 C1_PKD_rpt1 first protein kinase C conserved region 1 (C1 domain) found in the protein kinase D (PKD) family. PKDs are important regulators of many intracellular signaling pathways such as ERK and JNK, and cellular processes including the organization of the trans-Golgi network, membrane trafficking, cell proliferation, migration, and apoptosis. They are activated in a PKC-dependent manner by many agents including diacylglycerol (DAG), PDGF, neuropeptides, oxidative stress, and tumor-promoting phorbol esters, among others. Mammals harbor three types of PKDs: PKD1 (or PKCmu), PKD2, and PKD3 (or PKCnu). PKDs contain N-terminal tandem cysteine-rich zinc binding C1 (PKC conserved region 1), central PH (Pleckstrin Homology), and C-terminal catalytic kinase domains. This model corresponds to the first C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 56 matched cddid_all.tbl CDD cd20796 cd20796 410346 C1_PKD_rpt2 second protein kinase C conserved region 1 (C1 domain) found in the family of protein kinase D (PKD). PKDs are important regulators of many intracellular signaling pathways such as ERK and JNK, and cellular processes including the organization of the trans-Golgi network, membrane trafficking, cell proliferation, migration, and apoptosis. They are activated in a PKC-dependent manner by many agents including diacylglycerol (DAG), PDGF, neuropeptides, oxidative stress, and tumor-promoting phorbol esters, among others. Mammals harbor three types of PKDs: PKD1 (or PKCmu), PKD2, and PKD3 (or PKCnu). PKDs contain N-terminal tandem cysteine-rich zinc binding C1 (PKC conserved region 1), central PH (Pleckstrin Homology), and C-terminal catalytic kinase domains. This model corresponds to the second C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 54 matched cddid_all.tbl CDD cd20797 cd20797 410347 C1_CeDKF1-like_rpt1 first protein kinase C conserved region 1 (C1 domain) found in Caenorhabditis elegans serine/threonine-protein kinase DKF-1 and similar proteins. DKF-1 converts transient diacylglycerol (DAG) signals into prolonged physiological effects, independently of PKC. It plays a role in the regulation of growth and neuromuscular control of movement. It is involved in immune response to Staphylococcus aureus bacterium by activating transcription factor hlh-30 downstream of phospholipase plc-1. Members of this group contain two copies of the C1 domain. This model corresponds to the first one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 56 matched cddid_all.tbl CDD cd20798 cd20798 410348 C1_CeDKF1-like_rpt2 second protein kinase C conserved region 1 (C1 domain) found in Caenorhabditis elegans serine/threonine-protein kinase DKF-1 and similar proteins. DKF-1 converts transient diacylglycerol (DAG) signals into prolonged physiological effects, independently of PKC. It plays a role in the regulation of growth and neuromuscular control of movement. It is involved in immune response to Staphylococcus aureus bacterium by activating transcription factor hlh-30 downstream of phospholipase plc-1. Members of this group contain two copies of the C1 domain. This model corresponds to the second one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 54 matched cddid_all.tbl CDD cd20799 cd20799 410349 C1_DGK_typeI_rpt1 first protein kinase C conserved region 1 (C1 domain) found in type I diacylglycerol kinases. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. Type I DAG kinases (DGKs) contain EF-hand structures that bind Ca(2+) and recoverin homology domains, in addition to C1 and catalytic domains that are present in all DGKs. Type I DGKs, regulated by calcium binding, include three DGK isozymes (alpha, beta and gamma). DAG kinase alpha, also called 80 kDa DAG kinase, or diglyceride kinase alpha (DGK-alpha), is active upon cell stimulation, initiating the resynthesis of phosphatidylinositols and attenuating protein kinase C activity. DAG kinase beta, also called 90 kDa DAG kinase, or diglyceride kinase beta (DGK-beta), exhibits high phosphorylation activity for long-chain diacylglycerols. DAG kinase gamma, also called diglyceride kinase gamma (DGK-gamma), reverses the normal flow of glycerolipid biosynthesis by phosphorylating diacylglycerol back to phosphatidic acid. Members of this family contain two copies of the C1 domain. This model corresponds to the first one. DGK-alpha contains atypical C1 domains, while DGK-beta and DGK-gamma contain typical C1 domains that bind DAG and phorbol esters. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 62 matched cddid_all.tbl CDD cd20800 cd20800 410350 C1_DGK_typeII_rpt1 first protein kinase C conserved region 1 (C1 domain) found in type II diacylglycerol kinases. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. Type II DAG kinases (DGKs) contain pleckstrin homology (PH) and sterile alpha motifs (SAM) domains, in addition to C1 and catalytic domains that are present in all DGKs. The SAM domain mediates oligomerization of type II DGKs. Three DGK isozymes (delta, eta and kappa) are classified as type II. DAG kinase delta, also called 130 kDa DAG kinase, or diglyceride kinase delta (DGK-delta), is a residential lipid kinase in the endoplasmic reticulum. It promotes lipogenesis and is involved in triglyceride biosynthesis. DAG kinase eta, also called diglyceride kinase eta (DGK-eta), plays a key role in promoting cell growth. The DAG kinase eta gene, DGKH, is a replicated risk gene of bipolar disorder (BPD). DAG kinase kappa is also called diglyceride kinase kappa (DGK-kappa) or 142 kDa DAG kinase. Members of this family contain two copies of the C1 domain. This model corresponds to the first one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 60 matched cddid_all.tbl CDD cd20801 cd20801 410351 C1_DGKepsilon_typeIII_rpt1 first protein kinase C conserved region 1 (C1 domain) found in type III diacylglycerol kinase, DAG kinase epsilon, and similar proteins. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase epsilon, also called diglyceride kinase epsilon (DGK-epsilon), is the only isoform classified as type III; it possesses a hydrophobic domain in addition to C1 and catalytic domains that are present in all DGKs, and shows selectivity for acyl chains. It is highly selective for arachidonate-containing species of DAG. It may terminate signals transmitted through arachidonoyl-DAG or may contribute to the synthesis of phospholipids with defined fatty acid composition. DAG kinase epsilon contains two copies of the C1 domain. This model corresponds to the first one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 54 matched cddid_all.tbl CDD cd20802 cd20802 410352 C1_DGK_typeIV_rpt1 first protein kinase C conserved region 1 (C1 domain) found in type IV diacylglycerol kinases. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. Type IV DAG kinases (DGKs) contain myristoylated alanine-rich protein kinase C substrate (MARCKS), PDZ-binding, and ankyrin domains, in addition to C1 and catalytic domains that are present in all DGKs. The MARCKS domain regulates the nuclear localizations of type IV DGKs while the PDZ-binding and ankyrin domains regulate interactions with several proteins. Two DGK isozymes (zeta and iota) are classified as type IV. DAG kinase zeta, also called diglyceride kinase zeta (DGK-zeta), displays a strong preference for 1,2-diacylglycerols over 1,3-diacylglycerols, but lacks substrate specificity among molecular species of long chain diacylglycerols. DAG kinase iota, also called diglyceride kinase iota (DGK-iota), or DGKI, is a homolog of Drosophila DGK2, RdgA. It may have important cellular functions in the retina and brain. Members of this family contain two copies of the C1 domain. This model corresponds to the first one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 62 matched cddid_all.tbl CDD cd20803 cd20803 410353 C1_DGKtheta_typeV_rpt1 first protein kinase C conserved region 1 (C1 domain) found in type V diacylglycerol kinase, DAG kinase theta, and similar proteins. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase theta, also called diglyceride kinase theta (DGK-theta), is the only isoform classified as type V; it contains a pleckstrin homology (PH)-like domain and an additional C1 domain, compared to other DGKs. It may regulate the activity of protein kinase C by controlling the balance between the two signaling lipids, diacylglycerol and phosphatidic acid. DAG kinase theta contains three copies of the C1 domain. This model corresponds to the first one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 56 matched cddid_all.tbl CDD cd20804 cd20804 410354 C1_DGKtheta_typeV_rpt2 second protein kinase C conserved region 1 (C1 domain) found in type V diacylglycerol kinase, DAG kinase theta, and similar proteins. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase theta, also called diglyceride kinase theta (DGK-theta), is the only isoform classified as type V; it contains a pleckstrin homology (PH)-like domain and an additional C1 domain, compared to other DGKs. It may regulate the activity of protein kinase C by controlling the balance between the two signaling lipids, diacylglycerol and phosphatidic acid. DAG kinase theta contains three copies of the C1 domain. This model corresponds to the second one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 57 matched cddid_all.tbl CDD cd20805 cd20805 410355 C1_DGK_rpt2 second protein kinase C conserved region 1 (C1 domain) found in the diacylglycerol kinase family. The diacylglycerol kinase (DGK, EC 2.7.1.107) family of enzymes plays critical roles in lipid signaling pathways by converting diacylglycerol to phosphatidic acid, thereby downregulating signaling by the former and upregulating signaling by the latter second messenger. Ten DGK family isozymes have been identified to date, which possess different interaction motifs imparting distinct temporal and spatial control of DGK activity to each isozyme. They have been classified into five types (I-V), according to domain architecture and some common features. All DGK isozymes, except for DGKtheta, contain two copies of the C1 domain. This model corresponds to the second one. DGKtheta harbors three C1 domains. Its third C1 domain is included here. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 55 matched cddid_all.tbl CDD cd20806 cd20806 410356 C1_CHN protein kinase C conserved region 1 (C1 domain) found in the chimaerin family. Chimaerins are a family of phorbolester- and diacylglycerol-responsive GTPase activating proteins (GAPs) specific for the Rho-like GTPase Rac. Alpha1-chimerin (formerly known as N-chimerin) and alpha2-chimerin are alternatively spliced products of a single gene, as are beta1- and beta2-chimerin. Alpha1- and beta1-chimerin have a relatively short N-terminal region that does not encode any recognizable domains, whereas alpha2- and beta2-chimerin both include a functional SH2 domain that can bind to phosphotyrosine motifs within receptors. All the isoforms contain a GAP domain with specificity in vitro for Rac1 and a diacylglycerol (DAG)-binding C1 domain which allows them to translocate to membranes in response to DAG signaling and anchors them in close proximity to activated Rac. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 53 matched cddid_all.tbl CDD cd20807 cd20807 410357 C1_Munc13 protein kinase C conserved region 1 (C1 domain) found in the Munc13 family. The Munc13 gene family encodes a family of neuron-specific, synaptic molecules that bind to syntaxin, an essential mediator of neurotransmitter release. Munc13-1 is a component of presynaptic active zones in which it acts as an essential synaptic vesicle priming protein. Munc13-2 is essential for normal release probability at hippocampal mossy fiber synapses. Munc13-3 is almost exclusively expressed in the cerebellum. It acts as a tumor suppressor and plays a critical role in the formation of release sites with calcium channel nanodomains. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 53 matched cddid_all.tbl CDD cd20808 cd20808 410358 C1_RASGRP protein kinase C conserved region 1 (C1 domain) found in the RAS guanyl-releasing protein (RASGRP) family. The RASGRP family includes RASGRP1-4. They function as cation-, usually calcium-, and diacylglycerol (DAG)-regulated nucleotide exchange factor activating Ras through the exchange of bound GDP for GTP. RASGRP1, also called calcium and DAG-regulated guanine nucleotide exchange factor II (CalDAG-GEFII) or Ras guanyl-releasing protein, activates the Erk/MAP kinase cascade and regulates T-cell/B-cell development, homeostasis and differentiation by coupling T-lymphocyte/B-lymphocyte antigen receptors to Ras. RASGRP1 also regulates NK cell cytotoxicity and ITAM-dependent cytokine production by activation of Ras-mediated ERK and JNK pathways. RASGRP2, also called calcium and DAG-regulated guanine nucleotide exchange factor I (CalDAG-GEFI), Cdc25-like protein (CDC25L), or F25B3.3 kinase-like protein, specifically activates Rap and may also activate other GTPases such as RRAS, RRAS2, NRAS, KRAS but not HRAS. RASGRP2 is involved in aggregation of platelets and adhesion of T-lymphocytes and neutrophils probably through inside-out integrin activation, as well as in the muscarinic acetylcholine receptor M1/CHRM1 signaling pathway. RASGRP3, also called calcium and DAG-regulated guanine nucleotide exchange factor III (CalDAG-GEFIII), or guanine nucleotide exchange factor for Rap1, is a guanine nucleotide-exchange factor activating H-Ras, R-Ras and Ras-associated protein-1/2. It functions as an important mediator of signaling downstream from receptor coupled phosphoinositide turnover in B and T cells. RASGRP4 may function in mast cell differentiation. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 52 matched cddid_all.tbl CDD cd20809 cd20809 410359 C1_MRCK protein kinase C conserved region 1 (C1 domain) found in the Myotonic dystrophy kinase-related Cdc42-binding kinase (MRCK) family. MRCK is thought to be a coincidence detector of signaling by the small GTPase Cdc42 and phosphoinositides. MRCK/Cdc42 signaling mediates myosin-dependent cell motility. MRCK has been shown to promote cytoskeletal reorganization, which affects many biological processes. Three isoforms of MRCK are known, named alpha, beta and gamma. MRCKgamma is expressed in heart and skeletal muscles, unlike MRCKalpha and MRCKbeta, which are expressed ubiquitously. MRCK consists of a serine/threonine kinase domain, a cysteine rich (C1) region, a PH domain and a p21 binding motif. This model corresponds to C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 53 matched cddid_all.tbl CDD cd20810 cd20810 410360 C1_VAV protein kinase C conserved region 1 (C1 domain) found in VAV proteins. VAV proteins function both as cytoplasmic guanine nucleotide exchange factors (GEFs) for Rho GTPases and as scaffold proteins, and they play important roles in cell signaling by coupling cell surface receptors to various effector functions. They play key roles in processes that require cytoskeletal reorganization including immune synapse formation, phagocytosis, cell spreading, and platelet aggregation, among others. Vertebrates have three VAV proteins (VAV1, VAV2, and VAV3). VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 52 matched cddid_all.tbl CDD cd20811 cd20811 410361 C1_Raf protein kinase C conserved region 1 (C1 domain) found in the Raf (Rapidly Accelerated Fibrosarcoma) kinase family. Raf kinases are serine/threonine kinases (STKs) that catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. They act as mitogen-activated protein kinase kinase kinases (MAP3Ks, MKKKs, MAPKKKs), which phosphorylate and activate MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. They function in the linear Ras-Raf-MEK-ERK pathway that regulates many cellular processes including cycle regulation, proliferation, differentiation, survival, and apoptosis. Aberrant expression or activation of components in this pathway are associated with tumor initiation, progression, and metastasis. Raf proteins contain a Ras binding domain, a zinc finger cysteine-rich domain (C1), and a catalytic kinase domain. Vertebrates have three Raf isoforms (A-, B-, and C-Raf) with different expression profiles, modes of regulation, and abilities to function in the ERK cascade, depending on cellular context and stimuli. They have essential and non-overlapping roles during embryo- and organogenesis. Knockout of each isoform results in a lethal phenotype or abnormality in most mouse strains. This model describes the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 49 matched cddid_all.tbl CDD cd20812 cd20812 410362 C1_KSR protein kinase C conserved region 1 (C1 domain) found in the kinase suppressor of Ras (KSR) family. KSR is a scaffold protein that functions downstream of Ras and upstream of Raf in the Extracellular signal-Regulated Kinase (ERK) pathway that regulates many cellular processes including cycle regulation, proliferation, differentiation, survival, and apoptosis. KSR proteins regulate the assembly and activation of the Raf/MEK/ERK module upon Ras activation at the membrane by direct association of its components. They are widely regarded as pseudokinases, but there is some debate in this designation as a few groups have reported detecting kinase catalytic activity for KSRs, specifically KSR1. Vertebrates contain two KSR proteins, KSR1 and KSR2. KSR proteins contain a SAM-like domain, a zinc finger cysteine-rich domain (C1), and a pseudokinase domain. This model describes the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 48 matched cddid_all.tbl CDD cd20813 cd20813 410363 C1_ROCK protein kinase C conserved region 1 (C1 domain) found in the Rho-associated coiled-coil containing protein kinase (ROCK) family. ROCK is a serine/threonine protein kinase, catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. It is also referred to as Rho-associated kinase or simply as Rho kinase. It contains an N-terminal extension, a catalytic kinase domain, and a C-terminal extension, which contains a coiled-coil region encompassing a Rho-binding domain (RBD), a pleckstrin homology (PH) domain and a C1 domain. ROCK is auto-inhibited by the RBD and PH domain interacting with the catalytic domain. It is activated via interaction with Rho GTPases and is involved in many cellular functions including contraction, adhesion, migration, motility, proliferation, and apoptosis. The ROCK subfamily consists of two isoforms, ROCK1 and ROCK2, which may be functionally redundant in some systems, but exhibit different tissue distributions. Both isoforms are ubiquitously expressed in most tissues, but ROCK2 is more prominent in brain and skeletal muscle while ROCK1 is more pronounced in the liver, testes, and kidney. Studies in knockout mice result in different phenotypes, suggesting that the two isoforms do not compensate for each other during embryonic development. This model corresponds to C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 65 matched cddid_all.tbl CDD cd20814 cd20814 410364 CRIK protein kinase C conserved region 1 (C1 domain) found in citron Rho-interacting kinase (CRIK) and similar proteins. CRIK, also called serine/threonine-protein kinase 21, is an effector of the small GTPase Rho. It plays an important function during cytokinesis and affects its contractile process. CRIK-deficient mice show severe ataxia and epilepsy as a result of abnormal cytokinesis and massive apoptosis in neuronal precursors. A Down syndrome critical region protein TTC3 interacts with CRIK and inhibits CRIK-dependent neuronal differentiation and neurite extension. CRIK contains a catalytic domain, a central coiled-coil domain, and a C-terminal region containing a Rho-binding domain (RBD), a zinc finger (C1 domain), and a pleckstrin homology (PH) domain, in addition to other motifs. This model corresponds to C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 56 matched cddid_all.tbl CDD cd20815 cd20815 410365 C1_p190RhoGEF-like protein kinase C conserved region 1 (C1 domain) found in the 190 kDa guanine nucleotide exchange factor (p190RhoGEF)-like family. The p190RhoGEF-like protein family includes p190RhoGEF, Rho guanine nucleotide exchange factor 2 (ARHGEF2), A-kinase anchor protein 13 (AKAP-13) and similar proteins. p190RhoGEF is a brain-enriched, RhoA-specific guanine nucleotide exchange factor that regulates signaling pathways downstream of integrins and growth factor receptors. It is involved in axonal branching, synapse formation and dendritic morphogenesis, as well as in focal adhesion formation, cell motility and B-lymphocytes activation. ARHGEF2 acts as a guanine nucleotide exchange factor (GEF) that activates Rho-GTPases by promoting the exchange of GDP for GTP. It is thought to play a role in actin cytoskeleton reorganization in different tissues since its activation induces formation of actin stress fibers. AKAP-13 is a scaffold protein that plays an important role in assembling signaling complexes downstream of several types of G protein-coupled receptors. It activates RhoA in response to signaling via G protein-coupled receptors via its function as Rho guanine nucleotide exchange factor. It may also activate other Rho family members. AKAP-13 plays a role in cell growth, cell development and actin fiber formation. Members of this family share a common domain architecture containing C1, RhoGEF or Dbl-homologous (DH), and Pleckstrin Homology (PH) domains. Some members may contain additional domains such as the DUF5401 domain. This model describes the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 54 matched cddid_all.tbl CDD cd20816 cd20816 410366 C1_GMIP-like protein kinase C conserved region 1 (C1 domain) found in the GEM-interacting protein (GMIP)-like family. The GMIP-like family includes GMIP, Rho GTPase-activating protein 29 (ARHGAP29) and Rho GTPase-activating protein 45 (ARHGAP45). GMIP is a RhoA-specific GTPase-activating protein that acts as a key factor in saltatory neuronal migration. It associates with the Rab27a effector JFC1 and modulates vesicular transport and exocytosis. ARHGAP29, also called PTPL1-associated RhoGAP protein 1 (PARG1) or Rho-type GTPase-activating protein 29, is a GTPase activator for the Rho-type GTPases by converting them to an inactive GDP-bound state. It has strong activity toward RHOA, and weaker activity toward RAC1 and CDC42. ARHGAP29 may act as a specific effector of RAP2A to regulate Rho. In concert with RASIP1, ARHGAP29 suppresses RhoA signaling and dampens ROCK and MYH9 activities in endothelial cells and plays an essential role in blood vessel tubulogenesis. ARHGAP45, also called minor histocompatibility antigen HA-1 (mHag HA-1), is a Rac-GAP (GTPase-Activating Protein) in endothelial cells. It acts as a novel regulator of endothelial integrity. ARHGAP45 contains a GTPase activator for the Rho-type GTPases (RhoGAP) domain that would be able to negatively regulate the actin cytoskeleton as well as cell spreading. However, it also contains N-terminally a BAR-domin which can play an autoinhibitory effect on this RhoGAP activity. Members of this family contain a zinc-binding C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 51 matched cddid_all.tbl CDD cd20817 cd20817 410367 C1_Stac protein kinase C conserved region 1 (C1 domain) found in the SH3 and cysteine-rich domain-containing protein (Stac) family. Stac proteins are putative adaptor proteins that are important for neuronal function. There are three mammalian members (Stac1, Stac2 and Stac3) of this family. Stac1 and Stac3 contain two SH3 domains while Stac2 contains a single SH3 domain at the C-terminus. Stac1 and Stac2 have been found to be expressed differently in mature dorsal root ganglia (DRG) neurons. Stac1 is mainly expressed in peptidergic neurons while Stac2 is found in a subset of nonpeptidergic and all trkB+ neurons. Stac proteins contain a cysteine-rich C1 domain and one or two SH3 domains at the C-terminus. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 51 matched cddid_all.tbl CDD cd20818 cd20818 410368 C1_Myosin-IX protein kinase C conserved region 1 (C1 domain) found in the unconventional myosin-IX family. Myosins IX (Myo9) is a class of unique motor proteins with a common structure of an N-terminal extension preceding a myosin head homologous to the Ras-association (RA) domain, a head (motor) domain, a neck with IQ motifs that bind light chains, and a C-terminal tail containing cysteine-rich zinc binding (C1) and Rho-GTPase activating protein (RhoGAP) domains. There are two genes for myosins IX in humans, IXa and IXb, that are different in their expression and localization. IXa is expressed abundantly in brain and testis, and IXb is expressed abundantly in tissues of the immune system. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 56 matched cddid_all.tbl CDD cd20819 cd20819 410369 C1_DEF8 protein kinase C conserved region 1 (C1 domain) found in differentially expressed in FDCP 8 (DEF-8) and similar proteins. DEF-8 positively regulates lysosome peripheral distribution and ruffled border formation in osteoclasts. It is involved in bone resorption. DEF-8 contains a protein kinase C conserved region 1 (C1) domain followed by a putative zinc-RING and/or ribbon. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 62 matched cddid_all.tbl CDD cd20820 cd20820 410370 C1_RASSF1-like protein kinase C conserved region 1 (C1 domain) found in the Ras association domain-containing protein 1 (RASSF1)-like family. The RASSF1-like family includes RASSF1 and RASSF5. RASSF1 and RASSF5 are members of a family of RAS effectors, of which there are currently 8 members (RASSF1-8), all containing a Ras-association (RA) domain of the Ral-GDS/AF6 type. RASSF1 has eight transcripts (A-H) arising from alternative splicing and differential promoter usage. RASSF1A and 1C are the most extensively studied RASSF1; both are localized to microtubules and involved in the regulation of growth and migration. RASSF1 is a potential tumor suppressor that is required for death receptor-dependent apoptosis. RASSF5, also called new ras effector 1 (NORE1), or regulator for cell adhesion and polarization enriched in lymphoid tissues (RAPL), is expressed as three transcripts (A-C) via differential promoter usage and alternative splicing. RASSF5A is a pro-apoptotic Ras effector and functions as a Ras regulated tumor suppressor. RASSF5C is regulated by Ras related protein and modulates cellular adhesion. RASSF5 is a potential tumor suppressor that seems to be involved in lymphocyte adhesion by linking RAP1A activation upon T-cell receptor or chemokine stimulation to integrin activation. RASSF1 and RASSF5 contain a C1 domain, which is descibed in this model. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 52 matched cddid_all.tbl CDD cd20821 cd20821 410371 C1_MgcRacGAP protein kinase C conserved region 1 (C1 domain) found in male germ cell RacGap (MgcRacGAP) and similar proteins. MgcRacGAP, also called Rac GTPase-activating protein 1 (RACGAP1) or protein CYK4, plays an important dual role in cytokinesis: i) it is part of centralspindlin-complex, together with the mitotic kinesin MKLP1, which is critical for the structure of the central spindle by promoting microtuble bundling; and ii) after phosphorylation by aurora B, MgcRacGAP becomes an effective regulator of RhoA and plays an important role in the assembly of the contractile ring and the initiation of cytokinesis. MgcRacGAP-like proteins contain an N-terminal C1 domain, and a C-terminal RhoGAP domain. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 55 matched cddid_all.tbl CDD cd20822 cd20822 410372 C1_ScPKC1-like_rpt1 first protein kinase C conserved region 1 (C1 domain) found in Saccharomyces cerevisiae protein kinase C-like 1 (ScPKC1) and similar proteins. ScPKC1 is required for cell growth and for the G2 to M transition of the cell division cycle. It mediates a protein kinase cascade, activating BCK1 which itself activates MKK1/MKK2. The family also includes Schizosaccharomyces pombe PKC1 and PKC2, which are involved in the control of cell shape and act as targets of the inhibitor staurosporine. Members of this family contain two copies of the C1 domain. This model corresponds to the first one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 52 matched cddid_all.tbl CDD cd20823 cd20823 410373 C1_ScPKC1-like_rpt2 second protein kinase C conserved region 1 (C1 domain) found in Saccharomyces cerevisiae protein kinase C-like 1 (ScPKC1) and similar proteins. ScPKC1 is required for cell growth and for the G2 to M transition of the cell division cycle. It mediates a protein kinase cascade, activating BCK1 which itself activates MKK1/MKK2. The family also includes Schizosaccharomyces pombe PKC1 and PKC2, which are involved in the control of cell shape and act as targets of the inhibitor staurosporine. Members of this family contain two copies of C1 domain. This model corresponds to the second one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 59 matched cddid_all.tbl CDD cd20824 cd20824 410374 C1_SpBZZ1-like protein kinase C conserved region 1 (C1 domain) found in Schizosaccharomyces pombe protein BZZ1 and similar proteins. BZZ1 is a syndapin-like F-BAR protein that plays a role in endocytosis and trafficking to the vacuole. It functions with type I myosins to restore polarity of the actin cytoskeleton after NaCl stress. BZZ1 contains an N-terminal F-BAR (FES-CIP4 Homology and Bin/Amphiphysin/Rvs), a central coiled-coil, and two C-terminal SH3 domains. Schizosaccharomyces pombe BZZ1 also harbors a C1 domain, but Saccharomyces cerevisiae BZZ1 doesn't have any. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 53 matched cddid_all.tbl CDD cd20825 cd20825 410375 C1_PDZD8 protein kinase C conserved region 1 (C1 domain) found in PDZ domain-containing protein 8 (PDZD8) and similar proteins. PDZD8, also called Sarcoma antigen NY-SAR-84/NY-SAR-104, is a molecular tethering protein that connects endoplasmic reticulum (ER) and mitochondrial membranes. PDZD8-dependent ER-mitochondria membrane tethering is essential for ER-mitochondria Ca2+ transfer. In neurons, it is involved in the regulation of dendritic Ca2+ dynamics by regulating mitochondrial Ca2+ uptake. PDZD8 also plays an indirect role in the regulation of cell morphology and cytoskeletal organization. It contains a PDZ domain and a C1 domain. This model describes the C1 domain, a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 55 matched cddid_all.tbl CDD cd20826 cd20826 410376 C1_TNS2-like protein kinase C conserved region 1 (C1 domain) found in tensin-2 like (TNS2-like) proteins. The TNS2-like group includes TNS2, and variants of TNS1 and TNS3. Tensin-2 (TNS2), also called C1 domain-containing phosphatase and tensin (C1-TEN), or tensin-like C1 domain-containing phosphatase (TENC1), is an essential component for the maintenance of glomerular basement membrane (GBM) structures. It regulates cell motility and proliferation. It may have phosphatase activity. TNS2 reduces AKT1 phosphorylation, lowers AKT1 kinase activity and interferes with AKT1 signaling. Tensin-1 (TNS1) plays a role in fibrillar adhesion formation. It may be involved in cell migration, cartilage development and in linking signal transduction pathways to the cytoskeleton. Tensin-3 (TNS3), also called tensin-like SH2 domain-containing protein 1 (TENS1), or tumor endothelial marker 6 (TEM6), may play a role in actin remodeling. It is involved in the dissociation of the integrin-tensin-actin complex. Typical TNS1 and TNS3 do not contain C1 domains, but some isoforms/variants do. Members of this family contain an N-terminal region with a zinc finger (C1 domain), a protein tyrosine phosphatase (PTP)-like domain and a protein kinase 2 (C2) domain, and a C-terminal region with SH2 and pTyr binding (PTB) domains. This model corresponds to C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 52 matched cddid_all.tbl CDD cd20827 cd20827 410377 C1_Sbf-like protein kinase C conserved region 1 (C1 domain) found in the myotubularin-related protein Sbf and similar proteins. This group includes Drosophila melanogaster SET domain binding factor (Sbf), the single homolog of human MTMR5/MTMR13, and similar proteins, that show high sequence similarity to vertebrate myotubularin-related proteins (MTMRs) which may function as guanine nucleotide exchange factors (GEFs). Sbf is a pseudophosphatase that coordinates both phosphatidylinositol 3-phosphate (PI(3)P) turnover and Rab21 GTPase activation in an endosomal pathway that controls macrophage remodeling. It also functions as a GEF that promotes Rab21 GTPase activation associated with PI(3)P endosomes. Vertebrate MTMR5 and MTMR13 contain an N-terminal DENN domain, a PH-GRAM domain, an inactive PTP domain, a SET interaction domain, a coiled-coil domain, and a C-terminal PH domain. Members of this family contain these domains and have an additional C1 domain. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 53 matched cddid_all.tbl CDD cd20828 cd20828 410378 C1_MTMR-like protein kinase C conserved region 1 (C1 domain) found in uncharacterized proteins similar to myotubularin-related proteins. The family includes a group of uncharacterized proteins that show high sequence similarity to vertebrate myotubularin-related proteins (MTMRs), such as MTMR5 and MTMR13. MTMRs may function as guanine nucleotide exchange factors (GEFs). Vertebrate MTMR5 and MTMR13 contain an N-terminal DENN domain, a PH-GRAM domain, an inactive PTP domain, a SET interaction domain, a coiled-coil domain, and a C-terminal PH domain. Members of this family contain these domains and have an additional C1 domain. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 57 matched cddid_all.tbl CDD cd20829 cd20829 410379 C1_PIK3R-like_rpt1 first protein kinase C conserved region 1 (C1 domain) found in uncharacterized phosphatidylinositol 3-kinase regulatory subunit-like proteins. The family includes a group of uncharacterized proteins that show high sequence similarity to vertebrate phosphatidylinositol 3-kinase regulatory subunits (PIK3Rs), which bind to activated (phosphorylated) protein-tyrosine kinases through its SH2 domain and regulate their kinase activity. Unlike typical PIK3Rs, members of this family have two C1 domains. This model corresponds to the first one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 53 matched cddid_all.tbl CDD cd20830 cd20830 410380 C1_PIK3R-like_rpt2 second protein kinase C conserved region 1 (C1 domain) found in uncharacterized phosphatidylinositol 3-kinase regulatory subunit-like proteins. The family includes a group of uncharacterized proteins that show high sequence similarity to vertebrate phosphatidylinositol 3-kinase regulatory subunits (PIK3Rs), which bind to activated (phosphorylated) protein-tyrosine kinases through its SH2 domain and regulate their kinase activity. Unlike typical PIK3Rs, members of this family have two C1 domains. This model corresponds to the second one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 52 matched cddid_all.tbl CDD cd20831 cd20831 410381 C1_dGM13116p-like protein kinase C conserved region 1 (C1 domain) found in Drosophila melanogaster GM13116p and similar proteins. This group contains uncharacterized proteins including Drosophila melanogaster GM13116p and Caenorhabditis elegans hypothetical protein R11G1.4, both of which contain C2 (a calcium-binding domain) and C1 domains. This model describes the C1 domain, a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 58 matched cddid_all.tbl CDD cd20832 cd20832 410382 C1_ARHGEF-like protein kinase C conserved region 1 (C1 domain) found in uncharacterized Rho guanine nucleotide exchange factor (ARHGEF)-like proteins. The family includes a group of uncharacterized proteins that show high sequence similarity to vertebrate Rho guanine nucleotide exchange factors ARHGEF11 and ARHGEF12, which may play a role in the regulation of RhoA GTPase by guanine nucleotide-binding alpha-12 (GNA12) and alpha-13 (GNA13). Unlike typical ARHGEF11 and ARHGEF12, members of this family contain a C1 domain. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 53 matched cddid_all.tbl CDD cd20833 cd20833 410383 C1_cPKC_rpt1 first protein kinase C conserved region 1 (C1 domain) found in the classical (or conventional) protein kinase C (cPKC) family. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domains. cPKCs are potent kinases for histones, myelin basic protein, and protamine. They depend on calcium, DAG (1,2-diacylglycerol), and in most cases, phosphatidylserine (PS) for activation. There are four cPKC isoforms, named alpha, betaI, betaII, and gamma. PKC-alpha is expressed in many tissues and is associated with cell proliferation, apoptosis, and cell motility. It plays a role in the signaling of the growth factors PDGF, VEGF, EGF, and FGF. Abnormal levels of PKC-alpha have been detected in many transformed cell lines and several human tumors. In addition, PKC-alpha is required for HER2 dependent breast cancer invasion. The PKC beta isoforms (I and II), generated by alternative splicing of a single gene, are preferentially activated by hyperglycemia-induced DAG (1,2-diacylglycerol) in retinal tissues. This is implicated in diabetic microangiopathy such as ischemia, neovascularization, and abnormal vasodilator function. PKC-beta also plays an important role in VEGF signaling. In addition, glucose regulates proliferation in retinal endothelial cells via PKC-betaI. PKC-beta is also being explored as a therapeutic target in cancer. It contributes to tumor formation and is involved in the tumor host mechanisms of inflammation and angiogenesis. PKC-gamma is mainly expressed in neuronal tissues. It plays a role in protection from ischemia. Members of this family contain two copies of the C1 domain. This model corresponds to the first one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 58 matched cddid_all.tbl CDD cd20834 cd20834 410384 C1_nPKC_theta-like_rpt1 first protein kinase C conserved region 1 (C1 domain) found in novel protein kinase C (nPKC) theta, delta, and similar proteins. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domains. nPKCs are calcium-independent, but require DAG (1,2-diacylglycerol) and phosphatidylserine (PS) for activity. PKC-theta is selectively expressed in T-cells and plays an important and non-redundant role in several aspects of T-cell biology. PKC-delta plays a role in cell cycle regulation and programmed cell death in many cell types. Members of this family contain two copies of the C1 domain. This model corresponds to the first one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 61 matched cddid_all.tbl CDD cd20835 cd20835 410385 C1_nPKC_epsilon-like_rpt1 first protein kinase C conserved region 1 (C1 domain) found in novel protein kinase C (nPKC) epsilon, eta, and similar proteins. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domains. nPKCs are calcium-independent, but require DAG (1,2-diacylglycerol) and phosphatidylserine (PS) for activity. PKC-epsilon has been shown to behave as an oncoprotein. Its overexpression contributes to neoplastic transformation depending on the cell type. It contributes to oncogenesis by inducing disordered cell growth and inhibiting cell death. It also plays a role in tumor invasion and metastasis. PKC-epsilon has also been found to confer cardioprotection against ischemia and reperfusion-mediated damage. Other cellular functions include the regulation of gene expression, cell adhesion, and cell motility. PKC-eta is predominantly expressed in squamous epithelia, where it plays a crucial role in the signaling of cell-type specific differentiation. It is also expressed in pro-B cells and early-stage thymocytes, and acts as a key regulator in early B-cell development. PKC-eta increases glioblastoma multiforme (GBM) proliferation and resistance to radiation, and is being developed as a therapeutic target for the management of GBM. Members of this family contain two copies of the C1 domain. This model corresponds to the first one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 64 matched cddid_all.tbl CDD cd20836 cd20836 410386 C1_cPKC_rpt2 second protein kinase C conserved region 1 (C1 domain) found in the classical (or conventional) protein kinase C (cPKC) family. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. cPKCs are potent kinases for histones, myelin basic protein, and protamine. They depend on calcium, DAG (1,2-diacylglycerol), and in most cases, phosphatidylserine (PS) for activation. There are four cPKC isoforms, named alpha, betaI, betaII, and gamma. PKC-alpha is expressed in many tissues and is associated with cell proliferation, apoptosis, and cell motility. It plays a role in the signaling of the growth factors PDGF, VEGF, EGF, and FGF. Abnormal levels of PKC-alpha have been detected in many transformed cell lines and several human tumors. In addition, PKC-alpha is required for HER2 dependent breast cancer invasion. The PKC beta isoforms (I and II), generated by alternative splicing of a single gene, are preferentially activated by hyperglycemia-induced DAG (1,2-diacylglycerol) in retinal tissues. This is implicated in diabetic microangiopathy such as ischemia, neovascularization, and abnormal vasodilator function. PKC-beta also plays an important role in VEGF signaling. In addition, glucose regulates proliferation in retinal endothelial cells via PKC-betaI. PKC-beta is also being explored as a therapeutic target in cancer. It contributes to tumor formation and is involved in the tumor host mechanisms of inflammation and angiogenesis. PKC-gamma is mainly expressed in neuronal tissues. It plays a role in protection from ischemia. Members of this family contain two copies of C1 domain. This model corresponds to the second one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 54 matched cddid_all.tbl CDD cd20837 cd20837 410387 C1_nPKC_theta-like_rpt2 second protein kinase C conserved region 1 (C1 domain) found in novel protein kinase C (nPKC) theta, delta, and similar proteins. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. nPKCs are calcium-independent, but require DAG (1,2-diacylglycerol) and phosphatidylserine (PS) for activity. PKC-theta is selectively expressed in T-cells and plays an important and non-redundant role in several aspects of T-cell biology. PKC-delta plays a role in cell cycle regulation and programmed cell death in many cell types. Members of this family contain two copies of C1 domain. This model corresponds to the second one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 50 matched cddid_all.tbl CDD cd20838 cd20838 410388 C1_nPKC_epsilon-like_rpt2 second protein kinase C conserved region 1 (C1 domain) found in novel protein kinase C (nPKC) epsilon, eta, and similar proteins. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. nPKCs are calcium-independent, but require DAG (1,2-diacylglycerol) and phosphatidylserine (PS) for activity. PKC-epsilon has been shown to behave as an oncoprotein. Its overexpression contributes to neoplastic transformation depending on the cell type. It contributes to oncogenesis by inducing disordered cell growth and inhibiting cell death. It also plays a role in tumor invasion and metastasis. PKC-epsilon has also been found to confer cardioprotection against ischemia and reperfusion-mediated damage. Other cellular functions include the regulation of gene expression, cell adhesion, and cell motility. PKC-eta is predominantly expressed in squamous epithelia, where it plays a crucial role in the signaling of cell-type specific differentiation. It is also expressed in pro-B cells and early-stage thymocytes, and acts as a key regulator in early B-cell development. PKC-eta increases glioblastoma multiforme (GBM) proliferation and resistance to radiation, and is being developed as a therapeutic target for the management of GBM. Members of this family contain two copies of C1 domain. This model corresponds to the second one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 55 matched cddid_all.tbl CDD cd20839 cd20839 410389 C1_PKD1_rpt1 first protein kinase C conserved region 1 (C1 domain) found in protein kinase D (PKD) and similar proteins. PKD is also called PKD1, PRKD1, protein kinase C mu type (nPKC-mu), PRKCM, serine/threonine-protein kinase D1, or nPKC-D1. It is a serine/threonine-protein kinase that converts transient diacylglycerol (DAG) signals into prolonged physiological effects downstream of PKC, and is involved in the regulation of MAPK8/JNK1 and Ras signaling, Golgi membrane integrity and trafficking, cell survival through NF-kappa-B activation, cell migration, cell differentiation by mediating HDAC7 nuclear export, cell proliferation via MAPK1/3 (ERK1/2) signaling, and plays a role in cardiac hypertrophy, VEGFA-induced angiogenesis, genotoxic-induced apoptosis and flagellin-stimulated inflammatory response. PKD contains N-terminal tandem cysteine-rich zinc binding C1 (PKC conserved region 1), central PH (Pleckstrin Homology), and C-terminal catalytic kinase domains. This model corresponds to the first C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 72 matched cddid_all.tbl CDD cd20840 cd20840 410390 C1_PKD2_rpt1 first protein kinase C conserved region 1 (C1 domain) found in protein kinase D2 (PKD2) and similar proteins. PKD2, also called PRKD2, HSPC187, or serine/threonine-protein kinase D2 (nPKC-D2), is a serine/threonine-protein kinase that converts transient diacylglycerol (DAG) signals into prolonged physiological effects downstream of PKC, and is involved in the regulation of cell proliferation via MAPK1/3 (ERK1/2) signaling, oxidative stress-induced NF-kappa-B activation, inhibition of HDAC7 transcriptional repression, signaling downstream of T-cell antigen receptor (TCR) and cytokine production, and plays a role in Golgi membrane trafficking, angiogenesis, secretory granule release and cell adhesion. PKD2 contains N-terminal tandem cysteine-rich zinc binding C1 (PKC conserved region 1), central PH (Pleckstrin Homology), and C-terminal catalytic kinase domains. This model corresponds to the first C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 73 matched cddid_all.tbl CDD cd20841 cd20841 410391 C1_PKD3_rpt1 first protein kinase C conserved region 1 (C1 domain) found in protein kinase D3 (PKD3) and similar proteins. PKD3 is also called PRKD3, PRKCN, serine/threonine-protein kinase D3 (nPKC-D3), protein kinase C nu type (nPKC-nu), or protein kinase EPK2. It converts transient diacylglycerol (DAG) signals into prolonged physiological effects, downstream of PKC. It is involved in the regulation of the cell cycle by modulating microtubule nucleation and dynamics. PKD3 acts as a key mediator in several cancer development signaling pathways. PKD3 contains N-terminal tandem cysteine-rich zinc binding C1 (PKC conserved region 1), central PH (Pleckstrin Homology), and C-terminal catalytic kinase domains. This model corresponds to the first C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 75 matched cddid_all.tbl CDD cd20842 cd20842 410392 C1_PKD1_rpt2 second protein kinase C conserved region 1 (C1 domain) found in protein kinase D (PKD) and similar proteins. PKD is also called PKD1, PRKD1, protein kinase C mu type (nPKC-mu), PRKCM, serine/threonine-protein kinase D1, or nPKC-D1. It is a serine/threonine-protein kinase that converts transient diacylglycerol (DAG) signals into prolonged physiological effects downstream of PKC, and is involved in the regulation of MAPK8/JNK1 and Ras signaling, Golgi membrane integrity and trafficking, cell survival through NF-kappa-B activation, cell migration, cell differentiation by mediating HDAC7 nuclear export, cell proliferation via MAPK1/3 (ERK1/2) signaling, and plays a role in cardiac hypertrophy, VEGFA-induced angiogenesis, genotoxic-induced apoptosis and flagellin-stimulated inflammatory response. PKD contains N-terminal tandem cysteine-rich zinc binding C1 (PKC conserved region 1), central PH (Pleckstrin Homology), and C-terminal catalytic kinase domains. This model corresponds to the second C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 94 matched cddid_all.tbl CDD cd20843 cd20843 410393 C1_PKD2_rpt2 second protein kinase C conserved region 1 (C1 domain) found in protein kinase D2 (PKD2) and similar proteins. PKD2, also called PRKD2, HSPC187, or serine/threonine-protein kinase D2 (nPKC-D2), is a serine/threonine-protein kinase that converts transient diacylglycerol (DAG) signals into prolonged physiological effects downstream of PKC, and is involved in the regulation of cell proliferation via MAPK1/3 (ERK1/2) signaling, oxidative stress-induced NF-kappa-B activation, inhibition of HDAC7 transcriptional repression, signaling downstream of T-cell antigen receptor (TCR) and cytokine production, and plays a role in Golgi membrane trafficking, angiogenesis, secretory granule release and cell adhesion. PKD2 contains N-terminal tandem cysteine-rich zinc binding C1 (PKC conserved region 1), central PH (Pleckstrin Homology), and C-terminal catalytic kinase domains. This model corresponds to the second C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 79 matched cddid_all.tbl CDD cd20844 cd20844 410394 C1_PKD3_rpt2 second protein kinase C conserved region 1 (C1 domain) found in protein kinase D3 (PKD3) and similar proteins. PKD3 is also called PRKD3, PRKCN, serine/threonine-protein kinase D3 (nPKC-D3), protein kinase C nu type (nPKC-nu), or protein kinase EPK2. It converts transient diacylglycerol (DAG) signals into prolonged physiological effects, downstream of PKC. It is involved in the regulation of the cell cycle by modulating microtubule nucleation and dynamics. PKD3 acts as a key mediator in several cancer development signaling pathways. PKD3 contains N-terminal tandem cysteine-rich zinc binding C1 (PKC conserved region 1), central PH (Pleckstrin Homology), and C-terminal catalytic kinase domains. This model corresponds to the second C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 69 matched cddid_all.tbl CDD cd20845 cd20845 410395 C1_DGKbeta_rpt1 first protein kinase C conserved region 1 (C1 domain) found in diacylglycerol kinase beta (DAG kinase beta) and similar proteins. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase beta, also called 90 kDa diacylglycerol kinase, or diglyceride kinase beta (DGK-beta), exhibits high phosphorylation activity for long-chain diacylglycerols. It is classified as a type I DAG kinase (DGK), containing EF-hand structures that bind Ca(2+) and a recoverin homology domain, in addition to C1 and catalytic domains that are present in all DGKs. As a type I DGK, it is regulated by calcium binding. DAG kinase beta contains two copies of the C1 domain. This model corresponds to the first one. DGK-beta contains typical C1 domains that bind DAG and phorbol esters. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 66 matched cddid_all.tbl CDD cd20846 cd20846 410396 C1_DGKgamma_rpt1 first protein kinase C conserved region 1 (C1 domain) found in diacylglycerol kinase gamma (DAG kinase gamma) and similar proteins. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase gamma, also called diglyceride kinase gamma (DGK-gamma), reverses the normal flow of glycerolipid biosynthesis by phosphorylating diacylglycerol back to phosphatidic acid. It is classified as a type I DAG kinase (DGK), containing EF-hand structures that bind Ca(2+) and a recoverin homology domain, in addition to C1 and catalytic domains that are present in all DGKs. As a type I DGK, it is regulated by calcium binding. DGK-gamma contains two copies of the C1 domain. This model corresponds to the first one. DGK-gamma contains typical C1 domains that bind DAG and phorbol esters. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 73 matched cddid_all.tbl CDD cd20847 cd20847 410397 C1_DGKdelta_rpt1 first protein kinase C conserved region 1 (C1 domain) found in diacylglycerol kinase delta (DAG kinase delta) and similar proteins. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase delta, also called 130 kDa diacylglycerol kinase, or diglyceride kinase delta (DGK-delta), is a residential lipid kinase in the endoplasmic reticulum. It promotes lipogenesis and is involved in triglyceride biosynthesis. It is classified as a type II DAG kinase (DGK), containing pleckstrin homology (PH) and sterile alpha motifs (SAM) domains, in addition to C1 and catalytic domains that are present in all DGKs. The SAM domain mediates oligomerization of type II DGKs. DAG kinase delta contains two copies of the C1 domain. This model corresponds to the first one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 85 matched cddid_all.tbl CDD cd20848 cd20848 410398 C1_DGKeta_rpt1 first protein kinase C conserved region 1 (C1 domain) found in diacylglycerol kinase eta (DAG kinase eta) and similar proteins. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase eta, also called diglyceride kinase eta (DGK-eta), plays a key role in promoting cell growth. It is classified as a type II DAG kinase (DGK), containing pleckstrin homology (PH) and sterile alpha motifs (SAM) domains, in addition to C1 and catalytic domains that are present in all DGKs. The SAM domain mediates oligomerization of type II DGKs. The diacylglycerol kinase eta gene, DGKH, is a replicated risk gene of bipolar disorder (BPD). DAG kinase eta contains two copies of the C1 domain. This model corresponds to the first one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 86 matched cddid_all.tbl CDD cd20849 cd20849 410399 C1_DGKzeta_rpt1 first protein kinase C conserved region 1 (C1 domain) found in diacylglycerol kinase zeta (DAG kinase zeta) and similar proteins. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase zeta, also called diglyceride kinase zeta (DGK-zeta), displays a strong preference for 1,2-diacylglycerols over 1,3-diacylglycerols, but lacks substrate specificity among molecular species of long chain diacylglycerols. It is classified as a type IV DAG kinase (DGK), containing myristoylated alanine-rich protein kinase C substrate (MARCKS), PDZ-binding, and ankyrin domains, in addition to C1 and catalytic domains that are present in all DGKs. The MARCKS domain regulates the nuclear localizations of type IV DGKs while the PDZ-binding and ankyrin domains regulate interactions with several proteins. DAG kinase zeta contains two copies of the C1 domain. This model corresponds to the first one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 74 matched cddid_all.tbl CDD cd20850 cd20850 410400 C1_DGKiota_rpt1 first protein kinase C conserved region 1 (C1 domain) found in diacylglycerol kinase iota (DAG kinase iota) and similar proteins. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase iota, also called diglyceride kinase iota (DGK-iota), or DGKI, is a homolog of Drosophila DGK2, RdgA. It may have important cellular functions in the retina and brain. It is classified as a type IV DAG kinase (DGK), containing myristoylated alanine-rich protein kinase C substrate (MARCKS), PDZ-binding, and ankyrin domains, in addition to C1 and catalytic domains that are present in all DGKs. The MARCKS domain regulates the nuclear localizations of type IV DGKs while the PDZ-binding and ankyrin domains regulate interactions with several proteins. DAG kinase iota contains two copies of the C1 domain. This model corresponds to the first one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 73 matched cddid_all.tbl CDD cd20851 cd20851 410401 C1_DGK_typeI_like_rpt2 second protein kinase C conserved region 1 (C1 domain) found in type I diacylglycerol kinases. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. Type I DAG kinases (DGKs) contain EF-hand structures that bind Ca(2+) and recoverin homology domains, in addition to C1 and catalytic domains that are present in all DGKs. Type I DGKs, regulated by calcium binding, include three DGK isozymes (alpha, beta and gamma). DAG kinase alpha, also called 80 kDa DAG kinase, or diglyceride kinase alpha (DGK-alpha), is active upon cell stimulation, initiating the resynthesis of phosphatidylinositols and attenuating protein kinase C activity. DAG kinase beta, also called 90 kDa DAG kinase, or diglyceride kinase beta (DGK-beta), exhibits high phosphorylation activity for long-chain diacylglycerols. DAG kinase gamma, also called diglyceride kinase gamma (DGK-gamma), reverses the normal flow of glycerolipid biosynthesis by phosphorylating diacylglycerol back to phosphatidic acid. Members of this family contain two copies of the C1 domain. This model corresponds to the second one. DGK-alpha contains atypical C1 domains, while DGK-beta and DGK-gamma contain typical C1 domains that bind DAG and phorbol esters. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 52 matched cddid_all.tbl CDD cd20852 cd20852 410402 C1_DGK_typeII_rpt2 second protein kinase C conserved region 1 (C1 domain) found in type II diacylglycerol kinases. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. Type II DAG kinases (DGKs) contain pleckstrin homology (PH) and sterile alpha motifs (SAM) domains, in addition to C1 and catalytic domains that are present in all DGKs. The SAM domain mediates oligomerization of type II DGKs. Three DGK isozymes (delta, eta and kappa) are classified as type II. DAG kinase delta, also called 130 kDa DAG kinase, or diglyceride kinase delta (DGK-delta), is a residential lipid kinase in the endoplasmic reticulum. It promotes lipogenesis and is involved in triglyceride biosynthesis. DAG kinase eta, also called diglyceride kinase eta (DGK-eta), plays a key role in promoting cell growth. The DAG kinase eta gene, DGKH, is a replicated risk gene of bipolar disorder (BPD). DAG kinase kappa is also called diglyceride kinase kappa (DGK-kappa) or 142 kDa DAG kinase. Members of this family contain two copies of the C1 domain. This model corresponds to the second one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 54 matched cddid_all.tbl CDD cd20853 cd20853 410403 C1_DGKepsilon_typeIII_rpt2 second protein kinase C conserved region 1 (C1 domain) found in type III diacylglycerol kinase, DAG kinase epsilon, and similar proteins. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase epsilon, also called diglyceride kinase epsilon (DGK-epsilon), is the only isoform classified as type III; it possesses a hydrophobic domain in addition to C1 and catalytic domains that are present in all DGKs, and shows selectivity for acyl chains. It is highly selective for arachidonate-containing species of DAG. It may terminate signals transmitted through arachidonoyl-DAG or may contribute to the synthesis of phospholipids with defined fatty acid composition. DAG kinase epsilon contains two copies of the C1 domain. This model corresponds to the second one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 63 matched cddid_all.tbl CDD cd20854 cd20854 410404 C1_DGKtheta_typeV_rpt3 third protein kinase C conserved region 1 (C1 domain) found in type V diacylglycerol kinase, DAG kinase theta, and similar proteins. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase theta, also called diglyceride kinase theta (DGK-theta), is the only isoform classified as type V; it contains a pleckstrin homology (PH)-like domain and an additional C1 domain, compared to other DGKs. It may regulate the activity of protein kinase C by controlling the balance between the two signaling lipids, diacylglycerol and phosphatidic acid. DAG kinase theta contains three copies of the C1 domain. This model corresponds to the third one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 63 matched cddid_all.tbl CDD cd20855 cd20855 410405 C1_DGK_typeIV_rpt2 second protein kinase C conserved region 1 (C1 domain) found in type IV diacylglycerol kinases. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. Type IV DAG kinases (DGKs) contain myristoylated alanine-rich protein kinase C substrate (MARCKS), PDZ-binding, and ankyrin domains, in addition to C1 and catalytic domains that are present in all DGKs. The MARCKS domain regulates the nuclear localizations of type IV DGKs while the PDZ-binding and ankyrin domains regulate interactions with several proteins. Two DGK isozymes (zeta and iota) are classified as type IV. DAG kinase zeta, also called diglyceride kinase zeta (DGK-zeta), displays a strong preference for 1,2-diacylglycerols over 1,3-diacylglycerols, but lacks substrate specificity among molecular species of long chain diacylglycerols. DAG kinase iota, also called diglyceride kinase iota (DGK-iota), or DGKI, is a homolog of Drosophila DGK2, RdgA. It may have important cellular functions in the retina and brain. Members of this family contain two copies of the C1 domain. This model corresponds to the second one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 62 matched cddid_all.tbl CDD cd20856 cd20856 410406 C1_alphaCHN protein kinase C conserved region 1 (C1 domain) found in alpha-chimaerin and similar proteins. Alpha-chimaerin, also called A-chimaerin, N-chimaerin (CHN), alpha-chimerin, N-chimerin (NC), or Rho GTPase-activating protein 2 (ARHGAP2), is a GTPase-activating protein (GAP) for p21-rac and a phorbol ester receptor. It is involved in the assembly of neuronal locomotor circuits as a direct effector of EPHA4 in axon guidance. Alpha-chimaerin contains a functional SH2 domain that can bind to phosphotyrosine motifs within receptors, a GAP domain with specificity in vitro for Rac1 and a diacylglycerol (DAG)-binding C1 domain which allows them to translocate to membranes in response to DAG signaling and anchors them in close proximity to activated Rac. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 57 matched cddid_all.tbl CDD cd20857 cd20857 410407 C1_betaCHN protein kinase C conserved region 1 (C1 domain) found in beta-chimaerin and similar proteins. Beta-chimaerin, also called beta-chimerin (BCH) or Rho GTPase-activating protein 3 (ARHGAP3), is a GTPase-activating protein (GAP) for p21-rac. Insufficient expression of beta-2 chimaerin is expected to lead to higher Rac activity and could therefore play a role in the progression from low-grade to high-grade tumors. Beta-chimaerin contains a functional SH2 domain that can bind to phosphotyrosine motifs within receptors, a GAP domain with specificity in vitro for Rac1 and a diacylglycerol (DAG)-binding C1 domain which allows them to translocate to membranes in response to DAG signaling and anchors them in close proximity to activated Rac. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 61 matched cddid_all.tbl CDD cd20858 cd20858 410408 C1_Munc13-1 protein kinase C conserved region 1 (C1 domain) found in Munc13-1 and similar proteins. Munc13-1, also called protein unc-13 homolog A (Unc13A), is a diacylglycerol (DAG) receptor that plays a role in vesicle maturation during exocytosis as a target of the diacylglycerol second messenger pathway. It is involved in neurotransmitter release by acting in synaptic vesicle priming prior to vesicle fusion and participates in the activity-dependent refilling of readily releasable vesicle pool (RRP). Loss of MUNC13-1 function causes microcephaly, cortical hyperexcitability, and fatal myasthenia. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 60 matched cddid_all.tbl CDD cd20859 cd20859 410409 C1_Munc13-2-like protein kinase C conserved region 1 (C1 domain) found in Munc13-2, Munc13-3 and similar proteins. Munc13-2, also called protein unc-13 homolog B (Unc13B), plays a role in vesicle maturation during exocytosis as a target of the diacylglycerol second messenger pathway. It is involved in neurotransmitter release by acting in synaptic vesicle priming prior to vesicle fusion and participates in the activity-dependent refilling of readily releasable vesicle pool (RRP). Munc13-2 is essential for normal release probability at hippocampal mossy fiber synapses. Munc13-3 is almost exclusively expressed in the cerebellum. It acts as a tumor suppressor and plays a critical role in the formation of release sites with calcium channel nanodomains. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 82 matched cddid_all.tbl CDD cd20860 cd20860 410410 C1_RASGRP1 protein kinase C conserved region 1 (C1 domain) found in RAS guanyl-releasing protein 1 (RASGRP1) and similar proteins. RASGRP1, also called calcium and DAG-regulated guanine nucleotide exchange factor II (CalDAG-GEFII) or Ras guanyl-releasing protein, functions as a calcium- and diacylglycerol (DAG)-regulated nucleotide exchange factor specifically activating Ras through the exchange of bound GDP for GTP. It activates the Erk/MAP kinase cascade and regulates T-cell/B-cell development, homeostasis and differentiation by coupling T-lymphocyte/B-lymphocyte antigen receptors to Ras. RASGRP1 also regulates NK cell cytotoxicity and ITAM-dependent cytokine production by activation of Ras-mediated ERK and JNK pathways. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 55 matched cddid_all.tbl CDD cd20861 cd20861 410411 C1_RASGRP2 protein kinase C conserved region 1 (C1 domain) found in RAS guanyl-releasing protein 2 (RASGRP2) and similar proteins. RASGRP2, also called calcium and DAG-regulated guanine nucleotide exchange factor I (CalDAG-GEFI), Cdc25-like protein (CDC25L), or F25B3.3 kinase-like protein, functions as a calcium- and DAG-regulated nucleotide exchange factor specifically activating Rap through the exchange of bound GDP for GTP. It may also activate other GTPases such as RRAS, RRAS2, NRAS, KRAS but not HRAS. RASGRP2 is also involved in aggregation of platelets and adhesion of T-lymphocytes and neutrophils probably through inside-out integrin activation, as well as in the muscarinic acetylcholine receptor M1/CHRM1 signaling pathway. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 56 matched cddid_all.tbl CDD cd20862 cd20862 410412 C1_RASGRP3 protein kinase C conserved region 1 (C1 domain) found in RAS guanyl-releasing protein 3 (RASGRP3) and similar proteins. RASGRP3, also called calcium and DAG-regulated guanine nucleotide exchange factor III (CalDAG-GEFIII), or guanine nucleotide exchange factor for Rap1, is a guanine nucleotide-exchange factor activating H-Ras, R-Ras and Ras-associated protein-1/2. It functions as an important mediator of signaling downstream from receptor coupled phosphoinositide turnover in B and T cells. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 59 matched cddid_all.tbl CDD cd20863 cd20863 410413 C1_RASGRP4 protein kinase C conserved region 1 (C1 domain) found in RAS guanyl-releasing protein 4 (RASGRP4) and similar proteins. RASGRP4 functions as a cation- and diacylglycerol (DAG)-regulated nucleotide exchange factor activating Ras through the exchange of bound GDP for GTP. It may function in mast cell differentiation. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 57 matched cddid_all.tbl CDD cd20864 cd20864 410414 C1_MRCKalpha protein kinase C conserved region 1 (C1 domain) found in myotonic dystrophy kinase-related Cdc42-binding kinase alpha (MRCK alpha) and similar proteins. MRCK alpha, also called Cdc42-binding protein kinase alpha, DMPK-like alpha, or myotonic dystrophy protein kinase-like alpha, is a serine/threonine-protein kinase expressed ubiquitously in many tissues. It plays a role in the regulation of peripheral actin reorganization and neurite outgrowth. It may also play a role in the transferrin iron uptake pathway. MRCK alpha is an important downstream effector of Cdc42 and plays a role in the regulation of cytoskeleton reorganization and cell migration. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 60 matched cddid_all.tbl CDD cd20865 cd20865 410415 C1_MRCKbeta protein kinase C conserved region 1 (C1 domain) found in myotonic dystrophy kinase-related Cdc42-binding kinase beta (MRCK beta) and similar proteins. MRCK beta, also called Cdc42-binding protein kinase beta (Cdc42BP-beta), DMPK-like beta, or myotonic dystrophy protein kinase-like beta, is a serine/threonine-protein kinase expressed ubiquitously in many tissues. MRCK beta is an important downstream effector of Cdc42 and plays a role in the regulation of cytoskeleton reorganization and cell migration. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 53 matched cddid_all.tbl CDD cd20866 cd20866 410416 C1_MRCKgamma protein kinase C conserved region 1 (C1 domain) found in myotonic dystrophy kinase-related Cdc42-binding kinase gamma (MRCK gamma) and similar proteins. MRCK gamma (MRCKG), also called Cdc42-binding protein kinase gamma, DMPK-like gamma, myotonic dystrophy protein kinase-like gamma, or myotonic dystrophy protein kinase-like alpha, is a serine/threonine-protein kinase expressed in heart and skeletal muscles. It may act as a downstream effector of Cdc42 in cytoskeletal reorganization and contributes to the actomyosin contractility required for cell invasion, through the regulation of MYPT1 and thus MLC2 phosphorylation. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 52 matched cddid_all.tbl CDD cd20867 cd20867 410417 C1_VAV1 protein kinase C conserved region 1 (C1 domain) found in VAV1 protein. VAV1 is expressed predominantly in the hematopoietic system and plays an important role in the development and activation of B and T cells. It is activated by tyrosine phosphorylation to function as a guanine nucleotide exchange factor (GEF) for Rho GTPases following cell surface receptor activation, triggering various effects such as cytoskeletal reorganization, transcription regulation, cell cycle progression, and calcium mobilization. It also serves as a scaffold protein and has been shown to interact with Ku70, Socs1, Janus kinase 2, SIAH2, S100B, Abl gene, ZAP-70, SLP76, and Syk, among others. VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 57 matched cddid_all.tbl CDD cd20868 cd20868 410418 C1_VAV2 protein kinase C conserved region 1 (C1 domain) found in VAV2 protein. VAV2 is widely expressed and functions as a guanine nucleotide exchange factor (GEF) for RhoA, RhoB and RhoG and also activates Rac1 and Cdc42. It is implicated in many cellular and physiological functions including blood pressure control, eye development, neurite outgrowth and branching, EGFR endocytosis and degradation, and cell cluster morphology, among others. It has been reported to associate with Nek3. VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 58 matched cddid_all.tbl CDD cd20869 cd20869 410419 C1_VAV3 protein kinase C conserved region 1 (C1 domain) found in VAV3 protein. VAV3 is ubiquitously expressed and functions as a phosphorylation-dependent guanine nucleotide exchange factor (GEF) for RhoA, RhoG, and Rac1. Its function has been implicated in the hematopoietic, bone, cerebellar, and cardiovascular systems. VAV3 is essential in axon guidance in neurons that control blood pressure and respiration. It is overexpressed in prostate cancer cells and plays a role in regulating androgen receptor transcriptional activity. VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 59 matched cddid_all.tbl CDD cd20870 cd20870 410420 C1_A_C-Raf protein kinase C conserved region 1 (C1 domain) found in A- and C-Raf (Rapidly Accelerated Fibrosarcoma) kinases, and similar proteins. This group includes A-Raf and C-Raf, both of which are serine/threonine-protein kinases. A-Raf, also called proto-oncogene A-Raf or proto-oncogene A-Raf-1, cooperates with C-Raf in regulating ERK transient phosphorylation that is associated with cyclin D expression and cell cycle progression. Mice deficient in A-Raf are born alive but show neurological and intestinal defects. A-Raf demonstrates low kinase activity to MEK, compared with B- and C-Raf, and may also have alternative functions other than in the ERK signaling cascade. It regulates the M2 type pyruvate kinase, a key glycolytic enzyme. It also plays a role in endocytic membrane trafficking. C-Raf, also known as proto-oncogene Raf-1 or c-Raf-1, is ubiquitously expressed and was the first Raf identified. It was characterized as the acquired oncogene from an acutely transforming murine sarcoma virus (3611-MSV) and the transforming agent from the avian retrovirus MH2. C-Raf-deficient mice embryos die around mid-gestation with increased apoptosis of embryonic tissues, especially in the fetal liver. One of the main functions of C-Raf is restricting caspase activation to promote survival in response to specific stimuli such as Fas stimulation, macrophage apoptosis, and erythroid differentiation. Both A- and C-Raf are mitogen-activated protein kinase kinase kinases (MAP3K, MKKK, MAPKKK), which phosphorylate and activate MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. They function in the linear Ras-Raf-MEK-ERK pathway that regulates many cellular processes including cycle regulation, proliferation, differentiation, survival, and apoptosis. Raf proteins contain a Ras binding domain, a zinc finger cysteine-rich domain (C1), and a catalytic kinase domain. This model describes the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 52 matched cddid_all.tbl CDD cd20871 cd20871 410421 C1_B-Raf protein kinase C conserved region 1 (C1 domain) found in B-Raf (Rapidly Accelerated Fibrosarcoma) kinase and similar proteins. Serine/threonine-protein kinase B-Raf, also called proto-oncogene B-Raf, p94, or v-Raf murine sarcoma viral oncogene homolog B1, activates ERK with the strongest magnitude, compared with other Raf kinases. Mice embryos deficient in B-Raf die around midgestation due to vascular hemorrhage caused by apoptotic endothelial cells. Mutations in B-Raf have been implicated in initiating tumorigenesis and tumor progression, and are found in malignant cutaneous melanoma, papillary thyroid cancer, as well as in ovarian and colorectal carcinomas. Most oncogenic B-Raf mutations are located at the activation loop of the kinase and surrounding regions; the V600E mutation accounts for around 90% of oncogenic mutations. The V600E mutant constitutively activates MEK, resulting in sustained activation of ERK. B-Raf is a mitogen-activated protein kinase kinase kinase (MAP3K, MKKK, MAPKKK), which phosphorylates and activates MAPK kinases (MAPKKs or MKKs or MAP2Ks), which in turn phosphorylate and activate MAPKs during signaling cascades that are important in mediating cellular responses to extracellular signals. They function in the linear Ras-Raf-MEK-ERK pathway that regulates many cellular processes including cycle regulation, proliferation, differentiation, survival, and apoptosis. Raf proteins contain a Ras binding domain, a zinc finger cysteine-rich domain (C1), and a catalytic kinase domain. This model describes the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 60 matched cddid_all.tbl CDD cd20872 cd20872 410422 C1_KSR1 protein kinase C conserved region 1 (C1 domain) found in kinase suppressor of Ras 1 (KSR1) and similar proteins. KSR1 functions as a transducer of TNFalpha-stimulated C-Raf activation of ERK1/2 and NF-kB. Detected activity of KSR1 is cell type specific and context dependent. It is inactive in normal colon epithelial cells and becomes activated at the onset of inflammatory bowel disease (IBD). Similarly, KSR1 activity is undetectable prior to stimulation by EGF or ceramide in COS-7 or YAMC cells, respectively. KSR proteins are widely regarded as pseudokinases, however, this matter is up for debate as catalytic activity has been detected for KSR1 in some systems. KSR proteins contain a SAM-like domain, a zinc finger cysteine-rich domain (C1), and a pseudokinase domain. This model describes the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 47 matched cddid_all.tbl CDD cd20873 cd20873 410423 C1_KSR2 protein kinase C conserved region 1 (C1 domain) found in kinase suppressor of Ras 2 (KSR2) and similar proteins. KSR2 interacts with the protein phosphatase calcineurin and functions in calcium-mediated ERK signaling. It also functions in energy metabolism by regulating AMP kinase and AMPK-dependent processes such as glucose uptake and fatty acid oxidation. KSR proteins act as scaffold proteins that function downstream of Ras and upstream of Raf in the Extracellular signal-Regulated Kinase (ERK) pathway that regulates many cellular processes including cycle regulation, proliferation, differentiation, survival, and apoptosis. KSR proteins regulate the assembly and activation of the Raf/MEK/ERK module upon Ras activation at the membrane by direct association of its components. They are widely regarded as pseudokinases. KSR proteins contain a SAM-like domain, a zinc finger cysteine-rich domain (C1), and a pseudokinase domain. This model describes the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 57 matched cddid_all.tbl CDD cd20874 cd20874 410424 C1_ROCK1 protein kinase C conserved region 1 (C1 domain) found in Rho-associated coiled-coil containing protein kinase 1 (ROCK1) and similar proteins. ROCK1 is a serine/threonine kinase, catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. ROCK1, also called Rho-associated protein kinase 1, renal carcinoma antigen NY-REN-35, Rho-associated, coiled-coil-containing protein kinase I (ROCK-I), p160 ROCK-1, or p160ROCK, is preferentially expressed in the liver, lung, spleen, testes, and kidney. It mediates signaling from Rho to the actin cytoskeleton. It is implicated in the development of cardiac fibrosis, cardiomyocyte apoptosis, and hyperglycemia. Mice deficient with ROCK1 display eyelids open at birth (EOB) and omphalocele phenotypes due to the disorganization of actin filaments in the eyelids and the umbilical ring. ROCK proteins contain an N-terminal extension, a catalytic kinase domain, and a C-terminal extension, which contains a coiled-coil region encompassing a Rho-binding domain (RBD), a pleckstrin homology (PH) domain and a C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 69 matched cddid_all.tbl CDD cd20875 cd20875 410425 C1_ROCK2 protein kinase C conserved region 1 (C1 domain) found in Rho-associated coiled-coil containing protein kinase 2 (ROCK2) and similar proteins. ROCK2 is a serine/threonine kinase, catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. ROCK2, also called Rho-associated protein kinase 2, Rho kinase 2, Rho-associated, coiled-coil-containing protein kinase II (ROCK-II), or p164 ROCK-2, was the first identified target of activated RhoA, and was found to play a role in stress fiber and focal adhesion formation. It is prominently expressed in the brain, heart, and skeletal muscles. It is implicated in vascular and neurological disorders, such as hypertension and vasospasm of the coronary and cerebral arteries. ROCK2 is also activated by caspase-2 cleavage, resulting in thrombin-induced microparticle generation in response to cell activation. Mice deficient in ROCK2 show intrauterine growth retardation and embryonic lethality because of placental dysfunction. ROCK proteins contain an N-terminal extension, a catalytic kinase domain, and a C-terminal extension, which contains a coiled-coil region encompassing a Rho-binding domain (RBD), a pleckstrin homology (PH) domain and a C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 71 matched cddid_all.tbl CDD cd20876 cd20876 410426 C1_p190RhoGEF protein kinase C conserved region 1 (C1 domain) found in 190 kDa guanine nucleotide exchange factor (p190RhoGEF) and similar proteins. p190RhoGEF, also called Rho guanine nucleotide exchange factor (RGNEF), Rho guanine nucleotide exchange factor 28 (ARHGEF28), or RIP2, is a brain-enriched, RhoA-specific guanine nucleotide exchange factor that regulates signaling pathways downstream of integrins and growth factor receptors. It is involved in axonal branching, synapse formation and dendritic morphogenesis, as well as in focal adhesion formation, cell motility and B-lymphocytes activation. In addition to the Dbl homology (DH)-PH domain, p190RhoGEF contains an N-terminal C1 (Protein kinase C conserved region 1) domain. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 61 matched cddid_all.tbl CDD cd20877 cd20877 410427 C1_ARHGEF2 protein kinase C conserved region 1 (C1 domain) found in Rho guanine nucleotide exchange factor 2 (ARHGEF2) and similar proteins. ARHGEF2, also called guanine nucleotide exchange factor H1 (GEF-H1), microtubule-regulated Rho-GEF, or proliferating cell nucleolar antigen p40, acts as guanine nucleotide exchange factor (GEF) that activates Rho-GTPases by promoting the exchange of GDP for GTP. It is thought to play a role in actin cytoskeleton reorganization in different tissues since its activation induces formation of actin stress fibers. ARHGEF2 may be involved in epithelial barrier permeability, cell motility and polarization, dendritic spine morphology, antigen presentation, leukemic cell differentiation, cell cycle regulation, innate immune response, and cancer. It contains a C1 domain followed by Dbl-homology (DH) and pleckstrin-homology (PH) domains which bind and catalyze the exchange of GDP for GTP on RhoA. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 61 matched cddid_all.tbl CDD cd20878 cd20878 410428 C1_AKAP13 protein kinase C conserved region 1 (C1 domain) found in A-kinase anchor protein 13 (AKAP-13) and similar proteins. AKAP-13, also called AKAP-Lbc, breast cancer nuclear receptor-binding auxiliary protein (Brx-1), guanine nucleotide exchange factor Lbc, human thyroid-anchoring protein 31, lymphoid blast crisis oncogene (LBC oncogene), non-oncogenic Rho GTPase-specific GTP exchange factor, protein kinase A-anchoring protein 13 (PRKA13), or p47, is a scaffold protein that plays an important role in assembling signaling complexes downstream of several types of G protein-coupled receptors (GPCRs). It activates RhoA in response to GPCR signaling via its function as a Rho guanine nucleotide exchange factor. It may also activate other Rho family members. AKAP-13 plays a role in cell growth, cell development and actin fiber formation. Its Rho-GEF activity is regulated by protein kinase A (PKA), through binding and phosphorylation. Alternative splicing of this gene in humans has at least 3 transcript variants encoding different isoforms (i.e. proto-/onco-Lymphoid blast crisis, Lbc and breast cancer nuclear receptor-binding auxiliary protein, and Brx) that contain a C1 domain followed by a dbl oncogene homology (DH) domain and a PH domain which are required for full transforming activity. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 60 matched cddid_all.tbl CDD cd20879 cd20879 410429 C1_ARHGEF18-like protein kinase C conserved region 1 (C1 domain) found in uncharacterized Rho guanine nucleotide exchange factor 18 (ARHGEF18)-like proteins. The family includes a group of uncharacterized proteins that show high sequence similarity to vertebrate ARHGEF18, which is also called 114 kDa Rho-specific guanine nucleotide exchange factor (p114-Rho-GEF), p114RhoGEF, or septin-associated RhoGEF (SA-RhoGEF). ARHGEF18 acts as guanine nucleotide exchange factor (GEF) for RhoA GTPases. Its activation induces formation of actin stress fibers. ARHGEF18 also acts as a GEF for RAC1, inducing production of reactive oxygen species (ROS). Members of this family contain C1, RhoGEF or Dbl-homologous (DH), and Pleckstrin Homology (PH) domains, as well as a DUF5401 domain. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 53 matched cddid_all.tbl CDD cd20880 cd20880 410430 C1_Stac1 protein kinase C conserved region 1 (C1 domain) found in SH3 and cysteine-rich domain-containing protein (Stac1) and similar proteins. Stac1, also called Src homology 3 and cysteine-rich domain-containing protein, promotes expression of the ion channel CACNA1H at the cell membrane, and thereby contributes to the regulation of channel activity. It plays a minor and redundant role in promoting the expression of calcium channel CACNA1S at the cell membrane, and thereby contributes to increased channel activity. It slows down the inactivation rate of the calcium channel CACNA1C. Stac1 contains a cysteine-rich C1 domain and two SH3 domains at the C-terminus. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 57 matched cddid_all.tbl CDD cd20881 cd20881 410431 C1_Stac2 protein kinase C conserved region 1 (C1 domain) found in SH3 and cysteine-rich domain-containing protein 2 (Stac2) and similar proteins. Stac2, also called 24b2/Stac2, or Src homology 3 and cysteine-rich domain-containing protein 2, plays a redundant role in promoting the expression of calcium channel CACNA1S at the cell membrane, and thereby contributes to increased channel activity. It slows down the inactivation rate of the calcium channel CACNA1C. Stac2 contains a cysteine-rich C1 domain and one SH3 domain at the C-terminus. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 59 matched cddid_all.tbl CDD cd20882 cd20882 410432 C1_Stac3 protein kinase C conserved region 1 (C1 domain) found in SH3 and cysteine-rich domain-containing protein 3 (Stac3) and similar proteins. Stac3 is an essential component of the skeletal muscle excitation-contraction coupling (ECC) machinery. It is required for normal excitation-contraction coupling in skeletal muscle and for normal muscle contraction in response to membrane depolarization. It plays an essential role for normal Ca2+ release from the sarcplasmic reticulum, which ultimately leads to muscle contraction. Stac3 contains a cysteine-rich C1 domain and two SH3 domains at the C-terminus. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 59 matched cddid_all.tbl CDD cd20883 cd20883 410433 C1_Myosin-IXa protein kinase C conserved region 1 (C1 domain) found in unconventional myosin-IXa and similar proteins. Myosin-IXa, also called unconventional myosin-9a (Myo9a), is a single-headed, actin-dependent motor protein of the unconventional myosin IX class. It is expressed in several tissues and is enriched in the brain and testes. Myosin-IXa contains a Ras-associating (RA) domain, a motor domain, a protein kinase C conserved region 1 (C1), and a Rho GTPase activating domain (RhoGAP). Myosin-IXa binds the alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor (AMPAR) GluA2 subunit, and plays a key role in controlling the molecular structure and function of hippocampal synapses. Moreover, Myosin-IXa functions in epithelial cell morphology and differentiation, such that its knockout mice develop hydrocephalus and kidney dysfunction. Myosin-IXa regulates collective epithelial cell migration by targeting RhoGAP activity to cell-cell junctions. Myosin-IXa negatively regulates Rho GTPase signaling, and functions as a regulator of kidney tubule function. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 58 matched cddid_all.tbl CDD cd20884 cd20884 410434 C1_Myosin-IXb protein kinase C conserved region 1 (C1 domain) found in unconventional myosin-IXb and similar proteins. Myosin-IXb, also called unconventional myosin-9b (Myo9b), is an actin-dependent motor protein of the unconventional myosin IX class. It is expressed abundantly in tissues of the immune system, like lymph nodes, thymus, and spleen, and in several immune cells including dendritic cells, macrophages and CD4+ T cells. Myosin-IXb contains a Ras-associating (RA) domain, a motor domain, a protein kinase C conserved region 1 (C1), and a Rho GTPase activating (RhoGAP) domain. Myosin-IXb acts as a motorized signaling molecule that links Rho signaling to the dynamic actin cytoskeleton. It regulates leukocyte migration by controlling RhoA signaling. Myosin-IXb is also involved in the development of autoimmune diseases, including rheumatoid arthritis, systemic lupus erythematosus, and type 1 diabetes. Moreover, Myosin-IXb is a ROBO-interacting protein that suppresses RhoA activity in lung cancer cells. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 58 matched cddid_all.tbl CDD cd20885 cd20885 410435 C1_RASSF1 protein kinase C conserved region 1 (C1 domain) found in Ras association domain-containing protein 1 (RASSF1) and similar proteins. RASSF1 is a member of a family of RAS effectors, of which there are currently 8 members (RASSF1-8), all containing a Ras-association (RA) domain of the Ral-GDS/AF6 type. RASSF1 has eight transcripts (A-H) arising from alternative splicing and differential promoter usage. RASSF1A and 1C are the most extensively studied RASSF1 with both localized to microtubules and involved in regulation of growth and migration. RASSF1 is a potential tumor suppressor that is required for death receptor-dependent apoptosis. It contains a C1 domain, which is descibed in this model. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 54 matched cddid_all.tbl CDD cd20886 cd20886 410436 C1_RASSF5 protein kinase C conserved region 1 (C1 domain) found in Ras association domain-containing protein 5 (RASSF5) and similar proteins. RASSF5, also called new ras effector 1 (NORE1), or regulator for cell adhesion and polarization enriched in lymphoid tissues (RAPL), is a member of a family of RAS effectors, of which there are currently 8 members (RASSF1-8), all containing a Ras-association (RA) domain of the Ral-GDS/AF6 type. It is expressed as three transcripts (A-C) via differential promoter usage and alternative splicing. RASSF5A is a pro-apoptotic Ras effector and functions as a Ras regulated tumor suppressor. RASSF5C is regulated by Ras related protein and modulates cellular adhesion. RASSF5 is a potential tumor suppressor that seems to be involved in lymphocyte adhesion by linking RAP1A activation upon T-cell receptor or chemokine stimulation to integrin activation. It contains a C1 domain, which is descibed in this model. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 50 matched cddid_all.tbl CDD cd20887 cd20887 410437 C1_TNS2 protein kinase C conserved region 1 (C1 domain) found in tensin-2 and similar proteins. Tensin-2 (TNS2), also called C1 domain-containing phosphatase and tensin (C1-TEN), or tensin-like C1 domain-containing phosphatase (TENC1), is an essential component for the maintenance of glomerular basement membrane (GBM) structures. It regulates cell motility and proliferation. It may have phosphatase activity. TNS2 reduces AKT1 phosphorylation, lowers AKT1 kinase activity, and interferes with AKT1 signaling. It contains an N-terminal region with a zinc finger (C1 domain), a protein tyrosine phosphatase (PTP)-like domain and a protein kinase 2 (C2) domain, and a C-terminal region with SH2 and pTyr binding (PTB) domains. This model corresponds to the C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 53 matched cddid_all.tbl CDD cd20888 cd20888 410438 C1_TNS1_v protein kinase C conserved region 1 (C1 domain) found in tensin-1 (TNS1) variant and similar proteins. Tensin-1 (TNS1) plays a role in fibrillar adhesion formation. It may be involved in cell migration, cartilage development and in linking signal transduction pathways to the cytoskeleton. This model corresponds to the C1 domain found in TNS1 variant. Typical TNS1 does not contain C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 57 matched cddid_all.tbl CDD cd20889 cd20889 410439 C1_TNS3_v protein kinase C conserved region 1 (C1 domain) found in tensin-3 (TNS3) variant and similar proteins. Tensin-3 (TNS3), also called tensin-like SH2 domain-containing protein 1 (TENS1), or tumor endothelial marker 6 (TEM6), may play a role in actin remodeling. It is involved in the dissociation of the integrin-tensin-actin complex. This model corresponds to the C1 domain found in TNS3 variant. Typical TNS3 does not contain C1 domain. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 56 matched cddid_all.tbl CDD cd20890 cd20890 410440 C1_DGKalpha_rpt2 second protein kinase C conserved region 1 (C1 domain) found in diacylglycerol kinase alpha (DAG kinase alpha) and similar proteins. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase alpha, also called 80 kDa diacylglycerol kinase, or diglyceride kinase alpha (DGK-alpha), converts the second messenger diacylglycerol into phosphatidate upon cell stimulation, initiating the resynthesis of phosphatidylinositols and attenuating protein kinase C activity. It is classified as a type I DAG kinase (DGK), containing EF-hand structures that bind Ca(2+) and a recoverin homology domain, in addition to C1 and catalytic domains that are present in all DGKs. As a type I DGK, it is regulated by calcium binding. DAG kinase alpha contains two copies of the C1 domain. This model corresponds to the second one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 62 matched cddid_all.tbl CDD cd20891 cd20891 410441 C1_DGKbeta_rpt2 second protein kinase C conserved region 1 (C1 domain) found in diacylglycerol kinase beta (DAG kinase beta) and similar proteins. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase beta, also called 90 kDa diacylglycerol kinase, or diglyceride kinase beta (DGK-beta), exhibits high phosphorylation activity for long-chain diacylglycerols. It is classified as a type I DAG kinase (DGK), containing EF-hand structures that bind Ca(2+) and a recoverin homology domain, in addition to C1 and catalytic domains that are present in all DGKs. As a type I DGK, it is regulated by calcium binding. DAG kinase beta contains two copies of the C1 domain. This model corresponds to the second one. DGK-beta contains typical C1 domains that bind DAG and phorbol esters. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 59 matched cddid_all.tbl CDD cd20892 cd20892 410442 C1_DGKgamma_rpt2 second protein kinase C conserved region 1 (C1 domain) found in diacylglycerol kinase gamma (DAG kinase gamma) and similar proteins. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase gamma, also called diglyceride kinase gamma (DGK-gamma), reverses the normal flow of glycerolipid biosynthesis by phosphorylating diacylglycerol back to phosphatidic acid. It is classified as a type I DAG kinase (DGK), containing EF-hand structures that bind Ca(2+) and a recoverin homology domain, in addition to C1 and catalytic domains that are present in all DGKs. As a type I DGK, it is regulated by calcium binding. DGK-gamma contains two copies of the C1 domain. This model corresponds to the second one. DGK-gamma contains typical C1 domains that bind DAG and phorbol esters. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 61 matched cddid_all.tbl CDD cd20893 cd20893 410443 C1_DGKdelta_rpt2 second protein kinase C conserved region 1 (C1 domain) found in diacylglycerol kinase delta (DAG kinase delta) and similar proteins. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase delta, also called 130 kDa diacylglycerol kinase, or diglyceride kinase delta (DGK-delta), is a residential lipid kinase in the endoplasmic reticulum. It promotes lipogenesis and is involved in triglyceride biosynthesis. It is classified as a type II DAG kinase (DGK), containing pleckstrin homology (PH) and sterile alpha motifs (SAM) domains, in addition to C1 and catalytic domains that are present in all DGKs. The SAM domain mediates oligomerization of type II DGKs. DAG kinase delta contains two copies of the C1 domain. This model corresponds to the second one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 61 matched cddid_all.tbl CDD cd20894 cd20894 410444 C1_DGKeta_rpt2 second protein kinase C conserved region 1 (C1 domain) found in diacylglycerol kinase eta (DAG kinase eta) and similar proteins. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase eta, also called diglyceride kinase eta (DGK-eta), plays a key role in promoting cell growth. It is classified as a type II DAG kinase (DGK), containing pleckstrin homology (PH) and sterile alpha motifs (SAM) domains, in addition to C1 and catalytic domains that are present in all DGKs. The SAM domain mediates oligomerization of type II DGKs. The diacylglycerol kinase eta gene, DGKH, is a replicated risk gene of bipolar disorder (BPD). DAG kinase eta contains two copies of the C1 domain. This model corresponds to the second one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 62 matched cddid_all.tbl CDD cd20895 cd20895 410445 C1_DGKzeta_rpt2 second protein kinase C conserved region 1 (C1 domain) found in diacylglycerol kinase zeta (DAG kinase zeta) and similar proteins. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase zeta, also called diglyceride kinase zeta (DGK-zeta), displays a strong preference for 1,2-diacylglycerols over 1,3-diacylglycerols, but lacks substrate specificity among molecular species of long chain diacylglycerols. It is classified as a type IV DAG kinase (DGK), containing myristoylated alanine-rich protein kinase C substrate (MARCKS), PDZ-binding, and ankyrin domains, in addition to C1 and catalytic domains that are present in all DGKs. The MARCKS domain regulates the nuclear localizations of type IV DGKs while the PDZ-binding and ankyrin domains regulate interactions with several proteins. DAG kinase zeta contains two copies of the C1 domain. This model corresponds to the second one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 75 matched cddid_all.tbl CDD cd20896 cd20896 410446 C1_DGKiota_rpt2 second protein kinase C conserved region 1 (C1 domain) found in diacylglycerol kinase iota (DAG kinase iota) and similar proteins. Diacylglycerol (DAG) kinase (EC 2.7.1.107) is a lipid kinase that phosphorylates diacylglycerol to form phosphatidic acid. DAG kinase iota, also called diglyceride kinase iota (DGK-iota), or DGKI, is a homolog of Drosophila DGK2, RdgA. It may have important cellular functions in the retina and brain. It is classified as a type IV DAG kinase (DGK), containing myristoylated alanine-rich protein kinase C substrate (MARCKS), PDZ-binding, and ankyrin domains, in addition to C1 and catalytic domains that are present in all DGKs. The MARCKS domain regulates the nuclear localizations of type IV DGKs while the PDZ-binding and ankyrin domains regulate interactions with several proteins. DAG kinase iota contains two copies of the C1 domain. This model corresponds to the second one. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 75 matched cddid_all.tbl CDD cd20897 cd20897 411014 Smlt3025-like S. maltophilia immunity protein with unknown function (Smlt3025) and similar proteins. This family includes Smlt3025, an immunity protein of the type IV secretion system (T4SS) found in the multi-drug-resistant opportunistic pathogen Stenotrophomonas maltophilia. Experiments show that Smlt3025 counteracts Smlt3024, an effector protein transferred by the T4SS into target cells. The crystal structure of Smlt3025 reveals a topology similar to the iron-regulated protein FrpD from Neisseria meningitidis which has been shown to interact with the RTX protein FrpC, while its counterpart Smlt3024 is homologous to the N-terminal domain of large Ca2+-binding RTX proteins. 234 matched cddid_all.tbl CDD cd20900 cd20900 412054 HopBF1 "type III secretion system (T3SS) effector HopBF1 from Ewingella americana, and similar proteins. This family includes HopBF1 family of bacterial type III secretion system (T3SS) effectors identified as eukaryotic-specific HSP90 protein kinases. HopBF1 adopts a minimal and atypical protein kinase fold such that it is recognized by HSP90 as a host client. Utilizing this ""betrayal-like"" mechanism to achieve specificity, HopF1 phosphorylates and inactivates eukaryotic HSP90 by inhibiting the chaperone's ATPase activity. This prevents activation of immune receptors that trigger hypersensitive response in plants, thereby inducing severe disease symptoms in plants infected by certain plant pathogens." 169 matched cddid_all.tbl CDD cd20901 cd20901 411015 CC_AF10 coiled coil domain of ALL1-Fused gene from chromosome 10 protein (AF10) and similar proteins. This family includes AF10 (ALL1-Fused gene from chromosome 10 protein) which is one of mixed-lineage leukemia 1 (MLL1)-fusion partners that function in acute myeloid leukemia (ALL). Aberration of the mixed-lineage leukemia (MLL) gene is implicated in acute leukemia; chromosomal translocations of MLL1 generate oncogenic chimeric proteins, containing the non-catalytic N-terminal portion of MLL1 fused with many partners such as AF10. The MLL-AF10 fusion oncoprotein recruits DOT1L (disruptor of telomeric-silencing 1-like) to the homeobox A. The aberrant recruitment of DOT1L, a histone methyltransferase that methylates H3 lysine residues (H3K79), by MLL fusions and the resulting H3K79 methylation are thought to affect gene expression by altering chromatin accessibility. AF10 and DOT1L interact through their coiled coil domains. 64 matched cddid_all.tbl CDD cd20902 cd20902 411016 CC_DOT1L coiled coil domain of disruptor of telomeric-silencing 1-like (DOT1L) and similar proteins. This family contains DOT1L (disruptor of telomeric-silencing 1-like), a non-SET domain histone lysine methyltransferase (HKMT) that catalyzes monomethylation, dimethylation, and trimethylation of nucleosomal H3K79. DOT1L is recruited to the homeobox A by AF10 (ALL1-Fused gene from chromosome 10 protein), one of the mixed-lineage leukemia 1 (MLL1)-fusion partners that function in acute myeloid leukemia (ALL). Aberration of the MLL gene is implicated in acute leukemia; chromosomal translocations of MLL1 generate oncogenic chimeric proteins, containing the non-catalytic N-terminal portion of MLL1 fused with many partners such as AF10. The aberrant recruitment of DOT1L by MLL fusions and the resulting H3K79 methylation are thought to affect gene expression by altering chromatin accessibility. AF10 and DOT1L interact through their coiled coil domains. 65 matched cddid_all.tbl CDD cd20903 cd20903 411017 HCV_p7 Hepatitis C virus p7 protein. Hepatitis C virus (HCV) p7 protein is a viroporin essential for virus production. The p7 monomer is comprised of 2 trans-membrane helices connected by a cytosolic loop, and oligomerizes to form cation-specific ion channels. These ion channels dissipate pH gradients in secretory vesicles potentially protecting acid-labile intracellular virions during egress (the rupturing of the infected cell and release of viral contents). p7 protein has at least two different functions in culture, one via the formation of these ion channels, the other through its specific interaction with the non-structural viral protein NS2. Several compounds targeting p7 have been investigated as anti-HCV drugs. 58 matched cddid_all.tbl CDD cd20905 cd20905 411018 EHMT_ZBD Zinc-binding domain of euchromatic histone lysine methyltransferases EHMT1 and EHTM2. EHMT1 (also known as GLP) and EHMT2 (also known as NG36 and G9a) are histone methyltransferases that methylate the K9 position of histone H3, marking genomic regions for transcriptional repression. They may play a role in the G0/G1 cell cycle transition and are associated with promoting various types of cancer. Mutations in EHMT1 are associated with the genetic disorder Kleefstra syndrome. A functional role for the zinc-binding domain has not been established. 133 matched cddid_all.tbl CDD cd20907 cd20907 411019 CBM86 carbohydrate binding module family 86. This family describes what is most likely a xylan-binding module such as found in the Xyn10A protein of Roseburia intestinalis L1-82, which is involved in the extracellular capture and breakdown of xylan. 127 matched cddid_all.tbl CDD cd20908 cd20908 411020 SUF4-like N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins. Oryza sativa SUPPRESSOR OF FRI 4 (OsSUF4) is a C2H2-type zinc finger transcription factor which interacts with the major H3K36 methyltransferase SDG725 to promote H3K36me3 (tri-methylation at H3K9) establishment. The transcription factor OsSUF4 recognizes a specific 7-bp DNA element (5'-CGGAAAT-3'), which is contained in the promoter regions of many genes throughout the rice genome. Through interaction with OsSUF4, SDG725 is recruited to the promoters of key florigen genes, RICE FLOWERING LOCUS T1 (RFT1) and Heading date 3a (Hd3a), for H3K36 deposition to promote gene activation and rice plant flowering. OsSUF4 target genes include a number of genes involved in many biological processes. Flowering plant Arabidopsis SUF4 binds to a 15bp DNA element (5'-CCAAATTTTAAGTTT-3') within the promoter of the floral repressor gene FLOWERING LOCUS C (FLC) and recruits the FRI-C transcription activator complex to the FLC promoter. Although the DNA-binding element and target genes of AtSUF4 are different from those of OsSUF4, AtSUF4 is known to interact with the Arabidopsis H3K36 methyltransferase SDG8 (also known as ASHH2/EFS/SET8), and the methylation deposition mechanism mediated by the SUF4 transcription factor and H3K36 methyltransferase may be conserved in Arabidopsis and rice. Proteins in this family have two conserved C2H2-type zinc finger motifs at the N-terminus (included in this model), and a large proline-rich domain at the C-terminus; for OsSUF4, it has been shown that the N-terminal zinc-finger domain is responsible for DNA binding, and that the C-terminal domain interacts with SDG725. 82 matched cddid_all.tbl CDD cd20910 cd20910 411021 NCBD_CREBBP-p300_like Nuclear Coactivator Binding Domain (NCBD) of CREB (cyclic AMP response element binding protein) binding protein (CREBBP, also known as CBP) and its paralog p300. CREBBP (also called CBP) and its paralog p300, generally referred to as CREBBP/p300, are universal transcriptional coactivators that interact with many important transcription factors and comodulators to activate transcription. The NCBD domain [nuclear coactivator binding domain, also known as IRF-3 binding domain (IBiD) or SRC1 interaction domain (SID)] of CREBBP/p300 behaves as an intrinsically disordered domain in isolation, but folds into helical structures with different topologies upon binding to different ligands such as nuclear receptor coactivator p160, CREBBP interaction domain (CID) from nuclear receptor coactivator 1 (NCOA1 or Src1), NCOA2 (Tif2), and NCOA3 (ACTR), or interferon regulatory factor 3 (IRF-3). In Drosophila, there is only one CREB-binding protein ortholog and it is called nejire, dCBP, CBP/p300, or CBP. 43 matched cddid_all.tbl CDD cd20912 cd20912 411022 AIR_RAP80-like ABRAXAS Interacting Region (AIR) of Receptor-Associated Protein 80 (RAP80), and related domains. RAP80 and ABRAXAS are integral subunits of the BRCA1-A complex which also contains MERIT40 (Mediator of Rap80 Interactions and Targeting 40 kD, also known as BABAM1), BRE (also known as BABAM2, BRCC45 and BRCC4), and BRCC36 (also known as BRCC3). BRCA1-A functions in DNA double-strand break (DSB) repair. RAP80 interacts with the ABRAXAS, MERIT40, and BRE subunits. It is the interaction with ABRAXAS that drives specific incorporation of RAP80 into BRCA1-A. RAP80 contains one SUMO-interacting motif (SIM), two ubiquitin-interacting motifs (UIMs), this AIR, and two zinc finger motifs (ZnF). The SIM and UIM domains recruit BRCA1-A to sites of DNA damage. The AIR is integral in the interaction of RAP80 with the ABRAXAS, MERIT40, and BRE subunits. 59 matched cddid_all.tbl CDD cd20913 cd20913 411023 DCAF15-CTD C-terminal domain of DDB1- and CUL4-associated factor 15. This model represents the C-terminal domain of DCAF15 (DDB1- and CUL4-associated factor 15), the cullin RING ligase substrate receptor/adaptor that forms a complex with CUL4A or CUL4B, as part of the Rbx-Cul4-DDA1-DDB1-DCAF15 E3 ubiquitin ligase that is responsible for the proteasome degradation of certain proteins. Aryl sulfonamide anticancer agents such as indisulam, tasisulam, E7820, and chloroquinoxaline have been shown to recruit the essential mRNA-splicing factor RBM39 to DCAF15. These agents appear to promote binding of DCAF15 to the RNA-recognition motif (RRM) of RBM39, which suggests that derivatives of the aryl-sulfonamides may be used to target other RRM-containing proteins. Cell proliferation is inhibited by these aryl sulfonamides by causing degradation of RBM39, which leads to aberrant processing of pre-mRNA in hundreds of genes, primarily reflected by intron retention and exon skipping, thus collectively referred to as splicing inhibitor sulfonamides, or SPLAMs. 224 matched cddid_all.tbl CDD cd20917 cd20917 411024 DCAF15-NTD N-terminal domain of DDB1- and CUL4-associated factor 15. This model represents the N-terminal domain of DCAF15 (DDB1- and CUL4-associated factor 15), the cullin RING ligase substrate receptor/adaptor that forms a complex with CUL4A or CUL4B, as part of the Rbx-Cul4-DDA1-DDB1-DCAF15 E3 ubiquitin ligase that is responsible for the proteasome degradation of certain proteins. Aryl sulfonamide anticancer agents such as indisulam, tasisulam, E7820, and chloroquinoxaline have been shown to recruit the essential mRNA-splicing factor RBM39 to DCAF15. These agents appear to promote binding of DCAF15 to the RNA-recognition motif (RRM) of RBM39, which suggests that derivatives of the aryl-sulfonamides may be used to target other RRM-containing proteins. Cell proliferation is inhibited by these aryl sulfonamides by causing degradation of RBM39, which leads to aberrant processing of pre-mRNA in hundreds of genes, primarily reflected by intron retention and exon skipping, thus collectively referred to as splicing inhibitor sulfonamides, or SPLAMs. 225 matched cddid_all.tbl CDD cd20918 cd20918 410842 polyA_pol_NCLDV RNA polyadenylate polymerase of nucleocytoplasmic large DNA viruses. This model represents the poly(A) polymerases (PAPs) from nucleocytoplasmic large DNA viruses (NCLDV), a group of giant eukaryotic double-stranded DNA viruses that make up the phylum Nucleocytoviricota. They are referred to as nucleocytoplasmic because they are often able to replicate in both the host's cell nucleus and cytoplasm. PAPs catalyze the attachment of adenylates to the 3' ends of messenger RNA and other RNAs, forming poly(A) tails. PAP acts as a nucleic acid template-independent NMP-transferase, preferentially utilizing a single species of NTP, namely ATP. The polyadenylation state of an mRNA may correlate with the efficiency of its translation. This group includes PAPs from the Poxviridae and Mimiviridae family of viruses. In Vaccinia virus, from the Poxviridae family, polyadenylation is crucial for virion maturation and is carried out by a heterodimer, formed by the catalytic subunit VP55 and the processivity factor (VP39), which is required for the formation of long poly(A) tails. PAPs from Acanthamoeba polyphaga mimivirus and Megavirus chiliensis, which belong to the Mimiviridae family, are homodimeric and intrinsically self-processive, generating >700 nucleotides long poly(A) tails. Homodimerization is required for PAP activity; monomers are able to bind RNA but are enzymatically inactive. Thus, while other PAPs form heterodimers with processivity factors, the Mimiviridae PAPs become processive upon homodimerization. The catalytic subunit of NCLDV PAPs contains two topologically identical subdomains with a nucleotidyltransferase fold, suggesting that an ancestral duplication was at the origin of these viral PAPs. 335 matched cddid_all.tbl CDD cd20919 cd20919 410843 polyA_pol_Pox RNA polyadenylate polymerase catalytic subunit from the Poxviridae family of viruses. Poly(A) polymerases (PAPs) catalyze the attachment of adenylates to the 3' ends of messenger RNA and other RNAs, forming poly(A) tails. PAP acts as a nucleic acid template-independent NMP-transferase, preferentially utilizing a single species of NTP, namely ATP. The polyadenylation state of an mRNA may correlate with the efficiency of its translation. In Vaccinia virus, from the Poxviridae family of viruses, polyadenylation is crucial for virion maturation and is carried out by a heterodimer, formed by the catalytic subunit VP55 and the processivity factor (VP39). In the absence of VP39, oligo(A) tails are added to permissive primers by VP55 in a rapid processive burst, which ceases abruptly after tails have reached 30-35 nucleotides in length. With VP39, tails with lengths in the hundreds of nucleotides are processively synthesized with no abrupt termination of elongation. In contrast to mammalian cells, polyadenylation is not dependent on a multiprotein mRNA 3' end processing complex. VP55 translocates with respect to its single-stranded nucleic acid substrate during poly(A) tail addition. The catalytic subunit of Poxviridae PAPs contains two topologically identical subdomains with a nucleotidyltransferase fold, suggesting that an ancestral duplication was at the origin of these viral PAPs. 461 matched cddid_all.tbl CDD cd20920 cd20920 410844 polyA_pol_Mimi RNA polyadenylate polymerase from the Mimiviridae family of viruses. Poly(A) polymerases (PAPs) catalyze the attachment of adenylates to the 3' ends of messenger RNA and other RNAs, forming poly(A) tails. PAP acts as a nucleic acid template-independent NMP-transferase, preferentially utilizing a single species of NTP, namely ATP. The polyadenylation state of an mRNA may correlate with the efficiency of its translation. PAPs from Acanthamoeba polyphaga mimivirus and Megavirus chiliensis, which belong to the Mimiviridae family, are homodimeric and intrinsically self-processive, generating >700 nucleotides long poly(A) tails. Homodimerization is required for PAP activity; monomers are able to bind RNA but are enzymatically inactive. Thus, while other PAPs form heterodimers with processivity factors, the Mimiviridae PAPs become processive upon homodimerization. mRNA polyadenylation in Mimiviridae occurs at hairpin-forming palindromic sequences terminating viral transcripts. The catalytic subunit of Mimiviridae PAPs contains two topologically identical subdomains with a nucleotidyltransferase fold, suggesting that an ancestral duplication was at the origin of these viral PAPs. 449 matched cddid_all.tbl CDD cd20921 cd20921 410845 polyA_pol_Pycodna RNA polyadenylate polymerase from the Phycodnaviridae family of viruses. Poly(A) polymerases (PAPs) catalyze the attachment of adenylates to the 3' ends of messenger RNA and other RNAs, forming poly(A) tails. PAP acts as a nucleic acid template-independent NMP-transferase, preferentially utilizing a single species of NTP, namely ATP. The polyadenylation state of an mRNA may correlate with the efficiency of its translation. The catalytic subunit of NCLDV PAPs contains two topologically identical subdomains with a nucleotidyltransferase fold, suggesting that an ancestral duplication was at the origin of these viral PAPs. 357 matched cddid_all.tbl CDD cd20922 cd20922 410846 polyA_pol_Marseille RNA polyadenylate polymerase from the Marseilleviridae family of viruses. Poly(A) polymerases (PAPs) catalyze the attachment of adenylates to the 3' ends of messenger RNA and other RNAs, forming poly(A) tails. PAP acts as a nucleic acid template-independent NMP-transferase, preferentially utilizing a single species of NTP, namely ATP. The polyadenylation state of an mRNA may correlate with the efficiency of its translation. The catalytic subunit of NCLDV PAPs contains two topologically identical subdomains with a nucleotidyltransferase fold, suggesting that an ancestral duplication was at the origin of these viral PAPs. 316 matched cddid_all.tbl CDD cd20923 cd20923 410847 polyA_pol_Fausto RNA polyadenylate polymerase from Faustovirus. Poly(A) polymerases (PAPs) catalyze the attachment of adenylates to the 3' ends of messenger RNA and other RNAs, forming poly(A) tails. PAP acts as a nucleic acid template-independent NMP-transferase, preferentially utilizing a single species of NTP, namely ATP. The polyadenylation state of an mRNA may correlate with the efficiency of its translation. The catalytic subunit of NCLDV PAPs contains two topologically identical subdomains with a nucleotidyltransferase fold, suggesting that an ancestral duplication was at the origin of these viral PAPs. 351 matched cddid_all.tbl CDD cd20924 cd20924 410848 polyA_pol_Asfar RNA polyadenylate polymerase from the Asfarviridae family of viruses. Poly(A) polymerases (PAPs) catalyze the attachment of adenylates to the 3' ends of messenger RNA and other RNAs, forming poly(A) tails. PAP acts as a nucleic acid template-independent NMP-transferase, preferentially utilizing a single species of NTP, namely ATP. The polyadenylation state of an mRNA may correlate with the efficiency of its translation. The catalytic subunit of NCLDV PAPs contains two topologically identical subdomains with a nucleotidyltransferase fold, suggesting that an ancestral duplication was at the origin of these viral PAPs. 336 matched cddid_all.tbl CDD cd20925 cd20925 409519 IgV_CD28 "Immunoglobulin Variable (IgV) domain Cluster of Differentiation (CD) 28. The members here are composed of the immunoglobulin variable region (IgV) of Cluster of Differentiation (CD) 28). CD28 is one of the proteins expressed on T cells that provide co-stimulatory signals required for T cell activation and survival. CD28 is the receptor for CD80 (B7.1) and CD86 (B7.2) proteins. CD28 consists of a paired V-set of immunoglobulin (Ig) superfamily domains attached to single-transmembrane domains and cytoplasmic domains that contain the MYPPY motif, which is involved in binding B7.1 or B7.2. CD28 is very similar to CTLA-4 (cytotoxic T-lymphocyte-associated protein 4, also known as CD152 (cluster of differentiation 152)), which is involved in the regulation of T cell response, acting as an inhibitor of intracellular signaling. CTLA-4 also binds the B7 molecules (B7.1 and B7.2) with a higher affinity than does CD28. The B7/CTLA-4 interaction generates inhibitory signals down-regulating the response, and may prevent T cell activation by weak TCR signals. CD28 and CTLA-4 then elicit opposing signals in the regulation of T cell responsiveness and homeostasis. The IgSF is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. The two sheets are linked together by a conserved disulfide bond between B strand and F strand. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The N-terminal Ig-like domain of CD28 is a member of the V-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C'-C"" in the other. However, each CD28-B7 family member is slightly different, some have an IgV domain which lacks an A' or C"" strand." 117 matched cddid_all.tbl CDD cd20926 cd20926 409520 IgV_NKp30 Immunoglobulin variable (IgV) domain of Natural Killer cell activating receptor NKp30 and similar domains. The members here are composed of the immunoglobulin variable region (IgV) of Natural Killer cell activating receptor NKp30 (also known as Natural Cytotoxicity triggering Receptor 3 (NCR3)) and similar domains. NKp30 Recognizes the N-Terminal IgV Domain of B7-H6. In humans, the activating natural cytotoxicity receptor NKp30 plays a major role in NK cell-mediated tumor cell lysis. NKp30 recognizes the cell-surface protein B7-H6, which is expressed on tumor, but not healthy, cells. 112 matched cddid_all.tbl CDD cd20927 cd20927 409521 IgI_Titin_M1-like "Immunoglobulin-like M1 domain from Titin; a member of the I-set of IgSF domains. The members here are composed of the Immunoglobulin-like M1 I-set domain from Titin and similar proteins. Titin is a key component in the assembly and functioning of vertebrate striated muscles. By providing connections at the level of individual microfilaments, it contributes to the fine balance of forces between the two halves of the sarcomere. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C"" strand. The structure of the titin-M1 domain lacks this strand and thus it belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis." 90 matched cddid_all.tbl CDD cd20928 cd20928 409522 IgI_BTLA "Extracellular Immunoglobulin (Ig) domain of the B and T lymphocyte attenuator (BTLA); member of the I-set Ig superfamily domains. The members here are composed of the extracellular immunoglobulin (Ig) domain of the B and T lymphocyte attenuator (BTLA; also known as CD270). BTLA is a type I transmembrane glycoprotein that is structurally similar to the CD28 family of T cell co-stimulatory or coinhibitory molecules. BTLA is a coinhibitory molecule expressed on T cells, B cells, macrophages, dendritic and natural killer (NK) cells. Unlike CD28 family members, BTLA interacts with the tumor necrosis factor receptor superfamily member HVEM (herpes virus entry mediator) rather than with B7 family ligands. In addition, BTLA does not form a homodimer. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. In contrast to CD28 family members, the structure of the BTLA extracellular Ig domain lacks a C"" strand and thus is better described as a member of the I-set of Ig domains. I-set domains are found in several cell adhesion molecules, including vascular (VCAM), intercellular (ICAM), neural (NCAM) and mucosal addressin (MADCAM) cell adhesion molecules, as well as junction adhesion molecules (JAM)." 101 matched cddid_all.tbl CDD cd20929 cd20929 409523 IgV_CD22_d1 First immunoglobulin domain of Cluster of Differentiation (CD) 22; member of the V-set of IgSF domains. The members here are composed of the first immunoglobulin domain in Cluster of Differentiation (CD) 22 (also known as Siglec-2). CD22, a sialic-acid binding immunoglobulin type-lectin (Siglec) family member, is an inhibitory co-receptor of the B-cell receptor (BCR). The inhibitory function of CD22 and its restricted expression on B cells makes CD22 an attractive target against dysregulated B cells that cause autoimmune diseases and B-cell-derived cancers. CD22 plays a vital role in establishing a baseline level of B-cell inhibition, and thus is an important determinant of homeostasis in humoral immunity. Siglecs are primarily expressed on immune cells and recognize sialic acid-containing glycan ligands. Siglecs are organized as an extracellular module composed of Ig-like domains (an N-terminal variable set of Ig-like carbohydrate recognition domains, and 1 to 16 constant Ig-like domains), followed by transmembrane and short cytoplasmic domains. Human Siglecs are classified into two subgroups, one subgroup is comprised of sialoadhesin (Siglec-1), CD22 (Siglec-2), and MAG (Siglec-4, myelin-associated glycoprotein), the other subgroup is comprised of CD33-related Siglecs which include CD33 (Siglec-3) and human Siglecs 5-11. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. This group belongs to the V-set of IgSF domains. 114 matched cddid_all.tbl CDD cd20930 cd20930 409524 Ig3_Nectin-5_like Third immunoglobulin domain of Nectin-like Protein-5, and similar domains. The members here are composed of the third immunoglobulin domain of Nectin-like Protein-5 (also known as Cluster of Differentiation 155 (CD155)). Nectin-like Protein-5 mediates NK (Natural Killer) cell adhesion and triggers NK cell effector functions. CD155 binds two different NK cell receptors: CD96 and CD226. These interactions accumulate at the cell-cell contact site, leading to the formation of a mature immunological synapse between NK cell and target cell. This may trigger adhesion and secretion of lytic granules and IFN-gamma and activate cytotoxicity of activated NK cells. CD155 may also promote NK cell-target cell modular exchange, and PVR transfer to the NK cell. This transfer is more important in some tumor cells expressing a lot of PVR, and may trigger fratricide NK cell activation, providing tumors with a mechanism of immunoevasion. Moreover, CD155 plays a role in mediating tumor cell invasion and migration. 86 matched cddid_all.tbl CDD cd20931 cd20931 409525 Ig3_IL1RAP Third immunoglobulin domain of interleukin-1 receptor accessory protein (IL1RAP). The members here are composed of the third immunoglobulin Ig interleukin-1 receptor accessory protein (IL1RAP). The interleukin 1 receptor accessory protein (IL-1RAP), also known as IL-1R3, is a coreceptor of type 1 interleukin 1 receptor (IL-1R1) and is required for transmission of IL-1 signaling. The activated IL-1 receptor complex, which consists of IL-1R1 and IL-1RAP, induces multiple cellular responses including NF-kappa-B activation, IL-2 secretion, and IL-2 promoter activation. Signaling involves the recruitment of adapter molecules such as TOLLIP, MYD88, and IRAK1 or IRAK2 via the respective Toll/IL-1 receptor (TIR) domains of the receptor/coreceptor subunits. Moreover, IL1RAP is known to be the accessory co-receptor that activates signal transduction upon IL-36 binding to IL-36R. IL-36 cytokines, which are a subfamily of the IL-1 superfamily, bind to the IL-36 receptor (IL-36R) and use IL1RAP as a co-receptor. 107 matched cddid_all.tbl CDD cd20932 cd20932 409526 Ig3_IL1R_like Third immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R), and similar domains. The members here are composed of the third immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R) and similar proteins. Members of this family are characterized by extracellular immunoglobulin-like domains and intracellular Toll/Interleukin-1R (TIR) domain. Three naturally occurring ligands for the IL-1 receptor (IL1R) are known: the agonists IL-1alpha and IL-1beta and the IL-1-receptor antagonist IL1RA. IL-1Rs are involved in immune host defense and hematopoiesis. After binding to interleukin-1, IL1R associates with the coreceptor IL1RAP (interleukin 1 receptor accessory protein, also known as IL-1R3) to form the high affinity interleukin-1 receptor complex, which induces multiple cellular responses including NF-kappa-B activation, IL-2 secretion, and IL-2 promoter activation. Signaling involves the recruitment of adapter molecules such as TOLLIP, MYD88, and IRAK1 or IRAK2 via the respective TIR domains of the receptor/coreceptor subunits. IL1R binds ligands with comparable affinity to its antagonist IL1RA, and binding of IL1RA to IL1R, prevents association of the latter with IL1RAP to form a signaling complex. 104 matched cddid_all.tbl CDD cd20933 cd20933 409527 Ig_ch-CD3_epsilon_like Immunoglobulin (Ig)-like domain of chicken Cluster of Differentiation (CD) 3 epsilon chain and similar proteins. The members here are composed of the immunoglobulin (Ig)-like domain of chicken Cluster of Differentiation (CD) 3 epsilon chain and similar proteins. CD3 is a T cell surface receptor that is associated with alpha/beta T cell receptors (TCRs). The CD3 complex consists of one gamma, one delta, two epsilon, and two zeta chains. The CD3 subunits form heterodimers as gamma/epsilon, delta/epsilon, and zeta/zeta. The gamma, delta, and epsilon chains each contain an extracellular Ig domain, whereas the extracellular domains of the zeta chains are very small and have unknown structure. The CD3 domain participates in intracellular signaling once the TCR has bound an MHC/antigen complex. The chicken CD3epsilon Ig domain has low sequence identity with human (22%) and mouse (24%) CD3epsilon, but overall is structurally very similar over the entire domain. 63 matched cddid_all.tbl CDD cd20934 cd20934 409528 IgV_B7-H3 Immunoglobulin Variable (IgV) domain of B7-H3, a member of the B7 family of immune checkpoint molecules. The members here are composed of the immunoglobulin variable (IgV) domain of B7-H3 also known as CD276), a member of the B7 family of immune checkpoint molecules. B7-H3 is an important immune checkpoint member of the B7 family and shares homology with other B7 ligands such as programmed death ligand 1 (PD-L1). The B7 family molecules interact with CD28 on T-cells to provide co-stimulatory signals that regulate T-cell activation and T-helper cell differentiation. Although B7-H3 has been shown to have both co-stimulatory and co-inhibitory effects on T-cell responses, the most current studies describe B7-H3 as a T cell inhibitor that promotes tumor aggressiveness and proliferation. Moreover, B7-H3 is highly overexpressed on a wide range of human solid cancers and promotes tumor growth, metastasis, and drug resistance. Thus, B7-H3 expression in tumors often correlates with both negative prognosis and poor clinical outcome in cancer patients. B7-H3 protein contains a predicted signal peptide, V- and C-like Ig domains (IgV and IgC), a transmembrane region, and an intracellular tail. 115 matched cddid_all.tbl CDD cd20935 cd20935 409529 IgV_B7-H2 Immunoglobulin Variable (IgV) domain of B7-H2 (B7 homolog 2). The members here are composed of the immunoglobulin variable (IgV) domain of B7-H2 (B7 homolog 2 also known as ICOSL (inducible T cell costimulator ligand) or CD275). B7-H2 is a ligand for the T-cell-specific cell surface receptor ICOS and acts as a costimulatory signal for T-cell proliferation and cytokine secretion. The interaction of ICOS with ICOSL (B7-H2) regulates T cell activation and expansion, is involved in T cell dependent B cell activation, and T-helper cell differentiation. It is a member of the B7 family of immune regulatory proteins and shares homology with other B7 ligands, such as B7-1, B7-2, B7-H1 (PD-L1), PD-L2, and B7-H3. The extracellular domains of B7 proteins contain two Ig-like domains and all members have short cytoplasmic domains. These ligands are typically expressed on antigen presenting cells (such as macrophages, B cells and dendritic cells) and have the ability to regulate T-cell proliferation and function. Tumor cells are also capable of expressing the B7 family members in order to evade immune surveillance. 113 matched cddid_all.tbl CDD cd20936 cd20936 409530 IgI_3_CSF-1R Third immunoglobulin domain of the hematopoietic colony-stimulating factor 1 receptor (CSF-1R), and similar domains; member of the I-set of IgSF domains. The members here are composed of the third immunoglobulin domain of the hematopoietic colony-stimulating factor 1 receptor (CSF-1R) and similar proteins. CSF-1R, a class III receptor tyrosine kinase (RTKIII), is critical to the survival, proliferation, and differentiation of mononuclear phagocytic cells such as monocytes, tissue macrophages, muscularis macrophages, microglia, osteoclasts, Paneth cells, and myeloid dendritic cells. Human colony-stimulating factor 1 receptor (hCSF-1R) is unique among the hematopoietic receptors because it is activated by two distinct cytokines, CSF-1 and interleukin-34 (IL-34). The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. This group belongs to the I-set of IgSF domains. 93 matched cddid_all.tbl CDD cd20937 cd20937 409531 IgC2_CD22_d3 Third immunoglobulin domain in Cluster of Differentiation (CD) 22; member of the Constant 2 (C2)-set of IgSF domains. The members here are composed of the third immunoglobulin domain in Cluster of Differentiation (CD) 22 (also known as Siglec-2). CD22, a sialic-acid binding immunoglobulin type-lectin (Siglec) family member, is an inhibitory co-receptor of the B-cell receptor (BCR). The inhibitory function of CD22 and its restricted expression on B cells makes CD22 an attractive target against dysregulated B cells that cause autoimmune diseases and B-cell-derived cancers. CD22 plays a vital role in establishing a baseline level of B-cell inhibition, and thus is an important determinant of homeostasis in humoral immunity. Siglecs are primarily expressed on immune cells and recognize sialic acid-containing glycan ligands. Siglecs are organized as an extracellular module composed of Ig-like domains (an N-terminal variable set of Ig-like carbohydrate recognition domains, and 1 to 16 constant Ig-like domains), followed by transmembrane and short cytoplasmic domains. Human Siglecs are classified into two subgroups, one subgroup is comprised of sialoadhesin (Siglec-1), CD22 (Siglec-2), and MAG (Siglec-4, myelin-associated glycoprotein), the other subgroup is comprised of CD33-related Siglecs which include CD33 (Siglec-3) and human Siglecs 5-11. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. This group belongs to the C2-set of IgSF domains, having A, B, and E strands in one beta-sheet and A', G, F, C' in the other. Unlike other Ig domain sets, the C2-set lacks the D strand. 88 matched cddid_all.tbl CDD cd20938 cd20938 409532 IgC1_CD22_d2 Second immunoglobulin domain of Cluster of Differentiation (CD) 22; member of the Constant 1 (C1)-set of IgSF domains. The members here are composed of the second immunoglobulin domain of clusters of differentiation (CD) 22 (also known as Siglec-2). CD22, a sialic-acid binding immunoglobulin type-lectin (Siglec) family member, is an inhibitory co-receptor of the B-cell receptor (BCR). The inhibitory function of CD22 and its restricted expression on B cells makes CD22 an attractive target against dysregulated B cells that cause autoimmune diseases and B-cell-derived cancers. CD22 plays a vital role in establishing a baseline level of B-cell inhibition, and thus is an important determinant of homeostasis in humoral immunity. Siglecs are primarily expressed on immune cells and recognize sialic acid-containing glycan ligands. Siglecs are organized as an extracellular module composed of Ig-like domains (an N-terminal variable set of Ig-like carbohydrate recognition domains, and 1 to 16 constant Ig-like domains), followed by transmembrane and short cytoplasmic domains. Human Siglecs are classified into two subgroups, one subgroup is comprised of sialoadhesin (Siglec-1), CD22 (Siglec-2), and MAG (Siglec-4, myelin-associated glycoprotein), the other subgroup is comprised of CD33-related Siglecs which include CD33 (Siglec-3) and human Siglecs 5-11. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. This group belongs to the C1-set of IgSF domains. 98 matched cddid_all.tbl CDD cd20939 cd20939 409533 IgC2_D1_IL-6RA Immunoglobulin-like domain D1 of interleukin-6 receptor alpha-chain (IL-6RA, also known as CD126); member of the C2-set of IgSF domains. The members here are composed of the immunoglobulin-like domain D1 of interleukin-6 receptor alpha-chain (IL-6RA, also known as CD126). The IL-6RA ectodomain, which is highly modular, consisting of three domains (D1, D2, and D3). Interleukin-6 (IL-6) is a multifunctional cytokine that regulates the immune response, hemopoiesis, the acute phase response and inflammation. It is generated in an infectious lesion and sends out a warning signal to the entire body. IL-6 binds first to its cognate alpha-chain receptor (IL-6R), and then the IL-6/IL-6R complex which in turn induces homodimerization of gp130. As a result, a high-affinity functional receptor complex of IL-6, IL-6R and gp130 is formed, and subsequently the complex triggers a downstream signal cascade. Aberrant production of IL-6 and its receptor (IL-6R) are implicated in the pathogenesis of multiple myeloma, autoimmune diseases and prostate cancer. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. This group belongs to the C2-set of IgSF domains. Unlike other Ig domain sets, the C2-set lacks the D strand. 77 matched cddid_all.tbl CDD cd20940 cd20940 409534 Ig0_BSG1 Immunoglobulin-like Ig0 domain of basigin-1 (BSG1) and similar proteins. The members here are composed of the immunoglobulin (Ig) domain of the collagenase stimulatory factor, basigin-1 (BSG1; also known as Cluster of Differentiation 147 (CD147) and Extracellular Matrix Metalloproteinase Inducer (EMMPRIN)) and similar proteins. CD147 is a transmembrane glycoprotein that belongs to the immunoglobulin superfamily. It is expressed in nearly all cells including platelets and fibroblasts and is involved in inflammatory diseases, and cancer progression. CD147 is highly expressed in several cancers and used as a prognostic marker. The two primary isoforms of CD147 that are related to cancer progression have been identified: CD147 Ig1-Ig2 (also called Basigin-2) that is ubiquitously expressed in most tissues and CD147 Ig0-Ig1-Ig2 (also called Basigin-1) that is retinal specific and implicated in retinoblastoma. Studies showed that CD147 Ig0 domain is a potent stimulator of interleukin-6 and suggest that the CD147 Ig0 dimer is the functional unit required for activity. 116 matched cddid_all.tbl CDD cd20942 cd20942 409535 IgI_MAdCAM-1 "Immunoglobulin-like domain of Mucosal addressin cell-adhesion molecule (MAdCAM-1); member of the I-set of IgSF domains. The members here include the immunoglobulin-like domain of Mucosal addressin cell-adhesion molecule (MAdCAM-1). MadCAM-1 is an endothelial cell adhesion molecule that interacts preferentially with the leukocyte beta7 integrin LPAM-1 (alpha4beta7), L-selectin, and VLA-4 (alpha4beta1) on myeloid cells to direct leukocytes into mucosal and inflamed tissues. MadCAM-1 is expressed primarily on HEV of Peyer's patches and on venules in small intestinal lamina propria, on the marginal sinus of the spleen, and on HEV of embryonic lymph nodes. It is a member of the immunoglobulin superfamily (IgSF), which is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. The two sheets are linked together by a conserved disulfide bond between B strand and F strand. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The first Ig-like domain of MAdCAM-1 is a member of the I-set IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, the A strand of the I-set is discontinuous, but lacks a C"" strand." 88 matched cddid_all.tbl CDD cd20943 cd20943 409536 IgI_VCAM-1 "First immunoglobulin-like domain of vascular endothelial cell adhesion molecule-1 (VCAM-1), and similar domains; member of the I-set of IgSF domains. The members here include the first immunoglobulin-like domain of vascular endothelial cell adhesion molecule-1 (VCAM-1; also known as Cluster of Differentiation 106 (CD106)) and similar proteins. During the inflammation process, these molecules recruit leukocytes onto the vascular endothelium before extravasation to the injured tissues. The interaction of VCAM-1 binding to the beta1 integrin very late antigen (VLA-4) expressed by lymphocytes and monocytes mediates the adhesion of leucocytes to blood vessel walls, and regulates migration across the endothelium. During metastasis, some circulating cancer cells extravasate to a secondary site by a similar process. VCAM-1 may be involved in organ targeted tumor metastasis and may also act as host receptors for viruses and parasites. VCAM-1 contains seven Ig domains. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. The two sheets are linked together by a conserved disulfide bond between B strand and F strand. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The first Ig-like domain of VCAM-1 is a member of the I-set IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, the A strand of the I-set is discontinuous, but lacks a C"" strand." 89 matched cddid_all.tbl CDD cd20944 cd20944 409537 IgI_N_ICAM1-2-3 N-terminal immunoglobulin domain of the intercellular adhesion molecules ICAM-1 (Cluster of Differentiation 54 or CD54), ICAM-2 (CD102) and ICAM-3 (CD50); members of the I-set of IgSF domains. The members here are composed of the immunoglobulin (Ig) domain found in the N-terminus of the intercellular adhesion molecules ICAM-1 (Cluster of Differentiation 54 or CD54), ICAM-2 (CD102), and ICAM-3 (CD50). ICAM-1, ICAM-2, and ICAM-3 mediate a variety of critical intercellular adhesion events in the immune system through interactions with their counter-receptors, the beta2-integrins LFA-1 (CD11a/CD18), Mac-1 (CD11b/CD18), p150,95 (CD11c/CD18), and CD11d/CD18. The ICAMs are type I transmembrane glycoproteins belonging to the immunoglobulin superfamily (IgSF). The binding of the ICAM family members with the beta2-integrins physically stabilizes interactions between pairs of T and B cells, T cells and antigen-presenting cells (APCs), and brings effector cells such as cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells into close proximity to their target cells. All three ICAMs share a common polypeptide homology and structural motif, and the ability to bind LFA-1. The distinct functional role of each ICAM is affected by their relative affinities for LFA-1 (ICAM-1 > ICAM-2 > ICAM-3). ICAM-1 is expressed in most tissues at low levels, and expression is increased by inflammatory cytokines. In contrast, ICAM-2 is expressed predominantly on endothelium and leukocytes (except neutrophils), and its expression generally is not responsive to cytokines. ICAM-3 is expressed on leukocytes and Langerhans cells, but not on resting, cytokine-induced endothelium, or nonhematopoietic tissues. 81 matched cddid_all.tbl CDD cd20946 cd20946 409538 IgV_1_JAM1-like "First Ig-like domain of Junctional adhesion molecule-1 (JAM1)and similar domains; a member of the V-set of IgSF domains. The members here are composed of the first Ig-like domain of Junctional Adhesion Molecule-1 (JAM1)and similar domains. JAM1 is an immunoglobulin superfamily (IgSF) protein with two Ig-like domains in its extracellular region; it plays a role in the formation of endothelial and epithelial tight junction and acts as a receptor for mammalian reovirus sigma-1. The IgSF is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. The two sheets are linked together by a conserved disulfide bond between B strand and F strand. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The first Ig-like domain of JAM1 is a member of the V-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C'-C"" in the other." 102 matched cddid_all.tbl CDD cd20947 cd20947 409539 IgV_PDl1 Immunoglobulin Variable (IgV) domain of Programmed death ligand 1 (PD-L1). The members here are composed of the immunoglobulin variable (IgV) domain of Programmed death ligand 1 (PD-L1; also known as Cluster of Differentiation 274 (CD274)). PD-L1 is a cell-surface ligand that competes with PD-L2 for binding to the immunosuppressive receptor programmed death-1 (PD-1). PD-1 is a member of the B7 family that plays an important role in negatively regulating immune responses upon interaction with its two ligands, PD-L1 or PD-L2. Like PD-L2, PD-L1 interacts with PD-1 and suppresses T cell proliferation and cytokine production. The PD-1 receptor is expressed on the surface of activated T cells, while PD-L1 is expressed on cancer cells. When PD-1 and PD-L1 bind together, they form a molecular shield protecting tumor cells from being destroyed by the immune system. Thus, inhibiting the binding of PD-L1 to PD-1 with an antibody leads to killing of tumor cells by T cells. PD-1 inhibitors (such as Pembrolizumab, Nivolumab, and Cemiplimab) and PD-L1 inhibitors (such as Atezolizumab, Avelumab, and Durvalumab ) are an emerging class of immunotherapy that stimulate lymphocytes against tumor cells. 110 matched cddid_all.tbl CDD cd20948 cd20948 409540 IgC2_CEACAM5-like Fifth immunoglobulin (Ig)-like domain of the carcinoembryonic antigen (CEA) related cell adhesion molecule 5 (CEACAM5) and similar domains; member of the C2-set IgSF domains. The members here are composed of the fifth immunoglobulin (Ig)-like domain of the carcinoembryonic antigen (CEA) related cell adhesion molecule 5 (CEACAM5) and similar domains. The CEA family is a group of anchored or secreted glycoproteins, expressed by epithelial cells, leukocytes, endothelial cells and placenta. The CEA family is divided into the CEACAM and pregnancy-specific glycoprotein (PSG) subfamilies. Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5), also known as CD66e (Cluster of Differentiation 66e), is a cell surface glycoprotein that plays a role in cell adhesion, intracellular signaling and tumor progression. Diseases associated with CEACAM5 include lung cancer and rectum cancer. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. This group belongs to the C2-set of IgSF domains, having A, B, and E strands in one beta-sheet and A', G, F, C' in the other. Unlike other Ig domain sets, the C2-set lacks the D strand. 76 matched cddid_all.tbl CDD cd20949 cd20949 409541 IgI_Twitchin_like "C-terminal immunoglobulin-like domain of the myosin-associated giant protein kinase Twitchin, and similar domains; member of the I-set IgSF domains. The members here are composed of the C-terminal immunoglobulin-like domain of the myosin-associated giant protein kinase Twitchin and similar proteins, including Caenorhabditis elegans and Aplysia californica Twitchin, Drosophila melanogaster Projectin, and similar proteins. These are very large muscle proteins containing multiple immunoglobulin (Ig)-like and fibronectin type III (FN3) domains and a single kinase domain near the C-terminus. In humans these proteins are called Titin. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The Ig-like domain of the Twitchin is a member of the I-set IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C"" strand. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins (titin, telokin, and twitchin), the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D." 89 matched cddid_all.tbl CDD cd20950 cd20950 409542 IgI_2_JAM1 "Second Ig-like domain of Junctional adhesion molecule-1 (JAM1); a member of the I-set of IgSF domains. The members here are composed of the second Ig-like domain of Junctional adhesion molecule-1 (JAM1). JAM1 is an immunoglobulin superfamily (IgSF) protein with two Ig-like domains in its extracellular region; it plays a role in the formation of endothelial and epithelial tight junction and acts as a receptor for mammalian reovirus sigma-1. The IgSF is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. The two sheets are linked together by a conserved disulfide bond between B strand and F strand. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The second Ig-like domain of JAM1 is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, the A strand of the I-set is discontinuous but lacks a C"" strand. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors." 97 matched cddid_all.tbl CDD cd20951 cd20951 409543 IgI_titin_I1-like "Immunoglobulin domain I1 of the titin I-band and similar proteins; a member of the I-set of IgSF domains. The members here are composed of the immunoglobulin domain I1 of the titin I-band and similar proteins. Titin is a key component in the assembly and functioning of vertebrate striated muscles. By providing connections at the level of individual microfilaments, it contributes to the fine balance of forces between the two halves of the sarcomere. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. The two sheets are linked together by a conserved disulfide bond between B strand and F strand. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The Ig I1 domain of the titin I-band is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C"" strand. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis." 94 matched cddid_all.tbl CDD cd20952 cd20952 409544 IgI_5_Robo "Fifth Ig-like domain of Roundabout (Robo) homolog 1/2, and similar domains; a member of the I-set of IgSF domains. The members here are composed of the fifth Ig-like domain of Roundabout (Robo) homolog 1/2 and similar domains. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (Robo1, -2, and -3), and three mammalian Slit homologs (Slit-1,-2, -3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. Robo1, -2, and -3 are expressed by commissural neurons in the vertebrate spinal cord and Slits 1, -2, -3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of slit responsiveness, antagonizes slit responsiveness in precrossing axons. The Slit-Robo interaction is mediated by the second leucine-rich repeat (LRR) domain of Slit and the two N-terminal Ig domains of Robo, Ig1 and Ig2. The primary Robo binding site for Slit2 has been shown by surface plasmon resonance experiments and mutational analysis to be is the Ig1 domain, while the Ig2 domain has been proposed to harbor a weak secondary binding site. The fifth Ig-like domain of Robo 1 and 2 is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C"" strand. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors" 87 matched cddid_all.tbl CDD cd20953 cd20953 409545 IgI_2_Dscam "Second immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; a member of the I-set of IgSF domains. The members here are composed of the second immunoglobulin domain of the Drosophila melanogaster Down syndrome cell adhesion molecule (DSCAM) protein and similar proteins. DSCAM is a cell adhesion molecule that plays critical roles in neural development, including axon guidance and branching, axon target recognition, self-avoidance and synaptic formation. DSCAM belongs to the immunoglobulin superfamily and contributes to defects in the central nervous system in Down syndrome patients. Vertebrate DSCAMs differ from Drosophila Dscam1 in that they lack the extensive alternative splicing that occurs in the insect gene. Drosophila melanogaster Dscam has 38,016 isoforms generated by the alternative splicing of four variable exon clusters, which allows every neuron in the fly to display a distinctive set of Dscam proteins on its cell surface. Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is shown that thousands of isoforms bind themselves through specific homophilic (self-binding) interactions, a process which mediates cellular self-recognition. Drosophila Dscam2 is also alternatively spliced and plays a key role in the development of two visual system neurons, monopolar cells L1 and L2. This group is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C"" strand." 95 matched cddid_all.tbl CDD cd20954 cd20954 409546 IgI_7_Dscam "Seventh immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; a member of the I-set of IgSF domains. The members here are composed of the seventh immunoglobulin domain of the Drosophila melanogaster Down syndrome cell adhesion molecule (DSCAM) protein and similar proteins. Down syndrome cell adhesion molecule (DSCAM) is a cell adhesion molecule that plays critical roles in neural development, including axon guidance and branching, axon target recognition, self-avoidance and synaptic formation. DSCAM belongs to the immunoglobulin superfamily and contributes to defects in the central nervous system in Down syndrome patients. Vertebrate DSCAMs differ from Drosophila Dscam1 in that they lack the extensive alternative splicing that occurs in the insect gene. Drosophila melanogaster Dscam has 38,016 isoforms generated by the alternative splicing of four variable exon clusters, which allows every neuron in the fly to display a distinctive set of Dscam proteins on its cell surface. Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is shown that thousands of isoforms bind themselves through specific homophilic (self-binding) interactions, a process which mediates cellular self-recognition. Drosophila Dscam2 is also alternatively spliced and plays a key role in the development of two visual system neurons, monopolar cells L1 and L2. This group is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C"" strand." 96 matched cddid_all.tbl CDD cd20955 cd20955 409547 IgI_1_Dscam "First immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; a member of the I-set of IgSF domains. The members here are composed of the first immunoglobulin domain of the Drosophila melanogaster Down syndrome cell adhesion molecule (DSCAM) protein and similar proteins. Down syndrome cell adhesion molecule (DSCAM) is a cell adhesion molecule that plays critical roles in neural development, including axon guidance and branching, axon target recognition, self-avoidance and synaptic formation. DSCAM belongs to the immunoglobulin superfamily and contributes to defects in the central nervous system in Down syndrome patients. Vertebrate DSCAMs differ from Drosophila Dscam1 in that they lack the extensive alternative splicing that occurs in the insect gene. Drosophila melanogaster Dscam has 38,016 isoforms generated by the alternative splicing of four variable exon clusters, which allows every neuron in the fly to display a distinctive set of Dscam proteins on its cell surface. Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is shown that thousands of isoforms bind themselves through specific homophilic (self-binding) interactions, a process which mediates cellular self-recognition. Drosophila Dscam2 is also alternatively spliced and plays a key role in the development of two visual system neurons, monopolar cells L1 and L2. This group is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C"" strand." 99 matched cddid_all.tbl CDD cd20956 cd20956 409548 IgI_4_Dscam "Fourth immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; a member of the I-set of IgSF domains. The members here are composed of the fourth immunoglobulin domain of the Drosophila melanogaster Down syndrome cell adhesion molecule (DSCAM) protein and similar proteins. Down syndrome cell adhesion molecule (DSCAM) is a cell adhesion molecule that plays critical roles in neural development, including axon guidance and branching, axon target recognition, self-avoidance and synaptic formation. DSCAM belongs to the immunoglobulin superfamily and contributes to defects in the central nervous system in Down syndrome patients. Vertebrate DSCAMs differ from Drosophila Dscam1 in that they lack the extensive alternative splicing that occurs in the insect gene. Drosophila melanogaster Dscam has 38,016 isoforms generated by the alternative splicing of four variable exon clusters, which allows every neuron in the fly to display a distinctive set of Dscam proteins on its cell surface. Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is shown that thousands of isoforms bind themselves through specific homophilic (self-binding) interactions, a process which mediates cellular self-recognition. Drosophila Dscam2 is also alternatively spliced and plays a key role in the development of two visual system neurons, monopolar cells L1 and L2. This group is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C"" strand." 96 matched cddid_all.tbl CDD cd20957 cd20957 409549 IgC2_3_Dscam Third immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; a member of the Constant 2 (C2)-set of IgSF domains. The members here are composed of the third immunoglobulin domain of the Drosophila melanogaster Down syndrome cell adhesion molecule (DSCAM) protein and similar proteins. Down syndrome cell adhesion molecule (DSCAM) is a cell adhesion molecule that plays critical roles in neural development, including axon guidance and branching, axon target recognition, self-avoidance and synaptic formation. DSCAM belongs to the immunoglobulin superfamily and contributes to defects in the central nervous system in Down syndrome patients. Vertebrate DSCAMs differ from Drosophila Dscam1 in that they lack the extensive alternative splicing that occurs in the insect gene. Drosophila melanogaster Dscam has 38,016 isoforms generated by the alternative splicing of four variable exon clusters, which allows every neuron in the fly to display a distinctive set of Dscam proteins on its cell surface. Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is shown that thousands of isoforms bind themselves through specific homophilic (self-binding) interactions, a process which mediates cellular self-recognition. Drosophila Dscam2 is also alternatively spliced and plays a key role in the development of two visual system neurons, monopolar cells L1 and L2. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. This group belongs to the C2-set of IgSF domains, having A, B, and E strands in one beta-sheet and A', G, F, C, and C' in the other. Unlike other Ig domain sets, the C2-set lacks the D strand. 88 matched cddid_all.tbl CDD cd20958 cd20958 409550 IgI_5_Dscam "Fifth immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; a member of the I-set of IgSF domains. The members here are composed of the fifth immunoglobulin domain of the Drosophila melanogaster Down syndrome cell adhesion molecule (DSCAM) protein and similar proteins. Down syndrome cell adhesion molecule (DSCAM) is a cell adhesion molecule that plays critical roles in neural development, including axon guidance and branching, axon target recognition, self-avoidance and synaptic formation. DSCAM belongs to the immunoglobulin superfamily and contributes to defects in the central nervous system in Down syndrome patients. Vertebrate DSCAMs differ from Drosophila Dscam1 in that they lack the extensive alternative splicing that occurs in the insect gene. Drosophila melanogaster Dscam has 38,016 isoforms generated by the alternative splicing of four variable exon clusters, which allows every neuron in the fly to display a distinctive set of Dscam proteins on its cell surface. Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is shown that thousands of isoforms bind themselves through specific homophilic (self-binding) interactions, a process which mediates cellular self-recognition. Drosophila Dscam2 is also alternatively spliced and plays a key role in the development of two visual system neurons, monopolar cells L1 and L2. This group is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C"" strand." 89 matched cddid_all.tbl CDD cd20959 cd20959 409551 IgI_6_Dscam "Sixth immunoglobulin domain of the Drosophila melanogaster Dscam protein, and similar domains; a member of the I-set of IgSF domains. The members here are composed of the sixth immunoglobulin domain of the Drosophila melanogaster Down syndrome cell adhesion molecule (DSCAM) protein and similar proteins. Down syndrome cell adhesion molecule (DSCAM) is a cell adhesion molecule that plays critical roles in neural development, including axon guidance and branching, axon target recognition, self-avoidance and synaptic formation. DSCAM belongs to the immunoglobulin superfamily and contributes to defects in the central nervous system in Down syndrome patients. Vertebrate DSCAMs differ from Drosophila Dscam1 in that they lack the extensive alternative splicing that occurs in the insect gene. Drosophila melanogaster Dscam has 38,016 isoforms generated by the alternative splicing of four variable exon clusters, which allows every neuron in the fly to display a distinctive set of Dscam proteins on its cell surface. Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is shown that thousands of isoforms bind themselves through specific homophilic (self-binding) interactions, a process which mediates cellular self-recognition. Drosophila Dscam2 is also alternatively spliced and plays a key role in the development of two visual system neurons, monopolar cells L1 and L2. This group is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C"" strand." 94 matched cddid_all.tbl CDD cd20960 cd20960 409552 IgV_CAR_like "Immunoglobulin Variable (V) domain of the Coxsackievirus and Adenovirus Receptor (CAR), and similar proteins. The members here are composed of the Variable (V) domain of the Coxsackievirus and Adenovirus Receptor (CAR), and similar proteins. CAR, which is encoded by human CXADR gene, is a cell adhesion molecule of the Immunoglobulin (Ig) superfamily. The CAR acts as a type I membrane receptor for group B1-B6 coxsackie viruses and subgroup C adenoviruses. For instance, adenovirus interacts with the coxsackievirus and adenovirus receptor to enter epithelial airway cells. The CAR is also shown to be involved in physiological processes such as neuronal and heart development, epithelial tight junction integrity, and tumor suppression. The CAR is a component of the epithelial apical junction complex that may function as a homophilic cell adhesion molecule and is essential for tight junction integrity. The CAR is also involved in transepithelial migration of leukocytes through adhesive interactions with JAML a transmembrane protein of the plasma membrane of leukocytes. The interaction between both receptors also mediates the activation of gamma-delta T-cells, a subpopulation of T-cells residing in epithelia and involved in tissue homeostasis and repair. The CAR is composed of one V-set and one C2-set Ig module, a single transmembrane helix, and an intracellular domain. This group belongs to the V-set of IgSF domains, having A, B, E and D strands in one beta-sheet and A', G, F, C, C' and C"" in the other" 114 matched cddid_all.tbl CDD cd20961 cd20961 409553 Ig1_Tyro3_like First immunoglobulin (Ig)-like domain of Tyro3 receptor tyrosine kinase (RTK), and similar domains. The members here are composed of the first immunoglobulin (Ig)-like domain of Tyro3 receptor tyrosine kinase (RTK). Tyro3 together with Axl and Mer form the Axl/Tyro3 family of receptor tyrosine kinases (RTKs). This family includes Axl (also known as Ark, Ufo, and Tyro7), Tyro3 (also known as Sky, Rse, Brt, Dtk, and Tif), and Mer (also known as Nyk, c-Eyk, and Tyro12). Axl/Tyro3 family receptors have an extracellular portion with two Ig-like domains followed by two fibronectin-types III (FNIII) domains, a membrane-spanning single helix, and a cytoplasmic tyrosine kinase domain. Axl, Tyro3 and Mer are widely expressed in adult tissues, though they show higher expression in the brain, in the lymphatic and vascular systems, and in the testis. Axl, Tyro3, and Mer bind the vitamin K dependent protein Gas6 with high affinity, and in doing so activate their tyrosine kinase activity. Axl/Gas6 signaling may play a part in cell adhesion processes, prevention of apoptosis, and cell proliferation. 87 matched cddid_all.tbl CDD cd20962 cd20962 409554 IgI_C1_MyBP-C_like "Immunoglobulin Domain C1 of human cardiac Myosin Binding Protein C and similar proteins; a member of the I-set of IgSF domains. The members here are composed of the immunoglobulin domain C1 of human cardiac Myosin Binding Protein C (MyBP-C). MyBP-C is a thick filament protein involved in the regulation of muscle contraction. Mutations in cardiac MyBP-C gene are the second most frequent cause of hypertrophic cardiomyopathy. MyBP-C binds to myosin with two binding sites, one at its C-terminus and another at its N-terminus. The N-terminal binding site, consisting of immunoglobulin (lg) domains C1 and C2 connected by a flexible linker, interacts with the S2 segment of myosin in a phosphorylation-regulated manner. The C1 and C2 Ig domains can bind to and activate or inhibit the thin filament. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The C1 domain of the MyBP-C is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C"" strand. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors." 101 matched cddid_all.tbl CDD cd20963 cd20963 409555 IgV_VCBP "Immunoglobulin Variable region-containing chitin-binding proteins; an immunoglobulin V-set domain. The members here are composed of the immunoglobulin variable (IgV) region-containing chitin-binding proteins (VCBPs). VCBPs are secreted, immune-type molecules that have been identified in both amphioxus and sea squirt (Ciona intestinalis). VCBPs, which consist of a leader peptide, two tandem N-terminal immunoglobulin V-type domains and a single C-terminal chitin-binding domain, belong to a multigene family encoding secreted proteins. The VCBPs were identified first in the cephalochordate Branchiostoma floridae and show structural similarities with V-type domains of immunoglobulins and T cell receptors, suggesting that VCBPs represent a unique gut-associated form of innate immune proteins. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. This group belongs to the V-set of IgSF domains, having A, B, E and D strands in one beta-sheet and A', G, F, C, C' and C"" in the other." 123 matched cddid_all.tbl CDD cd20964 cd20964 409556 IgI_Tie2 "Immunoglobulin domain of Tie2 tyrosine kinase; a member of the I-set of IgSF domains. The members here are composed of the immunoglobulin (Ig) domain of Tie2 tyrosine kinase. The Tie receptor tyrosine kinases and their angiopoietin (Ang) ligands play central roles in developmental and tumor-induced angiogenesis. Tie2 contains three immunoglobulin (Ig) domains, which fold together with the three epidermal growth factor domains into a compact, arrowhead-shaped structure. Ang2-Tie2 recognition is similar to antibody-protein antigen recognition, including the location of the ligand-binding site within the Ig fold. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C"" strand. The structures of the Tie2 lacks this strand and thus it belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors." 92 matched cddid_all.tbl CDD cd20965 cd20965 409557 IgI_2_hemolin-like "Second immunoglobulin (Ig)-like domain of hemolin, and similar domains; a member of the I-set of IgSF domains. The members here are composed of the second immunoglobulin (Ig)-like domain of hemolin and similar proteins. Hemolin, an insect immunoglobulin superfamily (IgSF) member containing four Ig-like domains, is a lipopolysaccharide-binding immune protein induced during bacterial infection. Hemolin shares significant sequence similarity with the first four Ig-like domains of the transmembrane cell adhesion molecules (CAMs) of the L1 family. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C"" strand. The structures of this group show that the second Ig domain lacks this strand and thus belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules, including vascular (VCAM), intercellular (ICAM), neural (NCAM) and mucosal addressin (MADCAM) cell adhesion molecules, as well as junction adhesion molecules (JAM)." 101 matched cddid_all.tbl CDD cd20966 cd20966 409558 IgI_1_Axl_like "First immunoglobulin (Ig)-like domain of Axl receptor tyrosine kinase (RTK), and similar domains; member of the I-set Ig domains. The members here are composed of the first immunoglobulin (Ig)-like domain of Axl receptor tyrosine kinase (RTK). Axl together with Tyro3 and Mer form the Axl/Tyro3 family of receptor tyrosine kinases (RTKs). This family includes Axl (also known as Ark, Ufo, and Tyro7), Tyro3 (also known as Sky, Rse, Brt, Dtk, and Tif), and Mer (also known as Nyk, c-Eyk, and Tyro12). Axl/Tyro3 family receptors have an extracellular portion with two Ig-like domains followed by two fibronectin-types III (FNIII) domains, a membrane-spanning single helix, and a cytoplasmic tyrosine kinase domain. Axl, Tyro3 and Mer are widely expressed in adult tissues, though they show higher expression in the brain, in the lymphatic and vascular systems, and in the testis. Axl, Tyro3, and Mer bind the vitamin K dependent protein Gas6 with high affinity, and in doing so activate their tyrosine kinase activity. Axl/Gas6 signaling may play a part in cell adhesion processes, prevention of apoptosis, and cell proliferation. Ig superfamily domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The Ig-like domain of the Axl is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C"" strand." 101 matched cddid_all.tbl CDD cd20967 cd20967 409559 IgI_C2_MyBP-C-like "Domain C2 of human cardiac Myosin Binding Protein C and similar domains; a member of the I-set of IgSF domains. The members here are composed of the immunoglobulin (Ig) Domain C2 of human cardiac Myosin Binding Protein C (MyBP-C) and similar domains. MyBP-C is a thick filament protein involved in the regulation of muscle contraction. Mutations in cardiac MyBP-C gene are the second most frequent cause of hypertrophic cardiomyopathy. MyBP-C binds to myosin with two binding sites, one at its C-terminus and another at its N-terminus. The N-terminal binding site, consisting of immunoglobulin (lg) domains C1 and C2 connected by a flexible linker, interacts with the S2 segment of myosin in a phosphorylation-regulated manner. The C1 and C2 Ig domains can bind to and activate or inhibit the thin filament. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C"" strand. The structures of the Ig domains of MyBP-C lack this strand and thus belong to the I-set of Ig superfamily domains. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors." 82 matched cddid_all.tbl CDD cd20968 cd20968 409560 IgI_2_MuSK "agrin-responsive second immunoglobulin-like domains (Ig2) of the Muscle-specific kinase (MuSK) ectodomain; a member of the I-set of Ig superfamily domains. The members here are composed of the second immunoglobulin-like (Ig) domains of the Muscle-specific kinase (MuSK) ectodomain. MuSK is a receptor tyrosine kinase specifically expressed in skeletal muscle, where it plays a central role in the formation and maintenance of the neuromuscular junction (NMJ). MuSK is activated by agrin, a neuron-derived heparan sulfate proteoglycan. The activation of MUSK in myotubes regulates the formation of NMJs through the regulation of different processes including the specific expression of genes in subsynaptic nuclei, the reorganization of the actin cytoskeleton and the clustering of the acetylcholine receptors (AChR) in the postsynaptic membrane. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C"" strand. The structure of the MuSK lacks this strand and thus it belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis." 88 matched cddid_all.tbl CDD cd20969 cd20969 409561 IgI_Lingo-1 "Immunoglobulin I-set domain of the Leucine-rich repeat and immunoglobin-like domain-containing protein 1 (Lingo-1). The members here are composed of the immunoglobulin I-set (IgI) domain of the Leucine-rich repeat and immunoglobin-like domain-containing protein 1 (Lingo-1). Human Lingo-1 is a central nervous system-specific transmembrane glycoprotein also known as LERN-1, which functions as a negative regulator of neuronal survival, axonal regeneration, and oligodendrocyte differentiation and myelination. Lingo-1 is a key component of the Nogo receptor signaling complex (RTN4R/NGFR) in RhoA activation responsible for some inhibition of axonal regeneration by myelin-associated factors. The ligand-binding ectodomain of human Lingo-1 contains a bimodular, kinked structure composed of leucine-rich repeat (LRR) and immunoglobulin (Ig)-like modules. Diseases associated with Lingo-1 include mental retardation, autosomal recessive 64 and essential tremor. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C"" strand. The structure of the Lingo-1 lacks this strand and thus it belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis." 92 matched cddid_all.tbl CDD cd20970 cd20970 409562 IgI_1_MuSK "agrin-responsive first immunoglobulin-like domains (Ig1) of the MuSK ectodomain; a member of the I-set of IgSF domains. The members here are composed of the first immunoglobulin-like domains (Ig1) of the Muscle-specific kinase (MuSK). MuSK is a receptor tyrosine kinase specifically expressed in skeletal muscle, where it plays a central role in the formation and maintenance of the neuromuscular junction (NMJ). MuSK is activated by agrin, a neuron-derived heparan sulfate proteoglycan. The activation of MUSK in myotubes regulates the formation of NMJs through the regulation of different processes including the specific expression of genes in subsynaptic nuclei, the reorganization of the actin cytoskeleton and the clustering of the acetylcholine receptors (AChR) in the postsynaptic membrane. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C"" strand. The structure of the MuSK lacks this strand and thus it belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis." 92 matched cddid_all.tbl CDD cd20971 cd20971 409563 IgI_1_Titin-A168_like "First immunoglobulin-like domains A168 within the A-band segment of human cardiac titin, and similar domains; a member of the I-set of IgSF domains. The members here are composed of the first immunoglobulin-like domain A168 within the A-band segment of human cardiac titin. Titin is a key component in the assembly and functioning of vertebrate striated muscles. By providing connections at the level of individual microfilaments, it contributes to the fine balance of forces between the two halves of the sarcomere. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C"" strand. The structures of the titin-A168169 lacks this strand and thus it belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis." 93 matched cddid_all.tbl CDD cd20972 cd20972 409564 IgI_2_Titin_Z1z2-like "Second Ig-like domain of the giant muscle protein titin Z1z2 in the sarcomeric Z-disk, and similar domains; a member of the I-set of IgSF domains. The members here are composed of the second immunoglobulin (Ig)-like domain of the giant muscle protein titin Z1z2 in the sarcomeric Z-disk and similar proteins. Titin is a key component in the assembly and functioning of vertebrate striated muscles. By providing connections at the level of individual microfilaments, it contributes to the fine balance of forces between the two halves of the sarcomere. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C"" strand. The structure of the titin Z1z2 lacks this strand and thus it belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis." 91 matched cddid_all.tbl CDD cd20973 cd20973 409565 IgI_telokin-like "immunoglobulin-like domain of telokin and similar proteins; a member of the I-set of IgSF domains. The members here are composed of the immunoglobulin (Ig) domain in telokin, the C-terminal domain of myosin light chain kinase which is identical to telokin, and similar proteins. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C"" strand. The structure of the telokin Ig domain lacks this strand and thus it belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis." 88 matched cddid_all.tbl CDD cd20974 cd20974 409566 IgI_1_Titin_Z1z2-like "First Ig-like domain of the giant muscle protein titin Z1z2 in the sarcomeric Z-disk and similar proteins; a member of the I-set of IgSF domains. The members here are composed of the first immunoglobulin (Ig)-like domain of the giant muscle protein titin Z1z2 in the sarcomeric Z-disk and similar proteins. Titin is a key component in the assembly and functioning of vertebrate striated muscles. By providing connections at the level of individual microfilaments, it contributes to the fine balance of forces between the two halves of the sarcomere. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C"" strand. The structure of the titin Z1z2 lacks this strand and thus it belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis." 93 matched cddid_all.tbl CDD cd20975 cd20975 409567 IgI_APEG-1_like "Immunoglobulin-like domain of human Aortic Preferentially Expressed Protein-1 (APEG-1) and similar proteins; a member of the I-set of IgSF domains. The members here are composed of the immunoglobulin I-set (IgI) domain of the Human Aortic Preferentially Expressed Protein-1 (APEG-1) and similar proteins. APEG-1 is a novel specific smooth muscle differentiation marker predicted to play a role in the growth and differentiation of arterial smooth muscle cells (SMCs). The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C"" strand. The structure of the human APEG-1 lacks this strand and thus it belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis." 91 matched cddid_all.tbl CDD cd20976 cd20976 409568 IgI_4_MYLK-like "Fourth Ig-like domain from smooth muscle myosin light chain kinase and similar domains ; a member of the I-set of IgSF domains. The members here are composed of the fourth immunoglobulin (Ig)-like domain from smooth muscle myosin light chain kinase (MYLK) and similar domains. The Ig superfamily (IgSF) is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Unlike the V-set, one of the distinctive features of I-set domains is the lack of a C"" strand. The structure of this group shows that the fourth Ig-like domain from myosin light chain kinase lacks this strand and thus belongs to the I-set of the IgSF. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the hemolymph protein hemolin, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis." 90 matched cddid_all.tbl CDD cd20977 cd20977 409569 IgI_3_hemolin-like "Third immunoglobulin (Ig)-like domain of hemolin, and similar domains; a member of the I-set of IgSF domains. The members here are composed of the third immunoglobulin (Ig)-like domain of hemolin and similar proteins. Hemolin, an insect immunoglobulin superfamily (IgSF) member containing four Ig-like domains, is a lipopolysaccharide-binding immune protein induced during bacterial infection. Hemolin shares significant sequence similarity with the first four Ig-like domains of the transmembrane cell adhesion molecules (CAMs) of the L1 family. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The third Ig-like domain of hemolin is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C"" strand. I-set domains are found in several cell adhesion molecules, including vascular (VCAM), intercellular (ICAM), neural (NCAM) and mucosal addressin (MADCAM) cell adhesion molecules, as well as junction adhesion molecules (JAM)." 93 matched cddid_all.tbl CDD cd20978 cd20978 409570 IgI_4_hemolin-like "Fourth immunoglobulin (Ig)-like domain of hemolin, and similar domains; a member of the I-set of IgSF domains. The members here are composed of the fourth immunoglobulin (Ig)-like domain of hemolin and similar proteins. Hemolin, an insect immunoglobulin superfamily (IgSF) member containing four Ig-like domains, is a lipopolysaccharide-binding immune protein induced during bacterial infection. Hemolin shares significant sequence similarity with the first four Ig-like domains of the transmembrane cell adhesion molecules (CAMs) of the L1 family. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The fourth Ig-like domain of hemolin is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set domains, members of the I-set have a discontinuous A strand but lack a C"" strand. I-set domains are found in several cell adhesion molecules (such as VCAM, ICAM, and MADCAM), and are also present in numerous other diverse protein families, including several tyrosine-protein kinase receptors, the muscle proteins titin, telokin, and twitchin, the neuronal adhesion molecule axonin-1, and the signaling molecule semaphorin 4D that is involved in axonal guidance, immune function and angiogenesis." 88 matched cddid_all.tbl CDD cd20979 cd20979 409571 IgI_1_hemolin-like "First immunoglobulin (Ig)-like domain of hemolin, and similar domains; a member of the I-set of IgSF domains. The members here are composed of the first immunoglobulin (Ig)-like domain of hemolin and similar proteins. Hemolin, an insect immunoglobulin superfamily (IgSF) member containing four Ig-like domains, is a lipopolysaccharide-binding immune protein induced during bacterial infection. Hemolin shares significant sequence similarity with the first four Ig-like domains of the transmembrane cell adhesion molecules (CAMs) of the L1 family. IgSF domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. The first Ig-like domain of hemolin is a member of the I-set Ig domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand but lack a C"" strand. I-set domains are found in several cell adhesion molecules, including vascular (VCAM), intercellular (ICAM), neural (NCAM) and mucosal addressin (MADCAM) cell adhesion molecules, as well as junction adhesion molecules (JAM)." 91 matched cddid_all.tbl CDD cd20980 cd20980 409572 IgV_VISTA Immunoglobulin variable (IgV) domain of V-domain immunoglobulin suppressor of T cell activation (VISTA). The members here are composed of the immunoglobulin variable (IgV) domain of V-domain immunoglobulin suppressor of T cell activation (VISTA; also known as B7-H5, PD-1H, Gi24, Dies1, SISP1 and DD1alpha). VISTA is an immune checkpoint protein involved in the regulation of T cell activity and inhibits the T cell response against cancer. VISTA is a type I transmembrane protein with a single IgV domain with sequence homology to the IgV domains of the members of B7 family. VISTA is the only B7 family member that lacks an IgC domain. VISTA is primarily expressed in white blood cells and its transcription is partially controlled by p53. Similar to PD-1/PD-L1 and CTLA-4, a blockade of VISTA promotes tumor clearance by the immune system. Unlike the B7 family members, VISTA contains 10 beta-strands, instead of the nine that typically comprises of an IgV fold. Moreover, human VISTA contains the 21-residue extended loop between stands C and C', which does not align with any B7 family structure. 147 matched cddid_all.tbl CDD cd20981 cd20981 409573 IgV_B7-H6 Immunoglobulin variable (IgV) domain of B7-H6. The members here are composed of the immunoglobulin variable (IgV) domain of B7-H6 (also known as NCR3LG1). B7-H6 contains one IgV domain and one IgC domain (IgV-IgC) and belongs to the B7-family, which consists of structurally related cell-surface protein ligands which bind to receptors on lymphocytes that regulate immune responses. B7-H6 is a ligand of NKp30, which is a member of CD28 family and an activating receptor of natural killer (NK) cells. The expression of NKp30 has been found in most of NK cells, which is involved in the process of tumor cell killing and interaction with antigen presenting cells (APCs) such as dendritic cells. Studies showed that NK cells eliminate B7-H6-expressing tumor cells either directly via cytotoxicity or indirectly by cytokine secretion. For instance, chimeric NKp30-expressing T cells responded to B7-H6(+) tumor cells and those T cells produced IFN-gamma and killed B7-H6-expressing tumor cells in vivo. B7-H6 mRNA is not found in normal cells, while high expression of B7-H6 is found in certain type tumor cells, such as lymphoma, leukemia, ovarian cancer, brain tumors, breast cancers, and various sarcomas. Since B7-H6 can bind NKp30 to exert anti-tumor effects by NK cells, which are able to recognize the difference between cancer cells and normal cells, B7-H6 may serve as a promising target for cancer immunotherapy. 114 matched cddid_all.tbl CDD cd20982 cd20982 409574 IgV_TIM-3_like Immunoglobulin Variable (IgV) domain of T cell Immunoglobulin Domain and Mucin Domain 3 (Tim-3), and similar domains. The members here are composed of the immunoglobulin variable (IgV) domain of T cell immunoglobulin domain and mucin domain 3 (Tim-3; also known as Hepatitis A virus cellular receptor 2 (HAVcr-2) and Cluster of Differentiation 366 (CD366)) and similar proteins. TIM-3 is a checkpoint inhibitor in immune responses to tumors, as well as involved in chronic viral infections. Thus, Tim-3 has emerged as one of most promising immune checkpoint targets for cancer immunotherapy. Tim-3 is highly expressed on Th1 lymphocytes and CD11b(+) macrophages and is upregulated on activated T and myeloid cells. TIM-3 regulates macrophage, activation and inhibits Th1 mediated immune responses to promote immunological tolerance. There are three TIM family members in humans (TIM-1, TIM-3, and TIM-4) and eight members in mice (TIM-1 to TIM-8). The IgV domain of human TIM-3 has been shown to bind ligands such as carcinoembryonic antigen cell adhesion molecule 1 (CEACAM1), high mobility group protein B1 (HMGB1)and galectin-9 (GAL9). The binding of GAL9 to TIM-3 can negatively regulate Th1 immune response, enhance immune tolerance and inhibit anti#tumor immunity. Dysregulation of the TIM-3/GAL9 pathway is implicated in numerous chronic autoimmune diseases, such as multiple sclerosis and systemic lupus erythematosus. 107 matched cddid_all.tbl CDD cd20983 cd20983 409575 IgV_PD-L2 Immunoglobulin Variable (IgV) domain of Programmed death ligand 2 (PD-L2). The members here are composed of the immunoglobulin variable (IgV) domain of Programmed death ligand 2 (PD-L2; also known as B7-DC or CD273). Receptor-binding domain of PD-L2 is a cell-surface ligand that competes with PD-L1 for binding to the immunosuppressive receptor programmed death-1 (PD-1). PD-1 is a member of the CD28/B7 family that plays an important role in negatively regulating immune responses upon interaction with its two ligands, PD-L1 or PD-L2. PD-L2 has a higher affinity for PD-1 but is expressed at lower levels. PD-L2 interaction with PD-1 suppresses T cell proliferation, cytokine production and cytotoxic activity. PD-L2 is expressed on tumor cells, antigen-presenting cells or APCs (such as macrophages, B cells and dendritic cells), and a variety of other immune and nonimmune cells. Tumor expression of PD-L2 may contribute to tumor evasion of immune destruction by inactivating T cells. Thus, PD-L2 is a negative predictor for prognosis among solid cancer patients. 100 matched cddid_all.tbl CDD cd20984 cd20984 409576 IgV_B7-H4 Immunoglobulin Variable (IgV) domain of B7-H4. The members here are composed of the immunoglobulin variable (IgV) domain of B7-H4 (also known as B7-S1, B7x, or Vtcn1). B7-H4 is one of the B7 family of immune-regulatory ligands that act as negative regulators of T cell function; it contains one IgV domain and one IgC domain. The B7-family consists of structurally related cell-surface protein ligands, which bind to receptors on lymphocytes that regulate immune responses. The binding of B7-H4 to unidentified receptors results in the inhibition of TCR-mediated T cell proliferation, cell-cycle progression and IL-2 production. As a co-inhibitory molecule, B7-H4 is widely expressed in tumor tissues and its expression is significantly associated with poor prognosis in human cancers such as glioma, pancreatic cancer, oral squamous cell carcinoma, renal cell carcinoma, and lung cancer. 110 matched cddid_all.tbl CDD cd20985 cd20985 409577 IgV_CD200R-like Immunoglobulin Variable domain of cell surface glycoprotein CD200 receptor and similar proteins. The members here are composed of the immunoglobulin variable (IgV) domain of cell surface glycoprotein CD200 receptor and similar proteins. CD200 (also known as OX2) is a widely distributed membrane glycoprotein that regulates myeloid cell activity through its interaction with an inhibitory receptor (CD200R). CD200-CD200R interactions are involved in the control of myeloid cellular function. In the mouse, several CD200R-related genes have been identified, including CD200RL (for receptor like), CD200R1, and CD200R2. While CD200 gives good binding to CD200R, it does not bind CD200RLa, CD200RLb, CD200RLc, or CD200RLe. For instance, CD200RLa has a 50-fold lower binding affinity to CD200, although CD200RLa shares a high amino acid sequence identity with CD200R in the V-like domain. Furthermore, the CD200-CD200R regulatory interactions provide an attractive target for immunomodulation, because its manipulation can provoke either immune tolerance or autoimmune diseases. 107 matched cddid_all.tbl CDD cd20986 cd20986 409578 IgC1_PD-L2 Immunoglobulin Constant 1 (IgC1) domain of Programmed death ligand 2 (PD-L2). The members here are composed of the immunoglobulin Constant 1 (IgC1) domain of Programmed death ligand 2 (PD-L2; also known as B7-DC or CD273). PD-L2 is a cell-surface ligand that competes with PD-L1 for binding to the immunosuppressive receptor programmed death-1 (PD-1). PD-1 is a member of the CD28/B7 family that plays an important role in negatively regulating immune responses upon interaction with its two ligands, PD-L1 or PD-L2. PD-L2 has a higher affinity for PD-1 but is expressed at lower levels. PD-L2 interaction with PD-1 suppresses T cell proliferation, cytokine production and cytotoxic activity. PD-L2 is expressed on tumor cells, antigen-presenting cells or APCs (such as macrophages, B cells and dendritic cells), and a variety of other immune and nonimmune cells. Tumor expression of PD-L2 may contribute to tumor evasion of immune destruction by inactivating T cells. Thus, PD-L2 is a negative predictor for prognosis among solid cancer patients. 82 matched cddid_all.tbl CDD cd20987 cd20987 409579 IgC2_CD33_d2_like Second immunoglobulin domain of Cluster of Differentiation (CD) 33 and related Siglecs; member of the C2-set of IgSF domains. The members here are composed of the second immunoglobulin (Ig) domain of Cluster of Differentiation (CD) 33 (also known as sialic-acid binding immunoglobulin type-lectin 3 (Siglec-3)) and related Siglecs. CD33, a Siglec family member, is a well-known immunotherapeutic target in acute myeloid leukemia (AML). It is an inhibitory sialoadhesin expressed in human leukocytes of the myeloid lineage and some lymphoid subsets, including natural killer (NK) cells. Siglecs are primarily expressed on immune cells and recognize sialic acid-containing glycan ligands. Siglecs are organized as an extracellular module composed of Ig-like domains (an N-terminal variable set of Ig-like carbohydrate recognition domains, and 1 to 16 constant Ig-like domains), followed by transmembrane and short cytoplasmic domains. Human Siglecs are classified into two subgroups, one subgroup is comprised of sialoadhesin (Siglec-1), CD22 (Siglec-2), and MAG (Siglec-4, myelin-associated glycoprotein), the other subgroup is comprised of CD33-related Siglecs which include CD33 (Siglec-3) and human Siglecs 5-11. CD33 (Siglec-3) is the smallest Siglec member. It preferentially binds to alpha2-6- and alpha2-3-sialylated glycans and strongly binds to sialylated ligands on leukemic cell lines. Ig Superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. This group includes CD33-related Siglecs which belong to the C2-set of IgSF domains. Unlike the C1-set, the C2-set structures do not have a D strand. 94 matched cddid_all.tbl CDD cd20988 cd20988 409580 IgV_TCR_gammadelta "Gammadelta T-cell antigen receptor, variable (V) domain. The members here are composed of the immunoglobulin (Ig) variable (V) domain of the gamma/delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha/beta TCRs, but a small subset contain gamma/delta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma/delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing, and MHC independently of the bound peptide. Gamma/delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain standard Ig superfamily V-set AGFCC'C""/DEB domain topology. " 114 matched cddid_all.tbl CDD cd20989 cd20989 409581 IgV_1_Nectin-2_NecL-5_like_CD112_CD155 First immunoglobulin variable (IgV) domain of nectin-2, nectin-like protein 5, and similar domains. The members here are composed of the second immunoglobulin (Ig) domain of nectin-2 (also known as poliovirus receptor related protein 2 or Cluster of Differentiation 112 (CD112)), nectin-like protein 5 (CD155), and similar proteins. Nectins and Nectin-like molecules are a family of Ca(2+)-independent immunoglobulin-like transmembrane glycoproteins belonging to the class of adhesion receptors, consisting of nine members (nectins 1 through 4 and nectin-like proteins 1 through 5). Nectins are synaptic cell adhesion molecules (CAMs) which facilitate adhesion and signaling at various intracellular junctions. Nectins form homophilic cis-dimers, followed by homophilic and heterophilic trans-dimers involved in cell-cell adhesion. Nectin-2 and nectin-3 localize at Sertoli-spermatid junctions where they form heterophilic trans-interactions between the cells that are essential for the formation and maintenance of the junctions and for spermatid development. CD155 is the fifth member in the nectin-like molecule family, and functions as the receptor of poliovirus; therefore, CD155 is also referred to as Necl-5, or PVR. In contrast to all other family members, CD155 lacks self-adhesion capacity, yet it shares with nectins the feature to interact with other nectins. For instance, CD155 heterophilically trans-interacts with nectin-3, thereby contributing significantly to the establishment of adherens junctions between epithelial cells. This group belongs to the Constant 1 (C1)-set of IgSF domains, which has one beta-sheet that is formed by strands A-B-E-D and the other strands by G-F-C-C'. 112 matched cddid_all.tbl CDD cd20990 cd20990 409582 IgI_2_Palladin_C "Second C-terminal immunoglobulin (Ig)-like domain of palladin; member of the I-set of Ig superfamily (IgSF) domains. The members here are composed of the C-terminal immunoglobulin (Ig)-like domain of palladin. Palladin belongs to the palladin-myotilin-myopalladin family. Proteins belonging to this family contain multiple Ig-like domains and function as scaffolds, modulating actin cytoskeleton. Palladin binds to alpha-actinin ezrin, vasodilator-stimulated phosphoprotein VASP, SPIN90 (also known as DIP or mDia interacting protein), and Src. Palladin also binds F-actin directly, via its Ig3 domain. Palladin is expressed as several alternatively spliced isoforms, having various combinations of Ig-like domains, in a cell-type-specific manner. It has been suggested that palladin's different Ig-like domains may be specialized for distinct functions. This group belongs to the I-set of IgSF domains, having A-B-E-D strands in one beta-sheet and A'-G-F-C-C' in the other. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C"" strand." 91 matched cddid_all.tbl CDD cd20991 cd20991 409583 Ig1_IL1R_like First immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R), and similar domains. The members here are composed of the first immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R). IL-1 alpha and IL-1 beta are cytokines which participate in the regulation of inflammation, immune responses, and hematopoiesis. These cytokines bind to the IL-1 receptor type 1 (IL1R1), which is activated on additional association with interleukin-1 receptor accessory protein (IL1RAP). IL-1 also binds a second receptor designated type II (IL1R2). Mature IL1R1 consists of three Ig-like domains, a transmembrane domain, and a large cytoplasmic domain. Mature IL1R2 is organized similarly except that it has a short cytoplasmic domain. The latter does not initiate signal transduction. IL-1 receptor antagonist (IL-1RA), a naturally occurring cytokine, is widely expressed and binds to IL-1 receptors, inhibiting the binding of IL-1 alpha and IL-1 beta. 91 matched cddid_all.tbl CDD cd20992 cd20992 409584 Ig1_IL1R_like First immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R), and similar domains. The members here are composed of the first immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R). IL-1 alpha and IL-1 beta are cytokines which participate in the regulation of inflammation, immune responses, and hematopoiesis. These cytokines bind to the IL-1 receptor type 1 (IL1R1), which is activated on additional association with interleukin-1 receptor accessory protein (IL1RAP). IL-1 also binds a second receptor designated type II (IL1R2). Mature IL1R1 consists of three Ig-like domains, a transmembrane domain, and a large cytoplasmic domain. Mature IL1R2 is organized similarly except that it has a short cytoplasmic domain. The latter does not initiate signal transduction. A naturally occurring cytokine IL-1RA (IL-1 receptor antagonist) is widely expressed and binds to IL-1 receptors, inhibiting the binding of IL-1 alpha and IL-1 beta. 108 matched cddid_all.tbl CDD cd20993 cd20993 409585 Ig2_IL-1RAP_like Second immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R), and similar domains. The members here are composed of the second immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R). IL-1 alpha and IL-1 beta are cytokines which participate in the regulation of inflammation, immune responses, and hematopoiesis. These cytokines bind to the IL-1 receptor type 1 (IL1R1), which is activated on additional association with interleukin-1 receptor accessory protein (IL1RAP). IL-1 also binds a second receptor designated type II (IL1R2). Mature IL1R1 consists of three IG-like domains, a transmembrane domain, and a large cytoplasmic domain. Mature IL1R2 is organized similarly except that it has a short cytoplasmic domain. The latter does not initiate signal transduction. A naturally occurring cytokine IL-1RA (IL-1 receptor antagonist) is widely expressed and binds to IL-1 receptors, inhibiting the binding of IL-1 alpha and IL-1 beta. This group also contains ILIR-like 1 (IL1R1L) which maps to the same chromosomal location as IL1R1 and IL1R2. 93 matched cddid_all.tbl CDD cd20994 cd20994 409586 Ig2_IL1R_like Second immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R), and similar domains. The members here are composed of the second immunoglobulin (Ig)-like domain of interleukin-1 receptor (IL1R). IL-1 alpha and IL-1 beta are cytokines which participate in the regulation of inflammation, immune responses, and hematopoiesis. These cytokines bind to the IL-1 receptor type 1 (IL1R1), which is activated on additional association with interleukin-1 receptor accessory protein (IL1RAP). IL-1 also binds a second receptor designated type II (IL1R2). Mature IL1R1 consists of three IG-like domains, a transmembrane domain, and a large cytoplasmic domain. Mature IL1R2 is organized similarly except that it has a short cytoplasmic domain. The latter does not initiate signal transduction. A naturally occurring cytokine IL-1RA (IL-1 receptor antagonist) is widely expressed and binds to IL-1 receptors, inhibiting the binding of IL-1 alpha and IL-1 beta. This group also contains ILIR-like 1 (IL1R1L) which maps to the same chromosomal location as IL1R1 and IL1R2. 94 matched cddid_all.tbl CDD cd20995 cd20995 409587 IgI_N_ICAM-2 N-terminal immunoglobulin domain of the intercellular adhesion molecules ICAM-2 (Cluster of Differentiation 102 or CD102); member of the I-set of IgSF domains. The members here are composed of the N-terminal immunoglobulin domain of the intercellular adhesion molecules ICAM-2 (Cluster of Differentiation 102 or CD102). The intercellular adhesion molecules ICAM-1 (Cluster of Differentiation 54 or CD54), ICAM-2 and ICAM-3 (Cluster of Differentiation 50 or CD50) mediate a variety of critical intercellular adhesion events in the immune system through interactions with their counter-receptors, the beta2-integrins LFA-1 (CD11a/CD18), Mac-1 (CD11b/CD18), p150,95 (CD11c/CD18), and CD11d/CD18. The ICAMs are type I transmembrane glycoproteins belonging to the immunoglobulin superfamily (IgSF). The binding of the ICAM family members with the beta2-integrins physically stabilizes interactions between pairs of T and B cells, T cells and antigen-presenting cells (APCs), and brings effector cells such as cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells into close proximity to their target cells. All three ICAMs share a common polypeptide homology and structural motif, and the ability to bind LFA-1. The distinct functional role of each ICAM is affected by their relative affinities for LFA-1 (ICAM-1 > ICAM-2 > ICAM-3). ICAM-1 is expressed in most tissues at low levels, and expression is increased by inflammatory cytokines. In contrast, ICAM-2 is expressed predominantly on endothelium and leukocytes (except neutrophils), and its expression generally is not responsive to cytokines. ICAM-3 is expressed on leukocytes and Langerhans cells, but not on resting, cytokine-induced endothelium, or nonhematopoietic tissues. 83 matched cddid_all.tbl CDD cd20996 cd20996 409588 IgI_N_ICAM-1 N-terminal immunoglobulin domain of the intercellular adhesion molecules ICAM-1 (Cluster of Differentiation 54 or CD54); member of the I-set of IgSF domains. The members here are composed of the N-terminal immunoglobulin domain of the intercellular adhesion molecules ICAM-1 (Cluster of Differentiation 54 or CD54). The intercellular adhesion molecules ICAM-1, ICAM-2 (Cluster of Differentiation 102 or CD102) and ICAM-3 (Cluster of Differentiation 50 or CD50) mediate a variety of critical intercellular adhesion events in the immune system through interactions with their counter-receptors, the beta2-integrins LFA-1 (CD11a/CD18), Mac-1 (CD11b/CD18), p150,95 (CD11c/CD18), and CD11d/CD18. The ICAMs are type I transmembrane glycoproteins belonging to the immunoglobulin superfamily (IgSF). The binding of the ICAM family members with the beta2-integrins physically stabilizes interactions between pairs of T and B cells, T cells and antigen-presenting cells (APCs), and brings effector cells such as cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells into close proximity to their target cells. All three ICAMs share a common polypeptide homology and structural motif, and the ability to bind LFA-1. The distinct functional role of each ICAM is affected by their relative affinities for LFA-1 (ICAM-1 > ICAM-2 > ICAM-3). ICAM-1 is expressed in most tissues at low levels, and expression is increased by inflammatory cytokines. In contrast, ICAM-2 is expressed predominantly on endothelium and leukocytes (except neutrophils), and its expression generally is not responsive to cytokines. ICAM-3 is expressed on leukocytes and Langerhans cells, but not on resting, cytokine-induced endothelium, or nonhematopoietic tissues. 82 matched cddid_all.tbl CDD cd20997 cd20997 409589 IgI_N_ICAM-3 N-terminal immunoglobulin domain of the intercellular adhesion molecules ICAM-3 (Cluster of Differentiation 50 or CD50); member of the I-set of IgSF domains. The members here are composed of the N-terminal immunoglobulin domain of the intercellular adhesion molecules ICAM-3 (Cluster of Differentiation 50 or CD50). The intercellular adhesion molecules ICAM-1 (Cluster of Differentiation 54 or CD54), ICAM-2 (Cluster of Differentiation 102 or CD102) and ICAM-3 mediate a variety of critical intercellular adhesion events in the immune system through interactions with their counter-receptors, the beta2-integrins LFA-1 (CD11a/CD18), Mac-1 (CD11b/CD18), p150,95 (CD11c/CD18), and CD11d/CD18. The ICAMs are type I transmembrane glycoproteins belonging to the immunoglobulin superfamily (IgSF). The binding of the ICAM family members with the beta2-integrins physically stabilizes interactions between pairs of T and B cells, T cells and antigen-presenting cells (APCs), and brings effector cells such as cytotoxic T lymphocytes (CTLs) and natural killer (NK) cells into close proximity to their target cells. All three ICAMs share a common polypeptide homology and structural motif, and the ability to bind LFA-1. The distinct functional role of each ICAM is affected by their relative affinities for LFA-1 (ICAM-1 > ICAM-2 > ICAM-3). ICAM-1 is expressed in most tissues at low levels, and expression is increased by inflammatory cytokines. In contrast, ICAM-2 is expressed predominantly on endothelium and leukocytes (except neutrophils), and its expression generally is not responsive to cytokines. ICAM-3 is expressed on leukocytes and Langerhans cells, but not on resting, cytokine-induced endothelium, or nonhematopoietic tissues. 85 matched cddid_all.tbl CDD cd20998 cd20998 409590 IgC1_MHC_II_beta_I-E Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) I-E; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) I-E. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). I-A and I-E molecules have the same basic features insofar as peptide loading and presentation, although each interacts with distinctly different sets of peptides. They also differ in that there is a relatively high incidence of deletion of the I-E gene in both inbred strains of mice as well as wild mice and the lack of the reverse situation i.e. the deletion of I-A genes. A detailed structural understanding of the similarities and differences between I-A and the paralogous I-E could help illuminate the respective roles these molecules play in peptide presentation and T cell activation. Mouse I-Ag7 has a genetic susceptibility to autoimmune diabetes due to its small, uncharged amino acid residue at position 57 of their beta chain which results in the absence of a salt bridge between beta 57 and Arg alpha 76, which is adjacent to the P9 pocket of the peptide-binding groove. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure. 99 matched cddid_all.tbl CDD cd21000 cd21000 409591 IgC1_MHC_II_beta_HLA-DR Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DR; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DR. HLA-DR is an MHC class II cell surface receptor encoded by the human leukocyte antigen complex on chromosome 6 region 6p21.31. HLA-DR is also involved in several autoimmune conditions, disease susceptibility, and disease resistance including seronegative-rheumatoid arthritis, penicillamine-induced myasthenia, schizophrenia, Goodpasture syndrome, systemic lupus erythematosus, Alzheimers, tuberculoid leprosy, and Hashimoto's thyroiditis. HLA-DR molecules are upregulated in response to signaling. HLA-DR is an alphabeta heterodimer cell surface receptor, each subunit of which contains two extracellular domains, a membrane-spanning domain, and a cytoplasmic tail. Both alpha and beta chains are anchored in the membrane. The DR beta chain is encoded by 4 loci, however no more than 3 functional loci are present in a single individual, and no more than two on a single chromosome. Sometimes an individual may only possess 2 copies of the same locus, DRB1*. The HLA-DRB1 locus is ubiquitous and encodes a very large number of functionally variable gene products (HLA-DR1 to HLA-DR17). The HLA-DRB3 locus encodes the HLA-DR52 specificity, is moderately variable and is variably associated with certain HLA-DRB1 types. The HLA-DRB4 locus encodes the HLA-DR53 specificity, has some variation, and is associated with certain HLA-DRB1 types. The HLA-DRB5 locus encodes the HLA-DR51 specificity, which is typically invariable, and is linked to the HLA-DR2 types. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure. 96 matched cddid_all.tbl CDD cd21001 cd21001 409592 IgC1_MHC_II_beta_HLA-DQ_I-A Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DQ and I-A; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of human histocompatibility antigen (HLA) DQ and mouse I-A. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). I-A and I-E have the same basic features insofar as peptide loading and presentation, they differ in that each interacts with distinctly different sets of peptides, and in the incidence of deletion of their genes. A structural understanding of the similarities and differences between I-A and I-E may help with understanding their roles in peptide presentation and T cell activation. Mouse I-Ag7 has a genetic susceptibility to autoimmune diabetes due to its small, uncharged amino acid residue at position 57 of their beta chain which results in the absence of a salt bridge between beta 57 and Arg alpha 76, which is adjacent to the P9 pocket of the peptide-binding groove. Human HLA-DR, -DQ, and -DP are about 70% similar to each other. HLA-DQ (DQ) is a cell surface receptor protein found on antigen presenting cells. It is an alphabeta heterodimer of type MHC class II. The alpha and beta chains are encoded by two loci, HLA-DQA1 and HLA-DQB1, that are adjacent to each other on chromosome band 6p21.3. A person often produces two alpha-chain and two beta chain variants and thus 4 isoforms of DQ. HLA-DQ is involved in the autoimmune diseases celiac disease and diabetes mellitus type. DQ is one of several antigens involved in rejection of organ transplants. DQ2 is encoded by the HLA-DQB1*02 allele group. DQ6 is encoded by the HLA-DQB1*06 allele group. DQ2 beta-chains combine with alpha-chains, encoded by genetically linked HLA-DQA1 alleles, to form the cis-haplotype isoforms. These isoforms, nicknamed DQ2.2 and DQ2.5, are also encoded by the DQA1*0201 and DQA1*0501 genes, respectively. DQ6 beta-chains combine with alpha-chains, encoded by genetically linked HLA-DQA1 alleles, to form the cis-haplotype isoforms. For DQ6, however, cis-isoform pairing only occurs with DQ1 alpha-chains. There are many haplotypes of DQ6. Susceptibility to Leptospirosis infection was found associated with undifferentiated DQ6. DQ8 is determined by the antibody recognition of beta8 and this generally detects the gene product of DQB1*0302. DQ8 is commonly linked to autoimmune disease in the human population. DQ8 is the second most predominant isoform linked to celiac disease and the DQ most linked to Type 1 diabetes. DQ8 increases the risk for rheumatoid arthritis and is linked to the primary risk locus for RA, HLA-DR4. DR4 also plays an important role in Type 1 diabetes. DQ8 is a split antigen of the DQ3 broad antigen. MHC class II molecules play a key role in the initiation of the antigen-specific immune response. They are expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice, and induced in nonprofessional APCs, such as keratinocyctes; they are expressed on the surface of activated human T cells and on T cells from other species. MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes; these peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC, and bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure. 97 matched cddid_all.tbl CDD cd21002 cd21002 409593 IgC1_MHC_II_beta_HLA-DM Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DM; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DM. Human HLA-DM plays a critical role in antigen presentation to CD4 T cells by catalyzing the exchange of peptides bound to MHC class II molecules. Type 1 diabetes is correlated with DM activation and it is also implicated in viral infections such as herpes simplex virus, celiac disease, multiple sclerosis, other autoimmune diseases, and leukemia. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure. 97 matched cddid_all.tbl CDD cd21003 cd21003 409594 IgC1_MHC_II_beta_HLA-DP Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DP; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DP. HLA class II histocompatibility antigen, DP(W2) beta chain is a protein that in humans is encoded by the HLA-DPB1 gene. It plays a central role in the immune system by presenting peptides derived from extracellular proteins. MHC class II molecules are encoded by three different loci, HLA-DR, -DQ, and -DP, which are about 70% similar to each other. HLA-DP is an alphabeta heterodimer cell-surface receptor. Each DP subunit (alpha-subunit, beta-subunit) is composed of a alpha-helical N-terminal domain, an IgG-like beta sheet, a membrane spanning domain, and a cytoplasmic domain. The alpha-helical domain forms the sides of the peptide binding groove. The beta sheet regions form the base of the binding groove and the bulk of the molecule as well as the inter-subunit (non-covalent) binding region. Individuals carrying the MHCII allele, HLA-DP2, are at risk for chronic beryllium disease (CBD), a debilitating inflammatory lung condition caused by the reaction of CD4 T cells to inhaled beryllium. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure. 96 matched cddid_all.tbl CDD cd21004 cd21004 409595 IgC1_MHC_II_alpha_HLA_DO HLA class II histocompatibility antigen DO alpha; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the nonclassical MHC class II (MHCII) protein, HLA-DO, which binds HLA-DM and influences the repertoire of peptides presented by MHCII proteins. In complex with HLA-DM, HLA-DO adopts a classical MHCII structure, with alterations near the a subunit's 310 helix. HLA-DO binds to HLA-DM at the same sites implicated in MHCII interaction, and kinetic analysis showed that HLA-DO acts as a competitive inhibitor by acting as a substrate mimic. Though more remains to be elucidated about the function of HLA-DO, its unique distribution in the mammalian body namely, the exclusive expression of HLA-DO in B cells, thymic medullary epithelial cells, and dendritic cells indicate that it may be of physiological importance and has inspired further research. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. 95 matched cddid_all.tbl CDD cd21005 cd21005 409596 IgC1_MHC_II_alpha_I-EK Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) I-E; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) I-E. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure. 95 matched cddid_all.tbl CDD cd21006 cd21006 409597 IgC1_MHC_II_alpha_I-A Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) I-A; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) I-A. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). I-A and I-E molecules have the same basic features insofar as peptide loading and presentation, although each interacts with distinctly different sets of peptides. They also differ in that there is a relatively high incidence of deletion of the I-E a gene in both inbred strains of mice as well as wild mice and the lack of the reverse situation i.e. the deletion of I-A genes. A detailed structural understanding of the similarities and differences between I-A and the paralogous I-E could help illuminate the respective roles these molecules play in peptide presentation and T cell activation. Mouse I-Ag7 has a genetic susceptibility to autoimmune diabetes due to its small, uncharged amino acid residue at position 57 of their beta chain which results in the absence of a salt bridge between beta 57 and Arg alpha 76, which is adjacent to the P9 pocket of the peptide-binding groove. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure. 95 matched cddid_all.tbl CDD cd21007 cd21007 409598 IgC1_MHC_II_alpha_HLA-DR Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) DR; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) DR. MHC class II molecules are encoded by three different loci, HLA-DR, -DQ, and -DP, which are about 70% similar to each other. HLA-DR is a cell surface receptor protein found on antigen presenting cells. It is an alphabeta heterodimer of type MHC class II. The alpha and beta chains are encoded by two loci, HLA-DRA1 and HLA-DRB1, that are adjacent to each other on chromosome band 6p21.31. Susceptibility to multiple sclerosis and rheumatoid arthritis are associated with the human histocompatibility leukocyte antigen HLA-DR2 and HLA-DR4, respectively. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure. 95 matched cddid_all.tbl CDD cd21008 cd21008 409599 IgC1_MHC_II_alpha_HLA-DQ Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) DQ and related proteins; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) DQ. MHC class II molecules are encoded by three different loci, HLA-DR, -DQ, and -DP, which are about 70% similar to each other. HLA-DQ (DQ) is a cell surface receptor protein found on antigen presenting cells. It is an alphabeta heterodimer of type MHC class II. The alpha and beta chains are encoded by two loci, HLA-DQA1 and HLA-DQB1, that are adjacent to each other on chromosome band 6p21.3. A person often produces two alpha-chain and two beta chain variants and thus 4 isoforms of DQ. Two autoimmune diseases in which HLA-DQ is involved are celiac disease and diabetes mellitus type 1. DQ is one of several antigens involved in rejection of organ transplants. DQ8 is a split antigen of the DQ3 broad antigen. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure. 95 matched cddid_all.tbl CDD cd21009 cd21009 409600 IgC1_MHC_II_alpha_HLA-DM Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) DM; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) DM. Human HLA-DM, also known as H2-M in mice, plays a critical role in antigen presentation to CD4 T cells by catalyzing the exchange of peptides bound to MHC class II molecules. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure. 94 matched cddid_all.tbl CDD cd21010 cd21010 409601 IgC1_MHC-like_ZAG Immunoglobulin domain of Zn-alpha2-glycoprotein (ZAG); member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin domain of Zn-alpha2-glycoprotein (ZAG). ZAG is a soluble protein that is present in serum and other body fluids. ZAG stimulates lipid degradation in adipocytes and causes the extensive fat losses associated with some advanced cancers. The 2.8 angstrom crystal structure of ZAG resembles a class I major histocompatibility complex (MHC) heavy chain, but ZAG does not bind the class I light chain beta-2-microglobulin. The ZAG structure includes a large groove analogous to class I MHC peptide binding grooves. Instead of a peptide, the ZAG groove contains a nonpeptidic compound that may be implicated in lipid catabolism under normal or pathological conditions. IgC_MHC_I_alpha3; Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. 93 matched cddid_all.tbl CDD cd21011 cd21011 409602 IgC1_MHC-like_FcRn immunoglobulin domain of neonatal Fc receptor, major histocompatibility complex (MHC)-like; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin domain of neonatal Fc receptor (FcRn). FcRn performs two distinct functions: the transport of maternal immunoglobulin G (IgG) to pre- or neonatal mammals which provides passive immunity and protection of IgG from normal serum protein catabolism. FcRn is related to class I MHC proteins, but lacks a functional peptide binding groove. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. 93 matched cddid_all.tbl CDD cd21012 cd21012 409603 IgC1_MHC_H-2_TLA H-2 class I histocompatibility complex TLA (thymus leukemia antigen); member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the major histocompatibility complex (MHC) H-2 class I histocompatibility complex TLA (thymus leukemia antigen). The murine MHC class I histocompatibility TLA (Thymus leukemia antigen), which is encoded in the T region by T3 and T18 genes, is expressed mainly by intestinal epithelial cells and thymocytes. The murine TLAs are class I, beta-2-microglobulin-associated glycoproteins. The TLA function is not defined by antigen presentation, but rather by its relatively high affinity binding to CD8-alpha-alpha compared with CD8-alpha-beta. The existence of a human homolog for murine TLA remains unresolved. This group is a member of the C1-set Ig domains, which have one beta sheet that is formed by strands A, B, E, and D and the other strands by G, F, C, and C'. 95 matched cddid_all.tbl CDD cd21013 cd21013 409604 IgC1_MHC_Ib_Qa-1 Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1 and similar proteins; member of the C1-set of Ig superfamily (IgSF) domains. Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1 and similar proteins. Qa-1 presents hydrophobic peptides including Qdm derived from the leader sequence of classical MHC I molecules for immune surveillance by NK cells. Qa-1 bound peptides derived from the TCR Vbeta8.2 of activated T cells also activates CD8+ regulatory T cells to control autoimmunity and maintain self-tolerance. Four allotypes of Qa-1 (Qa-1a-d) are expressed that are highly conserved in sequence but have several variations that could affect peptide binding to Qa-1 or TCR recognition. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. 97 matched cddid_all.tbl CDD cd21014 cd21014 409605 IgC1_MHC_Ib_Qa-2 Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-2; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of QA-2. Qa-2 is a nonclassical MHC Ib antigen, which has been implicated in both innate and adaptive immune responses, as well as embryonic development. Qa-2 has an unusual peptide binding specificity in that it requires two dominant C-terminal anchor residues and is capable of associating with a substantially more diverse array of peptide sequences than other nonclassical MHC. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. 94 matched cddid_all.tbl CDD cd21015 cd21015 409606 IgC1_MHC_Ia_RT1-Aa Class Ia major histocompatibility complex (MHC) immunoglobulin domain of RT1-Aa; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of RT1-Aa. While most mammalian species transport these peptides into the ER via a single allele of TAP, rats have evolved different TAPs, TAP-A and TAP-B, RT1-Aa and RT1-A1c, which are associated with TAP-A and TAP-B. The rat MHC class Ia molecule RT1-Aa has the unusual capacity to bind long peptides ending in arginine, such as MTF-E, a thirteen-residue, maternally transmitted minor histocompatibility antigen. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. 95 matched cddid_all.tbl CDD cd21016 cd21016 409607 IgC1_MHC_Ib_T10_T22_like Class Ib major histocompatibility complex (MHC) immunoglobulin domain of T10, T22, and similar proteins; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of the murine H-2T-encoded T10, T22, and similar proteins. T10 and T22 are highly related nonclassical major histocompatibility complex (MHC) class Ib proteins that bind to certain gammadelta T cell receptors (TCRs) in the absence of other components. Classical MHC class I (class Ia) molecules participate in immune responses by presenting peptide antigens to cytolytic alpha beta T cells. Many nonclassical MHC class I (class Ib) molecules have distinct antigen-binding capabilities, suggesting that they have evolved for specific tasks that are distinct from those of MHC class Ia. Members of the IgC family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, and the IgC domain is involved in oligomerization and molecular interactions. 97 matched cddid_all.tbl CDD cd21017 cd21017 409608 IgC1_MHC_Ia_MIC-A_MIC-B Class Ia major histocompatibility complex (MHC) immunoglobulin domain of MIC-A and MIC-B; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of MIC-A and MIC-B. MIC-A and MIC-B are homologs that serve as stress-inducible antigens on epithelial and epithelially derived cells. Both serve as ligands for the widely expressed activating immunoreceptor NKG2D, a C-type lectin-like activating immunoreceptor. MIC-B is very similar in structure to MIC-A and likely interacts with NKG2D in an analogous manner. The interdomain flexibility observed in the MIC-A structures, a feature unique to MIC proteins among MHC class I proteins and homologs, is also displayed by MIC-B, with an interdomain relationship intermediate between the two examples of MIC-A structures. Mapping sequence variations onto the structures of MIC-A and MIC-B reveals patterns completely distinct from those displayed by classical MHC class I proteins, with a number of substitutions falling on positions likely to affect interactions with NKG2D, but with other positions lying distant from the NKG2D binding sites or buried within the core of the proteins. Members of the IgC family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding and the IgC domain is involved in oligomerization and molecular interactions. 95 matched cddid_all.tbl CDD cd21018 cd21018 409609 IgC1_MHC_Ia_H2Db_H2Ld Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) H2Db and H2Ld; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) H2Db and H2Ld. H-2Ld complexed with peptide QL9 (or p2Ca) and complexed with influenza virus peptide NP366-374 (ASNEN-METM), respectively are high-affinity alloantigens for the 2C T cell receptor (TCR). The a1-a2 super domains of H-2Ld, H-2Db, and H-2Kb closely superimpose. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. 95 matched cddid_all.tbl CDD cd21019 cd21019 409610 IgC1_MHC_Ia_H-2Kb Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H-2Kb; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H-2Kb. H-2Kb is an alloantigen for the 2C T cell receptor (TCR). H-2Kb forms a complex with beta-2-microglobulin, and a peptide, including VSV-8 (RGYVYNGL), SEV-9 (FAPGNYPAL), and OVA-8 (SIINFEKL). Comparison of the OVA-8, VSV-8, and SEV-9 complexes with H-2Kb indicates that four side chains (Lys-66, Glu-152, Arg-155, and Trp-167) adopt peptide-specific conformations. H-2Kb paralogs include H-2Db, H-2Kbml and H-2KbI1s. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. 94 matched cddid_all.tbl CDD cd21020 cd21020 409611 IgC1_MHC_Ia_H-2Dd Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H2-Dd; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H2-Dd. Mouse MHC is composed of 11 subclasses. It includes the classical MHC class I (MHC-Ia) that comprises H-2D, H-2K and H-2L subclasses, the non-classical MHC class I (MHCIb) that comprises H-2Q, H-2M and H-2T subclasses, the classical MHC class II (MHC-IIa) that includes H-2A(I-A) and H-2E(I-E) subclasses, and the non-classical MHC class II (MHC-IIb) comprises H-2M and H-2O. H-2K, H-2D, and H-2L are 80 to 90% homologous at the amino acid level yet appear to be involved in different recognition reactions and are differentially expressed on lymphoid cells. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. 95 matched cddid_all.tbl CDD cd21021 cd21021 409612 IgC1_MHC_Ib_HLA-H Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen H; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen H (HLA-H). HLA-H (also known as hereditary hemochromatosis protein; HFE) is a major histocompatibility complex (MHC) class I-like protein that is mutated in Hereditary Hemochromatosis. HFE is a protein of 343 amino acids that includes a signal peptide, an extracellular transferrin receptor-binding region (a1 and a2), an immunoglobulin-like domain (a3), a transmembrane region, and a short cytoplasmic tail. HFE binds beta-2-microglobulin to form a heterodimer expressed at the cell surface. It binds transferrin receptor (TFRC) in its extracellular alpha1-alpha2 domain. HFE plays an important part in the regulation of hepcidin expression in response to iron overload and the liver is important in the pathophysiology of HFE-associated hemochromatosis. Nine HFE splicing variants have been reported with transcripts lacking exon 2 or exon 3, or exons 2-3, 2-4, or 2-5. Diverse mutations involving HFE introns and exons discovered in persons with hemochromatosis or their family members cause or probably cause high iron phenotypes. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. 94 matched cddid_all.tbl CDD cd21022 cd21022 409613 IgC1_MHC_Ia_HLA-G Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) G; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) G. HLA-G histocompatibility antigen (also known as human leukocyte antigen G ; HLA-G) is a protein that in humans is encoded by the HLA-G gene. HLA-G belongs to the HLA nonclassical class I heavy chain paralogs. This class I molecule is a heterodimer consisting of a heavy chain and light chain, beta-2-microglobulin. The heavy chain is anchored in the membrane. HLA-G may play a role in immune tolerance in pregnancy, being expressed in the placenta by extravillous trophoblast cells (EVT), while the classical MHC class I genes (HLA-A and HLA-B) are not. Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I and class II. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. MHC class II molecules play a key role in the initiation of the antigen-specific immune repose. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure. 94 matched cddid_all.tbl CDD cd21023 cd21023 409614 IgC1_MHC_Ia_HLA-F Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) F; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen alpha chain F (HLA-F). HLA-F, encoded by the HLA-F gene in humans, belongs to the non-classical HLA class I heavy chain paralogs. This class I molecule mainly exists as a heterodimer associated with the invariant light chain beta-2-microglobulin. HLA-F molecules can interact with both activating and inhibitory receptors on immune cells, such as NK cells, and can present a diverse panel of peptides. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. 98 matched cddid_all.tbl CDD cd21024 cd21024 409615 IgC1_MHC_Ib_HLA-E Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) E; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) E. HLA-E is the first human class Ib major histocompatibility complex molecule to be crystallized. Like other MHC class I molecules, HLA-E is a heterodimer consisting of an a heavy chain and light chain beta-2-microglobulin. HLA-E is highly conserved and almost nonpolymorphic, and has recently been shown to be the first specialized ligand for natural killer cell receptors. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. 95 matched cddid_all.tbl CDD cd21025 cd21025 409616 IgC1_MHC_Ib_HLA-Cw3-4 Class Ib major histocompatibility complex (MHC) immunoglobulin domain of HLA-Cw3 and HLA-Cw4; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of HLA-Cw3 and HLA-Cw4. HLA-C belongs to the MHC class I heavy chain receptors. The C receptor is a heterodimer consisting of a HLA-C mature gene product and beta-2-microglobulin. The mature C chain is anchored in the membrane. MHC Class I molecules, like HLA-C, are expressed in nearly all cells, and present small peptides to the immune system which surveys for non-self peptides. HLA-C is a locus on chromosome 6, which encodes for a large number of HLA-C alleles that are Class-I MHC receptors. Class Ib histocompatibility leukocyte antigens (HLA)-Cw3 and (HLA)-Cw4 are ligands for the natural killer (NK) cell inhibitory receptors KIR2DL2 and KIR2DL1, respectively. HLA-Cw3 and related alleles (HLA-Cw1, -Cw7, and -Cw8) contain Ser77 and Asn80 and interact with KIR that are reactive with the GL183 antibody Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. HLA-Cw4 and related alleles (HLA-Cw2, -Cw5, and -Cw6) have Asn77 and Lys80 and are recognized by KIR reactive with the EB6 15 or HP-3E4 16 antibody. Members of the IgC family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, and the IgC domain is involved in oligomerization and molecular interactions. 96 matched cddid_all.tbl CDD cd21026 cd21026 409617 IgC1_MHC_Ia_HLA-B Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) B and similar proteins; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) B and similar proteins. The classical class I molecules (HLA-A, -B, and -C) are responsible for the presentation of endogenous antigen to CD8+ T cells. The receptor is a heterodimer, and is composed of a heavy alpha chain and smaller beta chain. The alpha chain is encoded by a variant HLA-B gene, and the beta chain (beta-2-microglobulin) is an invariant beta-2-microglobulin molecule. The beta-2-microglobulin protein is coded for by a separate region of the human genome. Human leukocyte antigen (HLA) B*3501 (B35) is a common human allele involved in mediating protective immunity against HIV. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. 97 matched cddid_all.tbl CDD cd21027 cd21027 409618 IgC1_MHC_Ia_HLA-A Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) A; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) A. The classical class I molecules (HLA-A, -B, and -C) are responsible for the presentation of endogenous antigen to CD8+ T cells. The receptor is a heterodimer, and is composed of a heavy alpha chain and smaller beta chain. The alpha chain is encoded by a variant HLA-A gene, and the beta chain (beta-2-microglobulin) is an invariant beta-2-microglobulin molecule. The beta-2-microglobulin protein is coded for by a separate region of the human genome. HLA-A2 is associated with spontaneous abortions, HIV, and Hodgkin lymphoma. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. 95 matched cddid_all.tbl CDD cd21028 cd21028 409619 IgC1_MHC_I_M144 Class I major histocompatibility complex (MHC) homolog m144; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) homolog m144 class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. 101 matched cddid_all.tbl CDD cd21029 cd21029 409620 IgC1_CD1 Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the immunoglobulin domain of Cluster of Differentiation (CD) 1. CD1 family of transmembrane glycoproteins, are structurally related to the major histocompatibility complex (MHC) proteins and form heterodimers with beta-2-microglobulin. They mediate the presentation of primarily lipid and glycolipid antigens of self or microbial origin to T cells. The human genome contains five CD1 family genes (CD1a, CD1b, CD1c, CD1d, and CD1e) organized in a cluster on chromosome 1. The CD1 family members are thought to differ in their cellular localization and specificity for particular lipid ligands. CD1a localizes to the plasma membrane and to recycling vesicles of the early endocytic system. Alternative splicing results in multiple transcript variants. Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. C1-set Ig domains have one beta sheet that is formed by strands A, B, E, and D and the other strands by G, F, C, and C'. 93 matched cddid_all.tbl CDD cd21030 cd21030 411025 V35-RBD_P-protein-C_like C-terminal RNA-binding domain (RBD) domain of Ebola virus VP35 phosphoprotein and related proteins. This family includes the C-terminal RNA-binding domain (RBD) of the P protein of viruses belonging to the Filoviridae family, such as Ebola virus or Marburg virus. VP35-RBD contains two subdomains: an alpha-helical subdomain and a beta-sheet subdomain. Virus infection typically activates host innate immunity, including the interferon (IFN) signaling pathway; VP35-RBD binds double-stranded RNA (dsRNA) inhibiting IFN-alpha/beta signaling. The family Filoviridae belongs to the order Mononegavirales which are nonsegmented negative-stranded RNA viruses (NNVs). The genomes of NNVs are encapsidated by their nucleocapsid (N) proteins to form N-RNA complexes which serve as a template for transaction and replication. The C-terminus of P protein binds nucleocapsid. P protein plays multiple roles in transcription and translation, which include acting as a chaperone of nascent nucleoprotein (N), and as a cofactor of the viral polymerase (L) where P forms a two-subunit polymerase with a large catalytic subunit (L) and stabilizes the polymerase on its template of N-RNA. 125 matched cddid_all.tbl CDD cd21031 cd21031 411026 MEV_P-protein-C_like C-terminal domain of Measles virus phosphoprotein and related proteins. This family includes the C-terminal domain of the P protein of plant viruses belonging to the Paramyxoviridae family such as measles virus and mumps virus. The family Paramyxoviridae belongs to the order Mononegavirales which are nonsegmented negative-stranded RNA viruses (NNVs). The genomes of NNVs are encapsidated by their nucleocapsid (N) proteins to form N-RNA complexes which serves as a template for transaction and replication. The C-terminus of P protein binds nucleocapsid. P protein plays multiple roles in transcription and translation, which include acting as a chaperone of nascent nucleoprotein (N), and as a cofactor of the viral polymerase (L) where P forms a two-subunit polymerase with a large catalytic subunit (L) and stabilizes the polymerase on its template of N-RNA. Paramyxoviruses have a polycistronic phosphoprotein (P) gene which encodes for proteins in addition to P protein; for example the measles virus P gene encodes for P protein and virulence factor V (MV-V). This domain family includes the unshared C-terminal domain of P protein not present in MV-V. 46 matched cddid_all.tbl CDD cd21032 cd21032 411027 RABV_P-protein-C_like C-terminal domain of Rabies virus phosphoprotein and related proteins. This family includes the C-terminal domain of the P protein of plant viruses belonging to the Rhabdoviridae animal family such as Rabies virus (RABV). RABV P protein is known to counteract the functions of various cellular factors involved in antiviral responses, including STAT1, and interferon-induced promyelocytic leukaemia (PML) protein; the C-terminal domain of the RABV P protein includes STAT1 and PML binding sites. The family Rhabdoviridae belongs to the order Mononegavirales which are nonsegmented negative-stranded RNA viruses (NNVs). The genomes of NNVs are encapsidated by their nucleocapsid (N) proteins to form N-RNA complexes which serves as a template for transaction and replication. The C-terminus of P protein binds nucleocapsid. P protein plays multiple roles in transcription and translation, which include acting as a chaperone of nascent nucleoprotein (N), and as a cofactor of the viral polymerase (L) where P forms a two-subunit polymerase with a large catalytic subunit (L) and stabilizes the polymerase on its template of N-RNA. 105 matched cddid_all.tbl CDD cd21033 cd21033 411028 VSV_P-protein-C_like C-terminal domain of Vesicular stomatitis Indiana virus phosphoprotein and related proteins. This family includes the C-terminal domain of the P protein of plant viruses belonging to the Rhabdoviridae animal family such as Vesicular stomatitis Indiana virus (VSV). The family Rhabdoviridae belongs to the order Mononegavirales which are nonsegmented negative-stranded RNA viruses (NNVs). The genomes of NNVs are encapsidated by their nucleocapsid (N) proteins to form N-RNA complexes which serves as a template for transaction and replication. The C-terminus of P protein binds nucleocapsid. P protein plays multiple roles in transcription and translation, which include acting as a chaperone of nascent nucleoprotein (N), and as a cofactor of the viral polymerase (L) where P forms a two-subunit polymerase with a large catalytic subunit (L) and stabilizes the polymerase on its template of N-RNA. 71 matched cddid_all.tbl CDD cd21035 cd21035 439137 BTHB basic tilted helix bundle (BTHB) domain. BTHB domain is found in the N-terminal region of FKBPs such as FKBP25 and in the core region of E3 ubiquitin ligase HectD1. It adopts a compact 5-helix bundle, hence termed BTHB (Basic Tilted Helix Bundle) domain. In FKBP25, it may have a role in regulating the association state of nucleosomes by interacting with nucleolin. This basic domain in FKBP25 also forms alternative complexes with other chromatin-related proteins, such as the HDAC1, HDAC2, and the transcriptional regulator YY1, the DNA binding activity of which is enhanced on binding FKBP25. Structural analysis of this fold suggests that the DNA binding properties of FKBP25 and HectD1 are presented by the conserved basic region. 64 matched cddid_all.tbl CDD cd21036 cd21036 411029 WH_MUS81 winged helix domain found in crossover junction endonuclease MUS81 and similar proteins. MUS81 is a crossover junction endonuclease that interacts with EME1 (essential meiotic structure-specific endonuclease 1) and EME2, to form a DNA structure-specific endonuclease with substrate preference for branched DNA structures with a 5'-end at the branch nick. The MUS80-EME1 endonuclease maintains genomic integrity in metazoans by cleaving branched DNA structures that can form during mitosis and fission yeast meiosis, and during processing of damaged replication folks. This model corresponds to the winged helix (WH) domain of MUS81, which is responsible for DNA binding. It comprises four helices and two beta strands. 94 matched cddid_all.tbl CDD cd21037 cd21037 411030 MLKL_NTD N-terminal domain of mixed lineage kinase domain-like protein (MLKL) and similar proteins. MLKL is a pseudokinase that does not have protein kinase activity and plays a key role in tumor necrosis factor (TNF)-induced necroptosis, a programmed cell death process. The model corresponds to the MLKL N-terminal region that reveals a four-helix bundle with an additional helix at the top which is likely key for MLKL function. The N-terminal domain binds directly to phospholipids and induces membrane permeabilization. 138 matched cddid_all.tbl CDD cd21039 cd21039 410951 NURR NURR (N-terminal unit for RNA recognition) domain. NURR domain is a self-folding globular RNA-binding domain with an all alpha-helix architecture with a highly conserved negatively charged surface area. It also contains a large hydrophobic cavity and a positively charged surface area as potential epitopes for inter-molecular interactions. NURR domain has been found in Drosophila melanogaster Syncrip and vertebrates heterogeneous nuclear ribonucleoproteins hnRNPR and hnRNPQ. 77 matched cddid_all.tbl CDD cd21044 cd21044 411031 Rab11BD_RAB3IP_like Rab11 binding domain of Rab-3A-interacting protein (RAB3IP), Rab-3A-interacting-like protein 1 (RAB3IL1) and similar proteins. The family includes RAB3IP and RAB3IL1, as well as Rab guanine nucleotide exchange factor SEC2 from yeast. RAB3IP, also called Rabin-3, or SSX2-interacting protein, or Rabin8, acts as a guanine nucleotide exchange factor (GEF) which promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. It mediates the release of GDP from RAB8A and RAB8B but not from RAB3A or RAB5. It modulates actin organization and promotes polarized transport of RAB8A-specific vesicles to the cell surface. RAB3IL1, also called guanine nucleotide exchange factor for Rab-3A (GRAB), or Rab3A-interacting-like protein 1, or Rabin3-like 1, acts as a guanine nucleotide exchange factor (GEF) which promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. As a dual Rab-binding protein, RAB3IL1 could potentially link Rab3 and Rab11 and/or Rab8 and Rab11-mediated intracellular trafficking processes. It may activate RAB3A, a GTPase that regulates synaptic vesicle exocytosis. It may also activate RAB8A and RAB8B. In addition, RAB3IL1 interacts with InsP6K1 and plays a role for InsP7 in vesicle exocytosis. SEC2 is a guanine nucleotide exchange factor for SEC4, catalyzing the dissociation of GDP from SEC4 and also potently promoting binding of GTP. Activation of SEC4 by SEC2 is needed for the directed transport of vesicles to sites of exocytosis. SEC2 binds the Rab GTPase YPT32 but does not have exchange activity on YPT32. The model corresponds to the Rab11a/Rab11b-binding region of family members which lies within the carboxy-terminus, a region distinct from their GEF domain and Rab3a-binding region. 178 matched cddid_all.tbl CDD cd21050 cd21050 410965 ELD_TRPML extracytosolic/lumenal domain (ELD) found in transient receptor potential channel mucolipins (TRPMLs). TRPML family proteins contain a linker between the first two transmembrane helices (S1 and S2), which is called TRPML I-II linker. It forms a tight tetramer that is crucial for full-length TRPMLs assembly and localization. In lysosomes and endosomes, this linker faces the lumen (it is therefore also referred to as the 'luminal linker'); on the plasma membrane, it faces the extracellular solution. TRPML I-II linker has been named as extracytosolic/lumenal domain (ELD). 167 matched cddid_all.tbl CDD cd21055 cd21055 411034 WH_NTD_SMARCB1_like N-terminal winged helix DNA-binding domain found in SMARCB1, PHF10 and similar proteins. The family includes SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (SMARCB1) and PHD finger protein 10 (PHF10), both of which have an N-terminal winged helix DNA-binding domain that is structurally related to the SKI/SNO/DAC domain found in a number of metazoan chromatin-associated proteins. SMARCB1, also termed BRG1-associated factor 47 (BAF47), or integrase interactor 1 protein (INI1), or SNF5, or SNF5L1, is a core component of the BAF (hSWI/SNF) complex, an ATP-dependent chromatin-remodeling complex that plays important roles in cell proliferation and differentiation, in cellular antiviral activities and inhibition of tumor formation. PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is involved in transcription activity regulation by chromatin remodeling. It is a component of the neural progenitors-specific chromatin remodeling complex (npBAF complex) and plays a role in the proliferation of neural progenitors. 80 matched cddid_all.tbl CDD cd21058 cd21058 411038 toxin_MLD_like membrane localization domain (MLD) of Vibrio MARTX, Pasteurella PMT, clostridial glycosylating cytotoxins, toxin effectors BteA (Bordetella T3SS effector A) and related proteins. This family includes membrane localization domains (MLDs) for toxin effectors such as the Rho-inactivation domain of Vibrio MARTX, Pasteurella mitogenic toxin (PMT), where it has been termed PMT C1 domain, and clostridial glycosylating cytotoxins including Clostridium difficile toxins A (TcdA) and B (TcdB), Clostridium novyi alpha-toxin (TcnA), and Clostridium sordellii lethal toxin (TcsL). It also includes the MLD located in the N-terminal minimal membrane-binding fragment of BteA, a type III secretion system (T3SS) effector protein from Bordetella pertussis, the causative agent of whooping cough. 78 matched cddid_all.tbl CDD cd21059 cd21059 411040 LciA-like lactococcin A immunity protein (LciA) and similar proteins. This family includes pore-forming bacteriocin class IId lactococcin A immunity protein (LciA) and similar proteins. The subclass IId is a linear, one-peptide bacteriocin that shares no sequence similarity to the other class II pediocin-like bacteriocins (class IIa), two-peptide bacteriocins (class IIb) or cyclic bacteriocins (class IIc). However, they all induce membrane leakage and cell death by specifically binding the mannose phosphotransferase system (man-PTS) on their target cells. LciA shares the same 4-helical bundle structure as the pediocin-like immunity proteins but has a shorter C-terminal helix and a different surface potential. Also, it has a flexible C-terminal tail that is important for the functionality of the immunity protein. 69 matched cddid_all.tbl CDD cd21060 cd21060 439140 CdiI_NC101 immunity protein of the contact-dependent growth inhibition (CDI) system of Escherichia coli NC101, and similar proteins. CDI toxins are expressed by gram-negative bacteria as part of a mechanism to inhibit the growth of neighboring cells. This model represents the inhibitor (CdiI, also called CdiI immunity protein) of the CdiA effector protein from Escherichia coli NC101. CdiA secretion is dependent on the outer membrane protein CdiB. Upon binding to a receptor on the surface of target bacteria, the CDI toxin is delivered via its C-terminal domain (CdiA-CT). CdiI immunity proteins are intracellular proteins that inactivate the toxin/effector protein. They are specific for their cognate CdiA-CT and do not protect cells from the toxins of other CDI+ bacteria. The CdiI immunity protein binds the CdiA toxin via its C-terminal domain to prevent auto-inhibition. Thus, CDI systems encode a complex network of toxin-immunity protein pairs that are deployed for intercellular competition. The E. coli NC101 CdiI exerts a unique ribonuclease activity that cleaves the single-stranded 3'-end from tRNAs that contain guanine discriminator nucleotides; for this, it requires elongation factor Tu (EF-Tu), an essential and highly conserved translation factor that delivers aminoacyl-tRNAs (aa-tRNA) to the ribosome during protein synthesis. Structure studies suggest the toxin remodels the GTP:EF-Tu:aa-tRNA complexes to free the 3'-end of aa-tRNA for entry into the nuclease active site. 99 matched cddid_all.tbl CDD cd21061 cd21061 410634 7tm_viral_rhodopsin viral rhodopsins and similar proteins, members of the seven-transmembrane GPCR superfamily. This subfamily is composed of viral homologs of proteorhodopsins (PRs), which are blue-light absorbing and green-light absorbing proteins acting as light-driven proton pumps that play a major role in supplying light energy for phototropic marine microorganisms, by a mechanism similar to that of bacteriorhodopsin. Viral proteorhodopsins are predicted to function as sensory rhodopsins that could affect signaling, for example, phototaxis in the infected protists, perhaps stimulating relocation of the infected protists to areas that are rich in nutrients required for virus reproduction. Viral proteorhodopsins are monophyletic and split into two distinct groups, I and II, represented by Phaeocystis globosa virus 12T VirRDTS and Organic Lake phycodnavirus OLPVRII, respectively. PRs belong to the microbial rhodopsin family, also known as type 1 rhodopsins, which also comprise the light-driven inward chloride pump halorhodopsin (HR), the light-gated cation channel channelrhodopsin (ChR), the light-sensor activating transmembrane transducer protein sensory rhodopsin II (SRII), the light-sensor activating soluble transducer protein Anabaena sensory rhodopsin (ASR), and the other light-driven proton pumps such as bacteriorhodopsin (BR). While microbial (type 1) and animal (type 2) rhodopsins have no sequence similarity with each other, they share a common architecture consisting of seven-transmembrane alpha-helices (TM) connected by extracellular loops and intracellular loops. Both types of rhodopsins consist of opsin and a covalently attached retinal (the aldehyde of vitamin A), a photoreactive chromophore, via a protonated Schiff base linkage to an amino group of lysine in the middle of the seventh transmembrane helix (TM7). Upon the absorption of light, microbial rhodopsins undergo light-induced photoisomerization of all-trans retinal into the 13-cis isomer, whereas the photoisomerization of 11-cis retinal to all-trans isomer occurs in the animal rhodopsins. While animal visual rhodopsins are activated by light to catalyze GDP/GTP exchange in the alpha subunit of the retinal G protein transducin (Gt), microbial rhodopsins do not activate G proteins, but instead can function as light-dependent ion pumps, cation channels, and sensors. 210 matched cddid_all.tbl CDD cd21062 cd21062 439138 BTHB_HectD1 basic tilted helix bundle (BTHB) domain found in HECT domain-containing protein 1 (HectD1) and similar proteins. HectD1, also called E3 ligase for inhibin receptor (EULIR), is a Hect-type E3 ubiquitin transferase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates. HectD1 is required for development of head mesenchyme and neural tube closure. 66 matched cddid_all.tbl CDD cd21063 cd21063 439139 BTHB_FKBP25 basic tilted helix bundle (BTHB) domain found in 25 kDa FK506-binding protein (FKBP25) and similar proteins. FKBP25, also called 25 kDa FKBP, FK506-binding protein 3 (FKBP-3), immunophilin FKBP-25, rapamycin-selective 25 kDa immunophilin or rotamase, acts as a peptidyl-prolyl cis-trans isomerase (PPIase, EC 5.2.1.8) that interconverts the cis and trans isomers of peptide bonds with the amino acid proline. FKBP25 binds both FK506 and rapamycin, and thus belongs to a family of receptors for the two immunosuppressants which inhibit T-cell proliferation by arresting two distinct cytoplasmic signal transmission pathways. 67 matched cddid_all.tbl CDD cd21064 cd21064 410952 NURR_hnRNPQ-like NURR (N-terminal unit for RNA recognition) domain found in heterogeneous nuclear ribonucleoproteins hnRNPQ, hnRNPR and similar proteins. The family includes hnRNPQ and hnRNPR. hnRNPQ, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NSAP1), or Synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP), is a highly conserved RNA-binding protein that mediates the exosomal partition of a set of miRNAs. It acts as a component of the hepatocyte exosomal miRNA sorting machinery. hnRNPR is a highly conserved RNA-binding protein that belongs to the heterogeneous nuclear ribonucleoprotein (hnRNP) family. hnRNP plays an important role in processing of precursor mRNA in the nucleus. hnRNPR acts as a general positive regulator of MHC class I expression. 78 matched cddid_all.tbl CDD cd21065 cd21065 410953 NURR_Syncrip-like NURR (N-terminal unit for RNA recognition) domain found in Drosophila melanogaster Syncrip and similar proteins. Syncrip is a conserved RNA-binding protein important in neuronal and muscular development in Drosophila. It is essential for the morphology and growth of the neuromuscular junction and regulates cytoplasmic vesicle-based messenger RNA (mRNA) transport. The model corresponds to NURR domain of Syncrip, which is a RNA-binding domain with a highly conserved RNA-binding surface. 83 matched cddid_all.tbl CDD cd21066 cd21066 410954 NURR_hnRNPQ NURR (N-terminal unit for RNA recognition) domain found in heterogeneous nuclear ribonucleoprotein Q (hnRNPQ) and similar proteins. hnRNPQ, also termed glycine- and tyrosine-rich RNA-binding protein (GRY-RBP), or NS1-associated protein 1 (NSAP1), or Synaptotagmin-binding, cytoplasmic RNA-interacting protein (SYNCRIP), is a highly conserved RNA-binding protein that mediates the exosomal partition of a set of miRNAs. It acts as a component of the hepatocyte exosomal miRNA sorting machinery. The model corresponds to NURR domain of hnRNPQ, which has structural similarity to bacterial protein Barstar and binds to Apobec1. 85 matched cddid_all.tbl CDD cd21067 cd21067 410955 NURR_hnRNPR NURR (N-terminal unit for RNA recognition) domain found in heterogeneous nuclear ribonucleoprotein R (hnRNPR) and similar proteins. hnRNPR is a highly conserved RNA-binding protein that belongs to the heterogeneous nuclear ribonucleoprotein (hnRNP) family. hnRNP plays an important role in processing of precursor mRNA in the nucleus. hnRNPR acts as a general positive regulator of MHC class I expression. The model corresponds to NURR domain of hnRNPR. 84 matched cddid_all.tbl CDD cd21068 cd21068 411032 Rab11BD_RAB3IP Rab11 binding domain of Rab-3A-interacting protein (RAB3IP). RAB3IP, also called Rabin-3, or SSX2-interacting protein, or Rabin8, acts as a guanine nucleotide exchange factor (GEF) which promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. It mediates the release of GDP from RAB8A and RAB8B but not from RAB3A or RAB5. It modulates actin organization and promotes polarized transport of RAB8A-specific vesicles to the cell surface. The model corresponds to the Rab11a/Rab11b-binding region of RAB3IP lies within its carboxy-terminus, a region distinct from its GEF domain and Rab3a-binding region. 193 matched cddid_all.tbl CDD cd21069 cd21069 411033 Rab11BD_RAB3IL1 Rab11 binding domain of Rab-3A-interacting-like protein 1 (RAB3IL1). RAB3IL1, also called guanine nucleotide exchange factor for Rab-3A (GRAB), or Rab3A-interacting-like protein 1, or Rabin3-like 1, acts as a guanine nucleotide exchange factor (GEF) which promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. As a dual Rab-binding protein, RAB3IL1 could potentially link Rab3 and Rab11 and/or Rab8 and Rab11-mediated intracellular trafficking processes. It may activate RAB3A, a GTPase that regulates synaptic vesicle exocytosis. It may also activate RAB8A and RAB8B. In addition, RAB3IL1 interacts with InsP6K1 and plays a role for InsP7 in vesicle exocytosis. The model corresponds to the Rab11a/Rab11b-binding region of RAB3IL1 lies within its carboxy-terminus, a region distinct from its GEF domain and Rab3a-binding region. 163 matched cddid_all.tbl CDD cd21070 cd21070 410966 ELD_TRPML1 extracytosolic/lumenal domain (ELD) found in transient receptor potential channel mucolipin 1 (TRPML1). TRPML1, also called mucolipin-1 (ML1), or MG-2, or Mucolipidin, may play a major role in Ca(2+) release from late endosome and lysosome vesicles to the cytoplasm, which is important for many lysosome-dependent cellular events, including the fusion and trafficking of these organelles, exocytosis and autophagy. The model corresponds to extracytosolic/lumenal domain (ELD), a linker located between the first two transmembrane segments (S1 and S2) of TRPML1. It forms a tight tetramer that is crucial for full-length TRPML1 assembly and localization. 171 matched cddid_all.tbl CDD cd21071 cd21071 410967 ELD_TRPML2 extracytosolic/lumenal domain (ELD) found in transient receptor potential channel mucolipin 2 (TRPML2). TRPML2, also called mucolipin-2 (ML2), acts as Ca(2+)-permeable cation channel with inwardly rectifying activity. It may activate ARF6 and be involved in the trafficking of GPI-anchored cargo proteins to the cell surface via the ARF6-regulated recycling pathway. The model corresponds to extracytosolic/lumenal domain (ELD), a linker located between the first two transmembrane segments (S1 and S2) of TRPML2. It forms a tight tetramer that is crucial for full-length TRPML2 assembly and localization. 167 matched cddid_all.tbl CDD cd21072 cd21072 410968 ELD_TRPML3 extracytosolic/lumenal domain (ELD) found in transient receptor potential channel mucolipin 3 (TRPML3). TRPML3, also called mucolipin-3 (ML3), acts as Ca(2+)-permeable cation channel with inwardly rectifying activity. It mediates release of Ca(2+) from endosomes to the cytoplasm, contributes to endosomal acidification and is involved in the regulation of membrane trafficking and fusion in the endosomal pathway. The model corresponds to extracytosolic/lumenal domain (ELD), a linker located between the first two transmembrane segments (S1 and S2) of TRPML3. It forms a tight tetramer that is crucial for full-length TRPML3 assembly and localization. 169 matched cddid_all.tbl CDD cd21073 cd21073 411039 toxin_BteA-MLD_like membrane localization domain (MLD) of BteA (Bordetella T3SS effector A) cytotoxin, the N-terminal domain of Photox toxin and related proteins. This family includes the MLD located in the N-terminal minimal membrane-binding segment of BteA (residues 1-131, BteA131), which has also been referred to as the lipid raft targeting (LRT) domain/motif. BteA is a type III secretion system (T3SS) effector protein from Bordetella pertussis, a bacterial respiratory pathogen and the causative agent of whooping cough. The BteA131 segment is multifunctional: in addition to targeting phosphatidylinositol (PI)-rich microdomains in the host membrane, it binds its cognate chaperone BtcA. The MLD adopts a four-helix bundle structure, with a positively charged surface that targets phosphatidylinositol 4,5-bisphosphate (PIP2) in the host membrane via critical arginine and lysine residues. A flexible region preceding the BteA helical bundle contains the characteristic beta-motif required for binding BtcA. This domain has significant sequence similarity to the N-terminal domain of effectors and the endo-domain of RTX-type toxins from Photorhabdus luminescens. This family includes the N-terminal domain of Photorhabdus laumondii Photox toxin; little is known about the N-terminus of Photox, but its C-terminus is an actin-targeting ADP-ribosyltransferase. 87 matched cddid_all.tbl CDD cd21074 cd21074 410781 DHD_Ski_Sno_Dac Dachshund-homology domain found in the Ski/Sno/Dac family of transcriptional regulators. The Dachshund-homology domain (DHD), also known as the N-terminal Ski/Sno/Dac domain, adopts a mixed alpha/beta structure containing a helix-turn-helix motif, similar to features found in the forkhead/winged-helix family of DNA binding proteins. It contains a conserved CLPQ motif and can bind co-factors. Its structure suggests that it may also bind DNA. Members of this family include the Ski protein, Ski-like protein (Sno), and Dachshund proteins. Ski may play a role in terminal differentiation of skeletal muscle cells but not in the determination of cells to the myogenic lineage. It functions as a repressor of transforming growth factor-beta (TGF-beta) signaling. Ski-like protein, also known as SKIL or Sno, is the ski proto-oncogene homolog. It may have regulatory roles in cell division or differentiation in response to extracellular signals. Dachshund proteins are essential components of a regulatory network controlling cell fate determination. They have been implicated in eye, limb, brain, and muscle development. 88 matched cddid_all.tbl CDD cd21075 cd21075 410961 DBD_XPA-like DNA-binding domain found in DNA repair protein complementing XP-A cells (XPA), yeast DNA repair protein RAD14 and similar proteins. The family includes DNA repair protein complementing XP-A cells (XPA), yeast DNA repair protein RAD14, zinc transporter 9 (ZNT9) and similar proteins. XPA, also known as xeroderma pigmentosum group A-complementing protein (XPAC), is involved in DNA excision repair. It initiates repair by binding to damaged sites with various affinities, depending on the photoproduct and the transcriptional state of the region. Rad14 is involved in nucleotide excision repair. It binds specifically to damaged DNA and is required for the incision step. Rad14 is a component of the nucleotide excision repair factor 1 (NEF1) complex consisting of Rad1, Rad10 and Rad14. ZNT9, also known as solute carrier family 30 member 9 (SLC30A9), may act as a zinc transporter involved in intracellular zinc homeostasis and may also play a role as nuclear receptor coactivator. The model corresponds to the DNA-binding domain found in XPA and Rad14. It consists of a conserved N-terminal zinc-binding subdomain and a C-terminal alpha/beta fold subdomain. ZNT9 contains only C-terminal alpha/beta fold subdomain but lacks of N-terminal zinc-binding subdomain. 67 matched cddid_all.tbl CDD cd21076 cd21076 410962 DBD_XPA DNA-binding domain found in DNA repair protein complementing XP-A cells (XPA) and similar proteins. XPA, also known as xeroderma pigmentosum group A-complementing protein (XPAC), is involved in DNA excision repair. It initiates repair by binding to damaged sites with various affinities, depending on the photoproduct and the transcriptional state of the region. 107 matched cddid_all.tbl CDD cd21077 cd21077 410963 DBD_Rad14 DNA-binding domain found in yeast DNA repair protein Rad14 and similar proteins. Rad14 is involved in nucleotide excision repair. It binds specifically to damaged DNA and is required for the incision step. Rad14 is a component of the nucleotide excision repair factor 1 (NEF1) complex consisting of Rad1, Rad10 and Rad14. 105 matched cddid_all.tbl CDD cd21078 cd21078 410964 NTD_ZNT9 N-terminal domain found in zinc transporter 9 (ZNT9) and similar proteins. ZNT9, also known as solute carrier family 30 member 9 (SLC30A9), may act as a zinc transporter involved in intracellular zinc homeostasis and may also play a role as nuclear receptor coactivator. 89 matched cddid_all.tbl CDD cd21079 cd21079 410782 DHD_Ski_Sno Dachshund-homology domain found in Ski, Ski-like protein (Sno), and similar proteins. Ski may play a role in terminal differentiation of skeletal muscle cells but not in the determination of cells to the myogenic lineage. It functions as a repressor of transforming growth factor-beta (TGF-beta) signaling. Ski-like protein, also known as SKIL or Sno, is the ski proto-oncogene homolog. It may have regulatory roles in cell division or differentiation in response to extracellular signals. The Dachshund-homology domain (DHD), also known as the N-terminal Ski/Sno/Dac domain, adopts a mixed alpha/beta structure containing a helix-turn-helix motif, similar to features found in the forkhead/winged-helix family of DNA binding proteins. It contains a conserved CLPQ motif and can bind co-factors. Its structure suggests that it may also bind DNA. 91 matched cddid_all.tbl CDD cd21080 cd21080 410783 DHD_Skor Dachshund-homology domain found in SKI family transcriptional corepressors, Skor1, Skor2 and similar proteins. Skor1, also known as functional Smad-suppressing element on chromosome 15 (Fussel-15), LBX1 corepressor 1, or ladybird homeobox corepressor 1, acts as a transcriptional corepressor of LBX1 and inhibits BMP signaling. Skor2, also known as functional Smad-suppressing element on chromosome 18 (Fussel-18), LBX1 corepressor 1-like protein, or ladybird homeobox corepressor 1-like protein, exhibits transcriptional repressor activity. It acts as a transforming growth factor-beta (TGF-beta) antagonist in the nervous system. The Dachshund-homology domain (DHD), also known as the N-terminal Ski/Sno/Dac domain, adopts a mixed alpha/beta structure containing a helix-turn-helix motif, similar to features found in the forkhead/winged-helix family of DNA binding proteins. It contains a conserved CLPQ motif and can bind co-factors. Its structure suggests that it may also bind DNA. 91 matched cddid_all.tbl CDD cd21081 cd21081 410784 DHD_Dac Dachshund-homology domain found in the retinal determination protein Dachshund and similar proteins. Dachshund proteins act as transcription factors involved in the regulation of organogenesis. They may be a regulator of SIX1, SIX6 and probably SIX5. The Dachshund-homology domain (DHD), also known as the N-terminal Ski/Sno/Dac domain, adopts a mixed alpha/beta structure containing a helix-turn-helix motif, similar to features found in the forkhead/winged-helix family of DNA binding proteins. It contains a conserved CLPQ motif and can bind co-factors. Its structure suggests that it may also bind DNA. It has been postulated that Dachshund proteins may bind to chromatin DNA via their DHD domains. 95 matched cddid_all.tbl CDD cd21082 cd21082 410785 DHD_SKIDA1 Dachshund-homology domain found in SKI/DACH domain-containing protein 1 (SKIDA1) and similar proteins. SKIDA1 is also known as protein DLN-1. Its biological function remains unclear. The Dachshund-homology domain (DHD), also known as the N-terminal Ski/Sno/Dac domain, adopts a mixed alpha/beta structure containing a helix-turn-helix motif, similar to features found in the forkhead/winged-helix family of DNA binding proteins. It contains a conserved CLPQ motif and can bind co-factors. Its structure suggests that it may also bind DNA. 91 matched cddid_all.tbl CDD cd21083 cd21083 410786 DHD_Ski Dachshund-homology domain found in Ski and similar proteins. Ski may play a role in terminal differentiation of skeletal muscle cells but not in the determination of cells to the myogenic lineage. It functions as a repressor of transforming growth factor-beta (TGF-beta) signaling. The Dachshund-homology domain (DHD), also known as the N-terminal Ski/Sno/Dac domain, adopts a mixed alpha/beta structure containing a helix-turn-helix motif, similar to features found in the forkhead/winged-helix family of DNA binding proteins. It contains a conserved CLPQ motif and can bind co-factors. Its structure suggests that it may also bind DNA. 102 matched cddid_all.tbl CDD cd21084 cd21084 410787 DHD_Sno Dachshund-homology domain found in Ski-like protein (Sno) and similar proteins. Ski-like protein, also known as SKIL, Ski-related oncogene (Sno), or Ski-related protein, is the ski proto-oncogene homolog. It may have regulatory roles in cell division or differentiation in response to extracellular signals. The Dachshund-homology domain (DHD), also known as the N-terminal Ski/Sno/Dac domain, adopts a mixed alpha/beta structure containing a helix-turn-helix motif, similar to features found in the forkhead/winged-helix family of DNA binding proteins. It contains a conserved CLPQ motif and can bind co-factors. Its structure suggests that it may also bind DNA. 100 matched cddid_all.tbl CDD cd21085 cd21085 411035 WH_NTD_PHF10 N-terminal winged helix DNA-binding domain found in PHD finger protein 10 (PHF10) and similar proteins. PHF10, also termed BRG1-associated factor 45a (BAF45a), or XAP135, is involved in transcription activity regulation by chromatin remodeling. It is a component of the neural progenitors-specific chromatin remodeling complex (npBAF complex) and plays a role in the proliferation of neural progenitors. The model corresponds to the N-terminal winged helix DNA-binding domain of PHF10, which is structurally related to the SKI/SNO/DAC domain that is found in a number of metazoan chromatin-associated proteins. 89 matched cddid_all.tbl CDD cd21086 cd21086 411036 WH_NTD_SMARCB1 N-terminal winged helix DNA-binding domain found in SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (SMARCB1) and similar proteins. SMARCB1, also termed BRG1-associated factor 47 (BAF47), or integrase interactor 1 protein (INI1), or SNF5, or SNF5L1, is a core component of the BAF (hSWI/SNF) complex, an ATP-dependent chromatin-remodeling complex that plays important roles in cell proliferation and differentiation, in cellular antiviral activities and inhibition of tumor formation. The model corresponds to the N-terminal winged helix DNA binding domain of SMARCB1, which is structurally related to the SKI/SNO/DAC domain that is found in a number of metazoan chromatin-associated proteins. 88 matched cddid_all.tbl CDD cd21087 cd21087 410635 7tm_viral_rhod_II_OLPVRII-like viral group II rhodopsins such as OLPVRII and similar proteins, members of the seven-transmembrane GPCR superfamily. The viral group II rhodopsins includes Organic Lake Phycodnavirus rhodopsin II (OLPVRII), a pentameric light-gated channel that is functionally analogous to well-studied pentameric ligand-gated ion channels playing crucial roles in many cellular processes. It is most likely specific for chloride. Members of this group are considered homologs of proteorhodopsins (PRs), which are blue-light absorbing and green-light absorbing proteins acting as light-driven proton pumps that play a major role in supplying light energy for phototropic marine microorganisms, by a mechanism similar to that of bacteriorhodopsin. Viral proteorhodopsins are predicted to function as sensory rhodopsins that could affect signaling, for example, phototaxis in the infected protists, perhaps stimulating relocation of the infected protists to areas that are rich in nutrients required for virus reproduction. PRs belong to the microbial rhodopsin family, also known as type 1 rhodopsins, which also comprise the light-driven inward chloride pump halorhodopsin (HR), the light-gated cation channel channelrhodopsin (ChR), the light-sensor activating transmembrane transducer protein sensory rhodopsin II (SRII), the light-sensor activating soluble transducer protein Anabaena sensory rhodopsin (ASR), and the other light-driven proton pumps such as bacteriorhodopsin (BR). While microbial (type 1) and animal (type 2) rhodopsins have no sequence similarity with each other, they share a common architecture consisting of seven-transmembrane alpha-helices (TM) connected by extracellular loops and intracellular loops. Both types of rhodopsins consist of opsin and a covalently attached retinal (the aldehyde of vitamin A), a photoreactive chromophore, via a protonated Schiff base linkage to an amino group of lysine in the middle of the seventh transmembrane helix (TM7). Upon the absorption of light, microbial rhodopsins undergo light-induced photoisomerization of all-trans retinal into the 13-cis isomer, whereas the photoisomerization of 11-cis retinal to all-trans isomer occurs in the animal rhodopsins. While animal visual rhodopsins are activated by light to catalyze GDP/GTP exchange in the alpha subunit of the retinal G protein transducin (Gt), microbial rhodopsins do not activate G proteins, but instead can function as light-dependent ion pumps, cation channels, and sensors. 210 matched cddid_all.tbl CDD cd21088 cd21088 410636 7tm_viral_rhod_I_VirRDTS-like viral group I rhodopsins such as VirRDTS and similar proteins, members of the seven-transmembrane GPCR superfamily. The viral group I rhodopsins includes Phaeocystis globosa virus 12T divergent type-1 DTS-motif rhodopsin (VirRDTS), a green light-absorbing proton pump that has a structure similar to that of bacteriorhodopsin (BR) and transfers light energy in a manner that substantially changes medium pH when expressed in a cell. Members of this group are considered homologs of proteorhodopsins (PRs), which are blue-light absorbing and green-light absorbing proteins acting as light-driven proton pumps that play a major role in supplying light energy for phototropic marine microorganisms, by a mechanism similar to that of bacteriorhodopsin. Viral proteorhodopsins are predicted to function as sensory rhodopsins that could affect signaling, for example, phototaxis in the infected protists, perhaps stimulating relocation of the infected protists to areas that are rich in nutrients required for virus reproduction. PRs belong to the microbial rhodopsin family, also known as type 1 rhodopsins, which also comprise the light-driven inward chloride pump halorhodopsin (HR), the light-gated cation channel channelrhodopsin (ChR), the light-sensor activating transmembrane transducer protein sensory rhodopsin II (SRII), the light-sensor activating soluble transducer protein Anabaena sensory rhodopsin (ASR), and the other light-driven proton pumps such as bacteriorhodopsin (BR). While microbial (type 1) and animal (type 2) rhodopsins have no sequence similarity with each other, they share a common architecture consisting of seven-transmembrane alpha-helices (TM) connected by extracellular loops and intracellular loops. Both types of rhodopsins consist of opsin and a covalently attached retinal (the aldehyde of vitamin A), a photoreactive chromophore, via a protonated Schiff base linkage to an amino group of lysine in the middle of the seventh transmembrane helix (TM7). Upon the absorption of light, microbial rhodopsins undergo light-induced photoisomerization of all-trans retinal into the 13-cis isomer, whereas the photoisomerization of 11-cis retinal to all-trans isomer occurs in the animal rhodopsins. While animal visual rhodopsins are activated by light to catalyze GDP/GTP exchange in the alpha subunit of the retinal G protein transducin (Gt), microbial rhodopsins do not activate G proteins, but instead can function as light-dependent ion pumps, cation channels, and sensors. 211 matched cddid_all.tbl CDD cd21089 cd21089 411041 Trm112-like eukaryotic tRNA methyltransferase 112, a partner protein of both rRNA/tRNA and protein methyltransferases, and similar proteins. This family contains eukaryotic tRNA methyltransferase 112 (Trm112)-like proteins such as human multifunctional methyltransferase subunit Trm112 protein, which acts as an activator of both rRNA/tRNA and protein methyltransferases. Trm112 acts as an obligate activating platform for at least four methyltransferases (MTase) involved in the modification of 18S rRNA (Bud23), tRNA (Trm9 and Trm11) and translation termination factor eRF1 (Mtq2) in eukaryotes. Hence, Trm112 is at a nexus between ribosome synthesis and function. Trm112 is a partner protein of N6amt1 (N6 -adenine-specific DNA methyltransferase 1), which is suggested to be the N6-adenine DNA methyltransferase (MTase) in human cells. Trm112 binds to a hydrophobic surface of N6amt1, stabilizing its structure but not directly contributing to substrate binding and catalysis. In Yarrowia lipolytica, it forms a complex with Trm9 methyltransferase, which is involved in the 5-methoxycarbonylmethyluridine (mcm(5)U) modification of the tRNA anticodon wobble position and hence promotes translational fidelity. In Saccharomyces cerevisiae, Trm112 (also called Ynr046w or tRNA methyltransferase 112) is a zinc binding protein that is plurifunctional and a component of the eRF1 methyltransferase, putatively containing a zinc finger signature motif. 117 matched cddid_all.tbl CDD cd21090 cd21090 411042 C11orf65 chromosome 11 open reading frame 65 and homologs. Chromosome 11 open reading frame 65 (C11orf65) is an uncharacterized protein that may be associated with potential sensitivity to metformin in type 2 diabetes (diabetes mellitus) patients without cancer. 260 matched cddid_all.tbl CDD cd21091 cd21091 411043 Fuzzy protein fuzzy and homologs. Protein fuzzy (or FUZ) is a planar cell polarity (PCP) effector that controls multiple cellular processes during development. PCP signalling is an evolutionarily conserved pathway by which directional information regarding polarized cell movement is provided to cells. The PCP signalling axis involves PCP core and PCP effector genes, which are activated consecutively to govern orientated cell migration and the establishment of cytoskeletal structures. Dishevelled (Dvl in mammals or Dsh in Drosophila) and Fuz (or fuzzy in Drosophila) are two representative PCP core and effector genes, respectively. PCP regulates mammalian nervous system development; Fuz-null mutant mice display neural tube defects due to failure of directional cell motility and cell fusion. 401 matched cddid_all.tbl CDD cd21092 cd21092 411044 TPT_S35C2 solute carrier family 35 member C2, member of the triose-phosphate transporter family. Solute carrier family 35 member C2 (S35C2 or Slc35c2), also called ovarian cancer-overexpressed gene 1 protein (OVCOV1), is a member of the triose-phosphate transporter (TPT) family, which is part of the drug/metabolite transporter (DMT) superfamily. It may function either as a GDP-fucose transporter that competes with Slc35c1 (S35C1) for GDP-fucose, or a factor that otherwise enhances the fucosylation of Notch and is required for optimal Notch signaling in mammalian cells. 248 matched cddid_all.tbl CDD cd21093 cd21093 410606 KLF8_12_N N-terminal domain of Kruppel-like factor (KLF) 8, KLF12, and similar proteins. Kruppel-like transcription factors (also known as Krueppel-like transcription factors, KLFs) belong to a family of proteins called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Although these factors bind to similar elements in vitro, they have distinct activities in vivo depending on their expression profile and the sequence of the N-terminal activation/repression domain, which differ between members. This model represents the related N-terminal activation/repression domains of KLF8 and KLF12. 172 matched cddid_all.tbl CDD cd21094 cd21094 410447 C1_aPKC_iota protein kinase C conserved region 1 (C1 domain) found in the atypical protein kinase C (aPKC) iota type. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. aPKCs only require phosphatidylserine (PS) for activation. They contain a C2-like region, instead of a calcium-binding (C2) region found in classical PKCs, in their regulatory domain. There are two aPKC isoforms, zeta and iota. aPKCs are involved in many cellular functions including proliferation, migration, apoptosis, polarity maintenance and cytoskeletal regulation. They also play a critical role in the regulation of glucose metabolism and in the pathogenesis of type 2 diabetes. PKC-iota is directly implicated in carcinogenesis. It is critical to oncogenic signaling mediated by Ras and Bcr-Abl. The PKC-iota gene is the target of tumor-specific gene amplification in many human cancers, and has been identified as a human oncogene. In addition to its role in transformed growth, PKC-iota also promotes invasion, chemoresistance, and tumor cell survival. Expression profiling of PKC-iota is a prognostic marker of poor clinical outcome in several human cancers. PKC-iota also plays a role in establishing cell polarity, and has critical embryonic functions. Members of this family contain C1 domain found in aPKC isoform iota. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 55 matched cddid_all.tbl CDD cd21095 cd21095 410448 C1_aPKC_zeta protein kinase C conserved region 1 (C1 domain) found in the atypical protein kinase C (aPKC) zeta type. PKCs are classified into three groups (classical, atypical, and novel) depending on their mode of activation and the structural characteristics of their regulatory domain. aPKCs only require phosphatidylserine (PS) for activation. They contain a C2-like region, instead of a calcium-binding (C2) region found in classical PKCs, in their regulatory domain. There are two aPKC isoforms, zeta and iota. aPKCs are involved in many cellular functions including proliferation, migration, apoptosis, polarity maintenance and cytoskeletal regulation. They also play a critical role in the regulation of glucose metabolism and in the pathogenesis of type 2 diabetes. PKC-zeta plays a critical role in activating the glucose transport response. It is activated by glucose, insulin, and exercise through diverse pathways. PKC-zeta also plays a central role in maintaining cell polarity in yeast and mammalian cells. In addition, it affects actin remodeling in muscle cells. Members of this family contain C1 domain found in aPKC isoform zeta. The C1 domain is a cysteine-rich zinc binding domain that does not bind DNA nor possess structural similarity to conventional zinc finger domains; it contains two separate Zn(2+)-binding sites. 55 matched cddid_all.tbl CDD cd21098 cd21098 467743 IQCG-IQCD IQ (isoleucine-glutamine) motif containing G and D (IQCG and IQCD). IQCG and IQCD belong to the IQ motif-containing protein family which contain a C-terminal conserved IQ (isoleucine-glutamine) motif and a coiled-coil domain. The IQCG protein (also known as DRC9 and CFAP122) is essential for sperm flagellum formation in mice. The IQCD protein (also known as DRC10) is involved in sperm fertilization and the acrosome reaction. Both proteins are components of the nexin-dynein regulatory complex (N-DRC), a key regulator of ciliary/flagellar motility. IQCG and IQCD proteins contain a central coiled-coil domain and a C-terminal IQ (isoleucine-glutamine) motif ([ILV]QxxxRxxxx[RK]), where x stands for any amino-acid residue, that interacts with calmodulin (CaM) in a calcium-independent manner. IQ motif-containing proteins that are known to bind calmodulin (CaM) have a wide diversity of biological functions, and they include neuronal growth proteins, myosins, voltage-operated channels, phosphatases, Ras exchange proteins, sperm surface proteins, Ras Gap-like proteins, spindle-associated proteins, and several proteins in plants. 25 matched cddid_all.tbl CDD cd21099 cd21099 467845 RXYLT1-like ribitol-5-phosphate xylosyltransferase 1, and related proteins. Ribitol-5-phosphate xylosyltransferase 1 (RXYLT1, also known as transmembrane protein 5, TMEM5) is a transmembrane protein which acts as a UDP-d-xylose:ribitol-5-phosphate beta1,4-xylosyltransferase in the biosynthetic pathway of O-mannosyl glycan. RXYLT1 catalyzes the transfer of UDP-D-xylose to ribitol 5-phosphate (Rbo5P) to form the Xylbeta1-4Rbo5P linkage on O-mannosyl glycan. O-mannosyl glycan is present in a number of glycoproteins, including alpha-dystroglycan. The TMEM5 gene has been associated with alpha-dystroglycanopathies, a diverse group of neuromuscular disorders caused by aberrant O-mannosylation of alpha-dystroglycan. 332 matched cddid_all.tbl CDD cd21101 cd21101 411045 MAF1-ALBA4_C C-terminal domain of mitochondrial association factor 1 (MAF1), Alba4, and related proteins. Mitochondria play a role in the regulation of the innate immune response. Host mitochondria are recruited to the membranes that surround certain intracellular bacteria and parasites during infection, a phenomenon termed host mitochondrial association (HMA). In Toxoplasma gondii, HMA is driven by a gene family that encodes mitochondrial association factor 1 (MAF1) proteins. MAF1 is the parasite protein needed to recruit host mitochondria to the Toxoplasma-containing vacuole during infection. The T. gondii MAF1 locus harbors multiple distinct paralogs that differ in their ability to mediate HMA; these fall into two broad groups designated MAF1a and MAF1b based on residue percent identity. MAF1b paralogs, but not MAF1a paralogs, have been shown to be responsible for the HMA phenotype. This family also includes Plasmodium yeolii ALBA4 which has been shown to modulate its stage-specific interactions and the fates of specific mRNAs during the parasite's growth and transmission, acting to regulate the development of the parasite's transmission stages. 264 matched cddid_all.tbl CDD cd21102 cd21102 411696 Arl6IP1_RETR3-like ADP-ribosylation factor-like protein 6-interacting protein 1, Reticulophagy regulator 3, and similar proteins. This family contains ADP-ribosylation factor-like 6 binding factor 1 (Arl6IP1 or Arl6ip-1) and the N-terminal reticulon-homology domain (RHD) of Reticulophagy regulators 1-3. Arl6IP1 is an endoplasmic reticulum (ER) protein that has an important role in cell conduction and material transport. Arl6IP1, a tetraspan membrane protein, is an anti-apoptotic protein specific to multicellular organisms, and is a potential player in shaping the ER tubules in mammalian cells. In Drosophila, knockdown of the Arl6IP1 gene leads to progressive motor deficit. An Arl6IP1 variant has also been associated with hereditary spastic paraplegia (HSP), motor and sensory polyneuropathy, and acromutilation. Reticulophagy regulator 1 (RETREG1/FAM134B) is an endoplasmic reticulum (ER)-anchored autophagy receptor that regulates the size and shape of the ER. It regulates turnover of the ER by selective phagocytosis, mediating ER delivery into lysosomes through sequestration into autophagosomes. It promotes membrane remodeling and ER scission through its membrane bending activity, and targets the fragments into autophagosomes by interacting with ATG8 family modifier proteins such as MAP1LC3A, MAP1LC3B, GABARAP, GABARAPL1 and GABARAPL2. RETREG2/FAM134A and RETREG3/FAM134C has been shown to interact with ATG8 family modifier proteins MAP1LC3A, MAP1LC3B, GABARAP, and GABARAPL1. Arl6IP1 shows some sequence similarity to the RHD of reticulophagy regulators, which may function in inducing membrane curvature. 178 matched cddid_all.tbl CDD cd21103 cd21103 439141 geminin-like_CC coiled-coil domain found in the geminin family. The geminin family includes geminin, geminin coiled-coil domain-containing protein 1 (GemC1), and McIdas. Together, geminin, GemC1, and McIdas (also called Idas or multicilin), controls both the cell cycle and differentiation decisions in cells. They were initially identified as cell cycle regulators associated with the chromosome cycle. Geminin is required to ensure once-per-cell-cycle genome replication, while McIdas and GemC1 bind to geminin and are implicated in DNA replication control. Geminin binds to Cdt1, a key component and crucial regulator of pre-replicative complexes (pre-RC), in a timely manner to inhibit DNA replication. Geminin family members also function as early regulators of multiciliogenesis. GemC1 and McIdas specify the multiciliate cell fate by forming complexes with the E2F4/5 transcription factors, resulting in centriole amplification and cilia formation. Geminin family proteins contain a homologous central coiled-coil domain that mediates homo- and heterodimerization; this ability is likely to be important for modulating their function in cycling and differentiating cells. This model represents the central coiled-coil domain of the geminin family. 58 matched cddid_all.tbl CDD cd21104 cd21104 411046 SNU13 U4/U6.U5 small nuclear ribonucleoprotein SNU13. U4/U6.U5 small nuclear ribonucleoprotein SNU13, also known as NHP2-like protein 1 or U4/U6.U5 tri-snRNP 15.5 kDa protein, is a component of the spliceosome B complex, involved in pre-mRNA splicing. It binds to the 5'-stem-loop of U4 snRNA. 122 matched cddid_all.tbl CDD cd21105 cd21105 409189 PGAP4-like Post-GPI attachment to proteins factor 4 and similar proteins. This family includes post-GPI attachment to proteins factor 4 (PGAP4), also known as post-GPI attachment to proteins GalNAc transferase 4 or transmembrane protein 246 (TMEM246). PGAP4 has been shown to be a Golgi-resident GPI-GalNAc transferase. Many eukaryotic proteins are anchored to the cell surface through glycolipid glycosylphosphatidylinositol (GPI). GPIs have a conserved core but exhibit diverse N-acetylgalactosamine (GalNAc) modifications. PGAP4 knockout cells lose GPI-GalNAc structures. PGAP4 is most likely involved in the initial steps of GPI-GalNAc biosynthesis. In contrast to other Golgi glycotransferases, it contains three transmembrane domains. This family also includes uncharacterized fungal proteins with similarity to PGAP4. 364 matched cddid_all.tbl CDD cd21106 cd21106 411047 TM6SF1-like transmembrane 6 superfamily member 1, member 2, and similar proteins. This family includes transmembrane 6 superfamily members 1 (TM6SF1) and 2 (TM6SF2), and similar proteins. TM6SF1 is a widely expressed lysosomal transmembrane protein that may be suitable as a lysosomal marker. Polymorphism of its paralog, TM6SF2, has been associated with the risk for hepatocellular carcinoma, and a variant of the gene has been found to impact the processing of lipids in the liver and the small intestine, causing non-alcoholic fatty liver disease (NAFLD). 356 matched cddid_all.tbl CDD cd21107 cd21107 411048 RsiG anti-sigma factor RsiG (AmfC). RsiG is an anti-sigma factor that binds and sequesters the sporulation-specific sigma factor WhiG in a fashion dependent on 3',5'-cyclic diguanylic acid (c-di-GMP). RsiG can bind the cyclic dinucleotide in the absence of sigma factor WhiG, and does so in a specific manner via a unique signature conserved in all Streptomyces. This gene was originally named amfC (aerial mycelium formation protein) but no specific role was established, and was later renamed rsiG (regulator of sigma WhiG). 145 matched cddid_all.tbl CDD cd21108 cd21108 439145 Lpg0189-like Legionella pneumophila Lpg0189 and similar proteins. Lpg0189 is a type II secretion system (T2SS)-dependent exoprotein of Legionella pneumophila and related Legionellales, encoded by the lpw02811 ORF. Homologs of this protein are present within ~65% of Legionella species and are absent from non-Legionella species. 260 matched cddid_all.tbl CDD cd21109 cd21109 410609 SPASM Iron-sulfur cluster-binding SPASM domain. This iron-sulfur cluster-binding domain is named SPASM after the biochemically characterized members, AlbA, PqqE, anSME, and MftC, which are involved in Subtilosin A, Pyrroloquinoline quinone, Anaerobic Sulfatase, and Mycofactocin maturation, respectively. SPASM occurs as an additional C-terminal domain in many peptide-modifying enzymes of the radical S-adenosylmethionine (SAM) superfamily. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. 65 matched cddid_all.tbl CDD cd21111 cd21111 411049 IFTase inulin fructotransferase. Inulin fructotransferase (IFTase; EC 4.2.2.17 and EC 4.2.2.18), a member of the glycoside hydrolase family 91, catalyzes depolymerization of beta-2,1-fructans inulin by successively removing the terminal difructosaccharide units as cyclic anhydrides via intramolecular fructosyl transfer. As a result, IFTase produces DFA-I (alpha-D-fructofuranose-beta-D-fructofuranose 2',1:2,1'-dianhydride) and DFA-III (alpha-D-fructofuranose-beta-D-fructofuranose 2',1:2,3'-dianhydride). 395 matched cddid_all.tbl CDD cd21112 cd21112 411050 alphaLP-like alpha-lytic protease (alpha-LP), a bacterial serine protease of the chymotrypsin family, and similar proteins. This family represents the catalytic domain of alpha-lytic protease (alpha-LP) and its closely-related homologs. Alpha-lytic protease (EC 3.4.21.12; also called alpha-lytic endopeptidase), originally isolated from the myxobacterium Lysobacter enzymogenes, belongs to the MEROPS peptidase family S1, subfamily S1E (streptogrisin A subfamily). It is synthesized as a pro-enzyme, thus having two domains; the N-terminal pro-domain acts as a foldase, required transiently for the correct folding of the protease domain, and also acts as a potent inhibitor of the mature enzyme, while the C-terminal domain catalyzes the cleavage of peptide bonds. Members of the alpha-lytic protease subfamily include Nocardiopsis alba protease (NAPase), a secreted chymotrypsin from the alkaliphile Cellulomonas bogoriensis, streptogrisins (SPG-A, SPG-B, SPG-C, and SPG-D), and Thermobifida fusca protease A (TFPA). These serine proteases have characteristic kinetic stability, exhibited by their extremely slow unfolding kinetics. The active site, characteristic of serine proteases, contains the catalytic triad consisting of serine acting as a nucleophile, aspartate as an electrophile, and histidine as a base, all required for activity. This model represents the C-terminal catalytic domain of alpha-lytic proteases. 188 matched cddid_all.tbl CDD cd21113 cd21113 439146 amidinotransferase-like L-arginine:glycine amidinotransferase, inosamine-phosphate amidinotransferase and similar proteins. This family contains amidinotransferase enzymes known to catalyze the transfer of the amidino group from a donor molecule (usually arginine) to an acceptor molecule bearing a primary amine. They are widespread in nature, occurring in essential metabolic pathways in eukaryotes as well as in biosynthetic pathways for antibiotics and virulence factors in prokaryotes. This family includes L-arginine:glycine amidinotransferase (EC 2.1.4.1; also called glycine amidinotransferase, arginine-glycine amidinotransferase, or arginine-glycine transamidinase), inosamine-phosphate amidinotransferase (EC 2.1.4.2; also called inosamine amidinotransferase, inosamine-P amidinotransferase, or scyllo-inosamine-4-phosphate amidinotransferase or L-arginine:inosamine phosphate amidinotransferase), and similar proteins. L-arginine:glycine amidinotransferase (AT or AGAT) catalyzes the committed step in creatine biosynthesis by formation of guanidinoacetic acid, the immediate precursor of creatine. Inosamine-phosphate amidinotransferases catalyze two nonconsecutive transamidination reactions in the biosynthesis of the streptomycin family of antibiotics. This family also includes L-arginine:inosamine-phosphate Streptomyces griseus amidinotransferase StrB1, which is structurally similar to human L-arginine:glycine amidinotransferase; AT and StrB1 share conserved residues involved in substrate binding and catalysis at equivalent topological positions, suggesting a similar reaction mechanism among amidinotransferases. 336 matched cddid_all.tbl CDD cd21114 cd21114 409232 NAC NAC domain. This family contains the NAC domain, named after the nascent polypeptide-associated complex (NAC) whose subunits contain NAC domains. In eukaryotes, the NAC complex, which plays an important role in co-translational targeting of nascent polypeptides to endoplasmic reticulum (ER), consists of 2 subunits: NAC alpha and a shortened splice variant of the basal transcription factor 3 (BTF3; also called BTF3b or NAC beta). The full length BTF3a protein excites transcription. 43 matched cddid_all.tbl CDD cd21115 cd21115 411051 legumain_C C-terminal prodomain of legumain. This family contains the C-terminal propeptide of legumain, a lysosomal endopeptidase with a specificity for hydrolysis of asparaginyl bonds. Legumain (also called vacuolar processing enzyme or VPE in plants, and asparaginyl endopeptidase or AEP in animals) is synthesized as a precursor with both N- and C-terminal propeptides. Prolegumain is directed to the lysosome or plant vacuole, where activation occurs at least partially by autolysis. The N-terminal catalytic domain is a cysteine protease from the C13 family. The C-terminal prodomain can be organized into an activation peptide (AP), spanning a helical region, and a C-terminal death domain-like fold, denoted as legumain stabilization and activity modulation (LSAM) domain. The C-terminal prodomain binds over the active site and inhibits the catalytic domain. During activation, the C-terminal prodomain is autocatalytically cleaved. This process is induced by pH changes. Human legumain has been shown to process the tetanus toxin generating the fragments found in class II antigen presentation. Legumain from plant seeds is thought to be responsible for the post-translational processing of seed proteins prior to storage. Legumain is highly expressed in some cancers such as colorectal cancer (CRC) and uveal melanoma (UM); it is associated with poor outcome in CRC and upregulation of legumain is associated with malignant behavior of UM. Thus, legumain may be used as a negative prognostic factor as well as a therapeutic target. 119 matched cddid_all.tbl CDD cd21116 cd21116 439149 ClyA-like "family of the cytolysin A (ClyA) family alpha pore-forming toxins (alpha-PFT) including Bacillus cereus HblB, Aeromonas hydrophila AhlB, Bacillus thuringiensis Cry6Aa and similar proteins. This family belongs to the ClyA family of alpha-PFT bacterial toxins. PFTs form the major group of virulence factors in many pathogenic bacteria and in general are critical components of the molecular offensive and defensive machinery of cells in all kingdoms of life. Bacterial PFTs facilitate the takeover of host resources by puncturing holes in the membrane. PFTs can be classified as alpha-PFTs and beta-PFTs depending on the secondary structures of their membrane component. Alpha-PFTs use a ring of amphipathic helices while beta-PFTs use a beta-barrel to construct the pore. Members of this family include the toxins: Bacillus cereus hemolysin binding component B (HblB or HBL-B) of the diarrheal enterotoxin hemolysin BL, Aeromonas hydrophila hemolytic (Ahl) component B (AhlB) of the tripartite AhlABC toxin, Vibrio cholerae cytotoxin motility associated killing factor A (MakA) cytotoxin, Xenorhabdus nematophila alpha-xenorhabdolysin (XaxA), Bacillus thuringiensis crystal 6Aa (Cry6Aa) parasporal crystal (Cry) toxin, and Bacillus cereus non-hemolytic enterotoxin (Nhe) component A (NheA) of the non-hemolytic enterotoxin Nhe, which, despite its name, is hemolytic, among others. In solution, ClyA proteins have an elongated, almost entirely alpha-helical structure, except for a short hydrophobic beta-hairpin known as the beta-tongue. Pore formation by ClyA requires circular oligomerization of the toxin by a sequential mechanism. This, in turn, concentrates the amphipathic helices in the center of the ring-like structure, forming a helical barrel that inserts into the membrane by a wedge-like mechanism. Compared with ClyA, NheA is almost entirely alpha-helical with an enlarged ""head"" domain, and an enlarged beta-tongue; it has been proposed that NheA could even form beta-barrel pores. Alpha-PFTs with similar structures are increasingly being found in eukaryotes, in particular as components of the immune systems of animals. This family may be distantly related to Escherichia coli alpha-PFT hemolysin E (HlyE, also known as ClyA or SheA)." 224 matched cddid_all.tbl CDD cd21117 cd21117 411052 Twitch_MoaA Iron-sulfur cluster-binding Twitch domain of GTP 3',8-cyclase. The iron-sulfur cluster-binding Twitch domain is found at the C-terminus of GTP 3',8-cyclase (EC 4.1.99.22), which is also called molybdenum cofactor biosynthesis protein A (MoaA) in bacteria and archaea, molybdenum cofactor biosynthesis protein 1 (MOCS1) in most eukaryotes, and molybdenum cofactor biosynthesis enzyme CNX2 in plants. GTP 3',8-cyclase is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the first step in molybdopterin biosynthesis, the cyclization of guanosine triphosphate to (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate, which is then converted to molybdopterin in subsequent steps. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. GTP 3',8-cyclase contains an additional iron-sulfur cluster at the C-terminal Twitch domain that is involved in substrate binding. The Twitch domain may be related to another iron-sulfur cluster-binding domain found at the C-terminus of some radical SAM enzymes, the SPASM domain, named after the biochemically characterized members, AlbA, PqqE, anSMEs, and MftC, which are involved in Subtilosin A, Pyrroloquinoline quinone, Anaerobic Sulfatase, and Mycofactocin maturation, respectively. 70 matched cddid_all.tbl CDD cd21118 cd21118 411053 dermokine dermokine. Dermokine, also known as epidermis-specific secreted protein SK30/SK89, is a skin-specific glycoprotein that may play a regulatory role in the crosstalk between barrier dysfunction and inflammation, and therefore play a role in inflammatory diseases such as psoriasis. Dermokine is one of the most highly expressed proteins in differentiating keratinocytes, found mainly in the spinous and granular layers of the epidermis, but also in the epithelia of the small intestine, macrophages of the lung, and endothelial cells of the lung. Mouse dermokine has been reported to be encoded by 22 exons, and its expression leads to alpha, beta, and gamma transcripts. 495 matched cddid_all.tbl CDD cd21119 cd21119 410610 SPASM_PqqE Iron-sulfur cluster-binding SPASM domain of coenzyme PQQ synthesis protein E. Coenzyme PQQ synthesis protein E (PqqE), also called pyrroloquinoline quinone (PQQ) biosynthesis protein E or PqqA peptide cyclase (EC 1.21.98.4), is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the formation of a C-C bond between C-4 of glutamate and C-3 of tyrosine residues of the PqqA protein, which is the first enzymatic step in the biosynthesis of the bacterial enzyme cofactor PQQ. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM (RS) enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. PqqE contains two auxiliary Fe-S clusters in its SPASM domain: one nearest the RS site (AuxI) is in the form of a 2Fe-2S cluster ligated by four cysteines; and a more remote cluster (AuxII) in the form of a 4Fe-4S center that is ligated by three cysteine residues and one aspartate residue. 114 matched cddid_all.tbl CDD cd21120 cd21120 410611 SPASM_anSME Iron-sulfur cluster-binding SPASM domain of anaerobic sulfatase maturating enzyme. Anaerobic sulfatase maturating enzyme (anSME) is a radical S-adenosylmethionine (SAM) enzyme that catalyzes, under anaerobic conditions, the co- or post-translational modification of arylsulfatases to form a catalytically essential formylglycine (FGly) residue to perform their hydrolysis function, removing sulfate groups from a wide array of substrates. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM (RS) enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster; anSME contains two auxillary 4Fe-4S clusters in its SPASM domain. 107 matched cddid_all.tbl CDD cd21121 cd21121 410612 SPASM_Cmo-like Iron-sulfur cluster-binding SPASM domain of tungsten-containing aldehyde ferredoxin oxidoreductase cofactor-modifying protein and similar proteins. This group is composed of Pyrococcus furiosus tungsten-containing aldehyde ferredoxin oxidoreductase (AOR; EC 1.2.7.5) cofactor-modifying protein, encoded by the cmo gene, and similar proteins. AOR cofactor-modifying protein is involved in the biosynthesis of a molybdopterin-based tungsten cofactor. Members of this group are radical S-adenosylmethionine (SAM) enzymes with a SPASM domain. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. This group appears to contain one auxillary Fe-S cluster, similar to the auxillary 4Fe-4S cluster in Bacillus circulans butirosin biosynthetic enzyme BtrN. 80 matched cddid_all.tbl CDD cd21122 cd21122 410613 SPASM_rSAM Iron-sulfur cluster-binding SPASM domain of an uncharacterized group of radical SAM proteins. Members of this group are radical S-adenosylmethionine (SAM) enzymes with a SPASM domain, named after the biochemically characterized members, AlbA, PqqE, anSME, and MftC, which are involved in Subtilosin A, Pyrroloquinoline quinone, Anaerobic Sulfatase, and Mycofactocin maturation, respectively. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. This group appears to contain one auxillary Fe-S cluster, similar to the auxillary 4Fe-4S cluster in Bacillus circulans butirosin biosynthetic enzyme BtrN. 71 matched cddid_all.tbl CDD cd21123 cd21123 410614 SPASM_MftC-like Iron-sulfur cluster-binding SPASM domain of mycofactocin radical SAM maturase MftC and similar proteins. This group is composed of Mycobacterium tuberculosis putative mycofactocin radical SAM maturase MftC and similar proteins. MftC is a radical S-adenosylmethionine (SAM) enzyme that may function to modify mycofactocin, a conserved polypeptide that might serve as an electron carrier. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. This group appears to contain one auxillary Fe-S cluster that is similar to the second auxillary 4Fe-4S cluster (AuxII) of Clostridium perfringens anaerobic sulfatase-maturating enzyme (anSME). 91 matched cddid_all.tbl CDD cd21124 cd21124 410615 SPASM_CteB-like Iron-sulfur cluster-binding SPASM domain of sactionine bond-forming enzyme CteB and similar proteins. Clostridium thermocellum sactionine bond-forming enzyme CteB is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the formation of the requisite thioether bridge between a cysteine and the alpha-carbon of an opposing amino acid that is required in sactipeptide biosynthesis. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM (RS) enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. CteB contains two auxillary 4Fe-4S clusters in its SPASM domain; the auxillary cluster nearest the RS site, called AuxI, exhibits an open coordination site in the absence of peptide substrate, which is coordinated by a peptidyl-cysteine residue in the bound state. 96 matched cddid_all.tbl CDD cd21125 cd21125 410616 SPASM_AlbA-like Iron-sulfur cluster-binding SPASM domain of antilisterial bacteriocin subtilosin biosynthesis protein AlbA and similar proteins. Bacillus subtilis antilisterial bacteriocin subtilosin biosynthesis protein AlbA is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the formation of three thioether bonds in the post-translational modification of a linear peptide into the cyclic peptide subtilosin A. The thioether bonds formed are between the sulfur of three cysteine residues and the alpha-carbons of two phenylalanines and one threonine to produce a rigid cyclic peptide. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. AlbA appears to contain one auxillary Fe-S cluster, similar to the auxillary 4Fe-4S cluster in Bacillus circulans butirosin biosynthetic enzyme BtrN. 97 matched cddid_all.tbl CDD cd21126 cd21126 410617 SPASM_rSAM Iron-sulfur cluster-binding SPASM domain of an uncharacterized group of radical SAM proteins. Members of this group are radical S-adenosylmethionine (SAM) enzymes with a SPASM domain, named after the biochemically characterized members, AlbA, PqqE, anSME, and MftC, which are involved in Subtilosin A, Pyrroloquinoline quinone, Anaerobic Sulfatase, and Mycofactocin maturation, respectively. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. This group appears to contain one auxillary Fe-S cluster, similar to the auxillary 4Fe-4S cluster in Bacillus circulans butirosin biosynthetic enzyme BtrN. 70 matched cddid_all.tbl CDD cd21127 cd21127 410618 SPASM_rSAM Iron-sulfur cluster-binding SPASM domain of an uncharacterized group of radical SAM proteins. Members of this group are radical S-adenosylmethionine (SAM) enzymes with a SPASM domain, named after the biochemically characterized members, AlbA, PqqE, anSME, and MftC, which are involved in Subtilosin A, Pyrroloquinoline quinone, Anaerobic Sulfatase, and Mycofactocin maturation, respectively. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. This group appears to contain one auxillary Fe-S cluster, similar to the auxillary 4Fe-4S cluster in Bacillus circulans butirosin biosynthetic enzyme BtrN. 83 matched cddid_all.tbl CDD cd21128 cd21128 410619 SPASM_rSAM Iron-sulfur cluster-binding SPASM domain of an uncharacterized group of radical SAM proteins. Members of this group are radical S-adenosylmethionine (SAM) enzymes with a SPASM domain, named after the biochemically characterized members, AlbA, PqqE, anSME, and MftC, which are involved in Subtilosin A, Pyrroloquinoline quinone, Anaerobic Sulfatase, and Mycofactocin maturation, respectively. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. This group may contain one auxillary Fe-S cluster with an open coordination site, similar to the auxillary 4Fe-4S cluster in Bacillus circulans butirosin biosynthetic enzyme BtrN, but missing one conserved cysteine in the binding site. 65 matched cddid_all.tbl CDD cd21129 cd21129 410620 SPASM_BtrN Iron-sulfur cluster-binding SPASM domain of butirosin biosynthesis protein N. Butirosin biosynthesis protein N (BtrN), also called S-adenosyl-L-methionine-dependent 2-deoxy-scyllo-inosamine dehydrogenase (EC 1.1.99.38), is a radical S-adenosylmethionine (SAM) enzyme that catalyzes the two-electron oxidation of 2-deoxy-scyllo-inosamine (DOIA) to amino-dideoxy-scyllo-inosose (amino-DOI) in the biosynthetic pathway of the aminoglycoside antibiotic butirosin. Radical SAM enzymes are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster that is involved in the reductive cleavage of SAM and generates a 5'-deoxyadenosyl radical, which in turn abstracts a hydrogen from the appropriately positioned carbon atom of the substrate. Radical SAM enzymes with a C-terminal SPASM domain contain at least one other iron-sulfur cluster. BtrN contains one auxillary 4Fe-4S cluster. 87 matched cddid_all.tbl CDD cd21130 cd21130 467846 parasporin-2-like_N-term N-terminal region of parasporin-2, hydralysin and similar aerolysin-type beta-barrel pore-forming proteins. Bacillus thuringiensis parasporin-2 (PS2, also named Cry46Aa1) is an anti-cancer protein which causes specific cell damage via PS2 oligomerization in the cell membrane. Glycosylphosphatidylinositol (GPI)-anchored proteins may be involved in the cytocidal action of PS2 as co-receptors for PS2's cytocidal action. This family also includes hydralysin (Hln-1) produced by the green hydra Chlorohydra viridissima. Hydralysin is a paralysis-inducing protein not found in the stinging cells (nematocytes), with a cell type-selective cytolytic activity; it binds erythrocyte membranes and forms discrete pores. They belong to the aerolysin family of beta-pore-forming proteins (beta-PFPs). PFPs are generally secreted as water-soluble monomers, which upon binding to target lipid membranes, oligomerize and form transmembrane pores harmful to cells. Beta-PFPs form pores by transmembrane beta-barrels. This model represents helix1 (H1), H2 and strand (S1) that forms part of a 4-stranded beta-sheet. 60 matched cddid_all.tbl CDD cd21131 cd21131 412055 TbPSSA-2-like ectodomain of Trypanosoma, including T. brucei Procyclic-Specific Surface Antigen-2 (TbPSSA-2), T. congolense Insect Stage Antigen (TcISA), and similar proteins. This family includes the ectodomains of Trypanosoma brucei Procyclic-Specific Surface Antigen-2 (TbPSSA-2) and homolog T. congolense Insect Stage Antigen (TcISA). Trypanosomal parasites transmit disease through the arthropod vector Glossina spp (the tsetse fly). Studies have shown that TbPSSA-2 plays an important role in parasite survival in the tsetse; TbPSSA-2 knock-out reduced the efficiency of trypanosome migration from the tsetse midgut to the salivary glands. The TbPSSA-2 and TcISA ectodomains adopt a novel architecture, having two lobes connected by a loop, exhibiting conformational flexibility. The inter-lobe hinge region displaying rotational flexibility suggests a potential mechanism for coordinating a binding partner. 208 matched cddid_all.tbl CDD cd21132 cd21132 410977 EVE-like EVE and YTH domains belong to the PUA superfamily. The EVE domain was formerly known as DUF55 and is thought to be involved in RNA binding. The YTH (YT521-B homology) domain is a novel RNA-binding domain that has been shown to bind to short, degenerate, single-stranded RNA motifs that loosely follow a consensus sequence. Both domains are part of the larger PUA superfamily. 138 matched cddid_all.tbl CDD cd21133 cd21133 410978 EVE EVE domains are putative RNA-binding domains that belong to the PUA superfamily. The EVE domain, formerly known as DUF55, has been revealed via structural similarity to be part of the PUA superfamily. It is most similar in three-dimensional fold to the YTH (YT521-B homology) domain, and is thought to be involved in RNA-binding. 148 matched cddid_all.tbl CDD cd21134 cd21134 410979 YTH YTH (YT521-B homology) domains are RNA-binding domains that belong to the PUA superfamily. Individual members of the YTH family have been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells. In general, eukaryotic YTH-family members may be involved in similar mechanisms to suppress gene regulation during gametogenesis or in other forms of silencing. The YTH domain is a novel RNA-binding domain that has been shown to bind to short, degenerate, single-stranded RNA motifs that loosely follow a consensus sequence. It belongs to the larger PUA superfamily. 133 matched cddid_all.tbl CDD cd21135 cd21135 439147 amidinotransferase_StrB1-like L-arginine:inosamine-phosphate amidinotransferase StrB1 from Streptomyces griseus (StrB1) and similar proteins. This subfamily includes inosamine-phosphate amidinotransferase (EC 2.1.4.2; also called inosamine amidinotransferase or inosamine-P amidinotransferase or scyllo-inosamine-4-phosphate amidinotransferase or L-arginine:inosamine phosphate amidinotransferase) from Streptomyces griseus (StrB1), among others. Inosamine-phosphate amidinotransferase catalyzes two non-consecutive transamidination reactions; it converts scyllo-inosamine 4-phosphate into N-amidino-scyllo-inosamine 4-phosphate, and N1-amidinostreptamine 6-phosphate into streptidine 6-phosphate. L-arginine:inosamine-phosphate amidinotransferase StrB1 is structurally similar to the human L-arginine:glycine amidinotransferase (AT), with residues involved in substrate binding and catalysis conserved in AT and StrB1 at equivalent topological positions, suggesting a similar reaction mechanism among amidinotransferases. This subfamily also includes putative inosamine-phosphate amidinotransferase 2 (StrB2), also called aminocyclitol amidinotransferase or inosamine-phosphate amidinotransferase II, from Streptomyces glaucescens. It is unclear if StrB2 participates in streptomycin biosynthesis as it contains an arginine residue instead of the nucleophilic cysteine that is a key residue for amidine transfer. 343 matched cddid_all.tbl CDD cd21136 cd21136 439148 amidinotransferase_AGAT-like L-arginine:glycine amidinotransferase and similar proteins. This subfamily includes eukaryotic L-arginine:glycine amidinotransferase (EC 2.1.4.1; also called glycine amidinotransferase or arginine-glycine amidinotransferase or arginine-glycine transamidinase or AT or AGAT) involved in creatine biosynthesis. L-arginine:glycine amidinotransferase (AGAT) catalyzes the committed step in creatine biosynthesis by formation of guanidinoacetic acid, the immediate precursor of creatine. Creatine plays a vital role in energy metabolism in muscle tissues, and may play a role in embryonic and central nervous system development and may be involved in the response to heart failure by elevating local creatine synthesis. This subfamily also contains bacterial proteins that include the virulence-associated protein HsvA from the fire blight pathogen Erwinia amylovora shown to be a polyamine amidinotransferase, and cyanobacterial SxtG, an amidinotransferase involved in the biosynthesis of paralytic shellfish toxins. The active sites of these enzymes are located in the core of the proteins at the base of a long, narrow substrate access channel. HsvA has a novel acceptor substrate specificity, with a clear preference for linear polyamines, especially putrescine and spermidine, as the amidino acceptor substrate. SxtG has a broad substrate promiscuity, operating on a wide variety of substrates and preferring alpha-amino ketones and alpha-amino methyl esters over alpha-amino acids. 352 matched cddid_all.tbl CDD cd21137 cd21137 412056 AA13_LPMO-like AA13 lytic polysaccharide monooxygenase, and similar proteins. This family contains starch-degrading (also called starch-active) lytic polysaccharide monooxygenase (LPMO), a representative of the new CAZy AA13 family and classified as an auxiliary activity enzyme. This enzyme acts on alpha-linked glycosidic bonds and displays a binding surface that is quite different from those of LPMOs acting on beta-linked glycosidic bonds, indicating that the AA13 family proteins interact with their substrate in a distinct fashion. The active site contains an amino-terminal histidine-ligated mononuclear copper. This enzyme generates aldonic acid-terminated malto-oligosaccharides from retrograded starch and significantly boosts the conversion of this recalcitrant substrate to maltose by beta-amylase. 233 matched cddid_all.tbl CDD cd21138 cd21138 411054 McdB-like Maintenance of carboxysome distribution (Mcd) protein B and similar proteins. This family contains maintenance of carboxysome distribution (Mcd) protein B (McdB), also called maintenance of carboxysome positioning B protein (McsB). It is found in cyanobacteria, where carboxysome maintenance is mediated by a DNA partition-like ParA-ParB system called the McdA-McdB. In order to actively position carboxysomes, McdB binds directly to McdA, a putative Walker-box ParA-like protein. McdB harbors a unique helical fold and it enables McdA dimer formation. 132 matched cddid_all.tbl CDD cd21140 cd21140 410981 Cas6_I-like Class 1 type I CRISPR-associated endoribonuclease Cas6. CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins) adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. These systems are divided into two classes: class 1 systems utilize multiple Cas proteins and CRISPR RNA (crRNA) to form an effector complex while class 2 systems employ a large, single effector with crRNA to mediate interference. Cas6 family endoribonucleases are metal-independent nucleases that catalyze RNA cleavage via a mechanism involving a 2'-3' cyclic intermediate. They share a common ferredoxin or RNA recognition motif (RRM) fold, and they recognize and excise CRISPR repeat RNAs that vary widely in primary and secondary structures. This subfamily contains Cas6 family endoribonucleases typically found within type I CRISPR-Cas systems and similar proteins. 243 matched cddid_all.tbl CDD cd21141 cd21141 410982 Cas6_III-like Class 1 type III CRISPR-associated endoribonuclease Cas6. CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins) adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. These systems are divided into two classes: class 1 systems utilize multiple Cas proteins and CRISPR RNA (crRNA) to form an effector complex while class 2 systems employ a large, single effector with crRNA to mediate interference. Cas6 family endoribonucleases are metal-independent nucleases that catalyze RNA cleavage via a mechanism involving a 2'-3' cyclic intermediate. They share a common ferredoxin or RNA recognition motif (RRM) fold, and they recognize and excise CRISPR repeat RNAs that vary widely in primary and secondary structures. This subfamily contains Cas6 family endoribonucleases typically found within type III CRISPR-Cas systems and similar proteins. 251 matched cddid_all.tbl CDD cd21142 cd21142 411055 Cas7fv type I-F variant CRISPR-associated backbone protein Cas7 (Cas7fv). Cas7fv is one of the CRISPR associated (Cas) proteins of type I-F variant CRISPR-Cas system. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas modules are adaptive immune systems found in archaea and bacteria against foreign nucleic acids such as phages and plasmids via RNA-guided endonucleases. CRISPR-Cas systems are classified based on Cas protein content and arrangement in CRISPR-Cas loci into two main classes (1 and 2) and at least six types (I, II, III, IV, V, VI). Class 1 systems utilize multiple Cas proteins and CRISPR RNA (crRNA) to form an effector complex while class 2 systems employ a large, single effector with crRNA to mediate interference. Type I CRISPR-Cas systems are most widespread in nature and the Cas protein composition of the employed Cascade interference complexes differ between seven subtypes (A-F, U). Type I-F variant (I-Fv) is a subtype that rely on a minimal set of five Cas proteins and has structural differences with I-F and I-E Cascades. Double strand DNA recruitment and recognition in the type I-Fv Cascade is facilitated from the major groove side by Cas5fv instead of the large subunit Cas8 and the finger domain of Cas7fv. 315 matched cddid_all.tbl CDD cd21143 cd21143 411056 Cas5fv type I-F variant CRISPR-associated protein Cas5 (Cas5fv). Cas5fv is one of the CRISPR-associated (Cas) proteins of type I-F variant CRISPR-Cas system. CRISPR (clustered regularly interspaced short palindromic repeats)-Cas modules are adaptive immune systems found in archaea and bacteria against foreign nucleic acids such as phages and plasmids via RNA-guided endonucleases. CRISPR-Cas systems are classified based on Cas protein content and arrangement in CRISPR-Cas loci into two main classes (1 and 2) and at least six types (I, II, III, IV, V, VI). Class 1 systems utilize multiple Cas proteins and CRISPR RNA (crRNA) to form an effector complex while class 2 systems employ a large, single effector with crRNA to mediate interference. Type I CRISPR-Cas systems are most widespread in nature and the Cas protein composition of the employed Cascade interference complexes differ between seven subtypes (A-F, U). Type I-F variant (I-Fv) is a subtype that rely on a minimal set of five Cas proteins and has structural differences with I-F and I-E Cascades. Double strand DNA recruitment and recognition in the type I-Fv Cascade is facilitated from the major groove side by Cas5fv instead of the large subunit Cas8 and the finger domain of Cas7fv. 335 matched cddid_all.tbl CDD cd21144 cd21144 439156 NendoU_XendoU-like Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural protein 15 (Nsp15), arterivirus Nsp11, torovirus endoribonuclease, Xenopus laevis endoribonuclease XendoU, and related proteins. Nidovirus endoribonucleases (NendoUs) and eukaryotic Xenopus laevis-like endoribonucleases (XendoUs) are uridylate-specific endoribonucleases which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. XendoU is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA. Except for turkey coronavirus (TCoV) Nsp15, Mn2+ is generally essential for the catalytic activity of coronavirus Nsp15. Mn2+ is dispensable, and to some extent inhibits the activity of arterivirus (Porcine Reproductive and Respiratory Syndrome virus) PRRSV Nsp11. XendoU also requires Mn2+. Coronavirus Nsp15 from Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), human Coronavirus 229E (HCoV229E), and murine hepatitis virus (MHV) forms a functional hexamer while Porcine DeltaCoronavirus (PDCoV) Nsp15 has been shown to exist as a dimer and a monomer in solution. Nsp11 from the arterivirus PRRSV is a dimer. 113 matched cddid_all.tbl CDD cd21146 cd21146 409283 Nip7_N_euk N-terminal domain of eukaryotic 60S ribosome subunit biogenesis protein Nip7 and similar proteins. This N-terminal domain of various proteins co-occurs with a PUA (PseudoUridine synthase and Archaeosine transglycosylase) RNA binding domain. This model contains eukaryotic Nip7, a protein that was shown to be required for efficient biogenesis of the 60S ribosome subunit in Saccharomyces cerevisiae. Recently, it was demonstrated that human Nip7 is essential in the accurate processing of pre-rRNA. Also included is KD93, a human homolog of Nip7. Nip7 and its homologs share a two-domain architecture with the C-terminal PUA domain mediating interaction with RNA, suggesting that Nip7 is an adaptor protein with the C-terminal domain interacting with RNA targets and the N-terminal domain mediating interaction with protein targets. 87 matched cddid_all.tbl CDD cd21147 cd21147 409284 RsmF_methylt_CTD1 RsmF rRNA methyltransferase first C-terminal domain. This model represents the first of two distinct C-terminal domains of the 16S rRNA methyltransferase RsmF and related RsmB/RsmF family ribosomal methyltransferases. It is necessary for stabilizing the N-terminal catalytic core (a SAM-dependent methyltransferase) and is related to the N-terminal domain of Nip7, a protein that was shown to be required for efficient biogenesis of the 60S ribosome subunit in Saccharomyces cerevisiae (human Nip7 is essential in the accurate processing of pre-rRNA). The second distinct C-terminal domain belongs to the PUA (PseudoUridine synthase and Archaeosine transglycosylase) RNA binding domain superfamily. 75 matched cddid_all.tbl CDD cd21148 cd21148 409290 PUA_Cbf5 PUA RNA-binding domain of the archaeal pseudouridine synthase component Cbf5. The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. Members of the archaeal and eukaryotic subfamily of pseudouridine synthases, including Cbf5 (dyskerin in humans) and similar proteins, are modules that assist in the binding and positioning (guide and/or substrate) of RNA to the pseudouridine synthase complex. Pseudouridine synthases are enzymes that are responsible for post-translational modifications of RNAs by specifically isomerizing uracil residues. In Pyrococcus furiosus H/ACA ribonucleoprotein (RNP) assembly with a single-hairpin H/ACA RNA, the lower stem and the ACA motif of the guide RNA are anchored at the PUA domain of Cbf5. In addition, the N-terminal extension of Cbf5, which is a hot spot for dyskeratosis congenita (a rare genetic form of bone marrow failure) mutation, forms an extra structural layer on the PUA domain. 75 matched cddid_all.tbl CDD cd21149 cd21149 409291 PUA_archaeosine_TGT PUA RNA-binding domain of archaeosine tRNA-guanine transglycosylase. The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. Members of this archaeosine tRNA-guanine transglycosylase (TGT) family are responsible for the exchange of a guanine residue in archaeal tRNAs with a preQ0 base (7-cyano-7-deazaguanine), which constitutes the initial step in archaeosine biosynthesis. Archaeosine is a modified RNA base specific to archaea (7-formamidino-7deazaguanosine), found at position 15 in tRNAs. It has been shown that the PUA domain of archaeosine TGT is not required for its specificity for position 15. 75 matched cddid_all.tbl CDD cd21150 cd21150 409292 PUA_NSun6-like PUA RNA-binding domain of the SAM-dependent methyltransferase NSun6 and similar proteins. The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. Members of this subfamily contain PUA domains that co-occur with SAM-dependent methyltransferase domains and may play roles as cytosine-C(5)-methyltransferases specific for tRNAs or rRNAs. Nsun6 binding to its tRNA substrates requires the presence of a 3'-CCA sequence, which is precisely recognized primarily through interactions with residues from the PUA domain, where the molecular surface of the PUA domain snugly fits onto each nucleotide residue of the CCA end. Human RNA:m5C methyltransferase NSun6 (hNSun6) plays a major role in bone metastasis and could be a valuable therapeutic target for bone metastasis and therapy-resistant tumors. 92 matched cddid_all.tbl CDD cd21151 cd21151 409293 PUA_Nip7-like PUA RNA binding domain of ribosome assembly factor Nip7 and similar proteins. The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. This eukaryotic and archaeal subfamily contains the conserved protein Nip7 and similar proteins, which are involved in ribosome biogenesis, taking part in 27S pre-rRNA processing and in formation of 60S ribosomal subunit. Nip7 orthologs share a two-domain architecture with the C-terminal PUA domain mediating interaction with RNA, suggesting that Nip7 is an adaptor protein with the C-terminal domain interacting with RNA targets and the N-terminal domain mediating interaction with protein targets. Structural analyses of the RNA-interacting surfaces of Saccharomyces cerevisiae and Pyrococcus abyssi Nip7 orthologs indicate that, in the archaeal PUA domain, C-terminal positively charged residues (arginines and lysines) are involved in RNA interaction while equivalent positions in eukaryotic orthologs are occupied by mostly hydrophobic residues. Both proteins can bind specifically to polyuridine, and RNA interaction requires specific residues of the PUA domain as determined by site-directed mutagenesis. 78 matched cddid_all.tbl CDD cd21152 cd21152 409294 PUA_TruB_bacterial PUA RNA-binding domain of bacterial pseudouridine synthase TruB and similar proteins. The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. Members of this bacterial subfamily of pseudouridine synthases, including TruB and similar proteins, are modules that assist in the binding and positioning (guide and/or substrate) of RNA to the pseudouridine synthase complex. Pseudouridine synthases are enzymes that are responsible for post-translational modifications of RNAs by specifically isomerizing uracil residues. The pseudouridine synthase TruB (also called tRNA pseudouridylate synthase B or Psi55 synthase) is responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of elongator tRNAs. 60 matched cddid_all.tbl CDD cd21153 cd21153 409295 PUA_RlmI PUA RNA-binding domain of the SAM-dependent methyltransferase RlmI and related proteins. The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. Members of this subfamily contain PUA domains that co-occur N-terminal to SAM-dependent methyltransferase domains and include Escherichia coli RlmI (rRNA large subunit methyltransferase gene I, also called YccW) and Thermus thermophilus methyltransferase RlmO, which are 5-methylcytosine methyltransferases (m5C MTases) that play a role in modifying 23S rRNA. This subfamily also includes Pyrococcus horikoshii PH1915 that may play a role as a 5-methyluridine MTase, and/or perform similar roles. 70 matched cddid_all.tbl CDD cd21154 cd21154 409296 PUA_MJ1432-like PUA RNA-binding domain of MJ1432, TA1423, PH0734, and similar proteins. The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. Members of this mostly archaeal family have not been characterized functionally; they may bind to RNA. This family includes Pyrococcus horikoshii PH0734 where the N-terminal domain may modulate the binding target of the C-terminal PUA domain using its characteristic electropositive surface. 84 matched cddid_all.tbl CDD cd21155 cd21155 409297 PUA_MCTS-1-like PUA RNA-binding domain of malignant T cell-amplified sequence 1 and related proteins. The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. Members of this eukaryotic family, labelled MCT-1 (malignant T cell-amplified sequence 1) or MCTS-1 (multiple copies T-cell lymphoma-1), contain a single PUA domain. They may play roles in the regulation of the cell cycle; human MCT-1 has been characterized for its oncogenic potential. MCT-1/MCTS1 expression is a new poor-prognosis marker in patients with aggressive breast cancers, and thus the MCT-1 pathway is a novel and promising therapeutic target for triple-negative breast cancer (TNBC). 97 matched cddid_all.tbl CDD cd21156 cd21156 409298 PUA_eIF2d-like PUA RNA-binding domain of eukaryotic translation initiation factor 2D and similar proteins. The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. Most members of this eukaryotic translation initiation factor 2D (eIF2d)-like family of eukaryotic proteins also contain a domain homologous to the translation initiation factor eIF1/SUI1, and a short uncharacterized N-terminal domain. eIF2D may function as a cytosolic GTP-independent initiation factor which delivers Met-tRNA (and non-initiating tRNAs) to the 40S ribosomal subunit. The family member from Drosophila melanogaster has been named ligatin, and this alias has been adopted for other family members as well, which are not homologous to the vertebrate ligatin (LGTN) that is a trafficking receptor for phosphoglycoproteins. 82 matched cddid_all.tbl CDD cd21157 cd21157 409299 PUA_G5K PUA domain of gamma-glutamyl kinase, found in archaea, bacteria, and eukarya. Gamma glutamyl kinase (G5K) is an enzyme essential for the biosynthesis of L-proline; it catalyzes the transfer of a phosphate group to glutamate. The resulting glutamate 5-phosphate cyclizes spontaneously to form 5-oxoproline. The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain functions as an RNA binding domain in many other proteins; however, its role in G5K is not understood. It might play a role in modulating the enzymatic properties of bacterial G5Ks. 104 matched cddid_all.tbl CDD cd21158 cd21158 439157 NendoU_nv Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural protein 15 (Nsp15), arterivirus Nsp11, torovirus endoribonuclease, and related proteins. Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. This family also includes torovirus NendoUs. Except for turkey coronavirus (TCoV) Nsp15, Mn2+ is generally essential for the catalytic activity of coronavirus Nsp15. Mn2+ is dispensable, and to some extent inhibits the activity of arterivirus (Porcine Reproductive and Respiratory Syndrome virus) PRRSV Nsp11. Coronavirus Nsp15 from Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), human Coronavirus 229E (HCoV229E), and murine hepatitis virus (MHV) form a functional hexamer while Porcine DeltaCoronavirus (PDCoV) Nsp15 has been shown to exist as a dimer and monomer in solution. Nsp11 from the arterivirus PRRSV is a dimer. NendoUs are distantly related to Xenopus laevis Mn(2+)-dependent uridylate-specific endoribonuclease (XendoU) which is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA. 151 matched cddid_all.tbl CDD cd21159 cd21159 394910 XendoU Xenopus laevis endoribonuclease XendoU, and related proteins. Xenopus laevis XendoU is a uridylate-specific endoribonuclease, which releases a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. XendoU is a monomer and requires Mn2+. It is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA. XendoU is distantly related to the Nidovirus uridylate-specific endoribonucleases (NendoUs) which include Nonstructural protein 15 (Nsp15) from coronaviruses, Nsp11 from arteriviruses, and torovirus endoribonuclease. 264 matched cddid_all.tbl CDD cd21160 cd21160 394911 NendoU_av_Nsp11-like Nidoviral uridylate-specific endoribonuclease (NendoU) domain of arterivirus PRRSV Nonstructural protein 11 (Nsp11), and related proteins. Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. Mn2+ is dispensable, and to some extent inhibits the activity of arterivirus (Porcine Reproductive and Respiratory Syndrome virus) PRRSV Nsp11. This Nsp11 exists as a dimer. NendoUs are distantly related to Xenopus laevis Mn(2+)-dependent uridylate-specific endoribonuclease (XendoU) which is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA. 120 matched cddid_all.tbl CDD cd21161 cd21161 439158 NendoU_cv_Nsp15-like Nidoviral uridylate-specific endoribonuclease (NendoU) domain of coronavirus Nonstructural Protein 15 (Nsp15) and related proteins. Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. Except for turkey coronavirus (TCoV) Nsp15, Mn2+ is generally essential for the catalytic activity of coronavirus Nsp15. Coronavirus Nsp15 from Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), human Coronavirus 229E (HCoV229E), and murine hepatitis virus (MHV) form a functional hexamer while Porcine DeltaCoronavirus (PDCoV) Nsp15 has been shown to exist as a dimer and a monomer in solution. NendoUs are distantly related to Xenopus laevis Mn(2+)-dependent uridylate-specific endoribonuclease (XendoU) which is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA. 151 matched cddid_all.tbl CDD cd21162 cd21162 394913 NendoU_tv_PToV-like Nidoviral uridylate-specific endoribonuclease (NendoU) domain of Porcine torovirus (PToV) endoribonuclease and related proteins. Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. The Porcine torovirus (PToV) strain PToV-NPL/2013 NendoU domain is located at the N-terminus of the ORF1ab replicase polyprotein, between regions annotated as Nonstructural proteins 11 (Nsp11) and 13 (Nsp13). This subfamily belongs to a family which includes Nsp15 from coronaviruses and Nsp11 from arteriviruses, which may participate in the viral replication process and in the evasion of the host immune system. These vary in their requirement for Mn2+. Coronavirus Nsp15 generally form functional hexamers, with the exception of Porcine DeltaCoronavirus (PDCoV) Nsp15 which exists as a dimer and a monomer in solution. Arterivirus (Porcine Reproductive and Respiratory Syndrome virus) PRRSV Nsp11 is a dimer. NendoUs are distantly related to Xenopus laevis Mn(2+)-dependent uridylate-specific endoribonuclease (XendoU) which is involved in the processing of intron-encoded box C/D U16 small, nucleolar RNA. 133 matched cddid_all.tbl CDD cd21163 cd21163 439159 M_cv_Nsp15-NTD_av_Nsp11-like middle (M) domain of coronavirus Nonstructural protein 15 (Nsp15) and the N-terminal domain (NTD) of arterivirus Nsp11 and related proteins. Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. Coronavirus Nsp15 NendoUs have an N-terminal domain, a middle (M) domain, and a C-terminal catalytic (NendoU) domain. Arterivirus Nsp11 has an N-terminal domain (NTD) and a C-terminal catalytic (NendoU) domain. The NTD of Nsp11 superimposes onto the M-domain of coronavirus Nsp15. Coronavirus Nsp15 from Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), human Coronavirus 229E (HCoV229E), and Murine Hepatitis Virus (MHV) form a functional hexamer. Oligomerization of Porcine DeltaCoronavirus (PDCoV) Nsp15 differs from that of other coronavirus members; it has been shown to exist as a dimer and a monomer in solution. Nsp11 from the arterivirus PRRSV functions as a dimer. 123 matched cddid_all.tbl CDD cd21165 cd21165 439160 M_cv-Nsp15-like middle domain of coronavirus Nonstructural protein 15 (Nsp15), and related proteins. Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. Coronavirus Nsp15 NendoUs have an N-terminal domain, a middle (M) domain and a C-terminal catalytic (NendoU) domain. Coronavirus Nsp15 from Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), human Coronavirus 229E (HCoV229E), and Murine Hepatitis Virus (MHV) form a functional hexamer. Oligomerization of Porcine DeltaCoronavirus (PDCoV) Nsp15 differs from that of the other coronavirus members; it has been shown to exist as a dimer and a monomer in solution. 126 matched cddid_all.tbl CDD cd21166 cd21166 394904 NTD_av_Nsp11-like N-terminal domain (NTD) of arterivirus Nonstructural protein 11 (Nsp11), and related proteins. Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. Coronavirus Nsp15 NendoUs have an N-terminal domain, a middle (M) domain and a C-terminal catalytic (NendoU) domain. Arterivirus Nsp11 has an N-terminal domain (NTD) and a C-terminal NendoU catalytic domain. The NTD of Nsp11 superimposes onto the M-domain of coronavirus Nsp15. Coronavirus Nsp15 from Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), human Coronavirus 229E (HCoV229E), and Murine Hepatitis Virus (MHV) form a functional hexamer. Oligomerization of Porcine DeltaCoronavirus (PDCoV) Nsp15 differs from that of the other coronaviruses; it has been shown to exist as a dimer and a monomer in solution. Nsp11 from the arterivirus PRRSV functions as a dimer. PRRSV Nsp11 has been shown to induce STAT2 degradation to inhibit interferon signaling; mutagenesis revealed that the amino acid residue K59 located at the NTD of Nsp11 is indispensable for inducing STAT2 reduction. 100 matched cddid_all.tbl CDD cd21167 cd21167 439161 M_alpha_beta_cv_Nsp15-like middle domain of alpha- and beta-coronavirus Nonstructural protein 15 (Nsp15), and related proteins. Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. Coronavirus Nsp15 NendoUs have an N-terminal domain, a middle (M) domain and a C-terminal catalytic (NendoU) domain. Coronavirus Nsp15 from Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), human Coronavirus 229E (HCoV229E), and Murine Hepatitis Virus (MHV) form a functional hexamer. This middle domain harbors residues involved in hexamer formation and in trimer stability. Oligomerization of Porcine DeltaCoronavirus (PDCoV) Nsp15 differs from that of the other coronaviruses; it has been shown to exist as a dimer and a monomer in solution. 127 matched cddid_all.tbl CDD cd21168 cd21168 394906 M_gcv_Nsp15-like middle domain of gammacoronavirus Nonstructural protein 15 (Nsp15), and related proteins. Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. Coronavirus Nsp15 NendoUs have an N-terminal domain, a middle (M) domain and a C-terminal catalytic (NendoU) domain. Coronavirus Nsp15 from Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), human Coronavirus 229E (HCoV229E), and Murine Hepatitis Virus (MHV) form a functional hexamer. This middle domain harbors residues involved in hexamer formation and in trimer stability. Oligomerization of Porcine DeltaCoronavirus (PDCoV) Nsp15 differs from that of the other coronaviruses; it has been shown to exist as a dimer and a monomer in solution. 123 matched cddid_all.tbl CDD cd21169 cd21169 394907 M_dcv_Nsp15-like middle domain of delta coronavirus Nonstructural protein 15 (Nsp15), and related proteins. Nidovirus endoribonucleases (NendoUs) are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include Nsp15 from coronaviruses and Nsp11 from arteriviruses, both of which may participate in the viral replication process and in the evasion of the host immune system. Coronavirus Nsp15 NendoUs have an N-terminal domain, a middle (M) domain and a C-terminal catalytic (NendoU) domain. Coronavirus Nsp15 from Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV), human Coronavirus 229E (HCoV229E), and Murine Hepatitis Virus (MHV) form a functional hexamer. Oligomerization of Porcine DeltaCoronavirus (PDCoV) Nsp15 differs from that of the other coronaviruses; it has been shown to exist as a dimer and a monomer in solution. 118 matched cddid_all.tbl CDD cd21170 cd21170 439162 NTD_CoV_Nsp15-like N-terminal domain of coronavirus Nonstructural protein 15 (Nsp15) and related proteins. Coronavirus (CoV) Nsp15 is a nidovirus endoribonuclease (NendoU). NendoUs are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include CoV Nsp15 and arterivirus Nsp11, both of which may participate in the viral replication process and in the evasion of the host immune system. This NTD structure (approximately 60 residues) present in CoV Nsp15, is missing in Nsp11. CoV Nsp15 has an N-terminal domain, a middle (M) domain, and a C-terminal catalytic (NendoU) domain. Nsp15 from Severe Acute Respiratory Syndrome (SARS)-CoV, human CoV 229E (HCoV229E), and Murine Hepatitis Virus (MHV) form a functional hexamer. Oligomerization of Porcine DeltaCoronavirus (PDCoV) Nsp15 differs from the Nsp15 of these alpha- and beta-coronavirus; it has been shown to exist as dimers and monomers in solution, and to function as a dimer. Nsp15 from Turkey CoV (TCoV), a gammaCoV, has been reported to be a homohexamer. 60 matched cddid_all.tbl CDD cd21171 cd21171 439163 NTD_alpha_betaCoV_Nsp15-like N-terminal domain of alpha- and beta-coronavirus Nonstructural protein 15 (Nsp15), and related proteins. Coronavirus (CoV) Nsp15 is a nidovirus endoribonuclease (NendoU). NendoUs are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include CoV Nsp15 and arterivirus Nsp11, both of which may participate in the viral replication process and in the evasion of the host immune system. This small NTD structure, present in coronavirus Nsp15, is missing in Nsp11. CoV Nsp15 has an N-terminal domain, a middle (M) domain, and a C-terminal catalytic (NendoU) domain. Nsp15 from Severe Acute Respiratory Syndrome (SARS)-CoV, human CoV229E (HCoV229E), and Murine Hepatitis Virus (MHV) form a functional hexamer. Residues in this N-terminal domain are important for hexamer (dimer of trimers) formation. 61 matched cddid_all.tbl CDD cd21172 cd21172 439164 NTD_deltaCoV_Nsp15-like N-terminal domain of deltacoronavirus Nonstructural protein 15 (Nsp15), and related proteins. Coronavirus (CoV) Nsp15 is a nidovirus endoribonuclease (NendoU). NendoUs are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include coronavirus Nsp15 and arterivirus Nsp11, both of which may participate in the viral replication process and in the evasion of the host immune system. This small NTD structure, present in CoV Nsp15, is missing in Nsp11. CoV Nsp15 has an N-terminal domain, a middle (M) domain, and a C-terminal catalytic (NendoU) domain. Oligomerization of Porcine DeltaCoronavirus (PDCoV) Nsp15 differs from the Nsp15 of alpha- and beta-coronavirus, such as Severe Acute Respiratory Syndrome (SARS)-CoV and Murine Hepatitis Virus (MHV) which form functional hexamers; PDCoV Nsp15 has been shown to exist as dimers and monomers in solution, and to function as a dimer. 60 matched cddid_all.tbl CDD cd21173 cd21173 411057 NucC-like cyclic oligonucleotide-based anti-phage signaling system-associated NucC nuclease and similar proteins. Cyclic oligonucleotide-based anti-phage signaling system (CBASS)-associated NucC nuclease kills phage-infected cells through genome destruction. It is allosterically activated by a cyclic triadenylate (cA3) second messenger that is synthesized by CBASS upon infection. NucC is related to restriction endonucleases but it adopts a homotrimeric structure. Binding of cA3 causes two NucC homotrimers to assemble into a homohexamer, which brings together a pair of active sites to activate DNA cleavage. NucC has also been integrated into type III CRISPR/Cas systems as an accessory nuclease. 231 matched cddid_all.tbl CDD cd21174 cd21174 410621 LPMO_auxiliary lytic polysaccharide monooxygenase auxiliary activity protein. Many proteins in this superfamily are copper-dependent lytic polysaccharide monooxygenases (LPMOs) and include lytic polysaccharide monooxygenase auxiliary activity families 9 (AA9) and 10 (AA10). The substrate-binding surface of this family is a flat beta-sandwich fold. 136 matched cddid_all.tbl CDD cd21175 cd21175 410622 LPMO_AA9 lytic polysaccharide monooxygenase (LPMO) auxiliary activity family 9 (AA9). AA9 proteins are copper-dependent lytic polysaccharide monooxygenases (LPMOs) involved in the cleavage of cellulose chains with oxidation of carbons C1 and/or C4 and C6. Activities include lytic cellulose monooxygenase (C1-hydroxylating) (EC 1.14.99.54) and lytic cellulose monooxygenase (C4-dehydrogenating) (EC 1.14.99.56). The family used to be called GH61 because weak endoglucanase activity had been demonstrated in some family members. 216 matched cddid_all.tbl CDD cd21176 cd21176 410623 LPMO_auxiliary-like fungal lytic polysaccharide monooxygenase (LPMO) auxiliary activity family protein. Proteins in this fungal family of copper-binding proteins may not function as lytic polysaccharide monooxygenases (LPMOs) or in specific binding of chitin and/or cellulose. A family member found in the ectomycorrhizal fungus Laccaria bicolor has been found to be located at the interface between tree rootlet cells and fungal hyphae. It does not perform oxidative cleavage of polysaccharides. Members of this family are related to LPMOs but have diverged to biological functions other than polysaccharide degradation. 121 matched cddid_all.tbl CDD cd21177 cd21177 410624 LPMO_AA10 lytic polysaccharide monooxygenase (LPMO) auxiliary activity family 10 (AA10). AA10 proteins are copper-dependent lytic polysaccharide monooxygenases (LPMOs), which may act on chitin or cellulose. The family used to be called CBM33. Activities in this family include lytic cellulose monooxygenase (C1-hydroxylating) (EC 1.14.99.54), lytic cellulose monooxygenase (C4-dehydrogenating) (EC 1.14.99.56), lytic chitin monooxygenase (EC 1.14.99.53), and lytic xylan monooxygenase/xylan oxidase (glycosidic bond-cleaving) (EC 1.14.99.-). Also included are viral chitin-binding glycoproteins such as fusolin and spheroidin-like proteins. 180 matched cddid_all.tbl CDD cd21178 cd21178 410625 Fusolin-like fusolin and similar proteins. Fusolin is a protein found in spindles of insect poxviruses that resembles the lytic polysaccharide monooxygenases of chitinovorous bacteria and may function to disrupt the chitin-rich peritrophic matrix that protects insects against oral infections. Thus, it is a component of the virus occlusion bodies (which are large proteinaceous polyhedra) that protect the virus from the outside environment for extended periods until they are ingested by insect larvae. 227 matched cddid_all.tbl CDD cd21179 cd21179 411059 LIC_1098-like putative DNA adenine methyltransferase similar to Leptospira interrogans LIC_1098. this uncharacterized family is structurally similar to DNA adenine methyltransferases such as FokI, EcoRV, or DpnIIA. 280 matched cddid_all.tbl CDD cd21180 cd21180 409666 GH2_GIPC GIPC-homology 2 (GH2) domain found in the GIPC family. The GIPC family includes PDZ domain-containing proteins, GIPC1 (also called GAIP C-terminus-interacting protein, RGS-GAIP-interacting protein, RGS19-interacting protein 1, RGS19IP1, synectin, tax interaction protein 2, or TIP-2), GIPC2, and GIPC3, which may act as scaffold proteins linking heterotrimeric G-proteins to seven-transmembrane-type WNT receptor or to receptor tyrosine kinases. They might play key roles in carcinogenesis and embryogenesis through modulation of growth factor signaling and cell adhesion. GIPCs are proteins with a GIPC homology 1 (GH1) domain, a central PDZ domain and a GH2 domain. This model corresponds to the GH2 domain, which mediates the interaction with myosin VI and is involved in homodimerization in the autoinhibited state. 65 matched cddid_all.tbl CDD cd21181 cd21181 410548 Tudor_SETDB1_rpt2 second Tudor domain found in SET domain bifurcated 1 (SETDB1) and similar proteins. SETDB1, also called ERG-associated protein with SET domain (ESET), histone H3-K9 methyltransferase 4, H3-K9-HMTase 4, or lysine N-methyltransferase 1E (KMT1E), acts as a histone-lysine N-methyltransferase that specifically trimethylates 'Lys-9' of histone H3 (H3K9me3). It mainly functions in euchromatin regions, thereby playing a central role in the silencing of euchromatic genes. It contains two Tudor domains. This model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 54 matched cddid_all.tbl CDD cd21182 cd21182 410549 Tudor_SMN_SPF30-like Tudor domain found in survival motor neuron protein (SMN), motor neuron-related-splicing factor 30 (SPF30), and similar proteins. This group contains SMN, SPF30, Tudor domain-containing protein 3 (TDRD3), DNA excision repair protein ERCC-6-like 2 (ERCC6L2), and similar proteins. SMN, also called component of gems 1, or Gemin-1, is part of a multimeric SMN complex that includes spliceosomal Sm core proteins and plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. SPF30, also called 30 kDa splicing factor SMNrp, SMN-related protein, or survival motor neuron domain-containing protein 1 (SMNDC1), is an essential pre-mRNA splicing factor required for assembly of the U4/U5/U6 tri-small nuclear ribonucleoprotein into the spliceosome. TDRD3 is a scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. ERCC6L2, also called DNA repair and recombination protein RAD26-like (RAD26L), may be involved in early DNA damage response. It regulates RNA Pol II-mediated transcription via its interaction with DNA-dependent protein kinase (DNA-PK) to resolve R loops and minimize transcription-associated genome instability. Members of this group contain a single Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. 50 matched cddid_all.tbl CDD cd21183 cd21183 409032 CH_FLN-like_rpt1 first calponin homology (CH) domain found in the filamin family. The filamin family includes filamin-A (FLN-A), filamin-B (FLN-B) and filamin-C (FLN-C). Filamins function to anchor various transmembrane proteins to the actin cytoskeleton. FLN-A is also called actin-binding protein 280 (ABP-280), alpha-filamin, endothelial actin-binding protein, filamin-1, or non-muscle filamin. It promotes orthogonal branching of actin filaments and links actin filaments to membrane glycoproteins. It also serves as a scaffold for a wide range of cytoplasmic signaling proteins. FLN-B is also called ABP-278, ABP-280 homolog, actin-binding-like protein, beta-filamin, filamin homolog 1 (Fh1), filamin-3, thyroid autoantigen, truncated actin-binding protein, or truncated ABP. It connects cell membrane constituents to the actin cytoskeleton and may also promote orthogonal branching of actin filaments as well as link actin filaments to membrane glycoproteins. FLN-C, also called FLNc, ABP-280-like protein, ABP-L, actin-binding-like protein, filamin-2, or gamma-filamin, is a muscle-specific filamin that plays a central role in muscle cells, probably by functioning as a large actin-cross-linking protein. It may be involved in reorganizing the actin cytoskeleton in response to signaling events, and may also display structural functions at the Z lines in muscle cells. FLN-C is critical for normal myogenesis and for maintaining the structural integrity of the muscle fibers. This family also includes Drosophila melanogaster protein jitterbug (Jbug), which is an actin-meshwork organizing protein containing three copies of the CH domain. Other members of this family contain two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 108 matched cddid_all.tbl CDD cd21184 cd21184 409033 CH_FLN-like_rpt2 second calponin homology (CH) domain found in the filamin family. The filamin family includes filamin-A (FLN-A), filamin-B (FLN-B) and filamin-C (FLN-C). Filamins function to anchor various transmembrane proteins to the actin cytoskeleton. FLN-A is also called actin-binding protein 280 (ABP-280), alpha-filamin, endothelial actin-binding protein, filamin-1, or non-muscle filamin. It promotes orthogonal branching of actin filaments and links actin filaments to membrane glycoproteins. It also serves as a scaffold for a wide range of cytoplasmic signaling proteins. FLN-B is also called ABP-278, ABP-280 homolog, actin-binding-like protein, beta-filamin, filamin homolog 1 (Fh1), filamin-3, thyroid autoantigen, truncated actin-binding protein, or truncated ABP. It connects cell membrane constituents to the actin cytoskeleton and may also promote orthogonal branching of actin filaments as well as link actin filaments to membrane glycoproteins. FLN-C, also called FLNc, ABP-280-like protein, ABP-L, actin-binding-like protein, filamin-2, or gamma-filamin, is a muscle-specific filamin that plays a central role in muscle cells, probably by functioning as a large actin-cross-linking protein. It may be involved in reorganizing the actin cytoskeleton in response to signaling events, and may also display structural functions at the Z lines in muscle cells. FLN-C is critical for normal myogenesis and for maintaining the structural integrity of the muscle fibers. This family also includes Drosophila melanogaster protein jitterbug (Jbug), which is an actin-meshwork organizing protein containing three copies of the CH domain. Other members of this family contain two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 103 matched cddid_all.tbl CDD cd21185 cd21185 409034 CH_jitterbug-like_rpt3 third calponin homology (CH) domain found in Drosophila melanogaster protein jitterbug and similar proteins. Protein jitterbug (Jbug) is an actin-meshwork organizing protein. It is required to maintain the shape and cell orientation of the Drosophila notum epithelium during flight muscle attachment to tendon cells. Jbug contains three copies of the CH domain. This model corresponds to the third CH domain. CH domains are actin filament (F-actin) binding motifs. 98 matched cddid_all.tbl CDD cd21186 cd21186 409035 CH_DMD-like_rpt1 first calponin homology (CH) domain found in the dystrophin family. The dystrophin family includes dystrophin and its paralog, utrophin. Dystrophin, encoded by the DMD gene, is a large, submembrane cytoskeletal protein that is the main component of the dystrophin-glycoprotein complex (DGC) in skeletal muscles. It links the transmembrane DGC to the actin cytoskeleton through binding strongly to the cytoplasmic tail of beta-dystroglycan, the transmembrane subunit of a highly O-glycosylated cell-surface protein. Dystrophin is also involved in maintaining the structural integrity of cells, as well as in the formation of the blood-brain barrier (BBB). Utrophin, also called dystrophin-related protein 1 (DRP-1), is an autosomal dystrophin homolog that increases dystrophic muscle function and reduces pathology. It is broadly expressed in both the mRNA and protein levels, and occurs in the cerebrovascular endothelium. Utrophin forms the utrophin-glycoprotein complex (UGC) by interacting with dystroglycans (DGs) and sarcoglycan-dystroglycans, as well as sarcoglycan and sarcospan (SG-SSPN) subcomplexes. It may act as a scaffolding protein that stabilizes lipid microdomains and clusters mechanosensitive channel subunits, and links the F-actin cytoskeleton to the cell membrane via the associated glycoprotein complex. Members of this family contain two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 107 matched cddid_all.tbl CDD cd21187 cd21187 409036 CH_DMD-like_rpt2 second calponin homology (CH) domain found in the dystrophin family. The dystrophin family includes dystrophin and its paralog, utrophin. Dystrophin, encoded by the DMD gene, is a large, submembrane cytoskeletal protein that is the main component of the dystrophin-glycoprotein complex (DGC) in skeletal muscles. It links the transmembrane DGC to the actin cytoskeleton through binding strongly to the cytoplasmic tail of beta-dystroglycan, the transmembrane subunit of a highly O-glycosylated cell-surface protein. Dystrophin is also involved in maintaining the structural integrity of cells, as well as in the formation of the blood-brain barrier (BBB). Utrophin, also called dystrophin-related protein 1 (DRP-1), is an autosomal dystrophin homolog that increases dystrophic muscle function and reduces pathology. It is broadly expressed in both the mRNA and protein levels, and occurs in the cerebrovascular endothelium. Utrophin forms the utrophin-glycoprotein complex (UGC) by interacting with dystroglycans (DGs) and sarcoglycan-dystroglycans, as well as sarcoglycan and sarcospan (SG-SSPN) subcomplexes. It may act as a scaffolding protein that stabilizes lipid microdomains and clusters mechanosensitive channel subunits, and link the F-actin cytoskeleton to the cell membrane via the associated glycoprotein complex. Members of this family contain two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 104 matched cddid_all.tbl CDD cd21188 cd21188 409037 CH_PLEC-like_rpt1 first calponin homology (CH) domain found in the plectin/dystonin/MACF1 family. This family includes plectin, dystonin and microtubule-actin cross-linking factor 1, isoforms 1/2/3/5 (MACF1). Plectin, also called PCN, PLTN, hemidesmosomal protein 1 (HD1), or plectin-1, is a structural component of muscle. It interlinks intermediate filaments with microtubules and microfilaments, and anchors intermediate filaments to desmosomes or hemidesmosomes. It could also bind muscle proteins such as actin to membrane complexes in muscle. Dystonin, also called 230 kDa bullous pemphigoid antigen, 230/240 kDa bullous pemphigoid antigen, bullous pemphigoid antigen 1 (BPA or BPAG1), dystonia musculorum protein, or hemidesmosomal plaque protein, is a cytoskeletal linker protein that acts as an integrator of intermediate filaments, actin, and microtubule cytoskeleton networks. It is required for anchoring either intermediate filaments to the actin cytoskeleton in neural and muscle cells, or keratin-containing intermediate filaments to hemidesmosomes in epithelial cells. MACF1, also called 620 kDa actin-binding protein (ABP620), actin cross-linking family protein 7 (ACF7), macrophin-1, or trabeculin-alpha, is a large protein containing numerous spectrin and leucine-rich repeat (LRR) domains. It facilitates actin-microtubule interactions at the cell periphery and couples the microtubule network to cellular junctions. Members of this family contain two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 105 matched cddid_all.tbl CDD cd21189 cd21189 409038 CH_PLEC-like_rpt2 second calponin homology (CH) domain found in the plectin/dystonin/MACF1 family. This family includes plectin, dystonin and microtubule-actin cross-linking factor 1, isoforms 1/2/3/5 (MACF1). Plectin, also called PCN, PLTN, hemidesmosomal protein 1 (HD1), or plectin-1, is a structural component of muscle. It interlinks intermediate filaments with microtubules and microfilaments, and anchors intermediate filaments to desmosomes or hemidesmosomes. It could also bind muscle proteins such as actin to membrane complexes in muscle. Dystonin, also called 230 kDa bullous pemphigoid antigen, 230/240 kDa bullous pemphigoid antigen, bullous pemphigoid antigen 1 (BPA or BPAG1), dystonia musculorum protein, or hemidesmosomal plaque protein, is a cytoskeletal linker protein that acts as an integrator of intermediate filaments, actin, and microtubule cytoskeleton networks. It is required for anchoring either intermediate filaments to the actin cytoskeleton in neural and muscle cells, or keratin-containing intermediate filaments to hemidesmosomes in epithelial cells. MACF1, also called 620 kDa actin-binding protein (ABP620), actin cross-linking family protein 7 (ACF7), macrophin-1, or trabeculin-alpha, is a large protein containing numerous spectrin and leucine-rich repeat (LRR) domains. It facilitates actin-microtubule interactions at the cell periphery and couples the microtubule network to cellular junctions. Members of this family contain two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 105 matched cddid_all.tbl CDD cd21190 cd21190 409039 CH_SYNE-like_rpt1 first calponin homology (CH) domain found in the synaptic nuclear envelope protein family. The synaptic nuclear envelope (SYNE) family includes SYNE-1, -2 and calmin. SYNE-1 (also called nesprin-1, enaptin, KASH domain-containing protein 1, KASH1, myocyte nuclear envelope protein 1, MYNE-1, or nuclear envelope spectrin repeat protein 1) and SYNE-2 (also called nesprin-2, KASH domain-containing protein 2, KASH2, nuclear envelope spectrin repeat protein 2, nucleus and actin connecting element protein, or protein NUANCE) may act redundantly. They are multi-isomeric modular proteins which form a linking network between organelles and the actin cytoskeleton to maintain subcellular spatial organization. They also act as components of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex, which is involved in the connection between the nuclear lamina and the cytoskeleton. Calmin, also called calponin-like transmembrane domain protein, is a protein with calponin homology (CH) and transmembrane domains expressed in maturing spermatogenic cells. It may be involved in the development and/or maintenance of neuronal functions. Members of this family contain two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 113 matched cddid_all.tbl CDD cd21191 cd21191 409040 CH_CLMN_rpt1 first calponin homology (CH) domain found in calmin and similar proteins. Calmin, also called calponin-like transmembrane domain protein, is a protein with calponin homology (CH) and transmembrane domains expressed in maturing spermatogenic cells. It may be involved in the development and/or maintenance of neuronal functions. Calmin contains two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 114 matched cddid_all.tbl CDD cd21192 cd21192 409041 CH_SYNE-like_rpt2 second calponin homology (CH) domain found in the synaptic nuclear envelope protein (SYNE) family. The SYNE family includes SYNE-1, -2 and calmin. SYNE-1 (also called nesprin-1, enaptin, KASH domain-containing protein 1, KASH1, myocyte nuclear envelope protein 1, MYNE-1, or nuclear envelope spectrin repeat protein 1) and SYNE-2 (also called nesprin-2, KASH domain-containing protein 2, KASH2, nuclear envelope spectrin repeat protein 2, nucleus and actin connecting element protein, or protein NUANCE) may act redundantly. They are multi-isomeric modular proteins which form a linking network between organelles and the actin cytoskeleton to maintain subcellular spatial organization. They also act as components of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex, which is involved in the connection between the nuclear lamina and the cytoskeleton. Calmin, also called calponin-like transmembrane domain protein, is a protein with calponin homology (CH) and transmembrane domains expressed in maturing spermatogenic cells. It may be involved in the development and/or maintenance of neuronal functions. Members of this family contain two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 107 matched cddid_all.tbl CDD cd21193 cd21193 409042 CH_beta_spectrin_rpt1 first calponin homology (CH) domain found in the beta spectrin family. The beta spectrin family includes beta-I, -II, -III, -IV and -V spectrins. Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is composed of two antiparallel dimers of alpha- and beta- subunits. Beta-I spectrin, also called spectrin beta chain, erythrocytic (SPTB), may be involved in anaemia pathogenesis. Beta-II spectrin, also called spectrin beta chain, non-erythrocytic 1 (SPTBN1), or fodrin beta chain, is a component of fodrin, which is the general spectrin-like protein that seems to be involved in secretion. Fodrin interacts with calmodulin in a calcium-dependent manner and is thus a candidate for the calcium-dependent movement of the cytoskeleton at the membrane. Beta-IV spectrin is also called spectrin, non-erythroid beta chain 3 (SPTBN3) or spectrin beta chain, non-erythrocytic 4 (SPTBN4). Its mutation associates with congenital myopathy, neuropathy, and central deafness. Beta-III spectrin is also called spectrin beta chain, non-erythrocytic 2 (SPTBN2), or spinocerebellar ataxia 5 protein (SCA5). Beta-V spectrin, also called spectrin beta chain, non-erythrocytic 5 (SPTBN5), is a mammalian ortholog of Drosophila beta H spectrin. Beta-III and Beta-V spectrins may play crucial roles as longer actin-membrane cross-linkers or fulfill the need for greater extensible flexibility than can be provided by the other smaller conventional spectrins. Members of this family contain two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 116 matched cddid_all.tbl CDD cd21194 cd21194 409043 CH_beta_spectrin_rpt2 second calponin homology (CH) domain found in the beta spectrin family. The beta spectrin family includes beta-I, -II, -III, -IV and -V spectrins. Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is composed of two antiparallel dimers of alpha- and beta- subunits. Beta-I spectrin, also called spectrin beta chain, erythrocytic (SPTB), may be involved in anaemia pathogenesis. Beta-II spectrin, also called spectrin beta chain, non-erythrocytic 1 (SPTBN1), or fodrin beta chain, is a component of fodrin, which is the general spectrin-like protein that seems to be involved in secretion. Fodrin interacts with calmodulin in a calcium-dependent manner and is thus a candidate for the calcium-dependent movement of the cytoskeleton at the membrane. Beta-IV spectrin is also called spectrin, non-erythroid beta chain 3 (SPTBN3) or spectrin beta chain, non-erythrocytic 4 (SPTBN4). Its mutation associates with congenital myopathy, neuropathy, and central deafness. Beta-III spectrin is also called spectrin beta chain, non-erythrocytic 2 (SPTBN2), or spinocerebellar ataxia 5 protein (SCA5). Beta-V spectrin, also called spectrin beta chain, non-erythrocytic 5 (SPTBN5), is a mammalian ortholog of Drosophila beta H spectrin. Beta-III and Beta-V spectrins may play crucial roles as longer actin-membrane cross-linkers or fulfill the need for greater extensible flexibility than can be provided by the other smaller conventional spectrins. Members of this family contain two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 105 matched cddid_all.tbl CDD cd21195 cd21195 409044 CH_MICAL2_3-like calponin homology (CH) domain found in molecule interacting with CasL protein 2 (MICAL-2), MICAL-3, and similar proteins. Molecule interacting with CasL protein (MICAL) is a large, multidomain, cytosolic protein with a single LIM domain, a calponin homology (CH) domain and a flavoprotein monooxygenase (MO) domain. In Drosophila, MICAL is expressed in axons, interacts with the neuronal A (PlexA) receptor and is required for Semaphorin 1a (Sema-1a)-PlexA-mediated repulsive axon guidance. The LIM and CH domains mediate interactions with the cytoskeleton, cytoskeletal adaptor proteins, and other signaling proteins. The flavoprotein MO is required for semaphorin-plexin repulsive axon guidance during axonal pathfinding in the Drosophila neuromuscular system. In addition, MICAL functions to interact with Rab13 and Rab8 to coordinate the assembly of tight junctions and adherens junctions in epithelial cells. Thus, MICAL is also called junctional Rab13-binding protein (JRAB). Members of this family, which includes MICAL-2, MICAL-3, and similar proteins, contain one CH domain. CH domains are actin filament (F-actin) binding motifs. 110 matched cddid_all.tbl CDD cd21196 cd21196 409045 CH_MICAL1 calponin homology (CH) domain found in molecule interacting with CasL protein 1. MICAL-1, also called NEDD9-interacting protein with calponin homology and LIM domains, acts as a [F-actin]-monooxygenase that promotes depolymerization of F-actin by mediating oxidation of specific methionine residues on actin to form methionine-sulfoxide, resulting in actin filament disassembly and preventing repolymerization. In the absence of actin, it also functions as a NADPH oxidase producing H(2)O(2). MICAL-1 acts as a cytoskeletal regulator that connects NEDD9 to intermediate filaments. It also acts as a negative regulator of apoptosis via its interaction with STK38 and STK38L. MICAL-1 is a Rab effector protein that plays a role in vesicle trafficking. It contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 106 matched cddid_all.tbl CDD cd21197 cd21197 409046 CH_MICALL calponin homology (CH) domain found in the MICAL-like protein family. The MICAL-L family includes MICAL-L1 and MICAL-L2. MICAL-L1, also called molecule interacting with Rab13 (MIRab13), is a probable lipid-binding protein with higher affinity for phosphatidic acid, a lipid enriched in recycling endosome membranes. It is a tubular endosomal membrane hub that connects Rab35 and Arf6 with Rab8a. It may be involved in a late step of receptor-mediated endocytosis regulating endocytosed-EGF receptor trafficking. Alternatively, it may regulate slow endocytic recycling of endocytosed proteins back to the plasma membrane. MICAL-L1 may indirectly play a role in neurite outgrowth. MICAL-L2, also called junctional Rab13-binding protein (JRAB), or molecule interacting with CasL-like 2, acts as an effector of small Rab GTPases which is involved in junctional complexes assembly through the regulation of cell adhesion molecule transport to the plasma membrane, and actin cytoskeleton reorganization. It regulates the endocytic recycling of occludins, claudins, and E-cadherin to the plasma membrane and may thereby regulate the establishment of tight junctions and adherens junctions. Members of this family contain a single copy of CH domain. CH domains are actin filament (F-actin) binding motifs. 105 matched cddid_all.tbl CDD cd21198 cd21198 409047 CH_EHBP calponin homology (CH) domain found in the EH domain-binding protein (EHBP) family. The EHBP family includes EHBP1 and EHBP1-like protein (EHBP1L1). EHBP1 is a regulator of endocytic recycling and may play a role in actin reorganization by linking clathrin-mediated endocytosis to the actin cytoskeleton. It may act as an effector of small GTPases, including RAB-10 (Rab10), and play a role in vesicle trafficking. EHBP1 is associated with aggressive prostate cancer and insulin-stimulated trafficking and cell migration. EHBP1L1 may also act as Rab effector protein and play a role in vesicle trafficking. It coordinates Rab8 and Bin1 to regulate apical-directed transport in polarized epithelial cells. Members of this family contain a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 105 matched cddid_all.tbl CDD cd21199 cd21199 409048 CH_CYTS calponin homology (CH) domain found in the cytospin family. The cytospin family includes cytospin-A and cytospin-B. Cytospin-A, also called renal carcinoma antigen NY-REN-22, sperm antigen with calponin homology and coiled-coil domains 1-like, or SPECC1-like (SPECC1L) protein, is involved in cytokinesis and spindle organization. It may play a role in actin cytoskeleton organization and microtubule stabilization and hence, is required for proper cell adhesion and migration. Cytospin-B, also called nuclear structure protein 5 (NSP5), sperm antigen HCMOGT-1, or sperm antigen with calponin homology and coiled-coil domains 1 (SPECC1), is a novel fusion partner to PDGFRB in juvenile myelomonocytic leukemia with translocation t(5;17)(q33;p11.2). Members of this family contain a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 112 matched cddid_all.tbl CDD cd21200 cd21200 409049 CH_SMTN-like calponin homology (CH) domain found in the smoothelin family. The smoothelin family includes smoothelin and smoothelin-like proteins. Smoothelins are actin-binding cytoskeletal proteins that are abundantly expressed in healthy visceral (smoothelin-A) and vascular (smoothelin-B) smooth muscle. SMTNL1, also called calponin homology-associated smooth muscle protein (CHASM), plays a role in the regulation of contractile properties of both striated and smooth muscles. It can bind to calmodulin and tropomyosin. When it is unphosphorylated, SMTNL1 may inhibit myosin dephosphorylation. SMTNL2 is highly expressed in skeletal muscle and could be associated with differentiating myocytes. Members of this family contain a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 107 matched cddid_all.tbl CDD cd21201 cd21201 409050 CH_VAV calponin homology (CH) domain found in VAV proteins. VAV proteins function both as cytoplasmic guanine nucleotide exchange factors (GEFs) for Rho GTPases and as scaffold proteins, and they play important roles in cell signaling by coupling cell surface receptors to various effector functions. They play key roles in processes that require cytoskeletal reorganization including immune synapse formation, phagocytosis, cell spreading, and platelet aggregation, among others. Vertebrates have three VAV proteins (VAV1, VAV2, and VAV3). VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. This model corresponds to the CH domain, an actin-binding domain which is present as a single copy in VAV proteins. 117 matched cddid_all.tbl CDD cd21202 cd21202 409051 CH_PIX calponin homology (CH) domain found in the Pak Interactive eXchange factor family. Pak Interactive eXchange factor (PIX) proteins are Rho guanine nucleotide exchange factors (GEFs), which activate small GTPases by exchanging bound GDP for free GTP. They act as GEFs for both Cdc42 and Rac1, and have been implicated in cell motility, adhesion, neurite outgrowth, and cell polarity. Vertebrates contain two proteins from the PIX family, alpha-PIX and beta-PIX. Alpha-PIX, also called Rho guanine nucleotide exchange factor 6 (ARHGEF6), is localized in dendritic spines where it regulates spine morphogenesis. It controls dendritic length and spine density in the hippocampus. Mutations in the ARHGEF6 gene cause X-linked intellectual disability in humans. Beta-PIX, also called Rho guanine nucleotide exchange factor 7 (ARHGEF7), plays important roles in regulating neuroendocrine exocytosis, focal adhesion maturation, cell migration, synaptic vesicle localization, and insulin secretion. Both alpha-PIX and beta-PIX contain a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs. 114 matched cddid_all.tbl CDD cd21203 cd21203 409052 CH_AtKIN14-like calponin homology (CH) domain found in Arabidopsis thaliana Kinesin-like KIN-14 protein family. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. This family includes a group of kinesin-like proteins belonging to KIN-14 protein family. They all contain a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs. 112 matched cddid_all.tbl CDD cd21204 cd21204 409053 CH_GAS2-like calponin homology (CH) domain found in the growth arrest-specific protein 2 family. The growth arrest-specific protein 2 (GAS-2) family includes GAS-2, and GAS-2 like proteins, GAS2L1-3. GAS-2 may play a role in apoptosis by acting as a cell death substrate for caspases. GAS2L1 (also called GAS2-related protein on chromosome 22 or growth arrest-specific protein 2-like 1) and GAS2L2 (also called GAS2-related protein on chromosome 17 or growth arrest-specific protein 2-like 2) may be involved in the cross-linking of microtubules and microfilaments. GAS2L3, also called GAS2-like protein 3, is a cytoskeletal linker protein that may promote and stabilize the formation of the actin and microtubule network. Members of this family contain a single copy of the CH domain at the N-terminal region. CH domains are actin filament (F-actin) binding motifs. 131 matched cddid_all.tbl CDD cd21205 cd21205 409054 CH_LRCH calponin homology (CH) domain found in the leucine-rich repeat and calponin homology domain-containing protein family. The leucine-rich repeat and calponin homology domain-containing protein (LRCH) family includes LRCH1-4. LRCH1, also called calponin homology domain-containing protein 1, or neuronal protein 81 (NP81), acts as a negative regulator of GTPase Cdc42 by sequestering Cdc42-guanine exchange factor DOCK8. LRCH2 may play a role in the organization of the cytoskeleton. LRCH3 is part of the DISP complex and may regulate the association of septins with actin and thereby regulate the actin cytoskeleton. LRCH4, also called leucine-rich repeat neuronal protein 4, or leucine-rich neuronal protein, acts as a novel Toll-like receptor (TLR) accessory protein that regulates the innate immune response. Members of this family contain a single copy of the CH domain at the C-terminus. CH domains are actin filament (F-actin) binding motifs. 107 matched cddid_all.tbl CDD cd21206 cd21206 409055 CH_IQGAP calponin homology (CH) domain found in the IQ motif containing GTPase activating protein family. Members of the IQ motif containing GTPase activating protein (IQGAP) family are associated with the Ras GTP-binding protein and act as essential regulators of cytoskeletal function. There are three known IQGAP family members: IQGAP1, IQGAP2, and IQGAP3. They are multi-domain molecules having a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeats, a single WW domain, four IQ motifs that mediate interactions with calmodulin, and a RasGAP related domain that binds active Rho family GTPases. IQGAP1 negatively regulates Ras family GTPases by stimulating their intrinsic GTPase activity. It lacks GAP activity. Both IQGAP1 and IQGAP2 specifically bind to Cdc42 and Rac1, but not to RhoA. Despite similarities to part of the sequence of RasGAP, neither IQGAP1 nor IQGAP2 interacts with Ras. IQGAP3 regulates the organization of the cytoskeleton under the regulation of Rac1 and Cdc42 in neuronal cells. The depletion of IQGAP3 is shown to impair neurite or axon outgrowth in neuronal cells with disorganized cytoskeleton. 118 matched cddid_all.tbl CDD cd21207 cd21207 409056 CH_dMP20-like calponin homology (CH) domain found in Drosophila melanogaster muscle-specific protein 20 (dMP20) and similar domains. This subfamily contains Drosophila melanogaster muscle-specific protein 20 (dMP20), Echinococcus granulosus myophilin, Dictyostelium discoideum Rac guanine nucleotide exchange factor B (also called Trix), and similar proteins. dMP20 is present only in the synchronous muscles of D. melanogaster. It may be involved in the system linking the nerve impulse with the contraction or the relaxation process. Trix is involved in the regulation of the late steps of the endocytic pathway. dMP20 contains a single copy of the CH domain, while Trix (triple CH-domain array exchange factor) contains three, two type 3 CH domains which are included in this model, and one type 1 CH domain that is not included in this subfamily, but is part of the superfamily. CH domains are actin filament (F-actin) binding motifs. 107 matched cddid_all.tbl CDD cd21208 cd21208 409057 CH_LMO7-like calponin homology (CH) domain found in LIM domain only protein 7 and similar proteins. This family includes LIM domain only protein 7 (LMO-7) and LIM and calponin homology domains-containing protein 1 (LIMCH1), and similar proteins. LMO-7, also called F-box only protein 20, or LOMP, is a transcription regulator for expression of many Emery-Dreifuss muscular dystrophy (EDMD)-relevant genes. It binds to alpha-actinin and AF6/afadin at adherens junctions for epithelial cell-cell adhesion. LIMCH1 acts as an actin stress fiber-associated protein that activates the non-muscle myosin IIa complex by promoting the phosphorylation of its regulatory subunit MRLC/MYL9. It positively regulates actin stress fiber assembly and stabilizes focal adhesions, and therefore negatively regulates cell spreading and cell migration. Members of this family contain a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs. 119 matched cddid_all.tbl CDD cd21209 cd21209 409058 CH_TAGLN-like calponin homology (CH) domain found in the transgelin family. The transgelin (TAGLN) family includes transgelin, transgelin-2 and transgelin-3. Transgelin, also called 22 kDa actin-binding protein, protein WS3-10, or smooth muscle protein 22-alpha (SM22-alpha), acts as an actin cross-linking/gelling protein that may be involved in calcium interactions and in regulating contractile properties of the cell. Transgelin-2, also called epididymis tissue protein Li 7e, or SM22-alpha homolog, acts as an actin-binding protein that induces actin gelation and regulates actin cytoskeleton. It may participate in the development and progression of multiple cancers. Transgelin-3, also called neuronal protein 22 (NP22), or neuronal protein NP25, may have a role in alcohol-related adaptations and may mediate regulatory signal transduction pathways in neurons. Members of this family contain a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 119 matched cddid_all.tbl CDD cd21210 cd21210 409059 CH_SCP1-like calponin homology (CH) domain found in Saccharomyces cerevisiae transgelin (SCP1) and similar proteins. The family includes transgelins from Saccharomyces cerevisiae and Schizosaccharomyces pombe, which are also called SCP1 and STG1, respectively. Transgelin, also called calponin homolog 1, has actin-binding and actin-bundling activity. It stabilizes actin filaments against disassembly. Transgelin contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 101 matched cddid_all.tbl CDD cd21211 cd21211 409060 CH_CNN calponin homology (CH) domain found in the calponin family. Calponin is an actin filament-associated regulatory protein expressed in smooth muscle and many types of non-muscle cells. There are three calponin isoforms, calponin-1, -2, -3. All of them are actin-binding proteins with functions in inhibiting actin-activated myosin ATPase and stabilizing the actin cytoskeleton. Calponin-1 is specifically expressed in smooth muscle cells and plays a role in fine-tuning smooth muscle contractility. Calponin-2 is expressed in both smooth muscle and non-muscle cells and regulates multiple actin cytoskeleton-based functions. Calponin-3 is expressed in the brain and participates in actin cytoskeleton-based activities in embryonic development and myogenesis. Members of this family contain a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 108 matched cddid_all.tbl CDD cd21212 cd21212 409061 CH_NAV2-like calponin homology (CH) domain found in neuron navigator (NAV) 2, NAV3, and similar proteins. This family includes neuron navigator 2 (NAV2) and NAV3, both of which contain a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs. NAV2, also called helicase APC down-regulated 1 (HELAD1), pore membrane and/or filament-interacting-like protein 2 (POMFIL2), retinoic acid inducible in neuroblastoma 1 (RAINB1), Steerin-2 (STEERIN2), or Unc-53 homolog 2 (unc53H2), possesses 3' to 5' helicase activity and exonuclease activity. It is involved in neuronal development, specifically in the development of different sensory organs. NAV3, also called pore membrane and/or filament-interacting-like protein 1 (POMFIL1), Steerin-3 (STEERIN3), or Unc-53 homolog 3 (unc53H3), may regulate IL2 production by T-cells. It may be involved in neuron regeneration. 105 matched cddid_all.tbl CDD cd21213 cd21213 409062 CH_DIXDC1 calponin homology (CH) domain found in Dixin and similar proteins. Dixin, also called coiled-coil protein DIX1, coiled-coil-DIX1, or DIX domain-containing protein 1, is a positive effector of the Wnt signaling pathway. It activates WNT3A signaling via DVL2 and regulates JNK activation by AXIN1 and DVL2. Members of this family contain a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs. 107 matched cddid_all.tbl CDD cd21214 cd21214 409063 CH_ACTN_rpt1 first calponin homology (CH) domain found in the alpha-actinin family. The alpha-actinin (ACTN) family includes alpha-actinin-1, -2, -3, and -4. They are F-actin cross-linking proteins which are thought to anchor actin to a variety of intracellular structures. ACTN1 mutations cause congenital macrothrombocytopenia. ACTN2 mutations are associated with cardiomyopathies, as well as skeletal muscle disorder. ACTN3 is critical in anchoring the myofibrillar actin filaments and plays a key role in muscle contraction. ACTN4 is associated with cell motility and cancer invasion. It is probably involved in vesicular trafficking via its association with the CART complex, which is necessary for efficient transferrin receptor recycling but not for epidermal growth factor receptor (EGFR) degradation. Members of this family contain two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 105 matched cddid_all.tbl CDD cd21215 cd21215 409064 CH_SpAIN1-like_rpt1 first calponin homology (CH) domain found in Schizosaccharomyces pombe alpha-actinin-like protein 1 and similar proteins. Schizosaccharomyces pombe alpha-actinin-like protein 1 (SpAIN1) binds to actin and is involved in actin-ring formation and organization. It plays a role in cytokinesis and is involved in septation. Members of this family contain two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 107 matched cddid_all.tbl CDD cd21216 cd21216 409065 CH_ACTN_rpt2 second calponin homology (CH) domain found in the alpha-actinin family. The alpha-actinin (ACTN) family includes alpha-actinin-1, -2, -3, and -4. They are F-actin cross-linking proteins which are thought to anchor actin to a variety of intracellular structures. ACTN1 mutations cause congenital macrothrombocytopenia. ACTN2 mutations are associated with cardiomyopathies, as well as skeletal muscle disorder. ACTN3 is critical in anchoring the myofibrillar actin filaments and plays a key role in muscle contraction. ACTN4 is associated with cell motility and cancer invasion. It is probably involved in vesicular trafficking via its association with the CART complex, which is necessary for efficient transferrin receptor recycling but not for epidermal growth factor receptor (EGFR) degradation. Members of this family contain two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 115 matched cddid_all.tbl CDD cd21217 cd21217 409066 CH_PLS_FIM_rpt1 first calponin homology (CH) domain found in the plastin/fimbrin family. This family includes plastin and fimbrin. Plastin has three isoforms, plastin-1, -2, and -3, which are all actin-bundling proteins. Plastin-1, also called intestine-specific plastin, or I-plastin, is an actin-bundling protein in the absence of calcium. Plastin-2, also called L-plastin, LC64P, or lymphocyte cytosolic protein 1 (LCP-1), plays a role in the activation of T-cells in response to costimulation through TCR/CD3 and CD2 or CD28. It modulates the cell surface expression of IL2RA/CD25 and CD69. Plastin-3, also called T-plastin, is found in intestinal microvilli, hair cell stereocilia, and fibroblast filopodia. It may play a role in the regulation of bone development. Fimbrin has been found in plants and fungi. Arabidopsis thaliana fimbrin (AtFIM) includes fimbrin-1, -2, -3, -4, and -5; they cross-link actin filaments (F-actin) in a calcium independent manner. They stabilize and prevent F-actin depolymerization mediated by profilin. They act as key regulators of actin cytoarchitecture, probably involved in cell cycle, cell division, cell elongation and cytoplasmic tractus. AtFIM5 is an actin bundling factor that is required for pollen germination and pollen tube growth. Fungal fimbrin binds to actin, and functionally associates with actin structures involved in the development and maintenance of cell polarity. Members of this family contain four copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 114 matched cddid_all.tbl CDD cd21218 cd21218 409067 CH_PLS_FIM_rpt2 second calponin homology (CH) domain found in the plastin/fimbrin family. This family includes plastin and fimbrin. Plastin has three isoforms, plastin-1, -2, and -3, which are all actin-bundling proteins. Plastin-1, also called intestine-specific plastin, or I-plastin, is an actin-bundling protein in the absence of calcium. Plastin-2, also called L-plastin, LC64P, or lymphocyte cytosolic protein 1 (LCP-1), plays a role in the activation of T-cells in response to costimulation through TCR/CD3 and CD2 or CD28. It modulates the cell surface expression of IL2RA/CD25 and CD69. Plastin-3, also called T-plastin, is found in intestinal microvilli, hair cell stereocilia, and fibroblast filopodia. It may play a role in the regulation of bone development. Fimbrin has been found in plants and fungi. Arabidopsis thaliana fimbrin (AtFIM) includes fimbrin-1, -2, -3, -4, and -5; they cross-link actin filaments (F-actin) in a calcium independent manner. They stabilize and prevent F-actin depolymerization mediated by profilin. They act as key regulators of actin cytoarchitecture, probably involved in cell cycle, cell division, cell elongation and cytoplasmic tractus. AtFIM5 is an actin bundling factor that is required for pollen germination and pollen tube growth. Fungal fimbrin binds to actin, and functionally associates with actin structures involved in the development and maintenance of cell polarity. Members of this family contain four copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 114 matched cddid_all.tbl CDD cd21219 cd21219 409068 CH_PLS_FIM_rpt3 third calponin homology (CH) domain found in the plastin/fimbrin family. This family includes plastin and fimbrin. Plastin has three isoforms, plastin-1, -2, and -3. Plastin-1, also called intestine-specific plastin, or I-plastin, is an actin-bundling protein in the absence of calcium. Plastin-2, also called L-plastin, or LC64P, or lymphocyte cytosolic protein 1 (LCP-1), is an actin-binding protein that plays a role in the activation of T-cells in response to costimulation through TCR/CD3 and CD2 or CD28. It modulates the cell surface expression of IL2RA/CD25 and CD69. Plastin-3, also called T-plastin, is an actin-bundling protein found in intestinal microvilli, hair cell stereocilia, and fibroblast filopodia. It may play a role in the regulation of bone development. Fimbrin has been found in plants and fungi. Arabidopsis thaliana fimbrin (AtFIM) includes fimbrin-1, -2, -3, -4, and -5, which cross-link actin filaments (F-actin) in a calcium independent manner. They stabilize and prevent F-actin depolymerization mediated by profilin. They act as key regulators of actin cytoarchitecture, probably involved in cell cycle, cell division, cell elongation and cytoplasmic tractus. AtFIM5 is an actin bundling factor that is required for pollen germination and pollen tube growth. Fungal fimbrin binds to actin, and functionally associates with actin structures involved in the development and maintenance of cell polarity. Members of this family contain four copies of the CH domain. This model corresponds to the third CH domain. CH domains are actin filament (F-actin) binding motifs. 113 matched cddid_all.tbl CDD cd21220 cd21220 409069 CH_PLS_FIM_rpt4 fourth calponin homology (CH) domain found in the plastin/fimbrin family. This family includes plastin and fimbrin. Plastin has three isoforms, plastin-1, -2, and -3. Plastin-1, also called intestine-specific plastin, or I-plastin, is an actin-bundling protein in the absence of calcium. Plastin-2, also called L-plastin, or LC64P, or lymphocyte cytosolic protein 1 (LCP-1), is an actin-binding protein that plays a role in the activation of T-cells in response to costimulation through TCR/CD3 and CD2 or CD28. It modulates the cell surface expression of IL2RA/CD25 and CD69. Plastin-3, also called T-plastin, is an actin-bundling protein found in intestinal microvilli, hair cell stereocilia, and fibroblast filopodia. It may play a role in the regulation of bone development. Fimbrin has been found in plants and fungi. Arabidopsis thaliana fimbrin (AtFIM) includes fimbrin-1, -2, -3, -4, and -5, which cross-link actin filaments (F-actin) in a calcium independent manner. They stabilize and prevent F-actin depolymerization mediated by profilin. They act as key regulators of actin cytoarchitecture, probably involved in cell cycle, cell division, cell elongation and cytoplasmic tractus. AtFIM5 is an actin bundling factor that is required for pollen germination and pollen tube growth. Fungal fimbrin binds to actin, and functionally associates with actin structures involved in the development and maintenance of cell polarity. Members of this family contain four copies of the CH domain. This model corresponds to the fourth CH domain. CH domains are actin filament (F-actin) binding motifs. 105 matched cddid_all.tbl CDD cd21221 cd21221 409070 CH_PARV_rpt1 first calponin homology (CH) domain found in the parvin family. The parvin family includes alpha-parvin, beta-parvin, and gamma-parvin. Alpha-parvin, also called actopaxin, calponin-like integrin-linked kinase-binding protein (CH-ILKBP), or matrix-remodeling-associated protein 2, plays a role in sarcomere organization and in smooth muscle cell contraction. It is required for normal development of the embryonic cardiovascular system, and for normal septation of the heart outflow tract. Beta-parvin, also called affixin, is an adapter protein that plays a role in integrin signaling via ILK and in activation of the GTPases Cdc42 and Rac1 by guanine exchange factors, such as ARHGEF6. Both alpha-parvin and beta-parvin are involved in the reorganization of the actin cytoskeleton and the formation of lamellipodia, and both play roles in cell adhesion, cell spreading, establishment or maintenance of cell polarity, and cell migration. Gamma-parvin probably plays a role in the regulation of cell adhesion and cytoskeleton organization. Members of this family contain two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 106 matched cddid_all.tbl CDD cd21222 cd21222 409071 CH_PARV_rpt2 second calponin homology (CH) domain found in the parvin family. The parvin family includes alpha-parvin, beta-parvin, and gamma-parvin. Alpha-parvin, also called actopaxin, calponin-like integrin-linked kinase-binding protein (CH-ILKBP), or matrix-remodeling-associated protein 2, plays a role in sarcomere organization and in smooth muscle cell contraction. It is required for normal development of the embryonic cardiovascular system, and for normal septation of the heart outflow tract. Beta-parvin, also called affixin, is an adapter protein that plays a role in integrin signaling via ILK and in activation of the GTPases Cdc42 and Rac1 by guanine exchange factors, such as ARHGEF6. Both alpha-parvin and beta-parvin are involved in the reorganization of the actin cytoskeleton and the formation of lamellipodia, and both play roles in cell adhesion, cell spreading, establishment or maintenance of cell polarity, and cell migration. Gamma-parvin probably plays a role in the regulation of cell adhesion and cytoskeleton organization. Members of this family contain two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 121 matched cddid_all.tbl CDD cd21223 cd21223 409072 CH_ASPM_rpt1 first calponin homology (CH) domain found in abnormal spindle-like microcephaly-associated protein (ASPM) and similar proteins. ASPM, also called abnormal spindle protein homolog, or Asp homolog, is involved in mitotic spindle regulation and coordination of mitotic processes. It may also have a preferential role in regulating neurogenesis. Members of this family contain two copies of the CH domain in the middle region. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 113 matched cddid_all.tbl CDD cd21224 cd21224 409073 CH_ASPM_rpt2 second calponin homology (CH) domain found in abnormal spindle-like microcephaly-associated protein (ASPM) and similar proteins. ASPM, also called abnormal spindle protein homolog, or Asp homolog, is involved in mitotic spindle regulation and coordination of mitotic processes. It may also have a preferential role in regulating neurogenesis. Members of this family contain two copies of CH domain in the middle region. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 138 matched cddid_all.tbl CDD cd21225 cd21225 409074 CH_CTX_rpt1 first calponin homology (CH) domain found in cortexillin. Cortexillins are actin-bundling proteins that play a critical role in regulating cell morphology and actin cytoskeleton reorganization. They play a major role in cytokinesis and contain two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 111 matched cddid_all.tbl CDD cd21226 cd21226 409075 CH_CTX_rpt2 second calponin homology (CH) domain found in cortexillin. Cortexillins are actin-bundling proteins that play a critical role in regulating cell morphology and actin cytoskeleton reorganization. They play a major role in cytokinesis and contain two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 103 matched cddid_all.tbl CDD cd21227 cd21227 409076 CH_jitterbug-like_rpt1 first calponin homology (CH) domain found in Drosophila melanogaster protein jitterbug and similar proteins. Protein jitterbug (Jbug) is an actin-meshwork organizing protein. It is required to maintain the shape and cell orientation of the Drosophila notum epithelium during flight muscle attachment to tendon cells. Jbug contains three copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 109 matched cddid_all.tbl CDD cd21228 cd21228 409077 CH_FLN_rpt1 first calponin homology (CH) domain found in filamins. The filamin family includes filamin-A (FLN-A), filamin-B (FLN-B) and filamin-C (FLN-C). Filamins function to anchor various transmembrane proteins to the actin cytoskeleton. FLN-A is also called actin-binding protein 280 (ABP-280), alpha-filamin, endothelial actin-binding protein, filamin-1, or non-muscle filamin. It promotes orthogonal branching of actin filaments and links actin filaments to membrane glycoproteins. It also serves as a scaffold for a wide range of cytoplasmic signaling proteins. FLN-B is also called ABP-278, ABP-280 homolog, actin-binding-like protein, beta-filamin, filamin homolog 1 (Fh1), filamin-3, thyroid autoantigen, truncated actin-binding protein, or truncated ABP. It connects cell membrane constituents to the actin cytoskeleton and may also promote orthogonal branching of actin filaments as well as link actin filaments to membrane glycoproteins. FLN-C, also called FLNc, ABP-280-like protein, ABP-L, actin-binding-like protein, filamin-2, or gamma-filamin, is a muscle-specific filamin that plays a central role in muscle cells, probably by functioning as a large actin-cross-linking protein. It may be involved in reorganizing the actin cytoskeleton in response to signaling events, and may also display structural functions at the Z lines in muscle cells. FLN-C is critical for normal myogenesis and for maintaining the structural integrity of the muscle fibers. Members of this family contain two copies of the CH domain. The model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 108 matched cddid_all.tbl CDD cd21229 cd21229 409078 CH_jitterbug-like_rpt2 second calponin homology (CH) domain found in Drosophila melanogaster protein jitterbug and similar proteins. Protein jitterbug (Jbug) is an actin-meshwork organizing protein. It is required to maintain the shape and cell orientation of the Drosophila notum epithelium during flight muscle attachment to tendon cells. Jbug contains three copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 105 matched cddid_all.tbl CDD cd21230 cd21230 409079 CH_FLN_rpt2 second calponin homology (CH) domain found in filamins. The filamin family includes filamin-A (FLN-A), filamin-B (FLN-B) and filamin-C (FLN-C). Filamins function to anchor various transmembrane proteins to the actin cytoskeleton. FLN-A is also called actin-binding protein 280 (ABP-280), alpha-filamin, endothelial actin-binding protein, filamin-1, or non-muscle filamin. It promotes orthogonal branching of actin filaments and links actin filaments to membrane glycoproteins. It also serves as a scaffold for a wide range of cytoplasmic signaling proteins. FLN-B is also called ABP-278, ABP-280 homolog, actin-binding-like protein, beta-filamin, filamin homolog 1 (Fh1), filamin-3, thyroid autoantigen, truncated actin-binding protein, or truncated ABP. It connects cell membrane constituents to the actin cytoskeleton and may also promote orthogonal branching of actin filaments as well as link actin filaments to membrane glycoproteins. FLN-C, also called FLNc, ABP-280-like protein, ABP-L, actin-binding-like protein, filamin-2, or gamma-filamin, is a muscle-specific filamin that plays a central role in muscle cells, probably by functioning as a large actin-cross-linking protein. It may be involved in reorganizing the actin cytoskeleton in response to signaling events, and may also display structural functions at the Z lines in muscle cells. FLN-C is critical for normal myogenesis and for maintaining the structural integrity of the muscle fibers. Members of this family contain two copies of the CH domain. The model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 103 matched cddid_all.tbl CDD cd21231 cd21231 409080 CH_DMD_rpt1 first calponin homology (CH) domain found in dystrophin and similar proteins. Dystrophin, encoded by the DMD gene, is a large, submembrane cytoskeletal protein that is the main component of the dystrophin-glycoprotein complex (DGC) in skeletal muscles. It links the transmembrane DGC to the actin cytoskeleton through binding strongly to the cytoplasmic tail of beta-dystroglycan, the transmembrane subunit of a highly O-glycosylated cell-surface protein. It is involved in maintaining the structural integrity of cells, as well as in the formation of the blood-brain barrier (BBB). Mutations in dystrophin lead to Duchenne muscular dystrophy (DMD). Moreover, dystrophin deficiency is associated with abnormal cerebral diffusion and perfusion, as well as in acute Trypanosoma cruzi infection. The dystrophin subfamily has been characterized by a compact cluster of domains comprising four EF-hand-like motifs and a ZZ-domain, followed by a looser region with two coiled-coils. These domains are believed to be involved in protein-protein interactions. In addition, dystrophin contains two syntrophin binding sites (SBSs) and a long N-terminal extension that comprises two actin-binding calponin homology (CH) domains, approximately 24 spectrin repeats (SRs) and a WW domain. This model corresponds to the first CH domain. 111 matched cddid_all.tbl CDD cd21232 cd21232 409081 CH_UTRN_rpt1 first calponin homology (CH) domain found in utrophin and similar proteins. Utrophin, also called dystrophin-related protein 1 (DRP-1), is an autosomal dystrophin homolog that increases dystrophic muscle function and reduces pathology. It is broadly expressed in both the mRNA and protein levels, and occurs in the cerebrovascular endothelium. Utrophin forms the utrophin-glycoprotein complex (UGC) by interacting with dystroglycans (DGs) and sarcoglycan-dystroglycans, as well as sarcoglycan and sarcospan (SG-SSPN) subcomplexes. It may act as a scaffolding protein that stabilizes lipid microdomains and clusters mechanosensitive channel subunits, and link the F-actin cytoskeleton to the cell membrane via the associated glycoprotein complex. Like dystrophin, utrophin has a compact cluster of domains comprising four EF-hand-like motifs and a ZZ-domain, followed by a looser region with two coiled-coils. These domains are believed to be involved in protein-protein interactions. In addition, it contains two syntrophin binding sites (SBSs) and a long N-terminal extension that comprises two actin-binding calponin homology (CH) domains, up to 24 spectrin repeats (SRs), and a WW domain. However, utrophin lacks the intrinsic microtubule binding activity of dystrophin SRs. This model corresponds to the first CH domain. 107 matched cddid_all.tbl CDD cd21233 cd21233 409082 CH_DMD_rpt2 second calponin homology (CH) domain found in dystrophin and similar proteins. Dystrophin, encoded by the DMD gene, is a large, submembrane cytoskeletal protein that is the main component of the dystrophin-glycoprotein complex (DGC) in skeletal muscles. It links the transmembrane DGC to the actin cytoskeleton through binding strongly to the cytoplasmic tail of beta-dystroglycan, the transmembrane subunit of a highly O-glycosylated cell-surface protein. It is involved in maintaining the structural integrity of cells, as well as in the formation of the blood-brain barrier (BBB). Mutations in dystrophin lead to Duchenne muscular dystrophy (DMD). Moreover, dystrophin deficiency is associated with abnormal cerebral diffusion and perfusion, as well as in acute Trypanosoma cruzi infection. The dystrophin subfamily has been characterized by a compact cluster of domains comprising four EF-hand-like motifs and a ZZ-domain, followed by a looser region with two coiled-coils. These domains are believed to be involved in protein-protein interactions. In addition, dystrophin contains two syntrophin binding sites (SBSs) and a long N-terminal extension that comprises two actin-binding calponin homology (CH) domains, approximately 24 spectrin repeats (SRs) and a WW domain. The model corresponds to the second CH domain. 111 matched cddid_all.tbl CDD cd21234 cd21234 409083 CH_UTRN_rpt2 second calponin homology (CH) domain found in utrophin and similar proteins. Utrophin, also called dystrophin-related protein 1 (DRP-1), is an autosomal dystrophin homolog that increases dystrophic muscle function and reduces pathology. It is broadly expressed in both the mRNA and protein levels, and occurs in the cerebrovascular endothelium. Utrophin forms the utrophin-glycoprotein complex (UGC) by interacting with dystroglycans (DGs) and sarcoglycan-dystroglycans, as well as sarcoglycan and sarcospan (SG-SSPN) subcomplexes. It may act as a scaffolding protein that stabilizes lipid microdomains and clusters mechanosensitive channel subunits, and link the F-actin cytoskeleton to the cell membrane via the associated glycoprotein complex. Like dystrophin, utrophin has a compact cluster of domains comprising four EF-hand-like motifs and a ZZ-domain, followed by a looser region with two coiled-coils. These domains are believed to be involved in protein-protein interactions. In addition, it contains two syntrophin binding sites (SBSs) and a long N-terminal extension that comprises two actin-binding calponin homology (CH) domains, up to 24 spectrin repeats (SRs), and a WW domain. However, utrophin lacks the intrinsic microtubule binding activity of dystrophin SRs. This model corresponds to the second CH domain. 104 matched cddid_all.tbl CDD cd21235 cd21235 409084 CH_PLEC_rpt1 first calponin homology (CH) domain found in plectin and similar proteins. Plectin, also called PCN, PLTN, hemidesmosomal protein 1 (HD1), or plectin-1, is a structural component of muscle. It interlinks intermediate filaments with microtubules and microfilaments, and anchors intermediate filaments to desmosomes or hemidesmosomes. It can also bind muscle proteins such as actin to membrane complexes in muscle. Plectin contains two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 119 matched cddid_all.tbl CDD cd21236 cd21236 409085 CH_DYST_rpt1 first calponin homology (CH) domain found in dystonin and similar proteins. Dystonin, also called 230 kDa bullous pemphigoid antigen, 230/240 kDa bullous pemphigoid antigen, bullous pemphigoid antigen 1 (BPA or BPAG1), dystonia musculorum protein, or hemidesmosomal plaque protein, is a cytoskeletal linker protein that acts as an integrator of intermediate filaments, actin, and microtubule cytoskeleton networks. It is required for anchoring either intermediate filaments to the actin cytoskeleton in neural and muscle cells, or keratin-containing intermediate filaments to hemidesmosomes in epithelial cells. Dystonin contains two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 128 matched cddid_all.tbl CDD cd21237 cd21237 409086 CH_MACF1_rpt1 first calponin homology (CH) domain found in microtubule-actin cross-linking factor 1, isoforms 1/2/3/5 (MACF1) and similar proteins. MACF1, also called 620 kDa actin-binding protein (ABP620), actin cross-linking family protein 7 (ACF7), macrophin-1, or trabeculin-alpha, is a large protein containing numerous spectrin and leucine-rich repeat (LRR) domains. It facilitates actin-microtubule interactions at the cell periphery and couples the microtubule network to cellular junctions. MACF1 contains two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 118 matched cddid_all.tbl CDD cd21238 cd21238 409087 CH_PLEC_rpt2 second calponin homology (CH) domain found in plectin and similar proteins. Plectin, also called PCN, PLTN, hemidesmosomal protein 1 (HD1), or plectin-1, is a structural component of muscle. It interlinks intermediate filaments with microtubules and microfilaments and anchors intermediate filaments to desmosomes or hemidesmosomes. It can also bind muscle proteins such as actin to membrane complexes in muscle. Plectin contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 106 matched cddid_all.tbl CDD cd21239 cd21239 409088 CH_DYST_rpt2 second calponin homology (CH) domain found in dystonin and similar proteins. Dystonin, also called 230 kDa bullous pemphigoid antigen, 230/240 kDa bullous pemphigoid antigen, bullous pemphigoid antigen 1 (BPA or BPAG1), dystonia musculorum protein, or hemidesmosomal plaque protein, is a cytoskeletal linker protein that acts as an integrator of intermediate filaments, actin, and microtubule cytoskeleton networks. It is required for anchoring either intermediate filaments to the actin cytoskeleton in neural and muscle cells, or keratin-containing intermediate filaments to hemidesmosomes in epithelial cells. Dystonin contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 104 matched cddid_all.tbl CDD cd21240 cd21240 409089 CH_MACF1_rpt2 second calponin homology (CH) domain found in microtubule-actin cross-linking factor 1, isoforms 1/2/3/5 (MACF1) and similar proteins. MACF1, also called 620 kDa actin-binding protein (ABP620), actin cross-linking family protein 7 (ACF7), macrophin-1, or trabeculin-alpha, is a large protein containing numerous spectrin and leucine-rich repeat (LRR) domains. It facilitates actin-microtubule interactions at the cell periphery and couples the microtubule network to cellular junctions. MACF1 contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 107 matched cddid_all.tbl CDD cd21241 cd21241 409090 CH_SYNE1_rpt1 first calponin homology (CH) domain found in synaptic nuclear envelope protein 1 and similar proteins. Synaptic nuclear envelope protein 1 (SYNE-1), also called nesprin-1, enaptin, KASH domain-containing protein 1 (KASH1), myocyte nuclear envelope protein 1 (MYNE-1), or nuclear envelope spectrin repeat protein 1, is a multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain subcellular spatial organization. SYNE-1 also acts as a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex, which is involved in the connection between the nuclear lamina and the cytoskeleton. SYNE-1 contains two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 113 matched cddid_all.tbl CDD cd21242 cd21242 409091 CH_SYNE2_rpt1 first calponin homology (CH) domain found in synaptic nuclear envelope protein 2. Synaptic nuclear envelope protein 2 (SYNE-2), also called nesprin-2, KASH domain-containing protein 2 (KASH2), nuclear envelope spectrin repeat protein 2, nucleus and actin connecting element protein, or protein NUANCE, is a multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain subcellular spatial organization. SYNE-2 also acts as a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex, which is involved in the connection between the nuclear lamina and the cytoskeleton. SYNE-2 contains two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 111 matched cddid_all.tbl CDD cd21243 cd21243 409092 CH_SYNE1_rpt2 second calponin homology (CH) domain found in synaptic nuclear envelope protein 1 (SYNE-1) and similar proteins. SYNE-1, also called nesprin-1, enaptin, KASH domain-containing protein 1 (KASH1), myocyte nuclear envelope protein 1 (MYNE-1), or nuclear envelope spectrin repeat protein 1, is a multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain subcellular spatial organization. SYNE-1 also acts as a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex, which is involved in the connection between the nuclear lamina and the cytoskeleton. SYNE-1 contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 109 matched cddid_all.tbl CDD cd21244 cd21244 409093 CH_SYNE2_rpt2 second calponin homology (CH) domain found in synaptic nuclear envelope protein 2 (SYNE-2) and similar proteins. SYNE-2, also called nesprin-2, KASH domain-containing protein 2 (KASH2), nuclear envelope spectrin repeat protein 2, nucleus and actin connecting element protein, or protein NUANCE, is a multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain subcellular spatial organization. SYNE-2 also acts as a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex, which is involved in the connection between the nuclear lamina and the cytoskeleton. SYNE-2 contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 109 matched cddid_all.tbl CDD cd21245 cd21245 409094 CH_CLMN_rpt2 second calponin homology (CH) domain found in calmin and similar proteins. Calmin, also called calponin-like transmembrane domain protein, is a protein with calponin homology (CH) and transmembrane domains expressed in maturing spermatogenic cells. It may be involved in the development and/or maintenance of neuronal functions. Calmin contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 106 matched cddid_all.tbl CDD cd21246 cd21246 409095 CH_SPTB-like_rpt1 first calponin homology (CH) domain found in the beta-I spectrin-like subfamily. The beta-I spectrin-like family includes beta-I, -II, -III and -IV spectrins. Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is composed of two antiparallel dimers of alpha- and beta- subunits. Beta-I spectrin, also called spectrin beta chain, erythrocytic (SPTB), may be involved in anaemia pathogenesis. Beta-II spectrin, also called spectrin beta chain, non-erythrocytic 1 (SPTBN1), or fodrin beta chain, is a component of fodrin, which is the general spectrin-like protein that seems to be involved in secretion. Fodrin interacts with calmodulin in a calcium-dependent manner and is thus a candidate for the calcium-dependent movement of the cytoskeleton at the membrane. Beta-III spectrin, also called spectrin beta chain, non-erythrocytic 2 (SPTBN2), or spinocerebellar ataxia 5 protein (SCA5), may play a crucial role as a longer actin-membrane cross-linker or fulfill the need for greater extensible flexibility than can be provided by the other smaller conventional spectrins. Beta-IV spectrin is also called spectrin, non-erythroid beta chain 3 (SPTBN3) or spectrin beta chain, non-erythrocytic 4 (SPTBN4). Its mutation associates with congenital myopathy, neuropathy, and central deafness. Members of this subfamily contain two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 117 matched cddid_all.tbl CDD cd21247 cd21247 409096 CH_SPTBN5_rpt1 first calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 5 (SPTBN5) and similar proteins. Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is composed of two antiparallel dimers of alpha- and beta- subunits. SPTBN5, also called beta-V spectrin, is a mammalian ortholog of Drosophila beta H spectrin that may play a crucial role as a longer actin-membrane cross-linker or to fulfill the need for greater extensible flexibility than can be provided by the other smaller conventional spectrins. SPTBN5 contains two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 125 matched cddid_all.tbl CDD cd21248 cd21248 409097 CH_SPTB_like_rpt2 second calponin homology (CH) domain found in the beta-I spectrin-like subfamily. The beta-I spectrin-like family includes beta-I, -II, -III and -IV spectrins. Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is composed of two antiparallel dimers of alpha- and beta- subunits. Beta-I spectrin, also called spectrin beta chain, erythrocytic (SPTB), may be involved in anaemia pathogenesis. Beta-II spectrin, also called spectrin beta chain, non-erythrocytic 1 (SPTBN1), or fodrin beta chain, is a component of fodrin, which is the general spectrin-like protein that seems to be involved in secretion. Fodrin interacts with calmodulin in a calcium-dependent manner and is thus a candidate for the calcium-dependent movement of the cytoskeleton at the membrane. Beta-III spectrin, also called spectrin beta chain, non-erythrocytic 2 (SPTBN2), or spinocerebellar ataxia 5 protein (SCA5), may play a crucial role as a longer actin-membrane cross-linker or fulfill the need for greater extensible flexibility than can be provided by the other smaller conventional spectrins. Beta-IV spectrin is also called spectrin, non-erythroid beta chain 3 (SPTBN3) or spectrin beta chain, non-erythrocytic 4 (SPTBN4). Its mutation associates with congenital myopathy, neuropathy, and central deafness. Members of this subfamily contain two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 105 matched cddid_all.tbl CDD cd21249 cd21249 409098 CH_SPTBN5_rpt2 second calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 5 (SPTBN5) and similar proteins. Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is composed of two antiparallel dimers of alpha- and beta- subunits. SPTBN5, also called beta-V spectrin, is a mammalian ortholog of Drosophila beta H spectrin that may play a crucial role as a longer actin-membrane cross-linker or to fulfill the need for greater extensible flexibility than can be provided by the other smaller conventional spectrins. SPTBN5 contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 109 matched cddid_all.tbl CDD cd21250 cd21250 409099 CH_MICAL2 calponin homology (CH) domain found in molecule interacting with CasL protein 2. MICAL-2 is a nuclear [F-actin]-monooxygenase that promotes depolymerization of F-actin by mediating oxidation of specific methionine residues on actin to form methionine-sulfoxide, resulting in actin filament disassembly and preventing repolymerization. In the absence of actin, it also functions as a NADPH oxidase producing H(2)O(2). MICAL-2 acts as a key regulator of the serum response factor (SRF) signaling pathway elicited by nerve growth factor and serum. It mediates oxidation and subsequent depolymerization of nuclear actin, leading to the increased MKL1/MRTF-A presence in the nucleus, promoting SRF:MKL1/MRTF-A-dependent gene transcription. MICAL-2 contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 110 matched cddid_all.tbl CDD cd21251 cd21251 409100 CH_MICAL3 calponin homology (CH) domain found in molecule interacting with CasL protein 3. MICAL-3 is a [F-actin]-monooxygenase that promotes depolymerization of F-actin by mediating oxidation of specific methionine residues on actin to form methionine-sulfoxide, resulting in actin filament disassembly and preventing repolymerization. In the absence of actin, it also functions as a NADPH oxidase producing H(2)O(2). MICAL-3 seems to act as a Rab effector protein and plays a role in vesicle trafficking. It is involved in exocytic vesicle tethering and fusion. MICAL3 contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 111 matched cddid_all.tbl CDD cd21252 cd21252 409101 CH_MICALL1 calponin homology (CH) domain found in MICAL-like protein 1. MICAL-like protein 1 (MICAL-L1), also called molecule interacting with Rab13 (MIRab13), is a probable lipid-binding protein with higher affinity for phosphatidic acid, a lipid enriched in recycling endosome membranes. It is a tubular endosomal membrane hub that connects Rab35 and Arf6 with Rab8a. It may be involved in a late step of receptor-mediated endocytosis regulating endocytosed-EGF receptor trafficking. Alternatively, it may regulate slow endocytic recycling of endocytosed proteins back to the plasma membrane. MICAL-L1 may indirectly play a role in neurite outgrowth. It contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 107 matched cddid_all.tbl CDD cd21253 cd21253 409102 CH_MICALL2 calponin homology (CH) domain found in MICAL-like protein 2 and similar proteins. MICAL-like protein 2 (MICAL-L2), also called junctional Rab13-binding protein (JRAB), or molecule interacting with CasL-like 2, acts as an effector of small Rab GTPases which is involved in junctional complexes assembly through the regulation of cell adhesion molecule transport to the plasma membrane, and actin cytoskeleton reorganization. It regulates the endocytic recycling of occludins, claudins, and E-cadherin to the plasma membrane and may thereby regulate the establishment of tight junctions and adherens junctions. Members of this subfamily contain a single copy of CH domain. CH domains are actin filament (F-actin) binding motifs. 106 matched cddid_all.tbl CDD cd21254 cd21254 409103 CH_EHBP1 calponin homology (CH) domain found in EH domain-binding protein 1 and similar proteins. EHBP1 is a regulator of endocytic recycling and may play a role in actin reorganization by linking clathrin-mediated endocytosis to the actin cytoskeleton. It may act as an effector of small GTPases, including RAB-10 (Rab10), and play a role in vesicle trafficking. EHBP1 is associated with aggressive prostate cancer and insulin-stimulated trafficking and cell migration. Members of this subfamily contain a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 107 matched cddid_all.tbl CDD cd21255 cd21255 409104 CH_EHBP1L1 calponin homology (CH) domain found in EH domain-binding protein 1-like protein 1 and similar proteins. EHBP1L1 may act as Rab effector protein and play a role in vesicle trafficking. It coordinates Rab8 and Bin1 to regulate apical-directed transport in polarized epithelial cells. Members of this subfamily contain a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 105 matched cddid_all.tbl CDD cd21256 cd21256 409105 CH_CYTSA calponin homology (CH) domain found in cytospin-A. Cytospin-A, also called renal carcinoma antigen NY-REN-22, or sperm antigen with calponin homology and coiled-coil domains 1-like, or SPECC1-like protein (SPECC1L), is involved in cytokinesis and spindle organization. It may play a role in actin cytoskeleton organization and microtubule stabilization and hence, is required for proper cell adhesion and migration. Cytospin-A contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 119 matched cddid_all.tbl CDD cd21257 cd21257 409106 CH_CYTSB calponin homology (CH) domain found in cytospin-B. Cytospin-B, also called nuclear structure protein 5 (NSP5), or sperm antigen HCMOGT-1, or sperm antigen with calponin homology and coiled-coil domains 1 (SPECC1), is a novel fusion Cytospin-B that contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 112 matched cddid_all.tbl CDD cd21258 cd21258 409107 CH_SMTNA calponin homology (CH) domain found in smoothelin-A and similar proteins. Smoothelins are actin-binding cytoskeletal proteins that are abundantly expressed in healthy visceral (smoothelin-A) and vascular (smoothelin-B) smooth muscle. This model corresponds to the single CH domain of smoothelin-A. CH domains are actin filament (F-actin) binding motifs. 111 matched cddid_all.tbl CDD cd21259 cd21259 409108 CH_SMTNB calponin homology (CH) domain found in smoothelin-B and similar proteins. Smoothelins are actin-binding cytoskeletal proteins that are abundantly expressed in healthy visceral (smoothelin-A) and vascular (smoothelin-B) smooth muscle. The human SMTN gene encodes smoothelin-A and smoothelin-B. This model corresponds to the single CH domain of smoothelin-B. CH domains are actin filament (F-actin) binding motifs. 112 matched cddid_all.tbl CDD cd21260 cd21260 409109 CH_SMTNL1 calponin homology (CH) domain found in smoothelin-like protein 1. Smoothelin-like protein 1 (SMTNL1), also called calponin homology-associated smooth muscle protein (CHASM), plays a role in the regulation of contractile properties of both striated and smooth muscles. It can bind to calmodulin and tropomyosin. When it is unphosphorylated, SMTNL1 may inhibit myosin dephosphorylation. SMTNL1 contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 116 matched cddid_all.tbl CDD cd21261 cd21261 409110 CH_SMTNL2 calponin homology (CH) domain found in smoothelin-like protein 2. Smoothelin-like protein 2 (SMTNL2) is highly expressed in skeletal muscle and could be associated with differentiating myocytes. It contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 107 matched cddid_all.tbl CDD cd21262 cd21262 409111 CH_VAV1 calponin homology (CH) domain found in VAV1 protein. VAV1 is expressed predominantly in the hematopoietic system and it plays an important role in the development and activation of B and T cells. It is activated by tyrosine phosphorylation to function as a guanine nucleotide exchange factor (GEF) for Rho GTPases following cell surface receptor activation, triggering various effects such as cytoskeletal reorganization, transcription regulation, cell cycle progression, and calcium mobilization. It also serves as a scaffold protein and has been shown to interact with Ku70, Socs1, Janus kinase 2, SIAH2, S100B, Abl gene, ZAP-70, SLP76, and Syk, among others. VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. This model corresponds to the CH domain, an actin-binding domain which is present as a single copy in VAV1 protein. 120 matched cddid_all.tbl CDD cd21263 cd21263 409112 CH_VAV2 calponin homology (CH) domain found in VAV2 protein and similar proteins. VAV2 is widely expressed and functions as a guanine nucleotide exchange factor (GEF) for RhoA, RhoB and RhoG and also activates Rac1 and Cdc42. It is implicated in many cellular and physiological functions including blood pressure control, eye development, neurite outgrowth and branching, EGFR endocytosis and degradation, and cell cluster morphology, among others. It has been reported to associate with Nek3. VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. The model corresponds to CH domain, an actin-binding domain which is present as a single copy in VAV2 protein. 119 matched cddid_all.tbl CDD cd21264 cd21264 409113 CH_VAV3 calponin homology (CH) domain found in VAV3 protein and similar proteins. VAV3 is ubiquitously expressed and functions as a phosphorylation-dependent guanine nucleotide exchange factor (GEF) for RhoA, RhoG, and Rac1. Its function has been implicated in the hematopoietic, bone, cerebellar, and cardiovascular systems. VAV3 is essential in axon guidance in neurons that control blood pressure and respiration. It is overexpressed in prostate cancer cells and it plays a role in regulating androgen receptor transcriptional activity. VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. The model corresponds to CH domain, an actin-binding domain which is present as a single copy in VAV3 protein. 117 matched cddid_all.tbl CDD cd21265 cd21265 409114 CH_alphaPIX calponin homology (CH) domain found in alpha-Pak Interactive eXchange factor. Alpha-Pak Interactive eXchange factor (alpha-PIX), also called PAK-interacting exchange factor alpha, Rho guanine nucleotide exchange factor 6 (ARHGEF6), Rac/Cdc42 guanine nucleotide exchange factor 6, or Cool (Cloned out of Library)-2, activates small GTPases by exchanging bound GDP for free GTP. It acts as a GEF for both Cdc42 and Rac1, and is localized in dendritic spines where it regulates spine morphogenesis. It controls dendritic length and spine density in the hippocampus. Mutations in the ARHGEF6 gene cause X-linked intellectual disability in humans. Alpha-PIX contains a single copy of the CH domain at its N-terminus. CH domains are actin filament (F-actin) binding motifs. 117 matched cddid_all.tbl CDD cd21266 cd21266 409115 CH_betaPIX calponin homology (CH) domain found in beta-Pak Interactive eXchange factor. Beta-Pak Interactive eXchange factor (beta-PIX), also called PAK-interacting exchange factor beta, Rho guanine nucleotide exchange factor 7 (ARHGEF7), p85, or Cool (Cloned out of Library)-1, activates small GTPases by exchanging bound GDP for free GTP. It acts as a GEF for both Cdc42 and Rac1, and plays important roles in regulating neuroendocrine exocytosis, focal adhesion maturation, cell migration, synaptic vesicle localization, and insulin secretion. Beta-PIX contains a single copy of the CH domain at its N-terminus. CH domains are actin filament (F-actin) binding motifs. 112 matched cddid_all.tbl CDD cd21267 cd21267 409116 CH_GAS2 calponin homology (CH) domain found in growth arrest-specific protein 2. Growth arrest-specific protein 2 (GAS-2) may play a role in apoptosis by acting as a cell death substrate for caspases. It contains a single copy of the CH domain at the N-terminal region. CH domains are actin filament (F-actin) binding motifs. 136 matched cddid_all.tbl CDD cd21268 cd21268 409117 CH_GAS2L1_2 calponin homology (CH) domain found in GAS2-like protein 1 (GAS2L1), GAS2L2, and similar proteins. This subfamily includes GAS2L1 (also called GAS2-related protein on chromosome 22 or growth arrest-specific protein 2-like 1) and GAS2L2 (also called GAS2-related protein on chromosome 17 or growth arrest-specific protein 2-like 2). They may be involved in the cross-linking of microtubules and microfilaments. Members of this subfamily contain a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs. 142 matched cddid_all.tbl CDD cd21269 cd21269 409118 CH_GAS2L3 calponin homology (CH) domain found in growth arrest-specific protein 2-like 3. Growth arrest-specific protein 2-like 3 (GAS2L3), also called GAS2-like protein 3, is a cytoskeletal linker protein that may promote and stabilize the formation of the actin and microtubule network. It contains a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs. 130 matched cddid_all.tbl CDD cd21270 cd21270 409119 CH_LRCH1 calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 1. Leucine-rich repeat and calponin homology domain-containing protein 1 (LRCH1), also called calponin homology domain-containing protein 1, or neuronal protein 81 (NP81), acts as a negative regulator of GTPase CDC42 by sequestering CDC42-guanine exchange factor DOCK8. LRCH1 contains a single copy of the CH domain at the C-terminus. CH domains are actin filament (F-actin) binding motifs. 112 matched cddid_all.tbl CDD cd21271 cd21271 409120 CH_LRCH2 calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 2. Leucine-rich repeat and calponin homology domain-containing protein 2 (LRCH2) may play a role in the organization of the cytoskeleton. It contains a single copy of the CH domain at the C-terminus. CH domains are actin filament (F-actin) binding motifs. 111 matched cddid_all.tbl CDD cd21272 cd21272 409121 CH_LRCH3 calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 3. Leucine-rich repeat and calponin homology domain-containing protein 3 (LRCH3) is part of the DISP (DOCK7-Induced Septin disPlacement) complex. It may regulate the association of septins with actin and thereby regulate the actin cytoskeleton. LRCH3 contains a single copy of the CH domain at the C-terminus. CH domains are actin filament (F-actin) binding motifs. 109 matched cddid_all.tbl CDD cd21273 cd21273 409122 CH_LRCH4 calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 4. Leucine-rich repeat and calponin homology domain-containing protein 4 (LRCH4), also called leucine-rich repeat neuronal protein 4, or leucine-rich neuronal protein, acts as a novel Toll-like receptor (TLR) accessory protein that regulates the innate immune response. LRCH4 contains a single copy of the CH domain at the C-terminus. CH domains are actin filament (F-actin) binding motifs. 109 matched cddid_all.tbl CDD cd21274 cd21274 409123 CH_IQGAP1 calponin homology (CH) domain found in Ras GTPase-activating-like protein IQGAP1. IQ motif containing GTPase activating protein 1 (IQGAP1), also called p195, is a homodimeric protein that is widely expressed among vertebrate cell types from early embryogenesis. It plays a crucial role in regulating the dynamics and assembly of the actin cytoskeleton. It belongs to the IQGAP family, which consists of multi-domain proteins having a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeats, a single WW domain, four IQ motifs that mediate interactions with calmodulin, and a RasGAP related domain that binds active Rho family GTPases. IQGAP1 negatively regulates Ras family GTPases by stimulating their intrinsic GTPase activity. It lacks GAP activity. Both, IQGAP1 and IQGAP2, specifically bind to Cdc42 and Rac1, but not to RhoA. Despite similarities to part of the sequence of RasGAP, neither IQGAP1 nor IQGAP2 interacts with Ras. IQGAP1 contains a single copy of the CH domain at the N-terminus. 154 matched cddid_all.tbl CDD cd21275 cd21275 409124 CH_IQGAP2 calponin homology (CH) domain found in Ras GTPase-activating-like protein IQGAP2. IQ motif containing GTPase activating protein 2 (IQGAP2) is a member of the IQGAP family, which consists of multi-domain proteins having a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeats, a single WW domain, four IQ motifs that mediate interactions with calmodulin, and a RasGAP related domain that binds active Rho family GTPases. IQGAP2 binds to activated Cdc42 and Rac1 but does not seem to stimulate their GTPase activity. It associates with calmodulin. IQGAP2 contains a single copy of the CH domain at the N-terminus. 156 matched cddid_all.tbl CDD cd21276 cd21276 409125 CH_IQGAP3 calponin homology (CH) domain found in Ras GTPase-activating-like protein IQGAP3. IQ motif containing GTPase activating protein 3 (IQGAP3) associates with Ras GTP-binding proteins. It regulates the organization of the cytoskeleton under the regulation of Rac1 and Cdc42 in neuronal cells. The depletion of IQGAP3 is shown to impair neurite or axon outgrowth in neuronal cells with disorganized cytoskeleton. It belongs to the IQGAP family, which consists of multi-domain proteins having a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeats, a single WW domain, four IQ motifs that mediate interactions with calmodulin, and a RasGAP related domain that binds active Rho family GTPases. IQGAP3 contains a single copy of the CH domain at the N-terminus. 152 matched cddid_all.tbl CDD cd21277 cd21277 409126 CH_LMO7 calponin homology (CH) domain found in LIM domain only protein 7. LIM domain only protein 7 (LMO-7), also called F-box only protein 20, or LOMP, is a transcription regulator for expression of many Emery-Dreifuss muscular dystrophy (EDMD)-relevant genes. It binds to alpha-actinin and AF6/afadin at adherens junctions for epithelial cell-cell adhesion. It contains a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs. 116 matched cddid_all.tbl CDD cd21278 cd21278 409127 CH_LIMCH1 calponin homology (CH) domain found in LIM and calponin homology domains-containing protein 1. LIM and calponin homology domains-containing protein 1 (LIMCH1) acts as an actin stress fiber-associated protein that activates the non-muscle myosin IIa complex by promoting the phosphorylation of its regulatory subunit MRLC/MYL9. It positively regulates actin stress fiber assembly and stabilizes focal adhesions, and therefore negatively regulates cell spreading and cell migration. LIMCH1 contains a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs. 118 matched cddid_all.tbl CDD cd21279 cd21279 409128 CH_TAGLN calponin homology (CH) domain found in transgelin. Transgelin, also called 22 kDa actin-binding protein, protein WS3-10, or smooth muscle protein 22-alpha (SM22-alpha), acts as an actin cross-linking/gelling protein that may be involved in calcium interactions and in regulating contractile properties of the cell. It may also contribute to replicative senescence. Transgelin contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 121 matched cddid_all.tbl CDD cd21280 cd21280 409129 CH_TAGLN2 calponin homology (CH) domain found in transgelin-2. Transgelin-2, also called epididymis tissue protein Li 7e, or SM22-alpha homolog, acts as an actin-binding protein that induces actin gelation and regulates the actin cytoskeleton. It may participate in the development and progression of multiple cancers. It contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 137 matched cddid_all.tbl CDD cd21281 cd21281 409130 CH_TAGLN3 calponin homology (CH) domain found in transgelin-3. Transgelin-3, also called neuronal protein 22 (NP22), or neuronal protein NP25, may have a role in alcohol-related adaptations and may mediate regulatory signal transduction pathways in neurons. It contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 119 matched cddid_all.tbl CDD cd21282 cd21282 409131 CH_CNN1 calponin homology (CH) domain found in calponin-1 and similar proteins. Calponin-1 (CNN1), also called basic calponin, or smooth muscle calponin H1, is a thin filament-associated protein that is implicated in the regulation and modulation of smooth muscle contraction. It is capable of binding to actin, calmodulin, troponin C, and tropomyosin. Calponin-1 contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 108 matched cddid_all.tbl CDD cd21283 cd21283 409132 CH_CNN2 calponin homology (CH) domain found in calponin-2. Calponin-2 (CNN2), also called neutral calponin, or smooth muscle calponin H2, is an actin cytoskeleton-associated regulatory protein that inhibits the activity of myosin-ATPase and cytoskeleton dynamics. It contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 109 matched cddid_all.tbl CDD cd21284 cd21284 409133 CH_CNN3 calponin homology (CH) domain found in calponin-3. Calponin-3 (CNN3), also called acidic isoform calponin, is an F-actin-binding protein that is expressed in the brain and has been shown to control dendritic spine morphology, density, and plasticity by regulating actin cytoskeletal reorganization and dynamics. It contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs. 111 matched cddid_all.tbl CDD cd21285 cd21285 409134 CH_NAV2 calponin homology (CH) domain found in neuron navigator 2. Neuron navigator 2 (NAV2), also called helicase APC down-regulated 1 (HELAD1), pore membrane and/or filament-interacting-like protein 2 (POMFIL2), retinoic acid inducible in neuroblastoma 1 (RAINB1), Steerin-2 (STEERIN2), or Unc-53 homolog 2 (unc53H2), possesses 3' to 5' helicase activity and exonuclease activity. It is involved in neuronal development, specifically in the development of different sensory organs. NAV2 contains a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs. 121 matched cddid_all.tbl CDD cd21286 cd21286 409135 CH_NAV3 calponin homology (CH) domain found in neuron navigator 3. Neuron navigator 3 (NAV3), also called pore membrane and/or filament-interacting-like protein 1 (POMFIL1), Steerin-3 (STEERIN3), or Unc-53 homolog 3 (unc53H3), may regulate IL2 production by T-cells. It may be involved in neuron regeneration. NAV3 contains a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs. 105 matched cddid_all.tbl CDD cd21287 cd21287 409136 CH_ACTN1_rpt2 second calponin homology (CH) domain found in alpha-actinin-1. Alpha-actinin-1 (ACTN1), also called alpha-actinin cytoskeletal isoform, or non-muscle alpha-actinin-1, is an F-actin cross-linking protein which is thought to anchor actin to a variety of intracellular structures. ACTN1 is a bundling protein. Its mutations cause congenital macrothrombocytopenia. It contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 124 matched cddid_all.tbl CDD cd21288 cd21288 409137 CH_ACTN2_rpt2 second calponin homology (CH) domain found in alpha-actinin-2. Alpha-actinin-2 (ACTN2), also called alpha-actinin skeletal muscle isoform 2, is an F-actin cross-linking protein which is thought to anchor actin to a variety of intracellular structures. ACTN2 is a bundling protein. Its mutations are associated with cardiomyopathies, as well as skeletal muscle disorder. It contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 124 matched cddid_all.tbl CDD cd21289 cd21289 409138 CH_ACTN3_rpt2 second calponin homology (CH) domain found in alpha-actinin-3. Alpha-actinin-3 (ACTN3), also called alpha-actinin skeletal muscle isoform 3, is an F-actin cross-linking protein which is thought to anchor actin to a variety of intracellular structures. ACTN3 is a bundling protein. It is critical in anchoring the myofibrillar actin filaments and plays a key role in muscle contraction. It contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 124 matched cddid_all.tbl CDD cd21290 cd21290 409139 CH_ACTN4_rpt2 second calponin homology (CH) domain found in alpha-actinin-4. Alpha-actinin-4 (ACTN4), also called non-muscle alpha-actinin 4, is an F-actin cross-linking protein which is thought to anchor actin to a variety of intracellular structures. It is associated with cell motility and cancer invasion. ACTN4 is probably involved in vesicular trafficking via its association with the CART complex, which is necessary for efficient transferrin receptor recycling but not for epidermal growth factor receptor (EGFR) degradation. It contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 125 matched cddid_all.tbl CDD cd21291 cd21291 409140 CH_SpAIN1-like_rpt2 second calponin homology (CH) domain found in Schizosaccharomyces pombe alpha-actinin-like protein 1 and similar proteins. Schizosaccharomyces pombe alpha-actinin-like protein 1 (SpAIN1) binds to actin and is involved in actin-ring formation and organization. It plays a role in cytokinesis and is involved in septation. Members of this family contain two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 115 matched cddid_all.tbl CDD cd21292 cd21292 409141 CH_PLS_rpt1 first calponin homology (CH) domain found in the plastin family. The plastin family includes plastin-1, -2, and -3, which are all actin-bundling proteins. Plastin-1, also called intestine-specific plastin, or I-plastin, is an actin-bundling protein in the absence of calcium. Plastin-2, also called L-plastin, LC64P, or lymphocyte cytosolic protein 1 (LCP-1), plays a role in the activation of T-cells in response to costimulation through TCR/CD3 and CD2 or CD28. It modulates the cell surface expression of IL2RA/CD25 and CD69. Plastin-3, also called T-plastin, is found in intestinal microvilli, hair cell stereocilia, and fibroblast filopodia. It may play a role in the regulation of bone development. Members of this family contain four copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 145 matched cddid_all.tbl CDD cd21293 cd21293 409142 CH_AtFIM_like_rpt1 first calponin homology (CH) domain found in the Arabidopsis thaliana fimbrin family. The Arabidopsis thaliana fimbrin (AtFIM) family includes fimbrin-1, -2, -3, -4, and -5, which cross-link actin filaments (F-actin) in a calcium independent manner. They stabilize and prevent F-actin depolymerization mediated by profilin. They act as key regulators of actin cytoarchitecture, and are probably involved in the cell cycle, cell division, cell elongation, and cytoplasmic tractus. AtFIM5 is an actin bundling factor that is required for pollen germination and pollen tube growth. Members of this family contain four copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 116 matched cddid_all.tbl CDD cd21294 cd21294 409143 CH_FIMB_rpt1 first calponin homology (CH) domain found in Saccharomyces cerevisiae fimbrin and similar proteins. Fimbrin binds to actin, and functionally associates with actin structures involved in the development and maintenance of cell polarity. Members of this family contain four copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 125 matched cddid_all.tbl CDD cd21295 cd21295 409144 CH_PLS_rpt2 second calponin homology (CH) domain found in the family of plastin. The plastin family includes plastin-1, -2, and -3. Plastin-1, also called intestine-specific plastin, or I-plastin, is an actin-bundling protein in the absence of calcium. Plastin-2, also called L-plastin, or LC64P, or lymphocyte cytosolic protein 1 (LCP-1), is an actin-binding protein that plays a role in the activation of T-cells in response to costimulation through TCR/CD3 and CD2 or CD28. It modulates the cell surface expression of IL2RA/CD25 and CD69. Plastin-3, also called T-plastin, is an actin-bundling protein found in intestinal microvilli, hair cell stereocilia, and fibroblast filopodia. It may play a role in the regulation of bone development. Members of this family contain four copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 113 matched cddid_all.tbl CDD cd21296 cd21296 409145 CH_AtFIM_like_rpt2 second calponin homology (CH) domain found in the Arabidopsis thaliana fimbrin family. The Arabidopsis thaliana fimbrin (AtFIM) family includes fimbrin-1, -2, -3, -4, and -5, which cross-link actin filaments (F-actin) in a calcium independent manner. They stabilize and prevent F-actin depolymerization mediated by profilin. They act as key regulators of actin cytoarchitecture, and are probably involved in the cell cycle, cell division, cell elongation, and cytoplasmic tractus. AtFIM5 is an actin bundling factor that is required for pollen germination and pollen tube growth. Members of this family contain four copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 109 matched cddid_all.tbl CDD cd21297 cd21297 409146 CH_FIMB_rpt2 second calponin homology (CH) domain found in Saccharomyces cerevisiae fimbrin and similar proteins. Fimbrin binds to actin, and functionally associates with actin structures involved in the development and maintenance of cell polarity. Members of this family contain four copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 109 matched cddid_all.tbl CDD cd21298 cd21298 409147 CH_PLS_rpt3 third calponin homology (CH) domain found in the plastin family. The plastin family includes plastin-1, -2, and -3. Plastin-1, also called intestine-specific plastin, or I-plastin, is an actin-bundling protein in the absence of calcium. Plastin-2, also called L-plastin, or LC64P, or lymphocyte cytosolic protein 1 (LCP-1), is an actin-binding protein that plays a role in the activation of T-cells in response to costimulation through TCR/CD3 and CD2 or CD28. It modulates the cell surface expression of IL2RA/CD25 and CD69. Plastin-3, also called T-plastin, is an actin-bundling protein found in intestinal microvilli, hair cell stereocilia, and fibroblast filopodia. It may play a role in the regulation of bone development. Members of this family contain four copies of the CH domain. This model corresponds to the third CH domain. CH domains are actin filament (F-actin) binding motifs. 117 matched cddid_all.tbl CDD cd21299 cd21299 409148 CH_AtFIM_like_rpt3 third calponin homology (CH) domain found in the Arabidopsis thaliana fimbrin family. The Arabidopsis thaliana fimbrin (AtFIM) family includes Fimbrin-1, -2, -3, -4, and -5, which cross-link actin filaments (F-actin) in a calcium independent manner. They stabilize and prevent F-actin depolymerization mediated by profilin. They act as key regulators of actin cytoarchitecture, probably involved in cell cycle, cell division, cell elongation and cytoplasmic tractus. AtFIM5 is an actin bundling factor that is required for pollen germination and pollen tube growth. Members of this family contain four copies of the CH domain. This model corresponds to the third CH domain. CH domains are actin filament (F-actin) binding motifs. 114 matched cddid_all.tbl CDD cd21300 cd21300 409149 CH_FIMB_rpt3 third calponin homology (CH) domain found in Saccharomyces cerevisiae fimbrin and similar proteins. Fimbrin binds to actin, and functionally associates with actin structures involved in the development and maintenance of cell polarity. Members of this family contain four copies of the CH domain. This model corresponds to the third CH domain. CH domains are actin filament (F-actin) binding motifs. 119 matched cddid_all.tbl CDD cd21301 cd21301 409150 CH_PLS_rpt4 fourth calponin homology (CH) domain found in the plastin family. The plastin family includes plastin-1, -2, and -3. Plastin-1, also called intestine-specific plastin, or I-plastin, is an actin-bundling protein in the absence of calcium. Plastin-2, also called L-plastin, or LC64P, or lymphocyte cytosolic protein 1 (LCP-1), is an actin-binding protein that plays a role in the activation of T-cells in response to costimulation through TCR/CD3 and CD2 or CD28. It modulates the cell surface expression of IL2RA/CD25 and CD69. Plastin-3, also called T-plastin, is an actin-bundling protein found in intestinal microvilli, hair cell stereocilia, and fibroblast filopodia. It may play a role in the regulation of bone development. Members of this family contain four copies of the CH domain. This model corresponds to the fourth CH domain. CH domains are actin filament (F-actin) binding motifs. 107 matched cddid_all.tbl CDD cd21302 cd21302 409151 CH_AtFIM_like_rpt4 fourth calponin homology (CH) domain found in the Arabidopsis thaliana fimbrin family. The Arabidopsis thaliana fimbrin (AtFIM) family includes fimbrin-1, -2, -3, -4, and -5, which cross-link actin filaments (F-actin) in a calcium independent manner. They stabilize and prevent F-actin depolymerization mediated by profilin. They act as key regulators of actin cytoarchitecture, probably involved in cell cycle, cell division, cell elongation and cytoplasmic tractus. AtFIM5 is an actin bundling factor that is required for pollen germination and pollen tube growth. Members of this family contain four copies of the CH domain. This model corresponds to the fourth CH domain. CH domains are actin filament (F-actin) binding motifs. 109 matched cddid_all.tbl CDD cd21303 cd21303 409152 CH_FIMB_rpt4 fourth calponin homology (CH) domain found in Saccharomyces cerevisiae fimbrin and similar proteins. Fimbrin binds to actin, and functionally associates with actin structures involved in the development and maintenance of cell polarity. Members of this family contain four copies of the CH domain. This model corresponds to the fourth CH domain. CH domains are actin filament (F-actin) binding motifs. 108 matched cddid_all.tbl CDD cd21304 cd21304 409153 CH_PARVA_B_rpt1 first calponin homology (CH) domain found in the alpha/beta parvin subfamily. The alpha/beta parvin subfamily includes alpha-parvin and beta-parvin. Alpha-parvin, also called actopaxin, calponin-like integrin-linked kinase-binding protein (CH-ILKBP), or matrix-remodeling-associated protein 2, plays a role in sarcomere organization and in smooth muscle cell contraction. It is required for normal development of the embryonic cardiovascular system, and for normal septation of the heart outflow tract. Beta-parvin, also called affixin, is an adapter protein that plays a role in integrin signaling via ILK and in activation of the GTPases Cdc42 and Rac1 by guanine exchange factors, such as ARHGEF6. Both alpha-parvin and beta-parvin are involved in the reorganization of the actin cytoskeleton and the formation of lamellipodia, and both play roles in cell adhesion, cell spreading, establishment or maintenance of cell polarity, and cell migration. Members of this subfamily contain two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 107 matched cddid_all.tbl CDD cd21305 cd21305 409154 CH_PARVG_rpt1 first calponin homology (CH) domain found in gamma-parvin. Gamma-parvin probably plays a role in the regulation of cell adhesion and cytoskeleton organization. It contains two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 106 matched cddid_all.tbl CDD cd21306 cd21306 409155 CH_PARVA_B_rpt2 second calponin homology (CH) domain found in the alpha/beta parvin subfamily. The alpha/beta parvin subfamily includes alpha-parvin and beta-parvin. Alpha-parvin, also called actopaxin, calponin-like integrin-linked kinase-binding protein (CH-ILKBP), or matrix-remodeling-associated protein 2, plays a role in sarcomere organization and in smooth muscle cell contraction. It is required for normal development of the embryonic cardiovascular system, and for normal septation of the heart outflow tract. Beta-parvin, also called affixin, is an adapter protein that plays a role in integrin signaling via ILK and in activation of the GTPases Cdc42 and Rac1 by guanine exchange factors, such as ARHGEF6. Both alpha-parvin and beta-parvin are involved in the reorganization of the actin cytoskeleton and the formation of lamellipodia, and both play roles in cell adhesion, cell spreading, establishment or maintenance of cell polarity, and cell migration. Members of this subfamily contain two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 121 matched cddid_all.tbl CDD cd21307 cd21307 409156 CH_PARVG_rpt2 second calponin homology (CH) domain found in gamma-parvin. Gamma-parvin probably plays a role in the regulation of cell adhesion and cytoskeleton organization. It contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 122 matched cddid_all.tbl CDD cd21308 cd21308 409157 CH_FLNA_rpt1 first calponin homology (CH) domain found in filamin-A (FLN-A) and similar proteins. Filamin-A (FLN-A) is also called actin-binding protein 280 (ABP-280), alpha-filamin, endothelial actin-binding protein, filamin-1, or non-muscle filamin. It promotes orthogonal branching of actin filaments and links actin filaments to membrane glycoproteins. It also anchors various transmembrane proteins to the actin cytoskeleton and serves as a scaffold for a wide range of cytoplasmic signaling proteins. FLN-A contains two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 129 matched cddid_all.tbl CDD cd21309 cd21309 409158 CH_FLNB_rpt1 first calponin homology (CH) domain found in filamin-B (FLN-B) and similar proteins. Filamin-B (FLN-B) is also called ABP-278, ABP-280 homolog, actin-binding-like protein, beta-filamin, filamin homolog 1 (Fh1), filamin-3, thyroid autoantigen, truncated actin-binding protein, or truncated ABP. It connects cell membrane constituents to the actin cytoskeleton. It may promote orthogonal branching of actin filaments and links actin filaments to membrane glycoproteins. It anchors various transmembrane proteins to the actin cytoskeleton. FLN-B contains two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 131 matched cddid_all.tbl CDD cd21310 cd21310 409159 CH_FLNC_rpt1 first calponin homology (CH) domain found in filamin-C (FLN-C) and similar proteins. Filamin-C (FLN-C), also called FLNc, ABP-280-like protein, ABP-L, actin-binding-like protein, filamin-2, or gamma-filamin, is a muscle-specific filamin that plays a central role in muscle cells, probably by functioning as a large actin-cross-linking protein. It may be involved in reorganizing the actin cytoskeleton in response to signaling events, and may also display structural functions at the Z lines in muscle cells. FLN-C is critical for normal myogenesis and for maintaining the structural integrity of the muscle fibers. FLN-C contains two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 125 matched cddid_all.tbl CDD cd21311 cd21311 409160 CH_dFLNA-like_rpt1 first calponin homology (CH) domain found in Drosophila melanogaster filamin-A (dFLNA) and similar proteins. Drosophila melanogaster filamin-A (dFLNA or dFLN-A), also called actin-binding protein 280 (ABP-280) or filamin-1, is involved in germline ring canal formation. It may tether actin microfilaments within the ovarian ring canal to the cell membrane and contributes to actin microfilament organization. dFLNA contains two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 124 matched cddid_all.tbl CDD cd21312 cd21312 409161 CH_FLNA_rpt2 second calponin homology (CH) domain found in filamin-A (FLN-A) and similar proteins. Filamin-A (FLN-A) is also called actin-binding protein 280 (ABP-280), alpha-filamin, endothelial actin-binding protein, filamin-1, or non-muscle filamin. It promotes orthogonal branching of actin filaments and links actin filaments to membrane glycoproteins. It also anchors various transmembrane proteins to the actin cytoskeleton and serves as a scaffold for a wide range of cytoplasmic signaling proteins. FLN-A contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 114 matched cddid_all.tbl CDD cd21313 cd21313 409162 CH_FLNB_rpt2 second calponin homology (CH) domain found in filamin-B (FLN-B) and similar proteins. Filamin-B (FLN-B) is also called ABP-278, ABP-280 homolog, actin-binding-like protein, beta-filamin, filamin homolog 1 (Fh1), filamin-3, thyroid autoantigen, truncated actin-binding protein, or truncated ABP. It connects cell membrane constituents to the actin cytoskeleton. It may promote orthogonal branching of actin filaments and links actin filaments to membrane glycoproteins. It anchors various transmembrane proteins to the actin cytoskeleton. FLN-B contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 110 matched cddid_all.tbl CDD cd21314 cd21314 409163 CH_FLNC_rpt2 second calponin homology (CH) domain found in filamin-C (FLN-C) and similar proteins. Filamin-C (FLN-C), also called FLNc, ABP-280-like protein, ABP-L, actin-binding-like protein, filamin-2, or gamma-filamin, is a muscle-specific filamin that plays a central role in muscle cells, probably by functioning as a large actin-cross-linking protein. It may be involved in reorganizing the actin cytoskeleton in response to signaling events, and may also display structural functions at the Z lines in muscle cells. FLN-C is critical for normal myogenesis and for maintaining the structural integrity of the muscle fibers. FLN-C contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 115 matched cddid_all.tbl CDD cd21315 cd21315 409164 CH_dFLNA-like_rpt2 second calponin homology (CH) domain found in Drosophila melanogaster filamin-A (dFLNA) and similar proteins. Drosophila melanogaster filamin-A (dFLNA or dFLN-A), also called actin-binding protein 280 (ABP-280) or filamin-1, is involved in germline ring canal formation. It may tether actin microfilaments within the ovarian ring canal to the cell membrane and contributes to actin microfilament organization. dFLNA contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 118 matched cddid_all.tbl CDD cd21316 cd21316 409165 CH_SPTBN1_rpt1 first calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 1 (SPTBN1) and similar proteins. Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is composed of two antiparallel dimers of alpha- and beta- subunits. SPTBN1, also called beta-II spectrin, fodrin beta chain, or spectrin, non-erythroid beta chain 1, is also a component of fodrin, which is the general spectrin-like protein that seems to be involved in secretion. Fodrin interacts with calmodulin in a calcium-dependent manner and is thus a candidate for the calcium-dependent movement of the cytoskeleton at the membrane. SPTBN1 contains two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 154 matched cddid_all.tbl CDD cd21317 cd21317 409166 CH_SPTBN2_rpt1 first calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 2 (SPTBN2) and similar proteins. Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is composed of two antiparallel dimers of alpha- and beta- subunits. SPTBN2, also called beta-III spectrin, or spinocerebellar ataxia 5 protein (SCA5), probably plays an important role in the neuronal membrane skeleton. Mutations in SPTBN2 is associated with spinocerebellar ataxia type 5. SPTBN2 contains two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 132 matched cddid_all.tbl CDD cd21318 cd21318 409167 CH_SPTBN4_rpt1 first calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 4 (SPTBN4) and similar proteins. Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is composed of two antiparallel dimers of alpha- and beta- subunits. SPTBN4, also called beta-IV spectrin, or spectrin, non-erythroid beta chain 3 (SPTBN3), is a novel spectrin isolated as an interactor of the receptor tyrosine phosphatase-like protein ICA512. Its mutation associates with congenital myopathy, neuropathy, and central deafness. SPTBN4 contains two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 139 matched cddid_all.tbl CDD cd21319 cd21319 409168 CH_SPTB_rpt2 second calponin homology (CH) domain found in spectrin beta chain, erythrocytic (SPTB) and similar proteins. Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is composed of two antiparallel dimers of alpha- and beta- subunits. SPTB, also called beta-I spectrin, may be involved in anaemia pathogenesis. SPTB contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 112 matched cddid_all.tbl CDD cd21320 cd21320 409169 CH_SPTBN1_rpt2 second calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 1 (SPTBN1) and similar proteins. Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is composed of two antiparallel dimers of alpha- and beta- subunits. SPTBN1, also called beta-II spectrin, fodrin beta chain, or spectrin, non-erythroid beta chain 1, is also a component of fodrin, which is the general spectrin-like protein that seems to be involved in secretion. Fodrin interacts with calmodulin in a calcium-dependent manner and is thus a candidate for the calcium-dependent movement of the cytoskeleton at the membrane. SPTBN1 contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 108 matched cddid_all.tbl CDD cd21321 cd21321 409170 CH_SPTBN2_rpt2 second calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 2 (SPTBN2) and similar proteins. Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is composed of two antiparallel dimers of alpha- and beta- subunits. SPTBN2, also called beta-III spectrin, or spinocerebellar ataxia 5 protein (SCA5), probably plays an important role in the neuronal membrane skeleton. Mutations in SPTBN2 is associated with spinocerebellar ataxia type 5. SPTBN2 contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 119 matched cddid_all.tbl CDD cd21322 cd21322 409171 CH_SPTBN4_rpt2 second calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 4 (SPTBN4) and similar proteins. Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is composed of two antiparallel dimers of alpha- and beta- subunits. SPTBN4, also called beta-IV spectrin, or spectrin, non-erythroid beta chain 3 (SPTBN3), is a novel spectrin isolated as an interactor of the receptor tyrosine phosphatase-like protein ICA512. Its mutation associates with congenital myopathy, neuropathy, and central deafness. SPTBN4 contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 130 matched cddid_all.tbl CDD cd21323 cd21323 409172 CH_PLS1_rpt1 first calponin homology (CH) domain found in plastin-1. Plastin-1, also called intestine-specific plastin, or I-plastin, is an actin-bundling protein in the absence of calcium. It contains four copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 145 matched cddid_all.tbl CDD cd21324 cd21324 409173 CH_PLS2_rpt1 first calponin homology (CH) domain found in plastin-2. Plastin-2, also called L-plastin, or LC64P, or lymphocyte cytosolic protein 1 (LCP-1), is an actin-binding protein that plays a role in the activation of T-cells in response to costimulation through TCR/CD3 and CD2 or CD28. It modulates the cell surface expression of IL2RA/CD25 and CD69. Plastin-2 contains four copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 145 matched cddid_all.tbl CDD cd21325 cd21325 409174 CH_PLS3_rpt1 first calponin homology (CH) domain found in plastin-3. Plastin-3, also called T-plastin, is an actin-bundling protein found in intestinal microvilli, hair cell stereocilia, and fibroblast filopodia. It may play a role in the regulation of bone development. Plastin- 3 contains four copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 148 matched cddid_all.tbl CDD cd21326 cd21326 409175 CH_PLS1_rpt2 second calponin homology (CH) domain found in plastin-1. Plastin-1, also called intestine-specific plastin, or I-plastin, is an actin-bundling protein in the absence of calcium. It contains four copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 121 matched cddid_all.tbl CDD cd21327 cd21327 409176 CH_PLS2_rpt2 second calponin homology (CH) domain found in plastin-2. Plastin-2, also called L-plastin, or LC64P, or lymphocyte cytosolic protein 1 (LCP-1), is an actin-binding protein that plays a role in the activation of T-cells in response to costimulation through TCR/CD3 and CD2 or CD28. It modulates the cell surface expression of IL2RA/CD25 and CD69. Plastin-2 contaisn four copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 125 matched cddid_all.tbl CDD cd21328 cd21328 409177 CH_PLS3_rpt2 second calponin homology (CH) domain found in plastin-3. Plastin-3, also called T-plastin, is an actin-bundling protein found in intestinal microvilli, hair cell stereocilia, and fibroblast filopodia. It may play a role in the regulation of bone development. Plastin-3 contains four copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 122 matched cddid_all.tbl CDD cd21329 cd21329 409178 CH_PLS1_rpt3 third calponin homology (CH) domain found in plastin-1. Plastin-1, also called intestine-specific plastin, or I-plastin, is an actin-bundling protein in the absence of calcium. It contains four copies of the CH domain. This model corresponds to the third CH domain. CH domains are actin filament (F-actin) binding motifs. 118 matched cddid_all.tbl CDD cd21330 cd21330 409179 CH_PLS2_rpt3 third calponin homology (CH) domain found in plastin-2. Plastin-2, also called L-plastin, or LC64P, or lymphocyte cytosolic protein 1 (LCP-1), is an actin-binding protein that plays a role in the activation of T-cells in response to costimulation through TCR/CD3 and CD2 or CD28. It modulates the cell surface expression of IL2RA/CD25 and CD69. Plastin-2 contains four copies of the CH domain. This model corresponds to the third CH domain. CH domains are actin filament (F-actin) binding motifs. 125 matched cddid_all.tbl CDD cd21331 cd21331 409180 CH_PLS3_rpt3 third calponin homology (CH) domain found in plastin-3. Plastin-3, also called T-plastin, is an actin-bundling protein found in intestinal microvilli, hair cell stereocilia, and fibroblast filopodia. It may play a role in the regulation of bone development. Plastin-3 contains four copies of the CH domain. This model corresponds to the third CH domain. CH domains are actin filament (F-actin) binding motifs. 134 matched cddid_all.tbl CDD cd21332 cd21332 409181 CH_PLS1_rpt4 fourth calponin homology (CH) domain found in plastin-1. Plastin-1, also called intestine-specific plastin, or I-plastin, is an actin-bundling protein in the absence of calcium. It contains four copies of the CH domain. This model corresponds to the fourth CH domain. CH domains are actin filament (F-actin) binding motifs. 115 matched cddid_all.tbl CDD cd21333 cd21333 409182 CH_PLS2_rpt4 fourth calponin homology (CH) domain found in plastin-2. Plastin-2, also called L-plastin, or LC64P, or lymphocyte cytosolic protein 1 (LCP-1), is an actin-binding protein that plays a role in the activation of T-cells in response to costimulation through TCR/CD3 and CD2 or CD28. It modulates the cell surface expression of IL2RA/CD25 and CD69. Plastin-2 contains four copies of the CH domain. This model corresponds to the fourth CH domain. CH domains are actin filament (F-actin) binding motifs. 115 matched cddid_all.tbl CDD cd21334 cd21334 409183 CH_PLS3_rpt4 fourth calponin homology (CH) domain found in plastin-3. Plastin-3, also called T-plastin, is an actin-bundling protein found in intestinal microvilli, hair cell stereocilia, and fibroblast filopodia. It may play a role in the regulation of bone development. Plastin-3 contains four copies of the CH domain. This model corresponds to the fourth CH domain. CH domains are actin filament (F-actin) binding motifs. 112 matched cddid_all.tbl CDD cd21335 cd21335 409184 CH_PARVA_rpt1 first calponin homology (CH) domain found in alpha-parvin. Alpha-parvin, also called actopaxin, calponin-like integrin-linked kinase-binding protein (CH-ILKBP), or matrix-remodeling-associated protein 2, plays a role in sarcomere organization and in smooth muscle cell contraction. It is required for normal development of the embryonic cardiovascular system, and for normal septation of the heart outflow tract. It is also involved in the reorganization of the actin cytoskeleton, the formation of lamellipodia and ciliogenesis, as well as in the establishement of cell polarity, cell adhesion, cell spreading, and directed cell migration. Alpha-parvin contains two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 115 matched cddid_all.tbl CDD cd21336 cd21336 409185 CH_PARVB_rpt1 first calponin homology (CH) domain found in beta-parvin. Beta-parvin, also called affixin, is an adapter protein that plays a role in integrin signaling via ILK and in activation of the GTPases Cdc42 and Rac1 by guanine exchange factors, such as ARHGEF6. It is involved in the reorganization of the actin cytoskeleton and the formation of lamellipodia and also plays a role in cell adhesion, cell spreading, establishment or maintenance of cell polarity, and cell migration. Beta-parvin contains two copies of the CH domain. This model corresponds to the first CH domain. CH domains are actin filament (F-actin) binding motifs. 106 matched cddid_all.tbl CDD cd21337 cd21337 409186 CH_PARVA_rpt2 second calponin homology (CH) domain found in alpha-parvin. Alpha-parvin, also called actopaxin, calponin-like integrin-linked kinase-binding protein (CH-ILKBP), or matrix-remodeling-associated protein 2, plays a role in sarcomere organization and in smooth muscle cell contraction. It is required for normal development of the embryonic cardiovascular system, and for normal septation of the heart outflow tract. It is also involved in the reorganization of the actin cytoskeleton, the formation of lamellipodia and ciliogenesis, as well as in the establishement of cell polarity, cell adhesion, cell spreading, and directed cell migration. Alpha-parvin contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 129 matched cddid_all.tbl CDD cd21338 cd21338 409187 CH_PARVB_rpt2 second calponin homology (CH) domain found in beta-parvin. Beta-parvin, also called affixin, is an adapter protein that plays a role in integrin signaling via ILK and in activation of the GTPases Cdc42 and Rac1 by guanine exchange factors, such as ARHGEF6. It is involved in the reorganization of the actin cytoskeleton and the formation of lamellipodia and also plays a role in cell adhesion, cell spreading, establishment or maintenance of cell polarity, and cell migration. Beta-parvin contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs. 130 matched cddid_all.tbl CDD cd21339 cd21339 410336 PPP2R3 "serine/threonine protein phosphatase 2A regulatory subunit B"". Heterotrimeric serine/threonine protein phosphatase 2A (PP2A) consists of scaffolding (A), catalytic (C), and variable (B, B', and B"") subunits. The variable subunits dictate subcellular localization and substrate specificity of the PP2A holoenzyme. This family includes PP2A regulatory B'' subunits alpha, beta and gamma, encoded by PPP2R3A, PPP2R3B and PPP2R3C, respectively. It also includes subunit delta encoded by PPP2R3D in mouse. These B-family regulatory subunits play various roles including regulation of cytoskeletal assembly, neuronal differentiation, mitogen-activated protein kinase signaling, and apoptosis. Subunits alpha and beta contain two-domain elongated structure with two calcium EF-hands which mediate Ca2+-dependent changes in phosphatase activity." 259 matched cddid_all.tbl CDD cd21340 cd21340 411060 PPP1R42 protein phosphatase 1 regulatory subunit 42. Protein phosphatase 1 regulatory subunit 42 (PPP1R42), also known as leucine-rich repeat-containing protein 67 (lrrc67) or testis leucine-rich repeat (TLRR) protein, plays a role in centrosome separation. PPP1R42 has been shown to interact with the well-conserved signaling protein phosphatase-1 (PP1) and thereby increasing PP1's activity, which counters centrosome separation. Inhibition of PPP1R42 expression increases the number of centrosomes per cell while its depletion reduces the activity of PP1 leading to activation of NEK2, the kinase responsible for phosphorylation of centrosomal linker proteins promoting centrosome separation. 220 matched cddid_all.tbl CDD cd21341 cd21341 411061 TTC8_N N-terminal domain of tetratricopeptide repeat domain 8. Tetratricopeptide repeat domain 8 (TTC80), also known a BBS8, has been directly linked to Bardet-Biedl syndrome, an autosomal recessive ciliopathy characterized by retinal degeneration, renal failure, obesity, diabetes, male infertility, polydactyly and cognitive impairment. Mutations in BBS8 cause early vision loss. In addition to C-terminal tetratricopeptide repeats, TTC8 also contains an N-terminal domain of unknown function. 139 matched cddid_all.tbl CDD cd21342 cd21342 409247 Syt1_2_N N-terminal domain of synaptotagmin-1 and -2. The synaptotagmins are integral membrane proteins of synaptic vesicles thought to serve as Ca(2+) sensors in the process of vesicular trafficking and exocytosis. Calcium binding to synaptotagmin-1 participates in triggering neurotransmitter release at the synapse. In general, synaptotagmins contain 2 calcium binding C2 domains. Synaptotagmin-1 and -2 have an additional N-terminal domain that has been shown to bind to Botulinum neurotoxin B. 93 matched cddid_all.tbl CDD cd21343 cd21343 439166 ZBD_UPF1_nv_SF1_Hel-like Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 helicase, nidovirus SF1 helicases including coronavirus Nsp13 and arterivirus Nsp10, and related proteins. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands, and are classified based on the arrangement of conserved motifs into six superfamilies. Members of this family belong to helicase superfamily 1 (SF1) and include nidoviral helicases such as Severe Acute Respiratory Syndrome coronavirus (SARS) non-structural protein 13 (SARS-Nsp13) and equine arteritis virus (EAV) Nsp10, as well as eukaryotic UPF1 helicase. The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. UPF1 participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. The CH/ZBD of UPF1 interacts with UPF2, a factor also involved in NMD. SARS-Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). The SARS-Nsp13 CH/ZBD is indispensable for helicase activity and interacts with SARS-Nsp12, the RNA-dependent RNA polymerase. SARS-Nsp12 can enhance the helicase activity of SARS-Nsp13. UPF1, SARS-Nsp13 and EAV Nsp10 are multidomain proteins; their other domains include a 1B regulatory domain and a SF1 helicase core. 70 matched cddid_all.tbl CDD cd21344 cd21344 439170 1B_UPF1_nv_SF1_Hel-like 1B domain of eukaryotic UPF1 helicase, nidovirus SF1 helicases including coronavirus Nsp13 and arterivirus Nsp10, and related proteins. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Members of this family belong to helicase superfamily 1 (SF1) and include nidoviral helicases such as Severe Acute Respiratory Syndrome coronavirus (SARS) non-structural protein 13 (SARS-Nsp13), Equine arteritis virus (EAV) Nsp10, and eukaryotic UPF1 RNA helicase. SARS-Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). UPF1 participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. UPF1, EAV Nsp10 and SARS-Nsp13 are multidomain proteins with an N-terminal Cys/His rich zinc-binding domain (CH/ZBD), a 1B domain and a SF1 helicase core. The 1B domain is involved in nucleic acid substrate binding; the 1B domain of EAV Nsp10 undergoes large conformational change upon substrate binding, and together with the 1A and 2A domains of the helicase core form a channel that accommodates the single stranded nucleic acids. 86 matched cddid_all.tbl CDD cd21369 cd21369 410596 cwf21 cwf21 domain. The cwf21 domain is involved in mRNA splicing; it binds directly to the spliceosomal protein Prp8. Mutations in the cwf21 domain prevents its binding to Prp8. The domain is composed of two alpha helices. Proteins containing the cwf21 domain include complexed with CEF1 protein 21 (CWC21) from budding yeast, complexed with cdc5 protein 21 (CWF21) from fission yeast, as well as their orthologs, serine/arginine repetitive matrix proteins (SRRM2 and SRRM3) from vertebrates. This domain family also includes U2-associated protein SR140 from Eumetazoa, protein RRC1, and similar proteins from plants. 48 matched cddid_all.tbl CDD cd21370 cd21370 410597 cwf21_SR140 cwf21 domain found in U2-associated protein SR140 and similar proteins. SR140, also called U2 snRNP-associated SURP motif-containing protein, U2SURP, or 140 kDa Ser/Arg-rich domain protein, is a putative splicing factor mainly found in higher eukaryotes. Although it was initially identified as a 17S U2 snRNP-associated protein, the molecular and physiological function of SR140 remains unclear. This model represents the cwf21 domain of SR140 and similar proteins. The cwf21 domain is involved in mRNA splicing; it binds directly to the spliceosomal protein Prp8. 50 matched cddid_all.tbl CDD cd21371 cd21371 410598 cwf21_RRC1-like cwf21 domain found in Arabidopsis thaliana protein RRC1 and similar proteins. RRC1, also called reduced red-light responses in cry1cry2 background 1, is a SR-like splicing factor required for phytochrome B (phyB) signal transduction and involved in phyB-dependent alternative splicing. This subfamily also includes protein RRC1-like, which may also function as a SR-like splicing factor. SR family splicing factors are characterized by the presence of a domain rich in arginine and serine dipeptides, called the RS domain. This model represents the cwf21 domain of RRC1 and similar proteins. The cwf21 domain is involved in mRNA splicing; it binds directly to the spliceosomal protein Prp8. 50 matched cddid_all.tbl CDD cd21372 cd21372 410599 cwf21_CWC21-like cwf21 domain found in fungal complexed with CEF1 protein 21 (CWC21) and similar proteins. This subfamily includes complexed with CEF1 protein 21 (CWC21) from budding yeast, complexed with cdc5 protein 21 (CWF21) from fission yeast, as well as their orthologs, serine/arginine repetitive matrix proteins (SRRM2 and SRRM3) from vertebrates. Both CWC21 and CWF21 are pre-mRNA-splicing factors that may function at or prior to the first catalytic step of splicing at the catalytic center of the spliceosome, together with ISY1. SRRM2 is required for pre-mRNA splicing as a component of the spliceosome. SRRM3 may play a role in regulating breast cancer cell invasiveness. It may be involved in RYBP-mediated breast cancer progression. Members of this family contain a cwf21 domain at the N-terminus. The cwf21 domain is involved in mRNA splicing; it binds directly to the spliceosomal protein Prp8. 49 matched cddid_all.tbl CDD cd21373 cd21373 410600 cwf21_SRRM2-like cwf21 domain found in serine/arginine repetitive matrix proteins, SRRM2, SRRM3 and similar proteins. This subfamily includes SRRM2 and SRRM3, both of which contain a cwf21 domain at the N-terminus. SRRM2, also called 300 kDa nuclear matrix antigen, serine/arginine-rich splicing factor-related nuclear matrix protein of 300 kDa, SR-related nuclear matrix protein of 300 kDa, Ser/Arg-related nuclear matrix protein of 300 kDa, splicing coactivator subunit SRm300, or Tax-responsive enhancer element-binding protein 803 (TaxREB803), is required for pre-mRNA splicing as component of the spliceosome. SRRM3 may play a role in regulating breast cancer cell invasiveness. It may be involved in RYBP-mediated breast cancer progression. The cwf21 domain is involved in mRNA splicing; it binds directly to the spliceosomal protein Prp8. 50 matched cddid_all.tbl CDD cd21375 cd21375 410601 cwf21_SRRM2 cwf21 domain found in serine/arginine repetitive matrix protein 2. Serine/arginine repetitive matrix protein 2 (SRRM2) is also called 300 kDa nuclear matrix antigen, serine/arginine-rich splicing factor-related nuclear matrix protein of 300 kDa, SR-related nuclear matrix protein of 300 kDa, Ser/Arg-related nuclear matrix protein of 300 kDa, splicing coactivator subunit SRm300, or Tax-responsive enhancer element-binding protein 803 (TaxREB803). It is required for pre-mRNA splicing as component of the spliceosome. It contains a cwf21 domain at the N-terminus. The cwf21 domain is involved in mRNA splicing; it binds directly to the spliceosomal protein Prp8. 64 matched cddid_all.tbl CDD cd21376 cd21376 410602 cwf21_SRRM3 cwf21 domain found in serine/arginine repetitive matrix protein 3 and similar proteins. Serine/arginine repetitive matrix protein 3 (SRRM3) may play a role in regulating breast cancer cell invasiveness. It may also be involved in RYBP-mediated breast cancer progression. SRRM3 contains a cwf21 domain at the N-terminus. The cwf21 domain is involved in mRNA splicing; it binds directly to the spliceosomal protein Prp8. 68 matched cddid_all.tbl CDD cd21377 cd21377 439173 CTWD_Cns1-like C-terminal wheel domain found in Saccharomyces cerevisiae Hsp70/Hsp90 co-chaperone Cns1, Homo sapiens tetratricopeptide repeat protein 4 (TTC4), and similar proteins. The family includes Hsp70/Hsp90 co-chaperone Cns1 from Saccharomyces cerevisiae and the human Cns1 homolog tetratricopeptide repeat protein 4 (TTC4), both of which contain a C-terminal wheel domain consisting of a twisted five-stranded beta sheet surrounded by several alpha helices. Cns1, also called cyclophilin seven suppressor 1, or STI1 stress-inducible protein homolog, binds to the molecular chaperones Hsp90 (HSC82 and HSP82) and Hsp70 (SSA1). It stimulates SSA1 ATPase activity, but not Hsp90 ATPase activity. It is involved in only a subset of Hsp90 functions. TTC4, also called TPR repeat protein 4, is a putative Hsp90 co-chaperone which interacts with CDC6 and shows alterations in transformed cells. It interacts with TBK1 and promotes Sendai virus (SeV)-induced host cell innate immune responses. 159 matched cddid_all.tbl CDD cd21378 cd21378 411062 eIF3E eukaryotic translation initiation factor 3 subunit E. Eukaryotic translation initiation factor 3 subunit E (eIF3E, also called INT6) is a subunit of eIF3, the largest initiation factor. eIF3 is involved in many steps of initiation, including ribosomal recruitment, attachment to mRNA, and scanning. The mammalian eIF3 complex has 13 subunits. Six subunits, including subunit E, contain PCI domains (N-terminal helical repeats and a winged helix domain or WHD) that mediates PCI polymerization. Mammalian eIF3e subunit interacts with eIF3C, eIF3D, eIF3L, and eIF3A subunits, as well as eIF4G and HERC2. It exhibits tumor suppressive or oncogenic functions depending on its expression level and/or tumor type; for example, decreased expression may cause breast cancer or non-small cell lung carcinoma while overexpression is correlated with colon cancer and glioblastoma. Decreased expression of eIF3E may also enable epithelial-mesenchymal transition (EMT), which is involved in adenomyosis by promoting cell invasion, and fibrogenesis by activating the TGF-beta1 signaling pathway. 416 matched cddid_all.tbl CDD cd21380 cd21380 439174 CTWD_Cns1 C-terminal wheel domain found in Saccharomyces cerevisiae Hsp70/Hsp90 co-chaperone Cns1 and similar proteins. Cns1, also called cyclophilin seven suppressor 1, or STI1 stress-inducible protein homolog, binds to the molecular chaperones Hsp90 (HSC82 and HSP82) and Hsp70 (SSA1). It stimulates SSA1 ATPase activity, but not Hsp90 ATPase activity. It is involved in only a subset of Hsp90 functions. The model corresponds to Cns1 C-terminal wheel domain consisting of a twisted five-stranded beta sheet surrounded by several alpha helices. 153 matched cddid_all.tbl CDD cd21381 cd21381 439175 CTWD_TTC4 C-terminal wheel domain found in Homo sapiens tetratricopeptide repeat protein 4 (TTC4) and similar proteins. TTC4, also called TPR repeat protein 4, is a putative Hsp90 co-chaperone which interacts with CDC6 and shows alterations in transformed cells. It interacts with TBK1 and promotes Sendai virus (SeV)-induced host cell innate immune responses. The model corresponds to TTC4 C-terminal wheel domain consisting of a twisted five-stranded beta sheet surrounded by several alpha helices. 150 matched cddid_all.tbl CDD cd21382 cd21382 412057 RING0_parkin RING finger-like zinc-binding domain 0 of parkin. Parkin, also called Parkinson juvenile disease protein 2, is a RBR (RING1-BRcat-Rcat)-type E3 ubiquitin-protein ligase that is associated with recessive early onset Parkinson's disease (PD), and exerts a protective effect against dopamine-induced alpha-synuclein-dependent cell toxicity. Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Parkin functions within a multiprotein E3 ubiquitin ligase complex, catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins. It is involved in regulating mitochondrial quality control. Its activation is a key regulatory event in the pathway to the clearance of depolarized or damaged mitochondria. Parkin contains an N-terminal ubiquitin-like domain, an acid linker, a RING finger-like domain 0 (RING0), and a C-terminal RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. This model represents RING0 of parkin. 84 matched cddid_all.tbl CDD cd21383 cd21383 410588 GAT_GGA_Tom1-like canonical GAT domain found in eukaryotic ADP-ribosylation factor (Arf)-binding proteins (GGAs), metazoan myb protein 1 (Tom1)-like proteins, and similar proteins. This model represents the canonical GAT (GGA and Tom1) domain found in GGAs from eukaryotes, Tom1-like proteins from metazoa, and LAS seventeen-binding protein 5 (Lsb5p)-like proteins from fungi. The canonical GAT domain is a monomeric three-helix bundle that binds ubiquitin. GGAs, also called Golgi-localized gamma-ear-containing Arf-binding proteins, belong to a family of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins that regulate clathrin-mediated trafficking of cargo proteins from the trans-Golgi network (TGN) to endosomes. GGAs play important roles in ubiquitin-dependent sorting of cargo proteins both in biosynthetic and endocytic pathways. Tom1 and its related proteins, Tom1L1 and Tom1L2, form a protein family sharing an N-terminal VHS-domain followed by a GAT domain. Tom1 family proteins bind to ubiquitin, ubiquitinated proteins, and Toll-interacting protein (Tollip) through its GAT domain. They do not associate with either Arf GTPases through its GAT domain nor with acidic cluster-dileucine sequences through its VHS domain. In addition, Tom1 family proteins recruit clathrin onto endosomes through their C-terminal region. The C-terminal clathrin-binding region of Tom1 and Tom1L2 are similar to each other, but distinguishable from Tom1L1. 80 matched cddid_all.tbl CDD cd21384 cd21384 410589 GAT_STAM_Vps27-like non-canonical GAT domain found in metazoan signal transducing adapter molecules (STAMs), fungal vacuolar protein sorting-associated protein 27 (Vps27), and similar proteins. This family includes several components of the ESCRT-0 complex, including STAMs, hepatocyte growth factor-regulated tyrosine kinase substrate (Hrs), as well as vacuolar protein sorting-associated protein 27 (Vps27) and class E vacuolar protein-sorting machinery protein Hse1 from fungi. The ESCRT-0 complex binds ubiquitin and acts as a sorting machinery that recognizes ubiquitinated receptors and transfers them for further sequential lysosomal sorting/trafficking processes. Members in this family contain a non-canonical GAT (GGA and Tom1) domain consisting of two helices. By contrast, a canonical GAT domain is a monomeric three-helix bundle that bind to ubiquitin. Hrs together with STAM forms a Hrs/STAM core complex. Vps27, together with Hse1, forms a Vps27/Hse1 core complex. Those complexes consist of two intertwined non-canonical GAT domains, each consisting of two helices from one subunit, and one from the other subunit. The intertwined GAT heterodimer acts as a scaffold for binding of ubiquitinated cargo proteins and coordinating ubiquitination and deubiquitination reactions that regulate sorting. 79 matched cddid_all.tbl CDD cd21385 cd21385 410590 GAT_Vps27 non-canonical GAT domain found in fungal vacuolar protein sorting-associated protein 27 (Vps27) and similar proteins. Vps27, also called Golgi retention defective protein 11 (GRD11), is a component of the ESCRT-0 complex which is the sorting receptor for ubiquitinated cargo proteins at the multivesicular body (MVB), and recruits ESCRT-I to the MVB outer membrane. It controls exit from the prevacuolar compartment (PVC) in both the forward direction to the vacuole and the return to the Golgi. Members of this family contain a non-canonical GAT (GGA and Tom1) domain consisting of two helices. A canonical GAT domain is a monomeric three-helix bundle that bind to ubiquitin. Vps27, together with another GAT domain-containing protein Hse1, forms a Vps27/Hse1 core complex that consists of two intertwined non-canonical GAT domains, each consisting of two helices from one subunit, and one from the other subunit. The two GAT domains are connected by a two-stranded coiled-coil. The Vps27/Hse1 complex, an intertwined GAT heterodimer, is a scaffold for binding of ubiquitinated cargo proteins and coordinating ubiquitination and deubiquitination reactions that regulate sorting. 84 matched cddid_all.tbl CDD cd21386 cd21386 410591 GAT_Hse1 non-canonical GAT domain found in fungal class E vacuolar protein-sorting machinery protein Hse1 and similar proteins. Hse1 is a component of the ESCRT-0 complex which is the sorting receptor for ubiquitinated cargo proteins at the multivesicular body (MVB), and recruits ESCRT-I to the MVB outer membrane. Members of this family contain a non-canonical GAT (GGA and Tom1) domain consisting of two helices. A canonical GAT domain is a monomeric three-helix bundle that bind to ubiquitin. Hse1, together with another GAT domain-containing protein Vps27, forms a Vps27/Hse1 core complex that consists of two intertwined non-canonical GAT domains, each consisting of two helices from one subunit, and one from the other subunit. The two GAT domains are connected by a two-stranded coiled-coil. The Vps27/Hse1 complex, an intertwined GAT heterodimer, is a scaffold for binding of ubiquitinated cargo proteins and coordinating ubiquitination and deubiquitination reactions that regulate sorting. 84 matched cddid_all.tbl CDD cd21387 cd21387 410592 GAT_Hrs non-canonical GAT domain found in metazoan hepatocyte growth factor-regulated tyrosine kinase substrate (Hrs) and similar proteins. Hrs, also called protein pp110, is a tyrosine kinase substrate in growth factor-stimulated cells. It is involved in intracellular signal transduction mediated by cytokines and growth factors. Hrs is a component of the ESCRT-0 complex that binds ubiquitin and acts as sorting machinery that recognizes ubiquitinated receptors and transfers them for further sequential lysosomal sorting/trafficking processes. Members of this family contain a non-canonical GAT (GGA and Tom1) domain consisting of two helices. A canonical GAT domain is a monomeric three-helix bundle that bind to ubiquitin. Hrs, together with another GAT domain-containing protein STAM, forms a Hrs/STAM core complex that consists of two intertwined GAT domains, each consisting of two helices from one subunit, and one from the other subunit. The two GAT domains are connected by a two-stranded coiled-coil. The Hrs/STAM complex, an intertwined GAT heterodimer, is a scaffold for binding of ubiquitinated cargo proteins and coordinating ubiquitination and deubiquitination reactions that regulate sorting. 96 matched cddid_all.tbl CDD cd21388 cd21388 410593 GAT_STAM non-canonical GAT domain found in metazoan signal transducing adapter molecules (STAMs) and similar proteins. STAMs are Hrs-binding proteins involved in intracellular signal transduction mediated by cytokines and growth factors. They are components of the ESCRT-0 complex that binds ubiquitin and acts as sorting machinery that recognizes ubiquitinated receptors and transfers them for further sequential lysosomal sorting/trafficking processes. Members of this family contain a non-canonical GAT (GGA and Tom1) domain consisting of two helices. A canonical GAT domain is a monomeric three-helix bundle that bind to ubiquitin. STAM, together with another GAT domain-containing protein Hrs, forms a Hrs/STAM core complex that consists of two intertwined GAT domains, each consisting of two helices from one subunit, and one from the other subunit. The two GAT domains are connected by a two-stranded coiled-coil. The Hrs/STAM complex, an intertwined GAT heterodimer, is a scaffold for binding of ubiquitinated cargo proteins and coordinating ubiquitination and deubiquitination reactions that regulate sorting. 77 matched cddid_all.tbl CDD cd21389 cd21389 410594 GAT_STAM1 non-canonical GAT domain found in signal transducing adapter molecule 1 (STAM-1) and similar proteins. STAM-1 is involved in intracellular signal transduction mediated by cytokines and growth factors. It may also play a role in T-cell development. STAM-1 is a component of the ESCRT-0 complex that binds ubiquitin and acts as sorting machinery that recognizes ubiquitinated receptors and transfers them for further sequential lysosomal sorting/trafficking processes. Members of this subfamily contain a non-canonical GAT (GGA and Tom1) domain consisting of two helices. A canonical GAT domain is a monomeric three-helix bundle that bind to ubiquitin. STAM-1, together with another GAT domain-containing protein Hrs, forms a Hrs/STAM1 core complex that consists of two intertwined GAT domains, each consisting of two helices from one subunit, and one from the other subunit. The two GAT domains are connected by a two-stranded coiled-coil. The Hrs/STAM1 complex, an intertwined GAT heterodimer, is a scaffold for binding of ubiquitinated cargo proteins and coordinating ubiquitination and deubiquitination reactions that regulate sorting. 77 matched cddid_all.tbl CDD cd21390 cd21390 410595 GAT_STAM2 non-canonical GAT domain found in signal transducing adapter molecule 2 (STAM-2) and similar proteins. STAM-2 is a Hrs-binding protein involved in intracellular signal transduction mediated by cytokines and growth factors. STAM-2 is a component of the ESCRT-0 complex that binds ubiquitin and acts as sorting machinery that recognizes ubiquitinated receptors and transfers them for further sequential lysosomal sorting/trafficking processes. Members of this family contain a non-canonical GAT (GGA and Tom1) domain consisting of two helices. A canonical GAT domain is a monomeric three-helix bundle that bind to ubiquitin. STAM-2, together with another GAT domain-containing protein Hrs, forms a Hrs/STAM2 core complex that consists of two intertwined GAT domains, each consisting of two helices from one subunit, and one from the other subunit. The two GAT domains are connected by a two-stranded coiled-coil. The Hrs/STAM2 complex, an intertwined GAT heterodimer, is a scaffold for binding of ubiquitinated cargo proteins and coordinating ubiquitination and deubiquitination reactions that regulate sorting. 91 matched cddid_all.tbl CDD cd21392 cd21392 409621 IgC2_CD160 Immunoglobulin Constant-2 domain of Cluster of Differentiation 160 (CD160). CD160 is expressed at the cell surface as a tightly disulfide-linked multimer and is tightly associated with peripheral blood NK cells and CD8 T lymphocytes with cytolytic effector activity. Structurally similar to The B and T lymphocyte attenuator (BTLA), which appears to act as a negative regulator of T cell activation and growth. CD160 is a ligand for HVEM (herpes virus entry mediator), and considered a proposed immune checkpoint inhibitor with anti-cancer activity along with anti-PD-1 antibodies. CD160 has also been proposed as a potential target in cases of human pathological ocular and tumor neoangiogenesis that do not respond or become resistant to existing antiangiogenic drugs. 119 matched cddid_all.tbl CDD cd21393 cd21393 411063 sm_acid_XPC-like small acidic domain of Xeroderma pigmentosum group C complementing protein and similar proteins. This model represents the small acidic domain of mammalian Xeroderma pigmentosum group C complementing protein (XPC), yeast Rad4, and similar proteins. XPC/Rad4 recruits transcription/repair factor IIH (TFIIH) to the nucleotide excision repair (NER) complex through interactions with its p62/Tfb1 and XPB/Ssl2 TFIIH subunits. Global genome repair (GGR), one of two NER initiation pathways in mammals, starts with DNA lesion detection by XPC. XPC is a structure specific DNA-binding factor that recognizes distortion of the damaged DNA double helix and recruits the TFIIH complex onto the lesion to open up the damaged DNA. The small acidic domain of XPC/Rad4 interacts with the pleckstrin homology (PH) domain of the p62/Tfb1 subunit of TFIIH. 42 matched cddid_all.tbl CDD cd21396 cd21396 412027 GINS_B beta-strand (B) domain of GINS complex proteins: Sld5, Psf1, Psf2, Psf3, Gins51 and Gins23. The GINS (named from the Japanese go-ichi-ni-san, meaning 5-1-2-3 for the Sld5, Psf1, Psf2, and Psf3 subunits) complex is involved in both the initiation and elongation stages of eukaryotic chromosome replication, with GINS being the component that most likely serves as the replicative helicase that unwinds duplex DNA ahead of the moving replication fork. This complex is found in eukaryotes and archaea, but not in bacteria. In eukaryotes, GINS is a tetrameric arrangement of four subunits Sld5, Psf1, Psf2 and Psf3, while in archaea, it consists of two different proteins named Gins51 and Gins23. The archaeal GINS complex can be either an alpha2beta2-type heterotetramer composed of Gins51 and Gins23, or a Gins51-only alpha4-type homotetramer. All GINS subunits are homologous and consist of two domains, called the alpha-helical (A) and beta-strand (B) domains. The A and B domains of Sld5/Psf1/Gins51 are permuted with respect to Psf1/Psf3/Gins23. The overall tetrameric assemblies of GINS are similar, but the relative locations of the C-terminal small domains are different with respect to the alpha-helical domain, resulting in different subunit contacts. However, the basic function of GINS in DNA replication is conserved across eukaryotes and archaea. This model represents the beta-strand domain (B-domain) of GINS complex proteins. 49 matched cddid_all.tbl CDD cd21397 cd21397 411064 cc_ERCC-6_N coiled-coil domain located near the N-terminus of human Excision Repair Cross Complementing 6 (ERCC-6) and related proteins. This model represents a coiled-coil domain located near the N-terminus of ERCC-6 and related proteins. ERCC-6 (also known as Cockayne syndrome group B, CSB) is a DNA-binding protein important in eukaryotic transcription-coupled repair (TCR). TCR is a well-conserved sub-pathway of nucleotide excision repair (NER) that preferentially removes DNA lesions from the template strand blocking translocation of RNA polymerase II (Pol II). In a model for TCR, the processing Pol II encounters the lesion on the transcribed DNA strand and stalls; it is then displaced by the TCR-initiation complex which includes ERCC-6, ERCC-8, UVSSA and USP7; TCR-specific factors then access the lesion for the DNA damage incision process. The N-terminal region, the ATPase domain and the C-terminal region of ERCC-6 all directly contribute to DNA association and catalytic activity. The ATPase domain functions in concert with either the N- or C-terminal region to mediate UV-induced chromatin association. The N-terminal region prevents ERCC-6 from stably associating with chromatin under normal growth conditions, and the C-terminal region of ERCC-6 promotes stable chromatin association in the presence of lesion-stalled transcription. In addition to this coiled-coil domain, the N-terminal region of ERCC-6 includes two lysine residues subject to SUMOylation, a nucleolar localization signal NoLS1, and a nuclear localization signal NLS1. ERCC-6 also includes a SWI/SNF-like ATPase domain, a nucleotide-binding domain and a ubiquitin-binding domain. This coiled-coil domain binds magnesium. This domain family does not include Saccharomyces cerevisiae RAD26, and Schizosaccharomyces pombe Rhp26. 77 matched cddid_all.tbl CDD cd21399 cd21399 394806 ZBD_nv_SF1_Hel-like Cys/His rich zinc-binding domain (CH/ZBD) of nidovirus helicases including coronavirus Nsp13 and arterivirus Nsp10, and related proteins. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. This nidovirus family includes Severe Acute Respiratory Syndrome coronavirus (SARS) non-structural protein 13 (SARS-Nsp13) and equine arteritis virus (EAV) Nsp10 helicase, and belongs to helicase superfamily 1 (SF1). The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. SARS-Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). The SARS-Nsp13 CH/ZBD is indispensable for helicase activity and interacts with SARS-Nsp12, the RNA-dependent RNA polymerase. SARS-Nsp12 can enhance the helicase activity of SARS-Nsp13. SARS-Nsp13 and EAV Nsp10 are multidomain proteins; their other domains include a 1B regulatory domain and a SF1 helicase core. 71 matched cddid_all.tbl CDD cd21400 cd21400 439167 ZBD_UPF1-like Cys/His rich zinc-binding domain (CH/ZBD) of eukaryotic UPF1 RNA helicase and related proteins. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. UPF1 belongs to helicase superfamily 1 (SF1). The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. UPF1 participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. The N-terminal CH/ZBD of UPF1 interacts with UPF2, a factor also involved in NMD. UPF1 has an N-terminal CH/ZBD, a 1B domain, and a SF1 helicase core. 120 matched cddid_all.tbl CDD cd21401 cd21401 439168 ZBD_cv_Nsp13-like Cys/His rich zinc-binding domain (CH/ZBD) of coronavirus SARS NSP13 helicase and related proteins. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. This coronavirus family includes Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) non-structural protein 13 (SARS-Nsp13) and belongs to helicase superfamily 1 (SF1) and to a family of nindoviral replication helicases. SARS-Nsp13 has an N-terminal CH/ZBD, a stalk domain, a 1B regulatory domain, and SF1 helicase core. The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. SARS-Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). The SARS-Nsp13 CH/ZBD is indispensable for helicase activity and interacts with SARS-Nsp12, the RNA-dependent RNA polymerase (RdRp). Structural studies of a stable SARS-CoV-2 RTC which included two molecules of Nsp13, the RdRp holoenzyme (Nsp7, two molecules of Nsp8, Nsp12), and an RNA template product, show that one Nsp13 CH/ZBD domain interacts with Nsp12, and both Nsp13-CH/ZBD domains interact with the Nsp8. This stable SARS-CoV-2 RTC suggests that the Nsp13 helicase may drive RTC backtracking, affecting proofreading and template switching. 95 matched cddid_all.tbl CDD cd21402 cd21402 394809 ZBD_mv_SF1_Hel-like Cys/His rich zinc-binding domain (CH/ZBD) of mesnidovirus SF1 helicase and related proteins. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. This mesnidovirus group includes the Bontag Baru virus (BBaV) replication helicase encoded on ORF1b and belongs to helicase superfamily 1 (SF1). The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. Members of this group belong to a family of nindoviral replication helicases which include includes Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) non-structural protein 13 (SARS-Nsp13), a component of the viral RNA synthesis replication and transcription complex (RTC). The SARS-Nsp13 CH/ZBD is indispensable for helicase activity and interacts with SARS-Nsp12, the RNA-dependent RNA polymerase. SARS-Nsp12 can enhance the helicase activity of SARS-Nsp13. 111 matched cddid_all.tbl CDD cd21403 cd21403 394810 ZBD_tv_SF1_Hel-like Cys/His rich zinc-binding domain (CH/ZBD) of tornidovirus SF1 helicase and related proteins. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. This tornidovirus group includes White bream virus (WBV) SF1 helicase encoded on ORF1b and belongs to helicase superfamily 1 (SF1). The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. Members of this group belong to a family of nindoviral replication helicases which include includes Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) non-structural protein 13 (SARS-Nsp13), a component of the viral RNA synthesis replication and transcription complex (RTC). The SARS-Nsp13 CH/ZBD is indispensable for helicase activity and interacts with SARS-Nsp12, the RNA-dependent RNA polymerase. 95 matched cddid_all.tbl CDD cd21404 cd21404 394811 ZBD_rv_SF1_Hel-like Cys/His rich zinc-binding domain (CH/ZBD) of ronidovirus SF1 helicase and related proteins. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. This ronidovirus group includes Gill-associated virus (GAV) replication helicase encoded on ORF1 and belongs to helicase superfamily 1 (SF1). The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. Members of this group belong to a family of nindoviral replication helicases which include includes Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) non-structural protein 13 (SARS-Nsp13), a component of the viral RNA synthesis replication and transcription complex (RTC). The SARS-Nsp13 CH/ZBD is indispensable for helicase activity and interacts with SARS-Nsp12, the RNA-dependent RNA polymerase. SARS-Nsp12 can enhance the helicase activity of SARS-Nsp13. 105 matched cddid_all.tbl CDD cd21405 cd21405 439169 ZBD_av_Nsp10-like Cys/His rich zinc-binding domain (CH/ZBD) of arterivirus EAV Nsp10 helicase and related proteins. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Members of this arterivirus group belong to helicase superfamily 1 (SF1) and include helicases such Equine arteritis virus (EAV) Nsp10 helicase encoded on ORF1b. The CH/ZBD has 3 zinc-finger (ZnF1-3) motifs. Members of this group belong to a family of nindoviral replication helicases which include includes Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) non-structural protein 13 (SARS-Nsp13), a component of the viral RNA synthesis replication and transcription complex (RTC). The SARS-Nsp13 CH/ZBD is indispensable for helicase activity and interacts with SARS-Nsp12, the RNA-dependent RNA polymerase. SARS-Nsp12 can enhance the helicase activity of SARS-Nsp13. 62 matched cddid_all.tbl CDD cd21406 cd21406 439171 1B_nv_SF1_Hel-like 1B domain of nidovirus helicases including coronavirus Nsp13 and arterivirus Nsp10, and related proteins. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Members of this nidoviral family belong to helicase superfamily 1 (SF1) and include nidoviral helicases such as Severe Acute Respiratory Syndrome coronavirus (SARS) non-structural protein 13 (SARS-Nsp13) and Equine arteritis virus (EAV) Nsp10. SARS-Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). They belong to a larger SF1 helicase family which also includes eukaryotic UPF1-like helicases. UPF1, EAV Nsp10 and SARS-Nsp13 are multidomain proteins with an N-terminal Cys/His rich zinc-binding domain (CH/ZBD), a 1B domain and a SF1 helicase core. The 1B domain is involved in nucleic acid substrate binding; the 1B domain of EAV Nsp10 undergoes large conformational change upon substrate binding, and together with the 1A and 2A domains of the helicase core form a channel that accommodates the single stranded nucleic acids. 48 matched cddid_all.tbl CDD cd21407 cd21407 394815 1B_UPF1-like 1B domain of eukaryotic UPF1 RNA helicase and related proteins. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. UPF1 belongs to helicase superfamily 1 (SF1). It participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons. UPF1 is a multidomain protein; it includes an N-terminal Cys/His rich zinc-binding domain (CH/ZBD), a regulatory 1B domain, and a SF1 helicase core. The 1B domain is involved in nucleic acid substrate binding; the 1B domain of the related Equine arteritis virus (EAV) Nsp10 undergoes large conformational change upon substrate binding, and together with the 1A and 2A domains of the helicase core form a channel that accommodates the single stranded nucleic acids. 90 matched cddid_all.tbl CDD cd21408 cd21408 394816 1B_Sen1p-like 1B domain of Saccharomyces cerevisiae Sen1p RNA helicase and related proteins. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Sen1p belongs to a UPF1-like family of helicase superfamily 1 (SF1). UPF1 participates in nonsense-mediated mRNA decay (NMD), a pathway which degrades transcripts with premature termination codons, Sen1p plays a role in the termination of non-coding transcription. UPF1 is a multidomain protein; it includes an N-terminal Cys/His rich zinc-binding domain (CH/ZBD), a 1B regulatory domain, and a SF1 helicase core. Sen1p has a similar domain organization and helicase mechanism to UPF1. However, it has distinct structural features including a more elaborate topology of the 1B barrel domain, and a distinct function from UPF1, an ATPase-dependent ability of promoting transcription termination in vitro. The 1B domain is involved in nucleic acid substrate binding; the 1B domain of the related Equine arteritis virus (EAV) Nsp10 undergoes large conformational change upon substrate binding, and together with the 1A and 2A domains of the helicase core form a channel that accommodates the single stranded nucleic acids. 106 matched cddid_all.tbl CDD cd21409 cd21409 394817 1B_cv_Nsp13-like 1B domain of coronavirus SARS NSP13 helicase and related proteins. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Members of this subfamily belong to helicase superfamily 1 (SF1) and include coronavirus helicases such as Severe Acute Respiratory Syndrome coronavirus (SARS) non-structural protein 13 (SARS-Nsp13). SARS-Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). Structural studies of a stable RTC which included the RNA-dependent RNA polymerase holoenzyme (Nsp7, two molecules of Nsp82, Nsp12), two molecules of Nsp13 helicase accessory factor and an RNA template product suggests that the Nsp13 helicase may drive RTC backtracking, affecting proofreading and template switching. SARS-Nsp13 is a multidomain protein; its other domains include an N-terminal Cys/His rich zinc-binding domain (CH/ZBD) and a SF1 helicase core. The 1B domain is involved in nucleic acid substrate binding; the 1B domain of the related Equine arteritis virus (EAV) Nsp10 undergoes large conformational change upon substrate binding, and together with the 1A and 2A domains of the helicase core form a channel that accommodates the single stranded nucleic acids. 79 matched cddid_all.tbl CDD cd21410 cd21410 439172 1B_av_Nsp10-like 1B domain of arterivirus EAV Nsp10 helicase and related proteins. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Members of this subfamily belong to helicase superfamily 1 (SF1) and include arterivirus helicases such Equine arteritis virus (EAV) Nsp10 helicase encoded on ORF1b. EAV Nsp10 is a multidomain protein; its other domains include an N-terminal Cys/His rich zinc-binding domain (CH/ZBD) and a SF1 helicase core. The 1B domain is involved in nucleic acid substrate binding; the 1B domain of EAV Nsp10 undergoes large conformational change upon substrate binding, and together with the 1A and 2A domains of the helicase core form a channel that accommodates the single stranded nucleic acids. 49 matched cddid_all.tbl CDD cd21411 cd21411 411058 NucC cyclic oligonucleotide-based anti-phage signaling system-associated NucC nuclease. Cyclic oligonucleotide-based anti-phage signaling system (CBASS)-associated NucC nuclease kills phage-infected cells through genome destruction. It is allosterically activated by a cyclic triadenylate (cA3) second messenger that is synthesized by CBASS upon infection. NucC is related to restriction endonucleases but it adopts a homotrimeric structure. Binding of cA3 causes two NucC homotrimers to assemble into a homohexamer, which brings together a pair of active sites to activate DNA cleavage. NucC has also been integrated into type III CRISPR/Cas systems as an accessory nuclease. 225 matched cddid_all.tbl CDD cd21413 cd21413 394819 unc_tv_SF1_Hel-like uncharacterized domain which connects the Cys/His rich zinc-binding (ZBD) and linker to the first helicase domain of tornidovirus SF1 helicase and related proteins. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Helicases in this family belong to helicase superfamily 1 (SF1) and include tornidovirus helicases such as Breda virus serotype 1 (BoTV-1) SF1 helicase encoded on ORF1b. They are related to the SF1 family nidoviral replication helicases which include Severe Acute Respiratory Syndrome coronavirus (SARS) non-structural protein 13 (SARS-Nsp13), a component of the viral RNA synthesis replication and transcription complex (RTC). SARS-Nsp13 is a multidomain protein; its other domains include an N-terminal Cys/His rich zinc-binding domain (ZBD) and a SF1 helicase core. The location of the uncharacterized domain represented in this tornidovirus group resembles that of the 1B domain in SARS-Nsp13 helicase; it connects the zinc-binding domain (ZBD) and linker to the first helicase domain. 79 matched cddid_all.tbl CDD cd21414 cd21414 394820 unc_rv_SF1_Hel-like uncharacterized domain which connects the Cys/His rich zinc-binding domain (ZBD) and linker to the first helicase domain of ronidovirus SF1 helicase and related proteins. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Members of this family belong to helicase superfamily 1 (SF1) and include ronidovirus helicases such as Gill-associated virus (GAV) replication helicase encoded on ORF1b. They are related to the SF1 family nidoviral replication helicases which include Severe Acute Respiratory Syndrome coronavirus (SARS) non-structural protein 13 (SARS-Nsp13), a component of the viral RNA synthesis replication and transcription complex (RTC). SARS-Nsp13 is a multidomain protein; its other domains include an N-terminal Cys/His rich zinc-binding domain (CH/ZBD) and a SF1 helicase core. The location and orientation of the uncharacterized domain represented in this ronidovirus group resembles that of the 1B domain in SARS-Nsp13 helicase; it connects the Cys/His zinc-binding domain (ZBD) and linker to the first helicase domain. 56 matched cddid_all.tbl CDD cd21416 cd21416 411065 HDC_protein histidine decarboxylase (HDC) gene cluster protein. This model includes an uncharacterized histidine decarboxylase (HDC) gene cluster protein. Lactobacillus parabuchneri is one of the major causes of elevated histamine levels in cheese. Histamine positive strain FAM21731 from L. parabuchneri has been shown to contain a histidine decarboxylase gene cluster present on a genomic island, which seems to have undergone transfer within the same species as well as between other lactobacilli. 380 matched cddid_all.tbl CDD cd21417 cd21417 411066 AvrRxo1 AvrRxo1, a type III effector with a polynucleotide kinase domain. This family contains AvrRxo1-ORF1 (also called AvrRxo1) which has been shown to be a type III-secreted virulence factor in Xanthomonas oryzae (Xoc) that causes bacterial leaf streak (BLS) disease in rice plants. AvrRxo1-ORF1 delivery in rice plant cells is recognized by disease resistance protein Rxo1, which triggers resistance to BLS disease. In the Xoc genome, AvrRxo1-ORF1 is adjacent to AvrRxo1-ORF2 (also called AvrRxo1-required chaperone, or Arc1) which appears to act as a molecular chaperone. AvrRxo1 has a T4 polynucleotide kinase (T4pnk) domain, while Arc1 has a kinase-binding domain with a structure that is atypical of effector-binding chaperones. AvrRxo1 and Arc1 comprise a toxin-antitoxin system similar to members of the zeta-epsilon family, with AvrRxo1 acting as the toxin. 330 matched cddid_all.tbl CDD cd21418 cd21418 411067 Arc1 Arc1, AvrRxo1-required chaperone. This family contains AvrRxo1-ORF2 (also called AvrRxo1-required chaperone or Arc1) which appears to act as a molecular chaperone for AvrRxo1-ORF1 (also called AvrRxo1), a type III-secreted virulence factor in Xanthomonas oryzae (Xoc), a bacteria that causes leaf streak (BLS) disease in rice plants. AvrRxo1-ORF1 delivery in rice plant cells is recognized by disease resistance protein Rxo1, which triggers resistance to BLS disease. In the Xoc genome, the Arc1 gene is found adjacent to AvrRxo1; Arc1 functions to suppress the bacteriostatic activity of AvrRxo1-ORF1 in bacterial cells. Arc1 has a kinase-binding domain with a structure that is atypical of effector-binding chaperones, while AvrRxo1 has a T4 polynucleotide kinase (T4pnk) domain. AvrRxo1 and Arc1 comprise a toxin-antitoxin system similar to members of the zeta-epsilon family, with Arc1 acting as the antitoxin. 97 matched cddid_all.tbl CDD cd21422 cd21422 412058 GatF mitochondrial glutamyl-tRNA(Gln) amidotransferase subunit F. Glutamyl-tRNA(Gln) amidotransferase subunit F (GatF), also called Glu-AdT subunit F, is the connector subunit of yeast mitochondrial tRNA-dependent amidotransferase (AdT) that is also composed of the GatA and GatB subunits. GatA and GatB are well conserved among bacteria and eukaryota, but the GatF subunit is a fungi-specific ortholog of the GatC subunit found in all other known heterotrimeric AdTs. AdT allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in the mitochondria. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). This model corresponds to the GatF subunit, which can be divided into two halves, the C-terminal GatC-like portion and the N-terminal appended domain (NTD). 128 matched cddid_all.tbl CDD cd21431 cd21431 467847 Med9-C Mediator complex subunit 9 (Med9) C-terminal domain family. Med9 is a member of the Middle module transcriptional mediator complex which has a species-specific amino-terminal and a well-conserved carboxy-terminal half. Med9 carboxy-terminal has a fundamental function involved in direct binding to other Med proteins and the assembly of Med9 into the Middle module. Med9 amino terminal plays a regulatory role in transcriptional regulation. Mediator co-activator complex plays an essential role in regulation of RNA polymerase II transcription in all eukaryotes. 82 matched cddid_all.tbl CDD cd21433 cd21433 439176 SARAH_Sav C-terminal SARAH domain of Drosophila melanogaster scaffold protein salvador (Sav) and similar proteins. Sav is a scaffold protein that is mainly found in metazoans. Drosophila melanogaster salvador, also called Shar-pei (SHRP), promotes both cell cycle exit and apoptosis in Drosophila. It plays a key role in the Hippo/SWH (Sav/Wts/Hpo) signaling pathway, a signaling pathway that plays a pivotal role in organ size control and tumor suppression by restricting proliferation and promoting apoptosis. Human protein salvador homolog 1, also called 45 kDa WW domain protein (WW45), acts as a mammalian sterile 20-like kinase 1 (MST1)-binding protein required to enhance MST1-mediated apoptosis. It is a regulator of STK3/MST2 and STK4/MST1 in the Hippo signaling pathway. It also plays a role in centrosome disjunction by regulating the localization of NEK2 to centrosomes, and its ability to phosphorylate CROCC and CEP250. This model corresponds to the C-terminal SARAH (Salvador-RassF-Hippo) domain of Sav, which mediates complex formation/heterodimerization between Hippo and Sav. 67 matched cddid_all.tbl CDD cd21435 cd21435 410603 SUN_cc1 coiled-coil domain 1 of SUN domain-containing proteins. SUN (Sad1 and UNC-84) proteins (SUN1 and SUN2) are components of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex which is involved in the connection between the nuclear lamina and the cytoskeleton. Besides the core SUN domain, SUN proteins contain two coiled-coil domains (CC1 and CC2), which act as intrinsic dynamic regulators controlling the activity of the SUN domain. The model corresponds to CC1 that functions as an activation segment to release CC2-mediated inhibition of the SUN domain. 55 matched cddid_all.tbl CDD cd21437 cd21437 467791 zf-HIT_ZNHIT1_like "HIT zinc finger found in zinc finger HIT domain-containing protein 1 (ZNHIT1) and similar proteins. The family includes ZNHIT1 and its yeast counterpart, the vacuolar protein sorting-associated protein 71 (Vps71p). ZNHIT1, also known as cyclin-G1-binding protein 1 (CGBP1), zinc finger protein subfamily 4A member 1 (ZNFN4A1), or p18 Hamlet, may have a role in inducing apoptosis through p53 signaling. It binds to Rev-erb beta and releases its inhibitory effect on the transcription of apolipoprotein C3 (APOC3) without affecting its DNA-binding activity. The yeast counterpart Vps71p, also referred to as SWR complex protein 6 (Swc6p), plays a role in the exchange of histone H2A for the H2A variant HZT1, a euchromatin-specific factor, leading to chromatin remodeling and transcriptional changes of targeted genes. It is indirectly involved in vacuolar protein sorting. Members of this family contain a zf-HIT domain characterized by a ""treble-clef"" fold through interleaved CCCC and CCHC zinc finger motifs, both of which bind a zinc ion." 43 matched cddid_all.tbl CDD cd21438 cd21438 410604 SUN2_cc1 coiled-coil domain 1 of SUN domain-containing protein 2 and similar proteins. SUN domain-containing protein 2 (SUN2), also called protein unc-84 homolog B, Rab5-interacting protein (Rab5IP), or Sad1/unc-84 protein-like 2, is a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex which is involved in the connection between the nuclear lamina and the cytoskeleton. Besides the core SUN domain, SUN2 contains two coiled-coil domains (CC1 and CC2), which act as the intrinsic dynamic regulators for controlling the activity of the SUN domain. This model corresponds to CC1 that functions as an activation segment to release CC2-mediated inhibition of the SUN domain. 55 matched cddid_all.tbl CDD cd21439 cd21439 410605 SUN1_cc1 coiled-coil domain 1 of SUN domain-containing protein 1 and similar proteins. SUN domain-containing protein 1 (SUN1), also called protein unc-84 homolog A, or Sad1/unc-84 protein-like 1, is a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex which is involved in the connection between the nuclear lamina and the cytoskeleton. Besides the core SUN domain, SUN1 contains two coiled-coil domains (CC1 and CC2), which act as the intrinsic dynamic regulators for controlling the activity of the SUN domain. This model corresponds to CC1 that may function as an activation segment to release CC2-mediated inhibition of the SUN domain. 55 matched cddid_all.tbl CDD cd21440 cd21440 410607 KLF8_N N-terminal domain of Kruppel-like factor 8. Kruppel-like factor 8 (also known as Krueppel-like transcription factor 8, KLF8) is a CACCC-box binding protein that associates with C-terminal Binding Protein (CtBP) and represses transcription. It plays an essential role in the regulation of the cell cycle, apoptosis, and differentiation. It has been identified as a key component of the transcription factor network that controls terminal differentiation during adipogenesis. It also plays an important role in the formation of several human tumors, including the promotion of tumorigenesis, invasion, and metastasis of colorectal cancer cells, and the progression of pancreatic cancer. KLF8 belongs to a family of proteins called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Although these factors bind to similar elements in vitro, they have distinct activities in vivo depending on their expression profile and the sequence of the N-terminal activation/repression domain, which differ between members. KLF8 contains an N-terminal repression domain that is related to that of KLF12. 169 matched cddid_all.tbl CDD cd21441 cd21441 410608 KLF12_N N-terminal domain of Kruppel-like factor 12. Kruppel-like factor 12 (also known as Krueppel-like transcription factor 12, KLF12) regulates, by transcriptionally repressing Nur77 expression, endometrial decidualization, which is a prerequisite for successful implantation and the establishment of pregnancy. It is involved in the maturation processes of kidney collecting ducts after birth, and is able to increase the promoter activity of the UT-A1 urea transporter promoter by binding to the CACCC motif. KLF12 has also been found to promote colorectal cancer growth is also involved in the invasion and apoptosis of basal-like breast carcinoma. KLF12 belongs to a family of proteins called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Although these factors bind to similar elements in vitro, they have distinct activities in vivo depending on their expression profile and the sequence of the N-terminal activation/repression domain, which differ between members. KLF12 contains an N-terminal domain that is related to the N-terminal repression domain of KLF8. 197 matched cddid_all.tbl CDD cd21442 cd21442 410568 SNARE_NTD_STX6-like N-terminal domain of syntaxin-6 and similar proteins. The family includes soluble NSF attachment protein receptor (SNARE) proteins, syntaxin-6 (STX6) and syntaxin-10 (STX10), and their homologs found in fungi and plants, such as Tlg1p, AtSYP61, and similar proteins. STX6 is involved in intracellular vesicle trafficking. STX10, also called Syn10, is involved in vesicular transport from the late endosomes to the trans-Golgi network. Tlg1p, also called syntaxin TLG1, is a SNARE protein (of Qc type) involved in membrane fusion probably in retrograde traffic of cytosolic double-membrane vesicles derived from both, early and possibly late endosomes/PVC (prevacuolar compartment) back to the trans-Golgi network (TGN or late Golgi). It has been reported to function both as a (target membrane) t-SNARE and as a (vesicle) v-SNARE. AtSYP61, also called osmotic stress-sensitive mutant 1 (OSM1), is a vesicle trafficking syntaxin protein that functions in the secretory pathway. It is involved in osmotic stress tolerance and in abscisic acid (ABA) regulation of stomatal responses in Arabidopsis. 103 matched cddid_all.tbl CDD cd21443 cd21443 410569 SNARE_NTD_STX6_STX10 N-terminal domain of syntaxin-6, syntaxin-10, and similar proteins. This subfamily includes two soluble NSF attachment protein receptor (SNARE) proteins, syntaxin-6 (STX6) and syntaxin-10 (STX10). STX6 is involved in intracellular vesicle trafficking. STX10, also called Syn10, is involved in vesicular transport from the late endosomes to the trans-Golgi network. This model corresponds to the N-terminal domain of STX6 and STX10, which is a regulatory domain named Habc. 103 matched cddid_all.tbl CDD cd21444 cd21444 410570 SNARE_NTD_Tlg1p-like N-terminal domain of t-SNARE affecting a late Golgi compartment protein 1 and similar proteins. t-SNARE affecting a late Golgi compartment protein 1 (Tlg1p), also called syntaxin TLG1, is a soluble NSF attachment protein receptor (SNARE) protein (of Qc type) involved in membrane fusion, probably in retrograde traffic of cytosolic double-membrane vesicles derived from both, early and possibly late endosomes/PVC (prevacuolar compartment) back to the trans-Golgi network (TGN or late Golgi). It has been reported to function both as a (target membrane) t-SNARE and as a (vesicle) v-SNARE. The model corresponds to the N-terminal domain of Tlg1p, which consists of a three-helix bundle. 93 matched cddid_all.tbl CDD cd21445 cd21445 410571 SNARE_NTD_AtSYP61-like N-terminal domain of Arabidopsis thaliana syntaxin-61 and similar proteins. Arabidopsis thaliana syntaxin-61 (AtSYP61), also called osmotic stress-sensitive mutant 1 (OSM1), is a vesicle trafficking syntaxin protein that functions in the secretory pathway. It is involved in osmotic stress tolerance and in abscisic acid (ABA) regulation of stomatal responses in Arabidopsis. This model corresponds to the N-terminal domain of AtSYP61, which shows high sequence similarity with the N-terminal domain of yeast Tlg1p, a soluble NSF attachment protein receptor (SNARE) protein (of Qc type) involved in membrane fusion. 99 matched cddid_all.tbl CDD cd21446 cd21446 410572 SNARE_NTD_STX10 N-terminal domain of syntaxin-10. Syntaxin-10 (STX10), also called Syn10, is part of a soluble NSF attachment protein receptor (SNARE) complex involved in vesicular transport from the late endosomes to the trans-Golgi network, such as the transport of mannose 6-phosphate receptors from endosomes to the Golgi after delivering lysosomal enzymes to the endocytic pathway. This model corresponds to the N-terminal domain of STX10, which is a regulatory domain named Habc. 103 matched cddid_all.tbl CDD cd21447 cd21447 410573 SNARE_NTD_STX6 N-terminal domain of syntaxin-6. Syntaxin-6 (STX6) is a component of a soluble NSF attachment protein receptor (SNARE) complex involved in intracellular vesicle trafficking and in the fusion of retrograde transport carriers with the trans-Golgi network (TGN). This model corresponds to N-terminal domain of STX6, which is a regulatory domain named Habc. 103 matched cddid_all.tbl CDD cd21448 cd21448 411996 DLC-like_DYNLT1-like dynein light chain (DLC)-like domain found in the dynein light chain Tctex-type 1 (DYNLT1) subfamily and similar proteins. The dynein light chain Tctex-type 1 (DYNLT1) subfamily includes two isoforms, DYNLT1 and DYNLT3, which contribute to the differential regulation of dynein cargo binding. They are non-catalytic accessory components of the cytoplasmic dynein 1 complex that are thought to be involved in linking dynein to cargos and to adapter proteins that regulate dynein function. The dynein complex contains either DYNLT1 or DYNLT3, but not both. The family also includes Schizosaccharomyces pombe dynein light chain Tctex-type (SpDlc1), Saccharomyces cerevisiae topoisomerase I damage affected protein 2 (TDA2) and similar proteins. SpDlc1 belongs to the 14-kDa Tctex-1 dynein light chain family. It acts as a non-catalytic accessory component of a dynein complex. It is required for regular oscillatory nuclear movement and efficient recombination during meiotic prophase in fission yeast. TDA2 is a novel protein of the endocytic machinery necessary for normal internalization of native cargo in yeast. It works independently of the dynein motor complex and microtubules. 98 matched cddid_all.tbl CDD cd21449 cd21449 411997 DLC-like_SF dynein light chain (DLC)-like domain superfamily. The superfamily corresponds to a class of proteins containing a dynein light chain (DLC)-like domain with anti-parallel beta-sheet packed against an alpha-helical hairpin. DLC-like domain-containing proteins includes cytoplasmic dynein light chain DYNLL1 and DYNLL2, axonemal dynein light chain 4 (DNAL4), tegumental-allergen-like proteins (TALs), dynein light chain Tctex-type DYNLT1 and DYNLT3, as well as Tctex1 domain-containing proteins (TCTEX1D). Both DYNLL1 and DYNLL2 are non-catalytic accessory components of the cytoplasmic dynein 1 complex that are thought to be involved in linking dynein to cargos and to adapter proteins that regulate dynein function. DNAL4 is a force generating protein of respiratory cilia. TALs may be involved in the transport of vesicles within the tegumental cytoplasm, probably within dynein motor complexes. DYNLT1 and DYNLT3, which contribute to the differential regulation of dynein cargo binding. They are non-catalytic accessory components of the cytoplasmic dynein 1 complex, which contains either DYNLT1 or DYNLT3, but not both. TCTEX1D family includes TCTEX1D1-4. TCTEX1D1 is a genetic modifier of disease progression in Duchenne muscular dystrophy (DMD). TCTEX1D2 is required for proper retrograde ciliary transport. TCTEX1D3 may be an accessory component of axonemal dynein and cytoplasmic dynein 1. TCTEX1D4 is a novel protein phosphatase 1 (PPP1) interactor. 96 matched cddid_all.tbl CDD cd21450 cd21450 411998 DLC-like_DYNLL1-like dynein light chain (DLC)-like domain found in cytoplasmic dynein light chain 1 (DYNLL1), axonemal dynein light chain 4 (DNAL4), tegumental-allergen-like proteins (TALs) and similar proteins. The family includes cytoplasmic dynein light chain 1 (DYNLL1), DYNLL2, axonemal dynein light chain 4 (DNAL4), and tegumental-allergen-like proteins (TALs). DYNLL1, also called protein inhibitor of neuronal nitric oxide synthase (PIN), or 8 kDa dynein light chain (DLC8), or dynein light chain LC8-type 1 (DLC1), is one of several non-catalytic accessory components of the cytoplasmic dynein 1 complex that are thought to be involved in linking dynein to cargos and to adapter proteins that regulate dynein function. It acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. It may play a role in changing or maintaining the spatial distribution of cytoskeletal structures. DYNLL2, also called cytoplasmic dynein light chain 2, or 8 kDa dynein light chain b (DLC8b), or dynein light chain LC8-type 2 (DLC2), is one of several non-catalytic accessory components of the cytoplasmic dynein 1 complex that are thought to be involved in linking dynein to cargos and to adapter proteins that regulate dynein function. DNAL4 is a force generating protein of respiratory cilia. It produces force towards the minus ends of microtubules. TALs, also called tegument antigens, are characterized by two N-terminal EF-hand motifs and a C-terminal region resembling a dynein light chain (DLC)-like domain. They were mainly found in parasitic platyhelminth species. TALs are strongly associated with the tegument, a syncytial structure that forms the outer layer of the organism. They may be involved in the transport of vesicles within the tegumental cytoplasm, probably within dynein motor complexes. 68 matched cddid_all.tbl CDD cd21451 cd21451 411999 DLC-like_TCTEX1D dynein light chain (DLC)-like domain found in the Tctex1 domain-containing protein (TCTEX1D) family. The Tctex1 domain-containing protein (TCTEX1D) family includes TCTEX1D1-4. TCTEX1D1 is a genetic modifier of disease progression in Duchenne muscular dystrophy (DMD). It can interact with ZMYND10 that stabilizes intermediate chain proteins in the cytoplasmic pre-assembly of dynein arms. TCTEX1D2 is required for proper retrograde ciliary transport. It associates with short-rib polydactyly syndrome proteins, such as Wdr34, Wdr60, and other dynein complex 1 and 2 subunits, and is required for ciliogenesis. TCTEX1D2 is a negative regulator of GLUT4 translocation and glucose uptake. TCTEX1D3, also called T-complex testis-specific protein 3, or T-complex-associated testis-expressed protein 3 (Tcte-3), may be an accessory component of axonemal dynein and cytoplasmic dynein 1. TCTEX1D4, also called protein N22.1, or Tctex-2-beta, is a novel protein phosphatase 1 (PPP1) interactor. It also interacts with ENG/endoglin, TGFBR2, and TGFBR3. The distribution of TCTEX1D4 in testis suggests its involvement in distinct functions, such as TGFbeta signaling at the blood-testis barrier and acrosome cap formation. The model corresponds to the dynein light chain (DLC)-like domain of TCTEX1Ds. 101 matched cddid_all.tbl CDD cd21452 cd21452 412000 DLC-like_DYNLL1_DYNLL2 dynein light chain (DLC)-like domain found in the cytoplasmic dynein light chain 1 (DYNLL1) family. The cytoplasmic dynein light chain 1 (DYNLL1) family includes DYNLL1 and DYNLL2. DYNLL1, also called protein inhibitor of neuronal nitric oxide synthase (PIN), or 8 kDa dynein light chain (DLC8), or dynein light chain LC8-type 1 (DLC1), acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. It may play a role in changing or maintaining the spatial distribution of cytoskeletal structures. Both DYNLL1 and DYNLL2 (also called 8 kDa dynein light chain b, or DLC8b, or dynein light chain LC8-type 2, or DLC2) are non-catalytic accessory components of the cytoplasmic dynein 1 complex that are thought to be involved in linking dynein to cargos and to adapter proteins that regulate dynein function. The model corresponds to the dynein light chain (DLC)-like domain of DYNLL1 and DYNLL2. 84 matched cddid_all.tbl CDD cd21453 cd21453 412001 DLC-like_DNAL4 dynein light chain (DLC)-like domain found in axonemal dynein light chain 4 (DNAL4) and similar proteins. Axonemal dynein light chain 4 (DNAL4) is a force generating protein of respiratory cilia. It produces force towards the minus ends of microtubules. The model corresponds to the dynein light chain (DLC)-like domain of DNAL4. 83 matched cddid_all.tbl CDD cd21454 cd21454 412002 DLC-like_TAL dynein light chain (DLC)-like domain found in the family of tegumental-allergen-like proteins (TALs). Tegumental-allergen-like proteins (TALs), also called tegument antigens, are characterized by two N-terminal EF-hand motifs and a C-terminal region resembling a dynein light chain (DLC)-like domain. They were mainly found in parasitic platyhelminth species. TALs are strongly associated with the tegument, a syncytial structure that forms the outer layer of the organism. They may be involved in the transport of vesicles within the tegumental cytoplasm, probably within dynein motor complexes. The model corresponds to the dynein light chain (DLC)-like domain of TAL. 87 matched cddid_all.tbl CDD cd21455 cd21455 412003 DLC-like_DYNLT1_DYNLT3 dynein light chain (DLC)-like domain found in the dynein light chain Tctex-type 1 (DYNLT1) family. The dynein light chain Tctex-type 1 (DYNLT1) family includes two isoforms, DYNLT1 and DYNLT3, which contribute to the differential regulation of dynein cargo binding. They are non-catalytic accessory components of the cytoplasmic dynein 1 complex that are thought to be involved in linking dynein to cargos and to adapter proteins that regulate dynein function. The dynein complex contains either DYNLT1 or DYNLT3, but not both. The model corresponds to the dynein light chain (DLC)-like domain of DYNLT1 and DYNLT3. 97 matched cddid_all.tbl CDD cd21456 cd21456 412004 DLC-like_SpDlc1-like dynein light chain (DLC)-like domain found in Schizosaccharomyces pombe dynein light chain Tctex-type (SpDlc1) and similar proteins. Schizosaccharomyces pombe dynein light chain 1 (SpDlc1) belongs to the 14-kDa Tctex-1 dynein light chain family. It acts as a non-catalytic accessory component of a dynein complex. It is required for regular oscillatory nuclear movement and efficient recombination during meiotic prophase in fission yeast. The model corresponds to the dynein light chain (DLC)-like domain found in SpDlc1 and similar proteins. 110 matched cddid_all.tbl CDD cd21457 cd21457 412005 DLC-like_TDA2 dynein light chain (DLC)-like domain found in topoisomerase I damage affected protein 2 (TDA2) and similar proteins. Topoisomerase I damage affected protein 2 (TDA2) is a novel protein of the endocytic machinery necessary for normal internalization of native cargo in yeast. It works independently of the dynein motor complex and microtubules. The model corresponds to the dynein light chain (DLC)-like domain of TDA2. 108 matched cddid_all.tbl CDD cd21458 cd21458 412006 DLC-like_TCTEX1D1 dynein light chain (DLC)-like domain found in Tctex1 domain-containing protein 1 (TCTEX1D1) and similar proteins. Tctex1 domain-containing protein 1 (TCTEX1D1) is a genetic modifier of disease progression in Duchenne muscular dystrophy (DMD). It can interact with ZMYND10 that stabilizes intermediate chain proteins in the cytoplasmic pre-assembly of dynein arms. The model corresponds to the (dynein light chain) DLC-like domain of TCTEX1D1. 104 matched cddid_all.tbl CDD cd21459 cd21459 412007 DLC-like_TCTEX1D2 dynein light chain (DLC)-like domain found in Tctex1 domain-containing protein 2 (TCTEX1D2) and similar proteins. Tctex1 domain-containing protein 2 (TCTEX1D2) is required for proper retrograde ciliary transport. It associates with short-rib polydactyly syndrome proteins, such as Wdr34, Wdr60, and other dynein complex 1 and 2 subunits, and is required for ciliogenesis. TCTEX1D2 is a negative regulator of GLUT4 translocation and glucose uptake. The model corresponds to the dynein light chain (DLC)-like domain of TCTEX1D2. 104 matched cddid_all.tbl CDD cd21460 cd21460 412008 DLC-like_TCTEX1D3 dynein light chain (DLC)-like domain found in Tctex1 domain-containing protein 3 (TCTEX1D3) and similar proteins. Tctex1 domain-containing protein 3 (TCTEX1D3), also called T-complex testis-specific protein 3, or T-complex-associated testis-expressed protein 3 (Tcte-3), may be an accessory component of axonemal dynein and cytoplasmic dynein 1. The model corresponds to the dynein light chain (DLC)-like domain of TCTEX1D3. 112 matched cddid_all.tbl CDD cd21461 cd21461 412009 DLC-like_TCTEX1D4 dynein light chain (DLC)-like domain found in Tctex1 domain-containing protein 4 (TCTEX1D4) and similar proteins. Tctex1 domain-containing protein 4 (TCTEX1D4), also called protein N22.1, or Tctex-2-beta, is a novel protein phosphatase 1 (PPP1) interactor. It also interacts with ENG/endoglin, TGFBR2 and TGFBR3. The distribution of TCTEX1D4 in testis suggests its involvement in distinct functions, such as TGFbeta signaling at the blood-testis barrier and acrosome cap formation. The model corresponds to the dynein light chain (DLC)-like domain of TCTEX1D4. 114 matched cddid_all.tbl CDD cd21462 cd21462 412010 DLC-like_DYNLT1 dynein light chain (DLC)-like domain found in dynein light chain Tctex-type 1 (DYNLT1) and similar proteins. Dynein light chain Tctex-type 1 (DYNLT1), also called TCTEL1, or TCTEX1, or protein CW-1, or T-complex testis-specific protein 1 homolog, is a non-catalytic accessory component of the cytoplasmic dynein 1 complex that are thought to be involved in linking dynein to cargos and to adapter proteins that regulate dynein function. It plays a role in neuronal morphogenesis. It is involved in intracellular targeting of D-type retrovirus gag polyproteins to the cytoplasmic assembly site. The model corresponds to the dynein light chain (DLC)-like domain of DYNLT1. 102 matched cddid_all.tbl CDD cd21463 cd21463 412011 DLC-like_DYNLT3 dynein light chain (DLC)-like domain found in dynein light chain Tctex-type 3 (DYNLT3) and similar proteins. Dynein light chain Tctex-type 3 (DYNLT3), also called rp3, or protein 91/23, or T-complex-associated testis-expressed 1-like, is a non-catalytic accessory component of the cytoplasmic dynein 1 complex that are thought to be involved in linking dynein to cargos and to adapter proteins that regulate dynein function. It has a potential role in chromosome congression in human mitosis and is required for chromosome alignment during mouse oocyte meiotic maturation. The DYNLT3 light chain directly links cytoplasmic dynein to a spindle checkpoint protein, Bub3. The model corresponds to the dynein light chain (DLC)-like domain of DYNLT3. 97 matched cddid_all.tbl CDD cd21464 cd21464 410550 7tm_GPR137 GPR137 family belonging to the seven-transmembrane G protein-coupled receptor superfamily. The GPR137 family includes GPR137A, GPR137B, and GPR137C, which are all orphan G protein-coupled receptors (GPCRs). GPR137A, also called GPR137 or transmembrane 7 superfamily member 1-like 1 protein (TM7SF1L1), is expressed in the central nervous system (CNS), endocrine gland, thymus, and lung. It is associated with different cancers including gastric cancer, pancreatic cancer, colon cancer, and malignant glioma. GPR137B, also called transmembrane 7 superfamily member 1 (TM7SF1), is a lysosome integral membrane protein that is strongly expressed in the heart, liver, kidney, and brain. It is associated with M2 macrophage polarization, and has been shown to perform a regulatory function in controlling dynamic Rag and mTORC1 localization and activity, as well as lysosome morphology. GPR137C, also called transmembrane 7 superfamily member 1-like 2 protein (TM7SF1L2), may be a key player in the prognosis of small cell lung cancer. GPCRs transmit physiological signals from the outside of the cell to the inside via G proteins. All GPCRs share a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 310 matched cddid_all.tbl CDD cd21465 cd21465 410574 LPS_wlbK-like Bordetella wlbK gene product domains involved in bacterial polysaccharide synthesis, and similar domains. This model includes gene wlbJ (also known as bplJ, bplK, wlbjK) product protein, one of 12 genes that is involved in liposaccharide (LPS) synthesis. The liposaccharides (LPS) of Bordetella species are pyrogenic, mitogenic, and toxic, and can activate and induce tumor necrosis factor production in macrophages, similar to endotoxins from other gram-negative bacteria. Also, while the family Enterobacteriaceae expresses smooth-type LPS, the Bordetella LPS molecules differ in chemical structure; B. bronchiseptica and B. parapertussis synthesize a long-chain polysaccharide consisting of a homopolymer of 2,3-dideoxy-2,3-diN-acetylgalactosaminuronic acid (2,3-diNAcGalA), known as O antigen, whereas B. pertussis does not and is therefore more similar to rough-type LPS. This substantial structural difference between the LPS molecules of the three main pathogenic bordetellae likely confers quite different surface properties on the different species. Gene characterization studies show that wlbJ and wlbK are two apparently separate genes in B. pertussis, but are fused into a single open reading frame in B. bronchiseptica and B. parapertussishu. Studies show that mutations in wlbJK do not affect LPS biosynthesis but their function remains unclear. 154 matched cddid_all.tbl CDD cd21466 cd21466 439190 Ubl2_PLpro_N_CoV_Nsp3-like second ubiquitin-like (Ubl) domain located N-terminal to the papain-like protease (PLpro) domain in coronavirus non-structural protein 3 (Nsp3) and related proteins. This model represents the second ubiquitin-like (Ubl) domain located N-terminal to the papain-like protease (PLpro) domain of non-structural protein 3 (Nsp3) from coronavirus (CoV), including highly pathogenic human CoVs such as Severe acute respiratory syndrome (SARS)-CoV and SARS-CoV-2 (also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus). SARS-CoV non-structural proteins (Nsps) are encoded in ORF1a and ORF1b. Post infection, the SARS-CoV genomic RNA is released into the cytoplasm of the cell and translated into two long polyproteins (pps), pp1a and pp1ab. Papain-like protease (PLpro) is one of two SARS-CoV proteases which process these polyproteins; it cleaves pp1a at three sites, releasing Nsp1, Nsp2, and Nsp3. Nsp3 is a large multi-functional multi-domain protein which is an essential component of the replication/transcription complex (RTC). This ubiquitin-like (Ubl) domain (sometimes referred to as Ubl2, the second Ubl domain of Nsp3) is located N-terminal to the PLpro domain of Nsp3. In addition to being a protease, SARS-CoV PLpro is a deubiquitinating enzyme (DUB), and may be involved in subverting cellular ubiquitination machinery to facilitate viral replication. A number of cellular DUBs have a Ubl domain, where it may serve a regulatory function. The exact functional role of this Ubl domain is unclear. 54 matched cddid_all.tbl CDD cd21467 cd21467 394822 Ubl1_cv_Nsp3_N-like first ubiquitin-like (Ubl) domain located at the N-terminus of coronavirus SARS-CoV non-structural protein 3 (Nsp3) and related proteins. This ubiquitin-like (Ubl) domain (Ubl1) is found at the N-terminus of coronavirus Nsp3, a large multi-functional multi-domain protein which is an essential component of the replication/transcription complex (RTC). The functions of Ubl1 in CoVs are related to single-stranded RNA (ssRNA) binding and to interacting with the nucleocapsid (N) protein. SARS-CoV Ubl1 has been shown to bind ssRNA having AUA patterns, and since the 5'-UTR of the SARS-CoV genome has a number of AUA repeats, it may bind there. In mouse hepatitis virus (MHV), this Ubl1 domain binds the cognate N protein. Adjacent to Ubl1 is a Glu-rich acidic region (also referred to as hypervariable region, HVR); Ubl1 together with HVR has been called Nsp3a. Currently, the function of HVR in CoVs is unknown. This model corresponds to one of two Ubl domains in Nsp3; the other is located N-terminal to the papain-like protease (PLpro) and is not represented by this model. 89 matched cddid_all.tbl CDD cd21468 cd21468 410575 LPS_wlbK_N-like N-terminal domain of Bordetella wlbK gene product involved in bacterial polysaccharide synthesis, and similar domains. This model includes the N-terminal domain of the gene wlbJ (also known as bplJ, bplK, wlbjK) product protein, one of 12 genes that is involved in liposaccharide (LPS) synthesis. The liposaccharides (LPS) of Bordetella species are pyrogenic, mitogenic, and toxic, and can activate and induce tumor necrosis factor production in macrophages, similar to endotoxins from other gram-negative bacteria. Also, while the family Enterobacteriaceae expresses smooth-type LPS, the Bordetella LPS molecules differ in chemical structure; B. bronchiseptica and B. parapertussis synthesize a long-chain polysaccharide consisting of a homopolymer of 2,3-dideoxy-2,3-diN-acetylgalactosaminuronic acid (2,3-diNAcGalA), known as O antigen, whereas B. pertussis does not and is therefore more similar to rough-type LPS. This substantial structural difference between the LPS molecules of the three main pathogenic bordetellae likely confers quite different surface properties on the different species. Gene characterization studies show that wlbJ and wlbK are two apparently separate genes in B. pertussis, but are fused into a single open reading frame in B. bronchiseptica and B. parapertussishu. Studies show that mutations in wlbJK do not affect LPS biosynthesis but their function remains unclear. 154 matched cddid_all.tbl CDD cd21469 cd21469 410576 LPS_wlbK_C-like C-terminal domain of Bordetella wlbK gene product involved in bacterial polysaccharide synthesis, and similar domains. This model includes the C-terminal domain of the gene wlbJ (also known as bplJ, bplK, wlbjK) product protein, one of 12 genes that is involved in liposaccharide (LPS) synthesis. The liposaccharides (LPS) of Bordetella species are pyrogenic, mitogenic, and toxic, and can activate and induce tumor necrosis factor production in macrophages, similar to endotoxins from other gram-negative bacteria. Also, while the family Enterobacteriaceae expresses smooth-type LPS, the Bordetella LPS molecules differ in chemical structure; B. bronchiseptica and B. parapertussis synthesize a long-chain polysaccharide consisting of a homopolymer of 2,3-dideoxy-2,3-diN-acetylgalactosaminuronic acid (2,3-diNAcGalA), known as O antigen, whereas B. pertussis does not and is therefore more similar to rough-type LPS. This substantial structural difference between the LPS molecules of the three main pathogenic bordetellae likely confers quite different surface properties on the different species. Gene characterization studies show that wlbJ and wlbK are two apparently separate genes in B. pertussis, but are fused into a single open reading frame in B. bronchiseptica and B. parapertussishu. Studies show that mutations in wlbJK do not affect LPS biosynthesis but their function remains unclear. 154 matched cddid_all.tbl CDD cd21470 cd21470 394823 CoV_Spike_S1_RBD receptor-binding domain of the S1 subunit of coronavirus spike (S) proteins. This family contains the receptor-binding domain (RBD) of the S1 subunit of coronavirus (CoV) spike (S) proteins from three highly pathogenic human coronaviruses (CoVs), including Middle East respiratory syndrome coronavirus (MERS-CoV), Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), and SARS coronavirus 2 (SARS-CoV-2), also known as a 2019 novel coronavirus (2019-nCoV), as well as S proteins from related coronaviruses. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. MHV uses mouse carcinoembryonic antigen related cell adhesion molecule 1a (mCEACAM1a) as the receptor, and the receptors for SARS-CoV and MERS-CoV are human angiotensin-converting enzyme 2 (ACE2) and human dipeptidyl peptidase 4 (DPP4), respectively. Recent studies found that the RBD of SARS-CoV-2 S protein binds strongly to human and bat angiotensin-converting enzyme 2 (ACE2) receptors. Moreover, SARS-CoV-2 RBD exhibited significantly higher binding affinity to the ACE2 receptor than SARS-CoV RBD. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs. 171 matched cddid_all.tbl CDD cd21471 cd21471 409193 CrtC-like carotenoid 1,2-hydratase and similar proteins. Carotenoid 1,2-hydratase (EC 4.2.1.131; CrtC; also known as acyclic carotenoid 1,2-hydratase, 1-hydroxyneurosporene hydratase, hydroxylycopene hydratase, hydroxyneurosporene synthase, lycopene hydratase, or neurosporene hydratase) is an enzyme with the systematic name lycopene hydro-lyase (1-hydroxy-1,2-dihydrolycopene-forming). It is involved in the biosynthesis of carotenoids such as lycopenes. It catalyzes the hydration of neurosporene to the corresponding hydroxylated carotenoids 1-HO-neurosporene and that of lycopene to 1-HO-lycopene. Studies suggest that CrtC may be bound to the membrane through an anchor so that a close distance to the substrate, which is synthesized in the cell membranes, is facilitated. 276 matched cddid_all.tbl CDD cd21472 cd21472 439191 CylC-like cyanobacterial acyl halogenase CylC and similar proteins. CylC has been characterized as a halogenase involved in the biosynthesis of cylindrocyclophane; another member, cyanobacterial NocO, has recently been implicated in the biosynthesis of chlorosphaerolactylates and nocuolactylates, NocO had been suggested to play a role in the synthesis of natural oxadiazines such as nocuolin A (NoA, exhibits anti-proliferative activity against human cancer cell lines). Members are also similar to cyanobacterial ColD and ColE, putative acyl halogenases involved in columbamide biosynthesis. 356 matched cddid_all.tbl CDD cd21473 cd21473 394836 cv_Nsp4_TM coronavirus non-structural protein 4 (Nsp4) transmembrane domain. Nsp4 may be involved in coronavirus-induced membrane remodeling. In order to assemble the replication-transcription complex (RTC), coronavirus induces the rearrangement of host endoplasmic reticulum (ER) membrane into double membrane vesicles (DMVs), zippered ER, or ER spherules. DMV formation has been observed in SARS-CoV cells overexpressing the three transmembrane-containing non-structural proteins of viral replicase polyprotein 1ab: Nsp3, Nsp4 and Nsp6. Together, Nsp3, Nsp4, and Nsp6 have the ability to induce the formation of DMVs that are similar to those seen in SARS-CoV-infected cells. 376 matched cddid_all.tbl CDD cd21474 cd21474 410551 7tm_GPR137A Integral membrane protein GPR137A, an orphan receptor member of the seven-transmembrane G protein-coupled receptor superfamily. GPR137A, also called GPR137 or transmembrane 7 superfamily member 1-like 1 protein (TM7SF1L1), is an orphan G protein-coupled receptor (GPCR) expressed in the central nervous system (CNS), endocrine gland, thymus, and lung. It is associated with different cancers including gastric cancer, pancreatic cancer, colon cancer, and malignant glioma. It is highly expressed in ovarian cancer and plays a pro-oncogenic role in the disease, promoting cell proliferation and metastasis through regulation of the PI3K/AKT pathway. GPCRs transmit physiological signals from the outside of the cell to the inside via G proteins. All GPCRs share a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 310 matched cddid_all.tbl CDD cd21475 cd21475 410552 7tm_GPR137C Integral membrane protein GPR137C, an orphan receptor member of the seven-transmembrane G protein-coupled receptor superfamily. GPR137C, also called transmembrane 7 superfamily member 1-like 2 protein (TM7SF1L2), is an orphan G protein-coupled receptor (GPCR) of unknown function. Bioinformatics analysis identified it as a likely key player in the prognosis of small cell lung cancer. GPCRs transmit physiological signals from the outside of the cell to the inside via G proteins. All GPCRs share a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 319 matched cddid_all.tbl CDD cd21476 cd21476 410553 7tm_GPR137B Integral membrane protein GPR137B, an orphan receptor member of the seven-transmembrane G protein-coupled receptor superfamily. GPR137B, also called transmembrane 7 superfamily member 1 (TM7SF1), is a lysosome integral membrane protein that is strongly expressed in the heart, liver, kidney, and brain. It is an orphan G protein-coupled receptor (GPCR) associated with M2 macrophage polarization, and has been shown to perform a regulatory function in controlling dynamic Rag and mTORC1 localization and activity, as well as lysosome morphology. It also plays a role in bone remodeling in mouse and zebrafish, functioning as a negative regulator of osteoclast activity essential for normal resorption and patterning of the skeleton. GPCRs transmit physiological signals from the outside of the cell to the inside via G proteins. All GPCRs share a common structural architecture comprising of seven-transmembrane (TM) alpha-helices interconnected by three extracellular and three intracellular loops. A general feature of GPCR signaling is agonist-induced conformational changes in the receptors, leading to activation of the heterotrimeric G proteins, which consist of the guanine nucleotide-binding G-alpha subunit and the dimeric G-beta-gamma subunits. The activated G proteins then bind to and activate numerous downstream effector proteins, which generate second messengers that mediate a broad range of cellular and physiological processes. 320 matched cddid_all.tbl CDD cd21477 cd21477 394824 SARS-CoV-like_Spike_S1_RBD receptor-binding domain of the S1 subunit of severe acute respiratory syndrome-related coronavirus Spike (S) protein and similar proteins. This subfamily contains the receptor-binding domain of the S1 subunit of coronavirus (CoV) spike (S) proteins from highly pathogenic human virus, severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), SARS coronavirus 2 (SARS-CoV-2), also known as 2019 novel coronavirus (2019-nCoV), and other SARS-like coronaviruses. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2 and SARS-CoV use the C-domain to bind their receptors. Recent studies found that the receptor-binding domain (RBD) of SARS-CoV-2 S protein binds strongly to human and bat angiotensin-converting enzyme 2 (ACE2) receptors. Moreover, SARS-CoV-2 RBD exhibited significantly higher binding affinity to the ACE2 receptor than SARS-CoV RBD. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for SARS-CoV, SARS-CoV-2, and most CoVs. 205 matched cddid_all.tbl CDD cd21478 cd21478 394825 HKU1-like_CoV_Spike_S1_RBD receptor-binding domain of the S1 subunit of the Spike (S) protein from human coronavirus HKU1 and related coronaviruses. This family contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from human coronavirus (CoV) HKU1, human coronavirus OC43 (HCoV-OC43), mouse hepatitis virus (MHV), porcine hemagglutinating encephalomyelitis virus (HEV), and other related coronaviruses. HKU1 is a human betacoronavirus that causes mild yet prevalent respiratory disease. HCoV-OC43 is of zoonotic origin and is endemic in the human population, causing mild respiratory tract infections and possible severe complications or fatalities in young children, the elderly, and immunocompromised individuals. MHV is the most common viral pathogen in contemporary laboratory mouse colonies manifesting as a primary infection in the upper respiratory tract. Porcine HEV is associated with acute outbreaks of wasting and encephalitis in nursing piglets from pig farms. These viruses are related to the zoonotic SARS and MERS betacoronaviruses, which have high fatality rates and pandemic potential. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBDs of MHV and HCoV-OC43 are located at the NTD, most CoVs use the C-domain to bind their receptors. Although a protein receptor has not yet been identified for HKU1, antibodies against the C-domain, but not those against the NTD, blocked HKU1 infection of cells, suggesting that the S1 C-domain is the primary HKU1 receptor-binding site. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs. 223 matched cddid_all.tbl CDD cd21479 cd21479 394826 MERS-like_CoV_Spike_S1_RBD receptor-binding domain of the S1 subunit of the Spike (S) protein from Middle East respiratory syndrome coronavirus. This family contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from the human coronavirus that causes Middle East Respiratory Syndrome (MERS-CoV) and related coronaviruses from animals. MERS-CoV causes severe pulmonary disease in humans. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including MERS-CoV use the C-domain to bind their receptors. MERS-CoV use human dipeptidyl peptidase 4 (DPP4), also called CD26, as its receptor. It binds DPP4 through the RBD of its S1 subunit and then fuses viral and host membranes through its S2 subunit. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs including MERS-CoV. 216 matched cddid_all.tbl CDD cd21480 cd21480 394827 SARS-CoV-2_Spike_S1_RBD receptor-binding domain of the S1 subunit of severe acute respiratory syndrome coronavirus 2 Spike (S) protein. This group contains the receptor-binding domain of the S1 subunit of the spike (S) protein from highly pathogenic human virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known as 2019 novel coronavirus (2019-nCoV). The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While RBD of mouse hepatitis virus (MHV) is located at the NTD, most of other CoVs, including SARS-CoV-2 use the C-domain to bind their receptors. Recent studies found that the receptor-binding domain (RBD) of SARS-CoV-2 S protein binds strongly to human and bat angiotensin-converting enzyme 2 (ACE2) receptors. Moreover, SARS-CoV-2 RBD exhibited significantly higher binding affinity to the ACE2 receptor than SARS-CoV RBD. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for SARS-CoV-2 and most CoVs. 223 matched cddid_all.tbl CDD cd21481 cd21481 394828 SARS-CoV_Spike_S1_RBD receptor-binding domain of the S1 subunit of severe acute respiratory syndrome-related coronavirus Spike (S) protein. This group contains the receptor-binding domain of the S1 subunit of the spike (S) protein from severe acute respiratory syndrome-related coronavirus (SARS-CoV) and similar coronaviruses. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV use the C-domain to bind their receptors. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for SARS-CoV and most CoVs. 222 matched cddid_all.tbl CDD cd21482 cd21482 394829 HKU1_N5-like_CoV_Spike_S1_RBD receptor-binding domain of the S1 subunit of the Spike (S) protein from human coronavirus HKU1, isolate N5 and isolate N2. This group contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from human coronavirus (CoV) HKU1, isolates N5 and N2. HKU1 is a human betacoronavirus that causes mild yet prevalent respiratory disease, and is related to the zoonotic SARS and MERS betacoronaviruses, which have high fatality rates and pandemic potential. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs use the C-domain to bind their receptors. Although a protein receptor has not yet been identified for HKU1, antibodies against the C-domain, but not those against the NTD, blocked HKU1 infection of cells, suggesting that the S1 C-domain is the primary HKU1 receptor-binding site. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs, and most likely, for HKU1. 304 matched cddid_all.tbl CDD cd21483 cd21483 394830 HKU1_N1_CoV_Spike_S1_RBD receptor-binding domain of the S1 subunit of the Spike (S) protein from human coronavirus HKU1, isolate N1. This group contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from human coronavirus (CoV) HKU1, isolate N1. HKU1 is a human betacoronavirus that causes mild yet prevalent respiratory disease, and is related to the zoonotic SARS and MERS betacoronaviruses, which have high fatality rates and pandemic potential. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs use the C-domain to bind their receptors. Although a protein receptor has not yet been identified for HKU1, antibodies against the C-domain, but not those against the NTD, blocked HKU1 infection of cells, suggesting that the S1 C-domain is the primary HKU1 receptor-binding site. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs, and most likely, for HKU1. 306 matched cddid_all.tbl CDD cd21484 cd21484 394831 MHV-like_Spike_S1_RBD receptor-binding domain of the S1 subunit of the Spike (S) protein from mouse hepatitis virus and other rodent coronaviruses. This group contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from mouse hepatitis virus (MHV) and other rodent coronaviruses. MHV is the most common viral pathogen in contemporary laboratory mouse colonies manifesting as a primary infection in the upper respiratory tract. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). MHV uses mouse carcinoembryonic antigen related cell adhesion molecule 1a (mCEACAM1a) as the receptor; the RBD of MHV is located at the NTD. Most CoVs, such as SARS-CoV and MERS-CoV, use the C-domain to bind their receptors. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs. 264 matched cddid_all.tbl CDD cd21485 cd21485 394832 HCoV-OC43-like_Spike_S1_RBD receptor-binding domain of the S1 subunit of the Spike (S) protein from human coronavirus OC43 and related proteins. This group contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from several betacoronaviruses including human coronavirus OC43 (HCoV-OC43) and bovine respiratory coronavirus (BCoV), among others. HCoV-OC43 is of zoonotic origin and is endemic in the human population, causing mild respiratory tract infections and possible severe complications or fatalities in young children, the elderly, and immunocompromised individuals. These viruses are related to the zoonotic SARS and MERS betacoronaviruses, which have high fatality rates and pandemic potential. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs use the C-domain to bind their receptors. It has been reported that HCoV-OC43 uses 9-O-acetyl-sialic acid (9-O-Ac-Sia) as a receptor, which is terminally linked to oligosaccharides decorating glycoproteins and gangliosides at the host cell surface. HCoV-OC43 appears to bind 9-O-Ac-Sia at the NTD. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs. 312 matched cddid_all.tbl CDD cd21486 cd21486 394833 human_MERS-CoV_Spike_S1_RBD receptor-binding domain of the S1 subunit of the Spike (S) protein from human Middle East respiratory syndrome coronavirus. This group contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from the human coronavirus that causes Middle East Respiratory Syndrome (MERS-CoV). MERS-CoV causes severe pulmonary disease in humans. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including MERS-CoV use the C-domain to bind their receptors. MERS-CoV use human dipeptidyl peptidase 4 (DPP4), also called CD26, as its receptor. It binds DPP4 through the RBD of its S1 subunit and then fuses viral and host membranes through its S2 subunit. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs including MERS-CoV. 219 matched cddid_all.tbl CDD cd21487 cd21487 394834 bat_HKU4-like_Spike_S1_RBD receptor-binding domain of the S1 subunit of the Spike (S) protein from Tylonycteris bat coronavirus HKU4 and similar proteins. This group contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from Tylonycteris bat coronavirus HKU4 and other Middle East Respiratory Syndrome (MERS)-related coronaviruses. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including human MERS-CoV that is phylogenetically closely related to bat CoV HKU4 use the C-domain to bind their receptors. HKU4 is able to bind the MERS-CoV receptor, human dipeptidyl peptidase 4 (DPP4), also called CD26. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs including MERS-CoV, and most likely, bat CoV HKU4. 219 matched cddid_all.tbl CDD cd21494 cd21494 411069 TMEM168 Transmembrane (TMEM) protein family 168. This family includes transmembrane protein 168 (TMEM168) and similar proteins. TMEM168 is a multi-pass membrane protein predicted to contain nine transmembrane helices. Its expression has been implicated in several diseases. It is upregulated in glioblastoma multiforme (GBM) and small interfering RNA (siRNA)-TMEM168 has been shown to prevent viability of human GBM cell lines, induce cell cycle arrest (G0/G1 phase), and promote apoptosis through the suppression of the Wnt/beta-catenin pathway. A TMEM168 point mutation has also been associated with arrhythmogenesis in familial Brugada syndrome. 681 matched cddid_all.tbl CDD cd21500 cd21500 412059 NleA-like bacterial effector protein NleA, and similar proteins. This family includes non-locus of enterocyte effacement (non-LEE) encoded effector A (NleA), a bacterial effector protein injected by enteropathogenic and enterohemorrhagic Escherichia coli (EPEC and EHEC), both related strains capable of inducing severe gastrointestinal disease. These pathogens modulate cellular functions via the deployment of effector proteins in a type three secretion system (T3SS)-dependent manner. In response, the host Nod-like receptor pyrin domain containing (NLRP) inflammasome activates caspase-1 and releases IL-1beta. NleA plays a role in controlling the host immune response through targeting of Nod-like receptor 3 (NLRP3); it has been identified as the effector that can subdue IL-1beta secretion by inhibiting caspase-1 activation, thus inhibiting NLRP inflammasome activation. NleA interacts with NLRP3 via regions containing the PYD and LRR domains. NleA has also been shown to associate with non-ubiquitinated and ubiquitinated NLRP3 and to interrupt de-ubiquitination of NLRP3, which is a required process for inflammasome activation. 425 matched cddid_all.tbl CDD cd21501 cd21501 411070 GtgE Salmonella enterica effector protein GtgE. The Salmonella enterica GtgE effector protein contributes to the virulence of this pathogen by modulating trafficking of the Salmonella-containing vacuole. GtgE, which exclusively targets inactive Rab GTPases, has been identified as a cysteine protease with the typical Cys-Hip-Asp catalytic triad. It functions by cleaving the Rab-family GTPases Rab29, Rab32 and Rab38, thereby preventing the delivery of antimicrobial factors to the bacteria-containing vacuole. It has been shown to solely process the inactive GDP-bound GTPase Rab32. However, weak binding of GtgE to the peptide encompassing the Rab29 cleavage site suggests that the function of GtgE may be dependent on other factors, such as a protein partner or interactions with the Salmonella-containing vacuole (SCV) membrane. 174 matched cddid_all.tbl CDD cd21502 cd21502 411071 vWA_BABAM1 Von-Willebrand factor A (vWA) domain found in BRISC and BRCA1-A complex member 1. BRISC and BRCA1 A complex member 1 (BABAM1) is also known as Mediator of RAP80 interactions and targeting subunit of 40 kDa (MERIT40), New component of the BRCA1-A complex (NBA1), HSPC142, or C19orf620. It is a core component of the BRCA1-A and BRISC complexes that function in DNA double-strand break repair and immune signaling, and contain the lysine-63 linkage-specific BRCC36 subunit that is functionalized by scaffold subunits Abraxas and ABRO1, respectively. BABAM1 interacts with Rap80, BRCC36, BRCC45, and Abraxas to form the BRCA1-A complex, a lysine-63-Ub specific deubiquitinating enzyme (DUB) which specifically recognizes lysine-63-linked ubiquitinated histones H2A and H2AX at DNA lesions sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at double-strand breaks (DSBs). BRISC is a DUB complex containing three other subunits, BRCC36, ABRO1 and BRCC45. It specifically hydrolyzes lysine-63 polyubiquitin chains, and is involved in multiple biological processes, including IFN-mediated antiviral immune regulation and inflammatory reaction. BABAM1 likely serves as a scaffold protein by integrating other components to form a functional complex. Furthermore, BABAM1 has been shown to play a critical role in BRISC-mediated regulation of Tankyrase1 (TNKS1) function during spindle assembly; it directly binds to the ankyrin repeat cluster V (ARC-V) domain of TNKS1 via its RXXPEG motif. BABAM1 contains a Von-Willebrand factor A (vWA) domain that is distantly related to classical vWA domains. 216 matched cddid_all.tbl CDD cd21503 cd21503 409631 ABC-2_lan_permease lantibiotic immunity ABC transporter permease (also called ABC-2 transporter permease) subunit. This family contains lantibiotic ABC transporter permease subunits which are highly hydrophobic, integral membrane proteins, and part of the bacitracin ABC transport system that confers resistance to the Gram-positive bacteria in which this system operates, particularly to type-A lantibiotics. Lantibiotics are small peptides, produced by Gram-positive bacteria, which are ribosomally-synthesized as pre-peptides and act by disrupting membrane integrity. Genes encoding the lantibiotic ABC transporter subunits are highly organized in operons containing all the genes required for maturation, transport, immunity, and synthesis. For example, in Lactococcus lactis, the lantibiotic nisin is active against other Gram-positive bacteria via various modes of actions; however, its self-protection against the pore-forming nisin is mediated by the ABC transporter composed of NisF, NisE and NisG subunits. This family includes the Lactococcus lactis NisG permease subunit that transports nisin to the surface and expels it from the membrane. This family also includes the lantibiotic ABC transporter permease subunits EpiE, MutE, MutG, and SlvE. Self-protection of the epidermin-producing strain Staphylococcus epidermidis Tu3298 against the pore-forming lantibiotic epidermin is mediated by an ABC transporter composed of the EpiF, EpiE, and EpiG proteins. In the mutacin I-producing strain Streptococcus mutans CH43, self-immunity against mutacin I is mediated by proteins MutF, MutE, and MutG, while in salivaricin D-producing strain Streptococcus salivarius 5M6c, mediation is via ABC transporter proteins SlvF, SlvE, and SlvG. 221 matched cddid_all.tbl CDD cd21504 cd21504 410337 PPP2R3A_B-like "serine/threonine protein phosphatase 2A regulatory subunit B"" alpha and beta subunits, and similar proteins. Heterotrimeric serine/threonine protein phosphatase 2A (PP2A) consists of scaffolding (A), catalytic (C), and variable (B, B', and B"") subunits. The variable subunits dictate subcellular localization and substrate specificity of the PP2A holoenzyme. These B-family regulatory subunits play various roles including regulation of cytoskeletal assembly, neuronal differentiation, mitogen-activated protein kinase signaling, and apoptosis. This subfamily includes protein phosphatase 2A regulatory subunit B'' subunits alpha and beta, encoded by PPP2R3A and PPP2R3B. It also includes subunit delta encoded by PPP2R3D in mouse. They contain two-domain elongated structures with two calcium EF-hands which mediate Ca2+-dependent changes in phosphatase activity." 274 matched cddid_all.tbl CDD cd21505 cd21505 410338 PPP2R3C "serine/threonine protein phosphatase 2A regulatory subunit B"" subunit gamma. Heterotrimeric serine/threonine protein phosphatase 2A (PP2A) consists of scaffolding (A), catalytic (C), and variable (B, B', and B"") subunits. The variable subunits dictate subcellular localization and substrate specificity of the PP2A holoenzyme. This subfamily includes protein phosphatase subunit G5PR (also known as serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit gamma, G4-1, G5pr, GDRM, SPGF36, or C14orf10) that is encoded by the PPP2R3C gene. It is involved in the control of the dynamic organization of the cortical cytoskeleton and plays an important role in the organization of interphase microtubule arrays in part through the regulation of nucleation geometry. G5PR is involved in the ontogeny of multiple organs, especially critical for testis development and spermatogenesis. PPP2R3C gene variants cause syndromic 46,XY gonadal dysgenesis and impaired spermatogenesis in humans, and thus is emerging as a potential therapeutic target for male infertility." 382 matched cddid_all.tbl CDD cd21506 cd21506 410339 PPP2R3A "serine/threonine protein phosphatase 2A regulatory subunit B"" subunit alpha. Heterotrimeric serine/threonine protein phosphatase 2A (PP2A) consists of scaffolding (A), catalytic (C), and variable (B, B', and B"") subunits. The variable subunits dictate subcellular localization and substrate specificity of the PP2A holoenzyme. This group contains protein phosphatase subunit PR130 (also known as protein phosphatase 2A regulatory subunit B'' subunit alpha, PR72, or PPP2R3) that is encoded by the PPP2R3A gene. PR130 and PR72 subunits are derived from the same gene through differential splicing; they harbor specific N-terminal domains of different lengths that are encoded by alternatively spliced exons and have identical C-termini. The common C-terminus contains a two-domain elongated structure with two calcium EF-hands which mediate Ca2+-dependent changes in phosphatase activity. The PR130 subunit has been shown to interact with the LIM domain of lipoma-preferred partner (LPP) through a conserved Zn2+-finger-like motif in the N-terminus of PR130." 284 matched cddid_all.tbl CDD cd21507 cd21507 410340 PPP2R3B "serine/threonine protein phosphatase 2A regulatory subunit B"" subunit beta. Heterotrimeric serine/threonine protein phosphatase 2A (PP2A) consists of scaffolding (A), catalytic (C), and variable (B, B', and B"") subunits. The variable subunits dictate subcellular localization and substrate specificity of the PP2A holoenzyme. This group contains protein phosphatase subunit PR70 (also known as protein phosphatase 2 regulatory subunit B'' subunit beta, PR48, NYREN8, PPP2R3L, or PPP2R3LY) that is encoded by the PPP2R3B gene. This substrate-recognizing subunit of PP2A has a two-domain elongated structure with two calcium EF-hands, each displaying different affinities to Ca2+. PPP2R3B/PR70 is a gonosomal melanoma tumor suppressor gene; PR70 decreased melanoma growth by negatively interfering with DNA replication and cell cycle progression through its role in stabilizing the cell division cycle 6 (CDC6)-chromatin licensing and DNA replication factor 1 (CDT1) interaction, which delays the firing of origins of DNA replication." 355 matched cddid_all.tbl CDD cd21508 cd21508 394835 HEV_Spike_S1_RBD receptor-binding domain of the S1 subunit of the Spike (S) protein from porcine hemagglutinating encephalomyelitis virus. This group contains the receptor-binding domain (RBD) of the S1 subunit of the spike (S) protein from porcine hemagglutinating encephalomyelitis virus (HEV), which is associated with acute outbreaks of wasting and encephalitis in nursing piglets from pig farms. Porcine HEV is related to the zoonotic SARS and MERS betacoronaviruses, which have high fatality rates and pandemic potential. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs use the C-domain to bind their receptors. The protein receptor for porcine HEV has not yet been identified. Due to the key role of the S protein RBD in viral attachment, it is the major target for antibody-mediated neutralization. This model corresponds to the S1 subunit C-domain that serves as the RBD for most CoVs. 298 matched cddid_all.tbl CDD cd21510 cd21510 411072 agarase_cat alpha-beta barrel catalytic domain of agarase, such as GH86-like endo-acting agarases identified in non-marine organisms. Typically, agarases (E.C. 3.2.1.81) are found in ocean-dwelling bacteria since agarose is a principle component of red algae cell wall polysaccharides. Agarose is a linear polymer of alternating D-galactose and 3,6-anhydro-L-galactopyranose. Endo-acting agarases, such as glycoside hydrolase 16 (GH16) and GH86 hydrolyze internal beta-1,4 linkages. GH86-like endo-acting agarase of this protein family has been identified in the human intestinal bacterium Bacteroides uniformis. This acquired metabolic pathway, as demonstrated by the prevalence of agar-specific genetic cluster called polysaccharide utilization loci (PULs), varies considerably between human populations, being much more prevalent in a Japanese sample than in North America, European, or Chinese samples. Agarase activity was also identified in the non-marine bacterium Cellvibrio sp. 321 matched cddid_all.tbl CDD cd21511 cd21511 439197 alpha_betaCoV_Nsp2 alpha- and betacoronavirus non-structural protein 2. Coronavirus Nsps are encoded in ORF1a and ORF1b. Post infection, the genomic RNA is released into the cytoplasm of the cell and translated into two long polyproteins (pp), pp1a and pp1ab, which are then autoproteolytically cleaved by two viral proteases Nsp3 and Nsp5 into smaller subunits. Nsp2 is one of these subunits. This alpha- and betacoronavirus family includes alphacoronavirus human coronavirus 229E (HCoV-229E) Nsp2, betacoronavirus Severe acute respiratory syndrome coronavirus (SARS-CoV) Nsp2, SARS-CoV-2 Nsp2, and Murine hepatitis virus (MHV) Nsp2 (also known as p65). The function of Nsp2 remains unclear. SARS-CoV Nsp2, rather than playing a role in viral replication, may be involved in altering the host cell environment; deletion of Nsp2 from the SARS-CoV genome results in only a modest reduction in viral titers. It has been shown to interact with two host proteins, prohibitin 1 (PHB1) and PHB2, which have been implicated in cellular functions, including cell-cycle progression, cell migration, cellular differentiation, apoptosis, and mitochondrial biogenesis. MHV Nsp2/p65, different from SARS-CoV Nsp2, may play an important role in the viral life cycle. This family may be distantly related to the gammacoronavirus Avian infectious bronchitis virus (IBV) Nsp2; IBV Nsp2 is a weak protein kinase R (PKR) antagonist, which may suggest that it plays a role in interfering with intracellular immunity. 399 matched cddid_all.tbl CDD cd21512 cd21512 394837 cv_gamma-delta_Nsp2_IBV-like gamma- and deltacoronavirus non-structural protein 2 (Nsp2), similar to IBV Nsp2 and related proteins. Coronavirus non-structural proteins (Nsps) are encoded in ORF1a and ORF1b. Post infection, the genomic RNA is released into the cytoplasm of the cell and translated into two long polyproteins (pp), pp1a and pp1ab, which are then autoproteolytically cleaved by two viral proteases Nsp3 and Nsp5 into smaller subunits. Nsp2 is one of these cleaved subunits. The functions of Nsp2 remain unclear. This gamma- and deltacoronavirus family includes Avian infectious bronchitis virus (IBV) Nsp2 which has been shown to be a weak protein kinase R (PKR) antagonist, which may suggest that it plays a role in interfering with intracellular immunity. This family may be distantly related to a family of alpha- and betacoronavirus Nsp2, which includes severe acute respiratory syndrome coronavirus (SARS-CoV) Nsp2, and Murine hepatitis virus (MHV) Nsp2 (also known as p65). SARS-CoV Nsp2, rather than playing a role in viral replication, may be involved in altering the host cell environment; deletion of Nsp2 from the SARS-CoV genome results in only a modest reduction in viral titers. It has been shown to interact with two host proteins, prohibitin 1 (PHB1) and PHB2, which have been implicated in cellular functions, including cell-cycle progression, cell migration, cellular differentiation, apoptosis, and mitochondrial biogenesis. MHV Nsp2/p65, different from SARS-CoV Nsp2, may play an important role in the viral life cycle. 365 matched cddid_all.tbl CDD cd21513 cd21513 394838 SUD_C_DPUP_CoV_Nsp3 C-terminal SARS-Unique Domain (SUD) of betacoronavirus non-structural protein 3 (Nsp3). This family contains the SUD-C of Nsp3 from Severe Acute Respiratory Syndrome (SARS) coronavirus (CoV), Middle East respiratory syndrome-related (MERS) CoV, and Rousettus bat CoV HKU9, as well as the DPUP (domain preceding Ubl2 and PLP2) of murine hepatitis virus (MHV) Nsp3. Though structurally similar, there is little sequence similarity between these four domain subfamilies: SARS SUD-C, MERS SUD-C, HKU9 SUD-C, and MHV DPUP. Non-structural protein 3 (Nsp3) is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. Nsp3 of SARS coronavirus includes a SARS-unique domain (SUD) consisting of three globular domains separated by short linker peptide segments: SUD-N, SUD-M, and SUD-C. SUD-N and SUD-M are macro domains which bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). The SUD-C domain adopts a frataxin-like fold and has structural similarity to DNA-binding domains of DNA-modifying enzymes. It binds to single-stranded RNA and recognizes purine bases more strongly than pyrimidine bases. SUD-C also regulates the RNA binding behavior of the SUD-M macrodomain. SUD-C is not as specific to SARS CoV Nsp3 as originally thought, and is conserved in the Nsp3s of all four lineages (A-D) of betacoronavirus. 71 matched cddid_all.tbl CDD cd21514 cd21514 394865 alphaCoV_Nsp2_HCoV-229E-like alphacoronavirus non-structural protein 2 (Nsp2), similar to HCoV-229E Nsp2 and related proteins. Coronavirus non-structural proteins (Nsps) are encoded in ORF1a and ORF1b. Post infection, the genomic RNA is released into the cytoplasm of the cell and translated into two long polyproteins (pp), pp1a and pp1ab, which are then autoproteolytically cleaved by two viral proteases Nsp3 and Nsp5 into smaller subunits. Nsp2 is one of these subunits. This subgroup includes alphacoronavirus human coronavirus 229E (HCoV-229E) Nsp2 and belongs to a family which includes betacoronavirus Severe acute respiratory syndrome coronavirus (SARS-CoV) Nsp2, SARS-CoV-2 Nsp2, and Murine hepatitis virus (MHV) Nsp2 (also known as p65). The function of Nsp2 remains unclear. SARS-CoV Nsp2, rather than playing a role in viral replication, may be involved in altering the host cell environment; deletion of Nsp2 from the SARS-CoV genome results in only a modest reduction in viral titers. It has been shown to interact with two host proteins, prohibitin 1 (PHB1) and PHB2, which have been implicated in cellular functions, including cell-cycle progression, cell migration, cellular differentiation, apoptosis, and mitochondrial biogenesis. MHV Nsp2/p65, different from SARS-CoV Nsp2, may play an important role in the viral life cycle. 503 matched cddid_all.tbl CDD cd21515 cd21515 439198 betaCoV_Nsp2_SARS_MHV-like betacoronavirus non-structural protein 2 (Nsp2), similar to SARS-CoV Nsp2 and MHV Nsp2 (p65), and related proteins. Coronavirus non-structural proteins (Nsps) are encoded in ORF1a and ORF1b. Post infection, the genomic RNA is released into the cytoplasm of the cell and translated into two long polyproteins (pp), pp1a and pp1ab, which are then autoproteolytically cleaved by two viral proteases Nsp3 and Nsp5 into smaller subunits. Nsp2 is one of these subunits. This family includes Severe acute respiratory syndrome coronavirus (SARS-CoV) Nsp2, SARS-CoV-2 Nsp2, and Murine hepatitis virus (MHV) Nsp2 (also known as p65). The function of Nsp2 remains unclear. SARS-CoV Nsp2 rather than playing a role in viral replication, may be involved in altering the host cell environment; deletion of Nsp2 from the SARS-CoV genome results in only a modest reduction in viral titers. It has been shown to interact with two host proteins, prohibitin 1 (PHB1) and PHB2 which have been implicated in cellular functions, including cell-cycle progression, cell migration, cellular differentiation, apoptosis, and mitochondrial biogenesis. MHV Nsp2/p65, different from SARS-CoV Nsp2, may play an important role in the viral life cycle. 562 matched cddid_all.tbl CDD cd21516 cd21516 439199 betaCoV_Nsp2_SARS-like betacoronavirus non-structural protein 2 (Nsp2) similar to SARS-CoV Nsp2, and related proteins from betacoronaviruses in the B lineage. Non-structural proteins (Nsps) from Severe acute respiratory syndrome coronavirus (SARS-CoV) and betacoronaviruses in the sarbecovirus subgenus (B lineage) are encoded in ORF1a and ORF1b. Post infection, the SARS-CoV genomic RNA is released into the cytoplasm of the cell and translated into two long polyproteins (pp), pp1a and pp1ab, which are then autoproteolytically cleaved by two viral proteases Nsp3 and Nsp5 into smaller subunits. Nsp2 is one of these subunits. The function of Nsp2 remains unknown. Deletion of Nsp2 from the SARS-CoV genome results in only a modest reduction in viral titers. Rather than playing a role in viral replication, SARS-CoV Nsp2 may be involved in altering the host cell environment; it has been shown to interact with two host proteins, prohibitin 1 (PHB1) and PHB2 which have been implicated in cellular functions, including cell-cycle progression, cell migration, cellular differentiation, apoptosis, and mitochondrial biogenesis. 637 matched cddid_all.tbl CDD cd21517 cd21517 394868 betaCoV_Nsp2_MERS-like betacoronavirus non-structural protein 2 (Nsp2) similar to MERS-CoV Nsp2, and related proteins from betacoronaviruses in the C lineage. Coronavirus non-structural proteins (Nsps) are encoded in ORF1a and ORF1b. Post infection, the genomic RNA is released into the cytoplasm of the cell and translated into two long polyproteins (pp), pp1a and pp1ab, which are then autoproteolytically cleaved by two viral proteases Nsp3 and Nsp5 into smaller subunits. Nsp2 is one of these subunits. This subgroup includes Nsp2 from Middle East respiratory syndrome-related coronavirus (MERS-CoV) and betacoronaviruses in the merbecovirus subgenus (C lineage). It belongs to a family which includes Severe acute respiratory syndrome coronavirus (SARS-CoV) Nsp2, and Murine hepatitis virus (MHV) Nsp2 (also known as p65). The function of Nsp2 remains unclear. SARS-CoV Nsp2, rather than playing a role in viral replication, may be involved in altering the host cell environment; deletion of Nsp2 from the SARS-CoV genome results in only a modest reduction in viral titers. It has been shown to interact with two host proteins, prohibitin 1 (PHB1) and PHB2, which have been implicated in cellular functions, including cell-cycle progression, cell migration, cellular differentiation, apoptosis, and mitochondrial biogenesis. MHV Nsp2/p65, different from SARS-CoV Nsp2, may play an important role in the viral life cycle. 660 matched cddid_all.tbl CDD cd21518 cd21518 394869 betaCoV_Nsp2_HKU9-like betacoronavirus non-structural protein 2 (Nsp2) similar to bat coronavirus HKU9 Nsp2, and related proteins from betacoronaviruses in the D lineage. Coronavirus non-structural proteins (Nsps) are encoded in ORF1a and ORF1b. Post infection, the genomic RNA is released into the cytoplasm of the cell and translated into two long polyproteins (pp), pp1a and pp1ab, which are then autoproteolytically cleaved by two viral proteases Nsp3 and Nsp5 into smaller subunits. Nsp2 is one of these subunits. This subgroup includes Nsp2 from Rousettus bat coronavirus HKU9 and betacoronaviruses in the nobecovirus subgenus (D lineage). It belongs to a family which includes Severe acute respiratory syndrome coronavirus (SARS-CoV) Nsp2, and Murine hepatitis virus (MHV) Nsp2 (also known as p65). The function of Nsp2 remains unclear. SARS-CoV Nsp2, rather than playing a role in viral replication, may be involved in altering the host cell environment; deletion of Nsp2 from the SARS-CoV genome results in only a modest reduction in viral titers. It has been shown to interact with two host proteins, prohibitin 1 (PHB1) and PHB2, which have been implicated in cellular functions, including cell-cycle progression, cell migration, cellular differentiation, apoptosis, and mitochondrial biogenesis. MHV Nsp2/p65, different from SARS-CoV Nsp2, may play an important role in the viral life cycle. 597 matched cddid_all.tbl CDD cd21519 cd21519 394870 betaCoV_Nsp2_MHV-like betacoronavirus non-structural protein 2 (Nsp2) similar to MHV Nsp2/p65 and related proteins from betacoronaviruses in the A lineage. Coronavirus non-structural proteins (Nsps) are encoded in ORF1a and ORF1b. Post infection, the genomic RNA is released into the cytoplasm of the cell and translated into two long polyproteins (pp), pp1a and pp1ab, which are then autoproteolytically cleaved by two viral proteases Nsp3 and Nsp5 into smaller subunits. Nsp2 is one of these subunits. This subgroup includes Nsp2 from Murine hepatitis virus (MHV) and betacoronaviruses in the embecovirus subgenus (A lineage). It belongs to a family which includes Severe acute respiratory syndrome coronavirus (SARS-CoV) Nsp2. The function of Nsp2 remains unclear. SARS-CoV Nsp2, rather than playing a role in viral replication, may be involved in altering the host cell environment; deletion of Nsp2 from the SARS-CoV genome results in only a modest reduction in viral titers, and it has been shown to interact with two host proteins, prohibitin 1 (PHB1) and PHB2 which have been implicated in cellular functions, including cell-cycle progression, cell migration, cellular differentiation, apoptosis, and mitochondrial biogenesis. MHV Nsp2, also known as p65, different from SARS-CoV Nsp2, may play an important role in the viral life cycle. 586 matched cddid_all.tbl CDD cd21520 cd21520 439200 SPOC_SF SPOC (Spen paralog and ortholog C-terminal) domain superfamily. The SPOC domain is involved in developmental signalling and has also been proposed to be a phosphorylation binding module. It has been found mainly in two protein families: transcription factor S-II (TFIIS) and Spen (split end). The TFIIS family includes SPOC domain-containing protein 1 (SPOCD1), yeast bypass of ESS1 protein 1 (Bye1p), PHD finger protein 3 (PHF3), and death-inducer obliterator (Dido) splicing variants, among others. They are characterized by having both a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal SPOC domain. The Spen protein family includes SMART/HDAC1-associated repressor protein (SHARP) and RNA binding motif protein 15 (RBM15)-like proteins from metazoans, as well as plant flowering time control protein FPA and yeast chromo domain-containing protein 1 (Chp1p). They are characterized by containing RNA recognition motifs (RRMs) and a SPOC domain. 138 matched cddid_all.tbl CDD cd21521 cd21521 439215 VEFS-box VEFS (VRN2-EMF2-FIS2-Su(z)12) box family. This family corresponds to a group of polycomb cluster proteins which control HOX gene transcription, as they function in heterochromatin-mediated repression. They are characterized by containing a VEFS-box in the C-terminal region, which is an acidic cluster and a tryptophan/methionine-rich sequence, the acidic-W/M domain. Some of these sequences are associated with a zinc-finger domain about 100 residues towards the N-terminus. Members include suppressor of zeste 12 protein (SUZ12) from vertebrates, plants, insects and fungi, as well as Polycomb group protein EMBRYONIC FLOWER 2 (EMF2), Polycomb group protein FERTILIZATION-INDEPENDENT SEED 2 (FIS2), and Polycomb group protein VERNALIZATION 2 (VRN2) from plants. 121 matched cddid_all.tbl CDD cd21523 cd21523 394839 SUD_C_MERS-CoV_Nsp3 C-terminal SARS-Unique Domain (SUD) of non-structural protein 3 (Nsp3) from Middle East respiratory syndrome-related coronavirus and related betacoronaviruses in the C lineage. This subfamily contains the SUD-C of Middle East respiratory syndrome-related (MERS) coronavirus (CoV) Nsp3 and other Nsp3s from betacoronaviruses in the merbecovirus subgenera (C lineage), including several bat-CoVs such as Tylonycteris bat CoV HKU4, Pipistrellus bat CoV HKU5, and Hypsugo bat CoV HKU25. Non-structural protein 3 (Nsp3) is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. Nsp3 of SARS coronavirus includes a SARS-unique domain (SUD) consisting of three globular domains separated by short linker peptide segments: SUD-N, SUD-M, and SUD-C. SUD-N and SUD-M are macro domains which bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). SUD is not as specific to SARS CoV as originally thought and is also found in MERS and related bat coronaviruses. Similar to SARS SUD-C, Tylonycteris bat-CoV HKU4 SUD-C (HKU4 C), a member of the MERS SUD-C group, also adopts a frataxin-like fold (DOI:10.1177/1934578X19849202) that has structural similarity to DNA-binding domains of DNA-modifying enzymes. However, there is little sequence similarity between the two domains. SARS SUD-C has been shown to bind to single-stranded RNA and recognize purine bases more strongly than pyrimidine bases; it also regulates the RNA binding behavior of the SARS SUD-M macrodomain. It is not known whether MERS SUD-C or HKU4 C functions in the same way. It has been suggested that HKU4 C engages in protein-protein interactions with HKU4 SUD-M. 76 matched cddid_all.tbl CDD cd21524 cd21524 394840 DPUP_MHV_Nsp3 DPUP (domain preceding Ubl2 and PLP2) of non-structural protein 3 (Nsp3) from murine hepatitis virus and related betacoronaviruses in the A lineage. This subfamily contains the DPUP (domain preceding Ubl2 and PLP2) of murine hepatitis virus (MHV) non-structural protein 3 (Nsp3) and other Nsp3s from betacoronaviruses in the embecovirus subgenera (A lineage), including human CoV OC43, rabbit CoV HKU14 and porcine hemagglutinating encephalomyelitis virus (HEV), among others. Non-structural protein 3 (Nsp3) is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. MHV Nsp3 contains a DPUP that is located N-terminal to the ubiquitin-like domain 2 (Ubl2) and papain-like protease 2 (PLP2) catalytic domain. It is structurally similar to the Severe Acute Respiratory Syndrome (SARS) CoV unique domain C (SUD-C), adopting a frataxin-like fold that has structural similarity to DNA-binding domains of DNA-modifying enzymes. SUD-C is also located N-terminal to Ubl2 and PLP2 in SARS Nsp3, similar to the DPUP of MHV Nsp3; however, unlike DPUP, it is preceded by SUD-N and SUD-M macrodomains that are absent in MHV Nsp3. Though structurally similar, there is little sequence similarity between DPUP and SUD-C. SARS SUD-C has been shown to bind to single-stranded RNA and recognize purine bases more strongly than pyrimidine bases; it also regulates the RNA binding behavior of the SARS SUD-M macrodomain. It is not known whether DPUP functions in the same way. 75 matched cddid_all.tbl CDD cd21525 cd21525 394841 SUD_C_SARS-CoV_Nsp3 C-terminal SARS-Unique Domain (SUD) of non-structural protein 3 (Nsp3) from Severe Acute Respiratory Syndrome coronavirus and related betacoronaviruses in the B lineage. This subfamily contains the SUD-C of Severe Acute Respiratory Syndrome (SARS) coronavirus (CoV) non-structural protein 3 (Nsp3) and other Nsp3s from betacoronaviruses in the sarbecovirus subgenera (B lineage), such as SARS-CoV-2 and related bat CoVs. Non-structural protein 3 (Nsp3) is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. Nsp3 of the Severe Acute Respiratory Syndrome (SARS) coronavirus includes a SARS-unique domain (SUD) consisting of three globular domains separated by short linker peptide segments: SUD-N, SUD-M, and SUD-C. SUD-N and SUD-M are macro domains which bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). The SUD-C domain adopts a frataxin-like fold and has structural similarity to DNA-binding domains of DNA-modifying enzymes. It binds to single-stranded RNA and recognizes purine bases more strongly than pyrimidine bases. SUD-C also regulates the RNA binding behavior of the SUD-M macrodomain. 67 matched cddid_all.tbl CDD cd21526 cd21526 394843 CoV_Nsp6 coronavirus non-structural protein 6. Coronaviruses (CoV) redirect and rearrange host cell membranes as part of the viral genome replication and transcription machinery; they induce the formation of double-membrane vesicles in infected cells. CoV non-structural protein 6 (Nsp6), a transmembrane-containing protein, together with Nsp3 and Nsp4, have the ability to induce double-membrane vesicles that are similar to those observed in severe acute respiratory syndrome (SARS) coronavirus-infected cells. By itself, Nsp6 can generate autophagosomes from the endoplasmic reticulum. Autophagosomes are normally generated as a cellular response to starvation to carry cellular organelles and long-lived proteins to lysosomes for degradation. Degradation through autophagy may provide an innate defense against virus infection, or conversely, autophagosomes can promote infection by facilitating the assembly of replicase proteins. In addition to initiating autophagosome formation, Nsp6 also limits autophagosome expansion regardless of how they were induced, i.e. whether they were induced directly by Nsp6, or indirectly by starvation or chemical inhibition of MTOR signaling. This may favor coronavirus infection by compromising the ability of autophagosomes to deliver viral components to lysosomes for degradation. 287 matched cddid_all.tbl CDD cd21527 cd21527 394949 CoV_Spike_S1_NTD N-terminal domain of the S1 subunit of coronavirus Spike (S) proteins. This family contains the N-terminal domain (NTD) of the S1 subunit of coronavirus (CoV) Spike (S) proteins from all four (A-D) lineages of betacoronaviruses, including three highly pathogenic human CoVs (HCoV) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2, also known as a 2019 novel coronavirus (2019-nCoV) or COVID-19 virus. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). Most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV, use the C-domain to bind their receptors. However, some CoVs from the A lineage, such as mouse hepatitis virus (MHV) uses the NTD to bind its receptor, mouse carcinoembryonic antigen related cell adhesion molecule 1a (mCEACAM1a). Bovine CoV and HCoV-OC43, also from the A lineage, recognize a sugar moiety, 5-N-acetyl-9-O-acetylneuraminic acid (Neu5,9Ac2), on cell-surface glycoproteins or glycolipids; this binding is also through the S1 NTD. The S1 NTD has also been the target for neutralizing antibodies, including human antibody CDC2-A2, and murine antibodies G2 and 5F9, which target MERS-CoV NTD. In addition, the S1 NTD contributes to the Spike trimer interface. 268 matched cddid_all.tbl CDD cd21528 cd21528 394955 CoV_Nsp14 nonstructural protein 14 of coronavirus. Nonstructural protein 14 (Nsp14) of coronavirus (CoV) plays an important role in viral replication and transcription. It consists of 2 domains with different enzymatic activities: an N-terminal exoribonuclease (ExoN) domain and a C-terminal cap (guanine-N7) methyltransferase (N7-MTase) domain. ExoN is important for proofreading and therefore, the prevention of lethal mutations. The association of Nsp14 with Nsp10 stimulates its ExoN activity; the complex hydrolyzes double-stranded RNA in a 3' to 5' direction as well as a single mismatched nucleotide at the 3'-end mimicking an erroneous replication product. The Nsp10/Nsp14 complex may function in a replicative mismatch repair mechanism. N7-MTase functions in mRNA capping. Nsp14 can methylate GTP, dGTP as well as cap analogs GpppG, GpppA and m7GpppG. The accumulation of m7GTP or Nsp14 has been found to interfere with protein translation of cellular mRNAs. 518 matched cddid_all.tbl CDD cd21529 cd21529 394849 CoV_M coronavirus Membrane (or Matrix) protein. This family contains the Membrane (M) protein of coronaviruses (CoVs) including three highly pathogenic human CoVs such as Middle East respiratory syndrome (MERS)-related CoV, severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2, also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the Orf1ab (a large polyprotein known as replicase/protease); all are required to produce a structurally complete viral particle. The M protein, a triple-spanning membrane protein, is the most abundant protein in the virion. It plays a central role in virion assembly and morphogenesis, and it defines the shape of the viral envelope. It is regarded as the central organizer of CoV assembly, interacting with all other major coronaviral structural proteins and turning cellular membranes into workshops where virus and host factors come together to make new virus particles. While homotypic interactions between the M proteins are the major driving force behind virion envelope formation, it needs to interact with other coronaviral structural proteins for complete virion formation. The interaction of the Spike protein with M is not required for the assembly process. However, binding of M to N protein stabilizes the nucleocapsid (N protein-RNA complex), as well as the internal core of virions, and thereby promotes completion of viral assembly. Thus, the M protein, and its interactions with other structural proteins, is necessary for the production and release of virus-like particles. 198 matched cddid_all.tbl CDD cd21530 cd21530 438015 CoV_RdRp coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome. This family contains the RNA-dependent RNA polymerase of alpha-, beta-, gamma-, delta-coronaviruses, including three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2, also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which shows potential for the treatment of SARS-CoV-2 viral infections. The structure of SARS-CoV-2 Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 928 matched cddid_all.tbl CDD cd21531 cd21531 394858 CoV_E Coronavirus Envelope (E) small membrane protein. This family contains the Envelope (E) small membrane protein of betacoronaviruses, including the E proteins from three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS) CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2, also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the Orf1ab (a large polyprotein known as replicase/protease); all are required to produce a structurally complete viral particle. The E protein is a small polypeptide (76-109 amino acids) that contains a single alpha-helical transmembrane domain. It plays a central role in virus morphogenesis and assembly. It acts as a viroporin and self-assembles in host membranes forming homopentameric protein-lipid pores that allow ion transport with poor selectivity. For some CoVs, such as mouse hepatitis virus (MHV) and SARS-CoV, deletion of the E gene did not completely abolish replication, but the virions were severely disabled from infecting new host cells with significantly reduced viral titers. In animal models, SARS-CoV lacking the E gene also showed significantly attenuated viral titers, likely due to its deficiency in suppressing host stress response and apoptosis induction. Moreover, the PDZ-binding motif (PBM) at the C-terminus of SARS-CoV E protein was shown to interact with a host PDZ protein called syntenin and lead to its relocation from nucleus to cytoplasm during SARS-CoV infection, thereby activating p38 kinase to induce the overexpression of inflammatory cytokines. Thus, the E protein is involved in both, viral replication and pathogenesis during CoV infection. 58 matched cddid_all.tbl CDD cd21532 cd21532 394859 HKU1-CoV-like_E human coronavirus HKU1 Envelope small membrane protein and similar proteins. This group contains the Envelope (E) small membrane protein of human coronavirus HKU1 and related coronaviruses (CoVs) from rodents. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the Orf1ab (a large polyprotein known as replicase/protease); all are required to produce a structurally complete viral particle. The E protein is a small polypeptide (76-109 amino acids) that contains a single alpha-helical transmembrane domain. It plays a central role in virus morphogenesis and assembly. It acts as a viroporin and self-assembles in host membranes forming homopentameric protein-lipid pores that allow ion transport with poor selectivity. For some CoVs, such as mouse hepatitis virus (MHV) and SARS-CoV, deletion of the E gene did not completely abolish replication, but the virions were severely disabled from infecting new host cells with significantly reduced viral titers. In animal models, SARS-CoV lacking the E gene also showed significantly attenuated viral titers, likely due to its deficiency in suppressing host stress response and apoptosis induction. Moreover, the PDZ-binding motif (PBM) at the C-terminus of SARS-CoV E protein was shown to interact with a host PDZ protein called syntenin and lead to its relocation from nucleus to cytoplasm during SARS-CoV infection, thereby activating p38 kinase to induce the overexpression of inflammatory cytokines. Thus, the E protein is involved in both, viral replication and pathogenesis during CoV infection. 74 matched cddid_all.tbl CDD cd21533 cd21533 394860 MERS-CoV-like_E Middle East respiratory syndrome-related coronavirus Envelope small membrane protein and similar proteins. This group contains the Envelope (E) small membrane protein of Middle East respiratory syndrome (MERS) coronavirus (CoV), as well as E proteins from related coronaviruses. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the Orf1ab (a large polyprotein known as replicase/protease); all are required to produce a structurally complete viral particle. The E protein is a small polypeptide (76-109 amino acids) that contains a single alpha-helical transmembrane domain. It plays a central role in virus morphogenesis and assembly. It acts as a viroporin and self-assembles in host membranes forming homopentameric protein-lipid pores that allow ion transport with poor selectivity. For some CoVs, such as mouse hepatitis virus (MHV) and SARS-CoV, deletion of the E gene did not completely abolish replication, but the virions were severely disabled from infecting new host cells with significantly reduced viral titers. In animal models, SARS-CoV lacking the E gene also showed significantly attenuated viral titers, likely due to its deficiency in suppressing host stress response and apoptosis induction. Moreover, the PDZ-binding motif (PBM) at the C-terminus of SARS-CoV E protein was shown to interact with a host PDZ protein called syntenin and lead to its relocation from nucleus to cytoplasm during SARS-CoV infection, thereby activating p38 kinase to induce the overexpression of inflammatory cytokines. Thus, the E protein is involved in both, viral replication and pathogenesis during CoV infection. 80 matched cddid_all.tbl CDD cd21534 cd21534 394861 SARS-CoV-like_E Severe acute respiratory syndrome coronavirus Envelope small membrane protein and similar proteins. This group contains the Envelope (E) small membrane protein of Severe acute respiratory syndrome (SARS) coronavirus (CoV) and SARS-CoV-2, also known as 2019 novel coronavirus (2019-nCoV) or COVID-19 virus, as well as E proteins from related CoVs. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the Orf1ab (a large polyprotein known as replicase/protease); all are required to produce a structurally complete viral particle. The E protein is a small polypeptide (76-109 amino acids) that contains a single alpha-helical transmembrane domain. It plays a central role in virus morphogenesis and assembly. It acts as a viroporin and self-assembles in host membranes forming homopentameric protein-lipid pores that allow ion transport with poor selectivity. For some CoVs, such as mouse hepatitis virus (MHV) and SARS-CoV, deletion of the E gene did not completely abolish replication, but the virions were severely disabled from infecting new host cells with significantly reduced viral titers. In animal models, SARS-CoV lacking the E gene also showed significantly attenuated viral titers, likely due to its deficiency in suppressing host stress response and apoptosis induction. Moreover, the PDZ-binding motif (PBM) at the C-terminus of SARS-CoV E protein was shown to interact with a host PDZ protein called syntenin and lead to its relocation from nucleus to cytoplasm during SARS-CoV infection, thereby activating p38 kinase to induce the overexpression of inflammatory cytokines. Thus, the E protein is involved in both, viral replication and pathogenesis during CoV infection. 62 matched cddid_all.tbl CDD cd21536 cd21536 394862 SARS-CoV-2_E Severe acute respiratory syndrome coronavirus 2 Envelope small membrane protein. This group contains the Envelope (E) small membrane protein of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known as 2019 novel coronavirus (2019-nCoV) or COVID-19 virus. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the Orf1ab (a large polyprotein known as replicase/protease); all are required to produce a structurally complete viral particle. The E protein is a small polypeptide (76-109 amino acids) that contains a single alpha-helical transmembrane domain. It plays a central role in virus morphogenesis and assembly. It acts as a viroporin and self-assembles in host membranes forming homopentameric protein-lipid pores that allow ion transport with poor selectivity. For some CoVs, such as mouse hepatitis virus (MHV) and SARS-CoV, deletion of the E gene did not completely abolish replication, but the virions were severely disabled from infecting new host cells with significantly reduced viral titers. In animal models, SARS-CoV lacking the E gene also showed significantly attenuated viral titers, likely due to its deficiency in suppressing host stress response and apoptosis induction. Moreover, the PDZ-binding motif (PBM) at the C-terminus of SARS-CoV E protein was shown to interact with a host PDZ protein called syntenin and lead to its relocation from nucleus to cytoplasm during SARS-CoV infection, thereby activating p38 kinase to induce the overexpression of inflammatory cytokines. Thus, the E protein is involved in both, viral replication and pathogenesis during CoV infection. 75 matched cddid_all.tbl CDD cd21537 cd21537 394842 SUD_C_HKU9_CoV_Nsp3 C-terminal SARS-Unique Domain (SUD) of non-structural protein 3 (Nsp3) from Rousettus bat coronavirus HKU9 and related betacoronaviruses in the D lineage. This subfamily contains the SUD-C of Rousettus bat coronavirus (CoV) HKU9 non-structural protein 3 (Nsp3) and other Nsp3s from betacoronaviruses in the nobecovirus subgenera (D lineage). Non-structural protein 3 (Nsp3) is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. Nsp3 of SARS coronavirus includes a SARS-unique domain (SUD) consisting of three globular domains separated by short linker peptide segments: SUD-N, SUD-M, and SUD-C. SUD-N and SUD-M are macro domains which bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). SUD is not as specific to SARS CoV as originally thought and is also found in Rousettus bat CoV HKU9 and related bat CoVs. Similar to SARS SUD-C, Rousettus bat CoV HKU9 SUD-C (HKU9 C), also adopts a frataxin-like fold that has structural similarity to DNA-binding domains of DNA-modifying enzymes. However, there is little sequence similarity between the two domains. SARS SUD-C has been shown to bind to single-stranded RNA and recognize purine bases more strongly than pyrimidine bases; it also regulates the RNA binding behavior of the SARS SUD-M macrodomain. It is not known whether HKU9 C functions in the same way. 73 matched cddid_all.tbl CDD cd21538 cd21538 439201 SPOC_TFIIS SPOC (Spen paralog and ortholog C-terminal) domain found in the transcription factor S-II (TFIIS) family. The transcription factor S-II (TFIIS) family includes SPOC domain-containing protein 1 (SPOCD1), yeast bypass of ESS1 protein 1 (Bye1p), PHD finger protein 3 (PHF3), and death-inducer obliterator (Dido) splicing variants, among others. They are characterized by having both a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling. SPOCD1 acts as a tumor-related factor that promotes cell proliferation and metastasis. Yeast Bye1p is a nuclear transcription factor with a domain resembling the central domain in transcription elongation factor TFIIS and plays an inhibitory role during transcription elongation. It functions as a multicopy suppressor of Ess1, a peptidyl-prolyl cis-trans isomerase involved in proline isomerization of the C-terminal domain (CTD) of RNA polymerase II (Pol II). PHF3 is a human homolog of the yeast protein Bye1p. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. The Dido/DIDO1 gene is implicated in several cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module. 146 matched cddid_all.tbl CDD cd21539 cd21539 439202 SPOC_Spen SPOC (Spen paralog and ortholog C-terminal) domain found in the Spen (split end) protein family. The Spen protein family includes a group of proteins characterized by containing RNA recognition motifs (RRMs) and a SPOC domain, such as SMART/HDAC1-associated repressor protein (SHARP) and RNA binding motif protein 15 (RBM15)-like proteins from metazoans, as well as plant flowering time control protein FPA and yeast chromo domain-containing protein 1 (Chp1p). SHARP, also called Msx2-interacting protein (MINT), or Spen homolog, is an estrogen-inducible transcriptional repressor that interacts directly with the nuclear receptor corepressor SMRT, histone deacetylases (HDACs), and components of the NuRD complex. RBM15, also called one-twenty two protein 1 (OTT1), is a novel mRNA export factor and component of the NXF1 pathway. RNA-binding protein 15B (RBM15B), also called one-twenty two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. Chp1p is a component of the kinetochore which plays a role in stabilizing microtubules and thus, allowing accurate chromosome segregation. It has a role in the RNA interference (RNAi) pathway which is important for heterochromatin formation and accurate chromosome segregation. FPA plays a role in the regulation of flowering time in the autonomous flowering pathway by decreasing FLOWERING LOCUS C mRNA levels. It is required for RNA-mediated chromatin silencing of a range of loci in the genome. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module. 148 matched cddid_all.tbl CDD cd21540 cd21540 439203 SPOC_SPOCD1 SPOC (Spen paralog and ortholog C-terminal) domain found in SPOC domain-containing protein 1 (SPOCD1) and similar proteins. SPOCD1 is a protein belonging to the transcription factor S-II (TFIIS) family of transcription factors. It acts as a tumor-related factor that promotes cell proliferation and metastasis. SPOCD1 was initially found to interact with testis protein phosphatase 1, which is a major eukaryotic serine/threonine-specific phosphatase that regulates cellular signaling. The model corresponds to the SPOC domain of SPOCD1; the SPOC domain is involved in developmental signaling and has also been proposed to be a phosphorylation binding module. 138 matched cddid_all.tbl CDD cd21541 cd21541 439204 SPOC_PHF3-like SPOC (Spen paralog and ortholog C-terminal) domain found in PHD finger protein 3 (PHF3), death-inducer obliterator (Dido) variants, and similar proteins. PHF3 is a human homolog of yeast protein bypass of Ess1 (Bye1), a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. This group also includes the protein products of the Dido gene that encodes three alternative splicing variants (Dido1, 2, and 3), which have been implicated in several cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. The Dido gene is a bone morphogenetic protein (BMP) target gene and promotes BMP-induced melanoma progression. Dido1 is important for maintaining embryonic stem (ES) cells and directly regulates the expression of pluripotency factors. It is the shortest isoform that contains only a highly conserved PHD finger responsible for the binding of histone H3 with a higher affinity for trimethylated lysine4 (H3K4me3). It also triggers apoptosis after nuclear translocation and caspase upregulation. Dido3 is the largest isoform and is ubiquitously expressed in all human tissues. It is dispensable for ES cell self-renewal and pluripotency, but is involved in the maintenance of stem cell genomic stability and tumorigenesis. This model corresponds to the SPOC domain of the PHF3-like group; the SPOC domain is involved in developmental signaling and has also been proposed to be a phosphorylation binding module. 141 matched cddid_all.tbl CDD cd21542 cd21542 439205 SPOC_Bye1p-like SPOC (Spen paralog and ortholog C-terminal) domain found in Saccharomyces cerevisiae bypass of ESS1 protein 1 (Bye1p) and similar proteins. Yeast Bye1p is a nuclear transcription factor with a domain resembling the central domain in the transcription elongation factor TFIIS. It plays an inhibitory role during transcription elongation. It functions as a multicopy suppressor of Ess1, a peptidyl-prolyl cis-trans isomerase involved in proline isomerization of the C-terminal domain (CTD) of RNA polymerase II (Pol II). Bye1p contains an N-terminal plant homeodomain (PHD) finger, a central Pol II-binding TFIIS-like domain (TLD) domain, and a C-terminal SPOC domain. This model corresponds to the SPOC domain which is involved in developmental signaling and has also been proposed to be a phosphorylation binding module. 153 matched cddid_all.tbl CDD cd21543 cd21543 439206 SPOC_SHARP SPOC (Spen paralog and ortholog C-terminal) domain found in SMART/HDAC1-associated repressor protein (SHARP) and similar proteins. SHARP, also called Msx2-interacting protein (MINT), or Spen homolog, is an estrogen-inducible transcriptional repressor that interacts directly with transcriptional corepressors silencing mediator for retinoid and thyroid receptor (SMRT)/nuclear receptor corepressor (NCoR), histone deacetylases (HDACs), and components of the NuRD complex. SHARP recruits HDAC activity and binds to the steroid receptor RNA coactivator SRA through four conserved N-terminal RNA recognition motifs (RRMs), also called RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), further suppressing SRA-potentiated steroid receptor transcription activity. Thus, SHARP has the capacity to modulate both liganded and nonliganded nuclear receptors. SHARP also has been identified as a component of transcriptional repression complexes in Notch/RBP-Jkappa signaling pathways. In addition to the N-terminal RRMs, SHARP possesses a C-terminal SPOC domain that binds to SMRT/NcoR. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module. 163 matched cddid_all.tbl CDD cd21544 cd21544 439207 SPOC_RBM15-like SPOC (Spen paralog and ortholog C-terminal) domain found in RNA binding motif protein 15 (RBM15) and similar proteins. This subfamily includes RBM15, RBM15B, and similar proteins found in metazoans. RBM15, also called one-twenty two protein 1 (OTT1), is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as a receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RNA-binding protein 15B (RBM15B), also called one-twenty two 3 (OTT3), is a paralog of RBM15 and therefore has post-transcriptional regulatory activity. It is a nuclear protein that shares with RBM15, the association with the splicing factor compartment and the nuclear envelope, as well as the binding to mRNA export factors NXF1 and Aly/REF. Members of this family have a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module. 164 matched cddid_all.tbl CDD cd21545 cd21545 439208 SPOC_Chp1p SPOC (Spen paralog and ortholog C-terminal) domain found in Schizosaccharomyces pombe chromo domain-containing protein 1 (Chp1p) and similar proteins. Chp1p is a component of the kinetochore that plays a role in stabilizing microtubules and thus, allowing accurate chromosome segregation. It has a role in the RNA interference (RNAi) pathway which is important for heterochromatin formation and accurate chromosome segregation. Chp1p is also a member of the RNA-induced transcriptional silencing (RITS) complex, which is involved in the biosynthesis of dsRNA from primer siRNAs provided by the RNA-directed RNA polymerase (RDRC) complex. The C-terminal portion of Chp1p contains three domains: SPOC, II, and PIN domains. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module. 133 matched cddid_all.tbl CDD cd21546 cd21546 439209 SPOC_FPA-like SPOC (Spen paralog and ortholog C-terminal) domain found in Arabidopsis thaliana flowering time control protein FPA and similar proteins. FPA plays a role in the regulation of flowering time in the autonomous flowering pathway by decreasing FLOWERING LOCUS C mRNA levels. It is required for RNA-mediated chromatin silencing of a range of loci in the genome. FPA cotranscriptionally recognizes aberrant RNA and marks it for silencing. It controls alternative cleavage and polyadenylation on pre-mRNAs and antisense RNAs. FPA functions redundantly with FCA to prevent the expression of distally polyadenylated antisense RNAs at the FLC locus. FPA belongs to the Spen (split end) protein family, whose members contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module. 125 matched cddid_all.tbl CDD cd21547 cd21547 439210 SPOC_DIDO1-like SPOC (Spen paralog and ortholog C-terminal) domain found in some death-inducer obliterator variants. The Dido/DIDO1 gene has been implicated in several cellular processes such as apoptosis and chromosomal segregation, particularly in the hematopoietic system. It encodes alternative splicing variants, including Dido1, 2, and 3, with Dido3 being the longest isoform and Dido1 being the shortest. Dido3 is ubiquitously expressed in all human tissues, is dispensable for embryonic stem (ES) cell self-renewal and pluripotency, but is involved in the maintenance of stem cell genomic stability and tumorigenesis. Dido3 contains a PHD finger, a transcription elongation factor S-II subunit M (TFSIIM) domain, a SPOC module, and a long C-terminal region (CT) of unknown homology. Dido2 and Dido1 are truncated at the C-terminus relative to Dido3, with Dido2 containing a partial SPOC domain whereas Dido1 is missing it completely. Dido1, also called DIO-1, or death-associated transcription factor 1 (DATF-1), is important for maintaining ES cells and directly regulates the expression of pluripotency factors. The conserved plant homeodomain (PHD) finger is responsible for the binding of histone H3 with a higher affinity for trimethylated lysine 4 (H3K4me3). The Dido/DIDO1 gene is a bone morphogenetic protein (BMP) target gene, which promotes BMP-induced melanoma progression. It also triggers apoptosis after nuclear translocation and caspase upregulation. This model corresponds to the SPOC domain which is involved in developmental signaling and has also been proposed to be a phosphorylation binding module. 143 matched cddid_all.tbl CDD cd21548 cd21548 439211 SPOC_PHF3 SPOC (Spen paralog and ortholog C-terminal) domain found in PHD finger protein 3 (PHF3). PHF3 is a human homolog of yeast protein bypass of Ess1 (Bye1), a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. It is ubiquitously expressed in normal tissues including brain, but its expression is significantly reduced or lost in glioblastomas. PHF3 contains an N-terminal plant homeodomain (PHD) finger, a central RNA polymerase II (Pol II)-binding TFIIS-like domain (TLD) domain, and a C-terminal SPOC domain. This model corresponds to the SPOC domain which is involved in developmental signaling and has also been proposed to be a phosphorylation binding module. 141 matched cddid_all.tbl CDD cd21549 cd21549 439212 SPOC_RBM15 SPOC (Spen paralog and ortholog C-terminal) domain found in vertebrate RNA binding motif protein 15 (RBM15). RBM15, also called one-twenty two protein 1 (OTT1), conserved in eukaryotes, is a novel mRNA export factor and component of the NXF1 pathway. It binds to NXF1 and serves as receptor for the RNA export element RTE. It also possesses mRNA export activity and can facilitate the access of DEAD-box protein DBP5 to mRNA at the nuclear pore complex (NPC). RBM15 belongs to the Spen (split end) protein family, which contain three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain. The model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module. 164 matched cddid_all.tbl CDD cd21550 cd21550 439213 SPOC_RBM15B SPOC (Spen paralog and ortholog C-terminal) domain found in putative RNA binding motif protein 15B (RBM15B). RBM15B, also called one-twenty two 3 (OTT3), is a paralog of RNA binding motif protein 15 (RBM15), which is also known as one-twenty two protein 1 (OTT1). Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein that shares with RBM15, the association with the splicing factor compartment and the nuclear envelope, as well as the binding to mRNA export factors NXF1 and Aly/REF. RBM15B belongs to the Spen (split end) protein family, which contains a domain architecture comprising of three N-terminal RNA recognition motifs (RRMs), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module. 167 matched cddid_all.tbl CDD cd21551 cd21551 439216 VEFS-box_SUZ12 VEFS (VRN2-EMF2-FIS2-Su(z)12) box found in suppressor of zeste 12 protein (SUZ12) and similar proteins. SUZ12, also called chromatin precipitated E2F target 9 protein (ChET 9 protein), or joined to JAZF1 protein, is a Polycomb group (PcG) protein that acts as a component of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. The PRC2/EED-EZH2 complex may also serve as a recruiting platform for DNA methyltransferases, thereby linking two epigenetic repression systems. This model corresponds to the VEFS (VRN2-EMF2-FIS2-Su(z)12) box at the C-terminus of SUZ12, which is responsible for binding to EED and EZH2. 122 matched cddid_all.tbl CDD cd21552 cd21552 439217 VEFS-box_ctSUZ12-like VEFS (VRN2-EMF2-FIS2-Su(z)12) box found in Chaetomium thermophilum suppressor of zeste 12 protein (ctSUZ12) and similar proteins. SUZ12 is a Polycomb group (PcG) protein that acts as a component of the Polycomb Repressive Complex 2 (PRC2), a histone methyltransferase complex composed of core subunits EZH2 (or EZH1), EED, SUZ12 and Rbbp4. PRC2 trimethylates histone H3K27 (H3K27me3) to mark developmentally repressed chromatin. This model corresponds to the VEFS (VRN2-EMF2-FIS2-Su(z)12) box at the C-terminus of SUZ12, which is responsible for binding to EED and EZH2 (or EZH1). 123 matched cddid_all.tbl CDD cd21553 cd21553 439218 VEFS-box_EMF2-like VEFS (VRN2-EMF2-FIS2-Su(z)12) box found in Arabidopsis thaliana Polycomb group protein EMBRYONIC FLOWER 2 (EMF2) and similar proteins. This subfamily includes a group of proteins similar to Arabidopsis thaliana Polycomb group (PcG) proteins, EMF2, Polycomb group protein FERTILIZATION-INDEPENDENT SEED 2 (FIS2), and Polycomb group protein VERNALIZATION 2 (VRN2). EMF2 is involved in flowering processes by repressing unknown target genes and preventing reproductive development. It participates in PcG protein complex-mediated (probably in complex with EMF1) silencing of the flower homeotic genes AGAMOUS (AG), PISTILLATA (PI), and APETALA3 (AP3), as well as of some regulatory genes such as ABSCISIC ACID INSENSITIVE3 (ABI3), LONG VEGETATIVE PHASE1 (LOV1), and FLOWERING LOCUS C (FLC) during vegetative development, by mediating trimethylation of histone 3 lysine 27 on the AG chromatin (H3K27me3). FIS2 is required to prevent the proliferation of the central cell by repressing unknown target genes before fertilization. It regulates the anteroposterior organization of the endosperm. VRN2 plays a central role in vernalization by maintaining repressed the homeotic gene FLC, a floral repressor, after cold treatment. PcG proteins act by forming multiprotein complexes, which are required to maintain the transcriptionally repressive state of homeotic genes throughout development. Members of this family contain a VEFS (VRN2-EMF2-FIS2-Su(z)12) box. 128 matched cddid_all.tbl CDD cd21554 cd21554 439219 CoV_N-NTD N-terminal domain of nucleocapsid (N) protein of coronavirus. The coronavirus nucleocapsid (N) protein is a major structural and multifunctional protein. It plays an important role in the virus replication cycle, by forming a complex with the viral RNA through its N-terminal domain (N-NTD), which makes this domain an important drug target. It also interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly. 123 matched cddid_all.tbl CDD cd21555 cd21555 411073 OmcS-like C-type cytochrome OmcS and similar proteins. This family includes C-type outer membrane cytochrome S (OmcS) which plays an important role in extracellular electron transfer. OmcS can transfer electrons to insoluble Fe(3+) oxides as well as other extracellular electron acceptors, including Mn(4+) oxide and humic substances. Recent studies show that Geobacter sulfurreducens hexaheme cytochrome OmcS proteins can assemble into filaments, known as microbial nanowires, similar to type IV pili composed of PilA protein. The coordination of a histidine in one subunit with the iron in the heme of an adjacent subunit is an important stabilizing element. The capacity of these bacteria to transport electrons to remote electron acceptors via these protein nanowires is of interest because of the environmental and practical significance of these microbes in soil. 382 matched cddid_all.tbl CDD cd21556 cd21556 438956 Macro_cv_SUD-N-M_Nsp3-like SUD-N and SUD-M macrodomains of the SARS-Unique Domain (SUD) of SARS-CoV non-structural protein 3 and related macrodomains. This family includes two macrodomains referred to as the SUD-N (N-terminal subdomain) and SUD-M (middle SUD subdomain) of the SARS-unique domain (SUD) which bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). It is found in non-structural protein 3 (Nsp3) of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and highly related coronaviruses. SUD consists of three globular domains separated by short linker peptide segments: SUD-N, SUD-M, and SUD-C. Among these, SUD-N and SUD-M are macrodomains. SUD-N (also called Mac2) is specific to the Nsp3 of SARS and betacoronaviruses of the sarbecovirus subgenera (B lineage), while SUD-M (also called Mac3) is present in most Nsp3 proteins except the Nsp3 from betacoronaviruses of the embecovirus subgenera (A lineage). SUD-C adopts a frataxin-like fold, has structural similarity to DNA-binding domains of DNA-modifying enzymes, binds single-stranded RNA, and regulates the RNA binding behavior of the SUD-M macrodomain. SARS-CoV Nsp3 contains a third macrodomain (the X-domain or Mac1) which is not included in this family. The X-domain may function as a module binding poly(ADP-ribose); however, SUD-N and SUD-M do not bind ADP-ribose, as the triple glycine sequence involved in its binding is not conserved in these. 108 matched cddid_all.tbl CDD cd21557 cd21557 438957 Macro_X_Nsp3-like "X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains. The X-domain, also called Mac1, is the macrodomain found in riboviral non-structural protein 3 (Nsp3), including the Nsp3 of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) as well as SARS-CoV-2, and other coronaviruses (alpha-, beta-, gamma-, and deltacoronavirus), among others. The SARS-CoV-2 Nsp3 Mac1 is highly conserved among all CoVs, and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. It appears to counter host-mediated antiviral ADP-ribosylation, a post-translational modification that is part of the host response to viral infections. Mac1 is essential for pathogenesis in multiple animal models of CoV infection, implicating it as a virulence factor and potential therapeutic target. Assays show that the de-MARylating activity leads to a rapid loss of substrate, and that Mac1 could not hydrolyze poly-ADP-ribose; thus, Mac1 is a MAR-hydrolase (mono-ADP ribosylhydrolase). Mac1 was originally named ADP-ribose-1""-phosphatase (ADRP) based on data demonstrating that it could remove the phosphate group from ADP-ribose-1""-phosphate; however, activity was modest and was unclear why this would impact a virus infection. This family also includes the X-domain of Avian infectious bronchitis virus (IBV) strain Beaudette coronavirus that does not bind ADP-ribose; the triple glycine sequence found in the X-domains of SARS-CoV and human coronavirus 229E (HCoV229E), which are involved in ADP-ribose binding, is not conserved in the IBV X-domain. SARS-CoVs have two other macrodomains referred to as the SUD-N (N-terminal subdomain, or Mac2) and SUD-M (middle SUD subdomain, or Mac3) of the SARS-unique domain (SUD), which also do not bind ADP-ribose; these bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). SARS-CoV SUD-N and SUD-M are not included in this group." 127 matched cddid_all.tbl CDD cd21558 cd21558 394844 alphaCoV-Nsp6 alphacoronavirus non-structural protein 6. Coronaviruses (CoV) redirect and rearrange host cell membranes as part of the viral genome replication and transcription machinery; they induce the formation of double-membrane vesicles in infected cells. CoV non-structural protein 6 (Nsp6), a transmembrane-containing protein, together with Nsp3 and Nsp4, have the ability to induce double-membrane vesicles that are similar to those observed in severe acute respiratory syndrome (SARS) coronavirus-infected cells. By itself, Nsp6 can generate autophagosomes from the endoplasmic reticulum. Autophagosomes are normally generated as a cellular response to starvation to carry cellular organelles and long-lived proteins to lysosomes for degradation. Degradation through autophagy may provide an innate defense against virus infection, or conversely, autophagosomes can promote infection by facilitating the assembly of replicase proteins. In addition to initiating autophagosome formation, Nsp6 also limits autophagosome expansion regardless of how they were induced, i.e. whether they were induced directly by Nsp6, or indirectly by starvation or chemical inhibition of MTOR signaling. This may favor coronavirus infection by compromising the ability of autophagosomes to deliver viral components to lysosomes for degradation. 293 matched cddid_all.tbl CDD cd21559 cd21559 394845 gammaCoV-Nsp6 gammacoronavirus non-structural protein 6. Coronaviruses (CoV) redirect and rearrange host cell membranes as part of the viral genome replication and transcription machinery; they induce the formation of double-membrane vesicles in infected cells. CoV non-structural protein 6 (Nsp6), a transmembrane-containing protein, together with Nsp3 and Nsp4, have the ability to induce double-membrane vesicles that are similar to those observed in severe acute respiratory syndrome (SARS) coronavirus-infected cells. By itself, Nsp6 can generate autophagosomes from the endoplasmic reticulum. Autophagosomes are normally generated as a cellular response to starvation to carry cellular organelles and long-lived proteins to lysosomes for degradation. Degradation through autophagy may provide an innate defense against virus infection, or conversely, autophagosomes can promote infection by facilitating the assembly of replicase proteins. In addition to initiating autophagosome formation, Nsp6 also limits autophagosome expansion regardless of how they were induced, i.e. whether they were induced directly by Nsp6, or indirectly by starvation or chemical inhibition of MTOR signaling. This may favor coronavirus infection by compromising the ability of autophagosomes to deliver viral components to lysosomes for degradation. 307 matched cddid_all.tbl CDD cd21560 cd21560 394846 betaCoV-Nsp6 betacoronavirus non-structural protein 6. Coronaviruses (CoV) redirect and rearrange host cell membranes as part of the viral genome replication and transcription machinery; they induce the formation of double-membrane vesicles in infected cells. CoV non-structural protein 6 (Nsp6), a transmembrane-containing protein, together with Nsp3 and Nsp4, have the ability to induce double-membrane vesicles that are similar to those observed in severe acute respiratory syndrome (SARS) coronavirus-infected cells. By itself, Nsp6 can generate autophagosomes from the endoplasmic reticulum. Autophagosomes are normally generated as a cellular response to starvation to carry cellular organelles and long-lived proteins to lysosomes for degradation. Degradation through autophagy may provide an innate defense against virus infection, or conversely, autophagosomes can promote infection by facilitating the assembly of replicase proteins. In addition to initiating autophagosome formation, Nsp6 also limits autophagosome expansion regardless of how they were induced, i.e. whether they were induced directly by Nsp6, or indirectly by starvation or chemical inhibition of MTOR signaling. This may favor coronavirus infection by compromising the ability of autophagosomes to deliver viral components to lysosomes for degradation. 290 matched cddid_all.tbl CDD cd21561 cd21561 394847 deltaCoV-Nsp6 deltacoronavirus non-structural protein 6. Coronaviruses (CoV) redirect and rearrange host cell membranes as part of the viral genome replication and transcription machinery; they induce the formation of double-membrane vesicles in infected cells. CoV non-structural protein 6 (Nsp6), a transmembrane-containing protein, together with Nsp3 and Nsp4, have the ability to induce double-membrane vesicles that are similar to those observed in severe acute respiratory syndrome (SARS) coronavirus-infected cells. By itself, Nsp6 can generate autophagosomes from the endoplasmic reticulum. Autophagosomes are normally generated as a cellular response to starvation to carry cellular organelles and long-lived proteins to lysosomes for degradation. Degradation through autophagy may provide an innate defense against virus infection, or conversely, autophagosomes can promote infection by facilitating the assembly of replicase proteins. In addition to initiating autophagosome formation, Nsp6 also limits autophagosome expansion regardless of how they were induced, i.e. whether they were induced directly by Nsp6, or indirectly by starvation or chemical inhibition of MTOR signaling. This may favor coronavirus infection by compromising the ability of autophagosomes to deliver viral components to lysosomes for degradation. 296 matched cddid_all.tbl CDD cd21562 cd21562 394883 Macro_cv_SUD-N_Nsp3-like SUD-N macrodomain (or Mac2 domain) of the SARS Unique Domain (SUD) of SARS-CoV non-structural protein 3 and related macrodomains. This subfamily includes the macrodomain referred to as SUD-N (N-terminal subdomain) of the SARS-unique domain (SUD) which binds G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). It is found in the non-structural protein 3 (Nsp3) of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and highly related coronaviruses. SUD consists of three globular domains separated by short linker peptide segments: SUD-N, SUD-M, and SUD-C. Among these, SUD-N and SUD-M are macrodomains: the SUD-M domain (not represented in this subfamily) is a related macrodomain which also binds G-quadruplexes. SUD-N (also called Mac2) is specific to the Nsp3 of SARS and betacoronaviruses of the sarbecovirus subgenera (B lineage), while SUD-M (also called Mac3) is present in most Nsp3 proteins except the Nsp3 from betacoronaviruses of the embecovirus subgenera (A lineage). SUD-C adopts a frataxin-like fold, has structural similarity to DNA-binding domains of DNA-modifying enzymes, binds single-stranded RNA, and regulates the RNA binding behavior of the SUD-M macrodomain. SARS-CoV Nsp3 contains a third macrodomain (the X-domain or Mac1) which is also not represented in this subfamily. The X-domain may function as a module binding poly(ADP-ribose); however, SUD-N and SUD-M do not bind ADP-ribose, as the triple glycine sequence involved in its binding is not conserved in these. 126 matched cddid_all.tbl CDD cd21563 cd21563 394884 Macro_cv_SUD-M_Nsp3-like SUD-M macrodomain (or Mac3 domain) of the SARS Unique Domain (SUD) of SARS-CoV non-structural protein 3 and related macrodomains. This subfamily includes the macrodomain referred to as SUD-M (middle SUD subdomain) of the SARS-unique domain (SUD) which binds G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). It is found in non-structural protein 3 (Nsp3) of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and related coronaviruses. SUD consists of three globular domains separated by short linker peptide segments: SUD-N, SUD-M, and SUD-C. Among these, SUD-N and SUD-M are macrodomains: The SUD-N domain (not represented in this subfamily) is a related macrodomain which also binds G-quadruplexes. While SUD-N (also called Mac2) is specific to the Nsp3 of SARS and betacoronaviruses of the sarbecovirus subgenera (B lineage), SUD-M (also called Mac3) is present in most Nsp3 proteins except the Nsp3 from betacoronaviruses of the embecovirus subgenera (A lineage). SUD-M, despite its name, is not specific to SARS. SUD-C adopts a frataxin-like fold, has structural similarity to DNA-binding domains of DNA-modifying enzymes, binds single-stranded RNA, and regulates the RNA binding behavior of the SUD-M macrodomain. SARS-CoV Nsp3 contains a third macrodomain (the X-domain or Mac1) which is also not represented in this subfamily. The X-domain may function as a module binding poly(ADP-ribose); however, SUD-N and SUD-M do not bind ADP-ribose, as the triple glycine sequence involved in its binding is not conserved in these. 120 matched cddid_all.tbl CDD cd21564 cd21564 394850 alphaCoV_M alphacoronavirus Membrane (or Matrix) protein. This subfamily contains the Membrane (M) protein of alphacoronaviruses including human coronaviruses (HCoVs), HCoV-229E and HCoV-NL63. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the Orf1ab (a large polyprotein known as replicase/protease); all are required to produce a structurally complete viral particle. The M protein, a triple-spanning membrane protein, is the most abundant protein in the virion. It plays a central role in virion assembly and morphogenesis, and it defines the shape of the viral envelope. It is regarded as the central organizer of CoV assembly, interacting with all other major coronaviral structural proteins and turning cellular membranes into workshops where virus and host factors come together to make new virus particles. While homotypic interactions between the M proteins are the major driving force behind virion envelope formation, it needs to interact with other coronaviral structural proteins for complete virion formation. The interaction of the Spike protein with M is not required for the assembly process. However, binding of M to N protein stabilizes the nucleocapsid (N protein-RNA complex), as well as the internal core of virions, and thereby promotes completion of viral assembly. Thus, the M protein, and its interactions with other structural proteins, is necessary for the production and release of virus-like particles. 218 matched cddid_all.tbl CDD cd21565 cd21565 394851 betaCoV_M betacoronavirus Membrane (or Matrix) protein. This subfamily contains the Membrane (M) protein of betacoronaviruses including the M proteins from three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS)-related CoV, severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2, also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the Orf1ab (a large polyprotein known as replicase/protease); all are required to produce a structurally complete viral particle. The M protein, a triple-spanning membrane protein, is the most abundant protein in the virion. It plays a central role in virion assembly and morphogenesis, and it defines the shape of the viral envelope. It is regarded as the central organizer of CoV assembly, interacting with all other major coronaviral structural proteins and turning cellular membranes into workshops where virus and host factors come together to make new virus particles. While homotypic interactions between the M proteins are the major driving force behind virion envelope formation, it needs to interact with other coronaviral structural proteins for complete virion formation. The interaction of the Spike protein with M is not required for the assembly process. However, binding of M to N protein stabilizes the nucleocapsid (N protein-RNA complex), as well as the internal core of virions, and thereby promotes completion of viral assembly. Thus, the M protein, and its interactions with other structural proteins, is necessary for the production and release of virus-like particles. 208 matched cddid_all.tbl CDD cd21566 cd21566 394852 gammaCoV_M gammacoronavirus Membrane (or Matrix) protein. This subfamily contains the Membrane (M) protein of gammacoronavirus including avian infectious bronchitis virus (IBV). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the Orf1ab (a large polyprotein known as replicase/protease); all are required to produce a structurally complete viral particle. The M protein, a triple-spanning membrane protein, is the most abundant protein in the virion. It plays a central role in virion assembly and morphogenesis, and it defines the shape of the viral envelope. It is regarded as the central organizer of CoV assembly, interacting with all other major coronaviral structural proteins and turning cellular membranes into workshops where virus and host factors come together to make new virus particles. While homotypic interactions between the M proteins are the major driving force behind virion envelope formation, it needs to interact with other coronaviral structural proteins for complete virion formation. The interaction of the Spike protein with M is not required for the assembly process. However, binding of M to N protein stabilizes the nucleocapsid (N protein-RNA complex), as well as the internal core of virions, and thereby promotes completion of viral assembly. Thus, the M protein, and its interactions with other structural proteins, is necessary for the production and release of virus-like particles. 212 matched cddid_all.tbl CDD cd21567 cd21567 394853 MERS-like-CoV_M Membrane (or Matrix) protein from Middle East respiratory syndrome-related coronavirus and related betacoronaviruses in the C lineage. This group contains the Membrane (M) protein of Middle East respiratory syndrome (MERS)-related CoV, bat-CoV HKU5, and similar proteins from betacoronaviruses in the merbecovirus subgenera (C lineage). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the Orf1ab (a large polyprotein known as replicase/protease); all are required to produce a structurally complete viral particle. The M protein, a triple-spanning membrane protein, is the most abundant protein in the virion. It plays a central role in virion assembly and morphogenesis, and it defines the shape of the viral envelope. It is regarded as the central organizer of CoV assembly, interacting with all other major coronaviral structural proteins and turning cellular membranes into workshops where virus and host factors come together to make new virus particles. While homotypic interactions between the M proteins are the major driving force behind virion envelope formation, it needs to interact with other coronaviral structural proteins for complete virion formation. The interaction of the Spike protein with M is not required for the assembly process. However, binding of M to N protein stabilizes the nucleocapsid (N protein-RNA complex), as well as the internal core of virions, and thereby promotes completion of viral assembly. Thus, the M protein, and its interactions with other structural proteins, is necessary for the production and release of virus-like particles. 216 matched cddid_all.tbl CDD cd21568 cd21568 394854 HCoV-like_M Membrane (or Matrix) protein from human coronavirus and related betacoronaviruses in the A lineage. This group contains the Membrane (M) protein of human coronaviruses (HCoVs), HCoV-OC43 and HCoV-HKU1, and similar proteins from betacoronaviruses in the embecovirus subgenera (A lineage). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the Orf1ab (a large polyprotein known as replicase/protease); all are required to produce a structurally complete viral particle. The M protein, a triple-spanning membrane protein, is the most abundant protein in the virion. It plays a central role in virion assembly and morphogenesis, and it defines the shape of the viral envelope. It is regarded as the central organizer of CoV assembly, interacting with all other major coronaviral structural proteins and turning cellular membranes into workshops where virus and host factors come together to make new virus particles. While homotypic interactions between the M proteins are the major driving force behind virion envelope formation, it needs to interact with other coronaviral structural proteins for complete virion formation. The interaction of the Spike protein with M is not required for the assembly process. However, binding of M to N protein stabilizes the nucleocapsid (N protein-RNA complex), as well as the internal core of virions, and thereby promotes completion of viral assembly. Thus, the M protein, and its interactions with other structural proteins, is necessary for the production and release of virus-like particles. 220 matched cddid_all.tbl CDD cd21569 cd21569 394855 SARS-like-CoV_M Membrane (or Matrix) protein from Severe acute respiratory syndrome (SARS) coronavirus, SARS-CoV-2, and related betacoronaviruses in the B lineage. This group contains the Membrane (M) protein of Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2 (also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus), and related proteins from betacoronaviruses in the sarbecovirus subgenera (B lineage). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the Orf1ab (a large polyprotein known as replicase/protease); all are required to produce a structurally complete viral particle. The M protein, a triple-spanning membrane protein, is the most abundant protein in the virion. It plays a central role in virion assembly and morphogenesis, and it defines the shape of the viral envelope. It is regarded as the central organizer of CoV assembly, interacting with all other major coronaviral structural proteins and turning cellular membranes into workshops where virus and host factors come together to make new virus particles. While homotypic interactions between the M proteins are the major driving force behind virion envelope formation, it needs to interact with other coronaviral structural proteins for complete virion formation. The interaction of the Spike protein with M is not required for the assembly process. However, binding of M to N protein stabilizes the nucleocapsid (N protein-RNA complex), as well as the internal core of virions, and thereby promotes completion of viral assembly. Thus, the M protein, and its interactions with other structural proteins, is necessary for the production and release of virus-like particles. 218 matched cddid_all.tbl CDD cd21570 cd21570 394856 batCoV_HKU9-like_M Membrane (or Matrix) protein from bat coronavirus HKU9 and related betacoronaviruses in the D lineage. This group contains the Membrane (M) protein of Rousettus bat coronavirus HKU9, and similar proteins from betacoronaviruses in the nobecovirus subgenera (D lineage). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the Orf1ab (a large polyprotein known as replicase/protease); all are required to produce a structurally complete viral particle. The M protein, a triple-spanning membrane protein, is the most abundant protein in the virion. It plays a central role in virion assembly and morphogenesis, and it defines the shape of the viral envelope. It is regarded as the central organizer of CoV assembly, interacting with all other major coronaviral structural proteins and turning cellular membranes into workshops where virus and host factors come together to make new virus particles. While homotypic interactions between the M proteins are the major driving force behind virion envelope formation, it needs to interact with other coronaviral structural proteins for complete virion formation. The interaction of the Spike protein with M is not required for the assembly process. However, binding of M to N protein stabilizes the nucleocapsid (N protein-RNA complex), as well as the internal core of virions, and thereby promotes completion of viral assembly. Thus, the M protein, and its interactions with other structural proteins, is necessary for the production and release of virus-like particles. 217 matched cddid_all.tbl CDD cd21571 cd21571 409236 KLF13_N N-terminal domain of Kruppel-like factor 13. Kruppel-like factor 13 (KLF13; also known as Krueppel-like factor 13, RANTES factor of late activated T lymphocytes 1/RFLAT-1, or Fetal Kruppel-like factor-2/FKLF-2), is a protein that in humans is encoded by the KLF13 gene. It was originally cloned from fetal globin-expressing tissues, though it has also been cloned from bone marrow, striated muscles, and a subset of T cells where it is highly expressed. KLF13 plays a role in heart development and morphogenesis and is thought to play a role in obesity. It regulates the expression of the chemokine RANTES in T lymphocytes and has been shown to interact with CREB-binding protein, heat shock protein 47, and PCAF. KLF9, KLF10, KLF11, KLF13, KLF14, and KLF16 share a conserved alpha-helical motif AA/VXXL that mediates their binding to Sin3A and their activities as transcriptional repressors. KLF13 belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF13. 136 matched cddid_all.tbl CDD cd21572 cd21572 409241 KLF10_N N-terminal domain of Kruppel-like factor 10. Kruppel-like factor 10 (KLF10; also known as Krueppel-like factor 10; early growth response(EGR)-alpha/EGRA; TGFbeta inducible early gene-1/TIEG1) is a protein that in humans is encoded by the KLF10 gene. KLF10 was first identified in human osteoblasts and plays a role in mediating estrogen (E2) signaling in bone and skeletal homeostasis and a regulatory role in tumor formation and metastasis. It may also play a role in adipocyte differentiation and adipose tissue function. KLF9, KLF10, KLF11, KLF13, KLF14, and KLF16 share a conserved a-helical motif AA/VXXL that mediates their binding to Sin3A and their activities as transcriptional repressors. KLF10 belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF10. 245 matched cddid_all.tbl CDD cd21573 cd21573 409237 KLF16_N N-terminal domain of Kruppel-like factor 16. Kruppel-like factor 16 (KLF16; also known as Krueppel-like factor 16, Basic transcription element binding protein 4/BTEB4, or Novel Sp1-like zinc finger transcription factor/2NSLP2) is a protein that in humans is encoded by the KLF16 gene. KLF16 functions as a transcription activator. It is thought to modulate dopaminergic transmission in the brain and also regulates the expression of several genes essential for metabolic and endocrine processes in sex steroid-sensitive uterine cells. KLF16 selectively binds three distinct KLF-binding sites (GC, CA, and BTE boxes). KLF9, KLF10, KLF11, KLF13, KLF14, and KLF16 share a conserved alpha-helical motif AA/VXXL that mediates their binding to Sin3A and their activities as transcriptional repressors. KLF16 belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF16. 125 matched cddid_all.tbl CDD cd21574 cd21574 410567 KLF17_N N-terminal domain of Kruppel-like factor 17. Kruppel-like factor 17 (KLF17), or Krueppel-like factor 17, is a protein that, in humans, is encoded by the KLF17 gene and acts as a tumor suppressor. It negatively regulates epithelial-mesenchymal transition and metastasis in breast cancer. KLF17 is thought to be the human ortholog of the mouse gene, zinc finger protein 393 (Zfp393), although it has diverged significantly. KLF17 can regulate gene transcription from CACCC-box elements. It belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF17. 286 matched cddid_all.tbl CDD cd21575 cd21575 410566 KLF18_N N-terminal domain of Kruppel-like factor 18. Kruppel-like factor 18 (KLF18), or Krueppel-like factor 18, is a product of a chromosomal neighbor of the KLF17 gene and is likely a product of its duplication. Phylogenetic analyses revealed that mammalian predicted KLF18 proteins and KLF17 proteins experienced elevated rates of evolution and are grouped with KLF1/KLF2/KLF4 and non-mammalian KLF17. KLF18 has been found in the human testis, though it was previously hypothesized to be a pseudogene in extant placental mammals. Mouse KLF18 expression data indicates that it may function in early embryonic development. It belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF18. Some KLF18 isoforms have duplicated N-terminal domains. 276 matched cddid_all.tbl CDD cd21576 cd21576 409238 KLF14_N N-terminal domain of Kruppel-like factor 14. Kruppel-like factor 14 (KLF14; also known as Krueppel-like factor 14 or basic transcription element-binding protein 5/BTEB5) is a protein that in humans is encoded by the KLF14 gene. KLF14 regulates the transcription of various genes, including TGFbetaRII (the type II receptor for TGFbeta). KLF14 is expressed in many tissues, lacks introns, and is subject to parent-specific expression. It also appears to be a master regulator of gene expression in adipose tissue. KLF14 is associated with coronary artery disease, hypercholesterolemia, and type 2 diabetes. KLF9, KLF10, KLF11, KLF13, KLF14, and KLF16 share a conserved alpha-helical motif AA/VXXL that mediates their binding to Sin3A and their activities as transcriptional repressors. KLF14 belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF14. 195 matched cddid_all.tbl CDD cd21577 cd21577 410554 KLF3_N N-terminal domain of Kruppel-like factor 3. Kruppel-like factor 3 (KLF3; also called Krueppel-like factor 3 and originally called Basic Kruppel-like Factor/BKLF), was the third member of the KLF family of zinc finger transcription factors to be discovered. KLF3 possesses a wide range of biological impacts on regulating apoptosis, differentiation, and proliferation in various tissues during the entire progression process. It has been proposed as a tumor suppressor in colorectal cancer. It appears to function predominantly as a repressor of transcription, turning genes off by recruiting the C-terminal Binding Protein co-repressors CtBP1 and CtBP2. CtBP docks onto a short motif (residues 61-65) in the N-terminus of KLF3, through the Proline-X-Aspartate-Leucine-Serine (PXDLS) motif. CtBP in turn recruits histone modifying enzymes to alter chromatin and repress gene expression. KLF3 belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF3. 214 matched cddid_all.tbl CDD cd21578 cd21578 409239 KLF9_N N-terminal domain of Kruppel-like factor 9. Kruppel-like factor 9 (KLF9; also known as Krueppel-like factor 9, or Basic Transcription Element Binding Protein 1/BTEB Protein 1) is a protein that in humans is encoded by the KLF9 gene. KLF9 is critical for the inhibition of growth and development of tumors. It is involved in cell differentiation of B cells, keratinocytes, and neurons. It is also a key transcriptional regulator for uterine endometrial cell proliferation, adhesion, and differentiation; these are processes essential for pregnancy success and are subverted during tumorigenesis. KLF9, KLF10, KLF11, KLF13, KLF14, and KLF16 share a conserved alpha-helical motif AA/VXXL that mediates their binding to Sin3A and their activities as transcriptional repressors. KLF9 belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF9. 142 matched cddid_all.tbl CDD cd21579 cd21579 410335 KLF5_N N-terminal domain of Kruppel-like factor 5. Kruppel-like factor 5 (KLF5; also known as also known as Krueppel-like factor 5; intestinal enriched Kruppel-like factor/IKLF; basic transcription element binding protein 2/BTEB2) a protein that in humans is encoded by the KLF5 gene. KLF5 is involved in numerous functions in eukaryotic cells, such as proliferation, migration, and differentiation. The loss of KLF5 expression is associated with tumors of the breast, cervix, endometrium, ovary, and prostate. KLF5 mediates the expression of several genes essential for proper cardiac structure and function, and plays a role in familial dilated cardiomyopathy. It functions as a transcriptional activator. KLF5 exhibits both transcriptional activation activity as well as trans-activating function. It belongs to a family of proteins called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF5. 273 matched cddid_all.tbl CDD cd21580 cd21580 410206 KLF15_N N-terminal domain of Kruppel-like factor 15. Kruppel-like factor 15 (KLF15; also known as Krueppel-like factor 15 or kidney-enriched Kruppel-like factor/KKLF) is a protein that in humans is encoded by the KLF15 gene. KLF15 plays a role in gluconeogenesis, adipogenesis, and may be a potential therapeutic target to reduce hepatitis B virus gene expression and viral replication, heart failure and aortic aneurysm formation, and endometrial, breast cancer, and other diseases related to estrogen. It belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF15. 213 matched cddid_all.tbl CDD cd21581 cd21581 409227 KLF1_N N-terminal domain of Kruppel-like Factor 1. Kruppel-like Factor 1 (KLF1, also known as Krueppel-like factor 1 or Erythroid Kruppel-like Factor/EKLF) was the first Kruppel-like factor discovered. It was found to be vitally important for embryonic erythropoiesis in promoting the switch from fetal hemoglobin (Hemoglobin F) to adult hemoglobin (Hemoglobin A) gene expression by binding to highly conserved CACCC domains. EKLF ablation in mouse embryos produces a lethal anemic phenotype, causing death by embryonic day 14, and natural mutations lead to beta+ thalassemia in humans. However, expression of embryonic hemoglobin and fetal hemoglobin genes is normal in EKLF-deficient mice, suggesting other factors may be involved. KLF1 functions as a transcriptional activator. It belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specifity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF1, which is related to the N-terminal domains of KLF2 and KLF4. 278 matched cddid_all.tbl CDD cd21582 cd21582 409228 KLF4_N N-terminal domain of Kruppel-like factor 4. Kruppel-like factor 4 (KLF4; also known as Krueppel-like factor 4 or gut-enriched Kruppel-like factor/GKLF) is a protein that, in humans, is encoded by the KLF4 gene. Evidence also suggests that KLF4 is a tumor suppressor in certain cancers, including colorectal cancer, gastric cancer, esophageal squamous cell carcinoma, intestinal cancer, prostate cancer, bladder cancer and lung cancer. It may act as a tumor promoter where increased KLF4 expression has been reported, such as in oral squamous cell carcinoma and in primary breast ductal carcinoma. KLF4 is one of four key factors that are essential for inducing pluripotent stem cells. KLF4 is highly expressed in non-dividing cells and its overexpression induces cell cycle arrest. KLF proteins KLF1, KLF2, KLF4, KLF5, KLF6, and KLF7 are transcriptional activators. KLF4 belongs to a family of proteins called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF4, which is related to the N-terminal domains of KLF1 and KLF2. 335 matched cddid_all.tbl CDD cd21583 cd21583 409229 KLF2_N N-terminal domain of Kruppel-like factor 2. Kruppel-like Factor 2 (KLF2, also known as Krueppel-like factor 2 or lung Kruppel-like Factor/LKLF) is a protein that, in humans, is encoded by the KLF2 gene on chromosome 19. It has been implicated in a variety of biochemical processes in the human body, including lung development, embryonic erythropoiesis, epithelial integrity, T-cell viability, and adipogenesis. KLF proteins KLF1, KLF2, KLF4, KLF5, KLF6, and KLF7 are transcriptional activators. KLF2 belongs to a family of proteins called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF2, which is related to the N-terminal domains of KLF1 and KLF4. 299 matched cddid_all.tbl CDD cd21584 cd21584 409242 KLF11_N N-terminal domain of Kruppel-like factor 11. Kruppel-like factor 11 (KLF11; also known as Krueppel-like factor 11; Fetal Kruppel-like factor-1/FKLF-1; maturity-onset diabetes of the young 7/MODY7; TGFbeta Inducible Early Growth Response 2/TIEG2) is a protein that in humans is encoded by the KLF11 gene. KLF11 is involved in cell growth, apoptosis, cellular inflammation and differentiation, endometriosis, and cholesterol, prostaglandin, neurotransmitter, fat, and sugar metabolism. KLF9, KLF10, KLF11, KLF13, KLF14, and KLF16 share a conserved a-helical motif AA/VXXL that mediates their binding to Sin3A and their activities as transcriptional repressors. KLF11 belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF11. 217 matched cddid_all.tbl CDD cd21585 cd21585 409244 KLF7_N N-terminal domain of Kruppel-like factor 7. Kruppel-like factor 7 (KLF7; also known as Krueppel-like factor 7, or ubiquitous Kruppel-like factor/UKLF) is a protein which, in humans, is encoded by the KLF7 gene. KLF7 is involved in regulation of the development and function of the nervous system and adipose tissue, type 2 diabetes, blood diseases, as well as pluripotent cell maintenance. It functions as a transcriptional activator. It belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF7. 160 matched cddid_all.tbl CDD cd21586 cd21586 409245 KLF6_N N-terminal domain of Kruppel-like factor 6. Kruppel-like factor 6 (KLF6; also known as Krueppel-like factor 6, BCD1, CBA1, COPEB, CPBP, GBF, PAC1, ST12, or ZF9) is a protein that, in humans, is encoded by the KLF6 gene. KLF6 contributes to cell proliferation, differentiation, cell death, and signal transduction. Hepatocyte expression of KLF6 regulates hepatic fatty acid and glucose metabolism via transcriptional activation of liver glucokinase and post-transcriptional regulation of the nuclear receptor peroxisome proliferator activated receptor alpha (PPARa). KLF6-expression contributes to hepatic insulin resistance and the progression of non-alcoholic fatty liver disease (NAFLD) to non-alcoholic steatohepatitis (NASH) and NASH-cirrhosis. KLF6 also affects peroxisome proliferator activated receptor gamma (PPARgamma)-signaling in NAFLD. KLF6 has also been identified as a tumor suppressor gene that is inactivated or downregulated in different cancers, including prostate, colon, and hepatocellular carcinomas. KLF6 transactivates genes controlling cell proliferation, including p21, E-cadherin, and pituary tumor-transforming gene 1 (PTTG1). KLF6 functions as a transcriptional activator. It belongs to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF6. 198 matched cddid_all.tbl CDD cd21587 cd21587 394891 gammaCoV_RdRp gammacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome. This subfamily contains the RNA-dependent RNA polymerase (RdRp) of gammacoronaviruses, including the RdRp of avian infectious bronchitis virus (IBV) and similar proteins. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 931 matched cddid_all.tbl CDD cd21588 cd21588 394892 alphaCoV_RdRp alphacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome. This subfamily contains the RNA-dependent RNA polymerase (RdRp) of alphacoronaviruses, including human coronaviruses (HCoVs), HCoV-NL63, and HCoV-229E. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 924 matched cddid_all.tbl CDD cd21589 cd21589 438016 betaCoV_RdRp betacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome. This subfamily contains the RNA-dependent RNA polymerase (RdRp) of betacoronaviruses, including the RdRps from three highly pathogenic human coronaviruses (CoVs) such as Middle East respiratory syndrome (MERS)-related CoV, Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2, also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which shows potential for the treatment of SARS-CoV-2 viral infections. The structure of SARS-CoV-2 Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 925 matched cddid_all.tbl CDD cd21590 cd21590 394894 deltaCoV_RdRp deltacoronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12: responsible for replication and transcription of the viral RNA genome. This subfamily contains the RNA-dependent RNA polymerase (RdRp) of deltacoronaviruses. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which has been shown to inhibit human endemic and zoonotic deltacoronaviruses with a highly divergent RdRp. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 928 matched cddid_all.tbl CDD cd21591 cd21591 394895 SARS-CoV-like_RdRp Severe acute respiratory syndrome coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the B lineage: responsible for replication and transcription of the viral RNA genome. This group contains the RNA-dependent RNA polymerase (RdRp) of Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV-2 (also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus), and similar proteins from betacoronaviruses in the sarbecovirus subgenera (B lineage). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which shows potential for the treatment of SARS-CoV-2 viral infections. The structure of SARS-CoV-2 Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. Recent studies have shown that the SARS-CoV-2 RdRp requires two iron-sulfur clusters to function optimally. Earlier studies had mistakenly identified these iron-sulfur cluster binding sites for zinc-binding sites, likely because iron-sulfur clusters degrade easily under standard experimental conditions.The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 928 matched cddid_all.tbl CDD cd21592 cd21592 394896 MERS-CoV-like_RdRp Middle East respiratory syndrome-related coronavirus RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the C lineage: responsible for replication and transcription of the viral RNA genome. This group contains the RNA-dependent RNA polymerase (RdRp) of Middle East respiratory syndrome (MERS)-related CoV, bat-CoV HKU5, and similar proteins from betacoronaviruses in the merbecovirus subgenera (C lineage). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir, which has been shown to potently inhibit MERS RdRp. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 931 matched cddid_all.tbl CDD cd21593 cd21593 394897 HCoV_HKU1-like_RdRp human coronavirus HKU1 RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the A lineage: responsible for replication and transcription of the viral RNA genome. This group contains the RNA-dependent RNA polymerase (RdRp) of human coronavirus HKU1, murine hepatitis virus, and similar proteins from betacoronaviruses in the embecovirus subgenera (A lineage). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 925 matched cddid_all.tbl CDD cd21594 cd21594 394857 deltaCoV_M deltacoronavirus Membrane (or Matrix) protein. This subfamily contains the Membrane (M) protein of deltacoronaviruses including porcine deltacoronavirus and Bulbul coronavirus HKU11. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the Orf1ab (a large polyprotein known as replicase/protease); all are required to produce a structurally complete viral particle. The M protein, a triple-spanning membrane protein, is the most abundant protein in the virion. It plays a central role in virion assembly and morphogenesis, and it defines the shape of the viral envelope. It is regarded as the central organizer of CoV assembly, interacting with all other major coronaviral structural proteins and turning cellular membranes into workshops where virus and host factors come together to make new virus particles. While homotypic interactions between the M proteins are the major driving force behind virion envelope formation, it needs to interact with other coronaviral structural proteins for complete virion formation. The interaction of the Spike protein with M is not required for the assembly process. However, binding of M to N protein stabilizes the nucleocapsid (N protein-RNA complex), as well as the internal core of virions, and thereby promotes completion of viral assembly. Thus, the M protein, and its interactions with other structural proteins, is necessary for the production and release of virus-like particles. 217 matched cddid_all.tbl CDD cd21595 cd21595 439220 CoV_N-CTD C-terminal domain of nucleocapsid (N) protein of coronavirus. The coronavirus nucleocapsid (N) protein is a major structural and multifunctional protein. It plays an important role in the virus replication cycle, by forming a complex with the viral RNA. It also interacts with the viral membrane protein during virion assembly and plays a critical role in enhancing the efficiency of virus transcription and assembly. The C-terminal domain of the N protein (N-CTD) is involved in dimerization, and is thus, also called the dimerization domain. 84 matched cddid_all.tbl CDD cd21596 cd21596 394898 batCoV-HKU9-like_RdRp Bat coronavirus HKU9 RNA-dependent RNA polymerase, also known as non-structural protein 12, and similar proteins from betacoronaviruses in the D lineage: responsible for replication and transcription of the viral RNA genome. This group contains the RNA-dependent RNA polymerase (RdRp) of bat coronavirus HKU9 and similar proteins from betacoronaviruses in the nobecovirus subgenera (D lineage). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. A key component, the RNA-dependent RNA polymerase (RdRp, also known as Nsp12), catalyzes the synthesis of viral RNA and thus plays a central role in the replication and transcription cycle of CoV, possibly interacting with its co-factors, Nsp7 and Nsp8. RdRp is therefore considered a primary target for nucleotide analog antiviral inhibitors such as remdesivir. Nsp12 contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 929 matched cddid_all.tbl CDD cd21597 cd21597 394948 SARS-CoV-2_Orf10 "Severe acute respiratory syndrome coronavirus 2 Orf10. This model represents the Orf10 protein of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), also known as 2019 novel coronavirus (2019-nCoV). SARS-CoV-2 causes the disease called ""coronavirus disease 2019"" (COVID-19). Orf10 appears to have no homologous proteins in SARS-CoV and other coronaviruses. It has been suggested that the genome sequence currently annotated as orf10 may not have a protein coding function in SARS-CoV-2, and instead may act, itself or as a precursor of other RNAs, in the regulation of gene expression, replication, or modulating cellular antiviral pathways (DOI:10.1101/2020.03.05.976167)." 36 matched cddid_all.tbl CDD cd21598 cd21598 394937 ORF7b_SARS_bat-CoV-like Severe Acute Respiratory Syndrome coronavirus structural accessory protein ORF7b and similar proteins from related betacoronaviruses in the B lineage. This family contains the structural accessory protein ORF7b, also called NS7b, of Severe Acute Respiratory Syndrome Coronaviruses (SARS-CoVs) from betacoronavirus lineage B, including SARS-CoV-2, also known as 2019-nCoV, and a bat coronavirus (BatCoV RaTG13), which was previously detected in Rhinolophus affinis from China's Yunnan province, as well as SARS-related virus from Rhinolophus bats in Europe and Kenya. ORF7b/NS7b from betacoronavirus in the B lineage are not related to NS7b proteins from other betacoronavirus lineages. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the ORF1ab (a large polyprotein known as replicase/protease); all required to produce a structurally complete viral particle. In addition, SARS-CoV contains a number of open reading frames that code for a total of eight accessory proteins, namely ORFs 3a, 3b, 6, 7a, 7b, 8a, 8b, and 9b. These ORFs are specific for SARS-CoV and do not show significant homology to accessory proteins of other coronaviruses. The SARS-CoV ORF7b protein is a highly hydrophobic 43 amino acid protein which is homologous to an accessory but structural component of SARS-CoV virion. While ORF7b is packaged into virions, it is not required for the virus budding process, as gene 7 deletion viruses replicate efficiently in vitro and in vivo. Moreover, ORF7b possesses a transmembrane helical domain (TMD), between 9-29 amino acid residues, is necessary for its Golgi complex localization, as replacing it with the TMD from the human endoprotease furin results in aberrant localization. 40 matched cddid_all.tbl CDD cd21599 cd21599 410178 RRM1_GNPTAB RNA recognition motif 1 (RRM1) found in N-acetylglucosamine-1-phosphotransferase subunits alpha/beta (GNPTAB) and similar proteins. GNPTAB, also termed GlcNAc-1-phosphotransferase subunits alpha/beta, or stealth protein GNPTAB, or UDP-N-acetylglucosamine-1-phosphotransferase subunits alpha/beta, catalyzes the formation of mannose 6-phosphate (M6P) markers on high mannose type oligosaccharides in the Golgi apparatus. M6P residues are required to bind to the M6P receptors (MPR), which mediate the vesicular transport of lysosomal enzymes to the endosomal/prelysosomal compartment. The model corresponds to the RNA recognition motif 1 (RRM1) of GNPTAB. Its functional significance remains to be investigated. 90 matched cddid_all.tbl CDD cd21600 cd21600 410179 RRM2_GNPTAB RNA recognition motif 2 (RRM2) found in N-acetylglucosamine-1-phosphotransferase subunits alpha/beta (GNPTAB) and similar proteins. GNPTAB, also termed GlcNAc-1-phosphotransferase subunits alpha/beta, or stealth protein GNPTAB, or UDP-N-acetylglucosamine-1-phosphotransferase subunits alpha/beta, catalyzes the formation of mannose 6-phosphate (M6P) markers on high mannose type oligosaccharides in the Golgi apparatus. M6P residues are required to bind to the M6P receptors (MPR), which mediate the vesicular transport of lysosomal enzymes to the endosomal/prelysosomal compartment. The model corresponds to the RNA recognition motif 2 (RRM2) of GNPTAB. Its functional significance remains to be investigated. 77 matched cddid_all.tbl CDD cd21601 cd21601 410180 RRM1_PES4_MIP6 RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins. The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif. 80 matched cddid_all.tbl CDD cd21602 cd21602 410181 RRM2_PES4_MIP6 RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins. The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif. 76 matched cddid_all.tbl CDD cd21603 cd21603 410182 RRM3_PES4_MIP6 RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins. The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif. 73 matched cddid_all.tbl CDD cd21604 cd21604 410183 RRM4_PES4_MIP6 RNA recognition motif 4 (RRM4) found in Saccharomyces cerevisiae protein PES4, protein MIP6 and similar proteins. The family includes PES4 (also called DNA polymerase epsilon suppressor 4) and MIP6 (also called MEX67-interacting protein 6), both of which are predicted RNA binding proteins that may act as regulators of late translation, protection, and mRNA localization. MIP6 acts as a novel factor for nuclear mRNA export, binds to both poly(A)+ RNA and nuclear pores. It interacts with MEX67. Members in this family contain four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the fourth RRM motif. 79 matched cddid_all.tbl CDD cd21605 cd21605 410184 RRM1_HRB1_GBP2 RNA recognition motif 1 (RRM1) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins. The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif. 77 matched cddid_all.tbl CDD cd21606 cd21606 410185 RRM2_HRB1_GBP2 RNA recognition motif 2 (RRM2) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins. The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif. 75 matched cddid_all.tbl CDD cd21607 cd21607 410186 RRM3_HRB1_GBP2 RNA recognition motif 3 (RRM3) found in Saccharomyces cerevisiae protein HRB1, G-strand-binding protein 2 (GBP2) and similar proteins. The family includes Saccharomyces cerevisiae protein HRB1 (also called protein TOM34) and GBP2, both of which are SR-like mRNA-binding proteins which shuttle from the nucleus to the cytoplasm when bound to the mature mRNA molecules. They act as quality control factors for spliced mRNAs. GBP2, also called RAP1 localization factor 6, is a single-strand telomeric DNA-binding protein that binds single-stranded telomeric sequences of the type (TG[1-3])n in vitro. It also binds to RNA. GBP2 influences the localization of RAP1 in the nuclei and plays a role in modulating telomere length. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the third RRM motif. 79 matched cddid_all.tbl CDD cd21608 cd21608 410187 RRM2_NsCP33_like RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins. The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif. 76 matched cddid_all.tbl CDD cd21609 cd21609 410188 RRM1_PSRP2_like RNA recognition motif 1 (RRM1) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins. PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). The family also includes Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (AtCP31A). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. Members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif. 80 matched cddid_all.tbl CDD cd21610 cd21610 410189 RRM2_PSRP2 RNA recognition motif 2 (RRM2) found in chloroplastic plastid-specific 30S ribosomal protein 2 (PSRP-2) and similar proteins. PSRP-2, also called chloroplastic 30S ribosomal protein 2, or chloroplastic small ribosomal subunit protein cS22, is a component of the chloroplast ribosome (chloro-ribosome), a dedicated translation machinery responsible for the synthesis of chloroplast genome-encoded proteins, including proteins of the transcription and translation machinery and components of the photosynthetic apparatus. It binds single strand DNA (ssDNA) and RNA in vitro. It exhibits RNA chaperone activity and regulates negatively resistance responses to abiotic stresses during seed germination (e.g. salt, dehydration, and low temperature) and seedling growth (e.g. salt). PSRP-2 contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif. 79 matched cddid_all.tbl CDD cd21611 cd21611 410190 RRM_SpPof8_like RNA recognition motif (RRM) found in Schizosaccharomyces pombe protein Pof8 and similar proteins. Pof8 is a La-related protein and a constitutive component of telomerase in fission yeast. It regulates telomerase assembly and poly(a)+TERRA expression in fission yeast. Members in this family contain an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 82 matched cddid_all.tbl CDD cd21612 cd21612 410191 RRM_AtRDRP1_like RNA recognition motif (RRM) found in Arabidopsis thaliana RNA-dependent RNA polymerase 1 (AtRDRP1) and similar proteins. AtRDRP1, also called RNA-directed RNA polymerase 1, is an RNA-dependent direct polymerase involved in antiviral silencing. It is required for the biogenesis of viral secondary siRNAs, process that follows the production of primary siRNAs derived from viral RNA replication. Members in this family contain an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 67 matched cddid_all.tbl CDD cd21613 cd21613 410192 RRM1_KSRP RNA recognition motif 1 (RRM1) found in Kinetoplastid-Specific Ribosomal Protein (KSRP) and similar proteins. KSRP is an essential protein located at the solvent face of the 40S subunit, where it binds and stabilizes kinetoplastid-specific domains of rRNA, suggesting its role in ribosome integrity. It also interacts with the kinetoplastid-specific C-terminal region of protein eS6. KSRP contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif. 71 matched cddid_all.tbl CDD cd21614 cd21614 410193 RRM2_KSRP RNA recognition motif 2 (RRM2) found in Kinetoplastid-Specific Ribosomal Protein (KSRP) and similar proteins. KSRP is an essential protein located at the solvent face of the 40S subunit, where it binds and stabilizes kinetoplastid-specific domains of rRNA, suggesting its role in ribosome integrity. It also interacts with the kinetoplastid-specific C-terminal region of protein eS6. KSRP contains two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif. 97 matched cddid_all.tbl CDD cd21615 cd21615 410194 RRM_SNP1_like RNA recognition motif (RRM) found in Saccharomyces cerevisiae U1 small nuclear ribonucleoprotein SNP1 and similar proteins. SNP1, also called U1 snRNP protein SNP1, or U1 small nuclear ribonucleoprotein 70 kDa homolog, or U1 70K, or U1 snRNP 70 kDa homolog, interacts with mRNA and is involved in nuclear mRNA splicing. It is a component of the spliceosome, where it is associated with snRNP U1 by binding stem loop I of U1 snRNA. Members in this family contain an N-terminal U1snRNP70 domain and an RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 118 matched cddid_all.tbl CDD cd21616 cd21616 410195 RRM_ScJSN1_like RNA recognition motif (RRM) found in Saccharomyces cerevisiae protein JSN1 and similar proteins. JSN1, also called Pumilio homology domain family member 1 (PUF1), is a member of the PUF family of proteins. It facilitates association of Arp2/3 complex to yeast mitochondria. It may play a role in mitosis, perhaps by affecting the stability of microtubules. Members in this family contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 118 matched cddid_all.tbl CDD cd21617 cd21617 410196 RRM_TDRD10 RNA recognition motif (RRM) found in Tudor domain-containing protein 10 (TDRD10) and similar proteins. TDRD10 is widely expressed and localized both to the nucleus and cytoplasm and may play general roles like regulation of RNA metabolism. It contains a Tudor domain and a RNA recognition motif (RRM). 69 matched cddid_all.tbl CDD cd21618 cd21618 410197 RRM_AtNSRA_like RNA recognition motif (RRM) found in Arabidopsis thaliana nuclear speckle RNA-binding protein A (AtNSRA) and similar protein. AtNSRA is an alternative splicing (AS) regulator that binds to specific mRNAs and modulates auxin effects on the transcriptome. It can be displaced from its targets upon binding to AS competitor long non-coding RNA (ASCO-RNA). Members in this family contain an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). 87 matched cddid_all.tbl CDD cd21619 cd21619 410198 RRM1_Crp79 RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe mRNA export factor Crp79 and similar proteins. Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif. 78 matched cddid_all.tbl CDD cd21620 cd21620 410199 RRM1_Mug28 RNA recognition motif 1 (RRM1) found in Schizosaccharomyces pombe meiotically up-regulated gene 28 protein (Mug28) and similar proteins. Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the first RRM motif. 84 matched cddid_all.tbl CDD cd21621 cd21621 410200 RRM2_Crp79_Mug28 RNA recognition motif 2 (RRM2) found in Schizosaccharomyces pombe mRNA export factor Crp79, meiotically up-regulated gene 28 protein (Mug28) and similar proteins. Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif. 74 matched cddid_all.tbl CDD cd21622 cd21622 410201 RRM3_Crp79_Mug28 RNA recognition motif 3 (RRM3) found in Schizosaccharomyces pombe mRNA export factor Crp79, meiotically up-regulated gene 28 protein (Mug28) and similar proteins. Crp79, also called meiotic expression up-regulated protein 5 (Mug5), or polyadenylate-binding protein crp79, or PABP, or poly(A)-binding protein, is an auxiliary mRNA export factor that binds the poly(A) tail of mRNA and is involved in the export of mRNA from the nucleus to the cytoplasm. Mug28 is a meiosis-specific protein that regulates spore wall formation. Members in this family contain three RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the three RRM motif. 92 matched cddid_all.tbl CDD cd21623 cd21623 394938 ORF7b_SARS-CoV-2 Structural accessory protein ORF7b of Severe Acute Respiratory Syndrome coronavirus 2 and similar proteins. This group contains the ORF7b, also called NS7b, of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), also known as 2019-nCoV, and a bat coronavirus (BatCoV RaTG13), which was previously detected in Rhinolophus affinis from China's Yunnan province and showed high sequence identity to SARS-CoV-2. ORF7b/NS7b from betacoronavirus in the B lineage are not related to NS7b proteins from other betacoronavirus lineages. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the ORF1ab (a large polyprotein known as replicase/protease); all required to produce a structurally complete viral particle. In addition, SARS coronavirus contains a number of open reading frames that code for a total of eight accessory proteins, namely ORFs 3a, 3b, 6, 7a, 7b, 8a, 8b, and 9b. These ORFs are specific for SARS-CoV and do not show significant homology to accessory proteins of other coronaviruses. The SARS-CoV ORF7b protein is a highly hydrophobic 43 amino acid protein which is homologous to an accessory but structural component of SARS-CoV virion. While ORF7b is packaged into virions, it is not required for the virus budding process, as gene 7 deletion viruses replicate efficiently in vitro and in vivo. Moreover, ORF7b possesses a transmembrane helical domain (TMD), between 9-29 amino acid residues, is necessary for its Golgi complex localization, as replacing it with the TMD from the human endoprotease furin results in aberrant localization. 43 matched cddid_all.tbl CDD cd21624 cd21624 394950 SARS-CoV-like_Spike_S1_NTD N-terminal domain of the S1 subunit of the Spike (S) protein from Severe acute respiratory syndrome coronavirus and related betacoronaviruses in the B lineage. This subfamily contains the N-terminal domain (NTD) of the S1 subunit of the Spike (S) proteins from betacoronaviruses in the sarbecovirus subgenera (B lineage), including the highly pathogenic human coronavirus (CoV), Severe acute respiratory syndrome (SARS) CoV, and SARS-CoV-2, also known as a 2019 novel coronavirus (2019-nCoV) or COVID-19 virus. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). Most CoVs, including SARS-CoV-2 and SARS-CoV, use the C-domain to bind their receptors. The S1 NTD contributes to the Spike trimer interface. 280 matched cddid_all.tbl CDD cd21625 cd21625 394951 MHV-like_Spike_S1_NTD N-terminal domain of the S1 subunit of the Spike (S) protein from murine hepatitis virus and related betacoronaviruses in the A lineage. This subfamily contains the N-terminal domain (NTD) of the S1 subunit of the Spike (S) proteins from betacoronaviruses in the embecovirus subgenera (A lineage), including murine hepatitis virus (MHV), human coronavirus (HCoV) HKU1 and OC43, and bovine CoV (BCoV). MHV is the most common viral pathogen in contemporary laboratory mouse colonies manifesting as a primary infection in the upper respiratory tract, while HCoV-HKU1 causes mild yet prevalent respiratory disease in humans. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While most CoVs, including SARS-CoV and MERS-CoV use the C-domain to bind their receptors, several CoVs in the A lineage use the NTD to bind their receptors. MHV binds its protein receptor, mouse carcinoembryonic antigen related cell adhesion molecule 1a (mCEACAM1a), through its S1 NTD. BCoV and HCoV-OC43 recognize a sugar moiety, 5-N-acetyl-9-O-acetylneuraminic acid (Neu5,9Ac2), on cell-surface glycoproteins or glycolipids; this binding is also through the S1 NTD. In addition, the S1 NTD contributes to the Spike trimer interface. 284 matched cddid_all.tbl CDD cd21626 cd21626 394952 MERS-CoV-like_Spike_S1_NTD N-terminal domain of the S1 subunit of the Spike (S) protein from Middle East respiratory syndrome-related coronavirus and related betacoronaviruses in the C lineage. This subfamily contains the N-terminal domain (NTD) of the S1 subunit of the Spike (S) proteins from betacoronaviruses in the merbecovirus subgenera (C lineage), including the highly pathogenic human coronavirus (CoV), Middle East respiratory syndrome (MERS)-related CoV, and related bat CoVs. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). Most CoVs, including MERS-CoV, use the C-domain to bind their receptors. Despite using the C-domain as its receptor, neutralizing antibodies targeting MERS-CoV S1-NTD have been reported, including human antibody CDC2-A2, murine antibodies G2 and 5F9, and macaque antibodies FIB-H1 and JC57-13. G2 has been shown to strongly disrupt the attachment of MERS-CoV S to its receptor, dipeptidyl peptidase-4 (DPP4). In addition, the S1 NTD contributes to the Spike trimer interface. 328 matched cddid_all.tbl CDD cd21627 cd21627 394953 batCoV-HKU9-like_Spike_S1_NTD N-terminal domain of the S1 subunit of the Spike (S) protein from Rousettus bat coronavirus HKU9 and related betacoronaviruses in the D lineage. This subfamily contains the N-terminal domain (NTD) of the S1 subunit of the Spike (S) proteins from betacoronaviruses in the nobecovirus subgenera (D lineage), including Rousettus bat coronavirus HKU9 and related bat CoVs. The CoV S protein is an envelope glycoprotein that plays the most important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains a hydrophobic fusion peptide and two heptad repeat regions. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). Most CoVs, including SARS-CoV-2, SARS-CoV, and MERS-CoV use the C-domain to bind their receptors. However, CoV such as mouse hepatitis virus (MHV) uses the NTD to bind its receptor, mouse carcinoembryonic antigen related cell adhesion molecule 1a (mCEACAM1a). The S1 NTD contributes to the Spike trimer interface. 289 matched cddid_all.tbl CDD cd21628 cd21628 394930 deltaCoV_NS7_NS7a deltacoronavirus accessory protein NS7 and NS7a. This family includes the accessory protein NS7 found in deltacoronaviruses from the Buldecovirus subgenus, such as porcine coronavirus HKU15, and several avian coronaviruses found in sparrow, pigeon, quail and falcon, among others. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered to be dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. Porcine deltacoronavirus (PDCoV) encodes three accessory proteins, NS6, NS7 and NS7a. NS7a is a 100 amino-acid polypeptide identical to the C-terminus of NS7; it remains unclear whether their functions are redundant. PDCoV HKU15, an emerging swine enteric coronavirus that causes diarrhea in neonatal piglets, has also been found in the respiratory tract of pigs and may be able to cause respiratory infections, thus possibly spreading through the respiratory route. NS7-specific mAbs that recognized cells transfected with an NS7 expression construct or infected with PDCoV also recognized NS7a, which is encoded by a separate subgenome mRNA with a non-canonical transcription regulatory sequence. The NS7 protein is extensively distributed in the mitochondria and may be involved in various cellular processes such as cytoskeleton networks and cell communication, metabolism, and protein biosynthesis. NS7-expressing and PDCoV-infected cells also show a substantial down-regulation of alpha-actinin-4. 195 matched cddid_all.tbl CDD cd21629 cd21629 394929 NS6_deltaCoV deltacoronavirus accessory protein NS6. This family includes the accessory protein NS6 from deltacoronaviruses such as porcine coronavirus HKU15, and several avian coronaviruses found in sparrow, pigeon, quail and falcon, among others. There are five essential genes in coronaviruses (CoVs) that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered to be dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. Porcine deltacoronavirus (PDCoV) encodes three accessory proteins, NS6, NS7, and NS7a. During PDCoV infection, NS6 antagonizes RIG-I-like receptor (RLR)-mediated IFN-beta production to evade host innate immune defense; it interacts with RIG-I and MDA5 to impede their association with double-stranded RNA. This is an important finding towards novel therapeutic targets and may lead to the development of more effective vaccines against PDCoV infection. 91 matched cddid_all.tbl CDD cd21630 cd21630 438634 Kunitz_TAP-like Tick anticoagulant peptide, and similar proteins. Tick anticoagulant peptide (TAP) is a competitive inhibitor of factor Xa, a serine protease that converts prothrombin into thrombin, which acts to convert fibrinogen into fibrin, the insoluble matrix of blood clots. TAP is one of the antihemostatic components evolved in the blood-feeding tick. This subfamily also includes the N-terminal Kunitz inhibitor domain of ornithodorin which binds to the active site of thrombin, while the C-terminal domain binds at the fibrinogen recognition exosite. The TAP structure is similar to that of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 60 matched cddid_all.tbl CDD cd21631 cd21631 409020 RHH_CopG_NikR-like ribbon-helix-helix domains of transcription repressor CopG, nickel responsive transcription factor NikR, and similar proteins. This family includes the ribbon-helix-helix (RHH) domains of transcriptional repressor CopG, nickel-responsive transcription factor NikR, several antitoxins such as Shewanella oneidensis CopA(SO), Burkholderia pseudomallei HicB, and Caulobacter crescentus ParD, and similar proteins. CopG, a homodimeric RHH protein of around 45 residues, constitutes one of the smallest natural transcriptional repressors characterized and is the prototype of a series of repressor proteins encoded by plasmids that exhibit a similar genetic structure at their leading strand initiation and control regions. It is involved in the control of plasmid copy number. NikR, which consists of the N-terminal DNA-binding RHH domain and the C-terminal metal-binding domain (MBD) with four nickel ions, regulates several genes; in Helicobacter pylori, NikR regulates the urease enzyme under extreme acidic conditions, and is involved in the intracellular physiology of nickel. Protein HicB is part of the HicAB toxin-antitoxin (TA) system, where the toxins are RNases, found in many bacteria. In Burkholderia pseudomallei, the HicAB system may play a role in disease by regulating the frequency of persister cells, while in Yersinia pestis HicB acts as an autoregulatory protein that inhibits HicA, which acts as an mRNase. In Escherichia coli, an excess of HicA has been shown to de-repress a HicB-DNA complex and restore transcription of HicB. The CopG family RHH domain, represented by this model, forms a homodimer and binds DNA. 42 matched cddid_all.tbl CDD cd21635 cd21635 394939 ORF7b_SARS-CoV-like Severe Acute Respiratory Syndrome coronavirus structural accessory protein ORF7b and related proteins. This group contains the ORF7b, also called NS7b, of Severe Acute Respiratory Syndrome coronaviruses (SARS-CoVs) and related betacoronaviruses identified in Chinese horseshoe bats, including bat SARS-like-CoV WIV1 and HKU3. ORF7b/NS7b from betacoronavirus in the B lineage are not related to NS7b proteins from other betacoronavirus lineages. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the ORF1ab (a large polyprotein known as replicase/protease); all required to produce a structurally complete viral particle. In addition, SARS coronavirus contains a number of open reading frames that code for a total of eight accessory proteins, namely ORFs 3a, 3b, 6, 7a, 7b, 8a, 8b, and 9b. These ORFs are specific for SARS-CoV and do not show significant homology to accessory proteins of other coronaviruses. The SARS-CoV ORF7b protein is a highly hydrophobic 43 amino acid protein which is homologous to an accessory but structural component of SARS-CoV virion. While ORF7b is packaged into virions, it is not required for the virus budding process, as gene 7 deletion viruses replicate efficiently in vitro and in vivo. Moreover, ORF7b possesses a transmembrane helical domain (TMD), between 9-29 amino acid residues, is necessary for its Golgi complex localization, as replacing it with the TMD from the human endoprotease furin results in aberrant localization. 44 matched cddid_all.tbl CDD cd21637 cd21637 394931 NS7_PDCoV Porcine deltacoronavirus (PDCoV) accessory protein NS7. This group includes the accessory protein NS7 found in Porcine coronavirus HKU15. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle., In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered to be dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. Porcine deltacoronavirus (PDCoV) encodes three accessory proteins, NS6, NS7 and NS7a. NS7a is a 100 amino-acid polypeptide identical to the C-terminus of NS7; it remains unclear whether their functions are redundant. PDCoV HKU15, an emerging swine enteric coronavirus that causes diarrhea in neonatal piglets, has also been found in the respiratory tract of pigs and may be able to cause respiratory infections, thus possibly spreading through the respiratory route. NS7-specific mAbs that recognized cells transfected with an NS7 expression construct or infected with PDCoV also recognized NS7a, which is encoded by a separate subgenome mRNA with a non-canonical transcription regulatory sequence. The NS7 protein is extensively distributed in the mitochondria and may be involved in various cellular processes such as cytoskeleton networks and cell communication, metabolism, and protein biosynthesis. NS7-expressing and PDCoV-infected cells also show a substantial down-regulation of alpha-actinin-4. 198 matched cddid_all.tbl CDD cd21638 cd21638 394932 NS7a_deltaCoV_HKU16-like accessory protein NS7a found in deltacoronavirus, including avian coronavirus HKU16 and related coronaviruses. This group includes the accessory protein NS7a from White-eye coronavirus HKU16, Falcon coronavirus UAE-HKU27, Houbara coronavirus UAE-HKU28 and Pigeon coronavirus UAE-HKU29, within the Buldecovirus subgenus of deltacoronaviruses (deltaCoVs). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered to be dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. In deltaCoVs, several avian species encode accessory protein NS7a, which is homologous to Porcine coronavirus (PDCoV) HKU15 accessory proteins NS7 and NS7a. PDCoV NS7a is a 100 amino-acid polypeptide identical to the C-terminus of NS7; it remains unclear whether their functions are redundant. The PDCoV NS7 protein is extensively distributed in the mitochondria and may be involved in various cellular processes such as cytoskeleton networks and cell communication, metabolism, and protein biosynthesis. NS7a proteins in this subfamily have yet to be characterized. 197 matched cddid_all.tbl CDD cd21639 cd21639 394933 NS7a_deltaCoV_HKU30-like accessory protein NS7a found in deltacoronavirus, including avian coronavirus HKU30 and related coronaviruses. This group includes the accessory protein NS7a from Quail deltacoronavirus (QdCoV) UAE-HKU30 and sparrow deltacoronavirus (SpCoV-HKU17) within the Buldecovirus subgenus of deltacoronaviruses. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered to be dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. In deltaCoVs, several avian species encode accessory protein NS7a, which is homologous to Porcine coronavirus (PDCoV) HKU15 accessory proteins NS7 and NS7a. PDCoV NS7a is a 100 amino-acid polypeptide identical to the C-terminus of NS7; it remains unclear whether their functions are redundant. The PDCoV NS7 protein is extensively distributed in the mitochondria and may be involved in various cellular processes such as cytoskeleton networks and cell communication, metabolism, and protein biosynthesis. NS7a proteins in this subfamily have yet to be characterized. Phylogenetic analysis revealed that QdCoV UAE-HKU30 belongs to the same CoV species as porcine deltacoronavirus (PdCoV) HKU15 and sparrow deltacoronavirus (SpdCoV) HKU17 within Buldecovirus subgenus, suggesting transmission between avian and swine hosts. 198 matched cddid_all.tbl CDD cd21640 cd21640 439221 ORF8-Ig_SARS-CoV-2-like "SARS-CoV-2 ORF8 immunoglobulin (Ig) domain protein and related proteins. This family includes the ORF8 immunoglobulin (Ig) domain protein of Severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2, also known as a 2019 novel coronavirus, 2019-nCoV) and related Sarbecovirus ORF8 proteins including those classified as type II, such as bat coronavirus Rf1 ORF8, and those classified as type III, such as Bat SARS coronavirus HKU3-1 ORF8. SARS-CoV-2 causes the disease called ""coronavirus disease 2019"" (COVID-19). SARS-CoV-2 ORF8 is a fast-evolving protein in SARS-related CoVs, and a potential pathogenicity factor which evolves rapidly to counter the immune response and facilitate the transmission between hosts. A 382 nucleotide deletion in SARS-CoV-2 ORF8 was found to correlate with milder disease and a lower incidence of hypoxia. SARS-CoV-2 ORF8 interacts with a variety of host proteins, including many factors involved in ERAD. It disrupts IFN-I signaling when exogenously overexpressed in cells, and downregulates MHC-I." 104 matched cddid_all.tbl CDD cd21641 cd21641 439222 ORF8-Ig_SARS-CoV-2-like "SARS-CoV-2 ORF8 immunoglobulin (Ig) domain protein and related proteins. This subfamily includes the ORF8 immunoglobulin (Ig) domain protein of Severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2, also known as a 2019 novel coronavirus, 2019-nCoV) and related Sarbecovirus ORF8 proteins. SARS-CoV-2 causes the disease called ""coronavirus disease 2019"" (COVID-19). SARS-CoV-2 ORF8 (also known as ns8 and accessory protein 8) is a fast-evolving protein in SARS-related CoVs, and a potential pathogenicity factor which evolves rapidly to counter the immune response and facilitate the transmission between hosts. A 382 nucleotide deletion in SARS-CoV-2 ORF8 was found to correlate with milder disease and a lower incidence of hypoxia. SARS-CoV-2 ORF8 interacts with a variety of host proteins, including many factors involved in ERAD. It disrupts IFN-I signaling when exogenously overexpressed in cells, and downregulates MHC-I. It belongs to a family which includes Sarbecovirus ORF8 proteins classified as type II, such as bat coronavirus Rf1 ORF8, and those classified as type III, such as Bat SARS coronavirus HKU3-1 ORF8." 104 matched cddid_all.tbl CDD cd21642 cd21642 394946 ORF8-Ig_Bat_SARS_CoV_Rf1_type-II-like "ORF8 immunoglobulin (Ig) domain protein of bat coronavirus Rf1, a type II ORF8, and related proteins. This subfamily includes the ORF8 immunoglobulin (Ig) domain proteins of bat coronavirus Rf1 (Bat SARS CoV Rf1) and Bat CoV 273/2005, which have been classified previously as type II ORF8 proteins. They belong to a family which includes the ORF8 immunoglobulin (Ig) domain protein of Severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2, also known as a 2019 novel coronavirus, 2019-nCoV) and other related Sarbecovirus ORF8's, such as Bat SARS coronavirus HKU3-1 ORF8 which has been classified previously as a type III ORF8. SARS-CoV-2 causes the disease called ""coronavirus disease 2019"" (COVID-19). SARS-CoV-2 ORF8 protein (also known as ns8 and accessory protein 8) is a fast-evolving protein in SARS-related CoVs, and a potential pathogenicity factor which evolves rapidly to counter the immune response and facilitate the transmission between hosts. A 382 nucleotide deletion in SARS-CoV-2 ORF8 was found to correlate with milder disease and a lower incidence of hypoxia. SARS-CoV-2 ORF8 interacts with a variety of host proteins, including many factors involved in ERAD. It disrupts IFN-I signaling when exogenously overexpressed in cells, and downregulates MHC-I. In most SARS-CoVs, ORF8 is split into overlapping ORF8a and ORF8b proteins; the N- and C-terminus of SARS-CoV-2 ORF8 is similar to SARS-CoV ORF8a and ORF8b, respectively." 119 matched cddid_all.tbl CDD cd21643 cd21643 394947 ORF8-Ig_bat_SARS-CoV_HKU3-1_type-III-like "ORF8 immunoglobulin (Ig) domain protein of bat SARS coronavirus HKU3-1 ORF8, a type III ORF8, and related proteins. This subfamily includes the ORF8 immunoglobulin (Ig) domain proteins of Bat SARS coronavirus HKU3-1 and Bat SARS-like coronavirus Rs3367, which have been classified previously as type III ORF8's. They belong to a family which includes the ORF8 immunoglobulin (Ig) domain protein of Severe acute respiratory syndrome (SARS) coronavirus 2 (SARS-CoV-2, also known as a 2019 novel coronavirus, 2019-nCoV) and other related Sarbecovirus ORF8's, such as bat coronavirus Rf1 (Bat SARS CoV Rf1) ORF8 which has been classified previously as a type II ORF8. SARS-CoV-2 causes the disease called ""coronavirus disease 2019"" (COVID-19). SARS-CoV-2 ORF8 protein (also known as ns8 and accessory protein 8) is a fast-evolving protein in SARS-related CoVs, and a potential pathogenicity factor which evolves rapidly to counter the immune response and facilitate the transmission between hosts. A 382 nucleotide deletion in SARS-CoV-2 ORF8 was found to correlate with milder disease and a lower incidence of hypoxia. SARS-CoV-2 ORF8 interacts with a variety of host proteins, including many factors involved in ERAD. It disrupts IFN-I signaling when exogenously overexpressed in cells, and downregulates MHC-I." 120 matched cddid_all.tbl CDD cd21644 cd21644 394940 batCoV-HKU9_NS7b NS7b protein from Rousettus bat coronavirus HKU9 and related betacoronaviruses in the D lineage. This model represents the NS7b protein of Rousettus bat coronavirus (CoV) HKU9 and related proteins from betacoronaviruses in the nobecovirus subgenera (D lineage). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered to be dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. The NS7b protein of lineage D betacoronavirus is an accessory protein whose function is unknown. It is not related to NS7b proteins from other betacoronavirus lineages. 178 matched cddid_all.tbl CDD cd21645 cd21645 394928 MERS-CoV-like_ORF5 Non-structural protein ORF5 from Middle East respiratory syndrome-related coronavirus and related betacoronaviruses in the C lineage. This model represents the non-structural protein ORF5 from Middle East respiratory syndrome-related coronavirus (MERS-CoV) and and similar proteins from betacoronaviruses in the merbecovirus subgenera (C lineage). ORF5 is also called non-structural protein 3d (NS3d) or accessory protein 3d in some bat merbecoviruses. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered to be dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. MERS-CoV is a highly pathogenic respiratory virus with pathogenic mechanisms that may be driven by innate immune pathways. MERS-CoV ORF5 acts as an interferon antagonist and may play a role in circumventing the innate immunity of host cells. It is also implicated to play a role in the modulation of NF-kappaB-mediated inflammation. ORF5/NS3d from merbecovirus (betacoronavirus, lineage C) may not be related to ORF5 proteins from other lineages. 223 matched cddid_all.tbl CDD cd21646 cd21646 394885 CoV_Nsp5_Mpro coronavirus non-structural protein 5, also called Main protease (Mpro). This family contains the coronavirus (CoV) non-structural protein 5 (Nsp5) also called the Main protease (Mpro), or 3C-like protease (3CLpro). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Mpro/Nsp5 is a key enzyme in this process, making it a high value target for the development of anti-coronavirus therapeutics. These enzymes belong to the MEROPS peptidase C30 family, where the active site residues His and Cys form a catalytic dyad. The structures of Mpro/Nsp5 consist of three domains with the first two containing anti-parallel beta barrels and the third consisting of an arrangement of alpha-helices. The catalytic residues are found in a cleft between the first two domains. Mpro/Nsp5 requires a Gln residue in the P1 position of the substrate and space for only small amino-acid residues such as Gly, Ala, or Ser in the P1' position; since there is no known human protease with a specificity for Gln at the cleavage site of the substrate, these viral proteases are suitable targets for the development of antiviral drugs. 292 matched cddid_all.tbl CDD cd21647 cd21647 394924 ORF4b_NS3c-betaCoV accessory protein ORF4b, also known as non-structural protein 3c (NS3c), of betacoronaviruses in the C lineage. This model represents the accessory protein 4b, ORF4b (also called NS3c protein) of Middle East respiratory syndrome (MERS)-related CoV and similar proteins from betacoronaviruses in the merbecovirus subgenera (C lineage), including Tylonycteris bat coronavirus HKU4 and Pipistrellus bat coronavirus HKU5. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered to be dispensable for viral replication, however several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. ORF4b/NS3c plays a role in the inhibition of host innate immunity by inhibiting the interaction between host IkappaB kinase epsilion (IKBKE or IKKE) and mitochondrial antiviral-signalling protein (MAVS). In turn, this inhibition prevents the production of host interferon beta. Additionally, it may also interfere with host antiviral response within the nucleus. The MERS-CoV ORF4b (also known as MERS-CoV 4b) has been shown to interfere with the NF-kappaB-dependent innate immune response during infection, as well as antagonizing the early antiviral alpha/beta interferon (IFN-alpha/beta) response, which may significantly contribute to MERS-CoV pathogenesis. 227 matched cddid_all.tbl CDD cd21648 cd21648 439223 SARS-CoV-like_ORF3a accessory protein ORF3a of severe acute respiratory syndrome-associated coronavirus and similar proteins from related betacoronavirus. This model represents the accessory protein ORF3a of Severe Acute Respiratory Syndrome-associated coronavirus (SARS-CoV), SARS-COV-2 (also called 2019 novel coronavirus or 2019-nCoV), and related betacoronaviruses in the Sarbecovirus subgenus (B lineage). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered to be dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. SARS-CoV mRNA 3 encodes the distinct proteins ORF3a and ORF3b, which are translated in different reading frames. Accessory protein ORF3a, also called protein 3a and protein X1, is the largest ORF protein in SARS-CoV. It is also called accessory protein 3 or protein 3 in some bat coronaviruses. SARS-CoV ORF3a promotes membrane rearrangement and cell death; it induces vesicle formation and is necessary for SARS-CoV-induced Golgi fragmentation. It has also been found to activate NF-kappaB and the NLRP3 inflammasome by promoting TNF receptor-associated factor 3 (TRAF3)-dependent ubiquitination of p105 and ASC (apoptosis-associated speck-like protein containing a caspase recruitment domain). The cytoplasmic domain of SARS-CoV ORF3a, composed of amino acids at the C-terminal region, has sequence similarity to a calcium pump present in Plasmodium falciparum and has been shown to bind calcium in vitro. SARS-CoV-2 3a is able to form ion channels; it is a Class IIIA viroporin, having 3 transmembrane helices per protomer and a lumenal amino terminus and cytosolic carboxyl terminus. It can form dimers, tetramers, and potentially higher order oligomers. It has been shown to form cation channels with modest selectivity for Ca2+ and K+ over Na+. 269 matched cddid_all.tbl CDD cd21649 cd21649 394923 SARS-CoV_ORF3b accessory protein ORF3b of severe acute respiratory syndrome-associated coronavirus. This model represents the accessory protein ORF3b of Severe acute respiratory syndrome-associated coronavirus (SARS-CoV). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered to be dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. SARS-CoV mRNA 3 encodes the distinct proteins ORF3a and ORF3b proteins, which are translated in different reading frames. SARS-CoV accessory protein ORF3b antagonizes interferon (IFN) function by modulating the activity of IFN regulatory factor 3 (IRF3). The IFN system functions as the first line of defense against viral infection in mammalian cells. Viral infection triggers a series of cellular events that lead to the production of IFN and several downstream antiviral genes, helping to establish an antiviral state. Viruses encode IFN antagonists to counteract the antiviral effects of IFN. SARS-CoV ORF3b, ORF6, and N proteins function as IFN antagonists. ORF3b inhibits both IFN synthesis and signaling. It localizes to the nucleus in transfected cells. 151 matched cddid_all.tbl CDD cd21650 cd21650 412060 CrtA-like spheroidene monooxygenase and similar proteins. Spheroidene monooxygenase (such as Rhodobacter sphaeroides monooxygenase CrtA) catalyzes the asymmetrical introduction of one keto group at the C-2 position of spheroidene and two keto groups at the C-2 and C-2' positions of spirilloxanthin in carotenoid pathways. Spectroscopic analysis suggests CrtA may have a 5-coordinated heme at its active site and that it may be a novel oxygenase and not a P450 enzyme. 225 matched cddid_all.tbl CDD cd21651 cd21651 394925 ORF4b_MERS-CoV-like accessory protein ORF4b, also known as non-structural protein 3c (NS3c) in Middle East respiratory syndrome (MERS)-related CoV. This model represents the accessory protein 4b, ORF4b (also called NS3c protein) of Middle East respiratory syndrome (MERS)-related CoV, as well as some bat coronaviruses. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered to be dispensable for viral replication, however several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. ORF4b/NS3c plays a role in the inhibition of host innate immunity by inhibiting the interaction between host IkappaB kinase epsilion (IKBKE or IKKE) and mitochondrial antiviral-signalling protein (MAVS). In turn, this inhibition prevents the production of host interferon beta. Additionally, it may also interfere with host antiviral response within the nucleus. The MERS-CoV ORF4b (also known as MERS-CoV 4b) has been shown to interfere with the NF-kappaB-dependent innate immune response during infection, as well as antagonizing the early antiviral alpha/beta interferon (IFN-alpha/beta) response, which may significantly contribute to MERS-CoV pathogenesis. 239 matched cddid_all.tbl CDD cd21652 cd21652 394926 ORF4b_HKU4-CoV accessory protein ORF4b, also known as non-structural protein 3c (NS3c), of Tylonycteris bat coronavirus HKU4 and similar proteins. This model represents the accessory protein 4b, ORF4b (also called NS3c protein) of Tylonycteris bat coronavirus HKU4 and related bat coronaviruses including Tylonycteris pachypus bat coronavirus HKU4-related. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered to be dispensable for viral replication, however several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. ORF4b/NS3c plays a role in the inhibition of host innate immunity by inhibiting the interaction between host IkappaB kinase epsilion (IKBKE or IKKE) and mitochondrial antiviral-signalling protein (MAVS). In turn, this inhibition prevents the production of host interferon beta. Additionally, it may also interfere with host antiviral response within the nucleus. ORF4b/NS3c proteins in this subgroup are similar to the MERS-CoV ORF4b (also known as MERS-CoV 4b) which has been shown to interfere with the NF-kappaB-dependent innate immune response during infection, as well as antagonizing the early antiviral alpha/beta interferon (IFN-alpha/beta) response, which may significantly contribute to MERS-CoV pathogenesis. 256 matched cddid_all.tbl CDD cd21653 cd21653 394927 ORF4b_HKU5-CoV accessory protein ORF4b, also known as non-structural protein 3c (NS3c), of Pipistrellus bat coronavirus HKU5 and similar proteins. This model represents the accessory protein 4b, ORF4b (also called NS3c protein) of Pipistrellus bat coronavirus HKU5 and related bat coronaviruses including Pipistrellus abramus bat coronavirus HKU5-related. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered to be dispensable for viral replication, however several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. ORF4b/NS3c plays a role in the inhibition of host innate immunity by inhibiting the interaction between host IkappaB kinase epsilion (IKBKE or IKKE) and mitochondrial antiviral-signalling protein (MAVS). In turn, this inhibition prevents the production of host interferon beta. Additionally, it may also interfere with host antiviral response within the nucleus. ORF4b/NS3c proteins in this subgroup are similar to the MERS-CoV ORF4b (also known as MERS-CoV 4b) which has been shown to interfere with the NF-kappaB-dependent innate immune response during infection, as well as antagonizing the early antiviral alpha/beta interferon (IFN-alpha/beta) response, which may significantly contribute to MERS-CoV pathogenesis. 249 matched cddid_all.tbl CDD cd21654 cd21654 394941 embe-merbe_CoV_ORF8b_protein-I-like MERS-CoV ORF8b, BECV protein I, and related Embecovirus and Merbecovirus proteins. This family includes the ORF8b accessory protein from Middle East respiratory syndrome-related coronavirus (MERS-CoV) and related merbecoviruses (C lineage), and protein I (also known as accessory protein N2) from bovine enteritic coronavirus-F15 strain (BECV-F15) and related Embecoviruses (A lineage). The gene encoding ORF8b is an internal ORF that is overlapped by the N (nucleocapsid) protein gene (ORF8a), and the gene encoding protein I is included in the N gene as an alternative ORF. ORF8b and protein I appear to have no homologous proteins in Sarbecovirus (lineage B), which includes Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) and SARS-CoV-2 (2019 novel coronavirus, 2019-nCoV). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. MERS-CoV ORF8b and BECV-F15 protein I are not essential for viral replication. 104 matched cddid_all.tbl CDD cd21657 cd21657 394956 deltaCoV_Nsp14 nonstructural protein 14 of deltacoronavirus. Nonstructural protein 14 (Nsp14) of coronavirus (CoV) plays an important role in viral replication and transcription. It consists of 2 domains with different enzymatic activities: an N-terminal exoribonuclease (ExoN) domain and a C-terminal cap (guanine-N7) methyltransferase (N7-MTase) domain. ExoN is important for proofreading and therefore, the prevention of lethal mutations. The association of Nsp14 with Nsp10 stimulates its ExoN activity; the complex hydrolyzes double-stranded RNA in a 3' to 5' direction as well as a single mismatched nucleotide at the 3'-end mimicking an erroneous replication product. The Nsp10/Nsp14 complex may function in a replicative mismatch repair mechanism. N7-MTase functions in mRNA capping. Nsp14 can methylate GTP, dGTP as well as cap analogs GpppG, GpppA and m7GpppG. The accumulation of m7GTP or Nsp14 has been found to interfere with protein translation of cellular mRNAs. 508 matched cddid_all.tbl CDD cd21658 cd21658 394957 gammaCoV_Nsp14 nonstructural protein 14 of gammacoronavirus. Nonstructural protein 14 (Nsp14) of coronavirus (CoV) plays an important role in viral replication and transcription. It consists of 2 domains with different enzymatic activities: an N-terminal exoribonuclease (ExoN) domain and a C-terminal cap (guanine-N7) methyltransferase (N7-MTase) domain. ExoN is important for proofreading and therefore, the prevention of lethal mutations. The association of Nsp14 with Nsp10 stimulates its ExoN activity; the complex hydrolyzes double-stranded RNA in a 3' to 5' direction as well as a single mismatched nucleotide at the 3'-end mimicking an erroneous replication product. The Nsp10/Nsp14 complex may function in a replicative mismatch repair mechanism. N7-MTase functions in mRNA capping. Nsp14 can methylate GTP, dGTP as well as cap analogs GpppG, GpppA and m7GpppG. The accumulation of m7GTP or Nsp14 has been found to interfere with protein translation of cellular mRNAs. 518 matched cddid_all.tbl CDD cd21659 cd21659 394958 betaCoV_Nsp14 nonstructural protein 14 of betacoronavirus. Nonstructural protein 14 (Nsp14) of coronavirus (CoV) plays an important role in viral replication and transcription. It consists of 2 domains with different enzymatic activities: an N-terminal exoribonuclease (ExoN) domain and a C-terminal cap (guanine-N7) methyltransferase (N7-MTase) domain. ExoN is important for proofreading and therefore, the prevention of lethal mutations. The association of Nsp14 with Nsp10 stimulates its ExoN activity; the complex hydrolyzes double-stranded RNA in a 3' to 5' direction as well as a single mismatched nucleotide at the 3'-end mimicking an erroneous replication product. The Nsp10/Nsp14 complex may function in a replicative mismatch repair mechanism. N7-MTase functions in mRNA capping. Nsp14 can methylate GTP, dGTP as well as cap analogs GpppG, GpppA and m7GpppG. The accumulation of m7GTP or Nsp14 has been found to interfere with protein translation of cellular mRNAs. 519 matched cddid_all.tbl CDD cd21660 cd21660 394959 alphaCoV_Nsp14 nonstructural protein 14 of alphacoronavirus. Nonstructural protein 14 (Nsp14) of coronavirus (CoV) plays an important role in viral replication and transcription. It consists of 2 domains with different enzymatic activities: an N-terminal exoribonuclease (ExoN) domain and a C-terminal cap (guanine-N7) methyltransferase (N7-MTase) domain. ExoN is important for proofreading and therefore, the prevention of lethal mutations. The association of Nsp14 with Nsp10 stimulates its ExoN activity; the complex hydrolyzes double-stranded RNA in a 3' to 5' direction as well as a single mismatched nucleotide at the 3'-end mimicking an erroneous replication product. The Nsp10/Nsp14 complex may function in a replicative mismatch repair mechanism. N7-MTase functions in mRNA capping. Nsp14 can methylate GTP, dGTP as well as cap analogs GpppG, GpppA and m7GpppG. The accumulation of m7GTP or Nsp14 has been found to interfere with protein translation of cellular mRNAs. 510 matched cddid_all.tbl CDD cd21661 cd21661 394942 merbe_CoV_ORF8b-like MERS-CoV ORF8b protein and related Merbecovirus proteins. This subfamily includes the ORF8b accessory protein from Middle East respiratory syndrome-related coronavirus (MERS-CoV) and related merbecoviruses (C lineage). The gene encoding ORF8b is an internal ORF that is overlapped by the N (nucleocapsid) protein gene (ORF8a). ORF8b appear to have no homologous proteins in Sarbecovirus (lineage B), which includes Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) and SARS-CoV-2 (2019 novel coronavirus, 2019-nCoV). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. MERS-CoV ORF8b is not essential for viral replication. It is related to protein I (also known as accessory protein N2) of bovine enteritic coronavirus-F15 strain (BECV-F15) and other related Embecoviruses; the gene encoding protein I is included in the N gene as an alternative ORF. 104 matched cddid_all.tbl CDD cd21662 cd21662 394943 embe-CoV_Protein-I_like BECV protein I and related Embecovirus proteins. This subfamily includes protein I (also known as accessory protein N2) from bovine enteritic coronavirus-F15 strain (BECV-F15) and related Embecoviruses (A lineage) including murine hepatitis virus. The gene encoding protein I is included in the N gene as an alternative ORF. Protein I appears to have no homologous proteins in Sarbecovirus lineage B, which includes Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) and SARS-CoV-2 (2019 novel coronavirus, 2019-nCoV). There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. BECV-F15 protein I is not essential for viral replication. It is related to the ORF8b accessory protein of Middle East respiratory syndrome-related coronavirus (MERS-CoV) and other related merbecoviruses (C lineage); the gene encoding ORF8b is an internal ORF that is overlapped by the N (nucleocapsid) protein gene (ORF8a). 115 matched cddid_all.tbl CDD cd21663 cd21663 394934 ORF7a_SARS-CoV-like Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) structural accessory protein ORF7a and similar proteins from related betacoronaviruses in the subgenera Sarbecovirus (B lineage). This family contains the structural accessory protein ORF7a, also called NS7a, of Severe Acute Respiratory Syndrome Coronaviruses (SARS-CoVs) from betacoronavirus subgenera Sarbecovirus (lineage B), including SARS-CoV-2, also known as 2019-nCoV, and a bat coronavirus (BatCoV RaTG13), which was previously detected in Rhinolophus affinis from China's Yunnan province, as well as SARS-related virus from Rhinolophus bats in Europe and Kenya. ORF7a/NS7a from betacoronavirus in the subgenera Sarbecovirus (lineage B) are not related to NS7a proteins from other coronavirus lineages. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the ORF1ab (a large polyprotein known as replicase/protease); all required to produce a structurally complete viral particle. In addition, SARS-CoV contains a number of open reading frames that code for a total of eight accessory proteins, namely ORFs 3a, 3b, 6, 7a, 7b, 8a, 8b, and 9b. These ORFs are specific for SARS-CoV and do not show significant homology to accessory proteins of other coronaviruses. Structurally, ORF7a possesses a distinctive immunoglobulin (Ig)-like domain which is related to extracellular metazoan Ig domains that are involved in adhesion, such as ICAM; it also contains a 15-amino acid signal peptide sequence at its N terminus, an 81-amino acid luminal domain, a 21-amino acid transmembrane domain, and a short C-terminal tail. Co-expression of SARS-CoV ORF7a with S, M, N and E proteins resulted in production of virus-like particles (VLPs) carrying ORF7a protein, indicating that ORF7a is a viral structural protein. Expression studies of ORF7a have shown that biological functions include induction of apoptosis through a caspase-dependent pathway, activation of the p38 mitogen-activated protein kinase signaling pathway, inhibition of host protein translation, and suppression of cell growth progression. These results collectively suggested that ORF7a protein may be involved in virus-host interactions. 83 matched cddid_all.tbl CDD cd21664 cd21664 439224 SMP_C2CD2-like synaptotagmin-like mitochondrial-lipid-binding protein (SMP) domain found in C2 domain-containing protein 2-like (C2CD2L) and similar proteins. This family includes C2 domain-containing protein 2 (C2CD2) and C2CD2-like (C2CD2L). C2CD2 (also called transmembrane protein 24-like or TMEM24L), may be a lipid-binding protein that shows high sequence similarity with C2 domain-containing protein 2-like (C2CD2L; also called transmembrane protein 24 or TMEM24). C2CD2L is a lipid-binding protein that transports phosphatidylinositol, the precursor of phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), from its site of synthesis in the endoplasmic reticulum (ER) to the cell membrane. It is a Ca2+-regulated component of ER-plasma membrane contacts in mammalian neurons. This model corresponds to the SMP domain of C2CD2 and C2CD2L which binds glycerolipids with a preference for phosphatidylinositol (PI). The bound PI is then transferred to the plasma membrane (PM) where it is converted to phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2] to replenish pools of this lipid hydrolyzed during glucose-stimulated signaling. PI(4,5)P2 is required for Ca2+-dependent exocytosis; hence, the SMP domain of TMEM24 is essential for sustaining the intracellular Ca2+ oscillations that trigger bursts of insulin granule release and subsequent insulin secretion. 175 matched cddid_all.tbl CDD cd21665 cd21665 394886 alphaCoV_Nsp5_Mpro alphacoronavirus non-structural protein 5, also called Main protease (Mpro). This subfamily contains the coronavirus (CoV) non-structural protein 5 (Nsp5) also called the Main protease (Mpro), or 3C-like protease (3CLpro), found in alphacoronaviruses. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Mpro/Nsp5 is a key enzyme in this process, making it a high value target for the development of anti-coronavirus therapeutics. These enzymes belong to the MEROPS peptidase C30 family, where the active site residues His and Cys form a catalytic dyad. The structures of Mpro/Nsp5 consist of three domains with the first two containing anti-parallel beta barrels and the third consisting of an arrangement of alpha-helices. The catalytic residues are found in a cleft between the first two domains. Mpro/Nsp5 requires a Gln residue in the P1 position of the substrate and space for only small amino-acid residues such as Gly, Ala, or Ser in the P1' position; since there is no known human protease with a specificity for Gln at the cleavage site of the substrate, these viral proteases are suitable targets for the development of antiviral drugs. 296 matched cddid_all.tbl CDD cd21666 cd21666 394887 betaCoV_Nsp5_Mpro betacoronavirus non-structural protein 5, also called Main protease (Mpro). This subfamily contains the coronavirus (CoV) non-structural protein 5 (Nsp5) also called the Main protease (Mpro), or 3C-like protease (3CLpro), found in betacoronaviruses. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Mpro/Nsp5 is a key enzyme in this process, making it a high value target for the development of anti-coronavirus therapeutics. These enzymes belong to the MEROPS peptidase C30 family, where the active site residues His and Cys form a catalytic dyad. The structures of Mpro/Nsp5 consist of three domains with the first two containing anti-parallel beta barrels and the third consisting of an arrangement of alpha-helices. The catalytic residues are found in a cleft between the first two domains. Mpro requires a Gln residue in the P1 position of the substrate and space for only small amino-acid residues such as Gly, Ala, or Ser in the P1' position; since there is no known human protease with a specificity for Gln at the cleavage site of the substrate, these viral proteases are suitable targets for the development of antiviral drugs. 297 matched cddid_all.tbl CDD cd21667 cd21667 394888 gammaCoV_Nsp5_Mpro gammacoronavirus non-structural protein 5, also called Main protease (Mpro). This subfamily contains the coronavirus (CoV) non-structural protein 5 (Nsp5) also called the Main protease (Mpro), or 3C-like protease (3CLpro), found in gammacoronaviruses. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Mpro/Nsp5 is a key enzyme in this process, making it a high value target for the development of anti-coronavirus therapeutics. These enzymes belong to the MEROPS peptidase C30 family, where the active site residues His and Cys form a catalytic dyad. The structures of Mpro/Nsp5 consist of three domains with the first two containing anti-parallel beta barrels and the third consisting of an arrangement of alpha-helices. The catalytic residues are found in a cleft between the first two domains. Mpro/Nsp5 requires a Gln residue in the P1 position of the substrate and space for only small amino-acid residues such as Gly, Ala, or Ser in the P1' position; since there is no known human protease with a specificity for Gln at the cleavage site of the substrate, these viral proteases are suitable targets for the development of antiviral drugs. 306 matched cddid_all.tbl CDD cd21668 cd21668 394889 deltaCoV_Nsp5_Mpro deltacoronavirus non-structural protein 5, also called Main protease (Mpro). This subfamily contains the coronavirus (CoV) non-structural protein 5 (Nsp5) also called the Main protease (Mpro), or 3C-like protease (3CLpro), found in deltacoronaviruses. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Mpro/Nsp5 is a key enzyme in this process, making it a high value target for the development of anti-coronavirus therapeutics. These enzymes belong to the MEROPS peptidase C30 family, where the active site residues His and Cys form a catalytic dyad. The structures of Mpro/Nsp5 consist of three domains with the first two containing anti-parallel beta barrels and the third consisting of an arrangement of alpha-helices. The catalytic residues are found in a cleft between the first two domains. Mpro/Nsp5 requires a Gln residue in the P1 position of the substrate and space for only small amino-acid residues such as Gly, Ala, or Ser in the P1' position; since there is no known human protease with a specificity for Gln at the cleavage site of the substrate, these viral proteases are suitable targets for the development of antiviral drugs. 302 matched cddid_all.tbl CDD cd21669 cd21669 439225 SMP_SF synaptotagmin-like mitochondrial-lipid-binding protein (SMP) domain superfamily. The SMP domain is a lipid transport domain found in phospholipid transfer proteins such as synaptotagmin family proteins, tricalbin (TCB) family proteins, maintenance of mitochondrial morphology protein 1 (MMM1), mitochondrial distribution and morphology protein 12 (MDM12), mitochondrial distribution and morphology protein 34 (MDM34), PDZ domain-containing protein 8 (PDZD8), testis-expressed protein 2 (TEX2), meiotically up-regulated gene 190 protein (Mug190), C2 domain-containing protein 2 (C2CD2) and C2 domain-containing protein 2-like (C2CD2L). The SMP domain belongs to a superfamily of lipid/hydrophobic ligand-binding domains called TULIP (tubular lipid-binding proteins). It adopts a TULIP fold with two alpha helices and a highly curved antiparallel beta sheet forming a cornucopia-like structure. 165 matched cddid_all.tbl CDD cd21670 cd21670 439226 SMP_ESyt synaptotagmin-like mitochondrial-lipid-binding protein (SMP) domain of the extended synaptotagmin (E-Syt) family. The extended synaptotagmin (E-Syt) family includes a group of Ca2+-regulated intrinsic membrane proteins, such as E-Syt1, E-Syt2 and E-Syt3. They are composed of an N-terminal endoplasmic reticulum (ER)-membrane anchor, a central SMP-domain, and five (E-Syt1) or three C-terminal cytoplasmic C2-domains (E-Syt2 and E-Syt3). The ER-membrane anchor and C2 domains are required for tethering, while the SMP domain is a lipid-binding domain that links the ER with other lipid bilayer-membranes within the cell. This model corresponds to the SMP domain, which has a beta-barrel structure like protein modules in the tubular-lipid-binding (TULIP) superfamily. It dimerizes to form an approximately 90-Angstrom-long cylinder traversed by a channel lined entirely with hydrophobic residues. The following two C2 domains then form arched structures flexibly linked to the SMP domain. 177 matched cddid_all.tbl CDD cd21671 cd21671 439227 SMP_Mmm1 synaptotagmin-like mitochondrial-lipid-binding protein (SMP) domain found in maintenance of mitochondrial morphology protein 1 (Mmm1) and similar proteins. Maintenance of mitochondrial morphology protein 1 (Mmm1), also called mitochondrial outer membrane protein Mmm1, or yeast mitochondrial escape protein 6 (YME6), is a mitochondrial outer membrane protein essential for establishing and maintaining the structure of mitochondria and maintenance of mtDNA nucleoids. It is a component of the ER-mitochondrion encounter structure/ mitochondrial distribution and morphology (ERMES/Mdm) complex, which serves as a molecular tether to connect the endoplasmic reticulum and mitochondria. Components of this complex are involved in the control of mitochondrial shape and protein biogenesis, and function in nonvesicular lipid trafficking between the ER and mitochondria. The Mdm12-Mmm1 subcomplex functions in the major beta-barrel assembly pathway that is responsible for biogenesis of all outer membrane beta-barrel proteins, and acts in a late step after the SAM complex. The Mdm10-Mdm12-Mmm1 subcomplex further acts in the TOM40-specific pathway after the action of the Mdm12-Mmm1 complex. This model corresponds to the SMP domain of Mmm1, which may be implicated in lipid transport. 216 matched cddid_all.tbl CDD cd21672 cd21672 439228 SMP_Mdm12 synaptotagmin-like mitochondrial-lipid-binding protein (SMP) domain found in mitochondrial distribution and morphology protein 12 (Mdm12) and similar proteins. Mitochondrial distribution and morphology protein 12 (Mdm12), also called mitochondrial inheritance component Mdm12, acts as a component of the endoplasmic reticulum-mitochondria encounter structure (ERMES)/Mdm complex, which serves as a molecular tether to connect the endoplasmic reticulum and mitochondria. Components of this complex are involved in the control of mitochondrial shape and protein biogenesis, and function in nonvesicular lipid trafficking between the endoplasmic reticulum (ER) and mitochondria. Mdm12 is required for the interaction of the ER-resident membrane protein Mmm1 and the outer mitochondrial membrane-resident beta-barrel protein Mdm10. The Mdm12-Mmm1 subcomplex functions in the major beta-barrel assembly pathway that is responsible for biogenesis of all mitochondrial outer membrane beta-barrel proteins, and acts in a late step after the SAM complex. The Mdm10-Mdm12-Mmm1 subcomplex further acts in the TOM40-specific pathway after the action of the Mdm12-Mmm1 complex. This model corresponds to the SMP domain of Mdm12, which adopts a head-to-head and tail-to-tail dimer configuration rather than existing solely as a monomer. It may be implicated in lipid transport. 206 matched cddid_all.tbl CDD cd21673 cd21673 439229 SMP_Mdm34 synaptotagmin-like mitochondrial-lipid-binding protein (SMP) domain found in mitochondrial distribution and morphology protein 34 (Mdm34) and similar proteins. Mitochondrial distribution and morphology protein 34 (Mdm34), also called mitochondrial outer membrane protein 2 (Mmm2), is a mitochondrial outer membrane protein required for yeast mitochondrial shape and maintenance of mtDNA nucleoids. It is a component of the ERMES/Mdm complex, which serves as a molecular tether to connect the endoplasmic reticulum (ER) and mitochondria. Components of this complex are involved in the control of mitochondrial shape and protein biogenesis, and function in nonvesicular lipid trafficking between the ER and mitochondria. Mdm34 is essential for the interaction of the ER-resident membrane protein Mmm1 and the outer mitochondrial membrane-resident beta-barrel protein Mdm10. This model corresponds to the SMP domain of Mdm34, which may be implicated in lipid transport. 193 matched cddid_all.tbl CDD cd21674 cd21674 439230 SMP_PDZD8 synaptotagmin-like mitochondrial-lipid-binding protein (SMP) domain found in PDZ domain-containing protein 8 (PDZD8) and similar proteins. PDZ domain-containing protein 8 (PDZD8), also called Sarcoma antigen NY-SAR-84/NY-SAR-104, is a molecular tethering protein that connects endoplasmic reticulum (ER) and mitochondria membranes. PDZD8-dependent endoplasmic reticulum-mitochondria membrane tethering is essential for ER-mitochondria Ca(2+) transfer. In neurons, PDZD8 is involved in the regulation of dendritic Ca(2+) dynamics by regulating mitochondrial Ca(2+) uptake in neurons. It plays an indirect role in the regulation of cell morphology and cytoskeletal organization. PDZD8 is also a novel Gag-interacting factor that promotes retroviral infection. It may act as a novel moesin-interacting cytoskeletal regulatory protein that suppresses infection by herpes simplex virus type 1 (HSV1). This model corresponds to the SMP domain of PDZD8, which may be implicated in lipid transport. 191 matched cddid_all.tbl CDD cd21675 cd21675 439231 SMP_TEX2 synaptotagmin-like mitochondrial-lipid-binding protein (SMP) domain found in testis-expressed protein 2 (TEX2) and similar proteins. testis-expressed protein 2 (TEX2), also called transmembrane protein 96 (TMEM96), is a transmembrane protein with uncharacterized biological function. Diseases associated with TEX2 include Wernicke-Korsakoff Syndrome. This model corresponds to the SMP domain of TEX2, which may be implicated in lipid transport. 186 matched cddid_all.tbl CDD cd21676 cd21676 439232 SMP_Mug190 synaptotagmin-like mitochondrial-lipid-binding protein (SMP) domain found in meiotically up-regulated gene 190 protein (Mug190) and similar proteins. Meiotically up-regulated gene 190 protein (Mug190) has a role in meiosis. This model corresponds to the SMP domain of Mug190, which may be implicated in lipid transport. 233 matched cddid_all.tbl CDD cd21677 cd21677 439233 SMP_SYT synaptotagmin-like mitochondrial-lipid-binding protein (SMP) domain found in the synaptotagmin family, mostly plants. The synaptotagmin family includes Arabidopsis thaliana synaptotagmins (AtSYT1-5) and similar proteins. AtSYT1, also called NTMC2T1.1, or synaptotagmin A (SYTA), plays an important role in maintaining plasma membrane integrity during freezing and osmotic stresses. It may function in membrane resealing during calcium-dependent freezing tolerance. It regulates endocytosis and endosome recycling at the plasma membrane and cell-to-cell trafficking of cabbage leaf curl virus (CaLCuV) and tobacco mosaic virus (TMV) movement proteins via plasmodesmata. AtSYT2, also called NTMC2T1.2, or synaptotagmin B (SYTB), may play an important role in regulating an unconventional protein trafficking from the cytosol to the extracellular matrix. AtSYT3 (also called NTMC2T1.3, or synaptotagmin C, or SYTC), AtSYT4 (also called NTMC2T2.2, or synaptotagmin D, or SYTD) and AtSYT5 (also called NTMC2T2.1, or synaptotagmin E, or SYTE) may also be involved in membrane trafficking. This model corresponds to the SMP domain of SYT family proteins, which may be implicated in lipid transport. 189 matched cddid_all.tbl CDD cd21678 cd21678 439234 SMP_TCB synaptotagmin-like mitochondrial-lipid-binding protein (SMP) domain found in the tricalbin (TCB) family. The tricalbin (TCB) family includes Saccharomyces cerevisiae TCB1-3 and similar proteins. They may play a role in membrane trafficking. This model corresponds to the SMP domain of TCB family proteins, which may be implicated in lipid transport. 203 matched cddid_all.tbl CDD cd21679 cd21679 439235 SMP_ESyt1 synaptotagmin-like mitochondrial-lipid-binding protein (SMP) domain found in extended synaptotagmin-1 (E-Syt1) and similar proteins. Extended synaptotagmin-1 (E-Syt1), also called membrane-bound C2 domain-containing protein (MBC2), binds glycerophospholipids in a barrel-like domain and may play a role in cellular lipid transport. It also binds calcium via the C2 domains and translocates to sites of contact between the endoplasmic reticulum and the cell membrane in response to increased cytosolic calcium levels. E-Syt1 tethers the endoplasmic reticulum to the cell membrane and promotes the formation of appositions between the endoplasmic reticulum and the cell membrane. E-Syt1 consists of an N-terminal endoplasmic reticulum (ER)-membrane anchor, a central SMP-domain, and five C-terminal cytoplasmic C2-domains. The ER-membrane anchor and C2 domains are required for tethering, and the SMP domain may be implicated in lipid transport. This model corresponds to the SMP domain. 176 matched cddid_all.tbl CDD cd21680 cd21680 439236 SMP_ESyt2 synaptotagmin-like mitochondrial-lipid-binding protein (SMP) domain found in extended synaptotagmin-2 (E-Syt2) and similar proteins. Extended synaptotagmin-2 (E-Syt2), also called Chr2Syt, tethers the endoplasmic reticulum to the cell membrane and promotes the formation of appositions between the endoplasmic reticulum and the cell membrane. It binds glycerophospholipids in a barrel-like domain and may play a role in cellular lipid transport. E-Syt2 plays a role in fibroblast growth factor (FGF) signaling via its role in the rapid internalization of FGFreceptor 1 (FGFR1) that has been activated by FGF1 binding; this occurs most likely via the AP-2 complex. E-Syt2 consists of an N-terminal endoplasmic reticulum (ER)-membrane anchor, a central SMP-domain, and three C-terminal cytoplasmic C2-domains. The ER-membrane anchor and C2 domains are required for tethering, and the SMP domain may be implicated in lipid transport. This model corresponds to SMP domain. 179 matched cddid_all.tbl CDD cd21681 cd21681 439237 SMP_ESyt3 synaptotagmin-like mitochondrial-lipid-binding protein (SMP) domain found in extended synaptotagmin-3 (E-Syt3) and similar proteins. Extended synaptotagmin-3 (E-Syt3), also called Chr3Syt, binds glycerophospholipids in a barrel-like domain and may play a role in cellular lipid transport. It tethers the endoplasmic reticulum to the cell membrane and promotes the formation of appositions between the endoplasmic reticulum and the cell membrane. E-Syt3 consists of an N-terminal endoplasmic reticulum (ER)-membrane anchor, a central SMP-domain, and three C-terminal cytoplasmic C2-domains. The ER-membrane anchor and C2 domains are required for tethering, and the SMP domain may be implicated in lipid transport. This model corresponds to the SMP domain. 177 matched cddid_all.tbl CDD cd21682 cd21682 439238 SMP_C2CD2 synaptotagmin-like mitochondrial-lipid-binding protein (SMP) domain found in C2 domain-containing protein 2 (C2CD2). C2CD2, also called transmembrane protein 24-like (TMEM24L), may be a lipid-binding protein that shows high sequence similarity with C2 domain-containing protein 2-like (C2CD2L; also transmembrane protein 24 or TMEM24). C2CD2L is a lipid-binding protein that transports phosphatidylinositol, the precursor of phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), from its site of synthesis in the endoplasmic reticulum to the cell membrane. It is a Ca2+-regulated component of endoplasmic reticulum (ER)-plasma membrane contacts in mammalian neurons. This model corresponds to the SMP domain of C2CD2, which may be implicated in lipid transport. 175 matched cddid_all.tbl CDD cd21683 cd21683 439239 SMP_C2CD2L synaptotagmin-like mitochondrial-lipid-binding protein (SMP) domain found in C2 domain-containing protein 2-like (C2CD2L). C2CD2L, also called phospholipid transfer protein C2CD2L, or C2CD2-like, or transmembrane protein 24 (TMEM24), is a lipid-binding protein that transports phosphatidylinositol, the precursor of phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2), from its site of synthesis in the endoplasmic reticulum to the cell membrane. It is a Ca2+-regulated component of endoplasmic reticulum (ER)-plasma membrane contacts in mammalian neurons. This model corresponds to the SMP domain of C2CD2L, which may be implicated in lipid transport. 177 matched cddid_all.tbl CDD cd21684 cd21684 394935 ORF7a_SARS-CoV-2-like Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) structural accessory protein ORF7a and a bat coronavirus (BatCoV RaTG13) from related betacoronaviruses in the subgenera Sarbecovirus (B lineage). This group contains the structural accessory protein ORF7a, also called NS7a, of Severe Acute Respiratory Syndrome Coronaviruses (SARS-CoV) from betacoronavirus subgenera Sarbecovirus (lineage B), including SARS-CoV-2, also known as 2019-nCoV, and a bat coronavirus (BatCoV RaTG13), which was previously detected in Rhinolophus affinis from China's Yunnan province. ORF7a/NS7a from betacoronavirus in the subgenera Sarbecovirus (B lineage) are not related to NS7a proteins from other coronavirus lineages. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the ORF1ab (a large polyprotein known as replicase/protease); all required to produce a structurally complete viral particle. In addition, SARS-CoV contains a number of open reading frames that code for a total of eight accessory proteins, namely ORFs 3a, 3b, 6, 7a, 7b, 8a, 8b, and 9b. These ORFs are specific for SARS-CoV and do not show significant homology to accessory proteins of other coronaviruses. Structurally, ORF7a possesses a distinctive immunoglobulin (Ig)-like domain which is related to extracellular metazoan Ig domains that are involved in adhesion, such as ICAM; it also contains a 15-aa signal peptide sequence at its N terminus, an 81-aa luminal domain, a 21-aa transmembrane domain, and a short C-terminal tail. Coexpression of SARS-CoV ORF7a with S, M, N, and E proteins resulted in production of virus-like particles (VLPs) carrying ORF7a protein, indicating that ORF7a is a viral structural protein. Expression studies of ORF7a have shown that biological functions include induction of apoptosis through a caspase-dependent pathway, activation of the p38 mitogen-activated protein kinase signaling pathway, inhibition of host protein translation, and suppression of cell growth progression. These results collectively suggested that ORF7a protein may be involved in virus-host interactions. 121 matched cddid_all.tbl CDD cd21685 cd21685 394936 ORF7a_SARS-CoV-like Severe Acute Respiratory Syndrome coronavirus (SARS-CoV-2) structural accessory protein ORF7a and similar proteins from betacoronaviruses in the subgenera Sarbecovirus (B lineage). This group contains the structural accessory protein ORF7a, also called NS7a, of Severe Acute Respiratory Syndrome Coronaviruses (SARS-CoVs) from betacoronavirus subgenera Sarbecovirus (lineage B). ORF7a/NS7a from betacoronavirus in the subgenera Sarbecovirus (B lineage) are not related to NS7a proteins from other coronavirus lineages. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and the ORF1ab (a large polyprotein known as replicase/protease); all required to produce a structurally complete viral particle. In addition, SARS-CoV contains a number of open reading frames that code for a total of eight accessory proteins, namely ORFs 3a, 3b, 6, 7a, 7b, 8a, 8b, and 9b. These ORFs are specific for SARS-CoV and do not show significant homology to accessory proteins of other coronaviruses. Structurally, ORF7a possesses a distinctive immunoglobulin (Ig)-like domain which is related to extracellular metazoan Ig domains that are involved in adhesion, such as ICAM; it also contains a 15-aa signal peptide sequence at its N terminus, an 81-aa luminal domain, a 21-aa transmembrane domain, and a short C-terminal tail. Coexpression of SARS-CoV ORF7a with S, M, N, and E proteins resulted in production of virus-like particles (VLPs) carrying ORF7a protein, indicating that ORF7a is a viral structural protein. Expression studies of ORF7a have shown that biological functions include induction of apoptosis through a caspase-dependent pathway, activation of the p38 mitogen-activated protein kinase signaling pathway, inhibition of host protein translation, and suppression of cell growth progression. These results collectively suggested that ORF7a protein may be involved in virus-host interactions. 83 matched cddid_all.tbl CDD cd21686 cd21686 409657 TM_Y_CoV_Nsp3_C C-terminus of coronavirus non-structural protein 3, including transmembrane and Y domains. This model represents the C-terminus of non-structural protein 3 (Nsp3) from alpha-, beta-, gamma-, and deltacoronavirus, including highly pathogenic betacoronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. This conserved C-terminus includes two transmembrane (TM) regions TM1 and TM2, an ectodomain (3Ecto) between the TM1 and TM2 that is glycosylated and located on the lumenal side of the ER, an amphiphatic region (AH1) that is not membrane-spanning, and a large Y domain of approximately 370 residues. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. In SARS-CoV and murine hepatitis virus (MHV), the TM1, 3Ecto and TM2 domains are important for the papain-like protease (PL2pro) domain to process Nsp3-Nsp4 cleavage. It has also been shown that the interaction of 3Ecto with the lumenal loop of Nsp4 is essential for ER rearrangements in cells infected with SARS-CoV or MHV. The Y domain, located at the cytosolic side of the ER, consists of the Y1 and CoV-Y subdomains, which are conserved in nidovirus and coronavirus, respectively. Functional information about the Y domain is limited; it has been shown that Nsp3 binding to Nsp4 is less efficient without the Y domain. 476 matched cddid_all.tbl CDD cd21687 cd21687 439284 TGEV-like_alphaCoV_Nsp1 non-structural protein 1 from transmissible gastroenteritis virus and similar alphacoronaviruses. This model represents the non-structural protein 1 (Nsp1) from transmissible gastroenteritis virus (TGEV) and similar alphacoronaviruses from the tegacovirus and minacovirus subgenera. CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. Nsp1 is the N-terminal cleavage product released from the ORF1a polyprotein by the action of papain-like protease (PLpro). Though Nsp1s of alphaCoVs and betaCoVs share structural similarity, they show no significant sequence similarity and may be considered as genus-specific markers. Despite low sequence similarity, the Nsp1s of alphaCoVs and betaCoVs exhibit remarkably similar biological functions, and are involved in the regulation of both host and viral gene expression. CoV Nsp1 induces suppression of host gene expression and interferes with host immune response. It inhibits host gene expression in two ways: by targeting the translation and stability of cellular mRNAs, and by inhibiting mRNA translation and inducing an endonucleolytic RNA cleavage in the 5'-UTR of cellular mRNAs through its tight association with the 40S ribosomal subunit, a key component of the cellular translation machinery. Inhibition of host mRNA translation includes that of type I interferons, major components of the host innate immune response. Nsp1 is critical in regulating viral replication and gene expression, as shown by multiple evidences, including: mutations in the Nsp1 coding region of the TGEV and murine hepatitis virus (MHV) genomes cause drastic reduction or elimination of infectious virus; bovine coronavirus (BCoV) Nsp1 is an RNA-binding protein that interacts with cis-acting replication elements in the 5'-UTR of the BCoV genome, implying its potential role in the regulation of viral translation or replication; and SARS-CoV Nsp1 enhances virus replication by binding to a stem-loop structure in the 5'-UTR of its genome. 104 matched cddid_all.tbl CDD cd21688 cd21688 409647 CoV_PLPro Coronavirus (CoV) papain-like protease (PLPro). This model represents the papain-like protease (PLPro) found in non-structural protein 3 (Nsp3) of alpha-, beta-, gamma-, and deltacoronavirus, including highly pathogenic betacoronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. PLPro is a key enzyme in this process, making it a high value target for the development of anti-coronavirus therapeutics. PLPro, which belongs to the MEROPS peptidase C16 family, participates in the proteolytic processing of the N-terminal region of the replicase polyprotein; it can cleave Nsp1|Nsp2, Nsp2|Nsp3, and Nsp3|Nsp4 sites and its activity is dependent on zinc. Besides cleaving the polyproteins, PLPro also possesses a related enzymatic activity to promote virus replication: deubiquitinating (DUB) and de-ISGylating activities. Both, ubiquitin (Ub) and Ub-like interferon-stimulated gene product 15 (ISG15), are involved in preventing viral infection; coronaviruses utilize Ubl-conjugating pathways to counter the pro-inflammatory properties of Ubl-conjugated host proteins via the action of PLPro, which processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. The Nsp3 PLPro domain in many of these CoVs has also been shown to antagonize host innate immune induction of type I interferon by interacting with IRF3 and blocking its activation. 299 matched cddid_all.tbl CDD cd21689 cd21689 410205 stalk_CoV_Nsp13-like stalk domain of coronavirus Nsp13 helicase and related proteins. This model represents the stalk domain of coronavirus non-structural protein 13 (Nsp13) helicase, found in the Nsp3s of alpha-, beta-, gamma-, and deltacoronaviruses, including Severe Acute Respiratory Syndrome coronavirus (SARS-CoV), SARS-CoV-2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome coronavirus (MERS-CoV). Helicases are classified based on the arrangement of conserved motifs into six superfamilies; coronavirus helicases in this family belong to superfamily 1 (SF1). Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It consists of an N-terminal ZBD (Cys/His rich zinc-binding domain), a stalk domain, a 1B regulatory domain, and SF1 helicase core. The stalk domain lies between the ZBD domain and the 1B domain; a short loop connects the ZBD to the stalk domain. The stalk domain is comprised of three tightly-interacting alpha-helices connected to the 1B domain, transferring the effect from the ZBD domain onto the helicase core domains. The ZBD and stalk domains are critical for the helicase activity of SARS-CoV Nsp13. 48 matched cddid_all.tbl CDD cd21690 cd21690 409667 GH2_like GIPC homology 2 (GH2) domain-like family. The GIPC (GAIP C-terminus-interacting protein) family of proteins mediate endocytosis by tethering cargo proteins to the motor myosin VI. This model represents the C-terminal GIPC homology 2 or GH2 domain (plus the linker to the PDZ domain located N-terminally of GH2), which mediates the interaction with myosin VI and is involved in homodimerization in the autoinhibited state. The family also includes DEAH box protein 8 (DHX8) and similar proteins. DHX8 (a human homolog of yeast Prp22), also called RNA helicase HRH1, is an ATP-dependent RNA helicase involved in pre-mRNA splicing as a component of the spliceosome. It facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 contains a GH2-like domain at the N-terminus, which shows high sequence similarity with the GH2 domain found in GIPC proteins. 62 matched cddid_all.tbl CDD cd21691 cd21691 409668 GH2-like_DHX8 GIPC-homology 2 (GH2)-like domain found in DEAH box protein 8 (DHX8) and similar proteins. DHX8 (a human homolog of yeast Prp22), also called RNA helicase HRH1, is an ATP-dependent RNA helicase involved in pre-mRNA splicing as a component of the spliceosome. It facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. This model corresponds to the GH2-like domain that shows high sequence similarity with the GH2 domain found in GIPC (GAIP C-terminus-interacting protein) family of proteins, which mediate endocytosis by tethering cargo proteins to the motor myosin VI. 68 matched cddid_all.tbl CDD cd21692 cd21692 412028 GINS_B_Sld5 beta-strand (B) domain of GINS complex protein Sld5. Sld5 is a component of the GINS (named from the Japanese go-ichi-ni-san, meaning 5-1-2-3 for the Sld5, Psf1, Psf2, and Psf3 subunits) tetrameric protein complex, within which Sld5 interacts with Psf1 via its N-terminal A-domain, and with Psf2 through a combination of the A and B domains. In Drosophila, Sld5 is required for normal cell cycle progression and the maintenance of genomic integrity. GINS is a complex of four subunits (Sld5, Psf1, Psf2 and Psf3) that is involved in both initiation and elongation stages of eukaryotic chromosome replication. Besides being essential for the maintenance of genomic integrity, GINS plays a central role in coordinating DNA replication with cell cycle checkpoints and is involved in cell growth. The eukaryotic GINS subunits Sld5, Psf1, Psf2 and Psf3 are homologous, and homologs are also found in archaea; the complex is not found in bacteria. Each subunit of the complex consists of two domains called the alpha-helical (A) and beta-strand (B) domains. The A and B domains of Sld5/Psf1 are permuted with respect to Psf1/Psf3. This model represents the B-domain of GINS subunit Sld5. 55 matched cddid_all.tbl CDD cd21693 cd21693 412029 GINS_B_Psf3 beta-strand (B) domain of GINS complex protein Psf3. Psf3 (partner of Sld5 3) is one of the proteins known to comprise the GINS (named from the Japanese go-ichi-ni-san, meaning 5-1-2-3 for the Sld5, Psf1, Psf2, and Psf3 subunits) complex, which is a macromolecular protein complex associated with DNA replication. Psf3 is dysregulated in cancer cells, and its overexpression may be related to tumor progression in some cancers including colon, breast, and lung cancers; its expression can be used as a prognostic indicator in some cancers. GINS is a complex of four subunits (Sld5, Psf1, Psf2 and Psf3) that is involved in both the initiation and elongation stages of eukaryotic chromosome replication. Besides being essential for the maintenance of genomic integrity, GINS plays a central role in coordinating DNA replication with cell cycle checkpoints and is involved in cell growth. The eukaryotic GINS subunits Sld5, Psf1, Psf2, and Psf3 are homologous, and homologs are also found in archaea; the complex is not found in bacteria. The four subunits of the complex consist of two domains each, called the alpha-helical (A) and beta-strand (B) domains. The A and B domains of Sld5/Psf1 are permuted with respect to Psf1/Psf3. This model represents the B-domain of GINS subunit Psf3. 64 matched cddid_all.tbl CDD cd21694 cd21694 412030 GINS_B_Psf2 beta-strand (B) domain of GINS complex protein Psf2. Psf2 (partner of Sld5 2) is a component of GINS (named from the Japanese go-ichi-ni-san, meaning 5-1-2-3 for the Sld5, Psf1, Psf2, and Psf3 subunits) tetrameric protein complex and has been found to play important roles in normal eye development in Xenopus laevis and in ICL (interstrand crosslinks) repair. ICLs are toxic lesions that covalently attach opposite strands of DNA. GINS is a complex of four subunits (Sld5, Psf1, Psf2 and Psf3) and is involved in both the initiation and elongation stages of eukaryotic chromosome replication. Besides being essential for the maintenance of genomic integrity, GINS plays a central role in coordinating DNA replication with cell cycle checkpoints and is involved in cell growth. The eukaryotic GINS subunits Sld5, Psf1, Psf2, and Psf3 are homologous, and homologs are also found in archaea; the complex is not found in bacteria. The four subunits of the complex consist of two domains each, called the alpha-helical (A) and beta-strand (B) domains. The A and B domains of Sld5/Psf1 are permuted with respect to Psf1/Psf3. This model represents the B-domain of GINS subunit Psf2. 62 matched cddid_all.tbl CDD cd21695 cd21695 412031 GINS_B_archaea_Gins51 beta-strand (B) domain of archaeal GINS complex protein Gins51. The GINS (named from the Japanese go-ichi-ni-san, meaning 5-1-2-3 for the Sld5, Psf1, Psf2, and Psf3 subunits) complex is involved in both initiation and elongation stages of eukaryotic chromosome replication, with GINS being the component that most likely serves as the replicative helicase that unwinds duplex DNA ahead of the moving replication fork. In archaeal DNA replication initiation, homo-hexameric MCM (mini-chromosome maintenance) unwinds the template double-stranded DNA to form the replication fork. MCM is activated by two proteins GINS and GAN (GINS-associated nuclease), which constitute the 'CMG' unwindosome complex together with the MCM core. While eukaryotic GINS complex is a tetrameric arrangement of four subunits Sld5, Psf1, Psf2 and Psf3, the archaeal complex consists of two different proteins, namely Gins51 and Gins23, and forms either an alpha2beta2-type heterotetramer composed of Gins51 and Gins23, or a Gins51-only alpha4-type homotetramer. The archaeal Gins51, as well as eukaryotic Sld5 and Psf1) have the alpha-helical (A) domain at the N-terminus and the beta-strand domain (B) at the C-terminus; this arrangement is called ABtype. Archaeal GINS contacts GAN by using the Gins51 B-domain as a hook, for the formation of the CMG helicase. The locations and contributions of the archaeal Gins subunit B domain to the tetramer formation, imply the possibility that the archaeal and eukaryotic GINS complexes contribute to DNA unwinding reactions by significantly different mechanisms in terms of the atomic details. This model represents the B-domain of Gins51. 52 matched cddid_all.tbl CDD cd21696 cd21696 412032 GINS_B_Psf1 beta-strand (B) domain of GINS complex protein Psf1. Psf1 (partner of Sld5 1) is a component of the GINS (named from the Japanese go-ichi-ni-san, meaning 5-1-2-3 for the Sld5, Psf1, Psf2, and Psf3 subunits) tetrameric protein complex, and is mainly expressed in highly proliferative tissues, such as blastocysts, adult bone marrow, and testis, in which the stem cell system is active. Psf1 has been reported to be a prognostic biomarker in breast cancer, prostate cancer, hepatocellular carcinoma, and non-small cell lung cancer (NSCLC) patients treated with surgery following preoperative chemotherapy or chemoradiotherapy. Loss of Psf1 causes embryonic lethality. GINS is a complex of four subunits (Sld5, Psf1, Psf2 and Psf3) and is involved in both the initiation and elongation stages of eukaryotic chromosome replication. Besides being essential for the maintenance of genomic integrity, GINS plays a central role in coordinating DNA replication with cell cycle checkpoints and is involved in cell growth. The eukaryotic GINS subunits Sld5, Psf1, Psf2 and Psf3 are homologous, and homologs are also found in archaea; the complex is not found in bacteria. The four subunits of the complex consist of two domains each, called the alpha-helical (A) and beta-strand (B) domains. The A and B domains of Sld5/Psf1 are permuted with respect to Psf1/Psf3. This model represents the B-domain of GINS subunit Psf1. 49 matched cddid_all.tbl CDD cd21697 cd21697 412033 GINS_B_archaea_Gins23 beta-strand (B) domain of archaeal GINS complex protein Gins23. The GINS (named from the Japanese go-ichi-ni-san, meaning 5-1-2-3 for the Sld5, Psf1, Psf2, and Psf3 subunits) complex is involved in both initiation and elongation stages of eukaryotic chromosome replication, with GINS being the component that most likely serves as the replicative helicase that unwinds duplex DNA ahead of the moving replication fork. In archaeal DNA replication initiation, homo-hexameric MCM (mini-chromosome maintenance) unwinds the template double-stranded DNA to form the replication fork. MCM is activated by two proteins GINS and GAN (GINS-associated nuclease), which constitute the 'CMG' unwindosome complex together with the MCM core. While eukaryotic GINS complex is a tetrameric arrangement of four subunits Sld5, Psf1, Psf2 and Psf3, the archaeal complex consists of two different proteins, namely Gins51 and Gins23, and forms either an alpha2beta2-type heterotetramer composed of Gins51 and Gins23, or a Gins51-only alpha4-type homotetramer. The archaeal Gins23, as well as eukaryotic Psf2 and Psf3, have the alpha-helical (A) domain at the C-terminus and the beta-strand domain (B) at the N-terminus; this arrangement is called BAtype. The locations and contributions of the archaeal Gins subunit B domain to the tetramer formation, imply the possibility that the archaeal and eukaryotic GINS complexes contribute to DNA unwinding reactions by significantly different mechanisms in terms of the atomic details. This model represents the B-domain of archaeal Gins23. 42 matched cddid_all.tbl CDD cd21698 cd21698 411955 CoV_Spike_S1-S2_S2 S1/S2 cleavage region and the S2 fusion subunit of coronavirus spike (S) proteins. This model represents the S1/S2 cleavage region and the S2 subunit of the spike (S) glycoprotein from coronavirus (CoVs), including three highly pathogenic human CoVs, Middle East respiratory syndrome coronavirus (MERS-CoV), Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), and SARS coronavirus 2 (SARS-CoV-2), also known as a 2019 novel coronavirus (2019-nCoV). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-terminal domain (C-domain). S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect S1 and S2. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV, and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP), and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. Notably, SARS-CoV-2 has a functional polybasic (furin) cleavage site through the insertion of PRRAR*SV (* indicates the cleavage site) at the S1/S2 interface, which is absent in SARS-CoV and other SARS-related CoVs. The S1/S2 cleavage region and the S2 fusion subunit play an essential role in viral entry by initiating fusion of the viral and cellular membranes. 523 matched cddid_all.tbl CDD cd21699 cd21699 411982 JMTM_APP_like juxtamembrane and transmembrane (JMTM) domain found in the amyloid-beta precursor protein (APP) family. The amyloid-beta precursor protein (APP) family includes amyloid-like proteins APLP-1 and APLP-2. APP (also called ABPP, APPI, Alzheimer disease (AD) amyloid protein, amyloid precursor protein, amyloid-beta A4 protein, cerebral vascular amyloid peptide (CVAP), PreA4, or protease nexin-II (PN-II)) functions as a cell surface receptor and performs physiological functions on the surface of neurons relevant to neurite growth, neuronal adhesion and axonogenesis. Amyloid-beta peptides are lipophilic metal chelators with metal-reducing activity; they bind transient metals such as copper, zinc and iron. APLP-1, also called APLP, may play a role in postsynaptic function. It couples to JIP signal transduction through C-terminal binding. APLP-1 may interact with cellular G-protein signaling pathways. It can regulate neurite outgrowth through binding to components of the extracellular matrix such as heparin and collagen I. APLP-2 (also called amyloid protein homolog (APPH), or CDEI box-binding protein (CDEBP)) may play a role in the regulation of hemostasis. Its soluble form may have inhibitory properties towards coagulation factors. APLP-2 may bind to the DNA 5'-GTCACATG-3'(CDEI box). It inhibits trypsin, chymotrypsin, plasmin, factor XIA, and plasma and glandular kallikrein. This model corresponds to juxtamembrane and transmembrane (JMTM) domain of APP, which consists of the intact transmembrane (TM) domain with adjacent N-terminal juxtamembrane (JM) region. More than half of all familial APP mutations of Alzheimer's disease are seen in its JMTM domain region. 41 matched cddid_all.tbl CDD cd21700 cd21700 411983 JMTM_Notch_APP juxtamembrane and transmembrane (JMTM) domain found in Notch and APP family proteins. The substrates of gamma-secretase include amyloid precursor protein (APP) and the Notch receptor. APP, also called APPI, or Alzheimer disease amyloid protein (ABPP), or amyloid precursor protein, or amyloid-beta A4 protein, or cerebral vascular amyloid peptide (CVAP), or PreA4, or protease nexin-II (PN-II), functions as a cell surface receptor and performs physiological functions on the surface of neurons relevant to neurite growth, neuronal adhesion and axonogenesis. Notch proteins are a family of type-1 transmembrane proteins that form a core component of the Notch signaling pathway. They operate in a variety of different tissues and play a role in a variety of developmental processes by controlling cell fate decisions. Successive cleavage of the APP carboxyl-terminal fragment generates amyloid-beta (Abeta) peptides of varying lengths. Accumulation of Abeta peptides such as Abeta42 and Abeta43 leads to formation of amyloid plaques in the brain, a hallmark of Alzheimer's disease. Notch cleavage is involved in cell-fate determination during development and neurogenesis. The model corresponds to the juxtamembrane and transmembrane (JMTM) domain found in Notch and APP family proteins. It comprises a transmembrane helix (TM) with adjacent juxtamembrane (JM) regions. The JMTM domain is likely to be recognized by gamma-secretase in a similar fashion to both Notch and APP family proteins. 41 matched cddid_all.tbl CDD cd21701 cd21701 411984 JMTM_Notch juxtamembrane and transmembrane (JMTM) domain found in Notch protein family. Neurogenic locus notch homolog (Notch) proteins are a family of type-1 transmembrane proteins that form a core component of the Notch signaling pathway. They operate in a variety of different tissues and play a role in a variety of developmental processes by controlling cell fate decisions. The model corresponds to the juxtamembrane and transmembrane (JMTM) domain of Notch proteins, which comprises an extended coil, a transmembrane helix (TM), and a beta-strand. 85 matched cddid_all.tbl CDD cd21702 cd21702 411985 JMTM_Notch1 juxtamembrane and transmembrane (JMTM) domain found in neurogenic locus notch homolog protein 1 (Notch1) and similar proteins. Neurogenic locus notch homolog protein 1 (Notch1), also called translocation-associated notch protein TAN-1, functions as a receptor for membrane-bound ligands Jagged-1 (JAG1), Jagged-2 (JAG2) and Delta-1 (DLL1) to regulate cell-fate determination. It affects the implementation of differentiation, proliferation and apoptotic programs. It is also involved in angiogenesis, and also negatively regulates endothelial cell proliferation and migration and angiogenic sprouting. This model corresponds to the juxtamembrane and transmembrane (JMTM) domain of Notch1, which comprises an extended coil, a transmembrane helix (TM), and a beta-strand. 80 matched cddid_all.tbl CDD cd21703 cd21703 411986 JMTM_Notch2 juxtamembrane and transmembrane (JMTM) domain found in neurogenic locus notch homolog protein 2 (Notch2) and similar proteins. Neurogenic locus notch homolog protein 2 (Notch2) functions as a receptor for membrane-bound ligands Jagged-1 (JAG1), Jagged-2 (JAG2) and Delta-1 (DLL1) to regulate cell-fate determination. Upon ligand activation through the released notch intracellular domain (NICD) it forms a transcriptional activator complex with RBPJ/RBPSUH and activates genes of the enhancer of split locus. Notch2 is involved in bone remodeling and homeostasis. In collaboration with RELA/p65, it enhances NFATc1 promoter activity and positively regulates RANKL-induced osteoclast differentiation. Notch2 positively regulates self-renewal of liver cancer cells. This model corresponds to the juxtamembrane and transmembrane (JMTM) domain of Notch2, which comprises an extended coil, a transmembrane helix (TM), and a beta-strand. 82 matched cddid_all.tbl CDD cd21704 cd21704 411987 JMTM_Notch3 juxtamembrane and transmembrane (JMTM) domain found in neurogenic locus notch homolog protein 3 (Notch3) and similar proteins. Neurogenic locus notch homolog protein 3 (Notch3) functions as a receptor for membrane-bound ligands Jagged1, Jagged2 and Delta1 to regulate cell-fate determination. Upon ligand activation through the released notch intracellular domain (NICD) it forms a transcriptional activator complex with RBPJ/RBPSUH and activates genes of the enhancer of split locus. The model corresponds to the juxtamembrane and transmembrane (JMTM) domain of Notch3, which comprises an extended coil, a transmembrane helix (TM), and a beta-strand. 90 matched cddid_all.tbl CDD cd21705 cd21705 411988 JMTM_Notch4 juxtamembrane and transmembrane (JMTM) domain found in neurogenic locus notch homolog protein 4 (Notch4) and similar proteins. Neurogenic locus notch homolog protein 4 (Notch4) functions as a receptor for membrane-bound ligands Jagged1, Jagged2 and Delta1 to regulate cell-fate determination. Upon ligand activation through the released notch intracellular domain (NICD) it forms a transcriptional activator complex with RBPJ/RBPSUH and activates genes of the enhancer of split locus. It affects the implementation of differentiation, proliferation and apoptotic programs. This model corresponds to the juxtamembrane and transmembrane (JMTM) domain of Notch4, which comprises an extended coil, a transmembrane helix (TM), and a beta-strand. 92 matched cddid_all.tbl CDD cd21706 cd21706 411989 JMTM_dNotch juxtamembrane and transmembrane (JMTM) domain found in Drosophila melanogaster neurogenic locus Notch protein (dNotch) and similar proteins. Drosophila melanogaster neurogenic locus Notch protein (dNotch) is an essential signaling protein which has a major role in many developmental processes. It functions as a receptor for membrane-bound ligands Delta and Serrate to regulate cell-fate determination. It regulates oogenesis, the differentiation of the ectoderm and the development of the central and peripheral nervous system, eye, wing disk, muscles and segmental appendages such as antennae and legs, through lateral inhibition or induction. It also regulates neuroblast self-renewal, identity and proliferation through the regulation of bHLH-O proteins; in larval brains, it is involved in the maintenance of type II neuroblast self-renewal and identity by suppressing erm expression together with pnt. It might also regulate dpn expression through the activation of the transcriptional regulator Su(H). This model corresponds to the juxtamembrane and transmembrane (JMTM) domain of dNotch, which comprises an extended coil, a transmembrane helix (TM), and a beta-strand. 90 matched cddid_all.tbl CDD cd21707 cd21707 411990 JMTM_APP juxtamembrane and transmembrane (JMTM) domain found in amyloid-beta precursor protein (APP) and similar proteins. Amyloid-beta precursor protein (APP), also called APPI, ABPP, Alzheimer disease amyloid protein, amyloid precursor protein, amyloid-beta A4 protein, cerebral vascular amyloid peptide (CVAP), PreA4, or protease nexin-II (PN-II), functions as a cell surface receptor and performs physiological functions on the surface of neurons relevant to neurite growth, neuronal adhesion and axonogenesis. Amyloid-beta peptides are lipophilic metal chelators with metal-reducing activity; they bind transient metals such as copper, zinc and iron. This model corresponds to juxtamembrane and transmembrane (JMTM) domain of APP, which consists of the intact transmembrane (TM) domain with adjacent N-terminal juxtamembrane (JM) region. More than half of all familial APP mutations of Alzheimer's disease are seen in its JMTM domain region. 40 matched cddid_all.tbl CDD cd21708 cd21708 411991 JMTM_APLP1 juxtamembrane and transmembrane (JMTM) domain found in amyloid-like protein 1 (APLP-1) and similar proteins. Amyloid-like protein 1 (APLP-1), also called APLP, may play a role in postsynaptic function. It couples to JIP signal transduction through C-terminal binding. APLP-1 may interact with cellular G-protein signaling pathways. It can regulate neurite outgrowth through binding to components of the extracellular matrix such as heparin and collagen I. This model corresponds to the juxtamembrane and transmembrane (JMTM) domain of APLP-1, which consists of the intact transmembrane (TM) domain with adjacent N-terminal juxtamembrane (JM) region. 85 matched cddid_all.tbl CDD cd21709 cd21709 411992 JMTM_APLP2 juxtamembrane and transmembrane (JMTM) domain found in amyloid-like protein 2 (APLP-2) and similar proteins. Amyloid-like protein 2 (APLP-2), also called amyloid protein homolog (APPH), or CDEI box-binding protein (CDEBP), may play a role in the regulation of hemostasis. Its soluble form may have inhibitory properties towards coagulation factors. APLP-2 may bind to the DNA 5'-GTCACATG-3'(CDEI box). It inhibits trypsin, chymotrypsin, plasmin, factor XIA, and plasma and glandular kallikrein. This model corresponds to juxtamembrane and transmembrane (JMTM) domain of APLP-2, which consists of the intact transmembrane (TM) domain with adjacent N-terminal juxtamembrane (JM) region. 81 matched cddid_all.tbl CDD cd21710 cd21710 409658 TM_Y_gammaCoV_Nsp3_C C-terminus of gammacoronavirus non-structural protein 3, including transmembrane and Y domains. This model represents the C-terminus of non-structural protein 3 (Nsp3) from gammacoronavirus, including Infectious bronchitis virus. This conserved C-terminus includes two transmembrane (TM) regions TM1 and TM2, an ectodomain (3Ecto) between the TM1 and TM2 that is glycosylated and located on the lumenal side of the ER, an amphiphatic region (AH1) that is not membrane-spanning, and a large Y domain of approximately 370 residues. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. In the related betacoronaviruses, Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and murine hepatitis virus (MHV), the TM1, 3Ecto and TM2 domains are important for the papain-like protease (PL2pro) domain to process Nsp3-Nsp4 cleavage. It has also been shown that the interaction of 3Ecto with the lumenal loop of Nsp4 is essential for ER rearrangements in cells infected with SARS-CoV or MHV. The Y domain, located at the cytosolic side of the ER, consists of the Y1 and CoV-Y subdomains, which are conserved in nidovirus and coronavirus, respectively. Functional information about the Y domain is limited; it has been shown that Nsp3 binding to Nsp4 is less efficient without the Y domain. 525 matched cddid_all.tbl CDD cd21711 cd21711 409659 TM_Y_deltaCoV_Nsp3_C C-terminus of deltacoronavirus non-structural protein 3, including transmembrane and Y domains. This model represents the C-terminus of non-structural protein 3 (Nsp3) from deltacoronavirus, including Magpie-robin coronavirus HKU18 and Bulbul coronavirus HKU11, among others. This conserved C-terminus includes two transmembrane (TM) regions TM1 and TM2, an ectodomain (3Ecto) between the TM1 and TM2 that is glycosylated and located on the lumenal side of the ER, an amphiphatic region (AH1) that is not membrane-spanning, and a large Y domain of approximately 370 residues. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. In the related betacoronaviruses, Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and murine hepatitis virus (MHV), the TM1, 3Ecto and TM2 domains are important for the papain-like protease (PL2pro) domain to process Nsp3-Nsp4 cleavage. It has also been shown that the interaction of 3Ecto with the lumenal loop of Nsp4 is essential for ER rearrangements in cells infected with SARS-CoV or MHV. The Y domain, located at the cytosolic side of the ER, consists of the Y1 and CoV-Y subdomains, which are conserved in nidovirus and coronavirus, respectively. Functional information about the Y domain is limited; it has been shown that Nsp3 binding to Nsp4 is less efficient without the Y domain. 490 matched cddid_all.tbl CDD cd21712 cd21712 409660 TM_Y_alphaCoV_Nsp3_C C-terminus of alphacoronavirus non-structural protein 3, including transmembrane and Y domains. This model represents the C-terminus of non-structural protein 3 (Nsp3) from alphacoronavirus, including Porcine epidemic diarrhea virus and Human coronavirus 229E, among others. This conserved C-terminus includes two transmembrane (TM) regions TM1 and TM2, an ectodomain (3Ecto) between the TM1 and TM2 that is glycosylated and located on the lumenal side of the ER, an amphiphatic region (AH1) that is not membrane-spanning, and a large Y domain of approximately 370 residues. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. In the related betacoronaviruses, Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and murine hepatitis virus (MHV), the TM1, 3Ecto and TM2 domains are important for the papain-like protease (PL2pro) domain to process Nsp3-Nsp4 cleavage. It has also been shown that the interaction of 3Ecto with the lumenal loop of Nsp4 is essential for ER rearrangements in cells infected with SARS-CoV or MHV. The Y domain, located at the cytosolic side of the ER, consists of the Y1 and CoV-Y subdomains, which are conserved in nidovirus and coronavirus, respectively. Functional information about the Y domain is limited; it has been shown that Nsp3 binding to Nsp4 is less efficient without the Y domain. 501 matched cddid_all.tbl CDD cd21713 cd21713 409661 TM_Y_betaCoV_Nsp3_C C-terminus of betacoronavirus non-structural protein 3, including transmembrane and Y domains. This model represents the C-terminus of non-structural protein 3 (Nsp3) from betacoronavirus, including highly pathogenic betacoronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. This conserved C-terminus includes two transmembrane (TM) regions TM1 and TM2, an ectodomain (3Ecto) between the TM1 and TM2 that is glycosylated and located on the lumenal side of the ER, an amphiphatic region (AH1) that is not membrane-spanning, and a large Y domain of approximately 370 residues. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. In SARS-CoV and murine hepatitis virus (MHV), the TM1, 3Ecto and TM2 domains are important for the papain-like protease (PL2pro) domain to process Nsp3-Nsp4 cleavage. It has also been shown that the interaction of 3Ecto with the lumenal loop of Nsp4 is essential for ER rearrangements in cells infected with SARS-CoV or MHV. The Y domain, located at the cytosolic side of the ER, consists of the Y1 and CoV-Y subdomains, which are conserved in nidovirus and coronavirus, respectively. Functional information about the Y domain is limited; it has been shown that Nsp3 binding to Nsp4 is less efficient without the Y domain. 545 matched cddid_all.tbl CDD cd21714 cd21714 409662 TM_Y_MHV-like_Nsp3_C C-terminus of non-structural protein 3, including transmembrane and Y domains, from murine hepatitis virus and betacoronavirus in the A lineage. This model represents the C-terminus of non-structural protein 3 (Nsp3) from betacoronavirus in the embecovirus subgenus (A lineage), including murine hepatitis virus (MHV) and Human coronavirus HKU1. This conserved C-terminus includes two transmembrane (TM) regions TM1 and TM2, an ectodomain (3Ecto) between the TM1 and TM2 that is glycosylated and located on the lumenal side of the ER, an amphiphatic region (AH1) that is not membrane-spanning, and a large Y domain of approximately 370 residues. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. In MHV and the related Severe acute respiratory syndrome-related coronavirus (SARS-CoV), the TM1, 3Ecto and TM2 domains are important for the papain-like protease (PL2pro) domain to process Nsp3-Nsp4 cleavage. It has also been shown that the interaction of 3Ecto with the lumenal loop of Nsp4 is essential for ER rearrangements in cells infected with SARS-CoV or MHV. The Y domain, located at the cytosolic side of the ER, consists of the Y1 and CoV-Y subdomains, which are conserved in nidovirus and coronavirus, respectively. Functional information about the Y domain is limited; it has been shown that Nsp3 binding to Nsp4 is less efficient without the Y domain. 555 matched cddid_all.tbl CDD cd21715 cd21715 409663 TM_Y_HKU9-like_Nsp3_C C-terminus of non-structural protein 3, including transmembrane and Y domains, from Rousettus bat coronavirus HKU9 and betacoronavirus in the D lineage. This model represents the C-terminus of non-structural protein 3 (Nsp3) from betacoronavirus in the nobecovirus subgenus (D lineage), including Rousettus bat coronavirus HKU9. This conserved C-terminus includes two transmembrane (TM) regions TM1 and TM2, an ectodomain (3Ecto) between the TM1 and TM2 that is glycosylated and located on the lumenal side of the ER, an amphiphatic region (AH1) that is not membrane-spanning, and a large Y domain of approximately 370 residues. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. In the related betacoronaviruses, Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and murine hepatitis virus (MHV), the TM1, 3Ecto and TM2 domains are important for the papain-like protease (PL2pro) domain to process Nsp3-Nsp4 cleavage. It has also been shown that the interaction of 3Ecto with the lumenal loop of Nsp4 is essential for ER rearrangements in cells infected with SARS-CoV or MHV. The Y domain, located at the cytosolic side of the ER, consists of the Y1 and CoV-Y subdomains, which are conserved in nidovirus and coronavirus, respectively. Functional information about the Y domain is limited; it has been shown that Nsp3 binding to Nsp4 is less efficient without the Y domain. 526 matched cddid_all.tbl CDD cd21716 cd21716 409664 TM_Y_MERS-CoV-like_Nsp3_C C-terminus of non-structural protein 3, including transmembrane and Y domains, from Middle East respiratory syndrome-related coronavirus and betacoronavirus in the C lineage. This model represents the C-terminus of non-structural protein 3 (Nsp3) from betacoronavirus in the merbecovirus subgenus (C lineage), including Middle East respiratory syndrome-related coronavirus (MERS-CoV) and Tylonycteris bat coronavirus HKU4. This conserved C-terminus includes two transmembrane (TM) regions TM1 and TM2, an ectodomain (3Ecto) between the TM1 and TM2 that is glycosylated and located on the lumenal side of the ER, an amphiphatic region (AH1) that is not membrane-spanning, and a large Y domain of approximately 370 residues. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. In the related betacoronaviruses, Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and murine hepatitis virus (MHV), the TM1, 3Ecto and TM2 domains are important for the papain-like protease (PL2pro) domain to process Nsp3-Nsp4 cleavage. It has also been shown that the interaction of 3Ecto with the lumenal loop of Nsp4 is essential for ER rearrangements in cells infected with SARS-CoV or MHV. The Y domain, located at the cytosolic side of the ER, consists of the Y1 and CoV-Y subdomains, which are conserved in nidovirus and coronavirus, respectively. Functional information about the Y domain is limited; it has been shown that Nsp3 binding to Nsp4 is less efficient without the Y domain. 566 matched cddid_all.tbl CDD cd21717 cd21717 409665 TM_Y_SARS-CoV-like_Nsp3_C C-terminus of non-structural protein 3, including transmembrane and Y domains, from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage. This model represents the C-terminus of non-structural protein 3 (Nsp3) from betacoronavirus in the sarbecovirus subgenus (B lineage), including highly pathogenic human coronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV). This conserved C-terminus includes two transmembrane (TM) regions TM1 and TM2, an ectodomain (3Ecto) between the TM1 and TM2 that is glycosylated and located on the lumenal side of the ER, an amphiphatic region (AH1) that is not membrane-spanning, and a large Y domain of approximately 370 residues. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. In SARS-CoV and the related murine hepatitis virus (MHV), the TM1, 3Ecto and TM2 domains are important for the papain-like protease (PL2pro) domain to process Nsp3-Nsp4 cleavage. It has also been shown that the interaction of 3Ecto with the lumenal loop of Nsp4 is essential for ER rearrangements in cells infected with SARS-CoV or MHV. The Y domain, located at the cytosolic side of the ER, consists of the Y1 and CoV-Y subdomains, which are conserved in nidovirus and coronavirus, respectively. Functional information about the Y domain is limited; it has been shown that Nsp3 binding to Nsp4 is less efficient without the Y domain. 531 matched cddid_all.tbl CDD cd21718 cd21718 409652 CoV_Nsp13-helicase helicase domain of coronavirus non-structural protein 13. This model represents the helicase domain of non-structural protein 13 (Nsp13) from alpha-, beta-, gamma-, and deltacoronavirus, including pathogenic human viruses such as Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core. 341 matched cddid_all.tbl CDD cd21719 cd21719 439240 CTNNAbd_CTNNB1-like alpha-catenin binding domain found in catenin beta-1 (CTNNB1), catenin gamma (CTNNG) and similar proteins. This family includes alpha-catenin binding domain found in catenin beta-1 (CTNNB1), catenin gamma (CTNNG), as well as Drosophila melanogaster armadillo segment polarity protein (dArm). CTNNB1, also called beta-catenin, is a key downstream component of the canonical Wnt signaling pathway. It is involved in the regulation of cell adhesion, as component of an E-cadherin:catenin adhesion complex. It acts as a negative regulator of centrosome cohesion. It is involved in the CDK2/PTPN6/CTNNB1/CEACAM1 pathway of insulin internalization. It blocks anoikis of malignant kidney and intestinal epithelial cells, and promotes their anchorage-independent growth by down-regulating DAPK2. It disrupts PML function and PML-NB formation by inhibiting RANBP2-mediated sumoylation of PML. CTNNG, also called junction plakoglobin (JUP), or desmoplakin III, or desmoplakin-3 (DP3), is a common junctional plaque protein. The membrane-associated plaques are architectural elements in an important strategic position to influence the arrangement and function of both the cytoskeleton and the cells within the tissue. The presence of plakoglobin in both the desmosomes and in the intermediate junctions suggests that it plays a central role in the structure and function of submembranous plaques. CTNNG acts as a substrate for VE-PTP and is required to stimulate VE-cadherin function in endothelial cells. It can replace beta-catenin in E-cadherin/catenin adhesion complexes which are proposed to couple cadherins to the actin cytoskeleton. dArm, which shows high sequence similarity with CTNNB1, is a Drosophila catenin that plays a role during central nervous system development. It can associate with alpha-catenin. Its neural isoform may associate with CadN and participate in the transmission of developmental information. Its cytoplasmic isoform accumulates through Wingless (Wg) signaling; arm function in Wg signal transduction is required early in development for determination of neuroblast fate. Arm and Abl proteins function cooperatively at adherens junctions in both the CNS and epidermis. This model corresponds to a small region at the C-termini of dArm, CTNNB1 and CTNNG; in CTNNB1, this region is responsible for alpha-catenin binding. 70 matched cddid_all.tbl CDD cd21720 cd21720 409653 gammaCoV_Nsp13-helicase helicase domain of gammacoronavirus non-structural protein 13. This model represents the helicase domain of non-structural protein 13 (Nsp13) from gammacoronavirus, including Avian infectious bronchitis virus. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. Coronavirus (CoV) Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core. 343 matched cddid_all.tbl CDD cd21721 cd21721 409654 deltaCoV_Nsp13-helicase helicase domain of deltacoronavirus non-structural protein 13. This model represents the helicase domain of non-structural protein 13 (Nsp13) from deltacoronavirus, including Bulbul coronavirus (CoV) HKU11 and Common moorhen CoV HKU21. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core. 342 matched cddid_all.tbl CDD cd21722 cd21722 409655 betaCoV_Nsp13-helicase helicase domain of betacoronavirus non-structural protein 13. This model represents the helicase domain of non-structural protein 13 (Nsp13) from betacoronavirus, including pathogenic human viruses such as Severe acute respiratory syndrome coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core. 340 matched cddid_all.tbl CDD cd21723 cd21723 409656 alphaCoV_Nsp13-helicase helicase domain of alphacoronavirus non-structural protein 13. This model represents the helicase domain of non-structural protein 13 (Nsp13) from alphacoronavirus, including Porcine epidemic diarrhea virus and Human coronavirus (CoV) NL63. Helicases catalyze NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified based on the arrangement of conserved motifs into six superfamilies. CoV Nsp13 is a member of the helicase superfamily 1 (SF1); SF1 and SF2 helicases do not form toroidal structures, while SF3-6 helicases do. Nsp13 is a component of the viral RNA synthesis replication and transcription complex (RTC). It is a multidomain protein containing a Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B domain involved in nucleic acid substrate binding, and a SF1 helicase core. 340 matched cddid_all.tbl CDD cd21724 cd21724 439241 CTNNAbd_CTNNB1 alpha-catenin binding domain found in catenin beta-1 (CTNNB1) and similar proteins. CTNNB1, also called beta-catenin, is a key downstream component of the canonical Wnt signaling pathway. In the absence of Wnt, it forms a complex with AXIN1, AXIN2, APC, CSNK1A1 and GSK3B that promotes phosphorylation on N-terminal Ser and Thr residues, and ubiquitination of CTNNB1 via BTRC and its subsequent degradation by the proteasome. In the presence of Wnt ligand, CTNNB1 is not ubiquitinated and accumulates in the nucleus, where it acts as a coactivator for transcription factors of the TCF/LEF family, leading to activation of Wnt responsive genes. CTNNB1 is involved in the regulation of cell adhesion as a component of an E-cadherin:catenin adhesion complex. It acts as a negative regulator of centrosome cohesion. It is involved in the CDK2/PTPN6/CTNNB1/CEACAM1 pathway of insulin internalization. It blocks anoikis of malignant kidney and intestinal epithelial cells and promotes their anchorage-independent growth by down-regulating DAPK2. It disrupts PML function and PML-NB formation by inhibiting RANBP2-mediated sumoylation of PML. This model corresponds to a small region at the C-terminus of CTNNB1, which is responsible for alpha-catenin binding. 74 matched cddid_all.tbl CDD cd21725 cd21725 439242 CTNNAbd_CTNNG alpha-catenin binding domain found in catenin gamma (CTNNG) and similar proteins. CTNNG, also called junction plakoglobin (JUP), or desmoplakin III, or desmoplakin-3 (DP3), is a common junctional plaque protein. The membrane-associated plaques are architectural elements in an important strategic position to influence the arrangement and function of both the cytoskeleton and the cells within the tissue. The presence of plakoglobin in both the desmosomes and in the intermediate junctions suggests that it plays a central role in the structure and function of submembranous plaques. CTNNG acts as a substrate for VE-PTP and is required to stimulate VE-cadherin function in endothelial cells. It can replace beta-catenin in E-cadherin/catenin adhesion complexes which are proposed to couple cadherins to the actin cytoskeleton. This model corresponds to a small region at the C-terminus of CTNNG, which shows high sequence similarity with alpha-catenin binding domain of catenin beta-1 (CTNNB1). 70 matched cddid_all.tbl CDD cd21726 cd21726 439243 CTNNAbd_dArm alpha-catenin binding domain found in Drosophila melanogaster armadillo segment polarity protein (dArm) and similar proteins. dArm is a Drosophila catenin that plays a role during central nervous system development. It can associate with alpha-catenin. The neural isoform of dArm may associate with CadN and participate in the transmission of developmental information. Its cytoplasmic isoform accumulates through Wingless (Wg) signaling; arm function in Wg signal transduction is required early in development for determination of neuroblast fate. Arm and Abl proteins function cooperatively at adherens junctions in both the CNS and epidermis. This model corresponds to a small region at the C-terminus of dArm, which shows high sequence similarity with alpha-catenin binding domain of catenin beta-1 (CTNNB1). 75 matched cddid_all.tbl CDD cd21727 cd21727 409626 betaCoV_Nsp3_betaSM betacoronavirus-specific marker of betacoronavirus non-structural protein 3. This model represents the betacoronavirus-specific marker (betaSM), also called group 2-specific marker (G2M), of non-structural protein 3 (Nsp3) from betacoronavirus, including highly pathogenic human coronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV). The betaSM/G2M is located C-terminal to the nucleic acid-binding (NAB) domain. This region is absent in alpha- and deltacoronavirus Nsp3; there is a gammacoronavirus-specific marker (gammaSM) at this position in gammacoronavirus Nsp3. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. Little is known about the betaSM/G2M domain; it is predicted to be non-enzymatic and may be an intrinsically disordered region. The betaSM/G2M domain is part of the predicted PLnc domain (made up of 385 amino acids) of SARS-CoV Nsp3 that may function as a replication/transcription scaffold, with interactions to Nsp5, Nsp12, Nsp13, Nsp14, and Nsp16. 125 matched cddid_all.tbl CDD cd21731 cd21731 409648 alphaCoV_PLPro alphacoronavirus papain-like protease. This model represents the papain-like protease (PLPro) found in non-structural protein 3 (Nsp3) of alphacoronavirus, including Swine acute diarrhea syndrome coronavirus (SADS-CoV) which causes severe diarrhea in piglets, and Human coronavirus 229E which infects humans and bats and causes the common cold. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. PLPro is a key enzyme in this process, making it a high value target for the development of anti-coronavirus therapeutics. PLPro, which belongs to the MEROPS peptidase C16 family, participates in the proteolytic processing of the N-terminal region of the replicase polyprotein; it can cleave Nsp1|Nsp2, Nsp2|Nsp3, and Nsp3|Nsp4 sites and its activity is dependent on zinc. Besides cleaving the polyproteins, PLPro also possesses a related enzymatic activity to promote virus replication: deubiquitinating (DUB) and de-ISGylating activities. Both, ubiquitin (Ub) and Ub-like interferon-stimulated gene product 15 (ISG15), are involved in preventing viral infection; coronaviruses utilize Ubl-conjugating pathways to counter the pro-inflammatory properties of Ubl-conjugated host proteins via the action of PLPro, which processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. The Nsp3 PLPro domain in SADS-CoV and many others has also been shown to antagonize host innate immune induction of type I interferon by interacting with IRF3 and blocking its activation. 289 matched cddid_all.tbl CDD cd21732 cd21732 409649 betaCoV_PLPro betacoronavirus papain-like protease. This model represents the papain-like protease (PLPro) found in non-structural protein 3 (Nsp3) of betacoronavirus, including highly pathogenic betacoronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. PLPro is a key enzyme in this process, making it a high value target for the development of anti-coronavirus therapeutics. PLPro, which belongs to the MEROPS peptidase C16 family, participates in the proteolytic processing of the N-terminal region of the replicase polyprotein; it can cleave Nsp1|Nsp2, Nsp2|Nsp3, and Nsp3|Nsp4 sites and its activity is dependent on zinc. In SARS-CoV and murine hepatitis virus (MHV), the C-terminal non-structural protein 3 region spanning transmembrane regions TM1 and TM2 with 3Ecto domain in between, are important for the PL2pro domain to process Nsp3-Nsp4 cleavage. Besides cleaving the polyproteins, PLPro also possesses a related enzymatic activity to promote virus replication: deubiquitinating (DUB) and de-ISGylating activities. Both, ubiquitin (Ub) and Ub-like interferon-stimulated gene product 15 (ISG15), are involved in preventing viral infection; coronaviruses utilize Ubl-conjugating pathways to counter the pro-inflammatory properties of Ubl-conjugated host proteins via the action of PLPro, which processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. The Nsp3 PLPro domain of many of these CoVs has also been shown to antagonize host innate immune induction of type I interferon by interacting with IRF3 and blocking its activation. Interactions of SARS-CoV and MERS-CoV with antiviral interferon (IFN) responses of human cells are remarkably different; high-dose IFN treatment (type I and type III) shows MERS-CoV was substantially more IFN sensitive than SARS-CoV. This may be due to differences in the architecture of the oxyanion hole and of the S3 as well as the S5 specificity sites, despite the overall structures of SARS-CoV and MERS-CoV PLPro being similar. 304 matched cddid_all.tbl CDD cd21733 cd21733 409650 gammaCoV_PLPro gammacoronavirus papain-like protease. This model represents the papain-like protease (PLPro) found in non-structural protein 3 (Nsp3) of gammacoronavirus, including Avian coronavirus, Canada goose coronavirus, and Beluga whale coronavirus SW1. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. PLPro is a key enzyme in this process, making it a high value target for the development of anti-coronavirus therapeutics. PLPro, which belongs to the MEROPS peptidase C16 family, participates in the proteolytic processing of the N-terminal region of the replicase polyprotein; it can cleave Nsp1|Nsp2, Nsp2|Nsp3, and Nsp3|Nsp4 sites and its activity is dependent on zinc. Besides cleaving the polyproteins, PLPro also possesses a related enzymatic activity to promote virus replication: deubiquitinating (DUB) and de-ISGylating activities. Both, ubiquitin (Ub) and Ub-like interferon-stimulated gene product 15 (ISG15), are involved in preventing viral infection; coronaviruses utilize Ubl-conjugating pathways to counter the pro-inflammatory properties of Ubl-conjugated host proteins via the action of PLPro, which processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. The Nsp3 PLPro domain in several CoVs has also been shown to antagonize host innate immune induction of type I interferon by interacting with IRF3 and blocking its activation. 304 matched cddid_all.tbl CDD cd21734 cd21734 409651 deltaCoV_PLPro deltacoronavirus papain-like protease. This model represents the papain-like protease (PLPro) found in the non-structural protein 3 (Nsp3) region of deltacoronavirus, including Porcine deltacoronavirus, Bulbul coronavirus HKU11, and Common moorhen coronavirus HKU21. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. PLPro is a key enzyme in this process, making it a high value target for the development of anti-coronavirus therapeutics. PLPro, which belongs to the MEROPS peptidase C16 family, participates in the proteolytic processing of the N-terminal region of the replicase polyprotein; it can cleave Nsp1|Nsp2, Nsp2|Nsp3, and Nsp3|Nsp4 sites and its activity is dependent on zinc. Besides cleaving the polyproteins, PLPro also possesses a related enzymatic activity to promote virus replication: deubiquitinating (DUB) and de-ISGylating activities. Both, ubiquitin (Ub) and Ub-like interferon-stimulated gene product 15 (ISG15), are involved in preventing viral infection; coronaviruses utilize Ubl-conjugating pathways to counter the pro-inflammatory properties of Ubl-conjugated host proteins via the action of PLPro, which processes both 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains from cellular substrates. The Nsp3 PLPro domain in many of these CoVs has also been shown to antagonize host innate immune induction of type I interferon by interacting with IRF3 and blocking its activation. 313 matched cddid_all.tbl CDD cd21735 cd21735 439244 ZnB-Zn_SUZ12-like zinc finger-binding (ZnB) and C2H2-type zinc finger (Zn) domain found in suppressor of zeste 12 protein (SUZ12), and similar proteins. This family includes a group of Polycomb group (PcG) proteins from metazoa and plants, such as suppressor of zeste 12 protein (SUZ12), and Polycomb group proteins EMBRYONIC FLOWER 2 (EMF2) and FERTILIZATION-INDEPENDENT SEED 2 (FIS2). SUZ12 (also called chromatin precipitated E2F target 9 protein (ChET 9 protein), or joined to JAZF1 protein) is a component of the Polycomb Repressive Complex 2 (PRC2)/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. The PRC2/EED-EZH2 complex may also serve as a recruiting platform for DNA methyltransferases, thereby linking two epigenetic repression systems. EMF2 is involved in flowering processes by repressing unknown target genes and preventing reproductive development. It participates in polycomb group (PcG) protein complex-mediated (probably in complex with EMF1) silencing of the flower homeotic genes AGAMOUS (AG), PISTILLATA (PI), and APETALA3 (AP3), as well as of some regulatory genes such as ABSCISIC ACID INSENSITIVE3 (ABI3), LONG VEGETATIVE PHASE1 (LOV1), and FLOWERING LOCUS C (FLC) during vegetative development, by mediating trimethylation of histone 3 lysine 27 on the AG chromatin (H3K27me3). FIS2 is required to prevent the proliferation of the central cell by repressing unknown target genes before fertilization. It regulates the anteroposterior organization of the endosperm. Members in this family contain a unique structural ZnB-Zn platform consisting of zinc finger-binding (ZnB) and C2H2-type zinc finger (Zn). 96 matched cddid_all.tbl CDD cd21739 cd21739 439286 NES2-NLS_ChREBP-like nuclear export signal 2 (NES2) and nuclear import signal (NLS) domains found in carbohydrate-responsive element-binding protein (ChREBP), MLX-interacting protein (MLXIP), and similar proteins. This family includes two transcription factors: ChREBP and MLXIP. ChREBP, also called class D basic helix-loop-helix protein 14 (bHLHd14), Max-like protein (MLX) interactor or MIO, MLX-interacting protein-like (MLXIPL), WS basic-helix-loop-helix leucine zipper protein (WS-bHLH), or Williams-Beuren syndrome chromosomal region 14 protein (WBSCR14), functions at two levels; nuclear localization and DNA binding. ChREBP binds to the canonical and non-canonical E box sequences 5'-CACGTG-3'. It also binds DNA as a heterodimer with TCFL4/MLX. MLXIP, also called class E basic helix-loop-helix protein 36 (bHLHe36), transcriptional activator MondoA, or MIR, is a novel basic helix-loop-helix-leucine zipper transcriptional activator that constitutes a positive branch of a max-like network. MLXIP binds DNA by forming a heterodimer with Max-like protein (MLX), and activates transcription. It binds to the canonical E box sequence 5'-CACGTG-3'. MLXIP plays a role in transcriptional activation of glycolytic target genes and is involved in glucose-responsive gene regulation. Members in this family may contain functional domains, including two nuclear export signals, NES1 and NES2, and a nuclear import signal (NLS) in the N-terminal region. This model corresponds to NES2 and NLS domains. 113 matched cddid_all.tbl CDD cd21740 cd21740 467848 C2_II_SUZ12 type II C2 domain found in suppressor of zeste 12 protein (SUZ12) and similar proteins. SUZ12, also called chromatin precipitated E2F target 9 protein (ChET 9 protein), or joined to JAZF1 protein, is a Polycomb group (PcG) protein that is a component of the PRC2/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. The PRC2/EED-EZH2 complex may also serve as a recruiting platform for DNA methyltransferases, thereby linking two epigenetic repression systems. SUZ12 is also involved in various cellular processes, including cell differentiation, proliferation, and apoptosis, and is frequently overexpressed in cancer cells. The model corresponds to the noncanonical type II C2 domain of SUZ12, which shares notable structural homology with the classical C2 domains and plays a role in protein-protein interactions that may contribute to its diverse functions. 167 matched cddid_all.tbl CDD cd21742 cd21742 439267 MobB_NDR_LATS-like "Mob-binding domain found in the NDR/LATS family serine/threonine protein kinases. The nuclear Dbf2-related (NDR)/large tumor suppressor (LATS) family includes NDR, LATS, CBK1, and Sid2p. They are involved in regulating many cellular functions including contraction, motility, division, proliferation, apoptosis, morphogenesis, and cytokinesis. NDR/LATS kinases bind to highly conserved Mob (Mps One binder) coactivators, forming regulatory complexes that control a diverse set of in vivo effector proteins, and are essential and evolutionarily conserved components of ""Hippo"" signaling pathways. Mob association creates a novel binding pocket that participates in the formation of the active state of NDR/LATS kinases. These kinases contain a regulatory domain located N-terminal to the serine/threonine kinase domain (called the N-terminal regulatory (NTR) domain) and an insert within the catalytic domain that contains an auto-inhibitory sequence. This model corresponds to the NTR or Mob-binding domain of NDR/LATS family serine/threonine protein kinases." 62 matched cddid_all.tbl CDD cd21743 cd21743 412023 CTD_KDM2A_2B-like C-terminal domain found in lysine-specific demethylase KDM2A, KDM2B, and similar proteins. This family includes lysine-specific demethylases KDM2A and KDM2B, as well as Drosophila melanogaster JmjC domain-containing histone demethylation protein 1 (Jhd1). KDM2A is a ubiquitously expressed histone H3 lysine 36 (H3K36) demethylase that has been implicated in gene silencing, cell cycle, cell growth, and cancer development. KDM2B is a ubiquitously expressed histone H3 lysine 4 (H3K4me2) or histone H3 lysine 36 (H3K36me2) demethylase that functions as a regulator of chemokine expression, cellular morphology, and the metabolome of fibroblasts. Jhd1, also called lysine (K)-specific demethylase 2 (KDM2), or [Histone-H3]-lysine-36 demethylase 1, is a histone demethylase (EC 1.14.11.27) that specifically demethylates 'Lys-36' of histone H3, thereby playing a central role in the histone code. Members in this family belong to the JmjC domain-containing histone demethylase family. They consist of two Jumonji domains (JmjN and JmjC), a CXXC zinc-finger domain, a plant homeodomain (PHD) finger, an F-box domain, followed by an antagonist of mitotic exit network protein 1 (AMN1) domain. This model corresponds to a small conserved region between the JmjC domain and the CXXC zinc-finger domain, which has been called the C-terminal domain by literature. 67 matched cddid_all.tbl CDD cd21744 cd21744 409643 RBD_KIF20A-like RAB6 binding domain (RBD) found in kinesin-like proteins KIF20A, KIF20B, and similar proteins. This family includes kinesin-like proteins KIF20A and KIF20B. KIF20A (also called GG10_2, mitotic kinesin-like protein 2 (MKlp2), Rab6-interacting kinesin-like protein, or rabkinesin-6) is a mitotic kinesin required for chromosome passenger complex (CPC)-mediated cytokinesis. Following phosphorylation by PLK1 (polo-like kinase 1), it is involved in recruitment of PLK1 to the central spindle. KIF20A interacts with guanosine triphosphate (GTP)-bound forms of RAB6A and RAB6B. It may act as a motor required for the retrograde RAB6 regulated transport of Golgi membranes and associated vesicles along microtubules. KIF20A has a microtubule plus-end-directed motility. KIF20B (also called cancer/testis antigen 90 (CT90), kinesin family member 20B, kinesin-related motor interacting with PIN1, or M-phase phosphoprotein 1 (MPP1)) is a plus-end-directed motor enzyme that is required for completion of cytokinesis. It is required for proper midbody organization and abscission in polarized cortical stem cells. KIF20B plays a role in the regulation of neuronal polarization by mediating the transport of specific cargoes. It participates in the mobilization of SHTN1 and in the accumulation of PIP3 in the growth cone of primary hippocampal neurons in a tubulin and actin-dependent manner. In the developing telencephalon, KIF20B cooperates with SHTN1 to promote both the transition from the multipolar to the bipolar stage and the radial migration of cortical neurons from the ventricular zone toward the superficial layer of the neocortex. This model corresponds to a conserved domain in the KIF20A subfamily, that shows RAB6 binding ability and has been called the RAB6 binding domain (RBD). KIF20A-RBD is a dimer composed of two parallel alpha helices that form a right-handed coiled-coil additionally stabilized by an inter-helical cysteine bridge. 56 matched cddid_all.tbl CDD cd21747 cd21747 439289 Rad21_Rec8_M Middle HEAT-repeat binding domain of Rad21/Rec8-like proteins. This family includes eukaryotic cohesins of the Rad21, Rec8, and Scc1 subfamilies. They mediate sister chromatid cohesion during mitosis and meiosis, as part of the cohesin complex. Cohesion is necessary for homologous recombination (including double-strand break repair) and correct chromatid segregation. These proteins may also be involved in chromosome condensation. Dissociation at the metaphase to anaphase transition causes loss of cohesion and chromatid segregation. This model corresponds to a conserved middle/central region of family members, consisting of short helices and two extended segments, which functions in binding to HEAT-repeat containing cohesin subunits. For example, human Scc1 homolog (NXP-1) binds to either SA1 or SA2, two homologous HEAT-containing proteins; the SA-Scc1 heterodimer mediates the binding between cohesin and its regulators, including Scc2-Scc4, Pds5, Wapl, and Sgo1. 79 matched cddid_all.tbl CDD cd21748 cd21748 439297 Kp60-NTD N-terminal domain (NTD) found in katanin p60 (Kp60) ATPase-containing subunit A1, and similar proteins. This model represents the N-terminal domain (NTD) of katanin p60 ATPase-containing subunit A1 (also called p60 katanin 1 or katanin p60 subunit A1), which is organized into an antiparallel three-helix bundle and is responsible for tubulin binding. Katanin p60 subunit A1 plays a key role in cytoskeletal reorganization during various cellular events in an ATP-dependent manner. It is a microtubule-severing protein (MTSP) that maintains the density of spindle microtubules at the poles in mitotic cells. MSTPs are a group of microtubule-associated proteins essential for multiple microtubule-related processes, including mitosis and meiosis. Microtubule severing may promote rapid reorganization of cellular microtubule arrays and the release of microtubules from the centrosome following nucleation. Microtubule release from the mitotic spindle poles allows depolymerization of the microtubule end proximal to the spindle pole, leading to poleward microtubule flux and poleward motion of chromosome. Microtubule release within the cell body of neurons may be required for their transport into neuronal processes by microtubule-dependent motor proteins. This transport is required for axonal growth. Katanin p60 has been implicated in several malignancies; it is aberrantly expressed in prostate cancer patients with bone metastasis where upregulation of katanin P60 inhibits cell proliferation but enhances cell migration. It promotes cell migration in breast cancer where high ketanin p60 expression in tumor tissue is correlated with lymph node metastasis and poor overall survival. Katanin p60 may also be a potential biomarker for lymph node metastasis and prognosis for non-small cell lung cancer. Katanin is a heterodimer with an AAA catalytic subunit katanin P60 and a non-AAA subunit katanin P80. In ASPM (known as Asp in fly and ASPM-1 in worm), a microcephaly-associated protein family that regulates spindle architecture, the N-terminal domain of katanin p60 subunit (kp60-NTD) and C-terminal domain of katanin p80 subunit form a heterodimer, which then binds conserved motifs in ASPM, thus forming a complex that controls microtubule disassembly at spindle poles; misregulation of this process can lead to microcephaly. p60 katanin-like 1 has been shown to be predominantly enriched within oocytes and ovaries, and essential for oocyte meiosis and maturation. The N-terminal domain of mouse katanin p60 (kp60-NTD) also binds to tubulin; structure studies of kp60-NTD reveal a striking similarity to the microtubule interacting and trafficking (MIT) domains, although their sequence similarities are low. 69 matched cddid_all.tbl CDD cd21749 cd21749 439245 ZnB-Zn_EMF2-like zinc finger-binding (ZnB) and C2H2-type zinc finger (Zn) domain found in Arabidopsis thaliana Polycomb group protein EMBRYONIC FLOWER 2 (EMF2), and similar proteins. This family includes a group of plant proteins similar to Arabidopsis thaliana Polycomb group (PcG) proteins EMF2 and FERTILIZATION-INDEPENDENT SEED 2 (FIS2). EMF2 is involved in flowering processes by repressing unknown target genes and preventing reproductive development. It participates in polycomb group (PcG) protein complex-mediated (probably in complex with EMF1) silencing of the flower homeotic genes AGAMOUS (AG), PISTILLATA (PI), and APETALA3 (AP3), as well as of some regulatory genes such as ABSCISIC ACID INSENSITIVE3 (ABI3), LONG VEGETATIVE PHASE1 (LOV1), and FLOWERING LOCUS C (FLC) during vegetative development, by mediating trimethylation of histone 3 lysine 27 on the AG chromatin (H3K27me3). FIS2 is required to prevent the proliferation of the central cell by repressing unknown target genes before fertilization. It regulates the anteroposterior organization of the endosperm. Members in this family show high sequence similarity with a unique structural ZnB-Zn platform found in metazoan, which consists of zinc finger-binding (ZnB) and C2H2-type zinc finger (Zn). 100 matched cddid_all.tbl CDD cd21750 cd21750 439246 ZnB-Zn_SUZ12 zinc finger-binding (ZnB) and C2H2-type zinc finger (Zn) domain found in suppressor of zeste 12 protein (SUZ12) and similar proteins. Suppressor of zeste 12 protein (SUZ12), also called chromatin precipitated E2F target 9 protein (ChET 9 protein), or joined to JAZF1 protein, is a Polycomb group (PcG) protein that acts as a component of the Polycomb Repressive Complex 2 (PRC2)/EED-EZH2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene. The PRC2/EED-EZH2 complex may also serve as a recruiting platform for DNA methyltransferases, thereby linking two epigenetic repression systems. This model corresponds to a unique structural ZnB-Zn platform consisting of zinc finger-binding (ZnB) and C2H2-type zinc finger (Zn), which forms an intramolecular complex that governs the mutual exclusive binding of Jarid2 and EPOP in PRC2 holo complexes. 96 matched cddid_all.tbl CDD cd21759 cd21759 409646 CBD_MYO6-like calmodulin binding domain found in unconventional myosin-VI and similar proteins. Myosins, which are actin-based motor molecules with ATPase activity, include unconventional myosins that serve in intracellular movements. Myosin-VI, also called unconventional myosin-6 (MYO6), is a reverse-direction motor protein that moves towards the minus-end of actin filaments. It is required for the structural integrity of the Golgi apparatus via the p53-dependent pro-survival pathway. Myosin-VI appears to be involved in a very early step of clathrin-mediated endocytosis in polarized epithelial cells. It modulates RNA polymerase II-dependent transcription. As part of the DISP (DOCK7-Induced Septin disPlacement) complex, Myosin-VI may regulate the association of septins with actin and thereby regulate the actin cytoskeleton. Myosin-VI is encoded by gene MYO6, the human homolog of the gene responsible for deafness in Snell's waltzer mice. It is mutated in autosomal dominant non-syndromic hearing loss. This family also includes Drosophila melanogaster unconventional myosin VI Jaguar (Jar; also called myosin heavy chain 95F (Mhc95F), or 95F MHC), which is a motor protein necessary for the morphogenesis of epithelial tissues during Drosophila development. Jar is required for basal protein targeting and correct spindle orientation in mitotic neuroblasts. It contributes to synaptic transmission and development at the Drosophila neuromuscular junction. Together with CLIP-190 (CAP-Gly domain-containing/cytoplasmic linker protein 190), Jar may coordinate the interaction between the actin and microtubule cytoskeleton. Jar may link endocytic vesicles to microtubules and possibly be involved in transport in the early embryo and in the dynamic process of dorsal closure; its function is believed to change during the life cycle. This model corresponds to the calmodulin (CaM) binding domain (CBD), which consists of three subdomains: a unique insert (Insert 2 or Ins2), an IQ motif, and a proximal tail domain (PTD, also known as lever arm extension or LAE). 149 matched cddid_all.tbl CDD cd21762 cd21762 409196 WH2 Wiskott-Aldrich Syndrome Homology (WASP) region 2 (WH2 motif), and similar proteins. This family contains the Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) as well as thymosin-beta (Tbeta; also called beta-thymosin or betaT) domains that are small, widespread intrinsically disordered actin-binding peptides displaying significant sequence variability and different regulations of actin self-assembly in motile and morphogenetic processes. These WH2/betaT peptides are identified by a central consensus actin-binding motif LKKT/V flanked by variable N-terminal and C-terminal extensions; the betaT shares a more extended and conserved C-terminal half than WH2. These single or repeated domains are found in actin-binding proteins (ABPs) such as the hematopoietic-specific protein WASP, its ubiquitously expressed ortholog neural-WASP (N-WASP), WASP-interacting protein (WAS/WASL-interacting protein family members 1 and 2), and WASP-family verprolin homologous protein (WAVE/SCAR) isoforms: WAVE1, WAVE2, and WAVE3. Also included are the WH2 domains found in inverted formin FH2 domain-containing protein (INF2), Cordon bleu (Cobl) protein, vasodilator-stimulated phosphoprotein (VASP) homology protein and actobindin (found in amoebae). These ABPs are commonly multidomain proteins that contain signaling domains and structurally conserved actin-binding motifs, the most important being the WH2 domain motif through which they bind actin in order to direct the location, rate, and timing for actin assembly in the cell into different structures, such as filopodia, lamellipodia, stress fibers, and focal adhesions. The WH2 domain motif is one of the most abundant actin-binding motifs in Wiskott-Aldrich syndrome proteins (WASPs) where they activate Arp2/3-dependent actin nucleation and branching in response to signals mediated by Rho-family GTPases. The thymosin beta (Tbeta) domains in metazoans act in cells as major actin-sequestering peptides; their complex with monomeric ATP-actin (G-ATP-actin) cannot polymerize at either filament (F-actin) end. 22 matched cddid_all.tbl CDD cd21764 cd21764 409640 CEN_USH1G_ANKS4B central domain found in usher syndrome type-1G protein, ankyrin repeat and SAM domain-containing protein 4B, and similar proteins. The family includes usher syndrome type-1G protein (USH1G), ankyrin repeat and SAM domain-containing protein 4B (ANKS4B), and similar proteins. USH1G, also called scaffold protein containing ankyrin repeats and SAM domain (Sans), is an anchoring/scaffolding protein that is a part of the functional network formed by USH1C, USH1G, CDH23 and MYO7A, that mediates mechanotransduction in cochlear hair cells. It is required for normal development and maintenance of cochlear hair cell bundles, as well as for normal hearing. ANKS4B, also called Harmonin-interacting ankyrin repeat-containing protein (Harp), is highly expressed in intestine and is essential for intermicrovillar adhesion. As part of the intermicrovillar adhesion complex (IMAC), ANKS4B plays a role in epithelial brush border differentiation, controlling microvilli organization and length. It may be involved in cellular response to endoplasmic reticulum stress. Both USH1G and ANKS4B contain four N-terminal ANK repeats, a central region, and a sterile alpha motif (SAM) followed by a C-terminal type I PDZ binding motif (PBM). This model corresponds to the central region (CEN), which contains the conserved regions CEN1 and CEN2. CEN is directly responsible for USH1G binding to the MYO7A MyTH4-FERM tandem, as well as for ANKS4B binding to the N-terminal MyTH4-FERM-SH3 supramodule of MYO7B. 41 matched cddid_all.tbl CDD cd21769 cd21769 409636 DEFL defensin-like domain family. This family includes a group of defensin-like proteins, including Arabidopsis thaliana protein LURE 1.2 (AtLURE1.2) and protein LURE 1.6 (AtLURE1.6), Mesobuthus martensii neurotoxin BmBKTx1, Arabidopsis thaliana defensin-like protein 32 (AtDEF32), as well as bactericidal proteins such as defensins, sapecins, tenecins, phormicins, and lucifensins. They are characterized by a defensin-like (DEFL) domain, which adopts a structure characterized by a cysteine-stabilized alpha/beta scaffold. AtLURE1.2 (also called cysteine-rich peptide 810_1.2 or defensin-like protein 213) and AtLURE1.6 (also called cysteine-rich peptide 810_1.6 or defensin-like protein 215) are pollen tube attractants guiding pollen tubes to the ovular micropyle. BmBKTx1, also called potassium channel toxin alpha-KTx 19.1 or BmK37, is a selective inhibitor of high conductance calcium-activated potassium channels KCa1.1/KCNMA1. Bactericidal proteins are host defense peptides produced in response to injury and are mostly active against Gram-positive bacteria. 29 matched cddid_all.tbl CDD cd21771 cd21771 439287 NES2-NLS_ChREBP nuclear export signal 2 (NES2) and nuclear import signal (NLS) domains found in carbohydrate-responsive element-binding protein (ChREBP), and similar proteins. ChREBP, also called class D basic helix-loop-helix protein 14 (bHLHd14), Max-like protein (MLX) interactor or MIO, MLX-interacting protein-like (MLXIPL), WS basic-helix-loop-helix leucine zipper protein (WS-bHLH), or Williams-Beuren syndrome chromosomal region 14 protein (WBSCR14), is a large transcription factor that functions at two levels, nuclear localization and DNA binding. It binds to the canonical and non-canonical E box sequences 5'-CACGTG-3'. It also binds DNA as a heterodimer with TCFL4/MLX. ChREBP contains functional domains, including two nuclear export signals, NES1 and NES2, and a nuclear import signal (NLS) in the N-terminal region. This model corresponds to NES2 and NLS domains. 116 matched cddid_all.tbl CDD cd21772 cd21772 439288 NES2-NLS_MLXIP nuclear export signal 2 (NES2) and nuclear import signal (NLS) domains found in MLX-interacting protein (MLXIP), and similar proteins. MLXIP, also called class E basic helix-loop-helix protein 36 (bHLHe36), transcriptional activator MondoA, or MIR, is a novel basic helix-loop-helix-leucine zipper transcriptional activator that constitutes a positive branch of a max-like network. It binds DNA by forming a heterodimer with Max-like protein (MLX) and activates transcription. It binds to the canonical E box sequence 5'-CACGTG-3'. MLXIP plays a role in transcriptional activation of glycolytic target genes and is involved in glucose-responsive gene regulation. MLXIP may contain functional domains, including two nuclear export signals, NES1 and NES2, and a nuclear import signal (NLS) in the N-terminal region. This model corresponds to NES2 and NLS domains. 117 matched cddid_all.tbl CDD cd21773 cd21773 439268 MobB_CBK1 "Mob-binding domain found in cell wall biosynthesis kinase CBK1 and similar proteins. This group is composed of fungal NDR/LATS family proteins including Saccharomyces cerevisiae CBK1 (or CBK1p), Schizosaccharomyces pombe Orb6 (or Orb6p) and Neurospora crassa Cot1. CBK1 is an essential component in the RAM (regulation of Ace2p activity and cellular morphogenesis) network. CBK1 and Orb6 play similar roles in coordinating cell morphology with cell cycle progression. Cot1 plays a role in polar tip extension. NDR/LATS kinases bind to highly conserved Mob (Mps One binder) coactivators, forming regulatory complexes that control a diverse set of in vivo effector proteins, and are essential and evolutionarily conserved components of ""Hippo"" signaling pathways. Mob association creates a novel binding pocket that participates in the formation of the active state of NDR/LATS kinases. Kinases in this subfamily contain a regulatory domain located N-terminal to the serine/threonine kinase domain (called the N-terminal regulatory (NTR) domain) and an insert within the catalytic domain that contains an auto-inhibitory sequence. This model corresponds to the NTR or Mob-binding domain of CBK1 and similar serine/threonine protein kinases." 80 matched cddid_all.tbl CDD cd21774 cd21774 439269 MobB_LATS "Mob-binding domain found in the large tumor suppressor (LATS) subfamily. LATS was originally identified in Drosophila using a screen for genes whose inactivation led to overproliferation of cells. In tetrapods, there are two LATS isoforms, LATS1 and LATS2. Inactivation of LATS1 in mice results in the development of various tumors, including sarcomas and ovarian cancer. LATS functions as a tumor suppressor and is implicated in cell cycle regulation. This subfamily belongs to the NDR/LATS family of kinases that bind to highly conserved Mob (Mps One binder) coactivators, forming regulatory complexes that control a diverse set of in vivo effector proteins, and are essential and evolutionarily conserved components of ""Hippo"" signaling pathways. Mob association creates a novel binding pocket that participates in the formation of the active state of NDR/LATS kinases. LATS proteins contain a regulatory domain located N-terminal to the serine/threonine kinase domain (called the N-terminal regulatory (NTR) domain) and an insert within the catalytic domain that contains an auto-inhibitory sequence. This model corresponds to the NTR or Mob-binding domain of LATS subfamily serine/threonine protein kinases." 62 matched cddid_all.tbl CDD cd21775 cd21775 439270 MobB_NDR-like "Mob-binding domain found in the nuclear Dbf2-related kinase (NDR) subfamily. NDR kinases regulate mitosis, cell growth, embryonic development, and neurological processes. They are also required for proper centrosome duplication. Higher eukaryotes contain two NDR isoforms, NDR1 and NDR2. This subfamily also includes Drosophila melanogaster tricorner, which is a serine/threonine-protein kinase that plays an important role in controlling cell structure and proliferation of a variety of polarized outgrowths including epidermal hairs, bristles, arista laterals, and dendrites. It affects cellular morphogenesis by regulating the expression of target genes that encode cytoskeleton-interacting proteins and not via the direct modification of the cytoskeleton. It maintains the integrity of epidermal hairs and is an essential component of the signaling pathway regulating dendritic branching of sensory neurons. The NDR subfamily belongs to the NDR/LATS family of kinases that bind to highly conserved Mob (Mps One binder) coactivators, forming regulatory complexes that control a diverse set of in vivo effector proteins, and are essential and evolutionarily conserved components of ""Hippo"" signaling pathways. Mob association creates a novel binding pocket that participates in the formation of the active state of NDR/LATS kinases. NDR-like kinases contain a regulatory domain located N-terminal to the serine/threonine kinase domain (called the N-terminal regulatory (NTR) domain) and an insert within the catalytic domain that contains an auto-inhibitory sequence. This model corresponds to the NTR or Mob-binding domain of NDR-like serine/threonine protein kinases." 65 matched cddid_all.tbl CDD cd21776 cd21776 439271 MobB_Sid2p-like "Mob-binding domain found in fungal Sid2p-like serine/threonine protein kinases. This group contains fungal kinases including Schizosaccharomyces pombe Sid2p and ppk35p, as well as Saccharomyces cerevisiae Dbf2p and Dbf20p. Sid2p plays a crucial role in the septum initiation network (SIN) and in the initiation of cytokinesis. Ppk35p, also called meiotically up-regulated gene 27 protein (mug27p), has a role in meiosis. Dbf2p is important in regulating the mitotic exit network (MEN) and in cytokinesis. Dbf20p may function in initiation of DNA synthesis and in late nuclear division. Kinases in this group belong to the NDR/LATS family of kinases that bind to highly conserved Mob (Mps One binder) coactivators, forming regulatory complexes that control a diverse set of in vivo effector proteins, and are essential and evolutionarily conserved components of ""Hippo"" signaling pathways. Mob association creates a novel binding pocket that participates in the formation of the active state of NDR/LATS kinases. These proteins contain a regulatory domain located N-terminal to the serine/threonine kinase domain (called the N-terminal regulatory (NTR) domain) and an insert within the catalytic domain that contains an auto-inhibitory sequence. This model corresponds to the NTR or Mob-binding domain of Sid2p-like serine/threonine protein kinases." 84 matched cddid_all.tbl CDD cd21777 cd21777 439272 MobB_LATS2 "Mob-binding domain found in large tumor suppressor homolog 2 (LATS2). LATS2, also called kinase phosphorylated during mitosis protein, serine/threonine-protein kinase kpm, or Warts-like kinase, is an essential mitotic regulator responsible for coordinating accurate cytokinesis completion and for governing the stabilization of other mitotic regulators. It is also critical in the maintenance of proper chromosome number, genomic stability, mitotic fidelity, and the integrity of centrosome duplication. Downregulation of LATS2 is associated with poor prognosis in acute lymphoblastic leukemia and breast cancer. LATS2 belongs to the NDR/LATS family of kinases that bind to highly conserved Mob (Mps One binder) coactivators, forming regulatory complexes that control a diverse set of in vivo effector proteins, and are essential and evolutionarily conserved components of ""Hippo"" signaling pathways. Mob association creates a novel binding pocket that participates in the formation of the active state of NDR/LATS kinases. LATS proteins contain a regulatory domain located N-terminal to the serine/threonine kinase domain (called the N-terminal regulatory (NTR) domain) and an insert within the catalytic domain that contains an auto-inhibitory sequence. This model corresponds to the NTR or Mob-binding domain of LATS2 serine/threonine protein kinase." 83 matched cddid_all.tbl CDD cd21778 cd21778 439273 MobB_LATS1 "Mob-binding domain found in large tumor suppressor homolog 1 (LATS1) and similar proteins. LATS1, also called WARTS protein kinase, is a serine/threonine-protein kinase that functions as a tumor suppressor and is implicated in cell cycle regulation. Inactivation of LATS1 in mice results in the development of various tumors, including sarcomas and ovarian cancer. Promoter methylation, loss of heterozygosity, and missense mutations targeting the LATS1 gene have also been found in human sarcomas and ovarian cancers. In addition, decreased expression of LATS1 is associated with an aggressive phenotype and poor prognosis. LATS1 induces G2 arrest and promotes cytokinesis. It may be a component of the mitotic exit network in higher eukaryotes. LATS1 belongs to the NDR/LATS family of kinases that bind to highly conserved Mob (Mps One binder) coactivators, forming regulatory complexes that control a diverse set of in vivo effector proteins, and are essential and evolutionarily conserved components of ""Hippo"" signaling pathways. Mob association creates a novel binding pocket that participates in the formation of the active state of NDR/LATS kinases. LATS proteins contain a regulatory domain located N-terminal to the serine/threonine kinase domain (called the N-terminal regulatory (NTR) domain) and an insert within the catalytic domain that contains an auto-inhibitory sequence. This model corresponds to the NTR or Mob-binding domain of LATS1 serine/threonine protein kinase and similar proteins." 76 matched cddid_all.tbl CDD cd21780 cd21780 439274 MobB_Trc-like "Mob-binding domain found in Drosophila melanogaster tricorner and similar proteins. Drosophila melanogaster tricorner, also called serine/threonine-protein kinase 38-like, or NDR protein kinase, is a serine/threonine-protein kinase that plays an important role in controlling cell structure and proliferation of a variety of polarized outgrowths including epidermal hairs, bristles, arista laterals, and dendrites. It affects cellular morphogenesis by regulating the expression of target genes that encode cytoskeleton-interacting proteins and not via the direct modification of the cytoskeleton. It maintains the integrity of epidermal hairs and is an essential component of the signaling pathway regulating dendritic branching of sensory neurons. Tricorner belongs to the NDR/LATS family of kinases that bind to highly conserved Mob (Mps One binder) coactivators, forming regulatory complexes that control a diverse set of in vivo effector proteins, and are essential and evolutionarily conserved components of ""Hippo"" signaling pathways. Mob association creates a novel binding pocket that participates in the formation of the active state of NDR/LATS kinases. These kinases contain a regulatory domain located N-terminal to the serine/threonine kinase domain (called the N-terminal regulatory (NTR) domain) and an insert within the catalytic domain that contains an auto-inhibitory sequence. This model corresponds to the NTR or Mob-binding domain of Tricorner-like serine/threonine protein kinases." 65 matched cddid_all.tbl CDD cd21781 cd21781 439275 MobB_NDR2 "Mob-binding domain found in nuclear Dbf2-related kinase 2 (NDR2). NDR2, also called serine/threonine-protein kinase 38-like (STK38L), plays a role in proper centrosome duplication. In addition, it is involved in regulating neuronal growth and differentiation, as well as in facilitating neurite outgrowth. NDR2 is also implicated in fear conditioning as it contributes to the coupling of neuronal morphological changes with fear-memory consolidation. NDR2 belongs to the NDR/LATS family of kinases that bind to highly conserved Mob (Mps One binder) coactivators, forming regulatory complexes that control a diverse set of in vivo effector proteins, and are essential and evolutionarily conserved components of ""Hippo"" signaling pathways. Mob association creates a novel binding pocket that participates in the formation of the active state of NDR/LATS kinases. NDR kinases contain a regulatory domain located N-terminal to the serine/threonine kinase domain (called the N-terminal regulatory (NTR) domain) and an insert within the catalytic domain that contains an auto-inhibitory sequence. This model corresponds to the NTR or Mob-binding domain of NDR2 serine/threonine protein kinase." 68 matched cddid_all.tbl CDD cd21782 cd21782 439276 MobB_NDR1 "Mob-binding domain found in nuclear Dbf2-related kinase 1 (NDR1) and similar proteins. NDR1, also called serine/threonine-protein kinase 38 (STK38), plays a role in proper centrosome duplication. It is highly expressed in thymus, muscle, lung and spleen. It is not an essential protein because mice deficient of NDR1 remain viable and fertile. However, these mice develop T-cell lymphomas and appear to be hypersensitive to carcinogenic treatment. NDR1 appears to also act as a tumor suppressor. NDR1 belongs to the NDR/LATS family of kinases that bind to highly conserved Mob (Mps One binder) coactivators, forming regulatory complexes that control a diverse set of in vivo effector proteins, and are essential and evolutionarily conserved components of ""Hippo"" signaling pathways. Mob association creates a novel binding pocket that participates in the formation of the active state of NDR/LATS kinases. NDR kinases contain a regulatory domain located N-terminal to the serine/threonine kinase domain (called the N-terminal regulatory (NTR) domain) and an insert within the catalytic domain that contains an auto-inhibitory sequence. This model corresponds to the NTR or Mob-binding domain of NDR1 serine/threonine protein kinase." 75 matched cddid_all.tbl CDD cd21783 cd21783 412024 CTD_Jhd1-like C-terminal domain found in Drosophila melanogaster JmjC domain-containing histone demethylation protein 1 and similar proteins. JmjC domain-containing histone demethylation protein 1 (Jhd1), also called lysine (K)-specific demethylase 2 (KDM2), or [Histone-H3]-lysine-36 demethylase 1, is a histone demethylase (EC 1.14.11.27) that specifically demethylates 'Lys-36' of histone H3, thereby playing a central role in the histone code. Jhd1 consists of two Jumonji domains (JmjN and JmjC), a CXXC zinc-finger domain, a plant homeodomain (PHD) finger, an F-box domain, followed by an antagonist of mitotic exit network protein 1 (AMN1) domain. This model corresponds to a small conserved region in Jhd1 between the JmjC domain and the CXXC zinc-finger domain, which has been called the C-terminal domain by literature. 67 matched cddid_all.tbl CDD cd21784 cd21784 412025 CTD_KDM2A C-terminal domain found in Lysine-specific demethylase 2A. Lysine-specific demethylase 2A (KDM2A) is also called CXXC-type zinc finger protein 8, F-box and leucine-rich repeat protein 11 (FBXL11), F-box protein FBL7, F-box protein Lilina, F-box/LRR-repeat protein 11, JmjC domain-containing histone demethylation protein 1A (Jhdm1a), or [Histone-H3]-lysine-36 demethylase 1A. It is a ubiquitously expressed histone H3 lysine 36 (H3K36) demethylase that has been implicated in gene silencing, cell cycle, cell growth, and cancer development. It acts as a key negative regulator of gluconeogenic gene expression and plays a critical role in the invasiveness, proliferation, and anchorage-independent growth of non-small cell lung cancer (NSCLC) cells, as well as in the osteo/dentinogenic differentiation of Mesenchymal stem cells (MSCs). KDM2A regulates rRNA transcription in response to starvation and functions as a negative regulator of NF-kappaB. It is a heterochromatin-associated and HP1-interacting protein that promotes Heterochromatin Protein 1 (HP1) localization to chromatin. It is specifically recruited to CpG islands to define a unique chromatin architecture, which requires direct and specific interaction with linker DNA. It also functions as a H3K4 demethylase that regulates cell proliferation through p15 (INK4B) and p27 (Kip1) in stem cells from apical papilla (SCAPs). KDM2A belongs to the JmjC domain-containing histone demethylase family. KDM2A consists of two Jumonji domains (JmjN and JmjC), a CXXC zinc-finger domain, a plant homeodomain (PHD) finger, an F-box domain, followed by an antagonist of mitotic exit network protein 1 (AMN1) domain. This model corresponds to a small conserved region in KDM2A between the JmjC domain and the CXXC zinc-finger domain, which has been called the C-terminal domain by literature. 68 matched cddid_all.tbl CDD cd21785 cd21785 412026 CTD_KDM2B C-terminal domain found in Lysine-specific demethylase 2B. Lysine-specific demethylase 2B (KDM2B) is also called Ndy1, CXXC-type zinc finger protein 2, F-box and leucine-rich (LRR) repeat protein 10 (FBXL10), F-box protein FBL10, JmjC domain-containing histone demethylation protein 1B (Jhdm1b), Jumonji domain-containing EMSY-interactor methyltransferase motif protein (protein JEMMA), or [Histone-H3]-lysine-36 demethylase 1B. It is a ubiquitously expressed histone H3 lysine 4 (H3K4me2) or histone H3 lysine 36 (H3K36me2) demethylase that functions as a regulator of chemokine expression, cellular morphology, and the metabolome of fibroblasts. It regulates the differentiation of Mesenchymal Stem Cells (MSCs) and has been implicated in cell cycle regulation by de-repressing cyclin-dependent kinase inhibitor 2B (CDKN2B or p15INK4B). It also plays a role in recruiting polycomb repressive complex 1 (PRC1) to CpG islands (CGIs) of developmental genes and regulates lysine 119 monoubiquitylation on H2A (H2AK119ub1) in embryonic stem cells (ESCs). KDM2B also acts as an oncogene that plays a critical role in leukemia development and maintenance. It consists of two Jumonji domains (JmjN and JmjC), a CXXC zinc-finger domain, a plant homeodomain (PHD) finger, an F-box domain, followed by an antagonist of mitotic exit network protein 1 (AMN1) domain. This model corresponds to a small conserved region in KDM2B between the JmjC domain and the CXXC zinc-finger domain, which has been called the C-terminal domain by literature. 67 matched cddid_all.tbl CDD cd21786 cd21786 409644 RBD_KIF20B RAB6 binding domain (RBD) found in kinesin-like protein KIF20B, and similar proteins. KIF20B (also called cancer/testis antigen 90 (CT90), kinesin family member 20B, kinesin-related motor interacting with PIN1, or M-phase phosphoprotein 1 (MPP1)) is a plus-end-directed motor enzyme that is required for completion of cytokinesis. It is required for proper midbody organization and abscission in polarized cortical stem cells. KIF20B plays a role in the regulation of neuronal polarization by mediating the transport of specific cargos. It participates in the mobilization of SHTN1 (shootin 1) and in the accumulation of PIP3 in the growth cone of primary hippocampal neurons in a tubulin and actin-dependent manner. In the developing telencephalon, KIF20B cooperates with SHTN1 to promote both the transition from the multipolar to the bipolar stage and the radial migration of cortical neurons from the ventricular zone toward the superficial layer of the neocortex. KIF20B acts as an oncogene for promoting bladder cancer cell proliferation, apoptosis inhibition, and carcinogenic progression. This model corresponds to a conserved region in KIF20B that shows some sequence similarity to the RAB6 binding domain (RBD) of KIF20A. KIF20A-RBD is a dimer composed of two parallel alpha helices that form a right-handed coiled-coil additionally stabilized by an inter-helical cysteine bridge. 56 matched cddid_all.tbl CDD cd21787 cd21787 409645 RBD_KIF20A RAB6 binding domain (RBD) found in kinesin-like protein KIF20A, and similar proteins. KIF20A, also called GG10_2, or mitotic kinesin-like protein 2 (MKlp2), or Rab6-interacting kinesin-like protein, or rabkinesin-6, is a mitotic kinesin required for chromosome passenger complex (CPC)-mediated cytokinesis. Following phosphorylation by PLK1, it is involved in recruitment of PLK1 (polo-like kinase 1) to the central spindle. KIF20A interacts with guanosine triphosphate (GTP)-bound forms of RAB6A and RAB6B. It may act as a motor required for the retrograde RAB6 regulated transport of Golgi membranes and associated vesicles along microtubules. KIF20A has a microtubule plus end-directed motility. This model corresponds to RAB6 binding domain (RBD) of KIF20A. KIF20A-RBD is a dimer composed of two parallel alpha helices that form a right-handed coiled-coil additionally stabilized by an inter-helical cysteine bridge. 56 matched cddid_all.tbl CDD cd21788 cd21788 439290 Rad21_Rec8_M_SpRad21p-like Middle HEAT-repeat binding domain found in Schizosaccharomyces pombe cohesin subunit rad21 (SpRad21p) and similar proteins. SpRad21p, also called double-strand-break (DSB) repair protein rad21, or SCC1 homolog, is a cleavable component of the cohesin complex, involved in chromosome cohesion during the cell cycle. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. It apparently forms a large proteinaceous ring within which sister chromatids can be trapped. At the metaphase-anaphase transition, SpRad21p is cleaved by cut1 and dissociates from chromatin, allowing sister chromatids to segregate. It is also involved in the DNA DSB repair system. This model corresponds to a small region in the middle of SpRad21p that shows high sequence similarity with the HEAT-repeat binding domain found in both Saccharomyces cerevisiae sister chromatid cohesion protein 1 (ScScc1p) and Homo sapiens nuclear matrix protein 1 (NXP-1), which consists of short helices and two long extended segments. 85 matched cddid_all.tbl CDD cd21789 cd21789 439291 Rad21_Rec8_M_SpRec8p-like Middle HEAT-repeat binding domain found in Schizosaccharomyces pombe meiotic recombination protein Rec8 (SpRec8p) and similar proteins. SpRec8p, also called cohesin rec8, is involved primarily in the early steps of meiotic recombination. It is required to ensure reductional chromosome segregation. This model corresponds to a small region in the middle of SpRec8p that shows high sequence similarity with the HEAT-repeat binding domain of Saccharomyces cerevisiae sister chromatid cohesion protein 1 (ScScc1p) and Homo sapiens nuclear matrix protein 1 (NXP-1), which consists of short helices and two long extended segments. 118 matched cddid_all.tbl CDD cd21790 cd21790 439292 Rad21_Rec8_M_ScRec8p-like Middle HEAT-repeat binding domain found in Saccharomyces cerevisiae meiotic recombination protein Rec8 (ScRec8p) and similar proteins. ScRec8p, also called cohesin REC8, or sporulation protein 69, replaces the SCC1 mitosis-specific cohesin to ensure sister chromatid cohesion during meiosis. It is cleaved by ESP1 shortly before the first meiotic division, and dissociates from chromatin, allowing sister chromatids to segregate. It is protected from cleavage by SPO13. This model corresponds to a small region in the middle of ScRec8p that shows high sequence similarity with the HEAT-repeat binding domain of Saccharomyces cerevisiae sister chromatid cohesion protein 1 (ScScc1p) and Homo sapiens nuclear matrix protein 1 (NXP-1), which consists of short helices and two long extended segments. 92 matched cddid_all.tbl CDD cd21791 cd21791 439293 Rad21_Rec8_M_ScScc1p-like Middle HEAT-repeat binding domain found in Saccharomyces cerevisiae sister chromatid cohesion protein 1 (ScScc1p) and similar proteins. ScScc1p, also called Mcd1, or Rhc21, or Pds3, is a cleavable component of the cohesin complex involved in chromosome cohesion during the cell cycle. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. The cohesin complex apparently forms a large proteinaceous ring within which sister chromatids can be trapped. At the metaphase-anaphase transition, ScScc1p is cleaved by ESP1 and dissociates from chromatin, allowing sister chromatids to segregate. This model corresponds to HEAT-repeat binding domain of ScScc1p in the middle region, which consists of short helices and two long extended segments. It is responsible for the binding of the budding yeast cohesin HEAT-repeat subunit Scc3. The Scc3-Scc1 subcomplex engages double-stranded DNA through a conserved, positively charged surface, and plays a central role in the recruitment of cohesin complexes to chromosomes and therefore for cohesin to faithfully execute its functions during cell division. 82 matched cddid_all.tbl CDD cd21792 cd21792 439294 Rad21_Rec8_M_NXP1-like Middle HEAT-repeat binding domain found in Homo sapiens nuclear matrix protein 1 (NXP-1) and similar proteins. NXP-1, also called double-strand-break repair protein Rad21 homolog (HR21), or Scc1 homolog, is related to Rad21/Scc1/Mcd1. As a component of the cohesin complex, it is involved in sister chromatid cohesion from the time of DNA replication in S phase to their segregation in mitosis, a function that is essential for proper chromosome segregation, post-replicative DNA repair, and the prevention of inappropriate recombination between repetitive regions. The cohesin complex may also play a role in spindle pole assembly during mitosis. The family also includes double-strand-break repair protein rad21-like protein 1 (RAD21L), which is a meiosis-specific component of some cohesin complex required during the initial steps of prophase I in male meiosis. This model corresponds to the HEAT-repeat binding domain of NXP-1 located in the middle/central region, which consists of four short helices and two long extended segments. It is responsible for the binding of cohesin HEAT-repeat subunit SA2. The SA2:NXP-1 heterodimer mediates the binding between cohesin and its regulators, including Scc2-Scc4, Pds5, Wapl, and Sgo1. 81 matched cddid_all.tbl CDD cd21793 cd21793 439295 Rad21_Rec8_M_AtSYN1-like Middle HEAT-repeat binding domain found in Arabidopsis thaliana sister chromatid cohesion 1 protein 1-4 (SYN1-4) and similar proteins. The family includes a group of plant chromosome cohesin proteins from the Rad21/Rec8 family, such as SYN1-4. SYN1, also called protein DETERMINATE INFERTILE 1 (DIF1), or SCC1 homolog 1, is involved in chromosome condensation, pairing, and segregation during meiosis. It is also responsible for cohesion between replicated sister chromatids. SYN4, also called AtRAD21-3, or AtRAD21.3, is involved in sister chromatid and centromere cohesion during mitosis. Similarly, SYN2 (also called SCC1 homolog 2, or AtRAD21-1) and SYN3 (also called SCC1 homolog 3, or AtRAD21-2) may also be involved in sister chromatid cohesion during mitosis. This model corresponds to a small region in the middle of SYN1-4 that shows high sequence similarity with the HEAT-repeat binding domain found in both the middle of Saccharomyces cerevisiae sister chromatid cohesion protein 1 (ScScc1p) and Homo sapiens nuclear matrix protein 1 (NXP-1), which consists of short helices and two long extended segments. 82 matched cddid_all.tbl CDD cd21794 cd21794 439296 Rad21_Rec8_M_Rec8 Middle HEAT-repeat binding domain found in Homo sapiens meiotic recombination protein REC8 homolog and similar proteins. Rec8, also called cohesin Rec8p, is a meiotic recombination and sister chromatid cohesion phosphoprotein of the Rad21p family conserved from fission yeast to humans. It is required during meiosis for separation of sister chromatids and homologous chromosomes. Proteolytic cleavage of Rec8 on chromosome arms by separin during anaphase I allows for homologous chromosome separation in meiosis I, and cleavage of Rec8 on centromeres during anaphase II allows for sister chromatid separation in meiosis II. This model corresponds to a small region in the middle of Rec8 that shows high sequence similarity with the HEAT-repeat binding domain found in both the middle of Saccharomyces cerevisiae sister chromatid cohesion protein 1 (ScScc1p) and Homo sapiens nuclear matrix protein 1 (NXP-1), which consists of short helices and two long extended segments. 75 matched cddid_all.tbl CDD cd21795 cd21795 409347 betaCoV_Nsp3_NAB nucleic acid binding domain of betacoronavirus non-structural protein 3. This model represents the nucleic acid binding (NAB) domain of non-structural protein 3 (Nsp3) from betacoronavirus including highly pathogenic human coronaviruses (CoVs) such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV). The NAB domain represents a new fold, with a parallel four-strand beta-sheet holding two alpha-helices of three and four turns that are oriented antiparallel to the beta-strands. NAB is a cytoplasmic domain located between the papain-like protease (PLPro) and betacoronavirus-specific marker (betaSM) domains of CoV Nsp3. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. The NAB domain both binds ssRNA and unwinds dsDNA. It prefers to bind ssRNA containing repeats of three consecutive guanines. A group of residues that form a positively charged patch on the protein surface of SARS-CoV Nsp3 NAB serves as the binding site of nucleic acids. This site is conserved in the NAB of Nsp3 from betacoronavirus in the sarbecovirus subgenus (B lineage), but may not be conserved in the Nsp3 NAB from betacoronaviruses in other lineages. 110 matched cddid_all.tbl CDD cd21796 cd21796 439285 SARS-CoV-like_Nsp1_N N-terminal domain of non-structural protein 1 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage. This model represents the N-terminal domain of non-structural protein 1 (Nsp1) from betacoronaviruses in the sarbecovirus subgenus (B lineage), including highly pathogenic coronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV). CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. Nsp1 is the N-terminal cleavage product released from the ORF1a polyprotein by the action of papain-like protease (PLpro). Though Nsp1s of alphaCoVs and betaCoVs share structural similarity, they show no significant sequence similarity and may be considered as genus-specific markers. Despite low sequence similarity, the Nsp1s of alphaCoVs and betaCoVs exhibit remarkably similar biological functions, and are involved in the regulation of both host and viral gene expression. CoV Nsp1 induces suppression of host gene expression and interferes with host immune response. It inhibits host gene expression in two ways: by targeting the translation and stability of cellular mRNAs, and by inhibiting mRNA translation and inducing an endonucleolytic RNA cleavage in the 5'-UTR of cellular mRNAs through its tight association with the 40S ribosomal subunit, a key component of the cellular translation machinery. Inhibition of host mRNA translation includes that of type I interferons, major components of the host innate immune response. Nsp1 is critical in regulating viral replication and gene expression, as shown by multiple evidences, including: mutations in the Nsp1 coding region of the transmissible gastroenteritis virus (TGEV) and murine hepatitis virus (MHV) genomes cause drastic reduction or elimination of infectious virus; bovine coronavirus (BCoV) Nsp1 is an RNA-binding protein that interacts with cis-acting replication elements in the 5'-UTR of the BCoV genome, implying its potential role in the regulation of viral translation or replication; and SARS-CoV Nsp1 enhances virus replication by binding to a stem-loop structure in the 5'-UTR of its genome. 115 matched cddid_all.tbl CDD cd21799 cd21799 409197 WH2_Wa_Cobl first Wiskott Aldrich syndrome homology region 2 (WH2 motif) repeat (called Wa) found in protein Cordon-Bleu (Cobl) and similar proteins. This family contains the first tandem Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2), called Wa, found in protein Cordon-Bleu (Cobl), a potent actin filament nucleator that plays an important role in the reorganization of the actin cytoskeleton. It regulates neuron morphogenesis and increases branching of axons and dendrites. It also modulates dendrite branching in Purkinje cells. Cobl binds to and sequesters actin monomers (G-actin). Cobl contains three tandem WH2 (or W) domains consisting of an N-terminal alpha helix and a C-terminal LRKV motif. The first two WH2 domains have the highest binding affinity for actin. They are functionally active in actin nucleation and polymerization. The model corresponds to the first WH2 domain. 33 matched cddid_all.tbl CDD cd21800 cd21800 409198 WH2_Wb_Cobl second Wiskott Aldrich syndrome homology region 2 (WH2 motif) repeat (called Wb) found in protein Cordon-Bleu (Cobl) and similar proteins. This family contains the second tandem Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2), called Wb, found in protein Cordon-Bleu (Cobl), a potent actin filament nucleator that plays an important role in the reorganization of the actin cytoskeleton. It regulates neuron morphogenesis and increases branching of axons and dendrites. It also modulates dendrite branching in Purkinje cells. Cobl binds to and sequesters actin monomers (G-actin). Cobl contains three tandem WH2 or W domains consisting of an N-terminal alpha helix and a C-terminal LRKV motif. The first two WH2 domains have the highest binding affinity for actin. They are functionally active in actin nucleation and polymerization. The model corresponds to the second WH2 domain. 44 matched cddid_all.tbl CDD cd21801 cd21801 409199 WH2_Wc_Cobl third Wiskott Aldrich syndrome homology region 2 (WH2 motif) repeat (called Wc) found in protein Cordon-Bleu (Cobl) and similar proteins. This family contains the third tandem Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2), called Wc, found in protein Cordon-Bleu (Cobl), a potent actin filament nucleator that plays an important role in the reorganization of the actin cytoskeleton. It regulates neuron morphogenesis and increases branching of axons and dendrites. It also modulates dendrite branching in Purkinje cells. Cobl binds to and sequesters actin monomers (G-actin). Cobl contains three tandem WH2 (or W) domains consisting of an N-terminal alpha helix and a C-terminal LRKV motif. The first two WH2 domains have the highest binding affinity for actin. They are functionally active in actin nucleation and polymerization. The model corresponds to the first WH2 domain. 26 matched cddid_all.tbl CDD cd21802 cd21802 409641 CEN_ANKS4B central domain found in ankyrin repeat and SAM domain-containing protein 4B. Ankyrin repeat and SAM domain-containing protein 4B (ANKS4B), also called Harmonin-interacting ankyrin repeat-containing protein (Harp), is highly expressed in intestine and is essential for intermicrovillar adhesion. As part of the intermicrovillar adhesion complex (IMAC), ANKS4B plays a role in epithelial brush border differentiation, controlling microvilli organization and length. It may be involved in cellular response to endoplasmic reticulum stress. ANKS4B consists of four N-terminal ANK repeats, a central region, and a sterile alpha motif (SAM) followed by a C-terminal type I PDZ binding motif (PBM). This model corresponds to the central region (CEN) of ANKS4B, which contains the conserved regions CEN1 and CEN2. CEN is directly responsible for binding to the N-terminal MyTH4-FERM-SH3 supramodule of MYO7B, with a mechanism highly analogous to the interaction between USH1G and MYO7A. 46 matched cddid_all.tbl CDD cd21803 cd21803 409642 CEN_USH1G central domain found in usher syndrome type-1G protein. Usher syndrome type-1G protein (USH1G), also called scaffold protein containing ankyrin repeats and SAM domain (Sans), is an anchoring/scaffolding protein that is part of the functional network formed by USH1C, USH1G, CDH23 and MYO7A, that mediates mechanotransduction in cochlear hair cells. It is required for normal development and maintenance of cochlear hair cell bundles, as well as for normal hearing. USH1G consists of four N-terminal ANK repeats, a central region, and a sterile alpha motif (SAM) followed by a C-terminal type I PDZ binding motif (PBM). This model corresponds to the central region (CEN) of USH1G, which contains the conserved regions CEN1 and CEN2. CEN is directly responsible for binding to the MYO7A MyTH4-FERM tandem. 57 matched cddid_all.tbl CDD cd21804 cd21804 409637 DEFL_AtLURE1-like defensin-like domain found in Arabidopsis thaliana proteins LURE 1.2, LURE 1.6, and similar proteins. This subfamily includes Arabidopsis thaliana (At) LURE1.2 (also called cysteine-rich peptide 810_1.2, CRP810_1.2, or defensin-like protein 213) and AtLURE1.6 (also called cysteine-rich peptide 810_1.6, CRP810_1.6, or defensin-like protein 215). They are pollen tube attractants guiding pollen tubes to the ovular micropyle. AtLURE1.2 attracts specifically pollen tubes from A. thaliana, but not those from A. lyrata. It triggers endocytosis of MDIS1 in the pollen tube tip. This model corresponds to the defensin-like (DEFL) domains of AtLURE1.2 and AtLURE1.6, which adopts a typical structure characterized by cysteine-stabilized alpha/beta scaffold. 38 matched cddid_all.tbl CDD cd21805 cd21805 409638 DEFL_BmBKTx1-like defensin-like domain found in Mesobuthus martensii neurotoxin BmBKTx1 and similar proteins. BmBKTx1, also called potassium channel toxin alpha-KTx 19.1, or BmK37, is a selective inhibitor of high conductance calcium-activated potassium channels KCa1.1/KCNMA1. It belongs to a family of short-chain alpha-KTx toxins of the potassium channel (also called alpha-KTx19) and may be insect specific. This subfamily also includes Arabidopsis thaliana defensin-like protein 32 (AtDEF32). Its biological function remains unclear. This model corresponds to the defensin-like (DEFL) domain of BmBKTx1 and AtDEF32, which adopts a typical structure characterized by cysteine-stabilized alpha/beta scaffold. 39 matched cddid_all.tbl CDD cd21806 cd21806 409639 DEFL_defensin-like defensin-like domain found in bilateria defensins, sapecins, tenecins, phormicins, and lucifensins. This subfamily includes a group of bactericidal proteins, such as defensins, sapecins, tenecins, phormicins, and lucifensins from bilateria. They are host defense peptides produced in response to injury and mostly active against Gram-positive bacteria. This model corresponds to the defensin-like (DEFL) domain, which adopts a typical structure characterized by cysteine-stabilized alpha/beta scaffold. 38 matched cddid_all.tbl CDD cd21807 cd21807 409632 ABC-2_lan_permease_MutE_EpiE-like lantibiotic immunity ABC transporter MutE/EpiE family permease (also called ABC-2 transporter MutE/EpiE family permease) subunit. This subfamily includes lantibiotic ABC transporter permease subunits EpiE, MutE, SlvE and NisE, which are highly hydrophobic, integral membrane proteins, and part of the bacitracin ABC transport system that confers resistance to the Gram-positive bacteria in which this system operates, specifically to the lantibiotics mutacin, epidermin, nisin and salivaricin, respectively. Lantibiotics are small peptides, produced by Gram-positive bacteria, which are ribosomally-synthesized as pre-peptides and act by disrupting membrane integrity. Genes encoding the lantibiotic ABC transporter subunits are highly organized in operons containing all the genes required for maturation, transport, immunity, and synthesis. For example, in Staphylococcus epidermidis Tu3298, the lantibiotic epidermin is active against other Gram-positive bacteria via various modes of actions; however, its self-protection against the pore-forming epidermin is mediated by the ABC transporter immunity proteins composed of EpiF, EpiE and EpiG; the EpiE permease subunit transports epidermin to the surface and expels it from the membrane. This subfamily also includes the lantibiotic ABC transporter permease subunits MutE, SlvF, and NisE. Self-protection of the mutacin-producing strain Streptococcus mutans CH43 against the pore-forming lantibiotic mutacin is mediated by an ABC transporter composed of MutF, MutE and MutG. In salivaricin D-producing strain Streptococcus salivarius 5M6c, self-immunity against the intrinsically trypsin-resistant salivaricin is mediated via ABC transporter proteins SlvF, SlvE and SlvG, while in Lactococcus lactis, self-immunity against nisin is mediated by the ABC transporter NisFEG. The MutE, NisE and SlvF permease subunits transport mutacin, nisin and salivaricin, respectively to the surface and expel them from the membrane. 234 matched cddid_all.tbl CDD cd21808 cd21808 409633 ABC-2_lan_permease_MutG lantibiotic immunity ABC transporter MutG family permease (also called ABC-2 transporter MutG family permease) subunit. This subfamily includes lantibiotic ABC transporter permease subunit MutG which is a highly hydrophobic, integral membrane protein, and part of the bacitracin ABC transport system that confers resistance to the Gram-positive bacteria in which this system operates, specifically to lantibiotic mutacin. Lantibiotics are small peptides, produced by Gram-positive bacteria, which are ribosomally-synthesized as pre-peptides and act by disrupting membrane integrity. Genes encoding the lantibiotic ABC transporter subunits are highly organized in operons containing all the genes required for maturation, transport, immunity, and synthesis. For example, in Streptococcus mutans CH43, the lantibiotic mutacin is active against other Gram-positive bacteria via various modes of actions; however, its self-protection against the pore-forming mutacin is mediated by the ABC transporter composed of MutF, MutE, and MutG. This subfamily includes the MutG permease subunit that transports mutacin to the surface and expels it from the membrane. 237 matched cddid_all.tbl CDD cd21809 cd21809 409634 ABC-2_lan_permease-like lantibiotic immunity ABC transporter permease (also called ABC-2 transporter permease) subunit and similar proteins. This subfamily contains lantibiotic ABC transporter permease subunits which are highly hydrophobic, integral membrane proteins, and part of the bacitracin ABC transport system that confers resistance to the Gram-positive bacteria in which this system operates, particularly to type-A lantibiotics. Lantibiotics are small peptides, produced by Gram-positive bacteria, which are ribosomally-synthesized as pre-peptides and act by disrupting membrane integrity. Genes encoding the lantibiotic ABC transporter subunits are highly organized in operons containing all the genes required for maturation, transport, immunity, and synthesis. For example, in Lactococcus lactis, the lantibiotic nisin is active against other Gram-positive bacteria via various modes of actions; however, its self-protection against the pore-forming nisin is mediated by the ABC transporter composed of NisF, NisE and NisG; the NisG permease subunit transports nisin to the surface and expels it from the membrane. This family includes mostly uncharacterized transport permease subunits that transport lantibiotics to the surface and expel them from the membrane. 235 matched cddid_all.tbl CDD cd21810 cd21810 409635 ABC-2_lan_permease_NisG-like lantibiotic immunity ABC transporter NisG family permease (also called ABC-2 transporter NisG family permease) subunit, and similar proteins. This subfamily contains lantibiotic ABC transporter permease subunits NisG and NsuG, which are highly hydrophobic, integral membrane proteins, and part of the bacitracin ABC transport system that confers resistance to the Gram-positive bacteria in which this system operates, particularly to the lantibiotic nisin. Lantibiotics are small peptides, produced by Gram-positive bacteria, which are ribosomally-synthesized as pre-peptides and act by disrupting membrane integrity. Genes encoding the lantibiotic ABC transporter subunits are highly organized in operons containing all the genes required for maturation, transport, immunity, and synthesis. In Lactococcus lactis and Streptococcus uberis, the lantibiotic nisin is active against other Gram-positive bacteria via various modes of actions; however, its self-protection against the pore-forming nisin is mediated by the ABC transporter composed of NisF, NisE and NisG. In Streptococcus uberis, similar proteins provide self-protection against the pore-forming lantibiotic nisin U. This subfamily contains the NisG and NsuG permease subunits that transport nisin to the surface and expel it from the membrane. 211 matched cddid_all.tbl CDD cd21811 cd21811 409251 CoV_Nsp7 coronavirus non-structural protein 7. This model represents the non-structural protein 7 (Nsp7) of alpha-, beta-, gamma- and deltacoronaviruses, including highly pathogenic betacoronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Upon processing of the Nsp7-10 region by protease M (Mpro), the released four small proteins Nsp7, Nsp8, Nsp9 and Nsp10 form functional complexes with CoV core enzymes and stimulate replication. Most importantly, a complex of Nsp7 with Nsp8 has been shown to activate and confer processivity to the RNA-synthesizing activity of Nsp12, the RNA-dependent RNA-polymerase (RdRp); in SARS-CoV, point mutations in the NSP7- or NSP8-coding region have been shown to delay virus growth. Nsp7 and Nsp8 cooperate in activating the primer-dependent activity of the Nsp12 RdRp such that the level of their association may constitute a limiting factor for obtaining a high RNA polymerase activity. The subsequent Nsp7/Nsp8/Nsp12 polymerase complex is then able to associate with an active bifunctional Nsp14, which includes N-terminal 3' to 5' exoribonuclease (ExoN) and C-terminal N7-guanine cap methyltransferase (N7-MTase) activities, thus representing a unique coronavirus Nsp assembly that incorporates RdRp, exoribonuclease, and N7-MTase activities. Interaction of Nsp7 with Nsp8 appears to be conserved across the coronavirus family, making these proteins interesting drug targets. Nsp7 has a 4-helical bundle conformation which is strongly affected by its interaction with Nsp8, especially where it concerns alpha-helix 4. SARS-CoV Nsp7 forms a 8:8 hexadecameric supercomplex with Nsp8 that adopts a hollow cylinder-like structure with a large central channel and positive electrostatic properties in the cylinder, while Feline infectious peritonitis virus Nsp7 forms a 2:1 heterotrimer with Nsp8. Regardless of their oligomeric structure, the Nsp7/Nsp8 complex functions as a noncanonical RNA polymerase capable of synthesizing RNA of up to template length. 83 matched cddid_all.tbl CDD cd21812 cd21812 409627 MHV-like_Nsp3_betaSM betacoronavirus-specific marker of non-structural protein 3 from murine hepatitis virus and betacoronavirus in the A lineage. This model represents the betacoronavirus-specific marker (betaSM), also called group 2-specific marker (G2M), of non-structural protein 3 (Nsp3) from betacoronavirus in the embecovirus subgenus (A lineage), including murine hepatitis virus (MHV) and Human coronavirus HKU1. The betaSM/G2M is located C-terminal to the nucleic acid-binding (NAB) domain. This region is absent in alpha- and deltacoronavirus Nsp3; there is a gammacoronavirus-specific marker (gammaSM) at this position in gammacoronavirus Nsp3. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. Little is known about the betaSM/G2M domain; it is predicted to be non-enzymatic and may be an intrinsically disordered region. The betaSM/G2M domain is part of the predicted PLnc domain (made up of 385 amino acids) of the related SARS-CoV Nsp3 that may function as a replication/transcription scaffold, with interactions to Nsp5, Nsp12, Nsp13, Nsp14, and Nsp16. 125 matched cddid_all.tbl CDD cd21813 cd21813 409628 HKU9-like_Nsp3_betaSM betacoronavirus-specific marker of non-structural protein 3 from Rousettus bat coronavirus HKU9 and betacoronavirus in the D lineage. This model represents the betacoronavirus-specific marker (betaSM), also called group 2-specific marker (G2M), of non-structural protein 3 (Nsp3) from betacoronavirus in the nobecovirus subgenus (D lineage), including Rousettus bat coronavirus HKU9. The betaSM/G2M is located C-terminal to the nucleic acid-binding (NAB) domain. This region is absent in alpha- and deltacoronavirus Nsp3; there is a gammacoronavirus-specific marker (gammaSM) at this position in gammacoronavirus Nsp3. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. Little is known about the betaSM/G2M domain; it is predicted to be non-enzymatic and may be an intrinsically disordered region. The betaSM/G2M domain is part of the predicted PLnc domain (made up of 385 amino acids) of the related SARS-CoV Nsp3 that may function as a replication/transcription scaffold, with interactions to Nsp5, Nsp12, Nsp13, Nsp14, and Nsp16. 135 matched cddid_all.tbl CDD cd21814 cd21814 409629 SARS-CoV-like_Nsp3_betaSM betacoronavirus-specific marker of non-structural protein 3 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage. This model represents the betacoronavirus-specific marker (betaSM), also called group 2-specific marker (G2M), of non-structural protein 3 (Nsp3) from betacoronavirus in the sarbecovirus subgenus (B lineage), including highly pathogenic human coronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV). The betaSM/G2M is located C-terminal to the nucleic acid-binding (NAB) domain. This region is absent in alpha- and deltacoronavirus Nsp3; there is a gammacoronavirus-specific marker (gammaSM) at this position in gammacoronavirus Nsp3. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. Little is known about the betaSM/G2M domain; it is predicted to be non-enzymatic and may be an intrinsically disordered region. The betaSM/G2M domain is part of the predicted PLnc domain (made up of 385 amino acids) of SARS-CoV Nsp3 that may function as a replication/transcription scaffold, with interactions to Nsp5, Nsp12, Nsp13, Nsp14, and Nsp16. 116 matched cddid_all.tbl CDD cd21815 cd21815 409630 MERS-CoV-like_Nsp3_betaSM betacoronavirus-specific marker of non-structural protein 3 from Middle East respiratory syndrome-related coronavirus and betacoronavirus in the C lineage. This model represents the betacoronavirus-specific marker (betaSM), also called group 2-specific marker (G2M), of non-structural protein 3 (Nsp3) from betacoronavirus in the merbecovirus subgenus (C lineage), including Middle East respiratory syndrome-related coronavirus (MERS-CoV) and Tylonycteris bat coronavirus HKU4. The betaSM/G2M is located C-terminal to the nucleic acid-binding (NAB) domain. This region is absent in alpha- and deltacoronavirus Nsp3; there is a gammacoronavirus-specific marker (gammaSM) at this position in gammacoronavirus Nsp3. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. Little is known about the betaSM/G2M domain; it is predicted to be non-enzymatic and may be an intrinsically disordered region. The betaSM/G2M domain is part of the predicted PLnc domain (made up of 385 amino acids) of the related SARS-CoV Nsp3 that may function as a replication/transcription scaffold, with interactions to Nsp5, Nsp12, Nsp13, Nsp14, and Nsp16. 124 matched cddid_all.tbl CDD cd21816 cd21816 409256 CoV_Nsp8 Coronavirus non-structural protein 8. This model represents the non-structural protein 8 (Nsp8) of alpha-, beta-, gamma- and deltacoronaviruses, including highly pathogenic betacoronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Upon processing of the Nsp7-10 region by protease M (Mpro), the released four small proteins Nsp7, Nsp8, Nsp9, and Nsp10 form functional complexes with CoV core enzymes and thereby stimulate replication. Most importantly, a complex of Nsp8 with Nsp7 has been shown to activate and confer processivity to the RNA-synthesizing activity of Nsp12, the RNA-dependent RNA-polymerase (RdRp); in SARS-CoV, point mutations in the genes encoding Nsp8 and Nsp7 have been shown to delay virus growth. Nsp8 and Nsp7 cooperate in activating the primer-dependent activity of the Nsp12 RdRp such that the level of their association may constitute a limiting factor for obtaining a high RNA polymerase activity. The subsequent Nsp7/Nsp8/Nsp12 polymerase complex is then able to associate with an active bifunctional Nsp14, which includes N-terminal 3' to 5' exoribonuclease (ExoN) and C-terminal N7-guanine cap methyltransferase (N7-MTase) activities, thus representing a unique coronavirus Nsp assembly that incorporates RdRp, exoribonuclease, and N7-MTase activities. Interaction of Nsp8 with Nsp7 appears to be conserved across the coronavirus family, making these proteins interesting drug targets. Nsp8 has a novel 'golf-club' fold composed of an N-terminal 'shaft' domain and a C-terminal 'head' domain. The shaft domain contains three helices, one of which is very long, while the head domain contains another three helices and seven beta-strands, forming an alpha/beta fold. SARS-CoV Nsp8 forms a 8:8 hexadecameric supercomplex with Nsp7 that adopts a hollow cylinder-like structure with a large central channel and positive electrostatic properties in the cylinder, while Feline infectious peritonitis virus Nsp8 forms a 1:2 heterotrimer with Nsp7. Regardless of their oligomeric structure, the Nsp7/Nsp8 complex functions as a noncanonical RNA polymerase capable of synthesizing RNA of up to the template length. 194 matched cddid_all.tbl CDD cd21817 cd21817 409622 IgC1_CH1_IgEG CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and gamma chain; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the first immunoglobulin constant-1 set domain of epsilon and gamma chains. It belongs to a family composed of the first immunoglobulin constant-1 set domain of alpha, delta, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors. 94 matched cddid_all.tbl CDD cd21818 cd21818 409623 IgC1_CH1_IgA CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the first immunoglobulin constant-1 set domain of alpha chains. It belongs to a family composed of the first immunoglobulin constant-1 set domain of alpha, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors. 94 matched cddid_all.tbl CDD cd21819 cd21819 409624 IgC1_CH1_IgM CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy mu chain; member of the C1-set of Ig superfamily (IgSF) domains. The members here are composed of the first immunoglobulin constant-1 set domain of mu chains. It belongs to a family composed of the first immunoglobulin constant-1 set domain of alpha, delta, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors. 95 matched cddid_all.tbl CDD cd21820 cd21820 409625 IgC1_MHC_1b_Qa-1b Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1b; member of the C1-set of Ig superfamily (IgSF) domains. The non-classical mouse MHC class I (MHC-I) molecule Qa-1b is a non-polymorphic MHC molecule with an important function in innate immunity. It binds and presents signal peptides of classical MHC-I molecules at the cell surface and, as such, act as an indirect sensor for the normal expression of MHC-I molecules. This signal peptide dominantly accommodated in the groove of Qa-1b is called Qdm, for Qa-1 determinant modifier, and its amino acid sequence AMAPRTLLL is highly conserved among mammalian species. The Qdm/Qa-1b complex serves as a ligand for the germ-line encoded heterodimeric CD94/NKG2A receptors expressed on natural killer (NK) cells and activated CD8+ T cells and transduces inhibitory signals to these lymphocytes. Thus, upon binding, Qa-1b signals NK cells not to engage in cell lysis. The molecular basis of Qa-1b function is unclear. 98 matched cddid_all.tbl CDD cd21821 cd21821 409352 MavE Dot/Icm type IV secretion system effector MavE. The Icm/Dot protein translocation apparatus is a type IVb secretion system, highly related to bacterial conjugative DNA transfer systems, and is important in establishing a replication vacuole. A complex of Icm/Dot proteins spans the bacterial envelope, allowing the transfer of proteins from the bacterial cytoplasm across membranes located in the target host eukaryotic cell. Icm/Dot-translocated substrates (IDTS) control construction of the replication compartment and have been shown to directly regulate membrane traffic associated with the movement of vesicles along steps in the early secretory system. Although the function of Legionella MavE is unknown, it has been shown to be an Icm/Dot-translocated substrate and is assumed to play a role in this type IV secretion system. 132 matched cddid_all.tbl CDD cd21822 cd21822 409348 SARS-CoV-like_Nsp3_NAB nucleic acid binding domain of non-structural protein 3 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage. This model represents the nucleic acid binding (NAB) domain of non-structural protein 3 (Nsp3) from betacoronavirus in the sarbecovirus subgenus (B lineage) and hibecovirus subgenus, including highly pathogenic human coronaviruses (CoVs) such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV). The NAB domain represents a new fold, with a parallel four-strand beta-sheet holding two alpha-helices of three and four turns that are oriented antiparallel to the beta-strands. NAB is a cytoplasmic domain located between the papain-like protease (PLPro) and betacoronavirus-specific marker (betaSM) domains of CoV Nsp3. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. The NAB domain both binds ssRNA and unwinds dsDNA. It prefers to bind ssRNA containing repeats of three consecutive guanines. A group of residues that form a positively charged patch on the protein surface of SARS-CoV Nsp3 NAB serves as the binding site of nucleic acids. This site is conserved in the NAB of Nsp3 from betacoronavirus in the B lineage. 107 matched cddid_all.tbl CDD cd21823 cd21823 409349 MERS-CoV-like_Nsp3_NAB nucleic acid binding domain of non-structural protein 3 from Middle East respiratory syndrome-related coronavirus and betacoronavirus in the C lineage. This model represents the nucleic acid binding (NAB) domain of non-structural protein 3 (Nsp3) from betacoronavirus in the merbecovirus subgenus (C lineage), including Middle East respiratory syndrome-related coronavirus (MERS-CoV) and Tylonycteris bat coronavirus HKU4. The NAB domain represents a new fold, with a parallel four-strand beta-sheet holding two alpha-helices of three and four turns that are oriented antiparallel to the beta-strands. NAB is a cytoplasmic domain located between the papain-like protease (PLPro) and betacoronavirus-specific marker (betaSM) domains of CoV Nsp3. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. The NAB domain both binds ssRNA and unwinds dsDNA. It prefers to bind ssRNA containing repeats of three consecutive guanines. A group of residues that form a positively charged patch on the protein surface of SARS-CoV Nsp3 NAB serves as the binding site of nucleic acids. This site is conserved in the NAB of Nsp3 from betacoronavirus in the sarbecovirus subgenus (B lineage), and appears to be partially conserved in the Nsp3 NAB from betacoronaviruses in the C lineage. 123 matched cddid_all.tbl CDD cd21824 cd21824 409350 MHV-like_Nsp3_NAB nucleic acid binding domain of non-structural protein 3 from murine hepatitis virus and betacoronavirus in the A lineage. This model represents the nucleic acid binding (NAB) domain of non-structural protein 3 (Nsp3) from betacoronavirus in the embecovirus subgenus (A lineage), including murine hepatitis virus (MHV) and Human coronavirus HKU1. The NAB domain represents a new fold, with a parallel four-strand beta-sheet holding two alpha-helices of three and four turns that are oriented antiparallel to the beta-strands. NAB is a cytoplasmic domain located between the papain-like protease (PLPro) and betacoronavirus-specific marker (betaSM) domains of CoV Nsp3. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. The NAB domain both binds ssRNA and unwinds dsDNA. It prefers to bind ssRNA containing repeats of three consecutive guanines. A group of residues that form a positively charged patch on the protein surface of SARS-CoV Nsp3 NAB serves as the binding site of nucleic acids. This site is conserved in the NAB of Nsp3 from betacoronavirus in the sarbecovirus subgenus (B lineage), but is not conserved in the Nsp3 NAB from betacoronaviruses in the A lineage. 119 matched cddid_all.tbl CDD cd21825 cd21825 409351 HKU9-like_Nsp3_NAB nucleic acid binding domain of non-structural protein 3 from Rousettus bat coronavirus HKU9 and betacoronavirus in the D lineage. This model represents the nucleic acid binding (NAB) domain of non-structural protein 3 (Nsp3) from betacoronavirus in the nobecovirus subgenus (D lineage), including Rousettus bat coronavirus HKU9. The NAB domain represents a new fold, with a parallel four-strand beta-sheet holding two alpha-helices of three and four turns that are oriented antiparallel to the beta-strands. NAB is a cytoplasmic domain located between the papain-like protease (PLPro) and betacoronavirus-specific marker (betaSM) domains of CoV Nsp3. Nsp3 is a large multi-functional multi-domain protein that is an essential component of the replication/transcription complex (RTC), which carries out RNA synthesis, RNA processing, and interference with the host cell innate immune system. The NAB domain both binds ssRNA and unwinds dsDNA. It prefers to bind ssRNA containing repeats of three consecutive guanines. A group of residues that form a positively charged patch on the protein surface of SARS-CoV Nsp3 NAB serves as the binding site of nucleic acids. This site is conserved in the NAB of Nsp3 from betacoronavirus in the sarbecovirus subgenus (B lineage), but is not conserved in the Nsp3 NAB from betacoronaviruses in the D lineage. 117 matched cddid_all.tbl CDD cd21826 cd21826 409252 alphaCoV_Nsp7 alphacoronavirus non-structural protein 7. This model represents the non-structural protein 7 (Nsp7) of alphacoronaviruses that include Feline infectious peritonitis virus (FCoV), Human coronavirus NL63 (HCoV-NL63), and Porcine transmissible gastroenteritis coronavirus (TGEV), among others. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Upon processing of the Nsp7-10 region by protease M (Mpro), the released four small proteins Nsp7, Nsp8, Nsp9 and Nsp10 form functional complexes with CoV core enzymes and stimulate replication. Most importantly, a complex of Nsp7 with Nsp8 has been shown to activate and confer processivity to the RNA-synthesizing activity of Nsp12, the RNA-dependent RNA-polymerase (RdRp); in SARS-CoV, point mutations in the NSP7- or NSP8-coding region have been shown to delay virus growth. Nsp7 and Nsp8 cooperate in activating the primer-dependent activity of the Nsp12 RdRp such that the level of their association may constitute a limiting factor for obtaining a high RNA polymerase activity. The subsequent Nsp7/Nsp8/Nsp12 polymerase complex is then able to associate with an active bifunctional Nsp14, which includes N-terminal 3' to 5' exoribonuclease (ExoN) and C-terminal N7-guanine cap methyltransferase (N7-MTase) activities, thus representing a unique coronavirus Nsp assembly that incorporates RdRp, exoribonuclease, and N7-MTase activities. Interaction of Nsp7 with Nsp8 appears to be conserved across the coronavirus family, making these proteins interesting drug targets. Nsp7 has a 4-helical bundle conformation which is strongly affected by its interaction with Nsp8, especially where it concerns alpha-helix 4. FCoV Nsp7 forms a 2:1 heterotrimer with Nsp8; the Nsp7/Nsp8 complex functions as a noncanonical RNA polymerase capable of synthesizing RNA of up to template length. 83 matched cddid_all.tbl CDD cd21827 cd21827 409253 betaCoV_Nsp7 betacoronavirus non-structural protein 7. This model represents the non-structural protein 7 (Nsp7) of betacoronaviruses including the highly pathogenic Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Upon processing of the Nsp7-10 region by protease M (Mpro), the released four small proteins Nsp7, Nsp8, Nsp9 and Nsp10 form functional complexes with CoV core enzymes and stimulate replication. Most importantly, a complex of Nsp7 with Nsp8 has been shown to activate and confer processivity to the RNA-synthesizing activity of Nsp12, the RNA-dependent RNA-polymerase (RdRp); in SARS-CoV, point mutations in the NSP7- or NSP8-coding region have been shown to delay virus growth. Nsp7 and Nsp8 cooperate in activating the primer-dependent activity of the Nsp12 RdRp such that the level of their association may constitute a limiting factor for obtaining a high RNA polymerase activity. The subsequent Nsp7/Nsp8/Nsp12 polymerase complex is then able to associate with an active bifunctional Nsp14, which includes N-terminal 3' to 5' exoribonuclease (ExoN) and C-terminal N7-guanine cap methyltransferase (N7-MTase) activities, thus representing a unique coronavirus Nsp assembly that incorporates RdRp, exoribonuclease, and N7-MTase activities. Interaction of Nsp7 with Nsp8 appears to be conserved across the coronavirus family, making these proteins interesting drug targets. Nsp7 has a 4-helical bundle conformation which is strongly affected by its interaction with Nsp8, especially where it concerns alpha-helix 4. SARS-CoV Nsp7 forms a 8:8 hexadecameric supercomplex with Nsp8 that adopts a hollow cylinder-like structure with a large central channel and positive electrostatic properties in the cylinder; the Nsp7/Nsp8 complex functions as a noncanonical RNA polymerase capable of synthesizing RNA of up to template length. 83 matched cddid_all.tbl CDD cd21828 cd21828 409254 gammaCoV_Nsp7 gammacoronavirus non-structural protein 7. This model represents the non-structural protein 7 (Nsp7) of gammacoronaviruses that include Avian infectious bronchitis virus (IBV) and Canada goose coronavirus (CGCoV), among others. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Upon processing of the Nsp7-10 region by protease M (Mpro), the released four small proteins Nsp7, Nsp8, Nsp9 and Nsp10 form functional complexes with CoV core enzymes and stimulate replication. Most importantly, a complex of Nsp7 with Nsp8 has been shown to activate and confer processivity to the RNA-synthesizing activity of Nsp12, the RNA-dependent RNA-polymerase (RdRp); in SARS-CoV, point mutations in the NSP7- or NSP8-coding region have been shown to delay virus growth. Nsp7 and Nsp8 cooperate in activating the primer-dependent activity of the Nsp12 RdRp such that the level of their association may constitute a limiting factor for obtaining a high RNA polymerase activity. The subsequent Nsp7/Nsp8/Nsp12 polymerase complex is then able to associate with an active bifunctional Nsp14, which includes N-terminal 3' to 5' exoribonuclease (ExoN) and C-terminal N7-guanine cap methyltransferase (N7-MTase) activities, thus representing a unique coronavirus Nsp assembly that incorporates RdRp, exoribonuclease, and N7-MTase activities. Interaction of Nsp7 with Nsp8 appears to be conserved across the coronavirus family, making these proteins interesting drug targets. Nsp7 has a 4-helical bundle conformation which is strongly affected by its interaction with Nsp8, especially where it concerns alpha-helix 4. SARS-CoV Nsp7 forms a 8:8 hexadecameric supercomplex with Nsp8 that adopts a hollow cylinder-like structure with a large central channel and positive electrostatic properties in the cylinder, while Feline infectious peritonitis virus Nsp7 forms a 2:1 heterotrimer with Nsp8. Regardless of their oligomeric structure, the Nsp7/Nsp8 complex functions as a noncanonical RNA polymerase capable of synthesizing RNA of up to template length. 83 matched cddid_all.tbl CDD cd21829 cd21829 409255 deltaCoV_Nsp7 deltacoronavirus non-structural protein 7. This model represents the non-structural protein 7 (Nsp7) of deltacoronaviruses that include White-eye coronavirus HKU16 and Quail coronavirus UAE-HKU30, among others. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Upon processing of the Nsp7-10 region by protease M (Mpro), the released four small proteins Nsp7, Nsp8, Nsp9 and Nsp10 form functional complexes with CoV core enzymes and stimulate replication. Most importantly, a complex of Nsp7 with Nsp8 has been shown to activate and confer processivity to the RNA-synthesizing activity of Nsp12, the RNA-dependent RNA-polymerase (RdRp); in SARS-CoV, point mutations in the NSP7- or NSP8-coding region have been shown to delay virus growth. Nsp7 and Nsp8 cooperate in activating the primer-dependent activity of the Nsp12 RdRp such that the level of their association may constitute a limiting factor for obtaining a high RNA polymerase activity. The subsequent Nsp7/Nsp8/Nsp12 polymerase complex is then able to associate with an active bifunctional Nsp14, which includes N-terminal 3' to 5' exoribonuclease (ExoN) and C-terminal N7-guanine cap methyltransferase (N7-MTase) activities, thus representing a unique coronavirus Nsp assembly that incorporates RdRp, exoribonuclease, and N7-MTase activities. Interaction of Nsp7 with Nsp8 appears to be conserved across the coronavirus family, making these proteins interesting drug targets. Nsp7 has a 4-helical bundle conformation which is strongly affected by its interaction with Nsp8, especially where it concerns alpha-helix 4. SARS-CoV Nsp7 forms a 8:8 hexadecameric supercomplex with Nsp8 that adopts a hollow cylinder-like structure with a large central channel and positive electrostatic properties in the cylinder, while Feline infectious peritonitis virus Nsp7 forms a 2:1 heterotrimer with Nsp8. Regardless of their oligomeric structure, the Nsp7/Nsp8 complex functions as a noncanonical RNA polymerase capable of synthesizing RNA of up to template length. 96 matched cddid_all.tbl CDD cd21830 cd21830 409257 alphaCoV_Nsp8 alphacoronavirus non-structural protein 8. This model represents the non-structural protein 8 (Nsp8) region of alphacoronaviruses that include Feline infectious peritonitis virus (FCoV), Human coronavirus NL63 (HCoV-NL63), and Porcine epidemic diarrhea coronavirus (PEDV), among others. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Upon processing of the Nsp7-10 region by protease M (Mpro), the released four small proteins Nsp7, Nsp8, Nsp9, and Nsp10 form functional complexes with CoV core enzymes and thereby stimulate replication. Most importantly, a complex of Nsp8 with Nsp7 has been shown to activate and confer processivity to the RNA-synthesizing activity of Nsp12, the RNA-dependent RNA-polymerase (RdRp); in SARS-CoV, point mutations in the genes encoding Nsp8 and Nsp7 have been shown to delay virus growth. Nsp8 and Nsp7 cooperate in activating the primer-dependent activity of the Nsp12 RdRp such that the level of their association may constitute a limiting factor for obtaining a high RNA polymerase activity. The subsequent Nsp7/Nsp8/Nsp12 polymerase complex is then able to associate with an active bifunctional Nsp14, which includes N-terminal 3' to 5' exoribonuclease (ExoN) and C-terminal N7-guanine cap methyltransferase (N7-MTase) activities, thus representing a unique coronavirus Nsp assembly that incorporates RdRp, exoribonuclease, and N7-MTase activities. Interaction of Nsp8 with Nsp7 appears to be conserved across the coronavirus family, making these proteins interesting drug targets. Nsp8 has a novel 'golf-club' fold composed of an N-terminal 'shaft' domain and a C-terminal 'head' domain. The shaft domain contains three helices, one of which is very long, while the head domain contains another three helices and seven beta-strands, forming an alpha/beta fold. FCoV Nsp8 forms a 1:2 heterotrimer with Nsp7; the Nsp7/Nsp8 complex functions as a noncanonical RNA polymerase capable of synthesizing RNA of up to the template length. 195 matched cddid_all.tbl CDD cd21831 cd21831 409258 betaCoV_Nsp8 betacoronavirus non-structural protein 8. This model represents the non-structural protein 8 (Nsp8) the highly pathogenic betacoronaviruses that include Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Upon processing of the Nsp7-10 region by protease M (Mpro), the released four small proteins Nsp7, Nsp8, Nsp9, and Nsp10 form functional complexes with CoV core enzymes and thereby stimulate replication. Most importantly, a complex of Nsp8 with Nsp7 has been shown to activate and confer processivity to the RNA-synthesizing activity of Nsp12, the RNA-dependent RNA-polymerase (RdRp); in SARS-CoV, point mutations in the genes encoding Nsp8 and Nsp7 have been shown to delay virus growth. Nsp8 and Nsp7 cooperate in activating the primer-dependent activity of the Nsp12 RdRp such that the level of their association may constitute a limiting factor for obtaining a high RNA polymerase activity. The subsequent Nsp7/Nsp8/Nsp12 polymerase complex is then able to associate with an active bifunctional Nsp14, which includes N-terminal 3' to 5' exoribonuclease (ExoN) and C-terminal N7-guanine cap methyltransferase (N7-MTase) activities, thus representing a unique coronavirus Nsp assembly that incorporates RdRp, exoribonuclease, and N7-MTase activities. Interaction of Nsp8 with Nsp7 appears to be conserved across the coronavirus family, making these proteins interesting drug targets. Nsp8 has a novel 'golf-club' fold composed of an N-terminal 'shaft' domain and a C-terminal 'head' domain. The shaft domain contains three helices, one of which is very long, while the head domain contains another three helices and seven beta-strands, forming an alpha/beta fold. SARS-CoV Nsp8 forms a 8:8 hexadecameric supercomplex with Nsp7 that adopts a hollow cylinder-like structure with a large central channel and positive electrostatic properties in the cylinder; the Nsp7/Nsp8 complex functions as a noncanonical RNA polymerase capable of synthesizing RNA of up to the template length. 196 matched cddid_all.tbl CDD cd21832 cd21832 409259 gammaCoV_Nsp8 gammacoronavirus non-structural protein 8. This model represents the non-structural protein 8 (Nsp8) region of gammacoronaviruses that include Avian infectious bronchitis virus (IBV) and Canada goose coronavirus (CGCoV), among others. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Upon processing of the Nsp7-10 region by protease M (Mpro), the released four small proteins Nsp7, Nsp8, Nsp9, and Nsp10 form functional complexes with CoV core enzymes and thereby stimulate replication. Most importantly, a complex of Nsp8 with Nsp7 has been shown to activate and confer processivity to the RNA-synthesizing activity of Nsp12, the RNA-dependent RNA-polymerase (RdRp); in SARS-CoV, point mutations in the genes encoding Nsp8 and Nsp7 have been shown to delay virus growth. Nsp8 and Nsp7 cooperate in activating the primer-dependent activity of the Nsp12 RdRp such that the level of their association may constitute a limiting factor for obtaining a high RNA polymerase activity. The subsequent Nsp7/Nsp8/Nsp12 polymerase complex is then able to associate with an active bifunctional Nsp14, which includes N-terminal 3' to 5' exoribonuclease (ExoN) and C-terminal N7-guanine cap methyltransferase (N7-MTase) activities, thus representing a unique coronavirus Nsp assembly that incorporates RdRp, exoribonuclease, and N7-MTase activities. Interaction of Nsp8 with Nsp7 appears to be conserved across the coronavirus family, making these proteins interesting drug targets. Nsp8 has a novel 'golf-club' fold composed of an N-terminal 'shaft' domain and a C-terminal 'head' domain. The shaft domain contains three helices, one of which is very long, while the head domain contains another three helices and seven beta-strands, forming an alpha/beta fold. SARS-CoV Nsp8 forms a 8:8 hexadecameric supercomplex with Nsp7 that adopts a hollow cylinder-like structure with a large central channel and positive electrostatic properties in the cylinder, while Feline infectious peritonitis virus Nsp8 forms a 1:2 heterotrimer with Nsp7. Regardless of their oligomeric structure, the Nsp7/Nsp8 complex functions as a noncanonical RNA polymerase capable of synthesizing RNA of up to the template length. 210 matched cddid_all.tbl CDD cd21833 cd21833 409260 deltaCoV_Nsp8 deltacoronavirus non-structural protein 8. This model represents the non-structural protein 8 (Nsp8) region of deltacoronaviruses that include White-eye coronavirus HKU16 and Quail coronavirus UAE-HKU30, among others. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Upon processing of the Nsp7-10 region by protease M (Mpro), the released four small proteins Nsp7, Nsp8, Nsp9, and Nsp10 form functional complexes with CoV core enzymes and thereby stimulate replication. Most importantly, a complex of Nsp8 with Nsp7 has been shown to activate and confer processivity to the RNA-synthesizing activity of Nsp12, the RNA-dependent RNA-polymerase (RdRp); in SARS-CoV, point mutations in the genes encoding Nsp8 and Nsp7 have been shown to delay virus growth. Nsp8 and Nsp7 cooperate in activating the primer-dependent activity of the Nsp12 RdRp such that the level of their association may constitute a limiting factor for obtaining a high RNA polymerase activity. The subsequent Nsp7/Nsp8/Nsp12 polymerase complex is then able to associate with an active bifunctional Nsp14, which includes N-terminal 3' to 5' exoribonuclease (ExoN) and C-terminal N7-guanine cap methyltransferase (N7-MTase) activities, thus representing a unique coronavirus Nsp assembly that incorporates RdRp, exoribonuclease, and N7-MTase activities. Interaction of Nsp8 with Nsp7 appears to be conserved across the coronavirus family, making these proteins interesting drug targets. Nsp8 has a novel 'golf-club' fold composed of an N-terminal 'shaft' domain and a C-terminal 'head' domain. The shaft domain contains three helices, one of which is very long, while the head domain contains another three helices and seven beta-strands, forming an alpha/beta fold. SARS-CoV Nsp8 forms a 8:8 hexadecameric supercomplex with Nsp7 that adopts a hollow cylinder-like structure with a large central channel and positive electrostatic properties in the cylinder, while Feline infectious peritonitis virus Nsp8 forms a 1:2 heterotrimer with Nsp7. Regardless of their oligomeric structure, the Nsp7/Nsp8 complex functions as a noncanonical RNA polymerase capable of synthesizing RNA of up to the template length. 189 matched cddid_all.tbl CDD cd21834 cd21834 411711 Hhal-like Restriction endonuclease HhaI and similar endonucleases. HhaI is a type II restriction endonuclease that recognizes the symmetric sequence 5'-GCG|C-3' (| denotes the cleavage site) and produces fragments with 2-base, 3'-overhangs. It domain belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and HindIII. 261 matched cddid_all.tbl CDD cd21835 cd21835 409346 SagF streptolysin S-associated protein SagF. Streptolysin S-associated protein SagF is encoded by the sagF gene, which has been identified to be a hemolytic activity-related gene in SEZ (Streptococcus equi ssp. zooepidemicus). The sagF gene is located in the same operon with sagD gene in the SEZ genome implying that it should play an important role in SEZ hemolytic activity and is an indispensable gene in the sag operon for streptolysin S (SLS) biosynthesis. 225 matched cddid_all.tbl CDD cd21836 cd21836 409345 adhesin_CP Neisseria gonorrhoeae Adhesin Complex Protein and similar proteins. This model contains adhesin complex protein found in Neisseria gonorrhoeae (Ng-ACP), the causative organism of the sexually transmitted disease gonorrhoea, and similar proteins. Studies have shown that Ng-ACP is conserved and expressed by over 50 gonococcal strains and that recombinant proteins induce antibodies in mice that killed the bacteria in vitro. Thus, recombinant Ng-ACP (rNg-ACP) is a potential vaccine candidate that induces antibodies that are bactericidal and prevent the gonococcus from inhibiting the lytic activity of an innate defense molecule. This protein is structurally similar to N. meningitidis adhesin complex protein as well as members of the MliC/PliC protein family of membrane-bound or periplasmic inhibitors of human C-type lysozyme (HL), suggesting that Ng-ACP may probably be located in the periplasm or phospholipid layer of the outer membrane. 93 matched cddid_all.tbl CDD cd21837 cd21837 409344 AvrRps4-like Pseudomonas syringae coiled-coil effector AvrRps4 C-terminal region, and regions in similar proteins. This model includes the C-terminal region of AvrRps4, a type III-secreted (T3S) effector protein originally identified in Pseudomonas syringae pv. pisi, a causal agent of bacterial blight in pea. AvrRps4 triggers RPS4 (resistance to P. syringae 4)-dependent immunity in resistant accessions of Arabidopsis. AvrRps4 is a bipartite effector, processed upon entry in planta by cleavage between two glycine residues, generating two protein parts, AvrRps4N and AvrRps4C. Mutation studies have shown that an electronegative surface patch in AvrRps4(C) is required for recognition by RPS4; mutations in this region have been shown to uncouple triggering of the hypersensitive response from disease resistance. The N-terminal part of AvrRps4 was previously assumed to only function in effector secretion into the host cell; however, in Arabidopsis, which uses a pair of resistance proteins, RRS1 and RPS4, both AvrRps4 parts are required for triggering resistance in Arabidopsis, and in fact, AvrRps4N on its own has some functions of an effector, implying that the fusion of the two AvrRps4 parts may have arisen to counteract plant defenses. 86 matched cddid_all.tbl CDD cd21839 cd21839 439298 BDD_Gal11-like beta-defensin domain found in gallinacin-11 (Gal-11) and gallinacin-13 (Gal-13). The family includes the beta-defensin domains of gallinacin 11 (Gal-11) and Gal-13. Gal-11, also called beta-defensin 11, or vitelline membrane outer layer protein 2 or vitelline membrane outer layer protein II (VMO-II or VMOII), is an antimicrobial peptide found in chicken egg. It is one of four major proteins in vitelline membranes, along with ovomucin, lysozyme, and VMO-1. Gal-11 has bactericidal activity toward both Gram-positive and Gram-negative bacteria. It is a compact fold composed of 2 packed beta-defensin domains, with the beta-defensin#related motifs, CX6CX5CX9CX6CC and CX6CX6CX7CX6CC, respectively. Gal-13, also called beta-defensin 13, has bactericidal activity against Escherichia coli, Listeria monocytogenes, Salmonella typhimurium and Streptococcus pyogenes but not against Staphylococcus aureus. Gal-13 contains only one beta-defensin domain. 32 matched cddid_all.tbl CDD cd21840 cd21840 439312 CAL1_NTD N-terminal domain of Drosophila melanogaster chromosome alignment defect 1 (CAL1). CAL1 is an evolutionarily distinct CENP-A histone chaperone that binds both CENP-A and the centromere receptor CENP-C, and functions in both pre-nucleosomal CENP-A recognition and its targeting to the centromere for deposition. Thus, it appears to combine the roles of HJURP as well as the Mis18 complex, which are CENP-A chaperones present in eukaryotes but absent in Drosophila. This model corresponds to the N-terminal domain of CAL1, which is responsible for binding to CENP-A/H4. 56 matched cddid_all.tbl CDD cd21844 cd21844 439313 JAK1bd_box_IFNLR1-like JAK1 binding box domain found in interferon lambda receptor 1 (IFNLR1), interleukin-10 receptor subunit alpha (IL10RA) and similar proteins. This family includes two class II cytokine receptors, IFNLR1 and IL10RA. IFNLR1 (also called IFN-lambda receptor 1, IFN-lambda-R1, cytokine receptor class-II member 12, cytokine receptor family 2 member 12, CRF2-12, interleukin-28 receptor subunit alpha, IL-28 receptor subunit alpha, IL-28R-alpha, IL-28RA, likely interleukin, cytokine receptor 2 or LICR2), together with IL10RB, forms a dimer. The IFNLR1/IL10RB dimer is a receptor for the cytokine ligands IFNL2 and IFNL3, and mediates their antiviral activity. The ligand/receptor complex stimulates the activation of the JAK/STAT signaling pathway, leading to expression of IFN-stimulated genes (ISG), which contribute to the antiviral state. IFNLR1 determines the cell type specificity of the lambda interferon action. It plays a significant role in the antiviral immune defense in the intestinal epithelium. IL10RA (also called IL-10 receptor subunit alpha, IL-10R subunit alpha, IL-10RA, CDw210a, interleukin-10 receptor subunit 1, IL-10R subunit 1, or IL-10R1) is a cell surface receptor for the cytokine IL10 that participates in IL10-mediated anti-inflammatory functions, limiting excessive tissue disruption caused by inflammation. Both, IFNLR1 and IL10RA, contain a box domain consisting of box1 and box2. The cytokine receptor box1 motif is critical for JAK kinase binding and activation. 49 matched cddid_all.tbl CDD cd21853 cd21853 439316 KNL1_NTD N-terminal domain found in kinetochore scaffold 1 (KNL1) and similar proteins. Kinetochore scaffold 1 (KNL1), also called ALL1-fused gene from chromosome 15q14 protein (AF15q14), Bub-linking kinetochore protein (Blinkin), cancer susceptibility candidate gene 5 protein (CASC5), cancer/testis antigen 29 (CT29), kinetochore-null protein 1, or protein D40/AF15q14, plays crucial roles during mitosis. It is essential for spindle-assembly checkpoint (SAC) signaling and for correct chromosome alignment. It is required for attachment of the kinetochores to the spindle microtubules. KNL1 directly links BUB1 and BUB1B to kinetochores. It is part of the MIS12 complex, which may be fundamental for kinetochore formation and proper chromosome segregation during mitosis. KNL1 also acts in coordination with CENPK to recruit the NDC80 complex to the outer kinetochore. This model corresponds to a small conserved region at the N-terminus of KNL1, which is responsible for the binding of protein phosphatase 1 (PP1). PP1 regulates SAC silencing and mitotic exit, and is targeted to kinetochores, in part, by KNL1. 56 matched cddid_all.tbl CDD cd21856 cd21856 439317 Plk4BD_Cep192 Plk4-binding domain found in centrosomal protein of 192 kDa (Cep192) and similar proteins. Cep192, also called SPD-2, plays a critical role in mitotic centrosome maturation and bipolar spindle assembly. It appears to be a major regulator of pericentriolar material (PCM) recruitment and centriole duplication. It is a centrosome-specific activating scaffold for Aurora kinase A (AURKA) and polo-like kinase 1 (Plk1). Cep192 also plays a key role in centrosome recruitment of both Cep152 and Polo-like kinase 4 (Plk4). This model corresponds to a conserved region in Cep192 that is responsible for binding to the cryptic polo box (CPB) of Plk4. 51 matched cddid_all.tbl CDD cd21864 cd21864 412061 GTSE1_CTD C-terminal domain of G2 and S phase-expressed protein 1. G2 and S phase-expressed protein 1 (GTSE-1), also called protein B99 homolog, is a cell cycle-regulated protein mainly localized in the cytoplasm and apparently associated with microtubules. It may be involved in p53-induced cell cycle arrest in G2/M phase by interfering with microtubule rearrangements that are required to enter mitosis. Overexpression of GTSE-1 delays G2/M phase progression. GTSE-1 is a clathrin adaptor protein; it is recruited to the spindle by clathrin, which stabilizes microtubules by inhibiting the microtubule depolymerase MCAK. This model corresponds to a conserved domain at the C-terminus of GTSE-1, which is required for clathrin binding and is only conserved in vertebrates. 56 matched cddid_all.tbl CDD cd21865 cd21865 439381 DEUBAD_NFRKB DEUBAD domain found in nuclear factor related to kappa-B-binding protein (NFRKB) and similar proteins. NFRKB, also called DNA-binding protein R kappa-B, or INO80 complex subunit G (INO80G), is a regulatory component of the metazoan INO80 complex involved in chromatin remodeling, transcription regulation, DNA replication and DNA repair. It modulates the deubiquitinase activity of UCHL5 in the INO80 complex. It binds to the DNA consensus sequence 5'-GGGGAATCTCC-3'. The model corresponds to the DEUBAD domain (conserved domain within the UCH regulatory proteins RPN13, NFRKB/INO80G, and ASX) of NFRKB, which binds primarily to the C-terminal ULD domain of UCH-L5. 112 matched cddid_all.tbl CDD cd21868 cd21868 409286 CC1_SLMAP-like first coiled-coil (CC1) domain found in Sarcolemmal membrane-associated protein and similar proteins. The family includes Sarcolemmal membrane-associated protein (SLMAP), its paralog TRAF3-interacting JNK-activating modulator (T3JAM), and similar proteins. SLMAP, also called Sarcolemmal membrane-associated protein, is a cardiac tail-anchored membrane protein that may play a role during myoblast fusion. T3JAM, also called TRAF3-interacting protein 3 (TRAF3IP3), is a novel protein that specifically interacts with TRAF3 and promotes the activation of JNK. It may function as an adapter molecule that regulates TRAF3-mediated JNK activation. SLMAP contains an N-terminal FHA domain, followed by four coiled-coil (CC) domains and a transmembrane domain. The model corresponds to the first CC (CC1) domain that is responsible for the binding of suppressor of IKBKE 1 (SIKE1). 38 matched cddid_all.tbl CDD cd21871 cd21871 409343 VscT2 type III secretion system apparatus protein VscT2 in Vibrio species. This model contains Vibrio type III secretion system (T3SS) apparatus protein VscT2. Vibrios, which include over 100 species, are ubiquitous in marine and estuarine environments, and many species such as Vibrio cholerae, V. parahaemolyticus and V. mimicus, are pathogens for humans. VscT2 co-occurs with vscS2, vscN2, vscC2 and vscR2 which are all essential for T3SS secretion. 130 matched cddid_all.tbl CDD cd21872 cd21872 409325 CoV_Nsp10 coronavirus non-structural protein 10. This model represents the non-structural protein 10 (Nsp10) of alpha-, beta-, gamma- and deltacoronaviruses, including highly pathogenic betacoronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Upon processing of the Nsp7-10 region by protease M (Mpro), the released four small proteins Nsp7, Nsp8, Nsp9, and Nsp10 form functional complexes with CoV core enzymes and thereby stimulate replication. Coronaviruses cap their mRNAs; RNA cap methylation may involve at least three proteins: Nsp10, Nsp14, and Nsp16. Nsp10 serves as a cofactor for both Nsp14 and Nsp16. Nsp14 consists of 2 domains with different enzymatic activities: an N-terminal ExoN domain and a C-terminal cap (guanine-N7) methyltransferase (N7-MTase) domain. The association of Nsp10 with Nsp14 enhances Nsp14's exoribonuclease (ExoN) activity, and not its N7-Mtase activity. ExoN is important for proofreading and therefore, the prevention of lethal mutations. The Nsp10/Nsp14 complex hydrolyzes double-stranded RNA in a 3' to 5' direction as well as a single mismatched nucleotide at the 3'-end, mimicking an erroneous replication product, and may function in a replicative mismatch repair mechanism. Nsp16 Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) acts sequentially to Nsp14 MTase in RNA capping methylation, and methylates the RNA cap at the ribose 2'-O position; it catalyzes the conversion of the cap-0 structure on m7GpppA-RNA to a cap-1 structure. The association of Nsp10 with Nsp16 enhances Nsp16's 2'OMTase activity, possibly through enhanced RNA binding affinity. Additionally, transmissible gastroenteritis virus (TGEV) Nsp10, Nsp16, and their complex can interact with DII4, which normally binds to Notch receptors; this interaction may disturb Notch signaling. Nsp10 also binds 2 zinc ions with high affinity. 131 matched cddid_all.tbl CDD cd21873 cd21873 409342 Ugr_9a-1-like includes Urticina grebelnyi Ugr 9a-1, Anemonia viridis Avd13a/b, Antheopsis maculata Amc1a peptide actitoxins. This model includes novel peptides isolated from venom of the sea anemone and include Urticina grebelnyi Ugr 9a-1 (also called pi-anemonetoxin (pi-AnmTX) Ugr 9a-1 or Pi-actitoxin-Ugr1a or Ugr 9-1), Antheopsis maculate Amc1a (also called delta-actitoxin-Amc1a, Delta-AITX-Amc1a, AnmTX Ama 9a-1 or peptide toxins Am-1) and Anemonia viridis Avd13b (also called U-actitoxin-Avd13b, AnmTX Avi 9a-1, or peptide toxin AV-2). These peptides belong to structural group 9a. Ugr 9a-1 has an uncommon beta-hairpin structure, stabilized by two S-S bridges. Its precursor protein appears to be processed in the following sequence: release of the signal peptide and of the propeptide, production of six identical 34-residue peptides by cleavage between Arg and Glu, release of four N-terminal and three C-terminal residues from each peptide and hydroxylation of each Pro in position 6 of the resulting 27-residue peptides. Ugr1a has been shown to produce a reversible inhibition effect on both the transient and the sustained current of human acid-sensing ion channel 3 (ASIC3) channels expressed in Xenopus laevis oocytes; it completely blocks the transient component and partially (48%) inhibits the amplitude of the sustained component. In mice, it significantly reversed inflammatory and acid-induced pain. 29 matched cddid_all.tbl CDD cd21874 cd21874 409336 alpha_betaCoV_Nsp1 non-structural protein 1 from alpha- and betacoronavirus. This model represents the non-structural protein 1 (Nsp1) from alpha- and betacoronaviruses, including highly pathogenic betacoronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. Gamma- and deltaCoVs do not have Nsp1. CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. Nsp1 is the N-terminal cleavage product released from the ORF1a polyprotein by the action of papain-like protease (PLpro). Though Nsp1s of alphaCoVs and betaCoVs share structural similarity, they show no significant sequence similarity and may be considered as genus-specific markers. Despite low sequence similarity, the Nsp1s of alphaCoVs and betaCoVs exhibit remarkably similar biological functions, and are involved in the regulation of both host and viral gene expression. CoV Nsp1 induces suppression of host gene expression and interferes with host immune response. It inhibits host gene expression in two ways: by targeting the translation and stability of cellular mRNAs, and by inhibiting mRNA translation and inducing an endonucleolytic RNA cleavage in the 5'-UTR of cellular mRNAs through its tight association with the 40S ribosomal subunit, a key component of the cellular translation machinery. Inhibition of host mRNA translation includes that of type I interferons, major components of the host innate immune response. Nsp1 is critical in regulating viral replication and gene expression, as shown by multiple evidences, including: mutations in the Nsp1 coding region of the transmissible gastroenteritis virus (TGEV) and murine hepatitis virus (MHV) genomes cause drastic reduction or elimination of infectious virus; bovine coronavirus (BCoV) Nsp1 is an RNA-binding protein that interacts with cis-acting replication elements in the 5'-UTR of the BCoV genome, implying its potential role in the regulation of viral translation or replication; and SARS-CoV Nsp1 enhances virus replication by binding to a stem-loop structure in the 5'-UTR of its genome. 103 matched cddid_all.tbl CDD cd21875 cd21875 409337 PEDV-like_alphaCoV_Nsp1 non-structural protein 1 from porcine epidemic diarrhea virus and similar alphacoronaviruses. This model represents the non-structural protein 1 (Nsp1) from porcine epidemic diarrhea virus (PEDV) and similar alphacoronaviruses from several subgenera including pedacovirus, setracovirus, duvinacovirus, decacovirus, colacovirus, myotacovirus, minunacovirus, and rhinacovirus. CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. Nsp1 is the N-terminal cleavage product released from the ORF1a polyprotein by the action of papain-like protease (PLpro). Though Nsp1s of alphaCoVs and betaCoVs share structural similarity, they show no significant sequence similarity and may be considered as genus-specific markers. Despite low sequence similarity, the Nsp1s of alphaCoVs and betaCoVs exhibit remarkably similar biological functions, and are involved in the regulation of both host and viral gene expression. CoV Nsp1 induces suppression of host gene expression and interferes with host immune response. It inhibits host gene expression in two ways: by targeting the translation and stability of cellular mRNAs, and by inhibiting mRNA translation and inducing an endonucleolytic RNA cleavage in the 5'-UTR of cellular mRNAs through its tight association with the 40S ribosomal subunit, a key component of the cellular translation machinery. Inhibition of host mRNA translation includes that of type I interferons, major components of the host innate immune response. Nsp1 is critical in regulating viral replication and gene expression, as shown by multiple evidences, including: mutations in the Nsp1 coding region of the transmissible gastroenteritis virus (TGEV) and murine hepatitis virus (MHV) genomes cause drastic reduction or elimination of infectious virus; bovine coronavirus (BCoV) Nsp1 is an RNA-binding protein that interacts with cis-acting replication elements in the 5'-UTR of the BCoV genome, implying its potential role in the regulation of viral translation or replication; and SARS-CoV Nsp1 enhances virus replication by binding to a stem-loop structure in the 5'-UTR of its genome. 108 matched cddid_all.tbl CDD cd21876 cd21876 409338 betaCoV_Nsp1 non-structural protein 1 from betacoronavirus. This model represents the non-structural protein 1 (Nsp1) from betacoronaviruses, including highly pathogenic coronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. Nsp1 is the N-terminal cleavage product released from the ORF1a polyprotein by the action of papain-like protease (PLpro). Though Nsp1s of alphaCoVs and betaCoVs share structural similarity, they show no significant sequence similarity and may be considered as genus-specific markers. Despite low sequence similarity, the Nsp1s of alphaCoVs and betaCoVs exhibit remarkably similar biological functions, and are involved in the regulation of both host and viral gene expression. CoV Nsp1 induces suppression of host gene expression and interferes with host immune response. It inhibits host gene expression in two ways: by targeting the translation and stability of cellular mRNAs, and by inhibiting mRNA translation and inducing an endonucleolytic RNA cleavage in the 5'-UTR of cellular mRNAs through its tight association with the 40S ribosomal subunit, a key component of the cellular translation machinery. Inhibition of host mRNA translation includes that of type I interferons, major components of the host innate immune response. Nsp1 is critical in regulating viral replication and gene expression, as shown by multiple evidences, including: mutations in the Nsp1 coding region of the transmissible gastroenteritis virus (TGEV) and murine hepatitis virus (MHV) genomes cause drastic reduction or elimination of infectious virus; bovine coronavirus (BCoV) Nsp1 is an RNA-binding protein that interacts with cis-acting replication elements in the 5'-UTR of the BCoV genome, implying its potential role in the regulation of viral translation or replication; and SARS-CoV Nsp1 enhances virus replication by binding to a stem-loop structure in the 5'-UTR of its genome. 114 matched cddid_all.tbl CDD cd21877 cd21877 409339 HKU9-like_Nsp1 non-structural protein 1 from Rousettus bat coronavirus HKU9 and betacoronavirus in the D lineage. This model represents the non-structural protein 1 (Nsp1) from betacoronavirus in the nobecovirus subgenus (D lineage), including Rousettus bat coronavirus HKU9. CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. Nsp1 is the N-terminal cleavage product released from the ORF1a polyprotein by the action of papain-like protease (PLpro). Though Nsp1s of alphaCoVs and betaCoVs share structural similarity, they show no significant sequence similarity and may be considered as genus-specific markers. Despite low sequence similarity, the Nsp1s of alphaCoVs and betaCoVs exhibit remarkably similar biological functions, and are involved in the regulation of both host and viral gene expression. CoV Nsp1 induces suppression of host gene expression and interferes with host immune response. It inhibits host gene expression in two ways: by targeting the translation and stability of cellular mRNAs, and by inhibiting mRNA translation and inducing an endonucleolytic RNA cleavage in the 5'-UTR of cellular mRNAs through its tight association with the 40S ribosomal subunit, a key component of the cellular translation machinery. Inhibition of host mRNA translation includes that of type I interferons, major components of the host innate immune response. Nsp1 is critical in regulating viral replication and gene expression, as shown by multiple evidences, including: mutations in the Nsp1 coding region of the transmissible gastroenteritis virus (TGEV) and murine hepatitis virus (MHV) genomes cause drastic reduction or elimination of infectious virus; bovine coronavirus (BCoV) Nsp1 is an RNA-binding protein that interacts with cis-acting replication elements in the 5'-UTR of the BCoV genome, implying its potential role in the regulation of viral translation or replication; and SARS-CoV Nsp1 enhances virus replication by binding to a stem-loop structure in the 5'-UTR of its genome. 165 matched cddid_all.tbl CDD cd21878 cd21878 409340 MERS-CoV-like_Nsp1 non-structural protein 1 from Middle East respiratory syndrome-related coronavirus and betacoronavirus in the C lineage. This model represents the non-structural protein 1 (Nsp1) from betacoronavirus in the merbecovirus subgenus (C lineage), including Middle East respiratory syndrome-related coronavirus (MERS-CoV) and Tylonycteris bat coronavirus HKU4. CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. Nsp1 is the N-terminal cleavage product released from the ORF1a polyprotein by the action of papain-like protease (PLpro). Though Nsp1s of alphaCoVs and betaCoVs share structural similarity, they show no significant sequence similarity and may be considered as genus-specific markers. Despite low sequence similarity, the Nsp1s of alphaCoVs and betaCoVs exhibit remarkably similar biological functions, and are involved in the regulation of both host and viral gene expression. CoV Nsp1 induces suppression of host gene expression and interferes with host immune response. It inhibits host gene expression in two ways: by targeting the translation and stability of cellular mRNAs, and by inhibiting mRNA translation and inducing an endonucleolytic RNA cleavage in the 5'-UTR of cellular mRNAs through its tight association with the 40S ribosomal subunit, a key component of the cellular translation machinery. Inhibition of host mRNA translation includes that of type I interferons, major components of the host innate immune response. Nsp1 is critical in regulating viral replication and gene expression, as shown by multiple evidences, including: mutations in the Nsp1 coding region of the transmissible gastroenteritis virus (TGEV) and murine hepatitis virus (MHV) genomes cause drastic reduction or elimination of infectious virus; bovine coronavirus (BCoV) Nsp1 is an RNA-binding protein that interacts with cis-acting replication elements in the 5'-UTR of the BCoV genome, implying its potential role in the regulation of viral translation or replication; and SARS-CoV Nsp1 enhances virus replication by binding to a stem-loop structure in the 5'-UTR of its genome. 170 matched cddid_all.tbl CDD cd21879 cd21879 409341 MHV-like_Nsp1 non-structural protein 1 from murine hepatitis virus and betacoronavirus in the A lineage. This model represents the non-structural protein 1 (Nsp1) from betacoronavirus in the embecovirus subgenus (A lineage), including murine hepatitis virus (MHV), bovine coronavirus (BCoV) and Human coronavirus HKU1. CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. Nsp1 is the N-terminal cleavage product released from the ORF1a polyprotein by the action of papain-like protease (PLpro). Though Nsp1s of alphaCoVs and betaCoVs share structural similarity, they show no significant sequence similarity and may be considered as genus-specific markers. Despite low sequence similarity, the Nsp1s of alphaCoVs and betaCoVs exhibit remarkably similar biological functions, and are involved in the regulation of both host and viral gene expression. CoV Nsp1 induces suppression of host gene expression and interferes with host immune response. It inhibits host gene expression in two ways: by targeting the translation and stability of cellular mRNAs, and by inhibiting mRNA translation and inducing an endonucleolytic RNA cleavage in the 5'-UTR of cellular mRNAs through its tight association with the 40S ribosomal subunit, a key component of the cellular translation machinery. Inhibition of host mRNA translation includes that of type I interferons, major components of the host innate immune response. Nsp1 is critical in regulating viral replication and gene expression, as shown by multiple evidences, including: mutations in the Nsp1 coding region of the transmissible gastroenteritis virus (TGEV) and MHV genomes cause drastic reduction or elimination of infectious virus; BCoV Nsp1 is an RNA-binding protein that interacts with cis-acting replication elements in the 5'-UTR of the BCoV genome, implying its potential role in the regulation of viral translation or replication; and SARS-CoV Nsp1 enhances virus replication by binding to a stem-loop structure in the 5'-UTR of its genome. 236 matched cddid_all.tbl CDD cd21880 cd21880 438580 OTU_RNAP_L_virus OTU (ovarian tumor) domain of viral RNA-directed RNA polymerase L. RNA-directed RNA polymerase L is also called protein L, large structural protein, replicase, transcriptase, or ubiquitin thioesterase. It displays RNA-directed RNA polymerase (EC 2.7.7.48), deubiquitinase (DUB)/ubiquitin thiolesterase (EC 3.4.19.12), and deISGylating activities. It is a viral homolog of ovarian tumor protease (vOTU) that has been implicated in the downregulation of type I interferon immune response by removing post-translational modifying proteins ubiquitin (Ub) and the Ub-like interferon-simulated gene 15 (ISG15) from host cellular proteins. The attachment of Ub and ISG15 to cellular proteins mediates important innate antiviral responses, and their removal inhibits these antiviral pathways. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 148 matched cddid_all.tbl CDD cd21881 cd21881 409329 CoV_Nsp9 coronavirus non-structural protein 9. This model represents the non-structural protein 9 (Nsp9) from coronaviruses, including highly pathogenic betacoronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. All of these Nsps, except for Nsp1 and Nsp2, are considered essential for transcription, replication, and translation of the viral RNA. Nsp9, with Nsp7, Nsp8, and Nsp10, localizes within the replication complex. Nsp9 is an essential single-stranded RNA-binding protein for CoV replication; it shares structural similarity to the oligosaccharide-binding (OB) fold, which is characteristic of proteins that bind to ssDNA or ssRNA. Nsp9 requires dimerization for binding and orienting RNA for subsequent use by the replicase machinery. CoV Nsp9s have diverse forms of dimerization that promote their biological function, which may help elucidate the mechanism underlying CoVs replication and contribute to the development of antiviral drugs. Generally, dimers are formed via interaction of the parallel alpha-helices containing the protein-protein interaction motif GXXXG at the C-terminus; additionally, the N-finger region may also play a critical role in dimerization as seen in porcine delta coronavirus (PDCoV) Nsp9. As a member of the replication complex, Nsp9 may not have a specific RNA-binding sequence but may act in conjunction with other Nsps as a processivity factor, as shown by mutation studies indicating that Nsp9 is a key ingredient that intimately engages other proteins in the replicase complex to mediate efficient virus transcription and replication. 111 matched cddid_all.tbl CDD cd21882 cd21882 411975 TRPV Transient Receptor Potential channel, Vanilloid subfamily (TRPV). The vanilloid TRP subfamily (TRPV), named after the vanilloid receptor 1 (TRPV1), consists of six members: four thermo-sensing channels (TRPV1, TRPV2, TRPV3, and TRPV4) and two Ca2+ selective channels (TRPV5 and TRPV6). The calcium-selective channels TRPV5 and TRPV6 can be heterotetramers and are important for general Ca2+ homeostasis. All four channels within the TRPV1-4 group show temperature-invoked currents when expressed in heterologous cell systems, ranging from activation at ~25C for TRPV4 to ~52C for TRPV2. The structure of TRPV shows the typical topology features of all Transient Receptor Potential (TRP) ion channel family members, such as six transmembrane regions, a short hydrophobic stretch between transmembrane segments 5 and 6 and large intracellular N- and C-terminal domains. The TRP family consists of membrane proteins that function as ion channels that communicate between the cell and its environment, by a vast array of physical or chemical stimuli, including radiation (in the form of temperature, infrared ,or light) and pressure (osmotic or mechanical). TRP channels are formed by a tetrameric complex of channel subunits. Based on sequence identity, the mammalian TRP channel family is classified into six subfamilies, with significant sequence similarity within the transmembrane domains, but very low similarity in their N- and C-terminal cytoplasmic regions. The six subfamilies are named based on their first member: TRPC (canonical), TRPV (vanilloid), TRPM (melastatin), TRPA (ankyrin), TRPML (mucolipin), and TRPP (polycystic). 600 matched cddid_all.tbl CDD cd21883 cd21883 439177 SARAH_SF C-terminal SARAH domain found in scaffold protein salvador (Sav), Ras-association domain proteins, and mammalian STE20-like protein kinases (MST). The SARAH (Salvador-RassF-Hippo) domain family includes scaffold protein salvador (Sav), Ras-association domain proteins (RASSF1-6), and mammalian STE20-like protein kinase (MST) subfamily members (MST1-2 and Hippo). Sav is a scaffold protein mainly found in metazoans. Drosophila melanogaster Sav, also called Shar-pei (SHRP), promotes both cell cycle exit and apoptosis in Drosophila. It plays a key role in the Hippo/SWH (Sav/Wts/Hpo) signaling pathway. Human protein salvador homolog 1, also called 45 kDa WW domain protein (WW45), acts as a mammalian sterile 20-like kinase 1 (MST1)-binding protein required to enhance MST1-mediated apoptosis. It is a regulator of STK3/MST2 and STK4/MST1 in the Hippo signaling pathway. Classical RASSF proteins interact either directly or indirectly with activated Ras. Ras proteins are small GTPases that are involved in cellular signal transduction. They seem to modulate some of the growth inhibitory responses mediated by Ras and may serve as tumor suppressor genes. RASSF1-6 contains a conserved SARAH motif adjacent to the RA domain that functions in scaffolding and regulatory interactions. MST1/2 and Hippo are involved in a conserved pathway that governs cell contact inhibition, organ size control, and tumor development. MST1 and MST2 are STE20 family stress-activated, pro-apoptotic serine/threonine-protein kinases which, following caspase-cleavage, enter the nucleus and induces chromatin condensation followed by internucleosomal DNA fragmentation. They are key components of the Hippo signaling pathway which plays a pivotal role in organ size control and tumor suppression by restricting proliferation and promoting apoptosis. Hippo (Hpo), also called STE20-like kinase MST (dMST), is the Drosophila homolog of STE20-like protein kinases, MST1 and MST2. It is a STE20 family serine/threonine-protein kinase that functions as a tumor suppressor by restricting cell proliferation and promotes apoptosis in conjunction with salvador and warts. Hpo also plays a key role in the Hippo/SWH signaling pathway. This model corresponds to the C-terminal SARAH domain, a characteristic coiled-coil structure. It is a small helical module that is important in signal-transduction networks. The central function of the SARAH domain seems to be the mediation of homo- and heterodimerization between SARAH domain-containing proteins. 45 matched cddid_all.tbl CDD cd21884 cd21884 439178 SARAH_MST_Hpo C-terminal SARAH domain found in the mammalian STE20-like protein kinase (MST) subfamily. The MST subfamily includes MST1 and MST2, as well as Drosophila melanogaster homolog protein, Hippo (Hpo). MST1/2 and Hippo are involved in a conserved pathway that governs cell contact inhibition, organ size control, and tumor development. MST1 and MST2 are STE20 family stress-activated, pro-apoptotic serine/threonine-protein kinases which, following caspase-cleavage, enter the nucleus and induces chromatin condensation followed by internucleosomal DNA fragmentation. They are key components of the Hippo signaling pathway which plays a pivotal role in organ size control and tumor suppression by restricting proliferation and promoting apoptosis. Hpo, also called STE20-like kinase MST (dMST), is the Drosophila homolog of STE20-like protein kinases, MST1 and MST2. It is a STE20 family serine/threonine-protein kinase that functions as a tumor suppressor by restricting cell proliferation, and promotes apoptosis in conjunction with salvador and warts. Hpo plays a key role in the Hippo/SWH (Sav/Wts/Hpo) signaling pathway. This model corresponds to the C-terminal SARAH (Salvador-RassF-Hippo) domain of mammalian STE20-like protein kinases and the Drosophila melanogaster homolog Hippo. 48 matched cddid_all.tbl CDD cd21885 cd21885 439179 SARAH_RASSF1-like C-terminal SARAH domain found in Ras-association domain proteins, RASSF1, RASSF3, and RASSF5. The RASSF subfamily of proteins shares a conserved RalGDS/AF6 Ras association (RA) domain which is located either at the C-terminus (RASSF1-6, the classical group) or at the N-terminus (RASSF7-10). Classical RASSF proteins interact either directly or indirectly with activated Ras. Ras proteins are small GTPases that are involved in cellular signal transduction. They seem to modulate some of the growth inhibitory responses mediated by Ras and may serve as tumor suppressor genes. RASSF1-6 contains a conserved SARAH (Salvador-RassF-Hippo) motif adjacent to the RA domain that functions in scaffolding and regulatory interactions. The RA domain of the classical RASSF proteins has a beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. This model corresponds to the SARAH domain of RASSF1, RASSF3, and RASSF5. It is a characteristic coiled-coil structure that is important in signal-transduction networks. The central function of the SARAH domain is the mediation of homo- and heterodimerization between SARAH domain-containing proteins. 45 matched cddid_all.tbl CDD cd21886 cd21886 439180 SARAH_RASSF2-like C-terminal SARAH domain found in Ras-association domain proteins, RASSF2, RASSF4, and RASSF6. The RASSF subfamily of proteins shares a conserved RalGDS/AF6 Ras association (RA) domain which is located either at the C-terminus (RASSF1-6, the classical group) or at the N-terminus (RASSF7-10). The classical RASSF proteins seem to modulate some of the growth inhibitory responses mediated by Ras and may serve as tumor suppressor genes. They interact either directly or indirectly with activated Ras. Ras proteins are small GTPases that are involved in cellular signal transduction. RASSF1-6 contain a conserved C-terminal SARAH (Salvador-RassF-Hippo) motif adjacent to the RA domain that functions in scaffolding and regulatory interactions. The RA domain of the classical RASSF proteins has a beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. This model corresponds to the SARAH domain of RASSF2, RASSF4, and RASSF6. It is a characteristic coiled-coil structure that is important in signal-transduction networks. The central function of the SARAH domain is the mediation of homo- and heterodimerization between SARAH domain-containing proteins. 45 matched cddid_all.tbl CDD cd21887 cd21887 439181 SARAH_MST1 C-terminal SARAH domain of mammalian STE20-like protein kinase 1 (MST1). MST1, also called serine/threonine-protein kinase 4, MST-1, STE20-like kinase MST1, or serine/threonine-protein kinase (STK) Krs-2, is a STE20 family stress-activated, pro-apoptotic STK which, following caspase-cleavage, enters the nucleus and induces chromatin condensation followed by internucleosomal DNA fragmentation. It is a key component of the Hippo signaling pathway which plays a pivotal role in organ size control and tumor suppression by restricting proliferation and promoting apoptosis. This model corresponds to the C-terminal SARAH (Salvador-RassF-Hippo) domain, which mediates homodimerization of MST1. The MST1 SARAH domain also interacts with Rassf1 and Rassf5 by forming a heterodimer which mediates the apoptosis process. 49 matched cddid_all.tbl CDD cd21888 cd21888 439182 SARAH_MST2 C-terminal SARAH domain of mammalian STE20-like protein kinase 2 (MST2). MST2, also called serine/threonine-protein kinase 3, MST-2, STE20-like kinase MST2, or serine/threonine-protein kinase (STK) Krs-1, is a STE20 family stress-activated, pro-apoptotic STK which, following caspase-cleavage, enters the nucleus and induces chromatin condensation followed by internucleosomal DNA fragmentation. It is a key component of the Hippo signaling pathway which plays a pivotal role in organ size control and tumor suppression by restricting proliferation and promoting apoptosis. This model corresponds to the C-terminal SARAH (Salvador-RassF-Hippo) domain, which mediates homodimerization of MST2. Similar to MST1, MST2 may also form heterodimers with other SARAH domain-containing proteins. 49 matched cddid_all.tbl CDD cd21889 cd21889 439183 SARAH_Hpo C-terminal SARAH domain of Drosophila melanogaster protein Hippo (Hpo) and similar proteins. Hpo, also called STE20-like kinase MST (dMST), is the Drosophila homolog of STE20-like protein kinases, MST1 and MST2. It is a STE20 family serine/threonine-protein kinase that functions as a tumor suppressor by restricting cell proliferation, and promotes apoptosis in conjunction with salvador and warts. Hpo plays a key role in the Hippo/SWH (Sav/Wts/Hpo) signaling pathway that plays a pivotal role in organ size control and tumor suppression by restricting proliferation and promoting apoptosis. This model corresponds to the C-terminal SARAH (Salvador-RassF-Hippo) domain of Hpo, which mediates complex formation between Hpo and Sav, as well as homodimerization. 56 matched cddid_all.tbl CDD cd21890 cd21890 439184 SARAH_RASSF1 C-terminal SARAH domain found in Ras-association domain-containing protein 1 (RASSF1). RASSF1 is one of six related proteins, the classical RASSF proteins (RASSF1-6), that contain a conserved RalGDS/AF6 Ras association (RA) domain located towards the C-terminus. It acts as a potential tumor suppressor that is required for death receptor-dependent apoptosis. It mediates activation of STK3/MST2 and STK4/MST1 during Fas-induced apoptosis by preventing their dephosphorylation. RASSF1 has eight transcripts (A-H) arising from alternative splicing and differential promoter usage. RASSF1A and 1C are the most extensively studied RASSF1, with both localized to microtubules and involved in regulation of growth and migration. With the exception of some minor splice variants (RASSF1F and RASSF1G), RASSF1 contains an RA domain and a C-terminal SARAH (Salvador-RassF-Hippo) protein-protein interaction motif. The RA domain of the classical RASSF proteins has a beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. The RA domain mediates interactions with Ras and other small GTPases, and the SARAH domain mediates protein-protein interactions crucial in the pathways that induce cell cycle arrest and apoptosis. This model corresponds to the SARAH domain of RASSF1. 46 matched cddid_all.tbl CDD cd21891 cd21891 439185 SARAH_RASSF3 C-terminal SARAH domain found in Ras-association domain-containing protein 3 (RASSF3). RASSF3 is one of six related proteins, the classical RASSF proteins (RASSF1-6), that contain a conserved RalGDS/AF6 Ras association (RA) domain located towards the C-terminus. RASSF3 has three transcripts (A-C) due to alternative splicing of the exons. The RASSF3B and 3C isoforms are shorter than RASSF3A, and unlike RASSF3A do not contain the RA or SARAH (Salvador-RassF-Hippo) domains. RASSF3A regulates apoptosis and the cell cycle via p53 stabilization and is possibly involved in DNA repair. The RA domain of the classical RASSF proteins has a beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. The RA domain mediates interactions with Ras and other small GTPases, and the SARAH domain mediates protein-protein interactions crucial in the pathways that induce cell cycle arrest and apoptosis. This model corresponds to the SARAH domain of RASSF3. 46 matched cddid_all.tbl CDD cd21892 cd21892 439186 SARAH_RASSF5 C-terminal SARAH domain found in Ras-association domain-containing protein 5 (RASSF5). RASSF5, also called New ras effector 1 (NORE1), or regulator for cell adhesion and polarization enriched in lymphoid tissues (RAPL), is one of six related proteins, the classical RASSF proteins (RASSF1-6), that contain a conserved RalGDS/AF6 Ras association (RA) domain located towards the C-terminus. It acts as a potential tumor suppressor that may be involved in lymphocyte adhesion by linking RAP1A activation upon T-cell receptor or chemokine stimulation to integrin activation. RASSF5 is expressed as three transcripts (A-C) via differential promoter usage and alternative splicing. RASSF5A is a pro-apoptotic Ras effector and functions as a Ras regulated tumor suppressor. RASSF5C is regulated by Ras related protein and modulates cellular adhesion. All transcript variants of RASSF5 contain the RA and SARAH (Salvador-RassF-Hippo) domains. The RA domain of the classical RASSF proteins has a beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. The RA domain mediates interactions with Ras and other small GTPases, and the SARAH domain mediates protein-protein interactions crucial in the pathways that induce cell cycle arrest and apoptosis. This model corresponds to the SARAH domain of RASSF5, that mediates homo- and heterodimerization. 48 matched cddid_all.tbl CDD cd21893 cd21893 439187 SARAH_RASSF2 C-terminal SARAH domain found in Ras-association domain-containing protein 2 (RASSF2). RASSF2 is one of six related proteins, the classical RASSF proteins (RASSF1-6), that contain a conserved RalGDS/AF6 Ras association (RA) domain located towards the C-terminus. It acts as a potential tumor suppressor that may promote apoptosis and cell cycle arrest. It is a KRAS-specific effector protein. It stabilizes STK3/MST2 by protecting it from proteasomal degradation. The RASSF2 gene is transcribed into two major isoforms (A and C). RASSF2 is structurally related to RASSF1A but unlike RASSF1A, it is primarily a nuclear protein. RASSF2 contains the RA and SARAH (Salvador-RassF-Hippo) domains. The RA domain of the classical RASSF proteins has a beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. RA domains mediate interactions with Ras and other small GTPases, and SARAH domains mediate protein-protein interactions crucial in the pathways that induce cell cycle arrest and apoptosis. This model corresponds to the SARAH domain of RASSF2. 46 matched cddid_all.tbl CDD cd21894 cd21894 439188 SARAH_RASSF4 C-terminal SARAH domain found in Ras-association domain-containing protein 4 (RASSF4). RASSF4 is one of six related proteins, the classical RASSF proteins (RASSF1-6), that contain a conserved RalGDS/AF6 Ras association (RA) domain located towards the C-terminus. It acts as a potential tumor suppressor that may promote apoptosis and cell cycle arrest. It also functions as a KRAS effector protein. RASSF4 is broadly expressed in normal tissues. Its expression is reduced in tumor cell lines and primary tumors by promoter specific hypermethylation. RASSF4 contains the RA and SARAH (Salvador-RassF-Hippo) domains. The RA domain of the classical RASSF proteins has a beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. RA domains mediate interactions with Ras and other small GTPases, and SARAH domains mediate protein-protein interactions crucial in the pathways that induce cell cycle arrest and apoptosis. This model corresponds to the SARAH domain of RASSF4. 46 matched cddid_all.tbl CDD cd21895 cd21895 439189 SARAH_RASSF6 C-terminal SARAH domain found in Ras-association domain-containing protein 6 (RASSF6). RASSF6 is one of six related proteins, the classical RASSF proteins (RASSF1-6), that contain a conserved RalGDS/AF6 Ras association (RA) domain located towards the C-terminus. It acts as a tumor suppressor protein involved in the induction of apoptosis, through both caspase-dependent and caspase-independent pathways. RASSF6 may function as a Ras effector protein. It is ubiquitinated and degraded by interacting with MDM2 to stabilize P53, and it regulates apoptosis and the cell cycle. RASSF6 is expressed as four transcripts via alternative splicing. All transcript variants of RASSF6 contain the RA and SARAH (Salvador-RassF-Hippo) domains. The RA domain of the classical RASSF proteins has the beta-grasp ubiquitin-like fold with low sequence similarity to ubiquitin. RA domains mediate interactions with Ras and other small GTPases. SARAH domains mediate protein-protein interactions crucial in the pathways that induce cell cycle arrest and apoptosis. This model corresponds to the SARAH domain of RASSF6. 46 matched cddid_all.tbl CDD cd21897 cd21897 409330 alphaCoV_Nsp9 alphacoronavirus non-structural protein 9. This model represents the non-structural protein 9 (Nsp9) of alphacoronaviruses, including Porcine epidemic diarrhea virus (PEDV), Porcine transmissible gastroenteritis coronavirus (TGEV), and Human coronavirus 229E. CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. All of these Nsps, except for Nsp1 and Nsp2, are considered essential for transcription, replication, and translation of the viral RNA. Nsp9, with Nsp7, Nsp8, and Nsp10, localizes within the replication complex. Nsp9 is an essential single-stranded RNA-binding protein for coronavirus replication; it shares structural similarity to the oligosaccharide-binding (OB) fold, which is characteristic of proteins that bind to ssDNA or ssRNA. Nsp9 requires dimerization for binding and orienting RNA for subsequent use by the replicase machinery. CoV Nsp9s have diverse forms of dimerization that promote their biological function, which may help elucidate the mechanism underlying CoVs replication and contribute to the development of antiviral drugs. Generally, dimers are formed via interaction of the parallel alpha-helices containing the protein-protein interaction motif GXXXG; additionally, the N-finger region may also play a critical role in dimerization as seen in porcine delta coronavirus (PDCoV) Nsp9. As a member of the replication complex, Nsp9 may not have a specific RNA-binding sequence but may act in conjunction with other Nsps as a processivity factor, as shown by mutation studies indicating that Nsp9 is a key ingredient that intimately engages other proteins in the replicase complex to mediate efficient virus transcription and replication. 108 matched cddid_all.tbl CDD cd21898 cd21898 409331 betaCoV_Nsp9 betacoronavirus non-structural protein 9. This model represents the non-structural protein 9 (Nsp9) from betacoronaviruses including highly pathogenic Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Middle East respiratory syndrome-related (MERS) CoV. CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. All of these Nsps, except for Nsp1 and Nsp2, are considered essential for transcription, replication, and translation of the viral RNA. Nsp9, with Nsp7, Nsp8, and Nsp10, localizes within the replication complex. Nsp9 is an essential single-stranded RNA-binding protein for coronavirus replication; it shares structural similarity to the oligosaccharide-binding (OB) fold, which is characteristic of proteins that bind to ssDNA or ssRNA. Nsp9 requires dimerization for binding and orienting RNA for subsequent use by the replicase machinery. CoV Nsp9s have diverse forms of dimerization that promote their biological function, which may help elucidate the mechanism underlying CoVs replication and contribute to the development of antiviral drugs. Generally, dimers are formed via interaction of the parallel alpha-helices containing the protein-protein interaction motif GXXXG; additionally, the N-finger region may also play a critical role in dimerization as seen in porcine delta coronavirus (PDCoV) Nsp9. As a member of the replication complex, Nsp9 may not have a specific RNA-binding sequence but may act in conjunction with other Nsps as a processivity factor, as shown by mutation studies indicating that Nsp9 is a key ingredient that intimately engages other proteins in the replicase complex to mediate efficient virus transcription and replication. 111 matched cddid_all.tbl CDD cd21899 cd21899 409332 gammaCoV_Nsp9 gammacoronavirus non-structural protein 9. This model represents the non-structural protein 9 (Nsp9) from gammacoronaviruses such as Avian infectious bronchitis virus (IBV). CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. All of these Nsps, except for Nsp1 and Nsp2, are considered essential for transcription, replication, and translation of the viral RNA. Nsp9, with Nsp7, Nsp8, and Nsp10, localizes within the replication complex. Nsp9 is an essential single-stranded RNA-binding protein for coronavirus replication; it shares structural similarity to the oligosaccharide-binding (OB) fold, which is characteristic of proteins that bind to ssDNA or ssRNA. Nsp9 requires dimerization for binding and orienting RNA for subsequent use by the replicase machinery. CoV Nsp9s have diverse forms of dimerization that promote their biological function, which may help elucidate the mechanism underlying CoVs replication and contribute to the development of antiviral drugs. Generally, dimers are formed via interaction of the parallel alpha-helices containing the protein-protein interaction motif GXXXG; additionally, the N-finger region may also play a critical role in dimerization as seen in porcine delta coronavirus (PDCoV) Nsp9. As a member of the replication complex, Nsp9 may not have a specific RNA-binding sequence but may act in conjunction with other Nsps as a processivity factor, as shown by mutation studies indicating that Nsp9 is a key ingredient that intimately engages other proteins in the replicase complex to mediate efficient virus transcription and replication. 113 matched cddid_all.tbl CDD cd21900 cd21900 409333 deltaCoV_Nsp9 deltacoronavirus non-structural protein 9. This model represents the non-structural protein 9 (Nsp9) from deltacoronaviruses such as the Porcine delta coronavirus (PDCoV) Porcine coronavirus HKU15. CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. All of these Nsps, except for Nsp1 and Nsp2, are considered essential for transcription, replication, and translation of the viral RNA. Nsp9, with Nsp7, Nsp8, and Nsp10, localizes within the replication complex. Nsp9 is an essential single-stranded RNA-binding protein for coronavirus replication; it shares structural similarity to the oligosaccharide-binding (OB) fold, which is characteristic of proteins that bind to ssDNA or ssRNA. Nsp9 requires dimerization for binding and orienting RNA for subsequent use by the replicase machinery. CoV Nsp9s have diverse forms of dimerization that promote their biological function, which may help elucidate the mechanism underlying CoVs replication and contribute to the development of antiviral drugs. Generally, dimers are formed via interaction of the parallel alpha-helices containing the protein-protein interaction motif GXXXG; additionally, the N-finger region may also play a critical role in dimerization as seen in porcine delta coronavirus (PDCoV) Nsp9. As a member of the replication complex, Nsp9 may not have a specific RNA-binding sequence but may act in conjunction with other Nsps as a processivity factor, as shown by mutation studies indicating that Nsp9 is a key ingredient that intimately engages other proteins in the replicase complex to mediate efficient virus transcription and replication. 109 matched cddid_all.tbl CDD cd21901 cd21901 409326 alpha_betaCoV_Nsp10 alphacoronavirus and betacoronavirus non-structural protein 10. This model represents the non-structural protein 10 (Nsp10) of alpha- and betacoronaviruses, including highly pathogenic betacoronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), Middle East respiratory syndrome-related (MERS) CoV, and alphacoronaviruses such as Human coronavirus 229E. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Upon processing of the Nsp7-10 region by protease M (Mpro), the released four small proteins Nsp7, Nsp8, Nsp9, and Nsp10 form functional complexes with CoV core enzymes and thereby stimulate replication. Coronaviruses cap their mRNAs; RNA cap methylation may involve at least three proteins: Nsp10, Nsp14, and Nsp16. Nsp10 serves as a cofactor for both Nsp14 and Nsp16. Nsp14 consists of 2 domains with different enzymatic activities: an N-terminal ExoN domain and a C-terminal cap (guanine-N7) methyltransferase (N7-MTase) domain. The association of Nsp10 with Nsp14 enhances Nsp14's exoribonuclease (ExoN) activity, and not its N7-Mtase activity. ExoN is important for proofreading and therefore, the prevention of lethal mutations. The Nsp10/Nsp14 complex hydrolyzes double-stranded RNA in a 3' to 5' direction as well as a single mismatched nucleotide at the 3'-end, mimicking an erroneous replication product, and may function in a replicative mismatch repair mechanism. Nsp16 Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) acts sequentially to Nsp14 MTase in RNA capping methylation, and methylates the RNA cap at the ribose 2'-O position; it catalyzes the conversion of the cap-0 structure on m7GpppA-RNA to a cap-1 structure. The association of Nsp10 with Nsp16 enhances Nsp16's 2'OMTase activity, possibly through enhanced RNA binding affinity. Additionally, transmissible gastroenteritis virus (TGEV) Nsp10, Nsp16 and their complex can interact with DII4, which normally binds to Notch receptors; this interaction may disturb Notch signaling. Nsp10 also binds 2 zinc ions with high affinity. 130 matched cddid_all.tbl CDD cd21902 cd21902 409327 gammaCoV_Nsp10 gammacoronavirus non-structural protein 10. This model represents the non-structural protein 10 (Nsp10) of gammacoronaviruses, including Infectious bronchitis virus (IBV)and Bottlenose dolphin coronavirus HKU22(BdCoV HKU22). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Upon processing of the Nsp7-10 region by protease M (Mpro), the released four small proteins Nsp7, Nsp8, Nsp9, and Nsp10 form functional complexes with CoV core enzymes and thereby stimulate replication. Coronaviruses cap their mRNAs; RNA cap methylation may involve at least three proteins: Nsp10, Nsp14, and Nsp16. Nsp10 serves as a cofactor for both Nsp14 and Nsp16. Nsp14 consists of 2 domains with different enzymatic activities: an N-terminal ExoN domain and a C-terminal cap (guanine-N7) methyltransferase (N7-MTase) domain. The association of Nsp10 with Nsp14 enhances Nsp14's exoribonuclease (ExoN) activity, and not its N7-Mtase activity. ExoN is important for proofreading and therefore, the prevention of lethal mutations. The Nsp10/Nsp14 complex hydrolyzes double-stranded RNA in a 3' to 5' direction as well as a single mismatched nucleotide at the 3'-end, mimicking an erroneous replication product, and may function in a replicative mismatch repair mechanism. Nsp16 Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) acts sequentially to Nsp14 MTase in RNA capping methylation and methylates the RNA cap at the ribose 2'-O position; it catalyzes the conversion of the cap-0 structure on m7GpppA-RNA to a cap-1 structure. The association of Nsp10 with Nsp16 enhances Nsp16's 2'OMTase activity, possibly through enhanced RNA binding affinity. Additionally, transmissible gastroenteritis virus (TGEV) Nsp10, Nsp16 and their complex can interact with DII4, which normally binds to Notch receptors; this interaction may disturb Notch signaling. Nsp10 also binds 2 zinc ions with high affinity. 134 matched cddid_all.tbl CDD cd21903 cd21903 409328 deltaCoV_Nsp10 deltacoronavirus non-structural protein 10. This model represents the non-structural protein 10 (Nsp10) of deltacoronaviruses, including Thrush coronavirus HKU12-600 and Wigeon coronavirus HKU20. CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Upon processing of the Nsp7-10 region by protease M (Mpro), the released four small proteins Nsp7, Nsp8, Nsp9, and Nsp10 form functional complexes with CoV core enzymes and thereby stimulate replication. Coronaviruses cap their mRNAs; RNA cap methylation may involve at least three proteins: Nsp10, Nsp14, and Nsp16. Nsp10 serves as a cofactor for both Nsp14 and Nsp16. Nsp14 consists of 2 domains with different enzymatic activities: an N-terminal ExoN domain and a C-terminal cap (guanine-N7) methyltransferase (N7-MTase) domain. The association of Nsp10 with Nsp14 enhances Nsp14's exoribonuclease (ExoN) activity, and not its N7-Mtase activity. ExoN is important for proofreading and therefore, the prevention of lethal mutations. The Nsp10/Nsp14 complex hydrolyzes double-stranded RNA in a 3' to 5' direction as well as a single mismatched nucleotide at the 3'-end, mimicking an erroneous replication product, and may function in a replicative mismatch repair mechanism. Nsp16 Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) acts sequentially to Nsp14 MTase in RNA capping methylation and methylates the RNA cap at the ribose 2'-O position; it catalyzes the conversion of the cap-0 structure on m7GpppA-RNA to a cap-1 structure. The association of Nsp10 with Nsp16 enhances Nsp16's 2'OMTase activity, possibly through enhanced RNA binding affinity. Additionally, transmissible gastroenteritis virus (TGEV) Nsp10, Nsp16 and their complex can interact with DII4, which normally binds to Notch receptors; this interaction may disturb Notch signaling. Nsp10 also binds 2 zinc ions with high affinity. 128 matched cddid_all.tbl CDD cd21904 cd21904 409324 TtfA-like Mycobacterial trehalose monomycolate transport factor A and similar proteins. TtfA (trehalose monomycolate transport factor A) plays a role in the transport of trehalose monomycolate across the inner membrane, potentially by forming a complex with the atypical lipid transporter MmpL3. Trehalose monomycolate is a component of the mycobacterial envelope. The core domain of TtfA shows strong structural similarity to class I type III secretion system (T3SS) chaperones, and TtfA may play other roles besides assisting in mycolate transport, given its phylogenetic distribution. 171 matched cddid_all.tbl CDD cd21905 cd21905 409300 PUA_TruB_thermotogae PUA RNA-binding domain of the thermotogae tRNA pseudouridine synthase B. The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. Members of the thermotogae subfamily of pseudouridine synthases TruB are modules that assist in the binding and positioning (guide and/or substrate) of RNA to the pseudouridine synthase complex. Pseudouridine synthases are enzymes that are responsible for post-translational modifications of RNAs by specifically isomerizing uracil residues. The pseudouridine synthase TruB (also called tRNA pseudouridylate synthase B or Psi55 synthase) is responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of elongator tRNAs. 78 matched cddid_all.tbl CDD cd21906 cd21906 439299 BDD2_Gal11 second beta-defensin domain found in gallinacin-11 (Gal-11). Gal-11, also called beta-defensin 11, or vitelline membrane outer layer protein 2 or vitelline membrane outer layer protein II (VMO-II or VMOII), is an antimicrobial peptide of the chicken egg. It is one of four major proteins in vitelline membranes, along with ovomucin, lysozyme, and VMO-1. Gal-11 has bactericidal activity toward both Gram-positive and Gram-negative bacteria. Gal-11 is a compact fold composed of 2 packed beta-defensin domains with the motifs CX6CX5CX9CX6CC and CX6CX6CX7CX6CC, respectively; this model corresponds to the second one. 37 matched cddid_all.tbl CDD cd21907 cd21907 439300 BDD1_Gal11 first beta-defensin domain found in gallinacin-11 (Gal-11). Gal-11, also called beta-defensin 11, or vitelline membrane outer layer protein 2 or vitelline membrane outer layer protein II (VMO-II or VMOII), is an antimicrobial peptide of the chicken egg. It is one of four major proteins in vitelline membranes, along with ovomucin, lysozyme, and VMO-1. Gal-11 has bactericidal activity toward both Gram-positive and Gram-negative bacteria. Gal-11 is a compact fold composed of 2 packed beta-defensin domains with motifs CX6CX5CX9CX6CC and CX6CX6CX7CX6CC, respectively; this model corresponds to the first one. 39 matched cddid_all.tbl CDD cd21908 cd21908 439301 BDD_Gal13 beta-defensin domain found in gallinacin-13 (Gal-13). Gal-13, also called beta-defensin 13, has bactericidal activity against Escherichia coli, Listeria monocytogenes, Salmonella typhimurium and Streptococcus pyogenes but not against Staphylococcus aureus. Gal-13 contains only one beta-defensin domain. 35 matched cddid_all.tbl CDD cd21909 cd21909 439314 JAK1bd_box_IL10RA JAK1 binding box domain found in interleukin-10 receptor subunit alpha (IL10RA) and similar proteins. IL10RA, also called IL-10 receptor subunit alpha, IL-10R subunit alpha, IL-10RA, CDw210a, interleukin-10 receptor subunit 1, IL-10R subunit 1, or IL-10R1, is a cell surface receptor for the cytokine IL10 that participates in IL10-mediated anti-inflammatory functions, limiting excessive tissue disruption caused by inflammation. This model corresponds to IL10RA box domain which consists of box1 and box2. 52 matched cddid_all.tbl CDD cd21910 cd21910 439315 JAK1bd_box_IFNLR1 JAK1 binding box domain found in interferon lambda receptor 1 (IFNLR1) and similar proteins. IFNLR1, also called IFN-lambda receptor 1, IFN-lambda-R1, cytokine receptor class-II member 12, cytokine receptor family 2 member 12, CRF2-12, interleukin-28 receptor subunit alpha, IL-28 receptor subunit alpha, IL-28R-alpha, IL-28RA, likely interleukin, or cytokine receptor 2 (LICR2), is a class II cytokine receptor that, together with IL10RB, forms a dimer. The IFNLR1/IL10RB dimer is a receptor for the cytokine ligands IFNL2 and IFNL3 and mediates their antiviral activity. The ligand/receptor complex stimulates the activation of the JAK/STAT signaling pathway leading to the expression of IFN-stimulated genes (ISG) which contribute to the antiviral state. IFNLR1 determines the cell type specificity of the lambda interferon action. It plays a significant role in the antiviral immune defense in the intestinal epithelium. This model corresponds to IFNLR1 box domain which consists of box1 and box2. Mutations within the box1 and box2 motifs disrupt Janus kinase (JAK) binding as well as signaling. 51 matched cddid_all.tbl CDD cd21911 cd21911 409287 CC1_SLMAP first coiled-coil (CC1) domain found in Sarcolemmal membrane-associated protein. Sarcolemmal membrane-associated protein (SLMAP), also called Sarcolemmal membrane-associated protein, is a cardiac tail-anchored membrane protein that may play a role during myoblast fusion. SLMAP contains an N-terminal FHA domain followed by four coiled-coil (CC) domains and a transmembrane domain. The model corresponds to the first CC (CC1) domain that is responsible for the binding of suppressor of IKBKE 1 (SIKE1). 63 matched cddid_all.tbl CDD cd21912 cd21912 409288 CC1_T3JAM first coiled-coil (CC1) domain found in TRAF3-interacting JNK-activating modulator. TRAF3-interacting JNK-activating modulator (T3JAM), also called TRAF3-interacting protein 3 (TRAF3IP3), is a novel protein that specifically interacts with TRAF3 and promotes the activation of JNK. It may function as an adapter molecule that regulates TRAF3-mediated JNK activation. The model corresponds to a conserved region that shows high sequence similarity with the first CC (CC1) domain of Sarcolemmal membrane-associated protein (SLMAP), which is responsible for the binding of suppressor of IKBKE 1 (SIKE1). 45 matched cddid_all.tbl CDD cd21913 cd21913 409285 Nip7_N_arch N-terminal domain of archaeal 60S ribosome subunit biogenesis protein Nip7. The N-terminal domain of archaeal 60S ribosome subunit biogenesis protein Nip7 co-occurs with a PUA (PseudoUridine synthase and Archaeosine transglycosylase) RNA binding domain. Nip7 is involved in ribosome biogenesis, taking part in 27S pre-rRNA processing and in formation of the 60S ribosomal subunit. Nip7 and its homologs share a two-domain architecture with the C-terminal PUA domain mediating interaction with RNA, suggesting that Nip7 is an adaptor protein with the C-terminal domain interacting with RNA targets and the N-terminal domain mediating interaction with protein targets. 85 matched cddid_all.tbl CDD cd21924 cd21924 467849 NBR_nanos NBR (NOT module binding region) found in Drosophila melanogaster protein nanos. Nanos is a maternal RNA-binding protein that is required for germ cells proliferation and self-renewal. It acts by forming a complex with pum and brat that regulates translation and mRNA stability. The complex binds to the Nanos Response Element (NRE), a 16 bp sequence in the hunchback (hb) mRNA 3'-UTR, and prevents its translation. Nanos is the localized posterior determinant in Drosophila. Drosophila Nanos contains a Nanos effector domain (NED) at its N-terminal half. This model corresponds to a central region of the NED (called the NOT module binding region, NBR) that bound to the NOT module revealed a bipartite interface that contacts both the NOT1 superfamily homology domain (SHD) and the NOT3 NOT-box domains. 49 matched cddid_all.tbl CDD cd21927 cd21927 409275 ZIP_TSC22D-like leucine zipper found in the TSC22 domain leucine zipper transcription factors, c-Myc-binding protein, and similar proteins. The family includes TGF-beta-stimulated clone-22 domain (TSC22D) leucine zipper transcription factors, TSC22D1-4, as well as c-Myc-binding protein (MycBP). TSC22D proteins have diverse physiological functions, including cell growth, development, homeostasis, and immune regulation. MycBP, also called associate of Myc 1 (AMY-1), is a novel c-Myc binding protein that may control the transcriptional activity of Myc. It stimulates the activation of E box-dependent transcription by Myc. Members of this family contain a conserved leucine zipper (ZIP) domain. Its first helix is not basic and does not contain the consensus sequence, NXX(A)(A)XX(C/S)R, found in most basic region/leucine zipper (bZIP) proteins. In the bZIP family of transcription factors, the leucine zipper acts as a dimerization domain and the upstream basic region as a DNA-binding domain. However, DNA-binding capability of TSC22D family proteins is not obvious, due to the lack of the basic region found in the original bZIP DNA-binding domains. Similar to bZIP, ZIP forms homo- and heterodimers, resulting in many dimers that may have different effects on transcription. 51 matched cddid_all.tbl CDD cd21928 cd21928 409272 LGNbd_FRMPD1_D4-like LGN tetratricopeptide repeat-binding domain found in FERM and PDZ domain-containing proteins FRMPD1, FRMPD4, and similar proteins. The family includes FRMPD1, FRMPD4, and similar proteins. FRMPD1, also called FERM domain-containing protein 2 (FRMD2), stabilizes membrane-bound GPSM1, and thereby promotes its interaction with GNAI1. It also acts as a regulatory binding partner of Activator of G-protein Signaling 3 (AGS3). FRMPD4, also called PDZ domain-containing protein 10 (PDZD10), PDZK10, or PSD-95-interacting regulator of spine morphogenesis (Preso), is a novel PSD-95-interacting FERM and PDZ domain-containing protein that regulates dendritic spine morphogenesis. It acts as a positive regulator of dendritic spine morphogenesis and density. It is required for the maintenance of excitatory synaptic transmission. It binds phosphatidylinositol 4,5-bisphosphate. This model corresponds to a conserved region in FRMPD1 and FRMPD4 that binds to tetratricopeptide (TPR) repeats present in the N-terminal domain of adaptor protein LGN. LGN plays a crucial role in mitotic spindle orientation and cell polarization via interaction with multiple targets including FRMPD1 and FRMPD4. 37 matched cddid_all.tbl CDD cd21930 cd21930 412018 IPD_PPP1R12 inhibitory phosphorylation domain of protein phosphatase 1 regulatory subunit 12 (PPP1R12) family. The PPP1R12 family includes PPP1R12A/MYPT1, PPP1R12B/MYPT2, and PPP1R12C. PPP1R12A/MYPT1, also called myosin phosphatase target subunit 1, or protein phosphatase myosin-binding subunit, is a substrate for the asparaginyl hydroxylase factor inhibiting hypoxia-inducible factor (FIH). It acts as a key regulator of protein phosphatase 1C (PPP1C). It mediates binding to myosin. As part of the PPP1C complex, PPP1R12A/MYPT1 is involved in dephosphorylation of PLK1. It is capable of inhibiting HIF1A inhibitor (HIF1AN)-dependent suppression of HIF1A activity. PPP1R12B/MYPT2, also called myosin phosphatase target subunit 2, is the targeting subunit of smooth-muscle myosin phosphatase that regulates myosin phosphatase activity and augments Ca(2+) sensitivity of the contractile apparatus. PPP1R12C, also called protein phosphatase 1 myosin-binding subunit of 85 kDa (MBS85), protein phosphatase 1 myosin-binding subunit p85, or LENG3, regulates myosin phosphatase activity. All family members contain an inhibitory phosphorylation domain. 47 matched cddid_all.tbl CDD cd21931 cd21931 409267 TD_EMAP-like trimerization domain of the echinoderm microtubule-associated protein-like family. The echinoderm microtubule-associated protein (EMAP)-like (EML) family includes EMAP-1, EMAP-2, EMAP-3, and EMAP-4. EMAP-1, also called EMAL1, EMAPL or EMAPL1, modulates the assembly and organization of the microtubule cytoskeleton, and probably plays a role in regulating the orientation of the mitotic spindle and the orientation of the plane of cell division. It is required for normal proliferation of neuronal progenitor cells in the developing brain and for normal brain development. EMAP-2, also called EML2 or EMAPL2, is a tubulin binding protein that inhibits microtubule nucleation and growth, resulting in shorter microtubules. EMAP-3, also called EML3, is a nuclear microtubule-binding protein required for the correct alignment of chromosomes in metaphase. EMAP-4, also called EML4, EMAPL4, restrictedly overexpressed proliferation-associated protein, or Ropp 120, may modify the assembly dynamics of microtubules, such that microtubules are slightly longer, but more dynamic. This model corresponds to a conserved trimerization domain located at the N-terminus of EML family members. 44 matched cddid_all.tbl CDD cd21932 cd21932 409264 MIU2_RNF168-like second motif interacting with ubiquitin domain found in RING finger protein 168 and similar domains. The domain family includes motif interacting with ubiquitin (MIU) domains of RING finger protein, RNF168 and RNF169. RNF168 is an E3 ubiquitin-protein ligase that promotes noncanonical K27 ubiquitination to signal DNA damage. It, together with RNF8, functions as a DNA damage response (DDR) factor that promotes monoubiquitination of H2A/H2AX at K13/15, facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. RNF169 is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. RNF169 recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to the regulation of the DSB repair pathway by competing with repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. RNF168 contains an N-terminal C3HC4-type RING-HC finger that catalyzes H2A-K15ub modification and interacts with H2A, and two MIU (motif interacting with ubiquitin) domains responsible for interaction with K63 linked poly-ubiquitin. RNF169 contains an N-terminal C3HC4-type RING-HC finger and a C-terminal MIU domain. This model corresponds to the second MIU (MIU2) domain of RNF168 and the C-terminal MIU domain of RNF169, which is responsible for bridging histone and ubiquitin surfaces. 42 matched cddid_all.tbl CDD cd21933 cd21933 409261 TBK1_IKKE-like_C C-terminal domain of non-canonical Inhibitor of kappa B kinases, IKK-E and TBK1, and similar proteins. Inhibitor of nuclear factor kappa-B kinase subunit epsilon (IKK-E or IKK-epsilon) and TANK-binding kinase 1 (TBK1) are non-canonical members of IKK family. They have been characterized as activators of nuclear factor-kappaB (NF-kappaB), but they are not essential for NF-kappaB activation. They play critical roles in antiviral response via phosphorylation and activation of transcription factors IRF3, IRF7, STAT1, and STAT3. They are also involved in the survival, tumorigenesis, and development of various cancers. Both IKK-epsilon and TBK1 contain an N-terminal protein kinase domain followed by a ubiquitin-like (Ubl) domain, a coiled-coil domain 1 (CCD1), and a C-terminal elongated alpha-helical domain. The model corresponds to the C-terminal elongated alpha-helical domain. It is responsible for the binding of adaptor proteins, optineurin (OPTN) and NAP1, to TBK1. 43 matched cddid_all.tbl CDD cd21936 cd21936 409276 ZIP_TSC22D leucine zipper domain found in the TSC22 domain family of leucine zipper transcription factors. The TGF-beta-stimulated clone-22 domain (TSC22D) family includes TSC22D1-4 and similar proteins. They have diverse physiological functions, including cell growth, development, homeostasis, and immune regulation. All family members contain a conserved leucine zipper (ZIP) domain located at the C-terminus. Its first helix is not basic and does not contain the consensus sequence, NXX(A)(A)XX(C/S)R, found in most basic region/leucine zipper (bZIP) proteins. In the bZIP family of transcription factors, the leucine zipper acts as a dimerization domain and the upstream basic region as a DNA-binding domain. However, DNA-binding capability of TSC22D family proteins is not obvious, due to the lack of the basic region found in the original bZIP DNA-binding domains. Similar to bZIP, ZIP forms homo- and heterodimers, resulting in many dimers that may have different effects on transcription. 49 matched cddid_all.tbl CDD cd21937 cd21937 409277 ZIP_MycBP-like leucine zipper domain found in c-Myc-binding protein and similar proteins. MycBP, also called associate of Myc 1 (AMY-1), is a novel c-Myc binding protein that may control the transcriptional activity of Myc. It stimulates the activation of E box-dependent transcription by Myc. This model corresponds to the conserved region that shows high sequence similarity with the leucine zipper (ZIP) domain located at the C-terminus of TGF-beta-stimulated clone-22 domain (TSC22D) family transcription factors. The first helix of ZIP is not basic and does not contain the consensus sequence, NXX(A)(A)XX(C/S)R, found in most basic region/leucine zipper (bZIP) proteins. Thus, the DNA-binding capability of the ZIP domain is not obvious. Similar to bZIP, ZIP forms homo- and heterodimers, resulting in many dimers that may have different effects on transcription. 53 matched cddid_all.tbl CDD cd21938 cd21938 409278 ZIP_TSC22D1 leucine zipper domain found in TSC22 domain family protein 1. TSC22 domain family protein 1 (TSC22D1) is also called cerebral protein 2, regulatory protein TSC-22, TGFB-stimulated clone 22, or transforming growth factor beta-1-induced transcript 4 protein (TGFB1I4). It is a transcriptional repressor that was reported to be present in both the cytoplasmic and the nuclear fraction. It is activated by transcription growth factor-beta1 and other growth factors of osteoblastic cells. TSC22D1 acts on the C-type natriuretic peptide (CNP) promoter. It enhances c-Myc-mediated activation of the telomerase reverse transcriptase (TERT) promoter. This model corresponds to the conserved leucine zipper (ZIP) domain located at the C-terminus of TSC22D1. Its first helix is not basic and does not contain the consensus sequence, NXX(A)(A)XX(C/S)R, found in most basic region/leucine zipper (bZIP) proteins. Thus, the DNA-binding capability of the ZIP domain is not obvious. Similar to bZIP, ZIP forms homo- and heterodimers, resulting in many dimers that may have different effects on transcription. 79 matched cddid_all.tbl CDD cd21939 cd21939 409279 ZIP_TSC22D2 leucine zipper domain found in TSC22 domain family protein 2. TSC22 domain family protein 2 (TSC22D2), also called transforming growth factor beta-stimulated clone 22 domain family member 2, or TSC22-related-inducible leucine zipper protein 4 (TILZ4), may participate in the regulation of cell growth. It interacts with pyruvate kinase isoform M2 (PKM2) and WD repeat domain 77 (WDR77). The model corresponds to the conserved leucine zipper (ZIP) domain located at the C-terminus of TSC22D2. Its first helix is not basic and does not contain the consensus sequence, NXX(A)(A)XX(C/S)R, found in most basic region/leucine zipper (bZIP) proteins. Thus, the DNA-binding capability of the ZIP domain is not obvious. Similar to bZIP, ZIP forms homo- and heterodimers, resulting in many dimers that may have different effects on transcription. 63 matched cddid_all.tbl CDD cd21940 cd21940 409280 ZIP_TSC22D3 leucine zipper domain found in TSC22 domain family protein 3. TSC22 domain family protein 3 (TSC22D3) is also called DSIP-immunoreactive peptide, protein DIP, delta sleep-inducing peptide immunoreactor, glucocorticoid-induced leucine zipper protein (GILZ), TSC-22-like protein, or TSC-22-related protein (TSC-22R). It protects T-cells from IL2 deprivation-induced apoptosis through the inhibition of FOXO3A transcriptional activity that leads to the down-regulation of the pro-apoptotic factor BCL2L11. In macrophages, it plays a role in the anti-inflammatory and immunosuppressive effects of glucocorticoids and IL10. In T-cells, it inhibits anti-CD3-induced NFKB1 nuclear translocation. TSC22D3 contains a leucine zipper motif, a Pro/Glu rich domain, and three potential phosphorylation sites. This model corresponds to the leucine zipper (ZIP) domain. Its first helix is not basic and does not contain the consensus sequence, NXX(A)(A)XX(C/S)R, found in most basic region/leucine zipper (bZIP) proteins. Thus, the DNA-binding capability of the ZIP domain is not obvious. Similar to bZIP, ZIP forms homo- and heterodimers, resulting in many dimers that may have different effects on transcription. 81 matched cddid_all.tbl CDD cd21941 cd21941 409281 ZIP_TSC22D4 leucine zipper domain found in TSC22 domain family protein 4. TSC22 domain family protein 4 (TSC22D4), also called TSC22-related-inducible leucine zipper protein 2 (TILZ2), or Tsc-22-like protein THG-1, is a transcriptional repressor that acts as a molecular determinant of insulin signalling and glucose handling. It also functions in hepatic lipid handling by regulating hepatic very-low-density-lipoprotein (VLDL) release and lipogenic gene expression. This model corresponds to the conserved leucine zipper (ZIP) domain located at the C-terminus of TSC22D4. Its first helix is not basic and does not contain the consensus sequence, NXX(A)(A)XX(C/S)R, found in most basic region/leucine zipper (bZIP) proteins. Thus, the DNA-binding capability of the ZIP domain is not obvious. Similar to bZIP, ZIP forms homo- and heterodimers, resulting in many dimers that may have different effects on transcription. 74 matched cddid_all.tbl CDD cd21942 cd21942 409273 LGNbd_FRMPD1 LGN tetratricopeptide repeat-binding domain found in FERM and PDZ domain-containing protein 1. FERM and PDZ domain-containing protein 1 (FRMPD1), also called FERM domain-containing protein 2 (FRMD2), stabilizes membrane-bound GPSM1, and thereby promotes its interaction with GNAI1. It also acts as a regulatory binding partner of Activator of G-protein Signaling 3 (AGS3). This model corresponds to a conserved region in FRMPD1 that binds to tetratricopeptide (TPR) repeats present in the N-terminal domain of adaptor protein LGN. LGN plays a crucial role in mitotic spindle orientation and cell polarization via interaction with multiple targets including FRMPD1. 38 matched cddid_all.tbl CDD cd21943 cd21943 409274 LGNbd_FRMPD4 LGN tetratricopeptide repeat-binding domain found in FERM and PDZ domain-containing protein 4. FRMPD4, also called PDZ domain-containing protein 10 (PDZD10), PDZK10, or PSD-95-interacting regulator of spine morphogenesis (Preso), is a novel PSD-95-interacting FERM and PDZ domain protein that regulates dendritic spine morphogenesis. It acts as a positive regulator of dendritic spine morphogenesis and density. It is required for the maintenance of excitatory synaptic transmission. It binds phosphatidylinositol 4,5-bisphosphate. FRMPD4 contains WW, PDZ and FERM domains in the N-terminal region. This model corresponds to a conserved region in the C-terminal region of FRMPD4 that binds to tetratricopeptide (TPR) repeats present in the N-terminal domain of adaptor protein LGN. LGN plays a crucial role in mitotic spindle orientation and cell polarization via interaction with multiple targets including FRMPD4. 49 matched cddid_all.tbl CDD cd21944 cd21944 412019 IPD_MYPT1 inhibitory phosphorylation domain of myosin phosphatase targeting subunit 1(MYPT1). MYPT1, also called protein phosphatase 1 regulatory subunit 12A (PPP1R12A), myosin phosphatase target subunit 1, or protein phosphatase myosin-binding subunit, is the targeting subunit of smooth-muscle myosin phosphatase. It is a substrate for the asparaginyl hydroxylase factor inhibiting hypoxia-inducible factor (FIH). MYPT1 acts as a key regulator of protein phosphatase 1C (PPP1C). It mediates binding to myosin. As part of the PPP1C complex, MYPT1 is involved in dephosphorylation of the mitosis regulator polo-like kinase 1 (PLK1). It is capable of inhibiting HIF1A inhibitor (HIF1AN)-dependent suppression of HIF1A activity. This model corresponds to the inhibitory phosphorylation domain of MYPT1. 57 matched cddid_all.tbl CDD cd21945 cd21945 412020 IPD_PPP1R12C inhibitory phosphorylation domain of protein phosphatase 1 regulatory subunit 12C (PPP1R12C). PPP1R12C, also called protein phosphatase 1 myosin-binding subunit of 85 kDa (MBS85), protein phosphatase 1 myosin-binding subunit p85, or LENG3, regulates myosin phosphatase activity. This model corresponds to a conserved region of PPP1R12C, which shows high sequence similarity to the inhibitory phosphorylation domain of MYPT1. 54 matched cddid_all.tbl CDD cd21946 cd21946 412021 IPD_MYPT2 inhibitory phosphorylation domain of myosin phosphatase targeting subunit 2 (MYPT2). MYPT2, also called protein phosphatase 1 regulatory subunit 12B (PPP1R12B), or myosin phosphatase target subunit 2, is the targeting subunit of smooth-muscle myosin phosphatase that regulates myosin phosphatase activity and augments Ca(2+) sensitivity of the contractile apparatus. This model corresponds to the inhibitory phosphorylation domain of MYPT2. 53 matched cddid_all.tbl CDD cd21947 cd21947 409268 TD_EMAP1 trimerization domain of echinoderm microtubule-associated protein-like 1. Echinoderm microtubule-associated protein-like 1 (EMAP-1), also called EMAL1, EMAPL, or EMAPL1, modulates the assembly and organization of the microtubule cytoskeleton, and probably plays a role in regulating the orientation of the mitotic spindle and the orientation of the plane of cell division. It is required for normal proliferation of neuronal progenitor cells in the developing brain and for normal brain development. This model corresponds to a conserved region located at the N-terminus of EMAP-1, which shows high sequence similarity with the N-terminal trimerization domain of EMAP-4 and EMAP-2. 58 matched cddid_all.tbl CDD cd21948 cd21948 409269 TD_EMAP2 trimerization domain of echinoderm microtubule-associated protein-like 2. Echinoderm microtubule-associated protein-like 2 (EMAP-2), also called EML2 or EMAPL2, is a tubulin binding protein that inhibits microtubule nucleation and growth, resulting in shorter microtubules. This model corresponds to the N-terminal trimerization domain of EMAP-2. 48 matched cddid_all.tbl CDD cd21949 cd21949 409270 TD_EMAP3 trimerization domain of echinoderm microtubule-associated protein-like 3. Echinoderm microtubule-associated protein-like 3 (EMAP-3), also called EML3, is a nuclear microtubule-binding protein required for the correct alignment of chromosomes in metaphase. It may modify the assembly dynamics of microtubules, such that microtubules are slightly longer, but more dynamic. This model corresponds to a conserved region located at the N-terminus of EMAP-3, which shows high sequence similarity with the N-terminal trimerization domain of EMAP-2 and EMAP-4. 48 matched cddid_all.tbl CDD cd21950 cd21950 409271 TD_EMAP4 trimerization domain of echinoderm microtubule-associated protein-like 4. Echinoderm microtubule-associated protein-like 4 (EMAP-4), also called EML4, EMAPL4, restrictedly overexpressed proliferation-associated protein, or Ropp 120, may modify the assembly dynamics of microtubules, such that microtubules are slightly longer, but more dynamic. This model corresponds to the N-terminal trimerization domain of EMAP-4. 59 matched cddid_all.tbl CDD cd21951 cd21951 409265 MIU_RNF169_C C-terminal motif interacting with ubiquitin domain found in RING finger protein 169. RING finger protein 169 (RNF169) is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. RNF169 recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to the regulation of the DSB repair pathway by competing with repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. RNF169 contains an N-terminal C3HC4-type RING-HC finger and a C-terminal MIU (motif interacting with ubiquitin) domain. This model corresponds to the MIU domain of RNF169, which shows high sequence similarity with the second MIU (MIU2) domain of RNF168, and is responsible for bridging histone and ubiquitin surfaces. 54 matched cddid_all.tbl CDD cd21952 cd21952 409266 MIU2_RNF168 second motif interacting with ubiquitin domain found in RING finger protein 168. RNF168 is an E3 ubiquitin-protein ligase that promotes noncanonical K27 ubiquitination to signal DNA damage. It, together with RNF8, functions as a DNA damage response (DDR) factor that promotes monoubiquitination of H2A/H2AX at K13/15, facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. Moreover, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. RNF168 contains an N-terminal C3HC4-type RING-HC finger that catalyzes H2A-K15ub modification and interacts with H2A, and two MIU (motif interacting with ubiquitin) domains responsible for the interaction with K63 linked poly-ubiquitin. This model corresponds to the second MIU (MIU2) domain of RNF168. The first MIU belongs to a different domain family and is not included here. 51 matched cddid_all.tbl CDD cd21953 cd21953 409262 IKKE_C C-terminal domain of inhibitor of nuclear factor kappa-B kinase subunit epsilon. Inhibitor of nuclear factor kappa-B kinase subunit epsilon (IKK-E) (EC 2.7.11.10) is also called I-kappa-B kinase epsilon, IKK-epsilon, IkBKE, inducible I kappa-B kinase, or IKK-I. It is an interferon regulatory factor-activating kinase that is a non-canonical member of the IKK family. It is involved in cellular innate immunity by inducing type I interferons. It is induced by the activation of nuclear factor-kappaB (NF-kappaB). IKK-E has also been implicated in antiviral immune response in higher vertebrates. It acts as a crucial pro-survival factor in human T cell leukemia virus type 1 (HTLV-1)-transformed T lymphocytes. Moreover, IKK-E plays an essential role in tumor initiation and progression. It inhibits protein kinase C (PKC) to promote Fascin-dependent actin bundling. IKK-E contains an N-terminal protein kinase domain followed by a ubiquitin-like (Ubl) domain, a coiled-coil domain 1 (CCD1), and a C-terminal elongated helical domain. This model corresponds to the C-terminal elongated helical domain of IKK-E that shows high sequence similarity with the C-terminal domain of TBK1, which is responsible for binding to its adaptor proteins, optineurin (OPTN) and NAP1. 48 matched cddid_all.tbl CDD cd21954 cd21954 409263 TBK1_C C-terminal domain of TANK-binding kinase 1. TANK-binding kinase 1 (TBK1), also called T2K and NF-kB-activating kinase, is a serine/threonine-protein kinase that is widely expressed in most cell types and acts as an IkappaB kinase (IKK)-activating kinase responsible for NF-kB activation in response to growth factors. It plays a role in modulating inflammatory responses through the NF-kB pathway. TKB1 is also a major player in innate immune responses since it functions as a virus-activated kinase necessary for establishing an antiviral state. It phosphorylates IRF-3 and IRF-7, which are important transcription factors for inducing type I interferon during viral infection. TBK1 may also play roles in cell transformation and oncogenesis. In addition, it regulates optineurin (OPTN), an important autophagy receptor involved in several selective autophagy processes. TBK1 contains N-terminal serine/threonine protein kinase, ubiquitin-like (Ubl), coiled-coil domain 1 (CCD1), and C-terminal alpha-helical domains. This model corresponds to a small conserved elongated alpha-helical domain at the C-terminus of TBK1, which is responsible for the binding of its adaptor proteins such as OPTN and NAP1. 47 matched cddid_all.tbl CDD cd21955 cd21955 409250 SARS-CoV_ORF9b accessory protein 9b of severe acute respiratory syndrome-associated coronavirus and similar proteins. This model represents the accessory protein 9b (ORF9b) from Severe acute respiratory syndrome-associated coronavirus (SARS-CoV) and some related betacoronaviruses such as bat coronavirus. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered to be dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. ORF9b is a product of an alternative open reading frame within the N gene from SARS coronavirus. It is a lipid-binding protein that has been shown to associate with intracellular vesicles in mammalian cells, consistent with a role in the assembly of the virion. ORF9b localizes to mitochondria and causes mitochondrial elongation by triggering ubiquitination and proteasomal degradation of dynamin-like protein 1, a host protein involved in mitochondrial fission. It also targets the mitochondrial-associated adaptor molecule MAVS signalosome to trigger the degradation of MAVS, TRAF3, and TRAF, which severely limits host cell interferon responses. There are slight differences in the genome organization of SARS-CoV-2 in different studies; not all SARS-CoV-2 isolates are reported as having ORF9b. 89 matched cddid_all.tbl CDD cd21956 cd21956 439318 MBD_Myo3a MORN4 binding domain (MBD) found in Myosin-IIIa and similar proteins. Myosin-IIIa, also called Myo3a, is a probable actin-based motor with ATPase and kinase activities. It may function as a cellular transporter capable of moving along actin bundles in sensory cells. Myosin-IIIa is highly expressed in retina and in inner ear hair cells. It is localized to the distal ends of actin-bundled structures. It is required for normal cochlear hair bundle development and hearing, and plays an important role in the early steps of cochlear hair bundle morphogenesis. Mutations in human myosin-IIIA are responsible for progressive nonsyndromic hearing loss. This model corresponds to the MORN4 binding domain (MBD) in the tail of myosin-IIIa. MORN4 and its Drosophila ortholog retinophilin (RTP) are binding partners/cargos of class III myosins. 49 matched cddid_all.tbl CDD cd21958 cd21958 439319 MyUb_Myo6 myosin VI ubiquitin-binding domain (MyUb) found in unconventional myosin-VI and similar proteins. Unconventional myosin VI, also called Myo6, or unconventional myosin-6, is a monomeric myosin, which moves towards the minus-end of actin filaments, in contrast to most other myosins which moves towards the plus-end of actin filaments. It is thought that myosin VI, unlike plus-end directed myosins, does not use a pure lever arm mechanism, but instead steps with a mechanism analogous to the kinesin neck-linker uncoupling model. It has been implicated in a myriad of functions including the transport of cytoplasmic organelles, maintenance of normal Golgi morphology, endocytosis, secretion, cell migration, border cell migration during development, cancer metastasis, deafness, and retinal development, among others. For example, the GIPC1 (GAIP interacting protein, C-terminus 1) adaptor protein mediates endocytosis by tethering PlexinD1, a transmembrane receptor that regulates neuronal and cardiovascular development and cargo protein of GIPC1, to myosin VI motor through a regulated oligomerization mechanism, forming a PlexinD1/GIPC/myosin VI complex. This model corresponds to the myosin VI ubiquitin-binding domain (MyUb) that binds to ubiquitin chains, especially those linked via K63, K11, and K29. 41 matched cddid_all.tbl CDD cd21963 cd21963 409248 Syt1_N N-terminal domain of synaptotagmin-1 (Syt1) and similar proteins. Syt1, also called synaptotagmin I (SytI), or p65, is a calcium sensor that participates in triggering neurotransmitter release at the synapse. It may have a regulatory role in the membrane interactions during trafficking of synaptic vesicles at the active zone of the synapse. Syt1 binds acidic phospholipids with a specificity that requires the presence of both an acidic head group and a diacyl backbone. A Ca(2+)-dependent interaction between synaptotagmin and putative receptors for activated protein kinase C has also been reported. It can bind to at least three additional proteins in a Ca(2+)-independent manner; these are neurexins, syntaxin and AP2. Syt1 also plays a role in dendrite formation by melanocytes. The model corresponds to N-terminal domain of Syt1, which is a recognition domain responsible for the binding of botulinum neurotoxin B (BoNT B). 108 matched cddid_all.tbl CDD cd21964 cd21964 409249 Syt2_N N-terminal domain of synaptotagmin-2 (Syt2) and similar proteins. Syt2, also called synaptotagmin II (SytII), exhibits calcium-dependent phospholipid and inositol polyphosphate binding properties. It may have a regulatory role in the membrane interactions during trafficking of synaptic vesicles at the active zone of the synapse. It plays a role in dendrite formation by melanocytes. The model corresponds to N-terminal domain of Syt2, which is a recognition domain responsible for the binding of botulinum neurotoxin B (BoNT B). 111 matched cddid_all.tbl CDD cd21965 cd21965 412012 Zn-C2H2_CALCOCO1_TAX1BP1_like autophagy receptor zinc finger-C2H2 domain found in calcium-binding and coiled-coil domain-containing proteins, TAX1BP1 and similar proteins. The family includes calcium-binding and coiled-coil domain-containing proteins (CALCOCO1 and CALCOCO2), TAX1BP1 and similar proteins. CALCOCO1, also called calphoglin, or coiled-coil coactivator protein, or Sarcoma antigen NY-SAR-3, functions as a coactivator for aryl hydrocarbon and nuclear receptors (NR). CALCOCO2, also called antigen nuclear dot 52 kDa protein, or nuclear domain 10 protein NDP52, or nuclear domain 10 protein 52, or nuclear dot protein 52, is an ubiquitin-binding autophagy receptor involved in the selective autophagic degradation of invading pathogens. TAX1BP1, also called TRAF6-binding protein (T6BP), is a novel ubiquitin-binding adaptor protein involved in the negative regulation of the NF-kappaB transcription factor, a key player in inflammatory responses, immunity and tumorigenesis. The family also includes Drosophila melanogaster Spindle-F (Spn-F) that is the central mediator of IK2 kinase-dependent dendrite pruning in drosophila sensory neurons. This model corresponds to the C2H2-type zinc binding domain found in family members. It is a typical C2H2-type zinc finger which specifically recognizes mono-ubiquitin or poly-ubiquitin chain. The overall ubiquitin-binding mode utilizes the C-terminal alpha-helix to interact with the solvent-exposed surface of the central beta-sheet of ubiquitin, similar to that observed in the RABGEF1/Rabex-5 or POLN/Pol-eta zinc finger. 24 matched cddid_all.tbl CDD cd21966 cd21966 439320 INSC_LBD LGN-binding domain (LBD) of protein Inscuteable (INSC) and similar proteins. Inscuteable (INSC) functions as an adapter protein linking the Par polarity complex (composed of Par3, Par6 and protein kinase C iota) to the Gpsm1/Gpsm2 complex, and is involved in cell polarity and spindle orientation during mitosis. Par3 interacts with INSC which binds directly to Pins (partner of Insc, homolog of vertebrate LGN/Gpsm2 and AGS3/Gpsm1). Pins then associates with the heterotrimeric G proteins and NuMA, which interacts directly with the cell spindle to control the orientation of the spindle and the division plane of mitotic cells. INSC may regulate cell proliferation and differentiation in the developing nervous system, may play a role in the asymmetric division of fibroblasts, and may also participate in the process of stratification of the squamous epithelium. This model corresponds to the Leu-Gly-Asn Repeat-Enriched Protein (LGN)-binding domain (LBD) of INSC. It interacts with the tetratricopeptide repeat (TPR) motifs of LGN, also called G-protein-signaling modulator 2 (Gpsm2). 300 matched cddid_all.tbl CDD cd21967 cd21967 412013 Zn-C2H2_CALCOCO1 C2H2-type zinc binding domain found in calcium-binding and coiled-coil domain-containing protein 1 (CALCOCO1) and similar proteins. CALCOCO1, also called calphoglin, or coiled-coil coactivator protein, or Sarcoma antigen NY-SAR-3, functions as a coactivator for aryl hydrocarbon and nuclear receptors (NR). It is recruited to promoters through its contact with the N-terminal basic helix-loop-helix-Per-Arnt-Sim (PAS) domain of transcription factors or coactivators, such as NCOA2. During ER-activation CALCOCO1 acts synergistically in combination with other NCOA2-binding proteins, such as EP300, CREBBP and CARM1. It is involved in the transcriptional activation of target genes in the Wnt/CTNNB1 pathway. It functions as a secondary coactivator in LEF1-mediated transcriptional activation via its interaction with CTNNB1. In association with CCAR1, CALCOCO1 enhances GATA1- and MED1-mediated transcriptional activation from the gamma-globin promoter during erythroid differentiation of K562 erythroleukemia cells. CALCOCO1 contains a C2H2-type zinc binding domain. 29 matched cddid_all.tbl CDD cd21968 cd21968 412014 Zn-C2H2_CALCOCO2 C2H2-type zinc binding domain found in calcium-binding and coiled-coil domain-containing protein 2 (CALCOCO2) and similar proteins. CALCOCO2, also called antigen nuclear dot 52 kDa protein, or nuclear domain 10 protein NDP52, or nuclear domain 10 protein 52, or nuclear dot protein 52, is an Xenophagy-specific receptor required for autophagy-mediated intracellular bacteria degradation. It acts as an effector protein of galectin-sensed membrane damage that restricts the proliferation of infecting pathogens such as Salmonella typhimurium upon entry into the cytosol by targeting LGALS8-associated bacteria for autophagy. It may play a role in ruffle formation and actin cytoskeleton organization and seems to negatively regulate constitutive secretion. CALCOCO2 contains a C2H2-type zinc binding domain. 27 matched cddid_all.tbl CDD cd21969 cd21969 412015 Zn-C2H2_TAX1BP1_rpt1 first C2H2-type zinc binding domain found in tax1-binding protein 1 (TAX1BP1) and similar proteins. TAX1BP1, also called TRAF6-binding protein (T6BP), is a novel ubiquitin-binding adaptor protein involved in the negative regulation of the NF-kappaB transcription factor, a key player in inflammatory responses, immunity and tumorigenesis. It inhibits TNF-induced apoptosis by mediating the TNFAIP3 anti-apoptotic activity. It may also play a role in the pro-inflammatory cytokine IL-1 signaling cascade. TAX1BP1 is degraded by caspase-3-like family proteins upon TNF-induced apoptosis. TAX1BP1 contains two C2H2-type zinc binding domains; this model corresponds to the first one. 24 matched cddid_all.tbl CDD cd21970 cd21970 412016 Zn-C2H2_TAX1BP1_rpt2 second C2H2-type zinc binding domain found in tax1-binding protein 1 (TAX1BP1) and similar proteins. TAX1BP1, also called TRAF6-binding protein (T6BP), is a novel ubiquitin-binding adaptor protein involved in the negative regulation of the NF-kappaB transcription factor, a key player in inflammatory responses, immunity and tumorigenesis. It inhibits TNF-induced apoptosis by mediating the TNFAIP3 anti-apoptotic activity. It may also play a role in the pro-inflammatory cytokine IL-1 signaling cascade. TAX1BP1 is degraded by caspase-3-like family proteins upon TNF-induced apoptosis. TAX1BP1 contains two C2H2-type zinc binding domains; this model corresponds to the second one. 27 matched cddid_all.tbl CDD cd21971 cd21971 412017 Zn-C2H2_spn-F C2H2-type zinc binding domain found in Drosophila melanogaster Spindle-F (Spn-F) and similar proteins. spn-F is the central mediator of IK2 kinase-dependent dendrite pruning in drosophila sensory neurons. It acts downstream of IKK-related kinase Ik2 in the same pathway for dendrite pruning. Spn-F is a coil-coiled protein containing a C2H2-type zinc binding domain. 30 matched cddid_all.tbl CDD cd21972 cd21972 409230 KLF1_2_4_N N-terminal domain of Kruppel-like factor (KLF) 1, KLF2, KLF4, and similar proteins. Kruppel/Krueppel-like transcription factors (KLFs) belong to a family of proteins called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specifity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the related N-terminal domains of KLF1, KLF2, KLF4, and similar proteins. 194 matched cddid_all.tbl CDD cd21973 cd21973 409246 KLF6_7_N-like N-terminal domain of Kruppel-like factor (KLF) 6, KLF7, and similar proteins. This subfamily is composed of Kruppel-like factor or Krueppel-like factor (KLF) 6, KLF7, and similar proteins, including KLF Luna, a Drosophila KLF6/KLF7. KLF6 contributes to cell proliferation, differentiation, cell death and signal transduction. Hepatocyte expression of KLF6 regulates hepatic fatty acid and glucose metabolism via transcriptional activation of liver glucokinase and post-transcriptional regulation of the nuclear receptor peroxisome proliferator activated receptor alpha (PPARa). KLF7 is involved in regulation of the development and function of the nervous system and adipose tissue, type 2 diabetes, blood diseases, as well as pluripotent cell maintenance. KLF Luna is maternally required for synchronized nuclear and centrosome cycles in the preblastoderm embryo. KLF6 and KLF7 are transcriptional activators. They belong to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the related N-terminal domains of KLF6, KLF7, and similar proteins. 138 matched cddid_all.tbl CDD cd21974 cd21974 409243 KLF10_11_N N-terminal domain of Kruppel-like factor (KLF) 10, KLF11, and similar proteins. This subfamily is composed of Kruppel-like factor or Krueppel-like factor (KLF) 10, KLF11, and similar proteins. KLF10 was first identified in human osteoblasts and plays a role in mediating estrogen (E2) signaling in bone and skeletal homeostasis and a regulatory role in tumor formation and metastasis. KLF11 is involved in cell growth, apoptosis, cellular inflammation and differentiation, endometriosis, and cholesterol, prostaglandin, neurotransmitter, fat, and sugar metabolism. KLF9, KLF10, KLF11, KLF13, KLF14, and KLF16 share a conserved a-helical motif AA/VXXL that mediates their binding to Sin3A and their activities as transcriptional repressors. KLF10/11 belong to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domain of KLF10, KLF11, and similar proteins. 229 matched cddid_all.tbl CDD cd21975 cd21975 409240 KLF9_13_N-like Kruppel-like factor (KLF) 9, KLF13, KLF14, KLF16, and similar proteins. Kruppel/Krueppel-like transcription factors (KLFs) belong to a family of proteins, called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. KLF9, KLF10, KLF11, KLF13, KLF14, and KLF16 share a conserved alpha-helical motif AA/VXXL that mediates their binding to Sin3A and their activities as transcriptional repressors. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specificity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the related N-terminal domains of KLF9, KLF13, KLF14, KLF16, and similar proteins. 163 matched cddid_all.tbl CDD cd21976 cd21976 409235 SARS-CoV_ORF9c accessory protein ORF9c (also referred to as ORF14) from Severe acute respiratory syndrome-associated coronavirus and related coronaviruses. This model represents the accessory protein 9c (ORF9c, also referred to as ORF14/protein 14) from Sarbecoviruses including Severe acute respiratory syndrome-associated coronavirus (SARS-CoV), SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV), and Bat SARS-like coronaviruses. There are five essential genes in CoVs that result in the following gene products: Spike (S) protein, Membrane (M) glycoprotein, Nucleocapsid (N), Envelope (E) protein, and replicase/protease polyproteins (ORF1ab); all are required to produce a structurally complete viral particle. In addition, CoV genomes also contain ORFs coding for accessory proteins that are specific for certain CoV lineages or for a particular CoV. In general, CoV accessory proteins are considered to be dispensable for viral replication; however, several accessory proteins have been shown to exhibit functions in virus-host interactions during CoV infection. ORF9c/protein 14 is a product of an alternative open reading frame (ORF) within the N gene from SARS coronavirus. A study of the SARS-CoV2-human protein-protein interaction network (including cloning, tagging and expressing SARS-CoV2 proteins in human cells followed by affinity-purification mass spectrometry) uncovered ORF9c/protein 14 interactions, including those with Sigma receptors (implicated in lipid remodeling and ER stress response), mitochondrial electron transport (ECSIT, ACAD9, NDUFAF1, NDUFB9 ), GPI-anchor biosynthesis (GPAA1, GIPS), and with innate immune signaling proteins (NLRX1, F2RL1, NDFIP2). A preliminary study, using a computational and knowledge-based approach to investigate the interplay between host and SARS-CoV2 in various signaling pathways, supports that SARS-CoV2 ORF9c protein may perturb host antiviral inflammatory cytokine and interferon production pathways (DOI:10.1101/2020.05.06.050260). There are slight differences in the genome organization of SARS-CoV2 in different studies; not all SARS-CoV2 isolates are reported as having ORF9c/protein 14. 70 matched cddid_all.tbl CDD cd21977 cd21977 438793 HMG-box_BHMG1 high mobility group (HMG)-box found in basic helix-loop-helix and HMG box domain-containing protein 1 (BHMG1) and similar proteins. BHMG1 is an uncharacterized HMG-box containing protein that contains a degenerate basic motif not likely to bind DNA. 66 matched cddid_all.tbl CDD cd21978 cd21978 438794 HMG-box_HMGB_rpt1 first high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family. HMGB proteins are chromatin-associated nuclear proteins that act as architectural factors in nucleoprotein structures, which regulate DNA-dependent processes including transcription. In mammals, four family members are present: HMGB1, HMGB2, HMGB3 and HMGB4. They regulate the expression of a wide range of genes through architectural remodeling of the chromatin structure. HMGB1, also called high mobility group protein 1 (HMG-1), is a prototypical alarmin or damage-associated molecular pattern (DAMP) molecule when released from cells. It plays important roles in the regulation of a wide range of processes, including transcription, replication, DNA repair, and nucleosome formation, in the nucleus. It also plays multiple roles in regulating inflammation and responses to cell and tissue stress. HMGB2, also called high mobility group protein 2 (HMG-2), has been implicated in numerous cellular processes, including proliferation, differentiation, apoptosis, and tumor growth. It acts as a chromatin-associated nonhistone protein involved in transcriptional regulation and nucleic-acid-mediated innate immune responses in mammalian cells. It binds DNA to stabilize nucleosomes and promote transcription. HMGB3, also called high mobility group protein 2a (HMG-2a), or high mobility group protein 4 (HMG-4), is an X-linked member of the HMGB family that functions as a universal sentinel for nucleic acid-mediated innate immune responses. HMGB3 has been implicated in the regulation of cellular proliferation and differentiation, as well as inflammatory responses. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. It is a factor that regulates chromatin and expression of neuronal differentiation markers. This family also includes high mobility group protein B1 pseudogene 1 (HMGB1P1) and nuclear auto-antigen Sp-100. HMGB1P1, also called putative high mobility group protein B1-like 1 (HMGB1L1), or putative high mobility group protein 1-like 1 (HMG-1L1), is an HMG-box containing protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. Sp-100, also called nuclear dot-associated Sp100 protein, or speckled 100 kDa, is a tumor suppressor that is a major constituent of promyelocytic leukemia (PML) bodies, a subnuclear organelle involved in many physiological processes including cell growth, differentiation and apoptosis. Through the regulation of ETS1, Sp-100 may play a role in angiogenesis, controlling endothelial cell motility and invasion. It may also play roles in the regulation of telomere lengthening, TP53-mediated transcription, FAS-mediated apoptosis, etc. In addition, the family includes Drosophila melanogaster high mobility group protein DSP1 (dDSP1) and similar proteins. dDSP1, also called protein dorsal switch 1, binds preferentially to single-stranded DNA and unwinds double-stranded DNA. It converts Dorsal and nuclear factor (NF)-kappa B from transcriptional activators to repressors. Members of the HMGB family contain two HMG-box domains. This model corresponds to the first one. 69 matched cddid_all.tbl CDD cd21979 cd21979 438795 HMG-box_HMGB_rpt2 second high mobility group (HMG)-box found in the high mobility group protein B (HMGB) family. HMGB proteins are chromatin-associated nuclear proteins that act as architectural factors in nucleoprotein structures, which regulate DNA-dependent processes including transcription. In mammals, four family members are present: HMGB1, HMGB2, HMGB3 and HMGB4. They regulate the expression of a wide range of genes through architectural remodeling of the chromatin structure. HMGB1, also called high mobility group protein 1 (HMG-1), is a prototypical alarmin or damage-associated molecular pattern (DAMP) molecule when released from cells. It plays important roles in the regulation of a wide range of processes, including transcription, replication, DNA repair, and nucleosome formation, in the nucleus. It also plays multiple roles in regulating inflammation and responses to cell and tissue stress. HMGB2, also called high mobility group protein 2 (HMG-2), has been implicated in numerous cellular processes, including proliferation, differentiation, apoptosis, and tumor growth. It acts as a chromatin-associated nonhistone protein involved in transcriptional regulation and nucleic-acid-mediated innate immune responses in mammalian. It binds DNA to stabilize nucleosomes and promote transcription. HMGB3, also called high mobility group protein 2a (HMG-2a), or high mobility group protein 4 (HMG-4), is an X-linked member of HMGB family and functions as a universal sentinel for nucleic acid-mediated innate immune responses. HMGB3 has been implicated in the regulation of cellular proliferation and differentiation, as well as inflammatory response. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. It is a factor that regulates chromatin and expression of neuronal differentiation markers. The family also includes high mobility group protein B1 pseudogene 1 (HMGB1P1) and nuclear auto-antigen Sp-100. HMGB1P1, also called putative high mobility group protein B1-like 1 (HMGB1L1), or putative high mobility group protein 1-like 1 (HMG-1L1), is an HMG-box containing protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. Sp-100, also called nuclear dot-associated Sp100 protein, or speckled 100 kDa. It is a tumor suppressor that is a major constituent of the promyelocytic leukemia (PML) bodies, a subnuclear organelle involved in many physiological processes including cell growth, differentiation and apoptosis. Through the regulation of ETS1, Sp-100 may play a role in angiogenesis, controlling endothelial cell motility and invasion. It may also play roles in the regulation of telomeres lengthening, TP53-mediated transcription, FAS-mediated apoptosis, etc. In addition, the family includes Drosophila melanogaster high mobility group protein DSP1 (dDSP1) and similar proteins. dDSP1, also called protein dorsal switch 1, is a Drosophila HMG1 protein that binds preferentially single-stranded DNA and unwinds double-stranded DNA. It converts Dorsal and nuclear factor (NF)-kappa B from transcriptional activators to repressors. Members of the HMGB family contain two HMG-box domains. This model corresponds to the second one. 71 matched cddid_all.tbl CDD cd21980 cd21980 438796 HMG-box_HMG20 high mobility group (HMG)-box found in the high mobility group protein 20 (HMG20) subfamily. The HMG20 subfamily includes HMG20A and HMG20B. HMG20A, also called HMG box-containing protein 20A, HMG domain-containing protein 1, HMG domain-containing protein HMGX1, HMGXB1, or iBRAF, is a chromatin-associated protein involved in neuronal differentiation and maturation. It is required for SNAI1-mediated epithelial to mesenchymal transition. HMG20A acts as an inhibitor of HMG20B. HMG20B, also called SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related, SMARCE1-related protein (SMARCE1R), BRCA2-associated factor 35 (BRAF35), HMG box-containing protein 20B, HMG domain-containing protein 2, HMG domain-containing protein HMGX2, Sox-like transcriptional factor, or structural DNA-binding protein BRAF35, is a DNA binding factor that acts as a repressor of erythroid differentiation. It is required for correct progression through the G2 phase of the cell cycle and entry into mitosis. It is also required for RCOR1/CoREST mediated repression of neuronal specific gene promoters. HMG20B is a core subunit of the Lys-specific demethylase 1/REST co-repressor 1 (LSD1-CoREST) histone demethylase complex. Both HMG20A and HMG20B contain one HMG-box. 81 matched cddid_all.tbl CDD cd21981 cd21981 438797 HMG-box_HMGXB3 high mobility group (HMG)-box found in HMG domain-containing protein 3 (HMGXB3) and similar proteins. HMGXB3, also called HMG box-containing protein 3, or protein SMF, is involved in DNA-damage repair and cell-cycle regulation. 105 matched cddid_all.tbl CDD cd21982 cd21982 438798 HMG-box_HMGXB4 high mobility group (HMG)-box found in HMG domain-containing protein 4 (HMGXB4) and similar proteins. HMGXB4, also called HMG box-containing protein 4, high mobility group protein 2-like 1 (HMG2L1), or protein HMGBCG, is a non-histone chromosomal protein that negatively regulates Wnt/beta-catenin signaling during development. It plays a role in the hematopoietic system. 61 matched cddid_all.tbl CDD cd21983 cd21983 438799 HMG-box_SMARCE1 high mobility group (HMG)-box found in SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 (SMARCE1) and similar proteins. SMARCE1, also called BRG1-associated factor 57 (BAF57), is a ubiquitously expressed protein involved in transcriptional activation and repression of select genes by chromatin remodeling. It is a component of SWI/SNF chromatin remodeling complexes that carry out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner. SMARCE1 has a single HMG domain that displays non-specific DNA-binding characteristics. It also contains a kinesin-like coiled-coil (KLCC) domain. 73 matched cddid_all.tbl CDD cd21984 cd21984 438800 HMG-box_PB1 high mobility group (HMG)-box found in protein polybromo-1 (PB1) and similar proteins. PB1, also called BRG1-associated factor 180 (BAF180), or polybromo-1D, is a subunit of the PBAF (polybromo/Brg1-associated factor) chromatin-remodeling complex required for kinetochore localization during mitosis and the transcription of estrogen-responsive genes. It is involved in transcriptional activation and repression of select genes by chromatin remodeling. It acts as a negative regulator of cell proliferation. 60 matched cddid_all.tbl CDD cd21985 cd21985 438801 HMG-box_PMS1 high mobility group (HMG)-box found in PMS1 protein homolog 1 (PMS1) and similar proteins. PMS1, also called DNA mismatch repair protein PMS1, is probably involved in the repair of mismatches in DNA. 73 matched cddid_all.tbl CDD cd21986 cd21986 438802 HMG-box_TFAM_rpt1 first high mobility group (HMG)-box found in mitochondrial transcription factor A (TFA) and similar proteins. TFA, also called TFAM, mitochondrial transcription factor 1 (TF1), transcription factor 6 (TCF-6), or transcription factor 6-like 2, binds to the mitochondrial light strand promoter and functions in mitochondrial transcription regulation. It is a component of the mitochondrial transcription initiation complex, composed of at least TFB2M, TFAM and POLRMT that is required for basal transcription of mitochondrial DNA. TFA is required for accurate and efficient promoter recognition by the mitochondrial RNA polymerase. It can unwind DNA. It bends the mitochondrial light strand promoter DNA into a U-turn shape via its HMG boxes. TFA is required for maintenance of normal levels of mitochondrial DNA and may play a role in organizing and compacting mitochondrial DNA. TFA contains two HMG-box domains. This model corresponds to the first one. 65 matched cddid_all.tbl CDD cd21987 cd21987 438803 HMG-box_TFAM_rpt2 second high mobility group (HMG)-box found in mitochondrial transcription factor A (TFA) and similar proteins. TFA, also called TFAM, mitochondrial transcription factor 1 (TF1), transcription factor 6 (TCF-6), or transcription factor 6-like 2, binds to the mitochondrial light strand promoter and functions in mitochondrial transcription regulation. It is a component of the mitochondrial transcription initiation complex, composed of at least TFB2M, TFAM and POLRMT that is required for basal transcription of mitochondrial DNA. TFA is required for accurate and efficient promoter recognition by the mitochondrial RNA polymerase. It can unwind DNA. It bends the mitochondrial light strand promoter DNA into a U-turn shape via its HMG boxes. TFA is required for maintenance of normal levels of mitochondrial DNA and may play a role in organizing and compacting mitochondrial DNA. TFA contains two HMG-box domains. This model corresponds to the second one. 100 matched cddid_all.tbl CDD cd21988 cd21988 438804 HMG-box_HBP1 high mobility group (HMG)-box found in HMG box-containing protein 1 (HBP1) and similar proteins. HBP1, also called HMG box transcription factor 1, or high mobility group box transcription factor 1, is a transcriptional repressor that binds to the promoter region of target genes. It plays a role in the regulation of the cell cycle and the Wnt pathway. HBP1 binds preferentially to the sequence 5'-TTCATTCATTCA-3'. 69 matched cddid_all.tbl CDD cd21989 cd21989 438805 HMG-box_HBP2 high mobility group (HMG)-box found in HMG box-containing protein 2 (HBP2) and similar proteins. HBP2, also called HMG box transcription factor BBX, or Bobby sox homolog, is a transcription factor that is necessary for cell cycle progression from the G1 to S phase. 69 matched cddid_all.tbl CDD cd21990 cd21990 438806 HMG-box_CIC-like high mobility group (HMG)-box found in protein capicua (CIC) and similar proteins. CIC is a transcriptional repressor which plays a role in the development of the central nervous system (CNS). In concert with ATXN1 and ATXN1L, CIC is involved in brain development. 78 matched cddid_all.tbl CDD cd21991 cd21991 438807 HMG-box_NSD2 high mobility group (HMG)-box found in nuclear SET domain-containing protein 2 (NSD2) and similar proteins. NSD2, also called multiple myeloma SET domain-containing protein (MMSET), protein trithorax-5 (TRX5), or wolf-Hirschhorn syndrome candidate 1 protein (WHSC1), acts as a histone-lysine N-methyltransferase with histone H3 'Lys-36' (H3K36me) methyltransferase activity. NSD2 has been shown to mediate di- and trimethylation of H3K36 and dimethylation of H4K20 in different systems and has been characterized as a transcriptional repressor interacting with histone deacetylase HDAC1 and histone demethylase LSD1. NSD2 mediates constitutive NF-kappaB signaling for cancer cell proliferation, survival and tumor growth. It is highly overexpressed in several types of human cancers, including small-cell lung cancers, neuroblastoma, carcinomas of stomach and colon, and bladder cancers, and its overexpression tends to be associated with tumor aggressiveness. 62 matched cddid_all.tbl CDD cd21992 cd21992 438808 HMG-box_MAEL high mobility group (HMG)-box found in protein maelstrom (MAEL) and similar proteins. MAEL is an RNA-binding protein that has evolved from an ancient nuclease active in protists. It plays a central role during spermatogenesis by repressing transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins and governs the methylation and subsequent repression of transposons. 61 matched cddid_all.tbl CDD cd21993 cd21993 438809 HMG-box_WDHD1 high mobility group (HMG)-box found in WD repeat and HMG-box DNA-binding protein 1 (WDHD1) and similar proteins. WDHD1, also called acidic nucleoplasmic DNA-binding protein 1 (And-1), acts as a replication initiation factor that brings together the MCM2-7 helicase and the DNA polymerase alpha/primase complex in order to initiate DNA replication. 62 matched cddid_all.tbl CDD cd21994 cd21994 438810 HMG-box_SSRP1-like high mobility group (HMG)-box found in structure-specific recognition protein 1 (SSRP1) and similar proteins. SSRP1, also called FACT complex subunit SSRP1, chromatin-specific transcription elongation factor 80 kDa subunit, facilitates chromatin transcription complex 80 kDa subunit (FACT 80 kDa subunit or FACTp80), facilitates chromatin transcription complex subunit SSRP1, recombination signal sequence recognition protein 1, or T160, is a factor that facilitates transcript elongation through nucleosomes. It is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair. 67 matched cddid_all.tbl CDD cd21995 cd21995 438811 HMG-box_TOX-like high mobility group (HMG)-box found in the TOX high mobility group box family. The TOX family includes four members: TOX, TOX2, TOX3 and TOX4. TOX, also called thymus high mobility group box protein TOX, is a transcriptional regulator with a major role in neural stem cell commitment and corticogenesis as well as in lymphoid cell development and lymphoid tissue organogenesis. It binds to GC-rich DNA sequences in the proximity of transcription start sites and may alter chromatin structure, modifying access of transcription factors to DNA. TOX2, also called granulosa cell HMG box protein 1 (GCX-1), is a putative transcriptional activator involved in the hypothalamic-pituitary-gonadal system. TOX3, also called CAG trinucleotide repeat-containing gene F9 protein (CAGF9), or trinucleotide repeat-containing gene 9 protein (TNRC9), is a transcriptional coactivator of the p300/CBP-mediated transcription complex. It activates transactivation through cAMP response element (CRE) sites. It protects against cell death by inducing anti-apoptotic and repressing pro-apoptotic transcripts. TOX4, also called epidermal Langerhans cell protein LCP1, is a component of the PTW/PP1 phosphatase complex, which plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase. All family members contain one HMG-box domain. 70 matched cddid_all.tbl CDD cd21996 cd21996 438812 HMG-box_TCF7-like high mobility group (HMG)-box found in the transcription factor 7 (TCF-7)-like family. The TCF7-like family includes TCF-7, TCF7-like 1 (TF7L1), lymphoid enhancer-binding factor 1 (LEF-1), and similar proteins. TCF-7, also called T-cell-specific transcription factor 1, or T-cell factor 1 (TCF-1), is a T lymphocyte-specific transcriptional activator involved in T-cell lymphocyte differentiation. It is necessary for the survival of CD4(+) CD8(+) immature thymocytes. It binds to the T-lymphocyte-specific enhancer element (5'-WWCAAAG-3') found in the promoter of the CD3E gene. TF7L1, also called HMG box transcription factor 3 (TCF-3), participates in the Wnt signaling pathway. It binds to DNA and acts as a repressor in the absence of CTNNB1, and as an activator in its presence. TF7L2, also called HMG box transcription factor 4, or T-cell-specific transcription factor 4, or T-cell factor 4, or TCF-4, participates in the Wnt signaling pathway and modulates MYC expression by binding to its promoter in a sequence-specific manner. It acts as a repressor in the absence of CTNNB1, and it activates transcription from promoters with several copies of the TCF motif 5'-CCTTTGATC-3' in the presence of CTNNB1. LEF-1, also called T cell-specific transcription factor 1-alpha (TCF1-alpha), is a transcription factor that binds DNA in a sequence-specific manner. It may participate in the Wnt signaling pathway. All family members contain one HMG-box domain. 85 matched cddid_all.tbl CDD cd21997 cd21997 438813 HMG_KMT2C-like high mobility group (HMG)-box found in histone-lysine N-methyltransferases KMT2C, KMT2D and similar proteins. This subfamily includes KMT2C and KMT2D. KMT2C, also called myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, and farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. KMT2D, also called ALL1-related protein (ALR), is encoded by the gene that was named MLL4, a fourth human homolog of Drosophila trithorax, located on chromosome 12. It enzymatically generates trimethylated histone H3 lysine 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. KMT2D is also a part of ASCOM. All subfamily members contain one HMG-box domain. 67 matched cddid_all.tbl CDD cd21998 cd21998 438814 HMG-box_UBF1_rpt1-like first high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar proteins. UBF1, also called UBTF, nucleolar transcription factor 1, or auto-antigen NOR-90, is a nucleolar transcription factor that recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element. UBF1 contains six HMG-box domains. This model corresponds to the first one. This model also includes the first HMG-box domain of upstream-binding factor 1-like protein 1 (UBTFL1), which contains two HMG-box domains. 77 matched cddid_all.tbl CDD cd21999 cd21999 438815 HMG-box_UBF1_rpt2 second high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar proteins. UBF1, also called UBTF, nucleolar transcription factor 1, or auto-antigen NOR-90, is a nucleolar transcription factor that recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element. UBF1 contains six HMG-box domains. This model corresponds to the second one. 73 matched cddid_all.tbl CDD cd22000 cd22000 438816 HMG-box_UBF1_rpt3 third high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar proteins. UBF1, also called UBTF, nucleolar transcription factor 1, or auto-antigen NOR-90, is a nucleolar transcription factor that recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element. UBF1 contains six HMG-box domains. This model corresponds to the third one. 83 matched cddid_all.tbl CDD cd22001 cd22001 438817 HMG-box_UBF1_rpt4 fourth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar proteins. UBF1, also called UBTF, nucleolar transcription factor 1, or auto-antigen NOR-90, is a nucleolar transcription factor that recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element. UBF1 contains six HMG-box domains. This model corresponds to the fourth one. 66 matched cddid_all.tbl CDD cd22002 cd22002 438818 HMG-box_UBF1_rpt5 fifth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar proteins. UBF1, also called UBTF, nucleolar transcription factor 1, or auto-antigen NOR-90, is a nucleolar transcription factor that recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element. UBF1 contains six HMG-box domains. This model corresponds to the fifth one. 72 matched cddid_all.tbl CDD cd22003 cd22003 438819 HMG-box_UBF1_rpt6-like sixth high mobility group (HMG)-box found in upstream-binding factor 1 (UBF1) and similar proteins. UBF1, also called UBTF, nucleolar transcription factor 1, or auto-antigen NOR-90, is a nucleolar transcription factor that recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element. UBF1 contains six HMG-box domains. This model corresponds to the sixth one. This model also includes the second HMG-box domain of upstream-binding factor 1-like protein 1 (UBTFL1), which contains two HMG-box domains. 86 matched cddid_all.tbl CDD cd22004 cd22004 438820 HMG-box_SOX high mobility group (HMG)-box found in sex-determining region Y (SRY)-box (SOX) family transcription factors. The SOX gene family of transcription factors are characterized by the evolutionarily conserved SRY-type HMG box, which is a DNA binding domain that binds the minor groove of DNA on a common consensus site, (A/T)(A/T)CAA(A/T)G but with different levels of efficiency. Members include SRY and its homologs identified in mammals that can be subdivided into 8 groups (A, B1, B2, C, D, E, F, G, H). They are involved in embryonic development, regulating processes such as cell differentiation, maintenance of stemness, sex determination, and development of the central nervous, haematopoietic and other organ systems. The SOX gene family has a crucial role in carcinogenesis and cancer progression. 75 matched cddid_all.tbl CDD cd22005 cd22005 438821 HMG-box_AtHMGB1-like high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 1 (HMGB1) and similar proteins. This subfamily contains a group of Arabidopsis thaliana HMGB family proteins, including HMGB1, 2, 3, 4, 5, 7, 12 and 14. They bind preferentially to double-stranded DNA. HMGB1 modulates general plant growth and stress tolerance and confers sensitivity to salt and genotoxic (methyl methanesulfonate, MMS) stresses. HMGB2 and HMGB5 confer sensitivity to salt and drought stresses. HMGB7 is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. Members of this subfamily contain only one HMG-box domain. 60 matched cddid_all.tbl CDD cd22006 cd22006 438822 HMG-box_AtHMGB6-like_rpt1 first high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins. HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the first one. 68 matched cddid_all.tbl CDD cd22007 cd22007 438823 HMG-box_AtHMGB6-like_rpt2 second high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins. HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the second one. 68 matched cddid_all.tbl CDD cd22008 cd22008 438824 HMG-box_AtHMGB6-like_rpt3 third high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 6 (HMGB6) and similar proteins. HMGB6, also called nucleosome/chromatin assembly factor group D 06 (or D 6), WRKY transcription factor 53 (WRKY53), or WRKY DNA-binding protein 53, is a master regulator of age-induced leaf senescence. It acts in a complex transcription factor signaling network regulating senescence specific gene expression; hydrogen peroxide might be involved in signal transduction. The subfamily also includes Arabidopsis thaliana HMGB13 (also known as nucleosome/chromatin assembly factor group D 13). Both HMGB6 and HMGB13 contain three HMG-box domains. This model corresponds to the third one. 78 matched cddid_all.tbl CDD cd22009 cd22009 438825 HMG-box_AtHMGB9-like high mobility group (HMG)-box found in Arabidopsis thaliana high mobility group B protein 9 (HMGB9) and similar proteins. This subfamily contains a group of Arabidopsis thaliana HMGB family proteins, including HMGB9, 10, 11, and 15. They are DNA-binding proteins containing both HMG-box and AT-rich interaction domains. They bind preferentially to DNA with A/T-rich content. HMGB9 is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. Members of this subfamily have only one HMG-box domain. 67 matched cddid_all.tbl CDD cd22010 cd22010 438826 HMG-box_ABF2-like_rpt1 first high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ARS-binding factor 2 (ABF2) and similar proteins. ABF2 is a close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. It specifically binds to the autonomously replicating sequence 1 (ARS1). It might play a positive role in gene expression and replication. ABF2 contains two HMG-box domains. This model corresponds to the first one. 68 matched cddid_all.tbl CDD cd22011 cd22011 438827 HMG-box_IXR1-like_rpt1 first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link recognition protein (Ixr1) and similar proteins. Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Ixr1 contains two HMG-box domains. This model corresponds to the first one. 75 matched cddid_all.tbl CDD cd22012 cd22012 438828 HMG-box_ABF2_IXR1-like_rpt2 second high mobility group (HMG)-box found in Saccharomyces cerevisiae mitochondrial ARS-binding factor 2 (ABF2), intrastrand cross-link recognition protein (Ixr1) and similar proteins. ABF2 is a close relative of the nuclear, chromosomal high-mobility group protein HMG1 in yeast mitochondria. It specifically binds to the autonomously replicating sequence 1 (ARS1). It might play a positive role in gene expression and replication. Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Both ABF2 and Ixr1 contain two HMG-box domains. This model corresponds to the second one. 64 matched cddid_all.tbl CDD cd22013 cd22013 438829 HMG-box_AtSSRP1 high mobility group (HMG)-box found in Arabidopsis thaliana FACT complex subunit SSRP1 and similar proteins. SSRP1, also called facilitates chromatin transcription complex subunit SSRP1, high mobility group B protein 8, nucleosome/chromatin assembly factor group D 08 (or D 8), protein NUCLEAR FUSION DEFECTIVE 8, or recombination signal sequence recognition protein 1, is a component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication, and DNA repair. SSRP1 may bind specifically to double-stranded DNA. It is required for karyogamy during female gametophyte development, when the two polar nuclei fuse to form the diploid central cell nucleus. SSRP1 contains only one HMG-box domain. 80 matched cddid_all.tbl CDD cd22014 cd22014 438830 HMG-box_CMB1-like high mobility group (HMG)-box found in Schizosaccharomyces pombe mismatch-binding protein cmb1 and similar proteins. Cmb1 binds to cytosines in base mismatches and opposite chemically altered guanines. It contains only one HMG-box domain. 62 matched cddid_all.tbl CDD cd22015 cd22015 438831 HMG-box_HMO1-like high mobility group (HMG)-box found in Saccharomyces cerevisiae high mobility group protein 1 (HMO1) and similar proteins. HMO1, also called high spontaneous mutagenesis protein 2 (HSM2), is a DNA-binding protein that is probably part of the rDNA transcription apparatus. It acts synergetically with the RPA49 subunit of RNA polymerase I during rDNA transcription. It may participate in mutagenesis control. 68 matched cddid_all.tbl CDD cd22016 cd22016 438832 HMG-box_NHP10-like high mobility group (HMG)-box found in Saccharomyces cerevisiae non-histone protein 10 (NHP10) and similar proteins. NHP10, also called high mobility group protein 2, is probably involved in transcription regulation via its interaction with the INO80 complex, a chromatin remodeling complex. 79 matched cddid_all.tbl CDD cd22017 cd22017 438833 HMG-box_HMG20A high mobility group (HMG)-box found in high mobility group protein 20A (HMG20A) and similar proteins. HMG20A, also called HMG box-containing protein 20A, HMG domain-containing protein 1 (HMGXB1), HMG domain-containing protein HMGX1, HMGXB1, or iBRAF, is a chromatin-associated protein involved in neuronal differentiation and maturation. It is required for SNAI1-mediated epithelial to mesenchymal transition. HMG20A acts as an inhibitor of HMG20B. 104 matched cddid_all.tbl CDD cd22018 cd22018 438834 HMG-box_HMG20B high mobility group (HMG)-box found in high mobility group protein 20B (HMG20B) and similar proteins. HMG20B, also called SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-related, SMARCE1-related protein (SMARCE1R), BRCA2-associated factor 35 (BRAF35), HMG box-containing protein 20B, HMG domain-containing protein 2 (HMGXB2), HMG domain-containing protein HMGX2, Sox-like transcriptional factor, or structural DNA-binding protein BRAF35, is a DNA binding factor that acts as a repressor of erythroid differentiation. It is required for correct progression through the G2 phase of the cell cycle and entry into mitosis. It is also required for RCOR1/CoREST mediated repression of neuronal specific gene promoters. HMG20B is a core subunit of the Lys-specific demethylase 1/REST co-repressor 1 (LSD1-CoREST) histone demethylase complex. 85 matched cddid_all.tbl CDD cd22026 cd22026 438835 HMG-box_KMT2C high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2C (KMT2C) and similar proteins. KMT2C, also called myeloid/lymphoid or mixed-lineage leukemia protein 3 (MLL3) or homologous to ALR protein, is a histone H3 lysine 4 (H3K4) lysine methyltransferase that functions as a circadian factor contributing to genome-scale circadian transcription. It is a component of a large complex that acts as a coactivator of multiple transcription factors, including the bile acid (BA)-activated nuclear receptor, farnesoid X receptor (FXR), a critical player in BA homeostasis. The MLL3 complex is essential for p53 transactivation of small heterodimer partner (SHP). KMT2C is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and its paralog MLL4. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. 81 matched cddid_all.tbl CDD cd22027 cd22027 438836 HMG-box_KMT2D high mobility group (HMG)-box found in histone-lysine N-methyltransferase 2D (KMT2D) and similar proteins. KMT2D, also called ALL1-related protein (ALR), is encoded by the gene that was named myeloid/lymphoid or mixed-lineage leukemia 4 (MLL4), a fourth human homolog of Drosophila trithorax, located on chromosome 12. KMT2D enzymatically generates trimethylated histone H3 Lys 4 (H3K4me3). It plays an essential role in differentiating the human pluripotent embryonal carcinoma cell line NTERA-2 clone D1 (NT2/D1) stem cells by activating differentiation-specific genes, such as HOXA1-3 and NESTIN. It is also a part of activating signal cointegrator-2 (ASC-2)-containing complex (ASCOM) that contains the transcriptional coactivator nuclear receptor coactivator 6 (NCOA6), KMT2C and KMT2D. The ASCOM complex is critical for nuclear receptor (NR) activation of bile acid transporter genes and is down regulated in cholestasis. 84 matched cddid_all.tbl CDD cd22028 cd22028 438837 HMG-box_SoxA_SoxB_SoxG high mobility group (HMG)-box found in group A, group B and group G of SRY-related high-mobility group (HMG) box (Sox) transcription factors. This subfamily includes SoxA, SoxB, and SoxG proteins. SRY is the only member of group A SRY-related high-mobility group (HMG) box (Sox) transcription factors. SRY, also called testis-determining factor, is a transcriptional regulator that controls a genetic switch in male development. It promotes DNA bending and is also involved in pre-mRNA splicing. The SRY HMG box recognizes DNA by partial intercalation in the minor groove. It binds to the DNA consensus sequence 5'-[AT]AACAA[AT]-3'. SoxB transcription factors play critical roles in the regulation of neurogenesis. They can be divided into two main subgroups, SoxB1 (Sox-1/Sox-2/Sox-3) and SoxB2 (SOX-14/SOX-21). SoxB1 proteins suppress neurogenesis by maintaining neural cells in an undifferentiated state. SoxB2 proteins may have the opposite activity and promote neuronal differentiation. SOX-5 is the only member of group G Sox transcription factors. It is also called SOX-12, SOX-20, SOX-26, or SOX-27. SOX-5 is a crucial transcription factor involved in the regulation of embryonic development and in cell fate determination. It binds to the 5'-AACAAT-3' sequence. SOX-15 can be a tumor suppressor in multiple cancer types. 76 matched cddid_all.tbl CDD cd22029 cd22029 438838 HMG-box_SoxC high mobility group (HMG)-box found in group C SRY-related high-mobility group (HMG) box (Sox) transcription factors. SoxC transcription factors includes three members: SOX4, SOX11 and SOX12. They play key roles, often in redundancy, in multiple developmental pathways, including neurogenesis and skeletogenesis. SOX-4 is a transcriptional activator that promotes neuronal differentiation both in the adult and embryonic neural progenitors. It binds with high affinity to the T-cell enhancer motif 5'-AACAAAG-3' motif. SOX-4 is abnormally expressed in various cancers. SOX-11 is a neural transcriptional factor involved in precursor survival, neuronal fate determination, migration and morphogenesis. SOX-12, also called SOX-22, is a transcription factor essential for embryonic development and cell fate determination. It binds to the sequence 5'-AACAAT-3'. 76 matched cddid_all.tbl CDD cd22030 cd22030 438839 HMG-box_SoxD high mobility group (HMG)-box found in group D SRY-related high-mobility group (HMG) box (Sox) transcription factors. SoxD transcription factors includes three members, Sox5, Sox6, and Sox13. They function as important transcriptional regulators of glial development in the central nervous system. SoxD proteins influence multiple stages of oligodendrocyte development and modulate SoxE protein function. This subfamily also contains SoxD transcription factor homolog EGL-13, which specifies distinct O2 and CO2 sensory neuron fates in Caenorhabditis elegans. SOX-5 plays important roles in various cancer types. It binds specifically to the DNA sequence 5'-AACAAT-3'. SOX-6 plays a key role in cell proliferation, differentiation, and cell fate determination, as well as neurogenesis and skeleton formation. It is a tumor suppressor and downregulated in various cancers. SOX-6 binds specifically to the DNA sequence 5'-AACAAT-3'. SOX-13, also called Islet cell antigen 12 (ICA12), or type 1 diabetes auto-antigen ICA12, modulates T cell specification and is an autoimmune antigen. It binds to the sequence 5'-AACAAT-3'. 77 matched cddid_all.tbl CDD cd22031 cd22031 438840 HMG-box_SoxE high mobility group (HMG)-box found in group E SRY-related high-mobility group (HMG) box (Sox) transcription factors. SoxE transcription factors includes three members: Sox8, Sox9, and Sox10. They function as important transcriptional regulators of neural differentiation and nervous system development. They regulate mammalian development directing sex determination, gliogenesis, pancreas specification and neural crest development. SOX-8 is specifically expressed by M cells in the intestinal epithelium. It acts as a transcription factor necessary for the maintenance of spermatogenesis. It may play a role in central nervous system, limb and facial development. SOX-9 is involved in cell differentiation, sex determination, and tumorigenesis. It plays a role in chondrocyte differentiation and skeletal development. SOX-10 plays a central role in the development of melanocytes and glial cells from neural crest precursors. 75 matched cddid_all.tbl CDD cd22032 cd22032 438841 HMG-box_SoxF high mobility group (HMG)-box found in group F SRY-related high-mobility group (HMG) box (Sox) transcription factors. SoxF transcription factors includes three members: Sox7, Sox17, and Sox18. They regulate endothelial cell fate as well as development and differentiation of the developing heart, blood cells, and lymphatic vessels. 76 matched cddid_all.tbl CDD cd22033 cd22033 438842 HMG-box_SoxH_SOX30 high mobility group (HMG)-box found in sex determining region Y (SRY)-box 30 (SOX30) and similar proteins. SOX-30 is a crucial transcription factor that controls the transition from a late meiotic to a post-meiotic gene expression program and subsequent round spermatid development. It specially prevents Wnt-signaling to suppress metastasis. SOX-30 binds to the DNA sequence 5'-ACAAT-3' and shows a preference for guanine residues surrounding this core motif. SOX-30 is the only member of the group H of SRY-related high-mobility group (HMG) box (Sox) transcription factors. 75 matched cddid_all.tbl CDD cd22034 cd22034 438843 HMG-box_SoxA_SRY high mobility group (HMG)-box found in sex-determining region Y protein (SRY) and similar proteins. SRY, also called testis-determining factor, is a transcriptional regulator that controls a genetic switch in male development. It promotes DNA bending and is also involved in pre-mRNA splicing. The SRY HMG box recognizes DNA by partial intercalation in the minor groove. It binds to the DNA consensus sequence 5'-[AT]AACAA[AT]-3'. SRY is the only member of group A SRY-related high-mobility group (HMG) box (Sox) transcription factors. 85 matched cddid_all.tbl CDD cd22035 cd22035 438844 HMG-box_SoxG_SOX15 high mobility group (HMG)-box found in sex determining region Y (SRY)-box 15 (SOX15) and similar proteins. SOX-15, also called SOX-12, SOX-20, SOX-26, or SOX-27, is a crucial transcription factor involved in the regulation of embryonic development and in cell fate determination. It binds to the 5'-AACAAT-3' sequence. SOX-15 can be a tumor suppressor in multiple cancer types. SOX-5 is the only member of group G SRY-related high-mobility group (HMG) box (Sox) transcription factors. 84 matched cddid_all.tbl CDD cd22036 cd22036 438845 HMG-box_SoxC_SOX4 high mobility group (HMG)-box found in sex determining region Y (SRY)-box 4 (SOX4) and similar proteins. SOX-4 is a transcriptional activator that promotes neuronal differentiation both in the adult and embryonic neural progenitors. It binds with high affinity to the T-cell enhancer motif 5'-AACAAAG-3' motif. SOX-4 is abnormally expressed in various cancers. SOX-4 belongs to group C SRY-related high-mobility group (HMG) box (Sox) transcription factors. 79 matched cddid_all.tbl CDD cd22037 cd22037 438846 HMG-box_SoxC_SOX11 high mobility group (HMG)-box found in sex determining region Y (SRY)-box 11 (SOX11) and similar proteins. SOX-11 is a neural transcriptional factor involved in precursor survival, neuronal fate determination, migration and morphogenesis. SOX-11 belongs to group C SRY-related high-mobility group (HMG) box (Sox) transcription factors. 92 matched cddid_all.tbl CDD cd22038 cd22038 438847 HMG-box_SoxC_SOX12 high mobility group (HMG)-box found in sex determining region Y (SRY)-box 12 (SOX12) and similar proteins. SOX-12, also called SOX-22, is a transcription factor essential for embryonic development and cell fate determination. It binds to the sequence 5'-AACAAT-3'. SOX-12 belongs to the group C of SRY-related high-mobility group (HMG) box (Sox) transcription factors. 88 matched cddid_all.tbl CDD cd22042 cd22042 438848 HMG-box_EGL13-like high mobility group (HMG)-box found in Caenorhabditis elegans protein egg laying defective 13 (EGL-13) and similar proteins. EGL-13 may act as a transcription factor that is required for uterine cell fate decisions in Caenorhabditis elegans. It controls genes required for the specification and differentiation of O(2) and CO(2)-sensing neurons and for maintaining URX sensory neuronal cell fate. 78 matched cddid_all.tbl CDD cd22046 cd22046 438849 HMG-box_SoxF_SOX7 high mobility group (HMG)-box found in sex determining region Y (SRY)-box 7 (SOX7) and similar proteins. SOX-7 is an endothelial-associated transcription factor that acts as a tumor suppressor in a number of cancer types. It binds the DNA sequence 5'-AACAAT-3'. SOX-7 belongs to the group F of SRY-related high-mobility group (HMG) box (Sox) transcription factors. 88 matched cddid_all.tbl CDD cd22047 cd22047 438850 HMG-box_SoxF_SOX17 high mobility group (HMG)-box found in sex determining region Y (SRY)-box 17 (SOX17) and similar proteins. SOX-17 is a developmental transcription regulator involved in endoderm formation, angiogenesis, and carcinogenesis. It acts as a tumor suppressor and modulates WNT signaling. SOX-17 binds target promoter DNA and bends the DNA. It binds to the sequences 5'-AACAAT-'3 or 5'-AACAAAG-3'. SOX-17 belongs to the group F of SRY-related high-mobility group (HMG) box (Sox) transcription factors. 81 matched cddid_all.tbl CDD cd22048 cd22048 438851 HMG-box_SoxF_SOX18 high mobility group (HMG)-box found in sex determining region Y (SRY)-box 18 (SOX18) and similar proteins. SOX-18 is a transcription factor involved in the development of cardiovascular and lymphatic vessels during embryonic development. It binds to the consensus sequence 5'-AACAAAG-3' and is able to trans-activate transcription via this site. SOX-18 belongs to the group F of SRY-related high-mobility group (HMG) box (Sox) transcription factors. 80 matched cddid_all.tbl CDD cd22054 cd22054 409233 NAC_NACA nascent polypeptide-associated complex (NAC), alpha subunit. The nascent polypeptide-associated complex (NAC) is a complex, conserved from archaea to human, that plays an important role in co translational targeting of nascent polypeptides to the endoplasmic reticulum (ER). In eukaryotes, under physiological conditions, the complex is a stable heterodimer of the NAC alpha subunit and the NAC beta subunit, also known as basal transcription factor 3b (BTF3b). An imbalance of the relative concentrations has been observed in diseases, like Alzheimer's, AIDS, and ulcerative colitis. NAC alpha consists of a NAC domain, also present in BTF3, and a unique C-terminal ubiquitin-associated (UBA) domain. 48 matched cddid_all.tbl CDD cd22055 cd22055 409234 NAC_BTF3 basal transcription factor BTF3. Basal transcription factor 3 (BTF3) plays an important role in the transcriptional regulation linked to growth and development in eukaryotes. In mammals, the BTF3 gene encodes two alternative splicing isoforms, BTF3a and BTF3b. The full length BTF3a protein excites transcription. The shortened BTF3b, which lacks the first 44 amino-terminal extension, is a component of the nascent polypeptide-associated complex (NAC), involved in regulating protein localization during translation. BTF3 is involved in oncogenesis; overexpression of BTF3 has been shown to be associated with a variety of malignancies such as cancer of the colon, pancreas, stomach, prostate and breast. It is upregulated in hypopharyngeal squamous cell carcinoma (HSCC) tumors correlating with lymph node metastasis and tumor promotion, thus indicating that BTF3 is a potential therapeutic target and prognostic biomarker for HSCC. BTF3 has also been implicated in the pathogenesis of osteosarcoma (OS), a malignant cancer that affects rapidly proliferating bones, and has a poor prognosis. 117 matched cddid_all.tbl CDD cd22056 cd22056 409231 KLF1_2_4_N-like N-terminal domain of Kruppel-like factors with similarity to the N-terminal domains of Kruppel-like factor (KLF)1, KLF2, and KLF4. Kruppel/Krueppel-like transcription factors (KLFs) belong to a family of proteins called the Specificity Protein (SP)/KLF family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. Members of the KLF family can act as activators or repressors of transcription depending on cell and promoter context. KLFs regulate various cellular functions, such as proliferation, differentiation, and apoptosis, as well as the development and homeostasis of several types of tissue. In addition to the C-terminal DNA-binding domain, each KLF also has a unique N-terminal activation/repression domain that confers specifity and allows it to bind specifically to a certain partner, leading to distinct activities in vivo. This model represents the N-terminal domains of an unknown subfamily of KLFs, predominantly found in fish, related to the N-terminal domains of KLF1, KLF2, and KLF4. 339 matched cddid_all.tbl CDD cd22057 cd22057 409200 WH2_WAVE Wiskott Aldrich syndrome homology region 2 (WH2 motif) found in Wiskott-Aldrich Syndrome Protein Family members 1 (WASP1 or WAVE1), 2 (WASP2 or WAVE2) and 3 (WASP3 or WAVE3). This family contains the Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) found in three Wiskott-Aldrich syndrome protein (WASP) family verprolin homologous protein (SCAR/WAVE) isoforms: WAVE1, WAVE2, and WAVE3. Members of this family activate actin related protein (Arp)2/3-dependent actin nucleation and branching in response to signals mediated by Rho-family GTPases. The domain structure of these proteins varies, reflecting different modes of regulation; however, they all share a common C-terminal WH2 region which constitutes the smallest fragment necessary for Arp2/3 activation. These proteins interact with actin via their WH2 domain. 28 matched cddid_all.tbl CDD cd22058 cd22058 409201 WH2_N_WASP first and second of two tandem Wiskott Aldrich syndrome homology region 2 (WH2 motif) repeats found in Neural Wiskott-Aldrich syndrome protein (N-WASP). This family contains both tandem Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) repeats found in the Neural Wiskott-Aldrich syndrome protein (N-WASP or Neural WASP); N-WASP contains two tandem WH2 domains. N-WASP integrates various extracellular signals to control actin dynamics and cytoskeletal reorganization through activation of the actin related protein (Arp)2/3 complex. It interacts with actin via the WH2 domain. N-WASP plays an important role in the deactivation or attenuation of B cell receptor signaling. N-WASP regulates filopodia formation and membrane invagination, as compared to WAVE proteins that serve as Rac1 effectors in the formation of lamellipodia. Filopodia are thin, actin-rich surface projections that are extended and maintained by N-WASP together with CDC42. N-WASP also plays a role in the nucleus by regulating gene transcription, probably by promoting nuclear actin polymerization. It binds to HSF1/HSTF1 and forms a complex on heat shock promoter elements (HSE) that negatively regulates HSP90 expression. It also plays a role in dendrite spine morphogenesis. Unphosphorylated N-WASP is preferentially localized in the nucleus and in the cytoplasm when phosphorylated; it is exported from the nucleus by a nuclear export signal (NES)-dependent mechanism to the cytoplasm. 23 matched cddid_all.tbl CDD cd22059 cd22059 409202 WH2_BetaT Wiskott Aldrich syndrome homology region 2 (WH2 motif) found in beta-Thymosin, and similar proteins. This family contains beta-thymosin (betaT; also called thymosin beta or Tbeta) domain which is similar to the Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2). Proteins in the beta-thymosin family are small peptides that act as actin monomer (G-actin) sequestering factors. They bind to G-actin into a 1:1 complex, rendering G-actin resistant to polymerization into filaments (F-actin). Thymosin beta 4 (Tbeta4 or TB4) and beta10 (Tbeta10) are minor variants of betaT that bind skeletal muscle actin and inhibit actin polymerization. Thymosin beta4 can also bind to polymerized F-actin. The roles of beta-thymosins also appear to extend beyond G-actin sequestration. Thymosin beta4 has also been linked to a number of additional biological events, including angiogenesis, wound healing, inflammation, and intracellular signaling through kinase activation. Research on thymosin beta10 in breast cancer cells has suggested a relationship with actin cytoskeletal remodeling and cell motility. In addition, thymosins beta4, beta10, and beta15 are highly expressed in several tumor cells, and these have been associated with a higher metastatic potential, possibly due to their function in cell proliferation. 34 matched cddid_all.tbl CDD cd22060 cd22060 409203 WH2_MTSS1 Wiskott Aldrich syndrome homology region 2 (WH2 motif) found in Metastasis suppressor protein 1 (MTSS-1). This family contains the first tandem Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) found in metastasis suppressor protein 1 (MTSS1, also called also known as missing in metastasis or MIM). MTSS1 may be related to cancer progression or tumor metastasis in a variety of organ sites, most likely through an interaction with the actin cytoskeleton. It interacts with actin via its WH2 domain. MTSS1 is a novel potential metastasis suppressor gene in several types of human cancers; its expression is down-regulated in ovarian cancer, colorectal cancer, oesophageal cancer, prostate cancer and breast cancer, whereas it has also been observed to be up-regulated in hepato-cellular carcinoma and breast cancer. 31 matched cddid_all.tbl CDD cd22061 cd22061 409204 WH2_INF2 Wiskott Aldrich syndrome homology region 2 (WH2 motif) found in Inverted formin-2 (INF2). This family contains the first tandem Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) found in inverted formin-2 (INF2, also known as HBEBP2-binding protein C). INF2 is a formin protein with the unique ability to accelerate both actin polymerization and depolymerization, the latter requiring severing of the filament. It interacts with actin at its formin homology 2 (FH2) domain, while the WH2 domain acts as the diaphanous autoregulatory domain (DAD) and binds to actin monomers. INF2 plays a role in mitochondrial fission and dorsal stress fiber formation. It accelerates actin nucleation and elongation by interacting with the fast-growing ends (barbed ends) of actin filaments, but also accelerates disassembly of actin through encircling and severing filaments. Mutations in INF2 lead to the kidney disease focal segmental glomerulosclerosis (FSGS) and the neurological disorder Charcot-Marie Tooth Disease (CMTD). 30 matched cddid_all.tbl CDD cd22062 cd22062 409205 WH2_DdVASP-like Wiskott Aldrich syndrome homology region 2 (WH2 motif) found in Dictyostelium discoideum Vasodilator-stimulated phosphoprotein (VASP) and similar proteins. This family contains the Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) found in Dictyostelium discoideum vasodilator-stimulated phosphoprotein (VASP) and similar proteins. VASP belongs to the Ena/VASP protein family whose members act as actin polymerases that drive the processive elongation of filament barbed ends in membrane protrusions or at the surface of bacterial pathogens. These actin-associated proteins are involved in a range of processes dependent on cytoskeleton remodeling and cell polarity such as lamellipodial and filopodial dynamics in migrating cells. VASP plays a crucial role in filopodia formation, cell-substratum adhesion, and proper chemotaxis. It nucleates and bundles actin filaments via oligomers that use their WH2 domains to effect both the tethering of actin filaments and their processive elongation in sites of active actin assembly. 31 matched cddid_all.tbl CDD cd22063 cd22063 409206 WH2_Actobindin Wiskott Aldrich syndrome homology region 2 (WH2 motif) found in Actobindin and similar proteins. This family contains the Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) found in actobindin, an actin-binding protein from amoeba. Actobindin is able to bind two actin monomers at high concentrations of G-actin. It inhibits actin polymerization by sequestering G-actin and stabilizing actin dimers, thus making it a more potent inhibitor of the early phase of actin polymerization than of F-actin elongation. 29 matched cddid_all.tbl CDD cd22064 cd22064 409207 WH2_WAS_WASL Wiskott Aldrich syndrome homology region 2 (WH2 motif) in WAS/WASL-interacting protein (WIP). This family contains the Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) found in WAS/WASL-interacting protein family (WIPF, also known as WASP-interacting protein or WIP). Human WIP protein is proline rich and has high sequence similarity to yeast protein verprolin (included in this model). WIP forms complexes with WASP/N-WASP and modulates their function in vivo. It is involved in the regulation of endocytosis and participates in several cellular processes, some of which are relevant in cancer and may be dependent on different oncogenic stimuli. WIP interacts directly with mammalian actin-binding protein-1 (mABP1) via the SH3 domain during platelet-derived growth factor (PDGF)-mediated dorsal ruffle formation. WIP family includes members 1 (WAS/WASL-interacting protein family member 1) or WIPF1), 2 (WIPF2) and 3 (WIPF3). Aberrant expression of WIPF1 contributes to the invasion and metastasis of several malignancies such breast cancer, glioma and colorectal cancer; it has been identified as an oncoprotein in human pancreatic ductal adenocarcinoma (PDAC) and is associated with poor survival. WIPF2 may be an important regulator of the actin cytoskeleton. WIPF2 binds to N-WASP, regulating actin dynamics close to the plasma membrane; N-WASP in turn controls the second phase insulin secretion through the regulation of the Arp2/3 complex. WIPF3, along with LIPA (lysosomal acid lipase A), are expressed in microphages and are involved in pathological abdominal aortic aneurysm (AAA), a serious condition of the aorta. In yeast, verprolin is involved in cytoskeletal organization and cellular growth. It may exert its effects on the cytoskeleton directly, or indirectly via proline-binding proteins, such as profilin, or via proteins possessing SH3 domains. 29 matched cddid_all.tbl CDD cd22065 cd22065 409208 WH2_Spire_1-2_r1 first tandem Wiskott-Aldrich Syndrome Homology (WASP) region 2 (WH2 motif) repeat of protein Spire homologs 1 and 2. This family contains the first tandem Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) domain in human Spire family proteins Spire-1 (also called Spir1) and Spire-2 (Spir2) and related proteins. Spire is an actin nucleator essential for establishing an actin mesh during oogenesis. It was first identified as a Drosophila maternal effect gene essential to establishment of both the anterior/posterior and dorsal/ventral body axes in developing oocytes and embryos. It has been found to sever filaments and sequester monomers in addition to nucleating new filaments; it remains associated with the slow-growing pointed end of the new filament. Spire is involved in intracellular vesicle transport along actin fibers, providing a novel link between actin cytoskeleton dynamics and intracellular transport. It is required for asymmetric spindle positioning and asymmetric cell division during oocyte meiosis. Spire contains four tandem WH2 domains. The mammalian genome encodes two Spire proteins, namely Spire-1 and Spire-2. This model contains WH2 domain 1 of human Spire-1 and Spire-2 . Major expression of both spire genes have been detected during embryogenesis in the developing nervous system). In addition, spire1 expression is found in the fetal liver, while spire2 expression is seen in early stages of intestinal development. In adult tissues, the spire2 gene shows a rather broad expression pattern, which includes the epithelial cells of the digestive tract, testical spermatocytes, and neuronal cells of the nervous system. In contrast, spire1 is mainly expressed in neuronal cells of the nervous system. Minor expression levels were detected in testis and spleen. Spire also acts in the nucleus where, together with Spire-1 and Spire-2, it promotes assembly of nuclear actin filaments in response to DNA damage in order to facilitate movement of chromatin and repair factors after DNA damage. High levels of spire1 expression are restricted to the nervous system, oocytes, and testis. Since function of Spire-1 and Spire-2 in oocyte maturation is redundant, spire1 mutant mice are fertile, overall brain anatomy is not altered, and visual and motor functions remain normal; however, detailed behavioral studies of the spire1 mutant mice unveiled a very specific and highly significant phenotype in terms of fear learning in male mice. 32 matched cddid_all.tbl CDD cd22066 cd22066 409209 WH2_Spire second, third, and fourth, tandem Wiskott-Aldrich Syndrome Homology (WASP) region 2 (WH2 motif) repeats of protein Spire. This family contains the Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) repeats 2-4 in human Spire (also called Spir), Drosophila Spire, and related proteins. Spire is an actin nucleator essential for establishing an actin mesh during oogenesis. This WH2-containing actin nucleator was first identified as a Drosophila maternal effect gene essential to establishment of both the anterior/posterior and dorsal/ventral body axes in developing oocytes and embryos. It has been found to sever filaments and sequester monomers in addition to nucleating new filaments; it remains associated with the slow-growing pointed end of the new filament. Spire is involved in intracellular vesicle transport along actin fibers, providing a novel link between actin cytoskeleton dynamics and intracellular transport. It is required for asymmetric spindle positioning and asymmetric cell division during oocyte meiosis. Spire contains four tandem WH2 domains. Several spire gene family members have been identified, including paralogs Spire-1 (Spir1) and Spire-2 (Spir2) in higher eukaryotes. Spire acts in the nucleus where, together with Spire-1 and Spire-2, it promotes assembly of nuclear actin filaments in response to DNA damage in order to facilitate movement of chromatin and repair factors after DNA damage. Spire-1 and Spire-2 encode a modified Fab1/YOTB/Vac1/EEA1 (FYVE)-type zinc finger membrane-binding domain at their C-termini that promiscuously interacts with negatively charged lipids and the interaction of these proteins with additional factors may provide the specificity for its targeting to the correct subpopulation of vesicles. 22 matched cddid_all.tbl CDD cd22067 cd22067 409210 WH2_DmSpire_r1-like first tandem Wiskott-Aldrich Syndrome Homology (WASP) region 2 (WH2 motif) repeat found in Drosophila melanogaster Spire, and similar proteins. This family contains the first of four tandem repeats of Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) in Drosophila melanogaster Spire (also called Spir), an actin nucleator essential for establishing an actin mesh during oogenesis. Spire was first identified as a Drosophila maternal effect gene essential to establishment of both the anterior/posterior and dorsal/ventral body axes in developing oocytes and embryos. It has been found to sever filaments and sequester monomers in addition to nucleating new filaments; it remains associated with the slow-growing pointed end of the new filament. Spire promotes dissociation of the actin nucleator Cappuccino (Capu) from the barbed end of actin filaments. Spire is involved in intracellular vesicle transport along actin fibers, providing a link between actin cytoskeleton dynamics and intracellular transport. Drosophila Spire contains four tandem WH2 domains which appear to function by determining the size of filament nuclei according to the number of WH2 repeats, suggesting that the WH2 domains of Spire line up actin subunits along a filament strand of the actin double helix, thereby generating nuclei for actin assembly. This model contains the first tandem WH2 domain of Spire (also called Spir-A or WH2-A). 27 matched cddid_all.tbl CDD cd22068 cd22068 409211 WH2_DmSpire_r3-like third tandem Wiskott-Aldrich Syndrome Homology (WASP) region 2 (WH2 motif) repeat found in Drosophila melanogaster Spire, and similar proteins. This family contains the third of four tandem repeats of Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) in Drosophila melanogaster Spire (also called Spir), an actin nucleator essential for establishing an actin mesh during oogenesis. Spire was first identified as a Drosophila maternal effect gene essential to establishment of both the anterior/posterior and dorsal/ventral body axes in developing oocytes and embryos. It has been found to sever filaments and sequester monomers in addition to nucleating new filaments; it remains associated with the slow-growing pointed end of the new filament. Spire promotes dissociation of the actin nucleator Cappuccino (Capu) from the barbed end of actin filaments. Spire is involved in intracellular vesicle transport along actin fibers, providing a link between actin cytoskeleton dynamics and intracellular transport. Drosophila Spire contains four tandem WH2 domains which appear to function by determining the size of filament nuclei according to the number of WH2 repeats, suggesting that the WH2 domains of Spire line up actin subunits along a filament strand of the actin double helix, thereby generating nuclei for actin assembly. This model contains the third tandem WH2 domain of Spire (also called Spir-C or WH2-C), which plays a unique role whereby two critical residues have been identified for activity for binding to actin with positive cooperativity. 26 matched cddid_all.tbl CDD cd22069 cd22069 409212 WH2_DmSpire_r4 fourth tandem Wiskott-Aldrich Syndrome Homology (WASP) region 2 (WH2 motif) repeat found in Drosophila melanogaster Spire, and similar proteins. This family contains the fourth of four tandem repeats of Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) in Drosophila melanogaster Spire (also called Spir), an actin nucleator essential for establishing an actin mesh during oogenesis. Spire was first identified as a Drosophila maternal effect gene essential to establishment of both the anterior/posterior and dorsal/ventral body axes in developing oocytes and embryos. It has been found to sever filaments and sequester monomers in addition to nucleating new filaments; it remains associated with the slow-growing pointed end of the new filament. Spire promotes dissociation of the actin nucleator Cappuccino (Capu) from the barbed end of actin filaments. Spire is involved in intracellular vesicle transport along actin fibers, providing a link between actin cytoskeleton dynamics and intracellular transport. Drosophila Spire contains four tandem WH2 domains which appear to function by determining the size of filament nuclei according to the number of WH2 repeats, suggesting that the WH2 domains of Spire line up actin subunits along a filament strand of the actin double helix, thereby generating nuclei for actin assembly. This model contains the fourth tandem WH2 domain of Spire (also called Spir-D or WH2-A). 29 matched cddid_all.tbl CDD cd22070 cd22070 409213 WH2_Pan1-like Wiskott-Aldrich Syndrome Homology (WASP) region 2 (WH2 motif) domain found in Actin cytoskeleton-regulatory complex protein Pan1, and similar proteins. This family contains the Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) found in actin cytoskeleton-regulatory complex protein Pan1, and similar proteins. Pan1 actin cytoskeleton-regulatory complex is a multi-domain scaffold that is required for the internalization of endosomes during actin-coupled endocytosis. It links the site of endocytosis to the cell membrane-associated actin cytoskeleton. Pan1 mediates uptake of external molecules and vacuolar degradation of plasma membrane proteins, may play a role in the proper organization of the cell membrane-associated actin cytoskeleton, and promotes its destabilization. 22 matched cddid_all.tbl CDD cd22071 cd22071 409214 WH2_WAVE-1 Wiskott Aldrich syndrome homology region 2 (WH2 motif) found in Wiskott-Aldrich Syndrome Protein Family Member 1 (WASP1 or WAVE1 or WASF1 or SCAR1). This family contains the Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) found in the Wiskott-Aldrich syndrome protein (WASP) relative WAVE 1 (also called WASP-family verprolin homologous protein 1 or SCAR1 or WAVE1). WAVE1 is a downstream effector protein involved in the transmission of signals from tyrosine kinase receptors and small GTPases to the actin cytoskeleton. It regulates lamellipodia formation via a hetero-pentameric WAVE regulatory complex (WRC) with additional proteins in the cell (Sra1/Cyfip1, Nap1/Hem-2, Abi and HSPC300) that regulates actin filament reorganization via its interaction with the actin related protein (Arp)2/3 complex. The WRC is stimulated by the Rac GTPase binding to CYFIP protein, allowing the release of WAVE1 from the complex. WAVE1 then binds and activates the Arp2/3 complex via its C-terminal domain. It interacts with actin via the WH2 domain. WAVE1 has been shown to be necessary for efficient transcriptional reprogramming in Xenopus oocytes and for normal development. 75 matched cddid_all.tbl CDD cd22072 cd22072 409215 WH2_WAVE-2 Wiskott Aldrich syndrome homology region 2 (WH2 motif) found in Wiskott-Aldrich Syndrome Protein Family Member 2 (WASP2 or WAVE2 or WASF2 or SCAR2). This family contains the Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) found in the Wiskott-Aldrich syndrome protein (WASP) relative WAVE 2 (also called WASP-family verprolin homologous protein 2 or WASF2 or SCAR2 or WAVE2). WAVE2 is a downstream effector protein involved in the transmission of signals from tyrosine kinase receptors and small GTPases to the actin cytoskeleton. It participates in multiple processes related to actin dynamics, such as lamellipodia and filopodium formation, cell migration and protrusion, and embryogenesis. It regulates lamellipodia formation via a hetero-pentameric WAVE regulatory complex (WRC) with additional proteins in the cell (Sra1/Cyfip1, Nap1/Hem-2, Abi and HSPC300) that regulates actin filament reorganization via its interaction with the actin related protein (Arp)2/3 complex. The WRC is stimulated by the Rac GTPase, kinases and phosphatidylinositols, and binds and activates the Arp2/3 complex via WAVE2 C-terminal domain. It interacts with actin via the WH2 domain. WAVE2 can also be phosphorylated by MAPK and forms a complex with PKA that regulates membrane protrusion. In mouse oocyte, WAVE2 regulates meiotic spindle stability, peripheral positioning and polar body emission, probably via an actin-mediated pathway. 30 matched cddid_all.tbl CDD cd22073 cd22073 409216 WH2_WAVE-3 Wiskott Aldrich syndrome homology region 2 (WH2 motif) found in Wiskott-Aldrich Syndrome Protein Family Member 3 (WASP-3 or WAVE3). This family contains the Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) found in the Wiskott-Aldrich syndrome protein (WASP) relative WAVE 3 (also called WASP-family verprolin homologous protein 3 or WASF3 or SCAR3 or WAVE3). WAVE3 is a downstream effector protein involved in the transmission of signals from tyrosine kinase receptors and small GTPases to the actin cytoskeleton. It plays a role in the regulation of cell morphology and cytoskeletal organization and is required in the control of cell shape. It forms a hetero-pentameric WAVE regulatory complex (WRC) with additional proteins in the cell (Sra1/Cyfip1, Nap1/Hem-2, Abi and HSPC300) that regulates actin filament reorganization via its interaction with the actin related protein (Arp)2/3 complex. The WRC is stimulated by the Rac GTPase, kinases and phosphatidylinositols, and binds and activates the Arp2/3 complex via WAVE3 C-terminal domain. It interacts with actin via the WH2 domain. This actin polymerization process is also involved in cancer cell invasion and metastasis. WASF3 has been shown to have a central role in cancer cell invasion and metastasis; elevated WAVE3 expression promotes metastasis in breast cancer and inactivation of WAVE3 in highly metastatic breast cancer cells has been shown to suppress invasion and metastasis. WAVE3 may also be pivotal in ovarian cancer cell motility, invasion and oncogenesis. In gastric cancer patients, WAVE3 expression correlates with poor outcome. In pancreatic cancer tissues, expression is prominently higher that in normal tissues and may be associated with lymphatic metastasis and poorly differentiated tumors; findings suggest that WAVE3 influences cell proliferation, migration and invasion via the AKT pathway. 66 matched cddid_all.tbl CDD cd22074 cd22074 409217 WH2_N-WASP_r1 first tandem Wiskott Aldrich syndrome homology region 2 (WH2 motif) repeat found in human Neural Wiskott-Aldrich syndrome protein (N-WASP) and related domains. This subfamily includes the first tandem Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) found in human Neural Wiskott-Aldrich syndrome protein (N-WASP or Neural WASP) and related domains. N-WASP integrates various extracellular signals to control actin dynamics and cytoskeletal reorganization through activation of the actin related protein (Arp)2/3 complex. It interacts with actin via the WH2 domain. N-WASP plays an important role in the deactivation or attenuation of B cell receptor signaling. N-WASP regulates filopodia formation and membrane invagination, as compared to WAVE proteins that serve as Rac1 effectors in the formation of lamellipodia. Filopodia are thin, actin-rich surface projections that are extended and maintained by N-WASP together with CDC42. N-WASP also plays a role in the nucleus by regulating gene transcription, probably by promoting nuclear actin polymerization. It binds to HSF1/HSTF1 and forms a complex on heat shock promoter elements (HSE) that negatively regulates HSP90 expression. It also plays a role in dendrite spine morphogenesis. Unphosphorylated N-WASP is preferentially localized in the nucleus and in the cytoplasm when phosphorylated; it is exported from the nucleus by a nuclear export signal (NES)-dependent mechanism to the cytoplasm. 27 matched cddid_all.tbl CDD cd22075 cd22075 409218 WH2_hN-WASP_r2_like second tandem Wiskott Aldrich syndrome homology region 2 (WH2 motif) repeat found in human Neural Wiskott-Aldrich syndrome protein (N-WASP) and related domains. This subfamily includes the second tandem Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) found in human Neural Wiskott-Aldrich syndrome protein (N-WASP or Neural WASP). N-WASP integrates various extracellular signals to control actin dynamics and cytoskeletal reorganization through activation of the actin related protein (Arp)2/3 complex. It interacts with actin via the WH2 domain. N-WASP plays an important role in the deactivation or attenuation of B cell receptor signaling. N-WASP regulates filopodia formation and membrane invagination, as compared to WAVE proteins that serve as Rac1 effectors in the formation of lamellipodia. Filopodia are thin, actin-rich surface projections that are extended and maintained by N-WASP together with CDC42. N-WASP also plays a role in the nucleus by regulating gene transcription, probably by promoting nuclear actin polymerization. It binds to HSF1/HSTF1 and forms a complex on heat shock promoter elements (HSE) that negatively regulates HSP90 expression. It also plays a role in dendrite spine morphogenesis. Unphosphorylated N-WASP is preferentially localized in the nucleus and in the cytoplasm when phosphorylated; it is exported from the nucleus by a nuclear export signal (NES)-dependent mechanism to the cytoplasm. This subfamily includes both tandem WH2 domains of mouse N-WASP. 25 matched cddid_all.tbl CDD cd22076 cd22076 409219 WH2_WAS_WASL-1 Wiskott Aldrich syndrome homology region 2 (WH2 motif) in WAS/WASL-interacting protein family member 1. This family contains the Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) in WAS/WASL-interacting protein family (WIPF, also known as WASP-interacting protein or WIP) member 1 (WIPF1). WIPF1 is a ubiquitously expressed proline-rich multidomain protein and is a binding partner and chaperone of WASP. It stabilizes actin filaments and regulates actin organization and polymerization which are associated with cell migration and invasion. Mutations in the WIPF1 binding site of WASP or in WIPF1 itself cause Wiskott-Aldrich syndrome (WAS), a rare X-linked recessive disease characterized by eczema, thrombocytopenia, immune deficiency, and bloody diarrhea. Aberrant expression of WIPF1 contributes to the invasion and metastasis of several malignancies such breast cancer, glioma and colorectal cancer; it has been identified as an oncoprotein in human pancreatic ductal adenocarcinoma (PDAC) and is associated with poor survival. 32 matched cddid_all.tbl CDD cd22077 cd22077 409220 WH2_WAS_WASL-2_3 Wiskott Aldrich syndrome homology region 2 (WH2 motif) in WAS/WASL-interacting protein (WIP) family members 2 and 3. WASF2 (WAS protein family, member 2), This family contains the Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) in WAS/WASL-interacting protein family (WIPF, also known as WASP-interacting protein or WIP) members 2 (WIPF2; also known as WIRE/WICH) and 3 (WIPF3). WIPF2 may be an important regulator of the actin cytoskeleton. It binds to N-WASP, regulating actin dynamics close to the plasma membrane; N-WASP in turn controls the second phase insulin secretion through the regulation of the Arp2/3 complex. Pathogenic properties of Shigella flexneri, a causative agent of intestinal infections worldwide, rely on its ability to invade the human colon where it spreads from cell to cell; WIPF2 has been shown to promote this via its contribution to the efficiency of actin-based motility in the cytosol and the resolution of the membrane protrusions into vacuoles. WIPF3, along with LIPA (lysosomal acid lipase A), are expressed in microphages and are involved in pathological abdominal aortic aneurysm (AAA), a serious condition of the aorta. 30 matched cddid_all.tbl CDD cd22078 cd22078 409221 WH2_Spire1_r2-like second tandem Wiskott-Aldrich Syndrome Homology (WASP) region 2 (WH2 motif) repeat of protein Spire homolog 1 (Spir1), and related proteins. This family contains the second tandem Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) domain in human Spire family protein Spire-1 (also called Spir1) and related proteins. Spire is an actin nucleator essential for establishing an actin mesh during oogenesis. It was first identified as a Drosophila maternal effect gene essential to establishment of both the anterior/posterior and dorsal/ventral body axes in developing oocytes and embryos. It has been found to sever filaments and sequester monomers in addition to nucleating new filaments; it remains associated with the slow-growing pointed end of the new filament. Spire is involved in intracellular vesicle transport along actin fibers, providing a novel link between actin cytoskeleton dynamics and intracellular transport. It is required for asymmetric spindle positioning and asymmetric cell division during oocyte meiosis. Spire contains four tandem WH2 domains. The mammalian genome encodes two Spire proteins, namely Spire-1 (Spir1) and Spire-2 (Spir2). This model contains WH2 domain 2 of human Spire-1 protein. Major expression of both spire genes have been detected during embryogenesis in the developing nervous system). In addition, spire1 expression is found in the fetal liver, and in adult tissues, spire1 is mainly expressed in neuronal cells of the nervous system. Minor expression levels were detected in testis and spleen. Spire also acts in the nucleus where, together with Spire-1 and Spire-2, it promotes assembly of nuclear actin filaments in response to DNA damage in order to facilitate movement of chromatin and repair factors after DNA damage. High levels of spire1 expression are restricted to the nervous system, oocytes, and testis. Since function of Spire-1 and Spire-2 in oocyte maturation is redundant, spire1 mutant mice are fertile, overall brain anatomy is not altered, and visual and motor functions remain normal; however, detailed behavioral studies of the spire1 mutant mice unveiled a very specific and highly significant phenotype in terms of fear learning in male mice. This family also contains the second of four tandem repeats of WH2 in Drosophila melanogaster Spire (also called Spir), an actin nucleator essential for establishing an actin mesh during oogenesis. 32 matched cddid_all.tbl CDD cd22079 cd22079 409222 WH2_Spire2_r2 second tandem Wiskott-Aldrich Syndrome Homology (WASP) region 2 (WH2 motif) repeat of protein Spire homolog 2. This family contains the second tandem Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) domain in human Spire family protein Spire-2 (also called Spir2) and related proteins. Spire is an actin nucleator essential for establishing an actin mesh during oogenesis. It was first identified as a Drosophila maternal effect gene essential to establishment of both the anterior/posterior and dorsal/ventral body axes in developing oocytes and embryos. It has been found to sever filaments and sequester monomers in addition to nucleating new filaments; it remains associated with the slow-growing pointed end of the new filament. Spire is involved in intracellular vesicle transport along actin fibers, providing a novel link between actin cytoskeleton dynamics and intracellular transport. It is required for asymmetric spindle positioning and asymmetric cell division during oocyte meiosis. Spire contains four tandem WH2 domains. The mammalian genome encodes two Spire proteins, namely Spire-1 (Spir1) and Spire-2 (Spir2). This model contains WH2 domain 2 of human Spire-2. Major expression of both spire genes have been detected during embryogenesis in the developing nervous system). In addition, spire2 expression is seen in early stages of intestinal development. In adult tissues, the spire2 gene shows a rather broad expression pattern, which includes the epithelial cells of the digestive tract, testical spermatocytes, and neuronal cells of the nervous system. Spire also acts in the nucleus where, together with Spire-1 and Spire-2, it promotes assembly of nuclear actin filaments in response to DNA damage in order to facilitate movement of chromatin and repair factors after DNA damage. 30 matched cddid_all.tbl CDD cd22080 cd22080 409223 WH2_Spire1_r4 fourth tandem Wiskott-Aldrich Syndrome Homology (WASP) region 2 (WH2 motif) repeat of protein Spire homolog 1. This family contains the fourth tandem Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) domain in human Spire family protein Spire-1 (also called Spir1) and related proteins. Spire is an actin nucleator essential for establishing an actin mesh during oogenesis. It was first identified as a Drosophila maternal effect gene essential to establishment of both the anterior/posterior and dorsal/ventral body axes in developing oocytes and embryos. It has been found to sever filaments and sequester monomers in addition to nucleating new filaments; it remains associated with the slow-growing pointed end of the new filament. Spire is involved in intracellular vesicle transport along actin fibers, providing a novel link between actin cytoskeleton dynamics and intracellular transport. It is required for asymmetric spindle positioning and asymmetric cell division during oocyte meiosis. Spire contains four tandem WH2 domains. The mammalian genome encodes two Spire proteins, namely Spire-1 (Spir1) and Spire-2 (Spir2). This model contains WH2 domain 4 of Spire-1 protein. Major expression of both spire genes have been detected during embryogenesis in the developing nervous system). In addition, spire1 expression is found in the fetal liver, and in adult tissues, spire1 is mainly expressed in neuronal cells of the nervous system. Minor expression levels were detected in testis and spleen. Spire also acts in the nucleus where, together with Spire-1 and Spire-2, it promotes assembly of nuclear actin filaments in response to DNA damage in order to facilitate movement of chromatin and repair factors after DNA damage. High levels of spire1 expression are restricted to the nervous system, oocytes, and testis. Since function of Spire-1 and Spire-2 in oocyte maturation is redundant, spire1 mutant mice are fertile, overall brain anatomy is not altered, and visual and motor functions remain normal; however, detailed behavioral studies of the spire1 mutant mice unveiled a very specific and highly significant phenotype in terms of fear learning in male mice. 24 matched cddid_all.tbl CDD cd22081 cd22081 409224 WH2_Spire2_r4 fourth tandem Wiskott-Aldrich Syndrome Homology (WASP) region 2 (WH2 motif) repeat of protein Spire homolog 2. This family contains the fourth tandem Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) domain in human Spire family protein Spire-2 (also called Spir2) and related proteins. Spire is an actin nucleator essential for establishing an actin mesh during oogenesis. It was first identified as a Drosophila maternal effect gene essential to establishment of both the anterior/posterior and dorsal/ventral body axes in developing oocytes and embryos. It has been found to sever filaments and sequester monomers in addition to nucleating new filaments; it remains associated with the slow-growing pointed end of the new filament. Spire is involved in intracellular vesicle transport along actin fibers, providing a novel link between actin cytoskeleton dynamics and intracellular transport. It is required for asymmetric spindle positioning and asymmetric cell division during oocyte meiosis. Spire contains four tandem WH2 domains. The mammalian genome encodes two Spire proteins, namely Spire-1 (Spir1) and Spire-2 (Spir2). This model contains WH2 domain 4 of Spire-2. Major expression of both spire genes have been detected during embryogenesis in the developing nervous system). In addition, spire2 expression is seen in early stages of intestinal development. In adult tissues, the spire2 gene shows a rather broad expression pattern, which includes the epithelial cells of the digestive tract, testical spermatocytes, and neuronal cells of the nervous system. Spire also acts in the nucleus where, together with Spire-1 and Spire-2, it promotes assembly of nuclear actin filaments in response to DNA damage in order to facilitate movement of chromatin and repair factors after DNA damage. 22 matched cddid_all.tbl CDD cd22082 cd22082 438854 F-box_FBXO1 F-box domain found in F-box only protein 1 (FBXO1) and similar proteins. FBXO1, also called FBX1, or cyclin-F, is a substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of CP110 during G2 phase, thereby acting as an inhibitor of centrosome reduplication. It is the largest among all cyclins and oscillates in the cell cycle like other cyclins. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 52 matched cddid_all.tbl CDD cd22083 cd22083 438855 F-box_FBA F-box domain found in the F-box associated (FBA) family of F-box proteins. The F-box associated (FBA) family is composed of FBXO2, FBXO6, FBXO17, FBXO27, and FBXO44, which contain a conserved G domain that mediates substrate binding. Members of this family play diverse roles in glycoprotein quality control. They bind high mannose and sulfated glycoproteins, with one FBA protein, FBXO44, failing to bind any glycans on the tested arrays. FBA proteins are components of canonical SCF (Skp1, Cullin1, and Rbx1) complexes, yet FBXO2 bound very little Cullin1, suggesting that FBXO2 may exist primarily as a heterodimer with Skp1. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 37 matched cddid_all.tbl CDD cd22084 cd22084 438856 F-box_FBXO3 F-box domain found in F-box only protein 3 (FBXO3) and similar proteins. FBXO3, also called FBX3, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It mediates the ubiquitination of HIPK2 and probably that of EP300, leading to rapid degradation by the proteasome. It also promotes ubiquitylation and transcriptional activity of AIRE (autoimmune regulator). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 49 matched cddid_all.tbl CDD cd22085 cd22085 438857 F-box_FBXO4 F-box domain found in F-box only protein 4 (FBXO4) and similar proteins. FBXO4, also called FBX4, is a specific substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex that catalyzes the ubiquitination and subsequent degradation of cyclin D1 and Trx1. It recognizes TERF1 and promotes its ubiquitination together with UBE2D1. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 50 matched cddid_all.tbl CDD cd22086 cd22086 438858 F-box_EMI F-box domain found in the early mitotic inhibitor (EMI) family of F-box proteins. The EMI family includes FBX5 (EMI1) and FBX43 (EMI2), which are anaphase-promoting complex/cyclosome (APC/C) inhibitors that bind APC/C-CCD20 (Cell division cycle protein 20) and/or APC/C-CDH1 (CDC20 homologue 1) complexes. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 48 matched cddid_all.tbl CDD cd22087 cd22087 438859 F-box_FBXO7 F-box domain found in F-box only protein 7 (FBXO7) and similar proteins. FBXO7, also called FBX7, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. It recognizes BIRC2 and DLGAP5. FBXO7 plays a role downstream of PINK1 in the clearance of damaged mitochondria via selective autophagy (mitophagy) by targeting PRKN to dysfunctional depolarized mitochondria. It promotes MFN1 ubiquitination. FBXO7 acts as a cell cycle regulator by enhancing cyclin D/cyclin-dependent kinase 6 (Cdk6) complex formation and stabilizing levels of p27, a cyclin-dependent kinase inhibitor. Mutations in the FBXO7 (PARK15) gene have been implicated in a juvenile form of parkinsonism called parkinsonian pyramidal syndrome (PPS), characterized by Parkinsonian symptoms and pyramidal tract signs. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 45 matched cddid_all.tbl CDD cd22088 cd22088 438860 F-box_FBXO8 F-box domain found in F-box only protein 8 (FBXO8) and similar proteins. FBXO8, also called FBX8, or F-box/SEC7 protein FBS, is a novel component of F-box proteins which contains an F-box domain and a putative Sec7 domain. FBX8 was originally identified as a Skp1-binding protein. It is involved in the ubiquitin-dependent proteolytic pathway. It acts as a metastasis suppressor that functions through mTOR signaling pathway. FBXO8 may promote the activation of ADP-ribosylation factor (ARF) through replacement of GDP with GTP. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 46 matched cddid_all.tbl CDD cd22089 cd22089 438861 F-box_FBXO9 F-box domain found in F-box only protein 9 (FBXO9) and similar proteins. FBXO9, also called FBX9, cross-immune reaction antigen 1, renal carcinoma antigen NY-REN-57, or VCIA1, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of TTI1 and TELO2 in a CK2-dependent manner, thereby directly regulating mTOR signaling. FBXO9 acts as an E3 ubiquitin ligase that regulates the stability and activity of peroxisome proliferator-activated receptor gamma (PPARgamma) through ubiquitination. It is also required for adipocyte differentiation. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 53 matched cddid_all.tbl CDD cd22090 cd22090 438862 F-box_FBXO10 F-box domain found in F-box only protein 10 (FBXO10) and similar proteins. FBXO10, also called FBX10, or PRMT11, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. The SCF(FBXO10) complex mediates ubiquitination and degradation of BCL2, an anti-apoptotic protein, thereby playing a role in apoptosis by controlling the stability of BCL2. It also associates with the receptor for advanced glycation end products (RAGE) to mediate its ubiquitination and degradation. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 50 matched cddid_all.tbl CDD cd22091 cd22091 438863 F-box_FBXO11 F-box domain found in F-box only protein 11 (FBXO11) and similar proteins. FBXO11, also called FBX11, protein arginine N-methyltransferase 9 (PRMT9), or vitiligo-associated protein 1 (VIT-1), is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins, such as DTL/CDT2, BCL6 and PRDM1/BLIMP1. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 45 matched cddid_all.tbl CDD cd22092 cd22092 438864 F-box_FBXO13 F-box domain found in F-box only protein 13 (FBXO13) and similar proteins. FBXO13, also called FBX13, F-box/LRR-repeat protein 17 (FBL17), or F-box and leucine-rich repeat protein 17 (FBXL17), is the substrate-recognition component of SCF(FBXL17) E3 ubiquitin ligase complex, a key component of a quality control pathway required to ensure functional dimerization of BTB domain-containing proteins (dimerization quality control, DQC). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 49 matched cddid_all.tbl CDD cd22093 cd22093 438865 F-box_FBXO15 F-box domain found in F-box only protein 15 (FBXO15) and similar proteins. FBXO15, also called FBX15, has a novel dual molecular function by controlling transcriptional repression and being part of SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligases, which is essential for stress response, gliotoxin production and virulence in the opportunistic human pathogen Aspergillus fumigatus. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 46 matched cddid_all.tbl CDD cd22094 cd22094 438866 F-box_FBXO16-like F-box domain found in F-box only protein 16 (FBXO16), epithelial cell-transforming sequence 2 oncogene-like (ECT2L) and similar proteins. This family includes FBXO16 and ECT2L. FBXO16, also called FBX16, is part of an SCF (SKP1-cullin-F-box) protein ligase complex. It probably recognizes and binds to some phosphorylated proteins and promotes their ubiquitination and degradation. It functions as a tumor suppressor by attenuating nuclear beta-catenin function. ECT2L, also called lung-specific F-box and DH domain-containing protein, or putative guanine nucleotide exchange factor LFDH, may act as a guanine nucleotide exchange factor (GEF). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 49 matched cddid_all.tbl CDD cd22095 cd22095 438867 F-box_FBXO18 F-box domain found in F-box only protein 18 (FBXO18) and similar proteins. FBXO18, also called FBX18, or F-box DNA helicase 1 (FBH1), is a 3'-5' DNA helicase and the substrate-recognition component of the SCF(FBH1) E3 ubiquitin ligase complex that plays a key role in response to stalled/damaged replication forks. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 48 matched cddid_all.tbl CDD cd22096 cd22096 438868 F-box_FBXO21 F-box domain found in F-box only protein 21 (FBXO21) and similar proteins. FBXO21, also called FBX21, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It facilitates Lys29-linkage and activation of ASK1 (apoptosis signal-regulating kinase 1) and promotes type I interferon production upon viral infection. It also polyubiquitylates EP300-interacting inhibitor of differentiation 1 (EID1) and is required for the efficient degradation of EID1 in both cycling and quiescent cells. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 48 matched cddid_all.tbl CDD cd22097 cd22097 438869 F-box_FBXO22 F-box domain found in F-box only protein 22 (FBXO22) and similar proteins. FBXO22, also called FBX22, or F-box protein FBX22p44, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It promotes the proteasome-dependent degradation of key sarcomeric proteins, such as alpha-actinin (ACTN2) and filamin-C (FLNC), essential for maintenance of normal contractile function. FBXO22 regulates histone H3 lysine 9 and 36 methylation levels by targeting histone demethylase KDM4A for ubiquitin-mediated proteasomal degradation. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 48 matched cddid_all.tbl CDD cd22098 cd22098 438870 F-box_FBXO24 F-box domain found in F-box only protein 24 (FBXO24) and similar proteins. FBXO24, also called FBX24, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It recognizes deacetylated nucleoside diphosphate kinase A (NDPK-A) to enhance its degradation. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 47 matched cddid_all.tbl CDD cd22099 cd22099 438871 F-box_FBXO25 F-box domain found in F-box only protein 25 (FBXO25) and similar proteins. FBXO25, also called FBX25, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It functions as a negative regulator of MAPK signaling though the reduction of ERK1/2 activation. It controls Tbx5 and Nkx2-5 transcriptional activity to regulate cardiomyocyte development. FBXO25 also plays a crucial role in tumorigenesis. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 45 matched cddid_all.tbl CDD cd22100 cd22100 438872 F-box_FBXO28 F-box domain found in F-box only protein 28 (FBXO28) and similar proteins. FBXO28, also called FBX28, is part of an SCF (SKP1-cullin-F-box) protein ligase complex. It probably recognizes and binds to some phosphorylated proteins and promotes their ubiquitination and degradation. It promotes mitotic progression and regulates topoisomerase IIalpha-dependent DNA decatenation. FBXO28 plays a crucial role in the pathogenesis of the 1q41q42 microdeletion syndrome. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 45 matched cddid_all.tbl CDD cd22101 cd22101 438873 F-box_FBXO30-like F-box domain found in F-box only protein 30 (FBXO30), F-box only protein 40 (FBXO40) and similar proteins. FBXO30, also called FBX30, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It is required for muscle atrophy following denervation. FBXO30 regulates mammopoiesis by targeting the bipolar mitotic kinesin Eg5. FBXO40, also called FBX40, or muscle disease-related protein, is a probable substrate-recognition component of an SCF-type E3 ubiquitin ligase complex that may function in myogenesis. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 45 matched cddid_all.tbl CDD cd22102 cd22102 438874 F-box_FBXO31 F-box domain found in F-box only protein 31 (FBXO31) and similar proteins. FBXO31, also called FBX31, or FBXO14, is a component of an SCF (SKP1-cullin-F-box) protein ligase complex that plays a central role in G1 arrest following DNA damage. It specifically recognizes phosphorylated cyclin-D1 (CCND1), promoting its ubiquitination and degradation by the proteasome, resulting in G1 arrest. FBXO31 may act as a tumor suppressor. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 48 matched cddid_all.tbl CDD cd22103 cd22103 438875 F-box_FBXO32 F-box domain found in F-box only protein 32 (FBXO32) and similar proteins. FBXO32, also called FBX32, atrogin-1, or muscle atrophy F-box protein (MAFbx), is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins during skeletal muscle atrophy. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 48 matched cddid_all.tbl CDD cd22104 cd22104 438876 F-box_FBXO33 F-box domain found in F-box only protein 33 (FBXO33) and similar proteins. FBXO33, also called FBX33, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. It exerts similar functions as F-box involved in polyQ pathogenesis (FipoQ) in modulating the ubiquitination and solubility of expanded SCA3-polyQ proteins. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 48 matched cddid_all.tbl CDD cd22105 cd22105 438877 F-box_FBXO34-like F-box domain found in F-box only protein 34 (FBXO34), F-box only protein 46 (FBXO46) and similar proteins. This family includes FBXO34 (also called FBX34) and FBXO46 (also called FBX46), both of which are substrate-recognition components of SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complexes. The SCF(FBOX46) complex mediates degradation of the tumor suppressor FBXO31 and thereby prevents premature cellular senescence. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 47 matched cddid_all.tbl CDD cd22106 cd22106 438878 F-box_FBXO36 F-box domain found in F-box only protein 36 (FBXO36) and similar proteins. FBXO36, also called FBX36, likely functions as the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 46 matched cddid_all.tbl CDD cd22107 cd22107 438879 F-box_FBXO38 F-box domain found in F-box only protein 38 (FBXO38) and similar proteins. FBXO38, also called FBX38, or modulator of KLF7 activity (MoKA), is part of an SCF (SKP1-cullin-F-box) protein ligase complex. It may coactivate the transcription factor Kruppel-like factor 7 (KLF7), but does not seem to promote KLF7 ubiquitination. FBXO38 acts as a crucial regulator of programmed cell death protein-1 (PD-1) protein turnover in T cells by mediating PD-1 ubiquitination and regulating anti-tumor immunity of T cells. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 44 matched cddid_all.tbl CDD cd22108 cd22108 438880 F-box_FBXO39 F-box domain found in F-box only protein 39 (FBXO39) and similar proteins. FBXO39, also called FBX39, likely functions as the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It acts as a cancer/testis antigen from colon cancer patients by serological analysis of recombinant cDNA expression libraries (SEREX). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 44 matched cddid_all.tbl CDD cd22109 cd22109 438881 F-box_FBXO41 F-box domain found in F-box only protein 41 (FBXO41) and similar proteins. FBXO41, also called FBX41, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It acts as a novel central nervous system (CNS)-specific F-box protein that localizes to the centrosome and the cytoplasm of neurons and promotes neuronal migration. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 47 matched cddid_all.tbl CDD cd22110 cd22110 438882 F-box_FBXO42 F-box domain found in F-box only protein 42 (FBXO42) and similar proteins. FBXO42, also called FBX42, or just one F-box and Kelch domain-containing protein (JFK), is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It specifically recognizes p53/TP53, promoting its ubiquitination and degradation. FBXO42 is also involved in the ubiquitin-proteasome system that may play a role in the pathogenesis of Parkinson's disease (PD). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 38 matched cddid_all.tbl CDD cd22111 cd22111 438883 F-box_FBXO45 F-box domain found in F-box only protein 45 (FBXO45) and similar proteins. FBXO45, also called FBX45, or F-box/SPRY domain-containing protein 1, functions as the substrate-recognition component of E3 ubiquitin ligase complexes. It is critical for synaptogenesis, neuronal migration, and synaptic transmission. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 36 matched cddid_all.tbl CDD cd22112 cd22112 438884 F-box_FBXO47 F-box domain found in F-box only protein 47 (FBXO47) and similar proteins. FBXO47, also called FBX47, functions as the substrate-recognition component of an SCF (SKP1-cullin-F-box) protein ligase complex. It probably recognizes and binds to some phosphorylated proteins and promotes their ubiquitination and degradation. It has a potential role as a tumor-suppressor gene. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 39 matched cddid_all.tbl CDD cd22113 cd22113 438885 F-box_FBXO48 F-box domain found in F-box only protein 48 (FBXO48) and similar proteins. FBXO48, also called FBX48, is one of the paralogs of the F-box only protein 7 (FBXO7), which is the causative gene for PARK15 (also known as Parkinsonian-pyramidal disease, PPD). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 46 matched cddid_all.tbl CDD cd22114 cd22114 438886 F-box_FBXL1 F-box domain found in F-box/LRR-repeat protein 1 (FBXL1) and similar proteins. FBXL1, also called S-phase kinase-associated protein 2, cyclin-A/CDK2-associated protein p45, F-box protein Skp2, or p45skp2, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins involved in cell cycle progression, signal transduction and transcription. It specifically recognizes phosphorylated CDKN1B/p27kip and is involved in regulation of G1/S transition. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 41 matched cddid_all.tbl CDD cd22115 cd22115 438887 F-box_FBXL2-like F-box domain found in F-box/LRR-repeat protein 2 (FBXL2), F-box/LRR-repeat protein 20 (FBXL20) and similar proteins. The family includes FBXL2 and FBXL30. FBXL2, also called F-box and leucine-rich repeat protein 2, or F-box protein FBL2/FBL3, is a calcium-activated substrate-recognition component of an SCF (SKP1-cullin-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Unlike many F-box proteins, FBXL2 does not seem to target phosphodegron within its substrates but rather calmodulin-binding motifs and is thereby antagonized by calmodulin. FBXL20, also called SCRAPPER, F-box and leucine-rich repeat protein 20, or F-box/LRR-repeat protein 2-like, is a component of a synapse-localized SCF-type E3 ubiquitin ligase which regulates neural transmission. It is widely expressed in the central nervous system and plays an important role in the ubiquitin-dependent degradation of regulating synaptic membrane exocytosis 1 (RIM1), which is an important factor in the release of synaptic vesicles. It may also mediate the ubiquitin degradation of E-cadherin resulting in an increased invasive ability of malignant cells. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 45 matched cddid_all.tbl CDD cd22116 cd22116 438888 F-box_FBXL3-like F-box domain found in F-box/LRR-repeat protein 3 (FBXL3), F-box/LRR-repeat protein 21 (FBXL21) and similar proteins. FBXL3, also called F-box and leucine-rich repeat protein 3A, or F-box/LRR-repeat protein 3A, is the substrate-recognition component of the SCF(FBXL3) E3 ubiquitin ligase complex that mainly acts in the nucleus and mediates ubiquitination and subsequent degradation of CRY1 and CRY2, and thus, is involved in circadian rhythm function. It plays a key role in the maintenance of both the speed and the robustness of the circadian clock oscillation. FBXL21, also called F-box and leucine-rich repeat protein 21, F-box and leucine-rich repeat protein 3B, or F-box/LRR-repeat protein 3B, is the substrate-recognition component of the SCF(FBXL21) E3 ubiquitin ligase complex that mainly acts in the cytosol and mediates ubiquitination of CRY proteins (CRY1 and CRY2), leading to CRY protein stabilization, and thus, is also involved in circadian rhythm function. It plays regulates the oscillation of the circadian clock through ubiquitination and stabilization of cryptochromes. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 39 matched cddid_all.tbl CDD cd22117 cd22117 438889 F-box_FBXL4 F-box domain found in F-box/LRR-repeat protein 4 (FBXL4) and similar proteins. FBXL4, also called F-box and leucine-rich repeat protein 4, or F-box protein FBL4/FBL5, is part of an SCF (SKP1-cullin-F-box) protein ligase complex. It serves as a clock output molecule that regulates sleep through promotion of rhythmic degradation of the GABA(A) receptor. Biallelic pathogenic variants in FBXL4 are associated with an encephalopathic mtDNA maintenance defect syndrome that is a multi-system disease characterized by lactic acidemia, developmental delay, and hypotonia. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 47 matched cddid_all.tbl CDD cd22118 cd22118 438890 F-box_FBXL5 F-box domain found in F-box/LRR-repeat protein 5 (FBXL5) and similar proteins. FBXL5, also called F-box and leucine-rich repeat protein 5, F-box protein FBL4/FBL5, or p45SKP2-like protein, is the substrate-recognition component of an SCF (SKP1-cullin-F-box) protein ligase complex that plays a central role in iron homeostasis by promoting the ubiquitination and subsequent degradation of IREB2/IRP2. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 41 matched cddid_all.tbl CDD cd22119 cd22119 438891 F-box_FBXL6 F-box domain found in F-box/LRR-repeat protein 6 (FBXL6) and similar proteins. FBXL6, also called F-box and leucine-rich repeat protein 6, or F-box protein FBL6 (FBL6A), is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 47 matched cddid_all.tbl CDD cd22120 cd22120 438892 F-box_FBXL7 F-box domain found in F-box/LRR-repeat protein 7 (FBXL7) and similar proteins. FBXL7, also called F-box and leucine-rich repeat protein 7, or F-box protein FBL6/FBL7, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of Aurora kinase A (AURKA) during mitosis, causing mitotic arrest. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 44 matched cddid_all.tbl CDD cd22121 cd22121 438893 F-box_FBXL8 F-box domain found in F-box/LRR-repeat protein 8 (FBXL8) and similar proteins. FBXL8, also called F-box and leucine-rich repeat protein 8, or F-box protein FBL8, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 35 matched cddid_all.tbl CDD cd22122 cd22122 438894 F-box_JHDM F-box domain found in the JmjC domain-containing histone demethylation protein (JHDM) family. The JHDM family includes F-box/LRR-repeat proteins FBXL10, FBXL11 and FBXL19. FBXL10 is also called lysine-specific demethylase 2B (KDM2B), CXXC-type zinc finger protein 2 (CXXC2), F-box and leucine-rich repeat protein 10 (FBL10), JmjC domain-containing histone demethylation protein 1B (JHDM1B), Jumonji domain-containing EMSY-interactor methyltransferase motif protein, protein JEMMA, protein-containing CXXC domain 2, [Histone-H3]-lysine-36 demethylase 1B, or NDY1. It is a histone demethylase that catalyzes the demethylation of H3K4me3 and H3K36me2, thereby playing a central role in the histone code. It preferentially binds the transcribed region of ribosomal RNA and represses the transcription of ribosomal RNA genes which inhibits cell growth and proliferation. FBXL10 may also serve as the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. FBXL11, also called KDM2A, CXXC8, F-box and leucine-rich repeat protein 11, F-box protein FBL7, F-box protein Lilina, JmjC domain-containing histone demethylation protein 1A (JHDM1A), or [Histone-H3]-lysine-36 demethylase 1A, is a histone H3 lysine 36 (H3K36) demethylase that regulates epithelial mesenchymal transition (EMT) and the metastasis of ovarian cancer. It plays an essential role in embryonic development and homeostasis by regulating cell proliferation and survival. FBXL11 may also recognize and bind to some phosphorylated proteins and promote their ubiquitination and degradation. It associates with centromeres and represses transcription of small non-coding RNAs that are encoded by the clusters of satellite repeats at the centromere. It is required to sustain centromeric integrity and genomic stability, particularly during mitosis. FBXL19, also called F-box and leucine-rich repeat protein 19, is the substrate-recognition component of an SCF-type E3 ubiquitin ligase complex. It acts as a CpG island-binding protein in mouse embryonic stem (ES) cells and has been shown to associate with the CDK-Mediator complex. It promotes H2Bub1 at the promoters of CpG island-containing genes by interacting with RNF20. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 43 matched cddid_all.tbl CDD cd22123 cd22123 438895 F-box_FBXL12 F-box domain found in F-box/LRR-repeat protein 12 (FBXL12) and similar proteins. FBXL12, also called F-box and leucine-rich repeat protein 12, or F-box protein FBL12, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It mediates the polyubiquitination and proteasomal degradation of calcium/calmodulin dependent protein kinase I (CAMK1) leading to disruption of cyclin D1/CDK4 complex assembly, which results in G1 cell cycle arrest in lung epithelia. It regulates T-cell differentiation in a cell-autonomous manner. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 42 matched cddid_all.tbl CDD cd22124 cd22124 438896 F-box_FBXL13 F-box domain found in F-box/LRR-repeat protein 13 (FBXL13) and similar proteins. FBXL13, also called F-box and leucine-rich repeat protein 13, or dynein regulatory complex subunit 6, is a component of the nexin-dynein regulatory complex (N-DRC), a key regulator of ciliary/flagellar motility which maintains the alignment and integrity of the distal axoneme and regulates microtubule sliding in motile axonemes. It is also the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 42 matched cddid_all.tbl CDD cd22125 cd22125 438897 F-box_FBXL14 F-box domain found in F-box/LRR-repeat protein 14 (FBXL14) and similar proteins. FBXL14, also called F-box and leucine-rich repeat protein 14, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin-protein ligase complex, which acts by mediating ubiquitination and subsequent degradation of SNAIL1. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 41 matched cddid_all.tbl CDD cd22126 cd22126 438898 F-box_FBXL15 F-box domain found in F-box/LRR-repeat protein 15 (FBXL15) and similar proteins. FBXL15, also called F-box only protein 37 (FBXO37), is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of Smad ubiquitination regulatory factor 1 (SMURF1), thereby acting as a positive regulator of the BMP signaling pathway. It is required for dorsal/ventral pattern formation and bone mass maintenance. It also mediates ubiquitination of SMURF2 and WWP2. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 44 matched cddid_all.tbl CDD cd22127 cd22127 438899 F-box_FBXL16 F-box domain found in F-box/LRR-repeat protein 16 (FBXL16) and similar proteins. FBXL16, also called F-box and leucine-rich repeat protein 16, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It acts as a repressor of one of the earliest steps in the cardiogenic lineage: FLK1+ progenitor formation. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 42 matched cddid_all.tbl CDD cd22128 cd22128 438900 F-box_FBXL18 F-box domain found in F-box/LRR-repeat protein 18 (FBXL18) and similar proteins. FBXL18, also called F-box and leucine-rich repeat protein 18, is a substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It promotes glioma progression by promoting K63-linked ubiquitination of Akt. It targets leucine-rich repeat kinase 2 (LRRK2) for proteasomal degradation and attenuates cell toxicity. FBXL18 also regulates apoptosis by mediating ubiquitin-dependent proteasomal degradation of the pro-apoptotic protein FBXL7 that may impact cellular processes involved in cell cycle progression. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 44 matched cddid_all.tbl CDD cd22129 cd22129 438901 F-box_FBXL22 F-box domain found in F-box/LRR-repeat protein 22 (FBXL22) and similar proteins. FBXL22, also called F-box and leucine-rich repeat protein 22, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex that promotes ubiquitination of sarcomeric proteins alpha-actinin-2 (ACTN2) and filamin-C (FLNC). It acts as a cardiac-enriched F-box protein that regulates sarcomeric protein turnover and is essential for maintenance of contractile function in vivo. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 43 matched cddid_all.tbl CDD cd22130 cd22130 438902 F-box_FBXW1 F-box domain found in F-box/WD repeat-containing proteins, FBXW1A, FBXW1B and similar proteins. FBXW1A, also called E3RSIkappaB, epididymis tissue protein Li 2a, F-box and WD repeats protein beta-TrCP, or pIkappaBalpha-E3 receptor subunit, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins, such as CTNNB1, NFKBIA, NFKBIB and NFKBIE, as well as phosphorylated NFKB1, ATF4, CDC25A, DLG1, FBXO5, PER1, SMAD3, SMAD4, SNAI1 and probably NFKB2. FBXW1B, also called F-box/WD repeat-containing protein 11 (FBXW11), F-box and WD repeats protein beta-TrCP2, or homologous to Slimb protein (HOS), is the substrate-recognition component of an SCF E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins, such as IFNAR1, CEP68 and CDC25A, as well as phosphorylated CTNNB1, NFKBIA, PER1 and PER2. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 51 matched cddid_all.tbl CDD cd22131 cd22131 438903 F-box_FBXW2 F-box domain found in F-box/WD repeat-containing protein 2 (FBXW2) and similar proteins. FBXW2, also called F-box and WD-40 domain-containing protein 2, or protein MD6, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It acts as a tumor suppressor by promoting SKP2 degradation. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 40 matched cddid_all.tbl CDD cd22132 cd22132 438904 F-box_FBXW5 F-box domain found in F-box/WD repeat-containing protein 5 (FBXW5) and similar proteins. FBXW5, also called F-box and WD-40 domain-containing protein 5, is the substrate-recognition component of both SCF (SKP1-CUL1-F-box protein) and DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complexes. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 46 matched cddid_all.tbl CDD cd22133 cd22133 438905 F-box_FBXW7 F-box domain found in F-box/WD repeat-containing protein 7 (FBXW7) and similar proteins. FBXW7, also called Archipelago homolog (Ago), F-box and WD-40 domain-containing protein 7, F-box protein FBX30, SEL-10, or Cdc4, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins, such as cyclin-E (CCNE1 or CCNE2), DISC1, JUN, MYC, NOTCH1 released notch intracellular domain (NICD), NOTCH2, MCL1, and probably PSEN1. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 59 matched cddid_all.tbl CDD cd22134 cd22134 438906 F-box_FBXW8 F-box domain found in F-box/WD repeat-containing protein 8 (FBXW8) and similar proteins. FBXW8, also called F-box and WD-40 domain-containing protein 8, or F-box only protein 29 (FBXO29), is the substrate-recognition component of a Cul7-RING ubiquitin-protein ligase complex, which mediates the ubiquitination and subsequent proteasomal degradation of target proteins, such as GORASP1, IRS1, MAP4K1/HPK1. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 48 matched cddid_all.tbl CDD cd22135 cd22135 438907 F-box_FBXW9 F-box domain found in F-box/WD repeat-containing protein 9 (FBXW9) and similar proteins. FBXW9, also called F-box and WD-40 domain-containing protein 9, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex that mediates the ubiquitination and subsequent proteasomal degradation of target proteins. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 45 matched cddid_all.tbl CDD cd22136 cd22136 438908 F-box_FBXW10 F-box domain found in F-box/WD repeat-containing protein 10 (FBXW10) and similar proteins. FBXW10, also called F-box and WD-40 domain-containing protein 10, or ubiquitin ligase-specificity factor, is a probable substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. Its overexpression leads to degradation of CBX5 and CBX1. FBXW10 is negatively regulated in transcription and expression levels by protein O-GlcNAcylation. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 40 matched cddid_all.tbl CDD cd22137 cd22137 438909 F-box_FBXW12 F-box domain found in F-box/WD repeat-containing protein 12 (FBXW12) and similar proteins. FBXW12, also called F-box and WD-40 domain-containing protein 12, or F-box only protein 35 (FBXO35), is the substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex that mediates the ubiquitination and subsequent proteasomal degradation of target proteins. It functions as an epithelial growth suppressor. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 44 matched cddid_all.tbl CDD cd22138 cd22138 438910 F-box_unchar F-box domain found in uncharacterized F-box protein group similar to F-box only protein 13 (FBXO13). The family corresponds to a group of uncharacterized F-box proteins which show sequence similarity to F-box only protein 13 (FBXO13). FBXO13, also called FBX13, or F-box/LRR-repeat protein 17 (FBL17), or F-box and leucine-rich repeat protein 17 (FBXL17), is the substrate-recognition component of the SCF(FBXL17) E3 ubiquitin ligase complex, a key component of a quality control pathway required to ensure functional dimerization of BTB domain-containing proteins (dimerization quality control, DQC). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 45 matched cddid_all.tbl CDD cd22139 cd22139 438911 F-box_unchar F-box domain found in uncharacterized F-box protein group similar to F-box only protein 3 (FBXO3). This subfamily corresponds to a group of uncharacterized F-box proteins which show sequence similarity to F-box only protein 3 (FBXO3). FBXO3, also called FBX3, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex, that mediates the ubiquitination of HIPK2 and probably that of EP300, leading to rapid degradation by the proteasome. It also promotes ubiquitylation and transcriptional activity of AIRE (autoimmune regulator). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 45 matched cddid_all.tbl CDD cd22140 cd22140 438912 F-box_D3-like F-box domain found in Oryza sativa F-box/LRR-repeat Max2 homolog (D3) and similar proteins. D3 is the ortholog of Arabidopsis MORE AXILLARY GROWTH2 (MAX2) and DWARF14 (AtD14) in rice. These proteins are essential signaling components to regulate strigolactone (SL)-repressed plant branching. In rice shoot branching inhibition, the SL-metabolizing alpha/beta hydrolase D14 interacts with the F-box protein D3 to ubiquitinate and degrade the transcription repressor D53. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 38 matched cddid_all.tbl CDD cd22141 cd22141 438913 F-box_ScCDC4-like F-box domain found in Saccharomyces cerevisiae cell division control protein 4 (ScCDC4) and similar proteins. ScCDC4 is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. It is essential for initiation of DNA replication and separation of the spindle pole bodies to form the poles of the mitotic spindle. It also plays a role in bud development, fusion of zygotic nuclei after conjugation and various aspects of sporulation. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 47 matched cddid_all.tbl CDD cd22142 cd22142 438914 F-box_ScDIA2-like F-box domain found in Saccharomyces cerevisiae protein Digs into agar protein 2 (ScDIA2) and similar proteins. ScDIA2 is a replication origin-binding protein that plays a role in regulating DNA replication. It is a component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 48 matched cddid_all.tbl CDD cd22143 cd22143 438915 F-box_ScMDM30-like F-box domain found in Saccharomyces cerevisiae mitochondrial distribution and morphology protein 30 (ScMDM30) and similar proteins. ScMDM30 is an F-box protein required for maintenance of fusion-competent mitochondria in yeast. It is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. ScMDM30 recognizes FZO1 and regulates the amount of FZO1. It acts as a regulatory factor for the mitochondrial fusion machinery and is required for mitochondrial DNA maintenance. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 44 matched cddid_all.tbl CDD cd22145 cd22145 438916 F-box_ScUFO1-like F-box domain found in Saccharomyces cerevisiae ubiquitin ligase complex F-box protein UFO1 (ScUFO1) and similar proteins. ScUFO1 is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. It probably recognizes and binds to phosphorylated target proteins. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 41 matched cddid_all.tbl CDD cd22146 cd22146 438917 F-box_ScMFB1-like F-box domain found in Saccharomyces cerevisiae mitochondrial F-box protein MFB1 (ScMFB1) and similar proteins. ScMFB1 is a novel mitochondria-associated F-box protein that functions to increase mitochondrial connectivity in yeast. ScMFB1 acts as a key component of a Skp1-Cdc53/Cullin-F-box protein (SCF) ubiquitin ligase complex machinery that regulates mitochondrial dynamics throughout the yeast's entire life cycle. It interacts with Skp1p in an F-box-dependent manner. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 42 matched cddid_all.tbl CDD cd22147 cd22147 438918 F-box_SpPof1-like F-box domain found in Schizosaccharomyces pombe Skp1-binding protein 1 (SpPof1) and similar proteins. SpPof1, also called F-box/WD repeat-containing protein pof1, probably recognizes and binds to some phosphorylated proteins and promotes their ubiquitination and degradation. It is required for the inactivation of zip1 via ubiquitination. This subfamily also includes Saccharomyces cerevisiae methionine-requiring protein 30 (ScMET30, also called E3 ubiquitin ligase complex SCF(Met30) subunit MET30), Aspergillus niger sulfur controller B (AnSCONB, also called sulfur metabolite repression control protein B) and Neurospora crassa sulfur controller 2 (NcSCON2, also called sulfur metabolite repression control protein 2). ScMET30 acts as a transcriptional inhibitor that negatively regulates the expression of sulfur amino acid biosynthesis genes. It controls cell cycle function (being required for the G1/S transition and M-phase but not the S-phase), sulfur metabolism, and methionine biosynthesis as part of the E3 ubiquitin ligase complex SCF(Met30). AnSCONB and NcSCON2 are components of the SCF (sconB/scon-2) E3 ubiquitin ligase complexes involved in the regulation of sulfur metabolite repression, probably by mediating the inactivation or degradation of the metR transcription factor. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 46 matched cddid_all.tbl CDD cd22148 cd22148 438919 F-box_DdgacFF-like F-box domain found in Dictyostelium discoideum Rho GTPase-activating protein gacFF (DdgacFF) and similar proteins. DdgacFF, also called GTPase activating factor for raC protein FF, is a Rho GTPase-activating protein involved in the signal transduction pathway. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 44 matched cddid_all.tbl CDD cd22149 cd22149 438920 F-box_DmSKP2-like F-box domain found in Drosophila melanogaster S-phase kinase-associated protein 2 (DmSKP2) and similar proteins. DmSKP2 is a Drosophila F-box protein that regulates cell proliferation by targeting Dacapo (Dap) for ubiquitination and proteasome-mediated degradation. It plays a role in maintaining diploidy of mitotic cells during development. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 43 matched cddid_all.tbl CDD cd22150 cd22150 438921 F-box_CeFBXA-like F-box domain found in Caenorhabditis elegans F-box domain-containing proteins (CeFBXA) and similar proteins. The family includes a group of uncharacterized Caenorhabditis elegans F-box domain-containing proteins. They may be components of SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complexes which mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 46 matched cddid_all.tbl CDD cd22151 cd22151 438922 F-box_AtGID2-like F-box domain found in Arabidopsis thaliana F-box protein GID2 and similar proteins. AtGID2, also called protein SLEEPY 1, is an essential component of the SCF-type E3 ligase complex, SCF(GID2), a complex that positively regulates the gibberellin signaling pathway. Upon gibberellin treatment, the SCF(GID2) complex mediates the ubiquitination and subsequent degradation of DELLA proteins (GAI, RGA and RGL2), some repressors of the gibberellin pathway, leading to the activation of the pathway. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 44 matched cddid_all.tbl CDD cd22152 cd22152 438923 F-box_AtAFR-like F-box domain found in Arabidopsis thaliana protein ATTENUATED FAR-RED RESPONSE (AtAFR) and similar proteins. AtAFR, also called SKP1-interacting partner 29 (AtSKIP29), or F-box protein AFR, is a component of SCF (SKP1/ASK-cullin-F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. It is part of the phyA-mediated signaling transduction pathway leading to the regulation of gene expression and hypocotyl elongation in response to red and far-red light exposure. This subfamily also includes many other Arabidopsis thaliana SKP1-interacting partner proteins. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 45 matched cddid_all.tbl CDD cd22153 cd22153 438924 F-box_AtTLP-like F-box domain found in Arabidopsis thaliana TUBBY-like proteins (AtTLPs) and similar proteins. The TUBBY-like protein gene family of Arabidopsis has 11 members, AtTLP1-11. They have conserved C-terminal tubby domains. All AtTLP members except AtTLP8 also contain a conserved F-box domain. AtTLPs are involved in responses to stress. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 45 matched cddid_all.tbl CDD cd22154 cd22154 438925 F-box_AtADO-like F-box domain found in Arabidopsis thaliana Adagio proteins (AtADO1/2/3) and similar proteins. This subfamily contains Arabidopsis thaliana Adagio proteins, including AtADO1, AtADO2 and AtADO3. They are components of E3 ubiquitin ligase complexes that play central roles in blue light-dependent circadian cycles. They act as blue light photoreceptors, due to the presence of FMN, that mediate light-regulated protein degradation of critical clock components by targeting them to the proteasome complex. AtADO1, also called clock-associated PAS protein ZTL, F-box only protein 2b (FBX2b), flavin-binding kelch repeat F-box protein 1-like protein 2 (FKL2), FKF1-like protein 2, LOV kelch protein 1 (LKP1), or protein ZEITLUPE, is a novel clock-associated PAS protein from Arabidopsis. Its circadian phase-specific degradation is mediated by the proteasome. AtADO2, also called F-box only protein 2c (FBX2c), flavin-binding kelch repeat F-box protein 1-like protein 1 (FKL1), FKF1-like protein 1, or LOV kelch protein 2 (LKP2), functions close to the circadian clock oscillator. AtADO3, also called F-box only protein 2a (FBX2a), or flavin-binding kelch repeat F-box protein 1 (FKF1), is essential for photoperiodic-specific light signaling and mediates cyclic degradation of a repressor of CONSTANS in Arabidopsis. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 47 matched cddid_all.tbl CDD cd22155 cd22155 438926 F-box_AtADLO1-like F-box domain found in Arabidopsis thaliana protein ARABIDILLO 1 (AtADLO1) and similar proteins. AtADLO1, also called F-box only protein 5 (FBX5), promotes lateral root initiation and development, independently of auxin (IAA) and abscisic acid (ABA). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 42 matched cddid_all.tbl CDD cd22156 cd22156 438927 F-box_AtARP8-like F-box domain found in Arabidopsis thaliana actin-related protein 8 (AtARP8) and similar proteins. AtARP8, also called F-box protein ARP8, is an F-box protein localized to the nucleolus in Arabidopsis. Unlike other plant nuclear actin-related proteins (ARPs), ARP8 is unique in having an F-box domain and an actin homology domain. It may play a role in nucleolar functions. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 45 matched cddid_all.tbl CDD cd22157 cd22157 438928 F-box_AtFBW1-like F-box domain found in Arabidopsis thaliana F-box/WD-40 repeat-containing protein 1 (AtFBW1) and similar proteins. AtFBW1, also called WD-40-associated F-box protein 1, is an F-box protein that contains four WD-40 repeats, which are separated from each other by a spacer region. Like other F-box proteins, AtFBW1 may be a component of SCF (Skp1 Cdc53 F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. This subfamily also contains many F-box only proteins that do not have any WD repeat. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 39 matched cddid_all.tbl CDD cd22158 cd22158 438929 F-box_AtFBW2-like F-box domain found in Arabidopsis thaliana F-box protein FBW2 (AtFBW2) and similar proteins. AtFBW2, also called SKP1-interacting partner 18 (SKIP18), is an F-box protein that contains four tandem WD-40 repeats. It is a component of SCF (SPK1/ASK-cullin-F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. It interacts with CUL1, CUL2 and SPK1B/ASK2. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 36 matched cddid_all.tbl CDD cd22159 cd22159 438930 F-box_AtTIR1-like F-box domain found in Arabidopsis thaliana transport inhibitor response 1 protein (TIR1), coronatine-insensitive protein 1 (COI1) and similar proteins. TIR1, also called F-box/LRR-repeat protein 1 (FBL1), is part of an SCF (SKP1-cullin-F-box) protein ligase complex that promotes the ubiquitin-dependent proteolysis of a family of transcriptional regulators known as Aux/IAAs in an auxin-dependent manner. TIR1 is an auxin receptor that plays a potential role in plant hormone signaling. COI1, also called F-box/LRR-repeat protein 2 (FBL2), is the substrate-recruiting module of an SCF ubiquitin E3 ligase complex. It mediates jasmonate signalling by promoting hormone-dependent ubiquitylation and degradation of transcriptional repressor JASMONATE ZIM-domain (JAZ) family proteins. This subfamily also includes Arabidopsis thaliana EIN3-binding F-box protein 1 (EBF1). EBF1, also called F-box/LRR-repeat protein 6 (FBL6), is a component of the SCF(EBF1) E3 ubiquitin ligase complex, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins (probably including EIN3 and EIL1). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 40 matched cddid_all.tbl CDD cd22160 cd22160 438931 F-box_AtFBL13-like F-box domain found in Arabidopsis thaliana F-box/LRR-repeat protein 13 (AtARP13), 25 (AtARP25) and similar proteins. AtARP13 and AtARP25 belong to the largest subfamily of plant F-box proteins, F-box/LRR-repeat protein (FBLs). It contains tandem leucine-rich repeats (LRRs). Like other F-box proteins, they may be components of SCF (Skp1 Cdc53 F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 36 matched cddid_all.tbl CDD cd22161 cd22161 438932 F-box_AtSKP2-like F-box domain found in Arabidopsis thaliana SKP2-like proteins (AtSKP2A and AtSKP2B) and similar proteins. AtSKP2A, also called FBL5-like protein (AtFBL5), is an F-box protein that regulates cell division and is degraded via the ubiquitin pathway. It acts as an auxin receptor. AtSKP2B, also called F-box/LRR-repeat protein 5 (AtFB5), is an F-box protein that does not interact with auxin. Both AtSKP2A and AtSKP2B are components of SCF(SKP2A/SKP2B) E3 ubiquitin ligase complexes, which mediate the ubiquitination and subsequent proteasomal degradation of target proteins (including cell cycle repressors). AtSKP2A regulates the stability of the transcription factors E2FC and DPB, repressors of cell proliferation. It confers increased tolerance to osmotic stress by promoting cell division, especially in meristems and promotes the formation of lateral root primordia. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 48 matched cddid_all.tbl CDD cd22162 cd22162 438933 F-box_AtSKIP3-like F-box domain found in Arabidopsis thaliana SKP1-interacting partner 3 (AtSKIP3) and similar proteins. AtSKIP3, also called F-box protein SKIP3, F-box protein PP2-B9, or protein PHLOEM PROTEIN 2-LIKE B9, is a component of SCF (SKP1-cullin-F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. It interacts with SKP1A/ASK1. This subfamily also includes many other Arabidopsis thaliana protein PHLOEM PROTEIN 2-LIKE proteins. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 46 matched cddid_all.tbl CDD cd22163 cd22163 438934 F-box_AtSKIP5-like F-box domain found in Arabidopsis thaliana SKP1-interacting partner 5 (AtSKIP5) and similar proteins. AtSKIP5, also called F-box protein SKIP5, is a component of SCF (SKP1-cullin-F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. It interacts with SKP1A/ASK1. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 46 matched cddid_all.tbl CDD cd22164 cd22164 438935 F-box_AtSKIP19-like F-box domain found in Arabidopsis thaliana SKP1-interacting partner 19 (AtSKIP19) and similar proteins. AtSKIP19, also called F-box protein SKIP19, or F-box/LRR-repeat protein 20 (FBL20), is a component of SCF (SPK1/ASK-cullin-F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. It interacts with CUL1 and SPK1B/ASK2. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 47 matched cddid_all.tbl CDD cd22165 cd22165 438936 F-box_AtSKIP22-like F-box domain found in Arabidopsis thaliana SKP1-interacting partner 22 (AtSKIP22) and similar proteins. AtSKIP22, also called F-box protein SKIP22, is a component of SCF (SKP1/ASK-cullin-F-box protein) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. It interacts with SKP1A/ASK1 and SPK1B/ASK2. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 46 matched cddid_all.tbl CDD cd22166 cd22166 438937 F-box_AtSKIP31-like F-box domain found in Arabidopsis thaliana SKP1-interacting partner 31 (AtSKIP31) and similar proteins. AtSKIP31, also called F-box protein SKIP31, is a component of SCF(ASK-cullin-F-box) E3 ubiquitin ligase complexes, which may mediate the ubiquitination and subsequent proteasomal degradation of target proteins. It interacts with SKP1A/ASK1 and SPK1B/ASK2. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 46 matched cddid_all.tbl CDD cd22167 cd22167 438938 F-box_FBXO2 F-box domain found in F-box only protein 2 (FBXO2) and similar proteins. FBXO2, also called FBX2, is a neuron-specific substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex that mediates the ubiquitination and subsequent proteasomal degradation of target proteins. It binds specifically to proteins attached with N-linked high-mannose type oligosaccharides, and subsequently contributes to ubiquitination of glycoproteins. FBXO2 regulates amyloid precursor protein (APP) levels and processing in the brain, and may play a role in modulating Alzheimer disease (AD) pathogenesis. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 72 matched cddid_all.tbl CDD cd22168 cd22168 438939 F-box_FBXO6-like F-box domain found in F-box only proteins FBXO6, FBXO44 and similar proteins. This subfamily includes FBXO6 and FBXO44. FBXO6, also called FBX6, F-box protein that recognizes sugar chains 2 (FBS2), or F-box/G-domain protein 2 (FBG2), is a substrate-recognition component of SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complexes. It is involved in the endoplasmic reticulum-associated degradation pathway (ERAD) for misfolded lumenal proteins, by recognizing and binding sugar chains on unfolded glycoproteins that are retro-translocated into the cytosol and promoting their ubiquitination and subsequent degradation. FBXO6 can recognize and bind denatured glycoproteins, which are modified with not only high-mannose but also complex-type oligosaccharides. It also recognizes sulfated glycans. FBXO6 is involved in DNA damage response by specifically recognizing activated CHEK1 (phosphorylated on 'Ser-345'), promoting its ubiquitination and degradation. FBXO44, also called FBXO6A, FBX44, or F-box/G-domain protein 3 (FBG3), is a substrate-recognition component of an SCF-type E3 ubiquitin ligase complex. It interacts with SKP1 and CUL1. FBXO44 mediates BRCA1 ubiquitination and degradation. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 82 matched cddid_all.tbl CDD cd22169 cd22169 438940 F-box_FBXO17-like F-box domain found in F-box only protein 17 (FBXO17), F-box only protein 27 (FBXO27) and similar proteins. This subfamily includes FBXO17 and FBXO27. FBXO17 is also called FBX17, F-box only protein 26 (FBX26/FBXO26), or FBG4, while FBXO27 is also called FBX27, or F-box/G-domain protein 5. FBXO17 and FBXO27 are the substrate-recognition components of SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complexes. They can recognize and bind denatured glycoproteins, which are modified with complex-type oligosaccharides. FBXO17 also recognizes sulfated glycans but does not bind high-mannose glycoproteins. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 48 matched cddid_all.tbl CDD cd22170 cd22170 438941 F-box_FBXO5 F-box domain found in F-box only protein 5 (FBXO5) and similar proteins. FBXO5, also called FBX5, or early mitotic inhibitor 1 (EMI1), acts as a regulator that inhibits the anaphase-promoting complex/cyclosome (APC/C), which controls cell cycle progression through the sequential degradation of various substrates from S phase to early mitosis. During mitotic cell cycle, it plays a role as both substrate and inhibitor of the APC-FZR1 complex. During G1 phase, it plays a role as substrate of the APC-FZR1 complex E3 ligase. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 49 matched cddid_all.tbl CDD cd22171 cd22171 438942 F-box_FBXO43 F-box domain found in F-box only protein 43 (FBXO43) and similar proteins. FBXO43, also called FBX43, or endogenous meiotic inhibitor 2 (EMI2), plays a key role during the meiotic cell cycle. It is required to establish and maintain the arrest of oocytes at the second meiotic metaphase until fertilization. It probably acts by inhibiting the anaphase-promoting complex/cyclosome (APC/C) ubiquitin ligase. It may recognize and bind to some phosphorylated proteins and promote their ubiquitination and degradation. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 49 matched cddid_all.tbl CDD cd22172 cd22172 438943 F-box_FBXO16 F-box domain found in F-box only protein 16 (FBXO16) and similar proteins. FBXO16, also called FBX16, is part of an SCF (SKP1-cullin-F-box) protein ligase complex. It probably recognizes and binds to some phosphorylated proteins and promotes their ubiquitination and degradation. It functions as a tumor suppressor by attenuating nuclear beta-catenin function. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 55 matched cddid_all.tbl CDD cd22173 cd22173 438944 F-box_ECT2L F-box domain found in epithelial cell-transforming sequence 2 oncogene-like (ECT2L) and similar proteins. ECT2L, also called lung-specific F-box and DH domain-containing protein, or putative guanine nucleotide exchange factor LFDH, may act as a guanine nucleotide exchange factor (GEF). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 52 matched cddid_all.tbl CDD cd22174 cd22174 438945 F-box_FBXO30 F-box domain found in F-box only protein 30 (FBXO30) and similar proteins. FBXO30, also called FBX30, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It is required for muscle atrophy following denervation. FBXO30 regulates mammopoiesis by targeting the bipolar mitotic kinesin Eg5. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 49 matched cddid_all.tbl CDD cd22175 cd22175 438946 F-box_FBXO40 F-box domain found in F-box only protein 40 (FBXO40) and similar proteins. FBXO40, also called FBX40, or muscle disease-related protein, is a probable substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex that may function in myogenesis. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 49 matched cddid_all.tbl CDD cd22176 cd22176 438947 F-box_FBXO34 F-box domain found in F-box only protein 34 (FBXO34) and similar proteins. FBXO34, also called FBX34, likely functions as the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 48 matched cddid_all.tbl CDD cd22177 cd22177 438948 F-box_FBXO46 F-box domain found in F-box only protein 46 (FBXO46) and similar proteins. FBXO46, also called FBX46, or F-box only protein 34-like, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex that mediates degradation of the tumor suppressor FBXO31 and thereby prevents premature cellular senescence. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 47 matched cddid_all.tbl CDD cd22178 cd22178 438949 F-box_FBXL3 F-box domain found in F-box/LRR-repeat protein 3 (FBXL3) and similar proteins. FBXL3, also called F-box and leucine-rich repeat protein 3A, or F-box/LRR-repeat protein 3A, is the substrate-recognition component of the SCF(FBXL3) E3 ubiquitin ligase complex that mainly acts in the nucleus and mediates ubiquitination and subsequent degradation of CRY1 and CRY2, and thus, is involved in circadian rhythm function. It plays a key role in the maintenance of both the speed and the robustness of the circadian clock oscillation. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 43 matched cddid_all.tbl CDD cd22179 cd22179 438950 F-box_FBXL21 F-box domain found in F-box/LRR-repeat protein 21 (FBXL21) and similar proteins. FBXL21, also called F-box and leucine-rich repeat protein 21, F-box and leucine-rich repeat protein 3B (FBXL3B), or F-box/LRR-repeat protein 3B, is the substrate-recognition component of the SCF(FBXL21) E3 ubiquitin ligase complex that mainly acts in the cytosol and mediates ubiquitination of CRY proteins (CRY1 and CRY2), leading to CRY protein stabilization, and thus, is involved in circadian rhythm function. It regulates the oscillation of the circadian clock through ubiquitination and stabilization of cryptochromes. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 43 matched cddid_all.tbl CDD cd22180 cd22180 438951 F-box_FBXL10 F-box domain found in F-box/LRR-repeat protein 10 (FBXL10) and similar proteins. FBXL10 is also called lysine-specific demethylase 2B (KDM2B), CXXC-type zinc finger protein 2 (CXXC2), F-box and leucine-rich repeat protein 10, F-box protein FBL10, JmjC domain-containing histone demethylation protein 1B (JHDM1B), Jumonji domain-containing EMSY-interactor methyltransferase motif protein, protein JEMMA, protein-containing CXXC domain 2, [Histone-H3]-lysine-36 demethylase 1B, or NDY1. It is a histone demethylase that catalyzes the demethylation of H3K4me3 and H3K36me2, thereby playing a central role in the histone code. It preferentially binds the transcribed region of ribosomal RNA and represses the transcription of ribosomal RNA genes which inhibits cell growth and proliferation. FBXL10 may also serve as the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 45 matched cddid_all.tbl CDD cd22181 cd22181 438952 F-box_FBXL11 F-box domain found in F-box/LRR-repeat protein 11 (FBXL11) and similar proteins. FBXL11, also called lysine-specific demethylase 2A (KDM2A), CXXC-type zinc finger protein (CXXC8), F-box and leucine-rich repeat protein 11, F-box protein FBL7, F-box protein Lilina, JmjC domain-containing histone demethylation protein 1A (JHDM1A), or [Histone-H3]-lysine-36 demethylase 1A, is a histone H3 lysine 36 (H3K36) demethylase that regulates epithelial mesenchymal transition (EMT) and the metastasis of ovarian cancer. It plays an essential role in embryonic development and homeostasis by regulating cell proliferation and survival. FBXL11 may also recognize and bind to some phosphorylated proteins and promote their ubiquitination and degradation. It associates with centromeres and represses transcription of small non-coding RNAs that are encoded by the clusters of satellite repeats at the centromere. It is required to sustain centromeric integrity and genomic stability, particularly during mitosis. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 47 matched cddid_all.tbl CDD cd22182 cd22182 438953 F-box_FBXW1A F-box domain found in F-box/WD repeat-containing protein 1A (FBXW1A) and similar proteins. FBXW1A, also called E3RSIkappaB, epididymis tissue protein Li 2a, F-box and WD repeats protein beta-TrCP, or pIkappaBalpha-E3 receptor subunit, is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins, such as CTNNB1, NFKBIA, NFKBIB and NFKBIE, as well as phosphorylated NFKB1, ATF4, CDC25A, DLG1, FBXO5, PER1, SMAD3, SMAD4, SNAI1 and probably NFKB2. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 60 matched cddid_all.tbl CDD cd22183 cd22183 438954 F-box_FBXW1B F-box domain found in F-box/WD repeat-containing protein 1B (FBXW1B) and similar proteins. FBXW1B, also called F-box/WD repeat-containing protein 11 (FBXW11), F-box and WD repeats protein beta-TrCP2, or homologous to Slimb protein (HOS), is the substrate-recognition component of an SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins, such as IFNAR1, CEP68 and CDC25A, as well as phosphorylated CTNNB1, NFKBIA, PER1 and PER2. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 51 matched cddid_all.tbl CDD cd22184 cd22184 409195 Af2093-like Archaeaoglobus fulgidus Af2093 and similar proteins. This family represents the uncharacterized protein Af2093, which has no known function. The three-dimensional fold of this protein family resembles that of PDDEXK nucleases, but it lacks the typical catalytic site. 245 matched cddid_all.tbl CDD cd22185 cd22185 409225 WH2_hVASP-like Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) of human Vasodilator-stimulated phosphoprotein and related proteins. This family contains the Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) of Ena/VASP family members including Protein enabled homolog (also known as Mena, mammalian enabled), VASP (vasodilator-stimulated phosphoprotein) and EVL (Ena-VASP-like or Enabled VASP or Ena/VASP). These are actin-associated proteins involved in a range of processes dependent on cytoskeleton remodeling and cell polarity such as axon guidance and lamellipodial and filopodial dynamics in migrating cells, platelet activation and cell migration. Ena/VASP proteins processively elongate F-actin barbed ends, promoting dissociation of barbed end assembly antagonists (uncapping). WH2 domains are small, widespread intrinsically disordered actin-binding peptides displaying significant sequence variability and different regulations of actin self-assembly in motile and morphogenetic processes. WH2 domains are identified by a central consensus actin-binding motif LKKT/V flanked by variable N-terminal and C-terminal extensions. 27 matched cddid_all.tbl CDD cd22186 cd22186 409226 WH2_Spire1-2_r3 third tandem Wiskott-Aldrich Syndrome Homology (WASP) region 2 (WH2 motif) repeat of protein Spire homologs 1 and 2. This family contains the third tandem Wiskott-Aldrich syndrome protein (WASP)-homology domain 2 (WH2) domain in human Spire family protein Spire-1 (also called Spir1) and Spire-2 (Spir2) and related proteins. Spire is an actin nucleator essential for establishing an actin mesh during oogenesis. It was first identified as a Drosophila maternal effect gene essential to establishment of both the anterior/posterior and dorsal/ventral body axes in developing oocytes and embryos. It has been found to sever filaments and sequester monomers in addition to nucleating new filaments; it remains associated with the slow-growing pointed end of the new filament. Spire is involved in intracellular vesicle transport along actin fibers, providing a novel link between actin cytoskeleton dynamics and intracellular transport. It is required for asymmetric spindle positioning and asymmetric cell division during oocyte meiosis. Spire contains four tandem WH2 domains. The mammalian genome encodes two Spire proteins, namely Spire-1 (Spir1) and Spire-2 (Spir2). This model contains WH2 domain 3 of human Spire-1 and Spire-2 . Major expression of both spire genes have been detected during embryogenesis in the developing nervous system). In addition, spire1 expression is found in the fetal liver, while spire2 expression is seen in early stages of intestinal development. In adult tissues, the spire2 gene shows a rather broad expression pattern, which includes the epithelial cells of the digestive tract, testical spermatocytes, and neuronal cells of the nervous system. In contrast, spire1 is mainly expressed in neuronal cells of the nervous system. Minor expression levels were detected in testis and spleen. Spire also acts in the nucleus where, together with Spire-1 and Spire-2, it promotes assembly of nuclear actin filaments in response to DNA damage in order to facilitate movement of chromatin and repair factors after DNA damage. High levels of spire1 expression are restricted to the nervous system, oocytes, and testis. Since function of Spire-1 and Spire-2 in oocyte maturation is redundant, spire1 mutant mice are fertile, overall brain anatomy is not altered, and visual and motor functions remain normal; however, detailed behavioral studies of the spire1 mutant mice unveiled a very specific and highly significant phenotype in terms of fear learning in male mice. 23 matched cddid_all.tbl CDD cd22187 cd22187 409194 asqI-like protein asqI and similar proteins. This family includes Aspergillus nidulans tyrosinase family protein asqI (aspoquinolone biosynthesis protein I) that is part of the gene cluster that mediates the biosynthesis of the aspoquinolone mycotoxins. 322 matched cddid_all.tbl CDD cd22188 cd22188 409192 arch-AMO_C-like subunit C of ammonia monooxygenase (AMO) from ammonia-oxidizing archaea, and related proteins. This model contains the subunit C of ammonia monooxygenase (AMO, EC 1.14.99.39) from ammonia-oxidizing archaea including Nitrososphaera viennensis gen. nov., sp. nov (also called Nitrososphaera viennensis EN76) that contains six variants (AmoC1-AmoC6) encoded by different genes. AMO catalyzes the conversion of ammonia to hydroxylamine. Nitrososphaera viennensis EN76 AMO is composed of four subunits: AmoA, AmoB, AmoX, and one of six variants of AmoC. The AMO subunit C belongs to a family which also includes subunit C of particulate methane monooxygenase (pMMO, also known as membrane-bound MMO, EC 1.14.18.3) from methanotrophic bacteria, and AMO from ammonia-oxidizing bacteria, which are not included in this model. Compared to its bacterial counterpart, archaeal AMO C subunit is significantly shorter at the N-terminal end. 181 matched cddid_all.tbl CDD cd22189 cd22189 409190 PGAP4-like_fungal uncharacterized fungal proteins similar to Post-GPI attachment to proteins factor 4. This subfamily contains uncharacterized fungal proteins with similarity to animal post-GPI attachment to proteins factor 4 (PGAP4), also known as post-GPI attachment to proteins GalNAc transferase 4 or transmembrane protein 246 (TMEM246). PGAP4 has been shown to be a Golgi-resident GPI-GalNAc transferase. Many eukaryotic proteins are anchored to the cell surface through glycolipid glycosylphosphatidylinositol (GPI). GPIs have a conserved core but exhibit diverse N-acetylgalactosamine (GalNAc) modifications. PGAP4 knockout cells lose GPI-GalNAc structures. PGAP4 is most likely involved in the initial steps of GPI-GalNAc biosynthesis. In contrast to other Golgi glycotransferases, it contains three transmembrane domains. Proteins from this subfamily contain the putative catalytic site of PGAP4 and may have similar activities. 375 matched cddid_all.tbl CDD cd22190 cd22190 409191 PGAP4 Post-GPI attachment to proteins factor 4. Post-GPI attachment to proteins factor 4 (PGAP4), also known as post-GPI attachment to proteins GalNAc transferase 4 or transmembrane protein 246 (TMEM246), has been shown to be a Golgi-resident GPI-GalNAc transferase. Many eukaryotic proteins are anchored to the cell surface through glycolipid glycosylphosphatidylinositol (GPI). GPIs have a conserved core but exhibit diverse N-acetylgalactosamine (GalNAc) modifications. PGAP4 knockout cells lose GPI-GalNAc structures. PGAP4 is most likely involved in the initial steps of GPI-GalNAc biosynthesis. In contrast to other Golgi glycotransferases (GTs), it contains three transmembrane domains. Structural modeling suggests that PGAP4 adopts a GT-A fold split by an insertion of tandem transmembrane domains. 379 matched cddid_all.tbl CDD cd22191 cd22191 439247 DPBB_RlpA_EXP_N-like double-psi beta-barrel fold of RlpA, N-terminal domain of expansins, and similar domains. The double-psi beta-barrel (DPBB) fold is found in a divergent group of proteins, including endolytic peptidoglycan transglycosylase RlpA (rare lipoprotein A), EG45-like domain containing proteins, kiwellins, Streptomyces papain inhibitor (SPI), the N-terminal domain of plant and bacterial expansins, GH45 family of endoglucanases, barwins, cerato-platanins, membrane-bound lytic murein transglycosylase A (MltA) and YuiC-like proteins. RlpA may work in tandem with amidases to degrade peptidoglycan (PG) in the division septum and lateral wall to facilitate daughter cell separation. An EG45-like domain containing protein from Arabidopsis thaliana, called plant natriuretic peptide A (AtPNP-A), functions in cell volume regulation. Kiwellin proteins comprise a widespread family of plant-defense proteins that target pathogenic bacterial/fungal effectors that down-regulate plant defense responses. SPI is a stress protein produced under hyperthermal stress conditions that serves as a glutamine and lysine donor substrate for microbial transglutaminase (MTG, EC 2.3.2.13) from Streptomycetes. Some expansin family proteins display cell wall loosening activity and are involved in cell expansion and other developmental events during which cell wall modification occurs. Endoglucanases (EC 3.2.1.4) catalyze the endohydrolysis of (1-4)-beta-D-glucosidic linkages in cellulose, lichenin, and cereal beta-D-glucans. Animal cellulases, such as endoglucanase EG27II, have great potential for industrial applications such as bioethanol production. Barwin is a basic protein from barley seed. It is a probable plant lectin that may be involved in a defense mechanism. Cerato-platanin is a phytotoxin which causes production of phytoalexin in platanus acerifolia, platanus occidentalis, and platanus orientalis. It also induces cell necrosis. MltA, also called murein hydrolase A, is a murein-degrading enzyme that may play a role in recycling of muropeptides during cell elongation and/or cell division. It degrades murein glycan strands and insoluble, high-molecular weight murein sacculi. YuiC is a Firmicute stationary phase survival (Sps) protein. 92 matched cddid_all.tbl CDD cd22192 cd22192 411976 TRPV5-6 Transient Receptor Potential channel, Vanilloid subfamily (TRPV), types 5 and 6. TRPV5 and TRPV6 (TRPV5/6) are two homologous members within the vanilloid subfamily of the transient receptor potential (TRP) family. TRPV5 and TRPV6 show only 30-40% homology with other members of the TRP family and have unique properties that differentiates them from other TRP channels. They mediate calcium uptake in epithelia and their expression is dramatically increased in numerous types of cancer. The structure of TRPV5/6 shows the typical topology features of all TRP family members, such as six transmembrane regions, a short hydrophobic stretch between transmembrane segments 5 and 6, which is predicted to form the Ca2+ pore, and large intracellular N- and C-terminal domains. The N-terminal domain of TRPV5/6 contains three ankyrin repeats. This structural element is present in several proteins and plays a role in protein-protein interactions. The N- and C-terminal tails of TRPV5/6 each contain an internal PDZ motif which can function as part of a molecular scaffold via interaction with PDZ-domain containing proteins. A major difference between the properties of TRPV5 and TRPV6 is in their tissue distribution: TRPV5 is predominantly expressed in the distal convoluted tubules (DCT) and connecting tubules (CNT) of the kidney, with limited expression in extrarenal tissues. In contrast, TRPV6 has a broader expression pattern such as expression in the intestine, kidney, placenta, epididymis, exocrine tissues, and a few other tissues. 609 matched cddid_all.tbl CDD cd22193 cd22193 411977 TRPV1-4 Transient Receptor Potential channel, Vanilloid subfamily (TRPV), types 1-4. TRPV1-4 are thermo-sensing channels that function directly in temperature-sensing and nociception; they share substantial structural and functional properties. Transient Receptor Potential (TRP) ion channels activated by temperature (thermo TRPs) are important molecular players in acute, inflammatory, and chronic pain states. So far, 11 TRP channels in mammalian cells have been identified as thermosensitive TRP (thermo-TRP) channels. TRPV1-4 channels are activated by different heat temperatures, for example, TRPV1 and TRPV2 are activated by high temperatures (>43C and >55C, respectively). TRPV1-4 belong to the vanilloid TRP subfamily (TRPV), named after the founding member vanilloid receptor 1 (TRPV1). The structure of TRPV shows the typical topology features of all TRP ion channel family members, such as six transmembrane regions, a short hydrophobic stretch between transmembrane segments 5 and 6 and large intracellular N- and C-terminal domains. 607 matched cddid_all.tbl CDD cd22194 cd22194 411978 TRPV3 Transient Receptor Potential channel, Vanilloid subfamily (TRPV), type 3. TRPV3 is a temperature-sensitive Transient Receptor Potential (TRP) ion channel that is activated by warm temperatures, synthetic small-molecule chemicals, and natural compounds from plants. TRPV3 function is regulated by physiological factors such as extracellular divalent cations and acidic pH, intracellular adenosine triphosphate, membrane voltage, and arachidonic acid. It is expressed in both neuronal and non-neuronal tissues including epidermal keratinocytes, epithelial cells in the gut, endothelial cells in blood vessels, and neurons in dorsal root ganglia and CNS. TRPV3 null mice have abnormal hair morphogenesis and compromised skin barrier function. It may play roles in inflammatory skin disorders, such as itch and pain sensation. TRPV3 is also expressed by many neuronal and non-neuronal tissues, showing that TRPV3 might play roles in other unknown cellular and physiological functions. TRPV3 belongs to the vanilloid TRP subfamily (TRPV), named after the founding member vanilloid receptor 1 (TRPV1). The structure of TRPV shows the typical topology features of all TRP ion channel family members, such as six transmembrane regions, a short hydrophobic stretch between transmembrane segments 5 and 6 and large intracellular N- and C-terminal domains. 680 matched cddid_all.tbl CDD cd22195 cd22195 411979 TRPV4 Transient Receptor Potential channel, Vanilloid subfamily (TRPV), type 4. TRPV4 is expressed broadly in neuronal and non-neuronal cells. It is activated by various stimuli, including hypo-osmolarity, warm temperature, and chemical ligands. TRPV4 acts in physiological functions such as osmoregulation and thermoregulation. It also has a role in mechanosensation in the vascular endothelium and urinary tract, and in cell barrier formation in vascular and epidermal tissues. Knockout mice studies suggested the functional importance of TRPV4 in the central nervous system, nociception, and bone formation. TRPV4 belongs to the vanilloid TRP subfamily (TRPV), named after the founding member vanilloid receptor 1 (TRPV1). The structure of TRPV shows the typical topology features of all Transient Receptor Potential (TRP) ion channel family members, such as six transmembrane regions, a short hydrophobic stretch between transmembrane segments 5 and 6 and large intracellular N- and C-terminal domains. 733 matched cddid_all.tbl CDD cd22196 cd22196 411980 TRPV1 Transient Receptor Potential channel, Vanilloid subfamily (TRPV), type 1. Vanilloid receptor 1 (TRPV1), a capsaicin (vanilloid) receptor, is the founding member of the vanilloid TRP subfamily (TRPV). In humans, it is expressed in the brain, kidney, pancreas, testis, uterus, spleen, stomach, small intestine, lung and liver. TRPV1 has been implicated to have function in thermo-sensation (heat), autonomic thermoregulation, nociception, food intake regulation, and multiple functions in the gastrointestinal (GI) tract. The receptor has also been involved in growth cone guidance, long-term depression, endocannabinoid signaling and osmosensing in the central nervous system. TRPV1 is up regulated in several human pathological conditions including vulvodynia, GI inflammation, Crohn's disease and ulcerative colitis. TRPV1 knock-out mice exhibit impaired sensation to thermal-mechanical acute pain. The structure of TRPV shows the typical topology features of all Transient Receptor Potential (TRP) ion channel family members, such as six transmembrane regions, a short hydrophobic stretch between transmembrane segments 5 and 6 and large intracellular N- and C-terminal domains. 649 matched cddid_all.tbl CDD cd22197 cd22197 411981 TRPV2 Transient Receptor Potential channel, Vanilloid subfamily (TRPV), type 2. TRPV2 is closely related to TRPV1, sharing high sequence identity (>50%), but TRPV2 shows a higher temperature threshold and sensitivity for activation than TRPV1. TRPV2 can be stimulated by ligands or lipids, and is involved in osmosensation and mechanosensation. TRPV2 is expressed in both neuronal and non-neuronal tissues, and it has been implicated in diverse physiological and pathophysiological processes, including cardiac-structure maintenance, innate immunity, and cancer. TRPV2 belongs to the vanilloid TRP subfamily (TRPV), named after the founding member vanilloid receptor 1 (TRPV1). The structure of TRPV shows the typical topology features of all Transient Receptor Potential (TRP) ion channel family members, such as six transmembrane regions, a short hydrophobic stretch between transmembrane segments 5 and 6 and large intracellular N- and C-terminal domains. 640 matched cddid_all.tbl CDD cd22198 cd22198 409188 CH_MICAL_EHBP-like calponin homology (CH) domain found in the MICAL and EHBP families. This group is composed of the molecule interacting with CasL protein (MICAL) and EH domain-binding protein (EHBP) families. MICAL is a large, multidomain, cytosolic protein with a single LIM domain, a calponin homology (CH) domain and a flavoprotein monooxygenase (MO) domain. In Drosophila, MICAL is expressed in axons, interacts with the neuronal A (PlexA) receptor and is required for Semaphorin 1a (Sema-1a)-PlexA-mediated repulsive axon guidance. The LIM and CH domains mediate interactions with the cytoskeleton, cytoskeletal adaptor proteins, and other signaling proteins. The flavoprotein MO is required for semaphorin-plexin repulsive axon guidance during axonal pathfinding in the Drosophila neuromuscular system. The EHBP family includes EHBP1 and EHBP1-like protein (EHBP1L1). EHBP1 is a regulator of endocytic recycling and may play a role in actin reorganization by linking clathrin-mediated endocytosis to the actin cytoskeleton. It may act as an effector of small GTPases, including RAB-10 (Rab10), and play a role in vesicle trafficking. EHBP proteins contain a single CH domain. CH domains are actin filament (F-actin) binding motifs. 105 matched cddid_all.tbl CDD cd22199 cd22199 439321 AcrVA4 Anti-CRISPR type V subtype A4. AcrVA4 is an anti-CRISPR (Acr) protein that was discovered via STSS (self-targeting spacers search) with further functional TXTL (cell-free transcription-translation) assay. The bioinformatic STSS method finds self-targeting CRISPR spacers in genomic DNA, predicts the type of CRISPR system involved, and obtains information about the targeted sequence. AcrVA4 block Cas12a activity; it inhibits recognition of double-stranded DNA (dsDNA), and drives dimerization of Cas12a. Cas12a (Cpf1) is a class 2 effector protein for the AcrVA subfamily that has high efficiency in genome editing. It possesses a single nuclease domain (RuvC) that is activated upon binding of the crRNA targeting sequence (or spacer) to a complementary single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) target molecule. In addition to gene editing, CRISPR-Cas12a has repurposed, in high eukaryotes, to carry out transcription regulation via a nuclease-dead Cas12a (dCas12a), AcrVAs were adopted to regulate (d)Cas12a activity; AcrVA4 is able to inhibit a dCas12a protein (dLbCas12a) in Saccharomyces cerevisiae. Type V systems fundamentally differ from type II by the domain architecture of their effector proteins. The type II effectors (Cas9) contain two nuclease domains that are each responsible for the cleavage of one strand of the target DNA, with the HNH nuclease inserted inside the RuvC-like nuclease domain sequence. By contrast, the type V effectors (Cas12) only contain a RuvC-like domain that cleaves both strands. Acr proteins have co-evolved with CRISPR-Cas proteins to provide bacteriophage with broad spectrum, or in some cases, highly selective protection from RNA-guided destruction. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Acr proteins are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 118 matched cddid_all.tbl CDD cd22200 cd22200 412062 NRDE2_MID MTR4-interacting domain (MID) found in nuclear exosome regulator NRDE2 and similar proteins. NRDE2 is a protein of the nuclear speckles that regulates RNA degradation and export from the nucleus through its interaction with MTREX, an essential factor directing various RNAs to exosomal degradation. NRDE2 negatively regulates exosome functions by inhibiting the RNA helicase MTR4 recruitment and exosome interaction. This model corresponds to the N-terminal MTR4-interacting domain (MID) of NRDE2. 99 matched cddid_all.tbl CDD cd22201 cd22201 412063 cubilin_NTD N-terminal domain of cubilin and similar proteins. Cubilin (CUBN, also called 460 kDa receptor, intestinal intrinsic factor receptor, intrinsic factor-cobalamin receptor, or intrinsic factor-vitamin B12 receptor) is an endocytic receptor which plays a role in lipoprotein, vitamin and iron metabolism by facilitating their uptake. It acts together with the 45-kDa transmembrane protein amnionless (AMN) to mediate endocytosis of the cobalamin (vitamin B12) binding intrinsic factor (CBLIF)-cobalamin complex. This model corresponds to the N-terminal domain of cubilin, which is responsible for the interaction with AMN. The cubilin interface with AMN is formed by the N-terminal strands of three cubilin chains. 129 matched cddid_all.tbl CDD cd22204 cd22204 409026 H1_KCTD12-like H1 domain found in potassium channel tetramerization domain-containing proteins. The H1 domain is found in potassium channel tetramerization domain-containing proteins such as KCTD8, KCTD12 (also called predominantly fetal expressed T1 domain/Pfetin), KCTD12b, and KCTD16. They serve as auxiliary gamma-aminobutyric acid type B (GABA-B) receptor subunits that constitute receptor subtypes with distinct functional properties. KCTD12 and -12b generate desensitizing receptor responses while KCTD8 and -16 generate largely non-desensitizing receptor responses. They control GABA-B signaling and regulate the rise time and duration of G protein-coupled inwardly rectifying potassium (GIRK) currents, as well as enhance receptor expression levels. KCTD12 regulates agonist potency and kinetics of GABA-B receptor signaling. It promotes tumorigenesis by facilitating CDC25B/CDK1/Aurora A-dependent G2/M transition. KCTD16 interacts with amyloid beta precursor protein (APP), a type I transmembrane protein involved in a variety of cellular processes such as cell adhesion and axon guidance. Members of this family consist of an N-terminal BTB domain followed by a region called the H1 domain. The BTB domain mediates interaction with the receptor. The C-terminal H1 domain, which possesses a beta-propeller-like fold, engages in interactions with G-protein beta-gamma subunits and is responsible for desensitization. This model corresponds to the H1 domain. 118 matched cddid_all.tbl CDD cd22207 cd22207 412064 pseudoGTPaseD_p190RhoGAP pseudoGTPase domain found in the family of p190RhoGAP. This family includes two p190RhoGAP proteins, A and B, which are Rho family GTPase-activating proteins (GAPs) that act as key regulators of Rho GTPase signaling and are essential for actin cytoskeletal structure and contractility. Rho family is one of five Ras superfamily subgroups (Ras, Rho, Rab, Ran and Arf). Each contains five highly conserved sequence motifs, termed 'G-motifs', required for nucleotide-binding and catalytic activity. PseudoGTPases consist of a GTPase fold lacking one or more of these G motifs. This model corresponds to the GTPase-like domain called pseudoGTPase domain that is located at the middle region of p190RhoGAP proteins. 166 matched cddid_all.tbl CDD cd22209 cd22209 412067 EMC10 ER membrane protein complex subunit 10 and similar proteins. Endoplasmic reticulum (ER) membrane protein complex subunit 10 (EMC10), also called hematopoietic signal peptide-containing membrane domain-containing protein 1 (HSM1) or INM02, is a bone marrow-derived angiogenic growth factor promoting angiogenesis and tissue repair in the heart after myocardial infarction. It stimulates cardiac endothelial cell migration and outgrowth via the activation of p38 MAPK, PAK, and MAPK2 signaling pathways. Yeast EMC10 is a non-essential component of the ER membrane protein complex (EMC), which may be involved in ER-associated degradation (ERAD) and proper assembly of multi-pass transmembrane proteins. 141 matched cddid_all.tbl CDD cd22210 cd22210 408999 HD_XRCC4-like_N N-terminal head domain found in the XRCC4 superfamily of proteins. The XRCC4 superfamily includes five families: XRCC4, XLF, PAXX, SAS6 and CCDC61. XRCC4 (X-ray repair cross-complementing protein 4), XLF (XRCC4-like factor) and PAXX (paralog of XRCC4 and XLF) play crucial roles in the non-homologous end-joining (NHEJ) DNA repair pathway. SAS6 (spindle assembly abnormal protein 6) and CCDC61 (coiled-coil domain-containing protein 61) have a centrosomal/centriolar function. Members of this superfamily have an N-terminal globular head domain, a centrally located coiled-coil, and a C-terminal low-complexity region. They form homodimers through two homodimerization domains: an N-terminal globular head domain and a parallel coiled-coil domain. In addition, some members such as XRCC4 and XLF form symmetric heterodimers that interact through their globular head domains at the opposite end of the homodimer interface, and may form XLF-XRCC4 filaments. This model corresponds to the N-terminal head domain of XRCC4 superfamily proteins. 115 matched cddid_all.tbl CDD cd22211 cd22211 411792 HkD_SF Hook domain-containing proteins superfamily. The Hook domain superfamily includes Hook adaptor proteins, Hook-related proteins and nuclear mitotic apparatus protein (NuMA). They share an N-terminal conserved globular Hook domain, which folds as a variant of the helical calponin homology (CH) domain with an extended alpha-helix. The Hook domain is responsible for the binding of microtubule. The Hook family includes microtubule-binding proteins, Hook1-3. Hook1 is required for spermatid differentiation. Hook2 contributes to the establishment and maintenance of centrosome function. Hook3 is an adaptor protein for microtubule-dependent intracellular vesicle and protein trafficking, and is involved in Golgi and endosome transport. Hook proteins are components of the FTS/Hook/FHIP complex (FHF complex), which may function to promote vesicle trafficking and/or fusion via the homotypic vesicular protein sorting (HOPS) complex. The Hook-related protein (HkRP) family includes Daple, Girdin and Gipie. Daple, also called Dvl-associating protein with a high frequency of leucine residues, or coiled-coil domain-containing protein 88C(CCDC88C), or Hook-related protein 2 (HkRP2), is a novel non-receptor nucleotide exchange factor (GEF) required for activation of guanine nucleotide-binding proteins (G-proteins) during non-canonical Wnt signaling. Girdin, also called Akt phosphorylation enhancer (APE), or coiled-coil domain-containing protein 88A (CCDC88A), or G alpha-interacting vesicle-associated protein (GIV), or Girders of actin filament, or Hook-related protein 1 (HkRP1), is a bifunctional modulator of guanine nucleotide-binding proteins (G proteins). Gipie, also called GRP78-interacting protein induced by ER stress, or coiled-coil domain-containing protein 88B(CCDC88B), or brain leucine zipper domain-containing protein, or Hook-related protein 3 (HkRP3), is a novel actin cytoskeleton-binding protein and Akt substrate that regulates cell migratory responses in various biological contexts. NuMA, also called nuclear mitotic apparatus protein 1, or nuclear matrix protein-22 (NMP-22), or SP-H antigen, is a microtubule (MT)-binding protein that plays a role in the formation and maintenance of the spindle poles and the alignment and the segregation of chromosomes during mitotic cell division. 145 matched cddid_all.tbl CDD cd22212 cd22212 412068 NDFIP-like NEDD4 family-interacting protein. The NEDD4 (neural precursor cell expressed, developmentally down-regulated protein 4)-family interacting proteins (NDFIPs) are adaptor proteins that recruit NEDD4 E3 ligases to specific substrate proteins, which leads to the ubiquitylation and subsequent degradation of these proteins. They also act as activators of the E3 ligase activity by releasing NEDD4 ligase from its auto-inhibitory conformation. NDFIP1/2 have been shown to be involved in neural development by regulating the expression of the Robo1 receptor. 171 matched cddid_all.tbl CDD cd22213 cd22213 439322 AcrIIC1 Anti-CRISPR type II subtype C1. AcrIIC1 was discovered via a guilt-by association (GBA) approach, which was based on the strong co-occurrence and clustering of acr and anti-CRISPR associated (aca) genes through proximity and homology searches. Subsequent structural and biochemical work has shown that AcrIIC1 is a broad-spectrum type II-C anti-CRISPR, inhibiting divergent Cas9 orthologs both in vitro and in vivo. AcrIIC1 interacts directly with the Cas9 HNH domain and blocks DNA cleavage via trapping it on its DNA target in a catalytically inactivated state. Type IIC CRISPR-Cas systems are the simplest of the type II systems, employing only three Cas proteins, Cas9, Cas1, and Cas2. Almost all type II Acrs characterized to date directly interact with the Cas9 endonuclease, although by distinct mechanisms. The type II CRISPR/Cas subtype has a distinct crRNA-guided surveillance complex encoded by cas9 (formerly csn1), cas1, cas2, and csn2 (for type IIA) or cas4 (for type IIB) genes, all located in a single transcriptional unit directly upstream of the CRISPR locus. Cleavage of the DNA target in type II systems is carried out by Cas9 which is an RNA-guided double-stranded DNase with two independent nuclease domains, HNH and RuvC. Due to the reliance of the type II system on a single protein for function, Cas9 homologs derived from different subtypes and species have been utilized for numerous gene editing applications. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 2 systems employ a single multi-domain effector Cas9 protein complex that performs target recognition and cleavage. Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 86 matched cddid_all.tbl CDD cd22214 cd22214 439323 AcrIIC2 Anti-CRISPR type II subtype C2. AcrIIC2 was discovered via a guilt-by association (GBA) approach, which was based on the strong co-occurrence and clustering of acr and anti-CRISPR associated (aca) genes through proximity and homology searches. Subsequent structural and biochemical work has shown that the AcrIIC2 dimer inhibits Cas9 complex assembly through interactions with the Cas9 positively charged bridge helix, that prevents crRNA binding and DNA loading into Cas9. Type IIC CRISPR-Cas systems are the simplest of the type II systems, employing only three Cas proteins, Cas9, Cas1, and Cas2. Almost all type II Acr proteins characterized to date directly interact with the Cas9 endonuclease, although by distinct mechanisms. The type II CRISPR/Cas subtype has a distinct crRNA-guided surveillance complex encoded by cas9 (formerly csn1), cas1, cas2, and csn2 (for type IIA) or cas4 (for type IIB) genes, all located in a single transcriptional unit directly upstream of the CRISPR locus. Cleavage of the DNA target in type II systems is carried out by Cas9 which is an RNA-guided double-stranded DNase with two independent nuclease domains, HNH and RuvC. Due to the reliance of the type II system on a single protein for function, Cas9 homologs derived from different subtypes and species have been utilized for numerous gene editing applications. AcrIIC1 and AcrIIC2 can target a broad spectrum of Cas9 orthologs from different subtypes which is important for designing AcrIIC1- and AcrIIC2-based molecular tools for biotechnological applications. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 2 systems employ a single multi-domain effector Cas9 protein complex that performs target recognition and cleavage. Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 111 matched cddid_all.tbl CDD cd22215 cd22215 439324 AcrIIC3 Anti-CRISPR type II subtype C3. AcrIIC3 was discovered via a guilt-by association (GBA) approach, which was based on the strong co-occurrence and clustering of acr and anti-CRISPR associated (aca) genes through proximity and homology searches. Subsequent structural and biochemical work has shown that AcrIIC3 binds opposite the active site on the HNH nuclease domain of Cas9 to inhibit its nuclease activity in an allosteric manner. AcrIIC3 employs a unique interface for HNH, which demonstrate the host specificity of AcrIIC3 that suggests potential applications in Cas9 control for gene editing. There is interest in engineered, light-dependent Acrs for optogenetic control of CRISPR-Cas9 systems; AcrIIC3-LOV2 hybrids (between AcrIIC3 and the LOV2 blue light sensory domain from Avena sativa) potently block Neisseria meningitidis Cas9 activity in mammalian cells in the dark, and permit robust genome editing at various endogenous loci upon blue light irradiation. Type IIC CRISPR-Cas systems are the simplest of the type II systems, employing only three Cas proteins, Cas9, Cas1, and Cas2. Almost all type II Acr proteins characterized to date directly interact with the Cas9 endonuclease, although by distinct mechanisms. The type II CRISPR/Cas subtype has a distinct crRNA-guided surveillance complex encoded by cas9 (formerly csn1), cas1, cas2, and csn2 (for type IIA) or cas4 (for type IIB) genes, and cas 9, cas1, cas2 (for type IIC) genes, all located in a single transcriptional unit directly upstream of the CRISPR locus. Cleavage of the DNA target in type II systems is carried out by Cas9 which is an RNA-guided double-stranded DNase with two independent nuclease domains, HNH and RuvC. Due to the reliance of the type II system on a single protein for function, Cas9 homologs derived from different subtypes and species have been utilized for numerous gene editing applications. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 2 systems employ a single multi-domain effector Cas9 protein complex that performs target recognition and cleavage. Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 111 matched cddid_all.tbl CDD cd22216 cd22216 409027 H1_KCTD12b H1 domain found in potassium channel tetramerization domain-containing protein 12b. Potassium channel tetramerization domain-containing protein 12b (KCTD12b) is a BTB/POZ domain-containing protein that is an auxiliary subunit of gamma-aminobutyric acid type B (GABA-B) receptors associated with mood disorders. KCTD12b consists of an N-terminal BTB domain followed by a region called the H1 domain. The BTB domain mediates interaction with the receptor. The C-terminal H1 domain, which possesses a beta-propeller-like fold, engages in interactions with G-protein beta-gamma subunits and is responsible for desensitization. This model corresponds to the H1 domain. 118 matched cddid_all.tbl CDD cd22217 cd22217 409028 H1_KCTD12 H1 domain found in potassium channel tetramerization domain-containing protein 12. Potassium channel tetramerization domain-containing protein 12 (KCTD12), also called predominantly fetal expressed T1 domain (Pfetin), is a BTB/POZ domain-containing protein that is an auxiliary subunit of gamma-aminobutyric acid type B (GABA-B) receptors associated with mood disorders. It regulates agonist potency and kinetics of GABA-B receptor signaling. It promotes tumorigenesis by facilitating CDC25B/CDK1/Aurora A-dependent G2/M transition. It also regulates colorectal cancer cell stemness through the ERK pathway. KCTD12 consists of an N-terminal BTB domain followed by a region called the H1 domain. The BTB domain mediates interaction with the receptor. The C-terminal H1 domain, which possesses a beta-propeller-like fold, engages in interactions with G-protein beta-gamma subunits and is responsible for desensitization. This model corresponds to the H1 domain. 119 matched cddid_all.tbl CDD cd22218 cd22218 409029 H1_KCTD8 H1 domain found in potassium channel tetramerization domain-containing protein 8. Potassium channel tetramerization domain-containing protein 8 (KCTD8), a BTB/POZ domain-containing protein, is an auxiliary subunit of gamma-aminobutyric acid type B (GABA-B) receptors that determine the pharmacology and kinetics of the receptor response. It generates largely non-desensitizing receptor responses. KCTD8 consists of an N-terminal BTB domain followed by a region called the H1 domain. The BTB domain mediates interaction with the receptor. The C-terminal H1 domain, which possesses a beta-propeller-like fold, engages in interactions with G-protein beta-gamma subunits. In the related protein KCTD12, the H1 domain is also responsible for desensitization. This model corresponds to the H1 domain of KCTD8, which may not be involved in desensitization. 122 matched cddid_all.tbl CDD cd22219 cd22219 409030 H1_KCTD16 H1 domain found in potassium channel tetramerization domain-containing protein 16. Potassium channel tetramerization domain-containing protein 16 (KCTD16) is a BTB/POZ domain-containing protein that is an auxiliary subunit of gamma-aminobutyric acid type B (GABA-) receptors associated with mood disorders. It interacts with amyloid beta precursor protein (APP), a type I transmembrane protein involved in a variety of cellular processes such as cell adhesion and axon guidance. KCTD16 generates largely non-desensitizing receptor responses. It consists of an N-terminal BTB domain followed by a region called the H1 domain. The BTB domain mediates interaction with the receptor. The C-terminal H1 domain, which possesses a beta-propeller-like fold, engages in interactions with G-protein beta-gamma subunits. In the related protein KCTD12, the H1 domain is also responsible for desensitization. This model corresponds to the H1 domain of KCTD16, which may not be involved in desensitization. 121 matched cddid_all.tbl CDD cd22220 cd22220 412065 pseudoGTPaseD_p190RhoGAP-B pseudoGTPase domain found in p190RhoGAP-B and similar proteins. p190RhoGAP protein B (p190RhoGAP-B), also called ARHGAP5, or p190-B, or Rho-type GTPase-activating protein 5 (RHOGAP5), is a Rho family GTPase-activating protein (GAP) that acts as a key regulator of Rho GTPase signaling and is essential for actin cytoskeletal structure and contractility. This model corresponds to the GTPase-like domain called pseudoGTPase domain that is located at the middle region of p190RhoGAP-B. Rho family GTPase-activating proteins normally have five highly conserved sequence motifs, termed 'G-motifs', required for nucleotide-binding and catalytic activity. PseudoGTPases consist of a GTPase fold lacking one or more of these G motifs. 171 matched cddid_all.tbl CDD cd22221 cd22221 412066 pseudoGTPaseD_p190RhoGAP-A pseudoGTPase domain found in p190RhoGAP-A and similar proteins. p190RhoGAP protein A (p190RhoGAP-A), also called Rho GTPase-activating protein 35(RHOGAP35), glucocorticoid receptor DNA-binding factor 1, or glucocorticoid receptor repression factor 1 (GRF-1), or Rho GAP p190A, or p190-A, is a Rho family GTPase-activating protein (GAP) that acts as a key regulator of Rho GTPase signaling and is essential for actin cytoskeletal structure and contractility. It binds several acidic phospholipids which inhibits the Rho GAP activity to promote the Rac GAP activity. This model corresponds to the GTPase-like domain called pseudoGTPase domain that is located at the middle region of p190RhoGAP-A. Rho family GTPase-activating proteins normally have five highly conserved sequence motifs, termed 'G-motifs', required for nucleotide-binding and catalytic activity. PseudoGTPases would consist of a GTPase fold lacking one or more of these G motifs. 172 matched cddid_all.tbl CDD cd22222 cd22222 411793 HkD_Hook Hook domain found in Hook family of microtubule-binding proteins. The Hook family includes Hook1-3. Hook1 is a microtubule-binding protein required for spermatid differentiation. Hook2, also a microtubule-binding protein, contributes to the establishment and maintenance of centrosome function. It may function in the positioning or formation of aggresomes, which are pericentriolar accumulations of misfolded proteins, proteasomes and chaperones. Hook3 is an adaptor protein for microtubule-dependent intracellular vesicle and protein trafficking. It is involved in Golgi and endosome transport. It acts as a scaffold for the opposite-polarity microtubule-based motors cytoplasmic dynein-1 and the kinesin KIF1C. It may participate in the turnover of the endocytosed scavenger receptor. Hook proteins are components of the FTS/Hook/FHIP complex (FHF complex), which may function to promote vesicle trafficking and/or fusion via the homotypic vesicular protein sorting (HOPS) complex. Hook adaptor proteins share an N-terminal conserved globular Hook domain, which folds as a variant of the helical calponin homology (CH) domain, and contacts the helix alpha1 of dynein light intermediate chain 1 (LIC1) in a hydrophobic groove. 147 matched cddid_all.tbl CDD cd22223 cd22223 411794 HkD_HkRP Hook domain found in the Hook-related protein (HkRP) family. The HkRP family includes Daple, Girdin and Gipie. Daple, also called Dvl-associating protein with a high frequency of leucine residues, or coiled-coil domain-containing protein 88C (CCDC88C), or Hook-related protein 2 (HkRP2), is a novel non-receptor nucleotide exchange factor (GEF) required for activation of guanine nucleotide-binding proteins (G-proteins) during non-canonical Wnt signaling. Girdin, also called Akt phosphorylation enhancer (APE), or coiled-coil domain-containing protein 88A (CCDC88A), or G alpha-interacting vesicle-associated protein (GIV), or Girders of actin filament, or Hook-related protein 1 (HkRP1), is a bifunctional modulator of guanine nucleotide-binding proteins (G proteins). It acts as a non-receptor guanine nucleotide exchange factor which binds to and activates guanine nucleotide-binding protein G(i) alpha subunits. It also acts as a guanine nucleotide dissociation inhibitor for guanine nucleotide-binding protein G(s) subunit alpha GNAS. In addition, Girdin plays an essential role in cell migration. Gipie, also called GRP78-interacting protein induced by ER stress, or coiled-coil domain-containing protein 88B (CCDC88B), or brain leucine zipper domain-containing protein, or Hook-related protein 3 (HkRP3), is a novel actin cytoskeleton-binding protein and Akt substrate that regulates cell migratory responses in various biological contexts. It acts as a positive regulator of T-cell maturation and inflammatory function. As a microtubule-binding protein, Gipie regulates lytic granule clustering and NK cell killing. All family members contain a conserved globular Hook domain which folds as a variant of the helical calponin homology (CH) domain. 149 matched cddid_all.tbl CDD cd22224 cd22224 411795 HkD_NuMA Hook domain found in nuclear mitotic apparatus protein (NuMA) and similar proteins. NuMA, also called nuclear mitotic apparatus protein 1, or nuclear matrix protein-22 (NMP-22), or SP-H antigen, is a microtubule (MT)-binding protein that plays a role in the formation and maintenance of the spindle poles, and the alignment and segregation of chromosomes during mitotic cell division. The model corresponds to the N-terminal conserved globular Hook domain of NuMA, which folds as a variant of the helical calponin homology (CH) domain. It directly binds dynein light intermediate chains LIC1 and LIC2 through a conserved hydrophobic patch shared among other Hook adaptors. 148 matched cddid_all.tbl CDD cd22225 cd22225 411796 HkD_Hook1 Hook domain found in protein Hook 1 (Hook1) and similar proteins. Hook1 is a microtubule-binding protein required for spermatid differentiation. It is a component of the FTS/Hook/FHIP complex (FHF complex), which may function to promote vesicle trafficking and/or fusion via the homotypic vesicular protein sorting (HOPS) complex. 150 matched cddid_all.tbl CDD cd22226 cd22226 411797 HkD_Hook3 Hook domain found in protein Hook 3 (Hook3) and similar proteins. Hook3 is an adaptor protein for microtubule-dependent intracellular vesicle and protein trafficking. It is involved in Golgi and endosome transport. It acts as a scaffold for the opposite-polarity microtubule-based motors cytoplasmic dynein-1 and the kinesin KIF1C. It may participate in the turnover of the endocytosed scavenger receptor. Hook3 is a component of the FTS/Hook/FHIP complex (FHF complex), which may function to promote vesicle trafficking and/or fusion via the homotypic vesicular protein sorting (HOPS) complex. 153 matched cddid_all.tbl CDD cd22227 cd22227 411798 HkD_Hook2 Hook domain found in protein Hook 2 (Hook2) and similar proteins. Hook2 is a microtubule-binding protein that contributes to the establishment and maintenance of centrosome function. It may function in the positioning or formation of aggresomes, which are pericentriolar accumulations of misfolded proteins, proteasomes and chaperones. Hook2 is a component of the FTS/Hook/FHIP complex (FHF complex), which may function to promote vesicle trafficking and/or fusion via the homotypic vesicular protein sorting (HOPS) complex. 150 matched cddid_all.tbl CDD cd22228 cd22228 411799 HkD_Daple Hook domain found in Daple (Dvl-associating protein with a high frequency of leucine residues) and similar proteins. Protein Daple, also called coiled-coil domain-containing protein 88C (CCDC88C), or Hook-related protein 2 (HkRP2), is a novel non-receptor nucleotide exchange factor (GEF) required for activation of guanine nucleotide-binding proteins (G-proteins) during non-canonical Wnt signaling. 153 matched cddid_all.tbl CDD cd22229 cd22229 411800 HkD_Girdin Hook domain found in Girdin and similar proteins. Girdin, also called Akt phosphorylation enhancer (APE), or coiled-coil domain-containing protein 88A (CCDC88A), or G alpha-interacting vesicle-associated protein (GIV), or Girders of actin filament, or Hook-related protein 1 (HkRP1), is a bifunctional modulator of guanine nucleotide-binding proteins (G proteins). It acts as a non-receptor guanine nucleotide exchange factor which binds to and activates guanine nucleotide-binding protein G(i) alpha subunits. It also acts as a guanine nucleotide dissociation inhibitor for guanine nucleotide-binding protein G(s) subunit alpha GNAS. In addition, Girdin plays an essential role in cell migration. 156 matched cddid_all.tbl CDD cd22230 cd22230 411801 HkD_Gipie Hook domain found in Gipie (GRP78-interacting protein induced by ER stress) and similar proteins. Gipie, also called coiled-coil domain-containing protein 88B (CCDC88B), or brain leucine zipper domain-containing protein, or Hook-related protein 3 (HkRP3), is a novel actin cytoskeleton-binding protein and Akt substrate that regulates cell migratory responses in various biological contexts. It acts as a positive regulator of T-cell maturation and inflammatory function. As a microtubule-binding protein, Gipie regulates lytic granule clustering and NK cell killing. 170 matched cddid_all.tbl CDD cd22231 cd22231 409021 RHH_NikR_HicB-like ribbon-helix-helix domains of nickel responsive transcription factor NikR, antitoxins HicB, ParD, and MazE, and similar proteins. This family includes the N-terminal domain of NikR, C-terminal domains of antitoxins HicB and ParD, as well as antitoxin MazE, and similar proteins, all of which belong to the ribbon-helix-helix (RHH) family of transcription factors. NikR is a nickel-responsive transcription factor that consists of an N-terminal DNA-binding RHH domain and a C-terminal metal-binding domain (MBD) with four nickel ions. In Helicobacter pylori, which colonizes the gastric epithelium of humans leading to gastric ulcers and gastric cancers, NikR (HpNikR) regulates multiple genes. It regulates urease, which protects H. pylori from acidic shock at low pH, by converting urea to ammonia and bicarbonate. It also plays a complex role in the intracellular physiology of nickel; occupation of nickel-binding sites results in NikR binding to its operator in the nickel permease nikABCDE promoter. Thus, there is weaker repression of NikABCDE transcription at low intracellular free nickel concentrations while strong repression prevails at higher concentrations, which would be potentially toxic. Antitoxin HicB is part of the HicAB toxin-antitoxin (TA) system, where the toxins are RNases, found in many bacteria. In the pathogen Burkholderia pseudomallei, the HicAB system plays a role in regulating the frequency of persister cells and may therefore play a role in disease. Structural studies of Yersinia pestis HicB show that it acts as an autoregulatory protein and HicA acts as an mRNase. In Escherichia coli, an excess of HicA has been shown to de-repress a HicB-DNA complex and restore transcription of HicB. Similarly, Caulobacter crescentus ParD antitoxin neutralizes the effect of cognate ParE toxin. In Bacillus subtilis, during stress conditions, antitoxin MazE binds to toxin MazF, an mRNA interferase, and inactivates it and cleaves mRNAs in a sequence-specific manner, resulting in cellular growth arrest. 44 matched cddid_all.tbl CDD cd22232 cd22232 409022 RHH_CopG_Cop6-like ribbon-helix-helix family transcriptional repressor protein CopG, uncharacterized Cop6, and similar proteins. This family includes the ribbon-helix-helix (RHH) family transcriptional repressor CopG, which is involved in the control of plasmid copy number, as well as uncharacterized proteins such as Cop6, which is found in a small plasmid that has been identified in methicillin-resistant Staphylococcus aureus (MRSA). CopG, a homodimeric protein of around 45 residues, constitutes one of the smallest natural transcriptional repressors characterized and is the prototype of a series of repressor proteins encoded by plasmids that exhibit a similar genetic structure at their leading strand initiation and control regions. It binds to and represses the single Pcr promoter that directs the synthesis of a bicistronic mRNA for CopG and the RepB initiator of replication, thereby regulating its own synthesis and that of RepB. 45 matched cddid_all.tbl CDD cd22233 cd22233 409023 RHH_CopAso-like ribbon-helix-helix domain of Shewanella oneidensis type II antitoxin CopA(SO), and similar proteins. This family includes the N-terminal ribbon-helix-helix (RHH) domain of Shewanella oneidensis CopA(SO), a newly identified type II antitoxin, as well as the N-terminal RHH domain of Escherichia coli PutA flavoprotein, among other similar proteins, many of which are as yet uncharacterized. CopA(SO) is a typical RHH antitoxin that includes an ordered N-terminal domain (CopA(SO)-N) and a disordered C-terminal domain (CopA(SO)-C). Biophysical investigation indicates allosteric effects of CopA(SO)-N on CopA(SO)-C; DNA binding of CopA(SO)-N appears to induce CopA(SO)-C to fold and self-associate the C-terminal domain. The multifunctional E. coli proline utilization A (PutA) flavoprotein functions as a membrane-associated proline catabolic enzyme as well as a transcriptional repressor of the proline utilization genes putA and putP. The N-terminal domain of PutA is a transcriptional regulator with an RHH fold; structure studies show that it forms a homodimer to bind one DNA duplex. This family also includes orphan antitoxin ParD2, an antitoxin component of a non-functional type II toxin-antitoxin (TA system); it does not neutralize the effect of any of the RelE or ParE toxins. 44 matched cddid_all.tbl CDD cd22234 cd22234 409024 RHH_MobB-like ribbon-helix-helix domain of mobilization protein MobB and similar proteins. This subfamily includes Pseudomonas syringae mobilization protein MobB, and mostly archaeal uncharacterized CopG family proteins. These proteins have a typical ribbon-helix-helix (RHH), similar to plasmid-encoded transcriptional repressor CopG, the protein that is encoded by the promiscuous streptococcal plasmid pMV158 and is involved in the control of plasmid copy number. 44 matched cddid_all.tbl CDD cd22235 cd22235 409025 RHH_CopG_archaea ribbon-helix-helix domain of CopG family transcriptional regulators found in archaea. This subfamily includes the N-terminal ribbon-helix-helix (RHH) domain of putative transcriptional repressor CopG from archaea, and similar proteins. These uncharacterized proteins have a typical RHH, similar to plasmid-encoded transcriptional repressor CopG, the protein that is encoded by the promiscuous streptococcal plasmid pMV158 and is involved in the control of plasmid copy number. 43 matched cddid_all.tbl CDD cd22236 cd22236 439325 AcrVA1-like Anti-CRISPR type V subtype A1 and similar proteins. This model represents AcrVA1 and similar uncharacterized proteins. AcrVA1 is an anti-CRISPR (Acr) protein that was discovered via STSS (self-targeting spacers search) with further functional TXTL (cell-free transcription-translation) assay. The bioinformatic STSS method finds self-targeting CRISPR spacers in genomic DNA, predicts the type of CRISPR system involved, and obtains information about the targeted sequence. AcrVA1 is a multiple-turnover inhibitor that triggers cleavage of the target recognition sequence of the Cas12a-bound guide RNA to irreversibly inactivate the Cas12a complex. Cas12a (Cpf1) is a class 2 effector protein for the AcrVA subfamily that has high efficiency in genome editing. It possesses a single nuclease domain (RuvC) that is activated upon binding of the crRNA targeting sequence (or spacer) to a complementary single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) target molecule. In addition to gene editing, CRISPR-Cas12a has repurposed, in high eukaryotes, to carry out transcription regulation via a nuclease-dead Cas12a (dCas12a), and AcrVAs have been adopted to regulate (d)Cas12a activity; AcrVA1 is able to inhibit two dCas12a proteins (denAsCas12a and dLbCas12a) in Saccharomyces cerevisiae. Type V systems fundamentally differ from type II by the domain architecture of their effector proteins. The type II effectors (Cas9) contain two nuclease domains that are each responsible for the cleavage of one strand of the target DNA, with the HNH nuclease inserted inside the RuvC-like nuclease domain sequence. By contrast, the type V effectors (Cas12) only contain a RuvC-like domain that cleaves both strands. Acr proteins have co-evolved with CRISPR-Cas proteins to provide bacteriophage with broad spectrum, or in some cases, highly selective protection from RNA-guided destruction. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Acr proteins are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 135 matched cddid_all.tbl CDD cd22238 cd22238 412071 AcrIF3 Anti-CRISPR type I subtype F3. AcrIF3 (also known as AcrF3) is an anti-CRISPR (Acr) protein that forms a homodimer and interacts directly with helicase-nuclease protein Cas3 and blocks its recruitment to the type I-F CRISPR-Cas surveillance complex (Csy). The type I-F Csy is a crRNA-guided surveillance complex, composed of a crRNA and nine Cas proteins (one Cas8f, one Cas5f, one Cas6f, and six Cas7f), which recruits a nuclease-helicase protein Cas3 for target degradation. Without Cas3 recruitment by the Csy-dsDNA complex, the CRISPR/Cas system is unable to efficiently destroy the invading DNA, resulting in escape from the immune response. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif which inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 1 systems utilize RNA-guided complexes consisting of multiple Cas proteins as the effector proteins to recognize and cleave target DNA. Type I CRISPR-Cas systems are the most widespread in nature, and the Cas protein composition of the employed CRISPR ribonucleoprotein (crRNP) complexes differs between seven subtypes (A to F, U). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 127 matched cddid_all.tbl CDD cd22239 cd22239 412072 NPHP4 Nephrocystin-4. Nephrocystin-4 (NPHP4), also known as nephroretinin, is a component of the nephronophthisis (NPHP) module which is part of the transition zone (TZ) of the cilia. NPHP4 forms complexes with alpha-tubulin, NPHP1 and RPGRIP1. The interaction with NPHP1 is crucial for cell-cell and cell-matrix adhesion signaling. Mutations in NPHP4 have been shown to cause nephronophthisis (NPHP), an autosomal recessive cause of kidney failure and earlier stages of chronic kidney disease among adults. 904 matched cddid_all.tbl CDD cd22240 cd22240 412034 akirin akirin. Akirins are small, highly conserved eumetazoan nuclear proteins that play a role in immune response and tumorigenesis. It is believed that they act as a connector between a variety of transcription factors and major chromatin remodeling complexes. In vertebrates, there are two orthologs, Akirin1 and Akirin2. 147 matched cddid_all.tbl CDD cd22241 cd22241 412073 AcrIF8 Anti-CRISPR type I subtype F8 (AcrIF8). AcrIF8 (also known as AcrF8) is an anti-CRISPR (Acr) protein that is positioned on the type I-F Csy spiral backbone surrounded by Cas5f, Cas7.4-7.6f, and Cas8f, and forms interactions with crRNA (CRISPR-RNA) to prevent the target DNA from binding to the Csy complex. The type I-F Csy complex is a crRNA-guided surveillance complex composed of a crRNA and nine Cas proteins (one Cas8f, one Cas5f, one Cas6f, and six Cas7f), which recruits a nuclease-helicase protein Cas3 for target degradation. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr Proteins are diverse with no common sequence or structural motif which inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 1 systems utilize RNA-guided complexes consisting of multiple Cas proteins as the effector proteins to recognize and cleave target DNA. Type I CRISPR-Cas systems are the most widespread in nature, and the Cas protein composition of the employed CRISPR ribonucleoprotein (crRNP) complexes differs between seven subtypes (A to F, U). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 77 matched cddid_all.tbl CDD cd22242 cd22242 439327 AcrIIA6 Anti-CRISPR type II subtype A6. AcrIIA6 is an anti-CRISPR (Acr) protein which was discovered via a self-targeting method that inhibits the type II-A CRISPR-Cas system (Csy). It is the largest known type II-A Acr, and it contains a helix-turn-helix (HTH) motif that is part of its dimerization interface. AcrIIA6 inhibits target DNA binding to Cas9 via an allosteric mechanism and can induce Cas9 dimerization. The protospacer adjacent motif (PAM) and AcrIIA6 recognition sites are structurally close and allosterically linked. AcrIIA6 affects Cas9 conformational dynamics associated with PAM binding. Almost all type II Acrs characterized to date directly interact with the Cas9 endonuclease, although by distinct mechanisms. The type II CRISPR/Cas subtype has a distinct crRNA-guided surveillance complex encoded by cas9 (formerly csn1), cas1, cas2, and csn2 (for type IIA) or cas4 (for type IIB) genes, all located in a single transcriptional unit directly upstream of the CRISPR locus. Cleavage of the DNA target in type II systems is carried out by Cas9 which is an RNA-guided double-stranded DNase with two independent nuclease domains, HNH and RuvC. Due to the reliance of the type II system on a single protein for function, Cas9 homologs derived from different subtypes and species have been utilized for numerous gene editing applications. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 178 matched cddid_all.tbl CDD cd22243 cd22243 412035 akirin-1 akirin-1. Akirins are small, highly conserved eumetazoan nuclear proteins that play a role in immune response and tumorigenesis. It is believed that they act as a connector between a variety of transcription factors and major chromatin remodeling complexes. Akirin-1 is one of the two orthologs in vertebrates that plays a role in immunity, myogenesis and meiosis. 188 matched cddid_all.tbl CDD cd22244 cd22244 412036 akirin-2 akirin-2. Akirins are small, highly conserved eumetazoan nuclear proteins that play a role in immune response and tumorigenesis. It is believed that they act as a connector between a variety of transcription factors and major chromatin remodeling complexes. Akirin-2 is one of the two orthologs in vertebrates that plays a role in immunity, myogenesis, and brain- and limb-development. Akirin-2 is partly cytosolic. It has been shown to interact with nuclear importins and therefore may play a role in proper transport between nucleus and cytoplasm. 184 matched cddid_all.tbl CDD cd22246 cd22246 412074 PI4KB_NTD N-terminal domain of phosphatidylinositol 4-kinase beta. Phosphatidylinositol 4-kinase beta (PI4K-beta, PI4Kbeta or PI4KB), also called PtdIns 4-kinase beta, NPIK, PI4K92, or PI4KIII, catalyzes the phosphorylation of phosphatidylinositol (PI) to form phosphatidylinositol 4-phosphate (PI4P), in the first committed step in the production of the second messenger inositol-1,4,5,-trisphosphate (PIP). It may regulate Golgi disintegration/reorganization during mitosis, possibly via its phosphorylation. PI4K-beta is critical for the maintenance of the Golgi and trans Golgi network (TGN) PI4P pools. It is recruited to membranes via its interaction with Golgi adaptor protein acyl-coenzyme A binding domain containing protein 3 (ACBD3). The ACBD3:PI4K-beta complex formation is essential for proper function of the Golgi. PI4K-beta also plays an essential role in Aichi virus RNA replication. It is recruited by ACBD3 at viral replication sites. This model corresponds to the N-terminal domain of PI4K-beta, which is responsible for interacting with ACBD3 by forming a complex with the Q domain. 65 matched cddid_all.tbl CDD cd22247 cd22247 439328 MCM8_WHD winged-helix domain (WHD) found in minichromosome maintenance 8 (MCM8) and similar proteins. MCM8 is a DNA helicase that is a component of the MCM8-MCM9 complex, which is involved in the repair of double-stranded DNA breaks (DBSs) and DNA interstrand cross-links (ICLs) by homologous recombination (HR). The MCM8-MCM9 complex is also required for DNA resection by the MRE11-RAD50-NBN/NBS1 (MRN) complex by recruiting the MRN complex to the repair site and by promoting its nuclease activity. This model corresponds to the C-terminal winged-helix domain (WHD) of MCM8, which mediates protein-nucleic acid interaction, as well as protein-protein interaction. 66 matched cddid_all.tbl CDD cd22248 cd22248 410202 Rcc_KIF21 regulatory coiled-coil domain found in the kinesin-like KIF21 family. The KIF21 family includes KIF21A and KIF21B. KIF21A (also called kinesin-like protein KIF2, or renal carcinoma antigen NY-REN-62) is a microtubule-binding motor protein involved in neuronal axonal transport. It works as a microtubule stabilizer that regulates axonal morphology, suppressing cortical microtubule dynamics in neurons. Mutations in KIF21A cause congenital fibrosis of the extraocular muscles type 1 (CFEOM1). In vitro, it has a plus-end directed motor activity. KIF21B is a plus-end directed microtubule-dependent motor protein which displays processive activity. It is involved in regulation of microtubule dynamics, synapse function, and neuronal morphology, including dendritic tree branching and spine formation. KIF21B plays a role in learning and memory. It is involved in the delivery of gamma-aminobutyric acid (GABA(A)) receptors to the cell surface. This model corresponds to the regulatory coiled-coil domain of KIF21A/KIF21B, which folds into an intramolecular antiparallel coiled-coil monomer in solution but crystallizes into a dimeric domain-swapped antiparallel coiled-coil. 81 matched cddid_all.tbl CDD cd22249 cd22249 409016 UDM1_RNF168_RNF169-like UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, RNF169 and similar proteins. This model represents the UDM1 (ubiquitin-dependent double-strand break [DSB] recruitment module 1) found in RING finger proteins, RNF168 and RNF169. RNF168 is an E3 ubiquitin-protein ligase that promotes non-canonical K27 ubiquitination to signal DNA damage. It functions, together with RNF8, as a DNA damage response (DDR) factor that promotes a series of ubiquitylation events on substrates such as H2A and H2AX. With H2AK13/15 ubiquitylation, it facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. In addition, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. RNF169 is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. RNF169 recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to the regulation of DSB repair pathway utilization via functionally competing with recruiting repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin, independent of its catalytic activity, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. The UDM1 domain comprises LRM1 (LR motif 1), UMI (ubiquitin-interacting motif [UIM]- and MIU-related UBD) and MIU1 (motif interacting with ubiquitin 1). Mutations of Ub-interacting residues in UDM1 have little effect on the accumulation of RNF168 to DSB sites, suggesting that it may not be the main site of binding ubiquitylated and polyubiquitylated targets. 66 matched cddid_all.tbl CDD cd22250 cd22250 409019 ROCK_SBD Shroom-binding domain found in Rho-associated coiled-coil containing protein kinase. Rho-associated coiled-coil containing protein kinase (ROCK) is a serine/threonine kinase (STK) that catalyzes the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. It is also referred to as Rho-associated protein kinase or simply as Rho kinase. The ROCK subfamily consists of two isoforms, ROCK1 and ROCK2, which may be functionally redundant in some systems, but exhibit different tissue distributions. Rho-associated protein kinase 1 (ROCK1) is also called renal carcinoma antigen NY-REN-35, Rho-associated, coiled-coil-containing protein kinase 1, ROCK-I, p160 ROCK-1, or p160ROCK, is preferentially expressed in the liver, lung, spleen, testes, and kidney. It mediates signaling from Rho to the actin cytoskeleton. It is implicated in the development of cardiac fibrosis, cardiomyocyte apoptosis, and hyperglycemia. Mice deficient in ROCK1 display eyelids open at birth (EOB) and omphalocele phenotypes due to the disorganization of actin filaments in the eyelids and the umbilical ring. Rho-associated protein kinase 2 (ROCK2), also called Rho kinase 2, Rho-associated, coiled-coil-containing protein kinase 2, ROCK-II, or p164 ROCK-2, is more prominent in brain and skeletal muscle. It is implicated in vascular and neurological disorders, such as hypertension and vasospasm of the coronary and cerebral arteries. Mice deficient in ROCK2 show intrauterine growth retardation and embryonic lethality because of placental dysfunction. ROCK subfamily proteins contain an N-terminal extension, a catalytic kinase domain, a coiled-coil (CC) region encompassing a Rho-binding domain (RBD), and a pleckstrin homology (PH) domain. ROCK is auto-inhibited by the RBD and PH domain interacting with the catalytic domain. It is activated via proteolytic cleavage, binding of lipids to the PH domain, or binding of GTP-bound RhoA to the CC region. More recently, the Shroom family of proteins have been identified as an additional regulator of ROCK. This model corresponds to the Shroom-binding domain (SBD) of ROCK, which forms a parallel coiled coil with the Shroom domain 2 (SD2) of Shroom. 75 matched cddid_all.tbl CDD cd22252 cd22252 412075 PARP2_NTR NTR (N-terminal region) domain of poly [ADP-ribose] polymerase 2 (PARP-2) and similar proteins. PARP-2 is also called ADP-ribosyltransferase diphtheria toxin-like 2 (ARTD2), DNA ADP-ribosyltransferase PARP2, NAD(+) ADP-ribosyltransferase 2 (ADPRT-2), poly[ADP-ribose] synthase 2 (pADPRT-2), or protein poly-ADP-ribosyltransferase PARP2. It is a poly-ADP-ribosyltransferase that mediates poly-ADP-ribosylation of proteins and plays a key role in DNA repair. It mainly mediates glutamate and aspartate ADP-ribosylation of target proteins. PARP-2 can also ADP-ribosylate DNA; it preferentially acts on 5'-terminal phosphates at DNA strand break termini in nicked duplex. This model corresponds to the NTR (N-terminal region) domain of PARP-2, which contains a nucleolar localization sequence (NoLS) and a putative nuclear localization signal (NLS). The NTR domain has a helical SAF-A/B, Acinus, and PIAS (SAP) domain fold and may participate in protein-protein interactions. 59 matched cddid_all.tbl CDD cd22254 cd22254 439329 CSB_WHD winged-helix domain (WHD) found in cockayne syndrome group B (CSB) and similar proteins. CSB, also called cockayne syndrome protein CSB, DNA excision repair protein ERCC-6, ERCC Excision Repair 6, or ATP-dependent helicase ERCC6, is involved in many DNA repair processes and is essential for transcription-coupled repair (TCR). It regulates DNA double-strand break (DSB) repair and checkpoint activation. Upon DNA-binding, it locally modifies DNA conformation by wrapping the DNA around itself, thereby modifying the interface between stalled RNA polymerase II and DNA. It is required for TCR complex formation. CSB also regulates transcription and chromatin remodeling activities that are essential for neuronal differentiation and neuritogenesis. This model corresponds to the winged-helix domain (WHD) of CSB, which is involved in the recruitment of CSB to DSBs. The CSB WHD folds as a single globular domain, defining a class of ubiquitin-binding domains (UBDs) different from other UBD classes. 72 matched cddid_all.tbl CDD cd22255 cd22255 439277 PBD_PPP1R3A PP1C binding domain found in protein phosphatase 1 regulatory subunit 3A (PPP1R3A) and similar proteins. PPP1R3A, also called protein phosphatase 1 glycogen-associated regulatory subunit (PP1G), protein phosphatase type-1 glycogen targeting subunit, or RG1, acts as a glycogen-targeting subunit for PP1 that is essential for cell division, and participates in the regulation of glycogen metabolism, muscle contractility, and protein synthesis. PPP1R3A plays an important role in glycogen synthesis but is not essential for insulin activation of glycogen synthase. It interacts with the PPP1CC catalytic subunit of PP1 and associates with glycogen. This model corresponds to the protein phosphatase 1 catalytic subunit (PP1C) binding domain of PPP1R3A, which contains a RVxF PP1C-binding motif that mediates interactions with PP1C. 82 matched cddid_all.tbl CDD cd22256 cd22256 412077 PrimPol_RBD C-terminal RPA-binding domain (RBD) of DNA-directed primase/polymerase protein and similar proteins. DNA-directed primase/polymerase protein (PrimPol), also called coiled-coil domain-containing protein 111, is a DNA primase-polymerase required for the maintenance of genome integrity. It facilitates mitochondrial and nuclear replication fork progression by initiating de novo DNA synthesis using dNTPs and acting as an error-prone DNA polymerase able to bypass certain DNA lesions. PrimPol is regulated by single-stranded DNA binding proteins. This model corresponds to the C-terminal RPA-binding domain (RBD) of PrimPol, which interacts directly with the RPA70N domain of RPA70. 81 matched cddid_all.tbl CDD cd22257 cd22257 412078 AcrIF6-like Anti-CRISPR type I subtype F6 and related uncharacterized proteins. AcrIF6 (also known as AcrF6) is an anti-CRISPR (Acr) protein that blocks invader DNA access by binding in the junction region between Cas7.6f and Cas8f subunits of the type I-F CRISPR-Cas surveillance complex (Csy) to compete for foreign DNA binding. The type I-F Csy is a crRNA-guided surveillance complex, composed of a crRNA and nine Cas proteins (one Cas8f, one Cas5f, one Cas6f, and six Cas7f), which recruits a nuclease-helicase protein Cas3 for target degradation. AcrIF6 can function as an inhibitor of both the type I-E and I-F CRISPR-Cas systems. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif which inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 1 systems utilize RNA-guided complexes consisting of multiple Cas proteins as the effector proteins to recognize and cleave target DNA. Type I CRISPR-Cas systems are the most widespread in nature, and the Cas protein composition of the employed CRISPR ribonucleoprotein (crRNP) complexes differs between seven subtypes (A to F, U). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 82 matched cddid_all.tbl CDD cd22259 cd22259 412079 AcrIF10 "Anti-CRISPR type I subtype F10. AcrIF10 (also known as AcrF10) is an anti-CRISPR (Acr) protein which acts as a ""DNA mimic protein"" (DMP) that binds in the junction region between Cas 7.6f and Cas8f subunits of the type I-F CRISPR-Cas surveillance complex (Csy) to inhibit foreign DNA binding to the CRISPR-Cas adaptive immune system. The key feature of DMPs is their DNA-like shape and charge distribution, and they affect the activity of DNA-binding proteins by occupying their DNA-binding domains. The type I-F Csy is a crRNA-guided surveillance complex composed of a crRNA and nine Cas proteins (one Cas8f, one Cas5f, one Cas6f, and six Cas7f), which recruits a nuclease-helicase protein Cas3 for target degradation. Without Cas3 recruitment by the Csy-dsDNA complex, the CRISPR/Cas system is unable to efficiently destroy the invading DNA, resulting in the escape from the immune response. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif which inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 1 systems utilize RNA-guided complexes consisting of multiple Cas proteins as the effector proteins to recognize and cleave target DNA. Type I CRISPR-Cas systems are the most widespread in nature, and the Cas protein composition of the employed CRISPR ribonucleoprotein (crRNP) complexes differs between seven subtypes (A to F, U). Acr families are named for their type and subtype which are numbered sequentially as they are discovered." 94 matched cddid_all.tbl CDD cd22260 cd22260 467850 AcrIF9 Anti-CRISPR type I subtype F9 (AcrIF9). AcrIF9 (also known as AcrF9) is an anti-CRISPR (Acr) protein that was discovered via the guilt-by association (GBA) method, and subsequently confirmed by structural and functional assays to inhibit the type I-F CRISPR-Cas system. GBA is based on the strong co-occurrence and clustering of acr and anti-CRISPR associated (aca) genes through proximity and homology searches. The AcrIF9 family is one of the largest and most diverse families of I-F Acrs. Among the 14 AcrIF proteins, at least nine (AcrIF1, AcrIF2, AcrIF4, AcrIF6, AcrIF7, AcrIF8, AcrIF9, AcrIF10 and AcrIF14) stably bind to the Cas surveillance complex (Csy) to inhibit recruitment of either target DNA or nuclease, suggesting direct association with the Csy complex is a major means for inhibition among AcrIF proteins. AcrIF9 exists in monomeric form in solution and can directly bind to DNA using a positively charged cleft. AcrIF9 binds to the Csy complex, thereby sterically blocking the hybridization of target DNA to the CRISPR RNA (crRNA). The Csy-AcrIF9 complex binds to dsDNA in a non-sequence specific manner, needing neither a protospacer associated motif (PAM) nor complementarity to the crRNA. AcrIF9 gives the Csy complex the ability to interact with non-sequence specific dsDNA, as does AcrIF14. The type I-F Csy complex is a crRNA-guided surveillance complex comprised of a crRNA and Cas proteins, which recruits a nuclease-helicase protein Cas3 for target degradation. Type I-F Cas proteins include Cas8f, Cas5f, Cas6f, and Cas7f, in the case of subtypes I-F1 and I-F3, and Cas5f, Cas6f, and Cas7f, in the case of subtype I-F2. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 1 systems utilize RNA-guided complexes consisting of multiple Cas proteins as the effector proteins to recognize and cleave target DNA. Type I CRISPR-Cas systems are the most widespread in nature, and the Cas protein composition of the employed CRISPR ribonucleoprotein (crRNP) complexes differs between nine subtypes (A, B, C, G, D, E, F1, F3, and F2). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 63 matched cddid_all.tbl CDD cd22261 cd22261 439330 AcrIIA2 Anti-CRISPR type II subtype A2. AcrIIA2 is an anti-CRISPR (Acr) protein which was discovered via a self-targeting method that inhibits the type II-A CRISPR-Cas system (Csy). AcrIIA2 and its more potent homolog, AcrIIA2b, interact with the protospacer adjacent motif (PAM) recognition residues of Cas9, preventing target double-stranded DNA (dsDNA) detection and Cas9 binding to DNA. Almost all type II Acr proteins characterized to date directly interact with the Cas9 endonuclease, although by distinct mechanisms. AcrIIA2 has been found to inhibit active gene drive systems in budding yeast; gene drive is one Cas9-based application of interest to the field of population control. The type II CRISPR/Cas subtype has a distinct crRNA-guided surveillance complex encoded by cas9 (formerly csn1), cas1, cas2, and csn2 (for type IIA) or cas4 (for type IIB) genes, all located in a single transcriptional unit directly upstream of the CRISPR locus. Cleavage of the DNA target in type II systems is carried out by Cas9 which is an RNA-guided double-stranded DNase with two independent nuclease domains, HNH and RuvC. Due to the reliance of the type II system on a single protein for function, Cas9 homologs derived from different subtypes and species have been utilized for numerous gene editing applications. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 2 systems employ a single multi-domain effector Cas9 protein complex that performs target recognition and cleavage. Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 116 matched cddid_all.tbl CDD cd22262 cd22262 410203 Rcc_KIF21B regulatory coiled-coil domain found in kinesin-like protein KIF21B. KIF21B is a plus-end directed microtubule-dependent motor protein which displays processive activity. It is involved in regulation of microtubule dynamics, synapse function, and neuronal morphology, including dendritic tree branching and spine formation. KIF21B plays a role in learning and memory. It is involved in the delivery of gamma-aminobutyric acid (GABA(A)) receptors to the cell surface. This model corresponds to a conserved region of KIF21B, which shows high sequence similarity to the regulatory coiled-coil domain of KIF21A. 82 matched cddid_all.tbl CDD cd22263 cd22263 410204 Rcc_KIF21A regulatory coiled-coil domain found in kinesin-like protein KIF21A. KIF21A, also called kinesin-like protein KIF2 or renal carcinoma antigen NY-REN-62, is a microtubule-binding motor protein involved in neuronal axonal transport. It works as a microtubule stabilizer that regulates axonal morphology, suppressing cortical microtubule dynamics in neurons. Mutations in KIF21A cause congenital fibrosis of the extraocular muscles type 1 (CFEOM1). In vitro, it has a plus-end directed motor activity. This model corresponds to the regulatory coiled-coil domain of KIF21A, which folds into an intramolecular antiparallel coiled-coil monomer in solution, but crystallizes into a dimeric domain-swapped antiparallel coiled-coil. 82 matched cddid_all.tbl CDD cd22264 cd22264 409017 UDM1_RNF169 UDM1 (ubiquitin-dependent DSB recruitment module 1) domain found in RING finger protein 169. RING finger protein 169 (RNF169) is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. It recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to the regulation of DSB repair pathway utilization via functionally competing with recruiting repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin independent of its catalytic activity, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. This model corresponds to the UDM1 (ubiquitin-dependent double-strand break [DSB] recruitment module 1) domain of RNF169, which comprises LRM1 (LR motif 1), UMI (ubiquitin-interacting motif [UIM]- and MIU-related UBD) and MIU1 (motif interacting with ubiquitin 1). Mutations of Ub-interacting residues in UDM1 have little effect on the accumulation of the related RNF168 to DSB sites, suggesting that it may not be the main site of binding ubiquitylated and polyubiquitylated targets. 70 matched cddid_all.tbl CDD cd22265 cd22265 409018 UDM1_RNF168 UDM1 (ubiquitin-dependent DSB recruitment module 1) domain found in RING finger protein 168. RING finger protein 168 (RNF168) is an E3 ubiquitin-protein ligase that promotes noncanonical K27 ubiquitination to signal DNA damage. Together with RNF8, RNF168 functions as a DNA damage response (DDR) factor that promotes a series of ubiquitylation events on substrates such as H2A and H2AX. With H2AK13/15 ubiquitylation, it facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. In addition, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. This model corresponds to the UDM1 (ubiquitin-dependent double-strand break [DSB] recruitment module 1) domain of RNF168, which comprises LRM1 (LR motif 1), UMI (ubiquitin-interacting motif [UIM]- and MIU-related UBD) and MIU1 (motif interacting with ubiquitin 1). Mutations of Ub-interacting residues in UDM1 have little effect on the accumulation of RNF168 to DSB sites, suggesting that it may not be the main site of binding ubiquitylated and polyubiquitylated targets. 73 matched cddid_all.tbl CDD cd22266 cd22266 412080 AcrIE1 Anti-CRISPR type I subtype E1. AcrIE1 (also known as AcrE1) is an anti-CRISPR (Acr) protein which binds as a homodimer to and inactivates the CRISPR-associated helicase/nuclease Cas3 protein. It has been shown that the C-terminal region of AcrIE1 is important for its inhibitory activity. AcrIE1 can convert the endogenous type I-E CRISPR system into a programmable transcriptional repressor. The type I-E Csy is a crRNA-guided surveillance complex, composed of a crRNA and eleven Cas proteins (one Cse1, two Cse2, one Cas5, six Cas7 and one Cas6e), which recruits a nuclease-helicase protein Cas3 for target degradation. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif which inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 1 systems utilize RNA-guided complexes consisting of multiple Cas proteins as the effector proteins to recognize and cleave target DNA. Type I CRISPR-Cas systems are the most widespread in nature, and the Cas protein composition of the employed CRISPR ribonucleoprotein (crRNP) complexes differs between seven subtypes (A to F, U). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 98 matched cddid_all.tbl CDD cd22267 cd22267 439332 AcrID1 Anti-CRISPR type I subtype D1 (AcrID1). AcrID1 is the first example of anti-CRISPR (Acr) protein found in the archaeal viral domain and the first against the CRISPR-Cas type I-D system discovered via functional assays. AcrID1 inhibits the type I-D system by interacting directly with the Cas10d protein, which is required for the interference stage. AcrID1 belongs to a conserved family of compact, dimeric alpha/beta-sandwich proteins characterized by extreme pH and temperature stability and a tendency to form protein fibers. The type I-D Csy complex is a CRISPR RNA (crRNA)-guided surveillance effector complex that includes a type I signature variant of helicase protein, Cas3, and a type III Cas10-like large subunit, Cas10d, in addition to Csc1 (Cas5) and the backbone protein Csc2 (Cas7). The Cas10d protein is predicted to function as the large subunit of the effector complex and the target-cleaving nuclease, but not as part of a signal transduction pathway as shown for the type III systems. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 1 systems utilize RNA-guided complexes consisting of multiple Cas proteins as the effector proteins to recognize and cleave target DNA. Type I CRISPR-Cas systems are the most widespread in nature, and the Cas protein composition of the employed CRISPR ribonucleoprotein (crRNP) complexes differs between seven subtypes (A to F, U). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 92 matched cddid_all.tbl CDD cd22268 cd22268 439248 DPBB_RlpA-like double-psi beta-barrel fold of endolytic peptidoglycan transglycosylase RlpA and similar proteins. Endolytic peptidoglycan transglycosylase RlpA (rare lipoprotein A, RlpA) is a lytic transglycosylase with a strong preference for naked glycan strands that lack stem peptides. It adopts a double-psi beta-barrel (DPBB) fold and is one of four SPOR-domain containing proteins in Escherichia coli (including FtsN, DedA and DamX) that bind peptidoglycan (PG) and are targeted to the septum during division. It directly interacts with the divisome protein FtsK in vitro, and deletion of the rlpA gene partially bypasses the requirement for functional FtsK, a large, multi-spanning membrane protein that facilitates double-stranded DNA translocation during division and sporulation in E. coli and Bacillus subtilis, respectively. In Pseudomonas aeruginosa, RlpA contributes to rod shape maintenance and daughter cell separation. The separation of daughter cells requires extensive PG remodeling. It has been suggested that amidases and RlpA work in tandem to degrade PG in the division septum and lateral wall to facilitate daughter cell separation. 92 matched cddid_all.tbl CDD cd22269 cd22269 439249 DPBB_EG45-like double-psi beta-barrel fold of EG45-like domain-containing proteins. This family contains plant EG45-like domain-containing proteins which show sequence similarity to expansins, and similar proteins. Citrus jambhiri EG45-like domain-containing protein was identified as a protein associated with citrus blight (CB), and is also called blight-associated protein p12 (CjBAp12) or plant natriuretic peptide (PNP). CjBAp12 does not display cell wall loosening activity of expansins. Arabidopsis thaliana EG45-like domain-containing protein 2, also called plant natriuretic peptide A (AtPNP-A), is a systemically mobile natriuretic peptide immunoanalog, recognized by antibodies against vertebrate atrial natriuretic peptides (ANPs), that functions in cell volume regulation. Thus, it has an important and systemic role in plant growth and homeostasis. Due to their similarity to the N-terminal domain of expansin and to endolytic peptidoglycan transglycosylase RlpA, EG45-like domain-containing proteins may adopt a double-psi beta-barrel fold. 106 matched cddid_all.tbl CDD cd22270 cd22270 439250 DPBB_kiwellin-like double-psi beta-barrel fold of the kiwellin family. Kiwellin (KWL) proteins comprise a widespread family of plant-defense proteins that target pathogenic bacterial/fungal effectors that down-regulate plant defense responses. They are part of a spatio-temporally coordinated, plant-wide defense response comprising KWL proteins with overlapping activities. Zea mays KWL1 specifically inhibits the enzymatic activity of the secreted chorismate mutase Cmu1, a virulence-promoting effector of the smut fungus Ustilago maydis. KWL proteins adopt a double-psi beta-barrel (DPBB) fold, which provides a versatile scaffold that can specifically counteract pathogen effectors such as Cmu1. 128 matched cddid_all.tbl CDD cd22271 cd22271 439251 DPBB_EXP_N-like N-terminal double-psi beta-barrel fold domain of the expansin family and similar domains. The plant expansin family consists of four subfamilies, alpha-expansin (EXPA), beta-expansin (EXPB), expansin-like A (EXLA), and expansin-like B (EXLB). EXPA and EXPB display cell wall loosening activity and are involved in cell expansion and other developmental events during which cell wall modification occurs. EXPA proteins function more efficiently on dicotyledonous cell walls, whereas EXPB proteins exhibit specificity for the cell walls of monocotyledons. Expansins also affect environmental stress responses. Expansin family proteins contain an N-terminal domain (D1) homologous to the catalytic domain of glycoside hydrolase family 45 (GH45) proteins but with no hydrolytic activity, and a C-terminal domain (D2) homologous to group-2 grass pollen allergens. This family also includes GH45 endoglucanases from mollusks. This model represents the N-terminal domain of expansins and similar proteins, which adopts a double-psi beta-barrel (DPBB) fold. 109 matched cddid_all.tbl CDD cd22272 cd22272 439252 DPBB_EXLX1-like N-terminal double-psi beta-barrel fold domain of bacterial expansins similar to Bacillus subtilis EXLX1. This subfamily is composed of bacterial expansins including Bacillus subtilis EXLX1, also called expansin-YoaJ. Similar to plant expansins, EXLX1 contains an N-terminal domain (D1) homologous to the catalytic domain of glycoside hydrolase family 45 (GH45) proteins but with no hydrolytic activity, and a C-terminal domain (D2) homologous to group-2 grass pollen allergens. It strongly binds to crystalline cellulose via D2, and weakly binds soluble cellooligosaccharides. Bacterial expansins, which are present in some plant pathogens, have the ability to loosen plant cell walls, but with weaker activity compared to plant expansins. They may have a role in plant-bacterial interactions. This model represents the N-terminal domain of EXLX1 and similar bacterial expansins, which adopts a double-psi beta-barrel (DPBB) fold. 95 matched cddid_all.tbl CDD cd22273 cd22273 439253 DPBB_SPI-like double-psi beta-barrel fold of Streptomyces papain inhibitor and similar proteins. Streptomyces papain inhibitor (SPI) adopts a rigid, thermo-resistant double-psi-beta-barrel (DPBB) fold that is stabilized by two cysteine bridges. SPI serves as a glutamine and lysine donor substrate for microbial transglutaminase (MTG, EC 2.3.2.13) from Streptomycetes, that is used to covalently and specifically link functional amines to glutamine donor sites of therapeutic proteins. SPI is a stress protein produced under hyperthermal stress conditions, and is able to inhibit the cysteine proteases, papain and bromelain, as well as the bovine serine protease trypsin. 101 matched cddid_all.tbl CDD cd22274 cd22274 439254 DPBB_EXPA_N N-terminal double-psi beta-barrel fold domain of the alpha-expansin subfamily. Alpha-expansins (EXPA, expansin-A) have cell wall loosening activity and are involved in cell expansion and other developmental events during which cell wall modification occurs. They also affect environmental stress responses. Arabidopsis thaliana EXPA1 is a cell wall modifying enzyme that controls the divisions marking lateral root initiation. Nicotiana tabacum EXPA4 positively regulates abiotic stress tolerance, and negatively regulates pathogen resistance. Wheat TaEXPA2 is involved in conferring cadmium tolerance. Alpha-expansins belong to the expansin family of proteins that contain an N-terminal domain (D1) homologous to the catalytic domain of glycoside hydrolase family 45 (GH45) proteins but with no hydrolytic activity, and a C-terminal domain (D2) homologous to group-2 grass pollen allergens. This model represents the N-terminal domain of alpha-expansins, which adopts a double-psi beta-barrel (DPBB) fold. 129 matched cddid_all.tbl CDD cd22275 cd22275 439255 DPBB_EXPB_N N-terminal double-psi beta-barrel fold domain of the beta-expansin subfamily. Beta-expansins (EXPB, expansin-B) have cell wall loosening activity and are involved in cell expansion and other developmental events during which cell wall modification occurs. They also affect environmental stress responses. The EXPB subfamily is known in the allergen literature as group-1 grass pollen allergens. EXPB of Bermuda, Johnson, and Para grass pollens, is a major cross-reactive allergen for allergic rhinitis patients in subtropical climate. EXPB1 induces extension and stress relaxation of grass cell walls. Wheat TaEXPB7-B is a beta-expansin gene involved in low-temperature stress and abscisic acid responses. Beta-expansins belong to the expansin family of proteins that contain an N-terminal domain (D1) homologous to the catalytic domain of glycoside hydrolase family 45 (GH45) proteins but with no hydrolytic activity, and a C-terminal domain (D2) homologous to group-2 grass pollen allergens. This model represents the N-terminal domain of beta-expansins, which adopts a double-psi beta-barrel (DPBB) fold. 121 matched cddid_all.tbl CDD cd22276 cd22276 439256 DPBB_EXLA_N N-terminal double-psi beta-barrel fold domain of the expansin-like A subfamily. Expansin-like A (EXLA) belongs to the plant expansin family that also includes alpha-expansin (EXPA), beta-expansin (EXPB), and expansin-like B (EXLB). Unlike EXPA and EXPB, EXLA proteins have not been shown to display cell wall loosening activity. EXLA2 is one of the three EXLA members in Arabidopsis. It lacks expansin activity, but contains a presumed cellulose-interacting domain. EXLA2 may function as a positive regulator of cell elongation in the dark-grown hypocotyl of Arabidopsis, possibly by interference with cellulose metabolism, deposition, or its organization. EXLA belongs to the expansin family of proteins that contain an N-terminal domain (D1) homologous to the catalytic domain of glycoside hydrolase family 45 (GH45) proteins but with no hydrolytic activity, and a C-terminal domain (D2) homologous to group-2 grass pollen allergens. This model represents the N-terminal domain of EXLA proteins, which adopts a double-psi beta-barrel (DPBB) fold. 127 matched cddid_all.tbl CDD cd22277 cd22277 439257 DPBB_EXLB_N N-terminal double-psi beta-barrel fold domain of the expansin-like B subfamily. Expansin-like B (EXLB) belongs to the plant expansin family that also includes alpha-expansin (EXPA), beta-expansin (EXPB), and expansin-like A (EXLA). Unlike EXPA and EXPB, EXLA proteins have not been shown to display cell wall loosening activity. Solanum tuberosum StEXLB6 showed differential expression under the treatments of abscisic acid (ABA), indoleacetic acid (IAA), and gibberellin acid 3 (GA3), as well as under drought and heat stresses, indicating that it is likely involved in potato stress resistance. Soybean GmEXLB1 improves phosphorus acquisition by regulating root elongation and architecture in Arabidopsis. EXLB belongs to the expansin family of proteins that contain an N-terminal domain (D1) homologous to the catalytic domain of glycoside hydrolase family 45 (GH45) proteins but with no hydrolytic activity, and a C-terminal domain (D2) homologous to group-2 grass pollen allergens. This model represents the N-terminal domain of EXLB proteins, which adopts a double-psi beta-barrel (DPBB) fold. 117 matched cddid_all.tbl CDD cd22278 cd22278 439258 DPBB_GH45_endoglucanase double-psi beta-barrel fold of glycoside hydrolase family 45 endoglucanase EG27II and similar proteins. This group is made up of endoglucanases from mollusks similar to Ampullaria crossean endoglucanase EG27II, a glycoside hydrolase family 45 (GH45) subfamily B protein. Endoglucanases (EC 3.2.1.4) catalyze the endohydrolysis of (1-4)-beta-D-glucosidic linkages in cellulose, lichenin, and cereal beta-D-glucans. Animal cellulases, such as endoglucanase EG27II, have great potential for industrial applications such as bioethanol production. GH45 endoglucanases from mollusks adopt a double-psi beta-barrel (DPBB) fold. 143 matched cddid_all.tbl CDD cd22279 cd22279 412081 AcrIF1 Anti-CRISPR type I subtype F1 (AcrIF1). AcrIF1 (also known as AcrF1) is an anti-CRISPR (Acr) protein that targets type I-F Csy and blocks CRISPR-RNA (crRNA) and invader DNA hybridization. It has been shown that multiple copies of AcrIF1 bind to the CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated protein) complex with different modes when working individually or cooperating with AcrIF2, which might exclude target DNA binding through different mechanisms. The type I-F Csy complex is a crRNA-guided surveillance complex composed of a crRNA and nine Cas proteins (one Cas8f, one Cas5f, one Cas6f, and six Cas7f), which recruits a nuclease-helicase protein Cas3 for target degradation. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps: the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif which inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 1 systems utilize RNA-guided complexes consisting of multiple Cas proteins as the effector proteins to recognize and cleave target DNA. Type I CRISPR-Cas systems are the most widespread in nature, and the Cas protein composition of the employed CRISPR ribonucleoprotein (crRNP) complexes differs between seven subtypes (A to F, U). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 77 matched cddid_all.tbl CDD cd22280 cd22280 412082 AcrIF2 "Anti-CRISPR type I subtype F2. AcrIF2 (also known as AcrF2) is an anti-CRISPR (Acr) protein which functions as a double-stranded ""DNA mimic protein"" (DMP) that binds to the type I-F CRISPR-Cas surveillance complex (Csy) and excludes target DNA binding. The key feature of DMPs is their DNA-like shape and charge distribution, and they affect the activity of DNA-binding proteins by occupying their DNA-binding domains. Acidic residues on the surface of AcrIF2 mimic the negative charge distribution on the helical backbone of a DNA duplex. The type I-F Csy complex is a crRNA-guided surveillance complex, composed of a crRNA and nine Cas proteins (one Cas8f, one Cas5f, one Cas6f, and six Cas7f), which recruits a nuclease-helicase protein Cas3 for target degradation. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif which inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 1 systems utilize RNA-guided complexes consisting of multiple Cas proteins as the effector proteins to recognize and cleave target DNA. Type I CRISPR-Cas systems are the most widespread in nature, and the Cas protein composition of the employed CRISPR ribonucleoprotein (crRNP) complexes differs between seven subtypes (A to F, U). Acr families are named for their type and subtype which are numbered sequentially as they are discovered." 86 matched cddid_all.tbl CDD cd22281 cd22281 439333 AcrllA4 Anti-CRISPR type II subtype A4. AcrIIA4 is an anti-CRISPR (Acr) protein which was discovered via a self-targeting method that inhibits the type II-A CRISPR-Cas system (Csy). AcrIIA4 interacts with Cas9-single-guide RNA (sgRNA) and inhibits Cas9 activity by structurally mimicking the protospacer adjacent motif (PAM) to occupy the PAM-interacting site in the PAM-interacting domain, thereby blocking recognition of double-stranded DNA substrates by Cas9. AcrIIA4 further inhibits the endonuclease activity of Cas9 by shielding its RuvC active site. The development of genome editing systems based on the Cas9 endonuclease has greatly facilitated gene knockouts and targeted genetic alterations. Co-expression of Cas9 and AcrIIA4 which is fused with the N terminal region of human Cdt1 (AcrIIA4-Cdt1) not only increases the frequency of homology-directed repair (HDR) but also suppresses off-targets effects. As AcrIIA4 interferes with Cas9 DNA binding activity, it may have use as a CRISPR controller of Cas9-mediated genome engineering: chemically inducible anti-CRISPR protein AcrIIA4 has been engineered to disable Cas9 DNA binding upon the addition of trimethoprim. Cas9-based application of interest to the field of population control is that of the 'gene drive'; CRISPR-Cas9 gene drives have been developed towards reducing the burden of pests and vector-borne diseases such as human malaria vector Anopheles gambiae. Germline expression of a phage-derived AcrIIA4 inactivated CRISPR-based gene drives and restore their inheritance to Mendelian rates in A. gambiae; and AcrIIA4 and AcrIIA2 proteins inhibit active gene drive systems in budding yeast. Almost all type II Acr proteins characterized to date directly interact with the Cas9 endonuclease, although by distinct mechanisms. The type II CRISPR/Cas subtype has a distinct crRNA-guided surveillance complex encoded by cas9 (formerly csn1), cas1, cas2, and csn2 (for type IIA) or cas4 (for type IIB) genes, type II-Cs are generally characterized by the absence of both cas4 and csn2; these genes are located all located in a single transcriptional unit directly upstream of the CRISPR locus. Cleavage of the DNA target in type II systems is carried out by Cas9 which is an RNA-guided double-stranded DNase with two independent nuclease domains, HNH and RuvC. Due to the reliance of the type II system on a single protein for function, Cas9 homologs derived from different subtypes and species have been utilized for numerous gene editing applications. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 2 systems employ a single multi-domain effector Cas9 protein complex that performs target recognition and cleavage. Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 76 matched cddid_all.tbl CDD cd22282 cd22282 439334 AcrllA1 Anti-CRISPR type II subtype A1. AcrIIA1 is an anti-CRISPR (Acr) protein which was discovered via a self-targeting method that inhibits the type II-A CRISPR-Cas system (Csy). AcrIIA1 contains an N-terminal domain that resembles the helix-turn-helix (HTH) motif of transcriptional factors and a C-terminal domain that adopts a fold of unknown function. This cd model spans both domains. AcrIIA1 from Listeria monocytogenes prophage forms a homodimer and it is anticipated that AcrIIA1 recognizes and associates with heterogeneous RNA molecules to abolish CRISPR-Cas immunity. Almost all type II Acrs characterized to date directly interact with the Cas9 endonuclease, although by distinct mechanisms. The type II CRISPR/Cas subtype has a distinct crRNA-guided surveillance complex encoded by cas9 (formerly csn1), cas1, cas2, and csn2 (for type IIA) or cas4 (for type IIB) genes, all located in a single transcriptional unit directly upstream of the CRISPR locus. Cleavage of the DNA target in type II systems is carried out by Cas9 which is an RNA-guided double-stranded DNase with two independent nuclease domains, HNH and RuvC. Due to the reliance of the type II system on a single protein for function, Cas9 homologs derived from different subtypes and species have been utilized for numerous gene editing applications. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 2 systems employ a single multi-domain effector Cas9 protein complex that performs target recognition and cleavage. Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 145 matched cddid_all.tbl CDD cd22283 cd22283 409000 HD_XRCC4_N N-terminal head domain found in X-ray repair cross-complementing protein 4 and similar proteins. X-ray repair cross-complementing protein 4 (XRCC4) is a DNA repair protein involved in DNA non-homologous end-joining (NHEJ), which is required for double-strand break repair and V(D)J recombination. The DNA ligase IV (LIG4)- XRCC4 complex is responsible for the ligation step of NHEJ, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends. XRCC4 monomers are comprised of an N-terminal globular head domain, a centrally located coiled-coil, and a C-terminal region. These monomers homodimerize through two dimerization domains, the N-terminal globular head domains and long extended alpha-helical coiled-coil regions. In addition, XRCC4 and XLF form symmetric heterodimers that interact through their globular head domains at the opposite end of the homodimer interface, and may form XLF-XRCC4 filaments. This model corresponds to the N-terminal head domain of XRCC4, which is structurally related to other XRCC4-superfamily members, PAXX, XLF, SAS6, and CCDC61. 117 matched cddid_all.tbl CDD cd22284 cd22284 409001 HD_CCDC61_N N-terminal head domain found in coiled-coil domain-containing protein 61 and similar proteins. Coiled-coil domain-containing protein 61 (CCDC61), also known as variable flagellar number 3 (VFL3), is a centrosomal protein required for spindle assembly and precise chromosome alignments in mitosis. It is the human ortholog of proteins required for anchoring distinct sets of cytoskeletal fibers to centrioles in unicellular eukaryotes. CCDC61 monomers are comprised of an N-terminal globular head domain, a centrally located coiled-coil, and a C-terminal region. These monomers homodimerize through two homodimerization domains, the N-terminal globular head domains and long extended alpha-helical coiled-coil regions. These CCDC61 homodimers assembles into linear filaments. This model corresponds to the N-terminal head domain of CCDC61, which is structurally related to other XRCC4-superfamily members, XRCC4, XLF, SAS6, and PAXX. 135 matched cddid_all.tbl CDD cd22285 cd22285 409002 HD_XLF_N N-terminal head domain found in XRCC4-like factor and similar proteins. XRCC4-like factor (XLF), also known as non-homologous end-joining factor 1 (NHEJ1) or protein cernunnos, is involved in DNA nonhomologous end joining (NHEJ), which is required for double-strand break (DSB) repair and V(D)J recombination. It interacts with the XRCC4-DNA ligase IV complex to promote NHEJ. It may act in concert with XRCC6/XRCC5 (Ku) to stimulate XRCC4-mediated joining of blunt ends and several types of mismatched ends that are non-complementary or partially complementary. XLF binds DNA in a length-dependent manner. Similar to XRCC4, XLF monomers are comprised of an N-terminal globular head domain, a centrally located coiled-coil, and a C-terminal region. These monomers homodimerize through two dimerization domains, the N-terminal globular head domains and long extended alpha-helical coiled-coil regions. In addition, XLF and XRCC4 form symmetric heterodimers that interact through their globular head domains at the opposite end of the homodimer interface, and may form XLF-XRCC4 filaments. This model corresponds to the N-terminal head domain of XLF, which is structurally related to other XRCC4-superfamily members, XRCC4, PAXX, SAS6, and CCDC61. 109 matched cddid_all.tbl CDD cd22286 cd22286 409003 HD_PAXX_N N-terminal head domain found in paralog of XRCC4 and XLF, and similar proteins. Paralog of XRCC4 and XLF (PAXX), also called XRCC4-like small protein, is a paralog of X-ray repair cross-complementing protein 4 (XRCC4) and XRCC4-like factor (XLF). It is involved in non-homologous end joining (NHEJ), a major pathway to repair double-strand breaks (DSBs) in DNA. It may act as a scaffold required to stabilize the DSB-repair protein Ku heterodimer, composed of XRCC5/Ku80 and XRCC6/Ku70, at double-strand break sites in cells. It functions with XRCC4 and XLF to bring about DSB repair and cell survival in response to DSB-inducing agents. Similar to XRCC4 and XLF, PAXX monomers are comprised of an N-terminal globular head domain, a centrally located coiled-coil, and a C-terminal region. These monomers homodimerize through two homodimerization domains, the N-terminal globular head domains and long extended alpha-helical coiled-coil regions. This model corresponds to the N-terminal head domain of PAXX, which is structurally related to other XRCC4-superfamily members, XRCC4, XLF, SAS6, and CCDC61. 102 matched cddid_all.tbl CDD cd22287 cd22287 412083 REV3L_RBD REV7 binding domain found in protein reversionless 3-like (REV3L) and similar proteins. REV3L, also called REV3-like, or REV3, or DNA polymerase zeta catalytic subunit (POLZ), is the catalytic subunit of the DNA polymerase zeta complex, an error-prone polymerase specialized in translesion DNA synthesis (TLS). REV3L lacks an intrinsic 3'-5' exonuclease activity and thus has no proofreading function. The model corresponds to a conserved region that is responsible for the binding of REV7. 23 matched cddid_all.tbl CDD cd22288 cd22288 412084 CWC27_CTD C-terminal domain of spliceosome-associated protein CWC27 and similar proteins. CWC27, also called antigen NY-CO-10, or probable inactive peptidyl-prolyl cis-trans isomerase CWC27, or PPIase CWC27, or serologically defined colon cancer antigen 10, is part of the spliceosome and plays a role in pre-mRNA splicing. It is a probable inactive PPIase with no peptidyl-prolyl cis-trans isomerase activity. This model corresponds to the C-terminal domain of CWC27, which interacts with CWC22 MIF4G domain. 56 matched cddid_all.tbl CDD cd22289 cd22289 412085 RecQL4_SLD2_NTD N-terminal homeodomain-like domain of metazoan RecQ protein-like 4 (RecQL4), fungal DNA replication regulator SLD2 and similar proteins. RecQL4, also called ATP-dependent DNA helicase Q4, or DNA helicase, RecQ-like type 4 (RecQ4), or RTS, is a DNA-dependent ATPase that may modulate chromosome segregation. This family also includes fungal DNA replication regulator SLD2, also known as DNA replication and checkpoint protein 1 (DRC1), which functions with DPB11 to control DNA replication and the S-phase checkpoint. It is also required for the proper activation of RAD53 in response to DNA damage and replication blocks. This model corresponds to the N-terminal domain of RecQL4 and SLD2, which is a homeodomain-like DNA interaction motif. 49 matched cddid_all.tbl CDD cd22290 cd22290 412086 cc_RasGRP1_C C-terminal coiled-coil domain of RAS guanyl-releasing protein 1 (RasGRP1) and similar proteins. RasGRP1, also called calcium and DAG-regulated guanine nucleotide exchange factor II (CalDAG-GEFII), or Ras guanyl-releasing protein, acts as a calcium- and diacylglycerol (DAG)-regulated nucleotide exchange factor, specifically activating Ras through the exchange of bound GDP for GTP. This model corresponds to the C-terminal coiled-coil domain of RasGRP1, which mediates oligomerization. 55 matched cddid_all.tbl CDD cd22291 cd22291 412087 cc_THAP11_C C-terminal coiled-coil domain of THAP domain-containing protein 11. THAP domain-containing protein 11 (THAP11) is a cell cycle and cell growth regulator differentially expressed in cancer cells. It acts as a transcriptional repressor that plays a central role for embryogenesis and the pluripotency of embryonic stem (ES) cells. This model corresponds to the C-terminal coiled-coil domain of THAP11, which is involved in protein dimerization. 61 matched cddid_all.tbl CDD cd22292 cd22292 412088 cc_Cep135_MBD coiled-coil microtubule binding domain of centrosomal protein of 135 kDa (Cep135) and similar proteins. Cep135, also called centrosomal protein 4, is involved in early centriole assembly, duplication, biogenesis, and formation. It is required for the recruitment of CEP295 to the proximal end of new-born centrioles at the centriolar microtubule wall during early S phase in a PLK4-dependent manner. This model corresponds to a conserved coiled-coil domain of Cep135, which is critical for microtubule binding. 62 matched cddid_all.tbl CDD cd22293 cd22293 412089 RBD_SHLD3_N N-terminal REV7-binding domain of Shieldin complex subunit 3 (SHLD3) and similar proteins. SHLD3, also called REV7-interacting novel NHEJ regulator 1, or Shield complex subunit 3, is a component of the shieldin complex, which plays an important role in the repair of DNA double-stranded breaks (DSBs). During G1 and S phase of the cell cycle, the complex functions downstream of TP53BP1 to promote non-homologous end joining (NHEJ) and suppress DNA end resection. SHLD3 mediates various NHEJ-dependent processes including immunoglobulin class-switch recombination, and fusion of unprotected telomeres. The model corresponds to the N-terminal REV7-binding domain of SHLD3, which contains a REV7-binding FXPWFP motif. 61 matched cddid_all.tbl CDD cd22294 cd22294 412090 MYO6_MIU_linker MIU-linker domain found in unconventional myosin-VI. Myosins are actin-based motor molecules with ATPase activity. Unconventional myosins function in intracellular movements. Myosin-VI, also called unconventional myosin-6 (MYO6), is a reverse-direction motor protein that moves towards the minus-end of actin filaments. It is required for the structural integrity of the Golgi apparatus via the p53-dependent pro-survival pathway. It appears to be involved in a very early step of clathrin-mediated endocytosis in polarized epithelial cells. It modulates RNA polymerase II-dependent transcription. As part of the DISP complex, Myosin-VI may regulate the association of septins with actin and thereby regulate the actin cytoskeleton. Myosin-VI is encoded by the MYO6 gene, the human homologue of the gene responsible for deafness in Snell's waltzer mice. It is mutated in autosomal dominant nonsyndromic hearing loss. This model corresponds to a conserved region of myosin-VI, which consist of three helices: MIU (Motif Interacting with Ubiquitin), a common linker helix (linker-alpha1) and an isoform-specific helix (linker-alpha2). 69 matched cddid_all.tbl CDD cd22295 cd22295 411969 cc_LAMB_C C-terminal coiled-coil domain found in the laminin subunit beta (LAMB) family. The LAMB family contains four members, LAMB1-4. They are components of laminin, a complex glycoprotein consisting of three different polypeptide chains (alpha, beta, gamma). Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration, and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components. This model corresponds to the C-terminal coiled-coil domain of LAMB, which may be involved in the integrin binding activity. 70 matched cddid_all.tbl CDD cd22296 cd22296 412091 CBD_TRPV5_C C-terminal CaM binding domain found in transient receptor potential cation channel subfamily V member 5 (TRPV5) and similar proteins. TRPV5, also called calcium transport protein 2 (CaT2), epithelial calcium channel 1 (ECaC1), or Osm-9-like TRP channel 3 (OTRPC3), is a constitutively active calcium selective cation channel that might be involved in Ca(2+) reabsorption in kidney and intestine. The channel is activated by low internal calcium levels, and the current exhibits an inward rectification. The model corresponds to the C-terminal calmodulin (CaM) binding domain of TRPV5, which contains several CaM binding sites in the N- and C-terminal tails. The binding of CaM to the C-terminal binding site is essential for the fast Ca2+-dependent inactivation of the channel. 73 matched cddid_all.tbl CDD cd22297 cd22297 412092 PSMD4_RAZUL RAZUL (Rpn10 AZUL-binding) domain of 26S proteasome non-ATPase regulatory subunit 4 (PSMD4) and similar proteins. PSMD4 is also called 26S proteasome regulatory subunit RPN10, 26S proteasome regulatory subunit S5A, antisecretory factor 1, AF, ASF, or multiubiquitin chain-binding protein (MCB1). It acts as a ubiquitin receptor subunit through ubiquitin-interacting motifs and selects ubiquitin-conjugates for destruction. It displays a preferred selectivity for longer polyubiquitin chains. PSMD4 is a component of the 26S proteasome, a multiprotein complex involved in the ATP-dependent degradation of ubiquitinated proteins. The proteasome participates in numerous cellular processes, including cell cycle progression, apoptosis, or DNA damage repair. The model corresponds to the C-terminal Rpn10 AZUL-binding domain (RAZUL) of PSMD4, which is responsible for binding the AZUL domain of E6AP/UBE3A. AZUL stands for amino-terminal zinc-binding domain of ubiquitin E3a ligase. 48 matched cddid_all.tbl CDD cd22298 cd22298 412093 NuMA_LGNBD LGN binding domain (LGNBD) of nuclear mitotic apparatus protein (NuMA) and similar proteins. NuMA, also called nuclear matrix protein-22 (NMP-22), nuclear mitotic apparatus protein 1 (NUMA1), or SP-H antigen, is a microtubule (MT)-binding protein that plays a role in the formation and maintenance of spindle poles and the alignment and segregation of chromosomes during mitotic cell division. It is involved in the establishment of mitotic spindle orientation during metaphase, and elongation during anaphase in a dynein-dynactin-dependent manner. NuMA, in complex with LGN, forms NuMA:LGN hetero-hexamers that promote spindle orientation. The model corresponds to the LGN binding domain (LGNBD) of NuMA. LGN (named for leu-gly-asn repeats) is also known as G protein signaling modulator 2. 56 matched cddid_all.tbl CDD cd22299 cd22299 411970 cc_LAMB2_C C-terminal coiled-coil domain found in laminin subunit beta-2 (LAMB2). LAMB2 is also called laminin B1s chain, laminin-11 subunit beta, laminin-14 subunit beta, laminin-15 subunit beta, laminin-3 subunit beta, laminin-4 subunit beta, laminin-7 subunit beta, laminin-9 subunit beta, S-laminin subunit beta, or S-LAM beta (LAMS). It is an important component of the interphotoreceptor matrix and plays a role in rod morphogenesis. It may also have an important function in the sarcolemmal basement membrane. Mutations of the LAMB2 gene mainly cause Pierson syndrome (microcoria-congenital nephrosis syndrome). LAMB2 is a component of laminin, a complex glycoprotein consisting of three different polypeptide chains (alpha, beta, gamma). Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration, and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components. This model corresponds to the C-terminal coiled-coil domain of LAMB2, which may be involved in the integrin binding activity. 72 matched cddid_all.tbl CDD cd22300 cd22300 411971 cc_LAMB1_C C-terminal coiled-coil domain found in laminin subunit beta-1 (LAMB1). LAMB1 is also called laminin B1 chain, laminin-1 subunit beta, laminin-10 subunit beta, laminin-12 subunit beta, laminin-2 subunit beta, laminin-6 subunit beta, or laminin-8 subunit beta. It is a glycoprotein that is involved in the pathogenesis of neurodevelopmental disorders. It also plays a crucial role in both lung morphogenesis and physiological function. Mutations in LAMB1 are associated with Cobblestone brain malformation (COB) with variable muscular or ocular abnormalities. LAMB1 is a component of laminin, a complex glycoprotein consisting of three different polypeptide chains (alpha, beta, gamma). Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration, and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components. This model corresponds to the C-terminal coiled-coil domain of LAMB1, which is involved in the integrin binding activity. 73 matched cddid_all.tbl CDD cd22301 cd22301 411972 cc_LAMB4_C C-terminal coiled-coil domain found in laminin subunit beta-4 (LAMB4). LAMB4, also called laminin beta-1-related protein, is a component of laminin, a complex glycoprotein consisting of three different polypeptide chains (alpha, beta, gamma). Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration, and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components. Mutations or loss of LAMB4 may be features of gastric and colorectal cancers. Reduced LAMB4 levels may contribute to colonic dysmotility associated with diverticulitis. This model corresponds to the C-terminal coiled-coil domain of LAMB4, which may be involved in the integrin binding activity. 70 matched cddid_all.tbl CDD cd22302 cd22302 411973 cc_DmLAMB1-like_C C-terminal coiled-coil domain found in Drosophila melanogaster laminin subunit beta-1 (DmLAMB1) and similar proteins. DmLAMB1, also called LanB1, is a glycoprotein required for nidogen (Ndg) localization to the basement membrane. It is a component of laminin, a complex glycoprotein consisting of three different polypeptide chains (alpha, beta, gamma). Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration, and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components. This model corresponds to the C-terminal coiled-coil domain of DmLAMB1, which may be involved in the integrin binding activity. 70 matched cddid_all.tbl CDD cd22303 cd22303 411974 cc_LAMB3_C C-terminal coiled-coil domain found in laminin subunit beta-3 (LAMB3). LAMB3 is also called epiligrin subunit beta, kalinin B1 chain, kalinin subunit beta, laminin B1k chain, laminin-5 subunit beta, or nicein subunit beta. It is a major component of the basement membrane in most adult tissues. Mutations in LAMB3 are associated with Herlitz junctional epidermolysis bullosa (H-JEB), a severe autosomal recessive disorder characterized by blister formation within the dermal-epidermal basement membrane. LAMB3 is a component of laminin, a complex glycoprotein consisting of three different polypeptide chains (alpha, beta, gamma). Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration, and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components. This model corresponds to the C-terminal coiled-coil domain of LAMB3, which may be involved in the integrin binding activity. 71 matched cddid_all.tbl CDD cd22304 cd22304 408997 VpdB_C C-terminal fragment of effector protein VpdB. This model represents the C-terminal fragment of the effector protein VpdB that binds the Legionella pneumophila Dot/Icm type IVB coupling protein (T4CP) complex which includes IcmS, IcmW, and LvgA. These L. pneumophila proteins are known to selectively assist the export of a subclass of effectors. The effector protein VpdB, like other L. pneumophila effectors VpdA, VpdC and VpdD, is a homolog of phospholipase A (PLA) patatin-like enzymes. However, VpdB does not appear to be involved in phospholipid metabolism. The structure reveals interactions between LvgA and a linear motif in the C-terminus of VpdB. This binding interface of LvgA also interacts with the C-terminal region of three additional L. pneumophila effectors, SidH, SetA, and PieA. 126 matched cddid_all.tbl CDD cd22305 cd22305 412069 NDFIP1 NEDD4 family-interacting protein 1. The NEDD4 (neural precursor cell expressed, developmentally down-regulated protein 4)-family interacting proteins (NDFIPs) are adaptor proteins that recruit NEDD4 E3 ligases to specific substrate proteins, which leads to the ubiquitylation and subsequent degradation of these proteins. They also act as activators of the E3 ligase activity by releasing NEDD4 ligase from its auto-inhibitory conformation. NDFIP1 has been shown to play a role in a variety of processes, including inflammation, immune signaling, and nuclear trafficking. 206 matched cddid_all.tbl CDD cd22306 cd22306 412070 NDFIP2 NEDD4 family-interacting protein 2. The NEDD4 (neural precursor cell expressed, developmentally down-regulated protein 4)-family interacting proteins (NDFIPs) are adaptor proteins that recruit NEDD4 E3 ligases to specific substrate proteins, which leads to the ubiquitylation and subsequent degradation of these proteins. They also act as activators of the E3 ligase activity by releasing NEDD4 ligase from its auto-inhibitory conformation. NDFIP2 may play a role in protein trafficking. 229 matched cddid_all.tbl CDD cd22307 cd22307 412094 Adgb_C_mid-like C-terminal middle region of Androglobins (Adgbs) and related proteins; including permuted globin domain and IQ motif. Androglobin (Adgb, also known as Calpain-7-like protein, CAPN7L) is a large multidomain protein consisting of an N-terminal peptidase C2 family calpain-like domain, an IQ calmodulin-binding motif, and an internal, circularly permuted globin domain. The canonical secondary structure of hemoglobins is an 3-over-3 alpha-helical sandwich structure, where the eight alpha-helical segments are conventionally labeled, A-H, according to their sequential order; Adgbs differ from this in having helices C-H followed by A-B. Adgbs and other phylogenetically ancient globins, such as neuroglobins and globin X, form hexacoordinated heme iron complexes. Globins contain various highly conserved residues of the heme pocket: including a Phe in the interhelical position CD1 (Phe CD1, first position in the loop between the helices C and D) that is packed against the heme, a His at the 7th position of the E-helix (His E7) that binds the heme iron distally, and a His at the 8th position of the F-helix (His F8) that binds the heme iron proximally. Unlike other hexacoordinated globins, Adgbs have an E7 Gln; their hexacoordination scheme is [Gln]-Fe-[His]. In mammals, Adgb is mainly expressed in the testes and may play an important role in spermatogenesis. Arthropod Adgbs have degenerate globin domains (DOI:10.3389/fgene.2020.00858). This model spans the permuted globin domain, the IQ motif, and a conserved region of about 200 amino acid residues located C-terminal to the globin domain; it does not include the N-terminal protease domain or the large uncharacterized C-terminal domain of approximately 500 residues. 416 matched cddid_all.tbl CDD cd22308 cd22308 411712 Af1548-like Archeoglobus fulgidus Af1548 and similar putative endonucleases. This family belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 165 matched cddid_all.tbl CDD cd22309 cd22309 411713 AgeI-like restriction endonuclease AgeI and similar endonucleases. Type IIP restriction endonuclease AgeI recognizes a palindromic sequence 5'-A|CCGGT-3' and cuts it ('|' denotes the cleavage site) producing staggered DNA ends. It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 205 matched cddid_all.tbl CDD cd22310 cd22310 411714 BcnI-like Restriction endonuclease BcnI and similar endonucleases. Restriction endonuclease BcnI cleaves duplex DNA containing the sequence 5'-CC|SGG-3' (S stands for C or G, | designates a cleavage position) to generate staggered products with single nucleotide 5'-overhangs. It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 229 matched cddid_all.tbl CDD cd22311 cd22311 411715 BglI-like Restriction endonuclease BglI and similar endonucleases. BglI is a type II restriction endonuclease that recognizes the interrupted DNA sequence GCCNNNNNGGC and cleaves between the fourth and fifth unspecified base pair to produce overhanging ends; it belongs to a superfamily of nucleases including very short patch repair (Vsr) Endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 284 matched cddid_all.tbl CDD cd22312 cd22312 411716 BglII-like Restriction endonuclease BglII and similar endonucleases. Restriction endonuclease BglII cleaves duplex DNA containing the sequence 5'-A|GATCT-3' (| designates the cleavage position) to generate staggered products with four nucleotide 5'-overhangs. It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 178 matched cddid_all.tbl CDD cd22313 cd22313 411717 BsaWI-like endonuclease BsaWI and similar endonucleases. The type II restriction endonuclease BsaWI recognizes a degenerated sequence 5'-W|CCGGW-3', where W stands for A or T and '|' denotes the cleavage site. It belongs to a family of restriction endonucleases that recognize a conserved CCGG tetranucleotide in their target and form homodimers or homotetramers, requiring binding of one, two or three DNA targets for optimal catalytic activity. They are part of a yet larger superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many other restriction endonucleases, such as EcoRI, BamHI, and FokI. 276 matched cddid_all.tbl CDD cd22314 cd22314 411718 Bse634I-like Restriction endonuclease Bse634I and similar endonucleases. Bacillus stearothermophilus restriction endonuclease Bse634I recognizes the nucleotide sequence R|CCGGY (R = A or G, Y = T or C, with | designating the cleavage site) and is an isoschisomer of Citrobacter freundii restriction endonuclease Cfr10I; it is active as a homotetramer and belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 281 matched cddid_all.tbl CDD cd22315 cd22315 411719 BsoBI-like Type II restriction endonuclease BsoBI and similar proteins. BsoBI is a thermophilic PDDEXK-family restriction endonuclease exhibiting both base-specific and degenerate recognition within the sequence C-Y-C-G-R-G. (R = A or G, Y = T or C) A conserved histidine has been proposed to act as a general base in the catalysis. BsoBI belongs to a wider superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 288 matched cddid_all.tbl CDD cd22316 cd22316 411720 BspD6I-like nicking endonuclease Nt.BspD6I and similar endonucleases. Heterodimeric type II restriction endonuclease nicking endonuclease BspD6I recognizes a pseudosymmetric DNA sequence (5'-GAGTC) and cuts both strands outside the recognition motif 4 nucleotides downstream. It forms the large subunit in a heterodimeric arrangement. This catalytic domain/subunit belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 345 matched cddid_all.tbl CDD cd22317 cd22317 411721 BstYI-like type II restriction endonuclease BstYI and similar proteins. BstYI is a thermophilic PDDExK-family restriction endonuclease with specificities that overlap those of BamHI and BglII; it cleaves the degenerate hexanucleotide R-G-A-T-C-Y (R = A or G, Y = T or C) and is part of a larger superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 188 matched cddid_all.tbl CDD cd22318 cd22318 411722 DNA2_N-like Nuclease domain of the nuclease/helicase DNA2 and related nucleases. The eukaryotic nuclease/helicase DNA2 processes double-strand breaks in DNA that have single-stranded ends/overhangs, as well as Okazaki fragments and stalled replication forks; it is therefore crucial for maintaining the integrity of the genome. The nuclease domain modeled here belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 234 matched cddid_all.tbl CDD cd22319 cd22319 411723 DpnI-like type II restriction endonuclease DpnI and similar proteins. This catalytic PD-(D/E)XK domain co-occurs with a C-terminal winged-helix DNA binding domain that is not included in the model. Both domains of R.DpnI bind DNA and are separately specific for the Gm6ATC sequences in Dam-methylated DNA. DpnI or Dam-replacing protein (DRP) is a restriction endonuclease flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis. Type II restriction endonuclease DpnI belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 174 matched cddid_all.tbl CDD cd22320 cd22320 411724 Ecl18kI-like Restriction endonuclease Ecl18kI and similar endonucleases. Restriction endonuclease Ecl18kI recognizes the sequence |CCNGG and cleaves it before the outer C (| designates the cleavage site) to generate 5 nt 5'-overhangs. It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 262 matched cddid_all.tbl CDD cd22321 cd22321 411725 EcoO109I-like Restriction endonuclease EcoO109I and related endonucleases. EcoO109I is a type II restriction endonuclease that recognizes ds DNA with a seven-base pair motif of both degenerate and discontinuous sequence, RG|GNCCY (R = A or G, Y = T or C, with | designating the cleavage site), and generates 5'-overhangs; it belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 232 matched cddid_all.tbl CDD cd22322 cd22322 411726 EcoRII-like Restriction endonuclease EcoRII and similar endonucleases. Restriction endonuclease EcoRII recognizes the sequence 5'-CCWGG-3' (W stands for A or T); it requires binding of a second target site as an allosteric effector in order to be active. EcoRII belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 211 matched cddid_all.tbl CDD cd22323 cd22323 411727 EcoRV-like Restriction endonuclease EcoRV and similar endonucleases. Type II restriction endonuclease EcoRV recognizes the site 5'-GAT|ATC-3' (| denotes the cleavage site) and functions as a homodimer; it belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 221 matched cddid_all.tbl CDD cd22324 cd22324 411728 Endonuclease_I Endonuclease I and similar nucleases. Junction-resolving T7 endonuclease I is a nuclease that is selective for the structure of the four-way DNA junction, it belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 114 matched cddid_all.tbl CDD cd22325 cd22325 411729 ERCC1_C-like Central domain of ERCC1. ERCC1 is a subunit of the DNA structure-specific endonuclease XPF-ERCC1, which incises a damaged DNA strand on the 5' side of a lesion during nucleotide excision repair. It also plays roles in DNA interstrand crosslink repair and homologous recombination. The ERCC1 central domain modeled here interacts tightly with XPF and may be involved in binding to single-stranded DNA. It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 128 matched cddid_all.tbl CDD cd22326 cd22326 411730 FAN1-like repair nuclease FAN1. This model characterizes a set of nucleases that resemble Holliday-junction resolving enzymes. They belong to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 652 matched cddid_all.tbl CDD cd22327 cd22327 411731 FokI_nuclease-like Nuclease domain of restriction endonuclease FokI and similar endonucleases. The type II restriction endonuclease FokI recognizes an asymmetric nucleotide sequence 5'-GGATG(N)9/13 and cleaves both DNA strands outside the recognition motif; its nuclease domain belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and HindIII. 161 matched cddid_all.tbl CDD cd22328 cd22328 411732 Hef-like Hef-like homing endonuclease and similar nucleases. Hef-like homing endonuclease such as I-Bth0305I, which is encoded within a group I intron in the recA gene of a Bacillus thuringiensis bacteriophage and cleaves a DNA target in the uninterrupted recA gene at a position immediately adjacent to the intron insertion site. It belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 99 matched cddid_all.tbl CDD cd22329 cd22329 411733 HincII-like Restriction endonuclease HincII and similar endonucleases. Type II restriction endonuclease HincII cleaves double-stranded DNA 5'-GTY|RAC-3' (| denotes the cleavage site, Y stands for C or T, R stand for A or G ) creating blunt ends. It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 252 matched cddid_all.tbl CDD cd22330 cd22330 411734 HindIII-like Restriction endonuclease HindIII and similar endonucleases. The type II restriction endonuclease HindIII cleaves DNA at the palindromic sequence A|AGCTT (| denotes the cleavage site). It belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 289 matched cddid_all.tbl CDD cd22331 cd22331 411735 HinP1I-like Restriction endonuclease HinP1I and similar endonucleases. HinP1I is a type II restriction endonuclease that recognizes and cleaves a palindromic tetranucleotide sequence (G|CGC) in double-stranded DNA, producing 2 nt 5' overhanging ends, it belongs to the PDDEXK superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 243 matched cddid_all.tbl CDD cd22332 cd22332 411736 HsdR_N N-terminal domain of HsdR motor subunit of type I restriction-modification enzyme EcoR124I and similar systems. The N-terminal endonuclease-like domain of HsdR motor subunit of type I restriction-modification enzyme EcoR124I belongs to a wider superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 226 matched cddid_all.tbl CDD cd22333 cd22333 411737 LlaBIII_nuclease-like nuclease domain of type ISB restriction-modification enzyme LlaBIII and similar nuclease domains. This N-terminal nuclease domain belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 149 matched cddid_all.tbl CDD cd22334 cd22334 411738 MspI-like Restriction endonuclease MspI and similar endonucleases. The type II restriction endonuclease MspI It recognizes and cleaves the palindromic tetranucleotide sequence 5'-C|CGG (| denotes the cleavage site) leaving 2 base 5' overhangs. It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 262 matched cddid_all.tbl CDD cd22335 cd22335 411739 MspjI-like Modification-dependent restriction endonuclease MspjI and similar endonucleases. MspJI recognizes 5-methylcytosine or 5-hydroxymethylcytosine as part of the motif CNN(G/A) and cleaves both strands at fixed distances (N(12)/N(16)) away from the modified cytosine at the 3'-side. It belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 185 matched cddid_all.tbl CDD cd22336 cd22336 411740 MunI-like restriction endonuclease MunI and similar proteins. MunI ( E.C. 3.1.21.4) is a type II restriction enzyme that catalyzes the hydrolysis of DNA, recognizing the palindromic hexanucleotide sequence CAATTG (with the cleavage site after C-1), and is very similar to EcoRI. They belong to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 200 matched cddid_all.tbl CDD cd22337 cd22337 411741 MvaI-like Restriction Endonuclease MvaI and similar endonucleases. Restriction endonuclease MvaI recognizes the sequence CC|WGG (W stands for A or T, '|' designates the cleavage site) and generates products with single nucleotide 5'-overhangs; it belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 239 matched cddid_all.tbl CDD cd22338 cd22338 411742 NaeI-like Restriction endonuclease NaeI and similar endonucleases. The type II restriction endonuclease NaeI recognizes and cleaves the DNA motif GCC|GGC (| denotes the cleavage site) and forms a covalent bond with the cleaved substrate. The enzyme binds two DNA recognition sites and only cleaves one DNA sequence. It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 256 matched cddid_all.tbl CDD cd22339 cd22339 411743 NciI-like Restriction endonuclease NciI and similar endonucleases. NciI is a type II restriction endonuclease that recognizes and cleaves the sequence CC|SGG (S stands for C or G, | denotes the cleavage site). It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 170 matched cddid_all.tbl CDD cd22340 cd22340 411744 NgoMIV-like Restriction endonuclease NgoMIV and similar endonucleases. Type II restriction endonuclease NgoMIV recognizes and cleaves the palindromic sequence 5'-G|CCGGC-3' (| denotes the cleavage site) to produce 4 bp 5' staggered ends. It is active as a homotetramer and belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 238 matched cddid_all.tbl CDD cd22341 cd22341 411745 NucS-like Mismatch restriction endonuclease NucS and similar nucleases. Archaeal mismatch restriction endonuclease NucS and its ortholog EndoMS specifically cleave dsDNA containing mismatched bases. They belong to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 237 matched cddid_all.tbl CDD cd22342 cd22342 411746 Pa4535-like putative restriction endonuclease similar to Pseudomonas aeruginosa Pa4535. These proteins belong to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 195 matched cddid_all.tbl CDD cd22343 cd22343 411747 PDDEXK_lambda_exonuclease-like Uncharacterized nucleases similar to lambda phage exonuclease. This model characterizes a diverse set of nucleases such as alkaline exonuclease from Laribacter hongkongensis, lambda phage exonuclease, or a Cas4-like protein from the Mimivirus virophage resistance element system. They belong to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 182 matched cddid_all.tbl CDD cd22344 cd22344 411748 PDDEXK_nuclease uncharacterized PDDEXK nuclease may function as a restriction endonuclease. This family belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 220 matched cddid_all.tbl CDD cd22345 cd22345 411749 PDDEXK_nuclease uncharacterized PDDEXK nuclease may function as a restriction endonuclease. This family belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 201 matched cddid_all.tbl CDD cd22346 cd22346 411750 PDDEXK_nuclease uncharacterized PDDEXK nuclease may function as a restriction endonuclease. This family belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 221 matched cddid_all.tbl CDD cd22347 cd22347 411751 PDDEXK_nuclease uncharacterized PDDEXK nuclease may function as a restriction endonuclease. This family belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 203 matched cddid_all.tbl CDD cd22348 cd22348 411752 PDDEXK_nuclease uncharacterized PDDEXK nuclease may function as a restriction endonuclease. This family belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 218 matched cddid_all.tbl CDD cd22349 cd22349 411753 PDDEXK_RNA_polymerase-like Endonuclease domain of segmented negative-strand RNA virus (sNSV) polymerases. The N-terminal endonuclease domain of sNSV polymerases is essential for viral cap-dependent transcription; it has endonuclease activity and belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 182 matched cddid_all.tbl CDD cd22350 cd22350 411754 PspGI-like Restriction endonuclease PspGI and similar nucleases. PspGI is an isoschizomer of EcoRII, it recognizes and cleaves the DNA sequence 5'-|CCWGG-3' (| denotes the cleavage site, W stands for A or T). It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 239 matched cddid_all.tbl CDD cd22351 cd22351 411755 PvuII-like Restriction endonuclease PvuII and similar nucleases. The type II restriction endonuclease PvuII recognizes and cleaves the DNA sequence 5'-CAG|CTG-3' leaving blunt ends (| denotes the cleavage site). It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 151 matched cddid_all.tbl CDD cd22352 cd22352 411756 RecB_C-like C-terminal nuclease domain of exodeoxyribonuclease V subunit RecB and similar proteins. Exodeoxyribonuclease V subunit beta (RecB) is a helicase/nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair; it binds to DSBs and unwinds DNA via a rapid and highly processive ATP-dependent bidirectional helicase. The C-terminal PDDEXK nuclease domain belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 215 matched cddid_all.tbl CDD cd22353 cd22353 411757 RecC_C-like C-terminal nuclease-like domain of exodeoxyribonuclease V subunit RecC and similar proteins. Exodeoxyribonuclease V subunit beta (RecC) is part of the RecBCD complex that processes DNA ends resulting from a double-strand break. Its C-terminal domain contacts the two separate strands of the DNA substrate and may be responsible for stabilizing RecD interactions with the complex. It belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 283 matched cddid_all.tbl CDD cd22354 cd22354 411758 RecU-like Holliday junction resolvase RecU (recombination protein U) and similar nucleases. Holliday junction (HJ) resolving enzyme RecU is involved in DNA repair and recombination. It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 157 matched cddid_all.tbl CDD cd22355 cd22355 411759 Sau3AI_C C-terminal allosteric effector domain of the restriction endonuclease Sau3AI. Sau3AI is a type II restriction enzyme that recognizes the 5'-|GATC-3' sequence in double-strand DNA (| denotes the cleavage site). The C-terminal domain modeled here does not have catalytic activity, it functions as an allosteric effector domain that assists in DNA binding and cleavage. It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methy-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 214 matched cddid_all.tbl CDD cd22356 cd22356 411760 Sau3AI_N-like N-terminal catalytic domain of type II restriction enzyme Sau3AI and similar endonucleases. Sau3AI is a type II restriction enzyme that recognizes the 5'-|GATC-3' sequence in double-strand DNA (| denotes the cleavage site). The N-terminal domain modeled here conveys the catalytic activity, it belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 188 matched cddid_all.tbl CDD cd22357 cd22357 411761 SfsA-like Sugar fermentation stimulation protein A and similar nucleases. Sugar fermentation stimulation protein A may bind to DNA in a non-specific manner and may act as a regulatory factor involved in the metabolism of sugars such as maltose. However, it contains a well-conserved PDDEXK nuclease active site and may have hydrolytic activity towards an unknown target. The putative catalytic domain belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 213 matched cddid_all.tbl CDD cd22358 cd22358 411762 SfsA-like_archaeal Sugar fermentation stimulation protein A and similar nucleases. Sugar fermentation stimulation protein A may bind to DNA in a non-specific manner and may act as a regulatory factor involved in the metabolism of sugars such as maltose. However, it contains a well-conserved PDDEXK nuclease active site and may have hydrolytic activity towards an unknown target. The putative catalytic domain belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 221 matched cddid_all.tbl CDD cd22359 cd22359 411763 SfsA-like_bacterial Sugar fermentation stimulation protein A and similar proteins. Sugar fermentation stimulation protein A may bind to DNA in a non-specific manner and may act as a regulatory factor involved in the metabolism of sugars such as maltose. However, it contains a well-conserved PDDEXK nuclease active site and may have hydrolytic activity towards an unknown target. The putative catalytic domain belongs to a superfamily of PDDEXK nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. The N-terminus of SfsA resembles a DNA-binding OB-fold domain. 218 matched cddid_all.tbl CDD cd22360 cd22360 411764 SgrAI-like Restriction endonuclease SgrAI and similar nucleases. The type II restriction endonuclease SgrAI binds and cleaves the target sequence CR|CCGGYG (| denotes the cleavage site, R stands for a purine and Y stands for a pyrimidine). It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 272 matched cddid_all.tbl CDD cd22361 cd22361 411765 ThaI-like type II restriction endonuclease subunit R of ThaI and similar endonucleases. The PD-(D/E)XK type II restriction endonuclease ThaI cuts the target sequence CG/CG with blunt ends. It belongs to a superfamily of PDDEXK nucleases that includes diverse members such as very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 200 matched cddid_all.tbl CDD cd22362 cd22362 411766 TnsA_endonuclease-like Transposon Tn7 transposition protein TnsA. TnsA is part of the Tn7 transposon mobile genetic element working together with TnsB, TnsC, and TnsD to facilitate insertion of the transposon. TnsA catalyzes cleavage at the transposon 5' ends, and TnsC is the activator of the composite TnsAB transposase. TnsA belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 234 matched cddid_all.tbl CDD cd22363 cd22363 411767 tRNA-intron_lyase_C catalytic C-terminal domain of the tRNA-intron lyase. This C-terminal catalytic domain of tRNA intron endonucleases cleaves pre tRNA at the 5' and 3' splice sites to release the intron (EC:3.1.27.9). It belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 91 matched cddid_all.tbl CDD cd22364 cd22364 411768 VC1899-like putative nuclease domain found in Vibrio cholerae VC1899 and similar proteins. A putative nuclease domain found in Vibrio cholerae VC1899 and similar proteins belongs to a superfamily of PDDEXK nucleases that includes diverse members such as very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 377 matched cddid_all.tbl CDD cd22365 cd22365 411769 VRR-NUC-like Virus-type replication repair nuclease. This model characterizes a set of nucleases that resemble Holliday-junction resolving enzymes. They belong to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 92 matched cddid_all.tbl CDD cd22366 cd22366 411770 XisH-like Endonuclease XisH and similar nucleases. XisH functions as an endonuclease in the control of expression of nitrogen fixation genes of certain Anabaena and Nostoc species of cyanobacteria. Together with XisI, it controls the cell-type specificity of the excision of the fdxN element by the recombinase XisF. XisH belongs to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 133 matched cddid_all.tbl CDD cd22367 cd22367 411771 XPF_ERCC4_MUS81-like XPF family DNA repair endonuclease. (Xeroderma Pigmentosum group F) DNA repair gene homologs are members of the XPF/Rad1/Mus81-dependent nuclease family which specifically cleave branched structures generated during DNA repair, replication, and recombination, and they are essential for maintaining genome stability. They belong to a wider superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 123 matched cddid_all.tbl CDD cd22368 cd22368 411772 YaeQ-like Nucleases similar to Escherichia coli YaeQ. This model characterizes a diverse set of poorly characterized nucleases such as Escherichia coli YaeQ. They belong to a superfamily of nucleases including very short patch repair (Vsr) endonucleases, archaeal Holliday junction resolvases, MutH methyl-directed DNA mismatch-repair endonucleases, and catalytic domains of many restriction endonucleases, such as EcoRI, BamHI, and FokI. 174 matched cddid_all.tbl CDD cd22369 cd22369 411956 alphaCoV_Spike_SD1-2_S1-S2_S2 SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) protein from alphacoronaviruses. This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from alphacoronaviruses including human coronaviruses (HCoVs), HCoV-NL63, and HCoV-229E, and porcine coronaviruses, transmissible gastroenteritis virus (TGEV) and porcine epidemic diarrhea virus (PEDV), among others. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP), and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HKU1 the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. 666 matched cddid_all.tbl CDD cd22370 cd22370 411957 betaCoV_Spike_SD1-2_S1-S2_S2 SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses. This family contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses, including three highly pathogenic human coronaviruses (CoVs), Middle East respiratory syndrome coronavirus (MERS-CoV), Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), and SARS coronavirus 2 (SARS-CoV-2), also known as a 2019 novel coronavirus (2019-nCoV). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HKU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. 667 matched cddid_all.tbl CDD cd22371 cd22371 411958 alphaCoV-HKU2-like_Spike_SD1-2_S1-S2_S2 SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the CoV spike (S) glycoprotein from Rhinolophus bat coronavirus HKU2 and related alphacoronaviruses. This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from Wencheng shrew coronavirus (WESV), Lucheng Rn rat coronavirus (LRNV), and two bat viruses (Rhinolophus bat coronavirus HKU2 and BtRf-AlphaCoV/YN2012). Members of this group form a distinct cluster that is separated from the other alphacoronaviruses. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Ro-BatCoV HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. 686 matched cddid_all.tbl CDD cd22372 cd22372 411959 gammaCoV_Spike_SD1-2_S1-S2_S2 SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from avian infectious bronchitis coronavirus (IBV) and related gammacoronaviruses. This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from gammacoronaviruses, including avian infectious bronchitis virus, and Beluga whale coronavirus SW1 (whale-CoV SW1). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Ro-BatCoV HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. 661 matched cddid_all.tbl CDD cd22373 cd22373 411960 delta-PDCoV-like_Spike_SD1-2_S1-S2_S2 SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from porcine coronavirus HKU15, avian coronaviruses, and related deltacoronaviruses. This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from porcine coronavirus PDCoV, and several avian coronaviruses such as quail deltacoronavirus (QdCoV) UAE-HKU30, white-eye coronavirus HKU16, common moorhen coronavirus HKU21, thrush CoV HKU12, and munia CoV HKU13, all from the Buldecovirus subgenus of deltacoronaviruses. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Ro-BatCoV HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. 648 matched cddid_all.tbl CDD cd22374 cd22374 411961 delta-PiCoV-like_Spike_SD1-2_S1-S2_S2 SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from Pigeon coronavirus UAE-HKU29, and related avian deltacoronaviruses. This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from Pigeon coronavirus UAE-HKU29, and related avian deltacoronaviruses including Falcon coronavirus UAE-HKU27, Magpie-robin coronavirus HKU18, Sparrow coronavirus HKU17, and Night heron coronavirus HKU19. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the (C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Ro-BatCoV HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. 739 matched cddid_all.tbl CDD cd22375 cd22375 411962 HCoV-NL63-229E-like_Spike_SD1-2_S1-S2_S2 SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoproteins from HCoV-NL63, HCoV-229E, and related alphacoronavirus. This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from alphacoronaviruses, including human coronaviruses (HCoVs), HCoV-NL63 and HCoV-229E. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HKU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. 677 matched cddid_all.tbl CDD cd22376 cd22376 411963 PDEV-like_Spike_SD1-2_S1-2_S2 SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from Porcine epidemic diarrhea virus and related alphacoronavirus. This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from alphacoronaviruses, including porcine epidemic diarrhea virus (PEDV), Scotophilus bat coronavirus, and swine enteric coronavirus, among others. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HKU1 the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. 673 matched cddid_all.tbl CDD cd22377 cd22377 411964 TGEV-like_Spike_SD1-2_S1-S2_S2 SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from transmissible gastroenteritis virus and related alphacoronaviruses. This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from porcine transmissible gastroenteritis virus (TGEV), canine coronavirus (CCoV), and feline coronavirus (FCoV). They display greater than 96% sequence identity and have been grouped in the same species, alphacoronavirus 1, within the Alphacoronavirus genus. The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HKU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. 751 matched cddid_all.tbl CDD cd22378 cd22378 411965 SARS-CoV-like_Spike_SD1-2_S1-S2_S2 SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from SARS-CoV-2 (COVID-19) and related betacoronaviruses in the B lineage. This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses in the sarbecovirus subgenus (B lineage), including highly pathogenic human CoVs such as Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV), and SARS-CoV-2 (also known as a 2019 novel coronavirus or 2019-nCoV). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. Notably, SARS-CoV-2 has a functional polybasic (furin) cleavage site through the insertion of PRRAR*SV (* indicates the cleavage site) at the S1/S2 interface, which is absent in SARS-CoV and other SARS-related coronaviruses. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. 662 matched cddid_all.tbl CDD cd22379 cd22379 411966 MERS-CoV-like_Spike_SD1-2_S1-S2_S2 SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from Middle East respiratory syndrome coronavirus and related betacoronaviruses in the C lineage. This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses in the merbecovirus subgenus (C lineage), including Middle East respiratory syndrome coronavirus (MERS-CoV). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. 682 matched cddid_all.tbl CDD cd22380 cd22380 411967 HKU1-CoV-like_Spike_SD1-2_S1-S2_S2 SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from human HKU1 and OC43 coronaviruses and related betacoronaviruses in the A lineage. This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses in the embecovirus subgenus (A lineage), including highly pathogenic human coronaviruses (CoVs), HKU1 and OC43 CoVs, as well as murine hepatitis virus (MHV). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of MHV is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Rousettus bat coronavirus HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. 663 matched cddid_all.tbl CDD cd22381 cd22381 411968 bat-HKU9-CoV-like_Spike_SD1-2_S1-S2_S2 SD-1 and SD-2 subdomains, the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from Rousettus bat coronavirus HKU9 and related betacoronaviruses in the D lineage. This group contains the SD-1 and SD-2 subdomains of the S1 subunit C-terminal domain (C-domain), the S1/S2 cleavage region, and the S2 fusion subunit of the spike (S) glycoprotein from betacoronaviruses in the nobecovirus subgenus (D lineage), including Rousettus bat coronavirus HKU9 (Ro-BatCoV HKU9). The CoV S protein is an envelope glycoprotein that plays a very important role in viral attachment, fusion, and entry into host cells, and serves as a major target for the development of neutralizing antibodies, inhibitors of viral entry, and vaccines. It is synthesized as a precursor protein that is cleaved into an N-terminal S1 subunit (~700 amino acids) and a C-terminal S2 subunit (~600 amino acids) that mediates attachment and membrane fusion, respectively. Three S1/S2 heterodimers assemble to form a trimer spike protruding from the viral envelope. The S1 subunit contains a receptor-binding domain (RBD), while the S2 subunit contains the coronavirus fusion machinery and is primarily alpha-helical. S1 contains two structurally independent domains, the N-terminal domain (NTD) and the C-domain. The S1 C-domain also contains two subdomains (SD-1 and SD-2), which connect the S1 and S2 subunits. Depending on the virus, either the NTD or the C-domain can serve as the receptor-binding domain (RBD). While the RBD of mouse hepatitis virus (MHV) is located at the NTD, most CoVs, including SARS-CoV-2, SARS-CoV and MERS-CoV use the C-domain to bind their receptors. The S2 subunit comprises the fusion peptide (FP), a second proteolytic site (S2'), followed by an internal fusion peptide (IFP) and two heptad-repeat domains (HR1 and HR2) preceding the transmembrane domain (TM). After binding of the S1 subunit RBD on the virion to its receptor on the target cell, the HR1 and HR2 domains interact with each other to form a six-helix bundle (6-HB) fusion core, bringing viral and cellular membranes into close proximity for fusion and infection. In order to catalyze the membrane fusion reaction, CoV S needs to be primed through cleavage at the S1/S2 and S2' sites. In the case of human-infecting coronaviruses such as SARS-CoV-2, HCoV-OC43, MERS-CoV, and HCoV-KU1, the spike protein contains an insertion of (R/K)-(2X)n-(R/K) (furin cleavage motif) at the S1/S2 site, which is absent in SARS-CoV and other SARS-related coronaviruses, as well as Ro-BatCoV HKU9. The region modeled in this cd (SD-1 and SD-2, the S1/S2 cleavage region, and the S2 fusion subunit) plays an essential role in viral entry by initiating fusion of the viral and cellular membranes. 731 matched cddid_all.tbl CDD cd22382 cd22382 411810 KH-I_SF1 type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins. SF1, also called branch point-binding protein, or BBP, or transcription factor ZFM1, or zinc finger gene in MEN1 locus, or zinc finger protein 162, is necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5'-UACUAAC-3' of the pre-mRNA. It may act as transcription repressor. 93 matched cddid_all.tbl CDD cd22383 cd22383 411811 KH-I_Hqk_like type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) family. The Hqk family includes Hqk and protein held out wings (how) found in Drosophila. Hqk, also called HqkI, is an RNA-binding protein that plays a central role in myelinization. It binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence and regulates target mRNA stability. It acts by regulating pre-mRNA splicing, mRNA export and protein translation. Hqk is a regulator of oligodendrocyte differentiation and maturation in the brain that may play a role in myelin and oligodendrocyte dysfunction in schizophrenia. How, also called KH domain protein KH93F, or protein muscle-specific, or protein Struthio, or protein wings held out (who), or Quaking-related 93F (qkr93F), is an RNA-binding protein involved in the control of muscular and cardiac activity. It is required for integrin-mediated cell-adhesion in wing blade. It plays essential roles during embryogenesis, in late stages of somatic muscle development, for myotube migration and during metamorphosis for muscle reorganization. 101 matched cddid_all.tbl CDD cd22384 cd22384 411812 KH-I_KHDRBS type I K homology (KH) RNA-binding domain found in the KH domain-containing, RNA-binding, signal transduction-associated protein (KHDRBS) family. The KHDRBS family includes three members, KHDRBS1-3. KHDRBS1, also called GAP-associated tyrosine phosphoprotein p62, or Src-associated in mitosis 68 kDa protein, or Sam68, or p21 Ras GTPase-activating protein-associated p62, or p68, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS1 acts as a putative regulator of mRNA stability and/or translation rates and mediates mRNA nuclear export. It is recruited and tyrosine phosphorylated by several receptor systems, for example the T-cell, leptin and insulin receptors. KHDRBS2, also called Sam68-like mammalian protein 1, or SLM-1, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds both poly(A) and poly(U) homopolymers. KHDRBS2 may function as an adapter protein for Src kinases during mitosis. KHDRBS3, also called RNA-binding protein T-Star, or Sam68-like mammalian protein 2, or SLM-2, or Sam68-like phosphotyrosine protein, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS3 may play a role as a negative regulator of cell growth. 102 matched cddid_all.tbl CDD cd22385 cd22385 411813 KH-I_KHDC4_rpt1 first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins. KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif. 84 matched cddid_all.tbl CDD cd22386 cd22386 411814 KH-I_KHDC4_rpt2 first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins. KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the second one. 102 matched cddid_all.tbl CDD cd22387 cd22387 411815 KH-I_DDX46_like type I K homology (KH) RNA-binding domain found in the family of DEAD box protein 46 (DDX46). The DDX46 family includes DEAD box protein 46 (DDX46), fungal pre-mRNA-processing ATP-dependent RNA helicase PRP5, Arabidopsis thaliana DEAD-box ATP-dependent RNA helicase RH42 and similar proteins. DDX46, also called PRP5 homolog, is an ATP-dependent RNA helicase that plays an essential role in splicing, either prior to, or during splicing A complex formation. It inhibits antiviral innate responses by entrapping selected antiviral transcripts in the nucleus. It is also involved in the development of several tumors. PRP5 is an ATP-dependent RNA helicase involved spliceosome assembly and in nuclear splicing. It catalyzes an ATP-dependent conformational change of U2 snRNP. PRP5 interacts with the U2 snRNP and HSH155. RH42, also called DEAD-box RNA helicase RCF1, or REGULATOR OF CBF GENE EXPRESSION 1, is a helicase required for pre-mRNA splicing, cold-responsive gene regulation and cold tolerance. Members in this family contain a divergent KH domain that lacks the RNA-binding GXXG motif. 82 matched cddid_all.tbl CDD cd22388 cd22388 411816 KH-I_N4BP1_like_rpt2 second type I K homology (KH) RNA-binding domain found in the family of NEDD4-binding protein 1 (N4BP1). The N4BP1 family includes N4BP1, NYN domain and retroviral integrase catalytic domain-containing protein (NYNRIN) and KH and NYN domain-containing protein (KHNYN). These proteins are probably of retroviral origin. N4BP1 interacts with and is a substrate of NEDD4 ubiquitin ligase (neural precursor cell expressed, developmentally downregulated 4, E3 ubiquitin protein ligase). It is also an inhibitor of the E3 ubiquitin-protein ligase ITCH, a NEDD4 structurally related E3. N4BP1 acts by interacting with the second WW domain of ITCH, leading to compete with ITCH's substrates and impairing ubiquitination of substrates. NYNRIN, also known as CGIN1/Cousin of GIN1, may contribute to retroviral resistance in mammals by regulating the ubiquitination of viral proteins. KHNYN acts as a novel cofactor for zinc finger antiviral protein (ZAP) to target CpG-containing retroviral RNA for degradation. Members of this family contains two type I K homology (KH) RNA-binding domain. The model corresponds to the second one. 63 matched cddid_all.tbl CDD cd22389 cd22389 411817 KH-I_Dim2p_like_rpt1 first type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and similar proteins. The family includes a group of conserved KH domain-containing protein mainly from archaea, such as Dim2p homologues from Pyrococcus horikoshii and Aeropyrum pernix. Dim2p acts as a preribosomal RNA processing factor that has been identified as an essential protein for the maturation of 40S ribosomal subunit in Saccharomyces cerevisiae. It is required for the cleavage at processing site A2 to generate the pre-20S rRNA and for the dimethylation of the 18S rRNA by 18S rRNA dimethyltransferase, Dim1p. Dim2p contains two K-homology (KH) RNA-binding domains. The model corresponds to the first one. 70 matched cddid_all.tbl CDD cd22390 cd22390 411818 KH-I_Dim2p_like_rpt2 second type I K homology (KH) RNA-binding domain found in Pyrococcus horikoshii Dim2p and similar proteins. The family includes a group of conserved KH domain-containing protein mainly from archaea, such as Dim2p homologues from Pyrococcus horikoshii and Aeropyrum pernix. Dim2p acts as a preribosomal RNA processing factor that has been identified as an essential protein for the maturation of 40S ribosomal subunit in Saccharomyces cerevisiae. It is required for the cleavage at processing site A2 to generate the pre-20S rRNA and for the dimethylation of the 18S rRNA by 18S rRNA dimethyltransferase, Dim1p. Dim2p contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one. 96 matched cddid_all.tbl CDD cd22391 cd22391 411819 KH-I_PNO1_rpt1 first type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar proteins. PNO1 is an RNA-binding protein that acts as a ribosome assembly factor and plays an important role in ribosome biogenesis. It positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA. PNO1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif. 80 matched cddid_all.tbl CDD cd22392 cd22392 411820 KH-I_PNO1_rpt2 second type I K homology (KH) RNA-binding domain found in partner of NOB1 (PNO1) and similar proteins. PNO1 is an RNA-binding protein that acts as a ribosome assembly factor and plays an important role in ribosome biogenesis. It positively regulates dimethylation of two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA. PNO1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one. 96 matched cddid_all.tbl CDD cd22393 cd22393 411821 KH-I_KRR1_rpt1 first type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome component and similar proteins. KRR1, also called HIV-1 Rev-binding protein 2, or KRR-R motif-containing protein 1, or Rev-interacting protein 1, or Rip-1, or ribosomal RNA assembly protein KRR1, is a ribosomal assembly factor required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. KRR1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif and is involved in binding another assembly factor, Kri1. 83 matched cddid_all.tbl CDD cd22394 cd22394 411822 KH-I_KRR1_rpt2 second type I K homology (KH) RNA-binding domain found in KRR1 small subunit processome component and similar proteins. KRR1, also called HIV-1 Rev-binding protein 2, or KRR-R motif-containing protein 1, or Rev-interacting protein 1, or Rip-1, or ribosomal RNA assembly protein KRR1, is a nucleolar protein required for 40S ribosome biogenesis. It is involved in nucleolar processing of pre-18S ribosomal RNA and ribosome assembly. KRR1 contains two K-homology (KH) RNA-binding domains. The model corresponds to the second one. 93 matched cddid_all.tbl CDD cd22395 cd22395 411823 KH-I_AKAP1 type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 (AKAP1) and similar proteins. AKAP1, also called A-kinase anchor protein 149 kDa, or AKAP 149, or dual specificity A-kinase-anchoring protein 1, or D-AKAP-1, or protein kinase A-anchoring protein 1 (PRKA1), or spermatid A-kinase anchor protein 84, or S-AKAP84, is a novel developmentally regulated A kinase anchor protein of male germ cells. It binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane. 68 matched cddid_all.tbl CDD cd22396 cd22396 411824 KH-I_FUBP_rpt1 first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins. The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the first one. 68 matched cddid_all.tbl CDD cd22397 cd22397 411825 KH-I_FUBP_rpt2 second type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins. The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the second one. 69 matched cddid_all.tbl CDD cd22398 cd22398 411826 KH-I_FUBP_rpt3 third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins. The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the third one. 67 matched cddid_all.tbl CDD cd22399 cd22399 411827 KH-I_FUBP_rpt4 fourth type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins. The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one. 67 matched cddid_all.tbl CDD cd22400 cd22400 411828 KH-I_IGF2BP_rpt1 first type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family. The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one. 68 matched cddid_all.tbl CDD cd22401 cd22401 411829 KH-I_IGF2BP_rpt2 second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family. The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one. 72 matched cddid_all.tbl CDD cd22402 cd22402 411830 KH-I_IGF2BP_rpt3 third type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family. The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one. 66 matched cddid_all.tbl CDD cd22403 cd22403 411831 KH-I_IGF2BP_rpt4 fourth type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family. The IGF2BP family includes three members: IGF2BP1/IMP-1/CRD-BP/VICKZ1, IGF2BP2/IMP-2/VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the fourth one. 66 matched cddid_all.tbl CDD cd22404 cd22404 411832 KH-I_MASK type I K homology (KH) RNA-binding domain found in Mask family proteins. The Mask family includes Drosophila melanogaster ankyrin repeat and KH domain-containing protein Mask, and its mammalian homologues Mask1/ANKHD1 and Mask2/ANKRD17. Mask, also called multiple ankyrin repeat single KH domain-containing protein, is a large ankyrin repeat and KH domain-containing protein involved in Drosophila receptor tyrosine kinase signaling. It acts as a mediator of receptor tyrosine kinase (RTK) signaling and may act either downstream of MAPK or transduce signaling through a parallel branch of the RTK pathway. Mask is required for the development and organization of indirect flight muscle sarcomeres by regulating the formation of M line and H zone and the correct assembly of thick and thin filaments in the sarcomere. Mask1/ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. Mask2/ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses. 71 matched cddid_all.tbl CDD cd22405 cd22405 411833 KH-I_Vigilin_rpt1 first type I K homology (KH) RNA-binding domain found in vigilin and similar proteins. Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the first one. 69 matched cddid_all.tbl CDD cd22406 cd22406 411834 KH-I_Vigilin_rpt2 second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins. Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the second one. 75 matched cddid_all.tbl CDD cd22407 cd22407 411835 KH-I_Vigilin_rpt3 third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins. Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the third one. 62 matched cddid_all.tbl CDD cd22408 cd22408 411836 KH-I_Vigilin_rpt4 fourth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins. Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourth one. 62 matched cddid_all.tbl CDD cd22409 cd22409 411837 KH-I_Vigilin_rpt5 fifth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins. Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fifth one. 70 matched cddid_all.tbl CDD cd22410 cd22410 411838 KH-I_Vigilin_rpt7 seventh type I K homology (KH) RNA-binding domain found in vigilin and similar proteins. Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the seventh one. 67 matched cddid_all.tbl CDD cd22411 cd22411 411839 KH-I_Vigilin_rpt8 eighth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins. Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eighth one. 62 matched cddid_all.tbl CDD cd22412 cd22412 411840 KH-I_Vigilin_rpt9 ninth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins. Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the ninth one. 70 matched cddid_all.tbl CDD cd22413 cd22413 411841 KH-I_Vigilin_rpt10 tenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins. Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the tenth one. 66 matched cddid_all.tbl CDD cd22414 cd22414 411842 KH-I_Vigilin_rpt11 eleventh type I K homology (KH) RNA-binding domain found in vigilin and similar proteins. Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the eleventh one. 66 matched cddid_all.tbl CDD cd22415 cd22415 411843 KH-I_Vigilin_rpt12 twelfth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins. Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the twelfth one. 92 matched cddid_all.tbl CDD cd22416 cd22416 411844 KH-I_Vigilin_rpt13 thirteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins. Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the thirteenth one. 78 matched cddid_all.tbl CDD cd22417 cd22417 411845 KH-I_Vigilin_rpt14 fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins. Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourteenth one. 72 matched cddid_all.tbl CDD cd22418 cd22418 411846 KH-I_Vigilin_rpt15 fifteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins. Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fifteenth one. 69 matched cddid_all.tbl CDD cd22419 cd22419 411847 KH-I_ASCC1 type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex subunit 1 (ASCC1) and similar proteins. ASCC1, also called ASC-1 complex subunit p50, or Trip4 complex subunit p50, plays a role in DNA damage repair as component of the ASCC complex. It is part of the ASC-1 complex that enhances NF-kappa-B, SRF and AP1 transactivation. In cells responding to gastrin-activated paracrine signals, it is involved in the induction of SERPINB2 expression by gastrin. ASCC1 may also play a role in the development of neuromuscular junction. 66 matched cddid_all.tbl CDD cd22420 cd22420 411848 KH-I_BICC1_rpt1 first type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins. BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one. 81 matched cddid_all.tbl CDD cd22421 cd22421 411849 KH-I_BICC1_rpt2 second type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins. BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one. 70 matched cddid_all.tbl CDD cd22422 cd22422 411850 KH-I_BICC1_rpt3 third type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins. BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one. 67 matched cddid_all.tbl CDD cd22423 cd22423 411851 KH-I_MEX3_rpt1 first type I K homology (KH) RNA-binding domain found in the family of MEX-3 RNA-binding proteins. The MEX-3 protein family includes four members, MEX3A/RKHD4, MEX3B/RKHD3/RNF195, MEX3C/ RKHD2/RNF194, and MEX3D/RKHD1/RNF193/TINO. They are homologous of Caenorhabditis elegans MEX-3 protein, a translational regulator that specifies the posterior blastomere identity in the early embryo and contributes to the maintenance of the germline totipotency. Mex-3 proteins are RNA-binding phosphoproteins involved in post-transcriptional regulatory mechanisms. They are characterized by containing two K-homology (KH) RNA-binding domains and a C-terminal RING finger. They bind RNA through their KH domains and shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway. The model corresponds to the first KH domain. 73 matched cddid_all.tbl CDD cd22424 cd22424 411852 KH-I_MEX3_rpt2 second type I K homology (KH) RNA-binding domain found in the family of MEX-3 RNA-binding proteins. The MEX-3 protein family includes four members, MEX3A/RKHD4, MEX3B/RKHD3/RNF195, MEX3C/ RKHD2/RNF194, and MEX3D/RKHD1/RNF193/TINO. They are homologous of Caenorhabditis elegans MEX-3 protein, a translational regulator that specifies the posterior blastomere identity in the early embryo and contributes to the maintenance of the germline totipotency. Mex-3 proteins are RNA-binding phosphoproteins involved in post-transcriptional regulatory mechanisms. They are characterized by containing two K-homology (KH) RNA-binding domains and a C-terminal RING finger. They bind RNA through their KH domains and shuttle between the nucleus and the cytoplasm via the CRM1-dependent export pathway. The model corresponds to the second KH domain. 72 matched cddid_all.tbl CDD cd22425 cd22425 411853 KH_I_FMR1_FXR_rpt1 first type I K homology (KH) RNA-binding domain found in a family of fragile X mental retardation protein (FMR1) and fragile X related (FXR) proteins. The FMR1/FXR family includes FMR1 (also known as FMRP) and its two homologues, fragile X related 1 (FXR1) and 2 (FXR2). They are involved in translational regulation, particularly in neuronal cells and play an important role in the regulation of glutamate-mediated neuronal activity and plasticity. Each of these three proteins can form heteromers with the others, and each can also form homomers. Lack of expression of FMR1 results in mental retardation and macroorchidism. FXR1 and FXR2 may play important roles in the function of FMR1 and in the pathogenesis of the Fragile X Mental Retardation Syndrome. Members of this family contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one. 77 matched cddid_all.tbl CDD cd22426 cd22426 411854 KH_I_FMR1_FXR_rpt2 second type I K homology (KH) RNA-binding domain found in a family of fragile X mental retardation protein (FMR1) and fragile X related (FXR) proteins. The FMR1/FXR family includes FMR1 (also known as FMRP) and its two homologues, fragile X related 1 (FXR1) and 2 (FXR2). They are involved in translational regulation, particularly in neuronal cells and play an important role in the regulation of glutamate-mediated neuronal activity and plasticity. Each of these three proteins can form heteromers with the others, and each can also form homomers. Lack of expression of FMR1 results in mental retardation and macroorchidism. FXR1 and FXR2 may play important roles in the function of FMR1 and in the pathogenesis of the Fragile X Mental Retardation Syndrome. Members of this family contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one. 63 matched cddid_all.tbl CDD cd22427 cd22427 411855 KH_I_FMR1_FXR_rpt3 third type I K homology (KH) RNA-binding domain found in a family of fragile X mental retardation protein (FMR1) and fragile X related (FXR) proteins. The FMR1/FXR family includes FMR1 (also known as FMRP) and its two homologues, fragile X related 1 (FXR1) and 2 (FXR2). They are involved in translational regulation, particularly in neuronal cells and play an important role in the regulation of glutamate-mediated neuronal activity and plasticity. Each of these three proteins can form heteromers with the others, and each can also form homomers. Lack of expression of FMR1 results in mental retardation and macroorchidism. FXR1 and FXR2 may play important roles in the function of FMR1 and in the pathogenesis of the Fragile X Mental Retardation Syndrome. Members of this family contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one. 79 matched cddid_all.tbl CDD cd22428 cd22428 411856 KH-I_TDRKH_rpt1 first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins. TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the first one. 74 matched cddid_all.tbl CDD cd22429 cd22429 411857 KH-I_TDRKH_rpt2 second type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins. TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the second one. 82 matched cddid_all.tbl CDD cd22430 cd22430 411858 KH-I_DDX43_DDX53 type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box protein 53 (DDX53) and similar proteins. DDX43 (also called cancer/testis antigen 13, or DEAD box protein HAGE, or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 (also called cancer-associated gene protein, or cancer/testis antigen 26, or DEAD box protein CAGE) shows high expression level in various tumors and is involved in anti-cancer drug resistance. Both DDX46 and DDX53 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. 66 matched cddid_all.tbl CDD cd22431 cd22431 411859 KH-I_RNaseY type I K homology (KH) RNA-binding domain found in ribonuclease Y (RNase Y) and similar proteins. RNase Y is an endoribonuclease that initiates mRNA decay. It initiates the decay of all SAM-dependent riboswitches, such as yitJ riboswitch. RNase Y is involved in processing of the gapA operon mRNA and it cleaves between cggR and gapA. It is also the decay-initiating endonuclease for rpsO mRNA. It plays a role in degradation of type I toxin-antitoxin system bsrG/SR4 RNAs and also a minor role in degradation of type I toxin-antitoxin system bsrE/SR5 degradation. 79 matched cddid_all.tbl CDD cd22432 cd22432 411860 KH-I_HNRNPK_rpt1 first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins. hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one. 64 matched cddid_all.tbl CDD cd22433 cd22433 411861 KH-I_HNRNPK_rpt2 second type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins. hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one. 70 matched cddid_all.tbl CDD cd22434 cd22434 411862 KH-I_HNRNPK_rpt3 third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins. hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one. 74 matched cddid_all.tbl CDD cd22435 cd22435 411863 KH-I_NOVA_rpt1 first type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova). The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one. 73 matched cddid_all.tbl CDD cd22436 cd22436 411864 KH-I_NOVA_rpt2 second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova). The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one. 70 matched cddid_all.tbl CDD cd22437 cd22437 411865 KH-I_BTR1_rpt2 second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins. BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one. 69 matched cddid_all.tbl CDD cd22438 cd22438 411866 KH-I_PCBP_rpt1 first type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs). The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one. 67 matched cddid_all.tbl CDD cd22439 cd22439 411867 KH-I_PCBP_rpt3 third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs). The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one. 68 matched cddid_all.tbl CDD cd22440 cd22440 411868 KH-I_KHDC1_like type I K homology (KH) RNA-binding domain found in KHDC1-like family. The KHDC1-like family corresponds to a group of structurally related proteins characterized by an atypical RNA-binding KH domain. They are unique to eutherian mammals and specifically expressed in oocytes and/or embryonic stem cells. Family members include KH homology domain-containing protein 1 (KHDC1), KHDC1-like protein (KHDC1L), KHDC3-like protein (KHDC3L, also called ES cell-associated transcript 1 protein or ECAT1), developmental pluripotency-associated 5 protein (DPPA5, also called embryonal stem cell-specific gene 1 protein or ESG-1), Oocyte-expressed protein (OOEP, also called KH homology domain-containing protein 2 or KHDC2, or Oocyte- and embryo-specific protein 19 or OEP19). KHDC3L is essential for human oocyte maturation and pre-implantation development of the resulting embryos. DPPA5 is involved in the maintenance of embryonic stem (ES) cell pluripotency. OOEP plays an essential role for zygotes to progress beyond the first embryonic cell divisions. 68 matched cddid_all.tbl CDD cd22441 cd22441 411869 KH-I_CeGLD3_rpt1 first type I K homology (KH) RNA-binding domain found in Caenorhabditis elegans defective in germ line development protein 3 (CeGLD-3) and similar proteins. CeGLD-3, also called germline development defective 3, is a Bicaudal-C (Bic-C) homolog that is involved in the translational control of germline-specific mRNAs during embryogenesis. It interacts with the cytoplasmic poly(A)-polymerase GLD-2. The two proteins cooperate to recognize target mRNAs and convert them into a polyadenylated, translationally active state. CeGLD-3 contains four K-homology (KH) RNA-binding domains, which are divergent KH domains that lacks the RNA-binding GXXG motif. The model corresponds to the first one. 71 matched cddid_all.tbl CDD cd22442 cd22442 411870 KH-I_CeGLD3_rpt2 second type I K homology (KH) RNA-binding domain found in Caenorhabditis elegans defective in germ line development protein 3 (CeGLD-3) and similar proteins. CeGLD-3, also called germline development defective 3, is a Bicaudal-C (Bic-C) homolog that is involved in the translational control of germline-specific mRNAs during embryogenesis. It interacts with the cytoplasmic poly(A)-polymerase GLD-2. The two proteins cooperate to recognize target mRNAs and convert them into a polyadenylated, translationally active state. CeGLD-3 contains four K-homology (KH) RNA-binding domains, which are divergent KH domains that lacks the RNA-binding GXXG motif. The model corresponds to the second one. 73 matched cddid_all.tbl CDD cd22443 cd22443 411871 KH-I_CeGLD3_rpt3 third type I K homology (KH) RNA-binding domain found in Caenorhabditis elegans defective in germ line development protein 3 (CeGLD-3) and similar proteins. CeGLD-3, also called germline development defective 3, is a Bicaudal-C (Bic-C) homolog that is involved in the translational control of germline-specific mRNAs during embryogenesis. It interacts with the cytoplasmic poly(A)-polymerase GLD-2. The two proteins cooperate to recognize target mRNAs and convert them into a polyadenylated, translationally active state. CeGLD-3 contains four K-homology (KH) RNA-binding domains, which are divergent KH domains that lacks the RNA-binding GXXG motif. The model corresponds to the third one. 74 matched cddid_all.tbl CDD cd22444 cd22444 411872 KH-I_CeGLD3_rpt4 fourth type I K homology (KH) RNA-binding domain found in Caenorhabditis elegans defective in germ line development protein 3 (CeGLD-3) and similar proteins. CeGLD-3, also called germline development defective 3, is a Bicaudal-C (Bic-C) homolog that is involved in the translational control of germline-specific mRNAs during embryogenesis. It interacts with the cytoplasmic poly(A)-polymerase GLD-2. The two proteins cooperate to recognize target mRNAs and convert them into a polyadenylated, translationally active state. CeGLD-3 contains four K-homology (KH) RNA-binding domains, which are divergent KH domains that lacks the RNA-binding GXXG motif. The model corresponds to the fourth one. 77 matched cddid_all.tbl CDD cd22445 cd22445 411873 KH-I_Rrp4_Rrp40 type I K homology (KH) RNA-binding domain found in exosome complex components Rrp4, Rrp40 and similar proteins. The family includes two ribosomal RNA-processing proteins, Rrp4 and Rrp40. They are non-catalytic components of the RNA exosome complex which has 3'-->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. Eukaryotic Rrp4 and Rrp40 contain a divergent KH domain that lacks the RNA-binding GXXG motif. 78 matched cddid_all.tbl CDD cd22446 cd22446 411874 KH-I_ScSCP160_rpt1 first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins. SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the first one. 86 matched cddid_all.tbl CDD cd22447 cd22447 411875 KH-I_ScSCP160_rpt2 second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins. SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the second one. 80 matched cddid_all.tbl CDD cd22448 cd22448 411876 KH-I_ScSCP160_rpt3 third type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins. SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the third one. 81 matched cddid_all.tbl CDD cd22449 cd22449 411877 KH-I_ScSCP160_rpt4 fourth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins. SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the fourth one. 70 matched cddid_all.tbl CDD cd22450 cd22450 411878 KH-I_ScSCP160_rpt5 fifth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins. SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the fifth one. 80 matched cddid_all.tbl CDD cd22451 cd22451 411879 KH-I_ScSCP160_rpt6 sixth type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins. SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the sixth one. 69 matched cddid_all.tbl CDD cd22452 cd22452 411880 KH-I_ScSCP160_rpt7 seventh type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins. SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the seventh one. 65 matched cddid_all.tbl CDD cd22453 cd22453 411881 KH-I_MUG60_like type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe meiotically up-regulated gene 60 protein (MUG60) and similar proteins. MUG60 is a KH domain-containing protein that has a role in meiosis. The family also contains Saccharomyces cerevisiae KH domain-containing protein YLL032C. 72 matched cddid_all.tbl CDD cd22454 cd22454 411882 KH-I_Mextli_like type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic translation initiation factor 4E-binding protein Mextli and similar proteins. Mextli is a novel eukaryotic translation initiation factor 4E-binding protein that promotes translation in Drosophila melanogaster. 71 matched cddid_all.tbl CDD cd22455 cd22455 411883 KH-I_Rnc1_rpt1 first type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins. Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one. 70 matched cddid_all.tbl CDD cd22456 cd22456 411884 KH-I_Rnc1_rpt2 second type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins. Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one. 69 matched cddid_all.tbl CDD cd22457 cd22457 411885 KH-I_Rnc1_rpt3 third type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins. Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one. 64 matched cddid_all.tbl CDD cd22458 cd22458 411886 KH-I_MER1_like type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae meiotic recombination 1 protein (MER1) and similar proteins. MER1 is required for chromosome pairing and genetic recombination. It may function to bring the axial elements of the synaptonemal complex corresponding to homologous chromosomes together by initiating recombination. MER1 might be responsible for regulating the MER2 gene and/or gene product. 65 matched cddid_all.tbl CDD cd22459 cd22459 411887 KH-I_PEPPER_rpt1_like first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins. The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH1 domain of PEPPER and FLK, as well as KH1 and KH3 domains of RCF3 and HEN4. 69 matched cddid_all.tbl CDD cd22460 cd22460 411888 KH-I_PEPPER_rpt2_like second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins. The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH2 domain of PEPPER and FLK, as well as KH2 and KH4 domains of RCF3 and HEN4. 73 matched cddid_all.tbl CDD cd22461 cd22461 411889 KH-I_PEPPER_like_rpt3 third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins. The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER and flowering locus K homology domain protein (FLK). PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. The model corresponds to the KH3 domain of PEPPER and FLK. 69 matched cddid_all.tbl CDD cd22462 cd22462 411890 KH-I_HEN4_like_rpt5 fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH domain-containing protein HEN4 and similar protein. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. HEN4 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of HEN4. 66 matched cddid_all.tbl CDD cd22463 cd22463 411891 KH-I_RCF3_like_rpt5 fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein RCF3 and similar protein. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of RCF3. 71 matched cddid_all.tbl CDD cd22464 cd22464 411892 KH-I_AtC3H36_like type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana zinc finger CCCH domain-containing proteins AtC3H36, AtC3H52 and similar proteins. The family corresponds to a group of plant CCCH family zinc finger proteins, such as AtC3H36 and AtC3H52, which contain one K homology (KH) RNA-binding domain. They may play important roles in RNA processing as RNA-binding proteins in animals. They may also have an effective role in stress tolerance. 66 matched cddid_all.tbl CDD cd22465 cd22465 411893 KH-I_Hqk type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins. Hqk, also called HqkI, is an RNA-binding protein that plays a central role in myelinization. It binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence and regulates target mRNA stability. It acts by regulating pre-mRNA splicing, mRNA export and protein translation. Hqk is a regulator of oligodendrocyte differentiation and maturation in the brain that may play a role in myelin and oligodendrocyte dysfunction in schizophrenia. 103 matched cddid_all.tbl CDD cd22466 cd22466 411894 KH-I_HOW type I K homology (KH) RNA-binding domain found in Drosophila protein held out wings (how) and similar proteins. How, also called KH domain protein KH93F, or protein muscle-specific, or protein Struthio, or protein wings held out (who), or Quaking-related 93F (qkr93F), is an RNA-binding protein involved in the control of muscular and cardiac activity. It is required for integrin-mediated cell-adhesion in wing blade. It plays essential roles during embryogenesis, in late stages of somatic muscle development, for myotube migration and during metamorphosis for muscle reorganization. 105 matched cddid_all.tbl CDD cd22467 cd22467 411895 KH-I_SPIN1_like type I K homology (KH) RNA-binding domain found in Oryza sativa SPL11-interacting protein 1 (SPIN1) and similar proteins. SPIN1 is a K homology domain protein negatively regulated and ubiquitinated by the E3 ubiquitin ligase SPL11. It is involved in flowering time control in rice. SPIN1 binds DNA and RNA in vitro. 101 matched cddid_all.tbl CDD cd22468 cd22468 411896 KH-I_KHDRBS1 type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 1 (KHDRBS1) and similar proteins. KHDRBS1, also called GAP-associated tyrosine phosphoprotein p62, or Src-associated in mitosis 68 kDa protein, or Sam68, or p21 Ras GTPase-activating protein-associated p62, or p68, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS1 acts as a putative regulator of mRNA stability and/or translation rates and mediates mRNA nuclear export. It is recruited and tyrosine phosphorylated by several receptor systems, for example the T-cell, leptin and insulin receptors. 106 matched cddid_all.tbl CDD cd22469 cd22469 411897 KH-I_KHDRBS2 type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 2 (KHDRBS2) and similar proteins. KHDRBS2, also called Sam68-like mammalian protein 1, or SLM-1, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds both poly(A) and poly(U) homopolymers. KHDRBS2 may function as an adapter protein for Src kinases during mitosis. 118 matched cddid_all.tbl CDD cd22470 cd22470 411898 KH-I_KHDRBS3 type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 3 (KHDRBS3) and similar proteins. KHDRBS3, also called RNA-binding protein T-Star, or Sam68-like mammalian protein 2, or SLM-2, or Sam68-like phosphotyrosine protein, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS3 may play a role as a negative regulator of cell growth. 113 matched cddid_all.tbl CDD cd22471 cd22471 411899 KH-I_RIK_like_rpt1 first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein RIK and similar proteins. RIK, also called rough sheath 2-interacting KH domain protein, or RS2-interacting KH domain protein, is a RNA binding protein that acts together with RS2/AS1 in the recruitment of HIRA. RIK contains two type I K homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif. 91 matched cddid_all.tbl CDD cd22472 cd22472 411900 KH-I_RIK_like_rpt2 second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein RIK and similar proteins. RIK, also called rough sheath 2-interacting KH domain protein, or RS2-interacting KH domain protein, is a RNA binding protein that acts together with RS2/AS1 in the recruitment of HIRA. RIK contains two type I K homology (KH) RNA-binding domains. The model corresponds to the second one. 96 matched cddid_all.tbl CDD cd22473 cd22473 411901 KH-I_DDX46 type I K homology (KH) RNA-binding domain found in DEAD box protein 46 (DDX46) and similar proteins. DDX46, also called PRP5 homolog, is an ATP-dependent RNA helicase that plays an essential role in splicing, either prior to, or during splicing A complex formation. It inhibits antiviral innate responses by entrapping selected antiviral transcripts in the nucleus. It is also involved in the development of several tumors. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif. 103 matched cddid_all.tbl CDD cd22474 cd22474 411902 KH-I_PRP5_like type I K homology (KH) RNA-binding domain found in fungal pre-mRNA-processing ATP-dependent RNA helicase PRP5 and similar proteins. PRP5 is an ATP-dependent RNA helicase involved spliceosome assembly and in nuclear splicing. It catalyzes an ATP-dependent conformational change of U2 snRNP. PRP5 interacts with the U2 snRNP and HSH155. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif. 89 matched cddid_all.tbl CDD cd22475 cd22475 411903 KH-I_AtRH42_like type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana DEAD-box ATP-dependent RNA helicase RH42 and similar proteins. RH42, also called DEAD-box RNA helicase RCF1, or REGULATOR OF CBF GENE EXPRESSION 1, is a helicase required for pre-mRNA splicing, cold-responsive gene regulation and cold tolerance. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif. 102 matched cddid_all.tbl CDD cd22476 cd22476 411904 KH-I_N4BP1 type I K homology (KH) RNA-binding domain found in NEDD4-binding protein 1 (N4BP1) and similar proteins. N4BP1 interacts with and is a substrate of NEDD4 ubiquitin ligase (neural precursor cell expressed, developmentally downregulated 4, E3 ubiquitin protein ligase). It is also an inhibitor of the E3 ubiquitin-protein ligase ITCH, a NEDD4 structurally related E3. N4BP1 acts by interacting with the second WW domain of ITCH, leading to compete with ITCH's substrates and impairing ubiquitination of substrates. 68 matched cddid_all.tbl CDD cd22477 cd22477 411905 KH-I_NYNRIN_like type I K homology (KH) RNA-binding domain found in the subfamily of NYN domain and retroviral integrase catalytic domain-containing protein (NYNRIN). The NYNRIN subfamily includes NYNRIN and KH and NYN domain-containing protein (KHNYN). NYNRIN, also known as CGIN1/Cousin of GIN1, may contribute to retroviral resistance in mammals by regulating the ubiquitination of viral proteins. KHNYN acts as a novel cofactor for zinc finger antiviral protein (ZAP) to target CpG-containing retroviral RNA for degradation. 66 matched cddid_all.tbl CDD cd22478 cd22478 411906 KH-I_FUBP1_rpt1 first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one. 75 matched cddid_all.tbl CDD cd22479 cd22479 411907 KH-I_FUBP2_rpt1 first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one. 71 matched cddid_all.tbl CDD cd22480 cd22480 411908 KH-I_FUBP3_rpt1 first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one. 71 matched cddid_all.tbl CDD cd22481 cd22481 411909 KH-I_FUBP1_rpt2 second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one. 71 matched cddid_all.tbl CDD cd22482 cd22482 411910 KH-I_FUBP2_rpt2 second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one. 73 matched cddid_all.tbl CDD cd22483 cd22483 411911 KH-I_FUBP3_rpt2 second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one. 83 matched cddid_all.tbl CDD cd22484 cd22484 411912 KH-I_FUBP1_rpt3 third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the third one. 68 matched cddid_all.tbl CDD cd22485 cd22485 411913 KH-I_FUBP2_rpt3 third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the third one. 68 matched cddid_all.tbl CDD cd22486 cd22486 411914 KH-I_FUBP3_rpt3 third type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the third one. 70 matched cddid_all.tbl CDD cd22487 cd22487 411915 KH-I_FUBP1_rpt4 fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 1 (FUBP1) and similar proteins. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP1 contains four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one. 72 matched cddid_all.tbl CDD cd22488 cd22488 411916 KH-I_FUBP2_rpt4 fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 2 (FUBP2) and similar proteins. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP2 contains four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one. 69 matched cddid_all.tbl CDD cd22489 cd22489 411917 KH-I_FUBP3_rpt4 fourth type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one. 69 matched cddid_all.tbl CDD cd22490 cd22490 411918 KH-I_IGF2BP1_rpt1 first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins. IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one. 76 matched cddid_all.tbl CDD cd22491 cd22491 411919 KH-I_IGF2BP2_rpt1 first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins. IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one. 74 matched cddid_all.tbl CDD cd22492 cd22492 411920 KH-I_IGF2BP3_rpt1 first type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins. IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the first one. 76 matched cddid_all.tbl CDD cd22493 cd22493 411921 KH-I_IGF2BP1_rpt2 second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins. IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one. 97 matched cddid_all.tbl CDD cd22494 cd22494 411922 KH-I_IGF2BP2_rpt2 second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins. IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one. 77 matched cddid_all.tbl CDD cd22495 cd22495 411923 KH-I_IGF2BP3_rpt2 second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins. IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one. 77 matched cddid_all.tbl CDD cd22496 cd22496 411924 KH-I_IGF2BP1_rpt3 third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins. IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one. 76 matched cddid_all.tbl CDD cd22497 cd22497 411925 KH-I_IGF2BP2_rpt3 third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins. IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one. 77 matched cddid_all.tbl CDD cd22498 cd22498 411926 KH-I_IGF2BP3_rpt3 third type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins. IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the third one. 78 matched cddid_all.tbl CDD cd22499 cd22499 411927 KH-I_IGF2BP1_rpt4 fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins. IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the fourth one. 76 matched cddid_all.tbl CDD cd22500 cd22500 411928 KH-I_IGF2BP2_rpt4 fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins. IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the fourth one. 78 matched cddid_all.tbl CDD cd22501 cd22501 411929 KH-I_IGF2BP3_rpt4 fourth type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins. IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the fourth one. 66 matched cddid_all.tbl CDD cd22502 cd22502 411930 KH-I_ANKRD17 type I K homology (KH) RNA-binding domain found in ankyrin repeat domain-containing protein 17 (ANKRD17) and similar proteins. ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses. 71 matched cddid_all.tbl CDD cd22503 cd22503 411931 KH-I_ANKHD1 type I K homology (KH) RNA-binding domain found in ankyrin repeat and KH domain-containing protein 1 (ANKHD1) and similar proteins. ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. It acts as a scaffolding protein that may be associated with the abnormal phenotype of leukemia cells. It may play might have a role in MM cell proliferation and cell cycle progression by regulating expression of p21. It also regulates cell cycle progression and proliferation in multiple myeloma cells. ANKHD1 is a component of Hippo signaling pathway. It functions as a positive regulator of YAP1 and promotes cell growth and cell cycle progression through Cyclin A upregulation in prostate cancer cells. 83 matched cddid_all.tbl CDD cd22504 cd22504 411932 KH_I_FXR1_rpt1 first type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins. FXR1 is an RNA-binding protein required for embryonic and postnatal development of muscle tissue. It may regulate intracellular transport and local translation of certain mRNAs. FXR1 protein may be present in amyloid form in brain of different species of mammals. It may regulate memory and emotions. FXR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif. 77 matched cddid_all.tbl CDD cd22505 cd22505 411933 KH_I_FXR2_rpt1 first type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 2 (FXR2) and similar proteins. FXR2, also known as FMR1L2, is an RNA-binding protein that plays a role in central nervous system function. It specifically regulates hippocampal neurogenesis by reducing the stability of Noggin mRNA. FXR2 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif. 77 matched cddid_all.tbl CDD cd22506 cd22506 411934 KH_I_FMR1_rpt1 first type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein 1 (FMR1) and similar proteins. FMR1, also called FMRP, or synaptic functional regulator FMR1, is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. It also plays a role in the alternative splicing of its own mRNA. FMR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif. 77 matched cddid_all.tbl CDD cd22507 cd22507 411935 KH_I_FXR1_rpt2 second type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins. FXR1 is an RNA-binding protein required for embryonic and postnatal development of muscle tissue. It may regulate intracellular transport and local translation of certain mRNAs. FXR1 protein may be present in amyloid form in brain of different species of mammals. It may regulate memory and emotions. FXR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one. 63 matched cddid_all.tbl CDD cd22508 cd22508 411936 KH_I_FXR2_rpt2 second type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 2 (FXR2) and similar proteins. FXR2, also known as FMR1L2, is an RNA-binding protein that plays a role in central nervous system function. It specifically regulates hippocampal neurogenesis by reducing the stability of Noggin mRNA. FXR2 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one. 63 matched cddid_all.tbl CDD cd22509 cd22509 411937 KH_I_FMR1_rpt2 second type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein 1 (FMR1) and similar proteins. FMR1, also called FMRP, or synaptic functional regulator FMR1, is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. It also plays a role in the alternative splicing of its own mRNA. FMR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one. 63 matched cddid_all.tbl CDD cd22510 cd22510 411938 KH_I_FXR1_rpt3 third type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 1 (FXR1) and similar proteins. FXR1 is an RNA-binding protein required for embryonic and postnatal development of muscle tissue. It may regulate intracellular transport and local translation of certain mRNAs. FXR1 protein may be present in amyloid form in brain of different species of mammals. It may regulate memory and emotions. FXR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one. 78 matched cddid_all.tbl CDD cd22511 cd22511 411939 KH_I_FXR2_rpt3 third type I K homology (KH) RNA-binding domain found in fragile X mental retardation syndrome-related protein 2 (FXR2) and similar proteins. FXR2, also known as FMR1L2, is an RNA-binding protein that plays a role in central nervous system function. It specifically regulates hippocampal neurogenesis by reducing the stability of Noggin mRNA. FXR2 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one. 78 matched cddid_all.tbl CDD cd22512 cd22512 411940 KH_I_FMR1_rpt3 third type I K homology (KH) RNA-binding domain found in fragile X mental retardation protein 1 (FMR1) and similar proteins. FMR1, also called FMRP, or synaptic functional regulator FMR1, is a multifunctional polyribosome-associated RNA-binding protein that plays a central role in neuronal development and synaptic plasticity through the regulation of alternative mRNA splicing, mRNA stability, mRNA dendritic transport and postsynaptic local protein synthesis of a subset of mRNAs. It also plays a role in the alternative splicing of its own mRNA. FMR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one. 78 matched cddid_all.tbl CDD cd22513 cd22513 411941 KH-I_BTR1_rpt1 first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins. BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one. 73 matched cddid_all.tbl CDD cd22514 cd22514 411942 KH-I_BTR1_rpt3 third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins. BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one. 71 matched cddid_all.tbl CDD cd22515 cd22515 411943 KH-I_PCBP1_2_rpt1 first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins. The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the first one. 70 matched cddid_all.tbl CDD cd22516 cd22516 411944 KH-I_PCBP3_rpt1 first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins. PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one. 77 matched cddid_all.tbl CDD cd22517 cd22517 411945 KH-I_PCBP4_rpt1 first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins. PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one. 70 matched cddid_all.tbl CDD cd22518 cd22518 411946 KH-I_PCBP1_2_rpt2 second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins. The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one. 78 matched cddid_all.tbl CDD cd22519 cd22519 411947 KH-I_PCBP3_rpt2 second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins. PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one. 79 matched cddid_all.tbl CDD cd22520 cd22520 411948 KH-I_PCBP4_rpt2 second type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins. PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one. 72 matched cddid_all.tbl CDD cd22521 cd22521 411949 KH-I_PCBP1_2_rpt3 third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins. The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one. 76 matched cddid_all.tbl CDD cd22522 cd22522 411950 KH-I_PCBP3_rpt3 third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins. PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one. 75 matched cddid_all.tbl CDD cd22523 cd22523 411951 KH-I_PCBP4_rpt3 third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 4 (PCBP4) and similar proteins. PCBP4, also called alpha-CP4, or heterogeneous nuclear ribonucleoprotein E4, or hnRNP E4, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It regulates both basal and stress-induced p21 expression through binding p21 3'-UTR and modulating p21 mRNA stability. It also plays a role in the cell cycle and is implicated in lung tumor suppression. PCBP4 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one. 68 matched cddid_all.tbl CDD cd22524 cd22524 411952 KH-I_Rrp4_prokar type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 mainly from archaea. The subfamily corresponds to ribosomal RNA-processing protein 4 (Rrp4) mainly from archaea. It is a non-catalytic component of the exosome, which is a phosphorolytic 3'-5' exoribonuclease complex involved in RNA degradation and processing. Rrp4 increases the RNA binding and the efficiency of RNA degradation and confers strong poly(A) specificity to the exosome. 82 matched cddid_all.tbl CDD cd22525 cd22525 411953 KH-I_Rrp4_eukar type I K homology (KH) RNA-binding domain found in exosome complex component Rrp4 from eukaryote. The subfamily corresponds to ribosomal RNA-processing protein 4 (Rrp4) mainly from eukaryote. Rrp4, also called exosome component 2 (EXOSC2), or ribosomal RNA-processing protein 4, is a non-catalytic component of the RNA exosome complex which has 3'-->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. Mutations in EXOSC2 gene are associated with a novel syndrome characterized by retinitis pigmentosa, progressive hearing loss, premature aging, short stature, mild intellectual disability and distinctive gestalt. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif. 123 matched cddid_all.tbl CDD cd22526 cd22526 411954 KH-I_Rrp40 type I K homology (KH) RNA-binding domain found in exosome complex component Rrp40 and similar proteins. Rrp40, also called exosome component 3 (EXOSC3), or ribosomal RNA-processing protein 40, is a non-catalytic component of the RNA exosome complex which has 3'-->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. Mutations of EXOSC3 gene are associated with neurological diseases. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif. 78 matched cddid_all.tbl CDD cd22527 cd22527 412022 IPD_PPP1R12A-like inhibitory phosphorylation domain of protein phosphatase 1 regulatory subunit 12A-like, and similar proteins. Protein phosphatase 1 regulatory subunit 12A-like (PPP1R12A-like) is a homolog of MYPT1, also called protein phosphatase 1 regulatory subunit 12A (PPP1R12A), myosin phosphatase target subunit 1, or protein phosphatase myosin-binding subunit. MYPT1 is the targeting subunit of smooth-muscle myosin phosphatase. It is a substrate for the asparaginyl hydroxylase factor inhibiting hypoxia-inducible factor (FIH). MYPT1 acts as a key regulator of protein phosphatase 1C (PPP1C). It mediates binding to myosin. As part of the PPP1C complex, MYPT1 is involved in dephosphorylation of the mitosis regulator polo-like kinase 1 (PLK1). It is capable of inhibiting HIF1A inhibitor (HIF1AN)-dependent suppression of HIF1A activity. This model corresponds to the inhibitory phosphorylation domain of PPP1R12A-like protein. 50 matched cddid_all.tbl CDD cd22528 cd22528 412095 av_Nsp3_ER-remodelling intracellular membrane remodeller motif of arterivirus non-structural protein 3 (Nsp3). This domain is present in subunit Nsp3 of RNA-arteriviruses, such as porcine arterivirus PRRSV and equine arterivirus EAV. Nsp3 proteins are localized to the ER and appear to be essential for formation of double-membrane vesicles that originate from the ER during the life-cycle of the virus. Arterivirus Nsp3 is a predicted tetra-spanning transmembrane protein containing four transmembrane helices, with the N- and C-termini of the protein residing in the cytoplasm. It contains a cluster of four highly conserved cysteine residues that are predicted to reside in the first luminal domain of the protein. These conserved cysteines play a key role in the formation of double-membrane vesicles (DMVs); mutagenesis of each completely blocked DMV formation. 57 matched cddid_all.tbl CDD cd22529 cd22529 411786 KH-II_NusA_rpt2 second type II K-homology (KH) RNA-binding domain found in transcription termination/antitermination protein NusA and similar proteins. NusA, also called N utilization substance protein A or transcription termination/antitermination L factor, is an essential multifunctional transcription elongation factor that participates in both transcription termination and antitermination. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNA polymerase pausing provides a mechanism for synchronizing transcription and translation. In prokaryotes, the N-terminal RNA polymerase-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, the S1 and two K-homology, KH1 and KH2. The K-homology (KH) domains of NusA belong to the type II KH RNA-binding domain superfamily. This model corresponds to the second KH domain of NusA and similar proteins. 61 matched cddid_all.tbl CDD cd22530 cd22530 411787 KH-II_NusA_arch_rpt1 first type II K-homology (KH) RNA-binding domain found in archaeal probable transcription termination protein NusA and similar proteins. NusA, also called N utilization substance protein A, is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. It participates in both transcription termination and antitermination. NusA homologs consisting of only the two type II K-homology (KH) domains are widely conserved in archaea. Although their function remains unclear, it has been found that Aeropyrum pernix NusA strongly binds to a certain CU-rich sequence near a termination signal. Archaeal NusA may have retained some functions of bacterial NusA, including ssRNA-binding ability. This model corresponds to the first KH domain of NusA found mainly in archaea. 69 matched cddid_all.tbl CDD cd22531 cd22531 411788 KH-II_NusA_arch_rpt2 second type II K-homology (KH) RNA-binding domain found in archaeal probable transcription termination protein NusA and similar proteins. NusA, also called N utilization substance protein A, is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. It participates in both transcription termination and antitermination. NusA homologs consisting of only the two type II K-homology (KH) domains are widely conserved in archaea. Although their function remains unclear, it has been found that Aeropyrum pernix NusA strongly binds to a certain CU-rich sequence near a termination signal. Archaeal NusA may have retained some functions of bacterial NusA, including ssRNA-binding ability. This model corresponds to the second KH domain of NusA mainly found in archaea. 67 matched cddid_all.tbl CDD cd22532 cd22532 411789 KH-II_CPSF_arch_rpt1 first type II K-homology (KH) RNA-binding domain found in archaeal cleavage and polyadenylation specificity factor (CPSF) and similar proteins. The archaeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup of enzymes within the metallo-beta-lactamase fold. Within the CPSF family, all archaeal genomes contain one member with two N-terminal type II K-homology (KH) domains and one without. This family includes the CPSF homologs from archaea possessing N-terminal KH domains. This model corresponds to the first KH domain, which is a non-canonical type II KH domain that does not contain the signature motif GXXG (where X represents any amino acid). 62 matched cddid_all.tbl CDD cd22533 cd22533 411790 KH-II_YlqC-like type II K-homology (KH) RNA-binding domain found in Bacillus subtilis UPF0109 protein YlqC and similar proteins. The family includes a group of uncharacterized proteins which show sequence similarity to Bacillus subtilis UPF0109 protein YlqC. They are mainly found in bacteria and contain only one canonical type II K-homology (KH) domain that has the signature motif GXXG (where X represents any amino acid). 75 matched cddid_all.tbl CDD cd22534 cd22534 411791 KH-II_Era type II K-homology (KH) RNA-binding domain found in GTPase Era and similar proteins. GTPase Era, also called ERA or GTP-binding protein Era, is an essential GTPase that binds both GDP and GTP, with nucleotide exchange occurring in the order of seconds whereas hydrolysis occurs in the order of minutes. It plays a role in numerous processes, including cell cycle regulation, energy metabolism, as a chaperone for 16S rRNA processing, and 30S ribosomal subunit biogenesis. Its presence in the 30S subunit may prevent translation initiation. GTPase Era may also be critical for maintaining cell growth and cell division rates. Members of this family contain only one canonical type II K-homology (KH) domain that has the signature motif GXXG (where X represents any amino acid). 87 matched cddid_all.tbl CDD cd22536 cd22536 411773 SP4_N N-terminal domain of transcription factor Specificity Protein (SP) 4. Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. Human SP4 is a risk gene of multiple psychiatric disorders including schizophrenia, bipolar disorder, and major depression. SP4 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP4. 623 matched cddid_all.tbl CDD cd22537 cd22537 411774 SP3_N N-terminal domain of transcription factor Specificity Protein (SP) 3. Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP1 and SP3 can interact with and recruit a large number of proteins including the transcription initiation complex, histone modifying enzymes, and chromatin remodeling complexes, which strongly suggest that SP1 and SP3 are important transcription factors in remodeling chromatin and the regulation of gene expression. SP3 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP3. 574 matched cddid_all.tbl CDD cd22538 cd22538 411690 SP8_N N-terminal domain of transcription factor Specificity Protein (SP) 8. Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP8 is crucial for limb outgrowth and neuropore closure. It is expressed during embryogenesis in the forming apical ectodermal ridge, restricted regions of the central nervous system, and tail bud. SP8 and SP9 are two closely related transcription factors that mediate FGF10 signaling, which in turn regulates FGF8 expression which is essential for normal limb development. Both SP8 and SP9 have been found in vertebrates, but only SP8 is present in invertebrates. SP8 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. This model represents the N-terminal domain of SP8. 303 matched cddid_all.tbl CDD cd22539 cd22539 411775 SP1_N N-terminal domain of transcription factor Specificity Protein (SP) 1. Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP1 has been shown to interact with a variety of proteins including myogenin, SMAD3, SUMO1, SF1, TAL1, and UBC. Some 12,000 SP1 binding sites are found in the human genome. SP1 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLF bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP1. 433 matched cddid_all.tbl CDD cd22540 cd22540 411776 SP2_N N-terminal domain of transcription factor Specificity Protein (SP) 2. Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP2 contains the least conserved DNA-binding domain within the SP subfamily of proteins, and its DNA sequence specificity differs from the other SP proteins. It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate, or in some cases, repress expression from different promoters. The transcription factor SP2 serves as a paradigm for indirect genomic binding. It does not require its DNA-binding domain for genomic DNA binding and occupies target promoters independently of whether they contain a cognate DNA-binding motif. SP2 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP2. 511 matched cddid_all.tbl CDD cd22541 cd22541 412096 SP5_N N-terminal domain of transcription factor Specificity Protein (SP) 5. Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. There are many SPs in vertebrates (9 SPs in humans and mice, 7 SPs in the chicken, and 11 SPs in teleost fish), but arthropods only have 3 SPs. All of them contain clade SP5, which plays a potential role in human cancers and was found in several human tumors including hepatocellular carcinoma, gastric cancer, and colon cancer. Leukemia inhibitor factor/Stat3 and Wnt/beta-catenin signaling pathways converge on SP5 to promote mouse embryonic stem cell self-renewal. SP5 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. This model represents the N-terminal domain of SP5. 143 matched cddid_all.tbl CDD cd22542 cd22542 411691 SP7_N N-terminal domain of transcription factor Specificity Protein (SP) 7. Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP7, also called Osterix (Osx) in humans, is highly conserved among bone-forming vertebrates. It plays a major role, along with Runx2 and Dlx5 in driving the differentiation of mesenchymal precursor cells into osteoblasts and eventually osteocytes. SP7 also plays a regulatory role by inhibiting chondrocyte differentiation, maintaining the balance between differentiation of mesenchymal precursor cells into ossified bone or cartilage. Mutations of this gene have been associated with multiple dysfunctional bone phenotypes in vertebrates. SP7 is thought to play a role in diseases such as Osteogenesis imperfecta. SP7 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. This model represents the N-terminal domain of SP7. 297 matched cddid_all.tbl CDD cd22543 cd22543 411692 SP6-9_N N-terminal domains of transcription factor Specificity Proteins (SP) 6-9, and similar proteins. Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. There are many SPs in vertebrates (9 SPs in humans and mice, 7 SPs in the chicken, and 11 SPs in teleost fish), but arthropods only have 3 SPs. SPs belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. This model represents the related N-terminal domains of SP6-SP9, and similar proteins. 162 matched cddid_all.tbl CDD cd22544 cd22544 411693 SP6_N N-terminal domain of transcription factor Specificity Protein (SP) 6. Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP6, also known as epiprofin, shows specific expression pattern in hair follicles and the apical ectodermal ridge (AER) of the developing limbs. SP6 null mice are nude and show defects in skin, teeth, limbs (syndactyly and oligodactyly), and lung alveoli. SP6 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. This model represents the N-terminal domain of SP6. 245 matched cddid_all.tbl CDD cd22545 cd22545 411777 SP1-4_N N-terminal domain of transcription factor Specificity Proteins (SP) 1-4. Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. There are many SPs in vertebrates (9 SPs in humans and mice, 7 SPs in chicken, and 11 SPs in teleost fish), but arthropods only have 3 SPs. SPs belong to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. SP1-4 have similar N-terminal transactivation domains characterized by glutamine-rich regions, which, in most cases, have adjacent serine/threonine-rich regions. This model represents the N-terminal domain of SP1-4. 82 matched cddid_all.tbl CDD cd22546 cd22546 412097 AcrIE2 Anti-CRISPR type I subtype E2. AcrIE2 (also known as AcrE2) is a phage anti-CRISPR (Acr) protein that has been shown to mediate inhibition of the type I-E CRISPR-Cas system of Pseudomonas aeruginosa. AcrIE2 was discovered via a guilt-by association (GBA) approach, which was based on the strong co-occurrence and clustering of acr and anti-CRISPR associated (aca) genes through proximity and homology searches, AcrIE2 was then confirmed functionally to be an type 1-E Acr. These anti-CRISPR gene clusters all contain a conserved putative promoter region at their 5' end and a conserved aca gene at their 3' end. Type I-E and I-F acr genes are located at the same position in the genomes of a large group of related phages, and they are found in a variety of combinations and arrangements. The type I-E CRISPR-Cas system Csy is a crRNA-guided surveillance complex, composed of a crRNA and eleven Cas proteins (one Cse1, two Cse2, one Cas5, six Cas7 and one Cas6e), which recruits a nuclease-helicase protein Cas3 for target degradation. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif which inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 1 systems utilize RNA-guided complexes consisting of multiple Cas proteins as the effector proteins to recognize and cleave target DNA. Type I CRISPR-Cas systems are the most widespread in nature, and the Cas protein composition of the employed CRISPR ribonucleoprotein (crRNP) complexes differs between seven subtypes (A to F, U). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 84 matched cddid_all.tbl CDD cd22547 cd22547 411694 SP6-9-like_N N-terminal domain of invertebrate transcription factor Specificity Proteins (SP) similar to SP6, SP8 and SP9. Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP6, also known as epiprofin, shows specific expression pattern in hair follicles and the apical ectodermal ridge (AER) of the developing limbs. SP6 null mice are nude and show defects in skin, teeth, limbs (syndactyly and oligodactyly), and lung alveoli. SP9 plays a role in limb outgrowth. It is expressed during embryogenesis in the forming AER, restricted regions of the central nervous system, and tail bud. SP8 and SP9 are two closely related transcription factors that mediate FGF10 signaling, which in turn regulates FGF8 expression which is essential for normal limb development. Both SP8 and SP9 have been found in vertebrates, but only SP8 is present in invertebrates. SPs belong to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. This model represents the N-terminal domain of invertebrate SPs similar to SP6, SP8, and SP9. 219 matched cddid_all.tbl CDD cd22549 cd22549 411695 SP9_N N-terminal domain of transcription factor Specificity Protein (SP) 9 and similar proteins. Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. SP9 plays a role in limb outgrowth. It is expressed during embryogenesis in the forming apical ectodermal ridge, restricted regions of the central nervous system, and tail bud. SP8 and SP9 are two closely related transcription factors that mediate FGF10 signaling, which in turn regulates FGF8 expression which is essential for normal limb development. Both SP8 and SP9 have been found in vertebrates, but only SP8 is present in invertebrates. SP9 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. SP factors may be separated into three groups based on their domain architecture and the similarity of their N-terminal transactivation domains: SP1-4, SP5, and SP6-9. The transactivation domains between the three groups are not homologous to one another. This model represents the N-terminal domain of SP9. 299 matched cddid_all.tbl CDD cd22551 cd22551 412098 AcrIE3 Anti-CRISPR type I subtype E3 (AcrIE3). AcrIE3 (also known as AcrE3) is an anti-CRISPR (Acr) protein that was discovered via guilt-by association (GBA) approach, which is based on the strong co-occurrence and clustering of acr and anti-CRISPR associated (aca) genes through proximity and homology searches. These anti-CRISPR gene clusters all contain a conserved putative promoter region at their 5' end and a conserved aca gene at their 3' end. Type I-E and I-F acr genes are located at the same position in the genomes of a large group of related phages, and they are found in a variety of combinations and arrangements. Functional assays confirmed AcrIE3 as a Type I-E Acr protein. AcrIE3 associates with the Cascade complex to hinder DNA binding, via an unknown mechanism. The type I-E CRISPR-Cas system Csy is a crRNA-guided surveillance complex, composed of a crRNA and eleven Cas proteins (one Cse1, two Cse2, one Cas5, six Cas7 and one Cas6e), which recruits a nuclease-helicase protein Cas3 for target degradation. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif which inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 1 systems utilize RNA-guided complexes consisting of multiple Cas proteins as the effector proteins to recognize and cleave target DNA. Type I CRISPR-Cas systems are the most widespread in nature, and the Cas protein composition of the employed CRISPR ribonucleoprotein (crRNP) complexes differs between seven subtypes (A to F, U). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 68 matched cddid_all.tbl CDD cd22552 cd22552 412099 AcrIE4 Anti-CRISPR type I subtype E4. AcrIE4, also known as AcrE4, anti-CRISPR protein 31 or ACR3112-31, is a phage anti-CRISPR (Acr) protein that has been shown to mediate inhibition of the type I-E CRISPR-Cas system of Pseudomonas aeruginosa. AcrIE4 was discovered via a guilt-by association (GBA) approach, which was based on the strong co-occurrence and clustering of acr and anti-CRISPR associated (aca) genes through proximity and homology searches. AcrIE4 was then confirmed functionally to be a type 1-E Acr. These anti-CRISPR gene clusters all contain a conserved putative promoter region at their 5' end and a conserved aca gene at their 3' end. Type I-E and I-F acr genes are located at the same position in the genomes of a large group of related phages, and they are found in a variety of combinations and arrangements. The type I-E Csy is a crRNA-guided surveillance complex, composed of a crRNA and eleven Cas proteins (one Cse1, two Cse2, one Cas5, six Cas7 and one Cas6e), which recruits a nuclease-helicase protein Cas3 for target degradation. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif which inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 1 systems utilize RNA-guided complexes consisting of multiple Cas proteins as the effector proteins to recognize and cleave target DNA. Type I CRISPR-Cas systems are the most widespread in nature, and the Cas protein composition of the employed CRISPR ribonucleoprotein (crRNP) complexes differs between seven subtypes (A to F, U). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 52 matched cddid_all.tbl CDD cd22553 cd22553 411778 SP1-4_arthropods_N N-terminal domain of transcription factor Specificity Protein (SP) 1-4 from arthropods. Specificity Proteins (SPs) are transcription factors that are involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling. There are many SPs in vertebrates (9 SPs in humans and mice, 7 SPs in the chicken, and 11 SPs in teleost fish), but arthropods only have 3 SPs. One SP is clade SP1-4, which is expressed ubiquitously throughout development. SP1-4 belongs to a family of proteins, called the SP/Kruppel or Krueppel-like Factor (KLF) family, characterized by a C-terminal DNA-binding domain of 81 amino acids consisting of three Kruppel-like C2H2 zinc fingers. These factors bind to a loose consensus motif, namely NNRCRCCYY (where N is any nucleotide; R is A/G, and Y is C/T), such as the recurring motifs in GC and GT boxes (5'-GGGGCGGGG-3' and 5-GGTGTGGGG-3') that are present in promoters and more distal regulatory elements of mammalian genes. SP factors preferentially bind GC boxes, while KLFs bind CACCC boxes. Another characteristic hallmark of SP factors is the presence of the Buttonhead (BTD) box CXCPXC, just N-terminal to the zinc fingers. The function of the BTD box is unknown, but it is thought to play an important physiological role. Another feature of most SP factors is the presence of a conserved amino acid stretch, the so-called SP box, located close to the N-terminus. This model represents the N-terminal domain of SP1-4 from arthropods. 384 matched cddid_all.tbl CDD cd22554 cd22554 412100 Slr4-like S (surface)-layer proteins similar to Pseudoalteromonas tunicata Slr4. Pseudoalteromonas tunicata D2 Slr4 (also known as EAR28894 protein) is an S-layer protein and the dominant protein within P. tunicata pellicle biofilm components. S-layers are self-assembling, paracrystalline proteinaceous lattices that form an interface between the cell and its extracellular environment; purified P. tunicata Slr4 protein is able to form square (p4 symmetry) paracrystalline lattices. Slr4 may protect cells and biofilm matrix components against stressors such as attack by viruses, bacteria or eukaryotes. The Slr4 family is widely distributed in gammaproteobacteria, including species of Pseudoalteromonas and Vibrio, and is found exclusively in marine metagenomes. It may play an important role in marine microbial physiology and ecology. 400 matched cddid_all.tbl CDD cd22555 cd22555 412101 Lpg2603_kinase Legionella pneumophila Dom/Icm type IV secretion system effector Lpg2603 kinase domain. This model contains the kinase domain of the type IV secretion system effector (T4SS) Lpg2603, an atypical kinase from the bacterial pathogen Legionella pneumophila. Lpg2603 is a remote member of the protein kinase superfamily having structural similarity, but notable differences in primary amino acid sequence. Studies show that Lpg2603 is an active protein kinase that requires the eukaryote-specific host signaling molecule inositol hexakisphosphate (IP6) for activity; IP6 binding rearranges the active site to allow for ATP binding and catalysis. The C-terminal domain of Lpg2603 is a PI4P-binding domain. 291 matched cddid_all.tbl CDD cd22556 cd22556 412102 AcrIE5 Anti-CRISPR type I subtype E5. AcrIE5 (also known as AcrE5) is an anti-CRISPR (Acr) protein that was discovered via guilt-by association (GBA) approach, which is based on the strong co-occurrence and clustering of acr and anti-CRISPR associated (aca) genes through proximity and homology searches. These anti-CRISPR gene clusters all contain a conserved putative promoter region at their 5' end and a conserved aca gene at their 3' end. Type I-E and I-F acr genes are located at the same position in the genomes of a large group of related phages, and they are found in a variety of combinations and arrangements. The type I-E CRISPR-Cas system Csy is a crRNA-guided surveillance complex, composed of a crRNA and eleven Cas proteins (one Cse1, two Cse2, one Cas5, six Cas7 and one Cas6e), which recruits a nuclease-helicase protein Cas3 for target degradation. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif which inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 1 systems utilize RNA-guided complexes consisting of multiple Cas proteins as the effector proteins to recognize and cleave target DNA. Type I CRISPR-Cas systems are the most widespread in nature, and the Cas protein composition of the employed CRISPR ribonucleoprotein (crRNP) complexes differs between seven subtypes (A to F, U). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 65 matched cddid_all.tbl CDD cd22557 cd22557 412103 AcrIF4 Anti-CRISPR type I subtype F4. AcrIF4 is a phage anti-CRISPR (Acr) protein that has been shown to associate with the type I-F Cascade surveillance complex (type I-F Csy complex) to inhibit DNA binding. AcrIF4 binds the Csy complex with affinities that are orders of magnitude weaker than Acr proteins like AcrIF1 and AcrIF2. The type I-F Csy complex is a crRNA-guided surveillance complex composed of a crRNA and nine Cas proteins (one Cas8f, one Cas5f, one Cas6f, and six Cas7f), which recruits a nuclease-helicase protein Cas3 for target degradation. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, which inhibit a wide range of CRISPR-Cas systems using various inhibition mechanisms. Weak and strong Acr-phages often cooperate to overcome CRISPR resistance, with a first phage blocking the host CRISPR-Cas immune system to allow a second Acr-phage to successfully replicate which leads to epidemiological tipping points. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 1 systems utilize RNA-guided complexes consisting of multiple Cas proteins as the effector proteins to recognize and cleave target DNA. Type I CRISPR-Cas systems are the most widespread in nature, and the Cas protein composition of the employed CRISPR ribonucleoprotein (crRNP) complexes differs between seven subtypes (A to F, U). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 95 matched cddid_all.tbl CDD cd22558 cd22558 411697 RETR_RHD N-terminal reticulon-homology domain of Reticulophagy regulators and similar proteins. This subfamily includes Reticulophagy regulators 1-3. Reticulophagy regulator 1 (RETREG1/FAM134B) is an endoplasmic reticulum (ER)-anchored autophagy receptor that regulates the size and shape of the ER. It regulates turnover of the ER by selective phagocytosis, mediating ER delivery into lysosomes through sequestration into autophagosomes. It promotes membrane remodeling and ER scission through its membrane bending activity, and targets the fragments into autophagosomes by interacting with ATG8 family modifier proteins such as MAP1LC3A, MAP1LC3B, GABARAP, GABARAPL1 and GABARAPL2. RETREG2/FAM134A and RETREG3/FAM134C has been shown to interact with ATG8 family modifier proteins MAP1LC3A, MAP1LC3B, GABARAP, and GABARAPL1. Members of this subfamily contain an N-terminal reticulon-homology domain (RHD) that shows sequence similarity to ADP-ribosylation factor-like 6 binding factor 1 (Arl6IP1 or Arl6ip-1), an ER protein that has an important role in cell conduction and material transport. The RHD may function in inducing membrane curvature. 192 matched cddid_all.tbl CDD cd22559 cd22559 411698 Arl6IP1 ADP-ribosylation factor-like protein 6-interacting protein 1. ADP-ribosylation factor-like 6 binding factor 1 (Arl6IP1 or Arl6ip-1), also called apoptotic regulator in the membrane of the endoplasmic reticulum (ARMER), is an endoplasmic reticulum (ER) protein that has an important role in cell conduction and material transport. Arl6IP1, a tetraspan membrane protein, is an anti-apoptotic protein specific to multicellular organisms, and is a potential player in shaping the ER tubules in mammalian cells. In neurons, Arl6IP1 has been associated with the regulation of glutamate, a major excitatory neurotransmitter in excitatory synapses. In Drosophila, knockdown of the Arl6IP1 gene leads to progressive motor deficit. An Arl6IP1 variant has also been associated with hereditary spastic paraplegia (HSP), motor and sensory polyneuropathy, and acromutilation. Arl6IP1 shows some sequence similarity to the reticulon-homology domain (RHD) of reticulophagy regulators, which may function in inducing membrane curvature. 167 matched cddid_all.tbl CDD cd22560 cd22560 411699 RETR1_RHD N-terminal reticulon-homology domain of Reticulophagy regulator 1. Reticulophagy regulator 1 (RETR1 or RETREG1), also called reticulophagy receptor 1 or FAM134B (family with sequence similarity 134, member B), is an endoplasmic reticulum (ER)-anchored autophagy receptor that regulates the size and shape of the ER. It regulates turnover of the ER by selective phagocytosis, mediating ER delivery into lysosomes through sequestration into autophagosomes. It promotes membrane remodeling and ER scission through its membrane bending activity, and targets the fragments into autophagosomes by interacting with ATG8 family modifier proteins such as MAP1LC3A, MAP1LC3B, GABARAP, GABARAPL1 and GABARAPL2. Loss of function of FAM134B is associated with diseases and cancer, including hereditary sensory and autonomic neuropathy type IIB (HSAN IIB), colorectal adenocarcinoma, and oesophageal squamous cell carcinoma, and other progressive neuronal degenerative diseases. FAM134B is also implicated in the suppression of viral replication during Ebola, Dengue, Zika, and West Nile viral infections. RETREG1/FAM134B contains an N-terminal reticulon-homology domain (RHD) that shows sequence similarity to ADP-ribosylation factor-like 6 binding factor 1 (Arl6IP1 or Arl6ip-1), an ER protein that has an important role in cell conduction and material transport. The RHD may function in inducing membrane curvature. 198 matched cddid_all.tbl CDD cd22561 cd22561 411700 RETR2_RHD N-terminal reticulon-homology domain of Reticulophagy regulator 2. Reticulophagy regulator 2 (RETR2 or RETREG2), also called FAM134A (family with sequence similarity 134, member A), C2orf17, or MAG2, interacts with ATG8 family modifier proteins MAP1LC3A, MAP1LC3B, GABARAP, and GABARAPL1. RETREG2/FAM134A contains an N-terminal reticulon-homology domain (RHD) that shows sequence similarity to ADP-ribosylation factor-like 6 binding factor 1 (Arl6IP1 or Arl6ip-1), an endoplasmic reticulum protein that has an important role in cell conduction and material transport. The RHD may function in inducing membrane curvature. 199 matched cddid_all.tbl CDD cd22562 cd22562 411701 RETR3_RHD N-terminal reticulon-homology domain of Reticulophagy regulator 3. Reticulophagy regulator 3 (RETR3 or RETREG3), also called FAM134C (family with sequence similarity 134, member C), mediates NRF1-enhanced neurite outgrowth. It interacts with ATG8 family modifier proteins MAP1LC3A, MAP1LC3B, GABARAP, and GABARAPL1. RETREG3/FAM134C contains an N-terminal reticulon-homology domain (RHD) that shows sequence similarity to ADP-ribosylation factor-like 6 binding factor 1 (Arl6IP1 or Arl6ip-1), an endoplasmic reticulum protein that has an important role in cell conduction and material transport. The RHD may function in inducing membrane curvature. 192 matched cddid_all.tbl CDD cd22563 cd22563 412104 CclA carnocyclin A. Carnocyclin A (CclA) is a potent ribosomally synthesized antimicrobial peptide, originally found in Carnobacterium maltaromaticum UAL307, that displays a broad spectrum of activity against numerous Gram-positive organisms. An amide bond links the N and C termini of this circular bacteriocin, giving it stability and structural integrity. CclA interacts with lipid bilayers in a voltage-dependent manner and forms anion selective pores that preferentially bind halide anions. The ABC transporter CclEFGH facilitates the production of CclA. 51 matched cddid_all.tbl CDD cd22564 cd22564 412105 AcrIF5 Anti-CRISPR type I subtype F5. AcrIF5, also known as AcrF5, is a phage anti-CRISPR (Acr) protein that has been shown to mediate inhibition of the type I-F CRISPR-Cas system of Pseudomonas aeruginosa. AcrIF5 is a weak anti-CRISPR and its gene always co-occurs with the AcrIF3 gene; however, the AcrIF3 gene often occurs in the absence of the AcrIF5 gene. The type I-F Csy complex is a crRNA-guided surveillance complex composed of a crRNA and nine Cas proteins (one Cas8f, one Cas5f, one Cas6f, and six Cas7f), which recruits a nuclease-helicase protein Cas3 for target degradation. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, which inhibit a wide range of CRISPR-Cas systems via various inhibition mechanisms. Weak and strong Acr-phages often cooperate to overcome CRISPR resistance, with a first phage blocking the host CRISPR-Cas immune system to allow a second Acr-phage to successfully replicate which leads to epidemiological tipping points. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 1 systems utilize RNA-guided complexes consisting of multiple Cas proteins as the effector proteins to recognize and cleave target DNA. Type I CRISPR-Cas systems are the most widespread in nature, and the Cas protein composition of the employed CRISPR ribonucleoprotein (crRNP) complexes differs between seven subtypes (A to F, U). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 79 matched cddid_all.tbl CDD cd22565 cd22565 412106 AcrIF7 Anti-CRISPR type I subtype F7. AcrIF7 (also known as AcrF7) is an anti-CRISPR (Acr) protein that was discovered via the guilt-by association (GBA) approach, which is based on the strong co-occurrence and clustering of acr and anti-CRISPR associated (aca) genes through proximity and homology searches. Functional assays show that AcrIF7 in Pseudomonas aeruginosa prophages strongly inhibits the type I-F CRISPR-Cas system. It has been classified as a broad-range type I-F Acr, as it is able to block the type I-F system of both P. aeruginosa and Pectobacterium atrosepticum. AcrIF7 targets the Cas8f subunit of the Csy complex and may compete for the same binding interface with AcrIF2. Extensive mutagenic analyses revealed that AcrIF7 associated with the highly conserved dsDNA binding site of Cas8f, primarily via electrostatic interactions. The type I-F Csy complex is a crRNA-guided surveillance complex composed of a crRNA and nine Cas proteins (one Cas8f, one Cas5f, one Cas6f, and six Cas7f), which recruits a nuclease-helicase protein Cas3 for target degradation. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 1 systems utilize RNA-guided complexes consisting of multiple Cas proteins as the effector proteins to recognize and cleave target DNA. Type I CRISPR-Cas systems are the most widespread in nature, and the Cas protein composition of the employed CRISPR ribonucleoprotein (crRNP) complexes differs between seven subtypes (A to F, U). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 69 matched cddid_all.tbl CDD cd22566 cd22566 412107 MrpH-like Mannose-resistant Proteus-like fimbriae (MR/P) tip adhesin (MrpH) and similar proteins. This model contains mannose-resistant Proteus-like fimbriae (MR/P) tip adhesin (MrpH) found in Proteus mirabilis, a Gram-negative uropathogen and a major causative agent in catheter-associated urinary tract infections. MrpH is required for MR/P-dependent adherence to surfaces. While MR/P belongs to a well-known class of adhesive fimbriae encoded by the chaperone-usher pathway, MrpH has a markedly different structure compared with other tip-located adhesins in this family. It is a novel class of metal-binding adhesin that requires zinc to mediate biofilm formation. 131 matched cddid_all.tbl CDD cd22568 cd22568 439335 EBM_STH1 ET-binding motif (EBM) of Saccharomyces cerevisiae ATP-dependent helicase STH1 and similar proteins. STH1/Sth1p (EC 3.6.4.12; also called nuclear protein STH1/NPS1, chromatin structure-remodeling complex protein STH1, or SNF2 homolog) is a Snf2p/Swi2p homolog that acts as a catalytic component of the chromatin structure-remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning. RSC is responsible for the transfer of a histone octamer from a nucleosome core particle to naked DNA. STH1 is an essential ATPase in RSC and differs from Snf/Swi in its interactions with histones and chromatin-associated proteins. It is a DNA translocase capable of nucleosome remodeling and is required for full expression of early meiotic genes. STH1 plays an essential role for mitotic growth and repression of CHA1 expression. It is also involved in G2 phase control. This model corresponds to a conserved region of STH1, which is responsible for the binding of the extra-terminal (ET) domain of TBP associated factor 14 (Taf14), a transcriptional regulator that controls diverse physiological processes and that physically interacts with at least seven nuclear complexes in yeast. 58 matched cddid_all.tbl CDD cd22569 cd22569 439336 TASOR_PBD periphilin binding domain of protein TASOR and similar proteins. TASOR, also called CTCL tumor antigen se89-1, retinoblastoma-associated protein RAP140, or transgene activation suppressor protein, is a component of the HUSH complex, a multiprotein complex that is at least composed of TASOR, PPHLN1 and MPHOSPH8, and mediates epigenetic repression. The HUSH complex is recruited to genomic loci rich in H3K9me3 and is required to maintain transcriptional silencing by promoting recruitment of SETDB1, a histone methyltransferase that mediates further deposition of H3K9me3, as well as MORC2. The HUSH complex is also involved in the silencing of unintegrated retroviral DNA by being recruited by ZNF638: some part of the retroviral DNA formed immediately after infection remains unintegrated in the host genome and is transcriptionally repressed. This model corresponds to a conserved region of TASOR, which is responsible for the binding of periphilin. 83 matched cddid_all.tbl CDD cd22570 cd22570 439337 CD4_CD cytoplasmic domain of T-cell surface glycoprotein CD4 and similar proteins. CD4, also called T-cell surface antigen T4/Leu-3, is an integral membrane glycoprotein that plays an essential role in the immune response and serves multiple functions in responses against both external and internal offenses. In T-cells, CD4 functions primarily as a coreceptor for MHC class II molecule:peptide complex. In other cells such as macrophages or NK cells, it plays a role in differentiation/activation, cytokine expression and cell migration in a TCR/LCK-independent pathway. CD4 participates in the development of T-helper cells in the thymus and triggers the differentiation of monocytes into functional mature macrophages. The model corresponds to cytoplasmic domain of CD4, which is responsible for the interaction with HIV-1 Nef protein that suppresses multiple immune surveillance mechanisms to promote viral pathogenesis. 44 matched cddid_all.tbl CDD cd22571 cd22571 439338 SNF6 transcription regulatory protein SNF6 domain family. SNF6 is a nuclear protein involved in transcriptional activation in Saccharomyces cerevisiae. It is a component of SWI/SNF complex, an ATP-dependent chromatin remodeling complex, which is required for the positive and negative regulation of gene expression of a large number of genes. It changes chromatin structure by altering DNA-histone contacts within a nucleosome, leading eventually to a change in nucleosome position, thus facilitating or repressing binding of gene-specific transcription factors. 198 matched cddid_all.tbl CDD cd22572 cd22572 439339 GCP5_NTD N-terminal domain of gamma-tubulin complex component 5 (GCP-5) and similar proteins. GCP-5, also called TUBGCP5, is a component of the gamma-tubulin ring complex (gamma-TuRC), which is necessary for microtubule nucleation at the centrosome. The model corresponds to the N-terminal domain (NTD) of GCP-5, which is involved in protein-protein interactions. GCP-5 binds Mozart1, a microprotein that regulates subcellular targeting and microtubule formation activity of gamma-TuRC at different cell cycle stages, through its NTD. 102 matched cddid_all.tbl CDD cd22573 cd22573 439340 RMP1_RBD RNA binding domain of Saccharomyces cerevisiae RNase MRP protein 1 (RMP1) and similar proteins. RMP1, also called RNA-processing protein RMP1, or RNase MRP 23.6 kDa subunit, functions as part of ribonuclease MRP (RNase MRP), which is involved in rRNA processing in mitochondria. RNase MRP complex consists of an RNA moiety and at least 10 protein subunits including POP1, POP3, POP4, POP5, POP6, POP7, POP8, RMP1, RPP1 and SNM1, many of which are shared with the RNase P complex. RMP1 is required for proper rRNA processing. The model corresponds to a conserved region of RMP1, which is responsible for the RNA binding. 116 matched cddid_all.tbl CDD cd22574 cd22574 439341 CNN1_HFD C-terminal histone fold domain of Saccharomyces cerevisiae co-purified with NNF1 protein 1 (CNN1). Cnn1, also called CENP-T homolog, or constitutive centromere-associated network protein Cnn1, is a component of the inner kinetochore, a multiprotein complex that assembles on centromeric DNA and attaches chromosomes to spindle microtubules, mediating chromosome segregation and sister chromatid segregation during meiosis and mitosis. Cnn1 is important for the recruitment of the outer kinetochore Ndc80 complex. The model corresponds to the C-terminal histone fold domain of Cnn1, which interacts with Wip1 to form a heterodimer. In budding yeast, the Cnn1-Wip1 heterodimer associated with the Ctf3 complex (Ctf3c) to form a sub-complex of the larger Ctf19 complex (Ctf19c). 90 matched cddid_all.tbl CDD cd22575 cd22575 439342 WIP1_HFD C-terminal histone fold domain of Saccharomyces cerevisiae W-like protein 1 (Wip1) and similar proteins. Wip1, also called CENP-W homolog, or constitutive centromere-associated network protein Wip1, is a component of the inner kinetochore, a multiprotein complex that assembles on centromeric DNA and attaches chromosomes to spindle microtubules, mediating chromosome segregation and sister chromatid segregation during meiosis and mitosis. The model corresponds to the C-terminal histone fold domain of Wip1, which interacts with Cnn1 to form a heterodimer. In budding yeast, the Cnn1-Wip1 heterodimer associated with the Ctf3 complex (Ctf3c) to form a sub-complex of the larger Ctf19 complex (Ctf19c). 73 matched cddid_all.tbl CDD cd22576 cd22576 439343 Edc3_Lsm Lsm domain of enhancer of mRNA-decapping protein 3 (Edc3) and similar proteins. Edc3 is an enhancer that stimulates decapping of both stable and unstable mRNA during mRNA decay. It does not affect nonsense-mediated mRNA decay. Edc3 also acts as a scaffold that aggregates mRNA ribonucleoproteins together for normal P-body assembly. The model corresponds to the N-terminal Lsm domain of Edc3, which is responsible for Dcp2 binding and decapping activation. 60 matched cddid_all.tbl CDD cd22577 cd22577 439344 Usa1_DBD C-terminal Der1-binding domain of U1 SNP1-associating protein 1 (Usa1) and similar proteins. Usa1 functions as a scaffold protein of the endoplasmic reticulum-associated degradation (ERAD; also known as endoplasmic reticulum quality control, ERQC) pathway involved in ubiquitin-dependent degradation of misfolded endoplasmic reticulum proteins. It is a component of the Hrd1 ubiquitin ligase complex, which is part of the ERAD-L and ERAD-M pathways responsible for the rapid degradation of soluble lumenal and membrane proteins with misfolded lumenal domains (ERAD-L), or ER-membrane proteins with misfolded transmembrane domains (ERAD-M). Usa1 plays essential roles in recruitment of Der1 to the Hrd1 ubiquitin ligase, as well as in regulation of the Hrd1p ubiquitin ligase. It is also involved in oligomerization of Hrd1 in its autoubiquitination and degradation. The model corresponds to the C-terminal Der1-binding domain of Usa1, which mediates the interaction with Der1 and is essential for ERAD-L in vivo. 49 matched cddid_all.tbl CDD cd22578 cd22578 439308 Mint1_CID CASK/Lin-2 interaction domain (CID) of Mint1 and similar proteins. Mint1, also called amyloid-beta A4 precursor protein-binding family A member 1 (Apba1), or adapter protein X11alpha, or neuron-specific X11 protein, or neuronal Munc18-1-interacting protein 1, functions in synaptic vesicle exocytosis by binding to Munc18-1, an essential component of the synaptic vesicle exocytotic machinery. It may modulate processing of the amyloid-beta precursor protein (APP) and hence formation of APP-beta. Mint1 is a component of the brain-specific heterotrimeric complex (LIN-10-LIN-2-LIN-7 complex), which associates with the motor protein KIF17 to transport vesicles containing N-methyl-D-aspartate (NMDA) receptor subunit NR2B along microtubules. It is also part of a multimeric complex containing Munc18-1 and syntaxin-1. The model corresponds to a conserved CASK/Lin-2 interaction domain (CID) of Mint1, which is responsible for CASK binding. 46 matched cddid_all.tbl CDD cd22579 cd22579 439345 MPEG1_P2 P2 domain of macrophage-expressed gene 1 protein (MPEG1) and similar proteins. Macrophage-expressed gene 1 protein (MPEG1), also called perforin-2 (P-2) or macrophage gene 1 protein (Mpg-1), is a pore-forming, antibacterial protein with broad-spectrum activity. It is a major antibacterial effector protein of the innate immune system in phagocytic as well as tissue forming cells. It plays an essential role in intracellular defense of parenchymal cells and phagocytes against pathogenic bacteria by inserting into the bacterial surface to form pores. This model corresponds to a unique membrane bound P2 domain of MPEG1, which helps to stabilize the pre-pore state by swapping between monomers and enables MPEG1 to bind its targeted membrane. 287 matched cddid_all.tbl CDD cd22580 cd22580 439346 AcrIF11 Anti-CRISPR type I subtype F11 (AcrIF11). AcrIF11 (also known as AcrF11) is an anti-CRISPR (Acr) protein that was discovered via the guilt-by association (GBA) method, and subsequently confirmed by functional assays to inhibit the type I-F CRISPR-Cas system. GBA is based on the strong co-occurrence and clustering of acr and anti-CRISPR associated (aca) genes through proximity and homology searches. AcrIF11 is often associated with genes encoding DNA-binding motifs, named Aca4 through Aca7. AcrIF11 is found in over 50 species of diverse proteobacteria; given its widespread nature it was used to discover acr loci encoding acr genes inhibiting types I-C and V-A CRISPR systems, where Acr proteins had not yet been found. Structure determination revealed that AcrIF11 binds NAD. The type I-F Csy complex is a crRNA-guided surveillance complex composed of a crRNA and nine Cas proteins (one Cas8f, one Cas5f, one Cas6f, and six Cas7f), which recruits a nuclease-helicase protein Cas3 for target degradation. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 1 systems utilize RNA-guided complexes consisting of multiple Cas proteins as the effector proteins to recognize and cleave target DNA. Type I CRISPR-Cas systems are the most widespread in nature, and the Cas protein composition of the employed CRISPR ribonucleoprotein (crRNP) complexes differs between seven subtypes (A to F, U). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 147 matched cddid_all.tbl CDD cd22581 cd22581 439214 SPOC_PPS-like SPOC (Spen paralog and ortholog C-terminal) domain found in Drosophila melanogaster protein partner of Sans-fille and similar proteins. Drosophila melanogaster protein partner of Sans-fille (PPS), also called protein partner of Snf, is a homolog of human DIDO. It mediates diverse chromatin activities, including the regulation of stemness genes in embryonic stem cells and splicing. PPS associates with spliceosomal RNAs including the U1 snRNP protein Sans-fille (Snf) to mediate sex determination gene Sex-lethal (Sxl) splicing autoregulation. Alternative splicing of the Sxl pre-mRNA determines gender during development in Drosophila, producing protein-encoding mRNAs in females but yielding inactive and truncated mRNAs in males. PPS contains a plant homeodomain (PHD) finger, Brahma and Kismet (BRK), a transcription elongation factor S-II subunit M (TFSIIM) domain, and a SPOC domain. This model corresponds to the SPOC domain that is involved in developmental signaling and has also been proposed to be a phosphorylation binding module. 142 matched cddid_all.tbl CDD cd22582 cd22582 439033 BRcat_RBR_unk BRcat domain found in an uncharacterized subfamily of RBR proteins. This subfamily contains uncharacterized members of the RBR family, including Arabidopsis thaliana mutator-like transposase, hypothetical protein F9K21.90, and hypothetical protein T16H5.30. The RBR family of RING-type E3 ligases are characterized by containing a RBR domain, which was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. It is composed of an extended RING domain (RING1) followed by an in-between RING (IBR) domain and the catalytic domain, which is structurally an IBR domain but is commonly designated RING2. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently, where the IBR and RING2 domains have been renamed as BRcat and Rcat domains, respectively. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. The BRcat domain adopts the same fold as the Rcat domain while lacking the catalytic cysteine residue and ubiquitination activity. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. 56 matched cddid_all.tbl CDD cd22583 cd22583 439034 Rcat_RBR_ARI7-like Rcat domain found in E3 ubiquitin-protein ligase ARI7 and similar proteins. This subfamily contains probable RBR-type E3 ubiquitin-protein ligases (EC 2.3.2.31) including Arabidopsis thaliana ARI5, ARI6, ARI7, and ARI8, as well as Dictyostelium discoideum RbrA (also called Ariadne-like ubiquitin ligase). They may function as part of E3 complexes, which accept ubiquitin from E2 ubiquitin-conjugating enzymes and then transfer it to substrates. RbrA may be required for normal cell-type proportioning and cell sorting during multicellular development, and is also necessary for spore cell viability. Members of this subfamily contain an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the Rcat domain of ARI7-like proteins that are essential for RBR E3 ligase activity and adopt the same fold as the BRcat domain. 55 matched cddid_all.tbl CDD cd22584 cd22584 439035 Rcat_RBR_unk Rcat domain found in an uncharacterized subfamily of RBR proteins. This subfamily contains uncharacterized members of the RBR family, including Arabidopsis thaliana mutator-like transposase and hypothetical protein At2g19610/F3P11.21. The RBR family of RING-type E3 ligases are characterized by containing a RBR domain, which was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. It is composed of an extended RING domain (RING1) followed by an in-between RING (IBR) domain and the catalytic domain, which is structurally an IBR domain but is commonly designated RING2. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been corrected as RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently, where the IBR and RING2 domains have been renamed as BRcat and Rcat domains, respectively. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. This model corresponds to the Rcat domain that is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain. 37 matched cddid_all.tbl CDD cd22585 cd22585 439036 Rcat_RBR_DEAH12-like Rcat domain of ATP-dependent RNA helicase DEAH12 and similar proteins. This group includes Arabidopsis thaliana ATP-dependent RNA helicases DEAH11 and DEAH12, which may be bifunctional proteins that function as DEAD-box RNA helicases (EC 3.6.4.13) and RBR-type E3 ubiquitin-protein ligases (EC 2.3.2.31). As RNA helicases, they may utilize the energy from ATP hydrolysis to unwind RNA (or DNA). DEAD-box RNA helicases participate in every aspect of RNA metabolism. As E3 ubiquitin-protein ligase, they may function as part of E3 complexes, which accept ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfer it to substrates. Other members of this group may not have an RNA helicase domain. All members contain an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the Rcat domain that is essential for RBR E3 ligase activity and adopts the same fold as the BRcat domain. 52 matched cddid_all.tbl CDD cd22586 cd22586 439037 Rcat_RBR_ARI1-like Rcat domain found in E3 ubiquitin-protein ligase ARI1 and similar proteins. This subfamily contains probable RBR-type E3 ubiquitin-protein ligases (EC 2.3.2.31) including Arabidopsis thaliana ARI1, ARI2, and ARI3. They may function as part of E3 complexes, which accept ubiquitin from E2 ubiquitin-conjugating enzymes and then transfer it to substrates. Members of this subfamily contain an RBR domain that was previously known as RING-BetweenRING-RING domain or TRIAD [two RING fingers and a DRIL (double RING finger linked)] domain. Based on current understanding of the structural biology of RBR ligases, the nomenclature of RBR has been changed to RING1-BRcat (benign-catalytic)-Rcat (required-for-catalysis) recently. The RBR domain uses an auto-inhibitory mechanism to modulate ubiquitination activity, as well as a hybrid mechanism that combines aspects from both RING and HECT E3 ligase functions to facilitate the ubiquitination reaction. This model corresponds to the Rcat domain of ARI1-like proteins that are essential for RBR E3 ligase activity and adopt the same fold as the BRcat domain. 54 matched cddid_all.tbl CDD cd22587 cd22587 439309 STING-like C-terminal domain of metazoan Stimulator Of Interferon Genes (STING) protein, bacterial STING, and similar proteins. This model represents the cytoplasmic ligand-binding domain (LBD, or cyclic-dinucleotide-binding domain) of Stimulator Of Interferon Genes (STING) protein, also called transmembrane protein 173 (TMEM173), mediator of IRF3 activation (MITA), endoplasmic reticulum IFN stimulator (ERIS), or N-terminal methionine-proline-tyrosine-serine plasma membrane tetraspanner (MYSA) of metazoa, as well as STING proteins in bacteria. STING is a receptor that senses foreign cyclic dinucleotides that are released during bacterial infections as well as in endogenous cyclic GMP-AMP (cGAMP) signaling during viral infection and anti-tumor immunity. STING activates downstream transcription factor IRF3 (interferon regulatory factor 3) and STAT (signal transducer and activator of transcription) via TBK1 ((Tank binding kinase 1), which are responsible for antiviral and innate immune response against intracellular pathogens. STING's activation of IRF3 and STAT induces the production of type 1 interferon and target genes involved in immune cell homing such as chemokines, respectively. STING may also function as a direct cytosolic DNA sensor. STING also has a role in B cell adaptive immunity through modulating B cell receptor signaling via PI3K (phosphatidylinositol 3-kinase). STING is encoded by the STING1 gene in mammals. It is an endoplasmic reticulum (ER) membrane protein that contains four transmembrane helices followed by a cytoplasmic ligand-binding and signaling domain. The cytoplasmic domain forms a homodimer, which undergoes conformational changes upon binding to cGAMP. Bacterial STING proteins are functional cyclic dinucleotide receptors and define a minimal homodimeric scaffold that selectively responds to cyclic di-GMP. They couple the recognition of cyclic dinucleotides with the formation of protein filaments to drive oligomerization of TIR effector domains and rapid NAD+ cleavage. Bacterial STING occurs primarily as a fusion to a Toll/interleukin-1 receptor (TIR, or Toll and IL-1 receptor) adaptor domain; TIR domains can function as beta-nicotinamide adenine dinucleotide (NAD+) hydrolases in plant and animal immunity. Bacterial STING homologs are 20% smaller and markedly compact, such that the metazoan insertions into the core bacterial fold are necessary for induction of autophagy, and the C-terminal tail contains motifs for the recruitment of kinases and transcription factors in vertebrates. 157 matched cddid_all.tbl CDD cd22588 cd22588 439142 GemC1_CC central coiled-coil domain of geminin coiled-coil domain-containing protein 1. Geminin coiled-coil domain-containing protein 1 (GemC1), which, together with McIdas (also called Idas or multicilin) and geminin, controls both the cell cycle and differentiation decisions in cells. GemC1 binds to geminin and is implicated in DNA replication control. It also functions as an early regulator of multiciliogenesis. GemC1 and Idas specify the multiciliate cell fate by forming complexes with the E2F4/5 transcription factors, resulting in centriole amplification and cilia formation. GemC1 belongs to the geminin family of proteins that also includes geminin and McIdas. They share a homologous central coiled-coil domain that mediates homo- and heterodimerization with other family members; this ability is likely to be important for modulating their function in cycling and differentiating cells. This model represents the central coiled-coil domain of GemC1. 61 matched cddid_all.tbl CDD cd22589 cd22589 439143 geminin_CC central coiled-coil domain of geminin. Geminin, together with geminin coiled-coil domain-containing protein 1 (GemC1) and McIdas (also called Idas or multicilin), controls both the cell cycle and differentiation decisions in cells. Geminin is an inhibitor of Cdt1, a key component and crucial regulator of pre-replicative complexes (pre-RC) that function in the duplication of chromosomal DNA. Pre-RC assembly culminates in the recruitment of the hexameric mini-chromosome maintenance complex (MCM) onto chromatin. Geminin tightly binds and sequesters Cdt1 in a complex that is unable to recruit MCM to origins, inhibiting DNA replication. It belongs to the geminin family of proteins that also includes GemC1 and McIdas. They share a homologous central coiled-coil domain that mediates homo- and heterodimerization with other family members; this ability is likely to be important for modulating their function in cycling and differentiating cells. This model represents the central coiled-coil domain of geminin. 65 matched cddid_all.tbl CDD cd22590 cd22590 439144 McIdas_CC central coiled-coil domain of McIdas (or multicilin). McIdas (also called Idas or multicilin), together with geminin coiled-coil domain-containing protein 1 (GemC1) and geminin, controls both the cell cycle and differentiation decisions in cells. Idas binds to geminin and is implicated in DNA replication control. It also functions as an early regulator of multiciliogenesis. GemC1 and McIdas specify the multiciliate cell fate by forming complexes with the E2F4/5 transcription factors, resulting in centriole amplification and cilia formation. Idas belongs to the geminin family of proteins that also includes geminin and GemC1. They share a homologous central coiled-coil domain that mediates homo- and heterodimerization with other family members; this ability is likely to be important for modulating their function in cycling and differentiating cells. This model represents the central coiled-coil domain of McIdas. 64 matched cddid_all.tbl CDD cd22591 cd22591 467851 AcrIIA5 "Anti-CRISPR type II subtype A5. AcrIIA5 is an anti-CRISPR (Acr) protein which was discovered in a virulent phage infecting Streptococcus thermophilus which strongly inhibits diverse Cas9 homologs. AcrIIA5 adopts a novel fold preceded by an intrinsically disordered region (IDR), which is required for Cas9 inhibition by AcrIIA5. Truncation of the IDR led to a complete loss of its Acr activity, and the length and charge of the IDR modulate AcrIIA5 binding to Cas9. The CRISPR Cas9-based cytosine base editors (CBEs) and adenine base editors (ABEs) are capable of catalyzing C-G to T-A or A-T to G-C base pair conversions, respectively, and are promising tools for achieving precise genetic changes in a wide range of organisms; however, the recognition of cognate DNA sequences near their target sites can cause severe off-target effects that greatly limit their clinical applications. Anti-CRISPRs, may have use in ameliorating the off-target effects of base editing systems. Anti-CRISPRs, AcrIIA2, AcrIIA4, and AcrIIA5 efficiently inhibit base editing systems in human cells. In particular, AcrIIA5 could efficiently inhibit different base editor variant systems, and diminish the off-target events of the base editor (CBE and ABE); suggesting that AcrIIA5 may have wide use for the precise control of base editing and to thoroughly ""shut off"" nuclease activity of both CBE and ABE systems. Almost all type II Acr proteins characterized to date directly interact with the Cas9 endonuclease, although by distinct mechanisms. The type II CRISPR/Cas subtype has a distinct crRNA-guided surveillance complex encoded by cas9 (formerly csn1), cas1, cas2, and csn2 (for type IIA) or cas4 (for type IIB) genes, type II-Cs are generally characterized by the absence of both cas4 and csn2; these genes are all located in a single transcriptional unit directly upstream of the CRISPR locus. However, variants of type II-C systems have been identified in archaea that contain cas4, and have cas1, cas2, cas4 downstream of the CRISPR locus. Cleavage of the DNA target in type II systems is carried out by Cas9 which is an RNA-guided double-stranded DNase with two independent nuclease domains, HNH and RuvC. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 2 systems are characterized by effector modules that consist of a single multidomain protein, such as Cas9 in type II. Acr families are named for their type and subtype which are numbered sequentially as they are discovered." 133 matched cddid_all.tbl CDD cd22592 cd22592 438635 Kunitz_BPTI bovine pancreatic trypsin inhibitor. This model contains bovine pancreatic trypsin inhibitor (BPTI, also known as pancreatic Kunitz inhibitor, aprotinin, or trypsin-kallikrein inhibitor), a small protein that inhibits the action of the trypsin, and is thus a member of the serine protease family of inhibitors. This class of enzymes contains conserved cysteine residues that form 3 disulfide bonds to stabilize the three-dimensional structure. BPTI has a relatively broad specificity, inhibiting trypsin as well as chymotrypsin, and elastase-like serine (pro)enzymes capable of very different primary specificity. It reacts rapidly with serine proteases to form stable complexes, but the enzyme:inhibitor complex formation may involve several intermediates corresponding to discrete reaction steps. Furthermore, BPTI inhibits the nitric oxide synthase type-I and -II action, and impairs K+ transport by Ca2+-activated K+ channels. Clinically, BPTI is used in certain surgical interventions, such as cardiopulmonary surgery and orthotopic liver transplantation since it significantly reduces hemorrhagic complications. 52 matched cddid_all.tbl CDD cd22593 cd22593 438636 Kunitz_conkunitzin conkunitzin-S1 and -S2, and similar proteins. This model includes Kunitz-type conkunitzin-S1 (Cs1) and -S2 (Cs2). Conkunitzins are pore-modulating toxins that block voltage-dependent potassium channels (Kvs) by exploiting inherent slow inactivation to block K+ channels. Cs1 binds to the channel turrets and disrupts the structural water hydrogen-bonding network, exposing the peripheral water pockets of ion channels and triggering an asymmetric collapse of the pore. Conus bullatus conkunitzin-B1, expressed in the venom duct, specifically blocks voltage-activated potassium channels (Kv) of the Shaker family. Members of this subfamily contain 2 disulfide bonds instead of the 3 present in most Kunitz domain proteins. 51 matched cddid_all.tbl CDD cd22594 cd22594 438637 Kunitz_textilinin-like venom Kunitz-type proteins such as textilinin, BF9 and PILP. This group includes toxins isolated from snake venoms, such as textilinin, vestiginin, spermatin, mulgin, venom basic protease inhibitor IX (BF9), and protease inhibitor-like protein (PILP), among others. Pseudonaja textilis textilinin-1 is a Kunitz-type serine protease inhibitor that binds to and blocks the activity of a range of serine proteases, including plasmin and trypsin. Ability of testilinin to inhibit plasmin, a protease involved in fibrinolysis, raises the possibility that it may be used as an alternative to aprotinin (Trasylol), which is a systemic antibleeding agent in surgery. Also included is the Bungarus fasciatus fraction IX (BF9), a chymotrypsin inhibitor that binds chymotrypsin but not trypsin. Protease inhibitor-like proteins PILP-1 and PILP-2 show weak binding and inhibition of matrix metalloproteinase-2 (MMP-2) and show an activity in inhibiting migration and invasion of neuroblastoma; they do not inhibit chymotrypsin or trypsin. The structures of these toxins are similar to those of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 56 matched cddid_all.tbl CDD cd22595 cd22595 438638 Kunitz_dendrotoxin dendrotoxins I, K, B and similar proteins. This group includes toxins isolated from snake venoms, such as dendrotoxins (DTXs) I, K and B, mambaquaretin-1 (MQ-1) and calcicludine. The dendrotoxins have little or no anti-protease activity but have been shown to block certain subtypes of voltage dependent potassium channels in neurons. Dendroaspis angusticeps (green mamba) alpha-dendrotoxin is a neurotoxin that enhances acetylcholine release at neuromuscular junctions. Studies with cloned K(+) channels show that this toxin blocks Kv1.1, Kv1.2 and Kv1.6 channels in the nanomolar range, whereas Dendroaspis polylepis (black mamba) dendrotoxin K preferentially blocks Kv1.1 channels. Also, structural analogs of dendrotoxins have facilitated defining the molecular recognition properties of different types of K(+) channels, and therefore, dendrotoxins are widely used as probes for studying the function of K(+) channels in physiology and pathophysiology. The structures of these toxins are similar to that of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 56 matched cddid_all.tbl CDD cd22596 cd22596 438639 Kunitz_bikunin_1-like first Kunitz domain of bikunin and similar proteins. This subfamily includes the N-terminal domain of bikunin (also known as inter-alpha-trypsin inhibitor light chain (ITI-LC) or urinary trypsin inhibitor), a plasma protease inhibitor, that is associated with inflammation and stabilizes the extracellular matrix. It is encoded together with alpha-1-microglobulin (A1M) by an alpha-1-microglobulin/bikunin precursor (AMBP) gene that is tightly controlled by several hepatocyte-enriched nuclear (HEN) factors, and cleaved by a furin-like protease that releases the two mature molecules. Bikunin is a Kunitz-type serine protease inhibitor, found in vertebrate serum and urine, modified by a chondroitin sulfate (CS) chain. The structures of these toxins are similar to that of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. Bikunin contains two Kunitz domains; this model represents the first repeat. 54 matched cddid_all.tbl CDD cd22597 cd22597 438640 Kunitz_bikunin_2-like second Kunitz domain of bikunin and similar proteins. This subfamily includes the C-terminal domain of bikunin (also known as inter-alpha-trypsin inhibitor light chain (ITI-LC) or urinary trypsin inhibitor), a plasma protease inhibitor, that is associated with inflammation and stabilizes the extracellular matrix. Bikunin is encoded together with alpha-1-microglobulin (A1M) by an alpha-1-microglobulin/bikunin precursor (AMBP) gene that is tightly controlled by several hepatocyte-enriched nuclear (HEN) factors, and cleaved by a furin-like protease that releases the two mature molecules. Bikunin is a Kunitz-type serine protease inhibitor, found in vertebrate serum and urine, modified by a chondroitin sulfate (CS) chain. The structures of these toxins are similar to that of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. Bikunin contains two Kunitz domains; this model represents the second repeat. 55 matched cddid_all.tbl CDD cd22598 cd22598 438641 Kunitz_huwentoxin Kunitz-type toxin huwentoxin-XI. This model contains Kunitz-type serine protease inhibitor huwentoxin-XI, including U15-theraphotoxin-Hs1g (also called U15-TRTX-Hs1g or Huwentoxin HW11c39), and kappaPI-theraphotoxin-Hs1a (also called KappaPI-TRTX-Hs1a or Huwentoxin-HW11g8). Huwentoxin-XI is a bifunctional toxin that inhibits both serine proteases (trypsin) and voltage-gated potassium channels (Kv) via surfaces displayed on opposite faces of the toxin. The structures of these domains are similar to those of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 53 matched cddid_all.tbl CDD cd22599 cd22599 438642 Kunitz_boophilin_1-like first Kunitz domain of Rhipicephalus microplus boophilin and similar proteins. This group includes venom serine protease inhibitors such as Rhipicephalus microplus and Ixodes scapularis boofilin, among others. Boophilin prevents blood clot formation to allow successful feeding and digestion through its inhibition activity of thrombin and other host anticoagulating factors like kallikrein, coagulation factor VII, or plasmin; it interacts with the host thrombin and trypsin. The structures of these domains are similar to those of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. Rhipicephalus microplus boophilin contains two Kunitz domains; this model represents the first repeat. 61 matched cddid_all.tbl CDD cd22600 cd22600 438643 Kunitz_boophilin_2-like second Kunitz domain of Rhipicephalus microplus boophilin and similar proteins. This group includes venom serine protease inhibitors such as Rhipicephalus microplus and Ixodes scapularis boofilin, among others. Boophilin prevents blood clot formation to allow successful feeding and digestion through its inhibition activity of thrombin and other host anticoagulating factors like kallikrein, coagulation factor VII, or plasmin; it interacts with the host thrombin and trypsin. The structures of these domains are similar to those of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. Rhipicephalus microplus boophilin contains two Kunitz domains; this model represents the second repeat. 54 matched cddid_all.tbl CDD cd22601 cd22601 438644 Kunitz_SmCI_1-like first Kunitz domain of Carboxypeptidase Inhibitor SmCI and similar domains. This group includes Sabellastarte magnifica carboxypeptidase inhibitor (SmCI), a tri-domain BPTI-Kunitz inhibitor capable of inhibiting serine proteases and A-like metallocarboxypeptidases. While the BPTI-Kunitz family of proteins includes voltage gated channel blockers and inhibitors of serine proteases, SmCI is the only BPTI-Kunitz protein capable of inhibiting metallocarboxypeptidases. Binding studies show that SmCI is able to bind three trypsin molecules under saturating conditions, but only one elastase interacts with the inhibitor. Additionally, SmCI can bind serine proteases and carboxypeptidases at the same time (at least in the ratio 1:1:1), thus becoming the first protease inhibitor that simultaneously blocks these two mechanistic classes of enzymes. This model contains the first Kunitz domain of SmCI, which has a structure similar to those of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 55 matched cddid_all.tbl CDD cd22602 cd22602 438645 Kunitz_SmCI_2-like second Kunitz domain of Carboxypeptidase Inhibitor SmCI and similar domains. This group includes Sabellastarte magnifica carboxypeptidase inhibitor (SmCI), a tri-domain BPTI-Kunitz inhibitor capable of inhibiting serine proteases and A-like metallocarboxypeptidases. While the BPTI-Kunitz family of proteins includes voltage gated channel blockers and inhibitors of serine proteases, SmCI is the only BPTI-Kunitz protein capable of inhibiting metallocarboxypeptidases. Binding studies show that SmCI is able to bind three trypsin molecules under saturating conditions, but only one elastase interacts with the inhibitor. Additionally, SmCI can bind serine proteases and carboxypeptidases at the same time (at least in the ratio 1:1:1), thus becoming the first protease inhibitor that simultaneously blocks these two mechanistic classes of enzymes. This model contains the second Kunitz domain of SmCI, which has a structure similar to those of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 51 matched cddid_all.tbl CDD cd22603 cd22603 438646 Kunitz_SmCI_3-like third Kunitz domain of Carboxypeptidase Inhibitor SmCI and similar domains. This group includes Sabellastarte magnifica carboxypeptidase inhibitor (SmCI), Bombyx mori cocoon shell-associated trypsin inhibitor (CSTI), Bombus terrestris Kunitz-type serine protease inhibitor Bt-KTI, and similar domains. SmCI is a tri-domain BPTI-Kunitz inhibitor capable of inhibiting serine proteases and A-like metallocarboxypeptidases. While the BPTI-Kunitz family of proteins includes voltage gated channel blockers and inhibitors of serine proteases, SmCI is the only BPTI-Kunitz protein capable of inhibiting metallocarboxypeptidases. Binding studies show that SmCI is able to bind three trypsin molecules under saturating conditions, but only one elastase interacts with the inhibitor. Additionally, SmCI can bind serine proteases and carboxypeptidases at the same time (at least in the ratio 1:1:1), thus becoming the first protease inhibitor that simultaneously blocks these two mechanistic classes of enzymes. CSTI and Bt-KTI are single Kunitz domain proteins that inhibit trypsin; in addition, Bt-KTI also inhibits plasmin. This model contains the third Kunitz domain of SmCI which has a structure similar to those of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 53 matched cddid_all.tbl CDD cd22604 cd22604 438647 Kunitz_BmTI-like Kunitz-type serine protease inhibitor 6 (BmTI-6), A (BmTI-A), and similar proteins. This group includes Kunitz-type serine protease inhibitors 6 (BmTI-6) and A (BmTI-A), both of which inhibit bovine trypsin, bovine chymotrypsin, human plasmin, human plasma kallikrein and human neutrophil elastase, but not bovine thrombin, human factor Xa or porcine pancreatic kallikrein. They may play a role in blocking blood coagulation during the larvae fixation on cattle. This subfamily also includes Rhipicephalus microplus protease inhibitor carrapatin. These proteins are similar to Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor) that shows an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 56 matched cddid_all.tbl CDD cd22605 cd22605 438648 Kunitz_WFIKKN_1-like first Kunitz domain of WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing proteins. This subfamily includes WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 1 (WFIKKN1, WFKN1), WFIKKN2 (WFKN2), and similar proteins. WFIKKN proteins are protease inhibitors that contain two distinct Kunitz-type protease inhibitor domains. They may have serine protease- and metalloprotease-inhibitor activity. This model represents the first Kunitz domain that is similar to Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor) that shows an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 52 matched cddid_all.tbl CDD cd22606 cd22606 438649 Kunitz_WFIKKN_2-like second Kunitz domain of WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing proteins. This subfamily includes WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 1 (WFIKKN1, WFKN1), WFIKKN2 (WFKN2), and similar proteins. WFIKKN proteins are protease inhibitors that contain two distinct Kunitz-type protease inhibitor domains. They may have serine protease- and metalloprotease-inhibitor activity. This model represents the second Kunitz (KU2) domain, which has been shown to inhibit trypsin, but not chymotrypsin, elastase, plasmin, pancreatic kallikrein, lung tryptase, plasma kallikrein, thrombin, urokinase or tissue plasminogen activator. However, the inhibition constant of this domain for bovine trypsin is about five orders of magnitudes lower than that of bovine pancreatic trypsin inhibitor (BPTI) for trypsin. This could be due to unfavorable side-chain conformation of a tryptophan at P2' site which is incompatible with a trypsin complex; typical trypsin inhibitors of the Kunitz family feature a tyrosine residue or other less bulky residues at this site. The structure of KU2 is similar to those of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 53 matched cddid_all.tbl CDD cd22607 cd22607 438650 Kunitz_ABPP-like Kunitz domain found in the amyloid-beta precursor protein (ABPP) subfamily. This subfamily includes the amyloid-beta precursor protein (ABPP, also called APP, APPI, Alzheimer disease amyloid protein, amyloid-beta A4 protein, cerebral vascular amyloid peptide (CVAP), protease nexin II (PN2)), as well as amyloid-like protein 2 (APLP2, also called amyloid protein homolog or APPH), among others. ABPP/APPI is an inhibitor of serine proteases such as anionic and cationic trypsins. For example, APPI-4M is a variant that specifically inhibits Kallikrein (KLK)-related peptidase 6 (KLK6), which is highly upregulated in several types of cancer where its increased activity promotes cancer invasion and metastasis. Amyloid-like protein 2 (APLP2) inhibits trypsin, chymotrypsin, plasmin, factor XIA, and plasma and glandular kallikrein, and may play a role in the regulation of hemostasis. Proteins in this subfamily contain a single Kunitz domain, with a structure similar to those of other Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 52 matched cddid_all.tbl CDD cd22608 cd22608 438651 Kunitz_PPTI-like Pseudocerastes persicus trypsin inhibitor (PPTI), Kunitz-type serine protease inhibitor bitisilin, and similar proteins. This group contains Pseudocerastes persicus trypsin inhibitor (PPTI), Bitis gabonica Kunitz-type serine protease inhibitor bitisilin-1 (BG-11), -2 (BG-15) and -3 (two-Kunitz protease inhibitor), Oxyuranus scutellatus scutellatus taicatoxin, and serine protease inhibitor component (TSPI, also called venom protease inhibitor 1 or venom protease inhibitor 2), among others. PPTI from P. persicus venom shows inhibitory effect against trypsin proteolytic activity and has similarities to dendrotoxins (DTXs), with corresponding functionally important residues. Studies have shown the ability of PPTI to inhibit voltage-gated potassium channels, and consequently have dual functionality. Bitilisins 1, 2, and 3 are serine protease inhibitors expressed in snake venom glands; bitsilin-3 consists of two Kunitz protease inhibitor domains. Taicatoxin inhibits trypsin, tissue kallikrein, elastase, plasmin and factor Xa, and is also known to block the voltage-dependent L-type calcium channels from the heart, and the small conductance calcium-activated potassium channels (KCa) in chromaffin cells and in the brain. The structures of these Kunitz-type proteins are similar to other Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 54 matched cddid_all.tbl CDD cd22609 cd22609 438652 Kunitz_TKDP-like trophoblast Kunitz domain protein (TKDP) and similar proteins. This model contains the trophoblast Kunitz domain protein 1 (TKDP-1) and splice variant TKDP-4, among others, which are Kunitz inhibitor domain proteins. TKDP-1 is expressed in the trophectoderm which forms the outer epithelial layer of the trophoblast, and may play a role in mediating maternal-conceptus interactions in the immediate preimplantation period. However, it does not appear to have proteinase inhibitory activity. These domains are similar to those of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor) that shows an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 52 matched cddid_all.tbl CDD cd22610 cd22610 438653 Kunitz_MitTx Micrurus tener tener Kunitz-type neurotoxin MitTx-alpha. Micrurus tener tener Kunitz-type neurotoxin MitTx-alpha is a subunit of the pain-inducing, heterodimeric polypeptide toxin that activates acid sensing ion channel a (ASIC1a) at nanomolar concentrations in a pH-independent manner. Acid sensing ion channels (ASICs) are sodium-selective, voltage-independent and amiloride-blockable ion channels that detect extracellular protons produced during inflammation or ischemic injury, and belong to the superfamily of degenerin/epithelial sodium channels. Subtype ASICa is expressed by primary afferent sensory neurons and is activated by MitTx. MitTx consists of two, non-covalently associated alpha and beta subunits that resemble Kunitz and phospholipase-A2 proteins, respectively, and together they function as a potent and selective ASIC1a agonist. The MitTx-alpha structures is similar to those of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 59 matched cddid_all.tbl CDD cd22611 cd22611 438654 Kunitz_eppin Kunitz domain of epididymal protease inhibitor eppin and similar proteins. This subfamily includes the Kunitz inhibitor domain protein eppin (also called Cancer/testis antigen 71 or CT71, epididymal protease inhibitor, protease inhibitor WAP7, serine protease inhibitor-like with Kunitz and WAP domains 1, or WAP four-disulfide core domain protein 7) as well as WAP four-disulfide core domain proteins 6A and 6B in mice, and similar proteins. Eppin is a serine protease inhibitor that plays an essential role in male reproduction and fertility. It modulates the hydrolysis of seminal fluid protein semenogelin 1 (SEMG1) by the serine protease kallikrein-related peptidase 3 (KLK3, PSA), provides antimicrobial protection for spermatozoa in the ejaculate coagulum, and binds SEMG1, thereby inhibiting sperm motility. Thus, eppin could potentially be used as a target for male contraception. These domains are similar to Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor) that shows an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 57 matched cddid_all.tbl CDD cd22612 cd22612 438655 Kunitz_ornithodorin_C-like C-terminal Kunitz domain of inhibitor ornithodorin and similar proteins. The Kunitz inhibitor ornithodorin is a highly selective and potent thrombin inhibitor isolated from blood sucking soft tick Ornithodoros moubata. Ornithodorin is a two-domain protein that resembles the tick anticoagulant peptide (TAP) isolated from the same organism, especially the N-terminal domain; this model contains the C-terminal domain. While the N-terminal domain binds to the active site of thrombin, this C-terminal domain binds at the fibrinogen recognition exosite. The structure of this domain is similar to those of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 49 matched cddid_all.tbl CDD cd22613 cd22613 438656 Kunitz_TFPI1_1-like "Kunitz protease inhibitor (KPI) domain 1 (KPI-1 or K1) of tissue factor pathway inhibitor (TFPI). This model represents the first Kunitz-type domain (K1 or KPI-1) of tissue factor pathway inhibitor (TFPI or TFPI1), also known as extrinsic pathway inhibitor (EPI) or lipoprotein-associated coagulation inhibitor (LACI). TFPI down-regulates the extrinsic coagulation pathway via inhibition of activated factor X (FXa or Xa) and FVIIa (VIIa). It inhibits activated FXa via a ""slow-tight binding mechanism"", i.e. rapid formation of a loose FXa-TFPI complex that then slowly isomerizes to a tight FXa-TFPI* complex. Subsequent inhibition of FVIIa is facilitated by the presence of tissue factor (TF) and FXa, which together rapidly and efficiently form a quaternary FXa-TFPI-TF-FVIIa complex in which the activity of FXa and FVIIa are inhibited. TFPI consists of 3 Kunitz-type protease inhibitor (KPI) domains in a tandem arrangement; The K1 domain of TFPI has been shown to bind and inhibit FVIIa while the K2 domain similarly inhibits FXa. Small peptide blocking inhibition of FXa and TF-FVIIa by TFPI shows that domain K1 is not only important for FVIIa inhibition but also for FXa inhibition, i.e. for the transition of the loose to the tight FXa-TFPI complex. The structure of the K1 domain is similar to those of other Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds." 55 matched cddid_all.tbl CDD cd22614 cd22614 438657 Kunitz_TFPI1_2-like "Kunitz protease inhibitor (KPI) domain 2 (KPI-2 or K2) of tissue factor pathway inhibitor (TFPI). This model represents the second Kunitz-type domain (K2 or KPI-2) of tissue factor pathway inhibitor (TFPI or TFPI1), also known as extrinsic pathway inhibitor (EPI) or lipoprotein-associated coagulation inhibitor (LACI). TFPI down-regulates the extrinsic coagulation pathway via inhibition of activated factor X (FXa or Xa) and FVIIa (VIIa). It inhibits activated FXa via a ""slow-tight binding mechanism"", i.e. rapid formation of a loose FXa-TFPI complex that then slowly isomerizes to a tight FXa-TFPI* complex. Subsequent inhibition of FVIIa is facilitated by the presence of tissue factor (TF) and FXa, which together rapidly and efficiently form a quaternary FXa-TFPI-TF-FVIIa complex in which the activity of FXa and FVIIa are inhibited. TFPI consists of 3 Kunitz-type protease inhibitor (KPI) domains in a tandem arrangement; the K2 domain is exposed on functionally active TFPI pools in circulation in blood, in platelets, and attached to the endothelium. While the K1 (or KPI-1) domain of TFPI has been shown to bind and inhibit FVIIa, the K2 domain inhibits FXa by binding directly to the active site and forming a FXa:TFPI complex. A close interaction between the TFPI K2 domain and the FXa active site is essential for the FXa inhibitory action of TFPI and for the formation of an inactive TF/FVIIa/FXa/TFPI complex which then prevents FXa generation. Thus, blockage of K2 would prevent TFPI binding to both FXa and FVIIa/TF, and fully abolish TFPI inhibition of the coagulation cascade. The structure of the K2 domain is similar to those of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds." 56 matched cddid_all.tbl CDD cd22615 cd22615 438658 Kunitz_TFPI1_TFPI2_3-like "Kunitz protease inhibitor (KPI) domain 3 (KPI-3 or K3) of tissue factor pathway inhibitor (TFPI) and TFPI2, and similar proteins. This model represents the third Kunitz-type domain (K3 or KPI-3) of tissue factor pathway inhibitor (TFPI or TFPI1), also known as extrinsic pathway inhibitor (EPI) or lipoprotein-associated coagulation inhibitor (LACI), and of TFPI2 (or TFPI-2). TFPI1 down-regulates the extrinsic coagulation pathway via inhibition of activated factor X (FXa or Xa) and FVIIa (VIIa). It inhibits activated FXa via a ""slow-tight binding mechanism"", i.e. rapid formation of a loose FXa-TFPI1 complex that then slowly isomerizes to a tight FXa-TFPI1* complex. Subsequent inhibition of FVIIa is facilitated by the presence of tissue factor (TF) and FXa, which together rapidly and efficiently form a quaternary FXa-TFPI1-TF-FVIIa complex in which the activity of FXa and FVIIa are inhibited. TFPI1 consists of 3 Kunitz-type protease inhibitor (KPI) domains in a tandem arrangement; while the K1 domain of TFPI has been shown to bind and inhibit FVIIa and the K2 domain similarly inhibits FXa, the K3 domain has no known inhibitory function. However, Protein S, which functions as a cofactor for TFPI to efficiently enhance TFPI inhibition of FXa and FXa activated TF-VIIa, is dependent on direct interactions with two important residues within K3, a Glutamate and an Arginine. This model also includes TFPI2 Kunitz domain 3 (KD3). TFPI2 exhibits inhibitory activity primarily toward trypsin, plasmin, and factor VIIa (FVIIa)/tissue factor (TF) via its KD1. It is believed to be the major inhibitor of plasmin in the extracellular matrix (ECM) but has little inhibitory activity toward urokinase-type plasminogen activator, tissue-type plasminogen activator, or thrombin. While TFPI2 specifically inhibits the proteases via the P1 arginine residue in KD1, domains KD2 and KD3 appear to have no discernible inhibitory activity and may serve to bind to nearby proteins to localize TFPI2 in the ECM. The structure of this domain is similar to that of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds." 54 matched cddid_all.tbl CDD cd22616 cd22616 438659 Kunitz_TFPI2_1-like Kunitz domain 1 (KD1) of tissue factor pathway inhibitor 2 (TFPI2) and similar proteins. This model represents the Kunitz-type domain 1 (KD1) of tissue factor pathway inhibitor 2 (TFPI2 or TFPI-2) and similar proteins. TFPI2 exhibits inhibitory activity primarily toward trypsin, plasmin, and factor VIIa (FVIIa)/tissue factor (TF) via its KD1. It is believed to be the major inhibitor of plasmin in the extracellular matrix (ECM) but has little inhibitory activity toward urokinase-type plasminogen activator, tissue-type plasminogen activator, or thrombin. TFPI2 specifically inhibits the proteases via the P1 arginine residue in KD1. The TFPI2 domains KD2 and KD3 appear to have no discernible inhibitory activity and may serve to bind to nearby proteins to localize TFPI2 in the ECM. Structure studies of KD1 complexed with proteases may help in the development of specific and potent KD1 domain protein that may have a large pharmacologic impact in preventing tumor metastasis, retinal degeneration, and degradation of collagen in the ECM. The structure of this domain is similar to that of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 57 matched cddid_all.tbl CDD cd22617 cd22617 438660 Kunitz_TFPI2_2-like Kunitz domain 2 (KD2) of tissue factor pathway inhibitor 2 (TFPI2) and similar proteins. This model represents the Kunitz-type domain 2 (KD2) of tissue factor pathway inhibitor 2 (TFPI2 or TFPI-2) and similar proteins. TFPI2 exhibits inhibitory activity primarily toward trypsin, plasmin, and factor VIIa (FVIIa)/tissue factor (TF) via its KD1. It is believed to be the major inhibitor of plasmin in the extracellular matrix (ECM) but has little inhibitory activity toward urokinase-type plasminogen activator, tissue-type plasminogen activator, or thrombin. While TFPI2 specifically inhibits the proteases via the P1 arginine residue in KD1, domains KD2 and KD3 appear to have no discernible inhibitory activity and may serve to bind to nearby proteins to localize TFPI2 in the ECM. This domain is similar to that of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor) that shows an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 54 matched cddid_all.tbl CDD cd22618 cd22618 438661 Kunitz_SHPI Stichodactyla helianthus Kunitz inhibitor protein ShPI-1, Heteractis crispa protease inhibitor stichotoxin-Hcr2e, and similar proteins. This model includes Kunitz inhibitor protein ShPI-1, the major protease inhibitor from the sea anemone Stichodactyla helianthus, as well as protease inhibitor stichotoxin-Hcr2e (also called PI- stichotoxin-Hcr2e, PI-SHTX-Hcr2e, or Kunitz-type serine protease inhibitor InhVJ) and HCRG1 from Heteractis crispa. ShPI-1 has an unusually broad specificity toward several serine proteases, including trypsin, chymotrypsin, human neutrophil elastase, kallikrein and plasmin, and can also bind aspartic and cysteine proteases, such as pepsin and papain, respectively. PI-SHTX-Hcr2e and HCRG1 inhibit trypsin and chymotrypsin, but do not inhibit the serine proteases plasmin, thrombin, kallikrein, the cysteine proteinase papain, and the aspartic protease pepsin. The structures of these domains are similar to those of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 53 matched cddid_all.tbl CDD cd22619 cd22619 438662 Kunitz_B2B Kunitz-type serine protease inhibitor subunit of beta 2-bungarotoxin, and similar proteins. This model includes the Kunitz inhibitor subunit of beta 2-bungarotoxin, a presynaptic neurotoxin of the Bungarus multicinctus venom. Beta-bungarotoxin is a heterodimeric neurotoxin consisting of a phospholipase subunit linked by a disulfide bond to the Kunitz protease inhibitor subunit; the latter subunit is homologous to venom basic protease inhibitors but has no protease inhibitor activity and is non-toxic. The beta-bungarotoxin Kunitz subunit serves to guide the toxin to its site of action on the presynaptic membrane by virtue of a high-affinity interaction with a specific subclass of voltage-sensitive potassium channels. This subfamily also includes Kunitz-type serine protease inhibitor homolog beta-bungarotoxin B1 chain and protease inhibitor-like protein 1 (PILP-1). The B1 chain also has no protease inhibitor activity but blocks voltage-gated potassium channels, while PILP-1 inhibits trypsin. The structures of these domains are similar to those of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 58 matched cddid_all.tbl CDD cd22620 cd22620 438663 Kunitz_KTT scorpion venom Kunitz-type toxin (KTT) such as LmKTT-1a, BmKTT-1, and BmKTT-2. This model includes scorpion Kunitz-type toxin (KTT) such as Lychas mucronatus LmKTT-1a (also called Delta-KTx 2.1 or SdPII), Mesobuthus martensii BmKTT-1 (also called Delta-KTx 2.4) and BmKTT-2 (also called Delta-KTx 3.1), all expressed by the venom gland. LmKTT-1a, BmKTT-1 and BmKTT-2 are all dual-function toxins that completely inhibit trypsin activity but have no effect on chymotrypsin or elastase. They also inhibit mKv1.3/KCNA3 potassium channel currents. The structures of these domains are similar to those of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor); however, they lack the conserved CysII-CysIV disulfide bond but contains 2 cysteine residues at the C-terminus that generate a new disulfide bond. 58 matched cddid_all.tbl CDD cd22621 cd22621 438664 Kunitz_HAI2_1-like Kunitz-type domain 1 (KD1) of hepatocyte growth factor activator inhibitor type 2 (HAI-2), and similar proteins. This model includes the Kunitz domain 1 (KD1) of hepatocyte growth factor activator inhibitor type 2 (HAI-2 or HAI2, also known as placental bikunin or Kunitz-type protease inhibitor 2). HAI-2 is composed of two Kunitz domains that strongly inhibit many serine proteases with sub-nanomolar affinities. HAI-2 Kunitz domain 1 (KD1) has been found to be the domain responsible for inhibition of hepatocyte growth factor (HGF) activator; activated HGF/scatter factor (HGF/SF) binds to its receptor tyrosine kinase MET to induce dimerization and initiate phosphorylation cascades leading to comprehensive cellular changes that, in the deregulated context of cancer, drive malignant transformation and progression. HAI-2 has been found to be a natural tumor suppressor in renal cell carcinoma, breast cancer and prostate cancer; its loss leads to tumor growth and progression in part due to increased MET signaling. HAI-2 is also a specific substrate for mesotrypsin, which is up-regulated with progression in prostate cancers and shown to contribute to invasion and metastasis; these activities of mesotrypsin may in part be mediated through cleavage and inactivation of HAI-2, resulting in increases in HGF/SF activation and MET signaling. HAI-2 is a physiological inhibitor of hepsin and matriptase, two type II transmembrane serine proteases that, like HGF activator, can convert latent pro-HGF/SF into the two-chain active signaling heterodimer. The structures of these KD1 domains are similar to those of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 53 matched cddid_all.tbl CDD cd22622 cd22622 438665 Kunitz_HAI2_2-like Kunitz-type domain 2 (KD2) of hepatocyte growth factor activator inhibitor type 2 (HAI-2), and similar proteins. This model includes Kunitz domain 2 (KD2) of hepatocyte growth factor activator inhibitor type 2 (HAI-2 or HAI2, also known as placental bikunin or Kunitz-type protease inhibitor 2). HAI-2 is composed of two Kunitz domains that strongly inhibit many serine proteases with sub-nanomolar affinities. It has been found to be a natural tumor suppressor in renal cell carcinoma, breast cancer and prostate cancer, the loss of which leads to tumor growth and progression attributable at least in part to increased MET signaling. HAI-2 is a specific substrate of mesotrypsin which is up-regulated with progression in prostate cancers and shown to contribute to invasion and metastasis; these activities of mesotrypsin may in part be mediated through cleavage and inactivation of HAI-2, resulting in increases in hetatocyte growth factor/scatter factor (HGF/SF) activation and MET signaling. HAI-2 is a physiological inhibitor of hepsin and matriptase, two type II transmembrane serine proteases that, like HGF activator, can convert latent pro-HGF/SF into the two-chain active signaling heterodimer. KD2 is similar to KD1, whose structure is similar to those of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 53 matched cddid_all.tbl CDD cd22623 cd22623 438666 Kunitz_HAI1_1-like Kunitz domain 1 of hepatocyte growth factor activator inhibitor-1 (HAI-1). This model includes Kunitz domain 1 (KD1) of hepatocyte growth factor activator inhibitor type 1 (HAI1 or HAI-1, also known as Kunitz-type protease inhibitor 1), a membrane-bound multidomain protein essential to the integrity of the basement membrane during placental development. HAI-1 contains an extracellular region and several internal domains that include two Kunitz domains separated in sequence but spatially closed to each other, and their interdomain interactions have evolved to stimulate the inhibitory activity of an integrated Kunitz. KD1, the major inhibitory domain of HAI-1, is involved in auto-inhibition of the extracellular region via steric blockage of its active site in the HAI-1 compact tertiary structure; presence of the target protease causes changes in the HAI-1 structure to an extended conformation. HAI-1 has been shown to inhibit several serine proteases such as matripase, hepsin, trypsin, hepatocyte growth factor activator (HGFA), and prostasin. It is also important in maintaining postnatal homeostasis in many tissues, including keratinization of the epidermis, hair development, colonic epithelium integrity, proliferation and cell fate of neural progenitor cells, and tissue injury and repair. The interaction between HAI-1 and matriptase is critical for tissue morphogenesis and cellular biology. HAI-1:matriptase ratio imbalance results in tumorigenesis; slight overexpression of matriptase relative to HAI-1 causes spontaneous squamous cell carcinoma, a phenotype that can be effectively reversed back to wild type by additional expression of HAI-1, indicating the need for a tight functional relationship between the two to maintain homeostasis. The structures of these domains are similar to those of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 59 matched cddid_all.tbl CDD cd22624 cd22624 438667 Kunitz_HAI1_2-like Kunitz domain 2 of hepatocyte growth factor activator inhibitor-1 (HAI1). This model includes Kunitz domain 2 (KD2) of hepatocyte growth factor activator inhibitor type 1 (HAI-1 or HAI1, also known as Kunitz-type protease inhibitor 1), a membrane-bound multidomain protein essential to the integrity of the basement membrane during placental development. HAI-1 contains an extracellular region and several internal domains that include two Kunitz domains separated in sequence but spatially closed to each other, and their interdomain interactions have evolved to stimulate the inhibitory activity of an integrated Kunitz. While the Kunitz domain 1 (KD1) is the major inhibitory domain of HAI-1 and involved in auto-inhibition of the extracellular region via steric blockage of its active site in the HAI-1 compact tertiary structure, studies show that deletion of HAI-1 Kunitz domain 2 (KD2) and the extracellular region enhanced inhibition of matriptase. HAI-1 KD2 has been shown to have potent inhibitory activity against trypsin, but it cannot inhibit hepatocyte growth factor activator (HGFA), and matriptase. HAI-1 is also important in maintaining postnatal homeostasis in many tissues, including keratinization of the epidermis, hair development, colonic epithelium integrity, proliferation and cell fate of neural progenitor cells, and tissue injury and repair. The interaction between HAI-1 and matriptase is critical for tissue morphogenesis and cellular biology. HAI-1:matriptase ratio imbalance results in tumorigenesis; slight overexpression of matriptase relative to HAI-1 causes spontaneous squamous cell carcinoma, a phenotype that can be effectively reversed back to wild type by additional expression of HAI-1, indicating the need for a tight functional relationship between the two to maintain homeostasis. The structure of KD2 is similar to those of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 61 matched cddid_all.tbl CDD cd22625 cd22625 438668 Kunitz_ixolaris_1 Kunitz-type domain 1 (K1) of Ixolaris, and similar proteins. This model includes the first Kunitz-type domain (K1) of ixolaris from the venomous organism Conus striatus. Ixolaris is a potent tick salivary anticoagulant that binds coagulation factor Xa (FXa) and zymogen FX, and forms a quaternary tissue factor (TF)/FVIIa/FX(a)/Ixolaris inhibitory complex. It blocks TF-induced coagulation and PAR2 (proteinase-activated receptor 2) signaling, and prevents thrombosis, tumor growth, and immune activation. Ixolaris consists of 2 Kunitz domains (K1 and K2), both of which recognize the heparin-binding (pro)exosite (HBE) on FX. While K2 is an extraordinarily dynamic domain that encompasses several residues involved in FX binding, K1 domain keeps as a rigid platform supporting the conformational dynamic of the K2 domain, forming a salt bridge with FXa. The structure of this domain is similar to that of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 53 matched cddid_all.tbl CDD cd22626 cd22626 438669 Kunitz_ixolaris_2 Kunitz-type domain 2 (K2) of Ixolaris, and similar proteins. This model includes the second Kunitz-type domain (K2) of ixolaris from the venomous organism Conus striatus. Ixolaris is a potent tick salivary anticoagulant that binds coagulation factor Xa (FXa) and zymogen FX, and forms a quaternary tissue factor (TF)/FVIIa/FX(a)/Ixolaris inhibitory complex. It blocks TF-induced coagulation and PAR2 (proteinase-activated receptor 2) signaling, and prevents thrombosis, tumor growth, and immune activation. Ixolaris consists of 2 Kunitz domains (K1 and K2), both of which recognize the heparin-binding (pro)exosite (HBE) on FX. This model contains K2, an extraordinarily dynamic domain that encompasses several residues involved in FX binding. Its backbone plasticity is critical for ixolaris biological activity. This domain contains 2 disulfide bonds instead of the 3 typical of Kunitz domain proteins. 51 matched cddid_all.tbl CDD cd22627 cd22627 438670 Kunitz_collagen_alpha1_VII Kunitz-type domain from the alpha1 chain of type VII collagen, and similar proteins. This model includes the Kunitz-type domain from the alpha1 chain of type VII collagen (collagen alpha-1(VII) chain also called long-chain collagen or LC collagen) and similar proteins. LC collagen, encoded by the COL7A1 gene, is a stratified squamous epithelial basement membrane protein that forms anchoring fibrils which may contribute to epithelial basement membrane organization and adherence by interacting with extracellular matrix (ECM) proteins such as type IV collagen. So far, over 800 COL7A1 mutations have been reported, including missense, nonsense, splicing, insertion, and deletion mutations which to varying degrees leads to deficiency of type VII collagen. Epidermolysis bullosa acquisita (EBA) is an autoimmune acquired blistering skin disease resulting from autoantibodies to type VII collagen. The COL7A1 protein contains a Kunitz domain, the deactivation of which induces tumorigenesis. This domain is similar to that of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), that shows an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 53 matched cddid_all.tbl CDD cd22628 cd22628 438671 Kunitz_collagen_alpha1_XXVIII Kunitz-type domain from the alpha1 chain of type XXVIII collagen, and similar proteins. This model includes the Kunitz-type domain from the alpha1 chain of type XXVIII collagen (collagen alpha-1(XXVIII) chain) and similar proteins. The zebrafish has four collagen XXVIII genes all of which are differentially expressed in the liver, thymus, muscle, intestine and skin; only the alpha1 chain contains the Kunitz domain which is often proteolytically processed. Mammals only contain the alpha1 collagen chain, expressed mostly in dorsal root ganglia and peripheral nerves. The Kunitz domain is found at the C-terminus, and is most related to Kunitz domains of papilin and alpha3(VI) collagen. This domain is similar to that of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor) that shows an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 51 matched cddid_all.tbl CDD cd22629 cd22629 438672 Kunitz_collagen_alpha3_VI Kunitz-type domain from the alpha3 chain of human type VI collagen, and similar proteins. This model includes the Kunitz-type domain from the alpha3 chain of type VI collagen (collagen alpha 3(VI) chain), encoded by COL6A3 gene. Collagen VI is a widely expressed member of the triple helix-containing protein superfamily of collagens and forms beaded microfibrils that anchor large interstitial structures. Immediately after fibril formation, the Kunitz domain can be cleaved off. Mutations in the alpha1, alpha2, and alpha3 chains of collagen VI cause myopathies ranging from the severe Ullrich congenital muscular dystrophy to the milder Bethlem myopathy, including intermediate forms. Early onset isolated dystonia, a neurological disease, has been shown to be caused by mutations in the alpha3 chain. Findings also indicated potential associations between COL6A3 polymorphisms and lung cancer risk. This domain is similar to that of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), showing an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 53 matched cddid_all.tbl CDD cd22630 cd22630 438673 Kunitz_collagen_alpha6_VI Kunitz-type domain from the alpha6 chain of human type VI collagen, and similar proteins. This model includes the Kunitz-type domain from the alpha6 chain of type VI collagen (collagen alpha 6(VI) chain), encoded by COL6A6 gene, and similar proteins. Collagen VI is a widely expressed member of the triple helix-containing protein superfamily of collagens and forms beaded microfibrils that anchor large interstitial structures. Immediately after fibril formation, the Kunitz domain can be cleaved off. This domain is similar to that of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor) that shows an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 55 matched cddid_all.tbl CDD cd22631 cd22631 438674 Kunitz_collagen_alpha6_VI-like Kunitz-type domain from the alpha6 chain of fish type VI collagen, and similar proteins. This model includes the Kunitz-type domain from the alpha6 chain of type VI collagen (collagen alpha 6(VI) chain) and similar proteins. Collagen VI is a widely expressed member of the triple helix-containing protein superfamily of collagens and forms beaded microfibrils that anchor large interstitial structures. Immediately after fibril formation, the Kunitz domain can be cleaved off. This domain is similar to that of Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor) that shows an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 51 matched cddid_all.tbl CDD cd22632 cd22632 438675 Kunitz_ELP-like early lactation protein (ELP), colostrum trypsin inhibitor (CTI), and similar proteins. This model includes the Kunitz-type proteins, colostrum trypsin inhibitor (CTI, also called colostrum BPI) and early lactation protein (ELP). In marsupials, the ELP gene is expressed in the mammary gland and the protein is secreted into milk during early lactation. Mature ELP shares approximately 55.4% similarity with the colostrum-specific bovine CTI protein. Marsupial ELP and eutherian CTI both have a single Kunitz domain and are secreted only during the early lactation phases, suggesting that this protein may have an important role in the immunologically immature young of these species. These proteins are similar to Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor) that shows an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 55 matched cddid_all.tbl CDD cd22633 cd22633 438676 Kunitz_actitoxin-like Kunitz-type actitoxins such as Anemonia viridis U-actitoxin-Avd3l, and similar proteins. This model includes the Kunitz-type actitoxins such as Anemonia viridis U-actitoxin-Avd3l (also called U-AITX-Avd3l or AsKC9), Anthopleura elegantissima KappaPI-actitoxin-Ael3a (also called KappaPI-AITX-Ael3a or Kunitz-type serine protease inhibitor APEKTx1) and Anthopleura aff. xanthogrammica PI-actitoxin-Axm2b (also called PI-AITX-Axm2b or Kunitz-type proteinase inhibitor AXPI-II). U-AITX-Avd3l and KappaPI-AITX-Ael3a are dual-function toxins that inhibit both the serine protease trypsin and voltage-gated potassium channels Kv1.2/KCNA2. These proteins are similar to Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor) that shows an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 55 matched cddid_all.tbl CDD cd22634 cd22634 438677 Kunitz_SCI-I-like chymotrypsin inhibitor SCI-I_III-like. This model includes the Kunitz-type chymotrypsin inhibitors SCI-III and SCI-I, and similar proteins in insects. SCI-III and SCI-I inhibit chymotrypsin, avoiding the accidental chymotrypsin-mediated activation of prophenoloxidase. This enzyme is required by the insect immune system to produce melanin which is used to engulf foreign objects. This subfamily also includes Kunitz-type male accessory gland peptide with protease inhibitory activity, synthesized and secreted by male accessory glands of Drosophila funebris; it may play a role as an acrosin inhibitor involved in reproduction. These proteins are similar to Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor) that shows an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 57 matched cddid_all.tbl CDD cd22635 cd22635 438678 Kunitz_papilin Kunitz domain of papilin, and similar proteins. This model includes the Kunitz domain found in human and mouse papilin, and similar proteins. Papilin is an extracellular matrix glycoprotein that has been found in many organisms to be involved in thin matrix layers during gastrulation, matrix associated with wandering, phagocytic hemocytes, basement membranes and space-filling matrix during Drosophila development. It is a multidomain protein that primarily occurs in basement membranes. Papilins interact with several extracellular matrix components and ADAMTS enzymes, influences cell rearrangements and may modulate metalloproteinases during organogenesis. Papilins exist in mammals and invertebrates as a set of related, though not necessarily identical proteins. Mammalian papilin contains a single Kunitz domain, while other papilins such as that from Caenorhabditis elegans, contains multiple Kunitz domains. These domains are similar to Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor) that shows an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 52 matched cddid_all.tbl CDD cd22637 cd22637 438679 Kunitz_papilin_mig6-like Drosophila melanogaster Kunitz domains 5, 6, 7, and Caenorhabditis elegans Kunitz domain 5 of papilin, and similar domains. This model includes Kunitz domains from papilins with multiple Kunitz domains, such as Drosophila melanogaster Kunitz domains 5, 6, 7, and Caenorhabditis elegans Kunitz domain 5 of papilin, among others. Papilins are essential for embryonic development. D. melanogaster papilin is an essential extracellular matrix (ECM) protein that influences cell rearrangements. It may act by modulating metalloproteinases action during organogenesis and is able to non-competitively inhibit procollagen N-proteinase, an ADAMTS metalloproteinase. C. elegans papilin (also called abnormal cell migration protein 6) mig-6 encodes long (MIG-6L) and short (MIG-6S) isoforms of the extracellular matrix protein papilin, each required for distinct aspects of distal tip cell (DTC) migration and both isoforms have an N-terminal papilin cassette, lagrin repeats and six C-terminal Kunitz-type serine proteinase inhibitory domains. It plays a role in embryogenesis, the second phase of distal cell tip migration and is required for distribution of the metalloproteinase, mig-17, during organogenesis. These domains are similar to Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor) that shows an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 51 matched cddid_all.tbl CDD cd22638 cd22638 438680 Kunitz_amblin-like Caenorhabditis elegans Kunitz domain 11 of papilin (also called abnormal cell migration protein 6 or mig-6), Amblyomma hebraeum amblin domain 1, and similar proteins. This model includes Caenorhabditis elegans Kunitz domain 11 of papilin (also called abnormal cell migration protein 6 or mig-6) and domain 1 of Amblyomma hebraeum amblin, and similar proteins. C. elegans papilin (also called abnormal cell migration protein 6) mig-6 encodes long (MIG-6L) and short (MIG-6S) isoforms of the extracellular matrix protein papilin, each required for distinct aspects of distal tip cell (DTC) migration and both isoforms have an N-terminal papilin cassette, lagrin repeats and six C-terminal Kunitz-type serine proteinase inhibitory domains. It plays a role in embryogenesis, the second phase of distal cell tip migration and is required for distribution of the metalloproteinase, mig-17, during organogenesis. Amblin contains two Kunitz-like domains and specifically inhibits thrombin. These domains are similar to Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor), that shows an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 51 matched cddid_all.tbl CDD cd22639 cd22639 438681 Kunitz_papilin_lacunin-like Drosophila melanogaster Kunitz domain 1, Manduca sexta lacunin Kunitz domain 1, and simialr proteins. This model includes Drosophila melanogaster Kunitz domain 1 of papilin and Manduca sexta Kunitz domain 1 of lacunin, and similar proteins. D. melanogaster papilin is an essential extracellular matrix (ECM) protein that influences cell rearrangements. It may act by modulating metalloproteinase action during organogenesis and is able to non-competitively inhibit procollagen N-proteinase, an ADAMTS metalloproteinase. M. sexta lacunin is a large multidomain ECM containing several domains including several Kunitz-type protease inhibitors, thrombospondin type I, immunoglobulin-like and others. It exerts multiple effects on a variety of cell behaviors associated with the complex phenomenon of epithelial morphogenesis. These domains are similar to Kunitz-type proteinase inhibitors such as BPTI (bovine pancreatic trypsin inhibitor) that shows an alpha/beta fold with irregular secondary structure stabilized by three disulfide bonds. 52 matched cddid_all.tbl CDD cd22641 cd22641 439347 C24-like Bizionia argentinensis C24 protein and similar proteins. C24 is a putative receptor-binding tip-like protein from Bizionia argentinensis JUB59. It may interact with lipopolysaccharide and membrane receptors. The C24 trimer binds a unique Mg2+ ion and shares structural similarity with the bacteriophage T4 long tail fiber receptor-binding tip, which adopts an overall rocket shape. However, there are marked differences in its domain organization, size and sequence identity. The C24 polypeptide chain contains four distinct domains: a globular proximal shoulder domain, a globular collar domain, an elongated, intertwined metal-binding needle domain and a globular receptor-binding-like unique distal head domain. This is a multi-domain model which includes all these four domains of C24 protein. 227 matched cddid_all.tbl CDD cd22643 cd22643 439348 DotY_NTD N-terminal domain of Legionella pneumophila DotY and similar proteins. DotY is a component of membrane-embedded T4 coupling complex (T4CC), which consists of the DotL ATPase, the DotM and DotN proteins,and DotY and DotZ. The DotLMNYZ hetero-pentamer and plays an essential role in the recruitment and delivery of effectors to the Type IV secretion (T4S) machinery in Legionella pneumophila, a bacterial pathogen that utilizes a T4S system to inject effector proteins into human macrophages. This model corresponds to the N-terminal domain of DotY, which is responsible for interaction with DotZ. DotY and DotZ are integral parts of the T4CC and play significant roles in the translocation of effectors. They are unique to the Legionella genus. 72 matched cddid_all.tbl CDD cd22644 cd22644 439349 DotZ Legionella pneumophila DotZ protein domain family. DotZ is a component of membrane-embedded T4 coupling complex (T4CC), which consists of the DotL ATPase, the DotM and DotN proteins,and DotY and DotZ. The DotLMNYZ hetero-pentamer plays an essential role in the recruitment and delivery of effectors to the Type IV secretion (T4S) machinery in Legionella pneumophila, a bacterial pathogen that utilizes a T4S system to inject effector proteins into human macrophages. DotZ is an integral part of the T4CC and plays a significant role in the translocation of effectors; this protein, along with DotZ, are unique to the Legionella genus. 279 matched cddid_all.tbl CDD cd22645 cd22645 439350 BIC1_CID CRY-interacting domain (CID) of protein BIC1 and similar proteins. BIC1, also called BLUE-LIGHT INHIBITOR OF CRYPTOCHROMES 1, interacts with photoexited CRY2 to inhibit its activity. It regulates the blue-light dependent dimerization of CRY2 and formation of photobodies. BIC1 inhibits CRY phosphorylation. This model corresponds to CRY-interacting domain (CID) of BIC1. 57 matched cddid_all.tbl CDD cd22646 cd22646 439351 MCM22_CTD C-terminal domain of inner kinetochore subunit MCM22 and similar proteins. MCM22, also called CENP-K homolog, or constitutive centromere-associated network protein MCM22, or minichromosome maintenance protein 22, is a component of the kinetochore, a multiprotein complex that assembles on centromeric DNA and attaches chromosomes to spindle microtubules, mediating chromosome segregation and sister chromatid segregation during meiosis and mitosis. It is a component of the inner kinetochore constitutive centromere-associated network (CCAN), which serves as a structural platform for outer kinetochore assembly. The model corresponds to the C-terminal domain of MCM22, which interacts with another three kinetochore subunits: CNN1, MCM16 and CTF3. 96 matched cddid_all.tbl CDD cd22647 cd22647 439352 CTF3_NTD_HEAT N-terminal HEAT repeat domain of inner kinetochore subunit CTF3 and similar proteins. CTF3 (also called CENP-I homolog, chromosome loss protein 3, chromosome transmission fidelity protein 3, or constitutive centromere-associated network protein CTF3) is a component of the central kinetochore, which mediates the attachment of the centromere to the mitotic spindle by forming essential interactions between the microtubule-associated outer kinetochore proteins and the centromere-associated inner kinetochore proteins. It is required for establishing bipolar spindle-microtubule attachments and proper chromosome segregation. The kinetochore is a multiprotein complex that assembles on centromeric DNA and attaches chromosomes to spindle microtubules, mediating chromosome segregation and sister chromatid segregation during meiosis and mitosis. CTF3 is a component of the inner kinetochore constitutive centromere-associated network (CCAN), which serves as a structural platform for outer kinetochore assembly. This model corresponds to the N-terminal HEAT repeat domain of CTF3, which interacts with another four kinetochore subunits, WIP1, CNN1, MCM16 and MCM22. 219 matched cddid_all.tbl CDD cd22648 cd22648 439353 Q4D6Q6-like Q4D6Q6-like domain family. This family includes Trypanosoma cruzi protein Q4D6Q6 and similar proteins. Q4D6Q6 is a conserved and kinetoplastid-specific protein essential for cell viability. Its monomers adopt a beta-beta-alpha-beta-beta-alpha-beta-beta topology and form a propeller-like tetramer. An oxidized cysteine, which is part of a cluster with phosphorylated serines and hydrophobic residues, has been identified as a highly reactive site, and may play a role as a nucleophile in a post-translational modification reaction. Since Q4D6Q6 is not present in mammals, it can be a potential drug target against kinetoplastid infection causing Chagas disease, Sleeping sickness and Leishmaniasis. 112 matched cddid_all.tbl CDD cd22649 cd22649 438713 DEXSMc_CoV_Nsp13 DEXSM-box helicase domain of coronavirus Nsp13 helicase. Helicases catalyze the NTP-dependent unwinding of nucleic acid duplexes into single strands and are classified into six superfamilies based on the arrangement of conserved motifs. This family contains coronavirus (CoV) non-structural protein 13 (Nsp13) helicase, including those from highly pathogenic human betaCoVs such as Severe Acute Respiratory Syndrome coronavirus (SARS) and SARS-CoV-2 (also known as 2019 novel CoV (2019-nCoV) or COVID-19 virus). Nsp13 helicase is a component of the viral RNA synthesis replication and transcription complex (RTC). SARS-Nsp13 is strongly inhibited by natural flavonoids, myricetin and scutellarein, and is emerging as a target for development of anti-SARS medications. It contains an N-terminal Cys/His rich zinc-binding domain (CH/ZBD), a stalk domain, a 1B regulatory domain, and an SF1 helicase core that carries a DEAD-box helicase domain. Nsp13 belongs to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region. 202 matched cddid_all.tbl CDD cd22650 cd22650 439165 NTD_gammaCoV_Nsp15-like N-terminal domain of gammacoronavirus Nonstructural protein 15 (Nsp15), and related proteins. Coronavirus (CoV) Nsp15 is a nidovirus endoribonuclease (NendoU). NendoUs are uridylate-specific endoribonucleases, which release a cleavage product containing a 2',3'-cyclic phosphate at the 3' terminal end. NendoUs include coronavirus Nsp15 and arterivirus Nsp11, both of which may participate in the viral replication process and in the evasion of the host immune system. This NTD structure (approximately 60 residues) present in coronavirus Nsp15, is missing in Nsp11. CoV Nsp15 has an N-terminal domain, a middle (M) domain, and a C-terminal catalytic (NendoU) domain. Nsp15 from alpha- and betaCoVs such as Severe Acute Respiratory Syndrome (SARS)-CoV, human Coronavirus 229E (HCoV229E), and Murine Hepatitis Virus (MHV) form a functional hexamer. The active form of the Nsp15 of Turkey CoV (TCoV), a gammaCoV, has been reported to be a homohexamer. Residues in this N-terminal domain may be important for hexamer formation. 60 matched cddid_all.tbl CDD cd22651 cd22651 439354 HlyE-like alpha pore-forming toxin (alpha-PFT) hemolysin E (HlyE, ClyA or SheA) in Escherichia coli, Salmonella typhi, and Shigella flexneri, and similar proteins. This family of alpha pore-forming toxins (alpha-PFTs) includes hemolysin E (HlyE; also called cytolysin (ClyA) or silent hemolysin A (SheA)), produced by certain strains of Escherichia coli, as well as by Salmonella enterica and Shigella flexneri, among others. HlyE is responsible for the hemolytic activity of certain strains of E. coli, including the pathogenic strain E. coli O157. Distinct from many secreted toxins and effectors, HlyE is delivered by outer-membrane vesicles (OMVs). HlyE is unrelated to the well-characterized pore-forming E. coli hemolysins of the RTX (repeats in toxin) family, hemolysin A (HlyA), and the enterohemolysin encoded by the plasmid borne ehxA gene of E. coli 0157. However, they all have the common structural features of an elongated, entirely alpha-helical domain, except for a short hydrophobic beta-hairpin known as the beta-tongue. The HlyE is monomeric in the periplasm where it forms a disulfide bond to prevent oligomerization. In the OMVs, it oligomerizes via a sequential mechanism to form a circular dodecameric pore structure that is active. The pore structure concentrates the amphipathic helices in the center of the ring-like structure, forming a helical barrel that inserts into the membrane by a wedge-like mechanism. HlyE/ClyA represents a prototype of the structural ClyA family of alpha-PFT which includes toxins that share structural similarity with HlyE, and includes Bacillus cereus HblB, Aeromonas hydrophila AhlB, and Bacillus thuringiensis Cry6Aa. Expression of HlyE in the absence of the RTX toxins is sufficient to give a hemolytic phenotype in E. coli. HlyE is expressed during anaerobic growth of E. coli. Anaerobic expression is controlled by the transcription factor, FNR (regulator of fumarate and nitrate reduction), such that, upon ingestion and entry into the anaerobic mammalian intestine, HlyE is produced and may then contribute to the colonization of the host. 247 matched cddid_all.tbl CDD cd22652 cd22652 439150 ClyA_AhlB-like Aeromonas hydrophila hemolytic component B (AhlB), and similar proteins. This model includes Aeromonas hydrophila hemolytic (Ahl) component B (AhlB) of the tripartite AhlABC toxin, a member of the cytolysin A (ClyA) family of alpha pore-forming toxins (alpha-PFTs). It consists of three proteins, AhlA, AhlB and AhlC, encoded by one operon containing the three genes. Functional and mutagenic studies support a model of pore assembly where the soluble tetrameric form of AhlC first disassociates into monomers, binds a single membrane leaflet, and then recruits AhlB to promote soluble to pore transition; AhlA then binds to form the active hydrophilic lined pore. The structure of AhlB shows an elongated, almost entirely alpha-helical protein, including a hydrophobic beta-hairpin known as a beta-tongue to shield membrane inserting hydrophobic residues. The head domain of AhlB undergoes a large conformational change involving the beta tongue becoming an extended alpha helix, and the tail domain helices sliding relative to one another as AhlB assembles into a hydrophobic pore. 332 matched cddid_all.tbl CDD cd22653 cd22653 439151 ClyA_HblB-like Bacillus cereus hemolysin binding component B (HblB), and similar proteins. This model includes Bacillus cereus hemolysin binding component B (HblB or HBL-B) of the diarrheal enterotoxin hemolysin BL (HBL), and is a member of the cytolysin A (ClyA) family of alpha pore-forming toxins (alpha-PFTs). HBL is composed of three distinct protein components, B, L1, and L2, which together possess hemolytic, cytotoxic, dermonecrotic, and vascular permeability activities in B. cereus. Although all three HBL components can individually bind to the membrane, it requires the three components to form a complex to form a pore. Structure of HblB shows an elongated, almost entirely alpha-helical protein, except for a short hydrophobic beta-hairpin known as the beta-tongue. HBL from Bacillus toyonensis BV-17 (a strain isolated from feces samples of healthy donors) has antitumor activity both in vitro and in vivo and may have potential as a treatment for colon cancer. For B. toyonesis HBL, combining HBL-B and HBL-L2 had no cytotoxicity but combining HBL-B and HBL-L1 does. 231 matched cddid_all.tbl CDD cd22654 cd22654 439152 ClyA_NheA-like "Bacillus cereus non-hemolytic enterotoxin (Nhe) component A (NheA), and similar proteins. This model contains Bacillus cereus tripartite non-hemolytic enterotoxin (Nhe) component A (NheA), a member of the cytolysin A (ClyA) family of alpha pore-forming toxins (alpha-PFTs). Non-hemolytic enterotoxin (Nhe), despite its name, is hemolytic and able to lyse erythrocytes from various mammalian organisms. It consists of three proteins, NheA, NheB and NheC, encoded by one operon containing three genes nheA, nheB and nheC, respectively. Separately, these three proteins show no toxicity; maximal activity is seen only when all three components are presented. The NheB and NheC components are able to bind to cell membranes while NheA is not; NheC primes the host cell for the formation of ion permeable NheB/C pores. Binding of NheA to NheB/NheC is thought to be the final stage of pore formation. Structure of NheA shows an elongated, almost entirely alpha-helical protein with an enlarged ""head"" domain compared with other cytolysins, displaying on its surface an enlarged beta-tongue which is of amphipathic rather than hydrophobic nature. It has been proposed that NheA could even form beta-barrel pores." 333 matched cddid_all.tbl CDD cd22655 cd22655 439153 ClyA_MakA-like Vibrio cholerae cytotoxin MakA (motility associated killing factor A), and similar proteins. This model includes Vibrio cholerae motility associated killing factor A (MakA) cytotoxin, a member of the cytolysin A (ClyA) family of alpha pore-forming toxins (alpha-PFTs). The MakA protein is encoded by the mak operon. Transport of the MakA protein from the bacteria is shown to occur by flagellum-dependent secretion, highlighting a non-conventional and direct role of flagella in pathogenesis of V. cholerae; a conserved N-terminal FTPP motif is essential for MakA secretion via the flagellum channel in a proton motive force-dependent manner. Structure of MakA shows an elongated, almost entirely alpha-helical protein, with the head domain consisting of two helices and three beta-strands that together with the short beta-strand of the tail domain forms a four-stranded sheet. MakA has been demonstrated to cause toxicity in both Caenorhabditis elegans and zebrafish. 342 matched cddid_all.tbl CDD cd22656 cd22656 439154 ClyA_Cry6Aa-like Bacillus thuringiensis crystal 6Aa (Cry6Aa) toxin, and similar proteins. This model includes pesticidal Cry6Aa toxin from Bacillus thuringiensis, one of the many parasporal crystal (Cry) toxins produced during the sporulation phase of growth. Many of these proteins are toxic to numerous insect species and have been effectively used as proteinaceous insecticides to directly kill insect pests; some have been used to control insect growth on transgenic agricultural plants. Cry6Aa exists as a protoxin, which is activated by cleavage using trypsin. Structure studies for Cry6Aa support a mechanism of action by pore formation, similar to cytolysin A (ClyA)-type alpha pore-forming toxins (alpha-PFTs) such as HblB, and bioassay and mutation studies show that Cry6Aa is an active pore-forming toxin. Cry6Aa shows atypical features compared to other members of alpha-PFTs, including internal repeat sequences and small loop regions within major alpha helices. 309 matched cddid_all.tbl CDD cd22657 cd22657 439155 ClyA_XaxA-like Xenorhabdus nematophila alpha-xenorhabdolysin (XaxA) and Yersinia enterocolitica YaxA, and similar proteins. This model includes Xenorhabdus nematophila alpha-xenorhabdolysin (XaxA) and Yersinia enterocolitica YaxA, both parts of two-component alpha-helical pore-forming toxins (alpha-PFTs). The xaxAB genes encoding the XaxAB toxin have also been also identified in various plant and human pathogens. XaxAB triggers necrosis and apoptosis in both insect hemocytes and mammalian cells. Structure studies show that component A binds to component B's back, forming a subunit; twelve to fifteen of these subunits then conjoin as the pore-forming toxin. Component A stabilizes each subunit on the membrane and activates component B, which then punctures the membrane by swinging out its lower end. Similarly, Yersinia enterocolitica YaxA, encoded by the yaxAB gene, forms a pore predominantly composed of decamers of YaxA-YaxB heterodimers. Although both subunits bear membrane-active moieties, only YaxA is capable of binding to membranes by itself and YaxB is subsequently recruited to membrane-associated YaxA and induced to present its lytic transmembrane helices; pore formation then progresses by further oligomerization of YaxA-YaxB dimers. YaxAB has been found to be strongly upregulated by the Yersinia master regulator RovA, a transcriptional activator of Yersinia outer membrane protein invasion which is involved in bacterial attachment and invasion across the intestinal epithelium. 306 matched cddid_all.tbl CDD cd22658 cd22658 439310 STING_C_metazoan-like C-terminal domain of Stimulator Of Interferon Genes (STING) protein in metazoans. This model represents the metazoan cytoplasmic ligand-binding domain (LBD, or cyclic-dinucleotide-binding domain) of Stimulator Of Interferon Genes (STING) protein, also called transmembrane protein 173 (TMEM173), mediator of IRF3 activation (MITA), endoplasmic reticulum IFN stimulator (ERIS), or N-terminal methionine-proline-tyrosine-serine plasma membrane tetraspanner (MYSA). STING is a receptor that senses foreign cyclic dinucleotides that are released during bacterial infections as well as in endogenous cyclic GMP-AMP (cGAMP) signaling during viral infection and anti-tumor immunity. STING activates downstream transcription factor IRF3 (interferon regulatory factor 3) and STAT (signal transducer and activator of transcription) via TBK1 ((Tank binding kinase 1), which are responsible for antiviral and innate immune response against intracellular pathogens. STING's activation of IRF3 and STAT induces the production of type 1 interferon and target genes involved in immune cell homing such as chemokines, respectively. STING may also function as a direct cytosolic DNA sensor. STING also has a role in B cell adaptive immunity through modulating B cell receptor signaling via PI3K (phosphatidylinositol 3-kinase). STING is encoded by the STING1 gene in mammals. It is an endoplasmic reticulum (ER) membrane protein that contains four transmembrane helices followed by a cytoplasmic ligand-binding and signaling domain. The cytoplasmic domain forms a homodimer, which undergoes conformational changes upon binding to cGAMP. Metazoan STING is larger and less compact than the bacterial homologs, so that the metazoan insertions into the core bacterial fold are necessary for induction of autophagy, and the C-terminal tail contains motifs for the recruitment of kinases and transcription factors in vertebrates. Bacterial STING proteins have also been shown to be functional cyclic dinucleotide receptors. 184 matched cddid_all.tbl CDD cd22659 cd22659 439311 STING_bact-like Stimulator Of Interferon Genes (STING) protein in bacteria. This model represents the bacterial Stimulator Of Interferon Genes (STING) protein that exhibits clear homology to the cyclic-dinucleotide-binding domain of human STING, and represents a newly identified prokaryotic member of the STING family of receptors. Bacterial STING occurs primarily as a fusion to a Toll/interleukin-1 receptor (TIR, or Toll and IL-1 receptor) adaptor domain, or more rarely are appended to predicted transmembrane segments; TIR domains can function as beta-nicotinamide adenine dinucleotide (NAD+) hydrolases in plant and animal immunity. Bacterial STING proteins define a minimal homodimeric scaffold that selectively responds to cyclic di-GMP synthesized by a neighboring cGAS/DncV-like nucleotidyltransferase (CD-NTase) enzyme. They couple the recognition of cyclic dinucleotides with the formation of protein filaments to drive oligomerization of TIR effector domains and rapid NAD+ cleavage. Structures of Flavobacteriaceae sp. STING (FsSTING) and Capnocytophaga granulosa STING (CgSTING) show that the overall architecture is conserved with metazoan STING; they adopt a canonical V-shaped, homodimeric architecture with a hydrophobic alpha-helix stem. However, bacterial STING proteins are 20% smaller and notably compact. Comparative structural analysis shows that metazoan-specific insertions into the core bacterial STING fold have enabled a switch from direct effector function to regulation of antiviral transcription. 155 matched cddid_all.tbl CDD cd22661 cd22661 439382 Cas12i CRISPR-associated protein (Cas) 12i. Cas12i1 and Cas12i2 are class 2 type V-I (class 2, type V family, subtype I; Cas12i) CRISPR effector proteins. Class 2, type V family members, have names each which begin with Cas12, and predominantly cleave the non-target strand of a double-stranded DNA (dsDNA) substrate. Two Cas12i proteins (Cas12i1 and Cas12i2), have CRISPR RNA (crRNA)-guided dsDNA cleavage activity. Cas12i1 and Cas12i2 cleave dsDNA adjacent to protospacer adjacent motif (PAM) sequences, preferring a 5' TTN PAM. They cleave the non-target DNA (NTD) strand prior to the target DNA (TD) strand to generate staggered double-strand breaks; for Cas12i1 the NTD strand was cleaved 13-15 nucleotides after the PAM duplex, and the TD strand was cleaved 24 nucleotides after the PAM duplex; for Cas12i2 the NTD strand was primarily cleaved 31 nucleotides after the PAM duplex and the TD strand was cleaved 24 nucleotides after the PAM duplex. In addition to dsDNA cleavage, Cas12i1 and Cas2i2 possess ssDNA cleavage activity, and pre-crRNA processing activity for crRNA maturation. The class 2 effector modules are single large proteins, distinguished by their domain architectures into type II, V and VI systems. Type V is the most diversified type and is further divided into subtypes A-I, K, and CRISPR-CasPhi. These subtypes, with the exception of subtype K, have ssDNA cleavage activity; after the effector protein cleaves the targeted dsDNA substance, the PAM-distal product is released, but the Cas protein is still bound to the PAM-proximal strand; at this point, the RuvC domain can still access ssDNA substrates and perform non-specific cleavage (also known as the promiscuous cleavage of collateral ssDNA or trans-cleavage. The type II effectors (Cas9) contain two nuclease domains that are each responsible for the cleavage of one strand of the target DNA, with the HNH nuclease inserted inside the RuvC-like nuclease domain sequence. By contrast, the type V effectors (Cas12) only contain a RuvC-like domain that cleaves both strands. Both type II and type V effectors adopt a similar architecture comprising a recognition lobe (REC) and a nuclease lobe (NUC). Cas9 endonucleases employ both the RuvC and HNH domains for DNA cleavage, however, Cas12 endonucleases use a single RuvC domain for DNA cleavage. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated protein) is an RNA guided adaptive immunity system present in bacteria and archaea, which defends its host against foreign nucleic acids that originate from phages or plasmids. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). 1071 matched cddid_all.tbl CDD cd22662 cd22662 439355 SARS-CoV-like_Nsp1_C C-terminal domain of non-structural protein 1 from Severe acute respiratory syndrome-related coronavirus and betacoronavirus in the B lineage. This model represents the C-terminal domain of non-structural protein 1 (Nsp1) from betacoronaviruses in the sarbecovirus subgenus (B lineage), including highly pathogenic coronaviruses such as Severe acute respiratory syndrome-related coronavirus (SARS-CoV) and SARS-CoV2 (also called 2019 novel CoV or 2019-nCoV). CoVs utilize a multi-subunit replication/transcription machinery assembled from a set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins. Nsp1 is the N-terminal cleavage product released from the ORF1a polyprotein by the action of papain-like protease (PLpro). Though Nsp1s of alphaCoVs and betaCoVs share structural similarity, they show no significant sequence similarity and may be considered as genus-specific markers. Despite low sequence similarity, the Nsp1s of alphaCoVs and betaCoVs exhibit remarkably similar biological functions, and are involved in the regulation of both host and viral gene expression. CoV Nsp1 induces suppression of host gene expression and interferes with host immune response. It inhibits host gene expression in two ways: by targeting the translation and stability of cellular mRNAs, and by inhibiting mRNA translation and inducing an endonucleolytic RNA cleavage in the 5'-UTR of cellular mRNAs through its tight association with the 40S ribosomal subunit, a key component of the cellular translation machinery. Inhibition of host mRNA translation includes that of type I interferons, major components of the host innate immune response. Nsp1 is critical in regulating viral replication and gene expression. SARS-CoV Nsp1 enhances virus replication by binding to a stem-loop structure in the 5'-UTR of its genome. When the SARS-CoV-2 5' UTR is bound to the Nsp1 N-terminus, the covalently linked Nsp1 C-terminus cannot bind the 40S ribosome, suggesting a bipartite mechanism whereby SARS-CoV-2 Nsp1 suppresses host but not viral translation. 53 matched cddid_all.tbl CDD cd22663 cd22663 438715 FHA_RNF8 forkhead associated (FHA) domain found in RING finger protein 8 (RNF8) and similar proteins. RNF8 is a telomere-associated E3 ubiquitin-protein ligase that plays an important role in DNA double-strand break (DSB) repair via histone ubiquitination. It is localized in the nucleus and interacts with class III E2s (UBE2E2, UbcH6, and UBE2E3), but not with other E2s (UbcH5, UbcH7, UbcH10, hCdc34, and hBendless). It recruits UBC13 for lysine 63-based self polyubiquitylation. Its deficiency causes neuronal pathology and cognitive decline, and its loss results in neuron degeneration. RNF8, together with RNF168, catalyzes a series of ubiquitylation events on substrates such as H2A and H2AX, with the H2AK13/15 ubiquitylation being particularly important for recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of DSBs. Specially, RNF8 mediates the ubiquitination of gammaH2AX, and recruits 53BP1 and BRCA1 to DNA damage sites which promotes DNA damage response (DDR) and inhibits chromosomal instability. Moreover, RNF8 interacts with retinoid X receptor alpha (RXR alpha) and enhances its transcription-stimulating activity. It also regulates the rate of exit from mitosis and cytokinesis. RNF8 contains an N-terminal FHA domain, which is a small phosphopeptide recognition module. 110 matched cddid_all.tbl CDD cd22664 cd22664 438716 FHA_TIFA-like forkhead associated (FHA) domain found in the family of TRAF-interacting protein with FHA domain-containing protein A (TIFA). The TIFA family includes TIFA and TIFA-like protein, TIFAB. TIFA, also called putative MAPK-activating protein PM14, putative NF-kappa-B-activating protein 20, or TRAF2-binding protein (T2BP), is an adapter molecule that plays a key role in the activation of proinflammatory NF-kappa-B signaling following detection of bacterial pathogen-associated molecular pattern metabolites (PAMPs). It promotes activation of an innate immune response by inducing the oligomerization and polyubiquitination of TRAF6, which leads to the activation of TAK1 and IKK through a proteasome-independent mechanism. TIFA-dependent innate immune response is triggered by ADP-D-glycero-beta-D-manno-heptose (ADP-heptose), a potent PAMP present in all Gram-negative and some Gram-positive bacteria: ADP-heptose is recognized by ALPK1, which phosphorylates TIFA at Thr-9, leading to TIFA homooligomerization and subsequent activation of proinflammatory NF-kappa-B signaling. TIFAB, also called TIFA-like protein, inhibits TIFA-mediated TRAF6 activation possibly by inducing a conformational change in TIFA. It regulates USP15-mediated p53 signaling during stressed and malignant hematopoiesis. Both TIFA and TIFAB harbor a conserved FHA domain, which is a small phosphopeptide recognition module. 133 matched cddid_all.tbl CDD cd22665 cd22665 438717 FHA_MDC1 forkhead associated (FHA) domain found in mediator of DNA damage checkpoint protein 1 (MDC1) and similar proteins. MDC1, also called nuclear factor with BRCT domains 1 (NFBD1), is a nuclear chromatin-associated protein that is required for checkpoint mediated cell cycle arrest in response to DNA damage within both the S and G2/M phases of the cell cycle. It directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-strand breaks. MDC1 contains a forkhead-associated (FHA) domain and two BRCT domains, as well as an internal 41-amino acid repeat sequence. The FHA domain is a small phosphopeptide recognition module. 97 matched cddid_all.tbl CDD cd22666 cd22666 438718 FHA_CHK2 forkhead associated (FHA) domain found in checkpoint kinase 2 (Chk2) and similar proteins. Chk2, also called Hucds1, Cds1 homolog, or serine/threonine-protein kinase Chk2, plays an important role in cellular responses to DNA double-strand breaks and related lesions. It is phosphorylated and activated by ATM kinase, resulting in its dissociation from sites of damage to phosphorylate downstream targets such as BRCA1, p53, cell cycle transcription factor E2F1, the promyelocytic leukemia protein (PML) involved in apoptosis, and CDC25 phosphatases, among others. Mutations in Chk2 is linked to a variety of cancers including familial breast cancer, myelodysplastic syndromes, prostate cancer, lung cancer, and osteosarcomas. Chk2 contains an N-terminal SQ/TQ cluster domain (SCD), a central forkhead-associated (FHA) domain, and a C-terminal catalytic kinase domain. The FHA domain is a small phosphopeptide recognition module. 112 matched cddid_all.tbl CDD cd22667 cd22667 438719 FHA_NBN forkhead associated (FHA) domain found in nibrin and similar proteins. Nibrin (NBN), also called cell cycle regulatory protein p95, or Nijmegen breakage syndrome protein 1 (NBS1), is a novel DNA double-strand break repair protein that is mutated in Nijmegen breakage syndrome. It is a component of the MRE11-RAD50-NBN (MRN complex) which plays a critical role in the cellular response to DNA damage and the maintenance of chromosome integrity. Nibrin modulates the DNA damage signal sensing by recruiting PI3/PI4-kinase family members ATM, ATR, and probably DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to the DNA damage sites and activating their functions. It can also recruit MRE11 and RAD50 to the proximity of DSBs by an interaction with the histone H2AX. Nibrin also functions in telomere length maintenance by generating the 3' overhang which serves as a primer for telomerase dependent telomere elongation. Nibrin is a major player in the control of intra-S-phase checkpoint. This subfamily also includes Schizosaccharomyces pombe DNA repair and telomere maintenance protein Nbs1 and Arabidopsis thaliana AtNbs1. SpNbs1 is an FHA domain-containing protein required for DNA damage repair and S-phase DNA damage checkpoint. It is involved in telomere length maintenance and maintenance of chromatin structure. AtNbs1 is a component of MRN complex. It also functions in the very early stages of meiosis. The FHA domain is a small phosphopeptide recognition module. 108 matched cddid_all.tbl CDD cd22668 cd22668 438720 FHA_FhaA-like forkhead associated (FHA) domain found in Mycobacterium tuberculosis FHA domain-containing protein FhaA and similar proteins. FhaA regulates cell growth and peptidoglycan synthesis by binding to MviN. It may inhibit the late stages of peptidoglycan synthesis. It contains an FHA domain, which is a small phosphopeptide recognition module. 91 matched cddid_all.tbl CDD cd22669 cd22669 438721 FHA_EmbR-like forkhead associated (FHA) domain found in Mycobacterium tuberculosis transcriptional regulatory protein EmbR and similar proteins. EmbR is a transcriptional regulator of the embCAB operon encoding cell wall arabinosyltransferases (EmbC, -A, and -B), and is phosphorylated by the cognate mycobacterial serine/threonine protein kinase PknH. It interacts with RNA polymerase and possesses a phosphorylation-dependent ATPase activity. EmbR contains a regulatory C-terminal forkhead-associated (FHA) domain, which mediates binding to a threonine-phosphorylated site in PknH. The FHA domain is a small phosphopeptide recognition module. 89 matched cddid_all.tbl CDD cd22670 cd22670 438722 FHA_MEK1-like forkhead associated (FHA) domain found in Saccharomyces cerevisiae meiosis-specific serine/threonine-protein kinase MEK1 and similar proteins. MEK1 (EC 2.7.11.1), also known as MRE4, is a meiosis-specific protein kinase required for chromosome synapsis and meiotic recombination. The recruitment and activation of MEK1 require the phosphorylation of the chromosome axis protein Hop1 at Thr318 (pT318), which is necessary for recognition by the MEK1 FHA domain. The FHA domain is a small phosphopeptide recognition module. 105 matched cddid_all.tbl CDD cd22671 cd22671 438723 FHA_APTX-like forkhead associated (FHA) domain found in aprataxin, bifunctional polynucleotide phosphatase/kinase (PNKP), aprataxin and PNK-like factor (APLF), and similar proteins. The family includes aprataxin, PNKP, and APLF. Aprataxin (EC 3.6.1.71/EC 3.6.1.72), also called forkhead-associated domain histidine triad-like protein (FHA-HIT), is a DNA-binding protein involved in single-strand DNA break repair, double-strand DNA break repair, and base excision repair. It catalyzes the release of adenylate groups covalently linked to 5'-phosphate termini, resulting in the production of 5'-phosphate termini that can be efficiently rejoined. It can also hydrolyze adenosine 5'-monophosphoramidate (AMP-NH(2)) and diadenosine tetraphosphate (AppppA), but with lower catalytic activity. Likewise, it catalyzes the release of 3'-linked guanosine (DNAppG) and inosine (DNAppI) from DNA but has higher specific activity with 5'-linked adenosine (AppDNA). PNKP (EC 3.1.3.32/EC 2.7.1.78), also called DNA 5'-kinase/3'-phosphatase, or polynucleotide kinase-3'-phosphatase, plays a key role in the repair of DNA damage, functioning as part of both the non-homologous end-joining (NHEJ) and base excision repair (BER) pathways. Through its two catalytic activities, PNKP ensures that DNA termini are compatible with extension and ligation by either removing 3'-phosphates from, or by phosphorylating 5'-hydroxyl groups on, the ribose sugar of the DNA backbone. APLF, also called apurinic-apyrimidinic endonuclease APLF, PNK and APTX-like FHA domain-containing protein, or XRCC1-interacting protein 1 (XIP1), is a novel apurinic-apyrimidinic (AP) endonuclease and 3'-5' exonuclease with conserved zinc-finger-like motifs involved in single-strand and double-strand DNA break repair. It is recruited to sites of DNA damage through interaction with poly(ADP-ribose), a polymeric post-translational modification synthesized transiently at sites of chromosomal damage to accelerate DNA strand break repair reactions. It can introduce nicks at hydroxyuracil and other types of pyrimidine base damage. Together with PARP3, APLF promotes the retention of the LIG4-XRCC4 complex on chromatin and accelerate DNA ligation during non-homologous end-joining (NHEJ). Members of this family contain an FHA domain at their N-terminus. The FHA domain is a small phosphopeptide recognition module. 101 matched cddid_all.tbl CDD cd22672 cd22672 438724 FHA_CHFR forkhead associated (FHA) domain found in checkpoint with forkhead and RING finger domains protein (CHFR). CHFR, also called RING finger protein 196 (RNF196), is a checkpoint protein that delays entry into mitosis in response to stress. It functions as an E3 ubiquitin ligase that ubiquitinates and degrades its target proteins, such as Aurora-A, Plk1, Kif22 and PARP-1, which are critical for proper mitotic transitions. It also plays an important role in cell cycle progression and tumor suppression and is negatively regulated by SUMOylation-mediated proteasomal ubiquitylation. Moreover, CHFR is involved in the early stage of the DNA damage response, which mediates the crosstalk between ubiquitination and poly-ADP-ribosylation. CHFR contains a fork head associated-(FHA) domain and a RING-HC finger. The CHFR FHA domain has been crystallized as a segment-swapped dimer. The FHA domain is a small phosphopeptide recognition module. 108 matched cddid_all.tbl CDD cd22673 cd22673 438725 FHA_Ki67 forkhead associated (FHA) domain found in proliferation marker protein Ki-67 and similar proteins. Ki-67, also called antigen identified by monoclonal antibody Ki-67, antigen KI-67, or antigen Ki67, acts as a biological surfactant to disperse mitotic chromosomes. It is required to maintain individual mitotic chromosomes dispersed in the cytoplasm following nuclear envelope disassembly. Ki-67 binds DNA with a preference for supercoiled DNA and AT-rich DNA. It may also play a role in chromatin organization. Ki-67 contains an FHA domain at its N-terminus. The FHA domain is a small phosphopeptide recognition module. 95 matched cddid_all.tbl CDD cd22674 cd22674 438726 FHA_PPP1R8 forkhead associated (FHA) domain found in protein phosphatase 1 regulatory inhibitor subunit 8 (PPP1R8) and similar proteins. PPP1R8, also called nuclear inhibitor of protein phosphatase 1 (NIPP-1), is an inhibitor subunit of the major nuclear protein phosphatase-1 (PP-1). It has RNA-binding activity but does not cleave RNA and may target PP-1 to RNA-associated substrates. It may also be involved in pre-mRNA splicing and binds DNA and might act as a transcriptional repressor. PPP1R8 seems to be required for cell proliferation. PPP1R8 contains an FHA domain that mediates interactions with threonine-phosphorylated maternal embryonic leucine zipper kinase (MELK). The FHA domain is a small phosphopeptide recognition module. 108 matched cddid_all.tbl CDD cd22675 cd22675 438727 FHA_Par42-like forkhead associated (FHA) domain found in Trypanosoma brucei Parvulin 42 (TbPar42) and similar proteins. TbPar42 is a nuclear protein that plays a key role in parasite cell proliferation. It exhibits an N-terminal forkhead associated (FHA)-domain and a peptidyl-prolyl-cis/trans-isomerase (PPIase) domain, both connected by a linker. Its PPIase domain adopts a parvulin fold and reflects structural elements of Pin1-type proteins but is catalytically inactive. Its FHA domain may be involved in the binding of phosphorylated target proteins. The FHA domain is a small phosphopeptide recognition module. 113 matched cddid_all.tbl CDD cd22676 cd22676 438728 FHA_SNIP1_DDL-like forkhead associated (FHA) domain found in Smad nuclear-interacting protein 1 (SNIP1), FHA domain-containing protein DDL, and similar proteins. SNIP1 is an FHA domain-containing protein required for pre-mRNA splicing as a component of the spliceosome. It inhibits NF-kappaB signaling by competing for its binding to the C/H1 domain of CBP/p300 transcriptional co-activators. It is involved in microRNA (miRNA) biogenesis. SNIP1 is a regulator of the cell cycle and cyclin D1 expression and may be involved in cyclin-D1/CCND1 mRNA stability through the SNARP complex which associates with both the 3'end of the CCND1 gene and its mRNA. This family also includes Arabidopsis thaliana FHA domain-containing protein DDL and similar proteins. DDL, also called protein DAWDLE, is involved in the microRNA (miRNA) and short interfering RNA (siRNA) biogenesis. It may facilitate DCL1 to access or recognize primary miRNAs. DDL binds RNA non-specifically. The FHA domain is a small phosphopeptide recognition module. 111 matched cddid_all.tbl CDD cd22677 cd22677 438729 FHA_Kanadaptin forkhead associated (FHA) domain found in kanadaptin and similar proteins. Kanadaptin, also called human lung cancer oncogene 3 protein (HLC-3), kidney anion exchanger adapter protein, or solute carrier family 4 anion exchanger member 1 adapter protein (SLC4A1AP), is a nuclear protein widely expressed in mammalian tissues. It was originally isolated as a kidney Cl-/HCO3- anion exchanger 1 (kAE1)-binding protein. It is a highly mobile nucleocytoplasmic shuttling and multilocalizing protein. Its role in mammalian cells remains unclear. It contains an FHA domain, which is a small phosphopeptide recognition module. 106 matched cddid_all.tbl CDD cd22678 cd22678 438730 FHA_PP2C70-like forkhead associated (FHA) domain found in Arabidopsis thaliana protein phosphatase 2C 70 (AtPP2C70) and similar proteins. AtPP2C70, also called kinase-associated protein phosphatase, or protein ROOT ATTENUATED GROWTH 1, dephosphorylates the serine/threonine receptor-like kinase RLK5. It may function as a signaling component in a pathway involving RLK5. It acts as a negative regulator of the CLAVATA1 signaling in plant development by binding and dephosphorylating CLAVATA1. It is also a component of a signaling pathway which mediates adaptation to NaCl stress. It contains an FHA domain, which is a small phosphopeptide recognition module. 102 matched cddid_all.tbl CDD cd22679 cd22679 438731 FHA_SLMAP forkhead associated (FHA) domain found in sarcolemmal membrane-associated protein (SLMAP) and similar proteins. SLMAP, also called sarcolemmal-associated protein (SLAP), is a tail-anchored protein involved in fundamental cellular processes, such as myoblast fusion, cell cycle progression, and chromosomal inheritance. It is a cardiac membrane protein that plays an important role in E-C coupling and the adrenergic response of the heart. Overexpression of the SLMAP gene has been associated with diabetes and endothelial dysfunction of macro- and micro-blood vessels. SLMAP contains an N-terminal FHA domain, which is a small phosphopeptide recognition module. 126 matched cddid_all.tbl CDD cd22680 cd22680 438732 FHA_ArnA-like forkhead associated (FHA) domain found in Sulfolobus Acidocaldarius FHA domain-containing protein ArnA and similar proteins. ArnA is an FHA domain-containing protein from Sulfolobus acidocaldarius that was shown to strongly interact with ArnB, a von Willebrand domain-containing protein. They act synergistically and negatively to modulate motility. ArnA is involved in regulating archaella expression in S. acidocaldarius. The FHA domain is a small phosphopeptide recognition module. 96 matched cddid_all.tbl CDD cd22681 cd22681 438733 FHA_PML1-like forkhead associated (FHA) domain found in Saccharomyces cerevisiae pre-mRNA leakage protein 1 (PML1) and similar proteins. PML1 is an FHA domain-containing protein required for efficient splicing and pre-mRNA nuclear retention. It is a component of the pre-mRNA retention and splicing (RES) complex composed of at least BUD13, IST3, and PML1. It contains an FHA domain, which is a small phosphopeptide recognition module. 129 matched cddid_all.tbl CDD cd22682 cd22682 438734 FHA_DgcB-like forkhead associated (FHA) domain found in Bdellovibrio bacteriovorus GGDEF domain protein DgcB and similar proteins. DgcB is a GGDEF enzyme that produces cyclic-di-GMP in response to an unknown stimulus. It appends the C-terminal GGDEF enzymatic domain with an N-terminal forkhead-associated (FHA) domain that acts as a consensus phosphopeptide sensor. The GGDEF and sensory FHA domains form an asymmetrical dimer. 96 matched cddid_all.tbl CDD cd22683 cd22683 438735 FHA_DUN1-like forkhead associated (FHA) domain found in Saccharomyces cerevisiae DNA damage response protein kinase DUN1 and similar proteins. DUN1 is a protein kinase that controls the DNA damage response in yeast. It phosphorylates SML1 on serine residues and cooperates with the PAN deadenylation complex in the regulation of RAD5 mRNA levels and cell survival in response to replicational stress. It contains an FHA domain, which is a small phosphopeptide recognition module. 96 matched cddid_all.tbl CDD cd22684 cd22684 438736 FHA_GarA_OdhI-like forkhead associated (FHA) domain found in Mycobacterium tuberculosis GarA, Corynebacterium glutamicum OdhI and similar proteins. This family includes Mycobacterium tuberculosis glycogen accumulation regulator GarA and Corynebacterium glutamicum oxoglutarate dehydrogenase inhibitor (OdhI). GarA is involved in the regulation of glutamate metabolism. It acts as a phosphorylation-dependent molecular switch that modulates the activities of Kgd, Gdh and GltB. GarA binds to Kgd, Gdh, GltB, PknB, and the N-terminal region of PknG via its FHA domain. OdhI is an essential component of the PknG signaling pathway. It can inhibit the activity of 2-oxoglutarate dehydrogenase only when it is unphosphorylated. The FHA domain is a small phosphopeptide recognition module. 94 matched cddid_all.tbl CDD cd22685 cd22685 438737 FHA_TCF19 forkhead associated (FHA) domain found in transcription factor 19 (TCF-19) and similar proteins. TCF-19, also called transcription factor SC1, was identified as a putative trans-activating factor with expression beginning at the late G1-S boundary in dividing cells. It also functions as a novel islet factor necessary for proliferation and survival in the INS-1 beta cell line. It plays an important role in susceptibility to both Type 1 Diabetes Mellitus (T1DM) and Type 2 Diabetes Mellitus (T2DM); it has been suggested that it may positively impact beta cell mass under conditions of beta cell stress and increased insulin demand. TCF-19 contains an N-terminal fork head association domain (FHA), a proline rich region, and a C-terminal plant homeodomain (PHD) finger. The FHA domain may serve as a nuclear signaling domain or as a phosphoprotein binding domain. The proline rich region is a common characteristic of trans-activating factors. The PHD finger may allow TCF-19 to interact with chromatin via methylated histone H3. 130 matched cddid_all.tbl CDD cd22686 cd22686 438738 FHA_AGGF1 forkhead associated (FHA) domain found in angiogenic factor with G patch and FHA domains 1 (AGGF1) and similar proteins. AGGF1, also called angiogenic factor VG5Q, or G patch domain-containing protein 7 (GPATC7), or vasculogenesis gene on 5q protein, is an angiogenic factor involved in vascular development, angiogenesis, specification of hemangioblasts, and differentiation of veins. It promotes angiogenesis and the proliferation of endothelial cells. It inhibits inflammatory effect and preserve vascular integrity in non-nervous system diseases. Mutated AGGF1 causes susceptibility to Klippel-Trenaunay syndrome, a vascular disorder. Increased AGGF1 expression is associated with tumor angiogenesis. The FHA domain is a small phosphopeptide recognition module. 123 matched cddid_all.tbl CDD cd22687 cd22687 438739 FHA_MCRS1 forkhead associated (FHA) domain found in microspherule protein 1 (MCRS1) and similar proteins. MCRS1, also called 58 kDa microspherule protein (MSP58), cell cycle-regulated factor p78, or INO80 complex subunit J, is a nuclear RNA-binding protein that interacts with fragile X mental retardation protein in polyribosomal ribonucleoparticles (mRNPs) from neurons. It is a cell-cycle-dependent protein that acts as an inhibitor of TERT telomerase activity. It associates with LPTS/PinX1 and reduces the telomere length. It modulates the transcription repressor activity of DAXX by recruiting it to the nucleolus. As part of the NSL complex, MCRS1 may be involved in acetylation of nucleosomal histone H4 on several lysine residues. MCRS1 is also a putative regulatory component of the chromatin remodeling INO80 complex, which is involved in transcriptional regulation, DNA replication, and probably DNA repair. MCRS1 contains an FHA domain at its C-terminus. The FHA domain is a small phosphopeptide recognition module. 105 matched cddid_all.tbl CDD cd22688 cd22688 438740 FHA_FOXK forkhead associated (FHA) domain found in the Forkhead box protein K (FOXK) subfamily. The FOXK subfamily includes two-winged helix transcription factors, FOXK1 and FOXK2. FOXK1, also called myocyte nuclear factor (MNF), acts as a transcriptional regulator that binds to the upstream enhancer region (CCAC box) of myoglobin genes. It positively regulates Wnt/beta-catenin signaling by translocating dishevelled (DVL) proteins into the nucleus. It also reduces virus replication, probably by binding the interferon stimulated response element (ISRE) to promote antiviral gene expression. In addition, FOXK1 plays important roles in multiple human cancers. FOXK2, also called cellular transcription factor ILF-1 or interleukin enhancer-binding factor 1, is a transcriptional regulator that recognizes the core sequence 5'-TAAACA-3'. It binds to NFAT-like motifs (purine-rich) in the IL2 promoter. It also binds to the HIV-1 long terminal repeat. FOXK2 may be involved in both positive and negative regulation of important viral and cellular promoter elements. In addition, FOXK2 plays a critical role in suppressing tumorigenesis. The Forkhead (FH) domain is a winged helix DNA-binding domain. FOX transcription factors recognize the core sequence 5'-(A/C)AA(C/T)A-3'. The FHA domain is a small phosphopeptide recognition module. 100 matched cddid_all.tbl CDD cd22689 cd22689 438741 FHA_RAD53-like_rpt1 first forkhead associated (FHA) domain found in Saccharomyces cerevisiae Serine/threonine-protein kinase RAD53 and similar proteins. RAD53, also called CHEK2 homolog, or serine-protein kinase 1 (Spk1), is a nuclear protein kinase that phosphorylates proteins on serine, threonine, and tyrosine. It controls S-phase checkpoint as well as G1 and G2 DNA damage checkpoints and prevents entry into anaphase and mitotic exit after DNA damage via regulation of the Polo kinase CDC5. It may be involved in the phosphorylation of RPH1. RAD53 contains two FHA domains. This model corresponds to the first one. The FHA domain is a small phosphopeptide recognition module. 132 matched cddid_all.tbl CDD cd22690 cd22690 438742 FHA_RAD53-like_rpt2 second forkhead associated (FHA) domain found in Saccharomyces cerevisiae Serine/threonine-protein kinase RAD53 and similar proteins. RAD53, also called CHEK2 homolog, or serine-protein kinase 1 (Spk1), is a nuclear protein kinase that phosphorylates proteins on serine, threonine, and tyrosine. It controls S-phase checkpoint as well as G1 and G2 DNA damage checkpoints and prevents entry into anaphase and mitotic exit after DNA damage via regulation of the Polo kinase CDC5. It may be involved in the phosphorylation of RPH1. RAD53 contains two FHA domains. This model corresponds to the second one. The FHA domain is a small phosphopeptide recognition module. 105 matched cddid_all.tbl CDD cd22691 cd22691 438743 FHA_PS1-like forkhead associated (FHA) domain found in Arabidopsis thaliana Protein PARALLEL SPINDLE 1 (PS1) and similar proteins. PS1 is an FHA domain-containing protein required for normal spindle orientation at male meiosis II and normal formation of tetrad of microspores. It is not involved in female meiosis. Mutations in PS1 lead to the production of diploid pollen grains. The FHA domain is a small phosphopeptide recognition module. 113 matched cddid_all.tbl CDD cd22692 cd22692 438744 FHA_DMA-like forkhead associated (FHA) domain found in Saccharomyces cerevisiae defective in mitotic arrest protein 1 (DMA1), 2 (DMA2) and similar proteins. DMA1 (also known as checkpoint forkhead associated with RING domains-containing protein 1, or CHF1) and DMA2 (also known as checkpoint forkhead associated with RING domains-containing protein 2, or CHF2) are E3 ubiquitin-protein ligases which function in cell cycle retarding in conjunction with the UBC4 and UBC13/MMS2 complex, two E2 ubiquitin conjugating enzymes. They are involved in nutritional control of the cell cycle and required for proper spindle positioning, likely regulating septin ring deposition at the bud neck. DMA1 targets the degradation of G1 cyclin PCL1. The FHA domain is a small phosphopeptide recognition module. 139 matched cddid_all.tbl CDD cd22693 cd22693 438745 FHA_FhaB-like forkhead associated (FHA) domain found in Mycobacterium tuberculosis FHA domain-containing protein FhaB and similar proteins. FhaB, also called FtsZ-interacting protein A (FipA), is a putative virulence factor involved in regulating cell shape. It can interact with polyketide-associated protein PapA5, a putative membrane protein involved in the biosynthesis of virulence enhancing lipids. FhaB regulates growth and cell division. It is probably required for divisomal protein assembly under oxidative stress. The FHA domain is a small phosphopeptide recognition module. 91 matched cddid_all.tbl CDD cd22694 cd22694 438746 FHA_Rv1747-like_rpt1 first forkhead associated (FHA) domain found in Mycobacterium tuberculosis ABC transporter ATP-binding/permease protein Rv1747 and similar proteins. Rv1747 is a putative ATP-binding cassette (ABC) transporter involved in the translocation of an unknown substrate across the membrane. It is required for normal virulent infection by M. tuberculosis. Rv1747 has a cytoplasmic regulatory module consisting of two pThr-interacting forkhead-associated (FHA) domains connected by a conformationally disordered linker with two phospho-acceptor threonines (pThr). Recruitment and phosphorylation of Rv1747 depend on the interaction between its two non-redundant FHA domains and the autophosphorylated form of serine/threonine protein kinase PknF. This model corresponds to the first FHA domain. The FHA domain is a small phosphopeptide recognition module. 93 matched cddid_all.tbl CDD cd22695 cd22695 438747 FHA_VPS64-like forkhead associated (FHA) domain found in Saccharomyces cerevisiae vacuolar protein sorting-associated protein 64 (VPS64) and similar proteins. This subfamily includes VPS64 (also called factor arrest protein 9 or FAR9) and factor arrest protein 10 (FAR10), which participate in the control of the re-entry into the cell cycle following pheromone treatment. VPS64 is also involved in vacuolar protein sorting. The FHA domain is a small phosphopeptide recognition module. 133 matched cddid_all.tbl CDD cd22696 cd22696 438748 FHA_Ct664-like forkhead associated (FHA) domain found in Chlamydia trachomatis Ct664 protein and similar proteins. This subfamily corresponds to a group of uncharacterized FHA domain-containing proteins which show high sequence similarity with Chlamydia trachomatis Ct664 protein. Ct664 situates within the type III secretion system cluster that also encodes an STPK (CT673 in C. trachomatis), suggesting a role of CT664 in the chlamydial type III secretion system by mediating phosphorylation-dependent protein-protein interactions. The FHA domain is a small phosphopeptide recognition module. 97 matched cddid_all.tbl CDD cd22697 cd22697 438749 FHA_Slr1951-like forkhead associated (FHA) domain found in Synechocystis sp. Slr1951 protein and similar proteins. This subfamily corresponds to a group of uncharacterized FHA domain-containing proteins which show high sequence similarity with Synechocystis sp. protein Slr1951 and protein Sll1895. The FHA domain is a small phosphopeptide recognition module. 102 matched cddid_all.tbl CDD cd22698 cd22698 438750 FHA_EspA-like forkhead associated (FHA) domain found in Myxococcus xanthus EspA and similar proteins. EspA is a histidine protein kinase with a fork head-associated (FHA) domain at the N-terminus and a receiver domain at the C-terminus. It functions as an inhibitor of sporulation during early fruiting body development while cells are aggregating into raised mounds. EspA is part of a two-component signal transduction system that regulates the timing of sporulation initiation. The FHA domain is a small phosphopeptide recognition module. 93 matched cddid_all.tbl CDD cd22699 cd22699 438751 FHA_PLM2-like forkhead associated (FHA) domain found in Saccharomyces cerevisiae plasmid maintenance protein 2 (PLM2) and similar proteins. This subfamily includes two homologs PLM2 and TOS4 (also called target of SBF protein 4), which are predicted to be chromatin-associated proteins. They bind to the promoters of genes with functions important for the G1/S (start) transition. PLM2 targets primarily genes involved in DNA synthesis and repair, chromosome segregation, nuclear division, and transcription. TOS4 targets primarily genes involved in pheromone response, polarized growth, and transcription. The FHA domain is a small phosphopeptide recognition module. 122 matched cddid_all.tbl CDD cd22700 cd22700 438752 FHA_FHAD1 forkhead associated (FHA) domain found in forkhead-associated domain-containing protein 1 (FHAD1) and similar proteins. FHAD1, also called FHA domain-containing protein 1, is an uncharacterized FHA domain-containing protein. The FHA domain is a small phosphopeptide recognition module. 96 matched cddid_all.tbl CDD cd22701 cd22701 438753 FHA_FKH1-like forkhead associated (FHA) domain found in Saccharomyces cerevisiae fork head protein homolog 1 (FKH1), 2 (FKH2) and similar proteins. This family includes FKH1 and FKH2, as well as pre-rRNA-processing protein FHL1. FKH1 and FKH2 are forkhead transcription factors that regulate the expression of the CLB2 cluster of genes during the G2/M phase of the mitotic cell cycle. The CLB2 cluster of genes includes mitotic regulators such as CLB1, CLB2, CDC5 and CDC20, as well as SWI5 and ACE2. FKH1 and FKH2 are involved in HMRa silencing. They associate with the coding regions of active genes and influence, in opposing ways, transcriptional elongation and termination, and coordinate early transcription elongation and pre-mRNA processing. Both FKH1 and FKH2 play a role as regulators of lifespan in collaboration with the anaphase-promoting complex (APC), likely through combined regulation of stress response, genomic stability, and cell cycle regulation. They also function in controlling yeast cell morphology by preventing pseudohyphal growth and act as rate-limiting replication origin activators via their interaction with the origin recognition complex (ORC). FHL1 is a forkhead protein that controls the pre-rRNA processing machinery in conjunction with IFH1. It might act as a transcriptional regulator of genes specifically involved in that process. IFH1 convert FHL1 from a repressor to an activator. This family also includes AtFHA1 and AtFHA2, which may play a role in the control of plant organ development. AtFHA2 is specifically involved in the regulation of stamen development. The FHA domain is a small phosphopeptide recognition module. 106 matched cddid_all.tbl CDD cd22702 cd22702 438754 FHA_ZEP-like forkhead associated (FHA) domain found in chloroplastic zeaxanthin epoxidase (ZEP) and similar proteins. ZEP, also called protein ABA DEFICIENT 1, ABA1, protein IMPAIRED IN BABA-INDUCED STERILITY 3, protein LOW EXPRESSION OF OSMOTIC STRESS-RESPONSIVE GENES 6, or protein NON-PHOTOCHEMICAL QUENCHING 2, plays an important role in the xanthophyll cycle and abscisic acid (ABA) biosynthesis. It converts zeaxanthin into antheraxanthin and subsequently violaxanthin. ZEP is required for resistance to osmotic and drought stresses, ABA-dependent stomatal closure, seed development and dormancy, modulation of defense gene expression, and disease resistance and non-photochemical quencing (NPQ). The FHA domain is a small phosphopeptide recognition module. 123 matched cddid_all.tbl CDD cd22703 cd22703 438755 FHA_PHF12 forkhead associated (FHA) domain found in PHD finger protein 12 (PHF12) and similar proteins. PHF12, also called PHD factor 1 (Pf1), is a plant homeodomain (PHD) zinc finger-containing protein that bridges the transducin-like enhancer of split (TLE) corepressor to the mSin3A-histone deacetylase (HDAC)-complex, and further represses transcription at targeted genes. PHF12 also interacts with MRG15 (mortality factor-related genes on chromosome 15), a member of the mortality factor (MORF) family of proteins implicated in regulating cellular senescence. It also contains an FHA domain, which is a small phosphopeptide recognition module. 129 matched cddid_all.tbl CDD cd22704 cd22704 438756 FHA_Cep170 forkhead associated (FHA) domain found in the centrosomal protein of 170 kDa protein (Cep170) family. The Cep170 family includes Cep170 and Cep170B. Cep170, also called Cep170A, KARP-1-binding protein, or KARP1-binding protein, is a protein that localizes to centrosomes as well as spindle microtubules and plays a role in microtubule organization and microtubule assembly. It is required for centriole subdistal appendage assembly. Cep170 is phosphorylated during M phase and interacts with Polo-like kinase 1 (Plk1). Cep170B, also called centrosomal protein 170B, plays a role in microtubule organization. The FHA domain is a small phosphopeptide recognition module. 102 matched cddid_all.tbl CDD cd22705 cd22705 438757 FHA_KIF1 forkhead associated (FHA) domain found in the kinesin-like protein KIF1 family. The KIF1 family includes KIF1A, KIF1B, and KIF1C. KIF1A, also called axonal transporter of synaptic vesicles (ATSV), microtubule-based motor KIF1A, Unc-104- and KIF1A-related protein, or Unc-104, is an axonal transporter of synaptic vesicles, which is mutated in hereditary sensory and autonomic neuropathy type 2. It is also required for neuronal dense core vesicle (DCV) transport to dendritic spines and axons. The calcium-dependent interaction with CALM1 increases vesicle motility, and interaction with the scaffolding proteins PPFIA2 and TANC2 recruits DCVs to synaptic sites. KIF1B, also called Klp, is a motor for anterograde transport of mitochondria. It has a microtubule plus end-directed motility. Isoform 1 mediates the transport of synaptic vesicles in neuronal cells, while isoform 2 is required for induction of neuronal apoptosis. KIF1C is a new kinesin-like protein involved in vesicle transport from the Golgi apparatus to the endoplasmic reticulum. It has a microtubule plus end-directed motility. The FHA domain is a small phosphopeptide recognition module, but this group may lack the conserved residues that are required for binding phosphothreonine. 101 matched cddid_all.tbl CDD cd22706 cd22706 438758 FHA_KIF13 forkhead associated (FHA) domain found in the kinesin-like protein KIF13 family. The KIF13 family includes KIF13A and KIF13B. KIF13A, also called kinesin-like protein RBKIN, is a plus end-directed microtubule-dependent motor protein involved in intracellular transport and in regulating various processes such as mannose-6-phosphate receptor (M6PR) transport to the plasma membrane, endosomal sorting during melanosome biogenesis, and cytokinesis. It mediates the transport of M6PR-containing vesicles from trans-Golgi network to the plasma membrane via direct interaction with the AP-1 complex. During melanosome maturation, KIF13A is required for delivering melanogenic enzymes from recycling endosomes to nascent melanosomes by creating peripheral recycling endosomal subdomains in melanocytes. It is also required for the abscission step in cytokinesis: it mediates translocation of ZFYVE26, and possibly TTC19, to the midbody during cytokinesis. KIF13B, also called kinesin-like protein GAKIN, is a novel kinesin-like protein that associates with the human homolog of the Drosophila discs large tumor suppressor in T lymphocytes. It is involved in reorganization of the cortical cytoskeleton. It regulates axon formation by promoting the formation of extra axons. KIF13B may be functionally important for the intracellular trafficking of membrane-associated guanylate kinase homologs (MAGUKs) and associated protein complexes. The FHA domain is a small phosphopeptide recognition module, but this group may lack the conserved residues that are required for binding phosphothreonine. 101 matched cddid_all.tbl CDD cd22707 cd22707 438759 FHA_KIF14 forkhead associated (FHA) domain found in kinesin-like protein KIF14 and similar proteins. KIF14 is a microtubule motor protein that binds to microtubules with high affinity through each tubulin heterodimer and has an ATPase activity. It plays a role in many processes like cell division, cytokinesis and in cell proliferation and apoptosis. KIF14 is a potential oncogene and is involved in the metastasis of various cancers. Mutations of KIF14 cause primary microcephaly by impairing cytokinesis. The FHA domain is a small phosphopeptide recognition module, but this group may lack the conserved residues that are required for binding phosphothreonine. 108 matched cddid_all.tbl CDD cd22708 cd22708 438760 FHA_KIF16 forkhead associated (FHA) domain found in the kinesin-like protein KIF16 family. The KIF16 family includes StARD9/KIF16A and KIF16B. StARD9, also called START domain-containing protein 9, or kinesin-like protein KIF16A, is a microtubule-dependent motor protein required for spindle pole assembly during mitosis. It is required to stabilize the pericentriolar material (PCM). KIF16B, also called sorting nexin-23, is a plus end-directed microtubule-dependent motor protein involved in endosome transport and receptor recycling and degradation. It regulates the plus end motility of early endosomes and the balance between recycling and degradation of receptors such as EGF receptor (EGFR) and FGF receptor (FGFR). It regulates the Golgi to endosome transport of FGFR-containing vesicles during early development, a key process for developing basement membrane and epiblast and primitive endoderm lineages during early postimplantation development. The FHA domain is a small phosphopeptide recognition module, but this group may lack the conserved residues that are required for binding phosphothreonine. 109 matched cddid_all.tbl CDD cd22709 cd22709 438761 FHA_KIF28P forkhead associated (FHA) domain found in kinesin-like protein KIF28P and similar proteins. KIF28P, also called kinesin-like protein 6 (KLP6), is a microtubule-dependent motor protein required for mitochondrion morphology and transport of mitochondria in neuronal cells. The FHA domain is a small phosphopeptide recognition module, but this group may lack the conserved residues that are required for binding phosphothreonine. 102 matched cddid_all.tbl CDD cd22710 cd22710 438762 FHA_YscD-like forkhead associated (FHA) domain found in Yersinia enterocolitica Yop proteins translocation protein D (YscD) and similar proteins. YscD protein is a single-pass inner membrane protein required for the export process of the Yop proteins. It is an essential component of the type III secretion system. YscD protein contains an N-terminal cytoplasmic domain, a transmembrane linker and a large periplasmic domain. The cytoplasmic domain consists of a forkhead-associated (FHA) fold. The FHA domain is a small phosphopeptide recognition module. Due to the lack of the conserved residues that are required for binding phosphothreonine, the cytoplasmic domain of YscD protein is therefore unlikely to function as a true FHA domain. 94 matched cddid_all.tbl CDD cd22711 cd22711 438763 FHA_AFDN forkhead associated (FHA) domain found in afadin and similar proteins. Afadin, also called ALL1-fused gene from chromosome 6 protein, protein AF-6, Afadin adherens junction formation factor, or MLLT4, is a nectin- and actin-filament-binding protein that connects nectin to the actin cytoskeleton. It is essential for the organization of adherens junctions. It may play a key role in the organization of epithelial structures of the embryonic ectoderm. The FHA domain is a small phosphopeptide recognition module, but this group may lack the conserved residues that are required for binding phosphothreonine. 106 matched cddid_all.tbl CDD cd22712 cd22712 438764 FHA_RADIL-like forkhead associated (FHA) domain found in the Ras-associating and dilute domain-containing protein (Radil)-like family. The Radil-like family includes Radil and Ras-interacting protein 1 (Rain). Radil acts as an important small GTPase Rap1 effector required for cell spreading and migration. It regulates neutrophil adhesion and motility by linking Rap1 to beta2-integrin activation. Rain, also called Rasip1, is an endothelial-specific Ras-interacting protein required for the proper formation of vascular structures that develop via both vasculogenesis and angiogenesis. It acts as a critical and vascular-specific regulator of GTPase signaling, cell architecture, and adhesion, which is essential for endothelial cell morphogenesis and blood vessel tubulogenesis. Rain interacts with Ras in a GTP-dependent manner and may serve as an effector for endomembrane-associated Ras. Both Radil and Rain contain an FHA domain. The FHA domain is a small phosphopeptide recognition module, but this group may lack the conserved residues that are required for binding phosphothreonine. 120 matched cddid_all.tbl CDD cd22713 cd22713 438765 FHA_PHLB1 forkhead associated (FHA) domain found in pleckstrin homology-like domain family B member 1 (PHLDB1) and similar proteins. PHLDB1, also called protein LL5-alpha (LL5A), acts as an insulin-responsive protein that enhances Akt activation. PHLDB1 contains a pleckstrin homology domain, which binds phosphatidylinositol PI(3,4)P(2), PI(3,5)P(2), and PI(3,4,5)P(3), as well as a Forkhead-associated (FHA) domain and coiled coil regions. The FHA domain is a small phosphopeptide recognition module, but this group may lack the conserved residues that are required for binding phosphothreonine. 120 matched cddid_all.tbl CDD cd22714 cd22714 438766 FHA_TIFA forkhead associated (FHA) domain found in TRAF-interacting protein with FHA domain-containing protein A (TIFA) and similar proteins. TIFA, also called putative MAPK-activating protein PM14, putative NF-kappa-B-activating protein 20, or TRAF2-binding protein (T2BP), is an adapter molecule that plays a key role in the activation of proinflammatory NF-kappa-B signaling following detection of bacterial pathogen-associated molecular pattern metabolites (PAMPs). It promotes activation of an innate immune response by inducing the oligomerization and polyubiquitination of TRAF6, which leads to the activation of TAK1 and IKK through a proteasome-independent mechanism. TIFA-dependent innate immune response is triggered by ADP-D-glycero-beta-D-manno-heptose (ADP-heptose), a potent PAMP present in all Gram-negative and some Gram-positive bacteria: ADP-heptose is recognized by ALPK1, which phosphorylates TIFA at Thr-9, leading to TIFA homooligomerization and subsequent activation of proinflammatory NF-kappa-B signaling. TIFA contains an FHA domain, which is a small phosphopeptide recognition module. 135 matched cddid_all.tbl CDD cd22715 cd22715 438767 FHA_TIFAB forkhead associated (FHA) domain found in TRAF-interacting protein with FHA domain-containing protein B (TIFAB). TIFAB, also called TIFA-like protein, inhibits TIFA-mediated TRAF6 activation possibly by inducing a conformational change in TIFA. It regulates USP15-mediated p53 signaling during stressed and malignant hematopoiesis. It contains an FHA domain, which is a small phosphopeptide recognition module. 129 matched cddid_all.tbl CDD cd22716 cd22716 438768 FHA_APTX_PNKP forkhead associated (FHA) domain found in aprataxin, bifunctional polynucleotide phosphatase/kinase (PNKP), and similar proteins. The subfamily includes aprataxin and PNKP. Aprataxin (EC 3.6.1.71/EC 3.6.1.72), also called forkhead-associated domain histidine triad-like protein (FHA-HIT), is a DNA-binding protein involved in single-strand DNA break repair, double-strand DNA break repair, and base excision repair. It catalyzes the release of adenylate groups covalently linked to 5'-phosphate termini, resulting in the production of 5'-phosphate termini that can be efficiently rejoined. It can also hydrolyze adenosine 5'-monophosphoramidate (AMP-NH(2)) and diadenosine tetraphosphate (AppppA), but with lower catalytic activity. Likewise, it catalyzes the release of 3'-linked guanosine (DNAppG) and inosine (DNAppI) from DNA but has higher specific activity with 5'-linked adenosine (AppDNA). PNKP (EC 3.1.3.32/EC 2.7.1.78), also called DNA 5'-kinase/3'-phosphatase, or polynucleotide kinase-3'-phosphatase, plays a key role in the repair of DNA damage, functioning as part of both the non-homologous end-joining (NHEJ) and base excision repair (BER) pathways. Through its two catalytic activities, PNKP ensures that DNA termini are compatible with extension and ligation by either removing 3'-phosphates from, or by phosphorylating 5'-hydroxyl groups on, the ribose sugar of the DNA backbone. Both aprataxin and PNKP contain an FHA domain at their N-terminus. The FHA domain is a small phosphopeptide recognition module. 97 matched cddid_all.tbl CDD cd22717 cd22717 438769 FHA_APLF forkhead associated (FHA) domain found in aprataxin and PNK-like factor (APLF) and similar proteins. APLF, also called apurinic-apyrimidinic endonuclease APLF, PNK and APTX-like FHA domain-containing protein, or XRCC1-interacting protein 1 (XIP1), is a novel apurinic-apyrimidinic (AP) endonuclease and 3'-5' exonuclease with conserved zinc-finger-like motifs involved in single-strand and double-strand DNA break repair. It is recruited to sites of DNA damage through interaction with poly(ADP-ribose), a polymeric post-translational modification synthesized transiently at sites of chromosomal damage to accelerate DNA strand break repair reactions. It can introduce nicks at hydroxyuracil and other types of pyrimidine base damage. Together with PARP3, APLF promotes the retention of the LIG4-XRCC4 complex on chromatin and accelerate DNA ligation during non-homologous end-joining (NHEJ). APLF contains an FHA domain at its N-terminus. The FHA domain is a small phosphopeptide recognition module. 99 matched cddid_all.tbl CDD cd22718 cd22718 438770 FHA_SNIP1 forkhead associated (FHA) domain found in Smad nuclear-interacting protein 1 (SNIP1) and similar proteins. SNIP1 is an FHA domain-containing protein required for pre-mRNA splicing as a component of the spliceosome. It inhibits NF-kappaB signaling by competing for its binding to the C/H1 domain of CBP/p300 transcriptional co-activators. It is involved in microRNA (miRNA) biogenesis. SNIP1 is a regulator of the cell cycle and cyclin D1 expression and may be involved in cyclin-D1/CCND1 mRNA stability through the SNARP complex, which associates with both the 3'end of the CCND1 gene and its mRNA. The FHA domain is a small phosphopeptide recognition module. 149 matched cddid_all.tbl CDD cd22719 cd22719 438771 FHA_DDL-like forkhead associated (FHA) domain found in Arabidopsis thaliana FHA domain-containing protein DDL and similar proteins. DDL, also called protein DAWDLE, is involved in microRNA (miRNA) and short interfering RNA (siRNA) biogenesis. It may facilitate DCL1 to access or recognize primary miRNAs. DDL binds RNA non-specifically. The FHA domain is a small phosphopeptide recognition module. 130 matched cddid_all.tbl CDD cd22720 cd22720 438772 FHA_GarA-like forkhead associated (FHA) domain found in Mycobacterium tuberculosis glycogen accumulation regulator GarA and similar proteins. GarA is an FHA domain-containing protein involved in the regulation of glutamate metabolism. It acts as a phosphorylation-dependent ON/OFF molecular switch that modulates the activities of KGD, GDH and GltB. Its FHA domain has dual specificity. It binds to both phosphorylated upstream partners, such as the kinases PknB and PknG, and nonphosphorylated downstream partners, such as the 2-oxoglutarate decarboxylase KGD. The FHA domain is a small phosphopeptide recognition module. 100 matched cddid_all.tbl CDD cd22721 cd22721 438773 FHA_OdhI-like forkhead associated (FHA) domain found in Corynebacterium glutamicum oxoglutarate dehydrogenase inhibitor (OdhI) and similar proteins. OdhI is an essential component of the PknG signaling pathway. It regulates glutamate production under biotin non-limiting conditions. It can inhibit the activity of 2-oxoglutarate dehydrogenase only when it is unphosphorylated. The FHA domain is a small phosphopeptide recognition module. 102 matched cddid_all.tbl CDD cd22722 cd22722 438774 FHA_FOXK1 forkhead associated (FHA) domain found in forkhead box protein K1 (FOXK1) and similar proteins. FOXK1, also called myocyte nuclear factor (MNF), acts as a transcriptional regulator that binds to the upstream enhancer region (CCAC box) of the myoglobin gene. It positively regulates Wnt/beta-catenin signaling by translocating DVL into the nucleus. It also reduces virus replication, probably by binding the interferon stimulated response element (ISRE) to promote antiviral gene expression. In addition, FOXK1 plays important roles in multiple human cancers. The FHA domain is a small phosphopeptide recognition module. 103 matched cddid_all.tbl CDD cd22723 cd22723 438775 FHA_FOXK2 forkhead associated (FHA) domain found in forkhead box protein K2 (FOXK2) and similar proteins. FOXK2, also called cellular transcription factor ILF-1, or interleukin enhancer-binding factor 1, is a transcriptional regulator that recognizes the core sequence 5'-TAAACA-3'. It binds to NFAT-like motifs (purine-rich) in the IL2 promoter. It also binds to HIV-1 long terminal repeat. FOXK2 may be involved in both positive and negative regulation of important viral and cellular promoter elements. In addition, FOXK2 plays a critical role in suppressing tumorigenesis. The FHA domain is a small phosphopeptide recognition module. 111 matched cddid_all.tbl CDD cd22724 cd22724 438776 FHA_Cep170A forkhead associated (FHA) domain found in centrosomal protein of 170 kDa (Cep170) and similar proteins. Cep170, also called Cep170A, KARP-1-binding protein, or KARP1-binding protein, is a protein that localizes to centrosomes as well as spindle microtubules and plays a role in microtubule organization and microtubule assembly. It is required for centriole subdistal appendage assembly. Cep170 is phosphorylated during M phase and interacts with Polo-like kinase 1 (Plk1). The FHA domain is a small phosphopeptide recognition module. 106 matched cddid_all.tbl CDD cd22725 cd22725 438777 FHA_Cep170B forkhead associated (FHA) domain found in centrosomal protein of 170 kDa protein B (Cep170B) and similar proteins. Cep170B, also called centrosomal protein 170B, plays a role in microtubule organization. The FHA domain is a small phosphopeptide recognition module. 106 matched cddid_all.tbl CDD cd22726 cd22726 438778 FHA_KIF1A forkhead associated (FHA) domain found in kinesin-like protein KIF1A. KIF1A, also called axonal transporter of synaptic vesicles (ATSV), microtubule-based motor KIF1A, Unc-104- and KIF1A-related protein, or Unc-104, is an axonal transporter of synaptic vesicles, which is mutated in hereditary sensory and autonomic neuropathy type 2. It is also required for neuronal dense core vesicle (DCV) transport to dendritic spines and axons. The calcium-dependent interaction with CALM1 increases vesicle motility, and interaction with the scaffolding proteins PPFIA2 and TANC2 recruits DCVs to synaptic sites. The FHA domain is a small phosphopeptide recognition module, but this group may lack the conserved residues that are required for binding phosphothreonine. 115 matched cddid_all.tbl CDD cd22727 cd22727 438779 FHA_KIF1B forkhead associated (FHA) domain found in kinesin-like protein KIF1B. KIF1B, also called Klp, is a motor for anterograde transport of mitochondria. It has a microtubule plus end-directed motility. Isoform 1 mediates the transport of synaptic vesicles in neuronal cells, while isoform 2 is required for induction of neuronal apoptosis. The FHA domain is a small phosphopeptide recognition module, but this group may lack the conserved residues that are required for binding phosphothreonine. 110 matched cddid_all.tbl CDD cd22728 cd22728 438780 FHA_KIF1C forkhead associated (FHA) domain found in kinesin-like protein KIF1C. KIF1C is a new kinesin-like protein involved in vesicle transport from the Golgi apparatus to the endoplasmic reticulum. It has a microtubule plus end-directed motility. The FHA domain is a small phosphopeptide recognition module, but this group may lack the conserved residues that are required for binding phosphothreonine. 102 matched cddid_all.tbl CDD cd22729 cd22729 438781 FHA_KIF13A forkhead associated (FHA) domain found in kinesin-like protein KIF13A. KIF13A, also called kinesin-like protein RBKIN, is a plus end-directed microtubule-dependent motor protein involved in intracellular transport and in regulating various processes such as mannose-6-phosphate receptor (M6PR) transport to the plasma membrane, endosomal sorting during melanosome biogenesis, and cytokinesis. It mediates the transport of M6PR-containing vesicles from trans-Golgi network to the plasma membrane via direct interaction with the AP-1 complex. During melanosome maturation, KIF13A is required for delivering melanogenic enzymes from recycling endosomes to nascent melanosomes by creating peripheral recycling endosomal subdomains in melanocytes. It is also required for the abscission step in cytokinesis: it mediates translocation of ZFYVE26, and possibly TTC19, to the midbody during cytokinesis. The FHA domain is a small phosphopeptide recognition module, but this group may lack the conserved residues that are required for binding phosphothreonine. 109 matched cddid_all.tbl CDD cd22730 cd22730 438782 FHA_KIF13B forkhead associated (FHA) domain found in kinesin-like protein KIF13B. KIF13B, also called kinesin-like protein GAKIN, is a novel kinesin-like protein that associates with the human homolog of the Drosophila discs large tumor suppressor in T lymphocytes. It is involved in reorganization of the cortical cytoskeleton. It regulates axon formation by promoting the formation of extra axons. KIF13B may be functionally important for the intracellular trafficking of membrane-associated guanylate kinase homologs (MAGUKs) and associated protein complexes. The FHA domain is a small phosphopeptide recognition module, but this group may lack the conserved residues that are required for binding phosphothreonine. 99 matched cddid_all.tbl CDD cd22731 cd22731 438783 FHA_KIF16A_STARD9 forkhead associated (FHA) domain found in StAR-related lipid transfer protein 9 (StARD9). StARD9, also called START domain-containing protein 9, or kinesin-like protein KIF16A, is a microtubule-dependent motor protein required for spindle pole assembly during mitosis. It is required to stabilize the pericentriolar material (PCM). The FHA domain is a small phosphopeptide recognition module, but this group may lack the conserved residues that are required for binding phosphothreonine. 119 matched cddid_all.tbl CDD cd22732 cd22732 438784 FHA_KIF16B forkhead associated (FHA) domain found in kinesin-like protein KIF16B. KIF16B, also called sorting nexin-23, is a plus end-directed microtubule-dependent motor protein involved in endosome transport and receptor recycling and degradation. It regulates the plus end motility of early endosomes and the balance between recycling and degradation of receptors such as EGF receptor (EGFR) and FGF receptor (FGFR). It regulates the Golgi to endosome transport of FGFR-containing vesicles during early development, a key process for developing basement membrane and epiblast and primitive endoderm lineages during early postimplantation development. The FHA domain is a small phosphopeptide recognition module, but this group may lack the conserved residues that are required for binding phosphothreonine. 117 matched cddid_all.tbl CDD cd22733 cd22733 438785 FHA_RADIL forkhead associated (FHA) domain found in Ras-associating and dilute domain-containing protein (Radil). Radil acts as an important small GTPase Rap1 effector required for cell spreading and migration. It regulates neutrophil adhesion and motility through linking Rap1 to beta2-integrin activation. It contains an FHA domain. The FHA domain is a small phosphopeptide recognition module, but this group may lack the conserved residues that are required for binding phosphothreonine. 113 matched cddid_all.tbl CDD cd22734 cd22734 438786 FHA_RAIN forkhead associated (FHA) domain found in Ras-interacting protein 1 (Rain). Rain, also called Rasip1, is an endothelial-specific Ras-interacting protein required for the proper formation of vascular structures that develop via both vasculogenesis and angiogenesis. It acts as a critical and vascular-specific regulator of GTPase signaling, cell architecture, and adhesion, which is essential for endothelial cell morphogenesis and blood vessel tubulogenesis. Rain interacts with Ras in a GTP-dependent manner and may serve as an effector for endomembrane-associated Ras. It contains an FHA domain. The FHA domain is a small phosphopeptide recognition module, but this group may lack the conserved residues that are required for binding phosphothreonine. 119 matched cddid_all.tbl CDD cd22735 cd22735 438787 FHA_APTX forkhead associated (FHA) domain found in aprataxin and similar proteins. Aprataxin (EC 3.6.1.71/EC 3.6.1.72), also called forkhead-associated domain histidine triad-like protein (FHA-HIT), is a DNA-binding protein involved in single-strand DNA break repair, double-strand DNA break repair, and base excision repair. It catalyzes the release of adenylate groups covalently linked to 5'-phosphate termini, resulting in the production of 5'-phosphate termini that can be efficiently rejoined. It can also hydrolyze adenosine 5'-monophosphoramidate (AMP-NH(2)) and diadenosine tetraphosphate (AppppA), but with lower catalytic activity. Likewise, it catalyzes the release of 3'-linked guanosine (DNAppG) and inosine (DNAppI) from DNA but has higher specific activity with 5'-linked adenosine (AppDNA). Mutations in the gene APTX have been associated with ataxia-ocular apraxia. Aprataxin contains an FHA domain at its N-terminus. The FHA domain is a small phosphopeptide recognition module. 100 matched cddid_all.tbl CDD cd22736 cd22736 438788 FHA_PNKP forkhead associated (FHA) domain found in bifunctional polynucleotide phosphatase/kinase (PNKP) and similar proteins. PNKP (EC 3.1.3.32/EC 2.7.1.78), also called DNA 5'-kinase/3'-phosphatase, or polynucleotide kinase-3'-phosphatase, plays a key role in the repair of DNA damage, functioning as part of both the non-homologous end-joining (NHEJ) and base excision repair (BER) pathways. Through its two catalytic activities, PNKP ensures that DNA termini are compatible with extension and ligation by either removing 3'-phosphates from, or by phosphorylating 5'-hydroxyl groups on, the ribose sugar of the DNA backbone. PNKP contains an FHA domain at its N-terminus. The FHA domain is a small phosphopeptide recognition module. 99 matched cddid_all.tbl CDD cd22737 cd22737 439356 FHA_Rv1747-like_rpt2 second forkhead associated (FHA) domain found in Mycobacterium tuberculosis ABC transporter ATP-binding/permease protein Rv1747 and similar proteins. Rv1747 is a putative ATP-binding cassette (ABC) transporter involved in the translocation of an unknown substrate across the membrane. It is required for normal virulent infection by M. tuberculosis. Rv1747 has a cytoplasmic regulatory module consisting of two pThr-interacting forkhead-associated (FHA) domains connected by a conformationally disordered linker with two phospho-acceptor threonines (pThr). Recruitment and phosphorylation of Rv1747 depend on the interaction between its two non-redundant FHA domains and the autophosphorylated form of serine/threonine protein kinase PknF. This model corresponds to the second FHA domain, which has a circularly permuted FHA domain fold with a conserved pThr-binding interface. 93 matched cddid_all.tbl CDD cd22738 cd22738 439305 KP6_alpha_beta KP6 killer toxin subunit alpha/beta family. KP6 is an anti-fungal protein produced by a double-stranded RNA virus. It is a neutral protein that is lethal to sensitive cells of the same or related species. KP6 is composed of two subunits: KP6alpha and KP6beta, which are produced after cleavage from a single precursor preprotoxin. The KP6alpha subunit is responsible for targeting while the KP6beta subunit is cytotoxic. KP6alpha can recognize some cellular receptors before interaction of the complex with KP6beta, precipitating cell death. Neither subunit is homologous in either sequence or structure to any other known cytotoxic protein, however, they have similar structures to each other. The major difference between the two subunits is that KP6alpha contains a hydrophobic helix at the N-terminus, which plays a key role in target recognition. 65 matched cddid_all.tbl CDD cd22740 cd22740 439281 Complexin_NTD N-terminal SNARE complex binding domain of the complexin family of SNARE regulators. Complexins (CPXs) are small, cytosolic proteins that bind to the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex to regulate synaptic vesicle exocytosis. There are four CPX isoforms: complexin I/synaphin-2, complexin II/synaphin-1, complexin III and complexin IV. CPXs I and II are highly homologous hydrophilic proteins that are enriched in neurons where they colocalize with syntaxin and SNAP25. They regulate the sequential interactions of alpha-SNAP and synaptotagmins with the SNAP receptor during exocytosis. CPXs III and IV are the only CPX isoforms present in retinal ribbon synapses. In addition, CPXs III and IV carry an extension with a functional CAAX-box farnesylation site that is absent in CPXs I and II. Their C-terminal farnesylation regulates their synaptic targeting and modulatory function in transmitter release. They may contribute to the unique release efficacy of retinal sensory neurons. CPXs III and IV can functionally replace CPXs I and II. Most of the invertebrate CPXs are more similar to CPXs I and II than to CPXs III and IV. This model corresponds to the N-terminal region of CPX that is responsible for SNARE complex binding. 41 matched cddid_all.tbl CDD cd22741 cd22741 439357 CART_CTD-like C-terminal domain of cocaine-and amphetamine-regulated transcript protein (CART) and similar proteins. Cocaine and amphetamine regulated transcript (CART) protein is a satiety factor closely associated with the actions of leptin and neuropeptide Y. It is an anorectic peptide that inhibits both normal and starvation-induced feeding and completely blocks the feeding response induced by neuropeptide Y. It is regulated by leptin in the hypothalamus. CART has been shown to promote neuronal development and survival in vitro. This model corresponds to the C-terminal domain (CTD) of CART, which belongs to the fold-family of small globular knottins. The CTD, containing the three disulfide bridges, is the biologically active part of the molecule affecting food intake. 41 matched cddid_all.tbl CDD cd22742 cd22742 439358 BUBL-like Bubble protein family. This family includes Penicillium brevicompactum bubble protein and similar proteins. Bubble protein (BP) is a small cysteine-rich protein that is a member of the growing class of defensins, and may act as a toxin. Studies show that P. brevicompactum BP inhibits growth of the yeast Saccharomyces cerevisiae in a dose-dependent manner, thus exhibiting anti-fungal effects. BP may recognize a molecule or part of a molecule with a negatively charged surface potential. It is a globular all-beta protein with a disulfide-bound Knottins fold, which contains a beta-hairpin with two adjacent disulfides. 64 matched cddid_all.tbl CDD cd22743 cd22743 439359 stomagen-like stomagen domain family. Stomagen, also called EPIDERMAL PATTERNING FACTOR-like protein 9 (EPFL9 or STOMAGEN), or EPF-like protein 9, is plant peptide hormone expressed in the mesophyll, that acts as a positive regulator of stomatal density and patterning. It competes with EPIDERMAL PATTERNING FACTORS 2 (EPF2) for binding to the ERECTA receptor, while it also competes with EPF1 and EPF2 for binding to TOO MANY MOUTHS (TMM), both receptors for the EPF peptides to initiate a signal cascade for stomatal development. EPFL9 cannot be cleaved by the protease CO2 RESPONSE SECRETED PROTEASE (CRSP). Stomagen is composed of a loop and a scaffold containing three disulphide bonds. It belongs to the fold-family of small globular knottins. 45 matched cddid_all.tbl CDD cd22744 cd22744 438581 OTU OTU (ovarian tumor) domain family. The OTU family of cysteine proteases use a conserved cysteine and histidine, and in most cases an aspartate, as the catalytic triad. OTU domains typically function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. 128 matched cddid_all.tbl CDD cd22745 cd22745 438582 OTU_OTU1 OTU (ovarian tumor) domain of ubiquitin thioesterase OTU1 and similar proteins. Ubiquitin thioesterase (EC 3.4.19.12) OTU1 is also called OTU domain-containing protein 1 in yeast, while human OTU1 is also called HIV-1-induced protease 7 (HIN7), DUBA-8, or OTU domain-containing protein 2 (OTUD2). OTU1 is a deubiquitinase (DUB) that catalyzes the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. OTU1 has been implicated in the ER-associated degradation (ERAD) pathway. In yeast, it counteracts the activity of Ufd2 by deubiquitinating Ufd2 substrates; Ufd2 is a E4 ubiquitin ligase that interacts with Cdc48, an AAA ATPase that plays a central role in the ERAD pathway by chaperoning proteins to the proteasome for destruction. OTU1 also functions as a substrate-processing factor of valosin-containing protein (VCP, the mammalian counterpart of yeast Cdc48) that is required for the retrotranslocation of the ERAD pathway. OTU1 has been shown to preferentially hydrolyze polyubiquitin chains with Lys48 linkages. It contains ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a C2H2-type zinc finger, and an OTU (ovarian tumor) domain. This model represents the OTU domain that interacts with ubiquitin and possesses catalytic activity. OTU1 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. This family also contains plant OTU1 and OTU2. 161 matched cddid_all.tbl CDD cd22746 cd22746 438583 OTU_plant_OTU3_4-like OTU (ovarian tumor) domain of deubiquitinating enzymes OTU3 and OTU4 from plants, and similar proteins. Deubiquitinating enzyme OTU3 (also called OTU domain-containing protein 3) and deubiquitinating enzyme OTU4 (also called OTU domain-containing protein 4) are deubiquitinases (DUBs) or ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. OTU3 and OTU4 may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 141 matched cddid_all.tbl CDD cd22747 cd22747 438584 OTU_OTUD1 OTU (ovarian tumor) domain of OTU domain-containing protein 1 and similar proteins. OTU domain-containing protein 1 (OTUD1), also called DUBA-7 in humans, is a deubiquitinating enzyme/ubiquitinyl hydrolase (EC 3.4.19.12) that specifically hydrolyzes 'Lys-63'-linked polyubiquitin to monoubiquitin; this specificity is facilitated by the C-terminal Ub-interacting motif (UIM) of OTUD1. It interacts and promotes the deubiquitination of myeloid cell leukemia 1 (MCL1), a pro-survival Bcl-2 family protein that plays important roles in cell survival, proliferation, differentiation and tumorigenesis. OTUD1 also deubiquitinates IFN regulatory factor 3 (IRF3) and attenuates its function; IRF3 is critical for the transcription of type I IFNs in defensing virus and promoting inflammatory responses. Loss-of-function mutations of OTUD1 associated with multiple autoimmune diseases including systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), ulcerative colitis (UC) and Hashimoto's thyroiditis (HT). OTUD1 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 149 matched cddid_all.tbl CDD cd22748 cd22748 438585 OTU_OTUD6-like OTU (ovarian tumor) domain of OTU domain-containing proteins 6A, 6B, and similar proteins. This subfamily is composed of mammalian OTU domain-containing protein 6A (OTUD6A, also called DUBA-2, vertebrate OTU domain-containing protein 6B (OTUD6B, also called DUBA-5), fungal OTU domain-containing protein 2 (OTU2), and similar proteins. OTUD6A, OTUD6B, and Schizosaccharomyces pombe OTU2 are deubiquitinating enzymes/ubiquitinyl hydrolases (EC 3.4.19.12). OTUD6A hydrolyzes 'Lys-27'-, 'Lys-29'-, and 'Lys-33'-linked polyubiquitin chains, and may also be able to hydrolyze 'Lys-11'-linked ubiquitin chains. It deubiquitylates and stabilizes dynamin-related protein 1 (Drp1), a cytosolic protein responsible for mitochondrial fission and is essential in the initiation and development of several human diseases including cancer, thereby facilitating tumorigenesis. OTUD6B is a functional deubiquitinase in in vitro enzyme assays. It may play a role in the ubiquitin-dependent regulation of protein synthesis downstream of mTORC1, and may modify the ubiquitination of the protein synthesis initiation complex to repress translation. Biallelic variants in OTUD6B cause an intellectual disability syndrome that is associated with seizures and dysmorphic features. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 144 matched cddid_all.tbl CDD cd22749 cd22749 438586 Otubain_C65 Otubain subfamily of ubiquitin thioesterases. The otubain subfamily is composed of otubain-1 (also called ubiquitin thioesterase OTUB1 or OTU domain-containing ubiquitin aldehyde-binding protein 1), otubain-2 (also called ubiquitin thioesterase OTUB2 or OTU domain-containing ubiquitin aldehyde-binding protein 2), and similar proteins. They function as deubiquitylases (DUBs)/ubiquitin thioesterases (EC 3.4.19.12). OTUB1 can specifically remove 'Lys-48'-linked conjugated ubiquitin from protein substrates, while OTUB2 mediates the deubiquitination of 'Lys-11'-,'Lys-48'- and 'Lys-63'-linked polyubiquitin chains, with a preference for 'Lys-63'-linked polyubiquitin chains. The otubain subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. Members of this subfamily are classified as family C65 cysteine proteases by MEROPS. 232 matched cddid_all.tbl CDD cd22750 cd22750 438587 OTU_C64 OTU (ovarian tumor) domain of family C64 cysteine proteases. This group includes proteins classified as family C64 cysteine protease by MEROPS, such as tumor necrosis factor (TNF) alpha-induced protein 3 (TNFAIP3), ZRANB1, OTU domain-containing protein 7A (OTUD7A), and OTUD7B. It also includes VCIP135. These proteins are deubiquitinases (DUBs)/ubiquitin thioesterases (EC 3.4.19.12) that mediates the deubiquitination of protein substrates. TNFAIP3 also contains ubiquitin ligase activity. It antagonizes IKK [IkappaB (inhibitor of kappaB) kinase] activation by modulating Lys63-linked polyubiquitination of cytokine-receptor-associated factors including TRAF2/6 (tumour-necrosis-factor-receptor-associated factor 2/6) and RIP1 (receptor-interacting protein 1). ZRANB1 binds, deubiquitinates, and stabilizes EZH2, which is the catalytic component of the Polycomb repressive complex 2 (PRC2) that silences gene transcription by methylating histone H3 at lysine 27 and is mutated or highly expressed in many types of cancer, including lymphoma, melanoma, prostate cancer, ovarian cancer, and breast cancer. OTUD7A has been identified as a critical gene for brain function, while OTUD7B functions as a negative regulator of the non-canonical NF-kappaB pathway by mediating the deubiquitination of TRAF3, an inhibitor of the NF-kappaB pathway, resulting in preventing TRAF3 proteolysis and over-activation of non-canonical NF-kappaB. VCIP135 controls Golgi membrane dynamics in the cell cycle and is required for Golgi and ER assembly. This group belongs to the OTU family of cysteine proteases that use a conserved cysteine and histidine, and in most cases an aspartate, as the catalytic triad. 185 matched cddid_all.tbl CDD cd22751 cd22751 438588 OTU_plant_OTU9-like OTU (ovarian tumor) domain of plant deubiquitinating enzyme OTU9 and similar proteins. This subfamily contains Arabidopsis thaliana deubiquitinating enzymes OTU8, OTU9, OTU10, OTU11, and OTU12, and similar proteins from plants and other eukaryotes. OTU8-OTU12 are deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 134 matched cddid_all.tbl CDD cd22752 cd22752 438589 OTU_OTUD5-like OTU (ovarian tumor) domain of OTU domain-containing protein 5 and similar proteins. OTU domain-containing protein 5 (OTUD5), also called deubiquitinating enzyme A (DUBA), is a phosphorylation-dependent deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that can hydrolyze 'Lys-48'- and 'Lys-63'-linked polyubiquitin chains, and may function as negative regulator of the innate immune system. It limits type I interferon production in macrophages and suppresses interleukin-17A production in T cells. OTUD5 also functions in an apoptotic signaling cascade by mediating the sequential activation of PDCD5 (programmed cell death 5) and p53 in response to genotoxic stress. In Drosophila, OTUD5/DUBA is essential for spermatogenesis. This subfamily also includes Arabidopsis thaliana OTU domain-containing protein 6, also called deubiquitinating enzyme OTU6 or otubain-like deubiquitinase 1 (OTLD1), which binds chromatin and has enzymatic histone deubiquitinase activity specific for the H2B histone. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. It also includes plant OTU6. 124 matched cddid_all.tbl CDD cd22753 cd22753 438590 OTU_ALG13-like OTU (ovarian tumor) domain of bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13 and similar proteins. Bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13 is alco called asparagine-linked glycosylation 13 homolog, glycosyltransferase 28 domain-containing protein 1 (GLT28D1), or UDP-N-acetylglucosamine transferase subunit ALG13 homolog. It displays both glycosyltransferase (EC 2.4.1.141) and deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) activities. With ALG14, it forms a UDP-N-acetylglucosamine transferase that catalyzes the second step of eukaryotic N-linked glycosylation in the endoplasmic reticulum. ALG13 variants cause a form of early infantile epileptic encephalopathy known as EIEE36 refractory seizures, neurodevelopmental impairment, and poor prognosis; given the essential role of ALG13 in glycosylation, it is also considered a congenital disorder of glycosylation (CDG). This subfamily also contains OTU domain-containing protein 4 (OTUD4), also called HIV-1-induced protein HIN-1, a DUB that specifically deubiquitinates 'Lys-63'-polyubiquitinated MYD88 adapter protein upon phosphorylation, triggering down-regulation of NF-kappa-B-dependent transcription of inflammatory mediators. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 130 matched cddid_all.tbl CDD cd22754 cd22754 438591 OTU_wMelOTU-like OTU (ovarian tumor) domain of Wolbachia pipientis OTU deubiquitinase wMelOTU and similar proteins. Bacterial OTU deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12), such as Wolbachia pipientis wMelOTU, play a role in the manipulation of host ubiquitin signaling, an evolutionary strategy employed by bacterial and viral pathogens. By removing host ubiquitin signals, invading pathogens can inactivate immune response pathways and evade detection. DUBs catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. wMelOTU belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 165 matched cddid_all.tbl CDD cd22755 cd22755 438592 OTU_CeDUB-like OTU (ovarian tumor) domain of Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and OTU domains, and similar proteins. This subfamily is composed of mostly uncharacterized proteins containing an OTU domain, similar to Caenorhabditis elegans deubiquitylating enzyme with USP/UBP and OTU domains. OTU domain-containing proteins function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 132 matched cddid_all.tbl CDD cd22756 cd22756 438593 OTU_OTUD3-like OTU (ovarian tumor) domain of OTU domain-containing protein 3 and similar proteins. This subfamily includes bilaterial OTU domain-containing protein 3 (OTUD3), Arabidopsis thaliana deubiquitinating enzyme OTU7, also called OTU domain-containing protein 7, and similar proteins. OTUD3 is a deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that hydrolyzes 'Lys-6'- and 'Lys-11'-linked polyubiquitin. It is an acetylation-dependent deubiquitinase that restricts innate antiviral immune signaling. It directly hydrolyzes lysine 63 (Lys63)-linked polyubiquitination of MAVS (mitochondrial antiviral-signaling protein) and shuts off innate antiviral immune response. OTUD3 can elicit tumor-suppressing or tumor-promoting activities in a cell- and tissue-dependent manner. It is a DUB for PTEN (phosphatase and tension homologue deleted on chromosome 10); the OTUD3-PTEN signaling axis plays a critical role in suppression of breast tumorigenesis. OTUD3 is also a DUB for glucose-regulated protein GRP78, stabilizing it and promoting lung tumorigenesis. OTU7 is a DUB that shows a preference for 'Lys-63' over 'Lys-48' over 'Met-1'-linked ubiquitin (UB) tetramers as substrates. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 131 matched cddid_all.tbl CDD cd22757 cd22757 438594 OTU_P87_VP80-like OTU (ovarian tumor) domain of nucleopolyhedrovirus P87/VP80 protein and similar proteins. The VP80 protein is a capsid-associated structural protein that was first identified as P87 in Orgyia pseudotsugata multicapsid nuclear polyhedrosis virus (OpMNPV); its homologs are found only in NPV genomes. The Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) VP80 protein is essential for the formation of both budded virus (BV) and occlusion-derived virus (ODV). It has also been shown to interact with the virus-triggered, nuclear F-actin cytoskeleton. P87/VP80 contains an N-terminal OTU domain. OTU domains typically function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 128 matched cddid_all.tbl CDD cd22758 cd22758 438595 OTU_232R-like OTU (ovarian tumor) domain of Invertebrate iridescent virus putative ubiquitin thioesterase 232R and similar proteins. This subfamily contains putative ubiquitin thioesterases 232R from Invertebrate iridescent virus and L96 from Tipula iridescent virus (TIV), Dictyostelium discoideum OTU domain-containing protein DDB_G0284757, and similar proteins. L96 may be involved in TIV genomic DNA packaging in a manner related to the Gag polyproteins of the mammalian viruses. Proteins in this subfamily contain an OTU domain. OTU domains typically function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. They belong to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 135 matched cddid_all.tbl CDD cd22759 cd22759 438596 OTU_plant_OTU3-like OTU (ovarian tumor) domain of deubiquitinating enzyme OTU3 from plants and similar proteins. Deubiquitinating enzyme OTU3, also called OTU domain-containing protein 3, is a deubiquitinase (DUB) or ubiquitin thiolesterase (EC 3.4.19.12) that catalyzes the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. OTU3 may play an important regulatory role at the level of protein turnover by preventing degradation. OTU3 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 159 matched cddid_all.tbl CDD cd22760 cd22760 438597 OTU_plant_OTU4-like OTU (ovarian tumor) domain of deubiquitinating enzyme OTU4 from plants and similar proteins. Deubiquitinating enzyme OTU4, also called OTU domain-containing protein 4, is a deubiquitinase (DUB) or ubiquitin thiolesterase (EC 3.4.19.12) that catalyzes the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. OTU4 may play an important regulatory role at the level of protein turnover by preventing degradation. OTU4 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 138 matched cddid_all.tbl CDD cd22761 cd22761 438598 OTU_OTUD6 OTU (ovarian tumor) domain of OTU domain-containing proteins 6A and 6B and similar proteins. This subfamily is composed of mammalian OTU domain-containing protein 6A (OTUD6A, also called DUBA-2) and vertebrate OTU domain-containing protein 6B (OTUD6B, also called DUBA-5), which are deubiquitinating enzymes/ubiquitinyl hydrolases (EC 3.4.19.12). OTUD6A hydrolyzes 'Lys-27'-, 'Lys-29'-, and 'Lys-33'-linked polyubiquitin chains, and may also be able to hydrolyze 'Lys-11'-linked ubiquitin chains. It deubiquitylates and stabilizes dynamin-related protein 1 (Drp1), a cytosolic protein responsible for mitochondrial fission and is essential in the initiation and development of several human diseases including cancer, thereby facilitating tumorigenesis. OTUD6B is a functional deubiquitinase in in vitro enzyme assays. It may play a role in the ubiquitin-dependent regulation of protein synthesis downstream of mTORC1, and may modify the ubiquitination of the protein synthesis initiation complex to repress translation. Biallelic variants in OTUD6B cause an intellectual disability syndrome that is associated with seizures and dysmorphic features. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 146 matched cddid_all.tbl CDD cd22762 cd22762 438599 OTU_fungi_OTU2-like OTU (ovarian tumor) domain of fungal OTU domain-containing protein 2 and similar proteins. This subfamily includes Schizosaccharomyces pombe and Saccharomyces cerevisiae OTU domain-containing protein 2 (OTU2) and similar proteins. S. pombe OTU2 is a ubiquitin thioesterase/hydrolase (EC 3.4.19.12) that can remove conjugated ubiquitin from protein substrates and may therefore play an important regulatory role at the level of protein turnover by preventing degradation. Fungal OTU2 bbelongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 142 matched cddid_all.tbl CDD cd22763 cd22763 438600 OTUB1 Ubiquitin Thioesterase Otubain-1. Otubain-1 is also called ubiquitin thioesterase OTUB1, deubiquitinating enzyme OTUB1, OTU domain-containing ubiquitin aldehyde-binding protein 1, or ubiquitin-specific-processing protease OTUB1. It is a deubiquitylase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that can specifically remove 'Lys-48'-linked conjugated ubiquitin from protein substrates. It is also capable of cleaving NEDD8 (neural-precursor-cell-expressed developmentally down-regulated 8), but not SUMO (small ubiquitin-related modifier) 1/2/3 and ISG15 (interferon-stimulated gene 15) conjugates. In addition, OTUB1 inhibits the DNA damage response independently of its catalytic activity by blocking ubiquitin transfer onto protein substrates via sequestration of E2 ubiquitin-conjugating enzymes. It also regulates many cancer-associated signaling pathways including MAPK, ERa, epithelial-mesenchymal transition (EMT), RHOa, mTORC1, FOXM1 and P53 to promote tumor cell survival, proliferation, invasiveness and therapeutic resistance. OTUB1 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. It is classified as a family C65 cysteine protease by MEROPS. 224 matched cddid_all.tbl CDD cd22764 cd22764 438601 OTUB2 Ubiquitin Thioesterase Otubain-2. Otubain-2 is also called ubiquitin thioesterase OTUB2, deubiquitinating enzyme OTUB2, OTU domain-containing ubiquitin aldehyde-binding protein 2, or ubiquitin-specific-processing protease OTUB2. It is a deubiquitylase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that mediates the deubiquitination of 'Lys-11'-,'Lys-48'- and 'Lys-63'-linked polyubiquitin chains, with a preference for 'Lys-63'-linked polyubiquitin chains. OTUB2 plays a role in DNA double-strand break (DSB) response (DDR); it enhances RNF8-mediated ubiquitination in an early phase of the DDR and promotes faster DSB repair but suppresses homologous recombination. It also functions as a cancer stemness and metastasis-promoting factor that deubiquitinates and activates the transcriptional regulators YAP/TAZ, which play important roles in development, physiology, and tumorigenesis and are negatively controlled by the Hippo pathway. OTUB2 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. It is classified as a family C65 cysteine protease by MEROPS. 222 matched cddid_all.tbl CDD cd22765 cd22765 438602 AtOTU1-like Arabidopsis thaliana Deubiquitinating enzyme OTU1 and similar plant proteins. This group contains plant otibain-like proteins including Oryza sativa Japonica group otubain-like deubiquitinase and Arabidopsis thaliana deubiquitinating enzyme OTU1 (AtOTU1), also called OVARIAN TUMOR DOMAIN-containing deubiquitinating enzyme 1 or OTU domain-containing protein 1. It is a deubiquitylase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that mediates the deubiquitination of protein substrates and may therefore play an important regulatory role at the level of protein turnover by preventing degradation. AtOTU1 shows a preference for Met-1 and 'Lys-48' over 'Lys-63'-linked ubiquitin tetramers as substrates. It belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. It is classified as a family C65 cysteine protease by MEROPS. 247 matched cddid_all.tbl CDD cd22766 cd22766 438603 OTU_TNFAIP3 OTU (ovarian tumor) domain of tumor necrosis factor alpha induced protein 3. Tumor necrosis factor (TNF) alpha-induced protein 3 (TNFAIP3) is also called OTU domain-containing protein 7C (OTUD7C), DNA-binding protein A20, or zinc finger protein A20. It is a ubiquitin-editing enzyme that contains both ubiquitin ligase and deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) activities. It antagonizes IKK [IkappaB (inhibitor of kappaB) kinase] activation by modulating Lys63-linked polyubiquitination of cytokine-receptor-associated factors including TRAF2/6 (tumour-necrosis-factor-receptor-associated factor 2/6) and RIP1 (receptor-interacting protein 1). It can also inhibit IKK through a non-catalytic mechanism which involves polyubiquitin. In vitro, TNFAIP3 is able to deubiquitinate 'Lys-11'-, 'Lys-48'- and 'Lys-63' polyubiquitin chains. TNFAIP3 contains several A20-type zinc fingers that mediate the ubiquitin ligase activity and an OTU (ovarian tumor) domain that contains the DUB activity. It belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. It is classified as a family C64 cysteine protease by MEROPS. 220 matched cddid_all.tbl CDD cd22767 cd22767 438604 OTU_ZRANB1 OTU (ovarian tumor) domain of Ubiquitin thioesterase ZRANB1 and similar proteins. ZRANB1 is also called TRAF-binding domain-containing protein, Trabid, or zinc finger Ran-binding domain-containing protein 1. It is a deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that specifically hydrolyzes 'Lys-29'-linked and 'Lys-33'-linked diubiquitin; it also cleaves 'Lys-63'-linked chains with less efficiency. ZRANB1 binds, deubiquitinates, and stabilizes EZH2, which is the catalytic component of the Polycomb repressive complex 2 (PRC2) that silences gene transcription by methylating histone H3 at lysine 27 and is mutated or highly expressed in many types of cancer, including lymphoma, melanoma, prostate cancer, ovarian cancer, and breast cancer. Drosophila Trabid interacts with TGF-beta Activating Kinase 1 (TAK1), which triggers both immunity and apoptosis, resulting in reduced immune signaling output and K63-linked ubiquitination. ZRANB1 belongs to the OTU family of cysteine proteases that use a conserved cysteine and histidine, and in most cases an aspartate, as the catalytic triad. ZRANB1 does not contain the conserved aspartate, and uses cysteine and histidine as a catalytic dyad. It is classified as a family C64 cysteine protease by MEROPS. 185 matched cddid_all.tbl CDD cd22768 cd22768 438605 OTU_OTUD7 OTU (ovarian tumor) domain of OTU domain-containing proteins 7A, 7B, and similar proteins. This subfamily consists of OTU domain-containing protein 7A (OTUD7A), OTUD7B, and similar proteins. OTUD7A and OTUD7B are deubiquitinases (DUBs)/ubiquitin thioesterases (EC 3.4.19.12) that specifically target Lys11-linked polyubiquitin. OTUD7A, also called zinc finger protein Cezanne 2, has been identified as a critical gene for brain function. It localizes to dendritic and spine compartments in cortical neurons, and its reduced levels contributed to dendritic spine and dendrite outgrowth deficits. OTUD7B, also called zinc finger protein Cezanne, functions as a negative regulator of the non-canonical NF-kappaB pathway by mediating the deubiquitination of TRAF3, an inhibitor of the NF-kappaB pathway, resulting in preventing TRAF3 proteolysis and over-activation of non-canonical NF-kappaB. OTUD7 proteins belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. They are classified as family C64 cysteine proteases by MEROPS. 208 matched cddid_all.tbl CDD cd22769 cd22769 438606 OTU_VCIP135 OTU (ovarian tumor) domain of deubiquitinating protein VCIP135. Deubiquitinating protein VCIP135 is also called valosin-containing protein p97/p47 complex-interacting protein 1, valosin-containing protein p97/p47 complex-interacting protein p135, or VCP/p47 complex-interacting 135-kDa protein. It is a deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that hydrolyzes 'Lys-11'- and 'Lys-48'-linked polyubiquitin chains. It is necessary for VCP-mediated reassembly of Golgi stacks after mitosis, and may play a role in VCP-mediated formation of transitional endoplasmic reticulum (tER). VCIP135 controls Golgi membrane dynamics in the cell cycle and is required for Golgi and ER assembly. It belongs to the OTU family of cysteine proteases that use a conserved cysteine and histidine, and in most cases an aspartate, as the catalytic triad. Not all members of this subfamily contain the active site. It is closely related to proteins classified as family C64 cysteine protease by MEROPS, such as TNFAIP3, ZRANB1, and OTUD7A/B. 197 matched cddid_all.tbl CDD cd22770 cd22770 438607 OTU_OTUD3 OTU (ovarian tumor) domain of OTU domain-containing protein 3 and similar proteins. OTU domain-containing protein 3 (OTUD3) is a deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that hydrolyzes 'Lys-6'- and 'Lys-11'-linked polyubiquitin. It is an acetylation-dependent deubiquitinase that restricts innate antiviral immune signaling. It directly hydrolyzes lysine 63 (Lys63)-linked polyubiquitination of MAVS (mitochondrial antiviral-signaling protein) and shuts off innate antiviral immune response. OTUD3 can elicit tumor-suppressing or tumor-promoting activities in a cell- and tissue-dependent manner. It is a DUB for PTEN (phosphatase and tension homologue deleted on chromosome 10); the OTUD3-PTEN signaling axis plays a critical role in suppression of breast tumorigenesis. OTUD3 is also a DUB for glucose-regulated protein GRP78, stabilizing it and promoting lung tumorigenesis. It belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 145 matched cddid_all.tbl CDD cd22771 cd22771 438608 OTU_plant_OTU7-like OTU (ovarian tumor) domain of Arabidopsis thaliana deubiquitinating enzyme OTU7 and similar proteins. Arabidopsis thaliana deubiquitinating enzyme OTU7, also called OTU domain-containing protein 7, is a deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that shows a preference for 'Lys-63' over 'Lys-48' over 'Met-1'-linked ubiquitin (UB) tetramers as substrates. DUBs catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. OTU7 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 124 matched cddid_all.tbl CDD cd22772 cd22772 438609 OTU_OTUD7B OTU (ovarian tumor) domain of OTU domain-containing protein 7B. OTU domain-containing protein 7B (OTUD7B) is also called cellular zinc finger anti-NF-kappa-B protein, zinc finger A20 domain-containing protein 1, or zinc finger protein Cezanne. It is a deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that specifically targets Lys11-linked polyubiquitin. It functions as a negative regulator of the non-canonical NF-kappaB pathway by mediating the deubiquitination of TRAF3, an inhibitor of the NF-kappaB pathway, resulting in preventing TRAF3 proteolysis and over-activation of non-canonical NF-kappaB. OTUD7B also deubiquitinates ZAP70, and thus, regulates T cell receptor (TCR) signaling. It belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. It is classified as a family C64 cysteine protease by MEROPS. 207 matched cddid_all.tbl CDD cd22773 cd22773 438610 OTU_OTUD7A OTU (ovarian tumor) domain of OTU domain-containing protein 7A. OTU domain-containing protein 7A (OTUD7A), also called zinc finger protein Cezanne 2, is a deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that specifically targets Lys11-linked polyubiquitin. OTUD7A has been identified as a critical gene for brain function. It localizes to dendritic and spine compartments in cortical neurons, and its reduced levels contributed to dendritic spine and dendrite outgrowth deficits. A homozygous OTUD7A missense variant located within the OTU catalytic domain is linked to early-onset epileptic encephalopathy and proteasome dysfunction. OTUD7A belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. It is classified as a family C64 cysteine protease by MEROPS. 207 matched cddid_all.tbl CDD cd22777 cd22777 439259 DPBB_barwin-like "double-psi beta-barrel fold of the barwin family. This family represents a group of double-psi beta-barrel (DPBB) fold proteins similar to Barwin, including Wheatwin-1/-2, pathogenesis-related protein P2, and the C-terminal domains of Pro-hevein, Wound-induced proteins WIN1/WIN2, and hevein-like preproprotein. Barwin is a basic protein from barley seed. It is a probable plant lectin that may be involved in a defense mechanism. Barwin binds weakly to a chitin analog. Pro-hevein, also called major hevein, is a rubber tree N-acetyl-D-glucosamine/N-acetyl-D-neuraminic acid binding lectin that can inhibit fungal growth. WIN1 and WIN2 from potato are cysteine-rich proteins which show striking homology to several chitin-binding proteins. Wheatwin-1 and Wheatwin-2 from bread wheat are also called pathogenesis-related protein 4a and 4b, respectively. They show antifungal activity towards B. cinerea and towards the wheat-specific pathogenic fungi F. culmorum and F. graminearum (groups 1 and 2). Wheatwin-1 has ribonuclease activity. Pathogenesis-related protein P2 (also called PR protein P2) from tomato is homologous to WINs and pro-hevein, but lack the N-terminal, chitin-binding ""hevein"" domain. Hevein-like preproprotein (also called HEL protein) from Arabidopsis is a fungal growth inhibitor. Neither its N-terminal hevein-like domain (CB-HEL) nor the C-terminal domain (CD-HEL) have chitinase activity, but both have antimicrobial activities. CD-HEL has RNase, but no DNase activity." 119 matched cddid_all.tbl CDD cd22778 cd22778 439260 DPBB_CEPL-like double-psi beta-barrel fold of the cerato-platanin family. This family represents a group of double-psi beta-barrel (DPBB) fold proteins similar to cerato-platanin, including protein SnodProt1, heat-stable 19 kDa antigen, allergen Asp f 15/Asp f 13, and Epl1 protein. They are involved in plant pathogenesis and elicitation of plant defense responses. Cerato-platanin is a phytotoxin which causes production of phytoalexin in Platanus acerifolia, P. occidentalis, and P. orientalis. It also induces cell necrosis. Cerato-platanin behaves as a fungal toxin. Protein SnodProt1 is also a phytotoxic protein. Heat-stable 19 kDa antigen is a Coccidioides-specific antigen (CS antigen) with serine proteinase activity. Epl1 protein is an elicitor of plant defence responses from Trichoderma virens. 117 matched cddid_all.tbl CDD cd22784 cd22784 439261 DPBB_MltA_YuiC-like "double-psi beta-barrel fold of membrane-bound lytic murein transglycosylase A (MltA) and YuiC-like proteins. This family includes two subfamilies of conserved double-psi beta-barrel (DPBB) domain proteins, such as membrane-bound lytic murein transglycosylase A (MltA)-like proteins and YuiC-like proteins. MltA, also called murein hydrolase A, is a murein-degrading enzyme that may play a role in the recycling of muropeptides during cell elongation and/or cell division. It degrades murein glycan strands and insoluble, high-molecular weight murein sacculi. Bacterial lytic transglycosylases (LTs) are classified into 4 families: family 1 includes slt70 MltC-MltF, family 2 includes MltA, family 3 includes MltB, and family 4 includes proteins of bacteriophage origin. MltA is distinct from other bacterial LTs, which are similar in structure and sequence with a lysozyme-like fold. MltA is a kidney bean-shaped monomeric protein comprised of two domains separated by a large groove, where the peptidoglycan strand binds. Domain A is made up of an N-terminal and a C-terminal portion, which corresponds to a double-psi beta-barrel (DPBB) fold. Domain B also has a beta-barrel fold topology, but it is inserted within the linear sequence of domain A. YuiC is a Firmicute stationary phase survival (Sps) protein that closely resembles the Barwin-like endoglucanase beta barrel of MltA. It is a DPBB fold that consists of two interlocked ""psi-structure"" motifs related by a pseudo-2-fold axis and may be involved in substrate binding and catalysis." 92 matched cddid_all.tbl CDD cd22785 cd22785 439262 DPBB_MltA-like "double-psi beta-barrel fold of membrane-bound lytic murein transglycosylase A (MltA) and similar proteins. MltA, also called murein hydrolase A, is a murein-degrading enzyme that may play a role in the recycling of muropeptides during cell elongation and/or cell division. It degrades murein glycan strands and insoluble, high-molecular weight murein sacculi. Bacterial lytic transglycosylases (LTs) are classified into 4 families: family 1 includes slt70 MltC-MltF, family 2 includes MltA, family 3 includes MltB, and family 4 includes proteins of bacteriophage origin. MltA is distinct from other bacterial LTs, which are similar in structure and sequence with a lysozyme-like fold. MltA is a kidney bean-shaped monomeric protein comprised of two domains separated by a large groove, where the peptidoglycan strand binds. Domain A is made up of an N-terminal and a C-terminal portion, which corresponds to a double-psi beta-barrel (DPBB) fold. Domain B also has a beta-barrel fold topology, but it is inserted within the linear sequence of domain A. This model corresponds to the DPBB fold that consists of two interlocked ""psi-structure"" motifs related by a pseudo-2-fold axis. It is involved in substrate binding and catalysis." 97 matched cddid_all.tbl CDD cd22786 cd22786 439263 DPBB_YuiC-like "double-psi beta-barrel fold of YuiC subfamily proteins. The YuiC subfamily includes a group of conserved double-psi beta-barrel (DPBB) fold proteins, such as Bacillus subtilis protein YuiC, cell wall shaping protein YabE, cell wall-binding protein YocH, as well as Clostridium tetani phosphatase-associated protein PapQ. YuiC is a Firmicute stationary phase survival (Sps) protein that closely resembles the Barwin-like endoglucanase beta barrel of MltA. It is a double-psi beta-barrel (DPBB) fold that consists of two interlocked ""psi-structure"" motifs related by a pseudo-2-fold axis and may be involved in substrate binding and catalysis." 96 matched cddid_all.tbl CDD cd22787 cd22787 439326 AcrVA1 Anti-CRISPR type V subtype A1. AcrVA1 is an anti-CRISPR (Acr) protein that was discovered via STSS (self-targeting spacers search) with further functional TXTL (cell-free transcription-translation) assay. The bioinformatic STSS method finds self-targeting CRISPR spacers in genomic DNA, predicts the type of CRISPR system involved, and obtains information about the targeted sequence. AcrVA1 is a multiple-turnover inhibitor that triggers cleavage of the target recognition sequence of the Cas12a-bound guide RNA to irreversibly inactivate the Cas12a complex. Cas12a (Cpf1) is a class 2 effector protein for the AcrVA subfamily that has high efficiency in genome editing. It possesses a single nuclease domain (RuvC) that is activated upon binding of the crRNA targeting sequence (or spacer) to a complementary single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) target molecule. In addition to gene editing, CRISPR-Cas12a has repurposed, in high eukaryotes, to carry out transcription regulation via a nuclease-dead Cas12a (dCas12a), and AcrVAs have been adopted to regulate (d)Cas12a activity; AcrVA1 is able to inhibit two dCas12a proteins (denAsCas12a and dLbCas12a) in Saccharomyces cerevisiae. Type V systems fundamentally differ from type II by the domain architecture of their effector proteins. The type II effectors (Cas9) contain two nuclease domains that are each responsible for the cleavage of one strand of the target DNA, with the HNH nuclease inserted inside the RuvC-like nuclease domain sequence. By contrast, the type V effectors (Cas12) only contain a RuvC-like domain that cleaves both strands. Acr proteins have co-evolved with CRISPR-Cas proteins to provide bacteriophage with broad spectrum, or in some cases, highly selective protection from RNA-guided destruction. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Acr proteins are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 161 matched cddid_all.tbl CDD cd22788 cd22788 439360 BBK32_C C-terminal domain of Borrelia burgdorferi protein BBK32, and similar proteins. This model includes the C-terminal domain of protein BBK32, termed BBK32-C, from Borrelia burgdorferi, the Lyme disease causing spirochete. The lipoprotein BBK32 blocks the activation of the classical pathway of complement in the host by binding to and inhibiting the initiating serine protease of the human classical complement pathway, C1r. It does so via the C-terminal domain (BBK32-C), and thereby prevents both its autocatalytic and C1s cleavage activities within the C1 complex. Mutation and comparative studies with BBK32-C homologs in B. garinii (BGD19) and B. afzelii (BAD16) identified three surface-exposed residues that are important in their potential relevance in C1r binding and inhibition, thus providing new insight into complement evasion mechanisms of Lyme-associated spirochetes of B. burgdorferi. BBK32-C adopts an anti-parallel four-helix bundle fold with a fifth alpha-helix protruding from the helical core. 149 matched cddid_all.tbl CDD cd22789 cd22789 439361 BORCS5-like BLOC-1-related complex subunit 5, and related proteins. This model includes BLOC-1-related complex subunit 5 (BORCS5), which is also called loss of heterozygosity 12 chromosomal region 1 (LOH12CR1), myristoylated lysosomal protein, or myrlysin. BORCS5 is a component of BLOC-1 related complex (BORC), a multisubunit complex that also contains Lyspersin/C17orf59, Diaskedin/C10orf32, KxDL1, MEF2BNB, BLOS1, BLOS2, and Snapin subunits. BLOC-1 is important for the biogenesis of lysosome-related organelles, and BORC is important for the positioning of the lysosome in the cytoplasm. The BORC complex associates with the lysosomal membrane where it recruits the small GTPase Arl8, which leads in turn to the kinesin-dependent movement of lysosomes toward the plus ends of microtubules in the peripheral cytoplasm. LOH12CR1 may function as a tumor suppressor by inhibiting tumor growth through deregulation of the G1/S checkpoint in human colorectal carcinoma. It has been shown to bind to LKB1, a well-known tumor suppressor gene in colorectal cancer; its expression level could be used as a promising biomarker in patients. This domain has also been found in many hypothetical proteins involved in loss of heterozygosity and thus tumor suppression. 157 matched cddid_all.tbl CDD cd22790 cd22790 438611 OTU_OTUL-like OTU (ovarian tumor) domain of ubiquitin thioesterase otulin family. Otulin family includes otulin and otulinl. Otulin, also called FAM105B, deubiquitinating enzyme otulin, OTU domain-containing deubiquitinase with linear linkage specificity, or ubiquitin thioesterase Gumby, is a deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that specifically removes linear ('Met-1'-linked) polyubiquitin chains to substrates and acts as a regulator of angiogenesis and innate immune response. It acts as a key negative regulator of inflammation by restricting spontaneous inflammation and maintaining immune homeostasis. Otulinl, also called FAM105A, is an OTU-class pseudo-deubiquitinase with a disrupted catalytic triad and undetectable cleavage activity for any diubiquitin linkage. It may play a role in endoplasmic reticulum (ER)-organelle communication. Otulin and otulinl belong to the OTU family of cysteine proteases that use a conserved cysteine and histidine, and in some cases an aspartate, as the catalytic dyad (or triad). 258 matched cddid_all.tbl CDD cd22791 cd22791 438612 OTU_VRTN OTU (ovarian tumor) domain of vertnin and similar proteins. Vertnin (VRTN) is an OTU domain-containing protein that is required for the development of thoracic vertebrae in mammals. OTU domains typically function as deubiquitinases (DUBs)/ubiquitin thiolesterases (EC 3.4.19.12) that catalyze the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. These DUBs may play important regulatory roles at the level of protein turnover by preventing degradation. Vertnin and some subfamily members do not possess the conserved catalytic residues and may not have DUB activity. VRTN gene is associated with variations in vertebral number. 137 matched cddid_all.tbl CDD cd22792 cd22792 438613 OTU_RDRP-like OTU (ovarian tumor) domain of the potexviruses/carlaviruses RNA replication protein family. RNA replication polyprotein (RDRP) is a viral homolog of ovarian tumor protease (vOTU), which displays RNA helicase (EC 3.6.4.13), RNA-directed RNA polymerase (EC 2.7.7.48), viral methyltransferase, Fe(2+) 2-oxoglutarate dioxygenase and protease activities. The central part of this protein possibly functions as an ATP-binding helicase. It is an RNA-directed RNA polymerase involved in viral RNA replication. It also acts as a thiol protease that cleaves the polyprotein. This subfamily belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 108 matched cddid_all.tbl CDD cd22793 cd22793 438614 OTU_plant_OTU1_2-like OTU (ovarian tumor) domain of deubiquitinating enzyme OTU1 and OTU2 from plants and similar proteins. Deubiquitinating enzyme OTU2, also called OTU domain-containing protein 2, is a deubiquitinase (DUB) or ubiquitin thiolesterase (EC 3.4.19.12) that catalyzes the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. OTU2 exhibited equivalent binding affinities for K48- and K63-linked ubiquitin chains and no cleavage activity toward linear UB chains. It may also be involved in endoplasmic-reticulum-associated protein degradation (ERAD). OTU2 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 163 matched cddid_all.tbl CDD cd22794 cd22794 438615 OTU_OTUD4 OTU (ovarian tumor) domain of OTU domain-containing protein 4 and similar proteins. OTU domain-containing protein 4 (OTUD4), also called HIV-1-induced protein HIN-1, is a deubiquitinase that specifically deubiquitinates 'Lys-63'-polyubiquitinated MYD88 adapter protein upon phosphorylation, triggering down-regulation of NF-kappa-B-dependent transcription of inflammatory mediators. OTUD4 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 130 matched cddid_all.tbl CDD cd22795 cd22795 438616 OTU_ALG13 OTU (ovarian tumor) domain of bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13. Bifunctional UDP-N-acetylglucosamine transferase and deubiquitinase ALG13 is also called asparagine-linked glycosylation 13 homolog, glycosyltransferase 28 domain-containing protein 1 (GLT28D1), or UDP-N-acetylglucosamine transferase subunit ALG13 homolog. It displays both glycosyltransferase (EC 2.4.1.141) and deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) activities. With ALG14, it forms a UDP-N-acetylglucosamine transferase that catalyzes the second step of eukaryotic N-linked glycosylation in the endoplasmic reticulum. ALG13 variants cause a form of early infantile epileptic encephalopathy known as EIEE36 refractory seizures, neurodevelopmental impairment, and poor prognosis; given the essential role of ALG13 in glycosylation, it is also considered a congenital disorder of glycosylation (CDG). ALG13 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 130 matched cddid_all.tbl CDD cd22796 cd22796 438617 OTU_plant_OTU6-like OTU (ovarian tumor) domain of deubiquitinating enzyme OTU6 from plants and similar proteins. Deubiquitinating enzyme OTU6, also called OTU domain-containing protein 6 or otubain-like deubiquitinase 1 (OTLD1), is a deubiquitinase (DUB) or ubiquitin thiolesterase (EC 3.4.19.12) that catalyzes the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. OTU6 binds chromatin and has enzymatic histone deubiquitinase activity specific for the H2B histone. OTU6 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 128 matched cddid_all.tbl CDD cd22797 cd22797 438618 OTU_plant_OTU5-like OTU (ovarian tumor) domain of deubiquitinating enzyme OTU5 from plants and similar proteins. Deubiquitinating enzyme OTU5, also called OTU domain-containing protein 6, is a deubiquitinase (DUB) or ubiquitin thiolesterase (EC 3.4.19.12) that catalyzes the thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin, a small regulatory protein that can be conjugated to a large range of target proteins. Protein ubiquitination is a post-translational modification of mostly Lys residues that regulates many cellular processes, including protein degradation, intracellular trafficking, cell signaling, autophagy, transcription, translation, and the DNA damage response. OTU5 is an inactive cysteine protease. It regulates gene expression by contributing to chromatin organization and DNA methylation patterns (e.g. H3K4me3 and H3K27me3). It is required for phosphate (Pi) homeostasis. OTU5 belongs to the OTU family of cysteine proteases that use a conserved cysteine, histidine, and an aspartate, as the catalytic triad. 149 matched cddid_all.tbl CDD cd22798 cd22798 438619 OTU_OTULL OTU (ovarian tumor) domain of inactive ubiquitin thioesterase Otulinl. Otulinl, also called FAM105A, is an OTU-class pseudo-deubiquitinase with a disrupted catalytic triad and undetectable cleavage activity for any diubiquitin linkage. It may play a role in endoplasmic reticulum (ER)-organelle communication. Otulinl belongs to the OTU family of cysteine proteases that use a conserved cysteine and histidine, and in some cases an aspartate, as the catalytic dyad (or triad). 261 matched cddid_all.tbl CDD cd22799 cd22799 438620 OTU_OTUL OTU (ovarian tumor) domain of ubiquitin thioesterase otulin and similar proteins. Otulin, also called FAM105B, deubiquitinating enzyme otulin, OTU domain-containing deubiquitinase with linear linkage specificity, or ubiquitin thioesterase Gumby, is a deubiquitinase (DUB)/ubiquitin thioesterase (EC 3.4.19.12) that specifically removes linear ('Met-1'-linked) polyubiquitin chains to substrates and acts as a regulator of angiogenesis and innate immune response. It acts as a key negative regulator of inflammation by restricting spontaneous inflammation and maintaining immune homeostasis. Otulin belongs to the OTU family of cysteine proteases that use a conserved cysteine and histidine, and in some cases an aspartate, as the catalytic dyad (or triad). 266 matched cddid_all.tbl CDD cd22802 cd22802 467852 AcrIIC4 Anti-CRISPR type II subtype C4. AcrIIC4 was discovered via a guilt-by association (GBA) approach, which was based on the strong co-occurrence and clustering of anti-CRISPR (acr) and anti-CRISPR associated (aca) genes through proximity and homology searches. AcrIIC4 inhibits Cas9 activity in vitro, as well as CRISPR interference activity in bacteria; it also prevents Cas9-mediated genome editing in mammalian cells. AcrIIC4 blocks CRISPR-Cas9 DNA cleavage activity. Structural studies on Haemophilus parainfluenzae AcrIIC4 show that it binds to the Cas9 Recognition Domain; this binding does not prevent the Cas9-anti-CRISPR complex from interacting with target DNA but does inhibit DNA cleavage. Type IIC CRISPR-Cas systems are the simplest of the type II systems, employing only three Cas proteins, Cas9, Cas1 and Cas2. Almost all type II Acrs characterized to date directly interact with the Cas9 endonuclease, although by distinct mechanisms. The type II CRISPR/Cas subtype has a distinct crRNA-guided surveillance complex encoded by cas9 (formerly csn1), cas1, cas2, and csn2 (for type IIA) or cas4 (for type IIB) genes, all located in a single transcriptional unit directly upstream of the CRISPR locus. Cleavage of the DNA target in type II systems is carried out by Cas9 which is an RNA-guided double-stranded DNase with two independent nuclease domains, HNH and RuvC. Due to the reliance of the type II system on a single protein for function, Cas9 homologs derived from different subtypes and species have been utilized for numerous gene editing applications. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 2 systems employ a single multi-domain effector Cas9 protein complex that performs target recognition and cleavage. Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 88 matched cddid_all.tbl CDD cd22803 cd22803 439362 AcrIIC5 Anti-CRISPR type II subtype C5. AcrIIC5 was discovered via a guilt-by association (GBA) approach, which was based on the strong co-occurrence and clustering of acr and anti-CRISPR associated (aca) genes through proximity and homology searches. AcrIIC5 inhibits Cas9 activity in vitro, as well as CRISPR interference activity in bacteria. It also prevents Cas9-mediated genome editing in mammalian cells. AcrIIC4 and AcrIIC5 are the most potent among the type II-C Acr proteins, preventing substrate DNA binding by Cas9, and exhibiting higher specificities for inhibition of type II-C Cas9s. Type IIC CRISPR-Cas systems are the simplest of the type II systems, employing only three Cas proteins, Cas9, Cas1, and Cas2. Almost all type II Acr proteins characterized to date directly interact with the Cas9 endonuclease, although by distinct mechanisms. The type II CRISPR/Cas subtype has a distinct crRNA-guided surveillance complex encoded by cas9 (formerly csn1), cas1, cas2, and csn2 (for type IIA) or cas4 (for type IIB) genes, all located in a single transcriptional unit directly upstream of the CRISPR locus. Cleavage of the DNA target in type II systems is carried out by Cas9 which is an RNA-guided double-stranded DNase with two independent nuclease domains, HNH and RuvC. Due to the reliance of the type II system on a single protein for function, Cas9 homologs derived from different subtypes and species have been utilized for numerous gene editing applications. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 2 systems employ a single multi-domain effector Cas9 protein complex that performs target recognition and cleavage. Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 115 matched cddid_all.tbl CDD cd22804 cd22804 439306 KP6_alpha KP6 killer toxin subunit alpha. KP6 is an anti-fungal protein produced by a double-stranded RNA virus. It is a neutral protein that is lethal to sensitive cells of the same or related species. KP6 is composed of two subunits: KP6alpha and KP6beta, which are produced after cleavage from a single precursor preprotoxin. The KP6alpha subunit is responsible for targeting while the KP6beta subunit is cytotoxic. KP6alpha can recognize some cellular receptors before interaction of the complex with KP6beta, precipitating cell death. Neither subunit is homologous in either sequence or structure to any other known cytotoxic protein, however, they have similar structures to each other. The major difference between the two subunits is that KP6alpha contains a hydrophobic helix at the N-terminus, which plays a key role in target recognition. This model corresponds to the KP6alpha subunit. 79 matched cddid_all.tbl CDD cd22805 cd22805 439307 KP6_beta KP6 killer toxin subunit beta. KP6 is an anti-fungal protein produced by a double-stranded RNA virus. It is a neutral protein lethal to sensitive cells of the same or related species. KP6 is composed of two subunits: KP6alpha and KP6beta, which are produced after cleavage from a single precursor preprotoxin. The KP6alpha subunit is responsible for targeting while the KP6beta subunit is cytotoxic. KP6alpha can recognize some cellular receptors before interaction of the complex with KP6beta, precipitating cell death. Neither subunit is homologous in either sequence or structure to any other known cytotoxic protein, however, they have highly similar structures to each other. The major difference between the two subunits is that KP6alpha contains a hydrophobic helix at the N-terminus, which plays a key role in target recognition. This model corresponds to the KP6beta subunit. 77 matched cddid_all.tbl CDD cd22808 cd22808 439282 Complexin_NTD_CPLX_I_II N-terminal SNARE complex binding domain found in complexins I and II. Complexins (CPXs, also called synaphins) are small, cytosolic proteins that bind to the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex to regulate synaptic vesicle exocytosis. Complexins I and II, also called synaphin-2 and synaphin-1, respectively, are highly homologous hydrophilic proteins that are enriched in neurons where they colocalize with syntaxin and SNAP25. They regulate the sequential interactions of alpha-SNAP and synaptotagmins with the SNAP receptor during exocytosis. They preferentially bind to syntaxin within the SNARE core complex containing SNAP25, VAMP2 and STX1A. This model corresponds to the N-terminal SNARE complex binding domain of complexins I and II. 41 matched cddid_all.tbl CDD cd22809 cd22809 439283 Complexin_NTD_CPLX_III_IV N-terminal SNARE complex binding domain found in complexins III and IV. Complexins (CPXs) are small, cytosolic proteins that bind to the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex to regulate synaptic vesicle exocytosis. Complexins III (CPX III) and IV (CPX IV) are the only CPX isoforms present in retinal ribbon synapses. They carry an extension with a functional CAAX-box farnesylation site that is absent in CPXs I and II. Their C-terminal farnesylation regulates their synaptic targeting and modulatory function in transmitter release. They may contribute to the unique release efficacy of retinal sensory neurons. CPXs III and IV can functionally replace CPXs I and II, which regulate a late step in the release process, most likely by stabilizing SNARE complexes and thus maintaining synaptic vesicles in a highly release competent state. This model corresponds to the N-terminal SNARE complex binding domain of CPXs III and IV. 44 matched cddid_all.tbl CDD cd22811 cd22811 439363 agbl-like alpha-galactosyl binding lectin, and similar proteins. This model includes alpha-galactosyl binding lectin from Lyophyllum decastes, an edible mushroom that has been shown to contain polysaccharide extracts with anti-tumor effects. Lyophyllum decastes lectin (LDL) is a homodimeric protein that recognizes non-reducing alpha-galactosyl groups, with specificity for alpha-1,4-linked galactose (Gal-alpha(1,4)Gal) epitopes. It shows no sequence similarity to any known lectin or other protein of known function, and its structure shows a novel fold. While other mushroom lectins have cytosolic location surmised, the presence of disulfide bridges in LDL suggests that this lectin may be secreted. 90 matched cddid_all.tbl CDD cd22813 cd22813 439278 PBD_PPP1R3 PP1C binding domain found in protein phosphatase 1 regulatory subunit 3 (PPP1R3) family. The PPP1R3 family includes three protein phosphatase 1 regulatory subunits, PPP1R3A, PPP1R3B and PPP1R3C, that act as glycogen-targeting subunits for protein phosphatase 1 (PP1). PPP1R3A, also called protein phosphatase 1 glycogen-associated regulatory subunit (PP1G), protein phosphatase type-1 glycogen targeting subunit, or RG1, is essential for cell division, and participates in the regulation of glycogen metabolism, muscle contractility, and protein synthesis. PPP1R3A plays an important role in glycogen synthesis but is not essential for insulin activation of glycogen synthase. PPP1R3B, also called hepatic glycogen-targeting protein phosphatase 1 regulatory subunit GL, protein phosphatase 1 regulatory subunit 4, PP1 subunit R4, or protein phosphatase 1 subunit GL, facilitates interaction of the PP1 with enzymes of the glycogen metabolism and regulates its activity. PPP1R3B suppresses the rate at which PP1 dephosphorylates (inactivates) glycogen phosphorylase and enhances the rate at which it activates glycogen synthase and therefore limits glycogen breakdown. Its activity is inhibited by glycogen phosphorylase liver form (PYGL), resulting in inhibition of the glycogen synthase and glycogen phosphorylase phosphatase activities of PP1. PPP1R3C, also called protein phosphatase 1 regulatory subunit 5 (PPP1R5), PP1 subunit R5, or protein targeting to glycogen (PTG), activates glycogen synthase, reduces glycogen phosphorylase activity and limits glycogen breakdown. It can dramatically increase basal and insulin-stimulated glycogen synthesis upon overexpression in a variety of cell types. This model corresponds to protein phosphatase 1 catalytic subunit (PP1C) binding domain, which contains a RVxF PP1C-binding motif that mediates interactions with PP1C. 31 matched cddid_all.tbl CDD cd22814 cd22814 439279 PBD_PPP1R3B PP1C binding domain found in protein phosphatase 1 regulatory subunit 3B (PPP1R3B). PPP1R3B, also called hepatic glycogen-targeting protein phosphatase 1 (PP1) regulatory subunit GL, protein phosphatase 1 regulatory subunit 4, PP1 subunit R4, or protein phosphatase 1 subunit GL, acts as a glycogen-targeting subunit for PP1. It facilitates interaction of the PP1 with enzymes of the glycogen metabolism and regulates its activity. PPP1R3B suppresses the rate at which PP1 dephosphorylates (inactivates) glycogen phosphorylase and enhances the rate at which it activates glycogen synthase and therefore limits glycogen breakdown. Its activity is inhibited by glycogen phosphorylase liver form (PYGL), resulting in inhibition of the glycogen synthase and glycogen phosphorylase phosphatase activities of PP1. It can dramatically increase basal and insulin-stimulated glycogen synthesis upon overexpression in hepatocytes. PPP1R3B interacts with glycogen, the PPP1CC catalytic subunit of PP1, and PYGL. It associates with glycogen particles. This model corresponds to the protein phosphatase 1 catalytic subunit (PP1C) binding domain of PPP1R3B, which contains a RVxF PP1C-binding motif that mediates interactions with PP1C. 74 matched cddid_all.tbl CDD cd22815 cd22815 439280 PBD_PPP1R3C PP1C binding domain found in protein phosphatase 1 regulatory subunit 3C (PPP1R3C). PPP1R3C, also called protein phosphatase 1 regulatory subunit 5 (PPP1R5), PP1 subunit R5, or protein targeting to glycogen (PTG), acts as a glycogen-targeting subunit for protein phosphatase 1 (PP1) and regulates its activity. It activates glycogen synthase, reduces glycogen phosphorylase activity, and limits glycogen breakdown. It can dramatically increase basal and insulin-stimulated glycogen synthesis upon overexpression in a variety of cell types. PPP1R3C interacts with the PPP1CC catalytic subunit of PP1 and associates with glycogen. This model corresponds to protein phosphatase 1 catalytic subunit (PP1C) binding domain of PPP1R3C, which contains a RVxF PP1C-binding motif that mediates interactions with PP1C. 79 matched cddid_all.tbl CDD cd22816 cd22816 439364 TMEM203 Transmembrane protein 203. Transmembrane protein 203 (TMEM203) is a conserved putative transmembrane protein that functions as a regulator of signaling pathways activated in response to diverse bacterial and viral stimuli. It has been shown in humans to be an intracellular regulator of STimulator of IFN Genes (STING)-mediated signaling and to interact with the pleiotropic inositol phosphate signaling pathway protein IP3R. In T-cells of patients with systemic lupus erythematosus (SLE), a disease characterized by the over-expression of type I interferons (IFN1), elevated TMEM203 mRNA levels are associated with disease activity. Thus, identification of TMEM203 may elucidate the control of STING-mediated innate immune responses, and provide a potential novel mechanism for therapeutic interventions in STING-associated inflammatory diseases. 131 matched cddid_all.tbl CDD cd22817 cd22817 467642 DRWD-N_Knl1 N-terminal double-RWD domain of kinetochore scaffold 1 and related proteins. Kinetochore scaffold 1 (KNL1 or Knl1, also known as Spc105, Spc7, and Blinkin) coordinates the spindle assembly checkpoint (SAC), a signaling pathway that delays chromosome segregation until all sister chromatids are properly attached to spindle microtubules (MTs). Knl1 is part of the KMN network, a conserved kinetochore protein complex that connects kinetochores to MTs. Knl1 has been shown to play an effective role in decreasing apoptosis and promoting the proliferation of colorectal cancer cells, suggesting that its inhibition may represent a promising therapeutic approach for colorectal cancer patients. Knl1 contains tandem RWD domains, also known as a double-RWD domain, DRWD, which has been shown to bind the Mis12 complex, consisting of Dsn1 and Nsl1, that tethers directly onto the underlying chromatin layer and mediates kinetochore targeting of Knl1. The model corresponds to N-terminal double-RWD domain (DRWD-N). 112 matched cddid_all.tbl CDD cd22818 cd22818 439365 AcrIIA11 Anti-CRISPR type II subtype A11. AcrIIA11 is an anti-CRISPR (Acr) protein which was discovered via a functional selection that inhibits the type II-A CRISPR-Cas system (Csy). AcrIIA11, a common anti-CRISPR in the human gut, uses a different mechanism than other previously characterized type II-A Acrs to inhibit Cas9 in bacteria and in human cells. It can be used to design phages that can infect bacteria which are otherwise difficult to destroy. These phages could be used to clear antibiotic-resistant infections in the future. Almost all type II Acrs characterized to date directly interact with the Cas9 endonuclease, although by distinct mechanisms. The type II CRISPR/Cas subtype has a distinct crRNA-guided surveillance complex encoded by cas9 (formerly csn1), cas1, cas2, and csn2 (for type IIA) or cas4 (for type IIB) genes, all located in a single transcriptional unit directly upstream of the CRISPR locus. Cleavage of the DNA target in type II systems is carried out by Cas9 which is an RNA-guided double-stranded DNase with two independent nuclease domains, HNH and RuvC. Due to the reliance of the type II system on a single protein for function, Cas9 homologs derived from different subtypes and species have been utilized for numerous gene editing applications. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 164 matched cddid_all.tbl CDD cd22819 cd22819 439331 AcrIIA2b Anti-CRISPR type II subtype A2b. AcrIIA2b is an anti-CRISPR (Acr) protein which is homolog to AcrIIA2 but they are different in the temperature dependence of Cas9 inhibition. AcrIIA2b, like AcrIIA2, interacts with the protospacer adjacent motif (PAM) recognition residues of Cas9, preventing target double-stranded DNA (dsDNA) detection and Cas9 binding to DNA. Differences in the temperature dependence of Cas9 inhibition by AcrIIA2 and AcrIIA2b arise from differences in both inhibitor structure and the local inhibitor-binding environment on Cas9. This difference expands the natural toolbox for regulating CRISPR-Cas9 genome editing temporally, spatially, and conditionally. Almost all type II Acr proteins characterized to date directly interact with the Cas9 endonuclease, although by distinct mechanisms. The type II CRISPR/Cas subtype has a distinct crRNA-guided surveillance complex encoded by cas9 (formerly csn1), cas1, cas2, and csn2 (for type IIA) or cas4 (for type IIB) genes, all located in a single transcriptional unit directly upstream of the CRISPR locus. Cleavage of the DNA target in type II systems is carried out by Cas9 which is an RNA-guided double-stranded DNase with two independent nuclease domains, HNH and RuvC. Due to the reliance of the type II system on a single protein for function, Cas9 homologs derived from different subtypes and species have been utilized for numerous gene editing applications. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 2 systems employ a single multi-domain effector Cas9 protein complex that performs target recognition and cleavage. Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 127 matched cddid_all.tbl CDD cd22823 cd22823 438682 Gal_Rha_Lectin Galactose/rhamnose-binding lectin domain. Galactose/rhamnose-binding lectin domain is formed from a four-stranded antiparallel beta-sheet which packs against an alpha-helix. It was originally described as galactose-binding lectin domain since it was found in a galactose-binding sea urchin egg lectin (SUEL). SUEL was first isolated as a D-galactoside binding lectin, it was later shown that it binds to L-rhamnose preferentially. Galactose/rhamnose-binding lectin domain is also found in many rhamnose-binding lectins, such as Oncorhynchus keta L-rhamnose-binding lectins (CSLs) and Silurus asotus rhamnose-binding lectin (SAL). In addition, the superfamily includes many SUEL/CSLs/SAL homologous proteins, such as plant beta-galactosidases, mammalian latrophilins, Caenorhabditis elegans protein EVA-1 and its homolog, human protein EVA-1 homolog C (also known as C21orf63). Due to the lack of galactose/rhamnose-binding key residues, some superfamily members may not form a binding pocket for galactose/rhamnose. Therefore, they are unlikely to act as galactose/rhamnose-binding lectins. 91 matched cddid_all.tbl CDD cd22825 cd22825 439376 Lge1_periphilin-like Eukaryotic transcriptional regulatory protein Lge1, periphilin, and similar proteins. This family includes transcriptional regulatory protein Lge1 found in fungi as well as periphilin-1, a component of the Human Silencing Hub (HUSH) complex, a multiprotein complex that mediates epigenetic repression. In yeasts, Lge1 is involved in the ubiquitination of histones H2A and H2B. This ubiquitination step is a vital one in the regulation of the transcriptional activity of RNA polymerase II. In Saccharomyces cerevisiae, Rad6 and Bre1 are present in a complex that contains Lge1; this complex is required for H2B ubiquitination. Bre1 is the H2B ubiquitin ligase that interacts with acidic activators, such as Gal4, and recruits Rad6 and its binding partner Lge1 to target promoters. In Schizosaccharomyces pombe, the equivalent protein to Lge1 appears to be Shf1. In human, periphilin acts a transcriptional co-repressor and regulates cell cycle progression. In human, periphilin-1 is involved in epithelial differentiation and contributes to epidermal integrity and barrier formation. It may act as transcriptional co-repressor involved in cell cycle progression. Chromosomal translocation of genes causing oncogenic fusion protein of Periphilin-1 and Fibroblast Growth Factor Receptor 2 (FGRF2) is associated with intrahepatic cholangiocarcinoma. 63 matched cddid_all.tbl CDD cd22826 cd22826 438683 Gal_Rha_Lectin_LPHNs galactose/rhamnose binding lectin domain found in latrophilins. Latrophilins, also called lectomedins or latrotoxin receptors, belong to Group I adhesion GPCRs, which also include ETL (EGF-TM7-latrophilin-related protein). These receptors are a member of the adhesion family (subclass B2) that belongs to the class B GPCRs. Three subtypes of latrophilins have been identified: latrophilin-1 (LPHN1), Latrophilin-2 (LPHN2), and Latrophilin-3 (LPHN3). The LPHN1 is a brain-specific calcium-independent receptor of alpha-latrotoxin, a potent presynaptic neurotoxin from the venom of the black widow spider that induces massive neurotransmitter release from sensory and motor neurons as well as endocrine cells, leading to nerve-terminal degeneration. LPHN2 and LPHN3, although sharing strong sequence homology to LPHN1, do not bind alpha-latrotoxin. While LPHN3 is also brain specific, LPHN2, is ubiquitously distributed. The endogenous ligands for these two receptors are unknown. All members in this family contain a galactose/rhamnose-binding lectin domain at N-terminus. 92 matched cddid_all.tbl CDD cd22827 cd22827 438684 Gal_Rha_Lectin_SUL-I-like galactose/rhamnose binding lectin domain found in Toxopneustes pileolus rhamnose-binding lectin SUL-I and similar proteins. SUL-I is a galactose/rhamnose-binding lectin with mitogenic, chemotactic, and cytotoxic activity. These activities can be triggered by binding of the lectin to specific carbohydrate chains on target cells. SUL-I may be involved in self-defense against invading microorganisms. SUL-I is composed of three distinctive domains with a folding structure similar to galactose/rhamnose-binding lectin domain found in proteins such as mammalian latrophilins, Oncorhynchus keta L-rhamnose-binding lectins (CSLs), and Silurus asotus rhamnose-binding lectin (SAL). The family also includes Heliocidaris crassispina D-galactoside-specific lectin, also known as sea urchin egg lectin or SUEL, and Echinometra lucunter L-rhamnose-binding lectin ELEL-1, both of which contain only one galactose/rhamnose-binding lectin domain. SUEL binds D-galactoside. It may play an important role in the activation of eggs triggered by fertilization, or in their subsequent differentiation. The dimeric form is essential for hemagglutination activity of SUEL. ELEL-1 is a rhamnose-binding lectin that also binds alpha-D-melibiose, alpha-D-lactose, beta-D-lactose, methyl-alpha-D-galactopyranoside, methyl-beta-D--galactopyranoside and D-galactose, but not D-arabinose, L-fucose, D-glucose, D-mannose, D-maltose, D-sucrose, N-acetyl-D-galactosamine, N-acetyl-D-glucosamine, N-acetyl-D-mannosamine-D-xylose, or by glycoproteins orosomucoid, thyroglobulin, ovomucoid and porcine stomach mucin. It shows cation-independent hemagglutinating activity against rabbit and human erythrocytes. ELEL-1 agglutinates cells of Gram-positive bacterial species S. aureus but not those of Gram-negative E. coli. 89 matched cddid_all.tbl CDD cd22828 cd22828 438685 Gal_Rha_Lectin_EVA1_EVA1C_rpt1 first galactose/rhamnose binding lectin domain found in Caenorhabditis elegans protein EVA-1, human protein EVA-1 homolog C and similar proteins. The family includes Caenorhabditis elegans protein EVA-1 and its homologs, such as human protein EVA-1 homolog C (also known as C21orf63). EVA-1 functions as an UNC-40 coreceptor to enhance attraction to the MADD-4 guidance cue in C. elegans. It also acts as a receptor for slt-1 and is required for the guidance of the AVM pioneer axon to the ventral nerve cord. Human C21orf63 is a type-1 transmembrane heparin-binding protein. Both human C21orf63 is a type-1 transmembrane heparin-binding protein. Members in this family contain two tandem galactose/rhamnose-binding lectin domains. This model corresponds to the first one. 105 matched cddid_all.tbl CDD cd22829 cd22829 438686 Gal_Rha_Lectin_EVA1_EVA1C_rpt2 second galactose/rhamnose binding lectin domain found in Caenorhabditis elegans protein EVA-1, human protein EVA-1 homolog C and similar proteins. The family includes Caenorhabditis elegans protein EVA-1 and its homologs, such as human protein EVA-1 homolog C (also known as C21orf63). EVA-1 functions as an UNC-40 coreceptor to enhance attraction to the MADD-4 guidance cue in C. elegans. It also acts as a receptor for slt-1 and is required for the guidance of the AVM pioneer axon to the ventral nerve cord. Human C21orf63 is a type-1 transmembrane heparin-binding protein. Members in this family contain two tandem galactose/rhamnose-binding lectin domains. This model corresponds to the second one. Due to the lack of rhamnose-binding key residues, the second galactose/rhamnose-binding domains of EVA-1 does not form a binding pocket for rhamnose. 99 matched cddid_all.tbl CDD cd22830 cd22830 438687 Gal_Rha_Lectin_dCirl galactose/rhamnose binding lectin domain found in Drosophila melanogaster Latrophilin Cirl and similar proteins. Latrophilin Cirl (calcium-independent receptor for latrotoxin) is an adhesion-type G-protein-coupled receptor (aGPCR) that acts as a molecular sensor and signal transducer that detects and converts mechanical stimuli into a metabotropic response. It functions in mechanosensory neurons by modulating ionotropic receptor currents, the initiating step of cellular mechanosensation. The model corresponds to a galactose/rhamnose-binding lectin domain found at the N-terminus of Latrophilin Cirl. 92 matched cddid_all.tbl CDD cd22831 cd22831 438688 Gal_Rha_Lectin_PKD1L2 galactose binding lectin domain found in polycystic kidney disease protein 1-like 2 (polycystin-1L2) and similar proteins. Polycystin-1L2 is a novel G-protein-coupled receptor that may function as an ion-channel regulator. This model corresponds to a galactose/rhamnose-binding lectin domain found at the N-terminal region of polycystin-1L2. Due to the lack of rhamnose-binding key residues, the galactose/rhamnose-binding domains of Polycystin-1L2 does not form a binding pocket for rhamnose. Therefore, Polycystin-1L2 is unlikely to act as a rhamnose-binding lectin. 98 matched cddid_all.tbl CDD cd22832 cd22832 438689 Gal_Rha_Lectin_CSL3_rpt1_rpt2-like first and second galactose/rhamnose binding lectin domain found in Oncorhynchus keta L-rhamnose-binding lectin CSL3 and similar proteins. The family includes a group of L-rhamnose-binding lectins, such as Oncorhynchus keta CSL1-3. CSL1 has hemagglutinating activity towards rabbit erythrocytes, but not human type B erythrocytes. CSL2 has hemagglutinating activity towards rabbit erythrocytes and human type B erythrocytes. CSL3 has hemagglutinating activity towards rabbit erythrocytes, human type A erythrocytes, human type B erythrocytes, human type O erythrocytes, and sheep erythrocytes. Their hemagglutinating activities are inhibited by smooth-type lipopolysaccharide (LPS) from different bacterial species. Members in this family contain two tandem galactose-binding lectin domains. This model corresponds to the first and second galactose/rhamnose-binding lectin domains found in Oncorhynchus keta CSL3, as well as the second galactose/rhamnose-binding lectin domain found in Oncorhynchus keta CSL2. 94 matched cddid_all.tbl CDD cd22833 cd22833 438690 Gal_Rha_Lectin_CSL1-2_RBL_SML_rpt1 first galactose/rhamnose binding lectin domain found in Oncorhynchus keta CSL1-2, Silurus asotus RBL, Scomberomorus niphonius SML and similar proteins. The family includes a group of L-rhamnose-binding lectins, such as Oncorhynchus keta CSL1 and CSL2. CSL1 has hemagglutinating activity towards rabbit erythrocytes, but not human type B erythrocytes. CSL2 has hemagglutinating activity towards rabbit erythrocytes and human type B erythrocytes. Their hemagglutinating activities are inhibited by smooth-type lipopolysaccharide (LPS) from different bacterial species. The family also includes Silurus asotus rhamnose-binding lectin (RBL) and Scomberomorus niphonius L-rhamnose-binding lectin (SML). RBL, also known as Silurus asotus (catfish) roe lectin (SAL), is a lectin that binds L-rhamnose. It also binds monosaccharides possessing steric similarity to the hydroxyl group orientation at C2 and C4 of the pyranose ring structure of L-rhamnose, such as L-mannose and L-lyxose. RBL does not require a Ca2+ ion or free thiol group for its agglutination activity. SML is a rhamnose-binding lectin that also binds melibiose, raffinose, D-galactose, L-arabinose, D-fucose, maltose, and D-glucose with decreasing affinity. It does not bind D-arabinose, L-fucose, lactose, xylose or 2-deoxy-D-galactose. SML shows strong hemagglutinating activity against rabbit erythrocytes. CSL1-2 and SML contain two tandem galactose/rhamnose-binding lectin domains. RBL contains three galactose/rhamnose-binding lectin domains. This model corresponds to the first one. 97 matched cddid_all.tbl CDD cd22834 cd22834 438691 Gal_Rha_Lectin_CSL1_rpt2 second galactose/rhamnose binding lectin domain found in Oncorhynchus keta CSL1 and similar proteins. The family includes a group of L-rhamnose-binding lectins, such as Oncorhynchus keta CSL1. CSL1 has hemagglutinating activity towards rabbit erythrocytes, but not human type B erythrocytes. Its hemagglutinating activity is inhibited by smooth-type lipopolysaccharide (LPS) from Klebsiella pneumoniae, Escherichia coli K-235, Shigella flexneri 1A, Aeromonas salmonicida and Salmonella minnesota and rough-type LPS from S. flexneri, but not by rough-type LPS from E. coli K12 and E. coli EH100. CSL1 agglutinates E. coli K12 and Bacillus subtilis. CSL1 contains two tandem galactose-binding lectin domains. This model corresponds to the second one. 95 matched cddid_all.tbl CDD cd22835 cd22835 438692 Gal_Rha_Lectin_SML_rpt2 second galactose/rhamnose binding lectin domain found in Scomberomorus niphonius L-rhamnose-binding lectin (SML) and similar proteins. SML is a rhamnose-binding lectin that also binds melibiose, raffinose, D-galactose, L-arabinose, D-fucose, maltose and D-glucose with decreasing affinity. It does not bind D-arabinose, L-fucose, lactose, xylose or 2-deoxy-D-galactose. SML shows strong hemagglutinating activity against rabbit erythrocytes. SML contains two tandem galactose/rhamnose-binding lectin domains. This model corresponds to the second one. 92 matched cddid_all.tbl CDD cd22836 cd22836 438693 Gal_Rha_Lectin_RBL_rpt2 second galactose/rhamnose binding lectin domain found in Silurus asotus rhamnose-binding lectin (RBL) and similar proteins. RBL, also known as Silurus asotus (catfish) roe lectin (SAL), is a lectin that binds L-rhamnose. It also binds monosaccharides possessing steric similarity to the hydroxyl group orientation at C2 and C4 of the pyranose ring structure of L-rhamnose, such as L-mannose and L-lyxose. RBL does not require a Ca2+ ion or free thiol group for its agglutination activity. RBL contains three galactose/rhamnose-binding lectin domains. This model corresponds to the second one. 95 matched cddid_all.tbl CDD cd22837 cd22837 438694 Gal_Rha_Lectin_RBL_rpt3 third galactose/rhamnose binding lectin domain found in Silurus asotus rhamnose-binding lectin (RBL) and similar proteins. RBL, also known as Silurus asotus (catfish) roe lectin (SAL), is a lectin that binds L-rhamnose. It also binds monosaccharides possessing steric similarity to the hydroxyl group orientation at C2 and C4 of the pyranose ring structure of L-rhamnose, such as L-mannose and L-lyxose. RBL does not require a Ca2+ ion or free thiol group for its agglutination activity. RBL contains three galactose/rhamnose-binding lectin domains. This model corresponds to the third one. 87 matched cddid_all.tbl CDD cd22838 cd22838 438695 Gal_Rha_Lectin_nemgal galactose/rhamnose binding lectin domain found in Hydra vulgaris nematogalectin and similar proteins. Nematogalectin, also called nemgal, is a nematocyst protein with an N-terminal GlyXY domain and a galactose/rhamnose binding lectin domain. There are two nematogalectins, A and B, in Hydra, and they are the products of alternative splicing. They are major components of the nematocyst tubule. Nematogalectin functions as a trimer that could bind to multiple chondroitin glycosaminoglycan molecules and stabilize the chondroitin proteoglycan layer. 100 matched cddid_all.tbl CDD cd22839 cd22839 438696 Gal_Rha_Lectin_LAT1 galactose/rhamnose binding lectin domain found in Caenorhabditis elegans latrophilin-like protein 1 (LAT1) and similar proteins. LAT1 plays a role in the establishment of anterior-posterior polarity in tissues during embryogenesis. It is required for the alignment of the mitotic spindles and division planes. It may have a role in cell death events and play an essential role in normal defection and oocyte fertilization. LAT1 is involved in sperm function. it operates in pharyngeal pumping during feeding. LAT1 contains a galactose/rhamnose binding lectin domain at the N-terminus. 95 matched cddid_all.tbl CDD cd22840 cd22840 438697 Gal_Rha_Lectin_LAT2 galactose/rhamnose binding lectin domain found in Caenorhabditis elegans latrophilin-like protein 2 (LAT2) and similar proteins. LAT2 may have a role in pharyngeal pumping during feeding. It contains a galactose/rhamnose binding lectin domain at the N-terminal region. Due to the lack of rhamnose-binding key residues, the galactose/rhamnose-binding domains of LAT2 does not form a binding pocket for rhamnose. Therefore, LAT2 is unlikely to act as a rhamnose-binding lectin. 96 matched cddid_all.tbl CDD cd22841 cd22841 438698 Gal_Rha_Lectin_REJ3 galactose/rhamnose binding lectin domain found in Strongylocentrotus purpuratus receptor for egg jelly 3 protein (REJ3) and similar proteins. REJ3 is a polycystin-1 protein (components of non-selective cation channels) that is cleaved at the GPS (G-protein-coupled receptor proteolytic site) domain and localizes to the acrosomal region of sea urchin sperm. REJ3 is a multidomain protein containing only one galactose/rhamnose-binding lectin domain at its N-terminus. 92 matched cddid_all.tbl CDD cd22842 cd22842 438699 Gal_Rha_Lectin_BGal galactose/rhamnose binding lectin domain found in plant beta-galactosidases and similar proteins. The family represents a group of plant beta-galactosidases (BGals), which belong to glycoside hydrolase family 35. They have a C-terminal domain homologous to animal galactose and rhamnose-binding lectins. BGals (EC 3.2.1.23), also called Exo-(1->4)-beta-D-galactanase, or lactase, catalyze hydrolysis of terminal non-reducing beta-D-galactose residues in beta-D-galactosides. Some family members contain more than one galactose/rhamnose binding lectin domain. Due to the lack of rhamnose-binding key residues, the galactose/rhamnose-binding lectin domains of BGals do not form a binding pocket for rhamnose. Therefore, BGals are unlikely to act as rhamnose-binding lectins. 91 matched cddid_all.tbl CDD cd22843 cd22843 438700 Gal_Rha_Lectin-like_P113 galactose/rhamnose binding lectin-like domain found in Plasmodium falciparum P113 and similar proteins. P113 is an abundant glycosylphosphatidylinositol (GPI)-anchored merozoite surface protein that tethers the RH5:CyRPA:RIPR complex to the merozoite surface. The N-terminal region of P113 contains two closely interacting domains, which resemble the galactose/rhamnose-binding lectin domains found in proteins such as sea urchin egg lectin (SUEL), plant beta-galactosidases, mammalian latrophilins, and catfish rhamnose-binding lectin (SAL) eggs. Due to the lack of rhamnose-binding key residues, the galactose/rhamnose binding lectin-like domains of P113 do not form a binding pocket for rhamnose. Therefore, P113 is unlikely to act as a rhamnose-binding lectin. This model corresponds to galactose/rhamnose binding lectin-like domain of P113. 89 matched cddid_all.tbl CDD cd22844 cd22844 438701 Gal_Rha_Lectin_LPHN1 galactose/rhamnose binding lectin domain found in latrophilin-1 and similar proteins. Latrophilin-1 (LPHN1), also called adhesion G protein-coupled receptor L1 (ADGRL1), or calcium-independent alpha-latrotoxin receptor 1 (CIRL-1), or lectomedin-2, is a brain-specific calcium-independent receptor that mediates the effect of alpha-latrotoxin, a potent presynaptic neurotoxin from the venom of the black widow spider that induces massive neurotransmitter release from sensory and motor neurons as well as endocrine cells, leading to nerve-terminal degeneration. This model corresponds to a galactose/rhamnose-binding lectin domain found at the N-terminus of LPHN1. 97 matched cddid_all.tbl CDD cd22845 cd22845 438702 Gal_Rha_Lectin_LPHN2 galactose/rhamnose binding lectin domain found in latrophilin-2 and similar proteins. Latrophilin-2 (LPHN2), also called adhesion G protein-coupled receptor L2 (ADGRL2), or calcium-independent alpha-latrotoxin receptor 2 (CIRL-2), or latrophilin homolog 1 (LPHH1), or lectomedin-1, is ubiquitously distributed calcium-independent receptor of low affinity for alpha-latrotoxin, an excitatory neurotoxin present in black widow spider venom which triggers massive exocytosis from neurons and neuroendocrine cells. It is probably implicated in the regulation of exocytosis. This model corresponds to a galactose/rhamnose-binding lectin domain found at the N-terminus of LPHN2. 97 matched cddid_all.tbl CDD cd22846 cd22846 438703 Gal_Rha_Lectin_LPHN3 galactose/rhamnose binding lectin domain found in latrophilin-3 and similar proteins. Latrophilin-3 (LPHN3), also called adhesion G protein-coupled receptor L3 (ADGRL3), or calcium-independent alpha-latrotoxin receptor 3 (CIRL-3), or lectomedin-3, is a brain-specific calcium-independent receptor that plays a role in cell-cell adhesion and neuron guidance via its interactions with FLRT2 and FLRT3 that are expressed at the surface of adjacent cells. It is involved in the development of glutamatergic synapses in the cortex. This model corresponds to a galactose/rhamnose-binding lectin domain found at the N-terminus of LPHN3. 99 matched cddid_all.tbl CDD cd22847 cd22847 438704 Gal_Rha_Lectin_like_P113_rpt1 first galactose/rhamnose binding lectin-like domain found in Plasmodium falciparum P113 and similar proteins. P113 is an abundant glycosylphosphatidylinositol (GPI)-anchored merozoite surface protein that tethers the RH5:CyRPA:RIPR complex to the merozoite surface. The N-terminal region of P113 contains two closely interacting domains, which resemble the galactose/rhamnose-binding lectin domains found in proteins such as sea urchin egg lectin (SUEL), plant beta-galactosidases, mammalian latrophilins, and catfish rhamnose-binding lectin (SAL) eggs. Due to the lack of rhamnose-binding key residues, the galactose/rhamnose-binding lectin-like domains of P113 do not form a binding pocket for rhamnose. Therefore, P113 is unlikely to act as a rhamnose-binding lectin. This model corresponds to the first galactose/rhamnose binding lectin-like domain of P113. 98 matched cddid_all.tbl CDD cd22848 cd22848 438705 Gal_Rha_Lectin_like-P113_rpt2 second galactose/rhamnose binding lectin-like domain found in Plasmodium falciparum P113 and similar proteins. P113 is an abundant glycosylphosphatidylinositol (GPI)-anchored merozoite surface protein that tethers the RH5:CyRPA:RIPR complex to the merozoite surface. The N-terminal region of P113 contains two closely interacting domains, which resemble the galactose/rhamnose-binding lectin domains found in proteins such as sea urchin egg lectin (SUEL), plant beta-galactosidases, mammalian latrophilins, and catfish rhamnose-binding lectin (SAL) eggs. Due to the lack of rhamnose-binding key residues, the galactose/rhamnose-binding lectin-like domains of P113 do not form a binding pocket for rhamnose. Therefore, P113 is unlikely to act as a rhamnose-binding lectin. This model corresponds to the second galactose/rhamnose binding lectin-like domain of P113. 96 matched cddid_all.tbl CDD cd22849 cd22849 439366 NuzM NuzM subunit of NADH:Ubiquinone Oxidoreductase. The NuzM subunit is a fungal specific subunit of NADH:ubiquinone oxidoreductase (respiratory complex I) which is a redox-driven proton pump that plays a central role in aerobic energy metabolism. Redox-linked proton translocation by complex I creates the electrochemical gradient that powers mitochondrial adenosine triphosphate synthesis. Loss of NuzM leads to disassembly of fungal complex I, thus making it a potential antifungal drug target. 159 matched cddid_all.tbl CDD cd22850 cd22850 439302 Nsa1_WDR74-like Ribosome biogenesis protein Nsa1 and similar proteins. Ribosome biogenesis protein Nsa1 (Nop7-associated 1) from fungi and WDR74 (WD repeat-containing protein 74) from mammals and plants, are homologous essential factors for ribosome assembly. In cooperation with the assembly factor Rix7/NVL2, Nsa1/WDR74 participates in an early cleavage of the pre-rRNA processing pathway. Rix7/NVL2 is a type II double ring, AAA-ATPase, that may mediate the release of Nsa1/WDR74 from nucleolar pre-60S particles. Nsa1/WDR74 contains an N-terminal seven-bladed beta-propeller WD40 domain that associates with the D1-AAA domain of the AAA-ATPase Rix7/NVL2, and a flexible lysine-rich C-terminus that extends outward from the WD40 domain, and is required for nucleolar localization. 333 matched cddid_all.tbl CDD cd22851 cd22851 439367 SMN_N N-terminal Gemin2-binding domain of the Survival Motor Neuron family. The survival motor neuron (SMN) protein family includes metazoan SMN and fungal SMN-like protein 1 (SMN1). SMN forms the oligomeric core of a multiprotein complex, called the SMN complex, that functions in the assembly and biogenesis of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. It is expressed in all tissues of metazoan organisms, but is particularly expressed at high levels in motor neurons. Schizosaccharomyces pombe SMN1 is essential for viability and has been shown to interact with human SMN and Sm proteins. Loss of function mutations in the SMN gene of humans cause spinal muscular atrophy (SMA), a leading genetic cause of infant mortality. While most eukaryotes have a single copy of the SMN gene, humans have two; the telomeric SMN1 gene is deleted or mutated in SMA patients, whereas the centromeric SMN2 gene is unaffected and can be present in multiple copies. SMN has three highly conserved domains: a short N-terminal region that is responsible for binding with high affinity to Gemin2; a central Tudor domain that recognizes symmetric dimethylarginine (sDMA) modifications in arginine/glycine rich regions of a number of proteins involved in RNA processing, including the Sm proteins; and a C-terminal domain called the YG-box that is primarily responsible for oligomerization. This model represents the N-terminal Gemin2-binding domain of SMN family proteins. 32 matched cddid_all.tbl CDD cd22852 cd22852 439368 SMN_C C-terminal oligomerization domain of the Survival Motor Neuron family. The survival motor neuron (SMN) protein family includes metazoan SMN and fungal SMN-like protein 1 (SMN1). SMN forms the oligomeric core of a multiprotein complex, called the SMN complex, that functions in the assembly and biogenesis of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. It is expressed in all tissues of metazoan organisms, but is particularly expressed at high levels in motor neurons. Schizosaccharomyces pombe SMN1 is essential for viability and has been shown to interact with human SMN and Sm proteins. Loss of function mutations in the SMN gene of humans cause spinal muscular atrophy (SMA), a leading genetic cause of infant mortality. While most eukaryotes have a single copy of the SMN gene, humans have two; the telomeric SMN1 gene is deleted or mutated in SMA patients, whereas the centromeric SMN2 gene is unaffected and can be present in multiple copies. SMN has three highly conserved domains: a short N-terminal region that is responsible for binding with high affinity to Gemin2; a central Tudor domain that recognizes symmetric dimethylarginine (sDMA) modifications in arginine/glycine rich regions of a number of proteins involved in RNA processing, including the Sm proteins; and a C-terminal domain called the YG-box that is primarily responsible for oligomerization. This model represents the C-terminal oligomerization domain of SMN family proteins. 29 matched cddid_all.tbl CDD cd22854 cd22854 439369 PfVFT1-like Plasmodium falciparum Venus Flytrap protein PfVFT1 and similar proteins. PfVFT1 is a highly immunogenic protein, but its biological role in the Plasmodium falciparum parasite is unknown. It is a parasite-specific antigen expressed by the P. falciparum 3D7 strain in both sexual and asexual stages and was identified as a major candidate for inclusion in a multicomponent blood stage malaria vaccine. Bioinformatic analysis predicts a signal peptide with no identifiable membrane anchors suggesting that it coordinates a membrane-associated partner to enable surface localization. Fractionation of detergent-resistance membranes showed that PfVFT1 clusters with GPI-anchored parasite proteins including Pf38, Pf92, Pf113, PfMSP-1, PfMSP-4, PfASP, and PfRAMA. 273 matched cddid_all.tbl CDD cd22857 cd22857 439303 WDR74 WD repeat-containing protein 74. WDR74 (WD repeat-containing protein 74) from mammals and plants is an essential factor for ribosome assembly. In cooperation with the assembly factor NVL2, WDR74 participates in an early cleavage of the pre-rRNA processing pathway. NVL2 is a type II double ring, AAA-ATPase, that may mediate the release of WDR74 from nucleolar pre-60S particles. WDR74 has been implicated in tumorigenesis. In lung cancer, it regulates cell proliferation, cell cycle progression, chemoresistance and cell aggressiveness, by inducing nuclear beta-catenin accumulation and driving downstream Wnt-responsive genes expression. In melanoma, it promotes apoptosis resistance and aggressive behavior by regulating the RPL5-MDM2-p53 pathway. WDR74 contains an N-terminal seven-bladed beta-propeller WD40 domain that associates with the D1-AAA domain of the AAA-ATPase NVL2, and a flexible lysine-rich C-terminus that extends outward from the WD40 domain, and is required for nucleolar localization. 325 matched cddid_all.tbl CDD cd22858 cd22858 439304 Nsa1 Ribosome Biogenesis Protein Nsa1. Ribosome biogenesis protein Nsa1 (Nop7-associated 1) from fungi is an essential factor for ribosome assembly. In cooperation with the assembly factor Rix7, Nsa1 participates in an early cleavage of the pre-rRNA processing pathway. Rix7 is a type II double ring, AAA-ATPase, that may mediate the release of Nsa1 from nucleolar pre-60S particles. The release of Nsa1 from a discrete preribosomal particle may trigger the progression of 60S ribosome biogenesis. Nsa1 is essential for cell viability in yeast. It contains an N-terminal seven-bladed beta-propeller WD40 domain that associates with the D1-AAA domain of the AAA-ATPase Rix7, and a flexible lysine-rich C-terminus that extends outward from the WD40 domain, and is required for nucleolar localization. 399 matched cddid_all.tbl CDD cd22860 cd22860 467471 PDRG1 p53 and DNA damage-regulated protein 1. p53 and DNA damage-regulated protein 1 (PDRG1) is a beta-type subunit of the prefoldin-like complex that is part of the PAQosome (Particle for Arrangement of Quaternary structure) complex. The PAQosome is a cochaperone that assists the chaperone HSP90 in assembly of large protein complexes. PDRG1 acts as a tumor marker in multiple cancer types, including testicular cancer, lung cancer, colorectal cancer, liver cancer, etc. Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. 103 matched cddid_all.tbl CDD cd22861 cd22861 439370 CYHR1_C C-terminal domain of cysteine and histidine-rich protein 1 and similar proteins. Cysteine and histidine-rich protein 1 (CYHR1) was first identified as an interaction partner of murine galectin-3. Its biological function is still unknown, but it has been shown to be a prognostic marker for esophageal squamous cell carcinoma and a biomarker in hemodialysis patients for the response to erythropoietin. CYHR1 contains an N-terminal C3HC4-type RING-HC finger. This model represents the conserved C-terminal domain of unknown function. 156 matched cddid_all.tbl CDD cd22863 cd22863 439379 Sir4_CC_C C-terminal coiled coil domain found in Saccharomyces cerevisiae silent information regulator 4 (Sir4p) and similar proteins. Sir4p is a regulatory protein that plays important roles in silent chromatin at telomeric and silent mating type loci. It physically interacts with another two silent information regulators, Sir2p and Sir3p, to form a complex that may regulate chromatin structure. The C-terminus of Sir4p is critical for its functions in vivo. This model corresponds to the C-terminal coiled coil domain of Sir4. Coiled coil dimerization is essential for telomeric and mating type silencing in Saccharomyces cerevisiae. 79 matched cddid_all.tbl CDD cd22868 cd22868 439371 Swc5_NTD N-terminal domain of Saccharomyces cerevisiae SWR1-complex protein 5 (Swc5), and similar proteins. SWR1-complex protein 5 (Swc5) is involved in chromosome stability. It is a component of the SWR1 complex which mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1, leading to transcriptional regulation of selected genes by chromatin remodeling. This model corresponds to a conserved D/E-rich region at the N-terminus of Swc5, which contains two consecutive DEF/Y motifs (defined here as 5 to 6 D or E residues followed by an aromatic F or Y residue). This region is responsible for the interaction with A-B dimer and participates in the eviction step of H2A-to-H2A.Z exchange reaction. 61 matched cddid_all.tbl CDD cd22869 cd22869 439372 SLX4_RIM2 second RIM (Rtt107 interaction motif) of Saccharomyces cerevisiae structure-specific endonuclease subunit SLX4 and similar proteins. SLX4 is the regulatory subunit that interacts with and increases the activity of different structure-specific endonucleases. It plays distinct roles in protecting genome stability by resolving diverse forms of deleterious DNA structures. SLX4 has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ssDNA. It is critical in maintaining the integrity of the ribosomal DNA (rDNA) loci, where it has a role in re-starting stalled replication forks. It also has Holliday junction resolvase activity in vitro. It interacts with the structure-specific RAD1-RAD10 endonuclease and promotes RAD1-RAD10-dependent 3'-non-homologous tail removal (NHTR) during repair of double-strand breaks by single-strand annealing. SLX4 also promotes recovery from DNA-alkylation-induced replisome stalling during DNA replication by facilitating the error-free mode of lesion bypass. This does not require SLX1 or RAD1-RAD10, but probably regulator of TY1 transposition protein 107 (Rtt107). SLX4 contains two Rtt107 interaction motif (RIM) regions, which are referred to as RIM1 and RIM2, respectively. This model corresponds to the second RIM region. 53 matched cddid_all.tbl CDD cd22875 cd22875 439373 IML3 IML3 domain found in Saccharomyces cerevisiae inner kinetochore subunit IML3 and similar proteins. Increased Minichromosome Loss 3 (IML3) protein, also called CENP-L homolog, constitutive centromere-associated network protein IML3, or minichromosome maintenance protein 19, is a component of the kinetochore, a multiprotein complex that assembles on centromeric DNA and attaches chromosomes to spindle microtubules, mediating chromosome segregation and sister chromatid segregation during meiosis and mitosis. IML3 forms a heterodimer with CHL4. CHL4-IML3 is part of a larger constitutive centromere-associated network (CCAN), also known as central kinetochore CTF19 complex in yeast, which serves as a structural platform for outer kinetochore assembly. 225 matched cddid_all.tbl CDD cd22876 cd22876 467853 Acm1_CIR CIR (central inhibitory region) domain of Saccharomyces cerevisiae APC/C-CDH1 modulator 1 (Acm1) and similar proteins. Acm1 functions as a negative regulator of Cdh1, which is an activator protein responsible for regulating the ubiquitin ligase activity and substrate specificity of the anaphase promoting complex/cyclosome (APC/C). Cdh1 is necessary for various cellular processes, such as exiting from mitosis, cytokinesis, and the formation of prereplicative complexes in G1. Acm1's central inhibitory region (CIR) plays a crucial role in inhibiting Cdh1, and it interacts with the WD40 domain of Cdh1. 67 matched cddid_all.tbl CDD cd22877 cd22877 467854 Srs2_C C-terminal domain of Saccharomyces cerevisiae structural ATP-dependent DNA helicase Srs2 and similar proteins. Srs2, also called RADH, or HPR5, is an ATP-dependent DNA helicase involved in DNA repair at least for UV-induced lesions. The polarity of the helicase activity was determined to be 3' to 5'. The model corresponds to Srs2 C-terminal domain, which harbors tandem receptor motifs that interact independently with proliferating cell nuclear antigen (PCNA) and SUMO; both motifs are required to specifically recognize SUMO-PCNA. 74 matched cddid_all.tbl CDD cd22879 cd22879 467855 Smc5_CC_C C-terminal coiled-coil domain of Saccharomyces cerevisiae structural maintenance of chromosomes protein 5 (Smc5) and similar proteins. Smc5 acts in a DNA repair pathway for removal of UV-induced DNA damage that is distinct from classical nucleotide excision repair and in repair of ionizing radiation damage. It functions in homologous recombination repair of DNA double strand breaks and in recovery of stalled replication forks. Smc5 is a component of the Smc5-Smc6 complex which plays a critical role in chromosome stability maintenance, DNA replication, homologous recombination, and double-stranded DNA damage repair. Smc5 contains N- and C-terminal coiled-coil (CC) domains, which wrap together to form an intertwined coiled-coil structure. The model corresponds to the C-terminal CC domain of Smc5. 73 matched cddid_all.tbl CDD cd22881 cd22881 467856 Mdv1_N N-terminal extended coiled-coil domain of Saccharomyces cerevisiae mitochondrial division protein 1 (Mdv1) and similar proteins. Mdv1, also known as mitochondrial fission 2 protein (FIS2), GAG3, or NET2, is involved in the mitochondrial fission machinery of the yeast Saccharomyces cerevisiae. Together with Fis1 and Dnm1, Mdv1 is an essential component of the machinery that mediates mitochondrial fission, a process crucial for mitochondrial maintenance and function. Mdv1 is an adapter protein that binds Fis1 and Dnm1 to form mitochondrial fission complexes, which facilitate the constriction and fission of the mitochondrial compartment during the late stages of mitochondrial division. Mdv1 works together with Caf4 to recruit Dnm1 to Fis1 on the mitochondrial outer membrane. Mdv1 protein has three domains: N-terminal extension, central coiled coil (CC), and C-terminal WD40 repeat region. The N-terminal extension binds to Fis1, while the CC domain facilitates dimerization of Mdv1 and is responsible for the recruitment of Dnm1 to the mitochondrial membrane. Both are included in this model. The C-terminal WD40 repeat region binds to Dnm1. 108 matched cddid_all.tbl CDD cd22882 cd22882 439374 Atg16_NTD N-terminal domain of Saccharomyces cerevisiae autophagy-related protein 16 (Atg16). Atg16, also called cytoplasm to vacuole targeting protein 11 (CVT11), or SAP18, stabilizes the Atg5-Atg12 conjugate and mediates the formation of the 350 kDa complex, which is necessary for autophagy. The Atg5-Atg12/Atg16 complex is required for efficient promotion of Atg8-conjugation to phosphatidylethanolamine and Atg8 localization to the pre-autophagosomal structure (PAS). Atg16 interacts with the Atg12-Atg5 protein conjugate through its N-terminal domain (NTD) and self-assembles through its coiled-coil (CC) domain. This model corresponds to the NTD of Saccharomyces cerevisiae Atg16; it does not include the NTD of Atg16 from other organisms. 52 matched cddid_all.tbl CDD cd22883 cd22883 439264 ANKRD27_zf Zn-fingernail found in ankyrin repeat domain-containing protein 27 (ANKRD27) and similar proteins. ANKRD27, also called VPS9 domain-containing protein, or VARP, is a multifunctional endosomal protein that acts as a regulatory/accessory factor for retromer-based coats. It may be a guanine exchange factor (GEF) for Rab21, Rab32 and Rab38 and may regulate endosome dynamics. It may also regulate the participation of VAMP7 in membrane fusion events and is involved in peripheral melanosomal distribution of TYRP1 in melanocytes. In addition, ANKRD27 participates in GLUT1 endosome-to-plasma membrane trafficking in a VPS29-dependent manner. ANKRD27 contains two conserved CHPLCxCxxC motifs which are referred to as Zn-fingernails. 38 matched cddid_all.tbl CDD cd22884 cd22884 439375 TOM22 Mitochondrial import receptor subunit TOM22 and similar proteins. Mitochondrial import receptor subunit TOM22, also called mitochondrial 17 kDa assembly protein, mitochondrial 22 kDa outer membrane protein (MOM22), protein MAS17, or translocase of outer membrane (TOM) 22 kDa subunit, is the central component of the TOM receptor complex responsible for the recognition and translocation of cytosolically synthesized mitochondrial preproteins. It may regulate the TOM machinery organization, stability and channel gating. Together with TOM20 and TOM70, TOM22 functions as the transit peptide receptor at the surface of the mitochondrion outer membrane and facilitates the movement of preproteins into the TOM40 translocation pore. The N-terminal region of TOM22 has been shown to have chaperone-like activity, and the C-terminal region faces the intermembrane face. 67 matched cddid_all.tbl CDD cd22885 cd22885 439265 ANKRD27_zf1 first Zn-fingernail found in ankyrin repeat domain-containing protein 27 (ANKRD27) and similar proteins. ANKRD27, also called VPS9 domain-containing protein, or VARP, is a multifunctional endosomal protein that acts as a regulatory/accessory factor for retromer-based coats. It may be a guanine exchange factor (GEF) for Rab21, Rab32 and Rab38 and may regulate endosome dynamics. It may also regulate the participation of VAMP7 in membrane fusion events and is involved in peripheral melanosomal distribution of TYRP1 in melanocytes. In addition, ANKRD27 participates in GLUT1 endosome-to-plasma membrane trafficking in a VPS29-dependent manner. ANKRD27 contains two conserved CHPLCxCxxC motifs which are referred to as Zn-fingernails. This model corresponds to the first Zn-fingernail of ANKRD27. 40 matched cddid_all.tbl CDD cd22886 cd22886 439266 ANKRD27_zf2 second Zn-fingernail found in ankyrin repeat domain-containing protein 27 (ANKRD27) and similar proteins. ANKRD27, also called VPS9 domain-containing protein, or VARP, is a multifunctional endosomal protein that acts as a regulatory/accessory factor for retromer-based coats. It may be a guanine exchange factor (GEF) for Rab21, Rab32 and Rab38 and may regulate endosome dynamics. It may also regulate the participation of VAMP7 in membrane fusion events and is involved in peripheral melanosomal distribution of TYRP1 in melanocytes. In addition, ANKRD27 participates in GLUT1 endosome-to-plasma membrane trafficking in a VPS29-dependent manner. ANKRD27 contains two conserved CHPLCxCxxC motifs which are referred to as Zn-fingernails. This model corresponds to the second Zn-fingernail of ANKRD27. 42 matched cddid_all.tbl CDD cd22887 cd22887 439196 Atg16_CCD Coiled-coiled domain of autophagy-related 16 (Atg16) family proteins. The Atg16 family includes Saccharomyces cerevisiae Atg16 (also called cytoplasm to vacuole targeting protein 11, CVT11, or SAP18), human autophagy-related protein 16-1 (also called APG16-like 1, ATG16L1, or APG16L) and autophagy-related protein 16-2 (also called APG16-like 2, ATG16L2, WD repeat-containing protein 80 or WDR80), and similar proteins. Atg16 stabilizes the Atg5-Atg12 conjugate and mediates the formation of the 350 kDa complex, which is necessary for autophagy. The Atg5-Atg12/Atg16 complex is required for efficient promotion of Atg8-conjugation to phosphatidylethanolamine and Atg8 localization to the pre-autophagosomal structure (PAS). Similarly, human ATG16L1 plays an essential role in autophagy and acts as a molecular scaffold which mediates protein-protein interactions essential for autophagosome formation. ATG16L2, though structurally similar to ATG16L1 and able to form a complex with the autophagy proteins Atg5 and Atg12, is not essential for autophagy. Single-nucleotide polymorphisms in ATG16L1 is associated with an increased risk of developing Crohn disease. Saccharomyces cerevisiae Atg16 contains an N-terminal domain (NTD) that interacts with the Atg5-Atg12 protein conjugate and a coiled-coil domain (CCD) that dimerizes and mediates self-assembly. Human ATG16L1 and ATG16L2 also contains an N-terminal region that binds Atg5, a CCD homologous to the yeast CCD, and a WD40 domain that represents approximately 50% of the full-length protein. This model corresponds to the CCD of Atg16 family proteins. 91 matched cddid_all.tbl CDD cd22888 cd22888 438622 CcO_VIIa_fungal fungal cytochrome c oxidase subunit VIIa. The fungal cytochrome c oxidase subunit VIIa, encoded by the gene COX9, is a subunit of the cytochrome c oxidase (CcO, also called complex IV or CIV), the terminal oxidase in the mitochondrial electron transport chain which drives oxidative phosphorylation. CcO is a multi-chain transmembrane protein complex located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 14 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 11 subunits are encoded within the nuclear genome. The VIIa subunit is the fungal homolog to subunit VIc in higher eukaryotes. It is a single-pass membrane protein and its specific function remains unclear. 53 matched cddid_all.tbl CDD cd22889 cd22889 438576 NDUFA3-like NADH:Ubiquinone Oxidoreductase, NDUFA3 subunit and related proteins. This family includes the NDUFA3 subunit of NADH:ubiquinone oxidoreductase (Respiratory complex I), which is a redox-driven proton pump that plays an important role in creating the electrochemical gradient that powers mitochondrial adenosine triphosphate synthesis. Complex I catalyzes the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD(+) + ubiquinol). Subunit NDUFA3 is a single-pass membrane protein and is considered an accessory subunit. This family also includes N9IM, the homologous subunit from fungi, as well as some plant homologs. 54 matched cddid_all.tbl CDD cd22890 cd22890 467857 ChiS-DBD ChiS-family DNA-Binding domain. This DNA-binding domain (DBD) is found in Vibrio cholerae sensor histidine kinase ChiS and related proteins. ChiS senses chitin, an abundant source of carbon and nitrogen for V. cholerae and other marine bacteria, and in response to chitin activates the expression of the chitin utilization program. ChiS can directly bind to DNA to regulate the expression of the chitobiose operon, chbBCARFG which is required for the uptake and degradation of the chitin disaccharide chitobiose. This ChiS DBD contains a distinct variant of the canonical helix-turn-helix domain (termed a helix-sheet-helix), in which the canonical tight turn of the HTH is replaced with an insertion containing a beta-sheet. Residues within the ChiS helix-sheet-helix are critical for DNA binding. The ChiS DBD is conserved in diverse proteobacterial proteins and may represent a novel group of transcriptional regulators. Unlike prototypical TCSs, that ChiS DNA binding is diminished, rather than stimulated, by phosphorylation, and ChiS may activates gene expression by directly recruiting RNA polymerase. 97 matched cddid_all.tbl CDD cd22891 cd22891 467643 DRWD-N_DmFANCL N-terminal double-RWD domain of Drosophila melanogaster Fanconi anemia group L protein (FANCL) and related proteins. FANCL, also called E3 ubiquitin-protein ligase FANCL, or RING-type E3 ubiquitin transferase FANCL, is an E3 ubiquitin-protein ligase component of the Fanconi anemia (FA) core complex which functions in the repair of interstrand crosslinks (ICLs) a toxic form of DNA damage. FANCL, works in conjunction with the E2 conjugating enzyme UBE2T (FANCT) to add a single ubiquitin to specific lysine residues on FANCD2 and FANCI. The mono-ubiquitinated FANCI-FANCD2 complex is thought to recruit downstream DNA-repair proteins for ICL processing. FANCL is composed of an N-terminal E2-like fold (ELF) domain, a novel double-RWD (DRWD) domain, and a C-terminal RING domain predicted to facilitate E2 binding. The DRWD domain is responsible for substrate binding. The model corresponds to the N-terminal DRWD domain (DRWD-N). 79 matched cddid_all.tbl CDD cd22892 cd22892 467644 DRWD-C_Knl1 C-terminal double-RWD domain of kinetochore scaffold 1 and related proteins. Kinetochore scaffold 1 (KNL1 or Knl1, also known as Spc105, Spc7, and Blinkin) coordinates the spindle assembly checkpoint (SAC), a signaling pathway that delays chromosome segregation until all sister chromatids are properly attached to spindle microtubules (MTs). Knl1 is part of the KMN network, a conserved kinetochore protein complex that connects kinetochores to MTs. Knl1 has been shown to play an effective role in decreasing apoptosis and promoting the proliferation of colorectal cancer cells, suggesting that its inhibition may represent a promising therapeutic approach for colorectal cancer patients. Knl1 contains tandem RWD domains, also known as a double-RWD domain, DRWD, which has been shown to bind the Mis12 complex, consisting of Dsn1 and Nsl1, that tethers directly onto the underlying chromatin layer and mediates kinetochore targeting of Knl1. The model corresponds to the C-terminal double-RWD domain (DRWD-C). 99 matched cddid_all.tbl CDD cd22893 cd22893 439192 PlcA-like phospholipase C similar to Legionella pneumophila PlcA. This family includes phospholipase C (PLC) from Legionella pneumophila (PlcA) and Pseudomonas fluorescens (PlcC), and similar proteins. PlcA and PlcC are secreted phosphatidylcholine-hydrolyzing PLCs. PlcC is involved in P. fluorescens's hemolytic activity. Its preferred substrates are 1-palmitoyl-2-arachidonoyl-phosphatidylcholine and dipalmitoyl-phosphatidylcholine. The active enzyme is a monomer that requires calcium and zinc ions for activity. 318 matched cddid_all.tbl CDD cd22896 cd22896 439377 periphilin-like Vertebrate periphilin-1 and similar proteins. This family contains periphilin (PPHLN1), a component of the Human Silencing Hub (HUSH) complex containing three proteins: periphilin, TASOR and MPP8 (also called MPHOSPH8) and mediates epigenetic repression. The HUSH complex is recruited to genomic loci rich in H3K9me3 and is required to maintain transcriptional silencing by promoting recruitment of SETDB1, a histone methyltransferase that mediates further deposition of H3K9me3 (histone H3 lysine 9 trimethylation), as well as MORC2, a DNA-binding ATPase. The HUSH complex is also involved in the silencing of unintegrated retroviral DNA by being recruited by ZNF638: some part of the retroviral DNA formed immediately after infection remains unintegrated in the host genome and is transcriptionally repressed. In human, periphilin-1, the protein encoded by the gene PPHLN1, is involved in epithelial differentiation and contributes to epidermal integrity and barrier formation. It is one of the several proteins that become sequentially incorporated into the cornified cell envelope during the terminal differentiation of keratinocyte at the outer layers of epidermis. This protein interacts with periplakin, which is known as a precursor of the cornified cell envelope. The cellular localization pattern and insolubility of this protein suggest that it may play a role in epithelial differentiation and contribute to epidermal integrity and barrier formation. Oncogenic fusion protein of Fibroblast Growth Factor Receptor 2 (FGRF2) joined to periphilin 1, that occurs through a chromosomal translocation, is associated with intrahepatic cholangiocarcinoma; FGFR2-PPHLN1 activity requiring FGRF2-driven tyrosine kinase domain and PPHLN1 dimerization domain strongly drives cellular proliferation. 74 matched cddid_all.tbl CDD cd22897 cd22897 439378 Lge1 Transcriptional regulatory protein Lge1 and similar proteins. This fungal transcriptional regulatory protein Lge1 is involved in the ubiquitination of histones H2A and H2B, a step that is vital in the regulation of the transcriptional activity of RNA polymerase II. In Saccharomyces cerevisiae, Lge1 (also called large cells protein 1), together with its interacting partner ubiquitin ligase Bre1, recruits Rad6, forming a complex that is required for H2B monoubiquitination, a process that regulates transcription, DNA replication, and DNA damage response and repair, ensuring the structural integrity of the genome. In S. pombe the equivalent protein to LGE1 appears to be small histone ubiquitination factor 1 (Shf1). 82 matched cddid_all.tbl CDD cd22898 cd22898 438630 Adeh_2942_sensor sensor domain of Anaeromyxobacter dehalogenans histidine kinase Adeh_2942. This model contains the periplasmic sensor domain of Anaeromyxobacter dehalogenans histidine kinase Adeh_2942, which has closest similarity to histidine kinase HK9 from Rhodopseudomonas palustris of an unknown function. Its structure reveals a four-helical bundle, similar to other members in this family. The response regulator of this prototypical two-component system has yet to be identified. 139 matched cddid_all.tbl CDD cd22899 cd22899 438631 NarQ_sensor ligand binding sensor domain of NarQ, and related chemoreceptors. The periplasmic ligand binding sensor domain of NarQ is a histidine kinase receptor that responds to nitrate and nitrite to effect regulation of anaerobic respiration in various bacteria and similar proteins. It forms a homodimer and binds to ligands such as nitrate via the dimerization interface, a feature that appears to be conserved in this domain superfamily. NarQ-NarP sensor-response regulator pair controls Escherichia coli gene expression in response to nitrate and nitrite. NarQ has been shown to interact equally with NarP and NarL response regulators; NarL is the sensor response partner of NarX. 116 matched cddid_all.tbl CDD cd22900 cd22900 438632 NarX_sensor ligand binding sensor domain of NarX, and related chemoreceptors. The periplasmic ligand binding sensor domain of NarX is a histidine kinase receptor that responds to nitrate and nitrite to effect regulation of anaerobic respiration in various bacteria and similar proteins. It forms a homodimer and binds to ligands such as nitrate via the dimerization interface, a feature that appears to be conserved in this domain superfamily. NarX-NarL sensor-response regulator pair controls Escherichia coli gene expression in response to nitrate and nitrite. NarX has been shown to exhibit a clear kinetic preference for NarL over NarP, the sensor response partner of NarQ. 116 matched cddid_all.tbl CDD cd22901 cd22901 438623 CcO_VIc Cytochrome c oxidase subunit VIc. Cytochrome c oxidase subunit VIc (COX6c) is a subunit of the cytochrome c oxidase (CcO, also called complex IV or CIV), the terminal oxidase in the mitochondrial electron transport chain which drives oxidative phosphorylation. CcO is a multi-chain transmembrane protein complex located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 14 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 11 subunits are encoded within the nuclear genome. The VIc subunit is a single-pass membrane protein found only in eukaryotes and its specific function remains unclear. 66 matched cddid_all.tbl CDD cd22902 cd22902 438577 NDUFA3 NADH dehydrogenase 1 alpha subcomplex subunit 3. NADH dehydrogenase 1 alpha subcomplex subunit 3 (NDUFA3) is a subunit of the of NADH:ubiquinone oxidoreductase (Respiratory complex I), which is a redox-driven proton pump that plays an important role in creating the electrochemical gradient that powers mitochondrial adenosine triphosphate synthesis. Subunit NDUFA3 is a single-pass membrane protein and is considered an accessory subunit. NDUFA3, along with subunit NDUFA5, have been shown to be necessary for assembly and/or stability of the matrix arm of human mitochondrial complex I. 80 matched cddid_all.tbl CDD cd22903 cd22903 438578 NI9M NADH:Ubiquinone Oxidoreductase, N9IM subunit. NI9M is a subunit of the NADH:ubiquinone oxidoreductase (Respiratory complex I), which is a redox-driven proton pump that plays an important role in creating the electrochemical gradient that powers mitochondrial adenosine triphosphate synthesis. NI9M is a single-pass membrane protein and a fungal subunit homologous to NADH dehydrogenase 1 alpha subcomplex subunit 3 (NDUFA3) that is considered an accessory subunit. 66 matched cddid_all.tbl CDD cd22904 cd22904 438579 NDUFA3_plant plant NADH:Ubiquinone Oxidoreductase, NDUFA3 subunit. This subfamily contains the NDUFA3-like subunit of plant NADH:Ubiquinone Oxidoreductase (Respiratory complex I), which is a redox-driven proton pump that plays an important role in creating the electrochemical gradient that powers mitochondrial adenosine triphosphate synthesis. NADH dehydrogenase 1 alpha subcomplex subunit 3 (NDUFA3) is a single-pass membrane protein and is considered an accessory subunit. 60 matched cddid_all.tbl CDD cd22905 cd22905 467030 HFD_Dr1 histone-fold domain found in protein Dr1 and similar proteins. Dr1, also called down-regulator of transcription 1 or negative cofactor 2-beta (NC2-beta), is a TATA-binding protein-associated phosphoprotein and inhibitor of class II gene transcription. It forms a heterodimer with DRAP1. The association of the Dr1/DRAP1 heterodimer with TBP results in functional repression of both activated and basal transcription of class II genes. Dr1 can bind to DNA on its own. Dr1 is a component of the ADA2A-containing complex (ATAC) that has histone acetyltransferase activity on histones H3 and H4. 129 matched cddid_all.tbl CDD cd22906 cd22906 467031 HFD_DRAP1 histone-fold domain found in Dr1-associated protein 1 (DRAP1) and similar proteins. DRAP1, also called Dr1-associated corepressor or negative cofactor 2-alpha (NC2-alpha), acts as a corepressor for Dr1 (down-regulator of transcription 1)-mediated repression of transcription. It forms a heterodimer with Dr1. The association of the Dr1/DRAP1 heterodimer with TBP results in a functional repression of both activated and basal transcription of class II genes. DRAP1 can bind to DNA on its own. It also binds TATA-binding protein-associated factor 172 (BTAF1). 75 matched cddid_all.tbl CDD cd22907 cd22907 467032 HFD_NFYB histone-fold domain found in nuclear transcription factor Y subunit beta (NF-YB) and similar proteins. NF-YB, also called CAAT box DNA-binding protein subunit B, or nuclear transcription factor Y subunit B, is a component of the sequence-specific heterotrimeric transcription factor (NF-Y), which specifically recognizes the 5'-CCAAT-3' box motif found in the promoters of its target genes. NF-Y can function as both an activator and a repressor, depending on its interacting cofactors. NF-Y is a heterotrimeric transcription factor composed of three components, NF-YA, NF-YB and NF-YC. NF-YB and NF-YC must interact and dimerize for NF-YA association and DNA binding. 91 matched cddid_all.tbl CDD cd22908 cd22908 467033 HFD_NFYC-like histone-fold domain found in nuclear transcription factor Y subunit gamma (NF-YC) and similar proteins. NF-YC, also called CAAT box DNA-binding protein subunit C, or nuclear transcription factor Y subunit C, or transactivator HSM-1/2, is a component of the sequence-specific heterotrimeric transcription factor (NF-Y) which specifically recognizes a 5'-CCAAT-3' box motif found in the promoters of its target genes. NF-Y can function as both an activator and a repressor, depending on its interacting cofactors. NF-Y is a heterotrimeric transcription factor composed of three components, NF-YA, NF-YB and NF-YC. NF-YB and NF-YC must interact and dimerize for NF-YA association and DNA binding. The family also includes NF-YC homologs such as Aspergillus fumigatus CCAAT-binding complex (CBC) subunit HapE and Saccharomyces cerevisiae transcriptional activator Hap5. HapE is a component of CBC, which is composed of the histone-like subunits HapC and HapE as well as the DNA specificity conferring subunit HapB. In yeast, Hap5 is a component of the CCAT-binding factor (CBF or HAP complex II), which is a transcriptional activator and binds to the upstream activation site (UAS2) of the CYC1 gene and other genes involved in mitochondrial electron transport and activates their expression. It recognizes the sequence 5'-CCAAT-3'. Hap5 is essential for DNA-binding activity. 84 matched cddid_all.tbl CDD cd22909 cd22909 467034 HFD_archaea_histone-like histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription regulators and similar proteins. The family includes many archaeal histone-fold proteins and histone-like transcription regulators, which may bind and compact DNA (95 to 150 base pairs) to form nucleosome-like structures that contain positive DNA supercoils. They can increase the resistance of DNA to thermal denaturation. 64 matched cddid_all.tbl CDD cd22910 cd22910 467035 HFD_H2B histone-fold domain found in histone H2B and similar proteins. Histone H2B is a core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called the histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4, assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Some histone H2B family members have broad antibacterial activity, which may contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid. 94 matched cddid_all.tbl CDD cd22911 cd22911 467036 HFD_H3 histone-fold domain found in histone H3 and similar proteins. Histone H3 is a core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called the histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. 95 matched cddid_all.tbl CDD cd22912 cd22912 467037 HFD_H4 histone-fold domain found in histone H4 and similar proteins. Histone H4 is a core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called the histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. 79 matched cddid_all.tbl CDD cd22913 cd22913 467038 HFD_ABTB2-like histone-fold domain found in ankyrin repeat and BTB/POZ domain-containing protein 2 (ABTB2) and similar proteins. ABTB2, also called Bood POZ containing gene type 2 (BPOZ-2), is a scaffold protein that controls the degradation of many biological proteins ranging from embryonic development to tumor progression. It may be involved in the initiation of hepatocyte growth. It inhibits the aggregation of alpha-synuclein, which has implications for Parkinson's disease. ABTB2 functions as an adaptor protein for the E3 ubiquitin ligase scaffold protein Cullin-3. It directly binds to eukaryotic elongation factor 1A1 (eEF1A1) to promote eEF1A1 ubiquitylation and degradation and prevent translation. It is also involved in the growth suppressive effect of the phosphatase and tensin homolog (PTEN). This subfamily also includes BTB/POZ domain-containing protein 11 (BTBD11), also called ankyrin repeat and BTB/POZ domain-containing protein BTBD11. It is a BTB-domain-containing Kelch-like protein with unknown function. 105 matched cddid_all.tbl CDD cd22914 cd22914 467039 HFD_SOS1_rpt1 first histone-fold domain found in son of sevenless homolog 1 (SOS-1) and similar proteins. SOS-1 is a guanine nucleotide exchange factor for Ras that binds to GRB2. It promotes the exchange of Ras-bound GDP by GTP. It is a catalytic component of a trimeric complex that participates in transduction of signals from Ras to Rac, by promoting the Rac-specific guanine nucleotide exchange factor (GEF) activity. SOS-1 contains tandem histone folds at the N-terminal region. The model corresponds to the first repeat. 78 matched cddid_all.tbl CDD cd22915 cd22915 467040 HFD_SOS1_rpt2 second histone-fold domain found in son of sevenless homolog 1 (SOS-1) and similar proteins. SOS-1 is a guanine nucleotide exchange factor for Ras that binds to GRB2. It promotes the exchange of Ras-bound GDP by GTP. It is a catalytic component of a trimeric complex that participates in transduction of signals from Ras to Rac, by promoting the Rac-specific guanine nucleotide exchange factor (GEF) activity. SOS-1 contains tandem histone folds at the N-terminal region. The model corresponds to the second repeat. 75 matched cddid_all.tbl CDD cd22916 cd22916 467041 HFD_TAF3 histone-fold domain found in transcription initiation factor TFIID subunit 3 (TAF3) and similar proteins. TAF3, also called TATA Binding Protein (TBP) associated factor 3, 140 kDa TATA box-binding protein-associated factor, TBP-associated factor 3, or transcription initiation factor TFIID 140 kDa subunit (TAF(II)140, TAF140, TAFII-140,TAFII140), is a component of the TFIID complex that is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). TFIID is one of the general transcription factors required for accurate and regulated initiation by RNA polymerase II. It plays a central role in mediating promoter responses to various activators and repressors. 92 matched cddid_all.tbl CDD cd22917 cd22917 467042 HFD_TAF6-like histone-fold domain found in transcription initiation factor TFIID subunit 6 (TAF6) and similar proteins. This subfamily includes TAF6 and TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L (TAF6L). TAF6, also called TATA Binding Protein (TBP) associated factor 6, RNA polymerase II TBP-associated factor subunit E, transcription initiation factor TFIID 70 kDa subunit (TAF(II)70, TAFII-70, TAFII70), or transcription initiation factor TFIID 80 kDa subunit, (TAF(II)80, TAFII-80, TAFII80), is a TBP-associated factor (TAF). TAFs are components of the transcription factor IID (TFIID) complex, PCAF histone acetylase complex, and TBP-free TAFII complex (TFTC). TIIFD is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. TFIID and PCAF are composed of TATA binding protein (TBP) and several TAFs. TBP is not part of TFTC. TAF6L, also called PCAF-associated factor 65-alpha (PAF65-alpha), is a component of the PCAF complex, which can efficiently acetylate histones in a nucleosomal context. The PCAF complex is composed of several TAFs and PCAF-associated factors (PAFs). It might be the human version of the yeast SAGA complex. With TAF5L, TAF6L acts as an epigenetic regulator essential for somatic reprogramming. It also regulates target genes through H3K9ac deposition and MYC recruitment, which trigger the MYC regulatory network to orchestrate gene expression programs to control embryonic stem cell state. 64 matched cddid_all.tbl CDD cd22918 cd22918 467043 HFD_TAF8 histone-fold domain found in transcription initiation factor TFIID subunit 8 (TAF8) and similar proteins. TAF8, also called TATA Binding Protein (TBP) associated factor 8, protein taube nuss, TBP-associated factor 43 kDa, TBP-associated factor 8, or transcription initiation factor TFIID 43 kDa subunit (TAFII-43, TAFII43), is a component of the TFIID complex that is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). TFIID is one of the general transcription factors required for accurate and regulated initiation by RNA polymerase II. It plays a central role in mediating promoter responses to various activators and repressors. TAF8 mediates both basal and activator-dependent transcription. It is involved in the differentiation of preadipocyte fibroblasts to adipocytes, however, it does not seem to play a role in differentiation of myoblasts. TAF8 is required for the integration of TAF10 in the TAF complex. It may be important for survival of cells of the inner cell mass which constitute the pluripotent cell population of the early embryo. 84 matched cddid_all.tbl CDD cd22919 cd22919 467044 HFD_CENP-S histone-fold domain found in centromere protein S (CENP-S) and similar proteins. CENP-S, also called MHF1, apoptosis-inducing TAF9-like domain-containing protein 1 (APITD1), FANCM-associated histone fold protein 1, FANCM-interacting histone fold protein 1, or Fanconi anemia-associated polypeptide of 16 kDa (FAAP16), is a DNA-binding component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. CENP-S, together with CENP-X, forms the MHF heterodimer, which can further assemble to form tetrameric structures. CENP-S acts as a crucial cofactor for FANCM, in both binding and ATP-dependent remodeling of DNA. It can stabilize FANCM. CENP-S also forms a discrete complex with FANCM and CENP-X, called FANCM-MHF. This interaction leads to synergistic activation of double-stranded DNA binding and strongly stimulates FANCM-mediated DNA remodeling. In complex with CENP-T, CENP-W and CENP-X (CENP-T-W-S-X heterotetramer), CENP-S is involved in the formation of a functional kinetochore outer plate, which is essential for kinetochore-microtubule attachment and faithful mitotic progression. As a component of MHF and CENP-T-W-S-X complexes, CENP-S binds DNA and bends it to form a nucleosome-like structure. Its DNA-binding function is fulfilled in the presence of CENP-X. It does not bind DNA on its own. 77 matched cddid_all.tbl CDD cd22920 cd22920 467045 HFD_CENP-T histone-fold domain found in centromere protein T (CENP-T) and similar proteins. CENP-T, also called interphase centromere complex protein 22 (ICEN22), is a component of the CENPA-NAC (nucleosome-associated) complex, which plays a central role in the assembly of kinetochore proteins, mitotic progression, and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. CENP-T is also part of a nucleosome-associated complex that binds specifically to histone H3-containing nucleosomes at the centromere, as opposed to nucleosomes containing CENPA. Moreover, CENP-T is a component of the heterotetrameric CENP-T-W-S-X complex that binds and supercoils DNA, and plays an important role in kinetochore assembly. CENP-T has a fundamental role in kinetochore assembly and function. It is one of the inner kinetochore proteins, with most further proteins binding downstream. It is required for normal chromosome organization and normal progress through mitosis. 94 matched cddid_all.tbl CDD cd22921 cd22921 467046 HFD_CENP-X histone-fold domain found in centromere protein X (CENP-X) and similar proteins. CENP-X, also called MHF2, FANCM-associated histone fold protein 2, FANCM-interacting histone fold protein 2, Fanconi anemia-associated polypeptide of 10 kDa, retinoic acid-inducible gene D9 protein homolog, or stimulated by retinoic acid gene 13 protein homolog, is a DNA-binding component of the Fanconi anemia (FA) core complex. It is required for the normal activation of the FA pathway, leading to monoubiquitination of the FANCI-FANCD2 complex in response to DNA damage, cellular resistance to DNA cross-linking drugs, and prevention of chromosomal breakage. CENP-X, together with CENP-S, forms the MHF heterodimer, which can further assemble to form tetrameric structures. CENP-X acts as a crucial cofactor for FANCM in both binding and ATP-dependent remodeling of DNA. It can stabilize FANCM. CENP-X also forms a discrete complex with FANCM and CENP-S, called FANCM-MHF. This interaction leads to synergistic activation of double-stranded DNA binding and strongly stimulates FANCM-mediated DNA remodeling. In complex with CENP-T, CENP-W and CENP-S (CENP-T-W-S-X heterotetramer), CENP-X is involved in the formation of a functional kinetochore outer plate, which is essential for kinetochore-microtubule attachment and faithful mitotic progression. As a component of the MHF and CENP-T-W-S-X complexes, CENP-X binds DNA and bends it to form a nucleosome-like structure. Its DNA-binding function is fulfilled in the presence of CENP-S. It does not bind DNA on its own. 73 matched cddid_all.tbl CDD cd22922 cd22922 467047 HFD_Aq328-like_rpt1 first histone-fold domain found in Aquifex Aeolicus protein Aq328 and similar proteins. This subfamily includes a group of uncharacterized DUF931 family proteins similar to Aquifex Aeolicus protein Aq328 and Thermus Thermophilus protein TTHA1479. Aq328 is possibly a DNA-binding protein that is involved in DNA packaging. The function of TTHA1479 remains unclear. All members contain two cross-shaped antiparallel histone-fold domains. This model corresponds to the first repeat. 72 matched cddid_all.tbl CDD cd22923 cd22923 467048 HFD_Aq328-like_rpt2 second histone-fold domain found in Aquifex Aeolicus protein Aq328 and similar proteins. This subfamily includes a group of uncharacterized DUF931 family proteins similar to Aquifex Aeolicus protein Aq328 and Thermus Thermophilus protein TTHA1479. Aq328 is possibly a DNA-binding protein that is involved in DNA packaging. The function of TTHA1479 remains unclear. All members contain two cross-shaped antiparallel histone-fold domains. The model corresponds to the second repeat. 66 matched cddid_all.tbl CDD cd22924 cd22924 467049 HFD_CHRAC1-like histone-fold domain found in chromatin accessibility complex protein 1 (CHRAC-1) and similar proteins. CHRAC-1, also called chromatin accessibility complex 15 kDa protein, or CHRAC-15, or DNA polymerase epsilon subunit p15, forms a complex with DNA polymerase epsilon subunit POLE3 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome remodeling activity of ISWI/SNF2H and ACF1. Together with POLE3, ACF1 and ISWI/SNF2H proteins, CHRAC-1 forms the ISWI chromatin-remodeling complex, CHRAC. This subfamily also includes Drosophila melanogaster chromatin accessibility complex 16kD protein (CHRAC-16), which is a histone-like protein that promotes nucleosome sliding of ATP-dependent nucleosome remodeling complexes. It is part of the CHRAC, composed of CHRAC-14, CHRAC-16, ACF and ISWI, which uses energy/ATP to increase the general accessibility of DNA in chromatin. It forms a heterodimer with CHRAC-14, binds DNA, and facilitates nucleosome sliding by ACF. It is required for oogenesis. 74 matched cddid_all.tbl CDD cd22925 cd22925 467050 HFD_HFI1-like histone-fold domain found in transcriptional coactivator HFI1, transcriptional adapter 1 (TADA1), and similar proteins. This subfamily includes HFI1 and TADA1. HFI1, also called ADA1, is a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. SAGA (Spt-Ada-Gcn5-acetyltransferase) is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TATA binding protein (TBP) interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA (SAGA altered, SPT8 absent), an altered form of SAGA, may be involved in positive transcriptional regulation. Besides lacking SPT8, SALSA contains an SPT7 subunit that is truncated. SLIK (SAGA-like) is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. HFI1/ADA1 and SPT20/ADA5 may recruit TATA binding protein (TBP) and possibly other basal factors to bind to the TATA box. TADA1, also called SPT3-associated factor 42, or STAF42, or transcriptional adapter 1-like protein (TADA1L), may be involved in transcriptional regulation. It functions as a component of the STAGA transcription coactivator-HAT complex, which is composed of at least SUPT3H, GCN5L2, TAF5L, TAF6L, SUPT7L, TADA3L, TAD1L, TAF10, TAF12, TRRAP, and TAF9. 53 matched cddid_all.tbl CDD cd22926 cd22926 467051 HFD_SPT3 histone-fold domain found in protein SPT3 and similar proteins. SPT3, also called suppressor of Ty 3 homolog, or positive regulator of Ty transcription, is a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. SAGA (Spt-Ada-Gcn5-acetyltransferase) is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TATA binding protein (TBP) interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA (SAGA altered, SPT8 absent), an altered form of SAGA, may be involved in positive transcriptional regulation. Besides lacking SPT8, SALSA contains an SPT7 subunit that is truncated. SPT3 is required for recruitment of TATA-binding protein (TBP) to SAGA-dependent promoters. During SAGA-mediated transcriptional inhibition, SPT3 and SPT8 prevent binding of TBP to the TATA box. SLIK (SAGA-like) is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. SPT factors 3, 7 and 8 are required for the initiation of Ty transcription from the delta promoter. SPT3 regulates Ty1 as well as mating factor genes. 81 matched cddid_all.tbl CDD cd22927 cd22927 467052 HFD_SPT7 histone-fold domain found in protein SPT7 and similar proteins. SPT7, also called suppressor of Ty 7 homolog, is a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. SAGA (Spt-Ada-Gcn5-acetyltransferase) is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TATA binding protein (TBP) interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA (SAGA altered, SPT8 absent), an altered form of SAGA, may be involved in positive transcriptional regulation. Besides lacking SPT8, SALSA contains an SPT7 subunit that is truncated. SLIK (SAGA-like) is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. SPT7 is transcriptional activator of TY elements and other genes. 117 matched cddid_all.tbl CDD cd22928 cd22928 467053 HFD_POLE3_DPB4 histone-fold domain found in DNA polymerase epsilon subunit 3 (POLE3) and similar proteins. POLE3, also called arsenic-transactivated protein (AsTP), chromatin accessibility complex 17 kDa protein (CHRAC-17), DNA polymerase II subunit 3, or DNA polymerase epsilon subunit p17, may participate in DNA repair and in chromosomal DNA replication. It is an accessory component of the DNA polymerase epsilon complex, which consists of four subunits: the catalytic subunit POLE and the accessory subunits POLE2, POLE3 and POLE4. It forms a complex with CHRAC1 and binds naked DNA, which is then incorporated into chromatin, aided by the nucleosome-remodeling activity of ISWI/SNF2H and ACF1. In fungi, POLE3 has been named as DNA polymerase epsilon subunit D (DPB4, also known as DNA polymerase II subunit D). DPB4 acts as an accessory component of the DNA polymerase epsilon (DNA polymerase II) that consists of POL2, DPB2, DPB3 and DPB4, and participates in chromosomal DNA replication. It also functions as a component of the ISW2 complex, which acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA. 87 matched cddid_all.tbl CDD cd22929 cd22929 467054 HFD_POLE4-like histone-fold domain found in DNA polymerase epsilon subunit 4 (POLE4) and similar proteins. POLE4, also called DNA polymerase II subunit 4, or DNA polymerase epsilon subunit p12, may participate in DNA repair and in chromosomal DNA replication. It is an accessory component of the DNA polymerase epsilon complex that consists of four subunits: the catalytic subunit POLE and the accessory subunits POLE2, POLE3 and POLE4. POLE4 forms a complex with POLE3. The POLE3-POLE4 is a histone chaperone that promotes tetrasome formation and DNA supercoiling in vitro. Interaction with POLE3 is a prerequisite for further binding with POLE and POLE2. In fungi, POLE4 has been named as DNA polymerase epsilon subunit C (DPB3, also known as DNA polymerase II subunit C). It is an accessory component of the DNA polymerase epsilon (DNA polymerase II) that participates in chromosomal DNA replication. DNA polymerase epsilon is a heterotetramer consisting of POL2, DPB2, DPB3 and DPB4. DPB3 is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. This subfamily also includes protein DLS1 (DPB3-like subunit of ISW2 complex 1). It functions as a component of the ISW2 complex, which at least consists of ISW2, ITC1, DLS1 and DPB4, and acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA. The ISW2 complex is involved in coordinating transcriptional repression and in inheritance of telomeric silencing. It is involved in repression of MAT a-specific genes, INO1, and early meiotic genes during mitotic growth dependent upon transcription factor UME6 and in a parallel pathway to the RPD3-SIN3 histone deacetylase complex. DLS1 is partially required for the ISW2 complex chromatin remodeling activity and is not required for its interaction with chromatin. 79 matched cddid_all.tbl CDD cd22931 cd22931 467055 HFD_TAF6 histone-fold domain found in transcription initiation factor TFIID subunit 6 (TAF6) and similar proteins. TAF6, also called TATA Binding Protein (TBP) associated factor 6, RNA polymerase II TBP-associated factor subunit E, transcription initiation factor TFIID 70 kDa subunit (TAF(II)70, TAFII-70, TAFII70), or transcription initiation factor TFIID 80 kDa subunit (TAF(II)80, TAFII-80, TAFII80), is a TBP-associated factor (TAF). TAFs are components of the transcription factor IID (TFIID) complex, PCAF histone acetylase complex, and TBP-free TAFII complex (TFTC). TIIFD is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. TFIID and PCAF are composed of TATA binding protein (TBP) and several TAFs. TBP is not part of TFTC. 66 matched cddid_all.tbl CDD cd22932 cd22932 467056 HFD_TAF6L histone-fold domain found in TAF6-like RNA polymerase II p300/CBP-associated factor-associated factor 65 kDa subunit 6L (TAF6L) and similar proteins. TAF6L, also called PCAF-associated factor 65-alpha (PAF65-alpha), is a component of the PCAF complex, which can efficiently acetylate histones in a nucleosomal context. The PCAF complex is composed of several TBP-associated factors (TAFs) and PCAF-associated factors (PAFs). It might be the human version of the yeast SAGA complex. With TAF5L, TAF6L acts as an epigenetic regulator essential for somatic reprogramming. It also regulates target genes through H3K9ac deposition and MYC recruitment, which trigger the MYC regulatory network to orchestrate gene expression programs to control embryonic stem cell state. 72 matched cddid_all.tbl CDD cd22933 cd22933 467057 HFD_HFI1 histone-fold domain found in transcriptional coactivator HFI1 and similar proteins. HFI1, also called ADA1, is a component of the transcription regulatory histone acetylation (HAT) complexes SAGA, SALSA and SLIK. SAGA (Spt-Ada-Gcn5-acetyltransferase) is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TATA binding protein (TBP) interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SALSA (SAGA altered, SPT8 absent), an altered form of SAGA, may be involved in positive transcriptional regulation. Besides lacking SPT8, SALSA contains an SPT7 subunit that is truncated. SLIK (SAGA-like) is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. HFI1/ADA1 and SPT20/ADA5 may recruit TATA binding protein (TBP) and possibly other basal factors to bind to the TATA box. 87 matched cddid_all.tbl CDD cd22934 cd22934 467058 HFD_TADA1 histone-fold domain found in transcriptional adapter 1 (TADA1) and similar proteins. TADA1, also called SPT3-associated factor 42, or STAF42, or transcriptional adapter 1-like protein (TADA1L), may be involved in transcriptional regulation. It functions as a component of the STAGA transcription coactivator-HAT complex, which is composed at least of SUPT3H, GCN5L2, TAF5L, TAF6L, SUPT7L, TADA3L, TAD1L, TAF10, TAF12, TRRAP and TAF9. 84 matched cddid_all.tbl CDD cd22935 cd22935 438575 SctA-like Sct family of secreted proteins similar to SctA. This family includes Dictyostelium discoideum secreted proteins SctA, SctB, SctC, SctD, and similar ptoteins. SctA, also called protein gp17, has been identified in Dictyostelium discoideum as the most abundant protein present in pycnosomes, which are dense structures consisting of membranous materials in endocytic compartments that are constitutively secreted into the extracellular medium. SctA is also found in multilamellar bodies (MLBs), which consist of structures of lysosomal origin composed of multiple concentric membrane layers, that are secreted by amoeba when fed digestible bacteria. The cellular function of pycnosomes and of SctA is as yet unknown. 149 matched cddid_all.tbl CDD cd22936 cd22936 438574 shulin_C20orf194-like Tetrahymena thermophila shulin, human uncharacterized protein C20orf194, and similar proteins. This family contains Tetrahymena thermophila shulin, human uncharacterized protein C20orf194, and similar proteins. Shulin is a negative regulator of the ciliary outer dynein arm (ODA). It binds newly synthesized ODAs, locks the dynein motors together by shutting off motor activity, and facilitates the delivery of ODAs from the cytoplasm to their final position in the cilia. ODAs, together with inner dynein arms (IDAs), are arrayed along a microtubule-based structure called the axoneme and drive the movement of cilia. Human C20orf194 interacts with the small GTPase Arf-like 3 (ARL3) and may act as its effector. The rs6051702 single nucleotide polymorphism (SNP) within the C20orf194 gene is associated with inosine triphosphatase (ITPA) functional gene polymorphisms that were found to influence RBV-induced hemoglobin (Hb)-decline during treatment of chronic hepatitis C patients with pegylated interferon (PEG-IFN) plus ribavirin (RBV). 1092 matched cddid_all.tbl CDD cd22937 cd22937 467858 AcrIF14 Anti-CRISPR type I subtype F14. AcrIF14 (also known as AcrF14) is an anti-CRISPR (Acr) protein that inhibits type I-F CRISPR-Cas surveillance complex (the Csy complex). AcrIF14 was discovered via the guilt-by association (GBA) method, and subsequently confirmed by functional assays to inhibit the type I-F CRISPR-Cas system. GBA is based on the strong co-occurrence and clustering of acr and anti-CRISPR associated (aca) genes through proximity and homology searches. AcrIF14 binds to the Csy complex to block the hybridization of target DNA to the CRISPR RNA (crRNA). Among the 14 AcrIF proteins, at least nine (AcrIF1, AcrIF2, AcrIF4, AcrIF6, AcrIF7, AcrIF8, AcrIF9, AcrIF10 and AcrIF14) stably bind to the Csy complex to inhibit recruitment of either target DNA or nuclease, suggesting direct association with the Csy complex is a major means for inhibition among AcrIF proteins. AcrIF14 also endows the Csy complex with the ability to interact with non-sequence specific dsDNA as AcrIF9 does. However, from structure and biochemical studies, the electropositive patches within the N-terminal domain of AcrIF14 and the PAM recognition loop of the Cas8f subunit of the Csy are essential for the non-sequence-specific dsDNA binding to the Csy-AcrIF14 complex, this is different from the mechanism of AcrIF9. The type I-F Csy complex is a crRNA-guided surveillance complex composed of a crRNA and nine Cas proteins (one Cas8f, one Cas5f, one Cas6f, and six Cas7f), which recruits a nuclease-helicase protein Cas3 for target degradation. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 1 systems utilize RNA-guided complexes consisting of multiple Cas proteins as the effector proteins to recognize and cleave target DNA. For Type I CRISPR-Cas systems which are the most widespread in nature, the Cas protein composition of the employed CRISPR ribonucleoprotein (crRNP) complexes differs between seven subtypes (A to F, G). Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 121 matched cddid_all.tbl CDD cd22938 cd22938 438571 Coatomer_WDAD Coatomer WD associated region. The coatomer, which is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunit. It is a heptameric complex that can polymerize into a cage to deform the membrane into a bud. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. This model corresponds to the WD-associated region (WDAD) found in coatomer subunits alpha, beta, and beta' and is composed of a beta-propeller and an alpha-solenoid. The WD40 domain is found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly. It typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40. Between the GH and WD lies a conserved core. It forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet. Each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade. The last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure. The residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands allowing them to bind either stably or reversibly. 474 matched cddid_all.tbl CDD cd22947 cd22947 438572 Coatomer_WDAD_beta-like Coatomer WD Associated Region from Coatomer Subunit Beta and Beta'. Coatomer subunit beta', also called beta'-coat protein; beta'-COP; p102, is a component of the coatomer, which is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunit. It is a heptameric complex that can polymerize into a cage to deform the membrane into a bud. This model corresponds to the WD-associated (WDAD) region found in coatomer subunits beta and beta' and is composed of a beta-propeller and an alpha-solenoid. The WD40 domain is found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly. It typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40. Between the GH and WD lies a conserved core. It forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet. Each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade. The last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure. The residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands allowing them to bind either stably or reversibly. 475 matched cddid_all.tbl CDD cd22948 cd22948 438573 Coatomer_WDAD_alpha Coatomer WD Associated Region from Coatomer Subunit Alpha. Coatomer subunit alpha, also called alpha-coat protein; Alpha-COP; HEPCOP, is a component of the coatomer, which is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunit. It is a heptameric complex that can polymerize into a cage to deform the membrane into a bud. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. This model corresponds to the WD-associated region (WDAD) found in coatomer subunit alpha and is composed of a beta-propeller and an alpha-solenoid. The WD40 domain is found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly. It typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40. Between the GH and WD lies a conserved core. It forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet. Each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade. The last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure. The residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands allowing them to bind either stably or reversibly. 452 matched cddid_all.tbl CDD cd22949 cd22949 439385 ELC_N N-terminal domain of Myosin essential light chain ELC. ELC is part of the apicomplexan membrane-associated protein complex called the glideosome, which is essential for parasite motility. The glideosome is composed of six proteins: myosin A (MyoA), essential light chain ELC, myosin light chain MLC1 (also called MTIP), and the glideosome-associated proteins GAP40, GAP45, and GAP50. MyoA is a Class XIV myosin implicated in gliding motility, as well as host cell and tissue invasion by parasites. ELC binds to the MyoA neck region adjacent to the MLC1-binding site, and both myosin light chains co-located to the glideosome. Although ELCs bind to a conserved MyoA sequence, P. falciparum ELC adopts a distinct structure in the free and MyoA-bound state. Therefore ELCs enhance MyoA performance by inducing alpha helical structure formation in MyoA and thus stiffening its lever arm. It has been shown that disruption of MyoA, MLC1, or ELC have dramatic effects on parasite motility but do not affect parasite shape or replication. The ELC N-terminal domain is part of the EF-hand calcium binding motif superfamily. Calcium binding has no effect on the structure of ELCs. 66 matched cddid_all.tbl CDD cd22950 cd22950 438570 petO Cytochrome b6-f complex subunit petO. Chloroplastic cytochrome b6-f complex subunit petO (or PETO), also called cytochrome b6-f complex subunit V (suV) or cytochrome b6-f-associated phosphoprotein, is a novel cytochrome b6-f subunit specific in green algae that is predicted by sequence analysis and biochemical characterization to have a one transmembrane alpha-helix topology with two large hydrophilic domains extending on the stromal and lumenal side of the thylakoid membranes, with a lumenal location of the N-terminus. It is reversibly phosphorylated upon state transition, and may have a possible role in signal transduction during redox-controlled short term and long term adaptation of the eukaryotic photosynthetic apparatus. PetO has been shown to contribute to the cyclic electron flow (CEF) around photosystem I (PSI) and cytochrome b6-f that generates ATP. 165 matched cddid_all.tbl CDD cd22951 cd22951 438569 C5_RaCI-like Rhipicephalus appendiculatus C5 Inhibitor (RaCI) and similar proteins. This family includes Rhipicephalus appendiculatus C5 inhibitors RaCI1 and RaCI2, Dermacentor andersoni RaCI3, and other homologs. These are novel tick-derived C5 inhibitors that do not share any similarity to previously characterized tick complement inhibitors such as OmCI. Complement C5 activation generates the potent anaphylatoxin C5a and leads to pathogen lysis, inflammation, and cell damage. RaCI binds human C5 and blocks the generation of C5a and membrane attack complex formation. The small size of RaCI compared with OmCI, and their different target sites on C5 (C5d-CUB and C5d-MG1-MG2, respectively), may help define better therapeutic complement 5 inhibitors. 65 matched cddid_all.tbl CDD cd22952 cd22952 438568 ART10-like Arrestin-related trafficking adapter 10 and similar proteins. Arrestin-related trafficking adaptors (ARTs) function by targeting specific plasma membrane proteins to the endocytic system. They contain multiple PY motifs that are required for recruitment of Rsp5/Nedd4-like ubiquitin ligase which modifies the cargoes. It has been proposed that ARTs remodel the cell surface in response to environmental cues and may serve as part of a quality-control system at the plasma membrane, targeting damaged and misfolded membrane proteins for ubiquitination and subsequent degradation in the lysosome/vacuole. The specific target protein for ART10 is not yet known. 409 matched cddid_all.tbl CDD cd22954 cd22954 438567 PLL_lectin PLL-type lectin with a 7-bladed beta-propeller topology. This model characterizes a family of lectins with a seven-bladed beta-propeller topology, which may specifically bind to O-methylated sugars, a carbohydrate modification whose function is not entirely understood. The pattern of methylation may be associated with defense agains pathogens, and family members such as PLL2 and PHL could play a role in circumventing host immune system defenses. Family member PLL3 has also been shown to interact with O-methylated glycans, but has higher affinity to L-fucose and its derivatives. 344 matched cddid_all.tbl CDD cd22955 cd22955 438566 TOS6 GPI-anchored protein TOS6. TOS6 is a glycosylphosphatidyl inositol (GPI)-anchored protein. The GPI-anchor is attached to the protein in the endoplasmic reticulum and serves to target the protein to the cell surface. The function of TOS6 is not known, but Saccharomyces cerevisiae Delta tos6 strains show significantly higher beta-glucosidase (BGL)-activity while maintaining wild type growth. 104 matched cddid_all.tbl CDD cd22957 cd22957 438526 DD_R_PKA_DPY30-like dimerization/docking (D/D) domains found in the cAMP-dependent protein kinase regulatory subunit (PRKAR) and the DPY30/SDC1-like family. This hierarchy includes the dimerization/docking (D/D) domains of type I and type II cAMP-dependent protein kinase (PKA) regulatory (R) subunits, DPY30 from animals and its homologs, SDC1 from yeasts, and similar domains. PKA is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of R subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. The R subunit contains an N-terminal D/D domain, a linker with an inhibitory sequence (IS), and two c-AMP binding domains. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. DPY30, also called dumpy-30, was initially discovered in Caenorhabditis elegans as a key player in X chromosome dosage compensation. Human DPY30 plays a dual function in moderately regulating the methyltransferase activity of SET1/COMPASS (COMplex of Proteins ASsociated with Set1) enzymes and contributing to the recruitment of the complex to chromatin. Yeast SDC1 (suppressor of CDC25 protein 1) is the smallest subunit of COMPASS (COMplex of Proteins ASsociated with Set1) and interacts exclusively with Bre2 at the distal end of the catalytic module. It positively regulates the COMPASS catalytic module by stabilizing the non-canonical Bre2 SPRY domain. DPY30/SDC1 contains a C-terminal helical bundle domain that directly interacts with Ash2L (in human)/Bre2 (in yeast) COMPASS through the DPY30-binding motif (DBM). The DPY30/SDC1 helical bundle domain, also called D/D domain, is formed of two alpha-helices that may be analogous to the D/D domain found in regulatory subunit of PKA. 29 matched cddid_all.tbl CDD cd22958 cd22958 438527 DD_DPY30_SDC1-like dimerization/docking (D/D) domain found in the DPY30/SDC1-like family. The DPY30/SDC1-like family includes DPY30 from animals and its homolog SDC1 from yeast, DPY30 domain-containing protein (DYDC), adenylate kinase 7 (AK7), IQ domain-containing protein K (IQCK), nucleoside diphosphate kinase homolog 5 (NDKH5), EF-hand calcium-binding domain-containing protein 5 (EFCAB5), and Chlamydomonas reinhardtii flagellar radial spoke proteins, RSP2 and RSP23. DPY30, also called dumpy-30, was initially discovered in Caenorhabditis elegans as a key player in X chromosome dosage compensation. Human DPY30 plays a dual function in moderately allosterically regulating the methyltransferase activity of SET1/COMPASS (COMplex of Proteins ASsociated with Set1) enzymes and contributing to the recruitment of the complex to chromatin. Yeast SDC1, also called complex proteins associated with SET1 protein SDC1, Set1C component SDC1, or suppressor of CDC25 protein 1, is the smallest subunit of COMPASS (COMplex of Proteins ASsociated with Set1) and interacts exclusively with Bre2 at the distal end of the catalytic module. It positively regulates the COMPASS catalytic module by stabilizing the non-canonical Bre2 SPRY domain. DYDC1 plays a crucial role during acrosome biogenesis. AK7 (EC2.7.4.3/EC 2.7.4.6), also called ATP-AMP transphosphorylase 7, is a nucleoside monophosphate (NMP) kinase that catalyzes the reversible transfer of the terminal phosphate group between nucleoside triphosphates and monophosphates. It is involved in maintaining ciliary structure and function. IQ motif-containing proteins may play an active role in cell polarization and migration, and even in ciliary function. The function of IQCK remains unclear. NDKH5, also called NME5, NDP kinase homolog 5, inhibitor of p53-induced apoptosis-beta (IPIA-beta), testis-specific nm23 homolog, or nm23-H5, is specifically expressed in testis germinal cells. It may not have NDK kinase activity. It confers protection from cell death by Bax and alters the cellular levels of several antioxidant enzymes including Gpx5. It may play a role in spermiogenesis by increasing the ability of late-stage spermatids to eliminate reactive oxygen species. RSP2 is a calmodulin binding spoke stalk protein required for motility in Chlamydomonas reinhardtii. It binds calmodulin in a calcium-dependent manner. RSP23, also called p61, is a functional Ca2+/calmodulin-regulated nucleoside diphosphate kinase (NDK) from the flagella of Chlamydomonas that is present in the radial spoke stalk. It binds calmodulin in a calcium-dependent manner. Members of this family contain a DPY30/SDC1 helical bundle domain that is formed by two alpha-helices. The DPY30/SDC1 helical bundle domain is also called D/D domain and might be analogous to the D/D domain found in the regulatory subunit of cAMP-dependent protein kinase (PKA). 40 matched cddid_all.tbl CDD cd22959 cd22959 438528 DD_C11orf49 dimerization/docking (D/D) domain found in UPF0705 protein C11orf49 and similar proteins. UPF0705 protein C11orf49 is an uncharacterized protein which contains an N-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domain of regulatory subunit of cAMP-dependent protein kinase (PKA). 53 matched cddid_all.tbl CDD cd22960 cd22960 438529 DD_TPGS1 dimerization/docking (D/D) domain found in tubulin polyglutamylase complex subunit 1 (TPGS1) and similar proteins. TPGS1 is part of the neuronal tubulin polyglutamylase complex which contains TPGS1, TPGS2, TTLL1, LRRC49 and NICN1. It is required for the development of the spermatid flagellum. TPGS1 contains an N-terminal domain which shows high sequence similarity to the dimerization/docking (D/D) domain of regulatory subunit of cAMP-dependent protein kinase (PKA). 39 matched cddid_all.tbl CDD cd22961 cd22961 438530 DD_TEX55-like dimerization/docking (D/D) domain found in the testis-specific expressed protein 55 (TEX55)-like family. The TEX55-like family includes TEX55, F-box/LRR-repeat protein 13 (FBXL13), adenylate kinase isoenzymes AK5 and AK8, as well as uncharacterized EF-hand calcium-binding domain-containing protein 10 (EFCAB10), and protein VEST-1. TEX55, also called testis-specific conserved cAMP-dependent type II PK-anchoring protein (TSCPA), is a putative A-kinase anchoring protein (AKAP) that is dispensable for male fertility. FBXL13, also called F-box and leucine-rich repeat protein 13, or dynein regulatory complex subunit 6 (DRC6), is a component of the nexin-dynein regulatory complex (N-DRC), a key regulator of ciliary/flagellar motility which maintains the alignment and integrity of the distal axoneme and regulates microtubule sliding in motile axonemes. It may also function as a substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. AK5 and AK8 act as nucleoside monophosphate (NMP) kinases that catalyze the reversible transfer of the terminal phosphate group between nucleoside triphosphates and monophosphates. Members of this family contain a conserved helical bundle domain that shows high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1. 43 matched cddid_all.tbl CDD cd22962 cd22962 438531 DD_AtENO3-like dimerization/docking (D/D) domain found in Arabidopsis thaliana cytosolic enolase 3 (ENO3) and similar proteins. Enolase (EC 4.2.1.11), also known as phosphopyruvate hydratase, is a metalloenzyme responsible for catalyzing the conversion of 2-phosphoglycerate (2-PG) to phosphoenolpyruvate (PEP), the ninth and penultimate step of glycolysis. The subfamily includes Arabidopsis thaliana ENO3, also called ENOC, 2-phospho-D-glycerate hydro-lyase 3, or 2-phosphoglycerate dehydratase 3. It contains an N-terminal domain which shows high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1. 45 matched cddid_all.tbl CDD cd22963 cd22963 438532 DD_CrRSP4-like dimerization/docking (D/D) domain found in Chlamydomonas reinhardtii flagellar radial spoke protein 4 (RSP4) and similar proteins. Flagellar radial spokes contribute to the regulation of dynein arm activity and thus the pattern of flagellar bending. They consist of a thin stalk, which is attached to a subfiber of the outer doublet microtubule, and a bulbous head, which is attached to the stalk and appears to interact with the projections from the central pair of microtubules. The radial spoke head is made of five different polypeptides (RSP1, RSP4, RSP6, RSP9, and RSP10). This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologs, including mammalian RSHL1 (also called RSPH6A) and RSHL3 (also called RSPH4A), the protein products of familial ciliary dyskinesia candidate genes. RSHL1 is essential for sperm flagellar assembly and male fertility. RSHL3 is a component of the axonemal radial spoke head which plays an important role in ciliary motility. It is required for triplet radial spokes (RS1, RS2 and RS3) head assembly in the motile cilia. Members of this family contain an N-terminal domain which shows high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1. 51 matched cddid_all.tbl CDD cd22964 cd22964 438533 DD_CrRSP_unchar dimerization/docking (D/D) domain of an uncharacterized subunit found in Chlamydomonas reinhardtii radial spoke 1. Flagellar radial spokes contribute to the regulation of dynein arm activity and thus the pattern of flagellar bending. They consist of a thin stalk, which is attached to a subfiber of the outer doublet microtubule, and a bulbous head, which is attached to the stalk and appears to interact with the projections from the central pair of microtubules. This subfamily includes an uncharacterized protein found in Chlamydomonas reinhardtii radial spoke 1. It contains a conserved domain that shows high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1. 46 matched cddid_all.tbl CDD cd22965 cd22965 438534 DD_DPY30_SDC1 dimerization/docking (D/D) domain found in the DPY30/SDC1 family. This family includes DPY30 from animals and its homologs, including SDC1 from yeast. DPY30, also called dumpy-30, was initially discovered in Caenorhabditis elegans as a key player in X chromosome dosage compensation. Human DPY30 plays a dual function in moderately allosterically regulating the methyltransferase activity of SET1/COMPASS (COMplex of Proteins ASsociated with Set1) enzymes and contributing to the recruitment of the complex to chromatin. DPY30 is the core component of several methyltransferase-containing complexes including MLL1/MLL, MLL2/3 (also named ASCOM complex) and MLL4/WBP7. As part of the MLL1/MLL complex, DPY30 is involved in the methylation of histone H3 at 'Lys-4', particularly trimethylation. Histone H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. In a teratocarcinoma cell, DPY30 plays a crucial role in retinoic acid-induced differentiation along the neural lineage, regulating gene induction and H3 'Lys-4' methylation at key developmental loci. It may also play an indirect or direct role in endosomal transport. Yeast SDC1, also called complex proteins associated with SET1 (COMPASS) protein SDC1, Set1C component SDC1, or suppressor of CDC25 protein 1, is the smallest subunit of COMPASS and interacts exclusively with Bre2 at the distal end of the catalytic module. It positively regulates the COMPASS catalytic module by stabilizing the non-canonical Bre2 SPRY domain. The COMPASS (Set1C) complex specifically mono-, di- and trimethylates histone H3 to form H3K4me1/2/3, which subsequently activates gene expression by regulating transcription elongation and plays a role in telomere length maintenance. This model corresponds to the C-terminal helical bundle domain of DPY30/SDC1, which is called dimerization/docking (D/D) domain. It forms a homodimer, which directly interacts with the Ash2L (Bre2 in yeast) subunit of COMPASS through its DPY30-binding motif (DBM). 41 matched cddid_all.tbl CDD cd22966 cd22966 438535 DD_DYDC-like dimerization/docking (D/D) domain found in the DPY30 domain-containing protein (DYDC)-like family. The DYDC-like family includes DYDC1 and DYDC2, as well as Chlamydomonas reinhardtii flagellar radial spoke protein 2 (RSP2) and similar proteins. DYDC1 plays a crucial role during acrosome biogenesis. RSP2 is a calmodulin binding spoke stalk protein required for motility in Chlamydomonas reinhardtii. It binds calmodulin in a calcium-dependent manner. Members of this family contain an N-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domain of protein DPY-30/SDC1. 44 matched cddid_all.tbl CDD cd22967 cd22967 438536 DD_AK7 dimerization/docking (D/D) domain found in adenylate kinase 7 and similar proteins. Adenylate kinase (AK7, EC2.7.4.3/EC 2.7.4.6), also called ATP-AMP transphosphorylase 7, is a nucleoside monophosphate (NMP) kinase that catalyzes the reversible transfer of the terminal phosphate group between nucleoside triphosphates and monophosphates. It has highest activity toward AMP, and weaker activity toward dAMP, CMP and dCMP. It also displays broad nucleoside diphosphate kinase activity. AK7 is involved in maintaining ciliary structure and function. This model corresponds to the C-terminal domain of AK7, which shows high sequence similarity to the dimerization/docking (D/D) domain of protein DPY-30/SDC1. 41 matched cddid_all.tbl CDD cd22968 cd22968 438537 DD_EFCAB5 dimerization/docking (D/D) domain found in EF-hand calcium-binding domain-containing protein 5 (EFCAB5) and similar proteins. EF-hand calcium-binding domain-containing protein 5 (EFCAB5) is an uncharacterized protein that contains an N-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domain of protein DPY-30/SDC1. 60 matched cddid_all.tbl CDD cd22969 cd22969 438538 DD_IQCK dimerization/docking (D/D) domain found in IQ domain-containing protein K (IQCK) and similar proteins. IQ motif-containing proteins may play an active role in cell polarization and migration, and even in ciliary function. Although its function remains unclear, IQCK contains a conserved region that shows high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1. 58 matched cddid_all.tbl CDD cd22970 cd22970 438539 DD_NDKH5-like dimerization/docking (D/D) domain found in nucleoside diphosphate kinase homolog 5 (NDKH5)-like family. The NDKH5 family includes NDKH5, Chlamydomonas reinhardtii flagellar radial spoke protein 23 (RSP23) and similar proteins. NDKH5, also called NME5, NDP kinase homolog 5, inhibitor of p53-induced apoptosis-beta (IPIA-beta), testis-specific nm23 homolog, or nm23-H5, is specifically expressed in testis germinal cells. It may not have NDK kinase activity. It confers protection from cell death by Bax and alters the cellular levels of several antioxidant enzymes including Gpx5. It may play a role in spermiogenesis by increasing the ability of late-stage spermatids to eliminate reactive oxygen species. RSP23, also called p61, is a functional Ca2+/calmodulin-regulated nucleoside diphosphate kinase (NDK) from the flagella of Chlamydomonas that is present in the radial spoke stalk. It binds calmodulin in a calcium-dependent manner. Members of this family contain a C-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domain of protein DPY-30/SDC1. 45 matched cddid_all.tbl CDD cd22971 cd22971 438540 DD_RIIAD1 dimerization/docking (D/D) domain found in RIIa domain-containing protein 1 (RIIAD1) and similar proteins. The family includes uncharacterized RIIa domain-containing protein 1 (RIIAD1), which contains a C-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domain of regulatory subunit of cAMP-dependent protein kinase (PKA). 41 matched cddid_all.tbl CDD cd22972 cd22972 438541 DD_ROP-like dimerization/docking (D/D) domain found in the ropporin (ROP)-like subfamily. The ROP-like family includes ropporin-1A (ROP1A, also called cancer/testis antigen 91, CT91, or rhophilin-associated protein 1A), ropporin-1B (ROP1B, also called rhophilin-associated protein 1B), and ropporin-1-like protein (ROPN1L, also called ROPN1-like protein, AKAP-associated sperm protein, or ASP), as well as Chlamydomonas reinhardtii flagellar radial spoke proteins, RSP7 and RSP11. ROP1A, ROP1B and ROPN1L play important roles in male fertility. They are involved in fibrous sheath integrity and sperm motility and play roles in cAMP-dependent protein kinase (PKA)-dependent signaling processes required for spermatozoa capacitation. RSP7 is a PKA RII-like protein. RSP11 is a non-PKA RIIa protein that contains a RII domain but lack any features required for cAMP signaling or phosphorylation. It is involved in the control of ciliary and flagellar beating. Members of this subfamily contain a conserved helical bundle domain that shows high sequence similarity to the dimerization/docking (D/D) domain of the regulatory subunit of PKA. 43 matched cddid_all.tbl CDD cd22973 cd22973 438542 DD_CATIP dimerization/docking (D/D) domain found in ciliogenesis-associated TTC17-interacting protein (CATIP) and similar proteins. CATIP, also called C2orf62, plays a role in primary ciliogenesis by modulating actin polymerization. It interacts with TTC17. Mutations in CATIP may contribute to asthenozoospermia through its involvement in actin polymerization and the actin cytoskeleton. CATIP contains a C-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domain of regulatory subunit of cAMP-dependent protein kinase (PKA). 40 matched cddid_all.tbl CDD cd22974 cd22974 438543 DD_ENO4 dimerization/docking (D/D) domain found in enolase 4 and similar proteins. Enolase (EC 4.2.1.11), also known as phosphopyruvate hydratase, is a metalloenzyme responsible for the catalyzing the conversion of 2-phosphoglycerate (2-PG) to phosphoenolpyruvate (PEP), the ninth and penultimate step of glycolysis. ENO4, also called 2-phospho-D-glycerate hydro-lyase, may be required for sperm motility and function. It contains an N-terminal domain which shows high sequence similarity to the dimerization/docking (D/D) domain of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1. 65 matched cddid_all.tbl CDD cd22975 cd22975 438544 DD_TEX55 dimerization/docking (D/D) domain found in testis-specific expressed protein 55 (TEX55) and similar proteins. TEX55, also called testis-specific conserved cAMP-dependent type II PK-anchoring protein (TSCPA), is a putative A-kinase anchoring protein (AKAP) that is dispensable for male fertility. It contains a C-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1. 50 matched cddid_all.tbl CDD cd22976 cd22976 438545 DD_EFCAB10 dimerization/docking (D/D) domain found in EF-hand calcium-binding domain-containing protein 10 (EFCAB10) and similar proteins. The subfamily includes uncharacterized EF-hand calcium-binding domain-containing protein 10 (EFCAB10), which contains an N-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1. 47 matched cddid_all.tbl CDD cd22977 cd22977 438546 DD_FBXL13 dimerization/docking (D/D) domain found in F-box/LRR-repeat protein 13 (FBXL13) and similar proteins. FBXL13, also called F-box and leucine-rich repeat protein 13, or dynein regulatory complex subunit 6 (DRC6), is a component of the nexin-dynein regulatory complex (N-DRC), a key regulator of ciliary/flagellar motility which maintains the alignment and integrity of the distal axoneme and regulates microtubule sliding in motile axonemes. It may also function as a substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. It contains an N-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1. 43 matched cddid_all.tbl CDD cd22978 cd22978 438547 DD_AK5 dimerization/docking (D/D) domain found in adenylate kinase isoenzyme 5 (AK5) and similar proteins. AK5 (EC 2.7.4.3/EC 2.7.4.6), also called ATP-AMP transphosphorylase 5, acts as a nucleoside monophosphate (NMP) kinase that catalyzes the reversible transfer of the terminal phosphate group between nucleoside triphosphates and monophosphates. It is active on AMP and dAMP with ATP as a donor. When GTP is used as phosphate donor, the enzyme phosphorylates AMP, CMP, and to a small extent dCMP. It also displays broad nucleoside diphosphate kinase activity. AK5 contains an N-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1. 44 matched cddid_all.tbl CDD cd22979 cd22979 438548 DD_AK8 dimerization/docking (D/D) domain found in adenylate kinase isoenzyme 8 (AK8) and similar proteins. AK8 (EC 2.7.4.3/EC 2.7.4.6), also called ATP-AMP transphosphorylase 8, acts as a nucleoside monophosphate (NMP) kinase that catalyzes the reversible transfer of the terminal phosphate group between nucleoside triphosphates and monophosphates. It has highest activity toward AMP, and weaker activity toward dAMP, CMP and dCMP. It also displays broad nucleoside diphosphate kinase activity. AK8 contains an N-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1. 45 matched cddid_all.tbl CDD cd22980 cd22980 438549 DD_VEST1 dimerization/docking (D/D) domain found in protein VEST-1 and similar proteins. VEST-1 (also called protein C8orf34) is an uncharacterized protein which contains an N-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1. 45 matched cddid_all.tbl CDD cd22981 cd22981 438550 DD_TbAK-like dimerization/docking (D/D) domain found in Trypanosoma brucei adenylate kinase (AK) and similar proteins. AK (EC 2.7.4.3), also called ATP-AMP transphosphorylase, ATP:AMP phosphotransferase, or adenylate monophosphate kinase, catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. It plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Members of this subfamily contain an N-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1. 44 matched cddid_all.tbl CDD cd22982 cd22982 438551 DD_CrRSP2-like dimerization/docking (D/D) domain found in Chlamydomonas reinhardtii flagellar radial spoke protein 2 (RSP2) and similar proteins. Flagellar radial spokes contribute to the regulation of dynein arm activity and thus the pattern of flagellar bending. They consist of a thin stalk, which is attached to the a subfiber of the outer doublet microtubule, and a bulbous head, which is attached to the stalk and appears to interact with the projections from the central pair of microtubules. RSP2 is a calmodulin binding spoke stalk protein required for motility in Chlamydomonas reinhardtii. It binds calmodulin in a calcium-dependent manner. This model corresponds to the C-terminal domain of RSP2, which shows high sequence similarity to the dimerization/docking (D/D) domain of protein DPY-30/SDC1. 53 matched cddid_all.tbl CDD cd22983 cd22983 438552 DD_CrRSP23-like dimerization/docking (D/D) domain found in Chlamydomonas reinhardtii flagellar radial spoke protein 23 (RSP23) and similar proteins. Flagellar radial spokes contribute to the regulation of dynein arm activity and thus the pattern of flagellar bending. They consist of a thin stalk, which is attached to the a subfiber of the outer doublet microtubule, and a bulbous head, which is attached to the stalk and appears to interact with the projections from the central pair of microtubules. RSP23, also called p61, is a functional Ca2+/calmodulin-regulated nucleoside diphosphate kinase (NDK) from flagella of Chlamydomonas that is present in the radial spoke stalk. It binds calmodulin in a calcium-dependent manner. RSP23 consists of an N-terminal catalytic NDK domain followed by a repetitive region that includes three IQ motifs and a highly acidic C-terminal segment, which shows high sequence similarity to the dimerization/docking (D/D) domain of protein DPY-30/SDC1. 58 matched cddid_all.tbl CDD cd22984 cd22984 438553 DD_CrRSP7-like dimerization/docking (D/D) domain found in Chlamydomonas reinhardtii flagellar radial spoke protein 7 (RSP7) and similar proteins. Flagellar radial spokes contribute to the regulation of dynein arm activity and thus the pattern of flagellar bending. They consist of a thin stalk, which is attached to a subfiber of the outer doublet microtubule, and a bulbous head, which is attached to the stalk and appears to interact with the projections from the central pair of microtubules. RSP7 is a cAMP-dependent protein kinase (PKA) RII-like protein. RSP7 contains an N-terminal domain which shows high sequence similarity to the dimerization/docking (D/D) domain of regulatory subunit of PKA. The D/D domain of RSP7 heterodimerizes with the D/D domain of RSP11 to form an X-type four-helix bundle within the radial spoke RS1 complex. 47 matched cddid_all.tbl CDD cd22985 cd22985 438554 DD_CrRSP11-like dimerization/docking (D/D) domain found in Chlamydomonas reinhardtii flagellar radial spoke protein 11 (RSP11) and similar proteins. Flagellar radial spokes contribute to the regulation of dynein arm activity and thus the pattern of flagellar bending. They consist of a thin stalk, which is attached to a subfiber of the outer doublet microtubule, and a bulbous head, which is attached to the stalk and appears to interact with the projections from the central pair of microtubules. RSP11 is a non-PKA (cAMP-dependent protein kinase) RIIa protein that contains a RII domain but lack any features required for cAMP signaling or phosphorylation. It is involved in the control of ciliary and flagellar beating. RSP11 contains an N-terminal domain which shows high sequence similarity to the dimerization/docking (D/D) domain of regulatory subunit of PKA. The D/D domain of RSP11 heterodimerizes with the D/D domain of RSP7 to form an X-type four-helix bundle within the radial spoke RS1 complex. 49 matched cddid_all.tbl CDD cd22987 cd22987 467859 AcrVA2-like Anti-CRISPR type V subtype A2 and similar proteins. AcrVA2 is an anti-CRISPR (Acr) protein that was discovered via STSS (self-targeting spacers search) with further functional TXTL (cell-free transcription-translation) assay. The bioinformatic STSS method finds self-targeting CRISPR spacers in genomic DNA, predicts the type of CRISPR system involved, and obtains information about the targeted sequence. AcrVA2 is found distributed throughout multiple classes of bacteria with orthologs present in Lachnospiraceae and Leptospira. Distant orthologs of AcrVA2 are also present on plasmids and conjugative elements in Escherichia coli, such as protein FinQ, a transcriptional inhibitor of the F plasmid transfer gene. AcrVA2 has been shown to inhibit a CRISPR-associated nuclease Cas12a ortholog MbCas12a in Pseudomonas aeruginosa strains. Cas12a (previously called Cpf1) is an effector protein for the class 2, subtype V-A CRISPR-Cas system that has high efficiency in genome editing. Cas12a has a single nuclease domain (RuvC) that is activated upon binding of the crRNA targeting sequence (or spacer) to a complementary single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA) target molecule; Cas12a also has non-specific ssDNA cleavage activity, known as promiscuous cleavage of collateral ssDNAs or trans-cleavage. In addition to gene editing, CRISPR-Cas12a has been re-purposed, in high eukaryotes, to carry out transcription regulation via a nuclease-dead Cas12a (dCas12a). Thus, AcrVAs have been adopted to regulate dCas12a activity. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Acr proteins are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). The distinguishing feature of types II, V and VI is a single, large, multi-domain effector protein, such as Cas12a in type V subtype A. Type V systems appear to have evolved, on multiple independent occasions, from TnpB proteins (predicted RuvC-like nucleases, encoded by IS605-like transposons) yielding a large pool of type V variants, many of which may become separate subtypes. Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 257 matched cddid_all.tbl CDD cd22990 cd22990 467860 mt-LAF21-like Trypanosoma brucei mitochondrial large subunit assembly factor 21 (mt-LAF21), and related proteins. mt-LAF21 is a Trypanosoma brucei mitochondrial large subunit (mt-LSU) assembly factor (mt-LAF) that plays a role in stabilizing partially mature 12S ribosomal RNA (rRNA) during the assembly process of the mt-LSU. Mitochondrial ribosomes (mitoribosomes) are ribonucleoprotein complexes and consist of a large (mt-LSU) and small subunit (mt-SSU). They differ markedly in composition and architecture from their bacterial counterparts and between different eukaryotic lineages, and their biogenesis involves exchange of assembly factors by ribosomal proteins. An investigation of native assembly intermediates of the mt-LSU from T. brucei identified 28 assembly factors, some of which are homologous to bacterial and eukaryotic ribosome assembly factors. mt-LAF21 is one of nine assembly factors identified as specific to an assembly intermediate referred to as state A, and which stabilizes the 12S rRNA in an immature conformation. Knockdown of mt-LAF21 protein levels in T. brucei cells by tetracycline-inducible RNAi results in a specific reduction of the mt-12S rRNA steady-state level, but not of the SSU mt-9S rRNA, suggesting that mt-LAF21 is required for mt-LSU, but not mt-SSU, maturation. Knockdown of LAF12 also results in a lower growth rate of cells, presumably due to retarded mt-LSU assembly. Mitochondrial biogenesis is biomedically important since mutations in mitoribosomal proteins, rRNAs, and assembly factors have been linked to a heterogeneous group of human multisystemic oxidative phosphorylation (OXPHOS) diseases and cancer development and progression. 473 matched cddid_all.tbl CDD cd22991 cd22991 467861 mt-LAF23-like Trypanosoma brucei mitochondrial large subunit assembly factor 23 (mt-LAF23), and related proteins. mt-LAF23 is a Trypanosoma brucei mitochondrial large subunit (mt-LSU) assembly factor (mt-LAF) that may play a role in stabilizing partially mature 12S ribosomal RNA (rRNA) during the assembly process of the mt-LSU. Mitochondrial ribosomes (mitoribosomes) are ribonucleoprotein complexes and consist of a large subunit (mt-LSU) and a small subunit (mt-SSU). They differ markedly in composition and architecture from their bacterial counterparts and between different eukaryotic lineages, and their biogenesis involves exchange of assembly factors by ribosomal proteins. An investigation of native assembly intermediates of the mt-LSU from T. brucei has identified 28 assembly factors, some of which are homologous to bacterial and eukaryotic ribosome assembly factors. mt-LAF23 is part of a cluster of nine assembly factors identified as specific to an assembly intermediate referred to as state A, and which stabilized the 12S rRNA in an immature conformation. Mitochondrial biogenesis is biomedically important since mutations in mitoribosomal proteins, rRNAs and assembly factors have been linked to a heterogeneous group of human multisystemic oxidative phosphorylation (OXPHOS) diseases, and cancer development and progression. 566 matched cddid_all.tbl CDD cd22992 cd22992 438565 MOC1 Monokaryotic chloroplast 1 protein (MOC1) and similar proteins. Monokaryotic chloroplast 1 protein (MOC1) is a Holliday junction (HJ) resolvase, originally identified from the green algae Chlamydomonas reinhardtii, but was later shown to be genetically conserved among green plants, such as Arabidopsis thaliana and Zea mays. Nicotiana tabacum MOC1 (NtMOC1) is exclusively localized to chloroplasts, and is essential for chloroplast nucleoid segregation. Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. NtMOC1 cleaves only four-way junctions and specifically introduces nicks between two cytosines at the homology core. NtMOC1 has the highest structural similarity to RuvC resolvase, suggesting their potentially similar HJ binding and resolution activities. However, the molecular basis for specific HJ resolution by MOC1 remains elusive. This family also includes bacterial homologs. 151 matched cddid_all.tbl CDD cd22997 cd22997 438557 GT_LH catalytic glycosyltransferase (GT) domain found in the lysyl hydroxylase (LH) family. The lysyl hydroxylase (LH) family includes LH1-3. LH1 (EC 1.14.11.4, also called procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 or PLOD1) and LH2 (EC 1.14.11.4, also called procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 or PLOD2) form hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines may serve as sites of attachment for carbohydrate units and are essential for stability of the intermolecular collagen cross-links. LH1 is part of a complex composed of PLOD1, P3H3 and P3H4 that catalyzes hydroxylation of lysine residues in collagen alpha chains and is required for normal assembly and cross-linking of collagen fibrils. LH3 (EC 1.14.11.4/EC 2.4.1.50/EC 2.4.1.66), also called procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 (PLOD3), or multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3, is a multifunctional enzyme that catalyzes a series of essential post-translational modifications on Lys residues in procollagen. It converts collagen lysines into 1,2-glucosylgalactosyl-5-hydroxylysines through three consecutive reactions: hydroxylation of collagen lysines (LH activity), N-linked conjugation of galactose to hydroxylysines (GT activity), and conjugation of glucose to galactosyl-5-hydroxylysines (GGT activity). LH3 monomer encompasses three domains; the first two N-terminal domains (catalytic glycosyltransferase domain and accessory domain) show Rossmann-fold architectures reminiscent of glycosyltransferases, whereas the C-terminal domain is characterized by a double-stranded beta-helix (DSBH) fold, highly conserved among the 2-oxoglutarate, Fe2+-dependent dioxygenases. This model corresponds to the N-terminal catalytic glycosyltransferase (GT) domain, which is solely responsible for glycosyltransferase activities (both GT and GGT). 247 matched cddid_all.tbl CDD cd22999 cd22999 439380 SAP_SLX4 SAP domain of structure-specific endonuclease subunit SLX4 and similar proteins. SLX4, also called BTB/POZ domain-containing protein 12 (BTBD12), is a Holliday junction resolvase subunit that binds multiple DNA repair/recombination endonucleases and is required for DNA repair. Mutations in the SLX4 gene are found in Fanconi anemia. This model corresponds to a conserved region called the SAP domain, which is responsible for the binding of MUS81, which plays a distinct role in interstrand crosslink repair. 51 matched cddid_all.tbl CDD cd23000 cd23000 439386 AVR-Pik_HID HMA interaction domain found in Pyricularia oryzae AVR-Pik and similar proteins. Microbial plant pathogens secrete effector proteins that can be recognized by plant intracellular nucleotide-binding leucine-rich repeat (NLR) receptors, initiating an immune response. AVR-Pik protein is an effector from the rice blast fungus Pyricularia oryzae (also known as Magnaporthe oryzae). It binds and stabilizes rice heavy metal-associated (HMA)-domain containing NLR proteins to co-opt their function to suppress immunity. AVR-Pik adopts a six-stranded beta-sandwich structure. There are four AVR-Pik alleles, AVR-PikA, AVR-PikC, AVR-PikD, AVR-PikE. 74 matched cddid_all.tbl CDD cd23002 cd23002 438558 GT_LH3 catalytic glycosyltransferase (GT) domain found in lysyl hydroxylase 3 (LH3) and similar proteins. Lysyl hydroxylase 3 (LH3; EC 1.14.11.4/EC 2.4.1.50/EC 2.4.1.66), also called procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 (PLOD3), or multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3, is a multifunctional enzyme that catalyzes a series of essential post-translational modifications on Lys residues in procollagen. It converts collagen lysines into 1,2-glucosylgalactosyl-5-hydroxylysines through three consecutive reactions: hydroxylation of collagen lysines (LH activity), N-linked conjugation of galactose to hydroxylysines (GT activity), and conjugation of glucose to galactosyl-5-hydroxylysines (GGT activity). LH3 monomer encompasses three domains; the first two N-terminal domains (catalytic glycosyltransferase domain and accessory domain) show Rossmann-fold architectures reminiscent of glycosyltransferases, whereas the C-terminal domain is characterized by a double-stranded beta-helix (DSBH) fold, highly conserved among the 2-oxoglutarate, Fe2+-dependent dioxygenases. This model corresponds to the N-terminal catalytic glycosyltransferase (GT) domain, which is solely responsible for glycosyltransferase activities (both GT and GGT). 230 matched cddid_all.tbl CDD cd23003 cd23003 438559 GT_LH2 catalytic glycosyltransferase (GT) domain found in lysyl hydroxylase 2 (LH2) and similar proteins. Lysyl hydroxylase 2 (LH2; EC 1.14.11.4), also called procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 (PLOD2), forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links. The model corresponds to the N-terminal conserved domain of LH2, which shows high sequence similarity with catalytic glycosyltransferase (GT) domain of LH3. 230 matched cddid_all.tbl CDD cd23004 cd23004 438560 GT_LH1 catalytic glycosyltransferase (GT) domain found in lysyl hydroxylase 1 (LH1) and similar proteins. LH1 (EC 1.14.11.4), also called procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1), forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines may serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links. LH1 is part of a complex composed of PLOD1, P3H3 and P3H4 that catalyzes hydroxylation of lysine residues in collagen alpha chains and is required for normal assembly and cross-linkling of collagen fibrils. This model corresponds to the N-terminal conserved domain of LH1, which shows high sequence similarity with catalytic glycosyltransferase (GT) domain of LH3. 230 matched cddid_all.tbl CDD cd23006 cd23006 438556 Dkkl1 Dickkopf-like protein 1. Dickkopf (Dkk) genes comprise an evolutionarily conserved small gene family of four members (Dkk1-4) and a unique Dkk3-related gene, Dkkl1, also called Dickkopf-like protein 1, cancer/testis antigen 34 (CT34), or sgy/soggy. Soggy is thought to play an important role in testicular development and spermatogenesis, and its abnormal expression may be an important factor in male infertility. It may promote spermatocyte apoptosis, thereby limiting sperm production. In adults, Dkkl1 may reduce testosterone synthesis in Leydig cells. Unlike the other members of the Dickkopf family, Soggy does not contain two conserved cysteine-rich domains (Cys-1 and Cys-2) separated by a linker region. It contains an N-terminal domain similar to that of the N-terminal region of Dkk3. 166 matched cddid_all.tbl CDD cd23008 cd23008 437995 CLPS_Dkk_Cys2 Colipase and the second cysteine-rich (Cys-2) domain of Dickkopf proteins. Colipase (also called CLPS) is a cysteine-rich protein that adopts a similar fold to a cysteine-rich domain (Cys-2) of the Dickkopf (Dkk) family proteins. Colipase functions to prevent the inhibitory effect of bile salts on lipase-catalyzed intraduodenal hydrolysis of dietary long-chain triglycerides. Dickkopf proteins are a discrete class of secreted Wnt inhibitors that are required for many developmental processes, including segmentation, endoderm development, limb polarity, neural crest differentiation, kidney morphogenesis, sex determination and brain development. They possess an N-terminal signal peptide and contain two conserved cysteine-rich domains (Cys-1 and Cys-2) separated by a linker region. The Dickkopf Cys-2 domain is similar to proteins in the colipase family and it has been suggested that the Cys-2 domain of Dkks may enable interaction with lipids in order to regulate Wnt function. 82 matched cddid_all.tbl CDD cd23009 cd23009 438006 Dkk_Cys1 first cysteine-rich (Cys-1) domain of Dickkopf proteins. The Dickkopf (Dkk) family comprises a discrete class of secreted Wnt inhibitors. The Wnt gene family is a large class of secreted proteins that are expressed in a variety of tissues and organs, and are required for many developmental processes, including segmentation, endoderm development, limb polarity, neural crest differentiation, kidney morphogenesis, sex determination and brain development. Dkks 1-4 each possesses an N-terminal signal peptide and contains two conserved cysteine-rich domains (Cys-1 and Cys-2) separated by a linker region. Each domain possesses 10 conserved cysteine residues. The Cys-2 domain is closely similar to those in the colipase family; it has been suggested that the Cys-2 domain of Dkks may enable interaction with lipids in order to regulate Wnt function. This model corresponds to the Cys-1 domain of Dickkopf proteins 1- 4. 52 matched cddid_all.tbl CDD cd23010 cd23010 467862 PM41-like Seed maturation protein PM41 and related proteins. Seed maturation is comprised of several developmental processes including the formation of the embryo pattern, the accumulation of reserves, the acquisition of tolerance to desiccation and the entry into dormancy. This cd includes seed maturation protein PM41 from Zea mays and related proteins 75 matched cddid_all.tbl CDD cd23011 cd23011 437996 CLPS Colipase. Colipase, also called CLPS, is a protein co-enzyme required for optimal enzyme activity of pancreatic lipase. It is secreted by the pancreas in an inactive form, procolipase, which is activated in the intestinal lumen by trypsin. Its function is to prevent the inhibitory effect of bile salts on the lipase-catalyzed intraduodenal hydrolysis of dietary long-chain triglycerides. Bile salts, at concentrations near their critical micellar concentration, desorb lipase from emulsified triacylglycerol and, thereby, inhibit lipolysis. Colipase functions by anchoring pancreatic lipase to the lipid-water interface through the formation of the stoichiometric colipase-lipase complex. 84 matched cddid_all.tbl CDD cd23012 cd23012 437997 Dkk_Cys2 second cysteine-rich (Cys-2) domain of Dickkopf proteins. The Dickkopf (Dkk) family comprises a discrete class of secreted Wnt inhibitors. The Wnt gene family is a large class of secreted proteins that are expressed in a variety of tissues and organs, and are required for many developmental processes, including segmentation, endoderm development, limb polarity, neural crest differentiation, kidney morphogenesis, sex determination and brain development. Dkks 1-4 each possesses an N-terminal signal peptide and contains two conserved cysteine-rich domains (Cys-1 and Cys-2) separated by a linker region. Each domain possesses 10 conserved cysteine residues. The Cys-2 domain is closely similar to those in the colipase family; it has been suggested that the Cys-2 domain of Dkks may enable interaction with lipids in order to regulate Wnt function. This model corresponds to the Cys-2 domain of Dickkopf proteins 1- 4. 77 matched cddid_all.tbl CDD cd23013 cd23013 438007 Dkk4_Cys1 first cysteine-rich (Cys-1) domain of Dickkopf-related protein 4. Dickkopf 4 (Dkk4) is a secreted protein which directly binds to LRP5/6 (low-density lipoprotein receptor related protein 5 and 6), and is an inhibitor of Wnt/beta-catenin signaling. Dkk4, which is upregulated by the activated Wnt pathway, contributes to tumor malignancy in variable tumors, promoting tumor cell invasion and progression. Aberrant accumulation of Dkk4 has been shown to promote tumor progression by forming the immune suppressive microenvironment in gastrointestinal stromal tumor, and thus Dkk4 may be used as a tumor biomarker for prognosis prediction and recurrence monitoring. Dkk4 belongs to the Dickkopf (Dkk) family that comprises a discrete class of secreted Wnt inhibitors. The Wnt gene family is a large class of secreted proteins that are expressed in a variety of tissues and organs, and are required for many developmental processes, including segmentation, endoderm development, limb polarity, neural crest differentiation, kidney morphogenesis, sex determination and brain development. Dkks 1-4 each possesses an N-terminal signal peptide and contains two conserved cysteine-rich domains (Cys-1 and Cys-2) separated by a linker region. Each domain possesses 10 conserved cysteine residues. The Cys-2 domain is closely similar to those in the colipase family; it has been suggested that the Cys-2 domain of Dkks may enable interaction with lipids in order to regulate Wnt function. This model corresponds to the Cys-1 domain of Dkk4. 55 matched cddid_all.tbl CDD cd23014 cd23014 438008 Dkk3_N_Cys1 N-terminus of Dickkopf-related protein 3; includes the first cysteine-rich (Cys-1) domain. Dickkopf 3 (Dkk3) is a secreted protein which, in contrast to Dkk1, Dkk2, and Dkk4, does not interact with LRP5/6 (low-density lipoprotein receptor related protein 5 and 6), and thus is a divergent family member that is not considered a true Wnt signaling antagonist. The role of Dkk proteins in cancer is considered mainly tumor suppressive since they are usually down-regulated in cancer cells. Dkk3 links heat shock factor 1 (HSF1) and YAP/TAZ signaling to control aggressive behaviors in cancer-associated fibroblasts; it does so via canonical Wnt signaling. It belongs to the Dickkopf (Dkk) family that comprises a discrete class of secreted Wnt inhibitors. The Wnt gene family is a large class of secreted proteins that are expressed in a variety of tissues and organs, and are required for many developmental processes, including segmentation, endoderm development, limb polarity, neural crest differentiation, kidney morphogenesis, sex determination and brain development. Dkks 1-4 each possesses an N-terminal signal peptide and contains two conserved cysteine-rich domains (Cys-1 and Cys-2) separated by a linker region. Each domain possesses 10 conserved cysteine residues. The Cys-2 domain is closely similar to those in the colipase family; it has been suggested that the Cys-2 domain of Dkks may enable interaction with lipids in order to regulate Wnt function. This model corresponds to the N-terminal region of Dkk3, including the Cys-1 domain and a region to its N-terminus that shows similarity to Dickkopf-like protein 1 (Dkkl1). 156 matched cddid_all.tbl CDD cd23015 cd23015 438009 Dkk2_Cys1 first cysteine-rich (Cys-1) domain of Dickkopf-related protein 2. Dickkopf 2 (Dkk2) is a secreted protein which directly binds to LRP5/6 (low-density lipoprotein receptor related protein 5 and 6), and is an inhibitor of Wnt/beta-catenin signaling. Dkk2 expression is modulated by expression of micro RNA-221 (miRNA-221) in esophageal cancer, and inactivation of Dkk2 may increase Wnt activity with accelerating tumor progression. Dkk2 belongs to the Dickkopf (Dkk) family that comprises a discrete class of secreted Wnt inhibitors. The Wnt gene family is a large class of secreted proteins that are expressed in a variety of tissues and organs, and are required for many developmental processes, including segmentation, endoderm development, limb polarity, neural crest differentiation, kidney morphogenesis, sex determination and brain development. Dkks 1-4 each possesses an N-terminal signal peptide and contains two conserved cysteine-rich domains (Cys-1 and Cys-2) separated by a linker region. Each domain possesses 10 conserved cysteine residues. The Cys-2 domain is closely similar to those in the colipase family; it has been suggested that the Cys-2 domain of Dkks may enable interaction with lipids in order to regulate Wnt function. This model corresponds to the Cys-1 domain of Dkk2. 55 matched cddid_all.tbl CDD cd23016 cd23016 467863 mt-LAF27 mitochondrial large subunit assembly factor 27 (mt-LAF27). mt-LAF27 is a mitochondrial large subunit assembly factor (mt-LAF) found in Trypanosomatids. In Trypanosoma brucei, mt-LAF27 is involved in the rearrangement of the H32-35 region of rRNA, together with other assembly factors such as mt-LAF21, mt-LAF22, KRIPP3, mt-LAF20, and mt-LAF28, as well as GTPases mt-EngA, mt-EngB, and Mtg1. The T. brucei mitochondrial ribosome (mitoribosome) has 28 assembly factors, 6 of which are homologous to bacterial and eukaryotic ribosome assembly factors. Mitoribosome assembly factors interact with the partially folded rRNA by specifically recognizing functionally important regions. The T. brucei mitoribosomal large subunit (mtLSU) accommodates the peptidyl transferase center (PTC) that catalyzes formation of peptide bonds between amino acids, tRNA-binding sites, the L7/L12 stalk that is responsible for the recruitment of translation factors, the L1 stalk, the central protuberance (CP) that facilitates communication between various functional sites, and the exit tunnel to egress a synthesized protein. Mitoribosomal biogenesis relies on an extensive protein network formed by the assembly factors that connect a premature PTC, the L1, and L7/L12 stalks with the CP, while the exit tunnel is blocked. The study of mitochondrial biogenesis in resource organisms is biomedically important since mutations in mitoribosomal proteins, rRNAs, and assembly factors have been linked to a heterogeneous group of human multi-systemic oxidative phosphorylation (OXPHOS) diseases and cancer development and progression. 98 matched cddid_all.tbl CDD cd23017 cd23017 467864 mt-LAF19-like mitochondrial large subunit assembly factor 19 (mt-LAF19) and related proteins. mt-LAF19 is a Trypanosoma brucei mitochondrial large subunit (mt-LSU) assembly factor (mt-LAF); in native mt-LSU assembly intermediates, the lariat-like structure of the 12S rRNA helix H88 is sandwiched between a loop of mt-LAF19, the core domain of mt-LAF4, and mt-LAF14. Mitochondrial ribosomes (mitoribosomes) are ribonucleoprotein complexes and consist of a large (mt-LSU) and small subunit (mt-SSU). They differ markedly in composition and architecture from their bacterial counterparts and between different eukaryotic lineages, and their biogenesis involves exchange of assembly factors by ribosomal proteins. An investigation of native assembly intermediates of the mt-LSU from T. brucei identified 28 assembly factors, some of which are homologous to bacterial and eukaryotic ribosome assembly factors. Mitochondrial biogenesis is biomedically important since mutations in mitoribosomal proteins, rRNAs, and assembly factors have been linked to a heterogeneous group of human multisystemic oxidative phosphorylation (OXPHOS) diseases and cancer development and progression. 97 matched cddid_all.tbl CDD cd23018 cd23018 467865 mt-LAF14 mitochondrial large subunit assembly factor 14 (mt-LAF14). Two Trypanosoma brucei mitochondrial large subunit assembly factors, mt-LAF14 and mt-LAF2, with five mitoribosomal proteins (bL28m, bL35m, bL19m, mL64 and mL74) make a protein mass to stabilize GTPase assembly factor mt-EngA at the pre-mtLSU (pre-mitoribosomal large subunit). Factor mt-LAF14 is an exclusively helical protein, comprised of at least 29 helices, which spans over the top of the central protuberance (CP), where it stabilizes unwound rRNA at the pre-mtLSU. The mtLSU accommodates the peptidyl transferase center (PTC) that catalyzes formation of peptide bonds between amino acids, tRNA-binding sites, the L7/L12 stalk that is responsible for the recruitment of translation factors, the L1 stalk, the CP that facilitates communication between various functional sites, and the exit tunnel to egress a synthesized protein. The process of mtLSU assembly relies on an extensive protein network formed by the assembly factors that connect a premature PTC, the L1, and L7/L12 stalks with the CP, while the exit tunnel is blocked. 669 matched cddid_all.tbl CDD cd23019 cd23019 438555 DD_ROP dimerization/docking (D/D) domain found in ropporins. The ROP subfamily includes ropporin-1A (ROP1A, also called cancer/testis antigen 91, CT91, or rhophilin-associated protein 1A), ropporin-1B (ROP1B, also called rhophilin-associated protein 1B), and ropporin-1-like protein (ROPN1L, also called ROPN1-like protein, AKAP-associated sperm protein, or ASP). ROP1A, ROP1B and ROPN1L play important roles in male fertility. They are involved in fibrous sheath integrity and sperm motility and play roles in cAMP-dependent protein kinase (PKA)-dependent signaling processes required for spermatozoa capacitation. Members of this subfamily contain a conserved helical bundle domain that shows high sequence similarity to the dimerization/docking (D/D) domain of the regulatory subunit of PKA, which dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs). ROP1A and ROP1B have been shown to bind AKAP3. 43 matched cddid_all.tbl CDD cd23020 cd23020 467792 zf-HIT "zinc finger HIT (zf-HIT) domain. The zinc finger HIT (zf-HIT) is a novel zinc-binding domain with about 50 amino acids. It is characterized by a fold in ""treble-clef"" through interleaved CCCC and CCHC zinc finger motifs that both bind a zinc ion. zf-HIT domain may function as a protein-protein interaction domain. It is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. The zf-HIT family includes six proteins containing zf-HIT domain present in human and three in yeast proteome, all belonging to multimodular RNA/protein complexes." 31 matched cddid_all.tbl CDD cd23021 cd23021 467793 zf-HIT_IN80B "zinc finger HIT (zf-HIT) found in INO80 complex subunit B (INO80B) and similar proteins. INO80B, also called high mobility group AT-hook 1-like 4 (HMGA1L4), or IES2 homolog, or PAP-1-associated protein 1 (PAPA-1), or zinc finger HIT domain-containing protein 4 (ZNHIT4), is a nucleolar protein that induces growth and cell cycle arrests at the G1 phase of the cell cycle. It is a core component of the chromatin remodeling INO80 complex, which is involved in transcriptional regulation, DNA replication and probably DNA repair. INO80B harbors a zf-HIT domain which is characterized by a fold in ""treble-clef"" through interleaved CCCC and CCHC ZnF motifs that both bind a zinc atom. The yeast counterpart of INO80B is Ies2p (Ino eighty subunit 2), which doesn't have zf-HIT domain." 33 matched cddid_all.tbl CDD cd23022 cd23022 467794 zf-HIT_DDX59 "zinc finger HIT (zf-HIT) found in DEAD box protein 59 (DDX59) and similar proteins. DDX59, also called zinc finger HIT domain-containing protein 5 (ZNHIT5), is a probable ATP-dependent RNA helicase (EC 3.6.4.13) that plays a role in nervous system development and function. It has an important role in lung cancer development through promoting DNA replication. Mutations in DDX59 implicate RNA helicase in the pathogenesis of oral-facial-digital syndrome (OFDS). DDX59 contains a zf-HIT domain which is characterized by a fold in ""treble-clef"" through interleaved CCCC and CCHC zinc finger motifs that both bind a zinc ion." 35 matched cddid_all.tbl CDD cd23023 cd23023 467795 zf-HIT_BCD1 "zinc finger HIT (zf-HIT) found in Box C/D snoRNA protein 1 (BCD1) and similar proteins. The zf-HIT domain-containing family includes BCD1 and its yeast counterpart Bcd1p, both of which have been characterized as assembly factors for box C/D snoRNPs. BCD1, also known as serologically defined breast cancer antigen NY-BR-75 or zinc finger HIT domain-containing protein 6 (ZNHIT6), is required for the accumulation, processing, transport, and biogenesis of box C/D snoRNAs, specifically U3 and U8, in the nucleoplasm. Bcd1p is essential for cellular viability in Saccharomyces cerevisiae and contributes to the specific stability of box C/D snoRNAs. Members of this family contain a zf-HIT domain, characterized by a fold in ""treble-clef"" through interleaved CCCC and CCHC ZnF motifs that both bind a zinc atom. The zf-HIT domain of Bcd1p is necessary but not sufficient for yeast growth, and although it lacks direct RNA-binding capacity, it helps Bcd1p maintain steady-state levels of box C/D snoRNAs. Additionally, the zf-HIT domain of Bcd1p is functionally interchangeable with that of Hit1p, another box C/D snoRNP assembly factor belonging to the zf-HIT family." 40 matched cddid_all.tbl CDD cd23024 cd23024 467796 zf-HIT_ZNHIT2-3 zinc finger HIT (zf-HIT) found in zinc finger HIT domain-containing protein 2 (ZNHIT2), 3 (ZNHIT3) and similar proteins. ZNHIT2 and ZNHIT3 are members of the zf-HIT domain-containing protein family that play crucial roles in various biological processes. ZNHIT2 acts as a bridging factor between the R2TP/PFDL complex and U5 snRNP, while ZNHIT3 interacts specifically with the ligand binding domain of the thyroid receptor and is involved in small nucleolar ribonucleoprotein particle assembly, transcriptional regulation, and snoRNP assembly. ZNHIT3 is also associated with HNF-4alpha and may play a role in MODY, while its dysfunction is linked to PEHO syndrome. Both proteins contain the zf-HIT domain and interact with other proteins through their HIT-type zinc finger in the presence of ATP, ADP, or other factors. 37 matched cddid_all.tbl CDD cd23026 cd23026 438010 Dkk1_N_Cys1 N-terminus of Dickkopf-related protein 1; includes the first cysteine-rich (Cys-1) domain. Dickkopf-1 (Dkk1) is a secreted protein which directly binds to LRP5/6 (low-density lipoprotein receptor related protein 5 and 6), and is an inhibitor of Wnt/beta-catenin signaling. Elevated expression of Dkk-1 may serve as a negative regulator for modulating the wnt/#-catenin signal pathway. Dkk1 is expressed in various human cancers. It has been studied extensively in mouse models of multiple myeloma that results in osteolytic bone lesions. Studies show that Dkk1 levels in bone marrow plasma and serum inhibit the differentiation of osteoblast precursors. Dkk1 belongs to the Dickkopf (Dkk) family that comprises a discrete class of secreted Wnt inhibitors. The Wnt gene family is a large class of secreted proteins that are expressed in a variety of tissues and organs, and are required for many developmental processes, including segmentation, endoderm development, limb polarity, neural crest differentiation, kidney morphogenesis, sex determination and brain development. Dkks 1-4 each possesses an N-terminal signal peptide and contains two conserved cysteine-rich domains (Cys-1 and Cys-2) separated by a linker region. Each domain possesses 10 conserved cysteine residues. The Cys-2 domain is closely similar to those in the colipase family; it has been suggested that the Cys-2 domain of Dkks may enable interaction with lipids in order to regulate Wnt function. This model corresponds to the N-terminal region of Dkk1, including the Cys-1 domain. 122 matched cddid_all.tbl CDD cd23058 cd23058 467271 PDZ2_Par3-like PDZ domain 2 of partitioning defective 3 (Par3), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Par3 (or PAR3 or Par-3, also known as Atypical PKC isotype-specific-interacting protein, ASIP, Drosophila Bazooka) and related domains. Par3 is a scaffold protein involved in organizing cell polarity across animals. Par3 binds numerous molecules both for its recruitment to one pole of the cell and for downstream contributions to polarized cell function. It regulates cell polarity by targeting the Par complex proteins Par6 and atypical protein kinase C (aPKC) to specific cortical sites. Physical interactions between Par3 and the Par complex include Par3 PDZ domain 1 binding to the Par6 PDZ domain, Par3 PDZ domain 1 and PDZ domain 3 binding the Par6's PDZ-binding motif, and an interaction with an undefined region of aPKC that requires both Par3 PDZ2 and PDZ3. The PDZ domains of Par3 have also been implicated as potential phosphoinositide signaling integrators, since its second PDZ domain binds to phosphoinositides, and the third PDZ interacts with phosphoinositide phosphatase PTEN. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Par3 family PDZ2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 93 matched cddid_all.tbl CDD cd23059 cd23059 467272 PDZ3_Par3-like PDZ domain 3 of partitioning defective 3 (Par3), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of Par3 (or PAR3 or Par-3, also known as Atypical PKC isotype-specific-interacting protein, ASIP, Drosophila Bazooka) and related domains. Par3 is a scaffold protein involved in organizing cell polarity across animals. Par3 binds numerous molecules both for its recruitment to one pole of the cell and for downstream contributions to polarized cell function. It regulates cell polarity by targeting the Par complex proteins Par6 and atypical protein kinase C (aPKC) to specific cortical sites. Physical interactions between Par-3 and the Par complex include Par3 PDZ domain 1 binding to the Par6 PDZ domain, Par3 PDZ domain 1 and PDZ domain 3 binding the Par6's PDZ-binding motif, and an interaction with an undefined region of aPKC that requires both Par3 PDZ2 and PDZ3. The PDZ domains of Par3 have also been implicated as potential phosphoinositide signaling integrators, since its second PDZ domain binds to phosphoinositides, and the third PDZ interacts with phosphoinositide phosphatase PTEN. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Par3 family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 103 matched cddid_all.tbl CDD cd23060 cd23060 467273 PDZ5_DrPTPN13-like PDZ domain 5 of Danio rerio tyrosine-protein phosphatase non-receptor type 13 (Ptpn13) and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of Danio rerio Ptpn13, and related domains. Protein-tyrosine phosphatases (PTPs) dephosphorylate phosphotyrosyl residues in proteins that are phosphorylated by protein tyrosine kinases (PTKs). Danio rerio Ptpn13 is a classical non-receptor-like PTP. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 80 matched cddid_all.tbl CDD cd23061 cd23061 467274 PDZ1_PDZD2-like PDZ domain 1 of PDZ domain containing 2 (PDZD2), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PDZD2, also known as KIAA0300, PIN-1, PAPIN, activated in prostate cancer (AIPC) and PDZ domain-containing protein 3 (PDZK3). PDZD2 has seven PDZ domains. PDZD2 is expressed at exceptionally high levels in the pancreas and certain cancer tissues such as prostate cancer. It promotes the proliferation of insulinoma cells and is upregulated during prostate tumorigenesis. In osteosarcoma (OS), the microRNA miR-363 acts as a tumor suppressor by inhibiting PDZD2. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PDZD2-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 94 matched cddid_all.tbl CDD cd23062 cd23062 467275 PDZ0_GgPro-IL-16-like PDZ domain 0 of Gallus gallus interleukin-16, and related domains. N-terminal PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1) of Gallus gallus IL16, and related domains. This IL16-PDZ0 domain is not found in the human pro-interleukin-16 (isoform 1, 1332 AA, pro-IL-16) which has 4 PDZ domains (PDZ1-4). Gallus gallus IL-16 has 5 PDZ domains: this N-terminal PDZ0, followed by 4 PDZ domains (PDZ1-4) which are homologous to human pro-IL-16 PDZ1-4. Precursor IL-16 is cleaved to produce pro-IL-16 and mature IL-16 (derived from the C-terminal 121 AA). Pro-IL-16 functions as a regulator of T cell growth; mature IL-16 is a CD4 ligand that induces chemotaxis and CD25 expression in CD4+ T cells. IL-16 bioactivity has been closely associated with the progression of several different cancers, including Gallus gallus IL-16 in the development of ovarian tumor and tumor-associated neoangiogenesis (TAN) in laying hens, an animal model of spontaneous ovarian cancer. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This IL16-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 83 matched cddid_all.tbl CDD cd23063 cd23063 467276 PDZ1_INAD-like PDZ domain 1 of inactivation-no-after-potential D (INAD), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of INAD, and related domains. INAD assembles key enzymes of the Drosophila compound eye photo-transduction pathway into a supramolecular complex, supporting efficient and fast light signaling. It contains 5 PDZ domains arranged in tandem (PDZ1-PDZ5) which independently bind various proteins. INAD PDZ2 binds eye-specific protein kinase C, INAD PDZ3 binds transient receptor potential (TRP) channel, and INAD PDZ4,5 tandem binds NORPA (phospholipase Cbeta, PLCbeta). Mutations of the inaD gene that lead to disruption of each of these interactions impair fly photo signal transduction. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This INAD-like family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 87 matched cddid_all.tbl CDD cd23064 cd23064 467277 PDZ3_INAD-like PDZ domain 3 of inactivation-no-after-potential D (INAD), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 3 of INAD, and related domains. INAD assembles key enzymes of the Drosophila compound eye photo-transduction pathway into a supramolecular complex, supporting efficient and fast light signaling. It contains 5 PDZ domains arranged in tandem (PDZ1-PDZ5) which independently bind various proteins. INAD PDZ2 binds eye-specific protein kinase C, INAD PDZ3 binds transient receptor potential (TRP) channel, and INAD PDZ4,5 tandem binds NORPA (phospholipase Cbeta, PLCbeta). Mutations of the inaD gene that lead to disruption of each of these interactions impair fly photo signal transduction. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This INAD-like family PDZ3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 80 matched cddid_all.tbl CDD cd23065 cd23065 467278 PDZ4_INAD-like PDZ domain 4 of inactivation-no-after-potential D (INAD), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 4 of INAD, and related domains. INAD assembles key enzymes of the Drosophila compound eye photo-transduction pathway into a supramolecular complex, supporting efficient and fast light signaling. It contains 5 PDZ domains arranged in tandem (PDZ1-PDZ5) which independently bind various proteins. INAD PDZ2 binds eye-specific protein kinase C, INAD PDZ3 binds transient receptor potential (TRP) channel, and INAD PDZ4,5 tandem binds NORPA (phospholipase Cbeta, PLCbeta). Mutations of the inaD gene that lead to disruption of each of these interactions impair fly photo signal transduction. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This INAD-like family PDZ4 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 82 matched cddid_all.tbl CDD cd23066 cd23066 467279 PDZ5_INAD-like PDZ domain 5 of inactivation no after potential D (INAD), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 5 of INAD, and related domains. INAD assembles key enzymes of the Drosophila compound eye photo-transduction pathway into a supramolecular complex, supporting efficient and fast light signaling. It contains 5 PDZ domains arranged in tandem (PDZ1-PDZ5) which independently bind various proteins. INAD PDZ2 binds eye-specific protein kinase C, INAD PDZ3 binds transient receptor potential (TRP) channel, and INAD PDZ45 tandem binds NORPA (phospholipase Cbeta, PLCbeta). Mutations of the inaD gene that lead to disruption of each of these interactions impair fly photo signal transduction. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This INAD-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 80 matched cddid_all.tbl CDD cd23067 cd23067 467280 PDZ_DEPTOR-like PDZ domain of DEP domain-containing mTOR-interacting protein (DEPTOR), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of DEPTOR, and related domains. DEPTOR (also known as DEP domain-containing protein 6, DEP6) is a regulatory protein of mTOR signaling; it is a negative regulator of both the mTORC1 and mTORC2 signaling pathways. DEPTOR's PDZ domain binds to mTOR's FAT domain to suppress mTOR's kinase activity. The DEPTOR PDZ domain also binds lysine-specific demethylase 4A (KDM4A), leucine-rich repeat containing 4 (LRRC4), p38gamma, and major intrinsically disordered Notch2-binding receptor 1 (MINAR1, also known as Ubtor). DEPTOR also interacts with salt-inducible kinase 3 (SIK3). PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This DEPTOR-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 75 matched cddid_all.tbl CDD cd23068 cd23068 467281 PDZ_ZASP52-like PDZ domain of Drosophila melanogaster PDZ and LIM domain protein Zasp52 (also known as Zasp), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Drosophila melanogaster Zasp52 and related domains. Drosophila melanogaster Zasp52 (also known as Z band alternatively spliced PDZ-motif protein or Zasp) colocalizes with integrins at myotendinous junctions and with alpha-actinin at Z-disks and is required for muscle attachment as well as Z-disk assembly and maintenance. The Zasp52 actin-binding site includes the extended PDZ domain and the ZM region. The Zasp52-PDZ domain is required for myofibril assembly. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This Zasp52-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 82 matched cddid_all.tbl CDD cd23069 cd23069 467282 PDZ_ARHGEF11-12-like PDZ domain of ARHGEF11, ARHGEF12, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ARHGEF11, ARHGEF12, and related domains. This subfamily includes the GEFs (guanine exchange factors) ARHGEF11 (Rho guanine nucleotide exchange factor 11, known as PDZ-RhoGEF) and ARHGEF12 (Rho guanine nucleotide exchange factor 12, also known as leukemia-associated RhoGEF). GEFs activate Rho GTPases by promoting GTP binding. ARHGEF11/12 are regulators of G protein signaling (RGS) domain-containing GEFs; the RGS domain mediates their binding to and activation of Galpha (and Gq also in the case of ARHGEF12), in response to G-protein coupled receptor activation. ARHGEF11 and 12 are involved in serum-signaling, and regulate Yes-Associated Protein (YAP1)-dependent transcription. The ARHGEF12 PDZ domain binds plexin-B1 and the receptor tyrosine kinase insulin-like growth factor receptor (IGF-R1) beta-subunit. ARHGEF12 also interacts with glutamate receptor delta-1(GluD1), a postsynaptic organizer of inhibitory synapses in cortical pyramidal neurons. The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This ARHGEF11-12-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 76 matched cddid_all.tbl CDD cd23070 cd23070 467283 PDZ_SNX27-like PDZ domain of sorting nexin-27 (SNX27), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of SNX27, and related domains. SNX27 is involved in retrograde transport from endosome to plasma membrane. The PDZ domain of SNX27 links cargo identification to retromer-mediated transport. SNX27 binds to the retromer complex (vacuolar protein sorting 26(VPS26)-VPS29-VPS35), via its PDZ domain binding to VPS26. The SNX27 PDZ domain also binds to cargo including the G-protein-coupled receptors (GPCRs): beta2-adrenergic receptor (beta2AR), beta1AR, parathyroid hormone receptor (PTHR), alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs), NMDA receptors, 5-hydroxytryptamine 4a receptors, frizzled receptors, and somatostatin receptor subtype 5 (SSTR5). Additional binding partners of the SNX27 PDZ domain include G protein-gated inwardly rectifying potassium (Kir3) channels, angiotensin-converting enzyme 2 (ACE2), and PTEN (phosphatase and tensin homolog deleted on chromosome 10); PTEN binding to SNX27 prevents SNX27's association with the retromer complex. SNX27 has been reported to be a host factor needed for efficient entry of an engineered SARS-CoV-2 variant, the spike protein of which contains a deletion at the S1/S2 subunit cleavage site; the PDZ domain of SNX27 binds angiotensin-converting enzyme 2 (ACE2), and may be involved in recycling ACE2 to the plasma membrane, thereby promoting viral entry. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This SNX27-like family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 93 matched cddid_all.tbl CDD cd23071 cd23071 467284 PDZ1_FRMPD2-like PDZ domain 1 of FERM and PDZ domain-containing protein 2 (FRMPD2), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of FRMPD2 (also known as PDZ domain-containing protein 4, and related domains. FRMPD2 is localized in the basolateral membranes of polarized epithelial cells and is associated with tight junction formation and immune response; it contains 3 PDZ domains. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 92 matched cddid_all.tbl CDD cd23072 cd23072 467285 PDZ1_PTPN13-like PDZ domain 1 of protein tyrosine phosphatase non-receptor type 13 (PTPN13), and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of PTPN13 [also known as Fas-associated protein-tyrosine phosphatase 1 (FAP-1), protein-tyrosine phosphatase 1E (PTP-E1), and protein-tyrosine phosphatase (PTPL1)], and related domains. PTPN13 regulates negative apoptotic signaling and mediates phosphoinositide 3-kinase (PI3K) signaling. PTPN13 has five PDZ domains. Proteins known to interact with PTPN13 PDZ domains include: PLEKHA1 and PLEKHA2 via PTPN13-PDZ domain 1, Fas receptor and thyroid receptor-interacting protein 6 via PTPN13-PDZ domain 2, nerve growth factor receptor and protein kinase N2 via PTPN13-PDZ domain 3, PDZ and LIM domain 4 (PDLIM4) via PTPN13-PDZ domains 2 and 4, and brain calpain-2 via PTPN13-PDZ domains 3, 4 and 5. Calpain-2-mediated PTPN13 fragments may be involved in abnormal tau aggregation and increased risk for Alzheimer's disease. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This PTPN13 family PDZ1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 92 matched cddid_all.tbl CDD cd23073 cd23073 467286 PDZ_MAST1 PDZ domain of microtubule-associated serine-threonine (MAST) protein kinase 1. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MAST family kinase MAST1, and related domains. MAST1 belongs to the MAST family kinases, which include MAST1-4. These MAST proteins contain a DUF1908 domain, a serine/threonine kinase domain, a AGC-kinase C-terminal domain, and a PDZ domain; MAST family member MASTL is a shorter protein lacking the PDZ domain. MAST1 functions as a scaffold protein to link the dystrophin/utrophin network with microfilaments via syntrophin, and it has been identified as a main driver of cisplatin resistance in human cancers. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAST1 family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F 95 matched cddid_all.tbl CDD cd23074 cd23074 467287 PDZ_MAST2 PDZ domain of microtubule-associated serine-threonine (MAST) protein kinase 2. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MAST2 (also known as microtubule-associated serine/threonine kinase-205 kD, MAST205) , and related domains. MAST2 belongs to the MAST family kinases, which include MAST1-4. These MAST proteins contain a DUF1908 domain, a serine/threonine kinase domain, a AGC-kinase C-terminal domain, and a PDZ domain. MAST2 may function to link the dystrophin/utrophin network with microtubule filaments via the syntrophins. Binding partners of MAST2 include beta2-syntrophin, TNF receptor-associated factor 6 (TRAF6), cAMP-regulated phosphoprotein (ARPP-16), Na+/H+ exchanger NHE3 (SLC9A3) and PTEN. MAST2 is also associated with microtubules of the spermatid manchette. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAST2 family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 93 matched cddid_all.tbl CDD cd23075 cd23075 467288 PDZ_MAST3 PDZ domain of microtubule-associated serine-threonine (MAST) protein kinase 3 (MAST3). PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MAST3, and related domains. MAST3 belongs to the MAST family kinases, which include MAST1-4. These MAST proteins contain a DUF1908 domain, a serine/threonine kinase domain, a AGC-kinase C-terminal domain, and a PDZ domain. MAST3 plays a critical role in regulating the immune response of inflammatory bowel disease (IBD), and is involved in the process of cytoskeleton organization, intracellular signal transduction and peptidyl-serine phosphorylation. MAST3 also promotes the proliferation and inflammation of fibroblast-like synoviocytes in rheumatoid arthritis. Binding partners of MAST3 include cAMP-regulated phosphoprotein (ARPP-16) and the tumor suppressor PTEN. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAST3 family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 94 matched cddid_all.tbl CDD cd23076 cd23076 467289 PDZ_MAST4 PDZ domain of microtubule-associated serine-threonine (MAST) protein kinase 4 (MAST4). PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of MAST4, and related domains. MAST4 belongs to the MAST family kinases, which include MAST1-4. These MAST proteins contain a DUF1908 domain, a serine/threonine kinase domain, a AGC-kinase C-terminal domain, and a PDZ domain. MAST4 is a component of the AICD-MAST4-FOXO1-RTKN2 neuroprotective pathway; MAST4 phosphorylation of forkhead box protein O1 (FOXO1) regulates rhotekin 2 (RTKN2) expression. As this pathway is repressed in Alzheimer's Disease (AD), MAST4 may play a role in preventing AD pathogenesis. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This MAST4 family domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 95 matched cddid_all.tbl CDD cd23077 cd23077 467290 PDZ_GIPC1 PDZ domain of PDZ domain-containing protein GIPC1. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of GIPC1, and related domains. GIPC1 (also known as GIPC, GAIP/RGS19-interacting protein or Tax-interacting protein 2) belongs to the GIPC family, members of which contain an N-terminal GIPC-homology 1 (GH1) domain, a central PDZ domain, and a C-terminal GH2 domain. GIPC1 functions as an adaptor molecule for loading PDZ-target cargoes on the MYO6 motor protein. The GIPC1 PDZ domain interacts with a variety of ligands, such as RGS19, NRP1, GLUT1, SEMA4C, SDC4 and IGF1R. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GIPC1 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 94 matched cddid_all.tbl CDD cd23078 cd23078 467291 PDZ_GIPC2 PDZ domain of PDZ domain-containing protein GIPC2, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of GIPC2, and related domains. GIPC2 belongs to the GIPC family, members of which contain an N-terminal GIPC-homology 1 (GH1) domain, a central PDZ domain, and a C-terminal GH2 domain. GIPC proteins function as adaptor molecules that assemble RTKs, GPCRs, integrins, transmembrane proteins and cytoplasmic signaling regulators as cargoes of MYO6-dependent endocytic transport. Mutations in the Gipc2 gene have been linked to cancer. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GIPC2 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 93 matched cddid_all.tbl CDD cd23079 cd23079 467292 PDZ_GIPC3 PDZ domain of PDZ domain-containing protein GIPC3, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of GIPC3, and related domains. GIPC3 (also known as C19orf64) belongs to the GIPC family, members of which contain an N-terminal GIPC-homology 1 (GH1) domain, a central PDZ domain, and a C-terminal GH2 domain. GIPC proteins function as adaptor molecules that assemble RTKs, GPCRs, integrins, transmembrane proteins and cytoplasmic signaling regulators as cargoes of MYO6-dependent endocytic transport. Mutations in the Gipc3 gene cause nonsyndromic hearing loss. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal end of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains as well as those with circular permutations and domain swapping mediated by beta-strands. This GIPC3 domain is a canonical PDZ domain containing six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2), arranged in the order: beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. 89 matched cddid_all.tbl CDD cd23080 cd23080 467637 cpPDZ_BsYlbL-like circularly permuted PDZ domain of Bacillus subtilis YlbL and related domains. Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Bacillus subtilis YlbL and related domains. YlbL is an S16 protease which participates with another unrelated S41 protease (CtpA) in a dual protease mechanism that promotes DNA damage checkpoint recovery. Deletion of both proteases leads to accumulation of the cell division inhibitor YneA. PDZ domains usually bind in sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This YlbL family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus. 83 matched cddid_all.tbl CDD cd23081 cd23081 467638 cpPDZ_EcRseP-like circularly permuted PDZ domains of Escherichia coli Regulator of sigma-E protease (RseP) and related domains. Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL), and related domains. RseP is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmE) protein RseA; it cleaves the peptide bond between the critical alanine and cysteine in the transmembrane region of RseA, releasing the cytoplasmic domain of RseA with its associated sigmaE. RseP contains two tandem-arranged periplasmic PDZ domains (PDZ-N/PDZ1 and PDZ-C/PDZ2) which act to negatively regulate protease action on intact RseA; they serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP. PDZ domains usually bind in sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus. 83 matched cddid_all.tbl CDD cd23082 cd23082 467639 cpPDZ1_EcRseP-like circularly permuted PDZ domain 1 (PDZ-N) of Escherichia coli Regulator of sigma-E protease (RseP) and related domains. Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL) and related domains. RseP is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmaE) protein RseA; it cleaves the peptide bond between the critical alanine and cysteine in the transmembrane region of RseA, releasing the cytoplasmic domain of RseA with it associated sigmaE. RseP contains two tandem-arranged periplasmic PDZ domains (PDZ-N/PDZ1 and PDZ-C/PDZ2) which act to negatively regulate protease action on intact RseA; they serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP. PDZ domains usually bind in sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus. 89 matched cddid_all.tbl CDD cd23083 cd23083 467640 cpPDZ2_EcRseP-like circularly permuted PDZ domain 2 (PDZ-C) of Escherichia coli Regulator of sigma-E protease (RseP) and related domains. Permuted PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of ResP (also known as Site-2 protease RseP, and YaeL) and related domains. RseP is involved in the regulation of an extracytoplasmic stress response through the cleavage of membrane-spanning anti-stress-response transcription factor (anti-sigmaE) protein RseA; it cleaves the peptide bond between the critical alanine and cysteine in the transmembrane region of RseA, releasing the cytoplasmic domain of RseA with it associated sigmaE. RseP contains two tandem-arranged periplasmic PDZ domains (PDZ-N/PDZ1 and PDZ-C/PDZ2) which act to negatively regulate protease action on intact RseA; they serve as a size-exclusion filter which prevents the access of an intact RseA into the active site of RseP. PDZ domains usually bind in sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as beta-strands A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This RseP family PDZ domain is a circularly permuted PDZ domain which places both beta-strands A and B at the C-terminus. Another permutation exists in the PDZ superfamily which places beta-strand A at the C-terminus. 85 matched cddid_all.tbl CDD cd23084 cd23084 467631 cpPDZ2_DegP-like circularly permuted second PDZ domain (PDZ2) of Escherichia coli periplasmic serine endoprotease DegP and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Escherichia coli DegP (also known as heat shock protein DegP and Protease Do), and related domains. DegP belongs to the HtrA family of housekeeping proteases. It acts as a protease, degrading transiently denatured and unfolded or misfolded proteins which accumulate in the periplasm following heat shock or other stress conditions, and as a molecular chaperone at low temperatures. DegP has two PDZ domains in addition to the protease domain; its PDZ1 domain is responsible for the identifying the distinct substrate sequences that affect degradation (degron) of the substrate sequence, and its PDZ2 domain is responsible for the combining with other DegP monomers to form a stable oligomer structure. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This DegP family PDZ domain 2 is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus. 83 matched cddid_all.tbl CDD cd23085 cd23085 467632 cpPDZ_AtDEGP14-like circularly permuted PDZ domain of Arabidopsis thaliana putative protease Do-like 14 (DEGP14) and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain of Arabidopsis thaliana putative protease DEGP14 and related domains. DEGP14 is a putative protease belonging to the HtrA family of housekeeping proteases. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This AtDEGP14-like PDZ domain is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus. 101 matched cddid_all.tbl CDD cd23086 cd23086 467633 cpPDZ2_MamE-like circularly permuted PDZ domain 2 of Magnetospirillum magneticum magnetosome formation protease MamE, and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 2 of Magnetospirillum magneticum MamE (also known as magnetochrome MamE and magnetosome serine protease MamE), and related domains. MamE is a serine protease required to produce magnetite crystals in the magnetotactic bacterium M. magneticum. It is involved in localization of some proteins (at least MamA, MamC, MamF, MamI and MamJ) to the magnetosome, and likely cleaves at least itself, MamO and MamP. Its autoproteolysis is stimulated by exogenous substrates or peptides that bind to its PDZ domains. Peptide binding to either the first or the second PDZ domain of MamE can activate proteolysis; activation through PDZ2 is much weaker. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This MamE-like PDZ domain 2 is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus. 96 matched cddid_all.tbl CDD cd23087 cd23087 467634 cpPDZ1_MamE-like circularly permuted PDZ domain 1 of Magnetospirillum magneticum magnetosome formation protease MamE and related domains. PDZ (PSD-95 (Postsynaptic density protein 95), Dlg (Discs large protein), and ZO-1 (Zonula occludens-1)) domain 1 of Magnetospirillum magneticum MamE (also known as magnetochrome MamE and magnetosome serine protease MamE), and related domains. MamE is a serine protease required to produce magnetite crystals in the magnetotactic bacterium M. magneticum. It is involved in localization of some proteins (at least MamA, MamC, MamF, MamI and MamJ) to the magnetosome, and likely cleaves at least itself, MamO and MamP. MamE-PDZ1 may bind MamB. Its autoproteolysis is stimulated by exogenous substrates or peptides that bind to its PDZ domains. Peptide binding to either the first or the second PDZ domain of MamE can activate proteolysis; activation through PDZ2 is much weaker. PDZ domains usually bind in a sequence-specific manner to short peptide sequences located at the C-terminal of their partner proteins (known as PDZ binding motifs). The PDZ superfamily includes canonical PDZ domains and as well as those with circular permutations and domain swapping of beta-strands. The canonical PDZ domain contains six beta-strands A-F and two alpha-helices (alpha-helix 1 and 2); arranged as A, B, C, alpha-helix 1, beta-strands D, E, alpha-helix 2 and beta-strand F. This MamE-like PDZ domain 1 is a circularly permuted PDZ domain which places beta-strand A on the C-terminus. Another permutation exists in the PDZ superfamily which places both beta-strands A and B on the C-terminus. 91 matched cddid_all.tbl CDD cd23088 cd23088 467866 mt-LAF8-like mitochondrial large subunit assembly factor 8 (mt-LAF8), and related proteins. mt-LAF8 is a Trypanosoma brucei mitochondrial large subunit (mt-LSU) assembly factor (mt-LAF) that plays a structural role in stabilizing a mt-LSU assembly intermediate (pre-mt-LSU), mt-LAF8, along with mt-LAF7, is bound at the L7/12 stalk base to the unfolded rRNA H41/42. Mitochondrial ribosomes (mitoribosomes) are ribonucleoprotein complexes and consist of a large (mt-LSU) and small subunit (mt-SSU). They differ markedly in composition and architecture from their bacterial counterparts and between different eukaryotic lineages, and their biogenesis involves exchange of assembly factors by ribosomal proteins. An investigation of native assembly intermediates of the mt-LSU from T. brucei identified 28 assembly factors, some of which are homologous to bacterial and eukaryotic ribosome assembly factors. Mitochondrial biogenesis is biomedically important since mutations in mitoribosomal proteins, rRNAs, and assembly factors have been linked to a heterogeneous group of human multisystemic oxidative phosphorylation (OXPHOS) diseases and cancer development and progression. 470 matched cddid_all.tbl CDD cd23089 cd23089 467867 mt-LAF15-like mitochondrial large subunit assembly factor 15a (mt-LAF15a), mt-LAF15b and related proteins. mt-LAF15 is a Trypanosoma brucei mitochondrial large subunit (mt-LSU) assembly factor (mt-LAF). In an mt-LSU assembly intermediate during maturation of the L7/L12 stalk, mt-LAF15 and an additional protein UNK6 form a protrusion similar to mtLSU factors bL10m:bL12m, and a protein module of mt-LAF15, mL75, and UNK6 protein form a continuum of at least 13 helices that is peripherally associated. Mitochondrial ribosomes (mitoribosomes) are ribonucleoprotein complexes and consist of a large (mt-LSU) and small subunit (mt-SSU). They differ markedly in composition and architecture from their bacterial counterparts and between different eukaryotic lineages, and their biogenesis involves exchange of assembly factors by ribosomal proteins. An investigation of native assembly intermediates of the mt-LSU from T. brucei identified 28 assembly factors, some of which are homologous to bacterial and eukaryotic ribosome assembly factors. Mitochondrial biogenesis is biomedically important since mutations in mitoribosomal proteins, rRNAs, and assembly factors have been linked to a heterogeneous group of human multisystemic oxidative phosphorylation (OXPHOS) diseases and cancer development and progression. 307 matched cddid_all.tbl CDD cd23090 cd23090 467868 mt-LAF7-like mitochondrial large subunit assembly factor 7 (mt-LAF7) and related proteins. mt-LAF7 is a Trypanosoma brucei mitochondrial large subunit (mt-LSU) assembly factor (mt-LAF) that plays a structural role in stabilizing a mt-LSU assembly intermediate (pre-mt-LSU); mt-LAFf7, along with mt-LAF8, is bound at the L7/12 stalk base to the unfolded rRNA H41/42. Mitochondrial ribosomes (mitoribosomes) are ribonucleoprotein complexes and consist of a large (mt-LSU) and small subunit (mt-SSU). They differ markedly in composition and architecture from their bacterial counterparts and between different eukaryotic lineages, and their biogenesis involves exchange of assembly factors by ribosomal proteins. An investigation of native assembly intermediates of the mt-LSU from T. brucei identified 28 assembly factors, some of which are homologous to bacterial and eukaryotic ribosome assembly factors. Mitochondrial biogenesis is biomedically important since mutations in mitoribosomal proteins, rRNAs, and assembly factors have been linked to a heterogeneous group of human multisystemic oxidative phosphorylation (OXPHOS) diseases and cancer development and progression. 152 matched cddid_all.tbl CDD cd23092 cd23092 467869 mt-LAF12-like mitochondrial large subunit assembly factor 12 (mt-LAF12) and related proteins. mt-LAF12 is a Trypanosoma brucei mitochondrial large subunit (mt-LSU) assembly factor (mt-LAF) which together with RPUSD4 and MRM performs a structural scaffolding role for binding GTPBP7, a GTPase assembly factor. Mitochondrial ribosomes (mitoribosomes) are ribonucleoprotein complexes and consist of a large (mt-LSU) and small subunit (mt-SSU). They differ markedly in composition and architecture from their bacterial counterparts and between different eukaryotic lineages, and their biogenesis involves exchange of assembly factors by ribosomal proteins. An investigation of native assembly intermediates of the mt-LSU from T. brucei identified 28 assembly factors, some of which are homologous to bacterial and eukaryotic ribosome assembly factors. Mitochondrial biogenesis is biomedically important since mutations in mitoribosomal proteins, rRNAs, and assembly factors have been linked to a heterogeneous group of human multisystemic oxidative phosphorylation (OXPHOS) diseases and cancer development and progression. 577 matched cddid_all.tbl CDD cd23105 cd23105 438516 GSAP gamma-secretase-activating protein and similar proteins. Gamma-secretase activating protein, also called GSAP or PION, selectively increases amyloid-beta production through a mechanism involving its interaction with both gamma-secretase and its substrate, the amyloid-beta precursor protein C-terminal fragment (APP-CTF). GSAP cleavage via caspase-3 is regulated and depends upon the availability of 5-lipoxygenase. Alzheimer's disease (AD), the most prevalent cause of dementia, is associated with accumulation of amyloid-beta peptide which is a major characteristic of the AD brain and responsible for some of its clinical manifestations. The anticancer drug imatinib had been shown to inhibit amyloid-beta formation without affecting Notch cleavage, by preventing GSAP interaction with the gamma-secretase substrate, APP-CTF. Thus, GSAP can serve as an amyloid-beta-lowering therapeutic target without affecting other key functions of gamma-secretase. 514 matched cddid_all.tbl CDD cd23106 cd23106 467870 neurotoxins_LC_scorpion long-chain neurotoxins from scorpions. Scorpion venoms contain groups of neurotoxins active specifically on mammals or insects. These peptide toxins can be classified into two main categories based on their molecular sizes and pharmacological actions. Short-chain toxins, composed of 30-40 amino acid residues with 3 or 4 disulfide bonds, affect mainly potassium or chloride channels, while long-chain toxins, composed of 60-70 amino acid residues with 4 disulfide bonds, affect mainly sodium channels and can be divided into two groups, the alpha and beta toxins. The alpha toxins bind in a voltage-dependent manner and modulate the sodium current inactivation stage, whereas binding of beta toxins is voltage-independent and interferes with the sodium current activation stage. The beta toxin class includes the groups of excitatory and depressant toxins, which differ in their mode of action and are highly specific against insects. They can selectively bind to the corresponding channels on the membrane of excitable cells, thus impairing the initial rapid depolarization phase of the action potential in nerve and muscle, resulting in neurotoxicity. This family contains the long-chain alpha and beta toxins from scorpion venom. 60 matched cddid_all.tbl CDD cd23110 cd23110 438513 GRP glucose/ribose porter family. The glucose/ribose porter (GRP) family (TC 2.A.7.5) includes two functionally characterized members, a glucose uptake permease from Staphylococcus xylosus, and a probable ribose uptake permease from Lactobacillus sakei. Both proteins probably function by H(+) symport. This family also includes several putative and hypothetical membrane proteins that are probably involved in sugar transport across bacterial membranes. GRP family proteins have a distinctive topology: 10 putative transmembrane (TM) alpha-helical spanning domains per polypeptide chain, which apparently arose by intragenic duplication of an element encoding a primordial five-TM polypeptide. In Lactococcus lactis, GlcU was identified as the sole non-PTS (phosphoenolpyruvate:phosphotransferase systems) permease involved in the transport of glucose, which is driven by the proton-motive force. A gene from Bacillus subtilis, ycxE, that is homologous to glcU, could substitute for glcU in Escherichia coli glucose growth experiments and restored glucose repression in Staphylococcus xylosus glcU mutants. RbsU is encoded on the rbsUDK gene cluster, which encodes proteins involved in ribose uptake and phosphorylation. RbsR has been annotated as the repressor of the rbsUDK operon, based on its homology with RbsR repressors. The GRP family belongs to the Drug/Metabolite Transporter (DMT) superfamily (TC 2.A.7). 279 matched cddid_all.tbl CDD cd23111 cd23111 438514 ribose_uptake_RbsU ribose uptake protein RbsU and similar proteins. This group includes ribose uptake protein RbsU and similar proteins. RbsU is encoded on the rbsUDK gene cluster, which encodes proteins involved in ribose uptake and phosphorylation. RbsR has been annotated as the repressor of the rbsUDK operon, based on its homology with RbsR repressors. RbsU belongs to the glucose/ribose porter (GRP) family (TC 2.A.7.5) and probably functions by H(+) symport. GRP family proteins have a distinctive topology: 10 putative transmembrane (TM) alpha-helical spanning domains per polypeptide chain, which apparently arose by intragenic duplication of an element encoding a primordial five-TM polypeptide. The GRP family belongs to the Drug/Metabolite Transporter (DMT) superfamily (TC 2.A.7). 285 matched cddid_all.tbl CDD cd23112 cd23112 438515 glucose_uptake_GlcU glucose uptake protein GlcU. Glucose uptake protein GlcU is part of the glucose/ribose porter (GRP) family (TC 2.A.7.5), which also includes ribose transport proteins, and several putative and hypothetical membrane proteins probably involved in sugar transport across bacterial membranes. GRP family proteins have a distinctive topology: 10 putative transmembrane (TM) alpha-helical spanning domains per polypeptide chain, which apparently arose by intragenic duplication of an element encoding a primordial five-TM polypeptide. In Lactococcus lactis, GlcU was identified as the sole non-PTS (phosphoenolpyruvate:phosphotransferase systems) permease involved in the transport of glucose, which is driven by the proton-motive force. A gene from Bacillus subtilis, ycxE, that is homologous to glcU, could substitute for glcU in Escherichia coli glucose growth experiments and restored glucose repression in Staphylococcus xylosus glcU mutants. The GRP family belongs to the Drug/Metabolite Transporter (DMT) superfamily (TC 2.A.7). 277 matched cddid_all.tbl CDD cd23113 cd23113 438475 RING-H2_MBR RING finger, H2 subclass, found in Arabidopsis thaliana MED25-binding RING-H2 protein (MBR) and similar proteins. This subfamily includes MBR1 and MBR2 (also called HAL3-interacting protein 1 or AtHIP1). They are E3 ubiquitin-protein ligases that function as regulators of MED25 stability by targeting MED25 for degradation in a RING-H2-dependent manner. Proteasome-dependent degradation of MED25 seems to activate its function as a positive regulator of FLOWERING LOCUS T (FT) and is important to induce the expression of FT, and consequently to promote flowering. MBR2 may also function downstream of HAL3 and be required for HAL3-regulated plant growth. Activation of MBR2 by HAL3 may lead to the degradation of cell cycle suppressors, resulting in enhancement of cell division and plant growth. Both MBR1 and MBR2 contain a C3H2C3-type RING-H2 finger. 50 matched cddid_all.tbl CDD cd23114 cd23114 438476 RING-H2_WAVH2 RING finger, H2 subclass, found in Arabidopsis thaliana protein WAV3 homolog 2 (WAVH2) and similar proteins. WAVH2, also known as RING-type E3 ubiquitin transferase WAVH2, is a probable E3 ubiquitin-protein ligase involved in the regulation of root growth. It acts as a positive regulator of root gravitropism. WAVH2 contains a C3H2C3-type RING-H2 finger. 56 matched cddid_all.tbl CDD cd23115 cd23115 438477 RING-H2_BB-like RING finger, H2 subclass, found in Arabidopsis thaliana RING-type E3 ubiquitin transferase BIG BROTHER (BB) and similar proteins. BB (also known as protein ENHANCER OF DA1-1 or EOD1) is an E3 ubiquitin-protein ligase that limits organ size, and possibly seed size, in a dose-dependent manner. It negatively regulates the duration of cell proliferation in leaves and petals independently of the major phytohormones (e.g. auxin, cytokinin, gibberellin, brassinosteroids, ethylene, abscisic acid, jasmonic acid), probably by targeting growth stimulators for degradation. It limits the proliferation of root meristematic cells. BB polyubiquitinates DA1. It is involved in the promotion of leaf senescence, in addition to its function in restricting plant growth. BB-related is an E3 ubiquitin-ligase probably involved in organ size regulation. Members of this subfamily contain a C3H2C3-type RING-H2 finger. 52 matched cddid_all.tbl CDD cd23116 cd23116 438478 RING-H2_AIRP1-like RING finger, H2 subclass, found in Arabidopsis thaliana protein ABA INSENSITIVE RING PROTEIN 1 (AIRP1) and similar proteins. This subfamily includes Arabidopsis thaliana AIRP1 and RING-H2 finger B1a (RHB1A). AIRP1, also known as RING-type E3 ubiquitin transferase AIRP1, possesses E3 ubiquitin-protein ligase activity in vitro when associated with the E2 enzyme UBC8. It plays combinatory roles with AIRP2 in the positive regulation of the abscisic acid-mediated drought stress response. RHB1A is a probable E3 ubiquitin-protein ligase. Members of this subfamily contain a C3H2C3-type RING-H2 finger. 49 matched cddid_all.tbl CDD cd23117 cd23117 438479 RING-H2_TUL1-like RING finger, H2 subclass, found in Saccharomyces cerevisiae transmembrane E3 ubiquitin-protein ligase 1 (TUL1) and similar proteins. This subfamily includes Saccharomyces cerevisiae TUL1, Schizosaccharomyces pombe DSC E3 ubiquitin ligase complex subunit 1 (DSC1), and Arabidopsis thaliana protein FLYING SAUCER 2 (FLY2). TUL1 is the catalytic component of DSC E3 ubiquitin ligase complexes that tag proteins present in Golgi, endosome and vacuole membranes and function in protein homeostasis under non-stress conditions, and support a role in protein quality control. It mediates ubiquitination of vacuolar proteins such as CPS1, PPN1, PEP12 and other proteins containing exposed hydrophilic residues within their transmembrane domains, leading to their sorting into internal vesicles in late endosomes. TUL1 also targets the unpalmitoylated endosomal SNARE TLG1 to the multivesicular body (MVB) pathway. DSC1, also known as defective for SREBP cleavage protein 1, is the catalytic component of the DSC E3 ubiquitin ligase complex required for the sre1 transcriptional activator proteolytic cleavage to release the soluble transcription factor from the membrane in low oxygen or sterol conditions. FLY2 acts as an E3 ubiquitin-protein ligase that may be involved in xylem development. Members of this subfamily contain a C3H2C3-type RING-H2 finger. 59 matched cddid_all.tbl CDD cd23118 cd23118 438480 RING-H2_SIS3 RING finger, H2 subclass, found in Arabidopsis thaliana protein SUGAR INSENSITIVE 3 (SIS3) and similar proteins. SIS3 is an E3 ubiquitin-protein ligase that acts as a positive regulator of sugar signaling during early seedling development. SIS3 contains a C3H2C3-type RING-H2 finger. 47 matched cddid_all.tbl CDD cd23119 cd23119 438481 RING-H2_NIPL1-like RING finger, H2 subclass, found in Arabidopsis thaliana NEP1-interacting protein-like 1 (NIPL1) and similar proteins. This subfamily includes Arabidopsis thaliana NIPL1 and MISFOLDED PROTEIN SENSING RING E3 LIGASE 1 (MPSR1). NIPL1, also called RING-H2 finger protein ATL27, may be involved in the early steps of the plant defense signaling pathway. MPSR1 is a cytoplasmic E3 ubiquitin-protein ligase involved in protein quality control (PQC) under proteotoxic stress. It is essential for plant survival under proteotoxic stress. It functions by removing damaged proteins before they form cytotoxic aggregates. It recognizes misfolded proteins selectively and tethers polyubiquitin chains to the proteins directly for subsequent degradation by the 26S proteasome pathway. Members of this subfamily contain a C3H2C3-type RING-H2 finger. 44 matched cddid_all.tbl CDD cd23120 cd23120 438482 RING-H2_ASR1 RING finger, H2 subclass, found in Saccharomyces cerevisiae alcohol-sensitive RING finger protein 1 (ASR1) and similar proteins. ASR1 is required for tolerance to alcohol. It signals alcohol stress to the nucleus. ASR1 contains a C3H2C3-type RING-H2 finger. 54 matched cddid_all.tbl CDD cd23121 cd23121 438483 RING-H2_RHA1-like RING finger, H2 subclass, found in Arabidopsis thaliana RING-H2 finger A1a (RHA1A), A1b (RHA1B) and similar proteins. This subfamily includes Arabidopsis thaliana RHA1A, RHA1B and XERICO. RHA1A is a probable E3 ubiquitin-protein ligase that may possess E3 ubiquitin ligase activity in vitro. RHA1B possesses E3 ubiquitin-protein ligase activity when associated with the E2 enzyme UBC8 in vitro. XERICO functions on abscisic acid homeostasis at post-translational level, probably through ubiquitin/proteasome-dependent substrate-specific degradation. Members of this subfamily contain a C3H2C3-type RING-H2 finger. 50 matched cddid_all.tbl CDD cd23122 cd23122 438484 RING-H2_RHF2A RING finger, H2 subclass, found in Arabidopsis thaliana RING-H2 zinc finger protein RHF2A and similar proteins. RHF2A is an E3 ubiquitin-protein ligase involved in the positive regulation of the gametogenesis progression. It is required for the degradation of KRP6, a cyclin-dependent kinase inhibitor which accumulates during meiosis and blocks the progression of subsequent mitoses during gametophytes development. It functions in association with RHF1A. Members of this subfamily contain a C3H2C3-type RING-H2 finger. 63 matched cddid_all.tbl CDD cd23123 cd23123 438485 RING-H2_RHA2B RING finger, H2 subclass, found in Saccharomyces cerevisiae RING-H2 zinc finger protein RHA2B and similar proteins. RHA2B is an E3 ubiquitin-protein ligase involved in the positive regulation of abscisic acid (ABA) signaling and responses to salt and osmotic stresses during seed germination and early seedling development. It acts additively with RHA2A in regulating ABA signaling and drought response. RHA2B contains a C3H2C3-type RING-H2 finger. 47 matched cddid_all.tbl CDD cd23124 cd23124 438486 mRING-HC-C3HC3D_arc-1-like Modified RING finger, HC subclass (C3HC3D-type), found in Caenorhabditis elegans putative GTP-binding protein trim-23 homolog (arc-1) and similar proteins. arc-1, also called RING-type E3 ubiquitin transferase arc-1, is an E3 ubiquitin-protein ligase that mediates E2-dependent protein ubiquitination. arc-1 contains a modified C3HC3D-type RING-HC finger. 55 matched cddid_all.tbl CDD cd23125 cd23125 438487 RING-HC_TRAF1-like RING finger, HC subclass, found in tumor necrosis factor (TNF) receptor-associated factor 1 (TRAF1)-like and similar proteins. TRAF1, also known as Epstein-Barr virus-induced protein 6 (EBI6), is an adapter molecule that regulates the activation of NF-kappa-B and JNK. It plays a role in the regulation of cell survival and apoptosis. The heterotrimer formed by TRAF1 and TRAF2 is part of an E3 ubiquitin-protein ligase complex that promotes ubiquitination of target proteins, such as MAP3K14. The TRAF1/TRAF2 complex recruits the antiapoptotic E3 protein-ubiquitin ligases BIRC2 and BIRC3 to TNFRSF1B/TNFR2. This subfamily corresponds a group of TRAF1-like proteins that contains an N-terminal domain with a typical C3HC4-type RING-HC finger. 51 matched cddid_all.tbl CDD cd23126 cd23126 438488 mRING-HC-C3HC3D_TRAF4-like Modified RING finger, HC subclass (C3HC3D-type), found in uncharacterized proteins similar to tumor necrosis factor (TNF) receptor-associated factor 4 (TRAF4). This subfamily corresponds to a group of uncharacterized proteins that shows high sequence similarity with tumor necrosis factor (TNF) receptor-associated factor 4 (TRAF4). TRAF4, also known as cysteine-rich domain associated with RING and Traf domains protein 1, or metastatic lymph node gene 62 protein (MLN 62), or RING finger protein 83 (RNF83), is a member of TRAF protein family, which mainly function in the immune system, where they mediate signaling through tumor necrosis factor receptors (TNFRs) and interleukin-1/Toll-like receptors (IL-1/TLRs). It also plays a critical role in the nervous system, as well as in carcinogenesis. Like TRAF4, members of this subfamily contain a modified C3HC3D-type RING-HC finger. 52 matched cddid_all.tbl CDD cd23127 cd23127 438489 RING-HC_BAH1-like RING finger, HC subclass, found in Arabidopsis thaliana protein BENZOIC ACID HYPERSENSITIVE 1 (BAH1) and similar proteins. This subfamily includes Arabidopsis thaliana BAH1 and BAH1-like. BAH1, also known as protein NITROGEN LIMITATION ADAPTATION (NLA), or RING-type E3 ubiquitin transferase BAH1, acts as an E3 ubiquitin-protein ligase that mediates E2-dependent protein ubiquitination. It plays a role in salicylic acid-mediated negative feedback regulation of salicylic acid (SA) accumulation. It may be involved in the overall regulation of SA, benzoic acid and phenylpropanoid biosynthesis. It controls the adaptability to nitrogen limitation by channeling the phenylpropanoid metabolic flux to the induced anthocyanin synthesis. BAH1-like, also known as RING finger protein 178, or RING-type E3 ubiquitin transferase BAH1-like, is a probable E3 ubiquitin-protein ligase. Members of this subfamily contain a typical C3HC4-type RING-HC finger. 74 matched cddid_all.tbl CDD cd23128 cd23128 438490 RING-HC_MIP1-like RING finger, HC subclass, found in Arabidopsis thaliana MND1-interacting protein 1 (MIP1) and similar proteins. This subfamily includes Arabidopsis thaliana MIP1, RING finger protein 4 (RF4) and RING finger protein 298 (RF298). MIP1 interacts with MND1, HOP2 and XRI1. RF4 and RF298 are putative E3 ubiquitin-protein ligase that may mediate E2-dependent protein ubiquitination. Members of this subfamily contain a typical C3HC4-type RING-HC finger. 55 matched cddid_all.tbl CDD cd23129 cd23129 438491 RING-HC_XBAT35-like RING finger, HC subclass, found in Arabidopsis thaliana protein XB3 homolog 5 (XBAT35) and similar proteins. XBAT35, also known as ankyrin repeat domain and RING finger-containing protein XBAT35, or RING-type E3 ubiquitin transferase XBAT35, has no E3 ubiquitin-protein ligase activity observed when associated with the E2 enzyme UBC8 in vitro. It contains a typical C3HC4-type RING-HC finger. 54 matched cddid_all.tbl CDD cd23130 cd23130 438492 RING-HC_EHV1-like RING finger, HC subclass, found in Equid alphaherpesvirus 1 (Equine herpesvirus 1/EHV-1) regulatory protein and similar proteins. EHV-1 regulatory protein belongs to the Vmw110 (IPC0) protein family. It contains a typical C3HC4-type RING-HC finger and binds zinc stably. 51 matched cddid_all.tbl CDD cd23131 cd23131 438493 RING-HC_RAD5 RING finger, HC subclass, found in radiation sensitivity protein 5 (RAD5) and similar proteins. RAD5, also known as revertibility protein 2 (REV2), or DNA repair protein RAD5, is a probable helicase, and a member of the UBC2/RAD6 epistasis group. It functions with the DNA repair protein RAD18 in error-free postreplication DNA repair. It is involved in the maintenance of wild-type rates of instability of simple repetitive sequences such as poly(GT) repeats. It may also be involved in maintaining a balance which acts in favor of error-prone non-homologous joining during DNA double-strand breaks repairs. It recruits the UBC13-MMS2 dimer to chromatin for DNA repair. RAD5 contains a typical C3HC4-type RING-HC finger. 65 matched cddid_all.tbl CDD cd23132 cd23132 438494 RING-HC_PRT1-like RING finger, HC subclass, found in Arabidopsis thaliana proteolysis 1 protein (PRT1) and similar proteins. PRT1, also called RING-type E3 ubiquitin transferase PRT1, is an E3 ubiquitin-protein ligase that mediates ubiquitination and subsequent proteasomal degradation of target proteins. It functions in the N-end rule pathway of protein degradation, where it specifically recognizes and ubiquitinates proteins with an N-terminal bulky aromatic amino acid (Phe). It does not act on aliphatic hydrophobic and basic N-terminal residues (Arg or Leu) containing proteins. PRT1 contains a typical C3HC4-type RING-HC finger. 52 matched cddid_all.tbl CDD cd23133 cd23133 438495 RING-HC_MmTRIM43-like RING finger, HC subclass, found in Mus musculus tripartite motif-containing protein 43 (TRIM43) and similar propteins. This subfamily includes TRIM43A, TRIM43B and TRIM43C, which are expressed specifically in mouse preimplantation embryos. They contain a typical C3HC4-type RING-HC finger. 57 matched cddid_all.tbl CDD cd23134 cd23134 438496 RING-HC_ITT1-like RING finger, HC subclass, found in Saccharomyces cerevisiae translation termination inhibitor protein ITT1 and similar proteins. ITT1 is a protein that modulates the efficiency of translation termination, resulting in the readthrough of all three types of nonsense codons UAA, UAG and UGA. ITT1 contains a typical C3HC4-type RING-HC finger. 60 matched cddid_all.tbl CDD cd23135 cd23135 438497 RING-HC_IRC20-like RING finger, HC subclass, found in Saccharomyces cerevisiae increased recombination centers protein 20 (IRC20) and similar proteins. IRC20 is an uncharacterized ATP-dependent helicase that is probably involved in a pathway contributing to genomic integrity. IRC20 contains a typical C3HC4-type RING-HC finger. 44 matched cddid_all.tbl CDD cd23136 cd23136 438498 RING-HC_ULS1-like RING finger, HC subclass, found in Saccharomyces cerevisiae ubiquitin ligase for SUMO conjugates protein 1 (ULS1) and similar proteins. ULS1, also called role in silencing protein 1, is an ATP-dependent helicase involved in mating type switching and in silencing interference through its interaction with the silencing regulator SIR4. It cooperates with UBC4 and UBC5 to mediate ubiquitination of SUMO conjugates. ULS1 contains a typical C3HC4-type RING-HC finger. 76 matched cddid_all.tbl CDD cd23137 cd23137 438499 RING-HC_TRY3-like RING finger, HC subclass, found in Candida albicans transcriptional regulator of yeast form adherence 3 (TRY3) and similar proteins. TRY3 acts as a transcription factor required for yeast cell adherence to silicone substrate. It contains a typical C3HC4-type RING-HC finger. 53 matched cddid_all.tbl CDD cd23138 cd23138 438500 RING-HC_ORTHRUS_rpt1 first RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins. This subfamily includes Arabidopsis thaliana ORTHRUS 1-5. They are E3 ubiquitin-protein ligases that may participate in CpG methylation-dependent transcriptional regulation and/or epigenetic transcriptional silencing. ORTHRUS 1 mediates ubiquitination with the E2 ubiquitin-conjugating enzymes UBC11, UBC8 and UBC8 homologs (e.g. UBC10, UBC11, UBC28 and UBC29) but not with UBC27, UBC30, UBC32, UBC34 and UBC36. ORTHRUS 2 and 5 mediate ubiquitination with the E2 ubiquitin-conjugating enzyme UBC11. ORTHRUS 1 and 2 promote methylation-mediated gene silencing leading, for example, to early flowering. They can bind to CpG, CpNpG, and CpNpN DNA motifs, with a strong preference for methylated forms, and with highest affinity for CpG substrates. Members of this subfamily contain two typical C3HC4-type RING-HC fingers. This model corresponds to the first one. 48 matched cddid_all.tbl CDD cd23139 cd23139 438501 RING-HC_ORTHRUS_rpt2 second RING finger, HC subclass, found in Arabidopsis thaliana ORTHRUS and similar proteins. This subfamily includes Arabidopsis thaliana ORTHRUS 1-5. They are E3 ubiquitin-protein ligases that may participate in CpG methylation-dependent transcriptional regulation and/or epigenetic transcriptional silencing. ORTHRUS 1 mediates ubiquitination with the E2 ubiquitin-conjugating enzymes UBC11, UBC8 and UBC8 homologs (e.g. UBC10, UBC11, UBC28 and UBC29) but not with UBC27, UBC30, UBC32, UBC34 and UBC36. ORTHRUS 2 and 5 mediate ubiquitination with the E2 ubiquitin-conjugating enzyme UBC11. ORTHRUS 1 and 2 promote methylation-mediated gene silencing leading, for example, to early flowering. They can bind to CpG, CpNpG, and CpNpN DNA motifs, with a strong preference for methylated forms, and with highest affinity for CpG substrates. Members of this subfamily contain two typical C3HC4-type RING-HC fingers. This model corresponds to the second one. 72 matched cddid_all.tbl CDD cd23140 cd23140 438502 RING-HC_KEG-like RING finger, HC subclass, found in Arabidopsis thaliana protein KEEP ON GOING (KEG) and similar proteins. KEG, also called RING-type E3 ubiquitin transferase KEG, is a RING E3 ubiquitin-protein ligase that mediates E2-dependent protein ubiquitination. It is essential for Arabidopsis growth and development. It acts as a negative regulator of abscisic acid signaling. It is required for ABSCISIC ACID-INSENSITIVE5 (ABI5) degradation, by mediating its ubiquitination. Together with EDR1, KEG may regulate endocytic trafficking and/or the formation of signaling complexes on trans-Golgi network (TGN)/ early endosome (EE) vesicles during stress responses. KEG is a multidomain protein that includes a C3HC4-type RING-HC finger, a kinase domain, ankyrin repeats, and 12 HERC2-like (for HECT and RCC1-like) repeats. 57 matched cddid_all.tbl CDD cd23141 cd23141 438503 RING-HC_ARI6-like RING finger, HC subclass, found in Arabidopsis thaliana protein ariadne homolog 6 (ARI6) and similar proteins. This subfamily includes ARI6 and ARI11. They might act as E3 ubiquitin-protein ligases, or as part of E3 complexes, which accept ubiquitin from specific E2 ubiquitin-conjugating enzymes and then transfer it to substrates. Members of this subfamily contain a typical C3HC4-type RING-HC finger. 62 matched cddid_all.tbl CDD cd23142 cd23142 438504 RING-HC_CHR27-like RING finger, HC subclass, found in Arabidopsis thaliana protein CHROMATIN REMODELING 27 (CHR27) and similar proteins. CHR27, also called protein SNF2-RING-HELICASE-LIKE 1, is a probable helicase-like transcription factor involved in transcriptional gene silencing. It associates with SUVR2 and contributes to transcriptional gene silencing at RNA-directed DNA methylation (RdDM) target loci but also at RdDM-independent target loci. It may be involved in nucleosome positioning to form ordered nucleosome arrays on chromatin. It associates with SUVR2 and functions redundantly with FRG2. It is required for the efficient methylation of a broad range of RdDM target loci. CHR27 contains a typical C3HC4-type RING-HC finger. 55 matched cddid_all.tbl CDD cd23143 cd23143 438505 RING-HC_CeBARD1-like RING finger, HC subclass, found in Caenorhabditis elegans BRCA1-associated RING domain protein 1 (CeBARD1) and similar proteins. CeBARD1, also called Ce-BRD-1, Cebrd-1, or RING-type E3 ubiquitin transferase BARD1, is a constituent of the CeBCD complex that possesses E3 ubiquitin-protein ligase activity. It plays a role in triggering cellular responses at damage sites in response to DNA damage that may be induced by ionizing radiation. It protects against chromosome non-disjunction and nuclear fragmentation during meiotic double-strand break repair to ensure sister chromatid recombination and aid chromosome stability. CeBARD1 contains a typical C3HC4-type RING-HC finger. 47 matched cddid_all.tbl CDD cd23144 cd23144 438506 RING-HC_XBAT31-like RING finger, HC subclass, found in Arabidopsis thaliana protein XB3 homolog 1 (XBAT31) and similar proteins. XBAT31, also called ankyrin repeat domain and RING finger-containing protein XBAT31, or RING-type E3 ubiquitin transferase XB31, has no E3 ubiquitin-protein ligase activity observed when associated with the E2 enzyme UBC8 in vitro. XBAT31 contains a typical C3HC4-type RING-HC finger. 65 matched cddid_all.tbl CDD cd23145 cd23145 438507 RING-HC_SPL2-like RING finger, HC subclass, found in Arabidopsis thaliana SP1-like protein 2 (SPL2) and similar proteins. SPL2, also known as RING-type E3 ubiquitin transferase SPL2, acts as an E3 ubiquitin-protein ligase that mediates E2-dependent protein ubiquitination. SPL2 contains a typical C3HC4-type RING-HC finger. 47 matched cddid_all.tbl CDD cd23146 cd23146 438508 RING-HC_AtBARD1-like RING finger, HC subclass, found in Arabidopsis thaliana BRCA1-associated RING domain protein 1 (AtBARD1) and similar proteins. AtBARD1, also called protein REPRESSOR OF WUSCHEL 1, binds specifically to H3K4me3 regions of target gene (e.g. WUS and WOX5) promoters to repress their transcription via chromatin remodeling. It is required for the shoot apical meristem (SAM) organization and maintenance, by confining WUS expression to the organizing center, and for the quiescent center (QC) development in the root apical meristem (RAM), by repressing WOX5 expression in the root proximal meristem. AtBARD1 plays a role in DNA repair and in cell-cycle control. It is required for the repair of DNA double-strand breaks (DSBs), both natural and induced by genotoxic stress, by homologous recombination (HR). AtBARD1 contains a typical C3HC4-type RING-HC finger. 54 matched cddid_all.tbl CDD cd23147 cd23147 438509 RING-HC_AtBRCA1-like RING finger, HC subclass, found in Arabidopsis thaliana protein BREAST CANCER SUSCEPTIBILITY 1 homolog (AtBRCA1) and similar proteins. AtBRCA1 plays a role in DNA repair and in cell-cycle control. It is required for the repair of DNA double-strand breaks (DSBs), both natural and induced by genotoxic stress, by homologous recombination (HR). AtBRCA1 contains a typical C3HC4-type RING-HC finger. 54 matched cddid_all.tbl CDD cd23148 cd23148 438510 RING-HC_ScRAD18-like RING finger, HC subclass, found in Saccharomyces cerevisiae radiation sensitivity protein 18 (RAD18) and similar proteins. RAD18, also called RING-type E3 ubiquitin transferase RAD18, acts as a postreplication repair E3 ubiquitin-protein ligase that associates with the E2 ubiquitin conjugating enzyme UBC2/RAD6 to form the UBC2-RAD18 ubiquitin ligase complex involved in postreplicative repair (PRR) of damaged DNA. The UBC2-RAD18 complex cooperates with RAD5 and the UBC13-MMS2 dimer to attach mono-ubiquitin chains on 'Lys-164' of POL30, which is necessary for PRR. The UBC2-RAD18 complex is also involved in prevention of spontaneous mutations caused by 7,8-dihydro-8-oxoguanine. RAD18 is an E3 RING-finger protein belonging to the UBC2/RAD6 epistasis group. It contains a typical C3HC4-type RING-HC finger. 52 matched cddid_all.tbl CDD cd23149 cd23149 438511 RING-Ubox_LubX-like_rpt1 first U-box domain, a modified RING finger, found in Legionella pneumophila U-box protein LubX and similar proteins. LubX, also called RING-type E3 ubiquitin transferase LubX, is part of the large arsenal of effectors in Legionella pneumophila that are translocated into the host cytosol during infection. LubX acts as an E3 ubiquitin-protein ligase (EC 2.3.2.27) that interferes with the host's ubiquitination pathway. LubX contains two RING-like U-box domains. U-box 1 is critical to the ubiquitin ligase activity, and U-box 2 mediates interaction with host target. This model corresponds to the first one. 55 matched cddid_all.tbl CDD cd23150 cd23150 438512 RING-Ubox_LubX-like_rpt2 second U-box domain, a modified RING finger, found in Legionella pneumophila U-box protein LubX and similar proteins. LubX, also called RING-type E3 ubiquitin transferase LubX, is part of the large arsenal of effectors in Legionella pneumophila that are translocated into the host cytosol during infection. LubX acts as an E3 ubiquitin-protein ligase (EC 2.3.2.27) that interferes with the host's ubiquitination pathway. LubX contains two RING-like U-box domains. U-box 1 is critical to the ubiquitin ligase activity, and U-box 2 mediates interaction with host target. This model corresponds to the second one. 69 matched cddid_all.tbl CDD cd23156 cd23156 467472 Prefoldin_3 Prefoldin subunit 3. Prefoldin subunit 3 is one of the alpha subunits of the eukaryotic prefoldin complex. Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils. 129 matched cddid_all.tbl CDD cd23157 cd23157 467473 Prefoldin_5 Prefoldin subunit 5. Prefoldin subunit 5 is one of the alpha subunits of the eukaryotic prefoldin complex. Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils. 124 matched cddid_all.tbl CDD cd23158 cd23158 467474 Prefoldin_UXT protein UXT. UXT is an alpha subunit of the prefoldin-like complex (PFDL). PFDL is involved in the cytoplasmic assembly of RNA polymerase I and can interact with other chaperone complexes, like R2TP, to form the PAQosome. UXT has an important role in the activation of the NF-kappaB pathway. UXT is also a component of the centrosome and is associated with gamma-tubulin. Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. 128 matched cddid_all.tbl CDD cd23159 cd23159 467475 Prefoldin_URI1 RNA polymerase II subunit 5-mediating protein homolog. URI (also called RNA polymerase II fifth subunit regulatory protein or RMP) is an alpha subunit of prefoldin-like complex (PFDL). PFDL is involved in the cytoplasmic assembly of RNA polymerase II and can interact with other chaperone complexes, like R2TP to form the PAQosome. In the cytoplasm, URI acts as a chaperone protein; in the nucleus, URI acts as a transcription regulator and can interact with RPB5 (a subunit of eukaryotic RNA polymerases) and RNA polymerase II (pol II). Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. 124 matched cddid_all.tbl CDD cd23160 cd23160 467476 Prefoldin_alpha_GimC Prefoldin alpha subunit, archaeal. Archaeal alpha subunit of prefoldin (GimC), a hexameric molecular chaperone complex, found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils. 127 matched cddid_all.tbl CDD cd23161 cd23161 467477 Prefoldin_6 Prefoldin subunit 6. Prefoldin subunit 6 is one of the beta subunits of the eukaryotic prefoldin complex. Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils. 101 matched cddid_all.tbl CDD cd23162 cd23162 467478 Prefoldin_beta_GimC Prefoldin beta subunit, archaeal. Archaeal beta subunit of prefoldin (GimC), a hexameric molecular chaperone complex, found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils. 102 matched cddid_all.tbl CDD cd23163 cd23163 467479 Prefoldin_2 prefoldin subunit 2. Prefoldin subunit 2 is one of the beta subunits of the eukaryotic prefoldin complex. Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils. 100 matched cddid_all.tbl CDD cd23164 cd23164 467480 Prefoldin_1 prefoldin subunit 1. Prefoldin subunit 1 is one of the beta subunits of the eukaryotic prefoldin complex. Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils. 99 matched cddid_all.tbl CDD cd23165 cd23165 467481 Prefoldin_4 prefoldin subunit 4. Prefoldin subunit 4 is one of the beta subunits of the eukaryotic prefoldin complex. Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils. 103 matched cddid_all.tbl CDD cd23166 cd23166 467482 ASDURF ASDURF. ASDURF is a beta-type subunit of the prefoldin-like complex (PFDL) that is part of the PAQosome (Particle for Arrangement of Quaternary structure) complex. The PAQosome is a cochaperone that assists the chaperone HSP90 in assembly of large protein complexes, like RNA polymerase I. Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. 80 matched cddid_all.tbl CDD cd23167 cd23167 438017 ps-ssRNAv_RdRp-like conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses. This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model. 73 matched cddid_all.tbl CDD cd23168 cd23168 438018 ps-ssRNAv_Nidovirales_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Nidovirales of positive-sense single-stranded RNA [(+)ssRNA] viruses. This family contains the catalytic core domain of RdRP of Nidovirales, an order of enveloped, (+)ssRNA viruses which infect vertebrates and invertebrates. Host organisms include mammals, birds, reptiles, amphibians, fish, arthropods, mollusks, and helminths. The order Nidovirales currently comprises 88 formally recognized virus species of (+)ssRNA viruses which are classified into nine virus families: Abyssoviridae, Arteriviridae, Coronaviridae, Euroniviridae, Medioniviridae, Mesoniviridae, Mononiviridae, Roniviridae, and Tobaniviridae. Based on the genome size, the members of the order Nidovirales can be divided into two groups, large and small nidoviruses. The genomes of the large nidoviruses are well over 25 kb in length with size differences in the 5 kb range. Planarian secretory cell nidovirus (PSCNV), only member of the Mononiviridae family, has the largest known non-segmented RNA genome of 41.1 kb; its host is the planarian flatworm. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 310 matched cddid_all.tbl CDD cd23169 cd23169 438019 ps-ssRNAv-Picornavirales catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of positive-sense single-stranded RNA [(+)ssRNA] viruses. This family contains the catalytic core domain of RdRp of Picornavirales, an order of (+)ssRNA viruses. The order Picornavirales comprises viruses that historically are referred to as picorna-like viruses and which are classified into eight virus families: Caliciviridae, Dicistroviridae, Iflaviridae, Marnaviridae, Picornaviridae, Polycipiviridae, Secoviridae, and Solinviviridae. All known genomes of Picornavirales members encode proteins with helicase, 3C-like protease, and RdRp domains, as well as capsid proteins with related structures, although the genome organizations can differ among viruses. The picornavirus genome is replicated via a negative-sense (-) RNA intermediate by the viral RdRp, named 3Dpol, which uses VPg (the product of 3B) as a primer to initiate the replication process. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 309 matched cddid_all.tbl CDD cd23170 cd23170 438020 ps-ssRNAv_Hypoviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Hypoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Hypoviridae. The Hypoviridae, comprising one genus, Hypovirus, is a family of capsidless viruses with (+)ssRNA genomes of 9.1-12.7 kb that possess either a single large ORF or two ORFs. Hypoviruses have been detected in ascomycetous or basidiomycetous filamentous fungi, and are considered to be replicated in host Golgi-derived, lipid vesicles that contain their double-stranded RNA (dsRNA) as a replicative form. Some hypoviruses induce hypovirulence to host fungi, while others do not. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 240 matched cddid_all.tbl CDD cd23171 cd23171 438021 ps-ssRNAv_EoPV-like_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the positive-sense single-stranded RNA [(+)ssRNA] picorna-like virus Ectropis obliqua, and related viruses. This group contains the catalytic core domain of RdRp of Ectropis obliqua picorna-like virus (EoPV), and related viruses. EoPV is an insect (+)ssRNA virus that causes a lethal granulosis infection of larvae of the tea looper (Ectropis obliqua), and related insect-infecting iflaviruses. Ectropis obliqua, a species of moth, is one of the most destructive pest insects on tea plants throughout growing areas of this crop in southern China. The EoPV genome contains a single large ORF encoding the capsid proteins at the 5' terminus of the genome with the non-structural proteins at the 3' end of the genome. This organization is similar to typical mammalian picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 239 matched cddid_all.tbl CDD cd23172 cd23172 438022 ps-ssRNAv_Astroviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Astroviridae, order, Stellavirales. Astrovirus has a non-segmented, (+)ssRNA genome within a non-enveloped icosahedral capsid. The family Astroviridae comprises two genera, Mamastrovirus, which infect mammals, and Avastrovirus, which infect birds. Astroviruses have been isolated from stools from a wide variety of mammals and birds. Human astroviruses have been shown to be an important cause of gastroenteritis in young children. Duck astrovirus causes an often-fatal hepatitis in ducklings. Astroviruses infecting turkeys, guinea fowl and chickens affect multiple organs, including the kidney and thymus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 243 matched cddid_all.tbl CDD cd23173 cd23173 438023 ps-ssRNAv_Nodaviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Nodaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Nodaviridae, order Nodamuvirales. The family name Nodaviridae, derives from the Japanese village of Nodamura where Nodamura virus was first isolated from Culex tritaeniorhynchus mosquitoes. Virions are non-enveloped and spherical in shape with icosahedral symmetry and diameters ranging from 25 to 33 nm. The members of the two genera in this family infect insects (Alphanodavirus) or fish (Betanodavirus). Alphanodavirus infection results in the stunting, paralysis and death of the insect host. The infection of fish by betanodaviruses such as striped jack nervous necrosis virus or red-spotted grouper nervous necrosis virus causes neural necrosis, encephalopathy or retinopathy and is associated with behavioral abnormalities and high mortality, posing significant problems for marine aquaculture. The genome consists of two molecules of (+)ssRNA: RNA1 and RNA2. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 236 matched cddid_all.tbl CDD cd23174 cd23174 438024 ps-ssRNAv_CBPV-like_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) chronic bee paralysis virus (CBPV) and related positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of the chronic bee paralysis virus (CBPV) and related (+)ssRNA viruses. The CBPV is the causative agent of severe, usually fatal, paralysis in adult honey bees. CBPV has not been assigned to any group or class of viruses because it has a unique genome organization and virion morphology. However, analyses of the nucleic acid sequence showed similarities between the RdRp of CBPV and the RdRps of Tombusviruses, Nodaviruses, Lake Sinai virus 1 and 2 as well as the Anopheline associated C virus (AACV). CBPV was one of the first viruses in honey bees to be described and isolated as it causes characteristic signs of disease in adult honey bees. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 229 matched cddid_all.tbl CDD cd23175 cd23175 438025 ps-ssRNAv_Potyviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Potyviridae, order: Patatavirales. Potyviridae, is the largest family of RNA plant viruses, members of which have (+)ssRNA genomes and flexuous filamentous particles. The family is divided into eight genera: Brambyvirus, Bymovirus, Ipomovirus, Macluravirus, Poacevirus, Potyvirus, Rymovirus, and Tritimovirus. Most genomes are monopartite but those of members of the genus Bymovirus are bipartite. Some members cause serious disease epidemics in cultivated plants. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 236 matched cddid_all.tbl CDD cd23176 cd23176 438026 ps-ssRNAv_Leviviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Leviviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Leviviridae, order Levivirales. Leviviridae is a family of (+)ssRNA viruses which are highly antigenic and are abundantly present in sewage, waste water, animal and human feces. Within this family two genera can be distinguished, Levivirus and Allolevivirus. Members of the family Leviviridae that propagate in Escherichia coli infect by adsorption to the sides of F(ertility) pili. This event leads to cleavage of the A-protein and release of the RNA from the virion into the bacterium. The infecting RNA encodes a replicase, which assembles with three host proteins, ribosomal protein S1 and translation elongation factors EF-Tu and EF-Ts, to form the active RNA polymerase. Leviviruses not only infect enterobacteria, but also species of the genera Caulobacter, Pseudomonas, and Acinetobacter, and probably many other Gram-negative bacteria. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 396 matched cddid_all.tbl CDD cd23177 cd23177 438027 ps-ssRNAv_Narnaviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Narnaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Narnaviridae, order Wolframvirales. Narnaviridae is a family of (+)ssRNA viruses which are the simplest of known RNA viruses, consisting of a single molecule of (+)ssRNA that may be as small as 2.3 kb and encoding only an RdRp to direct their own replication. They encode no protein capsid and no virus particles other than lipid vesicles are known to be associated with infection. The family Narnaviridae became the second virus family with members lacking a protein capsid, following the acceptance of the family Hypoviridae as the first such family. The two genera of the family, the genus Narnavirus and the genus Mitovirus, share basic genome organization properties. The single feature distinguishing the two genera is the site of translation of the RdRp, and presumably of replication: members of the genus Narnavirus are found in the cytosol (the cytoplasm exclusive of organelles) and the genus Mitovirus are confined to mitochondria. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 235 matched cddid_all.tbl CDD cd23178 cd23178 438028 ps-ssRNAv_Flaviviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Flaviviridae, order Amarillovirales. Flaviviridae, is a family of small, enveloped viruses with RNA genomes of 9-13 kb. Most infect mammals and birds. Many flaviviruses are host-specific and pathogenic, such as hepatitis C virus in the genus Hepacivirus. The majority of known members in the genus Flavivirus are arthropod borne, and many are important human and veterinary pathogens (e.g., yellow fever virus, dengue virus). Virions are typically spherical in shape with a lipid envelope. Virions have a single, small, basic capsid (C) protein and two (genera Flavivirus, Hepacivirus and Pegivirus) or three (genus Pestivirus) envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. Translational initiation of genomic RNA is cap dependent in the case of members of the genus Flavivirus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 284 matched cddid_all.tbl CDD cd23179 cd23179 438029 ps_ssRNAv_Tolivirales_RdRp "catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Toliovirales of positive-sense single-stranded RNA (+ssRNA) viruses. This family contains the catalytic core domain of RdRp of Tolivirales, an order of (+)ssRNA viruses which infect insects and plants. The virions are non-enveloped, spherical, and have an icosahedral capsid. The name Tolivirales, is derived from ""tombusvirus-like"" with the suffix -virales indicating a virus order. This order includes two families: Carmotetraviridae and Tombusviridae. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides." 227 matched cddid_all.tbl CDD cd23180 cd23180 438030 ps-ssRNAv_Solemoviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Solemoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the RdRp of RNA viruses belonging to the family Solemoviridae, order Sobelivirales. Plant viruses in the family Solemoviridae have stable icosahedral particles assembled on T=3 symmetry and a relatively small (4-4.6 kb) monopartite (+)ssRNA genome with 4-5 open reading frames (ORFs). The natural host range is relatively narrow for each virus. Viral transmission occurs via mechanical wounding, by vegetative propagation or abiotically through soil; insects (beetles, aphids, thrips, hoppers, mirid bugs, moths) can also be vectors. Viruses infecting legumes or plants from the family Chenopodiaceae may be seed-transmissible. Members of the family are classified into four genera: Sobemovirus, Polemovirus, Polerovirus, Enamovirus. The viral polyprotein contains domains of the membrane anchor, a serine protease, a genome-linked viral protein (VPg) and C-terminal protein(s) or an RdRp, expressed by means of ribosomal frameshifting. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 447 matched cddid_all.tbl CDD cd23181 cd23181 438031 ps-ssRNAv_Alvernaviridae_RdRp RNA-dependent RNA polymerase (RdRp) in the family Alvernaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the RdRp of RNA viruses belonging to the family Alvernaviridae, order Sobelivirales. Alvernaviridae is a family of non-enveloped [(+)ssRNA] viruses. Dinoflagellates serve as natural hosts. There is one genus in this family, Dinornavirus, which contains one species: Heterocapsa circularisquama RNA virus 01. Diseases associated with this family include host population control, possibly through lysis of the host cell. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 304 matched cddid_all.tbl CDD cd23182 cd23182 438032 ps-ssRNAv_Alsuviricetes_RdRp "catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the class Alsuviricetes of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the class Alsuviricetes, phylum: Kitrinoviricota. Alsuviricetes is a class of [(+)ssRNA] viruses which infect eukaryotes. The name of the group is a syllabic abbreviation of ""alpha supergroup"" with the suffix -viricetes indicating a virus class. The class Alsuviricetes includes three orders: Hepelivirales, Martellivirales, and Tymovirales. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides." 187 matched cddid_all.tbl CDD cd23183 cd23183 438033 ps-ssRNAv_Botourmiaviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Botourmiaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Botourmiaviridae, order Ourlivirales. The family includes six genera: Ourmiavirus, Botoulivirus, Magoulivirus, Penoulivirus, Rhizoulivirus and Scleroulivirus. Family Botourmiaviridae genomes can be monopartite (Botoulivirus, Magoulivirus, Penoulivirus, Rhizoulivirus and Scleroulivirus) (2-3 kb) or tripartate (Ourmiavirus). Members of genus Ourmiavirus infect plants and the other genera infect fungi. Members of the genera Botoulivirus, Magoulivirus and Scleroulivirus infect fungi from the genera Botrytis, Magnaporthe or Sclerotinia, respectively. Members of the genus Ourmiavirus infect plants: Ourmia melon virus infects melon, producing chlorotic spots and irregular ringspots, Epirus cherry virus produces rasp-leaf symptoms in cherry, and cassava virus C induces severe stunting and a yellow mosaic pattern in cassava. Ourmiavirus replication is dependent on the virus RdRp. Synthesis of the ourmiavirus coat protein from actively replicating RNA3 is necessary for both virion assembly and systemic infection of the host. The ourmiavirus movement protein determines symptoms and forms tubular structures involved in cell-to-cell movement and may undergo post-translational modification. Botoulivirus, magoulivirus and scleroulivirus replication is strictly dependent on the virus RNA-dependent RNA polymerase. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 223 matched cddid_all.tbl CDD cd23184 cd23184 438034 ps-ssRNAv_Barnaviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Barnaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Barnaviridae, order Sobelivirales, and related viruses. Barnaviridae is a family of non-enveloped, (+)ssRNA viruses. Cultivated mushrooms serve as natural hosts. The family has one genus, Barnavirus, which contains one species: Mushroom bacilliform virus (MBV) which infects the common cultivated button mushroom (Agaricus bisporus), and Bacilliform particles, which are morphologically similar to MBV, have been observed in the field mushroom Agaricus campestris. MBV viral transmission is horizontal via mycelium and possibly basidiospores. Distribution of MBV coincides with that of the commercial cultivation of Agaricus bisporus; the virus has been reported to occur in most major mushroom-growing countries. MBV is capable of autonomous replication, but commonly occurs as a double infection with a double-stranded RNA (dsRNA) virus (LaFrance isometric virus, LFIV) in mushrooms afflicted with La France disease. MBV is not required in pathogenesis involving LFIV, but it remains to be determined if it is a second, minor causal agent of LaFrance disease. MBV ssRNA and LFIV dsRNA do not share sequence homology. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 261 matched cddid_all.tbl CDD cd23185 cd23185 438035 dsRNAv_Picobirnaviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) of the family Picobirnaviridae of positive-sense double-stranded RNA [(+)dsRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Picobirnaviridae, order Durnavirales. Picobirnaviridae is a family of viruses with bi-segmented (rarely unsegmented) double-stranded RNA (dsRNA) genomes comprising about 4.4 kbp in total, with small, non-enveloped spherical virions. The family includes one genus (Picobirnavirus) grouping three genetic clusters with high sequence variability, two defined by viruses infecting vertebrates and a third with viruses found in invertebrates. Picobirnaviruses have been identified in feces of humans, rabbits, and a variety of other species of mammals, reptiles, birds, and invertebrates. The pathogenicity of picobirnaviruses has not been established; studies conducted with immunocompromised persons suggest that they are opportunistic pathogens that may cause diarrhea. A published phylogenetic tree constructed for RdRps of RNA viruses in the realm Riboviria, showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. The RdRp structure of double-stranded RNA picobirnavirus is highly homologous to the RdRp of (+)ssRNA viruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 444 matched cddid_all.tbl CDD cd23186 cd23186 438036 Tobaniviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRP) in the Tobaniviridae family of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Tobaniviridae, order Nidovirales. Tobaniviridae RNA viruses infect vertebrates; their host organisms include mammals, fish, and snakes. Member viruses have a viral envelope and (+)ssRNA genome. The genome size of Tobaniviruses ranges from 20 to 32 kilobases. The family is the only member of the suborder Tornidovirineae. The family Tobaniviridae has four subfamilies (Piscanivirinae, Remotovirinae, Remotovirinae, and Torovirinae) and eight genera (Bafinivirus, Oncotshavirus, Bostovirus, Infratovirus, Pregotovirus, Sectovirus, Tiruvirus, and Torovirus). The Tobaniviridae family belongs to the order Nidovirales, which currently comprises 88 formally recognized virus species of (+)ssRNA viruses, which are classified into nine virus families across seven different suborders. The structure of Tobaniviridae RdRp contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 401 matched cddid_all.tbl CDD cd23187 cd23187 438037 Mesoniviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the Mesoniviridae family of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Mesoniviridae, order Nidovirales. Member viruses have a viral envelope and (+)ssRNA genome. The family is named after the size of the genomes relative to other nidoviruses, which is intermediate between that of the families Arteriviridae and Coronaviridae, with meso- coming from the Greek word mesos, which means medium, while -ni is an abbreviation of nido. The family Mesoniviridae comprises of mosquito-specific viruses with extensive geographic distribution and host range. The family has only one subfamily, Hexponivirinae, which contains only one genus, Alphamesonivirus. There are 8 subgenera (Casualivirus, Enselivirus, Hanalivirus, Kadilivirus, Karsalivirus, Menolivirus, Namcalivirus, and Ofalivirus) and 10 species in Alphamesonivirus. The structure of Mesoniviridae RdRp contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 424 matched cddid_all.tbl CDD cd23188 cd23188 438038 Medioniviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the Medioniviridae family of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Medioniviridae, order Nidovirales. Member viruses have a viral envelope and (+)ssRNA genome. The Medioniviridae subgenera includes Turrinivirus and Balbicanovirus. The structure of Medioniviridae RdRp contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 391 matched cddid_all.tbl CDD cd23189 cd23189 438039 Arteriviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Arteriviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Arteriviridae, order Nidovirales. Member viruses have a viral envelope and (+)ssRNA genome. The overall genome organization of the Arteriviruses are highly similar to the Coronaviruses; however, they lack the spike proteins of the coronaviruses. The family members include equine arteritis virus (EAV), porcine reproductive and respiratory syndrome virus (PRRSV), lactate dehydrogenase elevating virus of mice, and simian hemorrhagic fever virus (SHFV). The structure of Arteriviridae RdRp contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 323 matched cddid_all.tbl CDD cd23190 cd23190 438040 Roniviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Roniviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Roniviridae, order Nidovirales. Member viruses have a viral envelope and (+)ssRNA genome. The family Roniviridae includes a single genus (Okavirus) for three species of viruses (Yellow head virus, Gill-associated virus and Okavirus 1) with enveloped, rod-shaped virions. Roniviruses infect penaeid and palaemonid shrimp. Natural infections are usually without apparent clinical signs. One member of the family (yellow head virus) is highly pathogenic for shrimp. Roniviruses are most closely related to other nidoviruses infecting arthropods, including members of the families Mesoniviridae (from mosquitoes) and Euroniviridae (from crustaceans). The structure of Roniviridae RdRp contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 379 matched cddid_all.tbl CDD cd23191 cd23191 438041 Euroniviridae_RdRp "catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Eunroniviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Eunroniviridae, order Nidovirales. Member viruses have a viral envelope and (+)ssRNA genome. Eunroniviridae is a closely related family of crustacean nidoviruses, within the suborder Ronidovirineae, which also includes the family Roniviridae. Ronidovirineae, named ""rod-shaped nidovirus"", is 150-200 nm long and approximately 60 nm thick. There are 3 viral species in the Euroniviridae family, all of which have been detected in crustaceans. The structure of Euroniviridae RdRp contains a RdRp domain as well as a large N-terminal extension that adopts a nidovirus RdRp-associated nucleotidyltransferase (NiRAN) architecture. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides." 345 matched cddid_all.tbl CDD cd23192 cd23192 438042 Caliciviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Caliciviridae, order Picornavirales. Member viruses have a viral (+)ssRNA genome, which is not segmented. The family Caliciviridae, includes eleven genera: seven genera of which infect mammals (Lagovirus, Norovirus, Nebovirus, Recovirus, Sapovirus, Valovirus, and Vesivirus), two genera of which infect birds (Bavovirus, Nacovirus), and two genera of which infect fish (Minovirus and Salovirus). Each genus includes 1-2 species. Human noroviruses are a leading cause of acute gastroenteritis in humans. Furthermore, unclassified caliciviruses have been detected in geese, yellowfin seabream, greater green snake, arctic lamprey, frogs and various Australian birds, highlighting the wide host range of viruses in the family Caliciviridae. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 310 matched cddid_all.tbl CDD cd23193 cd23193 438043 ps-ssRNA_Picornaviridae catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Picornaviridae, order Picornavirales. The Picornaviridae family consists of small, icosahedral viruses with (+)ssRNA genomes. Characteristic features of all members of the family Picornaviridae are three capsid proteins with beta-barrel folding, polyprotein processing by virus-encoded cysteine proteinase(s), and replication by an RdRp with a YGDD sequence motif. The family Picornaviridae comprises 68 genera containing 158 species, but many viruses are presently awaiting classification. The established genera of the family include: Aphthovirus, Avisivirus, Crohivirus, Enterovirus, Teschovirus, Cardiovirus, Erbovirus, Kobuvirus, Hepatovirus, Parechovirus, Aquamavirus, Avihepatovirus, Avisivirus, Cosavirus, Dicipivirus, Fipivirus, Gallivirus, Hunnivirus, Kunsagivirus, Limnipivirus, Megrivirus, Mischivirus, Mosavirus, Oscivirus, Pasivirus, Passerivirus, Rabovirus, Rosavirus, Sakobuvirus, Salivirus, Sapelovirus, Senecavirus, Sicinivirus, and Tremovirus. The Picornaviridae contains many important human and animal pathogens including enteroviruses (such as poliovirus, enterovirus, coxsackievirus, and rhinovirus), cardioviruses (such as encephalomyocarditis virus and Theiler's virus), hepatitis A virus and foot-and-mouth disease virus. Infection with various picornaviruses may cause encephalitis, febrile rash illnesses (hand-foot-and-mouth disease), aseptic meningitis, hepatitis, conjunctivitis, herpangina, myositis and myocarditis, and the common cold. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 345 matched cddid_all.tbl CDD cd23194 cd23194 438044 Dicistroviridae_RdRp RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales. This group contains the RdRp of RNA viruses belonging to the family Dicistroviridae, order Picornavirales. Dicistroviridae is a family of small non-enveloped viruses with a (+)ssRNA genome of approximately 8-10 kilobases. The family contains 3 genera: Aparavirus, Cripavirus, and Triatovirus. All members infect arthropod hosts with some having devastating economic consequences, such as acute bee paralysis virus, Kashmir bee virus, and Israeli acute paralysis virus in domesticated honeybees, and taura syndrome virus and mud crab virus in the seafood industry. On the contrary, host specificity and other desirable traits make several members of this group amenable to development as biopesticides for insect control, such as Solenopsis invicta virus 1 against fire ants, and triatoma virus against triatomine bugs that vector Chagas disease. Members in the family Dicistroviridae have similarity to viruses in the Picornavirales members (Iflaviridae, Picornaviridae, Marnaviridae and Secoviridae). The genomes of viruses of these taxa encode proteins with helicase, 3C-like protease, and RdRp domains, as well as capsid proteins with related structures, although the genome organizations can differ among viruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 315 matched cddid_all.tbl CDD cd23195 cd23195 438045 Marnaviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Marnaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Marnaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. They are mono- or dicistronic, have a polyadenylate tail and have conserved motifs for RNA helicase, RdRp, and structural protein domains. The first RNA virus isolated and characterized that infects a marine protist was Heterosigma akashiwo RNA virus (HaRNAV) in the genus Marnavirus, that infects the toxic bloom-forming Raphidophyte alga, Heterosigma akashiwo. Recently, it has undergone a major taxonomic revision and now includes 20 species within 7 genera, which include Bacillarnavirus, Kusarnavirus, Labyrnavirus, Locarnavirus, Marnavirus, Salisharnavirus, and Sogarnavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 310 matched cddid_all.tbl CDD cd23196 cd23196 438046 Secoviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Secoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Secoviridae, order Picornavirales. Members of the family Secoviridae are non-enveloped viruses with mono- or bipartite (RNA-1 and RNA-2) linear (+)ssRNA genomes of 9 to 13.7 kilobases in total. Secoviruses are related to picornaviruses and are classified in the order Picornavirales. The majority of known members infect dicotyledonous plants and many are important plant pathogens (e.g., grapevine fanleaf virus and rice tungro spherical virus). The Secoviridae includes 8 genera (Comovirus, Fabavirus, Nepovirus, Cheravirus, Sadwavirus, Torradovirus, Sequivirus, and Waikavirus) as well as unassigned species (strawberry latent ringspot virus-MEN 454, strawberry mottle virus-Thompson, black raspberry necrosis virus- 1, chocolate lily virus A-KP2, and Dioscorea mosaic associated virus-goiana). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 309 matched cddid_all.tbl CDD cd23197 cd23197 438047 Iflaviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Iflaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Iflaviridae, order Picornavirales. Iflaviridae is a family of small non-enveloped viruses with (+)ssRNA genomes of approximately 9-11 kilobases in length encoding a single polyprotein. All members infect arthropod hosts with the majority infecting insects. Beneficial and pest insects serve as hosts and infections can be symptomless (Nilaparvata lugens honeydew virus 1), cause developmental abnormalities (deformed wing virus, Varroa destructor virus 1, sacbrood virus), behavioral changes (deformed wing virus, Varroa destructor virus 1, slow bee paralysis virus, sacbrood virus) and premature mortality (deformed wing virus, Varroa destructor virus 1, slow bee paralysis virus, infectious flacherie virus, sacbrood virus). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 319 matched cddid_all.tbl CDD cd23198 cd23198 438048 Polycipiviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Polycipiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Polycipiviridae (polycistronic picorna-like viruses), order Picornavirales. Polycipiviridae is a family of picorna-like viruses with non-segmented, linear, (+)ssRNA genomes of approximately 10-12 kb. Their genomes are polycistronic, with four (or more) consecutive 5'-proximal open reading frames (ORFs) encoding structural (and possibly other) proteins and a long 3' ORF encoding the replication polyprotein. Members of species within the family are typically found in ants, with Apple picorna-like virus 1 and the unnamed Polycipiviridae virus in fruit bat stool as exceptions. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 317 matched cddid_all.tbl CDD cd23199 cd23199 438049 Solinviviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Solinviviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Solinviviridae, order Picornavirales. Solinviviridae is a family of picorna/calici-like viruses with non-segmented, linear, (+)ssRNA genomes of approximately 10-11 kb. Members of two species within the family infect ants but related unclassified virus sequences derive from a large variety of insects and other arthropods. Phylogenetic analysis of RdRp amino acid sequences shows that members of the two classified solinvivirus species form part of a large and very diverse group of arthropod-infecting viruses within the picorna/calici-like group of viruses. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg (viral protein genome-linked)-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 323 matched cddid_all.tbl CDD cd23200 cd23200 438050 Nora-virus_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in a novel picorna-like Drosophila virus, Nora virus. This group contains the catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the unclassified Nora virus, a new picorna-like virus family. Nora virus has a (+)ssRNA genome followed by a poly(A) tail. Unlike other picorna-like viruses, the genome has four open reading frames (ORFs). One ORF encodes a picornavirus-like cassette of proteins for virus replication, including an iflavirus-like RdRp and a helicase that is related to those of mammalian picornaviruses. The three other ORFs are not closely related to any previously described viruses. Nora virus is present as a persistent infection in several tested laboratory stocks and wild-caught flies. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 306 matched cddid_all.tbl CDD cd23201 cd23201 438051 Pestivirus_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Pestivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses. This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Pestivirus genus within the family Flaviviridae, order Amarillovirales. Members of the genus Pestivirus infect pigs and ruminants, including cattle, sheep, goats and wild ruminants, and are transmitted through contact with infected secretions (respiratory droplets, urine or feces). Infections may be subclinical or cause enteric, hemorrhagic or wasting diseases, including those by the economically important bovine viral diarrhea virus and classical swine fever virus. Virions of Pestivirus have a single, small, basic capsid (C) protein and three envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 579 matched cddid_all.tbl CDD cd23202 cd23202 438052 Hepacivirus_RdRp RNA-dependent RNA polymerase (RdRp) in the genus Hepacivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses. This group contains the RdRp of RNA viruses belonging to the Hepacivirus genus within the family Flaviviridae, order Amarillovirales. The genus Hepacivirus includes hepatitis C virus, a major human pathogen causing progressive liver disease, and several other viruses of unknown pathogenicity that infect horses, rodents, bats, cows and primates. Infections are typically persistent and target the liver. Virions of Hepacivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 518 matched cddid_all.tbl CDD cd23203 cd23203 438053 Pegivirus_RdRp RNA-dependent RNA polymerase (RdRp) in the genus Pegivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses. This group contains the RdRp of RNA viruses belonging to the Pegivirus genus within the family Flaviviridae, order Amarillovirales. Members of the Pegivirus genus are widely distributed in a range of mammalian species, in which they cause persistent infections. To date, they have not been clearly associated with disease. Virions of Pegivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 476 matched cddid_all.tbl CDD cd23204 cd23204 438054 Flavivirus_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Flavivirus, within the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses. This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Flavivirus genus within the family Flaviviridae, order Amarillovirales. The genus Flavivirus consists of more than 50 species of arthropod-borne viruses, with distinct groups infecting mosquitoes or ticks. Mammals and birds are the usual primary hosts, in which infections range from asymptomatic to severe or fatal hemorrhagic fever or neurological disease. Important human pathogens include yellow fever virus, dengue virus, Japanese encephalitis virus, West Nile virus and tick-borne encephalitis virus. Other members cause economically important diseases in domestic or wild animals. Virions of Flavivirus have a single, small, basic capsid (C) protein and two envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. Translational initiation of genomic RNA is cap dependent in the case of members of the genus Flavivirus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 565 matched cddid_all.tbl CDD cd23205 cd23205 438055 Carmotetraviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Carmotetraviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, and related Erinaceus virus H14. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Carmotetraviridae, and related Erinaceus virus H14, order Tolivirales. Carmotetraviridae includes only one genus, Alphacarmotetravirus, which has one species: Providence virus. Lepidopteran insects serve as the natural host. Recent studies indicated that Providence virus, a non-enveloped insect RNA virus, isolated from a lepidopteran midgut cell line can establish a productive infection in plants as well as in animal cells. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 268 matched cddid_all.tbl CDD cd23206 cd23206 438056 Tombusviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tombusviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Tombusviridae, order Tolivirales. The family Tombusviridae comprises plant viruses, and is classified into 3 subfamilies (Calvusvirinae, Procedovirinae, and Regressovirinae), 17 genera, and 95 species. One genus is unassigned to a subfamily: Luteovirus. The name of the family is derived from Tomato bushy stunt virus (TBSV). Members of Tombusviridae replicate in the cytoplasm, by use of negative strand templates. The replication process leaves a surplus of positive- sense (+)RNA strands, and it is thought that not only does the viral RNA act as a template for replication, but is also able to manipulate and regulate RNA synthesis. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 231 matched cddid_all.tbl CDD cd23207 cd23207 438057 ps-ssRNA_RdRp_Tymovirales catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Tymovirales of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Tymovirales. The Tymovirales order contains viruses that mostly infect plants, have a single molecule of (+)ssRNA, and which are united by the similarities in their replication-associated polyproteins. Tymovirales contains five families (Alpha-, Beta-, Delta- and Gammaflexiviridae and Tymoviridae) and groups mostly plant-infecting agents, although a few Tymovirales members have either fungal or insect hosts. Botrytis virus F (BVF), isolated from the fungus Botrytis cinerea, is a flexuous mycovirus that is typical of members of the genus Mycoflexivirus (family Gammaflexiviridae). The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 188 matched cddid_all.tbl CDD cd23208 cd23208 438058 ps-ssRNAv_Martellivirales_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Martellivirales of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Martellivirales, class Alsuviricetes. The order Martellivirales consists of seven families: Bromoviridae, Closteroviridae, Endornaviridae, Kitaviridae, Mayoviridae, Togaviridae, and Virgaviridae. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 190 matched cddid_all.tbl CDD cd23209 cd23209 438059 ps-ssRNAv_Hepelivirales_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Hepelivirales, class Alsuviricetes. This Hepelivirales order consists of four families: Alphatetraviridae, Benyviridae, Hepeviridae, and Matonaviridae. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 183 matched cddid_all.tbl CDD cd23210 cd23210 438060 Aphthovirus_RdRp RNA-dependent RNA polymerase (RdRp) in the Aphthovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the RdRp of RNA viruses belonging to the Aphthovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. This genus includes species such as bovine rhinitis A virus, bovine rhinitis B virus, equine rhinitis A virus, and food-and-mouth disease virus (FMDV). Aphthoviruses primarily infect via the upper respiratory tract. FMDV infects mainly cloven-hoofed animals, but has been isolated from at least 70 species of mammals. Aphthoviruses are non-enveloped and have an icosahedral capsid with a diameter of around 27 to 30 nm. The assembled viral capsid contains a single copy of the RNA genome and 60 copies of the four viral capsid proteins VP1, VP2, VP3, and VP4. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 458 matched cddid_all.tbl CDD cd23211 cd23211 438061 Cardiovirus_RdRp RNA-dependent RNA polymerase (RdRp) in the Cardiovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the RdRp of RNA viruses belonging to the Cardiovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. Vertebrates serve as natural hosts for the cardioviruses. There are currently six species in the genus: Cardiovirus A-F. Diseases associated with cardioviruses include: myocarditis, encephalitis, multiple sclerosis, and type 1 diabetes. Cardiovirus A is composed of only one serotype, encephalomycarditis virus (EMCV) which causes encephalomyocarditis and reproductive disease in pigs. Cardiovirus B comprises 15 genetic types, Theiler's murine encephalomyelitis virus (TMEV), Vilyuisk human encephalomyelitis virus (VHEV), thera virus (formerly named Theiler-like virus of rats), Saffold virus (SAFV) types 1 to 11, and genet fecal theilovirus (from Geneta geneta). Of these types, only VHEV and SAFV are thought to cause infection in humans. Thus far, Cardiovirus C has only been observed in the brown rat. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 460 matched cddid_all.tbl CDD cd23212 cd23212 438062 Teschovirus_RdRp RNA-dependent RNA polymerase (RdRp) in the Teschovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the RdRp of RNA viruses belonging to the Teschovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. Teschoviruses are emerging pathogens and infect the porcine population only. There are two species in this genus, including Teschovirus A (previously Porcine teschovirus), which is responsible for the porcine enteroviral encephalomyelitis disease caused in pigs, and Teschovirus B. Teschovirus is also known by several other names including Teschen disease, Talfan disease, poliomyelitis suum, benign enzootic paresis, Klobauk disease and contagious porcine paralysis. Teschovirus has a single-stranded, linear, non-segmented RNA genome. The RNA genome is positively sensed meaning that it has the same polarity as the mRNA and no reverse transcription is necessary. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 354 matched cddid_all.tbl CDD cd23213 cd23213 438063 Enterovirus_RdRp RNA-dependent RNA polymerase (RdRp) in the Enterovirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the RdRp of RNA viruses belonging to the Enterovirus genus within the family Picornaviridae, order Picornavirales. Enteroviruses have small, non-enveloped (+)ssRNA genomes, and replicate within the gastrointestinal tract or other mucosal surfaces. The genus Enterovirus has been divided into 15 species based on genetic divergence (EV A-L and Rhinovirus A-C), and its major members include poliovirus, coxsackievirus and rhinovirus. More than 100 enterovirus types have been associated with several human diseases, all of which are classified into four species (Enterovirus A, Enterovirus B, Enterovirus C, and Enterovirus D). RdRps are multi-domain proteins that play a pivotal role in enterovirus replication. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of enteroviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 453 matched cddid_all.tbl CDD cd23214 cd23214 438064 Kobuvirus_RdRp "RNA-dependent RNA polymerase (RdRp) in the Kobuvirus genus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the RdRp of RNA viruses belonging to the Kobuvirus genus within the family Picornaviridae, order Picornavirales. Kobuviruses are small, icosahedral and spherical viruses, with a (+)ssRNA genome. Unlike other picornaviruses, Kobuvirus capsids show a distinctive lumpy morphology when observed by electron microscopy; ""kobu"" means ""knob"" in Japanese. There are six species (Aichivirus A-F) in this genus. Initially, the genus Kobuvirus was divided into three species: Aichivirus A (AiVA, formerly Aichi virus), Aichivirus B (AivB, formerly Bovine kobuvirus) and Aichivirus C (AiVC, formerly Porcine kobuvirus) each possessing a single serotype. Canine kobuvirus belong to species Aichivirus A. Aichi virus infects humans, while bovine kobuvirus, porcine kobuvirus and canine kobuvirus infects cattle, swine, dogs and cats, respectively. Kobuviruses have also been detected in black goats, rabbits, European roller, and bats. RdRps are multi-domain proteins that play a pivotal role in enterovirus replication. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of kobuviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides." 459 matched cddid_all.tbl CDD cd23215 cd23215 438065 Hepatovirus_RdRp RNA-dependent RNA polymerase (RdRp) in the genus Hepatovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the RdRp of RNA viruses belonging to the Hepatovirus genus within the family Picornaviridae, order Picornavirales. Hepatoviruses are 27- to 32-nm, nonenveloped, icosahedral viruses with a (+)ssRNA linear genome of approximately 7.5-kb. The Hepatovirus genus has nine species, Hepatovirus A-I, of which Hepatovirus A is responsible for a self-limiting viral hepatitis in human beings and may be transmitted by the fecal-oral route during acute infection or by the ingestion of uncooked contaminated shellfish. RdRps are multi-domain proteins that play a pivotal role in enterovirus replication. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of hepatoviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 464 matched cddid_all.tbl CDD cd23216 cd23216 438066 Aalivirus_RdRp "RNA-dependent RNA polymerase (RdRp) in the genus Aalivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the RdRp of RNA viruses belonging to the Aalivirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. Aalivirus is a new picornavirus found in ducks in China. It is most closely related to duck hepatitis A virus (genus Avihepatovirus) and to avisivirus A1 (genus Avisivirus). The name ""aalivirus"" is derived from Avihepatovirus/Avisivirus-like virus. RdRps are multi-domain proteins that play a pivotal role in enterovirus replication. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides." 337 matched cddid_all.tbl CDD cd23217 cd23217 438067 Parechovirus_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Parechovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the Parechovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. The Parechovirus genus is comprised of six species, Parechovirus A (formerly named Human parechovirus), Parechovirus B (formerly named Ljungan virus), Parechovirus C (Sebokele virus) and Parechovirus D (ferret parechovirus), Parechovirus E (falcon parechovirus) and Parechovirus F (gecko parechovirus). Humans, ferrets, and various rodents serve as natural hosts. Human parechoviruses may cause gastrointestinal or respiratory illness in infants, and have been implicated in cases of myocarditis and encephalitis. Human parechoviruses replicate in the respiratory and gastrointestinal tract. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 371 matched cddid_all.tbl CDD cd23218 cd23218 438068 Sapelovirus_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Sapelovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Sapelovirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. Viruses in Sapelovirus are non-enveloped, with icosahedral, spherical, and round geometries, and T=pseudo3 symmetry. Sapelovirus, formerly known as porcine enterovirus (PEV)-8, is known to infect pigs asymptomatically but can cause reproductive failure and severe neurologic, enteric, or respiratory signs. Sapelovirus infections have been reported worldwide in pigs. The genus Sapelovirus contains three species, with a unique genome organization: Sapelovirus A, also known as porcine sapelovirus (PSV); Sapelovirus B as simian sapelovirus; and Avian sapelovirus represented by duck picornavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 366 matched cddid_all.tbl CDD cd23219 cd23219 438069 Kunsagivirus_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Kunsagivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Kunsagivirus genus within the family Picornaviridae, order Picornavirales. The Kunsagivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Kunsagivirus is a new picornavirus genus containing a three species. Viral RNA of kunsagivirus A1 was detected in feces of an apparently healthy European roller (Coracias garrulus), of kunsagivirus B1 (bat kunsagivirus) in feces of the fruit bat Eidolon helvum, and of kunsagivirus C1 (bakunsavirus) in wild baboons (Papio cynocephalus). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 346 matched cddid_all.tbl CDD cd23220 cd23220 438070 Aquamavirus_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Aquamavirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Aquamavirus genus within the family Picornaviridae, order Picornavirales. The Aquamavirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Aquamavirus is a genus containing a single species, Aquamavirus A. This species consists of the previously named seal picornavirus 1, now to be called seal aquamavirus A1. Recently other aquamaviruses have been discovered in bears and seals (unassigned aquamaviruses). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 338 matched cddid_all.tbl CDD cd23221 cd23221 438071 Rosavirus_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Rosavirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Rosavirus genus within the family Picornaviridae, order Picornavirales. The Rosavirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus contains three species Rosavirus A, Rosavirus B and Rosavirus C found in rats. The name rosavirus is derived from rodent stool-associated picornavirus. Viral RNA was detected in fecal samples of humans and rodents [canyon mouse (Peromyscus crinitus), brown rat (Rattus norvegicus), black rat (R. rattus), Sikkim rat (R. andamanensis), chestnut white-bellied rat (Niviventer fulvescens)]. Eight genetic types are distinguished by means of phylogenetic analysis (Rosavirus A: 2 types; Rosavirus B: 2 types; Rosavirus C: 4 types). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 381 matched cddid_all.tbl CDD cd23222 cd23222 438072 Dicipivirus_RdRp RNA-dependent RNA polymerase (RdRp) in the genus Dicipivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the RdRp of RNA viruses belonging to the Dicipivirus genus within the family Picornaviridae, order Picornavirales. The Dicipivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. The genus Dicipivirus contains two species, Cadicivirus A and Cadicivirus B. A new dicipivirus has been found in hedgehogs. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 451 matched cddid_all.tbl CDD cd23223 cd23223 438073 Megrivirus_RdRp RNA-dependent RNA polymerase (RdRp) in the genus Megrivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the RdRp of RNA viruses belonging to the Megrivirus genus within the family Picornaviridae, order Picornavirales. The Megrivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. The genus Megrivirus contains a five species Megrivirus A, Megrivirus B, Megrivirus C, Megrivirus D and Megrivirus E. The name Megrivirus is derived from the turkey genus name Meleagris. Megrivirus A is comprised of turkey hepatitis virus 1 (THV-1), duck megrivirus and goose megrivirus 1. Megrivirus B contains the mesiviruses. Megrivirus D contains harrier picornavirus 1 (HaPV-1). Megrivirus E was found in an Adelie penguin. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 432 matched cddid_all.tbl CDD cd23224 cd23224 438074 Passerivirus_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Passerivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Passerivirus genus within the family Picornaviridae, order Picornavirales. The Passerivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. There are two species in this genus: Passerivirus A and a second, novel passerivirus (Passerivirus B) that was discovered in 2018 in a population of Hungarian home-reared finches, where it achieved an over 50 percent mortality rate. Birds serve as natural hosts. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 380 matched cddid_all.tbl CDD cd23225 cd23225 438075 Mosavirus_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Mosavirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Mosavirus genus within the family Picornaviridae, order Picornavirales. The Mosavirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus includes two species: Mosavirus A, which found in the feces of a canyon mouse (Peromyscus crinitus), and Mosavirus B, which contains marmot mosavirus. Mosavirus stands for mouse stool-associated picornavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 378 matched cddid_all.tbl CDD cd23226 cd23226 438076 Cosavirus_RdRp RNA-dependent RNA polymerase (RdRp) in the genus Cosavirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the RdRp of RNA viruses belonging to the Cosavirus genus within the family Picornaviridae, order Picornavirales. The Cosavirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus consists of five species Cosavirus A, Cosavirus B, Cosavirus D, Cosavirus E and Cosavirus F. The candidate species, Cosavirus C, remains unclassified due to a lack of full genome sequence data. Cosaviruses (formerly called Dekaviruses) have been identified in the stools of south Asian children. Cosaviruses are most closely related to members of the Cardiovirus and Senecavirus genera, but they lack a leader polypeptide. The name Cosavirus stands for common stool-associated picornavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 461 matched cddid_all.tbl CDD cd23227 cd23227 438077 Mischivirus_RdRp RNA-dependent RNA polymerase (RdRp) in the genus Mischivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the RdRp of RNA viruses belonging to the Mischivirus genus within the family Picornaviridae, order Picornavirales. The Mischivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Mischivirus is a picornavirus genus containing five species Mischivirus A, Mischivirus B, Mischivirus C, Mischivirus D and the proposed Mischivirus E. The name is derived from the name originally given to the virus, Miniopterus schreibersii picornavirus, which was found in the common bent-wing bat (aka Schreiber's long-fingered bat or Schreiber's bat) in China and is most closely related to the cardioviruses. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 466 matched cddid_all.tbl CDD cd23228 cd23228 438078 Limnipivirus_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Limnipivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Limnipivirus genus within the family Picornaviridae, order Picornavirales. The Limnipivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus contains three species, Limnipivirus A (bluegill picornavirus 1), Limnipivirus B (carp picornavirus 1) and Limnipivirus C (fathead minnow picornavirus 1). Limnipiviruses infect freshwater fishes. The virus can be grown in various fish cell lines. Experimental infection of bluegills with bluegill picornavirus induces morbidity (inflammation and redness at the base of fins, exophthalmia, abdomen distension, internal hemorrhaging and ascites) and mortality. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 390 matched cddid_all.tbl CDD cd23229 cd23229 438079 Fipivirus_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Fipivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Fipivirus genus within the family Picornaviridae, order Picornavirales. The Fipivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus contains five species: Fipivirus A (Wuhan sharpbelly picornavirus 2), Fipivirus B (Wuhan sharpbelly picornavirus 3), Fipivirus C (Wenling crossorhombus picornavirus), Fipivirus D (Wenling jack mackerels picornavirus) and Fipivirus E (Wenling banjofish picornavirus 1). All contain viruses from fish. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 394 matched cddid_all.tbl CDD cd23230 cd23230 438080 Rabovirus_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Rabovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Rabovirus genus within the family Picornaviridae, order Picornavirales. The Rabovirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. The genus Rabovirus consists of four species Rabovirus A, Rabovirus B, Rabovirus C, and Rabovirus D. Viral RNA of this genus was detected in feces of Norway rats (Rattus norvegicus) and mice (Mus musculus) in USA and Germany, in intestinal contents of Himalayan marmots (Marmota himalayana), and in tissue samples of Gairdner's shrewmice (Mus pahari). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 361 matched cddid_all.tbl CDD cd23231 cd23231 438081 Avisivirus_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Avisivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Avisivirus genus within the family Picornaviridae, order Picornavirales. The Avisivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Avisivirus is a picornavirus genus containing three species Avisivirus A, Avisivirus B and Avisivirus C. The name Avisivirus is derived from Avihepato sister-clade. Turkeys serve as natural hosts. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 362 matched cddid_all.tbl CDD cd23232 cd23232 438082 Crohivirus_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Crohivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae. This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Crohivirus genus within the family Picornaviridae, order Picornavirales. The Crohivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. Crohivirus is a new genus containing two species, Crohivirus A and Crohivirus B. Crohivirus A (Crohivirus 1, CroV-1) is a novel picornavirus found the lesser red musk shrew (Crocidura hirta) which is found in southern Africa. The genome sequence is most closely related to the parechoviruses. Crohivirus B consists of a virus which has been found in the straw-colored fruit bat (Eidolon helvum). RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 373 matched cddid_all.tbl CDD cd23233 cd23233 438083 Luteovirus_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Luteovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Luteovirus genus within the family Tombusviridae, order Tolivirales. There are 13 species in the Luteovirus genus: Apple associated luteovirus, Apple luteovirus 1, Barley yellow dwarf virus kerII, Barley yellow dwarf virus kerIII, Barley yellow dwarf virus MAV, Barley yellow dwarf virus PAS, Barley yellow dwarf virus PAV, Bean leafroll virus, Cherry associated luteovirus, Nectarine stem pitting associated virus, Red clover associated luteovirus, Rose spring dwarf-associated virus, and Soybean dwarf virus. Plants serve as natural hosts. The geographical distribution of Luteoviruses is widespread, with the virus primarily infecting plants via transmission by aphid vectors. The virus only replicates within the host cell and not within the vector. The name 'luteovirus' is derived from the Latin luteus (yellow) due to the symptomatic yellowing of the plant that occurs as a result of infection. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 407 matched cddid_all.tbl CDD cd23234 cd23234 438084 Calvusvirinae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Calvusvirinae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the subfamily Calvusvirinae, family Tombusviridae, order Tolivirales. Umbravirus is a genus of plant viruses assigned to this subfamily. The genus includes nine distinct virus species: Carrot mottle mimic virus (CMoMV), Groundnut rosette virus (GRV), Ethiopian tobacco bushy top virus (ETBTV), Lettuce speckles mottle virus (LSMV), Opium poppy mosaic virus (OPMV), Pea enation mosaic virus-2 (PEMV-2), Tobacco mottle virus (TMoV), and Tobacco bushy top virus (TBTV). Umbraviruses differ from other plant viruses in that they do not encode a coat protein (CP), and thus no conventional virus particles are formed in the infected plants. However, they encode RdRp domain typical to that of other members of the family Tombusviridae, allowing to classify the genus Umbravirus within this family. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 471 matched cddid_all.tbl CDD cd23235 cd23235 438085 Regressovirinae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the subfamily Regressovirinae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the subfamily Regressovirinae, family Tombusviridae, order Tolivirales. Dianthovirus is a genus of plant viruses within this subfamily. All the genera in the family Tombusviridae have monopartite (+)ssRNA genomes, except the dianthoviruses which have bipartite (+)ssRNA genomes. The dianthoviruses are distributed worldwide. The genus Dianthovirus is composed of three viruses: Carnation ringspot virus, Red clover necrotic mosaic virus, and Sweet clover necrotic mosaic virus. The amino acid (aa) sequence of dianthovirus RdRp has higher homology with that of the luteoviruses, while the amino acid sequence of dianthovirus coat protein (CP) has high homology with those of the tombusviruses and aureusviruses that belong to the subfamily Procedovirinae. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 472 matched cddid_all.tbl CDD cd23236 cd23236 438086 Tombusvirus-like_RdRp RNA-dependent RNA polymerase (RdRp) in the genus Tombusvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within Procedovirinae subfamily; and related RdRps. This group contains the RdRp of RNA viruses belonging to the Tombusvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Tombusvirus is a genus of plant viruses. There are 17 species in the Tombusvirus genus: Artichoke mottled crinkle virus, Carnation Italian ringspot virus, Cucumber Bulgarian virus, Cucumber necrosis virus, Cymbidium ringspot virus, Eggplant mottled crinkle virus, Grapevine Algerian latent virus, Havel River virus, Lato River virus, Limonium flower distortion virus, Moroccan pepper virus, Neckar River virus, Pelargonium leaf curl virus, Pelargonium necrotic spot virus, Petunia asteroid mosaic virus, Sikte waterborne virus, and Tomato bushy stunt virus. Symptoms associated with this genus include mosaic. The name of the genus comes from Tomato bushy stunt virus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 474 matched cddid_all.tbl CDD cd23237 cd23237 438087 Alphanecrovirus_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Alphanecrovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the Alphanecrovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Alphanecroviruses are non-enveloped, with icosahedral and spherical geometries, and T=3 symmetry, and a diameter of around 28 nm. Their genomes are linear, around 4 kb in length. In the Alphanecrovirus genus plants serve as natural hosts. There are 4 species in this genus: Olive latent virus 1, Olive mild mosaic virus, Potato necrosis virus, and Tobacco necrosis virus A. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 439 matched cddid_all.tbl CDD cd23238 cd23238 438088 Panicovirus_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Panicovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the Panicovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. Viruses in Panicovirus are non-enveloped, with icosahedral and spherical geometries, and T=3 symmetry. Their host range is restricted to monocotyledonous plants. There are 3 species in this genus: Cocksfoot mild mosaic virus, Panicum mosaic virus, and Thin paspalum asymptomatic virus. The virus typically forms a systemic mosaic. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 692 matched cddid_all.tbl CDD cd23239 cd23239 438089 Alphacarmovirus_RdRp RNA-dependent RNA polymerase (RdRp) in the genus Alphacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily. This group contains the RdRp of RNA viruses belonging to the Alphacarmovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The Alphacarmovirus genus was split in 2015 into three genera, each retaining -carmovirus as part of their name: Alphacarmovirus, Betacarmovirus, and Gammacarmovirus. Different carmoviruses infect a wide range of both monocotyledonous and dicotyledonous plants. Viruses tend to remain localized, forming necrosis in artificially infected hosts. There are 8 species in the genus Alphacarmovirus: Adonis mosaic virus, Angelonia flower break virus, Calibrachoa mottle virus, Carnation mottle virus, Honeysuckle ringspot virus, Nootka lupine vein clearing virus, Pelargonium flower break virus, and Saguaro cactus virus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 470 matched cddid_all.tbl CDD cd23240 cd23240 438090 Betacarmovirus_RdRp RNA-dependent RNA polymerase (RdRp) in the genus Betacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily. This group contains the RdRp of RNA viruses belonging to the Betacarmovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The single genus Carmovirus was split in 2015 into three genera, each retaining -carmovirus as part of their name: Alphacarmovirus, Betacarmovirus, and Gammacarmovirus. Different carmoviruses infect a wide range of both monocotyledonous and dicotyledonous plants. Viruses tend to remain localized, forming necrosis in artificially infected hosts. There are 4 species in the genus Betacarmovirus: Cardamine chlorotic fleck virus, Hibiscus chlorotic ringspot virus, Japanese iris necrotic ring virus, and Turnip crinkle virus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 451 matched cddid_all.tbl CDD cd23241 cd23241 438091 Pelarspovirus_RdRp "RNA-dependent RNA polymerase (RdRp) in the genus Pelarspovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily. This group contains the RdRp of RNA viruses belonging to the Pelarspovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The genus name ""Pelarspovirus"" is derived from the pelargonium ringspot virus, which was the first virus to be named. There are 8 species in the Pelarspovirus genus: Clematis chlorotic mottle virus, Elderberry latent virus, Jasmine mosaic-associated virus, Jasmine virus H, Pelargonium chlorotic ring pattern virus, Pelargonium line pattern virus, Pelargonium ringspot virus, and Rosa rugosa leaf distortion virus. Members of the Pelarspovirus have monopartite genomes encoding five open reading frames (ORFs) that include two 5'-proximal replication proteins, two centrally located movement proteins (MP1 and MP2) and a 3'-proximal coat protein that, at least for pelargonium line pattern virus (PLPV), has been shown to act also as suppressor of RNA silencing. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides." 497 matched cddid_all.tbl CDD cd23242 cd23242 438092 Gammacarmovirus_RdRp RNA-dependent RNA polymerase (RdRp) in the genus Gammacarmovirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily. This group contains the RdRp of RNA viruses belonging to the Gammacarmovirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. The single genus Carmovirus was split in 2015 into three genera, each retaining -carmovirus as part of their name: Alphacarmovirus, Betacarmovirus, and Gammacarmovirus. Most species have a narrow natural host range. However, different carmoviruses infect a wide range of both monocotyledonous and dicotyledonous plants. Viruses tend to remain localized, forming necrosis in artificially infected hosts. There are 4 species in the genus Gammacarmovirus: Cowpea mottle virus, Melon necrotic spot virus, Pea stem necrosis virus, and Soybean yellow mottle mosaic virus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 476 matched cddid_all.tbl CDD cd23243 cd23243 438093 Aureusvirus_RdRp RNA-dependent RNA polymerase (RdRp) in the genus Aureusvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily. This group contains the RdRp of RNA viruses belonging to the Aureusvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. In the Aureusvirus genus plants serve as natural hosts. There are six species in this genus: Cucumber leaf spot virus (CLSV), Elderberry aureusvirus 1, Johnsongrass chlorotic stripe mosaic virus (JCSMV), Maize white line mosaic virus (MWLMV), Pothos latent virus (PoLV), and Yam spherical virus (YSV). Aureusviruses infect various natural host plants but their individual range is generally restricted to a few species, pothos and pigeon pea or lisianthus for PoLV, yam for YSV, sesame for SNMV, cucumber, melon or squash for CLSV and various Poaceae species, mainly maize (MWLMV) or johnsongrass (JCSMV). Aureusviruses are transmitted mechanically and by seeds. Transmission through the soil or by the water circulating in hydroponic systems for PoLV, CLSV and MWLMV, or by the fungus Olpidium bornovanus (for CLSV) have also been reported. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 488 matched cddid_all.tbl CDD cd23244 cd23244 438094 Betanecrovirus_RdRp RNA-dependent RNA polymerase (RdRp) in the genus Betanecrosvirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the Procedovirinae subfamily. This group contains the RdRp of RNA viruses belonging to the Betanecrosvirus genus within the subfamily Procedovirinae, family Tombusviridae, order Tolivirales. In the Betanecrosvirus genus plants serve as natural hosts, and transmission routes are mechanical, seed borne, and by contact. There are three species in this genus: Beet black scorch virus, Leek white stripe virus, and Tobacco necrosis virus D. Viral replication is cytoplasmic. Entry into the host cell is achieved by penetration into the host cell. Replication follows the positive stranded RNA virus replication model. Positive stranded RNA virus transcription, using the premature termination model of subgenomic RNA transcription is the method of transcription. The virus exits the host cell by tubule-guided viral movement. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 500 matched cddid_all.tbl CDD cd23245 cd23245 438095 Betaflexiviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Betaflexiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Tymovirales. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Betaflexiviridae, order Tymovirales. Virions within the Betaflexiviridae family are flexuous filaments, usually 12#13 nm in diameter (range 10#15 nm) and from 600 to over 1000 nm in length, depending on the genus. They infect plants which share a distinct lineage of alphavirus-like replication proteins. There are 108 species in the family Betaflexiviridae, assigned to 13 genera in two subfamilies (Quinvirinae and Trivirinae). Diseases associated with this family include: mosaic and ringspot symptoms. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides.. 318 matched cddid_all.tbl CDD cd23246 cd23246 438096 Alphaflexiviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Alphaflexiviridae of positive-sense single-stranded RNA (+ssRNA) viruses, in the order Tymovirales. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Alphaflexiviridae, order Tymovirales. Virions within the Alphaflexiviridae family are flexuous filaments, that are 470#800 nm long and 12#13 nm in diameter. They infect plants and plant-infecting fungi. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 294 matched cddid_all.tbl CDD cd23247 cd23247 438097 Tymoviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Tymoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Tymovirales. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Tymoviridae, order Tymovirales. Virions of the family Tymoviridae are isometric, non-enveloped, about 30 nm in diameter, and contain a single molecule of (+)ssRNA constituting 25#35% of the particle weight. There are 42 species in this family, assigned to three genera (Maculavirus, Marafivirus, and Tymovirus), with two species unassigned to a genus. Members of the Tymovirales order are mainly plant pathogens that are characterized by similarities in their replication-associated polyproteins, which account for the majority of their genomic coding capacity. They are considered to form a group, phylogenetically, referred to as flexiviruses, with filamentous virions. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 373 matched cddid_all.tbl CDD cd23248 cd23248 438098 Deltaflexiviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Deltaflexiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Tymovirales. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Deltaflexiviridae, order Tymovirales. Deltaflexiviridae consists of one genus (Deltaflexivirus) and three species: Fusarium deltaflexivirus 1, Sclerotinia deltaflexivirus 1, and Soybean-associated deltaflexivirus 1. Members of the Tymovirales order are mainly plant pathogens that are characterized by similarities in their replication-associated polyproteins, which account for the majority of their genomic coding capacity. They are considered to form a group, phylogenetically, referred to as flexiviruses, with filamentous virions. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 279 matched cddid_all.tbl CDD cd23249 cd23249 438099 Gammaflexiviridae_RdRp RNA-dependent RNA polymerase (RdRp) in the family Gammaflexiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Tymovirales. This group contains the RdRp of RNA viruses belonging to the family Gammaflexiviridae, order Tymovirales. Virions within the Gammaflexiviridae family are flexuous filaments of 720 nm modal length and about 13 nm in diameter. Members of the Tymovirales order are mainly plant pathogens that are characterized by similarities in their replication-associated polyproteins, which account for the majority of their genomic coding capacity. They are considered to form a group, phylogenetically, referred to as flexiviruses, with filamentous virions. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 354 matched cddid_all.tbl CDD cd23250 cd23250 438100 Togaviridae_RdRp RNA-dependent RNA polymerase (RdRp) in the family Togaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the RdRp of RNA viruses belonging to the family Togaviridae, order Martellivirales. Togaviridae is a family of small, enveloped viruses with [(+)ssRNA] genomes of 10-12 kb, and contains a single genus, Alphavirus. Alphavirus includes a large number of species that are mostly mosquito-borne and pathogenic in their vertebrate hosts. Many are important human and veterinary pathogens (e.g., chikungunya virus, eastern equine encephalitis virus). The genus Alphavirus mainly consists of mosquito-borne viruses although other hematophagous insects, including ticks, lice, and cliff swallow bugs, have been implicated in transmission. Vertebrate hosts include humans, non-human primates, equids, birds, amphibians, reptiles, rodents, and pigs. There are two aquatic alphaviruses, southern elephant seal virus and salmon pancreas disease virus, infecting sea mammals and fish respectively. Interestingly, Eilat virus (EILV) has been shown to only infect insect cells and is incapable of replicating in vertebrate cells. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 458 matched cddid_all.tbl CDD cd23251 cd23251 438101 Virgaviridae_RdRp RNA-dependent RNA polymerase (RdRp) in the family Virgaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the RdRp of RNA viruses belonging to the family Virgaviridae, order Martellivirales. The Virgaviridae is a family of plant viruses with rod-shaped virions, a (+)ssRNA genome with a 3'-terminal tRNA-like structure and a replication protein similar to those of the alpha-like supergroup. Plants serve as natural hosts. The name of the family is derived from the Latin word virga (rod), as all viruses in this family are rod-shaped. There are currently 59 species in this family, divided among seven genera: Goravirus, Furovirus, Hordeivirus, Pecluvirus, Pomovirus, Tobamovirus, and Tobravirus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 427 matched cddid_all.tbl CDD cd23252 cd23252 438102 Bromoviridae_RdRp RNA-dependent RNA polymerase (RdRp) in the family Bromoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the RdRp of RNA viruses belonging to the family Bromoviridae, order Martellivirales. The Bromoviridae family of plant viruses contains tri-segmented, (+)ssRNA viruses with a total genome size of about 8 kb. There are six genera in this family: Alfamovirus, Anulavirus, Bromovirus, Cucumovirus, Ilarvirus, and Oleavirus. Bromoviridae virions are variable in morphology (spherical or bacilliform) and are transmitted mechanically, in/on the pollen and non-persistently by insect vectors. Members of the family cause major disease epidemics in fruit, vegetable and fodder crops such as tomato, cucurbits, bananas, and alfalfa. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 332 matched cddid_all.tbl CDD cd23253 cd23253 438103 Closteroviridae_RdRp RNA-dependent RNA polymerase (RdRp) in the family Closteroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the RdRp of RNA viruses belonging to the family Closteroviridae, order Martellivirales. Viruses in the family Closteroviridae have a mono-, bi- or tripartite (+)ssRNA genome of 13-19 kb, and non-enveloped, filamentous particles 650-2200 nm long and 12 nm in diameter. They infect plants, mainly dicots, many of which are fruit crops. Members of the family are classified into four genera: Ampelovirus, Closterovirus, Crinivirus and Velarivirus. Their genetic diversity is primarily influenced by strong negative selection and recombination. Closteroviridae viruses are mostly phloem-restricted and induce specific cytoplasmic aggregates of virus particles intermingled with membranous vesicles derived from the endoplasmic reticulum and possibly mitochondria. Their transmission is by aphids, whiteflies, pseudococcid mealybugs or soft scale insects in a semi-persistent manner. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 266 matched cddid_all.tbl CDD cd23254 cd23254 438104 Kitaviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Kitaviridae, order Martellivirales. The family Kitaviridae is composed of five recognized species among the three genera: Blueberry necrotic ring blotch virus and Tea plant necrotic ring blotch virus (genus Blunervirus); Citrus leprosis virus C and Citrus leprosis virus C2 (genus Cilevirus); and Hibiscus green spot virus 2 (genus Higrevirus). Although related, there are considerable physical and genetic distinctions between members of the different genera. For example, cile- and higreviruses are associated with a bacilliform virion, whereas a spherical virion has been observed for the lone blunervirus for which microscopy has been reported. Moreover, the replication-associated polyproteins are encoded by a single genomic RNA for cile- and higreviruses, but are split between two genomic RNAs for blunerviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 267 matched cddid_all.tbl CDD cd23255 cd23255 438105 Endornaviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Endornaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Endornaviridae, order Martellivirales. The family Endornaviridae includes viruses with linear (+)ssRNA genomes that range from 9.7 to 17.6 kb. The family consists of two genera, Alphaendornavirus and Betaendornavirus. Alphaendornavirus includes species whose members infect plants, fungi and oomycetes, while the genus Betaendornavirus includes species whose members infect ascomycete fungi. Plant endornaviruses are transmitted only through the gametes. A conserved RNA-dependent RNA polymerase domain located in the C-terminal region of the polyprotein is a feature common to all endornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 237 matched cddid_all.tbl CDD cd23256 cd23256 438106 Mayoviridae_RdRp RNA-dependent RNA polymerase (RdRp) in the family Mayoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the RdRp of RNA viruses belonging to the family Mayoviridae, order Martellivirales. The Mayoviridae family consists of two genera, Idaeovirus and Pteridovirus. The genus Idaeovirus contains Raspberry bushy dwarf virus (RBDV), named after the host with which it was first associated (red raspberry, Rubus idaeu) and the disease which is characterized by bushiness (stunting and proliferation of canes); RBDV has recently been found causing an infection in grapevines. RBDV occurs in all tissues of the plant, including seed and pollen, and is transmitted in association with pollen, both vertically to the seed and horizontally to the pollinated plant; this is the only known method of natural spread of RBDV. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 329 matched cddid_all.tbl CDD cd23257 cd23257 438107 Benyviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Benyviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Benyviridae, order Hepelivirales. The Benyviridae is a family of plant viruses with rod-shaped virions. Their genomes are multipartite (+)ssRNAs with 5' m7G-cap and 3' poly(A) and there is post-translational cleavage of the viral replicase. Beet necrotic yellow vein virus belongs to the genus Benyvirus and is the cause of 'rhizomania' disease of sugar beet. This widespread soil-borne disease can severely reduce sugar beet growth and beet sucrose production. BNYVV RNA1 contains one open reading frame (ORF) encoding a replicase protein that harbors motifs for methyltransferase, helicase, papain-like protease, and RdRp. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 188 matched cddid_all.tbl CDD cd23258 cd23258 438108 Alphatetraviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Alphatetraviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Alphatetraviridae, order Hepelivirales. The Alphatetraviridae is a family of (+)ssRNA viruses with nonenveloped icosahedral T=4 viral particles; they restrictively infect insects, particularly the Lepidoptera. The Alphatetraviridae family includes two genera representing viruses with a monopartite (Betatetravirus) and bipartite (Omegatetravirus) genome organization. Under a previous classification, this Alphatetraviridae family was included in a single group of tetraviruses along with two other families: Carmotetraviridae (single species) and Permutotetraviridae. Neither of these two families is now included in this Alphatetraviridae family: Carmotetraviridae is now classified into a different order, Tolivirales; Permutotetraviridae is a permuted RdRp and not included in this RdRp hierarchy. Alphatetravirus replicases include three conserved functional domains, namely methytransferase (MT), helicase (HEL) and RdRp domains, that are characteristic of all members of the alpha-like virus superfamily. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 184 matched cddid_all.tbl CDD cd23259 cd23259 438109 Hepeviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Hepeviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Hepeviridae, order Hepelivirales. The family Hepeviridae includes enterically transmitted small non-enveloped [(+)ssRNA viruses. It includes the genera Piscihepevirus, whose members infect fish, and Orthohepevirus, whose members infect mammals and birds. Members of the genus Orthohepevirus include hepatitis E virus, which is responsible for self-limiting acute hepatitis in humans and several mammalian species; the infection may become chronic in immunocompromised individuals. Avian hepatitis E virus causes hepatitis-splenomegaly syndrome in chickens. Hepeviridae genomes (approximately 7.2 kb) have 5' methyl G caps and 3' poly (A) tails, and contain three ORFS. They have two mRNAs, a genome length and a subgenomic mRNA: the genome-length mRNA is translated to produce proteins required for RNA replication while the subgenomic mRNA is used to produce the capsid protein. Some of the capsid protein is glycosylated, which is an unusual finding for an unenveloped virus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 274 matched cddid_all.tbl CDD cd23260 cd23260 438110 Matonaviridae_RdRp catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Matonaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses. This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Matonaviridae, order Hepelivirales. Members of the family Matonaviridae have a (+)ssRNA genome enclosed by an icosahedral capsid. Matonaviridae has a single genus, Rubivirus, which contains three species: Rubivirus rubella (commonly called rubella virus), Rubivirus ruteetense (commonly called ruhugu virus), and Rubivirus strelense (commonly called rustrela virus). Rubella virus (RuV) is the etiologic agent of the disease rubella (also called German measles). RuV is transmitted only between humans via the respiratory route, and is the main cause of congenital rubella syndrome (severe congenital birth defects, miscarriage, and stillbirth) when infection occurs during the first trimester of pregnancy. In vitro studies with cell lines showed that RuV has an apoptotic effect on certain cell types; there is evidence for a p53-dependent mechanism. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. 257 matched cddid_all.tbl CDD cd23261 cd23261 467871 mt-LAF29-like Trypanosoma brucei mitochondrial large subunit assembly factor 29 (mt-LAF29), and related proteins. mt-LAF29 is a Trypanosoma brucei mitochondrial large subunit (mt-LSU) assembly factor (mt-LAF) that plays a role in stabilizing partially mature 12S ribosomal RNA (rRNA) during the assembly process of the mt-LSU. Mitochondrial ribosomes (mitoribosomes) are ribonucleoprotein complexes and consist of a large subunit (mt-LSU) and a small subunit (mt-SSU). They differ markedly in composition and architecture from their bacterial counterparts and between different eukaryotic lineages, and their biogenesis involves exchange of assembly factors by ribosomal proteins. An investigation of native assembly intermediates of the mt-LSU from T. brucei has identified 28 assembly factors, some of which are homologous to bacterial and eukaryotic ribosome assembly factors. mt-LAF29 is part of a cluster of nine assembly factors identified as specific to an assembly intermediate referred to as state A, and which stabilized the 12S rRNA in an immature conformation. Mitochondrial biogenesis is biomedically important since mutations in mitoribosomal proteins, rRNAs and assembly factors have been linked to a heterogeneous group of human multisystemic oxidative phosphorylation (OXPHOS) diseases, and cancer development and progression. 309 matched cddid_all.tbl CDD cd23262 cd23262 467872 mt-LAF20-like mitochondrial large subunit assembly factor 20 (mt-LAF20), and related proteins. mt-LAF20 is a Trypanosoma brucei mitochondrial large subunit (mt-LSU) assembly factor (mt-LAF) that, during the assembly process of the mt-LSU with other assembly factors such as mt-LAF21, mt-LAF22, KRIPP3, mt-LAF27, and mt-LAF28, as well as GTPases mt-EngA, mt-EngB, and Mtg1, is involved in the rearrangement of the region H32-35 of rRNA. Mitochondrial ribosomes (mitoribosomes) are ribonucleoprotein complexes and consist of a large (mt-LSU) and small subunit (mt-SSU). They differ markedly in composition and architecture from their bacterial counterparts, and between different eukaryotic lineages, and their biogenesis involves exchange of assembly factors by ribosomal proteins. An investigation of native assembly intermediates of the mt-LSU from T. brucei identified 28 assembly factors, some of which are homologous to bacterial and eukaryotic ribosome assembly factors. Mitochondrial biogenesis is biomedically important since mutations in mitoribosomal proteins, rRNAs, and assembly factors have been linked to a heterogeneous group of human multisystemic oxidative phosphorylation (OXPHOS) diseases and cancer development and progression. 56 matched cddid_all.tbl CDD cd23263 cd23263 467746 beta-trefoil_MIR MIR domain, beta-trefoil fold, found in the MIR (protein mannosyltransferase, IP3R and RyR) superfamily. The MIR superfamily includes dolichyl-phosphate-mannose-protein mannosyltransferases (PMTs), inositol 1,4,5-trisphosphate receptors (ITPRs/IP3R), ryanodine receptors (RyRs), and stromal cell-derived factor 2 (SDF-2)-like proteins. They all contain a MIR domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The MIR domain may have a ligand transferase function. 172 matched cddid_all.tbl CDD cd23265 cd23265 467807 beta-trefoil_ABD_ABFB-like Arabinose-binding domain (ABD), beta-trefoil fold, found in the ABFB family. The ABFB family includes alpha-L-arabinofuranosidase B (ABF B)-like proteins and otogelin-like proteins. Alpha-L-arabinofuranosidase (EC 3.2.1.55), also called ABF, or non-reducing end alpha-L-arabinofuranosidase, or arabinofuranosidase, or arabinosidase, is involved in the degradation of arabinoxylan, a major component of plant hemicellulose. It can hydrolyze 1,5-, 1,3- and 1,2-alpha-linkages not only in L-arabinofuranosyl oligosaccharides, but also in polysaccharides containing terminal non-reducing L-arabinofuranoses in side chains, like L-arabinan, arabinogalactan and arabinoxylan. ABF belongs to the glycosyl hydrolase 54 family. Hungateiclostridium thermocellum anti-sigma-I factor RsgI5 shows high sequence similarity with ABF B. It negatively regulates SigI5 activity through direct interaction. The OTOG subfamily includes otogelin (OTOG) and otogelin-like protein (OTOGL). OTOG is a glycoprotein specific to acellular membranes of the inner ear. It may be required for the anchoring of otoconial membranes and cupula to the underlying neuroepithelia in the vestibule. OTOG may be involved in the organization and/or stabilization of the fibrillar network that compose the tectorial membrane in the cochlea. OTOGL is a mucin glycoprotein that is a component of the tectorial membrane. It acts as a gel-forming mucin that forms high-molecular-weight complexes and is glycosylated through mucin-type O-glycosylation. Mutations in OTOG or OTOGL genes may cause hearing loss. Members of the ABFB family contain an ABD with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ABD binds two arabinose molecules in the beta and gamma subdomains. 135 matched cddid_all.tbl CDD cd23267 cd23267 467766 Toxin_R_bind_C C-terminal receptor binding domain, beta-trefoil fold, found in Clostridium neurotoxin family. The Clostridium neurotoxin (CNT) family is composed of tetanus neurotoxins (TeNT) and seven well-established serotypes (A-G) of botulinum neurotoxin (BoNT), which cause the diseases tetanus and botulism respectively. A new toxin serotype, BoNT/X, was recently identified. BoNTs are the primary virulence factors and vaccine components against botulism. They have been exploited as cosmetics and muscle-disorder treatment medicines for decades, are well known for their extreme neurotoxicity to humans. At motor neurons, BoNTs cleave neuronal soluble N-ethylmaleimide-sensitive-factor attachment protein receptor (SNARE) proteins that inhibits synaptic vesicle (SV) exocytosis, resulting in flaccid paralysis, whereas TeNT is subjected to retrograde transport into inhibitory neurons and blocks release of glycine and gamma-aminobutyric acid, which results in spastic paralysis. Uptake of BoNT/A, B, E, F, and G requires a dual interaction with complex polysialylated gangliosides found on neural tissue and specific membrane-anchored proteins found in synaptic vesicles, such as synaptotagmin or SV2 (synaptic vesicle glycoprotein 2), whereas little is known about the cell entry mechanisms of the serotypes C and D. The family also includes Enterococcus botulinum-like toxin eBoNT/J and Paraclostridium bifermentans mosquitocidal protein 1 (PMP1). eBoNT/J might be a precursor of a toxin that binds to an unknown eukaryotic cell receptor(s) and be taken up into the host cell via the endocytic pathway. PMP1 is a clostridial-like neurotoxin that selectively targets anopheline mosquitoes. All family members comprise three domains which are involved in catalysis (LC), translocation (HCT), and host receptor binding (HCR). The HCR domain is responsible for the highly specific targeting of the neurotoxin to neuronal cell membranes. It is a proven target for anti-BoNT antibody and vaccine development. This model corresponds to C-terminal HCR domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 190 matched cddid_all.tbl CDD cd23270 cd23270 438014 YPP1 cargo-transport protein YPP1. This family includes YGR198w (named YPP1, also called alpha-synuclein protective protein 1), which is essential in Saccharomyces cerevisiae. It has also been shown to perform fundamental functions in human and mouse. YPP1 is a cargo-transport protein involved in endocytosis. It interacts with genes involved in protein sorting and secretion, and plays a role in the assembly and recruitment of multiple copies of the kinase into phosphoinositide kinase (PIK) patches at the plasma membrane. It has been found to suppress the toxicity of alpha-synuclein (alpha-syn) mutant (A30P) that is associated with early onset of Parkinson's disease (PD) in humans, but not wild-type or the A53T mutant (also associated with early onset PD). 740 matched cddid_all.tbl CDD cd23271 cd23271 467839 GH55-like glycoside hydrolase family 55 (GH55) family domains and similar proteins. This family includes glycoside hydrolase family 55 (GH55) domains, which contains both endo- (EC 3.2.1.39) and exo-beta-1,3-glucanases (EC 3.2.1.58), based on the hydrolysis position. These enzymes hydrolyze beta-1,3-glucan bonds via inversion of stereochemistry at the anomeric carbon. GH55 is also called laminarinase due to its ability to hydrolyze laminarin, a beta-1,3-glucan with occasional beta-1,6 branching, found in brown algae such as Laminaria digitata. They have also been shown to react with the beta-1,3-glucans from fungal and plant cell walls. Also included in this family is SacteLam55A from the highly cellulolytic Streptomyces sp. SirexAA-E, a secreted protein encoded by SACTE_4363. Structural studies reveal an extended substrate-binding cleft with six or more subsites for sugar binding formed at the interface of two right handed beta-helical domains. Mutation studies support a critical glutamate as a catalytic acid and a proton relay network that activates water to serve as the catalytic base. Trichoderma harzianum and T. viride LamA1 have been characterized as endo-acting enzymes while Phanerochaete chrysosporium Lam55A, Chaetomium thermophilum CtLam55, as well as SacteLam55A, are exo-acting enzymes. 564 matched cddid_all.tbl CDD cd23272 cd23272 437998 Dkk1_Cys2 second cysteine-rich (Cys-2) domain of Dickkopf-related protein 1. Dickkopf-1 (Dkk1) is a secreted protein which directly binds to LRP5/6 (low-density lipoprotein receptor related protein 5 and 6), and is an inhibitor of Wnt/beta-catenin signaling. Elevated expression of Dkk-1 may serve as a negative regulator for modulating the wnt/#-catenin signal pathway. Dkk1 is expressed in various human cancers. It has been studied extensively in mouse models of multiple myeloma that results in osteolytic bone lesions. Studies show that Dkk1 levels in bone marrow plasma and serum inhibit the differentiation of osteoblast precursors. Dkk1 belongs to the Dickkopf (Dkk) family that comprises a discrete class of secreted Wnt inhibitors. The Wnt gene family is a large class of secreted proteins that are expressed in a variety of tissues and organs, and are required for many developmental processes, including segmentation, endoderm development, limb polarity, neural crest differentiation, kidney morphogenesis, sex determination and brain development. Dkks 1-4 each possesses an N-terminal signal peptide and contains two conserved cysteine-rich domains (Cys-1 and Cys-2) separated by a linker region. Each domain possesses 10 conserved cysteine residues. The Cys-2 domain is closely similar to those in the colipase family; it has been suggested that the Cys-2 domain of Dkks may enable interaction with lipids in order to regulate Wnt function. This model corresponds to the Cys-2 domain of Dkk1. 83 matched cddid_all.tbl CDD cd23273 cd23273 437999 Dkk2_Cys2 second cysteine-rich (Cys-2) domain of Dickkopf-related protein 2. Dickkopf 2 (Dkk2) is a secreted protein which directly binds to LRP5/6 (low-density lipoprotein receptor related protein 5 and 6), and is an inhibitor of Wnt/beta-catenin signaling. Dkk2 expression is modulated by expression of micro RNA-221 (miRNA-221) in esophageal cancer, and inactivation of Dkk2 may increase Wnt activity with accelerating tumor progression. Dkk2 belongs to the Dickkopf (Dkk) family that comprises a discrete class of secreted Wnt inhibitors. The Wnt gene family is a large class of secreted proteins that are expressed in a variety of tissues and organs, and are required for many developmental processes, including segmentation, endoderm development, limb polarity, neural crest differentiation, kidney morphogenesis, sex determination and brain development. Dkks 1-4 each possesses an N-terminal signal peptide and contains two conserved cysteine-rich domains (Cys-1 and Cys-2) separated by a linker region. Each domain possesses 10 conserved cysteine residues. The Cys-2 domain is closely similar to those in the colipase family; it has been suggested that the Cys-2 domain of Dkks may enable interaction with lipids in order to regulate Wnt function. This model corresponds to the Cys-2 domain of Dkk2. 84 matched cddid_all.tbl CDD cd23274 cd23274 438000 Dkk3_Cys2 second cysteine-rich (Cys-2) domain of Dickkopf-related protein 3. Dickkopf 3 (Dkk3) is a secreted protein which, in contrast to Dkk1, Dkk2, and Dkk4, does not interact with LRP5/6 (low-density lipoprotein receptor related protein 5 and 6), and thus is a divergent family member that is not considered a true Wnt signaling antagonist. The role of Dkk proteins in cancer is considered mainly tumor suppressive since they are usually down-regulated in cancer cells. Dkk3 links heat shock factor 1 (HSF1) and YAP/TAZ signaling to control aggressive behaviors in cancer-associated fibroblasts; it does so via canonical Wnt signaling. It belongs to the Dickkopf (Dkk) family that comprises a discrete class of secreted Wnt inhibitors. The Wnt gene family is a large class of secreted proteins that are expressed in a variety of tissues and organs, and are required for many developmental processes, including segmentation, endoderm development, limb polarity, neural crest differentiation, kidney morphogenesis, sex determination and brain development. Dkks 1-4 each possesses an N-terminal signal peptide and contains two conserved cysteine-rich domains (Cys-1 and Cys-2) separated by a linker region. Each domain possesses 10 conserved cysteine residues. The Cys-2 domain is closely similar to those in the colipase family; it has been suggested that the Cys-2 domain of Dkks may enable interaction with lipids in order to regulate Wnt function. This model corresponds to the Cys-2 domain of Dkk3. 86 matched cddid_all.tbl CDD cd23275 cd23275 438001 Dkk4_Cys2 second cysteine-rich (Cys-2) domain of Dickkopf-related protein 4. Dickkopf 4 (Dkk4) is a secreted protein which directly binds to LRP5/6 (low-density lipoprotein receptor related protein 5 and 6), and is an inhibitor of Wnt/beta-catenin signaling. Dkk4, which is upregulated by the activated Wnt pathway, contributes to tumor malignancy in variable tumors, promoting tumor cell invasion and progression. Aberrant accumulation of Dkk4 has been shown to promote tumor progression by forming the immune suppressive microenvironment in gastrointestinal stromal tumor, and thus Dkk4 may be used as a tumor biomarker for prognosis prediction and recurrence monitoring. Dkk4 belongs to the Dickkopf (Dkk) family that comprises a discrete class of secreted Wnt inhibitors. The Wnt gene family is a large class of secreted proteins that are expressed in a variety of tissues and organs, and are required for many developmental processes, including segmentation, endoderm development, limb polarity, neural crest differentiation, kidney morphogenesis, sex determination and brain development. Dkks 1-4 each possesses an N-terminal signal peptide and contains two conserved cysteine-rich domains (Cys-1 and Cys-2) separated by a linker region. Each domain possesses 10 conserved cysteine residues. The Cys-2 domain is closely similar to those in the colipase family; it has been suggested that the Cys-2 domain of Dkks may enable interaction with lipids in order to regulate Wnt function. This model corresponds to the Cys-2 domain of Dkk4. 94 matched cddid_all.tbl CDD cd23276 cd23276 467747 beta-trefoil_MIR_PMT MIR domain, beta-trefoil fold, found in the family of dolichyl-phosphate-mannose-protein mannosyltransferase (PMT). The PMT (EC 2.4.1.109) family includes mammalian protein O-mannosyl-transferases (POMT1 and POMT2) and yeast PMT1-7. PMTs are responsible for O-linked glycosylation of proteins. They catalyze the transfer of mannose to seryl and threonyl residues of secretory proteins. Protein O-glycosylation is essential for cell wall rigidity and cell integrity. Members in this family contain a MIR (protein mannosyltransferase, IP3R and RyR) domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 185 matched cddid_all.tbl CDD cd23277 cd23277 467748 beta-trefoil_MIR_ITPR MIR domain, beta-trefoil fold, found in the family of inositol 1,4,5-trisphosphate receptor (ITPR). Inositol 1,4,5 trisphosphate receptors (ITPRs) are a family of endoplasmic reticulum Ca2+ channels essential for the control of intracellular Ca2+ levels in virtually every mammalian cell type. Calcium-mediated signaling through ITPRs is essential for the regulation of numerous physiological processes, including fertilization, muscle contraction, apoptosis, secretion, and synaptic plasticity. The ITPR family includes three isoforms (ITPR1, ITPR2 and ITPR3), which can control different cellular processes due to their unique biophysical properties, subcellular localization, and tissue distribution. ITPRs contain an N-terminal MIR (protein mannosyltransferase, IP3R and RyR) domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 204 matched cddid_all.tbl CDD cd23278 cd23278 467749 beta-trefoil_MIR_RyR MIR domain, beta-trefoil fold, found in the family of ryanodine receptor (RyR). RyRs (also called RYRs) are intracellular Ca(2+) release channels located on the sarco/endoplasmic reticulum (SR/ER). They release calcium Ca(2+) intracellular stores to activate critical functions including muscle contraction and neurotransmitter release. The family includes three closely homologous proteins, RyR1, RyR2 and RyR3. RyR1 is present in skeletal muscle; RyR2 is in heart muscle; and RyR3 is expressed at low levels in many tissues including brain, smooth muscle, and slow-twitch skeletal muscle. RYR2 is the major cellular mediator of calcium-induced calcium release (CICR) in animal cells. RyR1 and RyR2 release Ca2+ from the ER in response to excitation of muscle membranes to promote muscle contraction. RYR3 is involved in force production and calcium handling in extraocular muscle. RYRs contain an N-terminal MIR (protein mannosyltransferase, IP3R and RyR) domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 180 matched cddid_all.tbl CDD cd23279 cd23279 467750 beta-trefoil_MIR_SDF2-like MIR domain, beta-trefoil fold, found in family of stromal cell-derived factor 2 (SDF-2). The SDF-2 family includes mammalian SDF-2 and SDF2-like protein 1 (SDF2L1) as well as similar proteins from plant, such as Arabidopsis thaliana stromal cell-derived factor 2-like protein (AtSDF2). SDF-2 is a secretory protein involved in multiple endoplasmic reticulum (ER) functions, including the misfolded protein catabolic process, protein glycosylation, and ER protein quality control. SDF2L1, also called PWP1-interacting protein 8, is an endoplasmic reticulum (ER)-localized protein that plays a role in ER-associated degradation (ERAD) of misfolded proinsulin in pancreatic beta-cells. It is a component of the endoplasmic reticulum (ER) chaperone complex and interacts with alpha- and beta-defensins. SDF2L1 may also act as a tumor suppressor that play an important role in a variety of cancers, such as breast cancer and ovarian cancer. AtSDF2, also called SDF2-like protein, acts as crucial component of the unfolded protein response (UPR) in Arabidopsis thaliana. It is involved in the endoplasmic reticulum (ER) protein quality control and unfolded protein response. It may be involved in the quality control of glycoproteins. AtSDF2 forms a complex in the ER with ERDJ3B and MED37A/BIP1 which is required for the proper accumulation and function of the surface-exposed leucine-rich repeat receptor kinases EFR involved in pathogen-associated molecular pattern (PAMP) triggered immunity. Members in this family contain a MIR (protein mannosyltransferase, IP3R and RyR) domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 173 matched cddid_all.tbl CDD cd23280 cd23280 467751 beta-trefoil_MIR_itr-1-like MIR domain, beta-trefoil fold, found in Caenorhabditis elegans inositol 1,4,5-trisphosphate receptor Itr-1 and similar proteins. Itr-1, also called IP3 receptor, or IP3R, or InsP3R, or LET-23 fertility effector 1, is a receptor for inositol 1,4,5-trisphosphate, a second messenger that regulates intracellular calcium homeostasis. It binds in vitro to both inositol 1,4,5-trisphosphate (1,4,5-InsP3) and inositol 2,4,5-trisphosphate (2,4,5-InsP3) with high affinity. It can also bind inositol 1,3,4,5-tetrakisphosphate (1,3,4,5-InsP4) and inositol 4,5-bisphosphate (4,5-InsP2), but with lower affinity. Itr-1 acts as a timekeeper/rhythm generator via calcium signaling, affecting the defecation cycle and pharyngeal pumping. It affects normal hermaphrodite and male fertility as a participant in intracellular signaling by acting downstream of let-23/lin-3 which regulates ovulation, spermathecal valve dilation and male mating behavior. It plays an important role in early embryonic development. It controls epidermal cell migration and may also regulate filopodial protrusive activity during epithelial morphogenesis. Itr-1 functions as a component of inositol trisphosphate (IP3)-mediated downstream signaling pathways that controls amphid sensory neuronal (ASH)-mediated response to nose touch and benzaldehyde, but no other ASH-mediated responses. Itr-1 contains an N-terminal MIR (protein mannosyltransferase, IP3R and RyR) domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 199 matched cddid_all.tbl CDD cd23281 cd23281 467752 beta-trefoil_MIR_POMT1 MIR domain, beta-trefoil fold, found in protein O-mannosyl-transferase 1 (POMT1) and similar proteins. POMT1 (EC 2.4.1.109), also called dolichyl-phosphate-mannose--protein mannosyltransferase 1, belongs to the glycosyltransferase 39 family. It transfers mannosyl residues to the hydroxyl group of serine or threonine residues. Coexpression of both POMT1 and POMT2 is necessary for enzyme activity, expression of either POMT1 or POMT2 alone is insufficient. It is essentially dedicated to O-mannosylation of alpha-DAG1 and few other proteins, but not of cadherins and protocaherins. POMT1 contains a MIR (protein mannosyltransferase, IP3R and RyR) domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 191 matched cddid_all.tbl CDD cd23282 cd23282 467753 beta-trefoil_MIR_POMT2 MIR domain, beta-trefoil fold, found in protein O-mannosyl-transferase 2 (POMT2) and similar proteins. POMT2 (EC 2.4.1.109), also called dolichyl-phosphate-mannose--protein mannosyltransferase 2, is a novel member of the PMT protein O-mannosyltransferase family specifically localized to the acrosome of mammalian spermatids. POMT2 transfers mannosyl residues to the hydroxyl group of serine or threonine residues. Coexpression of both POMT1 and POMT2 is necessary for enzyme activity, expression of either POMT1 or POMT2 alone is insufficient. It is essentially dedicated to O-mannosylation of alpha-DAG1 and few other proteins but not of cadherins and protocaherins. POMT2 contains a MIR (protein mannosyltransferase, IP3R and RyR) domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 183 matched cddid_all.tbl CDD cd23283 cd23283 467754 beta-trefoil_MIR_PMT1-like MIR domain, beta-trefoil fold, found in Saccharomyces cerevisiae dolichyl-phosphate-mannose--protein mannosyltransferase 1 (PMT1) and similar proteins. Dolichyl-phosphate-mannose-protein mannosyltransferases (EC 2.4.1.109), also called PMTs, are responsible for O-linked glycosylation of proteins. They catalyze the transfer of mannose to seryl and threonyl residues of secretory proteins. Protein O-glycosylation is essential for cell wall rigidity and cell integrity. In Saccharomyces cerevisiae, a family of protein mannosyltransferases coded for by seven genes (PMT1-7). The family includes PMT1 and PMT5. PMT1 forms a heterodimeric complex with PMT2 and more rarely with PMT5. The PMT1-PMT2 complex participates in oxidative protein folding, ER-associated protein degradation (ERAD), as well as ER export. It is required for incorporation of proteins in the cell wall. PMT5 form a functional heterodimer with PMT3 and more rarely with PMT1. Members in this family contain a MIR (protein mannosyltransferase, IP3R and RyR) domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 190 matched cddid_all.tbl CDD cd23284 cd23284 467755 beta-trefoil_MIR_PMT2-like MIR domain, beta-trefoil fold, found in Saccharomyces cerevisiae dolichyl-phosphate-mannose--protein mannosyltransferase 2 (PMT2) and similar proteins. Dolichyl-phosphate-mannose-protein mannosyltransferases (EC 2.4.1.109), also called PMTs, are responsible for O-linked glycosylation of proteins. They catalyze the transfer of mannose to seryl and threonyl residues of secretory proteins. Protein O-glycosylation is essential for cell wall rigidity and cell integrity. In Saccharomyces cerevisiae, a family of protein mannosyltransferases coded for by seven genes (PMT1-7). The family includes PMT2, PMT3 and PMT6. PMT2 forms a heterodimeric complex with PMT1 and more rarely with PMT5. The PMT1-PMT2 complex participates in oxidative protein folding, ER-associated protein degradation (ERAD), as well as ER export. It is required for incorporation of proteins in the cell wall. PMT3 form a functional heterodimer with PMT5 and more rarely with PMT1. It may have redundant activity to PMT2. PMT6 may form a heterodimer with PMT4. Members in this family contain a MIR (protein mannosyltransferase, IP3R and RyR) domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 192 matched cddid_all.tbl CDD cd23285 cd23285 467756 beta-trefoil_MIR_PMT4-like MIR domain, beta-trefoil fold, found in Saccharomyces cerevisiae dolichyl-phosphate-mannose--protein mannosyltransferase 4 (PMT4) and similar proteins. Dolichyl-phosphate-mannose-protein mannosyltransferases (EC 2.4.1.109), also called PMTs, are responsible for O-linked glycosylation of proteins. They catalyze the transfer of mannose to seryl and threonyl residues of secretory proteins. Protein O-glycosylation is essential for cell wall rigidity and cell integrity. In Saccharomyces cerevisiae, a family of protein mannosyltransferases coded for by seven genes (PMT1-7). The family includes PMT4. It forms a functional homodimer and may form a heterodimer with PMT6. PMT4 specifically acts on secretory proteins with an ER-luminally oriented Ser/Thr-rich region flanked by a membrane anchor such as FUS1, AXL2, GAS1, KEX2, MID2, WSC1, WSC2, OPY2, PRM5, RAX2, or YNL176. Members in this family contain a MIR (protein mannosyltransferase, IP3R and RyR) domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 187 matched cddid_all.tbl CDD cd23286 cd23286 467757 beta-trefoil_MIR_PMT7-like MIR domain, beta-trefoil fold, found in Saccharomyces cerevisiae dolichyl-phosphate-mannose--protein mannosyltransferase 7 (PMT7) and similar proteins. Dolichyl-phosphate-mannose-protein mannosyltransferases (EC 2.4.1.109), also called PMTs, are responsible for O-linked glycosylation of proteins. They catalyze the transfer of mannose to seryl and threonyl residues of secretory proteins. Protein O-glycosylation is essential for cell wall rigidity and cell integrity. In Saccharomyces cerevisiae, a family of protein mannosyltransferases coded for by seven genes (PMT1-7). The family includes PMT7. Members in this family contain a MIR (protein mannosyltransferase, IP3R and RyR) domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 192 matched cddid_all.tbl CDD cd23287 cd23287 467758 beta-trefoil_MIR_ITPR1 MIR domain, beta-trefoil fold, found in inositol 1,4,5-trisphosphate receptor type 1 (ITPR1) and similar proteins. ITPR1, also called IP3 receptor isoform 1 (IP3R 1), or InsP3R1, or type 1 inositol 1,4,5-trisphosphate receptor, or type 1 InsP3 receptor, is an intracellular channel that mediates calcium release from the endoplasmic reticulum following stimulation by inositol 1,4,5-trisphosphate. It is involved in the regulation of epithelial secretion of electrolytes and fluid through the interaction with AHCYL1. It plays a role in endoplasmic reticulum (ER) stress-induced apoptosis. ITPR1 contains an N-terminal MIR (protein mannosyltransferase, IP3R and RyR) domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 222 matched cddid_all.tbl CDD cd23288 cd23288 467759 beta-trefoil_MIR_ITPR2 MIR domain, beta-trefoil fold, found in inositol 1,4,5-trisphosphate receptor type 2 (ITPR2) and similar proteins. ITPR2, also called IP3 receptor isoform 2 (IP3R 2), or InsP3R2, or type 2 inositol 1,4,5-trisphosphate receptor, or type 2 InsP3 receptor, is a key regulator for the activity of calcium ion transmembrane transportation, which plays a critical role in cell cycle and proliferation. It is a receptor for inositol 1,4,5-trisphosphate, a second messenger that mediates the release of intracellular calcium. This release is regulated by cAMP both dependently and independently of cAMP-dependent protein kinase (PKA). ITPR2 contains an N-terminal MIR (protein mannosyltransferase, IP3R and RyR) domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 222 matched cddid_all.tbl CDD cd23289 cd23289 467760 beta-trefoil_MIR_ITPR3 MIR domain, beta-trefoil fold, found in inositol 1,4,5-trisphosphate receptor type 3 (ITPR3) and similar proteins. ITPR3, also called IP3 receptor isoform 3 (IP3R 3), or InsP3R3, or type 3 inositol 1,4,5-trisphosphate receptor, or type 3 InsP3 receptor, acts as anti-oncogenic channel by propelling pro-apoptotic Ca2+ signals to mitochondria. It is the principal intracellular Ca2+ release channel in cholangiocytes and plays a particularly important role in cancer. ITPR3 contains an N-terminal MIR (protein mannosyltransferase, IP3R and RyR) domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 215 matched cddid_all.tbl CDD cd23290 cd23290 467761 beta-trefoil_MIR_RyR1 MIR domain, beta-trefoil fold, found in ryanodine receptor 1 (RyR1) and similar proteins. RyR1, also called RYR-1, or skeletal muscle calcium release channel, or skeletal muscle ryanodine receptor, or skeletal muscle-type ryanodine receptor, or type 1 ryanodine receptor, is a calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm and thereby plays a key role in triggering muscle contraction following depolarization of T-tubules. It can also mediate the release of Ca(2+) from intracellular stores in neurons, and may thereby promote prolonged Ca(2+) signaling in the brain. It is required for normal embryonic development of muscle fibers and skeletal muscle, as well as for normal heart morphogenesis, skin development and ossification during embryogenesis. RYR-1 forms homotetramer and can also form heterotetramers with RYR-2. RYR-1 contains an N-terminal MIR (protein mannosyltransferase, IP3R and RyR) domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 192 matched cddid_all.tbl CDD cd23291 cd23291 467762 beta-trefoil_MIR_RyR2 MIR domain, beta-trefoil fold, found in ryanodine receptor 2 (RyR2) and similar proteins. RyR2, also called RYR-2, or cardiac muscle ryanodine receptor-calcium release channel, or cardiac muscle ryanodine receptor, or type 2 ryanodine receptor, is a calcium channel that mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm and thereby plays a key role in triggering cardiac muscle contraction. Aberrant channel activation can lead to cardiac arrhythmia. In cardiac myocytes, calcium release is triggered by increased Ca(2+) levels due to activation of the L-type calcium channel CACNA1C. The calcium channel activity of RYR-2 is modulated by formation of heterotetramers with RYR-3. RYR-2 is required for cellular calcium ion homeostasis. it plays an essential role in embryonic heart development. RYR-2 forms homotetramer and also forms heterotetramers with RYR-1 and RYR-3. RYR-2 contains an N-terminal MIR (protein mannosyltransferase, IP3R and RyR) domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 184 matched cddid_all.tbl CDD cd23292 cd23292 467763 beta-trefoil_MIR_RyR3 MIR domain, beta-trefoil fold, found in ryanodine receptor 3 (RyR3) and similar proteins. RyR3, also called RYR-3, or brain ryanodine receptor-calcium release channel, or brain-type ryanodine receptor, or type 3 ryanodine receptor, is a calcium channel that plays a role in cellular calcium signaling. It mediates the release of Ca(2+) from the sarcoplasmic reticulum into the cytoplasm in muscle and thereby plays a role in triggering muscle contraction. It also mediates Ca(2+)-induced Ca(2+) release from the endoplasmic reticulum in non-muscle cells. RYR-3 forms homotetramer and also forms heterotetramer with RYR-2. RYR-3 contains an N-terminal MIR (protein mannosyltransferase, IP3R and RyR) domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 187 matched cddid_all.tbl CDD cd23293 cd23293 467764 beta-trefoil_MIR_SDF2_meta MIR domain, beta-trefoil fold, found in family of metazoan stromal cell-derived factor 2 (SDF-2). The metazoan SDF-2 family includes SDF-2 and SDF2-like protein 1 (SDF2L1). SDF-2 is a secretory protein involved in multiple endoplasmic reticulum (ER) functions, including the misfolded protein catabolic process, protein glycosylation, and ER protein quality control. SDF2L1, also called PWP1-interacting protein 8, is an endoplasmic reticulum (ER)-localized protein that plays a role in ER-associated degradation (ERAD) of misfolded proinsulin in pancreatic beta-cells. It is a component of the endoplasmic reticulum (ER) chaperone complex and interacts with alpha- and beta-defensins. SDF2L1 may also act as a tumor suppressor that play an important role in a variety of cancers, such as breast cancer and ovarian cancer. Members in this family contain a MIR (protein mannosyltransferase, IP3R and RyR) domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 175 matched cddid_all.tbl CDD cd23294 cd23294 467765 beta-trefoil_MIR_AtSDF2-like MIR domain, beta-trefoil fold, found in Arabidopsis thaliana stromal cell-derived factor 2-like protein (AtSDF2) and similar proteins. AtSDF2, also called SDF2-like protein, acts as a crucial component of the unfolded protein response (UPR) in Arabidopsis thaliana. It is involved in the endoplasmic reticulum (ER) protein quality control and unfolded protein response. It may be involved in the quality control of glycoproteins. AtSDF2 forms a complex in the ER with ERDJ3B and MED37A/BIP1 which is required for the proper accumulation and function of the surface-exposed leucine-rich repeat receptor kinases EFR involved in pathogen-associated molecular pattern (PAMP) triggered immunity. AtSDF2 contains a MIR (protein mannosyltransferase, IP3R and RyR) domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 176 matched cddid_all.tbl CDD cd23295 cd23295 466777 beta-trefoil_IL1A beta-trefoil domain found in interleukin-1 alpha (IL-1 alpha) and similar proteins. IL-1 alpha, also called hematopoietin-1, is a potent inflammatory cytokine that activates the inflammatory process. It is produced by activated macrophages. IL-1 stimulates thymocyte proliferation by inducing IL-2 release, B-cell maturation and proliferation, and fibroblast growth factor activity. IL-1 proteins are involved in the inflammatory response, being identified as endogenous pyrogens, and are reported to stimulate the release of prostaglandin and collagenase from synovial cells. IL-1 alpha contains a C-terminal beta-trefoil domain, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 145 matched cddid_all.tbl CDD cd23296 cd23296 466778 beta-trefoil_IL1B beta-trefoil domain found in interleukin-1 beta (IL-1 beta) and similar proteins. IL-1 beta, also called catabolin, is a potent inflammatory cytokine that activates the inflammatory process. It was initially discovered as the major endogenous pyrogen. It induces prostaglandin synthesis, neutrophil influx and activation, T-cell activation and cytokine production, B-cell activation and antibody production, and fibroblast proliferation and collagen production. IL-1 beta promotes Th17 differentiation of T-cells and synergizes with IL12/interleukin-12 to induce IFN-gamma synthesis from T-helper 1 (Th1) cells. It plays a role in angiogenesis by inducing vascular endothelial growth factor (VEGF) production synergistically with tumor necrosis factor (TNF) and IL-6. IL-1 beta contains a C-terminal beta-trefoil domain, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 150 matched cddid_all.tbl CDD cd23297 cd23297 466779 beta-trefoil_IL1RA beta-trefoil domain found in interleukin-1 receptor antagonist protein (IL-1RA) and similar proteins. IL-1RA, also called IL-1RN, or IRAP, or ICIL-1RA, or IL1 inhibitor, inhibits the activity of interleukin-1 (IL-1) by binding to receptor IL1R1 and preventing its association with the co-receptor IL1RAP for signaling. It has no IL-1 like activity. IL-1RN binds functional interleukin-1 receptor IL1R1 with greater affinity than decoy receptor IL1R2; however, the physiological relevance of the latter association is unknown. IL-1RN contains a beta-trefoil domain, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 149 matched cddid_all.tbl CDD cd23298 cd23298 466780 beta-trefoil_IL18 beta-trefoil domain found in interleukin-18 (IL-18) and similar proteins. IL-18, also called Iboctadekin, or interferon gamma-inducing factor, or IFN-gamma-inducing factor, or interleukin-1 gamma, or IL-1 gamma, is a proinflammatory cytokine primarily involved in polarized T-helper 1 (Th1) cell and natural killer (NK) cell immune responses. Upon binding to IL18R1 and IL18RAP, it forms a signaling ternary complex which activates NF-kappa-B, triggering synthesis of inflammatory mediators. IL-18 works synergistically with IL12/interleukin-12 to induce IFN-gamma synthesis from Th1 cells and natural killer (NK) cells. IL-18 contains a beta-trefoil domain, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 149 matched cddid_all.tbl CDD cd23299 cd23299 466781 beta-trefoil_IL33 beta-trefoil domain found in interleukin-33 (IL-33) and similar proteins. IL-33, also called interleukin-1 family member 11, or IL-1F11, or nuclear factor from high endothelial venules (NF-HEV), acts as cytokine that binds to and signals through the IL1RL1/ST2 receptor which in turn activates NF-kappa-B and MAPK signaling pathways in target cells. It is involved in the maturation of Th2 cells inducing the secretion of T-helper type 2-associated cytokines. It is also involved in activation of mast cells, basophils, eosinophils, and natural killer cells. It acts as a chemoattractant for Th2 cells, and may function as an 'alarmin', that amplifies immune responses during tissue injury. IL-33 contains a beta-trefoil domain, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 153 matched cddid_all.tbl CDD cd23300 cd23300 466782 beta-trefoil_IL36 beta-trefoil domain found in the family of interleukin-36 (IL-36) and similar proteins. The IL-36 family includes three members, IL-36 alpha (also called FIL1 epsilon, or interleukin-1 epsilon, or IL-1 epsilon, or interleukin-1 family member 6, or IL-1F6), IL-36 beta (also called FIL1 eta, or interleukin-1 eta, or IL-1 eta, or interleukin-1 family member 8, or IL-1F8, or interleukin-1 homolog 2, or IL-1H2), and IL-36 gamma (also called IL-1-related protein 2, or IL-1RP2, or interleukin-1 epsilon, or IL-1 epsilon, or interleukin-1 family member 9, or IL-1F9, or interleukin-1 homolog 1, or IL-1H1). They act as cytokines that bind to and signals through the IL1RL2/IL-36R receptor which in turn activates NF-kappa-B and MAPK signaling pathways in target cells linked to a pro-inflammatory response. They are parts of the IL-36 signaling system that is thought to be present in epithelial barriers and to take part in local inflammatory response; like the IL-1 system with which they share the co-receptor IL1RAP. They may be involved in skin inflammatory response by acting on keratinocytes, dendritic cells, and indirectly on T-cells to drive tissue infiltration, cell maturation and cell proliferation. Members in this family contain a beta-trefoil domain, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 148 matched cddid_all.tbl CDD cd23301 cd23301 466783 beta-trefoil_IL37 beta-trefoil domain found in interleukin-37 (IL-37) and similar proteins. IL-37, also called FIL1 zeta, or IL-1X, or interleukin-1 family member 7, or IL-1F7, or interleukin-1 homolog 4, or IL-1H, or IL-1H4, or interleukin-1 zeta, or IL-1 zeta, or interleukin-1-related protein, or IL-1RP1, or interleukin-23, or IL-23, acts as a suppressor of innate inflammatory and immune responses involved in curbing excessive inflammation. This function requires SMAD3. It suppresses, or reduces, proinflammatory cytokine production, including IL1A and IL6, as well as CCL12, CSF1, CSF2, CXCL13, IL1B, IL23A, and IL1RN, but spares anti-inflammatory cytokines and inhibits dendritic cell activation. IL-37 contains a beta-trefoil domain, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 151 matched cddid_all.tbl CDD cd23302 cd23302 466784 beta-trefoil_IL38 beta-trefoil domain found in interleukin-38 (IL-38) and similar proteins. IL-38, also called interleukin-1 family member 10, or IL-1F10, or family of interleukin 1-theta, or FIL1 theta, or interleukin-1 HY2, or IL-1HY2, or interleukin-1 theta, or IL-1 theta, acts as cytokine with immunomodulatory activity. Alone, it does not induce cytokine production, but reduces IL22 and IL17A production by T-cells in response to heat-killed Candida albicans. It also reduces IL36G-induced production of IL8 by peripheral blood mononuclear cells. It increases IL6 production by dendritic cells stimulated by bacterial lipopolysaccharides (LPS). IL-38 contains a beta-trefoil domain, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 149 matched cddid_all.tbl CDD cd23303 cd23303 466785 beta-trefoil_IL36RA beta-trefoil domain found in interleukin-36 receptor antagonist protein (IL-36RA) and similar proteins. IL-36RA, also called FIL1 delta, or IL-1-related protein 3, or IL-1RP3, or interleukin-1 HY1, or IL-1HY1, or interleukin-1 delta, or IL-1 delta, or interleukin-1 family member 5, or IL-1F5, or interleukin-1 receptor antagonist homolog 1, or IL-1ra homolog 1, or interleukin-1-like protein 1, or IL-1L1, inhibits the activity of interleukin-36 (IL36 alpha,IL36 beta and IL36 gamma) by binding to receptor IL1RL2 and preventing its association with the coreceptor IL1RAP for signaling. It is part of the IL-36 signaling system that is thought to be present in epithelial barriers and to take part in local inflammatory response; like the IL-1 system with which it shares the coreceptor. It may play a role in skin inflammation, as well as in the innate immune response to fungal pathogens, such as Aspergillus fumigatus. It may activate an anti-inflammatory signaling pathway by recruiting SIGIRR. IL-36RA contains a beta-trefoil domain, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 146 matched cddid_all.tbl CDD cd23304 cd23304 466990 beta-trefoil_FGF1-like FGF domain, beta-trefoil fold, found in the fibroblast growth factor 1 (FGF1)-like family. The FGF1-like family includes FGF1 and FGF2. FGF1, also called acidic fibroblast growth factor (aFGF), or endothelial cell growth factor (ECGF), or heparin-binding growth factor 1 (HBGF-1), plays an important role in the regulation of cell survival, cell division, angiogenesis, cell differentiation, and cell migration. It functions as a potent mitogen in vitro. FGF1 acts as a ligand for fibroblast growth factor receptor 1 (FGFR1) and integrin. It interacts with FGFR1, FGFR2, FGFR3, and FGFR4. Affinity between fibroblast growth factors (FGFs) and their receptors is increased by heparan sulfate glycosaminoglycans that function as coreceptors. FGF1 also interacts with fibroblast growth factor-binding protein 1 (FGFBP1), FGF1, and FGF2. FGF2, also called basic fibroblast growth factor (bFGF), or heparin-binding growth factor 2 (HBGF2), acts as a ligand for FGFR1, FGFR2, FGFR3, and FGFR4. It also acts as an integrin ligand which is required for FGF2 signaling. FGF2 plays an important role in the regulation of cell survival, cell division, cell differentiation and cell migration. Both FGF1 and FGF2 contain a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 127 matched cddid_all.tbl CDD cd23305 cd23305 466991 beta-trefoil_FGF3-like FGF domain, beta-trefoil fold, found in the fibroblast growth factor 3 (FGF3)-like family. The FGF3-like family includes FGF3-6. FGF3, also called heparin-binding growth factor 3 (HBGF3), or proto-oncogene Int-2, plays an important role in the regulation of embryonic development, cell proliferation, and cell differentiation. It is required for normal ear development. FGF3 interacts with fibroblast growth factor receptors, FGFR1 and FGFR2. FGF4, also called heparin secretory-transforming protein 1 (HST-1), or HSTF-1, or heparin-binding growth factor 4 (HBGF4), or transforming protein KS3, plays an important role in the regulation of embryonic development, cell proliferation, and cell differentiation. It is required for normal limb and cardiac valve development during embryogenesis. It interacts with FGFR1, FGFR2, FGFR3, and FGFR4. FGF5, also called heparin-binding growth factor 5 (HBGF5), or Smag-82, plays an important role in the regulation of cell proliferation and cell differentiation. It is required for normal regulation of the hair growth cycle. It functions as an inhibitor of hair elongation by promoting progression from anagen, the growth phase of the hair follicle, into catagen the apoptosis-induced regression phase. FGF5 interacts with FGFR1 and FGFR2. FGF6, also called heparin secretory-transforming protein 2 (HST-2), or HSTF-2, or heparin-binding growth factor 6 (HBGF6), plays an important role in the regulation of cell proliferation, cell differentiation, angiogenesis and myogenesis, and is required for normal muscle regeneration. FGF6 interacts with FGFR1, FGFR2, and FGFR4. Affinity between FGFs and their receptors is increased by heparan sulfate glycosaminoglycans that function as coreceptors. Members in this family contain a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 127 matched cddid_all.tbl CDD cd23306 cd23306 466992 beta-trefoil_FGF7-like FGF domain, beta-trefoil fold, found in the fibroblast growth factor 7 (FGF7)-like family. The FGF7-like family includes FGF7, FGF10 and FGF22. FGF7, also called heparin-binding growth factor 7 (HBGF7), or keratinocyte growth factor (KGF), and FGF10 play important roles in the regulation of embryonic development, cell proliferation, and cell differentiation. They are required for normal branching morphogenesis. FGF7 is a growth factor active on keratinocytes. It may act as major paracrine effector of normal epithelial cell proliferation. FGF10 may play a role in wound healing. FGF22 plays a role in the fasting response, glucose homeostasis, lipolysis, and lipogenesis. It can stimulate cell proliferation (in vitro). It may be involved in hair development. FGF7 interacts with fibroblast growth factor receptor FGFR2 and fibroblast growth factor-binding protein 1 (FGFBP1). FGF10 and FGF22 interact with FGFR1, FGFR2 and FGFBP1. Members in this family contain a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 131 matched cddid_all.tbl CDD cd23307 cd23307 466993 beta-trefoil_FGF8-like FGF domain, beta-trefoil fold, found in the fibroblast growth factor 8 (FGF8)-like family. The FGF8-like family includes FGF8, FGF17 and FGF18. FGF8, also called androgen-induced growth factor (AIGF), or heparin-binding growth factor 8 (HBGF8), plays an important role in the regulation of embryonic development, cell proliferation, cell differentiation, and cell migration. It is required for normal brain, eye, ear,, and limb development during embryogenesis. It is also required for normal development of the gonadotropin-releasing hormone (GnRH) neuronal system. It plays a role in neurite outgrowth in hippocampal cells. FGF8 interacts with fibroblast growth factor receptors, FGFR1, FGFR2, FGFR3, and FGFR4. FGF17 plays an important role in the regulation of embryonic development and as signaling molecule in the induction and patterning of the embryonic brain. It is required for normal brain development. FGF17 interacts with FGFR3 and FGFR4. FGF18, also called zFGF5, plays an important role in the regulation of cell proliferation, cell differentiation, and cell migration. It is required for normal ossification and bone development. It stimulates hepatic and intestinal proliferation. FGF18 interacts FGFR3 and FGFR4. Members in this family contain a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 127 matched cddid_all.tbl CDD cd23308 cd23308 466994 beta-trefoil_FGF9-like FGF domain, beta-trefoil fold, found in the fibroblast growth factor 9 (FGF9)-like family. The FGF9-like family includes FGF9, FGF16, and FGF20. FGF9, also called glia-activating factor (GAF), or heparin-binding growth factor 9 (HBGF-9), plays an important role in the regulation of embryonic development, cell proliferation, cell differentiation, and cell migration. It acts as a heparin-binding glia-activating factor that may have a role in glial cell growth and differentiation during development, gliosis during repair and regeneration of brain tissue after damage, differentiation and survival of neuronal cells, and growth stimulation of glial tumors. FGF9 interacts with fibroblast growth factor receptors, FGFR1, FGFR2, FGFR3, and FGFR4. FGF16 plays an important role in the regulation of embryonic development, cell proliferation and cell differentiation. It is required for normal cardiomyocyte proliferation and heart development. FGF16 interacts with FGFR1 and FGFR2. FGF20 acts as a neurotrophic factor that regulates central nervous development and function. It interacts with FGFR2 and FGFR4. Affinity between fibroblast growth factors (FGFs) and their receptors is increased by heparan sulfate glycosaminoglycans that function as coreceptors. Members in this family contain a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 130 matched cddid_all.tbl CDD cd23309 cd23309 466995 beta-trefoil_FGF11-like FGF domain, beta-trefoil fold, found in the fibroblast growth factor 11 (FGF11)-like family. The FGF11-like family includes FGF11-14. FGF11, also called fibroblast growth factor homologous factor 3 (FHF3), may be involved in nervous system development and function. It plays roles in angiogenesis, tumorigenesis, adipogenesis, or liver regeneration. FGF12, also called fibroblast growth factor homologous factor 1 (FHF1), or myocyte-activating factor, is involved in nervous system development and function. It plays a role in the positive regulation of voltage-gated sodium channel activity. It promotes neuronal excitability by elevating the voltage dependence of neuronal sodium channel SCN8A fast inactivation. FGF12 interacts with the C-terminal region of SCN9A. FGF13, also called Fibroblast growth factor homologous factor 2 (FHF2), is a microtubule-binding protein which directly binds tubulin and is involved in both polymerization and stabilization of microtubules. Through its action on microtubules, it may participate in the refinement of axons by negatively regulating axonal and leading processes branching. FGF13 plays a crucial role in neuron polarization and migration in the cerebral cortex and the hippocampus. It may regulate voltage-gated sodium channels transport and function. It may also play a role in MAPK signaling. It is required for the development of axonal initial segment-targeting inhibitory GABAergic synapses made by chandelier neurons. FGF13 interacts with SCN1A, SCN5A, and SCN8A. It may also interact with SCN2A and SCN11A. FGF14, also called fibroblast growth factor homologous factor 4 (FH-4), may be involved in nervous system development and function. It interacts with SCN8A. Members in this family contain a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 130 matched cddid_all.tbl CDD cd23310 cd23310 466996 beta-trefoil_FGF19-like FGF domain, beta-trefoil fold, found in the fibroblast growth factor 19 (FGF19)-like family. The FGF19-like family includes FGF19, FGF21, and FGF23. FGF19 is involved in the suppression of bile acid biosynthesis through down-regulation of CYP7A1 expression, following positive regulation of the JNK and ERK1/2 cascades. It stimulates glucose uptake in adipocytes. Its activity requires the presence of beta-Klotho (KLB) and FGFR4. FGF-19 interacts with fibroblast growth factor receptors, FGFR1, FGFR2, FGFR3, and FGFR4. FGF21 stimulates glucose uptake in differentiated adipocytes via the induction of glucose transporter SLC2A1/GLUT1 expression (but not SLC2A4/GLUT4 expression). Its activity requires the presence of KLB. It interacts (via C-terminus) with KLB and fibroblast growth factor receptor FGFR4. FGF23, also called phosphatonin, or tumor-derived hypophosphatemia-inducing factor (HYPF), is a regulator of phosphate homeostasis. It inhibits renal tubular phosphate transport by reducing SLC34A1 levels. It upregulates EGR1 expression in the presence of alpha-Klotho (KL). It acts directly on the parathyroid to decrease PTH secretion. FGF23 acts as a regulator of vitamin-D metabolism. It negatively regulates osteoblast differentiation and matrix mineralization. FGF23 interacts with FGFR1, FGFR2, FGFR3, and FGFR4. Members in this family contain a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 121 matched cddid_all.tbl CDD cd23311 cd23311 466997 beta-trefoil_FGF_Bnl-like FGF domain, beta-trefoil fold, found in Drosophila melanogaster protein branchless (Bnl) and similar proteins. Protein Bnl is a homolog of mammalian fibroblast growth factors. It is a dosage-sensitive regulator of terminal branching. It functions as a chemoattractant that can guide terminal branches to new tissues and even to individual cells within a tissue. Bnl contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 129 matched cddid_all.tbl CDD cd23312 cd23312 466998 beta-trefoil_FGF_RP1 FGF domain, beta-trefoil fold, found in oxygen-regulated protein 1 (ORP1) and similar proteins. ORP1, also called retinitis pigmentosa 1 protein, or retinitis pigmentosa RP1 protein, is a microtubule-associated protein that regulates the stability and length of the microtubule-based axoneme of photoreceptors. It is required for the differentiation of photoreceptor cells. It plays a role in the organization of the outer segment of rod and cone photoreceptors ensuring the correct orientation and higher-order stacking of outer segment disks along the photoreceptor axoneme. Members in this family may contain one or two fibroblast growth factor (FGF) domain(s) in the middle region. The FGF domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 128 matched cddid_all.tbl CDD cd23313 cd23313 466999 beta-trefoil_FGF1 FGF domain, beta-trefoil fold, found in fibroblast growth factor 1 (FGF1) and similar proteins. FGF1, also called acidic fibroblast growth factor (aFGF), or endothelial cell growth factor (ECGF), or heparin-binding growth factor 1 (HBGF1), plays an important role in the regulation of cell survival, cell division, angiogenesis, cell differentiation, and cell migration. It functions as potent mitogen in vitro. FGF-1 acts as a ligand for fibroblast growth factor receptor 1 (FGFR1) and integrins. It interacts with FGFR1, FGFR2, FGFR3, and FGFR4. Affinity between fibroblast growth factors (FGFs) and their receptors is increased by heparan sulfate glycosaminoglycans that function as coreceptors. It also interacts with fibroblast growth factor-binding protein 1 (FGFBP1), FGF1, and FGF2. It can induce angiogenesis. FGF1 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 128 matched cddid_all.tbl CDD cd23314 cd23314 467000 beta-trefoil_FGF2 FGF domain, beta-trefoil fold, found in fibroblast growth factor 2 (FGF2) and similar proteins. FGF2, also called basic fibroblast growth factor (bFGF), or heparin-binding growth factor 2 (HBGF2), acts as a ligand for fibroblast growth factor receptors, FGFR1, FGFR2, FGFR3, and FGFR4. It also acts as an integrin ligand which is required for FGF2 signaling. FGF2 plays an important role in the regulation of cell survival, cell division, cell differentiation, and cell migration. It functions as a potent mitogen in vitro. It can induce angiogenesis. FGF2 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 125 matched cddid_all.tbl CDD cd23315 cd23315 467001 beta-trefoil_FGF3 FGF domain, beta-trefoil fold, found in fibroblast growth factor 3 (FGF3) and similar proteins. FGF3, also called heparin-binding growth factor 3 (HBGF3), or proto-oncogene Int-2, plays an important role in the regulation of embryonic development, cell proliferation, and cell differentiation. It is required for normal ear development. FGF3 interacts with fibroblast growth factor receptors, FGFR1 and FGFR2. Affinity between FGFs and their receptors is increased by heparan sulfate glycosaminoglycans that function as coreceptors. FGF3 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 140 matched cddid_all.tbl CDD cd23316 cd23316 467002 beta-trefoil_FGF4 FGF domain, beta-trefoil fold, found in fibroblast growth factor 4 (FGF4) and similar proteins. FGF4, also called heparin secretory-transforming protein 1 (HST-1), or HSTF-1, or heparin-binding growth factor 4 (HBGF4), or transforming protein KS3, plays an important role in the regulation of embryonic development, cell proliferation, and cell differentiation. It is required for normal limb and cardiac valve development during embryogenesis. It interacts with fibroblast growth factor receptors, FGFR1, FGFR2, FGFR3, and FGFR4. Affinity between fibroblast growth factors (FGFs) and their receptors is increased by heparan sulfate glycosaminoglycans that function as coreceptors. FGF4 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 125 matched cddid_all.tbl CDD cd23317 cd23317 467003 beta-trefoil_FGF5 FGF domain, beta-trefoil fold, found in fibroblast growth factor 5 (FGF5) and similar proteins. FGF5, also called heparin-binding growth factor 5 (HBGF5), or Smag-82, plays an important role in the regulation of cell proliferation and cell differentiation. It is required for normal regulation of the hair growth cycle. It functions as an inhibitor of hair elongation by promoting progression from anagen, the growth phase of the hair follicle, into catagen the apoptosis-induced regression phase. FGF5 interacts with fibroblast growth factor receptors, FGFR1 and FGFR2. Affinity between FGFs and their receptors is increased by heparan sulfate glycosaminoglycans that function as coreceptors. FGF-5 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 133 matched cddid_all.tbl CDD cd23318 cd23318 467004 beta-trefoil_FGF6 FGF domain, beta-trefoil fold, found in fibroblast growth factor 6 (FGF6) and similar proteins. FGF6, also called heparin secretory-transforming protein 2 (HST-2), or HSTF-2, or heparin-binding growth factor 6 (HBGF6), plays an important role in the regulation of cell proliferation, cell differentiation, angiogenesis, and myogenesis, and is required for normal muscle regeneration. FGF6 interacts with fibroblast growth factor receptors, FGFR1, FGFR2, and FGFR4. Affinity between fibroblast growth factors (FGFs) and their receptors is increased by heparan sulfate glycosaminoglycans that function as coreceptors. FGF6 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 125 matched cddid_all.tbl CDD cd23319 cd23319 467005 beta-trefoil_FGF7 FGF domain, beta-trefoil fold, found in fibroblast growth factor 7 (FGF7) and similar proteins. FGF7, also called heparin-binding growth factor 7 (HBGF7), or keratinocyte growth factor (KGF), plays an important role in the regulation of embryonic development, cell proliferation, and cell differentiation. It is required for normal branching morphogenesis. It is a growth factor active on keratinocytes. It may act as major paracrine effector of normal epithelial cell proliferation. FGF7 interacts with fibroblast growth factor receptor FGFR2 and fibroblast growth factor-binding protein 1 (FGFBP1). Affinity between fibroblast growth factors (FGFs) and their receptors is increased by heparan sulfate glycosaminoglycans that function as coreceptors. FGF7 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 136 matched cddid_all.tbl CDD cd23320 cd23320 467006 beta-trefoil_FGF10 FGF domain, beta-trefoil fold, found in fibroblast growth factor 10 (FGF10) and similar proteins. FGF10 plays an important role in the regulation of embryonic development, cell proliferation, and cell differentiation. It is required for normal branching morphogenesis. It may play a role in wound healing. FGF10 interacts with fibroblast growth factor receptors FGFR1 and FGFR2, as well as fibroblast growth factor-binding protein 1 (FGFBP1). FGF10 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 134 matched cddid_all.tbl CDD cd23321 cd23321 467007 beta-trefoil_FGF22 FGF domain, beta-trefoil fold, found in fibroblast growth factor 22 (FGF22) and similar proteins. FGF22 plays a role in the fasting response, glucose homeostasis, lipolysis, and lipogenesis. It can stimulate cell proliferation (in vitro). It may be involved in hair development. FGF22 interacts with fibroblast growth factor receptors, FGFR1 and FGFR2, as well as fibroblast growth factor-binding protein 1 (FGFBP1). FGF22 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 134 matched cddid_all.tbl CDD cd23322 cd23322 467008 beta-trefoil_FGF8 FGF domain, beta-trefoil fold, found in fibroblast growth factor 8 (FGF8) and similar proteins. FGF8, also called androgen-induced growth factor (AIGF), or heparin-binding growth factor 8 (HBGF8), plays an important role in the regulation of embryonic development, cell proliferation, cell differentiation, and cell migration. It is required for normal brain, eye, ear, and limb development during embryogenesis. It is also required for normal development of the gonadotropin-releasing hormone (GnRH) neuronal system. It plays a role in neurite outgrowth in hippocampal cells. FGF8 interacts with fibroblast growth factor receptors, FGFR1, FGFR2, FGFR3, and FGFR4. Affinity between fibroblast growth factors (FGFs) and their receptors is increased by heparan sulfate glycosaminoglycans that function as coreceptors. FGF8 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 147 matched cddid_all.tbl CDD cd23323 cd23323 467009 beta-trefoil_FGF17 FGF domain, beta-trefoil fold, found in fibroblast growth factor 17 (FGF17) and similar proteins. FGF17 plays an important role in the regulation of embryonic development and as signaling molecule in the induction and patterning of the embryonic brain. It is required for normal brain development. FGF17 interacts with fibroblast growth factor receptors, FGFR3 and FGFR4. FGF17 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 126 matched cddid_all.tbl CDD cd23324 cd23324 467010 beta-trefoil_FGF18 FGF domain, beta-trefoil fold, found in fibroblast growth factor 18 (FGF18) and similar proteins. FGF18, also called zFGF5, plays an important role in the regulation of cell proliferation, cell differentiation, and cell migration. It is required for normal ossification and bone development. It stimulates hepatic and intestinal proliferation. FGF18 interacts with fibroblast growth factor receptors, FGFR3 and FGFR4. FGF18 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 126 matched cddid_all.tbl CDD cd23325 cd23325 467011 beta-trefoil_FGF9 FGF domain, beta-trefoil fold, found in fibroblast growth factor 9 (FGF9) and similar proteins. FGF9, also called glia-activating factor (GAF), or heparin-binding growth factor 9 (HBGF-9), plays an important role in the regulation of embryonic development, cell proliferation, cell differentiation, and cell migration. It acts as a heparin-binding glia-activating factor that may have a role in glial cell growth and differentiation during development, gliosis during repair and regeneration of brain tissue after damage, differentiation and survival of neuronal cells, and growth stimulation of glial tumors. FGF9 interacts with fibroblast growth factor receptors, FGFR1, FGFR2, FGFR3, and FGFR4. Affinity between fibroblast growth factors (FGFs) and their receptors is increased by heparan sulfate glycosaminoglycans that function as coreceptors. FGF9 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 160 matched cddid_all.tbl CDD cd23326 cd23326 467012 beta-trefoil_FGF16 FGF domain, beta-trefoil fold, found in fibroblast growth factor 16 (FGF16) and similar proteins. FGF16 plays an important role in the regulation of embryonic development, cell proliferation, and cell differentiation. It is required for normal cardiomyocyte proliferation and heart development. FGF16 interacts with fibroblast growth factor receptors, FGFR1 and FGFR2. FGF16 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 150 matched cddid_all.tbl CDD cd23327 cd23327 467013 beta-trefoil_FGF20 FGF domain, beta-trefoil fold, found in fibroblast growth factor 20 (FGF20) and similar proteins. FGF20 acts as a neurotrophic factor that regulates central nervous development and function. It interacts with fibroblast growth factor receptors, FGFR2 and FGFR4. Affinity between fibroblast growth factors (FGFs) and their receptors is increased by heparan sulfate glycosaminoglycans that function as coreceptors. FGF20 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 153 matched cddid_all.tbl CDD cd23328 cd23328 467014 beta-trefoil_FGF12 FGF domain, beta-trefoil fold, found in fibroblast growth factor 12 (FGF12) and similar proteins. FGF12, also called fibroblast growth factor homologous factor 1 (FHF1), or myocyte-activating factor, is involved in nervous system development and function. It plays a role in the positive regulation of voltage-gated sodium channel activity. It promotes neuronal excitability by elevating the voltage dependence of neuronal sodium channel SCN8A fast inactivation. FGF12 interacts with the C-terminal region of SCN9A. FGF12 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 139 matched cddid_all.tbl CDD cd23329 cd23329 467015 beta-trefoil_FGF13 FGF domain, beta-trefoil fold, found in fibroblast growth factor 13 (FGF13) and similar proteins. FGF13, also called fibroblast growth factor homologous factor 2 (FHF2), is a microtubule-binding protein which directly binds tubulin and is involved in both polymerization and stabilization of microtubules. Through its action on microtubules, it may participate in the refinement of axons by negatively regulating axonal and leading processes branching. FGF13 plays a crucial role in neuron polarization and migration in the cerebral cortex and the hippocampus. It may regulate voltage-gated sodium channels transport and function. It may also play a role in MAPK signaling. It is required for the development of axonal initial segment-targeting inhibitory GABAergic synapses made by chandelier neurons. FGF13 interacts with SCN1A, SCN5A, and SCN8A. It may also interact with SCN2A and SCN11A. FGF-13 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 148 matched cddid_all.tbl CDD cd23330 cd23330 467016 beta-trefoil_FGF14 FGF domain, beta-trefoil fold, found in fibroblast growth factor 14 (FGF14) and similar proteins. FGF14, also called fibroblast growth factor homologous factor 4 (FH-4), may be involved in nervous system development and function. It interacts with SCN8A. FGF14 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 145 matched cddid_all.tbl CDD cd23331 cd23331 467017 beta-trefoil_FGF19 FGF domain, beta-trefoil fold, found in fibroblast growth factor 19 (FGF19) and similar proteins. FGF19 is involved in the suppression of bile acid biosynthesis through down-regulation of CYP7A1 expression, following positive regulation of the JNK and ERK1/2 cascades. It stimulates glucose uptake in adipocytes. Its activity requires the presence of beta-Klotho (KLB) and FGFR4. FGF-19 interacts with fibroblast growth factor receptors, FGFR1, FGFR2, FGFR3, and FGFR4. Affinity between fibroblast growth factors (FGFs) and their receptors is increased by alpha-Klotho (KL), KLB and heparan sulfate glycosaminoglycans that function as coreceptors. FGF19 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 128 matched cddid_all.tbl CDD cd23332 cd23332 467018 beta-trefoil_FGF21 FGF domain, beta-trefoil fold, found in fibroblast growth factor 21 (FGF21) and similar proteins. FGF21 stimulates glucose uptake in differentiated adipocytes via the induction of glucose transporter SLC2A1/GLUT1 expression (but not SLC2A4/GLUT4 expression). Its activity requires the presence of beta-Klotho (KLB). It interacts (via C-terminus) with KLB and fibroblast growth factor receptor FGFR4. FGF21 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 126 matched cddid_all.tbl CDD cd23333 cd23333 467019 beta-trefoil_FGF23 FGF domain, beta-trefoil fold, found in fibroblast growth factor 23 (FGF23) and similar proteins. FGF23, also called phosphatonin, or tumor-derived hypophosphatemia-inducing factor (HYPF), is a regulator of phosphate homeostasis. It inhibits renal tubular phosphate transport by reducing SLC34A1 levels. It upregulates EGR1 expression in the presence of alpha-Klotho (KL). It acts directly on the parathyroid to decrease PTH secretion. FGF23 acts as a regulator of vitamin-D metabolism. It negatively regulates osteoblast differentiation and matrix mineralization. FGF23 interacts with fibroblast growth factor receptors, FGFR1, FGFR2, FGFR3, and FGFR4. Affinity between fibroblast growth factors (FGFs) and their receptors is increased by KL and heparan sulfate glycosaminoglycans that function as coreceptors. FGF23 contains a FGF domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 148 matched cddid_all.tbl CDD cd23334 cd23334 467442 beta-trefoil_FSCN_rpt1 first fascin-like domain, beta-trefoil fold, found in the fascin subfamily. The fascin family includes fascin1-3 and Drosophila melanogaster protein singed. Fascin, also called fascin-1, 55 kDa actin-bundling protein, singed-like protein, or p55, is an actin-binding protein that contains 2 major actin binding sites. It is involved in the organization of actin filament bundles and the formation of microspikes, membrane ruffles, and stress fibers. It plays an important role for the formation of a diverse set of cell protrusions, such as filopodia, and for cell motility and migration. It mediates reorganization of the actin cytoskeleton and axon growth cone collapse in response to nerve growth factor (NGF). Fascin-2, also called retinal fascin, is a photoreceptor-specific paralog of the actin-bundling protein fascin. It may play a pivotal role in photoreceptor cell-specific events, such as disk morphogenesis. Fascin-3, also called testis fascin, is a novel paralog of the actin-bundling protein fascin expressed specifically in the elongate spermatid head. Protein singed acts as an actin-bundling protein that may have a role in the asymmetric organization and/or movement of cytoplasmic components. It has a role in somatic cells during the formation of adult bristles and hairs, and in the female germline during oogenesis. Members of this subfamily are composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the first fascin-like beta-trefoil domain. 125 matched cddid_all.tbl CDD cd23335 cd23335 467443 beta-trefoil_FSCN_rpt2 second fascin-like domain, beta-trefoil fold, found in the fascin subfamily. The fascin subfamily includes fascin1-3 and Drosophila melanogaster protein singed. Fascin, also called fascin-1, 55 kDa actin-bundling protein, singed-like protein, or p55, is an actin-binding protein that contains 2 major actin binding sites. It is involved in the organization of actin filament bundles and the formation of microspikes, membrane ruffles, and stress fibers. It plays an important role for the formation of a diverse set of cell protrusions, such as filopodia, and for cell motility and migration. It mediates reorganization of the actin cytoskeleton and axon growth cone collapse in response to nerve growth factor (NGF). Fascin-2, also called retinal fascin, is a photoreceptor-specific paralog of the actin-bundling protein fascin. It may play a pivotal role in photoreceptor cell-specific events, such as disk morphogenesis. Fascin-3, also called testis fascin, is a novel paralog of the actin-bundling protein fascin expressed specifically in the elongate spermatid head. Protein singed acts as an actin-bundling protein that may have a role in the asymmetric organization and/or movement of cytoplasmic components. It has a role in somatic cells during the formation of adult bristles and hairs, and in the female germline during oogenesis. Members of this subfamily are composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the second fascin-like beta-trefoil domain. 117 matched cddid_all.tbl CDD cd23336 cd23336 467444 beta-trefoil_FSCN_rpt3 third fascin-like domain, beta-trefoil fold, found in the fascin subfamily. The fascin subfamily includes fascin1-3 and Drosophila melanogaster protein singed. Fascin, also called fascin-1, 55 kDa actin-bundling protein, singed-like protein, or p55, is an actin-binding protein that contains 2 major actin binding sites. It is involved in the organization of actin filament bundles and the formation of microspikes, membrane ruffles, and stress fibers. It plays an important role for the formation of a diverse set of cell protrusions, such as filopodia, and for cell motility and migration. It mediates reorganization of the actin cytoskeleton and axon growth cone collapse in response to nerve growth factor (NGF). Fascin-2, also called retinal fascin, is a photoreceptor-specific paralog of the actin-bundling protein fascin. It may play a pivotal role in photoreceptor cell-specific events, such as disk morphogenesis. Fascin-3, also called testis fascin, is a novel paralog of the actin-bundling protein fascin expressed specifically in the elongate spermatid head. Protein singed acts as an actin-bundling protein that may have a role in the asymmetric organization and/or movement of cytoplasmic components. It has a role in somatic cells during the formation of adult bristles and hairs, and in the female germline during oogenesis. Members of this subfamily are composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the third fascin-like beta-trefoil domain. 124 matched cddid_all.tbl CDD cd23337 cd23337 467445 beta-trefoil_FSCN_rpt4 fourth fascin-like domain, beta-trefoil fold, found in the fascin subfamily. The fascin subfamily includes fascin1-3 and Drosophila melanogaster protein singed. Fascin, also called fascin-1, 55 kDa actin-bundling protein, singed-like protein, or p55, is an actin-binding protein that contains 2 major actin binding sites. It is involved in the organization of actin filament bundles and the formation of microspikes, membrane ruffles, and stress fibers. It plays an important role for the formation of a diverse set of cell protrusions, such as filopodia, and for cell motility and migration. It mediates reorganization of the actin cytoskeleton and axon growth cone collapse in response to nerve growth factor (NGF). Fascin-2, also called retinal fascin, is a photoreceptor-specific paralog of the actin-bundling protein fascin. It may play a pivotal role in photoreceptor cell-specific events, such as disk morphogenesis. Fascin-3, also called testis fascin, is a novel paralog of the actin-bundling protein fascin expressed specifically in the elongate spermatid head. Protein singed acts as an actin-bundling protein that may have a role in the asymmetric organization and/or movement of cytoplasmic components. It has a role in somatic cells during the formation of adult bristles and hairs, and in the female germline during oogenesis. Members in this family are composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the fourth fascin-like beta-trefoil domain. 114 matched cddid_all.tbl CDD cd23338 cd23338 467446 beta-trefoil_FSCN_FRG1 fascin-like domain, beta-trefoil fold, found in FSHD region gene 1 protein (FRG1) and similar proteins. Protein FRG1 binds to mRNA in a sequence-independent manner. It may play a role in the regulation of pre-mRNA splicing or in the assembly of rRNA into ribosomal subunits. It may be involved in mRNA transport, as well as in epigenetic regulation of muscle differentiation through regulation of activity of the histone-lysine N-methyltransferase KMT5B. FRG1 contains a fascin-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 141 matched cddid_all.tbl CDD cd23339 cd23339 467447 beta-trefoil_FSCN_fungal_FRG1-like fascin-like domain, beta-trefoil fold, found in fungal FRG1 and similar proteins. This group includes Schizosaccharomyces pombe protein FRG1 (SpFRG1), which may have a role in the processing of pre-rRNA or in the assembly of rRNA into ribosomal subunits. It is a component of the spliceosome and may be involved in pre-mRNA splicing. SpFRG1 contains a fascin-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 160 matched cddid_all.tbl CDD cd23340 cd23340 467448 beta-trefoil_FSCN_ACP-like fascin-like domain, beta-trefoil fold, found in Arabidopsis thaliana actin cross-linking protein (ACP) and similar proteins. This subfamily includes a group of uncharacterized proteins similar to Arabidopsis thaliana ACPs. ACPs organize actin filaments into dynamic and complex subcellular scaffolds that orchestrate important mechanical functions, including cell motility and adhesion. Members of this subfamily contain a fascin-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Some subfamily members contain two copies of the domain. 148 matched cddid_all.tbl CDD cd23341 cd23341 467449 beta-trefoil_FSCN_HatAB fascin-like domain, beta-trefoil fold, found in the hisactophilin subfamily. Hisactophilin is a histidine-rich actin-binding protein from Dictyostelium discoideum. It exists in two isoforms, hisactophilin-1 (HatA, also called HS I) and hisactophilin-2 (HatB, also called HS II), which are both myristoylated and distributed between plasma membrane and cytoplasm. Hisactophilin may act as an intracellular pH sensor that links chemotactic signals to responses in the microfilament system of the cells by nucleating actin polymerization or stabilizing the filaments. Hisactophilin contains a fascin-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 115 matched cddid_all.tbl CDD cd23342 cd23342 467450 beta-trefoil_FSCN_ZgPorA-like fascin-like domain, beta-trefoil fold, found in Zobellia galactanivorans beta-porphyranase A (PorA) and similar proteins. PorA (EC 3.2.1.178) cleaves the sulfated polysaccharide porphyran at the (1->4) linkages between beta-D-galactopyranose and alpha-L-galactopyranose-6-sulfate, forming mostly the disaccharide alpha-L-galactopyranose-6-sulfate-(1->3)-beta-D-galactose. It is inactive on the non-sulfated agarose portion of the porphyran backbone and displays a strict requirement for C6-sulfate in the -2 and +1-binding subsites. Members of this subfamily contain a fascin-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 122 matched cddid_all.tbl CDD cd23343 cd23343 467451 beta-trefoil_FSCN_BglX-like fascin-like domain, beta-trefoil fold, found in uncharacterized beta-glucosidase-like proteins. This subfamily includes a group of uncharacterized proteins which may be related to beta-glucosidase/glycosyl hydrolase 3 family. They contain a fascin-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 133 matched cddid_all.tbl CDD cd23344 cd23344 467452 beta-trefoil_FSCN1_rpt1 first fascin-like domain, beta-trefoil fold, found in fascin and similar proteins. Fascin, also called fascin-1, 55 kDa actin-bundling protein, singed-like protein, or p55, is an actin-binding protein that contains 2 major actin binding sites. It is involved in the organization of actin filament bundles and the formation of microspikes, membrane ruffles, and stress fibers. It plays an important role for the formation of a diverse set of cell protrusions, such as filopodia, and for cell motility and migration. It mediates reorganization of the actin cytoskeleton and axon growth cone collapse in response to nerve growth factor (NGF). Fascin is composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the first fascin-like beta-trefoil domain. 128 matched cddid_all.tbl CDD cd23345 cd23345 467453 beta-trefoil_FSCN2_rpt1 first fascin-like domain, beta-trefoil fold, found in fascin-2 and similar proteins. Fascin-2, also called retinal fascin, is a photoreceptor-specific paralog of the actin-bundling protein fascin. It may play a pivotal role in photoreceptor cell-specific events, such as disk morphogenesis. Fascin-2 is composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the first fascin-like beta-trefoil domain. 130 matched cddid_all.tbl CDD cd23346 cd23346 467454 beta-trefoil_FSCN3_rpt1 first fascin-like domain, beta-trefoil fold, found in fascin-3 and similar proteins. Fascin-3, also called testis fascin, is a novel paralog of the actin-bundling protein fascin expressed specifically in the elongate spermatid head. Fascin-3 is composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the first fascin-like beta-trefoil domain. 127 matched cddid_all.tbl CDD cd23347 cd23347 467455 beta-trefoil_singed_rpt1 first fascin-like domain, beta-trefoil fold, found in Drosophila melanogaster protein singed and similar proteins. Protein singed acts as an actin-bundling protein that may have a role in the asymmetric organization and/or movement of cytoplasmic components. It has a role in somatic cells during the formation of adult bristles and hairs, and in the female germline during oogenesis. It interacts with Rab35, with stronger binding to the Rab35-GTP form compared to the Rab35-GDP form. Protein singed is composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the first fascin-like beta-trefoil domain. 130 matched cddid_all.tbl CDD cd23348 cd23348 467456 beta-trefoil_FSCN1_rpt2 second fascin-like domain, beta-trefoil fold, found in fascin and similar proteins. Fascin, also called fascin-1, 55 kDa actin-bundling protein, singed-like protein, or p55, is an actin-binding protein that contains 2 major actin binding sites. It is involved in the organization of actin filament bundles and the formation of microspikes, membrane ruffles, and stress fibers. It plays an important role for the formation of a diverse set of cell protrusions, such as filopodia, and for cell motility and migration. It mediates reorganization of the actin cytoskeleton and axon growth cone collapse in response to nerve growth factor (NGF). Fascin is composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the second fascin-like beta-trefoil domain. 120 matched cddid_all.tbl CDD cd23349 cd23349 467457 beta-trefoil_FSCN2_rpt2 second fascin-like domain, beta-trefoil fold, found in fascin-2 and similar proteins. Fascin-2, also called retinal fascin, is a photoreceptor-specific paralog of the actin-bundling protein fascin. It may play a pivotal role in photoreceptor cell-specific events, such as disk morphogenesis. Fascin-2 is composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the second fascin-like beta-trefoil domain. 119 matched cddid_all.tbl CDD cd23350 cd23350 467458 beta-trefoil_FSCN3_rpt2 second fascin-like domain, beta-trefoil fold, found in fascin-3 and similar proteins. Fascin-3, also called testis fascin, is a novel paralog of the actin-bundling protein fascin expressed specifically in the elongate spermatid head. Fascin-3 is composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the second fascin-like beta-trefoil domain. 119 matched cddid_all.tbl CDD cd23351 cd23351 467459 beta-trefoil_singed_rpt2 second fascin-like domain, beta-trefoil fold, found in Drosophila melanogaster protein singed and similar proteins. Protein singed acts as an actin bundling protein that may have a role in the asymmetric organization and/or movement of cytoplasmic components. It has a role in somatic cells during the formation of adult bristles and hairs, and in the female germline during oogenesis. It interacts with Rab35, with stronger binding to the Rab35-GTP form compared to the Rab35-GDP form. Protein singed is composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the second fascin-like beta-trefoil domain. 119 matched cddid_all.tbl CDD cd23352 cd23352 467460 beta-trefoil_FSCN1_rpt3 third fascin-like domain, beta-trefoil fold, found in fascin and similar proteins. Fascin, also called fascin-1, 55 kDa actin-bundling protein, singed-like protein, or p55, is an actin-binding protein that contains 2 major actin binding sites. It is involved in the organization of actin filament bundles and the formation of microspikes, membrane ruffles, and stress fibers. It plays an important role for the formation of a diverse set of cell protrusions, such as filopodia, and for cell motility and migration. It mediates reorganization of the actin cytoskeleton and axon growth cone collapse in response to nerve growth factor (NGF). Fascin is composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the third fascin-like beta-trefoil domain. 123 matched cddid_all.tbl CDD cd23353 cd23353 467461 beta-trefoil_FSCN2_rpt3 third fascin-like domain, beta-trefoil fold, found in fascin-2 and similar proteins. Fascin-2, also called retinal fascin, is a photoreceptor-specific paralog of the actin-bundling protein fascin. It may play a pivotal role in photoreceptor cell-specific events, such as disk morphogenesis. Fascin-2 is composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the third fascin-like beta-trefoil domain. 123 matched cddid_all.tbl CDD cd23354 cd23354 467462 beta-trefoil_FSCN3_rpt3 third fascin-like domain, beta-trefoil fold, found in fascin-3 and similar proteins. Fascin-3, also called testis fascin, is a novel paralog of the actin-bundling protein fascin expressed specifically in the elongate spermatid head. Fascin-3 is composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the third fascin-like beta-trefoil domain. 123 matched cddid_all.tbl CDD cd23355 cd23355 467463 beta-trefoil_singed_rpt3 third fascin-like domain, beta-trefoil fold, found in Drosophila melanogaster protein singed and similar proteins. Protein singed acts as an actin-bundling protein that may have a role in the asymmetric organization and/or movement of cytoplasmic components. It has a role in somatic cells during the formation of adult bristles and hairs, and in the female germline during oogenesis. It interacts with Rab35, with stronger binding to the Rab35-GTP form compared to the Rab35-GDP form. Protein singed is composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the third fascin-like beta-trefoil domain. 125 matched cddid_all.tbl CDD cd23356 cd23356 467464 beta-trefoil_FSCN1_rpt4 fourth fascin-like domain, beta-trefoil fold, found in fascin and similar proteins. Fascin, also called fascin-1, 55 kDa actin-bundling protein, singed-like protein, or p55, is an actin-binding protein that contains 2 major actin binding sites. It is involved in the organization of actin filament bundles and the formation of microspikes, membrane ruffles, and stress fibers. It plays an important role for the formation of a diverse set of cell protrusions, such as filopodia, and for cell motility and migration. It mediates reorganization of the actin cytoskeleton and axon growth cone collapse in response to nerve growth factor (NGF). Fascin is composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the fourth fascin-like beta-trefoil domain. 111 matched cddid_all.tbl CDD cd23357 cd23357 467465 beta-trefoil_FSCN2_rpt4 fourth fascin-like domain, beta-trefoil fold, found in fascin-2 and similar proteins. Fascin-2, also called retinal fascin, is a photoreceptor-specific paralog of the actin-bundling protein fascin. It may play a pivotal role in photoreceptor cell-specific events, such as disk morphogenesis. Fascin-2 is composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the fourth fascin-like beta-trefoil domain. 112 matched cddid_all.tbl CDD cd23358 cd23358 467466 beta-trefoil_FSCN3_rpt4 fourth fascin-like domain, beta-trefoil fold, found in fascin-3 and similar proteins. Fascin-3, also called testis fascin, is a novel paralog of the actin-bundling protein fascin expressed specifically in the elongate spermatid head. Fascin-3 is composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the fourth fascin-like beta-trefoil domain. 113 matched cddid_all.tbl CDD cd23359 cd23359 467467 beta-trefoil_singed_rpt4 fourth fascin-like domain, beta-trefoil fold, found in Drosophila melanogaster protein singed and similar proteins. Protein singed acts as an actin-bundling protein that may have a role in the asymmetric organization and/or movement of cytoplasmic components. It has a role in somatic cells during the formation of adult bristles and hairs, and in the female germline during oogenesis. It interacts with Rab35, with stronger binding to the Rab35-GTP form compared to the Rab35-GDP form. Protein singed is composed of four fascin beta-trefoil domains, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the fourth fascin-like beta-trefoil domain. 113 matched cddid_all.tbl CDD cd23360 cd23360 467385 beta-trefoil_STI_WSCP_II soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in class II water-soluble chlorophyll proteins (WSCPs) and similar proteins. There are two kinds of water-soluble chlorophyll (Chl) proteins (WSCPs): Chenopodium-type (Class I, a WSCP from Chenopodium, Atriplex, Polygonum, and Amaranthus species) and Brassica-type (Class II, a WSCP from Brassica, Raphanus, and Lepidium species). Classes I and II WSCPs differ mainly in their photoconvertiblity. Class I WSCPs show a light-induced absorption change, whereas Class II WSCPs do not. This family includes Class II WSCPs. They possess the complete motif of the Kunitz-type proteinase inhibitor but may not inhibit trypsin, whose activity is inhibited strongly by one Kunitz-proteinase inhibitor, the soybean trypsin inhibitor (STI). Members of this subfamily contain a STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 176 matched cddid_all.tbl CDD cd23361 cd23361 467386 beta-trefoil_STI_WBA1 soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in Psophocarpus tetragonolobus albumin-1 and similar proteins. Albumin-1, also called WBA-1, or winged bean albumin 1, acts as a 2S seed storage protein that is homologous with Kunitz-type seed trypsin inhibitors. It contains a soybean trypsin inhibitor (STI)-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 174 matched cddid_all.tbl CDD cd23362 cd23362 467387 beta-trefoil_STI_WCI3-like soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in Psophocarpus tetragonolobus chymotrypsin inhibitor 3 (WCI-3) and similar proteins. This subfamily includes Psophocarpus tetragonolobus WCI-3, trypsin inhibitor 1 (WTI-1), and trypsin inhibitor DE-3 from Erythrina caffra (ETI). WTI-1 is a Kunitz type protease inhibitor that inhibits bovine trypsin stoichiometrically, but not bovine alpha-chymotrypsin. WCI-3 is a Kunitz-type winged bean chymotrypsin inhibitor (WbCI) that inhibits alpha-chymotrypsin at the molar ratio of 1:2 instead of 1:1, the usual ratio of 1:1 common to other members of the family. ETI is a trypsin inhibitor that shows high homology to other Kunitz trypsin protease inhibitors, but has the unique ability to bind and inhibit tissue plasminogen activator. Members of this subfamily contain an STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 170 matched cddid_all.tbl CDD cd23363 cd23363 467388 beta-trefoil_STI_SKTI soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in the soybean Kunitz trypsin inhibitor (SKTI) subfamily. SKTI is extracted from soybean (Glycine max L.) seeds. It shows inhibition of trypsin and possesses insect resistance and anti-tumor properties. This subfamily includes KTI1-3. KTI1 and KTI2 probably do not possess trypsin inhibitor activity. KTI3, also called trypsin inhibitor A, is responsible for most of the Kunitz trypsin inhibitor activity and protein found in soybean seeds. Members of this subfamily contain a soybean trypsin inhibitor (STI)-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 175 matched cddid_all.tbl CDD cd23364 cd23364 467389 beta-trefoil_STI_BbKI-like soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in Bauhinia bauhinioides Kunitz-type serine protease inhibitor BbKI and similar proteins. This subfamily includes Bauhinia bauhinioides BbKI, BbCI, Bauhinia rufa BrTI, and similar proteins. BbKI inhibits bovine trypsin, human plasma kallikrein and plasmin, and weakly inhibits bovine chymotrypsin. BbCI inhibits cruzipain, a cysteine proteinase from Trypanosoma cruzi. It also inhibits cathepsin L, a cysteine proteinase with high homology to cruzipain, but not cathepsin B, papain, bromelain, or ficin. BrTI acts as an inhibitor of trypsin and human plasma kallikrein. It does not inhibit chymotrypsin, porcine pancreatic elastase, human neutrophil elastase, coagulation factor Xa, human thrombin, porcine pancreatic kallikrein or plasmin. Members of this subfamily contain an STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 162 matched cddid_all.tbl CDD cd23365 cd23365 467390 beta-trefoil_STI_LlTI-like soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in Leucaena leucocephala trypsin inhibitor (LlTI) and similar proteins. LlTI is a Kunitz-type trypsin inhibitor that inhibits trypsin, plasmin, human plasma kallikrein, chymotrypsin, and factor XIIa activity. This subfamily also includes tamarind Kunitz inhibitor (TKI), Enterolobium contortisiliquum trypsin inhibitor (EcTI), Acacia confusa trypsin inhibitor (AcTI), Bauhinia ungulata factor Xa inhibitor BuXI, and Phanera variegata trypsin inhibitor BvTI. TKI is a Kunitz-type dual inhibitor (TKI) of factor Xa (FXa) and trypsin. It shows prolongation of blood coagulation time. EcTI also belongs to the Kunitz family of plant inhibitors, common in plant seeds. It inhibits trypsin, chymotrypsin, plasma kallikrein, plasmin, human neutrophil elastase, and Factor XIIa in the stoichiometric ratio 1:1, but not thrombin, bovine pancreatic elastase, or Factor Xa. It is involved in the inhibition of the invasion of gastric cancer cells through alterations in integrin-dependent cell signaling pathway. AcTI inhibits trypsin and alpha-chymotrypsin stoichiometrically at the molar ratio of 1:1 and 2:1 respectively. BuXI inhibits bovine trypsin and chymotrypsin, and human plasmin, plasma kallikrein, factor XIIa, and factor Xa. BvTI inhibits bovine trypsin and chymotrypsin, and human plasmin, plasma kallikrein and factor XIIa. Members of this subfamily contain an STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 170 matched cddid_all.tbl CDD cd23366 cd23366 467391 beta-trefoil_STI_AtTPI-like soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in Arabidopsis thaliana trypsin protease inhibitor (AtTPI) and similar proteins. AtTPI, also called kunitz trypsin inhibitor 4 (AtKTI4), or Kunitz trypsin inhibitor 1 (AtKTI1), exhibits Kunitz trypsin protease inhibitor activity. It is involved in modulating programmed cell death (PCD) in plant-pathogen interactions. It can also inhibit both serine proteases and cysteine proteases. It may be involved in the modulation of proteases that participate in the hydrolysis of dietary proteins in the gut of spider mites. Members of this subfamily contain an STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 195 matched cddid_all.tbl CDD cd23367 cd23367 467392 beta-trefoil_STI_KPI104-like soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in Medicago truncatula Kunitz type trypsin inhibitor 104 (KPI104) and similar proteins. This subfamily includes Medicago truncatula KPI104, KPI106, and KPI111. They are protease inhibitors involved in the control of mycorrhiza establishment and arbuscule development during root colonization by arbuscular mycorrhizal (AM) fungi (e.g. Rhizophagus irregularis). KPI104 interacts with cysteine protease (CP). It shows a stronger affinity for serine carboxypeptidase (SCP1) than for CP. KPI111 only interacts with SCP1. Members of this subfamily contain an STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 170 matched cddid_all.tbl CDD cd23368 cd23368 467393 beta-trefoil_STI_SPOR soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in Ipomoea batatas sporamin and similar proteins. This subfamily includes Ipomoea batatas sporamin A and sporamin B. They are major tuberous root proteins that belong to the soybean trypsin inhibitor (Kunitz) family of protease inhibitors. They exhibit antitumor activity in a number of types of tumor cells. Members of this subfamily contain an STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 174 matched cddid_all.tbl CDD cd23369 cd23369 467394 beta-trefoil_STI_AtKTI6-like soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in Arabidopsis thaliana Kunitz trypsin inhibitor 6 (AtKTI6) and similar proteins. This subfamily includes AtKTI6 and AtKTI7, which exhibit Kunitz trypsin protease inhibitor activity. Members of this subfamily contain an STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 170 matched cddid_all.tbl CDD cd23370 cd23370 467395 beta-trefoil_STI_MkMLP-like soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in Murraya koenigii miraculin-like protein (MkMLP) and similar proteins. This subfamily includes Theobroma cacao 21 kDa seed protein (TcASP) and Murraya koenigii miraculin-like protein (MkMLP). TcASP shows homology to the soybean trypsin inhibitor (Kunitz) family of protease inhibitors. MkMLP is closer to miraculin, a taste modifying protein, rather than classical Kunitz family members like soybean Kunitz-type trypsin inhibitor (STI). MkMLP is functionally unstable at higher temperatures. Members of this subfamily contain an STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 179 matched cddid_all.tbl CDD cd23371 cd23371 467396 beta-trefoil_STI_LSPI soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in Carica papaya latex serine proteinase inhibitor (LSPI) and similar proteins. LSPI, also called papaya protease inhibitor (PPI), is a double-headed Kunitz-type serine protease inhibitor. A single LSPI molecule can bind two trypsin units at the same time. LSPI may serve as a defense protein as it is induced by wounding and is inactive against endogenous proteases from C. papaya. LSPI belongs to the miraculin family of taste-modifying proteins, which are active against serine proteases. Members of this subfamily contain an STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 183 matched cddid_all.tbl CDD cd23372 cd23372 467397 beta-trefoil_STI_CPI-like soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in Solanum tuberosum cysteine protease inhibitor (CPI), serine protease inhibitor (SPI), aspartic protease inhibitor (API) and similar proteins. This subfamily includes Solanum tuberosum CPI, SPI, API, and similar proteins. CPI is a Kunitz-type potato cathepsin D inhibitor. It acts as a potent inhibitor of cathepsin l (cysteine protease) but does not inhibit trypsin or chymotrypsin (serine proteases). SPI is a potent inhibitor of serine proteases (chymotrypsin and trypsin). It inhibits tightly human leukocyte elastase (HLE). It does not inhibit papain, pepsin nor cathepsin D (cysteine and aspartic proteases). API functions as the inhibitor of cathepsin D (aspartic protease). It may also inhibit trypsin and chymotrypsin (serine proteases). CPI, SPI, and API protect plants by inhibiting proteases of invading organisms. Members of this subfamily contain an STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 171 matched cddid_all.tbl CDD cd23373 cd23373 467398 beta-trefoil_STI_ASI soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in alpha-amylase/subtilisin inhibitor (ASI) and similar proteins. This subfamily includes rice ASI (RASI) and barley ASI (BASI). RASI can inhibit alpha-amylase from larvae of the red flour beetle (Tribolium castaneum) and subtilisin from Bacillus subtilis. BASI is a bifunctional protein that can simultaneously inhibit alpha-amylase isozyme (AMY2) and serine proteases of the subtilisin family. Members of this subfamily contain an STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 176 matched cddid_all.tbl CDD cd23374 cd23374 467399 beta-trefoil_STI_CrataBL-like soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in Crateva tapia bark lectin (CrataBL) and similar proteins. CrataBL is both a Kunitz-type plant protease inhibitor and a glucose- and N-acetylglucosamine-binding lectin. It has hemagglutinating activity against human and rabbit erythrocytes which does not require divalent cations. It inhibits factor Xa and, to a lesser extent, trypsin. It does not inhibit neutrophil elastase, human plasma kallikrein, papain, human plasmin, porcine pancreatic kallikrein and bovine chymotrypsin. CrataBL has insecticidal activity against the termite species Nasutitermes corniger. It induces apoptosis in prostate cancer cell lines DU145 and PC3. The family includes CrataBL-form I and CrataBL-form II. This subfamily also includes Arabidopsis thaliana Kunitz trypsin inhibitor 3 (AtKTI3) that exhibits Kunitz trypsin protease inhibitor activity. Members of this subfamily contain an STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 160 matched cddid_all.tbl CDD cd23375 cd23375 467400 beta-trefoil_STI_VvMLP-like soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in Vitis vinifera miraculin-like protein (VvMLP) and similar proteins. This subfamily includes VvMLP, Synsepalum dulcificum miraculin (SdMIR), and Arabidopsis thaliana Kunitz trypsin inhibitor 5 (AtKTI5, also known as AtKTI2). VvMLP exhibits significant homology to miraculin. However, it exists as a monomer in solution with no detectable taste-modifying activity. It can act as a moderate trypsin inhibitor. SdMIR has the property of modifying a sour taste into a sweet taste. This alteration of taste perception persists for many minutes. AtKTI5 can inhibit both serine proteases and cysteine proteases. It may be involved in the modulation of the proteases that participate in the hydrolysis of dietary proteins in the gut of spider mites. Members of this subfamily contain an STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 177 matched cddid_all.tbl CDD cd23376 cd23376 467401 beta-trefoil_STI_DrTI soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in Delonix regia Kunitz-type serine protease inhibitor DrTI and similar proteins. DrTI is a Kunitz-type trypsin inhibitor that inhibits bovine trypsin and human plasma kallikrein, but not chymotrypsin and tissue kallikrein. Members of this subfamily contain an STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 174 matched cddid_all.tbl CDD cd23377 cd23377 467402 beta-trefoil_STI_MP4-like soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in Mucuna pruriens MP-4 and similar proteins. This subfamily includes Mucuna pruriens MP-4, Canavalia lineata subtilisin inhibitor CLSI-II, Cicer arietinum trypsin protein inhibitor 2 (CaTI2), Pisum sativum Kunitz-type trypsin inhibitor-like 1 protein (PIP20-1) and Kunitz-type trypsin inhibitor-like 2 protein (PIP20-2). MP-4 contributes significantly to the snake venom neutralization activity of Mucuna pruriens seeds through an indirect antibody-mediated mechanism and not through direct inhibition of venom proteases. CLSI-II inhibits subtilisin-type microbial serine proteases including proteinase K, subtilisin BPN', subtilisin Carlsberg and subtilisin E in a non-stoichiometric manner. It weakly inhibits Aspergillus oryzae protease and some metalloproteases including pronase E. It does not inhibit trypsin, chymotrypsin, Streptomyces griseus alkaline protease or Achromobacter lyticus lysyl endopeptidase. CLSI-II has a wider inhibitory specificity than CLSI-III. CaTI2 is a Kunitz trypsin inhibitor (KTI) with antifungal effect on Fusarium oxysporum f. sp. ciceris, a fungal pathogen known to cause severe damage to chickpea crop. It may be binding to the trypsin active pocket in a non-substrate like manner. PIP20-1 (also called protease inhibitor from pea 1 or FUC1) and PIP20-2 (also called protease inhibitor from pea 2 or FUC2) may act as protease inhibitors involved in plant defense responses. Members of this subfamily contain an STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 179 matched cddid_all.tbl CDD cd23378 cd23378 467403 beta-trefoil_STI_AMTIN Alocasia macrorrhizos trypsin/chymotrypsin inhibitor (AMTIN) and similar proteins. AMTIN, also called alocasin, is a multi-functional inhibitor that shows inhibition against proteases, amylases, and subtilisin. It inhibits the proteases, trypsin and chymotrypsin, and alpha-amylase. It also has antifungal activity against midgut proteases of Aedes aegypti. Members of this subfamily contain an STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 182 matched cddid_all.tbl CDD cd23379 cd23379 467404 beta-trefoil_STI_COTI soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in Senna obtusifolia trypsin inhibitor 1 (COTI) and similar proteins. COTI is a specific inhibitor of bovine trypsin. It also exhibits strong inhibitory effect on midgut trypsin from Pieris rapae, Helicoverpa armigera, Spodoptera exigua, and Spodoptera litura. Members of this subfamily contain an STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 172 matched cddid_all.tbl CDD cd23380 cd23380 467405 beta-trefoil_STI_GWIN3 soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in Populus sp. wound-responsive protein GWIN3 and similar proteins. GWIN3 may play a role in wound response. It shows high sequence similarity with sweet potato sporamins and legume Kunitz trypsin inhibitors. It remains unclear if GWIN3 is a trypsin inhibitor, but proteinase inhibitor function would be consistent with its wound-regulated behavior. Members of this subfamily contain an STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 168 matched cddid_all.tbl CDD cd23381 cd23381 467406 beta-trefoil_STI_API-A-like soybean trypsin inhibitor (STI)-like domain, beta-trefoil fold, found in Sagittaria sagittifolia proteinase inhibitor A (API-A) and similar proteins. API-A, also called double-headed proteinase inhibitor A, inhibits an equimolar amount of trypsin and chymotrypsin simultaneously, and inhibits kallikrein weakly. It possesses two distinct reactive sites, unlike other members of their family. API-A contains an STI-like domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 188 matched cddid_all.tbl CDD cd23383 cd23383 469560 ZF_RNaseIII_KREN_KREPB-like C2H2 zinc finger and Ribonuclease III-like domain of RNA-editing catalytic complex (RECC) proteins KREN1-3, KREPB4-KREPB10, and related proteins. KREN1-3 (KREPB1-3) and KREPB4-KREPB10 are components of the RNA-editing catalytic complex (RECC) involved in U-insertion/deletion mRNA editing during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastid species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The RECC core complex comprises a U-insertion subcomplex (KRET2 TUTase, KREPA1 zinc-finger protein, and KREL2 RNA ligase), a U-deletion subcomplex (KREX2 exonuclease, KREPA2 zinc-finger protein, and KREL1 RNA ligase), and six structural and/or RNA-binding proteins (KREPA3, KREPA4, KREPA5, KREPA6, KREPB4, and KREPB5). This core complex interacts with one of three RNase III family endonucleases (KREN1, KREN2, and KREN3) that may partner with one or more partner protein(s) with divergent RNase III domains, such as KREN1/KREPB8, KREN2/KREPB7, KREN3/KREPB6. KREPB4-KREPB10 have divergent RNase III domains. RECC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and the RNA-editing substrate-binding complex (RESC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. 195 matched cddid_all.tbl CDD cd23385 cd23385 467784 beta-trefoil_Ricin_MRC-like ricin B-type lectin domain, beta-trefoil fold, found in the macrophage mannose receptor (MRC) family. The MRC family includes MRC1-2, receptor-type tyrosine-protein phosphatase beta (PTPRB) isoform e, secretory phospholipase A2 receptor (PLA2R1), and lymphocyte antigen 75 (Ly-75). MRC1 mediates the endocytosis of glycoproteins by macrophages. It binds both sulfated and non-sulfated polysaccharide chains, and acts as a phagocytic receptor for bacteria, fungi, and other pathogens. It also acts as a receptor for Dengue virus envelope protein E. MRC2 may play a role as an endocytotic lectin receptor displaying calcium-dependent lectin activity. It internalizes glycosylated ligands from the extracellular space for release in an endosomal compartment via clathrin-mediated endocytosis. It may be involved in plasminogen activation system controlling the extracellular level of PLAUR/PLAU, and thus may regulate protease activity at the cell surface. It may contribute to cellular uptake, remodeling, and degradation of extracellular collagen matrices. It may play a role during cancer progression as well as in other chronic tissue destructive diseases acting on collagen turnover. It may participate in remodeling of extracellular matrix cooperating with the matrix metalloproteinases (MMPs). PTPRB (EC 3.1.3.48), also called protein-tyrosine phosphatase beta, plays an important role in blood vessel remodeling and angiogenesis. It is not necessary for the initial formation of the blood vessels but is essential for their maintenance and remodeling. It is also essential for the maintenance of endothelial cell contact integrity and for the adhesive function of VE-cadherin in endothelial cells that requires the presence of plakoglobin. PLA2R1 is a receptor for secretory phospholipase A2 (sPLA2). It acts as a receptor for phospholipase sPLA2-IB/PLA2G1B but not sPLA2-IIA/PLA2G2A. It can also bind to snake PA2-like toxins. It may be involved in responses in proinflammatory cytokine productions during endotoxic shock. It also has endocytic properties and rapidly internalizes sPLA2 ligands, which is particularly important for the clearance of extracellular sPLA2s to protect their potent enzymatic activities. Ly-75 acts as an endocytic receptor to direct captured antigens from the extracellular space to a specialized antigen-processing compartment. It causes reduced proliferation of B-lymphocytes. All family members contain a ricin B-type lectin domain at the N-terminus. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. One member of this family, MRC1, is missing the gamma subdomain. 119 matched cddid_all.tbl CDD cd23386 cd23386 467873 beta-trefoil_Ricin_LNBase ricin B-type lectin domain, beta-trefoil fold, found in Bifidobacterium bifidum lacto-N-biosidase (LNBase) and similar proteins. LNBase (EC2.3.1.140) belongs to the glycoside hydrolase 20 (GH20) family. It is a membrane-anchored extracellular enzyme that liberates lacto-N-biose I (LNB) from the non-reducing end of oligosaccharides and plays a key role in the metabolic pathway of these compounds. B. bifidum LNBase contains a signal peptide, a glycoside hydrolase family 20 (GH20) domain, a carbohydrate-binding module family 32 (CBM32) domain, a bacterial Ig-like domain, and a membrane anchor. The C-terminal region of the GH20 domain of LNBase has a unique ricin B-type lectin domain with a beta-trefoil-like fold. The typical beta-trefoil fold is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. In contrast, the second and third strands (alpha subdomain) and the last beta strand (part of gamma subdomain) are missing in the beta-trefoil fold of LNBase. 109 matched cddid_all.tbl CDD cd23387 cd23387 469574 beta-trefoil_Ricin_CdtAC ricin B-type lectin domain, beta-trefoil fold, found in cytolethal distending toxin subunit A (CdtA), subunit C (CdtC), and similar proteins. Cytolethal distending toxins (CDTs) are cytotoxins which induce host cell distension, growth arrest in G2/M phase, nucleus swelling, and chromatin fragmentation in HeLa cells. CDT is a heterotrimer consisting of the three subunits, CdtA, CdtB, and CdtC. CdtA, along with CdtC, probably forms a heterodimeric subunit required for the delivery of nuclease CdtB. Both CdtA and CdtC contain a ricin B-type lectin domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. The third beta strand is missing in CdtC. 133 matched cddid_all.tbl CDD cd23388 cd23388 467767 Toxin_R_bind_C_BoNTA_like C-terminal receptor binding domain, beta-trefoil fold, found in Clostridium botulinum neurotoxin type A (BoNT/A), type H (BoNT/H) and similar proteins. BoNT/A, also called bontoxilysin-A, or BOTOX, is a potent disease agent in botulism, a potential biological weapon and an effective therapeutic drug for a wide range of common medical conditions, such as migraines and a variety of ocular motility and movement disorders. It is also a licensed drug widely used for cosmetic applications. There are two types of BoNT/A receptor, gangliosides and members of the synaptic vesicle glycoprotein 2 (SV2) family. Both are required for BoNT/A toxicity and are therefore likely to cooperate with each other. SV2 family members are putative transporter proteins that are predicted to have 12 transmembrane domains, associate with the receptor-binding domain of the toxin. In addition, fibroblast growth factor receptor 3 (FGFR3) has also been reported to be a potential BoNT/A receptor. The family also includes BoNT/H, also known as BoNT/HA, or BoNT/FA, which shows high sequence/structure similarity to that of BoNT/A. However, they are different regarding their binding to cell-surface receptors including both polysialoganglioside (PSG) and SV2. BoNT/H also responds differently to some potent BoNT/A-neutralizing antibodies (e.g. CR2). Both BoNT/A and BoNT/H comprise three domains which are involved in catalysis (LC), translocation (HCT), and host receptor binding (HCR). The HCR domain is responsible for the highly specific targeting of the neurotoxin to neuronal cell membranes. It is a proven target for anti-BoNT antibody and vaccine development. This model corresponds to C-terminal HCR domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 196 matched cddid_all.tbl CDD cd23389 cd23389 467768 Toxin_R_bind_C_BoNTB C-terminal receptor binding domain, beta-trefoil fold, found in Clostridium botulinum neurotoxin type B (BoNT/B) and similar proteins. BoNT/B, also called bontoxilysin-B, is botulinum toxin that causes flaccid paralysis by inhibiting neurotransmitter (acetylcholine) release from the presynaptic membranes of nerve terminals of eukaryotic host skeletal and autonomic nervous system, with frequent heart or respiratory failure. There are two co-receptors of BoNT/B precursor, complex polysialylated gangliosides found on neural tissue and specific membrane-anchored proteins found in synaptic vesicles (e.g. synaptotagmin I and II). BoNT/B comprises three domains which are involved in catalysis (LC), translocation (HCT), and host receptor binding (HCR). The HCR domain is responsible for the highly specific targeting of the neurotoxin to neuronal cell membranes. It is a proven target for anti-BoNT antibody and vaccine development. This model corresponds to C-terminal HCR domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 198 matched cddid_all.tbl CDD cd23390 cd23390 467769 Toxin_R_bind_C_BoNTC C-terminal receptor binding domain, beta-trefoil fold, found in Clostridium botulinum neurotoxin type C (BoNT/C) and similar proteins. BoNT/C, also called bontoxilysin-C1, is botulinum toxin that causes flaccid paralysis by inhibiting neurotransmitter (acetylcholine) release from the presynaptic membranes of nerve terminals of the eukaryotic host skeletal and autonomic nervous system, with frequent heart or respiratory failure. BoNT/C is unique among characterized BoNTs in having 2 substrates, syntaxin (STX) and SNAP25. Unlike most BoNTs, precursor of BoNT/C seems not to have a proteinaceous co-receptor, and instead recognizes 2 different complex polysialylated gangliosides found on neural tissue probably in synaptic vesicles. Moreover, BoNT/C usually does not cause diseases in humans, but type C strains can be responsible for infant botulism. It has been shown to be a suitable drug for the treatment of dystonia. BoNT/C comprises three domains which are involved in catalysis (LC), translocation (HCT), and host receptor binding (HCR). The HCR domain is responsible for the highly specific targeting of the neurotoxin to neuronal cell membranes. It is a proven target for anti-BoNT antibody and vaccine development. This model corresponds to C-terminal HCR domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 188 matched cddid_all.tbl CDD cd23391 cd23391 467770 Toxin_R_bind_C_BoNTD_like C-terminal receptor binding domain, beta-trefoil fold, found in Clostridium botulinum neurotoxin type B (BoNT/D), C/D mosaic serotype (BoNT/CD) and similar proteins. BoNT/D, also called bontoxilysin-D, is botulinum toxin that causes flaccid paralysis by inhibiting neurotransmitter (acetylcholine) release from the presynaptic membranes of nerve terminals of the eukaryotic host skeletal and autonomic nervous system, with frequent heart or respiratory failure. BoNT/D activity is inhibited by GT1b. The protein receptor for BoNT/D has yet to be definitively proven. BoNT/CD is a BoNT subtype that is essentially a hybrid of the BoNT/C (about two-thirds) and BoNT/D (about one-third) serotypes. Both BoNT/D and BoNT/CD comprise three domains which are involved in catalysis (LC), translocation (HCT), and host receptor binding (HCR). The HCR domain is responsible for the highly specific targeting of the neurotoxin to neuronal cell membranes. It is a proven target for anti-BoNT antibody and vaccine development. This model corresponds to C-terminal HCR domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 181 matched cddid_all.tbl CDD cd23392 cd23392 467771 Toxin_R_bind_C_BoNTE C-terminal receptor binding domain, beta-trefoil fold, found in Clostridium botulinum neurotoxin type E (BoNT/E) and similar proteins. BoNT/E, also called bontoxilysin-E, is botulinum toxin that causes flaccid paralysis by inhibiting neurotransmitter (acetylcholine) release from the presynaptic membranes of nerve terminals of eukaryotic host skeletal and autonomic nervous system, with frequent heart or respiratory failure. There are two co-receptors of BoNT/E precursor, complex polysialylated gangliosides found on neural tissue and specific membrane-anchored proteins found in synaptic vesicles (e.g. synaptic vesicle protein 2). BoNT/E comprises three domains which are involved in catalysis (LC), translocation (HCT), and host receptor binding (HCR). The HCR domain is responsible for the highly specific targeting of the neurotoxin to neuronal cell membranes. It is a proven target for anti-BoNT antibody and vaccine development. This model corresponds to C-terminal HCR domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 177 matched cddid_all.tbl CDD cd23393 cd23393 467772 Toxin_R_bind_C_BoNTF C-terminal receptor binding domain, beta-trefoil fold, found in Clostridium botulinum neurotoxin type F (BoNT/F) and similar proteins. BoNT/F, also called bontoxilysin-F, is botulinum toxin that causes flaccid paralysis by inhibiting neurotransmitter (acetylcholine) release from the presynaptic membranes of nerve terminals of eukaryotic host skeletal and autonomic nervous system, with frequent heart or respiratory failure. There are two co-receptors of BoNT/F precursor, complex polysialylated gangliosides found on neural tissue and specific membrane-anchored proteins found in synaptic vesicles. BoNT/F was reported to bind synaptic vesicle protein 2 (SV2), but the functional relevance of SV2 for BoNT/F remains to be established. BoNT/F comprises three domains which are involved in catalysis (LC), translocation (HCT), and host receptor binding (HCR). The HCR domain is responsible for the highly specific targeting of the neurotoxin to neuronal cell membranes. It is a proven target for anti-BoNT antibody and vaccine development. This model corresponds to C-terminal HCR domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 184 matched cddid_all.tbl CDD cd23394 cd23394 467773 Toxin_R_bind_C_BoNTG C-terminal receptor binding domain, beta-trefoil fold, found in Clostridium botulinum neurotoxin type G (BoNT/G) and similar proteins. BoNT/G, also called bontoxilysin-G, is botulinum toxin that causes flaccid paralysis by inhibiting neurotransmitter (acetylcholine) release from the presynaptic membranes of nerve terminals of eukaryotic host skeletal and autonomic nervous system, with frequent heart or respiratory failure. There are two co-receptors of BoNT/G precursor, complex polysialylated gangliosides found on neural tissue and specific membrane-anchored proteins found in synaptic vesicles (e.g. synaptotagmin I and II). BoNT/G comprises three domains which are involved in catalysis (LC), translocation (HCT), and host receptor binding (HCR). The HCR domain is responsible for the highly specific targeting of the neurotoxin to neuronal cell membranes. It is a proven target for anti-BoNT antibody and vaccine development. This model corresponds to C-terminal HCR domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 195 matched cddid_all.tbl CDD cd23395 cd23395 467774 Toxin_R_bind_C_BoNTDC C-terminal receptor binding domain, beta-trefoil fold, found in Clostridium botulinum chimeric BoNT/DC neurotoxin and similar proteins. Botulinum toxin (BoNT) causes flaccid paralysis by inhibiting neurotransmitter (acetylcholine) release from the presynaptic membranes of nerve terminals of eukaryotic host skeletal and autonomic nervous system, with frequent heart or respiratory failure. BoNT/DC, also called D/C mosaic BoNT, is a BoNT subtype that is essentially a hybrid of the BoNT/C (about one-third) and BoNT/D (about two-thirds) serotypes. It is a pathogenic agent causing bovine botulism which exhibits the highest toxic activity to mice and possesses immunological specificity. BoNT/DC comprises three domains which are involved in catalysis (LC), translocation (HCT), and host receptor binding (HCR). The HCR domain is responsible for the highly specific targeting of the neurotoxin to neuronal cell membranes. It is a proven target for anti-BoNT antibody and vaccine development. The HCR domain of BoNT/DC is very similar to BoNT/C based on sequence. However, its crystal structure clearly shows that its HCR domain is more similar to BoNT/B than BoNT/C, which has been confirmed by functional studies. BoNT/DC does not share protein receptor with BoNT/C. Instead, it shares synaptotagmin (Syt) I and II as receptors with BoNT/B, despite their low sequence similarity. This model corresponds to C-terminal HCR domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 187 matched cddid_all.tbl CDD cd23396 cd23396 467775 Toxin_R_bind_C_BoNTX_like C-terminal receptor binding domain, beta-trefoil fold, found in Clostridium botulinum neurotoxin type X (BoNT/X) and similar proteins. BoNT/X, also called bontoxilysin-X, is a new serotype of botulinum toxin, which causes flaccid paralysis by inhibiting neurotransmitter (acetylcholine) release from the presynaptic membranes of nerve terminals of eukaryotic host skeletal and autonomic nervous system, with frequent heart or respiratory failure. There are two co-receptors of BoNT/X precursor, complex polysialylated gangliosides found on neural tissue and specific membrane-anchored proteins found in synaptic vesicles. Like BoNT/B/D/F/G, BoNT/X cleaves vesicle-associated membrane proteins (VAMP) 1, 2 and 3, but at a novel site (Arg66-Ala67 in VAMP2). Unlike other BoNTs, BoNT/X is the only toxin that also cleaves non-canonical substrates VAMP4, VAMP5, and Ykt6. The family also includes Enterococcus botulinum-like toxin eBoNT/J and Paraclostridium bifermentans mosquitocidal protein 1 (PMP1). eBoNT/J might be a precursor of a toxin that binds to an unknown eukaryotic cell receptor(s) and be taken up into the host cell via the endocytic pathway. It strongly resembles a botulinum-type toxin, with the appropriate domains and residues to have proteolytic function, although its C-terminus (which binds to a eukaryotic host cell) is different enough from clostrial botulinum toxins that it might bind another cell target. eBoNT/J shows no toxicity to mice, although it cleaves human VAMP-2 and SNAP-25 in neurons. PMP1 is a clostridial-like neurotoxin that selectively targets anopheline mosquitoes. It cleaves mosquito syntaxin but does not cleave human syntaxin despite the cleavage site being conserved. PMP1 is not implicated in toxicity, although it has conserved SxWY motif. Members in this family comprise three domains which are involved in catalysis (LC), translocation (HCT), and host receptor binding (HCR). The HCR domain is responsible for the highly specific targeting of the neurotoxin to neuronal cell membranes. It is a proven target for anti-BoNT antibody and vaccine development. This model corresponds to C-terminal HCR domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 188 matched cddid_all.tbl CDD cd23397 cd23397 467776 Toxin_R_bind_C_TeNT C-terminal receptor binding domain, beta-trefoil fold, found in Clostridium tetani tetanus toxin (TeNT) and similar proteins. TeNT (EC 3.4.24.68), also called tentoxylysin, is tetanus toxin that inhibits neurotransmission of inhibitory interneurons, causing spastic paralysis in the tetanus disease. It binds to peripheral neuronal synapses. It is internalized and moves by retrograde transport up the axon into the spinal cord where it can move between postsynaptic and presynaptic neurons. It inhibits neurotransmitter release by acting as a zinc endopeptidase that catalyzes the hydrolysis of the '76-Gln-|-Phe-77' bond of vesicle-associated membrane protein-2 (also known as synaptobrevin-2). TeNT comprises three domains which are involved in catalysis (LC), translocation (HCT), and host receptor binding (HCR). This model corresponds to C-terminal HCR domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 192 matched cddid_all.tbl CDD cd23398 cd23398 467808 beta-trefoil_ABD_OTOG-like Arabinose-binding domain (ABD), beta-trefoil fold, found in the otogelin (OTOG) family. The OTOG family includes otogelin (OTOG) and otogelin-like protein (OTOGL). OTOG is a glycoprotein specific to acellular membranes of the inner ear. It may be required for the anchoring of the otoconial membranes and cupula to the underlying neuroepithelia in the vestibule. OTOG may be involved in the organization and/or stabilization of the fibrillar network that compose the tectorial membrane in the cochlea. OTOGL is a mucin glycoprotein that is a component of the tectorial membrane. It acts as a gel-forming mucin that forms high-molecular-weight complexes and is glycosylated through mucin-type O-glycosylation. Mutations in the OTOG or OTOGL gene may cause hearing loss. Members of this family contain an ABD with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ABD of the related protein, alpha-L-arabinofuranosidase, binds two arabinose molecules in the beta and gamma subdomains. 143 matched cddid_all.tbl CDD cd23399 cd23399 467809 beta-trefoil_ABD_ABFB Arabinose-binding domain (ABD), beta-trefoil fold, found in alpha-L-arabinofuranosidase B (ABF B) and similar proteins. Alpha-L-arabinofuranosidase (EC 3.2.1.55), also called ABF, or non-reducing end alpha-L-arabinofuranosidase, or arabinofuranosidase, or arabinosidase, is involved in the degradation of arabinoxylan, a major component of plant hemicellulose. It can hydrolyze 1,5-, 1,3- and 1,2-alpha-linkages not only in L-arabinofuranosyl oligosaccharides, but also in polysaccharides containing terminal non-reducing L-arabinofuranoses in side chains, like L-arabinan, arabinogalactan and arabinoxylan. ABF belongs to the glycosyl hydrolase 54 family. The family also includes Hungateiclostridium thermocellum anti-sigma-I factor RsgI5. It negatively regulates SigI5 activity through direct interaction. Binding of the polysaccharide substrate to the extracellular C-terminal sensing domain of RsgI5 may induce a conformational change in its N-terminal cytoplasmic region, leading to the release and activation of SigI5. Members of the ABFB family contain an ABD with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ABD binds two arabinose molecules in the beta and gamma subdomains. 138 matched cddid_all.tbl CDD cd23400 cd23400 467810 beta-trefoil_ABD_OTOG Arabinose-binding domain (ABD), beta-trefoil fold, found in otogelin (OTOG) and similar proteins. OTOG is a glycoprotein specific to acellular membranes of the inner ear. It may be required for the anchoring of the otoconial membranes and cupula to the underlying neuroepithelia in the vestibule. OTOG may be involved in the organization and/or stabilization of the fibrillar network that compose the tectorial membrane in the cochlea. Mutations in the OTOG gene may cause hearing loss. OTOG contains an ABD with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ABD of the related protein, alpha-L-arabinofuranosidase, binds two arabinose molecules in the beta and gamma subdomains. 152 matched cddid_all.tbl CDD cd23401 cd23401 467811 beta-trefoil_ABD_OTOGL Arabinose-binding domain (ABD), beta-trefoil fold, found in otogelin-like protein (OTOGL) and similar proteins. OTOGL is a mucin glycoprotein that is a component of the tectorial membrane. It acts as a gel-forming mucin that forms high-molecular-weight complexes and is glycosylated through mucin-type O-glycosylation. Mutations in the OTOGL gene may cause hearing loss. OTOGL contains an ABD with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ABD of the related protein, alpha-L-arabinofuranosidase, binds two arabinose molecules in the beta and gamma subdomains. 154 matched cddid_all.tbl CDD cd23407 cd23407 467785 beta-trefoil_Ricin_MRC1 ricin B-type lectin domain, beta-trefoil fold, found in macrophage mannose receptor 1 (MRC1) and similar proteins. MRC1, also called MMR, C-type lectin domain family 13 member D (CLEC13D), C-type lectin domain family 13 member D-like (CLEC13DL), macrophage mannose receptor 1-like protein 1 (MRC1L1), or CD206, mediates the endocytosis of glycoproteins by macrophages. It binds both sulfated and non-sulfated polysaccharide chains. MRC1 acts as phagocytic receptor for bacteria, fungi and other pathogens. It also acts as a receptor for Dengue virus envelope protein E. MRC1 contains a ricin B-type lectin domain at the N-terminus. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. 123 matched cddid_all.tbl CDD cd23408 cd23408 467786 beta-trefoil_Ricin_MRC2 ricin B-type lectin domain, beta-trefoil fold, found in macrophage mannose receptor 2 (MRC2) and similar proteins. MRC2, also called C-type mannose receptor 2, C-type lectin domain family 13 member E (CLEC13E), endocytic receptor 180 (Endo180), urokinase-type plasminogen activator receptor-associated protein (UPARAP), UPAR-associated protein, urokinase receptor-associated protein, or CD280, may play a role as endocytotic lectin receptor displaying calcium-dependent lectin activity. It internalizes glycosylated ligands from the extracellular space for release in an endosomal compartment via clathrin-mediated endocytosis. It may be involved in plasminogen activation system controlling the extracellular level of PLAUR/PLAU, and thus may regulate protease activity at the cell surface. It may contribute to cellular uptake, remodeling, and degradation of extracellular collagen matrices. It may play a role during cancer progression as well as in other chronic tissue destructive diseases acting on collagen turnover. It may participate in remodeling of extracellular matrix cooperating with the matrix metalloproteinases (MMPs). MRC2 contains an atypical ricin B-type lectin domain at the N-terminus. The typical ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. In contrast, the ninth, tenth and eleventh beta strands, comprising the gamma subdomain, are missing in the ricin B-type lectin domain of MRC2. 124 matched cddid_all.tbl CDD cd23409 cd23409 467787 beta-trefoil_Ricin_PTPRB-like ricin B-type lectin domain, beta-trefoil fold, found in receptor-type tyrosine-protein phosphatase beta (PTPRB) isoform e and similar proteins. PTPRB (EC 3.1.3.48), also called protein-tyrosine phosphatase beta, R-PTP-beta, vascular endothelial protein tyrosine phosphatase, or VE-PTP, plays an important role in blood vessel remodeling and angiogenesis. It is not necessary for the initial formation of blood vessels but is essential for their maintenance and remodeling. It is also essential for the maintenance of endothelial cell contact integrity and for the adhesive function of VE-cadherin in endothelial cells, which requires the presence of plakoglobin. The subfamily corresponds to PTPRB isoform e, which contains an extra ricin B-type lectin domain at the N-terminus. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. 117 matched cddid_all.tbl CDD cd23410 cd23410 467788 beta-trefoil_Ricin_PLA2R1 ricin B-type lectin domain, beta-trefoil fold, found in secretory phospholipase A2 receptor (PLA2R1) and similar proteins. PLA2R1, also called PLA2-R, PLA2R, 180 kDa secretory phospholipase A2 receptor, C-type lectin domain family 13 member C (CLEC13C), or M-type receptor, is a receptor for secretory phospholipase A2 (sPLA2). It acts as a receptor for phospholipase sPLA2-IB/PLA2G1B but not sPLA2-IIA/PLA2G2A. It can also bind to snake PA2-like toxins. It may be involved in responses in proinflammatory cytokine production during endotoxic shock. It also has endocytic properties and rapidly internalizes sPLA2 ligands, which is particularly important for the clearance of extracellular sPLA2s to protect their potent enzymatic activities. PLA2R1 contains a ricin B-type lectin domain at the N-terminus. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. 118 matched cddid_all.tbl CDD cd23411 cd23411 467789 beta-trefoil_Ricin_LY75 ricin B-type lectin domain, beta-trefoil fold, found in lymphocyte antigen 75 (Ly-75) and similar proteins. Ly-75, also called C-type lectin domain family 13 member B, DEC-205, gp200-MR6, or CD205, acts as an endocytic receptor to direct captured antigens from the extracellular space to a specialized antigen-processing compartment. It causes reduced proliferation of B-lymphocytes. Ly-75 contains a ricin B-type lectin domain at the N-terminus. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. 116 matched cddid_all.tbl CDD cd23412 cd23412 467790 beta-trefoil_Ricin_unchar ricin B-type lectin domain, beta-trefoil fold, found in uncharacterized macrophage mannose receptor (MRC)-like proteins. The subfamily corresponds to a group of uncharacterized ricin B-type lectin beta-trefoil domain-containing proteins from Gnathostomata. They show high sequence similarity with macrophage mannose receptor (MRC) family proteins. 127 matched cddid_all.tbl CDD cd23413 cd23413 469575 beta-trefoil_Ricin_CdtC ricin B-type lectin domain, beta-trefoil fold, found in cytolethal distending toxin subunit C (CdtC) and similar proteins. Cytolethal distending toxins (CDTs) are cytotoxins which induce host cell distension, growth arrest in G2/M phase, nucleus swelling, and chromatin fragmentation in HeLa cells. CDT is a heterotrimer consisting of the three subunits, CdtA, CdtB, and CdtC. CdtA, along with CdtC, probably forms a heterodimeric subunit required for the delivery of nuclease CdtB. CdtC contains a ricin B-type lectin domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. The third beta strand is missing in CdtC. 148 matched cddid_all.tbl CDD cd23414 cd23414 469576 beta-trefoil_Ricin_CdtA ricin B-type lectin domain, beta-trefoil fold, found in cytolethal distending toxin subunit A (CdtA) and similar proteins. Cytolethal distending toxins (CDTs) are cytotoxins which induce host cell distension, growth arrest in G2/M phase, nucleus swelling, and chromatin fragmentation in HeLa cells. CDT is a heterotrimer consisting of the three subunits, CdtA, CdtB, and CdtC. CdtA, along with CdtC, probably forms a heterodimeric subunit required for the delivery of nuclease CdtB. CdtA contains a ricin B-type lectin domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. 147 matched cddid_all.tbl CDD cd23415 cd23415 467294 beta-trefoil_Ricin_AH ricin B-type lectin domain, beta-trefoil fold, found in Actinomycete actinohivin and similar proteins. Actinohivin is an actinomycete lectin with a potent specific anti-human immunodeficiency virus (anti-HIV) activity. It inhibits viral entry to cells by binding the high-mannose type sugar chains of gp120. Actinohivin contains a ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain contains a sugar-binding pocket. 120 matched cddid_all.tbl CDD cd23416 cd23416 467295 beta-trefoil_Ricin_MOA-like ricin B-type lectin domain, beta-trefoil fold, found in Marasmius oreades agglutinin (MOA) and similar proteins. The family includes Marasmius oreades agglutinin (MOA) and Polyporus squamosus Ricin B-related lectin (PSL). MOA is a lectin isolated from fruiting bodies of the mushroom M. oreades. It specifically binds non-reducing terminal Galalpha(1,3)Gal carbohydrates, such as that which occurs in the xenotransplantation epitope Galalpha(1,3)Galbeta(1,4)GlcNAc and the branched blood group B determinant Galalpha(1,3)[Fucalpha(1,2)]Gal. Polyporus squamosus Ricin B-related lectin (PSL) is a lectin specific for glycans terminating with the sequence Neu5Acalpha2-6Galbeta. Like MOA, PSL is a calcium-dependent cysteine protease. Both MOA and PSL contain an N-terminal ricin B-type lectin domain and a C-terminal agglutinin domain. The ricin B-type lectin domain is a beta-trefoil domain, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. 145 matched cddid_all.tbl CDD cd23417 cd23417 467296 beta-trefoil_Ricin_MytiLec-like ricin B-type lectin domain, beta-trefoil fold, found in Mytilus galloprovincialis lectin (MytiLec) and similar proteins. MytiLec is a D-galactose-binding lectin from the mussel Mytilus galloprovincialis with cytotoxicity against certain cancer cell types. It has hemagglutinating activity towards rabbit erythrocytes. It induces glycan-mediated cytotoxicity of human globotriaosylceramide-expressing lymphoma cells. The family also includes lectin from the mussel Mytilus californianus (MCL) and lectin from the sea mussel Crenomytilus grayanus (CGL). MCL is specific for binding D-galactose and N-Acetyl-d-galactosamine that contained carbohydrate moieties that were also inhibited by melibiose and raffinose. It can agglutinate all types of human erythrocytes, as well as rabbit red blood cells. CGL is specific for binding GalNAc/Gal-containing carbohydrate moieties. It displays antibacterial, antifungal, and antiviral activities. It also possesses anti-cancer activity through recognizing globotriose Gb3. Members of this family contain a ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. 132 matched cddid_all.tbl CDD cd23418 cd23418 467297 beta-trefoil_Ricin_XLN-like ricin B-type lectin domain, beta-trefoil fold, found in Streptomyces olivaceoviridis endo-1,4-beta-xylanase and similar proteins. The family includes Streptomyces olivaceoviridis endo-1,4-beta-xylanase (XLN, EC 3.2.1.8), Streptomyces avermitilis beta-L-arabinopyranosidase (EC 3.2.1.185), and Streptomyces coelicolor extracellular exo-alpha-L-arabinofuranosidase (ABF, EC 3.2.1.55). XLN, also called xylanase, or 1,4-beta-D-xylan xylanohydrolase, belongs to the glycosyl hydrolase 10 (cellulase F) family. It contributes to hydrolyze hemicellulose, the major component of plant cell walls. XLN contains a (beta/alpha)8-barrel as a catalytic domain, a family 13 carbohydrate binding module (CBM13) as a xylan binding domain (XBD) and a Gly/Pro-rich linker between them. Beta-L-arabinopyranosidase belongs to the glycosyl hydrolase 27 (GH27) family. It has a GH27 catalytic domain, an antiparallel beta-domain containing Greek key motifs, another antiparallel beta-domain forming a jellyroll structure, and a CBM13 module. ScAraf62A, also called ABF, or arabinosidase, or arabinoxylan arabinofuranohydrolase, belongs to the glycosyl hydrolase 62 (GH62) family. It is involved in the degradation of xylan and is a key enzyme in the complete degradation of the plant cell wall. It has a specific arabinofuranose-debranching activity on xylan from gramineae. It acts synergistically with xylanases and binds specifically to xylan. ScAraf62A comprises a CBM13 module at its N-terminus and a catalytic domain at its C-terminus. This model corresponds to the CBM13 module, which is a ricin B-type lectin domain with a beta-trefoil fold, characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may contain a potential sugar-binding pocket. 130 matched cddid_all.tbl CDD cd23419 cd23419 467298 beta-trefoil_Ricin_CELIII-like_rpt1 first ricin B-type lectin domain, beta-trefoil fold, found in Cucumaria echinata Ca2+-dependent hemolytic lectin CEL-III and similar proteins. CEL-III is a Ca2+-dependent and galactose-specific lectin that exhibits hemolytic and hemagglutinating activities. It functions as an oligomer that forms an ion-permeable pore in the cell membrane. CEL-III consists of three domains: two N-terminal ricin B-type lectin domains, and a C-terminal pore-forming domain. The ricin B-type lectin domains show a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (called alpha, beta, and gamma, respectively) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may contain a potential sugar-binding site. The model corresponds to the first ricin B-type lectin domain. 148 matched cddid_all.tbl CDD cd23420 cd23420 467299 beta-trefoil_Ricin_CELIII-like_rpt2 second ricin B-type lectin domain, beta-trefoil fold, found in Cucumaria echinata Ca2+-dependent hemolytic lectin CEL-III and similar proteins. CEL-III is a Ca2+-dependent and galactose-specific lectin that exhibits hemolytic and hemagglutinating activities. It functions as an oligomer that forms an ion-permeable pore in the cell membrane. CEL-III consists of three domains: two N-terminal ricin B-type lectin domains, and a C-terminal pore-forming domain. The ricin B-type lectin domains show a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (called alpha, beta, and gamma, respectively) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may contain a potential sugar-binding site. The model corresponds to the second ricin B-type lectin domain. 133 matched cddid_all.tbl CDD cd23422 cd23422 467300 beta-trefoil_Ricin_MPL_CNL ricin B-type lectin domain, beta-trefoil fold, found in Macrolepiota procera ricin B-like lectin (MPL), Clitocybe nebularis lectin (CNL), and similar proteins. MPL and CNL are a homodimeric ricin B-like lectins with a beta-trefoil fold that is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Their alpha subunit may harbor a sugar-binding pocket. MPL has the highest specificity for terminal N-acetyllactosamine and other beta-galactosides. CNL induces maturation and activation of dendritic cells via the toll-like receptor 4 pathway. It is specific for terminal, non-reducing N-acetylgalactosamine (Gal-NAc)-containing carbohydrates including N,N'-diacetyllactosediamine/LDN (GalNAcbeta1-4GlcNAc, LacdiNAc). It is also specific for carbohydrates containing N-acetylglucosamine (-GlcNAc) or N-acetyllactosamine (-Galbeta1-4GlcNAc) at the reducing end. 135 matched cddid_all.tbl CDD cd23423 cd23423 467301 beta-trefoil_Ricin_hemolysin "ricin B-type lectin domain, beta-trefoil fold, found in bacterial hemolysin and similar proteins. Bacterial hemolysins are exotoxins that attack blood cell membranes and cause cytolysis by forming heptameric pores in target host membranes. After binding to target membranes, the protein assembles into a heptameric pre-pore complex. Proteolytic cleavage triggers a conformation change that is required for membrane insertion and pore formation. Hemolysin may be called ""cytolysin"" or ""cytolytic toxin"", according to a specific action for certain cells. For example, this subfamily includes Vibrio vulnificus cytolysin that attack blood cell membranes and cause cell rupture, thereby liberating hemoglobins. Members of this subfamily contain a ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a putative sugar-binding pocket." 119 matched cddid_all.tbl CDD cd23424 cd23424 467302 beta-trefoil_Ricin_BEL-like ricin B-type lectin domain, beta-trefoil fold, found in Boletus edulis lectin (BEL), Laetiporus sulphureus lectin (LSL) and similar proteins. BEL has potent anti-proliferative effects on human cancer cells. It functions as a homodimer and each protomer folds as a beta-trefoil. The BEL beta-trefoil binds galactose and other galactose-containing carbohydrates. LSL is a lectin that exhibits hemolytic and hemagglutinating activities. It functions as a hexamer. Its monomeric protein consists of two distinct modules: an N-terminal beta-trefoil lectin module (LSL150) and a C-terminal membrane pore-forming module (PFM). All members of this subfamily contain a ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (called alpha, beta, and gamma, respectively) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may contain a potential sugar-binding site. Due to the lack of an aromatic residue, the sugar binding within alpha-site of LSL150 might be absent. 144 matched cddid_all.tbl CDD cd23425 cd23425 467303 beta-trefoil_Ricin_AglA ricin B-type lectin domain, beta-trefoil fold, found in alpha-galactosidase A (AglA) and similar proteins. AglA (EC 3.2.1.22), also called melibiase A, hydrolyzes a variety of simple alpha-D-galactosides as well as more complex molecules such as oligosaccharides and polysaccharides. It belongs to the glycosyl hydrolase 27 (GH27) family. AglA contains an N-terminal GH27 catalytic domain, an alpha galactosidase C-terminal beta sandwich domain in the middle region, and a carbohydrate-binding domain at the C-terminus. The carbohydrate-binding domain is also known as a ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may contain a potential sugar-binding pocket. 116 matched cddid_all.tbl CDD cd23426 cd23426 467304 beta-trefoil_Ricin_SSA ricin B-type lectin domain, beta-trefoil fold, found in Sclerotinia sclerotiorum agglutinin (SSA) and similar proteins. SSA acts as a lectin that primarily recognizes glycans with a non-reducing terminal N-acetylgalactosamine (GalNAc), with a preference for the alpha-over the beta-anomer. It can also bind non-reducing terminal galactose (Gal) residues but with a lower affinity. SSA strongly interacts with glycolipid type glycans with terminal non-reducing Gal or GalNAc but fails to bind sialylated or fucosylated forms of the same glycans. It also strongly interacts with galactosylated N-glycans, displaying highest affinity for alpha-1-3 branched mono-antennary N-glycans but also binding to multi-antennary glycans. SSA is a homodimeric protein. The monomer contains a ricin B-type lectin domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a putative sugar-binding pocket. 147 matched cddid_all.tbl CDD cd23427 cd23427 467305 beta-trefoil_Ricin_DCDC1 ricin B-type lectin domain, beta-trefoil fold, found in doublecortin domain-containing protein 1 (DCDC1) and similar proteins. DCDC1, also called doublecortin domain-containing 5 protein (DCDC5), is a microtubule-binding protein which plays an important role in mediating dynein-dependent transport of RAB8A-positive vesicles to the midbody during cytokinesis. In addition to doublecortin-like domains, DCDC1 may also contain a ricin B-type lectin domain in the middle region. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a putative sugar-binding pocket. 146 matched cddid_all.tbl CDD cd23428 cd23428 467306 beta-trefoil_Ricin_SPI ricin B-type lectin domain, beta-trefoil fold, found in Coprinopsis cinerea serine protease inhibitor 1 (PIC1) and similar proteins. PIC1, also called cospin, is a serine protease inhibitor that is active against beta-trypsin and alpha-chymotrypsin. This subfamily also includes Lentinula edodes serine protease inhibitor. In addition to beta-trypsin and alpha-chymotrypsin, it inhibits factor XIa, but not other enzymes involved in coagulation and fibrinolysis. It does not inhibit subtilisin, lysyl endopeptidase, arginyl endopeptidase or papain. Members of this family contain a ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a putative sugar-binding pocket. Protease inhibitors with the beta-trefoil fold may utilize their loops in various ways for the inhibition of serine proteases. 139 matched cddid_all.tbl CDD cd23429 cd23429 467307 beta-trefoil_Ricin_BinAB ricin B-type lectin domain, beta-trefoil fold, found in Lysinibacillus sphaericus BinA, BinB, and similar proteins. This subfamily includes Lysinibacillus sphaericus binary larvicide subunit BinA (also called 41.9 kDa insecticidal toxin, or larvicidal toxin protein P42) and subunit BinB (including 51.4 kDa insecticidal toxin and 63 kDa toxin crystal protein). They are components of a binary toxin active against Culex and some Aedes mosquito larvae. The individual subunits are not toxic. BinA forms a heterodimer with BinB. BinAB binds to the gastric caecum and posterior midgut of C. quinquefasciatus larvae. Binary toxin internalization into host gut cells requires both proteins. Both BinA and BinB have an N-terminal ricin B-type lectin domain and a C-terminal pore-forming domain. The ricin B-type lectin domain shows a beta-trefoil fold that has barrel and cap subdomains. The cap has 3 carbohydrate-binding modules while the barrel is involved in host cell receptor binding. At neutral pH, the carbohydrate-binding modules are accessible on the toxin surface, but the barrel subdomain is not. 167 matched cddid_all.tbl CDD cd23430 cd23430 467308 beta-trefoil_Ricin_CRYBG ricin B-type lectin domain, beta-trefoil fold, found in the beta/gamma crystallin domain-containing protein (CRYBG) family. The CRYBG family includes three members: CRYBG1, CRYBG2, and CRYBG3/vlAKAP. CRYBG1, also called absent in melanoma 1 protein (AIM1), may function as a suppressor of malignant melanoma. It may exert its effects through interactions with the cytoskeleton. CRYBG2 is also called absent in melanoma 1-like protein (AIM1L). CRYBG3/vlAKAP, also called very large A-kinase anchor protein, is an anchoring protein that mediates the subcellular compartmentation of protein kinase A (PKA). It binds to the dimeric RII-alpha regulatory subunit of PKA (PRKAR2A/PRKAR2B). CRYBG proteins belong to the beta/gamma-crystallin family. They all contain a ricin B-type lectin domain with a beta-trefoil fold at the C-terminus. The beta-trefoil fold is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. 133 matched cddid_all.tbl CDD cd23431 cd23431 467309 beta-trefoil_Ricin_AtEULS3-like ricin B-type lectin domain, beta-trefoil fold, found in Arabidopsis thaliana Ricin B-like lectin EULS3 (AtEULS3) and similar proteins. AtEULS3, also called euonymus lectin S3, is a Ricin B-like lectin that binds carbohydrates in vitro. It interacts through its lectin domain with glycan structures containing one or more Lewis X, Lewis Y or lactosamine motifs. It has been implicated in abiotic stress responses, abscisic acid-induced stomatal closure, as well as disease resistance against Pseudomonas syringae through its involvement in stomatal movement. All subfamily members contain a ricin B-type lectin domain at the C-terminus. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. 152 matched cddid_all.tbl CDD cd23432 cd23432 467310 beta-trefoil_Ricin_EndoBetaGal-like ricin B-type lectin domain, beta-trefoil fold, found in Clostridium perfringens GlcNac-alpha-1,4-Gal-releasing endo-beta-galactosidase (Endo-beta-Gal(GnGa)) and similar proteins. Endo-beta-Gal(GnGa) can release disaccharide GlcNAc-alpha-1,4Gal from O-glycans expressed in the gastric gland mucous cell-type mucin. It contains a C-terminal ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. 127 matched cddid_all.tbl CDD cd23433 cd23433 467311 beta-trefoil_Ricin_GALNT1-like ricin B-type lectin domain, beta-trefoil fold, found in the polypeptide N-acetylgalactosaminyltransferase 1 (GALNT1)-like subfamily. The GALNT1-like subfamily includes GALNT1 and GALNT13. They catalyze the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. GALNT1 has a broad spectrum of substrates for peptides such as EA2, Muc5AC, Muc1a, Muc1b and Muc7. GALNT13 has a much stronger activity than GALNT1 to transfer GalNAc to mucin peptides, such as Muc5Ac and Muc7. It can glycosylate SDC3. It may be responsible for the synthesis of Tn antigen in neuronal cells. Members of this subfamily comprise a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 127 matched cddid_all.tbl CDD cd23434 cd23434 467312 beta-trefoil_Ricin_GALNT2 ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase 2 (GALNT2) and similar proteins. GALNT2 (EC 2.4.1.41), also called polypeptide GalNAc transferase 2, GalNAc-T2, pp-GaNTase 2, protein-UDP acetylgalactosaminyltransferase 2, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 2, catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. GALNT2 has a broad spectrum of substrates for peptides such as EA2, Muc5AC, Muc1a, Muc1b. It is probably involved in O-linked glycosylation of the immunoglobulin A1 (IgA1) hinge region. It is also involved in O-linked glycosylation of APOC-III, ANGPTL3 and PLTP. It participates in the regulation of HDL-C metabolism. GALNT2 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 121 matched cddid_all.tbl CDD cd23435 cd23435 467313 beta-trefoil_Ricin_GALNT3-like ricin B-type lectin domain, beta-trefoil fold, found in the polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3)-like subfamily. The GALNT3-like subfamily includes GALNT3, GALNT4, GALNT6 and GALNT12. They act as GalNAc transferases (EC 2.4.1.41) that catalyze the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. GALNT3 has activity toward HIV envelope glycoprotein gp120, EA2, Muc2 and Muc5. It probably glycosylates fibronectin in vivo as well as FGF23. It plays a central role in phosphate homeostasis. GALNT4 shows highest activity towards Muc7, EA2 and Muc2, with a lower activity compared to GALNT2. It glycosylates 'Thr-57' of SELPLG. GALNT6 may participate in the synthesis of oncofetal fibronectin. It has activity toward Muc1a, Muc2, EA2 and fibronectin peptides. GALNT12 has activity toward non-glycosylated peptides such as Muc5AC, Muc1a and EA2, and no detectable activity with non-glycosylated Muc2 and Muc7. It displays enzymatic activity toward the Gal-NAc-Muc5AC glycopeptide, but no detectable activity to mono-GalNAc-glycosylated Muc1a, Muc2, Muc7 and EA2. It may play an important role in the initial step of mucin-type oligosaccharide biosynthesis in digestive organs. Members of this family comprise a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 128 matched cddid_all.tbl CDD cd23436 cd23436 467314 beta-trefoil_Ricin_GALNT5 ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase 5 (GALNT5) and similar proteins. GALNT5 (EC 2.4.1.41), also called polypeptide GalNAc transferase 5, GalNAc-T5, pp-GaNTase 5, protein-UDP acetylgalactosaminyltransferase 5, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 5, catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. GALNT5 has activity toward EA2 peptide substrate but has a weak activity toward Muc2 or Muc1b substrates. GALNT5 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 132 matched cddid_all.tbl CDD cd23437 cd23437 467315 beta-trefoil_Ricin_GALNT7 ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase 7 (GALNT7) and similar proteins. GALNT7 (EC 2.4.1.41), also called polypeptide GalNAc transferase 7, GalNAc-T7, pp-GaNTase 7, protein-UDP acetylgalactosaminyltransferase 7, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 7, acts as glycopeptide transferase involved in O-linked oligosaccharide biosynthesis, which catalyzes the transfer of an N-acetyl-D-galactosamine residue to an already glycosylated peptide. In contrast to other proteins of the family, it does not act as a peptide transferase that transfers GalNAc onto serine or threonine residue on the protein receptor, but instead requires the prior addition of a GalNAc on a peptide before adding additional GalNAc moieties. Its appropriate peptide substrate remains unidentified. GALNT7 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 124 matched cddid_all.tbl CDD cd23438 cd23438 467316 beta-trefoil_Ricin_GALNT8-like ricin B-type lectin domain, beta-trefoil fold, found in the polypeptide N-acetylgalactosaminyltransferase 8 (GALNT8)-like subfamily. The GALNT8-like subfamily includes GALNT8, GALNT9, GALNT17 and GALNT18. They act as GalNAc transferases (EC 2.4.1.41) that catalyze the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. GALNT9 does not glycosylate apomucin or SDC3. Members of this family comprise a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 134 matched cddid_all.tbl CDD cd23439 cd23439 467317 beta-trefoil_Ricin_GALNT10-like ricin B-type lectin domain, beta-trefoil fold, found in the polypeptide N-acetylgalactosaminyltransferase 10 (GALNT10)-like subfamily. The GALNT10-like subfamily includes GALNT10 and GALNTL6. They act as GalNAc transferases (EC 2.4.1.41) that catalyze the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. GALNT10 has activity toward Muc5Ac and EA2 peptide substrates. Members of this subfamily comprise a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 126 matched cddid_all.tbl CDD cd23440 cd23440 467318 beta-trefoil_Ricin_GALNT11 ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase 11 (GALNT11) and similar proteins. GALNT11 (EC 2.4.1.41), also called polypeptide GalNAc transferase 11, GalNAc-T11, pp-GaNTase 11, protein-UDP acetylgalactosaminyltransferase 11, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 11, catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. It is involved in left/right asymmetry by mediating O-glycosylation of NOTCH1. O-glycosylation of NOTCH1 promotes its activation, modulating the balance between motile and immotile (sensory) cilia at the left-right organizer (LRO). GALNT11 displays the same enzyme activity toward MUC1, MUC4, and EA2 as GALNT1. It is not involved in glycosylation of erythropoietin (EPO). GALNT11 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 127 matched cddid_all.tbl CDD cd23441 cd23441 467319 beta-trefoil_Ricin_GALNT14-like ricin B-type lectin domain, beta-trefoil fold, found in the polypeptide N-acetylgalactosaminyltransferase 14 (GALNT14)-like subfamily. The GALNT14-like subfamily includes GALNT14 and GALNT16. They act as GalNAc transferases (EC 2.4.1.41) that catalyze the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. GALNT14 displays activity toward mucin-derived peptide substrates such as Muc2, Muc5AC, Muc7, and Muc13 (-58). It may be involved in O-glycosylation in the kidney. Members of this subfamily comprise a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 122 matched cddid_all.tbl CDD cd23442 cd23442 467320 beta-trefoil_Ricin_GALNT15 ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase 15 (GALNT15) and similar proteins. GALNT15 (EC 2.4.1.41), also called polypeptide GalNAc transferase 15, GalNAc-T15, polypeptide GalNAc transferase-like protein 2, GalNAc-T-like protein 2, pp-GaNTase-like protein 2, polypeptide N-acetylgalactosaminyltransferase-like protein 2, protein-UDP acetylgalactosaminyltransferase-like protein 2, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-like protein 2, catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Although it displays a much weaker activity toward all substrates tested compared to GALNT2, GALNT15 can transfer up to seven GalNAc residues to the Muc5AC peptide, suggesting that it can fill vicinal Thr/Ser residues in cooperation with other GALNT proteins. It prefers Muc1a as its substrate. GALNT15 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 124 matched cddid_all.tbl CDD cd23443 cd23443 467321 beta-trefoil_Ricin_RIPs_II_rpt1 first ricin B-type lectin domain, beta-trefoil fold, found in type II ribosome-inactivating proteins (RIPs). Type II ribosome-inactivating proteins (RIPs) inhibit translation in eukaryotes by irreversibly inactivating the 28S rRNA and preventing the binding of elongation factor II to the ribosome. They consist of a catalytic A-chain which has rRNA N-glycosidase activity and a lectin B-chain containing two ricin B-type lectin domains with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The lectin chain facilitates the internalization of the catalytic chain on binding to the cell surface. The two chains are connected by a disulfide bridge. This model corresponds to the first ricin B-type lectin domain. Members of this subfamily includes Ricinus communis ricin, bitter gourd (Momordica charantia) seed lectin (BGSL), snake gourd (Trichosanthes anguina) seed lectin (SGSL), Sambucus ebulus ebulin I, Sambucus nigra nigrin b (also known as agglutinin V or SNAV), SNAI (also known as agglutinin I), SNAI' and SNAIf, Abrus precatorius abrin (ABR) and agglutinin-I (AAG), and Viscum album beta-galactoside-specific lectins 1-4 (also known as mistletoe lectins or MLs). 123 matched cddid_all.tbl CDD cd23444 cd23444 467322 beta-trefoil_Ricin_RIPs_II_rpt2 second ricin B-type lectin domain, beta-trefoil fold, found in type II ribosome-inactivating proteins (RIPs). Type II ribosome-inactivating proteins (RIPs) inhibit translation in eukaryotes by irreversibly inactivating the 28S rRNA and preventing the binding of elongation factor II to the ribosome. They consist of a catalytic A-chain which has rRNA N-glycosidase activity and a lectin B-chain containing two ricin B-type lectin domains with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The lectin chain facilitates the internalization of the catalytic chain on binding to the cell surface. The two chains are connected by a disulfide bridge. This model corresponds to the second ricin B-type lectin domain. Members of this family includes Ricinus communis ricin, bitter gourd (Momordica charantia) seed lectin (BGSL), snake gourd (Trichosanthes anguina) seed lectin (SGSL), Sambucus ebulus ebulin I, Sambucus nigra nigrin b (also known as agglutinin V or SNAV), SNAI (also known as agglutinin I), SNAI' and SNAIf, Abrus precatorius abrin (ABR) and agglutinin-I (AAG), and Viscum album beta-galactoside-specific lectins 1-4 (also known as mistletoe lectins or MLs). 122 matched cddid_all.tbl CDD cd23445 cd23445 467323 beta-trefoil_Ricin_HA17-like ricin B-type lectin domain, beta-trefoil fold, found in Clostridium botulinum hemagglutinating proteins, HA17 and HA33, and similar proteins. The subfamily includes Clostridium botulinum hemagglutinating proteins HA17 and HA33, Lysinibacillus sphaericus mosquitocidal toxin (MTX) and Pieris brassicae pierisin. The hemagglutinin (HA) component of the progenitor toxin protects the structural integrity of the neurotoxin. It may increase internalization of the neurotoxin into the bloodstream of the host. The hemagglutinin complex, composed of HA-70 (also known as HA3), HA-33 (also known as HA1) and HA-17 (also known as HA2), agglutinates erythrocytes, whereas the individual components do not. HA-33 is involved in recognition of cell-surface carbohydrates. HA-17 and HA-70 are involved in paracellular barrier disruption by E-cadherin binding. MTX acts as an ADP-ribosyl transferase. Pierisin, also called NAD--DNA ADP-ribosyltransferase, pierisin-2, or pierisin-B, catalyzes the ADP ribosylation of double-stranded DNA by targeting the N2 amino group of dG residues. It induces apoptosis in a range of human cell lines. Members of this subfamily contain at least one ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 133 matched cddid_all.tbl CDD cd23446 cd23446 467324 beta-trefoil_Ricin_1,3Gal43A ricin B-type lectin domain, beta-trefoil fold, found in Clostridium thermocellum 1,3Gal43A and similar proteins. 1,3Gal43A is an exo-beta-1,3-galactanase that specifically hydrolyses beta-1,3 glycosidic bonds in galactose-based oligosaccharides or polysaccharides, and shows maximum activity towards beta-1,3-galactotetraose. 1,3Gal43A consists of a glycoside hydrolase family 43 (GH43) catalytic domain, a CBM13 carbohydrate binding domain, and a type I dockerin domain. The CBM13 domain is also known as the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site. 137 matched cddid_all.tbl CDD cd23447 cd23447 467325 beta-trefoil_Ricin_AUDH ricin B-type lectin domain, beta-trefoil fold, found in Phanerodontia chrysosporium bifunctional aldos-2-ulose dehydratase/isomerase (AUDH) and similar proteins. AUDH participates in carbohydrate secondary metabolism, catalyzing the conversion of glucosone and 1,5-d-anhydrofructose to the secondary metabolites cortalcerone and microthecin, respectively. It is a homodimeric protein that consists of a seven-bladed beta-propeller domain, two cupin folds and a C-terminal ricin B-type lectin domain. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site. 139 matched cddid_all.tbl CDD cd23448 cd23448 467326 beta-trefoil_Ricin_Cry35Ab1 ricin B-type lectin domain, beta-trefoil fold, found in Bacillus thuringiensis Cry35Ab1 and similar proteins. Cry35Ab1 is an insecticidal protein belonging to the toxin_10 family (Pfam05431) that includes other insecticidal proteins such as the binary toxin BinA/BinB. It acts together with Cry34Ab1 to control corn rootworms. Cry35Ab1 contains a ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site. 133 matched cddid_all.tbl CDD cd23449 cd23449 467327 beta-trefoil_Ricin_EW29-like ricin B-type lectin domain, beta-trefoil fold, found in Lumbricus terrestris 29-kDa galactose-binding lectin (EW29) and similar proteins. EW29 is a galactose-binding lectin from the earthworm Lumbricus terrestris. It contains two ricin B-type lectin domains with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The second ricin B-type lectin domain may harbor two sugar-binding pockets in subdomains alpha and gamma. EW29 uses these two sugar-binding sites for its function as a single domain-type hemagglutinin. 128 matched cddid_all.tbl CDD cd23450 cd23450 467328 beta-trefoil_Ricin_EntTref ricin B-type lectin domain, beta-trefoil fold, found in Entamoeba histolytica lectin (EntTref) and similar proteins. EntTref is a ricin B-like lectin with a beta-trefoil fold that is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Only its alpha subdomain harbors a sugar-binding pocket. Its beta and gamma subdomains lack the carbohydrate-binding ability because of the absence of stacking interactions and other residues forming specific hydrogen bonds with the sugar atoms as in the alpha subdomain. EntTref binds to rhamnose, galactose and galactose-linked sugars. 125 matched cddid_all.tbl CDD cd23451 cd23451 467329 beta-trefoil_Ricin_laminarinase ricin B-type lectin domain, beta-trefoil fold, found in glucan endo-1,3-beta-glucosidase and similar proteins. Glucan endo-1,3-beta-glucosidase (EC 3.2.1.39), also called (1->3)-beta-glucan endohydrolase, or (1->3)-beta-glucanase, or laminarinase, belongs to the glycosyl hydrolase 64 (GH64) family. It catalyzes hydrolysis of (1->3)-beta-D-glucosidic linkages in (1->3)-beta-D-glucans. It has been implicated in the defense against fungal pathogens. Glucan endo-1,3-beta-glucosidase contains a C-terminal ricin B-type lectin domain with a beta-trefoil fold, characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site. 125 matched cddid_all.tbl CDD cd23452 cd23452 467330 beta-trefoil_Ricin_RPI ricin B-type lectin domain, beta-trefoil fold, found in Rarobacter faecitabidus serine protease I (RPI) and similar proteins. RPI, also called serine protease 1, is a major serine protease exhibiting lytic activity toward living yeast cells. It has a lectin-like affinity for mannose. Mannoproteins may be the native substrate for RPI. RPI contains a C-terminal ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site. 125 matched cddid_all.tbl CDD cd23453 cd23453 467331 beta-trefoil_Ricin_VPS13D ricin B-type lectin domain, beta-trefoil fold, found in vacuolar protein sorting-associated protein 13D (VPS13D) and similar proteins. VPS13D is a ubiquitin-binding protein that is required for the regulation of mitochondrial size and clearance. It promotes mitochondrial clearance by mitochondrial autophagy (mitophagy), also possibly by positively regulating mitochondrial fission. Mitophagy plays an important role in regulating cell health and mitochondrial size and homeostasis. Mutations in VPS13D lead to a new recessive ataxia with spasticity and mitochondrial defects. VPS13D contains a ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site. 159 matched cddid_all.tbl CDD cd23454 cd23454 467332 beta-trefoil_Ricin_GllA-1 GllA-1 domain, beta-trefoil fold, found in Mucor circinelloides Gellins and similar proteins. Gellin proteins act as central effectors of wound-induced protoplasmic gelation. They possess ten related N-terminal beta-trefoil domains (Gll-1 to Gll-10) that contribute to distinct gelation-related activities. The beta-trefoil domains show low sequence similarity to members of the functionally diverse ricin B lectin domain family. They are characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site. Gellin from M. circinelloides has been called GellinA (also known as GllA). The model corresponds to GllA-1 domain, which is a remote family member of the ricin B-type lectin domain. 136 matched cddid_all.tbl CDD cd23455 cd23455 467333 beta-trefoil_Ricin_RSA ricin B-type lectin domain, beta-trefoil fold, found in Rhizoctonia solani agglutinin (RSA) and similar proteins. RSA is a 15.5-kDa lectin accumulated in the mycelium and sclerotia of the soil born plant pathogenic fungus R. solani. It may act as a storage protein implicated in fungal insecticidal activity. It displays high selectivity towards terminal non-reducing N-acetylgalactosamine residues. RSA reveals a domain-swapping dimeric assembly. Each monomer contains a ricin B-type lectin domain that adopts a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site. 131 matched cddid_all.tbl CDD cd23456 cd23456 467334 beta-trefoil_Ricin_SCDase ricin B-type lectin domain, beta-trefoil fold, found in Shewanella algae sphingolipid ceramide N-deacylase (SCDase) and similar proteins. SCDase (EC 3.5.1.69) is an enzyme which hydrolyzes the N-acyl linkage between fatty acid and sphingosine in ceramide of various glycosphingolipids and sphingomyelin. Shewanella algae SCDase contains two ricin B-type lectin domains at its C-terminus. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. 122 matched cddid_all.tbl CDD cd23457 cd23457 467335 beta-trefoil_Ricin_SaAF-like ricin B-type lectin domain, beta-trefoil fold, found in Stigmatella aurantiaca alpha-L-arabinofuranosidase (SaAF) and similar proteins. Alpha-L-arabinofuranosidase (EC 3.2.1.55), also called non-reducing end alpha-L-arabinofuranosidase, or arabinosidase, catalyzes the hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides. It acts on alpha-L-arabinofuranosides, alpha-L-arabinans containing (1,3)- and/or (1,5)-linkages, arabinoxylans and arabinogalactans. Members of this subfamily contain a ricin B-type lectin domain that adopts a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site. 139 matched cddid_all.tbl CDD cd23458 cd23458 467336 beta-trefoil_Ricin_AgaB34-like ricin B-type lectin domain, beta-trefoil fold, found in Agarivorans albus beta-agarase AgaB34 and similar proteins. Beta-agarase (EC 3.2.1.81), also called endo-beta-agarase, is a glycosyl hydrolase family 16 (GH16) member that catalyzes the hydrolysis of (1->4)-beta-D-galactosidic linkages in agarose, a hydrophilic polysaccharide found in the cell wall of Rhodophyceaea (marine red algae), giving the tetramer as the predominant product. Beta-agarase contains a ricin B-type lectin domain that adopts a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site. 135 matched cddid_all.tbl CDD cd23459 cd23459 467337 beta-trefoil_Ricin_Pgant1-like ricin B-type lectin domain, beta-trefoil fold, found in Drosophila melanogaster polypeptide N-acetylgalactosaminyltransferase 1 (Pgant1) and similar proteins. Pgant1, also called pp-GaNTase 1, protein-UDP acetylgalactosaminyltransferase 1, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 1, functions as a GalNAc transferase (EC 2.4.1.41) that catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Pgant1 can both act as a peptide transferase that transfers GalNAc onto unmodified peptide substrates, and as a glycopeptide transferase that requires the prior addition of a GalNAc on a peptide before adding additional GalNAc moieties. It prefers the monoglycosylated Muc5AC-3 as a substrate. Members of this subfamily contain a ricin B-type lectin domain at the C-terminus. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site. 132 matched cddid_all.tbl CDD cd23460 cd23460 467338 beta-trefoil_Ricin_Pgant3-like ricin B-type lectin domain, beta-trefoil fold, found in Drosophila melanogaster polypeptide N-acetylgalactosaminyltransferase 3 (Pgant3) and similar proteins. Pgant3, also called pp-GaNTase 3, protein-UDP acetylgalactosaminyltransferase 3, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 3, functions as a GalNAc transferase (EC 2.4.1.41) that catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Pgant3 can both act as a peptide transferase that transfers GalNAc onto unmodified peptide substrates, and as a glycopeptide transferase that requires the prior addition of a GalNAc on a peptide before adding additional GalNAc moieties. It prefers EA2 as a substrate and has weak activity toward Muc5AC-3, -13 and -3/13 substrates. Pgant3 plays a critical role in the regulation of integrin-mediated cell adhesion during wing development by influencing, via glycosylation, the secretion and localization of the integrin ligand Tig to the basal cell layer interface. It may have a role in protein O-glycosylation in the Golgi and thereby in establishing and/or maintaining a proper secretory apparatus structure. Together with Pgant35A, Pgant3 regulates integrin levels and activity-dependent integrin signaling at the synapse in neurons and muscles. Members of this subfamily contain a ricin B-type lectin domain at the C-terminus. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site. 121 matched cddid_all.tbl CDD cd23461 cd23461 467339 beta-trefoil_Ricin_Pgant8-like ricin B-type lectin domain, beta-trefoil fold, found in Drosophila melanogaster polypeptide N-acetylgalactosaminyltransferase 8 (Pgant8) and similar proteins. This subfamily includes Pgant8 (also called pp-GaNTase 8, protein-UDP acetylgalactosaminyltransferase 8, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 8), Pgant10 (also called polypeptide N-acetylgalactosaminyltransferase 10, pp-GaNTase 10, protein-UDP acetylgalactosaminyltransferase 10, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 10), Pgant11 (also called polypeptide N-acetylgalactosaminyltransferase 11, pp-GaNTase 11, protein-UDP acetylgalactosaminyltransferase 11, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 11) and Pgant12 (also called polypeptide N-acetylgalactosaminyltransferase 12, pp-GaNTase 12, protein-UDP acetylgalactosaminyltransferase 12, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 12). They function as GalNAc transferases (EC 2.4.1.41) that catalyze the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Pgant8 can both act as a peptide transferase that transfers GalNAc onto unmodified peptide substrates, and as a glycopeptide transferase that requires the prior addition of a GalNAc on a peptide before adding additional GalNAc moieties. It prefers both EA2 and the diglycosylated Muc5AC-3/13 as substrates, albeit at very low levels for Muc5AC-3/13. Members of this subfamily contain a ricin B-type lectin domain at the C-terminus. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site. 128 matched cddid_all.tbl CDD cd23462 cd23462 467340 beta-trefoil_Ricin_Pgant9-like ricin B-type lectin domain, beta-trefoil fold, found in Drosophila melanogaster polypeptide N-acetylgalactosaminyltransferase 9 (Pgant9) and similar proteins. The subfamily includes Pgant9 (also called pp-GaNTase 9, protein-UDP acetylgalactosaminyltransferase 9, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 9), Pgant4 (also called pp-GaNTase 4, N-acetylgalactosaminyltransferase 4, protein-UDP acetylgalactosaminyltransferase 4, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 4) and Pgant6 (also called pp-GaNTase 6, N-acetylgalactosaminyltransferase 6, protein-UDP acetylgalactosaminyltransferase 6, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 6). They function as GalNAc transferases (EC 2.4.1.41) that catalyze the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. Pgant9 can both act as a peptide transferase that transfers GalNAc onto unmodified peptide substrates, and as a glycopeptide transferase that requires the prior addition of a GalNAc on a peptide before adding additional GalNAc moieties. Pgant4 and Pgant6 do not act as a peptide transferase, but instead requires the prior addition of a GalNAc on a peptide before adding additional GalNAc moieties. They prefer the diglycosylated Muc5AC-3/13 as a substrate. Pgant6 may have a role in protein O-glycosylation in the Golgi and thereby in establishing and/or maintaining a proper secretory apparatus structure. Members of this subfamily contain a ricin B-type lectin domain at the C-terminus. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site. 126 matched cddid_all.tbl CDD cd23463 cd23463 467341 beta-trefoil_Ricin_vlAKAP ricin B-type lectin domain, beta-trefoil fold, found in very large A-kinase anchor protein (vlAKAP) and similar proteins. vlAKAP, also called beta/gamma crystallin domain-containing protein 3 (CRYBG3), is an anchoring protein that mediates the subcellular compartmentation of protein kinase A (PKA). It binds to the dimeric RII-alpha regulatory subunit of PKA (PRKAR2A/PRKAR2B). vlAKAP belongs to the beta/gamma-crystallin family. It contains a ricin B-type lectin domain at the C-terminus. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. 136 matched cddid_all.tbl CDD cd23464 cd23464 467342 beta-trefoil_Ricin_CRYBG1 ricin B-type lectin domain, beta-trefoil fold, found in beta/gamma crystallin domain-containing protein 1 (CRYBG1) and similar proteins. CRYBG1, also called absent in melanoma 1 protein (AIM1), may function as a suppressor of malignant melanoma. It may exert its effects through interactions with the cytoskeleton. CRYBG1 belongs to the beta/gamma-crystallin family. It contains a ricin B-type lectin domain at the C-terminus. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. 137 matched cddid_all.tbl CDD cd23465 cd23465 467343 beta-trefoil_Ricin_CRYBG2 ricin B-type lectin domain, beta-trefoil fold, found in beta/gamma crystallin domain-containing protein 2 (CRYBG2) and similar proteins. CRYBG2, also called absent in melanoma 1-like protein (AIM1L), is a beta/gamma-crystallin family protein with a ricin B-type lectin domain at the C-terminus. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. 136 matched cddid_all.tbl CDD cd23466 cd23466 467344 beta-trefoil_Ricin_GALNT1 ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase 1 (GALNT1) and similar proteins. GALNT1 (EC 2.4.1.41), also called polypeptide GalNAc transferase 1, GalNAc-T1, pp-GaNTase 1, protein-UDP acetylgalactosaminyltransferase 1, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 1, catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. It has a broad spectrum of substrates for peptides such as EA2, Muc5AC, Muc1a, Muc1b and Muc7. GALNT1 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain is required in the glycopeptide specificity of enzyme activity but not for activity with naked peptide substrates, suggesting that it triggers the catalytic domain to act on GalNAc-glycopeptide substrates. 127 matched cddid_all.tbl CDD cd23467 cd23467 467345 beta-trefoil_Ricin_GALNT13 ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase 13 (GALNT13) and similar proteins. GALNT13 (EC 2.4.1.41), also called polypeptide GalNAc transferase 13, GalNAc-T13, pp-GaNTase 13, protein-UDP acetylgalactosaminyltransferase 13, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 13, catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. It has a much stronger activity than GALNT1 to transfer GalNAc to mucin peptides, such as Muc5Ac and Muc7. It can glycosylate SDC3. It may be responsible for the synthesis of Tn antigen in neuronal cells. GALNT13 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). The model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 127 matched cddid_all.tbl CDD cd23468 cd23468 467346 beta-trefoil_Ricin_GALNT3 ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase 3 (GALNT3) and similar proteins. GALNT3 (EC 2.4.1.41), also called polypeptide GalNAc transferase 3, GalNAc-T3, pp-GaNTase 3, protein-UDP acetylgalactosaminyltransferase 3, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 3, catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. GALNT3 has activity toward HIV envelope glycoprotein gp120, EA2, Muc2 and Muc5. It probably glycosylates fibronectin in vivo as well as FGF23. It plays a central role in phosphate homeostasis. GALNT3 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 129 matched cddid_all.tbl CDD cd23469 cd23469 467347 beta-trefoil_Ricin_GALNT4 ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase 4 (GALNT4) and similar proteins. GALNT4 (EC 2.4.1.41), also called polypeptide GalNAc transferase 4, GalNAc-T4, pp-GaNTase 4, protein-UDP acetylgalactosaminyltransferase 4, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 4, catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. GALNT4 shows highest activity towards Muc7, EA2 and Muc2, with a lower activity compared to GALNT2. It glycosylates 'Thr-57' of SELPLG. GALNT4 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 136 matched cddid_all.tbl CDD cd23470 cd23470 467348 beta-trefoil_Ricin_GALNT6 ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase 6 (GALNT6) and similar proteins. GALNT6 (EC 2.4.1.41), also called polypeptide GalNAc transferase 6, GalNAc-T6, pp-GaNTase 6, protein-UDP acetylgalactosaminyltransferase 6, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 6, catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. GALNT6 may participate in the synthesis of oncofetal fibronectin. It has activity toward Muc1a, Muc2, EA2 and fibronectin peptides. GALNT6 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 128 matched cddid_all.tbl CDD cd23471 cd23471 467349 beta-trefoil_Ricin_GALNT12 ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase 12 (GALNT12) and similar proteins. GALNT12 (EC 2.4.1.41), also called polypeptide GalNAc transferase 12, GalNAc-T12, pp-GaNTase 12, protein-UDP acetylgalactosaminyltransferase 12, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 12, catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. GALNT12 has activity toward non-glycosylated peptides such as Muc5AC, Muc1a and EA2, and no detectable activity with non-glycosylated Muc2 and Muc7. It displays enzymatic activity toward the Gal-NAc-Muc5AC glycopeptide, but no detectable activity to mono-GalNAc-glycosylated Muc1a, Muc2, Muc7 and EA2. It may play an important role in the initial step of mucin-type oligosaccharide biosynthesis in digestive organs. GALNT12 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 140 matched cddid_all.tbl CDD cd23472 cd23472 467350 beta-trefoil_Ricin_GALNT8 ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase 8 (GALNT8) and similar proteins. GALNT8 (EC 2.4.1.41), also called polypeptide GalNAc transferase 8, GalNAc-T8, pp-GaNTase 8, protein-UDP acetylgalactosaminyltransferase 8, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 8, may catalyze the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. GALNT8 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 146 matched cddid_all.tbl CDD cd23473 cd23473 467351 beta-trefoil_Ricin_GALNT9 ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase 9 (GALNT9) and similar proteins. GALNT9 (EC 2.4.1.41), also called polypeptide GalNAc transferase 9, GalNAc-T9, pp-GaNTase 9, protein-UDP acetylgalactosaminyltransferase 9, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 9, catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. GALNT9 does not glycosylate apomucin or SDC3. GALNT9 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 145 matched cddid_all.tbl CDD cd23474 cd23474 467352 beta-trefoil_Ricin_GALNT17 ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase 17 (GALNT17) and similar proteins. GALNT17 (EC 2.4.1.41), also called polypeptide GalNAc transferase-like protein 3, GalNAc-T-like protein 3, pp-GaNTase-like protein 3, protein-UDP acetylgalactosaminyltransferase-like protein 3, UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-like protein 3, or Williams-Beuren syndrome chromosomal region 17 protein, may catalyze the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. GALNT17 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 142 matched cddid_all.tbl CDD cd23475 cd23475 467353 beta-trefoil_Ricin_GALNT18 ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase 18 (GALNT18) and similar proteins. GALNT18 (EC 2.4.1.41), also called polypeptide GalNAc transferase 18, GalNAc-T18, polypeptide GalNAc transferase-like protein 4, GalNAc-T-like protein 4, pp-GaNTase-like protein 4, polypeptide N-acetylgalactosaminyltransferase-like protein 4, protein-UDP acetylgalactosaminyltransferase-like protein 4, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-like protein 4, catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. GALNT18 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 142 matched cddid_all.tbl CDD cd23476 cd23476 467354 beta-trefoil_Ricin_GALNT10 ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase 10 (GALNT10) and similar proteins. GALNT10 (EC 2.4.1.41), also called polypeptide GalNAc transferase 10, GalNAc-T10, pp-GaNTase 10, protein-UDP acetylgalactosaminyltransferase 10, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 10, catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. GALNT10 has activity toward Muc5Ac and EA2 peptide substrates. GALNT10 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 150 matched cddid_all.tbl CDD cd23477 cd23477 467355 beta-trefoil_Ricin_GALNTL6 ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase-like 6 (GALNTL6) and similar proteins. GALNTL6 (EC 2.4.1.41), also called polypeptide GalNAc transferase 17, GalNAc-T17, pp-GaNTase 17, protein-UDP acetylgalactosaminyltransferase 17, putative polypeptide N-acetylgalactosaminyltransferase 17, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 17, catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. GALNTL6 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 148 matched cddid_all.tbl CDD cd23478 cd23478 467356 beta-trefoil_Ricin_GALNT14 ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase 14 (GALNT14) and similar proteins. GALNT14 (EC 2.4.1.41), also called polypeptide GalNAc transferase 14, GalNAc-T14, pp-GaNTase 14, protein-UDP acetylgalactosaminyltransferase 14, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 14, catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. GALNT14 displays activity toward mucin-derived peptide substrates such as Muc2, Muc5AC, Muc7, and Muc13 (-58). It may be involved in O-glycosylation in the kidney. GALNT14 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 140 matched cddid_all.tbl CDD cd23479 cd23479 467357 beta-trefoil_Ricin_GALNT16 ricin B-type lectin domain, beta-trefoil fold, found in polypeptide N-acetylgalactosaminyltransferase 16 (GALNT16) and similar proteins. GALNT16 (EC 2.4.1.41), also called polypeptide GalNAc transferase 16, GalNAc-T16, polypeptide GalNAc transferase-like protein 1, GalNAc-T-like protein 1, pp-GaNTase-like protein 1, polypeptide N-acetylgalactosaminyltransferase-like protein 1, protein-UDP acetylgalactosaminyltransferase-like protein 1, or UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase-like protein 1, catalyzes the initial reaction in O-linked oligosaccharide biosynthesis, the transfer of an N-acetyl-D-galactosamine residue to a serine or threonine residue on the protein receptor. GALNT16 comprises a glycosyltransferase region and a ricin B-type lectin domain. The glycosyltransferase region contains two conserved domains, domain A (also called GT1 motif) and domain B (also called Gal/GalNAc-T motif). This model corresponds to the ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The ricin B-type lectin domain binds to GalNAc and contributes to the glycopeptide specificity. 129 matched cddid_all.tbl CDD cd23480 cd23480 467358 beta-trefoil_Ricin-like_rpt1 first ricin B-type lectin domain, beta-trefoil fold, found in Ricinus communis ricin, agglutinin and similar proteins. This subfamily includes ricin and agglutinin (RCA), which are toxic lectins from Ricinus communis. Ricin is highly toxic to animal cells, and to a lesser extent to plant cells. As a prototype AB toxin, ricin is composed of two polypeptide chains (A- and B-chain) linked by a disulfide bond. Ricin A chain acts as an RNA N-glycosidase that removes a specific adenine residue from an exposed loop of the 28S rRNA (A4324 in mammals), leading to rRNA breakage. Ricin B functions as a lectin that mediates cell binding via different oligosaccharide residues on the cell surface, including N-acetylglucosamine and galactose residues found in glycolipids and glycoproteins. It is also responsible for cell agglutination. Agglutinin shows high sequence similarity with ricin. It is only a weak toxin but a strong hemagglutinin. By contrast, ricin is a potent toxin but a weak hemagglutinin. Like ricin, agglutinin consists of a sugar-binding B chain linked via a disulfide bond to the catalytically active A chain. The B chain of ricin and agglutinin contains two ricin B-type lectin domains with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. This model corresponds to the first ricin B-type lectin domain. 137 matched cddid_all.tbl CDD cd23481 cd23481 467359 beta-trefoil_Ricin_BGSL_rpt1 first ricin B-type lectin domain, beta-trefoil fold, found in bitter gourd (Momordica charantia) seed lectin (BGSL) and similar proteins. Type II ribosome-inactivating proteins (RIPs) inhibit translation in eukaryotes by irreversibly inactivating the 28S rRNA and preventing the binding of elongation factor II to the ribosome. BGSL is a non-toxic four-chain type II RIP resulting from covalent association through a disulfide bridge between two identical copies of a two-chain unit. The two-chain unit consists of a catalytic A-chain and a lectin B-chain. The catalytic A-chain cannot firmly bind adenine due to the substitution of an aromatic residue involved in ensuring the proper orientation of the base in toxic RIPs, by a glycyl residue. BGSL is a galactose-specific lectin containing two ricin B-type lectin domains in its B-chain. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. This model corresponds to the first ricin B-type lectin domain. In BGSL, sugar does not bind at the 2gamma site. Its 1alpha site binds sugar, which is similar to that in snake gourd (Trichosanthes anguina) seed lectin (SGSL). 132 matched cddid_all.tbl CDD cd23482 cd23482 467360 beta-trefoil_Ricin_SGSL_rpt1 first ricin B-type lectin domain, beta-trefoil fold, found in snake gourd (Trichosanthes anguina) seed lectin (SGSL) and similar proteins. Type II ribosome-inactivating proteins (RIPs) inhibit translation in eukaryotes by irreversibly inactivating the 28S rRNA and preventing the binding of elongation factor II to the ribosome. SGSL is a non-toxic three-chain type II RIP consisting of Aalpha, Abeta and B chains with Abeta and B being disulfide-linked. The Aalpha and Abeta chains constitute the rRNA glycosidase domain and the B chain contains two ricin B-type carbohydrate-binding lectin domains. SGSL may have no glycosidase activity due to small changes in both the nucleotide binding and carbohydrate binding capabilities. It binds galactose and derivatives with a preference for the beta-anomeric forms. It also binds prophyrins. SGSL has hemagglutinating activity towards rabbit and human erythrocytes. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. This model corresponds to the first ricin B-type lectin domain. 135 matched cddid_all.tbl CDD cd23483 cd23483 467361 beta-trefoil_Ricin_ebulin-like_rpt1 first ricin B-type lectin domain, beta-trefoil fold, found in Sambucus ebulus ebulin I and similar proteins. The family includes Sambucus ebulus ebulin I and Sambucus nigra nigrin b (also known as agglutinin V or SNAV), SNAI (also known as agglutinin I), SNAI' and SNAIf. Ebulin l is a type II ribosome-inactivating protein (RIP) isolated from the leaves of Sambucus ebulus. It is a disulfide-linked heterodimer composed of a toxic A chain and a galactoside-specific lectin B chain. It is considered a nontoxic type II RIP due to a reduced cytotoxicity on whole cells and animals as compared with other toxic type II RIP like ricins. Ebulin l binds an A-chain substrate analogue, pteroic acid. It binds bind galactose and lactose in subdomain 1alpha in a similar manner to that of ricin. In contrast, it binds only the monosaccharide galactose, and not the disaccharide lactose in subdomain 2gamma. SNAV is a non-toxic GalNAc-specific type II RIP which strongly inhibits mammalian protein synthesis but does not affect plant nor bacterial protein synthesis. SNAI is a Neu5Ac(alpha2-6)Gal/GalNAc-specific agglutinin. It also acts as a type II RIP that strongly inhibits mammalian but not plant ribosomes. SNAI' is another NeuAc(alpha2,6)Gal/GalNAc binding type II RIP from elderberry (Sambucus nigra) bark. It is a minor bark protein which closely resembles the major Neu5Ac(alpha2,6)Gal/GalNAc binding type II RIP, SNAI, with respect to its carbohydrate-binding specificity and ribosome-inactivating activity but has a different molecular structure due to a single cysteine residue present in the B chain of SNAI but absent from SNAI'. SNAIf is a fruit-specific SNAI. It functions as a fetuin-binding fruit lectin. Like Ebulin l, SNAV, SNAI, SNAI' and SNAIf consist of a sugar-binding B chain linked via a disulfide bond to the catalytically active A chain. The A chain is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA. The B chain binds to cell receptors and probably facilitates the entry into the cell of the A chain. It may also be responsible for cell agglutination (lectin activity). The B chain contains two ricin B-type lectin domains with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. This model corresponds to the first ricin B-type lectin domain. 127 matched cddid_all.tbl CDD cd23484 cd23484 467362 beta-trefoil_Ricin_abrin-like_rpt1 first ricin B-type lectin domain, beta-trefoil fold, found in Abrus precatorius abrin, agglutinin-I and similar proteins. This subfamily includes Abrus precatorius abrin (ABR) and agglutinin-I (AAG), which share a high degree of sequence similarity and belong to the type II ribosome-inactivating protein (RIP) family. Type II RIPs inhibit protein synthesis in eukaryotic cells and can also induce apoptosis. They are two-polypeptide proteins with a toxic A chain and a lectin-like B chain linked by a disulfide bond. The A chain of abrin and agglutinin-I is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA. Agglutinin-I is less toxic than abrin. The B chain is a galactose-specific lectin that facilitates the binding to the cell membrane that precedes endocytosis. The B-chain contains two ricin B-type lectin domains with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. This model corresponds to the first ricin B-type lectin domain. 137 matched cddid_all.tbl CDD cd23485 cd23485 467363 beta-trefoil_Ricin_MLs_rpt1 first ricin B-type lectin domain, beta-trefoil fold, found in Viscum album B chain of beta-galactoside-specific lectins and similar proteins. This subfamily includes Viscum album beta-galactoside-specific lectins 1-4 (also known as mistletoe lectins or MLs), which inhibit growth of the human tumor cell line Molt4. They contain A and B chains. The A chain is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA. The B chain binds to cell receptors and probably facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (lectin activity). The B chain contains two ricin B-type lectin domains with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. This model corresponds to the first ricin B-type lectin domain. 134 matched cddid_all.tbl CDD cd23486 cd23486 467364 beta-trefoil_Ricin_cinnamomin_rpt1 first ricin B-type lectin domain, beta-trefoil fold, found in Cinnamomum camphora type II ribosome-inactivating protein (RIP) cinnamomin and similar proteins. RIPs are a group of ribotoxins that inhibit mammalian protein biosynthesis by irreversible inactivation of their 60S ribosomal subunit. Type II RIPs in plant cells comprise part of the plant's defense system towards animals. Cinnamomin is a type II RIP isolated from Cinnamomum camphora seeds. It shows inhibitory effects on cultured carcinoma cells and on the larvae of bollworm and mosquito. There are three cinnamomin isoforms (I, II, III). They are composed of two polypeptide chains (A- and B-chain) linked by a disulfide bond. The A-chain displays specific activity as an RNA N-glycosidase that blocks protein synthesis, whereas the B-chain is responsible for the binding to galactose-terminated receptors on cell membranes. The B-chain contains two ricin B-type lectin domains with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. This model corresponds to the first ricin B-type lectin domain. 129 matched cddid_all.tbl CDD cd23487 cd23487 467365 beta-trefoil_Ricin_like_rpt2 second ricin B-type lectin domain, beta-trefoil fold, found in Ricinus communis ricin, agglutinin and similar proteins. This subfamily includes ricin and agglutinin (RCA), toxic lectins from Ricinus communis. Ricin is highly toxic to animal cells, and to a lesser extent to plant cells. As a prototype AB toxin, ricin is composed of two polypeptide chains (A- and B-chain) linked by a disulfide bond. Ricin A chain acts as an RNA N-glycosidase that removes a specific adenine residue from an exposed loop of the 28S rRNA (A4324 in mammals), leading to rRNA breakage. Ricin B chain functions as a lectin that mediates cell binding via different oligosaccharide residues on the cell surface, including N-acetylglucosamine and galactose residues found on glycolipids and glycoproteins. It is also responsible for cell agglutination. Agglutinin shows high sequence similarity with ricin. It is only a weak toxin but a strong hemagglutinin. By contrast, ricin is a potent toxin but a weak hemagglutinin. Like ricin, agglutinin consists of a sugar-binding B chain linked via a disulfide bond to the catalytically active A chain. The B-chain of ricin and agglutinin contains two ricin B-type lectin domains with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. This model corresponds to the second ricin B-type lectin domain. 124 matched cddid_all.tbl CDD cd23488 cd23488 467366 beta-trefoil_Ricin_BGSL_rpt2 second ricin B-type lectin domain, beta-trefoil fold, found in bitter gourd (Momordica charantia) seed lectin (BGSL) and similar proteins. Type II ribosome-inactivating proteins (RIPs) inhibit translation in eukaryotes by irreversibly inactivating the 28S rRNA and preventing the binding of elongation factor II to the ribosome. BGSL is a non-toxic four-chain type II RIPs resulting from covalent association through a disulfide bridge between two identical copies of a two-chain unit. The two-chain unit consists of a catalytic A-chain and a lectin B-chain. The catalytic A-chain cannot firmly bind adenine due to the substitution of an aromatic residue involved in ensuring the proper orientation of the base in toxic RIPs, by a glycyl residue. BGSL is a galactose-specific lectin containing two ricin B-type lectin domains in B-chain. The ricin B-type lectin domain shows beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the second ricin B-type lectin domain. In BGSL, sugar does not bind at the 2gamma site. Its 1alpha site binds sugar, which is similar to that in snake gourd (Trichosanthes anguina) seed lectin (SGSL). 126 matched cddid_all.tbl CDD cd23489 cd23489 467367 beta-trefoil_Ricin_SGSL_rpt2 second ricin B-type lectin domain, beta-trefoil fold, found in snake gourd (Trichosanthes anguina) seed lectin (SGSL) and similar proteins. Type II ribosome-inactivating proteins (RIPs) inhibit translation in eukaryotes by irreversibly inactivating the 28S rRNA and preventing the binding of elongation factor II to the ribosome. SGSL is a non-toxic three-chain type II RIPs consisting of Aalpha, Abeta and B chains with Abeta and B being disulfide-linked. The Aalpha and Abeta chains constitute the rRNA glycosidase domain and the B chain contains two ricin B-type carbohydrate-binding lectin domains. SGSL may have no glycosidase activity due to small changes in both the nucleotide binding and carbohydrate binding capabilities. It binds galactose and derivatives with a preference for the beta-anomeric forms. It also binds prophyrins. SGSL has hemagglutinating activity towards rabbit and human erythrocytes. The ricin B-type lectin domain shows beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the second ricin B-type lectin domain. 128 matched cddid_all.tbl CDD cd23490 cd23490 467368 beta-trefoil_Ricin_ebulin-like_rpt2 second ricin B-type lectin domain, beta-trefoil fold, found in Sambucus ebulus ebulin I and similar proteins. This subfamily includes Sambucus ebulus ebulin I and Sambucus nigra nigrin b (also known as agglutinin V or SNAV), SNAI (also known as agglutinin I), SNAI' and SNAIf. Ebulin l is a type II ribosome-inactivating protein (RIP) isolated from the leaves of Sambucus ebulus. It is a disulfide-linked heterodimer composed of a toxic A chain and a galactoside-specific lectin B chain. It is considered a nontoxic type II RIP due to a reduced cytotoxicity on whole cells and animals as compared with other toxic type II RIP like ricin. Ebulin l binds an A-chain substrate analogue, pteroic acid. It binds bind galactose and lactose in subdomain 1alpha in a similar manner to that of ricin. In contrast, it binds only the monosaccharide galactose, and not the disaccharide lactose in subdomain 2gamma. SNAV is a non-toxic GalNAc-specific type II RIP which strongly inhibits mammalian protein synthesis but does not affect plant nor bacterial protein synthesis. SNAI is Neu5Ac(alpha2-6)Gal/GalNAc specific agglutinin. It also acts as a type II RIP that strongly inhibits mammalian but not plant ribosomes. SNAI' is another NeuAc(alpha2,6)Gal/GalNAc binding type II RIP from elderberry (Sambucus nigra) bark. It is a minor bark protein which closely resembles the major Neu5Ac(alpha2,6)Gal/GalNAc binding type II RIP, SNAI, with respect to its carbohydrate-binding specificity and ribosome-inactivating activity but has a different molecular structure due to a single cysteine residue present in the B chain of SNAI but absent from SNAI'. SNAIf is fruit specific SNAI. It functions as fetuin-binding fruit lectin. Like Ebulin l, SNAV, SNAI, SNAI' and SNAIf consist of a sugar-binding B chain linked via a disulfide bond to the catalytically active A chain. The A chain is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA. The B chain binds to cell receptors and probably facilitates the entry into the cell of the A chain. It may also be responsible for cell agglutination (lectin activity). The B chain contains two ricin B-type lectin domains with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the second ricin B-type lectin domain. 125 matched cddid_all.tbl CDD cd23491 cd23491 467369 beta-trefoil_Ricin_abrin-like_rpt2 second ricin B-type lectin domain, beta-trefoil fold, found in Abrus precatorius abrin, agglutinin-I and similar proteins. This subfamily includes Abrus precatorius abrin (ABR) and agglutinin-I (AAG), which share a high degree of sequence similarity and belong to the type II ribosome-inactivating protein (RIP) family. Type II RIPs inhibit protein synthesis in eukaryotic cells and can also induce apoptosis. They are composed of two polypeptide proteins with a toxic A chain and a lectin-like B chain linked by a disulfide bond. The A chain of abrin and agglutinin-I is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA. Agglutinin-I is less toxic than abrin. The B chain is a galactose-specific lectin that facilitates the binding to the cell membrane that precedes endocytosis. The B-chain contains two ricin B-type lectin domains with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the second ricin B-type lectin domain. 124 matched cddid_all.tbl CDD cd23492 cd23492 467370 beta-trefoil_Ricin_MLs_rpt2 second ricin B-type lectin domain, beta-trefoil fold, found in Viscum album B chain of beta-galactoside-specific lectins and similar proteins. This subfamily includes Viscum album beta-galactoside-specific lectins 1-4 (also known as mistletoe lectins or MLs), which inhibit growth of the human tumor cell line Molt4. They contain A and B chains. The A chain is responsible for inhibiting protein synthesis through the catalytic inactivation of 60S ribosomal subunits by removing adenine from position 4,324 of 28S rRNA. The B chain binds to cell receptors and probably facilitates the entry into the cell of the A chain; B chains are also responsible for cell agglutination (lectin activity). The B chain contains two ricin B-type lectin domains with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the second ricin B-type lectin domain. 124 matched cddid_all.tbl CDD cd23493 cd23493 467371 beta-trefoil_Ricin_cinnamomin_rpt2 second ricin B-type lectin domain, beta-trefoil fold, found in Cinnamomum camphora type II ribosome-inactivating protein (RIP) cinnamomin and similar proteins. RIPs are a group of ribotoxins that inhibit mammalian protein biosynthesis by irreversible inactivation of their 60S ribosomal subunit. Type II RIPs in plant cells comprise part of the plant's defense system towards animals. Cinnamomin is a type II RIP isolated from Cinnamomum camphora seeds. It shows inhibitory effects on cultured carcinoma cells and on the larva of the bollworm and mosquito. There are three cinnamomin isoforms (I, II, III). They are composed of two polypeptide chains (A- and B-chain) linked by a disulfide bond. The A-chain displays specific activity as an RNA N-glycosidase that blocks protein synthesis, whereas the B-chain is responsible for the binding to galactose-terminated receptors on cell membranes. The B-chain contains two ricin B-type lectin domains with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the second ricin B-type lectin domain. 125 matched cddid_all.tbl CDD cd23494 cd23494 467372 beta-trefoil_Ricin_HA17 ricin B-type lectin domain, beta-trefoil fold, found in Clostridium botulinum hemagglutinating protein HA17 and similar proteins. The hemagglutinin (HA) component of the progenitor toxin protects the structural integrity of the neurotoxin. It may increase internalization of the neurotoxin into the bloodstream of the host. The hemagglutinin complex, composed of HA-70 (also known as HA3), HA-33 (also known as HA1) and HA-17 (also known as HA2), agglutinates erythrocytes, whereas the individual components do not. HA-33 is involved in recognition of cell-surface carbohydrates. HA-17 and HA-70 are involved in paracellular barrier disruption by E-cadherin binding. HA-17 contains a ricin B-type lectin domain with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. 136 matched cddid_all.tbl CDD cd23495 cd23495 467373 beta-trefoil_Ricin_HA33_rpt1 first ricin B-type lectin domain, beta-trefoil fold, found in Clostridium botulinum hemagglutinating protein HA33 and similar proteins. HA33, also called HA1, is a hemagglutinin (HA) 33 kDa subcomponent, which is associated with the large botulinum neurotoxin secreted complexes and plays a critical role in toxin protection, internalization, and possibly activation. HA33 is involved with internalization of the toxin into the bloodstream by binding to oligosaccharides lining the intestine. HA33 contains two ricin B-type lectin domains with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a potential sugar binding site. The model corresponds to the first ricin B-type lectin domain. 133 matched cddid_all.tbl CDD cd23496 cd23496 467374 beta-trefoil_Ricin_HA33_rpt2 second ricin B-type lectin domain, beta-trefoil fold, found in Clostridium botulinum hemagglutinating protein HA33 and similar proteins. HA33, also called HA1, is a hemagglutinin (HA) 33 kDa subcomponent, which is associated with the large botulinum neurotoxin secreted complexes and plays a critical role in toxin protection, internalization, and possibly activation. HA33 is involved with internalization of the toxin into the bloodstream by binding to oligosaccharides lining the intestine. HA33 contains two ricin B-type lectin domains with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a potential sugar binding site. The model corresponds to the second ricin B-type lectin domain. 136 matched cddid_all.tbl CDD cd23497 cd23497 467375 beta-trefoil_Ricin_MTX-like_rpt1-3 first, second and third ricin B-type lectin domains, beta-trefoil fold, found in Lysinibacillus sphaericus mosquitocidal toxin (MTX) and similar proteins. This subfamily includes Lysinibacillus sphaericus MTX and Pieris brassicae pierisin. MTX acts as an ADP-ribosyl transferase. Pierisin, also called NAD--DNA ADP-ribosyltransferase, pierisin-2, or pierisin-B, catalyzes the ADP ribosylation of double-stranded DNA by targeting the N2 amino group of dG residues. It induces apoptosis in a range of human cell lines. Members of this family contain four ricin B-type lectin domains with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the first, second and third ricin B-type lectin domains. Each subdomain bears a potential sugar binding site. 139 matched cddid_all.tbl CDD cd23498 cd23498 467376 beta-trefoil_Ricin_MTX-like_rpt4 fourth ricin B-type lectin domain, beta-trefoil fold, found in Lysinibacillus sphaericus mosquitocidal toxin (MTX) and similar proteins. This subfamily includes Lysinibacillus sphaericus MTX and Pieris brassicae pierisin. MTX acts as an ADP-ribosyl transferase. Pierisin, also called NAD--DNA ADP-ribosyltransferase, pierisin-2, or pierisin-B, catalyzes the ADP ribosylation of double-stranded DNA by targeting the N2 amino group of dG residues. It induces apoptosis in a range of human cell lines. Members in this family contain four ricin B-type lectin domains with a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. The model corresponds to the fourth ricin B-type lectin domain. Each subdomain bears a potential sugar binding site. 134 matched cddid_all.tbl CDD cd23499 cd23499 467377 beta-trefoil_Ricin_SCDase_rpt1 first ricin B-type lectin domain, beta-trefoil fold, found in Shewanella algae sphingolipid ceramide N-deacylase (SCDase) and similar proteins. SCDase (EC 3.5.1.69) is an enzyme which hydrolyzes the N-acyl linkage between fatty acid and sphingosine in ceramide of various glycosphingolipids and sphingomyelin. Shewanella algae SCDase contains two ricin B-type lectin domains at its C-terminus. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. The model corresponds to the first lectin domain. 131 matched cddid_all.tbl CDD cd23500 cd23500 467378 beta-trefoil_Ricin_SCDase_rpt2 second ricin B-type lectin domain, beta-trefoil fold, found in Shewanella algae sphingolipid ceramide N-deacylase (SCDase) and similar proteins. SCDase (EC 3.5.1.69) is an enzyme which hydrolyzes the N-acyl linkage between fatty acid and sphingosine in ceramide of various glycosphingolipids and sphingomyelin. Shewanella algae SCDase contains two ricin B-type lectin domains at its C-terminus. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain may harbor a sugar-binding pocket. The model corresponds to the second lectin domain. 128 matched cddid_all.tbl CDD cd23501 cd23501 438013 TSLPI_Salp14_NTD N-terminal domain of the TSLPI/Salp14 family proteins. The TSLPI/Salp14 protein family includes several tick proteins, such as tick salivary lectin pathway inhibitor (TSLPI), the tick factor Xa (FXa) inhibitor Salp14, the fibrinolysis modulator Ixonnexin, as well as tick salivary protein BSAP1 (BaSO4-adsorbing protein 1). They all act as lectin pathway inhibitors. Those with an additional lysine-rich C terminus possess anticoagulant activity similar to the human natural anticoagulant tissue factor (TF) pathway inhibitor alpha (TFPIalpha) C terminus. BSAP1 is a distant homolog of the TSLPI/Salp14 family. The protein core region of BSAP1 adopts a noncanonical epidermal growth factor (EGF)-like domain fold, which is a novel motif for tick salivary proteins. The C-terminal region of BSAP1 has no homology with other TSLPI/Salp14 proteins. This model corresponds to the N-terminal domain of TSLPI/Salp14 family proteins. 59 matched cddid_all.tbl CDD cd23505 cd23505 438002 hydrophobin hydrophobins. Hydrophobins are a group of small cysteine-rich proteins that are expressed only by filamentous fungi and play important roles in fungal growth. They are characterized by the presence of 8 conserved cysteine residues that form 4 disulfide bonds. They contribute to surface hydrophobicity, which is important for processes such as association of hyphae in reproductive structures, dispersal of aerial spores and adhesion of pathogens to host structures. Hydrophobins have been divided into two classes based on their hydropathy patterns and biophysical properties. A key difference between class I and class II hydrophobins is that only class I hydrophobins form amyloid-like rodlets which have an underlying cross-beta amyloid structure. Class II hydrophobin films are significantly less robust and lack the rodlet morphology of class I hydrophobins. 77 matched cddid_all.tbl CDD cd23506 cd23506 439387 Sfi1p_helix Helix located at the middle N-terminal region of Sfi1p. Sfi1p is a single continuous alpha helix wrapped with centrins, which are calmodulin-like proteins present in centrosomes and spindle pole bodies (SPBs). Sfi1p is localized to the half-bridge of the yeast SPBs, and like Cdc31p (yeast centrin), it is required for the early steps of SPB duplication. Sfi1p contains a central domain composed of multiple conserved repeats which all can bind to Cdc31p. The Sfi1p C-terminus has an important role in separation or splitting of the duplicated SPBs during bipolar spindle assembly. 89 matched cddid_all.tbl CDD cd23507 cd23507 438003 hydrophobin_I class I hydrophobins. Class I hydrophobins are a unique family of fungal proteins that form a polymeric, water-repellent monolayer on the surface of structures such as spores and fruiting bodies. They form amyloid-like rodlets which have an underlying cross-beta amyloid structure. This subfamily includes the rodlet proteins of Neurospora crassa (gene eas) and Aspergillus nidulans (gene rodA). They are the main component of the hydrophobic sheath covering the surface of many fungal spores. The surface hydrophobicity is important for processes such as association of hyphae in reproductive structures, dispersal of aerial spores, and adhesion of pathogens to host structures. This subfamily also includes Schizophyllum commune fruiting body proteins and Agaricus bisporus hydrophobins. 78 matched cddid_all.tbl CDD cd23508 cd23508 438004 hydrophobin_II class II hydrophobins. Class II hydrophobins are a unique group of fungal proteins that can self-assemble into a monolayer on hydrophilic:hydrophobic interfaces. The monolayer is not fibrillar and it is not associated with formation of amyloid-structures, nor with large conformational changes. This subfamily includes Trichoderma reesei class II hydrophobins HFBI and HFBII, and Neurospora crassa class II hydrophobin NC2. HFBI and HFBII are responsible for spore hydrophobicity and protection. They form highly ordered monolayer films and crystalline fibrils. NC2 is a highly surface active protein that can form protein layers on a water:air interface that stabilize air bubbles. This subfamily also includes Cryphonectria parasitica cryparin and Ophiostoma ulmi cerato-ulmin (CU, also known as Dutch elm disease toxin). Cryparin is an abundant cell-surface protein from the chestnut blight fungus, Cryphonectria parasitica. CU has been implicated in Dutch elm disease pathogenesis. It is also a hydrophobin protein with high surface activity that acts as a parasitic fitness factor. 65 matched cddid_all.tbl CDD cd23509 cd23509 467874 Gnk2-like antifungal protein ginkbilobin-2-like domains found in plants. This family includes the antifungal protein ginkbilobin found in seeds of Ginkgo biloba. The full-length protein contains a signal peptide and is called ginkbilobin-2 (Gnk2 or stress-antifungal domain). Gnk2 is an extracellular domain harboring a conserved cysteine motif (C-8X-C-2X-C) in its core. This domain is present in three types of plant proteins: cysteine-rich receptor-like secreted proteins (CRRSPs), cysteine-rich receptor-like kinase (CRKs), and plasmodesmata-localized proteins (PDLPs). Gnk2 from Ginkgo biloba and maize AFP1 CRRSPs have been shown to bind mannose. CRKs that typically have two Gnk2 domains in the extracellular region, form part of a large subgroup of receptor-like protein kinases (RLKs) in plants and have been shown to participate in the control of stress responses and development in Arabidopsis. PDLPs contain two Gnk2 domains in their extracellular region and a transmembrane helix, but lack a kinase domain; they associate with plasmodesmata and are involved in symplastic intercellular signaling, pathogen response, systemic signaling, control of callose deposition and are targets for viral movement proteins. No ligand have been identified for PDLPs and CRKs. Although the precise biochemical functions of plant Gnk2 are not known, the conserved C-8X-C-2X-C motif may point to carbohydrate binding, similar to G. biloba Gnk2 inhibiting the growth of several fungi by binding mannose moieties of the fungal cell walls. 100 matched cddid_all.tbl CDD cd23510 cd23510 438012 MER1_2_10 Mating pheromones Er-1/Er-3, Er-2/Er-9, and Er-10. This model contains the structurally homologous pheromones Er-1/Er-3 (also known as euplomone R1/R3), Er-2/Er9 (also known as euplomone R2/R9) and Er-10 ((also known as euplomone R10) from the ciliated protozoan Euplotes raikovi. Mating ciliate pheromones (or gamones) are diffusible extracellular communication signals that distinguish different intraspecific classes of cells commonly referred to as 'mating types'. The pheromones prepare these cells for conjugation by changing their cell surface properties. The membrane-bound form promotes inter-cellular communication and adhesion for mating pair formation and may act as a binding site for the secreted form. Thermodynamic stability studies show that the structure, which consists of an up-down-up bundle of 3 short helices with three disulfide bridges, is stable. 36 matched cddid_all.tbl CDD cd23511 cd23511 438011 I-PpoI "homing endonuclease I-PpoI. Homing endonuclease I-PpoI is a member of the ""His-Cys box"" homing endonuclease family. In the slime mold Physarum polycephalum, I-PpoI is encoded by an open reading frame in the third intron of the nuclear, extrachromosomal 26 S rRNA gene. The ""His-Cys box"" sequence motifs are responsible for forming two structural zinc-binding sites per monomer and the enzyme is dependent on divalent cations (usually magnesium) for activity. I-PpoI is a homodimer that cleaves a partially symmetric 15 bp homing site generating four base, 3' cohesive overhangs of sequence 5'-TTAA-3'. Homing sites may vary in sequence at many of their individual nucleotide positions while still being recognized and cleaved. While I-PpoI tolerates base-pair substitutions at several positions within the homing site, it exhibits a strong preference for AT base-pairs in the central four positions of the homing site. I-PpoI severely bends its DNA target, resulting in significant deformations of the minor and major groove near the scissile phosphate groups, and only a smaller change in protein conformation." 159 matched cddid_all.tbl CDD cd23512 cd23512 467777 KREPA1 Kinetoplastid RNA Editing Protein A1 (KREPA1). The KREPA1 (TbMP81) protein is a crucial component of the parasitic protozoan's KREPA RNA editing complex. Kinetoplastid RNA editing (KRE) proteins occur as pairs or sets of related proteins in multiple complexes. KREPA complex is composed of six components (KREPA1-6), which share a conserved C-terminal region containing an oligonucleotide-binding (OB)-fold-like domain. KREPAs are responsible for the site-specific insertion and deletion of U nucleotides in the kinetoplastid mitochondria pre-messenger RNA. Apart from the conserved C-terminal OB-fold domain, KREPA1, KREPA2, and KREPA3 contain two conserved C2H2 zinc-finger domains. However, the C-terminal zinc-finger domain in KREPA1 has additional amino acids. KREPA1 is involved in the insertion sub-complex of editing activities and interacts with KREPA6 of the 20S editosome core complex. When KREPA1 is down-regulated, insertion editing is preferentially inhibited. 449 matched cddid_all.tbl CDD cd23513 cd23513 467778 KREPA4 Kinetoplastid RNA Editing Protein A4 (KREPA4). The KREPA4 (TbMP24) protein is a crucial component of the KREPA RNA editing catalytic complex (RECC) in parasitic protozoans. Kinetoplastid RNA editing (KRE) proteins occur as pairs or sets of related proteins in multiple complexes. This complex is composed of six components (KREPA1-6), which share a conserved C-terminal region containing an oligonucleotide-binding (OB)-fold-like domain. KREPA4 OB-fold domain plays a crucial role in the stable integration of KREPA4 into the editosomes, which are responsible for RNA editing in these parasites. KREPA4 is an RNA binding protein, and it is thought to be specific for the guide RNA (gRNA) Utail. KREPA4 interacts with KREPA6 via the alpha-helix region of its OB-fold, and the entire OB-fold is required for its integration into the functional editosome via additional protein-protein interactions. KREPA4 is also essential for the stability of the 20S editosome. 218 matched cddid_all.tbl CDD cd23514 cd23514 467779 KREPA Kinetoplastid RNA Editing Protein A (KREPA). The KREPA 1-6 (TbMP81, 63, 42, 24, 19, and 18, respectively) proteins are components of the RNA editing complex of parasitic protozoans such as Trypanosoma and Leishmania species. These parasites have a uniquely organized mitochondrial genome, the kinetoplast. Most kinetoplast-transcribed mRNAs are cryptic and encode multiple subunits for the electron transport chain following maturation through a uridine insertion/deletion process called RNA editing. KREPAs participate in the site-specific insertion and deletion of U nucleotides in the kinetoplastid mitochondria pre-messenger RNA. The editosome, a high molecular mass enzyme complex, carries out the reaction with the help of critical enzymes and structural proteins. Five related editosome proteins KREPA1 (TbMP81), KREPA2 (TbMP63), KREPA3 (TbMP42), KREPA4 (TbMP24), KREPA5 (TbMP19), and KREPA6 (TbMP18) play critical roles in the structure and auxiliary functions of the editing process without any predicted catalytic function. The KREPA1, KREPA2, and KREPA3 proteins contain C2H2 zinc finger motifs and KREPA4 and KREPA6, contain RNA-binding domains but all have a conserved C-terminal sequences that resemble an oligonucleotide-binding (OB)-fold domain. Thus, this group of five proteins is likely to be involved in protein-protein and/or protein-RNA interactions. RNA editing is crucial for the parasite's survival in both its bloodstream and procyclic form life cycle stages which allows the parasite to adapt to its environment and maintain its viability. 109 matched cddid_all.tbl CDD cd23515 cd23515 467875 MPSS2 mitochondrial 3' processome (MPsome) subunit 2. MPSS2 is a subunit of the mitochondrial 3' processome (MPsome) which is involved in 3'-5' trimming of messenger RNA (mRNA) precursors, in U-tailing of ribosomal RNA (rRNA) and some mRNAs, and in 3'-5' trimming and U-tailing of guide RNAs (gRNAs), during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode gRNAs involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. MPsome subunits include KDSS1 3'-5' exonuclease, RET1 terminal uridyltransferase (TUTase), and several subunits of as yet undefined functions (MPSS1-MPSS6). The maxicircle and minicircle RNAs are transcribed as 3' extended precursors and processed by MPsome-dependent 3'-5' degradation, and in the case of rRNAs and gRNAs also 3' uridylated. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The MPsome catalyzes the primary uridylation of about 800 nt gRNA precursor transcripts, their processive degradation to a mature size of 40-60 nt, and secondary U-tail addition. MPSS2 is predicted (AlphaFold) to be a predominantly alpha helical protein. 1532 matched cddid_all.tbl CDD cd23516 cd23516 438005 hydrophobin_I_eas-like Class I hydrophobin similar to Neurospora crassa eas. Class I hydrophobins are a unique family of fungal proteins that form a polymeric, water-repellent monolayer on the surface of structures such as spores and fruiting bodies. They form amyloid-like rodlets which have an underlying cross-beta amyloid structure. This group includes the rodlet protein of Neurospora crassa (gene eas), which is the main component of the hydrophobic sheath covering the surface of fungal spores. The surface hydrophobicity is important for processes such as association of hyphae in reproductive structures, dispersal of aerial spores, and adhesion of pathogens to host structures. 81 matched cddid_all.tbl CDD cd23517 cd23517 439383 Cas12i1 CRISPR-associated protein (Cas) 12i1. Cas12i1 is a class 2 type V-I (class 2, type V family, subtype I; Cas12i) CRISPR effector protein. Class 2, type V family members, have names each which begin with Cas12, and predominantly cleave the non-target strand of a double-stranded DNA (dsDNA) substrate. Two Cas12i proteins (Cas12i1 and Cas12i2), have CRISPR RNA (crRNA)-guided dsDNA cleavage activity. Cas12i1 and Cas12i2 cleave dsDNA adjacent to protospacer adjacent motif (PAM) sequences, preferring a 5' TTN PAM. They cleave the non-target DNA (NTD) strand prior to the target DNA (TD) strand to generate staggered double-strand breaks. For Cas12i1 the NTD strand was cleaved 13-15 nucleotides after the PAM duplex, and the TD strand was cleaved 24 nucleotides after the PAM duplex. In addition to dsDNA cleavage, Cas12i1 and Cas2i2 possess ssDNA cleavage activity, and pre-crRNA processing activity for crRNA maturation. The class 2 effector modules are single large proteins, distinguished by their domain architectures into type II, V and VI systems. Type V is the most diversified type and is further divided into subtypes A-I, K, and CRISPR-CasPhi. These subtypes, with the exception of subtype K, have ssDNA cleavage activity; after the effector protein cleaves the targeted dsDNA substance, the PAM-distal product is released, but the Cas protein is still bound to the PAM-proximal strand; at this point, the RuvC domain can still access ssDNA substrates and perform non-specific cleavage (also known as the promiscuous cleavage of collateral ssDNA or trans-cleavage. The type II effectors (Cas9) contain two nuclease domains that are each responsible for the cleavage of one strand of the target DNA, with the HNH nuclease inserted inside the RuvC-like nuclease domain sequence. By contrast, the type V effectors (Cas12) only contain a RuvC-like domain that cleaves both strands. Both type II and type V effectors adopt a similar architecture comprising a recognition lobe (REC) and a nuclease lobe (NUC). Cas9 endonucleases employ both the RuvC and HNH domains for DNA cleavage, however, Cas12 endonucleases use a single RuvC domain for DNA cleavage. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated protein) is an RNA guided adaptive immunity system present in bacteria and archaea, which defends its host against foreign nucleic acids that originate from phages or plasmids. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). 1076 matched cddid_all.tbl CDD cd23518 cd23518 439384 Cas12i2 CRISPR-associated protein (Cas) 12i2. Cas12i2 is a class 2 type V-I (class 2, type V family, subtype I; Cas12i) CRISPR effector protein. Class 2, type V family members have names each which begin with Cas12, and predominantly cleave the non-target strand of a double-stranded DNA (dsDNA) substrate. Two Cas12i proteins (Cas12i1 and Cas12i2), have CRISPR RNA (crRNA)-guided dsDNA cleavage activity. Cas12i1 and Cas12i2 cleave dsDNA adjacent to protospacer adjacent motif (PAM) sequences, preferring a 5' TTN PAM. They cleave the non-target DNA (NTD) strand prior to the target DNA (TD) strand to generate staggered double-strand breaks. For Cas12i2 the NTD strand was primarily cleaved 31 nucleotides after the PAM duplex and the TD strand was cleaved 24 nucleotides after the PAM duplex. In addition to dsDNA cleavage, Cas12 i1 and Cas12i2 possess ssDNA cleavage activity, and pre-crRNA processing activity for crRNA maturation. The class 2 effector modules are single large proteins, distinguished by their domain architectures into type II, V and VI systems. Type V is the most diversified type and is further divided into subtypes A-I, K, and CRISPR-CasPhi. These subtypes, with the exception of subtype K, have ssDNA cleavage activity; after the effector protein cleaves the targeted dsDNA substance, the PAM-distal product is released, but the Cas protein is still bound to the PAM-proximal strand; at this point, the RuvC domain can still access ssDNA substrates and perform non-specific cleavage (also known as the promiscuous cleavage of collateral ssDNA or trans-cleavage. The type II effectors (Cas9) contain two nuclease domains that are each responsible for the cleavage of one strand of the target DNA, with the HNH nuclease inserted inside the RuvC-like nuclease domain sequence. By contrast, the type V effectors (Cas12) only contain a RuvC-like domain that cleaves both strands. Both type II and type V effectors adopt a similar architecture comprising a recognition lobe (REC) and a nuclease lobe (NUC). Cas9 endonucleases employ both the RuvC and HNH domains for DNA cleavage, however, Cas12 endonucleases use a single RuvC domain for DNA cleavage. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated protein) is an RNA guided adaptive immunity system present in bacteria and archaea, which defends its host against foreign nucleic acids that originate from phages or plasmids. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). 1026 matched cddid_all.tbl CDD cd23519 cd23519 467802 Abraxas-like_domain Abraxas-like domain of BRCA1-A complex subunit Abraxas 1, BRISC complex subunit Abraxas 2, and similar domains found in insects and plants. BRCA1-A and BRISC complex subunit BRE (also known as BRISC and BRCA1 A complex member 2; BRCC4; BRCC45) is a core component of both the BRCA1-A and BRISC complexes. BRCA1-A and BRISC are separate complexes with diverging function; they use the same core of subunits to perform very distinct biological tasks, and are found in all vertebrates. BRCA1-A complex subunit Abraxas 1, also known as ABRA1, FAM175A, and CCDC98, is involved in DNA damage response and double-strand break (DSB) repair and acts as a central scaffold protein that assembles the various components of the complex and mediates the recruitment of BRCA1. The BRCA1-A complex consists of Abraxas-1, BRCC36, BRE, MERIT40, and RAP80. The BRCA1-A complex specifically recognizes 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesion sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at DSBs. This complex also possesses deubiquitinase (DUB) activity that specifically removes 'Lys-63'-linked ubiquitin on histones H2A and H2AX. BRCA1-A opposes homologous recombination (HR) by suppressing resection. It has been shown for BIR (break-induced replication), an HR-subtype that involves extensive DNA resection and mutagenic DNA synthesis, that Abraxas inhibits DNA end resection through regulating the levels of SLX4/MUS81 chromatin loading at DSBs in response to Topoisomerase I (TOP1) inhibitor-induced DNA damage. Familial mutations in the BRCA1-A proteins Abraxas-1 and RAP80 predispose carriers to early-onset breast cancer, analogous to mutations in BRCA1 and BRCA2. BRCA1-A requires the tandem ubiquitin (UIM2)- and SUMO-interacting motifs (SIM) in RAP80 and the BRCC36 DUB to function in DNA repair. BRCA1-A recruits BRCA1 by binding its BRCT domains upon phosphorylation of a motif near the C-terminus of Abraxas-1. BRCA1 binding to BRCA1-A sequesters the HR activator BRCA1 about 2-10 kb distal from DNA break sites, which is posited to limit HR. It is currently unclear how BRCA1-A is functionalized and targeted by RAP80 and Abraxas-1, and how BRCA1 is inhibited when bound to the complex. BRISC complex subunit Abraxas 2 is also known as ABRO1, FAM175B or KIAA0157. The BRISC complex consists of BRCC36, MERIT40, BRE, and Abraxas 2, and serves cellular stress response and immune signaling functions; it specifically cleaves 'Lys-63'-linked polyubiquitin, leaving the last ubiquitin chain attached to its substrates; In the BRISC complex, Abraxas 2 binds SHMT2a, a metabolic enzyme enabling cancer growth in hypoxic environments, which prevents the BRCC36 from binding and cleaving ubiquitin chains. BRCC36 is the DUB for both BRCA1-A and BRISC. BRCC36 associates with pseudo-DUB proteins (Abraxas 1 in BRCA1-A, Abraxas 2 in BRISC), which lack the essential Zn2+-coordinating residues required for DUB catalytic function. BRCC36 in BRCA1-A and BRISC is activated by assembly due to interaction between Glu30 of BRCC36 and Asn170 in Abraxas 1 and Asn164 in Abraxas 2, respectively, which structures the activation loop and positions the catalytic Glu33, For the BRISC complex it has been shown that higher-order association of BRCC36 and Abraxas2 into a dimer of heterodimers (superdimer) is required for BRCC36 DUB activity. A BRISC complex (containing of BRE/BRCC45, BRCC36, MERIT40, and Abraxas 2/KIAA0157) has been found in insects (Camponotus floridanus) and shown to efficiently degrade K63-linked chains. Homologs of genes encoding components of BRCA1-A and BRISC complexes have been found in plant genomes, including for BRE/BRCC45; plant homologs of BRCC36 have been shown to be involved in DNA repair, and BRCC36-KIAA0157 complexes have been found in Arabidopsis. 257 matched cddid_all.tbl CDD cd23520 cd23520 467820 BRE-like BRCA1-A and BRISC complex subunit BRE and related proteins. BRCA1-A and BRISC complex subunit BRE (also known as BRISC and BRCA1 A complex member 2; BRCC4; BRCC45) is a core component of both the BRCA1-A and BRISC complexes. BRCA1-A and BRISC are separate complexes with diverging function; they use the same core of subunits to perform very distinct biological tasks, and are found in all vertebrates. The BRCA1-A complex consists of BRE, Abraxas-1, BRCC36, MERIT40 and RAP80, and specifically recognizes 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesion sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at double-strand breaks (DSB)s. This complex also possesses deubiquitinase (DUB) activity that specifically removes 'Lys-63'-linked ubiquitin on histones H2A and H2AX. In BRCA1-A, two heteropentamers, composed of BRCC36, ABRAXAS, BRE and MERIT40, form an arc-shaped complex; the two half-arcs contact each other through BRCC36 and its scaffold partner ABRAXAS. BRCC36 is connected to this arc via the ABRAXAS MPN domain. BRE forms the central bridge between the ABRAXAS-BRCC36 MPN domain dimer and MERIT40. BRE's N-terminal ubiquitin-conjugating enzyme variants domain (UEV-N) binds the ABRAXAS MPN, and BRE's C-terminal UEV domain (UEV-C) holds MERIT40 at the extremity of the arc. Loss of BRE significantly impairs BRCA1-A function, resulting in DNA repair defects and loss of cancer suppression. The BRISC complex consists of BRE, BRCC36, MERIT40 and Abraxas 2, and serves cellular stress response and immune signaling functions; it specifically cleaves 'Lys-63'-linked polyubiquitin, leaving the last ubiquitin chain attached to its substrates. The BRISC core has the same 2-fold symmetrical arc shape and is structurally similar to BRCA1-A; however, the conformation of BRE UEV-C and MERIT40 differs markedly. BRE has different functionality in the BRCA1-A and BRISC complexes: in BRCA1, it is involved in RAP80 integration, BRCA1 sequestration and ubiquitin binding, while in BRISC, it is involved in dimerization, SHMT2 recruitment, DUB inhibition and ubiquitin binding. A BRISC complex (consisting of BRE/BRCC45, BRCC36, MERIT40 and Abraxas 2/KIAA0157) has been found in insects (Camponotus floridanus) and shown to efficiently degrade 'Lys-63'-linked chains. Homologs of genes encoding components of BRCA1-A and BRISC complexes have been found in plant genomes, including for BRE/BRCC45; plant homologs of BRCC36 have been shown to be involved in DNA repair; BRCC36-Abraxas 2 complexes have been found in Arabidopsis. 352 matched cddid_all.tbl CDD cd23523 cd23523 467803 Abraxas_1 BRCA1-A complex subunit Abraxas 1. BRCA1-A complex subunit Abraxas 1, also known as ABRA1, FAM175A, and CCDC98, is involved in DNA damage response and double-strand break (DSB) repair and acts as a central scaffold protein that assembles the various components of the complex and mediates the recruitment of BRCA1. The BRCA1-A complex consists of Abraxas 1, BRCC36, BRE, MERIT40, and RAP80, and specifically recognizes 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesion sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at DSBs. This complex also possesses deubiquitinase (DUB) activity that specifically removes 'Lys-63'-linked ubiquitin on histones H2A and H2AX; its DUB is BRCC36, which associates with pseudo-DUB protein Abraxas 1 which lacks the essential Zn2+-coordinating residues required for DUB catalytic function. BRCA1-A opposes homologous recombination (HR) by suppressing resection. It has been shown for BIR (break-induced replication), an HR-subtype that involves extensive DNA resection and mutagenic DNA synthesis; that Abraxas 1 inhibits DNA end resection through regulating the levels of SLX4/MUS81 chromatin loading at DSBs in response to Topoisomerase I (TOP1) inhibitor-induced DNA damage. Familial mutations in the BRCA1-A proteins Abraxas 1 and RAP80 predispose carriers to early-onset breast cancer, analogous to mutations in BRCA1 and BRCA2. BRCA1-A requires the tandem ubiquitin (UIM2)- and SUMO-interacting motifs (SIM) in RAP80 and the BRCC36 DUB to function in DNA repair. BRCA1-A recruits BRCA1 by binding its BRCT domains upon phosphorylation of a motif near the C-terminus of Abraxas 1. BRCA1 binding to BRCA1-A sequesters the HR activator BRCA1 about 2-10 kb distal from DNA break sites, which is posited to limit HR. It is currently unclear how BRCA1-A is functionalized and targeted by RAP80 and Abraxas 1 and how BRCA1 is inhibited when bound to the complex. BRCC36 in BRCA1-A is activated by assembly due to interaction between Glu30 of BRCC36 and Asn170 in Abraxas 1 which structures the activation loop and positions the catalytic Glu33. 379 matched cddid_all.tbl CDD cd23524 cd23524 467804 Abraxas_2 BRISC complex subunit Abraxas 2. BRISC complex subunit Abraxas 2 is also known as ABRO1, FAM175B, or KIAA0157. The BRISC complex consists of BRCC36, MERIT40, BRE, and Abraxas 2, and serves cellular stress response and immune signaling functions; it specifically cleaves 'Lys-63'-linked polyubiquitin, leaving the last ubiquitin chain attached to its substrates; BRISC's catalytic subunit is the deubiquitinase (DUB) BRCC36. BRCC36 associates with pseudo-DUB protein Abraxas2, which lacks the essential Zn2+-coordinating residues required for DUB catalytic function. Higher-order association of BRCC36 and Abraxas2 into a dimer of heterodimers (superdimer) is required for BRCC36 DUB activity. In the BRISC complex, Abraxas 2 binds SHMT2a, a metabolic enzyme enabling cancer growth in hypoxic environments, which prevents the BRCC36 from binding and cleaving ubiquitin chains. BRCC36 in BRISC is activated by assembly due to interaction between Glu30 of BRCC36 and Asn164 in Abraxas 2 which structures the activation loop and positions the catalytic Glu33. The members here include Abraxas 2 domains. 255 matched cddid_all.tbl CDD cd23525 cd23525 467805 Abraxas_2_insects BRISC complex subunit Abraxas 2 found in insects. BRISC complex subunit Abraxas 2 is also known as ABRO1, FAM175B or KIAA0157. The BRISC complex consists of BRCC36, MERIT40, BRE, and Abraxas 2, and serves cellular stress response and immune signaling functions; it specifically cleaves 'Lys-63'-linked polyubiquitin, leaving the last ubiquitin chain attached to its substrates; BRISC's catalytic subunit is the deubiquitinase (DUB) BRCC36. BRCC36 associates with pseudo-DUB protein Abraxas2, which lacks the essential Zn2+-coordinating residues required for DUB catalytic function. Higher-order association of BRCC36 and Abraxas2 into a dimer of heterodimers (superdimer) is required for BRCC36 DUB activity. In the BRISC complex, Abraxas 2 binds SHMT2a, a metabolic enzyme enabling cancer growth in hypoxic environments, which prevents the BRCC36 from binding and cleaving ubiquitin chains. BRCC36 in BRISC is activated by assembly due to interaction between Glu30 of BRCC36 and Asn164 in Abraxas 2 which structures the activation loop and positions the catalytic Glu33. The members in this subfamily include Camponotus floridanus KIAA0157 domain. 251 matched cddid_all.tbl CDD cd23526 cd23526 467738 capping_2-OMTase_CoV_Nsp16 Cap-0 specific (nucleoside-2'-O-)-methyltransferase of Coronavirus, also called non-structural protein 16. Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. Coronavirus (CoV) 2'OMTase activity is located in the non-structural protein 16 (Nsp16). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Nsp16 requires Nsp10 to bind both m7GpppA-RNA substrate and SAM cofactor; the structure suggests that Nsp10 may stabilize the SAM-binding pocket and extend the substrate RNA-binding groove of Nsp16. 191 matched cddid_all.tbl CDD cd23527 cd23527 467739 capping_2-OMTase_alphaCoV_Nsp16 Cap-0 specific (nucleoside-2'-O-)-methyltransferase of alphacoronavirus, also called non-structural protein 16. Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. The alphacoronavirus (alphaCoV) 2'OMTase activity is located in the non-structural protein 16 (Nsp16). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Nsp16 requires Nsp10 to bind both m7GpppA-RNA substrate and SAM cofactor; the structure suggests that Nsp10 may stabilize the SAM-binding pocket and extend the substrate RNA-binding groove of Nsp16. 193 matched cddid_all.tbl CDD cd23528 cd23528 467740 capping_2-OMTase_betaCoV_Nsp16 Cap-0 specific (nucleoside-2'-O-)-methyltransferase of betacoronavirus, also called non-structural protein 16. Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. The betacoronavirus (betaCoV) 2'OMTase activity is located in the non-structural protein 16 (Nsp16). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Nsp16 requires Nsp10 to bind both m7GpppA-RNA substrate and SAM cofactor; the structure suggests that Nsp10 may stabilize the SAM-binding pocket and extend the substrate RNA-binding groove of Nsp16. 216 matched cddid_all.tbl CDD cd23529 cd23529 467741 capping_2-OMTase_gammaCoV_Nsp16 Cap-0 specific (nucleoside-2'-O-)-methyltransferase of gammacoronavirus, also called non-structural protein 16. Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. The gammacoronavirus (gammaCoV) 2'OMTase activity is located in the non-structural protein 16 (Nsp16). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Nsp16 requires Nsp10 to bind both m7GpppA-RNA substrate and SAM cofactor; the structure suggests that Nsp10 may stabilize the SAM-binding pocket and extend the substrate RNA-binding groove of Nsp16. 196 matched cddid_all.tbl CDD cd23530 cd23530 467742 capping_2-OMTase_deltaCoV_Nsp16 Cap-0 specific (nucleoside-2'-O-)-methyltransferase of deltacoronavirus, also called non-structural protein 16. Cap-0 specific (nucleoside-2'-O-)-methyltransferase (2'OMTase) catalyzes the methylation of Cap-0 (m7GpppNp) at the 2'-hydroxyl of the ribose of the first nucleotide, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. This reaction is the fourth and last step in mRNA capping, the creation of the stabilizing five-prime cap (5' cap) on mRNA. The deltacoronavirus (deltaCoV) 2'OMTase activity is located in the non-structural protein 16 (Nsp16). CoVs utilize a multi-subunit replication/transcription machinery. A set of non-structural proteins (Nsps) generated as cleavage products of the ORF1a and ORF1ab viral polyproteins assemble to facilitate viral replication and transcription. Nsp16 requires Nsp10 to bind both m7GpppA-RNA substrate and SAM cofactor; the structure suggests that Nsp10 may stabilize the SAM-binding pocket and extend the substrate RNA-binding groove of Nsp16. 183 matched cddid_all.tbl CDD cd23531 cd23531 467876 AcrIIA14_C C-terminal domain of anti-CRISPR type II subtype A14. AcrIIA14 is an anti-CRISPR (Acr) protein which was discovered by a combination of self-targeting CRISPR screening and guilt-by-association Staphylococcus genomic searches. Staphylococcus genomes encode inhibitors of Staphylococcus aureus Cas9 (SauCas9), a genome editing alternative to Streptococcus pyogene Cas9 (SpyCas9); SauCas9 is highly active in mammalian cells, and easier to deliver than SpyCas9 due to its smaller size. AcrIIA14 is a potent inhibitor of SauCas9. AcrIIA14 consists of an N-terminal helix-turn-helix (HTH) domain and a C-terminal domain which inhibits SauCas9 activity in vivo and in vitro without affecting the binding of SauCas9 protein to single molecule guide RNA (sgRNA) and target DNA. The AcrIIA14 C-terminal domain binds to a non-conserved region of SauCas9 HNH nuclease domain sterically preventing the movement of the HNH domain toward the scissile phosphodiester linkage in the target DNA strand. In addition, the binding of AcrIIA14 triggers the conformational allostery of the HNH domain and the L1 linker within the SauCas9, driving them to make new interactions with the target-guide heteroduplex, enhancing the inhibitory ability of AcrIIA14. Almost all type II Acr proteins characterized to date directly interact with the Cas9 endonuclease, although by distinct mechanisms. The type II CRISPR/Cas subtype has a distinct CRISPR RNA (crRNA) guided surveillance complex encoded by cas9 (formerly csn1), cas1, cas2, and csn2 (for type IIA) or cas4 (for type IIB) genes, type II-Cs are generally characterized by the absence of both cas4 and csn2; these genes are all located in a single transcriptional unit directly upstream of the CRISPR locus. However, variants of type II-C systems have been identified in archaea that contain cas4, and have cas1, cas2, cas4 downstream of the CRISPR locus. Cleavage of the DNA target in type II systems is carried out by Cas9 which is an RNA-guided double-stranded DNase with two independent nuclease domains, HNH and RuvC. CRISPR-Cas immune systems are used by certain prokaryotes and archaea to resist the invasion of foreign nucleic acids such as phages or plasmids. Anti-CRISPRs are small proteins which are the natural inhibitors for CRISPR-Cas systems; encoded on bacterial and archaeal viruses, they allow the virus to evade host CRISPR-Cas systems. The CRISPR-Cas-mediated adaptive immune response can be divided into three steps, including the acquisition of spacer derived from invading nucleic acids, crRNA processing, and target degradation. Theoretically, Acr proteins could suppress any step to disrupt the CRISPR-Cas system. Acr proteins are diverse with no common sequence or structural motif, and they inhibit a wide range of CRISPR-Cas systems with various inhibition mechanisms. CRISPR-Cas systems are divided into two classes (1 and 2) and six types (class 1: types I, III and IV; class 2: types II, V and VI). Class 2 systems are characterized by effector modules that consist of a single multidomain protein, such as Cas9 in type II. Acr families are named for their type and subtype which are numbered sequentially as they are discovered. 97 matched cddid_all.tbl CDD cd23532 cd23532 467062 TFP_LU_ECD_BMPR1 extracellular domain (ECD) found in the family of bone morphogenetic protein receptor type-1 (BMPR1). The BMPR1 family includes BMPR-1A (also known as activin receptor-like kinase 3/ALK-3, or serine/threonine-protein kinase receptor R5/SKR5, or CD292) and BMPR-1B (also known as activin receptor-like kinase 6/ALK-6, or CDw293). They form a receptor complex consisting of two type II and two type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. BMPR-1A is the receptor for BMP2, BMP4, GDF5, and GDF6. It positively regulates chondrocyte differentiation through GDF5 interaction and mediates induction of adipogenesis by GDF6. BMPR-1B is the receptor for BMP7/OP-1 and GDF5. It positively regulates chondrocyte differentiation through GDF5 interaction. Members in this family contain an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 90 matched cddid_all.tbl CDD cd23533 cd23533 467063 TFP_LU_ECD_BMPR2_like extracellular domain (ECD) found in the bone morphogenetic protein receptor type-2 (BMPR2)-like family. The BMPR2-like family includes BMPR2, activin receptor type-2A (ACTR-IIA), activin receptor type-2B (ACTR-IIB), and anti-Muellerian hormone type-2 receptor (AMHR2). On ligand binding, they form a receptor complex consisting of two type II and two type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. BMPR2 binds to BMP7, BMP2, and less efficiently, BMP4. ACTR-IIA is the receptor for activin A, activin B, and inhibin A. It also interacts with type I receptor ACVR1 and bone morphogenetic protein 7 (BMP7). ACTR-IIB interacts with vacuolar protein sorting 39 (Vps39), dynein light chain Tctex-type 1 (DYNLT1), bone morphogenetic protein 2 (BMP2), and bone morphogenetic protein 3 (BMP3). AMHR2 is the receptor for anti-Muellerian hormone. Members in this family contain an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 93 matched cddid_all.tbl CDD cd23534 cd23534 467064 TFP_LU_ECD_ALK1 extracellular domain (ECD) found in activin receptor-like kinase 1 (ALK-1) and similar proteins. ALK-1 ((EC 2.7.11.30), also called ACVRL1, or ACVRLK1, or serine/threonine-protein kinase receptor R3 (SKR3), or TGF-B superfamily receptor type I (TSR-I)) acts as type I receptor for TGF-beta family ligands BMP9/GDF2 and BMP10 and important regulator of normal blood vessel development. On ligand binding, it forms a receptor complex consisting of two type II and two type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. ALK-1 may bind activin as well. This model corresponds to the extracellular domain (ECD) of ALK-1, which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 67 matched cddid_all.tbl CDD cd23535 cd23535 467065 TFP_LU_ECD_ALK2 extracellular domain (ECD) found in activin receptor-like kinase 2 (ALK-2) and similar proteins. ALK-2 (EC 2.7.11.30, also called ACVRLK2, or activin receptor type-1 (ACVR1), or activin receptor type I (ACTR-I), or serine/threonine-protein kinase receptor R1 (SKR1), or TGF-B superfamily receptor type I (TSR-I)) is bone morphogenetic protein (BMP) type I receptor that is involved in a wide variety of biological processes, including bone, heart, cartilage, nervous, and reproductive system development and regulation. As a type I receptor, ALK-2 forms heterotetrameric receptor complexes with the type II receptors AMHR2, ACVR2A, or ACVR2B. Upon binding of ligands such as BMP7 or GDF2/BMP9 to the heteromeric complexes, type II receptors transphosphorylate ACVR1 intracellular domain. In turn, ACVR1 kinase domain is activated and subsequently phosphorylates SMAD1/5/8 proteins that transduce the signal. In addition to its role in mediating BMP pathway-specific signaling, ALK-2 suppresses TGFbeta/activin pathway signaling by interfering with the binding of activin to its type II receptor. Besides canonical SMAD signaling, it can activate non-canonical pathways such as p38 mitogen-activated protein kinases/MAPKs. This model corresponds to the extracellular domain (ECD) of ALK-2, which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 71 matched cddid_all.tbl CDD cd23536 cd23536 467066 TFP_LU_ECD_ALK4 extracellular domain (ECD) found in activin receptor-like kinase 4 (ALK-4) and similar proteins. ALK-4 (EC 2.7.11.30, also called ACVRLK4, or activin receptor type-1B (ACVR1B), or activin receptor type IB (ACTR-IB), or serine/threonine-protein kinase receptor R2 (SKR2)) is the transmembrane serine/threonine kinase activin type-1 receptor forming an activin receptor complex with activin receptor type-2 (ACVR2A or ACVR2B). It transduces the activin signal from the cell surface to the cytoplasm and is thus regulating many physiological and pathological processes including neuronal differentiation and neuronal survival, hair follicle development and cycling, FSH production by the pituitary gland, wound healing, extracellular matrix production, immunosuppression, and carcinogenesis. This model corresponds to the extracellular domain (ECD) of ALK-4, which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 77 matched cddid_all.tbl CDD cd23537 cd23537 467067 TFP_LU_ECD_ALK5 extracellular domain (ECD) found in activin receptor-like kinase 5 (ALK-5) and similar proteins. ALK-5 (EC 2.7.11.30, also called TGF-beta receptor type-1 (TGFR-1), or activin A receptor type II-like protein kinase of 53kD, or serine/threonine-protein kinase receptor R4 (SKR4), or TGF-beta type I receptor, or transforming growth factor-beta receptor type I (TGFBR1), or TGF-beta receptor type I (TbetaR-I)) is the transmembrane serine/threonine kinase forming with the TGF-beta type II serine/threonine kinase receptor, TGFBR2, the non-promiscuous receptor for the TGF-beta cytokines TGFB1, TGFB2, and TGFB3. It transduces the TGFB1, TGFB2, and TGFB3 signal from the cell surface to the cytoplasm and is thus regulating a plethora of physiological and pathological processes including cell cycle arrest in epithelial and hematopoietic cells, control of mesenchymal cell proliferation and differentiation, wound healing, extracellular matrix production, immunosuppression, and carcinogenesis. This model corresponds to the extracellular domain (ECD) of ALK-5, which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 74 matched cddid_all.tbl CDD cd23538 cd23538 467068 TFP_LU_ECD_TGFR2 extracellular domain (ECD) found in TGF-beta receptor type-2 (TGFR-2) and similar proteins. TGFR-2 (also called transforming growth factor-beta receptor type II (TbetaR-II), or TGF-beta type II receptor, or TGF-beta receptor type II) belongs to a group of receptors for the TGFbeta family of secreted signaling molecules that includes TGFbeta, bone morphogenetic proteins, activins, growth and differentiation factors, and anti-Mullerian hormone, among others. These receptors contain an extracellular domain (ECD) that binds ligands, a single transmembrane region, and a cytoplasmic catalytic kinase domain. Type II receptors, such as TGFR-2, are high-affinity receptors which bind ligands, autophosphorylate, as well as trans-phosphorylate and activate low-affinity type I receptors. TGFR-2 acts as the receptor for TGFbeta, which is crucial in growth control and homeostasis in many different tissues. It plays roles in regulating apoptosis and in maintaining the balance between self-renewal and cell loss. It also plays a key role in maintaining vascular integrity and in regulating responses to genotoxic stress. Mutations in TGFR-2 can cause aortic aneurysm disorders such as Loeys-Dietz and Marfan syndromes. This model corresponds to the ECD of TGFR-2, which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 101 matched cddid_all.tbl CDD cd23539 cd23539 467069 TFP_LU_ECD_CinHb4_like extracellular domain (ECD) found in Ciona intestinalis globin CinHb4 and similar proteins. Four distinct globin genes have been identified in the Ciona genome. CinHb4 is encoded by the fourth globin gene. It shows an unusual extension at its N-terminus, which reveals a conserved region with similarity to the extracellular domain (ECD) of the TGF-beta receptor type I/II protein family involved in signal transduction. The functional relevance of these matches is currently unknown. The ECD belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 91 matched cddid_all.tbl CDD cd23540 cd23540 467070 TFP_LU_ECD_ALK7 extracellular domain (ECD) found in activin receptor-like kinase 7 (ALK-7) and similar proteins. ALK-7 (EC 2.7.11.30, also called activin receptor type-1C (ACVR1C), or activin receptor type IC (ACTR-IC)) is a serine/threonine protein kinase which forms a receptor complex on ligand binding. The receptor complex consisting of 2 type II and 2 type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators, SMAD2 and SMAD3. ALK-7 is the receptor for activin AB, activin B, and NODAL. It plays a role in cell differentiation, growth arrest and apoptosis. This model corresponds to the extracellular domain (ECD) of ALK-7, which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 76 matched cddid_all.tbl CDD cd23541 cd23541 467071 TFP_LU_ECD_Ly6A_like extracellular domain (ECD) found in mouse Ly-6A like lymphocyte antigens and similar proteins. The family includes mouse Ly-6 lymphocyte antigens, such as Ly-6A/Ly-6E, Ly-6B, Ly-6C1/6C2, Ly-6F, and Ly-6I/Ly-6M. Ly-6A/Ly-6E (also called stem cell antigen 1/SCA-1, or T-cell-activating protein/TAP) and Ly-6C are involved in T-cell activation. Members in this family contain an extracellular domain (ECD) which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 83 matched cddid_all.tbl CDD cd23542 cd23542 467072 TFP_LU_ECD_Ly6D extracellular domain (ECD) found in lymphocyte antigen 6D (Ly-6D) and similar proteins. Ly-6D (also called E48 antigen) is a GPI-anchored molecule apparently involved in keratinocyte cell-cell adhesion. It may act as a specification marker at earliest stage specification of lymphocytes between B- and T-cell development. Ly-6D contains an extracellular domain (ECD) which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 79 matched cddid_all.tbl CDD cd23543 cd23543 467073 TFP_LU_ECD_Ly6E extracellular domain (ECD) found in lymphocyte antigen 6E (Ly-6E) and similar proteins. Ly-6E (also called retinoic acid-induced gene E protein (RIG-E), or stem cell antigen 2 (SCA-2), or thymic shared antigen 1 (TSA-1)) is a GPI-anchored cell surface protein that regulates T-lymphocytes proliferation, differentiation, and activation. It restricts the entry of human coronaviruses, including SARS-CoV, MERS-CoV and SARS-CoV-2, by interfering with spike protein-mediated membrane fusion. It plays an essential role in placenta formation by acting as the main receptor for syncytin-A (SynA). It may also act as a modulator of nicotinic acetylcholine receptors (nAChRs) activity. Ly-6E contains an extracellular domain (ECD) which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 78 matched cddid_all.tbl CDD cd23544 cd23544 467074 TFP_LU_ECD_Ly6G5b extracellular domain (ECD) found in lymphocyte antigen 6 complex locus protein G5b (Ly6G5b) and similar proteins. Ly6G5b is a glycosylated, potentially secreted protein which could act as ligand for other cell-surface receptors and could thus potentially have a role in cell signaling. It contains an extracellular domain (ECD) which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 82 matched cddid_all.tbl CDD cd23545 cd23545 467075 TFP_LU_ECD_Ly6G5c extracellular domain (ECD) found in lymphocyte antigen 6 complex locus protein G5c (Ly6G5c) and similar proteins. Ly6G5c is a glycosylated, potentially secreted protein which could act as ligand for other cell-surface receptors and could thus potentially have a role in cell signaling. Ly6G5c may have a role in hematopoietic cell differentiation. It contains an extracellular domain (ECD) which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 88 matched cddid_all.tbl CDD cd23546 cd23546 467076 TFP_LU_ECD_Ly6G6c extracellular domain (ECD) found in lymphocyte antigen 6 complex locus protein G6c (Ly6G6c) and similar proteins. Ly6G6c is a glycosylated, GPI-anchored, cell surface molecule, located on filopodia, which could act as cell receptor with potential roles in signaling or cell-cell interactions. Ly6G6c contains an extracellular domain (ECD) which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 82 matched cddid_all.tbl CDD cd23547 cd23547 467077 TFP_LU_ECD_Ly6G6d extracellular domain (ECD) found in lymphocyte antigen 6 complex locus protein G6d (Ly6G6d) and similar proteins. Ly6G6d (also called protein Ly6-D, or megakaryocyte-enhanced gene transcript 1 protein) is a glycosylated, GPI-anchored, cell surface molecule, located on filopodia, which could act as cell receptor with potential roles in signaling or cell-cell interactions. Ly6G6d contains an extracellular domain (ECD) which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 92 matched cddid_all.tbl CDD cd23548 cd23548 467078 TFP_LU_ECD_Ly6G6e extracellular domain (ECD) found in lymphocyte antigen 6 complex locus protein G6e (Ly6G6e) and similar proteins. Ly6G6e (also called lymphocyte antigen 6G6e) is a glycosylated, GPI-anchored, cell surface molecule, located on filopodia, which could act as cell receptor with potential roles in signaling or cell-cell interactions. It may act as a modulator of nicotinic acetylcholine receptors (nAChRs) activity. In vitro it potentiates alpha-3:beta-4-containing nAChRs maximum response by increasing peak current and slowing down receptor desensitization; the activity is dependent on its cell surface localization. Ly6G6e contains an extracellular domain (ECD) which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 78 matched cddid_all.tbl CDD cd23549 cd23549 467079 TFP_LU_ECD_Ly6H extracellular domain (ECD) found in lymphocyte antigen 6H (Ly-6H) and similar proteins. Ly-6H may act as a modulator of nicotinic acetylcholine receptors (nAChRs) activity. In vitro it inhibits alpha-3:beta-4-containing nAChRs maximum response. Ly-6H may play a role in the intracellular trafficking of alpha-7-containing nAChRs and may inhibit their expression at the cell surface. It seems to inhibit alpha-7/CHRNA7 signaling in hippocampal neurons. Ly-6H contains an extracellular domain (ECD) which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 88 matched cddid_all.tbl CDD cd23550 cd23550 467080 TFP_LU_ECD_Ly6K extracellular domain (ECD) found in lymphocyte antigen 6K (Ly-6K) and similar proteins. Ly-6K is required for sperm migration into the oviduct and male fertility by controlling binding of sperm to zona pellucida. It may play a role in cell growth. Ly-6K contains an extracellular domain (ECD) which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 86 matched cddid_all.tbl CDD cd23551 cd23551 467081 TFP_LU_ECD_Ly6L extracellular domain (ECD) found in lymphocyte antigen 6L (Ly-6L) and similar proteins. Ly-6L (also called lymphocyte antigen 6 complex locus protein L) contains an extracellular domain (ECD) which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 86 matched cddid_all.tbl CDD cd23552 cd23552 467082 TFP_LU_ECD_Ly6M extracellular domain (ECD) found in Mus musculus Ly-6 family protein Ly-6M and similar proteins. Ly-6M is a novel member of the Ly-6 family of hematopoietic proteins. It contains an extracellular domain (ECD) which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 80 matched cddid_all.tbl CDD cd23553 cd23553 467083 TFP_LU_ECD_Ly6PGE extracellular domain (ECD) found in Danio rerio lymphocyte antigen 6 family member PGE (Ly6PGE) and similar proteins. Ly6PGE is an uncharacterized Ly-6/uPAR family protein. It contains an extracellular domain (ECD) which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 77 matched cddid_all.tbl CDD cd23554 cd23554 467084 TFP_LU_ECD_CD59 extracellular domain (ECD) found in CD59 glycoprotein and similar proteins. CD59 (also called 1F5 antigen, or 20 kDa homologous restriction factor, or HRF-20, or MAC-inhibitory protein (MAC-IP), or MEM43 antigen, or membrane attack complex inhibition factor (MACIF), or membrane inhibitor of reactive lysis (MIRL), or protectin) is an LY-6-like protein expressed in human lymphoid cells and inhibits the action of the complement membrane attack complex (MAC) on homologous cells. It acts by binding to the C8 and/or C9 complements of the assembling MAC, thereby preventing incorporation of the multiple copies of C9 required for complete formation of the osmolytic pore. This inhibitor appears to be species-specific. CD59 is also involved in signal transduction for T-cell activation complexed to a protein tyrosine kinase. CD59 contains an extracellular domain (ECD) which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 70 matched cddid_all.tbl CDD cd23555 cd23555 467085 TFP_LU_ECD_GML extracellular domain (ECD) found in glycosyl-phosphatidylinositol-anchored molecule-like protein (GML) and similar proteins. GML may play a role in the apoptotic pathway or cell-cycle regulation induced by p53/TP53 after DNA damage. It contains an extracellular domain (ECD) that belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 87 matched cddid_all.tbl CDD cd23556 cd23556 467086 TFP_LU_ECD_uPAR_rpt1 first extracellular domain (ECD) found in urokinase plasminogen activator surface receptor (uPAR) and similar proteins. uPAR (also called U-PAR, or monocyte activation antigen Mo3, or CD87) acts as a receptor for urokinase plasminogen activator. It plays a role in localizing and promoting plasmin formation. It mediates the proteolysis-independent signal transduction activation effects of U-PA. It is subject to negative-feedback regulation by U-PA which cleaves it into an inactive form. uPAR contains three extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). This model corresponds to the first ECD. 79 matched cddid_all.tbl CDD cd23557 cd23557 467087 TFP_LU_ECD_uPAR_rpt2 second extracellular domain (ECD) found in urokinase plasminogen activator surface receptor (uPAR) and similar proteins. uPAR (also called U-PAR, or monocyte activation antigen Mo3, or CD87) acts as a receptor for urokinase plasminogen activator. It plays a role in localizing and promoting plasmin formation. It mediates the proteolysis-independent signal transduction activation effects of U-PA. It is subject to negative-feedback regulation by U-PA which cleaves it into an inactive form. uPAR contains three extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). This model corresponds to the second ECD. 85 matched cddid_all.tbl CDD cd23558 cd23558 467088 TFP_LU_ECD_uPAR_rpt3 third extracellular domain (ECD) found in urokinase plasminogen activator surface receptor (uPAR) and similar proteins. uPAR (also called U-PAR, or monocyte activation antigen Mo3, or CD87) acts as a receptor for urokinase plasminogen activator. It plays a role in localizing and promoting plasmin formation. It mediates the proteolysis-independent signal transduction activation effects of U-PA. It is subject to negative-feedback regulation by U-PA which cleaves it into an inactive form. uPAR contains three extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). This model corresponds to the third ECD. 93 matched cddid_all.tbl CDD cd23559 cd23559 467089 TFP_LU_ECD_LYPD1 extracellular domain (ECD) found in Ly6/PLAUR domain-containing protein 1 (LYPD1) and similar proteins. LYPD1 (also called putative HeLa tumor suppressor (PHTS)) may act as a modulator of nicotinic acetylcholine receptors (nAChRs) activity. In vitro LYPD1 increases receptor desensitization and decreases affinity for ACh of alpha-4:beta-2-containing nAChRs. It may play a role in the intracellular trafficking of alpha-4:beta-2 and alpha-7-containing nAChRs and may inhibit their expression at the cell surface. It may be involved in the control of anxiety. LYPD1 also functions as a novel putative tumor suppressor involved in the transformation reversion of HeLaHF cells independently of the p53 pathway. LYPD1 contains an extracellular domain (ECD) that belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 85 matched cddid_all.tbl CDD cd23560 cd23560 467090 TFP_LU_ECD_SLURP1_like extracellular domain (ECD) found in the secreted Ly-6/uPAR-related protein 1 (SLURP-1)-like family. The SLURP-1-like family includes SLURP-1 and Ly6/PLAUR domain-containing protein 2 (LYPD2). SLURP-1 (also called ARS component B, or ARS (component B)-81/S, or anti-neoplastic urinary protein (ANUP)) has an antitumor activity. It was found to be a marker of late differentiation of the skin. It is implicated in maintaining the physiological and structural integrity of the keratinocyte layers of the skin. In vitro SLURP-1 down-regulates keratinocyte proliferation; the function may involve the proposed role as modulator of nicotinic acetylcholine receptors (nAChRs) activity. In vitro it inhibits alpha-7-dependent nAChR currents in an allosteric manner. In T cells SLURP-1 may be involved in regulation of intracellular Ca(2+) signaling. It may also have an immunomodulatory function in the cornea. The function may implicate a possible role as a scavenger receptor for PLAU thereby blocking PLAU-dependent functions of PLAUR such as in cell migration and proliferation. LYPD2 is a lymphocyte antigen-6 family protein and shows high sequence similarity with SLURP-1. Members in this family contain an extracellular domain (ECD) that belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 78 matched cddid_all.tbl CDD cd23561 cd23561 467091 TFP_LU_ECD_SLURP2 extracellular domain (ECD) found in Secreted Ly-6/uPAR-related protein 2 (SLURP-2) and similar proteins. SLURP-2 (also called Lynx1, or secreted Ly-6/uPAR domain-containing protein 2, or secreted LY6/PLAUR domain-containing protein 2) binds and may modulate the functional properties of nicotinic and muscarinic acetylcholine receptors. It may regulate keratinocytes proliferation, differentiation, and apoptosis. In vitro SLURP-2 moderately inhibits ACh-evoked currents of alpha-3:beta-2-containing nAChRs and strongly inhibits alpha-4:beta-2-containing nAChRs, modulates alpha-7-containing nAChRs, and inhibits nicotine-induced signaling probably implicating alpha-3:beta-4-containing nAChRs. It may act on alpha-3:beta-2 and alpha-7 nAChRs in an orthosteric, and on mAChRs, such as CHRM1 and CHRM3, in an allosteric manner. SLURP-2 contains an extracellular domain (ECD) that belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 75 matched cddid_all.tbl CDD cd23562 cd23562 467092 TFP_LU_ECD_LYPD3_rpt1 first extracellular domain (ECD) found in Ly6/PLAUR domain-containing protein 3 (LYPD3) and similar proteins. LYPD3 (also called GPI-anchored metastasis-associated protein C4.4A homolog, or matrigel-induced gene C4 protein (MIG-C4)) supports cell migration. It may be involved in urothelial cell-matrix interactions as well as in tumor progression. LYPD3 contains two extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). This model corresponds to the first ECD. 87 matched cddid_all.tbl CDD cd23563 cd23563 467093 TFP_LU_ECD_LYPD3_rpt2 second extracellular domain (ECD) found in Ly6/PLAUR domain-containing protein 3 (LYPD3) and similar proteins. LYPD3 (also called GPI-anchored metastasis-associated protein C4.4A homolog, or matrigel-induced gene C4 protein (MIG-C4)) supports cell migration. It may be involved in urothelial cell-matrix interactions as well as in tumor progression. LYPD3 contains two extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). This model corresponds to the second ECD. 88 matched cddid_all.tbl CDD cd23564 cd23564 467094 TFP_LU_ECD_LYPD4_rpt1_like first extracellular domain (ECD) found in the Ly6/PLAUR domain-containing protein 4 (LYPD4)-like family. The LYPD4-like family includes LYPD4, testis-expressed protein 101 (TEX101), and CD177 antigen. LYPD4 is an acrosome protein expressed specifically in mammalian testes and sperm. It plays an essential role in mammalian fertilization. TEX101 (also called cell surface receptor NYD-SP8, or scleroderma-associated autoantigen, or spermatogenesis-related gene protein (SGRG)) is a germ cell-specific glycosylphosphatidylinositol (GPI)-anchored protein essential for sperm fertility and spermatogenesis. It plays a role in fertilization by controlling binding of sperm to zona pellucida and migration of spermatozoa into the oviduct. It is associated with Ly6k during spermatogenesis in testis and is required for stable expression of lymphocyte antigen 6 family member K (Ly6k) on testicular germ cells. CD177, also called human neutrophil alloantigen 2a (HNA-2a), or NB1 glycoprotein (NB1 GP), or polycythemia rubra vera protein 1 (PRV-1), is a cell surface protein normally expressed on neutrophil. It modulates the function and homeostasis of tumor-infiltrating regulatory T cells. The expression of CD177 is an important biomarker of myeloproliferative diseases. HNA-2a is expressed on subpopulations of neutrophils. Gene CD177 has two alleles: NB1 and PRV-1, which encode a glycosylphoshatidylinositol (GPI)-anchored protein with three N-glycosylation sites that belongs to the uPAR/CD59/Ly6 snake toxin superfamily. NB1 glycoprotein binds to the endothelial cell adhesion molecule, platelet endothelial cell adhesion molecule-1 (PECAM-1) and participates in neutrophil transmigration. PRV-1 is a novel hematopoietic cell surface receptor which is overexpressed in polycythemia rubra vera. LYPD4 and TEX101 contain two extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). This model corresponds to the first ECD. CD177 contains four ECD domains. This model corresponds to the first ECD domain of LYPD4 and TEX101, as well as first and third ECD domains of CD177. 99 matched cddid_all.tbl CDD cd23565 cd23565 467095 TFP_LU_ECD_LYPD5_rpt1 first extracellular domain (ECD) found in Ly6/PLAUR domain-containing protein 5 (LYPD5) and similar proteins. LYPD5 (also called Haldisin (human antigen with LU-domains expressed in skin)) is a novel differentiation marker of stratum granulosum in squamous epithelia. LYPD5 contains two extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). This model corresponds to the first ECD. 95 matched cddid_all.tbl CDD cd23566 cd23566 467096 TFP_LU_ECD_LYPD5_rpt2 second extracellular domain (ECD) found in Ly6/PLAUR domain-containing protein 5 (LYPD5) and similar proteins. LYPD5 (also called Haldisin (human antigen with LU-domains expressed in skin)) is a novel differentiation marker of stratum granulosum in squamous epithelia. LYPD5 contains two extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). This model corresponds to the second ECD. 96 matched cddid_all.tbl CDD cd23567 cd23567 467097 TFP_LU_ECD_LYPD6_like extracellular domain (ECD) found in the Ly6/PLAUR domain-containing protein 6 (LYPD6)-like family. The LYPD6-like family includes LYPD6 and LYPD6B. LYPD6 acts as a modulator of nicotinic acetylcholine receptors (nAChRs) function in the brain. It inhibits nicotine-induced Ca(2+) influx through nAChRs. It functions as a positive regulator of Wnt/beta-catenin signaling. LYPD6B (also called LYPD7) may act as a modulator of nicotinic acetylcholine receptors (nAChRs) activity. In vitro it acts on nAChRs in a subtype- and stoichiometry-dependent manner. LYPD6B modulates specifically alpha-3(3):beta-4(2) nAChRs by enhancing the sensitivity to ACh, decreasing ACh-induced maximal current response and increasing the rate of desensitization to ACh; has no effect on alpha-7 homomeric nAChRs; modulates alpha-3(2):alpha-5:beta-4(2) nAChRs in the context of CHRNA5/alpha-5 variant Asn-398, but not its wild-type sequence. LYPD6B also activates AP1 (PMA)-mediated transcriptional activation. Members in this family contain an extracellular domain (ECD) that belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 88 matched cddid_all.tbl CDD cd23568 cd23568 467098 TFP_LU_ECD_LYPD8_rpt1 first extracellular domain (ECD) found in Ly6/PLAUR domain-containing protein 8 (LYPD8) and similar proteins. LYPD8 is a highly glycosylated glycosylphosphatidylinositol-anchored secreted protein selectively expressed on colonic enterocytes. It mediates segregation of intestinal bacteria and epithelial cells in the colon to preserve intestinal homeostasis. LYPD8 regulates the proliferation and migration of colorectal cancer cells through inhibiting the secretion of interleukin 6 (IL 6) and tumor necrosis factor alpha (TNF alpha). LYPD8 contains two extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). This model corresponds to the first ECD. 95 matched cddid_all.tbl CDD cd23569 cd23569 467099 TFP_LU_ECD_LYPD8_rpt2 second extracellular domain (ECD) found in Ly6/PLAUR domain-containing protein 8 (LYPD8) and similar proteins. LYPD8 is a highly glycosylated glycosylphosphatidylinositol-anchored secreted protein selectively expressed on colonic enterocytes. It mediates segregation of intestinal bacteria and epithelial cells in the colon to preserve intestinal homeostasis. LYPD8 regulates the proliferation and migration of colorectal cancer cells through inhibiting the secretion of interleukin 6 (IL 6) and tumor necrosis factor alpha (TNF alpha). LYPD8 contains two extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). This model corresponds to the second ECD. 78 matched cddid_all.tbl CDD cd23570 cd23570 467100 TFP_LU_ECD_LYPD9 extracellular domain (ECD) found in Mus musculus Ly6/PLAUR domain-containing protein 9 (LYPD9) and similar proteins. LYPD9 is a testis-specific secreted protein dispensable for spermatogenesis in mouse. It contains an extracellular domain (ECD) which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 86 matched cddid_all.tbl CDD cd23571 cd23571 467101 TFP_LU_ECD_PINLYP_rpt1 first extracellular domain (ECD) found in phospholipase A2 inhibitor and Ly6/PLAUR domain-containing protein (PINLYP) and similar proteins. PINLYP is a cytotoxic necrotizing factor (CNF)-like-inhibitor family protein which is the paralog of Ly6/PLAUR domain-containing protein 8 (LYPD8), a highly glycosylated glycosylphosphatidylinositol-anchored secreted protein that mediates segregation of intestinal bacteria and epithelial cells in the colon to preserve intestinal homeostasis. PINLYP contains two extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). This model corresponds to the first ECD. 89 matched cddid_all.tbl CDD cd23572 cd23572 467102 TFP_LU_ECD_PINLYP_rpt2 second extracellular domain (ECD) found in phospholipase A2 inhibitor and Ly6/PLAUR domain-containing protein (PINLYP) and similar proteins. PINLYP is a cytotoxic necrotizing factor (CNF)-like-inhibitor family protein which is the paralog of Ly6/PLAUR domain-containing protein 8 (LYPD8), a highly glycosylated glycosylphosphatidylinositol-anchored secreted protein that mediates segregation of intestinal bacteria and epithelial cells in the colon to preserve intestinal homeostasis. PINLYP contains two extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). This model corresponds to the second ECD. 80 matched cddid_all.tbl CDD cd23573 cd23573 467103 TFP_LU_ECD_PSCA extracellular domain (ECD) found in prostate stem cell antigen (PSCA) and similar proteins. PSCA may be involved in the regulation of cell proliferation. It has a cell-proliferation inhibition activity in vitro. PSCA may also act as a modulator of nicotinic acetylcholine receptors (nAChRs) activity. In vitro it inhibits nicotine-induced signaling probably implicating alpha-3:beta-2- or alpha-7-containing nAChRs. PSCA contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 78 matched cddid_all.tbl CDD cd23574 cd23574 467104 TFP_LU_ECD_SPACA4 extracellular domain (ECD) found in sperm acrosome membrane-associated protein 4 (SPACA4). SPACA4 (also called SAMP14) is a sperm surface membrane protein that may be involved in sperm-egg plasma membrane adhesion and fusion during fertilization. SPACA4 contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 79 matched cddid_all.tbl CDD cd23575 cd23575 467105 TFP_LU_ECD_GPIHBP1 extracellular domain (ECD) found in glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1 (GPI-HBP1) and similar proteins. GPI-HBP1 (also called GPI-anchored HDL-binding protein 1, or high density lipoprotein-binding protein 1) is an endothelial cell transporter for lipoprotein lipase. It mediates the transport of lipoprotein lipase LPL from the basolateral to the apical surface of endothelial cells in capillaries and anchors LPL on the surface of endothelial cells in the lumen of blood capillaries. GPI-HBP1 protects LPL against loss of activity, and against ANGPTL4-mediated unfolding. Thereby, it plays an important role in lipolytic processing of chylomicrons by LPL, triglyceride metabolism and lipid homeostasis. GPI-HBP1 binds chylomicrons and phospholipid particles that contain APOA5. It also binds high-density lipoprotein (HDL) and plays a role in the uptake of lipids from HDL. GPI-HBP1 contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 83 matched cddid_all.tbl CDD cd23576 cd23576 467106 TFP_LU_ECD_BAMBI extracellular domain (ECD) found in BMP and activin membrane-bound inhibitor (BAMBI) and similar proteins. BAMBI (also called non-metastatic gene A protein (NMA), or putative transmembrane protein NMA) is a transmembrane protein that acts as an important regulator of trabecular meshwork extracellular matrix and ocular hypertension. It negatively regulates the signaling activity of transforming growth factor (TGF)-beta, activin, and bone morphogenetic protein (BMP). BAMBI can function as a positive regulator of the Wnt/beta-catenin pathway to promote cell proliferation. It may be a reactive oxygen regulator to affect adipogenesis, thereby controlling obesity and metabolic syndrome. BAMBI contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 80 matched cddid_all.tbl CDD cd23577 cd23577 467107 TFP_LU_ECD_PATE1 extracellular domain (ECD) found in prostate and testis expressed protein 1 (PATE1) and similar proteins. PATE1 is a novel sperm-associated protein generally expressed in male genital tract and related to sperm development, maturation and fertilization. It contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 82 matched cddid_all.tbl CDD cd23578 cd23578 467108 TFP_LU_ECD_PATE2 extracellular domain (ECD) found in prostate and testis expressed protein 2 (PATE2) and similar proteins. PATE2 (also called PATE-like protein M (PATE-M)) is a member of the prostate and testis expression (PATE)-like family of proteins that likely play important roles in reproductive and neuronal physiology. They are expressed mainly in the male genital tract and involved in sperm-oolemma fusion and penetration, but not sperm-zona binding. PATE2 contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 82 matched cddid_all.tbl CDD cd23579 cd23579 467109 TFP_LU_ECD_PATE3 extracellular domain (ECD) found in prostate and testis expressed protein 3 (PATE3) and similar proteins. PATE3 (also called acrosomal vesicle protein HEL-127, or PATE-like protein DJ (PATE-DJ)) is a member of the prostate and testis expression (PATE)-like family of proteins that likely play important roles in reproductive and neuronal physiology. They are expressed mainly in the male genital tract and involved in sperm-oolemma fusion and penetration, but not sperm-zona binding. PATE3 contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 80 matched cddid_all.tbl CDD cd23580 cd23580 467110 TFP_LU_ECD_PATE4 extracellular domain (ECD) found in prostate and testis expressed protein 4 (PATE4) and similar proteins. PATE4, also called prostate and testis expressed 4, or PATE-like protein B) is a member of the prostate and testis expression (PATE)-like family of proteins that likely play important roles in reproductive and neuronal physiology. They are expressed mainly in the male genital tract and involved in sperm-oolemma fusion and penetration, but not sperm-zona binding. PATE4 may modulate the function of nicotinic acetylcholine receptors and enhance sperm motility. PATE4 contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 79 matched cddid_all.tbl CDD cd23581 cd23581 467111 TFP_LU_ECD_mPATE6_like extracellular domain (ECD) found in Mus musculus prostate and testis expressed protein 6 (PATE6) and similar proteins. The family includes Mus musculus PATE6 and PATE7. PATE6 (also called called prostate and testis expressed 6, or PATE-like protein C) acts as nicotinic acetylcholine receptor (nAChR) regulator. The biological function of PATE7 (also called called prostate and testis expressed 7) remains unclear. Members in this family contain an extracellular domain (ECD) which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 82 matched cddid_all.tbl CDD cd23582 cd23582 467112 TFP_LU_ECD_TRP extracellular domain (ECD) found in Acropora millepora threonine-rich protein (TRP) and similar proteins. TRP contains an extracellular domain (ECD) that belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 83 matched cddid_all.tbl CDD cd23583 cd23583 467113 TFP_LU_ECD_Prod1 extracellular domain (ECD) found in Notophthalmus viridescens Prod1 and similar proteins. Prod1 is a member of the three-finger protein superfamily implicated in salamander limb regeneration. It contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 68 matched cddid_all.tbl CDD cd23584 cd23584 467114 TFP_LU_ECD_PMF extracellular domain (ECD) found in Plethodon shermani plethodontid modulating factor (PMF) and similar proteins. PMF is a hypervariable salamander courtship pheromone that belongs to three-finger protein (TFP) superfamily. It affects female receptivity when delivered to the female's nares during courtship. PMF contains an extracellular domain (ECD) which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 65 matched cddid_all.tbl CDD cd23585 cd23585 467115 TFP_LU_ECD_LYNX1 extracellular domain (ECD) found in Ly-6/neurotoxin-like protein 1 (LYNX1) and similar protein. LYNX1 (also called testicular tissue protein Li 112) is an endogenous prototoxin that acts in different tissues through interaction to nicotinic acetylcholine receptors (nAChRs). It prevents plasticity in the primary visual cortex late in life. LYNX1 contains an extracellular domain (ECD) that belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 74 matched cddid_all.tbl CDD cd23586 cd23586 467116 TFP_LU_ECD_sma6 extracellular domain (ECD) found in Caenorhabditis elegans serine/threonine-protein kinase receptor sma-6 and similar proteins. Sma-6 (EC 2.7.11.30) is serine/threonine-protein kinase receptor that binds transforming growth factor-beta (TGF-beta)-like ligands dbl-1 and perhaps daf-7. Upon ligand binding, it probably activates a TGF-beta-like signaling pathway. Sma-6 contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 78 matched cddid_all.tbl CDD cd23588 cd23588 467117 TFP_LU_ECD_PLIG extracellular domain (ECD) found in Elaphe quadrivirgata phospholipase A2 inhibitor gamma subunit (gamma-PLI) family. The gamma-PLI family includes gamma-PLI A and gamma-PLI B. Gamma-PLI inhibits the enzymatic activity of all phospholipase A2 (PA2) groups. Gamma-PLI A and gamma-PLI B form a heterodimer. Members in this family contain an extracellular domain (ECD) that belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 82 matched cddid_all.tbl CDD cd23589 cd23589 467118 TFP_LU_ECD_Rtv extracellular domain (ECD) found in Drosophila melanogaster protein retroactive and similar proteins. Retroactive (Rtv) is a membrane-anchored extracellular protein required for cuticle organization in the larva of Drosophila melanogaster. It is a member of the Drosophila Ly6 superfamily. Retroactive contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 94 matched cddid_all.tbl CDD cd23590 cd23590 467119 TFP_LU_ECD_Bou extracellular domain (ECD) found in Drosophila melanogaster protein boudin and similar proteins. Boudin (Bou) is a glycosylphosphatidylinositol (GPI)-anchored membrane protein secreted extracellularly. It is a member of the Drosophila Ly6 superfamily. Boudin plays an essential role in the organization of septate junctions (SJs) and the maintenance of paracellular barriers in Drosophila epithelia and chordotonal organs. It is required for SJ formation in a non-cell-autonomous fashion. Boudin contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 88 matched cddid_all.tbl CDD cd23591 cd23591 467120 TFP_LU_ECD_Crim extracellular domain (ECD) found in Drosophila melanogaster protein crimpled and similar proteins. Crimpled (Crim) is a member of the Drosophila Ly6 superfamily. It is required for septate junction (SJ) formation and function in a tissue-autonomous manner. Crimpled contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 116 matched cddid_all.tbl CDD cd23592 cd23592 467121 TFP_LU_ECD_Crok extracellular domain (ECD), Ly6/uPAR superfamily, three finger domain (TFD) fold, found in Drosophila melanogaster protein crooked and similar proteins. Crooked (Crok) is a glycosylphosphatidylinositol (GPI)-anchored protein that plays an essential role in septa formation, the membrane accumulation of SJ components and paracellular barrier functions. It required for septate junction (SJ) formation and function in a tissue-autonomous manner. Crooked is specifically required for correct membrane trafficking of Neurexin IV, a central SJ component. Crooked is a member of the Drosophila Ly6 superfamily. It contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 104 matched cddid_all.tbl CDD cd23593 cd23593 467122 TFP_LU_ECD_Twit extracellular domain (ECD) found in Drosophila melanogaster Target of wit (Twit) and similar proteins. Twit is a GPI-anchored membrane ligand of the Ly6 family that participates in retrograde signalling as a downstream target of the bone morphogenetic protein (BMP) pathway receptor encoded by Wishful thinking (Wit). It acts in neurons, regulating spontaneous neurotransmitter release during the maturation of larval neuromuscular junctions. Twit contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 101 matched cddid_all.tbl CDD cd23594 cd23594 467123 TFP_LU_ECD_Atilla extracellular domain (ECD) found in Drosophila melanogaster protein atilla and similar proteins. Atilla is a glycosylphosphatidylinositol (GPI)-anchored protein, a member of the Drosophila Ly6 superfamily. It contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 101 matched cddid_all.tbl CDD cd23595 cd23595 467124 TFP_LU_ECD_Qvr extracellular domain (ECD) found in Drosophila melanogaster protein quiver and similar proteins. Quiver (Qvr, also called protein SLEEPLESS) is a glycosylphosphatidylinositol (GPI)-anchored protein required for homeostatic regulation of sleep under normal conditions and after sleep deprivation in Drosophila. It is a bifunctional regulator of excitability and cholinergic synaptic transmission. It is critical for regulating the levels, localization, and activity of the sleep-modulating potassium channel Shaker. Quiver is a member of the Drosophila Ly6 superfamily. It contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 90 matched cddid_all.tbl CDD cd23596 cd23596 467125 TFP_LU_ECD_Tkv extracellular domain (ECD) found in Drosophila melanogaster receptor protein serine/threonine kinase Thickveins and similar proteins. Thickveins (Tkv) is a decapentaplegic (dpp) type I receptor encoded by the thick veins (tkv) gene that is expressed in a highly localized and dynamic pattern during development. Thickveins is the ortholog of the human activin receptor-like kinase (ALK)-3/6. It contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 88 matched cddid_all.tbl CDD cd23597 cd23597 467126 TFP_LU_ECD_Bncr extracellular domain (ECD) found in Danio rerio protein Bouncer and similar proteins. Bouncer (bncr) is an oocyte-expressed fertilization factor that mediates sperm-egg binding and is essential for sperm entry into the egg. It is necessary and sufficient to mediate species-specific gamete recognition and fertilization, which is essential for vertebrate species performing external fertilization. Bouncer contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 78 matched cddid_all.tbl CDD cd23598 cd23598 467127 TFP_LU_ECD_Babo extracellular domain (ECD) found in Drosophila melanogaster Baboon and similar proteins. Baboon (Babo) is the Drosophila transforming growth factor-beta (TGF-beta)/activin-specific type I receptor that transmits signals through dSmad2. Baboon/dSmad2-mediated TGF-beta signaling is required during late larval stage for development of adult-specific neurons. In addition to dSmad2, it can Mad and bone morphogenetic protein (BMP)-specific R-Smad. Baboon is the ortholog of the human activin receptor-like kinase (ALK)-4/5/7. It contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 78 matched cddid_all.tbl CDD cd23599 cd23599 467128 TFP_LU_ECD_Cold extracellular domain (ECD) found in Drosophila melanogaster protein coiled and similar proteins. Coiled (Cold) is coded by the Drosophila cold gene that is expressed in a subset of glial cells. It is a member of the Drosophila Ly6 superfamily of extracellular ligands and could behave as a membrane component of the septate junctions (SJ). Cold is essential for tracheal morphogenesis and the organization of the insect SJ in a cell autonomous way. It is also required for organization of the blood-brain-barrier in the Drosophila nervous system. Coiled contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 95 matched cddid_all.tbl CDD cd23600 cd23600 467129 TFP_LU_ECD_Sax extracellular domain (ECD) found in Drosophila melanogaster Saxophone and similar proteins. Saxophone (Sax) is the Drosophila bone morphogenetic protein (BMP) type I receptor that transmits signal through Mad. It functions as a Dpp (Decapentaplegic) receptor in Drosophila embryos, but that its activity is normally inhibited by the O-linked glycosyltransferase Sxc (Super sex combs). Saxophone is the ortholog of the human activin receptor-like kinase (ALK)-1/2. It contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 89 matched cddid_all.tbl CDD cd23610 cd23610 467130 TFP_LU_ECD_C9orf57 extracellular domain (ECD) found in Homo sapiens uncharacterized protein C9orf57 and similar proteins. C9orf57 contains an extracellular domain (ECD) that belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 83 matched cddid_all.tbl CDD cd23611 cd23611 467131 TFP_LU_ECD_THFP5 extracellular domain (ECD) found in Danio rerio three-finger protein 5 (THFP5) and similar proteins. THFP5 contains an extracellular domain (ECD) which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 71 matched cddid_all.tbl CDD cd23612 cd23612 467132 TFP_LU_ECD_BMPR1A extracellular domain (ECD) found in bone morphogenetic protein receptor type-1A (BMPR-1A) and similar proteins. BMPR-1A (EC 2.7.11.30, also called BMP type-1A receptor, or activin receptor-like kinase 3 (ALK-3), or serine/threonine-protein kinase receptor R5 (SKR5), or CD292) on ligand binding, forms a receptor complex consisting of two type II, and two type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. BMPR-1A is the receptor for BMP2, BMP4, GDF5, and GDF6. It positively regulates chondrocyte differentiation through GDF5 interaction and mediates induction of adipogenesis by GDF6. This model corresponds to extracellular domain (ECD) of BMPR-1A, which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 84 matched cddid_all.tbl CDD cd23613 cd23613 467133 TFP_LU_ECD_BMPR1B extracellular domain (ECD) found in bone morphogenetic protein receptor type-1B (BMPR-1B) and similar proteins. BMPR-1B (EC 2.7.11.30, also called BMP type-1B receptor, or CDw293, or activin receptor-like kinase 6 (ALK-6)) on ligand binding forms a receptor complex consisting of two type II and two type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. BMPR-1B is the receptor for BMP7/OP-1 and GDF5. It positively regulates chondrocyte differentiation through GDF5 interaction. This model corresponds to extracellular domain (ECD) of BMPR-1B, which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 86 matched cddid_all.tbl CDD cd23614 cd23614 467134 TFP_LU_ECD_BMPR2 extracellular domain (ECD) found in bone morphogenetic protein receptor type-2 (BMPR-2) and similar proteins. BMPR2 (EC 2.7.11.30, also called BMP type-2 receptor, or bone morphogenetic protein receptor type II (BMPR-II), or BMP type II receptor) on ligand binding forms a receptor complex consisting of two type II and two type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. BMPR2 binds to BMP7, BMP2, and less efficiently, BMP4. The binding is weak, but enhanced by the presence of type I receptors for BMPs. It also mediates the induction of adipogenesis by GDF6. This model corresponds to the extracellular domain (ECD) of BMPR2, which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 101 matched cddid_all.tbl CDD cd23615 cd23615 467135 TFP_LU_ECD_ACVR2 extracellular domain (ECD) found in the activin receptor type-2 (ACTR-II) family. The ACTR-II family includes activin receptor type-2A (ACTR-IIA) and activin receptor type-2B (ACTR-IIB). They form a receptor complex consisting of two type II and two type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. ACTR-IIA is the receptor for activin A, activin B, and inhibin A. It mediates the induction of adipogenesis by GDF6. ACTR-IIA also interacts with type I receptor ACVR1 and bone morphogenetic protein 7 (BMP7). ACTR-IIB also interacts with vacuolar protein sorting 39 (Vps39), dynein light chain Tctex-type 1 (DYNLT1), bone morphogenetic protein 2 (BMP2), and bone morphogenetic protein 3 (BMP3). This model corresponds to the extracellular domain (ECD) of ACTR-IIA and ACTR-IIB, which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 94 matched cddid_all.tbl CDD cd23616 cd23616 467136 TFP_LU_ECD_AMHR2 extracellular domain (ECD) found in anti-Muellerian hormone type-2 receptor (AMHR2) and similar proteins. AMHR2 (EC 2.7.11.30, also called anti-Muellerian hormone type II receptor (MISRII), or AMH type II receptor, or MIS type II receptor, or MRII, on ligand binding) forms a receptor complex consisting of two type II and two type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. AMHR2 is the receptor for anti-Muellerian hormone. This model corresponds to the extracellular domain (ECD) of AMHR2, which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 89 matched cddid_all.tbl CDD cd23617 cd23617 467137 TFP_LU_ECD_Daf4 extracellular domain (ECD) found in Caenorhabditis elegans cell surface receptor Daf-4 and similar proteins. Daf-4 (also called abnormal dauer formation protein 4) is involved in a TGF-beta pathway. It may be a receptor for TGF-beta-like ligand Daf-7. Daf-4 controls the decision of whether or not larvae enter a developmentally arrested state, known as dauer, in response to environmental conditions. It regulates body size and male tail patterning. It is also involved in regulating entry into quiescence triggered by satiety and in sensitivity to CO2 levels. Members in this family contain an extracellular domain (ECD) that belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 102 matched cddid_all.tbl CDD cd23618 cd23618 467138 TFP_LU_ECD_Wit extracellular domain (ECD) found in Drosophila melanogaster Wishful thinking (Wit) and similar proteins. Wit is the Drosophila homolog to the mammalian bone morphogenetic protein (BMP) type II receptor, BMPRII. It is essential for nervous system development in Drosophila. It is necessary for BMP signaling and required for eggshell patterning. Wit contains an extracellular domain (ECD), which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 103 matched cddid_all.tbl CDD cd23619 cd23619 467139 TFP_LU_ECD_SLURP1 extracellular domain (ECD) found in secreted Ly-6/uPAR-related protein 1 (SLURP-1) and similar proteins. SLURP-1 (also called ARS component B, or ARS (component B)-81/S, or anti-neoplastic urinary protein (ANUP)) has antitumor activity. It was found to be a marker of late differentiation of the skin. It is implicated in maintaining the physiological and structural integrity of the keratinocyte layers of the skin. In vitro SLURP-1 down-regulates keratinocyte proliferation; the function may involve the proposed role as modulator of nicotinic acetylcholine receptors (nAChRs) activity. In vitro it inhibits alpha-7-dependent nAChR currents in an allosteric manner. In T cells SLURP-1 may be involved in regulation of intracellular Ca(2+) signaling. It may also have an immunomodulatory function in the cornea. The function may implicate a possible role as a scavenger receptor for PLAU thereby blocking PLAU-dependent functions of PLAUR such as in cell migration and proliferation. SLURP-1 contains an extracellular domain (ECD) that belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 78 matched cddid_all.tbl CDD cd23620 cd23620 467140 TFP_LU_ECD_LYPD2 extracellular domain (ECD) found in Ly6/PLAUR domain-containing protein 2 (LYPD2) and similar proteins. LYPD2 is a lymphocyte antigen-6 family protein. It contains an extracellular domain (ECD) that belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 79 matched cddid_all.tbl CDD cd23621 cd23621 467141 TFP_LU_ECD_LYPD4_rpt1 first extracellular domain (ECD) found in Ly6/PLAUR domain-containing protein 4 (LYPD4) and similar proteins. LYPD4 is an acrosome protein expressed specifically in mammalian testes and sperm. It plays an essential role in mammalian fertilization. LYPD4 contains two extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). This model corresponds to the first ECD. 103 matched cddid_all.tbl CDD cd23622 cd23622 467142 TFP_LU_ECD_TEX101_rpt1 first extracellular domain (ECD) found in testis-expressed protein 101 (TEX101) and similar proteins. TEX101 (also called cell surface receptor NYD-SP8, or scleroderma-associated autoantigen, or spermatogenesis-related gene protein (SGRG)) is a germ cell-specific glycosylphosphatidylinositol (GPI)-anchored protein essential for sperm fertility and spermatogenesis. It plays a role in fertilization by controlling binding of sperm to zona pellucida and migration of spermatozoa into the oviduct. It is associated with Ly6k during spermatogenesis in testis and is required for stable expression of lymphocyte antigen 6 family member K (Ly6k) on testicular germ cells. TEX101 contains two extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). This model corresponds to the first ECD. 99 matched cddid_all.tbl CDD cd23623 cd23623 467143 TFP_LU_ECD_CD177_rpt1 first extracellular domain (ECD) found in CD177 antigen and similar proteins. CD177 (also called human neutrophil alloantigen 2a (HNA-2a), or NB1 glycoprotein (NB1 GP), or polycythemia rubra vera protein 1 (PRV-1)) is a cell surface protein normally expressed on neutrophil. It modulates the function and homeostasis of tumor-infiltrating regulatory T cells. The expression of CD177 is an important biomarker of myeloproliferative diseases. HNA-2a is expressed on subpopulations of neutrophils. Gene CD177 has two alleles: NB1 and PRV-1, which encode a glycosylphoshatidylinositol (GPI)-anchored protein with three N-glycosylation sites that belongs to the uPAR/CD59/Ly6 snake toxin superfamily. NB1 glycoprotein binds to the endothelial cell adhesion molecule, platelet endothelial cell adhesion molecule-1 (PECAM-1) and participates in neutrophil transmigration. PRV-1 is a novel hematopoietic cell surface receptor which is overexpressed in polycythemia rubra vera. Members in this family contain four extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). This model corresponds to the first ECD. 100 matched cddid_all.tbl CDD cd23624 cd23624 467144 TFP_LU_ECD_CD177_rpt3 third extracellular domain (ECD) found in CD177 antigen and similar proteins. CD177 (also called human neutrophil alloantigen 2a (HNA-2a), or NB1 glycoprotein (NB1 GP), or polycythemia rubra vera protein 1 (PRV-1)) is a cell surface protein normally expressed on neutrophil. It modulates the function and homeostasis of tumor-infiltrating regulatory T cells. The expression of CD177 is an important biomarker of myeloproliferative diseases. HNA-2a is expressed on subpopulations of neutrophils. Gene CD177 has two alleles: NB1 and PRV-1, which encode a glycosylphoshatidylinositol (GPI)-anchored protein with three N-glycosylation sites that belongs to the uPAR/CD59/Ly6 snake toxin superfamily. NB1 glycoprotein binds to the endothelial cell adhesion molecule, platelet endothelial cell adhesion molecule-1 (PECAM-1) and participates in neutrophil transmigration. PRV-1 is a novel hematopoietic cell surface receptor which is overexpressed in polycythemia rubra vera. Members in this family contain four extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). This model corresponds to the third ECD. 102 matched cddid_all.tbl CDD cd23625 cd23625 467145 TFP_LU_ECD_LYPD6 extracellular domain (ECD) found in Ly6/PLAUR domain-containing protein 6 (LYPD6) and similar proteins. LYPD6 acts as a modulator of nicotinic acetylcholine receptors (nAChRs) function in the brain. It inhibits nicotine-induced Ca(2+) influx through nAChRs. It functions as a positive regulator of Wnt/beta-catenin signaling. LYPD6 contains an extracellular domain (ECD) that belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 89 matched cddid_all.tbl CDD cd23626 cd23626 467146 TFP_LU_ECD_LYPD6B extracellular domain (ECD) found in Ly6/PLAUR domain-containing protein 6B (LYPD6B) and similar proteins. LYPD6B (also called LYPD7) may act as a modulator of nicotinic acetylcholine receptors (nAChRs) activity. In vitro it acts on nAChRs in a subtype- and stoichiometry-dependent manner. LYPD6B modulates specifically alpha-3(3):beta-4(2) nAChRs by enhancing the sensitivity to ACh, decreasing ACh-induced maximal current response and increasing the rate of desensitization to ACh; has no effect on alpha-7 homomeric nAChRs; modulates alpha-3(2):alpha-5:beta-4(2) nAChRs in the context of CHRNA5/alpha-5 variant Asn-398, but not its wild-type sequence. LYPD6B also activates AP1 (PMA)-mediated transcriptional activation. LYPD6B contains an extracellular domain (ECD) that belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 88 matched cddid_all.tbl CDD cd23627 cd23627 467147 TFP_LU_ECD_UP extracellular domain (ECD) found in urinary proteins (UP1-3) and similar proteins. The family includes UP1 (also called liver regeneration-related protein LRRG05), UP2 and UP3, which are secreted proteins containing an extracellular domain (ECD) that belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 81 matched cddid_all.tbl CDD cd23628 cd23628 467148 TFP_LU_ECD_SP10_like extracellular domain (ECD) found in acrosomal protein SP-10, prostate and testis expressed protein 14 (Pate14) and similar proteins. The family includes SP-10 and Pate14. SP-10 (also called acrosomal vesicle protein 1 (ACRV1)) is a human intra-acrosomal protein that is first detected in the developing acrosome of round spermatids and is observed associated with the acrosomal membranes and matrix of mature sperm. Pate14 ( also called prostate and testis expressed 14, or secreted seminal-vesicle Ly-6 protein 1 (SSLP-1)) is a secreted Ly-6 protein purified from mouse seminal vesicle fluid. Members in this family contain an extracellular domain (ECD) which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 79 matched cddid_all.tbl CDD cd23629 cd23629 467149 TFP_LU_ECD_PLIGA extracellular domain (ECD) found in Elaphe quadrivirgata phospholipase A2 inhibitor gamma subunit A (gamma-PLI A) and similar proteins. Gamma-PLI inhibits the enzymatic activity of all phospholipase A2 (PA2) groups. There are two gamma-PLI subunits, subunit A and subunit B, which form a heterodimer. Members in this family contain an extracellular domain (ECD) that belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 83 matched cddid_all.tbl CDD cd23630 cd23630 467150 TFP_LU_ECD_PLIGB extracellular domain (ECD) found in Elaphe quadrivirgata phospholipase A2 inhibitor gamma subunit B (gamma-PLI B) and similar proteins. Gamma-PLI inhibits the enzymatic activity of all phospholipase A2 (PA2) groups. There are two gamma-PLI subunits, subunit A and subunit B, which form a heterodimer. Members in this family contain an extracellular domain (ECD) that belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 82 matched cddid_all.tbl CDD cd23631 cd23631 467151 TFP_LU_ECD_ACVR2A extracellular domain (ECD) found in activin receptor type-2A (ACTR-IIA) and similar proteins. ACTR-IIA (EC 2.7.11.30, also called activin receptor type IIA) on ligand binding forms a receptor complex consisting of two type II and two type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. ACTR-IIA is the receptor for activin A, activin B, and inhibin A. It mediates induction of adipogenesis by GDF6. ACTR-IIA also interacts with type I receptor ACVR1 and bone morphogenetic protein 7 (BMP7). This model corresponds to the extracellular domain (ECD) of ACTR-IIA, which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 95 matched cddid_all.tbl CDD cd23632 cd23632 467152 TFP_LU_ECD_ACVR2B extracellular domain (ECD) found in activin receptor type-2B (ACTR-IIB) and similar proteins. ACTR-IIB (EC 2.7.11.30, also called activin receptor type IIB) on ligand binding forms a receptor complex consisting of two type II and two type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. ACTR-IIB interacts with vacuolar protein sorting 39 (Vps39), dynein light chain Tctex-type 1 (DYNLT1), bone morphogenetic protein 2 (BMP2) and bone morphogenetic protein 3 (BMP3). This model corresponds to the extracellular domain (ECD) of ACTR-IIB, which belongs to Ly-6 antigen/uPA receptor-like (LU) superfamily and exhibits a snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). 91 matched cddid_all.tbl CDD cd23633 cd23633 467797 TFP_LU_ECD_LYPD4_rpt2_like second extracellular domain (ECD) found in the Ly6/PLAUR domain-containing protein 4 (LYPD4)-like family. The LYPD4-like family includes LYPD4, testis-expressed protein 101 (TEX101), and CD177 antigen. LYPD4 is an acrosome protein expressed specifically in mammalian testes and sperm. It plays an essential role in mammalian fertilization. TEX101, also called cell surface receptor NYD-SP8, or scleroderma-associated autoantigen, or spermatogenesis-related gene protein (SGRG), is a germ cell-specific glycosylphosphatidylinositol (GPI)-anchored protein essential for sperm fertility and spermatogenesis. It plays a role in fertilization by controlling binding of sperm to zona pellucida and migration of spermatozoa into the oviduct. It is associated with Ly6k during spermatogenesis in testes and is required for stable expression of lymphocyte antigen 6 family member K (Ly6k) on testicular germ cells. CD177, also called human neutrophil alloantigen 2a (HNA-2a), or NB1 glycoprotein (NB1 GP), or polycythemia rubra vera protein 1 (PRV-1), is a cell surface protein normally expressed on neutrophil. It modulates the function and homeostasis of tumor-infiltrating regulatory T cells. The expression of CD177 is an important biomarker of myeloproliferative diseases. HNA-2a is expressed on subpopulations of neutrophils. Gene CD177 has two alleles: NB1 and PRV-1, which encode a glycosylphoshatidylinositol (GPI)-anchored protein with three N-glycosylation sites that belongs to the uPAR/CD59/Ly6 snake toxin superfamily. NB1 glycoprotein binds to the endothelial cell adhesion molecule, platelet endothelial cell adhesion molecule-1 (PECAM-1), and participates in neutrophil transmigration. PRV-1 is a novel hematopoietic cell surface receptor which is overexpressed in polycythemia rubra vera. LYPD4 and TEX101 contain two extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and show snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). CD177 contains four ECD domains. The model corresponds to the second ECD domain of LYPD4 and TEX101, as well as second and fourth ECD domains of CD177. 76 matched cddid_all.tbl CDD cd23634 cd23634 467798 TFP_LU_ECD_TEX101_rpt2 second extracellular domain (ECD) found in testis-expressed protein 101 (TEX101) and similar proteins. TEX101, also called cell surface receptor NYD-SP8, or scleroderma-associated autoantigen, or spermatogenesis-related gene protein (SGRG), is a germ cell-specific glycosylphosphatidylinositol (GPI)-anchored protein essential for sperm fertility and spermatogenesis. It plays a role in fertilization by controlling binding of sperm to zona pellucida and migration of spermatozoa into the oviduct. It is associated with Ly6k during spermatogenesis in testes and is required for stable expression of lymphocyte antigen 6 family member K (Ly6k) on testicular germ cells. TEX101 contains two extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and show snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). The model corresponds to the second ECD domain of TEX101. 83 matched cddid_all.tbl CDD cd23635 cd23635 467799 TFP_LU_ECD_LYPD4_rpt2 second extracellular domain (ECD) found in Ly6/PLAUR domain-containing protein 4 (LYPD4) and similar proteins. LYPD4 is an acrosome protein expressed specifically in mammalian testes and sperm. It plays an essential role in mammalian fertilization. LYPD4 contains two extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and shows snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). This model corresponds to the second ECD domain of LYPD4. 88 matched cddid_all.tbl CDD cd23636 cd23636 467800 TFP_LU_ECD_CD177_rpt2 second extracellular domain (ECD) found in CD177 antigen and similar proteins. CD177, also called human neutrophil alloantigen 2a (HNA-2a), or NB1 glycoprotein (NB1 GP), or polycythemia rubra vera protein 1 (PRV-1), is a cell surface protein normally expressed on neutrophil. It modulates the function and homeostasis of tumor-infiltrating regulatory T cells. The expression of CD177 is an important biomarker of myeloproliferative diseases. HNA-2a is expressed on subpopulations of neutrophils. Gene CD177 has two alleles: NB1 and PRV-1, which encode a glycosylphoshatidylinositol (GPI)-anchored protein with three N-glycosylation sites that belongs to the uPAR/CD59/Ly6 snake toxin superfamily. NB1 glycoprotein binds to the endothelial cell adhesion molecule, platelet endothelial cell adhesion molecule-1 (PECAM-1), and participates in neutrophil transmigration. PRV-1 is a novel hematopoietic cell surface receptor which is overexpressed in polycythemia rubra vera. Members in this family contain four extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and show snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). The model corresponds to the second ECD domain of CD177. 77 matched cddid_all.tbl CDD cd23637 cd23637 467801 TFP_LU_ECD_CD177_rpt4 fourth extracellular domain (ECD) found in CD177 antigen and similar proteins. CD177, also called human neutrophil alloantigen 2a (HNA-2a), or NB1 glycoprotein (NB1 GP), or polycythemia rubra vera protein 1 (PRV-1), is a cell surface protein normally expressed on neutrophil. It modulates the function and homeostasis of tumor-infiltrating regulatory T cells. The expression of CD177 is an important biomarker of myeloproliferative diseases. HNA-2a is expressed on subpopulations of neutrophils. Gene CD177 has two alleles: NB1 and PRV-1, which encode a glycosylphoshatidylinositol (GPI)-anchored protein with three N-glycosylation sites that belongs to the uPAR/CD59/Ly6 snake toxin superfamily. NB1 glycoprotein binds to the endothelial cell adhesion molecule, platelet endothelial cell adhesion molecule-1 (PECAM-1) and participates in neutrophil transmigration. PRV-1 is a novel hematopoietic cell surface receptor which is overexpressed in polycythemia rubra vera. Members in this family contain four extracellular domains (ECDs) that belong to Ly-6 antigen/uPA receptor-like (LU) superfamily and show snake toxin-like fold (also known as three-finger toxin/3FTx fold or three-fingered protein/TFP domain fold). The model corresponds to the fourth ECD domain of CD177. 77 matched cddid_all.tbl CDD cd23640 cd23640 467877 uS3m uS3m domain family. Trypanosomal protein uS3m represents the only ribosomal protein encoded by the mitochondrial DNA. It is rich in hydrophobic amino acids and may serve as a hydrophobic core in the protein shell. uS3m is a component of Trypanosoma mitoribosome small subunits (SSUs). 65 matched cddid_all.tbl CDD cd23643 cd23643 467878 mS23 mS23 domain family. mS23 is an uncharacterized mitochondrial protein from Trypanosoma cruzi. It is a component of T. cruzi mitochondrial ribosome (mitoribosome) small subunits (Tb-mt-SSUs), which forms a complex with the C-terminal domain (CTD) of initiation factor IF-3 (Tb-mt-SSU/IF-3); it may be involved in mitoribosomal maturation. 253 matched cddid_all.tbl CDD cd23644 cd23644 467879 mS26 mS26 domain protein found in trypanosomal mitochondrial ribosomes. mS26 protein is a mitochondrial protein found in Trypanosoma, but its function has not yet been fully characterized. It is known to be a component of the small subunits of the Trypanosoma mitochondrial ribosome (Tb-mt-SSUs) and interacts with the C-terminal domain (CTD) of initiation factor IF-3 to form a complex called Tb-mt-SSU/IF-3. This complex may play a role in the maturation of the mitochondrial ribosome. 295 matched cddid_all.tbl CDD cd23645 cd23645 467059 HFD_Dpb3-like histone-fold domain found in Schizosaccharomyces pombe DNA polymerase epsilon subunit C (Dpb3) and similar proteins. Schizosaccharomyces pombe Dpb3 is an accessory component of the DNA polymerase epsilon (DNA polymerase II) that is a heterotetramer consisting of cdc20/Pol2, Dpb2, Dpb3, and Dpb4, and participates in chromosomal DNA replication. Dpb3 is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. The Dpb3-Dpb4 dimer associates with histone deacetylases, chromatin remodelers, and histones and plays a crucial role in the inheritance of histone hypoacetylation and H3K9 methylation in heterochromatin. The Dpb3-Dpb4 dimer is also required for the recruitment of sir2 to heterochromatin. 78 matched cddid_all.tbl CDD cd23649 cd23649 467880 Khc_CBD_cc cargo binding coiled-coil domain found in kinesin heavy chains. The family includes Drosophila kinesin-1, also called kinesin heavy chain (Khc), and Homo sapiens kinesin-1 heavy chain, also called conventional kinesin heavy chain/ubiquitous kinesin heavy chain (UKHC). Kinesin is a microtubule-associated force-producing protein that may play a role in organelle transport. Milt and Miro form an essential protein complex that links Khc to mitochondria for light chain-independent, anterograde transport of mitochondria. The family also includes kinesin heavy chain isoform 5A (KIF5A), also called kinesin heavy chain neuron-specific 1/neuronal kinesin heavy chain (NKHC1), and kinesin heavy chain isoform 5C (KIF5C), also called kinesin heavy chain neuron-specific 2 (NKHC2). KIF5A is a microtubule-dependent motor required for slow axonal transport of neurofilament proteins (NFH, NFM and NFL). It can induce formation of neurite-like membrane protrusions in non-neuronal cells in a ZFYVE27-dependent manner. KIF5C is involved in synaptic transmission and mediates dendritic trafficking of mRNAs. Khc comprises an N-terminal motor-domain, followed by a long coiled-coil stalk that mediates homodimerization, and an unstructured tail with regulatory function. The stalk includes the kinesin light chain (Klc) binding region and an alternative cargo binding region. The model corresponds to the cargo binding region, which is responsible for binding of the atypical tropomyosin, aTm1, a cargo adaptor that plays a stabilizing role in the interaction of Khc with RNA. 70 matched cddid_all.tbl CDD cd23650 cd23650 467881 TRP_CaM_bind1 Calmodulin binding site 1 (CBS1) found in Drosophila melanogaster transient receptor potential protein (TRP) and similar proteins. TRP is a light-sensitive calcium channel that is required for inositide-mediated Ca(2+) entry in the retina during phospholipase C (PLC)-mediated phototransduction. TRP and another retinal-specific protein, TRPL, act together in the light response, and are activated by fatty acids and metabolic stress. TRP is also required for olfactory adaptation and may be involved in olfactory system development. The TRP tail contains two calmodulin (CaM) binding sites (called CBS1 and CBS2), which binds to the CaM N-lobe and C-lobe, respectively. The model corresponds to CaM binding site 1. 66 matched cddid_all.tbl CDD cd23651 cd23651 467882 PiggyMac_CRD cysteine-rich domain (CRD) found in Paramecium tetraurelia PiggyMac, and similar proteins. PiggyMac is a domesticated PiggyBac transposase involved in programmed genome rearrangements. It contains a core catalytic domain typical of PiggyBac-related transposases and a short cysteine-rich domain (CRD), flanked by N- and C-terminal extensions. This model corresponds to CRD that is essential for PiggyMac activity in vivo. PiggyMac CRD does not bind DNA; instead, it interacts weakly with the N-terminus of histone H3, whatever its lysine methylation state. 81 matched cddid_all.tbl CDD cd23652 cd23652 467883 mS38 Trypanosomal mitochondrial ribosomal protein mS38 domain family, and similar proteins. mS38 protein is a mitochondrial protein found in Trypanosoma, but its function has not yet been fully characterized. It is known to be a component of the small subunits of the Trypanosoma brucei mitochondrial ribosome (Tb-mt-SSUs) and interacts with the C-terminal domain (CTD) of initiation factor IF-3 to form a complex called Tb-mt-SSU/IF-3. This complex may play a role in the maturation of the mitochondrial ribosome. 121 matched cddid_all.tbl CDD cd23653 cd23653 467884 mS65 mS65 domain rpotein found in trypanosomal mitochondrial ribosomes, and similar proteins. mS65 protein is a mitochondrial protein found in Trypanosoma, but its function has not yet been fully characterized. It is known to be a component of the small subunits of the Trypanosoma mitochondrial ribosome (Tb-mt-SSUs) and interacts with the C-terminal domain (CTD) of initiation factor IF-3 to form a complex called Tb-mt-SSU/IF-3. This complex may play a role in the maturation of the mitochondrial ribosome. 249 matched cddid_all.tbl CDD cd23654 cd23654 467885 uS19 Trypanosomal mitochondrial ribosome protein uS19 domain family, and similar proteins. uS19 is a mitochondrial protein found in Trypanosoma cruzi but its function has not been fully characterized yet. It has been shown to be a component of T. brucei mitoribosome small subunits (Tb-mt-SSUs), which forms a complex with the C-terminal domain (CTD) of initiation factor IF-3 (Tb-mt-SSU/IF-3) and may be involved in mitoribosomal maturation. 146 matched cddid_all.tbl CDD cd23655 cd23655 467886 mS61-like mS61 domain protein found in trypanosomal mitochondrial ribosomes, and similar proteins. mS61 protein is a mitochondrial protein found in Trypanosoma, but its function has not yet been fully characterized. It is known to be a component of the small subunits of the Trypanosoma mitochondrial ribosome (Tb-mt-SSUs) and interacts with the C-terminal domain (CTD) of initiation factor IF-3 to form a complex called Tb-mt-SSU/IF-3. This complex may play a role in the maturation of the mitochondrial ribosome. The mS61 domain protein also shows sequence similarity to trans-sialidase found in Trypanosoma as well as Perkinsela, an endosymbiotic kinetoplastid. However, while both the mitochondrial ms61 protein and trans-sialidase are proteins involved in cellular processes, they are not thought to have a common evolutionary origin or functional relationship. 282 matched cddid_all.tbl CDD cd23656 cd23656 467806 Abraxas_plant BRISC complex subunit Abro1-like protein in plants. BRISC complex subunit Abraxas 2 is also known as ABRO1, FAM175B or KIAA0157. The BRISC complex consists of BRCC36, MERIT40, BRE, and Abraxas 2, and serves cellular stress response and immune signaling functions; it specifically cleaves 'Lys-63'-linked polyubiquitin, leaving the last ubiquitin chain attached to its substrates; BRISC's catalytic subunit is the deubiquitinase (DUB) BRCC36. BRCC36 associates with pseudo-DUB protein Abraxas2, which lacks the essential Zn2+-coordinating residues required for DUB catalytic function. Higher-order association of BRCC36 and Abraxas2 into a dimer of heterodimers (superdimer) is required for BRCC36 DUB activity. In the BRISC complex, Abraxas 2 binds SHMT2a, a metabolic enzyme enabling cancer growth in hypoxic environments, which prevents the BRCC36 from binding and cleaving ubiquitin chains. BRCC36 in BRISC is activated by assembly due to interaction between Glu30 of BRCC36 and Asn164 in Abraxas 2 which structures the activation loop and positions the catalytic Glu33. Members in this subfamily include plant homologs of Abraxas 2 domains such as Arabidopsis thaliana BRCA1 (AtBRCA1). During plant evolution, BRCA1 acquired a PHD domain (absent in mammals), which might be involved in the transcriptional regulation of plant development, thus implicating participation of AtBRCA1 recruitment to damaged DNA. Arabidopsis thaliana harbors two homologs of the mammalian BRCA1 interaction partner BRCC36, AtBRCC36A and AtBRCC36B. Mutation of AtBRCC36A leads to a severe defect in intra- and interchromosomal homologous recombination (HR), which is also apparent in Atbrca1; in contrast, Atbrcc36b mutants showed no effect in HR. Atbrcc36a/Atbrca1 double mutant behaves like the single mutants of AtBRCA1 and AtBRCC36A and appears to be involved in a common pathway in the regulation of HR. AtBRCC36 is also epistatic to AtBRCA1 in DNA crosslink repair. 307 matched cddid_all.tbl CDD cd23657 cd23657 467504 USP-A-like "universal stress protein A and similar proteins. The universal stress protein UspA is a small cytoplasmic bacterial protein whose expression is enhanced several-fold when cellular viability is challenged with heat shock, nutrient starvation, stress agents which arrest cell growth, or DNA-damaging agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, suggesting that it asserts a general ""stress endurance"" activity. In general, these proteins form dimers and have domains for nucleotide binding activity. The crystal structure of Haemophilus influenzae UspA reveals an asymmetric dimer with a tertiary alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, but unlike MJ0577, it lacks ATP-binding activity." 138 matched cddid_all.tbl CDD cd23659 cd23659 467505 USP_At3g01520-like "universal stress protein At3g01520 and similar proteins. This subfamily includes plant and fungal proteins of unknown function, including Arabidopsis thaliana At3g01520. A. thaliana contains 44 USP domain-containing proteins; the USP domain is found either in a small protein with unknown physiological function or as an N-terminal portion of a multi-domain protein, usually a protein kinase. The gene At3g01520 of Arabidopsis thaliana encodes a 175-residue universal stress protein (USP)-like protein which is widely found in the genomes of bacteria, as well as fungi, protozoa, and plants. The bound AMP and conservation of residues in the ATP-binding loop suggest that the protein At3g01520 belongs to the ATP-binding USP subfamily. Universal stress proteins (USPs) are small cytoplasmic bacterial proteins whose expression is enhanced when the cell is exposed to stress agents. USP enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general ""stress endurance"" activity." 143 matched cddid_all.tbl CDD cd23660 cd23660 467506 USP-E_repeat2 "Universal stress protein E, repeat 2. UspE is a tandem-type USP that consists of two USP domains. The UspE expression levels of Escherichia coli become elevated in response to oxidative stress and DNA damaging agents, including exposure to mitomycin C, cadmium, and hydrogen peroxide. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general ""stress endurance"" activity." 148 matched cddid_all.tbl CDD cd23661 cd23661 467507 USP_Rv2623_repeat2 "universal stress protein Rv2623 and similar proteins, USP repeat 2. Mycobacterium tuberculosis universal stress protein Rv2623 regulates mycobacterial growth in vitro and in vivo and is required for the entry of the tubercle bacillus into the chronic phase of infection in the host. In addition, Rv2623 binds ATP and the growth-regulatory attribute of this USP is dependent on its ATP-binding activity. Rv2623 is thought to function as an ATP-dependent signaling intermediate in a pathway that promotes persistent infection. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general ""stress endurance"" activity. The crystal structure of Haemophilus influenzae Usp reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP, although Usp lacks ATP-binding activity." 133 matched cddid_all.tbl CDD cd23664 cd23664 467821 BRE BRCA1-A and BRISC complex subunit BRE. BRCA1-A and BRISC complex subunit BRE (also known as BRISC and BRCA1 A complex member 2; BRCC4; BRCC45) is a core component of both the BRCA1-A and BRISC complexes. BRCA1-A and BRISC are separate complexes with diverging function; they use the same core of subunits to perform very distinct biological tasks, and are found in all vertebrates. The BRCA1-A complex consists of BRE, Abraxas-1, BRCC36, MERIT40 and RAP80, and specifically recognizes 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesion sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at double-strand breaks (DSB)s. This complex also possesses deubiquitinase (DUB) activity that specifically removes 'Lys-63'-linked ubiquitin on histones H2A and H2AX. In BRCA1-A, two heteropentamers, composed of BRCC36, ABRAXAS, BRE and MERIT40, form an arc-shaped complex; the two half-arcs contact each other through BRCC36 and its scaffold partner ABRAXAS. BRCC36 is connected to this arc via the ABRAXAS MPN domain. BRE forms the central bridge between the ABRAXAS-BRCC36 MPN domain dimer and MERIT40. BRE's N-terminal ubiquitin-conjugating enzyme variants domain (UEV-N) binds the ABRAXAS MPN, and BRE's C-terminal UEV domain (UEV-C) holds MERIT40 at the extremity of the arc. Loss of BRE significantly impairs BRCA1-A function, resulting in DNA repair defects and loss of cancer suppression. The BRISC complex consists of BRE, BRCC36, MERIT40 and Abraxas 2, and serves cellular stress response and immune signaling functions; it specifically cleaves 'Lys-63'-linked polyubiquitin, leaving the last ubiquitin chain attached to its substrates. The BRISC core has the same 2-fold symmetrical arc shape and is structurally similar to BRCA1-A; however, the conformation of BRE UEV-C and MERIT40 differs markedly. BRE has different functionality in the BRCA1-A and BRISC complexes: in BRCA1, it is involved in RAP80 integration, BRCA1 sequestration and ubiquitin binding, while in BRISC, it is involved in dimerization, SHMT2 recruitment, DUB inhibition and ubiquitin binding. A BRISC complex (containing of BRE/BRCC45, BRCC36, MERIT40, and Abraxas 2/KIAA0157) has been found in insects (Camponotus floridanus) and shown to efficiently degrade 'Lys-63'-linked chains. Homologs of genes encoding components of BRCA1-A and BRISC complexes have been found in plant genomes, including for BRE/BRCC45; plant homologs of BRCC36 have been shown to be involved in DNA repair; BRCC36-Abraxas 2 complexes have been found in Arabidopsis. 364 matched cddid_all.tbl CDD cd23665 cd23665 467822 BRE-like_insects BRCA1-A and BRISC complex subunit BRE-like protein found in insects. BRCA1-A and BRISC complex subunit BRE (also known as BRISC and BRCA1 A complex member 2; BRCC4; BRCC45) is a core component of both the BRCA1-A and BRISC complexes. BRCA1-A and BRISC are separate complexes with diverging function; they use the same core of subunits to perform very distinct biological tasks, and are found in all vertebrates. The BRCA1-A complex consists of BRE, Abraxas-1, BRCC36, MERIT40 and RAP80, and specifically recognizes 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesion sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at double-strand breaks (DSB)s. This complex also possesses deubiquitinase (DUB) activity that specifically removes 'Lys-63'-linked ubiquitin on histones H2A and H2AX. In BRCA1-A, two heteropentamers, composed of BRCC36, ABRAXAS, BRE and MERIT40, form an arc-shaped complex; the two half-arcs contact each other through BRCC36 and its scaffold partner ABRAXAS. BRCC36 is connected to this arc via the ABRAXAS MPN domain. BRE forms the central bridge between the ABRAXAS-BRCC36 MPN domain dimer and MERIT40. BRE's N-terminal ubiquitin-conjugating enzyme variants domain (UEV-N) binds the ABRAXAS MPN, and BRE's C-terminal UEV domain (UEV-C) holds MERIT40 at the extremity of the arc. Loss of BRE significantly impairs BRCA1-A function, resulting in DNA repair defects and loss of cancer suppression. The BRISC complex consists of BRE, BRCC36, MERIT40 and Abraxas 2, and serves cellular stress response and immune signaling functions; it specifically cleaves 'Lys-63'-linked polyubiquitin, leaving the last ubiquitin chain attached to its substrates. The BRISC core has the same 2-fold symmetrical arc shape and is structurally similar to BRCA1-A; however, the conformation of BRE UEV-C and MERIT40 differs markedly. BRE has different functionality in the BRCA1-A and BRISC complexes: in BRCA1, it is involved in RAP80 integration, BRCA1 sequestration and ubiquitin binding; in BRISC, it is involved in dimerization, SHMT2 recruitment, DUB inhibition and ubiquitin binding. A BRISC complex (containing of BRE/BRCC45, BRCC36, MERIT40, and Abraxas 2/KIAA0157) has been found in insects (Camponotus floridanus) and shown to efficiently degrade 'Lys-63'-linked chains. This model contains the BRE domain of BRISC complexes found in insects. 364 matched cddid_all.tbl CDD cd23666 cd23666 467823 BRE-like_plant BRCA1-A and BRISC complex subunit BRE-like protein found in plants. BRCA1-A and BRISC complex subunit BRE (also known as BRISC and BRCA1 A complex member 2; BRCC4; BRCC45) is a core component of both the BRCA1-A and BRISC complexes. BRCA1-A and BRISC are separate complexes with diverging function; they use the same core of subunits to perform very distinct biological tasks, and are found in all vertebrates. The BRCA1-A complex consists of BRE, Abraxas-1, BRCC36, MERIT40, and RAP80 and specifically recognizes 'Lys-63'-linked ubiquitinated histones H2A and H2AX at DNA lesion sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at double-strand breaks (DSB)s. This complex also possesses deubiquitinase (DUB) activity that specifically removes 'Lys-63'-linked ubiquitin on histones H2A and H2AX. In BRCA1-A, two heteropentamers composed of BRCC36, ABRAXAS, BRE, and MERIT40 form an arc-shaped complex; the two half-arcs contact each other through BRCC36 and its scaffold partner ABRAXAS. BRCC36 is connected to this arc via the ABRAXAS MPN domain. BRE forms the central bridge between the ABRAXAS-BRCC36 MPN domain dimer and MERIT40. BRE's N-terminal ubiquitin-conjugating enzyme variants domain (UEV-N) binds the ABRAXAS MPN, and BRE's C-terminal UEV domain (UEV-C) holds MERIT40 at the extremity of the arc. Loss of BRE significantly impairs BRCA1-A function, resulting in DNA repair defects and loss of cancer suppression. The BRISC complex consists of BRE, BRCC36, MERIT40, and Abraxas 2, and serves cellular stress response and immune signaling functions; it specifically cleaves 'Lys-63'-linked polyubiquitin, leaving the last ubiquitin chain attached to its substrates. The BRISC core has the same 2-fold symmetrical arc shape and is structurally similar to BRCA1-A, however the conformation of BRE UEV-C and MERIT40 differs markedly. BRE has different functionality in the BRCA1-A and BRISC complexes: in BRCA1 it is involved in RAP80 integration, BRCA1 sequestration, and ubiquitin binding; in BRISC it is involved in dimerization, SHMT2 recruitment, DUB inhibition, and ubiquitin binding. Homologs of genes encoding components of BRCA1-A and BRISC complexes have been found in plant genomes, including for BRE/BRCC45; plant homologs of BRCC36 have been shown to be involved in DNA repair, and BRCC36-Abraxas 2 complexes have been found in Arabidopsis. This model contains the BRE domain of BRISC complexes found in plants. 370 matched cddid_all.tbl CDD cd23667 cd23667 467379 beta-trefoil_Ricin_CqDVP-like ricin B-type lectin domain, beta-trefoil fold, found in Culex quinquefasciatus salivary peptide (CqDVP) and similar proteins. CqDVP is a Cysteine and Tryptophan-Rich (CWRC) protein that is specific to adult female salivary glands and is secreted into vector saliva. It contains a ricin B-type lectin domain that shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site. 144 matched cddid_all.tbl CDD cd23668 cd23668 467840 GH55_beta13glucanase-like fungal glycoside hydrolase family 55 (GH55) family domains and similar proteins. This family includes fungal glycoside hydrolase family 55 (GH55) proteins, which contains both endo- (EC 3.2.1.39) and exo-beta-1,3-glucanases (EC 3.2.1.58), based on the hydrolysis position. These enzymes hydrolyze beta-1,3-glucan bonds via inversion of stereochemistry at the anomeric carbon. GH55 is also called laminarinase due to its ability to hydrolyze laminarin, a beta-1,3-glucan with occasional beta-1,6 branching found in brown algae such as Laminaria digitata. They have also been shown to react with the beta-1,3-glucans from fungal and plant cell walls. Trichoderma harzianum BGN13.1 and T. viride LamA1 in this family have been characterized as endo-acting enzymes while Phanerochaete chrysosporium Lam55A and Chaetomium thermophilum CtLam55 are exo-acting enzymes. The CtLam55 substrate binding cleft exhibits restricted access on one side, thus rendering the enzyme as an exo-beta-1,3-glucanase; this has been confirmed by thin layer chromatography experiments. Also, a binding pocket was identified that could explain binding of branched laminarin and accumulation of laminaritriose. A similar binding pocket has been observed in T. chrysosporium Lam55A through structural studies and site-directed mutagenesis; both support a critical glutamate as a catalytic acid and a proton relay network that activates water to serve as the catalytic base. 623 matched cddid_all.tbl CDD cd23669 cd23669 467841 GH55_SacteLam55A-like bacterial glycoside hydrolase family 55 (GH55) family domains and similar proteins. This family includes bacterial glycoside hydrolase family 55 (GH55) proteins, which contains both endo- (EC 3.2.1.39) and exo-beta-1,3-glucanases (EC 3.2.1.58), and hydrolyze beta-1,3-glucan bonds via inversion of stereochemistry at the anomeric carbon. Included in this family is Streptomyces sp. SirexAA-E (SacteLam55A), a secreted protein encoded by SACTE_4363. Structural studies reveal an extended substrate-binding cleft with six or more subsites for sugar binding formed at the interface of two right handed beta-helical domains. They also give insight into residues that enforce an exolytic reaction, interactions that potentially support a processive hydrolysis of the bound oligosaccharide, and the ability of the enzyme to accommodate substrates with beta-1,6 branching. Mutation studies support a critical glutamate as a catalytic acid and a proton relay network that activates water to serve as the catalytic base. Also included in this family are Saccharophagus degradans Gly5M, a novel protein identified as a beta-1,3-endoglucanase (EC 3.2.1.39) and bacterial beta-1,6-glucanase (EC 3.2.1.75) in GH5, and Corallococcus sp. strain EGB LamC, identified as a novel member of the GH16 family. 550 matched cddid_all.tbl CDD cd23670 cd23670 467887 MPSS1_C C-terminal region of mitochondrial 3' processome (MPsome) subunit 1. MPSS1 is a subunit of the mitochondrial 3' processome (MPsome) which is involved in 3'-5' trimming of messenger RNA (mRNA) precursors, in U-tailing of ribosomal RNA (rRNA) and some mRNAs, and in 3'-5' trimming and U-tailing of guide RNAs (gRNAs), during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode gRNAs involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. MPsome subunits include KDSS1 3'-5' exonuclease, RET1 terminal uridyltransferase (TUTase), and several subunits of as yet undefined functions (MPSS1-MPSS6). The maxicircle and minicircle RNAs are transcribed as 3' extended precursors and processed by MPsome-dependent 3'-5' degradation, and in the case of rRNAs and gRNAs, also 3' uridylated. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The MPsome catalyzes the primary uridylation of about 800 nt gRNA precursor transcripts, their processive degradation to a mature size of 40-60 nt, and secondary U-tail addition. This domain model spans the C-terminal region of MPSS1 and related proteins. MPSS1 is predicted (AlphaFold) to be a predominantly alpha helical protein with a C-terminal region containing helical hairpin motifs that structurally resemble HEAT repeats. 459 matched cddid_all.tbl CDD cd23671 cd23671 467888 MPSS3 mitochondrial 3' processome (MPsome) subunit 3. MPSS3 is a subunit of the mitochondrial 3' processome (MPsome) which is involved in 3'-5' trimming of messenger RNA (mRNA) precursors, in U-tailing of ribosomal RNA (rRNA) and some mRNAs, and in 3'-5' trimming and U-tailing of guide RNAs (gRNAs), during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode gRNAs involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. MPsome subunits include KDSS1 3'-5' exonuclease, RET1 terminal uridyltransferase (TUTase), and several subunits of as yet undefined functions (MPSS1-MPSS6). The maxicircle and minicircle RNAs are transcribed as 3' extended precursors and processed by MPsome-dependent 3'-5' degradation, and in the case of rRNAs and gRNAs also 3' uridylated. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The MPsome catalyzes the primary uridylation of about 800 nt gRNA precursor transcripts, their processive degradation to a mature size of 40-60 nt, and secondary U-tail addition. MPSS3 is predicted (AlphaFold) to have a structure of mostly alpha helices with a few beta strands. 1059 matched cddid_all.tbl CDD cd23672 cd23672 467889 MPSS5_OBF_C C-terminal oligonucleotide/oligosaccharide binding (OB) fold-like domain of mitochondrial 3' processome (MPsome) subunit 5. MPSS5 is a subunit of the mitochondrial 3' processome (MPsome) which is involved in 3'-5' trimming of messenger RNA (mRNA) precursors, in U-tailing of ribosomal RNA (rRNA) and some mRNAs, and in 3'-5' trimming and U-tailing of guide RNAs (gRNAs), during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode gRNAs involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. MPsome subunits include KDSS1 3'-5' exonuclease, RET1 terminal uridyltransferase (TUTase), and several subunits of as yet undefined functions (MPSS1-MPSS6). The maxicircle and minicircle RNAs are transcribed as 3' extended precursors and processed by MPsome-dependent 3'-5' degradation, and in the case of rRNAs and gRNAs also 3' uridylated. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The MPsome catalyzes the primary uridylation of about 800 nt gRNA precursor transcripts, their processive degradation to a mature size of 40-60 nt, and secondary U-tail addition. MPSS5 contains a C2H2-type zinc finger at the N-terminus and a predicted (AlphaFold) oligonucleotide/oligosaccharide binding (OB) fold-like domain at the C-terminus. This model represents the OB fold-like domain. 138 matched cddid_all.tbl CDD cd23673 cd23673 467890 MPSS6 mitochondrial 3' processome (MPsome) subunit 6. MPSS6 is a subunit of the mitochondrial 3' processome (MPsome) which is involved in 3'-5' trimming of messenger RNA (mRNA) precursors, in U-tailing of ribosomal RNA (rRNA) and some mRNAs, and in 3'-5' trimming and U-tailing of guide RNAs (gRNAs), during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode gRNAs involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. MPsome subunits include KDSS1 3'-5' exonuclease, RET1 terminal uridyltransferase (TUTase), and several subunits of as yet undefined functions (MPSS1-MPSS6). The maxicircle and minicircle RNAs are transcribed as 3' extended precursors and processed by MPsome-dependent 3'-5' degradation, and in the case of rRNAs and gRNAs also 3' uridylated. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The MPsome catalyzes the primary uridylation of about 800 nt gRNA precursor transcripts, their processive degradation to a mature size of 40-60 nt, and secondary U-tail addition. MPSS6 is predicted (AlphaFold) to contain a C-terminal oligonucleotide/oligosaccharide binding (OB) fold-like domain. 243 matched cddid_all.tbl CDD cd23674 cd23674 467891 MPSS4 mitochondrial 3' processome (MPsome) subunit 4. MPSS4 is a subunit of the mitochondrial 3' processome (MPsome) which is involved in 3'-5' trimming of messenger RNA (mRNA) precursors, in U-tailing of ribosomal RNA (rRNA) and some mRNAs, and in 3'-5' trimming and U-tailing of guide RNAs (gRNAs), during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode gRNAs involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. MPsome subunits include KDSS1 3'-5' exonuclease, RET1 terminal uridyltransferase (TUTase), and several subunits of as yet undefined functions (MPSS1-MPSS6). The maxicircle and minicircle RNAs are transcribed as 3' extended precursors and processed by MPsome-dependent 3'-5' degradation, and in the case of rRNAs and gRNAs also 3' uridylated. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The MPsome catalyzes the primary uridylation of about 800 nt gRNA precursor transcripts, their processive degradation to a mature size of 40-60 nt, and secondary U-tail addition. MPSS4 is predicted (AlphaFold) to have a structure containing only alpha helices, with nine domains (calculated by VAST). This model represents domains 3-5 (D3-D5), as well as parts of D2 and D6. No structure neighbors for the entire protein was detected, however, each domain showed many similar structures. Examples include similarity between MPSS4 D2 with Entamoeba histolytica diaphanous protein, D3 with domain 3 of Saccharomyces cerevisiae YPP1, and D4 with domain 3 of Human herpesvirus 2 envelope glycoprotein H, among others. 706 matched cddid_all.tbl CDD cd23675 cd23675 467892 KPAF2 kinetoplast polyadenylation factor 2 (KPAF2). KPAF2 is a component of the kinetoplast polyadenylation complex (KPAC) and plays a role in mRNA 3' adenylation/uridylation (addition of A/U-heteropolymers, referred to as A/U-tailing), during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. Kinetoplast RNA processing include 5' modification, 3'-5' degradation, internal sequence changes by U-insertion/deletion mRNA editing, and nontemplated 3' extensions. In T. brucei, mitochondrial RNA 3' modifications can be categorized into U-tailing by RET1 terminal uridyltransferase TUTase (gRNAs and rRNAs), A-tailing by KPAP1 poly(A) polymerase (most mRNAs), and A/U-extensions which require both enzymes and a complex of kinetoplast polyadenylation factors 1 and 2 (KPAF1/2). Pre-editing addition of the short (A) tail protects the edited transcript against 3'-5' degradation. KPAF1/2 induces the post-editing addition of A/U-heteropolymers by KPAP1 and RET1, which renders mRNA competent for translation. The KPAC complex includes KPAP1, KPAF1/2, and two additional factors KPAF3 and KPAF4. The latter two factors are involved in the pre-editing A-tailing function of KPAC: KPAF3 binds to and stabilizes the mRNA, and KPAF4 binds the A-tail impeding mRNA degradation. KPAF1-4 contain pentatricopeptide repeat (PPR) RNA-binding motifs. 528 matched cddid_all.tbl CDD cd23677 cd23677 467893 RESC3_ARM-like predicted ARM-like repeats of RNA-editing substrate-binding complex subunit 3. RESC3 (GRBC3, MRB8620) is a component of the RNA-editing substrate-binding complex (RESC), consisting of about 20 components, that is involved in kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. This alignment model represents the predicted (by AlphaFold) Armadillo (ARM)/beta-catenin-like repeats of RESC3, which makes up about 80 percent of the protein. ARM repeats are involved in mediating protein-protein interactions. 379 matched cddid_all.tbl CDD cd23678 cd23678 467894 RESC5 RNA-editing substrate-binding complex subunit 5 (RESC5). RESC5 (GRBC5, MRB11870) is a component of the RNA-editing substrate-binding complex (RESC) that is composed of about 20 components and is involved in kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. RESC5 is predicted (AlphaFold) to adopt a beta/alpha-propeller structure characteristic of the pentein superfamily, a mechanistically diverse superfamily encompassing both non-catalytic proteins and enzymes that catalyze hydrolase, dihydrolase and amidinotransfer reactions on guanidine substrates. 278 matched cddid_all.tbl CDD cd23679 cd23679 467895 RESC7 RNA-editing substrate-binding complex subunit 7 (RESC7); predicted alpha-helical domain. RESC7 (GRBC7, MRB0880) is a component of the RNA-editing substrate-binding complex (RESC), composed of about 20 components, that is involved in kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. RESC7 is also named RxLR effector protein and is predicted (by AlphaFold) to contain an alpha-helical domain in between disordered regions. This model represents the alpha-helical domain. 74 matched cddid_all.tbl CDD cd23680 cd23680 467896 RESC16 RNA-editing substrate-binding complex subunit 16 (RESC16). RESC16 (PAMC2) is a component of the RNA-editing substrate-binding complex (RESC) consisting of about 20-components that is involved in kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. RESC16 is predicted (by AlphaFold) to be an all alpha-helical protein that structurally resembles tetratricopeptide repeats (TPRs). It is structurally most similar to the human TPR protein, UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110, but shows low sequence identity (around 10 percent). 418 matched cddid_all.tbl CDD cd23681 cd23681 467816 RESC17_18-like RNA-editing substrate-binding complex subunit 17 (RESC17) and RESC18, and related proteins. RESC17 (PAMC3) AND RESC18 (PAMC4) are components of the RNA-editing substrate-binding complex (RESC), consisting of about 20-components, that is involved in kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. RESC17 and RESC18 show some sequence similarity and are both predicted (by AlphaFold) to contain four domains; their corresponding C-terminal domains 3 and 4 are structurally similar and superimposable. Domain 3 adopts a helical fold and shows similarity to helix-turn-helix DNA-binding motifs, while domain 4 adopts a 5-stranded beta sheet structure surrounded by helices. Domain 4, the largest domain and predicted with the highest confidence of the four domains, shows structural similarity to many proteins belonging to different domain superfamilies, including class I SAM-dependent methyltransferases and electron transfer flavoprotein (ETF) alpha belonging to the adenine nucleotide alpha hydrolase superfamily. Both RESC17 and RESC18 contain two N-terminal domains that adopt partial winged helix or helix-turn-helix folds, but are not directly superimposable to each other. These domains have structural similarities to various RNA- or DNA-binding domains. 257 matched cddid_all.tbl CDD cd23682 cd23682 467836 RESC1-2 RNA-editing substrate-binding complex subunit 1 (RESC1) and RESC2. RESC1 (GRBC1, GAP2) and RESC2 (GRBC2, GAP1) form a stable heterotetramer that directly binds guide RNAs (gRNAs) and is essential for the stability of gRNAs in U-insertion/deletion mRNA editing during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC1/2 is a core component of the RNA-editing substrate-binding complex (RESC) that consists of about 20 components. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. The predicted structures (by AlphaFold) of RESC1 and RESC2 contain a domain most structurally similar to fungal mRNA triphosphatases belonging to the CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) phosphatase superfamily; this domain adopts an eight-stranded antiparallel beta barrel tunnel (the triphosphate tunnel) with an active site located at the center of the tunnel. mRNA triphosphatase catalyzes the first step in the mRNA cap formation process, the removal of the gamma-phosphate of triphosphate terminated pre-mRNA. RESC1/2 lack the conserved mRNA triphosphatase active site residues and may not exhibit this enzymatic activity. 417 matched cddid_all.tbl CDD cd23683 cd23683 467897 IFT52_CTD C-terminal domain of intraflagellar transport protein 52 (IFT52) and similar proteins. IFT52 is involved in ciliogenesis as part of a complex involved in intraflagellar transport (IFT), the bi-directional movement of particles required for the assembly, maintenance, and functioning of primary cilia. It is required for the anterograde transport of IFT88. IFT52 is a component of the IFT complex B that consists of a 9-subunit salt-stable core and several peripheral subunits. The model corresponds to the C-terminal domain of IFT52, which is responsible for binding to the C-terminal domain of IFT46. 69 matched cddid_all.tbl CDD cd23684 cd23684 467898 ATP-synt_III_subunit8 Tetrahymena thermophila type III ATP synthase subunit 8 and similar proteins. The family includes Tetrahymena thermophila type III ATP synthase subunit 8, also known as Ymf56, and similar proteins. Type III mitochondrial ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization. 97 matched cddid_all.tbl CDD cd23685 cd23685 467899 uS7m Tetrahymena thermophila ribosomal protein uS7m and similar proteins. Ribosomal protein uS7m, also called Ymf63, is a component of small subunit (SSU) in Tetrahymena thermophila mitoribosome. The structure of the mitoribosomal complex reveals an assembly of 94-ribosomal proteins and four-rRNAs with an additional protein mass of ~700 kDa on the small subunit, while the large subunit (LSU) lacks 5S rRNA. 276 matched cddid_all.tbl CDD cd23686 cd23686 467900 mS82 Tetrahymena thermophila ribosomal protein mS82 and similar proteins. Ribosomal protein mS82 protein is a mitochondrial protein found in Trypanosoma, but its function has not yet been fully characterized. It is known to be a component of the small subunits of the Trypanosoma mitochondrial ribosome (Tb-mt-SSUs) and interacts with the C-terminal domain (CTD) of initiation factor IF-3 to form a complex called Tb-mt-SSU/IF-3. This complex may play a role in the maturation of the mitochondrial ribosome. 273 matched cddid_all.tbl CDD cd23687 cd23687 467901 uS3m_Ymf64 Tetrahymena thermophila ribosomal protein uS3m and similar proteins. Ribosomal protein uS3m, also called Ymf64, is a component of small subunit (SSU) in Tetrahymena thermophila mitochondrial ribosome (mitoribosome), which reveals an assembly of 94-ribosomal proteins and four-rRNAs with an additional protein mass of ~700 kDa on the small subunit (SSU); the large subunit lacks 5S rRNA. uS3m assembles together with mS31and mS92 to produce a full S3 protein. 330 matched cddid_all.tbl CDD cd23688 cd23688 467902 mL103 Tetrahymena thermophila ribosomal protein mL103 and similar proteins. Ribosomal protein mL103 is a component of large subunit (LSU) in Tetrahymena thermophila mitochondrial ribosomes (mitoribosomes). The structure of the mitoribosomal complex reveals an assembly of 94-ribosomal proteins and four-rRNAs with an additional protein mass of ~700 kDa on the small subunit, while the large subunit lacks 5S rRNA. 273 matched cddid_all.tbl CDD cd23689 cd23689 467903 mS81 Tetrahymena thermophila ribosomal protein mS81 and similar proteins. Ribosomal protein mS81 is a component of small subunit (SSU) in Tetrahymena thermophila mitochondrial ribosomes (mitoribosomes). The structure of the mitoribosomal SSU reveals an assembly of 94-ribosomal proteins and four-rRNAs with an additional protein mass of ~700 kDa on the small subunit, while the large subunit lacks 5S rRNA. 279 matched cddid_all.tbl CDD cd23690 cd23690 467904 mL101 Tetrahymena thermophila ribosomal protein mL101 and similar proteins. Ribosomal protein mL101 is a helical repeat protein binding partially unfolded H79. It acts as a component of large subunit (LSU) in Tetrahymena thermophila mitoribosome. The structure of the mitoribosomal complex reveals an assembly of 94-ribosomal proteins and four-rRNAs with an additional protein mass of ~700 kDa on the small subunit (SSU), while the large subunit (LSU) lacks 5S rRNA. 350 matched cddid_all.tbl CDD cd23691 cd23691 467905 uS4m Tetrahymena thermophila ribosomal protein uS4m, and similar proteins. Ribosomal protein uS4m, also called Ymf76, is a component of small subunit (SSU) in Tetrahymena thermophila mitochondrial ribosome (mitoribosome), which reveals an assembly of 94-ribosomal proteins and four-rRNAs with an additional protein mass of ~700 kDa on the small subunit; its large subunit (LSU) lacks 5S rRNA. 398 matched cddid_all.tbl CDD cd23692 cd23692 467906 mS89 Tetrahymena thermophila ribosomal protein mS89 and similar proteins. Ribosomal protein mS89 protein is a mitochondrial protein found in Trypanosoma, but its function has not yet been fully characterized. It is known to be a component of the small subunits of the Trypanosoma mitochondrial ribosome (Tb-mt-SSUs) and interacts with the C-terminal domain (CTD) of initiation factor IF-3 to form a complex called Tb-mt-SSU/IF-3. This complex may play a role in the maturation of the mitochondrial ribosome. 322 matched cddid_all.tbl CDD cd23693 cd23693 467907 mS45 Tetrahymena thermophila ribosomal protein mS45 and similar proteins. Ribosomal protein mS45 protein is a mitochondrial protein found in Trypanosoma, but its function has not yet been fully characterized. It is known to be a component of the small subunits of the Trypanosoma mitochondrial ribosome (Tb-mt-SSUs) and interacts with the C-terminal domain (CTD) of initiation factor IF-3 to form a complex called Tb-mt-SSU/IF-3. This complex may play a role in the maturation of the mitochondrial ribosome. 460 matched cddid_all.tbl CDD cd23694 cd23694 467908 mL106 Tetrahymena thermophila ribosomal protein mL106 and similar proteins. Ribosomal protein mL106 is a helical repeat protein binding large subunit (LSU) 3'-ES1. It acts as a component of LSU in the Tetrahymena thermophila mitoribosome, which reveals an assembly of 94-ribosomal proteins and four-rRNAs with an additional protein mass of ~700 kDa on the small subunit, while the large subunit lacks 5S rRNA. 480 matched cddid_all.tbl CDD cd23695 cd23695 467909 mS26_Tt Tetrahymena thermophila ribosomal protein mS26 and similar proteins. Ribosomal protein mS26 is a component of small subunit (SSU) in Tetrahymena thermophila mitochondrial ribosome (mitoribosome). The structure of the mitoribosome reveals an assembly of 94-ribosomal proteins and four-rRNAs with an additional protein mass of ~700 kDa on the small subunit; the large mitoribosomal subunit (LSU) lacks 5S rRNA. 496 matched cddid_all.tbl CDD cd23696 cd23696 467910 PsbW Chaetoceros gracilis photosystem II reaction center protein W (PsbW) and similar proteins. The centric diatom Chaetoceros gracilis photosystem II (PSII)- fucoxanthin (Fx) chlorophyll (Chl) a/c-binding protein (FCPII) supercomplex contains 35 protein subunits, as well as several pigments and cofactors. It catalyzes light-induced electron transfer and water-splitting reactions. PsbW is a component of the PSII core that contains 17 membrane-spanning subunits (D1, CP47, CP43, D2, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbW, PsbX, ycf12, and PsbZ). 64 matched cddid_all.tbl CDD cd23697 cd23697 467911 At5g55125 Arabidopsis thaliana mitochondrial ribosomal protein L31, and similar proteins. Mitochondrial ribosomal protein L31, also called bL31m or At5g55125, is a component of the large subunit (LSU) in RNA-rich Arabidopsis thaliana mitochondrial ribosome (mitoribosome). 65 matched cddid_all.tbl CDD cd23699 cd23699 467912 At5g63150_CTD C-terminal domain of Arabidopsis thaliana At5g63150 and similar proteins. At5g63150, also known as mS38, is a component of the small subunit (SSU) in RNA-rich Arabidopsis thaliana mitochondrial ribosome (mitoribosome). Thi model corresponds to the C-terminal domain of At5g63150. 30 matched cddid_all.tbl CDD cd23700 cd23700 467913 At3g51010 Arabidopsis thaliana At3g51010 and similar proteins. At3g51010, also known as mL87, is a component of the large subunit (LSU) in RNA-rich Arabidopsis thaliana mitochondrial ribosome (mitoribosome). 119 matched cddid_all.tbl CDD cd23701 cd23701 467914 At1g26750 Arabidopsis thaliana At1g26750 and similar proteins. At1g26750, also known as mS23, is a component of the small subunit (SSU) in RNA-rich Arabidopsis thaliana mitochondrial ribosome. 83 matched cddid_all.tbl CDD cd23702 cd23702 467915 eL14 Vairimorpha necatrix ribosomal protein eL14 and similar proteins. eL14 is a component of the large subunit (LSU) of the microsporidian ribosome that reveals a prokaryotic-like rRNA core covered with eukaryotic ribosomal proteins. 82 matched cddid_all.tbl CDD cd23703 cd23703 467916 mS26_PET12 Saccharomyces cerevisiae mitochondrial small ribosomal subunit protein mS26 and similar proteins. mS26, also known as mitochondrial 37S ribosomal protein PET12, is a component of the mitochondrial small ribosomal subunit (mt-SSU) of Saccharomyces cerevisiae mitochondrial ribosome (mitoribosome), a dedicated translation machinery responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. The mitoribosomes are attached to the mitochondrial inner membrane and translation products are cotranslationally integrated into the membrane. The family also includes a group of uncharacterized proteins from pezizomycotina, which show high sequence similarity with mS26. 179 matched cddid_all.tbl CDD cd23704 cd23704 467917 mS44 Saccharomyces cerevisiae mitochondrial small ribosomal subunit protein mS44, and similar proteins. mS44, also known as mitochondrial 37S ribosomal protein MRP13, is a component of the mitochondrial small ribosomal subunit (mt-SSU) of Saccharomyces cerevisiae mitochondrial ribosome (mitoribosome), a dedicated translation machinery responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. The mitoribosomes are attached to the mitochondrial inner membrane and translation products are cotranslationally integrated into the membrane. 279 matched cddid_all.tbl CDD cd23705 cd23705 467918 Flattop protein Flattop and similar proteins. Protein Flattop, also known as cilia- and flagella-associated protein 126 (CFAP126), or flagellum-associated protein 126 (FAP126), acts as a regulator of cilium basal body docking and positioning in mono- and multiciliated cells. It regulates basal body docking and cilia formation in multiciliated human lung cells. It also modulates kinocilium positioning and stereocilia bundle morphogenesis in the inner ear. 73 matched cddid_all.tbl CDD cd23706 cd23706 467919 FAP273 Chlamydomonas reinhardtii flagellum-associated protein 273 (FAP273), and similar proteins. The family includes Chlamydomonas reinhardtii FAP273 and similar proteins. Flagellum-associated protein 273 (FAP273) is a microtubule inner protein (MIP) that acts as a component of the decorated ciliary doublet microtubule, which reveals the identities, positions, repeat lengths and interactions of 38 associated proteins including 33 MIPs. 137 matched cddid_all.tbl CDD cd23707 cd23707 467920 Ten1_OBF telomere regulation protein Ten1 and similar proteins, with an oligonucleotide/oligosaccharide-binding (OB) fold. Telomere regulation protein Ten1 is required to regulate telomere length, as well as to prevent lethal damage to telomeric DNA. It interacts physically with both Stn1 and Cdc13 to form the Cdc13-Stn1-Ten1 (CST) complex that plays an essential role in telomere protection and maintenance in budding yeast. Stn1 and Ten1 also control a Cdc13-independent telomere capping mechanism that is coupled to the conventional DNA replication machinery. Ten1 adopts the oligonucleotide/oligosaccharide-binding (OB) fold. 131 matched cddid_all.tbl CDD cd23708 cd23708 467921 FAP276 Chlamydomonas reinhardtii flagellum-associated protein 276 (FAP276), and similar proteins. The family includes Chlamydomonas reinhardtii FAP276 and similar proteins. Flagellum-associated protein 276 (FAP276) is an inner junction (IJ) protein that acts as a component of the decorated ciliary doublet microtubule, which reveals the identities, positions, repeat lengths, and interactions of 38 associated proteins, including 33 microtubule inner proteins (MIPs). FAP276, together with PArkin Co-Regulated Gene (PACRG), FAP20, and FAP52, forms an IJ complex of the cilia, which is an interaction hub that involves tubulin post-translational modifications. 90 matched cddid_all.tbl CDD cd23709 cd23709 467922 Psrp5_CTD C-terminal domain of Spinacia oleracea chloroplastic PSRP5, and similar proteins. In spinach chlororibosome, four plastid-specific ribosomal proteins (PSRPs), PSRP1-4, were found to be associated with the small subunit (SSU) and two (PSRP5 and PSRP6) with the large subunit (LSU). PSRP5, also known as cL37, together with PSRP3 (cS23) and PSRP4 (bTHXc), is essential for plastid translation activity. This model corresponds to PSRP5 C-terminal domain, which consists of a short C-terminal alpha-helix connected by a linker to a long central alpha-helix. It is responsible for the binding of ribosomal RNA (rRNA). 53 matched cddid_all.tbl CDD cd23710 cd23710 467923 mL85 Trypanosoma brucei ribosomal protein mL85 and similar proteins. Ribosomal protein mL85 is a component of mitoribosomal large subunit (mtLSU) in Trypanosoma brucei mitochondrial ribosome (mitoribosome), which is composed of 127 mitoribosomal proteins and contains very small rRNAs. The family also includes Leishmania major ribosomal protein mL85. 141 matched cddid_all.tbl CDD cd23711 cd23711 467924 mL96 Trypanosoma brucei ribosomal protein mL96, and similar proteins. Ribosomal protein mL96 is a component of mitoribosomal large subunit (mtLSU) central protuberance (CP) in Trypanosoma brucei mitochondrial ribosome (mitoribosome), which is composed of 127 mitoribosomal proteins and contains very small rRNAs. The family also includes Leishmania major ribosomal protein mL96. 142 matched cddid_all.tbl CDD cd23712 cd23712 467925 mL63 Trypanosoma brucei ribosomal protein mL63, and similar proteins. Ribosomal protein mL63 is a component of mitoribosomal large subunit (mtLSU) in Trypanosoma brucei mitochondrial ribosome (mitoribosome), which is composed of 127 mitoribosomal proteins and contains very small rRNAs. The family also includes Leishmania major ribosomal protein mL63. 146 matched cddid_all.tbl CDD cd23713 cd23713 467926 RESC19 RNA-editing substrate-binding complex subunit 19 (RESC19). RESC19 (RBP7910) is a component of the RNA-editing substrate-binding complex (RESC), consisting of about 20 components, that is involved in kinetoplast RNA processing. RESC19 contains N- and C-terminal Z-DNA-binding domains (ZDBs) that bind RNA, and preferentially interacts with multiple mitochondrial RNA classes containing poly(U) and poly(AU)-rich sequences. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. This model includes both the N- and C-terminal Z-DNA-binding domains, which are both predicted (by AlphaFold) to adopt winged helix-turn-helix structures, consistent with their nucleic acid-binding properties. 174 matched cddid_all.tbl CDD cd23714 cd23714 467380 beta-trefoil_Ricin_MtaL ricin B-type lectin domain, beta-trefoil fold, found in Mushroom tyrosinase-associated lectin-like protein (MtaL) and similar proteins. Mushroom tyrosinase-associated lectin-like protein (MtaL) binds to mature Agaricus bisporus tyrosinase in vivo, but the exact physiological function of MtaL is poorly understood. MtaL contains a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site. The tyrosinase enzyme complex is comprised of a H(2)L(2) tetramer. The L subunit has a lectin-like fold, whereas the H subunit contains a binuclear copper-binding site in the deoxy-state, in which three histidine residues coordinate each copper ion. Comparison of the structures of MtaL and a ricin-B-like lectin with a bound disaccharide shows that MtaL may have a similar carbohydrate-binding site that may be involved in glycoreceptor activity. 129 matched cddid_all.tbl CDD cd23715 cd23715 467381 beta-trefoil_Ricin_CCL2 ricin B-type lectin domain, beta-trefoil fold, found in a novel fruiting body lectin CCL2 from the ink cap mushroom Coprinopsis cinerea and similar proteins. Coprinopsis cinerea lectin 2 (CCL2) is a fucoside-binding lectin from the basidiomycete C. cinerea. The fungal lectin CCL2 adopts a beta-trefoil fold and has been implicated in the defense of this mushroom against invertebrate predators based on its toxicity towards nematodes and insects. Toxicity of CCL2 towards the bacterivorous nematode Caenorhabditis elegans is dependent on the specific recognition of the alpha1,3 fucosylated cores of N-glycans on the nematode intestinal epithelium and results in developmental delay and premature death. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site. 130 matched cddid_all.tbl CDD cd23716 cd23716 467382 beta-trefoil_Ricin_Macrocypin ricin B-type lectin domain, beta-trefoil fold, found in Macrocypins from Macrolepiota procera. Macrocypins comprise a family of cysteine protease inhibitors from the basidiomycete Macrolepiota procera (parasol mushroom) that possess a beta-trefoil fold, the hallmark of Kunitz-type inhibitors. Macrocypins are effective inhibitors of papain and cysteine cathepsin endopeptidases, and also inhibit cathepsins B and H, which exhibit both exopeptidase and endopeptidase activities. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site. 165 matched cddid_all.tbl CDD cd23717 cd23717 467383 beta-trefoil_Ricin_SeviL ricin B-type lectin domain, beta-trefoil fold, found in a GM1b/asialo-GM1 binding lectin SeviL from the mussel Mytilisepta virgata. SeviL, a GM1b/asialo-GM1 binding ricin B-type lectin from the mussel Mytilisepta virgata (purplish bifurcate mussel), binds strongly to the linear saccharides of the ganglioside GM1b (Neu5Ac alpha(2-3)Gal beta(1-3)GalNAc beta(1-4)Gal beta(1-4)Glc) and its precursor, asialo-GM1 (Gal beta(1-3)GalNAc beta(1-4)Gal beta(1-4)Glc). SeviL is a dimeric member of the beta-trefoil superfamily and shows no interaction with GM1 due to steric hindrance with the sialic acid branch that is absent from GM1b. Thus, SeviL has a strong selectivity for asialo-GM1 over the closely related GM1. Moreover, SeviL displayed significant apoptotic effects against various cultured cell lines (human breast, ovarian, and colonic cancer) that possess asialo-GM1 oligosaccharide at the cell surface. This unusual specificity makes SeviL of great interest for the detection and control of certain cancer cells, and cells of the immune system, that display asialo-GM1. Furthermore, SeviL showed dose- and time-dependent activation of kinase MKK3/6, p38 MAPK, and caspase-3/9. The ricin B-type lectin domain shows a beta-trefoil fold, which is characterized by 12 beta strands folded into three similar trefoil subdomains (alpha, beta, and gamma) associated to give an overall structure with pseudo-3-fold symmetry. Each subdomain bears a potential sugar binding site. 124 matched cddid_all.tbl CDD cd23718 cd23718 469561 ZF_RNaseIII_KREPB9 C2H2 zinc finger and Ribonuclease III-like domain of RNA-editing catalytic complex (RECC) protein KREPB9. KREPB9 has a divergent RNase III domain and is a component of the RNA-editing catalytic complex (RECC) involved in U-insertion/deletion mRNA editing during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The RECC core complex comprises a U-insertion subcomplex (KRET2 TUTase, KREPA1 zinc-finger protein, and KREL2 RNA ligase), a U-deletion subcomplex (KREX2 exonuclease, KREPA2 zinc-finger protein, and KREL1 RNA ligase), and six structural and/or RNA-binding proteins (KREPA3, KREPA4, KREPA5, KREPA6, KREPB4, and KREPB5). This core complex interacts with one of three RNase III family endonucleases (KREN1, KREN2, and KREN3) that may partner with one or more partner protein(s) with divergent RNase III domains, such as KREN1/KREPB8, KREN2/KREPB7, KREN3/KREPB6. KREPB4-KREPB10 have divergent RNase III domains. RECC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and the RNA-editing substrate-binding complex (RESC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. 246 matched cddid_all.tbl CDD cd23719 cd23719 469562 ZF_RNaseIII_KREPB4-5 C2H2 zinc finger and Ribonuclease III-like domain of RNA-editing catalytic complex (RECC) proteins KREPB4-5. KREPB4 (MP46) and KREPB5 (MP44) have divergent RNase III domains and are components of the RNA-editing catalytic complex (RECC) involved in U-insertion/deletion mRNA editing during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The RECC core complex comprises a U-insertion subcomplex (KRET2 TUTase, KREPA1 zinc-finger protein, and KREL2 RNA ligase), a U-deletion subcomplex (KREX2 exonuclease, KREPA2 zinc-finger protein, and KREL1 RNA ligase), and six structural and/or RNA-binding proteins (KREPA3, KREPA4, KREPA5, KREPA6, KREPB4, and KREPB5). This core complex interacts with one of three RNase III family endonucleases (KREN1, KREN2, and KREN3) that may partner with one or more partner protein(s) with divergent RNase III domains, such as KREN1/KREPB8, KREN2/KREPB7, KREN3/KREPB6. KREPB4-KREPB10 have divergent RNase III domains. RECC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and the RNA-editing substrate-binding complex (RESC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. 261 matched cddid_all.tbl CDD cd23720 cd23720 469563 ZF_RNaseIII_KREPB10 C2H2 zinc finger and Ribonuclease III-like domain of RNA-editing catalytic complex (RECC) protein KREPB10. KREPB10 has a divergent RNase III domain and is a component of the RNA-editing catalytic complex (RECC) involved in U-insertion/deletion mRNA editing during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The RECC core complex comprises a U-insertion subcomplex (KRET2 TUTase, KREPA1 zinc-finger protein, and KREL2 RNA ligase), a U-deletion subcomplex (KREX2 exonuclease, KREPA2 zinc-finger protein, and KREL1 RNA ligase), and six structural and/or RNA-binding proteins (KREPA3, KREPA4, KREPA5, KREPA6, KREPB4, and KREPB5). This core complex interacts with one of three RNase III family endonucleases (KREN1, KREN2, and KREN3) that may partner with one or more partner protein(s) with divergent RNase III domains, such as KREN1/KREPB8, KREN2/KREPB7, KREN3/KREPB6. KREPB4-KREPB10 have divergent RNase III domains. RECC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and the RNA-editing substrate-binding complex (RESC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. 269 matched cddid_all.tbl CDD cd23721 cd23721 469564 ZF_RNaseIII_KREPB7 C2H2 zinc finger and Ribonuclease III-like domain of Ribonuclease III-like domain of RNA-editing catalytic complex (RECC) protein KREPB7. KREPB7 (MP47) has a divergent RNase III domain and is a component of the RNA-editing catalytic complex (RECC) involved in U-insertion/deletion mRNA editing during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The RECC core complex comprises a U-insertion subcomplex (KRET2 TUTase, KREPA1 zinc-finger protein, and KREL2 RNA ligase), a U-deletion subcomplex (KREX2 exonuclease, KREPA2 zinc-finger protein, and KREL1 RNA ligase), and six structural and/or RNA-binding proteins (KREPA3, KREPA4, KREPA5, KREPA6, KREPB4, and KREPB5). This core complex interacts with one of three RNase III family endonucleases (KREN1, KREN2, and KREN3) that may partner with one or more partner protein(s) with divergent RNase III domains, such as KREN1/KREPB8, KREN2/KREPB7, KREN3/KREPB6. KREPB4-KREPB10 have divergent RNase III domains. RECC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and the RNA-editing substrate-binding complex (RESC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. 301 matched cddid_all.tbl CDD cd23722 cd23722 469565 ZF_RNaseIII_KREPB8 C2H2 zinc finger and Ribonuclease III-like domain of RNA-editing catalytic complex (RECC) protein KREPB8. KREPB8 (MP41) has a divergent RNase III domain and is a component of the RNA-editing catalytic complex (RECC) involved in U-insertion/deletion mRNA editing during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The RECC core complex comprises a U-insertion subcomplex (KRET2 TUTase, KREPA1 zinc-finger protein, and KREL2 RNA ligase), a U-deletion subcomplex (KREX2 exonuclease, KREPA2 zinc-finger protein, and KREL1 RNA ligase), and six structural and/or RNA-binding proteins (KREPA3, KREPA4, KREPA5, KREPA6, KREPB4, and KREPB5). This core complex interacts with one of three RNase III family endonucleases (KREN1, KREN2, and KREN3) that may partner with one or more partner protein(s) with divergent RNase III domains, such as KREN1/KREPB8, KREN2/KREPB7, KREN3/KREPB6. KREPB4-KREPB10 have divergent RNase III domains. RECC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and the RNA-editing substrate-binding complex (RESC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. 259 matched cddid_all.tbl CDD cd23723 cd23723 469566 ZF_RNaseIII_KREPB6 C2H2 zinc finger and Ribonuclease III-like domain of Ribonuclease III-like domain of RNA-editing catalytic complex (RECC) protein KREPB6. KREPB6 (MP49) has a divergent RNase III domain and is a component of the RNA-editing catalytic complex (RECC) involved in U-insertion/deletion mRNA editing during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The RECC core complex comprises a U-insertion subcomplex (KRET2 TUTase, KREPA1 zinc-finger protein, and KREL2 RNA ligase), a U-deletion subcomplex (KREX2 exonuclease, KREPA2 zinc-finger protein, and KREL1 RNA ligase), and six structural and/or RNA-binding proteins (KREPA3, KREPA4, KREPA5, KREPA6, KREPB4, and KREPB5). This core complex interacts with one of three RNase III family endonucleases (KREN1, KREN2, and KREN3) that may partner with one or more partner protein(s) with divergent RNase III domains, such as KREN1/KREPB8, KREN2/KREPB7, KREN3/KREPB6. KREPB4-KREPB10 have divergent RNase III domains. RECC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and the RNA-editing substrate-binding complex (RESC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. 218 matched cddid_all.tbl CDD cd23724 cd23724 469567 ZF_RNaseIII_KREPB4 C2H2 zinc finger and Ribonuclease III-like domain of Ribonuclease III-like domain of RNA-editing catalytic complex (RECC) protein KREPB4. KREPB4 (MP46) has a divergent RNase III domain and is a component of the RNA-editing catalytic complex (RECC) involved in U-insertion/deletion mRNA editing during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The RECC core complex comprises a U-insertion subcomplex (KRET2 TUTase, KREPA1 zinc-finger protein, and KREL2 RNA ligase), a U-deletion subcomplex (KREX2 exonuclease, KREPA2 zinc-finger protein, and KREL1 RNA ligase), and six structural and/or RNA-binding proteins (KREPA3, KREPA4, KREPA5, KREPA6, KREPB4, and KREPB5). This core complex interacts with one of three RNase III family endonucleases (KREN1, KREN2, and KREN3) that may partner with one or more partner protein(s) with divergent RNase III domains, such as KREN1/KREPB8, KREN2/KREPB7, KREN3/KREPB6. KREPB4-KREPB10 have divergent RNase III domains, lacking the conserved catalytic residues. RECC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and the RNA-editing substrate-binding complex (RESC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. 251 matched cddid_all.tbl CDD cd23725 cd23725 469568 RNaseIII_KREPB5 Ribonuclease III-like domain of Ribonuclease III-like domain of RNA-editing catalytic complex (RECC) protein KREPB5. KREPB5 (MP44) has a divergent RNase III domain and is a component of the RNA-editing catalytic complex (RECC) involved in U-insertion/deletion mRNA editing during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The RECC core complex comprises a U-insertion subcomplex (KRET2 TUTase, KREPA1 zinc-finger protein, and KREL2 RNA ligase), a U-deletion subcomplex (KREX2 exonuclease, KREPA2 zinc-finger protein, and KREL1 RNA ligase), and six structural and/or RNA-binding proteins (KREPA3, KREPA4, KREPA5, KREPA6, KREPB4, and KREPB5). This core complex interacts with one of three RNase III family endonucleases (KREN1, KREN2, and KREN3) that may partner with one or more partner protein(s) with divergent RNase III domains, such as KREN1/KREPB8, KREN2/KREPB7, KREN3/KREPB6. KREPB4-KREPB10 have divergent RNase III domains. RECC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and the RNA-editing substrate-binding complex (RESC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. The C2H2 zinc finger that is present in related KREB proteins is not conserved in this subfamily. 259 matched cddid_all.tbl CDD cd23726 cd23726 469569 ZF_RNaseIII_KREN2 C2H2 zinc finger and Ribonuclease III domain of Kinetoplastid RNA Editing endonuclease 2 (KREN2). KREN2 (KRENB3) is an RNase III family endonuclease of the RNA-editing catalytic complex (RECC) involved in U-insertion/deletion mRNA editing during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The RECC core complex comprises a U-insertion subcomplex (KRET2 TUTase, KREPA1 zinc-finger protein, and KREL2 RNA ligase), a U-deletion subcomplex (KREX2 exonuclease, KREPA2 zinc-finger protein, and KREL1 RNA ligase), and six structural and/or RNA-binding proteins (KREPA3, KREPA4, KREPA5, KREPA6, KREPB4, and KREPB5). This core complex interacts with one of three RNase III family endonucleases (KREN1, KREN2, and KREN3) that may partner with one or more partner protein(s) with divergent RNase III domains, such as KREN1/KREPB8, KREN2/KREPB7, KREN3/KREPB6. KREPB4-KREPB10 have divergent RNase III domains. RECC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and the RNA-editing substrate-binding complex (RESC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. 259 matched cddid_all.tbl CDD cd23727 cd23727 469570 ZF_RNaseIII_KREN3 C2H2 zinc finger and Ribonuclease III domain of Kinetoplastid RNA Editing endonuclease 3 (KREN3). KREN3 (KREPB2) is an RNase III family endonuclease of the RNA-editing catalytic complex (RECC) involved in U-insertion/deletion mRNA editing during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The RECC core complex comprises a U-insertion subcomplex (KRET2 TUTase, KREPA1 zinc-finger protein, and KREL2 RNA ligase), a U-deletion subcomplex (KREX2 exonuclease, KREPA2 zinc-finger protein, and KREL1 RNA ligase), and six structural and/or RNA-binding proteins (KREPA3, KREPA4, KREPA5, KREPA6, KREPB4, and KREPB5). This core complex interacts with one of three RNase III family endonucleases (KREN1, KREN2, and KREN3) that may partner with one or more partner protein(s) with divergent RNase III domains, such as KREN1/KREPB8, KREN2/KREPB7, KREN3/KREPB6. KREPB4-KREPB10 have divergent RNase III domains. RECC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and the RNA-editing substrate-binding complex (RESC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. 256 matched cddid_all.tbl CDD cd23728 cd23728 469571 ZF_RNaseIII_KREN1 C2H2 zinc finger and Ribonuclease III domain of Kinetoplastid RNA Editing endonuclease 1 (KREN1). KREN1 (KREPB1) is an RNase III family endonuclease of the RNA-editing catalytic complex (RECC) involved in U-insertion/deletion mRNA editing during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The RECC core complex comprises a U-insertion subcomplex (KRET2 TUTase, KREPA1 zinc-finger protein, and KREL2 RNA ligase), a U-deletion subcomplex (KREX2 exonuclease, KREPA2 zinc-finger protein, and KREL1 RNA ligase), and six structural and/or RNA-binding proteins (KREPA3, KREPA4, KREPA5, KREPA6, KREPB4, and KREPB5). This core complex interacts with one of three RNase III family endonucleases (KREN1, KREN2, and KREN3) that may partner with one or more partner protein(s) with divergent RNase III domains, such as KREN1/KREPB8, KREN2/KREPB7, KREN3/KREPB6. KREPB4-KREPB10 have divergent RNase III domains. RECC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and the RNA-editing substrate-binding complex (RESC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. 294 matched cddid_all.tbl CDD cd23732 cd23732 467837 RESC1 RNA-editing substrate-binding complex subunit 1 (RESC1). RESC1 (GRBC1, GAP2) forms a stable heterotetramer with RESC2 (GRBC2, GAP1) that directly binds guide RNAs (gRNAs) and is essential for the stability of gRNAs in U-insertion/deletion mRNA editing during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC1/2 is a core component of the RNA-editing substrate-binding complex (RESC) that consists of about 20 components. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. The predicted structure (by AlphaFold) of RESC1 contains a domain most structurally similar to fungal mRNA triphosphatases belonging to the CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) phosphatase superfamily; this domain adopts an eight-stranded antiparallel beta barrel tunnel (the triphosphate tunnel) with an active site located at the center of the tunnel. mRNA triphosphatase catalyzes the first step in the mRNA cap formation process, the removal of the gamma-phosphate of triphosphate terminated pre-mRNA. RESC1 lacks the conserved mRNA triphosphatase active site residues and may not exhibit this enzymatic activity. 420 matched cddid_all.tbl CDD cd23733 cd23733 467838 RESC2 RNA-editing substrate-binding complex subunit 1 (RESC2). RESC2 (GRBC2, GAP1) forms a stable heterotetramer with RESC1 (GRBC1, GAP2) that directly binds guide RNAs (gRNAs) and is essential for the stability of gRNAs in U-insertion/deletion mRNA editing during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC1/2 is a core component of the RNA-editing substrate-binding complex (RESC) that consists of about 20 components. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. The predicted structure (by AlphaFold) of RESC2 contains a domain most structurally similar to fungal mRNA triphosphatases belonging to the CYTH-like (also known as triphosphate tunnel metalloenzyme (TTM)-like) phosphatase superfamily; this domain adopts an eight-stranded antiparallel beta barrel tunnel (the triphosphate tunnel) with an active site located at the center of the tunnel. mRNA triphosphatase catalyzes the first step in the mRNA cap formation process, the removal of the gamma-phosphate of triphosphate terminated pre-mRNA. RESC2 lacks the conserved mRNA triphosphatase active site residues and may not exhibit this enzymatic activity. 442 matched cddid_all.tbl CDD cd23734 cd23734 467927 RESC4 RNA-editing substrate-binding complex subunit 4 (RESC4). RESC4 (GRBC4, MRB5390) is a component of the RNA-editing substrate-binding complex (RESC) that is composed of about 20-components and is involved in kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. RESC4 is predicted (by AlphaFold) to adopt an all-helical structure with some disordered regions. The central region of RESC4 is predicted to adopt a 6-helical hairpin structure, resembling members of the Lanthionine synthetase C (LanC)-like/Six-hairpin glycosidase-like superfamily. The C-terminal region of RESC4 shows the highest amino acid conservation and is also predicted by AlphaFold with the highest confidence, to contain alpha helices that resemble Armadillo (ARM)/beta-catenin-like repeats. ARM repeats have been implicated in mediating protein-protein interactions. 1090 matched cddid_all.tbl CDD cd23735 cd23735 467928 RESC6-like RNA-editing substrate-binding complex subunit 6 (RESC6) and related proteins. RESC6 (GRBC6, MRB3010) is a component of the RNA-editing substrate-binding complex (RESC), that is composed of about 20 components and is involved in kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. RESC6 is predicted (by AlphaFold) to adopt an all-helical structure with a disordered region at the N-terminus. The helical structure that is predicted with high confidence resembles Armadillo (ARM)/beta-catenin-like repeats. ARM repeats have been implicated in mediating protein-protein interactions. 299 matched cddid_all.tbl CDD cd23736 cd23736 467929 RESC8-like RNA-editing substrate-binding complex subunit 8 (RESC8) and related proteins. RESC8 (REMC1, MRB10130) is a component of the RNA-editing substrate-binding complex (RESC) that is composed of about 20-components and is involved in kinetoplast RNA processing. RESC8 with RESC10, and RESC14 are RESC organizers which are important for modulating proper protein-protein-RNA rearrangements during editing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. RESC8 is predicted (by AlphaFold) to adopt an all-helical structure, with a lower confidence in prediction of the N-terminal 100 residues. The helical structure that is predicted with high confidence, representing the middle and most of the C-terminal region, resembles Armadillo (ARM)/beta-catenin-like repeats. ARM repeats have been implicated in mediating protein-protein interactions. 514 matched cddid_all.tbl CDD cd23737 cd23737 467930 RESC9 RNA-editing substrate-binding complex subunit 9 (RESC9). RESC9 (REMC2, MRB1860) is a component of the RNA-editing substrate-binding complex (RESC) that is composed of about 20 components and is involved in kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. RESC9 is predicted (by AlphaFold) to adopt an all-helical structure, with helices that resemble Armadillo (ARM)/beta-catenin-like repeats. ARM repeats have been implicated in mediating protein-protein interactions. Regions of the protein also show structural similarity to other alpha-helical proteins such as members of the glycosaminoglycan (GAG) polysaccharide lyase and alginate lyase families. 836 matched cddid_all.tbl CDD cd23738 cd23738 467931 RESC10 RNA-editing substrate-binding complex subunit 10 (RESC10). RESC10 (REMC3, MRB800) is a component of the RNA-editing substrate-binding complex (RESC) that is composed of about 20 components and is involved in kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. RESC10 is predicted (by AlphaFold) to adopt an all-helical structure with a disordered N-terminal region (of about 118 amino acids) that is predicted with low confidence. The rest of the protein is predicted with high confidence and shows a helical repeat structure that resembles proteins containing Armadillo (ARM)/beta-catenin-like repeats and tetratricopeptide (TPR) repeats. Both ARM and TPR repeats are implicated in mediating protein-protein interactions. 442 matched cddid_all.tbl CDD cd23739 cd23739 467932 TBRG4-like_N transforming growth factor beta (TGFbeta) regulator 4 (TBRG4) and similar proteins; predicted alpha-helical domain N-terminal to FAST kinase-like protein, subdomain 1 (FAST_1). TBRG4 also called cell cycle progression restoration protein 2 or Fas-activated serine-threonine (FAST) kinase domain-containing protein 4, is a regulator of TGFbeta and is implicated in numerous types of cancer. It serves a role in the tumorigenesis of lung cancer via deregulation of DNA damage-inducible transcript 3 (DDIT3), caveolin 1 (CAV1), and ribonucleotide reductase regulatory subunit M2 (RRM2). This domain lies N-terminal to the FAST_1 domain, and is predicted (by AlphaFold) to be alpha-helical, with similarity to structures of members of the 6-hairpin (6 helical hairpin) clan. 249 matched cddid_all.tbl CDD cd23740 cd23740 467833 RESC11A_12_12A RNA-editing substrate-binding complex subunit 11A (RESC11A), RESC12, RESC12A, and similar proteins. RESC11A (REMC4, MRB8180), RESC12 (REMC5, MRB4160), and RESC12A (REMC5A, MRB8170) are RNA-binding components of the RNA-editing substrate-binding complex (RESC), composed of about 20 components, that is involved in kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC), to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. RESC11A, RESC12, and RESC12A are predicted (by AlphaFold) to be helical repeat proteins, with predominantly alpha-helical structures that show similarity to each other but no similarity to experimentally determined structures. Shorter regions within the proteins show some structural similarity to various alpha-helical proteins including those containing containing Armadillo (ARM)/beta-catenin-like repeats and tetratricopeptide (TPR) repeats. Both ARM and TPR repeats are implicated in mediating protein-protein interactions. 579 matched cddid_all.tbl CDD cd23741 cd23741 467834 RESC11A RNA-editing substrate-binding complex subunit 11A (RESC11A) and similar proteins. RESC11A (REMC4, MRB8180) is an RNA-binding component of the RNA-editing substrate-binding complex (RESC), composed of about 20 components, that is involved in kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC), to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. RESC11A is predicted (by AlphaFold) to be a helical repeat protein, with a predominantly alpha-helical structure that shows no similarity to any experimentally determined structure. Shorter regions within the protein show some structural similarity to various alpha-helical proteins including those containing containing Armadillo (ARM)/beta-catenin-like repeats and tetratricopeptide (TPR) repeats. Both ARM and TPR repeats are implicated in mediating protein-protein interactions. 668 matched cddid_all.tbl CDD cd23742 cd23742 467835 RESC12-12A RNA-editing substrate-binding complex subunit 12 (RESC12), RESC12A, and similar proteins. RESC12 (REMC5, MRB4160) and RESC12A (REMC5A, MRB8170) are RNA-binding components of the RNA-editing substrate-binding complex (RESC), composed of about 20 components, that is involved in kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC), to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. RESC12 and RESC12A are predicted (by AlphaFold) to be helical repeat proteins, with predominantly alpha-helical structures that show similarity to each other but no similarity to experimentally determined structures. Shorter regions within the proteins show some structural similarity to various alpha-helical proteins including those containing containing Armadillo (ARM)/beta-catenin-like repeats and tetratricopeptide (TPR) repeats. Both ARM and TPR repeats are implicated in mediating protein-protein interactions. 682 matched cddid_all.tbl CDD cd23743 cd23743 467817 RESC18 RNA-editing substrate-binding complex subunit 18 (RESC18). RESC18 (PAMC4) is a component of the RNA-editing substrate-binding complex (RESC), consisting of about 20-components, that is involved in kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. RESC18 is predicted (AlphaFold) to contain four domains; the two C-terminal domains (domains 3 and 4) are structurally similar and superimposable to RESC17 domains 3 and 4. Domain 3 adopts a helical fold and shows similarity to helix-turn-helix DNA-binding motifs, while domain 4 adopts a 5-stranded beta sheet structure surrounded by helices. Domain 4, the largest domain and predicted with the highest confidence of the four domains, shows structural similarity to many proteins belonging to different domain superfamilies including class I SAM-dependent methyltransferases and electron transfer flavoprotein (ETF) alpha belonging to the adenine nucleotide alpha hydrolase superfamily. The two N-terminal domains adopt partial winged helix or helix-turn-helix folds with structural similarities to various RNA- or DNA-binding domains. 269 matched cddid_all.tbl CDD cd23744 cd23744 467818 RESC17 RNA-editing substrate-binding complex subunit 17 (RESC17). RESC17 (PAMC3) is a component of the RNA-editing substrate-binding complex (RESC), consisting of about 20-components, that is involved in kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. RESC17 is predicted (AlphaFold) to contain four domains; the two C-terminal domains (domains 3 and 4) are structurally similar and superimposable to RESC18 domains 3 and 4. Domain 3 adopts a helical fold and shows similarity to helix-turn-helix DNA-binding motifs, while domain 4 adopts a 5-stranded beta sheet structure surrounded by helices. Domain 4, the largest domain and predicted with the highest confidence of the four domains, shows structural similarity to many proteins belonging to different domain superfamilies including class I SAM-dependent methyltransferases and electron transfer flavoprotein (ETF) alpha belonging to the adenine nucleotide alpha hydrolase superfamily. The two N-terminal domains adopt partial winged helix or helix-turn-helix folds with structural similarities to various RNA- or DNA-binding domains. 324 matched cddid_all.tbl CDD cd23745 cd23745 467819 RESC17_18-like RNA-editing substrate-binding complex subunit 17 (RESC17) and RESC18 and related proteins; uncharacterized subgroup. RESC17 (PAMC3) AND RESC18 (PAMC4) are components of the RNA-editing substrate-binding complex (RESC), consisting of about 20-components, that is involved in kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. RESC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and RNA-editing catalytic complex (RECC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. RESC17 and RESC18 show some sequence similarity and are both predicted (AlphaFold) to contain four domains; their corresponding C-terminal domains 3 and 4 are structurally similar and superimposable. Domain 3 adopts a helical fold and shows similarity to helix-turn-helix DNA-binding motifs, while domain 4 adopts a 5-stranded beta sheet structure surrounded by helices. Domain 4, the largest domain and predicted with the highest confidence of the four domains, shows structural similarity to many proteins belonging to different domain superfamilies including class I SAM-dependent methyltransferases and electron transfer flavoprotein (ETF) alpha belonging to the adenine nucleotide alpha hydrolase superfamily. Both RESC17 and RESC18 contain two N-terminal domains that adopt partial winged helix or helix-turn-helix folds, but are not directly superimposable to each other. These domains have structural similarities to various RNA- or DNA-binding domains. 326 matched cddid_all.tbl CDD cd23746 cd23746 469572 ZF_RNaseIII_KREPB8-10 C2H2 zinc finger and Ribonuclease III-like domain of RNA-editing catalytic complex (RECC) protein KREPB9. KREPB8 (MP41), KREPB9, and KREPB10 have divergent RNase III domains, and are components of the RNA-editing catalytic complex (RECC) involved in U-insertion/deletion mRNA editing during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The RECC core complex comprises a U-insertion subcomplex (KRET2 TUTase, KREPA1 zinc-finger protein, and KREL2 RNA ligase), a U-deletion subcomplex (KREX2 exonuclease, KREPA2 zinc-finger protein, and KREL1 RNA ligase), and six structural and/or RNA-binding proteins (KREPA3, KREPA4, KREPA5, KREPA6, KREPB4, and KREPB5). This core complex interacts with one of three RNase III family endonucleases (KREN1, KREN2, and KREN3) that may partner with one or more partner protein(s) with divergent RNase III domains, such as KREN1/KREPB8, KREN2/KREPB7, KREN3/KREPB6. KREPB4-KREPB10 have divergent RNase III domains. RECC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and the RNA-editing substrate-binding complex (RESC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. 231 matched cddid_all.tbl CDD cd23747 cd23747 469573 ZF_RNaseIII_KREN1-3 C2H2 zinc finger and Ribonuclease III domain of Kinetoplastid RNA Editing endonuclease 1 (KREN1), KREN2, KREN3, and similar proteins. KREN1-3 (KREPB1-3) are RNase III family endonucleases of the RNA-editing catalytic complex (RECC) involved in U-insertion/deletion mRNA editing during kinetoplast RNA processing. The mitochondrial DNA of Trypanosomatids, known as the kinetoplast DNA (kDNA or mtDNA), consists of a network of dozens of maxicircles and thousands of minicircles concatenated together. Maxicircles are equivalent to other eukaryotic mitochondrial DNAs, while minicircles encode guide RNAs (gRNAs) involved in U-insertion/deletion editing processes exclusive of Trypanosomatids that produce the maturation of the maxicircle-encoded transcripts. Although most gRNAs are encoded by minicircles, varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Trypanosoma brucei maxicircles encode 9S and 12S rRNAs, two gRNAs, two ribosomal proteins and 16 subunits of respiratory complexes. 12 of the 18 maxicircle genes are present as cryptogenes whose transcripts require U-insertion/deletion editing, mediated by gRNAs, to restore a protein-coding capacity. The RECC core complex comprises a U-insertion subcomplex (KRET2 TUTase, KREPA1 zinc-finger protein, and KREL2 RNA ligase), a U-deletion subcomplex (KREX2 exonuclease, KREPA2 zinc-finger protein, and KREL1 RNA ligase), and six structural and/or RNA-binding proteins (KREPA3, KREPA4, KREPA5, KREPA6, KREPB4, and KREPB5). This core complex interacts with one of three RNase III family endonucleases (KREN1, KREN2, and KREN3) that may partner with one or more partner protein(s) with divergent RNase III domains, such as KREN1/KREPB8, KREN2/KREPB7, KREN3/KREPB6. KREPB4-KREPB10 have divergent RNase III domains. RECC interacts with two other complexes, the RNA-editing helicase 2 complex (REH2C) and the RNA-editing substrate-binding complex (RESC) to form an assembly (editosome/holoenzyme) that carries out U-insertion/deletion mRNA editing. 215 matched cddid_all.tbl CDD cd23763 cd23763 466849 ASKHA_ATPase_ROK ATPase-like domain of the ROK (Repressor, ORF, Kinase) domain family. The ROK family corresponds to a group of proteins including sugar kinases, transcriptional repressors, and yet uncharacterized open reading frames. ROK family sugar kinases phosphorylate a range of structurally distinct hexoses including the key carbon source D-glucose, various glucose epimers, and several acetylated hexosamines. The sugar kinases include N-acetyl-D-glucosamine kinase (NAGK; EC 2.7.1.59), polyphosphate glucokinase (PPGK; EC 2.7.1.63/EC 2.7.1.2), glucokinase (GLK; EC 2.7.1.2), fructokinase (FRK; EC 2.7.1.4), hexokinase (HK; EC 2.7.1.1), D-allose kinase (AlsK; EC 2.7.1.55), bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (GNE; EC 3.2.1.183/EC 2.7.1.60), N-acetylmannosamine kinase (NanK; EC 2.7.1.60), beta-glucoside kinase (BglK; EC 2.7.1.85), and N-acetylglucosamine kinase (EC 2.7.1.59). The family also contains the repressor proteins, such as N-acetylglucosamine repressor (NagC), xylose repressor (XylR), cyclobis-(1-6)-alpha-nigerosyl repressor (CYANR) and protein Mlc. ROK kinases harbor a conserved N-terminal ATP binding motif of sequence DxGxT, while ROK repressors possess a N-terminal extension that contains a canonical helix-turn-helix DNA binding motif. The ROK family proteins belong to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily of phosphotransferases, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 239 matched cddid_all.tbl CDD cd23766 cd23766 467744 IQCG IQ (isoleucine-glutamine) motif containing G (IQCG). IQCG, also called dynein regulatory complex protein 9 (DRC9), belongs to the IQ motif-containing protein family which contains a C-terminal conserved IQ (isoleucine-glutamine) motif and a coiled-coil domain. The IQ motif ([ILV]QxxxRxxxx[RK]), where x stands for any amino-acid residue, interacts with calmodulin (CaM) in a calcium-independent manner and is present in proteins with a wide diversity of biological functions. The expression of IQCG is reduced in the sperm of human asthenospermia patients whose sperm have reduced mobility. It has also been shown to have a role in the calmodulin-mediated calcium signaling pathway in zebrafish haematopoietic development. The human IQCG gene was first reported to be involved in chromosome translocation in a case of acute lymphoid/myeloid leukemia. It expresses predominantly at mice testis during spermatogenesis which interacts with calmodulin in a calcium-dependent manner in the mouse testis. IQCG knockout mice are sterile due to the total immobility of their spermatozoa. 40 matched cddid_all.tbl CDD cd23767 cd23767 467745 IQCD IQ (isoleucine-glutamine) motif containing D (IQCD). IQCD, also called dynein regulatory complex protein 10 (DRC10), belongs to the IQ motif-containing protein family which contains a C-terminal conserved IQ motif domain and two coiled-coil domains. The IQ motif ([ILV]QxxxRxxxx[RK]), where x stands for any amino-acid residue, interacts with calmodulin (CaM) in a calcium-independent manner and is present in proteins with a wide diversity of biological functions. The IQCD protein was found to primarily accumulate in the acrosome area of round and elongating spermatids of the testis during late stage of spermiogenesis and was then localized to the acrosome and tail regions of mature spermatozoa. The expression of IQCD follows the trajectory of acrosome development during spermatogenesis. IQCD is associated with neuroblastoma and neurodegenerative diseases, and is reported to interact with the nuclear retinoid X receptor in the presence of 9-cis-retinoic acid, thereby activating the transcriptional activity of the receptor. 37 matched cddid_all.tbl CDD cd23783 cd23783 467645 RWD_ScITT1-like RWD domain of Saccharomyces cerevisiae translation termination inhibitor protein ITT1 and related proteins. ITT1 is a novel protein inhibiting translation termination in Saccharomyces cerevisiae. It modulates the efficiency of translation termination, resulting in the readthrough of all three types of nonsense codons UAA, UAG and UGA. ITT1 modulates the efficiency of translation termination through physical interactions with two release factors eRF1 (Sup45) and eRF3 (Sup35). Deletion of the ITT1 gene increases yeast sensitivity to heavy metal, by modulating URE2 expression at the protein level; URE2 expression is critical to cell survival under heavy metal stress. 141 matched cddid_all.tbl CDD cd23784 cd23784 467646 RWD_Spc25 RWD domain of kinetochore protein Spc25 and related proteins. Spc25 is a component of the nuclear division cycle 80 (NDC80) kinetochore complex, which is essential for the stable formation of kinetochore-microtubule anchoring and correct chromosome segregation during mitosis. NDC80 has two subcomplexes, NDC80/NUF2 which binds directly to microtubules, and Spc24/Spc25 which interacts with the kinetochore. The inner kinetochore centromere protein T (CENP-T) has been shown to interact directly with the Spc24/25 RWD domains; these RWD domains serve as interaction modules at the kinetochores. 87 matched cddid_all.tbl CDD cd23785 cd23785 467647 DRWD-C_DmFANCL C-terminal double-RWD domain of Drosophila melanogaster Fanconi anemia group L protein (FANCL) and related proteins. FANCL, also called E3 ubiquitin-protein ligase FANCL, or RING-type E3 ubiquitin transferase FANCL, is an E3 ubiquitin-protein ligase component of the Fanconi anemia (FA) core complex which functions in the repair of interstrand crosslinks (ICLs), a toxic form of DNA damage. FANCL, works in conjunction with the E2 conjugating enzyme UBE2T (FANCT) to add a single ubiquitin to specific lysine residues on FANCD2 and FANCI. The mono-ubiquitinated FANCI-FANCD2 complex is thought to recruit downstream DNA-repair proteins for ICL processing. FANCL is composed of an N-terminal E2-like fold (ELF) domain, a novel double-RWD (DRWD) domain, and a C-terminal RING domain predicted to facilitate E2 binding. The DRWD domain is responsible for substrate binding. The model corresponds to the C-terminal DRWD domain (DRWD-C). 97 matched cddid_all.tbl CDD cd23786 cd23786 467648 ELF_FANCL N-terminal E2-like Fold (ELF) domain of Fanconi anemia group L protein (FANCL) and related proteins. FANCL, also called E3 ubiquitin-protein ligase FANCL, Fanconi anemia-associated polypeptide of 43 kDa (FAAP43), or RING-type E3 ubiquitin transferase FANCL, is an E3 ubiquitin-protein ligase component of the Fanconi anemia (FA) core complex which functions in the repair of interstrand crosslinks (ICLs), a toxic form of DNA damage. FANCL, works in conjunction with the E2 conjugating enzyme UBE2T (FANCT) to add a single ubiquitin to specific lysine residues on FANCD2 and FANCI. The mono-ubiquitinated FANCI-FANCD2 complex is thought to recruit downstream DNA-repair proteins for ICL processing. FANCL is composed of an N-terminal E2-like fold (ELF) domain, a novel double-RWD (DRWD) domain, and a C-terminal RING domain predicted to facilitate E2 binding. The model corresponds to the ELF domain which cannot bind the substrates. 86 matched cddid_all.tbl CDD cd23787 cd23787 467649 RWD_CSM1 RWD domain of Saccharomyces cerevisiae chromosome segregation in meiosis protein 1 (CSM1) and related proteins. Saccharomyces cerevisiae CSM1 is a component of the monopolin complex which promotes monoorientation during meiosis I, required for chromosome segregation during meiosis. It also plays a mitotic role in DNA replication. The family also includes Schizosaccharomyces pombe chromosome segregation protein 1 (PCS1), which is a component of a monopolin-like complex composed of PCS1 and MDE4. The PCS1/MDE4 complex associates with the kinetochore and is essential for accurate chromosome segregation during mitosis and meiosis II. PCS1 may clamp together microtubule binding sites on the same kinetochore, preventing merotelic attachment of microtubules. In contrast to its S. cerevisiae ortholog CSM1, PCS1 is not required for mono-orientation during meiosis I. 102 matched cddid_all.tbl CDD cd23788 cd23788 467650 DRWD-C_KlCTF19 C-terminal double-RWD domain of Kluyveromyces lactis chromosome transmission fidelity 19 (CTF19) and related proteins. CTF19, also called inner kinetochore subunit CTF19, CENP-P homolog, or constitutive centromere-associated network protein CTF19, is a component of the kinetochore, a multiprotein complex that assembles on centromeric DNA and attaches chromosomes to spindle microtubules, mediating chromosome segregation and sister chromatid segregation during meiosis and mitosis. KlCTF19 contains two RWD domains, also known as a double-RWD domain, DRWD, which is involved in interactions with other kinetochore proteins. The model corresponds to the C-terminal double-RWD domain (DRWD-C). 76 matched cddid_all.tbl CDD cd23789 cd23789 467651 DRWD-N_KlCTF19 N-terminal double-RWD domain of Kluyveromyces lactis chromosome transmission fidelity 19 (CTF19) and related proteins. CTF19, also called inner kinetochore subunit CTF19, CENP-P homolog, or constitutive centromere-associated network protein CTF19, is a component of the kinetochore, a multiprotein complex that assembles on centromeric DNA and attaches chromosomes to spindle microtubules, mediating chromosome segregation and sister chromatid segregation during meiosis and mitosis. KlCTF19 contains two RWD domains, also known as a double-RWD domain, DRWD, which is involved in interactions with other kinetochore proteins. The model corresponds to the N-terminal double-RWD domain (DRWD-N). 83 matched cddid_all.tbl CDD cd23790 cd23790 467410 UBCc_UBE2A_2B Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-conjugating enzymes E2A, E2B and related proteins. The E2A/2B subfamily includes mammalian ubiquitin-conjugating enzymes UBE2A/RAD6A and UBE2B/RAD6B, yeast ubiquitin-conjugating enzyme E2 2 (UBC2/RAD6), plant ubiquitin-conjugating enzyme E2 1-3 (UBC1-3), and similar proteins. They are ubiquitin-conjugating enzymes (EC 2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. Both UBE2A/RAD6A and UBE2B/RAD6B are required for post-replication repair of UV-damaged DNA. In vitro, they catalyze 'Lys-11', as well as 'Lys-48'-linked polyubiquitination. UBE2B might also catalyze 'Lys-63'-linked polyubiquitination. Saccharomyces cerevisiae UBC2 is required for DNA repair, damage-induced mutagenesis, and sporulation. 143 matched cddid_all.tbl CDD cd23791 cd23791 467411 UBCc_UBE2C Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-conjugating enzyme E2 C and related proteins. The E2C family includes mammalian ubiquitin-conjugating enzyme E2 C (UBE2C/UBCH10), yeast E2 ubiquitin-conjugating enzyme 11 (UBC11), plant ubiquitin-conjugating enzyme E2 19 (UBC19) and 20 (UBC20). They are ubiquitin-conjugating enzymes (EC 2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. UBE2C, also known as (E3-independent) E2 ubiquitin-conjugating enzyme C (EC 2.3.2.24), E2 ubiquitin-conjugating enzyme C, ubiquitin carrier protein C, or ubiquitin-protein ligase C, catalyzes 'Lys-11'- and 'Lys-48'-linked polyubiquitination in vitro. It is a ubiquitin carrier protein required for the destruction of mitotic cyclins and proteins that maintain sister chromatid cohesion in animal cells and in Schizosaccharomyces pombe. In Saccharomyces cerevisiae, UBC11 is not essential for mitotic cyclin destruction. Arabidopsis thaliana UBC19 is part of the anaphase-promoting complex (APC). It may have a key function during cell cycle and be involved in cyclin B1 degradation. 140 matched cddid_all.tbl CDD cd23792 cd23792 467412 UBCc_UBE2D Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin conjugating enzyme E2 D1-D3 and related proteins. The E2D family includes mammalian ubiquitin-conjugating enzyme E2 D1-4 (UBE2D1/SFT/UBC5A/UBCH5/UBCH5A, UBE2D2/PUBC1/UBC4/UBC5B/UBCH4/UBCH5B, UBE2D3/UBC5C/UBCH5C, UBE2D4/HBUCE1/UBCH5D), yeast E2 ubiquitin-conjugating enzyme 4 (UBC4) and 5 (UBC5), as well as plant counterpart ubiquitin-conjugating enzyme E2 8-12 (UBC8/UBCAT4A, UBC9/UBCAT4B, UBC10-12) and 28-30 (UBC28-30). They are ubiquitin-conjugating enzymes (EC 2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. In vitro, UBE2D1-3 (EC 2.3.2.23 and EC 2.3.2.24) catalyze 'Lys-48'-linked polyubiquitination. UBE2D3 also catalyzes 'Lys-11'-linked polyubiquitination. In vitro, UBE2D4 can promote polyubiquitination using all 7 ubiquitin Lys residues but may prefer 'Lys-11' and 'Lys-48'-linked polyubiquitination. Saccharomyces cerevisiae UBC4-5 and Arabidopsis thaliana UBC8-11 mediates the selective degradation of short-lived and abnormal proteins. 143 matched cddid_all.tbl CDD cd23793 cd23793 467413 UBCc_UBE2E Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin conjugating enzyme E2 E1-E3 and related proteins. The E2E subfamily includes mammalian ubiquitin-conjugating enzyme E2 E1-3 (UBE2E1/UBCH6, UBE2E2/UBCH8, UBE2E3/UBCH9) and similar proteins. UBE2E, also known as (E3-independent) E2 ubiquitin-conjugating enzyme E, or E2 ubiquitin-conjugating enzyme E, accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. UBE2E1 (EC 2.3.2.23 and EC 2.3.2.24) catalyzes the covalent attachment of ISG15 to other proteins. It mediates the selective degradation of short-lived and abnormal proteins. In vitro, it also catalyzes 'Lys-48'-linked polyubiquitination. In vitro, both UBE2E2 (EC 2.3.2.23) and UBE2E3 (EC 2.3.2.23) catalyze 'Lys-11'- and 'Lys-48'-, as well as 'Lys-63'-linked polyubiquitination. UBE2E2 catalyzes the ISGylation of influenza A virus NS1 protein. UBE2E3 participates in the regulation of trans-epithelial sodium transport in renal cells. It may be involved in cell growth arrest. 141 matched cddid_all.tbl CDD cd23794 cd23794 467414 UBCc_UBE2F_UBE2M Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin conjugating enzymes E2 F, E2 M and related proteins. The E2F/E2M subfamily includes mammalian ubiquitin-conjugating enzymes E2 F (UBE2F/NCE2, EC 2.3.2.32) and E2 M (UBE2M/UBC12, EC 2.3.2.34), yeast NEDD8-conjugating enzyme UBC12 (EC 2.3.2.24), plant RUB1-conjugating enzyme 1-2 (RCE1/UBC12 and RCE2/UBC12L, EC 2.3.2.-), and similar proteins. UBE2F (also called EDD8-conjugating enzyme UBE2F, NEDD8 carrier protein UBE2F, NEDD8 protein ligase UBE2F, NEDD8-conjugating enzyme 2, or RING-type E3 NEDD8 transferase UBE2F) and UBE2M (also called NEDD8-conjugating enzyme UBC12, or NEDD8 carrier protein) accept the ubiquitin-like protein NEDD8 from the UBA3-NAE1 E1 complex and catalyzes its covalent attachment to other proteins. The RBX2-UBE2F complex neddylates specific target proteins, such as CUL5. The RBX1-UBE2M complex neddylates specific target proteins, such as CUL1, CUL2, CUL3 and CUL4. UBE2M is involved in cell proliferation. Saccharomyces cerevisiae UBC12 and Arabidopsis thaliana RCE1/RCE2 accept the ubiquitin-like protein NEDD8/RUB1 from the UBA3-ULA1 E1 complex and the ECR1-AXR1 E1 complex, respectively. 138 matched cddid_all.tbl CDD cd23795 cd23795 467415 UBCc_UBE2G1 Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-conjugating enzyme E2 G1 and related proteins. The subfamily includes mammalian ubiquitin-conjugating enzymes E2 G1 (UBE2G1/UBC7/E217K), fission yeast ubiquitin-conjugating enzyme E2 15 (UBC15), plant ubiquitin-conjugating enzymes E2 7 (UBC7), E2 13 (UBC13) and E2 14 (UBC14). They are ubiquitin-conjugating enzymes (EC 2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. In vitro, UBE2G1 catalyzes 'Lys-48'-, as well as 'Lys-63'-linked polyubiquitination. It may be involved in the degradation of muscle-specific proteins and may mediate polyubiquitination of CYP3A4. Schizosaccharomyces pombe UBC15 has a role in the formation of chromatin structures that influence the localization of transcriptional silencing factors. Arabidopsis thaliana UBC7, UBC13 and UBC14 are involved in the formation of multiubiquitin chains. They signal the protein for selective degradation. 155 matched cddid_all.tbl CDD cd23796 cd23796 467416 UBCc_UBE2G2 Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-conjugating enzyme E2 G2 and related proteins. The subfamily includes mammalian ubiquitin-conjugating enzymes E2 G2 (UBE2G2/UBC7), yeast E2 ubiquitin-conjugating enzyme 7 (UBC7) and similar proteins. They are ubiquitin-conjugating enzymes (EC 2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. In vitro, UBE2G2 catalyzes 'Lys-48'-linked polyubiquitination. It is involved in endoplasmic reticulum-associated degradation (ERAD) and is required for sterol-induced ubiquitination of 3-hydroxy-3-methylglutaryl coenzyme A reductase and its subsequent proteasomal degradation. UBC7, also called ubiquitin-conjugating enzyme E2-18 kDa, functions in the degradation of misfolded or regulated proteins localized in the endoplasmic reticulum (ER) lumen or membrane via the ubiquitin-proteasome system. 158 matched cddid_all.tbl CDD cd23797 cd23797 467417 UBCc_UBE2H Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-conjugating enzyme E2 H and related proteins. The E2H subfamily includes mammalian ubiquitin-conjugating enzymes E2 H (UBE2H), yeast E2 ubiquitin-conjugating enzyme 8 (UBC8/GID3), and plant ubiquitin-conjugating enzyme E2 4-6 (UBC4-6). They are ubiquitin-conjugating enzymes (EC 2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. UBE2H (also E3-independent, EC 2.3.2.24) transfers ubiquitin to MAEA, a core component of the CTLH E3 ubiquitin-protein ligase complex. In vitro, UBE2H catalyzes 'Lys-11'- and 'Lys-48'-linked polyubiquitination. It might also ubiquitinate histone H2A. Saccharomyces cerevisiae UBC8 is required for the adaptation to the presence of glucose in the growth medium; it mediates the degradation of enzymes involved in gluconeogenesis when cells are shifted to glucose-containing medium. It is also required for proteasome-dependent catabolite degradation of fructose-1,6-bisphosphatase (FBP1). 138 matched cddid_all.tbl CDD cd23798 cd23798 467418 UBCc_UBE2I Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-conjugating enzyme E2 I and related proteins. The E2I subfamily includes mammalian ubiquitin-conjugating enzymes E2 I (UBE2I/UBC9/UBCE9, EC 2.3.2.-), yeast ubiquitin-conjugating enzyme E2-18 kDa (UBC9, EC2.3.2.-), and plant SUMO-conjugating enzyme 1 (SCE1/AHUS5, EC2.3.2.-). UBE2I, also called SUMO-conjugating enzyme UBC9, RING-type E3 SUMO transferase UBC9, SUMO-protein ligase, ubiquitin carrier protein 9, ubiquitin carrier protein I, or ubiquitin-protein ligase I, accepts the ubiquitin-like proteins SUMO1, SUMO2, SUMO3, SUMO4 and SUMO1P1/SUMO5 from the UBLE1A-UBLE1B E1 complex and catalyzes their covalent attachment to other proteins with the help of an E3 ligase such as RANBP2, CBX4 and ZNF451. It can catalyze the formation of poly-SUMO chains. It is necessary for sumoylation of FOXL2 and KAT5 and essential for nuclear architecture and chromosome segregation. UBE2I also sumoylates p53/TP53 at 'Lys-386' and mediates sumoylation of ERCC6 which is essential for its transcription-coupled nucleotide excision repair activity. Saccharomyces cerevisiae UBC9, also called SUMO-conjugating enzyme UBC9, RING-type E3 SUMO transferase UBC9, ubiquitin carrier protein 9, ubiquitin-conjugating enzyme E2-18 kDa, acts as an E2 ubiquitin-like--protein ligase that mediates SUMO/Smt3 attachment to septins and PCNA. It may be involved in degradation of S- (CLB5) and M-phase cyclins (CLB2). Arabidopsis thaliana SCE1, also called SUMO-conjugating enzyme SCE1, protein EMBRYO DEFECTIVE 1637, or protein hus5 homolog, is a SUMO-conjugating enzyme that accepts the SUMO proteins from the E1 SUMO-activating heterodimer SAE1/SAE2 and catalyzes its covalent attachment to other proteins with the E3 SUMO ligases SIZ1 and MMS21. It associates with SIZ1 for sumoylation of the transcription factor GTE3. 152 matched cddid_all.tbl CDD cd23799 cd23799 467419 UBCc_UBE2J Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-conjugating enzyme E2 J1, J2 and related proteins. The E2J subfamily includes mammalian ubiquitin-conjugating enzymes E2 J1 (UBE2J1/HSPC153/HSPC205/NCUBE1) and J2 (UBE2J2/NCUBE1), yeast ubiquitin-conjugating enzyme E2 6 (UBC6/DOA2), and plant ubiquitin-conjugating enzyme E2 32-34 (UBC32-34). They are ubiquitin-conjugating enzymes (EC 2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. UBE2J1 and UBE2J2 are non-canonical ubiquitin-conjugating enzyme (NCUBE), which function in the selective degradation of misfolded membrane proteins from the endoplasmic reticulum (ERAD). Saccharomyces cerevisiae UBC6 functions in degradation of misfolded or regulated proteins localized in the endoplasmic reticulum (ER) lumen or membrane via the ubiquitin-proteasome system. It is a cognate E2 conjugating enzyme for the DOA10 ubiquitin ligase complex, which is part of the ERAD-C pathway responsible for the rapid degradation of membrane proteins with misfolded cytoplasmic domains. 134 matched cddid_all.tbl CDD cd23800 cd23800 467420 UBCc_UBE2K Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-conjugating enzyme E2 K and related proteins. The E2J subfamily includes mammalian ubiquitin-conjugating enzymes E2 K (UBE2K/HIP2/LIG), yeast ubiquitin-conjugating enzyme E2 1 (UBC1), and plant ubiquitin-conjugating enzyme E2 27 (UBC27). They are ubiquitin-conjugating enzymes (EC 2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. UBE2K is also called huntingtin-interacting protein 2 (HIP-2), ubiquitin-conjugating enzyme E2-25 kDa, or ubiquitin-conjugating enzyme E2(25K). In vitro, in the presence or absence of BRCA1-BARD1 E3 ubiquitin-protein ligase complex, UBE2K catalyzes the synthesis of 'Lys-48'-linked polyubiquitin chains. It does not transfer ubiquitin directly, but elongates monoubiquitinated substrate proteins. Saccharomyces cerevisiae UBC1, also called ubiquitin-conjugating enzyme E2-24 kDa, functions in the degradation of misfolded or regulated proteins localized in the endoplasmic reticulum (ER) lumen or membrane via the ubiquitin-proteasome system. It is a cognate E2 conjugating enzyme for the HRD1 ubiquitin ligase complex, which is part of the ERAD-L and ERAD-M pathways responsible for the rapid degradation of soluble lumenal and membrane proteins with misfolded lumenal domains (ERAD-L), or ER-membrane proteins with misfolded transmembrane domains (ERAD-M). 145 matched cddid_all.tbl CDD cd23801 cd23801 467421 UBCc_UBE2L3 Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-conjugating enzyme E2 L3, L5, L6 and related proteins. The E2L3-like subfamily includes mammalian ubiquitin-conjugating enzymes E2 L3 (UBE2L3/UBCH7/UBCE7), L5 (UBE2L5), L6 (UBE2L6/UBCH8), and similar proteins. They are ubiquitin-conjugating enzymes (EC 2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. UBE2L3 specifically acts with HECT-type and RBR family E3 ubiquitin-protein ligases. It does not function with most RING-containing E3 ubiquitin-protein ligases because it lacks intrinsic E3-independent reactivity with lysine: in contrast, it has activity with the RBR family E3 enzymes, such as PRKN and ARIH1, that function like RING-HECT hybrids. In vitro, UBE2L3 catalyzes 'Lys-11'-linked polyubiquitination. It is involved in the selective degradation of short-lived and abnormal proteins. In addition to ubiquitin, UBE2L6 also catalyzes the covalent attachment of ISG15 to other proteins. It functions in the E6/E6-AP-induced ubiquitination of p53/TP53. It promotes ubiquitination and subsequent proteasomal degradation of FLT3. 147 matched cddid_all.tbl CDD cd23802 cd23802 467422 UBCc_UBE2Q Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-conjugating enzyme E2 Q1, Q2, and related proteins. The E2Q subfamily includes mammalian ubiquitin-conjugating enzymes E2 Q1 (UBE2Q1/NICE5/UBE2Q), Q2 (UBE2Q2), and similar proteins. They are ubiquitin-conjugating (EC 2.3.2.23) enzymes that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. UBE2Q1 may be involved in hormonal homeostasis in females. It is involved in regulation of B4GALT1 cell surface expression, B4GALT1-mediated cell adhesion to laminin and embryoid body formation. In vitro, UBE2Q2 catalyzes 'Lys-48'-linked polyubiquitination. This subfamily also includes ubiquitin-conjugating enzyme E2Q-like protein 1 (UBE2QL1), which is a probable E2 ubiquitin-protein ligase that may facilitate the monoubiquitination and degradation of MTOR and CCNE1 through interaction with FBXW7. 157 matched cddid_all.tbl CDD cd23803 cd23803 467423 UBCc_UBE2R Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-conjugating enzyme E2 R1-R2 and related proteins. The E2R subfamily includes mammalian ubiquitin-conjugating enzymes E2 R1 (UBE2R1/UBCH3/CDC34, EC 2.3.2.23 and EC 2.3.2.24), and E2 R2 (UBE2R2/UBC3B/CDC34B, EC 2.3.2.23), which accept ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro, UBE2R1 catalyzes 'Lys-48'-linked polyubiquitination. It also involved in the degradation of beta-catenin. In vitro, UBE2R2 catalyzes monoubiquitination and 'Lys-48'-linked polyubiquitination. It may be involved in the degradation of katenin. 170 matched cddid_all.tbl CDD cd23804 cd23804 467424 UBCc_UBE2S Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin conjugating enzyme E2 S and related domains. The E2S subfamily includes mammalian ubiquitin-conjugating enzymes E2 S (UBE2S/E2EPF), plant ubiquitin-conjugating enzyme E2 22 (UBC22), and similar proteins. They are ubiquitin-conjugating enzymes (EC2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. UBE2S catalyzes 'Lys-11'-linked polyubiquitination. It acts as an essential factor of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated ubiquitin ligase that controls progression through mitosis. UBE2S acts by specifically elongating 'Lys-11'-linked polyubiquitin chains initiated by the E2 enzyme UBE2C/UBCH10 on APC/C substrates, enhancing the degradation of APC/C substrates by the proteasome and promoting mitotic exit. It also acts by elongating ubiquitin chains initiated by the E2 enzyme UBE2D1/UBCH5 in vitro; it is however unclear whether UBE2D1/UBCH5 acts as an E2 enzyme for the APC/C in vivo. UBE2S is also involved in ubiquitination and subsequent degradation of VHL, resulting in an accumulation of HIF1A. In vitro, it can promote polyubiquitination using all 7 ubiquitin Lys residues, except 'Lys-48'-linked polyubiquitination. 146 matched cddid_all.tbl CDD cd23805 cd23805 467425 UBCc_UBE2T Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin conjugating enzyme E2 T and related enzymes. The E2T subfamily includes mammalian ubiquitin-conjugating enzymes E2 T (UBE2T/HSPC150/PIG50), plant ubiquitin-conjugating enzyme E2 37 (UBC37), and similar proteins. They are ubiquitin-conjugating enzymes (EC 2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. UBE2T, also called cell proliferation-inducing gene 50 protein, catalyzes monoubiquitination. It is involved in mitomycin-C (MMC)-induced DNA repair. It acts as a specific E2 ubiquitin-conjugating enzyme for the Fanconi anemia complex by associating with E3 ubiquitin-protein ligase FANCL and catalyzing monoubiquitination of FANCD2, a key step in the DNA damage pathway. UBE2T also mediates monoubiquitination of FANCL and FANCI. It may contribute to ubiquitination and degradation of BRCA1. In vitro, UBE2T can promote polyubiquitination using all 7 ubiquitin Lys residues, but may prefer 'Lys-11'-, 'Lys-27'-, 'Lys-48'- and 'Lys-63'-linked polyubiquitination. 146 matched cddid_all.tbl CDD cd23806 cd23806 467426 UBCc_UBE2U Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-conjugating enzyme E2 U and related proteins. The E2U subfamily includes mammalian ubiquitin-conjugating enzymes E2 U (UBE2U/, EC 2.3.2.23) and similar proteins. They are ubiquitin-conjugating enzymes that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. 141 matched cddid_all.tbl CDD cd23807 cd23807 467427 UEV_UBE2V ubiquitin E2 variant (UEV) domain of ubiquitin-conjugating enzyme E2 variant 1, 2 and related proteins. The E2V subfamily includes mammalian ubiquitin-conjugating enzyme E2 variant 1 (UBE2V1/CROC1/UBE2V/UEV1) and variant 2 (UBE2V2/MMS2/UEV2), yeast ubiquitin-conjugating enzyme variant MMS2, plant ubiquitin-conjugating enzyme E2 variant 1A (UEV1A/MMZ1) and variant 1B (UEV1B/MMZ2), and similar proteins. They have no ubiquitin ligase activity on their own. UBE2V1 (also called UEV-1, CROC-1, or TRAF6-regulated IKK activator 1 beta Uev1A) and UBE2V2 (also called DDVit 1, enterocyte differentiation-associated factor 1 (EDAF-1), enterocyte differentiation-promoting factor 1 (EDPF-1), MMS2 homolog, or vitamin D3-inducible protein) form heterodimers with UBE2N, respectively. Saccharomyces cerevisiae UEV MMS2 has a role in the DNA error-free postreplication repair (PRR) pathway. It forms a heterodimer with UBC13. Arabidopsis thaliana UEV1A and UEV1A form heterodimers with UBC35 or UBC36. The heterodimers possess ubiquitin-conjugating enzyme (EC 2.3.2.23) activity, catalyzing the synthesis of non-canonical poly-ubiquitin chains that are linked through 'Lys-63'. This type of poly-ubiquitination does not lead to protein degradation by the proteasome. Members of this subfamily may mediate transcriptional activation of target genes and plays a role in the control of progress through the cell cycle and differentiation. UEVs are homologous to E2 ubiquitin ligases but lack the conserved cysteine residue required for catalytic activity. 134 matched cddid_all.tbl CDD cd23808 cd23808 467428 UBCc_UBE2W Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin conjugating enzyme E2 W and related enzymes. The E2W subfamily includes mammalian ubiquitin-conjugating enzymes E2 W (UBE2W/UBC16), plant ubiquitin-conjugating enzyme E2 15-18 (UBC15-18), and similar proteins. They are ubiquitin-conjugating enzymes (EC 2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. UBE2W, also called FLJ11011, E2 ubiquitin-conjugating enzyme W, N-terminal E2 ubiquitin-conjugating enzyme (EC 2.3.2.25), N-terminus-conjugating E2, ubiquitin carrier protein W, ubiquitin-conjugating enzyme 16 (UBC-16), or ubiquitin-protein ligase W, specifically monoubiquitinates the N-terminus of various substrates, including ATXN3, MAPT/TAU, POLR2H/RPB8 and STUB1/CHIP, by recognizing backbone atoms of disordered N-termini. In vitro, UBE2W catalyzes 'Lys-11'-linked polyubiquitination. UBE2W is an important protein for early postnatal survival and for the normal functioning of multiple organ systems. 119 matched cddid_all.tbl CDD cd23809 cd23809 467429 UBCc_UBE2Z Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-conjugating enzyme E2 Z and related proteins. The E2Z subfamily includes mammalian ubiquitin-conjugating enzymes E2 Z (UBE2Z/HOYS7) and similar proteins. They are ubiquitin-conjugating enzymes (EC 2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. UBE2Z, also called Uba6-specific E2 conjugating enzyme 1 (Use1), acts as a ubiquitin-conjugating enzyme that accept ubiquitin from the E1 complex and catalyzes the covalent attachment to other proteins. It is a specific substrate for UBA6, not charged with ubiquitin by UBE1. It may be involved in apoptosis regulation. 151 matched cddid_all.tbl CDD cd23810 cd23810 467430 UBCc_BIRC6 Ubiquitin-conjugating enzyme E2, catalytic (UBCc)-like domain of baculoviral IAP repeat-containing protein 6 (BIRC6) and related proteins. BIRC6, also BIR repeat-containing ubiquitin-conjugating enzyme (BRUCE), RING-type E3 ubiquitin transferase (EC 2.3.2.27) BIRC6, or ubiquitin-conjugating BIR domain enzyme apollon (APOLLON), is an anti-apoptotic protein which can regulate cell death by controlling caspases and by acting as an E3 ubiquitin-protein ligase. It has an unusual ubiquitin conjugation system in that it could combine in a single polypeptide, ubiquitin conjugating (E2) with ubiquitin ligase (E3) activity, forming a chimeric E2/E3 ubiquitin ligase. Its targets include CASP9 and DIABLO/SMAC. BIRC6 acts as an inhibitor of CASP3, CASP7, and CASP9. BIRC6 is an important regulator for the final stages of cytokinesis. It is crucial for normal vesicle targeting to the site of abscission, but also for the integrity of the midbody and the midbody ring, and its striking ubiquitin modification. 205 matched cddid_all.tbl CDD cd23811 cd23811 467431 UBCc_ScCDC34-like Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of Saccharomyces cerevisiae CDC34 and related proteins. Saccharomyces cerevisiae CDC34 (EC 2.3.2.23), also called ubiquitin-conjugating enzyme E2-34 kDa, cell division control protein 34, E2 ubiquitin-conjugating enzyme 3 (UBC3), DNA6, or ubiquitin ligase complex SCF subunit CDC34, catalyzes the covalent attachment of ubiquitin to other proteins. In vitro, it may ubiquitinate histone H2A. CDC34 mediates the initiation of DNA replication (transition of G1 to S phase in cell cycle). It is the catalytic subunit of an SCF ubiquitin-protein ligase complex (together with Skp1p, Rbx1p, CDC53, and an F-box protein) that regulates cell cycle progression by targeting key substrates for degradation. Moreover, CDC34 is involved in the regulation of methionine biosynthesis genes and in the degradation of CDC6 together with CDC4 and CDC53. 170 matched cddid_all.tbl CDD cd23812 cd23812 467432 UBCc_ScPEX4-like Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of Saccharomyces cerevisiae Peroxin-4 (PEX4) protein and related proteins. Saccharomyces cerevisiae PEX4 (EC 2.3.2.23), also called ubiquitin-conjugating enzyme E2-21 kDa, UBC10, or PAS2, acts as a ubiquitin-conjugating enzyme that catalyzes the covalent attachment of ubiquitin to other proteins. It is essential for peroxisome biogenesis and is required for UBC4-independent ubiquitination of PEX5. This subfamily also includes Arabidopsis thaliana PEX4 (also known as UBC21, EC 2.3.2.23) that is required for peroxisome biogenesis. It is necessary for the developmental elimination of obsolete peroxisome matrix proteins. It may be involved in the ubiquitination of PEX5, targeting it for recycling. 145 matched cddid_all.tbl CDD cd23813 cd23813 467433 UBCc_UBE2N Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-conjugating enzyme E2 N and related proteins. The E2N subfamily includes mammalian ubiquitin-conjugating enzymes E2 N (UBE2N/UBCH13/UBC13/BLU), yeast ubiquitin-conjugating enzyme E2 13 (UBC13), and plant ubiquitin-conjugating enzyme E2 35-36 (UBC35/UBC13A/UBG13A, UBC36/UBC13B/UBG13B), which function as ubiquitin-conjugating enzymes (EC 2.3.2.23). UBE2N, also called Bendless-like ubiquitin-conjugating enzyme, forms heterodimers with UBE2V1 and UBE2V2, respectively. The UBE2V1/UBE2N and UBE2V2/UBE2N heterodimers catalyze the synthesis of non-canonical 'Lys-63'-linked polyubiquitin chains. This type of polyubiquitination does not lead to protein degradation by the proteasome. UBE2N also plays a role in the control of progress through the cell cycle and differentiation, as well as in the error-free DNA repair pathway, and contributes to the survival of cells after DNA damage. Saccharomyces cerevisiae UBC13 has a role in the DNA error-free post-replication repair (PRR) pathway. The UBC13/MMS2 heterodimer catalyzes the synthesis of non-canonical poly-ubiquitin chains that are linked through 'Lys-63'. Arabidopsis thaliana UBC35 and UBC36 catalyze the synthesis of non-canonical poly-ubiquitin chains that are linked through 'Lys-63'. They mediate transcriptional activation of target genes. They are required for post-replication repair of UV-damaged DNA and for adapting root developmental programs to suboptimal availability of iron. 144 matched cddid_all.tbl CDD cd23814 cd23814 467434 UEV_AKTIP ubiquitin E2 variant (UEV) domain of AKT-interacting protein and related proteins. AKTIP, also called Ft1, or fused toes protein homolog, is a component of the FTS/Hook/FHIP complex (FHF complex), which may function to promote vesicle trafficking and/or fusion via the homotypic vesicular protein sorting complex (the HOPS complex). AKTIP regulates apoptosis by enhancing phosphorylation and activation of AKT1. It increases release of TNFSF6 via the AKT1/GSK3B/NFATC1 signaling cascade. AKTIP contains a UEV domain that is homologous to E2 ubiquitin ligases but lacks the conserved cysteine residue required for catalytic activity. 112 matched cddid_all.tbl CDD cd23815 cd23815 467435 UBCc_SpUBC14-like Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of Schizosaccharomyces pombe UBC14 and related proteins. Schizosaccharomyces pombe UBC14 (EC 2.3.2.23), also called ubiquitin-conjugating enzyme E2 14, E2 ubiquitin-conjugating enzyme 14, ubiquitin carrier protein 14, or ubiquitin-protein ligase 14, acts as a ubiquitin-conjugating enzyme that catalyzes the covalent attachment of ubiquitin to other proteins. It mediates the selective degradation of short-lived and abnormal proteins. 143 matched cddid_all.tbl CDD cd23816 cd23816 467652 RWD_RWDD1 RWD domain of RWD domain-containing protein 1 (RWDD1) and related proteins. RWDD1, also called DRG family-regulatory protein 2 (DFRP2), or PTD013, interacts with DRG2 and protects DRG2 from proteolytic degradation. It is an androgen receptor-interacting protein that functions as a coactivator of androgen-dependent transcription. 118 matched cddid_all.tbl CDD cd23817 cd23817 467653 RWD-RWDD4 RWD domain of RWD domain-containing protein 4 (RWDD4) and related proteins. RWDD4, also called protein FAM28A, is a target of the tumor suppressor MicroRNA (MiR)-506 in bladder cancer cells. Downregulation of RWDD4 suppresses bladder cancer cell proliferation, migration and invasion. RWDD4 has also been identified as a modifier of metastasis in human prostate cancer. 104 matched cddid_all.tbl CDD cd23818 cd23818 467654 RWD_RNF25 RWD domain of RING finger protein 25 (RNF25) and related proteins. RNF25 (EC 2.3.2.27), also known as AO7, is a putative E3 ubiquitin-protein ligase that was initially identified as an interacting protein of the E2 ubiquitin-conjugating enzyme, Ubc5B. It is ubiquitously expressed in various tissues and is predominantly localized in the nucleus. RNF25 activates nuclear factor (NF)-kappaB-dependent gene expression upon stimulation with interleukin-1 beta (IL-1beta), or tumor necrosis factor (TNF), or overexpression of NF-kappaB-inducing kinase. It interacts with the p65 transactivation domain (TAD) and modulates its transcriptional activity. 109 matched cddid_all.tbl CDD cd23819 cd23819 467655 RWD_RWDD3 RWD domain of RWD domain-containing protein 3 (RWDD3) and related proteins. RWDD3, also called RWD domain-containing sumoylation enhancer (RSUME), acts as an enhancer of SUMO conjugation and has no effect on ubiquitination. It increases protein sumoylation (a dynamic ubiquitin-like post translational modification) of several proteins including HIF1alpha and I-kappa-B, through direct interaction with UBC9. Its RWD domain is required for the sumoylation enhancement activity. 106 matched cddid_all.tbl CDD cd23820 cd23820 467656 RWD_RNF14 RWD domain of RING finger protein 14 (RNF14) and related proteins. RNF14, also called androgen receptor (AR)-associated protein 54 (ARA54), HFB30, or Triad2 protein, is an RBR-type E3 ubiquitin-protein ligase (EC 2.3.2.31) that is highly expressed in the testis and interacts with class III E2s (UBE2E2, UbcH6, and UBE2E3). Its differential localization may play an important role in testicular development and spermatogenesis in humans. RNF14 functions as a transcriptional regulator of mitochondrial and immune function in muscles. It is a ligand-dependent AR co-activator that enhances AR-dependent transcriptional activation. It also may participate in enhancing cell cycle progression and cell proliferation via induction of cyclin D1. Moreover, RNF14 is crucial for colon cancer cell survival. It acts as a new enhancer of Wnt-dependent transcriptional outputs that act at the level of the T-cell factor/lymphoid enhancer factor (TCF/LEF)-beta-catenin complex. 125 matched cddid_all.tbl CDD cd23821 cd23821 467657 RWD_IMPACT RWD domain of protein IMPACT and related proteins. IMPACT, also imprinted and ancient gene protein homolog, acts as a translational regulator that ensures constant high levels of translation upon a variety of stress conditions, such as amino acid starvation, UV-C irradiation, proteasome inhibitor treatment, and glucose deprivation. It plays a role as a negative regulator of EIF2AK4/GCN2 kinase activity. It impairs GCN1-mediated EIF2AK4/GCN2 activation, and hence EIF2AK4/GCN2-mediated eIF-2-alpha phosphorylation and subsequent down-regulation of protein synthesis. IMPACT may be required to regulate translation in specific neuronal cells under amino acid starvation conditions by preventing GCN2 activation and therefore ATF4 synthesis. Through its inhibitory action on EIF2AK4/GCN2, IMPACT plays a role in differentiation of neuronal cells by stimulating neurite outgrowth. 101 matched cddid_all.tbl CDD cd23822 cd23822 467658 RWD_ScYIH1-like RWD domain of Saccharomyces cerevisiae protein YIH1 and related proteins. YIH1, also called protein IMPACT homolog, is an actin-binding protein that acts as a translational regulator which ensures constant high levels of translation under amino acid starvation. It plays a role as a negative regulator of GCN2 kinase activity. It impairs GCN1-mediated GCN2 activation, and hence GCN2-mediated eIF-2-alpha phosphorylation in amino acid-starved cells and subsequent down-regulation of protein synthesis. In normal conditions, it resides in an actin complex and has no activity. 97 matched cddid_all.tbl CDD cd23823 cd23823 467659 RWD_GCN2 RWD domain of eIF-2-alpha kinase GCN2 and related proteins. GCN2 (EC 2.7.11.1), also called eukaryotic translation initiation factor 2-alpha kinase 4 (EIF2AK4), acts as a metabolic-stress sensing protein kinase that phosphorylates the alpha subunit of eukaryotic translation initiation factor 2 (EIF2S1/eIF-2-alpha) in response to low amino acid availability. It also plays a role in modulating the adaptive immune response to yellow fever virus infection and promotes dendritic cells to initiate autophagy and antigene presentation to both CD4(+) and CD8(+) T-cells under amino acid starvation. 117 matched cddid_all.tbl CDD cd23824 cd23824 467660 RWD_ScGIR2-like RWD domain of Saccharomyces cerevisiae genetically interacts with ribosomal genes protein 2 (GIR2) and related proteins. GIR2, also called DRG family-regulatory protein 2, acts as a negative regulator of GCN2 kinase activity by interacting with GCN1 and disrupting the GCN1-GCN2 interaction in amino acid-starved cells. It also interacts with RBG1. The RBG1-GIR2 complex is responsible for efficient cell growth under conditions of amino acid depletion and binds the activator GCN1. Critical mutations in the RWD domain of GIR2 abolishes its interaction with GCN1. GIR2 may interact with ribosomes through GCN1, which binds directly to ribosomes. 159 matched cddid_all.tbl CDD cd23825 cd23825 467661 RWD_DHX57 RWD domain of DEAH box protein 57 (DHX57) and related proteins. DHX57 (EC 3.6.4.13) is a putative ATP-dependent RNA helicase. A genome-wide association study (GWAS) of cerebellar epigenetic age acceleration identified significant SNPs (single nucleotide polymorphisms) in a loci 2p22.1 inside the DHX57 gene, suggesting that variants in DHX57 are associated with epigenetic age in the cerebellum. 115 matched cddid_all.tbl CDD cd23826 cd23826 467436 UEV_Morgue-like ubiquitin E2 variant (UEV) domain of Drosophila melanogaster Morgue and related proteins. Morgue is an F-box/ubiquitin conjugase domain protein important for grim-reaper mediated apoptosis. It contains both an F-box and a UEV domain that is homologous to E2 ubiquitin ligases but lacks the conserved cysteine residue required for catalytic activity. 147 matched cddid_all.tbl CDD cd23827 cd23827 467662 RWD_YLR419W-like RWD domain of Saccharomyces cerevisiae putative ATP-dependent RNA helicase YLR419W and related proteins. YLR419W (EC 3.6.4.13) may act as an ATP-binding RNA helicase. The RWD domain may mediate protein-protein interactions. 104 matched cddid_all.tbl CDD cd23828 cd23828 467437 UBCc_TcUBE-like Ubiquitin-conjugating enzyme E2, putative catalytic (UBCc) domain of Trypanosoma cruzi putative ubiquitin-conjugating enzyme E2 and related proteins. This subfamily includes uncharacterized Trypanosoma cruzi putative ubiquitin-conjugating enzyme E2 and similar proteins. They may function as ubiquitin-conjugating enzymes (EC 2.3.2.23) that accept ubiquitin from the E1 complex and catalyze the covalent attachment to other proteins. 121 matched cddid_all.tbl CDD cd23829 cd23829 467663 RWD_RWDD2 RWD domain of RWD domain-containing protein 2A (RWDD2A), 2B (RWDD2B) and related proteins. This subfamily includes RWDD2A, previously known as RWD domain-containing 2 (RWDD2) and RWDD2B, previously known in humans as chromosome 21 open reading frame (C21orf6). C21orf6 appears to be involved in monosomy 21 phenotype. The RWD domain may mediate protein-protein interactions. 129 matched cddid_all.tbl CDD cd23830 cd23830 467664 DRWD-N_Mcm21 N-terminal double-RWD domain of minichromosome maintenance protein 21 (MCM21) and related proteins. MCM21, also called inner kinetochore subunit MCM21, CENP-O homolog, chromosome transmission fidelity protein 5 (CTF5), or constitutive centromere-associated network protein MCM21, is a component of the kinetochore, a multiprotein complex that assembles on centromeric DNA and attaches chromosomes to spindle microtubules, mediating chromosome segregation and sister chromatid segregation during meiosis and mitosis. MCM21 contains two RWD domains, also known as a double-RWD domain, DRWD, which is involved in interactions with other kinetochore proteins. The model corresponds to the N-terminal double-RWD domain (DRWD-N). 107 matched cddid_all.tbl CDD cd23831 cd23831 467665 DRWD-N_FANCL N-terminal double-RWD domain of Fanconi anemia group L protein (FANCL) and related proteins. FANCL, also called E3 ubiquitin-protein ligase FANCL, Fanconi anemia-associated polypeptide of 43 kDa (FAAP43), or RING-type E3 ubiquitin transferase FANCL, is an E3 ubiquitin-protein ligase component of the Fanconi anemia (FA) core complex which functions in the repair of interstrand crosslinks (ICLs), a toxic form of DNA damage. FANCL, works in conjunction with the E2 conjugating enzyme UBE2T (FANCT) to add a single ubiquitin to specific lysine residues on FANCD2 and FANCI. The mono-ubiquitinated FANCI-FANCD2 complex is thought to recruit downstream DNA-repair proteins for ICL processing. FANCL is composed of an N-terminal E2-like fold (ELF) domain, a novel double-RWD (DRWD) domain, and a C-terminal RING domain predicted to facilitate E2 binding. The DRWD domain is responsible for substrate binding. The model corresponds to the N-terminal DRWD domain (DRWD-N). 75 matched cddid_all.tbl CDD cd23832 cd23832 467666 DRWD-C_FANCL C-terminal double-RWD domain of Fanconi anemia group L protein (FANCL) and related proteins. FANCL, also called E3 ubiquitin-protein ligase FANCL, Fanconi anemia-associated polypeptide of 43 kDa (FAAP43), or RING-type E3 ubiquitin transferase FANCL, is an E3 ubiquitin-protein ligase component of the Fanconi anemia (FA) core complex which functions in the repair of interstrand crosslinks (ICLs), a toxic form of DNA damage. FANCL, works in conjunction with the E2 conjugating enzyme UBE2T (FANCT) to add a single ubiquitin to specific lysine residues on FANCD2 and FANCI. The mono-ubiquitinated FANCI-FANCD2 complex is thought to recruit downstream DNA-repair proteins for ICL processing. FANCL is composed of an N-terminal E2-like fold (ELF) domain, a novel double-RWD (DRWD) domain, and a C-terminal RING domain predicted to facilitate E2 binding. The DRWD domain is responsible for substrate binding. The model corresponds to the C-terminal DRWD domain (DRWD-C). 89 matched cddid_all.tbl CDD cd23833 cd23833 467438 UBCc_ApmR795-like Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of Acanthamoeba polyphaga mimivirus bifunctional E2/E3 enzyme R795 and related proteins. R795 (EC 2.3.2.23/EC 2.3.2.27) is a bifunctional enzyme which acts as an E2 ubiquitin-conjugating enzyme that catalyzes the covalent attachment of ubiquitin to other proteins. It also acts as a RING-type E3 ubiquitin-protein transferase. 117 matched cddid_all.tbl CDD cd23834 cd23834 467667 DRWD-C_Mcm21 C-terminal double-RWD domain of minichromosome maintenance protein 21 (MCM21) and related proteins. MCM21, also called inner kinetochore subunit MCM21, CENP-O homolog, chromosome transmission fidelity protein 5 (CTF5), or constitutive centromere-associated network protein MCM21, is a component of the kinetochore, a multiprotein complex that assembles on centromeric DNA and attaches chromosomes to spindle microtubules, mediating chromosome segregation and sister chromatid segregation during meiosis and mitosis. MCM21 contains two RWD domains, also known as a double-RWD domain, DRWD, which is involved in interactions with other kinetochore proteins. The model corresponds to the C-terminal double-RWD domain (DRWD-C). 88 matched cddid_all.tbl CDD cd23835 cd23835 467668 DRWD-N_CENP-O N-terminal double-RWD domain of centromere protein O (CENP-O) and related proteins. CENP-O, also called interphase centromere complex protein 36 (ICEN36), or MCM21R, is a component of the CENPA-CAD (nucleosome distal) complex, a complex recruited to centromeres which is involved in assembly of kinetochore proteins, mitotic progression, and chromosome segregation. It may be involved in incorporation of newly synthesized CENPA into centromeres via its interaction with the CENPA-NAC complex. It modulates the kinetochore-bound levels of NDC80 complex. CENP-O contains two RWD domains, also known as a double-RWD domain, DRWD, which is involved in interactions with other kinetochore proteins. The model corresponds to the N-terminal double-RWD domain (DRWD-N). 86 matched cddid_all.tbl CDD cd23836 cd23836 467669 DRWD-C_CENP-O C-terminal double-RWD domain of centromere protein O (CENP-O) and related proteins. CENP-O, also called interphase centromere complex protein 36 (ICEN36), or MCM21R, is a component of the CENPA-CAD (nucleosome distal) complex, a complex recruited to centromeres which is involved in assembly of kinetochore proteins, mitotic progression, and chromosome segregation. It may be involved in incorporation of newly synthesized CENPA into centromeres via its interaction with the CENPA-NAC complex. It modulates the kinetochore-bound levels of NDC80 complex. CENP-O contains two RWD domains, also known as a double-RWD domain, DRWD, which is involved in interactions with other kinetochore proteins. The model corresponds to the C-terminal double-RWD domain (DRWD-C). 98 matched cddid_all.tbl CDD cd23837 cd23837 467439 UBCc_UBE2O Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain of ubiquitin-conjugating enzyme E2 O and related proteins. The E2O subfamily includes mammalian ubiquitin-conjugating enzymes E2 O (UBE2O, EC 2.3.2.24), plant ubiquitin-conjugating enzyme E2 23-26 (UBC23-26, EC2.3.2.23) and E2 38-39 (UBC38-39, EC2.3.2.23), and similar proteins. UBE2O is an E2/E3 hybrid ubiquitin-protein ligase that displays both E2 and E3 ligase activities and mediates monoubiquitination of target proteins. Arabidopsis thaliana UBC proteins accept the ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. UBC24, also called PHO2, mediates PHO1 degradation through multivesicular body-mediated vacuolar proteolysis in response to inorganic phosphate (Pi) availability. It negatively regulates the protein abundance of PHF1 and PHT1s under Pi-sufficient conditions by facilitating the degradation of PHT1 proteins at the endomembrane. 198 matched cddid_all.tbl CDD cd23838 cd23838 467670 DRWD-N_ScCTF19 N-terminal double-RWD domain of Saccharomyces cerevisiae chromosome transmission fidelity 19 (CTF19) and related proteins. CTF19, also called inner kinetochore subunit CTF19, CENP-P homolog, chromosome transmission fidelity protein 19, constitutive centromere-associated network protein CTF19, or minichromosome maintenance protein 18, is a component of the kinetochore, a multiprotein complex that assembles on centromeric DNA and attaches chromosomes to spindle microtubules, mediating chromosome segregation and sister chromatid segregation during meiosis and mitosis. ScCTF19 contains two RWD domains, also known as a double-RWD domain, DRWD, which is involved in interactions with other kinetochore proteins. The model corresponds to the N-terminal double-RWD domain (DRWD-N). 100 matched cddid_all.tbl CDD cd23839 cd23839 467671 DRWD-C_ScCTF19 C-terminal double-RWD domain of Saccharomyces cerevisiae chromosome transmission fidelity 19 (CTF19) and related proteins. CTF19, also called inner kinetochore subunit CTF19, CENP-P homolog, chromosome transmission fidelity protein 19, constitutive centromere-associated network protein CTF19, or minichromosome maintenance protein 18, is a component of the kinetochore, a multiprotein complex that assembles on centromeric DNA and attaches chromosomes to spindle microtubules, mediating chromosome segregation and sister chromatid segregation during meiosis and mitosis. ScCTF19 contains two RWD domains, also known as a double-RWD domain, DRWD, which is involved in interactions with other kinetochore proteins. The model corresponds to the C-terminal double-RWD domain (DRWD-C). 104 matched cddid_all.tbl CDD cd23933 cd23933 467682 ALDH_C C-terminal catalytic domain of acetaldehyde dehydrogenase (ALDH) and similar proteins. Acetaldehyde dehydrogenase (ALDH; EC 1.2.1.10), also called acetaldehyde dehydrogenase (acetylating), acylating acetaldehyde dehydrogenase, or aldehyde dehydrogenase (acylating), catalyzes the conversion of acetaldehyde to acetyl-CoA, using NAD(+) and coenzyme A. It can also act on propanal and butanal to form propanoyl-CoA and butanoyl-CoA, respectively. ALDH is the final enzyme in the meta-cleavage pathway for the degradation of aromatic compounds such as phenols, cresols and catechols. NADP(+) can replace NAD(+) but the rate of reaction is much slower. ALDH contains two domains, an N-terminal Rossmann fold NAD+-binding domain and a C-terminal dimerization domain, which mediates dimerisation of the protein. The C-terminal dimerization domain is homologs to C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like catalytic domain. ALDHs are members of the GAPDH superfamily of proteins. 135 matched cddid_all.tbl CDD cd23934 cd23934 467683 AGPR_1_C C-terminal catalytic domain of N-acetyl-gamma-glutamyl-phosphate reductase (AGPR), type 1 and similar proteins. N-acetyl-gamma-glutamyl-phosphate reductase (AGPR; EC 1.2.1.38), also called N-acetyl-glutamate semialdehyde dehydrogenase, or NAGSA dehydrogenase, catalyzes the NADPH-dependent reduction of N-acetyl-gamma-glutamyl-phosphate phosphate, the third step of arginine biosynthesis. N-acetyl-gamma-glutamyl-phosphate phosphate, the product of the second step catalyzed by acetylglutamate kinase, undergoes reductive dephosphorylation to give N-acetylglutamic semialdehyde, which is converted to ornithine by acetylornithine aminotransferase and acetylornithine deacetylase. AGPR proteins contain an N-terminal Rossmann fold NAD(P)H-binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like catalytic domain and are members of the GAPDH superfamily of proteins. NADP(+) binds in a cleft between these domains and contacts both. There are two related families of N-acetyl-gamma-glutamyl-phosphate reductase, which differ by phylogeny, similarity clustering, and gap architecture in a multiple sequence alignment. The model corresponds to type 1 AGPR family. Bacterial members of this family tend to be found within Arg biosynthesis operons. The type 1 AGPR family also includes LysY (LysW-L-2-aminoadipate/LysW-L-glutamate phosphate reductase), which is involved in both, the arginine and lysine, biosynthetic pathways. 171 matched cddid_all.tbl CDD cd23935 cd23935 467684 AGPR_2_C C-terminal catalytic domain of N-acetyl-gamma-glutamyl-phosphate reductase (AGPR), type 2 and similar proteins. N-acetyl-gamma-glutamyl-phosphate reductase (AGPR; EC 1.2.1.38), also called N-acetyl-glutamate semialdehyde dehydrogenase, or NAGSA dehydrogenase, catalyzes the NADPH-dependent reduction of N-acetyl-gamma-glutamyl-phosphate phosphate, the third step of arginine biosynthesis. N-acetyl-gamma-glutamyl-phosphate phosphate, the product of the second step catalyzed by acetylglutamate kinase, undergoes reductive dephosphorylation to give N-acetylglutamic semialdehyde, which is converted to ornithine by acetylornithine aminotransferase and acetylornithine deacetylase. AGPR proteins contain an N-terminal Rossmann fold NAD(P)H-binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like catalytic domain and are members of the GAPDH superfamily of proteins. NADP(+) binds in a cleft between these domains and contacts both. There are two related families of N-acetyl-gamma-glutamyl-phosphate reductase, which differ by phylogeny, similarity clustering, and gap architecture in a multiple sequence alignment. The model corresponds to type 2 AGPR family. 178 matched cddid_all.tbl CDD cd23936 cd23936 467685 AGPR_C_ARG5_6_like C-terminal catalytic domain (AGPR region) of fungal bifunctional mitochondrial enzyme (gene ARG5,6, arg11 or arg-6) and similar proteins. The family includes bifunctional mitochondrial enzyme (gene ARG5,6, arg11 or arg-6) from fungi, which contains a N-terminal acetylglutamate kinase ( EC 2.7.2.8, also known as N-acetyl-L-glutamate 5-phosphotransferase/NAG kinase/AGK) domain and a C-terminal N-acetyl-gamma-glutamyl-phosphate reductase (AGPR; EC 1.2.1.38, also known as AGPR/N-acetyl-glutamate semialdehyde dehydrogenase/NAGSA dehydrogenase) domain. This model corresponds to the AGPR C-terminal catalytic domain. AGPR catalyzes the third step in the biosynthesis of arginine from glutamate, the NADP-dependent reduction of N-acetyl-5-glutamyl phosphate into N-acetylglutamate 5-semialdehyde. The budding yeast member, Arg5,6, is expressed as a precursor that is then maturated in the mitochondria into acetylglutamate kinase and acetylglutamyl-phosphate reductase. It is involved in the arginine biosynthesis pathway, catalyzing the second and third steps in the pathway. 161 matched cddid_all.tbl CDD cd23937 cd23937 467686 GAPDH_C_E4PDH C-terminal catalytic domain of D-erythrose-4-phosphate dehydrogenase (E4PDH) and similar proteins. D-erythrose-4-phosphate dehydrogenase (E4PDH; EC 1.2.1.72), also called E4P dehydrogenase, catalyzes the NAD-dependent conversion of D-erythrose 4-phosphate (E4P) to 4-phosphoerythronate, a precursor for the de novo synthesis of pyridoxine via 4-hydroxythreonine and D-1-deoxyxylulose. This enzyme activity appears to have evolved from glyceraldehyde-3-phosphate dehydrogenase (GADPH), whose substrate differs only in the lack of one carbon relative to E4P. E4PDH proteins contain an N-terminal Rossmann fold NAD(P) binding domain and a C-terminal GADPH-like catalytic domain and are members of the GAPDH superfamily of proteins. 165 matched cddid_all.tbl CDD cd23938 cd23938 467687 ASADH_C_bac_like C-terminal catalytic domain of bacterial aspartate beta-semialdehyde dehydrogenase (ASADH) and similar proteins. The family corresponds to a branch of bacterial aspartate beta-semialdehyde dehydrogenase (ASADH) enzymes mainly found in proteobacteria, such as Escherichia coli, Haemophilus influenzae, Pseudomonas aeruginosa and Vibrio cholerae. These proteins have similar overall folds and domain organizations but share less sequence homology with fungal and archaeal ASADHs. ASADH (EC 1.2.1.11), also called ASA dehydrogenase (ASD), or aspartate-beta-semialdehyde dehydrogenase, catalyzes the NADPH-dependent formation of L-aspartate-semialdehyde (ASA) by the reductive dephosphorylation of L-aspartyl-4-phosphate, which is the second step of the aspartate biosynthetic pathway. ASA can either be further reduced to homoserine, which leads to methionine, threonine, or isoleucine, or it can be condensed with pyruvate and cyclized into dihydrodipicolinate, and then converted into diaminopimelate, a component of bacterial cell walls, and finally decarboxylated to produce lysine. ASADH contains an N-terminal Rossmann fold NAD(P) binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like catalytic domain and are members of the GAPDH superfamily of proteins. 217 matched cddid_all.tbl CDD cd23939 cd23939 467688 AGPR_1_C_LysY C-terminal catalytic domain of [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase (LysY) and similar proteins. [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase (LysY; EC 1.2.1.103/EC 1.2.1.106) is involved in both, the arginine and lysine, biosynthetic pathways. LysY interacts with LysW. It may form a ternary complex with LysW and LysZ. Several bacteria and archaea utilize the amino group-carrier protein, LysW, for lysine biosynthesis from alpha-aminoadipate (AAA). In some cases, such as Sulfolobus, LysW is also used to protect the amino group of glutamate in arginine biosynthesis. After LysW modification, AAA and glutamate are converted to lysine and ornithine, respectively, by a single set of enzymes with dual functions. LysY is the third enzyme in lysine biosynthesis from AAA. LysY shows high sequence identity and functional similarities with ArgC, and they are considered to have evolved from a common ancestor. 174 matched cddid_all.tbl CDD cd23940 cd23940 467689 ASADH_C_MCR C-terminal catalytic domain of archaeal NADP-dependent malonyl-CoA reductase (MCR) and similar proteins. Archaeal NADP-dependent malonyl-CoA reductase (MCR; EC 1.2.1.75) catalyzes the reduction of malonyl-CoA to malonate semialdehyde, a key step in the 3-hydroxypropanoate and the 3-hydroxypropanoate/4-hydroxybutyrate cycles. It can also use succinyl-CoA and succinate semialdehyde as substrates but at a lower rate than malonyl-CoA. Sequence comparison suggests that the archaeal malonyl-CoA reductase gene (mcr) has evolved from the duplication of a common ancestral aspartate beta-semialdehyde dehydrogenase (ASADH) gene (asd). MCR contains an N-terminal Rossmann fold NAD(P) binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like catalytic domain and are members of the GAPDH superfamily of proteins. 185 matched cddid_all.tbl CDD cd23942 cd23942 467933 GarD bacterial effector GarD (gamma resistance determinant). GarD shields Chlamydia trachomatis inclusions from RNF213-mediated ubiquitylation and destruction, thereby providing protection from cell-autonomous immunity. 284 matched cddid_all.tbl CDD cd23943 cd23943 467508 USP-E_repeat1 "Universal stress protein E, repeat 1. UspE is a tandem-type USP that consists of two USP domains. The UspE expression levels of Escherichia coli become elevated in response to oxidative stress and DNA damaging agents, including exposure to mitomycin C, cadmium, and hydrogen peroxide. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general ""stress endurance"" activity." 143 matched cddid_all.tbl CDD cd23944 cd23944 467509 USP_Rv2623_repeat1 "universal stress protein Rv2623 and similar proteins, USP repeat 1. Mycobacterium tuberculosis universal stress protein Rv2623 regulates mycobacterial growth in vitro and in vivo and is required for the entry of the tubercle bacillus into the chronic phase of infection in the host. In addition Rv2623 binds ATP and the growth-regulatory attribute of this USP is dependent on its ATP-binding activity. Rv2623 is thought to function as an ATP-dependent signaling intermediate in a pathway that promotes persistent infection. The universal stress protein Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general ""stress endurance"" activity. The crystal structure of Haemophilus influenzae Usp reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP, although Usp lacks ATP-binding activity." 140 matched cddid_all.tbl CDD cd23945 cd23945 467510 PAPS_reductase Phosphoadenylyl-sulfate reductase (thioredoxin). Phosphoadenosine phosphosulfate (PAPS) reductase (or PAPS sulfotransferase EC 1.8.4.8) is part of the adenine nucleotide alpha hydrolase superfamily that also includes N-type ATP PPases and ATP sulfurylases. A highly modified version of the P loop, the fingerprint peptide of mononucleotide-binding proteins, is present in the active site of the protein, which appears to be a positively charged cleft containing a number of conserved arginine and lysine residues. Although PAPS reductase has no ATPase activity, it shows a striking similarity to the structure of the ATP pyrophosphatase (ATP PPase) domain of GMP synthetase, indicating that both enzyme families have evolved from a common ancestral nucleotide-binding fold. The enzyme uses thioredoxin as an electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP). 183 matched cddid_all.tbl CDD cd23946 cd23946 467511 Sulfate_adenylyltransferase_2 Sulfate adenylyltransferase subunit 2. Sulfate adenylyltransferase subunits 1 and 2 form ATP sulfurylase (ATPS) that catalyzes the adenylation of sulfate producing adenosine 5'-phosphosulfate (APS) and diphosphate, the first enzymatic step in the sulfur assimilation pathway. APS synthesis involves the formation of a high-energy phosphoric-sulfuric acid anhydride bond driven by GTP hydrolysis by CysN, coupled to ATP hydrolysis by CysD. CysD belongs to the ATP pyrophosphatase (ATP PPase) family of proteins, members of which include PAPS reductase, GMP synthetase, asparagine synthetase, and NAD(+) synthetase. This subunit is responsible for directly forming APS under control of the G protein. A modified version of the P loop (PP-loop), the fingerprint peptide of mononucleotide-binding proteins, is present in the active site of the protein, which appears to be a positively charged cleft containing a number of conserved arginine and lysine residues. 214 matched cddid_all.tbl CDD cd23947 cd23947 467512 PAPS_reductase-like_YbdN uncharacterized phosphoadenosine phosphosulfate reductase-like proteins, similar to Escherichia coli YbdN. This subgroup contains Escherichia coli YbdN and other phosphoadenosine phosphosulfate (PAPS) reductase (or PAPS sulfotransferase EC 1.8.4.8)-like proteins. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N-type ATP PPases and ATP sulfurylases. A highly modified version of the P loop, the fingerprint peptide of mononucleotide-binding proteins, is present in the active site of the protein, which appears to be a positively charged cleft containing a number of conserved arginine and lysine residues. Although PAPS reductase has no ATPase activity, it shows a striking similarity to the structure of the ATP pyrophosphatase (ATP PPase) domain of GMP synthetase, indicating that both enzyme families have evolved from a common ancestral nucleotide-binding fold. The enzyme uses thioredoxin as an electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP). 206 matched cddid_all.tbl CDD cd23948 cd23948 467513 FAD_synthase FAD synthase. FAD synthase (FMN:ATP adenylyl transferase (FMNAT); FAD pyrophosphorylase; Flavin adenine dinucleotide synthase (FADS); EC 2.7.7.2) is involved in the biochemical pathway for converting riboflavin into FAD. By sequence comparison, bacterial and eukaryotic FMNAT enzymes belong to two different protein superfamilies and apparently utilize different sets of active-site residues to accomplish the same chemistry. This subfamily includes eukaryotic FMNATs, which are members of the 3'-phosphoadenosine 5'-phosphosulfate (PAPS) reductase-like family belonging to the adenine nucleotide alpha hydrolase superfamily, which has conserved motifs different from those of nucleotidylyl transferases. 179 matched cddid_all.tbl CDD cd23949 cd23949 469558 Niban-like Niban-like protein. Niban-like proteins contain an N-terminal Pleckstrin-Homology (PH) domain that may be involved in binding to specific ligands. Phosphatidylinositol (3)-phosphate (PI3P) was recognized as the innate ligand of the PH domain of MINERVA (melanoma invasion by ERK, also known as FAM129B) PH. Niban family proteins have been found to regulate phosphorylation of a number of proteins involved in the regularion of translation, such as EIF2A, EIF4EBP1 and RPS6KB1. They may also be involved in the endoplasmic reticulum stress response (FAM129A, Niban-like protein 1), suggested to play a role in apoptosis suppression in cancer cells, while Niban-like protein 2 (FAM129C) is a B-cell membrane protein that is overexpressed in chronic lymphocytic leukemia. 550 matched cddid_all.tbl CDD cd23951 cd23951 467830 FBXL3_LRR-like Leucine-rich repeat domain of FBXL3 and related proteins. F-box/LRR-repeat proteins are part of Skp1-Cul1-F-box-protein (SCF) ubiquitin ligase complexes. They contain an F-Box, which binds to the core complex component SKP and a leucine-rich repeat (LRR) domain which gives substrate binding specificity. FBXL3 (F-box and leucine rich repeat protein 3) and FBXL21 have been shown to bind CRY1 repressors and are involved in regulation of circadian clock. 349 matched cddid_all.tbl CDD cd23952 cd23952 467934 Utp17_CTD C-terminal domain of Chaetomium thermophilum Utp17 and similar proteins. Utp17 is a double-propeller protein that acts as a component of the UTP-A complex, which consists of seven structural proteins (Utp4, Utp5, Utp8, Utp10, Utp9, Utp15, and Utp17). UTP-A, together with UTP-B (including Utp1, Utp6, Utp12, Utp13, Utp18, and Utp21) and U3 small nucleolar ribonucleoprotein (snoRNP, including U3 snoRNA, Nop1, Nop58, Nop56, Snu13, and Rrp9), forms a subset of 5' ETS-associated factors existing as pre-assembled subcomplexes in the 90S pre-ribosome (also referred to as the SSU processome), an early assembly intermediate formed during eukaryotic ribosome synthesis. UTP-A chaperones the nascent 5'-ETS as it emerges from the transcribing RNA polymerase I. The model corresponds to the C-terminal alpha-helical domain of Utp17, which is responsible for the binding of the N-terminal domain of Utp10. 42 matched cddid_all.tbl CDD cd23953 cd23953 467935 zuotin_NTD N-terminal domain of fungal ribosome associated J-protein zuotin and similar proteins. Zuotin, also known as DnaJ-related protein ZUO1, J protein ZUO1, or heat shock protein 40 homolog ZUO1, is a component of the ribosome-associated complex (RAC), which is a heterodimer of the Hsp70/DnaK-type chaperone SSZ1 and the Hsp40/DnaJ-type chaperone ZUO1. The RAC chaperone complex plays a role in regulating accurate translation termination and folding or maintaining nascent polypeptides in a folding-competent state. The ATPase activity of the ribosome-associated pool of Hsp70-type chaperones SSB1/SSB2 that bind to the nascent polypeptide chain is stimulated by the RAC chaperone complex. ZUO1 acts as a J-protein for SSB1/SSB2 only when it is associated with SSZ1. The N-terminal domain (NTD) of ZUO1 is responsible for its interaction with SSZ1, and it contains a conserved LP-motif that binds to the SSZ1 C-terminal SBD (substrate binding domain) beta-lid domain in the same way as canonical Hsp70s bind to their substrates. 38 matched cddid_all.tbl CDD cd23954 cd23954 467936 AMO1_CTD C-terminal domain of Chaetomium thermophilum nucleoporin AMO1 and similar proteins. AMO1, also known as nuclear pore protein AMO1, is a nucleoporin component of the nuclear pore complex (NPC), which is responsible for mediating the transport of macromolecules between the nucleus and the cytoplasm. Nucleoporins (NUPs) can act as both structural components of the NPC and docking or interaction partners for transiently associated nuclear transport factors. AMO1 is particularly essential for nuclear protein and mRNA export. The C-terminal domain (CTD) of AMO1 is responsible for interacting with the Nup-associated mRNA export factors Gle1. This interaction is important for coordinating the export of mRNA from the nucleus to the cytoplasm. The CTD of AMO1 is thought to play a crucial role in regulating the export of mRNAs, particularly those involved in stress responses. 63 matched cddid_all.tbl CDD cd23955 cd23955 467440 UBCc_invertebrate ubiquitin-conjugating enzyme family protein. This subfamily includes ubiquitin-conjugating enzyme E2, catalytic (UBCc) domains mostly found in non-vertebrate eukaryotes. They belong to the ubiquitin-conjugating (UBC) superfamily that represents a structural domain with an alpha-beta(4)-alpha(3) core fold. E2 is part of the ubiquitin-mediated protein degradation pathway in which a thioester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thioester linkages without the use of E3s. 120 matched cddid_all.tbl CDD cd23956 cd23956 467831 FBXL21_LRR Leucine-rich repeat domain of F-box/LRR-repeat protein 21. FBXL21 (F-box/LRR-repeat protein 21) stabilizes CRY repressor proteins through ubiquitination and therefore counteracts FBXL3. FBXL3 (F-box/LRR-repeat protein 3), together with SKP1 (S-phase-kinase-associated protein-1) and the cullin subunit CUL1, forms a Skp1-Cul1-F-box-protein (SCF) ubiquitin ligase complex that ubiquitinates CRYs mediating their degradation. This plays an important role in oscillation of the circadian clock. FBXL21 has also been shown to regulate myoblast differentiation and sarcomere architecture via Myozenin 1 (MYOZ1; calsarcin-2) ubiquitination and NFAT signaling. 350 matched cddid_all.tbl CDD cd23957 cd23957 467832 FBXL3_LRR Leucine-rich repeat domain of F-box/LRR-repeat protein 3. FBXL3 (F-box/LRR-repeat protein 3), together with SKP1 (S-phase-kinase-associated protein-1) and cullin subunit CUL1, forms a Skp1-Cul1-F-box-protein (SCF) ubiquitin ligase complex that ubiquitinates CRY repressor proteins and mediates their degradation. FBXL21 also ubiquitinates the cryptochromes (CRYs) but counteracts FBXL3. This plays an important role in regulating oscillation of the circadian clock. 350 matched cddid_all.tbl CDD cd23958 cd23958 467937 SCC2 Sister chromatid cohesion protein 2 and homologs. This family includes Sister chromatid cohesion protein 2 (Scc2) and its homolog (Scc2 homolog, also called Nipped-B-like protein or NIPBL). Scc2/NIPBL and Scc4 form a complex that is responsible for loading the cohesin protein onto sister chromatids during mitosis and meiosis. Cohesin is a ring-shaped protein complex that encircles the sister chromatids and helps to hold them together until they are ready to be separated during cell division. In addition to its role in chromosome segregation, cohesin also plays important roles in other cellular processes such as transcription, chromosome condensation, and DNA repair. 1197 matched cddid_all.tbl CDD cd23959 cd23959 467780 KREPA2 Kinetoplastid RNA Editing Protein A2 (KREPA2). The KREPA2 (TbMP63) protein is a component of the parasitic protozoan's KREPA RNA editing catalytic complex (RECC). Kinetoplastid RNA editing (KRE) proteins occur as pairs or sets of related proteins in multiple complexes. KREPA complex is composed of six components (KREPA1-6), which share a conserved C-terminal region containing an oligonucleotide-binding (OB)-fold-like domain. KREPAs are responsible for the site-specific insertion and deletion of U nucleotides in the kinetoplastid mitochondria pre-messenger RNA. Apart from the conserved C-terminal OB-fold domain, KREPA1, KREPA2, and KREPA3 contain two conserved C2H2 zinc-finger domains. KREPA2 and kinetoplastid RNA editing ligase 1 (KREL1) are specific for ligation post-U-deletion and are paralogous to KREL2 and KREPA1 that are specific for ligation post-U-insertion. KREPA2, is critical for RECC stability and KREL1 integration into the complex. 424 matched cddid_all.tbl CDD cd23960 cd23960 467781 KREPA3 Kinetoplastid RNA Editing Protein A3 (KREPA3). The KREPA3 (TbMP42) protein is a component of the parasitic protozoan's KREPA RNA editing catalytic complex (RECC). Kinetoplastid RNA editing (KRE) proteins occur as pairs or sets of related proteins in multiple complexes. KREPA complex is composed of six components (KREPA1-6), which share a conserved C-terminal region containing an oligonucleotide-binding (OB)-fold-like domain. Apart from the conserved C-terminal OB-fold domain, KREPA1, KREPA2, and KREPA3 contain two conserved C2H2 zinc-finger domains. KREPA3 zinc fingers and OB-fold domain are each essential for growth and in vivo editing in both procyclic (PF) and bloodstream (BF) life cycle stages of Trypanosoma brucei. KREPA3 may function in editosome organization and/or RNA positioning. 106 matched cddid_all.tbl CDD cd23961 cd23961 467782 KREPA5 Kinetoplastid RNA Editing Protein A5 (KREPA5). The KREPA5 (TbMP19) protein is a component of the KREPA RNA editing catalytic complex (RECC) in parasitic protozoans. Kinetoplastid RNA editing (KRE) proteins occur as pairs or sets of related proteins in multiple complexes. KREPA complex is composed of six components (KREPA1-6), which share a conserved C-terminal region containing an oligonucleotide-binding (OB)-fold-like domain. KRPEA5 is not found in Leishmania. 122 matched cddid_all.tbl CDD cd23962 cd23962 467783 KREPA6 Kinetoplastid RNA Editing Protein A6 (KREPA6). The KREPA6 (TbMP18) protein is a component of the KREPA RNA editing catalytic complex (RECC) in parasitic protozoans. Kinetoplastid RNA editing (KRE) proteins occur as pairs or sets of related proteins in multiple complexes. KREPA complex is composed of six components (KREPA1-6), which share a conserved C-terminal region containing an oligonucleotide-binding (OB)-fold-like domain. KREPA6 is the smallest of six editosome proteins that have OB-folds. Inactivation of KREPA6 expression results in disruption and ultimate loss of 20S editosomes and inhibition of procyclic form cell growth. KREPA6 is essential for the structural integrity and presence of 20S editosomes and for cell viability. 108 matched cddid_all.tbl CDD cd23963 cd23963 467691 GT29_ST8SIA alpha-N-acetylneuraminide alpha-2,8-sialyltransferase. ST8Sia family members are alpha-N-acetylneuraminidealpha-2,8-sialyltransferases that catalyze an alpha-2,8-linkage between sialic acid and the terminal sialic acid residues of glycochains, by transfering sialic acid from CMP-Sia. The family is subdivided into 3 classes of enzymes, depending on their catalytic activiy, the mono-STs (ST8Sia1, ST8Sia5 and ST8Sia6), the oligo-ST(ST8Sia3), and the poly-STs (ST8Sia2 and ST8Sia4). The ST8Sia family belongs to glycosyltransferase family 29 (GT29). 274 matched cddid_all.tbl CDD cd23964 cd23964 467692 GT29_ST6GALNAC1_2 alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1 and 2. ST6GalNAc family members are alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferases that catalyze an alpha-2,6-linkage between sialic acid and the N-acetylgalactosamine residues of glycochains through an 2,6-linkage, by transfering sialic acid from CMP-Sia. ST6GalNAc1 and 2 utilize mainly GalNAc-,Galbeta1,3GalNAc-, and Sia2,3Galbeta1,3GalNAc on O-glycans of glycoproteins as acceptors. The ST6GalNac family belongs to glycosyltransferase family 29 (GT29). 292 matched cddid_all.tbl CDD cd23965 cd23965 467693 GT29_ST6GALNAC3_4_5_6 alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3, 4, 5 and 6. ST6GalNAc family members are alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferases that catalyze an alpha-2,6-linkage between sialic acidand the N-acetylgalactosamine residues of glycochains through an 2,6-linkage, bytransfering sialic acid from CMP-Sia. ST6GalNAc3, 4, 5, and 6 utilizeSia2,3Galbeta1,3GalNAc as an acceptor with different individual substratespecificities. The ST6GalNac family belongs to glycosyltransferase family 29 (GT29). 225 matched cddid_all.tbl CDD cd23966 cd23966 467694 GT29_ST3GAL1_2 beta-galactoside alpha-2,3-sialyltransferase 1 and 2. ST3GAL family transfer sialic acid from CMP-Sia to the terminalgalactose residues of glycochains through an 2,3-linkage. ST3GAL1 and 2 preferentially utilize the Galbeta1,3GalNAc on O-glycans of glycoproteins (core1O-glycans) and on glycolipids as an acceptor substrate, respectively. Members ofthis family belong to glycosyltransferase family 29. 276 matched cddid_all.tbl CDD cd23967 cd23967 467695 GT29_ST3GAL3_4_5_6 beta-galactoside alpha-2,3-sialyltransferase 3,4,5 and 6. ST3GAL family transfers sialic acid from CMP-Sia to the terminalgalactose residues of glycochains through an 2,3-linkage. ST3GAL3 and 4 utilize bothGalbeta1,3GlcNAc and Galbeta1,4GlcNAc, mainly on glycoproteins and oligosaccharidesas acceptor substrates. ST3GAL5 is also known as GM3 ganglioside synthase. ST3GAL6 utilizes the Galbeta1,4GlcNAc on glycoproteins and glycolipids as an acceptor. Members of this family belong to glycosyltransferase family 29 (GT29). 205 matched cddid_all.tbl CDD cd23968 cd23968 467696 GT29_ST6GAL1_2 beta-galactoside alpha-2,6-sialyltransferase 1 and 2. ST6Gal family members are beta-galactosidealpha-2,6-sialyltransferases that catalyze an alpha-2,6-linkage between sialic acidand the terminal galactose residue of a glycochain, by transfering sialic acid fromCMP-Sia. The ST6Gal family belongs to the glycosyltransferase family 29 (GT29). 266 matched cddid_all.tbl CDD cd23969 cd23969 467697 GT29_ST8SIA_poly alpha-N-acetylneuraminide alpha-2,8-sialyltransferase 2 and 4. ST8Sia2 and 4 are known to be polysialyltransferases, and they can synthesize polysialic acid on neural cell adhesion molecules (NCAMs). ST8Sia family members are alpha-N-acetylneuraminide alpha-2,8-sialyltransferases that catalyze an alpha-2,8-linkage between sialic acid and the terminal sialic acid residues of glycochains, by transfering sialic acid from CMP-Sia and they belong to the glycosyltransferase family 29 (GT29). 276 matched cddid_all.tbl CDD cd23970 cd23970 467698 GT29_ST8SIA3_oligo alpha-N-acetylneuraminide alpha-2,8-sialyltransferase 3. Alpha-N-acetylneuraminide alpha-2,8-sialyltransferase 3 synthesizes polysialic acid and has been shown to autopolysialylate. ST8Sia3 utilizes the Siaalpha2,3Galbeta1,4GlcNAc structure on N-glycans of glycoproteins and glycolipids as acceptor substrates. ST8Sia family members are alpha-N-acetylneuraminidealpha-2,8-sialyltransferases that catalyze an alpha-2,8-linkage between sialic acidand the terminal sialic acid residues of glycochains, by transfering sialic acidfrom CMP-Sia and they belong to glycosyltransferase family 29 (GT29). 284 matched cddid_all.tbl CDD cd23971 cd23971 467699 GT29_ST8SIA_mono alpha-N-acetylneuraminide alpha-2,8-sialyltransferase 1, 5 and 6. ST8 Sia family members are alpha-N-acetylneuraminidealpha-2,8-sialyltransferases that catalyze an alpha-2,8-linkage between sialic acid and the terminal sialic acid residues of glycochains, by transfering sialic acid from CMP-Sia. The family is subdivided into 3 classes of enzymes, depending on theircatalytic activiy, the mono-STs (ST8Sia1, ST8Sia5 and ST8Sia6), the oligo-ST(ST8Sia3), and the poly-STs (ST8Sia2 and ST8Sia4). The ST8Sia family belongs to the glycosyltransferase family 29 (GT29). 271 matched cddid_all.tbl CDD cd23972 cd23972 467700 GT29_ST6GALNAC2 alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2. ST6GalNAc family members are alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferases that catalyze an alpha-2,6-linkage between sialic acid and the N-acetylgalactosamine residues of glycochains through an 2,6-linkage, by transfering sialic acid from CMP-Sia. ST6GalNAc2 utilize mainly GalNAc-,Galbeta1,3GalNAc-, and Sia2,3Galbeta1,3GalNAc on O-glycans of glycoproteins as acceptors. The ST6GalNac family belongs to glycosyltransferase family 29 (GT29). 308 matched cddid_all.tbl CDD cd23973 cd23973 467701 GT29_ST6GALNAC1 alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1. ST6GalNAc family members are alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferases that catalyze an alpha-2,6-linkage between sialic acid and the N-acetylgalactosamine residues of glycochains through an 2,6-linkage, by transfering sialic acid from CMP-Sia. ST6GalNAc1 utilize mainly GalNAc-,Galbeta1,3GalNAc-, and Sia2,3Galbeta1,3GalNAc on O-glycans of glycoproteins as acceptors. The ST6GalNac family belongs to glycosyltransferase family 29 (GT29). 309 matched cddid_all.tbl CDD cd23974 cd23974 467702 GT29_ST6GALNAC2L alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2-like. ST6GalNAc family members are alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferases that catalyze an alpha-2,6-linkage between sialic acid and the N-acetylgalactosamine residues of glycochains through an 2,6-linkage, by transfering sialic acid from CMP-Sia. The ST6GalNac family belongs to glycosyltransferase family 29 (GT29). 309 matched cddid_all.tbl CDD cd23975 cd23975 467703 GT29_ST6GALNAC3 alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3. ST6GalNAc family members are alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferases that catalyze an alpha-2,6-linkage between sialic acid and the N-acetylgalactosamine residues of glycochains through an 2,6-linkage, by transfering sialic acid from CMP-Sia. ST6GalNAc3, 4, 5, and 6 utilizeSia2,3Galbeta1,3GalNAc as an acceptor with different individual substrate specificities. The ST6GalNac family belongs to glycosyltransferase family 29 (GT29). 226 matched cddid_all.tbl CDD cd23976 cd23976 467704 GT29_ST6GALNAC5 alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5. ST6GalNAc family members are alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferases that catalyze an alpha-2,6-linkage between sialic acid and the N-acetylgalactosamine residues of glycochains through an 2,6-linkage, by transfering sialic acid from CMP-Sia. ST6GalNAc3, 4, 5, and 6 utilize Sia2,3Galbeta1,3GalNAc as an acceptor with different individual substrate specificities. The ST6GalNac family belongs to glycosyltransferase family 29 (GT29). 244 matched cddid_all.tbl CDD cd23977 cd23977 467705 GT29_ST6GALNAC4 alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 4. ST6GalNAc family members are alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferases that catalyze an alpha-2,6-linkage between sialic acid and the N-acetylgalactosamine residues of glycochains through an 2,6-linkage, by transfering sialic acid from CMP-Sia. ST6GalNAc3, 4, 5, and 6 utilizeSia2,3Galbeta1,3GalNAc as an acceptor with different individual substrate specificities. The ST6GalNac family belongs to glycosyltransferase family 29 (GT29). 228 matched cddid_all.tbl CDD cd23978 cd23978 467706 GT29_ST6GALNAC6 alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6. ST6GalNAc family members are alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferases that catalyze an alpha-2,6-linkage between sialic acid and the N-acetylgalactosamine residues of glycochains through an 2,6-linkage, by transfering sialic acid from CMP-Sia. ST6GalNAc3, 4, 5, and 6 utilizeSia2,3Galbeta1,3GalNAc as an acceptor with different individual substrate specificities. The ST6GalNac family belongs to glycosyltransferase family 29 (GT29). 229 matched cddid_all.tbl CDD cd23979 cd23979 467707 GT29_ST3GAL2 beta-galactoside alpha-2,3-sialyltransferase 2. ST3GAL family transfer sialic acid from CMP-Sia to the terminal galactose residues of glycochains through an 2,3-linkage. ST3GAL2 preferentially utilizes the Galbeta1,3GalNAc on glycolipids as an acceptor substrate. Members of this family belong to glycosyltransferase family 29 (GT29). 279 matched cddid_all.tbl CDD cd23980 cd23980 467708 GT29_ST3GAL1 beta-galactoside alpha-2,3-sialyltransferase 1. ST3GAL family transfer sialic acid from CMP-Sia to the terminal galactose residues of glycochains through an 2,3-linkage. ST3GAL1 preferentially utilizes the Galbeta1,3GalNAc on O-glycans of glycoproteins (core1 O-glycans) as an acceptor substrate. Members of this family belong to glycosyltransferase family29 (GT29). 280 matched cddid_all.tbl CDD cd23981 cd23981 467709 GT29_ST3GAL3 beta-galactoside alpha-2,3-sialyltransferase 3. ST3GAL family transfers sialic acid from CMP-Sia to the terminal galactose residues of glycochains through an 2,3-linkage. ST3GAL3 can utilize both Galbeta1,3GlcNAc and Galbeta1,4GlcNAc, mainly on glycoproteins and oligosaccharidesas acceptor substrates, but prefers the Galbeta1,3GlcNAc. Members of this family belong to glycosyltransferase family 29 (GT29). 207 matched cddid_all.tbl CDD cd23982 cd23982 467710 GT29_ST3GAL4 beta-galactoside alpha-2,3-sialyltransferase 4. ST3GAL family transfers sialic acid from CMP-Sia to the terminal galactose residues of glycochains through an 2,3-linkage. ST3GAL4 can utilize both Galbeta1,3GlcNAc and Galbeta1,4GlcNAc, mainly on glycoproteins and oligosaccharidesas acceptor substrates, but prefers the Galbeta1,4GlcNAc. Members of this family belong to glycosyltransferase family 29 (GT29). 204 matched cddid_all.tbl CDD cd23983 cd23983 467711 GT29_ST3GAL5 beta-galactoside alpha-2,3-sialyltransferase 5. ST3GAL family transfers sialic acid from CMP-Sia to the terminalgalactose residues of glycochains through an 2,3-linkage. ST3GAL5 is also known as GM3 ganglioside synthase. Members of this family belong to glycosyltransferase family 29 (GT29). 211 matched cddid_all.tbl CDD cd23984 cd23984 467712 GT29_ST3GAL6 beta-galactoside alpha-2,3-sialyltransferase 6. ST3GAL family transfers sialic acid from CMP-Sia to the terminal galactose residues of glycochains through an 2,3-linkage. ST3GAL6 utilizes the Galbeta1,4GlcNAc on glycoproteins and glycolipids as an acceptor. Members of this family belong to glycosyltransferase family 29 (GT29). 206 matched cddid_all.tbl CDD cd23985 cd23985 467713 GT29_ST6GAL1 beta-galactoside alpha-2,6-sialyltransferase 1. ST6Gal family members are beta-galactoside alpha-2,6-sialyltransferases that catalyze an alpha-2,6-linkage between sialic acid and the terminal galactose residue of a glycochain, by transfering sialic acid from CMP-Sia. ST6Gal1 play important roles in the immune system. The ST6Gal family belongs to the glycosyltransferase family 29 (GT29). 266 matched cddid_all.tbl CDD cd23986 cd23986 467714 GT29_ST6GAL2 beta-galactoside alpha-2,6-sialyltransferase 2. ST6Gal family members are beta-galactoside alpha-2,3-sialyltransferases that catalyze an alpha2,6-linkage between sialic acid and the terminal galactose residue of a glycochain, by a transfering sialic acid from CMP-Sia. Members of this family belong to glycosyltransferase family 29 (GT29). 270 matched cddid_all.tbl CDD cd23987 cd23987 467715 GT29_ST8SIA2 alpha-N-acetylneuraminide alpha-2,8-sialyltransferase 2. ST8Sia2 is a polysialyltransferase that can synthesize polysialic acid on neural cell adhesion molecules (NCAMs). ST8Sia2 catalyzes shorter polysialic acid formation of NCAMs than ST8Sia4. ST8Sia family members are alpha-N-acetylneuraminide alpha-2,8-sialyltransferases that catalyze an alpha-2,8-linkage between sialic acid and the terminal sialic acid residues of glycochains, by transfering sialic acid from CMP-Sia and they belong to the glycosyltransferase family 29 (GT29). 278 matched cddid_all.tbl CDD cd23988 cd23988 467716 GT29_ST8SIA4 alpha-N-acetylneuraminide alpha-2,8-sialyltransferase 4. ST8Sia4 is a polysialyltransferase that can synthesize polysialic acid on neural cell adhesion molecules (NCAMs). ST8Sia4 catalyzes longer polysialicacid formation of NCAMs than ST8Sia2. ST8Sia family members are alpha-N-acetylneuraminide alpha-2,8-sialyltransferases that catalyze an alpha-2,8-linkage between sialic acid and the terminal sialic acid residues of glycochains, by transfering sialic acid from CMP-Sia and they belong to the glycosyltransferase family 29 (GT29). 278 matched cddid_all.tbl CDD cd23989 cd23989 467717 GT29_ST8SIA1 alpha-N-acetylneuraminide alpha-2,8-sialyltransferase 1. Alpha-N-acetylneuraminide alpha-2,8-sialyltransferase 1 (also known as ganglioside GD3 synthase) adds sialic acids to GM3 ganglioside. ST8Sia family members are alpha-N-acetylneuraminide alpha-2,8-sialyltransferases that catalyze analpha-2,8-linkage between sialic acid and the terminal sialic acid residues of glycochains, by transfering sialic acid from CMP-Sia. The ST8Sia family belongs to the glycosyltransferase family 29 (GT29). 272 matched cddid_all.tbl CDD cd23990 cd23990 467718 GT29_ST8SIA5 alpha-N-acetylneuraminide alpha-2,8-sialyltransferase 5. alpha-N-acetylneuraminide alpha-2,8-sialyltransferase 5 (also known as alpha-2,8-sialyltransferase 8E) is involved in the biosynthesis of gangliosides, such as GD1c, GT1a, GQ1b, and GT3. ST8Sia family members are alpha-N-acetylneuraminide alpha-2,8-sialyltransferases that catalyze an alpha-2,8-linkage between sialic acid and the terminal sialic acid residues of glycochains, by transfering sialic acid from CMP-Sia. The ST8Sia family belongs to glycosyltransferase family 29 (GT29). 273 matched cddid_all.tbl CDD cd23991 cd23991 467719 GT29_ST8SIA6 alpha-N-acetylneuraminide alpha-2,8-sialyltransferase 6. alpha-N-acetylneuraminide alpha-2,8-sialyltransferase 6 (also known as alpha-2,8-sialyltransferase 8F) prefers O-glycans to N-glycans or glycolipids as acceptor substrates. ST8Sia family members are alpha-N-acetylneuraminide alpha-2,8-sialyltransferases that catalyze an alpha-2,8-linkage between sialic acid and the terminal sialic acid residues of glycochains, by transfering sialic acid from CMP-Sia. The ST8Sia family belongs to glycosyltransferase family 29(GT29). 273 matched cddid_all.tbl CDD cd23992 cd23992 467938 PBP_GOBP pheromone binding protein/general-odorant binding protein (PBP/GOBP) family proteins. Arthropod Odorant Binding Proteins (OBPs) extract odorants at the air-lymph interface and carry them to the olfactory receptors. In insects, OBPs are located in the antennal sensillary lymph. OBPs that bind insects' specific pheromones are called Pheromone Binding Proteins (PBPs), and OBPs that bind general odorant molecules are sometimes called General OBPs (GOPBs). The family includes PBPs and GOBPs mainly from insects, which are distinct from the vertebrate OBPs. PBPs are male-specific and associate with pheromone-sensitive neurons and GOBPs. GOBPs share a high level of sequence similarity with the PBPs. They may carry odorants rather than pheromones. 99 matched cddid_all.tbl CDD cd23993 cd23993 467827 Seipin Seipin and similar proteins. Seipin is a homo-oligomeric integral membrane protein in the endoplasmic reticulum (ER) that concentrates at junctions with cytoplasmic lipid droplets (LDs). It acts as a cell-autonomous regulator of lipolysis essential for adipocyte differentiation. Seipin is predicted to contain two transmembrane domains at N-terminus and C-terminus, respectively. Human seipin, also called Bernardinelli-Seip congenital lipodystrophy type 2 protein (BSCL2), may contain a third transmembrane domain in the middle region. Mutations in the seipin gene underlie human congenital generalized lipodystrophy. Seipin may also be implicated in Silver spastic paraplegia syndrome and distal hereditary motor neuropathy type V. Seipin homologs from fungi, plants, and insects are also included in this family. There are three SEIPIN homologs in Arabidopsis thaliana, designated SEIPIN1, SEIPIN2, and SEIPIN3. Saccharomyces cerevisiae Seipin (Sei1) is also called few lipid droplets protein 1 (Fld1p). Similar to their animal homologs, plant and yeast seipins also play roles in lipid droplet (LD) biogenesis. Human seipin exists as an undecamer, and this oligomerization state is critical for its physiological function. In contrast to Human seipin, S. cerevisiae Sei1-mediated LD formation depends on Ldb16, a yeast specific binding partner. Sei1 forms a homodecameric ring that scaffolds and positions Ldb16. 163 matched cddid_all.tbl CDD cd23994 cd23994 467828 Seipin_Sei1_like Saccharomyces cerevisiae Seipin and similar proteins. Seipin is a homo-oligomeric integral membrane protein in the endoplasmic reticulum (ER) that concentrates at junctions with cytoplasmic lipid droplets (LDs). It acts as a cell-autonomous regulator of lipolysis essential for adipocyte differentiation. Seipin is predicted to contain two transmembrane domains at N-terminus and C-terminus, respectively. This model corresponds to a group of seipins from Saccharomycotina. Saccharomyces cerevisiae seipin (Sei1), also called few lipid droplets protein 1 (Fld1p), is involved in lipid metabolism and lipid droplet (LD) morphology, number, and size. It facilitates initiation of LD formation and ensures that vectorial budding of LDs from the ER is directed towards the cytoplasm. In contrast to human seipin, Sei1-mediated LD formation depends on Ldb16, a yeast specific binding partner. Sei1 forms a homodecameric ring that scaffolds and positions Ldb16. 176 matched cddid_all.tbl CDD cd23995 cd23995 467829 Seipin_BSCL2_like Homo sapiens Seipin and similar proteins. Seipin is a homo-oligomeric integral membrane protein in the endoplasmic reticulum (ER) that concentrates at junctions with cytoplasmic lipid droplets (LDs). It acts as a cell-autonomous regulator of lipolysis essential for adipocyte differentiation. Seipin is predicted to contain two transmembrane domains at N-terminus and C-terminus, respectively. Human seipin, also called Bernardinelli-Seip congenital lipodystrophy type 2 protein (BSCL2), may contain a third transmembrane domain in the middle region. Mutations in the seipin gene underlie Human congenital generalized lipodystrophy. Seipin may also be implicated in Silver spastic paraplegia syndrome and distal hereditary motor neuropathy type V. Human seipin exists as an undecamer, and this oligomerization state is critical for its physiological function. Seipin homologs from fungi, plants and insects are also included in this family. There are three SEIPIN homologs in Arabidopsis thaliana, designated SEIPIN1, SEIPIN2, and SEIPIN3. 162 matched cddid_all.tbl CDD cd23996 cd23996 467939 LCL2-like Long chronological lifespan protein 2 and similar proteins. Proteins similar to Saccharomcyes cerevisiae long chronological lifespan protein 2 (LCL2), also called YLR104W, which may be a component of the endoplasmic reticulum-associated degradation (ERAD) pathway that acts upstream of HRD3 and USA1. 59 matched cddid_all.tbl CDD cd23997 cd23997 467824 CD19_double_Ig "CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold domain. CD19, also known as B-Lymphocyte Surface Antigen B4, T-Cell Surface Antigen Leu-12, and CVID3, is a transmembrane receptor present on various types of B cells, including progenitor, naive, and memory B cells, as well as plasmablasts. Until recently, it was believed to comprise two extracellular immunoglobulin (Ig) structural domains arranged in tandem with C2 topology. However, recent crystal structures have shown that the CD19 extracellular domain contains a unique double Ig domain that is responsible for its binding to proteins such as CD21, CD81, and CD225, which regulate B cell activation and survival. A recent analysis of the CD19 extracellular domain sequence reveals two ""Ig domains"", but the structure demonstrates that these two domains are not folded independently and connected in tandem. Rather, they fold together as one intertwined domain that can be referred to as a ""double Ig"" domain. Each of the two regular Ig domain sequences has a noticeably short linker that forms a loop between strands C' and D, rather than allowing the formation of a C"" strand. Additionally, the two Ig-domain sequences are separated by a long linker that is structured as a small insertion domain, enabling both Ig sequences to fold together as a unique double Ig-domain. The CD19 domain comprises four ""protodomains"": two formed by A'B-CC' strands and two by DE-FG strands that interdigitate to form a novel double Ig fold. When analyzing this double Ig domain in terms of the usual Ig-fold, A'B-CC' protodomain of the first Ig sequence combines with DE-FG protodomain of the second, and vice versa. Hence, the second combined Ig fold is inverted, with DE-FG protodomain of the first Ig sequence combining with A'B-CC' protodomain of the second Ig sequence and in that order, as if it were a circular permutation, obtained only through structural folding." 89 matched cddid_all.tbl CDD cd23998 cd23998 467825 CD19_protodomain_3_4 "CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold protodomain 3 and 4. CD19, also known as B-Lymphocyte Surface Antigen B4, T-Cell Surface Antigen Leu-12, and CVID3, is a transmembrane receptor present on various types of B cells, including progenitor, naive, and memory B cells, as well as plasmablasts. Until recently, it was believed to comprise two extracellular immunoglobulin (Ig) structural domains arranged in tandem with C2 topology. However, recent crystal structures have shown that the CD19 extracellular domain contains a unique double Ig domain that is responsible for its binding to proteins such as CD21, CD81, and CD225, which regulate B cell activation and survival. A recent analysis of the CD19 extracellular domain sequence reveals two ""Ig domains"", but the structure demonstrates that these two domains are not folded independently and connected in tandem. Rather, they fold together as one intertwined domain that can be referred to as a ""double Ig"" domain. Each of the two regular Ig domain sequences has a noticeably short linker that forms a loop between strands C' and D, rather than allowing the formation of a C"" strand. Additionally, the two Ig-domain sequences are separated by a long linker that is structured as a small insertion domain, enabling both Ig sequences to fold together as a unique double Ig-domain. The CD19 domain comprises four ""protodomains"": two formed by A'B-CC' strands and two by DE-FG strands that interdigitate to form a novel double Ig fold. When analyzing this double Ig domain in terms of the usual Ig-fold, A'B-CC' protodomain of the first Ig sequence combines with DE-FG protodomain of the second, and vice versa. Hence, the second combined Ig fold is inverted, with DE-FG protodomain of the first Ig sequence combining with A'B-CC' protodomain of the second Ig sequence and in that order, as if it were a circular permutation, obtained only through structural folding. This group contains the protodomains 3 and 4 of the CD19 double Ig domain." 95 matched cddid_all.tbl CDD cd23999 cd23999 467826 CD19_protodomain_1_2 "CD19 (Cluster of Differentiation 19), a unique double immunoglobulin (Ig)-fold protodomain 1 and 2. CD19, also known as B-Lymphocyte Surface Antigen B4, T-Cell Surface Antigen Leu-12, and CVID3, is a transmembrane receptor present on various types of B cells, including progenitor, naive, and memory B cells, as well as plasmablasts. Until recently, it was believed to comprise two extracellular immunoglobulin (Ig) structural domains arranged in tandem with C2 topology. However, recent crystal structures have shown that the CD19 extracellular domain contains a unique double Ig domain that is responsible for its binding to proteins such as CD21, CD81, and CD225, which regulate B cell activation and survival. A recent analysis of the CD19 extracellular domain sequence reveals two ""Ig domains"", but the structure demonstrates that these two domains are not folded independently and connected in tandem. Rather, they fold together as one intertwined domain that can be referred to as a ""double Ig"" domain. Each of the two regular Ig domain sequences has a noticeably short linker that forms a loop between strands C' and D, rather than allowing the formation of a C"" strand. Additionally, the two Ig-domain sequences are separated by a long linker that is structured as a small insertion domain, enabling both Ig sequences to fold together as a unique double Ig-domain. The CD19 domain comprises four ""protodomains"": two formed by A'B-CC' strands and two by DE-FG strands that interdigitate to form a novel double Ig fold. When analyzing this double Ig domain in terms of the usual Ig-fold, A'B-CC' protodomain of the first Ig sequence combines with DE-FG protodomain of the second, and vice versa. Hence, the second combined Ig fold is inverted, with DE-FG protodomain of the first Ig sequence combining with A'B-CC' protodomain of the second Ig sequence and in that order, as if it were a circular permutation, obtained only through structural folding. This group contains the protodomains 1 and 2 of the CD19 double Ig domain." 92 matched cddid_all.tbl CDD cd24000 cd24000 466850 ASKHA_NBD_HK nucleotide-binding domain (NBD) of the hexokinase (HK) domain family. Hexokinase (EC 2.7.1.1) possesses the ability to transfer an inorganic phosphate group from ATP to a substrate. It catalyzes the ATP-dependent phosphorylation of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). It can catalyze this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways. Hexokinase contains two structurally similar domains. Some members of the family have two copies of each of these domains. Hexokinases belong to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily of phosphotransferases, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 357 matched cddid_all.tbl CDD cd24001 cd24001 466851 ASKHA_NBD_Kae1_TsaB-like nucleotide-binding domain (NBD) of the Kae1/TsaB-like domain family. The family includes tRNA N6-adenosine threonylcarbamoyltransferase Kae1/TsaD, tRNA threonylcarbamoyladenosine biosynthesis protein TsaB (previously known as YeaZ), as well as proteins from the NodU/CmcH subfamily. tRNA N6-adenosine threonylcarbamoyltransferase (EC 2.3.1.234) is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. It is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37. TsaB is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. It may be involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaE. TsaB seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD. The NodU/CmcH family includes NodU from Rhizobium, CmcH from Amycolatopsis lactamdurans, the bifunctional carbamoyltransferase TobZ from Streptoalloteichus tenebrarius, NovN from Streptomyces niveus and NolNO from Sinorhizobium fredii. NodU is a Rhizobium nodulation protein involved in the synthesis of nodulation factors has 6-O-carbamoyltransferase-like activity. 3'-hydroxymethylcephem-O-carbamoyltransferase CmcH (EC 2.1.3.7) is involved in cephamycin (antibiotic) biosynthesis and has 3-hydroxymethylcephem carbamoyltransferase activity. nebramycin 5' synthase TobZ (EC 6.1.2.2) functions as an ATP carbamoyltransferase and tobramycin carbamoyltransferase. Novobiocin biosynthesis protein NovN (EC 2.1.3.12) acts as a carbamoyltransferase that mediates 3'-carbamoylation of the noviosyl ring to produce novobiocin, the final step in the novobiocin biosynthesis pathway. nodulation protein NolNO (EC 2.1.3.-) is involved in the O-carbamoylation of nod factors. The NodU/CmcH subfamily proteins consist of two domains. Only the N-terminal domain shows similarity with Kae1/TsaB-like domain, which belongs to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily of phosphotransferases, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 186 matched cddid_all.tbl CDD cd24002 cd24002 466852 ASKHA_NBD_BcrAD_BadFG-like nucleotide-binding domain (NBD) of the BcrAD/BadFG-like ATPase family. The BcrAD/BadFG-like ATPase family includes BcrA/BadF/BzdQ and BcrD/BadG/BzdP proteins, which are subunits of benzoyl-CoA reductase, that may be involved in ATP hydrolysis. The family also contains some dehydratase activators, such as Acidaminococcus fermentans (R)-2-hydroxyglutaryl-CoA dehydratase activating ATPase (HgdC), Clostridioides difficile 2-hydroxyisocaproyl-CoA dehydratase activator (HadI), Clostridium sporogenes (R)-phenyllactate dehydratase activator (FldI), and Anaerotignum propionicum activator of lactoyl-CoA dehydratase (LcdC). Uncharacterized proteins, such as Escherichia coli protein YjiL, Methanocaldococcus jannaschii protein MJ0800, and Aquifex aeolicus hypothetical protein O66634, are also includes in this family. The members of the O66634-like group contain two copies of the BcrAD/BadFG-like region suggesting that they may structurally dimerize. The BcrAD/BadFG-like ATPase family belongs to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 255 matched cddid_all.tbl CDD cd24003 cd24003 466853 ASKHA_NBD_GDA1_CD39_NTPase nucleotide-binding domain (NBD) of the GDA1/CD39 NTPase family. The GDA1/CD39 NTPase family contains a group of apyrases (also known as adenylpyrophophatase, or ATP-diphosphohydrolases; EC 3.6.1.5), which are enzymes that catalyze the hydrolysis of phosphoanhydride bonds of nucleoside tri- and diphosphates (NTPs and NDPs) in the presence of divalent cations. In vertebrate systems, especially in mammals, apyrases are more widely referred to as nucleoside triphosphate diphosphohydrolases (NTPDases). There are eight homologs of NTPDases (NTPDases 1-8) in mammals, two apyrase enzymes from yeast, GDA1 and YND1, and a total of seven homologs of apyrase, namely AtAPY1-7, found in Arabidopsis. The GDA1/CD39 NTPase family belongs to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 332 matched cddid_all.tbl CDD cd24004 cd24004 466854 ASKHA_NBD_PilM-like nucleotide-binding domain (NBD) of the PilM-like domain family. The PilM-like family includes type IV pilus inner membrane component PilM, cell division protein FtsA, and ethanolamine utilization protein EutJ. PilM is an inner membrane component of the type IV (T4S) secretion system that plays a role in surface and host cell adhesion, colonization, biofilm maturation, virulence, and twitching, a form of surface-associated motility. FtsA is an essential cell division protein that assists in the assembly of the Z ring. It may serve as the principal membrane anchor for the Z ring. It is also required for the recruitment to the septal ring of the downstream cell division proteins FtsK, FtsQ, FtsL, FtsI and FtsN. EutJ may protect ethanolamine ammonia-lyase (EAL, eutB-eutC) from inhibition. It may also function in assembling the bacterial microcompartment and/or in refolding EAL, suggesting it may have chaperone activity. Members in PilM-like family belong to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily of phosphotransferases, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 282 matched cddid_all.tbl CDD cd24005 cd24005 466855 ASKHA_NBD_ANMK-like nucleotide-binding domain (NBD) of the anhydro-N-acetylmuramic acid kinase (ANMK)-like domain family. The family includes anhydro-N-acetylmuramic acid kinase (ANMK) and levoglucosan kinase (LGK). ANMK (EC 2.7.1.170), also called AnhMurNAc kinase, catalyzes the specific phosphorylation of 1,6-anhydro-N-acetylmuramic acid (anhMurNAc) with the simultaneous cleavage of the 1,6-anhydro ring, generating MurNAc-6-P. It is required for the utilization of anhMurNAc either imported from the medium or derived from its own cell wall murein, and thus plays a role in cell wall recycling. LGK (EC 2.7.1.232) catalyzes the transfer of a phosphate group from ATP to levoglucosan (1,6-anhydro-beta-D-glucopyranose, LG) to yield glucose 6-phosphate in the presence of magnesium ion and ATP. In addition to the canonical kinase phosphotransfer reaction, the conversion requires cleavage of the 1,6-anhydro ring to allow ATP-dependent phosphorylation of the sugar O-6 atom. The ANMK-like family belongs to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily of phosphotransferases, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 358 matched cddid_all.tbl CDD cd24006 cd24006 466856 ASKHA_NBD_PPX_GppA nucleotide-binding domain (NBD) of the exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (PPX/GppA) domain family. Members of the PPX/GppA family are involved in bacterial survival and metabolism. They may play distinct biochemical roles involved in polyphosphate and (p)ppGpp metabolic pathways. Guanosine pentaphosphate (pppGpp) phosphohydrolase (GppA; EC 3.6.1.40) plays a key role in (p)ppGpp homeostasis. It specifically catalyzes the conversion of pppGpp to ppGpp (guanosine tetraphosphate). Sharing a similar domain structure, GppA is indistinguishable from exopolyphosphatase (PPX; EC 3.6.1.11), which mediates the metabolism of cellular inorganic polyphosphate. Especially, it is responsible for the maintenance of appropriate levels of cellular inorganic polyphosphate (PolyP). Some bacteria, such as Escherichia coli, possesses two homologs, EcGppA and EcPPX. Some others, such as Helicobacter pylori and Aquifex aeolicus, encode only one PPX/GppA homolog, which may play important roles in the homeostasis of both (p)ppGpp and PolyP. The PPX/GppA family belongs to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily of phosphotransferases, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 294 matched cddid_all.tbl CDD cd24007 cd24007 466857 ASKHA_NBD_eukNAGK-like nucleotide-binding domain (NBD) of the eukaryotic-type N-acetylglucosamine kinase (NAGK) family. The eukaryotic-type NAGK-like family includes a group of proteins similar to eukaryotic N-acetyl-D-glucosamine kinases, such as Vibrio cholerae glucosamine kinase GspK, Sulfurisphaera tokodaii ATP-dependent hexokinase (StHK), Thermoplasma acidophilum 2-dehydro-3-deoxygluconokinase (KdgK) and Clostridium acetobutylicum N-acetylmuramic acid/N-acetylglucosamine kinase (MurK). NAGK (EC 2.7.1.59), also called GlcNAc kinase, converts endogenous N-acetylglucosamine (GlcNAc), a major component of complex carbohydrates, from lysosomal degradation or nutritional sources into GlcNAc 6-phosphate. It is involved in the N-glycolylneuraminic acid (Neu5Gc) degradation pathway. NAGK also has ManNAc kinase activity. GspK (EC 2.7.1.8), also called GlcN kinase, acts as ATP-dependent kinase, which is specific for glucosamine. StHK is a novel hexokinase that can phosphorylate not only glucose but also GlcNAc, glucosamine, and mannose. KdgK (EC 2.7.1.45), also called 2-keto-3-deoxy-D-gluconate kinase, or KDG kinase, catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) to produce 2-keto-3-deoxy-6-phosphogluconate (KDPG). It is specific for KDG. MurK (EC 2.7.1.-/EC 2.7.1.59), also known MurNAc/GlcNAc kinase, or murein sugar kinase, catalyzes the ATP-dependent phosphorylation of both cell wall (peptidoglycan) amino sugars, N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc), at the 6-hydroxyl group. The eukaryotic-type N-acetylglucosamine kinase (NAGK) family belongs to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 295 matched cddid_all.tbl CDD cd24008 cd24008 466858 ASKHA_NBD_GLK nucleotide-binding domain (NBD) of glucokinase (GLK) and similar proteins. Glucokinase (EC 2.7.1.2), also called glucose kinase, acts as an ATP-dependent kinase that phosphorylates glucose using ATP as a donor to give glucose-6-phosphate and ADP. Glucokinases are mainly found in invertebrates and microorganisms and highly specific for glucose. Glucokinases belong to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 313 matched cddid_all.tbl CDD cd24009 cd24009 466859 ASKHA_NBD_MamK nucleotide-binding domain (NBD) of the actin-like protein MamK family. MamK, also called magnetosome cytoskeleton protein MamK, is a protein with ATPase activity which forms dynamic cytoplasmic filaments (probably with paralog MamK-like) that may organize magnetosomes into long chains running parallel to the long axis of the cell. Turnover of MamK filaments is probably promoted by MamK-like (e.g.. MamJ and/or LimJ), which provides a monomer pool. MamK forms twisted filaments in the presence of ATP or GTP. It serves to close gaps between magnetosomes in the chain. Interaction with MCP10 is involved in controlling the response to magnetic fields, possibly by controlling flagellar rotation. The MamK family belongs to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 328 matched cddid_all.tbl CDD cd24010 cd24010 466860 ASKHA_NBD_AcK_PK nucleotide-binding domain (NBD) of the acetate kinase (AcK)/propionate kinase (PK) domain family. The family corresponds to a group of proteins which transfer phosphate from ATP to a short chain aliphatic acid. It includes acetate kinase (AckA) and propionate kinase (TdcD and PduW). Acetate kinase (EC 2.7.2.1), also called acetokinase, catalyzes the formation of acetyl phosphate from acetate and ATP. It can also catalyze the reverse reaction in the presence of a divalent cation. During anaerobic growth of the organism, this enzyme is also involved in the synthesis of most of the ATP formed catabolically. Propionate kinase TdcD (EC 2.7.2.15) catalyzes the conversion of propionyl phosphate and ADP to propionate and ATP. It can also use acetyl phosphate as phosphate group acceptor. The family also includes propionate kinase PduW (EC 2.7.2.15) that works with phosphate acetyltransferase (pta) to capture exogenous propionate and regenerate propionyl-CoA during degradation of propionate and 1,2-propanediol (1,2-PD). This protein restores growth to an eutQ deletion on ethanolamine and tetrathionate under anoxic conditions. The AcK/PK family belongs to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily of phosphotransferases, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 392 matched cddid_all.tbl CDD cd24011 cd24011 466861 ASKHA_NBD_BK nucleotide-binding domain (NBD) of the butyrate kinase (BK) domain family. Butyrate kinase (EC 2.7.2.7) catalyzes the formation of butyryl-CoA by phosphorylating butyrate in the presence of ATP to form butyryl phosphate. Butyrate kinases exist in many fermentative species of the bacterial and archaeal families. They belong to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily of phosphotransferases, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 345 matched cddid_all.tbl CDD cd24012 cd24012 466862 ASKHA_NBD_KDGal-kinase nucleotide-binding domain (NBD) of the 2-keto-3-deoxy-galactonokinase (DgoK) domain family. 2-keto-3-deoxy-galactonokinase (EC 2.7.1.58), also called KDGal kinase, 2-dehydro-3-deoxygalactonokinase, or oxo-3-deoxygalactonate kinase, is a bacterial transferase which catalyzes the penultimate reaction in the Ley-Doudoroff pathway, where D-galactose is metabolized into pyruvate and d-glyceraldehyde 3-phosphate. This reaction involves the phosphorylation of 2-oxo-3-deoxygalactonate to 2-oxo-3-deoxygalactonate 6-phosphate using ATP as a phosphoryl-group donor. The N-terminal domain of 2-dehydro-3-deoxygalactonokinase reveals a putative substrate-binding site. Its C-terminal domain contains a nucleotide biding site. The KDGal kinase family belongs to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily of phosphotransferases, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 312 matched cddid_all.tbl CDD cd24013 cd24013 466863 ASKHA_ATPase_BT3980-like ATPase-like domain of DUF3822 family proteins. The DUF3822 family includes a group of uncharacterized bacterial proteins similar to Bacteroides thetaiotaomicron BT_3980, a protein with an actin-like ATPase fold and unknown function. They belong to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily of phosphotransferases, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 256 matched cddid_all.tbl CDD cd24014 cd24014 466864 ASKHA_NBD_Mk0840-like nucleotide-binding domain (NBD) of Methanopyrus kandleri sugar kinase Mk0840 and similar proteins. The family includes uncharacterized Methanopyrus kandleri sugar kinase Mk0840 that shows high similarity to bacterial anhydro-N-acetylmuramic acid kinase, which is involved in murein recycling. This family belongs to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily of phosphotransferases, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 313 matched cddid_all.tbl CDD cd24015 cd24015 466865 ASKHA_NBD_PanK-III nucleotide-binding domain (NBD) of type III pantothenate kinase (PanK-III) and similar proteins. PanK (EC 2.7.1.33), also called pantothenic acid kinase, is the first enzyme in the Coenzyme A (CoA) biosynthetic pathway. It catalyzes the phosphorylation of pantothenate (vitamin B5) to form 4'-phosphopantothenate at the expense of a molecule of adenosine triphosphate (ATP), which is the rate-limiting step in CoA biosynthesis. It cannot utilize a phosphoryl donor other than ATP. Three distinct types of PanK have been identified, PanK-I, PanK-II and PanK-III. The model corresponds to PanK-III that belongs to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily of phosphotransferases, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 241 matched cddid_all.tbl CDD cd24016 cd24016 466866 ASKHA_NBD_PanK-II nucleotide-binding domain (NBD) of type II pantothenate kinase (PanK-II) and similar proteins. PanK (EC 2.7.1.33), also called pantothenic acid kinase, is the first enzyme in the Coenzyme A (CoA) biosynthetic pathway. It catalyzes the phosphorylation of pantothenate (vitamin B5) to form 4'-phosphopantothenate at the expense of a molecule of adenosine triphosphate (ATP), which is the rate-limiting step in CoA biosynthesis. It cannot utilize a phosphoryl donor other than ATP. Three distinct types of PanK have been identified, PanK-I, PanK-II and PanK-III. Eukaryotic PanK-II enzymes often occur as different isoforms, such as PanK1, PanK2, PanK3 and PanK4. The model corresponds to PanK-II that belongs to the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily of phosphotransferases, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. 299 matched cddid_all.tbl CDD cd24017 cd24017 466867 ASKHA_T2SSL_N N-terminal domain of type II secretion system protein L (T2SSL) and similar proteins. Type II secretion system is composed of four main components: the outer membrane complex, the inner membrane complex, the cytoplasmic secretion ATPase and the periplasm-spanning pseudopilus. T2SSL, also called T2SS protein L, or general secretion pathway protein L, is an inner membrane component of the type II secretion system, also called secretion-dependent pathway (SDP), required for the energy-dependent secretion of extracellular factors such as proteases and toxins from the periplasm. T2SSL is predicted to contain a large cytoplasmic domain and has been shown to interact with the autophosphorylating cytoplasmic membrane protein T2SSE. It is thought that the tri-molecular complex of T2SSL, T2SSE and T2SSM might be involved in regulating the opening and closing of the secretion pore and/or transducing energy to the site of outer membrane translocation. The model corresponds to the N-terminal domain of T2SSL. It is a cytoplasmic domain that shows structural homology with the ASKHA (Acetate and Sugar Kinases/Hsc70/Actin) superfamily of phosphotransferases, all members of which share a common characteristic five-stranded beta sheet occurring in both the N- and C-terminal domains. T2SSL is entirely missing domains 1B and 2B of the typical ASKHA proteins. The domain 2B of the ASKHA superfamily is critically important for binding the adenosine part of ATP. Due to the absence of 2B domain in T2SSL, it is therefore unlikely that T2SSL is an ATP-binding protein. 226 matched cddid_all.tbl CDD cd24018 cd24018 466868 ASKHA_NBD_HK_fungi nucleotide-binding domain (NBD) of fungal hexokinase (HK) domain family. Hexokinase (EC 2.7.1.1) possesses the ability to transfer an inorganic phosphate group from ATP to a substrate. It catalyzes the ATP-dependent phosphorylation of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). It can catalyze this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways. Hexokinase contains two structurally similar domains. Some members of the family have two copies of each of these domains. There are three isozymes of hexokinase in yeast (PI, PII and glucokinase): isozymes PI and PII phosphorylate both aldo- and keto-sugars; glucokinase (EC 2.7.1.2) is specific for aldo-hexoses. Early meiotic induction protein 2 (EMI2, also known as glucokinase-2, EC 2.7.1.2) might be another isozyme of hexokinase in yeast. It is a putative glucokinase that functions in phosphorylation of aldohexoses and glucose uptake. It is involved in sporulation and required for the full activation of the early meiotic inducer IME1. Yeast hexokinases reveal a well-defined catalytic pocket that binds ATP and hexose, allowing easy transfer of the phosphate from ATP to the sugar. 431 matched cddid_all.tbl CDD cd24019 cd24019 466869 ASKHA_NBD_HK_meta nucleotide-binding domain (NBD) of metazoan hexokinase (HK) domain family. Hexokinase (EC 2.7.1.1) possesses the ability to transfer an inorganic phosphate group from ATP to a substrate. It catalyzes the ATP-dependent phosphorylation of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). It can catalyze this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways. Hexokinase contains two structurally similar domains. Some members of the family have two copies of each of these domains. For example, members from vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. Both the N- and C-terminal halves bind hexose and H6P. In types I and III only the C-terminal half supports catalysis. Their N-terminal half is the regulatory region. In type II, both halves support catalysis. Type IV hexokinase is similar to the yeast enzyme in containing only the two domains and is sometimes incorrectly referred to as glucokinase. Whereas types I to III can phosphorylate a variety of hexose sugars and are inhibited by glucose-6-phosphate (G6P), type IV is specific for glucose and shows no G6P inhibition. 427 matched cddid_all.tbl CDD cd24020 cd24020 466870 ASKHA_NBD_HK_plant nucleotide-binding domain (NBD) of plant hexokinase (HK) domain family. Hexokinase (EC 2.7.1.1) possesses the ability to transfer an inorganic phosphate group from ATP to a substrate. It catalyzes the ATP-dependent phosphorylation of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). It can catalyze this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways. Hexokinase contains two structurally similar domains. Some members of the family have two copies of each of these domains. Hexokinases act as sugar sensors in higher plants. They may regulate sugar-dependent gene repression or activation. They mediate the effects of sugar on plant growth and development independently of its catalytic activity or the sugar metabolism. They may also regulate the execution of program cell death in plant cells, as well as promote roots and leaves growth. 439 matched cddid_all.tbl CDD cd24021 cd24021 466871 ASKHA_NBD_ParM_Psk41-like nucleotide-binding domain (NBD) of Staphylococcus aureus pSK41 actin-like ParM protein and similar proteins from the ParM domain family. Type II plasmid partition systems utilize ParM NTPases in coordination with a centromere-binding protein called ParR to mediate accurate DNA segregation, a process critical for plasmid retention. The family corresponds to a group of uncharacterized proteins similar to Staphylococcus aureus pSK41 actin-like ParM protein, which is functionally homologous to R1 ParM, a known actin homologue, suggesting that it may also form filaments to drive partition. However, pSK41 ParM shows the strongest structural homology to the archaeal actin-like protein Thermoplasma acidophilum Ta0583, but not R1 ParM. 298 matched cddid_all.tbl CDD cd24022 cd24022 466872 ASKHA_NBD_ParM_R1-like nucleotide-binding domain (NBD) of Escherichia coli plasmid segregation protein ParM and similar proteins from ParM domain family. Type II plasmid partition systems utilize ParM NTPases in coordination with a centromere-binding protein called ParR to mediate accurate DNA segregation, a process critical for plasmid retention. The family corresponds to a group of uncharacterized proteins similar to Escherichia coli ParM, also called ParA locus 36 kDa protein, or protein StbA. It is a plasmid-encoded protein involved in the control of plasmid partition and required for accurate segregation of low-copy-number plasmid R1. 324 matched cddid_all.tbl CDD cd24023 cd24023 466873 ASKHA_NBD_ParM_Alp7A-like nucleotide-binding domain (NBD) of Bacillus subtilis actin-like protein Alp7A and similar proteins from the ParM domain family. The family corresponds to a group of uncharacterized proteins similar to Bacillus subtilis actin-like protein Alp7A, a plasmid partitioning protein that functions in plasmid segregation. The subfamily also includes Bacillus thuringiensis ParM hybrid fusion protein. 368 matched cddid_all.tbl CDD cd24024 cd24024 466874 ASKHA_NBD_ParM_AlfA-like nucleotide-binding domain (NBD) of Bacillus subtilis plasmid segregating actin AlfA and similar proteins from the ParM domain family. The family corresponds to a group of uncharacterized proteins similar to Bacillus subtilis plasmid segregating actin AlfA that forms ATP-dependent filaments both in vivo and in vitro. Unlike ParM, AlfA forms stable filaments that remain assembled indefinitely in the ADP-bound state, and it is structurally polar but grows at equal rates from both ends. In addition, AlfA lacks the canonical actin subdomain IIb, which plays important structural and functional roles in all other actins. Also, AlfA polymerization interfaces have diverged extensively from other actins, and AlfA binds ATP through completely novel interactions with the adenosine base. 264 matched cddid_all.tbl CDD cd24025 cd24025 466875 ASKHA_NBD_ParM_pCBH-like nucleotide-binding domain (NBD) of Clostridium botulinum plasmid segregation protein ParM and similar proteins from the ParM domain family. The family corresponds to a group of uncharacterized proteins similar to Clostridium botulinum pCBH plasmid segregation protein ParM, an actin-like polymerizing motor. pCBH ParM filament structure is far more complex in comparison to the known filament structures of actin, MreB, and other ParMs. It is bipolar and stiff and like microtubules. The 15 polymerizing strands are likely to exert greater combined force relative to typical two-stranded actin-like filaments. 326 matched cddid_all.tbl CDD cd24026 cd24026 466876 ASKHA_NBD_ParM_Alp12-like nucleotide-binding domain (NBD) of Clostridium tetani actin-like protein Alp12 and similar proteins from the ParM domain family. The family corresponds to a group of uncharacterized proteins similar to Clostridium tetani actin-like protein Alp12. It is a dynamically unstable force-generating motor involved in segregating the pE88 plasmid, which encodes the lethal tetanus toxin. Alp12 filaments have a unique polymer structure that is entirely different from F-actin and display dynamic behavior like microtubules. Alp12 can be repeatedly cycled between states of polymerization and dissociation, making it a novel candidate for incorporation into fuel-propelled nanobiopolymer machines. 308 matched cddid_all.tbl CDD cd24027 cd24027 466877 ASKHA_NBD_ParM_Ta0583-like nucleotide-binding domain (NBD) of Thermoplasma acidophilum archaeal actin homolog and similar proteins from the ParM domain family. The family corresponds to a group of uncharacterized proteins similar to Thermoplasma acidophilum archaeal actin homolog Ta0583, which is the archaeal counterpart of the eukaryotic structural protein actin, such as MreB and ParM. Ta0583 could have a function in cellular organization. It polymerizes into bundles of filaments, forming a helix with a filament width of 5.5 nm and an axial repeating unit of 5.5 nm. Polymerization of Ta0583 requires NTP and is optimal with ATP, but GTP, UTP, CTP, and even the deoxy form of NTP can also support the polymerization reaction. Nucleoside diphosphate or AMP-PNP does not support polymerization. 323 matched cddid_all.tbl CDD cd24028 cd24028 466878 ASKHA_NBD_HSP70_HSPA1-like "nucleotide-binding domain (NBD) of the 70-kDa heat shock protein 1 (HSPA1)-like family. The HSPA1-like family includes human HSPA1A (70-kDa heat shock protein 1A, also known as HSP72; HSPA1; HSP70I; HSPA1B; HSP70-1; HSP70-1A), HSPA1B (70-kDa heat shock protein 1B, also known as HSPA1A; HSP70-2; HSP70-1B), and HSPA1L (70-kDa heat shock protein 1-like, also known as HSP70T; hum70t; HSP70-1L; HSP70-HOM), HSPA2 (70-kDa heat shock protein 2, also known as HSP70-2; HSP70-3), BiP (also known as HSP70 family protein 5 /HSPA5; 70-kDa heat shock protein 5; glucose-regulated protein 78/GRP78; immunoglobulin heavy chain-binding protein), HSPA6 (also known as heat shock 70kDa protein 6; HSP70B'), HSPA7 (heat shock 70kDa protein 7 , also known as HSP70B), HSPA8 (heat shock 70kDa protein 8, also known as Lipopolysaccharide-associated protein 1/LAP1; HSC70; HSP73; HSPA10), HSPA13 (also known as 70-kDa heat shock protein 13; STCH; microsomal stress-70 protein ATPase core; stress-70 protein chaperone microsome-associated 60 kDa protein), as well as Saccharmoyces cerevisiae Hsp70 chaperone Ssb1-2 and heat shock protein Ssa1-4. HSPA1A/1B, HSPA1L, HSPA2 and HSPA6-8 are molecular chaperones implicated in a wide variety of cellular processes, including protection of the proteome from stress, folding and transport of newly synthesized polypeptides, activation of proteolysis of misfolded proteins and the formation and dissociation of protein complexes. They play pivotal roles in the protein quality control system, ensuring the correct folding of proteins, the re-folding of misfolded proteins and controlling the targeting of proteins for subsequent degradation. BiP plays a key role in protein folding and quality control in the endoplasmic reticulum lumen. It plays an auxiliary role in post-translational transport of small presecretory proteins across endoplasmic reticulum (ER). HSPA13 has peptide-independent ATPase activity. All family members belong to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly and can direct incompetent ""client"" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. HSP70 chaperone activity is regulated by various co-chaperones: J-domain proteins and nucleotide exchange factors (NEFs)." 376 matched cddid_all.tbl CDD cd24029 cd24029 466879 ASKHA_NBD_HSP70_DnaK_HscA_HscC "nucleotide-binding domain (NBD) of Escherichia coli chaperone proteins DnaK, HscA, HscC and similar proteins. Escherichia coli DnaK, also called heat shock 70 kDa protein/HSP70, plays an essential role in the initiation of phage lambda DNA replication, where it acts in an ATP-dependent fashion with the DnaJ protein to release lambda O and P proteins from the preprimosomal complex. DnaK is also involved in chromosomal DNA replication, possibly through an analogous interaction with the DnaA protein. Moreover, DnaK participates actively in the response to hyperosmotic shock. Escherichia coli HscA, also called Hsc66, acts as a chaperone involved in the maturation of iron-sulfur cluster-containing proteins. It has a low intrinsic ATPase activity which is markedly stimulated by HscB. It is involved in the maturation of IscU. Escherichia coli HscC, also called Hsc62, or YbeW, may act as the chaperone. It has ATPase activity. It cannot be stimulated by DnaJ. The family also includes Saccharomyces cerevisiae stress-seventy subfamily C proteins, Ssc1p (also called import motor subunit, mitochondrial; endonuclease SceI 75 kDa subunit; mtHSP70; ENS1; endonuclease SceI 75 kDa subunit) and Ssc3p (also called extracellular mutant protein 10/Ecm10), and Saccharomyces cerevisiae Stress-seventy subfamily Q protein 1/Ssq1p (also called Ssc2p; Ssh1p; mtHSP70 homolog). They all belong to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly, and can direct incompetent ""client"" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. Hsp70 chaperone activity is regulated by various co-chaperones: J-domain proteins and nucleotide exchange factors (NEFs); for Escherichia coli DnaK, these are the DnaJ and GrpE, respectively." 351 matched cddid_all.tbl CDD cd24030 cd24030 466880 ASKHA_NBD_HSP70_DDRA "nucleotide-binding domain (NBD) of diol dehydratase-reactivating factor large subunit (DDRA) and similar proteins. DDRA, also called DDR large subunit, diol dehydratase-reactivase large subunit, diol dehydratase-reactivating factor alpha subunit, or DDR alpha subunit, is the large subunit of the diol dehydratase-reactivating factor (DDR), which reactivates suicidally inhibited adenosylcobalamin-dependent diol dehydratase (DD, pddA, pddB, pddC). DDR acts as a chaperone, reactivating inactivated DD holoenzyme in the presence of ATP, Mg(2+) and free adenosylcobalamin (AdoCbl), by mediating the exchange of the tightly bound damaged cofactor AdoCbl for a free intact one. DDR has weak ATPase activity which is required for DD reactivation. DDRA contains the adenosine nucleotide binding site. DDRA has four domains, the ATPase domain, the swiveling domain, the linker domain, and the insert domain. The model corresponds to the ATPase domain. DDRA belongs to the heat shock protein 70 family of chaperones that assist in protein folding and assembly and can direct incompetent ""client"" proteins towards degradation." 260 matched cddid_all.tbl CDD cd24031 cd24031 466881 ASKHA_NBD_Kae1_TsaD nucleotide-binding domain (NBD) of the Kae1/TsaD family tRNA N6-adenosine threonylcarbamoyltransferase. tRNA N6-adenosine threonylcarbamoyltransferase (EC 2.3.1.234), also called N6-L-threonylcarbamoyladenine synthase, t(6)A synthase, t(6)A37 threonylcarbamoyladenosine biosynthesis protein, or tRNA threonylcarbamoyladenosine biosynthesis protein, is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. It is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37. The family includes different orthologous of tRNA N6-adenosine threonylcarbamoyltransferase, such as bacterial kinase-associated endopeptidase 1 (Kae1) and TsaD (also known as YgjD) protein, mammalian O-sialoglycoprotein endopeptidase (OSGEP) and yeast protein Kae1, as well as mammalian OSGEP-like protein 1 (OSGEPL1) and yeast protein Qri7, which are the mitochondrial versions of the universal Kae1/TsaD (also known as YgjD) protein and essential for mitochondrial genome maintenance. 304 matched cddid_all.tbl CDD cd24032 cd24032 466882 ASKHA_NBD_TsaB nucleotide-binding domain (NBD) of tRNA threonylcarbamoyladenosine biosynthesis protein TsaB (previously known as YeaZ) and similar proteins. TsaB, also called t(6)A37 threonylcarbamoyladenosine biosynthesis protein TsaB, is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. It may be involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaD and TsaE. TsaB seems to play an indirect role in the t(6)A biosynthesis pathway, possibly in regulating the core enzymatic function of TsaD. In fact, it can act as a protease that specifically degrades TsaD in vitro; therefore, TsaB may post-translationally regulate cellular pools of TsaD via proteolytic degradation. TsaB does not show sialoglycoprotease activity against glycophorin A. 205 matched cddid_all.tbl CDD cd24033 cd24033 466883 ASKHA_NBD_NodU_CmcH-like_N N-terminal nucleotide-binding domain (NBD) of the NodU/CmcH family proteins. The NodU/CmcH family includes NodU from Rhizobium, CmcH from Amycolatopsis lactamdurans, the bifunctional carbamoyltransferase TobZ from Streptoalloteichus tenebrarius, NovN from Streptomyces niveus and NolNO from Sinorhizobium fredii. NodU is a Rhizobium nodulation protein involved in the synthesis of nodulation factors has 6-O-carbamoyltransferase-like activity. 3'-hydroxymethylcephem-O-carbamoyltransferase CmcH (EC 2.1.3.7), also called 3'-hydroxymethylcephem-O-CASE (CCT), is involved in cephamycin (antibiotic) biosynthesis and has 3-hydroxymethylcephem carbamoyltransferase activity. nebramycin 5' synthase TobZ (EC 6.1.2.2), also called kanamycin A carbamoyltransferase, or tobramycin carbamoyltransferase, functions as an ATP carbamoyltransferase and tobramycin carbamoyltransferase. Novobiocin biosynthesis protein NovN (EC 2.1.3.12), also called decarbamoylnovobiocin carbamoyltransferase, acts as a carbamoyltransferase that mediates 3'-carbamoylation of the noviosyl ring to produce novobiocin, the final step in the novobiocin biosynthesis pathway. Nodulation protein NolNO (EC 2.1.3.-), also called NolO or Y4hD, is involved in the O-carbamoylation of nod factors. Members in this family consist of two domains. The model corresponds to the N-terminal Kae1-like domain. 268 matched cddid_all.tbl CDD cd24034 cd24034 466884 ASKHA_NBD_O66634-like_rpt1 nucleotide-binding domain (NBD) of the first repeat of Aquifex aeolicus hypothetical protein O66634 and similar proteins. The family includes a group of uncharacterized proteins similar to Aquifex aeolicus hypothetical protein O66634, which contains two copies of the BcrAD/BadFG-like domain, suggesting that the family may structurally dimerize. The model corresponds to the first copy of the BcrAD/BadFG-like domain. 258 matched cddid_all.tbl CDD cd24035 cd24035 466885 ASKHA_NBD_O66634-like_rpt2 nucleotide-binding domain (NBD) of the second repeat of Aquifex aeolicus hypothetical protein O66634 and similar proteins. The family includes a group of uncharacterized proteins similar to Aquifex aeolicus hypothetical protein O66634, which contains two copies of the BcrAD/BadFG-like domain, suggesting that the family may structurally dimerize. The model corresponds to the second copy of the BcrAD/BadFG-like domain. 258 matched cddid_all.tbl CDD cd24036 cd24036 466886 ASKHA_NBD_BcrAD_BadFG_HgdC_HadI nucleotide-binding domain (NBD) of the BcrAD/BadFG and HgdC/HadI family. The BcrAD/BadFG and HgdC/HadI family includes BcrA/BadF/BzdQ and BcrD/BadG/BzdP proteins which are subunits of benzoyl-CoA reductase, that may be involved in ATP hydrolysis. The family also contains some dehydratase activators, such as Acidaminococcus fermentans (R)-2-hydroxyglutaryl-CoA dehydratase activating ATPase (HgdC), Clostridioides difficile 2-hydroxyisocaproyl-CoA dehydratase activator (HadI), Clostridium sporogenes (R)-phenyllactate dehydratase activator (FldI), and Anaerotignum propionicum activator of lactoyl-CoA dehydratase (LcdC). Uncharacterized proteins, such as Escherichia coli protein YjiL and Methanocaldococcus jannaschii protein MJ0800, are also included in this family. 250 matched cddid_all.tbl CDD cd24037 cd24037 466887 ASKHA_NBD_TgNTPase-like nucleotide-binding domain (NBD) of Toxoplasma gondii nucleoside triphosphate hydrolase (NTPase) isoforms and similar proteins. The family corresponds a group of proteins similar to Toxoplasma gondii nucleoside triphosphate hydrolase (NTPase) isoforms, NTPase-I and NTPase-II. NTPase (EC 3.6.1.15), also called nucleoside-triphosphatase, may perform an important processing step in the conversion of high energy nucleotides prior to uptake by the parasite and may contribute to intracellular survival and virulence. NTPAse-I has a specific activity 4.5-fold higher than NTPAse-II in hydrolysis of ATP. The primary difference between these isozymes lies in their ability to hydrolyze nucleoside triphosphate versus diphosphate substrates. While NTPAse-II hydrolyzes ATP to ADP and ADP to AMP at almost the same rate, NTPAse-I hydrolyzes ADP to AMP at a much slower rate (0.7% of the rate for ATP). 565 matched cddid_all.tbl CDD cd24038 cd24038 466888 ASKHA_NBD_Lp1NTPDase-like nucleotide-binding domain (NBD) of Legionella pneumophila ectonucleoside triphosphate diphosphohydrolase I (Lp1NTPDase/Lpg1905) and similar proteins. The family corresponds to a group of proteins similar to Lp1NTPDase, which is a structural and functional homolog of the eukaryotic nucleoside triphosphate diphosphohydrolases (NTPDases) that control the extracellular levels of nucleotides (NTPs). Lp1NTPDase contributes to host-pathogen interactions through its NTPDase activity. Unlike most of the mammalian NTPDases, Lp1NTPDase is soluble and does not require membrane association to regulate its catalytic activity. 346 matched cddid_all.tbl CDD cd24039 cd24039 466889 ASKHA_NBD_YND1-like nucleotide-binding domain (NBD) of yeast nucleoside diphosphatase 1 (YND1) and similar proteins. YND1 (EC 3.6.1.5), also called Golgi apyrase, ATP-diphosphatase, ATP-diphosphohydrolase, adenosine diphosphatase, ADPase, or Golgi nucleoside diphosphatase, catalyzes the hydrolysis of phosphoanhydride bonds of nucleoside tri- and di-phosphates. YND1 is required for Golgi glycosylation and cell wall integrity. 373 matched cddid_all.tbl CDD cd24040 cd24040 466890 ASKHA_NBD_GDA1 nucleotide-binding domain (NBD) of yeast guanosine-diphosphatase (GDA1) and similar proteins. After transfer of sugars to endogenous macromolecular acceptors, GDA1 (EC 3.6.1.42), also called GDPase, converts nucleoside diphosphates to nucleoside monophosphates which in turn exit the Golgi lumen in a coupled antiporter reaction, allowing entry of additional nucleotide sugar from the cytosol. 409 matched cddid_all.tbl CDD cd24041 cd24041 466891 ASKHA_NBD_AtAPY1-like nucleotide-binding domain (NBD) of Arabidopsis thaliana apyrase 1 (AtAPY1), apyrase 2 (AtAPY2), and similar proteins. Apyrase (APY; EC 3.6.1.5), also called ATP-diphosphatase, ATP-diphosphohydrolase, adenosine diphosphatase, ADPase, NTPDase, or nucleoside triphosphate diphosphohydrolase, catalyzes the hydrolysis of phosphoanhydride bonds of nucleoside tri- and di-phosphates (NTPs and NDPs) in the presence of divalent cations. AtAPY1 and AtAPY2 are typical type II membrane proteins and function at the plasma membrane as ATPases and ADPases regulating ecto-ATP/ADP concentrations. They also act as endo-apyrases residing in the Golgi lumen with UDPase and GDPase activities. AtAPY1 and AtAPY2 play roles in the regulation of stomatal function by modulating extracellular ATP levels in guard cells. They work together to reduce extracellular ATP level which is essential for pollen germination and normal plant development. 399 matched cddid_all.tbl CDD cd24042 cd24042 466892 ASKHA_NBD_AtAPY3-like nucleotide-binding domain (NBD) of Arabidopsis thaliana apyrases 3-6 (AtAPY3-6) and similar proteins. Apyrase (APY; EC 3.6.1.5), also called ATP-diphosphatase, ATP-diphosphohydrolase, adenosine diphosphatase, ADPase, NTPDase, or nucleoside triphosphate diphosphohydrolase, catalyzes the hydrolysis of phosphoanhydride bonds of nucleoside tri- and di-phosphates (NTPs and NDPs). AtAPY3-5 exhibits a single putative N-terminal transmembrane domain typical of type II membrane proteins, whereas AtAPY6 appears to possess both an N- and a C- terminal transmembrane domain and to be type IV-A membrane protein. AtAPY5 exhibits the highest specific activities for NDPs of all the Arabidopsis apyrases. AtAPY4 may have the lowest NDPase activity, exhibiting a substrate preference for CTP. AtAPY6 plays an endo-apyrase role and is important in pollen exine formation. 393 matched cddid_all.tbl CDD cd24043 cd24043 466893 ASKHA_NBD_AtAPY7-like nucleotide-binding domain (NBD) of Arabidopsis thaliana apyrase 7 (AtAPY7) and similar proteins. Apyrase 7 (APY7; EC 3.6.1.5), also called ATP-diphosphatase, ATP-diphosphohydrolase, adenosine diphosphatase, ADPase, NTPDase, or nucleoside triphosphate diphosphohydrolase 7, catalyzes the hydrolysis of phosphoanhydride bonds of nucleoside tri- and di-phosphates (NTPs and NDPs). AtAPY7 has been classified as a type IV-A membrane protein. It is important in pollen exine formation. AtAPY7 does not appear to function as a typical apyrase. 418 matched cddid_all.tbl CDD cd24044 cd24044 466894 ASKHA_NBD_NTPDase1-like nucleotide-binding domain (NBD) of the ectonucleoside triphosphate diphosphohydrolase 1 (NTPDase1)-like subfamily. The NTPDase1-like subfamily includes NTPDases 1, 2, 3 and 8, which are localized to the cell surface with their catalytic domain facing the extracellular matrix. They are the ecto-apyrase group with NTPase activities. They participate in the regulation of purinergic signaling mediated by extracellular ATP and/or ADP (eATP and eADP) through the degradation of eATP and/or eADP into AMP. 411 matched cddid_all.tbl CDD cd24045 cd24045 466895 ASKHA_NBD_NTPDase4-like nucleotide-binding domain (NBD) of the ectonucleoside triphosphate diphosphohydrolase 4 (NTPDase4)-like subfamily. The NTPDase4-like subfamily includes NTPDase4 and NTPDase7. NTPDase4 (EC 3.6.1.15/EC 3.6.1.6/EC 3.6.1.42), also called Golgi UDPase, lysosomal apyrase-like protein of 70 kDa (LALP70), uridine-diphosphatase (UDPase), is located in the Golgi. It catalyzes the hydrolysis of nucleoside triphosphates and diphosphates in a calcium- or magnesium-dependent manner, with a preference for pyrimidines. It preferentially hydrolyzes UTP and TTP. NTPDase4 has at least one alternatively spliced variant, which has a broad substrate specificity with the ability of cleaving all nucleotide di- and triphosphates except for adenosine di- and triphosphate (ADP and ATP). It preferentially hydrolyzes CTP, UDP, CDP, GTP and GDP, and can use either calcium or magnesium equally. NTPDase7 (EC 3.6.1.15), also called lysosomal apyrase-like protein 1 (LALP1), is a novel mammalian endo-apyrase with substrate preference for nucleoside 5'-triphosphates UTP, GTP, and CTP. 450 matched cddid_all.tbl CDD cd24046 cd24046 466896 ASKHA_NBD_NTPDase5-like nucleotide-binding domain (NBD) of the ectonucleoside triphosphate diphosphohydrolase 5 (NTPDase5)-like subfamily. The NTPDase5-like subfamily includes NTPDase5 and NTPDase6. NTPDase5 (EC 3.6.1.6), also called nucleoside diphosphate phosphatase ENTPD5, CD39 antigen-like 4 (CD39L4), ER-UDPase, guanosine-diphosphatase ENTPD5, GDPase ENTPD5, inosine diphosphate phosphatase ENTPD5, nucleoside diphosphatase, uridine-diphosphatase ENTPD5, or UDPase ENTPD5, hydrolyzes nucleoside diphosphates with a preference for GDP, IDP and UDP compared to ADP and CDP. NTPDase6 (EC 3.6.1.6), also called CD39 antigen-like 2 (CD39L2), catalyzes the hydrolysis of nucleoside triphosphates and diphosphates in a calcium- or magnesium-dependent manner. It has a strong preference for nucleoside diphosphates, preferentially hydrolyzes GDP, IDP, and UDP, with slower hydrolysis of CDP, ITP, GTP, CTP, ADP, and UTP and virtually no hydrolysis of ATP. The membrane bound form might support glycosylation reactions in the Golgi apparatus and, when released from cells, might catalyze the hydrolysis of extracellular nucleotides. 372 matched cddid_all.tbl CDD cd24047 cd24047 466897 ASKHA_NBD_EutJ nucleotide-binding domain (NBD) of ethanolamine utilization protein EutJ and similar proteins. EutJ may protect ethanolamine ammonia-lyase (EAL, eutB-eutC) from inhibition. It may also function in assembling the bacterial microcompartment and/or in refolding EAL, suggesting it may have chaperone activity. 241 matched cddid_all.tbl CDD cd24048 cd24048 466898 ASKHA_NBD_FtsA nucleotide-binding domain (NBD) of cell division protein FtsA and similar proteins. FtsA is an essential cell division protein that assists in the assembly of the Z ring. It may serve as the principal membrane anchor for the Z ring. It is also required for the recruitment to the septal ring of the downstream cell division proteins FtsK, FtsQ, FtsL, FtsI and FtsN. FtsA binds ATP. FtsA interacts with FtsZ. This interaction plays an essential role in cell division. 372 matched cddid_all.tbl CDD cd24049 cd24049 466899 ASKHA_NBD_PilM nucleotide-binding domain (NBD) of type IV pilus inner membrane component PilM and similar proteins. PilM is an inner membrane component of the type IV (T4S) secretion system that plays a role in surface and host cell adhesion, colonization, biofilm maturation, virulence, and twitching, a form of surface-associated motility. PilN/PilO heterodimers form the foundation of the inner-membrane PilM/PilN/PilO/PilP complex which plays an essential role in the assembly of a functional T4 pilus. In turn, PilM associates with PilN and facilitates PilM functionally relevant structural changes that differentially impacts PilM binding to PilB, PilT, and PilC. 339 matched cddid_all.tbl CDD cd24050 cd24050 466900 ASKHA_NBD_ANMK nucleotide-binding domain (NBD) of anhydro-N-acetylmuramic acid kinase (ANMK) and similar proteins. ANMK (EC 2.7.1.170), also called AnhMurNAc kinase, catalyzes the specific phosphorylation of 1,6-anhydro-N-acetylmuramic acid (anhMurNAc) with the simultaneous cleavage of the 1,6-anhydro ring, generating MurNAc-6-P. It is required for the utilization of anhMurNAc either imported from the medium or derived from its own cell wall murein, and thus plays a role in cell wall recycling. 369 matched cddid_all.tbl CDD cd24051 cd24051 466901 ASKHA_NBD_LGK nucleotide-binding domain (NBD) of levoglucosan kinase (LGK) and similar proteins. LGK (EC 2.7.1.232) catalyzes the transfer of a phosphate group from ATP to levoglucosan (1,6-anhydro-beta-D-glucopyranose, LG) to yield glucose 6-phosphate in the presence of magnesium ion and ATP. In addition to the canonical kinase phosphotransfer reaction, the conversion requires cleavage of the 1,6-anhydro ring to allow ATP-dependent phosphorylation of the sugar O-6 atom. 409 matched cddid_all.tbl CDD cd24052 cd24052 466902 ASKHA_NBD_HpPPX-GppA-like nucleotide-binding domain (NBD) of Helicobacter pylori exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (HpPPX/GppA) and similar proteins. The PPX/GppA family proteins play essential roles in bacterial survival and metabolism. Guanosine pentaphosphate (pppGpp) phosphohydrolase (GppA; EC 3.6.1.40) plays a key role in (p)ppGpp homeostasis. It specifically catalyzes the conversion of pppGpp to ppGpp (guanosine tetraphosphate). Sharing a similar domain structure, GppA is indistinguishable from exopolyphosphatase (PPX; EC 3.6.1.11), which mediates the metabolism of cellular inorganic polyphosphate. Especially, it is responsible for the maintenance of appropriate levels of cellular inorganic polyphosphate (PolyP). The family corresponds a group of proteins similar to Helicobacter pylori PPX/GppA (HpPPX/GppA). HpPPX/GppA is phylogenetically distant from the Escherichia coli homologs. Unlike E. coli that possesses two homologs, EcGppA and EcPPX, H. pylori encodes only one PPX/GppA homolog, HpPPX/GppA. As such, HpPPX/GppA may play important roles in the homeostasis of both (p)ppGpp and PolyP. 298 matched cddid_all.tbl CDD cd24053 cd24053 466903 ASKHA_NBD_EcPPX-GppA-like nucleotide-binding domain (NBD) of Escherichia coli exopolyphosphatase (EcPPX), guanosine pentaphosphate phosphohydrolase (EcGppA) and similar proteins. The PPX/GppA family proteins play essential roles in bacterial survival and metabolism. Guanosine pentaphosphate (pppGpp) phosphohydrolase (GppA; EC 3.6.1.40) plays a key role in (p)ppGpp homeostasis. It specifically catalyzes the conversion of pppGpp to ppGpp (guanosine tetraphosphate). Sharing a similar domain structure, GppA is indistinguishable from exopolyphosphatase (PPX; EC 3.6.1.11), which mediates the metabolism of cellular inorganic polyphosphate. Especially, it is responsible for the maintenance of appropriate levels of cellular inorganic polyphosphate (PolyP). The family corresponds a group of proteins similar to Escherichia coli exopolyphosphatase (EcPPX) and guanosine pentaphosphate phosphohydrolase (EcGppA). Unlike other PPX/GppA family members containing one PPX/GppA homolog, E. coli possesses two homologs, EcGppA and EcPPX. 292 matched cddid_all.tbl CDD cd24054 cd24054 466904 ASKHA_NBD_AaPPX-GppA_MtPPX2-like nucleotide-binding domain (NBD) of Aquifex aeolicus PPX/GppA, Mycobacterium tuberculosis PPX2, Fusobacterium nucleatum AroB, and similar proteins. The PPX/GppA family proteins play essential roles in bacterial survival and metabolism. Guanosine pentaphosphate (pppGpp) phosphohydrolase (GppA; EC 3.6.1.40) plays a key role in (p)ppGpp homeostasis. It specifically catalyzes the conversion of pppGpp to ppGpp (guanosine tetraphosphate). Sharing a similar domain structure, GppA is indistinguishable from exopolyphosphatase (PPX; EC 3.6.1.11), which mediates the metabolism of cellular inorganic polyphosphate. Especially, it is responsible for the maintenance of appropriate levels of cellular inorganic polyphosphate (PolyP). The family corresponds to a group of proteins similar to Aquifex aeolicus exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (AaPPX/GppA), Mycobacterium tuberculosis exopolyphosphatase 2 (MtPPX2), Fusobacterium nucleatum bifunctional 3-dehydroquinate synthase/phosphatase (AroB) and similar proteins. 296 matched cddid_all.tbl CDD cd24055 cd24055 466905 ASKHA_NBD_ChPPX-like nucleotide-binding domain (NBD) of Cytophaga hutchinsonii exopolyphosphatase (ChPPX) and similar proteins. The PPX/GppA family proteins play essential roles in bacterial survival and metabolism. Guanosine pentaphosphate (pppGpp) phosphohydrolase (GppA; EC 3.6.1.40) plays a key role in (p)ppGpp homeostasis. It specifically catalyzes the conversion of pppGpp to ppGpp (guanosine tetraphosphate). Sharing a similar domain structure, GppA is indistinguishable from exopolyphosphatase (PPX; EC 3.6.1.11), which mediates the metabolism of cellular inorganic polyphosphate. Especially, it is responsible for the maintenance of appropriate levels of cellular inorganic polyphosphate (PolyP). The family corresponds a group of proteins similar to uncharacterized Cytophaga hutchinsonii exopolyphosphatase (ChPPX). 300 matched cddid_all.tbl CDD cd24056 cd24056 466906 ASKHA_NBD_MtPPX1-like nucleotide-binding domain (NBD) of Mycobacterium tuberculosis exopolyphosphatase 1 (MtPPX1) and similar proteins. The PPX/GppA family proteins play essential roles in bacterial survival and metabolism. Guanosine pentaphosphate (pppGpp) phosphohydrolase (GppA; EC 3.6.1.40) plays a key role in (p)ppGpp homeostasis. It specifically catalyzes the conversion of pppGpp to ppGpp (guanosine tetraphosphate). Sharing a similar domain structure, GppA is indistinguishable from exopolyphosphatase (PPX; EC 3.6.1.11), which mediates the metabolism of cellular inorganic polyphosphate. Especially, it is responsible for the maintenance of appropriate levels of cellular inorganic polyphosphate (PolyP). Mycobacterium tuberculosis encodes two PPX/GppA homologues, Rv0496 (MtPPX1) and Rv1026 (MtPPX2), which are analogous to the Escherichia coli PPX and GppA enzymes. MtPPX1 functions as an exopolyphosphatase, showing a distinct preference for relatively short-chain poly-P substrates. The exopolyphosphatase activities of MtPPX1 are inhibited by pppGpp. In contrast, MtPPX2 has no detectable exopolyphosphatase activities. Neither MtPPX1 nor MtPPX2 can hydrolyze pppGpp to ppGpp, which is a reaction catalyzed by E. coli PPX and GppA enzymes. Both the MtPPX1 and MtPPX2 proteins have modest ATPase and to a lesser extent ADPase activities. The family corresponds a group of proteins similar to MtPPX1. 302 matched cddid_all.tbl CDD cd24057 cd24057 466907 ASKHA_NBD_ROK_NAGK nucleotide-binding domain (NBD) of N-acetyl-D-glucosamine kinase (NAGK) and similar proteins. NAGK (EC 2.7.1.59), also called GlcNAc kinase, catalyzes the phosphorylation of N-acetyl-D-glucosamine (GlcNAc) derived from cell-wall degradation, yielding GlcNAc-6-P. Members of this subfamily belong to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. 298 matched cddid_all.tbl CDD cd24058 cd24058 466908 ASKHA_NBD_ROK_PPGK nucleotide-binding domain (NBD) of polyphosphate glucokinase (PPGK) and similar proteins. PPGK (EC 2.7.1.63/EC 2.7.1.2), also called poly(P)/ATP-glucomannokinase (GMK), poly(P) glucokinase, ATP-dependent glucokinase, or polyphosphate--glucose phosphotransferase, catalyzes the phosphorylation of glucose using polyphosphate or ATP as the phosphoryl donor. Polyphosphate, rather than ATP, seems to be the major phosphate donor for the enzyme in Mycobacterium tuberculosis. GTP, UTP and CTP can replace ATP as phosphoryl donor. PPGK belongs to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. Members of this family lack the cysteine-rich zinc-binding motif, which presents in other ROK families. 239 matched cddid_all.tbl CDD cd24059 cd24059 466909 ASKHA_NBD_ROK_TM1224-like nucleotide-binding domain (NBD) of Thermotoga maritima N-acetylglucosamine kinase (TM1224) and similar proteins. This subfamily includes a group of uncharacterized proteins similar to N-acetylglucosamine kinase (Tm1224; EC 2.7.1.59) from Thermotoga maritima, which belongs to kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. Tm1224 lacks the cysteine-rich zinc-binding motif, which presents in other family members. 305 matched cddid_all.tbl CDD cd24060 cd24060 466910 ASKHA_NBD_ROK_GNE nucleotide-binding domain (NBD) of bifunctional UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (GNE) and similar proteins. GNE (EC 3.2.1.183/EC 2.7.1.60), also called UDP-GlcNAc-2-epimerase/ManAc kinase, is a bi-functional enzyme that plays a key role in sialic acid biosynthesis. It regulates and initiates biosynthesis of N-acetylneuraminic acid (NeuAc), a precursor of sialic acids. It plays an essential role in early development and required for normal sialylation in hematopoietic cells. Sialylation is implicated in cell adhesion, signal transduction, tumorigenicity and metastatic behavior of malignant cells. GNE is the only human protein that contains a kinase domain belonging to the ROK (repressor, ORF, kinase) family. Mutations of the GNE protein cause sialurea or autosomal recessive inclusion body myopathy/Nonaka myopathy. 305 matched cddid_all.tbl CDD cd24061 cd24061 466911 ASKHA_NBD_ROK_SgGLK-like nucleotide-binding domain (NBD) of Streptomyces griseus glucokinase (GLK) and similar proteins. Glucokinase (EC 2.7.1.2), also called glucose kinase, acts as an ATP-dependent kinase that phosphorylates glucose using ATP as a donor to give glucose-6-phosphate and ADP. It is highly specific for glucose. Glucokinases are found in invertebrates and microorganisms. They belong to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. 306 matched cddid_all.tbl CDD cd24062 cd24062 466912 ASKHA_NBD_ROK_BsGLK-like nucleotide-binding domain (NBD) of Bacillus subtilis glucokinase (GLK) and similar proteins. Glucokinase (EC 2.7.1.2), also called glucose kinase, acts as an ATP-dependent kinase that phosphorylates glucose using ATP as a donor to give glucose-6-phosphate and ADP. It is highly specific for glucose. Glucokinases are found in invertebrates and microorganisms. They belong to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. 311 matched cddid_all.tbl CDD cd24063 cd24063 466913 ASKHA_NBD_ROK_ApGLK-like nucleotide-binding domain (NBD) of Aeropyrum pernix glucokinase (GLK) and similar proteins. Glucokinase (EC 2.7.1.2), also called glucose kinase, acts as an ATP-dependent kinase that phosphorylates glucose using ATP as a donor to give glucose-6-phosphate and ADP. It is highly specific for glucose. Glucokinases are found in invertebrates and microorganisms. They belong to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. 308 matched cddid_all.tbl CDD cd24064 cd24064 466914 ASKHA_NBD_ROK_TmGLK-like nucleotide-binding domain (NBD) of Thermotoga maritima glucokinase (GLK) and similar proteins. Glucokinase (EC 2.7.1.2), also called glucose kinase, acts as an ATP-dependent kinase that phosphorylates glucose using ATP as a donor to give glucose-6-phosphate and ADP. It is highly specific for glucose. Glucokinases are found in invertebrates and microorganisms. They belong to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. 301 matched cddid_all.tbl CDD cd24065 cd24065 466915 ASKHA_NBD_ROK_TtHK-like nucleotide-binding domain (NBD) of Thermus thermophilus hexokinase (HK) and similar proteins. HK (EC 2.7.1.1) possesses the ability to transfer an inorganic phosphate group from ATP to a substrate. It catalyzes the ATP-dependent phosphorylation of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). Thermus thermophilus HK possesses significant enzymatic activity against glucose and mannose. However, it shows little catalytic capacity for galactose and fructose. Members of this subfamily belong to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. 289 matched cddid_all.tbl CDD cd24066 cd24066 466916 ASKHA_NBD_ROK_EcFRK-like nucleotide-binding domain (NBD) of Escherichia coli fructokinase (FRK) and similar proteins. Escherichia coli FRK (EC 2.7.1.4), also called D-fructose kinase, manno(fructo)kinase, or MAK, catalyzes the phosphorylation of fructose to fructose-6-phosphate. It has also low level glucokinase activity in vitro. It is not able to phosphorylate D-ribose, D-mannitol, D-sorbitol, inositol, and L-threonine. Members of this subfamily belong to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. 294 matched cddid_all.tbl CDD cd24067 cd24067 466917 ASKHA_NBD_ROK_BsFRK-like nucleotide-binding domain (NBD) of Bacillus subtilis fructokinase (FRK) and similar proteins. Bacillus subtilis FRK (EC 2.7.1.4), also called glucomannan utilization protein E, catalyzes the phosphorylation of fructose to fructose-6-P. It seems to be involved in the degradation of glucomannan. Members of this subfamily belong to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. 285 matched cddid_all.tbl CDD cd24068 cd24068 466918 ASKHA_NBD_ROK_FnNanK-like nucleotide-binding domain (NBD) of Fusobacterium nucleatum N-acetylmannosamine kinase and similar proteins. The family includes Fusobacterium nucleatum N-acetylmannosamine kinase (NanK; EC 2.7.1.60) and beta-glucoside kinase (BglK; EC 2.7.1.85) from Klebsiella pneumoniae and Listeria innocua. NanK catalyzes the second step of the sialic acid catabolic pathway, transferring a phosphate group from adenosine 5'-triphosphate to the C6 position of N-acetylmannosamine to generate N-acetylmannosamine 6-phosphate. Unlike other NanK enzymes and ROK family members, F. nucleatum NanK does not have a conserved zinc-binding site. BglK catalyzes the ATP-dependent phosphorylation of cellobiose to produce cellobiose-6'-P. It may have a dual role of kinase and transcriptional regulator of the cellobiose-PTS operon. The subfamily belongs to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. Members of this subfamily lack the cysteine-rich zinc-binding motif, which presents in other ROK families. 294 matched cddid_all.tbl CDD cd24069 cd24069 466919 ASKHA_NBD_ROK_EcNanK-like nucleotide-binding domain (NBD) of Escherichia coli N-acetylmannosamine kinase and similar proteins. N-acetylmannosamine kinase (NanK; EC 2.7.1.60), also called ManNAc kinase, or N-acetyl-D-mannosamine kinase, catalyzes the phosphorylation of N-acetylmannosamine (ManNAc) to ManNAc-6-P. It has also low level glucokinase activity in vitro. This subfamily also contains Brucella melitensis bifunctional enzyme NanE/NanK (EC 5.1.3.9/EC 2.7.1.60), which also converts N-acetylmannosamine-6-phosphate (ManNAc-6-P) to N-acetylglucosamine-6-phosphate (GlcNAc-6-P). Members of this subfamily belong to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. 283 matched cddid_all.tbl CDD cd24070 cd24070 466920 ASKHA_NBD_ROK_AlsK nucleotide-binding domain (NBD) of D-allose kinase (AlsK) and similar proteins. AlsK (EC 2.7.1.55), also called allokinase, catalyzes the phosphorylation of D-allose to D-allose 6-phosphate. It has also low level glucokinase activity in vitro. Members of this subfamily belong to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. 293 matched cddid_all.tbl CDD cd24071 cd24071 466921 ASKHA_ATPase_ROK_Lmo0178-like ATPase-like domain of Listeria monocytogenes Lmo0178 and similar proteins. This subfamily includes a group of uncharacterized proteins similar to Listeria monocytogenes Lmo0178 protein, which is a predicted transcription repressor belonging to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. 312 matched cddid_all.tbl CDD cd24072 cd24072 466922 ASKHA_ATPase_ROK_YphH-like ATPase-like domain of Escherichia coli protein YphH and similar proteins. This subfamily includes a group of uncharacterized proteins similar to Escherichia coli protein YphH that belongs to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. 308 matched cddid_all.tbl CDD cd24073 cd24073 466923 ASKHA_ATPase_ROK_CYANR ATPase-like domain of cyclobis-(1-6)-alpha-nigerosyl repressor (CYANR) and similar proteins. CYANR acts as transcriptional repressor of cyclobis-(1-6)-alpha-nigerosyl (CNN) degrading enzymes. Members of this subfamily belong to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. 304 matched cddid_all.tbl CDD cd24074 cd24074 466924 ASKHA_ATPase_ROK_Mlc ATPase-like domain of protein Mlc and similar proteins. Mlc, also called making large colonies protein, acts as a transcriptional repressor that regulates the expression of proteins that are part of the phosphotransferase system for sugar uptake. It regulates the expression of malT. Members of this subfamily belong to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. 322 matched cddid_all.tbl CDD cd24075 cd24075 466925 ASKHA_ATPase_ROK_NagC ATPase-like domain of N-acetylglucosamine repressor (NagC) and similar proteins. NagC acts as a repressor of the nagEBACD operon involved in the uptake and degradation of the amino sugars, N-acetyl-D-glucosamine (GlcNAc) and glucosamine (GlcN). It acts both as an activator and a repressor for the transcription of the glmSU operon, encoding proteins necessary for the synthesis of GlcN (glmS) and the formation of UDP-GlcNAc (glmU). Members of this subfamily belong to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. 315 matched cddid_all.tbl CDD cd24076 cd24076 466926 ASKHA_ATPase_ROK_BsXylR-like ATPase-like domain of Bacillus subtilis xylose repressor (XylR) and similar proteins. This subfamily includes a group of uncharacterized proteins similar to Bacillus subtilis xylose repressor (BsXylR), which belongs to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. BsXylR acts as transcriptional repressor of xylose-utilizing enzymes. 303 matched cddid_all.tbl CDD cd24077 cd24077 466927 ASKHA_ATPase_ROK_SaXylR-like ATPase-like domain of Staphylococcus aureus xylose repressor (XylR) and similar proteins. This subfamily includes a group of uncharacterized proteins similar to Staphylococcus aureus xylose repressor (SaXylR), which belongs to the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. SaXylR acts as a transcriptional repressor of xylose-utilizing enzymes. It lacks the cysteine-rich zinc-binding motif, which presents in other family members. 295 matched cddid_all.tbl CDD cd24078 cd24078 466928 ASKHA_NBD_NAGK_meta nucleotide-binding domain (NBD) of N-acetyl-D-glucosamine kinase (NAGK) and similar proteins. NAGK (EC 2.7.1.59), also called N-acetylglucosamine kinase, or GlcNAc kinase, converts endogenous N-acetylglucosamine (GlcNAc), a major component of complex carbohydrates, from lysosomal degradation or nutritional sources into GlcNAc 6-phosphate. It is involved in the N-glycolylneuraminic acid (Neu5Gc) degradation pathway. NAGK also has ManNAc kinase activity. Members in this family are mainly from metazoa. 314 matched cddid_all.tbl CDD cd24079 cd24079 466929 ASKHA_NBD_PG1100-like nucleotide-binding domain (NBD) of Porphyromonas gingivalis putative N-acetylglucosamine kinase (PG1100) and similar proteins. The family includes a group of uncharacterized proteins similar to Porphyromonas gingivalis putative N-acetylglucosamine kinase (PG1100; EC 2.7.1.59), which may convert GlcNAc to GlcNAc-6-phosphate, a component utilized in UDP-GlcNAc biosynthesis or energy metabolism. 276 matched cddid_all.tbl CDD cd24080 cd24080 466930 ASKHA_NBD_StHK-like nucleotide-binding domain (NBD) of Sulfurisphaera tokodaii ATP-dependent hexokinase (StHK) and similar proteins. The family includes a group of uncharacterized proteins similar to Sulfurisphaera tokodaii ATP-dependent hexokinase (StHK). Hexokinase (EC 2.7.1.1) catalyzes the phosphorylation of glucose to glucose 6-phosphate by using ATP as a phosphoryl donor. StHK is a novel hexokinase that can phosphorylate not only glucose but also GlcNAc, glucosamine, and mannose. It differs from other known hexokinases and glucokinases in that its activity is strongly inhibited by ADP. It is distinct in its broad substrate specificity from the GlcNAc kinases, which are specific for GlcNAc. 291 matched cddid_all.tbl CDD cd24081 cd24081 466931 ASKHA_NBD_DdNAGK-like nucleotide-binding domain (NBD) of Dictyostelium discoideum N-acetyl-D-glucosamine kinase (NAGK) and similar proteins. The family includes a group of uncharacterized proteins similar to Dictyostelium discoideum N-acetyl-D-glucosamine kinase (NAGK). NAGK (EC 2.7.1.59), also called N-acetylglucosamine kinase, or GlcNAc kinase, converts N-acetylglucosamine (GlcNAc), a major component of complex carbohydrates, into GlcNAc 6-phosphate. It also has ManNAc kinase activity. 311 matched cddid_all.tbl CDD cd24082 cd24082 466932 ASKHA_NBD_GspK-like nucleotide-binding domain (NBD) of Vibrio cholerae glucosamine kinase GspK and similar proteins. The family includes a group of uncharacterized proteins similar to Vibrio cholerae glucosamine kinase GspK (EC 2.7.1.8), also called GlcN kinase. It acts as ATP-dependent kinase, which is specific for glucosamine. GspK does not show kinase activity with any other sugar. 279 matched cddid_all.tbl CDD cd24083 cd24083 466933 ASKHA_NBD_KdgK-like nucleotide-binding domain (NBD) of Thermoplasma acidophilum 2-dehydro-3-deoxygluconokinase (KdgK) and similar proteins. The family includes a group of uncharacterized proteins similar to Thermoplasma acidophilum 2-dehydro-3-deoxygluconokinase (KdgK; EC 2.7.1.45), also called 2-keto-3-deoxy-D-gluconate kinase, or KDG kinase. It catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) to produce 2-keto-3-deoxy-6-phosphogluconate (KDPG). It is specific for KDG. 284 matched cddid_all.tbl CDD cd24084 cd24084 466934 ASKHA_NBD_MurK-like nucleotide-binding domain (NBD) of Clostridium acetobutylicum N-acetylmuramic acid/N-acetylglucosamine kinase (MurK) and similar proteins. The family includes a group of uncharacterized proteins similar to Clostridium acetobutylicum N-acetylmuramic acid/N-acetylglucosamine kinase (MurK; EC 2.7.1.-/EC 2.7.1.59), also known MurNAc/GlcNAc kinase, or murein sugar kinase. It catalyzes the ATP-dependent phosphorylation of both cell wall (peptidoglycan) amino sugars, N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc), at the 6-hydroxyl group. Neither the non-N-acetylated forms of the cell wall sugars, i.e., glucosamine and/or muramic acid, nor epimeric hexoses or 1,6-anhydro-MurNAc are substrates for the enzyme. MurK may have a role in the rescue of the murein sugars GlcNAc and MurNAc released from muropeptides during cell wall turnover in C.acetobutylicum. 302 matched cddid_all.tbl CDD cd24085 cd24085 466935 ASKHA_NBD_PanK-II_bac nucleotide-binding domain (NBD) of type II pantothenate kinase (PanK-II) and similar proteins mainly from bacteria. PanK (EC 2.7.1.33), also called pantothenic acid kinase, is the first enzyme in the Coenzyme A (CoA) biosynthetic pathway. It catalyzes the phosphorylation of pantothenate (vitamin B5) to form 4'-phosphopantothenate at the expense of a molecule of adenosine triphosphate (ATP), which is the rate-limiting step in CoA biosynthesis. It cannot utilize a phosphoryl donor other than ATP. Three distinct types of PanK have been identified, PanK-I, PanK-II and PanK-III. The model corresponds to a group of PanK-II that is mainly from bacteria. 262 matched cddid_all.tbl CDD cd24086 cd24086 466936 ASKHA_NBD_PanK-II_euk nucleotide-binding domain (NBD) of type II pantothenate kinase (PanK-II) and similar proteins mainly from eukaryotes. PanK (EC 2.7.1.33), also called pantothenic acid kinase, is the first enzyme in the Coenzyme A (CoA) biosynthetic pathway. It catalyzes the phosphorylation of pantothenate (vitamin B5) to form 4'-phosphopantothenate at the expense of a molecule of adenosine triphosphate (ATP), which is the rate-limiting step in CoA biosynthesis. It cannot utilize a phosphoryl donor other than ATP. Three distinct types of PanK have been identified, PanK-I, PanK-II and PanK-III. The model corresponds to a group of PanK-II that is mainly from eukaryotes. Eukaryotic PanK-II enzymes often occur as different isoforms, such as PanK1, PanK2, PanK3 and PanK4. 327 matched cddid_all.tbl CDD cd24087 cd24087 466937 ASKHA_NBD_HK1-2_fungi nucleotide-binding domain (NBD) of hexokinase isozymes PI and PII from fungal hexokinase (HK) domain family. Hexokinase (EC 2.7.1.1) possesses the ability to transfer an inorganic phosphate group from ATP to a substrate. It catalyzes the ATP-dependent phosphorylation of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). It can catalyze this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways. Hexokinase contains two structurally similar domains. Some members of the family have two copies of each of these domains. There are three isozymes of hexokinase in yeast (PI, PII and glucokinase): isozymes PI and PII phosphorylate both aldo- and keto-sugars; glucokinase (EC 2.7.1.2) is specific for aldo-hexoses. Early meiotic induction protein 2 (EMI2, also known as glucokinase-2, EC 2.7.1.2) might be another isozyme of hexokinase in yeast. Yeast hexokinases reveal a well-defined catalytic pocket that binds ATP and hexose, allowing easy transfer of the phosphate from ATP to the sugar. The family corresponds to hexokinase PI and PII, which are also known as hexokinase-1/hexokinase-A and hexokinase-2/hexokinase-B, respectively. 428 matched cddid_all.tbl CDD cd24088 cd24088 466938 ASKHA_NBD_GLK1-2_fungi nucleotide-binding domain (NBD) of hexokinase isozymes glucokinase-1 (GLK-1) and glucokinase-2 (GLK-2) from fungal hexokinase (HK) domain family. Hexokinase (EC 2.7.1.1) possesses the ability to transfer an inorganic phosphate group from ATP to a substrate. It catalyzes the ATP-dependent phosphorylation of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). It can catalyze this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways. Hexokinase contains two structurally similar domains. Some members of the family have two copies of each of these domains. There are three isozymes of hexokinase in yeast (PI, PII and glucokinase): isozymes PI and PII phosphorylate both aldo- and keto-sugars; glucokinase (also known as glucokinase-1, EC 2.7.1.2) is specific for aldo-hexoses. Early meiotic induction protein 2 (EMI2, also known as glucokinase-2, EC 2.7.1.2) might be another isozyme of hexokinase in yeast. It is a putative glucokinase that functions in phosphorylation of aldohexoses and glucose uptake. It is involved in sporulation and required for the full activation of the early meiotic inducer IME1. Yeast hexokinases reveal a well-defined catalytic pocket that binds ATP and hexose, allowing easy transfer of the phosphate from ATP to the sugar. The family corresponds to glucokinase-1 and glucokinase-2. 445 matched cddid_all.tbl CDD cd24089 cd24089 466939 ASKHA_NBD_HK1-2_meta_rpt1 nucleotide-binding domain (NBD) of the first repeat of types I and II hexokinases from metazoan hexokinase (HK) domain family. Hexokinase (EC 2.7.1.1) possesses the ability to transfer an inorganic phosphate group from ATP to a substrate. It catalyzes the ATP-dependent phosphorylation of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). It can catalyze this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways. Hexokinase contains two structurally similar domains. Some members of the family have two copies of each of these domains. For example, members from vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. Both the N- and C-terminal halves bind hexose and H6P. In types I and III only the C-terminal half supports catalysis. Their N-terminal half is the regulatory region. In type II, both halves support catalysis. Type IV hexokinase is similar to the yeast enzyme in containing only the two domains and is sometimes incorrectly referred to as glucokinase. Whereas types I to III can phosphorylate a variety of hexose sugars and are inhibited by glucose-6-phosphate (G6P), type IV is specific for glucose and shows no G6P inhibition. The model corresponds to the first two domains of types I and II hexokinases. 429 matched cddid_all.tbl CDD cd24090 cd24090 466940 ASKHA_NBD_HK3_meta_rpt1 nucleotide-binding domain (NBD) of the first repeat of type III hexokinase from metazoan hexokinase (HK) domain family. Hexokinase (EC 2.7.1.1) possesses the ability to transfer an inorganic phosphate group from ATP to a substrate. It catalyzes the ATP-dependent phosphorylation of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). It can catalyze this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways. Hexokinase contains two structurally similar domains. Some members of the family have two copies of each of these domains. For example, members from vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. Both the N- and C-terminal halves bind hexose and H6P. In types I and III only the C-terminal half supports catalysis. Their N-terminal half is the regulatory region. In type II, both halves support catalysis. Type IV hexokinase is similar to the yeast enzyme in containing only the two domains and is sometimes incorrectly referred to as glucokinase. Whereas types I to III can phosphorylate a variety of hexose sugars and are inhibited by glucose-6-phosphate (G6P), type IV is specific for glucose and shows no G6P inhibition. The model corresponds to the first two domains of type III hexokinase. 431 matched cddid_all.tbl CDD cd24091 cd24091 466941 ASKHA_NBD_HK1-3_meta_rpt2 nucleotide-binding domain (NBD) of the second repeat of types I, II, and III hexokinases from metazoan hexokinase (HK) domain family. Hexokinase (EC 2.7.1.1) possesses the ability to transfer an inorganic phosphate group from ATP to a substrate. It catalyzes the ATP-dependent phosphorylation of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). It can catalyze this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways. Hexokinase contains two structurally similar domains. Some members of the family have two copies of each of these domains. For example, members from vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. Both the N- and C-terminal halves bind hexose and H6P. In types I and III only the C-terminal half supports catalysis. Their N-terminal half is the regulatory region. In type II, both halves support catalysis. Type IV hexokinase is similar to the yeast enzyme in containing only the two domains and is sometimes incorrectly referred to as glucokinase. Whereas types I to III can phosphorylate a variety of hexose sugars and are inhibited by glucose-6-phosphate (G6P), type IV is specific for glucose and shows no G6P inhibition. The model corresponds to the second two domains of types I to III hexokinases. Type I enzyme may have a catabolic function, producing H6P for energy production in glycolysis; it is bound to the mitochondrial membrane, which enables the coordination of glycolysis with the TCA cycle. Types II and III enzyme may have anabolic functions, providing H6P for glycogen or lipid synthesis. 433 matched cddid_all.tbl CDD cd24092 cd24092 466942 ASKHA_NBD_HK4_meta nucleotide-binding domain (NBD) of type IV hexokinase from metazoan hexokinase (HK) domain family. Hexokinase (EC 2.7.1.1) possesses the ability to transfer an inorganic phosphate group from ATP to a substrate. It catalyzes the ATP-dependent phosphorylation of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). It can catalyze this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways. Hexokinase contains two structurally similar domains. Some members of the family have two copies of each of these domains. For example, members from vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. Both the N- and C-terminal halves bind hexose and H6P. In types I and III only the C-terminal half supports catalysis. Their N-terminal half is the regulatory region. In type II, both halves support catalysis. Type IV hexokinase is similar to the yeast enzyme in containing only the two domains and is sometimes incorrectly referred to as glucokinase. Whereas types I to III can phosphorylate a variety of hexose sugars and are inhibited by glucose-6-phosphate (G6P), type IV is specific for glucose and shows no G6P inhibition. The model corresponds to type IV hexokinase. It is found in the liver and pancreatic beta-cells, where it is controlled by insulin (activation) and glucagon (inhibition). In pancreatic beta-cells, type IV enzyme acts as a glucose sensor to modify insulin secretion. Mutations in type IV hexokinase have been associated with diabetes mellitus. 444 matched cddid_all.tbl CDD cd24093 cd24093 466943 ASKHA_NBD_HSP70_Ssb "nucleotide-binding domain (NBD) of Saccharmoyces cerevisiae Hsp70 chaperone Ssb and similar proteins. Ssb is ribosome-bound, Hsp70-type chaperone that assists in the co-translational folding of newly synthesized proteins in the cytosol. It stimulates folding by interacting with nascent chains, binding to short, largely hydrophobic sequences exposed by unfolded proteins, thereby stabilizing longer, more slowly translated, and aggregation-prone nascent polypeptides and domains that cannot fold stably until fully synthesized. Ssb cooperates with a specific Hsp40/Hsp70 co-chaperone termed the ribosome-associated complex (RAC), which stimulates the ATPase activity of the ribosome-associated pool of Ssbs and switches it to the high affinity substrate binding state. Saccharmoyces cerevisiae Ssb are encoded by two genes, SSB1 and SSB2. Ssb1p is also known as cold-inducible protein YG101. Members in this subfamily belong to the heat shock protein 70 (HSP70) family of chaperones that assist in protein folding and assembly, and can direct incompetent ""client"" proteins towards degradation. Typically, HSP70s have a nucleotide-binding domain (NBD) and a substrate-binding domain (SBD). The nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. HSP70 chaperone activity is regulated by various co-chaperones: J-domain proteins and nucleotide exchange factors (NEFs)." 375 matched cddid_all.tbl CDD cd24094 cd24094 466944 ASKHA_NBD_HSP70_ScSse "nucleotide-binding domain (NBD) of Saccharomyces cerevisiae heat shock protein homolog Sse and similar proteins. The subgroup includes two Saccharomyces cerevisiae heat shock protein homologs, Sse1 and Sse2. They may have calcium-dependent calmodulin-binding activities. Both Sse1 and Sse2 belong to the 105/110 kDa heat shock protein (HSP105/110) subfamily of the HSP70-like family, and includes proteins believed to function generally as co-chaperones of HSP70 chaperones, acting as nucleotide exchange factors (NEFs), to remove ADP from their HSP70 chaperone partners during the ATP hydrolysis cycle. HSP70 chaperones assist in protein folding and assembly, and can direct incompetent ""client"" proteins towards degradation. Like HSP70 chaperones, HSP105/110s have an N-terminal nucleotide-binding domain (NBD) and a C-terminal substrate-binding domain (SBD). For HSP70 chaperones, the nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. Hsp70 chaperone activity is also regulated by J-domain proteins." 385 matched cddid_all.tbl CDD cd24095 cd24095 466945 ASKHA_NBD_HSP70_AtHsp70-14-like "nucleotide-binding domain (NBD) of Arabidopsis thaliana heat shock 70 kDa protein 14-16 and similar proteins. The subgroup includes Arabidopsis thaliana Hsp70-14, also known as heat shock 70 kDa protein 14; heat shock protein 91), Hsp70-15 (also known as heat shock 70 kDa protein 15), and Hsp70-16 (also known as heat shock 70 kDa protein 16). In cooperation with other chaperones, they are key components that facilitate folding of de novo synthesized proteins, assist translocation of precursor proteins into organelles, and are responsible for degradation of damaged protein under stress conditions. Members in this subgroup belong to the 105/110 kDa heat shock protein (HSP105/110) subfamily of the HSP70-like family, and includes proteins believed to function generally as co-chaperones of HSP70 chaperones, acting as nucleotide exchange factors (NEFs), to remove ADP from their HSP70 chaperone partners during the ATP hydrolysis cycle. HSP70 chaperones assist in protein folding and assembly, and can direct incompetent ""client"" proteins towards degradation. Like HSP70 chaperones, HSP105/110s have an N-terminal nucleotide-binding domain (NBD) and a C-terminal substrate-binding domain (SBD). For HSP70 chaperones, the nucleotide sits in a deep cleft formed between the two lobes of the NBD. The two subdomains of each lobe change conformation between ATP-bound, ADP-bound, and nucleotide-free states. ATP binding opens up the substrate-binding site; substrate-binding increases the rate of ATP hydrolysis. Hsp70 chaperone activity is also regulated by J-domain proteins." 389 matched cddid_all.tbl CDD cd24096 cd24096 466946 ASKHA_NBD_Kae1-like nucleotide-binding domain (NBD) of Kae1 and similar proteins. Kae1 (EC 2.3.1.234), also called kinase-associated endopeptidase 1, N6-L-threonylcarbamoyladenine synthase, t(6)A synthase, kinase-associated endopeptidase 1 (Kae1), t(6)A37 threonylcarbamoyladenosine biosynthesis protein Kae1, or tRNA threonylcarbamoyladenosine biosynthesis protein Kae1, is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. It is a component of the KEOPS complex that is probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37. Kae1 likely plays a direct catalytic role in this reaction but requires other protein(s) of the complex to fulfill this activity. OSGEP (EC 2.3.1.234), also called tRNA N6-adenosine threonylcarbamoyltransferase, N6-L-threonylcarbamoyladenine synthase, t(6)A synthase, t(6)A37 threonylcarbamoyladenosine biosynthesis protein OSGEP, tRNA threonylcarbamoyladenosine biosynthesis protein OSGEP, is the mammalian orthologue of kinase-associated endopeptidase Kae1. The family also includes bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein (EC 2.3.1.234/EC 2.7.11.1), which contains a Kae1 domain and a Bud32 domain. The Kae1 domain may play a catalytic role and the Bud32 domain probably displays kinase activity that regulates Kae1 function. 301 matched cddid_all.tbl CDD cd24097 cd24097 466947 ASKHA_NBD_TsaD-like nucleotide-binding domain (NBD) of TsaD and similar proteins. TsaD (EC 2.3.1.234), also called N6-L-threonylcarbamoyladenine synthase, t(6)A synthase, t(6)A37 threonylcarbamoyladenosine biosynthesis protein TsaD, or tRNA threonylcarbamoyladenosine biosynthesis protein TsaD, is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. It is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction. The family also includes mammalian OSGEP-like protein 1 (OSGEPL1) and yeast protein Qri7, which are the mitochondrial versions of the universal Kae1/TsaD (also known as YgjD) protein and essential for mitochondrial genome maintenance. 313 matched cddid_all.tbl CDD cd24098 cd24098 466948 ASKHA_NBD_TobZ_N N-terminal nucleotide-binding domain (NBD) of nebramycin 5' synthase (TobZ) and similar proteins. TobZ (EC 6.1.2.2), also called kanamycin A carbamoyltransferase, or tobramycin carbamoyltransferase, is involved in the biosynthesis of the 2-deoxystreptamine-containing aminoglycoside antibiotics such as nebramycin 5 and 6-O-carbamoylkanamycin. It catalyzes the hydrolysis of carbamoyl phosphate and its subsequent adenylation by ATP to yield O-carbamoyladenylate. Then it catalyzes the transfer of the carbamoyl moiety from O-carbamoyladenylate to the tobramycin 6-hydroxy group to yield nebramycin 5'. It catalyzes the same reaction with kanamycin A. These reactions are considerably slower in the presence of deoxy-ATP. TobZ consists of two major domains: the N-terminal Kae1-like domain is involved in the transfer of carbamoyl from O-carbamoyladenylate to tobramycin or kanamycin; the C-terminal YrdC-like domain is involved in the hydrolysis of carbamoyl phosphate and its subsequent adenylation by ATP. The model corresponds to the N-terminal domain. 243 matched cddid_all.tbl CDD cd24099 cd24099 466949 ASKHA_NBD_NovN-like_N N-terminal nucleotide-binding domain (NBD) of Streptomyces niveus novobiocin biosynthesis protein N (NovN) and similar proteins. The family includes a group of proteins similar to Streptomyces niveus novobiocin biosynthesis protein N (NovN) and Sinorhizobium fredii nodulation protein NolNO. NovN (EC 2.1.3.12), also called decarbamoylnovobiocin carbamoyltransferase, acts as a carbamoyltransferase that mediates 3'-carbamoylation of the noviosyl ring to produce novobiocin, the final step in the novobiocin biosynthesis pathway. Novobiocincin is an aminocoumarin family antibiotic that targets bacterial DNA gyrases. NolNO (EC 2.1.3.-), also called NolO or Y4hD, is involved in the O-carbamoylation of nod factors. Members of this family consist of two domains. The model corresponds to the N-terminal Kae1-like domain. 340 matched cddid_all.tbl CDD cd24100 cd24100 466950 ASKHA_NBD_MJ1051-like_N N-terminal nucleotide-binding domain (NBD) of Methanocaldococcus jannaschii protein MJ1051 and similar proteins. The family includes a group of uncharacterized proteins similar to Methanocaldococcus jannaschii protein MJ1051 and protein MJ1058. Members of this family consist of two domains. The model corresponds to the N-terminal Kae1-like domain. 238 matched cddid_all.tbl CDD cd24101 cd24101 466951 ASKHA_NBD_NodU_N N-terminal nucleotide-binding domain (NBD) of nodulation protein U (NodU) and similar proteins. NodU (EC 2.1.3.-) is a Rhizobium nodulation protein involved in the synthesis of nodulation factors has 6-O-carbamoyltransferase-like activity. Members of this family consist of two domains. The model corresponds to the N-terminal Kae1-like domain. 346 matched cddid_all.tbl CDD cd24102 cd24102 466952 ASKHA_NBD_CmcH_N N-terminal nucleotide-binding domain (NBD) of 3'-hydroxymethylcephem-O-carbamoyltransferase (CmcH) and similar proteins. CmcH (EC 2.1.3.7), also called 3'-hydroxymethylcephem-O-CASE (CCT), has 3-hydroxymethylcephem carbamoyltransferase activity. It catalyzes the carbamoylation reaction in the cephamycin (antibiotic) biosynthesis. Members of this family consist of two domains. The model corresponds to the N-terminal Kae1-like domain. 316 matched cddid_all.tbl CDD cd24103 cd24103 466953 ASKHA_NBD_HgdC_HadI-like nucleotide-binding domain (NBD) of the HgdC/HadI-like subfamily. The HgdC/HadI-like subfamily includes a group of proteins such as Acidaminococcus fermentans (R)-2-hydroxyglutaryl-CoA dehydratase activating ATPase (HgdC), Clostridioides difficile 2-hydroxyisocaproyl-CoA dehydratase activator (HadI), Clostridium sporogenes (R)-phenyllactate dehydratase activator (FldI), and Anaerotignum propionicum activator of lactoyl-CoA dehydratase (LcdC). HgdC (EC 3.6.1.-), also called (R)-2-hydroxyglutaryl-CoA dehydratase activase, (R)-2-hydroxyglutaryl-CoA dehydratase (component A), ATP-coupled electron transfer protein HgdC, or activator of (R)-2-hydroxyglutaryl-CoA dehydratase, is involved in the fermentation of L-glutamate via the hydroxyglutarate pathway. HgdC (CompA) has a very low ATPase activity. Its role is to activate dehydratase HgdA-HgdB complex and then maintain an appropriate redox state via an ATP-dependent electron transfer. The dehydratase requires only catalytic amounts of ATP and substoichiometric amounts of HgdC (CompA) to be functional. HadI is involved in the reductive branch of L-leucine fermentation. It is required for the activation of (R)-2-hydroxyisocaproyl-CoA dehydratase. The reduced activator transfers one electron to the dehydratase concomitant with hydrolysis of ATP. FldI (EC 3.6.1.-), also called initiator of phenyllactate dehydratase, is involved in the fermentation of L-phenylalanine via a Stickland reaction. It is required for the activation of the (R)-phenyllactate dehydratase complex FldABC. Only in the oxidized state, FldI exhibits significant ATPase activity, which appears to be essential for unidirectional electron transfer. LcdC, also called lactoyl-CoA dehydratase component E I, is required for the activation of lactoyl-CoA dehydratase. HadI, FldI and LcdC are extremely sensitive towards oxygen. 255 matched cddid_all.tbl CDD cd24104 cd24104 466954 ASKHA_NBD_benz_CoA_BcrA_BadF nucleotide-binding domain (NBD) of benzoyl-CoA reductase subunit A (BcrA/BadF) and similar proteins. Benzoyl-CoA reductase (EC 1.3.7.8), also called benzoyl-CoA reductase (dearomatizing), or 3-hydroxybenzoyl-CoA reductase, catalyzes the anaerobic reduction of benzoyl-CoA and 3-hydroxybenzoyl-CoA to form cyclohexa-1,5-diene-1-carbonyl-CoA and 3-hydroxycyclohexa-1,5-diene-1-carbonyl-CoA, respectively. The enzyme also reduces other benzoyl-CoA analogs with small substituents at the aromatic ring. The model corresponds to subunit A of benzoyl-CoA reductase. 253 matched cddid_all.tbl CDD cd24105 cd24105 466955 ASKHA_NBD_benz_CoA_BcrD_BadG nucleotide-binding domain (NBD) of benzoyl-CoA reductase subunit D (BcrD/BadG) and similar proteins. benzoyl-CoA reductase (EC 1.3.7.8), also called benzoyl-CoA reductase (dearomatizing), or 3-hydroxybenzoyl-CoA reductase, catalyzes the anaerobic reduction of benzoyl-CoA and 3-hydroxybenzoyl-CoA to form cyclohexa-1,5-diene-1-carbonyl-CoA and 3-hydroxycyclohexa-1,5-diene-1-carbonyl-CoA, respectively. The enzyme also reduces other benzoyl-CoA analogs with small substituents at the aromatic ring. The model corresponds to subunit D of benzoyl-CoA reductase. 256 matched cddid_all.tbl CDD cd24106 cd24106 466956 ASKHA_NBD_benz_CoA_BzdQ nucleotide-binding domain (NBD) of benzoyl-CoA reductase, bzd-type, Q subunit (BzdQ) and similar proteins. bzd-type benzoyl-CoA reductase BzdQ is encoded by the gene bzdQ from a benzoate-inducible catabolic operon in Azoarcus sp. The bzd-type benzoyl-CoA reductase system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for several different aromatic compounds, such as phenol and toluene. BzdQ may function the same as the A subunit of benzoyl-CoA reductase BcrA from Thauera aromatica and benzoyl-CoA reductase BadF from Rhodopseudomonas palustris. 253 matched cddid_all.tbl CDD cd24107 cd24107 466957 ASKHA_NBD_benz_CoA_BzdP nucleotide-binding domain (NBD) of benzoyl-CoA reductase, bzd-type, BzdP subunit and similar proteins. bzd-type benzoyl-CoA reductase BzdP is encoded by the gene bzdP from a benzoate-inducible catabolic operon in Azoarcus sp. The bzd-type benzoyl-CoA reductase system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for several different aromatic compounds, such as phenol and toluene. BzdP may function the same as the D subunit of benzoyl-CoA reductase BcrD from Thauera aromatica and benzoyl-CoA reductase BadG from Rhodopseudomonas palustris. 250 matched cddid_all.tbl CDD cd24108 cd24108 466958 ASKHA_NBD_MJ0800-like nucleotide-binding domain (NBD) of Methanocaldococcus jannaschii protein MJ0800 and similar proteins. The subfamily includes a group of uncharacterized proteins similar to Methanocaldococcus jannaschii protein MJ0800, which belongs to the BcrAD/BadFG-like ATPase family that also includes the BcrA/BadF/BzdQ and BcrD/BadG/BzdP proteins, which are subunits of benzoyl-CoA reductase that may be involved in ATP hydrolysis. 259 matched cddid_all.tbl CDD cd24109 cd24109 466959 ASKHA_NBD_YjiL-like nucleotide-binding domain (NBD) of Escherichia coli protein YjiL and similar proteins. The subfamily includes a group of uncharacterized proteins similar to Escherichia coli protein YjiL, which belongs to the BcrAD/BadFG-like ATPase family that also includes the BcrA/BadF/BzdQ and BcrD/BadG/BzdP proteins, which are subunits of benzoyl-CoA reductase that may be involved in ATP hydrolysis. 243 matched cddid_all.tbl CDD cd24110 cd24110 466960 ASKHA_NBD_NTPDase1 nucleotide-binding domain (NBD) of ectonucleoside triphosphate diphosphohydrolase 1 (NTPDase1) and similar proteins. NTPDase1 (EC 3.6.1.5), also called Ecto-ATP diphosphohydrolase 1, Ecto-ATPDase 1, Ecto-ATPase 1, Ecto-apyrase, or lymphoid cell activation antigen CD39, is a known E-type apyrase that could hydrolyze ATP and other nucleotides to regulate purinergic neurotransmission in the nervous system. It could also be implicated in the prevention of platelet aggregation by hydrolyzing platelet-activating ADP to AMP. NTPDase1 hydrolyzes ATP and ADP equally well. In addition, NTPDase1 can also hydrolyze ATP to AMP without the release of ADP. 422 matched cddid_all.tbl CDD cd24111 cd24111 466961 ASKHA_NBD_NTPDase2 nucleotide-binding domain (NBD) of ectonucleoside triphosphate diphosphohydrolase 2 (NTPDase2) and similar proteins. NTPDase2 (EC 3.6.1.-), also called CD39 antigen-like 1 (CD39L1), Ecto-ATP diphosphohydrolase 2 (ENTPD2), Ecto-ATPDase 2, or Ecto-ATPase 2, has E-type ecto-ATPase activity, by hydrolyzing extracellular ATP and other nucleotides to regulate purinergic neurotransmission in the nervous system. It hydrolyzes ADP only to a marginal extent. 418 matched cddid_all.tbl CDD cd24112 cd24112 466962 ASKHA_NBD_NTPDase3 nucleotide-binding domain (NBD) of ectonucleoside triphosphate diphosphohydrolase 3 (NTPDase3) and similar proteins. NTPDase3 (EC 3.6.1.5), also called CD39 antigen-like 3 (CD39L3), Ecto-ATP diphosphohydrolase 3, Ecto-ATPDase 3, Ecto-ATPase 3, Ecto-apyrase 3, or HB6, has a threefold preference for the hydrolysis of ATP over ADP. 411 matched cddid_all.tbl CDD cd24113 cd24113 466963 ASKHA_NBD_NTPDase8 nucleotide-binding domain (NBD) of ectonucleoside triphosphate diphosphohydrolase 8 (NTPDase8) and similar proteins. NTPDase8 (EC 3.6.1.5), also called E-NTPDase 8, or NTPDase 8, is a canalicular ectonucleoside NTPDase responsible for the main hepatic NTPDase activity. Ectonucleoside NTPDases catalyze the hydrolysis of gamma- and beta-phosphate residues of nucleotides, playing a central role in concentration of extracellular nucleotides. NTPDase8 has activity toward ATP, ADP, UTP and UDP, but not toward AMP. 433 matched cddid_all.tbl CDD cd24114 cd24114 466964 ASKHA_NBD_NTPDase5 nucleotide-binding domain (NBD) of ectonucleoside triphosphate diphosphohydrolase 5 (NTPDase5) and similar proteins. NTPDase5 (EC 3.6.1.6), also called nucleoside diphosphate phosphatase ENTPD5, CD39 antigen-like 4 (CD39L4), ER-UDPase, guanosine-diphosphatase ENTPD5, GDPase ENTPD5, inosine diphosphate phosphatase ENTPD5, nucleoside diphosphatase, uridine-diphosphatase ENTPD5, or UDPase ENTPD5, hydrolyzes nucleoside diphosphates with a preference for GDP, IDP and UDP compared to ADP and CDP. 375 matched cddid_all.tbl CDD cd24115 cd24115 466965 ASKHA_NBD_NTPDase6 nucleotide-binding domain (NBD) of ectonucleoside triphosphate diphosphohydrolase 6 (NTPDase6) and similar proteins. NTPDase6 (EC 3.6.1.6), also called CD39 antigen-like 2 (CD39L2), catalyzes the hydrolysis of nucleoside triphosphates and diphosphates in a calcium- or magnesium-dependent manner. It has a strong preference for nucleoside diphosphates, preferentially hydrolyzes GDP, IDP, and UDP, with slower hydrolysis of CDP, ITP, GTP, CTP, ADP, and UTP and virtually no hydrolysis of ATP. The membrane bound form might support glycosylation reactions in the Golgi apparatus and, when released from cells, might catalyze the hydrolysis of extracellular nucleotides. 374 matched cddid_all.tbl CDD cd24116 cd24116 466966 ASKHA_NBD_EcPPX-like nucleotide-binding domain (NBD) of Escherichia coli exopolyphosphatase (EcPPX) and similar proteins. EcPPX (EC 3.6.1.11), also called exopolyPase, or metaphosphatase, mediates the metabolism of cellular inorganic polyphosphate (polyP). It catalyzes degradation of polyP and releases orthophosphate processively from the ends of the polyP chain. It has a strong preference for long-chain polyphosphates and has only weak affinity for smaller size polyP of about 15 residues. Unlike other PPX/GppA family members containing one PPX/GppA homolog, E. coli possesses two homologs, EcGppA and EcPPX, which are indistinguishable in their domain arrangement. 299 matched cddid_all.tbl CDD cd24117 cd24117 466967 ASKHA_NBD_EcGppA-like nucleotide-binding domain (NBD) of Escherichia coli guanosine pentaphosphate phosphohydrolase (EcGppA) and similar proteins. EcGppA (EC 3.6.1.40), also called guanosine-5'-triphosphate,3'-diphosphate pyrophosphatase, or pppGpp-5'-phosphohydrolase, catalyzes the conversion of guanosine pentaphosphate (pppGpp) to guanosine tetraphosphate (ppGpp). pppGpp is a cytoplasmic signaling molecule which together with ppGpp controls the 'stringent response', an adaptive process that allows bacteria to respond to amino acid starvation, resulting in the coordinated regulation of numerous cellular activities. EcGppA also has exopolyphosphatase activity, catalyzing the release of orthophosphate by processive hydrolysis of the phosphoanyhydride bonds of polyphosphate chains. Unlike other PPX/GppA family members containing one PPX/GppA homolog, E. coli possesses two homologs, EcGppA and EcPPX, which are indistinguishable in their domain arrangement. 290 matched cddid_all.tbl CDD cd24118 cd24118 466968 ASKHA_NBD_AaPPX-GppA-like nucleotide-binding domain (NBD) of Aquifex aeolicus exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (AaPPX/GppA) and similar proteins. The PPX/GppA family proteins play essential roles in bacterial survival and metabolism. Guanosine pentaphosphate (pppGpp) phosphohydrolase (GppA; EC 3.6.1.40) plays a key role in (p)ppGpp homeostasis. It specifically catalyzes the conversion of pppGpp to ppGpp (guanosine tetraphosphate). Sharing a similar domain structure, GppA is indistinguishable from exopolyphosphatase (PPX; EC 3.6.1.11), which mediates the metabolism of cellular inorganic polyphosphate. Especially, it is responsible for the maintenance of appropriate levels of cellular inorganic polyphosphate (PolyP). The family corresponds to a group of proteins similar to Aquifex aeolicus PPX/GppA (AaPPX/GppA). AaPPX/GppA is phylogenetically distant from the Escherichia coli homologs. Unlike E. coli that possesses two homologs, EcGppA and EcPPX, A. aeolicus encodes only one PPX/GppA homolog, AaPPX/GppA. As such, AaPPX/GppA may play important roles in the homeostasis of both (p)ppGpp and PolyP. 293 matched cddid_all.tbl CDD cd24119 cd24119 466969 ASKHA_NBD_MtPPX2-like nucleotide-binding domain (NBD) of Mycobacterium tuberculosis exopolyphosphatase 2 (MtPPX2) and similar proteins. The PPX/GppA family proteins play essential roles in bacterial survival and metabolism. Guanosine pentaphosphate (pppGpp) phosphohydrolase (GppA; EC 3.6.1.40) plays a key role in (p)ppGpp homeostasis. It specifically catalyzes the conversion of pppGpp to ppGpp (guanosine tetraphosphate). Sharing a similar domain structure, GppA is indistinguishable from exopolyphosphatase (PPX; EC 3.6.1.11), which mediates the metabolism of cellular inorganic polyphosphate. Especially, it is responsible for the maintenance of appropriate levels of cellular inorganic polyphosphate (PolyP). Mycobacterium tuberculosis encodes two PPX/GppA homologues, Rv0496 (MtPPX1) and Rv1026 (MtPPX2), which are analogous to the Escherichia coli PPX and GppA enzymes. MtPPX1 functions as an exopolyphosphatase, showing a distinct preference for relatively short-chain poly-P substrates. The exopolyphosphatase activities of MtPPX1 are inhibited by pppGpp. In contrast, MtPPX2 has no detectable exopolyphosphatase activities. Neither MtPPX1 nor MtPPX2 can hydrolyze pppGpp to ppGpp, which is a reaction catalyzed by E. coli PPX and GppA enzymes. Both the MtPPX1 and MtPPX2 proteins have modest ATPase and to a lesser extent ADPase activities. The family corresponds a group of proteins similar to MtPPX2. 298 matched cddid_all.tbl CDD cd24120 cd24120 466970 ASKHA_NBD_AroB-like nucleotide-binding domain (NBD) of Fusobacterium nucleatum bifunctional 3-dehydroquinate synthase/phosphatase (AroB) and similar proteins. The family includes a group of PPX/GppA family proteins similar to Fusobacterium nucleatum bifunctional 3-dehydroquinate synthase/phosphatase (AroB; EC 4.2.3.4/EC 3.6.1.-). AroB contains 3-dehydroquinate synthase and an unknown phosphatase. 3-dehydroquinate synthase catalyzes the second step in the shikimate pathway, which is essential to produce aromatic amino acids in bacteria, plants, and fungi, but not mammals. 297 matched cddid_all.tbl CDD cd24121 cd24121 466971 ASKHA_NBD_FGGY_BaEryA-like nucleotide-binding domain (NBD) of Brucella abortus erythritol kinase (BaEryA) and similar proteins. The subfamily contains a group of uncharacterized proteins with similarity to Brucella abortus erythritol kinase (BaEryA; EC 2.7.1.215). It catalyzes the phosphorylation of erythritol to D-erythritol-1-phosphate. Members of this subfamily belong to the FGGY family of carbohydrate kinases, the monomers of which contain two large domains, which are separated by a deep cleft that forms the active site. This model includes both the N-terminal domain, which adopts a ribonuclease H-like fold, and the structurally related C-terminal domain. 452 matched cddid_all.tbl CDD cd24122 cd24122 466972 ASKHA_NBD_PanK-II_Pank1-like nucleotide-binding domain (NBD) of the pantothenate kinase 1 (Pank1)-like subfamily. PanK (EC 2.7.1.33), also called pantothenic acid kinase, is the first enzyme in the Coenzyme A (CoA) biosynthetic pathway. It catalyzes the phosphorylation of pantothenate (vitamin B5) to form 4'-phosphopantothenate at the expense of a molecule of adenosine triphosphate (ATP), which is the rate-limiting step in CoA biosynthesis. It cannot utilize a phosphoryl donor other than ATP. Three distinct types of PanK have been identified, PanK-I, PanK-II and PanK-III. Eukaryotic PanK-II enzymes often occur as different isoforms, such as PanK1, PanK2, PanK3 and PanK4. The Pank1-like subfamily includes PanK1-3. 303 matched cddid_all.tbl CDD cd24123 cd24123 466973 ASKHA_NBD_PanK-II_Pank4 nucleotide-binding domain (NBD) of pantothenate kinase 4 (Pank4) from type II pantothenate kinase (PanK-II) subfamily. PanK (EC 2.7.1.33), also called pantothenic acid kinase, is the first enzyme in the Coenzyme A (CoA) biosynthetic pathway. It catalyzes the phosphorylation of pantothenate (vitamin B5) to form 4'-phosphopantothenate at the expense of a molecule of adenosine triphosphate (ATP), which is the rate-limiting step in CoA biosynthesis. It cannot utilize a phosphoryl donor other than ATP. Three distinct types of PanK have been identified, PanK-I, PanK-II and PanK-III. Eukaryotic PanK-II enzymes often occur as different isoforms, such as PanK1, PanK2, PanK3 and PanK4. The model corresponds to PanK4, which is a putative bifunctional protein with a predicted amino-terminal pantothenate kinase (type II PanK) domain fused to a carboxy-terminal phosphatase domain. PanK4 homologs are found in animals, fungi, and plants. The human PanK4 kinase domain has catalytically-inactivating amino acid substitutions, thus it is characterized as a catalytically inactive pseudoPanK. 339 matched cddid_all.tbl CDD cd24124 cd24124 466974 ASKHA_NBD_HK1_meta_rpt1 nucleotide-binding domain (NBD) of the first repeat of type I hexokinase from metazoan hexokinase (HK) domain family. Hexokinase (EC 2.7.1.1) possesses the ability to transfer an inorganic phosphate group from ATP to a substrate. It catalyzes the ATP-dependent phosphorylation of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). It can catalyze this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways. Hexokinase contains two structurally similar domains. Some members of the family have two copies of each of these domains. For example, members from vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. Both the N- and C-terminal halves bind hexose and H6P. In types I and III only the C-terminal half supports catalysis. Their N-terminal half is the regulatory region. In type II, both halves support catalysis. Type IV hexokinase is similar to the yeast enzyme in containing only the two domains and is sometimes incorrectly referred to as glucokinase. Whereas types I to III can phosphorylate a variety of hexose sugars and are inhibited by glucose-6-phosphate (G6P), type IV is specific for glucose and shows no G6P inhibition. The model corresponds to the first two domains of type I hexokinase. 473 matched cddid_all.tbl CDD cd24125 cd24125 466975 ASKHA_NBD_HK2_meta_rpt1 nucleotide-binding domain (NBD) of the first repeat of type II hexokinase from metazoan hexokinase (HK) domain family. Hexokinase (EC 2.7.1.1) possesses the ability to transfer an inorganic phosphate group from ATP to a substrate. It catalyzes the ATP-dependent phosphorylation of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). It can catalyze this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways. Hexokinase contains two structurally similar domains. Some members of the family have two copies of each of these domains. For example, members from vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. Both the N- and C-terminal halves bind hexose and H6P. In types I and III only the C-terminal half supports catalysis. Their N-terminal half is the regulatory region. In type II, both halves support catalysis. Type IV hexokinase is similar to the yeast enzyme in containing only the two domains and is sometimes incorrectly referred to as glucokinase. Whereas types I to III can phosphorylate a variety of hexose sugars and are inhibited by glucose-6-phosphate (G6P), type IV is specific for glucose and shows no G6P inhibition. The model corresponds to the first two domains of type II hexokinase. 429 matched cddid_all.tbl CDD cd24126 cd24126 466976 ASKHA_NBD_HKDC1_meta_rpt1 nucleotide-binding domain (NBD) of the first repeat of hexokinase domain-containing protein 1 (HKDC1) from metazoan hexokinase (HK) domain family. Hexokinase (EC 2.7.1.1) possesses the ability to transfer an inorganic phosphate group from ATP to a substrate. It catalyzes the ATP-dependent phosphorylation of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). It can catalyze this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways. Hexokinase contains two structurally similar domains. Some members of the family have two copies of each of these domains. For example, members from vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. HKDC1 is a putative novel fifth hexokinase found in vertebrates. It may be involved in whole-body glucose use. The model corresponds to the first two domains of HKDC1. 429 matched cddid_all.tbl CDD cd24127 cd24127 466977 ASKHA_NBD_HK1_meta_rpt2 nucleotide-binding domain (NBD) of the second repeat of type I hexokinase from metazoan hexokinase (HK) domain family. Hexokinase (EC 2.7.1.1) possesses the ability to transfer an inorganic phosphate group from ATP to a substrate. It catalyzes the ATP-dependent phosphorylation of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). It can catalyze this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways. Hexokinase contains two structurally similar domains. Some members of the family have two copies of each of these domains. For example, members from vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. Both the N- and C-terminal halves bind hexose and H6P. In types I and III only the C-terminal half supports catalysis. Their N-terminal half is the regulatory region. In type II, both halves support catalysis. Type IV hexokinase is similar to the yeast enzyme in containing only the two domains and is sometimes incorrectly referred to as glucokinase. Whereas types I to III can phosphorylate a variety of hexose sugars and are inhibited by glucose-6-phosphate (G6P), type IV is specific for glucose and shows no G6P inhibition. The model corresponds to the second two domains of type I hexokinase. 434 matched cddid_all.tbl CDD cd24128 cd24128 466978 ASKHA_NBD_HK2_meta_rpt2 nucleotide-binding domain (NBD) of the second repeat of type II hexokinase from metazoan hexokinase (HK) domain family. Hexokinase (EC 2.7.1.1) possesses the ability to transfer an inorganic phosphate group from ATP to a substrate. It catalyzes the ATP-dependent phosphorylation of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). It can catalyze this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways. Hexokinase contains two structurally similar domains. Some members of the family have two copies of each of these domains. For example, members from vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. Both the N- and C-terminal halves bind hexose and H6P. In types I and III only the C-terminal half supports catalysis. Their N-terminal half is the regulatory region. In type II, both halves support catalysis. Type IV hexokinase is similar to the yeast enzyme in containing only the two domains and is sometimes incorrectly referred to as glucokinase. Whereas types I to III can phosphorylate a variety of hexose sugars and are inhibited by glucose-6-phosphate (G6P), type IV is specific for glucose and shows no G6P inhibition. The model corresponds to the second two domains of type II hexokinase. 435 matched cddid_all.tbl CDD cd24129 cd24129 466979 ASKHA_NBD_HK3_meta_rpt2 nucleotide-binding domain (NBD) of the second repeat of type III hexokinase from metazoan hexokinase (HK) domain family. Hexokinase (EC 2.7.1.1) possesses the ability to transfer an inorganic phosphate group from ATP to a substrate. It catalyzes the ATP-dependent phosphorylation of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). It can catalyze this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways. Hexokinase contains two structurally similar domains. Some members of the family have two copies of each of these domains. For example, members from vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. Both the N- and C-terminal halves bind hexose and H6P. In types I and III only the C-terminal half supports catalysis. Their N-terminal half is the regulatory region. In type II, both halves support catalysis. Type IV hexokinase is similar to the yeast enzyme in containing only the two domains and is sometimes incorrectly referred to as glucokinase. Whereas types I to III can phosphorylate a variety of hexose sugars and are inhibited by glucose-6-phosphate (G6P), type IV is specific for glucose and shows no G6P inhibition. The model corresponds to the second two domains of type III hexokinase. 430 matched cddid_all.tbl CDD cd24130 cd24130 466980 ASKHA_NBD_HKDC1_meta_rpt2 nucleotide-binding domain (NBD) of the second repeat of hexokinase domain-containing protein 1 (HKDC1) from metazoan hexokinase (HK) domain family. Hexokinase (EC 2.7.1.1) possesses the ability to transfer an inorganic phosphate group from ATP to a substrate. It catalyzes the ATP-dependent phosphorylation of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). It can catalyze this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways. Hexokinase contains two structurally similar domains. Some members of the family have two copies of each of these domains. For example, members from vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. HKDC1 is a putative novel fifth hexokinase found in vertebrates. It may be involved in whole-body glucose use. The model corresponds to the second two domains of HKDC1. 433 matched cddid_all.tbl CDD cd24131 cd24131 466981 ASKHA_NBD_Kae1_arch_bac nucleotide-binding domain (NBD) of tRNA N6-adenosine threonylcarbamoyltransferase (Kae1) and similar proteins mainly from archaea and bacteria. Kae1 (EC 2.3.1.234), also called N6-L-threonylcarbamoyladenine synthase, t(6)A synthase, t(6)A37 threonylcarbamoyladenosine biosynthesis protein Kae1, or tRNA threonylcarbamoyladenosine biosynthesis protein Kae1, is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. It is a component of the KEOPS complex that is probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37. Kae1 likely plays a direct catalytic role in this reaction but requires other protein(s) of the complex to fulfill this activity. The family also includes bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein (EC 2.3.1.234/EC 2.7.11.1), which contains a Kae1 domain and a Bud32 domain. The Kae1 domain may play a catalytic role and the Bud32 domain probably displays kinase activity that regulates Kae1 function. 323 matched cddid_all.tbl CDD cd24132 cd24132 466982 ASKHA_NBD_OSGEP_like_euk nucleotide-binding domain (NBD) of O-sialoglycoprotein endopeptidase (OSGEP) and similar proteins mainly from eukaryotes. OSGEP (EC 2.3.1.234), also called tRNA N6-adenosine threonylcarbamoyltransferase, N6-L-threonylcarbamoyladenine synthase, t(6)A synthase, t(6)A37 threonylcarbamoyladenosine biosynthesis protein OSGEP, tRNA threonylcarbamoyladenosine biosynthesis protein OSGEP, is a component of the EKC/KEOPS complex that is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. The complex is probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37. OSGEP likely plays a direct catalytic role in this reaction but requires other protein(s) of the complex to fulfill this activity. OSGEP is the mammalian orthologue of kinase-associated endopeptidase Kae1. 309 matched cddid_all.tbl CDD cd24133 cd24133 466983 ASKHA_NBD_TsaD_bac nucleotide-binding domain (NBD) of bacterial tRNA N6-adenosine threonylcarbamoyltransferase TsaD and similar proteins. TsaD (EC 2.3.1.234), also called N6-L-threonylcarbamoyladenine synthase, t(6)A synthase, t(6)A37 threonylcarbamoyladenosine biosynthesis protein TsaD, or tRNA threonylcarbamoyladenosine biosynthesis protein TsaD, is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. It is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction. 328 matched cddid_all.tbl CDD cd24134 cd24134 466984 ASKHA_NBD_OSGEPL1_QRI7_euk nucleotide-binding domain (NBD) of O-sialoglycoprotein endopeptidase-like protein 1 (OSGEPL1) and similar proteins from eukayotes. The family includes mammalian OSGEPL1 and yeast QRI7, which are the mitochondrial orthologs of the universal Kae1/ TsaD (also known as YgjD) protein. OSGEPL1/QRI7 (EC 2.3.1.234), also called mitochondrial tRNA N6-adenosine threonylcarbamoyltransferase, N6-L-threonylcarbamoyladenine synthase, t(6)A synthase, t(6)A37 threonylcarbamoyladenosine biosynthesis protein, or tRNA threonylcarbamoyladenosine biosynthesis protein, is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in mitochondrial tRNAs that read codons beginning with adenine. It is probably involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37. It is involved in mitochondrial genome maintenance. 330 matched cddid_all.tbl CDD cd24135 cd24135 466985 ASKHA_NBD_PanK-II_Pank1 nucleotide-binding domain (NBD) of pantothenate kinase 1 (Pank1) from type II pantothenate kinase (PanK-II) subfamily. PanK (EC 2.7.1.33), also called pantothenic acid kinase, is the first enzyme in the Coenzyme A (CoA) biosynthetic pathway. It catalyzes the phosphorylation of pantothenate (vitamin B5) to form 4'-phosphopantothenate at the expense of a molecule of adenosine triphosphate (ATP), which is the rate-limiting step in CoA biosynthesis. It cannot utilize a phosphoryl donor other than ATP. Three distinct types of PanK have been identified, PanK-I, PanK-II and PanK-III. Eukaryotic PanK-II enzymes often occur as different isoforms, such as PanK1, PanK2, PanK3 and PanK4. The model corresponds to PanK1. 352 matched cddid_all.tbl CDD cd24136 cd24136 466986 ASKHA_NBD_PanK-II_Pank2 nucleotide-binding domain (NBD) of pantothenate kinase 2 (Pank2) from type II pantothenate kinase (PanK-II) subfamily. PanK (EC 2.7.1.33), also called pantothenic acid kinase, is the first enzyme in the Coenzyme A (CoA) biosynthetic pathway. It catalyzes the phosphorylation of pantothenate (vitamin B5) to form 4'-phosphopantothenate at the expense of a molecule of adenosine triphosphate (ATP), which is the rate-limiting step in CoA biosynthesis. It cannot utilize a phosphoryl donor other than ATP. Three distinct types of PanK have been identified, PanK-I, PanK-II and PanK-III. Eukaryotic PanK-II enzymes often occur as different isoforms, such as PanK1, PanK2, PanK3 and PanK4. The model corresponds to PanK2. 354 matched cddid_all.tbl CDD cd24137 cd24137 466987 ASKHA_NBD_PanK-II_Pank3 nucleotide-binding domain (NBD) of pantothenate kinase 3 (Pank3) from type II pantothenate kinase (PanK-II) subfamily. PanK (EC 2.7.1.33), also called pantothenic acid kinase, is the first enzyme in the Coenzyme A (CoA) biosynthetic pathway. It catalyzes the phosphorylation of pantothenate (vitamin B5) to form 4'-phosphopantothenate at the expense of a molecule of adenosine triphosphate (ATP), which is the rate-limiting step in CoA biosynthesis. It cannot utilize a phosphoryl donor other than ATP. Three distinct types of PanK have been identified, PanK-I, PanK-II and PanK-III. Eukaryotic PanK-II enzymes often occur as different isoforms, such as PanK1, PanK2, PanK3 and PanK4. The model corresponds to PanK3. 353 matched cddid_all.tbl CDD cd24138 cd24138 467514 TtcA-like tRNA-cytidine(32) 2-sulfurtransferase and similar proteins. tRNA-cytidine(32) 2-sulfurtransferase, also called two-thiocytidine biosynthesis protein A or tRNA 2-thiocytidine biosynthesis protein TtcA, catalyzes the ATP-dependent 2-thiolation of cytidine in position 32 of tRNA, to form 2-thiocytidine (s(2)C32). TtcA belongs to the adenine nucleotide alpha hydrolase superfamily (AANH) that includes N-type ATP PPases and ATP sulfurylases. It forms an alpha/beta/alpha fold which binds to the adenosine group. This domain has a strongly conserved motif SGGKD at the N-terminus. 187 matched cddid_all.tbl CDD cd24139 cd24139 467940 SIP5-like SNF1-interacting protein 5 and similar proteins. Sip5 plays a role in the regulation of SNF1 kinase. It may negatively regulate SNF1 kinase under glucose-limiting conditions, by promoting the interaction of the REG1/GLC7 phosphatase complex with the kinase. It interacts directly with SNF1 kinase and the Reg1 component of the phosphatase complex. Sip5 also physically interacts with the N-terminus of Std1, an accessory subunit of the SNF1 kinase protein complex, in the absence of glucose. This prevents aggregation of Std1 and keeps it bound to SNF1, the catalytic subunit, keeping the SNF1 complex in an active state. Upon addition of glucose, Vhs1 kinase phosphorylates Sip5, inhibiting its binding to Std1. Once Sip5 is released, the N-terminal asparagine-rich part of Std1 aggregates, and Std1 exits the nucleus and localizes to cytoplasmic granules. SNF1 kinase is inactive in this state. 200 matched cddid_all.tbl CDD cd24140 cd24140 467812 Prp3_C-like C-terminal domain of Prp3 and related proteins. This group contains the C-terminal domains of Prp3 and RWD domain-containing proteins 2/3. Predicted structures (by AlphaFold) of the C-terminal domains of RWDD2 and RWDD3 reveal similarity to the C-terminal domain of Prp3, an essential U4/U6 di-snRNP-associated protein which plays a role in pre-mRNA splicing. The Prp3 C-terminal domain is a single-stranded RNA-binding domain. 117 matched cddid_all.tbl CDD cd24141 cd24141 467941 NDUFS5-like mitochondrial complex I subunit NDUFS5 and similar proteins. Ndufs5 (NADH dehydrogenase [ubiquinone] iron-sulfur protein 5) is an accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I). Complex I is a 45-subunit complex that functions in the transfer of electrons from NADH to the respiratory chain. It plays a key role in cellular energy metabolism, generating a major portion of the proton motive force that drives aerobic ATP synthesis. Ndufs5 is a component of the iron-sulfur (IP) subcomplex and does not seem to be involved in catalysis. 66 matched cddid_all.tbl CDD cd24142 cd24142 467942 ACL4-like Assembly chaperone of ribosomal protein L4 and similar proteins. Assembly chaperone of RPL4 (ACL4) acts as a chaperone for the L4 ribosomal subunit, encoded by RPL4A and RPL4B, and is required for hierarchical ribosome assembly. It is required for the soluble expression of newly synthesized RPL4 and for the protection of RPL4 from the Tom1-dependent cellular degradation machinery. ACL4 shields ribosomal protein L4 until timely release and insertion into the pre-ribosome is possible, once ribosomal protein L18 is present. 306 matched cddid_all.tbl CDD cd24143 cd24143 467943 LIP1-like ceramide synthase subunit LIP1 and similar proteins. Lip1 (or Lip1p) is an essential regulatory subunit of ceramide synthase (CerS), a multicomponent enzyme complex that also contains two catalytic subunits, Lag1 and Lac1. CerS catalyzes the synthesis of ceramides, which play a crucial role as basic building blocks of sphingolipids and as signalling molecules mediating the fate of the cell. Lip1 comprises a single-span ER membrane protein and its essential function is contained in the transmembrane or luminal part of the protein. 133 matched cddid_all.tbl CDD cd24144 cd24144 467944 BLOC1_CNL1 Biogenesis of lysosome-related organelles complex 1 subunit CNL1. Biogenesis of lysosome-related organelles complex 1 (BLOC-1) subunit CNL1, also called CNO-like protein 1, is part of a complex that is involved in endosomal cargo sorting. BLOC-1 is an endosomal Rab-GAP (GTPase-activating protein) adapter complex that is composed of at least BLI1, BLS1, CNL1, KXD1, SNN1 and VAB2. Saccharomyces cerevisiae CLN1 is believed to be the homolog to the cappuccino (cno) subunit of the BLOC-1 complex in higher eukaryotes. 87 matched cddid_all.tbl CDD cd24145 cd24145 467945 Mgr3-like Mitochondrial inner membrane i-AAA protease supercomplex subunit Mgr3 and similar proteins. Mgr3 (also called mitochondrial genome-required protein 3) is a component of the mitochondrial inner membrane i-AAA protease supercomplex, which degrades misfolded mitochondrial proteins. The supercomplex is composed of Mgr1, Mgr3, and Yme1. Mgr3, together with Mgr1, functions in an adapter complex that targets substrates to the i-AAA protease for degradation. 307 matched cddid_all.tbl CDD cd24146 cd24146 467616 nat-AmDH_N_like N-terminal NAD(P)-binding domain of native NAD(P)H-dependent amine dehydrogenases (nat-AmDHs) and similar proteins. The family corresponds to a group of native NAD(P)H-dependent amine dehydrogenases (nat-AmDHs) that catalyze the reductive amination of ketone and aldehyde substrates using NAD(P)H as the hydride source. nat-AmDHs can naturally catalyze the amination of 'neutral' carbonyl compounds using ammonia. They possess tremendous potential for the efficient asymmetric synthesis of alpha-chiral amines. The family also contains 2,4-diaminopentanoate dehydrogenase (DAPDH) and similar proteins. DAPDH, also known as ORD, is involved in the ornithine fermentation pathway. It catalyzes the oxidative deamination of (2R,4S)-2,4-diaminopentanoate ((2R,4S)-DAP) to yield 2-amino-4-ketopentanoate (AKP). Although DAPDH is more efficient with (2R,4S)-DAP, the diastereoisomer (2R,4R)-DAP can also be metabolized. Different forms of DAPDH exist which utilize NAD(+) (EC 1.4.1.26) or NAD(+)/NADP(+) (EC 1.4.1.12). Members of this family contain an N-terminal Rossmann fold NAD(P)-binding domain and a C-terminal dimerization domain. 157 matched cddid_all.tbl CDD cd24147 cd24147 467523 ASADH_N_like N-terminal NAD(P)-binding domain of aspartate beta-semialdehyde dehydrogenase (ASADH), USG-1 protein and similar proteins. The family includes aspartate beta-semialdehyde dehydrogenase (ASADH), NADP-dependent malonyl-CoA reductase (MCR), and USG-1 protein. They contain an N-terminal Rossmann fold NAD(P) binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like domain and are members of the GAPDH superfamily of proteins. ASADH (EC 1.2.1.11), also called ASA dehydrogenase (ASD), or aspartate-beta-semialdehyde dehydrogenase, catalyzes the NADPH-dependent formation of L-aspartate-semialdehyde (ASA) by the reductive dephosphorylation of L-aspartyl-4-phosphate, which is the second step of the aspartate biosynthetic pathway. ASA can either be further reduced to homoserine, which leads to methionine, threonine, or isoleucine, or it can be condensed with pyruvate and cyclized into dihydrodipicolinate, and then converted into diaminopimelate, a component of bacterial cell walls, and finally decarboxylated to produce lysine. NADP-dependent MCR (EC 1.2.1.75) is mainly found in Archaea. It catalyzes the reduction of malonyl-CoA to malonate semialdehyde, a key step in the 3-hydroxypropanoate and the 3-hydroxypropanoate/4-hydroxybutyrate cycles. It can also use succinyl-CoA and succinate semialdehyde as substrates but at a lower rate than malonyl-CoA. Sequence comparison suggests that the archaeal MCR gene (mcr) has evolved from the duplication of a common ancestral ASADH gene (asd). The biological function of USG-1 protein and homologs remains unclear. They are homologs to ASADH but lack the conserved active site residues of the ASADH protein C-terminal catalytic domain. 142 matched cddid_all.tbl CDD cd24148 cd24148 467524 AGPR_1_actinobacAGPR_like N-terminal NAD(P)-binding domain of actinobacterial N-acetyl-gamma-glutamyl-phosphate reductase (actinobacAGPR) and similar proteins. AGPR (EC 1.2.1.38), also called N-acetyl-glutamate semialdehyde dehydrogenase, or NAGSA dehydrogenase, catalyzes the third step in the biosynthesis of arginine from glutamate, the NADPH-dependent reduction of N-acetyl-5-glutamyl phosphate into N-acetylglutamate 5-semialdehyde. In bacteria it is a monofunctional protein of 35 to 38kDa (gene argC). There are two related families (type 1 and type 2) of N-acetyl-gamma-glutamyl-phosphate reductase, which differ by phylogeny, similarity clustering, and gap architecture in a multiple sequence alignment. The family includes N-acetyl-gamma-glutamyl-phosphate reductases mainly from actinobacteria. They belong to the type 1 AGPR family. Members in this family contain an N-terminal Rossmann fold NAD(P)-binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like domain. 164 matched cddid_all.tbl CDD cd24149 cd24149 467525 AGPR_N_ARG5_6_like N-terminal NAD(P)-binding domain (AGPR region) of fungal bifunctional mitochondrial enzyme (gene ARG5,6, arg11 or arg-6) and similar proteins. The family includes bifunctional mitochondrial enzyme (gene ARG5,6, arg11 or arg-6) from fungi, which contains a N-terminal acetylglutamate kinase ( EC 2.7.2.8, also known as N-acetyl-L-glutamate 5-phosphotransferase/NAG kinase/AGK) domain and a C-terminal N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38, also known as AGPR/N-acetyl-glutamate semialdehyde dehydrogenase/NAGSA dehydrogenase) domain. The model corresponds to the AGPR N-terminal NAD(P)-binding domain. AGPR catalyzes the third step in the biosynthesis of arginine from glutamate, the NADP-dependent reduction of N-acetyl-5-glutamyl phosphate into N-acetylglutamate 5-semialdehyde. The budding yeast member, Arg5,6, is expressed as a precursor that is then maturated in the mitochondria into acetylglutamate kinase and acetylglutamyl-phosphate reductase. It is involved in the arginine biosynthesis pathway, catalyzing the second and third steps in the pathway. 154 matched cddid_all.tbl CDD cd24150 cd24150 467526 ASADH_MCR_N N-terminal NAD(P)-binding domain of archaeal NADP-dependent malonyl-CoA reductase (MCR) and similar proteins. Archaeal NADP-dependent MCR (EC 1.2.1.75) catalyzes the reduction of malonyl-CoA to malonate semialdehyde, a key step in the 3-hydroxypropanoate and the 3-hydroxypropanoate/4-hydroxybutyrate cycles. It can also use succinyl-CoA and succinate semialdehyde as substrates but at a lower rate than malonyl-CoA. Sequence comparison suggests that the archaeal malonyl-CoA reductase gene (mcr) has evolved from the duplication of a common ancestral aspartate beta-semialdehyde dehydrogenase (ASADH) gene (asd). MCR contains an N-terminal Rossmann fold NAD(P) binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like catalytic domain. 163 matched cddid_all.tbl CDD cd24151 cd24151 467527 AGPR_1_N_LysY N-terminal NAD(P)-binding domain of [LysW]-L-2-aminoadipate/[LysW]-L-glutamate phosphate reductase (LysY) and similar proteins. LysY (EC 1.2.1.103/EC 1.2.1.106) is involved in both the arginine and lysine biosynthetic pathways. LysY interacts with LysW. It may form a ternary complex with LysW and LysZ. Several bacteria and archaea utilize the amino group-carrier protein, LysW, for lysine biosynthesis from alpha-aminoadipate (AAA). In some cases, such as Sulfolobus, LysW is also used to protect the amino group of glutamate in arginine biosynthesis. After LysW modification, AAA and glutamate are converted to lysine and ornithine, respectively, by a single set of enzymes with dual functions. LysY is the third enzyme in lysine biosynthesis from AAA. LysY shows high sequence identity and functional similarities with ArgC, and they are considered to have evolved from a common ancestor. Members in this subfamily belong to the type 1 AGPR family. They contain an N-terminal Rossmann fold NAD(P)-binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like domain. 170 matched cddid_all.tbl CDD cd24152 cd24152 466988 ASKHA_NBD_ROK-like nucleotide-binding domain (NBD) of an uncharacterized subgroup of the ROK family. This subfamily is composed of uncharacterized proteins belonging to the the kinase (ROK) family, a group of proteins that have sugar kinase and/or transcriptional repressor activities. Members of this subfamily lack the cysteine-rich zinc-binding motif, which presents in other ROK families. 286 matched cddid_all.tbl CDD cd24153 cd24153 467946 SARM1_N N-terminal ARM-repeat domain of SARM1 (sterile alpha and TIR motif containing 1). The nicotinamide adenine dinucleotidase SARM1 (sterile alpha and TIR motif containing 1) is involved in TLR (Toll-like receptor) signaling. It is responsible for targeted localization of the whole protein to post-synaptic regions of axons and plays a role in axon degeneration and therefore in several neurodegenerative conditions. Its NADase activity depletes the key cellular metabolite, NAD+, in response to nerve injury. SARM1 forms a homo-octamer, which avoids premature activation via a packed conformation that prevents dimerization and activation of the catalytic domains. The inactive conformation is stabilized by binding of the substrate NAD+ in an allosteric location distinct from the catalytic sites. This model characterizes the armadillo (ARM) repeat-containing N-terminal domain of SARM1. 308 matched cddid_all.tbl CDD cd24154 cd24154 467602 NUDIX_DR0079 "NUDIX domain family found in Deinococcus radiodurans, and similar proteins. Deinococcus radiodurans protein DR_0079 is one of 21 NUDIX hydrolases that it encodes, and it has been observed to have a marked preference for cytosine ribonucleoside 5'-diphosphate (CDP) and cytosine ribonucleoside 5'-triphosphate (CTP), and for their corresponding deoxyribose nucleotides, dCDP and dCTP, to a lesser degree. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & ""house-cleaning"" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required." 121 matched cddid_all.tbl CDD cd24155 cd24155 467603 NUDIX_ADPRase Adp Ribose Pyrophosphatase. ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. In humans, there are four distinct ADPRase activities, three putative cytosolic enzymes (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). Human ADPRase-II is also referred to as NUDT5. It lacks the N-terminal target sequence unique to mitochondrial ADPRase. The different cytosolic types are distinguished by their specificities for substrate and specific requirement for metal ions. NUDT5 forms a homodimer. It also contains a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the NUDIX motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. UDP-glucose pyrophosphatase (UGPPase) (EC 3.6.1.45; also known as nucleoside diphosphate-linked moiety X)) motif 14; Nudt14) hydrolyzes the pyrophosphate of the nucleoside diphosphate sugar to generate glucose-1-P and UMP. In mammals, UDP-glucose is the glucosyl donor for the synthesis of the storage polysaccharide glycogen. UGPPase, as a regulator of UDP-glucose, could play a regulatory role, but it has been shown to prefer ADP-ribose over UDP-glucose. Like other members of the NUDIX hydrolase superfamily, it requires a divalent cation, such as Mg2+, for its activity. It also contains a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. 187 matched cddid_all.tbl CDD cd24156 cd24156 467604 NUDIX_ADPRase_NudE "NUDIX domain family NudE found in Escherichia coli, and similar proteins. The adenosine nucleotide hydrolase NudE protein in Escherichia coli is a NUDIX hydrolase family member active against ADP ribose, NADH, AP2A and AP3A33, and is classified as a hydrolase (E.C. 3.6.1.-) based on gene annotations. It is an ADPRase (EC 3.6.1.13) catalyzes the hydrolysis of ADP-ribose to AMP and ribose-5-P. Like other members of the NUDIX hydrolase superfamily of enzymes, it is thought to require a divalent cation, such as Mg2+, for its activity. It also contains a 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the NUDIX motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & ""house-cleaning"" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required." 134 matched cddid_all.tbl CDD cd24157 cd24157 467605 NUDIX_GDPMK "GDP-mannose hydrolase (GDPMK), and similar proteins. GDP-mannose hydrolase (GDPMK) is a NUDIX enzyme that uses GDP-mannose as the preferred substrate. It is distinct from Nudix ADP-ribose hydrolases. GDPMK and ADP-ribose pyrophosphatase seem to use similar catalytic mechanism. However, GDPMK hydrolysis does not rely on a single glutamate as the catalytic base; rather, it is dependent on residues that coordinate the magnesium ions and residues that position the substrate properly for catalysis. Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & ""house-cleaning"" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required." 146 matched cddid_all.tbl CDD cd24158 cd24158 467606 NUDIX_ADPRase_Rv1700 ADP-ribose pyrophosphatase from Mycobacterium tuberculosis (Mt-ADPRase), and similar proteins. Mycobacterium tuberculosis ADP-ribose pyrophosphatase mt-ADPRase(also called Rv1700) is a NUDIX protein that catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. In humans, there are four distinct ADPRase activities, three putative cytosolic enzymes (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). Human ADPRase-II is also referred to as NUDT5. It lacks the N-terminal target sequence unique to mitochondrial ADPRase. The different cytosolic types are distinguished by their specificities for substrate and specific requirement for metal ions. NUDT5 forms a homodimer. It also contains a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the NUDIX motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. UDP-glucose pyrophosphatase (UGPPase) (EC 3.6.1.45; also known as nucleoside diphosphate-linked moiety X)) motif 14; Nudt14) hydrolyzes the pyrophosphate of the nucleoside diphosphate sugar to generate glucose-1-P and UMP. In mammals, UDP-glucose is the glucosyl donor for the synthesis of the storage polysaccharide glycogen. UGPPase, as a regulator of UDP-glucose, could play a regulatory role, but it has been shown to prefer ADP-ribose over UDP-glucose. Like other members of the NUDIX hydrolase superfamily, it requires a divalent cation, such as Mg2+, for its activity. It also contains a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. 174 matched cddid_all.tbl CDD cd24159 cd24159 467607 NUDIX_ADPRase_NudF Bdellovibrio Bacteriovorus nucleoside diphosphate sugar hydrolase, and similar proteins. Bdellovibrio bacteriovorus nucleoside diphosphate sugar (NDPS) hydrolase Bd3179 has been shown to similarities to the Escherichia coli adenosine diphosphate ribose (ADPR) hydrolase and the guanosine diphosphate mannose (GDPM) hydrolase. It may have a role when Bdellovibrio degrades and metabolizes host cell. ADP-ribose pyrophosphatase (ADPRase) catalyzes the hydrolysis of ADP-ribose and a variety of additional ADP-sugar conjugates to AMP and ribose-5-phosphate. In humans, there are four distinct ADPRase activities, three putative cytosolic enzymes (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). Human ADPRase-II is also referred to as NUDT5. It lacks the N-terminal target sequence unique to mitochondrial ADPRase. The different cytosolic types are distinguished by their specificities for substrate and specific requirement for metal ions. NUDT5 forms a homodimer. It also contains a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the NUDIX motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. UDP-glucose pyrophosphatase (UGPPase) (EC 3.6.1.45; also known as nucleoside diphosphate-linked moiety X)) motif 14; Nudt14) hydrolyzes the pyrophosphate of the nucleoside diphosphate sugar to generate glucose-1-P and UMP. In mammals, UDP-glucose is the glucosyl donor for the synthesis of the storage polysaccharide glycogen. UGPPase, as a regulator of UDP-glucose, could play a regulatory role, but it has been shown to prefer ADP-ribose over UDP-glucose. Like other members of the NUDIX hydrolase superfamily, it requires a divalent cation, such as Mg2+, for its activity. It also contains a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. 173 matched cddid_all.tbl CDD cd24160 cd24160 467608 NUDIX_ADPRase Adp-ribose pyrophosphatase (ADPRase) found in Thermus thermophilus, and similar proteins. ADP-ribose pyrophosphatase (ADPRase) such as found in extreme thermophile Thermus thermophilus (TtADPRase) catalyzes the hydrolysis of ADPR to AMP and ribose 5'-phosphate in the presence of Mg2+ and Zn2+ ions. In humans, there are four distinct ADPRase activities, three putative cytosolic enzymes (ADPRase-I, -II, and -Mn) and a single mitochondrial enzyme (ADPRase-m). Human ADPRase-II is also referred to as NUDT5. It lacks the N-terminal target sequence unique to mitochondrial ADPRase. The different cytosolic types are distinguished by their specificities for substrate and specific requirement for metal ions. NUDT5 forms a homodimer. It also contains a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the NUDIX motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity. UDP-glucose pyrophosphatase (UGPPase) (EC 3.6.1.45; also known as nucleoside diphosphate-linked moiety X)) motif 14; Nudt14) hydrolyzes the pyrophosphate of the nucleoside diphosphate sugar to generate glucose-1-P and UMP. In mammals, UDP-glucose is the glucosyl donor for the synthesis of the storage polysaccharide glycogen. UGPPase, as a regulator of UDP-glucose, could play a regulatory role, but it has been shown to prefer ADP-ribose over UDP-glucose. Like other members of the NUDIX hydrolase superfamily, it requires a divalent cation, such as Mg2+, for its activity. It also contains a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. 151 matched cddid_all.tbl CDD cd24161 cd24161 467609 NUDIX_ADPRase_Ndx2 "NUDIX family Ndx2. NUDIX family protein Ndx2 found in Thermus thermophilus has ADP-ribose pyrophosphatase (ADPRase) as well as flavin adenine dinucleotide (FAD) activity. ADPRase (EC 3.6.1.13) catalyzes the hydrolysis of ADP-ribose to AMP and ribose-5-P. Like other members of the NUDIX hydrolase superfamily of enzymes, it is thought to require a divalent cation, such as Mg2+, for its activity. It also contains a 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V) which functions as a metal binding site/catalytic site. In addition to the NUDIX motif, there are additional conserved amino acid residues, distal from the signature sequence, that correlate with substrate specificity.Members of the NUDIX hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue NUDIX motif (GX5EX7REUXEEXGU, where U = I, L or V), which functions as a metal binding and catalytic site. Substrates of NUDIX hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the NUDIX hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & ""house-cleaning"" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specificity are determined by the N-terminal extension or by residues in variable loop regions. Mechanistically, substrate hydrolysis occurs by a nucleophilic substitution reaction, with variation in the numbers and roles of divalent cations required." 137 matched cddid_all.tbl CDD cd24162 cd24162 467813 Prp3_C C-terminal domain of U4/U6 small nuclear ribonucleoprotein Prp3. Prp3 is an essential U4/U6 di-snRNP-associated protein which plays a role in pre-mRNA splicing. It may be involved in U4/U6 reassembly after splicing. The C-terminal domain of Prp3 is a single-stranded RNA-binding domain. 122 matched cddid_all.tbl CDD cd24163 cd24163 467814 RWDD2_C C-terminal domain of RWD domain-containing protein 2. RWDD2A, as well as RWDD2B, are small proteins that contain an N-terminal RWD domain and a C-terminal domain of unknown function. The C-terminal domain is predicted (by AlphaFold) to adopt a fold similar to the C-terminal domain of Prp3, an essential U4/U6 di-snRNP-associated protein which plays a role in pre-mRNA splicing. The Prp3 C-terminal domain is a single-stranded RNA-binding domain. 122 matched cddid_all.tbl CDD cd24164 cd24164 467815 RWDD3_C RWD domain-containing protein 3, C-terminal domain. RWDD3, also called RSUME, is a small protein containing an N-terminal RWD domain and a C-terminal domain of unknown function. RWDD3 acts by modulating post-translational modification (PTM) of proteins, and it also plays a role in tumorigenesis. The C-terminal domain is predicted (by AlphaFold) to adopt a fold similar to the C-terminal domain of Prp3, an essential U4/U6 di-snRNP-associated protein which plays a role in pre-mRNA splicing. The Prp3 C-terminal domain is a single-stranded RNA-binding domain. 110 matched cddid_all.tbl CDD cd24165 cd24165 467947 TfSGL-like endo-beta-1,2-glucanase. Endo-beta-1,2-Glucanase (SGL) is an enzyme that hydrolyzes beta-1,2-glucans. SGLs play an important role in some bacteria, but this model represents a group of eukaryotic SGLs, first identified and characterized in Talaromyces funiculosus (TfSGL), a soil fungus. TfSGL hydrolyzes reducing-end-modified beta-1,2-gluco-oligosaccharides to release a sophoroside with the modified moiety. This group is classified into a new family of glycoside hydrolases, GH162. 476 matched cddid_all.tbl CDD pfam00001 pfam00001 459624 7tm_1 7 transmembrane receptor (rhodopsin family). This family contains, amongst other G-protein-coupled receptors (GCPRs), members of the opsin family, which have been considered to be typical members of the rhodopsin superfamily. They share several motifs, mainly the seven transmembrane helices, GCPRs of the rhodopsin superfamily. All opsins bind a chromophore, such as 11-cis-retinal. The function of most opsins other than the photoisomerases is split into two steps: light absorption and G-protein activation. Photoisomerases, on the other hand, are not coupled to G-proteins - they are thought to generate and supply the chromophore that is used by visual opsins. 256 matched cddid_all.tbl CDD pfam00002 pfam00002 459625 7tm_2 7 transmembrane receptor (Secretin family). This family is known as Family B, the secretin-receptor family or family 2 of the G-protein-coupled receptors (GCPRs). They have been described in many animal species, but not in plants, fungi or prokaryotes. Three distinct sub-families are recognized. Subfamily B1 contains classical hormone receptors, such as receptors for secretin and glucagon, that are all involved in cAMP-mediated signalling pathways. Subfamily B2 contains receptors with long extracellular N-termini, such as the leukocyte cell-surface antigen CD97; calcium-independent receptors for latrotoxin, and brain-specific angiogenesis inhibitors amongst others. Subfamily B3 includes Methuselah and other Drosophila proteins. Other than the typical seven-transmembrane region, characteriztic structural features include an amino-terminal extracellular domain involved in ligand binding, and an intracellular loop (IC3) required for specific G-protein coupling. 248 matched cddid_all.tbl CDD pfam00003 pfam00003 459626 7tm_3 7 transmembrane sweet-taste receptor of 3 GCPR. This is a domain of seven transmembrane regions that forms the C-terminus of some subclass 3 G-coupled-protein receptors. It is often associated with a downstream cysteine-rich linker domain, NCD3G pfam07562, which is the human sweet-taste receptor, and the N-terminal domain, ANF_receptor pfam01094. The seven TM regions assemble in such a way as to produce a docking pocket into which such molecules as cyclamate and lactisole have been found to bind and consequently confer the taste of sweetness. 247 matched cddid_all.tbl CDD pfam00004 pfam00004 459627 AAA ATPase family associated with various cellular activities (AAA). AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes. 130 matched cddid_all.tbl CDD pfam00005 pfam00005 394964 ABC_tran ABC transporter. ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain pfam00664. These four domains may belong to a single polypeptide or belong in different polypeptide chains. 150 matched cddid_all.tbl CDD pfam00006 pfam00006 425417 ATP-synt_ab ATP synthase alpha/beta family, nucleotide-binding domain. This entry includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho. 212 matched cddid_all.tbl CDD pfam00007 pfam00007 394966 Cys_knot Cystine-knot domain. The family comprises glycoprotein hormones and the C-terminal domain of various extracellular proteins. It is believed to be involved in disulfide-linked dimerization. 105 matched cddid_all.tbl CDD pfam00008 pfam00008 394967 EGF EGF-like domain. There is no clear separation between noise and signal. pfam00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between swiss-prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains. 31 matched cddid_all.tbl CDD pfam00009 pfam00009 425418 GTP_EFTU Elongation factor Tu GTP binding domain. This domain contains a P-loop motif, also found in several other families such as pfam00071, pfam00025 and pfam00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains. 187 matched cddid_all.tbl CDD pfam00010 pfam00010 459628 HLH Helix-loop-helix DNA-binding domain. 53 matched cddid_all.tbl CDD pfam00011 pfam00011 459629 HSP20 Hsp20/alpha crystallin family. Not only do small heat-shock-proteins occur in eukaryotes and prokaryotes but they have also now been shown to occur in cyanobacterial phages as well as their bacterial hosts. 100 matched cddid_all.tbl CDD pfam00012 pfam00012 394970 HSP70 Hsp70 protein. Hsp70 chaperones help to fold many proteins. Hsp70 assisted folding involves repeated cycles of substrate binding and release. Hsp70 activity is ATP dependent. Hsp70 proteins are made up of two regions: the amino terminus is the ATPase domain and the carboxyl terminus is the substrate binding region. 598 matched cddid_all.tbl CDD pfam00013 pfam00013 459630 KH_1 KH domain. KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. 65 matched cddid_all.tbl CDD pfam00014 pfam00014 425421 Kunitz_BPTI Kunitz/Bovine pancreatic trypsin inhibitor domain. Indicative of a protease inhibitor, usually a serine protease inhibitor. Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure. Certain family members are similar to the tick anticoagulant peptide (TAP). This is a highly selective inhibitor of factor Xa in the blood coagulation pathways. TAP molecules are highly dipolar, and are arranged to form a twisted two- stranded antiparallel beta-sheet followed by an alpha helix. 53 matched cddid_all.tbl CDD pfam00015 pfam00015 333767 MCPsignal Methyl-accepting chemotaxis protein (MCP) signalling domain. This domain is thought to transduce the signal to CheA since it is highly conserved in very diverse MCPs. 172 matched cddid_all.tbl CDD pfam00016 pfam00016 459631 RuBisCO_large Ribulose bisphosphate carboxylase large chain, catalytic domain. The C-terminal domain of RuBisCO large chain is the catalytic domain adopting a TIM barrel fold. 292 matched cddid_all.tbl CDD pfam00017 pfam00017 425423 SH2 SH2 domain. 77 matched cddid_all.tbl CDD pfam00018 pfam00018 394975 SH3_1 SH3 domain. SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organization. First described in the Src cytoplasmic tyrosine kinase. The structure is a partly opened beta barrel. 47 matched cddid_all.tbl CDD pfam00019 pfam00019 459632 TGF_beta Transforming growth factor beta like domain. 102 matched cddid_all.tbl CDD pfam00020 pfam00020 459633 TNFR_c6 TNFR/NGFR cysteine-rich region. 39 matched cddid_all.tbl CDD pfam00021 pfam00021 394978 UPAR_LY6 u-PAR/Ly-6 domain. This extracellular disulphide bond rich domain is related to pfam00087. 77 matched cddid_all.tbl CDD pfam00022 pfam00022 394979 Actin Actin. 407 matched cddid_all.tbl CDD pfam00023 pfam00023 459634 Ank Ankyrin repeat. Ankyrins are multifunctional adaptors that link specific proteins to the membrane-associated, spectrin- actin cytoskeleton. This repeat-domain is a 'membrane-binding' domain of up to 24 repeated units, and it mediates most of the protein's binding activities. Repeats 13-24 are especially active, with known sites of interaction for the Na/K ATPase, Cl/HCO(3) anion exchanger, voltage-gated sodium channel, clathrin heavy chain and L1 family cell adhesion molecules. The ANK repeats are found to form a contiguous spiral stack such that ion transporters like the anion exchanger associate in a large central cavity formed by the ANK repeat spiral, while clathrin and cell adhesion molecules associate with specific regions outside this cavity. 34 matched cddid_all.tbl CDD pfam00024 pfam00024 459635 PAN_1 PAN domain. The PAN domain contains a conserved core of three disulphide bridges. In some members of the family there is an additional fourth disulphide bridge the links the N and C termini of the domain. The domain is found in diverse proteins, in some they mediate protein-protein interactions, in others they mediate protein-carbohydrate interactions. 76 matched cddid_all.tbl CDD pfam00025 pfam00025 459636 Arf ADP-ribosylation factor family. Pfam combines a number of different Prosite families together 160 matched cddid_all.tbl CDD pfam00026 pfam00026 394983 Asp Eukaryotic aspartyl protease. Aspartyl (acid) proteases include pepsins, cathepsins, and renins. Two-domain structure, probably arising from ancestral duplication. This family does not include the retroviral nor retrotransposon proteases (pfam00077), which are much smaller and appear to be homologous to a single domain of the eukaryotic asp proteases. 313 matched cddid_all.tbl CDD pfam00027 pfam00027 459637 cNMP_binding Cyclic nucleotide-binding domain. This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 89 matched cddid_all.tbl CDD pfam00028 pfam00028 394985 Cadherin Cadherin domain. 92 matched cddid_all.tbl CDD pfam00029 pfam00029 459638 Connexin Connexin. Connexin proteins form gap-junctions between cells. They carry four transmembrane regions, hence why this family now includes Connexin_CCC, which represented the second pair of TMs. 217 matched cddid_all.tbl CDD pfam00030 pfam00030 459639 Crystall Beta/Gamma crystallin. The alignment comprises two Greek key motifs since the similarity between them is very low. 82 matched cddid_all.tbl CDD pfam00031 pfam00031 425431 Cystatin Cystatin domain. Very diverse family. Attempts to define separate sub-families failed. Typically, either the N-terminal or C-terminal end is very divergent. But splitting into two domains would make very short families. pfam00666 is related to this family but has not been included. 92 matched cddid_all.tbl CDD pfam00032 pfam00032 459640 Cytochrom_B_C Cytochrome b(C-terminal)/b6/petD. 101 matched cddid_all.tbl CDD pfam00033 pfam00033 306530 Cytochrome_B Cytochrome b/b6/petB. 189 matched cddid_all.tbl CDD pfam00034 pfam00034 459641 Cytochrom_C Cytochrome c. The Pfam entry does not include all Prosite members. The cytochrome 556 and cytochrome c' families are not included. All these are now in a new clan together. The C-terminus of DUF989, pfam06181, has now been merged into this family. 89 matched cddid_all.tbl CDD pfam00035 pfam00035 425434 dsrm Double-stranded RNA binding motif. Sequences gathered for seed by HMM_iterative_training Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA. 66 matched cddid_all.tbl CDD pfam00036 pfam00036 425435 EF-hand_1 EF hand. The EF-hands can be divided into two classes: signalling proteins and buffering/transport proteins. The first group is the largest and includes the most well-known members of the family such as calmodulin, troponin C and S100B. These proteins typically undergo a calcium-dependent conformational change which opens a target binding site. The latter group is represented by calbindin D9k and do not undergo calcium dependent conformational changes. 29 matched cddid_all.tbl CDD pfam00037 pfam00037 459642 Fer4 4Fe-4S binding domain. Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. 24 matched cddid_all.tbl CDD pfam00038 pfam00038 459643 Filament Intermediate filament protein. 313 matched cddid_all.tbl CDD pfam00039 pfam00039 459644 fn1 Fibronectin type I domain. 40 matched cddid_all.tbl CDD pfam00040 pfam00040 459645 fn2 Fibronectin type II domain. 42 matched cddid_all.tbl CDD pfam00041 pfam00041 394996 fn3 Fibronectin type III domain. 85 matched cddid_all.tbl CDD pfam00042 pfam00042 459646 Globin Globin. 117 matched cddid_all.tbl CDD pfam00043 pfam00043 459647 GST_C Glutathione S-transferase, C-terminal domain. GST conjugates reduced glutathione to a variety of targets including S-crystallin from squid, the eukaryotic elongation factor 1-gamma, the HSP26 family of stress-related proteins and auxin-regulated proteins in plants. Stringent starvation proteins in E. coli are also included in the alignment but are not known to have GST activity. The glutathione molecule binds in a cleft between N and C-terminal domains. The catalytically important residues are proposed to reside in the N-terminal domain. In plants, GSTs are encoded by a large gene family (48 GST genes in Arabidopsis) and can be divided into the phi, tau, theta, zeta, and lambda classes. 93 matched cddid_all.tbl CDD pfam00044 pfam00044 459648 Gp_dh_N Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain. GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. N-terminal domain is a Rossmann NAD(P) binding fold. 101 matched cddid_all.tbl CDD pfam00045 pfam00045 395000 Hemopexin Hemopexin. Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metallopeptidases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of metallopeptidases (TIMPs). 44 matched cddid_all.tbl CDD pfam00046 pfam00046 459649 Homeodomain Homeodomain. 57 matched cddid_all.tbl CDD pfam00047 pfam00047 395002 ig Immunoglobulin domain. Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions. 86 matched cddid_all.tbl CDD pfam00048 pfam00048 459650 IL8 Small cytokines (intecrine/chemokine), interleukin-8 like. Includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity. Structure contains two highly conserved disulfide bonds. 60 matched cddid_all.tbl CDD pfam00049 pfam00049 459651 Insulin Insulin/IGF/Relaxin family. Superfamily includes insulins; relaxins; insulin-like growth factor; and bombyxin. All are secreted regulatory hormones. Disulfide rich, all-alpha fold. Alignment includes B chain, linker (which is processed out of the final product), and A chain. 77 matched cddid_all.tbl CDD pfam00050 pfam00050 395004 Kazal_1 Kazal-type serine protease inhibitor domain. Usually indicative of serine protease inhibitors. However, kazal-like domains are also seen in the extracellular part of agrins, which are not known to be protease inhibitors. Kazal domains often occur in tandem arrays. Small alpha+beta fold containing three disulphides. Alignment also includes a single domain from transporters in the OATP/PGT family. 49 matched cddid_all.tbl CDD pfam00051 pfam00051 395005 Kringle Kringle domain. Kringle domains have been found in plasminogen, hepatocyte growth factors, prothrombin, and apolipoprotein A. Structure is disulfide-rich, nearly all-beta. 79 matched cddid_all.tbl CDD pfam00052 pfam00052 459652 Laminin_B Laminin B (Domain IV). 136 matched cddid_all.tbl CDD pfam00053 pfam00053 395007 Laminin_EGF Laminin EGF domain. This family is like pfam00008 but has 8 conserved cysteines instead of six. 49 matched cddid_all.tbl CDD pfam00054 pfam00054 395008 Laminin_G_1 Laminin G domain. 131 matched cddid_all.tbl CDD pfam00055 pfam00055 459653 Laminin_N Laminin N-terminal (Domain VI). 230 matched cddid_all.tbl CDD pfam00056 pfam00056 395010 Ldh_1_N lactate/malate dehydrogenase, NAD binding domain. L-lactate dehydrogenases are metabolic enzymes which catalyze the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyze the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. N-terminus (this family) is a Rossmann NAD-binding fold. C-terminus is an unusual alpha+beta fold. 141 matched cddid_all.tbl CDD pfam00057 pfam00057 395011 Ldl_recept_a Low-density lipoprotein receptor domain class A. 37 matched cddid_all.tbl CDD pfam00058 pfam00058 459654 Ldl_recept_b Low-density lipoprotein receptor repeat class B. This domain is also known as the YWTD motif after the most conserved region of the repeat. The YWTD repeat is found in multiple tandem repeats and has been predicted to form a beta-propeller structure. 42 matched cddid_all.tbl CDD pfam00059 pfam00059 459655 Lectin_C Lectin C-type domain. This family includes both long and short form C-type 105 matched cddid_all.tbl CDD pfam00060 pfam00060 459656 Lig_chan Ligand-gated ion channel. This family includes the four transmembrane regions of the ionotropic glutamate receptors and NMDA receptors. 267 matched cddid_all.tbl CDD pfam00061 pfam00061 395015 Lipocalin Lipocalin / cytosolic fatty-acid binding protein family. Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel. 143 matched cddid_all.tbl CDD pfam00062 pfam00062 395016 Lys C-type lysozyme/alpha-lactalbumin family. Alpha-lactalbumin is the regulatory subunit of lactose synthase, changing the substrate specificity of galactosyltransferase from N-acetylglucosamine to glucose. C-type lysozymes are secreted bacteriolytic enzymes that cleave the peptidoglycan of bacterial cell walls. Structure is a multi-domain, mixed alpha and beta fold, containing four conserved disulfide bonds. 123 matched cddid_all.tbl CDD pfam00063 pfam00063 395017 Myosin_head Myosin head (motor domain). 674 matched cddid_all.tbl CDD pfam00064 pfam00064 459657 Neur Neuraminidase. Neuraminidases cleave sialic acid residues from glycoproteins. Belong to the sialidase family - but this alignment does not generalize to the other sialidases. Structure is a 6-sheet beta propeller. 334 matched cddid_all.tbl CDD pfam00066 pfam00066 459658 Notch LNR domain. The LNR (Lin-12/Notch repeat) domain is found in three tandem copies in Notch related proteins. The structure of the domain has been determined by NMR and was shown to contain three disulphide bonds and coordinate a calcium ion. Three repeats are also found in the PAPP-A peptidase. 35 matched cddid_all.tbl CDD pfam00067 pfam00067 395020 p450 Cytochrome P450. Cytochrome P450s are haem-thiolate proteins involved in the oxidative degradation of various compounds. They are particularly well known for their role in the degradation of environmental toxins and mutagens. They can be divided into 4 classes, according to the method by which electrons from NAD(P)H are delivered to the catalytic site. Sequence conservation is relatively low within the family - there are only 3 absolutely conserved residues - but their general topography and structural fold are highly conserved. The conserved core is composed of a coil termed the 'meander', a four-helix bundle, helices J and K, and two sets of beta-sheets. These constitute the haem-binding loop (with an absolutely conserved cysteine that serves as the 5th ligand for the haem iron), the proton-transfer groove and the absolutely conserved EXXR motif in helix K. While prokaryotic P450s are soluble proteins, most eukaryotic P450s are associated with microsomal membranes. their general enzymatic function is to catalyze regiospecific and stereospecific oxidation of non-activated hydrocarbons at physiological temperatures. 461 matched cddid_all.tbl CDD pfam00068 pfam00068 459659 Phospholip_A2_1 Phospholipase A2. Phospholipase A2 releases fatty acids from the second carbon group of glycerol. Perhaps the best known members are secreted snake venoms, but also found in secreted pancreatic and membrane-associated forms. Structure is all-alpha, with two core disulfide-linked helices and a calcium-binding loop. This alignment represents the major family of PLA2s. A second minor family, defined by the honeybee venom PLA2 PDB:1POC and related sequences from Gila monsters (Heloderma), is not recognized. This minor family conserves the core helix pair but is substantially different elsewhere. The PROSITE pattern PA2_HIS, specific to the first core helix, recognizes both families. 108 matched cddid_all.tbl CDD pfam00069 pfam00069 459660 Pkinase Protein kinase domain. 217 matched cddid_all.tbl CDD pfam00070 pfam00070 425450 Pyr_redox Pyridine nucleotide-disulphide oxidoreductase. This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain. 80 matched cddid_all.tbl CDD pfam00071 pfam00071 425451 Ras Ras family. Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices. 162 matched cddid_all.tbl CDD pfam00072 pfam00072 395025 Response_reg Response regulator receiver domain. This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain. 111 matched cddid_all.tbl CDD pfam00073 pfam00073 395026 Rhv picornavirus capsid protein. CAUTION: This alignment is very weak. It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognized. The family should probably be split up into sub-families. Capsid proteins of picornaviruses. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids. They include rhinovirus (common cold) and poliovirus. Common structure is an 8-stranded beta sandwich. Variations (one or two extra strands) occur. 170 matched cddid_all.tbl CDD pfam00074 pfam00074 459661 RnaseA Pancreatic ribonuclease. Ribonucleases. Members include pancreatic RNAase A and angiogenins. Structure is an alpha+beta fold -- long curved beta sheet and three helices. 121 matched cddid_all.tbl CDD pfam00075 pfam00075 395028 RNase_H RNase H. RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers. 141 matched cddid_all.tbl CDD pfam00076 pfam00076 425453 RRM_1 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteriztic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disease. 70 matched cddid_all.tbl CDD pfam00077 pfam00077 425454 RVP Retroviral aspartyl protease. Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases such as pepsins, cathepsins, and renins (pfam00026). 101 matched cddid_all.tbl CDD pfam00078 pfam00078 395031 RVT_1 Reverse transcriptase (RNA-dependent DNA polymerase). A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. 189 matched cddid_all.tbl CDD pfam00079 pfam00079 459662 Serpin Serpin (serine protease inhibitor). Structure is a multi-domain fold containing a bundle of helices and a beta sandwich. 368 matched cddid_all.tbl CDD pfam00080 pfam00080 459663 Sod_Cu Copper/zinc superoxide dismutase (SODC). superoxide dismutases (SODs) catalyze the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding family is one. Defects in the human SOD1 gene cause familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Structure is an eight-stranded beta sandwich, similar to the immunoglobulin fold. 129 matched cddid_all.tbl CDD pfam00081 pfam00081 425457 Sod_Fe_N Iron/manganese superoxide dismutases, alpha-hairpin domain. superoxide dismutases (SODs) catalyze the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. N-terminal domain is a long alpha antiparallel hairpin. A small fragment of YTRE_LEPBI matches well - sequencing error? 82 matched cddid_all.tbl CDD pfam00082 pfam00082 395035 Peptidase_S8 Subtilase family. Subtilases are a family of serine proteases. They appear to have independently and convergently evolved an Asp/Ser/His catalytic triad, like that found in the trypsin serine proteases (see pfam00089). Structure is an alpha/beta fold containing a 7-stranded parallel beta sheet, order 2314567. 287 matched cddid_all.tbl CDD pfam00083 pfam00083 395036 Sugar_tr Sugar (and other) transporter. 452 matched cddid_all.tbl CDD pfam00084 pfam00084 459664 Sushi Sushi repeat (SCR repeat). 56 matched cddid_all.tbl CDD pfam00085 pfam00085 395038 Thioredoxin Thioredoxin. Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. Some members with only the active site are not separated from the noise. 103 matched cddid_all.tbl CDD pfam00086 pfam00086 459665 Thyroglobulin_1 Thyroglobulin type-1 repeat. Thyroglobulin type 1 repeats are thought to be involved in the control of proteolytic degradation. The domain usually contains six conserved cysteines. These form three disulphide bridges. Cysteines 1 pairs with 2, 3 with 4 and 5 with 6. 66 matched cddid_all.tbl CDD pfam00087 pfam00087 395040 Toxin_TOLIP Snake toxin and toxin-like protein. This family predominantly includes venomous neurotoxins and cytotoxins from snakes, but also structurally similar (non-snake) toxin-like proteins (TOLIPs) such as Lymphocyte antigen 6D and Ly6/PLAUR domain-containing protein. Snake toxins are short proteins with a compact, disulphide-rich structure. TOLIPs have similar structural features (abundance of spaced cysteine residues, a high frequency of charge residues, a signal peptide for secretion and a compact structure) but, are not associated with a venom gland or poisonous function. They are endogenous animal proteins that are not restricted to poisonous animals. 70 matched cddid_all.tbl CDD pfam00088 pfam00088 459666 Trefoil Trefoil (P-type) domain. 43 matched cddid_all.tbl CDD pfam00089 pfam00089 459667 Trypsin Trypsin. 219 matched cddid_all.tbl CDD pfam00090 pfam00090 459668 TSP_1 Thrombospondin type 1 domain. 49 matched cddid_all.tbl CDD pfam00091 pfam00091 459669 Tubulin Tubulin/FtsZ family, GTPase domain. This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ and tubulin are GTPases. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules. 190 matched cddid_all.tbl CDD pfam00092 pfam00092 459670 VWA von Willebrand factor type A domain. 174 matched cddid_all.tbl CDD pfam00093 pfam00093 278520 VWC von Willebrand factor type C domain. The high cutoff was used to prevent overlap with pfam00094. 57 matched cddid_all.tbl CDD pfam00094 pfam00094 459671 VWD von Willebrand factor type D domain. Swiss:P17554 contains a vwd domain. Its function is unrelated but the similarity is very strong by several methods. 154 matched cddid_all.tbl CDD pfam00095 pfam00095 459672 WAP WAP-type (Whey Acidic Protein) 'four-disulfide core'. WAP belongs to the group of Elafin or elastase-specific inhibitors. 42 matched cddid_all.tbl CDD pfam00096 pfam00096 395048 zf-C2H2 Zinc finger, C2H2 type. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter. 23 matched cddid_all.tbl CDD pfam00097 pfam00097 395049 zf-C3HC4 Zinc finger, C3HC4 type (RING finger). The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid. Many proteins containing a RING finger play a key role in the ubiquitination pathway. 40 matched cddid_all.tbl CDD pfam00098 pfam00098 395050 zf-CCHC Zinc knuckle. The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger. 18 matched cddid_all.tbl CDD pfam00100 pfam00100 459673 Zona_pellucida Zona pellucida-like domain. 254 matched cddid_all.tbl CDD pfam00101 pfam00101 425465 RuBisCO_small Ribulose bisphosphate carboxylase, small chain. 97 matched cddid_all.tbl CDD pfam00102 pfam00102 459674 Y_phosphatase Protein-tyrosine phosphatase. 234 matched cddid_all.tbl CDD pfam00103 pfam00103 306585 Hormone_1 Somatotropin hormone family. 214 matched cddid_all.tbl CDD pfam00104 pfam00104 459675 Hormone_recep Ligand-binding domain of nuclear hormone receptor. This all helical domain is involved in binding the hormone in these receptors. 194 matched cddid_all.tbl CDD pfam00105 pfam00105 395055 zf-C4 Zinc finger, C4 type (two domains). In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other. 68 matched cddid_all.tbl CDD pfam00106 pfam00106 395056 adh_short short chain dehydrogenase. This family contains a wide variety of dehydrogenases. 195 matched cddid_all.tbl CDD pfam00107 pfam00107 395057 ADH_zinc_N Zinc-binding dehydrogenase. 129 matched cddid_all.tbl CDD pfam00108 pfam00108 459676 Thiolase_N Thiolase, N-terminal domain. Thiolase is reported to be structurally related to beta-ketoacyl synthase (pfam00109), and also chalcone synthase. 260 matched cddid_all.tbl CDD pfam00109 pfam00109 425468 ketoacyl-synt Beta-ketoacyl synthase, N-terminal domain. The structure of beta-ketoacyl synthase is similar to that of the thiolase family (pfam00108) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains. The N-terminal domain contains most of the structures involved in dimer formation and also the active site cysteine. 251 matched cddid_all.tbl CDD pfam00110 pfam00110 459677 wnt wnt family. Wnt genes have been identified in vertebrates and invertebrates but not in plants, unicellular eukaryotes or prokaryotes. In humans, 19 WNT proteins are known. Because of their insolubility little is known about Wnt protein structure, but all have 23 or 24 Cys residues whose spacing is highly conserved. Signal transduction by Wnt proteins (including the Wnt/beta-catenin, the Wnt/Ca++, and the Wnt/polarity pathway) is mediated by receptors of the Frizzled and LDL-receptor-related protein (LRP) families. 307 matched cddid_all.tbl CDD pfam00111 pfam00111 395061 Fer2 2Fe-2S iron-sulfur cluster binding domain. 77 matched cddid_all.tbl CDD pfam00112 pfam00112 425470 Peptidase_C1 Papain family cysteine protease. 214 matched cddid_all.tbl CDD pfam00113 pfam00113 395063 Enolase_C Enolase, C-terminal TIM barrel domain. 296 matched cddid_all.tbl CDD pfam00114 pfam00114 395064 Pilin Pilin (bacterial filament). Proteins with only the short N-terminal methylation site are not separated from the noise. The Prosite pattern detects those better. 108 matched cddid_all.tbl CDD pfam00115 pfam00115 459678 COX1 Cytochrome C and Quinol oxidase polypeptide I. Cytochrome c oxidase (E.C:7.1.1.9) is a key enzyme in aerobic metabolism. Proton pumping haem-copper oxidases represent the terminal, energy-transfer enzymes of respiratory chains in prokaryotes and eukaryotes. The CuB-haem a3 (or haem o) binuclear centre, associated with the largest subunit I of cytochrome c and ubiquinol oxidases (E.C:1.10.3.11), is directly involved in the coupling between dioxygen reduction and proton pumping. Some terminal oxidases generate a transmembrane proton gradient across the plasma membrane (prokaryotes) or the mitochondrial inner membrane (eukaryotes). The enzyme complex consists of 3-4 subunits (prokaryotes) up to 13 polypeptides (mammals) of which only the catalytic subunit (equivalent to mammalian subunit I (COXI) is found in all haem-copper respiratory oxidases. The presence of a bimetallic centre (formed by a high-spin haem and copper B) as well as a low-spin haem, both ligated to six conserved histidine residues near the outer side of four transmembrane spans within CO I is common to all family members. 432 matched cddid_all.tbl CDD pfam00116 pfam00116 395066 COX2 Cytochrome C oxidase subunit II, periplasmic domain. 120 matched cddid_all.tbl CDD pfam00117 pfam00117 395067 GATase Glutamine amidotransferase class-I. 188 matched cddid_all.tbl CDD pfam00118 pfam00118 395068 Cpn60_TCP1 TCP-1/cpn60 chaperonin family. This family includes members from the HSP60 chaperone family and the TCP-1 (T-complex protein) family. 489 matched cddid_all.tbl CDD pfam00119 pfam00119 459679 ATP-synt_A ATP synthase A chain. 216 matched cddid_all.tbl CDD pfam00120 pfam00120 425473 Gln-synt_C Glutamine synthetase, catalytic domain. 343 matched cddid_all.tbl CDD pfam00121 pfam00121 459680 TIM Triosephosphate isomerase. Triosephosphate isomerase (EC:5.3.1.1) (TIM) is the glycolytic enzyme that catalyzes the reversible interconversion of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. TIM plays an important role in several metabolic pathways and is essential for efficient energy production, present in eukaryotes and prokaryotes. TIM is a dimer of identical subunits, each of which is made up of about 250 amino-acid residues. A glutamic acid residue is involved in the catalytic mechanism. The tertiary structure of TIM has eight beta/alpha motifs folded into a barrel structure. The sequence around the active site residue is perfectly conserved in all known TIM's. Deficiencies in TIM are associated with haemolytic anaemia coupled with a progressive, severe neurological disorder. 244 matched cddid_all.tbl CDD pfam00122 pfam00122 425475 E1-E2_ATPase E1-E2 ATPase. 181 matched cddid_all.tbl CDD pfam00123 pfam00123 459681 Hormone_2 Peptide hormone. This family contains glucagon, GIP, secretin and VIP. 28 matched cddid_all.tbl CDD pfam00124 pfam00124 425477 Photo_RC Photosynthetic reaction centre protein. 260 matched cddid_all.tbl CDD pfam00125 pfam00125 459682 Histone Core histone H2A/H2B/H3/H4. 126 matched cddid_all.tbl CDD pfam00126 pfam00126 459683 HTH_1 Bacterial regulatory helix-turn-helix protein, lysR family. 60 matched cddid_all.tbl CDD pfam00127 pfam00127 395076 Copper-bind Copper binding proteins, plastocyanin/azurin family. 99 matched cddid_all.tbl CDD pfam00128 pfam00128 395077 Alpha-amylase Alpha amylase, catalytic domain. Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain. 334 matched cddid_all.tbl CDD pfam00129 pfam00129 395078 MHC_I Class I Histocompatibility antigen, domains alpha 1 and 2. 179 matched cddid_all.tbl CDD pfam00130 pfam00130 395079 C1_1 Phorbol esters/diacylglycerol binding domain (C1 domain). This domain is also known as the Protein kinase C conserved region 1 (C1) domain. 53 matched cddid_all.tbl CDD pfam00131 pfam00131 395080 Metallothio Metallothionein. 65 matched cddid_all.tbl CDD pfam00132 pfam00132 459684 Hexapep Bacterial transferase hexapeptide (six repeats). 30 matched cddid_all.tbl CDD pfam00133 pfam00133 459685 tRNA-synt_1 tRNA synthetases class I (I, L, M and V). Other tRNA synthetase sub-families are too dissimilar to be included. 602 matched cddid_all.tbl CDD pfam00134 pfam00134 459686 Cyclin_N Cyclin, N-terminal domain. Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the N-terminal domain. 127 matched cddid_all.tbl CDD pfam00135 pfam00135 395084 COesterase Carboxylesterase family. 513 matched cddid_all.tbl CDD pfam00136 pfam00136 395085 DNA_pol_B DNA polymerase family B. This region of DNA polymerase B appears to consist of more than one structural domain, possibly including elongation, DNA-binding and dNTP binding activities. 439 matched cddid_all.tbl CDD pfam00137 pfam00137 459687 ATP-synt_C ATP synthase subunit C. 60 matched cddid_all.tbl CDD pfam00139 pfam00139 459688 Lectin_legB Legume lectin domain. 245 matched cddid_all.tbl CDD pfam00140 pfam00140 425482 Sigma70_r1_2 Sigma-70 factor, region 1.2. 34 matched cddid_all.tbl CDD pfam00141 pfam00141 425483 peroxidase Peroxidase. 187 matched cddid_all.tbl CDD pfam00142 pfam00142 395090 Fer4_NifH 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family. 271 matched cddid_all.tbl CDD pfam00143 pfam00143 459689 Interferon Interferon alpha/beta domain. Type I interferons (alpha, beta) belong to the larger helical cytokine superfamily,which includes growth hormones, interleukins, several colony-stimulating factors and several other regulatory molecules. 160 matched cddid_all.tbl CDD pfam00144 pfam00144 395092 Beta-lactamase Beta-lactamase. This family appears to be distantly related to pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase. 327 matched cddid_all.tbl CDD pfam00145 pfam00145 395093 DNA_methylase C-5 cytosine-specific DNA methylase. 324 matched cddid_all.tbl CDD pfam00146 pfam00146 459690 NADHdh NADH dehydrogenase. 302 matched cddid_all.tbl CDD pfam00147 pfam00147 395095 Fibrinogen_C Fibrinogen beta and gamma chains, C-terminal globular domain. 221 matched cddid_all.tbl CDD pfam00148 pfam00148 395096 Oxidored_nitro Nitrogenase component 1 type Oxidoreductase. 398 matched cddid_all.tbl CDD pfam00149 pfam00149 459691 Metallophos Calcineurin-like phosphoesterase. This family includes a diverse range of phosphoesterases, including protein phosphoserine phosphatases, nucleotidases, sphingomyelin phosphodiesterases and 2'-3' cAMP phosphodiesterases as well as nucleases such as bacterial SbcD or yeast MRE11. The most conserved regions in this superfamily centre around the metal chelating residues. 114 matched cddid_all.tbl CDD pfam00150 pfam00150 395098 Cellulase Cellulase (glycosyl hydrolase family 5). 272 matched cddid_all.tbl CDD pfam00151 pfam00151 395099 Lipase Lipase. 336 matched cddid_all.tbl CDD pfam00152 pfam00152 425487 tRNA-synt_2 tRNA synthetases class II (D, K and N). 318 matched cddid_all.tbl CDD pfam00153 pfam00153 395101 Mito_carr Mitochondrial carrier protein. 96 matched cddid_all.tbl CDD pfam00154 pfam00154 425488 RecA recA bacterial DNA recombination protein. RecA is a DNA-dependent ATPase and functions in DNA repair systems. RecA protein catalyzes an ATP-dependent DNA strand-exchange reaction that is the central step in the repair of dsDNA breaks by homologous recombination. 262 matched cddid_all.tbl CDD pfam00155 pfam00155 395103 Aminotran_1_2 Aminotransferase class I and II. 351 matched cddid_all.tbl CDD pfam00156 pfam00156 425489 Pribosyltran Phosphoribosyl transferase domain. This family includes a range of diverse phosphoribosyl transferase enzymes. This family includes: Adenine phosphoribosyl-transferase EC:2.4.2.7. Hypoxanthine-guanine-xanthine phosphoribosyl-transferase. Hypoxanthine phosphoribosyl-transferase EC:2.4.2.8. Ribose-phosphate pyrophosphokinase i EC:2.7.6.1. Amidophosphoribosyltransferase EC:2.4.2.14. Orotate phosphoribosyl-transferase EC:2.4.2.10. Uracil phosphoribosyl-transferase EC:2.4.2.9. Xanthine-guanine phosphoribosyl-transferase EC:2.4.2.22. In Arabidopsis, At the very N-terminus of this domain is the P-Loop NTPase domain. 150 matched cddid_all.tbl CDD pfam00157 pfam00157 459692 Pou Pou domain - N-terminal to homeobox domain. 72 matched cddid_all.tbl CDD pfam00158 pfam00158 425491 Sigma54_activat Sigma-54 interaction domain. 168 matched cddid_all.tbl CDD pfam00159 pfam00159 459693 Hormone_3 Pancreatic hormone peptide. 35 matched cddid_all.tbl CDD pfam00160 pfam00160 459694 Pro_isomerase Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD. The peptidyl-prolyl cis-trans isomerases, also known as cyclophilins, share this domain of about 109 amino acids. Cyclophilins have been found in all organizms studied so far and catalyze peptidyl-prolyl isomerization during which the peptide bond preceding proline (the peptidyl-prolyl bond) is stabilized in the cis conformation. Mammalian cyclophilin A (CypA) is a major cellular target for the immunosuppressive drug cyclosporin A (CsA). Other roles for cyclophilins may include chaperone and cell signalling function. 149 matched cddid_all.tbl CDD pfam00161 pfam00161 459695 RIP Ribosome inactivating protein. 197 matched cddid_all.tbl CDD pfam00162 pfam00162 425495 PGK Phosphoglycerate kinase. 370 matched cddid_all.tbl CDD pfam00163 pfam00163 459696 Ribosomal_S4 Ribosomal protein S4/S9 N-terminal domain. This family includes small ribosomal subunit S9 from prokaryotes and S16 from metazoans. This domain is predicted to bind to ribosomal RNA. This domain is composed of four helices in the known structure. However the domain is discontinuous in sequence and the alignment for this family contains only the first three helices. 96 matched cddid_all.tbl CDD pfam00164 pfam00164 395112 Ribosom_S12_S23 Ribosomal protein S12/S23. This protein is known as S12 in bacteria and archaea and S23 in eukaryotes. 114 matched cddid_all.tbl CDD pfam00165 pfam00165 425497 HTH_AraC Bacterial regulatory helix-turn-helix proteins, AraC family. In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added. 42 matched cddid_all.tbl CDD pfam00166 pfam00166 395114 Cpn10 Chaperonin 10 Kd subunit. This family contains GroES and Gp31-like chaperonins. Gp31 is a functional co-chaperonin that is required for the folding and assembly of Gp23, a major capsid protein, during phage morphogenesis. 92 matched cddid_all.tbl CDD pfam00167 pfam00167 425498 FGF Fibroblast growth factor. Fibroblast growth factors are a family of proteins involved in growth and differentiation in a wide range of contexts. They are found in a wide range of organizms, from nematodes to humans. Most share an internal core region of high similarity, conserved residues in which are involved in binding with their receptors. On binding, they cause dimerization of their tyrosine kinase receptors leading to intracellular signalling. There are currently four known tyrosine kinase receptors for fibroblast growth factors. These receptors can each bind several different members of this family. Members of this family have a beta trefoil structure. Most have N-terminal signal peptides and are secreted. A few lack signal sequences but are secreted anyway; still others also lack the signal peptide but are found on the cell surface and within the extracellular matrix. A third group remain intracellular. They have central roles in development, regulating cell proliferation, migration and differentiation. On the other hand, they are important in tissue repair following injury in adult organizms. 124 matched cddid_all.tbl CDD pfam00168 pfam00168 425499 C2 C2 domain. 104 matched cddid_all.tbl CDD pfam00169 pfam00169 459697 PH PH domain. PH stands for pleckstrin homology. 105 matched cddid_all.tbl CDD pfam00170 pfam00170 395118 bZIP_1 bZIP transcription factor. The Pfam entry includes the basic region and the leucine zipper region. 60 matched cddid_all.tbl CDD pfam00171 pfam00171 425500 Aldedh Aldehyde dehydrogenase family. This family of dehydrogenases act on aldehyde substrates. Members use NADP as a cofactor. The family includes the following members: The prototypical members are the aldehyde dehydrogenases EC:1.2.1.3. Succinate-semialdehyde dehydrogenase EC:1.2.1.16. Lactaldehyde dehydrogenase EC:1.2.1.22. Benzaldehyde dehydrogenase EC:1.2.1.28. Methylmalonate-semialdehyde dehydrogenase EC:1.2.1.27. Glyceraldehyde-3-phosphate dehydrogenase EC:1.2.1.9. Delta-1-pyrroline-5-carboxylate dehydrogenase EC: 1.5.1.12. Acetaldehyde dehydrogenase EC:1.2.1.10. Glutamate-5-semialdehyde dehydrogenase EC:1.2.1.41. This family also includes omega crystallin, an eye lens protein from squid and octopus that has little aldehyde dehydrogenase activity. 459 matched cddid_all.tbl CDD pfam00172 pfam00172 395120 Zn_clus Fungal Zn(2)-Cys(6) binuclear cluster domain. 39 matched cddid_all.tbl CDD pfam00173 pfam00173 459698 Cyt-b5 Cytochrome b5-like Heme/Steroid binding domain. This family includes heme binding domains from a diverse range of proteins. This family also includes proteins that bind to steroids. The family includes progesterone receptors. Many members of this subfamily are membrane anchored by an N-terminal transmembrane alpha helix. This family also includes a domain in some chitin synthases. There is no known ligand for this domain in the chitin synthases. 74 matched cddid_all.tbl CDD pfam00174 pfam00174 459699 Oxidored_molyb Oxidoreductase molybdopterin binding domain. This domain is found in a variety of oxidoreductases. This domain binds to a molybdopterin cofactor. Xanthine dehydrogenases, that also bind molybdopterin, have essentially no similarity. 168 matched cddid_all.tbl CDD pfam00175 pfam00175 425503 NAD_binding_1 Oxidoreductase NAD-binding domain. Xanthine dehydrogenases, that also bind FAD/NAD, have essentially no similarity. 109 matched cddid_all.tbl CDD pfam00176 pfam00176 425504 SNF2-rel_dom SNF2-related domain. This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1). SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilizes energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors. 289 matched cddid_all.tbl CDD pfam00177 pfam00177 425505 Ribosomal_S7 Ribosomal protein S7p/S5e. This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes. 132 matched cddid_all.tbl CDD pfam00178 pfam00178 459700 Ets Ets-domain. 80 matched cddid_all.tbl CDD pfam00179 pfam00179 459701 UQ_con Ubiquitin-conjugating enzyme. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologs. TSG101 is one of several UBC homologs that lacks this active site cysteine. 139 matched cddid_all.tbl CDD pfam00180 pfam00180 425507 Iso_dh Isocitrate/isopropylmalate dehydrogenase. 346 matched cddid_all.tbl CDD pfam00181 pfam00181 395129 Ribosomal_L2 Ribosomal Proteins L2, RNA binding domain. 77 matched cddid_all.tbl CDD pfam00182 pfam00182 459702 Glyco_hydro_19 Chitinase class I. 232 matched cddid_all.tbl CDD pfam00183 pfam00183 459703 HSP90 Hsp90 protein. 516 matched cddid_all.tbl CDD pfam00184 pfam00184 459704 Hormone_5 Neurohypophysial hormones, C-terminal Domain. N-terminal Domain is in hormone5 79 matched cddid_all.tbl CDD pfam00185 pfam00185 425511 OTCace Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain. 154 matched cddid_all.tbl CDD pfam00186 pfam00186 425512 DHFR_1 Dihydrofolate reductase. 159 matched cddid_all.tbl CDD pfam00187 pfam00187 459705 Chitin_bind_1 Chitin recognition protein. 38 matched cddid_all.tbl CDD pfam00188 pfam00188 395136 CAP Cysteine-rich secretory protein family. This is a large family of cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins (CAP) that are found in a wide range of organizms, including prokaryotes and non-vertebrate eukaryotes, The nine subfamilies of the mammalian CAP 'super'family include: the human glioma pathogenesis-related 1 (GLIPR1), Golgi associated pathogenesis related-1 (GAPR1) proteins, peptidase inhibitor 15 (PI15), peptidase inhibitor 16 (PI16), cysteine-rich secretory proteins (CRISPs), CRISP LCCL domain containing 1 (CRISPLD1), CRISP LCCL domain containing 2 (CRISPLD2), mannose receptor like and the R3H domain containing like proteins. Members are most often secreted and have an extracellular endocrine or paracrine function and are involved in processes including the regulation of extracellular matrix and branching morphogenesis, potentially as either proteases or protease inhibitors; in ion channel regulation in fertility; as tumour suppressor or pro-oncogenic genes in tissues including the prostate; and in cell-cell adhesion during fertilization. The overall protein structural conservation within the CAP 'super'family results in fundamentally similar functions for the CAP domain in all members, yet the diversity outside of this core region dramatically alters the target specificity and, thus, the biological consequences. The Ca++-chelating function would fit with the various signalling processes (e.g. the CRISP proteins) that members of this family are involved in, and also the sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how Swiss:Q91055 blocks the Ca++ transporting ryanodine receptors. 117 matched cddid_all.tbl CDD pfam00189 pfam00189 425514 Ribosomal_S3_C Ribosomal protein S3, C-terminal domain. This family contains a central domain pfam00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain. Some are much longer. 83 matched cddid_all.tbl CDD pfam00190 pfam00190 395138 Cupin_1 Cupin. This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant. 151 matched cddid_all.tbl CDD pfam00191 pfam00191 395139 Annexin Annexin. This family of annexins also includes giardin that has been shown to function as an annexin. 66 matched cddid_all.tbl CDD pfam00193 pfam00193 459706 Xlink Extracellular link domain. 92 matched cddid_all.tbl CDD pfam00194 pfam00194 459707 Carb_anhydrase Eukaryotic-type carbonic anhydrase. 252 matched cddid_all.tbl CDD pfam00195 pfam00195 395142 Chal_sti_synt_N Chalcone and stilbene synthases, N-terminal domain. The C-terminal domain of Chalcone synthase is reported to be structurally similar to domains in thiolase and beta-ketoacyl synthase. The differences in activity are accounted for by differences in this N-terminal domain. 225 matched cddid_all.tbl CDD pfam00196 pfam00196 425517 GerE Bacterial regulatory proteins, luxR family. 57 matched cddid_all.tbl CDD pfam00197 pfam00197 395144 Kunitz_legume Trypsin and protease inhibitor. 174 matched cddid_all.tbl CDD pfam00198 pfam00198 425518 2-oxoacid_dh 2-oxoacid dehydrogenases acyltransferase (catalytic domain). These proteins contain one to three copies of a lipoyl binding domain followed by the catalytic domain. 212 matched cddid_all.tbl CDD pfam00199 pfam00199 459708 Catalase Catalase. 383 matched cddid_all.tbl CDD pfam00200 pfam00200 459709 Disintegrin Disintegrin. 74 matched cddid_all.tbl CDD pfam00201 pfam00201 278624 UDPGT UDP-glucoronosyl and UDP-glucosyl transferase. 499 matched cddid_all.tbl CDD pfam00202 pfam00202 395148 Aminotran_3 Aminotransferase class-III. 397 matched cddid_all.tbl CDD pfam00203 pfam00203 459710 Ribosomal_S19 Ribosomal protein S19. 80 matched cddid_all.tbl CDD pfam00204 pfam00204 425522 DNA_gyraseB DNA gyrase B. This family represents the second domain of DNA gyrase B which has a ribosomal S5 domain 2-like fold. This family is structurally related to PF01119. 173 matched cddid_all.tbl CDD pfam00205 pfam00205 425523 TPP_enzyme_M Thiamine pyrophosphate enzyme, central domain. The central domain of TPP enzymes contains a 2-fold Rossman fold. 137 matched cddid_all.tbl CDD pfam00206 pfam00206 425524 Lyase_1 Lyase. 312 matched cddid_all.tbl CDD pfam00207 pfam00207 459711 A2M Alpha-2-macroglobulin family. This family includes the C-terminal region of the alpha-2-macroglobulin family. 91 matched cddid_all.tbl CDD pfam00208 pfam00208 425526 ELFV_dehydrog Glutamate/Leucine/Phenylalanine/Valine dehydrogenase. 240 matched cddid_all.tbl CDD pfam00209 pfam00209 395155 SNF Sodium:neurotransmitter symporter family. These are twelve xTM-containing region transporters. 517 matched cddid_all.tbl CDD pfam00210 pfam00210 459712 Ferritin Ferritin-like domain. This family contains ferritins and other ferritin-like proteins such as members of the DPS family and bacterioferritins. 141 matched cddid_all.tbl CDD pfam00211 pfam00211 425528 Guanylate_cyc Adenylate and Guanylate cyclase catalytic domain. 183 matched cddid_all.tbl CDD pfam00212 pfam00212 459713 ANP Atrial natriuretic peptide. 31 matched cddid_all.tbl CDD pfam00213 pfam00213 459714 OSCP ATP synthase delta (OSCP) subunit. The ATP D subunit from E. coli is the same as the OSCP subunit which is this family. The ATP D subunit from metazoa are found in family pfam00401. 172 matched cddid_all.tbl CDD pfam00214 pfam00214 459715 Calc_CGRP_IAPP Calcitonin / CGRP / IAPP family. 130 matched cddid_all.tbl CDD pfam00215 pfam00215 395160 OMPdecase Orotidine 5'-phosphate decarboxylase / HUMPS family. This family includes Orotidine 5'-phosphate decarboxylase enzymes EC:4.1.1.23 that are involved in the final step of pyrimidine biosynthesis. The family also includes enzymes such as hexulose-6-phosphate synthase. This family appears to be distantly related to pfam00834. 215 matched cddid_all.tbl CDD pfam00216 pfam00216 425532 Bac_DNA_binding Bacterial DNA-binding protein. 88 matched cddid_all.tbl CDD pfam00217 pfam00217 459716 ATP-gua_Ptrans ATP:guanido phosphotransferase, C-terminal catalytic domain. The substrate binding site is located in the cleft between N and C-terminal domains, but most of the catalytic residues are found in the larger C-terminal domain. 203 matched cddid_all.tbl CDD pfam00218 pfam00218 395163 IGPS Indole-3-glycerol phosphate synthase. 252 matched cddid_all.tbl CDD pfam00219 pfam00219 459717 IGFBP Insulin-like growth factor binding protein. 53 matched cddid_all.tbl CDD pfam00220 pfam00220 395165 Hormone_4 Neurohypophysial hormones, N-terminal Domain. C-terminal is in hormone5 9 matched cddid_all.tbl CDD pfam00221 pfam00221 459718 Lyase_aromatic Aromatic amino acid lyase. This family includes proteins with phenylalanine ammonia-lyase, EC:4.3.1.24, histidine ammonia-lyase, EC:4.3.1.3, and tyrosine aminomutase, EC:5.4.3.6, activities. 464 matched cddid_all.tbl CDD pfam00223 pfam00223 459719 PsaA_PsaB Photosystem I psaA/psaB protein. 719 matched cddid_all.tbl CDD pfam00224 pfam00224 395168 PK Pyruvate kinase, barrel domain. This domain of the is actually a small beta-barrel domain nested within a larger TIM barrel. The active site is found in a cleft between the two domains. 348 matched cddid_all.tbl CDD pfam00225 pfam00225 459720 Kinesin Kinesin motor domain. 326 matched cddid_all.tbl CDD pfam00226 pfam00226 395170 DnaJ DnaJ domain. DnaJ domains (J-domains) are associated with hsp70 heat-shock system and it is thought that this domain mediates the interaction. DnaJ-domain is therefore part of a chaperone (protein folding) system. The T-antigens, although not in Prosite are confirmed as DnaJ containing domains from literature. 63 matched cddid_all.tbl CDD pfam00227 pfam00227 459721 Proteasome Proteasome subunit. The proteasome is a multisubunit structure that degrades proteins. Protein degradation is an essential component of regulation because proteins can become misfolded, damaged, or unnecessary. Proteasomes and their homologs vary greatly in complexity: from HslV (heat shock locus v), which is encoded by 1 gene in bacteria, to the eukaryotic 20S proteasome, which is encoded by more than 14 genes. Recently evidence of two novel groups of bacterial proteasomes was proposed. The first is Anbu, which is sparsely distributed among cyanobacteria and proteobacteria. The second is call beta-proteobacteria proteasome homolog (BPH). 188 matched cddid_all.tbl CDD pfam00228 pfam00228 425539 Bowman-Birk_leg Bowman-Birk serine protease inhibitor family. 23 matched cddid_all.tbl CDD pfam00229 pfam00229 425540 TNF TNF(Tumour Necrosis Factor) family. 127 matched cddid_all.tbl CDD pfam00230 pfam00230 395174 MIP Major intrinsic protein. MIP (Major Intrinsic Protein) family proteins exhibit essentially two distinct types of channel properties: (1) specific water transport by the aquaporins, and (2) small neutral solutes transport, such as glycerol by the glycerol facilitators. 223 matched cddid_all.tbl CDD pfam00231 pfam00231 459722 ATP-synt ATP synthase. 285 matched cddid_all.tbl CDD pfam00232 pfam00232 395176 Glyco_hydro_1 Glycosyl hydrolase family 1. 453 matched cddid_all.tbl CDD pfam00233 pfam00233 459723 PDEase_I 3'5'-cyclic nucleotide phosphodiesterase. 238 matched cddid_all.tbl CDD pfam00234 pfam00234 425543 Tryp_alpha_amyl Protease inhibitor/seed storage/LTP family. This family is composed of trypsin-alpha amylase inhibitors, seed storage proteins and lipid transfer proteins from plants. 74 matched cddid_all.tbl CDD pfam00235 pfam00235 459724 Profilin Profilin. 124 matched cddid_all.tbl CDD pfam00236 pfam00236 425545 Hormone_6 Glycoprotein hormone. 95 matched cddid_all.tbl CDD pfam00237 pfam00237 459725 Ribosomal_L22 Ribosomal protein L22p/L17e. This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes. 104 matched cddid_all.tbl CDD pfam00238 pfam00238 425547 Ribosomal_L14 Ribosomal protein L14p/L23e. 119 matched cddid_all.tbl CDD pfam00239 pfam00239 425548 Resolvase Resolvase, N terminal domain. The N-terminal domain of the resolvase family (this family) contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase - see pfam02796. 144 matched cddid_all.tbl CDD pfam00240 pfam00240 459726 ubiquitin Ubiquitin family. This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites. 72 matched cddid_all.tbl CDD pfam00241 pfam00241 459727 Cofilin_ADF Cofilin/tropomyosin-type actin-binding protein. Severs actin filaments and binds to actin monomers. 123 matched cddid_all.tbl CDD pfam00242 pfam00242 365972 DNA_pol_viral_N DNA polymerase (viral) N-terminal domain. 401 matched cddid_all.tbl CDD pfam00243 pfam00243 459728 NGF Nerve growth factor family. 112 matched cddid_all.tbl CDD pfam00244 pfam00244 459729 14-3-3 14-3-3 protein. 221 matched cddid_all.tbl CDD pfam00245 pfam00245 395188 Alk_phosphatase Alkaline phosphatase. 418 matched cddid_all.tbl CDD pfam00246 pfam00246 459730 Peptidase_M14 Zinc carboxypeptidase. 287 matched cddid_all.tbl CDD pfam00248 pfam00248 425554 Aldo_ket_red Aldo/keto reductase family. This family includes a number of K+ ion channel beta chain regulatory domains - these are reported to have oxidoreductase activity. 290 matched cddid_all.tbl CDD pfam00249 pfam00249 459731 Myb_DNA-binding Myb-like DNA-binding domain. This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family. 46 matched cddid_all.tbl CDD pfam00250 pfam00250 459732 Forkhead Forkhead domain. 86 matched cddid_all.tbl CDD pfam00251 pfam00251 425557 Glyco_hydro_32N Glycosyl hydrolases family 32 N-terminal domain. This domain corresponds to the N-terminal domain of glycosyl hydrolase family 32 which forms a five bladed beta propeller structure. 308 matched cddid_all.tbl CDD pfam00252 pfam00252 459733 Ribosomal_L16 Ribosomal protein L16p/L10e. 132 matched cddid_all.tbl CDD pfam00253 pfam00253 459734 Ribosomal_S14 Ribosomal protein S14p/S29e. This family includes both ribosomal S14 from prokaryotes and S29 from eukaryotes. 54 matched cddid_all.tbl CDD pfam00254 pfam00254 459735 FKBP_C FKBP-type peptidyl-prolyl cis-trans isomerase. 94 matched cddid_all.tbl CDD pfam00255 pfam00255 395197 GSHPx Glutathione peroxidase. 108 matched cddid_all.tbl CDD pfam00257 pfam00257 425561 Dehydrin Dehydrin. 144 matched cddid_all.tbl CDD pfam00258 pfam00258 425562 Flavodoxin_1 Flavodoxin. 142 matched cddid_all.tbl CDD pfam00260 pfam00260 365984 Protamine_P1 Protamine P1. 49 matched cddid_all.tbl CDD pfam00261 pfam00261 459736 Tropomyosin Tropomyosin. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites. The protein is best known for its role in regulating the interaction between actin and myosin in muscle contraction, but is also involved in the organization and dynamics of the cytoskeleton in non-muscle cells. There are multiple cell-specific isoforms, expressed by alternative promoters and alternative RNA processing of at least four genes. Muscle isoforms of tropomyosin are characterized by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. 235 matched cddid_all.tbl CDD pfam00262 pfam00262 459737 Calreticulin Calreticulin family. 369 matched cddid_all.tbl CDD pfam00263 pfam00263 459738 Secretin Bacterial type II and III secretion system protein. 159 matched cddid_all.tbl CDD pfam00264 pfam00264 425566 Tyrosinase Common central domain of tyrosinase. This family also contains polyphenol oxidases and some hemocyanins. Binds two copper ions via two sets of three histidines. This family is related to pfam00372. 209 matched cddid_all.tbl CDD pfam00265 pfam00265 306721 TK Thymidine kinase. 176 matched cddid_all.tbl CDD pfam00266 pfam00266 425567 Aminotran_5 Aminotransferase class-V. This domain is found in amino transferases, and other enzymes including cysteine desulphurase EC:4.4.1.-. 368 matched cddid_all.tbl CDD pfam00267 pfam00267 395205 Porin_1 Gram-negative porin. 335 matched cddid_all.tbl CDD pfam00268 pfam00268 425568 Ribonuc_red_sm Ribonucleotide reductase, small chain. 276 matched cddid_all.tbl CDD pfam00269 pfam00269 459739 SASP Small, acid-soluble spore proteins, alpha/beta type. 58 matched cddid_all.tbl CDD pfam00270 pfam00270 425570 DEAD DEAD/DEAH box helicase. Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. 165 matched cddid_all.tbl CDD pfam00271 pfam00271 459740 Helicase_C Helicase conserved C-terminal domain. The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. 109 matched cddid_all.tbl CDD pfam00272 pfam00272 425572 Cecropin Cecropin family. 30 matched cddid_all.tbl CDD pfam00273 pfam00273 459741 Serum_albumin Serum albumin family. 176 matched cddid_all.tbl CDD pfam00274 pfam00274 459742 Glycolytic Fructose-bisphosphate aldolase class-I. 349 matched cddid_all.tbl CDD pfam00275 pfam00275 395213 EPSP_synthase EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase). 415 matched cddid_all.tbl CDD pfam00276 pfam00276 459743 Ribosomal_L23 Ribosomal protein L23. 86 matched cddid_all.tbl CDD pfam00277 pfam00277 459744 SAA Serum amyloid A protein. The serum amyloid A (SAA) proteins comprise a family of vertebrate amphipathic alpha-helical apolipoproteins that associate predominantly with high density lipoproteins (HDL). They play a role in the mobilization of cholesterol for tissue repair and regeneration. The synthesis of these proteins is greatly increased (as much as a 1000 fold) in inflammation, being a major acute phase reactant together with C-reactive protein. They act as cytokine-like proteins that are involved in cell-cell communication and in inflammatory, immunologic, neoplastic and protective pathways. Prolonged elevation of plasma SAA levels, as in chronic inflammation, results in a pathological condition, called amyloidosis, which is characterized by the highly insoluble accumulation of SAA in several tissues. During chronic inflammation, SAA association with HDL can change its protein and lipid composition which abrogates the HDL anti-atherogenic properties, contributing to a pro-atherogenic state. 102 matched cddid_all.tbl CDD pfam00278 pfam00278 459745 Orn_DAP_Arg_deC Pyridoxal-dependent decarboxylase, C-terminal sheet domain. These pyridoxal-dependent decarboxylases act on ornithine, lysine, arginine and related substrates. 340 matched cddid_all.tbl CDD pfam00280 pfam00280 459746 potato_inhibit Potato inhibitor I family. 64 matched cddid_all.tbl CDD pfam00281 pfam00281 425579 Ribosomal_L5 Ribosomal protein L5. 57 matched cddid_all.tbl CDD pfam00282 pfam00282 395219 Pyridoxal_deC Pyridoxal-dependent decarboxylase conserved domain. 373 matched cddid_all.tbl CDD pfam00283 pfam00283 425580 Cytochrom_B559 Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits. 29 matched cddid_all.tbl CDD pfam00284 pfam00284 425581 Cytochrom_B559a Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit. This family is the lumenal portion of cytochrome b559 alpha chain, matches to this family should be accompanied by a match to the pfam00283 family also. The Prosite pattern pattern matches the transmembrane region of the cytochrome b559 alpha and beta subunits. 39 matched cddid_all.tbl CDD pfam00285 pfam00285 459747 Citrate_synt Citrate synthase, C-terminal domain. This is the long, C-terminal part of the enzyme. 357 matched cddid_all.tbl CDD pfam00286 pfam00286 425583 Flexi_CP Viral coat protein. Family includes coat proteins from Potexviruses and carlaviruses. 138 matched cddid_all.tbl CDD pfam00287 pfam00287 459748 Na_K-ATPase Sodium / potassium ATPase beta chain. 277 matched cddid_all.tbl CDD pfam00288 pfam00288 395225 GHMP_kinases_N GHMP kinases N terminal domain. This family includes homoserine kinases, galactokinases and mevalonate kinases. 64 matched cddid_all.tbl CDD pfam00289 pfam00289 425585 Biotin_carb_N Biotin carboxylase, N-terminal domain. This domain is structurally related to the PreATP-grasp domain. The family contains the N-terminus of biotin carboxylase enzymes, and propionyl-CoA carboxylase A chain. 108 matched cddid_all.tbl CDD pfam00290 pfam00290 395227 Trp_syntA Tryptophan synthase alpha chain. 258 matched cddid_all.tbl CDD pfam00291 pfam00291 459749 PALP Pyridoxal-phosphate dependent enzyme. Members of this family are all pyridoxal-phosphate dependent enzymes. This family includes: serine dehydratase EC:4.2.1.13 P20132, threonine dehydratase EC:4.2.1.16, tryptophan synthase beta chain EC:4.2.1.20, threonine synthase EC:4.2.99.2, cysteine synthase EC:4.2.99.8 P11096, cystathionine beta-synthase EC:4.2.1.22, 1-aminocyclopropane-1-carboxylate deaminase EC:4.1.99.4. 295 matched cddid_all.tbl CDD pfam00292 pfam00292 366005 PAX 'Paired box' domain. 125 matched cddid_all.tbl CDD pfam00293 pfam00293 395229 NUDIX NUDIX domain. 132 matched cddid_all.tbl CDD pfam00294 pfam00294 425587 PfkB pfkB family carbohydrate kinase. This family includes a variety of carbohydrate and pyrimidine kinases. 294 matched cddid_all.tbl CDD pfam00295 pfam00295 425588 Glyco_hydro_28 Glycosyl hydrolases family 28. Glycosyl hydrolase family 28 includes polygalacturonase EC:3.2.1.15 as well as rhamnogalacturonase A(RGase A), EC:3.2.1.-. These enzymes is important in cell wall metabolism. 319 matched cddid_all.tbl CDD pfam00296 pfam00296 425589 Bac_luciferase Luciferase-like monooxygenase. 313 matched cddid_all.tbl CDD pfam00297 pfam00297 395233 Ribosomal_L3 Ribosomal protein L3. 369 matched cddid_all.tbl CDD pfam00298 pfam00298 459750 Ribosomal_L11 Ribosomal protein L11, RNA binding domain. 69 matched cddid_all.tbl CDD pfam00299 pfam00299 395235 Squash Squash family serine protease inhibitor. 29 matched cddid_all.tbl CDD pfam00300 pfam00300 459751 His_Phos_1 Histidine phosphatase superfamily (branch 1). The histidine phosphatase superfamily is so named because catalysis centres on a conserved His residue that is transiently phosphorylated during the catalytic cycle. Other conserved residues contribute to a 'phosphate pocket' and interact with the phospho group of substrate before, during and after its transfer to the His residue. Structure and sequence analyses show that different families contribute different additional residues to the 'phosphate pocket' and, more surprisingly, differ in the position, in sequence and in three dimensions, of a catalytically essential acidic residue. The superfamily may be divided into two main branches. The larger branch 1 contains a wide variety of catalytic functions, the best known being fructose 2,6-bisphosphatase (found in a bifunctional protein with 2-phosphofructokinase) and cofactor-dependent phosphoglycerate mutase. The latter is an unusual example of a mutase activity in the superfamily: the vast majority of members appear to be phosphatases. The bacterial regulatory protein phosphatase SixA is also in branch 1 and has a minimal, and possible ancestral-like structure, lacking the large domain insertions that contribute to binding of small molecules in branch 1 members. 194 matched cddid_all.tbl CDD pfam00301 pfam00301 459752 Rubredoxin Rubredoxin. 46 matched cddid_all.tbl CDD pfam00302 pfam00302 425592 CAT Chloramphenicol acetyltransferase. 201 matched cddid_all.tbl CDD pfam00303 pfam00303 459753 Thymidylat_synt Thymidylate synthase. This is a family of proteins that are flavin-dependent thymidylate synthases. 259 matched cddid_all.tbl CDD pfam00304 pfam00304 395240 Gamma-thionin Gamma-thionin family. 44 matched cddid_all.tbl CDD pfam00305 pfam00305 459754 Lipoxygenase Lipoxygenase. 672 matched cddid_all.tbl CDD pfam00306 pfam00306 425595 ATP-synt_ab_C ATP synthase alpha/beta chain, C terminal domain. 126 matched cddid_all.tbl CDD pfam00307 pfam00307 425596 CH Calponin homology (CH) domain. The CH domain is found in both cytoskeletal proteins and signal transduction proteins. The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity. Most member proteins have from two to four copies of the CH domain, however some proteins such as calponin have only a single copy. 109 matched cddid_all.tbl CDD pfam00308 pfam00308 278724 Bac_DnaA Bacterial dnaA protein. 219 matched cddid_all.tbl CDD pfam00309 pfam00309 459755 Sigma54_AID Sigma-54 factor, Activator interacting domain (AID). The sigma-54 holoenzyme is an enhancer dependent form of the RNA polymerase. The AID is necessary for activator interaction. In addition, the AID also inhibits transcription initiation in the sigma-54 holoenzyme prior to interaction with the activator. 39 matched cddid_all.tbl CDD pfam00310 pfam00310 395245 GATase_2 Glutamine amidotransferases class-II. 420 matched cddid_all.tbl CDD pfam00311 pfam00311 425598 PEPcase Phosphoenolpyruvate carboxylase. 920 matched cddid_all.tbl CDD pfam00312 pfam00312 459756 Ribosomal_S15 Ribosomal protein S15. 81 matched cddid_all.tbl CDD pfam00313 pfam00313 278729 CSD 'Cold-shock' DNA-binding domain. 66 matched cddid_all.tbl CDD pfam00314 pfam00314 459757 Thaumatin Thaumatin family. 211 matched cddid_all.tbl CDD pfam00316 pfam00316 425601 FBPase Fructose-1-6-bisphosphatase, N-terminal domain. This family represents the N-terminus of this protein family. 191 matched cddid_all.tbl CDD pfam00317 pfam00317 459758 Ribonuc_red_lgN Ribonucleotide reductase, all-alpha domain. 75 matched cddid_all.tbl CDD pfam00318 pfam00318 459759 Ribosomal_S2 Ribosomal protein S2. 216 matched cddid_all.tbl CDD pfam00319 pfam00319 459760 SRF-TF SRF-type transcription factor (DNA-binding and dimerization domain). 48 matched cddid_all.tbl CDD pfam00320 pfam00320 425605 GATA GATA zinc finger. This domain uses four cysteine residues to coordinate a zinc ion. This domain binds to DNA. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contain a single copy of the domain. 36 matched cddid_all.tbl CDD pfam00321 pfam00321 395254 Thionin Plant thionin. 46 matched cddid_all.tbl CDD pfam00322 pfam00322 425606 Endothelin Endothelin family. 29 matched cddid_all.tbl CDD pfam00323 pfam00323 425607 Defensin_1 Mammalian defensin. 29 matched cddid_all.tbl CDD pfam00324 pfam00324 366028 AA_permease Amino acid permease. 467 matched cddid_all.tbl CDD pfam00325 pfam00325 425608 Crp Bacterial regulatory proteins, crp family. 32 matched cddid_all.tbl CDD pfam00326 pfam00326 459761 Peptidase_S9 Prolyl oligopeptidase family. 213 matched cddid_all.tbl CDD pfam00327 pfam00327 459762 Ribosomal_L30 Ribosomal protein L30p/L7e. This family includes prokaryotic L30 and eukaryotic L7. 51 matched cddid_all.tbl CDD pfam00328 pfam00328 395259 His_Phos_2 Histidine phosphatase superfamily (branch 2). The histidine phosphatase superfamily is so named because catalysis centres on a conserved His residue that is transiently phosphorylated during the catalytic cycle. Other conserved residues contribute to a 'phosphate pocket' and interact with the phospho group of substrate before, during and after its transfer to the His residue. Structure and sequence analyses show that different families contribute different additional residues to the 'phosphate pocket' and, more surprisingly, differ in the position, in sequence and in three dimensions, of a catalytically essential acidic residue. The superfamily may be divided into two main branches.The smaller branch 2 contains predominantly eukaryotic proteins. The catalytic functions in members include phytase, glucose-1-phosphatase and multiple inositol polyphosphate phosphatase. The in vivo roles of the mammalian acid phosphatases in branch 2 are not fully understood, although activity against lysophosphatidic acid and tyrosine-phosphorylated proteins has been demonstrated. 356 matched cddid_all.tbl CDD pfam00329 pfam00329 459763 Complex1_30kDa Respiratory-chain NADH dehydrogenase, 30 Kd subunit. 121 matched cddid_all.tbl CDD pfam00330 pfam00330 459764 Aconitase Aconitase family (aconitate hydratase). 460 matched cddid_all.tbl CDD pfam00331 pfam00331 425613 Glyco_hydro_10 Glycosyl hydrolase family 10. 310 matched cddid_all.tbl CDD pfam00332 pfam00332 366033 Glyco_hydro_17 Glycosyl hydrolases family 17. 309 matched cddid_all.tbl CDD pfam00333 pfam00333 459765 Ribosomal_S5 Ribosomal protein S5, N-terminal domain. 65 matched cddid_all.tbl CDD pfam00334 pfam00334 459766 NDK Nucleoside diphosphate kinase. 135 matched cddid_all.tbl CDD pfam00335 pfam00335 459767 Tetraspanin Tetraspanin family. 183 matched cddid_all.tbl CDD pfam00336 pfam00336 366036 DNA_pol_viral_C DNA polymerase (viral) C-terminal domain. 241 matched cddid_all.tbl CDD pfam00337 pfam00337 459768 Gal-bind_lectin Galactoside-binding lectin. This family contains galactoside binding lectins. The family also includes enzymes such as human eosinophil lysophospholipase (EC:3.1.1.5). 124 matched cddid_all.tbl CDD pfam00338 pfam00338 459769 Ribosomal_S10 Ribosomal protein S10p/S20e. This family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes. 98 matched cddid_all.tbl CDD pfam00339 pfam00339 425619 Arrestin_N Arrestin (or S-antigen), N-terminal domain. Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain. 148 matched cddid_all.tbl CDD pfam00340 pfam00340 395269 IL1 Interleukin-1 / 18. This family includes interleukin-1 and interleukin-18. 119 matched cddid_all.tbl CDD pfam00341 pfam00341 425620 PDGF PDGF/VEGF domain. 82 matched cddid_all.tbl CDD pfam00342 pfam00342 395271 PGI Phosphoglucose isomerase. Phosphoglucose isomerase catalyzes the interconversion of glucose-6-phosphate and fructose-6-phosphate. 487 matched cddid_all.tbl CDD pfam00343 pfam00343 459770 Phosphorylase Carbohydrate phosphorylase. The members of this family catalyze the formation of glucose 1-phosphate from one of the following polyglucoses; glycogen, starch, glucan or maltodextrin. 713 matched cddid_all.tbl CDD pfam00344 pfam00344 459771 SecY SecY. 322 matched cddid_all.tbl CDD pfam00345 pfam00345 425623 PapD_N Pili and flagellar-assembly chaperone, PapD N-terminal domain. C2 domain-like beta-sandwich fold. This domain is the n-terminal part of the PapD chaperone protein for pilus and flagellar assembly. 123 matched cddid_all.tbl CDD pfam00346 pfam00346 459772 Complex1_49kDa Respiratory-chain NADH dehydrogenase, 49 Kd subunit. 270 matched cddid_all.tbl CDD pfam00347 pfam00347 425625 Ribosomal_L6 Ribosomal protein L6. 78 matched cddid_all.tbl CDD pfam00348 pfam00348 459773 polyprenyl_synt Polyprenyl synthetase. 251 matched cddid_all.tbl CDD pfam00349 pfam00349 459774 Hexokinase_1 Hexokinase. Hexokinase (EC:2.7.1.1) contains two structurally similar domains represented by this family and pfam03727. Some members of the family have two copies of each of these domains. 197 matched cddid_all.tbl CDD pfam00350 pfam00350 459775 Dynamin_N Dynamin family. 168 matched cddid_all.tbl CDD pfam00351 pfam00351 459776 Biopterin_H Biopterin-dependent aromatic amino acid hydroxylase. This family includes phenylalanine-4-hydroxylase, the phenylketonuria disease protein. 331 matched cddid_all.tbl CDD pfam00352 pfam00352 425630 TBP Transcription factor TFIID (or TATA-binding protein, TBP). 84 matched cddid_all.tbl CDD pfam00353 pfam00353 459777 HemolysinCabind RTX calcium-binding nonapeptide repeat (4 copies). 36 matched cddid_all.tbl CDD pfam00354 pfam00354 278768 Pentaxin Pentaxin family. Pentaxins are also known as pentraxins. 194 matched cddid_all.tbl CDD pfam00355 pfam00355 425632 Rieske Rieske [2Fe-2S] domain. The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilizes the protein. 89 matched cddid_all.tbl CDD pfam00356 pfam00356 306791 LacI Bacterial regulatory proteins, lacI family. 46 matched cddid_all.tbl CDD pfam00357 pfam00357 459778 Integrin_alpha Integrin alpha cytoplasmic region. This family contains the short intracellular region of integrin alpha chains. 15 matched cddid_all.tbl CDD pfam00358 pfam00358 459779 PTS_EIIA_1 phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1. 121 matched cddid_all.tbl CDD pfam00359 pfam00359 459780 PTS_EIIA_2 Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2. 139 matched cddid_all.tbl CDD pfam00360 pfam00360 425635 PHY Phytochrome region. Phytochromes are red/far-red photochromic biliprotein photoreceptors which regulate plant development. They are widely represented in both photosynthetic and non-photosynthetic bacteria and are known in a variety of fungi. Although sequence similarities are low, this domain is structurally related to pfam01590, which is generally located immediately N-terminal to this domain. Compared with pfam01590, this domain carries an additional tongue-like hairpin loop between the fifth beta-sheet and the sixth alpha-helix which functions to seal the chromophore pocket and stabilize the photoactivated far-red-absorbing state (Pfr). The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue. 178 matched cddid_all.tbl CDD pfam00361 pfam00361 425636 Proton_antipo_M Proton-conducting membrane transporter. This is a family of membrane transporters that inlcudes some 7 of potentially 14-16 TM regions. In many instances the family forms part of complex I that catalyzes the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane, and in this context is a combination predominantly of subunits 2, 4, 5, 14, L, M and N. In many bacterial species these proteins are probable stand-alone transporters not coupled with oxidoreduction. The family in total represents homologs across the phyla. 291 matched cddid_all.tbl CDD pfam00362 pfam00362 459781 Integrin_beta Integrin beta chain VWA domain. Integrins have been found in animals and their homologs have also been found in cyanobacteria, probably due to horizontal gene transfer. This domain corresponds to the integrin beta VWA domain. 248 matched cddid_all.tbl CDD pfam00363 pfam00363 459782 Casein Casein. 87 matched cddid_all.tbl CDD pfam00364 pfam00364 395290 Biotin_lipoyl Biotin-requiring enzyme. This family covers two Prosite entries, the conserved lysine residue binds biotin in one group and lipoic acid in the other. Note that the HMM does not currently recognize the Glycine cleavage system H proteins. 73 matched cddid_all.tbl CDD pfam00365 pfam00365 459783 PFK Phosphofructokinase. 271 matched cddid_all.tbl CDD pfam00366 pfam00366 459784 Ribosomal_S17 Ribosomal protein S17. 68 matched cddid_all.tbl CDD pfam00367 pfam00367 459785 PTS_EIIB phosphotransferase system, EIIB. 32 matched cddid_all.tbl CDD pfam00368 pfam00368 459786 HMG-CoA_red Hydroxymethylglutaryl-coenzyme A reductase. The HMG-CoA reductases catalyze the conversion of HMG-CoA to mevalonate, which is the rate-limiting step in the synthesis of isoprenoids like cholesterol. Probably because of the critical role of this enzyme in cholesterol homeostasis, mammalian HMG-CoA reductase is heavily regulated at the transcriptional, translational, and post-translational levels. 368 matched cddid_all.tbl CDD pfam00370 pfam00370 395295 FGGY_N FGGY family of carbohydrate kinases, N-terminal domain. This domain adopts a ribonuclease H-like fold and is structurally related to the C-terminal domain. 245 matched cddid_all.tbl CDD pfam00372 pfam00372 459787 Hemocyanin_M Hemocyanin, copper containing domain. This family includes arthropod hemocyanins and insect larval storage proteins. 268 matched cddid_all.tbl CDD pfam00373 pfam00373 459788 FERM_M FERM central domain. This domain is the central structural domain of the FERM domain. 117 matched cddid_all.tbl CDD pfam00374 pfam00374 459789 NiFeSe_Hases Nickel-dependent hydrogenase. 495 matched cddid_all.tbl CDD pfam00375 pfam00375 425646 SDF Sodium:dicarboxylate symporter family. 388 matched cddid_all.tbl CDD pfam00376 pfam00376 425647 MerR MerR family regulatory protein. 38 matched cddid_all.tbl CDD pfam00377 pfam00377 425648 Prion Prion/Doppel alpha-helical domain. The prion protein is thought to be the infectious agent that causes transmissible spongiform encephalopathies, such as scrapie and BSE. It is thought that the prion protein can exist in two different forms: one is the normal cellular protein, and the other is the infectious form which can change the normal prion protein into the infectious form. It has been found that the prion alpha-helical domain is also found in the Doppel protein. 115 matched cddid_all.tbl CDD pfam00378 pfam00378 395302 ECH_1 Enoyl-CoA hydratase/isomerase. This family contains a diverse set of enzymes including: enoyl-CoA hydratase, napthoate synthase, carnitate racemase, 3-hydroxybutyryl-CoA dehydratase and dodecanoyl-CoA delta-isomerase. 251 matched cddid_all.tbl CDD pfam00379 pfam00379 459790 Chitin_bind_4 Insect cuticle protein. Many insect cuticular proteins include a 35-36 amino acid motif known as the R&R consensus. The extensive conservation of this region led to the suggestion that it functions to bind chitin. Provocatively, it has no sequence similarity to the well-known cysteine-containing chitin-binding domain found in chitinases and some peritrophic membrane proteins. Chitin binding has been shown experimentally for this region. Thus arthropods have two distinct classes of chitin binding proteins, those with the chitin-binding domain found in lectins, chitinases and peritrophic membranes (cysCBD) and those with the cuticular protein chitin-binding domain (non-cysCBD). 52 matched cddid_all.tbl CDD pfam00380 pfam00380 459791 Ribosomal_S9 Ribosomal protein S9/S16. This family includes small ribosomal subunit S9 from prokaryotes and S16 from eukaryotes. 121 matched cddid_all.tbl CDD pfam00381 pfam00381 459792 PTS-HPr PTS HPr component phosphorylation site. 79 matched cddid_all.tbl CDD pfam00382 pfam00382 425652 TFIIB Transcription factor TFIIB repeat. 92 matched cddid_all.tbl CDD pfam00383 pfam00383 395307 dCMP_cyt_deam_1 Cytidine and deoxycytidylate deaminase zinc-binding region. 100 matched cddid_all.tbl CDD pfam00384 pfam00384 395308 Molybdopterin Molybdopterin oxidoreductase. 359 matched cddid_all.tbl CDD pfam00385 pfam00385 459793 Chromo Chromo (CHRromatin organization MOdifier) domain. 52 matched cddid_all.tbl CDD pfam00386 pfam00386 395310 C1q C1q domain. C1q is a subunit of the C1 enzyme complex that activates the serum complement system. 126 matched cddid_all.tbl CDD pfam00387 pfam00387 459794 PI-PLC-Y Phosphatidylinositol-specific phospholipase C, Y domain. This associates with pfam00388 to form a single structural unit. 114 matched cddid_all.tbl CDD pfam00388 pfam00388 459795 PI-PLC-X Phosphatidylinositol-specific phospholipase C, X domain. This associates with pfam00387 to form a single structural unit. 142 matched cddid_all.tbl CDD pfam00389 pfam00389 425656 2-Hacid_dh D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain. This family represents the largest portion of the catalytic domain of 2-hydroxyacid dehydrogenases as the NAD binding domain is inserted within the structural domain. 311 matched cddid_all.tbl CDD pfam00390 pfam00390 395314 malic Malic enzyme, N-terminal domain. 182 matched cddid_all.tbl CDD pfam00391 pfam00391 459796 PEP-utilizers "PEP-utilizing enzyme, mobile domain. This domain is a ""swivelling"" beta/beta/alpha domain which is thought to be mobile in all proteins known to contain it." 73 matched cddid_all.tbl CDD pfam00392 pfam00392 306822 GntR Bacterial regulatory proteins, gntR family. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerization domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor. 64 matched cddid_all.tbl CDD pfam00393 pfam00393 459797 6PGD 6-phosphogluconate dehydrogenase, C-terminal domain. This family represents the C-terminal all-alpha domain of 6-phosphogluconate dehydrogenase. The domain contains two structural repeats of 5 helices each. 290 matched cddid_all.tbl CDD pfam00394 pfam00394 395317 Cu-oxidase Multicopper oxidase. Many of the proteins in this family contain multiple similar copies of this plastocyanin-like domain. 146 matched cddid_all.tbl CDD pfam00395 pfam00395 459798 SLH S-layer homology domain. 42 matched cddid_all.tbl CDD pfam00396 pfam00396 459799 Granulin Granulin. 42 matched cddid_all.tbl CDD pfam00397 pfam00397 459800 WW WW domain. The WW domain is a protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro. 30 matched cddid_all.tbl CDD pfam00398 pfam00398 395321 RrnaAD Ribosomal RNA adenine dimethylase. 263 matched cddid_all.tbl CDD pfam00399 pfam00399 395322 PIR Yeast PIR protein repeat. 17 matched cddid_all.tbl CDD pfam00400 pfam00400 459801 WD40 WD domain, G-beta repeat. 39 matched cddid_all.tbl CDD pfam00401 pfam00401 459802 ATP-synt_DE ATP synthase, Delta/Epsilon chain, long alpha-helix domain. Part of the ATP synthase CF(1). These subunits are part of the head unit of the ATP synthase. This subunit is called epsilon in bacteria and delta in mitochondria. In bacteria the delta (D) subunit is equivalent to the mitochondrial Oligomycin sensitive subunit, OSCP (pfam00213). 45 matched cddid_all.tbl CDD pfam00402 pfam00402 459803 Calponin Calponin family repeat. 25 matched cddid_all.tbl CDD pfam00403 pfam00403 459804 HMA Heavy-metal-associated domain. 58 matched cddid_all.tbl CDD pfam00404 pfam00404 459805 Dockerin_1 Dockerin type I domain. The dockerin repeat is the binding partner of the cohesin domain pfam00963. The cohesin-dockerin interaction is the crucial interaction for complex formation in the cellulosome. The dockerin repeats, each bearing homology to the EF-hand calcium-binding loop bind calcium. This family contains two copies of the repeat. 56 matched cddid_all.tbl CDD pfam00405 pfam00405 395328 Transferrin Transferrin. 328 matched cddid_all.tbl CDD pfam00406 pfam00406 395329 ADK Adenylate kinase. 184 matched cddid_all.tbl CDD pfam00407 pfam00407 395330 Bet_v_1 Pathogenesis-related protein Bet v 1 family. This family is named after Bet v 1, the major birch pollen allergen. This protein belongs to family 10 of plant pathogenesis-related proteins (PR-10), cytoplasmic proteins of 15-17 kd that are wide-spread among dicotyledonous plants. In recent years, a number of diverse plant proteins with low sequence similarity to Bet v 1 was identified. A classification by sequence similarity yielded several subfamilies related to pathogenesis-related proteins PR-10: These proteins were identified as major tree pollen allergens in birch and related species (hazel, alder), as plant food allergens expressed in high levels in fruits, vegetables and seeds (apple, celery, hazelnut), and as pathogenesis-related proteins whose expression is induced by pathogen infection, wounding, or abiotic stress. Hyp-1, an enzyme involved in the synthesis of the bioactive naphthodianthrone hypericin in St. John's wort (Hypericum perforatum) also belongs to this family. Most of these proteins were found in dicotyledonous plants. In addition, related sequences were identified in monocots and conifers. - Cytokinin-specific binding proteins: These legume proteins bind cytokinin plant hormones. - (S)-Norcoclaurine synthases are enzymes catalysing the condensation of dopamine and 4-hydroxyphenylacetaldehyde to (S)-norcoclaurine, the first committed step in the biosynthesis of benzylisoquinoline alkaloids such as morphine. -Major latex proteins and ripening-related proteins are proteins of unknown biological function that were first discovered in the latex of opium poppy (Papaver somniferum) and later found to be upregulated during ripening of fruits such as strawberry and cucumber. The occurrence of Bet v 1-related proteins is confined to seed plants with the exception of a cytokinin-binding protein from the moss Physcomitrella patens. 149 matched cddid_all.tbl CDD pfam00408 pfam00408 425666 PGM_PMM_IV Phosphoglucomutase/phosphomannomutase, C-terminal domain. 71 matched cddid_all.tbl CDD pfam00410 pfam00410 425667 Ribosomal_S8 Ribosomal protein S8. 127 matched cddid_all.tbl CDD pfam00411 pfam00411 306838 Ribosomal_S11 Ribosomal protein S11. 109 matched cddid_all.tbl CDD pfam00412 pfam00412 395333 LIM LIM domain. This family represents two copies of the LIM structural domain. 57 matched cddid_all.tbl CDD pfam00413 pfam00413 425668 Peptidase_M10 Matrixin. The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. 159 matched cddid_all.tbl CDD pfam00414 pfam00414 459806 MAP1B_neuraxin Neuraxin and MAP1B repeat. 17 matched cddid_all.tbl CDD pfam00415 pfam00415 395335 RCC1 Regulator of chromosome condensation (RCC1) repeat. 50 matched cddid_all.tbl CDD pfam00416 pfam00416 425669 Ribosomal_S13 Ribosomal protein S13/S18. This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes. 107 matched cddid_all.tbl CDD pfam00418 pfam00418 459807 Tubulin-binding Tau and MAP protein, tubulin-binding repeat. This family includes the vertebrate proteins MAP2, MAP4 and Tau, as well as other animal homologs. MAP4 is present in many tissues but is usually absent from neurons; MAP2 and Tau are mainly neuronal. Members of this family have the ability to bind to and stabilize microtubules. As a result, they are involved in neuronal migration, supporting dendrite elongation, and regulating microtubules during mitotic metaphase. Note that Tau is involved in neurofibrillary tangle formation in Alzheimer's disease and some other dementias. This family features a C-terminal microtubule binding repeat that contains a conserved KXGS motif. 30 matched cddid_all.tbl CDD pfam00419 pfam00419 425671 Fimbrial Fimbrial protein. 152 matched cddid_all.tbl CDD pfam00420 pfam00420 425672 Oxidored_q2 NADH-ubiquinone/plastoquinone oxidoreductase chain 4L. 95 matched cddid_all.tbl CDD pfam00421 pfam00421 425673 PSII Photosystem II protein. 499 matched cddid_all.tbl CDD pfam00423 pfam00423 278832 HN Haemagglutinin-neuraminidase. 539 matched cddid_all.tbl CDD pfam00424 pfam00424 366091 REV REV protein (anti-repression trans-activator protein). 91 matched cddid_all.tbl CDD pfam00425 pfam00425 425674 Chorismate_bind chorismate binding enzyme. This family includes the catalytic regions of the chorismate binding enzymes anthranilate synthase, isochorismate synthase, aminodeoxychorismate synthase and para-aminobenzoate synthase. 255 matched cddid_all.tbl CDD pfam00426 pfam00426 395342 VP4_haemagglut Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain. This entry represents the N-terminal concanavalin-like domain from the VP4 protein of rotavirus. 193 matched cddid_all.tbl CDD pfam00427 pfam00427 425675 PBS_linker_poly Phycobilisome Linker polypeptide. 125 matched cddid_all.tbl CDD pfam00428 pfam00428 459808 Ribosomal_60s 60s Acidic ribosomal protein. This family includes archaebacterial L12, eukaryotic P0, P1 and P2. 87 matched cddid_all.tbl CDD pfam00429 pfam00429 306850 TLV_coat ENV polyprotein (coat polyprotein). 560 matched cddid_all.tbl CDD pfam00430 pfam00430 425677 ATP-synt_B ATP synthase B/B' CF(0). Part of the CF(0) (base unit) of the ATP synthase. The base unit is thought to translocate protons through membrane (inner membrane in mitochondria, thylakoid membrane in plants, cytoplasmic membrane in bacteria). The B subunits are thought to interact with the stalk of the CF(1) subunits. This domain should not be confused with the ab CF(1) proteins (in the head of the ATP synthase) which are found in pfam00006 132 matched cddid_all.tbl CDD pfam00431 pfam00431 395345 CUB CUB domain. 110 matched cddid_all.tbl CDD pfam00432 pfam00432 395346 Prenyltrans Prenyltransferase and squalene oxidase repeat. 44 matched cddid_all.tbl CDD pfam00433 pfam00433 459809 Pkinase_C Protein kinase C terminal domain. 42 matched cddid_all.tbl CDD pfam00434 pfam00434 425679 VP7 Glycoprotein VP7. 323 matched cddid_all.tbl CDD pfam00435 pfam00435 395348 Spectrin Spectrin repeat. Spectrin repeat-domains are found in several proteins involved in cytoskeletal structure. These include spectrin, alpha-actinin and dystrophin. The sequence repeat used in this family is taken from the structural repeat in reference. The spectrin domain- repeat forms a three helix bundle. The second helix is interrupted by proline in some sequences. The repeats are defined by a characteriztic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues from the carboxyl end of helix C. Although the domain occurs in multiple repeats along sequences, the domains are actually stable on their own - ie they act, biophysically, like domains rather than repeats that along function when aggregated. 105 matched cddid_all.tbl CDD pfam00436 pfam00436 425680 SSB Single-strand binding protein family. This family includes single stranded binding proteins and also the primosomal replication protein N (PriB). PriB forms a complex with PriA, PriC and ssDNA. 103 matched cddid_all.tbl CDD pfam00437 pfam00437 425681 T2SSE Type II/IV secretion system protein. This family contains components of both the Type II protein secretion system (T2SS), including Type 4 pilus (T4P), and Type IV protein secretion system (T4SS) from Gram-negative bacteria. VirB11 ATPase is a subunit of the Agrobacterium tumefaciens transfer DNA (T-DNA) transfer system, a type IV secretion pathway required for delivery of T-DNA and effector proteins to plant cells during infection. The cytoplasmic T2S E ATPase is a Zn-containing protein thought to provide the mechanical force for the secretion process. T2S-E contains Walker A and B motifs, that are essential for secretion and ATPase activity. ATPase PulE and XcpR from Klebsiella oxytoca and Pseudomonas aeruginosa respectively are required for protein secretion via the T2SS. ATPase PilB is required for T4P extension. 269 matched cddid_all.tbl CDD pfam00438 pfam00438 459810 S-AdoMet_synt_N S-adenosylmethionine synthetase, N-terminal domain. The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold. 98 matched cddid_all.tbl CDD pfam00439 pfam00439 425683 Bromodomain Bromodomain. Bromodomains are 110 amino acid long domains, that are found in many chromatin associated proteins. Bromodomains can interact specifically with acetylated lysine. 84 matched cddid_all.tbl CDD pfam00440 pfam00440 425684 TetR_N Bacterial regulatory proteins, tetR family. 47 matched cddid_all.tbl CDD pfam00441 pfam00441 395354 Acyl-CoA_dh_1 Acyl-CoA dehydrogenase, C-terminal domain. C-terminal domain of Acyl-CoA dehydrogenase is an all-alpha, four helical up-and-down bundle. 149 matched cddid_all.tbl CDD pfam00443 pfam00443 425685 UCH Ubiquitin carboxyl-terminal hydrolase. 310 matched cddid_all.tbl CDD pfam00444 pfam00444 459811 Ribosomal_L36 Ribosomal protein L36. 38 matched cddid_all.tbl CDD pfam00445 pfam00445 459812 Ribonuclease_T2 Ribonuclease T2 family. 181 matched cddid_all.tbl CDD pfam00446 pfam00446 278853 GnRH Gonadotropin-releasing hormone. 10 matched cddid_all.tbl CDD pfam00447 pfam00447 459813 HSF_DNA-bind HSF-type DNA-binding. 98 matched cddid_all.tbl CDD pfam00448 pfam00448 459814 SRP54 SRP54-type protein, GTPase domain. This family includes relatives of the G-domain of the SRP54 family of proteins. 193 matched cddid_all.tbl CDD pfam00449 pfam00449 425689 Urease_alpha Urease alpha-subunit, N-terminal domain. The N-terminal domain is a composite domain and plays a major trimer stabilising role by contacting the catalytic domain of the symmetry related alpha-subunit. 120 matched cddid_all.tbl CDD pfam00450 pfam00450 459815 Peptidase_S10 Serine carboxypeptidase. 404 matched cddid_all.tbl CDD pfam00451 pfam00451 278858 Toxin_2 Scorpion short toxin, BmKK2. Members of this family, which are found in various scorpion toxins, confer potassium channel blocking activity. 32 matched cddid_all.tbl CDD pfam00452 pfam00452 459816 Bcl-2 Apoptosis regulator proteins, Bcl-2 family. 101 matched cddid_all.tbl CDD pfam00453 pfam00453 459817 Ribosomal_L20 Ribosomal protein L20. 104 matched cddid_all.tbl CDD pfam00454 pfam00454 395364 PI3_PI4_kinase Phosphatidylinositol 3- and 4-kinase. Some members of this family probably do not have lipid kinase activity and are protein kinases,. 241 matched cddid_all.tbl CDD pfam00455 pfam00455 395365 DeoRC DeoR C terminal sensor domain. The sensor domains of the DeoR are catalytically inactive versions of the ISOCOT fold, but retain the substrate binding site. DeorC senses diverse sugar derivatives such as deoxyribose nucleoside (DeoR), tagatose phosphate (LacR), galactosamine (AgaR), myo-inositol (Bacillus IolR) and L-ascorbate (UlaR). It can also bind L-ascorbate 6-phosphate, agrocinopines, sn-glycerol 3-phosphate, and sulfoquinovose (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 160 matched cddid_all.tbl CDD pfam00456 pfam00456 395366 Transketolase_N Transketolase, thiamine diphosphate binding domain. This family includes transketolase enzymes EC:2.2.1.1. and also partially matches to 2-oxoisovalerate dehydrogenase beta subunit EC:1.2.4.4. Both these enzymes utilize thiamine pyrophosphate as a cofactor, suggesting there may be common aspects in their mechanism of catalysis. 334 matched cddid_all.tbl CDD pfam00457 pfam00457 459818 Glyco_hydro_11 Glycosyl hydrolases family 11. 175 matched cddid_all.tbl CDD pfam00458 pfam00458 459819 WHEP-TRS WHEP-TRS domain. 53 matched cddid_all.tbl CDD pfam00459 pfam00459 459820 Inositol_P Inositol monophosphatase family. 271 matched cddid_all.tbl CDD pfam00460 pfam00460 459821 Flg_bb_rod Flagella basal body rod protein. 30 matched cddid_all.tbl CDD pfam00462 pfam00462 425695 Glutaredoxin Glutaredoxin. 60 matched cddid_all.tbl CDD pfam00463 pfam00463 278869 ICL Isocitrate lyase family. 526 matched cddid_all.tbl CDD pfam00464 pfam00464 395372 SHMT Serine hydroxymethyltransferase. 399 matched cddid_all.tbl CDD pfam00465 pfam00465 425696 Fe-ADH Iron-containing alcohol dehydrogenase. 362 matched cddid_all.tbl CDD pfam00466 pfam00466 459822 Ribosomal_L10 Ribosomal protein L10. 99 matched cddid_all.tbl CDD pfam00467 pfam00467 425698 KOW KOW motif. This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG. 32 matched cddid_all.tbl CDD pfam00468 pfam00468 425699 Ribosomal_L34 Ribosomal protein L34. 42 matched cddid_all.tbl CDD pfam00469 pfam00469 425700 F-protein Negative factor, (F-Protein) or Nef. Nef protein accelerates virulent progression of AIDS by its interaction with cellular proteins involved in signal transduction and host cell activation. Nef has been shown to bind specifically to a subset of the Src kinase family. 220 matched cddid_all.tbl CDD pfam00471 pfam00471 425701 Ribosomal_L33 Ribosomal protein L33. 46 matched cddid_all.tbl CDD pfam00472 pfam00472 459823 RF-1 RF-1 domain. This domain is found in peptide chain release factors such as RF-1 and RF-2, and a number of smaller proteins of unknown function. This domain contains the peptidyl-tRNA hydrolase activity. The domain contains a highly conserved motif GGQ, where the glutamine is thought to coordinate the water that mediates the hydrolysis. 111 matched cddid_all.tbl CDD pfam00473 pfam00473 425703 CRF Corticotropin-releasing factor family. 38 matched cddid_all.tbl CDD pfam00474 pfam00474 109527 SSF Sodium:solute symporter family. This family includes Swiss:P33413 which is not in the Prosite entry. Membership of this family is supported by a significant blast score. 406 matched cddid_all.tbl CDD pfam00475 pfam00475 459824 IGPD Imidazoleglycerol-phosphate dehydratase. 140 matched cddid_all.tbl CDD pfam00476 pfam00476 459825 DNA_pol_A DNA polymerase family A. 368 matched cddid_all.tbl CDD pfam00477 pfam00477 306882 LEA_5 Small hydrophilic plant seed protein. 109 matched cddid_all.tbl CDD pfam00478 pfam00478 459826 IMPDH IMP dehydrogenase / GMP reductase domain. This family is involved in biosynthesis of guanosine nucleotide. Members of this family contain a TIM barrel structure. In the inosine monophosphate dehydrogenases 2 CBS domains pfam00571 are inserted in the TIM barrel. This family is a member of the common phosphate binding site TIM barrel family. 463 matched cddid_all.tbl CDD pfam00479 pfam00479 459827 G6PD_N Glucose-6-phosphate dehydrogenase, NAD binding domain. 178 matched cddid_all.tbl CDD pfam00480 pfam00480 395384 ROK ROK family. This family, known as ROK (Repressor, ORF, Kinase) includes the xylose operon repressor, xylR, from Bacillus subtilis, Lactobacillus pentosus and Staphylococcus xylosus; N-acetylglucosamine repressor, nagC, from Escherichia coli; glucokinase from Streptomyces coelicolor; fructokinase from from Pediococcus pentosaceus, Streptococcus mutans and Zymomonas mobilis; allokinase and mlc from E. coli; and E. coli hypothetical proteins yajF and yhcI and the corresponding Haemophilus influenzae proteins. The repressor proteins (xylR and nagC) from this family possess an N-terminal region not present in the sugar kinases and which contains an helix-turn-helix DNA-binding motif. 292 matched cddid_all.tbl CDD pfam00481 pfam00481 395385 PP2C Protein phosphatase 2C. Protein phosphatase 2C is a Mn++ or Mg++ dependent protein serine/threonine phosphatase. 252 matched cddid_all.tbl CDD pfam00482 pfam00482 425708 T2SSF Type II secretion system (T2SS), protein F. The original family covered both the regions found by the current model. The splitting of the family has allowed the related FlaJ_arch (archaeal FlaJ family) to be merged with it. Proteins with this domain in form a platform for the machiney of the Type II secretion system, as well as the Type 4 pili and the archaeal flagella. This domain seems to show some similarity to PF00664 but this may just be due to similarities in the TM helices (personal obs: C Yeats). 119 matched cddid_all.tbl CDD pfam00483 pfam00483 425709 NTP_transferase Nucleotidyl transferase. This family includes a wide range of enzymes which transfer nucleotides onto phosphosugars. 243 matched cddid_all.tbl CDD pfam00484 pfam00484 459828 Pro_CA Carbonic anhydrase. This family includes carbonic anhydrases as well as a family of non-functional homologs related to YbcF. 156 matched cddid_all.tbl CDD pfam00485 pfam00485 425711 PRK Phosphoribulokinase / Uridine kinase family. This family matches three types of P-loop containing kinases: phosphoribulokinases, uridine kinases and bacterial pantothenate kinases(CoaA). Arabidopsis and other organizms have a dual uridine kinase/uracil phosphoribosyltransferase protein where the N-terminal region consists of a UK domain and the C-terminal region of a UPRT domain. 196 matched cddid_all.tbl CDD pfam00486 pfam00486 425712 Trans_reg_C Transcriptional regulatory protein, C terminal. 77 matched cddid_all.tbl CDD pfam00487 pfam00487 425713 FA_desaturase Fatty acid desaturase. Fatty acid desaturases are enzymes that catalyze the insertion of a double bond at the delta position of fatty acids. There seem to be two distinct families of fatty acid desaturases which do not seem to be evolutionary related: Family 1 composed of Stearoyl-CoA desaturases (SCD) and Family 2 composed of Bacterial fatty acid desaturases, Plant stearoyl-acyl-carrier-protein desaturase and Cyanobacterial DesA. Members of this entry are ER integral membrane proteins that share the same mushroom-shaped fold consisting of four transmembrane helices (TM1-TM4) which anchor them to the membrane, capped by a cytosolic domain containing a unique 9-10 histidine- coordinating di metal (di-iron) catalytic centre. The structure of mouse stearoyl-CoA desaturase (SDC) revealed that TM2 and TM4 are longer than TM1 and TM3 and protrude into the cytosolic domain, providing three of the nine histidine residues that coordinate the two metal ions, while the other histidine residues are provided by the soluble domain in this enzyme. 252 matched cddid_all.tbl CDD pfam00488 pfam00488 425714 MutS_V MutS domain V. This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam01624, pfam05188, pfam05192 and pfam05190. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain V of Thermus aquaticus MutS as characterized in, which contains a Walker A motif, and is structurally similar to the ATPase domain of ABC transporters. 188 matched cddid_all.tbl CDD pfam00489 pfam00489 395393 IL6 Interleukin-6/G-CSF/MGF family. 184 matched cddid_all.tbl CDD pfam00490 pfam00490 459829 ALAD Delta-aminolevulinic acid dehydratase. 315 matched cddid_all.tbl CDD pfam00491 pfam00491 425716 Arginase Arginase family. 272 matched cddid_all.tbl CDD pfam00493 pfam00493 459830 MCM MCM P-loop domain. 224 matched cddid_all.tbl CDD pfam00494 pfam00494 425717 SQS_PSY Squalene/phytoene synthase. 261 matched cddid_all.tbl CDD pfam00496 pfam00496 425718 SBP_bac_5 Bacterial extracellular solute-binding proteins, family 5 Middle. The borders of this family are based on the PDBSum definitions of the domain edges for Swiss:P06202. 368 matched cddid_all.tbl CDD pfam00497 pfam00497 425719 SBP_bac_3 Bacterial extracellular solute-binding proteins, family 3. This is a sensor domain found in solute-binding protein family 3 members from Gram-positive bacteria, Gram-negative bacteria and archaea. It can also be found in the N-terminal of the membrane-bound lytic murein transglycosylase F (MltF) protein. This domain recognizes Nicotinate, quidalnate, pyridine-2,5-dicarboxylate and salicylate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 221 matched cddid_all.tbl CDD pfam00498 pfam00498 459831 FHA FHA domain. The FHA (Forkhead-associated) domain is a phosphopeptide binding motif. 66 matched cddid_all.tbl CDD pfam00499 pfam00499 459832 Oxidored_q3 NADH-ubiquinone/plastoquinone oxidoreductase chain 6. 141 matched cddid_all.tbl CDD pfam00500 pfam00500 459833 Late_protein_L1 L1 (late) protein. 497 matched cddid_all.tbl CDD pfam00501 pfam00501 459834 AMP-binding AMP-binding enzyme. 417 matched cddid_all.tbl CDD pfam00502 pfam00502 425723 Phycobilisome Phycobilisome protein. 155 matched cddid_all.tbl CDD pfam00503 pfam00503 459835 G-alpha G-protein alpha subunit. G proteins couple receptors of extracellular signals to intracellular signaling pathways. The G protein alpha subunit binds guanyl nucleotide and is a weak GTPase. A set of residues that are unique to G-alpha as compared to its ancestor the Arf-like family form a ring of residues centered on the nucleotide binding site. A Ggamma is found fused to an inactive Galpha in the Dictyostelium protein gbqA. 316 matched cddid_all.tbl CDD pfam00504 pfam00504 459836 Chloroa_b-bind Chlorophyll A-B binding protein. 159 matched cddid_all.tbl CDD pfam00505 pfam00505 459837 HMG_box HMG (high mobility group) box. 68 matched cddid_all.tbl CDD pfam00506 pfam00506 278907 Flu_NP Influenza virus nucleoprotein. 520 matched cddid_all.tbl CDD pfam00507 pfam00507 459838 Oxidored_q4 NADH-ubiquinone/plastoquinone oxidoreductase, chain 3. 94 matched cddid_all.tbl CDD pfam00508 pfam00508 278909 PPV_E2_N E2 (early) protein, N terminal. 197 matched cddid_all.tbl CDD pfam00509 pfam00509 395409 Hemagglutinin Haemagglutinin. Haemagglutinin from influenza virus causes membrane fusion of the viral membrane with the host membrane. Fusion occurs after the host cell internalizes the virus by endocytosis. The drop of pH causes release of a hydrophobic fusion peptide and a large conformational change leading to membrane fusion. 504 matched cddid_all.tbl CDD pfam00510 pfam00510 395410 COX3 Cytochrome c oxidase subunit III. 258 matched cddid_all.tbl CDD pfam00511 pfam00511 395411 PPV_E2_C E2 (early) protein, C terminal. 80 matched cddid_all.tbl CDD pfam00512 pfam00512 459839 HisKA His Kinase A (phospho-acceptor) domain. dimerization and phospho-acceptor domain of histidine kinases. 66 matched cddid_all.tbl CDD pfam00513 pfam00513 278914 Late_protein_L2 Late Protein L2. 514 matched cddid_all.tbl CDD pfam00514 pfam00514 425727 Arm Armadillo/beta-catenin-like repeat. Approx. 40 amino acid repeat. Tandem repeats form super-helix of helices that is proposed to mediate interaction of beta-catenin with its ligands. CAUTION: This family does not contain all known armadillo repeats. 41 matched cddid_all.tbl CDD pfam00515 pfam00515 459840 TPR_1 Tetratricopeptide repeat. 34 matched cddid_all.tbl CDD pfam00516 pfam00516 278917 GP120 Envelope glycoprotein GP120. The entry of HIV requires interaction of viral GP120 with Swiss:P01730 and a chemokine receptor on the cell surface. 525 matched cddid_all.tbl CDD pfam00517 pfam00517 395415 GP41 Retroviral envelope protein. This family includes envelope protein from a variety of retroviruses. It includes the GP41 subunit of the envelope protein complex from human and simian immunodeficiency viruses (HIV and SIV) which mediate membrane fusion during viral entry. The family also includes bovine immunodeficiency virus, feline immunodeficiency virus and Equine infectious anaemia (EIAV). The family also includes the Gp36 protein from mouse mammary tumour virus (MMTV) and human endogenous retroviruses (HERVs). 197 matched cddid_all.tbl CDD pfam00518 pfam00518 425729 E6 Early Protein (E6). 110 matched cddid_all.tbl CDD pfam00519 pfam00519 459841 PPV_E1_C Papillomavirus helicase. This is the C-terminal ATPase/helicase domain of Papillomavirus E1 protein, a DNA helicase that is required for initiation of viral DNA replication. This protein forms a complex with the E2 protein pfam00508. The domain architecture of E1 is similar to that of the SV40 T-antigen. 289 matched cddid_all.tbl CDD pfam00520 pfam00520 459842 Ion_trans Ion transport protein. This family contains sodium, potassium and calcium ion channels. This family is 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times, whereas in others (e.g. K channels) the protein forms as a tetramer in the membrane. 238 matched cddid_all.tbl CDD pfam00521 pfam00521 459843 DNA_topoisoIV DNA gyrase/topoisomerase IV, subunit A. 432 matched cddid_all.tbl CDD pfam00522 pfam00522 278923 VPR VPR/VPX protein. 83 matched cddid_all.tbl CDD pfam00523 pfam00523 395418 Fusion_gly Fusion glycoprotein F0. 473 matched cddid_all.tbl CDD pfam00524 pfam00524 278925 PPV_E1_N E1 Protein, N terminal domain. 121 matched cddid_all.tbl CDD pfam00525 pfam00525 425732 Crystallin Alpha crystallin A chain, N terminal. 56 matched cddid_all.tbl CDD pfam00526 pfam00526 306912 Dicty_CTDC Dictyostelium (slime mold) repeat. 23 matched cddid_all.tbl CDD pfam00527 pfam00527 278928 E7 E7 protein, Early protein. 92 matched cddid_all.tbl CDD pfam00528 pfam00528 334128 BPD_transp_1 Binding-protein-dependent transport system inner membrane component. The alignments cover the most conserved region of the proteins, which is thought to be located in a cytoplasmic loop between two transmembrane domains. The members of this family have a variable number of transmembrane helices. 183 matched cddid_all.tbl CDD pfam00529 pfam00529 425733 CusB_dom_1 Cation efflux system protein CusB domain 1. The cation efflux system protein CusB from E. coli can be divided into four different domains, the first three domains of the protein are mostly beta-strands and the fourth forms an all alpha-helical domain. This entry represents the first beta-domain (domain 1) of CusB and it is formed by the N and C-terminal ends of the polypeptide (residues 89-102 and 324-385). CusB is part of the copper-transporting efflux system CusCFBA. This domain can also be found in other membrane-fusion proteins, such as HlyD, MdtN, MdtE and AaeA. HlyD is a component of the prototypical alpha-haemolysin (HlyA) bacterial type I secretion system, along with the other components HlyB and TolC. HlyD is anchored in the cytoplasmic membrane by a single transmembrane domain and has a large periplasmic domain within the carboxy-terminal 100 amino acids, HlyB and HlyD form a stable complex that binds the recombinant protein bearing a C-terminal HlyA signal sequence and ATP in the cytoplasm. HlyD, HlyB and TolC combine to form the three-component ABC transporter complex that forms a trans-membrane channel or pore through which HlyA can be transferred directly to the extracellular medium. Cutinase has been shown to be transported effectively through this pore. 322 matched cddid_all.tbl CDD pfam00530 pfam00530 459844 SRCR Scavenger receptor cysteine-rich domain. These domains are disulphide rich extracellular domains. These domains are found in several extracellular receptors and may be involved in protein-protein interactions. 98 matched cddid_all.tbl CDD pfam00531 pfam00531 459845 Death Death domain. 86 matched cddid_all.tbl CDD pfam00532 pfam00532 395423 Peripla_BP_1 Periplasmic binding proteins and sugar binding domain of LacI family. This family includes the periplasmic binding proteins, and the LacI family transcriptional regulators. The periplasmic binding proteins are the primary receptors for chemotaxis and transport of many sugar based solutes. The LacI family of proteins consist of transcriptional regulators related to the lac repressor. In this case, generally the sugar binding domain binds a sugar which changes the DNA binding activity of the repressor domain (pfam00356). 281 matched cddid_all.tbl CDD pfam00533 pfam00533 425736 BRCT BRCA1 C Terminus (BRCT) domain. The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilized head-to-tail BRCT-BRCT oligomerization mode. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants. 75 matched cddid_all.tbl CDD pfam00534 pfam00534 425737 Glycos_transf_1 Glycosyl transferases group 1. Mutations in this domain of Swiss:P37287 lead to disease (Paroxysmal Nocturnal haemoglobinuria). Members of this family transfer activated sugars to a variety of substrates, including glycogen, Fructose-6-phosphate and lipopolysaccharides. Members of this family transfer UDP, ADP, GDP or CMP linked sugars. The eukaryotic glycogen synthases may be distant members of this family. 158 matched cddid_all.tbl CDD pfam00535 pfam00535 425738 Glycos_transf_2 Glycosyl transferase family 2. Diverse family, transferring sugar from UDP-glucose, UDP-N-acetyl- galactosamine, GDP-mannose or CDP-abequose, to a range of substrates including cellulose, dolichol phosphate and teichoic acids. 166 matched cddid_all.tbl CDD pfam00536 pfam00536 425739 SAM_1 SAM domain (Sterile alpha motif). It has been suggested that SAM is an evolutionarily conserved protein binding domain that is involved in the regulation of numerous developmental processes in diverse eukaryotes. The SAM domain can potentially function as a protein interaction module through its ability to homo- and heterooligomerise with other SAM domains. 64 matched cddid_all.tbl CDD pfam00537 pfam00537 395428 Toxin_3 Scorpion toxin-like domain. This family contains both neurotoxins and plant defensins. The mustard trypsin inhibitor, MTI-2, is plant defensin. It is a potent inhibitor of trypsin with no activity towards chymotrypsin. MTI-2 is toxic for Lepidopteran insects, but has low activity against aphids. Brazzein is plant defensin-like protein. It is pH-stable, heat-stable and intensely sweet protein. The scorpion toxin (a neurotoxin) binds to sodium channels and inhibits the activation mechanisms of the channels, thereby blocking neuronal transmission. Scorpion toxins bind to sodium channels and inhibit the activation mechanisms of the channels, thereby blocking neuronal transmission 55 matched cddid_all.tbl CDD pfam00538 pfam00538 459846 Linker_histone linker histone H1 and H5 family. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures Histone H1 is replaced by histone H5 in some cell types. 71 matched cddid_all.tbl CDD pfam00539 pfam00539 306921 Tat Transactivating regulatory protein (Tat). The retroviral Tat protein binds to the Tar RNA. This activates transcriptional initiation and elongation from the LTR promoter. Binding is mediated by an arginine rich region. 64 matched cddid_all.tbl CDD pfam00540 pfam00540 249943 Gag_p17 gag gene protein p17 (matrix protein). The matrix protein forms an icosahedral shell associated with the inner membrane of the mature immunodeficiency virus. 140 matched cddid_all.tbl CDD pfam00541 pfam00541 459847 Adeno_knob Adenoviral fibre protein (knob domain). Specific attachment of adenovirus is achieved through interactions between host-cell receptors and the adenovirus fibre protein and is mediated by the globular carboxy-terminal domain of the adenovirus fibre protein, termed the carboxy-terminal knob domain. 193 matched cddid_all.tbl CDD pfam00542 pfam00542 425742 Ribosomal_L12 Ribosomal protein L7/L12 C-terminal domain. 67 matched cddid_all.tbl CDD pfam00543 pfam00543 459848 P-II Nitrogen regulatory protein P-II. P-II modulates the activity of glutamine synthetase. 108 matched cddid_all.tbl CDD pfam00544 pfam00544 366158 Pectate_lyase_4 Pectate lyase. This enzyme forms a right handed beta helix structure. Pectate lyase is an enzyme involved in the maceration and soft rotting of plant tissue. 211 matched cddid_all.tbl CDD pfam00545 pfam00545 459849 Ribonuclease ribonuclease. This enzyme hydrolyses RNA and oligoribonucleotides. 81 matched cddid_all.tbl CDD pfam00547 pfam00547 459850 Urease_gamma Urease, gamma subunit. Urease is a nickel-binding enzyme that catalyzes the hydrolysis of urea to carbon dioxide and ammonia. 99 matched cddid_all.tbl CDD pfam00548 pfam00548 278947 Peptidase_C3 3C cysteine protease (picornain 3C). Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral 3C cysteine protease. 174 matched cddid_all.tbl CDD pfam00549 pfam00549 395434 Ligase_CoA CoA-ligase. This family includes the CoA ligases Succinyl-CoA synthetase alpha and beta chains, malate CoA ligase and ATP-citrate lyase. Some members of the family utilize ATP others use GTP. 128 matched cddid_all.tbl CDD pfam00550 pfam00550 425746 PP-binding Phosphopantetheine attachment site. A 4'-phosphopantetheine prosthetic group is attached through a serine. This prosthetic group acts as a a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. This domain forms a four helix bundle. This family includes members not included in Prosite. The inclusion of these members is supported by sequence analysis and functional evidence. The related domain of Swiss:P19828 has the attachment serine replaced by an alanine. 62 matched cddid_all.tbl CDD pfam00551 pfam00551 395436 Formyl_trans_N Formyl transferase. This family includes the following members. Glycinamide ribonucleotide transformylase catalyzes the third step in de novo purine biosynthesis, the transfer of a formyl group to 5'-phosphoribosylglycinamide. Formyltetrahydrofolate deformylase produces formate from formyl- tetrahydrofolate. Methionyl-tRNA formyltransferase transfers a formyl group onto the amino terminus of the acyl moiety of the methionyl aminoacyl-tRNA. Inclusion of the following members is supported by PSI-blast. HOXX_BRAJA (P31907) contains a related domain of unknown function. PRTH_PORGI (P46071) contains a related domain of unknown function. Y09P_MYCTU (Q50721) contains a related domain of unknown function. 181 matched cddid_all.tbl CDD pfam00552 pfam00552 425747 IN_DBD_C Integrase DNA binding domain. Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain. The central domain is the catalytic domain pfam00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain. 45 matched cddid_all.tbl CDD pfam00553 pfam00553 425748 CBM_2 Cellulose binding domain. Two tryptophan residues are involved in cellulose binding. Cellulose binding domain found in bacteria. 101 matched cddid_all.tbl CDD pfam00554 pfam00554 425749 RHD_DNA_bind Rel homology DNA-binding domain. Proteins containing the Rel homology domain (RHD) are eukaryotic transcription factors. The RHD is composed of two structural domains. This is the N-terminal DNA-binding domain that is similar to that found in P53. The C-terminal domain has an immunoglobulin-like fold (See pfam16179) that functions as a dimerization domain. 169 matched cddid_all.tbl CDD pfam00555 pfam00555 395440 Endotoxin_M delta endotoxin. This family contains insecticidal toxins produced by Bacillus species of bacteria. During spore formation the bacteria produce crystals of this protein. When an insect ingests these proteins they are activated by proteolytic cleavage. The N terminus is cleaved in all of the proteins and a C terminal extension is cleaved in some members. Once activated the endotoxin binds to the gut epithelium and causes cell lysis leading to death. This activated region of the delta endotoxin is composed of three structural domains. The N-terminal helical domain is involved in membrane insertion and pore formation. The second and third domains are involved in receptor binding. 204 matched cddid_all.tbl CDD pfam00556 pfam00556 459851 LHC Antenna complex alpha/beta subunit. 38 matched cddid_all.tbl CDD pfam00557 pfam00557 459852 Peptidase_M24 Metallopeptidase family M24. This family contains metallopeptidases. It also contains non-peptidase homologs such as the N terminal domain of Spt16 which is a histone H3-H4 binding module. 208 matched cddid_all.tbl CDD pfam00558 pfam00558 109608 Vpu Vpu protein. The Vpu protein contains an N-terminal transmembrane spanning region and a C-terminal cytoplasmic region. The HIV-1 Vpu protein stimulates virus production by enhancing the release of viral particles from infected cells. The VPU protein binds specifically to CD4. 81 matched cddid_all.tbl CDD pfam00559 pfam00559 278957 Vif Retroviral Vif (Viral infectivity) protein. Human immunodeficiency virus type 1 (HIV-1) Vif is required for productive infection of T lymphocytes and macrophages. Virions produced in the absence of Vif have abnormal core morphology and those produced in primary T cells carry immature core proteins and low levels of mature capsid. 200 matched cddid_all.tbl CDD pfam00560 pfam00560 459853 LRR_1 Leucine Rich Repeat. CAUTION: This Pfam may not find all Leucine Rich Repeats in a protein. Leucine Rich Repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. These repeats are usually involved in protein-protein interactions. Each Leucine Rich Repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine Rich Repeats are often flanked by cysteine rich domains. 23 matched cddid_all.tbl CDD pfam00561 pfam00561 395444 Abhydrolase_1 alpha/beta hydrolase fold. This catalytic domain is found in a very wide range of enzymes. 245 matched cddid_all.tbl CDD pfam00562 pfam00562 459854 RNA_pol_Rpb2_6 RNA polymerase Rpb2, domain 6. RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII). 371 matched cddid_all.tbl CDD pfam00563 pfam00563 425752 EAL EAL domain. This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues. The EAL domain is a good candidate for a diguanylate phosphodiesterase function. The domain contains many conserved acidic residues that could participate in metal binding and might form the phosphodiesterase active site. 235 matched cddid_all.tbl CDD pfam00564 pfam00564 395447 PB1 PB1 domain. 84 matched cddid_all.tbl CDD pfam00565 pfam00565 395448 SNase Staphylococcal nuclease homolog. Present in all three domains of cellular life. Four copies in the transcriptional coactivator p100: these, however, appear to lack the active site residues of Staphylococcal nuclease. Positions 14 (Asp-21), 34 (Arg-35), 39 (Asp-40), 42 (Glu-43) and 110 (Arg-87) [SNase numbering in parentheses] are thought to be involved in substrate-binding and catalysis. 106 matched cddid_all.tbl CDD pfam00566 pfam00566 459855 RabGAP-TBC Rab-GTPase-TBC domain. Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases. 178 matched cddid_all.tbl CDD pfam00567 pfam00567 425754 TUDOR Tudor domain. 117 matched cddid_all.tbl CDD pfam00568 pfam00568 395450 WH1 "WH1 domain. WASp Homology domain 1 (WH1) domain. WASP is the protein that is defective in Wiskott-Aldrich syndrome (WAS). The majority of point mutations occur within the amino- terminal WH1 domain. The metabotropic glutamate receptors mGluR1alpha and mGluR5 bind a protein called homer, which is a WH1 domain homolog. A subset of WH1 domains has been termed a ""EVH1"" domain and appear to bind a polyproline motif." 111 matched cddid_all.tbl CDD pfam00569 pfam00569 395451 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300. ZZ in dystrophin binds calmodulin. Putative zinc finger; binding not yet shown. Four to six cysteine residues in its sequence are responsible for coordinating zinc ions, to reinforce the structure. 45 matched cddid_all.tbl CDD pfam00570 pfam00570 425755 HRDC HRDC domain. The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain cause human disease. It is interesting to note that the RecQ helicase in Deinococcus radiodurans has three tandem HRDC domains. 68 matched cddid_all.tbl CDD pfam00571 pfam00571 425756 CBS CBS domain. CBS domains are small intracellular modules that pair together to form a stable globular domain. This family represents a single CBS domain. Pairs of these domains have been termed a Bateman domain. CBS domains have been shown to bind ligands with an adenosyl group such as AMP, ATP and S-AdoMet. CBS domains are found attached to a wide range of other protein domains suggesting that CBS domains may play a regulatory role making proteins sensitive to adenosyl carrying ligands. The region containing the CBS domains in Cystathionine-beta synthase is involved in regulation by S-AdoMet. CBS domain pairs from AMPK bind AMP or ATP. The CBS domains from IMPDH and the chloride channel CLC2 bind ATP. 57 matched cddid_all.tbl CDD pfam00572 pfam00572 459856 Ribosomal_L13 Ribosomal protein L13. 119 matched cddid_all.tbl CDD pfam00573 pfam00573 425758 Ribosomal_L4 Ribosomal protein L4/L1 family. This family includes Ribosomal L4/L1 from eukaryotes and archaebacteria and L4 from eubacteria. L4 from yeast has been shown to bind rRNA. 190 matched cddid_all.tbl CDD pfam00574 pfam00574 425759 CLP_protease Clp protease. The Clp protease has an active site catalytic triad. In E. coli Clp protease, ser-111, his-136 and asp-185 form the catalytic triad. Swiss:P48254 has lost all of these active site residues and is therefore inactive. Swiss:P42379 contains two large insertions, Swiss:P42380 contains one large insertion. 181 matched cddid_all.tbl CDD pfam00575 pfam00575 425760 S1 S1 RNA binding domain. The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. 72 matched cddid_all.tbl CDD pfam00576 pfam00576 459857 Transthyretin HIUase/Transthyretin family. This family includes transthyretin that is a thyroid hormone-binding protein that transports thyroxine from the bloodstream to the brain. However, most of the sequences listed in this family do not bind thyroid hormones. They are actually enzymes of the purine catabolism that catalyze the conversion of 5-hydroxyisourate (HIU) to OHCU. HIU hydrolysis is the original function of the family and is conserved from bacteria to mammals; transthyretins arose by gene duplications in the vertebrate lineage. HIUases are distinguished in the alignment from the conserved C-terminal YRGS sequence. 108 matched cddid_all.tbl CDD pfam00577 pfam00577 425762 Usher Outer membrane usher protein. In Gram-negative bacteria the biogenesis of fimbriae (or pili) requires a two- component assembly and transport system which is composed of a periplasmic chaperone and an outer membrane protein which has been termed a molecular 'usher'. The usher protein is rather large (from 86 to 100 Kd) and seems to be mainly composed of membrane-spanning beta-sheets, a structure reminiscent of porins. Although the degree of sequence similarity of these proteins is not very high they share a number of characteriztics. One of these is the presence of two pairs of cysteines, the first one located in the N-terminal part and the second at the C-terminal extremity that are probably involved in disulphide bonds. The best conserved region is located in the central part of these proteins. 549 matched cddid_all.tbl CDD pfam00578 pfam00578 425763 AhpC-TSA AhpC/TSA family. This family contains proteins related to alkyl hydroperoxide reductase (AhpC) and thiol specific antioxidant (TSA). 124 matched cddid_all.tbl CDD pfam00579 pfam00579 395461 tRNA-synt_1b tRNA synthetases class I (W and Y). 292 matched cddid_all.tbl CDD pfam00580 pfam00580 395462 UvrD-helicase UvrD/REP helicase N-terminal domain. The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyze ATP dependent unwinding of double stranded DNA to single stranded DNA. Swiss:P23478, Swiss:P08394 have large insertions near to the carboxy-terminus relative to other members of the family. 267 matched cddid_all.tbl CDD pfam00581 pfam00581 425764 Rhodanese Rhodanese-like domain. Rhodanese has an internal duplication. This Pfam represents a single copy of this duplicated domain. The domain is found as a single copy in other proteins, including phosphatases and ubiquitin C-terminal hydrolases. 92 matched cddid_all.tbl CDD pfam00582 pfam00582 425765 Usp "Universal stress protein family. The universal stress protein UspA is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general ""stress endurance"" activity. The crystal structure of Haemophilus influenzae UspA reveals an alpha/beta fold similar to that of the Methanococcus jannaschii MJ0577 protein, which binds ATP, though UspA lacks ATP-binding activity." 137 matched cddid_all.tbl CDD pfam00583 pfam00583 395465 Acetyltransf_1 Acetyltransferase (GNAT) family. This family contains proteins with N-acetyltransferase functions such as Elp3-related proteins. 116 matched cddid_all.tbl CDD pfam00584 pfam00584 459858 SecE SecE/Sec61-gamma subunits of protein translocation complex. SecE is part of the SecYEG complex in bacteria which translocates proteins from the cytoplasm. In eukaryotes the complex, made from Sec61-gamma and Sec61-alpha translocates protein from the cytoplasm to the ER. Archaea have a similar complex. 55 matched cddid_all.tbl CDD pfam00585 pfam00585 395467 Thr_dehydrat_C C-terminal regulatory domain of Threonine dehydratase. Threonine dehydratases pfam00291 all contain a carboxy terminal region. This region may have a regulatory role. Some members contain two copies of this region. This family is homologous to the pfam01842 domain. 91 matched cddid_all.tbl CDD pfam00586 pfam00586 459859 AIRS AIR synthase related protein, N-terminal domain. This family includes Hydrogen expression/formation protein HypE, AIR synthases EC:6.3.3.1, FGAM synthase EC:6.3.5.3 and selenide, water dikinase EC:2.7.9.3. The N-terminal domain of AIR synthase forms the dimer interface of the protein, and is suggested as a putative ATP binding domain. 104 matched cddid_all.tbl CDD pfam00587 pfam00587 395469 tRNA-synt_2b tRNA synthetase class II core domain (G, H, P, S and T). tRNA-synt_2b is a family of largely threonyl-tRNA members. 181 matched cddid_all.tbl CDD pfam00588 pfam00588 425768 SpoU_methylase SpoU rRNA Methylase family. This family of proteins probably use S-AdoMet. 142 matched cddid_all.tbl CDD pfam00589 pfam00589 395471 Phage_integrase Phage integrase family. Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase are Arg-173, His-289, Arg-292 and Tyr-324. 169 matched cddid_all.tbl CDD pfam00590 pfam00590 425769 TP_methylase Tetrapyrrole (Corrin/Porphyrin) Methylases. This family uses S-AdoMet in the methylation of diverse substrates. This family includes a related group of bacterial proteins of unknown function. This family includes the methylase Dipthine synthase. 209 matched cddid_all.tbl CDD pfam00591 pfam00591 459860 Glycos_transf_3 Glycosyl transferase family, a/b domain. This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate. 253 matched cddid_all.tbl CDD pfam00593 pfam00593 395474 TonB_dep_Rec TonB dependent receptor. This model now only covers the conserved part of the barrel structure. 475 matched cddid_all.tbl CDD pfam00594 pfam00594 459861 Gla Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain. This domain is responsible for the high-affinity binding of calcium ions. This domain contains post-translational modifications of many glutamate residues by Vitamin K-dependent carboxylation to form gamma-carboxyglutamate (Gla). 41 matched cddid_all.tbl CDD pfam00595 pfam00595 395476 PDZ PDZ domain. PDZ domains are found in diverse signaling proteins. 81 matched cddid_all.tbl CDD pfam00596 pfam00596 459862 Aldolase_II Class II Aldolase and Adducin N-terminal domain. This family includes class II aldolases and adducins which have not been ascribed any enzymatic function. 178 matched cddid_all.tbl CDD pfam00598 pfam00598 395478 Flu_M1 Influenza Matrix protein (M1). This protein forms a continuous shell on the inner side of the lipid bilayer, but its function is unclear. 156 matched cddid_all.tbl CDD pfam00599 pfam00599 278994 Flu_M2 Influenza Matrix protein (M2). This protein spans the viral membrane with an extracellular amino-terminus external and a cytoplasmic carboxy-terminus. 97 matched cddid_all.tbl CDD pfam00600 pfam00600 366187 Flu_NS1 Influenza non-structural protein (NS1). NS1 is a homodimeric RNA-binding protein that is required for viral replication. NS1 binds polyA tails of mRNA keeping them in the nucleus. NS1 inhibits pre-mRNA splicing by tightly binding to a specific stem-bulge of U6 snRNA. 217 matched cddid_all.tbl CDD pfam00601 pfam00601 278996 Flu_NS2 Influenza non-structural protein (NS2). NS2 may play a role in promoting normal replication of the genomic RNAs by preventing the replication of short-length RNA species. 108 matched cddid_all.tbl CDD pfam00602 pfam00602 395479 Flu_PB1 Influenza RNA-dependent RNA polymerase subunit PB1. Two GTP binding sites exist in this protein. 732 matched cddid_all.tbl CDD pfam00603 pfam00603 395480 Flu_PA Influenza RNA-dependent RNA polymerase subunit PA. 694 matched cddid_all.tbl CDD pfam00604 pfam00604 395481 Flu_PB2 Influenza RNA-dependent RNA polymerase subunit PB2. PB2 can bind 5' end cap structure of RNA. 754 matched cddid_all.tbl CDD pfam00605 pfam00605 459863 IRF Interferon regulatory factor transcription factor. This family of transcription factors are important in the regulation of interferons in response to infection by virus and in the regulation of interferon-inducible genes. Three of the five conserved tryptophan residues bind to DNA. 106 matched cddid_all.tbl CDD pfam00606 pfam00606 425773 Glycoprotein_B Herpesvirus Glycoprotein B ectodomain. This domain corresponds to the ectodomain of glycoprotein B according to ECOD. 222 matched cddid_all.tbl CDD pfam00607 pfam00607 459864 Gag_p24 gag protein p24 N-terminal domain. p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro. 128 matched cddid_all.tbl CDD pfam00608 pfam00608 459865 Adeno_shaft Adenoviral fibre protein (repeat/shaft region). There is no separation between signal and noise. Specific attachment of adenovirus is achieved through interactions between host-cell receptors and the adenovirus fibre protein and is mediated by the globular carboxy-terminal domain of the adenovirus fibre protein, rather than the 'shaft' region represented by this family. The alignment of this family contains two copies of a fifteen residue repeat found in the 'shaft' region of adenoviral fibre proteins. 44 matched cddid_all.tbl CDD pfam00609 pfam00609 459866 DAGK_acc Diacylglycerol kinase accessory domain. Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. This domain is assumed to be an accessory domain: its function is unknown. 158 matched cddid_all.tbl CDD pfam00610 pfam00610 459867 DEP Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP). The DEP domain is responsible for mediating intracellular protein targeting and regulation of protein stability in the cell. The DEP domain is present in a number of signaling molecules, including Regulator of G protein Signaling (RGS) proteins, and has been implicated in membrane targeting. New findings in yeast, however, demonstrate a major role for a DEP domain in mediating the interaction of an RGS protein to the C-terminal tail of a GPCR, thus placing RGS in close proximity with its substrate G protein alpha subunit. 71 matched cddid_all.tbl CDD pfam00611 pfam00611 459868 FCH Fes/CIP4, and EFC/F-BAR homology domain. Alignment extended from. Highly alpha-helical. The cytosolic endocytic adaptor proteins in fungi carry this domain at the N-terminus; several of these have been referred to as muniscin proteins. These N-terminal BAR, N-BAR, and EFC/F-BAR domains are found in proteins that regulate membrane trafficking events by inducing membrane tubulation. The domain dimerizes into a curved structure that binds to liposomes and either senses or induces the curvature of the membrane bilayer to cause biophysical changes to the shape of the bilayer; it also thereby recruits other trafficking factors, such as the GTPase dynamin. Most EFC/F-BAR domain-family members localize to actin-rich structures. 78 matched cddid_all.tbl CDD pfam00612 pfam00612 459869 IQ IQ calmodulin-binding motif. Calmodulin-binding motif. 21 matched cddid_all.tbl CDD pfam00613 pfam00613 395488 PI3Ka Phosphoinositide 3-kinase family, accessory domain (PIK domain). PIK domain is conserved in all PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation. 185 matched cddid_all.tbl CDD pfam00614 pfam00614 395489 PLDc Phospholipase D Active site motif. Phosphatidylcholine-hydrolysing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homolog of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, and/or asparagine residues which may contribute to the active site. aspartic acid. An E. coli endonuclease (nuc) and similar proteins appear to be PLD homologs but possess only one of these motifs. The profile contained here represents only the putative active site regions, since an accurate multiple alignment of the repeat units has not been achieved. 28 matched cddid_all.tbl CDD pfam00615 pfam00615 459870 RGS Regulator of G protein signaling domain. RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits. 117 matched cddid_all.tbl CDD pfam00616 pfam00616 459871 RasGAP "GTPase-activator protein for Ras-like GTPase. All alpha-helical domain that accelerates the GTPase activity of Ras, thereby ""switching"" it into an ""off"" position." 207 matched cddid_all.tbl CDD pfam00617 pfam00617 459872 RasGEF RasGEF domain. Guanine nucleotide exchange factor for Ras-like small GTPases. 179 matched cddid_all.tbl CDD pfam00618 pfam00618 459873 RasGEF_N RasGEF N-terminal motif. A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this motif/domain N-terminal to the RasGef (Cdc25-like) domain. 104 matched cddid_all.tbl CDD pfam00619 pfam00619 459874 CARD Caspase recruitment domain. Motif contained in proteins involved in apoptotic signaling. Predicted to possess a DEATH (pfam00531) domain-like fold. 85 matched cddid_all.tbl CDD pfam00620 pfam00620 459875 RhoGAP RhoGAP domain. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases. 148 matched cddid_all.tbl CDD pfam00621 pfam00621 459876 RhoGEF RhoGEF domain. Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases Also called Dbl-homologous (DH) domain. It appears that pfam00169 domains invariably occur C-terminal to RhoGEF/DH domains. 176 matched cddid_all.tbl CDD pfam00622 pfam00622 459877 SPRY SPRY domain. SPRY Domain is named from SPla and the RYanodine Receptor and it is found in many eukaryotic proteins with a wide range of functions. It is a protein-interaction module involved in many important signalling pathways like RNA processing, regulation of histone H3 methylation, innate immunity or embryonic development. It can be divided into 11 subfamilies based on amino acid sequence similarity or the presence of additional protein domains. The greater SPRY family is divided into the SPRY/B30.2 (which contains a PRY extension at the N-terminal) and SPRY-only sub-families which are preceded by a subdomain that is structurally similar to the PRY region. SPRY/B30.2 structures revealed a bent beta-sandwich fold comprised of two beta-sheets. Distant homologs are domains in butyrophilin/ marenostrin/pyrin. 121 matched cddid_all.tbl CDD pfam00623 pfam00623 395498 RNA_pol_Rpb1_2 RNA polymerase Rpb1, domain 2. RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion. 166 matched cddid_all.tbl CDD pfam00624 pfam00624 395499 Flocculin Flocculin repeat. This short repeat is rich in serine and threonine residues. 39 matched cddid_all.tbl CDD pfam00625 pfam00625 395500 Guanylate_kin Guanylate kinase. 182 matched cddid_all.tbl CDD pfam00626 pfam00626 395501 Gelsolin Gelsolin repeat. 76 matched cddid_all.tbl CDD pfam00627 pfam00627 395502 UBA UBA/TS-N domain. This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280. 37 matched cddid_all.tbl CDD pfam00628 pfam00628 425785 PHD PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3. 51 matched cddid_all.tbl CDD pfam00629 pfam00629 459878 MAM MAM domain, meprin/A5/mu. An extracellular domain found in many receptors. The MAM domain along with the associated Ig domain in type IIB receptor protein tyrosine phosphatases forms a structural unit (termed MIg) with a seamless interdomain interface. It plays a major role in homodimerization of the phosphatase ectoprotein and in cell adhesion. MAM is a beta-sandwich consisting of two five-stranded antiparallel beta-sheets rotated away from each other by approx 25 degrees, and plays a similar role in meprin metalloproteinases. 159 matched cddid_all.tbl CDD pfam00630 pfam00630 395505 Filamin Filamin/ABP280 repeat. 89 matched cddid_all.tbl CDD pfam00631 pfam00631 459879 G-gamma GGL domain. G-protein gamma like domains (GGL) are found in the gamma subunit of the heterotrimeric G protein complex and in regulators of G protein signaling (RGS) proteins. It is also found fused to an inactive Galpha in the Dictyostelium protein gbqA. G-gamma likely shares a common origin with the helical N-terminal unit of G-beta. All organizms that posses a G-beta possess a G-gamma. 69 matched cddid_all.tbl CDD pfam00632 pfam00632 459880 HECT HECT-domain (ubiquitin-transferase). The name HECT comes from Homologous to the E6-AP Carboxyl Terminus. 304 matched cddid_all.tbl CDD pfam00633 pfam00633 425789 HHH Helix-hairpin-helix motif. The helix-hairpin-helix DNA-binding motif is found to be duplicated in the central domain of RuvA. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain. 30 matched cddid_all.tbl CDD pfam00634 pfam00634 459881 BRCA2 BRCA2 repeat. The alignment covers only the most conserved region of the repeat. 29 matched cddid_all.tbl CDD pfam00635 pfam00635 459882 Motile_Sperm MSP (Major sperm protein) domain. Major sperm proteins are involved in sperm motility. These proteins oligomerise to form filaments. This family contains many other proteins. 109 matched cddid_all.tbl CDD pfam00636 pfam00636 459883 Ribonuclease_3 Ribonuclease III domain. 101 matched cddid_all.tbl CDD pfam00637 pfam00637 459884 Clathrin Region in Clathrin and VPS. Each region is about 140 amino acids long. The regions are composed of multiple alpha helical repeats. They occur in the arm region of the Clathrin heavy chain. 142 matched cddid_all.tbl CDD pfam00638 pfam00638 395513 Ran_BP1 RanBP1 domain. 122 matched cddid_all.tbl CDD pfam00639 pfam00639 425792 Rotamase PPIC-type PPIASE domain. Rotamases increase the rate of protein folding by catalysing the interconversion of cis-proline and trans-proline. 96 matched cddid_all.tbl CDD pfam00640 pfam00640 395515 PID Phosphotyrosine interaction domain (PTB/PID). 133 matched cddid_all.tbl CDD pfam00641 pfam00641 395516 zf-RanBP Zn-finger in Ran binding protein and others. 30 matched cddid_all.tbl CDD pfam00642 pfam00642 459885 zf-CCCH Zinc finger C-x8-C-x5-C-x3-H type (and similar). 27 matched cddid_all.tbl CDD pfam00643 pfam00643 459886 zf-B_box B-box zinc finger. 42 matched cddid_all.tbl CDD pfam00644 pfam00644 395519 PARP Poly(ADP-ribose) polymerase catalytic domain. Poly(ADP-ribose) polymerase catalyzes the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active. 195 matched cddid_all.tbl CDD pfam00645 pfam00645 459887 zf-PARP Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region. Poly(ADP-ribose) polymerase is an important regulatory component of the cellular response to DNA damage. The amino-terminal region of Poly(ADP-ribose) polymerase consists of two PARP-type zinc fingers. This region acts as a DNA nick sensor. 87 matched cddid_all.tbl CDD pfam00646 pfam00646 425796 F-box F-box domain. This domain is approximately 50 amino acids long, and is usually found in the N-terminal half of a variety of proteins. Two motifs that are commonly found associated with the F-box domain are the leucine rich repeats (LRRs; pfam00560 and pfam07723) and the WD repeat (pfam00400). The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 43 matched cddid_all.tbl CDD pfam00647 pfam00647 459888 EF1G Elongation factor 1 gamma, conserved domain. 105 matched cddid_all.tbl CDD pfam00648 pfam00648 459889 Peptidase_C2 Calpain family cysteine protease. 295 matched cddid_all.tbl CDD pfam00649 pfam00649 425799 Copper-fist Copper fist DNA binding domain. 38 matched cddid_all.tbl CDD pfam00650 pfam00650 459890 CRAL_TRIO CRAL/TRIO domain. 151 matched cddid_all.tbl CDD pfam00651 pfam00651 395526 BTB BTB/POZ domain. The BTB (for BR-C, ttk and bab) or POZ (for Pox virus and Zinc finger) domain is present near the N-terminus of a fraction of zinc finger (pfam00096) proteins and in proteins that contain the pfam01344 motif such as Kelch and a family of pox virus proteins. The BTB/POZ domain mediates homomeric dimerization and in some instances heteromeric dimerization. The structure of the dimerized PLZF BTB/POZ domain has been solved and consists of a tightly intertwined homodimer. The central scaffolding of the protein is made up of a cluster of alpha-helices flanked by short beta-sheets at both the top and bottom of the molecule. POZ domains from several zinc finger proteins have been shown to mediate transcriptional repression and to interact with components of histone deacetylase co-repressor complexes including N-CoR and SMRT. The POZ or BTB domain is also known as BR-C/Ttk or ZiN. 107 matched cddid_all.tbl CDD pfam00652 pfam00652 395527 Ricin_B_lectin Ricin-type beta-trefoil lectin domain. 126 matched cddid_all.tbl CDD pfam00653 pfam00653 459891 BIR Inhibitor of Apoptosis domain. BIR stands for 'Baculovirus Inhibitor of apoptosis protein Repeat'. It is found repeated in inhibitor of apoptosis proteins (IAPs), and in fact it is also known as IAP repeat. These domains characteriztically have a number of invariant residues, including 3 conserved cysteines and one conserved histidine that coordinate a zinc ion. They are usually made up of 4-5 alpha helices and a three-stranded beta-sheet. BIR is also found in other proteins known as BIR-domain-containing proteins (BIRPs), such as Survivin. 68 matched cddid_all.tbl CDD pfam00654 pfam00654 425802 Voltage_CLC Voltage gated chloride channel. This family of ion channels contains 10 or 12 transmembrane helices. Each protein forms a single pore. It has been shown that some members of this family form homodimers. In terms of primary structure, they are unrelated to known cation channels or other types of anion channels. Three ClC subfamilies are found in animals. ClC-1 is involved in setting and restoring the resting membrane potential of skeletal muscle, while other channels play important parts in solute concentration mechanisms in the kidney. These proteins contain two pfam00571 domains. 344 matched cddid_all.tbl CDD pfam00656 pfam00656 425803 Peptidase_C14 Caspase domain. 213 matched cddid_all.tbl CDD pfam00657 pfam00657 459892 Lipase_GDSL GDSL-like Lipase/Acylhydrolase. 210 matched cddid_all.tbl CDD pfam00658 pfam00658 459893 PABP Poly-adenylate binding protein, unique domain. The region featured in this family is found towards the C-terminus of poly(A)-binding proteins (PABPs). These are eukaryotic proteins that, through their binding of the 3' poly(A) tail on mRNA, have very important roles in the pathways of gene expression. They seem to provide a scaffold on which other proteins can bind and mediate processes such as export, translation and turnover of the transcripts. Moreover, they may act as antagonists to the binding of factors that allow mRNA degradation, regulating mRNA longevity. PABPs are also involved in nuclear transport. PABPs interact with poly(A) tails via RNA-recognition motifs (pfam00076). Note that the PABP C-terminal region is also found in members of the hyperplastic discs protein (HYD) family of ubiquitin ligases that contain HECT domains - these are also included in this family. 66 matched cddid_all.tbl CDD pfam00659 pfam00659 459894 POLO_box POLO box duplicated region. 61 matched cddid_all.tbl CDD pfam00660 pfam00660 395534 SRP1_TIP1 Seripauperin and TIP1 family. 98 matched cddid_all.tbl CDD pfam00661 pfam00661 395535 Matrix Viral matrix protein. Found in Morbillivirus and paramyxovirus, pneumovirus. 340 matched cddid_all.tbl CDD pfam00662 pfam00662 459895 Proton_antipo_N NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus. This sub-family represents an amino terminal extension of pfam00361. Only NADH-Ubiquinone chain 5 and eubacterial chain L are in this family. This sub-family is part of complex I which catalyzes the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane. 51 matched cddid_all.tbl CDD pfam00664 pfam00664 459896 ABC_membrane ABC transporter transmembrane region. This family represents a unit of six transmembrane helices. Many members of the ABC transporter family (pfam00005) have two such regions. 274 matched cddid_all.tbl CDD pfam00665 pfam00665 459897 rve Integrase core domain. Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site. 98 matched cddid_all.tbl CDD pfam00666 pfam00666 395539 Cathelicidins Cathelicidin. A novel protein family, showing a conserved proregion and a variable carboxyl-terminal antimicrobial domain. This region shows similarity to cystatins. 101 matched cddid_all.tbl CDD pfam00667 pfam00667 395540 FAD_binding_1 FAD binding domain. This domain is found in sulfite reductase, NADPH cytochrome P450 reductase, Nitric oxide synthase and methionine synthase reductase. 219 matched cddid_all.tbl CDD pfam00668 pfam00668 395541 Condensation Condensation domain. This domain is found in many multi-domain enzymes which synthesize peptide antibiotics. This domain catalyzes a condensation reaction to form peptide bonds in non- ribosomal peptide biosynthesis. It is usually found to the carboxy side of a phosphopantetheine binding domain (pfam00550). It has been shown that mutations in the HHXXXDG motif abolish activity suggesting this is part of the active site. 454 matched cddid_all.tbl CDD pfam00669 pfam00669 425809 Flagellin_N Bacterial flagellin N-terminal helical region. Flagellins polymerize to form bacterial flagella. This family includes flagellins and hook associated protein 3. Structurally this family forms an extended helix that interacts with pfam00700. 139 matched cddid_all.tbl CDD pfam00670 pfam00670 395543 AdoHcyase_NAD S-adenosyl-L-homocysteine hydrolase, NAD binding domain. 162 matched cddid_all.tbl CDD pfam00672 pfam00672 459898 HAMP HAMP domain. 53 matched cddid_all.tbl CDD pfam00673 pfam00673 459899 Ribosomal_L5_C ribosomal L5P family C-terminus. This region is found associated with pfam00281. 94 matched cddid_all.tbl CDD pfam00674 pfam00674 395546 DUP DUP family. This family consists of several yeast proteins of unknown functions. Swiss-prot annotates these as belonging to the DUP family. Several members of this family contain an internal duplication of this region. 96 matched cddid_all.tbl CDD pfam00675 pfam00675 425812 Peptidase_M16 Insulinase (Peptidase family M16). 149 matched cddid_all.tbl CDD pfam00676 pfam00676 395548 E1_dh Dehydrogenase E1 component. This family uses thiamine pyrophosphate as a cofactor. This family includes pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase and 2-oxoisovalerate dehydrogenase. 300 matched cddid_all.tbl CDD pfam00677 pfam00677 459900 Lum_binding Lumazine binding domain. This domain binds to derivatives of lumazine in some proteins. Some proteins have lost the residues involved in binding lumazine. 83 matched cddid_all.tbl CDD pfam00679 pfam00679 425814 EFG_C Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold. 88 matched cddid_all.tbl CDD pfam00680 pfam00680 425815 RdRP_1 "Viral RNA-dependent RNA polymerase. This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the ""right hand"" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases." 450 matched cddid_all.tbl CDD pfam00681 pfam00681 459901 Plectin Plectin repeat. This family includes repeats from plectin, desmoplakin, envoplakin and bullous pemphigoid antigen. 39 matched cddid_all.tbl CDD pfam00682 pfam00682 459902 HMGL-like HMGL-like. This family contains a diverse set of enzymes. These include various aldolases and a region of pyruvate carboxylase. 264 matched cddid_all.tbl CDD pfam00683 pfam00683 459903 TB TB domain. This domain is also known as the 8 cysteine domain. This family includes the hybrid domains. This cysteine rich repeat is found in TGF binding protein and fibrillin. 44 matched cddid_all.tbl CDD pfam00684 pfam00684 459904 DnaJ_CXXCXGXG DnaJ central domain. The central cysteine-rich (CR) domain of DnaJ proteins contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DNAJ cysteine rich domain and various hydrophobic peptides has been found. 65 matched cddid_all.tbl CDD pfam00685 pfam00685 425820 Sulfotransfer_1 Sulfotransferase domain. 253 matched cddid_all.tbl CDD pfam00686 pfam00686 425821 CBM_20 Starch binding domain. 95 matched cddid_all.tbl CDD pfam00687 pfam00687 459905 Ribosomal_L1 Ribosomal protein L1p/L10e family. This family includes prokaryotic L1 and eukaryotic L10. 197 matched cddid_all.tbl CDD pfam00688 pfam00688 459906 TGFb_propeptide TGF-beta propeptide. This propeptide is known as latency associated peptide (LAP) in TGF-beta. LAP is a homodimer which is disulfide linked to TGF-beta binding protein. 239 matched cddid_all.tbl CDD pfam00689 pfam00689 376368 Cation_ATPase_C Cation transporting ATPase, C-terminus. Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport. This family represents 5 transmembrane helices. 175 matched cddid_all.tbl CDD pfam00690 pfam00690 459907 Cation_ATPase_N Cation transporter/ATPase, N-terminus. Members of this families are involved in Na+/K+, H+/K+, Ca++ and Mg++ transport. 68 matched cddid_all.tbl CDD pfam00691 pfam00691 425825 OmpA OmpA family. The Pfam entry also includes MotB and related proteins which are not included in the Prosite family. 95 matched cddid_all.tbl CDD pfam00692 pfam00692 395562 dUTPase dUTPase. dUTPase hydrolyses dUTP to dUMP and pyrophosphate. 129 matched cddid_all.tbl CDD pfam00693 pfam00693 395563 Herpes_TK Thymidine kinase from herpesvirus. 280 matched cddid_all.tbl CDD pfam00694 pfam00694 459908 Aconitase_C Aconitase C-terminal domain. Members of this family usually also match to pfam00330. This domain undergoes conformational change in the enzyme mechanism. 131 matched cddid_all.tbl CDD pfam00695 pfam00695 366252 vMSA Major surface antigen from hepadnavirus. 394 matched cddid_all.tbl CDD pfam00696 pfam00696 395565 AA_kinase Amino acid kinase family. This family includes kinases that phosphorylate a variety of amino acid substrates, as well as uridylate kinase and carbamate kinase. This family includes: Aspartokinase EC:2.7.2.4. Acetylglutamate kinase EC:2.7.2.8. Glutamate 5-kinase EC:2.7.2.11. Uridylate kinase EC:2.7.4.-. Carbamate kinase EC:2.7.2.2. 232 matched cddid_all.tbl CDD pfam00697 pfam00697 395566 PRAI N-(5'phosphoribosyl)anthranilate (PRA) isomerase. 193 matched cddid_all.tbl CDD pfam00698 pfam00698 395567 Acyl_transf_1 Acyl transferase domain. 319 matched cddid_all.tbl CDD pfam00699 pfam00699 459909 Urease_beta Urease beta subunit. This subunit is known as alpha in Heliobacter. 98 matched cddid_all.tbl CDD pfam00700 pfam00700 425827 Flagellin_C Bacterial flagellin C-terminal helical region. Flagellins polymerize to form bacterial flagella. There is some similarity between this family and pfam00669, particularly the motif NRFXSXIXXL. It has been suggested that these two regions associate and this is shown to be correct as structurally this family forms an extended helix that interacts with pfam00700. 86 matched cddid_all.tbl CDD pfam00701 pfam00701 395570 DHDPS Dihydrodipicolinate synthetase family. This family has a TIM barrel structure. 289 matched cddid_all.tbl CDD pfam00702 pfam00702 459910 Hydrolase haloacid dehalogenase-like hydrolase. This family is structurally different from the alpha/beta hydrolase family (pfam00561). This family includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure of the family consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of Swiss:P24069. The rest of the fold is composed of the core alpha/beta domain. Those members with the characteriztic DxD triad at the N-terminus are probably phosphatidylglycerolphosphate (PGP) phosphatases involved in cardiolipin biosynthesis in the mitochondria. 191 matched cddid_all.tbl CDD pfam00703 pfam00703 395572 Glyco_hydro_2 Glycosyl hydrolases family 2. This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities. 106 matched cddid_all.tbl CDD pfam00704 pfam00704 425828 Glyco_hydro_18 Glycosyl hydrolases family 18. 311 matched cddid_all.tbl CDD pfam00705 pfam00705 395574 PCNA_N Proliferating cell nuclear antigen, N-terminal domain. N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA. 125 matched cddid_all.tbl CDD pfam00706 pfam00706 109750 Toxin_4 Anenome neurotoxin. 43 matched cddid_all.tbl CDD pfam00707 pfam00707 459911 IF3_C Translation initiation factor IF-3, C-terminal domain. 86 matched cddid_all.tbl CDD pfam00708 pfam00708 425830 Acylphosphatase Acylphosphatase. 85 matched cddid_all.tbl CDD pfam00709 pfam00709 459912 Adenylsucc_synt Adenylosuccinate synthetase. 417 matched cddid_all.tbl CDD pfam00710 pfam00710 459913 Asparaginase Asparaginase, N-terminal. This is the N-terminal domain of this enzyme. 188 matched cddid_all.tbl CDD pfam00711 pfam00711 459914 Defensin_beta Beta defensin. The beta defensins are antimicrobial peptides implicated in the resistance of epithelial surfaces to microbial colonization. 36 matched cddid_all.tbl CDD pfam00712 pfam00712 395580 DNA_pol3_beta DNA polymerase III beta subunit, N-terminal domain. A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold. 121 matched cddid_all.tbl CDD pfam00713 pfam00713 307040 Hirudin Hirudin. 64 matched cddid_all.tbl CDD pfam00714 pfam00714 395581 IFN-gamma Interferon gamma. 138 matched cddid_all.tbl CDD pfam00715 pfam00715 425834 IL2 Interleukin 2. 145 matched cddid_all.tbl CDD pfam00716 pfam00716 279105 Peptidase_S21 Assemblin (Peptidase family S21). 336 matched cddid_all.tbl CDD pfam00717 pfam00717 425835 Peptidase_S24 Peptidase S24-like. 116 matched cddid_all.tbl CDD pfam00718 pfam00718 425836 Polyoma_coat Polyomavirus coat protein. 293 matched cddid_all.tbl CDD pfam00719 pfam00719 459915 Pyrophosphatase Inorganic pyrophosphatase. 154 matched cddid_all.tbl CDD pfam00720 pfam00720 425838 SSI Subtilisin inhibitor-like. 92 matched cddid_all.tbl CDD pfam00721 pfam00721 307047 TMV_coat Virus coat protein (TMV like). This family contains coat proteins from tobamoviruses, hordeiviruses, Tobraviruses, Furoviruses and Potyviruses. 163 matched cddid_all.tbl CDD pfam00722 pfam00722 395585 Glyco_hydro_16 Glycosyl hydrolases family 16. 168 matched cddid_all.tbl CDD pfam00723 pfam00723 395586 Glyco_hydro_15 Glycosyl hydrolases family 15. In higher organizms this family is represented by phosphorylase kinase subunits. 417 matched cddid_all.tbl CDD pfam00724 pfam00724 395587 Oxidored_FMN NADH:flavin oxidoreductase / NADH oxidase family. 341 matched cddid_all.tbl CDD pfam00725 pfam00725 395588 3HCDH 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain. This family also includes lambda crystallin. Some proteins include two copies of this domain. 97 matched cddid_all.tbl CDD pfam00726 pfam00726 334228 IL10 Interleukin 10. 170 matched cddid_all.tbl CDD pfam00727 pfam00727 459916 IL4 Interleukin 4. 116 matched cddid_all.tbl CDD pfam00728 pfam00728 425840 Glyco_hydro_20 Glycosyl hydrolase family 20, catalytic domain. This domain has a TIM barrel fold. 344 matched cddid_all.tbl CDD pfam00729 pfam00729 395591 Viral_coat Viral coat protein (S domain). 204 matched cddid_all.tbl CDD pfam00730 pfam00730 425841 HhH-GPD HhH-GPD superfamily base excision DNA repair protein. This family contains a diverse range of structurally related DNA repair proteins. The superfamily is called the HhH-GPD family after its hallmark Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This includes endonuclease III, EC:4.2.99.18 and MutY an A/G-specific adenine glycosylase, both have a C terminal 4Fe-4S cluster. The family also includes 8-oxoguanine DNA glycosylases. The methyl-CPG binding protein MBD4 also contains a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II EC:3.2.2.21 and other members of the AlkA family. 141 matched cddid_all.tbl CDD pfam00731 pfam00731 459917 AIRC AIR carboxylase. Members of this family catalyze the decarboxylation of 1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate (AIR). This family catalyze the sixth step of de novo purine biosynthesis. Some members of this family contain two copies of this domain. 147 matched cddid_all.tbl CDD pfam00732 pfam00732 366272 GMC_oxred_N GMC oxidoreductase. This family of proteins bind FAD as a cofactor. 218 matched cddid_all.tbl CDD pfam00733 pfam00733 395594 Asn_synthase Asparagine synthase. This family is always found associated with pfam00310. Members of this family catalyze the conversion of aspartate to asparagine. 279 matched cddid_all.tbl CDD pfam00734 pfam00734 459918 CBM_1 Fungal cellulose binding domain. 29 matched cddid_all.tbl CDD pfam00735 pfam00735 395596 Septin Septin. Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteriztic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerize to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis. 272 matched cddid_all.tbl CDD pfam00736 pfam00736 459919 EF1_GNE EF-1 guanine nucleotide exchange domain. This family is the guanine nucleotide exchange domain of EF-1 beta and EF-1 delta chains. 83 matched cddid_all.tbl CDD pfam00737 pfam00737 425845 PsbH Photosystem II 10 kDa phosphoprotein. This protein is phosphorylated in a light dependent reaction. 52 matched cddid_all.tbl CDD pfam00738 pfam00738 307060 Polyhedrin Polyhedrin. These proteins are found in occlusion bodies in various viruses. The polyhedrin protein protects the virus. 232 matched cddid_all.tbl CDD pfam00739 pfam00739 109783 X Trans-activation protein X. This protein is found in hepadnaviruses where it is indispensable for replication. 142 matched cddid_all.tbl CDD pfam00740 pfam00740 395599 Parvo_coat Parvovirus coat protein VP2. This protein, together with VP1 forms a capsomer. Both of these proteins are formed from the same transcript using alternative splicing. As a result, VP1 and VP2 differ only in the N-terminal region of VP1. VP2 is involved in packaging the viral DNA. 518 matched cddid_all.tbl CDD pfam00741 pfam00741 459920 Gas_vesicle Gas vesicle protein. This family includes gas vesicle proteins such as GvpJ. 39 matched cddid_all.tbl CDD pfam00742 pfam00742 459921 Homoserine_dh Homoserine dehydrogenase. 178 matched cddid_all.tbl CDD pfam00743 pfam00743 395602 FMO-like Flavin-binding monooxygenase-like. This family includes FMO proteins, cyclohexanone mono-oxygenase and a number of different mono-oxygenases. 531 matched cddid_all.tbl CDD pfam00745 pfam00745 459922 GlutR_dimer Glutamyl-tRNAGlu reductase, dimerization domain. 95 matched cddid_all.tbl CDD pfam00746 pfam00746 366278 Gram_pos_anchor LPXTG cell wall anchor motif. 43 matched cddid_all.tbl CDD pfam00747 pfam00747 395604 Viral_DNA_bp ssDNA binding protein. This protein is found in herpesviruses and is needed for replication. 1120 matched cddid_all.tbl CDD pfam00748 pfam00748 459923 Calpain_inhib Calpain inhibitor. This region is found multiple times in calpain inhibitor proteins. 129 matched cddid_all.tbl CDD pfam00749 pfam00749 395606 tRNA-synt_1c tRNA synthetases class I (E and Q), catalytic domain. Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organizms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln). 314 matched cddid_all.tbl CDD pfam00750 pfam00750 395607 tRNA-synt_1d tRNA synthetases class I (R). Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only arginyl tRNA synthetase. 348 matched cddid_all.tbl CDD pfam00751 pfam00751 459924 DM DM DNA binding domain. The DM domain is named after dsx and mab-3. dsx contains a single amino-terminal DM domain, whereas mab-3 contains two amino-terminal domains. The DM domain has a pattern of conserved zinc chelating residues C2H2C4. The dsx DM domain has been shown to dimerize and bind palindromic DNA. 47 matched cddid_all.tbl CDD pfam00752 pfam00752 395609 XPG_N XPG N-terminal domain. 100 matched cddid_all.tbl CDD pfam00753 pfam00753 425851 Lactamase_B Metallo-beta-lactamase superfamily. 196 matched cddid_all.tbl CDD pfam00754 pfam00754 459925 F5_F8_type_C F5/8 type C domain. This domain is also known as the discoidin (DS) domain family. 127 matched cddid_all.tbl CDD pfam00755 pfam00755 459926 Carn_acyltransf Choline/Carnitine o-acyltransferase. 570 matched cddid_all.tbl CDD pfam00756 pfam00756 395613 Esterase Putative esterase. This family contains Esterase D. However it is not clear if all members of the family have the same function. This family is related to the pfam00135 family. 246 matched cddid_all.tbl CDD pfam00757 pfam00757 395614 Furin-like Furin-like cysteine rich region. 143 matched cddid_all.tbl CDD pfam00758 pfam00758 459927 EPO_TPO Erythropoietin/thrombopoietin. 158 matched cddid_all.tbl CDD pfam00759 pfam00759 459928 Glyco_hydro_9 Glycosyl hydrolase family 9. 376 matched cddid_all.tbl CDD pfam00760 pfam00760 395617 Cucumo_coat Cucumovirus coat protein. 175 matched cddid_all.tbl CDD pfam00761 pfam00761 366290 Polyoma_coat2 Polyomavirus coat protein. 322 matched cddid_all.tbl CDD pfam00762 pfam00762 459929 Ferrochelatase Ferrochelatase. 315 matched cddid_all.tbl CDD pfam00763 pfam00763 459930 THF_DHG_CYH Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain. 115 matched cddid_all.tbl CDD pfam00764 pfam00764 279148 Arginosuc_synth Arginosuccinate synthase. This family contains a PP-loop motif. 386 matched cddid_all.tbl CDD pfam00765 pfam00765 366292 Autoind_synth Autoinducer synthase. 182 matched cddid_all.tbl CDD pfam00766 pfam00766 459931 ETF_alpha Electron transfer flavoprotein FAD-binding domain. This domain found at the C-terminus of electron transfer flavoprotein alpha chain and binds to FAD. The fold consists of a five-stranded parallel beta sheet as the core of the domain, flanked by alternating helices. A small part of this domain is donated by the beta chain. 81 matched cddid_all.tbl CDD pfam00767 pfam00767 279151 Poty_coat Potyvirus coat protein. 243 matched cddid_all.tbl CDD pfam00768 pfam00768 425859 Peptidase_S11 D-alanyl-D-alanine carboxypeptidase. 234 matched cddid_all.tbl CDD pfam00769 pfam00769 459932 ERM_C Ezrin/radixin/moesin family C terminal. This entry represents the C-terminal domain of the ERM family of proteins which consists of three closely-related proteins, ezrin, radixin and moesin. These proteins link actin filaments of cell surface structures to the plasma membrane, using a C-terminal F-actin binding segment and an N-terminal FERM domain (pfam00373), a common membrane binding module. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). This entry represents the C-terminal actin-binding tail domain. This entry also includes Ermin proteins, oligodendrocyte-specific proteins associated with the cytoskeleton whose C-terminal domain is similar to that in ERM family. 77 matched cddid_all.tbl CDD pfam00770 pfam00770 279154 Peptidase_C5 Adenovirus endoprotease. This family of adenovirus thiol endoproteases specifically cleave Gly-Ala peptides in viral precursor peptides. 179 matched cddid_all.tbl CDD pfam00771 pfam00771 459933 FHIPEP FHIPEP family. 645 matched cddid_all.tbl CDD pfam00772 pfam00772 395624 DnaB DnaB-like helicase N terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This N-terminal domain is required both for interaction with other proteins in the primosome and for DnaB helicase activity. 103 matched cddid_all.tbl CDD pfam00773 pfam00773 459934 RNB RNB domain. This domain is the catalytic domain of ribonuclease II. 314 matched cddid_all.tbl CDD pfam00775 pfam00775 425863 Dioxygenase_C Dioxygenase. 181 matched cddid_all.tbl CDD pfam00777 pfam00777 459935 Glyco_transf_29 Glycosyltransferase family 29 (sialyltransferase). Members of this family belong to glycosyltransferase family 29. 256 matched cddid_all.tbl CDD pfam00778 pfam00778 459936 DIX DIX domain. The DIX domain is present in Dishevelled and axin. This domain is involved in homo- and hetero-oligomerization. It is involved in the homo- oligomerization of mouse axin. The axin DIX domain also interacts with the dishevelled DIX domain. The DIX domain has also been called the DAX domain. 77 matched cddid_all.tbl CDD pfam00779 pfam00779 459937 BTK BTK motif. Zinc-binding motif containing conserved cysteines and a histidine. Always found C-terminal to PH domains. The crystal structure shows this motif packs against the PH domain. The PH+Btk module pair has been called the Tec homology (TH) region. 30 matched cddid_all.tbl CDD pfam00780 pfam00780 459938 CNH CNH domain. Domain found in NIK1-like kinase, mouse citron and yeast ROM1, ROM2. Unpublished observations. 261 matched cddid_all.tbl CDD pfam00781 pfam00781 425868 DAGK_cat Diacylglycerol kinase catalytic domain. Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The catalytic domain is assumed from the finding of bacterial homologs. YegS is the Escherichia coli protein in this family whose crystal structure reveals an active site in the inter-domain cleft formed by four conserved sequence motifs, revealing a novel metal-binding site. The residues of this site are conserved across the family. 125 matched cddid_all.tbl CDD pfam00782 pfam00782 395632 DSPc "Dual specificity phosphatase, catalytic domain. Ser/Thr and Tyr protein phosphatases. The enzyme's tertiary fold is highly similar to that of tyrosine-specific phosphatases, except for a ""recognition"" region." 127 matched cddid_all.tbl CDD pfam00784 pfam00784 459939 MyTH4 MyTH4 domain. Domain in myosin and kinesin tails, present twice in myosin-VIIa, and also present in 3 other myosins. 105 matched cddid_all.tbl CDD pfam00786 pfam00786 395634 PBD P21-Rho-binding domain. Small domains that bind Cdc42p- and/or Rho-like small GTPases. Also known as the Cdc42/Rac interactive binding (CRIB). 59 matched cddid_all.tbl CDD pfam00787 pfam00787 459940 PX PX domain. PX domains bind to phosphoinositides. 84 matched cddid_all.tbl CDD pfam00788 pfam00788 425871 RA Ras association (RalGDS/AF-6) domain. RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Recent evidence (not yet in MEDLINE) shows that some RA domains do NOT bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase. 93 matched cddid_all.tbl CDD pfam00789 pfam00789 395637 UBX UBX domain. This domain is present in ubiquitin-regulatory proteins and is a general Cdc48-interacting module. 80 matched cddid_all.tbl CDD pfam00790 pfam00790 395638 VHS VHS domain. Domain present in VPS-27, Hrs and STAM. 136 matched cddid_all.tbl CDD pfam00791 pfam00791 459941 ZU5 ZU5 domain. Domain present in ZO-1 and Unc5-like netrin receptors Domain of unknown function. 97 matched cddid_all.tbl CDD pfam00792 pfam00792 395640 PI3K_C2 Phosphoinositide 3-kinase C2. Phosphoinositide 3-kinase region postulated to contain a C2 domain. Outlier of pfam00168 family. 136 matched cddid_all.tbl CDD pfam00793 pfam00793 395641 DAHP_synth_1 DAHP synthetase I family. Members of this family catalyze the first step in aromatic amino acid biosynthesis from chorismate. E-coli has three related synthetases, which are inhibited by different aromatic amino acids. This family also includes KDSA which has very similar catalytic activity but is involved in the first step of liposaccharide biosynthesis. The enzyme is also part of the shikimate pathway, EC:2.5.1.54. 271 matched cddid_all.tbl CDD pfam00794 pfam00794 395642 PI3K_rbd PI3-kinase family, ras-binding domain. Certain members of the PI3K family possess Ras-binding domains in their N-termini. These regions show some similarity (although not highly significant similarity) to Ras-binding pfam00788 domains (unpublished observation). 106 matched cddid_all.tbl CDD pfam00795 pfam00795 425873 CN_hydrolase Carbon-nitrogen hydrolase. This family contains hydrolases that break carbon-nitrogen bonds. The family includes: Nitrilase EC:3.5.5.1, Aliphatic amidase EC:3.5.1.4, Biotidinase EC:3.5.1.12, Beta-ureidopropionase EC:3.5.1.6. Nitrilase-related proteins generally have a conserved E-K-C catalytic triad, and are multimeric alpha-beta-beta-alpha sandwich proteins. 257 matched cddid_all.tbl CDD pfam00796 pfam00796 425874 PSI_8 Photosystem I reaction centre subunit VIII. 24 matched cddid_all.tbl CDD pfam00797 pfam00797 395644 Acetyltransf_2 N-acetyltransferase. Arylamine N-acetyltransferase (NAT) is a cytosolic enzyme of approximately 30kDa. It facilitates the transfer of an acetyl group from Acetyl Coenzyme A on to a wide range of arylamine, N-hydroxyarylamines and hydrazines. Acetylation of these compounds generally results in inactivation. NAT is found in many species from Mycobacteria (M. tuberculosis, M. smegmatis etc) to man. It was the first enzyme to be observed to have polymorphic activity amongst human individuals. NAT is responsible for the inactivation of Isoniazid (a drug used to treat Tuberculosis) in humans. The NAT protein has also been shown to be involved in the breakdown of folic acid. 240 matched cddid_all.tbl CDD pfam00798 pfam00798 279177 Arena_glycoprot Arenavirus glycoprotein. 483 matched cddid_all.tbl CDD pfam00799 pfam00799 366313 Gemini_AL1 Geminivirus Rep catalytic domain. The AL1 proteins encodes the replication initiator protein (Rep) of geminiviruses, which is a replicon-specific initiator enzyme and is an essential component of the replisome. For geminivirus Rep protein, this N-terminal region is crucial for origin recognition and DNA cleavage and nucleotidyl transfer. 113 matched cddid_all.tbl CDD pfam00800 pfam00800 425875 PDT Prephenate dehydratase. This protein is involved in Phenylalanine biosynthesis. This protein catalyzes the decarboxylation of prephenate to phenylpyruvate. 181 matched cddid_all.tbl CDD pfam00801 pfam00801 395646 PKD PKD domain. This domain was first identified in the Polycystic kidney disease protein PKD1. This domain has been predicted to contain an Ig-like fold. 70 matched cddid_all.tbl CDD pfam00802 pfam00802 144411 Glycoprotein_G Pneumovirus attachment glycoprotein G. This family includes attachment proteins from respiratory synctial virus. Glycoprotein G has not been shown to have any neuraminidase or hemagglutinin activity (Swiss-Prot). The amino terminus is thought to be cytoplasmic, and the carboxyl terminus extracellular. The extracellular region contains four completely conserved cysteine residues. 263 matched cddid_all.tbl CDD pfam00803 pfam00803 279181 3A 3A/RNA2 movement protein family. This family includes movement proteins from various viruses. The 3A protein is found in bromoviruses and Cucumoviruses. The genome of these viruses contain 3 RNA segments. The third segment (RNA 3) contains two proteins, the coat protein and the 3A protein. The function of the 3A protein is uncertain but has been shown to be involved in cell-to- cell movement of the virus. The family also includes movement proteins from Dianthoviruses. 225 matched cddid_all.tbl CDD pfam00804 pfam00804 459942 Syntaxin Syntaxin. Syntaxins are the prototype family of SNARE proteins. They usually consist of three main regions - a C-terminal transmembrane region, a central SNARE domain which is characteriztic of and conserved in all syntaxins (pfam05739), and an N-terminal domain that is featured in this entry. This domain varies between syntaxin isoforms; in syntaxin 1A it is found as three alpha-helices with a left-handed twist. It may fold back on the SNARE domain to allow the molecule to adopt a 'closed' configuration that prevents formation of the core fusion complex - it thus has an auto-inhibitory role. The function of syntaxins is determined by their localization. They are involved in neuronal exocytosis, ER-Golgi transport and Golgi-endosome transport, for example. They also interact with other proteins as well as those involved in SNARE complexes. These include vesicle coat proteins, Rab GTPases, and tethering factors. 203 matched cddid_all.tbl CDD pfam00805 pfam00805 459943 Pentapeptide Pentapeptide repeats (8 copies). These repeats are found in many cyanobacterial proteins. The repeats were first identified in hglK. The function of these repeats is unknown. The structure of this repeat has been predicted to be a beta-helix. The repeat can be approximately described as A(D/N)LXX, where X can be any amino acid. 40 matched cddid_all.tbl CDD pfam00806 pfam00806 459944 PUF Pumilio-family RNA binding repeat. Puf repeats (aka PUM-HD, Pumilio homology domain) are necessary and sufficient for sequence specific RNA binding in fly Pumilio and worm FBF-1 and FBF-2. Both proteins function as translational repressors in early embryonic development by binding sequences in the 3' UTR of target mRNAs (e.g. the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA). Other proteins that contain Puf domains are also plausible RNA binding proteins. Swiss:P47135, for instance, appears to also contain a single RRM domain by HMM analysis. Puf domains usually occur as a tandem repeat of 8 domains. The Pfam model does not necessarily recognize all 8 repeats in all sequences; some sequences appear to have 5 or 6 repeats on initial analysis, but further analysis suggests the presence of additional divergent repeats. Structures of PUF repeat proteins show they consist of a two helix structure. 35 matched cddid_all.tbl CDD pfam00807 pfam00807 366317 Apidaecin Apidaecin. These antibacterial peptides are found in bees. These heat-stable, non-helical peptides are active against a wide range of plant-associated bacteria and some human pathogens. The Pfam alignment includes the propeptide and apidaecin sequence. 30 matched cddid_all.tbl CDD pfam00808 pfam00808 395650 CBFD_NFYB_HMF Histone-like transcription factor (CBF/NF-Y) and archaeal histone. This family includes archaebacterial histones and histone like transcription factors from eukaryotes. 65 matched cddid_all.tbl CDD pfam00809 pfam00809 395651 Pterin_bind Pterin binding enzyme. This family includes a variety of pterin binding enzymes that all adopt a TIM barrel fold. The family includes dihydropteroate synthase EC:2.5.1.15 as well as a group methyltransferase enzymes including methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) that catalyzes a key step in the Wood-Ljungdahl pathway of carbon dioxide fixation. It transfers the N5-methyl group from methyltetrahydrofolate (CH3-H4folate) to a cob(I)amide centre in another protein, the corrinoid iron-sulfur protein. MeTr is a member of a family of proteins that includes methionine synthase and methanogenic enzymes that activate the methyl group of methyltetra-hydromethano(or -sarcino)pterin. 243 matched cddid_all.tbl CDD pfam00810 pfam00810 459945 ER_lumen_recept ER lumen protein retaining receptor. 143 matched cddid_all.tbl CDD pfam00811 pfam00811 459946 Ependymin Ependymin. 127 matched cddid_all.tbl CDD pfam00812 pfam00812 459947 Ephrin Ephrin. 139 matched cddid_all.tbl CDD pfam00813 pfam00813 425882 FliP FliP family. 191 matched cddid_all.tbl CDD pfam00814 pfam00814 395656 TsaD tRNA N6-adenosine threonylcarbamoyltransferase. This domain can be found in Kae1/Qri7/YgjD, products of COG0533 that belong to a small group of 60 proteins that are present in all three domains of life. COG0533 proteins are suggest to play a role in a post translational modification of certain tRNAs. For example, YgjD along with YeaZ, YjeE, and YrdC have been deemed necessary and sufficient for the tRNA modification. This modification involves the formation of N6-threonyl carbamoyl adenosine (t6A) at position 37 in the anti-codon stem loop which is critical for translational speed and accuracy. Structural analysis indicate that YeaZ lacks resemblance to any known protease active site. Together with the absence of a putative zinc-binding motif. Thus the likelyhood of it being a protease, as previously thought, has been negated. EC:2.3.1.234 272 matched cddid_all.tbl CDD pfam00815 pfam00815 459948 Histidinol_dh Histidinol dehydrogenase. 410 matched cddid_all.tbl CDD pfam00816 pfam00816 425884 Histone_HNS H-NS histone family. 91 matched cddid_all.tbl CDD pfam00817 pfam00817 425885 IMS impB/mucB/samB family. These proteins are involved in UV protection (Swiss). 148 matched cddid_all.tbl CDD pfam00818 pfam00818 307113 Ice_nucleation Ice nucleation protein repeat. 15 matched cddid_all.tbl CDD pfam00819 pfam00819 109859 Myotoxins Myotoxin, crotamine. Crotamine is a family of cationic peptides expressed by the venom gland of, for example, Crotalus durissus terrificus. It acts as a cell-penetrating peptide (CPP) and as a potent voltage-gated potassium channel (Kv) inhibitor. 42 matched cddid_all.tbl CDD pfam00820 pfam00820 395660 Lipoprotein_1 Borrelia lipoprotein. This family of lipoproteins is found in Borrelia spirochetes. The function of these proteins is uncertain. 259 matched cddid_all.tbl CDD pfam00821 pfam00821 459949 PEPCK_GTP Phosphoenolpyruvate carboxykinase C-terminal P-loop domain. catalyzes the formation of phosphoenolpyruvate by decarboxylation of oxaloacetate. 356 matched cddid_all.tbl CDD pfam00822 pfam00822 395662 PMP22_Claudin PMP-22/EMP/MP20/Claudin family. 162 matched cddid_all.tbl CDD pfam00823 pfam00823 425887 PPE PPE family. This family named after a PPE motif near to the amino terminus of the domain. The PPE family of proteins all contain an amino-terminal region of about 180 amino acids. The carboxyl terminus of this family are variable, and on the basis of this region fall into at least three groups. The MPTR subgroup has tandem copies of a motif NXGXGNXG. The second subgroup contains a conserved motif at about position 350. The third group are only related in the amino terminal region. The function of these proteins is uncertain but it has been suggested that they may be related to antigenic variation of Mycobacterium tuberculosis. 158 matched cddid_all.tbl CDD pfam00825 pfam00825 425888 Ribonuclease_P Ribonuclease P. 107 matched cddid_all.tbl CDD pfam00827 pfam00827 459950 Ribosomal_L15e Ribosomal L15. 191 matched cddid_all.tbl CDD pfam00828 pfam00828 459951 Ribosomal_L27A Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A. This family includes higher eukaryotic ribosomal 60S L27A, archaeal 50S L18e, prokaryotic 50S L15, fungal mitochondrial L10, plant L27A, mitochondrial L15 and chloroplast L18-3 proteins. 125 matched cddid_all.tbl CDD pfam00829 pfam00829 459952 Ribosomal_L21p Ribosomal prokaryotic L21 protein. 99 matched cddid_all.tbl CDD pfam00830 pfam00830 459953 Ribosomal_L28 Ribosomal L28 family. The ribosomal 28 family includes L28 proteins from bacteria and chloroplasts. The L24 protein from yeast also contains a region of similarity to prokaryotic L28 proteins. L24 from yeast is also found in the large ribosomal subunit 58 matched cddid_all.tbl CDD pfam00831 pfam00831 459954 Ribosomal_L29 Ribosomal L29 protein. 56 matched cddid_all.tbl CDD pfam00832 pfam00832 425894 Ribosomal_L39 Ribosomal L39 protein. 41 matched cddid_all.tbl CDD pfam00833 pfam00833 425895 Ribosomal_S17e Ribosomal S17. 122 matched cddid_all.tbl CDD pfam00834 pfam00834 395672 Ribul_P_3_epim Ribulose-phosphate 3 epimerase family. This enzyme catalyzes the conversion of D-ribulose 5-phosphate into D-xylulose 5-phosphate. 198 matched cddid_all.tbl CDD pfam00835 pfam00835 459955 SNAP-25 SNAP-25 family. SNAP-25 (synaptosome-associated protein 25 kDa) proteins are components of SNARE complexes. Members of this family contain a cluster of cysteine residues that can be palmitoylated for membrane attachment. 56 matched cddid_all.tbl CDD pfam00836 pfam00836 459956 Stathmin Stathmin family. The Stathmin family of proteins play an important role in the regulation of the microtubule cytoskeleton. They regulate microtubule dynamics by promoting depolymerization of microtubules and/or preventing polymerization of tubulin heterodimers. 136 matched cddid_all.tbl CDD pfam00837 pfam00837 279210 T4_deiodinase Iodothyronine deiodinase. Iodothyronine deiodinase converts thyroxine (T4) to 3,5,3'-triiodothyronine (T3). 237 matched cddid_all.tbl CDD pfam00838 pfam00838 459957 TCTP Translationally controlled tumour protein. 163 matched cddid_all.tbl CDD pfam00839 pfam00839 425899 Cys_rich_FGFR Cysteine rich repeat. This cysteine rich repeat contains four cysteines. It is found in multiple copies in a protein that binds to fibroblast growth factors. The repeat is also found in MG160 and E-selectin ligand (ESL-1). 58 matched cddid_all.tbl CDD pfam00840 pfam00840 459958 Glyco_hydro_7 Glycosyl hydrolase family 7. 434 matched cddid_all.tbl CDD pfam00841 pfam00841 459959 Protamine_P2 Sperm histone P2. This protein also known as protamine P2 can substitute for histones in the chromatin of sperm (Swiss). The alignment contains both the sequence of the mature P2 protein and its propeptide. 89 matched cddid_all.tbl CDD pfam00842 pfam00842 459960 Ala_racemase_C Alanine racemase, C-terminal domain. 128 matched cddid_all.tbl CDD pfam00843 pfam00843 334282 Arena_nucleocap Arenavirus nucleocapsid N-terminal domain. This N-terminal domain folds into a novel structure with a deep cavity for binding the m7GpppN cap structure that is required for viral RNA transcription. 334 matched cddid_all.tbl CDD pfam00844 pfam00844 307130 Gemini_coat Geminivirus coat protein/nuclear export factor BR1 family. It has been shown that the 104 N-terminal amino acids of the maize streak virus coat protein bind DNA non- specifically. This family also includes various geminivirus movement proteins that are nuclear export factors or shuttles. One member BR1 facilitates the export of both ds and ss DNA form the nucleus. 244 matched cddid_all.tbl CDD pfam00845 pfam00845 307131 Gemini_BL1 Geminivirus BL1 movement protein. Geminiviruses encode two movement proteins that are essential for systemic infection of their host but dispensable for replication and encapsidation. 276 matched cddid_all.tbl CDD pfam00846 pfam00846 425903 Hanta_nucleocap Hantavirus nucleocapsid protein. 429 matched cddid_all.tbl CDD pfam00847 pfam00847 425904 AP2 AP2 domain. This 60 amino acid residue domain can bind to DNA and is found in transcription factor proteins. 52 matched cddid_all.tbl CDD pfam00848 pfam00848 425905 Ring_hydroxyl_A Ring hydroxylating alpha subunit (catalytic domain). This family is the catalytic domain of aromatic-ring- hydroxylating dioxygenase systems. The active site contains a non-heme ferrous ion coordinated by three ligands. 210 matched cddid_all.tbl CDD pfam00849 pfam00849 459961 PseudoU_synth_2 RNA pseudouridylate synthase. Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes RluD, a pseudouridylate synthase that converts specific uracils to pseudouridine in 23S rRNA. RluA from E. coli converts bases in both rRNA and tRNA. 151 matched cddid_all.tbl CDD pfam00850 pfam00850 425906 Hist_deacetyl Histone deacetylase domain. Histones can be reversibly acetylated on several lysine residues. Regulation of transcription is caused in part by this mechanism. Histone deacetylases catalyze the removal of the acetyl group. Histone deacetylases are related to other proteins. 298 matched cddid_all.tbl CDD pfam00851 pfam00851 279223 Peptidase_C6 Helper component proteinase. This protein is found in genome polyproteins of potyviruses. 440 matched cddid_all.tbl CDD pfam00852 pfam00852 459962 Glyco_transf_10 Glycosyltransferase family 10 (fucosyltransferase) C-term. This is the C-terminal domain of a family of fucosyltransferases. This enzyme transfers fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is known as glycosyltransferase family 10. The C-terminal domain is the likely binding-region for ADP (manuscript in publication). 176 matched cddid_all.tbl CDD pfam00853 pfam00853 459963 Runt Runt domain. 129 matched cddid_all.tbl CDD pfam00854 pfam00854 425909 PTR2 POT family. The POT (proton-dependent oligopeptide transport) family all appear to be proton dependent transporters. 392 matched cddid_all.tbl CDD pfam00855 pfam00855 459964 PWWP PWWP domain. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyzes all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organizing higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression. 92 matched cddid_all.tbl CDD pfam00856 pfam00856 459965 SET SET domain. SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases). A subset of SET domains have been called PR domains. These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction. The SET domain consists of two regions known as SET-N and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure. 115 matched cddid_all.tbl CDD pfam00857 pfam00857 376404 Isochorismatase Isochorismatase family. This family are hydrolase enzymes. 173 matched cddid_all.tbl CDD pfam00858 pfam00858 459966 ASC Amiloride-sensitive sodium channel. 439 matched cddid_all.tbl CDD pfam00859 pfam00859 459967 CTF_NFI CTF/NF-I family transcription modulation region. 288 matched cddid_all.tbl CDD pfam00860 pfam00860 395690 Xan_ur_permease Permease family. This family includes permeases for diverse substrates such as xanthine, uracil and vitamin C. However many members of this family are functionally uncharacterized and may transport other substrates. Members of this family have ten predicted transmembrane helices. 389 matched cddid_all.tbl CDD pfam00861 pfam00861 395691 Ribosomal_L18p Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast. This family includes the large subunit ribosomal proteins from bacteria, archaea, the mitochondria and the chloroplast. It does not include the 60S L18 or L5 proteins from Metazoa. 116 matched cddid_all.tbl CDD pfam00862 pfam00862 395692 Sucrose_synth Sucrose synthase. Sucrose synthases catalyze the synthesis of sucrose from UDP-glucose and fructose. This family includes the bulk of the sucrose synthase protein. However the carboxyl terminal region of the sucrose synthases belongs to the glycosyl transferase family pfam00534. 540 matched cddid_all.tbl CDD pfam00863 pfam00863 279235 Peptidase_C4 Peptidase family C4. This peptidase is present in the nuclear inclusion protein of potyviruses. 243 matched cddid_all.tbl CDD pfam00864 pfam00864 459968 P2X_receptor ATP P2X receptor. 362 matched cddid_all.tbl CDD pfam00865 pfam00865 459969 Osteopontin Osteopontin. 291 matched cddid_all.tbl CDD pfam00866 pfam00866 425916 Ring_hydroxyl_B Ring hydroxylating beta subunit. This subunit has a similar structure to NTF-2 and scytalone dehydratase. 144 matched cddid_all.tbl CDD pfam00867 pfam00867 459970 XPG_I XPG I-region. 87 matched cddid_all.tbl CDD pfam00868 pfam00868 459971 Transglut_N Transglutaminase family. 114 matched cddid_all.tbl CDD pfam00869 pfam00869 395698 Flavi_glycoprot Flavivirus glycoprotein, central and dimerization domains. 300 matched cddid_all.tbl CDD pfam00870 pfam00870 459972 P53 P53 DNA-binding domain. This family contains one anomalous member, viz: Zea mays (Q6JAD8). This sequence is identical to human P53 and would appear to be a a human contaminant within the Zea mays sampling effort. 191 matched cddid_all.tbl CDD pfam00871 pfam00871 395700 Acetate_kinase Acetokinase family. This family includes acetate kinase, butyrate kinase and 2-methylpropanoate kinase. 387 matched cddid_all.tbl CDD pfam00872 pfam00872 307151 Transposase_mut Transposase, Mutator family. 380 matched cddid_all.tbl CDD pfam00873 pfam00873 395701 ACR_tran AcrB/AcrD/AcrF family. Members of this family are integral membrane proteins. Some are involved in drug resistance. AcrB cooperates with a membrane fusion protein, AcrA, and an outer membrane channel TolC. The structure shows the AcrB forms a homotrimer. 1021 matched cddid_all.tbl CDD pfam00874 pfam00874 459973 PRD PRD domain. The PRD domain (for PTS Regulation Domain), is the phosphorylatable regulatory domain found in bacterial transcriptional antiterminator such as BglG, SacY and LicT, as well as in activators such as MtlR and LevR. The PRD is phosphorylated on one or two conserved histidine residues. PRD-containing proteins are involved in the regulation of catabolic operons in Gram+ and Gram- bacteria and are often characterized by a short N-terminal effector domain that binds to either RNA (CAT-RBD for antiterminators pfam03123) or DNA (for activators), and a duplicated PRD module which is phosphorylated by the sugar phosphotransferase system (PTS) in response to the availability of carbon source. The phosphorylations modify the conformation and stability of the dimeric proteins and thereby the RNA- or DNA-binding activity of the effector domain. The structure of the LicT PRD domains has been solved in both the active (pdb:1h99) and inactive state (pdb:1tlv), revealing massive structural rearrangements upon activation. 90 matched cddid_all.tbl CDD pfam00875 pfam00875 459974 DNA_photolyase DNA photolyase. This domain binds a light harvesting cofactor. 161 matched cddid_all.tbl CDD pfam00876 pfam00876 459975 Innexin Innexin. This family includes the Drosophila proteins Ogre and shaking-B, and the C. elegans proteins Unc-7 and Unc-9. Members of this family are integral membrane proteins which are involved in the formation of gap junctions. This family has been named the Innexins. 330 matched cddid_all.tbl CDD pfam00877 pfam00877 395705 NLPC_P60 NlpC/P60 family. The function of this domain is unknown. It is found in several lipoproteins. 105 matched cddid_all.tbl CDD pfam00878 pfam00878 425923 CIMR Cation-independent mannose-6-phosphate receptor repeat. The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat. 143 matched cddid_all.tbl CDD pfam00879 pfam00879 459976 Defensin_propep Defensin propeptide. 51 matched cddid_all.tbl CDD pfam00880 pfam00880 459977 Nebulin Nebulin repeat. 28 matched cddid_all.tbl CDD pfam00881 pfam00881 425926 Nitroreductase Nitroreductase family. The nitroreductase family comprises a group of FMN- or FAD-dependent and NAD(P)H-dependent enzymes able to metabolize nitrosubstituted compounds. 168 matched cddid_all.tbl CDD pfam00882 pfam00882 425927 Zn_dep_PLPC Zinc dependent phospholipase C. 173 matched cddid_all.tbl CDD pfam00883 pfam00883 459978 Peptidase_M17 Cytosol aminopeptidase family, catalytic domain. The two associated zinc ions and the active site are entirely enclosed within the C-terminal catalytic domain in leucine aminopeptidase. 304 matched cddid_all.tbl CDD pfam00884 pfam00884 459979 Sulfatase Sulfatase. 298 matched cddid_all.tbl CDD pfam00885 pfam00885 459980 DMRL_synthase 6,7-dimethyl-8-ribityllumazine synthase. This family includes the beta chain of 6,7-dimethyl-8- ribityllumazine synthase EC:2.5.1.9, an enzyme involved in riboflavin biosynthesis. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example Swiss:O28856. The family contains a number of different subsets including a family of proteins comprising archaeal lumazine and riboflavin synthases, type I lumazine synthases, and the eubacterial type II lumazine synthases. It has been established that lumazine synthase catalyzes the penultimate step in the biosynthesis of riboflavin in plants and microorganizms. The type I lumazine synthases area active in pentameric or icosahedral quaternary assemblies, whereas the type II are decameric. Brucella, a bacterial genus that causes brucellosis, and other Rhizobiales have an atypical riboflavin metabolic pathway. Brucella spp code for both a type-I and a type-II lumazine synthase, and it has been shown that at least one of these two has to be present in order for Brucella to be viable, showing that in the case of Brucella flavin metabolism is implicated in bacterial virulence. 134 matched cddid_all.tbl CDD pfam00886 pfam00886 459981 Ribosomal_S16 Ribosomal protein S16. 61 matched cddid_all.tbl CDD pfam00887 pfam00887 459982 ACBP Acyl CoA binding protein. 76 matched cddid_all.tbl CDD pfam00888 pfam00888 459983 Cullin Cullin family. 610 matched cddid_all.tbl CDD pfam00889 pfam00889 459984 EF_TS Elongation factor TS. 204 matched cddid_all.tbl CDD pfam00890 pfam00890 395718 FAD_binding_2 FAD binding domain. This family includes members that bind FAD. This family includes the flavoprotein subunits from succinate and fumarate dehydrogenase, aspartate oxidase and the alpha subunit of adenylylsulphate reductase. 398 matched cddid_all.tbl CDD pfam00891 pfam00891 395719 Methyltransf_2 O-methyltransferase domain. This family includes a range of O-methyltransferases. These enzymes utilize S-adenosyl methionine. 208 matched cddid_all.tbl CDD pfam00892 pfam00892 307170 EamA EamA-like transporter family. This family includes many hypothetical membrane proteins of unknown function. Many of the proteins contain two copies of the aligned region. The family used to be known as DUF6. Members of this family usually carry 5+5 transmembrane domains, and this domain attempts to model five of these. 136 matched cddid_all.tbl CDD pfam00893 pfam00893 459985 Multi_Drug_Res Small Multidrug Resistance protein. This family is the Small Multidrug Resistance (SMR) family. Several members have been shown to export a range of toxins, including ethidium bromide and quaternary ammonium compounds, through coupling with proton influx. 93 matched cddid_all.tbl CDD pfam00894 pfam00894 279266 Luteo_coat Luteovirus coat protein. 138 matched cddid_all.tbl CDD pfam00895 pfam00895 459986 ATP-synt_8 ATP synthase protein 8. 54 matched cddid_all.tbl CDD pfam00897 pfam00897 279268 Orbi_VP7 Orbivirus inner capsid protein VP7. In BTV, 260 trimers of VP7 are found in the core. The major proteins of the core are VP7 and VP3. VP7 forms an outer layer around VP3. 348 matched cddid_all.tbl CDD pfam00898 pfam00898 307171 Orbi_VP2 Orbivirus outer capsid protein VP2. VP2 acts as an anchor for VP1 and VP3. VP2 contains a non-specific DNA and RNA binding domain in the N-terminus. 946 matched cddid_all.tbl CDD pfam00899 pfam00899 459987 ThiF ThiF family. This domain is found in ubiquitin activating E1 family and members of the bacterial ThiF/MoeB/HesA family. It is repeated in Ubiquitin-activating enzyme E1. 238 matched cddid_all.tbl CDD pfam00900 pfam00900 459988 Ribosomal_S4e Ribosomal family S4e. 75 matched cddid_all.tbl CDD pfam00901 pfam00901 425937 Orbi_VP5 Orbivirus outer capsid protein VP5. cryoelectron microscopy indicates that VP5 is a trimer implying that there are 360 copies of VP5 per virion. 507 matched cddid_all.tbl CDD pfam00902 pfam00902 459989 TatC Sec-independent protein translocase protein (TatC). The bacterial Tat system has a remarkable ability to transport folded proteins even enzyme complexes across the cytoplasmic membrane. It is structurally and mechanistically similar to the Delta pH-driven thylakoidal protein import pathway. A functional Tat system or Delta pH-dependent pathway requires three integral membrane proteins: TatA/Tha4, TatB/Hcf106 and TatC/cpTatC. The TatC protein is essential for the function of both pathways. It might be involved in twin-arginine signal peptide recognition, protein translocation and proton translocation. Sequence analysis predicts that TatC contains six transmembrane helices (TMHs), and experimental data confirmed that N- and C-termini of TatC or cpTatC are exposed to the cytoplasmic or stromal face of the membrane. The cytoplasmic N-terminus and the first cytoplasmic loop region of the Escherichia coli TatC protein are essential for protein export. At least two TatC molecules co-exist within each Tat translocon. 210 matched cddid_all.tbl CDD pfam00903 pfam00903 395724 Glyoxalase Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily. 121 matched cddid_all.tbl CDD pfam00904 pfam00904 395725 Involucrin Involucrin repeat. 9 matched cddid_all.tbl CDD pfam00905 pfam00905 425939 Transpeptidase Penicillin binding protein transpeptidase domain. The active site serine (residue 337 in Swiss:P14677) is conserved in all members of this family. 296 matched cddid_all.tbl CDD pfam00906 pfam00906 279277 Hepatitis_core Hepatitis core antigen. The core antigen of hepatitis viruses possesses a carboxyl terminus rich in arginine. On this basis it was predicted that the core antigen would bind DNA. There is some experimental evidence to support this. 273 matched cddid_all.tbl CDD pfam00907 pfam00907 459990 T-box T-box. The T-box encodes a 180 amino acid domain that binds to DNA. Genes encoding T-box proteins are found in a wide range of animals, but not in other kingdoms such as plants. Family members are all thought to bind to the DNA consensus sequence TCACACCT. they are found exclusively in the nucleus, and perform DNA-binding and transcriptional activation/repression roles. They are generally required for development of the specific tissues they are expressed in, and mutations in T-box genes are implicated in human conditions such as DiGeorge syndrome and X-linked cleft palate, which feature malformations. 182 matched cddid_all.tbl CDD pfam00908 pfam00908 459991 dTDP_sugar_isom dTDP-4-dehydrorhamnose 3,5-epimerase. This family catalyze the isomerization of dTDP-4-dehydro-6-deoxy -D-glucose with dTDP-4-dehydro-6-deoxy-L-mannose. The EC number of this enzyme is 5.1.3.13. 164 matched cddid_all.tbl CDD pfam00909 pfam00909 395729 Ammonium_transp Ammonium Transporter Family. 399 matched cddid_all.tbl CDD pfam00910 pfam00910 459992 RNA_helicase RNA helicase. This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses. 102 matched cddid_all.tbl CDD pfam00912 pfam00912 459993 Transgly Transglycosylase. The penicillin-binding proteins are bifunctional proteins consisting of transglycosylase and transpeptidase in the N- and C-terminus respectively. The transglycosylase domain catalyzes the polymerization of murein glycan chains. 177 matched cddid_all.tbl CDD pfam00913 pfam00913 395732 Trypan_glycop Trypanosome variant surface glycoprotein (A-type). The trypanosome parasite expresses these proteins to evade the immune response. This family includes a variety of surface proteins such as Trypanosoma brucei VSGs such as expression site associated gene (ESAG) 6 and 7. 367 matched cddid_all.tbl CDD pfam00915 pfam00915 459994 Calici_coat Calicivirus coat protein. 291 matched cddid_all.tbl CDD pfam00916 pfam00916 459995 Sulfate_transp Sulfate permease family. This family of integral membrane proteins are known as the Sulfate Permease (SulP) family. SulP is a large family found in all domains of life. Although sulfate is a commonly transported ion there are many other activities in this family. See the TCDB description for a comprehensive summary. 379 matched cddid_all.tbl CDD pfam00917 pfam00917 425944 MATH MATH domain. This motif has been called the Meprin And TRAF-Homology (MATH) domain. This domain is hugely expanded in the nematode C. elegans. 113 matched cddid_all.tbl CDD pfam00918 pfam00918 459996 Gastrin Gastrin/cholecystokinin family. 127 matched cddid_all.tbl CDD pfam00919 pfam00919 459997 UPF0004 Uncharacterized protein family UPF0004. This family is the N terminal half of the Prosite family. The C-terminal half has been shown to be related to MiaB proteins. This domain is a nearly always found in conjunction with pfam04055 and pfam01938 although its function is uncertain. 98 matched cddid_all.tbl CDD pfam00920 pfam00920 459998 ILVD_EDD Dehydratase family. 513 matched cddid_all.tbl CDD pfam00921 pfam00921 376417 Lipoprotein_2 Borrelia lipoprotein. This family of lipoproteins is found in Borrelia spirochetes. The function of these proteins is uncertain. 299 matched cddid_all.tbl CDD pfam00922 pfam00922 366369 Phosphoprotein Vesiculovirus phosphoprotein. 204 matched cddid_all.tbl CDD pfam00923 pfam00923 395737 TAL_FSA Transaldolase/Fructose-6-phosphate aldolase. Transaldolase (TAL) is an enzyme of the pentose phosphate pathway (PPP) found almost ubiquitously in the three domains of life (Archaea, Bacteria, and Eukarya). TAL shares a high degree of structural similarity and sequence identity with fructose-6-phosphate aldolase (FSA). They both belong to the class I aldolase family. Their protein structures have been revealed. 226 matched cddid_all.tbl CDD pfam00924 pfam00924 459999 MS_channel Mechanosensitive ion channel. Two members of this protein family: Swiss:Q57634 and Swiss:Q58543 of M. jannaschii have been functionally characterized. Both proteins form mechanosensitive (MS) ion channels upon reconstitution into liposomes and functional examination by the patch-clamp technique. Therefore this family are likely to also be MS channel proteins. 203 matched cddid_all.tbl CDD pfam00925 pfam00925 460000 GTP_cyclohydro2 GTP cyclohydrolase II. GTP cyclohydrolase II catalyzes the first committed step in the biosynthesis of riboflavin. 123 matched cddid_all.tbl CDD pfam00926 pfam00926 460001 DHBP_synthase 3,4-dihydroxy-2-butanone 4-phosphate synthase. 3,4-Dihydroxy-2-butanone 4-phosphate is biosynthesized from ribulose 5-phosphate and serves as the biosynthetic precursor for the xylene ring of riboflavin. Sometimes found as a bifunctional enzyme with pfam00925. 192 matched cddid_all.tbl CDD pfam00927 pfam00927 460002 Transglut_C Transglutaminase family, C-terminal ig like domain. 106 matched cddid_all.tbl CDD pfam00928 pfam00928 395742 Adap_comp_sub Adaptor complexes medium subunit family. This family also contains members which are coatomer subunits. 259 matched cddid_all.tbl CDD pfam00929 pfam00929 395743 RNase_T Exonuclease. This family includes a variety of exonuclease proteins, such as ribonuclease T and the epsilon subunit of DNA polymerase III.; 164 matched cddid_all.tbl CDD pfam00930 pfam00930 395744 DPPIV_N Dipeptidyl peptidase IV (DPP IV) N-terminal region. This family is an alignment of the region to the N-terminal side of the active site. The Prosite motif does not correspond to this Pfam entry. 352 matched cddid_all.tbl CDD pfam00931 pfam00931 395745 NB-ARC NB-ARC domain. 245 matched cddid_all.tbl CDD pfam00932 pfam00932 460003 LTD Lamin Tail Domain. The lamin-tail domain (LTD), which has an immunoglobulin (Ig) fold, is found in Nuclear Lamins, Chlo1887 from Chloroflexus, and several bacterial proteins where it occurs with membrane associated hydrolases of the metallo-beta-lactamase,synaptojanin, and calcineurin-like phosphoesterase superfamilies. 108 matched cddid_all.tbl CDD pfam00933 pfam00933 395747 Glyco_hydro_3 Glycosyl hydrolase family 3 N terminal domain. 316 matched cddid_all.tbl CDD pfam00934 pfam00934 425952 PE PE family. This family named after a PE motif near to the amino terminus of the domain. The PE family of proteins all contain an amino-terminal region of about 110 amino acids. The carboxyl terminus of this family are variable and fall into several classes. The largest class of PE proteins is the highly repetitive PGRS class which have a high glycine content. The function of these proteins is uncertain but it has been suggested that they may be related to antigenic variation of Mycobacterium tuberculosis. The C-terminus of this domain contains the type VII secretion signal that has a YXXXD/E motif. 91 matched cddid_all.tbl CDD pfam00935 pfam00935 460004 Ribosomal_L44 Ribosomal protein L44. 76 matched cddid_all.tbl CDD pfam00936 pfam00936 425954 BMC BMC domain. Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure. 74 matched cddid_all.tbl CDD pfam00937 pfam00937 460005 CoV_nucleocap Coronavirus nucleocapsid. Coronavirus (CoV) nucleocapsid (N) proteins have 3 highly conserved domains. The N-terminal domain (NTD) (N1b), the C-terminal domain (CTD)(N2b) and the N3 region. The N1b and N2b domains from SARS CoV, infectious bronchitis virus (IBV), human CoV 229E and mouse hepatic virus (MHV) display similar topological organizations. N proteins form dimers, which are asymmetrically arranged into octamers via their N2b domains. Domains N1b and N2b are linked by another domain N2a that contains an SR-rich region in which phosphorylation of specific serine residues allows the N protein to associate with the RNA helicase DDX1 permitting template read-through, and enabling the transition from discontinuous transcription of subgenomic mRNAs (sgmRNAs) to continuous synthesis of longer sgmRNAs and genomic RNA (gRNA). It has been shown that N proteins interact with nonstructural protein 3 (NSP3) and thus are recruited to the replication-transcription complexes (RTCs). 343 matched cddid_all.tbl CDD pfam00938 pfam00938 279306 Lipoprotein_3 Lipoprotein. This family of lipoproteins is Mycoplasma specific. 85 matched cddid_all.tbl CDD pfam00939 pfam00939 279307 Na_sulph_symp Sodium:sulfate symporter transmembrane region. There are also some members in this family that do not match the Prosite motif, and belong to the subfamily SODIT1. 472 matched cddid_all.tbl CDD pfam00940 pfam00940 460006 RNA_pol DNA-dependent RNA polymerase. This is a family of single chain RNA polymerases. 411 matched cddid_all.tbl CDD pfam00941 pfam00941 460007 FAD_binding_5 FAD binding domain in molybdopterin dehydrogenase. 170 matched cddid_all.tbl CDD pfam00942 pfam00942 425958 CBM_3 Cellulose binding domain. 81 matched cddid_all.tbl CDD pfam00943 pfam00943 425959 Alpha_E2_glycop Alphavirus E2 glycoprotein. E2 forms a heterodimer with E1. The virus spikes are made up of 80 trimers of these heterodimers (sindbis virus). 403 matched cddid_all.tbl CDD pfam00944 pfam00944 366379 Peptidase_S3 Alphavirus core protein. Also known as coat protein C and capsid protein C. This makes the literature very confusing. Alphaviruses consist of a nucleoprotein core, a lipid membrane which envelopes the core, and glycoprotein spikes protruding from the lipid membrane. 156 matched cddid_all.tbl CDD pfam00945 pfam00945 395755 Rhabdo_ncap "Rhabdovirus nucleocapsid protein. The Nucleocapsid (N) Protein is said to have a ""tight"" structure. The carboxyl end of the N-terminal domain possesses an RNA binding domain. Sequence alignments show 2 regions of reasonable conservation, approx. 64-103 and 201-329. A whole functional protein is required for encapsidation to take place." 409 matched cddid_all.tbl CDD pfam00946 pfam00946 395756 Mononeg_RNA_pol Mononegavirales RNA dependent RNA polymerase. Members of the Mononegavirales including the Paramyxoviridae, like other non-segmented negative strand RNA viruses, have an RNA-dependent RNA polymerase composed of two subunits, a large protein L and a phosphoprotein P. This is a protein family of the L protein. The L protein confers the RNA polymerase activity on the complex. The P protein acts as a transcription factor. 1042 matched cddid_all.tbl CDD pfam00947 pfam00947 395757 Pico_P2A Picornavirus core protein 2A. This protein is a protease, involved in cleavage of the polyprotein. 127 matched cddid_all.tbl CDD pfam00948 pfam00948 279316 Flavi_NS1 Flavivirus non-structural Protein NS1. The NS1 protein is well conserved amongst the flaviviruses. It contains 12 cysteines, and undergoes glycosylation in a similar manner to other NS proteins. Mutational analysis has strongly implied a role for NS1 in the early stages of RNA replication. 360 matched cddid_all.tbl CDD pfam00949 pfam00949 395758 Peptidase_S7 Peptidase S7, Flavivirus NS3 serine protease. The viral genome is a positive strand RNA that encodes a single polyprotein precursor. Processing of the polyprotein precursor into mature proteins is carried out by the host signal peptidase and by NS3 serine protease, which requires NS2B (pfam01002) as a cofactor. 129 matched cddid_all.tbl CDD pfam00950 pfam00950 334323 ABC-3 ABC 3 transport family. 258 matched cddid_all.tbl CDD pfam00951 pfam00951 109986 Arteri_Gl Arterivirus GL envelope glycoprotein. Arteriviruses encode 4 envelope proteins, Gl, Gs, M and N. Gl envelope protein, is encoded in ORF5, and is 30- 45 kDa in size. Gl is heterogenously glycosylated with N-acetyllactosamine in a cell-type-specific manner. The Gl glycoprotein expresses the neutralization determinants. 179 matched cddid_all.tbl CDD pfam00952 pfam00952 395759 Bunya_nucleocap Bunyavirus nucleocapsid (N) protein. The bunyaviruses are enveloped viruses with a genome consisting of 3 ssRNA segments (called L, M and S). The nucleocapsid protein is encode on the small (S) genomic RNA. The N protein is the major component of the nucleocapsids. This protein is thought to interact with the L protein, virus RNA and/or other N proteins. 229 matched cddid_all.tbl CDD pfam00953 pfam00953 460008 Glycos_transf_4 Glycosyl transferase family 4. 158 matched cddid_all.tbl CDD pfam00954 pfam00954 395761 S_locus_glycop S-locus glycoprotein domain. In Brassicaceae, self-incompatible plants have a self/non-self recognition system. This is sporophytically controlled by multiple alleles at a single locus (S). S-locus glycoproteins, as well as S-receptor kinases, are in linkage with the S-alleles. This region is inferred to be a domain due to it having other domains adjacent to it. 111 matched cddid_all.tbl CDD pfam00955 pfam00955 460009 HCO3_cotransp HCO3- transporter family. This family contains Band 3 anion exchange proteins that exchange CL-/HCO3-. This family also includes cotransporters of Na+/HCO3-. 497 matched cddid_all.tbl CDD pfam00956 pfam00956 460010 NAP Nucleosome assembly protein (NAP). NAP proteins are involved in moving histones into the nucleus, nucleosome assembly and chromatin fluidity. They affect the transcription of many genes. 203 matched cddid_all.tbl CDD pfam00957 pfam00957 395764 Synaptobrevin Synaptobrevin. 89 matched cddid_all.tbl CDD pfam00958 pfam00958 425963 GMP_synt_C GMP synthase C terminal domain. GMP synthetase is a glutamine amidotransferase from the de novo purine biosynthetic pathway. This family is the C-terminal domain specific to the GMP synthases EC:6.3.5.2. In prokaryotes this domain mediates dimerization. Eukaryotic GMP synthases are monomers. This domain in eukaryotes includes several large insertions that may form globular domains. 92 matched cddid_all.tbl CDD pfam00959 pfam00959 395766 Phage_lysozyme Phage lysozyme. This family includes lambda phage lysozyme and E. coli endolysin. 107 matched cddid_all.tbl CDD pfam00960 pfam00960 366388 Neocarzinostat Neocarzinostatin family. 110 matched cddid_all.tbl CDD pfam00961 pfam00961 395767 LAGLIDADG_1 LAGLIDADG endonuclease. 101 matched cddid_all.tbl CDD pfam00962 pfam00962 425964 A_deaminase Adenosine deaminase. 330 matched cddid_all.tbl CDD pfam00963 pfam00963 395769 Cohesin Cohesin domain. Cohesin domains interact with a complementary domain, termed the dockerin domain. The cohesin-dockerin interaction is the crucial interaction for complex formation in the cellulosome. 139 matched cddid_all.tbl CDD pfam00964 pfam00964 460011 Elicitin Elicitin. Elicitins form a novel class of plant necrotic proteins which are secreted by Phytophthora and Pythium fungi, parasites of many economically important crops. These proteins induce leaf necrosis in infected plants and elicit an incompatible hypersensitive-like reaction, leading to the development of a systemic acquired resistance against a range of fungal and bacterial plant pathogens. 88 matched cddid_all.tbl CDD pfam00965 pfam00965 460012 TIMP Tissue inhibitor of metalloproteinase. Members of this family are common in extracellular regions of vertebrate species 183 matched cddid_all.tbl CDD pfam00967 pfam00967 395772 Barwin Barwin family. 116 matched cddid_all.tbl CDD pfam00969 pfam00969 425967 MHC_II_beta Class II histocompatibility antigen, beta domain. 75 matched cddid_all.tbl CDD pfam00970 pfam00970 425968 FAD_binding_6 Oxidoreductase FAD-binding domain. 99 matched cddid_all.tbl CDD pfam00971 pfam00971 250265 EIAV_GP90 EIAV coat protein, gp90. Equine infectious anaemia (EIAV). EIAV belongs to the family Retroviridae. EIAV gp90 is hypervariable in the carboxyl-end region and more stable in the amino-end region. This variability is a pathogenicity factor that allows the evasion of the host's immune response. 385 matched cddid_all.tbl CDD pfam00972 pfam00972 460013 Flavi_NS5 Flavivirus RNA-directed RNA polymerase, fingers and palm domains. Flaviviruses produce a large polyprotein from the ssRNA genome, encoding structural proteins required for virus assembly and non-structural (NS1-5) proteins involved in replication of the viral genome. This polyprotein is cleaved by viral and cellular proteases to produce mature viral proteins. NS5 is the largest mature viral protein and contains a N-terminal methyltransferase (MTase) domain separated by a short linker from the C-terminal RNA-directed RNA polymerase domain (RdRp) that adopts a characteriztic right-handed fingers-palm-thumb fold and possesses a number of short regions and motifs homologous to other RNA-directed RNA polymerases. This entry covers the fingers and palm domains of RNA-directed RNA polymerase (RdRp) from Flavivirus NS5. NS5 binds to a the stem loop A (SLA) at the 5' extremity of Flavivirus genome and regulates translation of the viral genome. 451 matched cddid_all.tbl CDD pfam00973 pfam00973 395775 Paramyxo_ncap Paramyxovirus nucleocapsid protein. The nucleocapsid protein is referred to as NP. NP is is the major structural component of the nucleocapsid. The protein is approx. 58 kDa. 2600 NP molecules go to tightly encapsidate the RNA. NP interacts with several other viral encoded proteins, all of which are involved in controlling replication. {NP-NP, NP-P, NP-(PL), and NP-V}. 524 matched cddid_all.tbl CDD pfam00974 pfam00974 425969 Rhabdo_glycop Rhabdovirus spike glycoprotein. Frequently abbreviated to G protein. The glycoprotein spike is made up of a trimer of G proteins. Channel formed by glycoprotein spike is thought to function in a similar manner to Influenza virus M2 protein channel, thus allowing a signal to pass across the viral membrane to signal for viral uncoating. 442 matched cddid_all.tbl CDD pfam00975 pfam00975 395776 Thioesterase Thioesterase domain. Peptide synthetases are involved in the non-ribosomal synthesis of peptide antibiotics. Next to the operons encoding these enzymes, in almost all cases, are genes that encode proteins that have similarity to the type II fatty acid thioesterases of vertebrates. There are also modules within the peptide synthetases that also share this similarity. With respect to antibiotic production, thioesterases are required for the addition of the last amino acid to the peptide antibiotic, thereby forming a cyclic antibiotic. Thioesterases (non-integrated) have molecular masses of 25-29 kDa. 223 matched cddid_all.tbl CDD pfam00976 pfam00976 460014 ACTH_domain Corticotropin ACTH domain. 19 matched cddid_all.tbl CDD pfam00977 pfam00977 425971 His_biosynth Histidine biosynthesis protein. Proteins involved in steps 4 and 6 of the histidine biosynthesis pathway are contained in this family. Histidine is formed by several complex and distinct biochemical reactions catalyzed by eight enzymes. The enzymes in this Pfam entry are called His6 and His7 in eukaryotes and HisA and HisF in prokaryotes. The structure of HisA is known to be a TIM barrel fold. In some archaeal HisA proteins the TIM barrel is composed of two tandem repeats of a half barrel. This family belong to the common phosphate binding site TIM barrel family. 228 matched cddid_all.tbl CDD pfam00978 pfam00978 395779 RdRP_2 RNA dependent RNA polymerase. This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins: 2A protein from bromoviruses putative RNA dependent RNA polymerase from tobamoviruses Non structural polyprotein from togaviruses 440 matched cddid_all.tbl CDD pfam00979 pfam00979 144537 Reovirus_cap Reovirus outer capsid protein, Sigma 3. Sigma 3 is the major outer capsid protein of reovirus. Sigma 3 is encoded by genome segment 4. Sigma 3 binds to double stranded RNA and associates with polypeptide u1 and its cleavage product u1C to form the outer shell of the virion. The Sigma 3 protein possesses a zinc-finger motif and an RNA-binding domain in the N and C termini respectively. This protein is also thought to play a role in pathogenesis. 367 matched cddid_all.tbl CDD pfam00980 pfam00980 395780 Rota_Capsid_VP6 Rotavirus major capsid protein VP6. Rotaviruses consist of three concentric protein shells. The intermediate (middle) protein layer consists 260 trimers of VP6. VP6 in the most abundant protein in the virion. VP6 is also involved in virion assembly, and possesses the ability to interact with VP2, VP4 and VP7. 396 matched cddid_all.tbl CDD pfam00981 pfam00981 144538 Rota_NS53 Rotavirus RNA-binding Protein 53 (NS53). This protein is also known as NSP1. NS53 is encoded by gene 5. It is made in low levels in the infected cells and is a component of early replication. The protein is known to accumulate on the cytoskeleton of the infected cell. NS53 is an RNA binding protein that contains a characteriztic cysteine rich region. 488 matched cddid_all.tbl CDD pfam00982 pfam00982 425972 Glyco_transf_20 Glycosyltransferase family 20. Members of this family belong to glycosyl transferase family 20. OtsA (Trehalose-6-phosphate synthase) is homologous to regions in the subunits of yeast trehalose-6-phosphate synthase/phosphate complex,. 471 matched cddid_all.tbl CDD pfam00983 pfam00983 395782 Tymo_coat Tymovirus coat protein. 179 matched cddid_all.tbl CDD pfam00984 pfam00984 460015 UDPG_MGDP_dh UDP-glucose/GDP-mannose dehydrogenase family, central domain. The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyze the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate. 92 matched cddid_all.tbl CDD pfam00985 pfam00985 144541 MSA_2 Merozoite Surface Antigen 2 (MSA-2) family. 171 matched cddid_all.tbl CDD pfam00986 pfam00986 460016 DNA_gyraseB_C DNA gyrase B subunit, carboxyl terminus. The amino terminus of eukaryotic and prokaryotic DNA topoisomerase II are similar, but they have a different carboxyl terminus. The amino-terminal portion of the DNA gyrase B protein is thought to catalyze the ATP-dependent super-coiling of DNA. See pfam00204. The carboxyl-terminal end supports the complexation with the DNA gyrase A protein and the ATP-independent relaxation. This family also contains Topoisomerase IV. This is a bacterial enzyme that is closely related to DNA gyrase,. 63 matched cddid_all.tbl CDD pfam00988 pfam00988 460017 CPSase_sm_chain Carbamoyl-phosphate synthase small chain, CPSase domain. The carbamoyl-phosphate synthase domain is in the amino terminus of protein. Carbamoyl-phosphate synthase catalyzes the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesize carbamoyl phosphate. See pfam00289. The small chain has a GATase domain in the carboxyl terminus. See pfam00117. 126 matched cddid_all.tbl CDD pfam00989 pfam00989 395786 PAS PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 113 matched cddid_all.tbl CDD pfam00990 pfam00990 425976 GGDEF Diguanylate cyclase, GGDEF domain. This domain is found linked to a wide range of non-homologous domains in a variety of bacteria. It has been shown to be homologous to the adenylyl cyclase catalytic domain and has diguanylate cyclase activity. This observation correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. In the WspR protein of Pseudomonas aeruginosa, the GGDEF domain acts as a diguanylate cyclase, PDB:3bre, when the whole molecule appears to form a tetramer consisting of two symmetrically-related dimers representing a biological unit. The active site is the GGD/EF motif, buried in the structure, and the cyclic dimeric guanosine monophosphate (c-di-GMP) bind to the inhibitory-motif RxxD on the surface. The enzyme thus catalyzes the cyclization of two guanosine triphosphate (GTP) molecules to one c-di-GMP molecule. 160 matched cddid_all.tbl CDD pfam00992 pfam00992 460018 Troponin Troponin. Troponin (Tn) contains three subunits, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT). this Pfam contains members of the TnT subunit. Troponin is a complex of three proteins, Ca2+ binding (TnC), inhibitory (TnI), and tropomyosin binding (TnT). The troponin complex regulates Ca++ induced muscle contraction. This family includes troponin T and troponin I. Troponin I binds to actin and troponin T binds to tropomyosin. 132 matched cddid_all.tbl CDD pfam00993 pfam00993 460019 MHC_II_alpha Class II histocompatibility antigen, alpha domain. 81 matched cddid_all.tbl CDD pfam00994 pfam00994 425979 MoCF_biosynth Probable molybdopterin binding domain. This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor. The domain is presumed to bind molybdopterin. The structure of this domain is known, and it forms an alpha/beta structure. In the known structure of Gephyrin this domain mediates trimerization. 143 matched cddid_all.tbl CDD pfam00995 pfam00995 460020 Sec1 Sec1 family. 506 matched cddid_all.tbl CDD pfam00996 pfam00996 395792 GDI GDP dissociation inhibitor. 436 matched cddid_all.tbl CDD pfam00997 pfam00997 460021 Casein_kappa Kappa casein. Kappa-casein is a mammalian milk protein involved in a number of important physiological processes. In the gut, the ingested protein is split into an insoluble peptide (para kappa-casein) and a soluble hydrophilic glycopeptide (caseinomacropeptide). Caseinomacropeptide is responsible for increased efficiency of digestion, prevention of neonate hypersensitivity to ingested proteins, and inhibition of gastric pathogens. 160 matched cddid_all.tbl CDD pfam00998 pfam00998 395794 RdRP_3 Viral RNA dependent RNA polymerase. This family includes viral RNA dependent RNA polymerase enzymes from hepatitis C virus and various plant viruses. 486 matched cddid_all.tbl CDD pfam00999 pfam00999 425982 Na_H_Exchanger Sodium/hydrogen exchanger family. Na/H antiporters are key transporters in maintaining the pH of actively metabolising cells. The molecular mechanisms of antiport are unclear. These antiporters contain 10-12 transmembrane regions (M) at the amino-terminus and a large cytoplasmic region at the carboxyl terminus. The transmembrane regions M3-M12 share identity with other members of the family. The M6 and M7 regions are highly conserved. Thus, this is thought to be the region that is involved in the transport of sodium and hydrogen ions. The cytoplasmic region has little similarity throughout the family. 377 matched cddid_all.tbl CDD pfam01000 pfam01000 425983 RNA_pol_A_bac RNA polymerase Rpb3/RpoA insert domain. Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal 117 matched cddid_all.tbl CDD pfam01001 pfam01001 110032 HCV_NS4b Hepatitis C virus non-structural protein NS4b. No precise function has been assigned to NS4b. However, it is known that NS4b interacts with NS4a and NS3 to form a large replicase complex to direct the viral RNA replication. 192 matched cddid_all.tbl CDD pfam01002 pfam01002 279357 Flavi_NS2B Flavivirus non-structural protein NS2B. Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. All, but two, are cleaved by the NS2B-NS3 protease complex. 127 matched cddid_all.tbl CDD pfam01003 pfam01003 366413 Flavi_capsid Flavivirus capsid protein C. Flaviviruses are small enveloped viruses with virions comprised of 3 proteins called C, M and E. Multiple copies of the C protein form the nucleocapsid, which contains the ssRNA molecule. 117 matched cddid_all.tbl CDD pfam01004 pfam01004 460022 Flavi_M Flavivirus envelope glycoprotein M. Flaviviruses are small enveloped viruses with virions comprised of 3 proteins called C, M and E. The envelope glycoprotein M is made as a precursor, called prM. The precursor portion of the protein is the signal peptide for the proteins entry into the membrane. prM is cleaved to form M in a late-stage cleavage event. Associated with this cleavage is a change in the infectivity and fusion activity of the virus. 74 matched cddid_all.tbl CDD pfam01005 pfam01005 279359 Flavi_NS2A Flavivirus non-structural protein NS2A. NS2A is a hydrophobic protein about 25 kDa is size. NS2A is cleaved from NS1 by a membrane bound host protease. NS2A has been found to associate with the dsRNA within the vesicle packages. It has also been found that NS2A associates with the known replicase components and so NS2A has been postulated to be part of this replicase complex. 215 matched cddid_all.tbl CDD pfam01006 pfam01006 366414 HCV_NS4a Hepatitis C virus non-structural protein NS4a. NS4a forms an integral part of the NS3 serine protease, as it is required in a number of cases as a cofactor of cleavage. It has also been reported that NS4a interacts with NS4b and NS3 to form a multi-subunit replicase complex. 55 matched cddid_all.tbl CDD pfam01007 pfam01007 460023 IRK Inward rectifier potassium channel transmembrane domain. 141 matched cddid_all.tbl CDD pfam01008 pfam01008 395798 IF-2B Initiation factor 2 subunit family. This family includes initiation factor 2B alpha, beta and delta subunits from eukaryotes, initiation factor 2B subunits 1 and 2 from archaebacteria and some proteins of unknown function from prokaryotes. Initiation factor 2 binds to Met-tRNA, GTP and the small ribosomal subunit. Members of this family have also been characterized as 5-methylthioribose- 1-phosphate isomerases, an enzyme of the methionine salvage pathway. The crystal structure of Ypr118w, a non-essential, low-copy number gene product from Saccharomyces cerevisiae, reveals a dimeric protein with two domains and a putative active site cleft. 281 matched cddid_all.tbl CDD pfam01010 pfam01010 366417 Proton_antipo_C NADH-dehyrogenase subunit F, TMs, (complex I) C-terminus. This sub-family represents a carboxyl terminal extension of pfam00361. It includes subunit 5 from chloroplasts, and bacterial subunit L. This sub-family is part of complex I which catalyzes the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane. This family is largely a few TM regions of the F subunit of NADH-Ubiquinone oxidoreductase from plants. The TMs form part of the anti-porter subunit. 244 matched cddid_all.tbl CDD pfam01011 pfam01011 395799 PQQ PQQ enzyme repeat. The family represent a single repeat of a beta propeller. This propeller has been found in several enzymes which utilize pyrrolo-quinoline quinone as a prosthetic group. 36 matched cddid_all.tbl CDD pfam01012 pfam01012 425985 ETF Electron transfer flavoprotein domain. This family includes the homologous domain shared between the alpha and beta subunits of the electron transfer flavoprotein. 178 matched cddid_all.tbl CDD pfam01014 pfam01014 460024 Uricase Uricase. 128 matched cddid_all.tbl CDD pfam01015 pfam01015 425987 Ribosomal_S3Ae Ribosomal S3Ae family. 191 matched cddid_all.tbl CDD pfam01016 pfam01016 460025 Ribosomal_L27 Ribosomal L27 protein. 77 matched cddid_all.tbl CDD pfam01017 pfam01017 460026 STAT_alpha STAT protein, all-alpha domain. STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. STAT proteins also include an SH2 domain pfam00017. 167 matched cddid_all.tbl CDD pfam01018 pfam01018 460027 GTP1_OBG GTP1/OBG. The N-terminal domain of Swiss:P20964 has the OBG fold, which is formed by three glycine-rich regions inserted into a small 8-stranded beta-sandwich these regions form six left-handed collagen-like helices packed and H-bonded together. 155 matched cddid_all.tbl CDD pfam01019 pfam01019 425991 G_glu_transpept Gamma-glutamyltranspeptidase. 499 matched cddid_all.tbl CDD pfam01020 pfam01020 395807 Ribosomal_L40e Ribosomal L40e family. Bovine L40 has been identified as a secondary RNA binding protein. L40 is fused to a ubiquitin protein. 48 matched cddid_all.tbl CDD pfam01021 pfam01021 425992 TYA Ty transposon capsid protein. Ty are yeast transposons. A 5.7kb transcript codes for p3 a fusion protein of TYA and TYB. The TYA protein is analogous to the gag protein of retroviruses. TYA a is cleaved to form 46kd protein which can form mature virion like particles. This entry corresponds to the capsid protein from Ty1 and Ty2 transposons. 384 matched cddid_all.tbl CDD pfam01022 pfam01022 425993 HTH_5 Bacterial regulatory protein, arsR family. Members of this family contains a DNA binding 'helix-turn-helix' motif. This family includes other proteins which are not included in the Prosite definition. 45 matched cddid_all.tbl CDD pfam01023 pfam01023 460028 S_100 S-100/ICaBP type calcium binding domain. The S-100 domain is a subfamily of the EF-hand calcium binding proteins. 45 matched cddid_all.tbl CDD pfam01024 pfam01024 425995 Colicin Colicin pore forming domain. 185 matched cddid_all.tbl CDD pfam01025 pfam01025 425996 GrpE GrpE. 165 matched cddid_all.tbl CDD pfam01026 pfam01026 425997 TatD_DNase TatD related DNase. This family of proteins are related to a large superfamily of metalloenzymes. TatD, a member of this family has been shown experimentally to be a DNase enzyme. 253 matched cddid_all.tbl CDD pfam01027 pfam01027 460029 Bax1-I Inhibitor of apoptosis-promoting Bax1. Programmed cell-death involves a set of Bcl-2 family proteins, some of which inhibit apoptosis (Bcl-2 and Bcl-XL) and some of which promote it (Bax and Bak). Human Bax inhibitor, BI-1, is an evolutionarily conserved integral membrane protein containing multiple membrane-spanning segments predominantly localized to intracellular membranes. It has 6-7 membrane-spanning domains. The C termini of the mammalian BI-1 proteins are comprised of basic amino acids resembling some nuclear targeting sequences, but otherwise the predicted proteins lack motifs that suggest a function. As plant BI-1 appears to localize predominantly to the ER, we hypothesized that plant BI-1 could also regulate cell death triggered by ER stress. BI-1 appears to exert its effect through an interaction with calmodulin. The budding yeast member of this family has been found unexpectedly to encode a BH3 domain-containing protein (Ybh3p) that regulates the mitochondrial pathway of apoptosis in a phylogenetically conserved manner. Examination of the crystal structure of a bacterial member of this family shows that these proteins mediate a calcium leak across the membrane that is pH-dependent. Calcium homoeostasis balances passive calcium leak with active calcium uptake. The structure exists in a pore-closed and pore-open conformation, at pHs of 8 and 6 respectively, and the pore can be opened by intracrystalline transition; together these findings suggest that pH controls the conformational transition. 207 matched cddid_all.tbl CDD pfam01028 pfam01028 460030 Topoisom_I Eukaryotic DNA topoisomerase I, catalytic core. Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination. 198 matched cddid_all.tbl CDD pfam01029 pfam01029 460031 NusB NusB family. The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination. 133 matched cddid_all.tbl CDD pfam01030 pfam01030 460032 Recep_L_domain Receptor L domain. The L domains from these receptors make up the bilobal ligand binding site. Each L domain consists of a single-stranded right hand beta-helix. This Pfam entry is missing the first 50 amino acid residues of the domain. 112 matched cddid_all.tbl CDD pfam01031 pfam01031 460033 Dynamin_M Dynamin central region. This is the stalk region which lies between the GTPase domain, see pfam00350, and the pleckstrin homology (PH) domain, see pfam00169. This region dimerizes in a cross-like fashion forming a dynamin dimer in which the two G-domains are oriented in opposite directions. 287 matched cddid_all.tbl CDD pfam01032 pfam01032 426003 FecCD FecCD transport family. This is a sub-family of bacterial binding protein-dependent transport systems family. This Pfam entry contains the inner components of this multicomponent transport system. 311 matched cddid_all.tbl CDD pfam01033 pfam01033 460034 Somatomedin_B Somatomedin B domain. 40 matched cddid_all.tbl CDD pfam01034 pfam01034 460035 Syndecan Syndecan domain. Syndecans are transmembrane heparin sulfate proteoglycans which are implicated in the binding of extracellular matrix components and growth factors. 63 matched cddid_all.tbl CDD pfam01035 pfam01035 460036 DNA_binding_1 6-O-methylguanine DNA methyltransferase, DNA binding domain. This is the C-terminal DNA-binding domain of 6-O-methylguanine-DNA methyltransferases. 81 matched cddid_all.tbl CDD pfam01036 pfam01036 460037 Bac_rhodopsin Bacteriorhodopsin-like protein. The bacterial opsins are retinal-binding proteins that provide light- dependent ion transport and sensory functions to a family of halophilic bacteria. They are integral membrane proteins believed to contain seven transmembrane (TM) domains, the last of which contains the attachment point for retinal (a conserved lysine). This family also includes distantly related proteins that do not contain the retinal binding lysine and so cannot function as opsins. Some fungal examples are: Swiss:O74870, Swiss:P25619, Swiss:P38079, Swiss:Q12117. 224 matched cddid_all.tbl CDD pfam01037 pfam01037 426007 AsnC_trans_reg Lrp/AsnC ligand binding domain. The l-leucine-responsive regulatory protein (Lrp/AsnC) family is a family of similar bacterial transcription regulatory proteins. The family is named after two E. coli proteins involved in regulating amino acid metabolism. This entry corresponds to the usually C-terminal regulatory ligand binding domain. Structurally this domain has a dimeric alpha/beta barrel fold. This domain binds almost exclusively amino acids but also 4-hydroxyphenylpyruvate and kynurenine (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 73 matched cddid_all.tbl CDD pfam01039 pfam01039 426008 Carboxyl_trans Carboxyl transferase domain. All of the members in this family are biotin dependent carboxylases. The carboxyl transferase domain carries out the following reaction; transcarboxylation from biotin to an acceptor molecule. There are two recognized types of carboxyl transferase. One of them uses acyl-CoA and the other uses 2-oxoacid as the acceptor molecule of carbon dioxide. All of the members in this family utilize acyl-CoA as the acceptor molecule. 491 matched cddid_all.tbl CDD pfam01040 pfam01040 460038 UbiA UbiA prenyltransferase family. 250 matched cddid_all.tbl CDD pfam01041 pfam01041 395827 DegT_DnrJ_EryC1 DegT/DnrJ/EryC1/StrS aminotransferase family. The members of this family are probably all pyridoxal-phosphate-dependent aminotransferase enzymes with a variety of molecular functions. The family includes StsA, StsC and StsS. The aminotransferase activity was demonstrated for purified StsC protein as the L-glutamine:scyllo-inosose aminotransferase EC:2.6.1.50, which catalyzes the first amino transfer in the biosynthesis of the streptidine subunit of streptomycin. 360 matched cddid_all.tbl CDD pfam01042 pfam01042 426010 Ribonuc_L-PSP Endoribonuclease L-PSP. Endoribonuclease active on single-stranded mRNA. Inhibits protein synthesis by cleavage of mRNA. Previously thought to inhibit protein synthesis initiation. This protein may also be involved in the regulation of purine biosynthesis. YjgF (renamed RidA) family members are enamine/imine deaminases. They hydrolyze reactive intermediates released by PLP-dependent enzymes, including threonine dehydratase. YjgF also prevents inhibition of transaminase B (IlvE) in Salmonella. 117 matched cddid_all.tbl CDD pfam01043 pfam01043 460039 SecA_PP_bind SecA preprotein cross-linking domain. The SecA ATPase is involved in the insertion and retraction of preproteins through the plasma membrane. This domain has been found to cross-link to preproteins, thought to indicate a role in preprotein binding. The pre-protein cross-linking domain is comprised of two sub domains that are inserted within the ATPase domain. 110 matched cddid_all.tbl CDD pfam01044 pfam01044 460040 Vinculin Vinculin family. 852 matched cddid_all.tbl CDD pfam01047 pfam01047 426012 MarR MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif. 59 matched cddid_all.tbl CDD pfam01048 pfam01048 426013 PNP_UDP_1 Phosphorylase superfamily. Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase) 233 matched cddid_all.tbl CDD pfam01049 pfam01049 460041 CADH_Y-type_LIR Cadherin, Y-type LIR-motif. LC3 Interacting Regions (LIRs), also known as ATG8-interacting motifs (AIMs), are short-linear motifs (SLiMs) of autophagy receptors and adaptor proteins that facilitates the selective recruitment of autophagy substrates to the autophagosome. LIRs are characterized by degenerated sequences with a four-residue core central sequence involved in ATG8-binding, with the W/Y/FxxL/I/V pattern. Based on the aromatic amino acid in position 1 they can be classified into W-type, Y-type and F-type. This entry includes three conserved LIR motifs of CADHs, which two are Y-type (YDxL/I) and one F-type (FKKL), while a fourth LIR (YGGV) is only present in CADH6 members. Cadherins (CADH) have a crucial role in epithelial-to-mesenchymal transition (EMT), involved in migration properties of tumour cells. CADH6 is an EMT marker in thyroid cancer that interacts with the ATG8 family members GABARAP, BNIP3 and BNIP3L restraining autophagy through LIR domains, a common feature among many cadherin family members. 60 matched cddid_all.tbl CDD pfam01050 pfam01050 426015 MannoseP_isomer Mannose-6-phosphate isomerase. All of the members of this Pfam entry belong to family 2 of the mannose-6-phosphate isomerases. The type II phosphomannose isomerases are bifunctional enzymes. This Pfam entry covers the isomerase domain. The guanosine diphospho-D-mannose pyrophosphorylase domain is in another Pfam entry, see pfam00483. 151 matched cddid_all.tbl CDD pfam01051 pfam01051 460042 Rep_3 Initiator Replication protein. This protein is an initiator of plasmid replication. RepB possesses nicking-closing (topoisomerase I) like activity. It is also able to perform a strand transfer reaction on ssDNA that contains its target. This family also includes RepA which is an E.coli protein involved in plasmid replication. The RepA protein binds to DNA repeats that flank the repA gene. 218 matched cddid_all.tbl CDD pfam01052 pfam01052 460043 FliMN_C Type III flagellar switch regulator (C-ring) FliN C-term. This family includes the C-terminal region of flagellar motor switch proteins FliN and FliM. It is associated with family FliM, pfam02154 and family FliN_N pfam16973. 66 matched cddid_all.tbl CDD pfam01053 pfam01053 395837 Cys_Met_Meta_PP Cys/Met metabolism PLP-dependent enzyme. This family includes enzymes involved in cysteine and methionine metabolism. The following are members: Cystathionine gamma-lyase, Cystathionine gamma-synthase, Cystathionine beta-lyase, Methionine gamma-lyase, OAH/OAS sulfhydrylase, O-succinylhomoserine sulfhydrylase All of these members participate is slightly different reactions. All these enzymes use PLP (pyridoxal-5'-phosphate) as a cofactor. 376 matched cddid_all.tbl CDD pfam01054 pfam01054 366439 MMTV_SAg Mouse mammary tumour virus superantigen. The mouse mammary tumour virus (MMTV) is a milk-transmitted type B retrovirus. The superantigen (SAg) is encoded by the long terminal repeat. The SAgs are also called PR73. 184 matched cddid_all.tbl CDD pfam01055 pfam01055 460044 Glyco_hydro_31 Glycosyl hydrolases family 31. Glycosyl hydrolases are key enzymes of carbohydrate metabolism. Family 31 comprises of enzymes that are, or similar to, alpha- galactosidases. 443 matched cddid_all.tbl CDD pfam01056 pfam01056 460045 Myc_N Myc amino-terminal region. The myc family belongs to the basic helix-loop-helix leucine zipper class of transcription factors, see pfam00010. Myc forms a heterodimer with Max, and this complex regulates cell growth through direct activation of genes involved in cell replication. Mutations in the C-terminal 20 residues of this domain cause unique changes in the induction of apoptosis, transformation, and G2 arrest. 339 matched cddid_all.tbl CDD pfam01057 pfam01057 426020 Parvo_NS1 Parvovirus non-structural protein NS1. This family also contains the NS2 protein. Parvoviruses encode two non-structural proteins, NS1 and NS2. The mRNA for NS2 contains the coding sequence for the first 87 amino acids of NS1, then by an alternative splicing mechanism mRNA from a different reading frame, encoding the last 78 amino acids, makes up the full length of the NS2 mRNA. NS1, is the major non-structural protein. It is essential for DNA replication. It is an 83-kDa nuclear phosphoprotein. It has DNA helicase and ATPase activity. 271 matched cddid_all.tbl CDD pfam01058 pfam01058 426021 Oxidored_q6 NADH ubiquinone oxidoreductase, 20 Kd subunit. 124 matched cddid_all.tbl CDD pfam01059 pfam01059 366442 Oxidored_q5_N NADH-ubiquinone oxidoreductase chain 4, amino terminus. 110 matched cddid_all.tbl CDD pfam01060 pfam01060 460046 TTR-52 Transthyretin-like family. TTR-52 was called family 2 in, and has weak similarity to transthyretin (formerly called pre-albumin) which transports thyroid hormones. The specific function of this protein is as a bridging molecule in apoptosis cross-linking dying cells to phagocytes. TTR-52 bridges by cross-linking surface-exposed phosphatidylserine (PtdSer) on apoptotic cells to the CED-1 receptor, a transmembrane receptor, on phagocytes. TTR-52 has an open beta-barrel-like structure. 79 matched cddid_all.tbl CDD pfam01061 pfam01061 426023 ABC2_membrane ABC-2 type transporter. 204 matched cddid_all.tbl CDD pfam01062 pfam01062 460047 Bestrophin Bestrophin, RFP-TM, chloride channel. Bestrophin is a 68-kDa basolateral plasma membrane protein expressed in retinal pigment epithelial cells (RPE). It is encoded by the VMD2 gene, which is mutated in Best macular dystrophy, a disease characterized by a depressed light peak in the electrooculogram. VMD2 encodes a 585-amino acid protein with an approximate mass of 68 kDa which has been designated bestrophin. Bestrophin shares homology with the Caenorhabditis elegans RFP gene family, named for the presence of a conserved arginine (R), phenylalanine (F), proline (P), amino acid sequence motif. Bestrophin is a plasma membrane protein, localized to the basolateral surface of RPE cells consistent with a role for bestrophin in the generation or regulation of the EOG light peak. Bestrophin and other RFP family members represent a new class of chloride channels, indicating a direct role for bestrophin in generating the light peak. The VMD2 gene underlying Best disease was shown to represent the first human member of the RFP-TM protein family. More than 97% of the disease-causing mutations are located in the N-terminal RFP-TM domain implying important functional properties. The bestrophins are four-pass transmembrane chloride-channel proteins, and the RFP-TM or bestrophin domain extends from the N-terminus through approximately 350 amino acids and contains all of the TM domains as well as nearly all reported disease causing mutations. Interestingly, the RFP motif is not conserved evolutionarily back beyond Metazoa, neither is it in plant members. 272 matched cddid_all.tbl CDD pfam01063 pfam01063 395844 Aminotran_4 Amino-transferase class IV. The D-amino acid transferases (D-AAT) are required by bacteria to catalyze the synthesis of D-glutamic acid and D-alanine, which are essential constituents of bacterial cell wall and are the building block for other D-amino acids. Despite the difference in the structure of the substrates, D-AATs and L-ATTs have strong similarity. 221 matched cddid_all.tbl CDD pfam01064 pfam01064 460048 Activin_recp Activin types I and II receptor domain. This Pfam entry consists of both TGF-beta receptor types. This is an alignment of the hydrophilic cysteine-rich ligand-binding domains, Both receptor types, (type I and II) posses a 9 amino acid cysteine box, with the the consensus CCX{4-5}CN. The type I receptors also possess 7 extracellular residues preceding the cysteine box. 78 matched cddid_all.tbl CDD pfam01065 pfam01065 395846 Adeno_hexon Hexon, adenovirus major coat protein, N-terminal domain. Hexon is the major coat protein from adenovirus type 2. Hexon forms a homo-trimer. The 240 copies of the hexon trimer are organized so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX. The penton complex, formed by the peripentonal hexons and base hexon (holding in place a fibre), lie at each of the 12 vertices. The N and C-terminal domains adopt the same PNGase F-like fold although they are significantly different in length. 586 matched cddid_all.tbl CDD pfam01066 pfam01066 460049 CDP-OH_P_transf CDP-alcohol phosphatidyltransferase. All of these members have the ability to catalyze the displacement of CMP from a CDP-alcohol by a second alcohol with formation of a phosphodiester bond and concomitant breaking of a phosphoride anhydride bond. 157 matched cddid_all.tbl CDD pfam01067 pfam01067 460050 Calpain_III Calpain large subunit, domain III. The function of the domain III and I are currently unknown. Domain II is a cysteine protease and domain IV is a calcium binding domain. Calpains are believed to participate in intracellular signaling pathways mediated by calcium ions. 136 matched cddid_all.tbl CDD pfam01068 pfam01068 426028 DNA_ligase_A_M ATP dependent DNA ligase domain. This domain belongs to a more diverse superfamily, including pfam01331 and pfam01653. 203 matched cddid_all.tbl CDD pfam01070 pfam01070 426029 FMN_dh FMN-dependent dehydrogenase. 350 matched cddid_all.tbl CDD pfam01071 pfam01071 395851 GARS_A Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain. Phosphoribosylglycinamide synthetase catalyzes the second step in the de novo biosynthesis of purine. The reaction catalyzed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the ATP-grasp domain of biotin carboxylase/carbamoyl phosphate synthetase (see pfam02786). 194 matched cddid_all.tbl CDD pfam01073 pfam01073 366449 3Beta_HSD 3-beta hydroxysteroid dehydrogenase/isomerase family. The enzyme 3 beta-hydroxysteroid dehydrogenase/5-ene-4-ene isomerase (3 beta-HSD) catalyzes the oxidation and isomerization of 5-ene-3 beta-hydroxypregnene and 5-ene-hydroxyandrostene steroid precursors into the corresponding 4-ene-ketosteroids necessary for the formation of all classes of steroid hormones. 279 matched cddid_all.tbl CDD pfam01074 pfam01074 426030 Glyco_hydro_38N Glycosyl hydrolases family 38 N-terminal domain. Glycosyl hydrolases are key enzymes of carbohydrate metabolism. 271 matched cddid_all.tbl CDD pfam01075 pfam01075 395853 Glyco_transf_9 Glycosyltransferase family 9 (heptosyltransferase). Members of this family belong to glycosyltransferase family 9. Lipopolysaccharide is a major component of the outer leaflet of the outer membrane in Gram-negative bacteria. It is composed of three domains; lipid A, Core oligosaccharide and the O-antigen. All of these enzymes transfer heptose to the lipopolysaccharide core. 247 matched cddid_all.tbl CDD pfam01076 pfam01076 395854 Mob_Pre Plasmid recombination enzyme. With some plasmids, recombination can occur in a site specific manner that is independent of RecA. In such cases, the recombination event requires another protein called Pre. Pre is a plasmid recombination enzyme. This protein is also known as Mob (conjugative mobilization). This family is also known as Mob-V. One of the family members, MobM, is encoded by a promiscuous plasmid actively involved in the spread of antibiotic resistance. Homologs of MobM are found in many plasmids and other mobile genetic elements of pathogenic bacteria, including S. aureus. MobM is a metal-dependent nuclease that uses histidine nitrogen for the nucleophilic attack on the scissile phosphate. Furthermore, in contrast to other DNA-processing enzymes, MobM is a histidine relaxase, a DNA-breaking and -joining enzyme, that operates through a phosphorus-nitrogen protein-DNA adduct for cell-to-cell DNA transfer. Mutational analysis indicate that the H(N/D)(Q/E)R N-terminal motif of MobM plays a crucial role in the cleavage and generation of stable DNA-protein adducts. 195 matched cddid_all.tbl CDD pfam01077 pfam01077 426031 NIR_SIR Nitrite and sulphite reductase 4Fe-4S domain. Sulphite and nitrite reductases are vital in the biosynthetic assimilation of sulphur and nitrogen, respectfully. They are also both important for the dissimilation of oxidized anions for energy transduction. 153 matched cddid_all.tbl CDD pfam01078 pfam01078 426032 Mg_chelatase Magnesium chelatase, subunit ChlI. Magnesium-chelatase is a three-component enzyme that catalyzes the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa. 207 matched cddid_all.tbl CDD pfam01079 pfam01079 460051 Hint Hint module. This is an alignment of the Hint module in the Hedgehog proteins. It does not include any Inteins which also possess the Hint module. 212 matched cddid_all.tbl CDD pfam01080 pfam01080 460052 Presenilin Presenilin. Mutations in presenilin-1 are a major cause of early onset Alzheimer's disease. It has been found that presenilin-1 binds to beta-catenin in-vivo. This family also contains SPE proteins from C.elegans. 394 matched cddid_all.tbl CDD pfam01081 pfam01081 395858 Aldolase KDPG and KHG aldolase. This family includes the following members: 4-hydroxy-2-oxoglutarate aldolase (KHG-aldolase) Phospho-2-dehydro-3-deoxygluconate aldolase (KDPG-aldolase) 196 matched cddid_all.tbl CDD pfam01082 pfam01082 460053 Cu2_monooxygen Copper type II ascorbate-dependent monooxygenase, N-terminal domain. The N and C-terminal domains of members of this family adopt the same PNGase F-like fold. 130 matched cddid_all.tbl CDD pfam01083 pfam01083 395860 Cutinase Cutinase. 173 matched cddid_all.tbl CDD pfam01084 pfam01084 460054 Ribosomal_S18 Ribosomal protein S18. 52 matched cddid_all.tbl CDD pfam01085 pfam01085 460055 HH_signal Hedgehog amino-terminal signalling domain. For the carboxyl Hint module, see pfam01079. Hedgehog is a family of secreted signal molecules required for embryonic cell differentiation. 161 matched cddid_all.tbl CDD pfam01086 pfam01086 460056 Clathrin_lg_ch Clathrin light chain. 223 matched cddid_all.tbl CDD pfam01087 pfam01087 426039 GalP_UDP_transf Galactose-1-phosphate uridyl transferase, N-terminal domain. SCOP reports fold duplication with C-terminal domain. Both involved in Zn and Fe binding. 182 matched cddid_all.tbl CDD pfam01088 pfam01088 460057 Peptidase_C12 Ubiquitin carboxyl-terminal hydrolase, family 1. 205 matched cddid_all.tbl CDD pfam01090 pfam01090 460058 Ribosomal_S19e Ribosomal protein S19e. 137 matched cddid_all.tbl CDD pfam01091 pfam01091 460059 PTN_MK_C PTN/MK heparin-binding protein family, C-terminal domain. 65 matched cddid_all.tbl CDD pfam01092 pfam01092 460060 Ribosomal_S6e Ribosomal protein S6e. 123 matched cddid_all.tbl CDD pfam01093 pfam01093 460061 Clusterin Clusterin. 418 matched cddid_all.tbl CDD pfam01094 pfam01094 460062 ANF_receptor Receptor family ligand binding region. This family includes extracellular ligand binding domains of a wide range of receptors. This family also includes the bacterial amino acid binding proteins of known structure. 347 matched cddid_all.tbl CDD pfam01095 pfam01095 395871 Pectinesterase Pectinesterase. 298 matched cddid_all.tbl CDD pfam01096 pfam01096 426046 TFIIS_C Transcription factor S-II (TFIIS). 39 matched cddid_all.tbl CDD pfam01097 pfam01097 395873 Defensin_2 Arthropod defensin. 34 matched cddid_all.tbl CDD pfam01098 pfam01098 426047 FTSW_RODA_SPOVE Cell cycle protein. This entry includes the following members; FtsW, RodA, SpoVE 356 matched cddid_all.tbl CDD pfam01099 pfam01099 460063 Uteroglobin Uteroglobin family. Uteroglobin is a homodimer of two identical 70 amino acid polypeptides linked by two disulphide bridges. The precise role of uteroglobin has still to be elucidated. 90 matched cddid_all.tbl CDD pfam01101 pfam01101 460064 HMG14_17 HMG14 and HMG17. 90 matched cddid_all.tbl CDD pfam01102 pfam01102 426050 Glycophorin_A Glycophorin A. 114 matched cddid_all.tbl CDD pfam01103 pfam01103 460065 Omp85 Omp85 superfamily domain. The Omp85 protein superfamily contains bacterial outer membrane proteins, which can function as protein translocases or as membrane protein assembly factors. The family includes the membrane bound beta barrel of proteins such as BamA and TamA from E. coli. 319 matched cddid_all.tbl CDD pfam01104 pfam01104 279449 Bunya_NS-S Bunyavirus non-structural protein NS-s. The NS-s protein is encoded by the S RNA. This segment also encodes for the N protein. These two proteins are encoded by overlapping reading frames. 91 matched cddid_all.tbl CDD pfam01105 pfam01105 426051 EMP24_GP25L emp24/gp25L/p24 family/GOLD. Members of this family are implicated in bringing cargo forward from the ER and binding to coat proteins by their cytoplasmic domains. This domain corresponds closely to the beta-strand rich GOLD domain described in. The GOLD domain is always found combined with lipid- or membrane-association domains. 181 matched cddid_all.tbl CDD pfam01106 pfam01106 460066 NifU NifU-like domain. This is an alignment of the carboxy-terminal domain. This is the only common region between the NifU protein from nitrogen-fixing bacteria and rhodobacterial species. The biochemical function of NifU is unknown. 67 matched cddid_all.tbl CDD pfam01107 pfam01107 279452 MP Viral movement protein (MP). This family includes a variety of movement proteins (MP)s. The MP is necessary for the initial cell-to-cell movement during the early stages of a viral infection. This movement is active, and it is known that the MP interacts with the plasmodesmata and possesses the ability to bind to RNA to achieve its role. This family also includes consists of virus movement proteins from the caulimovirus family. It has been suggested in cauliflower mosaic virus that these proteins mediated viral movement by modifying plasmodesmata and forming tubules in the channel that can accommodate the virus particles and references therein. The family contains a conserved DXR motif that is probably functionally important. 191 matched cddid_all.tbl CDD pfam01108 pfam01108 460067 Tissue_fac Tissue factor. This family is found in metazoa, and is very similar to the fibronectin type III domain. The family is found in cytokine receptors, interleukin and interferon receptors and coagulation factor III proteins. It occurs multiple times, as does fn3, family pfam00041. 107 matched cddid_all.tbl CDD pfam01109 pfam01109 144630 GM_CSF Granulocyte-macrophage colony-stimulating factor. 122 matched cddid_all.tbl CDD pfam01110 pfam01110 395881 CNTF Ciliary neurotrophic factor. 187 matched cddid_all.tbl CDD pfam01111 pfam01111 460068 CKS Cyclin-dependent kinase regulatory subunit. 68 matched cddid_all.tbl CDD pfam01112 pfam01112 426055 Asparaginase_2 Asparaginase. 308 matched cddid_all.tbl CDD pfam01113 pfam01113 460069 DapB_N Dihydrodipicolinate reductase, N-terminus. Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The N-terminal domain of DapB binds the dinucleotide NADPH. 121 matched cddid_all.tbl CDD pfam01114 pfam01114 279458 Colipase Colipase, N-terminal domain. SCOP reports duplication of common fold with Colipase C-terminal domain. 40 matched cddid_all.tbl CDD pfam01115 pfam01115 460070 F_actin_cap_B F-actin capping protein, beta subunit. 230 matched cddid_all.tbl CDD pfam01116 pfam01116 460071 F_bP_aldolase Fructose-bisphosphate aldolase class-II. 276 matched cddid_all.tbl CDD pfam01117 pfam01117 366474 Aerolysin Aerolysin toxin. This family represents the pore forming lobe of aerolysin. 359 matched cddid_all.tbl CDD pfam01118 pfam01118 426059 Semialdhyde_dh Semialdehyde dehydrogenase, NAD binding domain. This Pfam entry contains the following members: N-acetyl-glutamine semialdehyde dehydrogenase (AgrC) Aspartate-semialdehyde dehydrogenase 121 matched cddid_all.tbl CDD pfam01119 pfam01119 426060 DNA_mis_repair DNA mismatch repair protein, C-terminal domain. This family represents the C-terminal domain of the mutL/hexB/PMS1 family. This domain has a ribosomal S5 domain 2-like fold. 117 matched cddid_all.tbl CDD pfam01120 pfam01120 460072 Alpha_L_fucos Alpha-L-fucosidase. 333 matched cddid_all.tbl CDD pfam01121 pfam01121 426062 CoaE Dephospho-CoA kinase. This family catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form Coenzyme A EC:2.7.1.24. This enzyme uses ATP in its reaction. 180 matched cddid_all.tbl CDD pfam01122 pfam01122 460073 Cobalamin_bind Eukaryotic cobalamin-binding protein. 302 matched cddid_all.tbl CDD pfam01123 pfam01123 426064 Stap_Strp_toxin Staphylococcal/Streptococcal toxin, OB-fold domain. This entry represents an OB-fold domain found in enterotoxins. 86 matched cddid_all.tbl CDD pfam01124 pfam01124 460074 MAPEG MAPEG family. This family is has been called MAPEG (Membrane Associated Proteins in Eicosanoid and Glutathione metabolism). It includes proteins such as Prostaglandin E synthase. This enzyme catalyzes the synthesis of PGE2 from PGH2 (produced by cyclooxygenase from arachidonic acid). Because of structural similarities in the active sites of FLAP, LTC4 synthase and PGE synthase, substrates for each enzyme can compete with one another and modulate synthetic activity. 127 matched cddid_all.tbl CDD pfam01125 pfam01125 426066 G10 G10 protein. 146 matched cddid_all.tbl CDD pfam01126 pfam01126 395895 Heme_oxygenase Heme oxygenase. 204 matched cddid_all.tbl CDD pfam01127 pfam01127 426067 Sdh_cyt Succinate dehydrogenase/Fumarate reductase transmembrane subunit. This family includes a transmembrane protein from both the Succinate dehydrogenase and Fumarate reductase complexes. 122 matched cddid_all.tbl CDD pfam01128 pfam01128 460075 IspD 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase. Members of this family are enzymes which catalyze the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from cytidine triphosphate and 2-C-methyl-D-erythritol 4-phosphate (MEP). 219 matched cddid_all.tbl CDD pfam01129 pfam01129 279473 ART NAD:arginine ADP-ribosyltransferase. 222 matched cddid_all.tbl CDD pfam01130 pfam01130 460076 CD36 CD36 family. The CD36 family is thought to be a novel class of scavenger receptors. There is also evidence suggesting a possible role in signal transduction. CD36 is involved in cell adhesion. 454 matched cddid_all.tbl CDD pfam01131 pfam01131 426069 Topoisom_bac DNA topoisomerase. This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA. 410 matched cddid_all.tbl CDD pfam01132 pfam01132 460077 EFP Elongation factor P (EF-P) OB domain. 54 matched cddid_all.tbl CDD pfam01133 pfam01133 460078 ER Enhancer of rudimentary. Enhancer of rudimentary is a protein of unknown function that is highly conserved in plants and animals. This protein is found to be an enhancer of the rudimentary gene. 98 matched cddid_all.tbl CDD pfam01134 pfam01134 250388 GIDA Glucose inhibited division protein A. 391 matched cddid_all.tbl CDD pfam01135 pfam01135 395902 PCMT Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT). 205 matched cddid_all.tbl CDD pfam01136 pfam01136 426072 Peptidase_U32 Peptidase family U32. 233 matched cddid_all.tbl CDD pfam01137 pfam01137 460079 RTC RNA 3'-terminal phosphate cyclase. RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organizms. They catalyze the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation of the covalent AMP-cyclase intermediate. The structure of RTC demonstrates that RTCs are comprised two domain. The larger domain contains an insert domain of approximately 100 amino acids. 324 matched cddid_all.tbl CDD pfam01138 pfam01138 426074 RNase_PH 3' exoribonuclease family, domain 1. This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components contain a copy of this domain. A hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria. 129 matched cddid_all.tbl CDD pfam01139 pfam01139 460080 RtcB tRNA-splicing ligase RtcB. This family of RNA ligases (EC:6.5.1.3) join 2',3'-cyclic phosphate and 5'-OH ends. They catalyze the splicing of tRNA and may also participate in tRNA repair and recovery from stress-induced RNA damage. 416 matched cddid_all.tbl CDD pfam01140 pfam01140 426076 Gag_MA Matrix protein (MA), p15. The matrix protein, p15, is encoded by the gag gene. MA is involved in pathogenicity. 126 matched cddid_all.tbl CDD pfam01141 pfam01141 279483 Gag_p12 Gag polyprotein, inner coat protein p12. The retroviral p12 is a virion structural protein. p12 is proline rich. The function carried out by p12 in assembly and replication is unknown. p12 is associated with pathogenicity of the virus. 85 matched cddid_all.tbl CDD pfam01142 pfam01142 426077 TruD tRNA pseudouridine synthase D (TruD). TruD is responsible for synthesis of pseudouridine from uracil-13 in transfer RNAs. The structure of TruD reveals an overall V-shaped molecule which contains an RNA-binding cleft. 414 matched cddid_all.tbl CDD pfam01144 pfam01144 395909 CoA_trans Coenzyme A transferase. 216 matched cddid_all.tbl CDD pfam01145 pfam01145 426078 Band_7 SPFH domain / Band 7 family. This family has been called SPFH, Band 7 or PHB domain. Recent phylogenetic analysis has shown this domain to be a slipin or Stomatin-like integral membrane domain conserved from protozoa to mammals. 177 matched cddid_all.tbl CDD pfam01146 pfam01146 460081 Caveolin Caveolin. All three known Caveolin forms have the FEDVIAEP caveolin 'signature motif' within their hydrophilic N-terminal domain. Caveolin 2 (Cav-2) is co-localized and co-expressed with Cav-1/VIP21, forms heterodimers with it and needs Cav-1 for proper membrane localization. Cav-3 has greater protein sequence similarity to Cav-1 than to Cav-2. Cellular processes caveolins are involved in include vesicular transport, cholesterol homeostasis, signal transduction, and tumour suppression. 133 matched cddid_all.tbl CDD pfam01147 pfam01147 395912 Crust_neurohorm Crustacean CHH/MIH/GIH neurohormone family. 67 matched cddid_all.tbl CDD pfam01148 pfam01148 426080 CTP_transf_1 Cytidylyltransferase family. The members of this family are integral membrane protein cytidylyltransferases. The family includes phosphatidate cytidylyltransferase EC:2.7.7.41 as well as Sec59 from yeast. Sec59 is a dolichol kinase EC:2.7.1.108. 264 matched cddid_all.tbl CDD pfam01149 pfam01149 460082 Fapy_DNA_glyco Formamidopyrimidine-DNA glycosylase N-terminal domain. Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the N-terminal domain contains eight beta-strands, forming a beta-sandwich with two alpha-helices parallel to its edges. 116 matched cddid_all.tbl CDD pfam01150 pfam01150 426082 GDA1_CD39 GDA1/CD39 (nucleoside phosphatase) family. 416 matched cddid_all.tbl CDD pfam01151 pfam01151 460083 ELO GNS1/SUR4 family. Members of this family are involved in long chain fatty acid elongation systems that produce the 26-carbon precursors for ceramide and sphingolipid synthesis. Predicted to be integral membrane proteins, in eukaryotes they are probably located on the endoplasmic reticulum. Yeast ELO3 affects plasma membrane H+-ATPase activity, and may act on a glucose-signaling pathway that controls the expression of several genes that are transcriptionally regulated by glucose such as PMA1. 242 matched cddid_all.tbl CDD pfam01152 pfam01152 395917 Bac_globin Bacterial-like globin. This family of heme binding proteins are found mainly in bacteria. However they can also be found in some protozoa and plants as well. 121 matched cddid_all.tbl CDD pfam01153 pfam01153 460084 Glypican Glypican. 554 matched cddid_all.tbl CDD pfam01154 pfam01154 307348 HMG_CoA_synt_N Hydroxymethylglutaryl-coenzyme A synthase N terminal. 173 matched cddid_all.tbl CDD pfam01155 pfam01155 460085 HypA Hydrogenase/urease nickel incorporation, metallochaperone, hypA. HypA is a metallochaperone that binds nickel to bring it safely to its target. The targets for Hypa are the nickel-containing enzymes [Ni,Fe]-hydrogenase and urease. The nickel coordinates with four nitrogens within the protein. The four conserved cysteines towards the C-terminus bind one zinc moiety probably to stabilize the protein fold. 111 matched cddid_all.tbl CDD pfam01156 pfam01156 460086 IU_nuc_hydro Inosine-uridine preferring nucleoside hydrolase. 253 matched cddid_all.tbl CDD pfam01157 pfam01157 460087 Ribosomal_L21e Ribosomal protein L21e. 100 matched cddid_all.tbl CDD pfam01158 pfam01158 460088 Ribosomal_L36e Ribosomal protein L36e. 96 matched cddid_all.tbl CDD pfam01159 pfam01159 460089 Ribosomal_L6e Ribosomal protein L6e. 109 matched cddid_all.tbl CDD pfam01160 pfam01160 426090 Opiods_neuropep Vertebrate endogenous opioids neuropeptide. 47 matched cddid_all.tbl CDD pfam01161 pfam01161 460090 PBP Phosphatidylethanolamine-binding protein. 136 matched cddid_all.tbl CDD pfam01163 pfam01163 460091 RIO1 RIO1 family. This is a family of atypical serine kinases which are found in archaea, bacteria and eukaryotes. Activity of Rio1 is vital in Saccharomyces cerevisiae for the processing of ribosomal RNA, as well as for proper cell cycle progression and chromosome maintenance. The structure of RIO1 has been determined. 184 matched cddid_all.tbl CDD pfam01165 pfam01165 460092 Ribosomal_S21 Ribosomal protein S21. 51 matched cddid_all.tbl CDD pfam01166 pfam01166 460093 TSC22 TSC-22/dip/bun family. 57 matched cddid_all.tbl CDD pfam01167 pfam01167 460094 Tub Tub family. 251 matched cddid_all.tbl CDD pfam01168 pfam01168 460095 Ala_racemase_N Alanine racemase, N-terminal domain. 220 matched cddid_all.tbl CDD pfam01169 pfam01169 460096 UPF0016 Uncharacterized protein family UPF0016. This family contains integral membrane proteins of unknown function. Most members of the family contain two copies of a region that contains an EXGD motif. Each of these regions contains three predicted transmembrane regions. It has been suggested that these proteins are calcium transporters. 75 matched cddid_all.tbl CDD pfam01170 pfam01170 395932 UPF0020 Putative RNA methylase family UPF0020. This domain is probably a methylase. It is associated with the THUMP domain that also occurs with RNA modification domains. 184 matched cddid_all.tbl CDD pfam01171 pfam01171 426097 ATP_bind_3 PP-loop family. This family of proteins belongs to the PP-loop superfamily. 178 matched cddid_all.tbl CDD pfam01172 pfam01172 460097 SBDS Shwachman-Bodian-Diamond syndrome (SBDS) protein. This family is highly conserved in species ranging from archaea to vertebrates and plants. The family contains several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. It is characterized by bone marrow failure and leukemia predisposition. Members of this family play a role in RNA metabolism. In yeast these proteins have been shown to be critical for the release and recycling of the nucleolar shuttling factor Tif6 from pre-60S ribosomes, a key step in 60S maturation and translational activation of ribosomes. This data links defective late 60S subunit maturation to an inherited bone marrow failure syndrome associated with leukemia predisposition. 82 matched cddid_all.tbl CDD pfam01174 pfam01174 334414 SNO SNO glutamine amidotransferase family. This family and its amidotransferase domain was first described in. It is predicted that members of this family are involved in the pyridoxine biosynthetic pathway, based on the proximity and co-regulation of the corresponding genes and physical interaction between the members of pfam01174 and pfam01680. 188 matched cddid_all.tbl CDD pfam01175 pfam01175 460098 Urocanase Urocanase Rossmann-like domain. 209 matched cddid_all.tbl CDD pfam01176 pfam01176 460099 eIF-1a Translation initiation factor 1A / IF-1. This family includes both the eukaryotic translation factor eIF-1A and the bacterial translation initiation factor IF-1. 62 matched cddid_all.tbl CDD pfam01177 pfam01177 426101 Asp_Glu_race Asp/Glu/Hydantoin racemase. This family contains aspartate racemase, maleate isomerases EC:5.2.1.1, glutamate racemase, hydantoin racemase and arylmalonate decarboxylase EC:4.1.1.76. 210 matched cddid_all.tbl CDD pfam01179 pfam01179 460100 Cu_amine_oxid Copper amine oxidase, enzyme domain. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). This family corresponds to the catalytic domain of the enzyme. 403 matched cddid_all.tbl CDD pfam01180 pfam01180 426103 DHO_dh Dihydroorotate dehydrogenase. 291 matched cddid_all.tbl CDD pfam01182 pfam01182 460101 Glucosamine_iso Glucosamine-6-phosphate isomerases/6-phosphogluconolactonase. 222 matched cddid_all.tbl CDD pfam01183 pfam01183 426105 Glyco_hydro_25 Glycosyl hydrolases family 25. 180 matched cddid_all.tbl CDD pfam01184 pfam01184 426106 Gpr1_Fun34_YaaH GPR1/FUN34/yaaH family. The Ady2 protein in is required for acetate in Saccharomyces cerevisiae, and is probably an acetate transporter. A homolog in Yarrowia lipolytica (GPR1) has a role in acetic acid sensitivity. 207 matched cddid_all.tbl CDD pfam01185 pfam01185 426107 Hydrophobin Fungal hydrophobin. 79 matched cddid_all.tbl CDD pfam01186 pfam01186 460102 Lysyl_oxidase Lysyl oxidase. 204 matched cddid_all.tbl CDD pfam01187 pfam01187 395945 MIF Macrophage migration inhibitory factor (MIF). 114 matched cddid_all.tbl CDD pfam01189 pfam01189 426109 Methyltr_RsmB-F 16S rRNA methyltransferase RsmB/F. This is the catalytic core of this SAM-dependent 16S ribosomal methyltransferase RsmB/F enzyme. There is a catalytic cysteine residue at 180 in UniProtKB:Q5SII2, with another highly conserved cysteine at residue 230. It methylates the C(5) position of cytosine 2870 (m5C2870) in 25S rRNA. 199 matched cddid_all.tbl CDD pfam01190 pfam01190 460103 Pollen_Ole_e_1 Pollen protein Ole e 1 like. 94 matched cddid_all.tbl CDD pfam01191 pfam01191 426111 RNA_pol_Rpb5_C RNA polymerase Rpb5, C-terminal domain. The assembly domain of Rpb5. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain. 73 matched cddid_all.tbl CDD pfam01192 pfam01192 426112 RNA_pol_Rpb6 RNA polymerase Rpb6. Rpb6 is an essential subunit in the eukaryotic polymerases Pol I, II and III. This family also contains the bacterial equivalent to Rpb6, the omega subunit. Rpb6 and omega are structurally conserved and both function in polymerase assembly. 52 matched cddid_all.tbl CDD pfam01193 pfam01193 460104 RNA_pol_L RNA polymerase Rpb3/Rpb11 dimerization domain. The two eukaryotic subunits Rpb3 and Rpb11 dimerize to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerization domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some of the alpha subunits also contain iron-sulphur binding domains (pfam00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. 191 matched cddid_all.tbl CDD pfam01194 pfam01194 426114 RNA_pol_N RNA polymerases N / 8 kDa subunit. 58 matched cddid_all.tbl CDD pfam01195 pfam01195 460105 Pept_tRNA_hydro Peptidyl-tRNA hydrolase. 182 matched cddid_all.tbl CDD pfam01196 pfam01196 460106 Ribosomal_L17 Ribosomal protein L17. 97 matched cddid_all.tbl CDD pfam01197 pfam01197 460107 Ribosomal_L31 Ribosomal protein L31. 65 matched cddid_all.tbl CDD pfam01198 pfam01198 460108 Ribosomal_L31e Ribosomal protein L31e. 82 matched cddid_all.tbl CDD pfam01199 pfam01199 426119 Ribosomal_L34e Ribosomal protein L34e. 94 matched cddid_all.tbl CDD pfam01200 pfam01200 460109 Ribosomal_S28e Ribosomal protein S28e. 64 matched cddid_all.tbl CDD pfam01201 pfam01201 460110 Ribosomal_S8e Ribosomal protein S8e. 133 matched cddid_all.tbl CDD pfam01202 pfam01202 426122 SKI Shikimate kinase. 159 matched cddid_all.tbl CDD pfam01203 pfam01203 426123 T2SSN Type II secretion system (T2SS), protein N. Members of the T2SN family are involved in the Type II protein secretion system. The precise function of these proteins is unknown. 205 matched cddid_all.tbl CDD pfam01204 pfam01204 395961 Trehalase Trehalase. Trehalase (EC:3.2.1.28) is known to recycle trehalose to glucose. Trehalose is a physiological hallmark of heat-shock response in yeast and protects of proteins and membranes against a variety of stresses. This family is found in conjunction with pfam07492 in fungi. 509 matched cddid_all.tbl CDD pfam01205 pfam01205 460111 UPF0029 Uncharacterized protein family UPF0029. 105 matched cddid_all.tbl CDD pfam01206 pfam01206 426125 TusA Sulfurtransferase TusA. This family includes the TusA sulfurtransferases. 64 matched cddid_all.tbl CDD pfam01207 pfam01207 426126 Dus Dihydrouridine synthase (Dus). Members of this family catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA. Dihydrouridine modification of tRNA is widely observed in prokaryotes and eukaryotes, and also in some archae. Most dihydrouridines are found in the D loop of t-RNAs. The role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA. It is likely that different family members have different substrate specificities, which may overlap. Dus 1 from Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus 2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active as a single subunit, requiring NADPH or NADH, and is stimulated by the presence of FAD. Some family members may be targeted to the mitochondria and even have a role in mitochondria. 309 matched cddid_all.tbl CDD pfam01208 pfam01208 460112 URO-D Uroporphyrinogen decarboxylase (URO-D). 341 matched cddid_all.tbl CDD pfam01209 pfam01209 395966 Ubie_methyltran ubiE/COQ5 methyltransferase family. 228 matched cddid_all.tbl CDD pfam01210 pfam01210 395967 NAD_Gly3P_dh_N NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus. NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the N-terminal NAD-binding domain. 158 matched cddid_all.tbl CDD pfam01212 pfam01212 426128 Beta_elim_lyase Beta-eliminating lyase. 288 matched cddid_all.tbl CDD pfam01213 pfam01213 460113 CAP_N Adenylate cyclase associated (CAP) N terminal. 72 matched cddid_all.tbl CDD pfam01214 pfam01214 460114 CK_II_beta Casein kinase II regulatory subunit. 182 matched cddid_all.tbl CDD pfam01215 pfam01215 426131 COX5B Cytochrome c oxidase subunit Vb. 128 matched cddid_all.tbl CDD pfam01216 pfam01216 395972 Calsequestrin Calsequestrin. 350 matched cddid_all.tbl CDD pfam01217 pfam01217 460115 Clat_adaptor_s Clathrin adaptor complex small chain. 142 matched cddid_all.tbl CDD pfam01218 pfam01218 460116 Coprogen_oxidas Coproporphyrinogen III oxidase. 293 matched cddid_all.tbl CDD pfam01219 pfam01219 460117 DAGK_prokar Prokaryotic diacylglycerol kinase. 102 matched cddid_all.tbl CDD pfam01220 pfam01220 460118 DHquinase_II Dehydroquinase class II. 138 matched cddid_all.tbl CDD pfam01221 pfam01221 460119 Dynein_light Dynein light chain type 1. 83 matched cddid_all.tbl CDD pfam01222 pfam01222 250456 ERG4_ERG24 Ergosterol biosynthesis ERG4/ERG24 family. 429 matched cddid_all.tbl CDD pfam01223 pfam01223 460120 Endonuclease_NS DNA/RNA non-specific endonuclease. 220 matched cddid_all.tbl CDD pfam01225 pfam01225 460121 Mur_ligase Mur ligase family, catalytic domain. This family contains a number of related ligase enzymes which have EC numbers 6.3.2.*. This family includes: MurC, MurD, MurE, MurF, Mpl and FolC. MurC, MurD, Mure and MurF catalyze consecutive steps in the synthesis of peptidoglycan. Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide. The pentapeptide is is made of L-alanine, D-glutamic acid, Meso-diaminopimelic acid and D-alanyl alanine. The peptide moiety is synthesized by successively adding these amino acids to UDP-N-acetylmuramic acid. MurC transfers the L-alanine, MurD transfers the D-glutamate, MurE transfers the diaminopimelic acid, and MurF transfers the D-alanyl alanine. This family also includes Folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate. 84 matched cddid_all.tbl CDD pfam01226 pfam01226 460122 Form_Nir_trans Formate/nitrite transporter. Proteins in this entry belong to the Formate-Nitrite Transporter (FNT) family and includes the nitrite transport protein NirC and formate channel FocA. They have a pentameric architecture with structural similarity to aquaporins and glyceroporins. Proteins in this family transport the structurally related compounds, formate and nitrite. 244 matched cddid_all.tbl CDD pfam01227 pfam01227 426139 GTP_cyclohydroI GTP cyclohydrolase I. This family includes GTP cyclohydrolase enzymes and a family of related bacterial proteins. 176 matched cddid_all.tbl CDD pfam01228 pfam01228 426140 Gly_radical Glycine radical. 106 matched cddid_all.tbl CDD pfam01229 pfam01229 426141 Glyco_hydro_39 Glycosyl hydrolases family 39. 472 matched cddid_all.tbl CDD pfam01230 pfam01230 395984 HIT HIT domain. 98 matched cddid_all.tbl CDD pfam01231 pfam01231 460123 IDO Indoleamine 2,3-dioxygenase. 406 matched cddid_all.tbl CDD pfam01232 pfam01232 395986 Mannitol_dh Mannitol dehydrogenase Rossmann domain. 151 matched cddid_all.tbl CDD pfam01233 pfam01233 460124 NMT Myristoyl-CoA:protein N-myristoyltransferase, N-terminal domain. The N and C-terminal domains of NMT are structurally similar, each adopting an acyl-CoA N-acyltransferase-like fold. 158 matched cddid_all.tbl CDD pfam01234 pfam01234 395988 NNMT_PNMT_TEMT NNMT/PNMT/TEMT family. 261 matched cddid_all.tbl CDD pfam01235 pfam01235 460125 Na_Ala_symp Sodium:alanine symporter family. 385 matched cddid_all.tbl CDD pfam01237 pfam01237 460126 Oxysterol_BP Oxysterol-binding protein. 366 matched cddid_all.tbl CDD pfam01238 pfam01238 460127 PMI_typeI_C Phosphomannose isomerase type I C-terminal. This is the C-terminal domain of Phosphomannose isomerase type I enzymes (EC 5.3.1.8), which contains antiparallel beta-strands in an extended jelly roll topology with short loops connecting the strands. 48 matched cddid_all.tbl CDD pfam01239 pfam01239 460128 PPTA Protein prenyltransferase alpha subunit repeat. Both farnesyltransferase (FT) and geranylgeranyltransferase 1 (GGT1) recognize a CaaX motif on their substrates where 'a' stands for preferably aliphatic residues, whereas GGT2 recognizes a completely different motif. Important substrates for FT include, amongst others, many members of the Ras superfamily. GGT1 substrates include some of the other small GTPases and GGT2 substrates include the Rab family. 32 matched cddid_all.tbl CDD pfam01241 pfam01241 426147 PSI_PSAK Photosystem I psaG / psaK. 69 matched cddid_all.tbl CDD pfam01242 pfam01242 460129 PTPS 6-pyruvoyl tetrahydropterin synthase. 6-Pyruvoyl tetrahydrobiopterin synthase catalyzes the conversion of dihydroneopterin triphosphate to 6-pyruvoyl tetrahydropterin, the second of three enzymatic steps in the synthesis of tetrahydrobiopterin from GTP. The functional enzyme is a hexamer of identical subunits. 121 matched cddid_all.tbl CDD pfam01243 pfam01243 426149 Putative_PNPOx Pyridoxamine 5'-phosphate oxidase. Family of domains with putative PNPOx function. Family members were predicted to encode pyridoxamine 5'-phosphate oxidase, based on sequence similarity. However, there is no experimental data to validate the predicted activity and purified proteins, such as Swiss:Q06199 and its paralogs, do not possess this activity, nor do they bind to flavin mononucleotide (FMN). To date, the only time functional oxidase activity has been experimentally demonstrated is when the sequences contain both pfam01243 and pfam10590. Moreover, some of the family members that contain both domains have been shown to be involved in phenazine biosynthesis. While some molecular function has been experimentally validated for the proteins containing both domains, the role performed by each domain on its own is unknown. 88 matched cddid_all.tbl CDD pfam01244 pfam01244 395996 Peptidase_M19 Membrane dipeptidase (Peptidase family M19). 317 matched cddid_all.tbl CDD pfam01245 pfam01245 460130 Ribosomal_L19 Ribosomal protein L19. 108 matched cddid_all.tbl CDD pfam01246 pfam01246 460131 Ribosomal_L24e Ribosomal protein L24e. 63 matched cddid_all.tbl CDD pfam01247 pfam01247 460132 Ribosomal_L35Ae Ribosomal protein L35Ae. 94 matched cddid_all.tbl CDD pfam01248 pfam01248 426153 Ribosomal_L7Ae Ribosomal protein L7Ae/L30e/S12e/Gadd45 family. This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118. 95 matched cddid_all.tbl CDD pfam01249 pfam01249 460133 Ribosomal_S21e Ribosomal protein S21e. 79 matched cddid_all.tbl CDD pfam01250 pfam01250 460134 Ribosomal_S6 Ribosomal protein S6. 88 matched cddid_all.tbl CDD pfam01251 pfam01251 460135 Ribosomal_S7e Ribosomal protein S7e. 182 matched cddid_all.tbl CDD pfam01252 pfam01252 460136 Peptidase_A8 Signal peptidase (SPase) II. 140 matched cddid_all.tbl CDD pfam01253 pfam01253 460137 SUI1 Translation initiation factor SUI1. 75 matched cddid_all.tbl CDD pfam01254 pfam01254 426159 TP2 Nuclear transition protein 2. 133 matched cddid_all.tbl CDD pfam01255 pfam01255 460138 Prenyltransf Putative undecaprenyl diphosphate synthase. Previously known as uncharacterized protein family UPF0015, a single member of this family has been identified as an undecaprenyl diphosphate synthase. 220 matched cddid_all.tbl CDD pfam01256 pfam01256 396007 Carb_kinase Carbohydrate kinase. This family is related to pfam02110 and pfam00294 implying that it also is a carbohydrate kinase. (personal obs Yeats C). 242 matched cddid_all.tbl CDD pfam01257 pfam01257 460139 2Fe-2S_thioredx Thioredoxin-like [2Fe-2S] ferredoxin. 145 matched cddid_all.tbl CDD pfam01258 pfam01258 426162 zf-dskA_traR Prokaryotic dksA/traR C4-type zinc finger. 36 matched cddid_all.tbl CDD pfam01259 pfam01259 460140 SAICAR_synt SAICAR synthetase. Also known as Phosphoribosylaminoimidazole-succinocarboxamide synthase. 228 matched cddid_all.tbl CDD pfam01261 pfam01261 426164 AP_endonuc_2 Xylose isomerase-like TIM barrel. This TIM alpha/beta barrel structure is found in xylose isomerase and in endonuclease IV (EC:3.1.21.2). This domain is also found in the N termini of bacterial myo-inositol catabolism proteins. These are involved in the myo-inositol catabolism pathway, and is required for growth on myo-inositol in Rhizobium leguminosarum bv. viciae. 248 matched cddid_all.tbl CDD pfam01262 pfam01262 426165 AlaDh_PNT_C Alanine dehydrogenase/PNT, C-terminal domain. This family now also contains the lysine 2-oxoglutarate reductases. 213 matched cddid_all.tbl CDD pfam01263 pfam01263 396013 Aldose_epim Aldose 1-epimerase. 300 matched cddid_all.tbl CDD pfam01264 pfam01264 460141 Chorismate_synt Chorismate synthase. 344 matched cddid_all.tbl CDD pfam01265 pfam01265 426167 Cyto_heme_lyase Cytochrome c/c1 heme lyase. 296 matched cddid_all.tbl CDD pfam01266 pfam01266 426168 DAO FAD dependent oxidoreductase. This family includes various FAD dependent oxidoreductases: Glycerol-3-phosphate dehydrogenase EC:1.1.99.5, Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1. 339 matched cddid_all.tbl CDD pfam01267 pfam01267 460142 F-actin_cap_A F-actin capping protein alpha subunit. 263 matched cddid_all.tbl CDD pfam01268 pfam01268 460143 FTHFS Formate--tetrahydrofolate ligase. 555 matched cddid_all.tbl CDD pfam01269 pfam01269 396019 Fibrillarin Fibrillarin. 227 matched cddid_all.tbl CDD pfam01270 pfam01270 396020 Glyco_hydro_8 Glycosyl hydrolases family 8. 321 matched cddid_all.tbl CDD pfam01271 pfam01271 279595 Granin Granin (chromogranin or secretogranin). 584 matched cddid_all.tbl CDD pfam01272 pfam01272 426171 GreA_GreB Transcription elongation factor, GreA/GreB, C-term. This domain has an FKBP-like fold. 77 matched cddid_all.tbl CDD pfam01273 pfam01273 396022 LBP_BPI_CETP LBP / BPI / CETP family, N-terminal domain. The N and C terminal domains of the LBP/BPI/CETP family are structurally similar. 164 matched cddid_all.tbl CDD pfam01274 pfam01274 426172 Malate_synthase Malate synthase. 523 matched cddid_all.tbl CDD pfam01275 pfam01275 460144 Myelin_PLP Myelin proteolipid protein (PLP or lipophilin). 231 matched cddid_all.tbl CDD pfam01276 pfam01276 396025 OKR_DC_1 Orn/Lys/Arg decarboxylase, major domain. 417 matched cddid_all.tbl CDD pfam01277 pfam01277 396026 Oleosin Oleosin. 113 matched cddid_all.tbl CDD pfam01278 pfam01278 426174 Omptin Omptin family. The omptin family is a family of serine proteases. 282 matched cddid_all.tbl CDD pfam01279 pfam01279 460145 Parathyroid Parathyroid hormone family. 106 matched cddid_all.tbl CDD pfam01280 pfam01280 426176 Ribosomal_L19e Ribosomal protein L19e. 143 matched cddid_all.tbl CDD pfam01281 pfam01281 460146 Ribosomal_L9_N Ribosomal protein L9, N-terminal domain. 47 matched cddid_all.tbl CDD pfam01282 pfam01282 460147 Ribosomal_S24e Ribosomal protein S24e. 79 matched cddid_all.tbl CDD pfam01283 pfam01283 426179 Ribosomal_S26e Ribosomal protein S26e. 104 matched cddid_all.tbl CDD pfam01284 pfam01284 366555 MARVEL Membrane-associating domain. MARVEL domain-containing proteins are often found in lipid-associating proteins - such as Occludin and MAL family proteins. It may be part of the machinery of membrane apposition events, such as transport vesicle biogenesis. 136 matched cddid_all.tbl CDD pfam01285 pfam01285 426180 TEA TEA/ATTS domain. 68 matched cddid_all.tbl CDD pfam01286 pfam01286 460148 XPA_N XPA protein N-terminal. 32 matched cddid_all.tbl CDD pfam01287 pfam01287 396035 eIF-5a Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold. eIF5A, previously thought to be an initiation factor, has been shown to be required for peptide chain elongation in yeast. 69 matched cddid_all.tbl CDD pfam01288 pfam01288 460149 HPPK 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK). 128 matched cddid_all.tbl CDD pfam01289 pfam01289 426182 Thiol_cytolysin Thiol-activated cytolysin. 354 matched cddid_all.tbl CDD pfam01290 pfam01290 396038 Thymosin Thymosin beta-4 family. 39 matched cddid_all.tbl CDD pfam01291 pfam01291 396039 LIF_OSM LIF / OSM family. 162 matched cddid_all.tbl CDD pfam01292 pfam01292 426183 Ni_hydr_CYTB Prokaryotic cytochrome b561. This family includes cytochrome b561 and related proteins, in addition to the nickel-dependent hydrogenases b-type cytochrome subunit. Cytochrome b561 is a secretory vesicle-specific electron transport protein. It is an integral membrane protein, that binds two heme groups non-covalently. This is a prokaryotic family. Members of the 'eukaryotic cytochrome b561' family can be found in Pfam: PF03188. 180 matched cddid_all.tbl CDD pfam01293 pfam01293 426184 PEPCK_ATP Phosphoenolpyruvate carboxykinase. 465 matched cddid_all.tbl CDD pfam01294 pfam01294 460150 Ribosomal_L13e Ribosomal protein L13e. 180 matched cddid_all.tbl CDD pfam01295 pfam01295 426186 Adenylate_cycl Adenylate cyclase, class-I. 601 matched cddid_all.tbl CDD pfam01296 pfam01296 366564 Galanin Galanin. 29 matched cddid_all.tbl CDD pfam01297 pfam01297 460151 ZnuA Zinc-uptake complex component A periplasmic. ZnuA includes periplasmic solute binding proteins such as TroA that interacts with an ATP-binding cassette transport system in Treponema pallidum. ZnuA is part of the bacterial zinc-uptake complex ZnuABC, whose components are the following families, ZinT, pfam09223, pfam00950, pfam00005, all of which are regulated by the transcription-regulator family FUR, pfam01475. ZinT acts as a Zn2+-buffering protein that delivers Zn2+ to ZnuA (TroA), a high-affinity zinc-uptake protein. In Gram-negative bacteria the ZnuABC transporter system ensures an adequate import of zinc in Zn2+-poor environments, such as those encountered by pathogens within the infected host. 269 matched cddid_all.tbl CDD pfam01298 pfam01298 426188 TbpB_B_D "C-lobe and N-lobe beta barrels of Tf-binding protein B. Bacterial lipoproteins represent a large group of specialized membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis, and cell adherence. Pathogenic Gram-negative bacteria within the Neisseriaceae and Pasteurellaceae families rely on a specialized uptake system, characterized by an essential surface receptor complex that acquires iron from host transferrin (Tf) and transports the iron across the outer membrane. They have an iron uptake system composed of surface exposed lipoprotein, Tf-binding protein B (TbpB), and an integral outer-membrane protein, Tf-binding protein A (TbpA), that together function to extract iron from the host iron binding glycoprotein (Tf). TbpB is a bilobed (N and C lobe) lipid-anchored protein with each lobe consisting of an eight-stranded beta barrel flanked by a ""handle"" domain made up of four (N lobe) or eight (C lobe) beta strands. TbpB extends from the outer membrane surface by virtue of an N-terminal peptide region that is anchored to the outer membrane by fatty acyl chains on the N-terminal cysteine and is involved in the initial capture of iron-loaded Tf. This domain family is found in C and N lobe eight stranded beta barrel region of TbpB proteins. The eight-stranded barrel domains in N and C lobe draw comparisons to eight-stranded beta barrel outer-membrane protein W (OmpW). However, the barrel domains of TbpB have the hydrophobic residues line the inner surface of the beta barrels to create a stable hydrophobic core." 126 matched cddid_all.tbl CDD pfam01299 pfam01299 460152 Lamp Lysosome-associated membrane glycoprotein (Lamp). 148 matched cddid_all.tbl CDD pfam01300 pfam01300 460153 Sua5_yciO_yrdC Telomere recombination. This domain has been shown to bind preferentially to dsRNA. The domain is found in SUA5 as well as HypF and YrdC. It has also been shown to be required for telomere recombniation in yeast. 176 matched cddid_all.tbl CDD pfam01301 pfam01301 396048 Glyco_hydro_35 Glycosyl hydrolases family 35. 316 matched cddid_all.tbl CDD pfam01302 pfam01302 460154 CAP_GLY CAP-Gly domain. Cytoskeleton-associated proteins (CAPs) are involved in the organization of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove. 65 matched cddid_all.tbl CDD pfam01303 pfam01303 460155 Egg_lysin Egg lysin (Sperm-lysin). Egg lysin creates a hole in the envelope of the egg thereby allowing the sperm to pass through the envelope and fuse with the egg. 121 matched cddid_all.tbl CDD pfam01304 pfam01304 279626 Gas_vesicle_C Gas vesicles protein GVPc repeated domain. 33 matched cddid_all.tbl CDD pfam01306 pfam01306 396050 LacY_symp LacY proton/sugar symporter. This family is closely related to the sugar transporter family. 413 matched cddid_all.tbl CDD pfam01307 pfam01307 279627 Plant_vir_prot Plant viral movement protein. This family includes several known plant viral movement proteins from a number of different ssRNA plant virus families including potexviruses, hordeiviruses and carlaviruses. 100 matched cddid_all.tbl CDD pfam01308 pfam01308 279628 Chlam_OMP Chlamydia major outer membrane protein. The major outer membrane protein of Chlamydia contains four symmetrically spaced variable domains (VDs I to IV). This protein is believed to be an integral part to the pathogenesis, possibly adhesion. Along with the lipopolysaccharide, the major out membrane protein (MOMP) makes up the surface of the elementary body cell. The MOMP is the protein used to determine the different serotypes. 397 matched cddid_all.tbl CDD pfam01309 pfam01309 426192 EAV_GS Equine arteritis virus small envelope glycoprotein. Equine arteritis virus small envelope glycoprotein (Gs) is a class I transmembrane protein which adopts a number of different conformations. 196 matched cddid_all.tbl CDD pfam01310 pfam01310 366571 Adeno_PVIII Adenovirus hexon associated protein, protein VIII. See pfam01065. This family represents Hexon. 216 matched cddid_all.tbl CDD pfam01311 pfam01311 460156 Bac_export_1 Bacterial export proteins, family 1. This family includes the following members; FliR, MopE, SsaT, YopT, Hrp, HrcT and SpaR All of these members export proteins, that do not possess signal peptides, through the membrane. Although the proteins that these exporters move may be different, the exporters are thought to function in similar ways. 227 matched cddid_all.tbl CDD pfam01312 pfam01312 460157 Bac_export_2 FlhB HrpN YscU SpaS Family. This family includes the following members: FlhB, HrpN, YscU, SpaS, HrcU SsaU and YopU. All of these proteins export peptides using the type III secretion system. The peptides exported are quite diverse. 338 matched cddid_all.tbl CDD pfam01313 pfam01313 460158 Bac_export_3 Bacterial export proteins, family 3. This family includes the following members; FliQ, MopD, HrcS, Hrp, YopS and SpaQ All of these members export proteins, that do not possess signal peptides, through the membrane. Although the proteins that these exporters move may be different, the exporters are thought to function in similar ways. 72 matched cddid_all.tbl CDD pfam01314 pfam01314 426196 AFOR_C Aldehyde ferredoxin oxidoreductase, domains 2 & 3. Aldehyde ferredoxin oxidoreductase (AOR) catalyzes the reversible oxidation of aldehydes to their corresponding carboxylic acids with their accompanying reduction of the redox protein ferredoxin. This family is composed of two structural domains that bind the tungsten cofactor via DXXGL(C/D) motifs. In addition to maintaining specific binding interactions with the cofactor, another role for domains 2 and 3 may be to regulate substrate access to AOR. 388 matched cddid_all.tbl CDD pfam01315 pfam01315 426197 Ald_Xan_dh_C Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain. 107 matched cddid_all.tbl CDD pfam01316 pfam01316 396056 Arg_repressor Arginine repressor, DNA binding domain. 69 matched cddid_all.tbl CDD pfam01318 pfam01318 279637 Bromo_coat Bromovirus coat protein. 187 matched cddid_all.tbl CDD pfam01320 pfam01320 396057 Colicin_Pyocin Colicin immunity protein / pyocin immunity protein. 82 matched cddid_all.tbl CDD pfam01321 pfam01321 460159 Creatinase_N Creatinase/Prolidase N-terminal domain. This family includes the N-terminal non-catalytic domains from creatinase and prolidase. The exact function of this domain is uncertain. 128 matched cddid_all.tbl CDD pfam01322 pfam01322 460160 Cytochrom_C_2 Cytochrome C'. 118 matched cddid_all.tbl CDD pfam01323 pfam01323 426200 DSBA DSBA-like thioredoxin domain. This family contains a diverse set of proteins with a thioredoxin-like structure pfam00085. This family also includes 2-hydroxychromene-2-carboxylate (HCCA) isomerase enzymes catalyze one step in prokaryotic polyaromatic hydrocarbon (PAH) catabolic pathways. This family also contains members with functions other than HCCA isomerization, such as Kappa family GSTs, whose similarity to HCCA isomerases was not previously recognized. The sequence Swiss:O07298 has been annotated as a dioxygenase but is almost certainly an HCCA isomerase enzyme. Similarly, the sequence Swiss:Q9ZI67 has been annotated as a dehydrogenase, but is most probably also an HCCA isomerase enzyme. In addition, the Rhizobium leguminosarum Swiss:Q52782 protein has been annotated as a putative glycerol-3-phosphate transfer protein, but is also most likely to be an HCCA isomerase enzyme. 191 matched cddid_all.tbl CDD pfam01324 pfam01324 396061 Diphtheria_R Diphtheria toxin, R domain. C-terminal receptor binding (R) domain - binds to cell surface receptor, permitting the toxin to enter the cell by receptor mediated endocytosis. 167 matched cddid_all.tbl CDD pfam01325 pfam01325 396062 Fe_dep_repress Iron dependent repressor, N-terminal DNA binding domain. This family includes the Diphtheria toxin repressor. DNA binding is through a helix-turn-helix motif. 57 matched cddid_all.tbl CDD pfam01326 pfam01326 426201 PPDK_N Pyruvate phosphate dikinase, AMP/ATP-binding domain. This enzyme catalyzes the reversible conversion of ATP to AMP, pyrophosphate and phosphoenolpyruvate (PEP). The N-terminal domain has been shown to be the AMP/ATP-binding domain. 326 matched cddid_all.tbl CDD pfam01327 pfam01327 426202 Pep_deformylase Polypeptide deformylase. 153 matched cddid_all.tbl CDD pfam01328 pfam01328 426203 Peroxidase_2 Peroxidase, family 2. The peroxidases in this family do not have similarity to other peroxidases. 186 matched cddid_all.tbl CDD pfam01329 pfam01329 460161 Pterin_4a Pterin 4 alpha carbinolamine dehydratase. Pterin 4 alpha carbinolamine dehydratase is also known as DCoH (dimerization cofactor of hepatocyte nuclear factor 1-alpha). 88 matched cddid_all.tbl CDD pfam01330 pfam01330 460162 RuvA_N RuvA N terminal domain. The N terminal domain of RuvA has an OB-fold structure. This domain forms the RuvA tetramer contacts. 61 matched cddid_all.tbl CDD pfam01331 pfam01331 396068 mRNA_cap_enzyme mRNA capping enzyme, catalytic domain. This family represents the ATP binding catalytic domain of the mRNA capping enzyme. 194 matched cddid_all.tbl CDD pfam01333 pfam01333 426206 Apocytochr_F_C Apocytochrome F, C-terminal. This is a sub-family of cytochrome C. See pfam00034. 115 matched cddid_all.tbl CDD pfam01335 pfam01335 460163 DED Death effector domain. 82 matched cddid_all.tbl CDD pfam01336 pfam01336 460164 tRNA_anti-codon OB-fold nucleic acid binding domain. This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain. 75 matched cddid_all.tbl CDD pfam01337 pfam01337 460165 Barstar Barstar (barnase inhibitor). 82 matched cddid_all.tbl CDD pfam01338 pfam01338 396073 Bac_thur_toxin Bacillus thuringiensis toxin. 230 matched cddid_all.tbl CDD pfam01339 pfam01339 460166 CheB_methylest CheB methylesterase. 178 matched cddid_all.tbl CDD pfam01340 pfam01340 426211 MetJ Met Apo-repressor, MetJ. 97 matched cddid_all.tbl CDD pfam01341 pfam01341 426212 Glyco_hydro_6 Glycosyl hydrolases family 6. 293 matched cddid_all.tbl CDD pfam01342 pfam01342 460167 SAND SAND domain. The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerization. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain. 76 matched cddid_all.tbl CDD pfam01343 pfam01343 396077 Peptidase_S49 Peptidase family S49. 154 matched cddid_all.tbl CDD pfam01344 pfam01344 396078 Kelch_1 Kelch motif. The kelch motif was initially discovered in Kelch. In this protein there are six copies of the motif. It has been shown that Swiss:Q04652 is related to Galactose Oxidase for which a structure has been solved. The kelch motif forms a beta sheet. Several of these sheets associate to form a beta propeller structure as found in pfam00064, pfam00400 and pfam00415. 46 matched cddid_all.tbl CDD pfam01345 pfam01345 460168 DUF11 Domain of unknown function DUF11. A domain of unknown function found in multiple copies in several archaebacterial proteins. Conserved N-terminal lysine and C-terminal asparagine with central asp/glu suggests that many of these domain may contain an isopeptide bond. In Methanothermobacter sp. CaT2, a DUF11-containing repeat hypothetical protein encoded by MTCT_1020 plays a key role as a membrane-bound adhesion protein in the aggregation of CaT2. DUF11-containing repeat domains are not involved in aggregation, but may be important for stabilizing the surface cell wall structures of CaT2. 114 matched cddid_all.tbl CDD pfam01346 pfam01346 460169 FKBP_N Domain amino terminal to FKBP-type peptidyl-prolyl isomerase. This family is only found at the amino terminus of pfam00254. This entry represents the N-terminal domain found in FKBP-type peptidylprolyl isomerases (PPIase). The N-terminal domain forms the dimer interface by the mutual exchange of two beta-strands between monomers. 97 matched cddid_all.tbl CDD pfam01347 pfam01347 460170 Vitellogenin_N Lipoprotein amino terminal region. This family contains regions from: Vitellogenin, Microsomal triglyceride transfer protein and apolipoprotein B-100. These proteins are all involved in lipid transport. This family contains the LV1n chain from lipovitellin, that contains two structural domains. 582 matched cddid_all.tbl CDD pfam01348 pfam01348 279664 Intron_maturas2 Type II intron maturase. Group II introns use intron-encoded reverse transcriptase, maturase and DNA endonuclease activities for site-specific insertion into DNA. Although this type of intron is self splicing in vitro they require a maturase protein for splicing in vivo. It has been shown that a specific region of the aI2 intron is needed for the maturase function. This region was found to be conserved in group II introns and called domain X. 140 matched cddid_all.tbl CDD pfam01349 pfam01349 279665 Flavi_NS4B Flavivirus non-structural protein NS4B. Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4B protein is small and poorly conserved among the Flaviviruses. NS4B contains multiple hydrophobic potential membrane spanning regions. NS4B may form membrane components of the viral replication complex and could be involved in membrane localization of NS3 and pfam00972. 248 matched cddid_all.tbl CDD pfam01350 pfam01350 279666 Flavi_NS4A Flavivirus non-structural protein NS4A. Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4A protein is small and poorly conserved among the Flaviviruses. NS4A contains multiple hydrophobic potential membrane spanning regions. NS4A has only been found in cells infected by Kunjin virus. 144 matched cddid_all.tbl CDD pfam01351 pfam01351 396082 RNase_HII Ribonuclease HII. 199 matched cddid_all.tbl CDD pfam01352 pfam01352 460171 KRAB KRAB box. The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers. The KRAB domain is found to be involved in protein-protein interactions. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation. 42 matched cddid_all.tbl CDD pfam01353 pfam01353 426217 GFP Green fluorescent protein. 211 matched cddid_all.tbl CDD pfam01355 pfam01355 460172 HIPIP High potential iron-sulfur protein. 66 matched cddid_all.tbl CDD pfam01356 pfam01356 396086 A_amylase_inhib Alpha amylase inhibitor. 68 matched cddid_all.tbl CDD pfam01357 pfam01357 460173 Expansin_C Expansin C-terminal domain. This domain is found at the C-terminus of expansins, plant cell wall proteins involved in the non-enzymatic rearrangement of cell walls during cell growth. It contains the allergens lol PI, PII and PIII from Lolium perenne. 75 matched cddid_all.tbl CDD pfam01358 pfam01358 396088 PARP_regulatory Poly A polymerase regulatory subunit. 292 matched cddid_all.tbl CDD pfam01359 pfam01359 460174 Transposase_1 Transposase (partial DDE domain). This family includes the mariner transposase. 80 matched cddid_all.tbl CDD pfam01361 pfam01361 396090 Tautomerase Tautomerase enzyme. This family includes the enzyme 4-oxalocrotonate tautomerase that catalyzes the ketonization of 2-hydroxymuconate to 2-oxo-3-hexenedioate. 60 matched cddid_all.tbl CDD pfam01363 pfam01363 426221 FYVE FYVE zinc finger. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn++ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. We have included members which do not conserve these histidine residues but are clearly related. 68 matched cddid_all.tbl CDD pfam01364 pfam01364 396092 Peptidase_C25 Peptidase family C25. 343 matched cddid_all.tbl CDD pfam01365 pfam01365 460175 RYDR_ITPR RIH domain. The RIH (RyR and IP3R Homology) domain is an extracellular domain from two types of calcium channels. This region is found in the ryanodine receptor and the inositol-1,4,5- trisphosphate receptor. This domain may form a binding site for IP3. 199 matched cddid_all.tbl CDD pfam01366 pfam01366 426223 PRTP Herpesvirus processing and transport protein. The members of this family are associate with capsid intermediates during packaging of the virus. 654 matched cddid_all.tbl CDD pfam01367 pfam01367 460176 5_3_exonuc 5'-3' exonuclease, C-terminal SAM fold. 93 matched cddid_all.tbl CDD pfam01368 pfam01368 460177 DHH DHH family. It is predicted that this family of proteins all perform a phosphoesterase function. It included the single stranded DNA exonuclease RecJ. 145 matched cddid_all.tbl CDD pfam01369 pfam01369 460178 Sec7 Sec7 domain. The Sec7 domain is a guanine-nucleotide-exchange-factor (GEF) for the pfam00025 family. 183 matched cddid_all.tbl CDD pfam01370 pfam01370 396097 Epimerase NAD dependent epimerase/dehydratase family. This family of proteins utilize NAD as a cofactor. The proteins in this family use nucleotide-sugar substrates for a variety of chemical reactions. 238 matched cddid_all.tbl CDD pfam01371 pfam01371 426227 Trp_repressor Trp repressor protein. This protein binds to tryptophan and represses transcription of the Trp operon. 86 matched cddid_all.tbl CDD pfam01372 pfam01372 279683 Melittin Melittin. 26 matched cddid_all.tbl CDD pfam01373 pfam01373 366599 Glyco_hydro_14 Glycosyl hydrolase family 14. This family are beta amylases. 402 matched cddid_all.tbl CDD pfam01374 pfam01374 460179 Glyco_hydro_46 Glycosyl hydrolase family 46. This family are chitosanase enzymes. 210 matched cddid_all.tbl CDD pfam01375 pfam01375 366600 Enterotoxin_a Heat-labile enterotoxin alpha chain. 258 matched cddid_all.tbl CDD pfam01376 pfam01376 396100 Enterotoxin_b Heat-labile enterotoxin beta chain. 102 matched cddid_all.tbl CDD pfam01378 pfam01378 426228 IgG_binding_B B domain. This domain is found as a tandem repeat in Streptococcal cell surface proteins, such as the IgG binding protein G. 68 matched cddid_all.tbl CDD pfam01379 pfam01379 460180 Porphobil_deam Porphobilinogen deaminase, dipyromethane cofactor binding domain. 203 matched cddid_all.tbl CDD pfam01380 pfam01380 426230 SIS SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars. Presumably the SIS domains bind to the end-product of the pathway. 131 matched cddid_all.tbl CDD pfam01381 pfam01381 460181 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family. 55 matched cddid_all.tbl CDD pfam01382 pfam01382 460182 Avidin Avidin family. 113 matched cddid_all.tbl CDD pfam01383 pfam01383 460183 CpcD CpcD/allophycocyanin linker domain. 53 matched cddid_all.tbl CDD pfam01384 pfam01384 460184 PHO4 Phosphate transporter family. This family includes PHO-4 from Neurospora crassa which is a is a Na(+)-phosphate symporter. This family also contains the leukaemia virus receptor. 322 matched cddid_all.tbl CDD pfam01385 pfam01385 396108 OrfB_IS605 Probable transposase. This family includes IS891, IS1136 and IS1341. DUF1225, pfam06774, has now been merged into this family. 120 matched cddid_all.tbl CDD pfam01386 pfam01386 460185 Ribosomal_L25p Ribosomal L25p family. Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. This family includes Ctc from B. subtilis, which is induced by stress. 87 matched cddid_all.tbl CDD pfam01387 pfam01387 460186 Synuclein Synuclein. There are three types of synucleins in humans, these are called alpha, beta and gamma. Alpha synuclein has been found mutated in families with autosomal dominant Parkinson's disease. A peptide of alpha synuclein has also been found in amyloid plaques in Alzheimer's patients. 134 matched cddid_all.tbl CDD pfam01388 pfam01388 460187 ARID ARID/BRIGHT DNA binding domain. This domain is know as ARID for AT-Rich Interaction Domain, and also known as the BRIGHT domain. 87 matched cddid_all.tbl CDD pfam01389 pfam01389 396112 OmpA_membrane OmpA-like transmembrane domain. The structure of OmpA transmembrane domain shows that it consists of an eight stranded beta barrel. This family includes some other distantly related outer membrane proteins with low scores. 177 matched cddid_all.tbl CDD pfam01390 pfam01390 460188 SEA SEA domain. Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain. 100 matched cddid_all.tbl CDD pfam01391 pfam01391 460189 Collagen Collagen triple helix repeat (20 copies). Members of this family belong to the collagen superfamily. Collagens are generally extracellular structural proteins involved in formation of connective tissue structure. The alignment contains 20 copies of the G-X-Y repeat that forms a triple helix. The first position of the repeat is glycine, the second and third positions can be any residue but are frequently proline and hydroxy-proline. Collagens are post translationally modified by proline hydroxylase to form the hydroxy-proline residues. Defective hydroxylation is the cause of scurvy. Some members of the collagen superfamily are not involved in connective tissue structure but share the same triple helical structure. The family includes bacterial collagen-like triple-helix repeat proteins. 57 matched cddid_all.tbl CDD pfam01392 pfam01392 460190 Fz Fz domain. Also known as the CRD (cysteine rich domain), the C6 box in MuSK receptor. This domain of unknown function has been independently identified by several groups. The domain contains 10 conserved cysteines. 116 matched cddid_all.tbl CDD pfam01393 pfam01393 460191 Chromo_shadow Chromo shadow domain. This domain is distantly related to pfam00385. This domain is always found in association with a chromo domain. 52 matched cddid_all.tbl CDD pfam01394 pfam01394 460192 Clathrin_propel Clathrin propeller repeat. Clathrin is the scaffold protein of the basket-like coat that surrounds coated vesicles. The soluble assembly unit, a triskelion, contains three heavy chains and three light chains in an extended three-legged structure. Each leg contains one heavy and one light chain. The N-terminus of the heavy chain is known as the globular domain, and is composed of seven repeats which form a beta propeller. 37 matched cddid_all.tbl CDD pfam01395 pfam01395 460193 PBP_GOBP PBP/GOBP family. The olfactory receptors of terrestrial animals exist in an aqueous environment, yet detect odorants that are primarily hydrophobic. The aqueous solubility of hydrophobic odorants is thought to be greatly enhanced via odorant binding proteins which exist in the extracellular fluid surrounding the odorant receptors. This family is composed of pheromone binding proteins (PBP), which are male-specific and associate with pheromone-sensitive neurons and general-odorant binding proteins (GOBP). 109 matched cddid_all.tbl CDD pfam01396 pfam01396 307520 zf-C4_Topoisom Topoisomerase DNA binding C4 zinc finger. 39 matched cddid_all.tbl CDD pfam01397 pfam01397 460194 Terpene_synth Terpene synthase, N-terminal domain. It has been suggested that this gene family be designated tps (for terpene synthase). It has been split into six subgroups on the basis of phylogeny, called tpsa-tpsf. tpsa includes vetispiridiene synthase, 5-epi- aristolochene synthase, and (+)-delta-cadinene synthase. tpsb includes (-)-limonene synthase. tpsc includes kaurene synthase A. tpsd includes taxadiene synthase, pinene synthase and myrcene synthase. tpse includes kaurene synthase B. tpsf includes linalool synthase. 190 matched cddid_all.tbl CDD pfam01398 pfam01398 396120 JAB JAB1/Mov34/MPN/PAD-1 ubiquitin protease. Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain and PAD-1-like domain, JABP1 domain or JAMM domain. These are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based signalling and protein turnover pathways in eukaryotes. Versions of the domain in prokaryotic cognates of the ubiquitin-modification pathway are shown to have a similar role, and the archael protein from Haloferax volcanii is found to cleave ubiquitin-like small archaeal modifier proteins (SAMP1/2) from protein conjugates. 117 matched cddid_all.tbl CDD pfam01399 pfam01399 460195 PCI PCI domain. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15). 105 matched cddid_all.tbl CDD pfam01400 pfam01400 426242 Astacin Astacin (Peptidase family M12A). The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family contain two conserved disulphide bridges, these are joined 1-4 and 2-3. Members of this family have an amino terminal propeptide which is cleaved to give the active protease domain. All other linked domains are found to the carboxyl terminus of this domain. This family includes: Astacin, a digestive enzyme from Crayfish. Meprin, a multiple domain membrane component that is constructed from a homologous alpha and beta chain. Proteins involved in morphogenesis such as Swiss:P13497, and Tolloid from drosophila. 192 matched cddid_all.tbl CDD pfam01401 pfam01401 460196 Peptidase_M2 Angiotensin-converting enzyme. Members of this family are dipeptidyl carboxydipeptidases (cleave carboxyl dipeptides) and most notably convert angiotensin I to angiotensin II. Many members of this family contain a tandem duplication of the 600 amino acid peptidase domain, both of these are catalytically active. Most members are secreted membrane bound ectoenzymes. 581 matched cddid_all.tbl CDD pfam01402 pfam01402 426244 RHH_1 Ribbon-helix-helix protein, copG family. The structure of this protein repressor, which is the shortest reported to date and the first isolated from a plasmid, has a homodimeric ribbon-helix-helix arrangement. The helix-turn-helix-like structure is involved in dimerization and not DNA binding as might have been expected. 39 matched cddid_all.tbl CDD pfam01403 pfam01403 460197 Sema Sema domain. The Sema domain occurs in semaphorins, which are a large family of secreted and transmembrane proteins, some of which function as repellent signals during axon guidance. Sema domains also occur in the hepatocyte growth factor receptor and Swiss:P51805 180 matched cddid_all.tbl CDD pfam01404 pfam01404 460198 Ephrin_lbd Ephrin receptor ligand binding domain. The Eph receptors, which bind to ephrins pfam00812 are a large family of receptor tyrosine kinases. This family represents the amino terminal domain which binds the ephrin ligand. 177 matched cddid_all.tbl CDD pfam01405 pfam01405 426247 PsbT Photosystem II reaction centre T protein. The exact function of this protein is unknown. It probably consists of a single transmembrane spanning helix. The Swiss:P37256 protein, appears to be (i) a novel photosystem II subunit and (ii) required for maintaining optimal photosystem II activity under adverse growth conditions. 29 matched cddid_all.tbl CDD pfam01406 pfam01406 396128 tRNA-synt_1e tRNA synthetases class I (C) catalytic domain. This family includes only cysteinyl tRNA synthetases. 301 matched cddid_all.tbl CDD pfam01407 pfam01407 279715 Gemini_AL3 Geminivirus AL3 protein. Geminiviruses are small, ssDNA-containing plant viruses. Geminiviruses contain three ORFs (designated AL1, AL2, and AL3) that overlap and are specified by multiple polycistronic mRNAs. The AL3 protein comprises approximately 0.05% of the cellular proteins and is present in the soluble and organelle fractions. AL3 may form oligomers. Immunoprecipitation of AL3 in a baculovirus expression system extracts expressing both AL1 pfam00799 and AL3 showed that the two proteins also complex with each other. The AL3 protein is involved in viral replication. 119 matched cddid_all.tbl CDD pfam01408 pfam01408 426248 GFO_IDH_MocA Oxidoreductase family, NAD-binding Rossmann fold. This family of enzymes utilize NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot. 120 matched cddid_all.tbl CDD pfam01409 pfam01409 396130 tRNA-synt_2d tRNA synthetases class II core domain (F). Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only phenylalanyl-tRNA synthetases. This is the core catalytic domain. 245 matched cddid_all.tbl CDD pfam01410 pfam01410 460199 COLFI Fibrillar collagen C-terminal domain. Found at C-termini of fibrillar collagens: Ephydatia muelleri procollagen EMF1 alpha, vertebrate collagens alpha(1)III, alpha(1)II, alpha(2)V etc. 233 matched cddid_all.tbl CDD pfam01411 pfam01411 279719 tRNA-synt_2c tRNA synthetases class II (A). Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only alanyl-tRNA synthetases. 548 matched cddid_all.tbl CDD pfam01412 pfam01412 460200 ArfGap Putative GTPase activating protein for Arf. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs. 117 matched cddid_all.tbl CDD pfam01413 pfam01413 460201 C4 C-terminal tandem repeated domain in type 4 procollagen. Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome. 110 matched cddid_all.tbl CDD pfam01414 pfam01414 460202 DSL Delta serrate ligand. This family has been redefined to correspond to the EGF-like domain defined by structure. 46 matched cddid_all.tbl CDD pfam01415 pfam01415 460203 IL7 Interleukin 7. IL-7 is a cytokine that acts as a growth factor for early lymphoid cells of both B- and T-cell lineages. IL-7 and IL-7Ralpha bind the gamma-c receptor forming a complex crucial to several signaling cascades leading to the development and homeostasis of T and B cells. 152 matched cddid_all.tbl CDD pfam01416 pfam01416 460204 PseudoU_synth_1 tRNA pseudouridine synthase. Involved in the formation of pseudouridine at the anticodon stem and loop of transfer-RNAs Pseudouridine is an isomer of uridine (5-(beta-D-ribofuranosyl) uracil, and id the most abundant modified nucleoside found in all cellular RNAs. The TruA-like proteins also exhibit a conserved sequence with a strictly conserved aspartic acid, likely involved in catalysis. 108 matched cddid_all.tbl CDD pfam01417 pfam01417 426255 ENTH ENTH domain. The ENTH (Epsin N-terminal homology) domain is found in proteins involved in endocytosis and cytoskeletal machinery. The function of the ENTH domain is unknown. 124 matched cddid_all.tbl CDD pfam01418 pfam01418 334531 HTH_6 Helix-turn-helix domain, rpiR family. This domain contains a helix-turn-helix motif. The best characterized member of this family is Swiss:P39266. RpiR is a regulator of the expression of rpiB gene. 77 matched cddid_all.tbl CDD pfam01419 pfam01419 396138 Jacalin Jacalin-like lectin domain. Proteins containing this domain are lectins. It is found in 1 to 6 copies in these proteins. The domain is also found in the animal prostatic spermine-binding protein. 134 matched cddid_all.tbl CDD pfam01420 pfam01420 396139 Methylase_S Type I restriction modification DNA specificity domain. This domain is also known as the target recognition domain (TRD). Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The host genome is protected from cleavage by methylation of specific nucleotides in the target sites. In type I systems, both restriction and modification activities are present in one heteromeric enzyme complex composed of one DNA specificity subunit (this family), two modification (M) subunits and two restriction (R) subunits. 167 matched cddid_all.tbl CDD pfam01421 pfam01421 426256 Reprolysin Reprolysin (M12B) family zinc metalloprotease. The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis. Members of this family are also known as adamalysins. Most members of this family are snake venom endopeptidases, but there are also some mammalian proteins such as Swiss:P78325, and fertilin. Fertilin and closely related proteins appear to not have some active site residues and may not be active enzymes. 200 matched cddid_all.tbl CDD pfam01422 pfam01422 460205 zf-NF-X1 NF-X1 type zinc finger. This domain is presumed to be a zinc binding domain. The following pattern describes the zinc finger. C-X(1-6)-H-X-C-X3-C(H/C)-X(3-4)-(H/C)-X(1-10)-C Where X can be any amino acid, and numbers in brackets indicate the number of residues. Two position can be either his or cys. This family includes Swiss:P40798, Swiss:Q12986 and Swiss:P53971. The zinc fingers in Swiss:Q12986 bind to DNA. 19 matched cddid_all.tbl CDD pfam01423 pfam01423 426258 LSM LSM domain. The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings. 66 matched cddid_all.tbl CDD pfam01424 pfam01424 460206 R3H R3H domain. The name of the R3H domain comes from the characteriztic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to be binding ssDNA. 60 matched cddid_all.tbl CDD pfam01425 pfam01425 396144 Amidase Amidase. 442 matched cddid_all.tbl CDD pfam01426 pfam01426 460207 BAH BAH domain. This domain has been called BAH (Bromo adjacent homology) domain and has also been called ELM1 and BAM (Bromo adjacent motif) domain. The function of this domain is unknown but may be involved in protein-protein interaction. 120 matched cddid_all.tbl CDD pfam01427 pfam01427 279735 Peptidase_M15 D-ala-D-ala dipeptidase. 199 matched cddid_all.tbl CDD pfam01428 pfam01428 460208 zf-AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis. The following pattern describes the zinc finger. C-X2-C-X(9-12)-C-X(1-2)-C-X4-C-X2-H-X5-H-X-C Where X can be any amino acid, and numbers in brackets indicate the number of residues. 37 matched cddid_all.tbl CDD pfam01429 pfam01429 396147 MBD Methyl-CpG binding domain. The Methyl-CpG binding domain (MBD) binds to DNA that contains one or more symmetrically methylated CpGs. DNA methylation in animals is associated with alterations in chromatin structure and silencing of gene expression. MBD has negligible non-specific affinity for DNA. In vitro foot-printing with MeCP2 showed the MBD can protect a 12 nucleotide region surrounding a methyl CpG pair. MBDs are found in several Methyl-CpG binding proteins and also DNA demethylase. 76 matched cddid_all.tbl CDD pfam01430 pfam01430 460209 HSP33 Hsp33 protein. Hsp33 is a molecular chaperone, distinguished from all other known chaperones by its mode of functional regulation. Its activity is redox regulated. Hsp33 is a cytoplasmically localized protein with highly reactive cysteines that respond quickly to changes in the redox environment. Oxidising conditions like H2O2 cause disulfide bonds to form in Hsp33, a process that leads to the activation of its chaperone function. 271 matched cddid_all.tbl CDD pfam01431 pfam01431 279739 Peptidase_M13 Peptidase family M13. Mammalian enzymes are typically type-II membrane anchored enzymes which are known, or believed to activate or inactivate oligopeptide (pro)-hormones such as opioid peptides. The family also contains a bacterial member believed to be involved with milk protein cleavage. 205 matched cddid_all.tbl CDD pfam01432 pfam01432 396149 Peptidase_M3 Peptidase family M3. This is the Thimet oligopeptidase family, large family of mammalian and bacterial oligopeptidases that cleave medium sized peptides. The group also contains mitochondrial intermediate peptidase which is encoded by nuclear DNA but functions within the mitochondria to remove the leader sequence. 450 matched cddid_all.tbl CDD pfam01433 pfam01433 426262 Peptidase_M1 Peptidase family M1 domain. Members of this family are aminopeptidases. The members differ widely in specificity, hydrolysing acidic, basic or neutral N-terminal residues. This family includes leukotriene-A4 hydrolase, this enzyme also has an aminopeptidase activity. 219 matched cddid_all.tbl CDD pfam01434 pfam01434 460210 Peptidase_M41 Peptidase family M41. 190 matched cddid_all.tbl CDD pfam01435 pfam01435 426263 Peptidase_M48 Peptidase family M48. Peptidase_M48 is the largely extracellular catalytic region of CAAX prenyl protease homologs such as Human FACE-1 protease. These are metallopeptidases, with the characteriztic HExxH motif giving the two histidine-zinc-ligands and an adjacent glutamate on the next helix being the third. The whole molecule folds to form a deep groove/cleft into which the substrate can fit. 201 matched cddid_all.tbl CDD pfam01436 pfam01436 396153 NHL NHL repeat. The NHL (NCL-1, HT2A and LIN-41) repeat is found in multiple tandem copies. It is about 40 residues long and resembles the WD repeat pfam00400. The repeats have a catalytic activity in Swiss:P10731, proteolysis has shown that the Peptidyl-alpha-hydroxyglycine alpha-amidating lyase (PAL) activity is localized to the repeats. Swiss:Q13049 interacts with the activation domain of Tat. This interaction is me diated by the NHL repeats. 28 matched cddid_all.tbl CDD pfam01437 pfam01437 396154 PSI Plexin repeat. A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin. Two copies of the repeat are found in mahogany protein. A related C. elegans protein contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas some members show 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman). 52 matched cddid_all.tbl CDD pfam01439 pfam01439 396155 Metallothio_2 Metallothionein. Members of this family are metallothioneins. These proteins are cysteine rich proteins that bind to heavy metals. Members of this family appear to be closest to Class II metallothioneins, seed pfam00131. 80 matched cddid_all.tbl CDD pfam01440 pfam01440 279747 Gemini_AL2 Geminivirus AL2 protein. Geminiviruses are small, ssDNA-containing plant viruses. Geminiviruses contain three ORFs (designated AL1, AL2, and AL3) that overlap and are specified by multiple polycistronic mRNAs. The AL2 gene product transactivates expression of TGMV coat protein gene, and BR1 movement protein. 126 matched cddid_all.tbl CDD pfam01441 pfam01441 396156 Lipoprotein_6 Lipoprotein. Members of this family are lipoproteins that are probably involved in evasion of the host immune system by pathogens. 170 matched cddid_all.tbl CDD pfam01442 pfam01442 460211 Apolipoprotein Apolipoprotein A1/A4/E domain. These proteins contain several 22 residue repeats which form a pair of alpha helices. This family includes: Apolipoprotein A-I. Apolipoprotein A-IV. Apolipoprotein E. 175 matched cddid_all.tbl CDD pfam01443 pfam01443 366646 Viral_helicase1 Viral (Superfamily 1) RNA helicase. Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis. 227 matched cddid_all.tbl CDD pfam01445 pfam01445 279751 SH Viral small hydrophobic protein. The SH (small hydrophobic) protein is a membrane protein of uncertain function. 57 matched cddid_all.tbl CDD pfam01446 pfam01446 460212 Rep_1 Replication protein. Replication proteins (rep) are involved in plasmid replication. The Rep protein binds to the plasmid DNA and nicks it at the double strand origin (dso) of replication. The 3'-hydroxyl end created is extended by the host DNA replicase, and the 5' end is displaced during synthesis. At the end of one replication round, Rep introduces a second single stranded break at the dso and ligates the ssDNA extremities generating one double-stranded plasmid and one circular ssDNA form. Complementary strand synthesis of the circular ssDNA is usually initiated at the single-stranded origin by the host RNA polymerase. 249 matched cddid_all.tbl CDD pfam01447 pfam01447 460213 Peptidase_M4 Thermolysin metallopeptidase, catalytic domain. 147 matched cddid_all.tbl CDD pfam01448 pfam01448 460214 ELM2 ELM2 domain. The ELM2 (Egl-27 and MTA1 homology 2) domain is a small domain of unknown function. It is found in the MTA1 protein that is part of the NuRD complex. The domain is usually found to the N terminus of a myb-like DNA binding domain pfam00249. ELM2 is also found associated with an ARID DNA binding domain pfam01388 in Swiss:O82364. This suggests that ELM2 may also be involved in DNA binding, or perhaps is a protein-protein interaction domain. 53 matched cddid_all.tbl CDD pfam01450 pfam01450 460215 IlvC Acetohydroxy acid isomeroreductase, catalytic domain. Acetohydroxy acid isomeroreductase catalyzes the conversion of acetohydroxy acids into dihydroxy valerates. This reaction is the second in the synthetic pathway of the essential branched side chain amino acids valine and isoleucine. 138 matched cddid_all.tbl CDD pfam01451 pfam01451 460216 LMWPc Low molecular weight phosphotyrosine protein phosphatase. 142 matched cddid_all.tbl CDD pfam01452 pfam01452 279757 Rota_NSP4 Rotavirus non structural protein. This protein has been called NSP4, NSP5, NS28, and NCVP5. The final steps in the assembly of rotavirus occur in the lumen of the endoplasmic reticulum (ER). Targeting of the immature inner capsid particle (ICP) to this compartment is mediated by the cytoplasmic tail of NSP4, located in the ER membrane. 173 matched cddid_all.tbl CDD pfam01453 pfam01453 460217 B_lectin D-mannose binding lectin. These proteins include mannose-specific lectins from plants as well as bacteriocins from bacteria. 105 matched cddid_all.tbl CDD pfam01454 pfam01454 426270 MAGE MAGE homology domain. The MAGE (melanoma antigen-encoding gene) family are expressed in a wide variety of tumours but not in normal cells, with the exception of the male germ cells, placenta, and, possibly, cells of the developing embryo. The cellular function of this family is unknown. This family also contains the yeast protein, Nse3. The Nse3 protein is part of the Smc5-6 complex. Nse3 has been demonstrated to be important for meiosis. 205 matched cddid_all.tbl CDD pfam01455 pfam01455 460218 HupF_HypC HupF/HypC family. 64 matched cddid_all.tbl CDD pfam01456 pfam01456 250634 Mucin Mucin-like glycoprotein. This family of trypanosomal proteins resemble vertebrate mucins. The protein consists of three regions. The N and C terminii are conserved between all members of the family, whereas the central region is not well conserved and contains a large number of threonine residues which can be glycosylated. Indirect evidence suggested that these genes might encode the core protein of parasite mucins, glycoproteins that were proposed to be involved in the interaction with, and invasion of, mammalian host cells. This family contains an N-terminal signal peptide. 143 matched cddid_all.tbl CDD pfam01457 pfam01457 366652 Peptidase_M8 Leishmanolysin. 529 matched cddid_all.tbl CDD pfam01458 pfam01458 460219 SUFBD SUF system FeS cluster assembly, SufBD. Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S]. FeS cluster assembly is a complex process involving the mobilization of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. SufA is homologous to IscA, acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. This entry represents SufB and SufD proteins, which are homologous, and form part of the SufBCD complex in the SUF system. SufB accepts sulfur transferred from SufE, whereas SufD may play a role in iron acquisition. 218 matched cddid_all.tbl CDD pfam01459 pfam01459 460220 Porin_3 Eukaryotic porin. 269 matched cddid_all.tbl CDD pfam01462 pfam01462 396168 LRRNT Leucine rich repeat N-terminal domain. Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats. 28 matched cddid_all.tbl CDD pfam01463 pfam01463 279765 LRRCT Leucine rich repeat C-terminal domain. Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the C-terminus of tandem leucine rich repeats. 26 matched cddid_all.tbl CDD pfam01464 pfam01464 396169 SLT Transglycosylase SLT domain. This family is distantly related to pfam00062. Members are found in phages, type II, type III and type IV secretion systems. 114 matched cddid_all.tbl CDD pfam01465 pfam01465 460221 GRIP GRIP domain. The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi. The GRIP domain contains a completely conserved tyrosine residue. At least some of these domains have been shown to bind to GTPase Arl1, see structures in. 44 matched cddid_all.tbl CDD pfam01466 pfam01466 460222 Skp1 Skp1 family, dimerization domain. 48 matched cddid_all.tbl CDD pfam01467 pfam01467 396172 CTP_transf_like Cytidylyltransferase-like. This family includes: Cholinephosphate cytidylyltransferase; glycerol-3-phosphate cytidylyltransferase. It also includes putative adenylyltransferases, and FAD synthases. 134 matched cddid_all.tbl CDD pfam01468 pfam01468 396173 GA GA module. The GA (protein G-related Albumin-binding) module is composed of three alpha helices. This module is found in a range of bacterial cell surface proteins. The GA module from Swiss:Q51911 shows a strong affinity for albumin. 55 matched cddid_all.tbl CDD pfam01469 pfam01469 279771 Pentapeptide_2 Pentapeptide repeats (8 copies). These repeats are found in many mycobacterial proteins. These repeats are most common in the pfam00823 family of proteins, where they are found in the MPTR subfamily of PPE proteins. The function of these repeats is unknown. The repeat can be approximately described as XNXGX, where X can be any amino acid. These repeats are similar to pfam00805, however it is not clear if these two families are structurally related. 39 matched cddid_all.tbl CDD pfam01470 pfam01470 426276 Peptidase_C15 Pyroglutamyl peptidase. 203 matched cddid_all.tbl CDD pfam01471 pfam01471 460223 PG_binding_1 Putative peptidoglycan binding domain. This domain is composed of three alpha helices. This domain is found at the N or C terminus of a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. This family is found N-terminal to the catalytic domain of matrixins. The domain is found to bind peptidoglycan experimentally. 57 matched cddid_all.tbl CDD pfam01472 pfam01472 426278 PUA PUA domain. The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in the regulation of the expression of other genes. It is predicted that the PUA domain is an RNA binding domain. 74 matched cddid_all.tbl CDD pfam01473 pfam01473 366661 Choline_bind_1 Putative cell wall binding repeat. These repeats are characterized by conserved aromatic residues and glycines are found in multiple tandem copies in a number of proteins. The CW repeat is 20 amino acid residues long. The exact domain boundaries may not be correct. It has been suggested that these repeats in Swiss:P15057 might be responsible for the specific recognition of choline-containing cell walls. Similar but longer repeats are found in the glucosyltransferases and glucan-binding proteins of oral streptococci and shown to be involved in glucan binding as well as in the related dextransucrases of Leuconostoc mesenteroides. Repeats also occur in toxins of Clostridium difficile and other clostridia, though the ligands are not always known. 19 matched cddid_all.tbl CDD pfam01474 pfam01474 426279 DAHP_synth_2 Class-II DAHP synthetase family. Members of this family are aldolase enzymes that catalyze the first step of the shikimate pathway. 437 matched cddid_all.tbl CDD pfam01475 pfam01475 426280 FUR Ferric uptake regulator family. This family includes metal ion uptake regulator proteins, that bind to the operator DNA and controls transcription of metal ion-responsive genes. This family is also known as the FUR family. 121 matched cddid_all.tbl CDD pfam01476 pfam01476 396179 LysM LysM domain. The LysM (lysin motif) domain is about 40 residues long. It is found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. The structure of this domain is known. 43 matched cddid_all.tbl CDD pfam01477 pfam01477 396180 PLAT PLAT/LH2 domain. This domain is found in a variety of membrane or lipid associated proteins. It is called the PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology) domain. The known structure of pancreatic lipase shows this domain binds to procolipase pfam01114, which mediates membrane association. So it appears possible that this domain mediates membrane attachment via other protein binding partners. The structure of this domain is known for many members of the family and is composed of a beta sandwich. 115 matched cddid_all.tbl CDD pfam01478 pfam01478 426281 Peptidase_A24 Type IV leader peptidase family. Peptidase A24, or the prepilin peptidase as it is also known, processes the N-terminus of the prepilins. The processing is essential for the correct formation of the pseudopili of type IV bacterial protein secretion. The enzyme is found across eubacteria and archaea. 101 matched cddid_all.tbl CDD pfam01479 pfam01479 396182 S4 S4 domain. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation. The S4 domain probably mediates binding to RNA. 48 matched cddid_all.tbl CDD pfam01480 pfam01480 460224 PWI PWI domain. 71 matched cddid_all.tbl CDD pfam01481 pfam01481 396184 Arteri_nucleo Arterivirus nucleocapsid protein. 116 matched cddid_all.tbl CDD pfam01483 pfam01483 460225 P_proprotein Proprotein convertase P-domain. A unique feature of the eukaryotic subtilisin-like proprotein convertases is the presence of an additional highly conserved sequence of approximately 150 residues (P domain) located immediately downstream of the catalytic domain. 86 matched cddid_all.tbl CDD pfam01484 pfam01484 460226 Col_cuticle_N Nematode cuticle collagen N-terminal domain. The function of this domain is unknown. It is found in the N-terminal region of nematode cuticle collagens, see pfam01391. Cuticle is a tough elastic structure secreted by hypodermal cells and is primarily composed of collagen proteins. 50 matched cddid_all.tbl CDD pfam01485 pfam01485 460227 IBR IBR domain, a half RING-finger domain. The IBR (In Between Ring fingers) domain is often found to occur between pairs of ring fingers (pfam00097). This domain has also been called the C6HC domain and DRIL (for double RING finger linked) domain. Proteins that contain two Ring fingers and an IBR domain (these proteins are also termed RBR family proteins) are thought to exist in all eukaryotic organizms. RBR family members play roles in protein quality control and can indirectly regulate transcription. Evidence suggests that RBR proteins are often parts of cullin-containing ubiquitin ligase complexes. The ubiquitin ligase Parkin is an RBR family protein whose mutations are involved in forms of familial Parkinson's disease. 65 matched cddid_all.tbl CDD pfam01486 pfam01486 460228 K-box K-box region. The K-box region is commonly found associated with SRF-type transcription factors see pfam00319. The K-box is a possible coiled-coil structure. Possible role in multimer formation. 91 matched cddid_all.tbl CDD pfam01487 pfam01487 426287 DHquinase_I Type I 3-dehydroquinase. Type I 3-dehydroquinase, (3-dehydroquinate dehydratase or DHQase.) catalyzes the cis-dehydration of 3-dehydroquinate via a covalent imine intermediate giving dehydroshikimate. Dehydroquinase functions in the shikimate pathway which is involved in the biosynthesis of aromatic amino acids. Type II 3-dehydroquinase catalyzes the trans-dehydration of 3-dehydroshikimate see pfam01220. 227 matched cddid_all.tbl CDD pfam01488 pfam01488 460229 Shikimate_DH Shikimate / quinate 5-dehydrogenase. This family contains both shikimate and quinate dehydrogenases. Shikimate 5-dehydrogenase catalyzes the conversion of shikimate to 5-dehydroshikimate. This reaction is part of the shikimate pathway which is involved in the biosynthesis of aromatic amino acids. Quinate 5-dehydrogenase catalyzes the conversion of quinate to 5-dehydroquinate. This reaction is part of the quinate pathway where quinic acid is exploited as a source of carbon in prokaryotes and microbial eukaryotes. Both the shikimate and quinate pathways share two common pathway metabolites 3-dehydroquinate and dehydroshikimate. 136 matched cddid_all.tbl CDD pfam01490 pfam01490 279788 Aa_trans Transmembrane amino acid transporter protein. This transmembrane region is found in many amino acid transporters including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane domains. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance. Other members of this family include proline transporters and amino acid permeases. 410 matched cddid_all.tbl CDD pfam01491 pfam01491 460230 Frataxin_Cyay Frataxin-like domain. This family contains proteins that have a domain related to the globular C-terminus of Frataxin the protein that is mutated in Friedreich's ataxia. This domain is found in a family of bacterial proteins. The function of this domain is currently unknown. It has been suggested that this family is involved in iron transport. 106 matched cddid_all.tbl CDD pfam01492 pfam01492 279790 Gemini_C4 Geminivirus C4 protein. This family consists of the N terminal region of geminivirus C4 or AC4 proteins. In Tomato yellow leaf curl geminivirus (TYLCV) the C4 protein is necessary for efficient spreading of the virus in tomato plants. 84 matched cddid_all.tbl CDD pfam01493 pfam01493 460231 GXGXG GXGXG motif. This domain is found in glutamate synthase, tungsten formylmethanofuran dehydrogenase subunit c (FwdC) and molybdenum formylmethanofuran dehydrogenase subunit c (FmdC). A repeated G-XX-G-XXX-G motif is seen in the alignment. 190 matched cddid_all.tbl CDD pfam01494 pfam01494 396193 FAD_binding_3 FAD binding domain. This domain is involved in FAD binding in a number of enzymes. 348 matched cddid_all.tbl CDD pfam01496 pfam01496 460232 V_ATPase_I V-type ATPase 116kDa subunit family. This family consists of the 116kDa V-type ATPase (vacuolar (H+)-ATPases) subunits, as well as V-type ATP synthase subunit i. The V-type ATPases family are proton pumps that acidify intracellular compartments in eukaryotic cells for example yeast central vacuoles, clathrin-coated and synaptic vesicles. They have important roles in membrane trafficking processes. The 116kDa subunit (subunit a) in the V-type ATPase is part of the V0 functional domain responsible for proton transport. The a subunit is a transmembrane glycoprotein with multiple putative transmembrane helices it has a hydrophilic amino terminal and a hydrophobic carboxy terminal. It has roles in proton transport and assembly of the V-type ATPase complex. This subunit is encoded by two homologous gene in yeast VPH1 and STV1. 748 matched cddid_all.tbl CDD pfam01497 pfam01497 426291 Peripla_BP_2 Periplasmic binding protein. This is sensor domain found in bacterial periplasmic binding proteins, several of which are involved in iron and cobalamin transport. Among its ligands are siderophores bacillibactin, enterobactin and iron(III)-hydroxamates (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1 https://doi.org/10.1093/femsre/fuab043). 233 matched cddid_all.tbl CDD pfam01498 pfam01498 366677 HTH_Tnp_Tc3_2 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of C.elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in. Tc3 is a member of the Tc1/mariner family of transposable elements. 72 matched cddid_all.tbl CDD pfam01499 pfam01499 426292 Herpes_UL25 Herpesvirus UL25 family. The herpesvirus UL25 gene product is a virion component involved in virus penetration and capsid assembly. The product of the UL25 gene is required for packaging but not cleavage of replicated viral DNA. This family includes a number of herpesvirus proteins: EHV-1 36, EBV BVRF1, HCMV UL77, ILTV ORF2, and VZV gene 34. 527 matched cddid_all.tbl CDD pfam01500 pfam01500 366678 Keratin_B2 Keratin, high sulfur B2 protein. High sulfur proteins are cysteine-rich proteins synthesized during the differentiation of hair matrix cells, and form hair fibres in association with hair keratin intermediate filaments. This family has been divided up into four regions, with the second region containing 8 copies of a short repeat. This family is also known as B2 or KAP1. 161 matched cddid_all.tbl CDD pfam01501 pfam01501 279798 Glyco_transf_8 Glycosyl transferase family 8. This family includes enzymes that transfer sugar residues to donor molecules. Members of this family are involved in lipopolysaccharide biosynthesis and glycogen synthesis. This family includes Lipopolysaccharide galactosyltransferase, lipopolysaccharide glucosyltransferase 1, and glycogenin glucosyltransferase. 252 matched cddid_all.tbl CDD pfam01502 pfam01502 460233 PRA-CH Phosphoribosyl-AMP cyclohydrolase. This enzyme catalyzes the third step in the histidine biosynthetic pathway. It requires Zn ions for activity. 74 matched cddid_all.tbl CDD pfam01503 pfam01503 426294 PRA-PH Phosphoribosyl-ATP pyrophosphohydrolase. This enzyme catalyzes the second step in the histidine biosynthetic pathway. 83 matched cddid_all.tbl CDD pfam01504 pfam01504 460234 PIP5K Phosphatidylinositol-4-phosphate 5-Kinase. This family contains a region from the common kinase core found in the type I phosphatidylinositol-4-phosphate 5-kinase (PIP5K) family as described in. The family consists of various type I, II and III PIP5K enzymes. PIP5K catalyzes the formation of phosphoinositol-4,5-bisphosphate via the phosphorylation of phosphatidylinositol-4-phosphate a precursor in the phosphinositide signaling pathway. 227 matched cddid_all.tbl CDD pfam01505 pfam01505 460235 Vault Major Vault Protein repeat domain. The vault is a ubiquitous and highly conserved ribonucleoprotein particle of approximately 13 mDa of unknown function. This family corresponds to a repeated domain found in the amino terminal half of the major vault protein. 41 matched cddid_all.tbl CDD pfam01506 pfam01506 366682 HCV_NS5a Hepatitis C virus non-structural 5a protein membrane anchor. The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. The N-terminal region of the NS5a protein has been used in the construction of the alignment for this family. The C-terminal region has not been included because it is too heterogeneous. 23 matched cddid_all.tbl CDD pfam01507 pfam01507 396201 PAPS_reduct Phosphoadenosine phosphosulfate reductase family. This domain is found in phosphoadenosine phosphosulfate (PAPS) reductase enzymes or PAPS sulfotransferase. PAPS reductase is part of the adenine nucleotide alpha hydrolases superfamily also including N type ATP PPases and ATP sulphurylases. The enzyme uses thioredoxin as an electron donor for the reduction of PAPS to phospho-adenosine-phosphate (PAP). It is also found in NodP nodulation protein P from Rhizobium which has ATP sulfurylase activity (sulfate adenylate transferase). 173 matched cddid_all.tbl CDD pfam01508 pfam01508 279805 Paramecium_SA Paramecium surface antigen domain. This domain is a cysteine rich extracellular repeat found in surface antigens of Paramecium. The domain contains 8 cysteine residues. 62 matched cddid_all.tbl CDD pfam01509 pfam01509 426297 TruB_N TruB family pseudouridylate synthase (N terminal domain). Members of this family are involved in modifying bases in RNA molecules. They carry out the conversion of uracil bases to pseudouridine. This family includes TruB, a pseudouridylate synthase that specifically converts uracil 55 to pseudouridine in most tRNAs. This family also includes Cbf5p that modifies rRNA. 148 matched cddid_all.tbl CDD pfam01510 pfam01510 460236 Amidase_2 N-acetylmuramoyl-L-alanine amidase. This family includes zinc amidases that have N-acetylmuramoyl-L-alanine amidase activity EC:3.5.1.28. This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls (preferentially: D-lactyl-L-Ala). The structure is known for the bacteriophage T7 structure and shows that two of the conserved histidines are zinc binding. 122 matched cddid_all.tbl CDD pfam01512 pfam01512 460237 Complex1_51K Respiratory-chain NADH dehydrogenase 51 Kd subunit. 150 matched cddid_all.tbl CDD pfam01513 pfam01513 426300 NAD_kinase ATP-NAD kinase N-terminal domain. Members of this family include ATP-NAD kinases EC:2.7.1.23, which catalyzes the phosphorylation of NAD to NADP utilizing ATP and other nucleoside triphosphates as well as inorganic polyphosphate as a source of phosphorus. Also includes NADH kinases EC:2.7.1.86. 128 matched cddid_all.tbl CDD pfam01514 pfam01514 460238 YscJ_FliF Secretory protein of YscJ/FliF family. This family includes proteins that are related to the YscJ lipoprotein, and the amino terminus of FliF, the flageller M-ring protein. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flageller proteins, based on the similarity to YscJ proteins. 179 matched cddid_all.tbl CDD pfam01515 pfam01515 396207 PTA_PTB Phosphate acetyl/butaryl transferase. This family contains both phosphate acetyltransferase and phosphate butaryltransferase. These enzymes catalyze the transfer of an acetyl or butaryl group to orthophosphate. 318 matched cddid_all.tbl CDD pfam01516 pfam01516 279812 Orbi_VP6 Orbivirus helicase VP6. The VP6 protein a minor protein in the core of the virion is probably the viral helicase. 324 matched cddid_all.tbl CDD pfam01517 pfam01517 426302 HDV_ag Hepatitis delta virus delta antigen. The hepatitis delta virus (HDV) encodes a single protein, the hepatitis delta antigen (HDAg). The central region of this protein has been shown to bind RNA. Several interactions are also mediated by a coiled-coil region at the N terminus of the protein. 187 matched cddid_all.tbl CDD pfam01518 pfam01518 250679 PolyG_pol Sigma NS protein. This viral protein has a poly(C)-dependent poly(G) polymerase activity. 366 matched cddid_all.tbl CDD pfam01519 pfam01519 396208 DUF16 Protein of unknown function DUF16. The function of this protein is unknown. It appears to only occur in Mycoplasma pneumoniae. The crystal structure revealed that this domain is composed of two separated homotrimeric coiled-coils. 95 matched cddid_all.tbl CDD pfam01520 pfam01520 426303 Amidase_3 N-acetylmuramoyl-L-alanine amidase. This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls. 174 matched cddid_all.tbl CDD pfam01521 pfam01521 426304 Fe-S_biosyn Iron-sulphur cluster biosynthesis. This family is involved in iron-sulphur cluster biosynthesis. Its members include proteins that are involved in nitrogen fixation such as the HesB and HesB-like proteins. 111 matched cddid_all.tbl CDD pfam01522 pfam01522 426305 Polysacc_deac_1 Polysaccharide deacetylase. This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase. It also includes chitin deacetylase from yeast, and endoxylanases which hydrolyses glucosidic bonds in xylan. 124 matched cddid_all.tbl CDD pfam01523 pfam01523 426306 PmbA_TldD PmbA/TldA metallopeptidase domain 1. This entry represents a group of metalloproteases. The tertiary structure of the Escherichia coli TdlD/TdlE complex has been solved, and shows that the TdlD subunit is the active peptidase, binding a single zinc ion at an HEXXXH motif in which the glutamic acid is a substrate-binding residue and the two histidines are zinc ligands. The third zinc ligand is a cysteine, C-terminal to the HEXXXH motif. The TldE (also known as PmbA) by itself has no catalytic activity, does not bind zinc, and does not carry the HEXXXH motif. TldD and TldE were originally identified as regulators of DNA gyrase. Later, they are shown to be metalloproteases involved in CcdA degradation. 65 matched cddid_all.tbl CDD pfam01524 pfam01524 366689 Gemini_V2 Geminivirus V2 protein. Disruption of the V2 gene in Tomato yellow leaf curl virus (TYLCV) stopped its ability to systemically infect tomato plants, suggesting that the V2 gene product is required for successful infection of the host. 78 matched cddid_all.tbl CDD pfam01525 pfam01525 460239 Rota_NS26 Rotavirus NS26. Gene 11 product is a non-structural phosphoprotein designated as NS26. 198 matched cddid_all.tbl CDD pfam01526 pfam01526 426307 DDE_Tnp_Tn3 Tn3 transposase DDE domain. This family includes transposases of Tn3, Tn21, Tn1721, Tn2501, Tn3926 transposons from E-coli. The specific binding of the Tn3 transposase to DNA has been demonstrated. Sequence analysis has suggested that the invariant triad of Asp689, Asp765, Glu895 (numbering as in Tn3) may correspond to the D-D-35-E motif previously implicated in the catalysis of numerous transposases. 389 matched cddid_all.tbl CDD pfam01527 pfam01527 426308 HTH_Tnp_1 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family. 75 matched cddid_all.tbl CDD pfam01528 pfam01528 279822 Herpes_glycop Herpesvirus glycoprotein M. The herpesvirus glycoprotein M (gM) is an integral membrane protein predicted to contain 8 transmembrane segments. Glycoprotein M is not essential for viral replication. 373 matched cddid_all.tbl CDD pfam01529 pfam01529 396215 DHHC DHHC palmitoyltransferase. This entry refers to the DHHC domain, found in DHHC proteins which are palmitoyltransferases. Palmitoylation or, more specifically S-acylation, plays important roles in the regulation of protein localization, stability, and activity. It is a post-translational protein modification that involves the attachment of palmitic acid to Cys residues through a thioester linkage. Protein acyltransferases (PATs), also known as palmitoyltransferases, catalyze this reaction by transferring the palmitoyl group from palmitoyl-CoA to the thiol group of Cys residues. They are characterized by the presence of a 50-residue-long domain called the DHHC domain, which in most but not all cases is also cysteine-rich and gets its name from a highly conserved DHHC signature tetrapeptide (Asp-His-His-Cys). The Cys residue within the DHHC domain forms a stable acyl intermediate and transfers the acyl chain to the Cys residues of a target protein. Some proteins containing a DHHC domain include Drosophila DNZ1 protein, Mouse Abl-philin 2 (Aph2) protein, Mammalian ZDHHC9, Yeast ankyrin repeat-containing protein AKR1, Yeast Erf2 protein, and Arabidopsis thaliana tip growth defective 1. 132 matched cddid_all.tbl CDD pfam01530 pfam01530 460240 zf-C2HC Zinc finger, C2HC type. This is a DNA binding zinc finger domain. 29 matched cddid_all.tbl CDD pfam01531 pfam01531 250689 Glyco_transf_11 Glycosyl transferase family 11. This family contains several fucosyl transferase enzymes. 298 matched cddid_all.tbl CDD pfam01532 pfam01532 460241 Glyco_hydro_47 Glycosyl hydrolase family 47. Members of this family are alpha-mannosidases that catalyze the hydrolysis of the terminal 1,2-linked alpha-D-mannose residues in the oligo-mannose oligosaccharide Man(9)(GlcNAc)(2). 453 matched cddid_all.tbl CDD pfam01533 pfam01533 396218 Tospo_nucleocap Tospovirus nucleocapsid protein. The tospovirus genome consists of three linear ssRNA segments, denoted L, M and S complexed with the nucleocapsid protein. The S RNA encodes the nucleocapsid protein and another non-structural protein. 246 matched cddid_all.tbl CDD pfam01534 pfam01534 460242 Frizzled Frizzled/Smoothened family membrane region. This family contains the membrane spanning region of frizzled and smoothened receptors. This membrane region is predicted to contain seven transmembrane alpha helices. Proteins related to Drosophila frizzled are receptors for Wnt (mediating the beta-catenin signalling pathway), but also the planar cell polarity (PCP) pathway and the Wnt/calcium pathway. The predominantly alpha-helical Cys-rich ligand-binding region (CRD) of Frizzled is both necessary and sufficient for Wnt binding. The smoothened receptor mediates hedgehog signalling. 321 matched cddid_all.tbl CDD pfam01535 pfam01535 366695 PPR PPR repeat. This repeat has no known function. It is about 35 amino acids long and found in up to 18 copies in some proteins. This family appears to be greatly expanded in plants. This repeat occurs in PET309 that may be involved in RNA stabilization. This domain occurs in crp1 that is involved in RNA processing. This repeat is associated with a predicted plant protein Swiss:O49549 that has a domain organization similar to the human BRCA1 protein. The repeat has been called PPR. 31 matched cddid_all.tbl CDD pfam01536 pfam01536 460243 SAM_decarbox Adenosylmethionine decarboxylase. This is a family of S-adenosylmethionine decarboxylase (SAMDC) proenzymes. In the biosynthesis of polyamines SAMDC produces decarboxylated S-adenosylmethionine, which serves as the aminopropyl moiety necessary for spermidine and spermine biosynthesis from putrescine. The Pfam alignment contains both the alpha and beta chains that are cleaved to form the active enzyme. 331 matched cddid_all.tbl CDD pfam01537 pfam01537 426313 Herpes_glycop_D Herpesvirus glycoprotein D/GG/GX domain. This domain is found in several Herpes viruses glycoproteins. This is a family includes glycoprotein-D (gD or gIV) which is common to herpes simplex virus types 1 and 2, as well as equine herpes, bovine herpes and Marek's disease virus. Glycoprotein-D has been found on the viral envelope and the plasma membrane of infected cells. and gD immunization can produce an immune response to bovine herpes virus (BHV-1). This response is stronger than that of the other major glycoproteins gB (gI) and gC (gIII) in BHV-1. Glycoprotein G (gG)is one of the seven external glycoproteins of HSV1 and HSV2. This family also contains the glycoprotein GX, (gX), initially identified in Pseudorabies virus. 118 matched cddid_all.tbl CDD pfam01538 pfam01538 366698 HCV_NS2 Hepatitis C virus non-structural protein NS2. The viral genome is translated into a single polyprotein of about 3000 amino acids. Generation of the mature non-structural proteins relies on the activity of viral proteases. Cleavage at the NS2/NS3 junction is accomplished by a metal-dependent autoprotease encoded within NS2 and the N-terminus of NS3. 195 matched cddid_all.tbl CDD pfam01539 pfam01539 110536 HCV_env Hepatitis C virus envelope glycoprotein E1. 190 matched cddid_all.tbl CDD pfam01540 pfam01540 460244 Lipoprotein_7 Adhesin lipoprotein. This family consists of the p50 and variable adherence-associated antigen (Vaa) adhesins from Mycoplasma hominis. M. hominis is a mycoplasma associated with human urogenital diseases, pneumonia, and septic arthritis. An adhesin is a cell surface molecule that mediates adhesion to other cells or to the surrounding surface or substrate. The Vaa antigen is a 50-kDa surface lipoprotein that has four tandem repetitive DNA sequences encoding a periodic peptide structure, and is highly immunogenic in the human host. p50 is also a 50-kDa lipoprotein, having three repeats A,B and C, that may be a tetramer of 191-kDa in its native environment. 112 matched cddid_all.tbl CDD pfam01541 pfam01541 426314 GIY-YIG GIY-YIG catalytic domain. This domain called GIY-YIG is found in the amino terminal region of excinuclease abc subunit c (uvrC), bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage. The structure of I-TevI a GIY-YIG endonuclease, reveals a novel alpha/beta-fold with a central three-stranded antiparallel beta-sheet flanked by three helices. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site. 78 matched cddid_all.tbl CDD pfam01542 pfam01542 460245 HCV_core Hepatitis C virus core protein. The viral core protein forms the internal viral coat that encapsidates the genomic RNA and is enveloped in a host cell-derived lipid membrane. The core protein has been shown, by yeast two-hybrid assay to interact with cellular DEAD box helicases. The N terminus of the core protein is involved in transcriptional repression. 75 matched cddid_all.tbl CDD pfam01543 pfam01543 144947 HCV_capsid Hepatitis C virus capsid protein. 121 matched cddid_all.tbl CDD pfam01544 pfam01544 460246 CorA CorA-like Mg2+ transporter protein. The CorA transport system is the primary Mg2+ influx system of Salmonella typhimurium and Escherichia coli. CorA is virtually ubiquitous in the Bacteria and Archaea. There are also eukaryotic relatives of this protein. The family includes the MRS2 protein from yeast that is thought to be an RNA splicing protein. However its membership of this family suggests that its effect on splicing is due to altered magnesium levels in the cell. 292 matched cddid_all.tbl CDD pfam01545 pfam01545 426316 Cation_efflux Cation efflux family. Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are thought to be efflux pumps that remove these ions from cells. 189 matched cddid_all.tbl CDD pfam01546 pfam01546 460247 Peptidase_M20 Peptidase family M20/M25/M40. This family includes a range of zinc metallopeptidases belonging to several families in the peptidase classification. Family M20 are Glutamate carboxypeptidases. Peptidase family M25 contains X-His dipeptidases. 315 matched cddid_all.tbl CDD pfam01547 pfam01547 460248 SBP_bac_1 Bacterial extracellular solute-binding protein. This family also includes the bacterial extracellular solute-binding protein family POTD/POTF. 294 matched cddid_all.tbl CDD pfam01548 pfam01548 460249 DEDD_Tnp_IS110 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes an amino-terminal region of the pilin gene inverting protein (PIVML) and of members of the IS111A/IS1328/IS1533 family of transposases. The C-terminus is represented by family pfam02371. 155 matched cddid_all.tbl CDD pfam01549 pfam01549 426319 ShK ShK domain-like. This domain of is found in several C. elegans proteins. The domain is 30 amino acids long and rich in cysteine residues. There are 6 conserved cysteine positions in the domain that form three disulphide bridges. The domain is found in the potassium channel inhibitor ShK in sea anemone. 37 matched cddid_all.tbl CDD pfam01551 pfam01551 460250 Peptidase_M23 Peptidase family M23. Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Swiss:P33648 for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown. 96 matched cddid_all.tbl CDD pfam01552 pfam01552 279840 Pico_P2B Picornavirus 2B protein. Poliovirus infection leads to drastic alterations in membrane permeability late during infection. Proteins 2B and 2BC enhance membrane permeability. 101 matched cddid_all.tbl CDD pfam01553 pfam01553 366704 Acyltransferase Acyltransferase. This family contains acyltransferases involved in phospholipid biosynthesis and other proteins of unknown function. This family also includes tafazzin, the Barth syndrome gene. 131 matched cddid_all.tbl CDD pfam01554 pfam01554 334587 MatE MatE. The MatE domain 161 matched cddid_all.tbl CDD pfam01555 pfam01555 396230 N6_N4_Mtase DNA methylase. Members of this family are DNA methylases. The family contains both N-4 cytosine-specific DNA methylases and N-6 Adenine-specific DNA methylases. 221 matched cddid_all.tbl CDD pfam01556 pfam01556 460251 DnaJ_C DnaJ C terminal domain. This family consists of the C terminal region of the DnaJ protein. It is always found associated with pfam00226 and pfam00684. DnaJ is a chaperone associated with the Hsp70 heat-shock system involved in protein folding and renaturation after stress. The two C-terminal domains CTDI and CTDII, both incorporated in this family are necessary for maintaining the J-domains in their specific relative positions. Structural analysis of PDB:1nlt shows that PF00684 is nested within this DnaJ C-terminal region. 213 matched cddid_all.tbl CDD pfam01557 pfam01557 460252 FAA_hydrolase Fumarylacetoacetate (FAA) hydrolase family. This family consists of fumarylacetoacetate (FAA) hydrolase, or fumarylacetoacetate hydrolase (FAH) and it also includes HHDD isomerase/OPET decarboxylase from E. coli strain W. FAA is the last enzyme in the tyrosine catabolic pathway, it hydrolyses fumarylacetoacetate into fumarate and acetoacetate which then join the citric acid cycle. Mutations in FAA cause type I tyrosinemia in humans this is an inherited disorder mainly affecting the liver leading to liver cirrhosis, hepatocellular carcinoma, renal tubular damages and neurologic crises amongst other symptoms. The enzymatic defect causes the toxic accumulation of phenylalanine/tyrosine catabolites. The E. coli W enzyme HHDD isomerase/OPET decarboxylase contains two copies of this domain and functions in fourth and fifth steps of the homoprotocatechuate pathway; here it decarboxylates OPET to HHDD and isomerizes this to OHED. The final products of this pathway are pyruvic acid and succinic semialdehyde. This family also includes various hydratases and 4-oxalocrotonate decarboxylases which are involved in the bacterial meta-cleavage pathways for degradation of aromatic compounds. 2-hydroxypentadienoic acid hydratase encoded by mhpD in E. coli is involved in the phenylpropionic acid pathway of E. coli and catalyzes the conversion of 2-hydroxy pentadienoate to 4-hydroxy-2-keto-pentanoate and uses a Mn2+ co-factor. OHED hydratase encoded by hpcG in E. coli is involved in the homoprotocatechuic acid (HPC) catabolism. XylI in P. putida is a 4-Oxalocrotonate decarboxylase. 210 matched cddid_all.tbl CDD pfam01558 pfam01558 426323 POR Pyruvate ferredoxin/flavodoxin oxidoreductase. This family includes a region of the large protein pyruvate-flavodoxin oxidoreductase and the whole pyruvate ferredoxin oxidoreductase gamma subunit protein. It is not known whether the gamma subunit has a catalytic or regulatory role. Pyruvate oxidoreductase (POR) catalyzes the final step in the fermentation of carbohydrates in anaerobic microorganizms. This involves the oxidative decarboxylation of pyruvate with the participation of thiamine followed by the transfer of an acetyl moiety to coenzyme A for the synthesis of acetyl-CoA. The family also includes pyruvate flavodoxin oxidoreductase as encoded by the nifJ gene in cyanobacterium which is required for growth on molecular nitrogen when iron is limited. 172 matched cddid_all.tbl CDD pfam01559 pfam01559 366705 Zein Zein seed storage protein. Zeins are seed storage proteins. They are unusually rich in glutamine, proline, alanine, and leucine residues and their sequences show a series of tandem repeats. 244 matched cddid_all.tbl CDD pfam01560 pfam01560 110557 HCV_NS1 Hepatitis C virus non-structural protein E2/NS1. The hypervariable region of the E2/NS1 region of hepatitis C virus varies greatly between viral isolates. E2 is thought to encode a structurally unconstrained envelope protein. 344 matched cddid_all.tbl CDD pfam01561 pfam01561 460253 Hanta_G2 Hantavirus/Nairovirus glycoprotein G2. The medium (M) genome segment of hantaviruses (family Bunyaviridae) encodes the two virion glycoproteins G1 and G2, as a polyprotein precursor. This entry represents the polyprotein region which forms the G2 glycoprotein. The N-terminal region has a conserved CNP motif, suggested to be an integrin-binding motif. 457 matched cddid_all.tbl CDD pfam01562 pfam01562 460254 Pep_M12B_propep "Reprolysin family propeptide. This region is the propeptide for members of peptidase family M12B. The propeptide contains a sequence motif similar to the ""cysteine switch"" of the matrixins. This motif is found at the C terminus of the alignment but is not well aligned." 128 matched cddid_all.tbl CDD pfam01563 pfam01563 396236 Alpha_E3_glycop Alphavirus E3 glycoprotein. This protein is found in some alphaviruses as a virion associated spike protein. 59 matched cddid_all.tbl CDD pfam01564 pfam01564 396237 Spermine_synth Spermine/spermidine synthase domain. Spermine and spermidine are polyamines. This family includes spermidine synthase that catalyzes the fifth (last) step in the biosynthesis of spermidine from arginine, and spermine synthase. 183 matched cddid_all.tbl CDD pfam01565 pfam01565 426326 FAD_binding_4 FAD binding domain. This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyzes the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyzes the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidizes the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan. 139 matched cddid_all.tbl CDD pfam01566 pfam01566 426327 Nramp Natural resistance-associated macrophage protein. The natural resistance-associated macrophage protein (NRAMP) family consists of Nramp1, Nramp2, and yeast proteins Smf1 and Smf2. The NRAMP family is a novel family of functional related proteins defined by a conserved hydrophobic core of ten transmembrane domains. This family of membrane proteins are divalent cation transporters. Nramp1 is an integral membrane protein expressed exclusively in cells of the immune system and is recruited to the membrane of a phagosome upon phagocytosis. By controlling divalent cation concentrations Nramp1 may regulate the interphagosomal replication of bacteria. Mutations in Nramp1 may genetically predispose an individual to susceptibility to diseases including leprosy and tuberculosis conversely this might however provide protection form rheumatoid arthritis. Nramp2 is a multiple divalent cation transporter for Fe2+, Mn2+ and Zn2+ amongst others it is expressed at high levels in the intestine; and is major transferrin-independent iron uptake system in mammals. The yeast proteins Smf1 and Smf2 may also transport divalent cations. 356 matched cddid_all.tbl CDD pfam01567 pfam01567 279853 Hanta_G1 Hantavirus glycoprotein G1. The medium (M) genome segment of hantaviruses (family Bunyaviridae) encodes the two virion glycoproteins. G1 and G2, as a precursor protein in the complementary sense RNA. 523 matched cddid_all.tbl CDD pfam01568 pfam01568 426328 Molydop_binding Molydopterin dinucleotide binding domain. This domain is found in various molybdopterin - containing oxidoreductases and tungsten formylmethanofuran dehydrogenase subunit d (FwdD) and molybdenum formylmethanofuran dehydrogenase subunit (FmdD); where the domain constitutes almost the entire subunit. The formylmethanofuran dehydrogenase catalyzes the first step in methane formation from CO2 in methanogenic archaea and has a molybdopterin dinucleotide cofactor. This domain corresponds to the C-terminal domain IV in dimethyl sulfoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules. 110 matched cddid_all.tbl CDD pfam01569 pfam01569 426329 PAP2 PAP2 superfamily. This family includes the enzyme type 2 phosphatidic acid phosphatase (PAP2), Glucose-6-phosphatase EC:3.1.3.9, Phosphatidylglycerophosphatase B EC:3.1.3.27 and bacterial acid phosphatase EC:3.1.3.2. The family also includes a variety of haloperoxidases that function by oxidising halides in the presence of hydrogen peroxide to form the corresponding hypohalous acids. 124 matched cddid_all.tbl CDD pfam01570 pfam01570 366710 Flavi_propep Flavivirus polyprotein propeptide. The flaviviruses are small enveloped animal viruses containing a single positive strand genomic RNA. The genome encodes one large ORF a polyprotein which undergos proteolytic processing into mature viral peptide chains. This family consists of a propeptide region of approximately 90 amino acid length. 78 matched cddid_all.tbl CDD pfam01571 pfam01571 460255 GCV_T Aminomethyltransferase folate-binding domain. This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyzes the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase. 254 matched cddid_all.tbl CDD pfam01573 pfam01573 279858 Bromo_MP Bromovirus movement protein. 283 matched cddid_all.tbl CDD pfam01575 pfam01575 396243 MaoC_dehydratas MaoC like domain. The maoC gene is part of a operon with maoA which is involved in the synthesis of monoamine oxidase. The MaoC protein is found to share similarity with a wide variety of enzymes; estradiol 17 beta-dehydrogenase 4, peroxisomal hydratase-dehydrogenase-epimerase, fatty acid synthase beta subunit. Several bacterial proteins that are composed solely of this domain have (R)-specific enoyl-CoA hydratase activity. This domain is also present in the NodN nodulation protein N. 123 matched cddid_all.tbl CDD pfam01576 pfam01576 460256 Myosin_tail_1 Myosin tail. The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament. 1081 matched cddid_all.tbl CDD pfam01577 pfam01577 250716 Peptidase_S30 Potyvirus P1 protease. The potyviridae family positive stand RNA viruses with genome encoding a polyprotein. members include zucchini yellow mosaic virus, and turnip mosaic viruses which cause considerable losses of crops worldwide. This family consists of a C terminus region from various plant potyvirus P1 proteins (found at the N terminus of the polyprotein). The C terminus of P1 is a serine-type protease responsible for autocatalytic cleavage between P1 and the helper component protease pfam00851. The entire P1 protein may be involved in virus-host interactions. 245 matched cddid_all.tbl CDD pfam01578 pfam01578 307628 Cytochrom_C_asm Cytochrome C assembly protein. This family consists of various proteins involved in cytochrome c assembly from mitochondria and bacteria; CycK from Rhizobium, CcmC from E. coli and Paracoccus denitrificans.and orf240 from wheat mitochondria. The members of this family are probably integral membrane proteins with six predicted transmembrane helices. It has been proposed that members of this family comprise a membrane component of an ABC (ATP binding cassette) transporter complex. It is also proposed that this transporter is necessary for transport of some component needed for cytochrome c assembly. One member CycK contains a putative heme-binding motif, orf240 also contains a putative heme-binding motif and is a proposed ABC transporter with c-type heme as its proposed substrate. However it seems unlikely that all members of this family transport heme nor c-type apocytochromes because CcmC in the putative CcmABC transporter transports neither. CcmF forms a working module with CcmH and CcmI, CcmFHI, and itself is unlikely to bind haem directly. 211 matched cddid_all.tbl CDD pfam01579 pfam01579 426332 DUF19 Domain of unknown function (DUF19). This presumed domain has no known function. It is found in one or two copies in several Caenorhabditis elegans proteins. It is roughly 130 amino acids long. The domain contains 12 conserved cysteines which suggests that the domain is an extracellular domain and that these cysteines form six intradomain disulphide bridges. The GO annotation for this protein indicates that it has a function in nematode larval development and has a positive regulation of growth rate. 154 matched cddid_all.tbl CDD pfam01580 pfam01580 279863 FtsK_SpoIIIE FtsK/SpoIIIE family. FtsK has extensive sequence similarity to wide variety of proteins from prokaryotes and plasmids, termed the FtsK/SpoIIIE family. This domain contains a putative ATP binding P-loop motif. It is found in the FtsK cell division protein from E. coli and the stage III sporulation protein E SpoIIIE, which has roles in regulation of prespore specific gene expression in B. subtilis. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification. The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer. 219 matched cddid_all.tbl CDD pfam01581 pfam01581 110576 FARP FMRFamide related peptide family. The neuroactive peptide Phe-Met-Arg-Phe-NH2 (FMRF-amide) has a variety of effects on both mammalian and invertebrate tissues. 11 matched cddid_all.tbl CDD pfam01582 pfam01582 396246 TIR TIR domain. The Toll/interleukin-1 receptor (TIR) homology domain is an intracellular signalling domain found in MyD88, interleukin 1 receptor and the Toll receptor. It contains three highly-conserved regions, and mediates protein-protein interactions between the Toll-like receptors (TLRs) and signal-transduction components. TIR-like motifs are also found in plant proteins thought to be involved in resistance to disease. When activated, TIR domains recruit cytoplasmic adaptor proteins MyD88 and TOLLIP (Toll interacting protein). In turn, these associate with various kinases to set off signalling cascades. 165 matched cddid_all.tbl CDD pfam01583 pfam01583 396247 APS_kinase Adenylylsulphate kinase. Enzyme that catalyzes the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulfate. This domain contains an ATP binding P-loop motif. 154 matched cddid_all.tbl CDD pfam01584 pfam01584 460257 CheW CheW-like domain. CheW proteins are part of the chemotaxis signaling mechanism in bacteria. CheW interacts with the methyl accepting chemotaxis proteins (MCPs) and relays signals to CheY, which affects flageller rotation. This family includes CheW and other related proteins that are involved in chemotaxis. The CheW-like regulatory domain in CheA binds to CheW, suggesting that these domains can interact with each other. 131 matched cddid_all.tbl CDD pfam01585 pfam01585 396249 G-patch G-patch domain. This domain is found in a number of RNA binding proteins, and is also found in proteins that contain RNA binding domains. This suggests that this domain may have an RNA binding function. This domain has seven highly conserved glycines. 45 matched cddid_all.tbl CDD pfam01586 pfam01586 460258 Basic Myogenic Basic domain. This basic domain is found in the MyoD family of muscle specific proteins that control muscle development. The bHLH region of the MyoD family includes the basic domain and the Helix-loop-helix (HLH) motif. The bHLH region mediates specific DNA binding. With 12 residues of the basic domain involved in DNA binding. The basic domain forms an extended alpha helix in the structure. 81 matched cddid_all.tbl CDD pfam01588 pfam01588 396251 tRNA_bind Putative tRNA binding domain. This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1), human tyrosyl-tRNA synthetase, and endothelial-monocyte activating polypeptide II. G4p1 binds specifically to tRNA form a complex with methionyl-tRNA synthetases. In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme. This domain may perform a common function in tRNA aminoacylation. 96 matched cddid_all.tbl CDD pfam01589 pfam01589 279870 Alpha_E1_glycop Alphavirus E1 glycoprotein. E1 forms a heterodimer with E2 pfam00943. The virus spikes are made up of 80 trimers of these heterodimers (sindbis virus). 504 matched cddid_all.tbl CDD pfam01590 pfam01590 460259 GAF GAF domain. This domain is present in cGMP-specific phosphodiesterases, adenylyl and guanylyl cyclases, phytochromes, FhlA and NifA. Adenylyl and guanylyl cyclases catalyze ATP and GTP to the second messengers cAMP and cGMP, respectively, these products up-regulating catalytic activity by binding to the regulatory GAF domain(s). The opposite hydrolysis reaction is catalyzed by phosphodiesterase. cGMP-dependent 3',5'-cyclic phosphodiesterase catalyzes the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. Here too, cGMP regulates catalytic activity by GAF-domain binding. Phytochromes are regulatory photoreceptors in plants and bacteria which exist in two thermally-stable states that are reversibly inter-convertible by light: the Pr state absorbs maximally in the red region of the spectrum, while the Pfr state absorbs maximally in the far-red region. This domain is also found in FhlA (formate hydrogen lyase transcriptional activator) and NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54. This domain can bind biliverdine and phycocyanobilin (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 133 matched cddid_all.tbl CDD pfam01591 pfam01591 396253 6PF2K 6-phosphofructo-2-kinase. This enzyme occurs as a bifunctional enzyme with fructose-2,6-bisphosphatase. The bifunctional enzyme catalyzes both the synthesis and degradation of fructose-2,6-bisphosphate, a potent regulator of glycolysis. This enzyme contains a P-loop motif. 223 matched cddid_all.tbl CDD pfam01592 pfam01592 426336 NifU_N NifU-like N terminal domain. This domain is found in NifU in combination with pfam01106. This domain is found on isolated in several bacterial species. The nif genes are responsible for nitrogen fixation. However this domain is found in bacteria that do not fix nitrogen, so it may have a broader significance in the cell than nitrogen fixation. These proteins appear to be scaffold proteins for iron-sulfur clusters. 127 matched cddid_all.tbl CDD pfam01593 pfam01593 396255 Amino_oxidase Flavin containing amine oxidoreductase. This family consists of various amine oxidases, including maze polyamine oxidase (PAO)and various flavin containing monoamine oxidases (MAO). The aligned region includes the flavin binding site of these enzymes. The family also contains phytoene dehydrogenases and related enzymes. In vertebrates MAO plays an important role regulating the intracellular levels of amines via there oxidation; these include various neurotransmitters, neurotoxins and trace amines. In lower eukaryotes such as aspergillus and in bacteria the main role of amine oxidases is to provide a source of ammonium. PAOs in plants, bacteria and protozoa oxidase spermidine and spermine to an aminobutyral, diaminopropane and hydrogen peroxide and are involved in the catabolism of polyamines. Other members of this family include tryptophan 2-monooxygenase, putrescine oxidase, corticosteroid binding proteins and antibacterial glycoproteins. 446 matched cddid_all.tbl CDD pfam01594 pfam01594 279875 AI-2E_transport AI-2E family transporter. This family includes four different proteins from E. coli alone. One of them, YdgG or TqsA, has been shown to mediate transport of the quorum-sensing signal autoinducer 2 (AI-2). It is not clear if TqsA enhances secretion of AI-2 or inhibits AI-2 uptake. By altering the intracellular concentration of AI-2, TqsA affects gene expression in biofilms and biofilm formation. TsqA belongs to the AI-2 exporter (AI-2E) superfamily. 327 matched cddid_all.tbl CDD pfam01595 pfam01595 460260 CNNM Cyclin M transmembrane N-terminal domain. This transmembrane domain is found in metal transporter proteins such as cyclin M 1/2 (CNNM). CNNMs are integral membrane proteins that are conserved from bacteria to humans. CNNM family members influence metal ion homeostasis through mechanisms that may not involve direct membrane transport of the ions. Structurally, CNNMs are complex proteins that contain an extracellular N-terminal domain preceding a transmembrane domain, a 'Bateman module', which consists of two cystathionine- beta-synthase (CBS) domains pfam00571, and a C-terminal cNMP (cyclic nucleotide monophosphate) binding domain. This entry describes the CNNM transmembrane domain which contains four hydrophobic regions and forms a dimer through hydrophobic contacts between TM2 and TM3, in which each chain is composed of three transmembrane helices (TM1-3), a pair of short helices exposed on the intracellular side, and a juxtamembrane (JM) helix that forms a belt-like structure. The homodimer adopts an inward-facing conformation with a negatively charged cavity containing a conserved pi-helical turn in TM3 that coordinates a Mg2 ion. 183 matched cddid_all.tbl CDD pfam01596 pfam01596 396257 Methyltransf_3 O-methyltransferase. Members of this family are O-methyltransferases. The family includes catechol o-methyltransferase, caffeoyl-CoA O-methyltransferase and a family of bacterial O-methyltransferases that may be involved in antibiotic production. 203 matched cddid_all.tbl CDD pfam01597 pfam01597 396258 GCV_H Glycine cleavage H-protein. This is a family of glycine cleavage H-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyzes the catabolism of glycine in eukaryotes. A lipoyl group is attached to a completely conserved lysine residue. The H protein shuttles the methylamine group of glycine from the P protein to the T protein. 122 matched cddid_all.tbl CDD pfam01599 pfam01599 460261 Ribosomal_S27 Ribosomal protein S27a. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilization and is required for efficient ribosome biogenesis. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins. 43 matched cddid_all.tbl CDD pfam01600 pfam01600 460262 CoV_S1 Coronavirus spike glycoprotein S1. This family represents the spike glycoprotein (S) of coronaviruses. The spike protein is arranged in trimers on the surface of the viral membrane and is essential for viral entry. The spike protein is translated as a large polypeptide that is subsequently cleaved to the distal S1, responsible for receptor binding, and the membrane-anchored S2 responsible for membrane fusion. The coronavirus (SARS-CoV) S1 subunit is composed of two distinct domains: an N-terminal domain (S1 NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Each of these domains have been implicated in binding to host receptors. However, most coronaviruses are not known to utilize both the S1 NTD and S1 RBD for viral entry. This entry contains spike protein from both alpha and gamma coronaviruses but excludes the spike protein from beta-coronaviruses such as SARS-CoV. 412 matched cddid_all.tbl CDD pfam01601 pfam01601 460263 CoV_S2 Coronavirus spike glycoprotein S2. The coronavirus spike glycoprotein forms the characteriztic 'corona' after which the group is named. The Spike glycoprotein is translated as a large polypeptide that is subsequently cleaved to S1 pfam01600 and S2,. The S2 subunit normally contains multiple key components, including one or more fusion peptides (FP), a second proteolytic site (S2') and two conserved heptad repeats (HRs), driving membrane penetration and virus-cell fusion. The HRs can trimerize into a coiled-coil structure built of three HR1-HR2 helical hairpins presenting as a canonical six-helix bundle and drag the virus envelope and the host cell bilayer into close proximity, preparing for fusion to occur. 502 matched cddid_all.tbl CDD pfam01602 pfam01602 396262 Adaptin_N Adaptin N terminal region. This family consists of the N terminal region of various alpha, beta and gamma subunits of the AP-1, AP-2 and AP-3 adaptor protein complexes. The adaptor protein (AP) complexes are involved in the formation of clathrin-coated pits and vesicles. The N-terminal region of the various adaptor proteins (APs) is constant by comparison to the C-terminal which is variable within members of the AP-2 family; and it has been proposed that this constant region interacts with another uniform component of the coated vesicles. 523 matched cddid_all.tbl CDD pfam01603 pfam01603 460264 B56 Protein phosphatase 2A regulatory B subunit (B56 family). Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism. The ability of this widely distributed heterotrimeric enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits (See also pfam01240), this family is called the B56 family. 404 matched cddid_all.tbl CDD pfam01606 pfam01606 250739 Arteri_env Arterivirus envelope protein. This family consists of viral envelope proteins from the arterivirus genus; this includes porcine reproductive and respiratory virus (PRRSV) envelope protein GP3 and lactate dehydrogenase elevating virus (LDV) structural glycoprotein. Arteriviruses consists of positive ssRNA and do not have a DNA stage. 211 matched cddid_all.tbl CDD pfam01607 pfam01607 426342 CBM_14 Chitin binding Peritrophin-A domain. This domain is called the Peritrophin-A domain and is found in chitin binding proteins particularly peritrophic matrix proteins of insects and animal chitinases. Copies of the domain are also found in some baculoviruses. Relevant references that describe proteins with this domain include. It is an extracellular domain that contains six conserved cysteines that probably form three disulphide bridges. Chitin binding has been demonstrated for a protein containing only two of these domains. 53 matched cddid_all.tbl CDD pfam01608 pfam01608 460265 I_LWEQ I/LWEQ domain. I/LWEQ domains bind to actin. It has been shown that the I/LWEQ domains from mouse talin and yeast Sla2p interact with F-actin. I/LWEQ domains can be placed into four major groups based on sequence similarity: (1) Metazoan talin; (2) Dictyostelium TalA/TalB and SLA110; (3) metazoan Hip1p; and (4) yeast Sla2p. The domain has four conserved blocks, the name of the domain is derived from the initial conserved amino acid of each of the four blocks. 149 matched cddid_all.tbl CDD pfam01609 pfam01609 376573 DDE_Tnp_1 Transposase DDE domain. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. This family contains transposases for IS4, IS421, IS5377, IS427, IS402, IS1355, IS5, which was original isolated in bacteriophage lambda. 196 matched cddid_all.tbl CDD pfam01610 pfam01610 426344 DDE_Tnp_ISL3 Transposase. Transposase proteins are necessary for efficient DNA transposition. Contains transposases for IS204, IS1001, IS1096 and IS1165. 238 matched cddid_all.tbl CDD pfam01611 pfam01611 279888 Filo_glycop Filovirus glycoprotein. This family includes an extracellular region from the envelope glycoprotein of Ebola and Marburg viruses. This region is also produced as a separate transcript that gives rise to a non-structural, secreted glycoprotein, which is produced in large amounts and has an unknown function. Processing of this protein may be involved in viral pathogenicity. 395 matched cddid_all.tbl CDD pfam01612 pfam01612 396266 DNA_pol_A_exo1 3'-5' exonuclease. This domain is responsible for the 3'-5' exonuclease proofreading activity of E. coli DNA polymerase I (polI) and other enzymes, it catalyzes the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D). Werner syndrome is a human genetic disorder causing premature aging; the WRN protein has helicase activity in the 3'-5' direction. The FFA-1 protein is required for formation of a replication foci and also has helicase activity; it is a homolog of the WRN protein. RNase D is a 3'-5' exonuclease involved in tRNA processing. Also found in this family is the autoantigen PM/Scl thought to be involved in polymyositis-scleroderma overlap syndrome. 173 matched cddid_all.tbl CDD pfam01613 pfam01613 460266 Flavin_Reduct Flavin reductase like domain. This is a flavin reductase family consisting of enzymes known to be flavin reductases as well as various oxidoreductase and monooxygenase components. VlmR is a flavin reductase that functions in a two-component enzyme system to provide isobutylamine N-hydroxylase with reduced flavin and may be involved in the synthesis of valanimycin. SnaC is a flavin reductase that provides reduced flavin for the oxidation of pristinamycin IIB to pristinamycin IIA as catalyzed by SnaA, SnaB heterodimer. This flavin reductase region characterized by enzymes of the family is present in the C-terminus of potential FMN proteins from Synechocystis sp. suggesting it is a flavin reductase domain. 149 matched cddid_all.tbl CDD pfam01614 pfam01614 426346 IclR Bacterial transcriptional regulator. This family of bacterial transcriptional regulators includes the glycerol operon regulatory protein and acetate operon repressor both of which are members of the iclR family. These proteins have a Helix-Turn-Helix motif at the N-terminus. However this family covers the C-terminal region that binds to regulatory substrates including Glyoxylate, allantoin/ate, indole, aromatic hydrocarbons, sugar acids, succinic semialdehyde, benzoate derivatives, ascorbic acid, glycerol-3-phosphate, glyceraldehyde-3-phosphate and pyruvate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 128 matched cddid_all.tbl CDD pfam01616 pfam01616 460267 Orbi_NS3 Orbivirus NS3. The function of this Orbivirus non structural protein is uncertain. However it may play a role on release of the virus from infected cells. 193 matched cddid_all.tbl CDD pfam01617 pfam01617 366729 Surface_Ag_2 Surface antigen. This family includes a number of bacterial surface antigens expressed on the surface of pathogens. 247 matched cddid_all.tbl CDD pfam01618 pfam01618 460268 MotA_ExbB MotA/TolQ/ExbB proton channel family. This family groups together integral membrane proteins that appear to be involved translocation of proteins across a membrane. These proteins are probably proton channels. MotA is an essential component of the flageller motor that uses a proton gradient to generate rotational motion in the flageller. ExbB is part of the TonB-dependent transduction complex. The TonB complex uses the proton gradient across the inner bacterial membrane to transport large molecules across the outer bacterial membrane. 120 matched cddid_all.tbl CDD pfam01619 pfam01619 426348 Pro_dh Proline dehydrogenase. 296 matched cddid_all.tbl CDD pfam01620 pfam01620 460269 Pollen_allerg_2 Ribonuclease (pollen allergen). This family contains grass pollen proteins of group V. Swiss:Q40963 has been shown to possess ribonuclease activity. 155 matched cddid_all.tbl CDD pfam01621 pfam01621 279897 Fusion_gly_K Cell fusion glycoprotein K. This protein is probably an integral membrane bound glycoprotein that is involved in viral fusion with the host cell. 339 matched cddid_all.tbl CDD pfam01623 pfam01623 250753 Carla_C4 Carlavirus putative nucleic acid binding protein. This family of carlavirus nucleic acid binding proteins includes a motif for a potential C-4 type zinc finger this has four highly conserved cysteine residues and is a conserved feature of the carlaviruses 3' terminal ORF. These proteins may function as viral transcriptional regulators. The carlavirus family includes garlic latent virus and potato virus S and M, these viruses are positive strand, ssRNA with no DNA stage. 91 matched cddid_all.tbl CDD pfam01624 pfam01624 426350 MutS_I MutS domain I. This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam05188, pfam05192 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with globular domain I, which is involved in DNA binding, in Thermus aquaticus MutS as characterized in. 113 matched cddid_all.tbl CDD pfam01625 pfam01625 460270 PMSR Peptide methionine sulfoxide reductase. This enzyme repairs damaged proteins. Methionine sulfoxide in proteins is reduced to methionine. 153 matched cddid_all.tbl CDD pfam01627 pfam01627 426352 Hpt Hpt domain. The histidine-containing phosphotransfer (HPt) domain is a novel protein module with an active histidine residue that mediates phosphotransfer reactions in the two-component signaling systems. A multistep phosphorelay involving the HPt domain has been suggested for these signaling pathways. The crystal structure of the HPt domain of the anaerobic sensor kinase ArcB has been determined. The domain consists of six alpha helices containing a four-helix bundle-folding. The pattern of sequence similarity of the HPt domains of ArcB and components in other signaling systems can be interpreted in light of the three-dimensional structure and supports the conclusion that the HPt domains have a common structural motif both in prokaryotes and eukaryotes. In S. cerevisiae ypd1p this domain has been shown to contain a binding surface for Ssk1p (response regulator receiver domain containing protein pfam00072). 84 matched cddid_all.tbl CDD pfam01628 pfam01628 460271 HrcA HrcA protein C terminal domain. HrcA is found to negatively regulate the transcription of heat shock genes. HrcA contains an amino terminal helix-turn-helix domain, however this corresponds to the carboxy terminal domain. 221 matched cddid_all.tbl CDD pfam01629 pfam01629 426354 DUF22 Domain of unknown function DUF22. This domain is found in 1 to 3 copies in archaebacterial proteins. The function of the domain is unknown. This family appears to be expanded in Archaeoglobus fulgidus. 106 matched cddid_all.tbl CDD pfam01630 pfam01630 460272 Glyco_hydro_56 Hyaluronidase. 332 matched cddid_all.tbl CDD pfam01632 pfam01632 460273 Ribosomal_L35p Ribosomal protein L35. 61 matched cddid_all.tbl CDD pfam01633 pfam01633 396278 Choline_kinase Choline/ethanolamine kinase. Choline kinase catalyzes the committed step in the synthesis of phosphatidylcholine by the CDP-choline pathway. This alignment covers the protein kinase portion of the protein. The divergence of this family makes it very difficult to create a model that specifically predicts choline/ethanolamine kinases only. However if [add Pfam ID here for Choline_kinase_C] is also present then it is definitely a member of this family. 211 matched cddid_all.tbl CDD pfam01634 pfam01634 460274 HisG ATP phosphoribosyltransferase. 157 matched cddid_all.tbl CDD pfam01635 pfam01635 460275 CoV_M Coronavirus M matrix/glycoprotein. This family consists of various coronavirus matrix proteins which are transmembrane glycoproteins. The membrane (M) protein is the most abundant structural protein and defines the shape of the viral envelope, being the central organizer of coronavirus assembly. M proteins play a critical role in protein-protein interactions (as well as protein-RNA interactions) since virus-like particle (VLP) formation in many CoVs requires only the M and envelope (E) proteins for efficient virion assembly. Interaction of spike (S) with M is necessary for retention of S in the ER-Golgi intermediate compartment (ERGIC)/Golgi complex and its incorporation into new virions; binding of M to nucleocapsid (N) proteins stabilizes the nucleocapsid. Together, M and E protein make up the viral envelope and their interaction is sufficient for the production and release of virus-like particles (VLPs). 208 matched cddid_all.tbl CDD pfam01636 pfam01636 426359 APH Phosphotransferase enzyme family. This family consists of bacterial antibiotic resistance proteins, which confer resistance to various aminoglycosides they include: aminoglycoside 3'-phosphotransferase or kanamycin kinase / neomycin-kanamycin phosphotransferase and streptomycin 3''-kinase or streptomycin 3''-phosphotransferase. The aminoglycoside phosphotransferases inactivate aminoglycoside antibiotics via phosphorylation. This family also includes homoserine kinase. This family is related to fructosamine kinase pfam03881. 239 matched cddid_all.tbl CDD pfam01637 pfam01637 376582 ATPase_2 ATPase domain predominantly from Archaea. This family contain a conserved P-loop motif that is involved in binding ATP. There are eukaryote members as well as archaeal members in this family. 222 matched cddid_all.tbl CDD pfam01638 pfam01638 460276 HxlR HxlR-like helix-turn-helix. HxlR, a member of this family, is a DNA-binding protein that acts as a positive regulator of the formaldehyde-inducible hxlAB operon in Bacillus subtilis. 91 matched cddid_all.tbl CDD pfam01639 pfam01639 279910 v110 Viral family 110. This family of viral proteins is known as the 110 family. The function of members of this family is unknown. The family contains a central cysteine rich region with eight conserved cysteines. Some members of the family contains two copies of the cysteine rich region. 102 matched cddid_all.tbl CDD pfam01640 pfam01640 460277 Peptidase_C10 Peptidase C10 family. This family represents just the active peptide part of these proteins. Residues 1-120 are not part of the model as they form the pro-peptide, which before cleavage blocks the active site from the substrate. The catalytic residues of histidine and cysteine are brought close together at the active site by the folding of the active peptide. 187 matched cddid_all.tbl CDD pfam01641 pfam01641 460278 SelR SelR domain. Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterized with respect to structure and function. However, recent studies revealed that MsrA is only specific for methionine-S-sulfoxides. Because oxidized methionines occur in a mixture of R and S isomers in vivo, it was unclear how stereo-specific MsrA could be responsible for the reduction of all protein methionine sulfoxides. It appears that a second methionine sulfoxide reductase, SelR, evolved that is specific for methionine-R-sulfoxides, the activity that is different but complementary to that of MsrA. Thus, these proteins, working together, could reduce both stereoisomers of methionine sulfoxide. This domain is found both in SelR proteins and fused with the peptide methionine sulfoxide reductase enzymatic domain pfam01625. The domain has two conserved cysteine and histidines. The domain binds both selenium and zinc. The final cysteine is found to be replaced by the rare amino acid selenocysteine in some members of the family. This family has methionine-R-sulfoxide reductase activity. 120 matched cddid_all.tbl CDD pfam01642 pfam01642 460279 MM_CoA_mutase Methylmalonyl-CoA mutase. The enzyme methylmalonyl-CoA mutase is a member of a class of enzymes that uses coenzyme B12 (adenosylcobalamin) as a cofactor. The enzyme induces the formation of an adenosyl radical from the cofactor. This radical then initiates a free-radical rearrangement of its substrate, succinyl-CoA, to methylmalonyl-CoA. 503 matched cddid_all.tbl CDD pfam01643 pfam01643 366738 Acyl-ACP_TE Acyl-ACP thioesterase. This family consists of various acyl-acyl carrier protein (ACP) thioesterases (TE) these terminate fatty acyl group extension via hydrolysing an acyl group on a fatty acid. 248 matched cddid_all.tbl CDD pfam01644 pfam01644 426363 Chitin_synth_1 Chitin synthase. This region is found commonly in chitin synthases classes I, II and III. Chitin a linear homopolymer of GlcNAc residues, it is an important component of the cell wall of fungi and is synthesized on the cytoplasmic surface of the cell membrane by membrane bound chitin synthases. 163 matched cddid_all.tbl CDD pfam01645 pfam01645 396287 Glu_synthase Conserved region in glutamate synthase. This family represents a region of the glutamate synthase protein. This region is expressed as a separate subunit in the glutamate synthase alpha subunit from archaebacteria, or part of a large multidomain enzyme in other organizms. The aligned region of these proteins contains a putative FMN binding site and Fe-S cluster. 367 matched cddid_all.tbl CDD pfam01646 pfam01646 307668 Herpes_UL24 Herpes virus proteins UL24 and UL76. This family consists of various herpes virus proteins; the gene 20 product, U49 protein, UL24 and UL76 proteins and BXRF1. The UL24 gene (product of the 24th ORF) is not essential for virus replication, and mutants with lesions in UL24 show a reduced ability to replicate in tissue culture and have reduced thymidine kinase activity, as the UL24 gene overlaps with thymidine kinase. The family of proteins is involved in viral production, latency, and reactivation. Protein UL76 presents as globular aggresomes in the nuclei of transiently transfected cells. Bioinformatic analyses predict that UL76 has a propensity for aggregation and targets cellular proteins implicated in protein folding and ubiquitin-proteasome systems. UL76 interacts with the VWA domain of S5a, the 26S proteasome non-ATPase regulatory subunit 4 (or PSMD4, or Rpn10), forming a complex in the late phase of infection. 176 matched cddid_all.tbl CDD pfam01648 pfam01648 426364 ACPS 4'-phosphopantetheinyl transferase superfamily. Members of this family transfers the 4'-phosphopantetheine (4'-PP) moiety from coenzyme A (CoA) to the invariant serine of pfam00550. This post-translational modification renders holo-ACP capable of acyl group activation via thioesterification of the cysteamine thiol of 4'-PP. This superfamily consists of two subtypes: The ACPS type and the Sfp type. The structure of the Sfp type is known, which shows the active site accommodates a magnesium ion. The most highly conserved regions of the alignment are involved in binding the magnesium ion. 111 matched cddid_all.tbl CDD pfam01649 pfam01649 460280 Ribosomal_S20p Ribosomal protein S20. Bacterial ribosomal protein S20 interacts with 16S rRNA. 76 matched cddid_all.tbl CDD pfam01650 pfam01650 396290 Peptidase_C13 Peptidase C13 family. Members of this family are asparaginyl peptidases. The blood fluke parasite Schistosoma mansoni has at least five Clan CA cysteine peptidases in its digestive tract including cathepsins B (2 isoforms), C, F and L. All have been recombinantly expressed as active enzymes, albeit in various stages of activation. In addition, a Clan CD peptidase, termed asparaginyl endopeptidase or 'legumain' has been identified. This has formerly been characterized as a 'haemoglobinase', but this term is probably incorrect. Two cDNAs have been described for Schistosoma mansoni legumain; one encodes an active enzyme whereas the active site cysteine residue encoded by the second cDNA is substituted by an asparagine residue. Both forms have been recombinantly expressed. 257 matched cddid_all.tbl CDD pfam01652 pfam01652 460281 IF4E Eukaryotic initiation factor 4E. 158 matched cddid_all.tbl CDD pfam01653 pfam01653 396292 DNA_ligase_aden NAD-dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor. This domain is the catalytic adenylation domain. The NAD+ group is covalently attached to this domain at the lysine in the KXDG motif of this domain. This enzyme- adenylate intermediate is an important feature of the proposed catalytic mechanism. 318 matched cddid_all.tbl CDD pfam01654 pfam01654 460282 Cyt_bd_oxida_I Cytochrome bd terminal oxidase subunit I. This family are the alternative oxidases found in many bacteria which oxidize ubiquinol and reduce oxygen as part of the electron transport chain. This family is the subunit I of the oxidase E. coli has two copies of the oxidase, bo and bd', both of which are represented here In some nitrogen fixing bacteria, e.g. Klebsiella pneumoniae this oxidase is responsible for removing oxygen in microaerobic conditions, making the oxidase required for nitrogen fixation. This subunit binds a single b-haem, through ligands at His186 and Met393 (using SW:P11026 numbering). In addition His19 is a ligand for the haem b found in subunit II 428 matched cddid_all.tbl CDD pfam01655 pfam01655 460283 Ribosomal_L32e Ribosomal protein L32. This family includes ribosomal protein L32 from eukaryotes and archaebacteria. 108 matched cddid_all.tbl CDD pfam01656 pfam01656 426369 CbiA CobQ/CobB/MinD/ParA nucleotide binding domain. This family consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from S.typhimurium, and CobQ from R. capsulatus. These amidases catalyze amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria. The family also contains dethiobiotin synthetases as well as the plasmid partitioning proteins of the MinD/ParA family. 228 matched cddid_all.tbl CDD pfam01657 pfam01657 460284 Stress-antifung Salt stress response/antifungal. This domain is often found in association with the kinase domains pfam00069 or pfam07714. In many proteins it is duplicated. It contains six conserved cysteines which are involved in disulphide bridges. It has a role in salt stress response and has antifungal activity. 96 matched cddid_all.tbl CDD pfam01658 pfam01658 460285 Inos-1-P_synth Myo-inositol-1-phosphate synthase. This is a family of myo-inositol-1-phosphate synthases. Inositol-1-phosphate catalyzes the conversion of glucose-6- phosphate to inositol-1-phosphate, which is then dephosphorylated to inositol. Inositol phosphates play an important role in signal transduction. 104 matched cddid_all.tbl CDD pfam01659 pfam01659 279928 Luteo_Vpg Luteovirus putative VPg genome linked protein. This family consists of several putative genome linked proteins. The genomic RNA of luteoviruses are linked to virally encoded genome proteins (VPg). Open reading frame 4 is thought to encode the VPg in Soybean dwarf luteovirus. Luteoviruses have isometric capsids that contain a positive stand ssRNA genome, they have no DNA stage during their replication. 105 matched cddid_all.tbl CDD pfam01660 pfam01660 396298 Vmethyltransf Viral methyltransferase. This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily. 308 matched cddid_all.tbl CDD pfam01661 pfam01661 460286 Macro Macro domain. The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent: in certain cases it is believed to bind non-covalently; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein. This domain is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein 4 and also in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alpha-viruses and coronaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria and eukaryotes. The 3D structure of the SARS-CoV Macro domain has a mixed alpha/beta fold consisting of a central seven-stranded twisted mixed beta sheet sandwiched between two alpha helices on one face, and three on the other. The final alpha-helix, located on the edge of the central beta-sheet, forms the C terminus of the protein. The crystal structure of AF1521 (a Macro domain-only protein from Archaeoglobus fulgidus) has also been reported and compared with other Macro domain containing proteins. Several Macro domain only proteins are shorter than AF1521, and appear to lack either the first strand of the beta-sheet or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site. 116 matched cddid_all.tbl CDD pfam01663 pfam01663 396300 Phosphodiest Type I phosphodiesterase / nucleotide pyrophosphatase. This family consists of phosphodiesterases, including human plasma-cell membrane glycoprotein PC-1 / alkaline phosphodiesterase i / nucleotide pyrophosphatase (nppase). These enzymes catalyze the cleavage of phosphodiester and phosphosulfate bonds in NAD, deoxynucleotides and nucleotide sugars. Also in this family is ATX an autotaxin, tumour cell motility-stimulating protein which exhibits type I phosphodiesterases activity. The alignment encompasses the active site. Also present with in this family is 60-kDa Ca2+-ATPase form F. odoratum. 343 matched cddid_all.tbl CDD pfam01664 pfam01664 366748 Reo_sigma1 Reovirus viral attachment protein sigma 1. This family consists of the reovirus sigma 1 hemagglutinin, cell attachment protein. This glycoprotein is a minor capsid protein and also determines the serotype-specific humoral immune response. Sigma 1 consist of a fibrous tail and a globular head. The head has important roles in the cell attachment function of sigma 1 and determinant of the type-specific humoral immune response. Reovirus is part of the orthoreovirus group of retroviruses with, a dsRNA genome. Also present in this family is bacteriophage SF6 Lysozyme. 216 matched cddid_all.tbl CDD pfam01665 pfam01665 279933 Rota_NSP3 Rotavirus non-structural protein NSP3. This family consist of rotaviral non-structural RNA binding protein 34 (NS34 or NSP3). The NSP3 protein has been shown to bind viral RNA. The NSP3 protein consists of 3 conserved functional domains; a basic region which binds ssRNA, a region containing heptapeptide repeats mediating oligomerization and a leucine zipper motif. NSP3 may play a central role in replication and assembly of genomic RNA structures. Rotaviruses have a dsRNA genome and are a major cause cause of acute gastroenteritis in the young of many species. The rotavirus non-structural protein NSP3 is a sequence-specific RNA binding protein that binds the nonpolyadenylated 3' end of the rotavirus mRNAs. NSP3 also interacts with the translation initiation factor eIF4GI and competes with the poly(A) binding protein. 311 matched cddid_all.tbl CDD pfam01666 pfam01666 426373 DX DX module. This domain has no known function. It is found in several C. elegans proteins. The domain contains 6 conserved cysteines that probably form three disulphide bridges. 76 matched cddid_all.tbl CDD pfam01667 pfam01667 279935 Ribosomal_S27e Ribosomal protein S27. 55 matched cddid_all.tbl CDD pfam01668 pfam01668 460287 SmpB SmpB protein. 143 matched cddid_all.tbl CDD pfam01669 pfam01669 460288 Myelin_MBP Myelin basic protein. 144 matched cddid_all.tbl CDD pfam01670 pfam01670 396303 Glyco_hydro_12 Glycosyl hydrolase family 12. 207 matched cddid_all.tbl CDD pfam01671 pfam01671 460289 ASFV_360 African swine fever virus multigene family 360 protein. The multigene family 360 protein are found within the African swine fever virus (ASF) genome which consist of dsDNA and has similar structural features to the poxyviruses. The biological function of this family is not known. Although Swiss:Q65137 is a major structural protein. 215 matched cddid_all.tbl CDD pfam01672 pfam01672 376591 Plasmid_parti Putative plasmid partition protein. This family consists of conserved hypothetical proteins from Borrelia burgdorferi the lyme disease spirochaete, some of which are putative plasmid partition proteins. 85 matched cddid_all.tbl CDD pfam01673 pfam01673 279941 Herpes_env Herpesvirus putative major envelope glycoprotein. This family consists of probable major envelope glycoproteins from members of the herpesviridae including herpes simplex virus, human cytomegalovirus and varicella-zoster virus. Members of the herpesviridae have a dsDNA genome and do not have a RNA stage during there replication. 526 matched cddid_all.tbl CDD pfam01674 pfam01674 396304 Lipase_2 Lipase (class 2). This family consists of hypothetical C. elegans proteins and lipases. Lipases or triacylglycerol acylhydrolases hydrolyse ester bonds in triacylglycerol giving diacylglycerol, monoacylglycerol, glycerol and free fatty acids. Swiss:P37957 is an extracellular lipase from B. subtilis 168. 218 matched cddid_all.tbl CDD pfam01676 pfam01676 396305 Metalloenzyme Metalloenzyme superfamily. This family includes phosphopentomutase and 2,3-bisphosphoglycerate-independent phosphoglycerate mutase. This family is also related to pfam00245. The alignment contains the most conserved residues that are probably involved in metal binding and catalysis. 410 matched cddid_all.tbl CDD pfam01677 pfam01677 426376 Herpes_UL7 Herpesvirus UL7 like. This family consists of various functionally undefined proteins from the herpesviridae and UL7 from bovine herpes virus. UL7 is not essential for virus replication in cell culture, and is found localized in the cytoplasm of infected cells accumulated around the nucleus but could not be detected in purified virions. Members of the herpesviridae have a dsDNA genome and do not have a RNA stage during there replication. 213 matched cddid_all.tbl CDD pfam01678 pfam01678 396306 DAP_epimerase Diaminopimelate epimerase. Diaminopimelate epimerase contains two domains of the same alpha/beta fold, both contained in this family. 119 matched cddid_all.tbl CDD pfam01679 pfam01679 460290 Pmp3 Proteolipid membrane potential modulator. Pmp3 is an evolutionarily conserved proteolipid in the plasma membrane which, in S. pombe, is transcriptionally regulated by the Spc1 stress MAPK (mitogen-activated protein kinases) pathway. It functions to modulate the membrane potential, particularly to resist high cellular cation concentration. In eukaryotic organizms, stress-activated mitogen-activated protein kinases play crucial roles in transmitting environmental signals that will regulate gene expression for allowing the cell to adapt to cellular stress. Pmp3-like proteins are highly conserved in bacteria, yeast, nematode and plants. 49 matched cddid_all.tbl CDD pfam01680 pfam01680 460291 SOR_SNZ SOR/SNZ family. Members of this family are enzymes involved in a new pathway of pyridoxine/pyridoxal 5-phosphate biosynthesis. This family was formerly known as UPF0019. 206 matched cddid_all.tbl CDD pfam01681 pfam01681 460292 C6 C6 domain. This domain of unknown function is found in the C. elegans protein Swiss:Q19522. It is presumed to be an extracellular domain. The C6 domain contains six conserved cysteine residues in most copies of the domain. However some copies of the domain are missing cysteine residues 1 and 3 suggesting that these form a disulphide bridge. 90 matched cddid_all.tbl CDD pfam01682 pfam01682 460293 DB DB module. This domain has no known function. It is found in several C. elegans proteins. The domain contains 12 conserved cysteines that probably form six disulphide bridges. This domain is found associated with ig pfam00047 and fn3 pfam00041 domains, as well as in some lipases pfam00657. 98 matched cddid_all.tbl CDD pfam01683 pfam01683 460294 EB EB module. This domain has no known function. It is found in several C. elegans proteins. The domain contains 8 conserved cysteines that probably form four disulphide bridges. This domain is found associated with kunitz domains pfam00014. 52 matched cddid_all.tbl CDD pfam01684 pfam01684 366757 ET ET module. This domain has no known function. It is found in several C. elegans proteins. The domain contains 8-10 conserved cysteines that probably form 4-5 disulphide bridges. By inspection of the conservation of cysteines it looks like cysteines 1,2,3,4,9 and 10 are always present and that sometimes the pair 5 and 8 or the pair 6 and 7 are missing. This suggests that cysteines 5/8 and 6/7 make disulphide bridges. 78 matched cddid_all.tbl CDD pfam01686 pfam01686 396312 Adeno_Penton_B Adenovirus penton base protein. This family consists of various adenovirus penton base proteins, from both the Mastadenoviradae having mammalian hosts and the Aviadenoviradae having avian hosts. The penton base is a major structural protein forming part of the penton which consists of a base and a fibre, the pentons hold a morphologically prominent position at the vertex capsomer in the adenovirus particle. In mammalian adenovirus there is only one tail on each base where as in avian adenovirus there are two. 450 matched cddid_all.tbl CDD pfam01687 pfam01687 460295 Flavokinase Riboflavin kinase. This family represents the C-terminal region of the bifunctional riboflavin biosynthesis protein known as RibC in Bacillus subtilis. The RibC protein from Bacillus subtilis has both flavokinase and flavin adenine dinucleotide synthetase (FAD-synthetase) activities. RibC plays an essential role in the flavin metabolism. This domain is thought to have kinase activity. 123 matched cddid_all.tbl CDD pfam01688 pfam01688 279953 Herpes_gI Alphaherpesvirus glycoprotein I. This family consists of glycoprotein I form various members of the alphaherpesvirinae these include herpesvirus, varicella-zoster virus and pseudorabies virus. Glycoprotein I (gI) is important during natural infection, mutants lacking gI produce smaller lesions at the site of infection and show reduced neuronal spread. gI forms a heterodimeric complex with gE; this complex displays Fc receptor activity (binds to the Fc region of immunoglobulin). Glycoproteins are also important in the production of virus-neutralising antibodies and cell mediated immunity. The alphaherpesvirinae have a dsDNA gnome and have no RNA stage during viral replication. 155 matched cddid_all.tbl CDD pfam01690 pfam01690 279954 PLRV_ORF5 Potato leaf roll virus readthrough protein. This family consists mainly of the potato leaf roll virus readthrough protein. This is generated via a readthrough of open reading frame 3 a coat protein allowing transcription of open reading frame 5 to give an extended coat protein with a large c-terminal addition or read through domain. The readthrough protein is thought to play a role in the circulative aphid transmission of potato leaf roll virus. Also in the family is open reading frame 6 from beet western yellows virus and potato leaf roll virus both luteovirus and an unknown protein from cucurbit aphid-borne yellows virus a closterovirus. 524 matched cddid_all.tbl CDD pfam01691 pfam01691 279955 Adeno_E1B_19K Adenovirus E1B 19K protein / small t-antigen. This family consists of adenovirus E1B 19K protein or small t-antigen. The E1B 19K protein inhibits E1A induced apoptosis and hence prolongs the viability of the host cell. It can also inhibit apoptosis mediated by tumour necrosis factor alpha and Fas antigen. E1B 19K blocks apoptosis by interacting with and inhibiting the p53-inducible and death- promoting Bax protein. The E1B region of adenovirus encodes two proteins E1B 19K the small t-antigen as found in this family and E1B 55K the large t-antigen which is not found in this family; both of these proteins inhibit E1A induced apoptosis. 135 matched cddid_all.tbl CDD pfam01692 pfam01692 460296 Paramyxo_C Paramyxovirus non-structural protein C. This family consist of the C proteins (C', C, Y1, Y2) found in Paramyxovirinae; human parainfluenza, and sendai virus. The C proteins effect viral RNA synthesis having both a positive and negative effect during the course of infection. Paramyxovirus have a negative strand ssRNA genome of 15.3kb form which six mRNAs are transcribed, five of these are monocistronic. The P/C mRNA is polycistronic and has two overlapping open reading frames P and C, C encodes the nested C proteins C', C, Y1 and Y2. 204 matched cddid_all.tbl CDD pfam01693 pfam01693 460297 Cauli_VI Caulimovirus viroplasmin. This family consists of various caulimovirus viroplasmin proteins. The viroplasmin protein is encoded by gene VI and is the main component of viral inclusion bodies or viroplasms. Inclusions are the site of viral assembly, DNA synthesis and accumulation. Two domains exist within gene VI corresponding approximately to the 5' third and middle third of gene VI, these influence systemic infection in a light-dependent manner. 44 matched cddid_all.tbl CDD pfam01694 pfam01694 426384 Rhomboid Rhomboid family. This family contains integral membrane proteins that are related to Drosophila rhomboid protein. Members of this family are found in bacteria and eukaryotes. Rhomboid promotes the cleavage of the membrane-anchored TGF-alpha-like growth factor Spitz, allowing it to activate the Drosophila EGF receptor. Analysis has shown that Rhomboid-1 is an intramembrane serine protease (EC:3.4.21.105). Parasite-encoded rhomboid enzymes are also important for invasion of host cells by Toxoplasma and the malaria parasite. 147 matched cddid_all.tbl CDD pfam01695 pfam01695 426385 IstB_IS21 IstB-like ATP binding protein. This protein contains an ATP/GTP binding P-loop motif. It is found associated with IS21 family insertion sequences. The function of this protein is unknown, but it may perform a transposase function. 238 matched cddid_all.tbl CDD pfam01696 pfam01696 366761 Adeno_E1B_55K Adenovirus EB1 55K protein / large t-antigen. This family consists of adenovirus E1B 55K protein or large t-antigen. E1B 55K binds p53 the tumour suppressor protein converting it from a transcriptional activator which responds to damaged DNA in to an unregulated repressor of genes with a p53 binding site. This protects the virus against p53 induced host antiviral responses and prevents apoptosis as induced by the adenovirus E1A protein. The E1B region of adenovirus encodes two proteins E1B 55K the large t-antigen as found in this family and E1B 19K pfam01691 the small t-antigen which is not found in this family; both of these proteins inhibit E1A induced apoptosis. This family shows distant similarities to the pectate lyase superfamily. 387 matched cddid_all.tbl CDD pfam01697 pfam01697 426386 Glyco_transf_92 Glycosyltransferase family 92. Members of this family act as galactosyltransferases, belonging to glycosyltransferase family 92. The aligned region contains several conserved cysteine residues and several charged residues that may be catalytic residues. This is supported by the inclusion of this family in the GT-A glycosyl transferase superfamily. 250 matched cddid_all.tbl CDD pfam01698 pfam01698 396318 SAM_LFY Floricaula / Leafy protein SAM domain. This family consists of various plant development proteins which are homologs of floricaula (FLO) and Leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development. LFY proteins have been shown to binds semi-palindromic 19-bp DNA elements through its highly conserved C-terminal DBD. In addition to its well-characterized DBD, LFY possesses a second conserved domain at its amino terminus (LFY-N). This entry represents the SAM domain found in N -terminal of LFY proteins in plants. Crystallographic structure determination of LFY-N shows that LFY-N is a Sterile Alpha Motif (SAM) domain that mediates LFY oligomerization. It allows LFY to bind to regions lacking high-affinity LFYbs (LFY-binding sites) and confers on LFY the ability to access closed chromatin regions. Experiments carried out in plants, revealed that altering the capacity of LFY to oligomerize compromised its floral function and drastically reduced its genome-wide DNA binding. SAM oligomerization has been suggested to have a profound effect on a TF binding landscape by promoting cooperative binding of LFY to DNA, as was proposed for other oligomeric TFs, and it gives LFY access to closed chromatin regions that are notably refractory to TF binding. It has also been suggested that the biochemical properties of the SAM domain are evolutionary conserved in all plant species. 80 matched cddid_all.tbl CDD pfam01699 pfam01699 426387 Na_Ca_ex Sodium/calcium exchanger protein. This is a family of sodium/calcium exchanger integral membrane proteins. This family covers the integral membrane regions of the proteins. Sodium/calcium exchangers regulate intracellular Ca2+ concentrations in many cells; cardiac myocytes, epithelial cells, neurons retinal rod photoreceptors and smooth muscle cells. Ca2+ is moved into or out of the cytosol depending on Na+ concentration. In humans and rats there are 3 isoforms; NCX1 NCX2 and NCX3. 149 matched cddid_all.tbl CDD pfam01700 pfam01700 460298 Orbi_VP3 Orbivirus VP3 (T2) protein. The orbivirus VP3 protein is part of the virus core and makes a 'subcore' shell made up of 120 copies of the 100K protein. VP3 particles can also bind RNA and are fundamental in the early stages of viral core formation. Also found in the family is structural core protein VP2 from broadhaven virus which is similar to VP3 in bluetongue virus. Orbivirus are part of the larger reoviridae which have a dsRNA genome of 10-12 linear segments; orbivirus found in this family include bluetongue virus and epizootic hemorrhagic disease virus. 888 matched cddid_all.tbl CDD pfam01701 pfam01701 396320 PSI_PsaJ Photosystem I reaction centre subunit IX / PsaJ. This family consists of the photosystem I reaction centre subunit IX or PsaJ from various organizms including Synechocystis sp. (strain pcc 6803), Pinus thunbergii (green pine) and Zea mays (maize). PsaJ is a small 4.4kDa, chloroplastal encoded, hydrophobic subunit of the photosystem I reaction complex its function is not yet fully understood. PsaJ can be cross-linked to PsaF and has a single predicted transmembrane domain it has a proposed role in maintaining PsaF in the correct orientation to allow for fast electron transfer from soluble donor proteins to P700+. 37 matched cddid_all.tbl CDD pfam01702 pfam01702 460299 TGT Queuine tRNA-ribosyltransferase. This is a family of queuine tRNA-ribosyltransferases EC:2.4.2.29, also known as tRNA-guanine transglycosylase and guanine insertion enzyme. Queuine tRNA-ribosyltransferase modifies tRNAs for asparagine, aspartic acid, histidine and tyrosine with queuine. It catalyzes the exchange of guanine-34 at the wobble position with 7-aminomethyl-7-deazaguanine, and the addition of a cyclopentenediol moiety to 7-aminomethyl-7-deazaguanine-34 tRNA; giving a hypermodified base queuine in the wobble position. The aligned region contains a zinc binding motif C-x-C-x2-C-x29-H, and important tRNA and 7-aminomethyl-7deazaguanine binding residues. 358 matched cddid_all.tbl CDD pfam01704 pfam01704 460300 UDPGP UTP--glucose-1-phosphate uridylyltransferase. This family consists of UTP--glucose-1-phosphate uridylyltransferases, EC:2.7.7.9. Also known as UDP-glucose pyrophosphorylase (UDPGP) and Glucose-1-phosphate uridylyltransferase. UTP--glucose-1-phosphate uridylyltransferase catalyzes the interconversion of MgUTP + glucose-1-phosphate and UDP-glucose + MgPPi. UDP-glucose is an important intermediate in mammalian carbohydrate interconversion involved in various metabolic roles depending on tissue type. In Dictyostelium (slime mold) mutants in this enzyme abort the development cycle. Also within the family is UDP-N-acetylglucosamine or AGX1 and two hypothetical proteins from Borrelia burgdorferi the lyme disease spirochaete Swiss:O51893 and Swiss:O51036. 412 matched cddid_all.tbl CDD pfam01705 pfam01705 396323 CX CX module. This domain has no known function. It is found in several C. elegans proteins. The domain contains 6 conserved cysteines that probably form three disulphide bridges. 59 matched cddid_all.tbl CDD pfam01706 pfam01706 460301 FliG_C FliG C-terminal domain. FliG is a component of the flageller rotor, present in about 25 copies per flagellum. This domain functions specifically in motor rotation. 108 matched cddid_all.tbl CDD pfam01707 pfam01707 279970 Peptidase_C9 Peptidase family C9. 202 matched cddid_all.tbl CDD pfam01708 pfam01708 366768 Gemini_mov Geminivirus putative movement protein. This family consists of putative movement proteins from Maize streak and wheat dwarf virus. 92 matched cddid_all.tbl CDD pfam01709 pfam01709 460302 Transcrip_reg Transcriptional regulator. This is a family of transcriptional regulators. In mammals, it activates the transcription of mitochondrially-encoded COX1. In bacteria, it negatively regulates the quorum-sensing response regulator by binding to its promoter region. 235 matched cddid_all.tbl CDD pfam01710 pfam01710 279973 HTH_Tnp_IS630 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis PCC 6803 three of which are characterized as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily. 119 matched cddid_all.tbl CDD pfam01712 pfam01712 396326 dNK Deoxynucleoside kinase. This family consists of various deoxynucleoside kinases cytidine EC:2.7.1.74, guanosine EC:2.7.1.113, adenosine EC:2.7.1.76 and thymidine kinase EC:2.7.1.21 (which also phosphorylates deoxyuridine and deoxycytosine.) These enzymes catalyze the production of deoxynucleotide 5'-monophosphate from a deoxynucleoside. Using ATP and yielding ADP in the process. 201 matched cddid_all.tbl CDD pfam01713 pfam01713 460303 Smr Smr domain. This family includes the Smr (Small MutS Related) proteins, and the C-terminal region of the MutS2 protein. It has been suggested that this domain interacts with the MutS1 protein in the case of Smr proteins and with the N-terminal MutS related region of MutS2. This domain exhibits nicking endonuclease activity that might have a role in mismatch repair or genetic recombination. It shows no significant double strand cleavage or exonuclease activity. The full-length Swiss:Q86UW6 also has the polynucleotide kinase activity. 76 matched cddid_all.tbl CDD pfam01715 pfam01715 460304 IPPT IPP transferase. This is a family of IPP transferases EC:2.5.1.8 also known as tRNA delta(2)-isopentenylpyrophosphate transferase. These enzymes modify both cytoplasmic and mitochondrial tRNAs at A(37) to give isopentenyl A(37). 242 matched cddid_all.tbl CDD pfam01716 pfam01716 426394 MSP Manganese-stabilising protein / photosystem II polypeptide. This family consists of the 33 KDa photosystem II polypeptide from the oxygen evolving complex (OEC) of plants and cyanobacteria. The protein is also known as the manganese-stabilising protein as it is associated with the manganese complex of the OEC and may provide the ligands for the complex. 241 matched cddid_all.tbl CDD pfam01717 pfam01717 366771 Meth_synt_2 Cobalamin-independent synthase, Catalytic domain. This is a family of vitamin-B12 independent methionine synthases or 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferases, EC:2.1.1.14 from bacteria and plants. Plants are the only higher eukaryotes that have the required enzymes for methionine synthesis. This enzyme catalyzes the last step in the production of methionine by transferring a methyl group from 5-methyltetrahydrofolate to homocysteine. The aligned region makes up the carboxy region of the approximately 750 amino acid protein except in some hypothetical archaeal proteins present in the family, where this region corresponds to the entire length. This domain contains the catalytic residues of the enzyme. 323 matched cddid_all.tbl CDD pfam01718 pfam01718 396330 Orbi_NS1 Orbivirus non-structural protein NS1, or hydrophobic tubular protein. This family consists of orbivirus non-structural protein NS1, or hydrophobic tubular protein. NS1 has no specific function in virus replication, it is however thought to play a role in transport of mature virus particles from virus inclusion bodies to the cell membrane. Orbivirus are part of the larger reoviridae which have a dsRNA genome of at least 10 segments encoding at least 10 viral proteins; orbivirus found in this family include bluetongue virus, and African horsesickness virus. 548 matched cddid_all.tbl CDD pfam01719 pfam01719 396331 Rep_2 Plasmid replication protein. This family consists of various bacterial plasmid replication (Rep) proteins. These proteins are essential for replication of plasmids, the Rep proteins are topoisomerases that nick the positive stand at the plus origin of replication and also at the single-strand conversion sequence. 181 matched cddid_all.tbl CDD pfam01721 pfam01721 426395 Bacteriocin_II Class II bacteriocin. The bacteriocins are small peptides that inhibit the growth of various bacteria. Bacteriocins of lactic acid bacteria may inhibit their target cells by permeabilising the cell membrane. 33 matched cddid_all.tbl CDD pfam01722 pfam01722 460305 BolA BolA-like protein. This family consist of the morphoprotein BolA from E. coli and its various homologs. In E. coli over expression of this protein causes round morphology and may be involved in switching the cell between elongation and septation systems during cell division. The expression of BolA is growth rate regulated and is induced during the transition into the the stationary phase. BolA is also induced by stress during early stages of growth and may have a general role in stress response. It has also been suggested that BolA can induce the transcription of penicillin binding proteins 6 and 5. 75 matched cddid_all.tbl CDD pfam01723 pfam01723 279983 Chorion_1 Chorion protein. This family consists of the chorion superfamily proteins classes A, B, CA, CB and high-cysteine HCB from silk, gypsy and polyphemus moths. The chorion proteins make up the moths egg shell a complex extracellular structure. 169 matched cddid_all.tbl CDD pfam01724 pfam01724 426397 DUF29 Domain of unknown function DUF29. This family consists of various hypothetical proteins from cyanobacteria, none of which are functionally described. The aligned region is approximately 120-140 amino acids long corresponding to almost the entire length of the proteins in the family. Swiss:Q2RPE2, PDB:3fcn, is a small protein that has a novel all-alpha fold. The N-terminal helical hairpin is likely to function as a dimerization module. This protein is a member of PFam family PF01724. The function of this protein is unknown. One protein sequence contains a fusion of this protein and a DnaB domain, suggesting a possible role in DNA helicase activity (hypothetical). Dali hits have low Z and high rmsd, suggesting probably only topological similarities (not functional relevance) (details derived from TOPSAN). The family has several highly conserved sequence motifs, including YD/ExD, DxxNVxEEIE, and CPY/F/W, as well as conserved tryptophans. 138 matched cddid_all.tbl CDD pfam01725 pfam01725 460306 Ham1p_like Ham1 family. This family consists of the HAM1 protein and hypothetical archaeal bacterial and C. elegans proteins. HAM1 controls 6-N-hydroxylaminopurine (HAP) sensitivity and mutagenesis in S. cerevisiae. The HAM1 protein protects the cell from HAP, either on the level of deoxynucleoside triphosphate or the DNA level by a yet unidentified set of reactions. 186 matched cddid_all.tbl CDD pfam01726 pfam01726 396335 LexA_DNA_bind LexA DNA binding domain. This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA binding motif. This domain is found associated with pfam00717 the auto-proteolytic domain of LexA EC:3.4.21.88. 63 matched cddid_all.tbl CDD pfam01728 pfam01728 426399 FtsJ FtsJ-like methyltransferase. This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesized that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping. 179 matched cddid_all.tbl CDD pfam01729 pfam01729 396337 QRPTase_C Quinolinate phosphoribosyl transferase, C-terminal domain. Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase EC:2.4.2.19 is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyzes the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide. The QA substrate is bound between the C-terminal domain of one subunit, and the N-terminal domain of the other. The C-terminal domain has a 7 beta-stranded TIM barrel-like fold. 169 matched cddid_all.tbl CDD pfam01730 pfam01730 460307 UreF UreF. This family consists of the Urease accessory protein UreF. The urease enzyme (urea amidohydrolase) hydrolyses urea into ammonia and carbamic acid. UreF is proposed to modulate the activation process of urease by eliminating the binding of nickel irons to noncarbamylated protein. 141 matched cddid_all.tbl CDD pfam01731 pfam01731 334656 Arylesterase Arylesterase. This family consists of arylesterases (Also known as serum paraoxonase) EC:3.1.1.2. These enzymes hydrolyse organophosphorus esters such as paraoxon and are found in the liver and blood. They confer resistance to organophosphate toxicity. Human arylesterase (PON1) is associated with HDL and may protect against LDL oxidation. 86 matched cddid_all.tbl CDD pfam01732 pfam01732 426401 Mycop_pep_DUF31 Mycoplasma peptidase (DUF31). This domain is found in various uncharacterized proteins and putative lipoproteins from mycoplasmas. Although its function is not clear, it has been suggested that this is a serine protease domain; sequence analysis revealed that the amino acid sequence is similar to that of serine proteases. It is related to pathogenicity as this domain is present in proteins encoded by animal and human pathogenic Mycoplasmas. It has been proposed that the Ig binding protein M may function together with this domain playing a role in evading host Ig-mediated defense against the MIB-MIP (mycoplasma Ig binding protein (MIB) and mycoplasma Ig protease (MIP)) system, which is a novel mechanism that protects mycoplasma against host immune response. 353 matched cddid_all.tbl CDD pfam01733 pfam01733 396340 Nucleoside_tran Nucleoside transporter. This is a family of nucleoside transporters. In mammalian cells nucleoside transporters transport nucleoside across the plasma membrane and are essential for nucleotide synthesis via the salvage pathways for cells that lack their own de novo synthesis pathways. Also in this family is mouse and human nucleolar protein HNP36, a protein of unknown function; although it has been hypothesized to be a plasma membrane nucleoside transporter. 286 matched cddid_all.tbl CDD pfam01734 pfam01734 396341 Patatin Patatin-like phospholipase. This family consists of various patatin glycoproteins from plants. The patatin protein accounts for up to 40% of the total soluble protein in potato tubers. Patatin is a storage protein but it also has the enzymatic activity of lipid acyl hydrolase, catalysing the cleavage of fatty acids from membrane lipids. Members of this family have been found also in vertebrates. 190 matched cddid_all.tbl CDD pfam01735 pfam01735 366778 PLA2_B Lysophospholipase catalytic domain. This family consists of Lysophospholipase / phospholipase B EC:3.1.1.5 and cytosolic phospholipase A2 EC:3.1.4 which also has a C2 domain pfam00168. Phospholipase B enzymes catalyze the release of fatty acids from lysophsopholipids and are capable in vitro of hydrolysing all phospholipids extractable form yeast cells. Cytosolic phospholipase A2 associates with natural membranes in response to physiological increases in Ca2+ and selectively hydrolyses arachidonyl phospholipids, the aligned region corresponds the the carboxy-terminal Ca2+-independent catalytic domain of the protein as discussed in. 490 matched cddid_all.tbl CDD pfam01736 pfam01736 279993 Polyoma_agno Polyomavirus agnoprotein. This family consist of the DNA binding protein or agnoprotein from various polyomaviruses. This protein is highly basic and can bind single stranded and double stranded DNA. Mutations in the agnoprotein produce smaller viral plaques, hence its function is not essential for growth in tissue culture cells but something has slowed in the normal replication cycle. There is also evidence suggesting that the agnogene and agnoprotein act as regulators of structural protein synthesis. 62 matched cddid_all.tbl CDD pfam01737 pfam01737 460308 Ycf9 YCF9. This family consists of the hypothetical protein product of the YCF9 gene from chloroplasts and cyanobacteria. These proteins have no known function. 56 matched cddid_all.tbl CDD pfam01738 pfam01738 396343 DLH Dienelactone hydrolase family. 213 matched cddid_all.tbl CDD pfam01739 pfam01739 426403 CheR CheR methyltransferase, SAM binding domain. CheR proteins are part of the chemotaxis signaling mechanism in bacteria. CheR methylates the chemotaxis receptor at specific glutamate residues. CheR is an S-adenosylmethionine- dependent methyltransferase - the C-terminal domain (this one) binds SAM. 190 matched cddid_all.tbl CDD pfam01740 pfam01740 426404 STAS STAS domain. The STAS (after Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C terminal region of Sulphate transporters and bacterial antisigma factor antagonists. It has been suggested that this domain may have a general NTP binding function. 106 matched cddid_all.tbl CDD pfam01741 pfam01741 460309 MscL Large-conductance mechanosensitive channel, MscL. 126 matched cddid_all.tbl CDD pfam01742 pfam01742 396347 Peptidase_M27 Clostridial neurotoxin zinc protease. These toxins are zinc proteases that block neurotransmitter release by proteolytic cleavage of synaptic proteins such as synaptobrevins, syntaxin and SNAP-25. 420 matched cddid_all.tbl CDD pfam01743 pfam01743 396348 PolyA_pol Poly A polymerase head domain. This family includes nucleic acid independent RNA polymerases, such as Poly(A) polymerase, which adds the poly (A) tail to mRNA EC:2.7.7.19. This family also includes the tRNA nucleotidyltransferase that adds the CCA to the 3' of the tRNA EC:2.7.7.25. This family is part of the nucleotidyltransferase superfamily. 126 matched cddid_all.tbl CDD pfam01744 pfam01744 426406 GLTT GLTT repeat (6 copies). This short repeat of unknown function is found in multiple copies in several C. elegans proteins. The repeat is five residues long and consists of XGLTT where X can be any amino acid. 28 matched cddid_all.tbl CDD pfam01745 pfam01745 366786 IPT Isopentenyl transferase. Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid. 232 matched cddid_all.tbl CDD pfam01746 pfam01746 396350 tRNA_m1G_MT tRNA (Guanine-1)-methyltransferase. This is a family of tRNA (Guanine-1)-methyltransferases EC:2.1.1.31. In E.coli K12 this enzyme catalyzes the conversion of a guanosine residue to N1-methylguanine in position 37, next to the anticodon, in tRNA. 182 matched cddid_all.tbl CDD pfam01747 pfam01747 460310 ATP-sulfurylase ATP-sulfurylase. This domain is the catalytic domain of ATP-sulfurylase or sulfate adenylyltransferase EC:2.7.7.4 some of which are part of a bifunctional polypeptide chain associated with adenosyl phosphosulphate (APS) kinase pfam01583. Both enzymes are required for PAPS (phosphoadenosine-phosphosulfate) synthesis from inorganic sulphate. ATP sulfurylase catalyzes the synthesis of adenosine-phosphosulfate APS from ATP and inorganic sulphate. 213 matched cddid_all.tbl CDD pfam01749 pfam01749 460311 IBB Importin beta binding domain. This family consists of the importin alpha (karyopherin alpha), importin beta (karyopherin beta) binding domain. The domain mediates formation of the importin alpha beta complex; required for classical NLS import of proteins into the nucleus, through the nuclear pore complex and across the nuclear envelope. Also in the alignment is the NLS of importin alpha which overlaps with the IBB domain. 79 matched cddid_all.tbl CDD pfam01750 pfam01750 396353 HycI Hydrogenase maturation protease. The family consists of hydrogenase maturation proteases. In E. coli HypI the hydrogenase maturation protease is involved in processing of HypE the large subunit of hydrogenases 3, by cleavage of its C-terminal. 130 matched cddid_all.tbl CDD pfam01751 pfam01751 396354 Toprim Toprim domain. This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyze the relaxation of DNA supercoiling by causing transient double strand breaks. 93 matched cddid_all.tbl CDD pfam01752 pfam01752 426409 Peptidase_M9 Collagenase. This family of enzymes break down collagens. 285 matched cddid_all.tbl CDD pfam01753 pfam01753 460312 zf-MYND MYND finger. 39 matched cddid_all.tbl CDD pfam01754 pfam01754 460313 zf-A20 A20-like zinc finger. The A20 Zn-finger of bovine/human Rabex5/rabGEF1 is a Ubiquitin Binding Domain. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation. 24 matched cddid_all.tbl CDD pfam01755 pfam01755 366794 Glyco_transf_25 Glycosyltransferase family 25 (LPS biosynthesis protein). Members of this family belong to Glycosyltransferase family 25 This is a family of glycosyltransferases involved in lipopolysaccharide (LPS) biosynthesis. These enzymes catalyze the transfer of various sugars onto the growing LPS chain during its biosynthesis. 200 matched cddid_all.tbl CDD pfam01756 pfam01756 460314 ACOX Acyl-CoA oxidase. This is a family of Acyl-CoA oxidases EC:1.3.3.6. Acyl-coA oxidase converts acyl-CoA into trans-2- enoyl-CoA. 180 matched cddid_all.tbl CDD pfam01757 pfam01757 426413 Acyl_transf_3 Acyltransferase family. This family includes a range of acyltransferase enzymes. This domain is found in a wide range of acyltransferase enzymes, including, mainly, bacterial proteins which catalyze the transfer of acyl groups, other than amino-acyl, from one compound to another, such as Glucans biosynthesis protein C (OPGC) or protein OatA from Listeria monocytogenes serovar 1/2a and Staphylococcus aureus, an integral membrane protein which is responsible for O-acetylation at the C6-hydroxyl group of N-acetylmuramyl residues, forming the corresponding N,6-O-diacetylmuramic acid of the peptidoglycan, a modification that determines lysozyme resistance. This domain is also present in eukaryotic proteins, namely O-acyltransferase like protein (OACYL) from mouse and RHY1 (Regulator of hypoxia-inducible factor 1) and NRF6 (Nose resistant to fluoxetine protein 6) from Caenorhabditis elegans. 330 matched cddid_all.tbl CDD pfam01758 pfam01758 366796 SBF Sodium Bile acid symporter family. This family consists of Na+/bile acid co-transporters. These transmembrane proteins function in the liver in the uptake of bile acids from portal blood plasma a process mediated by the co-transport of Na+. Also in the family is ARC3 from S. cerevisiae; this is a putative transmembrane protein involved in resistance to arsenic compounds. 191 matched cddid_all.tbl CDD pfam01759 pfam01759 396359 NTR UNC-6/NTR/C345C module. Sequence similarity between netrin UNC-6 and C345C complement protein family members, and hence the existence of the UNC-6 module, was first reported in. Subsequently, many additional members of the family were identified on the basis of sequence similarity between the C-terminal domains of netrins, complement proteins C3, C4, C5, secreted frizzled-related proteins, and type I pro-collagen C-proteinase enhancer proteins (PCOLCEs), which are homologous with the N-terminal domains of tissue inhibitors of metalloproteinases (TIMPs). The TIMPs are classified as a separate family in Pfam (pfam00965). This expanded domain family has been named as the NTR module. 106 matched cddid_all.tbl CDD pfam01761 pfam01761 426414 DHQ_synthase 3-dehydroquinate synthase. The 3-dehydroquinate synthase EC:4.6.1.3 domain is present in isolation in various bacterial 3-dehydroquinate synthases and also present as a domain in the pentafunctional AROM polypeptide. 3-dehydroquinate (DHQ) synthase catalyzes the formation of dehydroquinate (DHQ) and orthophosphate from 3-deoxy-D-arabino heptulosonic 7 phosphate. This reaction is part of the shikimate pathway which is involved in the biosynthesis of aromatic amino acids. 260 matched cddid_all.tbl CDD pfam01762 pfam01762 426415 Galactosyl_T Galactosyltransferase. This family includes the galactosyltransferases UDP-galactose:2-acetamido-2-deoxy-D-glucose3beta-galactosyltransferase and UDP-Gal:beta-GlcNAc beta 1,3-galactosyltranferase. Specific galactosyltransferases transfer galactose to GlcNAc terminal chains in the synthesis of the lacto-series oligosaccharides types 1 and 2. 195 matched cddid_all.tbl CDD pfam01763 pfam01763 460315 Herpes_UL6 Herpesvirus UL6 like. This family consists of various proteins from the herpesviridae that are similar to herpes simplex virus type I UL6 virion protein. UL6 is essential for cleavage and packaging of the viral genome. 568 matched cddid_all.tbl CDD pfam01764 pfam01764 396362 Lipase_3 Lipase (class 3). 139 matched cddid_all.tbl CDD pfam01765 pfam01765 460316 RRF "Ribosome recycling factor. The ribosome recycling factor (RRF / ribosome release factor) dissociates the ribosome from the mRNA after termination of translation, and is essential bacterial growth. Thus ribosomes are ""recycled"" and ready for another round of protein synthesis." 158 matched cddid_all.tbl CDD pfam01766 pfam01766 280020 Birna_VP2 Birnavirus VP2 protein. VP2 is the major structural protein of birnaviruses. The large RNA segment of birnaviruses codes for a polyprotein (N-VP2-VP4-VP3-C). 440 matched cddid_all.tbl CDD pfam01767 pfam01767 426418 Birna_VP3 Birnavirus VP3 protein. VP3 is a minor structural component of the virus. The large RNA segment of birnaviruses codes for a polyprotein (N-VP2-VP4-VP3-C). 227 matched cddid_all.tbl CDD pfam01768 pfam01768 280022 Birna_VP4 Birnavirus VP4 protein. VP4 is a viral protease. The large RNA segment of birnaviruses codes for a polyprotein (N-VP2-VP4-VP3-C). 259 matched cddid_all.tbl CDD pfam01769 pfam01769 460317 MgtE Divalent cation transporter. This region is the integral membrane part of the eubacterial MgtE family of magnesium transporters. Related regions are found also in archaebacterial and eukaryotic proteins. All the archaebacterial and eukaryotic examples have two copies of the region. This suggests that the eubacterial examples may act as dimers. Members of this family probably transport Mg2+ or other divalent cations into the cell. The alignment contains two highly conserved aspartates that may be involved in cation binding (Bateman A unpubl.) 124 matched cddid_all.tbl CDD pfam01770 pfam01770 460318 Folate_carrier Reduced folate carrier. The reduced folate carrier (a transmembrane glycoprotein) transports reduced folate into mammalian cells via the carrier mediated mechanism (as opposed to the receptor mediated mechanism) it also transports cytotoxic folate analogues used in chemotherapy, such as methotrexate (MTX). Mammalian cells have an absolute requirement for exogenous folates which are needed for growth, and biosynthesis of macromolecules. 412 matched cddid_all.tbl CDD pfam01771 pfam01771 396366 Viral_alk_exo Viral alkaline exonuclease. This family includes various alkaline exonucleases from members of the Herpesviridae and Baculoviridae. Alkaline exonuclease appears to have an important role in the replication of herpes simplex virus. 460 matched cddid_all.tbl CDD pfam01773 pfam01773 460319 Nucleos_tra2_N Na+ dependent nucleoside transporter N-terminus. This family consists of nucleoside transport proteins. Swiss:Q62773 is a purine-specific Na+-nucleoside cotransporter localized to the bile canalicular membrane. Swiss:Q62674 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the N terminus of this family 73 matched cddid_all.tbl CDD pfam01774 pfam01774 460320 UreD UreD urease accessory protein. UreD is a urease accessory protein. Urease pfam00449 hydrolyses urea into ammonia and carbamic acid. UreD is involved in activation of the urease enzyme via the UreD-UreF-UreG-urease complex and is required for urease nickel metallocenter assembly. See also UreF pfam01730, UreG pfam01495. 164 matched cddid_all.tbl CDD pfam01775 pfam01775 396369 Ribosomal_L18A Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A. This family includes: archaeal 50S ribosomal protein L18Ae, often referred to as L20e or LX; fungal 60S ribosomal protein L20; and higher eukaryote 60S ribosomal protein L18A. 60 matched cddid_all.tbl CDD pfam01776 pfam01776 460321 Ribosomal_L22e Ribosomal L22e protein family. 100 matched cddid_all.tbl CDD pfam01777 pfam01777 460322 Ribosomal_L27e Ribosomal L27e protein family. The N-terminal region of the eukaryotic ribosomal L27 has the KOW motif. C-terminal region is represented by this family. 85 matched cddid_all.tbl CDD pfam01778 pfam01778 460323 Ribosomal_L28e Ribosomal L28e protein family. 115 matched cddid_all.tbl CDD pfam01779 pfam01779 460324 Ribosomal_L29e Ribosomal L29e protein family. 39 matched cddid_all.tbl CDD pfam01780 pfam01780 460325 Ribosomal_L37ae Ribosomal L37ae protein family. This ribosomal protein is found in archaebacteria and eukaryotes. It contains four conserved cysteine residues that may bind to zinc. 78 matched cddid_all.tbl CDD pfam01781 pfam01781 460326 Ribosomal_L38e Ribosomal L38e protein family. 67 matched cddid_all.tbl CDD pfam01782 pfam01782 460327 RimM RimM N-terminal domain. The RimM protein is essential for efficient processing of 16S rRNA. The RimM protein was shown to have affinity for free ribosomal 30S subunits but not for 30S subunits in the 70S ribosomes. This N-terminal domain is found associated with a PRC-barrel domain. 84 matched cddid_all.tbl CDD pfam01783 pfam01783 426430 Ribosomal_L32p Ribosomal L32p protein family. 56 matched cddid_all.tbl CDD pfam01784 pfam01784 426431 NIF3 NIF3 (NGG1p interacting factor 3). This family contains several NIF3 (NGG1p interacting factor 3) protein homologs. NIF3 interacts with the yeast transcriptional coactivator NGG1p which is part of the ADA complex, the exact function of this interaction is unknown. 236 matched cddid_all.tbl CDD pfam01785 pfam01785 250863 Closter_coat Closterovirus coat protein. This family consist of coat proteins from closteroviruses a member of the closteroviridae. The viral coat protein encapsulates and protects the viral genome. Both the large cp1 and smaller cp2 coat protein originate from the same primary transcript. Members of the closteroviridae include Sugar beet yellow virus and Grapevine leafroll-associated virus, closteroviruses have a positive strand ssRNA genome with no DNA stage during replication. 188 matched cddid_all.tbl CDD pfam01786 pfam01786 460328 AOX Alternative oxidase. The alternative oxidase is used as a second terminal oxidase in the mitochondria, electrons are transfered directly from reduced ubiquinol to oxygen forming water. This is not coupled to ATP synthesis and is not inhibited by cyanide, this pathway is a single step process. In rice the transcript levels of the alternative oxidase are increased by low temperature. 218 matched cddid_all.tbl CDD pfam01787 pfam01787 460329 Ilar_coat Ilarvirus coat protein. This family consists of various coat proteins from the ilarviruses part of the Bromoviridae, members include apple mosaic virus and prune dwarf virus. The ilarvirus coat protein is required to initiate replication of the viral genome in host plants. Members of the Bromoviridae have a positive stand ssRNA genome with no DNA stage in there replication. 204 matched cddid_all.tbl CDD pfam01788 pfam01788 460330 PsbJ PsbJ. This family consists of the photosystem II reaction centre protein PsbJ from plants and Cyanobacteria. In Synechocystis sp. PCC 6803 PsbJ regulates the number of photosystem II centres in thylakoid membranes, it is a predicted 4kDa protein with one membrane spanning domain. 39 matched cddid_all.tbl CDD pfam01789 pfam01789 426435 PsbP PsbP. This family consists of the 23 kDa subunit of oxygen evolving system of photosystem II or PsbP from various plants (where it is encoded by the nuclear genome) and Cyanobacteria. The 23 KDa PsbP protein is required for PSII to be fully operational in vivo, it increases the affinity of the water oxidation site for Cl- and provides the conditions required for high affinity binding of Ca2+. 155 matched cddid_all.tbl CDD pfam01790 pfam01790 460331 LGT Prolipoprotein diacylglyceryl transferase. 238 matched cddid_all.tbl CDD pfam01791 pfam01791 460332 DeoC DeoC/LacD family aldolase. This family includes diverse aldolase enzymes. This family includes the enzyme deoxyribose-phosphate aldolase EC:4.1.2.4, which is involved in nucleotide metabolism. The family also includes a group of related bacterial proteins of unknown function, see examples Swiss:Q57843 and Swiss:P76143. The family also includes tagatose 1,6-diphosphate aldolase (EC:4.1.2.40) is part of the tagatose-6-phosphate pathway of galactose-6-phosphate degradation. 230 matched cddid_all.tbl CDD pfam01793 pfam01793 396385 Glyco_transf_15 Glycolipid 2-alpha-mannosyltransferase. This is a family of alpha-1,2 mannosyl-transferases involved in N-linked and O-linked glycosylation of proteins. Some of the enzymes in this family have been shown to be involved in O- and N-linked glycan modifications in the Golgi. 313 matched cddid_all.tbl CDD pfam01794 pfam01794 426438 Ferric_reduct Ferric reductase like transmembrane component. This family includes a common region in the transmembrane proteins mammalian cytochrome B-245 heavy chain (gp91-phox), ferric reductase transmembrane component in yeast and respiratory burst oxidase from mouse-ear cress. This may be a family of flavocytochromes capable of moving electrons across the plasma membrane. The Frp1 protein from S. pombe is a ferric reductase component and is required for cell surface ferric reductase activity, mutants in frp1 are deficient in ferric iron uptake. Cytochrome B-245 heavy chain is a FAD-dependent dehydrogenase it is also has electron transferase activity which reduces molecular oxygen to superoxide anion, a precursor in the production of microbicidal oxidants. Mutations in the sequence of cytochrome B-245 heavy chain (gp91-phox) lead to the X-linked chronic granulomatous disease. The bacteriocidal ability of phagocytic cells is reduced and is characterized by the absence of a functional plasma membrane associated NADPH oxidase. The chronic granulomatous disease gene codes for the beta chain of cytochrome B-245 and cytochrome B-245 is missing from patients with the disease. 121 matched cddid_all.tbl CDD pfam01795 pfam01795 396387 Methyltransf_5 MraW methylase family. Members of this family are probably SAM dependent methyltransferases based on Swiss:P18595. This family appears to be related to pfam01596. 309 matched cddid_all.tbl CDD pfam01796 pfam01796 460333 OB_aCoA_assoc DUF35 OB-fold domain, acyl-CoA-associated. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain and a C-terminal OB fold domain represented in this entry. OB-folds are frequently found to bind nucleic acids suggesting this domain might bind to DNA or RNA (Topsan http://www.topsan.org/). Genomic context shows it to be adjacent to acyl-CoA transferase (http:/www.microbesonline.org/). 65 matched cddid_all.tbl CDD pfam01797 pfam01797 460334 Y1_Tnp Transposase IS200 like. Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS200 from E. coli. 119 matched cddid_all.tbl CDD pfam01798 pfam01798 460335 Nop snoRNA binding domain, fibrillarin. This family consists of various Pre RNA processing ribonucleoproteins. The function of the aligned region is unknown however it may be a common RNA or snoRNA or Nop1p binding domain. Nop5p (Nop58p) from yeast is the protein component of a ribonucleoprotein required for pre-18s rRNA processing and is suggested to function with Nop1p in a snoRNA complex. Nop56p and Nop5p interact with Nop1p and are required for ribosome biogenesis. Prp31p is required for pre-mRNA splicing in S. cerevisiae. Fibrillarin, or Nop, is the catalytic subunit responsible for the methyl transfer reaction of the site-specific 2'-O-methylation of ribosomal and spliceosomal RNA. 229 matched cddid_all.tbl CDD pfam01799 pfam01799 460336 Fer2_2 [2Fe-2S] binding domain. 73 matched cddid_all.tbl CDD pfam01801 pfam01801 280049 Cytomega_gL Cytomegalovirus glycoprotein L. Glycoprotein L from cytomegalovirus serves a chaperone for the correct folding and surface expression of glycoprotein H (gH). Glycoprotein L is a member of the heterotrimeric gCIII complex of glycoprotein which also includes gH and gO and has an essential role in viral fusion. 211 matched cddid_all.tbl CDD pfam01802 pfam01802 460337 Herpes_V23 Herpesvirus VP23 like capsid protein. This family consist of various capsid proteins from members of the herpesviridae. The capsid protein VP23 in herpes simplex virus forms a triplex together with VP19C these fit between and link together adjacent capsomers as formed by VP5 and VP26. VP3 along with the scaffolding proteins helps to form normal capsids by defining the curvature of the shell and size of the particle. 294 matched cddid_all.tbl CDD pfam01803 pfam01803 426444 LIM_bind LIM-domain binding protein. The LIM-domain binding protein, binds to the LIM domain pfam00412 of LIM homeodomain proteins which are transcriptional regulators of development. Nuclear LIM interactor (NLI) / LIM domain-binding protein 1 (LDB1) is located in the nuclei of neuronal cells during development, it is co-expressed with Isl1 in early motor neuron differentiation and has a suggested role in the Isl1 dependent development of motor neurons. It is suggested that these proteins act synergistically to enhance transcriptional efficiency by acting as co-factors for LIM homeodomain and Otx class transcription factors both of which have essential roles in development. The Drosophila protein Chip is required for segmentation and activity of a remote wing margin enhancer. Chip is a ubiquitous chromosomal factor required for normal expression of diverse genes at many stages of development. It is suggested that Chip cooperates with different LIM domain proteins and other factors to structurally support remote enhancer-promoter interactions. 242 matched cddid_all.tbl CDD pfam01804 pfam01804 460338 Penicil_amidase Penicillin amidase. Penicillin amidase or penicillin acylase EC:3.5.1.11 catalyzes the hydrolysis of benzylpenicillin to phenylacetic acid and 6-aminopenicillanic acid (6-APA) a key intermediate in the the synthesis of penicillins. Also in the family is cephalosporin acylase and aculeacin A acylase which are involved in the synthesis of related peptide antibiotics. 670 matched cddid_all.tbl CDD pfam01805 pfam01805 460339 Surp Surp module. This domain is also known as the SWAP domain. SWAP stands for Suppressor-of-White-APricot. It has been suggested that these domains may be RNA binding. 52 matched cddid_all.tbl CDD pfam01806 pfam01806 460340 Paramyxo_P Paramyxovirinae P phosphoprotein C-terminal region. The subfamily Paramyxovirinae of the family Paramyxoviridae now contains as main genera the Rubulaviruses, avulaviruses, respiroviruses, Henipavirus-es and morbilliviruses. Protein P is the best characterized, structurally of the replicative complex of N, P and L proteins and consists of two functionally distinct moieties, an N-terminal PNT, and a C-terminal PCT. The P protein is an essential part of the viral RNA polymerase complex formed from the P and L proteins. P protein plays a crucial role in the enzyme by positioning L onto the N/RNA template through an interaction with the C-terminal domain of N. Without P, L is not functional.The C-terminal part of P (PCT) is only functional as an oligomer and forms with L the polymerase complex. PNT is poorly conserved and unstructured in solution while PCT contains the oligomerization domain (PMD) that folds as a homotetrameric coiled coil (40) containing the L binding region and a C-terminal partially folded domain, PX (residues 474 to 568), identified as the nucleocapsid binding site. Interestingly, PX is also expressed as an independent polypeptide in infected cells. PX has a C-subdomain (residues 516 to 568) that consists of three {alpha}-helices arranged in an antiparallel triple-helical bundle linked to an unfolded flexible N-subdomain (residues 474 to 515). 248 matched cddid_all.tbl CDD pfam01807 pfam01807 426447 zf-CHC2 CHC2 zinc finger. This domain is principally involved in DNA binding in DNA primases. 95 matched cddid_all.tbl CDD pfam01808 pfam01808 460341 AICARFT_IMPCHas AICARFT/IMPCHase bienzyme. This is a family of bifunctional enzymes catalysing the last two steps in de novo purine biosynthesis. The bifunctional enzyme is found in both prokaryotes and eukaryotes. The second last step is catalyzed by 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase EC:2.1.2.3 (AICARFT), this enzyme catalyzes the formylation of AICAR with 10-formyl-tetrahydrofolate to yield FAICAR and tetrahydrofolate. This is catalyzed by a pair of C-terminal deaminase fold domains in the protein, where the active site is formed by the dimeric interface of two monomeric units. The last step is catalyzed by the N-terminal IMP (Inosine monophosphate) cyclohydrolase domain EC:3.5.4.10 (IMPCHase), cyclizing FAICAR (5-formylaminoimidazole-4-carboxamide ribonucleotide) to IMP. 308 matched cddid_all.tbl CDD pfam01809 pfam01809 460342 YidD Putative membrane protein insertion efficiency factor. This family consists of membrane insertion efficiency factor proteins. They contain three conserved cysteine residues. Family members such as YidD may be involved in insertion of integral membrane proteins into the membrane by assisting YidC (membrane protein insertase). Some members of the yidD family have been previously thought to posses alpha-hemolysin activity, however no sufficient evidence was found to corroborate this idea. Secondary structure prediction indicated the presence of three alpha-helices in YidD. None of the three alpha-helices appeared sufficiently hydrophobic to serve as a transmembrane, suggesting a cytoplasmic localization for YidD. However, a closer examination of the alpha-helical wheel projection of the predicted first alpha-helix in YidD suggested an amphipathic structure in its N-terminal region which might be involved in membrane targeting. 67 matched cddid_all.tbl CDD pfam01810 pfam01810 280058 LysE LysE type translocator. This family consists of various hypothetical proteins and an l-lysine exporter LysE from Corynebacterium glutamicum which is proposed to be the first of a novel family of translocators. LysE exports l-lysine from the cell into the surrounding medium and is predicted to span the membrane six times. The physiological function of the exporter is to excrete excess l-Lysine as a result of natural flux imbalances or peptide hydrolysis; and also after artificial deregulation of l-Lysine biosynthesis as used by the biotechnology. industry for the production of l-lysine. 193 matched cddid_all.tbl CDD pfam01812 pfam01812 396398 5-FTHF_cyc-lig 5-formyltetrahydrofolate cyclo-ligase family. 5-formyltetrahydrofolate cyclo-ligase or methenyl-THF synthetase EC:6.3.3.2 catalyzes the interchange of 5-formyltetrahydrofolate (5-FTHF) to 5-10-methenyltetrahydrofolate, this requires ATP and Mg2+. 5-FTHF is used in chemotherapy where it is clinically known as Leucovorin. 186 matched cddid_all.tbl CDD pfam01813 pfam01813 460343 ATP-synt_D ATP synthase subunit D. This is a family of subunit D form various ATP synthases including V-type H+ transporting and Na+ dependent. Subunit D is suggested to be an integral part of the catalytic sector of the V-ATPase. 194 matched cddid_all.tbl CDD pfam01814 pfam01814 396400 Hemerythrin Hemerythrin HHE cation binding domain. Iteration of the HHE family found it to be related to Hemerythrin. It also demonstrated that what has been described as a single domain in fact consists of two cation binding domains. Members of this family occur all across nature and are involved in a variety of processes. For instance, in Nereis diversicolor Swiss:P80255 binds Cadmium so as to protect the organizm from toxicity. However Hemerythrin is classically described as Oxygen-binding through two attached Fe2+ ions. And the bacterial Swiss:Q7WX96 is a regulator of response to NO, which suggests yet another set-up for its metal ligands. In Staphylococcus aureus P72360 has been noted to be important when the organizm switches to living in environments with low oxygen concentrations; perhaps this protein acts as an oxygen store or scavenger. This domain can bind oxygen (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043) 128 matched cddid_all.tbl CDD pfam01815 pfam01815 426451 Rop Rop protein. 57 matched cddid_all.tbl CDD pfam01816 pfam01816 460344 LRV Leucine rich repeat variant. The function of this repeat is unknown. It has an unusual structure of two helices. One is an alpha helix, the other is the much rarer 3-10 helix. 26 matched cddid_all.tbl CDD pfam01817 pfam01817 460345 CM_2 Chorismate mutase type II. Chorismate mutase EC:5.4.99.5 catalyzes the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine. 79 matched cddid_all.tbl CDD pfam01818 pfam01818 396402 Translat_reg Bacteriophage translational regulator. The translational regulator protein regA is encoded by the T4 bacteriophage and binds to a region of messenger RNA (mRNA) that includes the initiator codon. RegA is unusual in that it represses the translation of about 35 early T4 mRNAs but does not affect nearly 200 other mRNAs. 122 matched cddid_all.tbl CDD pfam01819 pfam01819 396403 Levi_coat Levivirus coat protein. The Levivirus coat protein forms the bacteriophage coat that encapsidates the viral RNA. 180 copies of this protein form the virion shell. The MS2 bacteriophage coat protein controls two distinct processes: sequence-specific RNA encapsidation and repression of replicase translation-by binding to an RNA stem-loop structure of 19 nucleotides containing the initiation codon of the replicase gene. The binding of a coat protein dimer to this hairpin shuts off synthesis of the viral replicase, switching the viral replication cycle to virion assembly rather than continued replication. 132 matched cddid_all.tbl CDD pfam01820 pfam01820 460346 Dala_Dala_lig_N D-ala D-ala ligase N-terminus. This family represents the N-terminal region of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4 which is thought to be involved in substrate binding. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF). This domain is structurally related to the PreATP-grasp domain. 118 matched cddid_all.tbl CDD pfam01821 pfam01821 460347 ANATO Anaphylotoxin-like domain. C3a, C4a and C5a anaphylatoxins are protein fragments generated enzymatically in serum during activation of complement molecules C3, C4, and C5. They induce smooth muscle contraction. These fragments are homologous to a three-fold repeat in fibulins. 36 matched cddid_all.tbl CDD pfam01822 pfam01822 460348 WSC WSC domain. This domain is involved in carbohydrate binding. 82 matched cddid_all.tbl CDD pfam01823 pfam01823 460349 MACPF MAC/Perforin domain. The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 complex binds to C8, which is composed of three chains (alpha, beta, and gamma), thus forming the C5b-8 complex. C5b-8 subsequently binds to C9 and acts as a catalyst in the polymerization of C9. Active MAC has a subunit composition of C5b-C6-C7-C8-C9{n}. Perforin is a protein found in cytolytic T-cell and killer cells. In the presence of calcium, perforin polymerizes into transmembrane tubules and is capable of lysing, non-specifically, a variety of target cells. There are a number of regions of similarity in the sequences of complement components C6, C7, C8-alpha, C8-beta, C9 and perforin. The X-ray crystal structure of a MACPF domain reveals that it shares a common fold with bacterial cholesterol dependent cytolysins (pfam01289) such as perfringolysin O. Three key pieces of evidence suggests that MACPF domains and CDCs are homologous: Functional similarity (pore formation), conservation of three glycine residues at a hinge in both families and conservation of a complex core fold. 211 matched cddid_all.tbl CDD pfam01824 pfam01824 280070 MatK_N MatK/TrnK amino terminal region. The function of this region is unknown. 331 matched cddid_all.tbl CDD pfam01825 pfam01825 460350 GPS GPCR proteolysis site, GPS, motif. The GPS motif is found in GPCRs, and is the site for auto-proteolysis, so is thus named, GPS. The GPS motif is a conserved sequence of ~40 amino acids containing canonical cysteine and tryptophan residues, and is the most highly conserved part of the domain. In most, if not all, cell-adhesion GPCRs these undergo autoproteolysis in the GPS between a conserved aliphatic residue (usually a leucine) and a threonine, serine, or cysteine residue. In higher eukaryotes this motif is found embedded in the C-terminal beta-stranded part of a GAIN domain - GPCR-Autoproteolysis INducing (GAIN). The GAIN-GPS domain adopts a fold in which the GPS motif, at the C-terminus, forms five beta-strands that are tightly integrated into the overall GAIN domain. The GPS motif, evolutionarily conserved from tetrahymena to mammals, is the only extracellular domain shared by all human cell-adhesion GPCRs and PKD proteins, and is the locus of multiple human disease mutations. The GAIN-GPS domain is both necessary and sufficient functionally for autoproteolysis, suggesting an autoproteolytic mechanism whereby the overall GAIN domain fine-tunes the chemical environment in the GPS to catalyze peptide bond hydrolysis. In the cell-adhesion GPCRs and PKD proteins, the GPS motif is always located at the end of their long N-terminal extracellular regions, immediately before the first transmembrane helix of the respective protein. 44 matched cddid_all.tbl CDD pfam01826 pfam01826 460351 TIL Trypsin Inhibitor like cysteine rich domain. This family contains trypsin inhibitors as well as a domain found in many extracellular proteins. The domain typically contains ten cysteine residues that form five disulphide bonds. The cysteine residues that form the disulphide bonds are 1-7, 2-6, 3-5, 4-10 and 8-9. 55 matched cddid_all.tbl CDD pfam01827 pfam01827 396410 FTH FTH domain. This presumed domain is likely to be a protein-protein interaction module. It is found in many proteins from C. elegans. The domain is found associated with the F-box pfam00646. This domain is named FTH after FOG-2 homology domain. 141 matched cddid_all.tbl CDD pfam01828 pfam01828 426460 Peptidase_A4 Peptidase A4 family. 206 matched cddid_all.tbl CDD pfam01829 pfam01829 460352 Peptidase_A6 Peptidase A6 family. 314 matched cddid_all.tbl CDD pfam01830 pfam01830 280076 Peptidase_C7 Peptidase C7 family. 243 matched cddid_all.tbl CDD pfam01831 pfam01831 460353 Peptidase_C16 Peptidase C16 family. 249 matched cddid_all.tbl CDD pfam01832 pfam01832 460354 Glucosaminidase Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase. This family includes Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase EC:3.2.1.96. As well as the flageller protein J that has been shown to hydrolyse peptidoglycan. 91 matched cddid_all.tbl CDD pfam01833 pfam01833 460355 TIG IPT/TIG domain. This family consists of a domain that has an immunoglobulin like fold. These domains are found in cell surface receptors such as Met and Ron as well as in intracellular transcription factors where it is involved in DNA binding. CAUTION: This family does not currently recognize a significant number of members. 84 matched cddid_all.tbl CDD pfam01834 pfam01834 460356 XRCC1_N XRCC1 N terminal domain. 148 matched cddid_all.tbl CDD pfam01835 pfam01835 426464 MG2 MG2 domain. This is the MG2 (macroglobulin) domain of alpha-2-macroglobulin in eukaryotes. Alpha-2-macroglobulins (A2Ms) are plasma proteins that trap and inhibit a broad range of proteases and are major components of the eukaryotic innate immune system. However, A2M-like proteins were identified in pathogenically invasive bacteria and species that colonize higher eukaryotes. This domain is found in eukaryotic and bacterial proteins. In human A2Ms, this domain is termed macroglobulin-like (MG) domain 2 and in Salmonella enterica ser A2Ms, this is domain 4. 95 matched cddid_all.tbl CDD pfam01837 pfam01837 426465 HcyBio Homocysteine biosynthesis enzyme, sulfur-incorporation. This presumed domain is about is about 360 residues long. The function of this domain is unknown. It is found in some proteins that have two C-terminal CBS pfam00571 domains. There are also proteins that contain two inserted Fe4S domains near the C-terminal end of the domain. The protein Swiss:O26943 has been misannotated as an inosine monophosphate dehydrogenase based on the similarity to the CBS domains. Based on genetic analyses in the methanogen Methanosarcina acetivorans, this family is a key component of the metabolic network for sulfide assimilation and trafficking in methanogens. It is essential to a novel, O-acetylhomoserine sulfhydrylase-independent pathway for homocysteine biosynthesis, and may catalyze sulfur incorporation into the side chain of an as yet unidentified amino acid precursor. The DUF39-CBS and DUF39-ferredoxin architectures repeatedly occur together in the genomes of methanogenic Archaea, suggesting they may be of diverged function. This is consistent with a phylogenetic reconstruction of the DUF39 family, which clearly distinguishes the CBS-associated and ferredoxin-associated DUF39s. 350 matched cddid_all.tbl CDD pfam01839 pfam01839 460357 FG-GAP FG-GAP repeat. This family contains the extracellular repeat that is found in up to seven copies in alpha integrins. This repeat has been predicted to fold into a beta propeller structure. The repeat is called the FG-GAP repeat after two conserved motifs in the repeat. The FG-GAP repeats are found in the N terminus of integrin alpha chains, a region that has been shown to be important for ligand binding. A putative Ca2+ binding motif is found in some of the repeats. 36 matched cddid_all.tbl CDD pfam01840 pfam01840 460358 TCL1_MTCP1 TCL1/MTCP1 family. Two related oncogenes, TCL-1 and MTCP-1, are overexpressed in T cell prolymphocytic leukaemias as a result of chromosomal rearrangements that involve the translocation of one T cell receptor gene to either chromosome 14q32 or Xq28. This family contains two repeated motifs that form a single globular domain. 118 matched cddid_all.tbl CDD pfam01841 pfam01841 376628 Transglut_core Transglutaminase-like superfamily. This family includes animal transglutaminases and other bacterial proteins of unknown function. Sequence conservation in this superfamily primarily involves three motifs that centre around conserved cysteine, histidine, and aspartate residues that form the catalytic triad in the structurally characterized transglutaminase, the human blood clotting factor XIIIa'. On the basis of the experimentally demonstrated activity of the Methanobacterium phage pseudomurein endoisopeptidase, it is proposed that many, if not all, microbial homologs of the transglutaminases are proteases and that the eukaryotic transglutaminases have evolved from an ancestral protease. 108 matched cddid_all.tbl CDD pfam01842 pfam01842 426468 ACT ACT domain. This family of domains generally have a regulatory role. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme. The ACT domain is found in: D-3-phosphoglycerate dehydrogenase EC:1.1.1.95, which is inhibited by serine. Aspartokinase EC:2.7.2.4, which is regulated by lysine. Acetolactate synthase small regulatory subunit, which is inhibited by valine. Phenylalanine-4-hydroxylase EC:1.14.16.1, which is regulated by phenylalanine. Prephenate dehydrogenase EC:4.2.1.51. formyltetrahydrofolate deformylase EC:3.5.1.10, which is activated by methionine and inhibited by glycine. GTP pyrophosphokinase EC:2.7.6.5 66 matched cddid_all.tbl CDD pfam01843 pfam01843 460359 DIL DIL domain. The DIL domain has no known function. 103 matched cddid_all.tbl CDD pfam01844 pfam01844 396422 HNH HNH endonuclease. His-Asn-His (HNH) proteins are a very common family of small nucleic acid-binding proteins that are generally associated with endonuclease activity. 47 matched cddid_all.tbl CDD pfam01845 pfam01845 426470 CcdB CcdB protein. 99 matched cddid_all.tbl CDD pfam01846 pfam01846 426471 FF FF domain. This domain has been predicted to be involved in protein-protein interaction. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions. 50 matched cddid_all.tbl CDD pfam01847 pfam01847 460360 VHL VHL beta domain. VHL forms a ternary complex with the elongin B and elongin C proteins. This complex binds Cul2, which then is involved in regulation of vascular endothelial growth factor mRNA. 82 matched cddid_all.tbl CDD pfam01848 pfam01848 426473 HOK_GEF Hok/gef family. 41 matched cddid_all.tbl CDD pfam01849 pfam01849 426474 NAC NAC domain. 54 matched cddid_all.tbl CDD pfam01850 pfam01850 426475 PIN PIN domain. 121 matched cddid_all.tbl CDD pfam01851 pfam01851 460361 PC_rep Proteasome/cyclosome repeat. 35 matched cddid_all.tbl CDD pfam01852 pfam01852 426476 START START domain. 205 matched cddid_all.tbl CDD pfam01853 pfam01853 460362 MOZ_SAS MOZ/SAS family. This region of these proteins has been suggested to be homologous to acetyltransferases. 179 matched cddid_all.tbl CDD pfam01855 pfam01855 396432 POR_N Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg. This family includes the N terminal structural domain of the pyruvate ferredoxin oxidoreductase. This domain binds thiamine diphosphate, and along with domains II and IV, is involved in inter subunit contacts. The family also includes pyruvate flavodoxin oxidoreductase as encoded by the nifJ gene in cyanobacterium which is required for growth on molecular nitrogen when iron is limited. 230 matched cddid_all.tbl CDD pfam01856 pfam01856 280099 HP_OMP Helicobacter outer membrane protein. This family seems confined to Helicobacter. It is predicted to be an outer membrane protein based on its pattern of alternating hydrophobic amino acids similar to porins. 154 matched cddid_all.tbl CDD pfam01857 pfam01857 460363 RB_B Retinoblastoma-associated protein B domain. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B domain. The B domain has a cyclin fold. 131 matched cddid_all.tbl CDD pfam01858 pfam01858 460364 RB_A Retinoblastoma-associated protein A domain. This domain has the cyclin fold as predicted. 195 matched cddid_all.tbl CDD pfam01861 pfam01861 396435 BpsA_C Branched-chain polyamine synthase A C-terminal domain. This domain is found in the C terminus of N(4)-bis(aminopropyl)spermidine synthase (EC:2.5.1.128, also known as Branched-chain polyamine synthase A, BpsA) from hyperthermophiles and in uncharacterized proteins from bacteria and archaea. 243 matched cddid_all.tbl CDD pfam01862 pfam01862 426480 PvlArgDC Pyruvoyl-dependent arginine decarboxylase (PvlArgDC). Methanococcus jannaschii contains homologs of most genes required for spermidine polyamine biosynthesis. Yet genomes from neither this organizm nor any other euryarchaeon have orthologues of the pyridoxal 5'-phosphate- dependent ornithine or arginine decarboxylase genes, required to produce putrescine. Instead,these organizms have a new class of arginine decarboxylase (PvlArgDC) formed by the self-cleavage of a proenzyme into a 5-kDa subunit and a 12-kDa subunit that contains a reactive pyruvoyl group. Although this extremely thermostable enzyme has no significant sequence similarity to previously characterized proteins, conserved active site residues are similar to those of the pyruvoyl-dependent histidine decarboxylase enzyme, and its subunits form a similar (alpha-beta)(3) complex. homologs of PvlArgDC are found in several bacterial genomes, including those of Chlamydia spp., which have no agmatine ureohydrolase enzyme to convert agmatine (decarboxylated arginine) into putrescine. In these intracellular pathogens, PvlArgDC may function analogously to pyruvoyl-dependent histidine decarboxylase; the cells are proposed to import arginine and export agmatine, increasing the pH and affecting the host cell's metabolism. Phylogenetic analysis of Pvl- ArgDC proteins suggests that this gene has been recruited from the euryarchaeal polyamine biosynthetic pathway to function as a degradative enzyme in bacteria. 161 matched cddid_all.tbl CDD pfam01863 pfam01863 396437 YgjP-like YgjP-like, metallopeptidase domain. This is a conserved domain containing the catalytic zinc-metallopeptidase (HExxH) catalytic motif. Proteins containing this domain are found in some archaebacteria, as well as Helicobacter pylori. The proteins are 190-240 amino acids long, with the C terminus being the most conserved region, containing three conserved histidines. This domain is found in YgjP from E. coli, a predicted metal-dependent hydrolase that hydrolyses UTP to UMP and diphosphate in vitro; and in MJ0123 from Methanocaldococcus jannaschii (also referred to as projannalysin). 207 matched cddid_all.tbl CDD pfam01864 pfam01864 280105 CarS-like CDP-archaeol synthase. CDP-archaeol synthase functions in the archaeal lipid biosynthetic pathway. It catalyzes the transfer of the nucleotide to its specific archaeal lipid substrate, leading to the formation of a CDP-activated precursor (CDP-archaeol) to which polar head groups are attached. Bacterial members of this family are uncharacterized. 175 matched cddid_all.tbl CDD pfam01865 pfam01865 280106 PhoU_div Protein of unknown function DUF47. This family includes prokaryotic proteins of unknown function, as well as a protein annotated as the pit accessory protein from Sinorhizobium meliloti. However, the function of this protein is also unknown (Pit stands for Phosphate transport). It is probably distantly related to pfam01895 (personal obs:Yeats C). 214 matched cddid_all.tbl CDD pfam01866 pfam01866 460365 Diphthamide_syn Putative diphthamide synthesis protein. Diphthamide_syn, diphthamide synthase, catalyzes the last amidation step of diphthamide biosynthesis using ammonium and ATP. Swiss:Q16439 is a candidate tumour suppressor gene. DPH2 from yeast, which confers resistance to diphtheria toxin has been found to be involved in diphthamide synthesis. Diphtheria toxin inhibits eukaryotic protein synthesis by ADP-ribosylating diphthamide, a post-translationally modified histidine residue present in EF2. Diphthamide synthase is evolutionarily conserved in eukaryotes. Diphthamide is a post-translationally modified histidine residue found on archaeal and eukaryotic translation elongation factor 2 (eEF-2). 302 matched cddid_all.tbl CDD pfam01867 pfam01867 460366 Cas_Cas1 CRISPR associated protein Cas1. Clustered regularly interspaced short palindromic repeats (CRISPRs) are a family of DNA direct repeats found in many prokaryotic genomes. This family of proteins corresponds to Cas1, a CRISPR-associated protein. Cas1 may be involved in linking DNA segments to CRISPR. 283 matched cddid_all.tbl CDD pfam01868 pfam01868 460367 RNase_P-MRP_p29 Ribonuclease P/MRP, subunit p29. This family consists of several archaeal and eukaryotic proteins. The archaeal proteins are found to be expressed within ribosomal operons and several of the sequences are described as ribonuclease P protein subunit p29 proteins. The structure of the RNase P subunit, Rpp29, from Methanobacterium thermoautotrophicum has been determined. Mth Rpp29 is a member of the oligonucleotide/oligosaccharide binding fold family. It contains a structured beta-barrel core and unstructured N- and C-terminal extensions bearing several highly conserved amino acid residues that could be involved in RNA contacts in the protein-RNA complex. Rpp29 catalyzes the endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. It interacts with the Rpp25 and Pop5 subunits. 84 matched cddid_all.tbl CDD pfam01869 pfam01869 396441 BcrAD_BadFG BadF/BadG/BcrA/BcrD ATPase family. This family includes the BadF and BadG proteins that are two subunits of Benzoyl-CoA reductase, that may be involved in ATP hydrolysis. The family also includes an activase subunit from the enzyme 2-hydroxyglutaryl-CoA dehydratase. The protein Swiss:O66634 contains two copies of this region suggesting that the family may structurally dimerize. This family appears to be related to pfam00370. 271 matched cddid_all.tbl CDD pfam01870 pfam01870 396442 Hjc Archaeal holliday junction resolvase (hjc). This family of archaebacterial proteins are holliday junction resolvases (hjc gene). The Holliday junction is an essential intermediate of homologous recombination. This protein is the archaeal equivalent of RuvC but is not sequence similar. 91 matched cddid_all.tbl CDD pfam01871 pfam01871 460368 AMMECR1 AMMECR1. This family consists of several AMMECR1 as well as several uncharacterized proteins. The contiguous gene deletion syndrome AMME is characterized by Alport syndrome, midface hypoplasia, mental retardation and elliptocytosis and is caused by a deletion in Xq22.3, comprising several genes including COL4A5, FACL4 and AMMECR1. This family contains sequences from several eukaryotic species as well as archaebacteria and it has been suggested that the AMMECR1 protein may have a basic cellular function, potentially in either the transcription, replication, repair or translation machinery. 167 matched cddid_all.tbl CDD pfam01872 pfam01872 396444 RibD_C RibD C-terminal domain. The function of this domain is not known, but it is thought to be involved in riboflavin biosynthesis. This domain is found in the C terminus of RibD/RibG, in combination with pfam00383, as well as in isolation in some archaebacterial proteins. This family appears to be related to pfam00186. 196 matched cddid_all.tbl CDD pfam01873 pfam01873 426485 eIF-5_eIF-2B Domain found in IF2B/IF5. This family includes the N terminus of eIF-5, and the C terminus of eIF-2 beta. This region corresponds to the whole of the archaebacterial eIF-2 beta homolog. The region contains a putative zinc binding C4 finger. 115 matched cddid_all.tbl CDD pfam01874 pfam01874 426486 CitG ATP:dephospho-CoA triphosphoribosyl transferase. The citG gene is found in a gene cluster with citrate lyase subunits. The function of the CitG protein was elucidated as ATP:dephospho-CoA triphosphoribosyl transferase. 256 matched cddid_all.tbl CDD pfam01875 pfam01875 280116 Memo Memo-like protein. This family contains members from all branches of life. The molecular function of this protein is unknown, but Memo (mediator of ErbB2-driven cell motility) a human protein is included in this family. It has been suggested that Memo controls cell migration by relaying extracellular chemotactic signals to the microtubule cytoskeleton. 271 matched cddid_all.tbl CDD pfam01876 pfam01876 396447 RNase_P_p30 RNase P subunit p30. This protein is part of the RNase P complex that is involved in tRNA maturation. 214 matched cddid_all.tbl CDD pfam01877 pfam01877 426487 RNA_binding RNA binding. PH1010 is composed of five alpha-helices (1-5) and eight beta-strands (1-8) with the following topology: beta-1, alpha-1, beta-2, beta-3, alpha-2, alpha-3, beta-4, beta-5, alpha-4, beta-6, alpha-5, beta-7, beta-8. The first six beta-strands (1-6) form a slightly twisted antiparallel beta-sheet and face five alpha-helices on one side. The last two beta-strands form an antiparallel beta-sheet in the C-terminus. PH1010 forms a characteriztic homodimer structure in the crystal. dimerization of the molecule is crucial for function. The structure resembles that of some ribosomal proteins such as the 50S ribosomal protein L5. Although the structure resembles that of the RRM-type RNA-binding domain of the ribosomal L5 protein, the residues involved in RNA-binding in the L5 protein are not conserved in this family. Despite this, these proteins bind to double-stranded RNA in a non-sequence specific manner. 113 matched cddid_all.tbl CDD pfam01878 pfam01878 396449 EVE EVE domain. This domain was formerly known as DUF55. Crystal structures have shown that this domain is part of the PUA superfamily. This domain has been named EVE and is thought to be RNA-binding. 146 matched cddid_all.tbl CDD pfam01880 pfam01880 396450 Desulfoferrodox Desulfoferrodoxin. Desulfoferrodoxins contains two types of iron: an Fe-S4 site very similar to that found in desulforedoxin from Desulfovibrio gigas and an octahedral coordinated high-spin ferrous site most probably with nitrogen/oxygen-containing ligands. Due to this rather unusual combination of active centres, this novel protein is named desulfoferrodoxin. 97 matched cddid_all.tbl CDD pfam01881 pfam01881 460369 Cas_Cas6_C CRISPR associated protein Cas6, C-terminal. This group of families is one of several protein families that are always found associated with prokaryotic CRISPRs, themselves a family of clustered regularly interspaced short palindromic repeats, DNA repeats found in nearly half of all bacterial and archaeal genomes. These DNA repeat regions have a remarkably regular structure: unique sequences of constant size, called spacers, sit between each pair of repeats. It has been shown that the CRISPRs are virus-derived sequences acquired by the host to enable them to resist viral infection. The Cas proteins from the host use the CRISPRs to mediate an antiviral response. After transcription of the CRISPR, a complex of Cas proteins termed Cascade cleaves a CRISPR RNA precursor in each repeat and retains the cleavage products containing the virus-derived sequence. Assisted by the helicase Cas3, these mature CRISPR RNAs then serve as small guide RNAs that enable Cascade to interfere with virus proliferation. Cas5 contains an endonuclease motif, whose inactivation leads to loss of resistance, even in the presence of phage-derived spacers. In Type I and III CRISPR/Cas systems, the Cas6 family of endoribonucleases generates functional CRISPR-derived RNAs by site-specific cleavage of repeat sequences in precursor transcripts. The structure of Cas6 showed it adopts a tandem ferredoxin/RRM fold. This entry represents the C-terminal domain. 87 matched cddid_all.tbl CDD pfam01882 pfam01882 426489 DUF58 Protein of unknown function DUF58. This family of prokaryotic proteins have no known function. Swiss:P71138 a protein of unknown function in the family has been misannotated as alpha-dextrin 6-glucanohydrolase. 86 matched cddid_all.tbl CDD pfam01883 pfam01883 460370 FeS_assembly_P Iron-sulfur cluster assembly protein. This family has an alpha/beta topology, with 13 conserved hydrophobic residues at its core and a putative active site containing a highly conserved cysteine. Members of this family are involved in a range of physiological functions. The family includes PaaJ (PhaH) from Pseudomonas putida. PaaJ forms a complex with PaaG (PhaF), PaaI (PhaG) and PaaK (PhaI), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid. It also includes PaaD from Escherichia coli, a member of a multicomponent oxygenase involved in phenylacetyl-CoA hydroxylation. Furthermore, several members of this family are shown to be involved in iron-sulfur (FeS) cluster assembly. Iron-sulfur (FeS) clusters are inorganic co-factors that are are able to transfer electrons and act as catalysts. They are involved in diverse cellular processes including cellular respiration, DNA replication and repair, antibiotic resistance, and dinitrogen fixation. The biogenesis of such clusters from elemental iron and sulfur is an enzymatic process that requires a set of specialized proteins. Proteins containing this domain include the chloroplast protein HCF101 (high chlorophyll fluorescence 101), which has been described as an essential and specific factor for assembly of [4Fe-4S]-cluster-containing protein complexes such as the membrane complex Photosystem I (PSI) and the heterodimeric FTR (ferredoxin-thioredoxin reductase) complex and is involved in the assembly of [4Fe-4S] clusters and their transfer to apoproteins. The mature HCF101 protein contains this domain at the N-terminal as well as eight cysteine residues along the sequence. All cysteine residues are conserved among higher plants, but of the two cysteine residues located in this domain only Cys128 is highly conserved and is present in the highly conserved P-loop domain of the plant HCF101 (CKGGVGKS). SufT protein from Staphylococcus aureus is composed of this domain solely and is shown to be involved in the maturation of FeS proteins. Given all this data, it is hypothesized that this domain might play a role in FeS cluster assembly. 73 matched cddid_all.tbl CDD pfam01884 pfam01884 396454 PcrB PcrB family. This family contains proteins that are related to PcrB. The function of these proteins is unknown. 226 matched cddid_all.tbl CDD pfam01885 pfam01885 460371 PTS_2-RNA "RNA 2'-phosphotransferase, Tpt1 / KptA family. Tpt1 catalyzes the last step of tRNA splicing in yeast. It transfers the splice junction 2'-phosphate from ligated tRNA to NAD, to produce ADP-ribose 1""-2""-cyclic phosphate. This is presumed to be followed by a transesterification step to release the RNA. The first step of this reaction is similar to that catalyzed by some bacterial toxins. E. coli KptA and mouse Tpt1 are likely to use the same reaction mechanism." 168 matched cddid_all.tbl CDD pfam01886 pfam01886 426492 DUF61 Protein of unknown function DUF61. This Domain of unknown function 61 (DUF61) family of proteins are widely distributed in archaea. In crenarchaea, the genes of DUF61 proteins are in an operon containing two genes of box C/D RNA protein complexes. The NMR structure of a DUF61 family member from the hyperthermophilic archaeon Sulfolobus solfataricus revealed a rigid core structure and flexible N- and C-terminal regions, including a negatively-charged independent C-terminal helix. The core structure consists of N- and C-terminal subdomains, in which the C-terminal subdomain shows significant structural similarity with several nucleic acid binding proteins. 121 matched cddid_all.tbl CDD pfam01887 pfam01887 460372 SAM_HAT_N SAM hydroxide adenosyltransferase N-terminal domain. This is a family of proteins, previously known as DUF62, found in archaebacteria and bacteria. The structure of proteins in this family is similar to that of a bacterial fluorinating enzyme. S-adenosyl-l-methionine hydroxide adenosyltransferases utilizes a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion. This family used to be known as DUF62. 145 matched cddid_all.tbl CDD pfam01888 pfam01888 460373 CbiD CbiD. CbiD is essential for cobalamin biosynthesis in both S. typhimurium and B. megaterium, no functional role has been ascribed to the protein. The CbiD protein has a putative S-AdoMet binding site. It is possible that CbiD might have the same role as CobF in undertaking the C-1 methylation and deacylation reactions required during the ring contraction process. 258 matched cddid_all.tbl CDD pfam01889 pfam01889 426495 DUF63 Membrane protein of unknown function DUF63. Proteins found in Archaebacteria of unknown function. These proteins are probably transmembrane proteins. 269 matched cddid_all.tbl CDD pfam01890 pfam01890 460374 CbiG_C Cobalamin synthesis G C-terminus. Members of this family are involved in cobalamin synthesis. The gene encoded by Swiss:P72862 has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyze adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyzes a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process. Within the cobalamin synthesis pathway CbiG catalyzes the both the opening of the lactone ring and the extrusion of the two-carbon fragment of cobalt-precorrin-5A from C-20 and its associated methyl group (deacylation) to give cobalt-precorrin-5B. This family is the C-terminal region, and the mid- and N-termival parts are conserved independently in other families. 120 matched cddid_all.tbl CDD pfam01891 pfam01891 460375 CbiM Cobalt uptake substrate-specific transmembrane region. This family of proteins forms part of the cobalt-transport complex in prokaryotes, CbiMNQO. CbiMNQO and NikMNQO are the most widespread groups of microbial transporters for cobalt and nickel ions and are unusual uptake systems as they consist of eg two transmembrane components (CbiM and CbiQ), a small membrane-bound component (CbiN) and an ATP-binding protein (CbiO) but no extracytoplasmic solute-binding protein. Similar components constitute the nickel transporters with some variability in the small membrane-bound component, either NikN or NikL, which are not similar to CbiN at the sequence level. CbiM is the substrate-specific component of the complex and is a seven-transmembrane protein. The CbiMNQO and NikMNQO systems form part of the coenzyme B12 biosynthesis pathway. The NikM protein is pfam10670. 202 matched cddid_all.tbl CDD pfam01893 pfam01893 426498 UPF0058 Uncharacterized protein family UPF0058. This archaebacterial protein has no known function. 86 matched cddid_all.tbl CDD pfam01894 pfam01894 460376 UPF0047 Uncharacterized protein family UPF0047. This family has no known function. The alignment contains a conserved aspartate and histidine that may be functionally important. 116 matched cddid_all.tbl CDD pfam01895 pfam01895 426500 PhoU PhoU domain. This family contains phosphate regulatory proteins including PhoU. PhoU proteins are known to play a role in the regulation of phosphate uptake. The PhoU domain is composed of a three helix bundle. The PhoU protein contains two copies of this domain. The domain binds to an iron cluster via its conserved E/DXXXD motif. 87 matched cddid_all.tbl CDD pfam01896 pfam01896 460377 DNA_primase_S DNA primase small subunit. DNA primase synthesizes the RNA primers for the Okazaki fragments in lagging strand DNA synthesis. DNA primase is a heterodimer of large and small subunits. This family also includes baculovirus late expression factor 1 or LEF-1 proteins. Baculovirus LEF-1 is a DNA primase enzyme. The family also contains many bacterial DNA primases. 158 matched cddid_all.tbl CDD pfam01899 pfam01899 460378 MNHE Na+/H+ ion antiporter subunit. Subunit of a Na+/H+ Prokaryotic antiporter complex. 150 matched cddid_all.tbl CDD pfam01900 pfam01900 460379 RNase_P_Rpp14 Rpp14/Pop5 family. tRNA processing enzyme ribonuclease P (RNase P) consists of an RNA molecule associated with at least eight protein subunits, hPop1, Rpp14, Rpp20, Rpp25, Rpp29, Rpp30, Rpp38, and Rpp40. This protein is known as Pop5 in eukaryotes. 102 matched cddid_all.tbl CDD pfam01901 pfam01901 396468 O_anti_polymase Putative O-antigen polymerase. Archaebacterial proteins of unknown function. Members of this family may be transmembrane proteins. These are potentially O-antigen assembly enzymes, with up to 11 transmembrane regions. 337 matched cddid_all.tbl CDD pfam01902 pfam01902 280139 Diphthami_syn_2 Diphthamide synthase. Diphthamide_syn, diphthamide synthase, catalyzes the last amidation step of diphthamide biosynthesis using ammonium and ATP. Diphthamide synthase is evolutionarily conserved in eukaryotes. Diphthamide is a post-translationally modified histidine residue found on archaeal and eukaryotic translation elongation factor 2 (eEF-2). In some members of this family, this domain is associated with pfam01042. The enzyme classification is EC:6.3.1.14. 219 matched cddid_all.tbl CDD pfam01903 pfam01903 396469 CbiX CbiX. The function of CbiX is uncertain, however it is found in cobalamin biosynthesis operons and so may have a related function. Some CbiX proteins contain a striking histidine-rich region at their C-terminus, which suggests that it might be involved in metal chelation. 106 matched cddid_all.tbl CDD pfam01904 pfam01904 426503 DUF72 Protein of unknown function DUF72. The function of this family is unknown. 220 matched cddid_all.tbl CDD pfam01905 pfam01905 396471 DevR CRISPR-associated negative auto-regulator DevR/Csa2. This group of families is one of several protein families that are always found associated with prokaryotic CRISPRs, themselves a family of clustered regularly interspaced short palindromic repeats, DNA repeats found in nearly half of all bacterial and archaeal genomes. These DNA repeat regions have a remarkably regular structure: unique sequences of constant size, called spacers, sit between each pair of repeats. It has been shown that the CRISPRs are virus-derived sequences acquired by the host to enable them to resist viral infection. The Cas proteins from the host use the CRISPRs to mediate an antiviral response. After transcription of the CRISPR, a complex of Cas proteins termed Cascade cleaves a CRISPR RNA precursor in each repeat and retains the cleavage products containing the virus-derived sequence. Assisted by the helicase Cas3, these mature CRISPR RNAs then serve as small guide RNAs that enable Cascade to interfere with virus proliferation. Cas5 contains an endonuclease motif, whose inactivation leads to loss of resistance, even in the presence of phage-derived spacers. This family used to be known as DUF73. DevR appears to be negative auto-regulator within the system. 268 matched cddid_all.tbl CDD pfam01906 pfam01906 426504 YbjQ_1 Putative heavy-metal-binding. From comparative structural analysis, this family is likely to be a heavy-metal binding domain. The domain oligomerises as a pentamer. The domain is about 100 amino acids long and is found in prokaryotes. 99 matched cddid_all.tbl CDD pfam01907 pfam01907 460380 Ribosomal_L37e Ribosomal protein L37e. This family includes ribosomal protein L37 from eukaryotes and archaebacteria. The family contains many conserved cysteines and histidines suggesting that this protein may bind to zinc. 53 matched cddid_all.tbl CDD pfam01909 pfam01909 396474 NTP_transf_2 Nucleotidyltransferase domain. Members of this family belong to a large family of nucleotidyltransferases. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase in-activates antibiotics by catalysing the addition of a nucleotidyl group onto the drug. 91 matched cddid_all.tbl CDD pfam01910 pfam01910 426506 Thiamine_BP Thiamine-binding protein. The crystal structure of two of these members shows that this domain has a ferredoxin like fold and is likely to exists as at least homodimers. Sulphate ions are are located at the dimer interfaces, which are thought to confer additional stability. Although the function of this domain remains to be identified, its structure suggests a role in protein-protein interactions possibly regulated by the binding of small-molecule ligands. Solution of the structure of the hyperthermophilic anaerobic Thermotoga maritima sequence, UniProtKB:Q9WYV6, shows that this has a beta-alpha-beta-beta-alpha-beta ferredoxin-like fold and assembles as a homotetramer. It was possible to identify a pocket in each monmer that bound an unidentified ligand. It was also found that it bound charged thiamine though not hydroxymethyl pyrimidine. It is proposed that it is transporting charged thiamine around the cytoplasm. Under oxidative conditions this bacterium is under stress, and the transcriiptional unit within which this protein is expressed is up-regulated in these conditions, suggesting that the chelation of cytoplasmic thaimine is part of the response mechanism to such oxidatvie stress, which is mediated by this family. 92 matched cddid_all.tbl CDD pfam01912 pfam01912 460381 eIF-6 eIF-6 family. This family includes eukaryotic translation initiation factor 6 as well as presumed archaebacterial homologs. 196 matched cddid_all.tbl CDD pfam01913 pfam01913 396477 FTR Formylmethanofuran-tetrahydromethanopterin formyltransferase. This enzyme EC:2.3.1.101 is involved in archaebacteria in the formation of methane from carbon dioxide. N-terminal distal lobe of alpha+beta ferredoxin-like fold. SCOP reports fold duplication with C-terminal proximal lobe. 144 matched cddid_all.tbl CDD pfam01914 pfam01914 280149 MarC MarC family integral membrane protein. Integral membrane protein family that includes the protein MarC. MarC was thought to be a multiple antibiotic resistance protein. Nevertheless, a study has shown that MarC is not involved in multiple antibiotic resistance. The function of this family is unclear. 203 matched cddid_all.tbl CDD pfam01915 pfam01915 396478 Glyco_hydro_3_C Glycosyl hydrolase family 3 C-terminal domain. This domain is involved in catalysis and may be involved in binding beta-glucan. This domain is found associated with pfam00933. 216 matched cddid_all.tbl CDD pfam01916 pfam01916 460382 DS Deoxyhypusine synthase. Eukaryotic initiation factor 5A (eIF-5A) contains an unusual amino acid, hypusine [N epsilon-(4-aminobutyl-2-hydroxy)lysine]. The first step in the post-translational formation of hypusine is catalyzed by the enzyme deoxyhypusine synthase (DS) EC:1.1.1.249. The modified version of eIF-5A, and DS, are required for eukaryotic cell proliferation. 287 matched cddid_all.tbl CDD pfam01917 pfam01917 396480 Arch_flagellin Archaebacterial flagellin. Archaeal motility occurs by the rotation of flagella that show similarity to bacterial type IV pili, including the multiflagellin nature of the flagellar filament, N-terminal sequence similarities, as well as the presence of homologous proteins in the two systems. Similar to type IV pilins, archaeal flagellins are initially synthesized with a short leader peptide that is cleaved by a membrane-located peptidase. The enzyme responsible for the removal of the this leader peptide is FlaK. Archaeal flagella are composed of a number of distinct flagellin proteins, specified by genes in two separate operons (A and B). 160 matched cddid_all.tbl CDD pfam01918 pfam01918 426509 Alba Alba. Alba is a novel chromosomal protein that coats archaeal DNA without compacting it. 66 matched cddid_all.tbl CDD pfam01920 pfam01920 396482 Prefoldin_2 Prefoldin subunit. This family includes prefoldin subunits that are not detected by pfam02996. 102 matched cddid_all.tbl CDD pfam01921 pfam01921 396483 tRNA-synt_1f tRNA synthetases class I (K). This family includes only lysyl tRNA synthetases from prokaryotes. 357 matched cddid_all.tbl CDD pfam01922 pfam01922 460383 SRP19 SRP19 protein. The signal recognition particle (SRP) binds to the signal peptide of proteins as they are being translated. The binding of the SRP halts translation and the complex is then transported to the endoplasmic reticulum's cytoplasmic surface. The SRP then aids translocation of the protein through the ER membrane. The SRP is a ribonucleoprotein that is composed of a small RNA and several proteins. One of these proteins is the SRP19 protein (Sec65 in yeast). 94 matched cddid_all.tbl CDD pfam01923 pfam01923 460384 Cob_adeno_trans Cobalamin adenosyltransferase. Cobalamin adenosyltransferase This family contains the gene products of PduO and EutT which are both cobalamin adenosyltransferases. PduO is a protein with ATP:cob(I)alamin adenosyltransferase activity. The main role of this protein is the conversion of inactive cobalamins to AdoCbl for 1,2-propanediol degradation.The EutT enzyme appears to be an adenosyl transferase, converting CNB12 to AdoB12. 163 matched cddid_all.tbl CDD pfam01924 pfam01924 460385 HypD Hydrogenase formation hypA family. HypD is involved in hydrogenase formation. It contains many possible metal binding residues, which may bind to nickel. Transposon Tn5 insertions into hypD resulted in R. leguminosarum mutants that lacked any hydrogenase activity in symbiosis with peas. 352 matched cddid_all.tbl CDD pfam01925 pfam01925 460386 TauE Sulfite exporter TauE/SafE. This is a family of integral membrane proteins where the alignment appears to contain two duplicated modules of three transmembrane helices. The proteins are involved in the transport of anions across the cytoplasmic membrane during taurine metabolism as an exporter of sulfoacetate. This family used to be known as DUF81. 235 matched cddid_all.tbl CDD pfam01926 pfam01926 460387 MMR_HSR1 50S ribosome-binding GTPase. The full-length GTPase protein is required for the complete activity of the protein of interacting with the 50S ribosome and binding of both adenine and guanine nucleotides, with a preference for guanine nucleotide. 113 matched cddid_all.tbl CDD pfam01927 pfam01927 426515 Mut7-C Mut7-C RNAse domain. RNAse domain of the PIN fold with an inserted Zinc Ribbon at the C terminus. 146 matched cddid_all.tbl CDD pfam01928 pfam01928 396490 CYTH CYTH domain. These sequences are functionally identified as members of the adenylate cyclase family, which catalyzes the conversion of ATP to 3',5'-cyclic AMP and pyrophosphate. Six distinct non-homologous classes of AC have been identified. The structure of three classes of adenylyl cyclases have been solved. 172 matched cddid_all.tbl CDD pfam01929 pfam01929 460388 Ribosomal_L14e Ribosomal protein L14. This family includes the eukaryotic ribosomal protein L14. 74 matched cddid_all.tbl CDD pfam01930 pfam01930 426517 Cas_Cas4 Domain of unknown function DUF83. This domain has no known function. The domain contains three conserved cysteines at its C terminus. 160 matched cddid_all.tbl CDD pfam01931 pfam01931 460389 NTPase_I-T Protein of unknown function DUF84. NTPase_I-T is a family of NTPases with supreme activity against ITP and XTP. Active site analysis and structure comparison of YjjX strongly suggested that it is an NTP binding protein with nucleoside triphosphatase activity. YjjX exhibits a mixed alpha-beta fold. 163 matched cddid_all.tbl CDD pfam01933 pfam01933 426519 CofD 2-phospho-L-lactate transferase CofD. This entry contains 2-phospho-L-lactate transferase (CofD), phosphoenolpyruvate transferase and related sequences. CofD catalyzes the fourth step in the biosynthesis of coenzyme F420, which is the transfer of the 2-phospholactate moiety from lactyl (2)diphospho-(5') guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) with the formation of the L-lactyl phosphodiester of 7,8-didemethyl- 8-hydroxy-5-deazariboflavin (F420-0) and GMP. F420 is a flavin derivative found in methanogens, Mycobacteria, and several other lineages. This enzyme is characterized so far in Methanocaldococcus jannaschii (Methanococcus jannaschii) but appears restricted to F420-containing species and is predicted to carry out the same function in these other species. CofD monomer contains 12 beta- strands, seven of them form a Rossmann fold, and 13 alpha-helices. 249 matched cddid_all.tbl CDD pfam01934 pfam01934 460390 HepT-like Ribonuclease HepT-like. This family includes the toxic component HepT of a type II toxin-antitoxin (TA) system, which has RNase activity. These proteins contain a HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain and are neutralized through tri-AMPylation by the cognate antitoxin MntA, containing a MNT (minimal nucleotidyltransferase) domain. HepT-MnA form an heterooctamer (at a 2:6 ratio), a rare organization for this kind of TA systems. HepT dimerizes and enables the formation of a deep cleft at the HEPN-domain interface, containing the RX4-6H motif (where X is any amino acid and the residue immediately after the conserved R is typically a polar amino acid) as the active site that functions as an RNA-cleaving RNase. This type II TA system regulates cell motility and confers plasmid stability. Due to the prevalence of these HEPN/MNT modules in bacteria and archaea, it has been suggested that these TA systems may also play a role in the environmental adaptation to extreme habitats. 120 matched cddid_all.tbl CDD pfam01935 pfam01935 376671 DUF87 Helicase HerA, central domain. This entry represents the central domain found in archaeal proteins such as DNA double-strand break repair helicase HerA (EC:3.6.4.12). HerA is a helicase which is able to utilize either 3' or 5' single-stranded DNA extensions for loading and subsequent DNA duplex unwinding. It forms a complex with NurA nuclease, this complex has the 5'-3' DNA end resection activity and is essential for cell viability in the crenarchaeon Sulfolobus islandicus. This domain includes the the central RecA-like catalytic core and a flanking four-helix bundle. The function of this prokaryotic domain is unknown. It contains several conserved aspartates and histidines that could be metal ligands. 220 matched cddid_all.tbl CDD pfam01936 pfam01936 426520 NYN NYN domain. These domains are found in the eukaryotic proteins typified by the Nedd4-binding protein 1 and the bacterial YacP-like proteins (Nedd4-BP1, YacP nucleases; NYN domains). The NYN domain shares a common protein fold with two other previously characterized groups of nucleases, namely the PIN (PilT N-terminal) and FLAP/5' --> 3' exonuclease superfamilies. These proteins share a common set of 4 acidic conserved residues that are predicted to constitute their active site. Based on the conservation of the acidic residues and structural elements Aravind and colleagues suggest that PIN and NYN domains are likely to bind only a single metal ion, unlike the FLAP/5' --> 3' exonuclease superfamily, which binds two metal ions. Based on conserved gene neighborhoods Aravind and colleagues infer that the bacterial members are likely to be components of the processome/degradsome that process tRNAs or ribosomal RNAs. 137 matched cddid_all.tbl CDD pfam01937 pfam01937 396496 ARMT1-like_dom "Damage-control phosphatase ARMT1-like domain. This domain is widely distributed in all domains of life and occur in stand-alone form and as C-terminal fusions to pantothenate kinase (PanK) in plants and animals. They are metal-dependent phosphatases involved in metabolic damage-control processes termed ""damage pre-emption"" or ""housecleaning"". S.cerevisiae Damage-control phosphatase YMR027W and the human orthologue Damage-control phosphatase ARMT1 (also known as C6orf211) are involved in response to DNA damage, a damage pre-emption function. Crystal structure of Damage-control phosphatase At2g17340 from Arabidopsis revealed a novel protein fold and several conserved residues coordinating a metal ion (probably Mg2+), which exhibits a high degree of conservation, suggesting that the metal-binding site is central for the function." 303 matched cddid_all.tbl CDD pfam01938 pfam01938 396497 TRAM TRAM domain. This small domain has no known function. However it may perform a nucleic acid binding role (Bateman A. unpublished observation). 59 matched cddid_all.tbl CDD pfam01939 pfam01939 280172 NucS Endonuclease NucS. Endonuclease NucS cleaves both 3' and 5' ssDNA extremities of branched DNA structures and it binds to ssDNA. 229 matched cddid_all.tbl CDD pfam01940 pfam01940 460391 DUF92 Integral membrane protein DUF92. Members of this family have several predicted transmembrane helices. One member of the family has been characterized as protein PGR (AtPGR). PGR is suggested to be a potential glucose-responsive regulator in carbohydrate metabolism in plants. This entry also includes protein VTE6, which is a Pphytyl-phosphate kinase catalysing the conversion of phytyl-monophosphate to phytyl-diphosphate. 237 matched cddid_all.tbl CDD pfam01941 pfam01941 460392 AdoMet_Synthase S-adenosylmethionine synthetase (AdoMet synthetase). This family consists of several archaebacterial S-adenosylmethionine synthetase C(AdoMet synthetase or MAT) (EC 2.5.1.6). S-Adenosylmethionine (AdoMet) occupies a central role in the metabolism of all cells. The biological roles of AdoMet include acting as the primary methyl group donor, as a precursor to the polyamines, and as a progenitor of a 5'-deoxyadenosyl radical. S-Adenosylmethionine synthetase catalyzes the only known route of AdoMet biosynthesis. The synthetic process occurs in a unique reaction in which the complete triphosphate chain is displaced from ATP and a sulfonium ion formed. MATs from various organizms contain ~400-amino acid polypeptide chains. 395 matched cddid_all.tbl CDD pfam01943 pfam01943 426523 Polysacc_synt Polysaccharide biosynthesis protein. Members of this family are integral membrane proteins. Many members of the family are implicated in production of polysaccharide. The family includes RfbX part of the O antigen biosynthesis operon. The family includes SpoVB from Bacillus subtilis, which is involved in spore cortex biosynthesis. 274 matched cddid_all.tbl CDD pfam01944 pfam01944 426524 SpoIIM Stage II sporulation protein M. SpoIIM is on e of four stage II sporulation proteins that is necessary for the forespore inside the mother-cell to be properly internalized through the breakdown of peptidoglycans trapped between the membranes of the septum separating the forespore and the mother-cell. The four proteins working in sequence are SpoIIB, pfam05036, SpoIIM, SpoIIP, pfam07454, and finally SpoIID, pfam08486. D, M and P are in a complex with each other and the complex assembles in a hierarchical manner such that M, which serves as a membrane anchor, recruits P to the septum and P, in turn, recruits D to the septum. 173 matched cddid_all.tbl CDD pfam01946 pfam01946 460393 Thi4 Thi4 family. This family includes Swiss:P32318 a putative thiamine biosynthetic enzyme. 232 matched cddid_all.tbl CDD pfam01947 pfam01947 366866 Rv2949c-like Chorismate pyruvate-lyase Rv2949c-like. This domain is found in chorismate pyruvate-lyases (EC:4.1.3.40, also known as 4-HB synthase and p-hydroxybenzoic acid synthase) such as those found in Mycobacterium tuberculosis where it removes the pyruvyl group from chorismate to provide 4-hydroxybenzoate (4HB). The chorismate pyruvate-lyase encoded by sll1797 in cyanobacteria Synechocystis sp., has been shown to catalyze the initial and essential step in plastoquinone biosynthesis. In E. coli, the chorismate lyase (UbiC) catalyzes the conversion of chorismate to p-hydroxybenzoate and pyruvate in the biosynthesis of ubiquinone as well. 149 matched cddid_all.tbl CDD pfam01948 pfam01948 460394 PyrI Aspartate carbamoyltransferase regulatory chain, allosteric domain. The regulatory chain is involved in allosteric regulation of aspartate carbamoyltransferase. The N-terminal domain has ferredoxin-like fold, and provides the regulatory chain dimerization interface. 93 matched cddid_all.tbl CDD pfam01949 pfam01949 426526 DUF99 Protein of unknown function DUF99. This family includes uncharacterized archaebacterial proteins. Sequence and structure analysis to identify RNase H-like superfamily members, has clustered this family in endonuclease Clade V, thus suggesting endonuclease activity of these proteins. 173 matched cddid_all.tbl CDD pfam01950 pfam01950 396504 FBPase_3 Fructose-1,6-bisphosphatase. This is a family of bacterial and archaeal fructose-1,6-bisphosphatases (FBPases). FBPase catalyzes the hydrolysis of D-fructose-1,6-bisphosphate (FBP) to D-fructose-6-phosphate (F6P) and orthophosphate and is an essential regulatory enzyme in the glyconeogenic pathway. 357 matched cddid_all.tbl CDD pfam01951 pfam01951 426527 Archease Archease protein family (MTH1598/TM1083). This archease family of proteins, has two SHS2 domains, with one inserted into another. It is predicted to be an enzyme. It is predicted to act as a chaperone in DNA/RNA metabolism. 136 matched cddid_all.tbl CDD pfam01954 pfam01954 426528 AF2212-like AF2212-like. This family includes short bacterial and archaebacterial proteins thought to be antitoxin components of the a type II toxin-antitoxin (TA) system. This entry includes AF2212 from Archaeoglobus fulgidus which has sequence similarity with the AbrB superfamily of DNA-binding proteins, identified as antitoxins. The secondary structure of AF2212 revealed at least three beta-strands that are most conserved in other AbrB superfamily members. 56 matched cddid_all.tbl CDD pfam01955 pfam01955 426529 CbiZ Adenosylcobinamide amidohydrolase. This prokaryotic protein family includes CbiZ which converts adenosylcobinamide (AdoCbi) to adenosylcobyric acid (AdoCby), an intermediate of the de novo coenzyme B12 biosynthetic route. 193 matched cddid_all.tbl CDD pfam01956 pfam01956 396507 EMC3_TMCO1 Integral membrane protein EMC3/TMCO1-like. This entry represents a group of eukaryotic and archaeal proteins. Eukaryotic members include EMC3, a subunit of the ER membrane protein complex (EMC) required for protein folding, and TMCO1, a ER calcium load-activated calcium channel. Archaeal members may function as insertases of the archaeal plasma membrane. 169 matched cddid_all.tbl CDD pfam01957 pfam01957 460395 NfeD NfeD-like C-terminal, partner-binding. NfeD-like proteins are widely distributed throughout prokaryotes and are frequently associated with genes encoding stomatin-like proteins (slipins). There appear to be three major groups: an ancestral group with only an N-terminal serine protease domain and this C-terminal beta sheet-rich domain which is structurally very similar to the OB-fold domain, associated with its neighbouring slipin cluster; a second major group with an additional middle, membrane-spanning domain, associated in some species with eoslipin and in others with yqfA; a final 'artificial' group which unites truncated forms lacking the protease region and associated with their ancestral gene partner, either yqfA or eoslipin. This NefD, C-terminal, domain appears to be the major one for relating to the associated protein. NfeD homologs are clearly reliant on their conserved gene neighbour which is assumed to be necessary for function, either through direct physical interaction or by functioning in the same pathway, possibly involve with lipid-rafts. 90 matched cddid_all.tbl CDD pfam01958 pfam01958 426531 Asp_DH_C Aspartate dehydrogenase, C-terminal. This entry represents the C-terminal domain of aspartate dehydrogenases that belong to a unique class of amino acid dehydrogenases. The structure of Thermotoga maritima TM1643 has been found to contain an N-terminal Rossmann fold domain (which binds the NAD(P)+ cofactor) and a C-terminal alpha/beta domain. Enzymatic characterization of TM1643 revealed that it possesses NAD or NADP-dependent dehydrogenase activity toward L-aspartate but no aspartate oxidase activity. Members of this group share some structural similarity to several other NAD(P)+-dependent oxidoreductases, including inositol 1-phosphate synthase, dihydrodipicolinate reductase, and ASA-DH. It has been proposed that in Thermotoga maritima, TM1643 catalyzes the first reaction of de novo biosynthesis of NAD from aspartate, and it produces iminoaspartate required for this pathway. 87 matched cddid_all.tbl CDD pfam01959 pfam01959 426532 DHQS 3-dehydroquinate synthase II. This family includes members of 3-dehydroquinate synthase II (EC:1.4.1.24), encoded by aroB genes in M. maripaludis which is widely distributed in methanogens. In M. jannaschii, proteins ADTH synthase (AroA) and DHQ synthase II (AroB) are required to convert 6-deoxy-5-ketofructose-1-phosphate (DKFP) and aspartate semialdehyde to 3-dehydroquinate (DHQ) in vitro. 347 matched cddid_all.tbl CDD pfam01960 pfam01960 460396 ArgJ ArgJ family. Members of the ArgJ family catalyze the first EC:2.3.1.1 and fifth steps EC:2.3.1.35 in arginine biosynthesis. 373 matched cddid_all.tbl CDD pfam01963 pfam01963 426534 TraB_PrgY_gumN TraB/PrgY/gumN family. This entry includes Tiki1/2 from humans, TraB/PrgY from the gut flora Enterococcusfaecalis and gumN from the plant pathogen Xanthomonas. Tiki1 is homologous to TraB/PrgY. They have a pair of widely spaced GX2H motifs and a conserved glutamate. From the structural study, this group of proteins have been identified as an ancient metalloprotease clan with a common protein architecture (cobbled from the folds of the EreA/ChaN/PMT group) that mediates proteolytic activities. Tiki1 is a membrane-associated protease that inhibits Wnt via the cleavage of its amino terminus, diminishing Wnt's binding to receptors. TraB/PrgY is an inhibitor peptide that may act as a protease to inactivate the mating pheromone. 262 matched cddid_all.tbl CDD pfam01964 pfam01964 460397 ThiC_Rad_SAM Radical SAM ThiC family. ThiC is found within the thiamine biosynthesis operon. ThiC is involved in pyrimidine biosynthesis. ThiC participates in the formation of 4-Amino-5-hydroxymethyl-2-methylpyrimidine from AIR, an intermediate in the de novo pyrimidine biosynthesis. Thic is a member of the radical SAM superfamily. 420 matched cddid_all.tbl CDD pfam01965 pfam01965 396514 DJ-1_PfpI DJ-1/PfpI family. The family includes the protease PfpI. This domain is also found in transcriptional regulators. 165 matched cddid_all.tbl CDD pfam01966 pfam01966 460398 HD HD domain. HD domains are metal dependent phosphohydrolases. 110 matched cddid_all.tbl CDD pfam01967 pfam01967 460399 MoaC MoaC family. Members of this family are involved in molybdenum cofactor biosynthesis. However their molecular function is not known. 136 matched cddid_all.tbl CDD pfam01968 pfam01968 396517 Hydantoinase_A Hydantoinase/oxoprolinase. This family includes the enzymes hydantoinase and oxoprolinase EC:3.5.2.9. Both reactions involve the hydrolysis of 5-membered rings via hydrolysis of their internal imide bonds. 288 matched cddid_all.tbl CDD pfam01969 pfam01969 426537 Ni_insertion Nickel insertion protein. Members of this family may be involved in the activation of nickel-pincer cofactor-dependent enzymes. LarC from Lactobacillus plantarum is involved, together with LarB and LarE, in the synthesis of the enzyme-bound cofactor of lactate racemase (LarA). Larc C binds Ni2+, and functions in nickel delivery to pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN), to form the mature cofactor. 380 matched cddid_all.tbl CDD pfam01970 pfam01970 426538 TctA Tripartite tricarboxylate transporter TctA family. This family, formerly known as DUF112, is a family of bacterial and archaeal tripartite tricarboxylate transporters of the extracytoplasmic solute binding receptor-dependent transporter group of families, distinct from the ABC and TRAP-T families. TctA is part of the tripartite TctABC system which, as characterized in S. typhimurium, is a secondary carrier that depends for activity on the extracytoplasmic tricarboxylate-binding receptor TctC as well as two integral membrane proteins, TctA and TctB. complete three-component systems are found only in bacteria. TctA is a large transmembrane protein with up to 12 predicted membrane spanning regions in bacteria and up to 11 such in archaea, with the N-terminal within the cytoplasm. TctA is thought to be a permease, and in most other bacteria functions without TctB and TctC molecules. 415 matched cddid_all.tbl CDD pfam01972 pfam01972 110924 SDH_sah Serine dehydrogenase proteinase. This family of archaebacterial proteins, formerly known as DUF114, has been found to be a serine dehydrogenase proteinase distantly related to ClpP proteinases that belong to the serine proteinase superfamily. The family has a catalytic triad of Ser, Asp, His residues, which shows an altered residue ordering compared with the ClpP proteinases but similar to that of the carboxypeptidase clan. 286 matched cddid_all.tbl CDD pfam01973 pfam01973 426539 MptE-like 6-hydroxymethylpterin diphosphokinase MptE-like. This domain can be found in a group of proteins, including archaeal 6-hydroxymethylpterin diphosphokinase (6-HMDPK), known as MptE, which catalyzes the formation of 6-hydroxymethyl-7,8-dihydropterin diphosphate (6-HMDP) from 6-HMD and ATP. 6-HMDP is the precursor of the pterin containing moiety of the essential C1-carriers tetrahydrofolate and tetrahydromethanopterin. This entry also includes a number of uncharacterized proteins from bacteria. 171 matched cddid_all.tbl CDD pfam01974 pfam01974 396521 tRNA_int_endo tRNA intron endonuclease, catalytic C-terminal domain. Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9. 85 matched cddid_all.tbl CDD pfam01975 pfam01975 460400 SurE Survival protein SurE. E. coli cells with the surE gene disrupted are found to survive poorly in stationary phase. It is suggested that SurE may be involved in stress response. Yeast also contains a member of the family Swiss:P38254. Swiss:P30887 can complement a mutation in acid phosphatase, suggesting that members of this family could be phosphatases. 187 matched cddid_all.tbl CDD pfam01976 pfam01976 426541 DUF116 Protein of unknown function DUF116. This archaebacterial protein has no known function. The protein contains seven conserved cysteines containing a CxxCxxC motif and may also be an integral membrane protein. 152 matched cddid_all.tbl CDD pfam01977 pfam01977 426542 UbiD 3-octaprenyl-4-hydroxybenzoate carboxy-lyase. This family has been characterized as 3-octaprenyl-4- hydroxybenzoate carboxy-lyase enzymes. This enzyme catalyzes the third reaction in ubiquinone biosynthesis. For optimal activity the carboxy-lase was shown to require Mn2+. 401 matched cddid_all.tbl CDD pfam01978 pfam01978 396525 TrmB Sugar-specific transcriptional regulator TrmB. One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis. 67 matched cddid_all.tbl CDD pfam01979 pfam01979 460401 Amidohydro_1 Amidohydrolase family. This family of enzymes are a a large metal dependent hydrolase superfamily. The family includes Adenine deaminase EC:3.5.4.2 that hydrolyses adenine to form hypoxanthine and ammonia. Adenine deaminases reaction is important for adenine utilization as a purine and also as a nitrogen source. This family also includes dihydroorotase and N-acetylglucosamine-6-phosphate deacetylases, EC:3.5.1.25 These enzymes catalyze the reaction N-acetyl-D-glucosamine 6-phosphate + H2O <=> D-glucosamine 6-phosphate + acetate. This family includes the catalytic domain of urease alpha subunit. Dihydroorotases (EC:3.5.2.3) are also included. 334 matched cddid_all.tbl CDD pfam01980 pfam01980 460402 TrmO tRNA-methyltransferase O. This family includes members such as TrmO (tRNA-methyltransferase O) also known as YaeB, which contains a single-sheeted beta-barrel structure. TrmO is an AdoMet-dependent methyltransferase responsible for m6t6A formation. Its human homolog, is responsible for formation of m6t6A37 in cytoplasmic tRNASer. Lack of TrmO decreases attenuation activity of the thr operon, indicating that N6 methylation of m6t6A37 ensures efficient decoding of ACY codons. In bacteria and eukaryotes, TrmO has a C-terminal domain containing the conserved DPRxxY motif. Where the Asp194 and Arg196 in this motif of E. coli TrmO are necessary for N6-methylation. However, no archaeal YaeB has a C-terminal domain containing the DPRxxY motif that is conserved in bacterial and mammalian TrmO homologs. 116 matched cddid_all.tbl CDD pfam01981 pfam01981 460403 PTH2 Peptidyl-tRNA hydrolase PTH2. Peptidyl-tRNA hydrolases are enzymes that release tRNAs from peptidyl-tRNA during translation. 115 matched cddid_all.tbl CDD pfam01982 pfam01982 426545 CTP-dep_RFKase Domain of unknown function DUF120. This domain is a CTP-dependent riboflavin kinase (RFK), found in archaea, that catalyzes the phosphorylation of riboflavin to form flavin mononucleotide in riboflavin biosynthesis EC:2.7.1.26. Its structure resembles a RIFT barrel, structurally similar to but topologically distinct from bacterial and eukaryotic examples. The N-terminal is a winged helix-turn-helix DNA-binding domain, and the C-terminal half is most similar in sequence to a group of cradle-loop barrels. Swiss:O28174 has this domain attached to pfam00325. 121 matched cddid_all.tbl CDD pfam01983 pfam01983 251014 CofC Guanylyl transferase CofC like. Coenzyme F420 is a hydride carrier cofactor that functions during methanogenesis. This family of proteins represents CofC, a nucleotidyl transferase that is involved in coenzyme F420 biosynthesis. CofC has been shown to catalyze the formation of lactyl-2-diphospho-5'-guanosine from 2-phospho-L-lactate and GTP. 217 matched cddid_all.tbl CDD pfam01984 pfam01984 460404 dsDNA_bind Double-stranded DNA-binding domain. This domain is believed to bind double-stranded DNA of 20 bases length. 106 matched cddid_all.tbl CDD pfam01985 pfam01985 460405 CRS1_YhbY CRS1 / YhbY (CRM) domain. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localizes to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. 84 matched cddid_all.tbl CDD pfam01986 pfam01986 460406 DUF123 Domain of unknown function DUF123. This archaebacterial domain has no known function. It is attached to an endonuclease domain in Swiss:Q58030. The domain contains several conserved cysteines and histidines. This suggests that the domain may be a zinc binding nucleic acid interaction domain (Bateman A unpubl.). 96 matched cddid_all.tbl CDD pfam01987 pfam01987 460407 AIM24 Mitochondrial biogenesis AIM24. In eukaryotes, this domain is involved in mitochondrial biogenesis. Its function in prokaryotes in unknown. 206 matched cddid_all.tbl CDD pfam01988 pfam01988 460408 VIT1 VIT family. This family includes the vacuolar Fe2+/Mn2+ uptake transporter Ccc1 and the vacuolar iron transporter VIT1. 212 matched cddid_all.tbl CDD pfam01989 pfam01989 426551 AcnX_swivel_put "Aconitase X swivel domain. This is a putative aconitase X swivel domain, which has been predicted by comparative genomic analysis. The domain is mainly found in archaeal and proteobacterial proteins. As such, the prediction should be treated with caution. One member of this entry from Aeropyrum pernix which has been annotated as a putative aconitase, has been characterized in vitro and catalyzes the dehydration of mevalonate 5-phosphate to form trans-anhydromevalonate 5-phosphate, a previously unknown intermediate, being involved in a ""modified"" mevalonate pathway." 75 matched cddid_all.tbl CDD pfam01990 pfam01990 460409 ATP-synt_F ATP synthase (F/14-kDa) subunit. This family includes 14-kDa subunit from vATPases, which is in the peripheral catalytic part of the complex. The family also includes archaebacterial ATP synthase subunit F. 91 matched cddid_all.tbl CDD pfam01991 pfam01991 396537 vATP-synt_E ATP synthase (E/31 kDa) subunit. This family includes the vacuolar ATP synthase E subunit, as well as the archaebacterial ATP synthase E subunit. 199 matched cddid_all.tbl CDD pfam01992 pfam01992 426553 vATP-synt_AC39 ATP synthase (C/AC39) subunit. This family includes the AC39 subunit from vacuolar ATP synthase, and the C subunit from archaebacterial ATP synthase. The family also includes subunit C from the Sodium transporting ATP synthase from Enterococcus hirae. 333 matched cddid_all.tbl CDD pfam01993 pfam01993 426554 MTD methylene-5,6,7,8-tetrahydromethanopterin dehydrogenase. This enzyme family is involved in formation of methane from carbon dioxide EC:1.5.99.9. The enzyme requires coenzyme F420. 274 matched cddid_all.tbl CDD pfam01994 pfam01994 426555 Trm56 tRNA ribose 2'-O-methyltransferase, aTrm56. This family is an aTrm56 that catalyzes the 2'-O-methylation of the cytidine residue in archaeal tRNA, using S-adenosyl-L-methionine. Biochemical assays showed that aTrm56 forms a dimer and prefers the L-shaped tRNA to the lambda form as its substrate. aTrm56 consists of the SPOUT domain, which contains the characteriztic deep trefoil knot for AdoMet binding, and a unique C-terminal beta-hairpin. 119 matched cddid_all.tbl CDD pfam01995 pfam01995 426556 NRD1_2 NrpR regulatory domains NRD1 and 2. This entry comprises two domains found in the nitrogen regulatory protein NrpR that bind DNA and repress transcription of nitrogen assimilation genes. The two NrpR regulatory domains (NRD1 and NRD2) that sense and bind 2-oxoglutarate (2OG) are both structurally and functionally homologous and share a high degree of sequence conservation. Mutational analysis of NrpR from Methanococcus maripaludis (MmNrpR) indicated that the two most critical residues for 2OG binding are Cys389 and His435 (Cys395 and His441, respectively in thermophilic archaeon Methanocaldococcus jannaschii (MjNrpR)). Both the Cys395 and His441 are conserved among NrpR proteins from diverse species. 238 matched cddid_all.tbl CDD pfam01996 pfam01996 426557 F420_ligase F420-0:Gamma-glutamyl ligase. F420-0:Gamma-glutamyl ligase (EC:6.3.2.-) is an enzyme involved in F420 biosynthesis pathway. It catalyzes the GTP-dependent successive addition of multiple gamma-linked L-glutamates to the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0). This reaction produces polyglutamated F420 derivatives. GTP + F420-0 + n L-glutamate -> GDP + phosphate + F420-n 218 matched cddid_all.tbl CDD pfam01997 pfam01997 460410 Translin Translin family. Members of this family include Translin that interacts with DNA and forms a ring around the DNA. This family also includes Swiss:Q99598, that was found to interact with translin with yeast two-hybrid screen. 197 matched cddid_all.tbl CDD pfam01998 pfam01998 396544 DUF131 Protein of unknown function DUF131. This archaebacterial protein family has no known function. The proteins are predicted to contain two transmembrane helices. 62 matched cddid_all.tbl CDD pfam02001 pfam02001 280223 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function. A study suggests that some members may be G-quadruplex binding proteins. 98 matched cddid_all.tbl CDD pfam02002 pfam02002 280224 TFIIE_alpha TFIIE alpha subunit. The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits TFIIE-alpha and TFIIE-beta and joins the pre-initiation complex after RNA polymerase II and TFIIF. This family consists of the conserved amino terminal region of eukaryotic TFIIE-alpha and proteins from archaebacteria that are presumed to be TFIIE-alpha subunits also Swiss:O29501. 105 matched cddid_all.tbl CDD pfam02005 pfam02005 396545 TRM N2,N2-dimethylguanosine tRNA methyltransferase. This enzyme EC:2.1.1.32 used S-AdoMet to methylate tRNA. The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs. The enzyme is found in both eukaryotes and archaebacteria 375 matched cddid_all.tbl CDD pfam02006 pfam02006 426559 PPS_PS Phosphopantothenate/pantothenate synthetase. This family of archaeal proteins includes pantothenate synthetase from Methanosarcina mazei and 4-phosphopantoate--beta-alanine ligase (phosphopantothenate synthetase) from Pyrococcus kodakaraensis. Pantothenate synthetase catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent and ADP-producing reaction. 4-phosphopantoate--beta-alanine ligase catalyzes the conversion of (R)-4-phosphopantoate and beta-alanine to 4'-phosphopantothenate in the CoA biosynthesis pathway. It cannot use (R)-pantoate as substrate and thus does not display pantothenate synthetase activity. 176 matched cddid_all.tbl CDD pfam02007 pfam02007 280227 MtrH Tetrahydromethanopterin S-methyltransferase MtrH subunit. The enzyme tetrahydromethanopterin S-methyltransferase EC:2.1.1.86 is composed of eight subunits. The enzyme is a membrane- associated enzyme complex which catalyzes an energy-conserving, sodium-ion-translocating step in methanogenesis from hydrogen and carbon dioxide. 299 matched cddid_all.tbl CDD pfam02008 pfam02008 366873 zf-CXXC CXXC zinc finger domain. This domain contains eight conserved cysteine residues that bind to two zinc ions. The CXXC domain is found in a variety of chromatin-associated proteins. This domain binds to nonmethyl-CpG dinucleotides. The domain is characterized by two repeats, and shows a peculiar internal duplication in which the second unit is inserted into the first one. Each of these units is characterized by four conserved cysteines, displaying a CXXCXXCX(n)C motif that chelate a Zn+2 ion. The DNA binding interface has been identified by NMR. In eukaryotes, the CXXC domain is found in stramenopiles, plants and metazoans. Plants possess a mono-CXXC domain that is present in distinct chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases. 48 matched cddid_all.tbl CDD pfam02009 pfam02009 396547 RIFIN Rifin. Plasmodium falciparum is the causative agent of deadly malaria disease. It encodes repetitive interspersed families of polypeptides (RIFINs), which are expressed on the surface of infected erythrocytes. All RIFIN sequences contain the PEXEL motif (a pentameric sequence RxLxE/Q/D, known as the Plasmodium export element) required for correct export and surface expression or host-targeting (HT) signal which plays a central role in the export of proteins into the host cell. It has been reported that PEXEL is preferably located 15-20 amino acids downstream of an N-terminal hydrophobic signal sequence. The RIFIN protein family can be divided into A and B types based on the presence or absence of a 25 amino acid motif located approximately 66 amino acids downstream of the PEXEL motif, with A- and B-types serving different roles in distinct parasite stages. The specific type B RIFIN variant (PF13_0006) is expressed on the surface of free merozoites, internally in developing gametocytes and on the surface of gametes at the point of emerging from activated, mature stage V gametocytes. While type A RIFIN are expressed on the infected erythrocyte surface, potentially contributing to the antigenic variation capacity of the parasite. 326 matched cddid_all.tbl CDD pfam02010 pfam02010 366875 REJ REJ domain. The REJ (Receptor for Egg Jelly) domain is found in PKD1, and the sperm receptor for egg jelly Swiss:Q26627. The function of this domain is unknown. The domain is 600 amino acids long so is probably composed of multiple structural domains. There are six completely conserved cysteine residues that may form disulphide bridges. This region contains tandem PKD-like domains. 448 matched cddid_all.tbl CDD pfam02011 pfam02011 426560 Glyco_hydro_48 Glycosyl hydrolase family 48. Members of this family are endoglucanase EC:3.2.1.4 and exoglucanase EC:3.2.1.91 enzymes that cleave cellulose or related substrate. 620 matched cddid_all.tbl CDD pfam02012 pfam02012 396549 BNR BNR/Asp-box repeat. Members of this family contain multiple BNR (bacterial neuraminidase repeat) repeats or Asp-boxes. The repeats are short, however the repeats are never found closer than 40 residues together suggesting that the repeat is structurally longer. These repeats are found in many glycosyl hydrolases as well as other extracellular proteins of unknown function. 12 matched cddid_all.tbl CDD pfam02013 pfam02013 251036 CBM_10 Cellulose or protein binding domain. This domain is found in two distinct sets of proteins with different functions. Those found in aerobic bacteria bind cellulose (or other carbohydrates); but in anaerobic fungi they are protein binding domains, referred to as dockerin domains or docking domains. They are believed to be responsible for the assembly of a multiprotein cellulase/hemicellulase complex, similar to the cellulosome found in certain anaerobic bacteria. 36 matched cddid_all.tbl CDD pfam02014 pfam02014 460411 Reeler Reeler domain. 130 matched cddid_all.tbl CDD pfam02015 pfam02015 280233 Glyco_hydro_45 Glycosyl hydrolase family 45. 214 matched cddid_all.tbl CDD pfam02016 pfam02016 460412 Peptidase_S66 LD-carboxypeptidase N-terminal domain. Muramoyl-tetrapeptide carboxypeptidase hydrolyses a peptide bond between a di-basic amino acid and the C-terminal D-alanine in the tetrapeptide moiety in peptidoglycan. This cleaves the bond between an L- and a D-amino acid. The function of this activity is in murein recycling. This family also includes the microcin c7 self-immunity protein Swiss:Q47511. This family corresponds to Merops family S66. 119 matched cddid_all.tbl CDD pfam02017 pfam02017 460413 CIDE-N CIDE-N domain. This domain is found in CAD nuclease, and ICAD, the inhibitor of CAD nuclease. The two proteins interact through this domain. 75 matched cddid_all.tbl CDD pfam02018 pfam02018 396553 CBM_4_9 Carbohydrate binding domain. This family includes diverse carbohydrate binding domains. 134 matched cddid_all.tbl CDD pfam02019 pfam02019 460414 WIF WIF domain. The WIF domain is found in the RYK tyrosine kinase receptors and WIF, the Wnt-inhibitory- factor. The domain is extracellular and contains two conserved cysteines that may form a disulphide bridge. This domain is Wnt binding in WIF, and it has been suggested that RYK may also bind to Wnt. The WIF domain is a member of the immunoglobulin superfamily, and it comprises nine beta-strands and two alpha-helices, with two of the beta-strands (6 and 9) interrupted by four and six residues of irregular secondary structure, respectively. Considering that the activity of Wnts depends on the presence of a palmitoylated cysteine residue in their amino-terminal polypeptide segment, Wnt proteins are lipid-modified and can act as stem cell growth factors, it is likely that the WIF domain recognizes and binds to Wnts that have been activated by palmitoylation and that the recognition of palmitoylated Wnts by WIF-1 is effected by its WIF domain rather than by its EGF domains. A strong binding affinity for palmitoylated cysteine residues would further explain the remarkably high affinity of human WIF-1 not only for mammalian Wnts, but also for Wnts from Xenopus and Drosophila. 126 matched cddid_all.tbl CDD pfam02020 pfam02020 460415 W2 eIF4-gamma/eIF5/eIF2-epsilon. This domain of unknown function is found at the C-terminus of several translation initiation factors. 76 matched cddid_all.tbl CDD pfam02021 pfam02021 460416 UPF0102 Uncharacterized protein family UPF0102. The function of this family is unknown. 92 matched cddid_all.tbl CDD pfam02022 pfam02022 426567 Integrase_Zn Integrase Zinc binding domain. Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain pfam00665. The carboxyl terminal domain is a DNA binding domain pfam00552. 36 matched cddid_all.tbl CDD pfam02023 pfam02023 460417 SCAN SCAN domain. The SCAN domain (named after SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in several pfam00096 proteins. The domain has been shown to be able to mediate homo- and hetero-oligomerization. 89 matched cddid_all.tbl CDD pfam02024 pfam02024 396559 Leptin Leptin. 142 matched cddid_all.tbl CDD pfam02025 pfam02025 460418 IL5 Interleukin 5. 112 matched cddid_all.tbl CDD pfam02026 pfam02026 460419 RyR RyR domain. This domain is called RyR for Ryanodine receptor. The domain is found in four copies in the ryanodine receptor. The function of this domain is unknown. 90 matched cddid_all.tbl CDD pfam02027 pfam02027 366884 RolB_RolC RolB/RolC glucosidase family. This family of proteins includes RolB and RolC. RolC releases cytokinins from glucoside conjugates. Whereas RolB hydrolyses indole glucosides. 184 matched cddid_all.tbl CDD pfam02028 pfam02028 460420 BCCT BCCT, betaine/carnitine/choline family transporter. 485 matched cddid_all.tbl CDD pfam02029 pfam02029 460421 Caldesmon Caldesmon. 495 matched cddid_all.tbl CDD pfam02030 pfam02030 307931 Lipoprotein_8 Hypothetical lipoprotein (MG045 family). This family includes hypothetical lipoproteins, the amino terminal part of this protein is related to pfam01547, a family of solute binding proteins. This suggests this family also has a solute binding function. 493 matched cddid_all.tbl CDD pfam02031 pfam02031 280248 Peptidase_M7 Streptomyces extracellular neutral proteinase (M7) family. 133 matched cddid_all.tbl CDD pfam02033 pfam02033 460422 RBFA Ribosome-binding factor A. 105 matched cddid_all.tbl CDD pfam02035 pfam02035 396565 Coagulin Coagulin. 172 matched cddid_all.tbl CDD pfam02036 pfam02036 460423 SCP2 SCP-2 sterol transfer family. This domain is involved in binding sterols. It is found in the SCP2 protein as well as the C terminus of the enzyme estradiol 17 beta-dehydrogenase EC:1.1.1.62. The UNC-24 protein contains an SPFH domain pfam01145. 100 matched cddid_all.tbl CDD pfam02037 pfam02037 460424 SAP SAP domain. The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins. 35 matched cddid_all.tbl CDD pfam02038 pfam02038 460425 ATP1G1_PLM_MAT8 ATP1G1/PLM/MAT8 family. 48 matched cddid_all.tbl CDD pfam02040 pfam02040 460426 ArsB Arsenical pump membrane protein. 423 matched cddid_all.tbl CDD pfam02041 pfam02041 396569 Auxin_BP Auxin binding protein. 164 matched cddid_all.tbl CDD pfam02042 pfam02042 460427 RWP-RK RWP-RK domain. This domain is named RWP-RK after a conserved motif at the C terminus of the presumed domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development. 49 matched cddid_all.tbl CDD pfam02043 pfam02043 460428 Bac_chlorC Bacteriochlorophyll C binding protein. 80 matched cddid_all.tbl CDD pfam02044 pfam02044 280257 Bombesin Bombesin-like peptide. 14 matched cddid_all.tbl CDD pfam02045 pfam02045 396572 CBFB_NFYA CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B. 56 matched cddid_all.tbl CDD pfam02046 pfam02046 426579 COX6A Cytochrome c oxidase subunit VIa. 112 matched cddid_all.tbl CDD pfam02048 pfam02048 307942 Enterotoxin_ST Heat-stable enterotoxin ST. This family consists of the heat stable enterotoxin ST from Escherichia coli. ST is a small peptide of 18 or 19 amino acid residues produced by enterotoxigenic E. coli and is one of the causes of acute diarrhoea in infants and travellers in developing countries. ST triggers a biological response by binding to a membrane-associated guanylyl cyclase C which is located on intestinal epithelial cell membranes. 54 matched cddid_all.tbl CDD pfam02049 pfam02049 460429 FliE Flagellar hook-basal body complex protein FliE. 89 matched cddid_all.tbl CDD pfam02050 pfam02050 426581 FliJ Flagellar FliJ protein. 123 matched cddid_all.tbl CDD pfam02052 pfam02052 110996 Gallidermin Gallidermin. 52 matched cddid_all.tbl CDD pfam02053 pfam02053 366894 Gene66 Gene 66 (IR5) protein. 209 matched cddid_all.tbl CDD pfam02055 pfam02055 307945 Glyco_hydro_30 Glycosyl hydrolase family 30 TIM-barrel domain. 348 matched cddid_all.tbl CDD pfam02056 pfam02056 396576 Glyco_hydro_4 Family 4 glycosyl hydrolase. 183 matched cddid_all.tbl CDD pfam02057 pfam02057 396577 Glyco_hydro_59 Glycosyl hydrolase family 59. 293 matched cddid_all.tbl CDD pfam02058 pfam02058 460430 Guanylin Guanylin precursor. 87 matched cddid_all.tbl CDD pfam02059 pfam02059 460431 IL3 Interleukin-3. 110 matched cddid_all.tbl CDD pfam02060 pfam02060 460432 ISK_Channel Slow voltage-gated potassium channel. 126 matched cddid_all.tbl CDD pfam02061 pfam02061 280268 Lambda_CIII Lambda Phage CIII. The CIII protein from bacteriophage lambda is an inhibitor of the FtsH peptidase. 42 matched cddid_all.tbl CDD pfam02063 pfam02063 460433 MARCKS MARCKS family. 289 matched cddid_all.tbl CDD pfam02064 pfam02064 460434 MAS20 MAS20 protein import receptor. 132 matched cddid_all.tbl CDD pfam02065 pfam02065 307952 Melibiase Melibiase. Glycoside hydrolase families GH27, GH31 and GH36 form the glycoside hydrolase clan GH-D. Glycoside hydrolase family 36 can be split into 11 families, GH36A to GH36K. This family includes enzymes from GH36A-B and GH36D-K and from GH27. 347 matched cddid_all.tbl CDD pfam02066 pfam02066 280272 Metallothio_11 Metallothionein family 11. 54 matched cddid_all.tbl CDD pfam02067 pfam02067 280273 Metallothio_5 Metallothionein family 5. 41 matched cddid_all.tbl CDD pfam02068 pfam02068 396582 Metallothio_PEC Plant PEC family metallothionein. 75 matched cddid_all.tbl CDD pfam02069 pfam02069 426585 Metallothio_Pro Prokaryotic metallothionein. 51 matched cddid_all.tbl CDD pfam02070 pfam02070 460435 NMU Neuromedin U. 25 matched cddid_all.tbl CDD pfam02071 pfam02071 366905 NSF Aromatic-di-Alanine (AdAR) repeat. This repeat is found in NSF attachment proteins. Its structure is similar to that found in TPR repeats pfam00515. 12 matched cddid_all.tbl CDD pfam02072 pfam02072 460436 Orexin Prepro-orexin. 129 matched cddid_all.tbl CDD pfam02073 pfam02073 426588 Peptidase_M29 Thermophilic metalloprotease (M29). 406 matched cddid_all.tbl CDD pfam02074 pfam02074 426589 Peptidase_M32 Carboxypeptidase Taq (M32) metallopeptidase. 488 matched cddid_all.tbl CDD pfam02075 pfam02075 366907 RuvC Crossover junction endodeoxyribonuclease RuvC. This entry includes endodeoxyribonucleases found in bacteria, such as RuvC. RuvC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli RuvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices. The Escherichia coli RuvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination. RuvC protein (EC:3.1.22.4) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo. 148 matched cddid_all.tbl CDD pfam02076 pfam02076 460437 STE3 Pheromone A receptor. 292 matched cddid_all.tbl CDD pfam02077 pfam02077 111019 SURF4 SURF4 family. 267 matched cddid_all.tbl CDD pfam02078 pfam02078 460438 Synapsin Synapsin, N-terminal domain. This family is structurally related to the PreATP-grasp domain. 97 matched cddid_all.tbl CDD pfam02079 pfam02079 460439 TP1 Nuclear transition protein 1. 51 matched cddid_all.tbl CDD pfam02080 pfam02080 460440 TrkA_C TrkA-C domain. This domain is often found next to the pfam02254 domain. The exact function of this domain is unknown. It has been suggested that it may bind an unidentified ligand. The domain is predicted to adopt an all beta structure. 70 matched cddid_all.tbl CDD pfam02081 pfam02081 396590 TrpBP Tryptophan RNA-binding attenuator protein. 68 matched cddid_all.tbl CDD pfam02082 pfam02082 396591 Rrf2 Iron-dependent Transcriptional regulator. Several proteins in this family form iron-sulfur clusters enabling iron dependent DNA transcription regulation. The iron binding is mediated by three conserved cysteine residues. Members of this family can also bind O-acetyl-L-serine, [Fe-S] and nitric oxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 131 matched cddid_all.tbl CDD pfam02083 pfam02083 426593 Urotensin_II Urotensin II. 12 matched cddid_all.tbl CDD pfam02084 pfam02084 251078 Bindin Bindin. 239 matched cddid_all.tbl CDD pfam02085 pfam02085 396592 Cytochrom_CIII Class III cytochrome C family. 103 matched cddid_all.tbl CDD pfam02086 pfam02086 396593 MethyltransfD12 D12 class N6 adenine-specific DNA methyltransferase. 254 matched cddid_all.tbl CDD pfam02087 pfam02087 111029 Nitrophorin Nitrophorin. 178 matched cddid_all.tbl CDD pfam02088 pfam02088 145317 Ornatin Ornatin. 41 matched cddid_all.tbl CDD pfam02089 pfam02089 460441 Palm_thioest Palmitoyl protein thioesterase. 248 matched cddid_all.tbl CDD pfam02090 pfam02090 280292 SPAM Salmonella surface presentation of antigen gene type M protein. 140 matched cddid_all.tbl CDD pfam02091 pfam02091 426595 tRNA-synt_2e Glycyl-tRNA synthetase alpha subunit. 276 matched cddid_all.tbl CDD pfam02092 pfam02092 460442 tRNA_synt_2f Glycyl-tRNA synthetase beta subunit. 536 matched cddid_all.tbl CDD pfam02093 pfam02093 426597 Gag_p30 Gag P30 core shell protein. According to Swiss-Prot annotation this protein is the viral core shell protein. P30 is essential for viral assembly. 208 matched cddid_all.tbl CDD pfam02095 pfam02095 396598 Extensin_1 Extensin-like protein repeat. 10 matched cddid_all.tbl CDD pfam02096 pfam02096 460443 60KD_IMP 60Kd inner membrane protein. 187 matched cddid_all.tbl CDD pfam02097 pfam02097 280298 Filo_VP35 Filoviridae VP35. 342 matched cddid_all.tbl CDD pfam02098 pfam02098 396600 His_binding Tick histamine binding protein. 150 matched cddid_all.tbl CDD pfam02099 pfam02099 460444 Josephin Josephin. 154 matched cddid_all.tbl CDD pfam02100 pfam02100 460445 ODC_AZ Ornithine decarboxylase antizyme. This family consists of ornithine decarboxylase antizyme proteins. The polyamine biosynthetic enzyme ornithine decarboxylase (ODC) is degraded by the 26 S proteasome via a ubiquitin-independent pathway. Its degradation is greatly accelerated by association with the polyamine-induced regulatory protein antizyme 1 (AZ1). 111 matched cddid_all.tbl CDD pfam02101 pfam02101 460446 Ocular_alb Ocular albinism type 1 protein. 402 matched cddid_all.tbl CDD pfam02102 pfam02102 251087 Peptidase_M35 Deuterolysin metalloprotease (M35) family. 352 matched cddid_all.tbl CDD pfam02104 pfam02104 460447 SURF1 SURF1 family. 195 matched cddid_all.tbl CDD pfam02106 pfam02106 426603 Fanconi_C Fanconi anaemia group C protein. 547 matched cddid_all.tbl CDD pfam02107 pfam02107 426604 FlgH Flagellar L-ring protein. 175 matched cddid_all.tbl CDD pfam02108 pfam02108 426605 FliH Flagellar assembly protein FliH. 124 matched cddid_all.tbl CDD pfam02109 pfam02109 460448 DAD DAD family. Members of this family are thought to be integral membrane proteins. Some members of this family have been shown to cause apoptosis if mutated, these proteins are known as DAD for defender against death. The family also includes the epsilon subunit of the oligosaccharyltransferase that is involved in N-linked glycosylation. 108 matched cddid_all.tbl CDD pfam02110 pfam02110 396609 HK Hydroxyethylthiazole kinase family. 247 matched cddid_all.tbl CDD pfam02112 pfam02112 396610 PDEase_II cAMP phosphodiesterases class-II. 339 matched cddid_all.tbl CDD pfam02113 pfam02113 396611 Peptidase_S13 D-Ala-D-Ala carboxypeptidase 3 (S13) family. This family of serine peptidases belong to MEROPS peptidase family S13 (D-Ala-D-Ala carboxypeptidase C, clan SE). The active site residues occur in the motif SXXK. D-Ala-D-Ala carboxypeptidase C is involved in the metabolism of cell components. There are three families of serine-type D-Ala-D-Ala peptidase (designated S11, S12 and S13), which are also known as low molecular weight penicillin-binding proteins. Family S13 comprises D-Ala-D-Ala peptidases that have sufficient sequence similarity around their active sites to assume a distant evolutionary relationship to other clan members; members of the S13 family also bind penicillin and have D-amino-peptidase activity. 444 matched cddid_all.tbl CDD pfam02114 pfam02114 251094 Phosducin Phosducin. 265 matched cddid_all.tbl CDD pfam02115 pfam02115 460449 Rho_GDI RHO protein GDP dissociation inhibitor. 191 matched cddid_all.tbl CDD pfam02116 pfam02116 426608 STE2 Fungal pheromone mating factor STE2 GPCR. 276 matched cddid_all.tbl CDD pfam02117 pfam02117 111054 7TM_GPCR_Sra Serpentine type 7TM GPCR chemoreceptor Sra. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Sra is part of the Sra superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. 328 matched cddid_all.tbl CDD pfam02118 pfam02118 396614 Srg Srg family chemoreceptor. 270 matched cddid_all.tbl CDD pfam02119 pfam02119 460450 FlgI Flagellar P-ring protein. 342 matched cddid_all.tbl CDD pfam02120 pfam02120 460451 Flg_hook Flagellar hook-length control protein FliK. This is the C terminal domain of FliK. FliK controls the length of the flagellar hook by directly measuring the hook length as a molecular ruler. This family also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems. 82 matched cddid_all.tbl CDD pfam02121 pfam02121 460452 IP_trans Phosphatidylinositol transfer protein. Along with the structurally unrelated Sec14p family (found in pfam00650), this family can bind/exchange one molecule of phosphatidylinositol (PI) or phosphatidylcholine (PC) and thus aids their transfer between different membrane compartments. There are three sub-families - all share an N-terminal PITP-like domain, whose sequence is highly conserved. It is described as consisting of three regions. The N-terminal region is thought to bind the lipid and contains two helices and an eight-stranded, mostly antiparallel beta-sheet. An intervening loop region, which is thought to play a role in protein-protein interactions, separates this from the C-terminal region, which exhibits the greatest sequence variation and may be involved in membrane binding. PITP alpha has a 16-fold greater affinity for PI than PC. Together with PITP beta, it is expressed ubiquitously in all tissues. 245 matched cddid_all.tbl CDD pfam02122 pfam02122 111059 Peptidase_S39 Peptidase S39. This family contains polyprotein processing endopeptidases from RNA viruses. 203 matched cddid_all.tbl CDD pfam02123 pfam02123 280316 RdRP_4 Viral RNA-directed RNA-polymerase. This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus. 465 matched cddid_all.tbl CDD pfam02124 pfam02124 460453 Marek_A Marek's disease glycoprotein A. This is the Ig-like domain found from Envelope glycoprotein C and glycoprotein A (GA) from Herpesvirus. GA is thought to play an immunoevasive role in the pathogenesis of Marek's disease. It is a candidate for causing the early-stage immunosuppression that occurs after MDHV infection. 90 matched cddid_all.tbl CDD pfam02126 pfam02126 396618 PTE Phosphotriesterase family. 298 matched cddid_all.tbl CDD pfam02127 pfam02127 396619 Peptidase_M18 Aminopeptidase I zinc metalloprotease (M18). 430 matched cddid_all.tbl CDD pfam02128 pfam02128 460454 Peptidase_M36 Fungalysin metallopeptidase (M36). 366 matched cddid_all.tbl CDD pfam02129 pfam02129 396621 Peptidase_S15 X-Pro dipeptidyl-peptidase (S15 family). 264 matched cddid_all.tbl CDD pfam02130 pfam02130 460455 YbeY Endoribonuclease YbeY. YbeY is a single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA. It acts together with the RNase R to eliminate defective 70S ribosomes, but not properly maturated 70S ribosomes or individual subunits, by a process mediated specifically by the 30S ribosomal subunit. It is involved in the processing of 16S, 23S and 5S rRNAs, with a particularly strong effect on maturation at both the 5'-and 3'-ends of 16S rRNA as well as maturation of the 5'-end of 23S and 5S rRNAs. The crystal structure of the protein from Aquifex aeolicus showed an overall fold consisting of one central alpha-helix surrounded by a four-stranded beta-sheet and four other alpha-helices. 125 matched cddid_all.tbl CDD pfam02132 pfam02132 460456 RecR RecR protein. 40 matched cddid_all.tbl CDD pfam02133 pfam02133 251109 Transp_cyt_pur Permease for cytosine/purines, uracil, thiamine, allantoin. 439 matched cddid_all.tbl CDD pfam02135 pfam02135 460457 zf-TAZ TAZ zinc finger. The TAZ2 domain of CBP binds to other transcription factors such as the p53 tumour suppressor protein, E1A oncoprotein, MyoD, and GATA-1. The zinc coordinating motif that is necessary for binding to target DNA sequences consists of HCCC. 72 matched cddid_all.tbl CDD pfam02136 pfam02136 396625 NTF2 Nuclear transport factor 2 (NTF2) domain. This family includes the NTF2-like Delta-5-3-ketosteroid isomerase proteins. 116 matched cddid_all.tbl CDD pfam02137 pfam02137 460458 A_deamin Adenosine-deaminase (editase) domain. Adenosine deaminases acting on RNA (ADARs) can deaminate adenosine to form inosine. In long double-stranded RNA, this process is non-specific; it occurs site-specifically in RNA transcripts. The former is important in defence against viruses, whereas the latter may affect splicing or untranslated regions. They are primarily nuclear proteins, but a longer isoform of ADAR1 is found predominantly in the cytoplasm. ADARs are derived from the Tad1-like tRNA deaminases that are present across eukaryotes. These in turn belong to the nucleotide/nucleic acid deaminase superfamily and are characterized by a distinct insert between the two conserved cysteines that are involved in binding zinc. 278 matched cddid_all.tbl CDD pfam02138 pfam02138 460459 Beach Beige/BEACH domain. 277 matched cddid_all.tbl CDD pfam02140 pfam02140 460460 Gal_Lectin Galactose binding lectin domain. 79 matched cddid_all.tbl CDD pfam02141 pfam02141 460461 DENN DENN (AEX-3) domain. DENN (after differentially expressed in neoplastic vs normal cells) is a domain which occurs in several proteins involved in Rab- mediated processes or regulation of MAPK signalling pathways. 186 matched cddid_all.tbl CDD pfam02142 pfam02142 460462 MGS MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes inosicase. The known structures in this family show a common phosphate binding site. 93 matched cddid_all.tbl CDD pfam02144 pfam02144 396631 Rad1 Repair protein Rad1/Rec1/Rad17. 257 matched cddid_all.tbl CDD pfam02145 pfam02145 460463 Rap_GAP Rap/ran-GAP. 179 matched cddid_all.tbl CDD pfam02146 pfam02146 426621 SIR2 Sir2 family. This region is characteriztic of Silent information regulator 2 (Sir2) proteins, or sirtuins. These are protein deacetylases that depend on nicotine adenine dinucleotide (NAD). They are found in many subcellular locations, including the nucleus, cytoplasm and mitochondria. Eukaryotic forms play in important role in the regulation of transcriptional repression. Moreover, they are involved in microtubule organization and DNA damage repair processes.i 179 matched cddid_all.tbl CDD pfam02148 pfam02148 460464 zf-UBP Zn-finger in ubiquitin-hydrolases and other protein. 63 matched cddid_all.tbl CDD pfam02149 pfam02149 460465 KA1 Kinase associated domain 1. 44 matched cddid_all.tbl CDD pfam02150 pfam02150 280336 RNA_POL_M_15KD RNA polymerases M/15 Kd subunit. 36 matched cddid_all.tbl CDD pfam02151 pfam02151 308001 UVR UvrB/uvrC motif. 36 matched cddid_all.tbl CDD pfam02152 pfam02152 460466 FolB Dihydroneopterin aldolase. This enzyme EC:4.1.2.25 catalyzes the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin in the biosynthetic pathway of tetrahydrofolate. 113 matched cddid_all.tbl CDD pfam02153 pfam02153 460467 PDH_N Prephenate dehydrogenase, nucleotide-binding domain. Members of this family are prephenate dehydrogenases (PDHs) EC:1.3.1.12 involved in tyrosine biosynthesis. This is the N-terminal nucleotide-binding domain of PDHs, which has a modified Rossmann nucleotide-binding fold with an extended beta-sheet sandwiched by three helices on each face. 154 matched cddid_all.tbl CDD pfam02154 pfam02154 111086 FliM Flagellar motor switch protein FliM. 192 matched cddid_all.tbl CDD pfam02155 pfam02155 426625 GCR Glucocorticoid receptor. 377 matched cddid_all.tbl CDD pfam02156 pfam02156 396639 Glyco_hydro_26 Glycosyl hydrolase family 26. 311 matched cddid_all.tbl CDD pfam02157 pfam02157 460468 Man-6-P_recep Mannose-6-phosphate receptor. This family includes both Cation-dependent and cation independent mannose-6-phosphate receptors. 254 matched cddid_all.tbl CDD pfam02158 pfam02158 426627 Neuregulin Neuregulin intracellular region. 360 matched cddid_all.tbl CDD pfam02159 pfam02159 460469 Oest_recep Oestrogen receptor. 138 matched cddid_all.tbl CDD pfam02160 pfam02160 280345 Peptidase_A3 Cauliflower mosaic virus peptidase (A3). 208 matched cddid_all.tbl CDD pfam02161 pfam02161 460470 Prog_receptor Progesterone receptor. 564 matched cddid_all.tbl CDD pfam02162 pfam02162 145362 XYPPX XYPPX repeat (two copies). This repeat is found in a wide variety of proteins and generally consists of the motif XYPPX where X can be any amino acid. The family includes annexin VII, the carboxy tail of certain rhodopsins. This family also includes plaque matrix proteins, however this motif is embedded in a ten residue repeat in Swiss:Q25460. The molecular function of this repeat is unknown. It is also not clear if all the members of this family share a common evolutionary ancestor due to its short length and biased amino acid composition. 15 matched cddid_all.tbl CDD pfam02163 pfam02163 426630 Peptidase_M50 Peptidase family M50. 291 matched cddid_all.tbl CDD pfam02165 pfam02165 460471 WT1 Wilm's tumour protein. 289 matched cddid_all.tbl CDD pfam02166 pfam02166 426632 Androgen_recep Androgen receptor. 501 matched cddid_all.tbl CDD pfam02167 pfam02167 426633 Cytochrom_C1 Cytochrome C1 family. 219 matched cddid_all.tbl CDD pfam02169 pfam02169 426634 LPP20 LPP20 lipoprotein. This family contains the LPP20 lipoprotein, which is a non-essential class of lipoprotein. 96 matched cddid_all.tbl CDD pfam02170 pfam02170 460472 PAZ PAZ domain. This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerization. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteriztic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway. 123 matched cddid_all.tbl CDD pfam02171 pfam02171 396649 Piwi Piwi domain. This domain is found in the protein Piwi and its relatives. The function of this domain is the dsRNA guided hydrolysis of ssRNA. Determination of the crystal structure of Argonaute reveals that PIWI is an RNase H domain, and identifies Argonaute as Slicer, the enzyme that cleaves mRNA in the RNAi RISC complex. In addition, Mg+2 dependence and production of 3'-OH and 5' phosphate products are shared characteriztics of RNaseH and RISC. The PIWI domain core has a tertiary structure belonging to the RNase H family of enzymes. RNase H fold proteins all have a five-stranded mixed beta-sheet surrounded by helices. By analogy to RNase H enzymes which cleave single-stranded RNA guided by the DNA strand in an RNA/DNA hybrid, the PIWI domain can be inferred to cleave single-stranded RNA, for example mRNA, guided by double stranded siRNA. 296 matched cddid_all.tbl CDD pfam02172 pfam02172 366953 KIX KIX domain. CBP and P300 bind to the CREB via a domain known as KIX. The KIX domain of CBP also binds to transactivation domains of other nuclear factors including Myb and Jun. 81 matched cddid_all.tbl CDD pfam02173 pfam02173 396650 pKID pKID domain. CBP and P300 bind to the pKID (phosphorylated kinase-inducible-domain) domain of CREB. 41 matched cddid_all.tbl CDD pfam02174 pfam02174 460473 IRS PTB domain (IRS-1 type). 99 matched cddid_all.tbl CDD pfam02175 pfam02175 111105 7TM_GPCR_Srb Serpentine type 7TM GPCR chemoreceptor Srb. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srb is part of the Sra superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. 236 matched cddid_all.tbl CDD pfam02176 pfam02176 280357 zf-TRAF TRAF-type zinc finger. 60 matched cddid_all.tbl CDD pfam02177 pfam02177 460474 APP_N Amyloid A4 N-terminal heparin-binding. This N-terminal domain of APP, amyloid precursor protein, is the heparin-binding domain of the protein. this region is also responsible for stimulation of neurite outgrowth. The structure reveals both a highly charged basic surface that may interact with glycosaminoglycans in the brain and an abutting hydrophobic surface that is proposed to play an important functional role such as in dimerization or ligand-binding. Structural similarities with cysteine-rich growth factors, taken together with its known growth-promoting properties, suggest the APP N-terminal domain could function as a growth factor in vivo. 100 matched cddid_all.tbl CDD pfam02178 pfam02178 308018 AT_hook AT hook motif. At hooks are DNA binding motifs with a preference for A/T rich regions. 13 matched cddid_all.tbl CDD pfam02179 pfam02179 460475 BAG BAG domain. Domain present in Hsp70 regulators. 77 matched cddid_all.tbl CDD pfam02180 pfam02180 426639 BH4 Bcl-2 homology region 4. 25 matched cddid_all.tbl CDD pfam02181 pfam02181 396655 FH2 Formin Homology 2 Domain. 372 matched cddid_all.tbl CDD pfam02182 pfam02182 460476 SAD_SRA SAD/SRA domain. The domain goes by several names including SAD, SRA and YDG. It adopts a beta barrel, modified PUA-like, fold that is widely present in eukaryotic chromatin proteins and in bacteria. Versions of this domain are known to bind hemi-methylated CpG dinucleotides and also other 5mC containing dinucleotides. The domain binds DNA by flipping out the methylated cytosine base from the DNA double helix.The conserved tyrosine and aspartate residues and a glycine rich patch are critical for recognition of the flipped out base. Mammalian UHRF1 that contains this domain plays an important role in maintenance of methylation at CpG dinucleotides by recruiting DNMT1 to hemimethylated sites associated with replication forks. The SAD/SRA domain has been combined with other domains involved in the ubiquitin pathway on multiple occasions and such proteins link recognition of DNA methylation to chromatin-protein ubiquitination. The domain is also found in species that lack DNA methylation, such as certain apicomplexans, suggestive of other DNA-binding modes or functions. A highly derived and distinct version of the domain is also found in fungi where it is fused to AlkB-type 2OGFeDO domains. In bacteria, the domain is usually fused or associated with restriction endonucleases, many of which target methylated or hemi-methylated DNA. 146 matched cddid_all.tbl CDD pfam02183 pfam02183 460477 HALZ Homeobox associated leucine zipper. 42 matched cddid_all.tbl CDD pfam02184 pfam02184 111114 HAT HAT (Half-A-TPR) repeat. The HAT (Half A TPR) repeat is found in several RNA processing proteins. 32 matched cddid_all.tbl CDD pfam02185 pfam02185 460478 HR1 Hr1 repeat. The HR1 repeat was first described as a three times repeated homology region of the N-terminal non-catalytic part of protein kinase PRK1(PKN). The first two of these repeats were later shown to bind the small G protein rho known to activate PKN in its GTP-bound form. Similar rho-binding domains also occur in a number of other protein kinases and in the rho-binding proteins rhophilin and rhotekin. Recently, the structure of the N-terminal HR1 repeat complexed with RhoA has been determined by X-ray crystallography. It forms an antiparallel coiled-coil fold termed an ACC finger. 67 matched cddid_all.tbl CDD pfam02186 pfam02186 460479 TFIIE_beta TFIIE beta subunit core domain. General transcription factor TFIIE consists of two subunits, TFIIE alpha pfam02002 and TFIIE beta. TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The structure of the DNA binding core region has been solved and has a winged helix fold. 66 matched cddid_all.tbl CDD pfam02187 pfam02187 460480 GAS2 Growth-Arrest-Specific Protein 2 Domain. The GAR2 domain is common in plakin family members and Gas2 family members. The GAR domain comprises around 57 amino acids and has been shown to bind to microtubules. 69 matched cddid_all.tbl CDD pfam02188 pfam02188 460481 GoLoco GoLoco motif. 22 matched cddid_all.tbl CDD pfam02189 pfam02189 426646 ITAM Immunoreceptor tyrosine-based activation motif. T cell receptor (TCR) is a complex multi-protein cell surface receptor composed of the ligand-sensing TCR heterodimer and three signaling subunits. These signaling subunits contain cytoplasmic immunoreceptor tyrosine-based activation motifs (ITAMs) with a consensus sequence of YxxL/Ix6-12YxxL/I. The two tyrosines are phosphorylated by a Src kinase, Lck or Fyn. Binding of the dually phosphorylated ITAM peptide reorients the two SH2 domains relative to each other, destabilizing inhibitory interactions made by the linker connecting the SH2 and kinase domains. 20 matched cddid_all.tbl CDD pfam02190 pfam02190 426647 LON_substr_bdg ATP-dependent protease La (LON) substrate-binding domain. This domain has been shown to be part of the PUA superfamily. This domain represents a general protein and polypeptide interaction domain for the ATP-dependent serine peptidase, LON, Peptidase_S16, pfam05362. ATP-dependent Lon proteases are conserved in all living organizms and catalyze rapid turnover of short-lived regulatory proteins and many damaged or denatured proteins. 195 matched cddid_all.tbl CDD pfam02191 pfam02191 460482 OLF Olfactomedin-like domain. 246 matched cddid_all.tbl CDD pfam02192 pfam02192 460483 PI3K_p85B PI3-kinase family, p85-binding domain. 74 matched cddid_all.tbl CDD pfam02194 pfam02194 460484 PXA PXA domain. This domain is associated with PX domains pfam00787. 181 matched cddid_all.tbl CDD pfam02195 pfam02195 426651 ParBc ParB/Sulfiredoxin domain. Proteins containing this domain include Escherichia coli plasmid protein ParB and mammalian Sulfiredoxin-1. ParB is involved in chromosome partition. It localizes to both poles of the predivisional cell following completion of DNA replication. Sulfiredoxin-1 contributes to oxidative stress resistance by reducing cysteine-sulfinic acid formed under exposure to oxidants in the peroxiredoxins PRDX1, PRDX2, PRDX3 and PRDX4. 90 matched cddid_all.tbl CDD pfam02196 pfam02196 460485 RBD Raf-like Ras-binding domain. 69 matched cddid_all.tbl CDD pfam02197 pfam02197 396669 RIIa Regulatory subunit of type II PKA R-subunit. 37 matched cddid_all.tbl CDD pfam02198 pfam02198 460486 SAM_PNT Sterile alpha motif (SAM)/Pointed domain. 83 matched cddid_all.tbl CDD pfam02199 pfam02199 460487 SapA Saposin A-type domain. 33 matched cddid_all.tbl CDD pfam02200 pfam02200 366975 STE STE like transcription factor. 109 matched cddid_all.tbl CDD pfam02201 pfam02201 460488 SWIB SWIB/MDM2 domain. This family includes the SWIB domain and the MDM2 domain. The p53-associated protein (MDM2) is an inhibitor of the p53 tumour suppressor gene binding the transactivation domain and down regulating the ability of p53 to activate transcription. This family contains the p53 binding domain of MDM2. 73 matched cddid_all.tbl CDD pfam02202 pfam02202 396673 Tachykinin Tachykinin family. 11 matched cddid_all.tbl CDD pfam02203 pfam02203 426656 TarH Tar ligand binding domain homolog. This entry represents the ligand-binding domain found in a number of methyl-accepting chemotaxis receptors, such as E.coli Tar (taxis to aspartate and repellents), which is a receptor for the attractant L-aspartate and also recognizes proteogenic amino acids, phthalic acid, Malic acid, 3,4-dihydroxymandelic acid, citrate, benzoate and derivatives, protocatechuate, vanillate, quinate, shikimate and dehydroshikimate (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 152 matched cddid_all.tbl CDD pfam02204 pfam02204 460489 VPS9 Vacuolar sorting protein 9 (VPS9) domain. This domain acts as a GDP-GTP exchange factor (GEF). It activates Rab GTPases by stimulating the release of GDP and allowing GTP to bind. 104 matched cddid_all.tbl CDD pfam02205 pfam02205 460490 WH2 WH2 motif. The WH2 motif (for Wiskott Aldrich syndrome homology region 2) has been shown in WASP and Scar1 (mammalian homolog) to be the region that interacts with actin. 28 matched cddid_all.tbl CDD pfam02206 pfam02206 426657 WSN Domain of unknown function. 66 matched cddid_all.tbl CDD pfam02207 pfam02207 460491 zf-UBR Putative zinc finger in N-recognin (UBR box). This region is found in E3 ubiquitin ligases that recognize N-recognins. 68 matched cddid_all.tbl CDD pfam02208 pfam02208 460492 Sorb Sorbin homologous domain. 45 matched cddid_all.tbl CDD pfam02209 pfam02209 460493 VHP Villin headpiece domain. 36 matched cddid_all.tbl CDD pfam02210 pfam02210 460494 Laminin_G_2 Laminin G domain. This family includes the Thrombospondin N-terminal-like domain, a Laminin G subfamily. 126 matched cddid_all.tbl CDD pfam02211 pfam02211 426662 NHase_beta Nitrile hydratase beta subunit. Nitrile hydratases EC:4.2.1.84 are unusual metalloenzymes that catalyze the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit. 223 matched cddid_all.tbl CDD pfam02212 pfam02212 460495 GED Dynamin GTPase effector domain. 91 matched cddid_all.tbl CDD pfam02213 pfam02213 460496 GYF GYF domain. The GYF domain is named because of the presence of Gly-Tyr-Phe residues. The GYF domain is a proline-binding domain in CD2-binding protein Swiss:O95400. 45 matched cddid_all.tbl CDD pfam02214 pfam02214 426665 BTB_2 BTB/POZ domain. In voltage-gated K+ channels this domain is responsible for subfamily-specific assembly of alpha-subunits into functional tetrameric channels. In KCTD1 this domain functions as a transcriptional repressor. It also mediates homomultimerization of KCTD1 and interaction of KCTD1 with the transcription factor AP-2-alpha. 93 matched cddid_all.tbl CDD pfam02216 pfam02216 396685 B B domain. This family contains the B domain of Staphylococcal protein A, which specifically binds to the Fc portion of immunoglobulin G. 51 matched cddid_all.tbl CDD pfam02217 pfam02217 280395 T_Ag_DNA_bind Origin of replication binding protein. This domain of large T antigen binds to the SV40 origin of DNA replication. 94 matched cddid_all.tbl CDD pfam02218 pfam02218 460497 HS1_rep Repeat in HS1/Cortactin. The function of this repeat is unknown. Seven copies are found in cortactin and four copies are found in HS1. The repeats are always found amino terminal to an SH3 domain pfam00018. 36 matched cddid_all.tbl CDD pfam02219 pfam02219 396687 MTHFR Methylenetetrahydrofolate reductase. This family includes the 5,10-methylenetetrahydrofolate reductase EC:1.7.99.5 from bacteria and methylenetetrahydrofolate reductase EC: 1.5.1.20 from eukaryotes. The structure for this domain is known to be a TIM barrel. 287 matched cddid_all.tbl CDD pfam02221 pfam02221 460498 E1_DerP2_DerF2 ML domain. ML domain - MD-2-related lipid recognition domain. This family consists of proteins from plants, animals and fungi, including dust mite allergen Der P 2. It has been implicate in lipid recognition, particularly in the recognition of pathogen related products. A mutation in Npc2 causes a rare form of Niemann-Pick type C2 disease. This domain has a similar topology to immunoglobulin domains. 133 matched cddid_all.tbl CDD pfam02222 pfam02222 396689 ATP-grasp ATP-grasp domain. This family does not contain all known ATP-grasp domain members. This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity. 169 matched cddid_all.tbl CDD pfam02223 pfam02223 396690 Thymidylate_kin Thymidylate kinase. 184 matched cddid_all.tbl CDD pfam02224 pfam02224 280401 Cytidylate_kin Cytidylate kinase. Cytidylate kinase EC:2.7.4.14 catalyzes the phosphorylation of cytidine 5'-monophosphate (dCMP) to cytidine 5'-diphosphate (dCDP) in the presence of ATP or GTP. 211 matched cddid_all.tbl CDD pfam02225 pfam02225 460499 PA PA domain. The PA (Protease associated) domain is found as an insert domain in diverse proteases. The PA domain is also found in a plant vacuolar sorting receptor Swiss:O22925 and members of the RZF family Swiss:O43567. It has been suggested that this domain forms a lid-like structure that covers the active site in active proteases, and is involved in protein recognition in vacuolar sorting receptors. 91 matched cddid_all.tbl CDD pfam02226 pfam02226 308053 Pico_P1A Picornavirus coat protein (VP4). VP1, VP2, VP3 and VP4 for the basic unit that forms the icosahedral coat of picornaviruses. Five symmetry-related N termini of coat protein VP4 form a ten-stranded, antiparallel beta barrel around the base of the icosahedral fivefold axis. 68 matched cddid_all.tbl CDD pfam02228 pfam02228 460500 Gag_p19 Major core protein p19. p19 is a component of the inner protein layer of the viral nucleocapsid. 92 matched cddid_all.tbl CDD pfam02229 pfam02229 460501 PC4 Transcriptional Coactivator p15 (PC4). p15 has a bipartite structure composed of an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. The DNA-binding activity of the carboxy-terminal is disguised by the amino-terminal p15 domain. Activity is controlled by protein kinases that target the regulatory domain. 52 matched cddid_all.tbl CDD pfam02230 pfam02230 396693 Abhydrolase_2 Phospholipase/Carboxylesterase. This family consists of both phospholipases and carboxylesterases with broad substrate specificity, and is structurally related to alpha/beta hydrolases pfam00561. 217 matched cddid_all.tbl CDD pfam02232 pfam02232 280407 Alpha_TIF Alpha trans-inducing protein (Alpha-TIF). Alpha-TIF, a virion protein (VP16), is involved in transcriptional activation of viral immediate early (IE) promoters (alpha genes). Specificity of Swiss:P23990 for IE genes is conferred by the 400 residue N-terminal, the 80 residue C-terminal is responsible for transcriptional activation. 343 matched cddid_all.tbl CDD pfam02233 pfam02233 460502 PNTB NAD(P) transhydrogenase beta subunit. This family corresponds to the beta subunit of NADP transhydrogenase in prokaryotes, and either the protein N- or C terminal in eukaryotes. The domain is often found in conjunction with pfam01262. Pyridine nucleotide transhydrogenase catalyzes the reduction of NAD+ to NADPH. A complete loss of activity occurs upon mutation of Gly314 in E. coli. 454 matched cddid_all.tbl CDD pfam02234 pfam02234 460503 CDI Cyclin-dependent kinase inhibitor. Cell cycle progression is negatively controlled by cyclin-dependent kinases inhibitors (CDIs). CDIs are involved in cell cycle arrest at the G1 phase. 46 matched cddid_all.tbl CDD pfam02236 pfam02236 280410 Viral_DNA_bi Viral DNA-binding protein, all alpha domain. This family represents a domain of the viral DNA- binding protein, a multi functional protein involved in DNA replication and transcription control. 79 matched cddid_all.tbl CDD pfam02237 pfam02237 426672 BPL_C Biotin protein ligase C terminal domain. The function of this structural domain is unknown. It is found to the C terminus of the biotin protein ligase catalytic domain pfam01317. 48 matched cddid_all.tbl CDD pfam02238 pfam02238 426673 COX7a Cytochrome c oxidase subunit VII. Cytochrome c oxidase, a 13 sub-unit complex, is the terminal oxidase in the mitochondrial electron transport chain. This family also contains both heart and liver isoforms of cytochrome c oxidase subunit VIIa. 53 matched cddid_all.tbl CDD pfam02239 pfam02239 366994 Cytochrom_D1 Cytochrome D1 heme domain. Cytochrome cd1 (nitrite reductase) catalyzes the conversion of nitrite to nitric oxide in the nitrogen cycle. This family represents the d1 heme binding domain of cytochrome cd1, in which His/Tyr side chains ligate the d1 heme iron of the active site in the oxidized state. 368 matched cddid_all.tbl CDD pfam02240 pfam02240 396698 MCR_gamma Methyl-coenzyme M reductase gamma subunit. Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (pfam02249), 2 beta (pfam02241), and 2 gamma (this family) subunits with two identical nickel porphinoid active sites. 246 matched cddid_all.tbl CDD pfam02241 pfam02241 460504 MCR_beta Methyl-coenzyme M reductase beta subunit, C-terminal domain. Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (pfam02249), 2 beta (this family), and 2 gamma (pfam02240) subunits with two identical nickel porphinoid active sites. The C-terminal domain of MCR beta has an all-alpha fold with buried central helix. 249 matched cddid_all.tbl CDD pfam02244 pfam02244 460505 Propep_M14 Carboxypeptidase activation peptide. Carboxypeptidases are found in abundance in pancreatic secretions. The pro-segment moiety (activation peptide) accounts for up to a quarter of the total length of the peptidase, and is responsible for modulation of folding and activity of the pro-enzyme. 73 matched cddid_all.tbl CDD pfam02245 pfam02245 460506 Pur_DNA_glyco Methylpurine-DNA glycosylase (MPG). Methylpurine-DNA glycosylase is a base excision-repair protein. It is responsible for the hydrolysis of the deoxyribose N-glycosidic bond, excising 3-methyladenine and 3-methylguanine from damaged DNA. 182 matched cddid_all.tbl CDD pfam02246 pfam02246 308063 B1 Protein L b1 domain. Protein L is a bacterial protein with immunoglobulin (Ig) light chain-binding properties. It contains a number of homologous b1 repeats towards the N-terminus. These repeats have been found to be responsible for the interaction of protein L with Ig light chains. 62 matched cddid_all.tbl CDD pfam02247 pfam02247 396702 Como_LCP Large coat protein. This family contains the large coat protein (LCP) of the comoviridae viral family. 369 matched cddid_all.tbl CDD pfam02248 pfam02248 396703 Como_SCP Small coat protein. This family contains the small coat protein (SCP) of the comoviridae viral family. 183 matched cddid_all.tbl CDD pfam02249 pfam02249 396704 MCR_alpha Methyl-coenzyme M reductase alpha subunit, C-terminal domain. Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (this family), 2 beta (pfam02241), and 2 gamma (pfam02240) subunits with two identical nickel porphinoid active sites. The C-terminal domain is comprised of an all-alpha multi-helical bundle. 127 matched cddid_all.tbl CDD pfam02250 pfam02250 396705 Orthopox_35kD 35kD major secreted virus protein. This family of orthopoxvirus secreted proteins (also known as T1 and A41) interact with members of both the CC and CXC superfamilies of chemokines. It has been suggested that these secreted proteins modulate leukocyte influx into virus-infected tissues. 224 matched cddid_all.tbl CDD pfam02251 pfam02251 460507 PA28_alpha Proteasome activator pa28 alpha subunit. PA28 activator complex (also known as 11s regulator of 20S proteasome) is a ring shaped hexameric structure of alternating alpha and beta subunits. This family represents the alpha subunit. The activator complex binds to the 20S proteasome ana simulates peptidase activity in and ATP-independent manner. 61 matched cddid_all.tbl CDD pfam02252 pfam02252 460508 PA28_beta Proteasome activator pa28 beta subunit. PA28 activator complex (also known as 11s regulator of 20S proteasome) is a ring shaped hexameric structure of alternating alpha and beta subunits. This family represents the beta subunit. The activator complex binds to the 20S proteasome ana simulates peptidase activity in and ATP-independent manner. 145 matched cddid_all.tbl CDD pfam02253 pfam02253 460509 PLA1 Phospholipase A1. Phospholipase A1 is a bacterial outer membrane bound acyl hydrolase with a broad substrate specificity EC:3.1.1.32. It has been proposed that Ser164 is the active site for Swiss:P00631. 248 matched cddid_all.tbl CDD pfam02254 pfam02254 426679 TrkA_N TrkA-N domain. This domain is found in a wide variety of proteins. These proteins include potassium channels, phosphoesterases, and various other transporters. This domain binds to NAD. 115 matched cddid_all.tbl CDD pfam02255 pfam02255 460510 PTS_IIA PTS system, Lactose/Cellobiose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIA PTS system enzymes. This family of proteins normally function as a homotrimer, stabilized by a centrally located metal ion. Separation into subunits is thought to occur after phosphorylation. 94 matched cddid_all.tbl CDD pfam02256 pfam02256 460511 Fe_hyd_SSU Iron hydrogenase small subunit. This family represents the small subunit of the Fe-only hydrogenases EC:1.18.99.1. The subunit is comprised of alternating random coil and alpha helical structures that encompasses the large subunit in a novel protein fold. 56 matched cddid_all.tbl CDD pfam02257 pfam02257 460512 RFX_DNA_binding RFX DNA-binding domain. RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer. It recognize X-boxes (DNA of the sequence 5'-GTNRCC(0-3N)RGYAAC-3', where N is any nucleotide, R is a purine and Y is a pyrimidine) using a highly conserved 76-residue DNA-binding domain (DBD). 79 matched cddid_all.tbl CDD pfam02258 pfam02258 460513 SLT_beta Shiga-like toxin beta subunit. This family represents the B subunit of shiga-like toxin (SLT or verotoxin) produced by some strains of E.coli associated with hemorrhagic colitis and hemolytic uremic syndrome. SLT's are composed of one enzymatic A subunit and five cell binding B subunits. 69 matched cddid_all.tbl CDD pfam02259 pfam02259 396714 FAT FAT domain. The FAT domain is named after FRAP, ATM and TRRAP. 342 matched cddid_all.tbl CDD pfam02260 pfam02260 460514 FATC FATC domain. The FATC domain is named after FRAP, ATM, TRRAP C-terminal. The solution structure of the FATC domain suggests it plays a role in redox-dependent structural and cellular stability. 32 matched cddid_all.tbl CDD pfam02261 pfam02261 460515 Asp_decarbox Aspartate decarboxylase. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme aspartate decarboxylase EC:4.1.1.11 which requires a pyruvoyl group for its activity. It is synthesized initially as a proenzyme which is then proteolytically cleaved to an alpha (C-terminal) and beta (N-terminal) subunit and a pyruvoyl group. This family contains both chains of aspartate decarboxylase. 107 matched cddid_all.tbl CDD pfam02262 pfam02262 426685 Cbl_N CBL proto-oncogene N-terminal domain 1. Cbl is an adaptor protein that binds EGF receptors (or other tyrosine kinases) and SH3 domains, functioning as a negative regulator of many signaling pathways. The N-terminal domain is evolutionarily conserved, and is known to bind to phosphorylated tyrosine residues. Cbl_N is comprised of 3 structural domains of which this is the first - a four helix bundle. 125 matched cddid_all.tbl CDD pfam02263 pfam02263 460516 GBP Guanylate-binding protein, N-terminal domain. Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP. 260 matched cddid_all.tbl CDD pfam02264 pfam02264 426687 LamB LamB porin. Maltoporin (LamB protein) forms a trimeric structure which facilitates the diffusion of maltodextrins across the outer membrane of Gram-negative bacteria. The membrane channel is formed by an antiparallel beta-barrel. 385 matched cddid_all.tbl CDD pfam02265 pfam02265 426688 S1-P1_nuclease S1/P1 Nuclease. This family contains both S1 and P1 nucleases (EC:3.1.30.1) which cleave RNA and single stranded DNA with no base specificity. 252 matched cddid_all.tbl CDD pfam02267 pfam02267 460517 Rib_hydrolayse ADP-ribosyl cyclase. ADP-ribosyl cyclase EC:3.2.2.5 (also know as cyclic ADP-ribose hydrolase or CD38) synthesizes cyclic-ADP ribose, a second messenger for glucose-induced insulin secretion. 229 matched cddid_all.tbl CDD pfam02268 pfam02268 460518 TFIIA_gamma_N Transcription initiation factor IIA, gamma subunit, helical domain. Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA box. The N-terminal domain of the gamma subunit is a 4 helix bundle. 46 matched cddid_all.tbl CDD pfam02269 pfam02269 190265 TFIID-18kDa Transcription initiation factor IID, 18kD subunit. This family includes the Spt3 yeast transcription factors and the 18kD subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold 93 matched cddid_all.tbl CDD pfam02270 pfam02270 426691 TFIIF_beta TFIIF, beta subunit HTH domain. Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter. 65 matched cddid_all.tbl CDD pfam02271 pfam02271 460519 UCR_14kD Ubiquinol-cytochrome C reductase complex 14kD subunit. The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex. This Pfam family represents the 14kD (or VI) subunit of the complex which is not directly involved in electron transfer, but has a role in assembly of the complex. 100 matched cddid_all.tbl CDD pfam02272 pfam02272 396724 DHHA1 DHHA1 domain. This domain is often found adjacent to the DHH domain pfam01368 and is called DHHA1 for DHH associated domain. This domain is diagnostic of DHH subfamily 1 members. This domains is also found in alanyl tRNA synthetase, suggesting that this domain may have an RNA binding function. The domain is about 60 residues long and contains a conserved GG motif. 139 matched cddid_all.tbl CDD pfam02273 pfam02273 111194 Acyl_transf_2 Acyl transferase. This bacterial family of Acyl transferases (or myristoyl-acp-specific thioesterases) catalyze the first step in the bioluminescent fatty acid reductase system. 294 matched cddid_all.tbl CDD pfam02274 pfam02274 426693 ADI Arginine deiminase. This family contains arginine deiminases, EC:3.5.3.6., enzymes that catalyze the reaction: arginine + H2O <=> citrulline + NH3. These enzymes belong to the amidinotranferase (AT) superfamily, which share the alpha/beta fold including structurally important residues, i.e buried hydrophobic residues, buried hydrophilic residues hydrogen-bonded with mainchain groups and a structural hallmark of three consecutive buried Gly residues near the C-terminus, conserved among these proteins. 377 matched cddid_all.tbl CDD pfam02275 pfam02275 396726 CBAH Linear amide C-N hydrolases, choloylglycine hydrolase family. This family includes several hydrolases which cleave carbon-nitrogen bonds, other than peptide bonds, in linear amides. These include choloylglycine hydrolase (conjugated bile acid hydrolase, CBAH) EC:3.5.1.24, penicillin acylase EC:3.5.1.11 and acid ceramidase EC:3.5.1.23. This domain forms the alpha-subunit for members from vertebral species, see family NAAA-beta, pfam15508. 316 matched cddid_all.tbl CDD pfam02276 pfam02276 396727 CytoC_RC Photosynthetic reaction centre cytochrome C subunit. Photosynthesis in purple bacteria is dependent on light-induced electron transfer in the reaction centre (RC), coupled to the uptake of protons from the cytoplasm. The RC contains a cytochrome molecule which re-reduces the oxidized electron donor. 309 matched cddid_all.tbl CDD pfam02277 pfam02277 460520 DBI_PRT Phosphoribosyltransferase. This family of proteins represent the nicotinate-nucleotide- dimethylbenzimidazole phosphoribosyltransferase (NN:DBI PRT) enzymes involved in dimethylbenzimidazole synthesis. This function is essential to de novo cobalamin (vitamin B12) production in bacteria. Nicotinate mononucleotide (NaMN):5,6-dimethylbenzimidazole (DMB) phosphoribosyltransferase (CobT) from Salmonella enterica plays a central role in the synthesis of alpha-ribazole-5'-phosphate, an intermediate for the lower ligand of cobalamin. 332 matched cddid_all.tbl CDD pfam02278 pfam02278 460521 Lyase_8 Polysaccharide lyase family 8, super-sandwich domain. This family consists of a group of secreted bacterial lyase enzymes EC:4.2.2.1 capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen. 249 matched cddid_all.tbl CDD pfam02281 pfam02281 426696 Dimer_Tnp_Tn5 Transposase Tn5 dimerization domain. Transposons are mobile DNA sequences capable of replication and insertion into the chromosome. Typically transposons code for the transposase enzyme, which catalyzes insertion, found between terminal inverted repeats. Tn5 has a unique method of self- regulation in which a truncated version of the transposase enzyme acts as an inhibitor. The catalytic domain of the Tn5 transposon is found in pfam01609. This domain mediates dimerization in the known structure. 99 matched cddid_all.tbl CDD pfam02282 pfam02282 396730 Herpes_UL42 DNA polymerase processivity factor (UL42). The DNA polymerase processivity factor (UL42) of herpes simplex virus forms a heterodimer with UL30 to create the viral DNA polymerase complex. UL42 functions to increase the processivity of polymerization and makes little contribution to the catalytic activity of the polymerase. 142 matched cddid_all.tbl CDD pfam02283 pfam02283 426697 CobU Cobinamide kinase / cobinamide phosphate guanyltransferase. This family is composed of a group of bifunctional cobalamin biosynthesis enzymes which display cobinamide kinase and cobinamide phosphate guanyltransferase activity. The crystal structure of the enzyme reveals the molecule to be a trimer with a propeller-like shape. 167 matched cddid_all.tbl CDD pfam02284 pfam02284 460522 COX5A Cytochrome c oxidase subunit Va. Cytochrome c oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit Va. 99 matched cddid_all.tbl CDD pfam02285 pfam02285 460523 COX8 Cytochrome oxidase c subunit VIII. Cytochrome c oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit VIII. 41 matched cddid_all.tbl CDD pfam02286 pfam02286 426700 Dehydratase_LU Dehydratase large subunit. This family contains the large subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances. 552 matched cddid_all.tbl CDD pfam02287 pfam02287 426701 Dehydratase_SU Dehydratase small subunit. This family contains the small subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances. 131 matched cddid_all.tbl CDD pfam02288 pfam02288 426702 Dehydratase_MU Dehydratase medium subunit. This family contains the medium subunit of the trimeric diol dehydratases and glycerol dehydratases. These enzymes are produced by some enterobacteria in response to growth substances. 108 matched cddid_all.tbl CDD pfam02289 pfam02289 426703 MCH Cyclohydrolase (MCH). Methenyl tetrahydromethanopterin cyclohydrolase EC:3.5.4.27 is involved in methanogenesis in bacteria and archaea, producing methane from carbon monoxide or carbon dioxide. 308 matched cddid_all.tbl CDD pfam02290 pfam02290 460524 SRP14 Signal recognition particle 14kD protein. The signal recognition particle (SRP) is a multimeric protein involved in targeting secretory proteins to the rough endoplasmic reticulum membrane. SRP14 and SRP9 form a complex essential for SRP RNA binding. 106 matched cddid_all.tbl CDD pfam02291 pfam02291 460525 TFIID-31kDa Transcription initiation factor IID, 31kD subunit. This family represents the N-terminus of the 31kD subunit (42kD in drosophila) of transcription initiation factor IID (TAFII31). TAFII31 binds to p53, and is an essential requirement for p53 mediated transcription activation. 122 matched cddid_all.tbl CDD pfam02293 pfam02293 426706 AmiS_UreI AmiS/UreI family transporter. This family includes UreI and proton gated urea channel as well as putative amide transporters. 165 matched cddid_all.tbl CDD pfam02294 pfam02294 280458 7kD_DNA_binding 7kD DNA-binding domain. This family contains members of the hyper-thermophilic archaebacterium 7kD DNA-binding/endoribonuclease P2 family. There are five 7kD DNA-binding proteins, 7a-7e, found as monomers in the cell. Protein 7e shows the tightest DNA-binding ability. 58 matched cddid_all.tbl CDD pfam02295 pfam02295 280459 z-alpha Adenosine deaminase z-alpha domain. This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA- editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this region to B-DNA has been shown to be disfavoured by steric hindrance. 67 matched cddid_all.tbl CDD pfam02296 pfam02296 426707 Alpha_adaptin_C Alpha adaptin AP2, C-terminal domain. Alpha adaptin is a hetero tetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. 113 matched cddid_all.tbl CDD pfam02297 pfam02297 426708 COX6B Cytochrome oxidase c subunit VIb. Cytochrome c oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of the potentially heme-binding subunit IVb of the oxidase. 65 matched cddid_all.tbl CDD pfam02298 pfam02298 280462 Cu_bind_like Plastocyanin-like domain. This family represents a domain found in flowering plants related to the copper binding protein plastocyanin. Some members of this family may not bind copper due to the lack of key residues. 84 matched cddid_all.tbl CDD pfam02300 pfam02300 426709 Fumarate_red_C Fumarate reductase subunit C. Fumarate reductase is a membrane-bound flavoenzyme consisting of four subunits, A-B. A and B comprise the membrane-extrinsic catalytic domain and C and D link the catalytic centres to the electron-transport chain. This family consists of the 15kD hydrophobic subunit C. 127 matched cddid_all.tbl CDD pfam02301 pfam02301 460526 HORMA HORMA domain. The HORMA (for Hop1p, Rev7p and MAD2) domain has been suggested to recognize chromatin states that result from DNA adducts, double stranded breaks or non-attachment to the spindle and acts as an adaptor that recruits other proteins. MAD2 is a spindle checkpoint protein which prevents progression of the cell cycle upon detection of a defect in mitotic spindle integrity. 209 matched cddid_all.tbl CDD pfam02302 pfam02302 396744 PTS_IIB PTS system, Lactose/Cellobiose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The lactose/cellobiose-specific family are one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes. The fold of IIB cellobiose shows similar structure to mammalian tyrosine phosphatases. This family also contains the fructose specific IIB subunit. 92 matched cddid_all.tbl CDD pfam02303 pfam02303 396745 Phage_DNA_bind Helix-destabilising protein. This family contains the bacteriophage helix-destabilising protein, or single-stranded DNA binding protein, required for DNA synthesis. 83 matched cddid_all.tbl CDD pfam02304 pfam02304 460527 Phage_B Scaffold protein B. This is a family of proteins from single-stranded DNA bacteriophages. Scaffold proteins B and D are required for procapsid formation. Sixty copies of the internal scaffold protein B are found in the procapsid. 117 matched cddid_all.tbl CDD pfam02305 pfam02305 308107 Phage_F Capsid protein (F protein). This is a family of proteins from single-stranded DNA bacteriophages. Protein F is the major capsid component, sixty copies of which are found in the virion. 510 matched cddid_all.tbl CDD pfam02306 pfam02306 280468 Phage_G Major spike protein (G protein). This is a family of proteins from single-stranded DNA bacteriophages. Five G proteins, each a tight beta barrel, from twelve surface spikes. 175 matched cddid_all.tbl CDD pfam02308 pfam02308 460528 MgtC MgtC family. The MgtC protein is found in an operon with the Mg2+ transporter protein MgtB. The function of MgtC and its homologs is not known. 120 matched cddid_all.tbl CDD pfam02309 pfam02309 460529 AUX_IAA AUX/IAA family. Transcription of the AUX/IAA family of genes is rapidly induced by the plant hormone auxin. Some members of this family are longer and contain an N terminal DNA binding domain. The function of this region is uncertain. 188 matched cddid_all.tbl CDD pfam02310 pfam02310 426713 B12-binding B12 binding domain. This domain binds to B12 (adenosylcobamide), it is found in several enzymes, such as glutamate mutase, methionine synthase and methylmalonyl-CoA mutase. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, which is important for B12 binding. 121 matched cddid_all.tbl CDD pfam02311 pfam02311 396749 AraC_binding AraC-like ligand binding domain. This family represents the arabinose-binding and dimerization domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif pfam00165. This domain is distantly related to the Cupin domain pfam00190. 134 matched cddid_all.tbl CDD pfam02312 pfam02312 396750 CBF_beta Core binding factor beta subunit. Core binding factor (CBF) is a heterodimeric transcription factor essential for genetic regulation of hematopoiesis and osteogenesis. The beta subunit enhances DNA-binding ability of the alpha subunit in vitro, and has been show to have a structure related to the OB fold. 166 matched cddid_all.tbl CDD pfam02313 pfam02313 426714 Fumarate_red_D Fumarate reductase subunit D. Fumarate reductase is a membrane-bound flavoenzyme consisting of four subunits, A-B. A and B comprise the membrane-extrinsic catalytic domain and C and D link the catalytic centres to the electron-transport chain. This family consists of the 13kD hydrophobic subunit D. 114 matched cddid_all.tbl CDD pfam02315 pfam02315 396752 MDH Methanol dehydrogenase beta subunit. Methanol dehydrogenase (MDH) is a bacterial periplasmic quinoprotein that oxidizes methanol to formaldehyde. MDH is a tetramer of two alpha and two beta subunits. This family contains the small beta subunit. 88 matched cddid_all.tbl CDD pfam02316 pfam02316 367032 HTH_Tnp_Mu_1 Mu DNA-binding domain. This family consists of MuA-transposase and repressor protein CI. These proteins contain homologous DNA-binding domains at their N-termini which compete for the same DNA site within the Mu bacteriophage genome. 134 matched cddid_all.tbl CDD pfam02317 pfam02317 426715 Octopine_DH NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain. This group of enzymes act on the CH-NH substrate bond using NAD(+) or NADP(+) as an acceptor. The Pfam family consists mainly of octopine and nopaline dehydrogenases from Ti plasmids. 149 matched cddid_all.tbl CDD pfam02318 pfam02318 426716 FYVE_2 FYVE-type zinc finger. This FYVE-type zinc finger is found at the N-terminus of effector proteins including rabphilin-3A and regulating synaptic membrane exocytosis protein 2. 118 matched cddid_all.tbl CDD pfam02319 pfam02319 460530 E2F_TDP E2F/DP family winged-helix DNA-binding domain. This family contains the transcription factor E2F and its dimerization partners TDP1 and TDP2, which stimulate E2F-dependent transcription. E2F binds to DNA as a homodimer or as a heterodimer in association with TDP1/2, the heterodimer having increased binding efficiency. The crystal structure of an E2F4-DP2-DNA complex shows that the DNA-binding domains of the E2F and DP proteins both have a fold related to the winged-helix DNA-binding motif. Recognition of the central c/gGCGCg/c sequence of the consensus DNA-binding site is symmetric, and amino acids that contact these bases are conserved among all known E2F and DP proteins. 65 matched cddid_all.tbl CDD pfam02320 pfam02320 460531 UCR_hinge Ubiquinol-cytochrome C reductase hinge protein. The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex. This Pfam family represents the 'hinge' protein of the complex which is thought to mediate formation of the cytochrome c1 and cytochrome c complex. 65 matched cddid_all.tbl CDD pfam02321 pfam02321 396757 OEP Outer membrane efflux protein. The OEP family (Outer membrane efflux protein) form trimeric channels that allow export of a variety of substrates in Gram negative bacteria. Each member of this family is composed of two repeats. The trimeric channel is composed of a 12 stranded all beta sheet barrel that spans the outer membrane, and a long all helical barrel that spans the periplasm. 181 matched cddid_all.tbl CDD pfam02322 pfam02322 460532 Cyt_bd_oxida_II Cytochrome bd terminal oxidase subunit II. This family consists of cytochrome bd type terminal oxidases that catalyze quinol-dependent, Na+-independent oxygen uptake. Members of this family are integral membrane proteins and contain a protohaem IX centre B558. One member of the family Swiss:O05192 is implicated in having an important role in micro-aerobic nitrogen fixation in the enteric bacterium Klebsiella pneumoniae. The family forms an integral functional unit with subunit I, family Bac_Ubq_Cox, pfam01654. 309 matched cddid_all.tbl CDD pfam02323 pfam02323 145463 ELH Egg-laying hormone precursor. This family consists of egg-laying hormone (ELH) precursor and atrial gland peptides form little and California sea hare. The family also includes ovulation prohormone precursor from great pond snail. This family thus represents a conserved gastropoda ovulation and egg production prohormone. Note that many of the proteins present are further cleaved to give individual peptides. Neuropeptidergic bag cells of the marine mollusk Aplysia californica synthesize an egg-laying hormone (ELH) precursor protein which is cleaved to generate several bioactive peptides including ELH, bag cell peptides (BCP) and acidic peptide (AP). 255 matched cddid_all.tbl CDD pfam02324 pfam02324 426720 Glyco_hydro_70 Glycosyl hydrolase family 70. Members of this family belong to glycosyl hydrolase family 70 Glucosyltransferases or sucrose 6-glycosyl transferases (GTF-S) catalyze the transfer of D-glucopyramnosyl units from sucrose onto acceptor molecules, EC:2.4.1.5. This family roughly corresponds to the N-terminal catalytic domain of the enzyme. Members of this family also contain the Putative cell wall binding domain pfam01473, which corresponds with the C-terminal glucan-binding domain. 831 matched cddid_all.tbl CDD pfam02325 pfam02325 460533 YGGT YGGT family. This family includes subunit CCB3 of cofactor assembly complex C, involved in c-type cytochrome maturation in photosynthetic organizms. This family also includes uncharacterized protein YggT, associated with bacteria outside the cyanobacteria. 71 matched cddid_all.tbl CDD pfam02326 pfam02326 396760 YMF19 Plant ATP synthase F0. This family corresponds to subunit 8 (YMF19) of the F0 complex of plant and algae mitochondrial F-ATPases (EC:3.6.1.34). 84 matched cddid_all.tbl CDD pfam02327 pfam02327 396761 BChl_A Bacteriochlorophyll A protein. Bacteriochlorophyll A protein is involved in the energy transfer system of green photosynthetic bacteria. The protein forms a homotrimer, with each monomer unit containing seven molecules of bacteriochlorophyll A. 354 matched cddid_all.tbl CDD pfam02329 pfam02329 426722 HDC Histidine carboxylase PI chain. Histidine carboxylase catalyzes the formation of histamine from histidine. Cleavage of the proenzyme PI chain yields two subunits, alpha and beta, which arrange as a hexamer (alpha beta)6. 293 matched cddid_all.tbl CDD pfam02330 pfam02330 460534 MAM33 Mitochondrial glycoprotein. This mitochondrial matrix protein family contains members of the MAM33 family which bind to the globular 'heads' of C1Q. It is thought to be involved in mitochondrial oxidative phosphorylation and in nucleus-mitochondrion interactions. 209 matched cddid_all.tbl CDD pfam02331 pfam02331 280489 P35 Apoptosis preventing protein. This viral protein functions to block the host apoptotic response caused by infection by the virus. The apoptosis preventing protein (or early 35kD protein, P35) acts by blocking caspase protease activity. 295 matched cddid_all.tbl CDD pfam02332 pfam02332 426724 Phenol_Hydrox Methane/Phenol/Toluene Hydroxylase. Bacterial phenol hydroxylase is a multicomponent enzyme that catabolizes phenol and some of its methylated derivatives. This Pfam family contains both the P1 and P3 polypeptides of phenol hydroxylase and the alpha and beta chain of methane hydroxylase protein A. 229 matched cddid_all.tbl CDD pfam02333 pfam02333 280491 Phytase Phytase. Phytase is a secreted enzyme which hydrolyses phytate to release inorganic phosphate. This family appears to represent a novel enzyme that shows phytase activity and has been shown to have a six- bladed propeller folding architecture. 375 matched cddid_all.tbl CDD pfam02334 pfam02334 426725 RTP Replication terminator protein. The bacterial replication terminator protein (RTP) plays a role in the termination of DNA replication by impeding replication fork movement. Two RTP dimers bind to the two inverted repeat regions at the termination site. 113 matched cddid_all.tbl CDD pfam02335 pfam02335 426726 Cytochrom_C552 Cytochrome c552. Cytochrome c552 (cytochrome c nitrite reductase) is a crucial enzyme in the nitrogen cycle catalysing the reduction of nitrite to ammonia. The crystal structure of cytochrome c552 reveals it to be a dimer, with with 10 close-packed type c haem groups. 435 matched cddid_all.tbl CDD pfam02336 pfam02336 280494 Denso_VP4 Capsid protein VP4. Four different translation initiation sites of the densovirus capsid protein mRNA give rise to four viral proteins, VP1 to VP4. This family represents VP4. 431 matched cddid_all.tbl CDD pfam02337 pfam02337 426727 Gag_p10 Retroviral GAG p10 protein. This family consists of various retroviral GAG (core) polyproteins and encompasses the p10 region producing the p10 protein upon proteolytic cleavage of GAG by retroviral protease. The p10 or matrix protein (MA) is associated with the virus envelope glycoproteins in most mammalian retroviruses and may be involved in virus particle assembly, transport and budding. Some of the GAG polyproteins have alternate cleavage sites leading to the production of alternative and longer cleavage products (e.g. p19) the alignment of this family only covers the approximately N-terminal (GAG) 100 amino acid region of homology to p10. 85 matched cddid_all.tbl CDD pfam02338 pfam02338 426728 OTU OTU-like cysteine protease. This family is comprised of a group of predicted cysteine proteases, homologous to the Ovarian Tumour (OTU) gene in Drosophila. Members include proteins from eukaryotes, viruses and pathogenic bacterium. The conserved cysteine and histidine, and possibly the aspartate, represent the catalytic residues in this putative group of proteases. 127 matched cddid_all.tbl CDD pfam02340 pfam02340 111251 PRRSV_Env PRRSV putative envelope protein. This family consists of a conserved probable envelope protein or ORF2 in porcine reproductive and respiratory syndrome virus (PRRSV) also in the family is a minor structural protein from lactate dehydrogenase-elevating virus. 234 matched cddid_all.tbl CDD pfam02341 pfam02341 426729 RbcX RbcX protein. The RBCX protein has been identified as having a possible chaperone-like function. The rbcX gene is juxtaposed to and cotranscribed with rbcL and rbcS encoding RuBisCO in Anabaena sp. CA. RbcX has been shown to possess a chaperone-like function assisting correct folding of RuBisCO in E. coli expression studies and is needed for RuBisCO to reach its maximal activity. 100 matched cddid_all.tbl CDD pfam02342 pfam02342 426730 TerD TerD domain. The TerD domain is found in TerD family proteins that include the paralogous TerD, TerA, TerE, TerF and TerZ proteins It is found in a stress response operon with TerB and TerC. TerD has a maximum of two calcium-binding sites depending on the conservation of aspartates. It has various fusions to nuclease domains, RNA binding domains, ubiquitin related domains, and metal binding domains. The ter gene products lie at the centre of membrane-linked metal recognition complexes with regulatory ramifications encompassing phosphorylation-dependent signal transduction, RNA-dependent regulation, biosynthesis of nucleoside-like metabolites and DNA processing linked to novel pathways. 187 matched cddid_all.tbl CDD pfam02343 pfam02343 460535 TRA-1_regulated TRA-1 regulated protein R03H10.4. This family of proteins represents the protein product of the gene R03H10.4 which is located near a sequence that matches the TRA-1 binding consensus. TRA-1 is a transcription factor which controls sexual differentiation in C.elegans. R03H10.4 shows male-enriched reporter gene expression and acts as a direct target of TRA-1 regulation. 129 matched cddid_all.tbl CDD pfam02344 pfam02344 460536 Myc-LZ Myc leucine zipper domain. This family consists of the leucine zipper dimerization domain found in both cellular c-Myc proto-oncogenes and viral v-Myc oncogenes. dimerization via the leucine zipper motif with other basic helix-loop-helix-leucine zipper (b/HLH/lz) proteins such as Max is required for efficient DNA binding. The Myc-Max dimer is a transactivating complex activating expression of growth related genes promoting cell proliferation. The dimerization is facilitated via interdigitating leucine residues every 7th position of the alpha helix. Like charge repulsion of adjacent residues in this region perturbs the formation of homodimers with heterodimers being promoted by opposing charge attractions. 27 matched cddid_all.tbl CDD pfam02346 pfam02346 280501 Vac_Fusion Chordopoxvirus multifunctional envelope protein A27. This is a family of viral fusion proteins from the chordopoxviruses. Swiss:P26312 a 14-kDa Vaccinia Virus protein has been demonstrated to function as a viral fusion protein mediating cell fusion at endosmomal (low) pH. More recently it has been shown that A27 forms disulfide-linked protein complexes with A26 protein providing an anchor for A26 protein packaging into mature virions. A27 regulates virion-membrane fusion rather than inducing it and is critical for the successful egress of mature virus particles. 56 matched cddid_all.tbl CDD pfam02347 pfam02347 396772 GDC-P Glycine cleavage system P-protein. This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1.2.10 (GDC) also annotated as glycine cleavage system or glycine synthase. GDC consists of four proteins P, H, L and T. The reaction catalyzed by this protein is:- Glycine + lipoylprotein <=> S-aminomethyldihydrolipoylprotein + CO2 428 matched cddid_all.tbl CDD pfam02348 pfam02348 396773 CTP_transf_3 Cytidylyltransferase. This family consists of two main Cytidylyltransferase activities: 1) 3-deoxy-manno-octulosonate cytidylyltransferase,, EC:2.7.7.38 catalysing the reaction:- CTP + 3-deoxy-D-manno-octulosonate <=> diphosphate + CMP-3-deoxy-D-manno-octulosonate, 2) acylneuraminate cytidylyltransferase EC:2.7.7.43,, catalysing the reaction:- CTP + N-acylneuraminate <=> diphosphate + CMP-N-acylneuraminate. NeuAc cytydilyltransferase of Mannheimia haemolytica has been characterized describing kinetics and regulation by substrate charge, energetic charge and amino-sugar demand. 217 matched cddid_all.tbl CDD pfam02349 pfam02349 396774 MSG Major surface glycoprotein. This is a novel repeat in Pneumocystis carinii Major surface glycoprotein (MSG) some members of the alignment have up to nine repeats of this family, the repeats containing several conserved cysteines. The MSG of P. carinii is an important protein in host-pathogen interactions. Surface glycoprotein A from Pneumocystis carinii is a main target for the host immune system, this protein is implicated in the attachment of Pneumocystis carinii to the host alveolar epithelial cells, alveolar macrophages, host surfactant and possibly accounts in part for the hypoxia seen in Pneumocystis carinii pneumonia (PCP). 76 matched cddid_all.tbl CDD pfam02350 pfam02350 426733 Epimerase_2 UDP-N-acetylglucosamine 2-epimerase. This family consists of UDP-N-acetylglucosamine 2-epimerases EC:5.1.3.14 this enzyme catalyzes the production of UDP-ManNAc from UDP-GlcNAc. Note that some of the enzymes is this family are bifunctional such as Swiss:O35826 and Swiss:Q9Z0P6 in this instance Pfam matches only the N-terminal half of the protein suggesting that the additional C-terminal part (when compared to mono-functional members of this family) is responsible for the UPD-N-acetylmannosamine kinase activity of these enzymes. This hypothesis is further supported by the assumption that the C-terminal part of Swiss:O35826 is the kinase domain. 336 matched cddid_all.tbl CDD pfam02351 pfam02351 460537 GDNF GDNF/GAS1 domain. This cysteine rich domain is found in multiple copies in GNDF and GAS1 proteins. GDNF and neurturin (NTN) receptors are potent survival factors for sympathetic, sensory and central nervous system neurons. GDNF and neurturin promote neuronal survival by signaling through similar multicomponent receptors that consist of a common receptor tyrosine kinase and a member of a GPI-linked family of receptors that determines ligand specificity. 87 matched cddid_all.tbl CDD pfam02352 pfam02352 367048 Decorin_bind Decorin binding protein. This family consists of decorin binding proteins from Borrelia. The decorin binding protein of Borrelia burgdorferi the lyme disease spirochetes adheres to the proteoglycan decorin found on collagen fibres. 141 matched cddid_all.tbl CDD pfam02353 pfam02353 396777 CMAS Mycolic acid cyclopropane synthetase. This family consist of Cyclopropane-fatty-acyl-phospholipid synthase or CFA synthase EC:2.1.1.79 this enzyme catalyze the reaction: S-adenosyl-L-methionine + phospholipid olefinic fatty acid <=> S-adenosyl-L-homocysteine + phospholipid cyclopropane fatty acid. 272 matched cddid_all.tbl CDD pfam02354 pfam02354 460538 Latrophilin Latrophilin Cytoplasmic C-terminal region. This family consists of the cytoplasmic C-terminal region in latrophilin. Latrophilin is a synaptic Ca2+ independent alpha- latrotoxin (LTX) receptor and is a novel member of the secretin family of G-protein coupled receptors that are involved in secretion. Latrophilin mRNA is present only in neuronal tissue. Lactrophillin interacts with G-alpha O. 378 matched cddid_all.tbl CDD pfam02355 pfam02355 280510 SecD_SecF Protein export membrane protein. This family consists of various prokaryotic SecD and SecF protein export membrane proteins. This SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC. SecD and SecF are required to maintain a proton motive force. 189 matched cddid_all.tbl CDD pfam02357 pfam02357 426736 NusG Transcription termination factor nusG. 96 matched cddid_all.tbl CDD pfam02358 pfam02358 426737 Trehalose_PPase Trehalose-phosphatase. This family consist of trehalose-phosphatases EC:3.1.3.12 these enzyme catalyze the de-phosphorylation of trehalose-6-phosphate to trehalose and orthophosphate. The aligned region is present in trehalose-phosphatases and comprises the entire length of the protein it is also found in the C-terminus of trehalose-6-phosphate synthase EC:2.4.1.15 adjacent to the trehalose-6-phosphate synthase domain - pfam00982. It would appear that the two equivalent genes in the E. coli otsBA operon otsA the trehalose-6-phosphate synthase and otsB trehalose-phosphatase (this family) have undergone gene fusion in most eukaryotes and Swiss:P93653. Trehalose is a common disaccharide of bacteria, fungi and invertebrates that appears to play a major role in desiccation tolerance. 234 matched cddid_all.tbl CDD pfam02359 pfam02359 426738 CDC48_N Cell division protein 48 (CDC48), N-terminal domain. This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the N-terminus. The VAT-N domain found in AAA ATPases pfam00004 is a substrate 185-residue recognition domain. 85 matched cddid_all.tbl CDD pfam02361 pfam02361 396782 CbiQ Cobalt transport protein. This family consists of various cobalt transport proteins Most of which are found in Cobalamin (Vitamin B12) biosynthesis operons. In Salmonella the cbiN cbiQ (product CbiQ in this family) and cbiO are likely to form an active cobalt transport system. 215 matched cddid_all.tbl CDD pfam02362 pfam02362 396783 B3 B3 DNA binding domain. This is a family of plant transcription factors with various roles in development, the aligned region corresponds the B3 DNA binding domain as described in this domain is found in VP1/AB13 transcription factors. Some proteins also have a second AP2 DNA binding domain pfam00847 such as RAV1. DNA binding activity was demonstrated by. 101 matched cddid_all.tbl CDD pfam02363 pfam02363 308140 C_tripleX Cysteine rich repeat. This Cysteine repeat C-X3-C-X3-C is repeated in sequences of this family, 34 times in Swiss:O17970. The function of these repeats is unknown as is the function of the proteins in which they occur. Most of the sequences in this family are from C. elegans. 17 matched cddid_all.tbl CDD pfam02364 pfam02364 426739 Glucan_synthase 1,3-beta-glucan synthase component. This family consists of various 1,3-beta-glucan synthase components including Gls1, Gls2 and Gls3 from yeast. 1,3-beta-glucan synthase EC:2.4.1.34 also known as callose synthase catalyzes the formation of a beta-1,3-glucan polymer that is a major component of the fungal cell wall. The reaction catalyzed is:- UDP-glucose + {(1,3)-beta-D-glucosyl}(N) <=> UDP + {(1,3)-beta-D-glucosyl}(N+1). 818 matched cddid_all.tbl CDD pfam02365 pfam02365 460539 NAM No apical meristem (NAM) protein. This is a family of no apical meristem (NAM) proteins these are plant development proteins. Mutations in NAM result in the failure to develop a shoot apical meristem in petunia embryos. NAM is indicated as having a role in determining positions of meristems and primordial. One member of this family NAP (NAC-like, activated by AP3/PI) is encoded by the target genes of the AP3/PI transcriptional activators and functions in the transition between growth by cell division and cell expansion in stamens and petals. 122 matched cddid_all.tbl CDD pfam02366 pfam02366 396786 PMT Dolichyl-phosphate-mannose-protein mannosyltransferase. This is a family of Dolichyl-phosphate-mannose-protein mannosyltransferase proteins EC:2.4.1.109. These proteins are responsible for O-linked glycosylation of proteins, they catalyze the reaction:- Dolichyl phosphate D-mannose + protein <=> dolichyl phosphate + O-D-mannosyl-protein. Also in this family is the Drosophila rotated abdomen protein which is a putative mannosyltransferase. This family appears to be distantly related to pfam02516 (A Bateman pers. obs.). This family also contains sequences from ArnTs (4-amino-4-deoxy-L-arabinose lipid A transferase). They catalyze the addition of 4-amino-4-deoxy-l-arabinose (l-Ara4N) to the lipid A moiety of the lipopolysaccharide. This is a critical modification enabling bacteria (e.g. Escherichia coli and Salmonella typhimurium) to resist killing by antimicrobial peptides such as polymyxins. Members such as Swiss:O52327 are predicted to have 12 trans-membrane regions. The N-terminal portion of these proteins is hypothesized to have a conserved glycosylation activity which is shared between distantly related oligosaccharyltransferases ArnT and PglB families. 245 matched cddid_all.tbl CDD pfam02367 pfam02367 460540 TsaE Threonylcarbamoyl adenosine biosynthesis protein TsaE. This family of proteins is involved in the synthesis of threonylcarbamoyl adenosine (t(6)A). 127 matched cddid_all.tbl CDD pfam02368 pfam02368 396788 Big_2 Bacterial Ig-like domain (group 2). This family consists of bacterial domains with an Ig-like fold. Members of this family are found in bacterial and phage surface proteins such as intimins. 77 matched cddid_all.tbl CDD pfam02369 pfam02369 460541 Big_1 Bacterial Ig-like domain (group 1). This family consists of bacterial domains with an Ig-like fold. Members of this family are found in bacterial surface proteins such as intimins and invasins involved in pathogenicity. 64 matched cddid_all.tbl CDD pfam02370 pfam02370 111279 M M protein repeat. This short repeat is found in multiple copies in bacterial M proteins. The M proteins bind to IgA and are closely associated with virulence. The M protein has been postulated to be a major group A Streptococcal (GAS) virulence factor because of its contribution to the bacterial resistance to opsonophagocytosis. 21 matched cddid_all.tbl CDD pfam02371 pfam02371 426743 Transposase_20 Transposase IS116/IS110/IS902 family. Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. This region is often found with pfam01548. The exact function of this region is uncertain. This family contains a HHH motif suggesting a DNA-binding function. 86 matched cddid_all.tbl CDD pfam02372 pfam02372 308146 IL15 Interleukin 15. Interleukin-15 (IL-15) is a cytokine that possesses a variety of biological functions, including stimulation and maintenance of cellular immune responses. Structurally these proteins are short-chain 4-helical cytokines. 129 matched cddid_all.tbl CDD pfam02373 pfam02373 396791 JmjC JmjC domain, hydroxylase. The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation. 114 matched cddid_all.tbl CDD pfam02374 pfam02374 396792 ArsA_ATPase Anion-transporting ATPase. This Pfam family represents a conserved domain, which is sometimes repeated, in an anion-transporting ATPase. The ATPase is involved in the removal of arsenate, antimonite, and arsenate from the cell. 302 matched cddid_all.tbl CDD pfam02375 pfam02375 460542 JmjN jmjN domain. 34 matched cddid_all.tbl CDD pfam02376 pfam02376 460543 CUT CUT domain. The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, often found downstream of the CUT domain. Multiple copies of the CUT domain can exist in one protein. 78 matched cddid_all.tbl CDD pfam02377 pfam02377 460544 Dishevelled Dishevelled specific domain. This domain is specific to the signalling protein dishevelled. The domain is found adjacent to the PDZ domain pfam00595, often in conjunction with DEP (pfam00610) and DIX (pfam00778). Much of it is disordered and yet conserved. 160 matched cddid_all.tbl CDD pfam02378 pfam02378 367061 PTS_EIIC Phosphotransferase system, EIIC. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The sugar-specific permease of the PTS consists of three domains (IIA, IIB and IIC). The IIC domain catalyzes the transfer of a phosphoryl group from IIB to the sugar substrate. 315 matched cddid_all.tbl CDD pfam02380 pfam02380 367062 Papo_T_antigen T-antigen specific domain. This domain represents a conserved region in papovavirus small and middle T-antigens. It is found as the N-terminal domain in the small T-antigen, and is centrally located in the middle T-antigen. 93 matched cddid_all.tbl CDD pfam02381 pfam02381 426747 MraZ MraZ protein, putative antitoxin-like. This small 70 amino acid domain is found duplicated in a family of bacterial proteins. These proteins may be DNA-binding transcription factors (Pers. comm. A Andreeva & A Murzin). It is likely, due to the similarity of fold, that this family acts as a bacterial antitoxin like the MazE antitoxin family. 72 matched cddid_all.tbl CDD pfam02382 pfam02382 396797 RTX N-terminal domain in RTX protein. The RTX family of bacterial toxins are a group of cytolysins and cytotoxins that have RTX (Repeat in ToXin repeats) pfam00353. This Pfam family represents a presumed domain which in some of these proteins. 312 matched cddid_all.tbl CDD pfam02383 pfam02383 460545 Syja_N SacI homology domain. This Pfam family represents a protein domain which shows homology to the yeast protein SacI. The SacI homology domain is most notably found at the amino terminal of the inositol 5'-phosphatase synaptojanin. 295 matched cddid_all.tbl CDD pfam02384 pfam02384 426749 N6_Mtase N-6 DNA Methylase. Restriction-modification (R-M) systems protect a bacterial cell against invasion of foreign DNA by endonucleolytic cleavage of DNA that lacks a site specific modification. The R-M system is a complex containing three polypeptides: M (this family), S (pfam01420), and R. This family consists of N-6 adenine-specific DNA methylase EC:2.1.1.72 from Type I and Type IC restriction systems. These methylases have the same sequence specificity as their corresponding restriction enzymes. 310 matched cddid_all.tbl CDD pfam02386 pfam02386 280534 TrkH Cation transport protein. This family consists of various cation transport proteins (Trk) and V-type sodium ATP synthase subunit J or translocating ATPase J EC:3.6.1.34. These proteins are involved in active sodium up-take utilizing ATP in the process. TrkH a member of the family from E. coli is a hydrophobic membrane protein and determines the specificity and kinetics of cation transport by the TrK system in E. coli. 491 matched cddid_all.tbl CDD pfam02387 pfam02387 426750 IncFII_repA IncFII RepA protein family. This protein is plasmid encoded and found to be essential for plasmid replication. 275 matched cddid_all.tbl CDD pfam02388 pfam02388 426751 FemAB FemAB family. The femAB operon codes for two nearly identical approximately 50-kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan. These proteins are also considered as a factor influencing the level of methicillin resistance. 406 matched cddid_all.tbl CDD pfam02389 pfam02389 280537 Cornifin Cornifin (SPRR) family. SPRR genes (formerly SPR) encode a novel class of polypeptides (small proline rich proteins) that are strongly induced during differentiation of human epidermal keratinocytes in vitro and in vivo. The most characteriztic feature of the SPRR gene family resides in the structure of the central segments of the encoded polypeptides that are built up from tandemly repeated units of either eight (SPRR1 and SPRR3) or nine (SPRR2) amino acids with the general consensus XKXPEPXX where X is any amino acid. In order to avoid bacterial contamination due to the high polar-nature of the HMM the threshold has been set very high. 135 matched cddid_all.tbl CDD pfam02390 pfam02390 367068 Methyltransf_4 Putative methyltransferase. This is a family of putative methyltransferases. The aligned region contains the GXGXG S-AdoMet binding site suggesting a putative methyltransferase activity. 173 matched cddid_all.tbl CDD pfam02391 pfam02391 460546 MoaE MoaE protein. This family contains the MoaE protein that is involved in biosynthesis of molybdopterin. Molybdopterin, the universal component of the pterin molybdenum cofactors, contains a dithiolene group serving to bind Mo. Addition of the dithiolene sulfurs to a molybdopterin precursor requires the activity of the converting factor. Converting factor contains the MoaE and MoaD proteins. 113 matched cddid_all.tbl CDD pfam02392 pfam02392 426753 Ycf4 Ycf4. This family consists of hypothetical Ycf4 proteins from various chloroplast genomes. It has been suggested that Ycf4 is involved in the assembly and/or stability of the photosystem I complex in chloroplasts. 176 matched cddid_all.tbl CDD pfam02393 pfam02393 396802 US22 US22 like. US22 proteins have been found across many animal DNA viruses and some vertebrates. The name sake of this family US22 is an early nuclear protein that is secreted from cells. The US22 family may have a role in virus replication and pathogenesis. Domain analysis showed that US22 proteins usually contain two copies of conserved modules which is homologous to several other families like SMI1 and SYD (commonly called SUKH superfamily). Bacterial operon analysis revealed that all bacterial SUKH members function as immunity proteins against various toxins. Thus US22 family is predicted to counter diverse anti-viral responses by interacting with specific host proteins. 124 matched cddid_all.tbl CDD pfam02394 pfam02394 426754 IL1_propep Interleukin-1 propeptide. The Interleukin-1 cytokines are translated as precursor proteins. The N terminal approx. 115 amino acids form a propeptide that is cleaved off to release the active interleukin-1. 106 matched cddid_all.tbl CDD pfam02395 pfam02395 396804 Peptidase_S6 Immunoglobulin A1 protease. This family consists of immunoglobulin A1 protease proteins. The immunoglobulin A1 protease cleaves immunoglobulin IgA and is found in pathogenic bacteria such as Neisseria gonorrhoeae. Not all of the members of this family are IgA proteases Swiss:O32555 from E. coli O157:H7 cleaves human coagulation factor V and Swiss:O88093 is a hemoglobin protease from E. coli EB1. 784 matched cddid_all.tbl CDD pfam02397 pfam02397 460547 Bac_transf Bacterial sugar transferase. This Pfam family represents a conserved region from a number of different bacterial sugar transferases, involved in diverse biosynthesis pathways. 180 matched cddid_all.tbl CDD pfam02398 pfam02398 280545 Corona_7 Coronavirus protein 7. This is a family of proteins from coronavirus which may function in viral assembly. 101 matched cddid_all.tbl CDD pfam02399 pfam02399 280546 Herpes_ori_bp Origin of replication binding protein. This Pfam family represents the herpesvirus origin of replication binding protein, probably involved in DNA replication. 820 matched cddid_all.tbl CDD pfam02401 pfam02401 460548 LYTB LytB protein. The mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis is essential in many eubacteria, plants, and the malaria parasite. The LytB gene is involved in the trunk line of the MEP pathway. 270 matched cddid_all.tbl CDD pfam02402 pfam02402 367072 Lysis_col Lysis protein. These small bacterial proteins are required for colicin release and partial cell lysis. This family contains lysis proteins for several different forms of colicin. Swiss:Q02112 has been included in this family, the similarity is not highly significant, however it is also a short protein, that is involved in secretion of other proteins (Bateman A pers. obs.). This family includes a signal peptide motif and a lipid attachment site. 49 matched cddid_all.tbl CDD pfam02403 pfam02403 426757 Seryl_tRNA_N Seryl-tRNA synthetase N-terminal domain. This domain is found associated with the Pfam tRNA synthetase class II domain (pfam00587) and represents the N-terminal domain of seryl-tRNA synthetase. 108 matched cddid_all.tbl CDD pfam02404 pfam02404 396808 SCF Stem cell factor. Stem cell factor (SCF) is a homodimer involved in hematopoiesis. SCF binds to and activates the SCF receptor (SCFR), a receptor tyrosine kinase. The crystal structure of human SCF has been resolved and a potential receptor-binding site identified. 275 matched cddid_all.tbl CDD pfam02405 pfam02405 460549 MlaE Permease MlaE. MlaE is a permease which in E. coli is a component of the Mla pathway, an ABC transport system that functions to maintain the asymmetry of the outer membrane. In Swiss:Q7DD59 it is involved in L-glutamate import into the cell. In Swiss:Q8L4R0 it is involved in lipid transfer within the cell. 212 matched cddid_all.tbl CDD pfam02406 pfam02406 426759 MmoB_DmpM MmoB/DmpM family. This family consists of monooxygenase components such as MmoB methane monooxygenase (EC:1.14.13.25) regulatory protein B. When MmoB is present at low concentration it converts methane monooxygenase from an oxidase to a hydroxylase and stabilizes intermediates required for the activation of dioxygen. Also found in this family is DmpM or Phenol hydroxylase (EC:1.14.13.7) protein component P2, this protein lacks redox co-factors and is required for optimal turnover of Phenol hydroxylase. 85 matched cddid_all.tbl CDD pfam02407 pfam02407 280553 Viral_Rep "Putative viral replication protein. This is a family of viral ORFs from various plant and animal ssDNA circoviruses. Published evidence to support the annotated function ""viral replication associated protein"" has not be found." 82 matched cddid_all.tbl CDD pfam02408 pfam02408 280554 CUB_2 CUB-like domain. This is a family of hypothetical C. elegans proteins. The aligned region has no known function nor do any of the proteins which possess it. However, this domain is related to the CUB domain. 120 matched cddid_all.tbl CDD pfam02410 pfam02410 460550 RsfS Ribosomal silencing factor during starvation. This family is expressed by almost all bacterial and eukaryotic genomes but not by archaea. Its function is to down-regulate protein synthesis under conditions of nutrient shortage, and it does this by binding to protein L14 of the large ribosomal subunit, thus acting as a ribosomal silencing factor (RsfS) by blocking the joining of the ribosomal subunits. This family is structurally homologous to nucleotidyltransferases. 97 matched cddid_all.tbl CDD pfam02411 pfam02411 111318 MerT MerT mercuric transport protein. MerT is an mercuric transport integral membrane protein and is responsible for transport of the Hg2+ iron from periplasmic MerP (also part of the transport system) to mercuric reductase (MerE). 116 matched cddid_all.tbl CDD pfam02412 pfam02412 367074 TSP_3 Thrombospondin type 3 repeat. The thrombospondin repeat is a short aspartate rich repeat which binds to calcium ions. The repeat was initially identified in thrombospondin proteins that contained 7 of these repeats. The repeat lacks defined secondary structure. 36 matched cddid_all.tbl CDD pfam02413 pfam02413 426761 Caudo_TAP Caudovirales tail fibre assembly protein, lambda gpK. This family contains bacterial and phage tail fibre assembly proteins. E.coli contains several members of this family although the function of these proteins is uncertain. Using the lambda phage members as examples, there are both gptfa and gpK tail proteins here. GpK forms part of the TTC or tail-tip complex that is located at the distal end of the tail. TTCs form the platform on which the tail-tube proteins self-assemble and are also the attachment point for fibres or receptor-binding proteins that mediate phage-adsorption to the surface of the host cell. TTC assembly starts with gpJ, which is also known as the central tail fibre and is involved in host-cell adsorption. It is the C-terminus of gpJ that interacts with the lamB receptor on host cells. A number of intermediates including gpK then interact with gpJ during tail morphogenesis. 130 matched cddid_all.tbl CDD pfam02414 pfam02414 396813 Borrelia_orfA Borrelia ORF-A. This protein is encoded by an open reading frame in plasmid borne DNA repeats of Borrelia species. This protein is known as ORF-A. The function of this putative protein is unknown. 285 matched cddid_all.tbl CDD pfam02415 pfam02415 308169 Chlam_PMP Chlamydia polymorphic membrane protein (Chlamydia_PMP) repeat. This family contains several Chlamydia polymorphic membrane proteins. Chlamydia pneumoniae is an obligate intracellular bacterium and a common human pathogen causing infection of the upper and lower respiratory tract. Common for the Pmps are the tetrapeptide GGA(I/V/L) motif repeated several times in the N-terminal part. The C-terminal half is characterized by conserved tryptophans and a carboxy-terminal phenylalanine. A signal peptide leader sequence is predicted in 20 C. pneumoniae Pmps, which indicates an outer membrane localization. Pmp10 and Pmp11 contain a signal peptidase II cleavage site suggesting lipid modification. The C. pneumoniae pmp genes represent 17.5% of the chlamydia-specific coding capacity and they are all transcribed during chlamydial growth but the function of Pmps remains unknown. This family shows some similarity to pfam05594 and hence is likely to also form a beta-helical structure (personal obs:C Yeats). 19 matched cddid_all.tbl CDD pfam02416 pfam02416 426762 TatA_B_E "mttA/Hcf106 family. Members of this protein family are involved in a sec independent translocation mechanism. This pathway has been called the DeltapH pathway in chloroplasts. Members of this family in E.coli are involved in export of redox proteins with a ""twin arginine"" leader motif." 53 matched cddid_all.tbl CDD pfam02417 pfam02417 460551 Chromate_transp Chromate transporter. Members of this family probably act as chromate transporters. Members of this family are found in both bacteria and archaebacteria. The proteins are composed of one or two copies of this region. The alignment contains two conserved motifs, FGG and PGP. 164 matched cddid_all.tbl CDD pfam02419 pfam02419 396815 PsbL PsbL protein. This family consists of the photosystem II reaction centre protein PsbJ from plants and Cyanobacteria. The function of this small protein is unknown. Interestingly the mRNA for this protein requires a post-transcriptional modification of an ACG triplet to form an AUG initiator codon. 37 matched cddid_all.tbl CDD pfam02420 pfam02420 111326 AFP Insect antifreeze protein repeat. This family of extracellular proteins is involved in stopping the formation of ice crystals at low temperatures. The proteins are composed of a 12 residue repeat that forms a structural repeat. The structure of the repeats is a beta helix. Each repeat contains two cys residues that form a disulphide bridge. 12 matched cddid_all.tbl CDD pfam02421 pfam02421 460552 FeoB_N Ferrous iron transport protein B. Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent. 156 matched cddid_all.tbl CDD pfam02422 pfam02422 460553 Keratin Keratin. This family represents avian keratin proteins, found in feathers, scale and claw. 81 matched cddid_all.tbl CDD pfam02423 pfam02423 426766 OCD_Mu_crystall Ornithine cyclodeaminase/mu-crystallin family. This family contains the bacterial Ornithine cyclodeaminase enzyme EC:4.3.1.12, which catalyzes the deamination of ornithine to proline. This family also contains mu-Crystallin the major component of the eye lens in several Australian marsupials, mRNA for this protein has also been found in human retina. 313 matched cddid_all.tbl CDD pfam02424 pfam02424 460554 ApbE ApbE family. This prokaryotic family of lipoproteins are related to ApbE from Salmonella typhimurium. ApbE is involved in thiamine synthesis. It acts as an FAD:protein FMN-transferase, catalysing the attachment of an FMN residue to a threonine residue of a protein via a phosphoester bond in such bacterial flavoproteins. 227 matched cddid_all.tbl CDD pfam02425 pfam02425 280567 GBP_PSP Paralytic/GBP/PSP peptide. This family includes insect peptides that are short (23 amino acids) and contain 1 disulphide bridge. The family includes growth-blocking peptide (GBP) of Pseudaletia separata and the paralytic peptides from Manduca sexta, Heliothis virescens, and Spodoptera exigua as well as plasmatocyte-spreading peptide (PSP1). These peptides function to halt metamorphosis from larvae to pupae. 23 matched cddid_all.tbl CDD pfam02426 pfam02426 426768 MIase Muconolactone delta-isomerase. This small enzyme forms a homodecameric complex, that catalyzes the third step in the catabolism of catechol to succinate- and acetyl-coa in the beta-ketoadipate pathway EC:5.3.3.4. The protein has a ferredoxin-like fold according to SCOP. 89 matched cddid_all.tbl CDD pfam02427 pfam02427 396821 PSI_PsaE Photosystem I reaction centre subunit IV / PsaE. PsaE is a 69 amino acid polypeptide from photosystem I present on the stromal side of the thylakoid membrane. The structure is comprised of a well-defined five-stranded beta-sheet similar to SH3 domains. 59 matched cddid_all.tbl CDD pfam02428 pfam02428 460555 Prot_inhib_II Potato type II proteinase inhibitor family. Members of this family are proteinase inhibitors that contain eight cysteines that form four disulphide bridges. The structure of the proteinase-inhibitor complex is known. 51 matched cddid_all.tbl CDD pfam02429 pfam02429 426770 PCP Peridinin-chlorophyll A binding protein. Peridinin-chlorophyll-protein, a water-soluble light-harvesting complex that has a blue-green absorbing carotenoid as its main pigment, is present in most photosynthetic dinoflagellates. These proteins are composed of two similar repeated domains. These domains constitute a scaffold with pseudo-twofold symmetry surrounding a hydrophobic cavity filled by two lipid, eight peridinin, and two chlorophyll a molecules. 145 matched cddid_all.tbl CDD pfam02430 pfam02430 396824 AMA-1 Apical membrane antigen 1. Apical membrane antigen 1 (AMA-1) is a Plasmodium asexual blood-stage antigen. It has been suggested that positive selection operates on the AMA-1 gene in regions coding for antigenic sites. 432 matched cddid_all.tbl CDD pfam02431 pfam02431 396825 Chalcone Chalcone-flavanone isomerase. Chalcone-flavanone isomerase is a plant enzyme responsible for the isomerization of chalcone to naringenin, 4',5,7-trihydroxyflavanone, a key step in the biosynthesis of flavonoids. 203 matched cddid_all.tbl CDD pfam02432 pfam02432 367084 Fimbrial_K88 Fimbrial, major and minor subunit. Fimbriae (also know as pili) are polar filaments found on the bacterial surface, allowing colonization of the host. This family consists of the minor and major fimbrial subunits. 155 matched cddid_all.tbl CDD pfam02433 pfam02433 460556 FixO Cytochrome C oxidase, mono-heme subunit/FixO. The bacterial oxidase complex, fixNOPQ or cytochrome cbb3, is thought to be required for respiration in endosymbiosis. FixO is a membrane bound mono-heme constituent of the fixNOPQ complex. 218 matched cddid_all.tbl CDD pfam02434 pfam02434 367085 Fringe Fringe-like. The drosophila protein fringe (FNG) is a glucosaminyltransferase that controls the response of the Notch receptor to specific ligands. FNG is localized to the Golgi apparatus (not secreted as previously thought). Modification of Notch occurs through glycosylation by FNG. The xenopus homolog, lunatic fringe, has been implicated in a variety of functions. 248 matched cddid_all.tbl CDD pfam02435 pfam02435 426772 Glyco_hydro_68 Levansucrase/Invertase. This Pfam family consists of the glycosyl hydrolase 68 family, including several bacterial levansucrase enzymes, and invertase from zymomonas. 419 matched cddid_all.tbl CDD pfam02436 pfam02436 460557 PYC_OADA Conserved carboxylase domain. This domain represents a conserved region in pyruvate carboxylase (PYC), oxaloacetate decarboxylase alpha chain (OADA), and transcarboxylase 5s subunit. The domain is found adjacent to the HMGL-like domain (pfam00682) and often close to the biotin_lipoyl domain (pfam00364) of biotin requiring enzymes. 201 matched cddid_all.tbl CDD pfam02437 pfam02437 460558 Ski_Sno SKI/SNO/DAC family. This family contains a presumed domain that is about 100 amino acids long. All members of this family contain a conserved CLPQ motif. The c-ski proto-oncogene has been shown to influence proliferation, morphological transformation and myogenic differentiation. Sno, a Ski proto-oncogene homolog, is expressed in two isoforms and plays a role in the response to proliferation stimuli. Dachshund also contains this domain. It is involved in various aspects of development. 100 matched cddid_all.tbl CDD pfam02438 pfam02438 308188 Adeno_100 Late 100kD protein. The late 100kD protein is a non-structural viral protein involved in the transport of hexon from the cytoplasm to the nucleus. 591 matched cddid_all.tbl CDD pfam02439 pfam02439 111345 Adeno_E3_CR2 Adenovirus E3 region protein CR2. Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host. This region called CR2 (conserved region 1) is found in Adenovirus type 19 (a subgroup D virus) 49 Kd protein in the E3 region. CR2 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 50 amino acid region is unknown. 38 matched cddid_all.tbl CDD pfam02440 pfam02440 367088 Adeno_E3_CR1 Adenovirus E3 region protein CR1. Early region 3 (E3) of human adenoviruses (Ads) codes for proteins that appear to control viral interactions with the host. This region called CR1 (conserved region 1) is found three times in Adenovirus type 19 (a subgroup D virus) 49 Kd protein in the E3 region. CR1 is also found in the 20.1 Kd protein of subgroup B adenoviruses. The function of this 80 amino acid region is unknown. This region is probably a divergent immunoglobulin domain (A. Bateman pers. observation). 95 matched cddid_all.tbl CDD pfam02441 pfam02441 426775 Flavoprotein Flavoprotein. This family contains diverse flavoprotein enzymes. This family includes epidermin biosynthesis protein, EpiD, which has been shown to be a flavoprotein that binds FMN. This enzyme catalyzes the removal of two reducing equivalents from the cysteine residue of the C-terminal meso-lanthionine of epidermin to form a --C==C-- double bond. This family also includes the B chain of dipicolinate synthase a small polar molecule that accumulates to high concentrations in bacterial endospores, and is thought to play a role in spore heat resistance, or the maintenance of heat resistance. dipicolinate synthase catalyzes the formation of dipicolinic acid from dihydroxydipicolinic acid. This family also includes phenyl-acrylic acid decarboxylase (EC:4.1.1.-). 177 matched cddid_all.tbl CDD pfam02442 pfam02442 396831 L1R_F9L Lipid membrane protein of large eukaryotic DNA viruses. The four families of large eukaryotic DNA viruses, Poxviridae, Asfarviridae, Iridoviridae, and Phycodnaviridae, referred to collectively as nucleocytoplasmic large DNA viruses or NCLDV, have all been shown to have a lipid membrane, in spite of the major differences in virion structure. The paralogous genes L1R and F9L encode membrane proteins that have a conserved domain architecture, with a single, C-terminal transmembrane helix, and an N-terminal, multiple-disulfide-bonded domain. The conservation of the myristoylated, disulfide-bonded protein L1R/F9L in most of the NCLDV correlates with the conservation of the thiol-disulfide oxidoreductase E10R which, in vaccinia virus, is required for the formation of disulfide bonds in L1R and F9L. 183 matched cddid_all.tbl CDD pfam02443 pfam02443 308191 Circo_capsid Circovirus capsid protein. Circoviruses are small circular single stranded viruses. This family is the capsid protein from viruses such as porcine circovirus and beak and feather disease virus. These proteins are about 220 amino acids long. 200 matched cddid_all.tbl CDD pfam02444 pfam02444 280583 HEV_ORF1 Hepatitis E virus ORF-2 (Putative capsid protein). The Hepatitis E virus (HEV) genome is a single-stranded, positive-sense RNA molecule of approximately 7.5 kb. Three open reading frames (ORF) were identified within the HEV genome: ORF1 encodes non-structural proteins, ORF2 encodes the putative structural protein(s), and ORF3 encodes a protein of unknown function. ORF2 contains a consensus signal peptide sequence at its amino terminus and a capsid-like region with a high content of basic amino acids similar to that seen with other virus capsid proteins. 114 matched cddid_all.tbl CDD pfam02445 pfam02445 460559 NadA "Quinolinate synthetase A protein. Quinolinate synthetase catalyzes the second step of the de novo biosynthetic pathway of pyridine nucleotide formation. In particular, quinolinate synthetase is involved in the condensation of dihydroxyacetone phosphate and iminoaspartate to form quinolinic acid. This synthesis requires two enzymes, a FAD-containing ""B protein"" and an ""A protein""." 287 matched cddid_all.tbl CDD pfam02446 pfam02446 460560 Glyco_hydro_77 4-alpha-glucanotransferase. These enzymes EC:2.4.1.25 transfer a segment of a (1,4)-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose or (1,4)-alpha-D-glucan. 458 matched cddid_all.tbl CDD pfam02447 pfam02447 308194 GntP_permease GntP family permease. This is a family of integral membrane permeases that are involved in gluconate uptake. E. coli contains several members of this family including GntU, a low affinity transporter and GntT, a high affinity transporter. 440 matched cddid_all.tbl CDD pfam02448 pfam02448 426778 L71 L71 family. This family of insect proteins are each about 100 amino acids long and have 6 conserved cysteine residues. They all have a predicted signal peptide and are probably excreted. The function of the proteins is unknown. 70 matched cddid_all.tbl CDD pfam02449 pfam02449 396834 Glyco_hydro_42 Beta-galactosidase. This group of beta-galactosidase enzymes belong to the glycosyl hydrolase 42 family. The enzyme catalyzes the hydrolysis of terminal, non-reducing terminal beta-D-galactosidase residues. 376 matched cddid_all.tbl CDD pfam02450 pfam02450 396835 LCAT Lecithin:cholesterol acyltransferase. Lecithin:cholesterol acyltransferase (LCAT) is involved in extracellular metabolism of plasma lipoproteins, including cholesterol. 383 matched cddid_all.tbl CDD pfam02451 pfam02451 308198 Nodulin Nodulin. Nodulin is a plant protein of unknown function. It is induced during nodulation in legume roots after rhizobium infection. 188 matched cddid_all.tbl CDD pfam02452 pfam02452 460561 PemK_toxin PemK-like, MazF-like toxin of type II toxin-antitoxin system. PemK is a growth inhibitor in E. coli known to bind to the promoter region of the Pem operon, auto-regulating synthesis. This family represents the toxin molecule of a typical bacterial toxin-antitoxin system pairing. The family includes a number of different toxins, such as MazF, Kid, PemK, ChpA, ChpB and ChpAK. 108 matched cddid_all.tbl CDD pfam02453 pfam02453 460562 Reticulon Reticulon. Reticulon, also know as neuroendocrine-specific protein (NSP), is a protein of unknown function which associates with the endoplasmic reticulum. This family represents the C-terminal domain of the three reticulon isoforms and their homologs. 157 matched cddid_all.tbl CDD pfam02454 pfam02454 111360 Sigma_1s Sigma 1s protein. The reoviral gene S1 encodes for haemagglutinin (sigma 1 protein), an outer capsid protein and a major factor in determining virus-host cell interactions. Sigma 1s is one of two translation products of the S1 gene. 116 matched cddid_all.tbl CDD pfam02455 pfam02455 308201 Hex_IIIa Hexon-associated protein (IIIa). The major capsid protein of the adenovirus strain is also known as a hexon. This is a family of hexon-associated proteins (protein IIIa). 539 matched cddid_all.tbl CDD pfam02456 pfam02456 280594 Adeno_IVa2 Adenovirus IVa2 protein. IVa2 protein can interact with the adenoviral packaging signal and that this interaction involves DNA sequences that have previously been demonstrated to be required for packaging. During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter. 370 matched cddid_all.tbl CDD pfam02457 pfam02457 460563 DAC DisA bacterial checkpoint controller nucleotide-binding. The DisA protein is a bacterial checkpoint protein that dimerizes into an octameric complex. The protein consists of three distinct domains. This domain is the first and is a globular, nucleotide-binding region; the next 146-289 residues constitute the DisA-linker family, pfam10635, that consists of an elongated bundle of three alpha helices (alpha-6, alpha-10, and alpha-11), one side of which carries an additional three helices (alpha7-9), which thus forms a spine like-linker between domains 1 and 3. The C-terminal residues, of domain 3, are represented by family HHH, pfam00633, the specific DNA-binding domain. The octameric complex thus has structurally linked nucleotide-binding and DNA-binding HhH domains and the nucleotide-binding domains are bound to a cyclic di-adenosine phosphate such that DisA is a specific di-adenylate cyclase. This N-terminal domain has been identified as a diadenylate cyclase (DAC) responsible for producing c-di-AMP from two molecules of ATP. The di-adenylate cyclase activity is strongly suppressed by binding to branched DNA, but not to duplex or single-stranded DNA, suggesting a role for DisA as a monitor of the presence of stalled replication forks or recombination intermediates via DNA structure-modulated c-di-AMP synthesis. 115 matched cddid_all.tbl CDD pfam02458 pfam02458 460564 Transferase Transferase family. This family includes a number of transferase enzymes. These include anthranilate N-hydroxycinnamoyl/benzoyltransferase that catalyzes the first committed reaction of phytoalexin biosynthesis. Deacetylvindoline 4-O-acetyltransferase EC:2.3.1.107 catalyzes the last step in vindoline biosynthesis is also a member of this family. The motif HXXXD is probably part of the active site. The family also includes trichothecene 3-O-acetyltransferase. 434 matched cddid_all.tbl CDD pfam02459 pfam02459 280597 Adeno_terminal Adenoviral DNA terminal protein. This protein is covalently attached to the terminii of replicating DNA in vivo. 543 matched cddid_all.tbl CDD pfam02460 pfam02460 308203 Patched Patched family. The transmembrane protein Patched is a receptor for the morphogene Sonic Hedgehog. This protein associates with the smoothened protein to transduce hedgehog signals. 793 matched cddid_all.tbl CDD pfam02461 pfam02461 426783 AMO Ammonia monooxygenase. Ammonia monooxygenase plays a key role in the nitrogen cycle and degrades a wide range of hydrocarbons and halogenated hydrocarbons. 238 matched cddid_all.tbl CDD pfam02462 pfam02462 308205 Opacity Opacity family porin protein. Pathogenic Neisseria spp. possess a repertoire of phase-variable Opacity proteins that mediate various pathogen--host cell interactions. These proteins are integral membrane proteins related to other porins. 126 matched cddid_all.tbl CDD pfam02463 pfam02463 426784 SMC_N RecF/RecN/SMC N terminal domain. This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. 1161 matched cddid_all.tbl CDD pfam02464 pfam02464 460565 CinA Competence-damaged protein. CinA is the first gene in the competence-inducible (cin) operon, and is thought to be specifically required at some stage in the process of transformation. This Pfam family consists of putative competence-damaged proteins from the cin operon. Some members of this family have nicotinamide mononucleotide (NMN) deamidase activity. 155 matched cddid_all.tbl CDD pfam02465 pfam02465 460566 FliD_N Flagellar hook-associated protein 2 N-terminus. The flagellar hook-associated protein 2 (HAP2 or FliD) forms the distal end of the flagella, and plays a role in mucin specific adhesion of the bacteria. This alignment covers the N-terminal region of this family of proteins. 97 matched cddid_all.tbl CDD pfam02466 pfam02466 460567 Tim17 Tim17/Tim22/Tim23/Pmp24 family. The pre-protein translocase of the mitochondrial outer membrane (Tom) allows the import of pre-proteins from the cytoplasm. Tom forms a complex with a number of proteins, including Tim17. Tim17, Tim22, and Tim23, are the central components of the widely conserved multi-subunit protein translocases, TIM23 and TIM22, which mediate protein transport across and into the inner mitochondrial membrane, respectively. In addition, several Tim17 family proteins occupy the inner and outer membranes of plastids. This family also includes Pmp24 a peroxisomal protein. The involvement of this domain in the targeting of PMP24 remains to be proved. PMP24 was known as Pmp27. Family members are suggested to be exclusive to eukaryotes, where the distribution in the eukaryotic subgroups of the mitochondrial Tim17, Tim22 and Tim23 proteins, as well as the peroxisomal Tim17 family proteins, suggests that they all likely to be present in the last eukaryotic common ancestor (LECA). 109 matched cddid_all.tbl CDD pfam02467 pfam02467 426788 Whib Transcription factor WhiB. WhiB is a putative transcription factor in Actinobacteria, required for differentiation and sporulation. 65 matched cddid_all.tbl CDD pfam02468 pfam02468 426789 PsbN Photosystem II reaction centre N protein (psbN). This is a family of small proteins encoded on the chloroplast genome. psbN is involved in photosystem II during photosynthesis, but its exact role is unknown. 43 matched cddid_all.tbl CDD pfam02469 pfam02469 396845 Fasciclin Fasciclin domain. This extracellular domain is found repeated four times in grasshopper fasciclin I as well as in proteins from mammals, sea urchins, plants, yeast and bacteria. 123 matched cddid_all.tbl CDD pfam02470 pfam02470 426790 MlaD MlaD protein. This family of proteins contains MlaD, which is a component of the Mla pathway, an ABC transport system that functions to maintain the asymmetry of the outer membrane. The family also contains the mce (mammalian cell entry) proteins from Mycobacterium tuberculosis. The archetype (Rv0169), was isolated as being necessary for colonization of, and survival within, the macrophage. This family contains proteins of unknown function from other bacteria. 81 matched cddid_all.tbl CDD pfam02471 pfam02471 396847 OspE Borrelia outer surface protein E. This is a family of outer surface proteins (Osp) from the Borrelia spirochete. The family includes OspE, and OspEF-related proteins (Erp). These proteins are coded for on different circular plasmids in the Borrelia genome. 107 matched cddid_all.tbl CDD pfam02472 pfam02472 426791 ExbD Biopolymer transport protein ExbD/TolR. This group of proteins are membrane bound transport proteins essential for ferric ion uptake in bacteria. The Pfam family consists of ExbD, and TolR which are involved in TonB-dependent transport of various receptor bound substrates including colicins. 128 matched cddid_all.tbl CDD pfam02474 pfam02474 426792 NodA Nodulation protein A (NodA). Rhizobia nodulation (nod) genes control the biosynthesis of Nod factors required for infection and nodulation of their legume hosts. Nodulation protein A (NodA) is a N-acetyltransferase involved in production of Nod factors that stimulate mitosis in various plant protoplasts. 195 matched cddid_all.tbl CDD pfam02475 pfam02475 396850 Met_10 Met-10+ like-protein. The methionine-10 mutant allele of N. crassa codes for a protein of unknown function, Swiss:O27901. However, homologous proteins have been found in yeast suggesting this protein may be involved in methionine biosynthesis, transport and/or utilization. 198 matched cddid_all.tbl CDD pfam02476 pfam02476 396851 US2 US2 family. This is a family of unique short (US) region proteins from the herpesvirus strain. The US2 family have no known function. 124 matched cddid_all.tbl CDD pfam02477 pfam02477 396852 Nairo_nucleo Nucleocapsid N protein. The nucleoprotein of the ssRNA negative-strand Nairovirus is an internal part of the virus particle. 443 matched cddid_all.tbl CDD pfam02478 pfam02478 280615 Pneumo_phosprot Pneumovirus phosphoprotein. This family represents the phosphoprotein of Paramyxoviridae, a putative RNA polymerase alpha subunit that may function in template binding. 286 matched cddid_all.tbl CDD pfam02479 pfam02479 280616 Herpes_IE68 Herpesvirus immediate early protein. This regulatory protein is expressed from an immediate early gene in the cell cycle of herpesvirus. The protein is known by various names including IE-68, US1, ICP22 and IR4. 132 matched cddid_all.tbl CDD pfam02480 pfam02480 460568 Herpes_gE Alphaherpesvirus glycoprotein E. Glycoprotein E (gE) of Alphaherpesvirus forms a complex with glycoprotein I (gI) (pfam01688), functioning as an immunoglobulin G (IgG) Fc binding protein. gE is involved in virus spread but is not essential for propagation. This entry represents the Ig-like domain of gE, identified as the Fc-binding domain. 175 matched cddid_all.tbl CDD pfam02481 pfam02481 426793 DNA_processg_A DNA recombination-mediator protein A. The SMF family, of DNA processing chain A, dprA, are a group of bacterial proteins. In H. pylori, dprA is required for natural chromosomal and plasmid transformation. It has now been shown that DprA is found to bind cooperatively to single-stranded DNA (ssDNA) and to interact with RecA. In the process, DprA-RecA-ssDNA filaments are produced and these filaments catalyze the homology-dependent formation of joint molecules. While the E.coli SSB protein limits access of RecA to ssDNA, DprA alleviates this barrier. It is proposed that DprA is a new member of the recombination-mediator protein family, dedicated to natural bacterial transformation. 210 matched cddid_all.tbl CDD pfam02482 pfam02482 460569 Ribosomal_S30AE Sigma 54 modulation protein / S30EA ribosomal protein. This Pfam family contains the sigma-54 modulation protein family and the S30AE family of ribosomal proteins which includes the light- repressed protein (lrtA). 87 matched cddid_all.tbl CDD pfam02484 pfam02484 280620 Rhabdo_NV Rhabdovirus Non-virion protein. Infectious hematopoietic necrosis virus (IHNV) is a member of the family Rhabdoviridae. The non-virion protein (NV) is coded for by one of the six genes of the IHNV genome, but is absent in vesiculovirus -like rhabdovirus. 111 matched cddid_all.tbl CDD pfam02485 pfam02485 426795 Branch Core-2/I-Branching enzyme. This is a family of two different beta-1,6-N-acetylglucosaminyltransferase enzymes, I-branching enzyme and core-2 branching enzyme. I-branching enzyme is responsible for the production of the blood group I-antigen during embryonic development. Core-2 branching enzyme forms crucial side-chain branches in O-glycans. This is a fmmily of glycosyl-transferases that are Type II membrane proteins that are found in the endoplasmic reticulum (ER) and Golgi apparatus. 250 matched cddid_all.tbl CDD pfam02486 pfam02486 426796 Rep_trans Replication initiation factor. Plasmid replication is initiated by the replication initiation factor (REP). This family represents a probable topoisomerase that makes a sequence-specific single-stranded nick in the plasmid DNA at the origin of replication. Human proteins also belong to this family, including myelin transcription factor 2 and cerebrin-50. 201 matched cddid_all.tbl CDD pfam02487 pfam02487 460570 CLN3 CLN3 protein. This is a family of proteins from the CLN3 gene. A mis-sense mutation of glutamic acid (E) to lysine (K) at position 295 in the human protein has been implicated in Juvenile neuronal ceroid lipofuscinosis (Batten disease). Batten disease is characterized by the accumulation of autofluorescent material in the lysosomes of most cells. Members of this family are transmembrane proteins functional in pre-vacuolar compartments. The protein in Sch.pombe is found to be localized to the vacuolar membrane, and a lack of functional protein clearly affects the size and pH of the vacuole. Thus the protein is necessary for vacuolar homeostasis. It is important for localization of late endosomal/lysosomal compartments, and it interacts with motor components driving both plus and minus end microtubular trafficking: tubulin, dynactin, dynein and kinesin-2. 383 matched cddid_all.tbl CDD pfam02488 pfam02488 280624 EMA Merozoite Antigen. This family represents the immunodominant surface antigen of Theileria parasites including equi merozoite antigen-1 (EMA-1) and equi merozoite antigen-2 (EMA-2). The protein shows variation at a putative glycosylation site, a potential mechanism for host immune response evasion. 250 matched cddid_all.tbl CDD pfam02489 pfam02489 396858 Herpes_glycop_H Herpesvirus glycoprotein H main domain. Herpesvirus glycoprotein H (gH) is a virion associated envelope glycoprotein. Complex formation between gH and gL has been demonstrated in both virions and infected cells. 500 matched cddid_all.tbl CDD pfam02491 pfam02491 460571 SHS2_FTSA SHS2 domain inserted in FTSA. FtsA is essential for bacterial cell division, and co-localizes to the septal ring with FtsZ. The SHS2 domain is inserted in to the RNAseH fold of FtsA, and is involved in protein-protein interaction. 73 matched cddid_all.tbl CDD pfam02492 pfam02492 396860 cobW CobW/HypB/UreG, nucleotide-binding domain. This domain is found in HypB, a hydrogenase expression / formation protein, and UreG a urease accessory protein. Both these proteins contain a P-loop nucleotide binding motif. HypB has GTPase activity and is a guanine nucleotide binding protein. It is not known whether UreG binds GTP or some other nucleotide. Both enzymes are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression. UreG is required for functional incorporation of the urease nickel metallocenter. GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins. This family of domains also contains P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the cobW gene product, which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans. 179 matched cddid_all.tbl CDD pfam02493 pfam02493 308220 MORN MORN repeat. The MORN (Membrane Occupation and Recognition Nexus) repeat is found in multiple copies in several proteins including junctophilins (See Takeshima et al. Mol. Cell 2000;6:11-22). A MORN-repeat protein has been identified in the parasite Toxoplasma gondiis a dynamic component of cell division apparatus in Toxoplasma gondii. It has been hypothesized to functions as a linker protein between certain membrane regions and the parasite's cytoskeleton. 23 matched cddid_all.tbl CDD pfam02494 pfam02494 460572 HYR HYR domain. This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion. 81 matched cddid_all.tbl CDD pfam02495 pfam02495 396861 TGBp3 Triple gene block 3. Family members include TGBp3 proteins found in many plant viruses. Triple gene block 3 proteins (TGBp3) are involved in virus momvement. TGBp3 is an integral ER membrane protein with a single transmembrane domain, and a C-terminal region exposed to the cytosol. TGBp3 is able to target TGBp2 to the cortical ER tubules of the cell periphery through the sorting signal in the C-terminal region of TGBp3. Moreover, it plays a key role in virus cell-to-cell movement by enhancing the TGBp2- and TGBp3-dependent plasmodesmata (PD) localization of TGBp1; however, the enhancement is abolished when one of the two conserved Cys residues in the C-terminal region of TGBp3 is replaced with Ala. 59 matched cddid_all.tbl CDD pfam02496 pfam02496 396862 ABA_WDS ABA/WDS induced protein. This is a family of plant proteins induced by water deficit stress (WDS), or abscisic acid (ABA) stress and ripening. 78 matched cddid_all.tbl CDD pfam02497 pfam02497 111400 Arteri_GP4 Arterivirus glycoprotein. This is a family of structural glycoproteins from arterivirus that corresponds to open reading frame 4 (ORF4) of the virus. 178 matched cddid_all.tbl CDD pfam02498 pfam02498 376797 Bro-N BRO family, N-terminal domain. This family includes the N-terminus of baculovirus BRO and ALI motif proteins. The function of BRO proteins is unknown. It has been suggested that BRO-A and BRO-C are DNA binding proteins that influence host DNA replication and/or transcription. This Pfam domain does not include the characteriztic invariant alanine, leucine, isoleucine motif of the ALI proteins. 96 matched cddid_all.tbl CDD pfam02499 pfam02499 426800 DNA_pack_C Probable DNA packing protein, C-terminus. This family includes proteins that are probably involved in DNA packing in herpesvirus. This domain is found at the C-terminus of the protein. 346 matched cddid_all.tbl CDD pfam02500 pfam02500 426801 DNA_pack_N Probable DNA packing protein, N-terminus. This family includes proteins that are probably involved in DNA packing in herpesvirus. This domain is normally found at the N-terminus of the protein. 274 matched cddid_all.tbl CDD pfam02501 pfam02501 426802 T2SSI Type II secretion system (T2SS), protein I. The Type II secretion system, also called Secretion-dependent pathway (SDP), is responsible for the transport of proteins across the outer membrane first exported to the periplasm by the Sec or Tat translocon in Gram-negative (diderm) bacteria. As members of the T2SJ family, members of the T2SI family are pseudopilins containing prepilin signal sequences. 80 matched cddid_all.tbl CDD pfam02502 pfam02502 460573 LacAB_rpiB Ribose/Galactose Isomerase. This family of proteins contains the sugar isomerase enzymes ribose 5-phosphate isomerase B (rpiB), galactose isomerase subunit A (LacA) and galactose isomerase subunit B (LacB). 134 matched cddid_all.tbl CDD pfam02503 pfam02503 460574 PP_kinase Polyphosphate kinase middle domain. Polyphosphate kinase (Ppk) catalyzes the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. 199 matched cddid_all.tbl CDD pfam02504 pfam02504 396866 FA_synthesis Fatty acid synthesis protein. The plsX gene is part of the bacterial fab gene cluster which encodes several key fatty acid biosynthetic enzymes. The exact function of the plsX protein in fatty acid synthesis is unknown. 324 matched cddid_all.tbl CDD pfam02505 pfam02505 426805 MCR_D Methyl-coenzyme M reductase operon protein D. Methyl coenzyme M reductase (MCR) catalyzes the final step in methanogenesis. MCR is composed of three subunits, alpha (pfam02249), beta (pfam02241) and gamma (pfam02240). Genes encoding the beta (mcrB) and gamma (mcrG) subunits are separated by two open reading frames coding for two proteins C and D. The function of proteins C and D (this family) is unknown. 142 matched cddid_all.tbl CDD pfam02507 pfam02507 367108 PSI_PsaF Photosystem I reaction centre subunit III. Photosystem I (PSI) is an integral membrane protein complex that uses light energy to mediate electron transfer from plastocyanin to ferredoxin. Subunit III (or PSI-F) is one of at least 14 different subunits that compose the PSI complex. 159 matched cddid_all.tbl CDD pfam02508 pfam02508 460575 Rnf-Nqr Rnf-Nqr subunit, membrane protein. This is a family of integral membrane proteins including Rhodobacter-specific nitrogen fixation (rnf) proteins RnfA and RnfE and Na+-translocating NADH:ubiquinone oxidoreductase (Na+-NQR) subunits NqrD and NqrE. 181 matched cddid_all.tbl CDD pfam02509 pfam02509 396869 Rota_NS35 Rotavirus non-structural protein 35. Rotavirus non-structural protein 35 (NS35) is a basic protein which possesses RNA-binding activity and is essential for genome replication. 317 matched cddid_all.tbl CDD pfam02510 pfam02510 280643 SPAN Surface presentation of antigens protein. Surface presentation of antigens protein (SPAN), also know as invasion protein invJ, is a Salmonella secretory pathway protein involved in presentation of determinants required for mammalian host cell invasion. 336 matched cddid_all.tbl CDD pfam02511 pfam02511 460576 Thy1 Thymidylate synthase complementing protein. Thymidylate synthase complementing protein (Thy1) complements the thymidine growth requirement of the organizms in which it is found, but shows no homology to thymidylate synthase. The bacterial members of this family at least are flavin-dependent thymidylate synthases. 186 matched cddid_all.tbl CDD pfam02512 pfam02512 280645 UK Virulence determinant. The UK protein is an African swine fever virus (ASFV) protein that is highly conserved amongst strains, and is an important viral virulence determinant for domestic pigs. 96 matched cddid_all.tbl CDD pfam02513 pfam02513 460577 Spin-Ssty Spin/Ssty Family. Spindlin (Spin) is a novel maternal transcript present in the unfertilized egg and early embryo. The Y-linked spermiogenesis -specific transcript (Ssty) is also expressed during gametogenesis and forms part of this Pfam family. Members of this family contain three copies of this 50 residue repeat. The repeat is predicted to contain four beta strands. 49 matched cddid_all.tbl CDD pfam02514 pfam02514 426809 CobN-Mg_chel CobN/Magnesium Chelatase. This family contains a domain common to the cobN protein and to magnesium protoporphyrin chelatase. CobN is implicated in the conversion of hydrogenobyrinic acid a,c-diamide to cobyrinic acid. Magnesium protoporphyrin chelatase is involved in chlorophyll biosynthesis. 1049 matched cddid_all.tbl CDD pfam02515 pfam02515 426810 CoA_transf_3 CoA-transferase family III. CoA-transferases are found in organizms from all lines of descent. Most of these enzymes belong to two well-known enzyme families, but recent work on unusual biochemical pathways of anaerobic bacteria has revealed the existence of a third family of CoA-transferases. The members of this enzyme family differ in sequence and reaction mechanism from CoA-transferases of the other families. Currently known enzymes of the new family are a formyl-CoA: oxalate CoA-transferase, a succinyl-CoA: (R)-benzylsuccinate CoA-transferase, an (E)-cinnamoyl-CoA: (R)-phenyllactate CoA-transferase, and a butyrobetainyl-CoA: (R)-carnitine CoA-transferase. In addition, a large number of proteins of unknown or differently annotated function from Bacteria, Archaea and Eukarya apparently belong to this enzyme family. Properties and reaction mechanisms of the CoA-transferases of family III are described and compared to those of the previously known CoA-transferases. 367 matched cddid_all.tbl CDD pfam02516 pfam02516 396873 STT3 Oligosaccharyl transferase STT3 subunit. This family consists of the oligosaccharyl transferase STT3 subunit and related proteins. The STT3 subunit is part of the oligosaccharyl transferase (OTase) complex of proteins and is required for its activity. In eukaryotes, OTase transfers a lipid-linked core-oligosaccharide to selected asparagine residues in the ER. In the archaea STT3 occurs alone, rather than in an OTase complex, and is required for N-glycosylation of asparagines. 478 matched cddid_all.tbl CDD pfam02517 pfam02517 460578 Rce1-like Type II CAAX prenyl endopeptidase Rce1-like. This family (also known as the ABI (abortive infection) family) contains putative IMPs and has homologs in all three domains of life, including Rce1 from S. cerevisiae. Rce1 is a type II CAAX prenyl protease that processes all farnesylated and geranylgeranylated CAAX proteins. It is an integral membrane endoprotease localized to the endoplasmic reticulum that mediates the cleavage of the carboxyl-terminal three amino acids from CaaX proteins. It is involved in processing the Ras family of small GTPases, the gamma-subunit of heterotrimeric GTPases, nuclear lamins, and protein kinases and phosphatases. Three residues of S. cerevisiae Rce1 -E156, H194 and H248- are critical for catalysis. The structure of Rce1 from the archaea Methanococcus (MmRce1) suggests that this group of proteins represents a novel IMP (intramembrane protease) family, the glutamate IMPs. There is a conserved sequence motif EExxxR. 92 matched cddid_all.tbl CDD pfam02518 pfam02518 460579 HATPase_c Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase. This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90. 109 matched cddid_all.tbl CDD pfam02519 pfam02519 460580 Auxin_inducible Auxin responsive protein. This family consists of the protein products of the ARG7 auxin responsive genes family none of which have any identified functional role. 92 matched cddid_all.tbl CDD pfam02520 pfam02520 396877 ANIS5_cation-bd SXP/RAL-2 family protein Ani s 5-like, metal-binding domain. This domain is found in proteins from nematodes, including SXP/RAL-2 family protein Ani s 5 (ANIS5) from Anisakis simplex, and comprises two conserved motifs: SXP1 and SXP2. Although the function of this domain is not clear, structural information from ANIS5 revealed an alpha helical arrangement with a Calmodulin-like fold. Functional studies indicates that ANIS5 can bind magnesium and calcium, suggesting that this domain plays a role in cation binding. These proteins are interesting targets to develop control strategies against the diseases caused by parasites. 107 matched cddid_all.tbl CDD pfam02521 pfam02521 426814 HP_OMP_2 Putative outer membrane protein. This family consists of putative outer membrane proteins from Helicobacter pylori (campylobacter pylori). 455 matched cddid_all.tbl CDD pfam02522 pfam02522 426815 Antibiotic_NAT Aminoglycoside 3-N-acetyltransferase. This family consists of bacterial aminoglycoside 3-N-acetyltransferases EC:2.3.1.81, these catalyze the reaction: Acetyl-Co + a 2-deoxystreptamine antibiotic <=> CoA + N3'-acetyl-2-deoxystreptamine antibiotic. The enzyme can use a range of antibiotics with 2-deoxystreptamine rings as acceptor for its acetyltransferase activity, this inactivates and confers resistance to gentamicin, kanamycin, tobramycin, neomycin and apramycin amongst others. 232 matched cddid_all.tbl CDD pfam02524 pfam02524 280656 KID KID repeat. This is family contains the KID repeat as found in Borrelia spirochete RepA / Rep+ proteins. The function of these proteins is unknown. RepA and related Borrelia proteins have been suggested to play an important genus-wide role in the biology of the Borrelia. 11 matched cddid_all.tbl CDD pfam02525 pfam02525 426816 Flavodoxin_2 Flavodoxin-like fold. This family consists of a domain with a flavodoxin-like fold. The family includes bacterial and eukaryotic NAD(P)H dehydrogenase (quinone) EC:1.6.99.2. These enzymes catalyze the NAD(P)H-dependent two-electron reductions of quinones and protect cells against damage by free radicals and reactive oxygen species. This enzyme uses a FAD co-factor. The equation for this reaction is:- NAD(P)H + acceptor <=> NAD(P)(+) + reduced acceptor. This enzyme is also involved in the bioactivation of prodrugs used in chemotherapy. The family also includes acyl carrier protein phosphodiesterase EC:3.1.4.14. This enzyme converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine residue from ACP. This family is related to pfam03358 and pfam00258. 193 matched cddid_all.tbl CDD pfam02526 pfam02526 280658 GBP_repeat Glycophorin-binding protein. This family contains glycophorin binding proteins from P. falciparum the malarial parasite. Glycophorin is a cell surface protein of erythrocytes. The Glycophorin binding protein contains a tandem 38 residue repeat. In Swiss:P02895 the repeat occurs 11 times. 38 matched cddid_all.tbl CDD pfam02527 pfam02527 396880 GidB rRNA small subunit methyltransferase G. This is a family of bacterial glucose inhibited division proteins these are probably involved in the regulation of cell devision. GidB has been shown to be a methyltransferase G specific to the rRNA small subunit. Previously identified as a glucose-inhibited division protein B that appears to be present and in a single copy in all complete eubacterial genomes so far sequenced. GidB specifically methylates the N7 position of a guanosine in 16S rRNA. 184 matched cddid_all.tbl CDD pfam02529 pfam02529 396881 PetG Cytochrome B6-F complex subunit 5. This family consists of cytochrome B6-F complex subunit 5 (PetG). The cytochrome bf complex found in green plants, eukaryotic algae and cyanobacteria, connects photosystem I to photosystem II in the electron transport chain, functioning as a plastoquinol:plastocyanin/cytochrome c6 oxidoreductase. PetG or subunit 5 is associated with the bf complex and the absence of PetG affects either the assembly or stability of the cytochrome bf complex in Chlamydomonas reinhardtii. 36 matched cddid_all.tbl CDD pfam02530 pfam02530 308243 Porin_2 Porin subfamily. This family consists of porins from the alpha subdivision of Proteobacteria the members of this family are related to pfam00267. The porins form large aqueous channels in the cell membrane allowing the selective entry of hydrophilic compounds this so called 'molecular sieve' is found in the cell walls of gram negative bacteria. 355 matched cddid_all.tbl CDD pfam02531 pfam02531 426817 PsaD PsaD. This family consists of PsaD from plants and cyanobacteria. PsaD is an extrinsic polypeptide of photosystem I (PSI) and is required for native assembly of PSI reaction clusters and is implicated in the electrostatic binding of ferredoxin within the reaction centre. PsaD forms a dimer in solution which is bound by PsaE however PsaD is monomeric in its native complexed PSI environment. 133 matched cddid_all.tbl CDD pfam02532 pfam02532 426818 PsbI Photosystem II reaction centre I protein (PSII 4.8 kDa protein). This family consists of various Photosystem II (PSII) reaction centre I proteins or PSII 4.8 kDa proteins, PsbI, from the chloroplast genome of many plants and Cyanobacteria. PsbI is a small, integral membrane component of PSII the role of which is not clear. Synechocystis mutants lacking PsbI have 20-30% loss of PSII activity however the PSII complex is not destabilized. 36 matched cddid_all.tbl CDD pfam02533 pfam02533 396883 PsbK Photosystem II 4 kDa reaction centre component. This family consists of various photosystem II 4 kDa reaction centre components (PsbK) from plant and Cyanobacteria. The photosystem II reaction centre is responsible for catalysing the core photosynthesis reaction the light-induced splitting of water and the consequential release of dioxygen. In C. reinhardtii the psbK product is required for the stable assembly and/or stability of the photosystem II complex. 41 matched cddid_all.tbl CDD pfam02534 pfam02534 367119 T4SS-DNA_transf Type IV secretory system Conjugative DNA transfer. These proteins contain a P-loop and walker-B site for nucleotide binding. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems. The C-terminus of this domain interacts with the relaxosome component TraM via the latter's tetramerization domain. TraD is a hexameric ring ATPase that forms the cytoplasmic face of the conjugative pore. The family contains a number of different DNA transfer proteins. 468 matched cddid_all.tbl CDD pfam02535 pfam02535 396884 Zip ZIP Zinc transporter. The ZIP family consists of zinc transport proteins and many putative metal transporters. The main contribution to this family is from the Arabidopsis thaliana ZIP protein family these proteins are responsible for zinc uptake in the plant. Also found within this family are C. elegans proteins of unknown function which are annotated as being similar to human growth arrest inducible gene product, although this protein in not found within this family. 325 matched cddid_all.tbl CDD pfam02536 pfam02536 460581 mTERF mTERF. This family contains one sequence of known function Human mitochondrial transcription termination factor (mTERF) the rest of the family consists of hypothetical proteins none of which have any functional information. mTERF is a multizipper protein possessing three putative leucine zippers one of which is bipartite. The protein binds DNA as a monomer. The leucine zippers are not implicated in a dimerization role as in other leucine zippers. 313 matched cddid_all.tbl CDD pfam02537 pfam02537 460582 CRCB CrcB-like protein, Camphor Resistance (CrcB). CRCB is a family of bacterial integral membrane proteins with four TMs.. Over expression in E. coli also leads to camphor resistance. 109 matched cddid_all.tbl CDD pfam02538 pfam02538 460583 Hydantoinase_B Hydantoinase B/oxoprolinase. This family includes N-methylhydaintoinase B which converts hydantoin to N-carbamyl-amino acids, and 5-oxoprolinase EC:3.5.2.9 which catalyzes the formation of L-glutamate from 5-oxo-L-proline. These enzymes are part of the oxoprolinase family and are related to pfam01968. 507 matched cddid_all.tbl CDD pfam02540 pfam02540 396888 NAD_synthase NAD synthase. NAD synthase (EC:6.3.5.1) is involved in the de novo synthesis of NAD and is induced by stress factors such as heat shock and glucose limitation. 241 matched cddid_all.tbl CDD pfam02541 pfam02541 396889 Ppx-GppA Ppx/GppA phosphatase family. This family consists of the N-terminal region of exopolyphosphatase (Ppx) EC:3.6.1.11 and guanosine pentaphosphate phospho-hydrolase (GppA) EC:3.6.1.40. 285 matched cddid_all.tbl CDD pfam02542 pfam02542 460584 YgbB YgbB family. The ygbB protein is a putative enzyme of deoxy-xylulose pathway (terpenoid biosynthesis). 155 matched cddid_all.tbl CDD pfam02543 pfam02543 426823 Carbam_trans_N Carbamoyltransferase N-terminus. This domain is found in NodU from Rhizobium, CmcH from Nocardia lactamdurans and the bifunctional carbamoyltransferase TobZ from Streptoalloteichus tenebrarius. NodU a Rhizobium nodulation protein involved in the synthesis of nodulation factors has 6-O-carbamoyltransferase-like activity. CmcH is involved in cephamycin (antibiotic) biosynthesis and has 3-hydroxymethylcephem carbamoyltransferase activity, EC:2.1.3.7 catalysing the reaction: Carbamoyl phosphate + 3-hydroxymethylceph-3-EM-4-carboxylate <=> phosphate + 3-carbamoyloxymethylcephem. TobZ functions as an ATP carbamoyltransferase and tobramycin carbamoyltransferase. These proteins contain two domains, this is the larger, N-terminal, domain. 352 matched cddid_all.tbl CDD pfam02544 pfam02544 460585 Steroid_dh 3-oxo-5-alpha-steroid 4-dehydrogenase. This family consists of 3-oxo-5-alpha-steroid 4-dehydrogenases, EC:1.3.99.5 Also known as Steroid 5-alpha-reductase, the reaction catalyzed by this enzyme is: 3-oxo-5-alpha-steroid + acceptor <=> 3-oxo-delta(4)-steroid + reduced acceptor. The Steroid 5-alpha-reductase enzyme is responsible for the formation of dihydrotestosterone, this hormone promotes the differentiation of male external genitalia and the prostate during fetal development. In humans mutations in this enzyme can cause a form of male pseudohermaphorditism in which the external genitalia and prostate fail to develop normally. A related enzyme is also found in plants is DET2, a steroid reductase from Arabidopsis. Mutations in this enzyme cause defects in light-regulated development. 150 matched cddid_all.tbl CDD pfam02545 pfam02545 460586 Maf Maf-like protein. Maf is a putative inhibitor of septum formation in eukaryotes, bacteria, and archaea. 174 matched cddid_all.tbl CDD pfam02547 pfam02547 460587 Queuosine_synth Queuosine biosynthesis protein. Queuosine (Q) biosynthesis protein, or S-adenosylmethionine:tRNA -ribosyltransferase-isomerase, is required for the synthesis of the queuosine precursor (oQ). It catalyzes the transfer and isomerization of the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to form epoxyqueuosine (oQ-tRNA). Q is a hypermodified nucleoside usually found at the first position of the anticodon of asparagine, aspartate, histidine, and tyrosine tRNAs. In Streptococcus gordonii, QueA has been shown to play a role in the regulation of arginine deiminase genes. 336 matched cddid_all.tbl CDD pfam02548 pfam02548 460588 Pantoate_transf Ketopantoate hydroxymethyltransferase. Ketopantoate hydroxymethyltransferase (EC:2.1.2.11) is the first enzyme in the pantothenate biosynthesis pathway. 259 matched cddid_all.tbl CDD pfam02550 pfam02550 251367 AcetylCoA_hydro Acetyl-CoA hydrolase/transferase N-terminal domain. This family contains several enzymes which take part in pathways involving acetyl-CoA. Acetyl-CoA hydrolase EC:3.1.2.1 catalyzes the formation of acetate from acetyl-CoA, CoA transferase (CAT1) EC:2.8.3.- produces succinyl-CoA, and acetate-CoA transferase EC:2.8.3.8 utilizes acyl-CoA and acetate to form acetyl-CoA. 198 matched cddid_all.tbl CDD pfam02551 pfam02551 396894 Acyl_CoA_thio Acyl-CoA thioesterase. This family represents the thioesterase II domain. Two copies of this domain are found in a number of acyl-CoA thioesterases. 132 matched cddid_all.tbl CDD pfam02552 pfam02552 251369 CO_dh CO dehydrogenase beta subunit/acetyl-CoA synthase epsilon subunit. This family consists of Carbon monoxide dehydrogenase I/II beta subunit EC:1.2.99.2 and acetyl-CoA synthase epsilon subunit. Carbon monoxide beta subunit catalyzes the reaction: CO + H2O + acceptor <=> CO2 + reduced acceptor. 168 matched cddid_all.tbl CDD pfam02553 pfam02553 426827 CbiN Cobalt transport protein component CbiN. CbiN is part of the active cobalt transport system involved in uptake of cobalt in to the cell involved with cobalamin biosynthesis (vitamin B12). It has been suggested that CbiN may function as the periplasmic binding protein component of the active cobalt transport system. 67 matched cddid_all.tbl CDD pfam02554 pfam02554 426828 CstA Carbon starvation protein CstA. This family consists of Carbon starvation protein CstA a predicted membrane protein. It has been suggested that CstA is involved in peptide utilization. 375 matched cddid_all.tbl CDD pfam02556 pfam02556 460589 SecB Preprotein translocase subunit SecB. This family consists of preprotein translocase subunit SecB. SecB is required for the normal export of envelope proteins out of the cell cytoplasm. 137 matched cddid_all.tbl CDD pfam02557 pfam02557 426830 VanY D-alanyl-D-alanine carboxypeptidase. 131 matched cddid_all.tbl CDD pfam02558 pfam02558 426831 ApbA Ketopantoate reductase PanE/ApbA. This is a family of 2-dehydropantoate 2-reductases also known as ketopantoate reductases, EC:1.1.1.169. The reaction catalyzed by this enzyme is: (R)-pantoate + NADP(+) <=> 2-dehydropantoate + NADPH. AbpA catalyzes the NADPH reduction of ketopantoic acid to pantoic acid in the alternative pyrimidine biosynthetic (APB) pathway. ApbA and PanE are allelic. ApbA, the ketopantoate reductase enzyme is required for the synthesis of thiamine via the APB biosynthetic pathway. 147 matched cddid_all.tbl CDD pfam02559 pfam02559 460590 CarD_CdnL_TRCF CarD-like/TRCF domain. CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes. This family includes the presumed N-terminal domain, CdnL. CarD interacts with the zinc-binding protein CarG to form a complex that regulates multiple processes in Myxococcus xanthus. This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF (transcription-repair-coupling factor) proteins. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription. This domain is involved in binding to the stalled RNA polymerase. The family includes members otherwise referred to as CdnL, for CarD N-terminal like, which differ functionally from CarD. The TRCF domain mentioned above is the RNA polymerase-interacting domain or RID. 89 matched cddid_all.tbl CDD pfam02560 pfam02560 426833 Cyanate_lyase Cyanate lyase C-terminal domain. Cyanate lyase (also known as cyanase) EC:4.2.1.104 is responsible for the hydrolysis of cyanate, allowing organizms that possess the enzyme to overcome the toxicity of environmental cyanate. This enzyme is composed of two domains, an N-terminal helix-turn-helix and this structurally unique C-terminal domain. 64 matched cddid_all.tbl CDD pfam02561 pfam02561 460591 FliS Flagellar protein FliS. FliS is coded for by the FliD operon and is transcribed in conjunction with FliD and FliT, however this protein has no known function. 115 matched cddid_all.tbl CDD pfam02562 pfam02562 460592 PhoH PhoH-like protein. PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation. 204 matched cddid_all.tbl CDD pfam02563 pfam02563 426836 Poly_export Polysaccharide biosynthesis/export protein. This is a family of periplasmic proteins involved in polysaccharide biosynthesis and/or export. 74 matched cddid_all.tbl CDD pfam02565 pfam02565 460593 RecO_C Recombination protein O C terminal. Recombination protein O (RecO) is involved in DNA repair and pfam00470 pathway recombination. 156 matched cddid_all.tbl CDD pfam02566 pfam02566 460594 OsmC OsmC-like protein. Osmotically inducible protein C (OsmC) is a stress -induced protein found in E. Coli. This family also contains a organic hydroperoxide detoxification protein that has a novel pattern of oxidative stress regulation. 99 matched cddid_all.tbl CDD pfam02567 pfam02567 396907 PhzC-PhzF Phenazine biosynthesis-like protein. PhzC/PhzF is involved in dimerization of two 2,3-dihydro-3-oxo-anthranilic acid molecules to create PCA by P. fluorescens. This family also contains Swiss:P28176, though there is no significant sequence similarity to pfam00303 members. This family appears to be distantly related to pfam01678, including containing a weak internal duplication. However members of this family do not contain the conserved cysteines that are hypothesized to be active site residues (Bateman A pers obs). 280 matched cddid_all.tbl CDD pfam02568 pfam02568 280691 ThiI Thiamine biosynthesis protein (ThiI). ThiI is required for thiazole synthesis, required for thiamine biosynthesis. 197 matched cddid_all.tbl CDD pfam02569 pfam02569 460595 Pantoate_ligase Pantoate-beta-alanine ligase. Pantoate-beta-alanine ligase, also know as pantothenate synthase, (EC:6.3.2.1) catalyzes the formation of pantothenate from pantoate and alanine. 277 matched cddid_all.tbl CDD pfam02570 pfam02570 426840 CbiC Precorrin-8X methylmutase. This is a family Precorrin-8X methylmutases also known as Precorrin isomerase, CbiC/CobH, EC:5.4.1.2. This enzyme catalyzes the reaction: Precorrin-8X <=> hydrogenobyrinate. This enzyme is part of the Cobalamin (vitamin B12) biosynthetic pathway and catalyzes a methyl rearrangement. 195 matched cddid_all.tbl CDD pfam02571 pfam02571 460596 CbiJ Precorrin-6x reductase CbiJ/CobK. This family consists of Precorrin-6x reductase EC:1.3.1.54. This enzyme catalyzes the reaction: precorrin-6Y + NADP(+) <=> precorrin-6X + NADPH. CbiJ and CobK both catalyze the reduction of macocycle in the colbalmin biosynthesis pathway. 248 matched cddid_all.tbl CDD pfam02572 pfam02572 460597 CobA_CobO_BtuR ATP:corrinoid adenosyltransferase BtuR/CobO/CobP. This family consists of the BtuR, CobO, CobP proteins all of which are Cob(I)alamin adenosyltransferase, EC:2.5.1.17, involved in cobalamin (vitamin B12) biosynthesis. These enzymes catalyze the adenosylation reaction: ATP + cob(I)alamin + H2O <=> phosphate + diphosphate + adenosylcobalamin. 171 matched cddid_all.tbl CDD pfam02574 pfam02574 460598 S-methyl_trans Homocysteine S-methyltransferase. This is a family of related homocysteine S-methyltransferases enzymes: 5-methyltetrahydrofolate--homocysteine S-methyltransferases also known EC:2.1.1.13; Betaine--homocysteine S-methyltransferase (vitamin B12 dependent), EC:2.1.1.5; and Homocysteine S-methyltransferase, EC:2.1.1.10,. 268 matched cddid_all.tbl CDD pfam02575 pfam02575 460599 YbaB_DNA_bd YbaB/EbfC DNA-binding family. This is a family of DNA-binding proteins. Members of this family form homodimers which bind DNA via a tweezer-like structure. The conformation of the DNA is changed when bound to these proteins. In bacteria, these proteins may play a role in DNA replication-recovery following DNA damage. 90 matched cddid_all.tbl CDD pfam02576 pfam02576 460600 RimP_N RimP N-terminal domain. This entry represents the N-terminal domain of the ribosome maturation factor RimP (also known as yhbC). RimP facilitates the maturation of the 30S ribosomal subunit. The N-terminal domain contains two alpha-helices and a three-stranded beta-sheet. It is suggested that the N-terminal domain of SP14.3 (RimP orthologue) could function as a protein module that binds to other proteins, especially those that contain highly positively charged surfaces.. 73 matched cddid_all.tbl CDD pfam02577 pfam02577 426845 BFN_dom Bifunctional nuclease domain. This entry represents the bifunctional nuclease (BFN) domain which is specific to bacteria and plant organizms. It has both RNase and DNase activities. The dimer of the BFN domain forms a wedge, each monomer being a basic triangular shape. The BFN domain is composed of an eight-stranded, distorted beta-sheet consisting of a four-stranded antiparallel beta-sheet, and a four-stranded mixed beta-sheet. This domain can be found in M. tuberculosis Carbon monoxide resistance (Cor) proteins. Cor consists entirely of this domain with homologs in a variety of organizms, including most mycobacteria, Bacteroides sp., Chlamydia sp., Streptomyces sp., and Rhodococcussp. One of the homologs from Oryza minuta protein OmBBD was reported to exhibit DNase and RNAse activity in vitro. OmBBD carries a C-terminal UvrB domain that is absent in the mycobacterial sequences. UvrB is one component of the UvrABC endonuclease system. Hence, it was proposed that OmBBD's observed nuclease activity may come not from this domain but from an interaction of the C-terminal UvrB with the catalytic UvrC nuclease. 112 matched cddid_all.tbl CDD pfam02578 pfam02578 460601 Cu-oxidase_4 Multi-copper polyphenol oxidoreductase laccase. Laccases are multi-copper oxidoreductases able to oxidize a wide variety of phenolic and non-phenolic compounds and are widely distributed among both prokaryotes and eukaryotes. There are two main active catalytic sites with conserved histidines that are capable of binding four copper atoms. 232 matched cddid_all.tbl CDD pfam02579 pfam02579 460602 Nitro_FeMo-Co Dinitrogenase iron-molybdenum cofactor. This family contains several NIF (B, Y and X) proteins which are iron-molybdenum cofactors (FeMo-co) in the dinitrogenase enzyme which catalyzes the reduction of dinitrogen to ammonium. Dinitrogenase is a hetero-tetrameric (alpha(2)beta(2)) enzyme which contains the iron-molybdenum cofactor (FeMo-co) at its active site. 93 matched cddid_all.tbl CDD pfam02580 pfam02580 460603 Tyr_Deacylase D-Tyr-tRNA(Tyr) deacylase. This family comprises of several D-Tyr-tRNA(Tyr) deacylase proteins. Cell growth inhibition by several d-amino acids can be explained by an in vivo production of d-aminoacyl-tRNA molecules. Escherichia coli and yeast cells express an enzyme, d-Tyr-tRNA(Tyr) deacylase, capable of recycling such d-aminoacyl-tRNA molecules into free tRNA and d-amino acid. Accordingly, upon inactivation of the genes of the above deacylases, the toxicity of d-amino acids increases. Orthologues of the deacylase are found in many cells.The D-aminoacyl-tRNA deacylase (DTD) enzyme is homodimeric with two active sites located at the dimeric interface. Each active site carries an invariant Gly-cisPro dipeptide motif in each monomer. The interaction between the dipeptide motifs from each monomer ensures substrate stereospecificity. This family also includes a subclass of DTDs which is present in Chordata and harbors a Gly-transPro motif. The cis to trans switch is the key to Animal DTDs (ATD) gaining of L-chiral selectivity. This 'gain of function' through relaxation of substrate chiral specificity underlies ATD's capability of correcting the error in tRNA selection. 144 matched cddid_all.tbl CDD pfam02581 pfam02581 426849 TMP-TENI Thiamine monophosphate synthase. Thiamine monophosphate synthase (TMP) (EC:2.5.1.3) catalyzes the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl)thiazole phosphate to yield thiamine phosphate. This Pfam family also includes the regulatory protein TENI, a protein from Bacillus subtilis that regulates the production of several extracellular enzymes by reducing alkaline protease production. While TenI shows high sequence similarity with thiamin phosphate synthase, the purified protein has no thiamin phosphate synthase activity. Instead, it is a thiazole tautomerase. 180 matched cddid_all.tbl CDD pfam02582 pfam02582 460604 DUF155 RMND1/Sif2-Sif3/Mrx10, DUF155. This entry represents a domain found in RMND1 from mammals, Sif2/Sif3 from fission yeasts and Rmd1/Rmd8/YDR282C (Mrx10) from budding yeasts. RMND1 and its yeast homolog, Mrx10, are mitochondrial proteins required for mitochondrial translation. Rmd1 and Rmd8 are cytoplasmic proteins required for sporulation. 173 matched cddid_all.tbl CDD pfam02583 pfam02583 426851 Trns_repr_metal Metal-sensitive transcriptional repressor. This is a family of metal-sensitive repressors, involved in resistance to metal ions. Members of this family bind copper, nickel or cobalt ions via conserved cysteine and histidine residues. In the absence of metal ions, these proteins bind to promoter regions and repress transcription. When bound to metal ions they are unable to bind DNA, leading to transcriptional derepression. 80 matched cddid_all.tbl CDD pfam02585 pfam02585 426852 PIG-L GlcNAc-PI de-N-acetylase. Members of this family are related to PIG-L an N-acetylglucosaminylphosphatidylinositol de-N-acetylase (EC:3.5.1.89) that catalyzes the second step in GPI biosynthesis. 128 matched cddid_all.tbl CDD pfam02586 pfam02586 460605 SRAP SOS response associated peptidase (SRAP). The SRAP family functions as a DNA-associated autoproteolytic switch that recruits diverse repair enzymes onto DNA damage. We propose that the human protein Q96FZ2:UniProtKB, the eukaryotic member of the SRAP family, which has been recently shown to bind specifically to DNA with 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxycytosine, is a sensor for these oxidized bases generated by the TET (tetrahedral aminopeptidase of the M42 family) enzymes from methylcytosine. Hence, its autoproteolytic activity might help it act as a switch that recruits DNA repair enzymes to remove these oxidized methylcytosine species as part of the DNA demethylation pathway downstream of the TET enzymes. 213 matched cddid_all.tbl CDD pfam02588 pfam02588 426854 YitT_membrane Uncharacterized 5xTM membrane BCR, YitT family COG1284. This is probably a bacterial ABC transporter permease (personal obs:Yeats C). 206 matched cddid_all.tbl CDD pfam02589 pfam02589 426855 LUD_dom LUD domain. This entry represents a domain found in lactate utilization proteins B (LutB) and C (LutC), as well as several uncharacterized proteins. LutB and LutC are encoded by th conserved LutABC operon in bacteria. They are involved in lactate utilization and is implicated in the oxidative conversion of L-lactate into pyruvate 188 matched cddid_all.tbl CDD pfam02590 pfam02590 460606 SPOUT_MTase Predicted SPOUT methyltransferase. This family of proteins are predicted to be SPOUT methyltransferases. 155 matched cddid_all.tbl CDD pfam02591 pfam02591 426857 zf-RING_7 C4-type zinc ribbon domain. Zn-ribbon_9 is a Zn-ribbon domain rich in aromatic and positively charged amino acid residues. This C-terminal Zn-ribbon domain consists of two beta-strands acting as a scaffold for the two Zn knuckles. Both pairs of cysteines making up the two Zn knuckles are situated at highly conserved sharp beta-turns, an arrangement that facilitates the tetrahedral coordination of the divalent Zn ion. The two Zn-knuckle cysteine motifs are separated by 20 residues, 9 of which form an alpha-helix (helix 4).Structural modelling suggests this domain may bind nucleic acids. The domain appears to bind flaA-mRNA, thus contributing to flagellum formation and motility. 33 matched cddid_all.tbl CDD pfam02592 pfam02592 460607 Vut_1 Putative vitamin uptake transporter. 154 matched cddid_all.tbl CDD pfam02593 pfam02593 367127 DUF166 Domain of unknown function. This family catalyzes the synthesis of thymidine monophosphate (dTMP) from deoxyuridine monophosphate (dUMP). The physiological co-substrate has not yet been identified. Previous designation of this famliy as being thymidylate synthase from one paper, PMID:10436953, has been shown to be erroneous. The proteins are uncharacterized. 218 matched cddid_all.tbl CDD pfam02594 pfam02594 460608 DUF167 Uncharacterized ACR, YggU family COG1872. 75 matched cddid_all.tbl CDD pfam02595 pfam02595 460609 Gly_kinase Glycerate kinase family. This is family of Glycerate kinases. 369 matched cddid_all.tbl CDD pfam02596 pfam02596 460610 DUF169 Uncharacterized ArCR, COG2043. 209 matched cddid_all.tbl CDD pfam02597 pfam02597 396932 ThiS ThiS family. ThiS (thiaminS) is a 66 aa protein involved in sulphur transfer. ThiS is coded in the thiCEFSGH operon in E. coli. This family of proteins have two conserved Glycines at the COOH terminus. Thiocarboxylate is formed at the last G in the activation process. Sulphur is transferred from ThiI to ThiS in a reaction catalyzed by IscS. MoaD, a protein involved sulphur transfer in molybdopterin synthesis, is about the same length and shows limited sequence similarity to ThiS. Both have the conserved GG at the COOH end. 74 matched cddid_all.tbl CDD pfam02598 pfam02598 460611 Methyltrn_RNA_3 Putative RNA methyltransferase. This family has a TIM barrel-like fold with a deep C-terminal trefoil knot. The arrangement of its hydrophilic and hydrophobic surfaces are opposite to that of the classic TIM barrel proteins. It is likely to bind RNA, and may function as a methyltransferase. 295 matched cddid_all.tbl CDD pfam02599 pfam02599 460612 CsrA Global regulator protein family. This is a family of global regulator proteins. This protein is a RNA-binding protein and a global regulator of carbohydrate metabolism genes facilitating mRNA decay. In E. coli CsrA binds the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara RmsA has been shown to regulate the production of virulence determinants, such extracellular enzymes. RmsA binds to RmsB regulatory RNA. 50 matched cddid_all.tbl CDD pfam02600 pfam02600 460613 DsbB Disulfide bond formation protein DsbB. This family consists of disulfide bond formation protein DsbB from bacteria. The DsbB protein oxidizes the periplasmic protein DsbA which in turn oxidizes cysteines in other periplasmic proteins in order to make disulfide bonds. DsbB acts as a redox potential transducer across the cytoplasmic membrane and is an integral membrane protein. DsbB posses six cysteines four of which are necessary for it proper function in vivo. 149 matched cddid_all.tbl CDD pfam02601 pfam02601 426865 Exonuc_VII_L Exonuclease VII, large subunit. This family consist of exonuclease VII, large subunit EC:3.1.11.6 This enzyme catalyzes exonucleolytic cleavage in either 5'->3' or 3'->5' direction to yield 5'-phosphomononucleotides. This exonuclease VII enzyme is composed of one large subunit and 4 small ones. 264 matched cddid_all.tbl CDD pfam02602 pfam02602 426866 HEM4 Uroporphyrinogen-III synthase HemD. This family consists of uroporphyrinogen-III synthase HemD EC:4.2.1.75 also known as Hydroxymethylbilane hydrolyase (cyclizing) from eukaryotes, bacteria and archaea. This enzyme catalyzes the reaction: Hydroxymethylbilane <=> uroporphyrinogen-III + H(2)O. Some members of this family are multi-functional proteins possessing other enzyme activities related to porphyrin biosynthesis, such as Swiss:Q59294 with pfam00590, however the aligned region corresponds with the uroporphyrinogen-III synthase EC:4.2.1.75 activity only. Uroporphyrinogen-III synthase is the fourth enzyme in the heme pathway. Mutant forms of the Uroporphyrinogen-III synthase gene cause congenital erythropoietic porphyria in humans a recessive inborn error of metabolism also known as Gunther disease. 230 matched cddid_all.tbl CDD pfam02603 pfam02603 460614 Hpr_kinase_N HPr Serine kinase N terminus. This family represents the N-terminal region of Hpr Serine/threonine kinase PtsK. This kinase is the sensor in a multicomponent phospho-relay system in control of carbon catabolic repression in bacteria. This kinase in unusual in that it recognizes the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating enzymes. X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller. The blades are formed by two N-terminal domains each, and the compact central hub assembles the C-terminal kinase domains. 125 matched cddid_all.tbl CDD pfam02604 pfam02604 460615 PhdYeFM_antitox Antitoxin Phd_YefM, type II toxin-antitoxin system. Members of this family act as antitoxins in type II toxin-antitoxin systems. When bound to their toxin partners, they can bind DNA via the N-terminus and repress the expression of operons containing genes encoding the toxin and the antitoxin. This domain complexes with Txe toxins containing pfam06769, Fic/DOC toxins containing pfam02661 and YafO toxins containing pfam13957. 67 matched cddid_all.tbl CDD pfam02605 pfam02605 426869 PsaL Photosystem I reaction centre subunit XI. This family consists of the photosystem I reaction centre subunit XI, PsaL, from plants and bacteria. PsaL is one of the smaller subunits in photosystem I with only two transmembrane alpha helices and interacts closely with PsaI. 143 matched cddid_all.tbl CDD pfam02606 pfam02606 460616 LpxK Tetraacyldisaccharide-1-P 4'-kinase. This family consists of tetraacyldisaccharide-1-P 4'-kinase also known as Lipid-A 4'-kinase or Lipid A biosynthesis protein LpxK, EC:2.7.1.130. This enzyme catalyzes the reaction: ATP + 2,3-bis(3-hydroxytetradecanoyl)-D -glucosaminyl-(beta-D-1,6)-2,3-bis(3-hydroxytetradecanoyl)-D-glu cosam inyl beta-phosphate <=> ADP + 2,3,2',3'-tetrakis(3-hydroxytetradecanoyl)-D- glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate. This enzyme is involved in the synthesis of lipid A portion of the bacterial lipopolysaccharide layer (LPS). The family contains a P-loop motif at the N terminus. 319 matched cddid_all.tbl CDD pfam02607 pfam02607 460617 B12-binding_2 B12 binding domain. This B12 binding domain is found in methionine synthase EC:2.1.1.13, and other shorter proteins that bind to B12. This domain is always found to the N-terminus of pfam02310. The structure of this domain is known, it is a 4 helix bundle. Many of the conserved residues in this domain are involved in B12 binding, such as those in the MXXVG motif. 68 matched cddid_all.tbl CDD pfam02608 pfam02608 396943 Bmp ABC transporter substrate-binding protein PnrA-like. Proteins containing this domain were originally annotated as basic membrane lipoproteins. However, several proteins containing this domain were later predicted as ABC transporter substrate-binding proteins, such as PnrA (also known as TmpC or TP0319) and RfuA (also known as Tpn38 or TP0298) from Treponema pallidum. PnrA transports purine nucleosides, while RfuA transports riboflavin. Proteins containing this domain also include Med from Bacillus subtilis. Med was annotated as a transcriptional activator protein that regulates comK. This domain can also found at the N terminus of glutamate receptor-like proteins from Dictyostelium (slime mold). 302 matched cddid_all.tbl CDD pfam02609 pfam02609 460618 Exonuc_VII_S Exonuclease VII small subunit. This family consist of exonuclease VII, small subunit EC:3.1.11.6 This enzyme catalyzes exonucleolytic cleavage in either 5'->3' or 3'->5' direction to yield 5'-phosphomononucleotides. This exonuclease VII enzyme is composed of one large subunit and 4 small ones. 51 matched cddid_all.tbl CDD pfam02610 pfam02610 426873 Arabinose_Isome L-arabinose isomerase. This is a family of L-arabinose isomerases, AraA, EC:5.3.1.4. These enzymes catalyze the reaction: L-arabinose <=> L-ribulose. This reaction is the first step in the pathway of L-arabinose utilization as a carbon source after entering the cell L-arabinose is converted into L-ribulose by the L-arabinose isomerases enzyme. 356 matched cddid_all.tbl CDD pfam02611 pfam02611 426874 CDH CDP-diacylglycerol pyrophosphatase. This is a family of CDP-diacylglycerol pyrophosphatases, EC:3.6.1.26. This enzyme catalyzes the reaction CDP-diacylglycerol + H2O <=> CMP + phosphatidate. 224 matched cddid_all.tbl CDD pfam02613 pfam02613 460619 Nitrate_red_del Nitrate reductase delta subunit. This family is the delta subunit of the nitrate reductase enzyme, The delta subunit is not part of the nitrate reductase enzyme but is most likely needed for assembly of the multi-subunit enzyme complex. In the absence of the delta subunit the core alpha beta enzyme complex is unstable. The delta subunit is essential for enzyme activity in vivo and in vitro. The nitrate reductase enzyme, EC:1.7.99.4 catalyze the conversion of nitrite to nitrate via the reduction of an acceptor. The nitrate reductase enzyme is composed of three subunits. Nitrate is the most widely used alternative electron acceptor after oxygen. This family also now contains the family TorD, a family of cytoplasmic chaperone proteins; like many prokaryotic molybdoenzymes, the TMAO reductase (TorA) of Escherichia coli requires the insertion of a bis(molybdopterin guanine dinucleotide) molybdenum (bis(MGD)Mo) cofactor in its catalytic site to be active and translocated to the periplasm. The TorD chaperone increases apoTorA activation up to four-fold, allowing maturation of most of the apoprotein. Therefore TorD is involved in the first step of TorA maturation to make it competent to receive the cofactor. 135 matched cddid_all.tbl CDD pfam02614 pfam02614 426876 UxaC Glucuronate isomerase. This is a family of Glucuronate isomerases also known as D-glucuronate isomerase, uronic isomerase, uronate isomerase, or uronic acid isomerase, EC:5.3.1.12. This enzyme catalyzes the reactions: D-glucuronate <=> D-fructuronate and D-galacturonate <=> D-tagaturonate. It is not however clear where the experimental evidence for this functional assignment came from and thus this family has no literature reference. 464 matched cddid_all.tbl CDD pfam02615 pfam02615 460620 Ldh_2 Malate/L-lactate dehydrogenase. This family consists of bacterial and archaeal Malate/L-lactate dehydrogenase. L-lactate dehydrogenase, EC:1.1.1.27, catalyzes the reaction (S)-lactate + NAD(+) <=> pyruvate + NADH. Malate dehydrogenase, EC:1.1.1.37 and EC:1.1.1.82, catalyzes the reactions: (S)-malate + NAD(+) <=> oxaloacetate + NADH, and (S)-malate + NADP(+) <=> oxaloacetate + NADPH respectively. 330 matched cddid_all.tbl CDD pfam02616 pfam02616 280735 SMC_ScpA Segregation and condensation protein ScpA. This is a family of proteins that from part of the condensin complex that regulates chromosome segregation. This is the A subunit, which binds to the ScpB subunit, pfam04079, and SMC, pfam02463, to participate in chromosomal partition during cell division. The condensin complex pulls DNA away from the mid-cell into both cell halves. These proteins are part of the Kleisin superfamily. 225 matched cddid_all.tbl CDD pfam02617 pfam02617 460621 ClpS ATP-dependent Clp protease adaptor protein ClpS. In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins. 80 matched cddid_all.tbl CDD pfam02618 pfam02618 460622 YceG YceG-like family. This family of proteins is found in bacteria. Proteins in this family are typically between 332 and 389 amino acids in length. This family was previously incorrectly annotated and names as aminodeoxychorismate lyase. The structure of Swiss:P28306 was solved by X-ray crystallography. 273 matched cddid_all.tbl CDD pfam02620 pfam02620 460623 YceD Large ribosomal RNA subunit accumulation protein YceD. This family is nearly universally conserved in bacteria and plants except the Chlorophyceae algae. Thus far, mutantional analysis in bacteria have not established a function. In contrast, mutants have embryo lethal phenotypes in maize and Arabidopsis. In maize, the mutant embryos arrest at an early transition stage.It has been suggested that family members specifically affect 23S rRNA accumulation in plastids as well as bacteria. 119 matched cddid_all.tbl CDD pfam02621 pfam02621 426881 VitK2_biosynth Menaquinone biosynthesis. This family includes two enzymes which are involved in menaquinone biosynthesis. One which catalyzes the conversion of cyclic de-hypoxanthine futalosine to 1,4-dihydroxy-6-naphthoate, and one which may be involved in the conversion of chorismate to futalosine. These enzymes comprise two domains with alpha/beta structures, a large domain and a small domain. A pocket between the two domains may form the active site, a conserved histidine located within this pocket could be the catalytic base. 252 matched cddid_all.tbl CDD pfam02622 pfam02622 460624 DUF179 Uncharacterized ACR, COG1678. 159 matched cddid_all.tbl CDD pfam02623 pfam02623 460625 FliW FliW protein. The protein BSU35380 from Bacillus subtilis (renamed FliW) was characterized as being a flagellar assembly factor. Experimental characterization was also carried out in Treponema pallidum (TP0658). In Campylobacter jejuni, Cj1075 has been shown to be involved in motility and flagellin biosynthesis. The two paralogues in Helicobacter pylori (HP1154 and HP1377) were found to be able to bind to flagellin. FliW proteins are involved in flagellar assembly. FliW is part of a three-part feedback loop: in Bacillus subtilis FliW inhibits CsrA (an RNA-binding protein) which inhibits FliC translation; hence FliW is required for FliC (flagellin) production. 121 matched cddid_all.tbl CDD pfam02624 pfam02624 426884 YcaO YcaO cyclodehydratase, ATP-ad Mg2+-binding. YcaO is an ATP- an Mg2+-binding protein involved in the peptidic biosynthesis of azoline. There three motifs involved in the binding are, in UniProtKB:P75838, 71-79: Sx3ExxER, 184-203: Sx6Ex3Qx3ExxER, and 286-290: RxxxE. Three slightly different functional families are represented in this family, proteins involved in TOMM (thiazole/oxazole-modified microcin) biogenesis, non-TOMM proteins such as UniProtKB:P75838, and TfuA-associated non-TOMM proteins involved in trifolitoxin biosynthesis. UniProtKB:P75838 hydrolyses ATP to AMP and pyrophosphate. 318 matched cddid_all.tbl CDD pfam02625 pfam02625 460626 XdhC_CoxI XdhC and CoxI family. This domain is often found in association with an NAD-binding region, related to TrkA-N (pfam02254; personal obs:C. Yeats). XdhC is believed to be involved in the attachment of molybdenum to Xanthine Dehydrogenase. 68 matched cddid_all.tbl CDD pfam02626 pfam02626 460627 CT_A_B Carboxyltransferase domain, subdomain A and B. Urea carboxylase (UC) catalyzes a two-step, ATP- and biotin-dependent carboxylation reaction of urea. It is composed of biotin carboxylase (BC), carboxyltransferase (CT), and biotin carboxyl carrier protein (BCCP) domains. The CT domain of UC consists of four subdomains, named A, B, C and D. This domain covers the A and B subdomains of the CT domain. This domain covers the whole length of KipA (kinase A) from Bacillus subtilis. It can also be found in S. cerevisiae urea amidolyase Dur1,2, which is a multifunctional biotin-dependent enzyme with domains for urea carboxylase and allophanate (urea carboxylate) hydrolase activity. 264 matched cddid_all.tbl CDD pfam02627 pfam02627 460628 CMD Carboxymuconolactone decarboxylase family. Carboxymuconolactone decarboxylase (CMD) EC:4.1.1.44 is involved in protocatechuate catabolism. In some bacteria a gene fusion event leads to expression of CMD with a hydrolase involved in the same pathway. In these bifunctional proteins CMD represents the C-terminal domain, pfam00561 represents the N-terminal domain. 84 matched cddid_all.tbl CDD pfam02628 pfam02628 460629 COX15-CtaA Cytochrome oxidase assembly protein. This is a family of integral membrane proteins. CtaA is required for cytochrome aa3 oxidase assembly in Bacillus subtilis. COX15 is required for cytochrome c oxidase assembly in yeast. 323 matched cddid_all.tbl CDD pfam02629 pfam02629 396961 CoA_binding CoA binding domain. This domain has a Rossmann fold and is found in a number of proteins including succinyl CoA synthetases, malate and ATP-citrate ligases. 97 matched cddid_all.tbl CDD pfam02630 pfam02630 460630 SCO1-SenC SCO1/SenC. This family is involved in biogenesis of respiratory and photosynthetic systems. SCO1 is required for a post-translational step in the accumulation of subunits COXI and COXII of cytochrome c oxidase. SenC is required for optimal cytochrome c oxidase activity and maximal induction of genes encoding the light-harvesting and reaction centre complexes of R. capsulatus. 134 matched cddid_all.tbl CDD pfam02631 pfam02631 460631 RecX RecX family. RecX is a putative bacterial regulatory protein. The gene encoding RecX is found downstream of recA, and is thought to interact with the RecA protein. 123 matched cddid_all.tbl CDD pfam02632 pfam02632 460632 BioY BioY family. A number of bacterial genes are involved in bioconversion of pimelate into dethiobiotin. BioY is a component of the BioMNY transport system involved in biotin uptake in prokaryotes. 139 matched cddid_all.tbl CDD pfam02633 pfam02633 426892 Creatininase Creatinine amidohydrolase. Creatinine amidohydrolase (EC:3.5.2.10), or creatininase, catalyzes the hydrolysis of creatinine to creatine. 226 matched cddid_all.tbl CDD pfam02634 pfam02634 460633 FdhD-NarQ FdhD/NarQ family. A pan-bacterial lineage of proteins. Nitrate assimilation protein, NarQ, and FdhD are required for formate dehydrogenase activity. Structurally, they possess a deaminase fold with a characteriztic binding pocket, suggesting that they might bind a nucleotide or related molecule allosterically to regulate the formate dehydrogenase catalytic subunit. 238 matched cddid_all.tbl CDD pfam02635 pfam02635 426894 DrsE DsrE/DsrF-like family. DsrE is a small soluble protein involved in intracellular sulfur reduction. This family also includes DsrF. 117 matched cddid_all.tbl CDD pfam02636 pfam02636 460634 Methyltransf_28 Putative S-adenosyl-L-methionine-dependent methyltransferase. This family is a putative S-adenosyl-L-methionine (SAM)-dependent methyltransferase. In eukaryotes it plays a role in mitochondrial complex I activity. 247 matched cddid_all.tbl CDD pfam02637 pfam02637 396969 GatB_Yqey GatB domain. This domain is found in GatB. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB, which transamidates Glu-tRNA to Gln-tRNA. 148 matched cddid_all.tbl CDD pfam02638 pfam02638 251441 GHL10 Glycosyl hydrolase-like 10. This is family of bacterial glycosyl-hydrolase-like proteins falling into the family GHL10 as described above,. 311 matched cddid_all.tbl CDD pfam02639 pfam02639 426896 DUF188 Uncharacterized BCR, YaiI/YqxD family COG1671. 130 matched cddid_all.tbl CDD pfam02641 pfam02641 460635 DUF190 Uncharacterized ACR, COG1993. 97 matched cddid_all.tbl CDD pfam02643 pfam02643 460636 DUF192 Uncharacterized ACR, COG1430. Two structures have been solved for members of this large (>500 members) family of bacterial proteins present mostly in environmental bacteria and metagenomes (distant homologs are also present in several Plasmodium species). TOPSAN analysis for pdb:3pjy shows that there is much similarity with the other solved structure, pdb:3m7a, solved for UniProt:Q2GA55 (Saro_0823), a homolog of Thermotoga maritima TM1668, UniProt:Q9X1Z6., The homolog in Caulobacter crescentus (CC1388), UniProt:Q9A8G6, is associated with CspD, a cold shock protein (CC1387), UniProt:Q9A8G7. However, the genomic context of UniProt:Q2GA55 is most conserved with a putative xylose isomerase, suggesting a possible role in extracellular sugar processing. Saro_0821, UniProt:Q2GA57, is annotated as an AMP-dependent synthetase and ligase. PDB:3m7a structure corresponds to the C-terminal (27-165) fragment of the YP_496102 (Saro_0823) protein and it is structurally unique, as the best hits from Dali have a Z-score of 3.8 (1nt0, 2j1t, 3kq4) and it is thus a likely candidate for a new fold. Interestingly, many of the top Dali hits are involved in sugar metabolism. There are no obvious active site-like cavities on the protein surface of 3m7a (http://www.topsan.org/Proteins/JCSG/). 104 matched cddid_all.tbl CDD pfam02645 pfam02645 426899 DegV Uncharacterized protein, DegV family COG1307. The structure of this protein revealed a bound fatty-acid molecule in a pocket between the two protein domains. The structure indicates that this family has the molecular function of fatty-acid binding and may play a role in the cellular functions of fatty acid transport or metabolism. 280 matched cddid_all.tbl CDD pfam02646 pfam02646 460637 RmuC RmuC family. This family contains several bacterial RmuC DNA recombination proteins. The function of the RMUC protein is unknown but it is suspected that it is either a structural protein that protects DNA against nuclease action, or is itself involved in DNA cleavage at the regions of DNA secondary structures 286 matched cddid_all.tbl CDD pfam02649 pfam02649 460638 GCHY-1 Type I GTP cyclohydrolase folE2. This is a family of prokaryotic proteins with type I GTP cyclohydrolase activity. GTP cyclohydrolase I is the first enzyme of the de novo tetrahydrofolate biosynthetic pathway present in bacteria, fungi, and plants, and encoded in Escherichia coli by the folE gene; it is also the first enzyme of the biopterin (BH4) pathway in Homo sapiens. The invariate, highly conserved glutamate residue at position 216 in Swiss:Q5F9K6 is likely to be the substrate ligand and the metal ligand is likely to be the cysteine at position 147. The enzyme is Zinc 2+ dependent. 262 matched cddid_all.tbl CDD pfam02650 pfam02650 460639 HTH_WhiA WhiA C-terminal HTH domain. This domain is found at the C-terminus of the sporulation regulator WhiA. It is predicted to form a DNA-binding helix-turn-helix structure. The WhiA protein also contains two N-terminal domains that are distant homologs of LAGLIDADG homing endonucleases. 83 matched cddid_all.tbl CDD pfam02652 pfam02652 280762 Lactate_perm L-lactate permease. L-lactate permease is an integral membrane protein probably involved in L-lactate transport. 522 matched cddid_all.tbl CDD pfam02653 pfam02653 396977 BPD_transp_2 Branched-chain amino acid transport system / permease component. This is a large family mainly comprising high-affinity branched-chain amino acid transporter proteins such as E. coli LivH and LivM, both of which are form the LIV-I transport system. Also found with in this family are proteins from the galactose transport system permease and a ribose transport system. 269 matched cddid_all.tbl CDD pfam02654 pfam02654 460640 CobS Cobalamin-5-phosphate synthase. This is family of Colbalmin-5-phosphate synthases, CobS, from bacteria. The CobS enzyme catalyzes the synthesis of AdoCbl-5'-p from AdoCbi-GDP and alpha-ribazole-5'-P. This enzyme is involved in the cobalamin (vitamin B12) biosynthesis pathway in particular the nucleotide loop assembly stage in conjunction with CobC, CobU and CobT. 215 matched cddid_all.tbl CDD pfam02655 pfam02655 396979 ATP-grasp_3 ATP-grasp domain. No functional information or experimental verification of function is known in this family. This family appears to be an ATP-grasp domain (Pers. obs. A Bateman). 160 matched cddid_all.tbl CDD pfam02656 pfam02656 396980 DUF202 Domain of unknown function (DUF202). This family consists of hypothetical proteins some of which are putative membrane proteins. No functional information or experimental verification of function is known. This domain is around 100 amino acids long. 68 matched cddid_all.tbl CDD pfam02657 pfam02657 426904 SufE Fe-S metabolism associated domain. This family consists of the SufE-related proteins. These have been implicated in Fe-S metabolism and export. 121 matched cddid_all.tbl CDD pfam02659 pfam02659 426905 Mntp Putative manganese efflux pump. MntP is a family of bacterial proteins with a signal peptide and four transmembrane domains. It is a putative manganese efflux pump, since deletion of the gene leads to profound manganese sensitivity and elevated intracellular manganese levels in bacteria. Manganese is a highly important trace nutrient for organizms from bacteria to humans, and acts as an important element in the defence against oxidative stress and as an enzyme cofactor. 152 matched cddid_all.tbl CDD pfam02660 pfam02660 460641 G3P_acyltransf Glycerol-3-phosphate acyltransferase. This family of enzymes catalyzes the transfer of an acyl group from acyl-ACP to glycerol-3-phosphate to form lysophosphatidic acid. 174 matched cddid_all.tbl CDD pfam02661 pfam02661 426907 Fic Fic/DOC family. This family consists of the Fic (filamentation induced by cAMP) protein and doc (death on curing). The Fic protein is involved in cell division and is suggested to be involved in the synthesis of PAB or folate, indicating that the Fic protein and cAMP are involved in a regulatory mechanism of cell division via folate metabolism. This family contains a central conserved motif HPFXXGNG in most members. The exact molecular function of these proteins is uncertain. P1 lysogens of Escherichia coli carry the prophage as a stable low copy number plasmid. The frequency with which viable cells cured of prophage are produced is about 10(-5) per cell per generation. A significant part of this remarkable stability can be attributed to a plasmid-encoded mechanism that causes death of cells that have lost P1. In other words, the lysogenic cells appear to be addicted to the presence of the prophage. The plasmid withdrawal response depends on a gene named doc (death on curing) that is represented by this family. Doc induces a reversible growth arrest of E. coli cells by targetting the protein synthesis machinery. Doc hosts the C-terminal domain of its antitoxin partner Phd (prevents host death) through fold complementation, a domain that is intrinsically disordered in solution but that folds into an alpha-helix on binding to Doc.This domain forms complexes with Phd antitoxins containing pfam02604. 94 matched cddid_all.tbl CDD pfam02662 pfam02662 460642 FlpD Methyl-viologen-reducing hydrogenase, delta subunit. This family consist of methyl-viologen-reducing hydrogenase, delta subunit / heterodisulphide reductase. No specific functions have been assigned to this subunit. The aligned region corresponds to almost the entire delta chain sequence and contains 4 conserved cysteine residues. However, in two Archaeoglobus sequences this region corresponds to only the C-terminus of these proteins Swiss:O29030 and Swiss:029595. 122 matched cddid_all.tbl CDD pfam02663 pfam02663 426909 FmdE FmdE, Molybdenum formylmethanofuran dehydrogenase operon. This entry represents the FmdE protein that is encode by the molybdenum formylmethanofuran dehydrogenase operon. FmdE does not co-purify with the molybdenum isozyme that is formed by FmdC and FmdB. The domain is typically found as a single copy, but is repeated in some sequence two to three times. It is also common place to find this domain co-occurs with a zinc-beta ribbon domain, suggesting that is may bind nucleic acid and be involved in transcription regulation. 89 matched cddid_all.tbl CDD pfam02664 pfam02664 426910 LuxS S-Ribosylhomocysteinase (LuxS). This family consists of the LuxS protein involved in autoinducer AI2 synthesis and its hypothetical relatives. S-ribosylhomocysteinase (LuxS) catalyzes the cleavage of the thioether bond in S-ribosylhomocysteine (SRH) to produce homocysteine and 4,5-dihydroxy-2,3-pentanedione (DPD), the precursor of type II bacterial quorum sensing molecule. 150 matched cddid_all.tbl CDD pfam02665 pfam02665 426911 Nitrate_red_gam Nitrate reductase gamma subunit. This family is the gamma subunit of the nitrate reductase enzyme, the gamma subunit is a b-type cytochrome that receives electrons from the quinone pool. It then transfers these via the iron-sulfur clusters of the beta subunit to the molybdenum cofactor found in the alpha subunit. The nitrate reductase enzyme, EC:1.7.99.4 catalyzes the conversion of nitrite to nitrate via the reduction of an acceptor. The nitrate reductase enzyme is composed of three subunits. Nitrate is the most widely used alternative electron acceptor after oxygen. 220 matched cddid_all.tbl CDD pfam02666 pfam02666 396989 PS_Dcarbxylase Phosphatidylserine decarboxylase. This is a family of phosphatidylserine decarboxylases, EC:4.1.1.65. These enzymes catalyze the reaction: Phosphatidyl-L-serine <=> phosphatidylethanolamine + CO2. Phosphatidylserine decarboxylase plays a central role in the biosynthesis of aminophospholipids by converting phosphatidylserine to phosphatidylethanolamine. 198 matched cddid_all.tbl CDD pfam02667 pfam02667 280776 SCFA_trans Short chain fatty acid transporter. This family consists of two sequences annotated as short chain fatty acid transporters, however, there are no references giving details of experimental characterization of this function. 453 matched cddid_all.tbl CDD pfam02668 pfam02668 367137 TauD Taurine catabolism dioxygenase TauD, TfdA family. This family consists of taurine catabolism dioxygenases of the TauD, TfdA family. TauD from E. coli is a alpha-ketoglutarate-dependent taurine dioxygenase. This enzyme catalyzes the oxygenolytic release of sulfite from taurine. TfdA from Burkholderia sp. is a 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase. TfdA from Alcaligenes eutrophus JMP134 is a 2,4-dichlorophenoxyacetate monooxygenase. Also included are gamma-Butyrobetaine hydroxylase enzymes EC:1.14.11.1. 264 matched cddid_all.tbl CDD pfam02669 pfam02669 460643 KdpC K+-transporting ATPase, c chain. This family consists of K+-transporting ATPase, c chain, KdpC. KdpC forms strong interactions with the KdpA subunit, serving to assemble and stabilize the Kdp complex. It has been suggested that KdpC could be one of the connecting links between the energy providing subunit KdpB and the K+-transporting subunit KdpA. The K+ transport system actively transports K+ ions via ATP hydrolysis. 179 matched cddid_all.tbl CDD pfam02670 pfam02670 460644 DXP_reductoisom 1-deoxy-D-xylulose 5-phosphate reductoisomerase. This is a family of 1-deoxy-D-xylulose 5-phosphate reductoisomerases. This enzyme catalyzes the formation of 2-C-methyl-D-erythritol 4-phosphate from 1-deoxy-D-xylulose-5-phosphate in the presence of NADPH. This reaction is part of the terpenoid biosynthesis pathway. 127 matched cddid_all.tbl CDD pfam02671 pfam02671 460645 PAH Paired amphipathic helix repeat. This family contains the paired amphipathic helix repeat. The family contains the yeast SIN3 gene (also known as SDI1) that is a negative regulator of the yeast HO gene. This repeat may be distantly related to the helix-loop-helix motif, which mediate protein-protein interactions. 45 matched cddid_all.tbl CDD pfam02672 pfam02672 426915 CP12 CP12 domain. The function of this domain is unknown, it does contain three conserved cysteines and a histidine, that suggests this may be a zinc binding domain (Bateman A pers. observation). This domain is found associated with CBS domains in some proteins pfam00571. 68 matched cddid_all.tbl CDD pfam02673 pfam02673 460646 BacA Bacitracin resistance protein BacA. Bacitracin resistance protein (BacA) is a putative undecaprenol kinase. BacA confers resistance to bacitracin, probably by phosphorylation of undecaprenol. More recent studies show that BacA has undecaprenyl pyrophosphate phosphatase activity. Undecaprenyl phosphate is a key lipid intermediate involved in the synthesis of various bacterial cell wall polymers. Bacitracin, a mixture of related cyclic polypeptide antibiotics, is used to treat surface tissue infections. Its primary mode of action is the inhibition of bacterial cell wall synthesis through sequestration of the essential carrier lipid undecaprenyl pyrophosphate, C55-PP, resulting in the loss of cell integrity and lysis. The characteriztic phosphatase sequence-motif in this family is likely to be the PGxSRSGG, compared with the PSGH of the PAP family of phosphatases. 259 matched cddid_all.tbl CDD pfam02674 pfam02674 460647 Colicin_V Colicin V production protein. Colicin V production protein is required in E. Coli for colicin V production from plasmid pColV-K30. This protein is coded for in the purF operon. 143 matched cddid_all.tbl CDD pfam02675 pfam02675 460648 AdoMet_dc S-adenosylmethionine decarboxylase. This family contains several S-adenosylmethionine decarboxylase proteins from bacterial and archaebacterial species. S-adenosylmethionine decarboxylase (AdoMetDC), a key enzyme in the biosynthesis of spermidine and spermine, is first synthesized as a proenzyme, which is cleaved post translationally to form alpha and beta subunits. The alpha subunit contains a covalently bound pyruvoyl group derived from serine that is essential for activity. 107 matched cddid_all.tbl CDD pfam02676 pfam02676 460649 TYW3 Methyltransferase TYW3. The methyltransferase TYW3 (tRNA-yW- synthesising protein 3) has been identified in yeast to be involved in wybutosine (yW) biosynthesis. yW is a complexly modified guanosine residue that contains a tricyclic base and is found at the 3' position adjacent the anticodon of phenylalanine tRNA. TYW3 is an N-4 methylase that methylates yW-86 to yield yW-72 in an Ado-Met-dependent manner. 206 matched cddid_all.tbl CDD pfam02677 pfam02677 460650 QueH Epoxyqueuosine reductase QueH. The reduction of epoxyqueuosine (oQ) is the last step in the synthesis of the tRNA modification queuosine (Q). members of this family were predicted to encode for an alternative epoxyqueuosine reductase. Furthermore, it has been suggested that family members are a non-orthologous replacement of queG, responsible for oQ to Q conversion. QueH contains conserved cysteines that could be involved in the coordination of a Fe/S center in a similar fashion to what has been identified in QueG. No cobalamin was identified associated with recombinant QueH protein, indicating that the reduction activity is independent from cobalamin. 175 matched cddid_all.tbl CDD pfam02678 pfam02678 426921 Pirin Pirin. This family consists of Pirin proteins from both eukaryotes and prokaryotes. The function of Pirin is unknown but the gene coding for this protein is known to be expressed in all tissues in the human body although it is expressed most strongly in the liver and heart. Pirin is known to be a nuclear protein, exclusively localized within the nucleoplasma and predominantly concentrated within dot-like subnuclear structures. A tomato homolog of human Pirin has been found to be induced during programmed cell death. Human Pirin interacts with Bcl-3 and NFI and hence is probably involved in the regulation of DNA transcription and replication. It appears to be an Fe(II)-containing member of the Cupin superfamily. 104 matched cddid_all.tbl CDD pfam02679 pfam02679 426922 ComA (2R)-phospho-3-sulfolactate synthase (ComA). In methanobacteria (2R)-phospho-3-sulfolactate synthase (ComA) catalyzes the first step of the biosynthesis of coenzyme M from phosphoenolpyruvate (P-enolpyruvate). This novel enzyme catalyzes the stereospecific Michael addition of sulfite to P-enolpyruvate, forming L-2-phospho-3-sulfolactate (PSL). It is suggested that the ComA-catalyzed reaction is analogous to those reactions catalyzed by beta-elimination enzymes that proceed through an enolate intermediate. 238 matched cddid_all.tbl CDD pfam02680 pfam02680 426923 DUF211 Uncharacterized ArCR, COG1888. 88 matched cddid_all.tbl CDD pfam02681 pfam02681 426924 DUF212 Divergent PAP2 family. This family is related to the pfam01569 family (personal obs: C Yeats). 134 matched cddid_all.tbl CDD pfam02682 pfam02682 426925 CT_C_D Carboxyltransferase domain, subdomain C and D. Urea carboxylase (UC) catalyzes a two-step, ATP- and biotin-dependent carboxylation reaction of urea. It is composed of biotin carboxylase (BC), carboxyltransferase (CT), and biotin carboxyl carrier protein (BCCP) domains. The CT domain of UC consists of four subdomains, named A, B, C and D. This domain covers the C and D subdomains of the CT domain. This domain covers the whole length of kipI (kinase A inhibitor) from Bacillus subtilis. It can also be found in S. cerevisiae urea amidolyase Dur1,2, which is a multifunctional biotin-dependent enzyme with domains for urea carboxylase and allophanate (urea carboxylate) hydrolase activity. 201 matched cddid_all.tbl CDD pfam02683 pfam02683 280792 DsbD Cytochrome C biogenesis protein transmembrane region. This family consists of the transmembrane (i.e. non-catalytic) region of Cytochrome C biogenesis proteins also known as disulphide interchange proteins. These proteins posses a protein disulphide isomerase like domain that is not found within the aligned region of this family. 213 matched cddid_all.tbl CDD pfam02684 pfam02684 397004 LpxB Lipid-A-disaccharide synthetase. This is a family of lipid-A-disaccharide synthetases, EC:2.4.2.128. These enzymes catalyze the reaction: UDP-2,3-bis(3-hydroxytetradecanoyl) glucosamine + 2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate <=> UDP + 2,3-bis(3-hydroxytetradecanoyl)-D-glucosaminyl-1,6 -beta-D-2,3-bis(3-hydroxytetradecanoyl)-beta-D-glucosaminyl 1-phosphate. These enzymes catalyze the fist disaccharide step in the synthesis of lipid-A-disaccharide. 374 matched cddid_all.tbl CDD pfam02685 pfam02685 397005 Glucokinase Glucokinase. This is a family of glucokinases or glucose kinases EC:2.7.1.2. These enzymes phosphorylate glucose using ATP as a donor to give glucose-6-phosphate and ADP. 314 matched cddid_all.tbl CDD pfam02686 pfam02686 460651 Glu-tRNAGln Glu-tRNAGln amidotransferase C subunit. This is a family of Glu-tRNAGln amidotransferase C subunits. The Glu-tRNA Gln amidotransferase enzyme itself is an important translational fidelity mechanism replacing incorrectly charged Glu-tRNAGln with the correct Gln-tRANGln via transmidation of the misacylated Glu-tRNAGln. This activity supplements the lack of glutaminyl-tRNA synthetase activity in gram-positive eubacterteria, cyanobacteria, Archaea, and organelles. 70 matched cddid_all.tbl CDD pfam02687 pfam02687 460652 FtsX FtsX-like permease family. This is a family of predicted permeases and hypothetical transmembrane proteins. Swiss:P57382 has been shown to transport lipids targeted to the outer membrane across the inner membrane. Both Swiss:P57382 and Swiss:O54500 have been shown to require ATP. This region contains three transmembrane helices. 120 matched cddid_all.tbl CDD pfam02689 pfam02689 280797 Herpes_Helicase Helicase. This family consists of Helicases from the Herpes viruses. Helicases are responsible for the unwinding of DNA and are essential for replication and completion of the viral life cycle. 809 matched cddid_all.tbl CDD pfam02690 pfam02690 460653 Na_Pi_cotrans Na+/Pi-cotransporter. This is a family of mainly mammalian type II renal Na+/Pi-cotransporters with other related sequences from lower eukaryotes and bacteria some of which are also Na+/Pi-cotransporters. In the kidney the type II renal Na+/Pi-cotransporters protein allows re-absorption of filtered Pi in the proximal tubule. 137 matched cddid_all.tbl CDD pfam02691 pfam02691 111576 VacA Vacuolating cyotoxin. This family consists of Vacuolating cyotoxin proteins form Proteobacteria. These proteins are an important virulence determinate in H. pylori and induce cytoplasmic vacuolation in a variety of mammalian cell lines. 1002 matched cddid_all.tbl CDD pfam02694 pfam02694 111577 UPF0060 Uncharacterized BCR, YnfA/UPF0060 family. Some members of this family have been proposed to function as a thallium-specific efflux pump. 107 matched cddid_all.tbl CDD pfam02696 pfam02696 426929 SelO Protein adenylyltransferase SelO. SelO and its homologs are widespread among most eukaryotic taxa, and are also common in many major bacterial taxa. SelO is a conserved pseudokinase that transfers AMP from ATP to Ser, Thr, and Tyr residues on protein substrates (AMPylation). It contains a protein kinase fold with ATP flipped in the active site. In eukaryotes, it is a mitochondrial protein that may be involved in redox biology. 459 matched cddid_all.tbl CDD pfam02697 pfam02697 397010 VAPB_antitox Putative antitoxin. Proteins in this family are possibly the antitoxin component of a VAPBC-like toxin-antitoxin (TA) module, which is widespread in the in both archaea and bacteria. 69 matched cddid_all.tbl CDD pfam02698 pfam02698 460654 DUF218 DUF218 domain. This large family of proteins contains several highly conserved charged amino acids, suggesting this may be an enzymatic domain (Bateman A pers. obs). The family includes SanA, which is involved in Vancomycin resistance. This protein may be involved in murein synthesis. 138 matched cddid_all.tbl CDD pfam02699 pfam02699 460655 YajC Preprotein translocase subunit. See. 78 matched cddid_all.tbl CDD pfam02700 pfam02700 426932 PurS Phosphoribosylformylglycinamidine (FGAM) synthase. This family forms a component of the de novo purine biosynthesis pathway. 77 matched cddid_all.tbl CDD pfam02701 pfam02701 397014 zf-Dof Dof domain, zinc finger. The Dof domain is a zinc finger DNA-binding domain, that shows resemblance to the Cys2 zinc finger. 57 matched cddid_all.tbl CDD pfam02702 pfam02702 460656 KdpD Osmosensitive K+ channel His kinase sensor domain. This is a family of KdpD sensor kinase proteins that regulate the kdpFABC operon responsible for potassium transport. The aligned region corresponds to the N-terminal cytoplasmic part of the protein which functions as the sensor domain responsible for sensing turgor pressure. It recognizes C-di-AMP and K+ (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 210 matched cddid_all.tbl CDD pfam02703 pfam02703 308370 Adeno_E1A Early E1A protein. This is a family of adenovirus early E1A proteins. The E1A protein is 32 kDa it can however be cleaved to yield the 28 kDa protein. The E1A protein is responsible for the transcriptional activation of the early genes with in the viral genome at the start of the infection process as well as some cellular genes. 289 matched cddid_all.tbl CDD pfam02704 pfam02704 460657 GASA Gibberellin regulated protein. This is the GASA gibberellin regulated cysteine rich protein family. The expression of these proteins is up-regulated by the plant hormone gibberellin, most of these proteins have some role in plant development. There are 12 cysteine residues conserved within the alignment giving the potential for these proteins to posses 6 disulphide bonds. 60 matched cddid_all.tbl CDD pfam02705 pfam02705 426935 K_trans K+ potassium transporter. This is a family of K+ potassium transporters that are conserved across phyla, having both bacterial (KUP), yeast (HAK), and plant (AtKT) sequences as members. 534 matched cddid_all.tbl CDD pfam02706 pfam02706 460658 Wzz Chain length determinant protein. This family includes proteins involved in lipopolysaccharide (lps) biosynthesis. This family comprises the whole length of chain length determinant protein (or wzz protein) that confers a modal distribution of chain length on the O-antigen component of lps. This region is also found as part of bacterial tyrosine kinases. 90 matched cddid_all.tbl CDD pfam02707 pfam02707 280810 MOSP_N Major Outer Sheath Protein N-terminal region. This is a family of spirochete major outer sheath protein N-terminal regions. These proteins are present on the bacterial cell surface. In T. denticola the major outer sheath protein (Msp) binds immobilized laminin and fibronectin supporting the hypothesis that Msp mediates the extracellular matrix binding activity of T. denticola. 196 matched cddid_all.tbl CDD pfam02709 pfam02709 460659 Glyco_transf_7C N-terminal domain of galactosyltransferase. This is the N-terminal domain of a family of galactosyltransferases from a wide range of Metazoa with three related galactosyltransferases activities, all three of which are possessed by one sequence in some cases. EC:2.4.1.90, N-acetyllactosamine synthase; EC:2.4.1.38, Beta-N-acetylglucosaminyl-glycopeptide beta-1,4- galactosyltransferase; and EC:2.4.1.22 Lactose synthase. Note that N-acetyllactosamine synthase is a component of Lactose synthase along with alpha-lactalbumin, in the absence of alpha-lactalbumin EC:2.4.1.90 is the catalyzed reaction. 78 matched cddid_all.tbl CDD pfam02710 pfam02710 397019 Hema_HEFG Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein. 155 matched cddid_all.tbl CDD pfam02711 pfam02711 367150 Pap_E4 E4 protein. This is is a family of Papillomavirus proteins, E4, coded for by ORF4. A splice variant, E1--E4, exists but neither the function of E4 or E1--E4 is known. 95 matched cddid_all.tbl CDD pfam02713 pfam02713 460660 DUF220 Domain of unknown function DUF220. This is family consists of a region in several Arabidopsis thaliana hypothetical proteins none of which have any known function. The aligned region contains two cysteine residues. This domain shows structural similarity to members of the Bet v1-like superfamily and may be involved in lipid binding. 73 matched cddid_all.tbl CDD pfam02714 pfam02714 460661 RSN1_7TM Calcium-dependent channel, 7TM region, putative phosphate. RSN1_7TM is the seven transmembrane domain region of putative phosphate transporter. The family is the 7TM region of osmosensitive calcium-permeable cation channels. 273 matched cddid_all.tbl CDD pfam02718 pfam02718 397022 Herpes_UL31 Herpesvirus UL31-like protein. This is a family of Herpesvirus proteins including UL31, UL53, and the product of ORF 69 in some strains. The proteins in this family have no known function. 251 matched cddid_all.tbl CDD pfam02719 pfam02719 426938 Polysacc_synt_2 Polysaccharide biosynthesis protein. This is a family of diverse bacterial polysaccharide biosynthesis proteins including the CapD protein, WalL protein mannosyl-transferase and several putative epimerases (e.g. WbiI). 284 matched cddid_all.tbl CDD pfam02720 pfam02720 397024 DUF222 Domain of unknown function (DUF222). This family is often found associated to the N-terminus of the HNH endonuclease domain pfam01844. The function of this domain is uncertain. This family has been called the 13E12 repeat family. 305 matched cddid_all.tbl CDD pfam02721 pfam02721 145722 DUF223 Domain of unknown function DUF223. 95 matched cddid_all.tbl CDD pfam02722 pfam02722 280819 MOSP_C Major Outer Sheath Protein C-terminal domain. This is a family of spirochete major outer sheath protein C-terminal regions. These proteins are present on the bacterial cell surface. In T. denticola the major outer sheath protein (Msp) binds immobilized laminin and fibronectin supporting the hypothesis that Msp mediates the extracellular matrix binding activity of T. denticola. This domain forms an amphipathic beta rich structure with channel forming activity. 205 matched cddid_all.tbl CDD pfam02723 pfam02723 460662 CoV_E Coronavirus small envelope protein E. This family includes E proteins, well conserved among Coronavirus strains. They are small, integral membrane proteins involved in several aspects of the virus' life cycle, such as assembly, budding, envelope formation, and pathogenesis. They act as a viroporin by oligomerizing after insertion in host membranes to create a hydrophilic pore that allows ion transport,. SARS-CoV E protein forms a Ca2+ permeable channel in the endoplasmic reticulum Golgi apparatus intermediate compartment (ERGIC)/Golgi membranes. The E protein ion channel activity alters Ca2+ homeostasis within cells boosting the activation of the NLRP3 inflammasome, leading to the overproduction of IL-beta. SARS-CoV overstimulates the NF-kappaB inflammatory pathway, triggering p38 MARK activation. 75 matched cddid_all.tbl CDD pfam02724 pfam02724 460663 CDC45 CDC45-like protein. CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. homologs of CDC45 have been identified in human, mouse and smut fungus among others. 529 matched cddid_all.tbl CDD pfam02725 pfam02725 460664 Paramyxo_NS_C Non-structural protein C. This family consists of the polymerase accessory protein C from members of the paramyxoviridae. 164 matched cddid_all.tbl CDD pfam02727 pfam02727 397027 Cu_amine_oxidN2 Copper amine oxidase, N2 domain. This domain is the first or second structural domain in copper amine oxidases, it is known as the N2 domain. Its function is uncertain. The catalytic domain can be found in pfam01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). 87 matched cddid_all.tbl CDD pfam02728 pfam02728 426941 Cu_amine_oxidN3 Copper amine oxidase, N3 domain. This domain is the second or third structural domain in copper amine oxidases, it is known as the N3 domain. Its function is uncertain. The catalytic domain can be found in pfam01179. Copper amine oxidases are a ubiquitous and novel group of quinoenzymes that catalyze the oxidative deamination of primary amines to the corresponding aldehydes, with concomitant reduction of molecular oxygen to hydrogen peroxide. The enzymes are dimers of identical 70-90 kDa subunits, each of which contains a single copper ion and a covalently bound cofactor formed by the post-translational modification of a tyrosine side chain to 2,4,5-trihydroxyphenylalanine quinone (TPQ). 100 matched cddid_all.tbl CDD pfam02729 pfam02729 460665 OTCace_N Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain. 140 matched cddid_all.tbl CDD pfam02730 pfam02730 426943 AFOR_N Aldehyde ferredoxin oxidoreductase, N-terminal domain. Aldehyde ferredoxin oxidoreductase (AOR) catalyzes the reversible oxidation of aldehydes to their corresponding carboxylic acids with their accompanying reduction of the redox protein ferredoxin. This domain interacts with the tungsten cofactor. 199 matched cddid_all.tbl CDD pfam02731 pfam02731 460666 SKIP_SNW SKIP/SNW domain. This domain is found in chromatin proteins. 152 matched cddid_all.tbl CDD pfam02732 pfam02732 426945 ERCC4 ERCC4 domain. This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase. EME1 interacts with MUS81 to form a DNA structure-specific endonuclease. 139 matched cddid_all.tbl CDD pfam02733 pfam02733 460667 Dak1 Dak1 domain. This is the kinase domain of the dihydroxyacetone kinase family EC:2.7.1.29. 312 matched cddid_all.tbl CDD pfam02734 pfam02734 460668 Dak2 DAK2 domain. This domain is the predicted phosphatase domain of the dihydroxyacetone kinase family. 175 matched cddid_all.tbl CDD pfam02735 pfam02735 460669 Ku Ku70/Ku80 beta-barrel domain. The Ku heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-binding beta-barrel domain. This domain is found in both the Ku70 and Ku80 proteins that form a DNA binding heterodimer. 197 matched cddid_all.tbl CDD pfam02736 pfam02736 460670 Myosin_N Myosin N-terminal SH3-like domain. This domain has an SH3-like fold. It is found at the N-terminus of many but not all myosins. The function of this domain is unknown. 45 matched cddid_all.tbl CDD pfam02737 pfam02737 397037 3HCDH_N 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain. This family also includes lambda crystallin. 180 matched cddid_all.tbl CDD pfam02738 pfam02738 460671 MoCoBD_1 Molybdopterin cofactor-binding domain. 244 matched cddid_all.tbl CDD pfam02739 pfam02739 460672 5_3_exonuc_N 5'-3' exonuclease, N-terminal resolvase-like domain. 163 matched cddid_all.tbl CDD pfam02740 pfam02740 426952 Colipase_C Colipase, C-terminal domain. SCOP reports duplication of common fold with Colipase N-terminal domain. 44 matched cddid_all.tbl CDD pfam02741 pfam02741 426953 FTR_C FTR, proximal lobe. The FTR (Formylmethanofuran--tetrahydromethanopterin formyltransferase) enzyme EC:2.3.1.101 is involved in archaebacteria in the formation of methane from carbon dioxide. C-terminal proximal lobe of alpha+beta ferredoxin-like fold. SCOP reports fold duplication with N-terminal distal lobe. 149 matched cddid_all.tbl CDD pfam02742 pfam02742 426954 Fe_dep_repr_C Iron dependent repressor, metal binding and dimerization domain. This family includes the Diphtheria toxin repressor. It acts as an iron-binding repressor of diphtheria toxin gene expression and may serve as a global regulator of gene expression. DTXR comprises an N-terminal DNA-binding domain, an interface domain (which contains two metal-binding sites) and a third, very flexible C-terminal domain. The second domain is responsible for dimerization and metal binding. Binding of DTXR to Tox operator requires a divalent metal ion such as cobalt, ferric, manganese and nickel whereas zinc shows weak activation. This domain can also bind Cd(II), Ca(II) and Cu(II) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 69 matched cddid_all.tbl CDD pfam02743 pfam02743 460673 dCache_1 Cache domain. Double cache domain 1 covers the last three strands from the membrane distal PAS-like domain, the first two strands of the membrane proximal domain, and the connecting elements between the two domains. This domain when present in chemoreceptors recognize several signals such as proteinogenic amino acids, GABA, Histamine and polyamines, decanoic acid, Autoinducer-2, purine derivatives, quaternary amines, citrate and taurine, among others. When associated with histidine kinases, it recognizes C3/C4-dicarboxylic acids, Spermine, guanosine and Autoinducer-2 (Mantilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1 https://doi.org/10.1093/femsre/fuab043). 237 matched cddid_all.tbl CDD pfam02744 pfam02744 397044 GalP_UDP_tr_C Galactose-1-phosphate uridyl transferase, C-terminal domain. SCOP reports fold duplication with N-terminal domain. Both involved in Zn and Fe binding. 166 matched cddid_all.tbl CDD pfam02745 pfam02745 397045 MCR_alpha_N Methyl-coenzyme M reductase alpha subunit, N-terminal domain. Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (this family), 2 beta (pfam02241), and 2 gamma (pfam02240) subunits with two identical nickel porphinoid active sites. The N-terminal domain has a ferredoxin-like fold. 269 matched cddid_all.tbl CDD pfam02746 pfam02746 397046 MR_MLE_N Mandelate racemase / muconate lactonizing enzyme, N-terminal domain. SCOP reports fold similarity with enolase N-terminal domain. 117 matched cddid_all.tbl CDD pfam02747 pfam02747 280843 PCNA_C Proliferating cell nuclear antigen, C-terminal domain. N-terminal and C-terminal domains of PCNA are topologically identical. Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA. 128 matched cddid_all.tbl CDD pfam02748 pfam02748 426956 PyrI_C Aspartate carbamoyltransferase regulatory chain, metal binding domain. The regulatory chain is involved in allosteric regulation of aspartate carbamoyltransferase. The C-terminal metal binding domain has a rubredoxin-like fold and provides the interface with the catalytic chain. 45 matched cddid_all.tbl CDD pfam02749 pfam02749 460674 QRPTase_N Quinolinate phosphoribosyl transferase, N-terminal domain. Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase EC:2.4.2.19 is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyzes the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide. The QA substrate is bound between the C-terminal domain of one subunit, and the N-terminal domain of the other. The N-terminal domain has an alpha/beta hammerhead fold. 88 matched cddid_all.tbl CDD pfam02750 pfam02750 308403 Synapsin_C Synapsin, ATP binding domain. Ca dependent ATP binding in this ATP grasp fold. Function unknown. 203 matched cddid_all.tbl CDD pfam02751 pfam02751 460675 TFIIA_gamma_C Transcription initiation factor IIA, gamma subunit. Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA box. The C-terminal domain of the gamma subunit is a 12 stranded beta-barrel. 43 matched cddid_all.tbl CDD pfam02752 pfam02752 460676 Arrestin_C Arrestin (or S-antigen), C-terminal domain. Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain. 135 matched cddid_all.tbl CDD pfam02753 pfam02753 426960 PapD_C Pili assembly chaperone PapD, C-terminal domain. Ig-like beta-sandwich fold. This domain is the C-terminal part of the pilus and flagellar-assembly chaperone protein PapD. 63 matched cddid_all.tbl CDD pfam02754 pfam02754 397052 CCG Cysteine-rich domain. The key element of this family is the CX31-38CCX33-34CXXC sequence motif normally found at the C-terminus in archaeal and bacterial Hdr-like proteins. There may be one or two copies, and the motif is probably an iron-sulfur binding cluster. In some instances one of the cysteines is replaced by an aspartate, and aspartate can in principle also function as a ligand of an iron-sulfur cluster. The family includes a subunit from heterodisulphide reductase and a subunit from glycolate oxidase and glycerol-3-phosphate dehydrogenase. 84 matched cddid_all.tbl CDD pfam02755 pfam02755 460677 RPEL RPEL repeat. The RPEL repeat is named after four conserved amino acids it contains. The RPEL motif binds to actin. 24 matched cddid_all.tbl CDD pfam02756 pfam02756 426962 GYR GYR motif. The GYR motif is found in several drosophila proteins. Its function is unknown, however the presence of completely conserved tyrosine residues may suggest it could be a substrate for tyrosine kinases. 18 matched cddid_all.tbl CDD pfam02757 pfam02757 426963 YLP YLP motif. The YLP motif is found in several drosophila proteins. Its function is unknown, however the presence of completely conserved tyrosine residues and its presence in Swiss:Q15303 may suggest it could be a substrate for tyrosine kinases. 9 matched cddid_all.tbl CDD pfam02758 pfam02758 460678 PYRIN PAAD/DAPIN/Pyrin domain. This domain is predicted to contain 6 alpha helices and to have the same fold as the pfam00531 domain. This similarity may mean that this is a protein-protein interaction domain. 76 matched cddid_all.tbl CDD pfam02759 pfam02759 460679 RUN RUN domain. This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases. 134 matched cddid_all.tbl CDD pfam02760 pfam02760 460680 HIN HIN-200/IF120x domain. This domain has no know function. It is found in one or two copies per protein, and is found associated with the PAAD/DAPIN domain pfam02758. 168 matched cddid_all.tbl CDD pfam02761 pfam02761 460681 Cbl_N2 CBL proto-oncogene N-terminus, EF hand-like domain. Cbl is an adaptor protein that binds EGF receptors (or other tyrosine kinases) and SH3 domains, functioning as a negative regulator of many signaling pathways. The N-terminal domain is evolutionarily conserved, and is known to bind to phosphorylated tyrosine residues. The so called N-terminal domain is actually 3 structural domains, of which this is the central EF hand domain. 84 matched cddid_all.tbl CDD pfam02762 pfam02762 460682 Cbl_N3 CBL proto-oncogene N-terminus, SH2-like domain. Cbl is an adaptor protein that binds EGF receptors (or other tyrosine kinases) and SH3 domains, functioning as a negative regulator of many signaling pathways. The N-terminal domain is evolutionarily conserved, and is known to bind to phosphorylated tyrosine residues. The so called N-terminal domain is actually 3 structural domains, of which this is the C-terminal SH2 domain. 86 matched cddid_all.tbl CDD pfam02763 pfam02763 397059 Diphtheria_C Diphtheria toxin, C domain. N-terminal catalytic (C) domain - blocks protein synthesis by transfer of ADP-ribose from NAD to a diphthamide residue of EF-2. 187 matched cddid_all.tbl CDD pfam02764 pfam02764 460683 Diphtheria_T Diphtheria toxin, T domain. Central domain of diphtheria toxin is the translocation (T) domain. pH induced conformational change in this domain triggers insertion into the endosomal membrane and facilitates the transfer of the catalytic domain into the cytoplasm. 161 matched cddid_all.tbl CDD pfam02765 pfam02765 397060 POT1 Telomeric single stranded DNA binding POT1/CDC13. This domain binds single stranded telomeric DNA and adopts an OB fold. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping. POT1 is one component of the shelterin complex that protects telomere-ends from attack by DNA-repair mechanisms. 140 matched cddid_all.tbl CDD pfam02767 pfam02767 397061 DNA_pol3_beta_2 DNA polymerase III beta subunit, central domain. A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold. 115 matched cddid_all.tbl CDD pfam02768 pfam02768 426968 DNA_pol3_beta_3 DNA polymerase III beta subunit, C-terminal domain. A dimer of the beta subunit of DNA polymerase beta forms a ring which encircles duplex DNA. Each monomer contains three domains of identical topology and DNA clamp fold. 118 matched cddid_all.tbl CDD pfam02769 pfam02769 460684 AIRS_C AIR synthase related protein, C-terminal domain. This family includes Hydrogen expression/formation protein HypE, AIR synthases EC:6.3.3.1, FGAM synthase EC:6.3.5.3 and selenide, water dikinase EC:2.7.9.3. The function of the C-terminal domain of AIR synthase is unclear, but the cleft formed between N and C domains is postulated as a sulphate binding site. 152 matched cddid_all.tbl CDD pfam02770 pfam02770 460685 Acyl-CoA_dh_M Acyl-CoA dehydrogenase, middle domain. Central domain of Acyl-CoA dehydrogenase has a beta-barrel fold. 95 matched cddid_all.tbl CDD pfam02771 pfam02771 460686 Acyl-CoA_dh_N Acyl-CoA dehydrogenase, N-terminal domain. The N-terminal domain of Acyl-CoA dehydrogenase is an all-alpha domain. 113 matched cddid_all.tbl CDD pfam02772 pfam02772 460687 S-AdoMet_synt_M S-adenosylmethionine synthetase, central domain. The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold. 118 matched cddid_all.tbl CDD pfam02773 pfam02773 460688 S-AdoMet_synt_C S-adenosylmethionine synthetase, C-terminal domain. The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold. 138 matched cddid_all.tbl CDD pfam02774 pfam02774 397067 Semialdhyde_dhC Semialdehyde dehydrogenase, dimerization domain. This Pfam entry contains the following members: N-acetyl-glutamine semialdehyde dehydrogenase (AgrC) Aspartate-semialdehyde dehydrogenase. 167 matched cddid_all.tbl CDD pfam02775 pfam02775 460689 TPP_enzyme_C Thiamine pyrophosphate enzyme, C-terminal TPP binding domain. 151 matched cddid_all.tbl CDD pfam02776 pfam02776 460690 TPP_enzyme_N Thiamine pyrophosphate enzyme, N-terminal TPP binding domain. 169 matched cddid_all.tbl CDD pfam02777 pfam02777 460691 Sod_Fe_C Iron/manganese superoxide dismutases, C-terminal domain. superoxide dismutases (SODs) catalyze the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the Mn/Fe-binding family is one. In humans, there is a cytoplasmic Cu/Zn SOD, and a mitochondrial Mn/Fe SOD. C-terminal domain is a mixed alpha/beta fold. 102 matched cddid_all.tbl CDD pfam02778 pfam02778 397071 tRNA_int_endo_N tRNA intron endonuclease, N-terminal domain. Members of this family cleave pre tRNA at the 5' and 3' splice sites to release the intron EC:3.1.27.9. 67 matched cddid_all.tbl CDD pfam02779 pfam02779 460692 Transket_pyr Transketolase, pyrimidine binding domain. This family includes transketolase enzymes, pyruvate dehydrogenases, and branched chain alpha-keto acid decarboxylases. 174 matched cddid_all.tbl CDD pfam02780 pfam02780 460693 Transketolase_C Transketolase, C-terminal domain. The C-terminal domain of transketolase has been proposed as a regulatory molecule binding site. 124 matched cddid_all.tbl CDD pfam02781 pfam02781 460694 G6PD_C Glucose-6-phosphate dehydrogenase, C-terminal domain. 295 matched cddid_all.tbl CDD pfam02782 pfam02782 426979 FGGY_C FGGY family of carbohydrate kinases, C-terminal domain. This domain adopts a ribonuclease H-like fold and is structurally related to the N-terminal domain. 197 matched cddid_all.tbl CDD pfam02783 pfam02783 426980 MCR_beta_N Methyl-coenzyme M reductase beta subunit, N-terminal domain. Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (pfam02249), 2 beta (this family), and 2 gamma (pfam02240) subunits with two identical nickel porphinoid active sites. The N-terminal domain has an alpha/beta ferredoxin-like fold. 182 matched cddid_all.tbl CDD pfam02784 pfam02784 397077 Orn_Arg_deC_N Pyridoxal-dependent decarboxylase, pyridoxal binding domain. These pyridoxal-dependent decarboxylases acting on ornithine, lysine, arginine and related substrates This domain has a TIM barrel fold. 241 matched cddid_all.tbl CDD pfam02785 pfam02785 426981 Biotin_carb_C Biotin carboxylase C-terminal domain. Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyzes the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference are in this C-terminal domain. 108 matched cddid_all.tbl CDD pfam02786 pfam02786 397079 CPSase_L_D2 Carbamoyl-phosphate synthase L chain, ATP binding domain. Carbamoyl-phosphate synthase catalyzes the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesize carbamoyl phosphate. See pfam00988. The small chain has a GATase domain in the carboxyl terminus. See pfam00117. The ATP binding domain (this one) has an ATP-grasp fold. 209 matched cddid_all.tbl CDD pfam02787 pfam02787 460695 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerization domain. Carbamoyl-phosphate synthase catalyzes the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. 79 matched cddid_all.tbl CDD pfam02788 pfam02788 426983 RuBisCO_large_N Ribulose bisphosphate carboxylase large chain, N-terminal domain. The N-terminal domain of RuBisCO large chain adopts a ferredoxin-like fold. 120 matched cddid_all.tbl CDD pfam02789 pfam02789 426984 Peptidase_M17_N Cytosol aminopeptidase family, N-terminal domain. 127 matched cddid_all.tbl CDD pfam02790 pfam02790 397083 COX2_TM Cytochrome C oxidase subunit II, transmembrane domain. The N-terminal domain of cytochrome C oxidase contains two transmembrane alpha-helices. 89 matched cddid_all.tbl CDD pfam02791 pfam02791 460696 DDT DDT domain. The DDT domain is named after (DNA binding homeobox and Different Transcription factors) and is approximately 60 residues in length. Along with the WHIM motifs, it comprises an entirely alpha helical module found in diverse eukaryotic chromatin proteins. Based on the structure of Ioc3, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. In particular, the DDT domain, in combination with the WHIM1 and WHIM2 motifs form the SLIDE domain binding pocket. 58 matched cddid_all.tbl CDD pfam02792 pfam02792 460697 Mago_nashi Mago nashi protein. This family was originally identified in Drosophila and called mago nashi, it is a strict maternal effect, grandchildless-like, gene. The human homolog has been shown to interact with an RNA binding protein. An RNAi knockout of the C. elegans homolog causes masculinization of the germ line (Mog phenotype) hermaphrodites, suggesting it is involved in hermaphrodite germ-line sex determination. Mago nashi has been found to be part of the exon-exon junction complex that binds 20 nucleotides upstream of exon-exon junctions. 142 matched cddid_all.tbl CDD pfam02793 pfam02793 397086 HRM Hormone receptor domain. This extracellular domain contains four conserved cysteines that probably for disulphide bridges. The domain is found in a variety of hormone receptors. It may be a ligand binding domain. 64 matched cddid_all.tbl CDD pfam02794 pfam02794 426986 HlyC RTX toxin acyltransferase family. Members of this family are enzymes EC:2.3.1.-. involved in fatty acylation of the protoxins (HlyA) at lysine residues, thereby converting them to the active toxin. Acyl-acyl carrier protein (ACP) is the essential acyl donor. This family show a number of conserved residues that are possible candidates for participation in acyl transfer. Site-directed mutagenesis of the single conserved histidine residue in Swiss:P06736 resulted in complete inactivation of the enzyme. 127 matched cddid_all.tbl CDD pfam02796 pfam02796 397088 HTH_7 Helix-turn-helix domain of resolvase. 45 matched cddid_all.tbl CDD pfam02797 pfam02797 397089 Chal_sti_synt_C Chalcone and stilbene synthases, C-terminal domain. This domain of chalcone synthase is reported to be structurally similar to domains in thiolase and beta-ketoacyl synthase. The differences in activity are accounted for by differences in the N-terminal domain. 151 matched cddid_all.tbl CDD pfam02798 pfam02798 460698 GST_N Glutathione S-transferase, N-terminal domain. Function: conjugation of reduced glutathione to a variety of targets. Also included in the alignment, but not GSTs: S-crystallins from squid (similarity to GST previously noted); eukaryotic elongation factors 1-gamma (not known to have GST activity and similarity not previously recognized); HSP26 family of stress-related proteins including auxin-regulated proteins in plants and stringent starvation proteins in E. coli (not known to have GST activity and similarity not previously recognized). The glutathione molecule binds in a cleft between the N- and C-terminal domains - the catalytically important residues are proposed to reside in the N-terminal domain. 76 matched cddid_all.tbl CDD pfam02799 pfam02799 460699 NMT_C Myristoyl-CoA:protein N-myristoyltransferase, C-terminal domain. The N and C-terminal domains of NMT are structurally similar, each adopting an acyl-CoA N-acyltransferase-like fold. 194 matched cddid_all.tbl CDD pfam02800 pfam02800 460700 Gp_dh_C Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain. GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. C-terminal domain is a mixed alpha/antiparallel beta fold. 158 matched cddid_all.tbl CDD pfam02801 pfam02801 426989 Ketoacyl-synt_C Beta-ketoacyl synthase, C-terminal domain. The structure of beta-ketoacyl synthase is similar to that of the thiolase family (pfam00108) and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains. 118 matched cddid_all.tbl CDD pfam02803 pfam02803 397094 Thiolase_C Thiolase, C-terminal domain. Thiolase is reported to be structurally related to beta-ketoacyl synthase (pfam00109), and also chalcone synthase. 123 matched cddid_all.tbl CDD pfam02805 pfam02805 460701 Ada_Zn_binding Metal binding domain of Ada. The Escherichia coli Ada protein repairs O6-methylguanine residues and methyl phosphotriesters in DNA by direct transfer of the methyl group to a cysteine residue. This domain contains four conserved cysteines that form a zinc binding site. One of these cysteines is a methyl group acceptor. The methylated domain can then specifically bind to the ada box on a DNA duplex. 62 matched cddid_all.tbl CDD pfam02806 pfam02806 426991 Alpha-amylase_C Alpha amylase, C-terminal all-beta domain. Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain. 94 matched cddid_all.tbl CDD pfam02807 pfam02807 460702 ATP-gua_PtransN ATP:guanido phosphotransferase, N-terminal domain. The N-terminal domain has an all-alpha fold. 67 matched cddid_all.tbl CDD pfam02809 pfam02809 460703 UIM Ubiquitin interaction motif. This motif is called the ubiquitin interaction motif. One of the proteins containing this motif is a receptor for poly-ubiquitination chains for the proteasome. This motif has a pattern of conservation characteriztic of an alpha helix. 17 matched cddid_all.tbl CDD pfam02810 pfam02810 460704 SEC-C SEC-C motif. The SEC-C motif found in the C-terminus of the SecA protein, in the middle of some SWI2 ATPases and also solo in several proteins. The motif is predicted to chelate zinc with the CXC and C[HC] pairs that constitute the most conserved feature of the motif. It is predicted to be a potential nucleic acid binding domain. 19 matched cddid_all.tbl CDD pfam02811 pfam02811 460705 PHP PHP domain. The PHP (Polymerase and Histidinol Phosphatase) domain is a putative phosphoesterase domain. 171 matched cddid_all.tbl CDD pfam02812 pfam02812 460706 ELFV_dehydrog_N Glu/Leu/Phe/Val dehydrogenase, dimerization domain. 129 matched cddid_all.tbl CDD pfam02813 pfam02813 460707 Retro_M Retroviral M domain. Retroviruses contain a small protein, MA (matrix), which forms a protein lining immediately beneath the phospholipid membrane of the mature virus particle. MA is located in the N-terminal region of the Gag precursor polyprotein. The N-terminal segment of MA proteins directs the Gag protein to the plasma membrane where budding takes place, and has been called the M domain. This domain forms an alpha helical bundle structure. 86 matched cddid_all.tbl CDD pfam02814 pfam02814 460708 UreE_N UreE urease accessory protein, N-terminal domain. UreE is a urease accessory protein. Urease pfam00449 hydrolyses urea into ammonia and carbamic acid. 62 matched cddid_all.tbl CDD pfam02815 pfam02815 397103 MIR MIR domain. The MIR (protein mannosyltransferase, IP3R and RyR) domain is a domain that may have a ligand transferase function. 185 matched cddid_all.tbl CDD pfam02816 pfam02816 460709 Alpha_kinase Alpha-kinase family. This family is a novel family of eukaryotic protein kinase catalytic domains, which have no detectable similarity to conventional kinases. The family contains myosin heavy chain kinases and Elongation Factor-2 kinase and a bifunctional ion channel. This family is known as the alpha-kinase family. The structure of the kinase domain revealed unexpected similarity to eukaryotic protein kinases in the catalytic core as well as to metabolic enzymes with ATP-grasp domains. 185 matched cddid_all.tbl CDD pfam02817 pfam02817 460710 E3_binding e3 binding domain. This family represents a small domain of the E2 subunit of 2-oxo-acid dehydrogenases responsible for the binding of the E3 subunit. 36 matched cddid_all.tbl CDD pfam02818 pfam02818 460711 PPAK PPAK motif. These motifs are found in the PEVK region of titin. 27 matched cddid_all.tbl CDD pfam02819 pfam02819 111689 Toxin_9 Spider toxin. This family of spider neurotoxins are thought to be calcium ion channel inhibitors. 43 matched cddid_all.tbl CDD pfam02820 pfam02820 460712 MBT mbt repeat. The function of this repeat is unknown, but is found in a number of nuclear proteins such as drosophila sex comb on midleg protein. The repeat is found in up to four copies as in Swiss:Q9UHJ3. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function. 66 matched cddid_all.tbl CDD pfam02821 pfam02821 427002 Staphylokinase Staphylokinase/Streptokinase family. 116 matched cddid_all.tbl CDD pfam02822 pfam02822 460713 Antistasin Antistasin family. Members of this family are inhibitors of trypsin family proteases. This domain is highly disulphide bonded. The domain is also found in some large extracellular proteins in multiple copies. 26 matched cddid_all.tbl CDD pfam02823 pfam02823 460714 ATP-synt_DE_N ATP synthase, Delta/Epsilon chain, beta-sandwich domain. Part of the ATP synthase CF(1). These subunits are part of the head unit of the ATP synthase. The subunit is called epsilon in bacteria and delta in mitochondria. In bacteria the delta (D) subunit is equivalent to the mitochondrial Oligomycin sensitive subunit, OSCP (pfam00213). 80 matched cddid_all.tbl CDD pfam02824 pfam02824 427005 TGS TGS domain. The TGS domain is named after ThrRS, GTPase, and SpoT. Interestingly, TGS domain was detected also at the amino terminus of the uridine kinase from the spirochaete Treponema pallidum (but not any other organizm, including the related spirochaete Borrelia burgdorferi). TGS is a small domain that consists of ~50 amino acid residues and is predicted to possess a predominantly beta-sheet structure. There is no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role. 60 matched cddid_all.tbl CDD pfam02825 pfam02825 460715 WWE WWE domain. The WWE domain is named after three of its conserved residues and is predicted to mediate specific protein- protein interactions in ubiquitin and ADP ribose conjugation systems. 66 matched cddid_all.tbl CDD pfam02826 pfam02826 427007 2-Hacid_dh_C D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain. This domain is inserted into the catalytic domain, the large dehydrogenase and D-lactate dehydrogenase families in SCOP. N-terminal portion of which is represented by family pfam00389. 178 matched cddid_all.tbl CDD pfam02827 pfam02827 460716 PKI cAMP-dependent protein kinase inhibitor. Members of this family are extremely potent competitive inhibitors of camp-dependent protein kinase activity. These proteins interact with the catalytic subunit of the enzyme after the cAMP-induced dissociation of its regulatory chains. 69 matched cddid_all.tbl CDD pfam02828 pfam02828 460717 L27 L27 domain. The L27 domain is found in receptor targeting proteins Lin-2 and Lin-7. 52 matched cddid_all.tbl CDD pfam02829 pfam02829 460718 3H 3H domain. This domain is predicted to be a small molecule binding domain, based on its occurrence with other domains. The domain is named after its three conserved histidine residues. 97 matched cddid_all.tbl CDD pfam02830 pfam02830 427011 V4R V4R domain. The V4R (vinyl 4 reductase) domain is a predicted small molecular binding domain, that may bind to hydrocarbons. 62 matched cddid_all.tbl CDD pfam02831 pfam02831 397116 gpW gpW. gpW is a 68 residue protein known to be present in phage particles. Extracts of phage-infected cells lacking gpW contain DNA-filled heads, and active tails, but no infectious virions. gpW is required for the addition of gpFII to the head, which is, in turn, required for the attachment of tails. Since gpFII and tails are known to be attached at the connector, gpW is also likely to assemble at this site. The addition of gpW to filled heads increases the DNase resistance of the packaged DNA, suggesting that gpW either forms a plug at the connector to prevent ejection of the DNA, or binds directly to the DNA. The large number of positively charged residues in gpW (its calculated pI is 10.8) is consistent with a role in DNA interaction. 62 matched cddid_all.tbl CDD pfam02832 pfam02832 280922 Flavi_glycop_C Flavivirus glycoprotein, immunoglobulin-like domain. 97 matched cddid_all.tbl CDD pfam02833 pfam02833 460719 DHHA2 DHHA2 domain. This domain is often found adjacent to the DHH domain pfam01368 and is called DHHA2 for DHH associated domain. This domain is diagnostic of DHH subfamily 2 members. The domain is about 120 residues long and contains a conserved DXK motif at its amino terminus. 124 matched cddid_all.tbl CDD pfam02834 pfam02834 397118 LigT_PEase LigT like Phosphoesterase. Members of this family are bacterial and archaeal RNA ligases that are able to ligate tRNA half molecules containing 2',3'-cyclic phosphate and 5' hydroxyl termini to products containing the 2',5' phosphodiester linkage. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family. The structure of a related protein is known. They belong to the 2H phosphoesterase superfamily. They share a common active site, characterized by two conserved histidines, with vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins. 87 matched cddid_all.tbl CDD pfam02836 pfam02836 397119 Glyco_hydro_2_C Glycosyl hydrolases family 2, TIM barrel domain. This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities. 302 matched cddid_all.tbl CDD pfam02837 pfam02837 397120 Glyco_hydro_2_N Glycosyl hydrolases family 2, sugar binding domain. This family contains beta-galactosidase, beta-mannosidase and beta-glucuronidase activities and has a jelly-roll fold. The domain binds the sugar moiety during the sugar-hydrolysis reaction. 169 matched cddid_all.tbl CDD pfam02838 pfam02838 427013 Glyco_hydro_20b Glycosyl hydrolase family 20, domain 2. This domain has a zincin-like fold. 124 matched cddid_all.tbl CDD pfam02839 pfam02839 427014 CBM_5_12 Carbohydrate binding domain. This short domain is found in many different glycosyl hydrolase enzymes and is presumed to have a carbohydrate binding function. The domain has six aromatic groups that may be important for binding. 25 matched cddid_all.tbl CDD pfam02840 pfam02840 460720 Prp18 Prp18 domain. The splicing factor Prp18 is required for the second step of pre-mRNA splicing. The structure of a large fragment of the Saccharomyces cerevisiae Prp18 is known. This fragment is fully active in yeast splicing in vitro and includes the sequences of Prp18 that have been evolutionarily conserved. The core structure consists of five alpha-helices that adopt a novel fold. The most highly conserved region of Prp18, a nearly invariant stretch of 19 aa, forms part of a loop between two alpha-helices and may interact with the U5 small nuclear ribonucleoprotein particles. 142 matched cddid_all.tbl CDD pfam02841 pfam02841 460721 GBP_C Guanylate-binding protein, C-terminal domain. Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP. 297 matched cddid_all.tbl CDD pfam02843 pfam02843 460722 GARS_C Phosphoribosylglycinamide synthetase, C domain. Phosphoribosylglycinamide synthetase catalyzes the second step in the de novo biosynthesis of purine. The reaction catalyzed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the C-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (see pfam02787). 88 matched cddid_all.tbl CDD pfam02844 pfam02844 460723 GARS_N Phosphoribosylglycinamide synthetase, N domain. Phosphoribosylglycinamide synthetase catalyzes the second step in the de novo biosynthesis of purine. The reaction catalyzed by Phosphoribosylglycinamide synthetase is the ATP- dependent addition of 5-phosphoribosylamine to glycine to form 5'phosphoribosylglycinamide. This domain is related to the N-terminal domain of biotin carboxylase/carbamoyl phosphate synthetase (see pfam00289). This domain is structurally related to the PreATP-grasp domain. 102 matched cddid_all.tbl CDD pfam02845 pfam02845 427018 CUE CUE domain. CUE domains have been shown to bind ubiquitin. It has been suggested that CUE domains are related to pfam00627 and this has been confirmed by the structure of the domain. CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. 42 matched cddid_all.tbl CDD pfam02847 pfam02847 397128 MA3 MA3 domain. Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains. 113 matched cddid_all.tbl CDD pfam02852 pfam02852 427019 Pyr_redox_dim Pyridine nucleotide-disulphide oxidoreductase, dimerization domain. This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. 109 matched cddid_all.tbl CDD pfam02854 pfam02854 397130 MIF4G MIF4G domain. MIF4G is named after Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. 203 matched cddid_all.tbl CDD pfam02861 pfam02861 460724 Clp_N Clp amino terminal domain, pathogenicity island component. This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site. In many bacterial species, including E.coli, this region represents the N-terminus of one of the key components of the pathogenicity island complex that injects toxin from one bacterium into another. 53 matched cddid_all.tbl CDD pfam02862 pfam02862 460725 DDHD DDHD domain. The DDHD domain is 180 residues long and contains four conserved residues that may form a metal binding site. The domain is named after these four residues. This pattern of conservation of metal binding residues is often seen in phosphoesterase domains. This domain is found in retinal degeneration B proteins, as well as a family of probable phospholipases. It has been shown that this domain is found in a longer C terminal region that binds to PYK2 tyrosine kinase. These proteins have been called N-terminal domain-interacting receptor (Nir1, Nir2 and Nir3). This suggests that this region is involved in functionally important interactions in other members of this family. 241 matched cddid_all.tbl CDD pfam02863 pfam02863 460726 Arg_repressor_C Arginine repressor, C-terminal domain. This is the C-terminal domain of the arginine repressor, responsible for arginine binding and multimerization. It binds mainly Arg, but also ornithine, Pro and Tyr (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 68 matched cddid_all.tbl CDD pfam02864 pfam02864 460727 STAT_bind STAT protein, DNA binding domain. STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. This family represents the DNA binding domain of STAT, which has an ig-like fold. STAT proteins also include an SH2 domain pfam00017. 132 matched cddid_all.tbl CDD pfam02865 pfam02865 460728 STAT_int STAT protein, protein interaction domain. STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. STAT proteins also include an SH2 domain pfam00017. 119 matched cddid_all.tbl CDD pfam02866 pfam02866 397136 Ldh_1_C lactate/malate dehydrogenase, alpha/beta C-terminal domain. L-lactate dehydrogenases are metabolic enzymes which catalyze the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyze the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. 173 matched cddid_all.tbl CDD pfam02867 pfam02867 460729 Ribonuc_red_lgC Ribonucleotide reductase, barrel domain. 487 matched cddid_all.tbl CDD pfam02868 pfam02868 427026 Peptidase_M4_C Thermolysin metallopeptidase, alpha-helical domain. 167 matched cddid_all.tbl CDD pfam02870 pfam02870 397139 Methyltransf_1N 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain. This entry represents the N-terminal ribonuclease-like domain associated with 6-O-methylguanine DNA methyltransferase activity. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (also known as O-6-methylguanine-DNA-alkyltransferase) 77 matched cddid_all.tbl CDD pfam02872 pfam02872 427027 5_nucleotid_C 5'-nucleotidase, C-terminal domain. 155 matched cddid_all.tbl CDD pfam02873 pfam02873 460730 MurB_C UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain. Members of this family are UDP-N-acetylenolpyruvoylglucosamine reductase enzymes EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan. 99 matched cddid_all.tbl CDD pfam02874 pfam02874 427029 ATP-synt_ab_N ATP synthase alpha/beta family, beta-barrel domain. This family includes the ATP synthase alpha and beta subunits the ATP synthase associated with flagella. 69 matched cddid_all.tbl CDD pfam02875 pfam02875 460731 Mur_ligase_C Mur ligase family, glutamate ligase domain. This family contains a number of related ligase enzymes which have EC numbers 6.3.2.*. This family includes: MurC, MurD, MurE, MurF, Mpl and FolC. MurC, MurD, Mure and MurF catalyze consecutive steps in the synthesis of peptidoglycan. Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide. The pentapeptide is is made of L-alanine, D-glutamic acid, Meso-diaminopimelic acid and D-alanyl alanine. The peptide moiety is synthesized by successively adding these amino acids to UDP-N-acetylmuramic acid. MurC transfers the L-alanine, MurD transfers the D-glutamate, MurE transfers the diaminopimelic acid, and MurF transfers the D-alanyl alanine. This family also includes Folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate. 87 matched cddid_all.tbl CDD pfam02876 pfam02876 427030 Stap_Strp_tox_C Staphylococcal/Streptococcal toxin, beta-grasp domain. 107 matched cddid_all.tbl CDD pfam02877 pfam02877 460732 PARP_reg Poly(ADP-ribose) polymerase, regulatory domain. Poly(ADP-ribose) polymerase catalyzes the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins, which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active. 135 matched cddid_all.tbl CDD pfam02878 pfam02878 427032 PGM_PMM_I Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I. 138 matched cddid_all.tbl CDD pfam02879 pfam02879 427033 PGM_PMM_II Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II. 102 matched cddid_all.tbl CDD pfam02880 pfam02880 460733 PGM_PMM_III Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III. 115 matched cddid_all.tbl CDD pfam02881 pfam02881 460734 SRP54_N SRP54-type protein, helical bundle domain. 75 matched cddid_all.tbl CDD pfam02882 pfam02882 427036 THF_DHG_CYH_C Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain. 160 matched cddid_all.tbl CDD pfam02883 pfam02883 460735 Alpha_adaptinC2 Adaptin C-terminal domain. Alpha adaptin is a heterotetramer which regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This ig-fold domain is found in alpha, beta and gamma adaptins. 111 matched cddid_all.tbl CDD pfam02884 pfam02884 460736 Lyase_8_C Polysaccharide lyase family 8, C-terminal beta-sandwich domain. This family consists of a group of secreted bacterial lyase enzymes EC:4.2.2.1 capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen. 69 matched cddid_all.tbl CDD pfam02885 pfam02885 460737 Glycos_trans_3N Glycosyl transferase family, helical bundle domain. This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate. 63 matched cddid_all.tbl CDD pfam02886 pfam02886 397154 LBP_BPI_CETP_C LBP / BPI / CETP family, C-terminal domain. The N and C terminal domains of the LBP/BPI/CETP family are structurally similar. 238 matched cddid_all.tbl CDD pfam02887 pfam02887 460738 PK_C Pyruvate kinase, alpha/beta domain. As well as being found in pyruvate kinase this family is found as an isolated domain in some bacterial proteins. 114 matched cddid_all.tbl CDD pfam02888 pfam02888 460739 CaMBD Calmodulin binding domain. Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM). CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other. 75 matched cddid_all.tbl CDD pfam02889 pfam02889 460740 Sec63 Sec63 Brl domain. This domain (also known as the Brl domain) is required for assembly of functional endoplasmic reticulum translocons. 307 matched cddid_all.tbl CDD pfam02890 pfam02890 308504 DUF226 Borrelia family of unknown function DUF226. This family of proteins are found in Borrelia. The proteins are about 190 amino acids long and have no known function. 139 matched cddid_all.tbl CDD pfam02891 pfam02891 460741 zf-MIZ MIZ/SP-RING zinc finger. This domain has SUMO (small ubiquitin-like modifier) ligase activity and is involved in DNA repair and chromosome organization. 50 matched cddid_all.tbl CDD pfam02892 pfam02892 427043 zf-BED BED zinc finger. 44 matched cddid_all.tbl CDD pfam02893 pfam02893 397160 GRAM GRAM domain. The GRAM domain is found in in glucosyltransferases, myotubularins and other putative membrane-associated proteins. Note the alignment is lacking the last two beta strands and alpha helix. 112 matched cddid_all.tbl CDD pfam02894 pfam02894 427044 GFO_IDH_MocA_C Oxidoreductase family, C-terminal alpha/beta domain. This family of enzymes utilize NADP or NAD. This family is called the GFO/IDH/MOCA family in swiss-prot. 203 matched cddid_all.tbl CDD pfam02895 pfam02895 427045 H-kinase_dim Signal transducing histidine kinase, homodimeric domain. This helical bundle domain is the homodimer interface of the signal transducing histidine kinase family. 66 matched cddid_all.tbl CDD pfam02896 pfam02896 397163 PEP-utilizers_C PEP-utilizing enzyme, PEP-binding domain. This entry represents a TIM barrel domain found at the C terminus of a number of PEP (phosphoenolpyruvate)-utilizing proteins. In PPDK (Pyruvate phosphate dikinase) this C-terminal domain has been shown to be a PEP-binding domain. 292 matched cddid_all.tbl CDD pfam02897 pfam02897 397164 Peptidase_S9_N Prolyl oligopeptidase, N-terminal beta-propeller domain. This unusual 7-stranded beta-propeller domain protects the catalytic triad of prolyl oligopeptidase (see pfam00326), excluding larger peptides and proteins from proteolysis in the cytosol. 414 matched cddid_all.tbl CDD pfam02898 pfam02898 460742 NO_synthase Nitric oxide synthase, oxygenase domain. 362 matched cddid_all.tbl CDD pfam02899 pfam02899 427047 Phage_int_SAM_1 Phage integrase, N-terminal SAM-like domain. 83 matched cddid_all.tbl CDD pfam02900 pfam02900 397167 LigB Catalytic LigB subunit of aromatic ring-opening dioxygenase. 260 matched cddid_all.tbl CDD pfam02901 pfam02901 427048 PFL-like Pyruvate formate lyase-like. This family of enzymes includes pyruvate formate lyase, choline trimethylamine lyase, glycerol dehydratase, 4-hydroxyphenylacetate decarboxylase, and benzylsuccinate synthase. 647 matched cddid_all.tbl CDD pfam02902 pfam02902 397169 Peptidase_C48 Ulp1 protease family, C-terminal catalytic domain. This domain contains the catalytic triad Cys-His-Asn. 202 matched cddid_all.tbl CDD pfam02903 pfam02903 397170 Alpha-amylase_N Alpha amylase, N-terminal ig-like domain. 120 matched cddid_all.tbl CDD pfam02905 pfam02905 397171 EBV-NA1 Epstein Barr virus nuclear antigen-1, DNA-binding domain. This domain has a ferredoxin-like fold. 139 matched cddid_all.tbl CDD pfam02906 pfam02906 397172 Fe_hyd_lg_C Iron only hydrogenase large subunit, C-terminal domain. 277 matched cddid_all.tbl CDD pfam02907 pfam02907 427049 Peptidase_S29 Hepatitis C virus NS3 protease. Hepatitis C virus NS3 protein is a serine protease which has a trypsin-like fold. The non-structural (NS) protein NS3 is one of the NS proteins involved in replication of the HCV genome. NS2-3 proteinase, a zinc-dependent enzyme, performs a single proteolytic cut to release the N-terminus of NS3. The action of NS3 proteinase (NS3P), which resides in the N-terminal one-third of the NS3 protein, then yields all remaining non-structural proteins. The C-terminal two-thirds of the NS3 protein contain a helicase. The functional relationship between the proteinase and helicase domains is unknown. NS3 has a structural zinc-binding site and requires cofactor NS4A. 149 matched cddid_all.tbl CDD pfam02909 pfam02909 397174 TetR_C_1 Tetracyclin repressor-like, C-terminal domain. 144 matched cddid_all.tbl CDD pfam02910 pfam02910 460743 Succ_DH_flav_C Fumarate reductase flavoprotein C-term. This family contains fumarate reductases, succinate dehydrogenases and L-aspartate oxidases. 129 matched cddid_all.tbl CDD pfam02911 pfam02911 460744 Formyl_trans_C Formyl transferase, C-terminal domain. 99 matched cddid_all.tbl CDD pfam02912 pfam02912 460745 Phe_tRNA-synt_N Aminoacyl tRNA synthetase class II, N-terminal domain. 69 matched cddid_all.tbl CDD pfam02913 pfam02913 397178 FAD-oxidase_C FAD linked oxidases, C-terminal domain. This domain has a ferredoxin-like fold. 248 matched cddid_all.tbl CDD pfam02914 pfam02914 397179 DDE_2 Bacteriophage Mu transposase. This transposase is essential for integration, replication-transposition and excision of Bacteriophage Mu DNA. The crystal structure of the core domain of Mu transposase, MuA, exhibits that the first of two subdomains contains the active site and, despite very limited sequence homology, exhibits a striking similarity to the core domain of Human immunodeficiency virus 1 integrase. The enzymatic activity of MuA is known to be activated by formation of a DNA-bound tetramer of the protein. 221 matched cddid_all.tbl CDD pfam02915 pfam02915 397180 Rubrerythrin Rubrerythrin. This domain has a ferritin-like fold. 137 matched cddid_all.tbl CDD pfam02916 pfam02916 397181 DNA_PPF DNA polymerase processivity factor. 115 matched cddid_all.tbl CDD pfam02917 pfam02917 397182 Pertussis_S1 Pertussis toxin, subunit 1. 239 matched cddid_all.tbl CDD pfam02918 pfam02918 280986 Pertussis_S2S3 Pertussis toxin, subunit 2 and 3, C-terminal domain. 109 matched cddid_all.tbl CDD pfam02919 pfam02919 460746 Topoisom_I_N Eukaryotic DNA topoisomerase I, DNA binding fragment. Topoisomerase I promotes the relaxation of DNA superhelical tension by introducing a transient single-stranded break in duplex DNA and are vital for the processes of replication, transcription, and recombination. This family may be more than one structural domain. 213 matched cddid_all.tbl CDD pfam02920 pfam02920 427054 Integrase_DNA DNA binding domain of tn916 integrase. 58 matched cddid_all.tbl CDD pfam02921 pfam02921 460747 UCR_TM Ubiquinol cytochrome reductase transmembrane region. Each subunit of the cytochrome bc1 complex provides a single helix (this family) to make up the transmembrane region of the complex. 66 matched cddid_all.tbl CDD pfam02922 pfam02922 427056 CBM_48 Carbohydrate-binding module 48 (Isoamylase N-terminal domain). This domain is found in a range of enzymes that act on branched substrates - isoamylase, pullulanase and branching enzyme. This family also contains the beta subunit of 5' AMP activated kinase. 80 matched cddid_all.tbl CDD pfam02923 pfam02923 280991 BamHI Restriction endonuclease BamHI. 157 matched cddid_all.tbl CDD pfam02924 pfam02924 427057 HDPD Bacteriophage lambda head decoration protein D. 115 matched cddid_all.tbl CDD pfam02925 pfam02925 460748 gpD Bacteriophage scaffolding protein D. 141 matched cddid_all.tbl CDD pfam02926 pfam02926 460749 THUMP THUMP domain. The THUMP domain is named after after thiouridine synthases, methylases and PSUSs. The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterized RNA-binding domains. It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets. 143 matched cddid_all.tbl CDD pfam02927 pfam02927 427058 CelD_N Cellulase N-terminal ig-like domain. 83 matched cddid_all.tbl CDD pfam02928 pfam02928 460750 zf-C5HC2 C5HC2 zinc finger. Predicted zinc finger with eight potential zinc ligand binding residues. This domain is found in Jumonji. This domain may have a DNA binding function. 54 matched cddid_all.tbl CDD pfam02929 pfam02929 460751 Bgal_small_N Beta galactosidase small chain. This domain comprises the small chain of dimeric beta-galactosidases EC:3.2.1.23. This domain is also found in single chain beta-galactosidase. 223 matched cddid_all.tbl CDD pfam02931 pfam02931 460752 Neur_chan_LBD Neurotransmitter-gated ion-channel ligand binding domain. This family is the extracellular ligand binding domain of these ion channels. This domain forms a pentameric arrangement in the known structure. 215 matched cddid_all.tbl CDD pfam02932 pfam02932 460753 Neur_chan_memb Neurotransmitter-gated ion-channel transmembrane region. This family includes the four transmembrane helices that form the ion channel. 232 matched cddid_all.tbl CDD pfam02933 pfam02933 427063 CDC48_2 Cell division protein 48 (CDC48), domain 2. This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the C-terminus. The VAT-N domain found in AAA ATPases pfam00004 is a substrate 185-residue recognition domain. 64 matched cddid_all.tbl CDD pfam02934 pfam02934 460754 GatB_N GatB/GatE catalytic domain. This domain is found in the GatB and GatE proteins. 284 matched cddid_all.tbl CDD pfam02935 pfam02935 427065 COX7C Cytochrome c oxidase subunit VIIc. Cytochrome c oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit VIIc. The yeast member of this family is called COX VIII. 57 matched cddid_all.tbl CDD pfam02936 pfam02936 460755 COX4 Cytochrome c oxidase subunit IV. Cytochrome c oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit IV. The Dictyostelium member of this family is called COX VI. The yeast protein Swiss:P53077 appears to be the yeast COX IV subunit. 100 matched cddid_all.tbl CDD pfam02937 pfam02937 460756 COX6C Cytochrome c oxidase subunit VIc. Cytochrome c oxidase, a 13 sub-unit complex, EC:1.9.3.1 is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit VIc. 69 matched cddid_all.tbl CDD pfam02938 pfam02938 397199 GAD GAD domain. This domain is found in some members of the GatB and aspartyl tRNA synthetases. 94 matched cddid_all.tbl CDD pfam02939 pfam02939 460757 UcrQ UcrQ family. The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is a respiratory multienzyme complex. This family represents the 9.5 kDa subunit of the complex. 76 matched cddid_all.tbl CDD pfam02940 pfam02940 397201 mRNA_triPase mRNA capping enzyme, beta chain. The beta chain of mRNA capping enzyme has triphosphatase activity. The function of the capping enzyme also depends on the guanylyltransferase activity conferred by the alpha chain (see pfam01331) 221 matched cddid_all.tbl CDD pfam02941 pfam02941 427069 FeThRed_A Ferredoxin thioredoxin reductase variable alpha chain. 67 matched cddid_all.tbl CDD pfam02942 pfam02942 281009 Flu_B_NS1 Influenza B non-structural protein (NS1). A specific region of the influenza B virus NS1 protein, which includes part of its effector domain, blocks the covalent linkage of ISG15 to its target proteins both in vitro and in infected cells. Of the several hundred proteins induced by interferon (IFN) alpha/beta, the ubiquitin-like ISG15 protein is one of the most predominant. Influenza A virus employs a different strategy: its NS1 protein does not bind the ISG15 protein, but little or no ISG15 protein is produced during infection. 247 matched cddid_all.tbl CDD pfam02943 pfam02943 427070 FeThRed_B Ferredoxin thioredoxin reductase catalytic beta chain. 106 matched cddid_all.tbl CDD pfam02944 pfam02944 460758 BESS BESS motif. The BESS motif is named after the proteins in which it is found (BEAF, Suvar(3)7 and Stonewall). The motif is 40 amino acid residues long and is composed of two predicted alpha helices. Based on the protein in which it is found and the presence of conserved positively charged residues it is predicted to be a DNA binding domain. This domain appears to be specific to drosophila. 35 matched cddid_all.tbl CDD pfam02945 pfam02945 397205 Endonuclease_7 Recombination endonuclease VII. 82 matched cddid_all.tbl CDD pfam02946 pfam02946 460759 GTF2I GTF2I-like repeat. This region of sequence similarity is found up to six times in a variety of proteins including GTF2I. It has been suggested that this may be a DNA binding domain. 75 matched cddid_all.tbl CDD pfam02947 pfam02947 460760 Flt3_lig flt3 ligand. The flt3 ligand is a short chain cytokine with a 4 helical bundle fold. 131 matched cddid_all.tbl CDD pfam02948 pfam02948 460761 Amelogenin Amelogenin. Amelogenins play a role in biomineralization. They seem to regulate the formation of crystallites during the secretory stage of tooth enamel development. thought to play a major role in the structural organization and mineralization of developing enamel. They are found in the extracellular matrix. Mutations in X-chromosomal amelogenin can cause Amelogenesis imperfecta. 179 matched cddid_all.tbl CDD pfam02949 pfam02949 251636 7tm_6 7tm Odorant receptor. This family is composed of 7 transmembrane receptors, that are probably drosophila odorant receptors. 313 matched cddid_all.tbl CDD pfam02950 pfam02950 367269 Conotoxin Conotoxin. Conotoxins are small snail toxins that block ion channels. 74 matched cddid_all.tbl CDD pfam02951 pfam02951 460762 GSH-S_N Prokaryotic glutathione synthetase, N-terminal domain. 116 matched cddid_all.tbl CDD pfam02952 pfam02952 460763 Fucose_iso_C L-fucose isomerase, C-terminal domain. 141 matched cddid_all.tbl CDD pfam02953 pfam02953 460764 zf-Tim10_DDP Tim10/DDP family zinc finger. Putative zinc binding domain with four conserved cysteine residues. This domain is found in the human disease protein Swiss:O60220. Members of this family such as Tim9 and Tim10 are involved in mitochondrial protein import. Members of this family seem to be localized to the mitochondrial intermembrane space. 64 matched cddid_all.tbl CDD pfam02954 pfam02954 427077 HTH_8 Bacterial regulatory protein, Fis family. 40 matched cddid_all.tbl CDD pfam02955 pfam02955 427078 GSH-S_ATP Prokaryotic glutathione synthetase, ATP-grasp domain. 175 matched cddid_all.tbl CDD pfam02956 pfam02956 367272 TT_ORF1 TT viral orf 1. TT virus (TTV), isolated initially from a Japanese patient with hepatitis of unknown aetiology, has since been found to infect both healthy and diseased individuals and numerous prevalence studies have raised questions about its role in unexplained hepatitis. ORF1 is a large 750 residue protein. The N-terminal half of this protein corresponds to the capsid protein. 526 matched cddid_all.tbl CDD pfam02957 pfam02957 251643 TT_ORF2 TT viral ORF2. TT virus (TTV), isolated initially from a Japanese patient with hepatitis of unknown aetiology, has since been found to infect both healthy and diseased individuals, and numerous prevalence studies have raised questions about its role in unexplained hepatitis. ORF2 is a 150 residue protein. This family also includes the VP2 protein from the chicken anaemia virus which is a gyrovirus. Gyroviruses are small circular single stranded viruses. The proteins contain a set of conserved cysteine and histidine residues suggesting a zinc binding domain. 103 matched cddid_all.tbl CDD pfam02958 pfam02958 397213 EcKL Ecdysteroid kinase-like family. This family includes ecdysteroid 22-kinase, an enzyme responsible for the phosphorylation of ecdysteroids (insect growth and moulting hormones) at C-22, to form physiologically inactive ecdysteroid 22-phosphates. Most insects contain 12 to 105 genes encoding this family and yet so far only one enzyme (ecdysteroid 22-kinase from Bombyx mori) has characterized substrates (2-deoxyecdysone, ecdysone, 20-hydroxyecdysone). There are good reasons to believe that this family includes kinases that act on other small molecule substrates and that they may function in detoxification processes. 293 matched cddid_all.tbl CDD pfam02959 pfam02959 281024 Tax HTLV Tax. Human T-cell leukaemia virus type I (HTLV-I) is the etiological agent for adult T-cell leukaemia (ATL), as well as for tropical spastic paraparesis (TSP) and HTLV-I associate myelopathy (HAM). A biological understanding of the involvement of HTLV-I and in ATL has focused significantly on the workings of the virally-encoded 40 kDa phospho-oncoprotein, Tax. Tax is a transcriptional activator. Its ability to modulate the expression and function of many cellular genes has been reasoned to be a major contributory mechanism explaining HTLV-I-mediated transformation of cells. In activating cellular gene expression, Tax impinges upon several cellular signal-transduction pathways, including those for CREB/ATF and NF-kappaB. 222 matched cddid_all.tbl CDD pfam02960 pfam02960 460765 K1 K1 glycoprotein. 120 matched cddid_all.tbl CDD pfam02961 pfam02961 460766 BAF Barrier to autointegration factor. The BAF protein has a SAM-domain-like bundle of orthogonally packed alpha-hairpins - one classic and one pseudo helix-hairpin-helix motif. The protein is involved in the prevention of retroviral DNA integration. 88 matched cddid_all.tbl CDD pfam02962 pfam02962 427080 CHMI 5-carboxymethyl-2-hydroxymuconate isomerase. 124 matched cddid_all.tbl CDD pfam02963 pfam02963 427081 EcoRI Restriction endonuclease EcoRI. 257 matched cddid_all.tbl CDD pfam02964 pfam02964 427082 MeMO_Hyd_G Methane monooxygenase, hydrolase gamma chain. 161 matched cddid_all.tbl CDD pfam02965 pfam02965 460767 Met_synt_B12 Vitamin B12 dependent methionine synthase, activation domain. 273 matched cddid_all.tbl CDD pfam02966 pfam02966 460768 DIM1 Mitosis protein DIM1. 133 matched cddid_all.tbl CDD pfam02969 pfam02969 427084 TAF TATA box binding protein associated factor (TAF). TAF proteins adopt a histone-like fold. 66 matched cddid_all.tbl CDD pfam02970 pfam02970 460769 TBCA Tubulin binding cofactor A. 99 matched cddid_all.tbl CDD pfam02971 pfam02971 460770 FTCD Formiminotransferase domain. 146 matched cddid_all.tbl CDD pfam02972 pfam02972 145886 Phycoerythr_ab Phycoerythrin, alpha/beta chain. This family represents the non-globular alpha and beta chain components of phycoerythrin. The structure is a long beta-hairpin and a single alpha-helix. 57 matched cddid_all.tbl CDD pfam02973 pfam02973 281035 Sialidase Sialidase, N-terminal domain. 188 matched cddid_all.tbl CDD pfam02974 pfam02974 427087 Inh Protease inhibitor Inh. The Inh inhibitor is secreted into the periplasm where its presumed physiological function is to protect periplasmic proteins against the action of secreted proteases. A range of proteases including A, B and C from E. chrysanthemi, alkaline protease from Pseudomonas aeruginosa and the 50 kDa protease from Serratia marcescens are inhibited. 95 matched cddid_all.tbl CDD pfam02975 pfam02975 427088 Me-amine-dh_L Methylamine dehydrogenase, L chain. 113 matched cddid_all.tbl CDD pfam02976 pfam02976 427089 MutH DNA mismatch repair enzyme MutH. 103 matched cddid_all.tbl CDD pfam02977 pfam02977 397224 CarbpepA_inh Carboxypeptidase A inhibitor. 40 matched cddid_all.tbl CDD pfam02978 pfam02978 460771 SRP_SPB Signal peptide binding domain. 95 matched cddid_all.tbl CDD pfam02979 pfam02979 427091 NHase_alpha Nitrile hydratase, alpha chain. 178 matched cddid_all.tbl CDD pfam02980 pfam02980 397227 FokI_dom_2 FokI, recognition domain, subdomain 2. Type IIS restriction endonuclease FokI is a member of an unusual class of bipartite restriction enzymes that recognizes the double-stranded DNA sequence 5'-GGATG-3' and cleave DNA phosphodiester groups 9 base pairs away on this strand and 13 base pairs away on the complementary strand. FokI contains amino- and carboxy-terminal domains corresponding to the DNA- recognition and cleavage functions, respectively. The recognition domain is made of three smaller subdomains (D1, D2 and D3) which are evolutionarily related to the helix-turn-helix-containing DNA-binding domain of the catabolite gene activator protein CAP. This entry represents the subdomain D2 of FokI. D1 and D2 make almost all of the base-specific contacts with the DNA. 136 matched cddid_all.tbl CDD pfam02981 pfam02981 397228 FokI_D1 FokI, recognition domain, subdomain 1. Type IIS restriction endonuclease FokI is a member of an unusual class of bipartite restriction enzymes that recognizes the double-stranded DNA sequence 5'-GGATG-3' and cleave DNA phosphodiester groups 9 base pairs away on this strand and 13 base pairs away on the complementary strand. FokI contains amino- and carboxy-terminal domains corresponding to the DNA- recognition and cleavage functions, respectively. The recognition domain is made of three smaller subdomains (D1, D2 and D3) which are evolutionarily related to the helix-turn-helix- containing DNA-binding domain of the catabolite gene activator protein CAP. This entry represents the subdomain D1 of FokI. Subdomain D1 of the recognition domain covers the DNA major groove, recognizing base pairs at the 3' end of the recognition sequence (GGATG). 135 matched cddid_all.tbl CDD pfam02982 pfam02982 202497 Scytalone_dh Scytalone dehydratase. Scytalone dehydratases are structurally related to the NTF2 family (see pfam02136). 160 matched cddid_all.tbl CDD pfam02983 pfam02983 460772 Pro_Al_protease Alpha-lytic protease prodomain. 55 matched cddid_all.tbl CDD pfam02984 pfam02984 397230 Cyclin_C Cyclin, C-terminal domain. Cyclins regulate cyclin dependent kinases (CDKs). Swiss:P22674 is a Uracil-DNA glycosylase that is related to other cyclins. Cyclins contain two domains of similar all-alpha fold, of which this family corresponds with the C-terminal domain. 119 matched cddid_all.tbl CDD pfam02985 pfam02985 460773 HEAT HEAT repeat. The HEAT repeat family is related to armadillo/beta-catenin-like repeats (see pfam00514). 31 matched cddid_all.tbl CDD pfam02986 pfam02986 397232 Fn_bind Fibronectin binding repeat. The ability of bacteria to bind fibronectin is thought to enable the colonization of wound tissue and blood clots. The fibronectin binding repeat is found in bacterial fibronectin binding proteins and serum opacity factor. Bacterial fibronectin binding proteins are surface proteins that covalently link to the bacterial cell wall, mediate adherence of the bacteria to host cells and trigger the fibronectin/integrin-mediated uptake of bacteria by host cells. Each fibronectin binding repeat is an array of short motifs that bind to fibronectin type I domains. Fibronectin binding repeats are natively unfolded in the absence of fibronectin and are thought to adopt a well-defined conformation (tandem beta-zipper) upon binding. 33 matched cddid_all.tbl CDD pfam02987 pfam02987 111833 LEA_4 Late embryogenesis abundant protein. Different types of LEA proteins are expressed at different stages of late embryogenesis in higher plant seed embryos and under conditions of dehydration stress. The function of these proteins is unknown. 44 matched cddid_all.tbl CDD pfam02988 pfam02988 190495 PLA2_inh Phospholipase A2 inhibitor. 83 matched cddid_all.tbl CDD pfam02989 pfam02989 281047 DUF228 Lyme disease proteins of unknown function. 182 matched cddid_all.tbl CDD pfam02990 pfam02990 460774 EMP70 Endomembrane protein 70. 512 matched cddid_all.tbl CDD pfam02991 pfam02991 281049 ATG8 Autophagy protein Atg8 ubiquitin like. Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity. Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. The yeast proteins are involved in the autophagosome, and Atg8 binds Atg19, via its N-terminus and the C-terminus of Atg19. 104 matched cddid_all.tbl CDD pfam02992 pfam02992 460775 Transposase_21 Transposase family tnp2. Transposase_21 proteins are present mostly in plants, with members horizontally transferred to Bifidobacterium breve (GI: 291457831). Both DUF1258 pfam06869 and Transposase_21 have conserved active site residues similar to RNase H-like proteins, which suggests that they are functional transposases (1). 211 matched cddid_all.tbl CDD pfam02993 pfam02993 367287 MCPVI Minor capsid protein VI. This minor capsid protein may act as a link between the external capsid and the internal DNA-protein core. The C-terminal 11 residues may function as a protease cofactor leading to enzyme activation. 225 matched cddid_all.tbl CDD pfam02994 pfam02994 460776 Transposase_22 L1 transposable element RBD-like domain. This entry represents the RBD-like domain. 98 matched cddid_all.tbl CDD pfam02995 pfam02995 397236 DUF229 Protein of unknown function (DUF229). Members of this family are uncharacterized. They are 500-1200 amino acids in length and share a long region conservation that probably corresponds to several domains. The Go annotation for the protein indicates that it is involved in nematode larval development and has a positive regulation on growth rate. 496 matched cddid_all.tbl CDD pfam02996 pfam02996 427096 Prefoldin Prefoldin subunit. This family comprises of several prefoldin subunits. The biogenesis of the cytoskeletal proteins actin and tubulin involves interaction of nascent chains of each of the two proteins with the oligomeric protein prefoldin (PFD) and their subsequent transfer to the cytosolic chaperonin CCT (chaperonin containing TCP-1). Electron microscopy shows that eukaryotic PFD, which has a similar structure to its archaeal counterpart, interacts with unfolded actin along the tips of its projecting arms. In its PFD-bound state, actin seems to acquire a conformation similar to that adopted when it is bound to CCT. 120 matched cddid_all.tbl CDD pfam02998 pfam02998 111843 Lentiviral_Tat Lentiviral Tat protein. This family contains retroviral transactivating (Tat) proteins, from a variety of Lentiviruses. 86 matched cddid_all.tbl CDD pfam02999 pfam02999 308571 Borrelia_orfD Borrelia orf-D family. Borrelia burgdorferi supercoiled plasmids encode multicopy tandem open reading frames called Orf-A, Orf-B, Orf-C and Orf-D. This family corresponds to Orf-D. The putative product of this gene has no known function. 100 matched cddid_all.tbl CDD pfam03000 pfam03000 460777 NPH3 NPH3 family. Phototropism of Arabidopsis thaliana seedlings in response to a blue light source is initiated by nonphototropic hypocotyl 1 (NPH1), a light-activated serine-threonine protein kinase. Mutations in NPH3 disrupt early signaling occurring downstream of the NPH1 photoreceptor. The NPH3 gene encodes a NPH1-interacting protein. NPH3 is a member of a large protein family, apparently specific to higher plants, and may function as an adapter or scaffold protein to bring together the enzymatic components of a NPH1-activated phosphorelay. 218 matched cddid_all.tbl CDD pfam03002 pfam03002 367290 Somatostatin Somatostatin/Cortistatin family. Members of this family are hormones. Somatostatin inhibits the release of somatotropin. Cortistatin is a peptide that is related to the Somatostatins that is found to depresses neuronal electrical activity but, unlike somatostatin, induces low-frequency waves in the cerebral cortex and antagonizes the effects of acetylcholine on hippocampal and cortical measures of excitability. 18 matched cddid_all.tbl CDD pfam03003 pfam03003 281058 Pox_G9-A16 Pox virus entry-fusion-complex G9/A16. Pox_G9-A16 is a family of two of the eight entry-fusion complex proteins of pox viruses. the viral fusion proteins are components of the mature virion, MV, membrane. Extracellular enveloped virions (EVs), the infecting particles are MVs with an additional membrane that is opened or removed prior to the fusion of the MV and cell membrane during virus entry. G9 and A16 interact closely with each other and each is required for membrane fusion and virus entry as well as for interaction with A56/K2. 128 matched cddid_all.tbl CDD pfam03004 pfam03004 367291 Transposase_24 Plant transposase (Ptta/En/Spm family). Transposase proteins are necessary for efficient DNA transposition. This family includes various plant transposases from the Ptta and En/Spm families. 137 matched cddid_all.tbl CDD pfam03006 pfam03006 427098 HlyIII Haemolysin-III related. Members of this family are integral membrane proteins. This family includes a protein with hemolytic activity from Bacillus cereus. It has been proposed that YOL002c encodes a Saccharomyces cerevisiae protein that plays a key role in metabolic pathways that regulate lipid and phosphate metabolism. In eukaryotes, members are seven-transmembrane pass molecules found to encode functional receptors with a broad range of apparent ligand specificities, including progestin and adipoQ receptors, and hence have been named PAQR proteins. The mammalian members include progesterone binding proteins. Unlike the case with GPCR receptor proteins, the evolutionary ancestry of the members of this family can be traced back to the Archaea. This family belongs to the CREST superfamily, which are distantly related to GPCRs. 222 matched cddid_all.tbl CDD pfam03007 pfam03007 281060 WES_acyltransf Wax ester synthase-like Acyl-CoA acyltransferase domain. This domain is found in wax ester synthase genes. In these proteins this domain catalyzes the CoA dependent acyltransferase reaction with fatty alcohols to form wax esters. 261 matched cddid_all.tbl CDD pfam03008 pfam03008 427099 DUF234 Archaea bacterial proteins of unknown function. 91 matched cddid_all.tbl CDD pfam03009 pfam03009 397241 GDPD Glycerophosphoryl diester phosphodiesterase family. E. coli has two sequence related isozymes of glycerophosphoryl diester phosphodiesterase (GDPD) - periplasmic and cytosolic. This family also includes agrocinopine synthase, the similarity to GDPD has been noted. This family appears to have weak but not significant matches to mammalian phospholipase C pfam00388, which suggests that this family may adopt a TIM barrel fold. 244 matched cddid_all.tbl CDD pfam03010 pfam03010 281063 GP4 GP4. GP4 is a minor membrane-associated glycoproteins. This family contains envelope protein GP4 from equine arteritis virus. 152 matched cddid_all.tbl CDD pfam03011 pfam03011 281064 PFEMP PFEMP1 DBL domain. PfEMP1 (Plasmodium falciparum erythrocyte membrane protein) has been identified as the rosetting ligand of the malaria parasite P. falciparum. Rosetting is the adhesion of infected erythrocytes with uninfected erythrocytes in the vasculature of the infected organ, and is associated with severe malaria. PfEMP1 interacts with Complement Receptor One on uninfected erythrocytes to form rosettes. The extreme variation within these proteins and the grouping of var genes implies that var gene recombination preferentially occurs within var gene groups. These groups reflect a functional diversification that has evolved to cope with the varying conditions of transmission and host immune response met by the parasite. A recombination hotspot was uncovered between Duffy-binding-like (DBL) subdomains. Solution of the crystal structure of the N-terminal and first DBL region of PfEMP1 from the VarO variant of the PfEMP1 protein is found to be directly implicated in rosetting as the heparin-binding site. 154 matched cddid_all.tbl CDD pfam03012 pfam03012 397242 PP_M1 Phosphoprotein. This family includes the M1 phosphoprotein non-structural RNA polymerase alpha subunit, which is thought to be a component of the active polymerase, and may be involved in template binding. 296 matched cddid_all.tbl CDD pfam03013 pfam03013 460778 Pyr_excise Pyrimidine dimer DNA glycosylase. Pyrimidine dimer DNA glycosylases excise pyrimidine dimers by hydrolysis of the glycosylic bond of the 5' pyrimidine, followed by the intra-pyrimidine phosphodiester bond. Pyrimidine dimers are the major UV-lesions of DNA. 81 matched cddid_all.tbl CDD pfam03014 pfam03014 367296 SP2 Structural protein 2. This family represents structural protein 2 of the hepatitis E virus. The high basic amino acid content of this protein has lead to the suggestion of a role in viral genomic RNA encapsidation. 709 matched cddid_all.tbl CDD pfam03015 pfam03015 460779 Sterile Male sterility protein. This family represents the C-terminal region of the male sterility protein in a number of arabidopsis and drosophila. A sequence-related jojoba acyl CoA reductase is also included. 92 matched cddid_all.tbl CDD pfam03016 pfam03016 397245 Exostosin Exostosin family. The EXT family is a family of tumour suppressor genes. Mutations of EXT1 on 8q24.1, EXT2 on 11p11-13, and EXT3 on 19p have been associated with the autosomal dominant disorder known as hereditary multiple exostoses (HME). This is the most common known skeletal dysplasia. The chromosomal locations of other EXT genes suggest association with other forms of neoplasia. EXT1 and EXT2 have both been shown to encode a heparan sulphate polymerase with both D-glucuronyl (GlcA) and N-acetyl-D-glucosaminoglycan (GlcNAC) transferase activities. The nature of the defect in heparan sulphate biosynthesis in HME is unclear. 290 matched cddid_all.tbl CDD pfam03017 pfam03017 427102 Transposase_23 TNP1/EN/SPM transposase. 64 matched cddid_all.tbl CDD pfam03018 pfam03018 460780 Dirigent Dirigent-like protein. This family contains a number of proteins which are induced during disease response in plants. Members of this family are involved in lignification. 145 matched cddid_all.tbl CDD pfam03020 pfam03020 460781 LEM LEM domain. The LEM domain is 50 residues long and is composed of two parallel alpha helices. This domain is found in inner nuclear membrane proteins. It is called the LEM domain after LAP2, Emerin and Man1. 40 matched cddid_all.tbl CDD pfam03021 pfam03021 281073 CM2 Influenza C virus M2 protein. Influenza C virus M1 protein is encoded by a spliced mRNA. The unspliced mRNA is also found in small quantities and can encode the protein represented by this family. 139 matched cddid_all.tbl CDD pfam03022 pfam03022 308585 MRJP Major royal jelly protein. Royal jelly is the food of queen bee larvae, and is responsible for the high reproductive ability of the queen. Major royal jelly proteins make up around 90% of larval jelly proteins. This family also the sequence-related yellow protein of drosophila which controls pigmentation of the adult cuticle and larval mouth parts. 288 matched cddid_all.tbl CDD pfam03023 pfam03023 397249 MurJ Lipid II flippase MurJ. Peptidoglycan synthesis (PG) biosynthesis involves the formation of peptidoglycan precursor lipid II (undecaprenyl-pyrophosphate-linked N-acetyl glucosamine-N-acetyl muramic acid-pentapeptide) on the cytosolic face of the cell membrane. Lipid II is then translocated across the membrane and its glycopeptide moiety becomes incorporated into the growing cell wall mesh. MviN, renamed as MurJ, is a lipid II flippase essential for cell wall peptidoglycan synthesis. MurJ belongs to the MVF (mouse virulence factor) family of MOP superfamily transporters, which also includes the MATE (multidrug and toxic compound extrusion) transporter and eukaryotic OLF (oligosaccharidyl-lipid flippase) families. In addition to the canonical MOP transporter core consisting of 12 transmembrane helices (TMs), MurJ has two additional C-terminal TMs (13 and 14) of unknown function. Structural analysis indicates that the N lobe (TMs 1-6) and C lobe (TMs 7-14) are arranged in an inward-facing N-shape conformation, rather than the outward-facing V-shape conformation observed in all existing MATE transporter structures. Furthermore, a hydrophobic groove is formed by two C-terminal transmembrane helices, which leads into a large central cavity that is mostly cationic. Mutagenesis studies, revealed a solvent-exposed cavity that is essential for function. Mutation of conserved residues (Ser17, Arg18, Arg24, Arg52, and Arg255) at the proximal site failed to complement MurJ function, consistent with the idea that these residues are important for recognizing the diphosphate and/or sugar moieties of lipid II. It has also been suggested that the chloride ion in the central cavity and a zinc ion at the beginning of TM 7 might be functionally important. 451 matched cddid_all.tbl CDD pfam03024 pfam03024 397250 Folate_rec Folate receptor family. This family includes the folate receptor which binds to folate and reduced folic acid derivatives and mediates delivery of 5-methyltetrahydrofolate to the interior of cells. These proteins are attached to the membrane by a GPI-anchor. The proteins contain 16 conserved cysteines that form eight disulphide bridges. 172 matched cddid_all.tbl CDD pfam03025 pfam03025 145918 Papilloma_E5 Papillomavirus E5. The E5 protein from papillomaviruses is about 80 amino acids long. The proteins are contain three regions that are predicted to be transmembrane alpha helices. The function of this protein is unknown. 72 matched cddid_all.tbl CDD pfam03026 pfam03026 281077 CM1 Influenza C virus M1 protein. This family represents the matrix 1 protein of influenza C virus. The protein is the product of a spliced mRNA. Small quantities of the unspliced mRNA are found in the cell additionally encoding the M2 protein (see pfam03021). 235 matched cddid_all.tbl CDD pfam03028 pfam03028 460782 Dynein_heavy Dynein heavy chain region D6 P-loop domain. This family represents the C-terminal region of dynein heavy chain. The chain also contains ATPase activity and microtubule binding ability and acts as a motor for the movement of organelles and vesicles along microtubules. Dynein is also involved in cilia and flagella movement. The dynein subunit consists of at least two heavy chains and a number of intermediate and light chains. The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This C-terminal domain carries the D6 region of the dynein motor where the P-loop has been lost in evolution but the general structure of a potential ATP binding site appears to be retained. 115 matched cddid_all.tbl CDD pfam03029 pfam03029 397252 ATP_bind_1 Conserved hypothetical ATP binding protein. Members of this family are found in a range of archaea and eukaryotes and have hypothesized ATP binding activity. 238 matched cddid_all.tbl CDD pfam03030 pfam03030 427106 H_PPase Inorganic H+ pyrophosphatase. The H+ pyrophosphatase is an transmembrane proton pump involved in establishing the H+ electrochemical potential difference between the vacuole lumen and the cell cytosol. Vacuolar-type H(+)-translocating inorganic pyrophosphatases have long been considered to be restricted to plants and to a few species of photo-trophic bacteria. However, in recent investigations, these pyrophosphatases have been found in organizms as disparate as thermophilic Archaea and parasitic protists. 663 matched cddid_all.tbl CDD pfam03031 pfam03031 397254 NIF NLI interacting factor-like phosphatase. This family contains a number of NLI interacting factor isoforms and also an N-terminal regions of RNA polymerase II CTC phosphatase and FCP1 serine phosphatase. This region has been identified as the minimal phosphatase domain. 160 matched cddid_all.tbl CDD pfam03032 pfam03032 281082 FSAP_sig_propep Frog skin active peptide family signal and propeptide. This family contains a number of defence peptides secreted from the skin of amphibians, including the opiate-like dermorphins and deltorphins, and the antimicrobial dermoseptins and temporins. The alignment for this family consists of the signal peptide and propeptide regions and does not include the active peptides.Family members such as the peptide leucine arginine (pLR) belongs to a class of cyclic peptides isolated from frog skin. Its primary sequence is similar to the reactive loop of plant Bowman-Birk inhibitors (BBI), and the circular sunflower trypsin inhibitor-1 (SFTI-1) and to HV-BBI, an isolated peptide from amphibian skin with trypsin-inhibitory activity. pLR is a highly potent trypsin inhibitor, with therapeutic potential. A study describing immunomodulatory properties of pLR showed that the peptide is a potent activator of histamine release. Other members such as Phylloseptins are antimicrobial peptides of 19-20 residues and carry an amidated C-terminus. 46 matched cddid_all.tbl CDD pfam03033 pfam03033 427107 Glyco_transf_28 Glycosyltransferase family 28 N-terminal domain. The glycosyltransferase family 28 includes monogalactosyldiacylglycerol synthase (EC 2.4.1.46) and UDP-N-acetylglucosamine transferase (EC 2.4.1.-). This N-terminal domain contains the acceptor binding site and likely membrane association site. This family also contains a large number of proteins that probably have quite distinct activities. 139 matched cddid_all.tbl CDD pfam03034 pfam03034 460783 PSS Phosphatidyl serine synthase. Phosphatidyl serine synthase is also known as serine exchange enzyme. This family represents eukaryotic PSS I and II which are membrane bound proteins which catalyzes the replacement of the head group of a phospholipid (phosphotidylcholine or phosphotidylethanolamine) by L-serine. 273 matched cddid_all.tbl CDD pfam03035 pfam03035 367308 RNA_capsid Calicivirus putative RNA polymerase/capsid protein. 226 matched cddid_all.tbl CDD pfam03036 pfam03036 460784 Perilipin Perilipin family. The perilipin family includes lipid droplet-associated protein (perilipin), adipose differentiation-related protein (adipophilin) and TIP47, also known as perilin-3, altogether form the PAT family of proteins. They predominantly localize to the surface of intracellular neutral lipid droplets. Perilipin is a modulator of adipocyte lipid metabolism and adipophilinis and are involved in the development and maintenance of adipose tissue. This family appears to share some similarity with pfam08618. 400 matched cddid_all.tbl CDD pfam03037 pfam03037 367310 KMP11 Kinetoplastid membrane protein 11. Kinetoplastid membrane protein 11 is a major cell surface glycoprotein of the parasite Leishmania donovani. 90 matched cddid_all.tbl CDD pfam03038 pfam03038 281088 Herpes_UL95 UL95 family. Members of this family, found in several herpesviruses, include EBV BGLF3 and other UL95 proteins (e.g. HCMV UL95, HVS-1 34, HSV6 U67). Their function is unknown. 319 matched cddid_all.tbl CDD pfam03039 pfam03039 460785 IL12 Interleukin-12 alpha subunit. Interleukin 12 (IL-12) is a disulphide-bonded heterodimer consisting of a 35kDa alpha subunit and a 40kDa beta subunit. It is involved in the stimulation and maintenance of Th1 cellular immune responses, including the normal host defence against various intracellular pathogens, such as Leishmania, Toxoplasma, measles virus and HIV. IL-12 also has an important role in pathological Th1 responses, such as in inflammatory bowel disease and multiple sclerosis. Suppression of IL-12 activity in such diseases may have therapeutic benefit. On the other hand, administration of recombinant IL-12 may have therapeutic benefit in conditions associated with pathological Th2 responses. 214 matched cddid_all.tbl CDD pfam03040 pfam03040 427111 CemA CemA family. Members of this family are probable integral membrane proteins. Their molecular function is unknown. CemA proteins are found in the inner envelope membrane of chloroplasts but not in the thylakoid membrane. A cyanobacterial member of this family has been implicated in CO2 transport, but is probably not a CO2 transporter itself. They are predicted to be haem-binding however this has not been proven experimentally. 228 matched cddid_all.tbl CDD pfam03041 pfam03041 281091 Baculo_LEF-2 lef-2. The lef-2 gene (for late expression factor 2) from baculovirus is required for expression of late genes. This gene has been shown to be specifically required for expression from the vp39 and polh promoters. LEF-1 is a DNA primase and there is some evidence to suggest that LEF-2 may bind to both DNA and LEF-1. 184 matched cddid_all.tbl CDD pfam03042 pfam03042 281092 Birna_VP5 Birnavirus VP5 protein. Birnaviruses are ds RNA viruses. Non structural protein VP5 is found in RNA segment A. The function of this small viral protein is unknown. The proteins are about 150 amino acids long and contain several conserved histidines and cysteines that might form a zinc binding site (Bateman A pers. obs.). 139 matched cddid_all.tbl CDD pfam03043 pfam03043 281093 Herpes_UL87 Herpesvirus UL87 family. Members of this family are functionally uncharacterized. This family groups together EBV BcRF1, HSV-6 U58, HVS-1 24 and HCMV UL87. The proteins range from 575 to 950 amino acids in length. 523 matched cddid_all.tbl CDD pfam03044 pfam03044 281094 Herpes_UL16 Herpesvirus UL16/UL94 family. This family groups together HSV-1 UL16, HSV-6 ORF11R, EHV-1 46, HCMV UL94, EBV BGLF2 and VZV 44. UL16 protein may play a role in capsid maturation including DNA packaging/cleavage. In immunofluorescence studies, UL16 was localized to the nucleus of infected cells in areas containing high concentrations of HSV capsid proteins. These nuclear compartments have been described previously as viral assemblons and are distinct from compartments containing replicating DNA. localization within assemblons argues for a role of UL16 encoded protein in capsid assembly or maturation. 328 matched cddid_all.tbl CDD pfam03045 pfam03045 460786 DAN DAN domain. This domain contains 9 conserved cysteines and is extracellular. Therefore the cysteines may form disulphide bridges. This family of proteins has been termed the DAN family after the first member to be reported. This family includes DAN, Cerberus and Gremlin. The gremlin protein is an antagonist of bone morphogenetic protein signaling. It is postulated that all members of this family antagonize different TGF beta pfam00019 ligands. Recent work shows that the DAN protein is not an efficient antagonist of BMP-2/4 class signals, we found that DAN was able to interact with GDF-5 in a frog embryo assay, suggesting that DAN may regulate signaling by the GDF-5/6/7 class of BMPs in vivo. 108 matched cddid_all.tbl CDD pfam03047 pfam03047 335196 ComC COMC family. This family consists exclusively of streptococcal competence stimulating peptide precursors, which are generally up to 50 amino acid residues long. In all the members of this family, the leader sequence is cleaved after two conserved glycine residues; thus the leader sequence is of the double- glycine type. Competence stimulating peptides (CSP) are small (less than 25 amino acid residues) cationic peptides. The N-terminal amino acid residue is negatively charged, either glutamate or aspartate. The C-terminal end is positively charged. The third residue is also positively charged: a highly conserved arginine. A few COMC proteins and their precursors (not included in this family) do not fully follow the above description. In particular: the leader sequence in the CSP precursor from Streptococcus sanguis NCTC 7863 is not of the double-glycine type; the CSP from Streptococcus gordonii NCTC 3165 does not have a negatively charged N-terminus residue and has a lysine instead of arginine at the third position. Functionally, CSP act as pheromones, stimulating competence for genetic transformation in streptococci. In streptococci, the (CSP mediated) competence response requires exponential cell growth at a critical density, a relatively simple requirement when compared to the stationary-phase requirement of Haemophilus, or the late-logarithmic- phase of Bacillus. All bacteria induced to competence by a particular CSP are said to belong to the same pherotype, because each CSP is recognized by a specific receptor (the signalling domain of a histidine kinase ComD). Pherotypes are not necessarily species-specific. In addition, an organizm may change pherotype. There are two possible mechanisms for pherotype switching: horizontal gene transfer, and accumulation of point mutations. The biological significance of pherotypes and pherotype switching is not definitively determined. Pherotype switching occurs frequently enough in naturally competent streptococci to suggest that it may be an important contributor to genetic exchange between different bacterial species. The family Antibacterial16, streptolysins from group A streptococci, has been merged into this family. 31 matched cddid_all.tbl CDD pfam03048 pfam03048 281097 Herpes_UL92 UL92 family. Members of this family, found in several herpesviruses, include EBV BDLF4, HCMV UL92, HHV8 31, HSV6 U63. Their function is unknown. The N terminus of this protein contains 6 conserved cysteines and histidines that might form a zinc binding domain (A Bateman pers. obs.). 189 matched cddid_all.tbl CDD pfam03049 pfam03049 281098 Herpes_UL79 UL79 family. Members of this family are functionally uncharacterized proteins from herpesviruses. This family groups together HSV-6 U52, HVS-1 18 and HCMV UL79. 254 matched cddid_all.tbl CDD pfam03050 pfam03050 427113 DDE_Tnp_IS66 Transposase IS66 family. Transposase proteins are necessary for efficient DNA transposition. This family includes IS66 from Agrobacterium tumefaciens. 281 matched cddid_all.tbl CDD pfam03051 pfam03051 397262 Peptidase_C1_2 Peptidase C1-like family. This family is closely related to the Peptidase_C1 family pfam00112, containing several prokaryotic and eukaryotic aminopeptidases and bleomycin hydrolases. 438 matched cddid_all.tbl CDD pfam03052 pfam03052 308597 Adeno_52K Adenoviral protein L1 52/55-kDa. The adenoviral protein L1 52/55-kDa is expressed in both the early and late stages of infection which suggests that it could play multiple roles in the viral life cycle. The L1 52/55 kDa protein interacts with the viral IVa2 protein and is required for DNA packaging. L1 53/55-kDa is required to mediate stable association between the viral DNA and empty capsid. 198 matched cddid_all.tbl CDD pfam03053 pfam03053 251695 Corona_NS3b ORF3b coronavirus protein. Members of this family are non-structural proteins, approximately 250 amino acid residues long. They are found in transmissible gastroenteritis coronavirus (TGEV) and porcine respiratory coronavirus (PRCV) isolates. These proteins are found on the same mRNA as another product, designated ORF3a. While ORF3a/b has been implicated in TGEV and PRCV pathogenesis, its precise role remains unclear (see.. 226 matched cddid_all.tbl CDD pfam03054 pfam03054 460787 tRNA_Me_trans tRNA methyl transferase HUP domain. This family represents the N-terminal HUP domain in tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs. 202 matched cddid_all.tbl CDD pfam03055 pfam03055 460788 RPE65 Retinal pigment epithelial membrane protein. This family represents a retinal pigment epithelial membrane receptor which is abundantly expressed in retinal pigment epithelium, and binds plasma retinal binding protein. The family also includes the sequence related neoxanthin cleavage enzyme in plants and lignostilbene-alpha,beta-dioxygenase in bacteria. 449 matched cddid_all.tbl CDD pfam03057 pfam03057 460789 DUF236 DUF236 repeat. This family represents a short repeat region found a number of C. elegans proteins of unknown function. 31 matched cddid_all.tbl CDD pfam03058 pfam03058 251699 Sar8_2 Sar8.2 family. Members of this family are found in Solanaceae plants, a taxonomic group (family) that includes pepper and tobacco plant species. Synthesis of these proteins is induced by tobacco mosaic virus (TMV) and salicylic acid; indeed they are thought to be involved in the development of systemic acquired resistance (SAR) after an initial hypersensitive response to microbial infection. SAR is characterized by long-lasting resistance to infection by a wide range of pathogens, extending to plant tissues distant from the initial infection site. 85 matched cddid_all.tbl CDD pfam03059 pfam03059 308600 NAS Nicotianamine synthase protein. Nicotianamine synthase EC:2.5.1.43 catalyzes the trimerization of S-adenosylmethionine to yield one molecule of nicotianamine. Nicotianamine has an important role in plant iron uptake mechanisms. Plants adopt two strategies (termed I and II) of iron acquisition. Strategy I is adopted by all higher plants except graminaceous plants, which adopt strategy II. In strategy I plants, the role of nicotianamine is not fully determined: possible roles include the formation of more stable complexes with ferrous than with ferric ion, which might serve as a sensor of the physiological status of iron within a plant, or which might be involved in the transport of iron. In strategy II (graminaceous) plants, nicotianamine is the key intermediate (and nicotianamine synthase the key enzyme) in the synthesis of the mugineic family (the only known family in plants) of phytosiderophores. Phytosiderophores are iron chelators whose secretion by the roots is greatly increased in instances of iron deficiency. The 3D structures of five example NAS from Methanothermobacter thermautotrophicus reveal the monomer to consist of a five-helical bundle N-terminal domain on top of a classic Rossmann fold C-terminal domain. The N-terminal domain is unique to the NAS family, whereas the C-terminal domain is homologous to the class I family of SAM-dependent methyltransferases. An active site is created at the interface of the two domains, at the rim of a large cavity that corresponds to the nucleotide binding site such as is found in other proteins adopting a Rossmann fold. 276 matched cddid_all.tbl CDD pfam03060 pfam03060 367316 NMO Nitronate monooxygenase. Nitronate monooxygenase (NMO), formerly referred to as 2-nitropropane dioxygenase (NPD) (EC:1.13.11.32), is an FMN-dependent enzyme that uses molecular oxygen to oxidize (anionic) alkyl nitronates and, in the case of the enzyme from Neurospora crassa, (neutral) nitroalkanes to the corresponding carbonyl compounds and nitrite. Previously classified as 2-nitropropane dioxygenase, but it is now recognized that this was the result of the slow ionization of nitroalkanes to their nitronate (anionic) forms. The enzymes from the fungus Neurospora crassa and the yeast Williopsis saturnus var. mrakii (formerly classified as Hansenula mrakii) contain non-covalently bound FMN as the cofactor. Active towards linear alkyl nitronates of lengths between 2 and 6 carbon atoms and, with lower activity, towards propyl-2-nitronate. The enzyme from N. crassa can also utilize neutral nitroalkanes, but with lower activity. One atom of oxygen is incorporated into the carbonyl group of the aldehyde product. The reaction appears to involve the formation of an enzyme-bound nitronate radical and an a-peroxynitroethane species, which then decomposes, either in the active site of the enzyme or after release, to acetaldehyde and nitrite. 331 matched cddid_all.tbl CDD pfam03061 pfam03061 427116 4HBT Thioesterase superfamily. This family contains a wide variety of enzymes, principally thioesterases. This family includes 4HBT (EC 3.1.2.23) which catalyzes the final step in the biosynthesis of 4-hydroxybenzoate from 4-chlorobenzoate in the soil dwelling microbe Pseudomonas CBS-3. This family includes various cytosolic long-chain acyl-CoA thioester hydrolases. Long-chain acyl-CoA hydrolases hydrolyse palmitoyl-CoA to CoA and palmitate, they also catalyze the hydrolysis of other long chain fatty acyl-CoA thioesters. 79 matched cddid_all.tbl CDD pfam03062 pfam03062 427117 MBOAT MBOAT, membrane-bound O-acyltransferase family. The MBOAT (membrane bound O-acyl transferase) family of membrane proteins contains a variety of acyltransferase enzymes. A conserved histidine has been suggested to be the active site residue. 334 matched cddid_all.tbl CDD pfam03063 pfam03063 460790 Prismane Prismane/CO dehydrogenase family. This family includes both hybrid-cluster proteins and the beta chain of carbon monoxide dehydrogenase. The hybrid-cluster proteins contain two Fe/S centres - a [4Fe-4S] cubane cluster, and a hybrid [4Fe-2S-2O] cluster. The physiological role of this protein is as yet unknown, although a role in nitrate/nitrite respiration has been suggested. The prismane protein from Escherichia coli was shown to contain hydroxylamine reductase activity (NH2OH + 2e + 2 H+ -> NH3 + H2O). This activity is rather low. Hydroxylamine reductase activity was also found in CO-dehydrogenase in which the active site Ni was replaced by Fe. The CO dehydrogenase contains a Ni-3Fe-2S-3O centre. 539 matched cddid_all.tbl CDD pfam03064 pfam03064 460791 U79_P34 HSV U79 / HCMV P34. This family represents herpes virus protein U79 and cytomegalovirus early phosphoprotein P34 (UL112). 134 matched cddid_all.tbl CDD pfam03065 pfam03065 397267 Glyco_hydro_57 Glycosyl hydrolase family 57. This family includes alpha-amylase (EC:3.2.1.1), 4--glucanotransferase (EC:2.4.1.-) and amylopullulanase enzymes. 293 matched cddid_all.tbl CDD pfam03066 pfam03066 460792 Nucleoplasmin Nucleoplasmin/nucleophosmin domain. Nucleoplasmins are also known as chromatin decondensation proteins. They bind to core histones and transfer DNA to them in a reaction that requires ATP. This is thought to play a role in the assembly of regular nucleosomal arrays. 102 matched cddid_all.tbl CDD pfam03067 pfam03067 460793 LPMO_10 Lytic polysaccharide mono-oxygenase, cellulose-degrading. This domain is found associated with a wide variety of cellulose binding domains. This is a family of two very closely related proteins that together act as both a C1- and a C4-oxidising lytic polysaccharide mono-oxygenase, degrading cellulose. This domain is also found in baculoviral spheroidins and spindolins, protein of unknown function. 184 matched cddid_all.tbl CDD pfam03068 pfam03068 460794 PAD Protein-arginine deiminase (PAD). Members of this family are found in mammals. In the presence of calcium ions, PAD enzymes EC:3.5.3.15 catalyze the post-translational modification reaction responsible for the formation of citrulline residues: Protein L-arginine + H2O <=> Protein L-citrulline + NH3. Several types are recognized (and included in the family) on the basis of molecular mass, substrate specificity, and tissue localization. The expression of type I PAD is known to be under the control of oestrogen. 393 matched cddid_all.tbl CDD pfam03069 pfam03069 397271 FmdA_AmdA Acetamidase/Formamidase family. This family includes amidohydrolases of formamide EC:3.5.1.49 and acetamide. Swiss:Q50228 forms a homotrimer suggesting all the members of this family also do. 271 matched cddid_all.tbl CDD pfam03070 pfam03070 397272 TENA_THI-4 TENA/THI-4/PQQC family. Members of this family are found in all the three major phyla of life: archaebacteria, eubacteria, and eukaryotes. In Bacillus subtilis, TENA is one of a number of proteins that enhance the expression of extracellular enzymes, such as alkaline protease, neutral protease and levansucrase. The THI-4 protein, which is involved in thiamine biosynthesis, is also a member of this family. The C-terminal part of these proteins consistently show significant sequence similarity to TENA proteins. This similarity was first noted with the Neurospora crassa THI-4. This family includes bacterial coenzyme PQQ synthesis protein C or PQQC proteins. Pyrroloquinoline quinone (PQQ) is the prosthetic group of several bacterial enzymes,including methanol dehydrogenase of methylotrophs and the glucose dehydrogenase of a number of bacteria. PQQC has been found to be required in the synthesis of PQQ but its function is unclear. The exact molecular function of members of this family is uncertain. 210 matched cddid_all.tbl CDD pfam03071 pfam03071 397273 GNT-I GNT-I family. Alpha-1,3-mannosyl-glycoprotein beta-1,2-N-acetylglucosaminyltransferase (GNT-I, GLCNAC-T I) EC:2.4.1.101 transfers N-acetyl-D-glucosamine from UDP to high-mannose glycoprotein N-oligosaccharide. This is an essential step in the synthesis of complex or hybrid-type N-linked oligosaccharides. The enzyme is an integral membrane protein localized to the Golgi apparatus, and is probably distributed in all tissues. The catalytic domain is located at the C-terminus. 434 matched cddid_all.tbl CDD pfam03072 pfam03072 281117 DUF237 Domain of unknown function (DUF237). This is a domain of unknown function found in mycoplasma. It is found at the C-terminal region. 137 matched cddid_all.tbl CDD pfam03073 pfam03073 460795 TspO_MBR TspO/MBR family. Tryptophan-rich sensory protein (TspO) is an integral membrane protein that acts as a negative regulator of the expression of specific photosynthesis genes in response to oxygen/light. It is involved in the efflux of porphyrin intermediates from the cell. This reduces the activity of coproporphyrinogen III oxidase, which is thought to lead to the accumulation of a putative repressor molecule that inhibits the expression of specific photosynthesis genes. Several conserved aromatic residues are necessary for TspO function: they are thought to be involved in binding porphyrin intermediates. In, the rat mitochondrial peripheral benzodiazepine receptor (MBR) was shown to not only retain its structure within a bacterial outer membrane, but also to be able to functionally substitute for TspO in TspO- mutants, and to act in a similar manner to TspO in its in situ location: the outer mitochondrial membrane. The biological significance of MBR remains unclear, however. It is thought to be involved in a variety of cellular functions, including cholesterol transport in steroidogenic tissues. 144 matched cddid_all.tbl CDD pfam03074 pfam03074 460796 GCS Glutamate-cysteine ligase. This family represents the catalytic subunit of glutamate-cysteine ligase (E.C. 6.3.2.2), also known as gamma-glutamylcysteine synthetase (GCS). This enzyme catalyzes the rate limiting step in the biosynthesis of glutathione. The eukaryotic enzyme is a dimer of a heavy chain and a light chain with all the catalytic activity exhibited by the heavy chain (this family). 369 matched cddid_all.tbl CDD pfam03076 pfam03076 281120 GP3 Equine arteritis virus GP3. This protein is encoded by ORF3 of equine arteritis virus. The function is unknown. 160 matched cddid_all.tbl CDD pfam03077 pfam03077 427124 VacA2 Putative vacuolating cytotoxin. This family contains a number of Helicobacter outer membrane proteins with multiple copies of this small conserved region. 58 matched cddid_all.tbl CDD pfam03078 pfam03078 251715 ATHILA ATHILA ORF-1 family. ATHILA is a group of Arabidopsis thaliana retrotransposons belonging to the Ty3/gypsy family of the long terminal repeat (LTR) class of eukaryotic retrotransposons. The central region of ATHILA retrotransposons contains two or three open reading frames (ORFs). This family represents the ORF1 product. The function of ORF1 is unknown. 456 matched cddid_all.tbl CDD pfam03079 pfam03079 281122 ARD ARD/ARD' family. The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+. ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion. The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions. ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalyzed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels. This family also contains other members, whose functions are not well characterized. 157 matched cddid_all.tbl CDD pfam03080 pfam03080 460797 Neprosin Neprosin. Pitcher plants are insectivorous and secrete a digestive fluid into the pitcher. This fluid contains a mixture of enzymes including peptidases. One of these is neprosin, characterized from the pitcher plant Nepenthes ventrata. This peptidase is of unknown catalytic type and is unaffected by standard peptidase inhibitors. Unusually, activity is directed towards prolyl bonds, but unlike most peptidase that cleave after proline, there is no restriction on sequence length or position of the proline residue. The peptidase is secreted and is presumed to possess an N-terminal activation peptide. The neprosin domain corresponds to the mature peptidase. It is not known if other proteins with this domain are peptidases. 211 matched cddid_all.tbl CDD pfam03081 pfam03081 460798 Exo70 Exo70 exocyst complex subunit. The Exo70 protein forms one subunit of the exocyst complex. First discovered in S. cerevisiae, Exo70 and other exocyst proteins have been observed in several other eukaryotes, including humans. In S. cerevisiae, the exocyst complex is involved in the late stages of exocytosis, and is localized at the tip of the bud, the major site of exocytosis in yeast. Exo70 interacts with the Rho3 GTPase. This interaction mediates one of the three known functions of Rho3 in cell polarity: vesicle docking and fusion with the plasma membrane (the other two functions are regulation of actin polarity and transport of exocytic vesicles from the mother cell to the bud). In humans, the functions of Exo70 and the exocyst complex are less well characterized: Exo70 is expressed in several tissues and is thought to also be involved in exocytosis. 373 matched cddid_all.tbl CDD pfam03082 pfam03082 281125 MAGSP Male accessory gland secretory protein. The accessory gland of male insects is a genital tissue that secretes many components of the ejaculatory fluid, some of which affect the female's receptivity to courtship and her rate of oviposition. This protein is expressed exclusively in the male accessory glands of adult Drosophila melanogaster. The proteins are transferred to the female fly during copulation and are rapidly altered in the female genital tract. 267 matched cddid_all.tbl CDD pfam03083 pfam03083 397278 MtN3_slv Sugar efflux transporter for intercellular exchange. This family includes proteins such as drosophila saliva, MtN3 involved in root nodule development and a protein involved in activation and expression of recombination activation genes (RAGs). Although the molecular function of these proteins is unknown, they are almost certainly transmembrane proteins. This family contains a region of two transmembrane helices that is found in two copies in most members of the family. This family also contains specific sugar efflux transporters that are essential for the maintenance of animal blood glucose levels, plant nectar production, and plant seed and pollen development. In many organizims it meditaes gluose transport; in Arabidopsis it is necessary for pollen viability; and two of the rice homologs are specifically exploited by bacterial pathogens for virulence by means of direct binding of a bacterial effector to the SWEET promoter. 87 matched cddid_all.tbl CDD pfam03084 pfam03084 460799 Sigma_1_2 Reoviral Sigma1/Sigma2 family. Reoviruses are double-stranded RNA viruses. They lack a membrane envelope and their capsid is organized in two concentric icosahedral layers: an inner core and an outer capsid layer. The sigma1 protein is found in the outer capsid, and the sigma2 protein is found in the core. There are four other kinds of protein (besides sigma2) in the core, termed lambda 1-3, mu2. Interactions between sigma2 and lambda 1 and lambda 3 are thought to initiate core formation, followed by mu2 and lambda2. Sigma1 is a trimeric protein, and is positioned at the 12 vertices of the icosahedral outer capsid layer. Its N-terminal fibrous tail, arranged as a triple coiled coil, anchors it in the virion, and a C-terminal globular head interacts with the cellular receptor. These two parts form by separate trimerization events. The N-terminal fibrous tail forms on the polysome, without the involvement of ATP or chaperones. The post- translational assembly of the C-terminal globular head involves the chaperone activity of Hsp90, which is associated with phosphorylation of Hsp90 during the process. Sigma1 protein acts as a cell attachment protein, and determines viral virulence, pathways of spread, and tropism. Junctional adhesion molecule has been identified as a receptor for sigma1. In type 3 reoviruses, a small region, predicted to form a beta sheet, in the N-terminal tail was found to bind target cell surface sialic acid (i.e. sialic acid acts as a co-receptor) and promote apoptosis. The sigma1 protein also binds to the lambda2 core protein. 443 matched cddid_all.tbl CDD pfam03085 pfam03085 367327 RAP-1 Rhoptry-associated protein 1 (RAP-1). Members of this family are found in Babesia species. Though not in this Pfam family, rhoptry-associated proteins are also found in Plasmodium falciparum. Indeed, animal infection with Babesia may produce a pattern similar to human malaria. Rhoptry organelles form part of the apical complex in apicomplexan parasites. Rhoptry-associated proteins are antigenic, and generate partially protective immune responses in infected mammals. Thus RAPs are among the targeted vaccine antigens for babesial (and malarial) parasites. However, RAP-1 proteins are encoded by by a multigene family; thus RAP-1 proteins are polymorphic, with B and T cell epitopes that are conserved among strains, but not across species. Antibodies to Babesia RAP-1 may also be helpful in the serological detection of Babesia infections. 241 matched cddid_all.tbl CDD pfam03086 pfam03086 281129 DUF240 Domain of unknown function (DUF240). This is a domain of unknown function found in mycoplasma. It is found at the N-terminal region. 119 matched cddid_all.tbl CDD pfam03087 pfam03087 427127 BPS1 Protein BPS1. This family includes protein BPS1 (Protein BYPASS 1) from Arabidopsis, which is required for normal root and shoot development. It prevents constitutive production of a root mobile carotenoid-derived signalling compound that is capable of arresting shoot and leaf development. 239 matched cddid_all.tbl CDD pfam03088 pfam03088 281131 Str_synth Strictosidine synthase. Strictosidine synthase (E.C. 4.3.3.2) is a key enzyme in alkaloid biosynthesis. It catalyzes the condensation of tryptamine with secologanin to form strictosidine. 89 matched cddid_all.tbl CDD pfam03089 pfam03089 427128 RAG2 Recombination activating protein 2. V-D-J recombination is the combinatorial process by which the huge range of immunoglobulin and T cell binding specificity is generated from a limited amount of genetic material. This process is synergistically activated by RAG1 and RAG2 in developing lymphocytes. Defects in RAG2 in humans are a cause of severe combined immunodeficiency B cell negative and Omenn syndrome. 339 matched cddid_all.tbl CDD pfam03090 pfam03090 427129 Replicase Replicase family. This is a family of bacterial plasmid DNA replication initiator proteins. Pfam: PF01051 is a similar family. These RepA proteins exist as monomers and dimers in equilibrium: monomers bind directly to repeated DNA sequences and thus activate replication; dimers repress repA transcription by binding an inversely repeated DNA operator. Dimer dissociation can occur spontaneously or be mediated by Hsp70 chaperones. 128 matched cddid_all.tbl CDD pfam03091 pfam03091 460800 CutA1 CutA1 divalent ion tolerance protein. Several gene loci with a possible involvement in cellular tolerance to copper have been identified. One such locus in eubacteria and archaebacteria, cutA, is thought to be involved in cellular tolerance to a wide variety of divalent cations other than copper. The cutA locus consists of two operons, of one and two genes. The CutA1 protein is a cytoplasmic protein, encoded by the single-gene operon and has been linked to divalent cation tolerance. It has no recognized structural motifs. This family also contains putative proteins from eukaryotes (human and Drosophila). 98 matched cddid_all.tbl CDD pfam03092 pfam03092 308617 BT1 BT1 family. Members of this family are transmembrane proteins. Several are Leishmania putative proteins that are thought to be pteridine transporters. One such protein Swiss:Q25272, previously termed (and is still annotated as) ORFG, was shown to encode a biopterin transport protein using null mutants, thus being subsequently renamed BT1. The significant similarity of ORFG/BT1 to Trypanosoma brucei ESAG10 (a putative transmembrane protein and another member of this family) was previously noted. This family also contains five putative Arabidopsis thaliana proteins of unknown function. In addition, it also contains two predicted prokaryotic proteins (from the cyanobacteria Synechocystis and Synechococcus). 432 matched cddid_all.tbl CDD pfam03094 pfam03094 460801 Mlo Mlo family. A family of plant integral membrane proteins, first discovered in barley. Mutants lacking wild-type Mlo proteins show broad spectrum resistance to the powdery mildew fungus, and dysregulated cell death control, with spontaneous cell death in response to developmental or abiotic stimuli. Thus wild-type Mlo proteins are thought to be inhibitors of cell death whose deficiency lowers the threshold required to trigger the cascade of events that result in plant cell death. Mlo proteins are localized in the plasma membrane and possess seven transmembrane regions; thus the Mlo family is the only major higher plant family to possess 7 transmembrane domains. It has been suggested that Mlo proteins function as G-protein coupled receptors in plants; however the molecular and biological functions of Mlo proteins remain to be fully determined. 483 matched cddid_all.tbl CDD pfam03095 pfam03095 460802 PTPA Phosphotyrosyl phosphate activator (PTPA) protein. Phosphotyrosyl phosphatase activator (PTPA) proteins stimulate the phosphotyrosyl phosphatase (PTPase) activity of the dimeric form of protein phosphatase 2A (PP2A). PTPase activity in PP2A (in vitro) is relatively low when compared to the better recognized phosphoserine/ threonine protein phosphorylase activity. The specific biological role of PTPA is unknown, Basal expression of PTPA depends on the activity of a ubiquitous transcription factor, Yin Yang 1 (YY1). The tumour suppressor protein p53 can inhibit PTPA expression through an unknown mechanism that negatively controls YY1. 293 matched cddid_all.tbl CDD pfam03096 pfam03096 397285 Ndr Ndr family. This family consists of proteins from different gene families: Ndr1/RTP/Drg1, Ndr2, and Ndr3. Their similarity was previously noted. The precise molecular and cellular function of members of this family is still unknown. Yet, they are known to be involved in cellular differentiation events. The Ndr1 group was the first to be discovered. Their expression is repressed by the proto-oncogenes N-myc and c-myc, and in line with this observation, Ndr1 protein expression is down-regulated in neoplastic cells, and is reactivated when differentiation is induced by chemicals such as retinoic acid. Ndr2 and Ndr3 expression is not under the control of N-myc or c-myc. Ndr1 expression is also activated by several chemicals: tunicamycin and homocysteine induce Ndr1 in human umbilical endothelial cells; nickel induces Ndr1 in several cell types. Members of this family are found in wide variety of multicellular eukaryotes, including an Ndr1 type protein in Helianthus annuus (sunflower), known as Sf21. Interestingly, the highest scoring matches in the noise are all alpha/beta hydrolases pfam00561, suggesting that this family may have an enzymatic function (Bateman A pers. obs.). 285 matched cddid_all.tbl CDD pfam03097 pfam03097 460803 BRO1 BRO1-like domain. This domain is found in a number proteins including Rhophilin and BRO1. It is known to have a role in endosomal targeting. ESCRT-III subunit Snf7 binds to a conserved hydrophobic patch in the BRO1 domain that is required for protein complex formation and for the protein-sorting function of BRO1. 366 matched cddid_all.tbl CDD pfam03098 pfam03098 460804 An_peroxidase Animal haem peroxidase. 531 matched cddid_all.tbl CDD pfam03099 pfam03099 427135 BPL_LplA_LipB Biotin/lipoate A/B protein ligase family. This family includes biotin protein ligase, lipoate-protein ligase A and B. Biotin is covalently attached at the active site of certain enzymes that transfer carbon dioxide from bicarbonate to organic acids to form cellular metabolites. Biotin protein ligase (BPL) is the enzyme responsible for attaching biotin to a specific lysine at the active site of biotin enzymes. Each organizm probably has only one BPL. Biotin attachment is a two step reaction that results in the formation of an amide linkage between the carboxyl group of biotin and the epsilon-amino group of the modified lysine. Lipoate-protein ligase A (LPLA) catalyzes the formation of an amide linkage between lipoic acid and a specific lysine residue in lipoate dependent enzymes. The unusual biosynthesis pathway of lipoic acid is mechanistically intertwined with attachment of the cofactor. 132 matched cddid_all.tbl CDD pfam03100 pfam03100 460805 CcmE CcmE. CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organizms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor. 129 matched cddid_all.tbl CDD pfam03101 pfam03101 335217 FAR1 FAR1 DNA-binding domain. This domain contains a WRKY like fold and is therefore most likely a zinc binding DNA-binding domain. 90 matched cddid_all.tbl CDD pfam03102 pfam03102 427137 NeuB NeuB family. NeuB is the prokaryotic N-acetylneuraminic acid (Neu5Ac) synthase. It catalyzes the direct formation of Neu5Ac (the most common sialic acid) by condensation of phosphoenolpyruvate (PEP) and N-acetylmannosamine (ManNAc). This reaction has only been observed in prokaryotes; eukaryotes synthesize the 9-phosphate form, Neu5Ac-9-P, and utilize ManNAc-6-P instead of ManNAc. Such eukaryotic enzymes are not present in this family. This family also contains SpsE spore coat polysaccharide biosynthesis proteins. 239 matched cddid_all.tbl CDD pfam03103 pfam03103 460806 DUF243 Domain of unknown function (DUF243). This family of uncharacterized proteins is only found in fly proteins. It is found associated with YLP motifs pfam02757 in some proteins. 98 matched cddid_all.tbl CDD pfam03104 pfam03104 397292 DNA_pol_B_exo1 DNA polymerase family B, exonuclease domain. This domain has 3' to 5' exonuclease activity and adopts a ribonuclease H type fold. 333 matched cddid_all.tbl CDD pfam03105 pfam03105 460807 SPX SPX domain. We have named this region the SPX domain after SYG1, Pho81 and XPR1. This 180 residue long domain is found at the amino terminus of a variety of proteins. In the yeast protein SYG1, the N-terminus directly binds to the G-protein beta subunit and inhibits transduction of the mating pheromone signal. Similarly, the N-terminus of the human XPR1 protein binds directly to the beta subunit of the G-protein heterotrimer leading to increased production of cAMP. These findings suggest that all the members of this family are involved in G-protein associated signal transduction. The N-termini of several proteins involved in the regulation of phosphate transport, including the putative phosphate level sensors PHO81 from Saccharomyces cerevisiae and NUC-2 from Neurospora crassa, are also members of this family. The SPX domain of S. cerevisiae low-affinity phosphate transporters Pho87 and Pho90 auto-regulates uptake and prevents efflux. This SPX dependent inhibition is mediated by the physical interaction with Spl2 NUC-2 contains several ankyrin repeats pfam00023. Several members of this family are annotated as XPR1 proteins: the xenotropic and polytropic retrovirus receptor confers susceptibility to infection with murine xenotropic and polytropic leukaemia viruses (MLV). Infection by these retroviruses can inhibit XPR1-mediated cAMP signalling and result in cell toxicity and death. The similarity between SYG1, phosphate regulators and XPR1 sequences has been previously noted, as has the additional similarity to several predicted proteins, of unknown function, from Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans, Schizosaccharomyces pombe, and Saccharomyces cerevisiae, and many other diverse organizms. In addition, given the similarities between XPR1 and SYG1 and phosphate regulatory proteins, it has been proposed that XPR1 might be involved in G-protein associated signal transduction and may itself function as a phosphate sensor. 339 matched cddid_all.tbl CDD pfam03106 pfam03106 460808 WRKY WRKY DNA -binding domain. 57 matched cddid_all.tbl CDD pfam03107 pfam03107 427141 C1_2 C1 domain. This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in pfam00130, therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol (A Bateman pers. obs.). This family are found in plant proteins. 48 matched cddid_all.tbl CDD pfam03108 pfam03108 427142 DBD_Tnp_Mut MuDR family transposase. This region is found in plant proteins that are presumed to be the transposases for Mutator transposable elements. These transposons contain two ORFs. The molecular function of this region is unknown. 67 matched cddid_all.tbl CDD pfam03109 pfam03109 427143 ABC1 ABC1 atypical kinase-like domain. This family includes ABC1 from yeast and AarF from E. coli. These proteins have a nuclear or mitochondrial subcellular location in eukaryotes. The exact molecular functions of these proteins is not clear, however yeast ABC1 suppresses a cytochrome b mRNA translation defect and is essential for the electron transfer in the bc 1 complex and E. coli AarF is required for ubiquinone production. It has been suggested that members of the ABC1 family are novel chaperonins. These proteins are unrelated to the ABC transporter proteins. 245 matched cddid_all.tbl CDD pfam03110 pfam03110 460809 SBP SBP domain. SBP domains (for SQUAMOSA-pROMOTER BINDING PROTEIN) are found in plant proteins. It is a sequence specific DNA-binding domain. Members of family probably function as transcription factors involved in the control of early flower development. The domain contains 10 conserved cysteine and histidine residues that probably are zinc ligands. 75 matched cddid_all.tbl CDD pfam03112 pfam03112 281152 DUF244 Uncharacterized protein family (ORF7) DUF. Several members of this family are Borrelia burgdorferi plasmid proteins of uncharacterized function. 161 matched cddid_all.tbl CDD pfam03113 pfam03113 427145 RSV_NS2 Respiratory synctial virus non-structural protein NS2. The molecular structure and function of the NS2 protein is not known. However, mutants lacking the NS2 grow at slower rates when compared to the wild-type. Nevertheless, NS2 is not essential for viral replication. 124 matched cddid_all.tbl CDD pfam03114 pfam03114 460810 BAR BAR domain. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different protein families. A BAR domain with an additional N-terminal amphipathic helix (an N-BAR) can drive membrane curvature. These N-BAR domains are found in amphiphysin, endophilin, BRAP and Nadrin. BAR domains are also frequently found alongside domains that determine lipid specificity, like pfam00169 and pfam00787 domains in beta centaurins and sorting nexins respectively. 235 matched cddid_all.tbl CDD pfam03115 pfam03115 367340 Astro_capsid_N Astrovirus capsid protein precursor. This product is encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The 87kD precursor protein undergoes an intracellular cleavage to form a 79kD protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion. 431 matched cddid_all.tbl CDD pfam03116 pfam03116 460811 NQR2_RnfD_RnfE NQR2, RnfD, RnfE family. This family of bacterial proteins includes a sodium-translocating NADH-ubiquinone oxidoreductase (i.e. a respiration linked sodium pump). In Vibrio cholerae, it negatively regulates the expression of virulence factors through inhibiting (by an unknown mechanism) the transcription of the transcriptional activator ToxT. The family also includes proteins involved in nitrogen fixation, RnfD and RnfE. The similarity of these proteins to NADH-ubiquinone oxidoreductases was previously noted. 304 matched cddid_all.tbl CDD pfam03117 pfam03117 281157 Herpes_UL49_1 UL49 family. Members of this family, found in several herpesviruses, include EBV BFRF2 and other UL49 proteins (e.g. HCMVA UL49, HSV6 U33). There are eight conserved cysteine residues in this alignment, all lying towards the C-terminus. Their function is unknown. 243 matched cddid_all.tbl CDD pfam03118 pfam03118 427148 RNA_pol_A_CTD Bacterial RNA polymerase, alpha chain C terminal domain. The alpha subunit of RNA polymerase consists of two independently folded domains, referred to as amino-terminal and carboxyl terminal domains. The amino terminal domain is involved in the interaction with the other subunits of the RNA polymerase. The carboxyl-terminal domain interacts with the DNA and activators. The amino acid sequence of the alpha subunit is conserved in prokaryotic and chloroplast RNA polymerases. There are three regions of particularly strong conservation, two in the amino-terminal and one in the carboxyl- terminal. 63 matched cddid_all.tbl CDD pfam03119 pfam03119 460812 DNA_ligase_ZBD NAD-dependent DNA ligase C4 zinc finger domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor. This family is a small zinc binding motif that is presumably DNA binding. IT is found only in NAD dependent DNA ligases. 26 matched cddid_all.tbl CDD pfam03120 pfam03120 460813 DNA_ligase_OB NAD-dependent DNA ligase OB-fold domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor. This family is a small domain found after the adenylation domain pfam01653 in NAD dependent ligases. OB-fold domains generally are involved in nucleic acid binding. 79 matched cddid_all.tbl CDD pfam03121 pfam03121 367342 Herpes_UL52 Herpesviridae UL52/UL70 DNA primase. Herpes simplex virus type 1 DNA replication in host cells is known to be mediated by seven viral-encoded proteins, three of which form a heterotrimeric DNA helicase-primase complex. This complex consists of UL5, UL8, and UL52 subunits. Heterodimers consisting of UL5 and UL52 have been shown to retain both helicase and primase activities. Nevertheless, UL8 is still essential for replication: though it lacks any DNA binding or catalytic activities, it is involved in the transport of UL5-UL52 and it also interacts with other replication proteins. The molecular mechanisms of the UL5-UL52 catalytic activities are not known. While UL5 is associated with DNA helicase activity and UL52 with DNA primase activity, the helicase activity requires the interaction of UL5 and UL52. It is not known if the primase activity can be maintained by UL52 alone. The region encompassed by residues 610-636 of HSV1 UL52 is thought to contain a divalent metal cation binding motif. Indeed, this region contains several aspartate and glutamate residues that might be involved in divalent cation binding. The biological significance of UL52-UL8 interaction is not known. Yeast two-hybrid analysis together with immunoprecipitation experiments have shown that the HSV1 UL52 region between residues 366-914 is essential for this interaction, while the first 349 N-terminal residues are dispensable. This family also includes protein UL70 from cytomegalovirus (CMV, a subgroup of the Herpesviridae) strains, which, by analogy with UL52, is thought to have DNA primase activity. Indeed, CMV strains also possess a DNA helicase-primase complex, the other subunits being protein UL105 (with known similarity to HSV1 UL5) and protein UL102. 75 matched cddid_all.tbl CDD pfam03122 pfam03122 460814 Herpes_MCP Herpes virus major capsid protein. This family represents the major capsid protein (MCP) of herpes viruses. The capsid shell consists of 150 MCP hexamers and 12 MCP pentamers. One pentamer is found at each of the 12 apices of the icosahedral shell, and the hexamers form the edges and 20 faces. 1368 matched cddid_all.tbl CDD pfam03123 pfam03123 460815 CAT_RBD CAT RNA binding domain. This RNA binding domain is found at the amino terminus of transcriptional antitermination proteins such as BglG, SacY and LicT. These proteins control the expression of sugar metabolising operons in Gram+ and Gram- bacteria. This domain has been called the CAT (Co-AntiTerminator) domain. It binds as a dimer to short Ribonucleotidic Anti-Terminator (RAT) hairpin, each monomer interacting symmetrically with both strands of the RAT hairpin. In the full-length protein, CAT is followed by two phosphorylatable PTS regulation domains (pfam00874) that modulate the RNA binding activity of CAT. Upon activation, the dimeric proteins bind to RAT targets in the nascent mRNA, thereby preventing abortive dissociation of the RNA polymerase from the DNA template. 56 matched cddid_all.tbl CDD pfam03124 pfam03124 460816 EXS EXS family. We have named this region the EXS family after (ERD1, XPR1, and SYG1). This family includes C-terminus portions from the SYG1 G-protein associated signal transduction protein from Saccharomyces cerevisiae, and sequences that are thought to be murine leukaemia virus (MLV) receptors (XPR1). N-terminus portions from these proteins are aligned in the SPX pfam03105 family. The previously noted similarity between SYG1 and MLV receptors over their whole sequences is thus borne out in pfam03105 and this family. While the N-termini aligned in pfam03105 are thought to be involved in signal transduction, the role of the C-terminus sequences aligned in this family is not known. This region of similarity contains several predicted transmembrane helices. This family also includes the ERD1 (ERD: ER retention defective) yeast proteins. ERD1 proteins are involved in the localization of endogenous endoplasmic reticulum (ER) proteins. erd1 null mutants secrete such proteins even though they possess the C-terminal HDEL ER lumen localization label sequence. In addition, null mutants also exhibit defects in the Golgi-dependent processing of several glycoproteins, which led to the suggestion that the sorting of luminal ER proteins actually occurs in the Golgi, with subsequent return of these proteins to the ER via `salvage' vesicles. 331 matched cddid_all.tbl CDD pfam03125 pfam03125 251743 Sre C. elegans Sre G protein-coupled chemoreceptor. Caenorhabditis elegans Sre proteins are candidate chemosensory receptors. There are four main recognized groups of such receptors: Odr-10, Sra, Sro, and Srg. Sre (this family), Sra pfam02117 and Srb pfam02175 comprise the Sra group. All of the above receptors are thought to be G protein-coupled seven transmembrane domain proteins. The existence of several different chemosensory receptors underlies the fact that in spite of having only 20-30 chemosensory neurones, C. elegans detects hundreds of different chemicals, with the ability to discern individual chemicals among combinations. 363 matched cddid_all.tbl CDD pfam03126 pfam03126 460817 Plus-3 Plus-3 domain. This domain is about 90 residues in length and is often found associated with the pfam02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively charged residues, hence this domain has been named the plus-3 domain. It is found in yeast Rtf1 which may be a transcription elongation factor. 103 matched cddid_all.tbl CDD pfam03127 pfam03127 460818 GAT GAT domain. The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 and ARF3. The GAT domain stabilizes membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins. 76 matched cddid_all.tbl CDD pfam03128 pfam03128 427156 CXCXC CXCXC repeat. This repeat contains the conserved pattern CXCXC where X can be any amino acid. The repeat is found in up to five copies in Vascular endothelial growth factor C. In the salivary glands of the dipteran Chironomus tentans, a specific messenger ribonucleoprotein (mRNP) particle, the Balbiani ring (BR) granule, can be visualized during its assembly on the gene and during its nucleocytoplasmic transport. This repeat is found over 70 copies in the balbiani ring protein 3. It is also found in some silk proteins. 13 matched cddid_all.tbl CDD pfam03129 pfam03129 460819 HGTP_anticodon Anticodon binding domain. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases it is probably the anticodon binding domain. 94 matched cddid_all.tbl CDD pfam03130 pfam03130 308641 HEAT_PBS PBS lyase HEAT-like repeat. This family contains a short bi-helical repeat that is related to pfam02985. Cyanobacteria and red algae harvest light energy using macromolecular complexes known as phycobilisomes (PBS), peripherally attached to the photosynthetic membrane. The major components of PBS are the phycobiliproteins. These heterodimeric proteins are covalently attached to phycobilins: open-chain tetrapyrrole chromophores, which function as the photosynthetic light-harvesting pigments. Phycobiliproteins differ in sequence and in the nature and number of attached phycobilins to each of their subunits. This family includes the lyase enzymes that specifically attach particular phycobilins to apophycobiliprotein subunits. The most comprehensively studied of these is the CpcE/F lyase, which attaches phycocyanobilin (PCB) to the alpha subunit of apophycocyanin. Similarly, MpeU/V attaches phycoerythrobilin to phycoerythrin II, while CpeY/Z is thought to be involved in phycoerythrobilin (PEB) attachment to phycoerythrin (PE) I (PEs I and II differ in sequence and in the number of attached molecules of PEB: PE I has five, PE II has six). All the reactions of the above lyases involve an apoprotein cysteine SH addition to a terminal delta 3,3'-double bond. Such a reaction is not possible in the case of phycoviolobilin (PVB), the phycobilin of alpha-phycoerythrocyanin (alpha-PEC). It is thought that in this case, PCB, not PVB, is first added to apo-alpha-PEC, and is then isomerized to PVB. The addition reaction has been shown to occur in the presence of either of the components of alpha-PEC-PVB lyase PecE or PecF (or both). The isomerization reaction occurs only when both PecE and PecF components are present, i.e. the PecE/F phycobiliprotein lyase is also a phycobilin isomerase. Another member of this family is the NblB protein, whose similarity to the phycobiliprotein lyases was previously noted. This constitutively expressed protein is not known to have any lyase activity. It is thought to be involved in the coordination of PBS degradation with environmental nutrient limitation. It has been suggested that the similarity of NblB to the phycobiliprotein lyases is due to the ability to bind tetrapyrrole phycobilins via the common repeated motif. 27 matched cddid_all.tbl CDD pfam03131 pfam03131 427158 bZIP_Maf bZIP Maf transcription factor. Maf transcription factors contain a conserved basic region leucine zipper (bZIP) domain, which mediates their dimerization and DNA binding property. Thus, this family is probably related to pfam00170. This family also includes the DNA_binding domain of Skn-1, this domain lacks the leucine zipper found in other bZip domains, and binds DNA is a monomer. 92 matched cddid_all.tbl CDD pfam03133 pfam03133 397308 TTL Tubulin-tyrosine ligase family. Tubulins and microtubules are subjected to several post-translational modifications of which the reversible detyrosination/tyrosination of the carboxy-terminal end of most alpha-tubulins has been extensively analysed. This modification cycle involves a specific carboxypeptidase and the activity of the tubulin-tyrosine ligase (TTL). The true physiological function of TTL has so far not been established. Tubulin-tyrosine ligase (TTL) catalyzes the ATP-dependent post-translational addition of a tyrosine to the carboxy terminal end of detyrosinated alpha-tubulin. In normally cycling cells, the tyrosinated form of tubulin predominates. However, in breast cancer cells, the detyrosinated form frequently predominates, with a correlation to tumour aggressiveness. On the other hand, 3-nitrotyrosine has been shown to be incorporated, by TTL, into the carboxy terminal end of detyrosinated alpha-tubulin. This reaction is not reversible by the carboxypeptidase enzyme. Cells cultured in 3-nitrotyrosine rich medium showed evidence of altered microtubule structure and function, including altered cell morphology, epithelial barrier dysfunction, and apoptosis. Bacterial homologs of TTL are predicted to form peptide tags. Some of these are fused to a 2-oxoglutarate Fe(II)-dependent dioxygenase domain. 291 matched cddid_all.tbl CDD pfam03134 pfam03134 460820 TB2_DP1_HVA22 TB2/DP1, HVA22 family. This family includes members from a wide variety of eukaryotes. It includes the TB2/DP1 (deleted in polyposis) protein, which in humans is deleted in severe forms of familial adenomatous polyposis, an autosomal dominant oncological inherited disease. The family also includes the plant protein of known similarity to TB2/DP1, the HVA22 abscisic acid-induced protein, which is thought to be a regulatory protein. 77 matched cddid_all.tbl CDD pfam03135 pfam03135 367350 CagE_TrbE_VirB CagE, TrbE, VirB family, component of type IV transporter system. This family includes the Helicobacter pylori protein CagE, which together with other proteins from the cag pathogenicity island (PAI), encodes a type IV transporter secretion system. The precise role of CagE is not known, but studies in animal models have shown that it is essential for pathogenesis in Helicobacter pylori induced gastritis and peptic ulceration. Indeed, the expression of the cag PAI has been shown to be essential for stimulating human gastric epithelial cell apoptosis in vitro. Similar type IV transport systems are also found in other bacteria. This family includes the TrbE and VirB proteins from the respective trb and Vir conjugal transfer systems in Agrobacterium tumefaciens. homologs of VirB proteins from other species are also members of this family, e.g. VirB from Brucella suis. 202 matched cddid_all.tbl CDD pfam03136 pfam03136 427160 Pup_ligase Pup-ligase protein. Pupylation is a novel protein modification system found in some bacteria. This family of proteins are the enzyme that can conjugate proteins of the Pup family to lysine residues in target proteins marking them for degradation. The archetypal protein in this family is PafA (proteasome accessory factor) from Mycobacterium tuberculosis. It has been suggested that these proteins are related to gamma-glutamyl-cysteine synthetases. 406 matched cddid_all.tbl CDD pfam03137 pfam03137 460821 OATP Organic Anion Transporter Polypeptide (OATP) family. This family consists of several eukaryotic Organic-Anion-Transporting Polypeptides (OATPs). Several have been identified mostly in human and rat. Different OATPs vary in tissue distribution and substrate specificity. Since the numbering of different OATPs in particular species was based originally on the order of discovery, similarly numbered OATPs in humans and rats did not necessarily correspond in function, tissue distribution and substrate specificity (in spite of the name, some OATPs also transport organic cations and neutral molecules). Thus, Tamai et al. initiated the current scheme of using digits for rat OATPs and letters for human ones. Prostaglandin transporter (PGT) proteins are also considered to be OATP family members. In addition, the methotrexate transporter OATK is closely related to OATPs. This family also includes several predicted proteins from Caenorhabditis elegans and Drosophila melanogaster. This similarity was not previously noted. Note: Members of this family are described (in the Swiss-Prot database) as belonging to the SLC21 family of transporters. 526 matched cddid_all.tbl CDD pfam03139 pfam03139 460822 AnfG_VnfG Vanadium/alternative nitrogenase delta subunit. The nitrogenase complex EC:1.18.6.1 catalyzes the conversion of molecular nitrogen to ammonia (nitrogen fixation) as follows: 8 reduced ferredoxin + 8 H(+) + N(2) + 16 ATP <=> 8 oxidized ferredoxin + 2 NH(3) + 16 ADP + 16 phosphate. The complex is hexameric, consisting of 2 alpha, 2 beta, and 2 delta subunits. This family represents the delta subunit of a group of nitrogenases that do not utilize molybdenum (Mo) as a cofactor, but instead use either vanadium (V nitrogenases), or iron (alternative nitrogenases). V nitrogenases are encoded by vnf operons, and alternative nitrogenases by anf operons. The delta subunits are VnfG and AnfG, respectively. 111 matched cddid_all.tbl CDD pfam03140 pfam03140 460823 DUF247 Plant protein of unknown function. The function of the plant proteins constituting this family is unknown. 390 matched cddid_all.tbl CDD pfam03141 pfam03141 335237 Methyltransf_29 Putative S-adenosyl-L-methionine-dependent methyltransferase. This family is a putative S-adenosyl-L-methionine (SAM)-dependent methyltransferase. 506 matched cddid_all.tbl CDD pfam03142 pfam03142 367353 Chitin_synth_2 Chitin synthase. Members of this family are fungal chitin synthase EC:2.4.1.16 enzymes. They catalyze chitin synthesis as follows: UDP-N-acetyl-D-glucosamine + {(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N) <=> UDP + {(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N+1). 527 matched cddid_all.tbl CDD pfam03143 pfam03143 397314 GTP_EFTU_D3 Elongation factor Tu C-terminal domain. Elongation factor Tu consists of three structural domains, this is the third domain. This domain adopts a beta barrel structure. This the third domain is involved in binding to both charged tRNA and binding to EF-Ts pfam00889. 105 matched cddid_all.tbl CDD pfam03144 pfam03144 427163 GTP_EFTU_D2 Elongation factor Tu domain 2. Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to pfam03143, and in fact has weak sequence matches to this domain. 73 matched cddid_all.tbl CDD pfam03145 pfam03145 460824 Sina Seven in absentia protein family. The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non- neuronal cell type. The Sina protein contains an N-terminal RING finger domain pfam00097. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that thus Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologs of Sina have also been identified. The human homolog Siah-1 also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is described in pfam00097, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologs, whose similarity was noted previously, this family also includes putative homologs from Caenorhabditis elegans, Arabidopsis thaliana. 198 matched cddid_all.tbl CDD pfam03146 pfam03146 460825 NtA Agrin NtA domain. Agrin is a multidomain heparan sulphate proteoglycan, that is a key organizer for the induction of postsynaptic specializations at the neuromuscular junction. Binding of agrin to basement membranes requires the amino terminal (NtA) domain. This region mediates high affinity interaction with the coiled-coil domain of laminins. The binding of agrin to laminins via the NtA domain is subject to tissue-specific regulation. The NtA domain-containing form of agrin is expressed in non-neuronal cells or in neurons that project to non-neuronal cell such as motor neurons. The structure of this domain is an OB-fold. 109 matched cddid_all.tbl CDD pfam03147 pfam03147 460826 FDX-ACB Ferredoxin-fold anticodon binding domain. This is the anticodon binding domain found in some phenylalanyl tRNA synthetases. The domain has a ferredoxin fold. 94 matched cddid_all.tbl CDD pfam03148 pfam03148 460827 Tektin Tektin family. Tektins are cytoskeletal proteins. They have been demonstrated in such cellular sites as centrioles, basal bodies, and along ciliary and flagellar doublet microtubules. Tektins form unique protofilaments, organized as longitudinal polymers of tektin heterodimers with axial periodicity matching tubulin. Tektin polypeptides consist of several alpha-helical regions that are predicted to form coiled coils. Indeed, tektins share considerable structural similarities with intermediate filament proteins. Possible functional roles for tektins are: stabilization of tubulin protofilaments; attachment of A and B-tubules in ciliary/flagellar microtubule doublets and C-tubules in centrioles; binding of axonemal components. 383 matched cddid_all.tbl CDD pfam03150 pfam03150 427168 CCP_MauG Di-haem cytochrome c peroxidase. This is a family of distinct cytochrome c peroxidases (CCPs) that contain two haem groups. Similar to other cytochrome c peroxidases, they reduce hydrogen peroxide to water using c-type haem as an oxidisable substrate. However, since they possess two, instead of one, haem prosthetic groups, bacterial CCPs reduce hydrogen peroxide without the need to generate semi-stable free radicals. The two haem groups have significantly different redox potentials. The high potential (+320 mV) haem feeds electrons from electron shuttle proteins to the low potential (-330 mV) haem, where peroxide is reduced (indeed, the low potential site is known as the peroxidatic site). The CCP protein itself is structured into two domains, each containing one c-type haem group, with a calcium-binding site at the domain interface. This family also includes MauG proteins, whose similarity to di-haem CCP was previously recognized. 151 matched cddid_all.tbl CDD pfam03151 pfam03151 308657 TPT Triose-phosphate Transporter family. This family includes transporters with a specificity for triose phosphate. 290 matched cddid_all.tbl CDD pfam03152 pfam03152 460828 UFD1 Ubiquitin fusion degradation protein UFD1. Post-translational ubiquitin-protein conjugates are recognized for degradation by the ubiquitin fusion degradation (UFD) pathway. Several proteins involved in this pathway have been identified. This family includes UFD1, a 40kD protein that is essential for vegetative cell viability. The human UFD1 gene is expressed at high levels during embryogenesis, especially in the eyes and in the inner ear primordia and is thought to be important in the determination of ectoderm-derived structures, including neural crest cells. In addition, this gene is deleted in the CATCH-22 (cardiac defects, abnormal facies, thymic hypoplasia, cleft palate and hypocalcaemia with deletions on chromosome 22) syndrome. This clinical syndrome is associated with a variety of developmental defects, all characterized by microdeletions on 22q11.2. Two such developmental defects are the DiGeorge syndrome OMIM:188400, and the velo-cardio- facial syndrome OMIM:145410. Several of the abnormalities associated with these conditions are thought to be due to defective neural crest cell differentiation. 174 matched cddid_all.tbl CDD pfam03153 pfam03153 460829 TFIIA Transcription factor IIA, alpha/beta subunit. Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. 344 matched cddid_all.tbl CDD pfam03154 pfam03154 460830 Atrophin-1 Atrophin-1 family. Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. 991 matched cddid_all.tbl CDD pfam03155 pfam03155 460831 Alg6_Alg8 ALG6, ALG8 glycosyltransferase family. N-linked (asparagine-linked) glycosylation of proteins is mediated by a highly conserved pathway in eukaryotes, in which a lipid (dolichol phosphate)-linked oligosaccharide is assembled at the endoplasmic reticulum membrane prior to the transfer of the oligosaccharide moiety to the target asparagine residues. This oligosaccharide is composed of Glc(3)Man(9)GlcNAc(2). The addition of the three glucose residues is the final series of steps in the synthesis of the oligosaccharide precursor. Alg6 transfers the first glucose residue, and Alg8 transfers the second one. In the human alg6 gene, a C->T transition, which causes Ala333 to be replaced with Val, has been identified as the cause of a congenital disorder of glycosylation, designated as type Ic OMIM:603147. 477 matched cddid_all.tbl CDD pfam03157 pfam03157 367362 Glutenin_hmw High molecular weight glutenin subunit. Members of this family include high molecular weight subunits of glutenin. This group of gluten proteins is thought to be largely responsible for the elastic properties of gluten, and hence, doughs. Indeed, glutenin high molecular weight subunits are classified as elastomeric proteins, because the glutenin network can withstand significant deformations without breaking, and return to the original conformation when the stress is removed. Elastomeric proteins differ considerably in amino acid sequence, but they are all polymers whose subunits consist of elastomeric domains, composed of repeated motifs, and non-elastic domains that mediate cross-linking between the subunits. The elastomeric domain motifs are all rich in glycine residues in addition to other hydrophobic residues. High molecular weight glutenin subunits have an extensive central elastomeric domain, flanked by two terminal non-elastic domains that form disulphide cross-links. The central elastomeric domain is characterized by the following three repeated motifs: PGQGQQ, GYYPTS[P/L]QQ, GQQ. It possesses overlapping beta-turns within and between the repeated motifs, and assumes a regular helical secondary structure with a diameter of approx. 1.9 nm and a pitch of approx. 1.5 nm. 786 matched cddid_all.tbl CDD pfam03158 pfam03158 281192 DUF249 Multigene family 530 protein. Members of this family are multigene family 530 proteins from African swine fever viruses. These proteins may be involved in promoting survival of infected macrophages. 192 matched cddid_all.tbl CDD pfam03159 pfam03159 460832 XRN_N XRN 5'-3' exonuclease N-terminus. This family aligns residues towards the N-terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity EC:3.1.11.-. Thus, the aligned region may be necessary for 5' to 3' exonuclease function. The family also contains several Xrn1 and Xrn2 proteins. The 5'-3' exoribonucleases Xrn1p and Xrn2p/Rat1p function in the degradation and processing of several classes of RNA in Saccharomyces cerevisiae. Xrn1p is the main enzyme catalysing cytoplasmic mRNA degradation in multiple decay pathways, whereas Xrn2p/Rat1p functions in the processing of rRNAs and small nucleolar RNAs (snoRNAs) in the nucleus. 231 matched cddid_all.tbl CDD pfam03160 pfam03160 397326 Calx-beta Calx-beta domain. 91 matched cddid_all.tbl CDD pfam03161 pfam03161 427174 LAGLIDADG_2 LAGLIDADG DNA endonuclease family. This is a family of site-specific DNA endonucleases encoded by DNA mobile elements. Similar to pfam00961, the members of this family are also LAGLIDADG endonucleases. 168 matched cddid_all.tbl CDD pfam03162 pfam03162 397328 Y_phosphatase2 Tyrosine phosphatase family. This family is closely related to the pfam00102 and pfam00782 families. 150 matched cddid_all.tbl CDD pfam03165 pfam03165 460833 MH1 MH1 domain. The MH1 (MAD homology 1) domain is found at the amino terminus of MAD related proteins such as Smads. This domain is separated from the MH2 domain by a non-conserved linker region. The crystal structure of the MH1 domain shows that a highly conserved 11 residue beta hairpin is used to bind the DNA consensus sequence GNCN in the major groove, shown to be vital for the transcriptional activation of target genes. Not all examples of MH1 can bind to DNA however. Smad2 cannot bind DNA and has a large insertion within the hairpin that presumably abolishes DNA binding. A basic helix (H2) in MH1 with the nuclear localization signal KKLKK has been shown to be essential for Smad3 nuclear import. Smads also use the MH1 domain to interact with transcription factors such as Jun, TFE3, Sp1, and Runx. 103 matched cddid_all.tbl CDD pfam03166 pfam03166 460834 MH2 MH2 domain. This is the MH2 (MAD homology 2) domain found at the carboxy terminus of MAD related proteins such as Smads. This domain is separated from the MH1 domain by a non-conserved linker region. The MH2 domain mediates interaction with a wide variety of proteins and provides specificity and selectivity to Smad function and also is critical for mediating interactions in Smad oligomers. Unlike MH1, MH2 does not bind DNA. The well-studied MH2 domain of Smad4 is composed of five alpha helices and three loops enclosing a beta sandwich. Smads are involved in the propagation of TGF-beta signals by direct association with the TGF-beta receptor kinase which phosphorylates the last two Ser of a conserved 'SSXS' motif located at the C-terminus of MH2. 172 matched cddid_all.tbl CDD pfam03167 pfam03167 397331 UDG Uracil DNA glycosylase superfamily. 154 matched cddid_all.tbl CDD pfam03168 pfam03168 427176 LEA_2 Late embryogenesis abundant protein. Different types of LEA proteins are expressed at different stages of late embryogenesis in higher plant seed embryos and under conditions of dehydration stress. The function of these proteins is unknown. This family represents a group of LEA proteins that appear to be distinct from those in pfam02987. The family DUF1511, pfam07427, has now been merged into this family. 99 matched cddid_all.tbl CDD pfam03169 pfam03169 367370 OPT OPT oligopeptide transporter protein. The OPT family of oligopeptide transporters is distinct from the ABC pfam00005 and PTR pfam00854 transporter families. OPT transporters were first recognized in fungi (Candida albicans and Schizosaccharomyces pombe), but this alignment also includes orthologues from Arabidopsis thaliana. OPT transporters are thought to have 12-14 transmembrane domains and contain the following motif: SPYxEVRxxVxxxDDP. 614 matched cddid_all.tbl CDD pfam03170 pfam03170 427177 BcsB Bacterial cellulose synthase subunit. This family includes bacterial proteins involved in cellulose synthesis. Cellulose synthesis has been identified in several bacteria. In Agrobacterium tumefaciens, for instance, cellulose has a pathogenic role: it allows the bacteria to bind tightly to their host plant cells. While several enzymatic steps are involved in cellulose synthesis, potentially the only step unique to this pathway is that catalyzed by cellulose synthase. This enzyme is a multi subunit complex. This family encodes a subunit that is thought to bind the positive effector cyclic di-GMP. This subunit is found in several different bacterial cellulose synthase enzymes. The first recognized sequence for this subunit is BcsB. In the AcsII cellulose synthase, this subunit and the subunit corresponding to BcsA are found in the same protein. Indeed, this alignment only includes the C-terminal half of the AcsAII synthase, which corresponds to BcsB. 607 matched cddid_all.tbl CDD pfam03171 pfam03171 397334 2OG-FeII_Oxy 2OG-Fe(II) oxygenase superfamily. This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalysing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 <=> procollagen trans- 4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site. The family also includes lysyl hydrolases, isopenicillin synthases and AlkB. 101 matched cddid_all.tbl CDD pfam03172 pfam03172 460835 HSR HSR domain. The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots (NDs). An ND-targeting region that coincides with a homodimerization domain was mapped in Sp100. Sequences similar to the Sp100 homodimerization/ND-targeting region occur in several other proteins and constitute a novel protein motif, termed HSR domain (for homogeneously-staining region). The HSR domain has also been named ASS (AIRE, Sp-100 and Sp140). This domain is usually found at the amino terminus of proteins that contain a SAND domain pfam01342. 99 matched cddid_all.tbl CDD pfam03173 pfam03173 427179 CHB_HEX Putative carbohydrate binding domain. This domain represents the N terminal domain in chitobiases and beta-hexosaminidases EC:3.2.1.52. It is composed of a beta sandwich structure that is similar in structure to the cellulose binding domain of cellulase from Cellulomonas fimi. This suggests that this may be a carbohydrate binding domain. 153 matched cddid_all.tbl CDD pfam03174 pfam03174 427180 CHB_HEX_C Chitobiase/beta-hexosaminidase C-terminal domain. This short domain represents the C terminal domain in chitobiases and beta-hexosaminidases EC:3.2.1.52. It is composed of a beta sandwich structure. The function of this domain is unknown. 75 matched cddid_all.tbl CDD pfam03175 pfam03175 367375 DNA_pol_B_2 DNA polymerase type B, organellar and viral. Like pfam00136, members of this family are also DNA polymerase type B proteins. Those included here are found in plant and fungal mitochondria, and in viruses. 455 matched cddid_all.tbl CDD pfam03176 pfam03176 308676 MMPL MMPL family. Members of this family are putative integral membrane proteins from bacteria. Several of the members are mycobacterial proteins. Many of the proteins contain two copies of this aligned region. The function of these proteins is not known, although it has been suggested that they may be involved in lipid transport. 332 matched cddid_all.tbl CDD pfam03177 pfam03177 427181 Nucleoporin_C Non-repetitive/WGA-negative nucleoporin C-terminal. This is the C-termainl half of a family of nucleoporin proteins. Nucleoporins are the main components of the nuclear pore complex in eukaryotic cells, and mediate bidirectional nucleocytoplasmic transport, especially of mRNA and proteins. Two nucleoporin classes are known: one is characterized by the FG repeat pfam03093; the other is represented by this family, and lacks any repeats. RNA undergoing nuclear export first encounters the basket of the nuclear pore and many nucleoporins are accessible on the basket side of the pore. 559 matched cddid_all.tbl CDD pfam03178 pfam03178 427182 CPSF_A CPSF A subunit region. This family includes a region that lies towards the C-terminus of the cleavage and polyadenylation specificity factor (CPSF) A (160 kDa) subunit. CPSF is involved in mRNA polyadenylation and binds the AAUAAA conserved sequence in pre-mRNA. CPSF has also been found to be necessary for splicing of single-intron pre-mRNAs. The function of the aligned region is unknown but may be involved in RNA/DNA binding. 319 matched cddid_all.tbl CDD pfam03179 pfam03179 460836 V-ATPase_G Vacuolar (H+)-ATPase G subunit. This family represents the eukaryotic vacuolar (H+)-ATPase (V-ATPase) G subunit. V-ATPases generate an acidic environment in several intracellular compartments. Correspondingly, they are found as membrane-attached proteins in several organelles. They are also found in the plasma membranes of some specialized cells. V-ATPases consist of peripheral (V1) and membrane integral (V0) heteromultimeric complexes. The G subunit is part of the V1 subunit, but is also thought to be strongly attached to the V0 complex. It may be involved in the coupling of ATP degradation to H+ translocation. 105 matched cddid_all.tbl CDD pfam03180 pfam03180 427184 Lipoprotein_9 NlpA lipoprotein. This entry represents bacterial lipoproteins that belong to the NlpA family. It contains several antigenic members, that may be involved in bacterial virulence. This entry includes the D-methionine binding lipoprotein MetQ, which is the substrate-binding component of a D-methionine permease, a binding protein-dependent, ATP-driven transport system. Other members of this family, such as NlpA, have been identified as putative substrate-binding components of ABC transporters. NlpA, is an inner-membrane-anchored lipoprotein that has been shown to have a minor role in methionine import. 236 matched cddid_all.tbl CDD pfam03181 pfam03181 460837 BURP BURP domain. The BURP domain is found at the C-terminus of several different plant proteins. It was named after the proteins in which it was first identified: the BNM2 clone-derived protein from Brassica napus; USPs and USP-like proteins; RD22 from Arabidopsis thaliana; and PG1beta from Lycopersicon esculentum. This domain is around 230 amino acid residues long. It possesses the following conserved features: two phenylalanine residues at its N-terminus; two cysteine residues; and four repeated cysteine-histidine motifs, arranged as: CH-X(10)-CH-X(25-27)-CH-X(25-26)-CH, where X can be any amino acid. The function of this domain is unknown. 215 matched cddid_all.tbl CDD pfam03183 pfam03183 112017 Borrelia_rep Borrelia repeat protein. 18 matched cddid_all.tbl CDD pfam03184 pfam03184 367380 DDE_1 DDE superfamily endonuclease. This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. Interestingly this family also includes the CENP-B protein. This domain in that protein appears to have lost the metal binding residues and is unlikely to have endonuclease activity. Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. 177 matched cddid_all.tbl CDD pfam03185 pfam03185 460838 CaKB Calcium-activated potassium channel, beta subunit. 195 matched cddid_all.tbl CDD pfam03186 pfam03186 460839 CobD_Cbib CobD/Cbib protein. This family includes CobD proteins from a number of bacteria, in Salmonella this protein is called Cbib. Salmonella CobD is a different protein. This protein is involved in cobalamin biosynthesis and is probably an enzyme responsible for the conversion of adenosylcobyric acid to adenosylcobinamide or adenosylcobinamide phosphate. 280 matched cddid_all.tbl CDD pfam03187 pfam03187 281216 Corona_I Corona nucleocapsid I protein. 207 matched cddid_all.tbl CDD pfam03188 pfam03188 427188 Cytochrom_B561 Eukaryotic cytochrome b561. Cytochrome b561 is a secretory vesicle-specific electron transport protein. It is an integral membrane protein, that binds two heme groups non-covalently. This is a eukaryotic family. Members of the 'prokaryotic cytochrome b561' family can be found in Pfam: PF01292. 137 matched cddid_all.tbl CDD pfam03189 pfam03189 460840 Otopetrin Otopetrin. 433 matched cddid_all.tbl CDD pfam03190 pfam03190 460841 Thioredox_DsbH Protein of unknown function, DUF255. 163 matched cddid_all.tbl CDD pfam03192 pfam03192 367385 DUF257 Pyrococcus protein of unknown function, DUF257. 205 matched cddid_all.tbl CDD pfam03193 pfam03193 427191 RsgA_GTPase RsgA GTPase. RsgA (also known as EngC and YjeQ) represents a protein family whose members are broadly conserved in bacteria and are indispensable for growth. The GTPase domain of RsgA is very similar to several P-loop GTPases, but differs in having a circular permutation of the GTPase structure described by a G4-G1-G3 pattern. 174 matched cddid_all.tbl CDD pfam03194 pfam03194 460842 LUC7 LUC7 N_terminus. This family contains the N terminal region of several LUC7 protein homologs and only contains eukaryotic proteins. LUC7 has been shown to be a U1 snRNA associated protein with a role in splice site recognition. The family also contains human and mouse LUC7 like (LUC7L) proteins and human cisplatin resistance-associated overexpressed protein (CROP). 246 matched cddid_all.tbl CDD pfam03195 pfam03195 460843 LOB Lateral organ boundaries (LOB) domain. The lateral organ boundaries (LOB) gene encodes a plant-specific protein of unknown function that is expressed at the adaxial base of initiating lateral organs. The N-terminal of the LOB protein contains an approximately 100-amino acid conserved domain (the LOB domain) that is present in 42 other Arabidopsis thaliana proteins as well as in proteins from a variety of other plant species. The LOB domain contains conserved blocks of amino acids that identify the LOB domain (LBD) gene family. In particular, a conserved C-x(2)-C-x(6)-C-x(3)-C motif, which is the defining feature of the LOB domain, is present in all LBD proteins. 99 matched cddid_all.tbl CDD pfam03196 pfam03196 281224 DUF261 Protein of unknown function, DUF261. 137 matched cddid_all.tbl CDD pfam03197 pfam03197 460844 FRD2 Bacteriophage FRD2 protein. 103 matched cddid_all.tbl CDD pfam03198 pfam03198 397351 Glyco_hydro_72 Glucanosyltransferase. This is a family of glycosylphosphatidylinositol-anchored beta(1-3)glucanosyltransferases. The active site residues in the Aspergillus fumigatus example Swiss:B0XT72 are the two glutamate residues at 160 and 261. 315 matched cddid_all.tbl CDD pfam03199 pfam03199 460845 GSH_synthase Eukaryotic glutathione synthase. 102 matched cddid_all.tbl CDD pfam03200 pfam03200 397353 Glyco_hydro_63 Glycosyl hydrolase family 63 C-terminal domain. This is a family of eukaryotic enzymes belonging to glycosyl hydrolase family 63. They catalyze the specific cleavage of the non-reducing terminal glucose residue from Glc(3)Man(9)GlcNAc(2). Mannosyl oligosaccharide glucosidase EC:3.2.1.106 is the first enzyme in the N-linked oligosaccharide processing pathway. This family represents the C-terminal catalytic domain. 494 matched cddid_all.tbl CDD pfam03201 pfam03201 397354 HMD H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase. 88 matched cddid_all.tbl CDD pfam03202 pfam03202 397355 Lipoprotein_10 Putative mycoplasma lipoprotein, C-terminal region. 129 matched cddid_all.tbl CDD pfam03203 pfam03203 427195 MerC MerC mercury resistance protein. 105 matched cddid_all.tbl CDD pfam03205 pfam03205 427196 MobB Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop. 133 matched cddid_all.tbl CDD pfam03206 pfam03206 427197 NifW Nitrogen fixation protein NifW. Nitrogenase is a complex metalloenzyme composed of two proteins designated the Fe-protein and the MoFe-protein. Apart from these two proteins, a number of accessory proteins are essential for the maturation and assembly of nitrogenase. Even though experimental evidence suggests that these accessory proteins are required for nitrogenase activity, the exact roles played by many of these proteins in the functions of nitrogenase are unclear. Using yeast two-hybrid screening it has been shown that NifW can interact with itself as well as NifZ. 99 matched cddid_all.tbl CDD pfam03207 pfam03207 367392 OspD Borrelia outer surface protein D (OspD). 254 matched cddid_all.tbl CDD pfam03208 pfam03208 460846 PRA1 PRA1 family protein. This family includes the PRA1 (Prenylated rab acceptor) protein which is a Rab guanine dissociation inhibitor (GDI) displacement factor. This family also includes the glutamate transporter EAAC1 interacting protein GTRAP3-18. 141 matched cddid_all.tbl CDD pfam03209 pfam03209 367394 PUCC PUCC protein. This protein is required for high-level transcription of the PUC operon. 401 matched cddid_all.tbl CDD pfam03210 pfam03210 281237 Paramyx_P_V_C Paramyxovirus P/V phosphoprotein C-terminal. Paramyxoviridae P genes are able to generate more than one product, using alternative reading frames and RNA editing. The P gene encodes the structural phosphoprotein P. In addition, it encodes several non-structural proteins present in the infected cell but not in the virus particle. This family includes phosphoprotein P and the non-structural phosphoprotein V from different paramyxoviruses. Phosphoprotein P is essential for the activity of the RNA polymerase complex which it forms with another subunit, L pfam00946. Although all the catalytic activities of the polymerase are associated with the L subunit, its function requires specific interactions with phosphoprotein P. The P and V phosphoproteins are amino co-terminal, but diverge at their C-termini. This difference is generated by an RNA-editing mechanism in which one or two non-templated G residues are inserted into P-gene-derived mRNA. In measles virus and Sendai virus, one G residue is inserted and the edited transcript encodes the V protein. In mumps, simian virus type 5 and Newcastle disease virus, two G residues are inserted, and the edited transcript codes for the P protein. Being phosphoproteins, both P and V are rich in serine and threonine residues over their whole lengths. In addition, the V proteins are rich in cysteine residues at the C-termini. This C-terminal region of the P phosphoprotein is likely to be the nucleocapsid-binding domain, and is found to be intrinsically disordered and thus liable to induced folding. 154 matched cddid_all.tbl CDD pfam03211 pfam03211 460847 Pectate_lyase Pectate lyase. 202 matched cddid_all.tbl CDD pfam03212 pfam03212 460848 Pertactin Pertactin. 121 matched cddid_all.tbl CDD pfam03213 pfam03213 281240 Pox_P35 Poxvirus P35 protein. 323 matched cddid_all.tbl CDD pfam03214 pfam03214 367397 RGP Reversibly glycosylated polypeptide. 340 matched cddid_all.tbl CDD pfam03215 pfam03215 367398 Rad17 Rad17 P-loop domain. 186 matched cddid_all.tbl CDD pfam03216 pfam03216 397361 Rhabdo_ncap_2 Rhabdovirus nucleoprotein. 295 matched cddid_all.tbl CDD pfam03217 pfam03217 460849 SlpA Surface layer protein A domain. This short domain is found in a variety of bacterial cell surface proteins. The domain is about 60 residues in length (although previously defined as 2 copies of this domain). It usually occurs in tandem pairs. It may be distantly related to the SH3 domain. 54 matched cddid_all.tbl CDD pfam03219 pfam03219 397363 TLC TLC ATP/ADP transporter. 491 matched cddid_all.tbl CDD pfam03220 pfam03220 397364 Tombus_P19 Tombusvirus P19 core protein. 171 matched cddid_all.tbl CDD pfam03221 pfam03221 460850 HTH_Tnp_Tc5 Tc5 transposase DNA-binding domain. 63 matched cddid_all.tbl CDD pfam03222 pfam03222 367404 Trp_Tyr_perm Tryptophan/tyrosine permease family. 393 matched cddid_all.tbl CDD pfam03223 pfam03223 460851 V-ATPase_C V-ATPase subunit C. 367 matched cddid_all.tbl CDD pfam03224 pfam03224 460852 V-ATPase_H_N V-ATPase subunit H. The yeast Saccharomyces cerevisiae vacuolar H+-ATPase (V-ATPase) is a multisubunit complex responsible for acidifying organelles. It functions as an ATP dependent proton pump that transports protons across a lipid bilayer. This domain corresponds to the N terminal domain of the H subunit of V-ATPase. The N-terminal domain is required for the activation of the complex whereas the C-terminal domain is required for coupling ATP hydrolysis to proton translocation. 314 matched cddid_all.tbl CDD pfam03225 pfam03225 251809 Viral_Hsp90 Viral heat shock protein Hsp90 homolog. 511 matched cddid_all.tbl CDD pfam03226 pfam03226 427204 Yippee-Mis18 Yippee zinc-binding/DNA-binding /Mis18, centromere assembly. This family includes both Yippee-type proteins and Mis18 kinetochore proteins. Yippee are putative zinc-binding/DNA-binding proteins. Mis18 are proteins involved in the priming of centromeres for recruiting CENP-A. Mis18-alpha and beta form part of a small complex with Mis18-binding protein. Mis18-alpha is found to interact with DNA de-methylases through a Leu-rich region located at its carboxyl terminus. This entry also includes the CULT domain proteins such as Cereblon. 99 matched cddid_all.tbl CDD pfam03227 pfam03227 460853 GILT Gamma interferon inducible lysosomal thiol reductase (GILT). This family includes the two characterized human gamma-interferon-inducible lysosomal thiol reductase (GILT) sequences: Swiss:P13284 and Swiss:Q9UL08. It also contains several other eukaryotic putative proteins with similarity to GILT. The aligned region contains three conserved cysteine residues. In addition, the two GILT sequences possess a C-X(2)-C motif that is shared by some of the other sequences in the family. This motif is thought to be associated with disulphide bond reduction. 102 matched cddid_all.tbl CDD pfam03228 pfam03228 281252 Adeno_VII Adenoviral core protein VII. The function of this protein is unknown. It has a conserved amino terminus of 50 residues followed by a positively charged tail, suggesting it may interact with nucleic acid. The major core protein of the adenovirus, protein VII, was found to be associated with viral DNA throughout infection. The precursor to protein VII were shown to be in vivo and in vitro acceptors of ADP-ribose. The ADP-ribosylated core proteins were assembled into mature virus particles. ADP-ribosylation of adenovirus core proteins may have a role in virus decapsidation. 142 matched cddid_all.tbl CDD pfam03229 pfam03229 251813 Alpha_GJ Alphavirus glycoprotein J. 126 matched cddid_all.tbl CDD pfam03230 pfam03230 427206 Antirestrict Antirestriction protein. This family includes various protein that are involved in antirestriction. The ArdB protein efficiently inhibits restriction by members of the three known families of type I systems of E. coli. 92 matched cddid_all.tbl CDD pfam03231 pfam03231 251815 Bunya_NS-S_2 Bunyavirus non-structural protein NS-S. This family represents the Bunyavirus NS-S family. Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. 444 matched cddid_all.tbl CDD pfam03232 pfam03232 460854 COQ7 Ubiquinone biosynthesis protein COQ7. Members of this family contain two repeats of about 90 amino acids, that contains two conserved motifs. One of these DXEXXH may be part of an enzyme active site. 167 matched cddid_all.tbl CDD pfam03233 pfam03233 251817 Cauli_AT Aphid transmission protein. This protein is found in various caulimoviruses. It codes for an 18 kDa protein (PII), which is dispensable for infection but which is required for aphid transmission of the virus. This protein interacts with the PIII protein. 163 matched cddid_all.tbl CDD pfam03234 pfam03234 427208 CDC37_N Cdc37 N terminal kinase binding. Cdc37 is a molecular chaperone required for the activity of numerous eukaryotic protein kinases. This domain corresponds to the N terminal domain which binds predominantly to protein kinases and is found N terminal to the Hsp (Heat shocked protein) 90-binding domain pfam08565. Expression of a construct consisting of only the N-terminal domain of Saccharomyces pombe Cdc37 results in cellular viability. This indicates that interactions with the cochaperone Hsp90 may not be essential for Cdc37 function. 124 matched cddid_all.tbl CDD pfam03235 pfam03235 427209 DUF262 Protein of unknown function DUF262. 78 matched cddid_all.tbl CDD pfam03237 pfam03237 427210 Terminase_6N Terminase large subunit, T4likevirus-type, N-terminal. This entry represents the N-terminal domain of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. It includes the terminase large subunit of Bacteriophage T4 (terminase gene 17, Gp17). homologs are also found in Gene Transfer Agents (GTA), including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata). 214 matched cddid_all.tbl CDD pfam03238 pfam03238 281258 ESAG1 ESAG protein. Expression-site-associated gene (ESAG) proteins are thought to be involved in VSG activation. This family includes ESAG 117A as well as ESAG IM 5. 227 matched cddid_all.tbl CDD pfam03239 pfam03239 251822 FTR1 Iron permease FTR1 family. 284 matched cddid_all.tbl CDD pfam03241 pfam03241 460855 HpaB 4-hydroxyphenylacetate 3-hydroxylase C terminal. HpaB encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli. HpaB is part of a heterodimeric enzyme that also requires HpaC. The enzyme is NADH-dependent and uses FAD as the redox chromophore. This family also includes PvcC, which may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis. 196 matched cddid_all.tbl CDD pfam03242 pfam03242 460856 LEA_3 Late embryogenesis abundant protein. Members of this family are similar to late embryogenesis abundant proteins. Members of the family have been isolated in a number of different screens. However, the molecular function of these proteins remains obscure. 93 matched cddid_all.tbl CDD pfam03243 pfam03243 460857 MerB Alkylmercury lyase. Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. 126 matched cddid_all.tbl CDD pfam03244 pfam03244 460858 PSI_PsaH Photosystem I reaction centre subunit VI. Photosystem I (PSI) is an integral membrane protein complex that uses light energy to mediate electron transfer from plastocyanin to ferredoxin. 139 matched cddid_all.tbl CDD pfam03245 pfam03245 427215 Phage_lysis Bacteriophage Rz lysis protein. This protein is involved in host lysis. This family is not considered to be a peptidase according to the MEROPs database. This family Rz and the Rz1 protein (pfam06085) represent a unique example of two genes located in different reading frames in the same nucleotide sequence, which encode different proteins that are both required in the same physiological pathway. 126 matched cddid_all.tbl CDD pfam03246 pfam03246 397378 Pneumo_ncap Pneumovirus nucleocapsid protein. 390 matched cddid_all.tbl CDD pfam03247 pfam03247 460859 Prothymosin Prothymosin/parathymosin family. Prothymosin alpha and parathymosin are two ubiquitous small acidic nuclear proteins that are thought to be involved in cell cycle progression, proliferation, and cell differentiation. 109 matched cddid_all.tbl CDD pfam03248 pfam03248 460860 Rer1 Rer1 family. RER1 family protein are involved in involved in the retrieval of some endoplasmic reticulum membrane proteins from the early golgi compartment. The C terminus of yeast Rer1p interacts with a coatomer complex. 167 matched cddid_all.tbl CDD pfam03249 pfam03249 460861 TSA Type specific antigen. There are several antigenic variants in Rickettsia tsutsugamushi, and a type-specific antigen (TSA) of 56-kilodaltons located on the rickettsial surface is responsible for the variation. TSA56 is found in Orientia tsutsugamushi (O. tsutsugamushi), the causative agent of scrub typhus, an obligate intracellular pathogen. TSA56 is one of the three major outer membrane proteins of O. tsutsugamushi. It is required for adhesion. Furthermore, it has been demonstrated that O. tsutsugamushi, can bind to fibronectin (Fn) via the antigenic membrane protein, TSA56. There are 3 extracellular antigen domains (ADs), where ADIII and adjacent C-terminal region of TSA56 waswere shown to be sufficient for Fn interaction and prohibiting Fn-enhanced invasion. 510 matched cddid_all.tbl CDD pfam03250 pfam03250 460862 Tropomodulin Tropomodulin. Tropomodulin is a novel tropomyosin regulatory protein that binds to the end of erythrocyte tropomyosin and blocks head-to-tail association of tropomyosin along actin filaments. Limited proteolysis shows this protein is composed of two domains. The amino terminal domain contains the tropomyosin binding function. 142 matched cddid_all.tbl CDD pfam03251 pfam03251 281269 Tymo_45kd_70kd Tymovirus 45/70Kd protein. Tymoviruses are single stranded RNA viruses. This family includes a protein of unknown function that has been named based on its molecular weight. Tymoviruses such as the ononis yellow mosaic tymovirus encode only three proteins. Of these two are overlapping this protein overlaps a larger ORF that is thought to be the polymerase. 468 matched cddid_all.tbl CDD pfam03252 pfam03252 281270 Herpes_UL21 Herpesvirus UL21. The UL21 protein appears to be a dispensable component in herpesviruses. 524 matched cddid_all.tbl CDD pfam03253 pfam03253 460863 UT Urea transporter. Members of this family transport urea across membranes. The family includes a bacterial homolog Swiss:Q9S408. 292 matched cddid_all.tbl CDD pfam03254 pfam03254 427220 XG_FTase Xyloglucan fucosyltransferase. Plant cell walls are crucial for development, signal transduction, and disease resistance in plants. Cell walls are made of cellulose, hemicelluloses, and pectins. Xyloglucan (XG), the principal load-bearing hemicellulose of dicotyledonous plants, has a terminal fucosyl residue. This fucosyltransferase adds this residue. 475 matched cddid_all.tbl CDD pfam03255 pfam03255 427221 ACCA Acetyl co-enzyme A carboxylase carboxyltransferase alpha subunit. Acetyl co-enzyme A carboxylase carboxyltransferase is composed of an alpha and beta subunit. 144 matched cddid_all.tbl CDD pfam03256 pfam03256 367420 ANAPC10 Anaphase-promoting complex, subunit 10 (APC10). 185 matched cddid_all.tbl CDD pfam03257 pfam03257 460864 Adhesin_P1_C Mycoplasma adhesin P1, C-terminal. This domain is found towards the C-terminal of adhesins from Mycoplasmas, such as adhesin P1, first identified as the major determinant for cytoadherence and gliding motility in M. pneumoniae. P1 forms a transmembrane adhesion complex with P40/P90, called 'Nap', which mediates motility and infectivity in these organizms. The C-terminal domain is smaller than the large N-terminal domain and is mostly conserved. It is followed by a transmembrane domain and acts as a stalk connecting the large N-terminal domain with the outer surface of the cell membranes. P1 N-terminal domain is highly variable (pfam12378). 116 matched cddid_all.tbl CDD pfam03258 pfam03258 367421 Baculo_FP Baculovirus FP protein. The FP protein is missing in baculovirus (Few Polyhedra) mutants. 147 matched cddid_all.tbl CDD pfam03259 pfam03259 397386 Robl_LC7 Roadblock/LC7 domain. This family includes proteins that are about 100 amino acids long and have been shown to be related. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions. This family also includes Golgi-associated MP1 adapter protein and MglB from Myxococcus xanthus, a protein involved in gliding motility. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role. 91 matched cddid_all.tbl CDD pfam03260 pfam03260 460865 Lipoprotein_11 Lepidopteran low molecular weight (30 kD) lipoprotein. 231 matched cddid_all.tbl CDD pfam03261 pfam03261 460866 CDK5_activator Cyclin-dependent kinase 5 activator protein. 340 matched cddid_all.tbl CDD pfam03262 pfam03262 281280 Corona_6B_7B Coronavirus 6B/7B protein. 206 matched cddid_all.tbl CDD pfam03263 pfam03263 460867 Cucumo_2B Cucumovirus protein 2B. This protein may be a viral movement protein. 105 matched cddid_all.tbl CDD pfam03264 pfam03264 427224 Cytochrom_NNT NapC/NirT cytochrome c family, N-terminal region. Within the NapC/NirT family of cytochrome c proteins, some members, such as NapC and NirT, bind four haem groups, while others, such as TorC, bind five haems. This family aligns the common N-terminal region that contains four haem-binding C-X(2)-CH motifs. 174 matched cddid_all.tbl CDD pfam03265 pfam03265 460868 DNase_II Deoxyribonuclease II. 316 matched cddid_all.tbl CDD pfam03266 pfam03266 460869 NTPase_1 NTPase. This domain is found across all species from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme. The sequence carries both a Walker A and Walker B motif which together are characteriztic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue. 168 matched cddid_all.tbl CDD pfam03268 pfam03268 367428 DUF267 Caenorhabditis protein of unknown function, DUF267. 360 matched cddid_all.tbl CDD pfam03269 pfam03269 367429 DUF268 Caenorhabditis protein of unknown function, DUF268. 176 matched cddid_all.tbl CDD pfam03270 pfam03270 427226 DUF269 Protein of unknown function, DUF269. Members of this family may be involved in nitrogen fixation, since they are found within nitrogen fixation operons. 121 matched cddid_all.tbl CDD pfam03271 pfam03271 460870 EB1 EB1-like C-terminal motif. This motif is found at the C-terminus of proteins that are related to the EB1 protein. The EB1 proteins contain an N-terminal CH domain pfam00307. The human EB1 protein was originally discovered as a protein interacting with the C-terminus of the APC protein. This interaction is often disrupted in colon cancer, due to deletions affecting the APC C-terminus. Several EB1 orthologues are also included in this family. The interaction between EB1 and APC has been shown to have a potent synergistic effect on microtubule polymerization. Neither of EB1 or APC alone has this effect. It is thought that EB1 targets APC to the + ends of microtubules, where APC promotes microtubule polymerization. This process is regulated by APC phosphorylation by Cdc2, which disrupts APC-EB1 binding. Human EB1 protein can functionally substitute for the yeast EB1 homolog Mal3. In addition, Mal3 can substitute for human EB1 in promoting microtubule polymerization with APC. 41 matched cddid_all.tbl CDD pfam03272 pfam03272 460871 Mucin_bdg Putative mucin or carbohydrate-binding module. This family is the putative binding domain for the substrates of enhancin, and other similar metallopeptidases. This is not the enzymically active, peptidase, part of the proteins - see pfam13402. 116 matched cddid_all.tbl CDD pfam03273 pfam03273 397395 Baculo_gp64 Baculovirus gp64 envelope glycoprotein family. This family includes the gp64 glycoprotein from baculovirus as well as other viruses. 506 matched cddid_all.tbl CDD pfam03274 pfam03274 281291 Foamy_BEL Foamy virus BEL 1/2 protein. 301 matched cddid_all.tbl CDD pfam03275 pfam03275 427229 GLF UDP-galactopyranose mutase. 203 matched cddid_all.tbl CDD pfam03276 pfam03276 460872 Gag_spuma Spumavirus gag protein. 614 matched cddid_all.tbl CDD pfam03277 pfam03277 281294 Herpes_UL4 Herpesvirus UL4 family. 187 matched cddid_all.tbl CDD pfam03278 pfam03278 281295 IpaB_EvcA IpaB/EvcA family. This family includes IpaB, which is an invasion plasmid antigen from Shigella, as well as EvcA from E. coli. Members of this family seem to be involved in pathogenicity of some enterobacteria. However the exact function of this component is not clear. 144 matched cddid_all.tbl CDD pfam03279 pfam03279 281296 Lip_A_acyltrans Bacterial lipid A biosynthesis acyltransferase. 294 matched cddid_all.tbl CDD pfam03280 pfam03280 427230 Lipase_chap Proteobacterial lipase chaperone protein. 185 matched cddid_all.tbl CDD pfam03281 pfam03281 460873 Mab-21 Mab-21 protein nucleotidyltransferase domain. This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development. 191 matched cddid_all.tbl CDD pfam03283 pfam03283 460874 PAE Pectinacetylesterase. 345 matched cddid_all.tbl CDD pfam03284 pfam03284 397400 PHZA_PHZB Phenazine biosynthesis protein A/B. 161 matched cddid_all.tbl CDD pfam03285 pfam03285 460875 Paralemmin Paralemmin. 301 matched cddid_all.tbl CDD pfam03286 pfam03286 281302 Pox_Ag35 Pox virus Ag35 surface protein. 196 matched cddid_all.tbl CDD pfam03287 pfam03287 308745 Pox_C7_F8A Poxvirus C7/F8A protein. 147 matched cddid_all.tbl CDD pfam03288 pfam03288 367437 Pox_D5 Poxvirus D5 protein-like. This family includes D5 from Poxviruses which is necessary for viral DNA replication, and is a nucleic acid independent nucleoside triphosphatase. Members of this family are also found outside of poxviruses. This domain is a DNA-binding winged HTH domain. 85 matched cddid_all.tbl CDD pfam03289 pfam03289 281305 Pox_I1 Poxvirus protein I1. 307 matched cddid_all.tbl CDD pfam03290 pfam03290 281306 Peptidase_C57 Vaccinia virus I7 processing peptidase. 425 matched cddid_all.tbl CDD pfam03291 pfam03291 281307 Pox_MCEL mRNA capping enzyme. This family of enzymes are related to pfam03919. 332 matched cddid_all.tbl CDD pfam03292 pfam03292 281308 Pox_P4B Poxvirus P4B major core protein. 657 matched cddid_all.tbl CDD pfam03293 pfam03293 397402 Pox_RNA_pol Poxvirus DNA-directed RNA polymerase, 18 kD subunit. 160 matched cddid_all.tbl CDD pfam03294 pfam03294 397403 Pox_Rap94 RNA polymerase-associated transcription specificity factor, Rap94. 796 matched cddid_all.tbl CDD pfam03295 pfam03295 281311 Pox_TAA1 Poxvirus trans-activator protein A1 C-terminal. 63 matched cddid_all.tbl CDD pfam03296 pfam03296 281312 Pox_polyA_pol Poxvirus poly(A) polymerase nucleotidyltransferase domain. 147 matched cddid_all.tbl CDD pfam03297 pfam03297 460876 Ribosomal_S25 S25 ribosomal protein. 100 matched cddid_all.tbl CDD pfam03298 pfam03298 397405 Stanniocalcin Stanniocalcin family. 200 matched cddid_all.tbl CDD pfam03299 pfam03299 460877 TF_AP-2 Transcription factor AP-2. 196 matched cddid_all.tbl CDD pfam03300 pfam03300 281316 Tenui_NS4 Tenuivirus non-structural, movement protein NS4. 282 matched cddid_all.tbl CDD pfam03301 pfam03301 281317 Trp_dioxygenase Tryptophan 2,3-dioxygenase. 346 matched cddid_all.tbl CDD pfam03302 pfam03302 146106 VSP Giardia variant-specific surface protein. 397 matched cddid_all.tbl CDD pfam03303 pfam03303 460878 WTF WTF protein. This is a family of hypothetical Schizosaccharomyces pombe proteins. Their function is unknown. 224 matched cddid_all.tbl CDD pfam03304 pfam03304 308750 Mlp Mlp lipoprotein family. The Mlp (for Multicopy Lipoprotein) family of lipoproteins is found in Borrelia species. This family were previously known as 2.9 lipoprotein genes. These surface expressed genes may represent new candidate vaccinogens for Lyme disease. Members of this family generally are downstream of four ORFs called A,B,C and D that are involved in hemolytic activity. 121 matched cddid_all.tbl CDD pfam03305 pfam03305 397407 Lipoprotein_X Mycoplasma MG185/MG260 protein. Most of the aligned regions in this family are found towards the middle of the member proteins. 183 matched cddid_all.tbl CDD pfam03306 pfam03306 460879 AAL_decarboxy Alpha-acetolactate decarboxylase. 219 matched cddid_all.tbl CDD pfam03307 pfam03307 460880 Adeno_E3_15_3 Adenovirus 15.3kD protein in E3 region. 117 matched cddid_all.tbl CDD pfam03308 pfam03308 281323 MeaB Methylmalonyl Co-A mutase-associated GTPase MeaB. Family members were previously thought to be ArgK proteins acting as ATPase enzymes and kinases. They are now believed to be methylmalonyl Co-A mutase-associated GTPase MeaB. Structural studies of MeaB and the human ortholog (methylmalonyl associated protein A) MMAA, reveal alpha-helical domains at the N- and C-termini as well as a Ras-like GTPase domain. Mutational analysis of MeaB, show prohibited growth in Methylobacterium due to the inability to convert methylmalonyl-CoA to succinyl-CoA caused by an inactive form of methylmalonyl-CoA mutatase (mcm). In humans, mutations in (MMAA) are associated with the fatal disease methylmalonyl aciduria. 272 matched cddid_all.tbl CDD pfam03309 pfam03309 460881 Pan_kinase Type III pantothenate kinase. Type III pantothenate kinase catalyzes the phosphorylation of pantothenate (Pan), the first step in the universal pathway of CoA biosynthesis. 205 matched cddid_all.tbl CDD pfam03310 pfam03310 460882 Cauli_DNA-bind Caulimovirus DNA-binding protein. The gene III product of cauliflower mosaic virus (CaMV) is known as virion-associated protein or P3, which is tightly associated with the virus particles and has a regulatory function in the virus infection cycle. P3 decorate the virions; its N-terminal domain forms an antiparallel alpha-helical coiled-coil network at the surface and the C-terminal domain interacts with the C-terminal half of the coat protein. It is a DNA binding protein in which the DNA binding activity is located on its C-terminal part. 117 matched cddid_all.tbl CDD pfam03311 pfam03311 460883 Cornichon Cornichon protein. 122 matched cddid_all.tbl CDD pfam03312 pfam03312 397411 DUF272 Protein of unknown function (DUF272). This family of proteins is restricted to C.elegans and has no known function. The protein contains a ubiquitin fold. The GO annotation for the protein indicates that it has a function in nematode larval development. 123 matched cddid_all.tbl CDD pfam03313 pfam03313 427238 SDH_alpha Serine dehydratase alpha chain. L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyzes the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway. 259 matched cddid_all.tbl CDD pfam03314 pfam03314 367444 DUF273 Protein of unknown function, DUF273. 219 matched cddid_all.tbl CDD pfam03315 pfam03315 427239 SDH_beta Serine dehydratase beta chain. L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyzes the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway. 146 matched cddid_all.tbl CDD pfam03317 pfam03317 460884 ELF ELF protein. This is a family of hypothetical proteins from cereal crops. 123 matched cddid_all.tbl CDD pfam03318 pfam03318 427241 ETX_MTX2 Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2. This family appears to be distantly related to pfam01117. 222 matched cddid_all.tbl CDD pfam03319 pfam03319 427242 EutN_CcmL Ethanolamine utilization protein EutN/carboxysome. The crystal structure of EutN contains a central five-stranded beta-barrel, with an alpha-helix at the open end of this barrel (PDB:2HD3). The structure also contains three additional beta-strands, which help the formation of a tight hexamer, with a hole in the center. this suggests that EutN forms a pore, with an opening of 26 Angstrom in diameter on one face and 14 Angstrom on the other face. EutN is involved in the cobalamin-dependent degradation of ethanolamine. 83 matched cddid_all.tbl CDD pfam03320 pfam03320 427243 FBPase_glpX Bacterial fructose-1,6-bisphosphatase, glpX-encoded. 304 matched cddid_all.tbl CDD pfam03321 pfam03321 460885 GH3 GH3 auxin-responsive promoter. 531 matched cddid_all.tbl CDD pfam03323 pfam03323 427245 GerA Bacillus/Clostridium GerA spore germination protein. 467 matched cddid_all.tbl CDD pfam03324 pfam03324 367447 Herpes_HEPA Herpesvirus DNA helicase/primase complex associated protein. This family includes HSV UL8, EHV-1 54, VZV 52 AND HCMV 102. 95 matched cddid_all.tbl CDD pfam03325 pfam03325 397420 Herpes_PAP Herpesvirus polymerase accessory protein. The same proteins are also known as polymerase processivity factors. 166 matched cddid_all.tbl CDD pfam03326 pfam03326 308764 Herpes_TAF50 Herpesvirus transcription activation factor (transactivator). This family includes EBV BRLF1 and similar ORF 50 proteins from other herpesviruses. 568 matched cddid_all.tbl CDD pfam03327 pfam03327 427246 Herpes_VP19C Herpesvirus capsid shell protein VP19C. 262 matched cddid_all.tbl CDD pfam03328 pfam03328 427247 HpcH_HpaI HpcH/HpaI aldolase/citrate lyase family. This family includes 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase and 4-hydroxy-2-oxovalerate aldolase. 221 matched cddid_all.tbl CDD pfam03330 pfam03330 427248 DPBB_1 Lytic transglycolase. Rare lipoprotein A (RlpA) contains a conserved region that has the double-psi beta-barrel (DPBB) fold. The function of RlpA is not well understood, but it has been shown to act as a prc mutant suppressor in Escherichia coli. The DPBB fold is often an enzymatic domain. The members of this family are quite diverse, and if catalytic this family may contain several different functions. Another example of this domain is found in the N terminus of pollen allergen. Recent studies show that the full-length RlpA protein from Pseudomonas Aeruginosa is an outer membrane protein that is a lytic transglycolase with specificity for peptidoglycan lacking stem peptides. Residue D157 in UniProtKB:Q9X6V6 is critical for lytic activity. 82 matched cddid_all.tbl CDD pfam03331 pfam03331 460886 LpxC UDP-3-O-acyl N-acetylglycosamine deacetylase. The enzymes in this family catalyze the second step in the biosynthetic pathway for lipid A. 271 matched cddid_all.tbl CDD pfam03332 pfam03332 397425 PMM Eukaryotic phosphomannomutase. This enzyme EC:5.4.2.8 is involved in the synthesis of the GDP-mannose and dolichol-phosphate-mannose required for a number of critical mannosyl transfer reactions. 220 matched cddid_all.tbl CDD pfam03333 pfam03333 377022 PapB Adhesin biosynthesis transcription regulatory protein. This family includes PapB, DaaA, FanA, FanB, and AfaA. 91 matched cddid_all.tbl CDD pfam03334 pfam03334 460887 PhaG_MnhG_YufB Na+/H+ antiporter subunit. This family includes PhaG from Rhizobium meliloti, MnhG from Staphylococcus aureus, YufB from Bacillus subtilis. 82 matched cddid_all.tbl CDD pfam03335 pfam03335 335296 Phage_fiber Phage tail fibre repeat. 14 matched cddid_all.tbl CDD pfam03336 pfam03336 281347 Pox_C4_C10 Poxvirus C4/C10 protein. This family represents proteins found in Poxvirus, including Protein C10 and Protein C4. Vaccinia virus protein C4 plays a role in the inhibition of host NF-kappa-B activation. It blocks the subunit p65/RELA translocation into the host nucleus. 322 matched cddid_all.tbl CDD pfam03337 pfam03337 281348 Pox_F12L Poxvirus F12L protein. 649 matched cddid_all.tbl CDD pfam03338 pfam03338 281349 Pox_J1 Poxvirus J1 protein. 145 matched cddid_all.tbl CDD pfam03339 pfam03339 281350 Pox_L3_FP4 Poxvirus L3/FP4 protein. 316 matched cddid_all.tbl CDD pfam03340 pfam03340 397427 Pox_Rif Poxvirus rifampicin resistance protein. 542 matched cddid_all.tbl CDD pfam03341 pfam03341 281352 Pox_mRNA-cap Poxvirus mRNA capping enzyme, small subunit. The small subunit of the poxvirus mRNA capping enzyme has been found to have a structure which suggests that it started life as an RNA cap 2-prime O-methyltransferase. It has subsequently evolved to a catalytically inactive form that has been retained in order to help stabilize the large subunit, D1, and to enhance its methyltransferase activity through an allosteric mechanism. 286 matched cddid_all.tbl CDD pfam03342 pfam03342 281353 Rhabdo_M1 Rhabdovirus M1 matrix protein (M1 polymerase-associated protein). 227 matched cddid_all.tbl CDD pfam03343 pfam03343 460888 SART-1 SART-1 family. SART-1 is a protein involved in cell cycle arrest and pre-mRNA splicing. It has been shown to be a component of U4/U6 x U5 tri-snRNP complex in human, Schizosaccharomyces pombe and Saccharomyces cerevisiae. SART-1 is a known tumour antigen in a range of cancers recognized by T cells. 569 matched cddid_all.tbl CDD pfam03344 pfam03344 460889 Daxx Daxx N-terminal Rassf1C-interacting domain. The Daxx protein (also known as the Fas-binding protein) is thought to play a role in apoptosis. Daxx forms a complex with Axin. Remodelling of the family to a short domain based on the PDB:2kzs structure gives a more representative family. DAXX is a scaffold protein shown to play diverse roles in transcription and cell cycle regulation. This N-terminal domain folds into a left-handed four-helix bundle (H1, H2, H4, H5) that binds to the N-terminal residues of the tumour-suppressor Rassf1C. 95 matched cddid_all.tbl CDD pfam03345 pfam03345 460890 DDOST_48kD Oligosaccharyltransferase 48 kDa subunit beta. Members of this family are involved in asparagine-linked protein glycosylation. In particular, dolichyl-diphosphooligosaccharide-protein glycosyltransferase (DDOST), also known as oligosaccharyltransferase EC:2.4.1.119, transfers the high-mannose sugar GlcNAc(2)-Man(9)-Glc(3) from a dolichol-linked donor to an asparagine acceptor in a consensus Asn-X-Ser/Thr motif. In most eukaryotes, the DDOST complex is composed of three subunits, which in humans are described as a 48kD subunit, ribophorin I, and ribophorin II. However, the yeast DDOST appears to consist of six subunits (alpha, beta, gamma, delta, epsilon, zeta). The yeast beta subunit is a 45kD polypeptide, previously discovered as the Wbp1 protein, with known sequence similarity to the human 48kD subunit and the other orthologues. This family includes the 48kD-like subunits from several eukaryotes; it also includes the yeast DDOST beta subunit Wbp1. 406 matched cddid_all.tbl CDD pfam03347 pfam03347 281357 TDH Vibrio thermostable direct hemolysin. 165 matched cddid_all.tbl CDD pfam03348 pfam03348 460891 Serinc Serine incorporator (Serinc). This is a family of eukaryotic membrane proteins which incorporate serine into membranes and facilitate the synthesis of the serine-derived lipids phosphatidylserine and sphingolipid. Members of this family contain 11 transmembrane domains and form intracellular complexes with key enzymes involved in serine and sphingolipid biosynthesis. 434 matched cddid_all.tbl CDD pfam03349 pfam03349 427255 Toluene_X Outer membrane protein transport protein (OMPP1/FadL/TodX). This family includes TodX from Pseudomonas putida F1 and TbuX from Ralstonia pickettii PKO1. These are membrane proteins of uncertain function that are involved in toluene catabolism. Related proteins involved in the degradation of similar aromatic hydrocarbons are also in this family, such as CymD. This family also includes FadL involved in translocation of long-chain fatty acids across the outer membrane. It is also a receptor for the bacteriophage T2. 421 matched cddid_all.tbl CDD pfam03350 pfam03350 460892 UPF0114 Uncharacterized protein family, UPF0114. 118 matched cddid_all.tbl CDD pfam03351 pfam03351 460893 DOMON DOMON domain. The DOMON (named after dopamine beta-monooxygenase N-terminal) domain is 110-125 residues long. It is predicted to form an all beta fold with up to 11 strands and is secreted to the extracellular compartment. The beta-strand folding produces a hydrophobic pocket which appears to bind soluble haem. This is consistent with the predominant architectures where the protein is associated with cytochromes or enzymatic domains whose activity involves redox or electron transfer reactions potentially as a direct participant in the electron transfer process. The DOMON domain superfamily, of which this is just one member, shows (1) multiple hydrophobic residues that contribute to the hydrophobic core of the strands of the beta-sandwich, and small residues found at the boundaries of strands and loops, (2) a strongly conserved charged residue (usually arginine/lysine) at the end of strand 9, which possibly stabilizes the loop between 9 and 10, and (3) a polar residue (usually histidine, lysine or arginine), that interacts or coordinates with ligands. The suggested superfamily includes both haem- and sugar-binding members: the haem-binding families being the ethyl-Benzoate dehydrogenase family EB_dh, pfam09459, the cellobiose dehydrogenase family CBDH and this family, and the sugar-binding families being the xylanases, CBM_4_9, pfam02018. The common feature of the superfamily is the 11-beta-strand structure, although the first and eleventh strands are not well conserved either within families or between families. 116 matched cddid_all.tbl CDD pfam03352 pfam03352 460894 Adenine_glyco Methyladenine glycosylase. The DNA-3-methyladenine glycosylase I is constitutively expressed and is specific for the alkylated 3-methyladenine DNA. 177 matched cddid_all.tbl CDD pfam03353 pfam03353 397436 Lin-8 Ras-mediated vulval-induction antagonist. LIN-8 is a nuclear protein, present at the sites of transcriptional repressor complexes, which interacts with LIN-35 Rb. Lin35 Rb is a product of the class B synMuv gene lin-35 which silences genes required for vulval specification through chromatin modification and remodelling. The biological role of the interaction has not yet been determined however predictions have been made. The interaction shows that class A synMuv genes control vulval induction through the transcriptional regulation of gene expression. LIN-8 normally functions as part of a protein complex however when the complex is absent, other family members can partially replace LIN-8 activity. 309 matched cddid_all.tbl CDD pfam03354 pfam03354 460895 TerL_ATPase "Terminase large subunit, ATPase domain. Terminase large subunit (TerL) from bacteriophages and evolutionarily related viruses, is an important component of the DNA packing machinery and comprises an ATPase domain, which powers DNA translocation and a nuclease domain that cuts concatemeric DNA. TerL forms pentamers in which the ATPase domains form a ring distal to the capsid. This is the ATPase domain which contains a C-terminal subdomain that sits above the ATPase active site, called the ""Lid subdomain"" with reference to analogous lid subdomains found in other ATPases. It contains a hydrophobic patch (Trp and Tyr residues) that mediates critical interactions in the interface between adjacent ATPase subunits and assists the positioning of the arginine finger residue that catalyzes ATP hydrolysis. This entry also includes bacterial proteins of unknown function." 178 matched cddid_all.tbl CDD pfam03355 pfam03355 146143 Pox_TAP Viral Trans-Activator Protein. These proteins function as a trans-activator of viral late genes. 260 matched cddid_all.tbl CDD pfam03356 pfam03356 281365 Pox_LP_H2 Viral late protein H2. All Members of this family show similarity to the vaccinia virus late protein H2. This protein is often referred to by its gene name of H2R. Members from this family all belong to the viral taxon Poxviridae. 188 matched cddid_all.tbl CDD pfam03357 pfam03357 460896 Snf7 Snf7. This family of proteins are involved in protein sorting and transport from the endosome to the vacuole/lysosome in eukaryotic cells. Vacuoles/lysosomes play an important role in the degradation of both lipids and cellular proteins. In order to perform this degradative function, vacuoles/lysosomes contain numerous hydrolases which have been transported in the form of inactive precursors via the biosynthetic pathway and are proteolytically activated upon delivery to the vacuole/lysosome. The delivery of transmembrane proteins, such as activated cell surface receptors to the lumen of the vacuole/lysosome, either for degradation/downregulation, or in the case of hydrolases, for proper localization, requires the formation of multivesicular bodies (MVBs). These late endosomal structures are formed by invaginating and budding of the limiting membrane into the lumen of the compartment. During this process, a subset of the endosomal membrane proteins is sorted into the forming vesicles. Mature MVBs fuse with the vacuole/lysosome, thereby releasing cargo containing vesicles into its hydrolytic lumen for degradation. Endosomal proteins that are not sorted into the intralumenal MVB vesicles are either recycled back to the plasma membrane or Golgi complex, or remain in the limiting membrane of the MVB and are thereby transported to the limiting membrane of the vacuole/lysosome as a consequence of fusion. Therefore, the MVB sorting pathway plays a critical role in the decision between recycling and degradation of membrane proteins. A few archaeal sequences are also present within this family. 168 matched cddid_all.tbl CDD pfam03358 pfam03358 427259 FMN_red NADPH-dependent FMN reductase. 152 matched cddid_all.tbl CDD pfam03359 pfam03359 460897 GKAP Guanylate-kinase-associated protein (GKAP) protein. 341 matched cddid_all.tbl CDD pfam03360 pfam03360 460898 Glyco_transf_43 Glycosyltransferase family 43. 202 matched cddid_all.tbl CDD pfam03361 pfam03361 281370 Herpes_IE2_3 Herpes virus intermediate/early protein 2/3. These viral sequences are similar to UL117 protein of human and chimpanzee cytomegalovirus, and to intermediate/early proteins 2 and 3 of certain herpes viruses. UL117 is thought to be a glycoprotein that is expressed at early and late times after infection. This region is close to the C-terminus of the protein and may be a transmembrane region. 162 matched cddid_all.tbl CDD pfam03362 pfam03362 281371 Herpes_UL47 Herpesvirus UL47 protein. 448 matched cddid_all.tbl CDD pfam03363 pfam03363 281372 Herpes_LP Herpesvirus leader protein. 174 matched cddid_all.tbl CDD pfam03364 pfam03364 397441 Polyketide_cyc Polyketide cyclase / dehydrase and lipid transport. This family contains polyketide cylcases/dehydrases which are enzymes involved in polyketide synthesis. The family also includes proteins which are involved in the binding/transport of lipids. 125 matched cddid_all.tbl CDD pfam03366 pfam03366 460899 YEATS YEATS family. We have named this family the YEATS family, after `YNK7', `ENL', `AF-9', and `TFIIF small subunit'. This family also contains the GAS41 protein. All these proteins are thought to have a transcription stimulatory activity 80 matched cddid_all.tbl CDD pfam03367 pfam03367 427263 zf-ZPR1 ZPR1 zinc-finger domain. The zinc-finger protein ZPR1 is ubiquitous among eukaryotes. It is indeed known to be an essential protein in yeast. In quiescent cells, ZPR1 is localized to the cytoplasm. But in proliferating cells treated with EGF or with other mitogens, ZPR1 accumulates in the nucleolus. ZPR1 interacts with the cytoplasmic domain of the inactive EGF receptor (EGFR) and is thought to inhibit the basal protein tyrosine kinase activity of EGFR. This interaction is disrupted when cells are treated with EGF, though by themselves, inactive EGFRs are not sufficient to sequester ZPR1 to the cytoplasm. Upon stimulation by EGF, ZPR1 directly binds the eukaryotic translation elongation factor-1alpha (eEF-1alpha) to form ZPR1/eEF-1alpha complexes. These move into the nucleus, localising particularly at the nucleolus. Indeed, the interaction between ZPR1 and eEF-1alpha has been shown to be essential for normal cellular proliferation, and ZPR1 is thought to be involved in pre-ribosomal RNA expression. The ZPR1 domain consists of an elongation initiation factor 2-like zinc finger and a double-stranded beta helix with a helical hairpin insertion. ZPR1 binds preferentially to GDP-bound eEF1A but does not directly influence the kinetics of nucleotide exchange or GTP hydrolysis. The alignment for this family shows a domain of which there are two copies in ZPR1 proteins. This family also includes several hypothetical archaeal proteins (from both Crenarchaeota and Euryarchaeota), which only contain one copy of the aligned region. This similarity between ZPR1 and archaeal proteins was not previously noted. 161 matched cddid_all.tbl CDD pfam03368 pfam03368 460900 Dicer_dimer Dicer dimerization domain. This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules. It is essential for the activity of Dicer. It is a divergent double stranded RNA-binding domain. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity. This domain has weak dsRNA-binding activity. It mediates heterodimerization of Dicer proteins with their respective protein partners. 89 matched cddid_all.tbl CDD pfam03369 pfam03369 281377 Herpes_UL3 Herpesvirus UL3 protein. 135 matched cddid_all.tbl CDD pfam03370 pfam03370 427265 CBM_21 Carbohydrate/starch-binding module (family 21). This family consists of several eukaryotic proteins that are thought to be involved in the regulation of glycogen metabolism. For instance, the mouse PTG protein has been shown to interact with glycogen synthase, phosphorylase kinase, phosphorylase a: these three enzymes have key roles in the regulation of glycogen metabolism. PTG also binds the catalytic subunit of protein phosphatase 1 (PP1C) and localizes it to glycogen. Subsets of similar interactions have been observed with several other members of this family, such as the yeast PIG1, PIG2, GAC1 and GIP2 proteins. While the precise function of these proteins is not known, they may serve a scaffold function, bringing together the key enzymes in glycogen metabolism. This family is a carbohydrate binding domain. 112 matched cddid_all.tbl CDD pfam03371 pfam03371 460901 PRP38 PRP38 family. Members of this family are related to the pre mRNA splicing factor PRP38 from yeast. Therefore all the members of this family could be involved in splicing. This conserved region could be involved in RNA binding. The putative domain is about 180 amino acids in length. PRP38 is a unique component of the U4/U6.U5 tri-small nuclear ribonucleoprotein (snRNP) particle and is necessary for an essential step late in spliceosome maturation. 165 matched cddid_all.tbl CDD pfam03372 pfam03372 460902 Exo_endo_phos Endonuclease/Exonuclease/phosphatase family. This large family of proteins includes magnesium dependent endonucleases and a large number of phosphatases involved in intracellular signalling. This family includes: AP endonuclease proteins EC:4.2.99.18, DNase I proteins EC:3.1.21.1, Synaptojanin an inositol-1,4,5-trisphosphate phosphatase EC:3.1.3.56, Sphingomyelinase EC:3.1.4.12 and Nocturnin. 183 matched cddid_all.tbl CDD pfam03373 pfam03373 281381 Octapeptide Octapeptide repeat. This octapeptide repeat is found in several bacterial proteins. The function of this repeat is unknown. 8 matched cddid_all.tbl CDD pfam03374 pfam03374 460903 ANT Phage antirepressor protein KilAC domain. This domain was called the KilAC domain by Iyer and colleagues. 105 matched cddid_all.tbl CDD pfam03376 pfam03376 460904 Adeno_E3B Adenovirus E3B protein. 67 matched cddid_all.tbl CDD pfam03377 pfam03377 397449 TAL_effector TAL effector repeat. The proteins in this family bind to DNA. Each repeat binds to a base pair in a predictable way. The structure shows that each repeat is composed of two alpha helices. 33 matched cddid_all.tbl CDD pfam03378 pfam03378 367469 CAS_CSE1 CAS/CSE protein, C-terminus. Mammalian cellular apoptosis susceptibility (CAS) proteins are homologous to the yeast chromosome-segregation protein, CSE1. This family aligns the C-terminal halves (approximately). CAS is involved in both cellular apoptosis and proliferation. Apoptosis is inhibited in CAS-depleted cells, while the expression of CAS correlates to the degree of cellular proliferation. Like CSE1, it is essential for the mitotic checkpoint in the cell cycle (CAS depletion blocks the cell in the G2 phase), and has been shown to be associated with the microtubule network and the mitotic spindle, as is the protein MEK, which is thought to regulate the intracellular localization (predominantly nuclear vs. predominantly cytosolic) of CAS. In the nucleus, CAS acts as a nuclear transport factor in the importin pathway. The importin pathway mediates the nuclear transport of several proteins that are necessary for mitosis and further progression. CAS is therefore thought to affect the cell cycle through its effect on the nuclear transport of these proteins. Since apoptosis also requires the nuclear import of several proteins (such as P53 and transcription factors), it has been suggested that CAS also enables apoptosis by facilitating the nuclear import of at least a subset of these essential proteins. 435 matched cddid_all.tbl CDD pfam03379 pfam03379 427269 CcmB CcmB protein. CcmB is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organizms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor. CcmB is required for the export of haem to the periplasm. 215 matched cddid_all.tbl CDD pfam03380 pfam03380 460905 DUF282 Caenorhabditis protein of unknown function, DUF282. 38 matched cddid_all.tbl CDD pfam03381 pfam03381 460906 CDC50 LEM3 (ligand-effect modulator 3) family / CDC50 family. Members of this family have been predicted to contain transmembrane helices. The family member LEM3 is a ligand-effect modulator, mutation of which increases glucocorticoid receptor activity in response to dexamethasone and also confers increased activity on other intracellular receptors including the progesterone, oestrogen and mineralocorticoid receptors. LEM3 is thought to affect a downstream step in the glucocorticoid receptor pathway. Factors that modulate ligand responsiveness are likely to contribute to the context-specific actions of the glucocorticoid receptor in mammalian cells. The products of genes YNR048w, YNL323w and YCR094w (CDC50) show redundancy of function and are involved in regulation of transcription via CDC39. CDC39 (also known as NOT1) is normally a negative regulator of transcription either by affecting the general RNA polymerase II machinery or by altering chromatin structure. One function of CDC39 is to block activation of the mating response pathway in the absence of pheromone, and mutation causes arrest in G1 by activation of the pathway. It may be that the cold-sensitive arrest in G1 noticed in CDC50 mutants may be due to inactivation of CDC39. The effects of LEM3 on glucocorticoid receptor activity may also be due to effects on transcription via CDC39. 292 matched cddid_all.tbl CDD pfam03382 pfam03382 427272 DUF285 Mycoplasma protein of unknown function, DUF285. This region appears distantly related to leucine rich repeats. 120 matched cddid_all.tbl CDD pfam03383 pfam03383 251914 Serpentine_r_xa Caenorhabditis serpentine receptor-like protein, class xa. This family contains various Caenorhabditis proteins, some of which are annotated as being serpentine receptors, mainly of the xa class. 153 matched cddid_all.tbl CDD pfam03384 pfam03384 146165 DUF287 Drosophila protein of unknown function, DUF287. 55 matched cddid_all.tbl CDD pfam03385 pfam03385 427273 STELLO STELLO glycosyltransferases. This domain family is found in Metazoa and in Virdiplantae. Two of the family members are characterized in Arabidopsis thaliana, named STELLO1 (STL1) and STELLO2 (STL2) respectively. They are Golgi-localized proteins that can interact with CesAs (cellulose synthase A) and control cellulose quantity. In the absence of STELLO function, the spatial distribution within the Golgi, secretion and activity of the CSCs are impaired indicating a central role of the STELLO proteins in CSC assembly. Point mutations in the predicted catalytic domains of the STELLO proteins indicate that they are glycosyltransferases facing the Golgi lumen. STL homologs are present throughout the plant kingdom, but STL proteins are distinct from distantly related proteins in nematodes, fungi and molluscs. 387 matched cddid_all.tbl CDD pfam03386 pfam03386 460907 ENOD93 Early nodulin 93 ENOD93 protein. 78 matched cddid_all.tbl CDD pfam03387 pfam03387 281391 Herpes_UL46 Herpesvirus UL46 protein. 435 matched cddid_all.tbl CDD pfam03388 pfam03388 397453 Lectin_leg-like Legume-like lectin family. Lectins are structurally diverse proteins that bind to specific carbohydrates. This family includes the VIP36 and ERGIC-53 lectins. These two proteins were the first recognized members of a family of animal lectins similar (19-24%) to the leguminous plant lectins. The alignment for this family aligns residues lying towards the N-terminus, where the similarity of VIP36 and ERGIC-53 is greatest. However, while Fiedler and Simons identified these proteins as a new family of animal lectins, our alignment also includes yeast sequences. ERGIC-53 is a 53kD protein, localized to the intermediate region between the endoplasmic reticulum and the Golgi apparatus (ER-Golgi-Intermediate Compartment, ERGIC). It was identified as a calcium-dependent, mannose-specific lectin. Its dysfunction has been associated with combined factors V and VIII deficiency OMIM:227300 OMIM:601567, suggesting an important and substrate-specific role for ERGIC-53 in the glycoprotein- secreting pathway. 226 matched cddid_all.tbl CDD pfam03389 pfam03389 427275 MobA_MobL MobA/MobL family. This family includes of the MobA protein from the E. coli plasmid RSF1010, and the MobL protein from the Thiobacillus ferrooxidans plasmid PTF1. These sequences are mobilization proteins, which are essential for specific plasmid transfer. 217 matched cddid_all.tbl CDD pfam03390 pfam03390 427276 2HCT 2-hydroxycarboxylate transporter family. The 2-hydroxycarboxylate transporter family is a family of secondary transporters found exclusively in the bacterial kingdom. They function in the metabolism of the di- and tricarboxylates malate and citrate, mostly in fermentative pathways involving decarboxylation of malate or oxaloacetate. 414 matched cddid_all.tbl CDD pfam03391 pfam03391 397456 Nepo_coat Nepovirus coat protein, central domain. The members of this family are derived from nepoviruses. Together with comoviruses and picornaviruses, nepoviruses are classified in the picornavirus superfamily of plus strand single-stranded RNA viruses. This family aligns several nepovirus coat protein sequences. In several cases, this is found at the C-terminus of the RNA2-encoded viral polyprotein. The coat protein consists of three trapezoid-shaped beta-barrel domains, and forms a pseudo T = 3 icosahedral capsid structure. 167 matched cddid_all.tbl CDD pfam03392 pfam03392 460908 OS-D Insect pheromone-binding family, A10/OS-D. 93 matched cddid_all.tbl CDD pfam03393 pfam03393 308800 Pneumo_matrix Pneumovirus matrix protein. 252 matched cddid_all.tbl CDD pfam03394 pfam03394 281397 Pox_E8 Poxvirus E8 protein. 238 matched cddid_all.tbl CDD pfam03395 pfam03395 281398 Pox_P4A Poxvirus P4A protein. 882 matched cddid_all.tbl CDD pfam03396 pfam03396 397458 Pox_RNA_pol_35 Poxvirus DNA-directed RNA polymerase, 35 kD subunit. 293 matched cddid_all.tbl CDD pfam03397 pfam03397 460909 Rhabdo_matrix Rhabdovirus matrix protein. 168 matched cddid_all.tbl CDD pfam03398 pfam03398 460910 Ist1 Regulator of Vps4 activity in the MVB pathway. ESCRT-I, -II, and -III are endosomal sorting complexes required for transporting proteins and carry out cargo sorting and vesicle formation in the multivesicular bodies, MVBs, pathway. These complexes are transiently recruited from the cytoplasm to the endosomal membrane where they bind transmembrane proteins previously marked for degradation by mono-ubiquitination. Assembly of ESCRT-III, a complex composed of at least four subunits (Vps2, Vps24, Vps20, Snf7), is intimately linked with MVB vesicle formation, its disassembly being an essential step in the MVB vesicle formation, a reaction that is carried out by Vps4, an AAA-type ATPase. The family Ist1 is a regulator of Vps4 activity; by interacting with Did2 and Vps4, Ist1 appears to regulate the recruitment and oligomerization of Vps4. Together Ist1, Did2, and Vta1 form a network of interconnected regulatory proteins that modulate Vps4 activity, thereby regulating the flow of cargo through the MVB pathway. 164 matched cddid_all.tbl CDD pfam03399 pfam03399 460911 SAC3_GANP SAC3/GANP family. This family includes diverse proteins involved in large complexes. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3, and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localization of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. 287 matched cddid_all.tbl CDD pfam03400 pfam03400 281403 DDE_Tnp_IS1 IS1 transposase. Transposase proteins are necessary for efficient DNA transposition. This family represents bacterial IS1 transposases. 131 matched cddid_all.tbl CDD pfam03401 pfam03401 397461 TctC Tripartite tricarboxylate transporter family receptor. These probable extra-cytoplasmic solute receptors are strongly overrepresented in several beta-proteobacteria. This family, formerly known as Bug - Bordetella uptake gene (bug) product - is a family of bacterial tripartite tricarboxylate receptors of the extracytoplasmic solute binding receptor-dependent transporter group of families, distinct from the ABC and TRAP-T families. The TctABC system has been characterized in S. typhimurium, and TctC is the extracytoplasmic tricarboxylate-binding receptor which binds the transporters TctA and TctB, two integral membrane proteins. Complete three-component systems are found only in bacteria. 274 matched cddid_all.tbl CDD pfam03402 pfam03402 460912 V1R Vomeronasal organ pheromone receptor family, V1R. This family represents one of two known vomeronasal organ receptor families, the V1R family. 292 matched cddid_all.tbl CDD pfam03403 pfam03403 397462 PAF-AH_p_II Platelet-activating factor acetylhydrolase, isoform II. Platelet-activating factor acetylhydrolase (PAF-AH) is a subfamily of phospholipases A2, responsible for inactivation of platelet-activating factor through cleavage of an acetyl group. Three known PAF-AHs are the brain heterotrimeric PAF-AH Ib, whose catalytic beta and gamma subunits are aligned in pfam02266, the extracellular, plasma PAF-AH (pPAF-AH), and the intracellular PAF-AH isoform II (PAF-AH II). This family aligns pPAF-AH and PAF-AH II, whose similarity was previously noted. 372 matched cddid_all.tbl CDD pfam03404 pfam03404 427280 Mo-co_dimer Mo-co oxidoreductase dimerization domain. This domain is found in molybdopterin cofactor (Mo-co) oxidoreductases. It is involved in dimer formation, and has an Ig-fold structure. 136 matched cddid_all.tbl CDD pfam03405 pfam03405 460913 FA_desaturase_2 Fatty acid desaturase. 318 matched cddid_all.tbl CDD pfam03406 pfam03406 427282 Phage_fiber_2 Phage tail fibre repeat. This repeat is found in the tail fibres of phage. For example protein K. The repeats are about 40 residues long. 38 matched cddid_all.tbl CDD pfam03407 pfam03407 367480 Nucleotid_trans Nucleotide-diphospho-sugar transferase. Proteins in this family have been been predicted to be nucleotide-diphospho-sugar transferases. 208 matched cddid_all.tbl CDD pfam03408 pfam03408 460914 Foamy_virus_ENV Foamy virus envelope protein. Expression of the envelope (Env) glycoprotein is essential for viral particle egress. This feature is unique to the Spumavirinae, a subclass of the Retroviridae. 984 matched cddid_all.tbl CDD pfam03409 pfam03409 397466 Glycoprotein Transmembrane glycoprotein. This family of proteins has some GO annotations for positive regulation of growth rate and nematode larval development. This is probably a family of membrane glycoproteins. 351 matched cddid_all.tbl CDD pfam03410 pfam03410 281411 Peptidase_M44 Metallopeptidase from vaccinia pox. This is a family of Poxviridae metalloendopeptidases. The members were often originally named as G1 proteins. The family carries three zinc-binding ligands and a catalytic glutamate. The first two zinc ligands are histidine residues, found together with the catalytic glutamate in a HXXEH motif, an inverse of the classical metallopeptidase motif, HEXXH. The third zinc ligand is a glutamate C-terminal to the HXXEH motif within a motif ELENEY (see MEROPS). 596 matched cddid_all.tbl CDD pfam03411 pfam03411 427283 Peptidase_M74 Penicillin-insensitive murein endopeptidase. 242 matched cddid_all.tbl CDD pfam03412 pfam03412 367483 Peptidase_C39 Peptidase C39 family. Lantibiotic and non-lantibiotic bacteriocins are synthesized as precursor peptides containing N-terminal extensions (leader peptides) which are cleaved off during maturation. Most non-lantibiotics and also some lantibiotics have leader peptides of the so-called double-glycine type. These leader peptides share consensus sequences and also a common processing site with two conserved glycine residues in positions -1 and -2. The double- glycine-type leader peptides are unrelated to the N-terminal signal sequences which direct proteins across the cytoplasmic membrane via the sec pathway. Their processing sites are also different from typical signal peptidase cleavage sites, suggesting that a different processing enzyme is involved. Peptide bacteriocins are exported across the cytoplasmic membrane by a dedicated ATP-binding cassette (ABC) transporter. The ABC transporter is the maturation protease and its proteolytic domain resides in the N-terminal part of the protein. This peptidase domain is found in a wide range of ABC transporters, however the presumed catalytic cysteine and histidine are not conserved in all members of this family. 133 matched cddid_all.tbl CDD pfam03413 pfam03413 427284 PepSY Peptidase propeptide and YPEB domain. This region is likely to have an protease inhibitory function (personal obs:C Yeats). This model is likely to miss some members of this family as the separation from signal to noise is not clear. The name is derived from Peptidase & Bacillus subtilis YPEB. 59 matched cddid_all.tbl CDD pfam03414 pfam03414 427285 Glyco_transf_6 Glycosyltransferase family 6. 289 matched cddid_all.tbl CDD pfam03415 pfam03415 427286 Peptidase_C11 Clostripain family. 359 matched cddid_all.tbl CDD pfam03416 pfam03416 460915 Peptidase_C54 Peptidase family C54. 269 matched cddid_all.tbl CDD pfam03417 pfam03417 397472 AAT Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase. 223 matched cddid_all.tbl CDD pfam03418 pfam03418 367487 Peptidase_A25 Germination protease. 354 matched cddid_all.tbl CDD pfam03419 pfam03419 460916 Peptidase_U4 Sporulation factor SpoIIGA. 274 matched cddid_all.tbl CDD pfam03420 pfam03420 397474 Peptidase_S77 Prohead core protein serine protease. 198 matched cddid_all.tbl CDD pfam03421 pfam03421 427289 Acetyltransf_14 YopJ Serine/Threonine acetyltransferase. The Yersinia effector YopJ inhibits the innate immune response by blocking MAP kinase and NFkappaB signaling pathways. YopJ is a serine/threonine acetyltransferase which regulates signalling pathways by blocking phosphorylation. Specifically, YopJ has been shown to block phosphorylation of active site residues. It has also been shown that YopJ acetyltransferase is activated by eukaryotic host cell inositol hexakisphosphate. This family was previously incorrectly annotated in Pfam as being a peptidase family. 174 matched cddid_all.tbl CDD pfam03422 pfam03422 397476 CBM_6 Carbohydrate binding module (family 6). 125 matched cddid_all.tbl CDD pfam03423 pfam03423 367491 CBM_25 Carbohydrate binding domain (family 25). 101 matched cddid_all.tbl CDD pfam03424 pfam03424 397477 CBM_17_28 Carbohydrate binding domain (family 17/28). 204 matched cddid_all.tbl CDD pfam03425 pfam03425 427290 CBM_11 Carbohydrate binding domain (family 11). 175 matched cddid_all.tbl CDD pfam03426 pfam03426 367493 CBM_15 Carbohydrate binding domain (family 15). 153 matched cddid_all.tbl CDD pfam03427 pfam03427 112252 CBM_19 Carbohydrate binding domain (family 19). 61 matched cddid_all.tbl CDD pfam03428 pfam03428 427291 RP-C Replication protein C N-terminal domain. Replication protein C is involved in the early stages of viral DNA replication. 174 matched cddid_all.tbl CDD pfam03429 pfam03429 367495 MSP1b Major surface protein 1B. The major surface protein (MSP1) of the cattle pathogen Anaplasma is a heterodimer comprised of MSP1a and MSP1b. This family is the MSP1b chain. There MSP1 proteins are putative adhesins for bovine erythrocytes. 769 matched cddid_all.tbl CDD pfam03430 pfam03430 281430 TATR Trans-activating transcriptional regulator. This family of trans-activating transcriptional regulator (TATR), also known as intermediate early protein 1, are common to the Nucleopolyhedroviruses. 575 matched cddid_all.tbl CDD pfam03431 pfam03431 367496 RNA_replicase_B RNA replicase, beta-chain. This family is of Leviviridae RNA replicases. The replicase is also known as RNA dependent RNA polymerase. 538 matched cddid_all.tbl CDD pfam03432 pfam03432 367497 Relaxase Relaxase/mobilization nuclease domain. Relaxases/mobilization proteins are required for the horizontal transfer of genetic information contained on plasmids that occurs during bacterial conjugation. The relaxase, in conjunction with several auxiliary proteins, forms the relaxation complex or relaxosome. Relaxases nick duplex DNA in a specific manner by catalysing trans-esterification. 240 matched cddid_all.tbl CDD pfam03433 pfam03433 427292 EspA EspA-like secreted protein. EspA is the prototypical member of this family. EspA, together with EspB, EspD and Tir are exported by a type III secretion system. These proteins are essential for attaching and effacing lesion formation. EspA is a structural protein and a major component of a large, transiently expressed, filamentous surface organelle which forms a direct link between the bacterium and the host cell. 180 matched cddid_all.tbl CDD pfam03434 pfam03434 308824 DUF276 DUF276. This family is specific to Borrelia burgdorferi. The protein is encoded on extra-chromosomal DNA. This domain has no known function. 291 matched cddid_all.tbl CDD pfam03435 pfam03435 397480 Sacchrp_dh_NADP Saccharopine dehydrogenase NADP binding domain. This family contains the NADP binding domain of saccharopine dehydrogenase. In some organizms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase. The saccharopine dehydrogenase can also function as a saccharopine reductase. 120 matched cddid_all.tbl CDD pfam03436 pfam03436 427293 DUF281 Domain of unknown function (DUF281). This family of worm domain has no known function. The boundaries of the presumed domain are rather uncertain. 55 matched cddid_all.tbl CDD pfam03437 pfam03437 281436 BtpA BtpA family. The BtpA protein is tightly associated with the thylakoid membranes, where it stabilizes the reaction centre proteins of photosystem I. 254 matched cddid_all.tbl CDD pfam03438 pfam03438 367500 Pneumo_NS1 Pneumovirus NS1 protein. This non-structural protein is one of two found in pneumoviruses. The protein is about 140 amino acids in length. The NS1 protein appears to be important for efficient replication but not essential. The NS1 protein has been shown by yeast two-hybrid to interact with the viral P protein. This protein is also known as the 1C protein. It has also been shown that NS1 can potently inhibit transcription and RNA replication. 136 matched cddid_all.tbl CDD pfam03439 pfam03439 397481 Spt5-NGN Early transcription elongation factor of RNA pol II, NGN section. Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit. 84 matched cddid_all.tbl CDD pfam03440 pfam03440 367501 APT Aerolysin/Pertussis toxin (APT) domain. This family represents the N-terminal domain of aerolysin and pertussis toxin and has a type-C lectin like fold. 87 matched cddid_all.tbl CDD pfam03441 pfam03441 460917 FAD_binding_7 FAD binding domain of DNA photolyase. 201 matched cddid_all.tbl CDD pfam03442 pfam03442 427295 CBM_X2 Carbohydrate binding domain X2. This domain binds to cellulose and to bacterial cell walls. It is found in glycosyl hydrolases and in scaffolding proteins of cellulosomes (multiprotein glycosyl hydrolase complexes). In the cellulosome it may aid cellulose degradation by anchoring the cellulosome to the bacterial cell wall and by binding it to its substrate. This domain has an Ig-like fold. 83 matched cddid_all.tbl CDD pfam03443 pfam03443 460918 AA9 Auxiliary Activity family 9 (formerly GH61). Although weak endoglucanase activity has been demonstrated in several members of this family, they lack the clustered conserved catalytic acidic amino acids present in most glycoside hydrolases. Many members of this family lack measurable cellulase activity on their own, but enhance the activity of other cellulolytic enzymes. They are therefore unlikely to be true glycoside hydrolases. The substrate-binding surface of this family is a flat Ig-like fold. This family of enzymes were originally classified as glycoside hydrolases (GH61) and they have been reclassified as the Auxiliary Activity Family 9 (AA9) of CAZy. 208 matched cddid_all.tbl CDD pfam03444 pfam03444 281443 HrcA_DNA-bdg Winged helix-turn-helix transcription repressor, HrcA DNA-binding. This domain is always found with a pair of CBS domains pfam00571. 79 matched cddid_all.tbl CDD pfam03445 pfam03445 460919 DUF294 Putative nucleotidyltransferase DUF294. This domain is found associated with pfam00571. This region is uncharacterized, however it seems to be similar to pfam01909, conserving the DXD motif. This strongly suggests that members of this family are also nucleotidyltransferases (Bateman A pers. obs.). 138 matched cddid_all.tbl CDD pfam03446 pfam03446 427298 NAD_binding_2 NAD binding domain of 6-phosphogluconate dehydrogenase. The NAD binding domain of 6-phosphogluconate dehydrogenase adopts a Rossmann fold. 159 matched cddid_all.tbl CDD pfam03447 pfam03447 281446 NAD_binding_3 Homoserine dehydrogenase, NAD binding domain. This domain adopts a Rossmann NAD binding fold. The C-terminal domain of homoserine dehydrogenase contributes a single helix to this structural domain, which is not included in the Pfam model. 116 matched cddid_all.tbl CDD pfam03448 pfam03448 427299 MgtE_N MgtE intracellular N domain. This domain is found at the N-terminus of eubacterial magnesium transporters of the MgtE family pfam01769. This domain is an intracellular domain that has an alpha-helical structure. The crystal structure of the MgtE transporter shows two of 5 magnesium ions are in the interface between the N domain and the CBS domains. In the absence of magnesium there is a large shift between the N and CBS domains. 102 matched cddid_all.tbl CDD pfam03449 pfam03449 460920 GreA_GreB_N Transcription elongation factor, N-terminal. This domain adopts a long alpha-hairpin structure. 71 matched cddid_all.tbl CDD pfam03450 pfam03450 460921 CO_deh_flav_C CO dehydrogenase flavoprotein C-terminal domain. 102 matched cddid_all.tbl CDD pfam03451 pfam03451 460922 HELP HELP motif. The founding member of the EMAP protein family is the 75 kDa Echinoderm Microtubule-Associated Protein, so-named for its abundance in sea urchin, sand dollar and starfish eggs. The Hydrophobic EMAP-Like Protein (HELP) motif was identified initially in the human EMAP-Like Protein 2 (EML2) and subsequently in the entire EMAP Protein family. The HELP motif is approximately 60-70 amino acids in length and is conserved amongst metazoans. Although the HELP motif is hydrophobic, there is no evidence that EMAP-Like Proteins are membrane-associated. All members of the EMAP-Like Protein family, identified to-date, are constructed with an amino terminal HELP motif followed by a WD domain. In C. elegans, EMAP-Like Protein-1 (ELP-1) is required for touch sensation indicating that ELP-1 may play a role in mechanosensation. The localization of ELP-1 to microtubules and adhesion sites implies that ELP-1 may transmit forces between the body surface and the touch receptor neurons. 72 matched cddid_all.tbl CDD pfam03452 pfam03452 427303 Anp1 Anp1. The members of this family (Anp1, Van1 and Mnn9) are membrane proteins required for proper Golgi function. These proteins co-localize within the cis Golgi, and that they are physically associated in two distinct complexes. 265 matched cddid_all.tbl CDD pfam03453 pfam03453 460923 MoeA_N MoeA N-terminal region (domain I and II). This family contains two structural domains. One of these contains the conserved DGXA motif. This region is found in proteins involved in biosynthesis of molybdopterin cofactor however the exact molecular function of this region is uncertain. 147 matched cddid_all.tbl CDD pfam03454 pfam03454 460924 MoeA_C MoeA C-terminal region (domain IV). This domain is found in proteins involved in biosynthesis of molybdopterin cofactor however the exact molecular function of this domain is uncertain. The structure of this domain is known and forms an incomplete beta barrel. 72 matched cddid_all.tbl CDD pfam03455 pfam03455 460925 dDENN dDENN domain. This region is always found associated with pfam02141. It is predicted to form a globular domain. Although not statistically supported it has been suggested that this domain may be similar to members of the Rho/Rac/Cdc42 GEF family. This N-terminal region of DENN folds into a longin module, consisting of a central antiparallel beta-sheet layered between helix H1 and helices H2 and H3 (strands S1-S5). Rab35 interacts with dDENN via residues in helix 1 and in the loop S3-S4. 48 matched cddid_all.tbl CDD pfam03456 pfam03456 460926 uDENN uDENN domain. This region is always found associated with pfam02141. It is predicted to form an all beta domain. 59 matched cddid_all.tbl CDD pfam03457 pfam03457 427308 HA Helicase associated domain. This short domain is found in multiple copies in bacterial helicase proteins. The domain is predicted to contain 3 alpha helices. The function of this domain may be to bind nucleic acid. 63 matched cddid_all.tbl CDD pfam03458 pfam03458 460927 Gly_transporter Glycine transporter. This domain contains three transmembrane helices. Proteins containing this domain are important for glycine utilization, being identified as glycine transporters. Some members of the family are also important for alanine utilization. In these proteins this domain is found in pairs. An archaeal member of this family which contains this domain is a TRIC-type potassium channel. 74 matched cddid_all.tbl CDD pfam03459 pfam03459 427310 TOBE TOBE domain. The TOBE domain (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum and sulfate. Found in ABC transporters immediately after the ATPase domain. 60 matched cddid_all.tbl CDD pfam03460 pfam03460 377044 NIR_SIR_ferr Nitrite/Sulfite reductase ferredoxin-like half domain. Sulfite and Nitrite reductases are key to both biosynthetic assimilation of sulfur and nitrogen and dissimilation of oxidized anions for energy transduction. Two copies of this repeat are found in Nitrite and Sulfite reductases and form a single structural domain. 67 matched cddid_all.tbl CDD pfam03461 pfam03461 460928 TRCF TRCF domain. 95 matched cddid_all.tbl CDD pfam03462 pfam03462 460929 PCRF PCRF domain. This domain is found in peptide chain release factors. 192 matched cddid_all.tbl CDD pfam03463 pfam03463 460930 eRF1_1 eRF1 domain 1. The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification. 122 matched cddid_all.tbl CDD pfam03464 pfam03464 397502 eRF1_2 eRF1 domain 2. The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification. 133 matched cddid_all.tbl CDD pfam03465 pfam03465 397503 eRF1_3 eRF1 domain 3. The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown. Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification. 100 matched cddid_all.tbl CDD pfam03466 pfam03466 460931 LysR_substrate LysR substrate binding domain. The structure of this domain is known and is similar to the periplasmic binding proteins. This domain binds a variety of ligands that caries in size and structure, such as amino acids, sugar phosphates, organic acids, metal cations, flavonoids, C6-ring carboxylic acids, H2O2, HOCl, homocysteine, NADPH, ATP, sulphate, muropeptides, acetate, salicylate, citrate, phenol- and quinolone derivatives, acetylserines, fatty acid CoA, shikimate, chorismate, homocysteine, indole-3-acetic acid, Na(I), c-di-GMP, ppGpp and hydrogen peroxide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 205 matched cddid_all.tbl CDD pfam03467 pfam03467 460932 Smg4_UPF3 Smg-4/UPF3 family. This family contains proteins that are involved in nonsense mediated mRNA decay. A process that is triggered by premature stop codons in mRNA. The family includes Smg-4 and UPF3. 168 matched cddid_all.tbl CDD pfam03468 pfam03468 460933 XS XS domain. The XS (rice gene X and SGS3) domain is found in a family of plant proteins including gene X and SGS3. SGS3 is thought to be involved in post-transcriptional gene silencing (PTGS). This domain contains a conserved aspartate residue that may be functionally important. The XS domain has recently been predicted to possess an RRM-like RNA-binding domain by fold recognition. 113 matched cddid_all.tbl CDD pfam03469 pfam03469 460934 XH XH domain. The XH (rice gene X Homology) domain is found in a family of plant proteins including gene X. The molecular function of these proteins is unknown. However these proteins usually contain an XS domain that is also found in the PTGS protein SGS3. This domain contains a conserved glutamate residue that may be functionally important. 131 matched cddid_all.tbl CDD pfam03470 pfam03470 251981 zf-XS XS zinc finger domain. This domain is a putative nucleic acid binding zinc finger found in proteins that also contain an XS domain. 43 matched cddid_all.tbl CDD pfam03471 pfam03471 460935 CorC_HlyC Transporter associated domain. This small domain is found in a family of proteins with the pfam01595 domain and two CBS domains with this domain found at the C-terminus of the proteins, the domain is also found at the C terminus of some Na+/H+ antiporters. This domain is also found in CorC that is involved in Magnesium and cobalt efflux. The function of this domain is uncertain but might be involved in modulating transport of ion substrates. 81 matched cddid_all.tbl CDD pfam03472 pfam03472 427319 Autoind_bind Autoinducer binding domain. This domain is found a a large family of transcriptional regulators. This domain specifically binds to autoinducer molecules (N-Acyl homoserine lactones, chlorolactone and rosmarinic acid) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 148 matched cddid_all.tbl CDD pfam03473 pfam03473 460936 MOSC MOSC domain. The MOSC (MOCO sulfurase C-terminal) domain is a superfamily of beta-strand-rich domains identified in the molybdenum cofactor sulfurase and several other proteins from both prokaryotes and eukaryotes. These MOSC domains contain an absolutely conserved cysteine and occur either as stand-alone forms such as Swiss:P32157, or fused to other domains such as NifS-like catalytic domain in Molybdenum cofactor sulfurase. The MOSC domain is predicted to be a sulfur-carrier domain that receives sulfur abstracted by the pyridoxal phosphate-dependent NifS-like enzymes, on its conserved cysteine, and delivers it for the formation of diverse sulfur-metal clusters. 116 matched cddid_all.tbl CDD pfam03474 pfam03474 460937 DMA DMRTA motif. This region is found to the C-terminus of the pfam00751. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown. 36 matched cddid_all.tbl CDD pfam03475 pfam03475 460938 3-alpha 3-alpha domain. This small triple helical domain has been predicted to assume a topology similar to helix-turn-helix domains. These domains are found at the C-terminus of proteins related to Swiss:P32157. 44 matched cddid_all.tbl CDD pfam03476 pfam03476 281474 MOSC_N MOSC N-terminal beta barrel domain. This domain is found to the N-terminus of pfam03473. The function of this domain is unknown, however it is predicted to adopt a beta barrel fold. 118 matched cddid_all.tbl CDD pfam03477 pfam03477 397513 ATP-cone ATP cone domain. 86 matched cddid_all.tbl CDD pfam03478 pfam03478 460939 DUF295 Protein of unknown function (DUF295). This domain is found in plant proteins of unknown function. It can be found in association with F-box domain pfam00646. 57 matched cddid_all.tbl CDD pfam03479 pfam03479 460940 PCC Plants and Prokaryotes Conserved (PCC) domain. This is a Plants and Prokaryotes Conserved (PPC) domain found in proteins that contain AT-hook motifs pfam02178 which strongly suggests a DNA-binding function for the proteins as a whole. Proteins with PPC domains are found in Bacteria, Archaea and the plant kingdom.The PPC domain has a single alpha-helix packed against an antiparallel beta-sheet, which is formed by five beta-strands. There are three highly conserved histidine residues, eg at 117, 119 and 133 in Swiss:Q46QL5 which appear to form a zinc-binding site, and the domain has been observed to form homotrimers. The domain co-occurs with a thioredoxin-like domain in uncharacterized cyanobacterial proteins. 115 matched cddid_all.tbl CDD pfam03480 pfam03480 427325 DctP Bacterial extracellular solute-binding protein, family 7. This family of proteins is involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes Swiss:P37735, a C4-dicarboxylate-binding protein and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component. 286 matched cddid_all.tbl CDD pfam03481 pfam03481 460941 Sua5_C Threonylcarbamoyl-AMP synthase, C-terminal domain. This domain can be found in the C terminus of threonylcarbamoyl-AMP synthases, including Sua5 from Saccharomyces cerevisiae and YwlC from Bacillus subtilis. Threonylcarbamoyl-AMP synthase is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t6A37) in tRNAs that read codons beginning with adenine. This domain adopts the Rossmann fold and may be involved in GTP and/or tRNA binding based on structural similarity with both GTP and tRNA binding proteins. 134 matched cddid_all.tbl CDD pfam03482 pfam03482 281480 SIC sic protein repeat. Serotype M1 group A Streptococcus strains cause epidemic waves of human infections. This 30 aa repeat occurs in the sic protein, an extracellular protein (streptococcal inhibitor of complement) that inhibits human complement. 30 matched cddid_all.tbl CDD pfam03483 pfam03483 427327 B3_4 B3/4 domain. This domain is found in tRNA synthetase beta subunits as well as in some non tRNA synthetase proteins. 174 matched cddid_all.tbl CDD pfam03484 pfam03484 460942 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits. 67 matched cddid_all.tbl CDD pfam03485 pfam03485 460943 Arg_tRNA_synt_N Arginyl tRNA synthetase N terminal domain. This domain is found at the amino terminus of Arginyl tRNA synthetase, also called additional domain 1 (Add-1). It is about 140 residues long and it has been suggested that this domain will be involved in tRNA recognition. 83 matched cddid_all.tbl CDD pfam03486 pfam03486 427330 HI0933_like HI0933-like protein. 406 matched cddid_all.tbl CDD pfam03487 pfam03487 460944 IL13 Interleukin-13. 110 matched cddid_all.tbl CDD pfam03488 pfam03488 112313 Ins_beta Nematode insulin-related peptide beta type. 48 matched cddid_all.tbl CDD pfam03489 pfam03489 460945 SapB_2 Saposin-like type B, region 2. Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. It is one of the most studied members of the saposin protein family and it is involved in the hydrolysis of glycolipids and glycerolipids. SapB is unique in the saposin family in that it facilitates degradation by interacting with the substrate, not the enzymes. 34 matched cddid_all.tbl CDD pfam03491 pfam03491 397524 5HT_transport_N Serotonin (5-HT) neurotransmitter transporter, N-terminus. This short domain lies at the very N-terminus of many serotonin and other transporter proteins, eg SNF, pfam00209. 41 matched cddid_all.tbl CDD pfam03492 pfam03492 460946 Methyltransf_7 SAM dependent carboxyl methyltransferase. This family of plant methyltransferases contains enzymes that act on a variety of substrates including salicylic acid, jasmonic acid and 7-Methylxanthine. Caffeine is synthesized through sequential three-step methylation of xanthine derivatives at positions 7-N, 3-N, and 1-N. The protein 7-methylxanthine methyltransferase (designated as CaMXMT) catalyzes the second step to produce theobromine. 326 matched cddid_all.tbl CDD pfam03493 pfam03493 460947 BK_channel_a Calcium-activated BK potassium channel alpha subunit. 90 matched cddid_all.tbl CDD pfam03494 pfam03494 427335 Beta-APP Beta-amyloid peptide (beta-APP). 39 matched cddid_all.tbl CDD pfam03495 pfam03495 367526 Binary_toxB Clostridial binary toxin B/anthrax toxin PA Ca-binding domain. This domain is a calcium binding domain in the anthrax toxin protective antigen. 78 matched cddid_all.tbl CDD pfam03496 pfam03496 427336 ADPrib_exo_Tox ADP-ribosyltransferase exoenzyme. This is a family of bacterial and viral bi-glutamic acid ADP-ribosyltransferases, where, in Swiss:Q93Q17, E403 is the catalytic residue and E401 contributes to the transfer of ADP-ribose to the target protein. In clostridial species it is actin that is being ADP-ribosylated; this result is lethal and dermonecrotic in infected mammals. 199 matched cddid_all.tbl CDD pfam03497 pfam03497 397528 Anthrax_toxA Anthrax toxin LF subunit. 174 matched cddid_all.tbl CDD pfam03498 pfam03498 397529 CDtoxinA Cytolethal distending toxin A/C domain. 149 matched cddid_all.tbl CDD pfam03500 pfam03500 281496 Cellsynth_D Cellulose synthase subunit D. 144 matched cddid_all.tbl CDD pfam03501 pfam03501 427337 S10_plectin Plectin/S10 domain. This presumed domain is found at the N-terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding. 92 matched cddid_all.tbl CDD pfam03502 pfam03502 427338 Channel_Tsx Nucleoside-specific channel-forming protein, Tsx. 238 matched cddid_all.tbl CDD pfam03503 pfam03503 460948 Chlam_OMP3 Chlamydia cysteine-rich outer membrane protein 3. 54 matched cddid_all.tbl CDD pfam03504 pfam03504 281500 Chlam_OMP6 Chlamydia cysteine-rich outer membrane protein 6. 91 matched cddid_all.tbl CDD pfam03505 pfam03505 308877 Clenterotox Clostridium enterotoxin. 197 matched cddid_all.tbl CDD pfam03506 pfam03506 460949 Flu_C_NS1 Influenza C non-structural protein (NS1). The influenza C virus genome consists of seven single-stranded RNA segments. The shortest RNA segment encodes a 286 amino acid non-structural protein NS1. This protein contains 6 conserved cysteines that may be functionally important, perhaps binding to a metal ion. 162 matched cddid_all.tbl CDD pfam03507 pfam03507 397531 CagA CagA exotoxin phosphopeptide substrate mimic region. Helicobacter pylori is the most common world-wide infection and plays an important role in pathogenesis of peptic ulcers. The CagA (cytotoxin-associated gene A) protein is a cell-surface antigen which may play a role in determining the relative virulence of the viral strains. This entry represents the phosphopeptide substrate mimic region of CagA. 39 matched cddid_all.tbl CDD pfam03508 pfam03508 460950 Connexin43 Gap junction alpha-1 protein (Cx43). 79 matched cddid_all.tbl CDD pfam03509 pfam03509 460951 Connexin50 Gap junction alpha-8 protein (Cx50). 65 matched cddid_all.tbl CDD pfam03510 pfam03510 281505 Peptidase_C24 2C endopeptidase (C24) cysteine protease family. 105 matched cddid_all.tbl CDD pfam03511 pfam03511 460952 Fanconi_A Fanconi anaemia group A protein. 63 matched cddid_all.tbl CDD pfam03512 pfam03512 397535 Glyco_hydro_52 Glycosyl hydrolase family 52. 414 matched cddid_all.tbl CDD pfam03513 pfam03513 427342 Cloacin_immun Cloacin immunity protein. 80 matched cddid_all.tbl CDD pfam03514 pfam03514 397536 GRAS GRAS domain family. Proteins in the GRAS (GAI, RGA, SCR) family are known as major players in gibberellin (GA) signaling, which regulates various aspects of plant growth and development. Mutation of the SCARECROW (SCR) gene results in a radial pattern defect, loss of a ground tissue layer, in the root. The PAT1 protein is involved in phytochrome A signal transduction. A sequence, structure and evolutionary analysis showed that the GRAS family emerged in bacteria and belongs to the Rossmann-fold, AdoMET (SAM)-dependent methyltransferase superfamily. All bacterial, and a subset of plant GRAS proteins, are predicted to be active and function as small-molecule methylases. Several plant GRAS proteins lack one or more AdoMet (SAM)-binding residues while preserving their substrate-binding residues. Although GRAS proteins are implicated to function as transcriptional factors, the above analysis suggests that they instead might either modify or bind small molecules. 374 matched cddid_all.tbl CDD pfam03515 pfam03515 367536 Cloacin Colicin-like bacteriocin tRNase domain. The C-terminal region of colicin-like bacteriocins is either a pore-forming or an endonuclease-like domain. Cloacin and Pyocins have similar structures and activities to the colicins from E coli and the klebicins from Klebsiella spp. Colicins E5 and D cleave the anticodon loops of distinct tRNAs of Escherichia coli both in vivo and in vitro. The full-length molecule has an N-terminal translocation domain and a middle, double alpha-helical region which is receptor-binding. 273 matched cddid_all.tbl CDD pfam03516 pfam03516 460953 Filaggrin Filaggrin. 56 matched cddid_all.tbl CDD pfam03517 pfam03517 427344 Voldacs Regulator of volume decrease after cellular swelling. ICln is a ubiquitously expressed multi-functional protein that plays a critical role in regulating volume decrease in cells after cellular swelling. In plants, ICln induces Cl- currents, thus regulating Cl- homoeostasis in eukaryotes. Structurally, the fold resembles a pleckstrin homology fold, on of whose roles is to recruit and tether their host protein to the cell membrane; and although the surface charges of the ICln fold are not equivalent to those of the PH domain, ICln can be phosphorylated in vitro and the PH-nature of the domain may be the part involving it in the transposition from cytosol to cell membrane during cytotonic swelling. 139 matched cddid_all.tbl CDD pfam03519 pfam03519 427345 Invas_SpaK Invasion protein B family. 78 matched cddid_all.tbl CDD pfam03520 pfam03520 460954 KCNQ_channel KCNQ voltage-gated potassium channel. This family matches to the C-terminal tail of KCNQ type potassium channels. 190 matched cddid_all.tbl CDD pfam03521 pfam03521 397541 Kv2channel Kv2 voltage-gated K+ channel. 288 matched cddid_all.tbl CDD pfam03522 pfam03522 460955 SLC12 Solute carrier family 12. 414 matched cddid_all.tbl CDD pfam03523 pfam03523 460956 Macscav_rec Macrophage scavenger receptor. 49 matched cddid_all.tbl CDD pfam03524 pfam03524 427348 CagX Conjugal transfer protein. This family includes type IV secretion system CagX conjugation protein. Other members of this family are involved in conjugal transfer to plant cells of T-DNA. 216 matched cddid_all.tbl CDD pfam03525 pfam03525 460957 Meiotic_rec114 Meiotic recombination protein Rec7 N-terminal domain. This entry represents the N-terminal domain of the S. pombe Rec7 protein as predicted by AlphaFold. This domain adopts a PH-like domain fold. 135 matched cddid_all.tbl CDD pfam03526 pfam03526 112349 Microcin Colicin E1 (microcin) immunity protein. 55 matched cddid_all.tbl CDD pfam03527 pfam03527 427349 RHS RHS protein. 38 matched cddid_all.tbl CDD pfam03528 pfam03528 367545 Rabaptin Rabaptin. 486 matched cddid_all.tbl CDD pfam03529 pfam03529 427350 TF_Otx Otx1 transcription factor. 91 matched cddid_all.tbl CDD pfam03530 pfam03530 460958 SK_channel Calcium-activated SK potassium channel. 111 matched cddid_all.tbl CDD pfam03531 pfam03531 460959 SSrecog Structure-specific recognition protein (SSRP1). SSRP1 has been implicated in transcriptional initiation and elongation and in DNA replication and repair. This domain belongs to the Pleckstrin homology fold superfamily. 69 matched cddid_all.tbl CDD pfam03532 pfam03532 460960 OMS28_porin OMS28 porin. 253 matched cddid_all.tbl CDD pfam03533 pfam03533 460961 SPO11_like SPO11 homolog. 43 matched cddid_all.tbl CDD pfam03534 pfam03534 427354 SpvB Salmonella virulence plasmid 65kDa B protein. 286 matched cddid_all.tbl CDD pfam03535 pfam03535 460962 Paxillin Paxillin family. Paxillin is a multi-domain protein that localizes in cultured cells primarily to sites of cell adhesion to the extracellular matrix (ECM) called focal adhesions. The family here represents the N-terminal regions with the proline-rich part as well as the Paxillin part. Focal adhesions form a structural link between the ECM and the actin cytoskeleton and are also important sites of signal transduction; their components propagate signals arising from the activation of integrins following their engagement with ECM proteins, such as fibronectin, collagen and laminin. Importantly, focal adhesion proteins including paxillin also serve as a point of convergence for signals resulting from stimulation of various classes of growth factor receptor. 198 matched cddid_all.tbl CDD pfam03536 pfam03536 427356 VRP3 Salmonella virulence-associated 28kDa protein. 218 matched cddid_all.tbl CDD pfam03537 pfam03537 460963 Glyco_hydro_114 Glycoside-hydrolase family GH114. This family is recognized as a glycosyl-hydrolase family, number 114. It is endo-alpha-1,4-polygalactosaminidase, a rare enzyme. It is proposed to be TIM-barrel, the most common structure amongst the catalytic domains of glycosyl-hydrolases. 218 matched cddid_all.tbl CDD pfam03538 pfam03538 427358 VRP1 Salmonella virulence plasmid 28.1kDa A protein. 318 matched cddid_all.tbl CDD pfam03539 pfam03539 112362 Spuma_A9PTase Spumavirus aspartic protease (A9). 163 matched cddid_all.tbl CDD pfam03540 pfam03540 460964 TFIID_30kDa Transcription initiation factor TFIID 23-30kDa subunit. 49 matched cddid_all.tbl CDD pfam03542 pfam03542 460965 Tuberin Tuberin. Tuberous sclerosis complex (TSC) is an autosomal dominant disorder and is characterized by the presence of hamartomas in many organs, such as brain, skin, heart, lung, and kidney. It is caused by mutation either TSC1 or TSC2 tumour suppressor gene. The TSC2 gene codes for tuberin and interacts with hamartin pfam04388, containing two coiled-coil regions, which have been shown to mediate binding to tuberin. These two proteins function within the same pathway(s) regulating cell cycle, cell growth, adhesion, and vesicular trafficking. 349 matched cddid_all.tbl CDD pfam03543 pfam03543 460966 Peptidase_C58 Yersinia/Haemophilus virulence surface antigen. 203 matched cddid_all.tbl CDD pfam03544 pfam03544 427361 TonB_C Gram-negative bacterial TonB protein C-terminal. The TonB_C domain is the well-characterized C-terminal region of the TonB receptor molecule. This protein is bound to an inner membrane-bound protein ExbB via a globular domain and has a flexible middle region that is likely to help in positioning the C-terminal domain into the iron-transporter barrel in the outer membrane. TonB_C interacts with the N-terminal TonB box of the outer membrane transporter that binds the Fe3+-siderophore complex. The barrel of the transporter, consisting of 22 beta-sheets and an inside plug, binds the iron complex in the barrel entrance. 79 matched cddid_all.tbl CDD pfam03545 pfam03545 397557 YopE Yersinia virulence determinant (YopE). 70 matched cddid_all.tbl CDD pfam03546 pfam03546 460967 Treacle Treacher Collins syndrome protein Treacle. 531 matched cddid_all.tbl CDD pfam03547 pfam03547 308904 Mem_trans Membrane transport protein. This family includes auxin efflux carrier proteins and other transporter proteins from all domains of life. 341 matched cddid_all.tbl CDD pfam03548 pfam03548 427363 LolA Outer membrane lipoprotein carrier protein LolA. 165 matched cddid_all.tbl CDD pfam03549 pfam03549 460968 Tir_receptor_M Translocated intimin receptor (Tir) intimin-binding domain. Intimin and its translocated intimin receptor (Tir) are bacterial proteins that mediate adhesion between mammalian cells and attaching and effacing (A/E) pathogens. A unique and essential feature of A/E bacterial pathogens is the formation of actin-rich pedestals beneath the intimately adherent bacteria and localized destruction of the intestinal brush border. The bacterial outer membrane adhesin, intimin, is necessary for the production of the A/E lesion and diarrhoea. The A/E bacteria translocate their own receptor for intimin, Tir, into the membrane of mammalian cells using the type III secretion system. The translocated Tir triggers additional host signalling events and actin nucleation, which are essential for lesion formation. This family represents the Tir intimin-binding domain (Tir IBD) which is needed to bind intimin and support the predicted topology for Tir, with both N- and C-terminal regions in the mammalian cell cytosol. 65 matched cddid_all.tbl CDD pfam03550 pfam03550 460969 LolB Outer membrane lipoprotein LolB. 149 matched cddid_all.tbl CDD pfam03551 pfam03551 397561 PadR Transcriptional regulator PadR-like family. Members of this family are transcriptional regulators that appear to be related to the pfam01047 family. This family includes PadR, a protein that is involved in negative regulation of phenolic acid metabolism. 74 matched cddid_all.tbl CDD pfam03552 pfam03552 460970 Cellulose_synt Cellulose synthase. Cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues, is the major component of wood and thus paper, and is synthesized by plants, most algae, some bacteria and fungi, and even some animals. The genes that synthesize cellulose in higher plants differ greatly from the well-characterized genes found in Acetobacter and Agrobacterium sp. More correctly designated as 'cellulose synthase catalytic subunits', plant cellulose synthase (CesA) proteins are integral membrane proteins, approximately 1,000 amino acids in length. There are a number of highly conserved residues, including several motifs shown to be necessary for processive glycosyltransferase activity. 715 matched cddid_all.tbl CDD pfam03553 pfam03553 281542 Na_H_antiporter Na+/H+ antiporter family. This family includes integral membrane proteins, some of which are NA+/H+ antiporters. 303 matched cddid_all.tbl CDD pfam03554 pfam03554 281543 Herpes_UL73 UL73 viral envelope glycoprotein. This family groups together the viral proteins BLRF1, U46, 53, and UL73. The UL73-like envelope glycoproteins, which associates in a high molecular mass complex with its counterpart, gM, induce neutralising antibody responses in the host. These glycoprotein are highly polymorphic, particularly in the N-terminal region. 74 matched cddid_all.tbl CDD pfam03555 pfam03555 281544 Flu_C_NS2 Influenza C non-structural protein (NS2). The influenza C virus genome consists of seven single-stranded RNA segments. The shortest RNA segment encodes a 286 amino acid non-structural protein NS1 pfam03506 as well as the NS2 protein. The NS2 protein is only about 60 amino acids in length and of unknown function. 57 matched cddid_all.tbl CDD pfam03556 pfam03556 460971 Cullin_binding Cullin binding. This domain binds to cullins and to Rbx-1, components of an E3 ubiquitin ligase complex for neddylation. Neddylation is the process by which the C-terminal glycine of the ubiquitin-like protein Nedd8 is covalently linked to lysine residues in a protein through an isopeptide bond. The structure of this domain is composed entirely of alpha helices. 117 matched cddid_all.tbl CDD pfam03557 pfam03557 281546 Bunya_G1 Bunyavirus glycoprotein G1. Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. This family contains the G1 glycoprotein which is the viral attachment protein. 879 matched cddid_all.tbl CDD pfam03558 pfam03558 367561 TBSV_P22 TBSV core protein P21/P22. This protein is required for cell-to-cell movement in plants. Furthermore, the membrane-associated protein is dispensable for both replication and transcription. 187 matched cddid_all.tbl CDD pfam03559 pfam03559 397563 Hexose_dehydrat NDP-hexose 2,3-dehydratase. This family includes a range of proteins from antibiotic production pathways. The family includes gra-ORF27 product that probably functions at an early step, most likely as a dTDP-4-keto-6- deoxyglucose-2,3-dehydratase. Its homologs include dnmT from the daunorubicin biosynthetic gene cluster in S. peucetius, a similar gene from the daunomycin biosynthetic cluster in Streptomyces sp. strain C5 Swiss:Q53880, eryBVI from the erythromycin cluster in S. erythraea and snoH from the nogalamycin cluster in S. nogalater. The proteins in this family are composed of two copies of a 200 amino acid long unit that may be a structural domain. 203 matched cddid_all.tbl CDD pfam03561 pfam03561 460972 Allantoicase Allantoicase repeat. This family is found in pairs in Allantoicases, forming the majority of the protein. These proteins allow the use of purines as secondary nitrogen sources in nitrogen-limiting conditions through the reaction: allantoate + H(2)0 = (-)-ureidoglycolate + urea. 150 matched cddid_all.tbl CDD pfam03562 pfam03562 460973 MltA MltA specific insert domain. This beta barrel domain is found inserted in the MltA a murein degrading transglycosylase enzyme. This domain may be involved in peptidoglycan binding. 231 matched cddid_all.tbl CDD pfam03563 pfam03563 397566 Bunya_G2 Bunyavirus glycoprotein G2. Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. This family contains the G2 glycoprotein which interacts with the pfam03557 G1 glycoprotein. 281 matched cddid_all.tbl CDD pfam03564 pfam03564 281552 DUF1759 Protein of unknown function (DUF1759). This is a family of proteins of unknown function. Most of the members are gag-polyproteins. 148 matched cddid_all.tbl CDD pfam03566 pfam03566 397567 Peptidase_A21 Peptidase family A21. 574 matched cddid_all.tbl CDD pfam03567 pfam03567 427369 Sulfotransfer_2 Sulfotransferase family. This family includes a variety of sulfotransferase enzymes. Chondroitin 6-sulfotransferase catalyzes the transfer of sulfate to position 6 of the N-acetylgalactosamine residue of chondroitin. This family also includes Heparan sulfate 2-O-sulfotransferase (HS2ST) and Heparan sulfate 6-sulfotransferase (HS6ST). Heparan sulfate (HS) is a co-receptor for a number of growth factors, morphogens, and adhesion proteins. HS biosynthetic modifications may determine the strength and outcome of HS-ligand interactions. Mice that lack HS2ST undergo developmental failure only after midgestation,the most dramatic effect being the complete failure of kidney development. Heparan sulphate 6- O -sulfotransferase (HS6ST) catalyzes the transfer of sulphate from adenosine 3'-phosphate, 5'-phosphosulphate to the 6th position of the N -sulphoglucosamine residue in heparan sulphate. 238 matched cddid_all.tbl CDD pfam03568 pfam03568 460974 Peptidase_C50 Peptidase family C50. 389 matched cddid_all.tbl CDD pfam03569 pfam03569 460975 Peptidase_C8 Peptidase family C8. 208 matched cddid_all.tbl CDD pfam03571 pfam03571 460976 Peptidase_M49 Peptidase family M49. 550 matched cddid_all.tbl CDD pfam03572 pfam03572 460977 Peptidase_S41 Peptidase family S41. 165 matched cddid_all.tbl CDD pfam03573 pfam03573 460978 OprD outer membrane porin, OprD family. This family includes outer membrane proteins related to OprD. OprD has been described as a serine type peptidase. However the proposed catalytic residues are not conserved suggesting that many of these proteins are not peptidases. 393 matched cddid_all.tbl CDD pfam03574 pfam03574 427373 Peptidase_S48 Peptidase family S48. 149 matched cddid_all.tbl CDD pfam03575 pfam03575 397574 Peptidase_S51 Peptidase family S51. 206 matched cddid_all.tbl CDD pfam03576 pfam03576 427374 Peptidase_S58 Peptidase family S58. 309 matched cddid_all.tbl CDD pfam03577 pfam03577 427375 Peptidase_C69 Peptidase family C69. 402 matched cddid_all.tbl CDD pfam03578 pfam03578 460979 HGWP HGWP repeat. This short (30 amino acids) repeat is found in a number of plant proteins. It contains a conserved HGWP motif, hence its name. The function of these proteins is unknown. 28 matched cddid_all.tbl CDD pfam03579 pfam03579 281565 SHP Small hydrophobic protein. The small hydrophobic integral membrane protein, SH (previously designated 1A) is found to have a variety of glycosylated forms. This protein is a component of the mature virion. 64 matched cddid_all.tbl CDD pfam03580 pfam03580 281566 Herpes_UL14 Herpesvirus UL14-like protein. This is a family of Herpesvirus proteins including UL14. UL14 protein is a minor component of the virion tegument and is expressed late in infection. UL14 protein can influence the intracellular localization patterns of a number of proteins belonging to the capsid or the DNA encapsidation machinery. 146 matched cddid_all.tbl CDD pfam03581 pfam03581 427377 Herpes_UL33 Herpesvirus UL33-like protein. This is a family of Herpesvirus proteins including UL33,UL51. The proteins in this family are involved in packaging viral DNA. 72 matched cddid_all.tbl CDD pfam03583 pfam03583 367570 LIP Secretory lipase. These lipases are expressed and secreted during the infection cycle of these pathogens. In particular, C. albicans has a large number of different lipases, possibly reflecting broad lipolytic activity, which may contribute to the persistence and virulence of C. albicans in human tissue. 286 matched cddid_all.tbl CDD pfam03584 pfam03584 367571 Herpes_ICP4_N Herpesvirus ICP4-like protein N-terminal region. The immediate-early protein ICP4 (infected-cell polypeptide 4) is required for efficient transcription of early and late viral genes and is thus essential for productive infection. ICP4 is a large phosphoprotein that binds DNA in a sequence specific manner as a homodimer. ICP4 represses transcription from LAT, ICP4 and ORF-P that have high-affinity a ICP4 binding site that spans the transcription initiation site. ICP4 proteins have two highly conserved regions, this family contains the N-terminal region that contains sites for DNA binding and homodimerization. 163 matched cddid_all.tbl CDD pfam03585 pfam03585 281570 Herpes_ICP4_C Herpesvirus ICP4-like protein C-terminal region. The immediate-early protein ICP4 (infected-cell polypeptide 4) is required for efficient transcription of early and late viral genes and is thus essential for productive infection. ICP4 is a large phosphoprotein that binds DNA in a sequence specific manner as a homodimer. ICP4 represses transcription from LAT, ICP4 and ORF-P that have high-affinity a ICP4 binding site that spans the transcription initiation site. ICP4 proteins have two highly conserved regions, this family contains the C-terminal region that probably acts as an enhancer for the N-terminal region. 444 matched cddid_all.tbl CDD pfam03586 pfam03586 427378 Herpes_UL36 Herpesvirus UL36 tegument protein. The UL36 open reading frame (ORF) encodes the largest herpes simplex virus type 1 (HSV-1) protein, a 270-kDa polypeptide designated VP1/2, which is also a component of the virion tegument. A null mutation in the UL36 gene of herpes simplex virus type 1 results in accumulation of unenveloped DNA-filled capsids in the cytoplasm of infected cells. This family only covers a small central part of this large protein. 251 matched cddid_all.tbl CDD pfam03587 pfam03587 460980 EMG1 EMG1/NEP1 methyltransferase. Members of this family are essential for 40S ribosomal biogenesis. The structure of EMG1 has revealed that it is a novel member of the superfamily of alpha/beta knot fold methyltransferases. 205 matched cddid_all.tbl CDD pfam03588 pfam03588 460981 Leu_Phe_trans Leucyl/phenylalanyl-tRNA protein transferase. 171 matched cddid_all.tbl CDD pfam03589 pfam03589 427381 Antiterm Antitermination protein. 85 matched cddid_all.tbl CDD pfam03590 pfam03590 427382 AsnA Aspartate-ammonia ligase. 228 matched cddid_all.tbl CDD pfam03591 pfam03591 460982 AzlC AzlC protein. 135 matched cddid_all.tbl CDD pfam03592 pfam03592 427384 Terminase_2 Terminase small subunit. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site. 143 matched cddid_all.tbl CDD pfam03594 pfam03594 427385 BenE Benzoate membrane transport protein. 378 matched cddid_all.tbl CDD pfam03595 pfam03595 460983 SLAC1 Voltage-dependent anion channel. This family of transporters has ten alpha helical transmembrane segments. The structure of a bacterial homolog of SLAC1 shows it to have a trimeric arrangement. The pore is composed of five helices with a conserved Phe residue involved in gating. One homolog, Mae1 from the yeast Schizosaccharomyces pombe, functions as a malate uptake transporter; another, Ssu1 from Saccharomyces cerevisiae and other fungi including Aspergillus fumigatus, is characterized as a sulfite efflux pump; and TehA from Escherichia coli is identified as a tellurite resistance protein by virtue of its association in the tehA/tehB operon. In plants, this family is found in the stomatal guard cells functioning as an anion-transporting pore. Many homologs are incorrectly annotated as tellurite resistance or dicarboxylate transporter (TDT) proteins. 321 matched cddid_all.tbl CDD pfam03596 pfam03596 281580 Cad Cadmium resistance transporter. 192 matched cddid_all.tbl CDD pfam03597 pfam03597 460984 FixS Cytochrome oxidase maturation protein cbb3-type. 44 matched cddid_all.tbl CDD pfam03598 pfam03598 427388 CdhC CO dehydrogenase/acetyl-CoA synthase complex beta subunit. 155 matched cddid_all.tbl CDD pfam03599 pfam03599 397588 CdhD CO dehydrogenase/acetyl-CoA synthase delta subunit. 384 matched cddid_all.tbl CDD pfam03600 pfam03600 460985 CitMHS Citrate transporter. 342 matched cddid_all.tbl CDD pfam03601 pfam03601 427390 Cons_hypoth698 Conserved hypothetical protein 698. 304 matched cddid_all.tbl CDD pfam03602 pfam03602 427391 Cons_hypoth95 Conserved hypothetical protein 95. 179 matched cddid_all.tbl CDD pfam03603 pfam03603 427392 DNA_III_psi DNA polymerase III psi subunit. 126 matched cddid_all.tbl CDD pfam03604 pfam03604 427393 DNA_RNApol_7kD DNA directed RNA polymerase, 7 kDa subunit. 32 matched cddid_all.tbl CDD pfam03605 pfam03605 427394 DcuA_DcuB Anaerobic c4-dicarboxylate membrane transporter. 365 matched cddid_all.tbl CDD pfam03606 pfam03606 427395 DcuC C4-dicarboxylate anaerobic carrier. 454 matched cddid_all.tbl CDD pfam03607 pfam03607 460986 DCX Doublecortin. 60 matched cddid_all.tbl CDD pfam03608 pfam03608 427397 EII-GUT PTS system enzyme II sorbitol-specific factor. 162 matched cddid_all.tbl CDD pfam03609 pfam03609 460987 EII-Sor PTS system sorbose-specific iic component. 233 matched cddid_all.tbl CDD pfam03610 pfam03610 427399 EIIA-man PTS system fructose IIA component. 113 matched cddid_all.tbl CDD pfam03611 pfam03611 460988 EIIC-GAT PTS system sugar-specific permease component. This family includes bacterial transmembrane proteins with a putative sugar-specific permease function, including and analogous to the IIC component of the PTS system. It has been suggested that this permease may form part of an L-ascorbate utilization pathway, with proposed specificity for 3-keto-L-gulonate (formed by hydrolysis of L-ascorbate). This family includes the IIC component of the galactitol specific GAT family PTS system. 397 matched cddid_all.tbl CDD pfam03612 pfam03612 427401 EIIBC-GUT_N Sorbitol phosphotransferase enzyme II N-terminus. 184 matched cddid_all.tbl CDD pfam03613 pfam03613 460989 EIID-AGA PTS system mannose/fructose/sorbose family IID component. 263 matched cddid_all.tbl CDD pfam03614 pfam03614 281597 Flag1_repress Repressor of phase-1 flagellin. 170 matched cddid_all.tbl CDD pfam03615 pfam03615 397602 GCM GCM motif protein. 140 matched cddid_all.tbl CDD pfam03616 pfam03616 308938 Glt_symporter Sodium/glutamate symporter. 368 matched cddid_all.tbl CDD pfam03617 pfam03617 281600 IBV_3A IBV 3A protein. The gene product of gene 3 from Avian infectious bronchitis virus. Currently, the function of this protein remains unknown. 57 matched cddid_all.tbl CDD pfam03618 pfam03618 460990 Kinase-PPPase Kinase/pyrophosphorylase. This family of regulatory proteins has ADP-dependent kinase and inorganic phosphate-dependent pyrophosphorylase activity. 256 matched cddid_all.tbl CDD pfam03619 pfam03619 460991 Solute_trans_a Organic solute transporter Ostalpha. This family is a transmembrane organic solute transport protein. In vertebrates these proteins form a complex with Ostbeta, and function as bile transporters. In plants they may transport brassinosteroid-like compounds and act as regulators of cell death. 251 matched cddid_all.tbl CDD pfam03620 pfam03620 281603 IBV_3C IBV 3C protein. Product of ORF 3C from Avian infectious bronchitis virus (IBV). Currently, the function of this protein remains unknown. 92 matched cddid_all.tbl CDD pfam03621 pfam03621 427405 MbtH MbtH-like protein. This domain is found in the MbtH protein as well as at the N terminus of the antibiotic synthesis protein NIKP1. MbtH and its homologs were first noted in gene clusters involved in non-ribosomal peptides and other secondary metabolites by Quadri et al. This domain is about 70 amino acids long and contains 3 fully conserved tryptophan residues. The structure of the PA2412 protein shows it adopts a beta-beta-beta-alpha-alpha topology with the short C-terminal helix forming the tip of an overall arrowhead shape. MbtH proteins have been shown to be required for the synthesis of antibiotics, siderophores and glycopeptidolipids. 53 matched cddid_all.tbl CDD pfam03622 pfam03622 281605 IBV_3B IBV 3B protein. Product of ORF 3B from Avian infectious bronchitis virus (IBV). Currently, the function of this protein remains unknown. 64 matched cddid_all.tbl CDD pfam03623 pfam03623 460992 Focal_AT Focal adhesion targeting region. Focal adhesion kinase (FAK) is a tyrosine kinase found in focal adhesions, intracellular signaling complexes that are formed following engagement of the extracellular matrix by integrins. The C-terminal 'focal adhesion targeting' (FAT) region is necessary and sufficient for localising FAK to focal adhesions. The crystal structure of FAT shows it forms a four-helix bundle that resembles those found in two other proteins involved in cell adhesion, alpha-catenin and vinculin. The binding of FAT to the focal adhesion protein, paxillin, requires the integrity of the helical bundle, whereas binding to another focal adhesion protein, talin, does not. 130 matched cddid_all.tbl CDD pfam03625 pfam03625 460993 DUF302 Domain of unknown function DUF302. Domain is found in an undescribed set of proteins. Normally occurs uniquely within a sequence, but is found as a tandem repeat. Shows interesting phylogenetic distribution with majority of examples in bacteria and archaea, but it is also found in some fungal proteins. The hypothetical protein TT1751 from Thermus thermophilus has a beta-alpha-beta(4)-alpha structural fold. 63 matched cddid_all.tbl CDD pfam03626 pfam03626 427408 COX4_pro Prokaryotic Cytochrome C oxidase subunit IV. Cytochrome c oxidase (COX) is a multi-subunit enzyme complex that catalyzes the final step of electron transfer through the respiratory chain on the mitochondrial inner membrane. This family is composed of cytochrome c oxidase subunit 4 from prokaryotes. 72 matched cddid_all.tbl CDD pfam03627 pfam03627 460994 PapG_N PapG carbohydrate binding domain. PapG, the adhesin of the P-pili, is situated at the tip and is only a minor component of the whole pilus structure. A two-domain structure has been postulated for PapG; a carbohydrate binding N-terminus (this domain) and chaperone binding C-terminus. The carbohydrate-binding domain interacts with the receptor glycan. 226 matched cddid_all.tbl CDD pfam03628 pfam03628 397609 PapG_C PapG chaperone-binding domain. PapG, the adhesin of the P-pili, is situated at the tip and is only a minor component of the whole pilus structure. A two-domain structure has been postulated for PapG; a carbohydrate binding N-terminus and chaperone binding C-terminus (this domain). The chaperone-binding domain is highly conserved, and is essential for the correct assembly of the pili structure when aided by the chaperone molecule PapD. 108 matched cddid_all.tbl CDD pfam03629 pfam03629 427409 SASA Carbohydrate esterase, sialic acid-specific acetylesterase. The catalytic triad of this esterase enzyme comprises residues Ser127, His403 and Asp391 in UniProtKB:P70665. 227 matched cddid_all.tbl CDD pfam03630 pfam03630 460995 Fumble Fumble. Fumble is required for cell division in Drosophila. Mutants lacking fumble exhibit abnormalities in bipolar spindle organization, chromosome segregation, and contractile ring formation. Analyses have demonstrated that encodes three protein isoforms, all of which contain a domain with high similarity to the pantothenate kinases of A. nidulans and mouse. A role of fumble in membrane synthesis has been proposed. 311 matched cddid_all.tbl CDD pfam03631 pfam03631 460996 Virul_fac_BrkB Virulence factor BrkB. This family acts as a virulence factor. In Bordetella pertussis, Swiss:Q45339 is essential for resistance to complement-dependent killing by serum. This family was originally predicted to be ribonuclease BN, but this prediction has since been shown to be incorrect. 256 matched cddid_all.tbl CDD pfam03632 pfam03632 281612 Glyco_hydro_65m Glycosyl hydrolase family 65 central catalytic domain. This family of glycosyl hydrolases contains vacuolar acid trehalase and maltose phosphorylase.Maltose phosphorylase (MP) is a dimeric enzyme that catalyzes the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The central domain is the catalytic domain, which binds a phosphate ion that is proximal the the highly conserved Glu. The arrangement of the phosphate and the glutamate is thought to cause nucleophilic attack on the anomeric carbon atom. The catalytic domain also forms the majority of the dimerization interface. 387 matched cddid_all.tbl CDD pfam03633 pfam03633 460997 Glyco_hydro_65C Glycosyl hydrolase family 65, C-terminal domain. This family of glycosyl hydrolases contains vacuolar acid trehalase and maltose phosphorylase.Maltose phosphorylase (MP) is a dimeric enzyme that catalyzes the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. The C-terminal domain forms a two layered jelly roll motif. This domain is situated at the base of the catalytic domain, however its function remains unknown. 51 matched cddid_all.tbl CDD pfam03634 pfam03634 460998 TCP TCP family transcription factor. This is a family of TCP plant transcription factors. TCP proteins were named after the first characterized members (TB1, CYC and PCFs) and they are involved in multiple developmental control pathways. This region contains a DNA binding basic-Helix-Loop-Helix (bHLP) structure. 152 matched cddid_all.tbl CDD pfam03635 pfam03635 427414 Vps35 Vacuolar protein sorting-associated protein 35. Vacuolar protein sorting-associated protein (Vps) 35 is one of around 50 proteins involved in protein trafficking. In particular, Vps35 assembles into a retromer complex with at least four other proteins Vps5, Vps17, Vps26 and Vps29. Vps35 contains a central region of weaker sequence similarity, thought to indicate the presence of at least three domains. 733 matched cddid_all.tbl CDD pfam03636 pfam03636 460999 Glyco_hydro_65N Glycosyl hydrolase family 65, N-terminal domain. This family of glycosyl hydrolases contains vacuolar acid trehalase and maltose phosphorylase.Maltose phosphorylase (MP) is a dimeric enzyme that catalyzes the conversion of maltose and inorganic phosphate into beta-D-glucose-1-phosphate and glucose. This domain is believed to be essential for catalytic activity although its precise function remains unknown. 237 matched cddid_all.tbl CDD pfam03637 pfam03637 461000 Mob1_phocein Mob1/phocein family. Mob1 is an essential Saccharomyces cerevisiae protein, identified from a two-hybrid screen, that binds Mps1p, a protein kinase essential for spindle pole body duplication and mitotic checkpoint regulation. Mob1 contains no known structural motifs; however MOB1 is a member of a conserved gene family and shares sequence similarity with a nonessential yeast gene, MOB2. Mob1 is a phosphoprotein in vivo and a substrate for the Mps1p kinase in vitro. Conditional alleles of MOB1 cause a late nuclear division arrest at restrictive temperature. This family also includes phocein, a rat protein that by yeast two hybrid interacts with striatin. 171 matched cddid_all.tbl CDD pfam03638 pfam03638 461001 TCR Tesmin/TSO1-like CXC domain, cysteine-rich domain. This family includes proteins that have two copies of a cysteine rich motif as follows: C-X-C-X4-C-X3-YC-X-C-X6-C-X3-C-X-C-X2-C. The family includes Tesmin and TSO1. This family is called a CXC domain in. 38 matched cddid_all.tbl CDD pfam03639 pfam03639 427418 Glyco_hydro_81 Glycosyl hydrolase family 81 N-terminal domain. Family of eukaryotic beta-1,3-glucanases. Within the Aspergillus fumigatus protein Swiss:Q9UVV0 two perfectly conserved Glu residues (E550 or E554) have been proposed as putative nucleophiles of the active site of the Engl1 endoglucanase, while the proton donor would be D475. The endo-beta-1,3-glucanase activity is essential for efficient spore release. This entry represents the N-terminal beta sandwich domain. 321 matched cddid_all.tbl CDD pfam03640 pfam03640 427419 Lipoprotein_15 Secreted repeat of unknown function. This family occurs as tandem repeats in a set of lipoproteins. The alignment contains a Y-X4-D motif. 45 matched cddid_all.tbl CDD pfam03641 pfam03641 397621 Lysine_decarbox Possible lysine decarboxylase. The members of this family share a highly conserved motif PGGXGTXXE that is probably functionally important. This family includes proteins annotated as lysine decarboxylases, although the evidence for this is not clear. 130 matched cddid_all.tbl CDD pfam03642 pfam03642 367591 MAP MAP domain. This presumed 110 amino acid residue domain is found in multiple copies in MAP (MHC class II analogue protein). The protein has been found in a wide range of extracellular matrix proteins. 87 matched cddid_all.tbl CDD pfam03643 pfam03643 397622 Vps26 Vacuolar protein sorting-associated protein 26. Vacuolar protein sorting-associated protein (Vps) 26 is one of around 50 proteins involved in protein trafficking. In particular, Vps26 assembles into a retromer complex with at least four other proteins Vps5, Vps17, Vps29 and Vps35. This family also contains Down syndrome critical region 3/A. 275 matched cddid_all.tbl CDD pfam03644 pfam03644 461002 Glyco_hydro_85 Glycosyl hydrolase family 85. Family of endo-beta-N-acetylglucosaminidases. These enzymes work on a broad spectrum of substrates. 292 matched cddid_all.tbl CDD pfam03645 pfam03645 461003 Tctex-1 Tctex-1 family. Tctex-1 is a dynein light chain. It has been shown that Tctex-1 can bind to the cytoplasmic tail of rhodopsin. C-terminal rhodopsin mutations responsible for retinitis pigmentosa inhibit this interaction. 96 matched cddid_all.tbl CDD pfam03646 pfam03646 427422 FlaG FlaG protein. Although important for flagella the exact function of this protein is unknown. 101 matched cddid_all.tbl CDD pfam03647 pfam03647 461004 Tmemb_14 Transmembrane proteins 14C. This family of short membrane proteins are as yet uncharacterized. 89 matched cddid_all.tbl CDD pfam03648 pfam03648 397627 Glyco_hydro_67N Glycosyl hydrolase family 67 N-terminus. Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. This family represents the N-terminal region of alpha-glucuronidase. The N-terminal domain forms a two-layer sandwich, each layer being formed by a beta sheet of five strands. A further two helices form part of the interface with the central, catalytic, module (pfam07488). 120 matched cddid_all.tbl CDD pfam03649 pfam03649 427424 UPF0014 Uncharacterized protein family (UPF0014). characterized proteins in this family include probable iron export permease protein FetB, which is part of the ABC transporter complex FetAB, probably involved in iron export, and aluminium sensitive 3 protein, also part of an ABC transporter required for aluminum (Al) resistance. This family also includes integral membrane proteins currently uncharacterized. 242 matched cddid_all.tbl CDD pfam03650 pfam03650 427425 MPC Mitochondrial pyruvate carriers. This family includes mitochondrial pyruvate carrier proteins, such as Mpc 1/2 and their homologs. They mediate the uptake of pyruvate into mitochondria. In humans, Mpc1 and Mpc2 associate to form an ~150-kilodalton complex in the inner mitochondrial membrane. MPC1 contains two predicted transmembrane regions. MPC2 contains three predicted transmembrane regions. Several studies have demonstrated MPC involvement in the control of cell fate in cancer and gluconeogenesis in models of type 2 diabetes. 110 matched cddid_all.tbl CDD pfam03652 pfam03652 461005 RuvX Holliday junction resolvase. The central intermediate formed during mitotic and meiotic recombination is a four stranded DNA structure, also known as the Holliday junction (HJ), and its efficient resolution is essential for proper segregation of chromosomes. Resolution of HJs is mediated by a diverse group of DNA structure specific endonucleases known as Holliday junction resolvases (HJR). This entry is specific for RuvX also known as YqgF a family of nucleases which resolves the Holliday junction intermediates in genetic recombination. Studies carried out in M. tuberculosis, have shown that YqgF/RuvX is a genuine HJR analogous to RuvC from E. coli. Furthermore, a single cysteine present in M. tuberculosis RuvX was found to be required for disulfide-bond mediated intermolecular dimerization and HJ resolution activity, suggesting that M. tuberculosis RuvX has adapted its YqgF protein to function like a typical RuvC family HJR. 134 matched cddid_all.tbl CDD pfam03653 pfam03653 427427 UPF0093 Uncharacterized protein family (UPF0093). 146 matched cddid_all.tbl CDD pfam03656 pfam03656 252088 Pam16 Pam16. The Pam16 protein is the fifth essential subunit of the pre-sequence translocase-associated protein import motor (PAM). In Saccharomyces cerevisiae, Pam16 is required for preprotein translocation into the matrix, but not for protein insertion into the inner membrane. Pam16 has a degenerate J domain. J-domain proteins play important regulatory roles as co-chaperones, recruiting Hsp70 partners and accelerating the ATP-hydrolysis step of the chaperone cycle. Pam16's J-like domain strongly interacts with Pam18's J domain, leading to a productive interaction of Pam18 with mtHsp70 at the mitochondria import channel. Pam18 stimulates the ATPase activity of mtHsp70. 127 matched cddid_all.tbl CDD pfam03657 pfam03657 461006 UPF0113 UPF0113 PUA domain. 73 matched cddid_all.tbl CDD pfam03658 pfam03658 427429 Ub-RnfH RnfH family Ubiquitin. A member of the RnfH family of the ubiquitin superfamily. Members of this family strongly co-occur in two distinct gene neighborhood contexts. In one it is associated with a START domain protein, a membrane protein SmpA and the transfer mRNA binding protein SmpB. This association suggests a possible role in the SmpB-tmRNA-based tagging and degadation system of bacteria, which is interesting given that other members of the ubiquitin system are analogously involved in protein-tagging and degradation across eukaryotes and various prokaryotes. The second context in which the RnfH genes are present is in a membrane associated complex involved in transporting electrons for various reductive reactions such as nitrogen fixation. 83 matched cddid_all.tbl CDD pfam03659 pfam03659 461007 Glyco_hydro_71 Glycosyl hydrolase family 71. Family of alpha-1,3-glucanases. 372 matched cddid_all.tbl CDD pfam03660 pfam03660 461008 PHF5 PHF5-like protein. This family of proteins the superfamily of PHD-finger proteins. At least one example, from mouse, may act as a chromatin-associated protein. The S. pombe ini1 gene is essential, required for splicing. It is localized in the nucleus, but not detected in the nucleolus and can be complemented by human ini1. 104 matched cddid_all.tbl CDD pfam03661 pfam03661 461009 TMEM33_Pom33 Transmembrane protein 33/Nucleoporin POM33. This is an integral membrane protein family. Family members include TMEM33/Pom33 proteins. Budding yeast Pom33 is a transmembrane nucleoporin that contributes to proper distribution and/or efficient assembly of nuclear pores. Proteins in this entry also include Tts1 from fission yeasts, Kr-h2 (krueppel homolog 2) from flies and TMEM33 from vertebrates. Tts1 is required for the correct positioning of the cellular division plane by delimiting the actomyosin ring assembly at the cell equator. Kr-h2 is a member of the dosage-dependent hierarchy effective upon white gene expression. TMEM33 regulates the tubular structure of endoplasmic reticulum by suppressing the membrane-shaping activity of reticulons. 237 matched cddid_all.tbl CDD pfam03662 pfam03662 461010 Glyco_hydro_79n Glycosyl hydrolase family 79, N-terminal domain. Family of endo-beta-N-glucuronidase, or heparanase. Heparan sulfate proteoglycans (HSPGs) play a key role in the self- assembly, insolubility and barrier properties of basement membranes and extracellular matrices. Hence, cleavage of heparan sulfate (HS) affects the integrity and functional state of tissues and thereby fundamental normal and pathological phenomena involving cell migration and response to changes in the extracellular micro-environment. Heparanase degrades HS at specific intra-chain sites. The enzyme is synthesized as a latent approximately 65 kDa protein that is processed at the N-terminus into a highly active approximately 50 kDa form. Experimental evidence suggests that heparanase may facilitate both tumour cell invasion and neovascularization, both critical steps in cancer progression. The enzyme is also involved in cell migration associated with inflammation and autoimmunity. 318 matched cddid_all.tbl CDD pfam03663 pfam03663 397638 Glyco_hydro_76 Glycosyl hydrolase family 76. Family of alpha-1,6-mannanases. 348 matched cddid_all.tbl CDD pfam03664 pfam03664 281639 Glyco_hydro_62 Glycosyl hydrolase family 62. Family of alpha -L-arabinofuranosidase (EC 3.2.1.55). This enzyme hydrolysed aryl alpha-L-arabinofuranosides and cleaves arabinosyl side chains from arabinoxylan and arabinan. 272 matched cddid_all.tbl CDD pfam03665 pfam03665 461011 UPF0172 Uncharacterized protein family (UPF0172). In Chlamydomonas reinhardtii the protein TLA1 (truncated light-harvesting chlorophyll antenna size) apparently regulates genes that define the chlorophyll-a antenna size in the photosynthetic apparatus. This family was formerly known as UPF0172. 189 matched cddid_all.tbl CDD pfam03666 pfam03666 427435 NPR3 Nitrogen Permease regulator of amino acid transport activity 3. This family, also known in yeasts as Rmd11, complexes with NPR2, pfam06218. This complex heterodimer is responsible for inactivating TORC1. an evolutionarily conserved protein complex that controls cell size via nutritional input signals, specifically, in response to amino acid starvation. 442 matched cddid_all.tbl CDD pfam03668 pfam03668 397641 ATP_bind_2 P-loop ATPase protein family. This family contains an ATP-binding site and could be an ATPase (personal obs:C Yeats). 284 matched cddid_all.tbl CDD pfam03669 pfam03669 461012 ASTER PAT complex subunit Asterix. This family represents Asterix proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes. The PAT complex acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins. Asterix is the substrate-interacting subunit of the PAT complex and associates with the first TMD of the nascent chain. The PAT complex favors the binding to TMDs with exposed hydrophilic amino acids within the lipid bilayer and provides a membrane-embedded partially hydrophilic environment in which TMD1 binds. 96 matched cddid_all.tbl CDD pfam03670 pfam03670 112485 UPF0184 Uncharacterized protein family (UPF0184). 83 matched cddid_all.tbl CDD pfam03671 pfam03671 397643 Ufm1 Ubiquitin fold modifier 1 protein. This is a family of short ubiquitin-like proteins, that is like neither type-1 or type-2. It is a ubiquitin-fold modifier 1 (Ufm1) that is synthesized in a precursor form of 85 amino-acid residues. In humans the enzyme for Ufm1 is Uba5 and the conjugating enzyme is Ufc1. Prior to activation by Uba5 the extra two amino acids at the C-terminal region of the human pro-Ufm1 protein are removed to expose Gly whose residue is necessary for conjugation to target molecule(s). The mature Ufm1 is conjugated to yet unidentified endogenous proteins,. While Ubiquitin and many Ubls possess the conserved C-terminal di-glycine that is adenylated by each specific E1 or E1-like enzyme, respectively, in an ATP-dependent manner, Ufm1(1-83) possesses a single glycine at its C-terminus, which is followed by a Ser-Cys dipeptide in the precursor form of Ufm1. The C-terminally processed Ufm1(1-83) is specifically activated by Uba5, an E1-like enzyme, and then transferred to its cognate Ufc1, an E2-like enzyme. 75 matched cddid_all.tbl CDD pfam03672 pfam03672 427437 UPF0154 Uncharacterized protein family (UPF0154). This family contains a set of short bacterial proteins of unknown function. 60 matched cddid_all.tbl CDD pfam03673 pfam03673 427438 UPF0128 Uncharacterized protein family (UPF0128). The members of this family are about 240 amino acids in length. The proteins are as yet uncharacterized. 221 matched cddid_all.tbl CDD pfam03676 pfam03676 461013 PHAF1 Phagosome assembly factor 1. PHAF1 and BCAS3 form a complex that affects the recruitment of several core autophagy proteins to the phagophore assembly site. 392 matched cddid_all.tbl CDD pfam03677 pfam03677 281647 UPF0137 Uncharacterized protein family (UPF0137). This family includes GP6-D a virulence plasmid encoded protein. 237 matched cddid_all.tbl CDD pfam03678 pfam03678 308977 Adeno_hexon_C Hexon, adenovirus major coat protein, C-terminal domain. Hexon is the major coat protein from adenovirus type 2. Hexon forms a homo-trimer. The 240 copies of the hexon trimer are organized so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX. The penton complex, formed by the peripentonal hexons and base hexon (holding in place a fibre), lie at each of the 12 vertices. The N and C-terminal domains adopt the same PNGase F-like fold although they are significantly different in length. 241 matched cddid_all.tbl CDD pfam03682 pfam03682 308978 UPF0158 Uncharacterized protein family (UPF0158). 157 matched cddid_all.tbl CDD pfam03683 pfam03683 427440 UPF0175 Uncharacterized protein family (UPF0175). This family contains small proteins of unknown function. 75 matched cddid_all.tbl CDD pfam03684 pfam03684 427441 UPF0179 Uncharacterized protein family (UPF0179). The function of this family is unknown, however the proteins contain two cysteine clusters that may be iron sulphur redox centres. 139 matched cddid_all.tbl CDD pfam03685 pfam03685 427442 UPF0147 Uncharacterized protein family (UPF0147). This family of small proteins have no known function. 81 matched cddid_all.tbl CDD pfam03686 pfam03686 397649 UPF0146 Uncharacterized protein family (UPF0146). The function of this family of proteins is unknown. 129 matched cddid_all.tbl CDD pfam03687 pfam03687 281654 UPF0164 Uncharacterized protein family (UPF0164). This family of uncharacterized proteins are only found in Treponema pallidum. These proteins belong to the membrane beta barrel superfamily. 326 matched cddid_all.tbl CDD pfam03688 pfam03688 397650 Nepo_coat_C Nepovirus coat protein, C-terminal domain. The members of this family are derived from nepoviruses. Together with comoviruses and picornaviruses, nepoviruses are classified in the picornavirus superfamily of plus strand single-stranded RNA viruses. This family aligns several nepovirus coat protein sequences. In several cases, this is found at the C-terminus of the RNA2-encoded viral polyprotein. The coat protein consists of three trapezoid-shaped beta-barrel domains, and forms a pseudo T = 3 icosahedral capsid structure. 163 matched cddid_all.tbl CDD pfam03689 pfam03689 397651 Nepo_coat_N Nepovirus coat protein, N-terminal domain. The members of this family are derived from nepoviruses. Together with comoviruses and picornaviruses, nepoviruses are classified in the picornavirus superfamily of plus strand single-stranded RNA viruses. This family aligns several nepovirus coat protein sequences. In several cases, this is found at the C-terminus of the RNA2-encoded viral polyprotein. The coat protein consists of three trapezoid-shaped beta-barrel domains, and forms a pseudo T = 3 icosahedral capsid structure. 91 matched cddid_all.tbl CDD pfam03690 pfam03690 461014 UPF0160 Uncharacterized protein family (UPF0160). This family of proteins contains a large number of metal binding residues. The patterns are suggestive of a phosphoesterase function. The conserved DHH motif may mean this family is related to pfam01368. 315 matched cddid_all.tbl CDD pfam03691 pfam03691 397653 UPF0167 Uncharacterized protein family (UPF0167). The proteins in this family are about 200 amino acids long and each contain 3 CXXC motifs. 174 matched cddid_all.tbl CDD pfam03692 pfam03692 308985 CxxCxxCC Putative zinc- or iron-chelating domain. This family of proteins contains 8 conserved cysteines. It has in the past been annotated as being one of the complex of proteins of the flagellar Fli complex. However this was due to a mis-annotation of the original Salmonella LT2 Genbank entry of 'fliB'. With all its conserved cysteines it is possibly a domain that chelates iron or zinc ions. 85 matched cddid_all.tbl CDD pfam03693 pfam03693 281658 ParD_antitoxin Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH. ParD is the antitoxin of a bacterial toxin-antitoxin gene pair. The cognate toxin is ParE in, pfam05016. The family contains several related antitoxins from Cyanobacteria, Proteobacteria and Actinobacteria. Antitoxins of this class carry an N-terminal ribbon-helix-helix domain, RHH, that is highly conserved across all type II bacterial antitoxins, which dimerizes with the RHH domain of a second VapB molecule. A hinge section follows the RHH, with an additional pair of flexible alpha helices at the C-terminus. This C-terminus is the toxin-binding region of the dimer, and so is specific to the cognate toxin, whereas the RHH domain has the specific function of lying across the RNA-binding groove of the toxin dimer and inactivating the active-site - a more general function of all type II antitoxins. 80 matched cddid_all.tbl CDD pfam03694 pfam03694 461015 Erg28 Erg28 like protein. This is a family of integral membrane proteins, which may contain four transmembrane helices. Members of this family are thought to be involved in sterol C-4 demethylation. In S. cerevisiae they may tether Erg26p (sterol dehydrogenase/decarboxylase) and Erg27p (3-ketoreductase) to the endoplasmic reticulum or may facilitate interaction between these proteins. The family contains a conserved arginine and histidine that may be functionally important. 111 matched cddid_all.tbl CDD pfam03695 pfam03695 427445 UPF0149 Uncharacterized protein family (UPF0149). The protein in this family are about 190 amino acids long. The function of these proteins is unknown. 170 matched cddid_all.tbl CDD pfam03698 pfam03698 427446 UPF0180 Uncharacterized protein family (UPF0180). The members of this family are small uncharacterized proteins. 73 matched cddid_all.tbl CDD pfam03699 pfam03699 427447 UPF0182 Uncharacterized protein family (UPF0182). This family contains uncharacterized integral membrane proteins. 752 matched cddid_all.tbl CDD pfam03700 pfam03700 461016 Sorting_nexin Sorting nexin, N-terminal domain. These proteins bins to the cytoplasmic domain of plasma membrane receptors. and are involved in endocytic protein trafficking. The N-terminal domain appears to be specific to sorting nexins 1 and 2. 75 matched cddid_all.tbl CDD pfam03701 pfam03701 427449 UPF0181 Uncharacterized protein family (UPF0181). This family contains small proteins of about 50 amino acids of unknown function. The family includes YoaH. 50 matched cddid_all.tbl CDD pfam03702 pfam03702 397660 AnmK Anhydro-N-acetylmuramic acid kinase. Anhydro-N-acetylmuramic acid kinase catalyzes the specific phosphorylation of 1,6-anhydro-N-acetylmuramic acid (anhMurNAc) with the simultaneous cleavage of the 1,6-anhydro ring, generating MurNAc-6-P. It is also required for the utilization of anhMurNAc, either imported from the medium, or derived from its own cell wall murein, and in so doing plays a role in cell wall recycling. 364 matched cddid_all.tbl CDD pfam03703 pfam03703 427450 bPH_2 Bacterial PH domain. Domain found in uncharacterized family of membrane proteins. 1-3 copies found in each protein, with each copy flanked by transmembrane helices. Members of this family have a PH domain like structure. 78 matched cddid_all.tbl CDD pfam03704 pfam03704 397662 BTAD Bacterial transcriptional activator domain. Found in the DNRI/REDD/AFSR family of regulators. This region of AFSR along with the C terminal region is capable of independently directing actinorhodin production. This family contains TPR repeats. 146 matched cddid_all.tbl CDD pfam03705 pfam03705 461017 CheR_N CheR methyltransferase, all-alpha domain. CheR proteins are part of the chemotaxis signaling mechanism in bacteria. CheR methylates the chemotaxis receptor at specific glutamate residues. CheR is an S-adenosylmethionine- dependent methyltransferase. 53 matched cddid_all.tbl CDD pfam03706 pfam03706 461018 LPG_synthase_TM Lysylphosphatidylglycerol synthase TM region. LPG_synthase_TM is the N-terminal region of this family of bacterial phosphatidylglycerol lysyltransferases. The function of the family is to add lysyl groups to membrane lipids, and this region is the transmembrane domain of 7xTMs. In order to counteract attack by membrane-damaging external cationic antimicrobial molecules - from host immune systems, bacteriocins, defensins, etc - bacteria modify their anionic membrane phosphatidylglycerol with positively-charged L-lysine; this results in repulsion of the foreign cationic peptides. 302 matched cddid_all.tbl CDD pfam03707 pfam03707 427453 MHYT Bacterial signalling protein N terminal repeat. Found as an N terminal triplet tandem repeat in bacterial signalling proteins. Family includes CoxC and CoxH from P.carboxydovorans. Each repeat contains two transmembrane helices. Domain is also described as the MHYT domain. 54 matched cddid_all.tbl CDD pfam03708 pfam03708 461019 Avian_gp85 Avian retrovirus envelope protein, gp85. Family of a vain specific viral glycoproteins that forms a receptor-binding gp85 polypeptide that is linked through disulfide to a membrane-spanning gp37 spike. Gp85 confers a high degree of subgroup specificity for interaction with distinct cell receptors. 246 matched cddid_all.tbl CDD pfam03709 pfam03709 427454 OKR_DC_1_N "Orn/Lys/Arg decarboxylase, N-terminal domain. This domain has a flavodoxin-like fold, and is termed the ""wing"" domain because of its position in the overall 3D structure." 111 matched cddid_all.tbl CDD pfam03710 pfam03710 397667 GlnE Glutamate-ammonia ligase adenylyltransferase. Conserved repeated domain found in GlnE proteins. These proteins adenylate and deadenylate glutamine synthases: ATP + {L-Glutamate:ammonia ligase (ADP-forming)} = Diphosphate + Adenylyl-{L-Glutamate:Ammonia ligase (ADP-forming)}. The family is related to the pfam01909 domain. 249 matched cddid_all.tbl CDD pfam03711 pfam03711 461020 OKR_DC_1_C Orn/Lys/Arg decarboxylase, C-terminal domain. 132 matched cddid_all.tbl CDD pfam03712 pfam03712 461021 Cu2_monoox_C Copper type II ascorbate-dependent monooxygenase, C-terminal domain. The N and C-terminal domains of members of this family adopt the same PNGase F-like fold. 157 matched cddid_all.tbl CDD pfam03713 pfam03713 427457 DUF305 Domain of unknown function (DUF305). Domain found in small family of bacterial secreted proteins with no known function. Also found in Paramecium bursaria chlorella virus 1. This domain is short and found in one or two copies. The domain has a conserved HH motif that may be functionally important. This domain belongs to the ferritin superfamily. It contains two sequence similar repeats each of which is composed of two alpha helices. 151 matched cddid_all.tbl CDD pfam03714 pfam03714 461022 PUD Bacterial pullanase-associated domain. Domain is found in pullanase - carbohydrate de-branching - proteins. It is found both to the N or the C terminii of of the alpha-amylase active site region. This domain contains several conserved aromatic residues that are suggestive of a carbohydrate binding function. 97 matched cddid_all.tbl CDD pfam03715 pfam03715 461023 Noc2 Noc2p family. At least one member, Noc2p from yeast, is required for a late step in 60S subunit export from the nucleus. It has also been shown to co-precipitate with Nug1p, a nuclear GTPase also required for ribosome nucleus export. This family was formerly known as UPF0120. 296 matched cddid_all.tbl CDD pfam03716 pfam03716 202737 WCCH WCCH motif. The WCCH motif is found in a retrotransposons and Gemini viruses. A specific function has not been associated to this motif. 25 matched cddid_all.tbl CDD pfam03717 pfam03717 427460 PBP_dimer Penicillin-binding Protein dimerization domain. This domain is found at the N terminus of Class B High Molecular Weight Penicillin-Binding Proteins. Its function has not been precisely defined, but is strongly implicated in PBP polymerization. The domain forms a largely disordered 'sugar tongs' structure. 178 matched cddid_all.tbl CDD pfam03718 pfam03718 397674 Glyco_hydro_49 Glycosyl hydrolase family 49. Family of dextranase (EC 3.2.1.11) and isopullulanase (EC 3.2.1.57). Dextranase hydrolyses alpha-1,6-glycosidic bonds in dextran polymers. This domain corresponds to the C-terminal pectate lyase like domain. 118 matched cddid_all.tbl CDD pfam03719 pfam03719 461024 Ribosomal_S5_C Ribosomal protein S5, C-terminal domain. 71 matched cddid_all.tbl CDD pfam03720 pfam03720 427462 UDPG_MGDP_dh_C UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain. The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyze the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate. 103 matched cddid_all.tbl CDD pfam03721 pfam03721 397677 UDPG_MGDP_dh_N UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain. The UDP-glucose/GDP-mannose dehydrogenaseses are a small group of enzymes which possesses the ability to catalyze the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate. 186 matched cddid_all.tbl CDD pfam03722 pfam03722 461025 Hemocyanin_N Hemocyanin, all-alpha domain. This family includes arthropod hemocyanins and insect larval storage proteins. 124 matched cddid_all.tbl CDD pfam03723 pfam03723 461026 Hemocyanin_C Hemocyanin, ig-like domain. This family includes arthropod hemocyanins and insect larval storage proteins. 243 matched cddid_all.tbl CDD pfam03724 pfam03724 461027 META META domain. Small domain family found in proteins of of unknown function. Some are secreted and implicated in motility in bacteria. Also occurs in Leishmania spp. as an essential gene. Over-expression in L.amazonensis increases virulence. A pair of cysteine residues show correlated conservation, suggesting that they form a disulphide bond. 109 matched cddid_all.tbl CDD pfam03725 pfam03725 427466 RNase_PH_C 3' exoribonuclease family, domain 2. This family includes 3'-5' exoribonucleases. Ribonuclease PH contains a single copy of this domain, and removes nucleotide residues following the -CCA terminus of tRNA. Polyribonucleotide nucleotidyltransferase (PNPase) contains two tandem copies of the domain. PNPase is involved in mRNA degradation in a 3'-5' direction. The exosome is a 3'-5' exoribonuclease complex that is required for 3' processing of the 5.8S rRNA. Three of its five protein components, Swiss:P46948 Swiss:Q12277 and Swiss:P25359 contain a copy of this domain. Swiss:Q10205, a hypothetical protein from S. pombe appears to belong to an uncharacterized subfamily. This subfamily is found in both eukaryotes and archaebacteria. 67 matched cddid_all.tbl CDD pfam03726 pfam03726 397682 PNPase Polyribonucleotide nucleotidyltransferase, RNA binding domain. This family contains the RNA binding domain of Polyribonucleotide nucleotidyltransferase (PNPase) PNPase is involved in mRNA degradation in a 3'-5' direction. 80 matched cddid_all.tbl CDD pfam03727 pfam03727 461028 Hexokinase_2 Hexokinase. Hexokinase (EC:2.7.1.1) contains two structurally similar domains represented by this family and pfam00349. Some members of the family have two copies of each of these domains. 236 matched cddid_all.tbl CDD pfam03728 pfam03728 281690 Viral_DNA_Zn_bi Viral DNA-binding protein, zinc binding domain. This family represents the zinc binding domain of the viral DNA- binding protein, a multi functional protein involved in DNA replication and transcription control. Two copies of this domain are found at the C-terminus of many members of the family. 94 matched cddid_all.tbl CDD pfam03729 pfam03729 427468 DUF308 Short repeat of unknown function (DUF308). Family of short repeats that occurs in a limited number of membrane proteins. It may divide further in short repeats of around 7-10 residues of the pattern G-#-X(2)-#(2)-X (#=hydrophobic). 73 matched cddid_all.tbl CDD pfam03730 pfam03730 461029 Ku_C Ku70/Ku80 C-terminal arm. The Ku heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the C terminal arm. This alpha helical region embraces the beta-barrel domain pfam02735 of the opposite subunit. 79 matched cddid_all.tbl CDD pfam03731 pfam03731 427470 Ku_N Ku70/Ku80 N-terminal alpha/beta domain. The Ku heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold. 220 matched cddid_all.tbl CDD pfam03732 pfam03732 367628 Retrotrans_gag Retrotransposon gag protein. Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved. 97 matched cddid_all.tbl CDD pfam03733 pfam03733 461030 YccF Inner membrane component domain. Domain occurs as one or more copies in bacterial and eukaryotic proteins. These are membrane proteins of four TM regions, two appearing in each of the two copies when both are present. Many of the latter members also carry the sodium/calcium exchanger protein family pfam01699, which have multipass membrane regions. 51 matched cddid_all.tbl CDD pfam03734 pfam03734 461031 YkuD L,D-transpeptidase catalytic domain. This family of proteins are found in a range of bacteria. It has been shown that this domain can act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. This gives bacteria resistance to beta-lactam antibiotics that inhibit PBPs which usually carry out the cross-linking reaction. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue. Several members of this family contain peptidoglycan binding domains. The molecular structure of YkuD protein shows this domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This family was formerly called the ErfK/YbiS/YcfS/YnhG family, but is now named after the first protein of known structure. 89 matched cddid_all.tbl CDD pfam03735 pfam03735 461032 ENT ENT domain. This presumed domain is named after Emsy N Terminus (ENT). Emsy is a protein that is amplified in breast cancer and interacts with BRCA2. The N terminus of this protein is found to be similar to other vertebrate and plant proteins of unknown function. This domain has a completely conserved histidine residue that may be functionally important. 71 matched cddid_all.tbl CDD pfam03736 pfam03736 461033 EPTP EPTP domain. Mutations in the LGI/Epitempin gene can result in a special form of epilepsy, autosomal dominant lateral temporal epilepsy. The Epitempin protein contains a large repeat in its C terminal section. The architecture and structural features of this repeat make it a likely member 7-bladed beta-propeller fold. 41 matched cddid_all.tbl CDD pfam03737 pfam03737 427475 RraA-like Aldolase/RraA. Members of this family include regulator of ribonuclease E activity A (RraA) and 4-hydroxy-4-methyl-2-oxoglutarate (HMG)/4-carboxy- 4-hydroxy-2-oxoadipate (CHA) aldolase, also known as RraA-like protein. RraA acts as a trans-acting modulator of RNA turnover, binding essential endonuclease RNase E and inhibiting RNA processing. RraA-like proteins seem to contain aldolase and/or decarboxylase activity either in place of or in addition to the RNase E inhibitor functions. 148 matched cddid_all.tbl CDD pfam03738 pfam03738 427476 GSP_synth Glutathionylspermidine synthase preATP-grasp. This region contains the Glutathionylspermidine synthase enzymatic activity EC:6.3.1.8. This is the C-terminal region in bi-enzymes. Glutathionylspermidine (GSP) synthetases of Trypanosomatidae and Escherichia coli couple hydrolysis of ATP (to ADP and Pi) with formation of an amide bond between spermidine and the glycine carboxylate of glutathione (gamma-Glu-Cys-Gly). In the pathogenic trypanosomatids, this reaction is the penultimate step in the biosynthesis of the antioxidant metabolite, trypanothione (N1,N8-bis-(glutathionyl)spermidine), and is a target for drug design. This region, the pre-ATP grasp region, probably carries the substrate-binding site. 371 matched cddid_all.tbl CDD pfam03739 pfam03739 427477 LptF_LptG Lipopolysaccharide export system permease LptF/LptG. Members of this family are predicted integral membrane proteins of about 350 amino acids long and containing about 6 trans-membrane regions. characterized members include LptF and LptG, two homologous tandem-encoded permeases of an export ATP transporter for lipopolysaccharide (LPS) assembly in most Gram-negative bacteria. 352 matched cddid_all.tbl CDD pfam03740 pfam03740 461034 PdxJ Pyridoxal phosphate biosynthesis protein PdxJ. Members of this family belong to the PdxJ family that catalyzes the condensation of 1-deoxy-d-xylulose-5-phosphate (DXP) and 1-amino-3-oxo-4-(phosphohydroxy)propan-2-one to form pyridoxine 5'-phosphate (PNP). This reaction is involved in de novo synthesis of pyridoxine (vitamin B6) and pyridoxal phosphate. 234 matched cddid_all.tbl CDD pfam03741 pfam03741 461035 TerC Integral membrane protein TerC family. This family contains a number of integral membrane proteins that also contains the TerC protein. TerC has been implicated in resistance to tellurium. This protein may be involved in efflux of tellurium ions. The tellurite-resistant Escherichia coli strain KL53 was found during testing of the group of clinical isolates for antibiotics and heavy metal ion resistance. Determinant of the tellurite resistance of the strain was located on a large conjugative plasmid. Analyses showed, the genes terB, terC, terD and terE are essential for conservation of the resistance. The members of the family contain a number of conserved aspartates that could be involved in binding to metal ions. 178 matched cddid_all.tbl CDD pfam03742 pfam03742 397695 PetN PetN. PetN is a small hydrophobic protein, crucial for cytochrome b6-f complex assembly and/or stability. 29 matched cddid_all.tbl CDD pfam03743 pfam03743 427480 TrbI Bacterial conjugation TrbI-like protein. Although not essential for conjugation, the TrbI protein greatly increase the conjugational efficiency. 187 matched cddid_all.tbl CDD pfam03744 pfam03744 427481 BioW 6-carboxyhexanoate--CoA ligase. This family contains the enzyme 6-carboxyhexanoate--CoA ligase EC:6.2.1.14. This enzyme is involved in the first step of biotin synthesis, where it converts pimelate into pimeloyl-CoA. The enzyme requires magnesium as a cofactor and forms a homodimer. 239 matched cddid_all.tbl CDD pfam03745 pfam03745 427482 DUF309 Domain of unknown function (DUF309). This domain is found in eubacterial and archaebacterial proteins of unknown function. The proteins contain a motif HXXXEXX(W/Y) where X can be any amino acid. This motif is likely to be functionally important and may be involved in metal binding. 59 matched cddid_all.tbl CDD pfam03746 pfam03746 461036 LamB_YcsF LamB/YcsF family. This family includes LamB. The lam locus of Aspergillus nidulans consists of two divergently transcribed genes, lamA and lamB, involved in the utilization of lactams such as 2-pyrrolidinone. Both genes are under the control of the positive regulatory gene amdR and are subject to carbon and nitrogen metabolite repression. The exact molecular function of the proteins in this family is unknown. 238 matched cddid_all.tbl CDD pfam03747 pfam03747 461037 ADP_ribosyl_GH ADP-ribosylglycohydrolase. This family includes enzymes that ADP-ribosylations, for example ADP-ribosylarginine hydrolase EC:3.2.2.19 cleaves ADP-ribose-L-arginine. The family also includes dinitrogenase reductase activating glycohydrolase. Most surprisingly the family also includes jellyfish crystallins, these proteins appear to have lost the presumed active site residues. 200 matched cddid_all.tbl CDD pfam03748 pfam03748 461038 FliL Flagellar basal body-associated protein FliL. This FliL protein controls the rotational direction of the flagella during chemotaxis. FliL is a cytoplasmic membrane protein associated with the basal body. 98 matched cddid_all.tbl CDD pfam03749 pfam03749 427486 SfsA Sugar fermentation stimulation protein RE domain. This family contains Sugar fermentation stimulation proteins. Which is probably a regulatory factor involved in maltose metabolism. SfsA has been shown to bind DNA and it contains a helix-turn-helix motif that probably binds DNA at its C-terminus. 138 matched cddid_all.tbl CDD pfam03750 pfam03750 461039 Csm2_III-A Csm2 Type III-A. Clusters of short DNA repeats with non-homologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-associated) proteins. This entry represents Csm2 Type III-A, a family of Cas proteins also known as TM1810/Csm2. 111 matched cddid_all.tbl CDD pfam03752 pfam03752 461040 ALF Short repeats of unknown function. This set of repeats is found in a small family of secreted proteins of no known function, though they are possibly involved in signal transduction. ALF stands for Alanine-rich (AL) - conserved Phenylalanine (F). 39 matched cddid_all.tbl CDD pfam03753 pfam03753 367637 HHV6-IE Human herpesvirus 6 immediate early protein. The proteins in this family are poorly characterized, but an investigation has indicated that the immediate early protein is required the down-regulation of MHC class I expression in dendritic cells. Human herpesvirus 6 immediate early protein is also referred to as U90. 964 matched cddid_all.tbl CDD pfam03754 pfam03754 281714 At2g31720-like B3 domain-containing protein At2g31720-like. This entry represents a group of uncharacterized plant proteins, including B3 domain-containing protein At2g31720 (also known as Protein AUXIN RESPONSE FACTOR 70) from Arabidopsis. These are DNA-binding proteins likely to be involved in stress response. 113 matched cddid_all.tbl CDD pfam03755 pfam03755 461041 YicC_N YicC-like family, N-terminal region. Family of bacterial proteins. Although poorly characterized, the members of this protein family have been demonstrated to play a role in stationary phase survival. These proteins are not essential during stationary phase. 155 matched cddid_all.tbl CDD pfam03756 pfam03756 461042 AfsA A-factor biosynthesis hotdog domain. The AfsA family are key enzymes in A-factor biosynthesis, which is essential for streptomycin production and resistance. This domain is distantly related to the thioester dehydratase FabZ family and therefore has a HotDog domain. 133 matched cddid_all.tbl CDD pfam03759 pfam03759 427490 PRONE PRONE (Plant-specific Rop nucleotide exchanger). This is a functional guanine exchange factor (GEF) of plant Rho GTPase. 361 matched cddid_all.tbl CDD pfam03760 pfam03760 427491 LEA_1 Late embryogenesis abundant (LEA) group 1. Family members are conserved along the entire coding region, especially within the hydrophobic internal 20 amino acid motif, which may be repeated. 71 matched cddid_all.tbl CDD pfam03761 pfam03761 367641 DUF316 Nematode trypsin-6-like family. This is a family of trypsin-6-like proteins found in nematodes that are part of the chymotrypsin family S1, ie a serine peptidase. The C. elegans sequence UniProt:O01566 is trypsin-6: all the active site residues are present (His90, Asp168, Ser267). 281 matched cddid_all.tbl CDD pfam03762 pfam03762 427492 VOMI Vitelline membrane outer layer protein I (VOMI). VOMI binds tightly to ovomucin fibrils of the egg yolk membrane. The structure that consists of three beta-sheets forming Greek key motifs, which are related by an internal pseudo three-fold symmetry. Furthermore, the structure of VOMI has strong similarity to the structure of the delta-endotoxin, as well as a carbohydrate-binding site in the top region of the common fold. 166 matched cddid_all.tbl CDD pfam03763 pfam03763 427493 Remorin_C Remorin, C-terminal region. Remorins are plant-specific plasma membrane-associated proteins. In tobacco remorin co-purifies with lipid rafts. Most remorins have a variable, proline-rich N-half and a more conserved C-half that is predicted to form coiled coils. Consistent with this, circular dichroism studies have demonstrated that much of the protein is alpha-helical. Remorins exist in plasma membrane preparations as oligomeric structures and form filaments in vitro. The proteins can bind polyanions including the extracellular matrix component oligogalacturonic acid (OGA). In vitro, remorin in plasma membrane preparations is phosphorylated (principally on threonine residues) in the presence of OGA and thus co-purifies with a protein kinases(s). The biological functions of remorins are unknown but roles as components of the membrane/cytoskeleton are possible. 106 matched cddid_all.tbl CDD pfam03764 pfam03764 397710 EFG_IV Elongation factor G, domain IV. This domain is found in elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopts a ribosomal protein S5 domain 2-like fold. 121 matched cddid_all.tbl CDD pfam03765 pfam03765 461043 CRAL_TRIO_N CRAL/TRIO, N-terminal domain. This all-alpha domain is found to the N-terminus of pfam00650. 53 matched cddid_all.tbl CDD pfam03766 pfam03766 367646 Remorin_N Remorin, N-terminal region. Remorins are plant-specific plasma membrane-associated proteins. In tobacco remorin co-purifies with lipid rafts. Most remorins have a variable, proline-rich C-half and a more conserved N-half that is predicted to form coiled coils. Consistent with this, circular dichroism studies have demonstrated that much of the protein is alpha-helical. Remorins exist in plasma membrane preparations as oligomeric structures and form filaments in vitro. The proteins can bind polyanions including the extracellular matrix component oligogalacturonic acid (OGA). In vitro, remorin in plasma membrane preparations is phosphorylated (principally on threonine residues) in the presence of OGA and thus co-purifies with a protein kinases(s). The biological functions of remorins are unknown but roles as components of the membrane/cytoskeleton are possible. 51 matched cddid_all.tbl CDD pfam03767 pfam03767 397712 Acid_phosphat_B HAD superfamily, subfamily IIIB (Acid phosphatase). This family proteins includes acid phosphatases and a number of vegetative storage proteins. 213 matched cddid_all.tbl CDD pfam03768 pfam03768 397713 Attacin_N Attacin, N-terminal region. This family includes attacin and sarcotoxin, but not diptericin (which share similarity to the C-terminal region of attacin). All members of this family are insect antibacterial proteins which are induced by the fat body and subsequently released into secreted into the hemolymph where they act synergistically to kill the invading microorganizm. 64 matched cddid_all.tbl CDD pfam03769 pfam03769 397714 Attacin_C Attacin, C-terminal region. This family includes attacin, sarcotoxin and diptericin. All members of this family are insect antibacterial proteins which are induced by the fat body and subsequently released into secreted into the hemolymph where they act synergistically to kill the invading microorganizm. 120 matched cddid_all.tbl CDD pfam03770 pfam03770 397715 IPK Inositol polyphosphate kinase. ArgRIII has has been demonstrated to be an inositol polyphosphate kinase. 190 matched cddid_all.tbl CDD pfam03771 pfam03771 367651 SPDY Domain of unknown function (DUF317). This a sequence family found in a set of bacterial proteins with no known function. This domain is currently only found in streptomyces bacteria. Most proteins contain two copies of this domain. 59 matched cddid_all.tbl CDD pfam03772 pfam03772 461044 Competence Competence protein. Members of this family are integral membrane proteins with 6 predicted transmembrane helices. Some members of this family have been shown to be essential for bacterial competence in uptake of extracellular DNA. These proteins may transport DNA across the cell membrane. These proteins contain a highly conserved motif in the amino terminal transmembrane region that has two histidines that may form a metal binding site. 269 matched cddid_all.tbl CDD pfam03773 pfam03773 281730 ArsP_1 Predicted permease. This family of integral membrane proteins are predicted to be permeases of unknown specificity. 316 matched cddid_all.tbl CDD pfam03775 pfam03775 461045 MinC_C Septum formation inhibitor MinC, C-terminal domain. In Escherichia coli Swiss:P06138 assembles into a Z ring at midcell while assembly at polar sites is prevented by the min system. MinC, a component of this system, is an inhibitor of FtsZ assembly that is positioned within the cell by interaction with MinDE. MinC is an oligomer, probably a dimer. The C terminal half of MinC is the most conserved and interacts with MinD. The N terminal half is thought interact with FtsZ. 101 matched cddid_all.tbl CDD pfam03776 pfam03776 461046 MinE Septum formation topological specificity factor MinE. The E. coli minicell locus was shown to code for three gene products (MinC, MinD, and MinE) whose coordinate action is required for proper placement of the division septum. The minE gene codes for a topological specificity factor that, in wild-type cells, prevents the division inhibitor from acting at internal division sites while permitting it to block septation at polar sites. 67 matched cddid_all.tbl CDD pfam03777 pfam03777 397719 ChpA-C ChpA-C. Small domain found in a family of secreted streptomyces proteins. It occurs singly or as a pair. Many of the domains have two cysteines that may form a disulphide bridge. This domain is found in chaplins ChpA-C (coelicolor hydrophobic aerial) proteins. ChpA-C contain a canonical C-terminal sortase signal, which is recognized by sortase enzymes that covalently couple their substrates to the peptidoglycan present in the cell wall. Indeed, direct evidence for sortase-mediated coupling of ChpC has been demonstrated, and it is expected that ChpA and ChpB are also anchored to the cell wall. 55 matched cddid_all.tbl CDD pfam03778 pfam03778 461047 DUF321 Protein of unknown function (DUF321). This family may be related to the FARP (FMRFamide) family, pfam01581. 23 matched cddid_all.tbl CDD pfam03779 pfam03779 427499 SPW SPW repeat. A short repeat found in a small family of membrane-bound proteins. This repeat contains a conserved SPW motif in the first of two transmembrane helices. 48 matched cddid_all.tbl CDD pfam03780 pfam03780 427500 Asp23 Asp23 family, cell envelope-related function. The alkaline shock protein Asp23 was identified as an alkaline shock protein that was expressed in a sigmaB-dependent manner in Staphylococcus aureus. Following an alkaline shock Asp23 accumulates in the soluble protein fraction of the S. aureus cell. Asp23 is one of the most abundant proteins in the cytosolic protein fraction of stationary S. aureus cells, with a copy-number of >25000 per cell. A second Asp23-family protein, AmaP, which is encoded within the asp23-operon, is required to localize Asp23 to the cell membrane. The overall function for the family is thus a cell envelope-related one in Gram-positive bacteria. UniProtKB:Q2FW64. 108 matched cddid_all.tbl CDD pfam03781 pfam03781 397722 FGE-sulfatase Sulfatase-modifying factor enzyme 1. This domain is found in eukaryotic proteins required for post-translational sulfatase modification (SUMF1). These proteins are associated with the rare disorder multiple sulfatase deficiency (MSD). The protein product of the SUMF1 gene is FGE, formylglycine (FGly),-generating enzyme, which is a sulfatase. Sulfatases are enzymes essential for degradation and remodelling of sulfate esters, and formylglycine (FGly), the key catalytic in the active site, is unique to sulfatases. FGE is localized to the endoplasmic reticulum (ER) and interacts with and modifies the unfolded form of newly synthesized sulfatases. FGE is a single-domain monomer with a surprising paucity of secondary structure that adopts a unique fold which is stabilized by two Ca2+ ions. The effect of all mutations found in MSD patients is explained by the FGE structure, providing a molecular basis for MSD. A redox-active disulfide bond is present in the active site of FGE. An oxidized cysteine residue, possibly cysteine sulfenic acid, has been detected that may allow formulation of a structure-based mechanism for FGly formation from cysteine residues in all sulfatases. In Mycobacteria and Treponema denticola this enzyme functions as an iron(II)-dependent oxidoreductase. 259 matched cddid_all.tbl CDD pfam03782 pfam03782 461048 AMOP AMOP domain. This domain may have a role in cell adhesion. It is called the AMOP domain after Adhesion associated domain in MUC4 and Other Proteins. This domain is extracellular and contains a number of cysteines that probably form disulphide bridges. 143 matched cddid_all.tbl CDD pfam03783 pfam03783 427502 CsgG Curli production assembly/transport component CsgG. CsgG is an outer membrane-located lipoprotein that is highly resistant to protease digestion. During curli assembly, an adhesive surface fibre, CsgG is required to maintain the stability of CsgA and CsgB. 209 matched cddid_all.tbl CDD pfam03784 pfam03784 461049 Cyclotide Cyclotide family. This family contains a set of cyclic peptides with a variety of activities. The structure consists of a distorted triple-stranded beta-sheet and a cysteine-knot arrangement of the disulfide bonds. Cyclotides can be separated into two subfamilies, namely bracelet and moebius. The bracelet cyclotide subfamily tends to contain a larger number of positively charged residues and has a bracelet-like circularization of the backbone. The moebius cyclotide subfamily contains a backbone twist due to a cis-Pro peptide bond and may conceptually be regarded as a molecular Moebius strip. 29 matched cddid_all.tbl CDD pfam03785 pfam03785 367657 Peptidase_C25_C Peptidase family C25, C terminal ig-like domain. 74 matched cddid_all.tbl CDD pfam03786 pfam03786 397726 UxuA D-mannonate dehydratase (UxuA). UxuA (this family) and UxuB are required for hexuronate degradation. 351 matched cddid_all.tbl CDD pfam03787 pfam03787 397727 RAMPs RAMP superfamily. The molecular function of these proteins is not yet known. However, they have been identified and called the RAMP (Repair Associated Mysterious Proteins) superfamily. The members of this family have no known function they are around 300 amino acids in length and have several conserved motifs. 188 matched cddid_all.tbl CDD pfam03788 pfam03788 461050 LrgA LrgA family. This family is uncharacterized. It contains the protein LrgA that has been hypothesized to export murein hydrolases. 94 matched cddid_all.tbl CDD pfam03789 pfam03789 427504 ELK ELK domain. This domain is required for the nuclear localization of these proteins. All of these proteins are members of the Tale/Knox homeodomain family, a subfamily within homeobox pfam00046. 22 matched cddid_all.tbl CDD pfam03790 pfam03790 461051 KNOX1 KNOX1 domain. The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization. 40 matched cddid_all.tbl CDD pfam03791 pfam03791 427506 KNOX2 KNOX2 domain. The MEINOX region is comprised of two domains, KNOX1 and KNOX2. KNOX1 plays a role in suppressing target gene expression. KNOX2, essential for function, is thought to be necessary for homo-dimerization. 48 matched cddid_all.tbl CDD pfam03792 pfam03792 461052 PBC PBC domain. The PBC domain is a member of the TALE (three-amino-acid loop extension) superclass of homeodomain proteins. 181 matched cddid_all.tbl CDD pfam03793 pfam03793 461053 PASTA PASTA domain. This domain is found at the C termini of several Penicillin-binding proteins and bacterial serine/threonine kinases. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. It is a small globular fold consisting of 3 beta-sheets and an alpha-helix. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain. 63 matched cddid_all.tbl CDD pfam03795 pfam03795 397734 YCII YCII-related domain. The majority of proteins in this family consist of a single copy of this domain, though it is also found as a repeat. A strongly conserved histidine and a aspartate suggest that the domain has an enzymatic function. This family also now includes the family formerly known as the DGPF domain (COG3795). Although its function is unknown it is found fused to a sigma-70 factor family domain in Swiss:Q9A8M4. Suggesting that this domain plays a role in transcription initiation (Bateman A per. obs.). This domain is named after the most conserved motif in the alignment. 94 matched cddid_all.tbl CDD pfam03796 pfam03796 427509 DnaB_C DnaB-like helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. 254 matched cddid_all.tbl CDD pfam03797 pfam03797 461054 Autotransporter Autotransporter beta-domain. Secretion of protein products occurs by a number of different pathways in bacteria. One of these pathways known as the type V pathway was first described for the IgA1 protease. The protein component that mediates secretion through the outer membrane is contained within the secreted protein itself, hence the proteins secreted in this way are called autotransporters. This family corresponds to the presumed integral membrane beta-barrel domain that transports the protein. This domain is found at the C terminus of the proteins it occurs in. The N terminus contains the variable passenger domain that is translocated across the membrane. Once the passenger domain is exported it is cleaved auto-catalytically in some proteins, in others a different protease is used and in some cases no cleavage occurs. 255 matched cddid_all.tbl CDD pfam03798 pfam03798 461055 TRAM_LAG1_CLN8 TLC domain. 200 matched cddid_all.tbl CDD pfam03799 pfam03799 461056 FtsQ_DivIB_C Cell division protein FtsQ/DivIB, C-terminal. FtsQ is an essential cell division protein. It may link together the upstream cell division proteins, which are predominantly cytoplasmic, with the downstream cell division proteins, which are predominantly periplasmic. FtsQ may control the correct divisome assembly. DivIB is a cell division protein from Gram-positive bacteria, probably homologous to Escherichia coli FtsQ. DivIB interacts with FtsL, DivIC and PBP-2B. DivIB plays an essential role in division at high temperatures, maybe by protecting FtsL from degradation or by promoting formation of the FtsL-DivIC complex. It is also required for efficient sporulation at all temperatures. FtsQ and DivIB have a short N-terminal cytoplasmic domain and a larger C-terminal periplasmic domain. This entry represents the C-terminal region. 113 matched cddid_all.tbl CDD pfam03800 pfam03800 461057 Nuf2 Nuf2 family. Members of this family are components of the mitotic spindle. It has been shown that Nuf2 from yeast is part of a complex called the Ndc80p complex. This complex is thought to bind to the microtubules of the spindle. An arabidopsis protein has been included in this family that has previously not been identified as a member of this family, Swiss:Q9C953. The match is not strong, but in common with other members of this family contains coiled-coil to the C terminus of this region. 139 matched cddid_all.tbl CDD pfam03801 pfam03801 461058 Ndc80_HEC HEC/Ndc80p family. Members of this family are components of the mitotic spindle. It has been shown that Ndc80/HEC from yeast is part of a complex called the Ndc80p complex. This complex is thought to bind to the microtubules of the spindle. 159 matched cddid_all.tbl CDD pfam03802 pfam03802 427515 CitX Apo-citrate lyase phosphoribosyl-dephospho-CoA transferase. 164 matched cddid_all.tbl CDD pfam03803 pfam03803 252175 Scramblase Scramblase. Scramblase is palmitoylated and contains a potential protein kinase C phosphorylation site. Scramblase exhibits Ca2+-activated phospholipid scrambling activity in vitro. There are also possible SH3 and WW binding motifs. Scramblase is involved in the redistribution of phospholipids after cell activation or injury. 221 matched cddid_all.tbl CDD pfam03804 pfam03804 281756 DUF325 Viral proteins of unknown function. This is a family of uncharacterized proteins from Alphabaculovirus. 73 matched cddid_all.tbl CDD pfam03805 pfam03805 427516 CLAG Cytoadherence-linked asexual protein. Clag (cytoadherence linked asexual gene) is a malaria surface protein which has been shown to be involved in the binding of Plasmodium falciparum infected erythrocytes to host endothelial cells, a process termed cytoadherence. The cytoadherence phenomenon is associated with the sequestration of infected erythrocytes in the blood vessels of the brain, cerebral malaria. Clag is a multi-gene family in Plasmodium falciparum with at least 9 members identified to date. Orthologous proteins in the rodent malaria species Plasmodium chabaudi (Lawson D Unpubl. obs.) suggest that the gene family is found in other malaria species and may play a more generic role in cytoadherence. 1285 matched cddid_all.tbl CDD pfam03806 pfam03806 397742 ABG_transport AbgT putative transporter family. 502 matched cddid_all.tbl CDD pfam03807 pfam03807 397743 F420_oxidored NADP oxidoreductase coenzyme F420-dependent. 92 matched cddid_all.tbl CDD pfam03808 pfam03808 461059 Glyco_tran_WecG Glycosyl transferase WecG/TagA/CpsF family. The WecG member of this family, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway. Also included in this group is Xanthomonas campestris pv. campestris GumM, a glycosyltransferase participating in the biosynthesis of the exopolysaccharide xanthan. 168 matched cddid_all.tbl CDD pfam03810 pfam03810 397745 IBN_N Importin-beta N-terminal domain. 72 matched cddid_all.tbl CDD pfam03811 pfam03811 281762 Zn_Tnp_IS1 InsA N-terminal domain. This appears to be a short zinc binding domain found in IS1 InsA family protein. It is found at the N-terminus of the protein and may be a DNA-binding domain. 35 matched cddid_all.tbl CDD pfam03812 pfam03812 461060 KdgT 2-keto-3-deoxygluconate permease. 298 matched cddid_all.tbl CDD pfam03813 pfam03813 461061 Nrap Nrap protein domain 1. Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localized in the nucleolus. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript. This domain has a nucleotidyltransferase structure. 144 matched cddid_all.tbl CDD pfam03814 pfam03814 461062 KdpA Potassium-transporting ATPase A subunit. 548 matched cddid_all.tbl CDD pfam03815 pfam03815 427521 LCCL LCCL domain. 96 matched cddid_all.tbl CDD pfam03816 pfam03816 427522 LytR_cpsA_psr LytR_cpsA_psr family. The entry represents a domain found in a number of LCP (LytR-Cps2A-Psr) family proteins. LCP family is also known as TagU family. LCP family proteins have been reported to be required for the synthesis of anionic cell wall polymers. 149 matched cddid_all.tbl CDD pfam03817 pfam03817 427523 MadL Malonate transporter MadL subunit. 117 matched cddid_all.tbl CDD pfam03818 pfam03818 427524 MadM Malonate/sodium symporter MadM subunit. 249 matched cddid_all.tbl CDD pfam03819 pfam03819 427525 MazG MazG nucleotide pyrophosphohydrolase domain. This domain is about 100 amino acid residues in length. It is found in the MazG protein from E. coli. It contains four conserved negatively charged residues that probably form an active site or metal binding site. This domain is found in isolation in some proteins as well as associated with pfam00590. This domain is clearly related to pfam01503 another pyrophosphohydrolase involved in histidine biosynthesis. This family may be structurally related to the NUDIX domain pfam00293 (Bateman A pers. obs.). 74 matched cddid_all.tbl CDD pfam03820 pfam03820 461063 SFXNs Sideroflexins. This family contains sideroflexin 1, 2 and 3 (SFXN1/2/3). SFXN1 is a multipass mitochondrial membrane protein and is part of the sideroflexin family of proteins conserved throughout eukaryotes. In humans, SFXN1 is highly expressed in the blood, liver, and kidney, which are tissues with high one-carbon metabolism activity. SFXN1 functions as a mitochondrial serine transporter in one-carbon metabolism. SFXN1 and SFXN3 (and perhaps SFXN2) are the main mitochondrial serine transporters in human cells and Sfxn1-3 also have this function in D. melanogaster. SFXN1 and SFXN3 likely have other physiologically relevant substrates besides serine, such as alanine or cysteine. Because SFXN1 is expressed in many cancers most highly in leukemias and lymphomas and its expression is likely regulated by the Myc transcription factor, it is suggested that it may have roles in cancer cell growth. Furthermore, Myc-binding sites were found in the promoters of SFXN1, SFXN2, and SFXN3. 319 matched cddid_all.tbl CDD pfam03821 pfam03821 461064 Mtp Golgi 4-transmembrane spanning transporter. 229 matched cddid_all.tbl CDD pfam03822 pfam03822 427528 NAF NAF domain. 56 matched cddid_all.tbl CDD pfam03823 pfam03823 461065 Neurokinin_B Neurokinin B. 58 matched cddid_all.tbl CDD pfam03824 pfam03824 397758 NicO High-affinity nickel-transport protein. High affinity nickel transporters involved in the incorporation of nickel into H2-uptake hydrogenase and urease enzymes. Essential for the expression of catalytically active hydrogenase and urease. Ion uptake is dependent on proton motive force. HoxN in Alcaligenes eutrophus is thought to be an integral membrane protein with seven transmembrane helices. The family also includes a cobalt transporter. 287 matched cddid_all.tbl CDD pfam03825 pfam03825 461066 Nuc_H_symport Nucleoside H+ symporter. 399 matched cddid_all.tbl CDD pfam03826 pfam03826 461067 OAR OAR motif. The entry represents the OAR motif. 19 matched cddid_all.tbl CDD pfam03827 pfam03827 427531 Orexin_rec2 Orexin receptor type 2. 57 matched cddid_all.tbl CDD pfam03828 pfam03828 427532 PAP_assoc Cid1 family poly A polymerase. This domain is found in poly(A) polymerases and has been shown to have polynucleotide adenylyltransferase activity. Proteins in this family have been located to both the nucleus and the cytoplasm. 60 matched cddid_all.tbl CDD pfam03829 pfam03829 427533 PTSIIA_gutA PTS system glucitol/sorbitol-specific IIA component. 113 matched cddid_all.tbl CDD pfam03830 pfam03830 461068 PTSIIB_sorb PTS system sorbose subfamily IIB component. 148 matched cddid_all.tbl CDD pfam03831 pfam03831 427535 YjdM PhnA domain. 69 matched cddid_all.tbl CDD pfam03832 pfam03832 461069 WSK WSK motif. This short motif is names after three conserved residues found in a WXSXK motif in protein kinase A anchoring proteins. 29 matched cddid_all.tbl CDD pfam03833 pfam03833 427537 PolC_DP2 DNA polymerase II large subunit DP2. 866 matched cddid_all.tbl CDD pfam03834 pfam03834 461070 Rad10 Binding domain of DNA repair protein Ercc1 (rad10/Swi10). Ercc1 and XPF (xeroderma pigmentosum group F-complementing protein) are two structure-specific endonucleases of a class of seven containing an ERCC4 domain. Together they form an obligate complex that functions primarily in nucleotide excision repair (NER), a versatile pathway able to detect and remove a variety of DNA lesions induced by UV light and environmental carcinogens, and secondarily in DNA interstrand cross-link repair and telomere maintenance. This domain in fact binds simultaneously to both XPF and single-stranded DNA; this ternary complex explains the important role of Ercc1 in targeting its catalytic XPF partner to the NER pre-incision complex. 114 matched cddid_all.tbl CDD pfam03835 pfam03835 427539 Rad4 Rad4 transglutaminase-like domain. 146 matched cddid_all.tbl CDD pfam03836 pfam03836 461071 RasGAP_C RasGAP C-terminus. This domain can be found in the C terminus of the IQGAP family members, including human IQGAP1/2/3, S. cerevisiae Iqg1 and S. pombe Rng2. Some members function in cytoskeletal remodelling. Human IQGAP1 is a scaffolding protein that can assemble multi-protein complexes involved in cell-cell interaction, cell adherence, and movement via actin/tubulin-based cytoskeletal reorganization. IQGAP1 is also a regulator of the MAPK and Wnt/beta-catenin signaling pathways.Iqg1 and Rng2 are required for actomyosin ring construction during cytokinesis. 137 matched cddid_all.tbl CDD pfam03837 pfam03837 397770 RecT RecT family. The DNA single-strand annealing proteins (SSAPs), such as RecT, Red-beta, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. This family includes proteins related to RecT. 192 matched cddid_all.tbl CDD pfam03838 pfam03838 461072 RecU Recombination protein U. 162 matched cddid_all.tbl CDD pfam03839 pfam03839 461073 Sec62 Translocation protein Sec62. 191 matched cddid_all.tbl CDD pfam03840 pfam03840 461074 SecG Preprotein translocase SecG subunit. 69 matched cddid_all.tbl CDD pfam03841 pfam03841 309101 SelA L-seryl-tRNA selenium transferase. 367 matched cddid_all.tbl CDD pfam03842 pfam03842 146463 Silic_transp Silicon transporter. 513 matched cddid_all.tbl CDD pfam03843 pfam03843 427544 Slp Outer membrane lipoprotein Slp family. 151 matched cddid_all.tbl CDD pfam03845 pfam03845 281794 Spore_permease Spore germination protein. 321 matched cddid_all.tbl CDD pfam03846 pfam03846 397775 SulA Cell division inhibitor SulA. 111 matched cddid_all.tbl CDD pfam03847 pfam03847 367691 TFIID_20kDa Transcription initiation factor TFIID subunit A. 68 matched cddid_all.tbl CDD pfam03848 pfam03848 397776 TehB Tellurite resistance protein TehB. 193 matched cddid_all.tbl CDD pfam03849 pfam03849 461075 Tfb2 Transcription factor Tfb2. 360 matched cddid_all.tbl CDD pfam03850 pfam03850 461076 Tfb4 Transcription factor Tfb4. This family appears to be distantly related to the VWA domain. 270 matched cddid_all.tbl CDD pfam03851 pfam03851 252205 UvdE UV-endonuclease UvdE. 275 matched cddid_all.tbl CDD pfam03852 pfam03852 281799 Vsr DNA mismatch endonuclease Vsr. 74 matched cddid_all.tbl CDD pfam03853 pfam03853 427546 YjeF_N YjeF-related protein N-terminus. YjeF-N domain is a novel version of the Rossmann fold with a set of catalytic residues and structural features that are different from the conventional dehydrogenases. YjeF-N domain is fused to Ribokinases in bacteria (YjeF), where they may be phosphatases, and to divergent Sm and the FDF domain in eukaryotes (Dcp3p and FLJ21128), where they may be involved in decapping and catalyze hydrolytic RNA-processing reactions. 168 matched cddid_all.tbl CDD pfam03854 pfam03854 281801 zf-P11 P-11 zinc finger. 50 matched cddid_all.tbl CDD pfam03855 pfam03855 281802 M-factor M-factor. The M-factor is a pheromone produce upon nitrogen starvation. The production of M-factor is increased by the pheromone signal. The protein undergoes post-translational modification, to remove the C-terminal signal peptide, the carboxy-terminal cysteine residue is carboxy-methylated and S-alkylated, with a farnesyl residue. 43 matched cddid_all.tbl CDD pfam03856 pfam03856 427547 SUN Beta-glucosidase (SUN family). Members of this family include Nca3, Sun4 and Sim1. This is a family of yeast proteins, involved in a diverse set of functions (DNA replication, aging, mitochondrial biogenesis and cell septation). BGLA from Candida wickerhamii has been characterized as a Beta-glucosidase EC:3.2.1.21. 244 matched cddid_all.tbl CDD pfam03857 pfam03857 367697 Colicin_im Colicin immunity protein. Colicin immunity proteins are plasmid-encoded proteins necessary for protecting the cell against colicins. Colicins are toxins released by bacteria during times of stress. 138 matched cddid_all.tbl CDD pfam03858 pfam03858 367698 Crust_neuro_H Crustacean neurohormone H. These proteins are referred to as precursor-related peptides as they are typically co-transcribed and translated with the CHH neurohormone (pfam01147). However, in some species this neuropeptide is synthesized as a separate protein. Furthermore, neurohormone H can undergo proteolysis to give rise to 5 different neuropeptides. 41 matched cddid_all.tbl CDD pfam03859 pfam03859 461077 CG-1 CG-1 domain. CG-1 domains are highly conserved domains of about 130 amino-acid residues containing a predicted bipartite NLS and named after a partial cDNA clone isolated from parsley encoding a sequence-specific DNA-binding protein. CG-1 domains are associated with CAMTA proteins (for CAlModulin -binding Transcription Activator) that are transcription factors containing a calmodulin -binding domain and ankyrins (ANK) motifs. 114 matched cddid_all.tbl CDD pfam03860 pfam03860 427549 DUF326 Domain of Unknown Function (DUF326). This family is a small cysteine-rich repeat. The cysteines mostly follow a C-X(2)-C-X(3)-C-X(2)-C-X(3) pattern, though they often appear at other positions in the repeat as well. 21 matched cddid_all.tbl CDD pfam03861 pfam03861 427550 ANTAR ANTAR domain. ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins. The majority of the domain consists of a coiled-coil. 46 matched cddid_all.tbl CDD pfam03862 pfam03862 427551 SpoVAC_SpoVAEB SpoVAC/SpoVAEB sporulation membrane protein. Members of this family are all transcribed from the spoVA operon. Bacillus and Clostridium are two well studied endospore forming bacteria. Spore formation provides a resistance mechanism in response to extreme or unfavourable environmental conditions such as heat, radiation, and chemical agents or nutrient deprivation. The reverse process termed germination takes place where spores develop into growing cells in response to nutrient availability or stress reduction. Nutrient germinant receptors (GRs) and the SpoVA proteins are important players in the germination process. In B.subtilis the SpoVAC and SpoVAEB, belonging to this domain family, are predicted to be membrane proteins, with two to five membrane spanning. Biophysical and biochemical studies suggest that SpoVAC acts as a mechano-sensitive channel with properties that would allow the release of Ca-DPA (dipicolinic acid) and amino acids during germination of the spore. The release of Ca-DPA is a crucial event during spore germination. When expressed in E.coli SpoVAC provides protection against osmotic downshift. Furthermore, SpoVAC acts as channel that facilitates the efflux down the concentration gradient of osmolytes up to a mass of at least 600 Da. Another conserved SpoVA protein in all spore-forming bacteria is SpoVAEb, which appears to be an integral membrane protein with no known function. 116 matched cddid_all.tbl CDD pfam03863 pfam03863 281809 Phage_mat-A Phage maturation protein. 446 matched cddid_all.tbl CDD pfam03864 pfam03864 427552 Phage_cap_E Phage major capsid protein E. Major capsid protein E is involved with the stabilization of the condensed form of the DNA molecule in phage heads. 335 matched cddid_all.tbl CDD pfam03865 pfam03865 461078 ShlB Haemolysin secretion/activation protein ShlB/FhaC/HecB. This family represents a group of sequences that are related to ShlB from Serratia marcescens. ShlB is an outer membrane protein pore involved in the Type Vb or Two-partner secretion system where it is functions to secrete and activate the haemolysin ShlA. The activation of ShlA occurs during secretion when ShlB imposes a conformational change in the inactive haemolysin to form the active protein. 317 matched cddid_all.tbl CDD pfam03866 pfam03866 146478 HAP Hydrophobic abundant protein (HAP). Expression of HAP is thought to be developmentally regulated and possibly involved in spherule cell wall formation. 167 matched cddid_all.tbl CDD pfam03867 pfam03867 397787 FTZ Fushi tarazu (FTZ), N-terminal region. This region contains the important motif (LXXLL) necessary for the interaction of FTZ with the nuclear receptor FTZ-F1. FTZ is thought to represents a category of LXXLL motif-dependent co-activators for nuclear receptors. 269 matched cddid_all.tbl CDD pfam03868 pfam03868 427554 Ribosomal_L6e_N Ribosomal protein L6, N-terminal domain. 60 matched cddid_all.tbl CDD pfam03869 pfam03869 397789 Arc Arc-like DNA binding domain. Arc repressor act by he cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognize bases in the major groove. 50 matched cddid_all.tbl CDD pfam03870 pfam03870 461079 RNA_pol_Rpb8 RNA polymerase Rpb8. Rpb8 is a subunit common to the three yeast RNA polymerases, pol I, II and III. Rpb8 interacts with the largest subunit Rpb1, and with Rpb3 and Rpb11, two smaller subunits. 136 matched cddid_all.tbl CDD pfam03871 pfam03871 427556 RNA_pol_Rpb5_N RNA polymerase Rpb5, N-terminal domain. Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure. This module is important for positioning the downstream DNA. 89 matched cddid_all.tbl CDD pfam03872 pfam03872 427557 RseA_N Anti sigma-E protein RseA, N-terminal domain. Sigma-E is important for the induction of proteins involved in heat shock response. RseA binds sigma-E via its N-terminal domain, sequestering sigma-E and preventing transcription from heat-shock promoters. The C-terminal domain is located in the periplasm, and may interact with other protein that signal periplasmic stress. 87 matched cddid_all.tbl CDD pfam03873 pfam03873 427558 RseA_C Anti sigma-E protein RseA, C-terminal domain. Sigma-E is important for the induction of proteins involved in heat shock response. RseA binds sigma-E via its N-terminal domain, sequestering sigma-E and preventing transcription from heat-shock promoters. The C-terminal domain is located in the periplasm, and may interact with other protein that signal periplasmic stress. 53 matched cddid_all.tbl CDD pfam03874 pfam03874 461080 RNA_pol_Rpb4 RNA polymerase Rpb4. This family includes the Rpb4 protein. This family also includes C17 (aka CGRP-RCP) is an essential subunit of RNA polymerase III. C17 forms a subcomplex with C25 which is likely to be the counterpart of subcomplex Rpb4/7 in Pol II. 115 matched cddid_all.tbl CDD pfam03875 pfam03875 397795 Statherin Statherin. Statherin functions biologically to inhibit the nucleation and growth of calcium phosphate minerals. The N-terminus of statherin is highly charge, the glutamic acids of which have been shown to be important in the recognition hydroxyapatite. 41 matched cddid_all.tbl CDD pfam03876 pfam03876 427560 SHS2_Rpb7-N SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397. Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction. 57 matched cddid_all.tbl CDD pfam03878 pfam03878 461081 YIF1 YIF1. YIF1 (Yip1 interacting factor) is an integral membrane protein that is required for membrane fusion of ER derived vesicles. It also plays a role in the biogenesis of ER derived COPII transport vesicles. 243 matched cddid_all.tbl CDD pfam03879 pfam03879 427562 Cgr1 Cgr1 family. Members of this family are coiled-coil proteins that are involved in pre-rRNA processing. 107 matched cddid_all.tbl CDD pfam03880 pfam03880 461082 DbpA DbpA RNA binding domain. This RNA binding domain is found at the C-terminus of a number of DEAD helicase proteins. It is sufficient to confer specificity for hairpin 92 of 23S rRNA, which is part of the ribosomal A-site. However, several members of this family lack specificity for 23S rRNA. These can proteins can generally be distinguished by a basic region that extends beyond this domain [Karl Kossen, unpublished data]. 72 matched cddid_all.tbl CDD pfam03881 pfam03881 427564 Fructosamin_kin Fructosamine kinase. This family includes eukaryotic fructosamine-3-kinase enzymes. The family also includes bacterial members that have not been characterized but probably have a similar or identical function. 288 matched cddid_all.tbl CDD pfam03882 pfam03882 397801 KicB MukF winged-helix domain. The kicA and kicB genes are found upstream of mukB. It has been suggested that the kicB gene encodes a killing factor and the kicA gene codes for a protein that suppresses the killing function of the kicB gene product. It was also demonstrated that KicA and KicB can function as a post-segregational killing system, when the genes are transferred from the E. coli chromosome onto a plasmid. 115 matched cddid_all.tbl CDD pfam03883 pfam03883 461083 H2O2_YaaD Peroxide stress protein YaaA. YaaA is a key element of the stress response to H2O2. It acts by reducing the level of intracellular iron levels after peroxide stress, thereby attenuating the Fenton reaction and the DNA damage that this would cause. The molecular mechanism of action is not known. 233 matched cddid_all.tbl CDD pfam03884 pfam03884 427566 YacG DNA gyrase inhibitor YacG. YacG inhibits all the catalytic activities of DNA gyrase by preventing its interaction with DNA. It acts by binding directly to the C-terminal domain of GyrB, which probably disrupts DNA binding by the gyrase. YacG has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins. The conserved four cysteine motif in this protein (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures. 48 matched cddid_all.tbl CDD pfam03885 pfam03885 461084 DUF327 Protein of unknown function (DUF327). The proteins in this family are around 140-170 residues in length. The proteins contain many conserved residues. with the most conserved motifs found in the central and C-terminal region. The function of these proteins is unknown. 141 matched cddid_all.tbl CDD pfam03886 pfam03886 427568 ABC_trans_aux ABC-type transport auxiliary lipoprotein component. ABC_trans_aux is a family of bacterial proteins that act as auxiliarires to the ABC-transporter in the gamma-hexachlorocyclohexane uptake permease system in Sphingobium japonicum. Gamma-hexachlorocyclohexane, or Lindane, can be used as the sole source of carbon in S.japonicum in aerobic conditions. Lindane is an insecticide. 155 matched cddid_all.tbl CDD pfam03887 pfam03887 427569 YfbU YfbU domain. This presumed domain is about 160 residues long. It is found in archaebacteria and eubacteria. In Swiss:Q9EUM2 it is associated with a helix-turn-helix domain. This suggests that this may be a ligand binding domain. 165 matched cddid_all.tbl CDD pfam03888 pfam03888 427570 MucB_RseB MucB/RseB N-terminal domain. Members of this family are regulators of the anti-sigma E protein RseD. 178 matched cddid_all.tbl CDD pfam03889 pfam03889 427571 ArfA Alternative ribosome-rescue factor A. During translation of messenger RNAs by ribosomes, translation sometimes pauses or stalls. Ribosomes stalled on mRNAs need to be rescued for reuse in order to maintain proper translation capacity. Rescue systems such as ArfA-RF2 and ArfB (formerly known as YaeJ) are present in many bacterial species. Family members such as ArfA cooperates with the canonical peptide release factor RF2 to hydrolyse the peptidyl-tRNA in the non-stop complex. Structural and biochemical analysis show that ArfA anchors its positively charged C-terminal in the mRNA entry channel of the ribosome. Whereas its N terminus is sandwiched between the decoding centre and the switch loop of RF2, leading to marked conformational changes in both the decoding centre and RF2 thereby triggering RF2 peptidyl-hydrolysing activity. 44 matched cddid_all.tbl CDD pfam03891 pfam03891 427572 DUF333 Domain of unknown function (DUF333). This small domain of about 70 residues is found in a number of bacterial proteins. It is found at the N-terminus the of Swiss:O28332 protein. The proteins containing this domain are uncharacterized. 46 matched cddid_all.tbl CDD pfam03892 pfam03892 427573 NapB Nitrate reductase cytochrome c-type subunit (NapB). The napB gene encodes a dihaem cytochrome c, the small subunit of a heterodimeric periplasmic nitrate reductase. 122 matched cddid_all.tbl CDD pfam03893 pfam03893 427574 Lipase3_N Lipase 3 N-terminal region. N terminal region to pfam01764, found on a subset of Lipase 3 containing proteins. 75 matched cddid_all.tbl CDD pfam03894 pfam03894 427575 XFP D-xylulose 5-phosphate/D-fructose 6-phosphate phosphoketolase. Bacterial enzyme splits fructose-6-P and/or xylulose-5-P with the aid of inorganic phosphate into either acetyl-P and erythrose-4-P and/or acetyl-P and glyeraldehyde-3-P EC:4.1.2.9, EC:4.1.2.22. This family is distantly related to transketolases e.g. pfam02779. 176 matched cddid_all.tbl CDD pfam03895 pfam03895 427576 YadA_anchor YadA-like membrane anchor domain. This region represents the C-terminal 120 amino acids of a family of surface-exposed bacterial proteins. YadA, an adhesin from Yersinia, was the first member of this family to be characterized. UspA2 from Moraxella was second. The Eib immunoglobulin-binding proteins from E. coli were third, followed by the DsrA proteins of Haemophilus ducreyi and others. These proteins are homologous at their C-terminal and have predicted signal sequences, but they diverge elsewhere. The C-terminal 9 amino acids, consisting of alternating hydrophobic amino acids ending in F or W, comprise a targeting motif for the outer membrane of the Gram negative cell envelope. This region is important for oligomerization. 60 matched cddid_all.tbl CDD pfam03896 pfam03896 461085 TRAP_alpha Translocon-associated protein (TRAP), alpha subunit. The alpha-subunit of the TRAP complex (TRAP alpha) is a single-spanning membrane protein of the endoplasmic reticulum (ER) which is found in proximity of nascent polypeptide chains translocating across the membrane. 279 matched cddid_all.tbl CDD pfam03898 pfam03898 146498 TNV_CP Satellite tobacco necrosis virus coat protein. 198 matched cddid_all.tbl CDD pfam03899 pfam03899 461086 ATP-synt_I ATP synthase I chain. The atp operon of alkaliphilic Bacillus pseudofirmus OF4, as in most prokaryotes, contains the eight structural genes for the F-ATPase (ATP synthase), which are preceded by an atpI gene that encodes a membrane protein with 2 TMSs. A tenth gene, atpZ, has been found in this operon, which is upstream of and overlapping with atpI. AtpI is a Ca2+/Mg2+ transporter. 99 matched cddid_all.tbl CDD pfam03900 pfam03900 461087 Porphobil_deamC Porphobilinogen deaminase, C-terminal domain. 72 matched cddid_all.tbl CDD pfam03901 pfam03901 281842 Glyco_transf_22 Alg9-like mannosyltransferase family. Members of this family are mannosyltransferase enzymes. At least some members are localized in endoplasmic reticulum and involved in GPI anchor biosynthesis. 414 matched cddid_all.tbl CDD pfam03902 pfam03902 397816 Gal4_dimer Gal4-like dimerization domain. 44 matched cddid_all.tbl CDD pfam03903 pfam03903 397817 Phage_T4_gp36 Phage T4 tail fibre. Irreversible binding of T-even bacteriophages to Escherichia coli is mediated by the short and long tail fibres, important for DNA injection. Long tail fibres consist of a phage-proximal (gp34) and a phage-distal rod, the latter containing two protein trimers (gp36 and gp37). Gp36 is present in the upper part of the distal rod, it forms a complex with gp35 and gp37, binding them through the N-terminal and C-terminal regions, respectively. The upper part of the distal rod has a beta-structure. 131 matched cddid_all.tbl CDD pfam03904 pfam03904 461088 DUF334 Domain of unknown function (DUF334). Staphylococcus aureus plasmid proteins with no characterized function. 121 matched cddid_all.tbl CDD pfam03905 pfam03905 146503 Corona_NS4 Coronavirus non-structural protein NS4. 45 matched cddid_all.tbl CDD pfam03906 pfam03906 427579 Phage_T7_tail Phage T7 tail fibre protein. The bacteriophage T7 tail complex consists of a conical tail-tube surrounded by six kinked tail-fibres, which are oligomers of the viral protein gp17. 157 matched cddid_all.tbl CDD pfam03907 pfam03907 427580 Spo7 Spo7-like protein. S. cerevisiae Spo7 has an unknown function, but has a role in formation of a spherical nucleus and meiotic division. 205 matched cddid_all.tbl CDD pfam03908 pfam03908 112708 Sec20 Sec20. Sec20 is a membrane glycoprotein associated with secretory pathway. 92 matched cddid_all.tbl CDD pfam03909 pfam03909 461089 BSD BSD domain. This domain contains a distinctive -FW- motif. It is found in a family of eukaryotic transcription factors as well as a set of proteins of unknown function. 55 matched cddid_all.tbl CDD pfam03910 pfam03910 367721 Adeno_PV Adenovirus minor core protein PV. 355 matched cddid_all.tbl CDD pfam03911 pfam03911 427582 Sec61_beta Sec61beta family. This family consists of homologs of Sec61beta - a component of the Sec61/SecYEG protein secretory system. The domain is found in eukaryotes and archaea and is possibly homologous to the bacterial SecG. It consists of a single putative transmembrane helix, preceded by a short stretch containing various charged residues; this arrangement may help determine orientation in the cell membrane. 38 matched cddid_all.tbl CDD pfam03912 pfam03912 427583 Psb28 Psb28 protein. Psb28 is a 13 kDa soluble protein that is directly assembled in dimeric PSII supercomplexes. The negatively charged N-terminal region is essential for this process. This protein was formerly known as PsbW, but PsbW is now reserved for pfam07123. 106 matched cddid_all.tbl CDD pfam03913 pfam03913 112713 Ragweed_pollen Ragweed group 5 pollen allergen. This family contains several ragweed allergens including Amb a 5, Amb t 5 and Amb p 5. 44 matched cddid_all.tbl CDD pfam03914 pfam03914 461090 CBF CBF/Mak21 family. 151 matched cddid_all.tbl CDD pfam03915 pfam03915 427585 AIP3 Actin interacting protein 3. 407 matched cddid_all.tbl CDD pfam03916 pfam03916 397824 NrfD Polysulphide reductase, NrfD. NrfD is an integral transmembrane protein with loops in both the periplasm and the cytoplasm. NrfD is thought to participate in the transfer of electrons, from the quinone pool into the terminal components of the Nrf pathway. 313 matched cddid_all.tbl CDD pfam03917 pfam03917 461091 GSH_synth_ATP Eukaryotic glutathione synthase, ATP binding domain. 465 matched cddid_all.tbl CDD pfam03918 pfam03918 461092 CcmH Cytochrome C biogenesis protein. Members of this family include NrfF, CcmH, CycL, Ccl2. 143 matched cddid_all.tbl CDD pfam03919 pfam03919 461093 mRNA_cap_C mRNA capping enzyme, C-terminal domain. 108 matched cddid_all.tbl CDD pfam03920 pfam03920 461094 TLE_N Groucho/TLE N-terminal Q-rich domain. The N-terminal domain of the Grouch/TLE co-repressor proteins are involved in oligomerization. 117 matched cddid_all.tbl CDD pfam03921 pfam03921 397829 ICAM_N Intercellular adhesion molecule (ICAM), N-terminal domain. ICAMs normally functions to promote intercellular adhesion and signalling. However, The N-terminal domain of the receptor binds to the rhinovirus 'canyon' surrounding the icosahedral 5-fold axes, during the viral attachment process. This family is a family that is part of the Ig superfamily and is therefore related to the family ig (pfam00047). 86 matched cddid_all.tbl CDD pfam03922 pfam03922 397830 OmpW OmpW family. This family includes outer membrane protein W (OmpW) proteins from a variety of bacterial species. This protein may form the receptor for S4 colicins in E. coli. 193 matched cddid_all.tbl CDD pfam03923 pfam03923 427590 Lipoprotein_16 Uncharacterized lipoprotein. The function of this presumed lipoprotein is unknown. The family includes E. coli YajG. 149 matched cddid_all.tbl CDD pfam03924 pfam03924 427591 CHASE CHASE domain. This domain is found in the extracellular portion of receptor-like proteins - such as serine/threonine kinases and adenylyl cyclases. This is a ligand-binding domain that binds cytokinin (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 184 matched cddid_all.tbl CDD pfam03925 pfam03925 427592 SeqA SeqA protein C-terminal domain. The binding of SeqA protein to hemimethylated GATC sequences is important in the negative modulation of chromosomal initiation at oriC, and in the formation of SeqA foci necessary for Escherichia coli chromosome segregation. SeqA tetramers are able to aggregate or multimerize in a reversible, concentration-dependent manner. Apart from its function in the control of DNA replication, SeqA may also be a specific transcription factor. 110 matched cddid_all.tbl CDD pfam03927 pfam03927 427593 NapD NapD protein. Uncharacterized protein involved in formation of periplasmic nitrate reductase. 71 matched cddid_all.tbl CDD pfam03928 pfam03928 461095 HbpS-like Haem degrading protein HbpS-like. This entry includes haem degrading protein HbpS from Streptomyces reticuli (swiss:Q9RIM2) and and GlcG from Escherichia coli. HbpS is up-regulated in response to haemin- and peroxide-based oxidative stress. It interacts with the SenS/SenR two-component signal transduction system. Iron binds to surface-exposed lysine residues of an octomeric assembly of the protein. The structure of GlcG is composed of an alpha-beta(2)-alpha(3)-beta(2)-alpha fold, similar to the Roadblock/LC7 domain. 116 matched cddid_all.tbl CDD pfam03929 pfam03929 427595 PepSY_TM PepSY-associated TM region. The PepSY_TM family is so named because it is an alignment of up to five transmembranes helices found in bacterial species some of which carry a nested PepSY domain, pfam03413. 355 matched cddid_all.tbl CDD pfam03930 pfam03930 397837 Flp_N Recombinase Flp protein N-terminus. 82 matched cddid_all.tbl CDD pfam03931 pfam03931 397838 Skp1_POZ Skp1 family, tetramerization domain. 60 matched cddid_all.tbl CDD pfam03932 pfam03932 427596 CutC CutC family. Copper transport in Escherichia coli is mediated by the products of at least six genes, cutA, cutB, cutC, cutD, cutE, and cutF. A mutation in one or more of these genes results in an increased copper sensitivity. Members of this family are between 200 and 300 amino acids in length are found in both eukaryotes and bacteria. 201 matched cddid_all.tbl CDD pfam03934 pfam03934 427597 T2SSK Type II secretion system (T2SS), protein K. Members of this family are involved in the Type II protein secretion system. The T2SK family includes proteins such as ExeK, PulK, OutX and XcpX. 283 matched cddid_all.tbl CDD pfam03935 pfam03935 397841 SKN1_KRE6_Sbg1 Beta-glucan synthesis-associated protein SKN1/KRE6/Sbg1. This family consists of the beta-glucan synthesis-associated proteins KRE6, SKN1 and Sbg1. Beta1,6-Glucan is a key component of the yeast cell wall, interconnecting cell wall proteins, beta1,3-glucan, and chitin. SKN1 and KRE6 show similarities to glycoside hydrolase family 16 glycoside hydrolases, suggesting that they are glycosyl hydrolases or transglycosylases. They are related with the synthesis and anchorage of cell wall proteins of glucan polymers of the yeast cell wall, although they play redundant roles. SKN1, KRE6 and Sbg1 share the SKN1 domain which is conserved in SKN1 and KRE6 proteins of many fungal species. Sbg1 is an integral membrane protein essential for contractile-ring constriction and septum formation during cytokinesis, which interacts with the conserved beta-glucan synthase Bgs1 and regulates its protein levels ans localization. 500 matched cddid_all.tbl CDD pfam03936 pfam03936 461096 Terpene_synth_C Terpene synthase family, metal binding domain. It has been suggested that this gene family be designated tps (for terpene synthase). It has been split into six subgroups on the basis of phylogeny, called tpsa-tpsf. tpsa includes vetispiridiene synthase, 5-epi- aristolochene synthase, and (+)-delta-cadinene synthase. tpsb includes (-)-limonene synthase. tpsc includes kaurene synthase A. tpsd includes taxadiene synthase, pinene synthase, and myrcene synthase. tpse includes kaurene synthase B. tpsf includes linalool synthase. 266 matched cddid_all.tbl CDD pfam03937 pfam03937 461097 Sdh5 Flavinator of succinate dehydrogenase. This family includes the highly conserved mitochondrial and bacterial proteins Sdh5/SDHAF2/SdhE. Both yeast and human Sdh5/SDHAF2 interact with the catalytic subunit of the succinate dehydrogenase (SDH) complex, a component of both the electron transport chain and the tricarboxylic acid cycle. Sdh5 is required for SDH-dependent respiration and for Sdh1 flavination (incorporation of the flavin adenine dinucleotide cofactor). Mutational inactivation of Sdh5 confers tumor susceptibility in humans. Bacterial homologs of Sdh5, termed SdhE, are functionally conserved being required for the flavinylation of SdhA and succinate dehydrogenase activity. Like Sdh5, SdhE interacts with SdhA. Furthermore, SdhE was characterized as a FAD co-factor chaperone that directly binds FAD to facilitate the flavinylation of SdhA. Phylogenetic analysis demonstrates that SdhE/Sdh5 proteins evolved only once in an ancestral alpha-proteobacteria prior to the evolution of the mitochondria and now remain in subsequent descendants including eukaryotic mitochondria and the alpha, beta and gamma proteobacteria. This family was previously annotated in Pfam as being a divergent TPR repeat but structural evidence has indicated this is not true. The E. coli protein, YgfY also acts as the antitoxin to the membrane-bound toxin family Cpta, pfam13166, whose E. coli member YgfX, expressed from the same operon as YgfY. 76 matched cddid_all.tbl CDD pfam03938 pfam03938 461098 OmpH Outer membrane protein (OmpH-like). This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery. 140 matched cddid_all.tbl CDD pfam03939 pfam03939 461099 Ribosomal_L23eN Ribosomal protein L23, N-terminal domain. The N-terminal domain appears to be specific to the eukaryotic ribosomal proteins L25, L23, and L23a. 50 matched cddid_all.tbl CDD pfam03940 pfam03940 281873 MSSP Male specific sperm protein. This family of drosophila proteins are typified by the repetitive motif C-G-P. 51 matched cddid_all.tbl CDD pfam03941 pfam03941 461100 INCENP_ARK-bind Inner centromere protein, ARK binding region. This region of the inner centromere protein has been found to be necessary and sufficient for binding to aurora-related kinase. This interaction has been implicated in the coordination of chromosome segregation with cell division in yeast. 53 matched cddid_all.tbl CDD pfam03942 pfam03942 461101 DTW DTW domain. This presumed domain is found in bacterial and eukaryotic proteins. Its function is unknown. The domain contains multiple conserved motifs including a DTXW motif that this domain has been named after. 195 matched cddid_all.tbl CDD pfam03943 pfam03943 461102 TAP_C TAP C-terminal domain. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for nuclear export of mRNA. Tap has a modular structure, and its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling. The structure of the C-terminal domain is composed of four helices. The structure is related to the UBA domain. 49 matched cddid_all.tbl CDD pfam03944 pfam03944 397849 Endotoxin_C delta endotoxin. This family contains insecticidal toxins produced by Bacillus species of bacteria. During spore formation the bacteria produce crystals of this protein. When an insect ingests these proteins they are activated by proteolytic cleavage. The N terminus is cleaved in all of the proteins and a C terminal extension is cleaved in some members. Once activated the endotoxin binds to the gut epithelium and causes cell lysis leading to death. This activated region of the delta endotoxin is composed of three structural domains. The N-terminal helical domain is involved in membrane insertion and pore formation. The second and third domains are involved in receptor binding. 142 matched cddid_all.tbl CDD pfam03945 pfam03945 397850 Endotoxin_N delta endotoxin, N-terminal domain. This family contains insecticidal toxins produced by Bacillus species of bacteria. During spore formation the bacteria produce crystals of this protein. When an insect ingests these proteins they are activated by proteolytic cleavage. The N terminus is cleaved in all of the proteins and a C terminal extension is cleaved in some members. Once activated the endotoxin binds to the gut epithelium and causes cell lysis leading to death. This activated region of the delta endotoxin is composed of three structural domains. The N-terminal helical domain is involved in membrane insertion and pore formation. The second and third domains are involved in receptor binding. 218 matched cddid_all.tbl CDD pfam03946 pfam03946 461103 Ribosomal_L11_N Ribosomal protein L11, N-terminal domain. The N-terminal domain of Ribosomal protein L11 adopts an alpha/beta fold and is followed by the RNA binding C-terminal domain. 58 matched cddid_all.tbl CDD pfam03947 pfam03947 427606 Ribosomal_L2_C Ribosomal Proteins L2, C-terminal domain. 123 matched cddid_all.tbl CDD pfam03948 pfam03948 461104 Ribosomal_L9_C Ribosomal protein L9, C-terminal domain. 86 matched cddid_all.tbl CDD pfam03949 pfam03949 427608 Malic_M Malic enzyme, NAD binding domain. 257 matched cddid_all.tbl CDD pfam03950 pfam03950 427609 tRNA-synt_1c_C tRNA synthetases class I (E and Q), anti-codon binding domain. Other tRNA synthetase sub-families are too dissimilar to be included. This family includes only glutamyl and glutaminyl tRNA synthetases. In some organizms, a single glutamyl-tRNA synthetase aminoacylates both tRNA(Glu) and tRNA(Gln). 175 matched cddid_all.tbl CDD pfam03951 pfam03951 427610 Gln-synt_N Glutamine synthetase, beta-Grasp domain. 82 matched cddid_all.tbl CDD pfam03952 pfam03952 461105 Enolase_N Enolase, N-terminal domain. 131 matched cddid_all.tbl CDD pfam03953 pfam03953 397858 Tubulin_C Tubulin C-terminal domain. This family includes the tubulin alpha, beta and gamma chains. Members of this family are involved in polymer formation. Tubulins are GTPases. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. Tubulin is the major component of microtubules. (The FtsZ GTPases have been split into their won family). 125 matched cddid_all.tbl CDD pfam03954 pfam03954 461106 Lectin_N Hepatic lectin, N-terminal domain. This is the N-terminal domain found in hepatic lectins, also known as Asialoglycoprotein receptors (ASGRs). ASGRs function as scavengers to mediate the endocytosis of plasma glycoproteins with terminal galactose and N-acetylgalactosamine units. ASGR is composed of a major (ASGR1) and a minor (ASGR2) subunits, both of which are type II, single-pass transmembrane proteins. ASGR is highly expressed in liver but has been also identified in human peripheral blood monocytes, representing a mobile pool of the receptor reaching distant sites from the liver to play a scavenger function where there is an infection or a damaged tissue. This domain includes the short, single transmembrane domain and the stalk region which mediates the oligomerization between subunits. 140 matched cddid_all.tbl CDD pfam03955 pfam03955 461107 Adeno_PIX Adenovirus hexon-associated protein (IX). Hexon (PF01065) is the major coat protein from adenovirus type 2. Hexon forms a homo-trimer. The 240 copies of the hexon trimer are organized so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX. 110 matched cddid_all.tbl CDD pfam03956 pfam03956 427613 Lys_export Lysine exporter LysO. Members of this family contain a conserved core of four predicted transmembrane segments. Some members have an additional pair of N-terminal transmembrane helices. This family includes lysine exporter LysO (YbjE) from E. coli. 190 matched cddid_all.tbl CDD pfam03957 pfam03957 461108 Jun Jun-like transcription factor. 231 matched cddid_all.tbl CDD pfam03958 pfam03958 461109 Secretin_N Bacterial type II/III secretion system short domain. This is a short, often repeated, domain found in bacterial type II/III secretory system proteins. All previous NolW-like domains fall into this family. 68 matched cddid_all.tbl CDD pfam03959 pfam03959 461110 FSH1 Serine hydrolase (FSH1). This is a family of serine hydrolases. 208 matched cddid_all.tbl CDD pfam03960 pfam03960 427617 ArsC ArsC family. This family is related to glutaredoxins pfam00462. 109 matched cddid_all.tbl CDD pfam03961 pfam03961 461111 FapA Flagellar Assembly Protein A beta solenoid domain. This entry represents the C-terminal beta solenoid domain of FapA and its homologs. Members of this family include FapA (flagellar assembly protein A) found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction. This entry shows similarity to pfam03775 suggesting a similar functional role. 272 matched cddid_all.tbl CDD pfam03962 pfam03962 461112 Mnd1 Mnd1 HTH domain. This family of proteins includes MND1 from S. cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair. 60 matched cddid_all.tbl CDD pfam03963 pfam03963 427619 FlgD Flagellar hook capping protein - N-terminal region. FlgD is known to be absolutely required for hook assembly, yet it has not been detected in the mature flagellum. It appears to act as a hook-capping protein to enable assembly of hook protein subunits. FlgD regulates the assembly of the hook cap structure to prevent leakage of hook monomers into the medium and hook monomer polymerization and also plays a role in determination of the correct hook length, with the help of the FliK protein. This family represents the N-terminal conserved region of FlgD. A recent crystal structure showed that this region was likely to be flexible and was cleaved off during crystallization. 75 matched cddid_all.tbl CDD pfam03964 pfam03964 461113 Chorion_2 Chorion family 2. The chorion genes of Drosophila are amplified in response to developmental signals in the follicle cells of the ovary. 129 matched cddid_all.tbl CDD pfam03965 pfam03965 427620 Penicillinase_R Penicillinase repressor. The penicillinase repressor negatively regulates expression of the penicillinase gene. The N-terminal region of this protein is involved in operator recognition, while the C-terminal is responsible for dimerization of the protein. 115 matched cddid_all.tbl CDD pfam03966 pfam03966 397869 Trm112p Trm112p-like protein. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. Trm112p is required for tRNA methylation in S. cerevisiae and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices. 44 matched cddid_all.tbl CDD pfam03967 pfam03967 397870 PRCH Photosynthetic reaction centre, H-chain N-terminal region. The family corresponds the N-terminal cytoplasmic domain. 133 matched cddid_all.tbl CDD pfam03968 pfam03968 427621 LptD_N LptA/(LptD N-terminal domain) LPS transport protein. This family of proteins are involved in lipopolysaccharide transport across the gram negative inner and outer membranes. The type examples for this family are E. coli LptA and the N-terminal domain of LptD. 113 matched cddid_all.tbl CDD pfam03969 pfam03969 397872 AFG1_ATPase AFG1-like ATPase. This P-loop motif-containing family of proteins includes AFG1, LACE1 and ZapE. ATPase family gene 1 (AFG1) is a 377 amino acid yeast protein with an ATPase motif typical of the family. LACE1, the mammalian homolog of AFG1, is a mitochondrial integral membrane protein that is essential for maintenance of fused mitochondrial reticulum and lamellar cristae morphology. It has also been demonstrated that LACE1 mediates degradation of nuclear-encoded complex IV subunits COX4 (cytochrome c oxidase 4), COX5A and COX6A, and is required for normal activity of complexes III and IV of the respiratory chain. ZapE is a cell division protein found in Gram-negative bacteria. The bacterial cell division process relies on the assembly, positioning, and constriction of FtsZ ring (the so-called Z-ring), a ring-like network that marks the future site of the septum of bacterial cell division. ZapE is a Z-ring associated protein required for cell division under low-oxygen conditions. It is an ATPase that appears at the constricting Z-ring late in cell division. It reduces the stability of FtsZ polymers in the presence of ATP in vitro. 361 matched cddid_all.tbl CDD pfam03970 pfam03970 281903 Herpes_UL37_1 Herpesvirus UL37 tegument protein. UL37 interacts with UL36, which is thought to be an important early step in tegumentation during virion morphogenesis in the cytoplasm. 267 matched cddid_all.tbl CDD pfam03971 pfam03971 461114 IDH Monomeric isocitrate dehydrogenase. NADP(+)-dependent isocitrate dehydrogenase (ICD) is an important enzyme of the intermediary metabolism, as it controls the carbon flux within the citric acid cycle and supplies the cell with 2-oxoglutarate EC:1.1.1.42 and NADPH for biosynthetic purposes. 733 matched cddid_all.tbl CDD pfam03972 pfam03972 461115 MmgE_PrpD MmgE/PrpD N-terminal domain. This entry represents the N-terminal domain of 2-methylcitrate dehydratase EC:4.2.1.79 (PrpD) that is required for propionate catabolism. It catalyzes the third step of the 2-methylcitric acid cycle. 244 matched cddid_all.tbl CDD pfam03973 pfam03973 397875 Triabin Triabin. Triabin is a serine-protease inhibitor with a calycin fold. 147 matched cddid_all.tbl CDD pfam03974 pfam03974 427624 Ecotin Ecotin. Ecotin is a broad range serine protease inhibitor, which forms homodimers. The C-terminal region contains the dimerization motif. Interestingly, the binding sites show a fluidity of protein contacts binding sites show a fluidity of protein contacts derived from ecotin's innate flexibility in fitting itself to proteases while. 122 matched cddid_all.tbl CDD pfam03975 pfam03975 461116 CheD CheD chemotactic sensory transduction. This chemotaxis protein stimulates methylation of MCP proteins. The chemotaxis machinery of Bacillus subtilis is similar to that of the well characterized system of Escherichia coli. However, B. subtilis contains several chemotaxis genes not found in the E. coli genome, such as CheC and CheD, indicating that the B. subtilis chemotactic system is more complex. CheD plays an important role in chemotactic sensory transduction for many organizms. CheD deamidates other B. subtilis chemoreceptors including McpB and McpC. Deamidation by CheD is required for B. subtilis chemoreceptors to effectively transduce signals to the CheA kinase. The structure of a complex between the signal-terminating phosphatase, CheC, and the receptor-modifying deamidase, CheD, reveals how CheC mimics receptor substrates to inhibit CheD and how CheD stimulates CheC phosphatase activity. CheD resembles other cysteine deamidases from bacterial pathogens that inactivate host Rho-GTPases. Phospho-CheY, the intracellular signal and CheC target, stabilizes the CheC-CheD complex and reduces availability of CheD. A model is proposed whereby CheC acts as a CheY-P-induced regulator of CheD; CheY-P would cause CheC to sequester CheD from the chemoreceptors, inducing adaptation of the chemotaxis system. 106 matched cddid_all.tbl CDD pfam03976 pfam03976 397878 PPK2 Polyphosphate kinase 2 (PPK2). Inorganic polyphosphate (polyP) plays a role in metabolism and regulation and has been proposed to serve as a energy source in a pre-ATP world. In prokaryotes, the synthesis and utilization of polyP are catalyzed by PPK1, PPK2 and polyphosphatases. Proteins with a single PPK2 domain catalyze polyP-dependent phosphorylation of ADP to ATP, whereas proteins containing 2 fused PPK2 domains phosphorylate AMP to ADP. The structure of PPK2 from Pseudomonas aeruginosa has revealed a a 3-layer alpha/beta/alpha sandwich fold with an alpha-helical lid similar to the structures of microbial thymidylate kinases. 229 matched cddid_all.tbl CDD pfam03977 pfam03977 427626 OAD_beta Na+-transporting oxaloacetate decarboxylase beta subunit. Members of this family are integral membrane proteins. The decarboxylation reactions they catalyze are coupled to the vectorial transport of Na+ across the cytoplasmic membrane, thereby creating a sodium ion motive force that is used for ATP synthesis. 344 matched cddid_all.tbl CDD pfam03978 pfam03978 397880 Borrelia_REV Borrelia burgdorferi REV protein. This family consists of several REV proteins from Borrelia burgdorferi (Lyme disease spirochete). The function of REV is unknown although it known that gene is induced during the ingesting of host blood suggesting a role in the metabolic activation of borreliae to adapt to physiological stimuli. 157 matched cddid_all.tbl CDD pfam03979 pfam03979 461117 Sigma70_r1_1 Sigma-70 factor, region 1.1. Region 1.1 modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase. Region 1.1 is also involved in promoter binding 69 matched cddid_all.tbl CDD pfam03980 pfam03980 461118 Nnf1 Nnf1. NNF1 is an essential yeast gene that is necessary for chromosome segregation. It is associated with the spindle poles and forms part of a kinetochore subcomplex called MIND. 103 matched cddid_all.tbl CDD pfam03981 pfam03981 461119 Ubiq_cyt_C_chap Ubiquinol-cytochrome C chaperone. 137 matched cddid_all.tbl CDD pfam03982 pfam03982 112781 DAGAT Diacylglycerol acyltransferase. The terminal step of triacylglycerol (TAG) formation is catalyzed by the enzyme diacylglycerol acyltransferase (DAGAT). 297 matched cddid_all.tbl CDD pfam03983 pfam03983 427630 SHD1 SLA1 homology domain 1, SHD1. NPFXD peptides specifically interact with the SHD1 domain. NPFXD is a clathrin-facilitated endocytic targeting signal. NPFXD was originally discovered in the cytoplasmic domain of the furin-like protease Kex2p. Sla1 is thought to function as an endocytic adaptor. 67 matched cddid_all.tbl CDD pfam03984 pfam03984 367755 DUF346 Repeat of unknown function (DUF346). This repeat was found as seven tandem copies in one protein. It is predicted to be composed of beta-strands. Thus it is likely that it forms a beta-propeller structure. It is found in association with BNR repeats, which also form a beta-propeller. 36 matched cddid_all.tbl CDD pfam03985 pfam03985 397885 Paf1 Paf1. Members of this family are components of the RNA polymerase II associated Paf1 complex. The Paf1 complex functions during the elongation phase of transcription in conjunction with Spt4-Spt5 and Spt16-Pob3i. 416 matched cddid_all.tbl CDD pfam03987 pfam03987 461120 Autophagy_act_C Autophagocytosis associated protein, active-site domain. Autophagocytosis is a starvation-induced process responsible for transport of cytoplasmic proteins to the vacuole. The cysteine residue within the HPC motif is the putative active-site residue for recognition of the Apg5 subunit of the autophagosome complex. 151 matched cddid_all.tbl CDD pfam03988 pfam03988 427632 DUF347 Repeat of Unknown Function (DUF347). This repeat is found as four tandem repeats in a family of bacterial membrane proteins. Each repeat contains two transmembrane regions and a conserved tryptophan. 50 matched cddid_all.tbl CDD pfam03989 pfam03989 427633 DNA_gyraseA_C DNA gyrase C-terminal domain, beta-propeller. This repeat is found as 6 tandem copies at the C-termini of GyrA and ParC DNA gyrases. It is predicted to form 4 beta strands and to probably form a beta-propeller structure. This region has been shown to bind DNA non-specifically and may stabilize the DNA-topoisomerase complex. 48 matched cddid_all.tbl CDD pfam03990 pfam03990 461121 DUF348 G5-linked-Ubiquitin-like domain. This domain normally occurs as tandem repeats; however it is found as a single copy in the S. cerevisiae DNA-binding nuclear protein YCR593. This protein is involved in sporulation part of the SET3C complex, which is required to repress early/middle sporulation genes during meiosis. The bacterial proteins are likely to be involved in a cell wall function as they are found in conjunction with the pfam07501 domain, which is involved in various cell surface processes. This domain is also present in the resuscitation-promoting factors RpfB from Mycobacterium tuberculosis and Rpf2 from Corynebacterium glutamicum. These are factors that stimulate resuscitation of dormant cells. This domain has a beta grasp fold. Structural description of this domain revealed a structural conservation between these domains and ubiquitin, hence it is termed UBL-G5. 41 matched cddid_all.tbl CDD pfam03991 pfam03991 112790 Prion_octapep Copper binding octapeptide repeat. This repeat is found at the amino terminus of prion proteins. It has been shown to bind to copper. 8 matched cddid_all.tbl CDD pfam03992 pfam03992 427635 ABM Antibiotic biosynthesis monooxygenase. This domain is found in monooxygenases involved in the biosynthesis of several antibiotics by Streptomyces species. It's occurrence as a repeat in Streptomyces coelicolor SCO1909 is suggestive that the other proteins function as multimers. There is also a conserved histidine which is likely to be an active site residue. 74 matched cddid_all.tbl CDD pfam03993 pfam03993 427636 DUF349 Domain of Unknown Function (DUF349). This domain is found singly or as up to five tandem repeats in a small set of bacterial proteins. There are two or three alpha-helices, and possibly a beta-strand. 73 matched cddid_all.tbl CDD pfam03994 pfam03994 427637 DUF350 Domain of Unknown Function (DUF350). This domain occurs in a small set of of bacterial proteins. It has two transmembrane regions, and often occurs as tandem repeats. The are no conserved catalytic residues. 54 matched cddid_all.tbl CDD pfam03995 pfam03995 427638 Inhibitor_I36 Peptidase inhibitor family I36. This domain is currently only found in a small set of S. coelicolor secreted proteins. There are four conserved cysteines that probably form two disulphide bonds. Proteins 2SCK31.15C and SCO3675 also have probable beta-propellers at their C-termini. This family includes Swiss:P01077 a known peptidase inhibitor of known structure. This protein has a crystallin like fold pfam00030 and is distantly related by sequence. It is not known whether other members of this family are peptidase inhibitors. 69 matched cddid_all.tbl CDD pfam03996 pfam03996 397893 Hema_esterase Hemagglutinin esterase. 384 matched cddid_all.tbl CDD pfam03997 pfam03997 427639 VPS28 VPS28 protein. 187 matched cddid_all.tbl CDD pfam03998 pfam03998 461122 Utp11 Utp11 protein. This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. 241 matched cddid_all.tbl CDD pfam03999 pfam03999 427641 MAP65_ASE1 Microtubule associated protein (MAP65/ASE1 family). 477 matched cddid_all.tbl CDD pfam04000 pfam04000 461123 Sas10_Utp3 Sas10/Utp3/C1D family. This family contains Utp3 and LCP5 which are components of the U3 ribonucleoprotein complex. It also includes the human C1D protein and Saccharomyces cerevisiae YHR081W (rrp47), an exosome-associated protein required for the 3' processing of stable RNAs, and Sas10 which has been identified as a regulator of chromatin silencing. This family also includes the human protein Neuroguidin an initiation factor 4E (eIF4E) binding protein. 83 matched cddid_all.tbl CDD pfam04001 pfam04001 397898 Vhr1 Transcription factor Vhr1. Vhr1 is a transcription factor which regulates the biotin-dependent expression of transporters VHT1 and BIO5. 91 matched cddid_all.tbl CDD pfam04002 pfam04002 461124 RadC RadC-like JAB domain. A family of proteins present widely across the bacteria. This family was named initially with reference to the E. coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions. However the relevant mutation has subsequently been shown to be in recG, where radC is in fact an allele of recG. In addition, a personal communication from Claverys, J-P, et al, indicates a total failure of all attempts to characterize a radiation-related function for RadC in Streptococcus pneumoniae, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair. Computational analysis, however, provides a possible function. The RadC-like family belong to the JAB superfamily of metalloproteins. The domain shows fusions to an N-terminal Helix-hairpin-Helix (HhH) domain in most instances. Other domain combinations include fusions to the anti-restriction module ArdC, the DinG/RAD3-like superfamily II helicases and the DNAG-like primase. In some bacteria, closely related DinG/Rad3- like superfamily II helicases are fused to a 3'-5' exonuclease in the same position as the RadC-like JAB domain. These conserved domain associations lead to the hypothesis that the RadC-like JAB domains might function as a nuclease. 113 matched cddid_all.tbl CDD pfam04003 pfam04003 461125 Utp12 Dip2/Utp12 Family. This domain is found at the C-terminus of proteins containing WD40 repeats. These proteins are part of the U3 ribonucleoprotein the yeast protein is called Utp12 or DIP2. 106 matched cddid_all.tbl CDD pfam04004 pfam04004 461126 Leo1 Leo1-like protein. Members of this family are part of the Paf1/RNA polymerase II complex. The Paf1 complex probably functions during the elongation phase of transcription. The Leo1 subunit of the yeast Paf1-complex binds RNA and contributes to complex recruitment. The subunit acts by co-ordinating co-transcriptional chromain modifications and helping recruitment of mRNA 3prime-end processing factors. 163 matched cddid_all.tbl CDD pfam04005 pfam04005 461127 Hus1 Hus1-like protein. Hus1, Rad1, and Rad9 are three evolutionarily conserved proteins required for checkpoint control in fission yeast. These proteins are known to form a stable complex in vivo. Hus1-Rad1-Rad9 complex may form a PCNA-like ring structure, and could function as a sliding clamp during checkpoint control. 288 matched cddid_all.tbl CDD pfam04006 pfam04006 461128 Mpp10 Mpp10 protein. This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites. 506 matched cddid_all.tbl CDD pfam04007 pfam04007 281936 DUF354 Protein of unknown function (DUF354). Members of this family are around 350 amino acids in length. They are found in archaebacteria and have no known function. 349 matched cddid_all.tbl CDD pfam04008 pfam04008 427648 Adenosine_kin Adenosine specific kinase. The structure of a member of this family from the hyperthermophilic archaeon Pyrobaculum aerophilum contains a modified histidine residue which is interpreted as stable phosphorylation. In vitro binding studies confirmed that adenosine and AMP but not ADP or ATP bind to the protein. 154 matched cddid_all.tbl CDD pfam04009 pfam04009 397905 DUF356 Protein of unknown function (DUF356). Members of this family are around 120 amino acids in length and are found in some archaebacteria. The function of this family is unknown. However it contains a conserved motif IHPPAH that may be involved in its function. 106 matched cddid_all.tbl CDD pfam04010 pfam04010 427649 DUF357 Protein of unknown function (DUF357). Members of this family are short (less than 100 amino acid) proteins found in archaebacteria. The function of these proteins is unknown. 73 matched cddid_all.tbl CDD pfam04011 pfam04011 461129 LemA LemA family. The members of this family are related to the LemA protein. LemA contains an amino terminal predicted transmembrane helix. It has been predicted that the small amino terminus is extracellular. The exact molecular function of this protein is uncertain. 149 matched cddid_all.tbl CDD pfam04012 pfam04012 461130 PspA_IM30 PspA/IM30 family. This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homolog in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma(54) containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator. 215 matched cddid_all.tbl CDD pfam04013 pfam04013 397908 Methyltrn_RNA_2 Putative SAM-dependent RNA methyltransferase. This family is likely to be an S-adenosyl-L-methionine (SAM)-dependent RNA methyltransferase. It is responsible for N1-methylation of pseudouridine 54 in archaeal tRNAs. 198 matched cddid_all.tbl CDD pfam04014 pfam04014 397909 MazE_antitoxin Antidote-toxin recognition MazE, bacterial antitoxin. AbrB-like is a family of small proteins that operate in conjunction with a cognate toxin molecule. The commonly attributed role of toxin-antitoxin systems is to maintain low-copy number plasmids from one generation to the next. Such gene-pairs are also found on chromosomes and to be associated with a number of biological functions such as: reduction of protein synthesis, gene regulation and retardation of cell growth under nutritional stress. This family includes proteins from a number of different pairings, eg MazE, AbrB, VapB, PhoU, PemI-like and SpoVT. MazE is the antidote to the toxin MazF of E. coli. MazE-MazF in E. coli is a regulated prokaryotic chromosomal addiction module. MazE antidote is degraded by the ClpPA protease of the bacterial proteasome. MazE-MazF is thought to play a role in programmed cell death when cells suffer nutrient deprivation, and MazE-MazF modules have also been implicated in the bacteriostatic effects of other addiction modules. 44 matched cddid_all.tbl CDD pfam04015 pfam04015 461131 DUF362 Domain of unknown function (DUF362). Domain that is sometimes present in iron-sulphur proteins. 199 matched cddid_all.tbl CDD pfam04016 pfam04016 397911 DUF364 Putative heavy-metal chelation. This domain of unknown function has a PLP-dependent transferase-like fold. Its genomic context suggests that it may have a role in anaerobic vitamin B12 biosynthesis. This domain is often found at the C-terminus of proteins containing DUF4213, pfam13938. The structure of UnioProtKB:B8FUJ5, PDB:3l5o, suggests that the protein has an enolase N-terminal-like fold and this Rossmann-like C-terminal domain. Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The protein may be playing a role in heavy-metal chelation. 147 matched cddid_all.tbl CDD pfam04017 pfam04017 427652 DUF366 Domain of unknown function (DUF366). Archaeal domain of unknown function. 183 matched cddid_all.tbl CDD pfam04018 pfam04018 427653 DUF368 Domain of unknown function (DUF368). Predicted transmembrane domain of unknown function. Family members have between 6 and 9 predicted transmembrane segments. 241 matched cddid_all.tbl CDD pfam04019 pfam04019 427654 DUF359 Protein of unknown function (DUF359). This family of archaebacterial proteins are about 170 amino acids in length. They have no known function. The most conserved portion of the protein contains the sequence GEEDL that may be important for its function. 122 matched cddid_all.tbl CDD pfam04020 pfam04020 461132 Phage_holin_4_2 Mycobacterial 4 TMS phage holin, superfamily IV. These proteins are predicted transmembrane proteins with probably four transmembrane spans. The 1.E.40 is represented by the mycobacterial 4 phage holin, but it also contains many cyanobacterial. proteobacterial and firmicute proteins. Holins are encoded within the genomes of Gram-positive and Gram-negative bacteria as well as in those of the bacteriophage of these organizms. The primary function of holins appears to be transport of murein hydrolases across the cytoplasmic membrane to the cell wall where these enzymes hydrolyse the cell wall polymer as a prelude to cell lysis. When chromosomally encoded the enzymes are therefore autolysins. Holins may also facilitate leakage of electrolytes and nutrients from the cell cytoplasm, thereby promoting cell death. Some may catalyze export of nucleases. 105 matched cddid_all.tbl CDD pfam04021 pfam04021 397916 Class_IIIsignal Class III signal peptide. This family of archaeal proteins contains. an amino terminal motif QXSXEXXXL that has been suggested to be part of a class III signal sequence. With the Q being the +1 residue of the signal peptidase cleavage site. Two members of this family are cleaved by a type IV pilin-like signal peptidase. 27 matched cddid_all.tbl CDD pfam04022 pfam04022 281951 Staphylcoagulse Staphylocoagulase repeat. 27 matched cddid_all.tbl CDD pfam04023 pfam04023 461133 FeoA FeoA domain. This family includes FeoA a small protein, probably involved in Fe2+ transport. This presumed short domain is also found at the C-terminus of a variety of metal dependent transcriptional regulators. This suggests that this domain may be metal-binding. In most cases this is likely to be either iron or manganese. 74 matched cddid_all.tbl CDD pfam04024 pfam04024 461134 PspC PspC domain. This family includes Phage shock protein C (PspC) that is thought to be a transcriptional regulator. The presumed domain is 60 amino acid residues in length. 57 matched cddid_all.tbl CDD pfam04025 pfam04025 461135 DUF370 Domain of unknown function (DUF370). Bacterial domain of unknown function. 73 matched cddid_all.tbl CDD pfam04026 pfam04026 427659 SpoVG SpoVG. Stage V sporulation protein G. Essential for sporulation and specific to stage V sporulation in Bacillus megaterium and subtilis. In B. subtilis, expression decreases after 30-60 minutes of cold shock. 82 matched cddid_all.tbl CDD pfam04027 pfam04027 427660 DUF371 Domain of unknown function (DUF371). Archaeal domain of unknown function. 133 matched cddid_all.tbl CDD pfam04028 pfam04028 461136 DUF374 Domain of unknown function (DUF374). Bacterial domain of unknown function. 69 matched cddid_all.tbl CDD pfam04029 pfam04029 461137 2-ph_phosp 2-phosphosulpholactate phosphatase. Thought to catalyze 2-phosphosulpholactate = sulpholactate + phosphate. Probable magnesium cofactor. Involved in the second step of coenzyme M biosynthesis. Inhibited by vanadate in Methanococcus jannaschii. Also known as the ComB family. 222 matched cddid_all.tbl CDD pfam04030 pfam04030 427663 ALO D-arabinono-1,4-lactone oxidase. This domain is specific to D-arabinono-1,4-lactone oxidase EC:1.1.3.-, which is involved in the final step of the D-erythroascorbic acid biosynthesis pathway. 258 matched cddid_all.tbl CDD pfam04031 pfam04031 461138 Las1 Las1-like. Las1 is an essential nuclear protein involved in cell morphogenesis and cell surface growth. 148 matched cddid_all.tbl CDD pfam04032 pfam04032 427665 Rpr2 RNAse P Rpr2/Rpp21/SNM1 subunit domain. This family contains a ribonuclease P subunit of humans and yeast. Other members of the family include the probable archaeal homologs. This family includes SNM1. It is a subunit of RNase MRP (mitochondrial RNA processing), a ribonucleoprotein endoribonuclease that has roles in both mitochondrial DNA replication and nuclear 5.8S rRNA processing. SNM1 is an RNA binding protein that binds the MRP RNA specifically. This subunit possibly binds the precursor tRNA. 88 matched cddid_all.tbl CDD pfam04033 pfam04033 427666 DUF365 Domain of unknown function (DUF365). Archaeal domain of unknown function. 96 matched cddid_all.tbl CDD pfam04034 pfam04034 461139 Ribo_biogen_C Ribosome biogenesis protein, C-terminal. This family represents the C-terminal domain of some putative ribosome biogenesis proteins in archaea. It has also been identified in the eukaryotic protein Tsr3, which is involved in ribosomal RNA biogenesis. 127 matched cddid_all.tbl CDD pfam04037 pfam04037 461140 DUF382 Domain of unknown function (DUF382). This domain is specific to the human splicing factor 3b subunit 2 and it's orthologues. Splicing factor 3b subunit 2 or SAP145 is a suppressor of U2 snRNA mutations. Pre-mRNA splicing is catalyzed by a large ribonucleoprotein complex called the spliceosome. Spliceosomes are multi-component enzymes that catalyze pre-mRNA splicing and form step-wise by the ordered interaction of UsnRNPs and non-snRNP proteins with short conserved regions of the pre-mRNA at the 5' and 3' splice sites and branch site. 126 matched cddid_all.tbl CDD pfam04038 pfam04038 427669 DHNA Dihydroneopterin aldolase. 108 matched cddid_all.tbl CDD pfam04039 pfam04039 461141 MnhB Domain related to MnhB subunit of Na+/H+ antiporter. Possible subunit of Na+/H+ antiporter,. Predicted integral membrane protein, usually four transmembrane regions in this domain. Often found in bacterial NADH dehydrogenase subunit. 125 matched cddid_all.tbl CDD pfam04041 pfam04041 397932 Glyco_hydro_130 beta-1,4-mannooligosaccharide phosphorylase. This is a family of glycosyl-hydrolases of the CAZy GH130 family. Several have been characterized as mannosylglucose phosphorylase. This enzyme is part of the mannan catalytic pathway and feeds into the glycolysis cycle. Specifically it catalyzes the reversible phosphorolysis of beta-1,4-D-mannosyl-N-acetyl-D-glucosamine. This family was noted to belong to the Beta fructosidase superfamily in. 315 matched cddid_all.tbl CDD pfam04042 pfam04042 461142 DNA_pol_E_B DNA polymerase alpha/epsilon subunit B. This family contains a number of DNA polymerase subunits. The B subunit of the DNA polymerase alpha plays an essential role at the initial stage of DNA replication in S. cerevisiae and is phosphorylated in a cell cycle-dependent manner. DNA polymerase epsilon is essential for cell viability and chromosomal DNA replication in budding yeast. In addition, DNA polymerase epsilon may be involved in DNA repair and cell-cycle checkpoint control. The enzyme consists of at least four subunits in mammalian cells as well as in yeast. The largest subunit of DNA polymerase epsilon is responsible for polymerase epsilon is responsible for polymerase activity. In mouse, the DNA polymerase epsilon subunit B is the second largest subunit of the DNA polymerase. A part of the N-terminal was found to be responsible for the interaction with SAP18. Experimental evidence suggests that this subunit may recruit histone deacetylase to the replication fork to modify the chromatin structure. 210 matched cddid_all.tbl CDD pfam04043 pfam04043 461143 PMEI Plant invertase/pectin methylesterase inhibitor. This domain inhibits pectin methylesterases (PMEs) and invertases through formation of a non-covalent 1:1 complex. It has been implicated in the regulation of fruit development, carbohydrate metabolism and cell wall extension. It may also be involved in inhibiting microbial pathogen PMEs. It has been observed that it is often expressed as a large inactive preprotein. It is also found at the N-termini of PMEs predicted from DNA sequences (personal obs:C Yeats), suggesting that both PMEs and their inhibitor are expressed as a single polyprotein and subsequently processed. It has two disulphide bridges and is mainly alpha-helical. 148 matched cddid_all.tbl CDD pfam04045 pfam04045 461144 P34-Arc Arp2/3 complex, 34 kD subunit p34-Arc. Arp2/3 protein complex has been implicated in the control of actin polymerization in cells. The human complex consists of seven subunits which include the actin related Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. This family represents the p34-Arc subunit. 238 matched cddid_all.tbl CDD pfam04046 pfam04046 461145 PSP PSP. Proline rich domain found in numerous spliceosome associated proteins. 46 matched cddid_all.tbl CDD pfam04048 pfam04048 367782 Sec8_exocyst Sec8 exocyst complex component specific domain. 141 matched cddid_all.tbl CDD pfam04049 pfam04049 427675 ANAPC8 Anaphase promoting complex subunit 8 / Cdc23. The anaphase-promoting complex is composed of eight protein subunits, including BimE (APC1), CDC27 (APC3), CDC16 (APC6), and CDC23 (APC8). 140 matched cddid_all.tbl CDD pfam04050 pfam04050 461146 Upf2 Up-frameshift suppressor 2. Transcripts harbouring premature signals for translation termination are recognized and rapidly degraded by eukaryotic cells through a pathway known as nonsense-mediated mRNA decay. In Saccharomyces cerevisiae, three trans-acting factors (Upf1 to Upf3) are required for nonsense-mediated mRNA decay. 133 matched cddid_all.tbl CDD pfam04051 pfam04051 461147 TRAPP Transport protein particle (TRAPP) component. TRAPP plays a key role in the targeting and/or fusion of ER-to-Golgi transport vesicles with their acceptor compartment. TRAPP is a large multimeric protein that contains at least 10 subunits. This family contains many TRAPP family proteins. The Bet3 subunit is one of the better characterized TRAPP proteins and has a dimeric structure with hydrophobic channels. The channel entrances are located on a putative membrane-interacting surface that is distinctively flat, wide and decorated with positively charged residues. Bet3 is proposed to localize TRAPP to the Golgi. 148 matched cddid_all.tbl CDD pfam04052 pfam04052 461148 TolB_N TolB amino-terminal domain. TolB is an essential periplasmic component of the tol-dependent translocation system. This function of this amino terminal domain is uncertain. 105 matched cddid_all.tbl CDD pfam04053 pfam04053 427679 Coatomer_WDAD Coatomer WD associated region. This region is composed of WD40 repeats. 439 matched cddid_all.tbl CDD pfam04054 pfam04054 427680 Not1 CCR4-Not complex component, Not1. The Ccr4-Not complex is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID. 365 matched cddid_all.tbl CDD pfam04055 pfam04055 427681 Radical_SAM Radical SAM superfamily. Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation. 159 matched cddid_all.tbl CDD pfam04056 pfam04056 461149 Ssl1 Ssl1-like. Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex. 178 matched cddid_all.tbl CDD pfam04057 pfam04057 397945 Rep-A_N Replication factor-A protein 1, N-terminal domain. 99 matched cddid_all.tbl CDD pfam04059 pfam04059 112856 RRM_2 RNA recognition motif 2. 97 matched cddid_all.tbl CDD pfam04060 pfam04060 461150 FeS Putative Fe-S cluster. This family includes a domain with four conserved cysteines that probably form an Fe-S redox cluster. 33 matched cddid_all.tbl CDD pfam04061 pfam04061 461151 ORMDL ORMDL family. Evidence form suggests that ORMDLs are involved in protein folding in the ER. Orm proteins have been identified as negative regulators of sphingolipid synthesis that form a conserved complex with serine palmitoyltransferase, the first and rate-limiting enzyme in sphingolipid production. This novel and conserved protein complex, has been termed the SPOTS complex (serine palmitoyltransferase, Orm1/2, Tsc3, and Sac1). 135 matched cddid_all.tbl CDD pfam04062 pfam04062 461152 P21-Arc ARP2/3 complex ARPC3 (21 kDa) subunit. The seven component ARP2/3 actin-organizing complex is involved in actin assembly and function. 174 matched cddid_all.tbl CDD pfam04063 pfam04063 461153 DUF383 Domain of unknown function (DUF383). 188 matched cddid_all.tbl CDD pfam04064 pfam04064 461154 DUF384 Domain of unknown function (DUF384). 55 matched cddid_all.tbl CDD pfam04065 pfam04065 461155 Not3 Not1 N-terminal domain, CCR4-Not complex component. 228 matched cddid_all.tbl CDD pfam04066 pfam04066 461156 MrpF_PhaF Multiple resistance and pH regulation protein F (MrpF / PhaF). Members of the PhaF / MrpF family are predicted to be an integral membrane proteins with three transmembrane regions, involved in regulation of pH. PhaF is part of a potassium efflux system involved in pH regulation. It is also involved in symbiosis in Rhizobium meliloti. MrpF is part of a Na+/H+ antiporter complex, also involved in pH homeostasis. MrpF is thought to be an efflux system for Na+ and cholate. The Mrp system in Bacilli may also have primary energization capacities. 52 matched cddid_all.tbl CDD pfam04068 pfam04068 427689 RLI Possible Fer4-like domain in RNase L inhibitor, RLI. Possible metal-binding domain in endoribonuclease RNase L inhibitor. Found at the N-terminal end of RNase L inhibitor proteins, adjacent to the 4Fe-4S binding domain, fer4, pfam00037. Also often found adjacent to the DUF367 domain pfam04034 in uncharacterized proteins. The RNase L system plays a major role in the anti-viral and anti-proliferative activities of interferons, and could possibly play a more general role in the regulation of RNA stability in mammalian cells. Inhibitory activity requires concentration-dependent association of RLI with RNase L. 35 matched cddid_all.tbl CDD pfam04069 pfam04069 397954 OpuAC Substrate binding domain of ABC-type glycine betaine transport system. Part of a high affinity multicomponent binding-protein-dependent transport system involved in bacterial osmoregulation. This domain is often fused to the permease component of the transporter complex. Family members are often integral membrane proteins or predicted to be attached to the membrane by a lipid anchor. Glycine betaine is involved in protection from high osmolarity environments for example in Bacillus subtilis. The family member OpuBC is closely related, and involved in choline transport. Choline is necessary for the biosynthesis of glycine betaine. L-carnitine is important for osmoregulation in Listeria monocytogenes. Family also contains proteins binding l-proline (ProX), histidine (HisX) and taurine (TauA). 257 matched cddid_all.tbl CDD pfam04070 pfam04070 461157 DUF378 Domain of unknown function (DUF378). Predicted transmembrane domain of unknown function. The majority of the family have two predicted transmembrane regions. 60 matched cddid_all.tbl CDD pfam04071 pfam04071 427691 zf-like Cysteine-rich small domain. Probable metal-binding domain. 80 matched cddid_all.tbl CDD pfam04072 pfam04072 427692 LCM Leucine carboxyl methyltransferase. Family of leucine carboxyl methyltransferases EC:2.1.1.-. This family may need divides a the full alignment contains a significantly shorter mouse sequence. 188 matched cddid_all.tbl CDD pfam04073 pfam04073 427693 tRNA_edit Aminoacyl-tRNA editing domain. This domain is found either on its own or in association with the tRNA synthetase class II core domain (pfam00587). It is involved in the tRNA editing of mis-charged tRNAs including Cys-tRNA(Pro), Cys-tRNA(Cys), Ala-tRNA(Pro). The structure of this domain shows a novel fold. 123 matched cddid_all.tbl CDD pfam04074 pfam04074 461158 DUF386 YhcH/YjgK/YiaL. This family consists of bacterial proteins. YjgK (TabA) influences biofilm formation by toxin-antitoxin systems. Another member of this family, YhcH, is a possible sugar isomerase of sialic acid catabolism. 148 matched cddid_all.tbl CDD pfam04075 pfam04075 281995 F420H2_quin_red F420H(2)-dependent quinone reductase. This family of proteins is found in the genera Mycobacterium and Streptomyces. Member protein Rv3547 has been characterized as a deazaflavin-dependent nitroreductase. Rv1558 is an F420H(2)-dependent quinone reductase involved in oxidative stress protection. 129 matched cddid_all.tbl CDD pfam04076 pfam04076 281996 BOF Bacterial OB fold (BOF) protein. Proteins in this family form an OB-fold. Analysis of the predicted binding site of BOF family proteins implies that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localize in the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesized for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the BOF ligand-binding site may be associated with the presence of BOF proteins in mobile genetic elements and their potential role in bacterial pathogenicity. 103 matched cddid_all.tbl CDD pfam04077 pfam04077 461159 DsrH DsrH like protein. DsrH is involved in oxidation of intracellular sulphur in the phototrophic sulphur bacterium Chromatium vinosum D. 87 matched cddid_all.tbl CDD pfam04078 pfam04078 461160 Rcd1 Cell differentiation family, Rcd1-like. Two of the members in this family have been characterized as being involved in regulation of Ste11 regulated sex genes. Mammalian Rcd1 is a novel transcriptional cofactor that mediates retinoic acid-induced cell differentiation. 259 matched cddid_all.tbl CDD pfam04079 pfam04079 427697 SMC_ScpB Segregation and condensation complex subunit ScpB. This is a family of prokaryotic proteins that form one of the subunits, ScpB, of the segregation and condensation complex, condensin, that plays a key role in the maintenance of the chromosome. In prokaryotes the complex consists of three proteins, SMC, ScpA (kleisin) and ScpB. ScpB dimerizes and binds to ScpA. As originally predicted, ScpB is structurally a winged-helix at both its N- and C-terminal halves. IN Bacillus subtilis,one Smc dimer is bridged by a single ScpAB to generate asymmetric tripartite rings analogous to eukaryotic SMC complex ring-shaped assemblies. 159 matched cddid_all.tbl CDD pfam04080 pfam04080 461161 Per1 Per1-like family. PER1 is required for GPI-phospholipase A2 activity and is involved in lipid remodelling of GPI-anchored proteins. PER1 is part of the CREST superfamily. 254 matched cddid_all.tbl CDD pfam04081 pfam04081 367800 DNA_pol_delta_4 DNA polymerase delta, subunit 4. 131 matched cddid_all.tbl CDD pfam04082 pfam04082 397964 Fungal_trans Fungal specific transcription factor domain. This domain is found in a number of fungal transcription factors including transcriptional activator xlnR, yeast regulatory protein GAL4, and nicotinate catabolism cluster-specific transcription factor HxnR. 262 matched cddid_all.tbl CDD pfam04083 pfam04083 461162 Abhydro_lipase Partial alpha/beta-hydrolase lipase region. This family corresponds to a N-terminal part of an alpha/beta hydrolase domain. 63 matched cddid_all.tbl CDD pfam04084 pfam04084 461163 ORC2 Origin recognition complex subunit 2. All DNA replication initiation is driven by a single conserved eukaryotic initiator complex termed he origin recognition complex (ORC). The ORC is a six protein complex. The function of ORC is reviewed in. 323 matched cddid_all.tbl CDD pfam04085 pfam04085 461164 MreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. 148 matched cddid_all.tbl CDD pfam04086 pfam04086 461165 SRP-alpha_N Signal recognition particle, alpha subunit, N-terminal. SRP is a complex of six distinct polypeptides and a 7S RNA that is essential for transferring nascent polypeptide chains that are destined for export from the cell to the translocation apparatus of the endoplasmic reticulum (ER) membrane. SRP binds hydrophobic signal sequences as they emerge from the ribosome, and arrests translation. 281 matched cddid_all.tbl CDD pfam04087 pfam04087 461166 DUF389 Domain of unknown function (DUF389). Family of hypothetical bacterial proteins with an undetermined function. 137 matched cddid_all.tbl CDD pfam04088 pfam04088 461167 Peroxin-13_N Peroxin 13, N-terminal region. Both termini of the Peroxin-13 are oriented to the cytosol. Peroxin-13 is required for peroxisomal association of peroxin-14. 142 matched cddid_all.tbl CDD pfam04089 pfam04089 461168 BRICHOS BRICHOS domain. The BRICHOS domain is about 100 amino acids long. It is found in a variety of proteins implicated in dementia, respiratory distress and cancer. Its exact function is unknown; roles that have been proposed for it include (a) in targeting of the protein to the secretory pathway, (b) intramolecular chaperone-like function, and (c) assisting the specialized intracellular protease processing system. This C-terminal domain is embedded in the endoplasmic reticulum lumen, and binds to the N-terminal, transmembrane, SP_C, pfam08999, provided that it is in non-helical conformation. Thus the Brichos domain of proSP-C is a chaperone that induces alpha-helix formation of an aggregation-prone TM region. 91 matched cddid_all.tbl CDD pfam04090 pfam04090 367807 RNA_pol_I_TF RNA polymerase I specific initiation factor. 199 matched cddid_all.tbl CDD pfam04091 pfam04091 461169 Sec15 Exocyst complex subunit Sec15-like. 308 matched cddid_all.tbl CDD pfam04092 pfam04092 461170 SAG SRS domain. Toxoplasma gondii is a persistent protozoan parasite capable of infecting almost any warm-blooded vertebrate. The surface of Toxoplasma is coated with a family of developmentally regulated glycosylphosphatidylinositol (GPI)-linked proteins (SRSs), of which SAG1 is the prototypic member. SRS proteins mediate attachment to host cells and interface with the host immune response to regulate the virulence of the parasite. SAG1 is composed of two disulphide linked SRS domains. These have 6 cysteines that form 1-6,2-5 and 3-4 pairings. The structure of the immunodominant SAG1 antigen reveals a homodimeric configuration. The SRS domain is found in a single copy in the SAG2 proteins. This family of surface antigens are found in other apicomplexans. 132 matched cddid_all.tbl CDD pfam04093 pfam04093 282013 MreD rod shape-determining protein MreD. MreD (murein formation D) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. 160 matched cddid_all.tbl CDD pfam04095 pfam04095 397974 NAPRTase Nicotinate phosphoribosyltransferase (NAPRTase) family. Nicotinate phosphoribosyltransferase (EC:2.4.2.11) is the rate limiting enzyme that catalyzes the first reaction in the NAD salvage synthesis. This family also includes Pre-B cell enhancing factor that is a cytokine Swiss:P43490. This family is related to Quinolinate phosphoribosyltransferase pfam01729. 235 matched cddid_all.tbl CDD pfam04096 pfam04096 461171 Nucleoporin2 Nucleoporin autopeptidase. The nuclear pore complex protein plays a role in bidirectional transport across the nucleoporin complex in nucleocytoplasmic transport. The mammalian nuclear pore complex (NPC) is comprised of approximately 30 unique proteins, collectively known as nucleoporins. This family includes yeast family members such as Nup145p as well as vertebrate Nup98. The NUP C-terminal domains of Nup98 and Nup145 possess peptidase S59 autoproteolytic activity. The autoproteolytic sites of Nup98 and Nup145 each occur immediately C-terminal to the NUP C-terminal domain. Thus, although this domain occurs in the middle of each precursor polypeptide, it winds up at the C-terminal end of the N-terminal cleavage product. Cleavage of the peptide chains are necessary for the proper targeting to the nuclear pore. 143 matched cddid_all.tbl CDD pfam04097 pfam04097 461172 Nic96 Nup93/Nic96. Nup93/Nic96 is a component of the nuclear pore complex. It is required for the correct assembly of the nuclear pore complex. In Saccharomyces cerevisiae, Nic96 has been shown to be involved in the distribution and cellular concentration of the GTPase Gsp1. The structure of Nic96 has revealed a mostly alpha helical structure. 613 matched cddid_all.tbl CDD pfam04098 pfam04098 367812 Rad52_Rad22 Rad52/22 family double-strand break repair protein. The DNA single-strand annealing proteins (SSAPs), such as RecT, Red-beta, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. This family includes proteins related to Rad52. These proteins contain two helix-hairpin-helix motifs. 140 matched cddid_all.tbl CDD pfam04099 pfam04099 282019 Sybindin Sybindin-like family. Sybindin is a physiological syndecan-2 ligand on dendritic spines, the small protrusions on the surface of dendrites that receive the vast majority of excitatory synapses. 134 matched cddid_all.tbl CDD pfam04100 pfam04100 427710 Vps53_N Vps53-like, N-terminal. Vps53 complexes with Vps52 and Vps54 to form a multi- subunit complex involved in regulating membrane trafficking events. 372 matched cddid_all.tbl CDD pfam04101 pfam04101 427711 Glyco_tran_28_C Glycosyltransferase family 28 C-terminal domain. The glycosyltransferase family 28 includes monogalactosyldiacylglycerol synthase (EC 2.4.1.46) and UDP-N-acetylglucosamine transferase (EC 2.4.1.-). Structural analysis suggests the C-terminal domain contains the UDP-GlcNAc binding site. 166 matched cddid_all.tbl CDD pfam04102 pfam04102 461173 SlyX SlyX. The SlyX protein has no known function. It is short less than 80 amino acids and is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C-terminus. The protein may be a coiled-coil structure. 66 matched cddid_all.tbl CDD pfam04103 pfam04103 461174 CD20 CD20-like family. This family includes the CD20 protein and the beta subunit of the high affinity receptor for IgE Fc. The high affinity receptor for IgE is a tetrameric structure consisting of a single IgE-binding alpha subunit, a single beta subunit, and two disulfide-linked gamma subunits. The alpha subunit of Fc epsilon RI and most Fc receptors are homologous members of the Ig superfamily. By contrast, the beta and gamma subunits from Fc epsilon RI are not homologous to the Ig superfamily. Both molecules have four putative transmembrane segments and a probably topology where both amino- and carboxy termini protrude into the cytoplasm. This family also includes LR8 like proteins from humans, mice and rats. The function of the human LR8 protein is unknown although it is known to be strongly expressed in the lung fibroblasts. This family also includes sarcospan is a transmembrane component of dystrophin-associated glycoprotein. Loss of the sarcoglycan complex and sarcospan alone is sufficient to cause muscular dystrophy. The role of the sarcoglycan complex and sarcospan is thought to be to strengthen the dystrophin axis connecting the basement membrane with the cytoskeleton. 155 matched cddid_all.tbl CDD pfam04104 pfam04104 397980 DNA_primase_lrg Eukaryotic and archaeal DNA primase, large subunit. DNA primase is the polymerase that synthesizes small RNA primers for the Okazaki fragments made during discontinuous DNA replication. DNA primase is a heterodimer of two subunits, the small subunit Pri1 (48 kDa in yeast), and the large subunit Pri2 (58 kDa in the yeast S. cerevisiae). The large subunit of DNA primase forms interactions with the small subunit and the structure implicates that it is not directly involved in catalysis, but plays roles in correctly positioning the primase/DNA complex, and in the transfer of RNA to DNA polymerase. 222 matched cddid_all.tbl CDD pfam04106 pfam04106 461175 APG5 Autophagy protein Apg5. Apg5 is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway. 197 matched cddid_all.tbl CDD pfam04107 pfam04107 461176 GCS2 Glutamate-cysteine ligase family 2(GCS2). Also known as gamma-glutamylcysteine synthetase and gamma-ECS (EC:6.3.2.2). This enzyme catalyzes the first and rate limiting step in de novo glutathione biosynthesis. Members of this family are found in archaea, bacteria and plants. May and Leaver discuss the possible evolutionary origins of glutamate-cysteine ligase enzymes in different organizms and suggest that it evolved independently in different eukaryotes, from an ancestral bacterial enzyme. They also state that Arabidopsis thaliana gamma-glutamylcysteine synthetase is structurally unrelated to mammalian, yeast and Escherichia coli homologs. In plants, there are separate cytosolic and chloroplast forms of the enzyme. 289 matched cddid_all.tbl CDD pfam04108 pfam04108 427715 ATG17_like Autophagy protein ATG17-like domain. This domain is found in the autophagy-related proteins ATG17 and ATG11, conserved across eukaryotes. ATG17 forms a complex with ATG29 and ATG31, critical for both PAS (preautophagosomal structure) formation and autophagy. Together with ATG13, it is required for ATG1 kinase activation. ATG11 is a scaffold protein required for the cytoplasm-to-vacuole targeting (Cvt) pathway during starvation and to recruit ATG proteins to the pre-autophagosome. It is also required for ATG1 kinase activation. In many eukaryotes, ATG11 (the orthologue in mammals is RB1-inducible coiled-coil protein 1 (RB1CC1) and in S. pombe is Taz1-interacting factor 1 (taf1)) is essential for bulk autophagy, except in S.cerevisiae. ATG17 and ATG11 are large similar proteins, both predicted to be almost entirely helical, containing conserved coiled-coil regions and lack obvious functional motifs. 360 matched cddid_all.tbl CDD pfam04109 pfam04109 461177 ATG9 Autophagy protein ATG9. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg9 plays a direct role in the formation of the cytoplasm to vacuole targeting and autophagic vesicles, and it is the sole transmembrane protein in the autophagosome-forming machinery. It colocalizes with Atg2 at the expanding edge of the isolation membrane where Atg2 receives phospholipids from the endoplasmic reticulum (ER). Atg9 is a lipid scramblase that translocates phospholipids between outer and inner leaflets of liposomes. Phospholipids delivered by Atg2 are translocated from the cytoplasmic to the luminal leaflet by Atg9, driving autophagosomal membrane expansion. 478 matched cddid_all.tbl CDD pfam04110 pfam04110 397985 APG12 Ubiquitin-like autophagy protein Apg12. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. The Apg12 system is one of the ubiquitin-like protein conjugation systems conserved in eukaryotes. It was first discovered in yeast during systematic analyses of the apg mutants defective in autophagy. Covalent attachment of Apg12-Apg5 is essential for autophagy. 87 matched cddid_all.tbl CDD pfam04111 pfam04111 461178 APG6 Apg6 BARA domain. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway. This entry is the Beta-Alpha repeated, autophagy-specific (BARA) domain. 176 matched cddid_all.tbl CDD pfam04112 pfam04112 461179 Mak10 Mak10 subunit, NatC N(alpha)-terminal acetyltransferase. NatC N(alpha)-terminal acetyltransferases contains Mak10p, Mak31p and Mak3p subunits. All three subunits are associated with each other to form the active complex. 162 matched cddid_all.tbl CDD pfam04113 pfam04113 461180 Gpi16 Gpi16 subunit, GPI transamidase component. GPI (glycosyl phosphatidyl inositol) transamidase is a multi-protein complex. Gpi16, Gpi8 and Gaa1 for a sub-complex of the GPI transamidase. GPI transamidase that adds glycosylphosphatidylinositols (GPIs) to newly synthesized proteins. Gpi16 is an essential N-glycosylated transmembrane glycoprotein. Gpi16 is largely found on the lumenal side of the ER. It has a single C-terminal transmembrane domain and a small C-terminal, cytosolic extension with an ER retrieval motif. 524 matched cddid_all.tbl CDD pfam04114 pfam04114 461181 Gaa1 Gaa1-like, GPI transamidase component. GPI (glycosyl phosphatidyl inositol) transamidase is a multi-protein complex. Gpi16, Gpi8 and Gaa1 for a sub-complex of the GPI transamidase. GPI transamidase that adds glycosylphosphatidylinositols (GPIs) to newly synthesized proteins. 496 matched cddid_all.tbl CDD pfam04115 pfam04115 427721 Ureidogly_lyase Ureidoglycolate lyase. Ureidoglycolate lyase (EC:4.3.2.3) is one of the enzymes that acts upon ureidoglycolate, an intermediate of purine catabolism, releasing urea. The enzyme has in the past been wrongly assigned to EC:3.5.3.19, enzymes which release ammonia from ureidoglycolate. 162 matched cddid_all.tbl CDD pfam04116 pfam04116 397991 FA_hydroxylase Fatty acid hydroxylase. This entry includes fatty acid and carotene hydroxylases and sterol desaturases. Beta-carotene hydroxylase is involved in zeaxanthin synthesis by hydroxylating beta-carotene, but the enzyme may be involved in other pathways. This family includes C-5 sterol desaturase and C-4 sterol methyl oxidase. Members of this family are involved in cholesterol biosynthesis and biosynthesis a plant cuticular wax. These enzymes contain two copies of a HXHH motif which coordinate two irons at the catalytic centre. Members of this family are ER integral membrane proteins that share a novel mushroom-shaped fold consisting of four transmembrane (TM1-TM4) helices that anchor them to the membrane capped by a cytosolic domain containing the unique histidine- coordinating di metal centre. 134 matched cddid_all.tbl CDD pfam04117 pfam04117 461182 Mpv17_PMP22 Mpv17 / PMP22 family. The 22-kDa peroxisomal membrane protein (PMP22) is a major component of peroxisomal membranes. PMP22 seems to be involved in pore forming activity and may contribute to the unspecific permeability of the organelle membrane. PMP22 is synthesized on free cytosolic ribosomes and then directed to the peroxisome membrane by specific targeting information. Mpv17 is a closely related peroxisomal protein. In mouse, the Mpv17 protein is involved in the development of early-onset glomerulosclerosis. More recently a homolog of Mpv17 in S. cerevisiae has been been found to be an integral membrane protein of the inner mitochondrial membrane where it has been proposed to have a role in ethanol metabolism and tolerance during heat-shock. Defects in MPV17 is associated with mitochondrial DNA depletion syndrome (MDDS) and Navajo neurohepatopathy (NNH). MDDS is a clinically heterogeneous group of disorders characterized by a reduction in mitochondrial DNA (mtDNA) copy number. Primary mtDNA depletion is inherited as an autosomal recessive trait and may affect single organs, typically muscle or liver, or multiple tissues. Individuals with the hepatocerebral form of mitochondrial DNA depletion syndrome have early progressive liver failure and neurologic abnormalities, hypoglycemia, and increased lactate in body fluids. NNH is an autosomal recessive disease that is prevalent among Navajo children in the South Western states of America. The major clinical features are hepatopathy, peripheral neuropathy, corneal anesthesia and scarring, acral mutilation, cerebral leukoencephalopathy, failure to thrive, and recurrent metabolic acidosis with intercurrent infections. Infantile, childhood, and classic forms of NNH have been described. Mitochondrial DNA depletion was detected in the livers of patients, suggesting a primary defect in mtDNA maintenance. 62 matched cddid_all.tbl CDD pfam04118 pfam04118 461183 Dopey_N Dopey, N-terminal. DopA is the founding member of the Dopey family and is required for correct cell morphology and spatiotemporal organization of multicellular structures in the filamentous fungus Aspergillus nidulans. DopA homologs are found in mammals. S. cerevisiae DOP1 is essential for viability and, affects cellular morphogenesis. 302 matched cddid_all.tbl CDD pfam04119 pfam04119 427724 HSP9_HSP12 Heat shock protein 9/12. These heat shock proteins (Hsp9 and Hsp12) are strongly expressed, an increase of 100 fold, upon entry into stationary phase in yeast. 59 matched cddid_all.tbl CDD pfam04120 pfam04120 427725 Iron_permease Low affinity iron permease. 128 matched cddid_all.tbl CDD pfam04121 pfam04121 461184 Nup84_Nup100 Nuclear pore protein 84 / 107. Nup84p forms a complex with five proteins, of which Nup120p, Nup85p, Sec13p, and a Sec13p homologs. This Nup84p complex in conjunction with Sec13-type proteins is required for correct nuclear pore biogenesis. 702 matched cddid_all.tbl CDD pfam04122 pfam04122 461185 CW_binding_2 ell wall binding domain 2 (CWB2). This domain is found in 1 to 3 tandem copies in a wide variety of bacterial cell surface proteins. It has been show the three tandem repeats of the CWB2 domain are essential for correct anchoring to the cell wall. It was shown that in SlpA and Cwp2 that these domains were essential for the binding of PSII an anionic teichoic acid-like component of the cell wall. The structure of the Cwp8 and Cwp6 proteins shows that this domain forms a trimeric arrangement with each domain adopting a structure with some similarity to the Toprim fold. A groove containing many conserved residues was predicted to be the site of the PSII molecule. 80 matched cddid_all.tbl CDD pfam04123 pfam04123 427728 DUF373 Domain of unknown function (DUF373). Archaeal domain of unknown function. Predicted to be an integral membrane protein with six transmembrane regions. 336 matched cddid_all.tbl CDD pfam04124 pfam04124 427729 Dor1 Dor1-like family. Dor1 is involved in vesicle targeting to the yeast Golgi apparatus and complexes with a number of other trafficking proteins, which include Sec34 and Sec35. 315 matched cddid_all.tbl CDD pfam04126 pfam04126 309308 Cyclophil_like Cyclophilin-like. This domain has a cyclophilin-like fold, consisting of an eight-stranded beta-barrel with an alpha helix located between the beta-2 and beta-3 strands and a 310 helix located between the beta-7 and beta-8 strands. The catalytic site found in human cyclophilin is not conserved in this domain, suggesting a different function for this domain. 119 matched cddid_all.tbl CDD pfam04127 pfam04127 461186 DFP DNA / pantothenate metabolism flavoprotein. The DNA/pantothenate metabolism flavoprotein (EC:4.1.1.36) affects synthesis of DNA, and pantothenate metabolism. 183 matched cddid_all.tbl CDD pfam04129 pfam04129 282044 Vps52 Vps52 / Sac2 family. Vps52 complexes with Vps53 and Vps54 to form a multi- subunit complex involved in regulating membrane trafficking events. 508 matched cddid_all.tbl CDD pfam04130 pfam04130 461187 GCP_C_terminal Gamma tubulin complex component C-terminal. This is the C-terminal domain found in components of the gamma-tubulin complex proteins (GCPs). Family members include spindle pole body (SBP) components such as Spc97 and Spc98 which function as the microtubule-organizing center in yeast. Furthermore, family members such as human GCP4 (Gamma-tubulin complex component 4) have been structurally elucidated. Structure-based sequence analysis revealed the existence of an exposed surface area conserved in all human GCPs and in GCP4 orthologs. This area is located in the C-terminal domain of GCP4, which was confirmed in vitro to bind directly to gamma-tubulin. Sequence alignment of human GCPs based on the GCP4 structure helped delineate conserved regions in the N- and C-terminal domains. 297 matched cddid_all.tbl CDD pfam04131 pfam04131 427732 NanE Putative N-acetylmannosamine-6-phosphate epimerase. This family represents a putative ManNAc-6-P-to-GlcNAc-6P epimerase in the N-acetylmannosamine (ManNAc) utilization pathway found mainly in pathogenic bacteria. 192 matched cddid_all.tbl CDD pfam04133 pfam04133 461188 Vps55 Vacuolar protein sorting 55. Vps55 is involved in the secretion of the Golgi form of the soluble vacuolar carboxypeptidase Y, but not the trafficking of the membrane-bound vacuolar alkaline phosphatase. Both Vps55 and obesity receptor gene-related protein are important for functioning membrane trafficking to the vacuole/lysosome of eukaryotic cells. 118 matched cddid_all.tbl CDD pfam04134 pfam04134 461189 DCC1-like DCC1-like thiol-disulfide oxidoreductase. Members of this family have two highly conserved cysteine residues within the DxxCxxC motif at the N-terminal. This motif is conserved in the thiol-disulfide oxidoreductase family. This family includes At5g50100 (also known as DCC1) from Arabidopsis thaliana, a thioredoxin that modulates ROS homeostasis resulting in de novo shoot initiation and may be involved in the improvement of the capacity of plant regeneration. Uncharacterized proteins from bacteria are also included in this family. 112 matched cddid_all.tbl CDD pfam04135 pfam04135 427735 Nop10p Nucleolar RNA-binding protein, Nop10p family. Nop10p is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10p is probably necessary for the stability of these RNPs. 51 matched cddid_all.tbl CDD pfam04136 pfam04136 461190 Sec34 Sec34-like family. Sec34 and Sec35 form a sub-complex, in a seven protein complex that includes Dor1 (pfam04124). This complex is thought to be important for tethering vesicles to the Golgi. 146 matched cddid_all.tbl CDD pfam04137 pfam04137 461191 ERO1 Endoplasmic Reticulum Oxidoreductin 1 (ERO1). Members of this family are required for the formation of disulphide bonds in the ER. 352 matched cddid_all.tbl CDD pfam04138 pfam04138 427738 GtrA GtrA-like protein. Members of this family are predicted to be integral membrane proteins with three or four transmembrane spans. They are involved in the synthesis of cell surface polysaccharides. The GtrA family are a subset of this family. GtrA is predicted to be an integral membrane protein with 4 transmembrane spans. It is involved is in O antigen modification by Shigella flexneri bacteriophage X (SfX), but does not determine the specificity of glucosylation. Its function remains unknown, but it may play a role in translocation of undecaprenyl phosphate linked glucose (UndP-Glc) across the cytoplasmic membrane. Another member of this family is a DTDP-glucose-4-keto-6-deoxy-D-glucose reductase, which catalyzes the conversion of dTDP-4-keto-6-deoxy-D-glucose to dTDP-D-fucose, which is involved in the biosynthesis of the serotype-specific polysaccharide antigen of Actinobacillus actinomycetemcomitans Y4 (serotype b). This family also includes the teichoic acid glycosylation protein, GtcA, which is a serotype-specific protein in some Listeria innocua and monocytogenes strains. Its exact function is not known, but it is essential for decoration of cell wall teichoic acids with glucose and galactose. 116 matched cddid_all.tbl CDD pfam04139 pfam04139 427739 Rad9 Rad9. Rad9 is required for transient cell-cycle arrests and transcriptional induction of DNA repair in response to DNA damage. It contains a Bcl-2 homology domain 3 (BH3). 253 matched cddid_all.tbl CDD pfam04140 pfam04140 427740 ICMT Isoprenylcysteine carboxyl methyltransferase (ICMT) family. The isoprenylcysteine o-methyltransferase (EC:2.1.1.100) family carry out carboxyl methylation of cleaved eukaryotic proteins that terminate in a CaaX motif. In Saccharomyces cerevisiae this methylation is carried out by Ste14p, an integral endoplasmic reticulum membrane protein. Ste14p is the founding member of the isoprenylcysteine carboxyl methyltransferase (ICMT) family, whose members share significant sequence homology. 95 matched cddid_all.tbl CDD pfam04142 pfam04142 398009 Nuc_sug_transp Nucleotide-sugar transporter. This family of membrane proteins transport nucleotide sugars from the cytoplasm into Golgi vesicles. Swiss:P78382 transports CMP-sialic acid, Swiss:P78381 transports UDP-galactose and Swiss:Q9Y2D2 transports UDP-GlcNAc. 315 matched cddid_all.tbl CDD pfam04143 pfam04143 461192 Sulf_transp Sulphur transport. This is an integral membrane protein. It is predicted to have a function in the transport of sulphur-containing molecules. It contains several conserved glycines and an invariant cysteine that is probably an important functional residue. 310 matched cddid_all.tbl CDD pfam04144 pfam04144 461193 SCAMP SCAMP family. In vertebrates, secretory carrier membrane proteins (SCAMPs) 1-3 constitute a family of putative membrane-trafficking proteins composed of cytoplasmic N-terminal sequences with NPF repeats, four central transmembrane regions (TMRs), and a cytoplasmic tail. SCAMPs probably function in endocytosis by recruiting EH-domain proteins to the N-terminal NPF repeats but may have additional functions mediated by their other sequences. 172 matched cddid_all.tbl CDD pfam04145 pfam04145 461194 Ctr Ctr copper transporter family. The redox active metal copper is an essential cofactor in critical biological processes such as respiration, iron transport, oxidative stress protection, hormone production, and pigmentation. A widely conserved family of high-affinity copper transport proteins (Ctr proteins) mediates copper uptake at the plasma membrane. A series of clustered methionine residues in the hydrophilic extracellular domain, and an MXXXM motif in the second transmembrane domain, are important for copper uptake. These methionine probably coordinate copper during the process of metal transport. 151 matched cddid_all.tbl CDD pfam04146 pfam04146 461195 YTH YT521-B-like domain. A protein of the YTH family has been shown to selectively remove transcripts of meiosis-specific genes expressed in mitotic cells. It has been speculated that in higher eukaryotic YTH-family members may be involved in similar mechanisms to suppress gene regulation during gametogenesis or general silencing. The rat protein YT521-B is a tyrosine-phosphorylated nuclear protein, that interacts with the nuclear transcriptosomal component scaffold attachment factor B, and the 68-kDa Src substrate associated during mitosis, Sam68. In vivo splicing assays demonstrated that YT521-B modulates alternative splice site selection in a concentration-dependent manner. The YTH domain has been identified as part of the PUA superfamily. 135 matched cddid_all.tbl CDD pfam04147 pfam04147 461196 Nop14 Nop14-like family. Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production. 835 matched cddid_all.tbl CDD pfam04148 pfam04148 461197 Erv26 Transmembrane adaptor Erv26. Erv26 is an integral membrane protein that is packed into COPII vesicles and cycles between the ER and Golgi compartments. It directs pro-alkaline phosphatase into endoplasmic reticulum-derived COPII transport vesicles. 202 matched cddid_all.tbl CDD pfam04149 pfam04149 427747 DUF397 Domain of unknown function (DUF397). The function of this family is unknown. 50 matched cddid_all.tbl CDD pfam04151 pfam04151 427748 PPC Bacterial pre-peptidase C-terminal domain. This domain is normally found at the C-terminus of secreted bacterial peptidases. They are not present in the active peptidase. It is possible that they fulfill a similar role to the PKD (pfam00801) domain, which also are found in this context. Visual analysis suggests that PKD and PPC are distantly related (personal obs:Bateman A, Yeats C). 68 matched cddid_all.tbl CDD pfam04152 pfam04152 461198 Mre11_DNA_bind Mre11 DNA-binding presumed domain. The Mre11 complex is a multi-subunit nuclease that is composed of Mre11, Rad50 and Nbs1/Xrs2, and is involved in checkpoint signalling and DNA replication. Mre11 has an intrinsic DNA-binding activity that is stimulated by Rad50 on its own or in combination with Nbs1. 175 matched cddid_all.tbl CDD pfam04153 pfam04153 461199 NOT2_3_5 NOT2 / NOT3 / NOT5 family. NOT1, NOT2, NOT3, NOT4 and NOT5 form a nuclear complex that negatively regulates the basal and activated transcription of many genes. This family includes NOT2, NOT3 and NOT5. 121 matched cddid_all.tbl CDD pfam04155 pfam04155 461200 Ground-like Ground-like domain. This family consists of the ground-like domain and is specific to C.elegans. It has been proposed that the ground-like domain containing proteins may bind and modulate the activity of Patched-like membrane molecules, reminiscent of the modulating activities of neuropeptides. 73 matched cddid_all.tbl CDD pfam04157 pfam04157 461201 EAP30 EAP30/Vps36 family. This family includes EAP30 as well as the Vps36 protein. Vps36 is involved in Golgi to endosome trafficking. EAP30 is a subunit of the ELL complex. The ELL is an 80-kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. 210 matched cddid_all.tbl CDD pfam04158 pfam04158 427753 Sof1 Sof1-like domain. Sof1 is essential for cell growth and is a component of the nucleolar rRNA processing machinery. 87 matched cddid_all.tbl CDD pfam04159 pfam04159 282069 NB NB glycoprotein. The NB glycoprotein is found in Influenza type B virus. Its function is unknown. 100 matched cddid_all.tbl CDD pfam04160 pfam04160 282070 Borrelia_orfX Orf-X protein. This short protein has no known function and is found in Jaagsiekte sheep retrovirus. Jaagsiekte sheep retrovirus (JSRV) is the etiological agent of a contagious lung tumour of sheep known as sheep pulmonary adenomatosis. JSRV exhibits a simple genetic organization, characteriztic of the type D and type B retroviruses, with the canonical retroviral sequences gag, pro, pol and env encoding the structural proteins of the virion. An additional open reading frame (orf-x), of approximately 500 bp overlapping pol. 154 matched cddid_all.tbl CDD pfam04161 pfam04161 461202 Arv1 Arv1-like family. Arv1 is a transmembrane protein with potential zinc-binding motifs. ARV1 is a novel mediator of eukaryotic sterol homeostasis. 204 matched cddid_all.tbl CDD pfam04162 pfam04162 282072 Gyro_capsid Gyrovirus capsid protein (VP1). Gyroviruses are small circular single stranded viruses. This family includes the VP1 protein from the chicken anaemia virus which is the viral capsid protein. 449 matched cddid_all.tbl CDD pfam04163 pfam04163 282073 Tht1 Tht1-like nuclear fusion protein. 595 matched cddid_all.tbl CDD pfam04165 pfam04165 282074 DUF401 Protein of unknown function (DUF401). Members if this family are predicted to have 10 transmembrane regions. 393 matched cddid_all.tbl CDD pfam04166 pfam04166 461203 PdxA Pyridoxal phosphate biosynthetic protein PdxA. In Escherichia coli the coenzyme pyridoxal 5'-phosphate is synthesized de novo by a pathway that is thought to involve the condensation of 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose, catalyzed by the enzymes PdxA and PdxJ, to form either pyridoxine (vitamin B6) or pyridoxine 5'-phosphate. 251 matched cddid_all.tbl CDD pfam04167 pfam04167 461204 DUF402 Protein of unknown function (DUF402). Family member FomD is a predicted protein from a fosfomycin biosynthesis gene cluster in Streptomyces wedmorensis. Its function is unknown. 68 matched cddid_all.tbl CDD pfam04168 pfam04168 461205 Alpha-E A predicted alpha-helical domain with a conserved ER motif. An uncharacterized alpha helical domain containing a highly conserved ER motif and typically found as a tandem duplication. Contextual analysis suggests that it functions in a distinct peptide synthesis/modification system comprising of a transglutaminase, a peptidase of the NTN-hydrolase superfamily, an active and inactive circularly permuted ATP-grasp domains and a transglutaminase fused N-terminal to a circularly permuted COOH-NH2 ligase domain. 303 matched cddid_all.tbl CDD pfam04170 pfam04170 461206 NlpE NlpE N-terminal domain. This family represents a bacterial outer membrane lipoprotein that is necessary for signalling by the Cpx pathway. This pathway responds to cell envelope disturbances and increases the expression of periplasmic protein folding and degradation factors. While the molecular function of the NlpE protein is unknown, it may be involved in detecting bacterial adhesion to abiotic surfaces. In Escherichia coli and Salmonella typhi, NlpE is also known to confer copper tolerance in copper-sensitive strains of Escherichia coli, and may be involved in copper efflux and delivery of copper to copper-dependent enzymes. 86 matched cddid_all.tbl CDD pfam04172 pfam04172 461207 LrgB LrgB-like family. The two products of the lrgAB operon are potential membrane proteins, and LrgA and LrgB are both thought to control of murein hydrolase activity and penicillin tolerance. 206 matched cddid_all.tbl CDD pfam04173 pfam04173 282080 DoxD TQO small subunit DoxD. Swiss:P97207 is a subunit of the terminal quinol oxidase present in the plasma membrane of Acidianus ambivalens, with calculated molecular mass of 20.4 kDa. Thiosulphate:quinone oxidoreductase (TQO) is one of the early steps in elemental sulphur oxidation. A novel TQO enzyme was purified from the thermo-acidophilic archaeon Acidianus ambivalens and shown to consist of a large subunit (DoxD) and a smaller subunit (DoxA). The DoxD- and DoxA-like two subunits are fused together in a single polypeptide in Swiss:Q8AAF0. 167 matched cddid_all.tbl CDD pfam04174 pfam04174 398029 CP_ATPgrasp_1 A circularly permuted ATPgrasp. An ATP-grasp family that is present both as catalytically active and inactive versions. Contextual analysis suggests that it functions in a distinct peptide synthesis/modification system that additionally contains a transglutaminase, an NTN-hydrolase, the Alpha-E domain, and a transglutaminase fused N-terminal to a circularly permuted COOH-NH2 ligase. The inactive forms are often fused N-terminal to the Alpha-E domain. 332 matched cddid_all.tbl CDD pfam04175 pfam04175 427760 DUF406 Protein of unknown function (DUF406). Members of this family appear to be found only in gamma proteobacteria. The function of this protein family is undetermined. Solution of the structures of the two members of this family investigated bear some resemblance to that of the single domain enzyme pterin-4a-carbinolamine dehydratase, PDC. Although the residues of PCDs involved in binding of metabolite are not conserved in the two structures under study, they do correspond to a surface-region structurally aligned with residues that are highly conserved, eg Glu 89, suggesting that this region is also involved in binding of a ligand, thereby possibly constituting a catalytic site of a yet uncharacterized enzyme specific for gamma proteobacteria. 81 matched cddid_all.tbl CDD pfam04176 pfam04176 461208 TIP41 TIP41-like family. The TOR signalling pathway activates a cell-growth program in response to nutrients. TIP41 interacts with TAP42 and negatively regulates the TOR signaling pathway. 168 matched cddid_all.tbl CDD pfam04177 pfam04177 461209 TAP42 TAP42-like family. The TOR signalling pathway activates a cell-growth program in response to nutrients. TIP41 (pfam04176) interacts with TAP42 and negatively regulates the TOR signaling pathway. 305 matched cddid_all.tbl CDD pfam04178 pfam04178 461210 Got1 Got1/Sft2-like family. Traffic through the yeast Golgi complex depends on a member of the syntaxin family of SNARE proteins, Sed5, present in early Golgi cisternae. Got1 is thought to facilitate Sed5-dependent fusion events. This is a family of sequences derived from eukaryotic proteins. They are similar to a region of a SNARE-like protein required for traffic through the Golgi complex, SFT2 protein. This is a conserved protein with four putative transmembrane helices, thought to be involved in vesicular transport in later Golgi compartments. 110 matched cddid_all.tbl CDD pfam04179 pfam04179 427764 Init_tRNA_PT Rit1 DUSP-like domain. This enzyme (EC:2.4.2.-) modifies exclusively the initiator tRNA in position 64 using 5'-phosphoribosyl-1'-pyrophosphate as the modification donor. As the initiator tRNA participates both in the initiation and elongation of translation, the 2'-O-ribosyl phosphate modification discriminates the initiator tRNAs from the elongator tRNAs. This C-terminal domain shows similarity to dual specificity phosphatases. 110 matched cddid_all.tbl CDD pfam04180 pfam04180 461211 LTV Low temperature viability protein. The low-temperature viability protein LTV1 is involved in ribosome biogenesis 40S subunit production. 370 matched cddid_all.tbl CDD pfam04181 pfam04181 461212 RPAP2_Rtr1 Rtr1/RPAP2 family. This family includes the human RPAP2 (RNAP II associated polypeptide) protein and the yeast Rtr1 protein. It has been suggested that this family of proteins are regulators of core RNA polymerase II function. 75 matched cddid_all.tbl CDD pfam04182 pfam04182 367858 B-block_TFIIIC B-block binding subunit of TFIIIC. Yeast transcription factor IIIC (TFIIIC) is a multi-subunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding. 75 matched cddid_all.tbl CDD pfam04183 pfam04183 461213 IucA_IucC IucA / IucC family. IucA and IucC catalyze discrete steps in biosynthesis of the siderophore aerobactin from N epsilon-acetyl-N epsilon-hydroxylysine and citrate. This family represents the N-terminal region. The C-terminal region appears to be related to iron transporter proteins. 210 matched cddid_all.tbl CDD pfam04184 pfam04184 461214 ST7 ST7 protein. The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene. The molecular function of this protein is uncertain. 532 matched cddid_all.tbl CDD pfam04185 pfam04185 309350 Phosphoesterase Phosphoesterase family. This family includes both bacterial phospholipase C enzymes EC:3.1.4.3, but also eukaryotic acid phosphatases EC:3.1.3.2. 348 matched cddid_all.tbl CDD pfam04186 pfam04186 427769 FxsA FxsA cytoplasmic membrane protein. This is a bacterial family of cytoplasmic membrane proteins. It includes two transmembrane regions. The molecular function of FxsA is unknown, but in Escherichia coli its over-expression has been shown to alleviate the exclusion of phage T7 in those cells with an F plasmid. 109 matched cddid_all.tbl CDD pfam04187 pfam04187 461215 Cofac_haem_bdg Haem-binding uptake, Tiki superfamily, ChaN. This is a family of putative bacterial lipoproteins necessary for the uptake of haem-iron. The structure of UniProtKB:Q0PBW2, PDB:2g5g, comprises a large parallel beta-sheet with flanking alpha-helices and a smaller domain consisting of alpha-helices. Two cofacial haem groups (~3.5 Angstom apart with an inter-iron distance of 4.4 Angstrom) bind in a pocket formed by a dimer of two ChaN monomers. 211 matched cddid_all.tbl CDD pfam04188 pfam04188 282094 Mannosyl_trans2 Mannosyltransferase (PIG-V). This is a family of eukaryotic ER membrane proteins that are involved in the synthesis of glycosylphosphatidylinositol (GPI), a glycolipid that anchors many proteins to the eukaryotic cell surface. Proteins in this family are involved in transferring the second mannose in the biosynthetic pathway of GPI. 439 matched cddid_all.tbl CDD pfam04189 pfam04189 461216 Gcd10p Gcd10p family. eIF-3 is a multi-subunit complex that stimulates translation initiation in vitro at several different steps. This family corresponds to the gamma subunit if eIF3. The Yeast protein Gcd10p has also been shown to be part of a complex with the methyltransferase Gcd14p that is involved in modifying tRNA. 295 matched cddid_all.tbl CDD pfam04190 pfam04190 461217 GET4 Golgi to ER traffic protein 4. In budding yeast, Get4 is part of the GET complex that inserts the tail-anchored (TA) proteins into the endoplasmic reticulum membrane. In humans, Get4 is part the BAG6/BAT3 complex, maintains misfolded and hydrophobic patches-containing proteins in a soluble state and facilitates their proper delivery to the endoplasmic reticulum, or alternatively promotes their sorting to the proteasome where they undergo degradation. The BAG6/BAT3 complex is involved in the post-translational delivery of tail-anchored/type II transmembrane proteins to the endoplasmic reticulum membrane. 251 matched cddid_all.tbl CDD pfam04191 pfam04191 461218 PEMT Phospholipid methyltransferase. The S. cerevisiae phospholipid methyltransferase (EC:2.1.1.16) has a broad substrate specificity of unsaturated phospholipids. 105 matched cddid_all.tbl CDD pfam04192 pfam04192 461219 Utp21 Utp21 specific WD40 associated putative domain. Utp21 is a subunit of U3 snoRNP, which is essential for synthesis of 18S rRNA. 209 matched cddid_all.tbl CDD pfam04193 pfam04193 461220 PQ-loop PQ loop repeat. Members of this family are all membrane bound proteins possessing a pair of repeats each spanning two transmembrane helices connected by a loop. The PQ motif found on loop 2 is critical for the localization of cystinosin to lysosomes. However, the PQ motif appears not to be a general lysosome-targeting motif. It is thought likely to possess a more general function. Most probably this involves a glutamine residue. Family members are membrane transporters since two members, cystinosin and PQLC2, transport cystine and cationic amino acids, respectively, across the lysosomal membrane. The 2nd PQ-loop of cystinosin hosts the substrate-coupled H+ binding site underlying its H+ symport mechanism, suggesting that PQ-loop repeats have functional significance. It is thus likely that PQ-loop-containing proteins act as a family of membrane transporters. Some transport cystine and cationic amino acids, respectively, across the lysosomal membrane. Others transport lysine and or arginine across the lysosomal membrane in order to maintain the acidic homoeostasis. 61 matched cddid_all.tbl CDD pfam04194 pfam04194 461221 PDCD2_C Programmed cell death protein 2, C-terminal putative domain. 111 matched cddid_all.tbl CDD pfam04195 pfam04195 461222 Transposase_28 Putative gypsy type transposon. This family of plant genes are thought to be related to gypsy type transposons. 69 matched cddid_all.tbl CDD pfam04196 pfam04196 282102 Bunya_RdRp Bunyavirus RNA dependent RNA polymerase. The bunyaviruses are enveloped viruses with a genome consisting of 3 ssRNA segments (called L, M and S). The nucleocapsid protein is encode on the small (S) genomic RNA. The L segment codes for an RNA polymerase. This family contains the RNA dependent RNA polymerase on the L segment. 739 matched cddid_all.tbl CDD pfam04197 pfam04197 461223 Birna_RdRp_palm "Birnavirus RNA dependent RNA polymerase (VP1), palm domain. Birnaviruses are dsRNA viruses. This entry corresponds to the ""palm"" domain of the RNA dependent RNA polymerase, also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic ""palm"" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. The catalytic motifs are arranged in a permuted order in sequence." 531 matched cddid_all.tbl CDD pfam04198 pfam04198 427778 Sugar-bind Putative sugar-binding domain. This probable domain is found in bacterial transcriptional regulators such as DeoR and SorC. These proteins have an amino-terminal helix-turn-helix pfam00325 that binds to DNA. This domain is probably the ligand regulator binding region. SorC is regulated by sorbose and other members of this family are likely to be regulated by other sugar substrates. 256 matched cddid_all.tbl CDD pfam04199 pfam04199 461224 Cyclase Putative cyclase. Proteins in this family are thought to be cyclase enzymes. They are found in proteins involved in antibiotic synthesis. However they are also found in organizms that do not make antibiotics pointing to a wider role for these proteins. The proteins contain a conserved motif HXGTHXDXPXH that is likely to form part of the active site. 159 matched cddid_all.tbl CDD pfam04200 pfam04200 398051 Lipoprotein_17 Lipoprotein associated domain. This presumed domain is about 100 amino acids in length. It is found in lipoprotein of unknown function and is greatly expanded in Mycoplasma pulmonis. The domain is found in up to five copies in some proteins. This family also includes the Mycoplasma arthritidis MAA2 variable surface protein. MAA2 is implicated in in cytoadherence and virulence and has been shown to exhibit both size and phase variability. 84 matched cddid_all.tbl CDD pfam04201 pfam04201 461225 TPD52 Tumour protein D52 family. The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologs from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologs of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family. These proteins have an amino terminal coiled-coil that allows members to form homo- and heterodimers with each other. 99 matched cddid_all.tbl CDD pfam04202 pfam04202 112992 Mfp-3 Foot protein 3. Mytilus foot protein-3 (Mfp-3) is a highly polymorphic protein family located in the byssal adhesive plaques of blue mussels. 71 matched cddid_all.tbl CDD pfam04203 pfam04203 427781 Sortase Sortase domain. The founder member of this family is S. aureus sortase, a transpeptidase that attaches surface proteins by the threonine of an LPXTG motif to the cell wall. 121 matched cddid_all.tbl CDD pfam04204 pfam04204 427782 HTS Homoserine O-succinyltransferase. The activation of homoserine through succinylation of homoserine in some bacteria, such as Escherichia coli and Bacillus cereus, is carried out by homoserine O-succinyltransferase (HTS, EC:2.3.1.46), while other bacteria, such as Haemophilus influenzae, Pseudomonas aeruginosa, and Mycobacterium tuberculosis, acetylate homoserine via homoserine O-acetyltransferase (HTA;EC:2.3.1.31). This family also includes serine acetyltransferase CysE (EC:2.3.1.30) from Lactobacillus casei, which catalyzes the formation of O-acetyl serine from L-serine and acetyl-CoA, and is involved in cysteine biosynthesis. 298 matched cddid_all.tbl CDD pfam04205 pfam04205 461226 FMN_bind FMN-binding domain. This conserved region includes the FMN-binding site of the NqrC protein as well as the NosR and NirI regulatory proteins. This domain is post-translationally flavinylated that may facilitate electron transfer, and thus, resembles multiheme cytochromes. 71 matched cddid_all.tbl CDD pfam04206 pfam04206 427784 MtrE Tetrahydromethanopterin S-methyltransferase, subunit E. The N5-methyltetrahydromethanopterin: coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump. 271 matched cddid_all.tbl CDD pfam04207 pfam04207 427785 MtrD Tetrahydromethanopterin S-methyltransferase, subunit D. The N5-methyltetrahydromethanopterin: coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump. 218 matched cddid_all.tbl CDD pfam04208 pfam04208 427786 MtrA Tetrahydromethanopterin S-methyltransferase, subunit A. The N5-methyltetrahydromethanopterin: coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump. 165 matched cddid_all.tbl CDD pfam04209 pfam04209 461227 HgmA_C Homogentisate 1,2-dioxygenase C-terminal. Homogentisate dioxygenase cleaves the aromatic ring during the metabolic degradation of Phe and Tyr. Homogentisate dioxygenase deficiency causes alkaptonuria. The structure of homogentisate dioxygenase shows that the enzyme forms a hexamer arrangement comprised of a dimer of trimers. The active site iron ion is coordinated near the interface between the trimers. This entry represents the C-terminal active site domain. 153 matched cddid_all.tbl CDD pfam04210 pfam04210 427787 MtrG Tetrahydromethanopterin S-methyltransferase, subunit G. The N5-methyltetrahydromethanopterin: coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump. 64 matched cddid_all.tbl CDD pfam04211 pfam04211 427788 MtrC Tetrahydromethanopterin S-methyltransferase, subunit C. The N5-methyltetrahydromethanopterin: coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump. 266 matched cddid_all.tbl CDD pfam04212 pfam04212 461228 MIT MIT (microtubule interacting and transport) domain. The MIT domain forms an asymmetric three-helix bundle and binds ESCRT-III (endosomal sorting complexes required for transport) substrates. 66 matched cddid_all.tbl CDD pfam04213 pfam04213 427790 HtaA Htaa. This domain is found in HtaA, a secreted protein implicated in iron acquisition and transport. 162 matched cddid_all.tbl CDD pfam04214 pfam04214 427791 DUF411 Protein of unknown function, DUF. The function of the members of this bacterial protein family is unknown. Some members may be involved in conferring cation resistance. 69 matched cddid_all.tbl CDD pfam04216 pfam04216 427792 FdhE Protein involved in formate dehydrogenase formation. The function of these proteins is unknown. They may possibly be involved in the formation of formate dehydrogenase. 286 matched cddid_all.tbl CDD pfam04217 pfam04217 427793 DUF412 Protein of unknown function, DUF412. This family consists of bacterial proteins, including yfbV from E. coli. YfbV is a membrane protien involved in insulating the chromosome from the TerR macrodomain. 140 matched cddid_all.tbl CDD pfam04218 pfam04218 461229 CENP-B_N CENP-B N-terminal DNA-binding domain. Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure. 53 matched cddid_all.tbl CDD pfam04219 pfam04219 427794 DUF413 Protein of unknown function, DUF. 90 matched cddid_all.tbl CDD pfam04220 pfam04220 427795 YihI Der GTPase activator (YihI). YihI activates the GTPase activity of Der, a 50S ribosomal subunit stability factor. The stimulation is specific to Der as YihI does not stimulate the GTPase activity of Era or ObgE. The interaction of YihI with Der requires only the C-terminal 78 amino acids of YihI. A yihI deletion mutant is viable and shows a shorter lag period, but the same post-lag growth rate as a wild-type strain. yihI is expressed during the lag period. Overexpression of yihI inhibits cell growth and biogenesis of the 50S ribosomal subunit. YihI is an unusual, highly hydrophilic protein with an uneven distribution of charged residues, resulting in an N-terminal region with high pI and a C-terminal region with low pI. 155 matched cddid_all.tbl CDD pfam04221 pfam04221 427796 RelB RelB antitoxin. RelE and RelB form a toxin-antitoxin system. RelE represses translation, probably through binding ribosomes. RelB stably binds RelE, presumably deactivating it. 83 matched cddid_all.tbl CDD pfam04222 pfam04222 427797 DUF416 Protein of unknown function (DUF416). This is a bacterial protein family of unknown function. Proteins in this family adopt an alpha helical structure. Genome context analysis has suggested a high probability of a functional association with histidine kinases, which implicates proteins in this family to play a role in signalling (information from TOPSAN 2Q9R). 183 matched cddid_all.tbl CDD pfam04223 pfam04223 427798 CitF Citrate lyase, alpha subunit (CitF). In citrate-utilizing prokaryotes, citrate lyase EC:4.1.3.6 cleaves intracellular citrate into acetate and oxaloacetate, and is organized as a functional complex consisting of alpha, beta, and gamma subunits. The gamma subunit serves as an acyl carrier protein (ACP), and has a 2'-(5''-phosphoribosyl)-3'-dephospho-CoA prosthetic group. The citrate lyase is active only if this prosthetic group is acetylated; this acetylation is catalyzed by an acetate:SH-citrate lyase ligase. The alpha subunit substitutes citryl for the acetyl group to form citryl-S-ACP. The beta subunit completes the reaction by cleaving the citryl to yield oxaloacetate and (regenerated) acetyl-S-ACP. This family represents the alpha subunit EC:2.8.3.10. 466 matched cddid_all.tbl CDD pfam04224 pfam04224 282127 DUF417 Protein of unknown function, DUF417. This family of uncharacterized proteins appears to be restricted to proteobacteria. 175 matched cddid_all.tbl CDD pfam04225 pfam04225 427799 OapA Opacity-associated protein A LysM-like domain. The OapA domain gets its name from the Haemophilus influenzae protein OapA, which is required for the expression of colony opacity, thus opacity- associated protein A. The OapA protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation. The OapA domain has been shown to bind to peptidoglycan in the E. coli protein YtfB. A screen to identify factors that affect cell division in E. coli discovered that overproducing a fragment of YtfB, including its OapA domain, caused cells to grow as long filaments. OapA domains are commonly associated with other domains that are involved in breaking peptidoglycan cross-links. The OapA domain is distantly related to pfam01476. 85 matched cddid_all.tbl CDD pfam04226 pfam04226 461230 Transgly_assoc Transglycosylase associated protein. Bacterial protein, predicted to be an integral membrane protein. Some family members have been annotated as transglycosylase associated proteins, but no experimental evidence is provided. This family was annotated based on the information in Swiss:P76011. 49 matched cddid_all.tbl CDD pfam04227 pfam04227 461231 Indigoidine_A Indigoidine synthase A like protein. Indigoidine is a blue pigment synthesized by Erwinia chrysanthemi implicated in pathogenicity and protection from oxidative stress. IdgA is involved in indigoidine biosynthesis, but its specific function is unknown. The recommended name for this protein is now pseudouridine-5'-phosphate glycosidase. 289 matched cddid_all.tbl CDD pfam04228 pfam04228 427802 Zn_peptidase Putative neutral zinc metallopeptidase. Members of this family have a predicted zinc binding motif characteriztic of neutral zinc metallopeptidases (Prosite:PDOC00129). 290 matched cddid_all.tbl CDD pfam04229 pfam04229 461232 GrpB GrpB protein. This family has been suggested to belong to the nucleotidyltransferase superfamily. It occurs at the C-terminus of dephospho-CoA kinase (CoaE) in a number of cases, where it plays a role in the proper folding of the enzyme. 161 matched cddid_all.tbl CDD pfam04230 pfam04230 427804 PS_pyruv_trans Polysaccharide pyruvyl transferase. Pyruvyl-transferases involved in peptidoglycan-associated polymer biosynthesis. CsaB in Bacillus anthracis is necessary for the non-covalent anchoring of proteins containing an SLH (S-layer homology) domain to peptidoglycan-associated pyruvylated polysaccharides. WcaK and AmsJ are involved in the biosynthesis of colanic acid in Escherichia coli and of amylovoran in Erwinia amylovora. 233 matched cddid_all.tbl CDD pfam04231 pfam04231 398077 Endonuclease_1 Endonuclease I. Bacterial periplasmic or secreted endonuclease I (EC:3.1.21.1) E. coli endonuclease I (EndoI) is a sequence independent endonuclease located in the periplasm. It is inhibited by different RNA species. It is thought to normally generate double strand breaks in DNA, except in the presence of high salt concentrations and RNA, when it generates single strand breaks in DNA. Its biological role is unknown. Other family members are known to be extracellular. This family also includes a non-specific, Mg2+ activated ribonuclease precursor. 235 matched cddid_all.tbl CDD pfam04232 pfam04232 427805 SpoVS Stage V sporulation protein S (SpoVS). In Bacillus subtilis this protein interferes with sporulation at an early stage and this inhibitory effect is overcome by SpoIIB and SpoVG. SpoVS seems to play a positive role in allowing progression beyond stage V of sporulation. Null mutations in the spoVS gene block sporulation at stage V, impairing the development of heat resistance and coat assembly. 81 matched cddid_all.tbl CDD pfam04233 pfam04233 309383 Phage_Mu_F Phage Mu protein F like protein. Members of this family are found in double-stranded DNA bacteriophages, and in some bacteria. A member of this family is required for viral head morphogenesis in bacteriophage SPP1. This family is possibly a minor head protein. This family may be related to the family TT_ORF1 (pfam02956). 110 matched cddid_all.tbl CDD pfam04234 pfam04234 427806 CopC CopC domain. CopC is a bacterial blue copper protein that binds 1 atom of copper per protein molecule. Along with CopA, CopC mediates copper resistance by sequestration of copper in the periplasm. 92 matched cddid_all.tbl CDD pfam04235 pfam04235 427807 DUF418 Protein of unknown function (DUF418). Probable integral membrane protein. 163 matched cddid_all.tbl CDD pfam04236 pfam04236 398081 Transp_Tc5_C Tc5 transposase C-terminal domain. This family corresponds to a C-terminal cysteine rich region that probably binds to a metal ion and could be DNA binding (pers. obs. A Bateman). 63 matched cddid_all.tbl CDD pfam04237 pfam04237 461233 YjbR YjbR. YjbR has a CyaY-like fold. 91 matched cddid_all.tbl CDD pfam04238 pfam04238 427809 DUF420 Protein of unknown function (DUF420). Predicted membrane protein with four transmembrane helices. 130 matched cddid_all.tbl CDD pfam04239 pfam04239 427810 DUF421 Protein of unknown function (DUF421). YDFR family 119 matched cddid_all.tbl CDD pfam04240 pfam04240 427811 Caroten_synth Carotenoid biosynthesis protein. The representative member of this family is CruF, a C50 carotenoid 2',3'-hydratase involved in the synthesis of the C50 carotenoid bacterioruberin in the halophilic archaeon Haloarcula japonica. 209 matched cddid_all.tbl CDD pfam04241 pfam04241 461234 DUF423 Protein of unknown function (DUF423). This family of proteins with unknown function is a possible integral membrane protein from Caenorhabditis elegans. This family of proteins has GO references indicating the protein is involved in nematode larval development and is a positive regulator of growth rate. 86 matched cddid_all.tbl CDD pfam04242 pfam04242 377260 DUF424 Protein of unknown function (DUF424). This is a family of uncharacterized proteins. 92 matched cddid_all.tbl CDD pfam04244 pfam04244 461235 DPRP Deoxyribodipyrimidine photo-lyase-related protein. This family appears to be related to pfam00875. 221 matched cddid_all.tbl CDD pfam04245 pfam04245 427814 NA37 37-kD nucleoid-associated bacterial protein. 312 matched cddid_all.tbl CDD pfam04246 pfam04246 461236 RseC_MucC Positive regulator of sigma(E), RseC/MucC. This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions). In Pseudomonas aeruginosa, de-repression of sigma(E) is associated with the alginate-overproducing phenotype characteriztic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains an ApbE domain pfam02424, which is itself involved in thiamine biosynthesis. 130 matched cddid_all.tbl CDD pfam04247 pfam04247 427816 SirB Invasion gene expression up-regulator, SirB. SirB up-regulates Salmonella typhimurium invasion gene transcription. It is, however, not essential for the expression of these genes. Its function is unknown. 118 matched cddid_all.tbl CDD pfam04248 pfam04248 461237 NTP_transf_9 Domain of unknown function (DUF427). This domain contains a beta-tent fold. 93 matched cddid_all.tbl CDD pfam04250 pfam04250 427818 DUF429 Protein of unknown function (DUF429). 209 matched cddid_all.tbl CDD pfam04252 pfam04252 427819 RNA_Me_trans Predicted SAM-dependent RNA methyltransferase. This family of proteins are predicted to be alpha/beta-knot SAM-dependent RNA methyltransferases. 200 matched cddid_all.tbl CDD pfam04253 pfam04253 461238 TFR_dimer Transferrin receptor-like dimerization domain. This domain is involved in dimerization of the transferrin receptor as shown in its crystal structure. 116 matched cddid_all.tbl CDD pfam04254 pfam04254 427821 DUF432 Protein of unknown function (DUF432). Archaeal protein of unknown function. 120 matched cddid_all.tbl CDD pfam04255 pfam04255 427822 DUF433 Protein of unknown function (DUF433). 54 matched cddid_all.tbl CDD pfam04256 pfam04256 461239 DUF434 Protein of unknown function (DUF434). 56 matched cddid_all.tbl CDD pfam04257 pfam04257 461240 Exonuc_V_gamma Exodeoxyribonuclease V, gamma subunit. The Exodeoxyribonuclease V enzyme is a multi-subunit enzyme comprised of the proteins RecB, RecC (this family) and RecD. This enzyme plays an important role in homologous genetic recombination, repair of double strand DNA breaks resistance to UV irradiation and chemical DNA-damage. The enzyme (EC:3.1.11.5) catalyzes ssDNA or dsDNA-dependent ATP hydrolysis, hydrolysis of ssDNA or dsDNA and unwinding of dsDNA. This subunit recognizes and binds DNA forks containing Chi sequences in a sequence specific manner while Chi interactions with the phosphodiester backbone (mainly arginine side chains) stabilize the twisted conformation of the DNA. These interactions induce conformational changes that switch RecBCD from bacteriophage destruction and CRISPR spacer acquisition, to constructive host DNA repair. 308 matched cddid_all.tbl CDD pfam04258 pfam04258 282158 Peptidase_A22B Signal peptide peptidase. The members of this family are membrane proteins. In some proteins this region is found associated with pfam02225. This family corresponds with Merops subfamily A22B, the type example of which is signal peptide peptidase. There is a sequence-similarity relationship with pfam01080. 286 matched cddid_all.tbl CDD pfam04259 pfam04259 367886 SASP_gamma Small, acid-soluble spore protein, gamma-type. The SASP family is a family of small, glutamine and asparagine-rich peptides that store amino acids in the spores of Bacillus subtilis and related bacteria. 84 matched cddid_all.tbl CDD pfam04260 pfam04260 427825 DUF436 Protein of unknown function (DUF436). Family of bacterial proteins with undetermined function. 170 matched cddid_all.tbl CDD pfam04261 pfam04261 461241 Dyp_perox Dyp-type peroxidase family. This family of dye-decolourising peroxidases lack a typical heme-binding region. 315 matched cddid_all.tbl CDD pfam04262 pfam04262 427826 Glu_cys_ligase Glutamate-cysteine ligase. Family of bacterial f glutamate-cysteine ligases (EC:6.3.2.2) that carry out the first step of the glutathione biosynthesis pathway. 371 matched cddid_all.tbl CDD pfam04263 pfam04263 461242 TPK_catalytic Thiamin pyrophosphokinase, catalytic domain. Family of thiamin pyrophosphokinase (EC:2.7.6.2). Thiamin pyrophosphokinase (TPK) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggest that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis. 112 matched cddid_all.tbl CDD pfam04264 pfam04264 461243 YceI YceI-like domain. E. coli YceI is a base-induced periplasmic protein. The recent structure of a member of this family shows that it binds to poly-isoprenoid. The structure consists of an extended, eight-stranded, antiparallel beta-barrel that resembles the lipocalin fold. 118 matched cddid_all.tbl CDD pfam04265 pfam04265 461244 TPK_B1_binding Thiamin pyrophosphokinase, vitamin B1 binding domain. Family of thiamin pyrophosphokinase (EC:2.7.6.2). Thiamin pyrophosphokinase (TPK) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggest that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis. 66 matched cddid_all.tbl CDD pfam04266 pfam04266 398105 ASCH ASCH domain. The ASCH domain adopts a beta-barrel fold similar to the pfam01472 domain. It is thought to function as an RNA-binding domain during coactivation, RNA-processing and possibly during prokaryotic translation regulation. 102 matched cddid_all.tbl CDD pfam04267 pfam04267 427830 SoxD Sarcosine oxidase, delta subunit family. Sarcosine oxidase is a hetero-tetrameric enzyme that contains both covalently bound FMN and non-covalently bound FAD and NAD(+). This enzyme catalyzes the oxidative demethylation of sarcosine to yield glycine, H2O2, and 5,10-CH2-tetrahydrofolate (H4folate) in a reaction requiring H4folate and O2. 82 matched cddid_all.tbl CDD pfam04268 pfam04268 461245 SoxG Sarcosine oxidase, gamma subunit family. Sarcosine oxidase is a hetero-tetrameric enzyme that contains both covalently bound FMN and non-covalently bound FAD and NAD(+). This enzyme catalyzes the oxidative demethylation of sarcosine to yield glycine, H2O2, and 5,10-CH2-tetrahydrofolate (H4folate) in a reaction requiring H4folate and O2. 152 matched cddid_all.tbl CDD pfam04269 pfam04269 427831 DUF440 Protein of unknown function, DUF440. This family consists of uncharacterized bacterial proteins. 101 matched cddid_all.tbl CDD pfam04270 pfam04270 461246 Strep_his_triad Streptococcal histidine triad protein. All members of this family are proteins from Streptococcal species. The proteins are characterized by having a HxxHxH motif that usually occurs multiple times throughout the protein. The histidine triad is predicted to bind metal cations, in particular Zn2+. The zinc is transferred, on the surface of the streptococcus from the Strep_his_triad protein, a zinc scavenger, to apo-ADCAII, a cell-surface lipoprotein transporter that leads to Zn2+ uptake into the bacterium. 51 matched cddid_all.tbl CDD pfam04272 pfam04272 367891 Phospholamban Phospholamban. The regulation of calcium levels across the membrane of the sarcoplasmic reticulum involves the interplay of many membrane proteins. Phospholamban is a 52 residue integral membrane protein that is involved in reversibly inhibiting the Ca(2+) pump and regulating the flow of Ca ions across the sarcoplasmic reticulum membrane during muscle contraction and relaxation. Phospholamban is thought to form a pentamer in the membrane. 52 matched cddid_all.tbl CDD pfam04273 pfam04273 398110 BLH_phosphatase Beta-lactamase hydrolase-like protein, phosphatase-like domain. This domain is found N-terminal to a beta-lactamase domain, and it may have phosphatase activity. This domain is found in Beta-lactamase hydrolase-like protein from Agrobacterium fabrum, which may play a role in cell adherence or biofilm development. 110 matched cddid_all.tbl CDD pfam04275 pfam04275 461247 P-mevalo_kinase Phosphomevalonate kinase. Phosphomevalonate kinase (EC:2.7.4.2) catalyzes the phosphorylation of 5-phosphomevalonate into 5-diphosphomevalonate, an essential step in isoprenoid biosynthesis via the mevalonate pathway. This family represents the animal type of the enzyme. The other is the ERG8 type, found in plants and fungi, and some bacteria (see pfam00288). 112 matched cddid_all.tbl CDD pfam04276 pfam04276 398112 DUF443 Protein of unknown function (DUF443). Family of uncharacterized proteins. 202 matched cddid_all.tbl CDD pfam04277 pfam04277 461248 OAD_gamma Oxaloacetate decarboxylase, gamma chain. 76 matched cddid_all.tbl CDD pfam04278 pfam04278 398114 Tic22 Tic22-like family. The preprotein translocation at the inner envelope membrane of chloroplasts so far involves five proteins: Tic110, Tic55, Tic40, Tic22 (this family) and Tic20. The molecular function of these proteins has not yet been established. 244 matched cddid_all.tbl CDD pfam04279 pfam04279 461249 IspA Intracellular septation protein A. Inner membrane-spanning protein YciB (also known as intracellular septation protein A) is a family of proteins which are essential for both normal cell division and bacterial virulence and are believed to play a role in the septation process. These proteins play a role in cell envelope biogenesis, maintenance of cell envelope integrity and membrane homeostasis. 176 matched cddid_all.tbl CDD pfam04280 pfam04280 427835 Tim44 Tim44-like domain. Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane. Tim44 is thought to bind phospholipids of the mitochondrial inner membrane both by electrostatic interactions and by penetrating the polar head group region. This family includes the C-terminal region of Tim44 that has been shown to form a stable proteolytic fragment in yeast. This region is also found in a set of smaller bacterial proteins. The molecular function of the bacterial members of this family is unknown but transport seems likely. The crystal structure of the C terminal of Tim44 has revealed a large hydrophobic pocket which might play an important role in interacting with the acyl chains of lipid molecules in the mitochondrial membrane. 145 matched cddid_all.tbl CDD pfam04281 pfam04281 427836 Tom22 "Mitochondrial import receptor subunit Tom22. The mitochondrial protein translocase family, which is responsible for movement of nuclear encoded pre-proteins into mitochondria, is very complex with at least 19 components. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three ""motor"" proteins. This family represents the Tom22 proteins. The N terminal region of Tom22 has been shown to have chaperone-like activity, and the C terminal region faces the intermembrane face." 138 matched cddid_all.tbl CDD pfam04282 pfam04282 427837 DUF438 Family of unknown function (DUF438). 67 matched cddid_all.tbl CDD pfam04283 pfam04283 398119 CheF-arch Chemotaxis signal transduction system protein F from archaea. This is a family of proteins that are archaea-specific components of the bacterial-like chemotaxis signal transduction system of archaea. In H. salinarum, the CheF proteins interact with the chemotaxis proteins CheY, CheD and CheC2 as well as the flagella-accessory proteins FlaCE and FlaD, and are essential for any tactic response. CheF probably functions at the interface between the bacterial-like chemotaxis signal transduction system and the archaeal flagellar apparatus. 217 matched cddid_all.tbl CDD pfam04284 pfam04284 461250 DUF441 Protein of unknown function (DUF441). Predicted to be an integral membrane protein. 139 matched cddid_all.tbl CDD pfam04285 pfam04285 427839 DUF444 Protein of unknown function (DUF444). Bacterial protein of unknown function. One family member is predicted to contain a von Willebrand factor (vWF) type A domain (Smart:VWA). Another family member YeaH is predicted to be part of a conserved signalling pathway with the kinase YeaG and the SpoVR protein YcgB. The pathway may be involved in nitrogen metabolism (see Supplementary note 5 in.) 409 matched cddid_all.tbl CDD pfam04286 pfam04286 427840 DUF445 Protein of unknown function (DUF445). Predicted to be a membrane protein. 368 matched cddid_all.tbl CDD pfam04287 pfam04287 427841 DUF446 tRNA pseudouridine synthase C. This family is suggested to be the catalytic domain of tRNA pseudouridine synthase C by association. The structure has been solved for one member, as PDB:2HGK, which by inference is designated in this way. 97 matched cddid_all.tbl CDD pfam04288 pfam04288 427842 MukE MukE-like family. Bacterial protein involved in chromosome partitioning, MukE 229 matched cddid_all.tbl CDD pfam04289 pfam04289 398125 DUF447 Protein of unknown function (DUF447). Archaeal protein of unknown function. A fungal member UniProtKB:M2LN89 is clearly a Flavine-reductase enzyme by homology, and UniProtKB:O28442 has been shown to bind riboflavin 5'-phosphate (unpublished structural Xray analysis). 174 matched cddid_all.tbl CDD pfam04290 pfam04290 427843 DctQ Tripartite ATP-independent periplasmic transporters, DctQ component. The function of the members of this family is unknown, but DctQ homologs are invariably found in the tripartite ATP-independent periplasmic transporters. 132 matched cddid_all.tbl CDD pfam04293 pfam04293 427844 SpoVR SpoVR like protein. Family member Swiss:P37875 is Bacillus subtilis stage V sporulation protein R, which is involved in spore cortex formation. Little is known about cortex biosynthesis, except that it depends on several sigma E controlled genes, including spoVR. Another family member is an uncharacterized protein YcgB. YcgB has been suggested to be part of a conserved signalling pathway with YeaH and YeaG. This pathway may be involved in nitrogen metabolism (see Supplementary note 5 in.) 419 matched cddid_all.tbl CDD pfam04294 pfam04294 461251 VanW VanW like protein. Family members include vancomycin resistance protein W (VanW). Genes encoding members of this family have been found in vancomycin resistance gene clusters vanB and vanG. The function of VanW is unknown. 130 matched cddid_all.tbl CDD pfam04295 pfam04295 461252 GD_AH_C D-galactarate dehydratase / Altronate hydrolase, C terminus. Family members include the C termini of D-galactarate dehydratase (EC:4.2.1.42) which is thought to catalyze the reaction D-galactarate = 5-keto-4-deoxy-D-glucarate + H2O, and altronate hydrolase (altronic acid hydratase, EC:4.2.1.7), which catalyzes D-altronate = 2-keto-2-deoxygluconate + H2O. As purified, both enzymes are catalytically inactive in the absence of added Fe2+, Mn2+, and beta-mercaptoethanol. Synergistic activation of altronate hydrolase activity is seen in the presence of both iron and manganese ions, suggesting that the enzyme may have two ion binding sites. Mn2+ appears to be part of the enzyme active centre, but the function of the single bound Fe2+ ion is unknown. The hydratase has no Fe-S core. 393 matched cddid_all.tbl CDD pfam04296 pfam04296 427847 YlxR Protein of unknown function (DUF448). The YlxR family has been demonstrated to regulate metabolic gene expression. 75 matched cddid_all.tbl CDD pfam04297 pfam04297 282193 UPF0122 Putative helix-turn-helix protein, YlxM / p13 like. Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13. Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway. 98 matched cddid_all.tbl CDD pfam04298 pfam04298 461253 Zn_peptidase_2 Putative neutral zinc metallopeptidase. Zinc metallopeptidase zinc binding regions have been predicted in some family members by a pattern match (Prosite:PS00142), of the characteriztic HEXXH motif. 217 matched cddid_all.tbl CDD pfam04299 pfam04299 461254 FMN_bind_2 Putative FMN-binding domain. In Bacillus subtilis, family member PAI 2/ORF-2 was found to be essential for growth. The SUPERFAMILY database finds that this domain is related to FMN-binding domains, suggesting this protein is also FMN-binding. 166 matched cddid_all.tbl CDD pfam04300 pfam04300 461255 FBA F-box associated region. Members of this family are associated with F-box domains, hence the name FBA. This domain is probably involved in binding other proteins that will be targeted for ubiquitination. Swiss:Q9UK22 is involved in binding to N-glycosylated proteins. 175 matched cddid_all.tbl CDD pfam04301 pfam04301 113085 DUF452 Protein of unknown function (DUF452). 213 matched cddid_all.tbl CDD pfam04303 pfam04303 398133 PrpF PrpF protein. PrpF is a protein found in the 2-methylcitrate pathway. It is structurally similar to DAP epimerase and proline racemase. This protein is likely to acts to isomerize trans-aconitate to cis-aconitate. 384 matched cddid_all.tbl CDD pfam04304 pfam04304 427851 DUF454 Protein of unknown function (DUF454). Predicted membrane protein. 115 matched cddid_all.tbl CDD pfam04305 pfam04305 461256 DUF455 Protein of unknown function (DUF455). 247 matched cddid_all.tbl CDD pfam04306 pfam04306 461257 DUF456 Protein of unknown function (DUF456). This family is a putative membrane protein that contains glycine zipper motifs. 135 matched cddid_all.tbl CDD pfam04307 pfam04307 427854 YdjM LexA-binding, inner membrane-associated putative hydrolase. YdjM is a family of putative LexA-binding proteins. Members are predicted to be membrane-bound metal-dependent hydrolases that may be acting as phospholipases. It is a member of the SOS network, that rescues cells from UV and other DNA-damage. Expression of YdjM is regulated by LexA. 172 matched cddid_all.tbl CDD pfam04308 pfam04308 398138 RNaseH_like Ribonuclease H-like. RNaseH_like is a family of uncharacterized eubacterial proteins that are distant homologs of Ribonuclease H-like. The family maintains all the core secondary structure elements of the RNase H-like fold and shares several conserved, presumably active site residues with RNase HI. This finding suggests that it functions as a nuclease. 145 matched cddid_all.tbl CDD pfam04309 pfam04309 427855 G3P_antiterm Glycerol-3-phosphate responsive antiterminator. Intracellular glycerol is usually converted to glycerol-3-phosphate in an ATP-requiring phosphorylation reaction catalyzed by glycerol kinase (GlpK) glycerol-3-phosphate activates the antiterminator GlpP. 173 matched cddid_all.tbl CDD pfam04310 pfam04310 427856 MukB MukB N-terminal. This family represents the N-terminal region of MukB, one of a group of bacterial proteins essential for the movement of nucleoids from mid-cell towards the cell quarters (i.e. chromosome partitioning). The structure of the N-terminal domain consists of an antiparallel six-stranded beta sheet surrounded by one helix on one side and by five helices on the other side. It contains an exposed Walker A loop in an unexpected helix-loop-helix motif (in other proteins, Walker A motifs generally adopt a P loop conformation as part of a strand-loop-helix motif embedded in a conserved topology of alternating helices and (parallel) beta strands). 226 matched cddid_all.tbl CDD pfam04311 pfam04311 461258 DUF459 Protein of unknown function (DUF459). Putative periplasmic protein. 322 matched cddid_all.tbl CDD pfam04312 pfam04312 427857 DUF460 Protein of unknown function (DUF460). Archaeal protein of unknown function. 135 matched cddid_all.tbl CDD pfam04313 pfam04313 427858 HSDR_N Type I restriction enzyme R protein N terminus (HSDR_N). This family consists of a number of N terminal regions found in type I restriction enzyme R (HSDR) proteins. Restriction and modification (R/M) systems are found in a wide variety of prokaryotes and are thought to protect the host bacterium from the uptake of foreign DNA. Type I restriction and modification systems are encoded by three genes: hsdR, hsdM, and hsdS. The three polypeptides, HsdR, HsdM, and HsdS, often assemble to give an enzyme (R2M2S1) that modifies hemimethylated DNA and restricts unmethylated DNA. 151 matched cddid_all.tbl CDD pfam04314 pfam04314 461259 PCuAC Copper chaperone PCu(A)C. PCu(A)C is a periplasmic copper chaperone. Its role may be to capture and transfer copper to two other copper chaperones, PrrC and Cox11, which in turn deliver Cu(I) to cytochrome c oxidase. 107 matched cddid_all.tbl CDD pfam04315 pfam04315 427860 EpmC Elongation factor P hydroxylase. This family catalyzes the final step in the elongation factor P modification pathway. It hydroxylates Lys-34 of elongation factor P. Members of this family have a conserved HEXXH motif, suggesting they are putative peptidases of zincin fold. 162 matched cddid_all.tbl CDD pfam04316 pfam04316 461260 FlgM Anti-sigma-28 factor, FlgM. FlgM binds and inhibits the activity of the transcription factor sigma 28. Inhibition of sigma 28 prevents the expression of genes from flagellar transcriptional class 3, which include genes for the filament and chemotaxis. Correctly assembled basal body-hook structures export FlgM, relieving inhibition of sigma 28 and allowing expression of class 3 genes. NMR studies show that free FlgM is mostly unfolded, which may facilitate its export. The C terminal half of FlgM adopts a tertiary structure when it binds to sigma 28. All mutations in FlgM that prevent sigma 28 inhibition affect the C-terminal domain and is the region thought to constitute the binding domain. A minimal binding domain has been identified between Glu 64 and Arg 88 in Salmonella typhimurium. The N-terminal portion remains unstructured and may be necessary for recognition by the export machinery. 54 matched cddid_all.tbl CDD pfam04317 pfam04317 427862 DUF463 YcjX-like family, DUF463. This family represents a group of uncharacterized proteins including a bacterial stress protein YcjX. The crystal structure of YcjX from Shewanella oneidensis has now been solved, and shows it to be a Ras-like GTP-binding protein. However, YcjX utilizes a non-canonical switch 2' motif not found in any other G protein. 443 matched cddid_all.tbl CDD pfam04318 pfam04318 367903 DUF468 Protein of unknown function (DUF468). These conserved ORFs probably are probably not translated into protein [Personal communication, Val Wood]. 84 matched cddid_all.tbl CDD pfam04319 pfam04319 427863 NifZ NifZ domain. This short protein is found in the nif (nitrogen fixation) operon. Its function is unknown but is probably involved in nitrogen fixation or regulating some component of this process. This 75 residue region is presumed to be a domain. It is found in isolation in some members and in the amino terminal half of the longer NifZ proteins. 70 matched cddid_all.tbl CDD pfam04320 pfam04320 427864 YggL_50S_bp YggL 50S ribosome-binding protein. This family represents bacterial proteins predominantly found in Gammaproteobacteria. YggL from E.coli has been characterized and it interacts with ribosome subunits 50S and 70S. It is a 50S-binding protein likely to be involved in particle assembly. It is a small protein extremely conserved in Gammaproteobacteria but also present in orders Burkholderiales and Neisseriales from Betaproteobacteria. 102 matched cddid_all.tbl CDD pfam04321 pfam04321 427865 RmlD_sub_bind RmlD substrate binding domain. L-rhamnose is a saccharide required for the virulence of some bacteria. Its precursor, dTDP-L-rhamnose, is synthesized by four different enzymes the final one of which is RmlD. The RmlD substrate binding domain is responsible for binding a sugar nucleotide. 284 matched cddid_all.tbl CDD pfam04322 pfam04322 427866 DUF473 Protein of unknown function (DUF473). Family of uncharacterized Archaeal proteins. 118 matched cddid_all.tbl CDD pfam04324 pfam04324 461261 Fer2_BFD BFD-like [2Fe-2S] binding domain. The two Fe ions are each coordinated by two conserved cysteine residues. This domain occurs alone in small proteins such as Bacterioferritin-associated ferredoxin (BFD). The function of BFD is not known, but it may may be a general redox and/or regulatory component involved in the iron storage or mobilization functions of bacterioferritin in bacteria. This domain is also found in nitrate reductase proteins in association with Nitrite and sulphite reductase 4Fe-4S domain (pfam01077), Nitrite/Sulfite reductase ferredoxin-like half domain (pfam03460) and Pyridine nucleotide-disulphide oxidoreductase (pfam00070). It is also found in NifU nitrogen fixation proteins, in association with NifU-like N terminal domain (pfam01592) and NifU-like domain (pfam01106). 50 matched cddid_all.tbl CDD pfam04325 pfam04325 461262 DUF465 Protein of unknown function (DUF465). Family members are found in small bacterial proteins, and also in the heavy chains of eukaryotic myosin and kinesin, C terminal of the motor domain (Myosin pfam00063, Kinesin pfam00225). Members of this family may form coiled coil structures. 48 matched cddid_all.tbl CDD pfam04326 pfam04326 461263 AlbA_2 Putative DNA-binding domain. This family belongs to the AlbA clan of DNA-binding domains. 116 matched cddid_all.tbl CDD pfam04327 pfam04327 461264 Peptidase_Prp Cysteine protease Prp. This is a family of cysteine protease that are found to cleave the N-terminus extension of ribosomal subunit L27 in eubacteria. Proteins in this family are distinguished by a pair of invariant histidine and cysteine residues with conserved spacing that form the classic catalytic dyad of a cysteine protease. 102 matched cddid_all.tbl CDD pfam04328 pfam04328 427871 Sel_put Selenoprotein, putative. This entry includes a group of putative selenoproteins from Proteobacteria, Actinobacteria and Firmicutes. The invariant cysteine at the C terminus is encoded by a TGA Sec codon in some Epsilonproteobacteria, suggesting a redox activity for the protein. Some members of this family have been suggested to be required for pyruvate transport in diverse bacteria, along with a CstA-like transporter found adjacent in the genome (see Supplementary note 5 in.) 58 matched cddid_all.tbl CDD pfam04332 pfam04332 367905 DUF475 Protein of unknown function (DUF475). Predicted to be an integral membrane protein with multiple membrane spans. 295 matched cddid_all.tbl CDD pfam04333 pfam04333 461265 MlaA MlaA lipoprotein. MlaA is a component of the Mla pathway, an ABC transport system that functions to maintain the asymmetry of the outer membrane. MlaA is required for the intercellular spreading of Shigella flexneri. It is attached to the outer membrane by a lipid anchor. 194 matched cddid_all.tbl CDD pfam04334 pfam04334 113117 DUF478 Protein of unknown function (DUF478). This family contains uncharacterized protein encoded on Trypanosoma kinetoplast minicircles. 68 matched cddid_all.tbl CDD pfam04335 pfam04335 427873 VirB8 VirB8 protein. VirB8 is a bacterial virulence protein with cytoplasmic, transmembrane, and periplasmic regions. It is thought that it is a primary constituent of a DNA transporter. The periplasmic region interacts with VirB9, VirB10, and itself. This family also includes the conjugal transfer protein family TrbF, a family of proteins known to be involved in conjugal transfer. The TrbF protein is thought to compose part of the pilus required for transfer. This domain has a similar fold to the NTF2 protein. 211 matched cddid_all.tbl CDD pfam04336 pfam04336 461266 ACP_PD Acyl carrier protein phosphodiesterase. YajB, now renamed acpH, encodes an ACP hydrolase that converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine prosthetic group from ACP. 105 matched cddid_all.tbl CDD pfam04337 pfam04337 427875 DUF480 Protein of unknown function, DUF480. This family consists of several proteins of uncharacterized function. 148 matched cddid_all.tbl CDD pfam04338 pfam04338 427876 DUF481 Protein of unknown function, DUF481. This family includes several proteins of uncharacterized function. 206 matched cddid_all.tbl CDD pfam04339 pfam04339 461267 FemAB_like Peptidogalycan biosysnthesis/recognition. FemAB_like is a family of both baterial and Viridiplantae proteins with responsibility for building interpeptide bridges in peptidoglycan. Such a function is feasible for bacteria but less likely for the plant members of this family. Perhaps the plant-members are using homologous proteins to recognize bacterial peptidoglcans as part of their innate immune system. 369 matched cddid_all.tbl CDD pfam04340 pfam04340 282228 DUF484 Protein of unknown function, DUF484. This family consists of several proteins of uncharacterized function. 219 matched cddid_all.tbl CDD pfam04341 pfam04341 461268 DUF485 Protein of unknown function, DUF485. This family represents a putative component of ActP-like carboxylate transporters. Several members are cofit with adjacent ActP-like permeases, and the family appears to represent a membrane protein. It has been suggested to be involved in pyruvate utilization. 89 matched cddid_all.tbl CDD pfam04342 pfam04342 461269 DMT_6 Putative member of DMT superfamily (DUF486). This family contains several proteins of uncharacterized function. The family is represented in the Transport classification database as 2.A.7.34, though the exact nature of what is transported is not known. 104 matched cddid_all.tbl CDD pfam04343 pfam04343 427880 DUF488 Protein of unknown function, DUF488. This family includes several proteins of uncharacterized function. 123 matched cddid_all.tbl CDD pfam04344 pfam04344 427881 CheZ Chemotaxis phosphatase, CheZ. This family represents the bacterial chemotaxis phosphatase, CheZ. This protein forms a dimer characterized by a long four-helix bundle, composed of two helices from each monomer. CheZ dephosphorylates CheY in a reaction that is essential to maintain a continuous chemotactic response to environmental changes. It is thought that CheZ's conserved residue Gln 147 orientates a water molecule for nucleophilic attack at the CheY active site. 203 matched cddid_all.tbl CDD pfam04345 pfam04345 113128 Chor_lyase Chorismate lyase. Chorismate lyase catalyzes the first step in ubiquinone synthesis, i.e. the removal of pyruvate from chorismate, to yield 4-hydroxybenzoate. 168 matched cddid_all.tbl CDD pfam04346 pfam04346 427882 EutH Ethanolamine utilization protein, EutH. EutH is a bacterial membrane protein whose molecular function is unknown. It has been suggested that it may act as an ethanolamine transporter, responsible for carrying ethanolamine from the periplasm to the cytoplasm. 351 matched cddid_all.tbl CDD pfam04347 pfam04347 427883 FliO Flagellar biosynthesis protein, FliO. FliO is an essential component of the flagellum-specific protein export apparatus. It is an integral membrane protein that acts as an assembly chaperone for the flagellar protein FliP (pfam00813). It is crucial, although not strictly required, for efficient FliP assembly and, thus flagellar assembly and function. 87 matched cddid_all.tbl CDD pfam04348 pfam04348 367906 LppC LppC putative lipoprotein. This family includes several bacterial outer membrane antigens, whose molecular function is unknown. 532 matched cddid_all.tbl CDD pfam04349 pfam04349 427884 MdoG Periplasmic glucan biosynthesis protein, MdoG. This family represents MdoG, a protein that is necessary for the synthesis of periplasmic glucans. The function of MdoG remains unknown. It has been suggested that it may catalyze the addition of branches to a linear glucan backbone. 474 matched cddid_all.tbl CDD pfam04350 pfam04350 427885 PilO Pilus assembly protein, PilO. PilO proteins are involved in the assembly of pilin. However, the precise function of this family of proteins is not known. 146 matched cddid_all.tbl CDD pfam04351 pfam04351 427886 PilP Pilus assembly protein, PilP. The PilP family are periplasmic proteins involved in the biogenesis of type IV pili. 146 matched cddid_all.tbl CDD pfam04352 pfam04352 461270 ProQ ProQ/FINO family. This family includes ProQ, which is required for full activation of the osmoprotectant transporter, ProP, in Escherichia coli. This family includes several bacterial fertility inhibition (FINO) proteins. The conjugative transfer of F-like plasmids is repressed by FinO, an RNA binding protein. FinO interacts with the F-plasmid encoded traJ mRNA and its antisense RNA, FinP, stabilising FinP against endonucleolytic degradation and facilitating sense-antisense RNA recognition. ProQ operates as an RNA-chaperone, binding RNA and bringing about both RNA strand-exchange and RNA duplexing. This suggests that in fact it does not regulate ProP transcription but rather regulates ProP translation through activity as an RNA-binding protein. 106 matched cddid_all.tbl CDD pfam04353 pfam04353 427888 Rsd_AlgQ Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ. This family includes bacterial transcriptional regulators that are thought to act through an interaction with the conserved region 4 of the sigma(70) subunit of RNA polymerase. The Pseudomonas aeruginosa homolog, AlgQ, positively regulates virulence gene expression and is associated with the mucoid phenotype observed in Pseudomonas aeruginosa isolates from cystic fibrosis patients. 149 matched cddid_all.tbl CDD pfam04354 pfam04354 427889 ZipA_C ZipA, C-terminal FtsZ-binding domain. This family represents the ZipA C-terminal domain. ZipA is involved in septum formation in bacterial cell division. Its C-terminal domain binds FtsZ, a major component of the bacterial septal ring. The structure of this domain is an alpha-beta fold with three alpha helices and a beta sheet of six antiparallel beta strands. The major loops protruding from the beta sheet surface are thought to form a binding site for FtsZ. 127 matched cddid_all.tbl CDD pfam04355 pfam04355 461271 SmpA_OmlA SmpA / OmlA family. Lipoprotein Bacterial outer membrane lipoprotein, possibly involved in in maintaining the structural integrity of the cell envelope. Lipid attachment site is a conserved N terminal cysteine residue. Sometimes found adjacent to the OmpA domain (pfam00691). 69 matched cddid_all.tbl CDD pfam04356 pfam04356 427891 DUF489 Protein of unknown function (DUF489). Protein of unknown function, cotranscribed with purB in Escherichia coli, but with function unrelated to purine biosynthesis. 192 matched cddid_all.tbl CDD pfam04357 pfam04357 461272 TamB TamB, inner membrane protein subunit of TAM complex. TamB is an integral inner membrane protein that forms a complex - the translocation and assembly module or TAM - with the outer membrane protein, TamA. TAM is responsible for the efficient secretion of the adhesin protein Ag43 in E.coli K-12. 383 matched cddid_all.tbl CDD pfam04358 pfam04358 461273 DsrC DsrC like protein. Family member Swiss:P45573 has been observed to co-purify with Desulfovibrio vulgaris dissimilatory sulfite reductase, and many members of this family are annotated as the third (gamma) subunit of dissimilatory sulphite reductase. However, this protein appears to be only loosely associated to the sulfite reductase, which suggests that DsrC may not be an integral part of the dissimilatory sulphite reductase. Members of this family are found in organizms such as E. coli and H. influenzae which do not contain dissimilatory sulphite reductases but can synthesize assimilatory sirohaem sulphite and nitrite reductases. It is speculated that DsrC may be involved in the assembly, folding or stabilization of sirohaem proteins. The strictly conserved cysteine in the C terminus suggests that DsrC may have a catalytic function in the metabolism of sulphur compounds. 107 matched cddid_all.tbl CDD pfam04359 pfam04359 461274 DUF493 Protein of unknown function (DUF493). This domain is likely to act in a regulatory capacity like pfam01842 domains. This domain has a remarkable property in that the C-terminal residue of every protein in the family lies up in the alignment. This suggests that the C-terminal residue plays some important functional role (Bateman A pers obs). 84 matched cddid_all.tbl CDD pfam04360 pfam04360 427895 Serglycin Serglycin. Serglycin is the most prevalent proteoglycan produced in haemopoietic cells. Serglycin is a proteinase resistant secretory granule proteoglycan. 149 matched cddid_all.tbl CDD pfam04361 pfam04361 427896 DUF494 Protein of unknown function (DUF494). Members of this family of uncharacterized proteins are often named Smg. 153 matched cddid_all.tbl CDD pfam04362 pfam04362 461275 Iron_traffic Bacterial Fe(2+) trafficking. This is a family of bacterial Fe(2+) trafficking proteins. 85 matched cddid_all.tbl CDD pfam04363 pfam04363 427898 DUF496 Protein of unknown function (DUF496). 93 matched cddid_all.tbl CDD pfam04364 pfam04364 461276 DNA_pol3_chi DNA polymerase III chi subunit, HolC. The DNA polymerase III holoenzyme (EC:2.7.7.7) is the polymerase responsible for the replication of the Escherichia coli chromosome. The holoenzyme is composed of the DNA polymerase III core, the sliding clamp, and the DnaX clamp loading complex. The DnaX complex contains either either the tau or gamma product of gene dnax, complexed to delta.delta' and to chi psi. Chi forms a 1:1 heterodimer with psi. The chi psi complex functions by increasing the affinity of tau and gamma for delta.delta' allowing a functional clamp-loading complex to form at physiological subunit concentrations. Psi is responsible for the interaction with DnaX (gamma/tau), but psi is insoluble unless it is in a complex with chi. 135 matched cddid_all.tbl CDD pfam04365 pfam04365 461277 BrnT_toxin Ribonuclease toxin, BrnT, of type II toxin-antitoxin system. BrnT is a ribonuclease toxin of a type II toxin-antitoxin system that exhibits a RelE-like fold. The antitoxin that neutralizes this toxin is pfam14384. BrnT is found in bacteria, archaea, bacteriophage, and plasmids. BrnT-BrnA forms a 2:2 tetrameric complex and autoregulates its own expression, which is induced by a number of different environmental stresses. Expression of BrnT alone results in cessation of bacterial growth which can be rescued after subsequent expression of BrnA. 77 matched cddid_all.tbl CDD pfam04366 pfam04366 461278 Ysc84 Las17-binding protein actin regulator. Ysc84 is a family of Las17-binding proteins found in metazoa. Together, Las17 and Ysc84 are essential for proper polymerization of actin; Ysc84 is able to bind to and stabilize the actin dimer presented by Las17 and thereby promote polymerization. An active actin cytoskeleton is necessary for adequate endocytosis. (pfam00018), or a FYVE zinc finger (pfam01363). 127 matched cddid_all.tbl CDD pfam04367 pfam04367 461279 DUF502 Protein of unknown function (DUF502). Predicted to be an integral membrane protein. 106 matched cddid_all.tbl CDD pfam04368 pfam04368 427903 DUF507 Protein of unknown function (DUF507). Bacterial protein of unknown function. 182 matched cddid_all.tbl CDD pfam04369 pfam04369 113152 Lactococcin Lactococcin-like family. Family of bacteriocins from lactic acid bacteria. 60 matched cddid_all.tbl CDD pfam04370 pfam04370 367915 DUF508 Domain of unknown function (DUF508). This is a family of uncharacterized proteins from C. elegans. 142 matched cddid_all.tbl CDD pfam04371 pfam04371 461280 PAD_porph Porphyromonas-type peptidyl-arginine deiminase. Peptidyl-arginine deiminase (PAD) enzymes catalyze the deimination of the guanidino group from carboxy-terminal arginine residues of various peptides to produce ammonia. PAD from Porphyromonas gingivalis (PPAD) appears to be evolutionarily unrelated to mammalian PAD (pfam03068), which is a metalloenzyme. PPAD is thought to belong to the same superfamily as aminotransferase and arginine deiminase, and to form an alpha/beta propeller structure. This family has previously been named PPADH (Porphyromonas peptidyl-arginine deiminase homologs). The predicted catalytic residues in PPAD are Asp130, Asp187, His236, Asp238 and Cys351. These are absolutely conserved with the exception of Asp187 which is absent in two family members. PPAD is also able to catalyze the deimination of free L-arginine, but has primarily peptidyl-arginine specificity. It may have a FMN cofactor. 324 matched cddid_all.tbl CDD pfam04375 pfam04375 427905 HemX HemX, putative uroporphyrinogen-III C-methyltransferase. This is a family of bacterial putative uroporphyrinogen-III C-methyltransferase proteins. It forms one of the members of a complex of proteins involved in the biogenesis of the inner membrane in E.coli. Uroporphorphyrin-III C-methyltransferase (HemX) is a single spanning inner membrane protein that regulates the activity of NAD(P)H:glutamyl-tRNA reductase (HemA) in the tetrapyrrole biosynthesis pathway. 236 matched cddid_all.tbl CDD pfam04376 pfam04376 461281 ATE_N Arginine-tRNA-protein transferase, N terminus. This family represents the N terminal region of the enzyme arginine-tRNA-protein transferase (EC 2.3.2.8), which catalyzes the post-translational conjugation of arginine to the N terminus of a protein. In eukaryotes, this functions as part of the N-end rule pathway of protein degradation by conjugating a de-stabilising amino acid to the amino terminal aspartate or glutamate of a protein, targeting the protein for ubiquitin-dependent proteolysis. N terminal cysteine is sometimes modified. In S cerevisiae, Cys20, 23, 94 and/or 95 are thought to be important for activity. Of these, only Cys 94 appears to be completely conserved in this family. 71 matched cddid_all.tbl CDD pfam04377 pfam04377 461282 ATE_C Arginine-tRNA-protein transferase, C terminus. This family represents the C terminal region of the enzyme arginine-tRNA-protein transferase (EC 2.3.2.8), which catalyzes the post-translational conjugation of arginine to the N terminus of a protein. In eukaryotes, this functions as part of the N-end rule pathway of protein degradation by conjugating a destabilising amino acid to the amino terminal aspartate or glutamate of a protein, targeting the protein for ubiquitin-dependent proteolysis. N terminal cysteine is sometimes modified. 122 matched cddid_all.tbl CDD pfam04378 pfam04378 398191 RsmJ Ribosomal RNA large subunit methyltransferase D, RlmJ. RlmJ is ribosomal RNA large subunit methyltransferase J is required for full methylation of 23S ribosomal RNA (rRNA) during ribosome biogenesis. The ribosomal RNA of E. coli carries 24 residues that require methylation, and this methyltransferase is the last to be described, that modifies A2030. RlmJ displays a variant of the Rossmann-like methyltransferase (MTase) fold with an inserted helical subdomain. On binding cofactor and substrate a large shift of the N-terminal motif X tail is induced in order to make it cover the cofactor-binding site and to trigger active-site changes in motifs IV and VIII. 245 matched cddid_all.tbl CDD pfam04379 pfam04379 461283 DUF525 ApaG domain. The apaG domain is a ~125 amino acids domain present in bacterial apaG proteins and in eukaryotic F-box proteins. The domain is named after the bacterial apaG protein, of which it forms the core. The domain also occurs in the C-terminal part of eukaryotic proteins with an N-terminal F-box domain. The Salmonella typhimurium apaG domain protein corD is involved in Co(2+) resistance and Mg(2+) efflux. Tertiary structures from different apaG proteins show a fold of several beta-sheets. The apaG domain may be involved in protein-protein interactions which could be implicated in substrate-specificity. 87 matched cddid_all.tbl CDD pfam04380 pfam04380 461284 BMFP Membrane fusogenic activity. BMFP consists of two structural domains, a coiled-coil C-terminal domain via which the protein self-associates as a trimer, and an N-terminal domain disordered at neutral pH but adopting an amphipathic alpha-helical structure in the presence of phospholipid vesicles, high ionic strength, acidic pH or SDS. BMFP interacts with phospholipid vesicles though the predicted amphipathic alpha-helix induced in the N-terminal half of the protein and promotes aggregation and fusion of vesicles in vitro. 70 matched cddid_all.tbl CDD pfam04381 pfam04381 427910 RdgC Putative exonuclease, RdgC. Members of the RdgC family may have exonuclease activity. RdgC is required for efficient pilin variation in Neisseria gonorrhoeae, suggesting that it may be involved in recombination reactions. In Escherichia coli, RdgC is required for growth in recombination-deficient exonuclease-depleted strains. Under these conditions, RdgC may act as an exonuclease to remove collapsed replication forks, in the absence of the normal repair mechanisms. 298 matched cddid_all.tbl CDD pfam04382 pfam04382 461285 SAB SAB domain. This presumed domain is found in proteins containing FERM domains pfam00373. This domain is found to bind to both spectrin and actin, hence the name SAB (Spectrin and Actin Binding) domain. 50 matched cddid_all.tbl CDD pfam04383 pfam04383 367917 KilA-N KilA-N domain. The amino-terminal module of the D6R/N1R proteins defines a novel, conserved DNA-binding domain (the KilA-N domain) that is found in a wide range of proteins of large bacterial and eukaryotic DNA viruses. The KilA-N domain family also includes the previously defined APSES domain. The KilA-N and APSES domains may also share a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease. 107 matched cddid_all.tbl CDD pfam04384 pfam04384 427912 Fe-S_assembly Iron-sulphur cluster assembly. This family of proteins is likely to be involved in the assembly of iron-sulphur clusters. It may function as an adaptor protein. In Escherichia coli Swiss:P0C0L9 forms part of the isc operon, which encodes genes involved in iron-sulphur cluster assembly. Its structure is entirely alpha helical, and it contains a modified wing-helix structure, usually found in DNA-binding proteins. It binds to Fe2+ and Fe3+ ions and to the cysteine desulfurase IscS, the same surface of the protein is involved in both binding to iron and to IscS. 64 matched cddid_all.tbl CDD pfam04385 pfam04385 252557 FAINT Domain of unknown function, DUF529. This family represents a repeated region found in several Theileria parva proteins. The repeat is normally about 70 residues long and contains a conserved aromatic residue in the middle. 78 matched cddid_all.tbl CDD pfam04386 pfam04386 427913 SspB Stringent starvation protein B. Escherichia coli stringent starvation protein B (SspB), is thought to enhance the specificity of degradation of tmRNA-tagged proteins by the ClpXP protease. The tmRNA tag, also known as ssrA, is an 11-aa peptide added to the C terminus of proteins stalled during translation, targets proteins for degradation by ClpXP and ClpAP. SspB a cytoplasmic protein that specifically binds to residues 1-4 and 7 of the tag. Binding of SspB enhances degradation of tagged proteins by ClpX, and masks sequence elements important for ClpA interactions, inhibiting degradation by ClpA. However, more recent work has cast doubt on the importance of SspB in wild-type cells. SspB is encoded in an operon whose synthesis is stimulated by carbon, amino acid, and phosphate starvation. SspB may play a special role during nutrient stress, for example by ensuring rapid degradation of the products of stalled translation, without causing a global increase in degradation of all ClpXP substrates. 144 matched cddid_all.tbl CDD pfam04387 pfam04387 461286 PTPLA Protein tyrosine phosphatase-like protein, PTPLA. This family includes the mammalian protein tyrosine phosphatase-like protein, PTPLA. A significant variation of PTPLA from other protein tyrosine phosphatases is the presence of proline instead of catalytic arginine at the active site. It is thought that PTPLA proteins have a role in the development, differentiation, and maintenance of a number of tissue types. 163 matched cddid_all.tbl CDD pfam04388 pfam04388 461287 Hamartin Hamartin protein. This family includes the hamartin protein which is thought to function as a tumour suppressor. The hamartin protein interacts with the tuberin protein pfam03542. Tuberous sclerosis complex (TSC) is an autosomal dominant disorder and is characterized by the presence of hamartomas in many organs, such as brain, skin, heart, lung, and kidney. It is caused by mutation either TSC1 or TSC2 tumour suppressor gene. TSC1 encodes a protein, hamartin, containing two coiled-coil regions, which have been shown to mediate binding to tuberin. The TSC2 gene codes for tuberin pfam03542. These two proteins function within the same pathway(s) regulating cell cycle, cell growth, adhesion, and vesicular trafficking. 730 matched cddid_all.tbl CDD pfam04389 pfam04389 461288 Peptidase_M28 Peptidase family M28. 192 matched cddid_all.tbl CDD pfam04390 pfam04390 461289 LptE Lipopolysaccharide-assembly. LptE (formerly known as RplB) is involved in lipopolysaccharide-assembly on the outer membrane of Gram-negative organizms. The lipopolysaccharide component of the outer bacterial membrane is transported from its source of origin to the outer membrane by a set of proteins constituting a transport machinery that is made up of LptA, LptB, LptC, LptD, LptE. LptD appears to be anchored in the outer membrane, and LptE forms a complex with it. This part of the machinery complex is involved in the assembly of lipopolysaccharide in the outer leaflet of the outer membrane. 84 matched cddid_all.tbl CDD pfam04391 pfam04391 427917 DUF533 Protein of unknown function (DUF533). Some family members may be secreted or integral membrane proteins. 177 matched cddid_all.tbl CDD pfam04392 pfam04392 427918 ABC_sub_bind ABC transporter substrate binding protein. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins. 293 matched cddid_all.tbl CDD pfam04393 pfam04393 427919 DUF535 Protein of unknown function (DUF535). Family member Shigella flexneri VirK is a virulence protein required for the expression, or correct membrane localization of IcsA (VirG) on the bacterial cell surface,. This family also includes Pasteurella haemolytica lapB, which is thought to be membrane-associated. 279 matched cddid_all.tbl CDD pfam04394 pfam04394 282276 DUF536 Protein of unknown function, DUF536. This family aligns the C-terminal region from several bacterial proteins of unknown function that may be involved in a theta-type replication mechanism. 43 matched cddid_all.tbl CDD pfam04395 pfam04395 282277 Poxvirus_B22R Poxvirus B22R protein. This is highly conserved C-rich, central region of poxvirus proteins from eg, Fowlpox virus, Myxoma virus, Lumpy skin disease, Variola virus and other members of the Poxviridae family of double-stranded, no-RNA stage poxviruses. There are three pairs of conserved cysteine residues. 204 matched cddid_all.tbl CDD pfam04397 pfam04397 427920 LytTR LytTr DNA-binding domain. This domain is found in a variety of bacterial transcriptional regulators. The domain binds to a specific DNA sequence pattern. 98 matched cddid_all.tbl CDD pfam04398 pfam04398 461290 DUF538 Protein of unknown function, DUF538. This family consists of several plant proteins of unknown function. 109 matched cddid_all.tbl CDD pfam04399 pfam04399 461291 Glutaredoxin2_C Glutaredoxin 2, C terminal domain. Glutaredoxins are a multifunctional family of glutathione-dependent disulphide oxidoreductases. Unlike other glutaredoxins, glutaredoxin 2 (Grx2) cannot reduce ribonucleotide reductase. Grx2 has significantly higher catalytic activity in the reduction of mixed disulphides with glutathione (GSH) compared with other glutaredoxins. The active site residues (Cys9-Pro10-Tyr11-Cys12, in Escherichia coli Grx2, Swiss:P39811), which are found at the interface between the N- and C-terminal domains are identical to other glutaredoxins, but there is no other similarity between glutaredoxin 2 and other glutaredoxins. Grx2 is structurally similar to glutathione-S-transferases (GST), but there is no obvious sequence similarity. The inter-domain contacts are mainly hydrophobic, suggesting that the two domains are unlikely to be stable on their own. Both domains are needed for correct folding and activity of Grx2. It is thought that the primary function of Grx2 is to catalyze reversible glutathionylation of proteins with GSH in cellular redox regulation including the response to oxidative stress. 130 matched cddid_all.tbl CDD pfam04400 pfam04400 427923 NqrM (Na+)-NQR maturation NqrM. The NqrM gene is often found adjacent to the nqr operons that encode (Na+)-NQR subunits. It is involved in the maturation of (Na+) translocating NADH:quinone oxidoreductase in proteobacteria. The four conserved Cys residues found in NqrM are required for (Na+)- NQR maturation and may serve as ligands for a metal ion or metal cluster used to build up the (Na+)-NQR molecule. 41 matched cddid_all.tbl CDD pfam04402 pfam04402 461292 SIMPL Protein of unknown function (DUF541). Members of this family have so far been found in bacteria and mouse SwissProt or TrEMBL entries. However possible family members have also been identified in translated rat (Genbank:AW144450) and human (Genbank:AI478629) ESTs. A mouse family member has been named SIMPL (signalling molecule that associates with mouse pelle-like kinase). SIMPL appears to facilitate and/or regulate complex formation between IRAK/mPLK (IL-1 receptor-associated kinase) and IKK (inhibitor of kappa-B kinase) containing complexes, and thus regulate NF-kappa-B activity. Separate experiments demonstrate that a mouse family member (named LaXp180) binds the Listeria monocytogenes surface protein ActA, which is a virulence factor that induces actin polymerization. It may also bind stathmin, a protein involved in signal transduction and in the regulation of microtubule dynamics. In bacteria its function is unknown, but it is thought to be located in the periplasm or outer membrane. 159 matched cddid_all.tbl CDD pfam04403 pfam04403 461293 PqiA Paraquat-inducible protein A. Paraquat is a superoxide radical-generating agent. The promoter for the pqiA gene is also inducible by other known superoxide generators. This is predicted to be a family of integral membrane proteins, possibly located in the inner membrane. This family is related to NADH dehydrogenase subunit 2 (pfam00361). 154 matched cddid_all.tbl CDD pfam04404 pfam04404 427926 ERF ERF superfamily. The DNA single-strand annealing proteins (SSAPs), such as RecT, Red-beta, ERF and Rad52, function in RecA-dependent and RecA-independent DNA recombination pathways. This family includes proteins related to ERF. 153 matched cddid_all.tbl CDD pfam04405 pfam04405 427927 ScdA_N Domain of Unknown function (DUF542). This domain is always found in conjunction with the HHE domain (pfam03794) at the N-terminus. 55 matched cddid_all.tbl CDD pfam04406 pfam04406 461294 TP6A_N Type IIB DNA topoisomerase. Type II DNA topoisomerases are ubiquitous enzymes that catalyze the ATP-dependent transport of one DNA duplex through a second DNA segment via a transient double-strand break. Type II DNA topoisomerases are now subdivided into two sub-families, type IIA and IIB DNA topoisomerases. TP6A_N is present in type IIB topoisomerase and is thought to be involved in DNA binding owing to its sequence similarity to E. coli catabolite activator protein (CAP). 62 matched cddid_all.tbl CDD pfam04407 pfam04407 427929 DUF531 Protein of unknown function (DUF531). Family of hypothetical archaeal proteins. 170 matched cddid_all.tbl CDD pfam04408 pfam04408 461295 HA2 Helicase associated domain (HA2). This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding. 104 matched cddid_all.tbl CDD pfam04409 pfam04409 398215 DUF530 Protein of unknown function (DUF530). Family of hypothetical archaeal proteins. 521 matched cddid_all.tbl CDD pfam04410 pfam04410 461296 Gar1 Gar1/Naf1 RNA binding region. Gar1 is a small nucleolar RNP that is required for pre-mRNA processing and pseudouridylation. It is co-immunoprecipitated with the H/ACA families of snoRNAs. This family represents the conserved central region of Gar1. This region is necessary and sufficient for normal cell growth, and specifically binds two snoRNAs snR10 and snR30. This region is also necessary for nucleolar targeting, and it is thought that the protein is co-transported to the nucleolus as part of a nucleoprotein complex. In humans, Gar1 is also component of telomerase in vivo. Naf1 is an essential protein that plays a role in ribosome biogenesis, modification of spliceosomal small nuclear RNAs and telomere synthesis, and is homologous to Gar1. 89 matched cddid_all.tbl CDD pfam04411 pfam04411 427932 PDDEXK_7 PD-(D/E)XK nuclease superfamily. This domain has been identified as a member of the PD-(D/E)XK nuclease superfamily through transitive meta profile searches. The domain has two additional beta-strands inserted to the core fold after the first core alpha-helix. It has been speculated that it could function as s methylation-dependent restriction. The domain has two additional beta-strands inserted into the core fold after the first core alpha-helix. The PD-(D/E)XK signature is clearly conserved corresponding to an invariant PD (motif II) and DAK (motif III) motifs. There is also a conserved glutamic acid in motif I that is most likely to be involved in metal ion binding. The second core alpha-helix contains an invariant MHXYRD motif. It has been speculated that it could function as s methylation-dependent restriction enzyme. 161 matched cddid_all.tbl CDD pfam04412 pfam04412 461297 AcnX Aconitase X. Aconitase X (AcnX) is a subfamily of Acn superfamily. It is encoded in the genomes of many archaea, proteobacteria and fungi. Among archaea, the pattern of aconitase X occurrence complements that of aconitase A such that together the two enzymes account for aconitase activity in all archaea. This protein catalyzes the dehydration of cis-3-hydroxy-L-proline to delta1-pyrroline-2-carboxylate. 385 matched cddid_all.tbl CDD pfam04413 pfam04413 461298 Glycos_transf_N 3-Deoxy-D-manno-octulosonic-acid transferase (kdotransferase). Members of this family transfer activated sugars to a variety of substrates, including glycogen, fructose-6-phosphate and lipopolysaccharides. Members of the family transfer UDP, ADP, GDP or CMP linked sugars. The Glycos_transf_N region is flanked at the N-terminus by a signal peptide and at the C-terminus by Glycos_transf_1 (pfam00534). The eukaryotic glycogen synthases may be distant members of this bacterial family. 178 matched cddid_all.tbl CDD pfam04414 pfam04414 427935 tRNA_deacylase D-aminoacyl-tRNA deacylase. Several aminoacyl-tRNA synthetases have the ability to transfer the D-isomer of their amino acid onto their cognate tRNA. D-aminoacyl-tRNA deacylases hydrolyse the ester bond between the polynucleotide and the D-amino acid, thereby preventing the accumulation of such mis-acylated and metabolically inactive tRNA molecules. 204 matched cddid_all.tbl CDD pfam04415 pfam04415 282295 DUF515 Protein of unknown function (DUF515). Family of hypothetical Archaeal proteins. 449 matched cddid_all.tbl CDD pfam04417 pfam04417 461299 DUF501 Protein of unknown function (DUF501). Family of uncharacterized bacterial proteins. 137 matched cddid_all.tbl CDD pfam04418 pfam04418 461300 DUF543 Domain of unknown function (DUF543). This family of short eukaryotic proteins has no known function. Most of the members of this family are only 80 amino acid residues long. However the Arabidopsis homolog is over 300 residues long. The presumed domain contains a conserved amino terminal cysteine and a conserved motif GXGXGXG in the carboxy terminal half that may be functionally important. 75 matched cddid_all.tbl CDD pfam04419 pfam04419 398223 4F5 4F5 protein related disordered region. Members of this family are short proteins that are rich in aspartate, glutamate, lysine and arginine. Although the function of these proteins is unknown, they are found to be ubiquitously expressed. This entry is named after the H4F5 protein UniProt:O75920. This region appears to be found at the N-terminus of some longer proteins. Many proteins contain a C-terminal zinc finger domain pfam12907. 38 matched cddid_all.tbl CDD pfam04420 pfam04420 427938 CHD5 CHD5-like protein. Members of this family are probably coiled-coil proteins that are similar to the CHD5 (Congenital heart disease 5) protein. In Saccharomyces cerevisiae this protein localizes to the ER and is thought to play a homeostatic role. 158 matched cddid_all.tbl CDD pfam04421 pfam04421 461301 Mss4 Mss4 protein. 94 matched cddid_all.tbl CDD pfam04422 pfam04422 461302 FrhB_FdhB_N Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term. Coenzyme F420 hydrogenase (EC:1.12.99.1) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the N termini of F420 hydrogenase and dehydrogenase beta subunits,. The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain (EC:1.2.1.2) is also a member of this family. This region is often found in association with the 4Fe-4S binding domain, fer4 (pfam00037). 78 matched cddid_all.tbl CDD pfam04423 pfam04423 427940 Rad50_zn_hook Rad50 zinc hook motif. The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side. 52 matched cddid_all.tbl CDD pfam04424 pfam04424 461303 MINDY_DUB MINDY deubiquitinase. This entry represents a group of deubiquitinating (DUB) enzymes known as the MINDY family (MIU-containing novel DUB). Ubiquitin (Ub) is released one molecule at a time from the distal end of proteins with Lys48-linked polyubiquitin chains. Long polyubiquitin chains are preferred. The catalytic Cys and His residues have been identified by site-directed mutagenesis, as has the Gln that participates in formation of the oxyanion hole during catalysis. Despite the structural similarity to papain-like cysteine peptidases, a residue corresponding to the Asn that orientates the imidazolium ring of the catalytic His has not been identified. Members of the MINDY family of DUBs contain an MIU (motif interacting with Ub) motif, which is a helical motif that binds mono-Ub. 110 matched cddid_all.tbl CDD pfam04425 pfam04425 398229 Bul1_N Bul1 N terminus. This family contains the N terminus of Saccharomyces cerevisiae Bul1. Bul1 binds the ubiquitin ligase Rsp5, via an N terminal PPSY motif (157-160 in Swiss:P48524). The complex containing Bul1 and Rsp5 is involved in intracellular trafficking of the general amino acid permease Gap1, degradation of Rog1 in cooperation with Bul2 and GSK-3, and mitochondrial inheritance. Bul1 may contain HEAT repeats. 445 matched cddid_all.tbl CDD pfam04426 pfam04426 367936 Bul1_C Bul1 C terminus. This family contains the C terminus of Saccharomyces cerevisiae Bul1. Bul1 binds the ubiquitin ligase Rsp5, via an N terminal PPSY motif (157-160 in Swiss:P48524). The complex containing Bul1 and Rsp5 is involved in intracellular trafficking of the general amino acid permease Gap1, degradation of Rog1 in cooperation with Bul2 and GSK-3, and mitochondrial inheritance. Bul1 may contain HEAT repeats. 271 matched cddid_all.tbl CDD pfam04427 pfam04427 461304 Brix Brix domain. 180 matched cddid_all.tbl CDD pfam04428 pfam04428 367938 Choline_kin_N Choline kinase N terminus. Found N terminal to choline/ethanolamine kinase regions (pfam01633) in some plant and fungal choline kinase enzymes (EC:2.7.1.32). This region is only found in some members of the choline kinase family, and is therefore unlikely to contribute to catalysis. 51 matched cddid_all.tbl CDD pfam04430 pfam04430 461305 DUF498 Protein of unknown function (DUF498/DUF598). This is a large family of uncharacterized proteins found in all domains of life. The structure shows a novel fold with three beta sheets. A dimeric form is found in the crystal structure. It was suggested that the cleft in between the two monomers might bing nucleic acid. 106 matched cddid_all.tbl CDD pfam04431 pfam04431 398232 Pec_lyase_N Pectate lyase, N terminus. This region is found N terminal to the pectate lyase domain (pfam00544) in some plant pectate lyase enzymes. 52 matched cddid_all.tbl CDD pfam04432 pfam04432 461306 FrhB_FdhB_C Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus. Coenzyme F420 hydrogenase (EC:1.12.99.1) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the C termini of F420 hydrogenase and dehydrogenase beta subunits,. The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain (EC:1.2.1.2) is also a member of this family. This region is often found in association with the 4Fe-4S binding domain, fer4 (pfam00037). 145 matched cddid_all.tbl CDD pfam04433 pfam04433 461307 SWIRM SWIRM domain. This SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in chromosomal proteins. It contains a helix-turn helix motif and binds to DNA. 78 matched cddid_all.tbl CDD pfam04434 pfam04434 309540 SWIM SWIM zinc finger. This domain is found in bacterial, archaeal and eukaryotic proteins. It is predicted to be organized into two N-terminal beta-strands and a C-terminal alpha helix, thus possibly adopting a fold similar to that of the C2H2 zinc finger (pfam00096). SWIM is thought to be a versatile domain that can interact with DNA or proteins in different contexts. 38 matched cddid_all.tbl CDD pfam04435 pfam04435 461308 SPK Domain of unknown function (DUF545). Family of uncharacterized C. elegans proteins. The region represented by this family can is found to be repeated up to four time in some proteins. 104 matched cddid_all.tbl CDD pfam04437 pfam04437 461309 RINT1_TIP1 RINT-1 / TIP-1 family. This family includes RINT-1, a Rad50 interacting protein which participates in radiation induced checkpoint control, as well as the TIP-1 protein from yeast that seems to be involved in a complex with Sec20p that is required for Golgi transport. 511 matched cddid_all.tbl CDD pfam04438 pfam04438 461310 zf-HIT HIT zinc finger. This presumed zinc finger contains up to 6 cysteine residues that could coordinate zinc. The domain is named after the HIT protein. This domain is also found in the Thyroid receptor interacting protein 3 (TRIP-3) that specifically interact with the ligand binding domain of the thyroid receptor. 30 matched cddid_all.tbl CDD pfam04439 pfam04439 461311 Adenyl_transf Streptomycin adenylyltransferase. Also known as Aminoglycoside 6- adenylyltransferase (EC:2.7.7.-), this protein confers resistance to aminoglycoside antibiotics. 278 matched cddid_all.tbl CDD pfam04440 pfam04440 461312 Dysbindin Dysbindin (Dystrobrevin binding protein 1). Dysbindin is an evolutionary conserved 40-kDa coiled-coil-containing protein that binds to alpha- and beta-dystrobrevin in muscle and brain. Dystrophin and alpha-dystrobrevin are co-immunoprecipitated with dysbindin, indicating that dysbindin is DPC-associated in muscle. Dysbindin co-localizes with alpha-dystrobrevin at the sarcolemma and is up-regulated in dystrophin-deficient muscle. In the brain, dysbindin is found primarily in axon bundles and especially in certain axon terminals, notably mossy fibre synaptic terminals in the cerebellum and hippocampus. Dysbindin may have implications for the molecular pathology of Duchenne muscular dystrophy and may provide an alternative route for anchoring dystrobrevin and the DPC to the muscle membrane. Genetic variation in the human dysbindin gene is also thought to be associated with Schizophrenia. 143 matched cddid_all.tbl CDD pfam04441 pfam04441 398240 Pox_VERT_large Poxvirus early transcription factor (VETF), large subunit. The poxvirus early transcription factor (VETF), in addition to the viral RNA polymerase, is required for efficient transcription of early genes in vitro. VETF is a heterodimeric protein that binds specifically to early gene promoters. The heterodimer is comprised of an 82 kDa (this family) subunit and a 70 kDa subunit. 697 matched cddid_all.tbl CDD pfam04442 pfam04442 461313 CtaG_Cox11 Cytochrome c oxidase assembly protein CtaG/Cox11. Cytochrome c oxidase assembly protein is essential for the assembly of functional cytochrome oxidase protein. In eukaryotes it is an integral protein of the mitochondrial inner membrane. Cox11 is essential for the insertion of Cu(I) ions to form the CuB site. This is essential for the stability of other structures in subunit I, for example haems a and a3, and the magnesium/manganese centre. Cox11 is probably only required in sub-stoichiometric amounts relative to the structural units. The C terminal region of the protein is known to form a dimer. Each monomer coordinates one Cu(I) ion via three conserved cysteine residues (111, 208 and 210) in Saccharomyces cerevisiae. Met 224 is also thought to play a role in copper transfer or stabilising the copper site. 148 matched cddid_all.tbl CDD pfam04443 pfam04443 282319 LuxE Acyl-protein synthetase, LuxE. LuxE is an acyl-protein synthetase found in bioluminescent bacteria. LuxE catalyzes the formation of an acyl-protein thioester from a fatty acid and a protein. This is the second step in the bioluminescent fatty acid reduction system, which converts tetradecanoic acid to the aldehyde substrate of the luciferase-catalyzed bioluminescence reaction A conserved cysteine found at position 364 in Photobacterium phosphoreum LuxE is thought to be acylated during the transfer of the acyl group from the synthetase subunit to the reductase. The carboxyl terminal of the synthetase is though to act as a flexible arm to transfer acyl groups between the sites of activation and reduction. This family also includes Vibrio cholerae RBFN protein, which is involved in the biosynthesis of the O-antigen component 3-deoxy-L-glycero-tetronic acid. 386 matched cddid_all.tbl CDD pfam04444 pfam04444 427951 Dioxygenase_N Catechol dioxygenase N terminus. This family consists of the N termini of catechol, chlorocatechol or hydroxyquinol 1,2-dioxygenase proteins. This region is always found adjacent to the dioxygenase domain (pfam00775). 75 matched cddid_all.tbl CDD pfam04445 pfam04445 427952 SAM_MT Putative SAM-dependent methyltransferase. This is a family of putative SAM-dependent methyltransferases. 230 matched cddid_all.tbl CDD pfam04446 pfam04446 461314 Thg1 tRNAHis guanylyltransferase. The Thg1 protein from Saccharomyces cerevisiae is responsible for adding a GMP residue to the 5' end of tRNA His. The catalytic domain Thg1 contains a RRM (ferredoxin) fold palm domain, just like the viral RNA-dependent RNA polymerases, reverse transcriptases, family A and B DNA polymerases, adenylyl cyclases, diguanylate cyclases (GGDEF domain) and the predicted polymerase of the CRISPR system. Thg1 possesses an active site with three acidic residues that chelate Mg++ cations. Thg1 catalyzes polymerization similar to the 5'-3' polymerases. 130 matched cddid_all.tbl CDD pfam04447 pfam04447 367945 dATP-dGTP_PPHyd dATP/dGTP pyrophosphohydrolase. This domain is found in phage proteins, such as A0A2H5BHG5 from Acinetobacter phage SH-Ab 15497, which are associated with PurZ, an enzyme that catalyzes the synthesis of diaminopurine (Z), a DNA modification that gives phages an advantage for evading host restriction enzymes activity. This domain has dATP and dGTP pyrophosphohydrolase activity; it catalyzes the hydrolysis of dATP/dGTP to pyrophosphate and dAMP/dGMP, respectively, with little or no activities for NTPs and pyrimidine dNTPs. It is suggested that enzymes containing this domain supply dGMP as the substrate for PurZ, elevating dZTP level to promote Z incorporation. 97 matched cddid_all.tbl CDD pfam04448 pfam04448 427954 DUF551 Protein of unknown function (DUF551). This family represents the carboxy terminus of a protein of unknown function, found in dsDNA viruses with no RNA stage, including bacteriophages lambda and P22, and also in some Escherichia coli prophages. 66 matched cddid_all.tbl CDD pfam04449 pfam04449 427955 Fimbrial_CS1 CS1 type fimbrial major subunit. Fimbriae, also known as pili, form filaments radiating from the surface of the bacterium to a length of 0.5-1.5 micrometres. They enable the cell to colonize host epithelia. This family constitutes the major subunits of CS1 like pili, including CS2 and CFA1 from Escherichia coli, and also the Cable type II pilin major subunit from Burkholderia cepacia. The major subunit of CS1 pili is called CooA. Periplasmic CooA is mostly complexed with the assembly protein CooB. In addition, a small pool of CooA multimers, and CooA-CooD complexes exists, but the functional significance is unknown. A member of this family has also been identified in Salmonella typhi and Salmonella enterica. 134 matched cddid_all.tbl CDD pfam04450 pfam04450 427956 BSP Peptidase of plants and bacteria. These basic secretory proteins (BSPs) are believed to be part of the plants defence mechanism against pathogens. 207 matched cddid_all.tbl CDD pfam04451 pfam04451 398248 Capsid_NCLDV Large eukaryotic DNA virus major capsid protein. This family includes the major capsid protein of iridoviruses, chlorella virus and Spodoptera ascovirus, which are all dsDNA viruses with no RNA stage. This is the most abundant structural protein and can account for up to 45% of virion protein. In Chlorella virus PBCV-1 the major capsid protein is a glycoprotein. The four families of large eukaryotic DNA viruses, Poxviridae, Asfarviridae, Iridoviridae, and Phycodnaviridae, are referred to collectively as nucleocytoplasmic large DNA viruses or NCLDV. The virions of different NCLDV have dramatically different structures. The major capsid proteins of iridoviruses and phycodnaviruses, both of which have icosahedral capsids surrounding an inner lipid membrane, showed a high level of sequence conservation. A more limited, but statistically significant sequence similarity was observed between these proteins and the major capsid protein (p72) of ASFV, which also has an icosahedral capsid. It was surprising, however, to find that all of these proteins shared a conserved domain with the poxvirus protein D13L, which is an integral virion component thought to form a scaffold for the formation of viral crescents and immature virion. 192 matched cddid_all.tbl CDD pfam04452 pfam04452 461315 Methyltrans_RNA RNA methyltransferase domain. RNA methyltransferases modify nucleotides during ribosomal RNA maturation in a site-specific manner. The Escherichia coli member is specific for U1498 methylation. 165 matched cddid_all.tbl CDD pfam04453 pfam04453 427958 LptD LPS transport system D. Lipopolysaccharide (LPS) is essential for most Gram-negative bacteria and has crucial roles in protection of the bacteria from harsh environments and toxic compounds, including antibiotics. This family includes members such as LPTD found in Shigella flexneri and Yersinia pestis. Structural analysis indicates that LptD forms a novel 26-stranded beta-barrel. It interacts with LPTE where LptE adopts a roll-like structure located inside the barrel of LptD. The LPS translocon LptD is unable to fold properly in the absence of LptE and the two proteins form a unique barrel and plug architecture for LPS transport and insertion. LptD is an essential outer membrane protein that mediates the final transport of lipopolysaccharide (LPS) to outer leaflet. It has been suggested that LptD is a promising target for the development of effective vaccines and antibody-based therapies to control Vibrio infection. 384 matched cddid_all.tbl CDD pfam04454 pfam04454 427959 Linocin_M18 Encapsulating protein for peroxidase. The Linocin_M18 is found in eubacteria and archaea. These proteins, referred to as encapsulins, form nanocompartments within the bacterium which contain ferritin-like proteins or peroxidases, enzymes involved in oxidative-stress response. These enzymes are targeted to the interior of encapsulins via unique C-terminal extensions. 253 matched cddid_all.tbl CDD pfam04455 pfam04455 427960 Saccharop_dh_N LOR/SDH bifunctional enzyme conserved region. Lysine-oxoglutarate reductase/Saccharopine dehydrogenase (LOR/SDH) is a bifunctional enzyme. This conserved region is commonly found immediately N-terminal to Saccharop_dh (pfam03435) in eukaryotes. 93 matched cddid_all.tbl CDD pfam04456 pfam04456 461316 DUF503 Protein of unknown function (DUF503). Family of hypothetical bacterial proteins. 82 matched cddid_all.tbl CDD pfam04457 pfam04457 461317 MJ1316 MJ1316 RNA cyclic group end recognition domain. RNA repair domain predicted to be involved specifically in the recognition of RNA 3' ends with 2'-3' cyclic phosphate groups. 75 matched cddid_all.tbl CDD pfam04458 pfam04458 427963 DUF505 Protein of unknown function (DUF505). Family of uncharacterized prokaryotic proteins. 622 matched cddid_all.tbl CDD pfam04459 pfam04459 461318 DUF512 Protein of unknown function (DUF512). Family of uncharacterized prokaryotic proteins. 203 matched cddid_all.tbl CDD pfam04461 pfam04461 461319 DUF520 Protein of unknown function (DUF520). The structure of the DUF520 family of uncharacterized proteins shows that it has composed of two domains each of which has the same topology. 161 matched cddid_all.tbl CDD pfam04463 pfam04463 461320 2-thiour_desulf 2-thiouracil desulfurase. This family of proteins, predominantly found in Bacteria, are involved in the desulfuration of 2-thiouracil into uracil in the 2-thiouridine degradation pathway. It has been demonstrated that these proteins contain a Fe-S cluster required for their activity. 137 matched cddid_all.tbl CDD pfam04464 pfam04464 398259 Glyphos_transf CDP-Glycerol:Poly(glycerophosphate) glycerophosphotransferase. Wall-associated teichoic acids are a heterogeneous class of phosphate-rich polymers that are covalently linked to the cell wall peptidoglycan of gram-positive bacteria. They consist of a main chain of phosphodiester-linked polyols and/or sugar moieties attached to peptidoglycan via a linkage unit. CDP-glycerol:poly(glycerophosphate) glycerophosphotransferase is responsible for the polymerization of the main chain of the teichoic acid by sequential transfer of glycerol-phosphate units from CDP-glycerol to the linkage unit lipid. 360 matched cddid_all.tbl CDD pfam04465 pfam04465 367954 DUF499 Protein of unknown function (DUF499). Family of uncharacterized hypothetical prokaryotic proteins. 1016 matched cddid_all.tbl CDD pfam04466 pfam04466 335802 Terminase_3 Phage terminase large subunit. Initiation of packaging of double-stranded viral DNA involves the specific interaction of the prohead with viral DNA in a process mediated by a phage-encoded terminase protein. The terminase enzymes are usually hetero-oligomers composed of a small and a large subunit. This region is found on the large subunit and possess an endonuclease and ATPase activity that require Mg2+ and a neutral or slightly basic reaction. This region is also found in bacterial sequences. 201 matched cddid_all.tbl CDD pfam04467 pfam04467 367955 DUF483 Protein of unknown function (DUF483). Family of uncharacterized prokaryotic proteins. 119 matched cddid_all.tbl CDD pfam04468 pfam04468 461321 PSP1 PSP1 C-terminal conserved region. This region is present in both eukaryotes and eubacteria. The yeast PSP1 protein is involved in suppressing mutations in the DNA polymerase alpha subunit in yeast. 86 matched cddid_all.tbl CDD pfam04471 pfam04471 461322 Mrr_cat Restriction endonuclease. Prokaryotic family found in type II restriction enzymes containing the hallmark (D/E)-(D/E)XK active site. Presence of catalytic residues implicates this region in the enzymatic cleavage of DNA. 114 matched cddid_all.tbl CDD pfam04472 pfam04472 461323 SepF Cell division protein SepF. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This family also includes archaeal related proteins of unknown function. 72 matched cddid_all.tbl CDD pfam04473 pfam04473 282345 DUF553 Transglutaminase-like domain. This family of uncharacterized archaeal proteins are related to Transglutaminase-like domains. This family has previously been called DUF553 and UPF0252. 140 matched cddid_all.tbl CDD pfam04474 pfam04474 461324 DUF554 Protein of unknown function (DUF554). Family of uncharacterized prokaryotic proteins. Multiple predicted transmembrane regions suggest that the region is membrane associated. 220 matched cddid_all.tbl CDD pfam04475 pfam04475 427971 DUF555 Protein of unknown function (DUF555). Family of uncharacterized, hypothetical archaeal proteins. 101 matched cddid_all.tbl CDD pfam04476 pfam04476 427972 4HFCP_synth 4-HFC-P synthase. (5-formylfuran-3-yl)methyl phosphate synthase, also known as 4-HFC-P synthase, is involved in the production of methanofuran. This family has a classical TIM-barrel structure whose biological unit is a homohexamer. 228 matched cddid_all.tbl CDD pfam04478 pfam04478 398266 Mid2 Mid2 like cell wall stress sensor. This family represents a region near the C terminus of Mid2, which contains a transmembrane region. The remainder of the protein sequence is serine-rich and of low complexity, and is therefore impossible to align accurately. Mid2 is thought to act as a mechanosensor of cell wall stress. The C-terminal cytoplasmic region of Mid2 is known to interact with Rom2, a guanine nucleotide exchange factor (GEF) for Rho1, which is part of the cell wall integrity signalling pathway. 150 matched cddid_all.tbl CDD pfam04479 pfam04479 461325 RTA1 RTA1 like protein. This family is comprised of fungal proteins with multiple transmembrane regions. RTA1 is involved in resistance to 7-aminocholesterol, while RTM1 confers resistance to an an unknown toxic chemical in molasses. These proteins may bind to the toxic substance, and thus prevent toxicity. They are not thought to be involved in the efflux of xenobiotics. 210 matched cddid_all.tbl CDD pfam04480 pfam04480 398268 DUF559 Protein of unknown function (DUF559). 95 matched cddid_all.tbl CDD pfam04481 pfam04481 113257 DUF561 Protein of unknown function (DUF561). Protein of unknown function found in a cyanobacterium, and the chloroplasts of algae. 243 matched cddid_all.tbl CDD pfam04483 pfam04483 461326 DUF565 Protein of unknown function (DUF565). Predicted transmembrane protein found in plants, chloroplasts and cyanobacteria. This family is also known as YCF20. 57 matched cddid_all.tbl CDD pfam04484 pfam04484 461327 QWRF QWRF family. AUG8 belongs to the plant QWRF motif-containing protein family, which also includes microtubule-associated protein ENDOSPERM DEFECTIVE 1 and SNOWY COTYLEDON 3. AUG8 binds the microtubule plus-end and participates in the reorientation of microtubules in hypocotyls (the stem of a germinating seedling). 304 matched cddid_all.tbl CDD pfam04485 pfam04485 427976 NblA Phycobilisome degradation protein nblA. In the cyanobacterium Synechococcus PCC 7942, nblA triggers degradation of light-harvesting phycobiliproteins in response to deprivation nutrients including nitrogen, phosphorus and sulphur. The mechanism of nblA function is not known, but it has been hypothesized that nblA may act by disrupting phycobilisome structure, activating a protease or tagging phycobiliproteins for proteolysis. Members of this family have also been identified in the chloroplasts of some red algae. 50 matched cddid_all.tbl CDD pfam04486 pfam04486 398272 SchA_CurD SchA/CurD like domain. Members of this family have only been identified in species of the Streptomyces genus. Two family members are known to be part of gene clusters involved in the synthesis of polyketide-based spore pigments, homologous to clusters involved in the synthesis of polyketide antibiotics. The function of this protein is unknown, but it has been speculated to contain a NAD(P) binding site. Many of these proteins contain two copies of this presumed domain. 118 matched cddid_all.tbl CDD pfam04487 pfam04487 461328 CITED CITED. CITED, CBP/p300-interacting transactivator with ED-rich tail, are characterized by a conserved 32-amino acid sequence at the C-terminus. CITED proteins do not bind DNA directly and are thought to function as transcriptional co-activators. 211 matched cddid_all.tbl CDD pfam04488 pfam04488 398274 Gly_transf_sug Glycosyltransferase sugar-binding region containing DXD motif. The DXD motif is a short conserved motif found in many families of glycosyltransferases, which add a range of different sugars to other sugars, phosphates and proteins. DXD-containing glycosyltransferases all use nucleoside diphosphate sugars as donors and require divalent cations, usually manganese. The DXD motif is expected to play a carbohydrate binding role in sugar-nucleoside diphosphate and manganese dependent glycosyltransferases. 93 matched cddid_all.tbl CDD pfam04489 pfam04489 282358 DUF570 Protein of unknown function (DUF570). Protein of unknown function, found in herpesvirus and cytomegalovirus. 456 matched cddid_all.tbl CDD pfam04490 pfam04490 282359 Pox_T4_C Poxvirus T4 protein, C terminus. This family of poxvirus proteins are thought to be retained in the endoplasmic reticulum. M-T4 of myxoma virus is thought to protect infected lymphocytes from apoptosis and modulate the inflammatory response to virus infection. 146 matched cddid_all.tbl CDD pfam04491 pfam04491 282360 Pox_T4_N Poxvirus T4 protein, N terminus. This family of poxvirus proteins are thought to be secreted or retained in the endoplasmic reticulum if the protein also contains an additional C terminal region (pfam04490). M-T4 of myxoma virus is thought to protect infected lymphocytes from apoptosis and modulate the inflammatory response to virus infection. 46 matched cddid_all.tbl CDD pfam04492 pfam04492 461329 Phage_rep_O Bacteriophage replication protein O. Replication protein O is necessary for the initiation of bacteriophage DNA replication. Protein O interacts with the lambda replication origin, and also with replication protein P to form an oligomer. It is speculated that the N-terminal half interacts with the replication origin while the C terminal half mediates protein-protein interaction (annotation of Swiss: P14815). 92 matched cddid_all.tbl CDD pfam04493 pfam04493 427979 Endonuclease_5 Endonuclease V. Endonuclease V is specific for single-stranded DNA or for duplex DNA that contains uracil or that is damaged by a variety of agents. 198 matched cddid_all.tbl CDD pfam04494 pfam04494 461330 TFIID_NTD2 WD40 associated region in TFIID subunit, NTD2 domain. This region is an all-alpha domain associated with the WD40 helical bundle of the TAF5 subunit of transcription factor TFIID. The domain has distant structural similarity to RNA polymerase II CTD interacting factors. It contains several conserved clefts that are likely to be critical for TFIID complex assembly. The TAF5 subunit is present twice in the TFIID complex and is critical for the function and assembly of the complex, and the NTD2 and N-terminal domain is crucial for homodimerization. 130 matched cddid_all.tbl CDD pfam04495 pfam04495 427981 GRASP55_65 GRASP55/65 PDZ-like domain. GRASP55 (Golgi re-assembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide- sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system. This region appears to be related to the PDZ domain. 138 matched cddid_all.tbl CDD pfam04496 pfam04496 282365 Herpes_UL35 Herpesvirus UL35 family. UL35 represents a true late gene which encodes a 12-kDa capsid protein. 109 matched cddid_all.tbl CDD pfam04497 pfam04497 461331 Pox_E2-like Poxviridae protein. This family of proteins is restricted to Poxviridae. It contains a number of differently named uncharacterized proteins. 727 matched cddid_all.tbl CDD pfam04498 pfam04498 282367 Pox_VP8_L4R Poxvirus nucleic acid binding protein VP8/L4R. The 25 kDa product of Vaccinia virus gene L4R is also known as VP8. VP8 is found in the cores of Vaccinia virions and is essential for the formation of transcriptionally competent viral particles. It binds both single stranded and double stranded DNA and RNA with similar affinities. Binding is thought to involve cooperative interactions between protein subunits. The protein is proteolytically cleaved during viral assembly at an Ala-Gly-Ala site. Possible roles for VP8 include packaging and maintaining the DNA genome in a transcribable configuration; binding ssDNA during transcription initiation; and cooperation with I8R protein to unwind early promoter regions. VP8 may also function in either transcription elongation or release of mRNA molecules from viral particles. 217 matched cddid_all.tbl CDD pfam04499 pfam04499 398279 SAPS SIT4 phosphatase-associated protein. This family includes a conserved region from a group of yeast proteins that associate with the SIT4 phosphatase. This association is required for SIT4's role in G1 cyclin transcription and for bud formation. This family also includes homologous regions from other eukaryotes. 383 matched cddid_all.tbl CDD pfam04500 pfam04500 461332 FLYWCH FLYWCH zinc finger domain. Mutations in the mod(mdg4) gene have effects on variegation (PEV), the properties of insulator sequences, correct path-finding of growing nerve cells, meiotic pairing of chromosomes, and apoptosis. The occurrence of FLYWCH motifs in mod(mdg4) gene product and other proteins is discussed in. 62 matched cddid_all.tbl CDD pfam04501 pfam04501 367967 Baculo_VP39 Baculovirus major capsid protein VP39. This family constitutes the 39 kDa major capsid protein of the Baculoviridae. 240 matched cddid_all.tbl CDD pfam04502 pfam04502 461333 Saf4_Yju2 Saf4/Yju2 protein. This is a family of eukaryotic proteins that includes CCDC130 and CCDC94 from humans, Saf4 from fission yeasts and Yju2 from budding yeasts. Saf4 (also known as cwc16) is involved in mRNA splicing where it associates with cdc5 and the other cwf proteins as part of the spliceosome. Yju2 is a splicing factor that is associated with the Prp 19-associated complex and acts after Prp2 in promoting the first catalytic reaction of pre-mRNA splicing. 328 matched cddid_all.tbl CDD pfam04503 pfam04503 461334 SSDP Single-stranded DNA binding protein, SSDP. This is a family of eukaryotic single-stranded DNA binding proteins with specificity to a pyrimidine-rich element found in the promoter region of the alpha2(I) collagen gene. 293 matched cddid_all.tbl CDD pfam04504 pfam04504 461335 DUF573 Protein of unknown function, DUF573. 95 matched cddid_all.tbl CDD pfam04505 pfam04505 461336 CD225 Interferon-induced transmembrane protein. This family includes the human leukocyte antigen CD225, which is an interferon inducible transmembrane protein, and is associated with interferon induced cell growth suppression. 68 matched cddid_all.tbl CDD pfam04506 pfam04506 427987 Rft-1 Rft protein. 513 matched cddid_all.tbl CDD pfam04507 pfam04507 398286 DUF576 Csa1 family. This family contains several uncharacterized staphylococcal proteins. These proteins have been called conserved staphylococcal antigens (Csa). 225 matched cddid_all.tbl CDD pfam04508 pfam04508 282377 Pox_A_type_inc Viral A-type inclusion protein repeat. The repeat is found in the A-type inclusion protein of the Poxvirus family. 22 matched cddid_all.tbl CDD pfam04509 pfam04509 398287 CheC CheC-like family. The restoration of pre-stimulus levels of the chemotactic response regulator, CheY-P, is important for allowing bacteria to respond to new environmental stimuli. The members of this family, CheC, CheX, CheA and FliY are CheY-P phosphatase. CheC appears to be primarily involved in restoring normal CheY-P levels, whereas FliY seems to act on CheY-P constitutively. CheD enhances the activity of CheC 5-fold, which is normally relatively low. In some cases, the region represented by this entry is present as multiple copies. 38 matched cddid_all.tbl CDD pfam04510 pfam04510 367974 DUF577 Family of unknown function (DUF577). This domain is found in Arabidopsis thaliana proteins, which are specifically expressed during meiosis. Many of these members contain a repeated region. 173 matched cddid_all.tbl CDD pfam04511 pfam04511 427988 DER1 Der1-like family. The endoplasmic reticulum (ER) of the yeast Saccharomyces cerevisiae contains of proteolytic system able to selectively degrade misfolded lumenal secretory proteins. For examination of the components involved in this degradation process, mutants were isolated. They could be divided into four complementation groups. The mutations led to stabilization of two different substrates for this process. The mutant classes were called 'der' for 'degradation in the ER'. DER1 was cloned by complementation of the der1-2 mutation. The DER1 gene codes for a novel, hydrophobic protein, that is localized to the ER. Deletion of DER1 abolished degradation of the substrate proteins. The function of the Der1 protein seems to be specifically required for the degradation process associated with the ER. Interestingly this family seems distantly related to the Rhomboid family of membrane peptidases. Suggesting that this family may also mediate degradation of misfolded proteins (Bateman A pers. obs.). 191 matched cddid_all.tbl CDD pfam04512 pfam04512 398289 Baculo_PEP_N Baculovirus polyhedron envelope protein, PEP, N terminus. Polyhedra are large crystalline occlusion bodies containing nucleopolyhedrovirus virions, and surrounded by an electron-dense structure called the polyhedron envelope or polyhedron calyx. The polyhedron envelope (associated) protein PEP is thought to be an integral part of the polyhedron envelope. PEP is concentrated at the surface of polyhedra, and is thought to be important for the proper formation of the periphery of polyhedra. It is thought that PEP may stabilize polyhedra and protect them from fusion or aggregation. 91 matched cddid_all.tbl CDD pfam04513 pfam04513 309591 Baculo_PEP_C Baculovirus polyhedron envelope protein, PEP, C terminus. Polyhedra are large crystalline occlusion bodies containing nucleopolyhedrovirus virions, and surrounded by an electron-dense structure called the polyhedron envelope or polyhedron calyx. The polyhedron envelope (associated) protein PEP is thought to be an integral part of the polyhedron envelope. PEP is concentrated at the surface of polyhedra, and is thought to be important for the proper formation of the periphery of polyhedra. It is thought that PEP may stabilize polyhedra and protect them from fusion or aggregation. 140 matched cddid_all.tbl CDD pfam04514 pfam04514 282383 BTV_NS2 Bluetongue virus non-structural protein NS2. This family includes NS2 proteins from other members of the Orbivirus genus. NS2 is a non-specific single-stranded RNA-binding protein that forms large homomultimers and accumulates in viral inclusion bodies of infected cells. Three RNA binding regions have been identified in Bluetongue virus serotype 17 at residues 2-11, 153-166 and 274-286. NS2 multimers also possess nucleotidyl phosphatase activity. The precise function of NS2 is not known, but it may be involved in the transport and condensation of viral mRNAs. 349 matched cddid_all.tbl CDD pfam04515 pfam04515 461337 Choline_transpo Plasma-membrane choline transporter. This family represents a high-affinity plasma-membrane choline transporter in C.elegans which is thought to be rate-limiting for ACh synthesis in cholinergic nerve terminals. 325 matched cddid_all.tbl CDD pfam04516 pfam04516 461338 CP2 CP2 transcription factor. This family represents a conserved region in the CP2 transcription factor family. 214 matched cddid_all.tbl CDD pfam04517 pfam04517 461339 Microvir_lysis Microvirus lysis protein (E), C terminus. E protein causes host cell lysis by inhibiting MraY, a peptidoglycan biosynthesis enzyme. This leads to cell wall failure at septation. The N terminal transmembrane region matches the signal peptide model and must be omitted from the family. 42 matched cddid_all.tbl CDD pfam04518 pfam04518 309594 Effector_1 Effector from type III secretion system. This is a family of effector proteins which are secreted by the type III secretion system. The precise function of this family is unknown. 352 matched cddid_all.tbl CDD pfam04519 pfam04519 461340 Bactofilin Polymer-forming cytoskeletal. This is a family of bactofilins, a functionally diverse class of cytoskeletal, polymer-forming, proteins that is widely conserved among bacteria. In the example species C. crescentus, two bactofilins assemble into a membrane-associated laminar structure that shows cell-cycle-dependent polar localization and acts as a platform for the recruitment of a cell wall biosynthetic enzyme involved in polar morphogenesis. Bactofilins display distinct subcellular distributions and dynamics in different bacterial species, suggesting that they are versatile structural elements that have adopted a range of different cellular functions. 89 matched cddid_all.tbl CDD pfam04520 pfam04520 461341 Senescence_reg Senescence regulator. This protein regulates the expression of proteins associated with leaf senescence in plants. 171 matched cddid_all.tbl CDD pfam04521 pfam04521 282390 Viral_P18 ssRNA positive strand viral 18kD cysteine rich protein. 137 matched cddid_all.tbl CDD pfam04522 pfam04522 461342 BBMV_Gp1_N Broad bean mottle virus, Gp1, N-terminal. This region represents the N terminus of Broad bean mottle virus, Gp1 (2a protein), and is always found N terminal to a predicted RNA-dependent RNA polymerase region (pfam00978). 234 matched cddid_all.tbl CDD pfam04523 pfam04523 282392 Herpes_U30 Herpes virus tegument protein U30. This family is named after the human herpesvirus protein, but has been characterized in cytomegalovirus as UL47. Cytomegalovirus UL47 is a component of the tegument, which is a protein layer surrounding the viral capsid. UL47 co-precipitates with UL48 and UL69 tegument proteins, and the major capsid protein UL86. A UL47-containing complex is thought to be involved in the release of viral DNA from the disassembling virus particle. 906 matched cddid_all.tbl CDD pfam04525 pfam04525 398294 LOR LURP-one-related. The structure of this family has been solved. It comprises a 12-stranded beta barrel with a central C-terminal alpha helix. This helix is thought to be a transmembrane helix. It is structurally similar to the C-terminal domain of the Tubby protein. In plants it plays a role in defense against pathogens. 186 matched cddid_all.tbl CDD pfam04526 pfam04526 461343 DUF568 Protein of unknown function (DUF568). Family of uncharacterized plant proteins. 100 matched cddid_all.tbl CDD pfam04527 pfam04527 427994 Retinin_C Drosophila Retinin like protein. Family of Drosophila proteins related to the C-terminal region of the Drosophila Retinin protein. Conserved region is found towards the C-terminus of the member proteins. 63 matched cddid_all.tbl CDD pfam04528 pfam04528 461344 Adeno_E4_34 Adenovirus early E4 34 kDa protein conserved region. Conserved region found in the Adenovirus E4 34 kDa protein. 145 matched cddid_all.tbl CDD pfam04529 pfam04529 398296 Herpes_U59 Herpesvirus U59 protein. The proteins in this family have no known function. Cytomegalovirus UL88 is also a member of this family. 365 matched cddid_all.tbl CDD pfam04530 pfam04530 282398 Viral_Beta_CD Viral Beta C/D like family. Family of ssRNA positive-strand viral proteins. Conserved region found in the Beta C and Beta D transcripts. 123 matched cddid_all.tbl CDD pfam04531 pfam04531 398297 Phage_holin_1 Bacteriophage holin. This family of holins is found in several staphylococcal and streptococcal bacteriophages. Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis. It is thought that the temporal precision of holin-mediated lysis may occur through the buildup of a holin oligomer which causes the lysis. 82 matched cddid_all.tbl CDD pfam04532 pfam04532 282400 DUF587 Protein of unknown function (DUF587). This family consists of the N termini of some human herpesvirus U58 proteins, and some cytomegalovirus UL87 proteins. This region is always found N terminal to the Pfam family UL87 (pfam03043), which has no known function. 227 matched cddid_all.tbl CDD pfam04533 pfam04533 282401 Herpes_U44 Herpes virus U44 protein. This is a family of proteins from dsDNA beta-herpesvirinae and gamma-herpesvirinae viruses. The function is not known, and the proteins are named variously as U44, BSRF1, UL71, and M71. The family BSRF1 has been merged into this. 202 matched cddid_all.tbl CDD pfam04534 pfam04534 398298 Herpes_UL56 Herpesvirus UL56 protein. In herpes simplex virus type 2, UL56 is thought to be a tail-anchored type II membrane protein involved in vesicular trafficking. The C terminal hydrophobic region is required for association with the cytoplasmic membrane, and the N terminal proline-rich region is important for the translocation of UL56 to the Golgi apparatus and cytoplasmic vesicles. 197 matched cddid_all.tbl CDD pfam04535 pfam04535 367980 CASP_dom Casparian strip membrane protein domain. This domain is found mainly in plant proteins known as Casparian strip membrane proteins (CASPs) and CASP-like proteins (CASPLs). CASPs are four-membrane-span proteins that mediate the deposition of Casparian strips in the endodermis by recruiting the lignin polymerization machinery. Interestingly, the CASP first extracellular loop was found conserved in euphyllophytes but absent in plants lacking Casparian strips. 150 matched cddid_all.tbl CDD pfam04536 pfam04536 461345 TPM_phosphatase TPM domain. This family was first named TPM domain after its founding proteins: TLP18.3, Psb32 and MOLO-1. In Arabidopsis, this domain is called the thylakoid acid phosphatase -TAP - domain and has a Rossmann-like fold. In plants, the family resides in the thylakoid lumen attached to the outer membrane of the chloroplast/plastid. It is active in the photosystem II. 125 matched cddid_all.tbl CDD pfam04537 pfam04537 282405 Herpes_UL55 Herpesvirus UL55 protein. In infected cells, UL55 is associated with the nuclear matrix, and found adjacent to compartments containing the capsid protein ICP35. UL55 was not detected in assembled virions. It is thought that UL55 may play a role in virion assembly or maturation. 164 matched cddid_all.tbl CDD pfam04538 pfam04538 461346 BEX Brain expressed X-linked like family. This is a family of transcription elongation factors which includes those referred to as Bex proteins as well as those named TCEAL7. Bex1 was shown to be a novel link between neurotrophin signalling, the cell cycle, and neuronal differentiation, suggesting it might function by coordinating internal cellular states with the ability of cells to respond to external signals. TCEAL7 has been shown negatively to regulate the NF-kappaB pathway, hence being important in ovarian cancer as it one of the genes frequently downregulated in this cancer. A closely related protein, TFIIS/TCEA, found in pfam07500 is involved in transcription elongation and transcript fidelity. TFIIS/TCEA promotes 3' endoribonuclease activity of RNA polymerase II (pol II) and allows pol II to bypass transcript pause or 'arrest' during elongation process. It is thus possible that BEX is also acting in this way. 103 matched cddid_all.tbl CDD pfam04539 pfam04539 427997 Sigma70_r3 Sigma-70 region 3. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme. 78 matched cddid_all.tbl CDD pfam04540 pfam04540 282408 Herpes_UL51 Herpesvirus UL51 protein. UL51 protein is a virion protein. In pseudorabies virus, UL51 was identified as a component of the capsid. In herpes simplex virus type 1 there is evidence for post-translational modification of UL51. 158 matched cddid_all.tbl CDD pfam04541 pfam04541 398302 Herpes_U34 Herpesvirus virion protein U34. The virion proteins in this family include membrane phosphoprotein-like proteins such as UL34, Epstein-Barr and R50, from dsDNA viruses, no RNA stage, Herpesvirales. The family Herpes_BFRF1, pfam05900, has been merged in. 182 matched cddid_all.tbl CDD pfam04542 pfam04542 427998 Sigma70_r2 Sigma-70 region 2. Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation. 71 matched cddid_all.tbl CDD pfam04544 pfam04544 282411 Herpes_UL20 Herpesvirus egress protein UL20. UL20 is predicted to be a transmembrane protein with multiple membrane spans. It is involved in the trans-cellular transport of enveloped virions, and is therefore important for viral egress. However, UL20 operates in different cellular compartments and different stages of egress in pseudorabies virus and herpes simplex virus. This is thought to be due to differences in egress pathways between these two viruses. 179 matched cddid_all.tbl CDD pfam04545 pfam04545 461347 Sigma70_r4 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives. 50 matched cddid_all.tbl CDD pfam04546 pfam04546 461348 Sigma70_ner Sigma-70, non-essential region. The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function. 169 matched cddid_all.tbl CDD pfam04547 pfam04547 461349 Anoctamin Calcium-activated chloride channel. The family carries eight putative transmembrane domains, and, although it has no similarity to other known channel proteins, it is clearly a calcium-activated ionic channel. It is expressed in various secretory epithelia, the retina and sensory neurons, and mediates receptor-activated chloride currents in diverse physiological processes. 377 matched cddid_all.tbl CDD pfam04548 pfam04548 398307 AIG1 AIG1 family. Arabidopsis protein AIG1 appears to be involved in plant resistance to bacteria. 200 matched cddid_all.tbl CDD pfam04549 pfam04549 367985 CD47 CD47 transmembrane region. This family represents the transmembrane region of CD47 leukocyte antigen. 147 matched cddid_all.tbl CDD pfam04550 pfam04550 428002 Phage_holin_3_2 Phage holin family 2. Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis. It is thought that the temporal precision of holin-mediated lysis may occur through the buildup of a holin oligomer which causes the lysis. 86 matched cddid_all.tbl CDD pfam04551 pfam04551 428003 GcpE GcpE protein. In a variety of organizms, including plants and several eubacteria, isoprenoids are synthesized by the mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. Although different enzymes of this pathway have been described, the terminal biosynthetic steps of the MEP pathway have not been fully elucidated. GcpE gene of Escherichia coli is involved in this pathway. 343 matched cddid_all.tbl CDD pfam04552 pfam04552 428004 Sigma54_DBD Sigma-54, DNA binding domain. This DNA binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore this region contains a putative helix-turn-helix motif. At the C-terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins. 159 matched cddid_all.tbl CDD pfam04553 pfam04553 461350 Tis11B_N Tis11B like protein, N terminus. Members of this family always contain a tandem repeat of CCCH zinc fingers pfam00642. Tis11B, Tis11D and their homologs are thought to be regulatory proteins involved in the response to growth factors. The function of the N terminus is unknown. 114 matched cddid_all.tbl CDD pfam04554 pfam04554 252669 Extensin_2 Extensin-like region. 57 matched cddid_all.tbl CDD pfam04555 pfam04555 461351 XhoI Restriction endonuclease XhoI. This family consists of type II restriction enzymes (EC:3.1.21.4) that recognize the double-stranded sequence CTCGAG and cleave after C-1. 191 matched cddid_all.tbl CDD pfam04556 pfam04556 428007 DpnII DpnII restriction endonuclease. Members of this family are type II restriction enzymes (EC:3.1.21.4). They recognize the double-stranded unmethylated sequence GATC and cleave before G-1. http://rebase.neb.com/rebase/enz/DpnII.html 276 matched cddid_all.tbl CDD pfam04557 pfam04557 461352 tRNA_synt_1c_R2 Glutaminyl-tRNA synthetase, non-specific RNA binding region part 2. This is a region found N terminal to the catalytic domain of glutaminyl-tRNA synthetase (EC 6.1.1.18) in eukaryotes but not in Escherichia coli. This region is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function. 87 matched cddid_all.tbl CDD pfam04558 pfam04558 461353 tRNA_synt_1c_R1 Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1. This is a region found N terminal to the catalytic domain of glutaminyl-tRNA synthetase (EC 6.1.1.18) in eukaryotes but not in Escherichia coli. This region is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function. 161 matched cddid_all.tbl CDD pfam04559 pfam04559 461354 Herpes_UL17 Herpesvirus UL17 protein. UL17 protein is required for DNA cleavage and packaging in herpes viruses. It has been shown to associate with immature B-type capsids, and is required for the the localization of capsids and capsid proteins to the intranuclear sites where viral DNA is cleaved and packaged. In the virion, UL17 is a component of the tegument, which is a protein layer surrounding the viral capsid. 497 matched cddid_all.tbl CDD pfam04560 pfam04560 461355 RNA_pol_Rpb2_7 "RNA polymerase Rpb2, domain 7. RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed ""switch 4"". The switches within the polymerase are thought to signal different stages of transcription." 87 matched cddid_all.tbl CDD pfam04561 pfam04561 398318 RNA_pol_Rpb2_2 RNA polymerase Rpb2, domain 2. RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI). 185 matched cddid_all.tbl CDD pfam04562 pfam04562 398319 Dicty_spore_N Dictyostelium spore coat protein, N terminus. The Dictyostelium spore coat is a polarised extracellular matrix composed of glycoproteins and cellulose. Four of the major coat glycoproteins exist as a multi-protein complex within the prespore vesicles before secretion. Of these, SP96 and SP70 are members of this family. The presence of SP96 and SP70 in the complex is necessary for the cellulose binding activity of the complex, which is in turn necessary for normal spore coat assembly. The function of this region of these proteins is not known. 114 matched cddid_all.tbl CDD pfam04563 pfam04563 367994 RNA_pol_Rpb2_1 RNA polymerase beta subunit. RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain. 396 matched cddid_all.tbl CDD pfam04564 pfam04564 398320 U-box U-box domain. The U-box is a domain of ~70 amino acids that is present in proteins from yeast to human. It consists of the beta-beta-alpha-beta-alpha- fold typical of U-box and RING domains. The central alpha helix is flanked by two prominent surface-exposed loop regions. This domain is one class of E3 ligases, involved in the ubiquitination process. This domain is related to the Ring finger pfam00097 but lacks the zinc binding residues. 73 matched cddid_all.tbl CDD pfam04565 pfam04565 428011 RNA_pol_Rpb2_3 RNA polymerase Rpb2, domain 3. RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site. 67 matched cddid_all.tbl CDD pfam04566 pfam04566 428012 RNA_pol_Rpb2_4 RNA polymerase Rpb2, domain 4. RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain. 62 matched cddid_all.tbl CDD pfam04567 pfam04567 428013 RNA_pol_Rpb2_5 RNA polymerase Rpb2, domain 5. RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain. 53 matched cddid_all.tbl CDD pfam04568 pfam04568 428014 IATP Mitochondrial ATPase inhibitor, IATP. ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP. The minimum inhibitory region for bovine inhibitor is from residues 39 to 72. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH, the inhibitor forms a dimer via antiparallel coiled coil interactions between the C terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity. 98 matched cddid_all.tbl CDD pfam04569 pfam04569 367998 DUF591 Protein of unknown function. This family represents a conserved region in a number of uncharacterized plant proteins. 41 matched cddid_all.tbl CDD pfam04570 pfam04570 428015 zf-FLZ zinc-finger of the FCS-type, C2-C2. zf-FLZ is a FCS-like zinc-finger domain found in higher plants. It is bryophitic in origin. It carries a zf-FCS-like C2-C2 zinc finger, consisting of a consensus cysteine-signature sequence with conserved phenyl alanine and serine residue associated with a third cysteine. It acts as a protein-protein interaction module. 53 matched cddid_all.tbl CDD pfam04571 pfam04571 461356 Lipin_N lipin, N-terminal conserved region. Mutations in the lipin gene lead to fatty liver dystrophy in mice. The protein has been shown to be phosphorylated by the TOR Ser/Thr protein kinases in response to insulin stimulation. The conserved region is found at the N-terminus of the member proteins. 103 matched cddid_all.tbl CDD pfam04572 pfam04572 428017 Gb3_synth Alpha 1,4-glycosyltransferase conserved region. The glycosphingolipids (GSL) form part of eukaryotic cell membranes. They consist of a hydrophilic carbohydrate moiety linked to a hydrophobic ceramide tail embedded within the lipid bilayer of the membrane. Lactosylceramide, Gal1,4Glc1Cer (LacCer), is the common synthetic precursor to the majority of GSL found in vertebrates. Alpha 1.4-glycosyltransferases utilize UDP donors and transfer the sugar to a beta-linked acceptor. This region appears to be confined to higher eukaryotes. No function has been yet assigned to this region. 130 matched cddid_all.tbl CDD pfam04573 pfam04573 461357 SPC22 Signal peptidase subunit. Translocation of polypeptide chains across the endoplasmic reticulum membrane is triggered by signal sequences. During translocation of the nascent chain through the membrane, the signal sequence of most secretory and membrane proteins is cleaved off. Cleavage occurs by the signal peptidase complex (SPC) which consists of four subunits in yeast and five in mammals. This family is common to yeast and mammals. 172 matched cddid_all.tbl CDD pfam04574 pfam04574 368003 DUF592 Protein of unknown function (DUF592). This region is found in some SIR2 family proteins (pfam02146). 153 matched cddid_all.tbl CDD pfam04575 pfam04575 398328 SlipAM Surface lipoprotein assembly modifier. Surface lipoprotein assembly modifier (Slam) is a surface lipoprotein that may have a role in virulence. In Neisseria, it is required for the surface display of lipidated virulence factors. Proteins in this family contain an eight-stranded beta-barrel domain. 288 matched cddid_all.tbl CDD pfam04576 pfam04576 428019 Zein-binding Zein-binding. This domain binds to zein proteins, pfam01559. Zein proteins are seed storage proteins. 92 matched cddid_all.tbl CDD pfam04577 pfam04577 428020 Glyco_transf_61 Glycosyltransferase 61. This family represents the Glycosyltransferase Family 61. Members in this family are further processed into a mature form. It includes O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 (POMGnT2, also known as AGO61 or EOGLT) and EGF domain-specific O-linked N-acetylglucosamine transferase (EOGT). This family also includes plant beta-1,2-xylosyltransferases. 124 matched cddid_all.tbl CDD pfam04578 pfam04578 461358 DUF594 Protein of unknown function, DUF594. 55 matched cddid_all.tbl CDD pfam04579 pfam04579 461359 Keratin_matx Keratin, high-sulphur matrix protein. Family of Keratin, high-sulfur matrix proteins. The keratin products of mammalian epidermal derivatives such as wool and hair consist of microfibrils embedded in a rigid matrix of other proteins. The matrix proteins include the high-sulphur and high-tyrosine keratins, having molecular weights of 6-20 kDa, whereas microfibrils contain the larger, low-sulphur keratins (40-56 kDa). 96 matched cddid_all.tbl CDD pfam04580 pfam04580 282445 Pox_D3 Chordopoxvirinae D3 protein. Chordopoxvirinae D3 protein conserved region. Region occupies entire length of D3 protein. 248 matched cddid_all.tbl CDD pfam04582 pfam04582 368009 Reo_sigmaC Reovirus sigma C capsid protein C-terminal domain. 130 matched cddid_all.tbl CDD pfam04583 pfam04583 368010 Baculo_p74 Baculoviridae p74 conserved region. Baculoviruses are distinct from other virus families in that there are two viral phenotypes: budded virus (BV) and occlusion-derived virus (ODV). BVs disseminate viral infection throughout the tissues of the host and ODVs transmit baculovirus between insect hosts. GFP tagging experiments implicate p74 as an ODV envelope protein. 218 matched cddid_all.tbl CDD pfam04584 pfam04584 282447 Pox_A28 Poxvirus A28 family. Family of conserved Poxvirus A28 family proteins. Conserved region spans entire protein in the majority of family members. 140 matched cddid_all.tbl CDD pfam04586 pfam04586 309640 Peptidase_S78 Caudovirus prohead serine protease. Family of Caudovirus prohead serine proteases also found in a number of bacteria possibly as the result of horizontal transfer. 160 matched cddid_all.tbl CDD pfam04587 pfam04587 461360 ADP_PFK_GK ADP-specific Phosphofructokinase/Glucokinase conserved region. In archaea a novel type of glycolytic pathway exists that is deviant from the classical Embden-Meyerhof pathway. This pathway utilizes two novel proteins: an ADP-dependent Glucokinase and an ADP-dependent Phosphofructokinase. This conserved region is present at the C-terminal of both these proteins. Interestingly this family contains sequences from higher eukaryotes.. 427 matched cddid_all.tbl CDD pfam04588 pfam04588 461361 HIG_1_N Hypoxia induced protein conserved region. This family is found in proteins thought to be involved in the response to hypoxia. Family members mostly come from diverse eukaryotic organizms however eubacterial members have been identified. This region is found at the N-terminus of the member proteins which are predicted to be transmembrane. 52 matched cddid_all.tbl CDD pfam04589 pfam04589 461362 RFX1_trans_act RFX1 transcription activation region. The RFX family is a family of winged-helix DNA binding proteins. RFX1 is a regulatory factor essential for expression of MHC class II genes. This region is to found N terminal to the RFX DNA binding region (pfam02257) in some mammalian RFX proteins, and is thought to activate transcription when associated with DNA. Deletion analysis has identified the region 233-351 in human RFX1 as being required for maximal activation. 163 matched cddid_all.tbl CDD pfam04591 pfam04591 428026 DUF596 Protein of unknown function, DUF596. This family contains several uncharacterized proteins. 73 matched cddid_all.tbl CDD pfam04592 pfam04592 461363 SelP_N Selenoprotein P, N terminal region. SelP is the only known eukaryotic selenoprotein that contains multiple selenocysteine (Sec) residues, and accounts for more than 50% of the selenium content of rat and human plasma. It is thought to be glycosylated. SelP may have antioxidant properties. It can attach to epithelial cells, and may protect vascular endothelial cells against peroxynitrite toxicity. The high selenium content of SelP suggests that it may be involved in selenium intercellular transport or storage. The promoter structure of bovine SelP suggest that it may be involved in countering heavy metal intoxication, and may also have a developmental function. The N-terminal region of SelP can exist independently of the C terminal region. Zebrafish selenoprotein Pb lacks the C terminal Sec-rich region, and a protein encoded by the rat SelP gene and lacking this region has also been reported. N-terminal region contains a conserved SecxxCys motif, which is similar to the CysxxCys found in thioredoxins. It is speculated that the N terminal region may adopt a thioredoxin fold and catalyze redox reactions. The N-terminal region also contains a His-rich region, which is thought to mediate heparin binding. Binding to heparan proteoglycans could account for the membrane binding properties of SelP. The function of the bacterial members of this family is uncharacterized. 233 matched cddid_all.tbl CDD pfam04593 pfam04593 335847 SelP_C Selenoprotein P, C terminal region. SelP is the only known eukaryotic selenoprotein that contains multiple selenocysteine (Sec) residues, and accounts for more than 50% of the selenium content of rat and human plasma. It is thought to be glycosylated. SelP may have antioxidant properties. It can attach to epithelial cells, and may protect vascular endothelial cells against peroxynitrite toxicity. The high selenium content of SelP suggests that it may be involved in selenium intercellular transport or storage. The promoter structure of bovine SelP suggest that it may be involved in countering heavy metal intoxication, and may also have a developmental function. The N terminal region always contains one Sec residue, and this is separated from the C terminal region (9-16 sec residues) by a histidine-rich sequence. The large number of Sec residues in the C-terminal portion of SelP suggest CC that it may be involved in selenium transport or storage. However, it is also possible that this region has a redox function. 133 matched cddid_all.tbl CDD pfam04595 pfam04595 252691 Pox_I6 Poxvirus I6-like family. This family includes I6 proteins as well as the related F5L proteins. 320 matched cddid_all.tbl CDD pfam04596 pfam04596 282455 Pox_F15 Poxvirus protein F15. 136 matched cddid_all.tbl CDD pfam04597 pfam04597 428028 Ribophorin_I Ribophorin I. Ribophorin I is an essential subunit of oligosaccharyltransferase (OST), which is also known as Dolichyl-diphosphooligosaccharide--protein glycosyltransferase, (EC:2.4.1.119). OST catalyzes the transfer of an oligosaccharide from dolichol pyrophosphate to selected asparagine residues of nascent polypeptides as they are translocated into the lumen of the rough endoplasmic reticulum. Ribophorin I and OST48 are though to be responsible for OST catalytic activity. Both yeast and mammalian proteins are glycosylated but the sites are not conserved. Glycosylation may contribute towards general solubility but is unlikely to be involved in a specific biochemical function Most family members are predicted to have a transmembrane helix at the C terminus of this region. 438 matched cddid_all.tbl CDD pfam04598 pfam04598 398339 Gasdermin Gasdermin pore forming domain. The precise function of this protein is unknown. A deletion/insertion mutation is associated with an autosomal dominant non-syndromic hearing impairment form. In addition, this protein has also been found to contribute to acquired etoposide resistance in melanoma cells. This family also includes the gasdermin protein 240 matched cddid_all.tbl CDD pfam04599 pfam04599 282458 Pox_G5 Poxvirus G5 protein. This protein has been predicted to be related to the FEN-1 endonuclease. 425 matched cddid_all.tbl CDD pfam04601 pfam04601 282459 DUF569 Domain of unknown function (DUF569). Family of hypothetical proteins. Some family members contain a two copies of the domain. 142 matched cddid_all.tbl CDD pfam04602 pfam04602 377388 Arabinose_trans Mycobacterial cell wall arabinan synthesis protein. Arabinosyltransferase is involved in arabinogalactan (AG) biosynthesis pathway in mycobacteria. AG is a component of the macromolecular assembly of the mycolyl-AG-peptidoglycan complex of the cell wall. This enzyme has important clinical applications as it is believed to be the target of the antimycobacterial drug Ethambutol. 459 matched cddid_all.tbl CDD pfam04603 pfam04603 461364 Mog1 Ran-interacting Mog1 protein. Segregation of nuclear and cytoplasmic processes facilitates regulation of many eukaryotic cellular functions such as gene expression and cell cycle progression. Trafficking through the nuclear pore requires a number of highly conserved soluble factors that escort macromolecular substrates into and out of the nucleus. The Mog1 protein has been shown to interact with RanGTP which stimulates guanine nucleotide release, suggesting Mog1 regulates the nuclear transport functions of Ran. The human homolog of Mog1 is thought to be alternatively spliced. 137 matched cddid_all.tbl CDD pfam04604 pfam04604 368018 L_biotic_typeA Type-A lantibiotic. Lantibiotics are antibiotic peptides distinguished by the presence of the rare thioether amino acids lanthionine and/or methyl-lanthionine. They are produced by Gram-positive bacteria as gene-encoded precursor peptides and undergo post-translational modification to generate the mature peptide. Based on their structural and functional features lantibiotics are currently divided into two major groups: the flexible amphiphilic type-A and the rather rigid and globular type-B. Type-A lantibiotics act primarily by pore formation in the bacterial membrane by a mechanism involving the interaction with specific docking molecules such as the membrane precursor lipid II. 51 matched cddid_all.tbl CDD pfam04606 pfam04606 428030 Ogr_Delta Ogr/Delta-like zinc finger. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F. This family also includes zinc fingers in recombinase proteins. 47 matched cddid_all.tbl CDD pfam04607 pfam04607 428031 RelA_SpoT Region found in RelA / SpoT proteins. This region of unknown function is found in RelA and SpoT of Escherichia coli, and their homologs in plants and in other eubacteria. RelA is a guanosine 3',5'-bis-pyrophosphate (ppGpp) synthetase (EC:2.7.6.5) while SpoT is thought to be a bifunctional enzyme catalysing both ppGpp synthesis and degradation (ppGpp 3'-pyrophosphohydrolase, (EC:3.1.7.2)). This region is often found in association with HD (pfam01966), a metal-dependent phosphohydrolase, TGS (pfam02824) which is a possible nucleotide-binding region, and the ACT regulatory domain (pfam01842). 113 matched cddid_all.tbl CDD pfam04608 pfam04608 461365 PgpA Phosphatidylglycerophosphatase A. This family represents a family of bacterial phosphatidylglycerophosphatases (EC:3.1.3.27), known as PgpA. It appears that bacteria possess several phosphatidylglycerophosphatases, and thus, PgpA is not essential in Escherichia coli. 136 matched cddid_all.tbl CDD pfam04609 pfam04609 428033 MCR_C Methyl-coenzyme M reductase operon protein C. Methyl coenzyme M reductase (MCR) catalyzes the final step in methanogenesis. MCR is composed of three subunits, alpha (pfam02249), beta (pfam02241) and gamma (pfam02240). Genes encoding the beta (mcrB) and gamma (mcrG) subunits are separated by two open reading frames coding for two proteins C and D. The function of proteins C and D (this family) is unknown. This family nowalso includes family MtrC_related, 270 matched cddid_all.tbl CDD pfam04610 pfam04610 377390 TrbL TrbL/VirB6 plasmid conjugal transfer protein. 214 matched cddid_all.tbl CDD pfam04611 pfam04611 282467 AalphaY_MDB Mating type protein A alpha Y mating type dependent binding region. This region is important for the mating type dependent binding of Y protein to the A alpha Z protein of another mating type in Schizophyllum commune. 145 matched cddid_all.tbl CDD pfam04612 pfam04612 428034 T2SSM Type II secretion system (T2SS), protein M. This family of membrane proteins consists of Type II secretion system protein M sequences from several Gram-negative (diderm) bacteria. The precise function of these proteins is unknown, though in Vibrio cholerae, the T2SM (EpsM) protein interacts with the T2SL (EpsL) protein, and also forms homodimers. 160 matched cddid_all.tbl CDD pfam04613 pfam04613 461366 LpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD. UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase (EC 2.3.1.-) catalyzes an early step in lipid A biosynthesis: UDP-3-O-(3-hydroxytetradecanoyl)glucosamine + (R)-3-hydroxytetradecanoyl- [acyl carrier protein] -> UDP-2,3-bis(3-hydroxytetradecanoyl)glucosamine + [acyl carrier protein]. Members of this family also contain a hexapeptide repeat (pfam00132). This family constitutes the non-repeating region of LPXD proteins. 69 matched cddid_all.tbl CDD pfam04614 pfam04614 461367 Pex19 Pex19 protein family. 245 matched cddid_all.tbl CDD pfam04615 pfam04615 461368 Utp14 Utp14 protein. This protein is found to be part of a large ribonucleoprotein complex containing the U3 snoRNA. Depletion of the Utp proteins impedes production of the 18S rRNA, indicating that they are part of the active pre-rRNA processing complex. This large RNP complex has been termed the small subunit (SSU) processome. 704 matched cddid_all.tbl CDD pfam04616 pfam04616 398349 Glyco_hydro_43 Glycosyl hydrolases family 43. The glycosyl hydrolase family 43 contains members that are arabinanases. Arabinanases hydrolyse the alpha-1,5-linked L-arabinofuranoside backbone of plant cell wall arabinans. The structure of arabinanase Arb43A from Cellvibrio japonicus reveals a five-bladed beta-propeller fold. A long V-shaped groove, partially enclosed at one end, forms a single extended substrate-binding surface across the face of the propeller. 281 matched cddid_all.tbl CDD pfam04617 pfam04617 461369 Hox9_act Hox9 activation region. This family constitutes the N termini of the paralogous homeobox proteins HoxA9, HoxB9, HoxC9 and HoxD9. The N terminal region is found to act as a transcription activation region. Btg1 and Btg2 - the B-cell translocation gene products - may function as cofactors for Hoxb9-mediated transcription. The Btg proteins modulate Hoxb9 transcriptional activity by recruiting a multiprotein Ccr4-like complex. 182 matched cddid_all.tbl CDD pfam04618 pfam04618 461370 HD-ZIP_N HD-ZIP protein N terminus. This family consists of the N termini of plant homeobox-leucine zipper proteins. Its function is unknown. 99 matched cddid_all.tbl CDD pfam04619 pfam04619 309663 Adhesin_Dr Dr-family adhesin. This family of adhesins bind to the Dr blood group antigen component of decay-accelerating factor. This mediates adherence of uropathogenic Escherichia coli to the urinary tract. This family contains both fimbriated and afimbriated adherence structures. This protein also confers the phenotype of mannose-resistant hemagglutination, which can be inhibited by chloramphenicol. The N terminal portion of the protein is though to be responsible for chloramphenicol sensitivity. 139 matched cddid_all.tbl CDD pfam04620 pfam04620 309664 FlaA Flagellar filament outer layer protein Flaa. Periplasmic flagella are the organelles of spirochete mobility, and are structurally different from the flagella of other motile bacteria. They reside inside the cell within the periplasmic space, and confer mobility in viscous gel-like media such connective tissue. The flagella are composed of an outer sheath of FlaA proteins and a core filament of FlaB proteins. Each species usually has several FlaA protein species. 230 matched cddid_all.tbl CDD pfam04621 pfam04621 461371 ETS_PEA3_N PEA3 subfamily ETS-domain transcription factor N terminal domain. The N terminus of the PEA3 transcription factors is implicated in transactivation and in inhibition of DNA binding. Transactivation is potentiated by activation of the Ras/MAP kinase and protein kinase A signalling cascades. The N terminal region contains conserved MAP kinase phosphorylation sites. 344 matched cddid_all.tbl CDD pfam04622 pfam04622 461372 ERG2_Sigma1R ERG2 and Sigma1 receptor like protein. This family consists of the fungal C-8 sterol isomerase and mammalian sigma1 receptor. C-8 sterol isomerase (delta-8--delta-7 sterol isomerase), catalyzes a reaction in ergosterol biosynthesis, which results in unsaturation at C-7 in the B ring of sterols. Sigma 1 receptor is a low molecular mass mammalian protein located in the endoplasmic reticulum, which interacts with endogenous steroid hormones, such as progesterone and testosterone. It also binds the sigma ligands, which are are a set of chemically unrelated drugs including haloperidol, pentazocine, and ditolylguanidine. Sigma1 effectors are not well understood, but sigma1 agonists have been observed to affect NMDA receptor function, the alpha-adrenergic system and opioid analgesia. 192 matched cddid_all.tbl CDD pfam04623 pfam04623 113396 Adeno_E1B_55K_N Adenovirus E1B protein N-terminus. This family constitutes the amino termini of E1B 55 kDa (pfam01696). E1B 55K binds p53 the tumour suppressor protein converting it from a transcriptional activator which responds to damaged DNA in to an unregulated repressor of genes with a p53 binding site. This protects the virus against p53 induced host antiviral responses and prevents apoptosis as induced by the by the adenovirus E1A protein. The role of the N terminus in the function of E1B is not known. 71 matched cddid_all.tbl CDD pfam04624 pfam04624 309667 Dec-1 Dec-1 repeat. The defective chorion-1 gene (dec-1) in Drosophila encodes follicle cell proteins necessary for proper eggshell assembly. Multiple products of the dec-1 gene are formed by alternative RNA splicing and proteolytic processing. Cleavage products include S80 (80 kDa) which is incorporated into the eggshell, and further proteolysis of S80 gives S60 (60 kDa). This repeat is usually found in 12 copies in the central region of the protein. Its function is unknown. Length polymorphisms of Dec-1 have been observed in wild-type strains, and are caused by changes in the numbers of the first five repeats. 27 matched cddid_all.tbl CDD pfam04625 pfam04625 368028 DEC-1_N DEC-1 protein, N-terminal region. The defective chorion-1 gene (dec-1) in Drosophila encodes follicle cell proteins necessary for proper eggshell assembly. Multiple products of the dec-1 gene are formed by alternative RNA splicing and proteolytic processing. Cleavage products include S80 (80 kDa) which is incorporated into the eggshell, and further proteolysis of S80 gives S60 (60 kDa). 403 matched cddid_all.tbl CDD pfam04626 pfam04626 282480 DEC-1_C Dec-1 protein, C terminal region. The defective chorion-1 gene (dec-1) in Drosophila encodes follicle cell proteins necessary for proper eggshell assembly. Multiple products of the dec-1 gene are formed by alternative RNA splicing and proteolytic processing. Cleavage products include S80 (80 kDa) which is incorporated into the eggshell, and further proteolysis of S80 gives S60 (60 kDa). Alternative splicing generates different carboxyl terminal ends in different protein isoforms, so this is region is the most C terminal region that is present in the main isoforms. 131 matched cddid_all.tbl CDD pfam04627 pfam04627 461373 ATP-synt_Eps Mitochondrial ATP synthase epsilon chain. This family constitutes the mitochondrial ATP synthase epsilon subunit. This is not to be confused with the bacterial epsilon subunit, which is homologous to the mitochondrial delta subunit (pfam00401 and pfam02823) The epsilon subunit is located in the extrinsic membrane section F1, which is the catalytic site of ATP synthesis. The epsilon subunit was not well ordered in the crystal structure of bovine F1, but it is known to be located in the stalk region of F1. E subunit is thought to be involved in the regulation of ATP synthase, since a null mutation increased oligomycin sensitivity and decreased inhibition by inhibitor protein IF1. 49 matched cddid_all.tbl CDD pfam04628 pfam04628 335859 Sedlin_N Sedlin, N-terminal conserved region. Mutations in this protein are associated with the X-linked spondyloepiphyseal dysplasia tarda syndrome (OMIM:313400). This family represents an N-terminal conserved region. 129 matched cddid_all.tbl CDD pfam04629 pfam04629 461374 ICA69 Islet cell autoantigen ICA69, C-terminal domain. This family includes a 69 kD protein which has been identified as an islet cell autoantigen in type I diabetes mellitus. Its precise function is unknown. 241 matched cddid_all.tbl CDD pfam04630 pfam04630 309671 Phage_TTP_1 Phage tail tube protein. This is a family of phage tail tube proteins from Myoviridae. 199 matched cddid_all.tbl CDD pfam04631 pfam04631 282484 PIF2 Per os infectivity factor 2. This family includes several hypothetical baculoviral proteins, with predicted molecular weights of approximately 44 kD. Family members include per os infectivity factor 2 (PIF2). PIF2 forms a stable complex with PIF1, PIF3, PIF4 which is essential for oral infectivity of Autographa californica multinucleocapsid nucleopolyhedrovirus (AcMNPV) in insect larvae, and P74 is also associated with this complex. 372 matched cddid_all.tbl CDD pfam04632 pfam04632 428044 FUSC Fusaric acid resistance protein family. This family includes a conserved region found in two proteins associated with fusaric acid resistance, from Burkholderia cepacia and Klebsiella oxytoca. These proteins are likely to be membrane transporter proteins. 655 matched cddid_all.tbl CDD pfam04633 pfam04633 282486 Herpes_BMRF2 Herpesvirus BMRF2 protein. 349 matched cddid_all.tbl CDD pfam04634 pfam04634 398357 DUF600 Protein of unknown function, DUF600. This conserved region is found in several uncharacterized proteins from Gram positive bacteria. 144 matched cddid_all.tbl CDD pfam04636 pfam04636 461375 PA26 PA26 p53-induced protein (sestrin). PA26 is a p53-inducible protein. Its function is unknown. It has similarity to pfam04636 in its N-terminus. 442 matched cddid_all.tbl CDD pfam04637 pfam04637 282489 Herpes_pp85 Herpesvirus phosphoprotein 85 (HHV6-7 U14/HCMV UL25). This family includes UL25 proteins from HCMV, as well as U14 proteins from HHV 6 and HHV7. These 85 kD phosphoproteins appear to act as structural antigens, but their precise function is otherwise unknown. 542 matched cddid_all.tbl CDD pfam04639 pfam04639 282490 Baculo_E56 Baculoviral E56 protein, specific to ODV envelope. This family represents the E56 protein, which is localizes to the occlusion derived virus (ODV) envelope, but not to the budded virus (BV) envelope. 293 matched cddid_all.tbl CDD pfam04640 pfam04640 461376 PLATZ PLATZ transcription factor. Plant AT-rich sequence and zinc-binding proteins (PLATZ) are zinc dependant DNA binding proteins. They bind to AT rich sequences and functions in transcriptional repression. Included in this family is the protein RGF1 INDUCIBLE TRANSCRIPTION FACTOR 1 (RITF1), a transcription factor that plays a central role in mediating RGF1 hormone peptide signalling, leading to the production of reactive oxygen species (ROS) in roots to modulate meristem size and root growth, probably via oxidative post-translational modification of the transcription factor PLETHORA. 79 matched cddid_all.tbl CDD pfam04641 pfam04641 398360 Rtf2 Rtf2 RING-finger. It is vital for effective cell-replication that replication is not stalled at any point by, for instance, damaged bases. Replication termination factor 2 (Rtf2) stabilizes the replication fork stalled at the site-specific replication barrier RTS1 by preventing replication restart until completion of DNA synthesis by a converging replication fork initiated at a flanking origin. The RTS1 element terminates replication forks that are moving in the cen2-distal direction while allowing forks moving in the cen2-proximal direction to pass through the region. Rtf2 contains a C2HC2 motif related to the C3HC4 RING-finger motif, and would appear to fold up, creating a RING finger-like structure but forming only one functional Zn2+ ion-binding site. This domain is also found at the N-terminus of peptidyl-prolyl cis-trans isomerase 4, a divergent cyclophilin family. 258 matched cddid_all.tbl CDD pfam04642 pfam04642 282493 DUF601 Protein of unknown function, DUF601. This family represents a conserved region found in several uncharacterized plant proteins. 327 matched cddid_all.tbl CDD pfam04643 pfam04643 368034 Motilin_assoc Motilin/ghrelin-associated peptide. This family represents a peptide sequence that lies C-terminal to motilin/ghrelin on the respective precursor peptide. Its function is unknown. 59 matched cddid_all.tbl CDD pfam04644 pfam04644 461377 Motilin_ghrelin Motilin/ghrelin. Motilin is a gastrointestinal regulatory polypeptide produced by motilin cells in the duodenal epithelium. It is released into the general circulation at about 100-min intervals during the inter-digestive state and is the most important factor in controlling the inter-digestive migrating contractions. Motilin also stimulates endogenous release of the endocrine pancreas. This family also includes ghrelin, a growth hormone secretagogue synthesized by endocrine cells in the stomach. Ghrelin stimulates growth hormone secretagogue receptors in the pituitary. These receptors are distinct from the growth hormone-releasing hormone receptors, and thus provide a means of controlling pituitary growth hormone release by the gastrointestinal system. 28 matched cddid_all.tbl CDD pfam04645 pfam04645 282496 DUF603 Protein of unknown function, DUF603. This family includes several uncharacterized proteins from Borrelia species. 181 matched cddid_all.tbl CDD pfam04646 pfam04646 461378 DUF604 Protein of unknown function, DUF604. This family includes a conserved region found in several uncharacterized plant proteins. 256 matched cddid_all.tbl CDD pfam04647 pfam04647 461379 AgrB Accessory gene regulator B. The arg locus consists of two transcripts: RNAII and RNAIII. RNAII encodes four genes (agrA, B, C, and D) whose gene products assemble a quorum sensing system. AgrB and AgrD are essential for the production of the autoinducing peptide which functions as a signal for quorum sensing. AgrB is a transmembrane protein. 185 matched cddid_all.tbl CDD pfam04648 pfam04648 398364 MF_alpha Yeast mating factor alpha hormone. The hormone is excreted into the culture medium by haploid cells of the alpha mating type and acts on cells of the opposite mating type (type A). It inhibits DNA synthesis in type A cells synchronising them with type alpha, and so mediates the conjugation process. 13 matched cddid_all.tbl CDD pfam04649 pfam04649 68229 VlpA_repeat Mycoplasma hyorhinis VlpA repeat. This repeat is found in the extracellular (C-terminal) region of the variant surface antigen A (VlpA) of Mycoplasma hyorhinis. Mutations that change the number of repeats in the protein are involved in antigenic variation and immune evasion of this swine pathogen. 13 matched cddid_all.tbl CDD pfam04650 pfam04650 428049 YSIRK_signal YSIRK type signal peptide. Many surface proteins found in Streptococcus, Staphylococcus, and related lineages share apparently homologous signal sequences. A motif resembling [YF]SIRKxxxGxxS[VIA] appears at the start of the transmembrane domain. The GxxS motif appears perfectly conserved, suggesting a specific function and not just homology. There is a strong correlation between proteins carrying this region at the N-terminus and those carrying the Gram-positive anchor domain with the LPXTG sortase processing site at the C-terminus. 26 matched cddid_all.tbl CDD pfam04651 pfam04651 282501 Pox_A12 Poxvirus A12 protein. 183 matched cddid_all.tbl CDD pfam04652 pfam04652 461380 Vta1 Vta1 like. Vta1 (VPS20-associated protein 1) is a positive regulator of Vps4. Vps4 is an ATPase that is required in the multivesicular body (MVB) sorting pathway to dissociate the endosomal sorting complex required for transport (ESCRT). Vta1 promotes correct assembly of Vps4 and stimulates its ATPase activity through its conserved Vta1/SBP1/LIP5 region. 133 matched cddid_all.tbl CDD pfam04654 pfam04654 461381 DUF599 Protein of unknown function, DUF599. This family includes several uncharacterized proteins. 211 matched cddid_all.tbl CDD pfam04655 pfam04655 398368 APH_6_hur Aminoglycoside/hydroxyurea antibiotic resistance kinase. The aminoglycoside phosphotransferases achieve inactivation of their antibiotic substrates by phosphorylation utilizing ATP. Likewise hydroxyurea is inactivated by phosphorylation of the hydroxy group in the hydroxylamine moiety. 250 matched cddid_all.tbl CDD pfam04656 pfam04656 282505 Pox_E6 Pox virus E6 protein. Family of pox virus E6 proteins. 566 matched cddid_all.tbl CDD pfam04657 pfam04657 428052 DMT_YdcZ Putative inner membrane exporter, YdcZ. DMT_YdcZ is a family of putative inner membrane exporters from both Gram-positive and Gram-negative bacteria. 140 matched cddid_all.tbl CDD pfam04658 pfam04658 461382 TAFII55_N TAFII55 protein conserved region. The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. TAFII55 binds to TAFII250 and inhibits it acetyltransferase activity. The exact role of TAFII55 is currently unknown. The conserved region is situated towards the N-terminus of the protein. 160 matched cddid_all.tbl CDD pfam04659 pfam04659 398371 Arch_fla_DE Archaeal flagella protein. Family of archaeal flaD and flaE proteins. Conserved region found at N-terminus of flaE but towards the C-terminus of flaD. 96 matched cddid_all.tbl CDD pfam04660 pfam04660 282509 Nanovirus_coat Nanovirus coat protein. Family of conserved Nanoviral coat proteins. 177 matched cddid_all.tbl CDD pfam04661 pfam04661 282510 Pox_I3 Poxvirus I3 ssDNA-binding protein. 257 matched cddid_all.tbl CDD pfam04662 pfam04662 252728 Luteo_PO Luteovirus P0 protein. This family of proteins may be involved in suppression of PTGS a plant defence mechanism. 208 matched cddid_all.tbl CDD pfam04663 pfam04663 428054 Phenol_monoox Phenol hydroxylase conserved region. Under aerobic conditions, phenol is usually hydroxylated to catechol and degraded via the meta or ortho pathways. Two types of phenol hydroxylase are known: one is a multi-component enzyme the other is a single-component monooxygenase. This region is found in both types of enzymes. 66 matched cddid_all.tbl CDD pfam04664 pfam04664 461383 OGFr_N Opioid growth factor receptor (OGFr) conserved region. Opioid peptides act as growth factors in neural and non-neural cells and tissues, in addition to serving in neurotransmission/neuromodulation in the nervous system. The Opioid growth factor receptor is an integral membrane protein associated with the nucleus. The conserved region is situated at the N-terminus of the member proteins with a series of imperfect repeats lying immediately to its C-terminus. 208 matched cddid_all.tbl CDD pfam04665 pfam04665 282513 Pox_A32 Poxvirus A32 protein. The A32 protein is thought to be involved in viral DNA packaging. 241 matched cddid_all.tbl CDD pfam04666 pfam04666 461384 Glyco_transf_54 N-Acetylglucosaminyltransferase-IV (GnT-IV) conserved region. The complex-type of oligosaccharides are synthesized through elongation by glycosyltransferases after trimming of the precursor oligosaccharides transferred to proteins in the endoplasmic reticulum. N-Acetylglucosaminyltransferases (GnTs) take part in the formation of branches in the biosynthesis of complex-type sugar chains. In vertebrates, six GnTs, designated as GnT-I to -VI, which catalyze the transfer of GlcNAc to the core mannose residues of Asn-linked sugar chains, have been identified. GnT-IV (EC:2.4.1.145) catalyzes the transfer of GlcNAc from UDP-GlcNAc to the GlcNAc1-2Man1-3 arm of core oligosaccharide [Gn2(22)core oligosaccharide] and forms GlcNAc1-4(GlcNAc1-2)Man1-3 structure on the core oligosaccharide (Gn3(2,4,2)core oligosaccharide). In some members the conserved region occupies all but the very for N-terminal, where there is a signal sequence on all members. For other members the conserved region does not occupy the entire protein but is still to the N-terminus of the protein. 278 matched cddid_all.tbl CDD pfam04667 pfam04667 398375 Endosulfine cAMP-regulated phosphoprotein/endosulfine conserved region. Conserved region found in both cAMP-regulated phosphoprotein 19 (ARPP-19) and Alpha/Beta endosulfine. No function has yet been assigned to ARPP-19. Endosulfine is the endogenous ligand for the ATP-dependent potassium (K ATP) channels which occupy a key position in the control of insulin release from the pancreatic beta cell by coupling cell polarity to metabolism. In both cases the region occupies the majority of the protein. 80 matched cddid_all.tbl CDD pfam04668 pfam04668 461385 Tsg Twisted gastrulation (Tsg) protein conserved region. Tsg was identified in Drosophila as being required to specify the dorsal-most structures in the embryo, for example amnioserosa. Biochemical experiments have revealed three key properties of Tsg: it can synergistically inhibit Dpp/BMP action in both Drosophila and vertebrates by forming a tripartite complete between itself, SOG/chordin and a BMP ligand; Tsg seems to enhance the Tld/BMP-1-mediated cleavage rate of SOG/chordin and may change the preference of site utilization; Tsg can promote the dissociation of chordin cysteine-rich-containing fragments from the ligand to inhibit BMP signalling. 99 matched cddid_all.tbl CDD pfam04669 pfam04669 368048 Polysacc_synt_4 Polysaccharide biosynthesis. This family of proteins plays a role in xylan biosynthesis in plant cell walls. IRX15/IRX15-L precise role in xylan biosynthesis is unknown. Glucuronoxylan methyltransferase (GXMT) catalyzes 4-O-methylation of the glucuronic acid substituents of this polysaccharide. AtGXMT1 specifically transfers the methyl group from S-adenosyl-l-methionine to O-4 of alpha-d-glucopyranosyluronic acid residues that are linked to O-2 of the xylan backbone. The function of members of this family in animals and fungi is not known. 177 matched cddid_all.tbl CDD pfam04670 pfam04670 398377 Gtr1_RagA Gtr1/RagA G protein conserved region. GTR1 was first identified in S. cerevisiae as a suppressor of a mutation in RCC1. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologs of Gtr1. Included in this family is the human Rag C, a novel protein that has been shown to interact with RagA/B. 231 matched cddid_all.tbl CDD pfam04671 pfam04671 309696 Ag332 Erythrocyte membrane-associated giant protein antigen 332. To date many different Plasmodium antigens recognized by the hyperimmune system human sera have been cloned, sequenced and characterized. The majority contain tandemly repeated amino acid sequences which make up a considerable portion of the protein sequence. It has been suggested that these repeat-containing antigens may provide an immunological 'smokescreen' to the parasite in order to evade the human immune system. This repeat is found exclusively in the Plasmodium falciparum Ag332 protein and occupies most of its length. 21 matched cddid_all.tbl CDD pfam04672 pfam04672 252734 Methyltransf_19 S-adenosyl methyltransferase. This family contains a SAM (S-adenosyl methyltransferase) domain, with a central beta sheet with 3 alpha-helices on both sides. Crystal packing analysis of the structure PDB:3giw from Swiss:Q82L35 suggests that a monomer is the solution state oligomeric form. An unidentified ligand (UNL, cyan) was found at the putative active site surrounded by the residues His57, His170, Phe171, Tyr216 and Met22. The UNL is likely to be a phenylalanine or phenylalanine-like molecule. (details derived from TOPSAN). 268 matched cddid_all.tbl CDD pfam04673 pfam04673 428058 Cyclase_polyket Polyketide synthesis cyclase. This family represents a number of cyclases involved in polyketide synthesis in a number of actinobacterial species. 104 matched cddid_all.tbl CDD pfam04674 pfam04674 461386 Phi_1 Phosphate-induced protein 1 conserved region. Family of conserved plant proteins. Conserved region identified in a phosphate-induced protein of unknown function. 265 matched cddid_all.tbl CDD pfam04675 pfam04675 461387 DNA_ligase_A_N DNA ligase N terminus. This region is found in many but not all ATP-dependent DNA ligase enzymes (EC:6.5.1.1). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I, and in Saccharomyces cerevisiae, this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In vaccinia virus this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation. 174 matched cddid_all.tbl CDD pfam04676 pfam04676 461388 CwfJ_C_2 Protein similar to CwfJ C-terminus 2. This region is found in the N terminus of Schizosaccharomyces pombe protein CwfJ. CwfJ is part of the Cdc5p complex involved in mRNA splicing. 96 matched cddid_all.tbl CDD pfam04677 pfam04677 428062 CwfJ_C_1 Protein similar to CwfJ C-terminus 1. This region is found in the N terminus of Schizosaccharomyces pombe protein CwfJ. CwfJ is part of the Cdc5p complex involved in mRNA splicing. 122 matched cddid_all.tbl CDD pfam04678 pfam04678 461389 MCU Mitochondrial calcium uniporter. MCU functions with MICU1, an essential gatekeeper component of calcium-channel transport, to facilitate Ca2+ uptake into the mitochondrion. 181 matched cddid_all.tbl CDD pfam04679 pfam04679 398383 DNA_ligase_A_C ATP dependent DNA ligase C terminal region. This region is found in many but not all ATP-dependent DNA ligase enzymes (EC:6.5.1.1). It is thought to constitute part of the catalytic core of ATP dependent DNA ligase. 94 matched cddid_all.tbl CDD pfam04680 pfam04680 282527 OGFr_III Opioid growth factor receptor repeat. Proline-rich repeat found only in a human opioid growth factor receptor. 20 matched cddid_all.tbl CDD pfam04681 pfam04681 113449 Bys1 Blastomyces yeast-phase-specific protein. The molecular function of this protein is not known. Its expression is specific to the high temperature, unicellular yeast morphology (as opposed to the lower temperature, multicellular mycelium form). 155 matched cddid_all.tbl CDD pfam04682 pfam04682 282528 Herpes_BTRF1 Herpesvirus BTRF1 protein conserved region. Herpesvirus protein. 258 matched cddid_all.tbl CDD pfam04683 pfam04683 461390 Proteasom_Rpn13 Proteasome complex subunit Rpn13 ubiquitin receptor. This family was thought originally to be involved in cell-adhesion, but the members are now known to be proteasome subunit Rpn13, a novel ubiquitin receptor. The 26S proteasome is a huge macromolecular protein-degradation machine consisting of a proteolytically active 20S core, in the form of four disc-like proteins, and one or two 19S regulatory particles. The regulatory particle(s) sit on the top and or bottom of the core, de-ubiquitinate the substrate peptides, unfold them and guide them into the narrow channel through the centre of the core. Rpn13 and its homologs dock onto the regulatory particle through the N-terminal region which binds Rpn2. The C-terminal part of the domain binds de-ubiquitinating enzyme Uch37/UCHL5 and enhances its isopeptidase activity. Rpn13 binds ubiquitin via a conserved amino-terminal region called the pleckstrin-like receptor for ubiquitin, termed Pru, domain. The domain forms two contiguous anti-parallel beta-sheets with a configuration similar to the pleckstrin-homology domain (PHD) fold. Rpn13's ability to bind ubiquitin and the proteasome subunit Rpn2/S1 simultaneously supports evidence of its role as a ubiquitin receptor. Finally, when complexed to di-ubiquitin, via the Pru, and Uch37 via the C-terminal part, it frees up the distal ubiquitin for de-ubiquitination by the Uch37. 87 matched cddid_all.tbl CDD pfam04684 pfam04684 398385 BAF1_ABF1 BAF1 / ABF1 chromatin reorganizing factor. ABF1 is a sequence-specific DNA binding protein involved in transcription activation, gene silencing and initiation of DNA replication. ABF1 is known to remodel chromatin, and it is proposed that it mediates its effects on transcription and gene expression by modifying local chromatin architecture. These functions require a conserved stretch of 20 amino acids in the C-terminal region of ABF1 (amino acids 639 to 662 S. cerevisiae ). The N-terminal two thirds of the protein are necessary for DNA binding, and the N-terminus (amino acids 9 to 91 in S. cerevisiae) is thought to contain a novel zinc-finger motif which may stabilize the protein structure. 501 matched cddid_all.tbl CDD pfam04685 pfam04685 461391 DUF608 Glycosyl-hydrolase family 116, catalytic region. This represents a family of archaeal, bacterial and eukaryotic glycosyl hydrolases, that belong to superfamily GH116. The primary catabolic pathway for glucosylceramide is catalysis by the lysosomal enzyme glucocerebrosidase. In higher eukaryotes, glucosylceramide is the precursor of glycosphingolipids, a complex group of ubiquitous membrane lipids. Mutations in the human protein cause motor-neurone defects in hereditary spastic paraplegia. The catalytic nucleophile, identified in UniProtKB:Q97YG8_SULSO, is a glutamine-335, with the likely acid/base at Asp-442 and the aspartates at Asp-406 and Asp-458 residues also playing a role in the catalysis of glucosides and xylosides that are beta-bound to hydrophobic groups. The family is defined as GH116, which presently includes enzymes with beta-glucosidase, EC:3.2.1.21, beta-xylosidase, EC:3.2.1.37, and glucocerebrosidase EC:3.2.1.45 activity. 362 matched cddid_all.tbl CDD pfam04686 pfam04686 461392 SsgA Streptomyces sporulation and cell division protein, SsgA. The precise function of SsgA is unknown. It has been found to be essential for spore formation, and to stimulate cell division. 98 matched cddid_all.tbl CDD pfam04687 pfam04687 282533 Microvir_H Microvirus H protein (pilot protein). A single molecule of H protein is found on each of the 12 spikes on the microvirus shell. H is involved in the ejection of the phage DNA, and at least one copy is injected into the host's periplasmic space along with the ssDNA viral genome. Part of H is thought to lie outside the shell, where it recognizes lipopolysaccharide from virus-sensitive strains. Part of H may lie within the capsid, since mutations in H can influence the DNA ejection mechanism by affecting the DNA-protein interactions. H may span the capsid through the hydrophilic channels formed by G proteins. Elucidation of the DNA-ejection mechanism from the crystal structure of part of the H protein shows that this tail-less icosahedral, single-stranded DNA phiX174-like coliphage bacteriophage requires H as a pilot protein for its DNA-delivery. H oligomerises to form a tube the function of which seems to be the delivery of the DNA genome across the host's periplasmic space into the host cytoplasm. The tube is constructed of ten alpha-helices with their amino termini arrayed in a right-handed super-helical coiled-coil and their carboxy termini arrayed in a left-handed super-helical coiled-coil. The tube spans the periplasmic space and is present while the genome is being delivered into the host cell's cytoplasm. 310 matched cddid_all.tbl CDD pfam04688 pfam04688 398388 Holin_SPP1 SPP1 phage holin. This family constitutes holin proteins from the dsDNA Siphidoviridae group bacteriophages with two transmembrane segments. Most bacteriophages require an endolysin and a holin for host lysis. During late gene expression, holins accumulate and oligomerise in the host cell membrane. They then suddenly trigger to permeablise the membrane, which causes lysis by allowing endolysin to attach the peptidoglycan. There are thought to be at least 35 different families of holin genes. 74 matched cddid_all.tbl CDD pfam04689 pfam04689 282535 S1FA DNA binding protein S1FA. S1FA is a DNA-binding protein found in plants that specifically recognizes the negative promoter element S1F. 66 matched cddid_all.tbl CDD pfam04690 pfam04690 461393 YABBY YABBY protein. YABBY proteins are a group of plant-specific transcription involved in the specification of abaxial polarity in lateral organs. 163 matched cddid_all.tbl CDD pfam04691 pfam04691 428068 ApoC-I Apolipoprotein C-I (ApoC-1). Apolipoprotein C-I (ApoC-1) is a water-soluble protein component of plasma lipoprotein. It solubalises lipids and regulates lipid metabolism. ApoC-1 transfers among HDL (high density lipoprotein), VLDL (very low-density lipoprotein) and chylomicrons. ApoC-1 activates lecithin:choline acetyltransferase (LCAT), inhibits cholesteryl ester transfer protein, can inhibit hepatic lipase and phospholipase 2 and can stimulate cell growth. ApoC-1 delays the clearance of beta-VLDL by inhibiting its uptake via the LDL receptor-related pathway. ApoC-1 has been implicated in hypertriglyceridemia, and Alzheimer's disease. 61 matched cddid_all.tbl CDD pfam04692 pfam04692 461394 PDGF_N Platelet-derived growth factor, N terminal region. This family consists of the amino terminal regions of platelet-derived growth factor (PDGF, pfam00341) A and B chains. 78 matched cddid_all.tbl CDD pfam04693 pfam04693 147046 DDE_Tnp_2 Archaeal putative transposase ISC1217. 327 matched cddid_all.tbl CDD pfam04694 pfam04694 282539 Corona_3 Coronavirus ORF3 protein. 59 matched cddid_all.tbl CDD pfam04695 pfam04695 461395 Pex14_N Pex14 N-terminal domain. Family of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N-terminus of the protein. 46 matched cddid_all.tbl CDD pfam04696 pfam04696 461396 Pinin_SDK_memA pinin/SDK/memA/ protein conserved region. Members of this family have very varied localizations within the eukaryotic cell. pinin is known to localize at the desmosomes and is implicated in anchoring intermediate filaments to the desmosomal plaque. SDK2/3 is a dynamically localized nuclear protein thought to be involved in modulation of alternative pre-mRNA splicing. memA is a tumour marker preferentially expressed in human melanoma cell lines. A common feature of the members of this family is that they may all participate in regulating protein-protein interactions. 130 matched cddid_all.tbl CDD pfam04697 pfam04697 461397 Pinin_SDK_N pinin/SDK conserved region. SDK2/3 is localized in nuclear speckles where as pinin is known to localize at the desmosomes where it is thought to be involved in anchoring intermediate filaments to the desmosomal plaque. The role of SDK2/3 in the nucleus is thought to be concerned with modulation of alternative pre-mRNA splicing. pinin has also been implicated as a tumour suppressor. The conserved region is found at the N-terminus of the member proteins. 132 matched cddid_all.tbl CDD pfam04698 pfam04698 461398 Rab_eff_C Rab effector MyRIP/melanophilin C-terminus. This domain is found at the C-terminus of the Rab effector proteins MyRIP and melanophilin. 717 matched cddid_all.tbl CDD pfam04699 pfam04699 461399 P16-Arc ARP2/3 complex 16 kDa subunit (p16-Arc). The Arp2/3 protein complex has been implicated in the control of actin polymerization. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. The precise function of p16-Arc is currently unknown. Its structure consists of a single domain containing a bundle of seven alpha helices. 146 matched cddid_all.tbl CDD pfam04700 pfam04700 282545 Baculo_gp41 Structural glycoprotein p40/gp41 conserved region. Family of viral structural glycoproteins. 185 matched cddid_all.tbl CDD pfam04701 pfam04701 282546 Pox_D2 Pox virus D2 protein. 139 matched cddid_all.tbl CDD pfam04702 pfam04702 252749 Vicilin_N Vicilin N terminal region. This region is found in plant seed storage proteins, N-terminal to the Cupin domain (pfam00190). In Macadamia integrifolia, this region is processed into peptides of approximately 50 amino acids containing a C-X-X-X-C-(10-12)X-C-X-X-X-C motif. These peptides exhibit antimicrobial activity in vitro. 147 matched cddid_all.tbl CDD pfam04703 pfam04703 398397 FaeA FaeA-like protein. This family represents a number of fimbrial protein transcription regulators found in Gram-negative bacteria. These proteins are thought to facilitate binding of the leucine-rich regulatory protein to regulatory elements, possibly by inhibiting deoxyadenosine methylation of these elements by deoxyadenosine methylase. 61 matched cddid_all.tbl CDD pfam04704 pfam04704 461400 Zfx_Zfy_act Zfx / Zfy transcription activation region. Zfx and Zfy are transcription factors implicated in mammalian sex determination. This region is found N terminal to multiple copies of a C2H2 Zinc finger (pfam00096). This region has been shown to activate transcription when fused to a GAL4 DNA binding domain. 328 matched cddid_all.tbl CDD pfam04705 pfam04705 368067 TSNR_N Thiostrepton-resistance methylase, N terminus. This region is found in some members of the SpoU-type rRNA methylase family (pfam00588). 111 matched cddid_all.tbl CDD pfam04706 pfam04706 461401 Dickkopf_N Dickkopf N-terminal cysteine-rich region. Dickkopf proteins are a class of Wnt antagonists. They possess two conserved cysteine-rich regions. This family represents the N-terminal one. The C-terminal region has been found to share significant sequence similarity to the colipase fold, pfam01114, pfam02740. 51 matched cddid_all.tbl CDD pfam04707 pfam04707 398400 PRELI PRELI-like family. This family includes a conserved region found in the PRELI protein and yeast YLR168C gene MSF1 product. The function of this protein is unknown, though it is thought to be involved in intra-mitochondrial protein sorting. This region is also found in a number of other eukaryotic proteins. 156 matched cddid_all.tbl CDD pfam04708 pfam04708 282551 Pox_F16 Poxvirus F16 protein. 215 matched cddid_all.tbl CDD pfam04709 pfam04709 461402 AMH_N Anti-Mullerian hormone, N terminal region. Anti-Mullerian hormone, AMH is a signalling molecule involved in male and female sexual differentiation. Defects in synthesis or action of AMH cause persistent Mullerian duct syndrome (PMDS), a rare form of male pseudohermaphroditism. This family represents the N terminal part of the protein, which is not thought to be essential for activity. AMH contains a TGF-beta domain (pfam00019), at the C terminus. 389 matched cddid_all.tbl CDD pfam04710 pfam04710 461403 Pellino Pellino. Pellino is involved in Toll-like signalling pathways, and associates with the kinase domain of the Pelle Ser/Thr kinase. 409 matched cddid_all.tbl CDD pfam04711 pfam04711 461404 ApoA-II Apolipoprotein A-II (ApoA-II). Apolipoprotein A-II (ApoA-II) is the second major apolipoprotein of high density lipoprotein in human plasma. Mature ApoA-II is present as a dimer of two 77-amino acid chains joined by a disulphide bridge. ApoA-II regulates many steps in HDL metabolism, and its role in coronary heart disease is unclear. In bovine serum, the ApoA-II homolog is present in almost free form. Bovine ApoA-II shows antimicrobial activity against Escherichia coli and yeasts in phosphate buffered saline (PBS). 99 matched cddid_all.tbl CDD pfam04712 pfam04712 461405 Radial_spoke Radial spokehead-like protein. This family includes the radial spoke head proteins RSP4 and RSP6 from Chlamydomonas reinhardtii, and several eukaryotic homologs, including mammalian RSHL1, the protein product of a familial ciliary dyskinesia candidate gene. 406 matched cddid_all.tbl CDD pfam04713 pfam04713 282556 Pox_I5 Poxvirus protein I5. 75 matched cddid_all.tbl CDD pfam04714 pfam04714 461406 BCL_N BCL7, N-terminal conserver region. Members of the BCL family have significant sequence similarity at their N-terminus, represented in this family. The function of BCL7 proteins is unknown. They may be involved in early development. In addition, BCL7B is commonly hemizygously deleted in patients with Williams syndrome. 48 matched cddid_all.tbl CDD pfam04715 pfam04715 428082 Anth_synt_I_N Anthranilate synthase component I, N terminal region. Anthranilate synthase (EC:4.1.3.27) catalyzes the first step in the biosynthesis of tryptophan. Component I catalyzes the formation of anthranilate using ammonia and chorismate. The catalytic site lies in the adjacent region, described in the chorismate binding enzyme family (pfam00425). This region is involved in feedback inhibition by tryptophan. This family also contains a region of Para-aminobenzoate synthase component I (EC 4.1.3.-). 140 matched cddid_all.tbl CDD pfam04716 pfam04716 461407 ETC_C1_NDUFA5 ETC complex I subunit conserved region. Family of eukaryotic NADH-ubiquinone oxidoreductase subunits (EC:1.6.5.3) (EC:1.6.99.3) from complex I of the electron transport chain initially identified in Neurospora crassa as a 29.9 kDa protein. The conserved region is found at the N-terminus of the member proteins. 67 matched cddid_all.tbl CDD pfam04717 pfam04717 428084 Phage_base_V Type VI secretion system/phage-baseplate injector OB domain. Family of bacterial and phage baseplate assembly proteins responsible for forming the small spike at the end of the tail or bacterial pathogenic needle-shaft. This entry represents the OB fold part of the structure. This structure contains an unusual extra beta hairpin that forms the foundation of the spike protein's beta helix. 75 matched cddid_all.tbl CDD pfam04718 pfam04718 461408 ATP-synt_G Mitochondrial ATP synthase g subunit. The Fo sector of the ATP synthase is a membrane bound complex which mediates proton transport. It is composed of nine different polypeptide subunits (a, b, c, d, e, f, g F6, A6L). The function of subunit g is currently unknown. The conserved region covers all but the very N-terminus of the member sequences. No prokaryotic members have been identified thus far. 92 matched cddid_all.tbl CDD pfam04719 pfam04719 428086 TAFII28 hTAFII28-like protein conserved region. The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C-terminal of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3. 86 matched cddid_all.tbl CDD pfam04720 pfam04720 428087 PDDEXK_6 PDDEXK-like family of unknown function. PDDEXK_6 is a family of plant proteins that are distant homologs of the PD-(D/E)XK nuclease superfamily. The core structure is retained, as alpha-beta-beta-beta-alpha-beta. It retains the characteriztic PDDEXK motifs II and III in modified forms - xDxxx motif located in the second core beta-strand, where x is any hydrophobic residue, and a D/E)X(D/N/S/C/G) pattern. The missing positively charged residue in motif III is possibly replaced by a conserved arginine in motif IV located in the proceeding alpha-helix. The family is not in general fused with any other domains, so its function cannot be predicted. 215 matched cddid_all.tbl CDD pfam04721 pfam04721 461409 PAW PNGase C-terminal domain, mannose-binding module PAW. The PAW domain is found at the C-terminus of PGNase, or peptide-N-glycanase, enzymes. It was named for 'domain present in PNGases and other worm proteins'. PNGase catalyzes the deglycosylation of several misfolded N-linked glycoproteins by cleaving off the bulky glycan chain before these proteins are degraded by the proteasome. PNGase specifically acts on the unfolded form of high-mannose type N-glycosylated proteins, and this domain appears to be the mannose-binding domain, which contributes to the oligosaccharide-binding specificity of PNGase. 197 matched cddid_all.tbl CDD pfam04722 pfam04722 461410 Ssu72 Ssu72-like protein. The highly conserved and essential protein Ssu72 has intrinsic phosphatase activity and plays an essential role in the transcription cycle. Ssu72 was originally identified in a yeast genetic screen as enhancer of a defect caused by a mutation in the transcription initiation factor TFIIB. It binds to TFIIB and is also involved in mRNA elongation. Ssu72 is further involved in both poly(A) dependent and independent termination. It is a subunit of the yeast cleavage and polyadenylation factor (CPF), which is part of the machinery for mRNA 3'-end formation. Ssu72 is also essential for transcription termination of snRNAs. 189 matched cddid_all.tbl CDD pfam04723 pfam04723 377402 GRDA Glycine reductase complex selenoprotein A. Found in clostridia, this protein contains one active site selenocysteine and catalyzes the reductive deamination of glycine, which is coupled to the esterification of orthophosphate resulting in the formation of ATP. A member of this family may also exist in Treponema denticola. 147 matched cddid_all.tbl CDD pfam04724 pfam04724 428090 Glyco_transf_17 Glycosyltransferase family 17. This family represents beta-1,4-mannosyl-glycoprotein beta-1,4-N-acetylglucosaminyltransferase (EC:2.4.1.144). This enzyme transfers the bisecting GlcNAc to the core mannose of complex N-glycans. The addition of this residue is regulated during development and has functional consequences for receptor signalling, cell adhesion, and tumour progression. 349 matched cddid_all.tbl CDD pfam04725 pfam04725 309736 PsbR Photosystem II 10 kDa polypeptide PsbR. This protein is associated with the oxygen-evolving complex of photosystem II. Its function in photosynthesis is not known. The C-terminal hydrophobic region functions as a thylakoid transfer signal but is not removed. 98 matched cddid_all.tbl CDD pfam04726 pfam04726 282569 Microvir_J Microvirus J protein. This small protein is involved in DNA packaging, interacting with DNA via its hydrophobic carboxyl terminus. In bacteriophage phi-X174, J is present in 60 copies, and forms an S-shaped polypeptide chain without any secondary structure. It is thought to interact with DNA through simple charge interactions. 37 matched cddid_all.tbl CDD pfam04727 pfam04727 461411 ELMO_CED12 ELMO/CED-12 family. This family represents a conserved domain which is found in a number of eukaryotic proteins including CED-12, ELMO I and ELMO II. ELMO1 is a component of signalling pathways that regulate phagocytosis and cell migration and is the mammalian orthologue of the C. elegans gene, ced-12. CED-12 is required for the engulfment of dying cells and cell migration. In mammalian cells, ELMO1 interacts with Dock180 as part of the CrkII/Dock180/Rac pathway responsible for phagocytosis and cell migration. ELMO1 is ubiquitously expressed, although its expression is highest in the spleen, an organ rich in immune cells. ELMO1 has a PH domain and a polyproline sequence motif at its C terminus which are not present in this alignment. 161 matched cddid_all.tbl CDD pfam04728 pfam04728 428092 LPP Lipoprotein leucine-zipper. This is leucine-zipper is found in the enterobacterial outer membrane lipoprotein LPP. It is likely that this domain oligomerises and is involved in protein-protein interactions. As such it is a bundle of alpha-helical coiled-coils, which are known to play key roles in mediating specific protein-protein interactions for in molecular recognition and the assembly of multi-protein complexes. 53 matched cddid_all.tbl CDD pfam04729 pfam04729 461412 ASF1_hist_chap ASF1 like histone chaperone. This family includes the yeast and human ASF1 protein. These proteins have histone chaperone activity. ASF1 participates in both the replication-dependent and replication-independent pathways. The structure three-dimensional has been determined as a a compact immunoglobulin-like beta sandwich fold topped by three helical linkers. 154 matched cddid_all.tbl CDD pfam04730 pfam04730 368086 Agro_virD5 Agrobacterium VirD5 protein. The virD operon in Agrobacterium encodes a site-specific endonuclease, and a number of other poorly characterized products. This family represents the VirD5 protein. 672 matched cddid_all.tbl CDD pfam04731 pfam04731 461413 Caudal_act Caudal like protein activation region. This family consists of the amino termini of proteins belonging to the caudal-related homeobox protein family. This region is thought to mediate transcription activation. The level of activation caused by mouse Cdx2 is affected by phosphorylation at serine 60 via the mitogen-activated protein kinase pathway. Caudal family proteins are involved in the transcriptional regulation of multiple genes expressed in the intestinal epithelium, and are important in differentiation and maintenance of the intestinal epithelial lining. Caudal proteins always have a homeobox DNA binding domain (pfam00046). 136 matched cddid_all.tbl CDD pfam04732 pfam04732 461414 Filament_head Intermediate filament head (DNA binding) region. This family represents the N-terminal head region of intermediate filaments. Intermediate filament heads bind DNA. Vimentin heads are able to alter nuclear architecture and chromatin distribution, and the liberation of heads by HIV-1 protease liberates may play an important role in HIV-1 associated cytopathogenesis and carcinogenesis. Phosphorylation of the head region can affect filament stability. The head has been shown to interaction with the rod domain of the same protein. 83 matched cddid_all.tbl CDD pfam04733 pfam04733 398419 Coatomer_E Coatomer epsilon subunit. This family represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex. 288 matched cddid_all.tbl CDD pfam04734 pfam04734 461415 Ceramidase_alk Neutral/alkaline non-lysosomal ceramidase, N-terminal. This family represents N-terminal domain of a group of neutral/alkaline ceramidases found in both bacteria and eukaryotes. The EC classification is EC:3.5.1.23. The enzyme hydrolyses ceramide to generate sphingosine and fatty acid. The enzyme plays a regulatory role in a variety of physiological events in eukaryotes and also functions as an exotoxin in particular bacteria. This N-terminal domain carries two metal-binding sites, the first for Zn2+ residing within the domain, and the second, for Mg2+/Ca2+ lying at the interface between the two domains. 473 matched cddid_all.tbl CDD pfam04735 pfam04735 282577 Baculo_helicase Baculovirus DNA helicase. 1307 matched cddid_all.tbl CDD pfam04736 pfam04736 428097 Eclosion Eclosion hormone. Eclosion hormone is an insect neuropeptide that triggers the performance of ecdysis behaviour, which causes shedding of the old cuticle at the end of a molt,. 60 matched cddid_all.tbl CDD pfam04738 pfam04738 428098 Lant_dehydr_N Lantibiotic dehydratase, N terminus. Lantibiotics are ribosomally synthesized antimicrobial agents derived from ribosomally synthesized peptides. They are produced by bacteria of the Firmicutes phylum, and include mutacin, subtilin, and nisin. Lantibiotic peptides contain thioether bridges termed lanthionines that are thought to be generated by dehydration of serine and threonine residues followed by addition of cysteine residues. This family constitutes the N-terminus of the enzyme proposed to catalyze the dehydration step via glutamylation of the substrate during lantibiotic biosynthesis. The enzyme dehydrates Ser/Thr residues in the precursor by glutamylation. 648 matched cddid_all.tbl CDD pfam04739 pfam04739 461416 AMPKBI 5'-AMP-activated protein kinase beta subunit, interaction domain. This region is found in the beta subunit of the 5'-AMP-activated protein kinase complex, and its yeast homologs Sip1, Sip2 and Gal83, which are found in the SNF1 kinase complex. This region is sufficient for interaction of this subunit with the kinase complex, but is not solely responsible for the interaction, and the interaction partner is not known. The isoamylase N-terminal domain (pfam02922) is sometimes found in proteins belonging to this family. 70 matched cddid_all.tbl CDD pfam04740 pfam04740 428100 LXG LXG domain of WXG superfamily. This domain is present is the N-terminal region of a group of polymorphic toxin proteins in bacteria. It is predicted to use Type VII secretion pathway to mediate export of bacterial toxins. 202 matched cddid_all.tbl CDD pfam04741 pfam04741 282582 InvH InvH outer membrane lipoprotein. This family represents the Salmonella outer membrane lipoprotein InvH. The molecular function of this protein is unknown, but it is required for the localization to outer membrane of InvG, which is involved in a type III secretion apparatus mediating host cell invasion. 147 matched cddid_all.tbl CDD pfam04744 pfam04744 428101 Monooxygenase_B Monooxygenase subunit B protein. Family of membrane associated monooxygenases (EC 1.13.12.-) which utilize O(2) to oxidize their substrate. Family members include both ammonia and methane monooxygenases involved in the oxidation of their respective substrates. These enzymes are multi-subunit complexes. This family represents the B subunit of the enzyme; the A subunit is thought to contain the active site.. 381 matched cddid_all.tbl CDD pfam04745 pfam04745 282584 Pox_A8 VITF-3 subunit protein. Family of Chordopoxvirus proteins composing one of the two subunits that make up VITF-3, a virally encoded complex necessary for intermediate stage transcription. 289 matched cddid_all.tbl CDD pfam04746 pfam04746 113513 DUF575 Protein of unknown function (DUF575). Family of uncharacterized proteins. Contains several chlamydial members. 101 matched cddid_all.tbl CDD pfam04747 pfam04747 282585 DUF612 Protein of unknown function, DUF612. This family includes several uncharacterized proteins from Caenorhabditis elegans. 511 matched cddid_all.tbl CDD pfam04748 pfam04748 428102 Polysacc_deac_2 Divergent polysaccharide deacetylase. This family is divergently related to pfam01522 (personal obs:Yeats C). 214 matched cddid_all.tbl CDD pfam04749 pfam04749 461417 PLAC8 PLAC8 family. This family includes the Placenta-specific gene 8 protein. 99 matched cddid_all.tbl CDD pfam04750 pfam04750 428104 Far-17a_AIG1 FAR-17a/AIG1-like protein. This family includes the hamster androgen-induced FAR-17a protein, and its human homolog, the AIG1 protein. The function of these proteins is unknown. This family also includes homologous regions from a number of other metazoan proteins. 206 matched cddid_all.tbl CDD pfam04751 pfam04751 461418 DUF615 Protein of unknown function (DUF615). This family of bacterial proteins has no known function. 139 matched cddid_all.tbl CDD pfam04752 pfam04752 398428 ChaC ChaC-like protein. The ChaC family of proteins function as gamma-glutamyl cyclotransferases acting specifically to degrade glutathione but not other gamma-glutamyl peptides. It is is conversed across all phyla and represents a new pathway for glutathione degradation in living cells. 176 matched cddid_all.tbl CDD pfam04753 pfam04753 461419 Corona_NS12-7 Coronavirus non-structural protein NS12.7 family. This entry corresponds to a non-structural protein found in some beta coronaviruses. It is known as the NS12.7 family after its predicted molecular weight. The function of this protein is unknown. 109 matched cddid_all.tbl CDD pfam04754 pfam04754 428107 Transposase_31 Putative transposase, YhgA-like. This family of putative transposases includes the YhgA sequence from Escherichia coli and several prokaryotic homologs. 202 matched cddid_all.tbl CDD pfam04755 pfam04755 309752 PAP_fibrillin PAP_fibrillin. This family identifies a conserved region found in a number of plastid lipid-associated proteins (PAPs), and in a number of putative fibrillin proteins. 196 matched cddid_all.tbl CDD pfam04756 pfam04756 461420 OST3_OST6 OST3 / OST6 family, transporter family. The proteins in this family are part of a complex of eight ER proteins that transfers core oligosaccharide from dolichol carrier to Asn-X-Ser/Thr motifs. This family includes both OST3 and OST6, each of which contains four predicted transmembrane helices. Disruption of OST3 and OST6 leads to a defect in the assembly of the complex. Hence, the function of these genes seems to be essential for recruiting a fully active complex necessary for efficient N-glycosylation. These proteins are also thought to be novel Mg2+ transporters. 294 matched cddid_all.tbl CDD pfam04757 pfam04757 398431 Pex2_Pex12 Pex2 / Pex12 amino terminal region. This region is found at the N terminal of a number of known and predicted peroxins including Pex2, Pex10 and Pex12. This conserved region is usually associated with a C terminal ring finger (pfam00097) domain. 213 matched cddid_all.tbl CDD pfam04758 pfam04758 398432 Ribosomal_S30 Ribosomal protein S30. 58 matched cddid_all.tbl CDD pfam04759 pfam04759 428109 DUF617 Protein of unknown function, DUF617. This family represents a conserved region in a number of uncharacterized plant proteins. 162 matched cddid_all.tbl CDD pfam04760 pfam04760 428110 IF2_N Translation initiation factor IF-2, N-terminal region. This conserved feature at the N-terminus of bacterial translation initiation factor IF2 has recently had its structure solved. It shows structural similarity to the tRNA anticodon Stem Contact Fold domains of the methionyl-tRNA and glutaminyl-tRNA synthetases, and a similar fold is also found in the B5 domain of the phenylalanine-tRNA synthetase. 52 matched cddid_all.tbl CDD pfam04761 pfam04761 282599 Phage_Treg Lactococcus bacteriophage putative transcription regulator. This family represents a number of putative transcription repressor proteins found in several Lactococcus bacteriophages. Horizontal transfer may account for the presence of similar proteins in Lactococcus. 61 matched cddid_all.tbl CDD pfam04762 pfam04762 428111 IKI3 IKI3 family. Members of this family are components of the elongator multi-subunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation. This region contains WD40 like repeats. 933 matched cddid_all.tbl CDD pfam04763 pfam04763 368104 DUF562 Protein of unknown function (DUF562). Family of uncharacterized proteins. 146 matched cddid_all.tbl CDD pfam04764 pfam04764 252787 DUF613 Protein of unknown function (DUF613). Family of chloroplast proteins of unknown function. Some members have two copies of the conserved region. 120 matched cddid_all.tbl CDD pfam04765 pfam04765 428112 DUF616 Protein of unknown function (DUF616). Family of uncharacterized proteins. 303 matched cddid_all.tbl CDD pfam04766 pfam04766 309761 Baculo_p26 Nucleopolyhedrovirus p26 protein. Family of Baculovirus p26 proteins. 234 matched cddid_all.tbl CDD pfam04767 pfam04767 282602 Pox_F17 DNA-binding 11 kDa phosphoprotein. Family of poxvirus proteins required for virus morphogenesis. Protein function necessary for proteolytic processing of the major viral structural proteins, P4a and P4b. 93 matched cddid_all.tbl CDD pfam04768 pfam04768 398437 NAT NAT, N-acetyltransferase, of N-acetylglutamate synthase. This is the C-terminal NAT or N-acetyltransferase domain of bifunctional N-acetylglutamate synthase/kinases. It catalyzes the first two steps in arginine biosynthesis. This domain contains the putative NAGS - N-acetylglutamate synthase - active site. It is found at the C-terminus of Neurospora crassa acetylglutamate synthase - amino-acid acetyltransferase, EC: 2.3.1.1. It is also found C-terminal to the amino acid kinase region (pfam00696) in some fungal acetylglutamate kinase enzymes. it stabilizes the yeast NAGK, N-acetyl-L-glutamate kinase, slows catalysis and modulates feed-back inhibition by arginine. This domain is found to be the N-acetyltransferase (NAT) domain, and it has a typical GCN5-related NAT fold and a site that catalyzes NAG synthesis which is located >25 Angstrom away from the L-arginine binding site in the N-temrinal domain pfam00696. 166 matched cddid_all.tbl CDD pfam04769 pfam04769 398438 MATalpha_HMGbox Mating-type protein MAT alpha 1 HMG-box. This family includes Saccharomyces cerevisiae mating type protein alpha 1. Mat alpha 1 is a transcription activator which activates mating-type alpha-specific genes. MAT alpha 1 and MCM 1 bind cooperatively to PQ elements upstream of alpha-specific genes. Alpha 1 interacts in vivo with STE12, linking expression of alpha-specific genes to the alpha-pheromone (pfam04648) response pathway. In silico modelling of the MAT_Alpha1 domain indicates that its best scoring templates were structures of HMG-box proteins, and DOI: 10.4236/ojbiphy.2013.31001. Phylogenetic analysis suggests that the MAT_Alpha1 domain diverged from the MATA_HMG-box subfamily. The name of MATalpha_HMG-box was proposed for the MAT_alpha1 domain. 186 matched cddid_all.tbl CDD pfam04770 pfam04770 398439 ZF-HD_dimer ZF-HD protein dimerization region. This family of proteins has are plant transcription factors, and have been named ZF-HD for zinc finger homeodomain proteins, on the basis of similarity to proteins of known structure. This region is thought to be involved in the formation of homo and heterodimers, and may form a zinc finger. 55 matched cddid_all.tbl CDD pfam04771 pfam04771 282606 CAV_VP3 Chicken anaemia virus VP-3 protein. This protein is found in the nucleus of infected cells and may act as a transcriptional regulator. It induces apoptosis, and is also known as apoptin [SwissProt annotation for Swiss:P54094]. 121 matched cddid_all.tbl CDD pfam04772 pfam04772 282607 Flu_B_M2 Influenza B matrix protein 2 (BM2). M2 is synthesized in the late phase of infection and incorporated into the virion. It may be phosphorylated in vivo. The function of BM2 is unknown. 109 matched cddid_all.tbl CDD pfam04773 pfam04773 428113 FecR FecR protein. FecR is involved in regulation of iron dicitrate transport. In the absence of citrate FecR inactivates FecI. FecR is probably a sensor that recognizes iron dicitrate in the periplasm. 96 matched cddid_all.tbl CDD pfam04774 pfam04774 461421 HABP4_PAI-RBP1 Hyaluronan / mRNA binding family. This family includes the HABP4 family of hyaluronan-binding proteins, and the PAI-1 mRNA-binding protein, PAI-RBP1. HABP4 has been observed to bind hyaluronan (a glucosaminoglycan), but it is not known whether this is its primary role in vivo. It has also been observed to bind RNA, but with a lower affinity than that for hyaluronan. PAI-1 mRNA-binding protein specifically binds the mRNA of type-1 plasminogen activator inhibitor (PAI-1), and is thought to be involved in regulation of mRNA stability. However, in both cases, the sequence motifs predicted to be important for ligand binding are not conserved throughout the family, so it is not known whether members of this family share a common function. 108 matched cddid_all.tbl CDD pfam04775 pfam04775 461422 Bile_Hydr_Trans Acyl-CoA thioester hydrolase/BAAT N-terminal region. This family consists of the amino termini of acyl-CoA thioester hydrolase and bile acid-CoA:amino acid N-acetyltransferase (BAAT). This region is not thought to contain the active site of either enzyme. Thioesterase isoforms have been identified in peroxisomes, cytoplasm and mitochondria, where they are thought to have distinct functions in lipid metabolism. For example, in peroxisomes, the hydrolase acts on bile-CoA esters. 127 matched cddid_all.tbl CDD pfam04776 pfam04776 428116 protein_MS5 Protein MS5. Proteins are known only from species of Brassicaceae. Protein MS5 is essential for pairing of homologs during early prophase stage of meiosis but not necessary for the initiation of DNA double-strand breaks. 118 matched cddid_all.tbl CDD pfam04777 pfam04777 461423 Evr1_Alr Erv1 / Alr family. Biogenesis of Fe/S clusters involves a number of essential mitochondrial proteins. Erv1p of Saccharomyces cerevisiae mitochondria is required for the maturation of Fe/S proteins in the cytosol. The ALR (augmenter of liver regeneration) represents a mammalian orthologue of yeast Erv1p. Both Erv1p and full-length ALR are located in the mitochondrial intermembrane an d it thought to operate downstream of the mitochondrial ABC transporter. 93 matched cddid_all.tbl CDD pfam04778 pfam04778 461424 LMP LMP repeated region. This family consists of a repeated sequence element found in the LMP group of surface-located membrane proteins of Mycoplasma hominis. The the number of repeats in the protein affects the tendency of cells to spontaneously aggregate. Agglutination may be an important factor in colonization. Non-agglutinating microorganizms might easily be distributed whereas aggregation might provide a better chance to avoid an antibody response since some of the epitopes may be buried. 158 matched cddid_all.tbl CDD pfam04780 pfam04780 428119 DUF629 Protein of unknown function (DUF629). This family represents a region of several plant proteins of unknown function. A C2H2 zinc finger is predicted in this region in some family members, but the spacing between the cysteine residues is not conserved throughout the family. 464 matched cddid_all.tbl CDD pfam04781 pfam04781 428120 DUF627 Protein of unknown function (DUF627). This family represents the N-terminal region of several plant proteins of unknown function. 108 matched cddid_all.tbl CDD pfam04782 pfam04782 461425 DUF632 Protein of unknown function (DUF632). This plant protein may be a leucine zipper, but there is no experimental evidence for this. 311 matched cddid_all.tbl CDD pfam04783 pfam04783 461426 DUF630 Protein of unknown function (DUF630). This region is sometimes found at the N-terminus of putative plant bZIP proteins. Its function is not known. Structural modelling suggests this domain may bind nucleic acids. 59 matched cddid_all.tbl CDD pfam04784 pfam04784 461427 DUF547 Protein of unknown function, DUF547. Family of uncharacterized proteins from C. elegans and A. thaliana. 119 matched cddid_all.tbl CDD pfam04785 pfam04785 282619 Rhabdo_M2 Rhabdovirus matrix protein M2. M protein is involved in condensing and targeting the ribonucleoprotein (RNP) coil to the plasma membrane. M interacts specifically with the transmembrane spike protein (G) is important for the incorporation of G protein into budding virions. 202 matched cddid_all.tbl CDD pfam04786 pfam04786 398451 Baculo_DNA_bind ssDNA binding protein. Family of Baculovirus ssDNA binding proteins. 248 matched cddid_all.tbl CDD pfam04787 pfam04787 282621 Pox_H7 Late protein H7. Family of poxvirus late H7 proteins. 143 matched cddid_all.tbl CDD pfam04788 pfam04788 398452 DUF620 Protein of unknown function (DUF620). Family of uncharacterized proteins. 243 matched cddid_all.tbl CDD pfam04789 pfam04789 398453 DUF621 Protein of unknown function (DUF621). Family of uncharacterized proteins. Some are annotated as having possible G-protein-coupled receptor-like activity. 301 matched cddid_all.tbl CDD pfam04790 pfam04790 461428 Sarcoglycan_1 Sarcoglycan complex subunit protein. The dystrophin glycoprotein complex (DGC) is a membrane-spanning complex that links the interior cytoskeleton to the extracellular matrix in muscle. The sarcoglycan complex is a subcomplex within the DGC and is composed of several muscle-specific, transmembrane proteins (alpha-, beta-, gamma-, delta- and zeta-sarcoglycan). The sarcoglycans are asparagine-linked glycosylated proteins with single transmembrane domains. This family contains beta, gamma and delta members. 255 matched cddid_all.tbl CDD pfam04791 pfam04791 461429 LMBR1 LMBR1-like membrane protein. Members of this family are integral membrane proteins that are around 500 residues in length. LMBR1 is not involved in preaxial polydactyly, as originally thought. Vertebrate members of this family may play a role in limb development. Lysosomal cobalamin transport escort protein LMBD1 is a lysosomal membrane chaperone required to export cobalamin from lysosome to the cytosol, allowing its conversion to cofactors. A member of this family has been shown to be a lipocalin membrane receptor. 471 matched cddid_all.tbl CDD pfam04792 pfam04792 398456 LcrV V antigen (LcrV) protein. Yersinia pestis, the aetiologic agent of plague, secretes a set of environmentally regulated, plasmid pCD1-encoded virulence proteins termed Yops and V antigen (LcrV) by a type III secretion mechanism. LcrV is a multifunctional protein that has been shown to act at the level of secretion control by binding the Ysc inner-gate protein LcrG and to modulate the host immune response by altering cytokine production. LcrV is also necessary for full induction of low-calcium response (LCR) stimulon virulence gene transcription. Family members are not confined to Yersinia pestis. 298 matched cddid_all.tbl CDD pfam04793 pfam04793 368123 Herpes_BBRF1 BRRF1-like protein. Family of herpesvirus proteins including Epstein-barr virus protein BBRF1. 282 matched cddid_all.tbl CDD pfam04794 pfam04794 461430 YdjC YdjC-like protein. Family of YdjC-like proteins. This region is possibly involved in the the cleavage of cellobiose-phosphate. 187 matched cddid_all.tbl CDD pfam04795 pfam04795 461431 PAPA-1 PAPA-1-like conserved region. Family of proteins with a conserved region found in PAPA-1, a PAP-1 binding protein. 78 matched cddid_all.tbl CDD pfam04796 pfam04796 309782 RepA_C Plasmid encoded RepA protein. Family of plasmid encoded proteins involved in plasmid replication. The role of RepA in the replication process is not clearly understood. 161 matched cddid_all.tbl CDD pfam04797 pfam04797 309783 Herpes_ORF11 Herpesvirus dUTPase protein. This family of proteins are found in Herpesvirus proteins. This family includes proteins called ORF10 and ORF11 amongst others. However, these proteins seem to be related to other dUTPases pfam00692 suggesting that these proteins are also dUTPases (Bateman A pers. obs.). 372 matched cddid_all.tbl CDD pfam04798 pfam04798 282632 Baculo_19 Baculovirus 19 kDa protein conserved region. Family of Baculovirus proteins of approximate mass 19 kDa. 143 matched cddid_all.tbl CDD pfam04799 pfam04799 461432 Fzo_mitofusin fzo-like conserved region. Family of putative transmembrane GTPase. The fzo protein is a mediator of mitochondrial fusion. This conserved region is also found in the human mitofusin protein. 159 matched cddid_all.tbl CDD pfam04800 pfam04800 461433 NDUS4 NADH dehydrogenase ubiquinone Fe-S protein 4. This entry represents NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, an accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), initially identified in Neurospora crassa as a 21 kDa protein. It is believed that members of this family are not to be involved in catalysis. 93 matched cddid_all.tbl CDD pfam04801 pfam04801 461434 RPC5 RPC5 protein. This family represents the RPC5 protein which is part of the RNA polymerase III complex. 427 matched cddid_all.tbl CDD pfam04802 pfam04802 461435 PP4R3 Phosphatase 4 regulatory subunit 3. This entry represents the Serine/threonine-protein phosphatase 4 regulatory subunit 3 (also known as SMEK homolog) PP4R3, which forms a complex with the phosphatase 4 catalytic subunit (PP4c), localising it to the DNA damage repair machinery and regulates its activity. PP4c is involved in developmental progression, chemotaxis, expression of stress response genes and cell movement. 191 matched cddid_all.tbl CDD pfam04803 pfam04803 461436 Cor1 Cor1/Xlr/Xmr conserved region. Cor1 is a component of the chromosome core in the meiotic prophase chromosomes. Xlr is a lymphoid cell specific protein. Xlm is abundantly transcribed in testis in a tissue-specific and developmentally regulated manner. The protein is located in the nuclei of spermatocytes, early in the prophase of the first meiotic division, and later becomes concentrated in the XY nuclear subregion where it is in particular associated with the axes of sex chromosomes. 124 matched cddid_all.tbl CDD pfam04805 pfam04805 282638 Pox_E10 E10-like protein conserved region. Family of poxvirus proteins. 69 matched cddid_all.tbl CDD pfam04806 pfam04806 398464 EspF EspF protein repeat. The enteropathogenic Escherichia coli EspF secreted protein induces host cell apoptosis. Its proline-rich structure suggests that it may act by binding to SH3 domains or EVH1 domains of host cell signalling proteins. 47 matched cddid_all.tbl CDD pfam04807 pfam04807 147122 Gemini_AC4_5 Geminivirus AC4/5 conserved region. 33 matched cddid_all.tbl CDD pfam04808 pfam04808 113574 CTV_P23 Citrus tristeza virus (CTV) P23 protein. This family consists of protein P23 from the citrus tristeza virus, which is a member of the Closteroviridae. CTV viruses produce more positive than negative RNA strands, and P23 controls this asymmetrical RNA accumulation. Amino acids 42-180 are essential for function and are thought to contain RNA-binding and zinc finger domains. 209 matched cddid_all.tbl CDD pfam04809 pfam04809 428133 HupH_C HupH hydrogenase expression protein, C-terminal conserved region. This family represents a C-terminal conserved region found in these bacterial proteins necessary for hydrogenase synthesis. Their precise function is unknown. 109 matched cddid_all.tbl CDD pfam04810 pfam04810 461437 zf-Sec23_Sec24 Sec23/Sec24 zinc finger. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is found to be zinc binding domain. 38 matched cddid_all.tbl CDD pfam04811 pfam04811 398467 Sec23_trunk Sec23/Sec24 trunk domain. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is known as the trunk domain and has an alpha/beta vWA fold and forms the dimer interface. 241 matched cddid_all.tbl CDD pfam04812 pfam04812 461438 HNF-1B_C Hepatocyte nuclear factor 1 (HNF-1), beta isoform C terminus. This family consists of a region found within the alpha isoform and at the C terminus of the beta isoform of the homeobox-containing transcription factor of HNF-1. Different isoforms of HNF-1 are generated by the differential use of polyadenylation sites and by alternative splicing. The C-terminal region of HNF-1 is responsible for the activation of transcription. Mutations and polymorphisms in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3). 258 matched cddid_all.tbl CDD pfam04813 pfam04813 461439 HNF-1A_C Hepatocyte nuclear factor 1 (HNF-1), alpha isoform C terminus. This family consists of an alternative C terminus of homeobox-containing transcription factor HNF-1, found in the HNF-1A isoform. Different isoforms of HNF-1 are generated by the differential use of polyadenylation sites and by alternative splicing. The C-terminal region of HNF-1 is responsible for the activation of transcription, and HNF-1A, which has this C-terminal extension, transactivates less well than the B and C isoforms. Mutations and polymorphisms in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3). 85 matched cddid_all.tbl CDD pfam04814 pfam04814 461440 HNF-1_N Hepatocyte nuclear factor 1 (HNF-1), N terminus. This family consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerization sequence and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3). 178 matched cddid_all.tbl CDD pfam04815 pfam04815 461441 Sec23_helical Sec23/Sec24 helical domain. COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is composed of five alpha helices. 103 matched cddid_all.tbl CDD pfam04816 pfam04816 428139 TrmK tRNA (adenine(22)-N(1))-methyltransferase. tRNA_MT is a family of bacterial tRNA (adenine(22)-N(1))-methyltransferase enzymes with a Rossmann-like fold. This enzyme carries out the function of N1-adenosine methylation at position 22 of bacterial tRNA. 205 matched cddid_all.tbl CDD pfam04817 pfam04817 113583 Umbravirus_LDM Umbravirus long distance movement (LDM) family. The long distance movement protein of Umbraviruses mediates the movement of viral RNA through the phloem of infected plants. 231 matched cddid_all.tbl CDD pfam04818 pfam04818 461442 CID CID domain. This domain binds to the phosphorylated C-terminal domain (CTD) of RNA polymerase II. This domain is known as the CTD-interacting domain (CID). 117 matched cddid_all.tbl CDD pfam04819 pfam04819 461443 DUF716 Family of unknown function (DUF716). This family is equally distributed in both metazoa and plants. Annotation associated with Swiss:Q9SLW7 suggest that it may be involved in response to viral attack in plants. However, no clear function has been assigned to this family. 138 matched cddid_all.tbl CDD pfam04820 pfam04820 398475 Trp_halogenase Tryptophan halogenase. Tryptophan halogenase catalyzes the chlorination of tryptophan to form 7-chlorotryptophan. This is the first step in the biosynthesis of pyrrolnitrin, an antibiotic with broad-spectrum anti-fungal activity. Tryptophan halogenase is NADH-dependent. 457 matched cddid_all.tbl CDD pfam04821 pfam04821 461444 TIMELESS Timeless protein. The timeless gene in Drosophila melanogaster and its homologs in a number of other insects and mammals (including human) are involved in circadian rhythm control. This family includes a related proteins from a number of fungal species. 273 matched cddid_all.tbl CDD pfam04822 pfam04822 461445 Takusan Takusan. This domain is named takusan, which is a Japanese word meaning 'many'. Members of this family regulate synaptic activity. 85 matched cddid_all.tbl CDD pfam04823 pfam04823 398478 Herpes_UL49_2 Herpesvirus UL49 tegument protein. 82 matched cddid_all.tbl CDD pfam04824 pfam04824 335912 Rad21_Rec8 Conserved region of Rad21 / Rec8 like protein. This family represents a conserved region found in eukaryotic cohesins of the Rad21, Rec8 and Scc1 families. Members of this family mediate sister chromatid cohesion during mitosis and meiosis, as part of the cohesin complex. Cohesion is necessary for homologous recombination (including double-strand break repair) and correct chromatid segregation. These proteins may also be involved in chromosome condensation. Dissociation at the metaphase to anaphase transition causes loss of cohesion and chromatid segregation. 55 matched cddid_all.tbl CDD pfam04825 pfam04825 461446 Rad21_Rec8_N N terminus of Rad21 / Rec8 like protein. This family represents a conserved N-terminal region found in eukaryotic cohesins of the Rad21, Rec8 and Scc1 families. Members of this family mediate sister chromatid cohesion during mitosis and meiosis, as part of the cohesin complex. Cohesion is necessary for homologous recombination (including double-strand break repair) and correct chromatid segregation. These proteins may also be involved in chromosome condensation. Dissociation at the metaphase to anaphase transition causes loss of cohesion and chromatid segregation. 104 matched cddid_all.tbl CDD pfam04826 pfam04826 461447 Arm_2 Armadillo-like. This domain contains armadillo-like repeats. Proteins containing this domain interact with numerous other proteins, through these interactions they are involved in a wide variety of processes including carcinogenesis, control of cellular ageing and survival, regulation of circadian rhythm and lysosomal sorting of G protein-coupled receptors. 221 matched cddid_all.tbl CDD pfam04827 pfam04827 203098 Plant_tran Plant transposon protein. This family contains plant transposases which are putative members of the PIF / Ping-Pong family. 205 matched cddid_all.tbl CDD pfam04828 pfam04828 428146 GFA Glutathione-dependent formaldehyde-activating enzyme. The GFA enzyme catalyzes the first step in the detoxification of formaldehyde. This domain has a beta-tent fold. 93 matched cddid_all.tbl CDD pfam04829 pfam04829 428147 PT-VENN Pre-toxin domain with VENN motif. This family represents a conserved region found in many bacterial porlymorphic toxins which is located before the C-terminal toxin modules. 52 matched cddid_all.tbl CDD pfam04830 pfam04830 428148 DUF637 Possible hemagglutinin (DUF637). This family represents a conserved region found in a bacterial protein which may be a hemagglutinin or hemolysin. 166 matched cddid_all.tbl CDD pfam04831 pfam04831 461448 Popeye Popeye protein conserved region. The function of Popeye proteins is not well understood. They are predominantly expressed in cardiac and skeletal muscle. This family represents a conserved region which includes three potential transmembrane domains. 227 matched cddid_all.tbl CDD pfam04832 pfam04832 461449 SOUL SOUL heme-binding protein. This family represents a group of putative heme-binding proteins. Our family includes archaeal and bacterial homologs. 173 matched cddid_all.tbl CDD pfam04833 pfam04833 461450 COBRA COBRA-like protein. Family of plant proteins are designated COBRA-like (COBL) proteins. The 12 Arabidopsis members of the family are all GPI-liked. Some members of this family are annotated as phytochelatin synthase, but these annotations are incorrect. 167 matched cddid_all.tbl CDD pfam04834 pfam04834 461451 Adeno_E3_14_5 Early E3 14.5 kDa protein. The E3B 14.5 kDa was first identified in Human adenovirus type 5. It is an integral membrane protein oriented with its C terminus in the cytoplasm. It functions to down-regulate the epidermal growth factor receptor and prevent tumour necrosis factor cytolysis. It achieves this through the interaction with E3 10.4 kDa protein. 100 matched cddid_all.tbl CDD pfam04835 pfam04835 282664 Pox_A9 A9 protein conserved region. Family of Chordopoxvirus A9 proteins. 53 matched cddid_all.tbl CDD pfam04836 pfam04836 461452 IFRD_C Interferon-related protein conserved region. Family of proteins thought to be involved in regulating gene activity in the proliferative and/or differentiative pathways induced by NGF. 52 matched cddid_all.tbl CDD pfam04837 pfam04837 113603 MbeB_N MbeB-like, N-term conserved region. This family represents an N-terminal conserved region of MbeB/MobB proteins. These proteins are essential for specific plasmid transfer. 52 matched cddid_all.tbl CDD pfam04838 pfam04838 282666 Baculo_LEF5 Baculoviridae late expression factor 5. 156 matched cddid_all.tbl CDD pfam04839 pfam04839 398487 PSRP-3_Ycf65 Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65). This small acidic protein is found in 30S ribosomal subunit of cyanobacteria and plant plastids. In plants it has been named plastid-specific ribosomal protein 3 (PSRP-3), and in cyanobacteria it is named Ycf65. Plastid-specific ribosomal proteins may mediate the effects of nuclear factors on plastid translation. The acidic PSRPs are thought to contribute to protein-protein interactions in the 30S subunit, and are not thought to bind RNA. 47 matched cddid_all.tbl CDD pfam04840 pfam04840 282668 Vps16_C Vps16, C-terminal region. This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport. The role of VPS16 in this complex is not known. 320 matched cddid_all.tbl CDD pfam04841 pfam04841 252829 Vps16_N Vps16, N-terminal region. This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport. The role of VPS16 in this complex is not known. 408 matched cddid_all.tbl CDD pfam04842 pfam04842 368150 DUF639 Plant protein of unknown function (DUF639). Plant protein of unknown function. 230 matched cddid_all.tbl CDD pfam04843 pfam04843 461453 Herpes_teg_N Herpesvirus tegument protein, N-terminal conserved region. 183 matched cddid_all.tbl CDD pfam04844 pfam04844 461454 Ovate Transcriptional repressor, ovate. This is a family of transcriptional repressors. In plants, these proteins are important regulators of growth and development. 58 matched cddid_all.tbl CDD pfam04845 pfam04845 282672 PurA PurA ssDNA and RNA-binding protein. This family represents most of the length of the protein. 219 matched cddid_all.tbl CDD pfam04846 pfam04846 282673 Herpes_pp38 Herpesvirus pp38 phosphoprotein. This protein represents a conserved region found in most herpesvirus pp38 phosphoproteins. 63 matched cddid_all.tbl CDD pfam04847 pfam04847 282674 Calcipressin Calcipressin. Calcipressin is also known as calcineurin-binding protein, since it inhibits calcineurin-mediated transcriptional modulation by binding to calcineurin's catalytic domain. 183 matched cddid_all.tbl CDD pfam04848 pfam04848 428155 Pox_A22 Poxvirus A22 protein. 140 matched cddid_all.tbl CDD pfam04849 pfam04849 461455 HAP1_N HAP1 N-terminal conserved region. This family represents an N-terminal conserved region found in several huntingtin-associated protein 1 (HAP1) homologs. HAP1 binds to huntingtin in a polyglutamine repeat-length-dependent manner. However, its possible role in the pathogenesis of Huntington's disease is unclear. This family also includes a similar N-terminal conserved region from hypothetical protein products of ALS2CR3 genes found in the human juvenile amyotrophic lateral sclerosis critical region 2q33-2q34. 309 matched cddid_all.tbl CDD pfam04850 pfam04850 398491 Baculo_E66 Baculovirus E66 occlusion-derived virus envelope protein. 387 matched cddid_all.tbl CDD pfam04851 pfam04851 398492 ResIII Type III restriction enzyme, res subunit. 162 matched cddid_all.tbl CDD pfam04852 pfam04852 398493 ALOG_dom ALOG domain. The 125-residue ALOG (Arabidopsis LSH1 and oryza G1) domain is rich in basic amino acids, especially arginine, and is highly conserved among land plants. Members of the ALOG family of proteins function as key developmental regulators. It has been proposed that the ALOG domain originated from the N-terminal DNA-binding domains of integrases belonging to the tyrosine recombinase superfamily encoded by a distinct type of DIRS1-like LTR retrotransposon found in several eukaryotes. Secondary structure predictions revealed an all-alpha helical domain with four conserved helices. Some proteins known to contain an ALOG domain are Arabidopsis thaliana LIGHT_DEPENDENT SHORT HYPOCOTYLS1 (LSH1),involved in phytochrome- dependent light signalling; Oryza G1, involved in the specification of sterile lemma identity and Plant defence proteins. 126 matched cddid_all.tbl CDD pfam04854 pfam04854 428157 DUF624 Protein of unknown function, DUF624. This family includes several uncharacterized bacterial proteins. 77 matched cddid_all.tbl CDD pfam04855 pfam04855 428158 SNF5 SNF5 / SMARCB1 / INI1. SNF5 is a component of the yeast SWI/SNF complex, which is an ATP-dependent nucleosome-remodelling complex that regulates the transcription of a subset of yeast genes. SNF5 is a key component of all SWI/SNF-class complexes characterized so far. This family consists of the conserved region of SNF5, including a direct repeat motif. SNF5 is essential for the assembly promoter targeting and chromatin remodelling activity of the SWI-SNF complex. SNF5 is also known as SMARCB1, for SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily b, member 1, and also INI1 for integrase interactor 1. Loss-of function mutations in SNF5 are thought to contribute to oncogenesis in malignant rhabdoid tumours (MRTs). 186 matched cddid_all.tbl CDD pfam04856 pfam04856 461456 Securin Securin sister-chromatid separation inhibitor. Securin is also known as pituitary tumour-transforming gene product. Over-expression of securin is associated with a number of tumours, and it has been proposed that this may be due to erroneous chromatid separation leading to chromosome gain or loss. 197 matched cddid_all.tbl CDD pfam04857 pfam04857 461457 CAF1 CAF1 family ribonuclease. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the polyA tail. CAF1 encodes a critical component of the major cytoplasmic deadenylase in yeast. Both Caf1p is required for normal mRNA deadenylation in vivo and localizes to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent polyA-specific exonuclease activity. Some members of this family include and inserted RNA binding domain pfam01424. This family of proteins is related to other exonucleases pfam00929 (Bateman A pers. obs.). The crystal structure of Saccharomyces cerevisiae Pop2 has been resolved at 2.3 Angstrom resolution. 375 matched cddid_all.tbl CDD pfam04858 pfam04858 398497 TH1 TH1 protein. TH1 is a highly conserved but uncharacterized metazoan protein. No homolog has been identified in Caenorhabditis elegans. TH1 binds specifically to A-Raf kinase. 579 matched cddid_all.tbl CDD pfam04859 pfam04859 461458 DUF641 Plant protein of unknown function (DUF641). Plant protein of unknown function. 127 matched cddid_all.tbl CDD pfam04860 pfam04860 461459 Phage_portal Phage portal protein. Bacteriophage portal proteins form a dodecamer and is located at a five-fold vertex of the viral capsid. The portal complex forms a channel through which the viral DNA is packaged into the capsid, and exits during infection. The portal protein is though to rotate during DNA packaging. Portal proteins from different phage show little sequence homology, so this family does not represent all portal proteins. 281 matched cddid_all.tbl CDD pfam04862 pfam04862 398500 DUF642 Protein of unknown function (DUF642). This family represents a duplicated conserved region found in a number of uncharacterized plant proteins, potentially in the stem. There is a conserved CGP sequence motif. 157 matched cddid_all.tbl CDD pfam04863 pfam04863 398501 EGF_alliinase Alliinase EGF-like domain. Allicin is a thiosulphinate that gives rise to dithiines, allyl sulphides and ajoenes, the three groups of active compounds in Allium species. Allicin is synthesized from sulfoxide cysteine derivatives by alliinase (EC:4.4.1.4), whose C-S lyase activity cleaves C(beta)-S(gamma) bonds. It is thought that this enzyme forms part of a primitive plant defence system. This family represents the N-terminal EGF-like domain. 56 matched cddid_all.tbl CDD pfam04864 pfam04864 398502 Alliinase_C Allinase. Allicin is a thiosulphinate that gives rise to dithiines, allyl sulphides and ajoenes, the three groups of active compounds in Allium species. Allicin is synthesized from sulfoxide cysteine derivatives by alliinase (EC:4.4.1.4), whose C-S lyase activity cleaves C(beta)-S(gamma) bonds. It is thought that this enzyme forms part of a primitive plant defence system. 363 matched cddid_all.tbl CDD pfam04865 pfam04865 428162 Baseplate_J Baseplate J-like protein. The P2 bacteriophage J protein lies at the edge of the baseplate. This family also includes a number of bacterial homologs, which are thought to have been horizontally transferred. 254 matched cddid_all.tbl CDD pfam04866 pfam04866 282690 Rota_NS6 Rotavirus non-structural protein 6. 92 matched cddid_all.tbl CDD pfam04867 pfam04867 282691 DUF643 Protein of unknown function (DUF643). Protein of unknown function found in Borrelia burgdorferi, the Lyme disease spirochete. 114 matched cddid_all.tbl CDD pfam04868 pfam04868 428163 PDE6_gamma Retinal cGMP phosphodiesterase, gamma subunit. Retinal rod and cone cGMP phosphodiesterases function as the effector enzymes in the vertebrate visual transduction cascade. This family represents the inhibitory gamma subunit, which is also expressed outside retinal tissues and has been shown to interact with the G-protein-coupled receptor kinase 2 signalling system to regulate the epidermal growth factor- and thrombin-dependent stimulation of p42/p44 mitogen-activated protein kinase in human embryonic kidney 293 cells. 82 matched cddid_all.tbl CDD pfam04869 pfam04869 461460 Uso1_p115_head Uso1 / p115 like vesicle tethering protein, head region. Also known as General vesicular transport factor, Transcytosis associated protein (TAP) and Vesicle docking protein, this myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerization, and a short C-terminal acidic region. p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region. It is required for intercisternal transport in the golgi stack. This family consists of part of the head region. The head region is highly conserved, but its function is unknown. It does not seem to be essential for vesicle tethering. The N-terminal part of the head region, not within this family, contains context-detected Armadillo/beta-catenin-like repeats (pfam00514). 310 matched cddid_all.tbl CDD pfam04870 pfam04870 428165 Moulting_cycle Moulting cycle. This family of proteins plays a role in the moulting cycle of nematodes, which involves the synthesis of a new collagen-rich cuticle underneath the existing cuticle and the subsequent removal of the old cuticle. 343 matched cddid_all.tbl CDD pfam04871 pfam04871 461461 Uso1_p115_C Uso1 / p115 like vesicle tethering protein, C terminal region. Also known as General vesicular transport factor, Transcytosis associate protein (TAP) and Vesicle docking protein, this myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerization, and a short C-terminal acidic region. p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region. It is required for intercisternal transport in the golgi stack. This family consists of the acidic C-terminus, which binds to the golgins giantin and GM130. p115 is thought to juxtapose two membranes by binding giantin with one acidic region, and GM130 with another. 121 matched cddid_all.tbl CDD pfam04872 pfam04872 282696 Pox_L5 Poxvirus L5 protein family. This family includes variola (smallpox) and vaccinia virus L5 proteins. However, not all proteins in this family are called L5. L5 is thought to contain a metal-binding region. 79 matched cddid_all.tbl CDD pfam04873 pfam04873 398508 EIN3 Ethylene insensitive 3. Ethylene insensitive 3 (EIN3) proteins are a family of plant DNA-binding proteins that regulate transcription in response to the gaseous plant hormone ethylene, and are essential for ethylene-mediated responses including the triple response, cell growth inhibition, and accelerated senescence. 252 matched cddid_all.tbl CDD pfam04874 pfam04874 461462 Mak16 Mak16 protein C-terminal region. The precise function of this eukaryotic protein family is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni Mak16 has been shown to target protein transport to the nucleolus. 97 matched cddid_all.tbl CDD pfam04875 pfam04875 282699 DUF645 Protein of unknown function, DUF645. This family includes several uncharacterized proteins from Vibrio cholerae. There is some doubt regarding the existence of these proteins, they are encoded by open reading frames contained within a repeated region in the Vibrio superintegron. 59 matched cddid_all.tbl CDD pfam04876 pfam04876 461463 Tenui_NCP Tenuivirus major non-capsid protein. This protein of unknown function accumulates in large amounts in tenuivirus infected cells. It is found in all forms of the inclusion bodies that are formed after infection. 173 matched cddid_all.tbl CDD pfam04877 pfam04877 368170 Harpin HrpZ. HrpZ from the plant pathogen Pseudomonas syringae binds to lipid bilayers and forms a cation-conducting pore in vivo. This pore-forming activity may allow nutrient release or delivery of virulence factors during bacterial colonization of host plants. The family of hairpinN proteins, Harpin, has been merged into this family. HrpN is a virulence determinant which elicits lesion formation in Arabidopsis and tobacco and triggers systemic resistance in Arabidopsis. 277 matched cddid_all.tbl CDD pfam04878 pfam04878 282702 Baculo_p48 Baculovirus P48 protein. 370 matched cddid_all.tbl CDD pfam04879 pfam04879 428168 Molybdop_Fe4S4 Molybdopterin oxidoreductase Fe4S4 domain. This domain is found in formate dehydrogenase H for which the structure is known. This first domain (residues 1 to 60) of PDB:1aa6 is an Fe4S4 cluster just below the protein surface. 55 matched cddid_all.tbl CDD pfam04880 pfam04880 461464 NUDE_C NUDE protein, C-terminal conserved region. This family represents the C-terminal conserved region of the NUDE proteins. NUDE proteins are involved in nuclear migration. 169 matched cddid_all.tbl CDD pfam04881 pfam04881 461465 Adeno_GP19K Adenovirus GP19K. This 19 kDa glycoprotein binds the major histocompatibility (MHC) class I antigens in the endoplasmic reticulum (ER). The ER retention signal at the C-terminus of GP19K causes retention of the complex in the ER, preventing lysis of the cell by cytotoxic T lymphocytes. 132 matched cddid_all.tbl CDD pfam04882 pfam04882 428171 Peroxin-3 Peroxin-3. Peroxin-3 is a peroxisomal protein. It is thought to be involve in membrane vesicle assembly prior to the translocation of matrix proteins. 451 matched cddid_all.tbl CDD pfam04883 pfam04883 428172 HK97-gp10_like Bacteriophage HK97-gp10, putative tail-component. This family of proteins is found in the caudovirales. It may be a tail component. 80 matched cddid_all.tbl CDD pfam04884 pfam04884 428173 UVB_sens_prot Vitamin B6 photo-protection and homoeostasis. In plants, this domain plays a role in auxin-transport, plant growth and development and appears to be expressed by all cells in the plant as well as in plastids. The family has been shown to play a role in vitamin B6 photo-protection and homoeostasis in plants. 240 matched cddid_all.tbl CDD pfam04885 pfam04885 461466 Stig1 Stigma-specific protein, Stig1. This family represents the Stig1 cysteine rich plant protein. The STIG1 gene is developmentally regulated and expressed specifically in the stigmatic secretory zone. 136 matched cddid_all.tbl CDD pfam04886 pfam04886 282710 PT PT repeat. This short repeat is composed on the tetrapeptide XPTX. This repeat is found in a variety of proteins, however it is not clear if these repeats are homologous to each other. The alignment represents nine copies of this repeat. 36 matched cddid_all.tbl CDD pfam04887 pfam04887 282711 Pox_M2 Poxvirus M2 protein. This family includes M2 protein from variola virus. The function of this protein is not known. 196 matched cddid_all.tbl CDD pfam04888 pfam04888 428175 SseC Secretion system effector C (SseC) like family. SseC is a secreted protein that forms a complex together with SecB and SecD on the surface of Salmonella. All these proteins are secreted by the type III secretion system. Many mucosal pathogens use type III secretion systems for the injection of effector proteins into target cells. SecB, SseC and SecD are inserted into the target cell membrane. where they form a small pore or translocon. In addition to SseC, this family includes the bacterial secreted proteins PopB, PepB, YopB and EspD which are thought to be directly involved in pore formation, and type III secretion system translocon. 312 matched cddid_all.tbl CDD pfam04889 pfam04889 428176 Cwf_Cwc_15 Cwf15/Cwc15 cell cycle control protein. This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologs. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing. 244 matched cddid_all.tbl CDD pfam04890 pfam04890 309840 DUF648 Family of unknown function (DUF648). Family of hypothetical Chlamydia proteins. This family may well comprise of two domains, as some members only match the N-terminus. 289 matched cddid_all.tbl CDD pfam04891 pfam04891 428177 NifQ NifQ. NifQ is involved in early stages of the biosynthesis of the iron-molybdenum cofactor (FeMo-co), which is an integral part of the active site of dinitrogenase. The conserved C-terminal cysteine residues may be involved in metal binding. 159 matched cddid_all.tbl CDD pfam04892 pfam04892 461467 VanZ VanZ like family. This family contains several examples of the VanZ protein, but also contains examples of phosphotransbutyrylases. 79 matched cddid_all.tbl CDD pfam04893 pfam04893 461468 Yip1 Yip1 domain. The Yip1 integral membrane domain contains four transmembrane alpha helices. The domain is characterized by the motifs DLYGP and GY. The Yip1 protein is a golgi protein involved in vesicular transport that interacts with GTPases. 173 matched cddid_all.tbl CDD pfam04894 pfam04894 428180 Nre_N Archaeal Nre, N-terminal. This conserved region is found in the N-terminal region of archaeal Nre proteins. While most archaeal organizms encode only a single Nre protein, some encode two, NreA and NreB. 270 matched cddid_all.tbl CDD pfam04895 pfam04895 428181 Nre_C Archaeal Nre, C-terminal. This conserved region is found in the C-terminal region of archaeal Nre proteins. While most archaeal organizms encode only a single Nre protein, some encode two, NreA and NreB. 110 matched cddid_all.tbl CDD pfam04896 pfam04896 428182 AmoC Ammonia monooxygenase/methane monooxygenase, subunit C. Ammonia monooxygenase plays a key role in the nitrogen cycle and degrades a wide range of hydrocarbons and halogenated hydrocarbons. This family represents the AmoC subunit. It also includes the particulate methane monooxygenase subunit PmoC from methanotrophic bacteria. 245 matched cddid_all.tbl CDD pfam04898 pfam04898 461469 Glu_syn_central Glutamate synthase central domain. The central domain of glutamate synthase connects the amino terminal amidotransferase domain with the FMN-binding domain and has an alpha / beta overall topology. This domain appears to be a rudimentary form of the FMN-binding TIM barrel according to SCOP. 281 matched cddid_all.tbl CDD pfam04899 pfam04899 113664 MbeD_MobD MbeD/MobD like. The MbeD and MobD proteins are plasmid encoded, and are involved in the plasmids mobilization and transfer in the presence of conjugative plasmids. 70 matched cddid_all.tbl CDD pfam04900 pfam04900 461470 Fcf1 Fcf1. Fcf1 is a nucleolar protein involved in pre-rRNA processing. Depletion of yeast Fcf1 and Fcf2 leads to a decrease in synthesis of the 18S rRNA and results in a deficit in 40S ribosomal subunits. 99 matched cddid_all.tbl CDD pfam04901 pfam04901 461471 RAMP Receptor activity modifying family. The calcitonin-receptor-like receptor can function as either a calcitonin-gene-related peptide or an adrenomedullin receptor. The receptors function is modified by receptor-activity-modifying protein or RAMP. RAMPs are single-transmembrane-domain proteins. 109 matched cddid_all.tbl CDD pfam04902 pfam04902 461472 Nab1 Conserved region in Nab1. Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of transcription factors. This C-terminal region is found only in the Nab1 subfamily. 180 matched cddid_all.tbl CDD pfam04904 pfam04904 461473 NCD1 NAB conserved region 1 (NCD1). Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of transcription factors. This region consists of the N-terminal NAB conserved region 1, which interacts with the EGR1 inhibitory domain (R1). It may also mediate multimerization. 79 matched cddid_all.tbl CDD pfam04905 pfam04905 461474 NCD2 NAB conserved region 2 (NCD2). Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of transcription factors. This family consists of NAB conserved region 2, near the C-terminus of the protein. It is necessary for transcriptional repression by the Nab proteins. It is also required for transcription activation by Nab proteins at Nab-activated promoters. 125 matched cddid_all.tbl CDD pfam04906 pfam04906 461475 Tweety Tweety. The tweety (tty) gene has not been characterized at the protein level. However, it is thought to form a membrane protein with five potential membrane-spanning regions. A number of potential functions have been suggested in. 429 matched cddid_all.tbl CDD pfam04908 pfam04908 398530 SH3BGR SH3-binding, glutamic acid-rich protein. 92 matched cddid_all.tbl CDD pfam04909 pfam04909 428190 Amidohydro_2 Amidohydrolase. These proteins are amidohydrolases that are related to pfam01979. 283 matched cddid_all.tbl CDD pfam04910 pfam04910 461476 Tcf25 Transcriptional repressor TCF25. Members of this family are transcriptional repressors. They may act by increasing histone deacetylase activity at promoter regions. 323 matched cddid_all.tbl CDD pfam04911 pfam04911 428192 ATP-synt_J ATP synthase j chain. 51 matched cddid_all.tbl CDD pfam04912 pfam04912 461477 Dynamitin Dynamitin. Dynamitin is a subunit of the microtubule-dependent motor complex and in implicated in cell adhesion by binding to macrophage-enriched myristoylated alanine-rice C kinase substrate (MacMARCKS). 390 matched cddid_all.tbl CDD pfam04913 pfam04913 282731 Baculo_Y142 Baculovirus Y142 protein. This domain family is found in Baculovirus proteins including protein AC142, which is expressed in the cytoplasm and nucleus throughout infection. It is required for nucleocapsid envelopment in the budding virus to form the occlusion-derived virus and subsequent embedding of virions into polyhedra. 440 matched cddid_all.tbl CDD pfam04914 pfam04914 461478 DltD DltD protein. DltD is and integral membrane protein involved in the biosynthesis of D-alanyl-lipoteichoic acid. This is important in controlling the net ionic charge in lipoteichoic acid (LTA). This family is found in bacteria of the Bacillus/Clostridium group. DltD binds Dcp and ligates it with D-alanine. DltD does not ligate acyl carrier protein (ACP) with D-alanine. It also has thioesterase activity for mischarged D-alanyl-acyl carrier protein (ACP). DltD is thought to be responsible for discriminating between Dcp involved in the D-alanylation of LTA, and ACP involved in fatty acid biosynthesis. 349 matched cddid_all.tbl CDD pfam04916 pfam04916 461479 Phospholip_B Phospholipase B. Phospholipase B (PLB) catalyzes the hydrolytic cleavage of both acylester bonds of glycerophospholipids. This family of PLB enzymes has been identified in mammals, flies and nematodes but not in yeast. In Drosophila this protein was named LAMA for laminin ancestor since it is expressed in the neuronal and glial precursors that surround the lamina. 483 matched cddid_all.tbl CDD pfam04917 pfam04917 309860 Shufflon_N Bacterial shufflon protein, N-terminal constant region. This family represents the high-similarity N-terminal 'constant region' shared by shufflon proteins. 324 matched cddid_all.tbl CDD pfam04919 pfam04919 282736 DUF655 Protein of unknown function (DUF655). This family includes several uncharacterized archaeal proteins. This protein appears to contain two HHH motifs. 181 matched cddid_all.tbl CDD pfam04920 pfam04920 282737 BNYVV_p31 Beet necrotic yellow vein virus, p31. This is a family of hypothetical proteins known as p31, mostly from Beet necrotic yellow vein virus. P31, encoded by RNA4, is involved in efficient vector transmission, symptom severity and silencing suppression in roots. 126 matched cddid_all.tbl CDD pfam04921 pfam04921 461480 XAP5 XAP5, circadian clock regulator. This protein is found in a wide range of eukaryotes. It is a nuclear protein previously suggested to be DNA binding but recent studies suggest that they play a role in the spliceosome complex. In plants, this family is essential for correct circadian clock functioning by acting as a light-quality regulator coordinating the activities of blue and red light signalling pathways during plant growth - inhibiting growth in red light but promoting growth in blue light. 238 matched cddid_all.tbl CDD pfam04922 pfam04922 461481 DIE2_ALG10 DIE2/ALG10 family. The ALG10 protein from Saccharomyces cerevisiae encodes the alpha-1,2 glucosyltransferase of the endoplasmic reticulum. This protein has been characterized in rat as potassium channel regulator 1. 383 matched cddid_all.tbl CDD pfam04923 pfam04923 461482 Ninjurin Ninjurin. Ninjurin (nerve injury-induced protein) is involved in nerve regeneration and in the formation and function in some tissues. 102 matched cddid_all.tbl CDD pfam04924 pfam04924 282741 Pox_A6 Poxvirus A6 protein. 370 matched cddid_all.tbl CDD pfam04925 pfam04925 461483 SHQ1 SHQ1 protein. S. cerevisiae SHQ1 protein is required for SnoRNAs of the box H/ACA Quantitative accumulation (unpublished). 186 matched cddid_all.tbl CDD pfam04926 pfam04926 461484 PAP_RNA-bind Poly(A) polymerase predicted RNA binding domain. Based on its similarity structurally to the RNA recognition motif this domain is thought to be RNA binding. 177 matched cddid_all.tbl CDD pfam04927 pfam04927 461485 SMP Seed maturation protein. Plant seed maturation protein. 59 matched cddid_all.tbl CDD pfam04928 pfam04928 461486 PAP_central Poly(A) polymerase central domain. The central domain of Poly(A) polymerase shares structural similarity with the allosteric activity domain of ribonucleotide reductase R1, which comprises a four-helix bundle and a three-stranded mixed beta- sheet. Even though the two enzymes bind ATP, the ATP-recognition motifs are different. 344 matched cddid_all.tbl CDD pfam04929 pfam04929 282746 Herpes_DNAp_acc Herpes DNA replication accessory factor. Replicative DNA polymerases are capable of polymerizing tens of thousands of nucleotides without dissociating from their DNA templates. The high processivity of these polymerases is dependent upon accessory proteins that bind to the catalytic subunit of the polymerase or to the substrate. The Epstein-Barr virus (EBV) BMRF1 protein is an essential component of the viral DNA polymerase and is absolutely required for lytic virus replication. BMRF1 is also a transactivator. This family is predicted to have a UL42 like structure. 400 matched cddid_all.tbl CDD pfam04930 pfam04930 461487 FUN14 FUN14 family. This family of short proteins are found in eukaryotes and some archaea. Although the function of these proteins is not known they may contain transmembrane helices. 95 matched cddid_all.tbl CDD pfam04931 pfam04931 461488 DNA_pol_phi DNA polymerase phi. This family includes the fifth essential DNA polymerase in yeast EC:2.7.7.7. Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units. 765 matched cddid_all.tbl CDD pfam04932 pfam04932 461489 Wzy_C O-Antigen ligase. This group of bacterial proteins is involved in the synthesis of O-antigen, a lipopolysaccharide found in the outer membrane in gram-negative bacteria. This family includes O-antigen ligases such as E. coli RfaL. 148 matched cddid_all.tbl CDD pfam04934 pfam04934 461490 Med6 MED6 mediator sub complex component. Component of RNA polymerase II holoenzyme and mediator sub complex. 134 matched cddid_all.tbl CDD pfam04935 pfam04935 461491 SURF6 Surfeit locus protein 6. The surfeit locus protein SURF-6 is shown to be a component of the nucleolar matrix and has a strong binding capacity for nucleic acids. 197 matched cddid_all.tbl CDD pfam04936 pfam04936 282752 DUF658 Protein of unknown function (DUF658). Protein of unknown function found in Lactococcus lactis bacteriophages. 186 matched cddid_all.tbl CDD pfam04937 pfam04937 461492 DUF659 Protein of unknown function (DUF 659). Transposase-like protein with no known function. 152 matched cddid_all.tbl CDD pfam04938 pfam04938 461493 SIP1 Survival motor neuron (SMN) interacting protein 1 (SIP1). Survival motor neuron (SMN) interacting protein 1 (SIP1) interacts with SMN protein and plays a crucial role in the biogenesis of spliceosomes. There is evidence that the protein is linked to spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis(ALS) in humans. 211 matched cddid_all.tbl CDD pfam04939 pfam04939 461494 RRS1 Ribosome biogenesis regulatory protein (RRS1). This family consists of several eukaryotic ribosome biogenesis regulatory (RRS1) proteins. RRS1 is a nuclear protein that is essential for the maturation of 25 S rRNA and the 60 S ribosomal subunit assembly in Saccharomyces cerevisiae. 163 matched cddid_all.tbl CDD pfam04940 pfam04940 461495 BLUF Sensors of blue-light using FAD. The BLUF domain has been shown to bind FAD in the AppA protein. AppA is involved in the repression of photosynthesis genes in response to blue-light. 89 matched cddid_all.tbl CDD pfam04941 pfam04941 282757 LEF-8 Late expression factor 8 (LEF-8). Late expression factor 8 (LEF-8) is one of the primary components of RNA polymerase produced by polyhedrosis viruses. LEF-8 shows homology to the second largest subunit of prokaryotic DNA-directed RNA polymerase. 730 matched cddid_all.tbl CDD pfam04942 pfam04942 428212 CC CC domain. This short domain contains four conserved cysteines that probably for two disulphide bonds. The domain is named after the characteriztic CC motif. 34 matched cddid_all.tbl CDD pfam04943 pfam04943 282759 Pox_F11 Poxvirus F11 protein. The protein F11 is an early virus protein. 409 matched cddid_all.tbl CDD pfam04945 pfam04945 461496 YHS YHS domain. This short presumed domain is about 50 amino acid residues long. It often contains two cysteines that may be functionally important. This domain is found in copper transporting ATPases, some phenol hydroxylases and in a set of uncharacterized membrane proteins including Swiss:Q9CNI0. This domain is named after three of the most conserved amino acids it contains. The domain may be metal binding, possibly copper ions. This domain is duplicated in some copper transporting ATPases. 46 matched cddid_all.tbl CDD pfam04947 pfam04947 282761 Pox_VLTF3 Poxvirus Late Transcription Factor VLTF3 like. Members of this family are approximately 26 KDa, and are involved in trans-activator of late transcription. 168 matched cddid_all.tbl CDD pfam04948 pfam04948 282762 Pox_A51 Poxvirus A51 protein. 337 matched cddid_all.tbl CDD pfam04949 pfam04949 398553 Transcrip_act Transcriptional activator. This family of proteins may act as a transcriptional activator. It plays a role in stress response in plants. 154 matched cddid_all.tbl CDD pfam04950 pfam04950 461497 RIBIOP_C 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal. RIBIOP_C is a family of eukaryotic proteins from the C-terminus of pre-rRNA-processing protein or ribosome biogenesis proteins BMS1 and TSR1. These proteins act, in the nucleolus, as a molecular switch during maturation of the 40S ribosomal subunit. This domain, domain IV of translation elongation factor selb, adopts the same fold as translation proteins such as domain II of GTP-elongation factor Tu proteins. 284 matched cddid_all.tbl CDD pfam04951 pfam04951 428215 Peptidase_M55 D-aminopeptidase. Bacillus subtilis DppA is a binuclear zinc-dependent, D-specific aminopeptidase. The structure reveals that DppA is a new example of a 'self-compartmentalising protease', a family of proteolytic complexes. Proteasomes are the most extensively studied representatives of this family. The DppA enzyme is composed of identical 30 kDa subunits organized in a decamer with 52 point-group symmetry. A 20 A wide channel runs through the complex, giving access to a central chamber holding the active sites. The structure shows DppA to be a prototype of a new family of metalloaminopeptidases characterized by the SXDXEG key sequence. The only known substrates are D-ala-D-ala and D-ala-gly-gly. 263 matched cddid_all.tbl CDD pfam04952 pfam04952 428216 AstE_AspA Succinylglutamate desuccinylase / Aspartoacylase family. This family includes Succinylglutamate desuccinylase EC:3.1.-.- that catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway. The family also include aspartoacylase EC:3.5.1.15 which cleaves acylaspartate into a fatty acid and aspartate. Mutations in Swiss:P45381 lead to Canavan disease. This family is probably structurally related to pfam00246 (Bateman A pers. obs.). 289 matched cddid_all.tbl CDD pfam04954 pfam04954 428217 SIP Siderophore-interacting protein. 119 matched cddid_all.tbl CDD pfam04955 pfam04955 428218 HupE_UreJ HupE / UreJ protein. This family of proteins are hydrogenase / urease accessory proteins. The alignment contains many conserved histidines that are likely to be involved in nickel binding. The members usually have five membrane-spanning regions. 179 matched cddid_all.tbl CDD pfam04956 pfam04956 398559 TrbC TrbC/VIRB2 pilin. TrbC is a pilin found in bacterial type IV secretion systems. The protein undergoes three processing steps before gaining its mature cyclic structure. This family also contains VIRB2 type IV secretion proteins. This alignment contains two predicted transmembrane helices. 98 matched cddid_all.tbl CDD pfam04957 pfam04957 428219 RMF Ribosome modulation factor. This protein associates with 70s ribosomes and converts them to a dimeric form (100S ribosomes) which appear during the transition from the exponential growth phase to the stationary phase of Escherichia coli cells. 54 matched cddid_all.tbl CDD pfam04958 pfam04958 428220 AstA Arginine N-succinyltransferase beta subunit. Arginine N-succinyltransferase EC:2.3.1.109 catalyzes the transfer of succinyl-CoA to arginine to produce succinyl-arginine. This is the first step in arginine catabolism by the arginine succinyltransferase pathway. 336 matched cddid_all.tbl CDD pfam04959 pfam04959 461498 ARS2 Arsenite-resistance protein 2. Arsenite is a carcinogenic compound which can act as a co-mutagen by inhibiting DNA repair. Arsenite-resistance protein 2 is thought to play a role in arsenite resistance. 195 matched cddid_all.tbl CDD pfam04960 pfam04960 461499 Glutaminase Glutaminase. This family of enzymes deaminates glutamine to glutamate EC:3.5.1.2. 283 matched cddid_all.tbl CDD pfam04961 pfam04961 461500 FTCD_C Formiminotransferase-cyclodeaminase. Members of this family are thought to be Formiminotransferase- cyclodeaminase enzymes EC:4.3.1.4. This domain is found in the C-terminus of the bifunctional animal members of the family. 182 matched cddid_all.tbl CDD pfam04962 pfam04962 398565 KduI KduI/IolB family. This family includes the 5-keto 4-deoxyuronate isomerase enzyme EC:5.3.1.17 that is involved in pectin degradation. This family aldo includes bacterial Myo-inositol catabolism (IolB) proteins. The Bacillus subtilis inositol operon (iolABCDEFGHIJ) is involved in myo-inositol catabolism. Glucose repression of the iol operon induced by inositol is exerted through catabolite repression mediated by CcpA and the iol induction system mediated by IolR. The exact function of IolB is unknown. Members of this family possess a Cupin like structure. 260 matched cddid_all.tbl CDD pfam04963 pfam04963 461501 Sigma54_CBD Sigma-54 factor, core binding domain. This domain makes a direct interaction with the core RNA polymerase, to form an enhancer dependent holoenzyme. The centre of this domain contains a very weak similarity to a helix-turn-helix motif which may represent the other DNA binding domain. 182 matched cddid_all.tbl CDD pfam04964 pfam04964 398567 Flp_Fap Flp/Fap pilin component. 46 matched cddid_all.tbl CDD pfam04965 pfam04965 428225 GPW_gp25 Baseplate wedge protein gp25. This family represents T4 phage gp25 protein and gp25-like proteins, found in several systems, including contractile tail bacteriophages, the type VI secretion system (T6SS) and R-type pyocins, which constitute a multiprotein tubular apparatus to attach to and penetrate host cell membranes. Gp25 is a component of the conserved wedge in the inner part of the baseplate and serves as a nucleus for sheath polymerization, playing a critical role in sheath assembly and contraction. The EPR motif (Glu-Pro-Arg, residues 85-87 of gp25) is conserved across all members of the family including orthologs from the RpoS-mediated general stress response system (called IraD). This motif interacts with the 'core bundle' composed of orthologs of T4 gp6 and gp7 proteins in contractile injection systems. 93 matched cddid_all.tbl CDD pfam04966 pfam04966 335962 OprB Carbohydrate-selective porin, OprB family. 373 matched cddid_all.tbl CDD pfam04967 pfam04967 282780 HTH_10 HTH DNA binding domain. 53 matched cddid_all.tbl CDD pfam04968 pfam04968 461502 CHORD CHORD. CHORD represents a Zn binding domain. Silencing of the C. elegans CHORD-containing gene results in semisterility and embryo lethality, suggesting an essential function of the wild-type gene in nematode development. 62 matched cddid_all.tbl CDD pfam04969 pfam04969 461503 CS CS domain. The CS and CHORD (pfam04968) are fused into a single polypeptide chain in metazoans but are found in separate proteins in plants; this is thought to be indicative of an interaction between CS and CHORD. It has been suggested that the CS domain is a binding module for HSP90, implying that CS domain-containing proteins are involved in recruiting heat shock proteins to multiprotein assemblies. Two CS domains are found at the N-terminus of Ubiquitin carboxyl-terminal hydrolase 19 (USP19), these domains may play a role in the interaction of USP19 with cellular inhibitor of apoptosis 2. 76 matched cddid_all.tbl CDD pfam04970 pfam04970 398571 LRAT Lecithin retinol acyltransferase. The full-length members of this family, eg Swiss:P53816, are representatives of a novel class II tumour-suppressor family, designated as H-REV107-like. This domain is the catalytic N-terminal proline-rich region of the protein. The downstream region is a putative C-terminal transmembrane domain which is found to be crucial for cellular localization, but not necessary for the enzyme activity. H-REV107-like proteins are homologous to lecithin retinol acyltransferase (LRAT), an enzyme that catalyzes the transfer of the sn-1 acyl group of phosphatidylcholine to all-trans-retinol and forming a retinyl ester. 106 matched cddid_all.tbl CDD pfam04971 pfam04971 428228 Phage_holin_2_1 Bacteriophage P21 holin S. Phage_holin_2_1 is a family of small hydrophobic holin proteins with one or more transmembrane domains. Members of this family fall into the holin superfamily II, and Phage 21 S holin is the prototype for this superfamily. It has two transmembrane segments with both the N- and C-termini on the cytoplasmic side of the inner membrane in E. coli. Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis. It is thought that the temporal precision of holin-mediated lysis may occur through the build up of a holin oligomer which causes the lysis. 64 matched cddid_all.tbl CDD pfam04972 pfam04972 428229 BON BON domain. This domain is found in a family of osmotic shock protection proteins. It is also found in some Secretins and a group of potential haemolysins. Its likely function is attachment to phospholipid membranes. 69 matched cddid_all.tbl CDD pfam04973 pfam04973 428230 NMN_transporter Nicotinamide mononucleotide transporter. Members of this family are integral membrane proteins that are involved in transport of nicotinamide mononucleotide. 176 matched cddid_all.tbl CDD pfam04976 pfam04976 398575 DmsC DMSO reductase anchor subunit (DmsC). The terminal electron transfer enzyme Me2SO reductase of Escherichia coli is a heterotrimeric enzyme composed of a membrane extrinsic catalytic dimer (DmsAB) and a membrane intrinsic polytopic anchor subunit (DmsC). 275 matched cddid_all.tbl CDD pfam04977 pfam04977 428231 DivIC Septum formation initiator. DivIC from B. subtilis is necessary for both vegetative and sporulation septum formation. These proteins are mainly composed of an amino terminal coiled-coil. 69 matched cddid_all.tbl CDD pfam04978 pfam04978 428232 DUF664 Protein of unknown function (DUF664). This family is commonly found in Streptomyces coelicolor and is of unknown function. These proteins contain several conserved histidines at their N-terminus that may form a metal binding site. 148 matched cddid_all.tbl CDD pfam04979 pfam04979 461504 IPP-2 Protein phosphatase inhibitor 2 (IPP-2). Protein phosphotase inhibitor 2 (IPP-2) is a phosphoprotein conserved among all eukaryotes, and it appears in both the nucleus and cytoplasm of tissue culture cells. 130 matched cddid_all.tbl CDD pfam04981 pfam04981 461505 NMD3 NMD3 family. The NMD3 protein is involved in nonsense mediated mRNA decay. This amino terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway. 242 matched cddid_all.tbl CDD pfam04982 pfam04982 461506 HPP HPP family. These proteins are integral membrane proteins with four transmembrane spanning helices. The most conserved region of the alignment is a motif HPP. The function of these proteins is uncertain but they may be transporters. 122 matched cddid_all.tbl CDD pfam04983 pfam04983 461507 RNA_pol_Rpb1_3 RNA polymerase Rpb1, domain 3. RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking. 158 matched cddid_all.tbl CDD pfam04984 pfam04984 428236 Phage_sheath_1 Phage tail sheath protein subtilisin-like domain. This entry represents the second domain in a variety of phage tail sheath proteins. According to ECOD this domain has a subtilisin-like structure. 157 matched cddid_all.tbl CDD pfam04985 pfam04985 428237 Phage_tube Phage tail tube protein FII. The major structural components of the contractile tail of bacteriophage P2 are proteins FI and FII, which are believed to be the tail sheath and tube proteins, respectively. 161 matched cddid_all.tbl CDD pfam04986 pfam04986 428238 Y2_Tnp Putative transposase. Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases IS1294 and IS801. This is a rolling-circle transposase. 183 matched cddid_all.tbl CDD pfam04987 pfam04987 461508 PigN Phosphatidylinositolglycan class N (PIG-N). Phosphatidylinositolglycan class N (PIG-N) is a mammalian homolog of the yeast protein MCD4P and is expressed in the endoplasmic reticulum. PIG-N is essential for glycosylphosphatidylinositol anchor synthesis. Glycosylphosphatidylinositol (GPI)-anchored proteins are cell surface-localized proteins that serve many important cellular functions. 454 matched cddid_all.tbl CDD pfam04988 pfam04988 461509 AKAP95 A-kinase anchoring protein 95 (AKAP95). A-kinase (or PKA)-anchoring protein AKAP95 is implicated in mitotic chromosome condensation by acting as a targeting molecule for the condensin complex. The protein contains two zinc fingers which are thought to mediate the binding of AKAP95 to DNA. 136 matched cddid_all.tbl CDD pfam04989 pfam04989 428241 CmcI Cephalosporin hydroxylase. Members of this family are about 220 amino acids long. The CmcI protein is presumed to represent the cephalosporin-7--hydroxylase. However this has not been experimentally verified. 206 matched cddid_all.tbl CDD pfam04990 pfam04990 461510 RNA_pol_Rpb1_7 RNA polymerase Rpb1, domain 7. RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (pfam04561). 136 matched cddid_all.tbl CDD pfam04991 pfam04991 428243 LicD LicD family. The LICD family of proteins show high sequence similarity and are involved in phosphorylcholine metabolism. There is evidence to show that LicD2 mutants have a reduced ability to take up choline, have decreased ability to adhere to host cells and are less virulent. These proteins are part of the nucleotidyltransferase superfamily. 228 matched cddid_all.tbl CDD pfam04992 pfam04992 461511 RNA_pol_Rpb1_6 RNA polymerase Rpb1, domain 6. RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II. 188 matched cddid_all.tbl CDD pfam04993 pfam04993 428245 TfoX_N TfoX N-terminal domain. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes. This family corresponds to the N-terminal presumed domain of TfoX. The domain is found as an isolated domain in some proteins suggesting this is an autonomous domain. 91 matched cddid_all.tbl CDD pfam04994 pfam04994 461512 TfoX_C TfoX C-terminal domain. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found associated with pfam00383 in Swiss:Q9JZR1. It is also found as an isolated domain in some proteins suggesting this is an autonomous domain. 77 matched cddid_all.tbl CDD pfam04995 pfam04995 428247 CcmD Heme exporter protein D (CcmD). The CcmD protein is part of a C-type cytochrome biogenesis operon. The exact function of this protein is uncertain. It has been proposed that CcmC, CcmD and CcmE interact directly with each other, establishing a cytoplasm to periplasm haem delivery pathway for cytochrome c maturation. This protein is found fused to CcmE in Swiss:P52224. These proteins contain a predicted transmembrane helix. 44 matched cddid_all.tbl CDD pfam04996 pfam04996 428248 AstB Succinylarginine dihydrolase. This enzyme transforms N(2)-succinylglutamate into succinate and glutamate. This is the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway. 442 matched cddid_all.tbl CDD pfam04997 pfam04997 398595 RNA_pol_Rpb1_1 RNA polymerase Rpb1, domain 1. RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand. 320 matched cddid_all.tbl CDD pfam04998 pfam04998 398596 RNA_pol_Rpb1_5 RNA polymerase Rpb1, domain 5. RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound. 516 matched cddid_all.tbl CDD pfam04999 pfam04999 428249 FtsL Cell division protein FtsL. In Escherichia coli, nine gene products are known to be essential for assembly of the division septum. One of these, FtsL, is a bitopic membrane protein whose precise function is not understood. It has been proposed that FtsL interacts with the DivIC protein pfam04977, however this interaction may be indirect. 97 matched cddid_all.tbl CDD pfam05000 pfam05000 398598 RNA_pol_Rpb1_4 RNA polymerase Rpb1, domain 4. RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors. 108 matched cddid_all.tbl CDD pfam05001 pfam05001 461513 RNA_pol_Rpb1_R RNA polymerase Rpb1 C-terminal repeat. The repetitive C-terminal domain (CTD) of Rpb1 (RNA polymerase Pol II) plays a critical role in the regulation of gene expression. The activity of the CTD is dependent on its state of phosphorylation. 12 matched cddid_all.tbl CDD pfam05002 pfam05002 461514 SGS SGS domain. This domain was thought to be unique to the SGT1-like proteins, but is also found in calcyclin binding proteins. 81 matched cddid_all.tbl CDD pfam05003 pfam05003 428251 DUF668 Protein of unknown function (DUF668). This entry represents the C-terminal domain of PSI proteins from Arabidopsis. This domain is found associated with pfam11961. PSI1 was identified as a gene that is co-expressed with the phytosulfokine (PSK) receptor genes PSKR1 and PSKR2 in Arabidopsis thaliana. PSI proteins are plant-specific and promote growth. 88 matched cddid_all.tbl CDD pfam05004 pfam05004 461515 IFRD Interferon-related developmental regulator (IFRD). Interferon-related developmental regulator (IFRD1) is the human homolog of the rat early response protein PC4 and its murine homolog TIS7. The exact function of IFRD1 is unknown but it has been shown that PC4 is necessary to muscle differentiation and that it might have a role in signal transduction. This family also contains IFRD2 and its murine equivalent SKMc15 which are highly expressed soon after gastrulation and in the hepatic primordium, suggesting an involvement in early hematopoiesis. 297 matched cddid_all.tbl CDD pfam05005 pfam05005 428253 Ocnus Janus/Ocnus family (Ocnus). This family is comprised of the Ocnus, Janus-A and Janus-B proteins. These proteins have been found to be testes specific in Drosophila melanogaster. 108 matched cddid_all.tbl CDD pfam05006 pfam05006 368236 PIF3 Per os infectivity factor 3. This family contains viral proteins and includes Baculovirus Per os infectivity factor 3 (PIF3). PIF3 forms a complex on the occlusion-derived virus surface with PIF1, PIF2, and P74 which has an essential function in the initial stages of baculovirus oral infection. 149 matched cddid_all.tbl CDD pfam05007 pfam05007 252941 Mannosyl_trans Mannosyltransferase (PIG-M). PIG-M has a DXD motif. The DXD motif is found in many glycosyltransferases that utilize nucleotide sugars. It is thought that the motif is involved in the binding of a manganese ion that is required for association of the enzymes with nucleotide sugar substrates. 259 matched cddid_all.tbl CDD pfam05008 pfam05008 461516 V-SNARE Vesicle transport v-SNARE protein N-terminus. V-SNARE proteins are required for protein traffic between eukaryotic organelles. The v-SNAREs on transport vesicles interact with t-SNAREs on target membranes in order to facilitate this. This domain is the N-terminal half of the V-Snare proteins. 79 matched cddid_all.tbl CDD pfam05009 pfam05009 282817 EBV-NA3 Epstein-Barr virus nuclear antigen 3 (EBNA-3). This family contains EBNA-3A, -3B, and -3C which are latent infection nuclear proteins important for Epstein-Barr virus (EBV)-induced B-cell immortalization and the immune response to EBV infection. 254 matched cddid_all.tbl CDD pfam05010 pfam05010 461517 TACC_C Transforming acidic coiled-coil-containing protein (TACC), C-terminal. This entry represents a C-terminal domain found in the the proteins TACC 1, 2 and 3 (TACC1-3). TACC1 is found concentrated in the centrosomes of eukaryotes which may play a conserved role in organizing centrosomal microtubules. The human TACC proteins have been linked to cancer and TACC2 has been identified as a possible tumour suppressor (AZU-1). TACC 3 from Xenopus laevis, also known as maskin, associates XMAP215 and promotes efficient microtubule elongation during mitosis. Maskin is also found to bind CPEB and elF-4E. Interestingly, the functional homolog (Alp7) in Schizosaccharomyces pombe (not included in this entry) has been shown to be required for organization of bipolar spindles. 201 matched cddid_all.tbl CDD pfam05011 pfam05011 461518 DBR1 Lariat debranching enzyme, C-terminal domain. This presumed domain is found at the C-terminus of lariat debranching enzyme. This domain is always found in association with pfam00149. 136 matched cddid_all.tbl CDD pfam05013 pfam05013 461519 FGase N-formylglutamate amidohydrolase. Formylglutamate amidohydrolase (FGase) catalyzes the terminal reaction in the five-step pathway for histidine utilization in Pseudomonas putida. By this action, N-formyl-L-glutamate (FG) is hydrolysed to produce L-glutamate plus formate. 219 matched cddid_all.tbl CDD pfam05014 pfam05014 461520 Nuc_deoxyrib_tr Nucleoside 2-deoxyribosyltransferase. Nucleoside 2-deoxyribosyltransferase EC:2.4.2.6 catalyzes the cleavage of the glycosidic bonds of 2`-deoxyribonucleosides. 117 matched cddid_all.tbl CDD pfam05015 pfam05015 398609 HigB-like_toxin RelE-like toxin of type II toxin-antitoxin system HigB. This family carries several different examples of type II bacterial toxins of toxin-antitoxin systems including many HigB-like ones. The fold is referred to as the RelE/YoeB/Txe/Yeeu fold suggesting all examples of these are present in this family. Several plasmids with proteic killer gene-systems have been reported. All of them encode a stable toxin and an unstable antidote. Upon loss of the plasmid, the less stable inhibitor is inactivated more rapidly than the toxin, allowing the toxin to be activated. The activation of these systems results in cell filamentation and cessation of viable cell production. It has been verified that both the stable killer and the unstable inhibitor of the systems are short polypeptides. This family corresponds to the toxin. 93 matched cddid_all.tbl CDD pfam05016 pfam05016 398610 ParE_toxin ParE toxin of type II toxin-antitoxin system, parDE. ParE is the toxin family of a type II toxin-antitoxin family. It is toxic towards DNA gyrase, but is neutralized by the antitoxin ParD. The family also encompasses RelE/ParE described in. 91 matched cddid_all.tbl CDD pfam05017 pfam05017 368241 TMP TMP repeat. This short repeat consists of the motif WXXh where X can be any residue and h is a hydrophobic residue. The repeat is name TMP after its occurrence in the tape measure protein (TMP). Tape measure protein is a component of phage tail and probably forms a beta-helix. Truncated forms of TMP lead to shortened tail fibres. This repeat is also found in non-phage proteins where it may play a structural role. 11 matched cddid_all.tbl CDD pfam05018 pfam05018 461521 CFA20_dom CFA20 domain. This domain is characteriztic of cilia- and flagella-associated protein 20 (CFA20). CFA20 is a cilium- and flagellum-specific protein that plays a role in axonemal structure organization and motility. In Chlamydomonas reinhardtii, it stabilizes outer doublet microtubules (DMTs) of the axoneme and may work as a scaffold for intratubular proteins, such as tektin and PACRG, to produce the beak structures in DMT1. Other proteins contain a domain with homology to CFA20. WDR90/POC16 contains such a domain in its N terminus, followed by a large C-terminal domain with multiple WD40 repeats. This domain is also present in the N terminus of uncharacterized protein C3orf67. 185 matched cddid_all.tbl CDD pfam05019 pfam05019 461522 Coq4 Coenzyme Q (ubiquinone) biosynthesis protein Coq4. Coq4p was shown to peripherally associate with the matrix face of the mitochondrial inner membrane. The putative mitochondrial- targeting sequence present at the amino-terminus of the polypeptide efficiently imported it to mitochondria. The function of Coq4p is unknown, although its presence is required to maintain a steady-state level of Coq7p, another component of the Q biosynthetic pathway. The overall structure of Coq4 is alpha helical and shows resemblance to haemoglobin/myoglobin (information from TOPSAN). 213 matched cddid_all.tbl CDD pfam05020 pfam05020 461523 zf-NPL4 NPL4 family, putative zinc binding region. The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterized step in ER-associated degradation after ubiquitination of target proteins but before their recognition by the 26S proteasome. This region of the protein contains possibly two zinc binding motifs (Bateman A pers. obs.). Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing. 145 matched cddid_all.tbl CDD pfam05021 pfam05021 461524 NPL4 NPL4 family. The HRD4 gene was identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterized step in ER-associated degradation after ubiquitination of target proteins but before their recognition by the 26S proteasome. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing. 309 matched cddid_all.tbl CDD pfam05022 pfam05022 461525 SRP40_C SRP40, C-terminal domain. This presumed domain is found at the C-terminus of the S. cerevisiae SRP40 protein and its homologs. SRP40/nopp40 is a chaperone involved in nucleocytoplasmic transport. SRP40 is also a suppressor of mutant AC40 subunit of RNA polymerase I and III. 75 matched cddid_all.tbl CDD pfam05023 pfam05023 461526 Phytochelatin Phytochelatin synthase. Phytochelatin synthase is the enzyme responsible for the synthesis of heavy-metal-binding peptides (phytochelatins) from glutathione and related thiols. The crystal structure of a member of this family shows it to possess a papain fold. The enzyme catalyzes the deglycination of a GSH donor molecule. The enzyme contains a catalytic triad of cysteine, histidine and aspartate residues. 206 matched cddid_all.tbl CDD pfam05024 pfam05024 461527 Gpi1 N-acetylglucosaminyl transferase component (Gpi1). Glycosylphosphatidylinositol (GPI) represents an important anchoring molecule for cell surface proteins.The first step in its synthesis is the transfer of N-acetylglucosamine (GlcNAc) from UDP-N-acetylglucosamine to phosphatidylinositol (PI). This chemically simple step is genetically complex because three or four genes are required in both yeast (GPI1, GPI2 and GPI3) and mammals (GPI1, PIG A, PIG H and PIG C), respectively. 273 matched cddid_all.tbl CDD pfam05025 pfam05025 428264 RbsD_FucU RbsD / FucU transport protein family. The Escherichia coli high-affinity ribose-transport system consists of six proteins encoded by the rbs operon (rbsD, rbsA, rbsC, rbsB, rbsK and rbsR). RbsD was originally thought to be a high affinity ribose transport protein, but further analysis shows that it is a D-ribose pyranase. It catalyzes the interconversion of beta-pyran and beta-furan forms of D-ribose. It also catalyzes the conversion between beta-allofuranose and beta-allopyranose. This family also includes FucU a component of the fucose operon and is a L-fucose mutarotase, involved in the anomeric conversion of L-fucose. It also exhibits a pyranase activity for D-ribose. Both have been classified in the RbsD/FucU family of proteins. Members of this family are ubiquitous having been found in organizms from eubacteria to mammals. 132 matched cddid_all.tbl CDD pfam05026 pfam05026 428265 DCP2 Dcp2, box A domain. This domain is always found to the amino terminal side of pfam00293. This domain is specific to mRNA decapping protein 2 and this region has been termed Box A. Removal of the cap structure is catalyzed by the Dcp1-Dcp2 complex. 83 matched cddid_all.tbl CDD pfam05028 pfam05028 461528 PARG_cat Poly (ADP-ribose) glycohydrolase (PARG). Poly(ADP-ribose) glycohydrolase (PARG), is a ubiquitously expressed exo- and endoglycohydrolase which mediates oxidative and excitotoxic neuronal death. 329 matched cddid_all.tbl CDD pfam05029 pfam05029 461529 TIMELESS_C Timeless PAB domain. The timeless (tim) gene is essential for circadian function in Drosophila. Putative homologs of Drosophila tim have been identified in both mice and humans (mTim and hTIM, respectively). Mammalian TIM is not the true orthologue of Drosophila TIM, but is the likely orthologue of a fly gene, timeout (also called tim-2). mTim has been shown to be essential for embryonic development, but does not have substantiated circadian function. This entry corresponds to the PAB (PARP-1-binding domain). 87 matched cddid_all.tbl CDD pfam05030 pfam05030 428268 SSXT SSXT protein (N-terminal region). The SSXT or SS18 protein is involved in synovial sarcoma in humans. A SYT-SSX fusion gene resulting from the chromosomal translocation t(X;18) (p11;q11) is characteriztic of synovial sarcomas. This translocation fuses the SSXT (SYT) gene from chromosome 18 to either of two homologous genes at Xp11, SSX1 or SSX2. 60 matched cddid_all.tbl CDD pfam05031 pfam05031 428269 NEAT Iron Transport-associated domain. NEAT domains are heme and/or hemoprotein-binding modules highly conserved in secondary structure. They have roles in hemoprotein binding, heme extraction and heme transfer 116 matched cddid_all.tbl CDD pfam05032 pfam05032 398624 Spo12 Spo12 family. This family of proteins includes Spo12 from S. cerevisiae. The Spo12 protein plays a regulatory role in two of the most fundamental processes of biology, mitosis and meiosis, and yet its biochemical function remains elusive. Spo12 is a nuclear protein. Spo12 is a component of the FEAR (Cdc fourteen early anaphase release) regulatory network, that promotes Cdc14 release from the nucleolus during early anaphase. The FEAR network is comprised of the polo kinase Cdc5, the separase Esp1, the kinetochore-associated protein Slk19, and Spo12. 33 matched cddid_all.tbl CDD pfam05033 pfam05033 461530 Pre-SET Pre-SET motif. This protein motif is a zinc binding motif. It contains 9 conserved cysteines that coordinate three zinc ions. It is thought that this region plays a structural role in stabilising SET domains. 99 matched cddid_all.tbl CDD pfam05034 pfam05034 398626 MAAL_N Methylaspartate ammonia-lyase N-terminus. Methylaspartate ammonia-lyase EC:4.3.1.2 catalyzes the second step of fermentation of glutamate. It is a homodimer. This family represents the N-terminal region of Methylaspartate ammonia-lyase. This domain is structurally related to pfam03952. This domain is associated with the catalytic domain pfam07476. 160 matched cddid_all.tbl CDD pfam05035 pfam05035 428271 DGOK 2-keto-3-deoxy-galactonokinase. 2-keto-3-deoxy-galactonokinase EC:2.7.1.58 catalyzes the second step in D-galactonate degradation. 286 matched cddid_all.tbl CDD pfam05036 pfam05036 461531 SPOR SPOR domain. Bacterial SPOR domains bind peptidoglycan (PG) and target proteins to the cell division site by binding to denuded glycan strands that lack stem peptides. This 70 residue domain is composed of two 35 residue repeats found in proteins involved in sporulation and cell division such as FtsN, DedD, and CwlM. This domain is involved in binding peptidoglycan. Two tandem repeats fold into a pseudo-2-fold symmetric single-domain structure containing numerous contacts between the repeats. FtsN is an essential cell division protein with a simple bitopic topology, a short N-terminal cytoplasmic segment fused to a large carboxy periplasmic domain through a single transmembrane domain. These repeats lay at the periplasmic C-terminus. FtsN localizes to the septum ring complex. 76 matched cddid_all.tbl CDD pfam05037 pfam05037 398629 DUF669 Protein of unknown function (DUF669). Members of this family are found in various phage proteins. 126 matched cddid_all.tbl CDD pfam05038 pfam05038 461532 Cytochrom_B558a Cytochrome Cytochrome b558 alpha-subunit. Cytochrome b-245 light chain (p22-phox) is one of the key electron transfer elements of the NADPH oxidase in phagocytes. 184 matched cddid_all.tbl CDD pfam05039 pfam05039 428273 Agouti Agouti protein. The agouti protein regulates pigmentation in the mouse hair follicle producing a black hair with a subapical yellow band. A highly homologous protein agouti signal protein (ASIP)is present in humans and is expressed at highest levels in adipose tissue where it may play a role in energy homeostasis and possibly human pigmentation. 43 matched cddid_all.tbl CDD pfam05041 pfam05041 461533 Pecanex_C Pecanex protein (C-terminus). This family consists of C terminal region of the pecanex protein homologs. The pecanex protein is a maternal-effect neurogenic gene found in Drosophila. 227 matched cddid_all.tbl CDD pfam05042 pfam05042 428275 Caleosin Caleosin related protein. This family contains plant proteins related to caleosin. Caleosins contain calcium-binding domains and have an oleosin-like association with lipid bodies. Caleosins are present at relatively low levels and are mainly bound to microsomal membrane fractions at the early stages of seed development. As the seeds mature, overall levels of caleosins increased dramatically and they were associated almost exclusively with storage lipid bodies. This family is probably related to EF hands pfam00036. 169 matched cddid_all.tbl CDD pfam05043 pfam05043 428276 Mga Mga helix-turn-helix domain. M regulator protein trans-acting positive regulator (Mga) is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions. This domain is found in the centre of the Mga proteins. This family also contains a number of bacterial RofA transcriptional regulators that seem to be largely restricted to streptococci. These proteins have been shown to regulate the expression of important bacterial adhesins. This is presumably a DNA-binding domain. 87 matched cddid_all.tbl CDD pfam05044 pfam05044 461534 HPD Homeo-prospero domain. Prospero is a large drosophila transcription factor protein that is expressed in all neural lineages of drosophila embryos. It is needed for correct expression of several neural proteins and in determining the cell fates of neural stem cells. homologs of prospero are found in a wide range of animals including humans with the highest level of similarity being found in the C-terminal 160 amino acids. This region was identified as containing an atypical homeobox domain followed by a prospero domain. However, the structure shows that these two regions form a single stable structural domain as defined here. This homeo-prospero domain binds to DNA. 154 matched cddid_all.tbl CDD pfam05045 pfam05045 428278 RgpF Rhamnan synthesis protein F. This family consists of a group of proteins which are related to the Streptococcus rhamnose-glucose polysaccharide assembly protein (RgpF). Rhamnan backbones are found in several O polysaccharides of phytopathogenic bacteria and are regarded as pathogenic factors. 500 matched cddid_all.tbl CDD pfam05046 pfam05046 461535 Img2 Mitochondrial large subunit ribosomal protein (Img2). This family of proteins have been identified as part of the mitochondrial large ribosomal subunit in yeast. 83 matched cddid_all.tbl CDD pfam05047 pfam05047 428280 L51_S25_CI-B8 Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain. The proteins in this family are located in the mitochondrion. The family includes ribosomal protein L51, and S25. This family also includes mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) EC:1.6.5.3. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins. Structurally related to thioredoxin-fold. 52 matched cddid_all.tbl CDD pfam05048 pfam05048 428281 NosD Periplasmic copper-binding protein (NosD). NosD is a periplasmic protein which is thought to insert copper into the exported reductase apoenzyme (NosZ). This region forms a parallel beta helix domain. 215 matched cddid_all.tbl CDD pfam05049 pfam05049 461536 IIGP Interferon-inducible GTPase (IIGP). Interferon-inducible GTPase (IIGP) is thought to play a role in in intracellular defence. IIGP is predominantly associated with the Golgi apparatus and also localizes to the endoplasmic reticulum and exerts a distinct role in IFN-induced intracellular membrane trafficking or processing. 375 matched cddid_all.tbl CDD pfam05050 pfam05050 428282 Methyltransf_21 Methyltransferase FkbM domain. This family has members from bacteria to human, and appears to be a methyltransferase. 170 matched cddid_all.tbl CDD pfam05051 pfam05051 428283 COX17 Cytochrome C oxidase copper chaperone (COX17). Cox17 is essential for the assembly of functional cytochrome c oxidase (CCO) and for delivery of copper ions to the mitochondrion for insertion into the enzyme in yeast. The structure of Cox17 shows the protein to have an unstructured N-terminal region followed by two helices and several unstructured C-terminal residues. The Cu(I) binding site has been modelled as two-coordinate with ligation by conserved residues Cys23 and Cys26. 47 matched cddid_all.tbl CDD pfam05052 pfam05052 309965 MerE MerE protein. The prokaryotic MerE (or URF-1) protein is part of the mercury resistance operon. The protein is thought not to have any direct role in conferring mercury resistance to the organizm but may be a mercury resistance transposon. 75 matched cddid_all.tbl CDD pfam05053 pfam05053 398642 Menin Menin. MEN1, the gene responsible for multiple endocrine neoplasia type 1, is a tumour suppressor gene that encodes a protein called Menin which may be an atypical GTPase stimulated by nm23. 617 matched cddid_all.tbl CDD pfam05054 pfam05054 282858 AcMNPV_Ac109 Autographa californica nuclear polyhedrosis virus (AcMNPV) protein. This domain family is found in viral proteins such as Ac109 from Autographa californica nuclear polyhedrosis virus (AcMNPV). The gene (Orf1090) is essential and transcribed late in virus assembly, and protein AC109 has been shown to be important for the transport of the budded virion to the host nucleus. In mutants lacking the AC109 gene, virions are unable to enter the nucleus and remain in the cytoplasm. Although addition of AC109 allowed virions to enter the nucleus, the occlusion bodies were empty, indicating that AC109 is also important for the production of infectious budded virus. The exact function of this domain family remains unknown. 418 matched cddid_all.tbl CDD pfam05055 pfam05055 252976 DUF677 Protein of unknown function (DUF677). This family consists of AT14A like proteins from Arabidopsis thaliana. At14a has a small domain that has sequence similarities to integrins from fungi, insects and humans. Transcripts of At14a are found in all Arabidopsis tissues and localizes partly to the plasma membrane. 336 matched cddid_all.tbl CDD pfam05056 pfam05056 461537 DUF674 Protein of unknown function (DUF674). This family is found in Arabidopsis thaliana and contains several uncharacterized proteins. 449 matched cddid_all.tbl CDD pfam05057 pfam05057 309968 DUF676 Putative serine esterase (DUF676). This family of proteins are probably serine esterase type enzymes with an alpha/beta hydrolase fold. 212 matched cddid_all.tbl CDD pfam05058 pfam05058 282861 ActA ActA Protein. The ActA family is found in Listeria and is associated with motility. ActA protein acts as a scaffold to assemble and activate host cell actin cytoskeletal factors at the bacterial surface, resulting in directional actin polymerization and propulsion of the bacterium through the cytoplasm of the host cell. 633 matched cddid_all.tbl CDD pfam05059 pfam05059 461538 Orbi_VP4 Orbivirus VP4 core protein. Orbiviruses are double stranded RNA retroviruses of which the bluetongue virus is a member. The core of bluetongue virus (BTV) is a multienzyme complex composed of two major proteins (VP7 and VP3) and three minor proteins (VP1, VP4 and VP6) in addition to the viral genome. VP4 has been shown to perform all RNA capping activities and has both methyltransferase type 1 and type 2 activities associated with it. 640 matched cddid_all.tbl CDD pfam05060 pfam05060 461539 MGAT2 N-acetylglucosaminyltransferase II (MGAT2). UDP-N-acetyl-D-glucosamine:alpha-6-D-mannoside beta-1,2-N- acetylglucosaminyltransferase II (EC 2.4.1.143) (GnT II/MGAT2) is a Golgi resident enzyme that catalyzes an essential step in the biosynthetic pathway leading from high mannose to complex N-linked oligosaccharides. Mutations in the MGAT2 gene lead to congenital disorder of glycosylation (CDG IIa). CDG IIa patients have an increased bleeding tendency, unrelated to coagulation factors. 349 matched cddid_all.tbl CDD pfam05061 pfam05061 282864 Pox_A11 Poxvirus A11 Protein. Family of conserved Chordopoxvirinae A11 family proteins. Conserved region spans entire protein in the majority of family members. 315 matched cddid_all.tbl CDD pfam05062 pfam05062 428286 RICH RICH domain. This presumed domain is about 85 residues in length and very rich in charged residues, hence the name RICH (Rich In CHarged residues). It is found in secreted proteins such as PspC, SpsA and IgA FC receptor from Streptococcus agalactiae. This domain could be involved in bacterial adherence or cell wall binding. 81 matched cddid_all.tbl CDD pfam05063 pfam05063 368270 MT-A70 MT-A70. MT-A70 is the S-adenosylmethionine-binding subunit of human mRNA:m6A methyl-transferase (MTase), an enzyme that sequence-specifically methylates adenines in pre-mRNAs. 174 matched cddid_all.tbl CDD pfam05064 pfam05064 461540 Nsp1_C Nsp1-like C-terminal region. This family probably forms a coiled-coil. This important region of Nsp1 is involved in binding Nup82. 114 matched cddid_all.tbl CDD pfam05065 pfam05065 428287 Phage_capsid Phage capsid family. Family of bacteriophage hypothetical proteins and capsid proteins. 272 matched cddid_all.tbl CDD pfam05066 pfam05066 461541 HARE-HTH HB1, ASXL, restriction endonuclease HTH domain. A winged helix-turn-helix domain present in the plant HB1, vertebrate ASXL, the H. pylori restriction endonuclease HpyAIII(HgrA), the RNA polymerase delta subunit(RpoE) of Gram positive bacteria and several restriction endonucleases. The domain is distinguished by the presence of a conserved one-turn helix between helix-3 and the preceding conserved turn. Its diverse architectures in eukaryotic species with extensive gene body methylation is suggestive of a chromatin function. The genetic interaction of the HARE-HTH containing ASXL with the methyl cytosine hydroxylating Tet2 protein is suggestive of a role for the domain in discriminating sequences with DNA modifications such as hmC. Bacterial versions include fusions to diverse restriction endonucleases, and a DNA glycosylase where it may play a similar role in detecting modified DNA. Certain bacterial version of the HARE-HTH domain show fusions to the helix-hairpin-helix domain of the RNA polymerase alpha subunit and the HTH domains found in regions 3 and 4 of the sigma factors. These versions are predicted to function as a novel inhibitor of the binding of RNA polymerase to transcription start sites, similar to the Bacillus delta protein. 71 matched cddid_all.tbl CDD pfam05067 pfam05067 252986 Mn_catalase Manganese containing catalase. Catalases are important antioxidant metalloenzymes that catalyze disproportionation of hydrogen peroxide, forming dioxygen and water. Two families of catalases are known, one having a heme cofactor, and this family that is a structurally distinct family containing non-heme manganese. 283 matched cddid_all.tbl CDD pfam05068 pfam05068 428289 MtlR Mannitol repressor. The mannitol operon of Escherichia coli, encoding the mannitol-specific enzyme II of the phosphotransferase system (MtlA) and mannitol phosphate dehydrogenase (MtlD) contains an additional downstream open reading frame which encodes the mannitol repressor (MtlR). 164 matched cddid_all.tbl CDD pfam05069 pfam05069 428290 Phage_tail_S Phage virion morphogenesis family. Protein S of phage P2 is thought to be involved in tail completion and stable head joining. 149 matched cddid_all.tbl CDD pfam05071 pfam05071 461542 NDUFA12 NADH ubiquinone oxidoreductase subunit NDUFA12. This family contains the 17.2 kD subunit of complex I (NDUFA12) and its homologs. The family also contains a second related eukaryotic protein of unknown function,. 96 matched cddid_all.tbl CDD pfam05072 pfam05072 282873 Herpes_UL43 Herpesvirus UL43 protein. UL43 genes are expressed with true-late (gamma2) kinetics and have been identified as a virion tegument component. 373 matched cddid_all.tbl CDD pfam05073 pfam05073 368276 Baculo_p24 Baculovirus P24 capsid protein. Baculovirus P24 is associated with nucleocapsids of budded and polyhedra-derived virions. 165 matched cddid_all.tbl CDD pfam05075 pfam05075 368277 DUF684 Protein of unknown function (DUF684). This family contains several uncharacterized proteins from Caenorhabditis elegans. The GO annotation suggests that the protein is involved in nematode larval development and has a positive regulation on growth rate. 338 matched cddid_all.tbl CDD pfam05076 pfam05076 461543 SUFU Suppressor of fused protein (SUFU). SUFU, encoding the human orthologue of Drosophila suppressor of fused, appears to have a conserved role in the repression of Hedgehog signaling. SUFU exerts its repressor role by physically interacting with GLI proteins in both the cytoplasm and the nucleus. SUFU has been found to be a tumour-suppressor gene that predisposes individuals to medulloblastoma by modulating the SHH signaling pathway. Genomic contextual analysis of bacterial SUFU versions revealed that they are immunity proteins against diverse nuclease toxins in polymorphic toxin systems. 171 matched cddid_all.tbl CDD pfam05077 pfam05077 282877 DUF678 Protein of unknown function (DUF678). This family contains several poxvirus proteins of unknown function. 73 matched cddid_all.tbl CDD pfam05078 pfam05078 461544 DUF679 Protein of unknown function (DUF679). This family includes members such as plant proteins AtDMPs 1-10 (Arabidopsis thaliana DUF679 domain membrane proteins 1 -10). The AtDMP proteins are predicted to have four transmembrane spans, with cytosolic amino- and carboxy-termini. DMP1 is a membrane protein that may be involved in membrane fission during breakdown of the ER and the tonoplast during leaf senescence and in membrane fusion during vacuole biogenesis in roots. Several DMP proteins are expressed in senescing organs (DMP1, -3, -4) or tissues that will stall later in development (DMP1, -2, -4, -7). These expression patterns strongly suggest involvement of several DMPs in various programmed cell death processes, e.g. senescence, dehiscence and abscission. AtDMP8 and AtDMP9 however, have been shown to facilitate gamete fusion during double fertilization in flowering plants. 163 matched cddid_all.tbl CDD pfam05079 pfam05079 428294 DUF680 Protein of unknown function (DUF680). This family contains several uncharacterized proteins which seem to be found exclusively in Rhizobium loti. 54 matched cddid_all.tbl CDD pfam05080 pfam05080 113835 DUF681 Protein of unknown function (DUF681). This family contains several uncharacterized beak and feather disease virus proteins. 101 matched cddid_all.tbl CDD pfam05081 pfam05081 282879 AcMNPV_P18 Autographa californica nuclear polyhedrosis virus (AcMNPV), P18. This family is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), P18; it is a family of uncharacterized viral proteins. 157 matched cddid_all.tbl CDD pfam05082 pfam05082 428295 Rop-like Rop-like. This family contains several uncharacterized bacterial proteins. These proteins are found in nitrogen fixation operons so are likely to play some role in this process. They consist of two alpha helices which are joined by a four residue linker. The helices form an antiparallel bundle and cross towards their termini. They are likely to form a rod-like dimer. They have structural similarity to the regulatory protein Rop, pfam01815. 60 matched cddid_all.tbl CDD pfam05083 pfam05083 398655 LST1 LST-1 protein. B144/LST1 is a gene encoded in the human major histocompatibility complex that produces multiple forms of alternatively spliced mRNA and encodes peptides fewer than 100 amino acids in length. B144/LST1 is strongly expressed in dendritic cells. Transfection of B144/LST1 into a variety of cells induces morphologic changes including the production of long, thin filopodia. 78 matched cddid_all.tbl CDD pfam05084 pfam05084 428296 GRA6 Granule antigen protein (GRA6). This family contains the granule antigen protein GRA6 which is found in the parasitic protozoa Toxoplasma gondii and Neospora caninum. GRA6 protein plays an important role in the antigenicity and pathogenicity in these organizms. 215 matched cddid_all.tbl CDD pfam05085 pfam05085 282883 DUF685 Protein of unknown function (DUF685). This family consists of several uncharacterized proteins from Borrelia burgdorferi (Lyme disease spirochete). There is some evidence to suggest that the proteins may be outer surface proteins. 265 matched cddid_all.tbl CDD pfam05086 pfam05086 252996 Dicty_REP Dictyostelium (Slime Mold) REP protein. This family consists of REP proteins from Dictyostelium (Slime molds). REP protein is likely involved in transcription regulation and control of DNA replication, specifically amplification of plasmid at low copy numbers. The formation of homomultimers may be required for their regulatory activity. 910 matched cddid_all.tbl CDD pfam05087 pfam05087 398657 Rota_VP2 Rotavirus VP2 protein. Rotavirus particles consist of three concentric proteinaceous capsid layers. The innermost capsid (core) is made of VP2. The genomic RNA and the two minor proteins VP1 and VP3 are encapsidated within this layer. The N-terminus of rotavirus VP2 is necessary for the encapsidation of VP1 and VP3. 882 matched cddid_all.tbl CDD pfam05088 pfam05088 428297 Bac_GDH Bacterial NAD-glutamate dehydrogenase. This family consists of several bacterial proteins which are closely related to NAD-glutamate dehydrogenase found in Streptomyces clavuligerus. Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyze the reversible oxidative deamination of glutamate to ketoglutarate and ammonia. 1530 matched cddid_all.tbl CDD pfam05089 pfam05089 461545 NAGLU Alpha-N-acetylglucosaminidase (NAGLU) tim-barrel domain. Alpha-N-acetylglucosaminidase, a lysosomal enzyme required for the stepwise degradation of heparan sulfate. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterized by neurological dysfunction but relatively mild somatic manifestations. The structure shows that the enzyme is composed of three domains. This central domain has a tim barrel fold. 332 matched cddid_all.tbl CDD pfam05090 pfam05090 461546 VKG_Carbox Vitamin K-dependent gamma-carboxylase. Using reduced vitamin K, oxygen, and carbon dioxide, gamma-glutamyl carboxylase post-translationally modifies certain glutamates by adding carbon dioxide to the gamma position of those amino acids. In vertebrates, the modification of glutamate residues of target proteins is facilitated by an interaction between a propeptide present on target proteins and the gamma-glutamyl carboxylase. 432 matched cddid_all.tbl CDD pfam05091 pfam05091 461547 eIF-3_zeta Eukaryotic translation initiation factor 3 subunit 7 (eIF-3). This family is made up of eukaryotic translation initiation factor 3 subunit 7 (eIF-3 zeta/eIF3 p66/eIF3d). Eukaryotic initiation factor 3 is a multi-subunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilization of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits. These functions and the complex nature of eIF3 suggest multiple interactions with many components of the translational machinery. The gene coding for the protein has been implicated in cancer in mammals. 521 matched cddid_all.tbl CDD pfam05092 pfam05092 282889 PIF Per os infectivity. This is a family of dsDNA Baculovirus proteins. It is required for the infectivity of the OBs or occlusion bodies. It is a structural protein of the ODV envelope required only in the first steps of per os larva infection, as viruses being produced in cells expressing the gene for this protein but not containing it in their genomes are able to produce successful infections. Baculoviruses are large DNA viruses that infect arthropods, mainly members of the order Lepidoptera. In their life cycle, they produce two kinds of particles, a budded, non-occluded virus (BV), which buds out of the infected cell and is responsible for the cell-to-cell transmission of the virus, and an occluded form, the occlusion body (OB), which is responsible for protecting the virus between encounters with larvae. A variable number of virions are included in the para-crystalline structure of the OB, mainly constituted by the virus-encoded polyhedrin protein; these virions are called occlusion body-derived virions or ODVs. 519 matched cddid_all.tbl CDD pfam05093 pfam05093 398662 CIAPIN1 Cytokine-induced anti-apoptosis inhibitor 1, Fe-S biogenesis. Anamorsin, subsequently named CIAPIN1 for cytokine-induced anti-apoptosis inhibitor 1, in humans is the homolog of yeast Dre2, a conserved soluble eukaryotic Fe-S cluster protein, that functions in cytosolic Fe-S protein biogenesis. It is found in both the cytoplasm and in the mitochondrial intermembrane space (IMS). CIAPIN1 is found to be up-regulated in hepatocellular cancer, is considered to be a downstream effector of the receptor tyrosine kinase-Ras signalling pathway, and is essential in mouse definitive haematopoiesis. Dre2 has been found to interact with the yeast reductase Tah18, forming a tight cytosolic complex implicated in the response to high levels of oxidative stress. 99 matched cddid_all.tbl CDD pfam05094 pfam05094 282891 LEF-9 Late expression factor 9 (LEF-9). Late expression factor 9 (LEF-9) is one of the primary components of RNA polymerase produced by baculoviruses. LEF-9 is homologous to the largest beta-subunit of prokaryotic DNA-directed RNA polymerase. 493 matched cddid_all.tbl CDD pfam05095 pfam05095 309989 DUF687 Protein of unknown function (DUF687). This family contains several uncharacterized Chlamydia proteins. 537 matched cddid_all.tbl CDD pfam05096 pfam05096 428301 Glu_cyclase_2 Glutamine cyclotransferase. This family of enzymes EC:2.3.2.5 catalyze the cyclization of free L-glutamine and N-terminal glutaminyl residues in proteins to pyroglutamate (5-oxoproline) and pyroglutamyl residues respectively. This family includes plant and bacterial enzymes and seems unrelated to the mammalian enzymes. 249 matched cddid_all.tbl CDD pfam05097 pfam05097 368284 DUF688 Protein of unknown function (DUF688). This family contains several uncharacterized proteins found in Arabidopsis thaliana. 443 matched cddid_all.tbl CDD pfam05098 pfam05098 282893 LEF-4 Late expression factor 4 (LEF-4). Late expression factor 4 (LEF-4) is one of the Baculovirus late expression factor proteins. LEF-4 carries out all the enzymatic functions related to mRNA capping. 471 matched cddid_all.tbl CDD pfam05099 pfam05099 428302 TerB Tellurite resistance protein TerB. This family contains the TerB tellurite resistance proteins from a a number of bacteria. 118 matched cddid_all.tbl CDD pfam05100 pfam05100 282895 Phage_tail_L Phage minor tail protein L. 206 matched cddid_all.tbl CDD pfam05101 pfam05101 428303 VirB3 Type IV secretory pathway, VirB3-like protein. This family includes the Type IV secretory pathway VirB3 protein, that is found associated with bacterial inner and outer membranes. The family also includes the conjugal transfer protein TrbD family that contains a nucleotide binding motif and may provide energy for the export of DNA or the export of other Trb proteins. 82 matched cddid_all.tbl CDD pfam05102 pfam05102 309993 Holin_BlyA holin, BlyA family. BlyA, a small holin found in Borrelia circular plasmids that is encoded by a prophage. BlyA contains two largely hydrophobic helices and a highly charged C-terminus and has two transmembrane segments. 61 matched cddid_all.tbl CDD pfam05103 pfam05103 428304 DivIVA DivIVA protein. The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate mini-cells. Inactivation of divIVA produces a mini-cell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype. These proteins appear to contain coiled-coils. 131 matched cddid_all.tbl CDD pfam05104 pfam05104 461548 Rib_recp_KP_reg Ribosome receptor lysine/proline rich region. This highly conserved region is found towards the C-terminus of the transmembrane domain. The function is unclear. 140 matched cddid_all.tbl CDD pfam05105 pfam05105 428306 Phage_holin_4_1 Bacteriophage holin family. Phage holins and lytic enzymes are both necessary for bacterial lysis and virus dissemination. This family also includes TcdE/UtxA involved in toxin secretion in Clostridium difficile. The 1.E.10 family is represented by Bacillus subtilis phi29 holin. 1.E.16 represents the Cph1 holin; and the 1.E.19 family is represented by the Clostridium difficile TcdE holin. Toxigenic strains of C. difficile produce two large toxins (TcdA and TcdB) encoded within a pathogenicity locus. tcdE, encoded between tcdA and tcdB, encodes a 166 aa protein which causes death to E. coli when expressed, and the structure of TcdE resembles holins. TcdE acts on the bacterial membrane. Since TcdA and TcdB lack signal peptides, they may be released via TcdE either prior to or subsequent to cell lysis. 109 matched cddid_all.tbl CDD pfam05106 pfam05106 428307 Phage_holin_3_1 Phage holin family (Lysis protein S). This family represents one of a large number of mutually dissimilar families of phage holins. Holins act against the host cell membrane to allow lytic enzymes of the phage to reach the bacterial cell wall. This family includes the product of the S gene of phage lambda. 99 matched cddid_all.tbl CDD pfam05107 pfam05107 461549 Cas_Cas7 CRISPR-associated protein Cas7. CRISPR-associated protein Cas7 is one of the components of the type I-B cascade-like antiviral defence complex. In Haloferax volcanii, Cas5, Cas6 and Cas7 form a small complex that aids the stability of CRISPR-derived RNA. 253 matched cddid_all.tbl CDD pfam05108 pfam05108 428309 T7SS_ESX1_EccB Type VII secretion system ESX-1, transport TM domain B. EccB is a family of largely Gram-positive bacterial transmembrane componenets of the type VII secretion system characterized in Mycobacterium tuberculosis, systems ESX1-5. Translocation of virulent peptides through the membranes is thought to be mediated via a complex that includes EccB, EccC, EccD, EccE, and MycP. EccB, EccC, EccD, and EccE form a stable complex in the mycobacterial cell envelope. 405 matched cddid_all.tbl CDD pfam05109 pfam05109 282904 Herpes_BLLF1 Herpes virus major outer envelope glycoprotein (BLLF1). This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo. 886 matched cddid_all.tbl CDD pfam05110 pfam05110 461550 AF-4 AF-4 proto-oncoprotein N-terminal region. This family consists of AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental retardation syndrome) nuclear proteins. These proteins have been linked to human diseases such as acute lymphoblastic leukaemia and mental retardation. The family also contains a Drosophila AF4 protein homolog Lilliputian which contains an AT-hook domain. Lilliputian represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila. 514 matched cddid_all.tbl CDD pfam05111 pfam05111 461551 Amelin Ameloblastin precursor (Amelin). This family consists of several mammalian Ameloblastin precursor (Amelin) proteins. Matrix proteins of tooth enamel consist mainly of amelogenin but also of non-amelogenin proteins, which, although their volumetric percentage is low, have an important role in enamel mineralization. One of the non-amelogenin proteins is ameloblastin, also known as amelin and sheathlin. Ameloblastin (AMBN) is one of the enamel sheath proteins which is though to have a role in determining the prismatic structure of growing enamel crystals. 411 matched cddid_all.tbl CDD pfam05112 pfam05112 282907 Baculo_p47 Baculovirus P47 protein. This family consists of several Baculovirus P47 proteins which is one of the primary components of Baculovirus encoded RNA polymerase, which initiates transcription from late and very late promoters. 306 matched cddid_all.tbl CDD pfam05113 pfam05113 310001 DUF693 Protein of unknown function (DUF693). This family consists of several uncharacterized proteins from Borrelia burgdorferi (Lyme disease spirochete). 313 matched cddid_all.tbl CDD pfam05114 pfam05114 428312 DUF692 Protein of unknown function (DUF692). This family consists of several uncharacterized bacterial proteins. 263 matched cddid_all.tbl CDD pfam05115 pfam05115 428313 PetL Cytochrome B6-F complex subunit VI (PetL). This family consists of several Cytochrome B6-F complex subunit VI (PetL) proteins found in several plant species. PetL is one of the small subunits which make up The cytochrome b(6)f complex. PetL is strictly required neither for the accumulation nor for the function of cytochrome b6f; in its absence, however, the complex becomes unstable in vivo in aging cells and labile in vitro. It has been suggested that the N-terminus of the protein is likely to lie in the thylakoid lumen. 31 matched cddid_all.tbl CDD pfam05116 pfam05116 428314 S6PP Sucrose-6F-phosphate phosphohydrolase. This family consists of Sucrose-6F-phosphate phosphohydrolase proteins found in plants and cyanobacteria. Sucrose-6(F)-phosphate phosphohydrolase catalyzes the final step in the pathway of sucrose biosynthesis. 246 matched cddid_all.tbl CDD pfam05117 pfam05117 428315 DUF695 Family of unknown function (DUF695). Family of uncharacterized bacterial proteins. 129 matched cddid_all.tbl CDD pfam05118 pfam05118 461552 Asp_Arg_Hydrox Aspartyl/Asparaginyl beta-hydroxylase. Iron (II)/2-oxoglutarate (2-OG)-dependent oxygenases catalyze oxidative reactions in a range of metabolic processes. Proline 3-hydroxylase hydroxylates proline at position 3, the first of a 2-OG oxygenase catalysing oxidation of a free alpha-amino acid. The structure of proline 3-hydroxylase contains the conserved motifs present in other 2-OG oxygenases including a jelly roll strand core and residues binding iron and 2-oxoglutarate, consistent with divergent evolution within the extended family. This family represent the arginine, asparagine and proline hydroxylases. The aspartyl/asparaginyl beta-hydroxylase (EC:1.14.11.16) specifically hydroxylates one aspartic or asparagine residue in certain epidermal growth factor-like domains of a number of proteins. 157 matched cddid_all.tbl CDD pfam05119 pfam05119 461553 Terminase_4 Phage terminase, small subunit. 96 matched cddid_all.tbl CDD pfam05120 pfam05120 428318 GvpG Gas vesicle protein G. Gas vesicles are intracellular, protein-coated, and hollow organelles found in cyanobacteria and halophilic archaea. They are permeable to ambient gases by diffusion and provide buoyancy, enabling cells to move upwards in water to access oxygen and/or light. Proteins containing this family are found in gas vesicles and play a role in the formation of gas vesicles. 72 matched cddid_all.tbl CDD pfam05121 pfam05121 428319 GvpK Gas vesicle protein K. These proteins are involved in the formation of gas vesicles. 81 matched cddid_all.tbl CDD pfam05122 pfam05122 398681 SpdB Mobile element transfer protein. This proteins are involved in transferring a group of integrating conjugative DNA elements, such as pSAM2 from Streptomyces ambofaciens. Their precise role is not known. 50 matched cddid_all.tbl CDD pfam05123 pfam05123 368294 S_layer_N S-layer like family, N-terminal region. 284 matched cddid_all.tbl CDD pfam05124 pfam05124 368295 S_layer_C S-layer like family, C-terminal region. 221 matched cddid_all.tbl CDD pfam05125 pfam05125 461554 Phage_cap_P2 Phage major capsid protein, P2 family. 327 matched cddid_all.tbl CDD pfam05127 pfam05127 461555 Helicase_RecD Helicase. This domain contains a P-loop (Walker A) motif, suggesting that it has ATPase activity, and a Walker B motif. In tRNA(Met) cytidine acetyltransferase (TmcA) it may function as an RNA helicase motor (driven by ATP hydrolysis) which delivers the wobble base to the active centre of the GCN5-related N-acetyltransferase (GNAT) domain. It is found in the bacterial exodeoxyribonuclease V alpha chain (RecD), which has 5'-3' helicase activity. It is structurally similar to the motor domain 1A in other SF1 helicases. 171 matched cddid_all.tbl CDD pfam05128 pfam05128 368297 DUF697 Domain of unknown function (DUF697). Family of bacterial hypothetical proteins that is sometimes associated with GTPase domains. 162 matched cddid_all.tbl CDD pfam05129 pfam05129 461556 Elf1 Transcription elongation factor Elf1 like. This family of short proteins contains a putative zinc binding domain with four conserved cysteines. Swiss:P36053 has been identified as a transcription elongation factor in Saccharomyces cerevisiae. 77 matched cddid_all.tbl CDD pfam05130 pfam05130 428323 FlgN FlgN protein. This family includes the FlgN protein and export chaperone involved in flagellar synthesis. 140 matched cddid_all.tbl CDD pfam05131 pfam05131 461557 Pep3_Vps18 Pep3/Vps18/deep orange family. This region is found in a number of protein identified as involved in golgi function and vacuolar sorting. The molecular function of this region is unknown. The members of this family contain a C-terminal ring finger domain. 147 matched cddid_all.tbl CDD pfam05132 pfam05132 461558 RNA_pol_Rpc4 RNA polymerase III RPC4. Specific subunit for Pol III, the tRNA specific polymerase. 138 matched cddid_all.tbl CDD pfam05133 pfam05133 398687 Phage_prot_Gp6 Phage portal protein, SPP1 Gp6-like. This bacteriophage protein forms a gateway that enables DNA passage during packaging and ejection of the phage genome. It also forms the junction between the phage head (capsid) and the tail proteins. During SPP1 morphogenesis, the portal protein, Gp6, participates in the procapsid assembly reaction. In the mature SPP1 virion, Gp6 exists as a dodecamer, while recombinant SPP1 Gp6 has been shown to form 13-subunit assemblies. This protein is common to Siphoviridae (phages with long non-contractile tails) and Myoviridae (phages with contractile tails). It is also found in a number of bacterial species. This family also includes the old Pfam family Phage_min_cap (PF:PF05126). RC Paper describing PDB structure 2jes 416 matched cddid_all.tbl CDD pfam05134 pfam05134 282928 T2SSL Type II secretion system (T2SS), protein L. This family consists of Type II secretion system protein L sequences from several Gram-negative (diderm) bacteria. The Type II secretion system, also called Secretion-dependent pathway (SDP), is responsible for extracellular secretion of a number of different proteins, including proteases and toxins. This pathway supports secretion of proteins across the cell envelope in two distinct steps, in which the second step, involving translocation through the outer membrane, is assisted by at least 13 different gene products. T2SL is predicted to contain a large cytoplasmic domain represented by this family and has been shown to interact with the autophosphorylating cytoplasmic membrane protein T2SE. It is thought that the tri-molecular complex of T2SL, T2SE (pfam00437) and T2SM (pfam04612) might be involved in regulating the opening and closing of the secretion pore and/or transducing energy to the site of outer membrane translocation. 230 matched cddid_all.tbl CDD pfam05135 pfam05135 428326 Phage_connect_1 Phage gp6-like head-tail connector protein. This family of proteins contain head-tail connector proteins related to gp6 from bacteriophage HK97. A structure of this protein shows similarity to gp15 a well characterized connector component of bacteriophage SPP1. 93 matched cddid_all.tbl CDD pfam05136 pfam05136 428327 Phage_portal_2 Phage portal protein, lambda family. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage capsid and the tail proteins. 348 matched cddid_all.tbl CDD pfam05137 pfam05137 428328 PilN Fimbrial assembly protein (PilN). 77 matched cddid_all.tbl CDD pfam05138 pfam05138 428329 PaaA_PaaC Phenylacetic acid catabolic protein. This family includes proteins such as PaaA and PaaC that are part of a catabolic pathway of phenylacetic acid. These proteins may form part of a dioxygenase complex. 251 matched cddid_all.tbl CDD pfam05139 pfam05139 428330 Erythro_esteras Erythromycin esterase. This family includes erythromycin esterase enzymes that confer resistance to the erythromycin antibiotic. 311 matched cddid_all.tbl CDD pfam05140 pfam05140 428331 ResB ResB-like family. This family includes both ResB and cytochrome c biogenesis proteins. Mutations in ResB indicate that they are essential for growth. ResB is predicted to be a transmembrane protein. 445 matched cddid_all.tbl CDD pfam05141 pfam05141 461559 DIT1_PvcA Pyoverdine/dityrosine biosynthesis protein. DIT1 is involved in synthesising dityrosine. Dityrosine is a sporulation-specific component of the yeast ascospore wall that is essential for the resistance of the spores to adverse environmental conditions. Pyoverdine biosynthesis protein PvcA is involved in the biosynthesis of pyoverdine, a cyclized isocyano derivative of tyrosine. It has a modified Rossmann fold. 270 matched cddid_all.tbl CDD pfam05142 pfam05142 461560 DUF702 Domain of unknown function (DUF702). Members of this family are found in various putative zinc finger proteins. 154 matched cddid_all.tbl CDD pfam05144 pfam05144 461561 Phage_CRI Phage replication protein CRI. The phage replication protein CRI, is also known as Gene II, is essential for DNA replication. 232 matched cddid_all.tbl CDD pfam05145 pfam05145 428334 AbrB Transition state regulatory protein AbrB. Bacillus subtilis respond to a multitude of environmental stimuli by using transcription factors called transition state regulators (TSRs). They play an essential role in cell survival by regulating spore formation, competence, and biofilm development. AbrB is one of the most known TSRs, acting as a pleotropic regulator for over 60 different genes where it directly binds to their promoter or regulatory regions. Many other genes are indirectly controlled by AbrB since it is a regulator of other regulatory proteins, including ScoC, Abh, SinR and SigH. Hence, AbrB is considered a global regulatory protein controlling processes such as Bacillus subtilis growth and cell division as well as production of extracellular degradative enzymes, nitrogen utilization and amino acid metabolism, motility, synthesis of antibiotics and their resistant determinants, development of competence, transport systems, oxidative stress response, phosphate metabolism, cell surface components and sporulation. AbrB is a tetramer consisting of identical 94 residue monomers. Its DNA-binding function resides solely in the N-terminal domain (AbrBN) of 53 residues. Although it does not recognize a well-defined DNA base-pairing sequence, instead, it appears to target a very weak pseudo consensus nucleotide sequence, TGGNA-5bp-TGGNA, which allows it to be rather promiscuous in binding. The N-terminal domains of very similar sequences are present in two more Bacillus subtilis proteins, Abh and SpoVT. Mutagenesis studies suggest that the role of the C-terminal domain is in forming multimers. 312 matched cddid_all.tbl CDD pfam05147 pfam05147 398697 LANC_like Lanthionine synthetase C-like protein. Lanthionines are thioether bridges that are putatively generated by dehydration of Ser and Thr residues followed by addition of cysteine residues within the peptide. This family contains the lanthionine synthetase C-like proteins 1 and 2 which are related to the bacterial lanthionine synthetase components C (LanC). LANCL1 (P40 seven-transmembrane-domain protein) and LANCL2 (testes-specific adriamycin sensitivity protein) are thought to be peptide-modifying enzyme components in eukaryotic cells. Both proteins are produced in large quantities in the brain and testes and may have role in the immune surveillance of these organs. Lanthionines are found in lantibiotics, which are peptide-derived, post-translationally modified antimicrobials produced by several bacterial strains. This region contains seven internal repeats. 350 matched cddid_all.tbl CDD pfam05148 pfam05148 398698 Methyltransf_8 Hypothetical methyltransferase. This family consists of several uncharacterized eukaryotic proteins which are related to methyltransferases pfam01209. 214 matched cddid_all.tbl CDD pfam05149 pfam05149 368306 Flagellar_rod Paraflagellar rod protein. This family consists of several eukaryotic paraflagellar rod component proteins. The eukaryotic flagellum represents one of the most complex macromolecular structures found in any organizm and contains more than 250 proteins. In addition to its locomotive role, the flagellum is probably involved in nutrient uptake since receptors for host low-density lipoproteins are localized on the flagellar membrane as well as on the flagellar pocket membrane. 287 matched cddid_all.tbl CDD pfam05150 pfam05150 428335 Legionella_OMP Legionella pneumophila major outer membrane protein precursor. This family consists of major outer membrane protein precursors from Legionella pneumophila. 294 matched cddid_all.tbl CDD pfam05151 pfam05151 398700 PsbM Photosystem II reaction centre M protein (PsbM). This family consists of several Photosystem II reaction centre M proteins (PsbM) from plants and cyanobacteria. During the photosynthetic light reactions in the thylakoid membranes of cyanobacteria, algae, and plants, photosystem II (PSII), a multi-subunit membrane protein complex, catalyzes oxidation of water to molecular oxygen and reduction of plastoquinon. 31 matched cddid_all.tbl CDD pfam05152 pfam05152 282943 DUF705 Protein of unknown function (DUF705). This family contains several uncharacterized Baculovirus proteins. 302 matched cddid_all.tbl CDD pfam05153 pfam05153 461562 MIOX Myo-inositol oxygenase. MIOX is the enzyme myo-inositol oxygenase. It catalyzes the first committed step in the glucuronate-xylulose pathway, It is a di-iron oxygenase with a key role in inositol metabolism. The structure reveals a monomeric, single-domain protein with a mostly helical fold that is distantly related to the diverse HD domain superfamily. The structural core is of five alpha-helices that contribute six ligands, four His and two Asp, to the di-iron centre where the two iron atoms are bridged by a putative hydroxide ion and one of the Asp ligands. The substrate is myo-inositol is bound in a terminal substrate-binding mode to a di-iron cluster. Within the structure are two additional proteinous lids that cover and shield the enzyme's active site. 249 matched cddid_all.tbl CDD pfam05154 pfam05154 428337 TM2 TM2 domain. This family is composed of a pair of transmembrane alpha helices connected by a short linker. The function of this domain is unknown, however it occurs in a wide range or protein contexts. 50 matched cddid_all.tbl CDD pfam05155 pfam05155 428338 Phage_X Phage X family. This family is the product of Gene X. The function of this protein is unknown. 88 matched cddid_all.tbl CDD pfam05157 pfam05157 428339 T2SSE_N Type II secretion system (T2SS), protein E, N-terminal domain. This domain is found at the N-terminus of members of the Type II secretion system protein E. Proteins in this subfamily are typically involved in Type 4 pilus biogenesis, though some are involved in other processes; for instance aggregation in Myxococcus xanthus. The structure of this domain is now known. 108 matched cddid_all.tbl CDD pfam05158 pfam05158 398703 RNA_pol_Rpc34 RNA polymerase Rpc34 subunit. Subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of yeast RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and is therefore participates in Pol III recruitment. 317 matched cddid_all.tbl CDD pfam05159 pfam05159 282949 Capsule_synth Capsule polysaccharide biosynthesis protein. This family includes export proteins involved in capsule polysaccharide biosynthesis, such as KpsS and LipB. 310 matched cddid_all.tbl CDD pfam05160 pfam05160 461563 DSS1_SEM1 DSS1/SEM1 family. This family contains the breast cancer tumour suppressor BRCA2-interacting protein DSS1 and its homolog SEM1, both of which are short acidic proteins. DSS1 has been shown to be a conserved component of the Rae1 mediated mRNA export pathway in Schizosaccharomyces pombe. 59 matched cddid_all.tbl CDD pfam05161 pfam05161 461564 MOFRL MOFRL family. MOFRL(multi-organizm fragment with rich Leucine) family exists in bacteria and eukaryotes. The function of this domain is not clear, although it exists in some putative enzymes such as reductases and kinases. 106 matched cddid_all.tbl CDD pfam05162 pfam05162 428342 Ribosomal_L41 Ribosomal protein L41. 24 matched cddid_all.tbl CDD pfam05163 pfam05163 398707 DinB DinB family. DNA damage-inducible (din) genes in Bacillus subtilis are coordinately regulated and together compose a global regulatory network that has been termed the SOS-like or SOB regulon. This family includes DinB from B. subtilis. 163 matched cddid_all.tbl CDD pfam05164 pfam05164 461565 ZapA Cell division protein ZapA. ZapA is a cell division protein which interacts with FtsZ. FtsZ is part of a mid-cell cytokinetic structure termed the Z-ring that recruits a hierarchy of fission related proteins early in the bacterial cell cycle. The interaction of FtsZ with ZapA drives its polymerization and promotes FtsZ filament bundling thereby contributing to the spatio-temporal tuning of the Z-ring. 85 matched cddid_all.tbl CDD pfam05165 pfam05165 147379 GCH_III GTP cyclohydrolase III. GTP cyclohydrolase (GCH) III from Methanocaldococcus jannaschi catalyzes the conversion of GTP to 2-amino-5-formylamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (FAPy). The reaction requires two bound magnesium ions for the catalysis and is activated by monovalent cations such as potassium and ammonium. The enzyme is a tetramer of identical subunits; each monomer is composed of an N- and a C-terminal domain that adopt nearly superimposible structures, suggesting that the protein has arisen by gene duplication. The family is found in archaea and bacteria. 246 matched cddid_all.tbl CDD pfam05166 pfam05166 428344 YcgL YcgL domain. This family of proteins formerly called DUF709 includes the E. coli gene ycgL. homologs of YcgL are found in gammaproteobacteria. The structure of this protein shows a novel alpha/beta/alpha sandwich structure. 73 matched cddid_all.tbl CDD pfam05167 pfam05167 461566 DUF711 Uncharacterized ACR (DUF711). The proteins in this family are functionally uncharacterized. The proteins are around 450 amino acids long. It is likely that this family represents a group of glycerol-3-phosphate dehydrogenases. 402 matched cddid_all.tbl CDD pfam05168 pfam05168 398711 HEPN HEPN domain. 117 matched cddid_all.tbl CDD pfam05170 pfam05170 428346 AsmA AsmA family. The AsmA gene, whose product is involved in the assembly of outer membrane proteins in Escherichia coli. AsmA mutations were isolated as extragenic suppressors of an OmpF assembly mutant. AsmA may have a role in LPS biogenesis. 607 matched cddid_all.tbl CDD pfam05171 pfam05171 461567 HemS Haemin-degrading HemS.ChuX domain. The Yersinia enterocolitica O:8 periplasmic binding-protein- dependent transport system consisted of four proteins: the periplasmic haemin-binding protein HemT, the haemin permease protein HemU, the ATP-binding hydrophilic protein HemV and the haemin-degrading protein HemS (this family). The structure for HemS has been solved and consists of a tandem repeat of this domain. 128 matched cddid_all.tbl CDD pfam05172 pfam05172 398713 Nup35_RRM Nup53/35/40-type RNA recognition motif. Members of this family belong to the nucleor pore complex, NPC, the only gateway between the nucleus and the cytoplasm. The NPC consists of several subcomplexes each one of which is made up of multiple copies of several individual Nup, Nic or Sec protein subunits. In yeast, this Nup or nucleoporin subunit is numbered Nup53, Nup40 in Schizo. pombe and in vertebrates as Nup35. This subunit forms part of the inner ring within the membrane and interacts directly with Nup-Ndc1, considered to be an anchor for the NPC in the pore membrane. This region of the Nup is the RNA-recognition region. 81 matched cddid_all.tbl CDD pfam05173 pfam05173 461568 DapB_C Dihydrodipicolinate reductase, C-terminus. Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The C-terminal domain of DapB has been proposed to be the substrate- binding domain. 122 matched cddid_all.tbl CDD pfam05175 pfam05175 428349 MTS Methyltransferase small domain. This domain is found in ribosomal RNA small subunit methyltransferase C as well as other methyltransferases. 170 matched cddid_all.tbl CDD pfam05176 pfam05176 398716 ATP-synt_10 ATP10 protein. ATP 10 is essential for the assembly of a functional mitochondrial ATPase complex. 255 matched cddid_all.tbl CDD pfam05177 pfam05177 428350 RCSD RCSD region. Proteins contain this region include C.elegans UNC-89. This region is found repeated in UNC-89 and shows conservation in prolines, lysines and glutamic acids. Proteins with RCSD are involved in muscle M-line assembly, but the function of this region RCSD is not clear. 101 matched cddid_all.tbl CDD pfam05178 pfam05178 461569 Kri1 KRI1-like family. The yeast member of this family (Kri1p) is found to be required for 40S ribosome biogenesis in the nucleolus. 103 matched cddid_all.tbl CDD pfam05179 pfam05179 461570 CDC73_C RNA pol II accessory factor, Cdc73 family, C-terminal. CDC73 is an RNA polymerase II accessory factor, and forms part of the Paf1 complex that has roles in post-initiation events. More specifically, crystal structure analysis shows the C-terminus to be a Ras-like domain that adopts a fold that is highly similar to GTPases of the Ras superfamily. The canonical nucleotide binding pocket is altered in CDC73, and there is no nucleotide ligand, but it contributes to histone methylation and Paf1C recruitment to active genes. Thus together with Rtf1 it combines to couple the Paf1 complex to elongating polymerase. The family has been added to the P-loop clan on the basis of the topology of the b-stranded core, and its similarity to Ras. 157 matched cddid_all.tbl CDD pfam05180 pfam05180 461571 zf-DNL DNL zinc finger. The domain is named after a short C-terminal motif of D(N/H)L. This domain is a novel zinc-finger protein essential for protein import into mitochondria. 64 matched cddid_all.tbl CDD pfam05181 pfam05181 461572 XPA_C XPA protein C-terminus. 51 matched cddid_all.tbl CDD pfam05182 pfam05182 461573 Fip1 Fip1 motif. This short motif is about 40 amino acids in length. In the Fip1 protein that is a component of a yeast pre-mRNA polyadenylation factor that directly interacts with poly(A) polymerase. This region of Fip1 is needed for the interaction with the Th1 subunit of the complex and for specific polyadenylation of the cleaved mRNA precursor. 43 matched cddid_all.tbl CDD pfam05183 pfam05183 461574 RdRP RNA dependent RNA polymerase. This family of proteins are eukaryotic RNA dependent RNA polymerases. These proteins are involved in post transcriptional gene silencing where they are thought to amplify dsRNA templates. 557 matched cddid_all.tbl CDD pfam05184 pfam05184 461575 SapB_1 Saposin-like type B, region 1. Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. It is one of the most studied members of the saposin protein family and it is involved in the hydrolysis of glycolipids and glycerolipids. SapB is unique in the saposin family in that it facilitates degradation by interacting with the substrate, not the enzymes. 38 matched cddid_all.tbl CDD pfam05185 pfam05185 428356 PRMT5 PRMT5 arginine-N-methyltransferase. The human homolog of yeast Skb1 (Shk1 kinase-binding protein 1) is PRMT5, an arginine-N-methyltransferase. These proteins appear to be key mitotic regulators. They play a role in Jak signalling in higher eukaryotes. 171 matched cddid_all.tbl CDD pfam05186 pfam05186 428357 Dpy-30 Dpy-30 motif. This motif is found in a wide variety of domain contexts. It is found in the Dpy-30 proteins hence the motifs name. It is about 40 residues long and is probably formed of two alpha-helices. It may be a dimerization motif analogous to pfam02197 (Bateman A pers obs). 42 matched cddid_all.tbl CDD pfam05187 pfam05187 461576 ETF_QO Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S. Electron-transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) in the inner mitochondrial membrane accepts electrons from electron-transfer flavoprotein which is located in the mitochondrial matrix and reduces ubiquinone in the mitochondrial membrane. The two redox centres in the protein, FAD and a [4Fe4S] cluster, are present in a 64-kDa monomer. 104 matched cddid_all.tbl CDD pfam05188 pfam05188 398728 MutS_II MutS domain II. This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam01624, pfam05192 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. This domain corresponds to domain II in Thermus aquaticus MutS as characterized in, and has similarity resembles RNAse-H-like domains (see pfam00075). 133 matched cddid_all.tbl CDD pfam05189 pfam05189 461577 RTC_insert RNA 3'-terminal phosphate cyclase (RTC), insert domain. RNA cyclases are a family of RNA-modifying enzymes that are conserved in all cellular organizms. They catalyze the ATP-dependent conversion of the 3'-phosphate to the 2',3'-cyclic phosphodiester at the end of RNA, in a reaction involving formation of the covalent AMP-cyclase intermediate. The structure of RTC demonstrates that RTCs are comprised two domain. The larger domain contains an insert domain of approximately 100 amino acids. 102 matched cddid_all.tbl CDD pfam05190 pfam05190 398730 MutS_IV MutS family domain IV. This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam01624, pfam05188, pfam05192 and pfam00488. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds in part with globular domain IV, which is involved in DNA binding, in Thermus aquaticus MutS as characterized in. 92 matched cddid_all.tbl CDD pfam05191 pfam05191 461578 ADK_lid Adenylate kinase, active site lid. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organizms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain, is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function. 36 matched cddid_all.tbl CDD pfam05192 pfam05192 461579 MutS_III MutS domain III. This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam05188, pfam01624 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain III, which is central to the structure of Thermus aquaticus MutS as characterized in. 291 matched cddid_all.tbl CDD pfam05193 pfam05193 428362 Peptidase_M16_C Peptidase M16 inactive domain. Peptidase M16 consists of two structurally related domains. One is the active peptidase, whereas the other is inactive. The two domains hold the substrate like a clamp. 181 matched cddid_all.tbl CDD pfam05194 pfam05194 461580 UreE_C UreE urease accessory protein, C-terminal domain. UreE is a urease accessory protein. Urease pfam00449 hydrolyses urea into ammonia and carbamic acid. The C-terminal region of members of this family contains a His rich Nickel binding site. 86 matched cddid_all.tbl CDD pfam05195 pfam05195 461581 AMP_N Aminopeptidase P, N-terminal domain. This domain is structurally very similar to the creatinase N-terminal domain (pfam01321). However, little or no sequence similarity exists between the two families. 121 matched cddid_all.tbl CDD pfam05196 pfam05196 461582 PTN_MK_N PTN/MK heparin-binding protein family, N-terminal domain. 57 matched cddid_all.tbl CDD pfam05197 pfam05197 461583 TRIC TRIC channel. TRIC (trimeric intracellular cation) channels are differentially expressed in intracellular stores in animal cell types. TRIC subtypes contain three proposed transmembrane segments, and form homo-trimers with a bullet-like structure. Electrophysiological measurements with purified TRIC preparations identify a monovalent cation-selective channel. 185 matched cddid_all.tbl CDD pfam05198 pfam05198 461584 IF3_N Translation initiation factor IF-3, N-terminal domain. 70 matched cddid_all.tbl CDD pfam05199 pfam05199 398739 GMC_oxred_C GMC oxidoreductase. This domain found associated with pfam00732. 143 matched cddid_all.tbl CDD pfam05201 pfam05201 461585 GlutR_N Glutamyl-tRNAGlu reductase, N-terminal domain. 144 matched cddid_all.tbl CDD pfam05202 pfam05202 398741 Flp_C Recombinase Flp protein. 254 matched cddid_all.tbl CDD pfam05203 pfam05203 368334 Hom_end_hint Hom_end-associated Hint. Homing endonucleases are encoded by mobile DNA elements that are found inserted within host genes in all domains of life. The crystal structure of the homing nuclease PI-Sce revealed two domains: an endonucleolytic centre resembling the C-terminal domain of Drosophila melanogaster Hedgehog protein, and a second domain containing the protein-splicing active site. This Domain corresponds to the latter protein-splicing domain. 444 matched cddid_all.tbl CDD pfam05204 pfam05204 368335 Hom_end Homing endonuclease. Homing endonucleases are encoded by mobile DNA elements that are found inserted within host genes in all domains of life. 110 matched cddid_all.tbl CDD pfam05205 pfam05205 461586 COMPASS-Shg1 COMPASS (Complex proteins associated with Set1p) component shg1. The Shg1 subunit is one of the eight subunits of the COMPASS complex, complex associated with SET1, conserved in yeasts and in other eukaryotes up to humans. It is associated with the region of the Set1 protein that is N-terminal to the C-terminus, ie Set1-560-900. The function of Shg1 seems to be to slightly inhibit histone 3 lysine 4 (H3K4) di- and tri-methylation, and it is a pioneer protein. The COMPASS complex functions to methylate the fourth lysine of Histone 3 and for silencing of genes close to the telomeres of chromosomes. 100 matched cddid_all.tbl CDD pfam05206 pfam05206 398743 TRM13 Methyltransferase TRM13. This is a family of eukaryotic proteins which are responsible for 2'-O-methylation of tRNA at position 4. TRM13 shows no sequence similarity to other known methyltransferases. 256 matched cddid_all.tbl CDD pfam05207 pfam05207 398744 zf-CSL CSL zinc finger. This is a zinc binding motif which contains four cysteine residues which chelate zinc. This domain is often found associated with a pfam00226 domain. This domain is named after the conserved motif of the final cysteine. 55 matched cddid_all.tbl CDD pfam05208 pfam05208 461587 ALG3 ALG3 protein. The formation of N-glycosidic linkages of glycoproteins involves the ordered assembly of the common Glc3Man9GlcNAc2 core-oligosaccharide on the lipid carrier dolichyl pyrophosphate. Whereas early mannosylation steps occur on the cytoplasmic side of the endoplasmic reticulum with GDP-Man as donor, the final reactions from Man5GlcNAc2-PP-Dol to Man9GlcNAc2-PP-Dol on the lumenal side use Dol-P-Man. ALG3 gene encodes the Dol-P-Man:Man5GlcNAc2-PP-Dol mannosyltransferase. 358 matched cddid_all.tbl CDD pfam05209 pfam05209 461588 MinC_N Septum formation inhibitor MinC, N-terminal domain. In Escherichia coli Swiss:P06138 assembles into a Z ring at midcell while assembly at polar sites is prevented by the min system. MinC, a component of this system, is an inhibitor of FtsZ assembly that is positioned within the cell by interaction with MinDE. MinC is an oligomer, probably a dimer. The C terminal half of MinC is the most conserved and interacts with MinD. The N terminal half is thought to interact with FtsZ. 71 matched cddid_all.tbl CDD pfam05210 pfam05210 461589 Sprouty Sprouty protein (Spry). This family consists of eukaryotic Sprouty protein homologs. Sprouty proteins have been revealed as inhibitors of the Ras/mitogen-activated protein kinase (MAPK) cascade, a pathway crucial for developmental processes initiated by activation of various receptor tyrosine kinases. The sprouty gene has found to be expressed in the the brain, cochlea, nasal organs, teeth, salivary gland, lungs, digestive tract, kidneys and limb buds in mice. 101 matched cddid_all.tbl CDD pfam05211 pfam05211 428371 NLBH Neuraminyllactose-binding hemagglutinin precursor (NLBH). This family is comprised of several flagellar sheath adhesin proteins also called neuraminyllactose-binding hemagglutinin precursor (NLBH) or N-acetylneuraminyllactose-binding fibrillar hemagglutinin receptor-binding subunits. NLBH is found exclusively in Helicobacter which are gut colonising bacteria and bind to sialic acid rich macromolecules present on the gastric epithelium. 238 matched cddid_all.tbl CDD pfam05212 pfam05212 461590 DUF707 Protein of unknown function (DUF707). This family consists of several uncharacterized proteins from Arabidopsis thaliana. 292 matched cddid_all.tbl CDD pfam05213 pfam05213 282997 Corona_NS2A Coronavirus NS2A protein. This family contains a number of corona virus non-structural proteins of unknown function. The family also includes a polymerase protein fragment from Berne virus and does not seem to be related to the pfam04753 Coronavirus NS2 family. This family is part of the 2H phosphoesterase superfamily. 267 matched cddid_all.tbl CDD pfam05214 pfam05214 282998 Baculo_p33 Baculovirus P33. This family consists of a series of Baculovirus P33 protein homologs of unknown function. 247 matched cddid_all.tbl CDD pfam05215 pfam05215 461591 Spiralin Spiralin domain. This entry represents a repeated domain found in Spiralin proteins found in spiroplasma bacteria. Spiroplasmas are helically shaped pathogenic bacteria related to the mycoplasmas. The surface of spiroplasma bacteria is crowded with the membrane-anchored lipoprotein spiralin whose structure and function are unknown although its cellular function is thought to be a structural and mechanical one rather than a catalytic one. 81 matched cddid_all.tbl CDD pfam05216 pfam05216 461592 UNC-50 UNC-50 family. Gmh1p from S. cerevisiae is located in the Golgi membrane and interacts with ARF exchange factors. 223 matched cddid_all.tbl CDD pfam05217 pfam05217 310081 STOP STOP protein. Neurons contain abundant subsets of highly stable microtubules that resist de-polymerizing conditions such as exposure to the cold. Stable microtubules are thought to be essential for neuronal development, maintenance, and function. STOP is a major factor responsible for the intriguing stability properties of neuronal microtubules and is important for synaptic plasticity. Additionally knowledge of STOPs function and properties may help in the treatment of neuroleptics in illnesses such as schizophrenia, currently thought to result from synaptic defects. 35 matched cddid_all.tbl CDD pfam05218 pfam05218 368344 DUF713 Protein of unknown function (DUF713). This family contains several proteins of unknown function from C.elegans. The GO annotation suggests that this protein is involved in nematode development and has a positive regulation on growth rate. 185 matched cddid_all.tbl CDD pfam05219 pfam05219 253097 DREV DREV methyltransferase. This family contains DREV protein homologs from several eukaryotes. The function of this protein is unknown. However, these proteins appear to be related to other methyltransferases (Bateman A pers obs). 265 matched cddid_all.tbl CDD pfam05220 pfam05220 461593 MgpC MgpC adhesin. This family contains several Mycoplasma MgpC like-proteins. The structure of MGP3 shows that this entry is a partial match to a large beta propeller domain that binds to sialic acid. 226 matched cddid_all.tbl CDD pfam05221 pfam05221 461594 AdoHcyase S-adenosyl-L-homocysteine hydrolase. 429 matched cddid_all.tbl CDD pfam05222 pfam05222 461595 AlaDh_PNT_N Alanine dehydrogenase/PNT, N-terminal domain. This family now also contains the lysine 2-oxoglutarate reductases. 135 matched cddid_all.tbl CDD pfam05223 pfam05223 428377 MecA_N NTF2-like N-terminal transpeptidase domain. The structure of this domain from MecA is known and is found to be similar to that found in NTF2 pfam02136. This domain seems unlikely to have an enzymatic function, and its role remains unknown. 117 matched cddid_all.tbl CDD pfam05224 pfam05224 398753 NDT80_PhoG NDT80 / PhoG like DNA-binding family. This family includes the DNA-binding region of NDT80 as well as PhoG and its homologs. The family contains VIB-1. VIB-1 is thought to be a regulator of conidiation in Neurospora crassa and shares a region of similarity to PHOG, a possible phosphate nonrepressible acid phosphatase in Aspergillus nidulans. It has been found that vib-1 is not the structural gene for nonrepressible acid phosphatase, but rather may regulate nonrepressible acid phosphatase activity. 180 matched cddid_all.tbl CDD pfam05225 pfam05225 283007 HTH_psq helix-turn-helix, Psq domain. This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster. In pipsqueak this domain binds to GAGA sequence. 45 matched cddid_all.tbl CDD pfam05226 pfam05226 428378 CHASE2 CHASE2 domain. CHASE2 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are parts of signal transduction pathways in bacteria. Specifically, CHASE2 domains are found in histidine kinases, adenylate cyclases, serine/threonine kinases and predicted diguanylate cyclases/phosphodiesterases. Environmental factors that are recognized by CHASE2 domains are not known at this time. 264 matched cddid_all.tbl CDD pfam05227 pfam05227 428379 CHASE3 CHASE3 domain. CHASE3 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are parts of signal transduction pathways in bacteria. Specifically, CHASE3 domains are found in histidine kinases, adenylate cyclases, methyl-accepting chemotaxis proteins and predicted diguanylate cyclases/phosphodiesterases. This domain recognizes pyrene (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 138 matched cddid_all.tbl CDD pfam05228 pfam05228 428380 CHASE4 CHASE4 domain. CHASE4. This is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are parts of signal transduction pathways in prokaryotes. Specifically, CHASE4 domains are found in histidine kinases in Archaea and in predicted diguanylate cyclases/phosphodiesterases in Bacteria. Environmental factors that are recognized by CHASE4 domains are not known at this time. 139 matched cddid_all.tbl CDD pfam05229 pfam05229 428381 SCPU Spore Coat Protein U domain. This domain is found in a bacterial family of spore coat proteins, as well as a family of secreted pili proteins involved in motility and biofilm formation. This family is distantly related to fimbrial proteins. 137 matched cddid_all.tbl CDD pfam05230 pfam05230 428382 MASE2 MASE2 domain. Predicted integral membrane sensory domain found in histidine kinases, diguanylate cyclases and other bacterial signaling proteins. 89 matched cddid_all.tbl CDD pfam05231 pfam05231 428383 MASE1 MASE1. Predicted integral membrane sensory domain found in histidine kinases, diguanylate cyclases and other bacterial signaling proteins. This entry also includes members of the 8 transmembrane UhpB type (8TMR-UT) domain family. 299 matched cddid_all.tbl CDD pfam05232 pfam05232 428384 BTP Chlorhexidine efflux transporter. This family represents a conserved pair of two transmembrane alpha-helices. All members carry the two pairs of TMs. BTP is a form of drug efflux pump, that actively tranports chlorhexidine out of the cell. Chlorhexidine, a bisbiguanide antimicrobial agent, is commonly used as an antiseptic and disinfectant in hospitals, and there is an increasing problem with resistance to it in some pathogenic bacteria. BTP is localized in the cytoplasmic membrane. 64 matched cddid_all.tbl CDD pfam05233 pfam05233 461596 PHB_acc PHB accumulation regulatory domain. The proteins this domain is found in are typically involved in regulating polymer accumulation in bacteria, particularly poly-beta-hydroxybutyrate (PHB). The N-terminal region is likely to be the DNA-binding domain (pfam07879) while this domain probably binds PHB (personal obs:C Yeats). 40 matched cddid_all.tbl CDD pfam05234 pfam05234 113985 UAF_Rrn10 UAF complex subunit Rrn10. The protein Rrn10 has been identified as a component of the Upstream Activating Factor (UAF), an RNA polymerase I (pol I) specific transcription stimulatory factor 122 matched cddid_all.tbl CDD pfam05235 pfam05235 461597 CHAD CHAD domain. The CHAD domain is an alpha-helical domain functionally associated with the pfam01928 domains. It has conserved histidines that may chelate metals. 164 matched cddid_all.tbl CDD pfam05236 pfam05236 461598 TAF4 Transcription initiation factor TFIID component TAF4 family. This region of similarity is found in Transcription initiation factor TFIID component TAF4. 264 matched cddid_all.tbl CDD pfam05238 pfam05238 398764 CENP-N Kinetochore protein CHL4 like. CHL4 is a protein involved in chromosome segregation. It is a component of the central kinetochore which mediates the attachment of the centromere to the mitotic spindle. CENP-N is one of the components that assembles onto the CENP-A-nucleosome-associated (NAC) centromere. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-A, the centromere-specific histone H3 variant, assembles an array of nucleosomes and it is this that seems to be the prime candidate for specifying centromere identity. CENP-A nucleosomes directly recruit a proximal CENP-A nucleosome associated complex (NAC) comprised of CENP-M, CENP-N and CENP-T, CENP-U(50), CENP-C and CENP-H. Assembly of the CENP-A NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Additionally, there are seven other subunits which make up the CENP-A-nucleosome distal (CAD) centromere, CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S, also assembling on the CENP-A NAC. 403 matched cddid_all.tbl CDD pfam05239 pfam05239 398765 PRC PRC-barrel domain. The PRC-barrel is an all beta barrel domain found in photosystem reaction centre subunit H of the purple bacteria and RNA metabolism proteins of the RimM group. PRC-barrels are approximately 80 residues long, and found widely represented in bacteria, archaea and plants. This domain is also present at the carboxyl terminus of the pan-bacterial protein RimM, which is involved in ribosomal maturation and processing of 16S rRNA. A family of small proteins conserved in all known euryarchaea are composed entirely of a single stand-alone copy of the domain. 78 matched cddid_all.tbl CDD pfam05240 pfam05240 461599 APOBEC_C APOBEC-like C-terminal domain. This domain is found at the C-termini of the Apolipoprotein B mRNA editing enzyme. 78 matched cddid_all.tbl CDD pfam05241 pfam05241 461600 EBP EXPERA (EXPanded EBP superfamily). The EXPERA (EXPanded EBP superfamily) domain is conserved among the following protein families: TM6SF1 (Transmembrane 6 Superfamily Member 1), TM6SF2 (Transmembrane 6 Superfamily Member 2), MAC30 (Meningioma-associated protein 30 also known as TMEM97, or Transmembrane protein 97), and EBP (Emopamil binding protein). EBP is an enzyme with a D8, D7 sterol isomerase activity that catalyzes the transposition of a double bond from C8=C9 to C7=C8 in the sterol B-ring. Mutations of EBP are known to cause the genetic disorder of X-linked dominant chondrodysplasia punctata (CDPX2). This syndrome of humans is lethal in most males, and affected females display asymmetric hyperkeratotic skin and skeletal abnormalities. 112 matched cddid_all.tbl CDD pfam05242 pfam05242 368355 GLYCAM-1 Glycosylation-dependent cell adhesion molecule 1 (GlyCAM-1). This family consists of the lactophorin precursors proteose peptone component 3 (PP3) and glycosylation-dependent cell adhesion molecule 1 (GlyCAM-1). GlyCAM-1 functions as a ligand for L-selectin, a saccharide-binding protein on the surface of circulating leukocytes, and mediates the trafficking of blood-born lymphocytes into secondary lymph nodes. In this context, sulphatation of the carbohydrates of GlyCAM-1 has been shown to be a critical structural requirement to be recognized by L-selectin. GlyCAM-1 is also expressed in pregnant and lactating mammary glands of mouse and in an unknown site in the lung, in the bovine uterus and rat cochlea. 135 matched cddid_all.tbl CDD pfam05244 pfam05244 113995 Brucella_OMP2 Brucella outer membrane protein 2. This family consists of several outer membrane proteins (2a and 2b) from brucella bacteria. Brucellae are Gram-negative, facultative intracellular bacteria that can infect many species of animals and man. 240 matched cddid_all.tbl CDD pfam05246 pfam05246 283023 DUF735 Protein of unknown function (DUF735). This family consists of several uncharacterized Borrelia burgdorferi (Lyme disease spirochete) proteins of unknown function. 211 matched cddid_all.tbl CDD pfam05247 pfam05247 428390 FlhD Flagellar transcriptional activator (FlhD). This family consists of several bacterial flagellar transcriptional activator (FlhD) proteins. FlhD combines with FlhC to form a regulatory complex in E. coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator. 101 matched cddid_all.tbl CDD pfam05248 pfam05248 310102 Adeno_E3A Adenovirus E3A. 104 matched cddid_all.tbl CDD pfam05250 pfam05250 461601 UPF0193 Uncharacterized protein family (UPF0193). This family of proteins is functionally uncharacterized. 217 matched cddid_all.tbl CDD pfam05251 pfam05251 461602 Ost5 Oligosaccharyltransferase subunit 5. Eukaryotic N-glycosylation is catalyzed in the ER lumen, where the enzyme oligosaccharyltransferase (OTase) transfers donor glycans from a dolichol pyrophosphate (DolP) carrier (Lipid-linked oligosaccharide; LLO) to polypeptides. The yeast OTase is a hetero-oligomeric complex composed of essential (Ost1, Ost2, Wbp1, Stt3, and Swp1) and nonessential (Ost3, Ost4, Ost5, and Ost6) subunits. This domain family is found in Ost5. The precise function of this subunit is not known, however Ost5 appears to form a sub-complex with Ost1, and this sub-complex associates with the catalytic Stt3 subunit of OTase. Down regulation of Ost5 resulted in a limited effect on glycosylation and no effect on the stability of Ost1 or Stt3 subunits. 73 matched cddid_all.tbl CDD pfam05253 pfam05253 461603 zf-U11-48K U11-48K-like CHHC zinc finger. This zinc binding domain has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function. 25 matched cddid_all.tbl CDD pfam05254 pfam05254 461604 UPF0203 Uncharacterized protein family (UPF0203). This family of proteins is functionally uncharacterized. 69 matched cddid_all.tbl CDD pfam05255 pfam05255 428395 UPF0220 Uncharacterized protein family (UPF0220). This family of proteins is functionally uncharacterized. 160 matched cddid_all.tbl CDD pfam05256 pfam05256 428396 UPF0223 Uncharacterized protein family (UPF0223). This family of proteins is functionally uncharacterized. 85 matched cddid_all.tbl CDD pfam05257 pfam05257 461605 CHAP CHAP domain. This domain corresponds to an amidase function. Many of these proteins are involved in cell wall metabolism of bacteria. This domain is found at the N-terminus of Swiss:P43675, where it functions as a glutathionylspermidine amidase EC:3.5.1.78. This domain is found to be the catalytic domain of PlyCA. CHAP is the amidase domain of bifunctional Escherichia coli glutathionylspermidine synthetase/amidase, and it catalyzes the hydrolysis of Gsp (glutathionylspermidine) into glutathione and spermidine. 83 matched cddid_all.tbl CDD pfam05258 pfam05258 461606 DciA Dna[CI] antecedent, DciA. This family contains several actinomycete proteins. Family members such as DciA (dna[CI] antecedent) found in Pseudomonas aeruginosa, has been shown to share a common function with DnaC (in Escherichia coli) and DnaI (in Bacillus subtilis), acting as a replicative helicase. Furthermore, functional analysis revealed that DciA is essential for replication initiation and protein depletion resulted in a blockage of the initiation of replication after the formation of the open complex. 88 matched cddid_all.tbl CDD pfam05259 pfam05259 283034 Herpes_UL1 Herpesvirus glycoprotein L. This family consists of several herpesvirus glycoprotein L or UL1 proteins. Glycoprotein L is known to form a complex with glycoprotein H but the function of this complex is poorly understood. 103 matched cddid_all.tbl CDD pfam05261 pfam05261 398777 Tra_M TraM protein, DNA-binding. The TraM protein is an essential part of the DNA transfer machinery of the conjugative resistance plasmid R1 (IncFII). On the basis of mutational analyses, it was shown that the essential transfer protein TraM has at least two functions. First, a functional TraM protein was found to be required for normal levels of transfer gene expression. Second, experimental evidence was obtained that TraM stimulates efficient site-specific single-stranded DNA cleavage at the oriT, in vivo. Furthermore, a specific interaction of the cytoplasmic TraM protein with the membrane protein TraD was demonstrated, suggesting that the TraM protein creates a physical link between the relaxosomal nucleoprotein complex and the membrane-bound DNA transfer apparatus. 126 matched cddid_all.tbl CDD pfam05262 pfam05262 114011 Borrelia_P83 Borrelia P83/100 protein. This family consists of several Borrelia P83/P100 antigen proteins. 489 matched cddid_all.tbl CDD pfam05263 pfam05263 428399 DUF722 Protein of unknown function (DUF722). This family contains several bacteriophage proteins of unknown function. 134 matched cddid_all.tbl CDD pfam05264 pfam05264 310112 CfAFP Choristoneura fumiferana antifreeze protein (CfAFP). This family consists of several antifreeze proteins from the insect Choristoneura fumiferana (Spruce budworm). Antifreeze proteins (AFPs) and antifreeze glycoproteins (AFGPs) are present in many organizms that must survive sub-zero temperatures. These proteins bind to seed ice crystals and inhibit their growth through an adsorption-inhibition mechanism. 137 matched cddid_all.tbl CDD pfam05265 pfam05265 283037 DUF723 Protein of unknown function (DUF723). This family contains several uncharacterized proteins from Neisseria meningitidis. These proteins may have a role in DNA-binding. 60 matched cddid_all.tbl CDD pfam05266 pfam05266 428400 DUF724 Protein of unknown function (DUF724). This family contains several uncharacterized proteins found in Arabidopsis thaliana and other plants. This region is often found associated with Agenet domains and may contain coiled-coil. 188 matched cddid_all.tbl CDD pfam05267 pfam05267 398779 DUF725 Protein of unknown function (DUF725). This family contains several Drosophila proteins of unknown function. 121 matched cddid_all.tbl CDD pfam05268 pfam05268 147458 GP38 Phage tail fibre adhesin Gp38. This family contains several Gp38 proteins from T-even-like phages. Gp38, together with a second phage protein, gp57, catalyzes the organization of gp37 but is absent from the phage particle. Gp37 is responsible for receptor recognition. 261 matched cddid_all.tbl CDD pfam05269 pfam05269 398780 Phage_CII Bacteriophage CII protein. This family consists of several phage CII regulatory proteins. CII plays a key role in the lysis-lysogeny decision in bacteriophage lambda and related phages. 79 matched cddid_all.tbl CDD pfam05270 pfam05270 428401 AbfB Alpha-L-arabinofuranosidase B (ABFB) domain. This family consists of several fungal alpha-L-arabinofuranosidase B proteins. L-Arabinose is a constituent of plant-cell-wall poly-saccharides. It is found in a polymeric form in L-arabinan, in which the backbone is formed by 1,5-a- linked l-arabinose residues that can be branched via 1,2-a- and 1,3-a-linked l-arabinofuranose side chains. AbfB hydrolyses 1,5-a, 1,3-a and 1,2-a linkages in both oligosaccharides and polysaccharides, which contain terminal non-reducing l-arabinofuranoses in side chains. 137 matched cddid_all.tbl CDD pfam05271 pfam05271 147459 Tobravirus_2B Tobravirus 2B protein. This family consists of several tobravirus 2B proteins. It is known that the 2B protein is required for transmission by both Paratrichodorus pachydermus and P. anemones nematodes. 117 matched cddid_all.tbl CDD pfam05272 pfam05272 461607 VirE Virulence-associated protein E. This family contains several bacterial virulence-associated protein E like proteins. These proteins contain a P-loop motif. 217 matched cddid_all.tbl CDD pfam05273 pfam05273 428403 Pox_RNA_Pol_22 Poxvirus RNA polymerase 22 kDa subunit. This family consists of several poxvirus DNA-dependent RNA polymerase 22 kDa subunits. 184 matched cddid_all.tbl CDD pfam05274 pfam05274 283043 Baculo_E25 Occlusion-derived virus envelope protein E25. This family consists of several nucleopolyhedrovirus occlusion-derived virus envelope E25 proteins. 190 matched cddid_all.tbl CDD pfam05275 pfam05275 428404 CopB Copper resistance protein B precursor (CopB). This family consists of several bacterial copper resistance proteins. Copper is essential and serves as cofactor for more than 30 enzymes yet a surplus of copper is toxic and leads to radical formation and oxidation of biomolecules. Therefore, copper homeostasis is a key requisite for every organizm. CopB serves to extrude copper when it approaches toxic levels. 208 matched cddid_all.tbl CDD pfam05276 pfam05276 461608 SH3BP5 SH3 domain-binding protein 5 (SH3BP5). This family consists of several eukaryotic SH3 domain-binding protein 5 or c-Jun N-terminal kinase (JNK)-interacting proteins (SH3BP5 or Sab). Sab binds to and serves as a substrate for JNK in vitro, and has been found to interact with the Src homology 3 (SH3) domain of Bruton's tyrosine kinase (Btk). Inspection of the sequence of Sab reveals the presence of two putative mitogen-activated protein kinase interaction motifs (KIMs) similar to that found in the JNK docking domain of the c-Jun transcription factor, and four potential serine-proline JNK phosphorylation sites in the C-terminal half of the molecule. 231 matched cddid_all.tbl CDD pfam05277 pfam05277 368366 DUF726 Protein of unknown function (DUF726). This family consists of several uncharacterized eukaryotic proteins. 341 matched cddid_all.tbl CDD pfam05278 pfam05278 253129 PEARLI-4 Arabidopsis phospholipase-like protein (PEARLI 4). This family contains several phospholipase-like proteins from Arabidopsis thaliana which are homologous to PEARLI 4. 234 matched cddid_all.tbl CDD pfam05279 pfam05279 428406 Asp-B-Hydro_N Aspartyl beta-hydroxylase N-terminal region. This family includes the N-terminal regions of the junctin, junctate and aspartyl beta-hydroxylase proteins. Junctate is an integral ER/SR membrane calcium binding protein, which comes from an alternatively spliced form of the same gene that generates aspartyl beta-hydroxylase and junctin. Aspartyl beta-hydroxylase catalyzes the post-translational hydroxylation of aspartic acid or asparagine residues contained within epidermal growth factor (EGF) domains of proteins. 66 matched cddid_all.tbl CDD pfam05280 pfam05280 428407 FlhC Flagellar transcriptional activator (FlhC). This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in E. coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator. 171 matched cddid_all.tbl CDD pfam05281 pfam05281 368368 Secretogranin_V Neuroendocrine protein 7B2 precursor (Secretogranin V). The neuroendocrine protein 7B2 has a critical role in the proteolytic conversion and activation of proPC2, the enzyme responsible for the proteolytic conversion of many peptide hormone precursors. The 7B2 protein acts as an intracellular binding protein for proPC2, facilitates its maturation, and is required for its enzymatic activity. Processing of many important peptide precursors does not occur in 7B2 nulls. 7B2 null mice exhibit a unique form of Cushing's disease with many atypical symptoms, such as hypoglycemia. 230 matched cddid_all.tbl CDD pfam05282 pfam05282 461609 AAR2 AAR2 protein. This family consists of several eukaryotic AAR2-like proteins. The yeast protein AAR2 is involved in splicing pre-mRNA of the a1 cistron and other genes that are important for cell growth. 356 matched cddid_all.tbl CDD pfam05283 pfam05283 461610 MGC-24 Multi-glycosylated core protein 24 (MGC-24), sialomucin. This family consists of several MGC-24 (or Cd164 antigen) proteins from eukaryotic organizms. MGC-24/CD164 is a sialomucin expressed in many normal and cancerous tissues. In humans, soluble and transmembrane forms of MGC-24 are produced by alternative splicing. 140 matched cddid_all.tbl CDD pfam05284 pfam05284 428410 DUF736 Protein of unknown function (DUF736). This family consists of several uncharacterized bacterial proteins of unknown function. 98 matched cddid_all.tbl CDD pfam05285 pfam05285 461611 SDA1 SDA1. This family consists of several SDA1 protein homologs. SDA1 is a Saccharomyces cerevisiae protein which is involved in the control of the actin cytoskeleton. The protein is essential for cell viability and is localized in the nucleus. 257 matched cddid_all.tbl CDD pfam05287 pfam05287 283053 PMG PMG protein. This family consists of several mouse anagen-specific protein mKAP13 (PMG1 and PMG2). PMG1 and 2 contain characteriztic repeats reminiscent of the keratin-associated proteins (KAPs). Both genes are expressed in growing hair follicles in skin as well as in sebaceous and eccrine sweat glands. Interestingly, expression is also detected in the mammary epithelium where it is limited to the onset of the pubertal growth phase and is independent of ovarian hormones. Their broad, developmentally controlled expression pattern, together with their unique amino acid composition, demonstrate that pmg-1 and pmg-2 constitute a novel KAP gene family participating in the differentiation of all epithelial cells forming the epidermal appendages. 180 matched cddid_all.tbl CDD pfam05288 pfam05288 283054 Pox_A3L Poxvirus A3L Protein. This family consists of several poxvirus A3L or A2_5L proteins. 70 matched cddid_all.tbl CDD pfam05289 pfam05289 368373 BLYB Borrelia hemolysin accessory protein. This family consists of several borrelia hemolysin accessory proteins (BLYB). BLYB was thought to be an accessory protein, which was proposed to comprise a hemolysis system but it is now thought that BlyA and BlyB function instead as a prophage-encoded holin or holin-like system. 120 matched cddid_all.tbl CDD pfam05290 pfam05290 368374 Baculo_IE-1 Baculovirus immediate-early protein (IE-0). The Autographa californica multinucleocapsid nuclear polyhedrosis virus (AcMNPV) ie-1 gene product (IE-1) is thought to play a central role in stimulating early viral transcription. IE-1 has been demonstrated to activate several early viral gene promoters and to negatively regulate the promoters of two other AcMNPV regulatory genes, ie-0 and ie-2. It is thought that that IE-1 negatively regulates the expression of certain genes by binding directly, or as part of a complex, to promoter regions containing a specific IE-1-binding motif (5'-ACBYGTAA-3') near their mRNA start sites. 141 matched cddid_all.tbl CDD pfam05291 pfam05291 461612 Bystin Bystin. Trophinin and tastin form a cell adhesion molecule complex that potentially mediates an initial attachment of the blastocyst to uterine epithelial cells at the time of implantation. Trophinin and tastin bind to an intermediary cytoplasmic protein called bystin. Bystin may be involved in implantation and trophoblast invasion because bystin is found with trophinin and tastin in the cells at human implantation sites and also in the intermediate trophoblasts at invasion front in the placenta from early pregnancy. This family also includes the yeast protein ENP1. ENP1 is an essential protein in Saccharomyces cerevisiae and is localized in the nucleus. It is thought that ENP1 plays a direct role in the early steps of rRNA processing as enp1 defective yeast cannot synthesize 20S pre-rRNA and hence 18S rRNA, which leads to reduced formation of 40S ribosomal subunits. 290 matched cddid_all.tbl CDD pfam05292 pfam05292 461613 MCD Malonyl-CoA decarboxylase C-terminal domain. This family consists of several eukaryotic malonyl-CoA decarboxylase (MLYCD) proteins. Malonyl-CoA, in addition to being an intermediate in the de novo synthesis of fatty acids, is an inhibitor of carnitine palmitoyltransferase I, the enzyme that regulates the transfer of long-chain fatty acyl-CoA into mitochondria, where they are oxidized. After exercise, malonyl-CoA decarboxylase participates with acetyl-CoA carboxylase in regulating the concentration of malonyl-CoA in liver and adipose tissue, as well as in muscle. Malonyl-CoA decarboxylase is regulated by AMP-activated protein kinase (AMPK). 245 matched cddid_all.tbl CDD pfam05293 pfam05293 114041 ASFV_L11L African swine fever virus (ASFV) L11L protein. L11L is an integral membrane protein of the African swine fever virus (ASFV) which is expressed late in the virus replication cycle. The protein is thought to be non-essential for growth in vitro and for virus virulence in domestic swine. 78 matched cddid_all.tbl CDD pfam05294 pfam05294 253137 Toxin_5 Scorpion short toxin. This family contains various secreted scorpion short toxins and seems to be unrelated to pfam00451. 32 matched cddid_all.tbl CDD pfam05295 pfam05295 253138 Luciferase_N Luciferase/LBP N-terminal domain. This family consists of a presumed N-terminal domain that is conserved between dinoflagellate luciferase and luciferin binding proteins. Luciferase is involved in catalysing the light emitting reaction in bioluminescence and luciferin binding protein (LBP) is known to bind to luciferin (the substrate for luciferase) to stop it reacting with the enzyme and therefore switching off the bioluminescence function. The expression of these two proteins is controlled by a circadian clock at the translational level, with synthesis and degradation occurring on a daily basis. However This domain is not the catalytic part of the protein. It has been suggested that this region may mediate an interaction between LBP and Luciferase or their association with the vacuolar membrane. 82 matched cddid_all.tbl CDD pfam05296 pfam05296 283059 TAS2R Taste receptor protein (TAS2R). This family consists of several forms of eukaryotic taste receptor proteins (TAS2Rs). TAS2Rs are G protein-coupled receptors expressed in subsets of taste receptor cells of the tongue and palate epithelia in humans and mice, and are organized in the genome in clusters. The proteins are genetically linked to loci that influence bitter perception in mice and humans. 303 matched cddid_all.tbl CDD pfam05297 pfam05297 283060 Herpes_LMP1 Herpesvirus latent membrane protein 1 (LMP1). This family consists of several latent membrane protein 1 or LMP1s mostly from Epstein-Barr virus. LMP1 of EBV is a 62-65 kDa plasma membrane protein possessing six membrane spanning regions, a short cytoplasmic N-terminus and a long cytoplasmic carboxy tail of 200 amino acids. EBV latent membrane protein 1 (LMP1) is essential for EBV-mediated transformation and has been associated with several cases of malignancies. EBV-like viruses in Cynomolgus monkeys (Macaca fascicularis) have been associated with high lymphoma rates in immunosuppressed monkeys 386 matched cddid_all.tbl CDD pfam05298 pfam05298 114046 Bombinin Bombinin. This family consists of Bombinin and Maximin proteins from Bombina maxima (Chinese red belly toad). Two groups of antimicrobial peptides have been isolated from skin secretions of Bombina maxima. Peptides in the first group, named maximins 1, 2, 3, 4 and 5, are structurally related to bombinin-like peptides (BLPs). Unlike BLPs, sequence variations in maximins occurred all through the molecules. In addition to the potent antimicrobial activity, cytotoxicity against tumour cells and spermicidal action of maximins, maximin 3 possessed a significant anti-HIV activity. Maximins 1 and 3 have been found to be toxic to mice. Peptides in the second group, termed maximins H1, H2, H3 and H4, are homologous with bombinin H peptides. 141 matched cddid_all.tbl CDD pfam05299 pfam05299 461614 Peptidase_M61 M61 glycyl aminopeptidase. Glycyl aminopeptidase is an unusual peptidase in that it has a preference for substrates with an N-terminal glycine or alanine. These proteins are found in Bacteria and in Archaea. 116 matched cddid_all.tbl CDD pfam05300 pfam05300 461615 MIC19_MIC25 MICOS complex subunit MIC19/MIC25. MIC19 (also known as ChChd3) and MIC25 (also known as ChChd6) are components of the MICOS complex, a large protein complex of the mitochondrial inner membrane that plays crucial roles in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane. MIC19 plays an important role in the maintenance of the MICOS complex stability and the mitochondrial cristae morphology. 173 matched cddid_all.tbl CDD pfam05301 pfam05301 461616 Acetyltransf_16 GNAT acetyltransferase, Mec-17. Mec-17 is the protein product of one of the 18 genes required for the development and function of the touch receptor neuron for gentle touch. Mec-17 is specifically required for maintaining the differentiation of the touch receptor. The family shares all the residue-motifs characteriztic of Gcn5-related acetyl-transferases, though the exact unction is still unknown. 176 matched cddid_all.tbl CDD pfam05302 pfam05302 310131 DUF720 Protein of unknown function (DUF720). This family consists of several uncharacterized Chlamydia proteins of unknown function. 128 matched cddid_all.tbl CDD pfam05303 pfam05303 398795 GSKIP_dom GSKIP domain. This domain is found in GSK3-beta interaction protein (GSKIP), which binds to GSK3beta. It is also found as a short domain towards the N terminus in clustered mitochondria protein, also known as clueless in Drosophila, which is involved in proper cytoplasmic distribution of mitochondria. 103 matched cddid_all.tbl CDD pfam05304 pfam05304 461617 DUF728 Protein of unknown function (DUF728). This family consists of several uncharacterized tobravirus proteins of unknown function. 139 matched cddid_all.tbl CDD pfam05305 pfam05305 461618 DUF732 Protein of unknown function (DUF732). This family consists of several uncharacterized Mycobacterium tuberculosis and leprae proteins of unknown function. 72 matched cddid_all.tbl CDD pfam05306 pfam05306 428418 DUF733 Protein of unknown function (DUF733). This family consists of several uncharacterized Drosophila melanogaster proteins of unknown function. 85 matched cddid_all.tbl CDD pfam05307 pfam05307 461619 Bundlin Bundlin. This family consists of several bundlin proteins from E. coli. Bundlin is a type IV pilin protein that is the only known structural component of enteropathogenic Escherichia coli bundle-forming pili (BFP). BFP play a role in virulence, antigenicity, autoaggregation, and localized adherence to epithelial cells. These proteins contain an N-terminal methylation motif. 151 matched cddid_all.tbl CDD pfam05308 pfam05308 461620 Mito_fiss_reg Mitochondrial fission regulator. In eukaryotes, this family of proteins induces mitochondrial fission. 245 matched cddid_all.tbl CDD pfam05309 pfam05309 428420 TraE TraE protein. This family consists of several bacterial sex pilus assembly and synthesis proteins (TraE). Conjugal transfer of plasmids from donor to recipient cells is a complex process in which a cell-to-cell contact plays a key role. Many genes encoded by self-transmissible plasmids are required for various processes of conjugation, including pilus formation, stabilization of mating pairs, conjugative DNA metabolism, surface exclusion and regulation of transfer gene expression. The exact function of the TraE protein is unknown. 178 matched cddid_all.tbl CDD pfam05310 pfam05310 191255 Tenui_NS3 Tenuivirus movement protein. This family of ssRNA negative-strand crop plant tenuivirus proteins appears to combine PV2, NS2, NS3, and PV3 proteins. Plant viruses encode specific proteins known as movement proteins (MPs) to control their spread through plasmodesmata (PD) in walls between cells as well as from leaf to leaf via vascular-dependent transport. During this movement process, the virally encoded MPs interact with viral genomes for transport from the viral replication sites to the PDs in the walls of infected cells along the cytoskeleton and/or endoplasmic reticulum (ER) network. The virus is then thought to move through the PDs in the form of MP-associated ribonucleoprotein complexes or as virions. The NS3 protein appears to function as an RNA silencing suppressor. 186 matched cddid_all.tbl CDD pfam05311 pfam05311 253146 Baculo_PP31 Baculovirus 33KDa late protein (PP31). Autographa californica nuclear polyhedrosis virus (AcMNPV) pp31 is a nuclear phosphoprotein that accumulates in the virogenic stroma, which is the viral replication centre in the infected-cell nucleus, binds to DNA, and serves as a late expression factor. 267 matched cddid_all.tbl CDD pfam05313 pfam05313 283071 Pox_P21 Poxvirus P21 membrane protein. The P21 membrane protein of vaccinia virus, encoded by the A17L (or A18L) gene, has been reported to localize on the inner of the two membranes of the intracellular mature virus (IMV). It has also been shown that P21 acts as a membrane anchor for the externally located fusion protein P14 (A27L gene). 189 matched cddid_all.tbl CDD pfam05314 pfam05314 283072 Baculo_ODV-E27 Baculovirus occlusion-derived virus envelope protein EC27. This family consists of several baculovirus occlusion-derived virus envelope proteins (EC27 or E27). The ODV-E27 protein has distinct functional characteriztics compared to cellular and viral cyclins. Depending on the cdk protein, and perhaps other viral or cellular proteins yet to be described, the kinase-EC27 complex may have either cyclin B- or D-like activity. 295 matched cddid_all.tbl CDD pfam05315 pfam05315 398800 ICEA ICEA Protein. This family consists of several ICEA proteins from Helicobacter pylori. Helicobacter pylori infection causes gastritis and peptic ulcer disease, and is classified as a definite carcinogen of gastric cancer. ICEA1 is speculated to be associated with peptic ulcer disease. 218 matched cddid_all.tbl CDD pfam05316 pfam05316 461621 VAR1 Mitochondrial ribosomal protein (VAR1). This family consists of the yeast mitochondrial ribosomal proteins VAR1. Mitochondria possess their own ribosomes responsible for the synthesis of a small number of proteins encoded by the mitochondrial genome. In yeast the two ribosomal RNAs and a single ribosomal protein, VAR1, are products of mitochondrial genes, and the remaining approximately 80 ribosomal proteins are encoded in the nucleus. VAR1 along with 15S rRNA are necessary for the formation of mature 37S subunits. 197 matched cddid_all.tbl CDD pfam05317 pfam05317 368384 Thermopsin Thermopsin. This family consists of several thermopsin proteins from archaebacteria. Thermopsin is a thermostable acid protease which is capable of hydrolysing the following bonds: Leu-Val, Leu-Tyr, Phe-Phe, Phe-Tyr, and Tyr-Thr. The specificity of thermopsin is therefore similar to that of pepsin, that is, it prefers large hydrophobic residues at both sides of the scissile bond. 253 matched cddid_all.tbl CDD pfam05318 pfam05318 253150 Tombus_movement Tombusvirus movement protein. This family consists of several Tombusvirus movement proteins. These proteins allow the virus to move from cell-to-cell and allow host-specific systemic spread. 68 matched cddid_all.tbl CDD pfam05320 pfam05320 398801 Pox_RNA_Pol_19 Poxvirus DNA-directed RNA polymerase 19 kDa subunit. This family contains several DNA-directed RNA polymerase 19 kDa polypeptides. The Poxvirus DNA-directed RNA polymerase (EC: 2.7.7.6) catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. 164 matched cddid_all.tbl CDD pfam05321 pfam05321 428422 HHA Haemolysin expression modulating protein. This family consists of haemolysin expression modulating protein (HHA) homologs. YmoA and Hha are highly similar bacterial proteins downregulating gene expression in Yersinia enterocolitica and Escherichia coli, respectively. 56 matched cddid_all.tbl CDD pfam05322 pfam05322 283078 NinE NINE Protein. This family consists of NINE proteins from several bacteriophages and from E. coli. 58 matched cddid_all.tbl CDD pfam05323 pfam05323 283079 Pox_A21 Poxvirus A21 Protein. This family consists of several poxvirus A21 proteins. 111 matched cddid_all.tbl CDD pfam05324 pfam05324 461622 Sperm_Ag_HE2 Sperm antigen HE2. This family consists of several variants of the human and chimpanzee sperm antigen proteins (HE2 and EP2 respectively). The EP2 gene codes for a family of androgen-dependent, epididymis-specific secretory proteins.The EP2 gene uses alternative promoters and differential splicing to produce a family of variant messages. The translated putative protein variants differ significantly from each other. Some of these putative proteins have similarity to beta-defensins, a family of antimicrobial peptides. 70 matched cddid_all.tbl CDD pfam05325 pfam05325 114071 DUF730 Protein of unknown function (DUF730). This family consists of several uncharacterized Arabidopsis thaliana proteins of unknown function. 122 matched cddid_all.tbl CDD pfam05326 pfam05326 398804 SVA Seminal vesicle autoantigen (SVA). This family consists of seminal vesicle autoantigen and prolactin-inducible (PIP) proteins. Seminal vesicle autoantigen (SVA) is specifically present in the seminal plasma of mice. This 19-kDa secretory glycoprotein suppresses the motility of spermatozoa by interacting with phospholipid. PIP, has several known functions. In saliva, this protein plays a role in host defence by binding to microorganizms such as Streptococcus. PIP is an aspartyl proteinase and it acts as a factor capable of suppressing T-cell apoptosis through its interaction with CD4. 124 matched cddid_all.tbl CDD pfam05327 pfam05327 461623 RRN3 RNA polymerase I specific transcription initiation factor RRN3. This family consists of several eukaryotic proteins which are homologous to the yeast RRN3 protein. RRN3 is one of the RRN genes specifically required for the transcription of rDNA by RNA polymerase I (Pol I) in Saccharomyces cerevisiae. 548 matched cddid_all.tbl CDD pfam05328 pfam05328 461624 CybS CybS, succinate dehydrogenase cytochrome B small subunit. This family consists of several eukaryotic succinate dehydrogenase [ubiquinone] cytochrome B small subunit, mitochondrial precursor (CybS) proteins. SDHD encodes the small subunit (cybS) of cytochrome b in succinate-ubiquinone oxidoreductase (mitochondrial complex II). Mitochondrial complex II is involved in the Krebs cycle and in the aerobic electron transport chain. It contains four proteins. The catalytic core consists of a flavoprotein and an iron-sulfur protein; these proteins are anchored to the mitochondrial inner membrane by the large subunit of cytochrome b (cybL) and cybS, which together comprise the heme-protein cytochrome b. Mutations in the SDHD gene can lead to hereditary paraganglioma, characterized by the development of benign, vascularised tumours in the head and neck. 131 matched cddid_all.tbl CDD pfam05331 pfam05331 398806 DUF742 Protein of unknown function (DUF742). This family consists of several uncharacterized Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown. 114 matched cddid_all.tbl CDD pfam05332 pfam05332 428426 Vesi_VP2 Vesivirus VP2 protein. This family consists of several Calicivirus VP2 proteins. VP2 is a minor capsid protein encoded by all caliciviruses. forms a large portal-like assembly at a unique three-fold axis of symmetry, following receptor engagement. This assembly-which was not detected in undecorated virions-is formed of twelve copies of VP2, arranged with their hydrophobic N termini pointing away from the virion surface. 105 matched cddid_all.tbl CDD pfam05334 pfam05334 461625 DUF719 Protein of unknown function (DUF719). This family consists of several eukaryotic proteins of unknown function. 181 matched cddid_all.tbl CDD pfam05335 pfam05335 398808 DUF745 Protein of unknown function (DUF745). This family consists of several uncharacterized Drosophila melanogaster proteins of unknown function. 180 matched cddid_all.tbl CDD pfam05336 pfam05336 428428 rhaM L-rhamnose mutarotase. This family contains L-rhamnose mutarotase which is a glycosyl hydrolase that converts the monosaccharide L-rhamnopyranose from the alpha to the beta stereoisomer. In Escherichia coli this enzyme is the product of the rhaM gene (also known as yiiL). The tertiary structure has been solved, in complex with L-rhamnose, and the catalytic mechanism determined. His22 is the proton donor. The enzyme naturally exists as a dimer. 100 matched cddid_all.tbl CDD pfam05337 pfam05337 398810 CSF-1 Macrophage colony stimulating factor-1 (CSF-1). Colony stimulating factor 1 (CSF-1) is a homodimeric polypeptide growth factor whose primary function is to regulate the survival, proliferation, differentiation, and function of cells of the mononuclear phagocytic lineage. This lineage includes mononuclear phagocytic precursors, blood monocytes, tissue macrophages, osteoclasts, and microglia of the brain, all of which possess cell surface receptors for CSF-1. The protein has also been linked with male fertility and mutations in the Csf-1 gene have been found to cause osteopetrosis and failure of tooth eruption. Structurally these are short-chain 4-helical cytokines. 140 matched cddid_all.tbl CDD pfam05338 pfam05338 283089 DUF717 Protein of unknown function (DUF717). This family consists of several herpesvirus proteins of unknown function. 55 matched cddid_all.tbl CDD pfam05339 pfam05339 428429 DUF739 Protein of unknown function (DUF739). This family contains several bacteriophage proteins. Some of the proteins in this family have been labeled putative cro repressor proteins. 68 matched cddid_all.tbl CDD pfam05340 pfam05340 398811 DUF740 Protein of unknown function (DUF740). This family consists of several uncharacterized plant proteins of unknown function. 610 matched cddid_all.tbl CDD pfam05341 pfam05341 283092 PIF6 Per os infectivity factor 6. Family members include Autographa californica nuclear polyhedrosis virus (AcMNPV) Orf68 (also known as per os infectivity factor 6, PIF6 or ac68). PIF6 is present in both the budded virus (BV) and the occluded-derived virus (ODV). The ac68 gene overlaps the lef3 gene which encodes the single-stranded DNA binding protein, and knockout experiments of ac68 have to ensure that a functional lef3 gene is present. In ac68KO experiments, viral DNA replication and BV levels were unaffected as were mortality rates if caterpillars were injected with BV directly into the hemolymph bypassing the gut. However, in oral bioassays the ac68KO occlusion bodies failed to kill larvae, indicating that PIF6 is a per os infectivity factor. 105 matched cddid_all.tbl CDD pfam05342 pfam05342 461626 Peptidase_M26_N M26 IgA1-specific Metallo-endopeptidase N-terminal region. These peptidases, which cleave mammalian IgA, are found in Gram-positive bacteria. Often found associated with pfam00746, they may be attached to the cell wall. 250 matched cddid_all.tbl CDD pfam05343 pfam05343 428431 Peptidase_M42 M42 glutamyl aminopeptidase. These peptidases are found in Archaea and Bacteria. The example in Lactococcus lactis, PepA, aids growth on milk. Pyrococcus horikoshii contain a thermostable de-blocking aminopeptidase member of this family used commercially for N-terminal protein sequencing. 292 matched cddid_all.tbl CDD pfam05344 pfam05344 283095 DUF746 Domain of Unknown Function (DUF746). This is a short conserved region found in some transposons. Structural modelling suggests this domain may bind nucleic acids. 64 matched cddid_all.tbl CDD pfam05345 pfam05345 398814 He_PIG Putative Ig domain. This alignment represents the conserved core region of ~90 residue repeat found in several haemagglutinins and other cell surface proteins. Sequence similarities to (pfam02494) and (pfam00801) suggest an Ig-like fold (personal obs:C. Yeats). So this family may be similar in function to the (pfam02639) and (pfam02638) domains. This domain is also found in the WisP family of proteins of Tropheryma whipplei. 95 matched cddid_all.tbl CDD pfam05346 pfam05346 398815 DUF747 Eukaryotic membrane protein family. This family is a family of eukaryotic membrane proteins. It was previously annotated as including a putative receptor for human cytomegalovirus gH but this has has since been disputed. Analysis of the mouse Tapt1 protein (transmembrane anterior posterior transformation 1) has shown it to be involved in patterning of the vertebrate axial skeleton. 311 matched cddid_all.tbl CDD pfam05347 pfam05347 428432 Complex1_LYR Complex 1 protein (LYR family). Proteins in this family include an accessory subunit of the higher eukaryotic NADH dehydrogenase complex. In Saccharomyces cerevisiae, the Isd11 protein has been shown to play a role in Fe/S cluster biogenesis in mitochondria. We have named this family LYR after a highly conserved tripeptide motif close to the N-terminus of these proteins. 59 matched cddid_all.tbl CDD pfam05348 pfam05348 461627 UMP1 Proteasome maturation factor UMP1. UMP1 is a short-lived chaperone present in the precursor form of the 20S proteasome and absent in the mature complex. UMP1 is required for the correct assembly and enzymatic activation of the proteasome. UMP1 seems to be degraded by the proteasome upon its formation 115 matched cddid_all.tbl CDD pfam05349 pfam05349 461628 GATA-N GATA-type transcription activator, N-terminal. GATA transcription factors mediate cell differentiation in a diverse range of tissues. Mutation are often associated with certain congenital human disorders. The six classical vertebrate GATA proteins, GATA-1 to GATA-6, are highly homologous and have two tandem zinc fingers. The classical GATA transcription factors function transcription activators. In lower metazoans GATA proteins carry a single canonical zinc finger. This family represents the N-terminal domain of the family of GATA transcription activators. 174 matched cddid_all.tbl CDD pfam05350 pfam05350 428435 GSK-3_bind Glycogen synthase kinase-3 binding. Glycogen synthase kinase-3 (GSK-3) sequentially phosphorylates four serine residues on glycogen synthase (GS), in the sequence SxxxSxxxSxxx-SxxxS(p), by recognising and phosphorylating the first serine in the sequence motif SxxxS(P) (where S(p) represents a phosphoserine). Interaction of GSK-3 with a peptide derived from GSK-3 binding protein (this family) prevents GSK-3 interaction with Axin. This interaction thereby inhibits the Axin-dependent phosphorylation of beta-catenin by GSK-3. 237 matched cddid_all.tbl CDD pfam05351 pfam05351 428436 GMP_PDE_delta GMP-PDE, delta subunit. GMP-PDE delta subunit was originally identified as a fourth subunit of rod-specific cGMP phosphodiesterase (PDE)(EC:3.1.4.35). The precise function of PDE delta subunit in the rod specific GMP-PDE complex is unclear. In addition, PDE delta subunit is not confined to photoreceptor cells but is widely distributed in different tissues. PDE delta subunit is thought to be a specific soluble transport factor for certain prenylated proteins and Arl2-GTP a regulator of PDE-mediated transport. 153 matched cddid_all.tbl CDD pfam05352 pfam05352 147504 Phage_connector Phage Connector (GP10). The head-tail connector of bacteriophage 29 is composed of 12 36 kDa subunits with 12 fold symmetry. It is the central component of a rotary motor that packages the genomic dsDNA into pre-formed proheads. This motor consists of the head-tail connector, surrounded by a 29-encoded, 174-base, RNA and a viral ATPase protein. 281 matched cddid_all.tbl CDD pfam05353 pfam05353 398821 Atracotoxin Delta Atracotoxin. Delta atracotoxin produces potentially fatal neurotoxic symptoms in primates by slowing he inactivation of voltage-gated sodium channels. The structure of atracotoxin comprises a core beta region containing a triple-stranded a thumb-like extension protruding from the beta region and a C-terminal helix. The beta region contains a cystine knot motif, a feature seen in other neurotoxic polypeptides. 42 matched cddid_all.tbl CDD pfam05354 pfam05354 283102 Phage_attach Phage Head-Tail Attachment. The phage head-tail attachment protein is required for the joining of phage heads and tails at the last step of morphogenesis. 117 matched cddid_all.tbl CDD pfam05355 pfam05355 428437 Apo-CII Apolipoprotein C-II. Apolipoprotein C-II (ApoC-II) is the major activator of lipoprotein lipase, a key enzyme in the regulation of triglyceride levels in human serum. 77 matched cddid_all.tbl CDD pfam05356 pfam05356 428438 Phage_Coat_B Inovirus Coat protein B. The major coat protein in the capsid of filamentous bacteriophage forms a helical assembly of about 7000 identical protomers, with each protomer comprised of 46 amino acid, after the cleavage of the signal peptide. Each protomer forms a slightly curved helix that combine to form a tubular structure that encapsulates the viral DNA. 56 matched cddid_all.tbl CDD pfam05357 pfam05357 368403 Phage_Coat_A Phage Coat Protein A. Infection of Escherichia coli by filamentous bacteriophages is mediated by the minor phage coat protein A and involves two distinct cellular receptors, the F' pilus and the periplasmic protein TolA. These two receptors are contacted in a sequential manner, such that binding of TolA by the extreme N-terminal domain is conditional on a primary interaction of the second coat protein A domain with the F' pilus. 62 matched cddid_all.tbl CDD pfam05358 pfam05358 283105 DicB DicB protein. DicB is part of the dic operon, which resides on cryptic prophage Kim. Under normal conditions, expression of dicB is actively repressed. When expression is induced, however, cell division rapidly ceases, and this division block is dependent on MinC with which it interacts. 62 matched cddid_all.tbl CDD pfam05359 pfam05359 461629 DUF748 Domain of Unknown Function (DUF748). 152 matched cddid_all.tbl CDD pfam05360 pfam05360 428440 YiaAB yiaA/B two helix domain. This domain consists of two transmembrane helices and a conserved linking section. 53 matched cddid_all.tbl CDD pfam05361 pfam05361 461630 PP1_inhibitor PKC-activated protein phosphatase-1 inhibitor. Contractility of vascular smooth muscle depends on phosphorylation of myosin light chains, and is modulated by hormonal control of myosin phosphatase activity. Signaling pathways activate kinases such as PKC or Rho-dependent kinases that phosphorylate the myosin phosphatase inhibitor protein called CPI-17. Phosphorylation of CPI-17 at Thr-38 enhances its inhibitory potency 1000-fold, creating a molecular switch for regulating contraction. 141 matched cddid_all.tbl CDD pfam05362 pfam05362 428442 Lon_C Lon protease (S16) C-terminal proteolytic domain. The Lon serine proteases must hydrolyse ATP to degrade protein substrates. In Escherichia coli, these proteases are involved in turnover of intracellular proteins, including abnormal proteins following heat-shock. The active site for protease activity resides in a C-terminal domain. The Lon proteases are classified as family S16 in Merops. 205 matched cddid_all.tbl CDD pfam05363 pfam05363 398827 Herpes_US12 Herpesvirus US12 family. US12 a key factor in the evasion of cellular immune response against HSV-infected cells. Specific inhibition of the transporter associated with antigen processing (TAP) by US12 prevents peptide transport into the endoplasmic reticulum and subsequent loading of major histocompatibility complex (MHC) class I molecules. US12 is comprised of three helices and is associated with cellular membranes. 82 matched cddid_all.tbl CDD pfam05364 pfam05364 461631 SecIII_SopE_N Salmonella type III secretion SopE effector N-terminus. Salmonella typhimurium employs a type III secretion system to inject bacterial toxins into the host cell cytosol. These toxins transiently activate Rho family GTP-binding protein-dependent signaling cascades to induce cytoskeletal rearrangements. SopE, one of these toxins, can activate Cdc42 in a Dbl-like fashion via its C-terminal GEP domain pfam07487. This family represents the N-terminal region of SopE. The function of this domain is unknown. 74 matched cddid_all.tbl CDD pfam05365 pfam05365 461632 UCR_UQCRX_QCR9 Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like. The UQCRX/QCR9 protein is the 9/10 subunit of complex III, encoding a protein of about 7-kDa. Deletion of QCR9 results in the inability of cells to grow on grow on-fermentable carbon source n yeast. 50 matched cddid_all.tbl CDD pfam05366 pfam05366 368407 Sarcolipin Sarcolipin. Sarcolipin is a 31 amino acid integral membrane protein that regulates Ca-ATPase activity in skeletal muscle. 31 matched cddid_all.tbl CDD pfam05367 pfam05367 368408 Phage_endo_I Phage endonuclease I. The bacteriophage endonuclease I is a nuclease that is selective for the structure of the four-way Holliday DNA junction. 149 matched cddid_all.tbl CDD pfam05368 pfam05368 398829 NmrA NmrA-like family. NmrA is a negative transcriptional regulator involved in the post-translational modification of the transcription factor AreA. NmrA is part of a system controlling nitrogen metabolite repression in fungi. This family only contains a few sequences as iteration results in significant matches to other Rossmann fold families. 236 matched cddid_all.tbl CDD pfam05369 pfam05369 461633 MtmB Monomethylamine methyltransferase MtmB. Monomethylamine methyltransferase of the archaebacterium Methanosarcina barkeri contains a novel amino acid, pyrrolysine, encoded by the termination codon UAG. The structure reveals a homohexamer comprised of individual subunits with a TIM barrel fold. 450 matched cddid_all.tbl CDD pfam05370 pfam05370 398830 DUF749 Domain of unknown function (DUF749). Archaeal domain of unknown function. This domain has been solved as part of a structural genomics project and comprises of segregated helical and anti-parallel beta sheet regions. 87 matched cddid_all.tbl CDD pfam05372 pfam05372 398831 Delta_lysin Delta lysin family. Delta-lysin is a 26 amino acid, hemolytic peptide toxin secreted by Staphylococcus aureus. It is thought that delta-toxin forms an amphipathic helix upon binding to lipid bilayers. The precise mode of action of delta-lysis is unclear. 25 matched cddid_all.tbl CDD pfam05373 pfam05373 398832 Pro_3_hydrox_C L-proline 3-hydroxylase, C-terminal. Iron (II)/2-oxoglutarate (2-OG)-dependent oxygenases catalyze oxidative reactions in a range of metabolic processes. Proline 3-hydroxylase hydroxylates proline at position 3, the first of a 2-OG oxygenase catalysing oxidation of a free alpha-amino acid. The structure contains conserved motifs present in other 2-OG oxygenases including a jelly roll strand core and residues binding iron and 2-oxoglutarate, consistent with divergent evolution within the extended family. The structure differs significantly from many other 2-OG oxygenases in possessing a discrete C-terminal helical domain. 101 matched cddid_all.tbl CDD pfam05374 pfam05374 428445 Mu-conotoxin Mu-Conotoxin. Mu-conotoxins are peptide inhibitors of voltage-sensitive sodium channels. 22 matched cddid_all.tbl CDD pfam05375 pfam05375 253170 Pacifastin_I Pacifastin inhibitor (LCMII). Structures of members of this family show that they are comprised of a triple-stranded antiparallel beta-sheet connected by three disulfide bridges, which defines this as a novel family of serine protease inhibitors. 40 matched cddid_all.tbl CDD pfam05377 pfam05377 428446 FlaC_arch Flagella accessory protein C (FlaC). Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells). 55 matched cddid_all.tbl CDD pfam05378 pfam05378 398834 Hydant_A_N Hydantoinase/oxoprolinase N-terminal region. This family is found at the N-terminus of the pfam01968 family. 176 matched cddid_all.tbl CDD pfam05379 pfam05379 283122 Peptidase_C23 Carlavirus endopeptidase. A peptidase involved in auto-proteolysis of a polyprotein from the plant pathogen blueberry scorch carlavirus (BBScV). Corresponds to Merops family C23. 88 matched cddid_all.tbl CDD pfam05380 pfam05380 461634 Peptidase_A17 Pao retrotransposon peptidase. Corresponds to Merops family A17. These proteins are homologous to aspartic proteinases encoded by retroposons and retroviruses. 162 matched cddid_all.tbl CDD pfam05381 pfam05381 398836 Peptidase_C21 Tymovirus endopeptidase. Corresponds to Merops family C21. The best-studied plant alpha-like virus proteolytic enzyme is the proteinase of turnip yellow mosaic virus (TYMV). The TYMV replicase protein undergoes auto-cleavage to yield two products. The auto-peptidase activity has been mapped to the central part of this polyprotein. 100 matched cddid_all.tbl CDD pfam05382 pfam05382 283125 Amidase_5 Bacteriophage peptidoglycan hydrolase. At least one of the members of this family, the Pal protein from the pneumococcal bacteriophage Dp-1 has been shown to be a N-acetylmuramoyl-L-alanine amidase. According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside at the N-terminal domain whereas the C-terminal domain binds to the choline residues of the cell wall teichoic acids. This family appears to be related to pfam00877. 142 matched cddid_all.tbl CDD pfam05383 pfam05383 461635 La La domain. This presumed domain is found at the N-terminus of La RNA-binding proteins as well as other proteins. The function of this region is uncertain. 59 matched cddid_all.tbl CDD pfam05384 pfam05384 428449 DegS Sensor protein DegS. This is small family of Bacillus DegS proteins. The DegS-DegU two-component regulatory system of Bacillus subtilis controls various processes that characterize the transition from the exponential to the stationary growth phase, including the induction of extracellular degradative enzymes, expression of late competence genes and down-regulation of the sigma D regulon. The family also contains one sequence Swiss:Q8R9D3 from Thermoanaerobacter tengcongensis which are described as sensory transduction histidine kinases. 159 matched cddid_all.tbl CDD pfam05385 pfam05385 283128 Adeno_E4 Mastadenovirus early E4 13 kDa protein. This family consists of human and simian mastadenovirus early E4 13 kDa proteins. Human adenovirus type 9 (Ad9) is unique in eliciting exclusively estrogen-dependent mammary tumours in rats and in not requiring viral E1 region transforming genes for tumorigenicity. E4 codes for an oncoprotein essential for tumourigenesis by Ad9. 108 matched cddid_all.tbl CDD pfam05386 pfam05386 428450 TEP1_N TEP1 N-terminal domain. This short sequence region is found in four copies at the N-terminus of the TEP1 telomerase component. The functional significance of the region is uncertain. However the conservation of two histidines and a cysteine suggests it is a potential zinc binding domain. 29 matched cddid_all.tbl CDD pfam05387 pfam05387 310175 Chorion_3 Chorion family 3. This family consists of several Drosophila chorion proteins S36 and S38. The chorion genes of Drosophila are amplified in response to developmental signals in the follicle cells of the ovary. 277 matched cddid_all.tbl CDD pfam05388 pfam05388 398840 Carbpep_Y_N Carboxypeptidase Y pro-peptide. This family is found at the N terminus of several carboxypeptidase Y proteins and contains a signal peptide and pro-peptide regions. 126 matched cddid_all.tbl CDD pfam05389 pfam05389 461636 MecA Negative regulator of genetic competence (MecA). This family contains several bacterial MecA proteins. The development of competence in Bacillus subtilis is regulated by growth conditions and several regulatory genes. In complex media competence development is poor, and there is little or no expression of late competence genes. Mec mutations permit competence development and late competence gene expression in complex media, bypassing the requirements for many of the competence regulatory genes. The mecA gene product acts negatively in the development of competence. Null mutations in mecA allow expression of a late competence gene comG, under conditions where it is not normally expressed, including in complex media and in cells mutant for several competence regulatory genes. Overexpression of MecA inhibits comG transcription. 168 matched cddid_all.tbl CDD pfam05390 pfam05390 398842 Kre9_KNH1_C Yeast cell wall synthesis protein KRE9/KNH1 C-terminal. This is the C-terminal domain found in KRE9 and KNH1 proteins which are involved in encoding cell surface O glycoproteins, required for beta -1,6-glucan synthesis in yeast. In Saccharomyces cerevisiae, a kre9 null mutation leads to severe growth defects, aberrant multi-budded morphology, and mating defects. Over-expression of Knh1 suppresses growth defects of a kre9 null mutant. Knh1 is required for propionic acid resistance. 101 matched cddid_all.tbl CDD pfam05391 pfam05391 398843 Lsm_interact Lsm interaction motif. This short motif is found at the C-terminus of Prp24 proteins and probably interacts with the Lsm proteins to promote U4/U6 formation. 19 matched cddid_all.tbl CDD pfam05392 pfam05392 461637 COX7B Cytochrome C oxidase chain VIIB. 78 matched cddid_all.tbl CDD pfam05393 pfam05393 428453 Hum_adeno_E3A Human adenovirus early E3A glycoprotein. This family consists of several early glycoproteins from human adenoviruses. 100 matched cddid_all.tbl CDD pfam05394 pfam05394 368421 AvrB_AvrC Avirulence protein. This family consists of several avirulence proteins from Pseudomonas syringae and Xanthomonas campestris. 326 matched cddid_all.tbl CDD pfam05395 pfam05395 428454 DARPP-32 Protein phosphatase inhibitor 1/DARPP-32. This family consists of several mammalian protein phosphatase inhibitor 1 (IPP-1) and dopamine- and cAMP-regulated neuronal phosphoprotein (DARPP-32) proteins. Protein phosphatase inhibitor-1 is involved in signal transduction and is an endogenous inhibitor of protein phosphatase-1. It has been demonstrated that DARPP-32, if phosphorylated, can inhibit protein-phosphatase-1. DARPP-32 has a key role in many neurotransmitter pathways throughout the brain and has been shown to be involved in controlling receptors, ion channels and other physiological factors including the brain's response to drugs of abuse, such as cocaine, opiates and nicotine. DARPP-32 is reciprocally regulated by the two neurotransmitters that are most often implicated in schizophrenia - dopamine and glutamate. Dopamine activates DARPP-32 through the D1 receptor pathway and disables DARPP-32 through the D2 receptor. Glutamate, acting through the N-methyl-d-aspartate receptor, renders DARPP-32 inactive. A mutant form of DARPP-32 has been linked with gastric cancers. 136 matched cddid_all.tbl CDD pfam05396 pfam05396 461638 Phage_T7_Capsid Phage T7 capsid assembly protein. 188 matched cddid_all.tbl CDD pfam05397 pfam05397 398846 Med15_fungi Mediator complex subunit 15. GAL11 or MED15 is one of the up to 32 or subunits of the Mediator complex which is found from fungi to humans. The Mediator complex interacts with RNA polymerase II and other general transcription factors to form the RNA polymerase II holoenzyme, thereby affecting transcription through targetting of activators and repressors. This family is found in fungi and the small metazoan starlet anemone. 112 matched cddid_all.tbl CDD pfam05398 pfam05398 310184 PufQ PufQ cytochrome subunit. This family consists of bacterial PufQ proteins. PufQ id required for bacteriochlorophyll biosynthesis serving a regulatory function in the formation of photosynthetic complexes. 74 matched cddid_all.tbl CDD pfam05399 pfam05399 461639 EVI2A Ectropic viral integration site 2A protein (EVI2A). This family contains several mammalian ectropic viral integration site 2A (EVI2A) proteins. The function of this protein is unknown although it is thought to be a membrane protein and may function as an oncogene in retrovirus induced myeloid tumours. 232 matched cddid_all.tbl CDD pfam05400 pfam05400 461640 FliT Flagellar protein FliT. This family contains several bacterial flagellar FliT proteins. The flagellar proteins FlgN and FliT have been proposed to act as substrate specific export chaperones, facilitating incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum. In Salmonella typhimurium flgN and fliT mutants, the export of target HAPs is reduced, concomitant with loss of unincorporated flagellin into the surrounding medium. 86 matched cddid_all.tbl CDD pfam05401 pfam05401 428457 NodS Nodulation protein S (NodS). This family consists of nodulation S (NodS) proteins. The products of the rhizobial nodulation genes are involved in the biosynthesis of lipochitin oligosaccharides (LCOs), which are host-specific signal molecules required for nodule formation. NodS is an S-adenosyl-L-methionine (SAM)-dependent methyltransferase involved in N methylation of LCOs. NodS uses N-deacetylated chitooligosaccharides, the products of the NodBC proteins, as its methyl acceptors. 201 matched cddid_all.tbl CDD pfam05402 pfam05402 461641 PqqD Coenzyme PQQ synthesis protein D (PqqD). This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis. 65 matched cddid_all.tbl CDD pfam05403 pfam05403 253181 Plasmodium_HRP Plasmodium histidine-rich protein (HRPII/III). This family consists of several histidine-rich protein II and III sequence from Plasmodium falciparum. 218 matched cddid_all.tbl CDD pfam05404 pfam05404 398850 TRAP-delta Translocon-associated protein, delta subunit precursor (TRAP-delta). This family consists of several eukaryotic translocon-associated protein, delta subunit precursors (TRAP-delta or SSR-delta). The exact function of this protein is unknown. 162 matched cddid_all.tbl CDD pfam05405 pfam05405 368426 Mt_ATP-synt_B Mitochondrial ATP synthase B chain precursor (ATP-synt_B). The Fo sector of the ATP synthase is a membrane bound complex which mediates proton transport. It is composed of nine different polypeptide subunits (a, b, c, d, e, f, g F6, A6L). 163 matched cddid_all.tbl CDD pfam05406 pfam05406 398851 WGR WGR domain. This domain is found in a variety of polyA polymerases as well as the E. coli molybdate metabolism regulator Swiss:P33345 and other proteins of unknown function. I have called this domain WGR after the most conserved central motif of the domain. The domain is found in isolation in proteins such as Swiss:Q9JN21 and is between 70 and 80 residues in length. I propose that this may be a nucleic acid binding domain. 79 matched cddid_all.tbl CDD pfam05407 pfam05407 461642 Peptidase_C27 Rubella virus endopeptidase. Corresponds to Merops family C27. Required for processing of the rubella virus replication protein. 164 matched cddid_all.tbl CDD pfam05408 pfam05408 283147 Peptidase_C28 Foot-and-mouth virus L-proteinase. Corresponds to Merops family C28. Protein fold of the peptidase unit for members of this family resembles that of papain. The leader proteinase of foot and mouth disease virus (FMDV) cleaves itself from the growing polyprotein and also cleaves the host translation initiation factor 4GI (eIF4G), thus inhibiting 5'-cap dependent translation. 201 matched cddid_all.tbl CDD pfam05409 pfam05409 398852 Peptidase_C30 Coronavirus endopeptidase C30. This Coronavirus (CoV) domain, peptidase C30, is also known as 3C-like proteinase (3CL-pro), or CoV main protease (M-pro) domain. CoV M-pro is a dimer where each subunit is composed of three domains I, II and III,,. Domains I and II consist of six-stranded antiparallel beta barrels and together resemble the architecture of chymotrypsin, and of picornaviruses 3C proteinases. The substrate-binding site is located in a cleft between these two domains. The catalytic site is situated at the centre of the cleft. A long loop connects domain II to the C-terminal domain (domain III). This latter domain has been implicated in the proteolytic activity of M-pro. In the active site of M-pro, Cys and His form a catalytic dyad,. 274 matched cddid_all.tbl CDD pfam05410 pfam05410 461643 Peptidase_C31 Porcine arterivirus-type cysteine proteinase alpha. Corresponds to Merops family C31. These peptidases are involved in viral polyprotein processing in replication. 105 matched cddid_all.tbl CDD pfam05411 pfam05411 398854 Peptidase_C32 Equine arteritis virus putative proteinase. These proteins are characterized by a region that has been proposed to have peptidase activity involved in viral polyprotein processing in replication. 127 matched cddid_all.tbl CDD pfam05412 pfam05412 114153 Peptidase_C33 Equine arterivirus Nsp2-type cysteine proteinase. Corresponds to Merops family C33. These peptidases are involved in viral polyprotein processing in replication. 108 matched cddid_all.tbl CDD pfam05413 pfam05413 147545 Peptidase_C34 Putative closterovirus papain-like endopeptidase. Corresponds to Merops family C34. Putative closterovirus papain-like endopeptidase from the apple chlorotic leaf spot closterovirus. 92 matched cddid_all.tbl CDD pfam05414 pfam05414 461644 DUF1717 Viral domain of unknown function (DUF1717). This domain is found in viral proteins of unknown function. 78 matched cddid_all.tbl CDD pfam05415 pfam05415 461645 Peptidase_C36 Beet necrotic yellow vein furovirus-type papain-like endopeptidase. Corresponds to Merops family C36. This protease involved in processing the viral polyprotein. 104 matched cddid_all.tbl CDD pfam05416 pfam05416 253185 Peptidase_C37 Southampton virus-type processing peptidase. Corresponds to Merops family C37. Norwalk-like viruses (NLVs), including the Southampton virus, cause acute non-bacterial gastroenteritis in humans. The NLV genome encodes three open reading frames (ORFs). ORF1 encodes a polyprotein, which is processed by the viral protease into six proteins. 535 matched cddid_all.tbl CDD pfam05417 pfam05417 461646 Peptidase_C41 Hepatitis E cysteine protease. Corresponds to MEROPs family C41. This papain-like protease cleaves the viral polyprotein encoded by ORF1 of the hepatitis E virus (HEV). 161 matched cddid_all.tbl CDD pfam05418 pfam05418 428460 Apo-VLDL-II Apovitellenin I (Apo-VLDL-II). This family consists of several avian apovitellenin I sequences. As part of the avian reproductive effort, large quantities of triglyceride-rich very-low-density lipoprotein (VLDL) particles are transported by receptor-mediated endocytosis into the female germ cells. Although the oocytes are surrounded by a layer of granulosa cells harbouring high levels of active lipoprotein lipase, non-lipolysed VLDL is transported into the yolk. This is because VLDL particles from laying chickens are protected from lipolysis by apolipoprotein (apo)-VLDL-II, a potent dimeric lipoprotein lipase inhibitor. Apo-VLDL-II is produced in the liver and secreted into the blood stream when induced by estrogen production in female birds. 79 matched cddid_all.tbl CDD pfam05419 pfam05419 428461 GUN4 GUN4-like. In Arabidopsis, GUN4 is required for the functioning of the plastid mediated repression of nuclear transcription that is involved in controlling the levels of magnesium- protoporphyrin IX. GUN4 binds the product and substrate of Mg-chelatase, an enzyme that produces Mg-Proto, and activates Mg-chelatase. GUN4 is thought to participates in plastid-to-nucleus signaling by regulating magnesium-protoporphyrin IX synthesis or trafficking. 138 matched cddid_all.tbl CDD pfam05420 pfam05420 461647 BCSC_C Cellulose synthase operon protein C C-terminus (BCSC_C). This family contains the C-terminal regions of several bacterial cellulose synthase operon C (BCSC) proteins. BCSC is involved in cellulose synthesis although the exact function of this protein is unknown. 336 matched cddid_all.tbl CDD pfam05421 pfam05421 428463 DUF751 Protein of unknown function (DUF751). This family contains several plant, cyanobacterial and algal proteins of unknown function. The family is exclusively found in phototrophic organizms and may therefore play a role in photosynthesis (personal obs:Moxon SJ). 60 matched cddid_all.tbl CDD pfam05422 pfam05422 461648 SIN1 Stress-activated map kinase interacting protein 1 (SIN1). SIN1 is the N-terminus of stress-activated map kinase interacting protein 1 (MAPKAP1 OR SIN1) sequences. This domain is likely to be the Ras-binding domain. The fission yeast Sty1/Spc1 mitogen-activated protein (MAP) kinase is a member of the eukaryotic stress-activated MAP kinase (SAPK) family. Sin1 interacts with Sty1/Spc1. Cells lacking Sin1 display many, but not all, of the phenotypes of cells lacking the Sty1/Spc1 MAP kinase including sterility, multiple stress sensitivity and a cell-cycle delay. Sin1 is phosphorylated after stress but this is not Sty1/Spc1-dependent. The separate CRIM and PH, pleckstrin-homology domains of the full-length SIN1 proteins have been separated into distinct families. 136 matched cddid_all.tbl CDD pfam05423 pfam05423 283157 Mycobact_memb Mycobacterium membrane protein. This family contains several membrane proteins from Mycobacterium species. 138 matched cddid_all.tbl CDD pfam05424 pfam05424 428465 Duffy_binding Duffy binding domain. This domain is found in Plasmodium Duffy binding proteins. Plasmodium vivax and Plasmodium knowlesi merozoites invade human erythrocytes that express Duffy blood group surface determinants. The Duffy receptor family is localized in micronemes, an organelle found in all organizms of the phylum Apicomplexa. This family is closely associated on PfEMP1 proteins with PFEMP, pfam03011. 178 matched cddid_all.tbl CDD pfam05425 pfam05425 428466 CopD Copper resistance protein D. Copper sequestering activity displayed by some bacteria is determined by copper-binding protein products of the copper resistance operon (cop). CopD, together with CopC, perform copper uptake into the cytoplasm. 96 matched cddid_all.tbl CDD pfam05426 pfam05426 398861 Alginate_lyase Alginate lyase. This family contains several bacterial alginate lyase proteins. Alginate is a family of 1-4-linked copolymers of beta -D-mannuronic acid (M) and alpha -L-guluronic acid (G). It is produced by brown algae and by some bacteria belonging to the genera Azotobacter and Pseudomonas. Alginate lyases catalyze the depolymerization of alginates by beta -elimination, generating a molecule containing 4-deoxy-L-erythro-hex-4-enepyranosyluronate at the nonreducing end. This family adopts an all alpha fold. 274 matched cddid_all.tbl CDD pfam05427 pfam05427 461649 FIBP Acidic fibroblast growth factor binding (FIBP). Acidic fibroblast growth factor (aFGF) intracellular binding protein (FIBP) is a protein found mainly in the nucleus that is thought to be involved in the intracellular function of aFGF. 360 matched cddid_all.tbl CDD pfam05428 pfam05428 461650 CRF-BP Corticotropin-releasing factor binding protein (CRF-BP). This family consists of several eukaryotic corticotropin-releasing factor binding proteins (CRF-BP or CRH-BP). Corticotropin-releasing hormone (CRH) plays multiple roles in vertebrate species. In mammals, it is the major hypothalamic releasing factor for pituitary adrenocorticotropin secretion, and is a neurotransmitter or neuromodulator at other sites in the central nervous system. In non-mammalian vertebrates, CRH not only acts as a neurotransmitter and hypophysiotropin, it also acts as a potent thyrotropin-releasing factor, allowing CRH to regulate both the adrenal and thyroid axes, especially in development. CRH-BP is thought to play an inhibitory role in which it binds CRH and other CRH-like ligands and prevents the activation of CRH receptors. There is however evidence that CRH-BP may also exhibit diverse extra and intracellular roles in a cell specific fashion and at specific times in development. 298 matched cddid_all.tbl CDD pfam05430 pfam05430 398864 Methyltransf_30 S-adenosyl-L-methionine-dependent methyltransferase. This family is a S-adenosyl-L-methionine (SAM)-dependent methyltransferase. It is often found in association with pfam01266, where it is responsible for catalysing the transfer of a methyl group from S-adenosyl-L-methionine to 5-aminomethyl-2-thiouridine to form 5-methylaminomethyl-2-thiouridine. 124 matched cddid_all.tbl CDD pfam05431 pfam05431 398865 Toxin_10 Insecticidal Crystal Toxin, P42. Family of Bacillus insecticidal crystal toxins. Strains of Bacillus that have this insecticidal activity use a binary toxin comprised of two proteins, P51 and P42 (this family). Members of this family are highly conserved between strains of different serotypes and phage groups. 169 matched cddid_all.tbl CDD pfam05432 pfam05432 461651 BSP_II Bone sialoprotein II (BSP-II). Bone sialoprotein (BSP) is a major structural protein of the bone matrix that is specifically expressed by fully-differentiated osteoblasts. The expression of bone sialoprotein (BSP) is normally restricted to mineralized connective tissues of bones and teeth where it has been associated with mineral crystal formation. However, it has been found that ectopic expression of BSP occurs in various lesions, including oral and extraoral carcinomas, in which it has been associated with the formation of microcrystalline deposits and the metastasis of cancer cells to bone. 299 matched cddid_all.tbl CDD pfam05433 pfam05433 428470 Rick_17kDa_Anti Glycine zipper 2TM domain. This family includes a putative two transmembrane alpha-helical region that contains glycine zipper motifs. This family includes several Rickettsia genus specific 17 kDa surface antigen proteins. 43 matched cddid_all.tbl CDD pfam05434 pfam05434 428471 Tmemb_9 TMEM9. This family contains several eukaryotic transmembrane proteins which are homologous to human transmembrane protein 9. The TMEM9 gene encodes a 183 amino-acid protein that contains an N-terminal signal peptide, a single transmembrane region, three potential N-glycosylation sites and three conserved cys-rich domains in the N-terminus, but no known functional domains. The protein is highly conserved between species from Caenorhabditis elegans to man and belongs to a novel family of transmembrane proteins. The exact function of TMEM9 is unknown although it has been found to be widely expressed and localized to the late endosomes and lysosomes. Members of this family contain pfam03128 repeats in their N-terminal region. 145 matched cddid_all.tbl CDD pfam05435 pfam05435 368442 Phi-29_GP3 Phi-29 DNA terminal protein GP3. This family consists of DNA terminal protein GP3 sequences from Phi-29 like bacteriophages. DNA terminal protein GP3 is linked to the 5' ends of both strands of the genome through a phosphodiester bond between the beta-hydroxyl group of a serine residue and the 5'-phosphate of the terminal deoxyadenylate. This protein is essential for DNA replication and is involved in the priming of DNA elongation. 266 matched cddid_all.tbl CDD pfam05436 pfam05436 398869 MF_alpha_N Mating factor alpha precursor N-terminus. This family contains the N-terminal regions of the Saccharomyces mating factor alpha precursor protein. All proteins in this family contain one or more copies pfam04648 further toward their C terminus. 87 matched cddid_all.tbl CDD pfam05437 pfam05437 461652 AzlD Branched-chain amino acid transport protein (AzlD). This family consists of a number of bacterial and archaeal branched-chain amino acid transport proteins. AzlD is known to be involved in conferring resistance to 4-azaleucine although its exact role is uncertain. 99 matched cddid_all.tbl CDD pfam05438 pfam05438 461653 TRH Thyrotropin-releasing hormone (TRH). This family consists of several thyrotropin-releasing hormone (TRH) proteins. Thyrotropin-Releasing Hormone (TRH; pyroGlu-His-Pro-NH2), originally isolated as a hypothalamic neuropeptide hormone, most likely acts also as a neuromodulator and/or neurotransmitter in the central nervous system (CNS). This interpretation is supported by the identification of a peptidase localized on the surface of neuronal cells which has been termed TRH-degrading ectoenzyme (TRH-DE) since it selectively inactivates TRH. TRH has been used clinically for the treatment of spinocerebellar degeneration and disturbance of consciousness in humans. 220 matched cddid_all.tbl CDD pfam05439 pfam05439 398872 JTB Jumping translocation breakpoint protein (JTB). This family contains several jumping translocation breakpoint proteins or JTBs. Jumping translocation (JT) is an unbalanced translocation that comprises amplified chromosomal segments jumping to various telomeres. JTB, located at 1q21, has been found to fuse with the telomeric repeats of acceptor telomeres in a case of JT. hJTB (human JTB) encodes a trans-membrane protein that is highly conserved among divergent eukaryotic species. JT results in a hJTB truncation, which potentially produces an hJTB product devoid of the trans-membrane domain. hJTB is located in a gene-rich region at 1q21, called EDC (Epidermal Differentiation Complex). JTB has also been implicated in prostatic carcinomas. 110 matched cddid_all.tbl CDD pfam05440 pfam05440 428474 MtrB Tetrahydromethanopterin S-methyltransferase subunit B. The N5-methyltetrahydromethanopterin: coenzyme M (EC:2.1.1.86) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump. 93 matched cddid_all.tbl CDD pfam05443 pfam05443 428475 ROS_MUCR ROS/MUCR transcriptional regulator protein. This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti. This gene encodes a 15.5-kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid and is necessary for succinoglycan production. Sinorhizobium meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of alfalfa nodules. MucR from Sinorhizobium meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan. 122 matched cddid_all.tbl CDD pfam05444 pfam05444 461654 DUF753 Protein of unknown function (DUF753). This family contains sequences with are repeated in several uncharacterized proteins from Drosophila melanogaster. 146 matched cddid_all.tbl CDD pfam05445 pfam05445 283176 Pox_ser-thr_kin Poxvirus serine/threonine protein kinase. 434 matched cddid_all.tbl CDD pfam05448 pfam05448 398876 AXE1 Acetyl xylan esterase (AXE1). This family consists of several bacterial acetyl xylan esterase proteins. Acetyl xylan esterases are enzymes that hydrolyse the ester linkages of the acetyl groups in position 2 and/or 3 of the xylose moieties of natural acetylated xylan from hardwood. These enzymes are one of the accessory enzymes which are part of the xylanolytic system, together with xylanases, beta-xylosidases, alpha-arabinofuranosidases and methylglucuronidases; these are all required for the complete hydrolysis of xylan. 316 matched cddid_all.tbl CDD pfam05449 pfam05449 428477 Phage_holin_3_7 Putative 3TM holin, Phage_holin_3. This is a family of putative proteobacterial phage three-transmembrane-domain holins. 80 matched cddid_all.tbl CDD pfam05450 pfam05450 310213 Nicastrin Nicastrin. Nicastrin and presenilin are two major components of the gamma-secretase complex, which executes the intramembrane proteolysis of type I integral membrane proteins such as the amyloid precursor protein (APP) and Notch. Nicastrin is synthesized in fibroblasts and neurons as an endoglycosidase-H-sensitive glycosylated precursor protein (immature nicastrin) and is then modified by complex glycosylation in the Golgi apparatus and by sialylation in the trans-Golgi network (mature nicastrin). A region featured in this family has a fold similar to human transferrin receptor (TfR) and a bacterial aminopeptidase. It is implicated in the pathogenesis of Alzheimer's disease. 227 matched cddid_all.tbl CDD pfam05451 pfam05451 283180 Phytoreo_Pns Phytoreovirus nonstructural protein Pns10/11. This family consists of Phytoreovirus nonstructural proteins Pns10 and Pns11. Genome segment S11 of rice gall dwarf virus (RGDV), a member of Phytoreovirus encodes a putative protein of 40 kDa that exhibits approximately 37% homology at the amino acid level to the nonstructural proteins Pns10 of rice dwarf and wound tumour viruses, which are other members of Phytoreovirus. 359 matched cddid_all.tbl CDD pfam05452 pfam05452 147565 Clavanin Clavanin. This family consists of clavanin proteins from the haemocytes of the invertebrate Styela clava, a solitary tunicate. The family is made up of four alpha-helical antimicrobial peptides, clavanins A, B, C and D. The tunicate peptides resemble magainins in size, primary sequence and antibacterial activity. Synthetic clavanin A displays comparable antimicrobial activity to magainins and cecropins. The presence of alpha-helical antimicrobial peptides in the haemocytes of a urochordate suggests that such peptides are primeval effectors of innate immunity in the vertebrate lineage. 80 matched cddid_all.tbl CDD pfam05453 pfam05453 398878 Toxin_6 BmTXKS1/BmP02 toxin family. This family consists of toxin-like peptides that are isolated from the venom of Buthus martensii Karsch scorpion. The precursor consists of 60 amino acid residues, with a putative signal peptide of 28 residues and an extra residue, and a mature peptide of 31 residues with an amidated C-terminal. The peptides share close homology with other scorpion K+ channel toxins and should present a common three-dimensional fold - the Cysteine -stabilized alphabeta (CSalphabeta) motif. This family acts by blocking small conductance calcium activated potassium ion channels in their victim. 28 matched cddid_all.tbl CDD pfam05454 pfam05454 461655 DAG1 Dystroglycan (Dystrophin-associated glycoprotein 1). Dystroglycan is one of the dystrophin-associated glycoproteins, which is encoded by a 5.5 kb transcript in human. The protein product is cleaved into two non-covalently associated subunits, [alpha] (N-terminal) and [beta] (C-terminal). In skeletal muscle the dystroglycan complex works as a transmembrane linkage between the extracellular matrix and the cytoskeleton. [alpha]-dystroglycan is extracellular and binds to merosin ([alpha]-2 laminin) in the basement membrane, while [beta]-dystroglycan is a transmembrane protein and binds to dystrophin, which is a large rod-like cytoskeletal protein, absent in Duchenne muscular dystrophy patients. Dystrophin binds to intracellular actin cables. In this way, the dystroglycan complex, which links the extracellular matrix to the intracellular actin cables, is thought to provide structural integrity in muscle tissues. The dystroglycan complex is also known to serve as an agrin receptor in muscle, where it may regulate agrin-induced acetylcholine receptor clustering at the neuromuscular junction. There is also evidence which suggests the function of dystroglycan as a part of the signal transduction pathway because it is shown that Grb2, a mediator of the Ras-related signal pathway, can interact with the cytoplasmic domain of dystroglycan. In general, aberrant expression of dystrophin-associated protein complex underlies the pathogenesis of Duchenne muscular dystrophy, Becker muscular dystrophy and severe childhood autosomal recessive muscular dystrophy. Interestingly, no genetic disease has been described for either [alpha]- or [beta]-dystroglycan. Dystroglycan is widely distributed in non-muscle tissues as well as in muscle tissues. During epithelial morphogenesis of kidney, the dystroglycan complex is shown to act as a receptor for the basement membrane. Dystroglycan expression in mouse brain and neural retina has also been reported. However, the physiological role of dystroglycan in non-muscle tissues has remained unclear. 290 matched cddid_all.tbl CDD pfam05455 pfam05455 310215 GvpH GvpH. This family consists of archaeal GvpH proteins which are thought to be involved in gas vesicle synthesis. 177 matched cddid_all.tbl CDD pfam05456 pfam05456 461656 eIF_4EBP Eukaryotic translation initiation factor 4E binding protein (EIF4EBP). This family consists of several eukaryotic translation initiation factor 4E binding proteins (EIF4EBP1,2 and 3). Translation initiation in eukaryotes is mediated by the cap structure (m7GpppN, where N is any nucleotide) present at the 5' end of all cellular mRNAs, except organellar. The cap is recognized by eukaryotic initiation factor 4F (eIF4F), which consists of three polypeptides, including eIF4E, the cap-binding protein subunit. The interaction of the cap with eIF4E facilitates the binding of the ribosome to the mRNA. eIF4E activity is regulated in part by translational repressors, 4E-BP1, 4E-BP2 and 4E-BP3 which bind to it and prevent its assembly into eIF4F. 110 matched cddid_all.tbl CDD pfam05458 pfam05458 283184 Siva Cd27 binding protein (Siva). Siva binds to the CD27 cytoplasmic tail. It has a DD homology region, a box-B-like ring finger, and a zinc finger-like domain. Overexpression of Siva in various cell lines induces apoptosis, suggesting an important role for Siva in the CD27-transduced apoptotic pathway. Siva-1 binds to and inhibits BCL-X(L)-mediated protection against UV radiation-induced apoptosis. Indeed, the unique amphipathic helical region (SAH) present in Siva-1 is required for its binding to BCL-X(L) and sensitising cells to UV radiation. Natural complexes of Siva-1/BCL-X(L) are detected in HUT78 and murine thymocyte, suggesting a potential role for Siva-1 in regulating T cell homeostasis. This family contains both Siva-1 and the shorter Siva-2 lacking the sequence coded by exon 2. It has been suggested that Siva-2 could regulate the function of Siva-1. 173 matched cddid_all.tbl CDD pfam05459 pfam05459 398881 Herpes_UL69 Herpesvirus transcriptional regulator family. This family includes UL69 and IE63 that are transcriptional regulator proteins. 217 matched cddid_all.tbl CDD pfam05460 pfam05460 368452 ORC6 Origin recognition complex subunit 6 (ORC6). This family consists of several eukaryotic origin recognition complex subunit 6 (ORC6) proteins. Despite differences in their structure and sequences among eukaryotic replicators, ORC is a conserved feature of replication initiation in all eukaryotes. ORC-related genes have been identified in organizms ranging from S. pombe to plants to humans. All DNA replication initiation is driven by a single conserved eukaryotic initiator complex termed he origin recognition complex (ORC). The ORC is a six protein complex. The function of ORC is reviewed in. 288 matched cddid_all.tbl CDD pfam05461 pfam05461 461657 ApoL Apolipoprotein L. Apo L belongs to the high density lipoprotein family that plays a central role in cholesterol transport. The cholesterol content of membranes is important in cellular processes such as modulating gene transcription and signal transduction both in the adult brain and during neurodevelopment. There are six apo L genes located in close proximity to each other on chromosome 22q12 in humans. 22q12 is a confirmed high-susceptibility locus for schizophrenia and close to the region associated with velocardiofacial syndrome that includes symptoms of schizophrenia. 298 matched cddid_all.tbl CDD pfam05462 pfam05462 283188 Dicty_CAR Slime mold cyclic AMP receptor. This family consists of cyclic AMP receptor (CAR) proteins from slime molds. CAR proteins are responsible for controlling development in Dictyostelium discoideum. 305 matched cddid_all.tbl CDD pfam05463 pfam05463 398883 Sclerostin Sclerostin (SOST). This family contains several mammalian sclerostin (SOST) proteins. SOST is thought to suppress bone formation. Mutations of the SOST gene lead to sclerosteosis, a progressive sclerosing bone dysplasia with an autosomal recessive mode of inheritance. Radiologically, it is characterized by a generalized hyperostosis and sclerosis leading to a markedly thickened and sclerotic skull, with mandible, ribs, clavicles and all long bones also being affected. Due to narrowing of the foramina of the cranial nerves, facial nerve palsy, hearing loss and atrophy of the optic nerves can occur. Sclerosteosis is clinically and radiologically very similar to van Buchem disease, mainly differentiated by hand malformations and a large stature in sclerosteosis patients. 198 matched cddid_all.tbl CDD pfam05464 pfam05464 398884 Phi-29_GP4 Phi-29-like late genes activator (early protein GP4). This family consists of phi-29-like late genes activator (or early protein GP4). This protein is thought to be a positive regulator of late transcription and may function as a sigma like component of the host RNA polymerase. 123 matched cddid_all.tbl CDD pfam05465 pfam05465 310220 Halo_GVPC Halobacterial gas vesicle protein C (GVPC) repeat. This family consists of Halobacterium gas vesicle protein C sequences which are thought to confer stability to the gas vesicle membranes. 32 matched cddid_all.tbl CDD pfam05466 pfam05466 461658 BASP1 Brain acid soluble protein 1 (BASP1 protein). This family consists of several brain acid soluble protein 1 (BASP1) or neuronal axonal membrane protein NAP-22. The BASP1 is a neuron enriched Ca(2+)-dependent calmodulin-binding protein of unknown function. 238 matched cddid_all.tbl CDD pfam05467 pfam05467 283192 Herpes_U47 Herpesvirus glycoprotein U47. 677 matched cddid_all.tbl CDD pfam05470 pfam05470 428482 eIF-3c_N Eukaryotic translation initiation factor 3 subunit 8 N-terminus. The largest of the mammalian translation initiation factors, eIF3, consists of at least eight subunits ranging in mass from 35 to 170 kDa. eIF3 binds to the 40 S ribosome in an early step of translation initiation and promotes the binding of methionyl-tRNAi and mRNA. 593 matched cddid_all.tbl CDD pfam05472 pfam05472 428483 Ter DNA replication terminus site-binding protein (Ter protein). This family contains several bacterial Ter proteins. The Ter protein specifically binds to DNA replication terminus sites on the host and plasmid genome and then blocks progress of the DNA replication fork. 295 matched cddid_all.tbl CDD pfam05473 pfam05473 368457 UL45 UL45 protein, carbohydrate-binding C-type lectin-like. This family consists of several UL45 proteins. The herpes simplex virus UL45 gene encodes an 18 kDa virion envelope protein whose function remains unknown. It has been suggested that the 18 kDa UL45 gene product is required for efficient growth in the central nervous system at low doses and may play an important role under the conditions of a naturally acquired infection. This family also contains several Varicellovirus UL45 or gene 15 proteins. The Equine herpesvirus 1 UL45 protein represents a type II membrane glycoprotein which has been found to be non-essential for EHV-1 growth in vitro but deletion reduces the viruses' replication efficiency. Studies have shown that UL45 has a C-type lectin-like fold, suggesting that it might have a carbohydrate-binding function. 191 matched cddid_all.tbl CDD pfam05474 pfam05474 368458 Semenogelin Semenogelin. This family consists of several mammalian secreted seminal proteins including semenogelin I and II. Freshly ejaculated human semen has the appearance of a loose gel in which the predominant structural protein components are the seminal vesicle secreted semenogelins (Sg). This family also includes seminal vesicle secretory protein 3A from mouse, which has been shown to be involved in the coagulation of semen resulting in the formation of the copulatory plug. 582 matched cddid_all.tbl CDD pfam05475 pfam05475 368459 Chlam_vir Pgp3 C-terminal domain. This family consists of Chlamydia virulence proteins which are thought to be required for growth within mammalian cells. The C-terminal domain shows distant homology to the TNF superfamily. 146 matched cddid_all.tbl CDD pfam05476 pfam05476 368460 PET122 PET122. The nuclear PET122 gene of S. cerevisiae encodes a mitochondrial-localized protein that activates initiation of translation of the mitochondrial mRNA from the COX3 gene, which encodes subunit III of cytochrome c oxidase. 259 matched cddid_all.tbl CDD pfam05477 pfam05477 461659 SURF2 Surfeit locus protein 2 (SURF2). Surfeit locus protein 2 is part of a group of at least six sequence unrelated genes (Surf-1 to Surf-6). The six Surfeit genes have been classified as housekeeping genes, being expressed in all tissue types tested and not containing a TATA box in their promoter region. The exact function of SURF2 is unknown. 240 matched cddid_all.tbl CDD pfam05478 pfam05478 461660 Prominin Prominin. The prominins are an emerging family of proteins that among the multispan membrane proteins display a novel topology. Mouse prominin and human prominin (mouse)-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration. 799 matched cddid_all.tbl CDD pfam05479 pfam05479 398889 PsaN Photosystem I reaction centre subunit N (PSAN or PSI-N). This family contains several Photosystem I reaction centre subunit N (PSI-N) proteins. The protein has no known function although it is localized in the thylakoid lumen. PSI-N is a small extrinsic subunit at the lumen side and is very likely involved in the docking of plastocyanin. 132 matched cddid_all.tbl CDD pfam05480 pfam05480 428486 PSMbeta Phenol-soluble modulin beta protein. This family consists of several different short Staphylococcal proteins known as the phenol-soluble modulin beta proteins. The family contains SLUSH A, B and C proteins as well as haemolysin and gonococcal growth inhibitor. Some strains of the coagulase-negative Staphylococcus lugdunensis produce a synergistic hemolytic activity (SLUSH), phenotypically similar to the delta-hemolysin of S. aureus. Gonococcal growth inhibitor from Staphylococcus act on the cytoplasmic membrane of the gonococcal cell causing cytoplasmic leakage and, eventually, death. 43 matched cddid_all.tbl CDD pfam05481 pfam05481 461661 Myco_19_kDa Mycobacterium 19 kDa lipoprotein antigen. Most of the antigens of Mycobacterium leprae and M. tuberculosis that have been identified are members of stress protein families, which are highly conserved throughout many diverse species. Of the M. leprae and M. tuberculosis antigens identified by monoclonal antibodies, all except the 18-kDa M. leprae antigen and the 19-kDa M. tuberculosis antigen are strongly cross-reactive between these two species and are coded within very similar genes. 116 matched cddid_all.tbl CDD pfam05482 pfam05482 368466 Serendipity_A Serendipity locus alpha protein (SRY-A). The Drosophila serendipity alpha (sry alpha) gene is specifically transcribed at the blastoderm stage, from nuclear cycle 11 to the onset of gastrulation, in all somatic nuclei. SRY-A is required for the cellularization of the embryo and is involved in the localization of the actin filaments just prior to and during plasma membrane invagination. This family forms a different clade of the Vinculin superfamily with an evolutionary relationship that is functionally consistent with a role for sry alpha at the actin cortex during cellularization. 542 matched cddid_all.tbl CDD pfam05483 pfam05483 114219 SCP-1 Synaptonemal complex protein 1 (SCP-1). Synaptonemal complex protein 1 (SCP-1) is the major component of the transverse filaments of the synaptonemal complex. Synaptonemal complexes are structures that are formed between homologous chromosomes during meiotic prophase. 787 matched cddid_all.tbl CDD pfam05484 pfam05484 428488 LRV_FeS LRV protein FeS4 cluster. This Iron sulphur cluster is found at the N-terminus of some proteins containing pfam01816 repeats. 53 matched cddid_all.tbl CDD pfam05485 pfam05485 461662 THAP THAP domain. The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes. 76 matched cddid_all.tbl CDD pfam05486 pfam05486 428490 SRP9-21 "Signal recognition particle 9 kDa protein (SRP9). This family consists of several eukaryotic SRP9 proteins. SRP9 together with the Alu-homologous region of 7SL RNA and SRP14 comprise the ""Alu domain"" of SRP, which mediates pausing of synthesis of ribosome associated nascent polypeptides that have been engaged by the targeting domain of SRP. This family also contains the homologous fungal SRP21." 83 matched cddid_all.tbl CDD pfam05488 pfam05488 428491 PAAR_motif PAAR motif. This motif is found usually in pairs in a family of bacterial membrane proteins. It is also found as a triplet of tandem repeats comprising the entire length in a another family of hypothetical proteins. 71 matched cddid_all.tbl CDD pfam05489 pfam05489 283209 Phage_tail_X Phage Tail Protein X. This domain is found in a family of phage tail proteins. Visual analysis suggests that it is related to pfam01476 (personal obs: C Yeats). The functional annotation of family members further confirms this hypothesis. 60 matched cddid_all.tbl CDD pfam05491 pfam05491 398896 RuvB_C RuvB C-terminal winged helix domain. The RuvB protein makes up part of the RuvABC revolvasome which catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalyzed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family consists of the C-terminal region of the RuvB protein which is thought to be helicase DNA-binding domain. 72 matched cddid_all.tbl CDD pfam05493 pfam05493 461663 ATP_synt_H ATP synthase subunit H. ATP synthase subunit H is an extremely hydrophobic of approximately 9 kDa. This subunit may be required for assembly of vacuolar ATPase. 59 matched cddid_all.tbl CDD pfam05494 pfam05494 461664 MlaC MlaC protein. MlaC is a component of the Mla pathway, an ABC transport system that functions to maintain the asymmetry of the outer membrane. This family of proteins is involved in toluene tolerance, which is mediated by increased cell membrane rigidity resulting from changes in fatty acid and phospholipid compositions, exclusion of toluene from the cell membrane, and removal of intracellular toluene by degradation. Many proteins are involved in these processes. 165 matched cddid_all.tbl CDD pfam05495 pfam05495 461665 zf-CHY CHY zinc finger. This family of domains are likely to bind to zinc ions. They contain many conserved cysteine and histidine residues. We have named this domain after the N-terminal motif CXHY. This domain can be found in isolation in some proteins, but is also often associated with pfam00097. One of the proteins in this family is a mitochondrial intermembrane space protein called Hot13. This protein is involved in the assembly of small TIM complexes. 75 matched cddid_all.tbl CDD pfam05496 pfam05496 398900 RuvB_N Holliday junction DNA helicase RuvB P-loop domain. The RuvB protein makes up part of the RuvABC revolvasome which catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalyzed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein. 159 matched cddid_all.tbl CDD pfam05497 pfam05497 461666 Destabilase Destabilase. Destabilase is an endo-epsilon(gamma-Glu)-Lys isopeptidase, which cleaves isopeptide bonds formed by transglutaminase (Factor XIIIa) between glutamine gamma-carboxamide and the epsilon-amino group of lysine. 118 matched cddid_all.tbl CDD pfam05498 pfam05498 428496 RALF Rapid ALkalinization Factor (RALF). Family members found in Arabidopsis include RALF23. It has been shown to reduce plant growth upon overexpression while mature plants were dwarfed and bushy. It has also been suggested that RALF23 of Arabidopsis, counteracts brassinosteroid (BR) growth-promoting effects which may be relieved by the down-regulation of RALF23 65 matched cddid_all.tbl CDD pfam05499 pfam05499 398903 DMAP1 DNA methyltransferase 1-associated protein 1 (DMAP1). DNA methylation can contribute to transcriptional silencing through several transcriptionally repressive complexes, which include methyl-CpG binding domain proteins (MBDs) and histone deacetylases (HDACs). The chief enzyme that maintains mammalian DNA methylation, DNMT1, can also establish a repressive transcription complex. The non-catalytic amino terminus of DNMT1 binds to HDAC2 and DMAP1 (for DNMT1 associated protein), and can mediate transcriptional repression. DMAP1 has intrinsic transcription repressive activity, and binds to the transcriptional co-repressor TSG101. DMAP1 is targeted to replication foci through interaction with the far N terminus of DNMT1 throughout S phase, whereas HDAC2 joins DNMT1 and DMAP1 only during late S phase, providing a platform for how histones may become deacetylated in heterochromatin following replication. 163 matched cddid_all.tbl CDD pfam05501 pfam05501 368473 DUF755 Domain of unknown function (DUF755). This family is predominated by ORFs from Circoviridae. The function of this family remains to be determined. 122 matched cddid_all.tbl CDD pfam05502 pfam05502 428497 Dynactin_p62 Dynactin p62 family. Dynactin is a multi-subunit complex and a required cofactor for most, or all, of the cellular processes powered by the microtubule-based motor cytoplasmic dynein. p62 binds directly to the Arp1 subunit of dynactin. 474 matched cddid_all.tbl CDD pfam05503 pfam05503 283219 Pox_G7 Poxvirus G7-like. 367 matched cddid_all.tbl CDD pfam05504 pfam05504 428498 Spore_GerAC Spore germination B3/ GerAC like, C-terminal. The GerAC protein of the Bacillus subtilis spore is required for the germination response to L-alanine. Members of this family are thought to be located in the inner spore membrane. Although the function of this family is unclear, they are likely to encode the components of the germination apparatus that respond directly to this germinant, mediating the spore's response. 167 matched cddid_all.tbl CDD pfam05505 pfam05505 398905 Ebola_NP Ebola nucleoprotein. This family consists of Ebola and Marburg virus nucleoproteins. These proteins are responsible for encapsidation of genomic RNA. It has been found that nucleoprotein DNA vaccines can offer protection from the virus. 717 matched cddid_all.tbl CDD pfam05506 pfam05506 428499 PLipase_C_C Bacterial phospholipase C, C-terminal domain. This domain is found, normally as a tandem repeat, at the C-terminus of bacterial phospholipase C proteins. 86 matched cddid_all.tbl CDD pfam05507 pfam05507 461667 MAGP Microfibril-associated glycoprotein (MAGP). This family consists of several mammalian microfibril-associated glycoprotein (MAGP) 1 and 2 proteins. MAGP1 and 2 are components of elastic fibres. MAGP-1 has been proposed to bind a C-terminal region of tropoelastin, the soluble precursor of elastin. MAGP-2 was found to interact with fibrillin-1 and -2, as well as fibulin-1, another component of elastic fibres this suggests that MAGP-2 may be important in the assembly of microfibrils. 137 matched cddid_all.tbl CDD pfam05508 pfam05508 428501 Ran-binding RanGTP-binding protein. The small Ras-like GTPase Ran plays an essential role in the transport of macromolecules in and out of the nucleus and has been implicated in spindle and nuclear envelope formation during mitosis in higher eukaryotes. The S. cerevisiae ORF YGL164c encoding a novel RanGTP-binding protein, termed Yrb30p was identified. The protein competes with yeast RanBP1 (Yrb1p) for binding to the GTP-bound form of yeast Ran (Gsp1p) and is, like Yrb1p, able to form trimeric complexes with RanGTP and some of the karyopherins. 308 matched cddid_all.tbl CDD pfam05509 pfam05509 428502 TraY TraY domain. This family consists of several enterobacterial TraY proteins. TraY is involved in bacterial conjugation where it is required for efficient nick formation in the F plasmid. These proteins have a ribbon-helix-helix fold and are likely to be DNA-binding proteins. 49 matched cddid_all.tbl CDD pfam05510 pfam05510 461668 Sarcoglycan_2 Sarcoglycan alpha/epsilon. Sarcoglycans are a subcomplex of transmembrane proteins which are part of the dystrophin-glycoprotein complex. They are expressed in the skeletal, cardiac and smooth muscle. Although numerous studies have been conducted on the sarcoglycan subcomplex in skeletal and cardiac muscle, the manner of the distribution and localization of these proteins along the nonjunctional sarcolemma is not clear. This family contains alpha and epsilon members. 410 matched cddid_all.tbl CDD pfam05511 pfam05511 461669 ATP-synt_F6 Mitochondrial ATP synthase coupling factor 6. Coupling factor 6 (F6) is a component of mitochondrial ATP synthase which is required for the interactions of the catalytic and proton-translocating segments. 96 matched cddid_all.tbl CDD pfam05512 pfam05512 398911 AWPM-19 AWPM-19-like family. Members of this family are 19 kDa membrane proteins. The levels of the plant protein AWPM-19 increase dramatically when there is an increase level of abscisic acid. The increase presence of this protein leads to greater tolerance of freezing. 142 matched cddid_all.tbl CDD pfam05513 pfam05513 283228 TraA TraA. Conjugative transfer of a bacteriocin plasmid, pPD1, of Enterococcus faecalis is induced in response to a peptide sex pheromone, cPD1, secreted from plasmid-free recipient cells. cPD1 is taken up by a pPD1 donor cell and binds to an intracellular receptor, TraA. Once a recipient cell acquires pPD1, it starts to produce an inhibitor of cPD1, termed iPD1, which functions as a TraA antagonist and blocks self-induction in donor cells. TraA transduces the signal of cPD1 to the mating response. 120 matched cddid_all.tbl CDD pfam05514 pfam05514 283229 HR_lesion HR-like lesion-inducing. Family of plant proteins that are associated with the hypersensitive response (HR) pathway of defence against plant pathogens. 138 matched cddid_all.tbl CDD pfam05515 pfam05515 283230 Viral_NABP Viral nucleic acid binding. This family is common to ssRNA positive-strand viruses and are commonly described as nucleic acid binding proteins (NABP). 190 matched cddid_all.tbl CDD pfam05517 pfam05517 461670 p25-alpha p25-alpha. This family encodes a 25 kDa protein that is phosphorylated by a Ser/Thr-Pro kinase. It has been described as a brain specific protein, but it is found in Tetrahymena thermophila. 155 matched cddid_all.tbl CDD pfam05518 pfam05518 428505 Totivirus_coat Totivirus coat protein. 727 matched cddid_all.tbl CDD pfam05520 pfam05520 114252 Citrus_P18 Citrus tristeza virus P18 protein. 167 matched cddid_all.tbl CDD pfam05521 pfam05521 428506 Phage_H_T_join Phage head-tail joining protein. 96 matched cddid_all.tbl CDD pfam05522 pfam05522 114254 Metallothio_6 Metallothionein. This family consists of metallothioneins from several worm and sea urchin species. Metallothioneins are low molecular weight, cysteine rich proteins known to be involved in heavy metal detoxification and homeostasis. 65 matched cddid_all.tbl CDD pfam05523 pfam05523 428507 FdtA WxcM-like, C-terminal. This family includes FdtA from Aneurinibacillus thermoaerophilus, which has been characterized as a dtdp-6-deoxy-3,4-keto-hexulose isomerase. It also includes WxcM from Xanthomonas campestris (pv. campestris). 129 matched cddid_all.tbl CDD pfam05524 pfam05524 461671 PEP-utilizers_N PEP-utilizing enzyme, N-terminal. 125 matched cddid_all.tbl CDD pfam05525 pfam05525 428509 Branch_AA_trans Branched-chain amino acid transport protein. This family consists of several bacterial branched-chain amino acid transport proteins which are responsible for the transport of leucine, isoleucine and valine via proton motive force. 425 matched cddid_all.tbl CDD pfam05526 pfam05526 398915 R_equi_Vir Rhodococcus equi virulence-associated protein. This family consists of several virulence-associated proteins from Rhodococcus equi. Rhodococcus equi is an important pulmonary pathogen of foals and is increasingly isolated from pneumonic infections and other infections in human immunodeficiency virus (HIV)-infected patients. Isolates from foals possess a large virulence plasmid, varying in size from 80 to 90 kb. Isolates lacking the plasmid are avirulent to foals. Little is known about the function of the plasmid apart from its encoding a virulence associated surface proteins. 177 matched cddid_all.tbl CDD pfam05527 pfam05527 461672 DUF758 Domain of unknown function (DUF758). Family of eukaryotic proteins with unknown function, which are induced by tumour necrosis factor. 160 matched cddid_all.tbl CDD pfam05528 pfam05528 283238 Acc5b_avian_CoV Accessory protein 5b, avian coronavirus. Avian infectious bronchitis virus, a member of Coronaviridae family, has a single-stranded positive-sense RNA genome, which is 27 kb in length. Gene 5 contains two (5a and 5b) open reading frames. This entry represents the host translation inhibitor 5b (ORF 5b, also known as accessory protein 5b) which is involved in host translation shut off without degrading host RNA. It suppresses host gene expression which facilitates evasion from host type I interferon immune response. 82 matched cddid_all.tbl CDD pfam05529 pfam05529 461673 Bap31 Bap31/Bap29 transmembrane region. Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31. This family also contains the Bap29 protein that forms a heterodimer with Bap 31. 137 matched cddid_all.tbl CDD pfam05531 pfam05531 368485 NPV_P10 Nucleopolyhedrovirus P10 protein. This family consists of several nucleopolyhedrovirus P10 proteins which are thought to be involved in the morphogenesis of the polyhedra. 75 matched cddid_all.tbl CDD pfam05532 pfam05532 428512 CsbD CsbD-like. CsbD is a bacterial general stress response protein. It's expression is mediated by sigma-B, an alternative sigma factor. The role of CsbD in stress response is unclear. 53 matched cddid_all.tbl CDD pfam05533 pfam05533 114264 Peptidase_C42 Beet yellows virus-type papain-like endopeptidase C42. Members of the Closteroviridae and Potyviridae families of plant positive-strand RNA viruses encode one or two papain-like leader proteinases, belonging to Merops peptidase family C42. 88 matched cddid_all.tbl CDD pfam05534 pfam05534 310261 HicB HicB family. This family consists of several bacterial HicB related proteins. The function of HicB is unknown although it is thought to be involved in pilus formation. It has been speculated that HicB performs a function antagonistic to that of pili and yet is necessary for invasion of certain niches. 51 matched cddid_all.tbl CDD pfam05535 pfam05535 398919 Chromadorea_ALT Chromadorea ALT protein. This family consists of several ALT protein homologs found in nematodes. Lymphatic filariasis is a major tropical disease caused by the mosquito borne nematodes Brugia and Wuchereria. About 120 million people are infected and at risk of lymphatic pathology such as acute lymphangitis and elephantiasis. Expression of alt-1 and alt-2 is initiated midway through development in the mosquito, peaking in the infective larva and declining sharply following entry into the host. ALT-1 and the closely related ALT-2 have been found to be strong candidates for a future vaccine against human filariasis. 77 matched cddid_all.tbl CDD pfam05536 pfam05536 336138 Neurochondrin Neurochondrin. This family contains several eukaryotic neurochondrin proteins. Neurochondrin induces hydroxyapatite resorptive activity in bone marrow cells resistant to bafilomycin A1, an inhibitor of macrophage- and osteoclast-mediated resorption. Expression of the gene is localized to chondrocyte, osteoblast, and osteocyte in the bone and to the hippocampus and Purkinje cell layer of cerebellum in the brain. 605 matched cddid_all.tbl CDD pfam05537 pfam05537 283245 DUF759 Borrelia burgdorferi protein of unknown function (DUF759). This family consists of several uncharacterized proteins from the Lyme disease spirochete Borrelia burgdorferi. 429 matched cddid_all.tbl CDD pfam05538 pfam05538 368487 Campylo_MOMP Campylobacter major outer membrane protein. This family consists of Campylobacter major outer membrane proteins. The major outer membrane protein (MOMP), a putative porin and a multifunction surface protein of Campylobacter jejuni, may play an important role in the adaptation of the organizm to various host environments. 421 matched cddid_all.tbl CDD pfam05539 pfam05539 114270 Pneumo_att_G Pneumovirinae attachment membrane glycoprotein G. 408 matched cddid_all.tbl CDD pfam05540 pfam05540 428513 Serpulina_VSP Serpulina hyodysenteriae variable surface protein. This family consists of several variable surface proteins from Serpulina hyodysenteriae. 401 matched cddid_all.tbl CDD pfam05541 pfam05541 253243 Spheroidin Entomopoxvirus spheroidin protein. Entomopoxviruses (EPVs) are large (300-400 nm) oval-shaped viruses replicating in the cytoplasm of their insect host cells. At the end of their replicative cycle EPVs virions are occluded in a highly expressed protein called spheroidin. This protein forms large (5-20 mm long) oval-shaped occlusion bodies (OBs) called spherules. The infectious cycle of EPVs begins with the ingestion by the insect host of the spherules, their dissolution by the alkaline reducing conditions of the midgut fluid and the release of virions in the midgut lumen. The infective particles first replicate in midgut epithelial cells, then pass the gut barrier to colonize the internal tissues, mainly the fat body cells. Whilst spheroidin has been demonstrated to be non-essential for viral replication, it plays an essential role in the natural biological cycle of the virus in protecting virions from adverse environmental conditions (e.g. UV degradation) and thus improving transmission efficacy. In this respect, spheroidins are functionally similar to polyhedrins of baculoviruses or cypoviruses. 943 matched cddid_all.tbl CDD pfam05542 pfam05542 461674 DUF760 Protein of unknown function (DUF760). This family contains several uncharacterized plant proteins. 83 matched cddid_all.tbl CDD pfam05543 pfam05543 398922 Peptidase_C47 Staphopain peptidase C47. Staphopains are one of four major families of proteinases secreted by the Gram-positive Staphylococcus aureus. These staphylococcal cysteine proteases are secreted as preproenzymes that are proteolytically cleaved to generate the mature enzyme. 174 matched cddid_all.tbl CDD pfam05544 pfam05544 398923 Pro_racemase Proline racemase. This family consists of proline racemase (EC 5.1.1.4) proteins which catalyze the interconversion of L- and D-proline in bacteria. This family also contains several similar eukaryotic proteins including Swiss:Q9NCP4 a sequence with B-cell mitogenic properties which has been characterized as a co-factor-independent proline racemase. 325 matched cddid_all.tbl CDD pfam05545 pfam05545 428515 FixQ Cbb3-type cytochrome oxidase component FixQ. This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon. 49 matched cddid_all.tbl CDD pfam05546 pfam05546 428516 She9_MDM33 She9 / Mdm33 family. Members of this family are mitochondrial inner membrane proteins with a role in inner mitochondrial membrane organization and biogenesis. 198 matched cddid_all.tbl CDD pfam05547 pfam05547 398926 Peptidase_M6 Immune inhibitor A peptidase M6. The insect pathogenic Gram-positive Bacillus thuringiensis secretes immune inhibitor A, a metallopeptidase, which specifically cleaves host antibacterial proteins. A homolog of immune inhibitor A, PrtV, has been identified in the Gram-negative human pathogen Vibrio cholerae. 644 matched cddid_all.tbl CDD pfam05548 pfam05548 336143 Peptidase_M11 Gametolysin peptidase M11. In the unicellular biflagellated alga, Chlamydomonas reinhardtii, gametolysin, a zinc-containing metallo-protease, is responsible for the degradation of the cell wall. homologs of gametolysin have also been reported in the simple multicellular organizm, Volvox. 303 matched cddid_all.tbl CDD pfam05549 pfam05549 253247 Allexi_40kDa Allexivirus 40kDa protein. 271 matched cddid_all.tbl CDD pfam05550 pfam05550 283255 Peptidase_C53 Pestivirus Npro endopeptidase C53. Unique to pestiviruses, the N-terminal protein encoded by the bovine viral diarrhoea virus genome is a cysteine protease (Npro) responsible for a self-cleavage that releases the N terminus of the core protein. This unique protease is dispensable for viral replication, and its coding region can be replaced by a ubiquitin gene directly fused in frame to the core. 168 matched cddid_all.tbl CDD pfam05551 pfam05551 368495 zf-His_Me_endon Zinc-binding loop region of homing endonuclease. This domain is the short zinc-binding loops region of a number of much longer chain homing endonucleases. Such loops are probably stabilized by the zinc and may be viewed as small but separate domains. The common structural feature of these domains is that at least three zinc ligands lie very close to each other in the sequence and are not incorporated into regular secondary structural elements. The biological roles played by these small zinc-binding domains are presently unknown. 131 matched cddid_all.tbl CDD pfam05552 pfam05552 428517 TM_helix Conserved TM helix. This alignment represents a conserved transmembrane helix as well as some flanking sequence. It is often found in association with pfam00924. 48 matched cddid_all.tbl CDD pfam05553 pfam05553 461675 DUF761 Cotton fibre expressed protein. This family consists of several plant proteins of unknown function. Three of the sequences (from Gossypium hirsutum) in this family are described as cotton fibre expressed proteins. The remaining sequences, found in Arabidopsis thaliana, are uncharacterized. 35 matched cddid_all.tbl CDD pfam05554 pfam05554 147629 Novirhabdo_Nv Viral hemorrhagic septicemia virus non-virion protein. This family consists of several viral hemorrhagic septicemia virus non-virion (Nv) proteins. The NV protein is a nonstructural protein absent from mature virions although it is present in infected cells. The function of this protein is unknown. 122 matched cddid_all.tbl CDD pfam05555 pfam05555 283259 DUF762 Coxiella burnetii protein of unknown function (DUF762). This family consists several of several uncharacterized proteins from the bacterium Coxiella burnetii. Coxiella burnetii is the causative agent of the Q fever disease. 244 matched cddid_all.tbl CDD pfam05556 pfam05556 461676 Calsarcin Calcineurin-binding protein (Calsarcin). This family consists of several mammalian calcineurin-binding proteins. The calcium- and calmodulin-dependent protein phosphatase calcineurin has been implicated in the transduction of signals that control the hypertrophy of cardiac muscle and slow fibre gene expression in skeletal muscle. Calsarcin-1 and calsarcin-2 are expressed in developing cardiac and skeletal muscle during embryogenesis, but calsarcin-1 is expressed specifically in adult cardiac and slow-twitch skeletal muscle, whereas calsarcin-2 is restricted to fast skeletal muscle. Calsarcins represent a novel family of sarcomeric proteins that link calcineurin with the contractile apparatus, thereby potentially coupling muscle activity to calcineurin activation. Calsarcin-3, is expressed specifically in skeletal muscle and is enriched in fast-twitch muscle fibres. Like calsarcin-1 and calsarcin-2, calsarcin-3 interacts with calcineurin, and the Z-disc proteins alpha-actinin, gamma-filamin, and telethonin. 255 matched cddid_all.tbl CDD pfam05557 pfam05557 461677 MAD Mitotic checkpoint protein. This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated. 660 matched cddid_all.tbl CDD pfam05558 pfam05558 368499 DREPP DREPP plasma membrane polypeptide. This family contains several plant plasma membrane proteins termed DREPPs as they are developmentally regulated plasma membrane polypeptides. 206 matched cddid_all.tbl CDD pfam05559 pfam05559 461678 DUF763 Protein of unknown function (DUF763). This family consists of several uncharacterized bacterial and archaeal proteins of unknown function. 318 matched cddid_all.tbl CDD pfam05560 pfam05560 114291 Bt_P21 Bacillus thuringiensis P21 molecular chaperone protein. This family contains several Bacillus thuringiensis P21 proteins. These proteins are thought to be molecular chaperones and have mosquitocidal properties. 182 matched cddid_all.tbl CDD pfam05561 pfam05561 310276 DUF764 Borrelia burgdorferi protein of unknown function (DUF764). This family consists of proteins of unknown function from Borrelia burgdorferi (Lyme disease spirochete). 182 matched cddid_all.tbl CDD pfam05562 pfam05562 398931 WCOR413 Cold acclimation protein WCOR413. This family consists of several WCOR413-like plant cold acclimation proteins. 181 matched cddid_all.tbl CDD pfam05563 pfam05563 461679 SpvD Salmonella plasmid virulence protein SpvD. This family consists of several SpvD plasmid virulence proteins from different Salmonella species.The structure of the protein from Salmonella typhimurium has been solved and shows a papain-like fold, with a predicted catalytic triad of Cys73, His162 and Asp182. The protein has been shown to have deubiquitinating-like activity, releasing aminoluciferin (AML) from Ub-AML. 212 matched cddid_all.tbl CDD pfam05564 pfam05564 398933 Auxin_repressed Dormancy/auxin associated protein. This family contains several plant dormancy-associated and auxin-repressed proteins the function of which are poorly understood. 117 matched cddid_all.tbl CDD pfam05565 pfam05565 398934 Sipho_Gp157 Siphovirus Gp157. This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophages. It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage. 162 matched cddid_all.tbl CDD pfam05566 pfam05566 283269 Pox_vIL-18BP Orthopoxvirus interleukin 18 binding protein. Interleukin-18 (IL-18) is a proinflammatory cytokine that plays a key role in the activation of natural killer and T helper 1 cell responses principally by inducing interferon-gamma (IFN-gamma). Several poxvirus genes encode proteins with sequence similarity to IL-18BPs. It has been shown that vaccinia, ectromelia and cowpox viruses secrete from infected cells a soluble IL-18BP (vIL-18BP) that may modulate the host antiviral response. The expression of vIL-18BPs by distinct poxvirus genera that cause local or general viral dissemination, or persistent or acute infections in the host, emphasizes the importance of IL-18 in response to viral infections. 126 matched cddid_all.tbl CDD pfam05567 pfam05567 398935 Neisseria_PilC Neisseria PilC beta-propeller domain. This family consists of several PilC protein sequences from Neisseria gonorrhoeae and N. meningitidis. PilC is a phase-variable protein associated with pilus-mediated adherence of pathogenic Neisseria to target cells. This domain has been shown to adopt a beta-propeller structure. 411 matched cddid_all.tbl CDD pfam05568 pfam05568 114299 ASFV_J13L African swine fever virus J13L protein. This family consists of several African swine fever virus J13L proteins. 189 matched cddid_all.tbl CDD pfam05569 pfam05569 428523 Peptidase_M56 BlaR1 peptidase M56. Production of beta-Lactamase and penicillin-binding protein 2a (which mediate staphylococcal resistance to beta-lactam antibiotics) is regulated by a signal-transducing integral membrane protein and a transcriptional repressor. The signal transducer is a fusion protein with penicillin-binding and zinc metalloprotease domains. The signal for protein expression is transmitted by site-specific proteolytic cleavage of both the transducer, which auto-activates, and the repressor, which is inactivated, unblocking gene transcription. homologs to this peptidase domain, which corresponds to Merops family M56, are also found in a number of other bacterial genome sequences. 296 matched cddid_all.tbl CDD pfam05570 pfam05570 114301 DUF765 Circovirus protein of unknown function (DUF765). This family consists of several short (27-30aa) porcine and bovine circovirus ORF6 proteins of unknown function. 29 matched cddid_all.tbl CDD pfam05571 pfam05571 398936 JAMP JNK1/MAPK8-associated membrane protein. This family consists of several eukaryotic proteins including JAMP, a Jun N-terminal kinase 1 (JNK1)-associated membrane protein. It associates with JNK1 through its C-terminal domain and regulates the duration of JNK1 activity in response to diverse stress stimuli. It is an important component for coordinated clearance of misfolded proteins from the ER. 292 matched cddid_all.tbl CDD pfam05572 pfam05572 368506 Peptidase_M43 Pregnancy-associated plasma protein-A. Pregnancy-associated plasma protein A (PAPP-A) is a metallo-protease belonging to Merops family M43. It cleaves insulin-like growth factor (IGF) binding protein-4 (IGFBP-4), causing a dramatic reduction in its affinity for IGF-I and -II. Through this mechanism, PAPP-A is a regulator of IGF bioactivity in several systems, including the human ovary and the cardiovascular system. 152 matched cddid_all.tbl CDD pfam05573 pfam05573 461680 NosL NosL. NosL is one of the accessory proteins of the nos (nitrous oxide reductase) gene cluster. NosL is a monomeric protein of 18,540 MW that specifically and stoichiometrically binds Cu(I). The copper ion in NosL is ligated by a Cys residue, and one Met and one His are thought to serve as the other ligands. It is possible that NosL is a copper chaperone involved in metallo-centre assembly. 129 matched cddid_all.tbl CDD pfam05575 pfam05575 114305 V_cholerae_RfbT Vibrio cholerae RfbT protein. This family consists of several RfbT proteins from Vibrio cholerae. It has been found that genetic alteration of the rfbT gene is responsible for serotype conversion of Vibrio cholerae O1 and determines the difference between the Ogawa and Inaba serotypes, in that the presence of rfbT is sufficient for Inaba-to-Ogawa serotype conversion. 286 matched cddid_all.tbl CDD pfam05576 pfam05576 461681 Peptidase_S37 PS-10 peptidase S37. These serine proteases have been found in Streptomyces species. 448 matched cddid_all.tbl CDD pfam05577 pfam05577 310284 Peptidase_S28 Serine carboxypeptidase S28. These serine proteases include several eukaryotic enzymes such as lysosomal Pro-X carboxypeptidase, dipeptidyl-peptidase II, and thymus-specific serine peptidase. 434 matched cddid_all.tbl CDD pfam05578 pfam05578 398938 Peptidase_S31 Pestivirus NS3 polyprotein peptidase S31. These serine peptidases are involved in processing of the flavivirus polyprotein. 211 matched cddid_all.tbl CDD pfam05579 pfam05579 253263 Peptidase_S32 Equine arteritis virus serine endopeptidase S32. Serine peptidases involved in processing nidovirus polyprotein. 297 matched cddid_all.tbl CDD pfam05580 pfam05580 461682 Peptidase_S55 SpoIVB peptidase S55. The protein SpoIVB plays a key role in signalling in the final sigma-K checkpoint of Bacillus subtilis. 210 matched cddid_all.tbl CDD pfam05582 pfam05582 428526 Peptidase_U57 YabG peptidase U57. YabG is a protease involved in the proteolysis and maturation of SpoIVA and YrbA proteins, conserved with the cortex and/or coat assembly by Bacillus subtilis. 280 matched cddid_all.tbl CDD pfam05584 pfam05584 283279 Sulfolobus_pRN Sulfolobus plasmid regulatory protein. This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus. 72 matched cddid_all.tbl CDD pfam05585 pfam05585 147642 DUF1758 Putative peptidase (DUF1758). This is a family of nematode proteins of unknown function. However, it seems likely that these proteins act as aspartic peptidases. 164 matched cddid_all.tbl CDD pfam05586 pfam05586 461683 Ant_C Anthrax receptor C-terminus region. This region is found in the putatively cytoplasmic C-terminus of the anthrax receptor. 93 matched cddid_all.tbl CDD pfam05587 pfam05587 461684 Anth_Ig Anthrax receptor extracellular domain. This region is found in the putatively extracellular N-terminal half of the anthrax receptor. It is probably part of the Ig superfamily and most closely related to pfam01833 (personal obs: C Yeats). 102 matched cddid_all.tbl CDD pfam05588 pfam05588 283282 Botulinum_HA-17 Clostridium botulinum HA-17 domain. This family consists of several Clostridium botulinum hemagglutinin (HA) subcomponents. Clostridium botulinum type D strain 4947 produces two different sizes of progenitor toxins (M and L) as intact forms without proteolytic processing. The M toxin is composed of neurotoxin (NT) and nontoxic-nonhemagglutinin (NTNHA), whereas the L toxin is composed of the M toxin and hemagglutinin (HA) subcomponents (HA-70, HA-17, and HA-33). 145 matched cddid_all.tbl CDD pfam05589 pfam05589 398943 DUF768 Protein of unknown function (DUF768). This family consists of several uncharacterized hypothetical proteins from Rhizobium loti. 67 matched cddid_all.tbl CDD pfam05590 pfam05590 283284 DUF769 Xylella fastidiosa protein of unknown function (DUF769). This family consists of several uncharacterized hypothetical proteins of unknown function from Xylella fastidiosa, the organizm that causes Pierce's disease in plants. 259 matched cddid_all.tbl CDD pfam05591 pfam05591 428529 T6SS_VipA Type VI secretion system, VipA, VC_A0107 or Hcp2. T6SSs are toxin delivery systems. It is a multiprotein complex requiring numerous core proteins (Tss proteins) including cytoplasmic, transmembrane, and outer membrane components. The needle or tube apparatus is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex. VipA is a family of Gram-negative bacterial proteins that form part of the type VI pathogenic secretion system. Members have been variously defined as VC_A0107 family, Hcp2, TssB and VipA, for ClpV-interacting proteins. VipB and VipA proteins interact very closely to form the shaft of the pathogenic penetrating needle system. VipA and VipB (TssB and TssC) proteins were shown to form a cog-wheel like tubular structure in V. cholerae that was noticed to resemble T4 phage gp18 polysheath. Two beta-strands of VipA and four beta-strands of VipB intertwine forming the middle layer of the sheath. The sheath assembles around an inner Hcp tube and is attached to a structure called a baseplate that spans the bacterial membranes. Importantly, VipA/VipB sheath was shown to form a long contractile organelle in V. cholerae and in E. coli, suggesting that sheath contraction powers the secretion. 154 matched cddid_all.tbl CDD pfam05592 pfam05592 336149 Bac_rhamnosid Bacterial alpha-L-rhamnosidase concanavalin-like domain. This family consists of bacterial rhamnosidase A and B enzymes. L-Rhamnose is abundant in biomass as a common constituent of glycolipids and glycosides, such as plant pigments, pectic polysaccharides, gums or biosurfactants. Some rhamnosides are important bioactive compounds. For example, terpenyl glycosides, the glycosidic precursor of aromatic terpenoids, act as important flavouring substances in grapes. Other rhamnosides act as cytotoxic rhamnosylated terpenoids, as signal substances in plants or play a role in the antigenicity of pathogenic bacteria. 102 matched cddid_all.tbl CDD pfam05593 pfam05593 461685 RHS_repeat RHS Repeat. RHS proteins contain extended repeat regions. These repeats often appear to be involved in ligand binding. Note that this model may not find all the repeats in a protein and that it covers two RHS repeats. The 3D structure of an RHS-repeat-containing protein (the B and C components of an ABC toxin complex) has been determined. The RHS repeats form an extended strip of beta-sheet that spirals around to form a hollow shell, encapsulating the variable C-terminal domain. 37 matched cddid_all.tbl CDD pfam05594 pfam05594 461686 Fil_haemagg Haemagglutinin repeat. This highly divergent repeat occurs in number of proteins implicated in cell aggregation. The Pfam alignment probably contains three such repeats (personal obs: C Yeats). These are likely to have a beta-helical structure. 68 matched cddid_all.tbl CDD pfam05595 pfam05595 428532 DUF771 Domain of unknown function (DUF771). Family of uncharacterized ORFs found in Bacteriophage and Lactococcus lactis. 90 matched cddid_all.tbl CDD pfam05596 pfam05596 398948 Taeniidae_ag Taeniidae antigen. This family consists of several antigen proteins from Taenia and Echinococcus (tapeworm) species. 64 matched cddid_all.tbl CDD pfam05597 pfam05597 428533 Phasin Poly(hydroxyalcanoate) granule associated protein (phasin). Polyhydroxyalkanoates (PHAs) are storage polyesters synthesized by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon. 126 matched cddid_all.tbl CDD pfam05598 pfam05598 461687 DUF772 Transposase domain (DUF772). This presumed domain is found at the N-terminus of many proteins found in transposons. 71 matched cddid_all.tbl CDD pfam05599 pfam05599 191311 Deltaretro_Tax Deltaretrovirus Tax protein. This family consists of Rex/Tax proteins from human and simian T-cell leukaemia viruses. The exact function of these proteins is unknown. Tax is the viral transactivator; is it a nuclear phosphoprotein that interacts with CREB, coactivator CBP/p300 and PCAF to form a multiprotein complex, which activates viral LTR and stimulates virus expression. Tax is also involved in deregulated expression of numerous cellular genes leading to T-cell leukaemia. Rex is a nucleolar post transcriptional regulator that facilitates export to the cytoplasm of viral RNA not or incompletely spliced [personal communication, Dr. S Nicot]. 87 matched cddid_all.tbl CDD pfam05600 pfam05600 461688 CDK5RAP3 CDK5 regulatory subunit-associated protein 3. This family contains several eukaryotic sequences such as CDK5RAP3 (also known as C53 or LZAP) which serves as a probable tumour suppressor. Initially identified as a CDK5R1 interactor controlling cell proliferation. It negatively regulates NF-kappa-B-mediated gene transcription through the control of RELA phosphorylation. It also regulates mitotic G2/M transition checkpoint and mitotic G2 DNA damage checkpoint. It has been shown to bind Wip1 and stimulates its phosphatase activity. 506 matched cddid_all.tbl CDD pfam05602 pfam05602 461689 CLPTM1 Cleft lip and palate transmembrane protein 1 (CLPTM1). This family consists of several eukaryotic cleft lip and palate transmembrane protein 1 sequences. Cleft lip with or without cleft palate is a common birth defect that is genetically complex. The nonsyndromic forms have been studied genetically using linkage and candidate-gene association studies with only partial success in defining the loci responsible for orofacial clefting. CLPTM1 encodes a transmembrane protein and has strong homology to two Caenorhabditis elegans genes, suggesting that CLPTM1 may belong to a new gene family. This family also contains the human cisplatin resistance related protein CRR9p which is associated with CDDP-induced apoptosis. 431 matched cddid_all.tbl CDD pfam05603 pfam05603 461690 DUF775 Protein of unknown function (DUF775). This family consists of several eukaryotic proteins of unknown function. 199 matched cddid_all.tbl CDD pfam05604 pfam05604 428538 DUF776 Protein of unknown function (DUF776). This family consists of several highly related mouse and human proteins of unknown function. 182 matched cddid_all.tbl CDD pfam05605 pfam05605 428539 zf-Di19 Drought induced 19 protein (Di19), zinc-binding. This family consists of several drought induced 19 (Di19) like proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought. This domain is a zinc-binding domain. 54 matched cddid_all.tbl CDD pfam05606 pfam05606 368518 DUF777 Borrelia burgdorferi protein of unknown function (DUF777). This family consists of several hypothetical proteins of unknown function from Borrelia burgdorferi (Lyme disease spirochete). 135 matched cddid_all.tbl CDD pfam05608 pfam05608 428540 DUF778 Protein of unknown function (DUF778). This family consists of several eukaryotic proteins of unknown function. 136 matched cddid_all.tbl CDD pfam05609 pfam05609 461691 LAP1_C Lamina-associated polypeptide 1, AAA+ activator domain. Torsin-1A-interacting proteins 1 and 2 (TOIP 1/2), also known as LAP1 proteins (Lamina-associated polypeptide 1) are type 2 integral membrane proteins with a single membrane-spanning region of the inner nuclear membrane. These proteins interact with and activate Torsin A, an AAA+ ATPase localized to the endoplasmic reticulum (ER) through a perinuclear domain and forms a heterohexameric (LAP1-Torsin)3 ring that targets Torsin to the nuclear envelope. LAP1 has an atypical AAA+ fold and provides an arginine finger to the Torsin A active site to promote its ATPase activity. A single mutation in Torsin A causes early onset primary dystonia, a painful and severely disabling neuromuscular disease. This entry represents the C-terminal AAA+ activator domain of LAP1. 233 matched cddid_all.tbl CDD pfam05610 pfam05610 428542 DUF779 Protein of unknown function (DUF779). This family consists of several bacterial proteins of unknown function. 94 matched cddid_all.tbl CDD pfam05611 pfam05611 368521 DUF780 Caenorhabditis elegans protein of unknown function (DUF780). This family consists of several short C. elegans proteins of unknown function. 71 matched cddid_all.tbl CDD pfam05612 pfam05612 428543 Leg1 Leg1. Protein liver-enriched gene 1 (Leg1) has been suggested to function as a novel secreted regulator for the liver development. 331 matched cddid_all.tbl CDD pfam05613 pfam05613 283304 Herpes_U15 Human herpesvirus U15 protein. 110 matched cddid_all.tbl CDD pfam05614 pfam05614 114342 Circovir_ORF3 Circovirus ORF3. This family consists porcine circovirus ORF3 protein which plays a role in modulating host cell signalling by binding to and degrading host RGS16. This protein is not necessary for virus replication. 104 matched cddid_all.tbl CDD pfam05615 pfam05615 461692 THOC7 Tho complex subunit 7. The Tho complex is involved in transcription elongation and mRNA export from the nucleus. 135 matched cddid_all.tbl CDD pfam05616 pfam05616 283306 Neisseria_TspB Neisseria meningitidis TspB protein. This family consists of several Neisseria meningitidis TspB virulence factor proteins. 517 matched cddid_all.tbl CDD pfam05617 pfam05617 461693 Prolamin_like Prolamin-like. Prolamin_like (in which DUF784 and DUF1278 have been merged) is found to be expressed in the plant embryo sac and to be regulated by the Myb98 transcription factor. Computational analysis has revealed that members are homologous to the plant prolamin superfamily (Protease inhibitor-seed storage-LTP family, pfam00234). In contrast to typical prolamin members that have eight conserved Cys residues forming four pairs of disulfide bonds, this domain contains only six conserved Cys residues that may form three pairs of disulfide bonds. The domain may have a potential function in lipid transfer or protection during plant embryo sac development and reproduction. 70 matched cddid_all.tbl CDD pfam05618 pfam05618 283308 Zn_protease Putative ATP-dependant zinc protease. Proteins in this family are annotated as being ATP-dependant zinc proteases. 138 matched cddid_all.tbl CDD pfam05619 pfam05619 310307 DUF787 Borrelia burgdorferi protein of unknown function (DUF787). This family consists of several hypothetical proteins of unknown function from Borrelia burgdorferi (Lyme disease spirochete). 369 matched cddid_all.tbl CDD pfam05620 pfam05620 428546 TMEM208_SND2 SRP-independent targeting protein 2/TMEM208. This family includes SRP-independent targeting protein 2 (SND2) from yeast and transmembrane protein 208 (TMEM208) from mammals. Both are localized to the endoplasmic reticulum (ER). SND2 works together with SND1 and SND3 in an alternative targeting route to the ER. TMEM208 regulates both ER stress and autophagy. It contains three predicted transmembrane regions. SND2 also known as Env10 in Saccharomyces cerevisiae, and its homolog as Mug69 in Schizosaccharomyces pombe. They were identified as proteins involved in vacuolar processing and morphology and meiosis, respectively. 167 matched cddid_all.tbl CDD pfam05621 pfam05621 428547 TniB Bacterial TniB protein. This family consists of several bacterial TniB NTP-binding proteins. TniB is a probable ATP-binding protein which is involved in Tn5053 mercury resistance transposition. This entry represents a P-loop domain. 189 matched cddid_all.tbl CDD pfam05622 pfam05622 461694 HOOK HOOK protein coiled-coil region. This family consists of several HOOK1, 2 and 3 proteins from different eukaryotic organizms. The different members of the human gene family are HOOK1, HOOK2 and HOOK3. Different domains have been identified in the three human HOOK proteins, and it was demonstrated that the highly conserved NH2-domain mediates attachment to microtubules, whereas this central coiled-coil motif mediates homodimerization and the more divergent C-terminal domains are involved in binding to specific organelles (organelle-binding domains). It has been demonstrated that endogenous HOOK3 binds to Golgi membranes, whereas both HOOK1 and HOOK2 are localized to discrete but unidentified cellular structures. In mice the Hook1 gene is predominantly expressed in the testis. Hook1 function is necessary for the correct positioning of microtubular structures within the haploid germ cell. Disruption of Hook1 function in mice causes abnormal sperm head shape and fragile attachment of the flagellum to the sperm head. This entry includes the central coiled-coiled domain and the divergent C-terminal domain. 528 matched cddid_all.tbl CDD pfam05623 pfam05623 461695 DUF789 Protein of unknown function (DUF789). This family consists of several plant proteins of unknown function. 295 matched cddid_all.tbl CDD pfam05624 pfam05624 428550 LSR Lipolysis stimulated receptor (LSR). The lipolysis-stimulated receptor (LSR) is a lipoprotein receptor primarily expressed in the liver and activated by free fatty acids. It is thought to be involved in the clearance of triglyceride-rich lipoproteins, and has been shown in mice to be critical for liver and embryonic development. 48 matched cddid_all.tbl CDD pfam05625 pfam05625 461696 PAXNEB PAXNEB protein. PAXNEB or PAX6 neighbour is found in several eukaryotic organizms. PAXNED is an RNA polymerase II Elongator protein subunit. It is part of the HAP subcomplex of Elongator, which is a six-subunit component of the RNA polymerase II holoenzyme. The HAP subcomplex is required for Elongator structural integrity and histone acetyltransferase activity. This protein family has a P-loop-like motif and adopts a RecA-ATPase-like fold, lacking the conserved sequence signature of ATPases. 359 matched cddid_all.tbl CDD pfam05626 pfam05626 428551 DUF790 Protein of unknown function (DUF790). This family consists of several hypothetical archaeal proteins of unknown function. 385 matched cddid_all.tbl CDD pfam05627 pfam05627 398967 AvrRpt-cleavage Cleavage site for pathogenic type III effector avirulence factor Avr. This domain is conserved in small families of otherwise unrelated proteins in both mono-cots and di-cots, suggesting that it has a conserved, plant-specific function. It is found both in the plant RIN4 (resistance R membrane-bound host-target protein) where it appears to contribute to the binding of the protein to both RCS (AvrRpt2 auto-cleavage site) and AvrB, the virulence factor from the infecting bacterium. The cleavage site for the AvrRpt2 avirulence protein would appear to be the sequence motifs VPQFGDW and LPKFGEW, both of which are highly conserved within the domain. 36 matched cddid_all.tbl CDD pfam05628 pfam05628 310316 Borrelia_P13 Borrelia membrane protein P13. This family consists of P13 proteins from Borrelia species. P13 is a 13kDa integral membrane protein which is post-translationally processed at both ends and modified by an unknown mechanism. 138 matched cddid_all.tbl CDD pfam05629 pfam05629 283319 Nanovirus_C8 Nanovirus component 8 (C8) protein. This family consists of a group of 17.4 kDa nanovirus proteins which are highly related to the faba bean necrotic yellows virus component 8 protein whose function is unknown. 154 matched cddid_all.tbl CDD pfam05630 pfam05630 461697 NPP1 Necrosis inducing protein (NPP1). This family consists of several NPP1 like necrosis inducing proteins from oomycetes, fungi and bacteria. Infiltration of NPP1 into leaves of Arabidopsis thaliana plants result in transcript accumulation of pathogenesis-related (PR) genes, production of ROS and ethylene, callose apposition, and HR-like cell death. 198 matched cddid_all.tbl CDD pfam05631 pfam05631 283321 MFS_5 Sugar-tranasporters, 12 TM. MFS_5 is a family of sugar-transporters from both prokaryotes and eukaryotes. 356 matched cddid_all.tbl CDD pfam05632 pfam05632 368533 DUF792 Borrelia burgdorferi protein of unknown function (DUF792). This family consists of several hypothetical proteins from the Lyme disease spirochete Borrelia burgdorferi. 184 matched cddid_all.tbl CDD pfam05633 pfam05633 428553 ROH1-like Protein ROH1-like. This family consists of several plant proteins and includes RHO1, an interactor of the exocyst subunit Exo70A1 and has been shown to be required for seed coat mucilage deposition. 383 matched cddid_all.tbl CDD pfam05634 pfam05634 428554 APO_RNA-bind APO RNA-binding. This domain contains conserved cysteine and histidine residues. It resembles zinc fingers, and binds to zinc. This domain functions as an RNA-binding domain. 194 matched cddid_all.tbl CDD pfam05635 pfam05635 461698 23S_rRNA_IVP 23S rRNA-intervening sequence protein. This family consists of bacterial proteins encoded within an intervening sequence present within some 23S rRNA genes. It folds into an anti-parallel four-helix bundle and forms homopentamers. 106 matched cddid_all.tbl CDD pfam05636 pfam05636 428556 HIGH_NTase1 HIGH Nucleotidyl Transferase. This family consists of HIGH Nucleotidyl Transferases 386 matched cddid_all.tbl CDD pfam05637 pfam05637 368535 Glyco_transf_34 galactosyl transferase GMA12/MNN10 family. This family contains a number of glycosyltransferase enzymes that contain a DXD motif. This family includes a number of C. elegans homologs where the DXD is replaced by DXH. Some members of this family are included in glycosyltransferase family 34. 238 matched cddid_all.tbl CDD pfam05638 pfam05638 428557 T6SS_HCP Type VI secretion system effector, Hcp. HCP is a family of proteins which are expressed in up to 1000 copies in Gram-negative bacteria. Together these copies aggregate into a needle-like shaft or tube that will penetrate other bacteria via a puncturing protein attached to its head. Initially Hcp forms a hexameric structure with a central channel of 40 Angstroms. These hexamers pile up one on top of each other forming nanotubes resembling the gp19 tail phage tube. 129 matched cddid_all.tbl CDD pfam05639 pfam05639 428558 Pup Pup-like protein. This family consists of several short bacterial proteins formely known as (DUF797). It was recently shown that Mycobacterium tuberculosis contains a small protein, Pup (Rv2111c), that is covalently conjugated to the e-NH2 groups of lysines on several target proteins (pupylation) such as the malonyl CoA acyl carrier protein (FabD). Pupylation of FabD was shown to result in its recruitment to the mycobacterial proteasome and subsequent degradation analogous to eukaryotic ubiquitin-conjugated proteins. Searches recovered Pup orthologs in all major actinobacteria lineages including the basal bifidobacteria and also sporadically in certain other bacterial lineages. The Pup proteins were all between 50-90 residues in length and a multiple alignment shows that they all contain a conserved motif with a G [EQ] signature at the C-terminus. Thus, all of them are suitable for conjugation via the terminal glutamate or the deamidated glutamine (as shown in the case of the Mycobacterium). The conserved globular core of Pup is predicted to form a bihelical unit with the extreme C-terminal 6-7 residues forming a tail in the extended conformation. Thus, Pup is structurally unrelated to the ubiquitin fold and has convergently evolved the function of protein modifier. 64 matched cddid_all.tbl CDD pfam05640 pfam05640 461699 NKAIN Na,K-Atpase Interacting protein. NKAIN (Na,K-Atpase INteracting) proteins are a family of evolutionary conserved transmembrane proteins that localize to neurons, that are critical for neuronal function, and that interact with the beta subunits, beta1 in vertebrates and beta in Drosophila, of Na,K-ATPase. NKAINs have highly conserved trans-membrane domains but otherwise no other characterized domains. NKAINs may function as subunits of pore or channel structures in neurons or they may affect the function of other membrane proteins. They are likely to function within the membrane bilayer. 206 matched cddid_all.tbl CDD pfam05641 pfam05641 461700 Agenet Agenet domain. This domain is related to the TUDOR domain pfam00567. The function of the agenet domain is unknown. This family now matches both the two Agenet domains in the FMR proteins. 61 matched cddid_all.tbl CDD pfam05642 pfam05642 253298 Sporozoite_P67 Sporozoite P67 surface antigen. This family consists of several Theileria P67 surface antigens. A stage specific surface antigen of Theileria parva, p67, is the basis for the development of an anti-sporozoite vaccine for the control of East Coast fever (ECF) in cattle. The antigen has been shown to contain five distinct linear peptide sequences recognized by sporozoite-neutralising murine monoclonal antibodies. 727 matched cddid_all.tbl CDD pfam05643 pfam05643 428561 DUF799 Putative bacterial lipoprotein (DUF799). This family consists of several bacterial proteins of unknown function. Some of the family members are described as putative lipoproteins. 185 matched cddid_all.tbl CDD pfam05644 pfam05644 461701 Miff Mitochondrial and peroxisomal fission factor Mff. This protein has a role in mitochondrial and peroxisomal fission. 292 matched cddid_all.tbl CDD pfam05645 pfam05645 398977 RNA_pol_Rpc82 RNA polymerase III subunit RPC82. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa. 233 matched cddid_all.tbl CDD pfam05647 pfam05647 461702 Epiglycanin_TR Tandem-repeating region of mucin, epiglycanin-like. The unusual mucin, epiglycanin, is membrane-bound at the C-terminus but has a long region of this tandem-repeat at the N-terminus. It was the first mucin identified to be associated with the malignant behaviour of carcinoma cells. Mouse Muc21/epiglycanin is thought to be a highly glycosylated molecule, which makes it likely that its function is dependent on its glycoforms. Cells expressing Muc21 are significantly less adherent to each other and to extracellular matrix components than control cells, and this loss of adhesion is mediated by the TR portion of Muc21. This family also now contains the repeat that was the C. elegans protein of unknown function (DUF801). 68 matched cddid_all.tbl CDD pfam05648 pfam05648 398979 PEX11 Peroxisomal biogenesis factor 11 (PEX11). This family consists of several peroxisomal biogenesis factor 11 (PEX11) proteins from several eukaryotic species. The PEX11 peroxisomal membrane proteins promote peroxisome division in multiple eukaryotes. 223 matched cddid_all.tbl CDD pfam05649 pfam05649 461703 Peptidase_M13_N Peptidase family M13. M13 peptidases are well-studied proteases found in a wide range of organizms including mammals and bacteria. In mammals they participate in processes such as cardiovascular development, blood-pressure regulation, nervous control of respiration, and regulation of the function of neuropeptides in the central nervous system. In bacteria they may be used for digestion of milk. 382 matched cddid_all.tbl CDD pfam05650 pfam05650 428565 DUF802 Domain of unknown function (DUF802). This region is found as two or more repeats in a small number of hypothetical proteins. 53 matched cddid_all.tbl CDD pfam05651 pfam05651 461704 Diacid_rec Putative sugar diacid recognition. This region is found in several proteins characterized as carbohydrate diacid regulators. An HTH DNA-binding motif is found at the C-terminus of these proteins suggesting that this region includes the sugar recognition region. 129 matched cddid_all.tbl CDD pfam05652 pfam05652 461705 DcpS Scavenger mRNA decapping enzyme (DcpS) N-terminal. This family consists of several scavenger mRNA decapping enzymes (DcpS) and is the N-terminal domain of these proteins. DcpS is a scavenger pyrophosphatase that hydrolyses the residual cap structure following 3' to 5' decay of an mRNA. The association of DcpS with 3' to 5' exonuclease exosome components suggests that these two activities are linked and there is a coupled exonucleolytic decay-dependent decapping pathway. 103 matched cddid_all.tbl CDD pfam05653 pfam05653 398984 Mg_trans_NIPA Magnesium transporter NIPA. NIPA (nonimprinted in Prader-Willi/Angelman syndrome) is a family of integral membrane proteins which function as magnesium transporters. 295 matched cddid_all.tbl CDD pfam05655 pfam05655 398985 AvrD Pseudomonas avirulence D protein (AvrD). This family consists of several avirulence D (AvrD) proteins primarily found in Pseudomonas syringae. 330 matched cddid_all.tbl CDD pfam05656 pfam05656 461706 DUF805 Protein of unknown function (DUF805). This family consists of several bacterial proteins of unknown function. 110 matched cddid_all.tbl CDD pfam05657 pfam05657 428569 DUF806 Protein of unknown function (DUF806). This family consists of several Siphovirus and Lactococcus proteins of unknown function. The viral sequences are thought to be tail component proteins. 121 matched cddid_all.tbl CDD pfam05658 pfam05658 461707 YadA_head YadA head domain repeat (2 copies). This entry represents two copies of a fourteen residue repeat that makes up the head domain of bacterial haemagglutinins and invasins. 27 matched cddid_all.tbl CDD pfam05659 pfam05659 398988 RPW8 Arabidopsis broad-spectrum mildew resistance protein RPW8. This family consists of several broad-spectrum mildew resistance proteins from Arabidopsis thaliana. Plant disease resistance (R) genes control the recognition of specific pathogens and activate subsequent defence responses. The Arabidopsis thaliana locus Resistance To Powdery Mildew 8 (RPW8) contains two naturally polymorphic, dominant R genes, RPW8.1 and RPW8.2, which individually control resistance to a broad range of powdery mildew pathogens. They induce localized, salicylic acid-dependent defences similar to those induced by R genes that control specific resistance. Apparently, broad-spectrum resistance mediated by RPW8 uses the same mechanisms as specific resistance. 139 matched cddid_all.tbl CDD pfam05660 pfam05660 283346 DUF807 Coxiella burnetii protein of unknown function (DUF807). This family consists of several proteins of unknown function from Coxiella burnetii (the causative agent of a zoonotic disease called Q fever). 142 matched cddid_all.tbl CDD pfam05661 pfam05661 428571 DUF808 Protein of unknown function (DUF808). This family consists of several bacterial proteins of unknown function. 302 matched cddid_all.tbl CDD pfam05662 pfam05662 428572 YadA_stalk Coiled stalk of trimeric autotransporter adhesin. This short motif is found in invasins and haemagglutinins, normally associated with (pfam05658). 43 matched cddid_all.tbl CDD pfam05663 pfam05663 147685 DUF809 Protein of unknown function (DUF809). This family consists of several proteins of unknown function Raphanus sativus (Radish) and Brassica napus (Rape). 138 matched cddid_all.tbl CDD pfam05666 pfam05666 428573 Fels1 Fels-1 Prophage Protein-like. 42 matched cddid_all.tbl CDD pfam05667 pfam05667 461708 CCDC22 Coiled-coil domain-containing protein 22. Human coiled-coil domain-containing protein 22 (CCDC22) is involved in regulation of NF-kappa-B signalling; the function may involve association with COMMD8 and a CUL1-dependent E3 ubiquitin ligase complex. It is part of the OMMD/CCDC22/CCDC93 (CCC) complex, which interacts with the multisubunit WASH complex required for endosomal deposition of F-actin and cargo trafficking in conjunction with the retromer. This entry also includes CCDC22 homologs from animals and plants. 600 matched cddid_all.tbl CDD pfam05669 pfam05669 428575 Med31 SOH1. The family consists of Saccharomyces cerevisiae SOH1 homologs. SOH1 is responsible for the repression of temperature sensitive growth of the HPR1 mutant and has been found to be a component of the RNA polymerase II transcription complex. SOH1 not only interacts with factors involved in DNA repair, but transcription as well. Thus, the SOH1 protein may serve to couple these two processes. 95 matched cddid_all.tbl CDD pfam05670 pfam05670 428576 NFACT-R_1 NFACT protein RNA binding domain. This domain occurs in proteins that have been annotated as Fibronectin/fibrinogen binding protein by similarity. This annotation comes from Swiss:O34693 where the N-terminal region is involved in this activity. It is an RNA binding domain of the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins. This NFACT-R family is found in two eukaryotic gene contexts: fused to the NFACT-N and NFACT-C domains in the NFACT protein involved in the ribosomal quality control pathway which contributes to CAT-tailing and as a standalone domain. Additionally this domain contains a conserved motif D/E-X-W/Y-X-H that may be functionally important. 111 matched cddid_all.tbl CDD pfam05671 pfam05671 398995 GETHR GETHR pentapeptide repeat (5 copies). This pentapeptide repeat is found mainly in Plasmodium spp. The most conserved amino acid at each position leads to its name GETHR (Bateman A unpublished obs.). The function of this repeat is unknown. 25 matched cddid_all.tbl CDD pfam05672 pfam05672 461709 MAP7 MAP7 (E-MAP-115) family. The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. 153 matched cddid_all.tbl CDD pfam05673 pfam05673 428578 DUF815 Protein of unknown function (DUF815). This family consists of several bacterial proteins of unknown function. 250 matched cddid_all.tbl CDD pfam05674 pfam05674 283357 DUF816 Baculovirus protein of unknown function (DUF816). This family includes proteins that are about 200 amino acids in length. The proteins are all from baculoviruses. This family includes ORF107 from Orgyia pseudotsugata multicapsid polyhedrosis virus (OpMNPV) and a variety of other numbered ORF proteins, such as ORF52, ORF140. The function of these proteins is unknown. 176 matched cddid_all.tbl CDD pfam05675 pfam05675 428579 DUF817 Protein of unknown function (DUF817). This family consists of several bacterial proteins of unknown function. 234 matched cddid_all.tbl CDD pfam05676 pfam05676 461710 NDUF_B7 NADH-ubiquinone oxidoreductase B18 subunit (NDUFB7). This family consists of several NADH-ubiquinone oxidoreductase B18 subunit proteins from different eukaryotic organizms. Oxidative phosphorylation is the well-characterized process in which ATP, the principal carrier of chemical energy of individual cells, is produced due to a mitochondrial proton gradient formed by the transfer of electrons from NADH and FADH2 to molecular oxygen. The oxidative phosphorylation (OXPHOS) system is located in the mitochondrial inner membrane and consists of five multi-subunit enzyme complexes and two small electron carriers: coenzyme Q10 and cytochrome C. At least 70 structural proteins involved in the formation of the whole OXPHOS system are encoded by nuclear genes, whereas 13 structural proteins are encoded by the mitochondrial genome. Deficiency of NADH ubiquinone oxidoreductase, the first enzyme complex of the mitochondrial respiratory chain, is one of the most frequent causes of human mitochondrial encephalomyopathies. 62 matched cddid_all.tbl CDD pfam05677 pfam05677 253315 DUF818 Chlamydia CHLPS protein (DUF818). This family consists of several Chlamydia CHLPS proteins, the function of which are unknown. 364 matched cddid_all.tbl CDD pfam05678 pfam05678 461711 VQ VQ motif. This short motif is found in a variety of plant proteins. These proteins vary greatly in length and are mostly composed of low complexity regions. They all conserve a short motif FXhVQChTG, where X is any amino acid and h is a hydrophobic amino acid. The function of this motif is uncertain, however one protein in this family has been found to bind the SigA sigma factor Swiss:Q9LDH1. It would seem plausible that this motif is needed for this activity and that this whole family might be involved in modulating plastid sigma factors (Bateman A pers. obs.). 28 matched cddid_all.tbl CDD pfam05679 pfam05679 461712 CHGN Chondroitin N-acetylgalactosaminyltransferase. 500 matched cddid_all.tbl CDD pfam05680 pfam05680 368558 ATP-synt_E ATP synthase E chain. This family consists of several ATP synthase E chain sequences which are components of the CF(0) subunit. 83 matched cddid_all.tbl CDD pfam05681 pfam05681 461713 Fumerase Fumarate hydratase (Fumerase). This family consists of several bacterial fumarate hydratase proteins FumA and FumB. Fumarase, or fumarate hydratase (EC 4.2.1.2), is a component of the citric acid cycle. In facultative anaerobes such as Escherichia coli, fumarase also engages in the reductive pathway from oxaloacetate to succinate during anaerobic growth. Three fumarases, FumA, FumB, and FumC, have been reported in E. coli. fumA and fumB genes are homologous and encode products of identical sizes which form thermolabile dimers of Mr 120,000. FumA and FumB are class I enzymes and are members of the iron-dependent hydrolases, which include aconitase and malate hydratase. The active FumA contains a 4Fe-4S centre, and it can be inactivated upon oxidation to give a 3Fe-4S centre. 267 matched cddid_all.tbl CDD pfam05683 pfam05683 461714 Fumerase_C Fumarase C-terminus. This family consists of the C terminal region of several bacterial fumarate hydratase proteins (FumA and FumB). Fumarase, or fumarate hydratase (EC 4.2.1.2), is a component of the citric acid cycle. In facultative anaerobes such as Escherichia coli, fumarase also engages in the reductive pathway from oxaloacetate to succinate during anaerobic growth. 204 matched cddid_all.tbl CDD pfam05684 pfam05684 114410 DUF819 Protein of unknown function (DUF819). This family contains proteins of unknown function from archaeal, bacterial and plant species. 379 matched cddid_all.tbl CDD pfam05685 pfam05685 428585 Uma2 Putative restriction endonuclease. This entry includes a group of putative nuclease, including hypothetical protein TT1808 (also known as Uma2 or TTHA1514), an AT-rich DNA-binding protein from Thermus thermophilus. This domain has a 3-layer alpha/beta/alpha topology similar to that found in restriction endonucleases. The nuclease domain is ubiquitously found in enzymes involved in metabolism of nucleic acids, mostly in nucleases with diverse biological functions. 169 matched cddid_all.tbl CDD pfam05686 pfam05686 310354 Glyco_transf_90 Glycosyl transferase family 90. This family of glycosyl transferases are specifically (mannosyl) glucuronoxylomannan/galactoxylomannan -beta 1,2-xylosyltransferases, EC:2.4.2.-. 396 matched cddid_all.tbl CDD pfam05687 pfam05687 461715 BES1_N BES1/BZR1 plant transcription factor, N-terminal. This family consists of the N terminal regions of several plant transcription factors. It is classified as BES1/BZR1, a plant-specific transcription factor that cooperates with transcription factors such as BIM1 to regulate brassinosteroid-induced genes. 143 matched cddid_all.tbl CDD pfam05688 pfam05688 428587 BIg21 Bacterial Immunoglobulin-like 21. This entry represents BIg21(Bacterial Immunoglobulin-like 21) found in InvasinE (InvE). Invasins are members of the inverse autotransporter (IAT) family also referred to as type Ve secretion system. In general, they consist of an N-terminal beta-barrel-like domain, which is responsible for attachment of invasin to the outer membrane region of bacteria, repetitive Immunoglobuli-like (Ig) domains, which vary significantly in number among all the invasins, and the C-terminal domain/adhesion domain (AD) pfam05689, which provides invasins with the specificity to bind to its host target molecules. The overall structure of InvE shows that it comprises of three domain architecture in which the domains BIg20 (Bacterial Immunoglobulin-like 20) and BIg21 adopt two layer beta-sandwich fold resembling eukaryotic members of Immunoglobulin-superfamily (IgSF), while the AD is a globular, alpha/beta-domain. The structure of BIg21 belongs to the I2 set of IgSF with a unique modification in the C-E interstrand loop, important for its interaction with AD. BIg21 and AD form a functional super-domain as well, necessary to target the host receptor. 108 matched cddid_all.tbl CDD pfam05689 pfam05689 428588 InvE_AD "Adhesion domain. This entry represents the Adhesion domain found in InvasinE (invE). Invasins are members of the inverse autotransporter (IAT) family also referred to as type Ve secretion system. In general, they consist of an N-terminal beta-barrel-like domain, which is responsible for attachment of invasin to the outer membrane region of bacteria, repetitive Immunoglobulin-like (Ig) domains, which vary significantly in number among all the invasins, and the C-terminal domain/adhesion domain (AD), which provides invasins with the specificity to bind to its host target molecules. InvE-AD adopts a C-type lectin-like domain (CTLD)fold with unique modifications. The core structure of the adhesion domain (AD) is made up of a globular alpha/beta fold and can be divided into three sub-sections. The first is a lasso-shaped loop structure termed the ""adaptor ring"" since it forms a ring-shaped platform that connects BIg21 pfam05688 with the two residual sub-sections in the AD. These two residual subsections are the ""C-type lectin-like domain"" and the ""wedge module"". InvE-CTLD lacks the ability to coordinate Ca2+, and motifs such as EPN, QPD, and WND that are responsible for the specificity of carbohydrate recognition are also absent, giving rise to the notion that the InvE-CTLD is not a carbohydrate binding domain." 135 matched cddid_all.tbl CDD pfam05690 pfam05690 428589 ThiG Thiazole biosynthesis protein ThiG. This family consists of several bacterial thiazole biosynthesis protein G sequences. ThiG, together with ThiF and ThiH, is proposed to be involved in the synthesis of 4-methyl-5-(b-hydroxyethyl)thiazole (THZ) which is an intermediate in the thiazole production pathway. This family also includes triosephosphate isomerase and pyridoxal 5'-phosphate synthase subunit PdxS. 247 matched cddid_all.tbl CDD pfam05691 pfam05691 283371 Raffinose_syn Raffinose synthase or seed imbibition protein Sip1. This family consists of several raffinose synthase proteins, also known as seed imbibition (Sip1) proteins. Raffinose (O-alpha- D-galactopyranosyl- (1-->6)- O-alpha- D-glucopyranosyl-(1<-->2)- O-beta- D-fructofuranoside) is a widespread oligosaccharide in plant seeds and other tissues. Raffinose synthase (EC:2.4.1.82) is the key enzyme that channels sucrose into the raffinose oligosaccharide pathway. Raffinose family oligosaccharides (RFOs) are ubiquitous in plant seeds and are thought to play critical roles in the acquisition of tolerance to desiccation and seed longevity. Raffinose synthases are alkaline alpha-galactosidases and are solely responsible for RFO breakdown in germinating maize seeds, whereas acidic galactosidases appear to have other functions. Glycoside hydrolase family 36 can be split into 11 families, GH36A to GH36K. This family includes enzymes from GH36C. 749 matched cddid_all.tbl CDD pfam05692 pfam05692 368561 Myco_haema Mycoplasma haemagglutinin. This family consists of several haemagglutinin sequences from Mycoplasma synoviae and Mycoplasma gallisepticum. The major plasma membrane proteins, pMGAs, of Mycoplasma gallisepticum are cell adhesin (hemagglutinin) molecules. It has been shown that the genetic determinants that code for the haemagglutinins are organized into a large family of genes and that only one of these genes is predominately expressed in any given strain. 424 matched cddid_all.tbl CDD pfam05693 pfam05693 399009 Glycogen_syn Glycogen synthase. This family consists of the eukaryotic glycogen synthase proteins GYS1, GYS2 and GYS3. Glycogen synthase (GS) is the enzyme responsible for the synthesis of -1,4-linked glucose chains in glycogen. It is the rate limiting enzyme in the synthesis of the polysaccharide, and its activity is highly regulated through phosphorylation at multiple sites and also by allosteric effectors, mainly glucose 6-phosphate (G6P). 639 matched cddid_all.tbl CDD pfam05694 pfam05694 461716 SBP56 56kDa selenium binding protein (SBP56). This family consists of several eukaryotic selenium binding proteins as well as three sequences from archaea. The exact function of this protein is unknown although it is thought that SBP56 participates in late stages of intra-Golgi protein transport. The Lotus japonicus homolog of SBP56, LjSBP is thought to have more than one physiological role and can be implicated in controlling the oxidation/reduction status of target proteins, in vesicular Golgi transport. 453 matched cddid_all.tbl CDD pfam05695 pfam05695 283375 DUF825 Plant protein of unknown function (DUF825). This family consists of several plant proteins greater than 1000 residues in length. The function of this family is unknown. 1486 matched cddid_all.tbl CDD pfam05696 pfam05696 368563 DUF826 Protein of unknown function (DUF826). This family consists of several enterobacterial and siphoviral sequences of unknown function. 65 matched cddid_all.tbl CDD pfam05697 pfam05697 461717 Trigger_N Bacterial trigger factor protein (TF). In the E. coli cytosol, a fraction of the newly synthesized proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains. This family represents the N-terminal region of the protein. 144 matched cddid_all.tbl CDD pfam05698 pfam05698 428592 Trigger_C Bacterial trigger factor protein (TF) C-terminus. In the E. coli cytosol, a fraction of the newly synthesized proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains. This family represents the C-terminal region of the protein. 162 matched cddid_all.tbl CDD pfam05699 pfam05699 399013 Dimer_Tnp_hAT hAT family C-terminal dimerization region. This dimerization region is found at the C terminus of the transposases of elements belonging to the Activator superfamily (hAT element superfamily). The isolated dimerization region forms extremely stable dimers in vitro. 83 matched cddid_all.tbl CDD pfam05700 pfam05700 428593 BCAS2 Breast carcinoma amplified sequence 2 (BCAS2). This family consists of several eukaryotic sequences of unknown function. The mammalian members of this family are annotated as breast carcinoma amplified sequence 2 (BCAS2) proteins. BCAS2 is a putative spliceosome associated protein. 204 matched cddid_all.tbl CDD pfam05701 pfam05701 461718 WEMBL "Weak chloroplast movement under blue light. WEMBL consists of several plant proteins required for the chloroplast avoidance response under high intensity blue light. This avoidance response consists in the relocation of chloroplasts on the anticlinal side of exposed cells. Acts in association with PMI2 to maintain the velocity of chloroplast photo-relocation movement via the regulation of cp-actin filaments. Thus several member-sequences are described as ""myosin heavy chain-like""." 562 matched cddid_all.tbl CDD pfam05702 pfam05702 368568 Herpes_UL49_5 Herpesvirus UL49.5 envelope/tegument protein. UL49.5 protein consists of 98 amino acids with a calculated molecular mass of 10,155 Da. It contains putative signal peptide and transmembrane domains but lacks a consensus sequence for N glycosylation. UL49.5 protein is an O-glycosylated structural component of the viral envelope. 98 matched cddid_all.tbl CDD pfam05703 pfam05703 399016 Auxin_canalis Auxin canalization. This domain is frequently found at the N-terminus of proteins containing pfam08458 at the C-terminus. It is a component of the auto-regulatory loop which enables auxin canalization by recruitment of the PIN1 auxin efflux protein to the cell membrane. 258 matched cddid_all.tbl CDD pfam05704 pfam05704 368570 Caps_synth Capsular polysaccharide synthesis protein. This family consists of several capsular polysaccharide proteins. Capsular polysaccharide (CPS) is a major virulence factor in Streptococcus pneumoniae. 278 matched cddid_all.tbl CDD pfam05705 pfam05705 461719 DUF829 Eukaryotic protein of unknown function (DUF829). This family consists of several uncharacterized eukaryotic proteins. 241 matched cddid_all.tbl CDD pfam05706 pfam05706 399018 CDKN3 Cyclin-dependent kinase inhibitor 3 (CDKN3). This family consists of cyclin-dependent kinase inhibitor 3 or kinase associated phosphatase proteins from several mammalian species. The cyclin-dependent kinase (Cdk)-associated protein phosphatase (KAP) is a human dual specificity protein phosphatase that dephosphorylates Cdk2 on threonine 160 in a cyclin-dependent manner. 168 matched cddid_all.tbl CDD pfam05707 pfam05707 283385 Zot Zonular occludens toxin (Zot). This family consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot). Zot is elaborated by bacteriophages present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers 195 matched cddid_all.tbl CDD pfam05708 pfam05708 461720 Peptidase_C92 Permuted papain-like amidase enzyme, YaeF/YiiX, C92 family. Amidase_YiiX is a family of permuted papain-like amidases. It has amidase specificity for the amide bond between a lipid and an amino acid (or peptide). From the structure, a tetramer, each monomer is made up of a layered alpha-beta fold with a central, 6-stranded, antiparallel beta-sheet that is protected by helices on either side. The catalytic Cys154 in UniProtKB:Q74NK7, PDB:3kw0, is located on the N-terminus of helix alphaF. The two additional helices located above Cys154 contribute to the formation of the active site, where the lysine ligand is bound. 164 matched cddid_all.tbl CDD pfam05709 pfam05709 428597 Sipho_tail Phage tail protein. This family consists of several Siphovirus and other phage tail component proteins as well as some bacterial proteins of unknown function. 259 matched cddid_all.tbl CDD pfam05710 pfam05710 283388 Coiled Coiled coil. This region is found in a group of Dictyostelium discoideum proteins. It is likely to form a coiled-coil. Some of the proteins are regulated by cyclic AMP and are expressed late in development. 90 matched cddid_all.tbl CDD pfam05711 pfam05711 428598 TylF Macrocin-O-methyltransferase (TylF). This family consists of bacterial macrocin O-methyltransferase (TylF) proteins. TylF is responsible for the methylation of macrocin to produce tylosin. Tylosin is a macrolide antibiotic used in veterinary medicine to treat infections caused by Gram-positive bacteria and as an animal growth promoter in the swine industry. It is produced by several Streptomyces species. As with other macrolides, the antibiotic activity of tylosin is due to the inhibition of protein biosynthesis by a mechanism that involves the binding of tylosin to the ribosome, preventing the formation of the mRNA-aminoacyl-tRNA-ribosome complex. The structure of one representative sequence from this family, NovP, shows it to be an S-adenosyl-l-methionine-dependent O-methyltransferase that catalyzes the penultimate step in the biosynthesis of the aminocoumarin antibiotic novobiocin. Specifically, it methylates at 4-OH of the noviose moiety, and the resultant methoxy group is important for the potency of the mature antibiotic. It is likely that the key structural features of NovP are common to the rest of the family and include: a helical 'lid' region that gates access to the co-substrate binding pocket and an active centre that contains a 3-Asp putative metal binding site. A further conserved Asp probably acts as the general base that initiates the reaction by de-protonating the 4-OH group of the noviose unit. 255 matched cddid_all.tbl CDD pfam05712 pfam05712 461721 MRG MRG. This family consists of three different eukaryotic proteins (mortality factor 4 (MORF4/MRG15), male-specific lethal 3(MSL-3) and ESA1-associated factor 3(EAF3)). It is thought that the MRG family is involved in transcriptional regulation via histone acetylation. It contains 2 chromo domains and a leucine zipper motif. 185 matched cddid_all.tbl CDD pfam05713 pfam05713 428600 MobC Bacterial mobilization protein (MobC). This family consists of several bacterial MobC-like, mobilization proteins. MobC proteins belong to the group of relaxases. Together with MobA and MobB they bind to a single cis-active site of a mobilising plasmid, the origin of transfer (oriT) region. The absence of MobC has several different effects on oriT DNA. Site- and strand-specific nicking by MobA protein is severely reduced, accounting for the lower frequency of mobilization. The localized DNA strand separation required for this nicking is less affected, but becomes more sensitive to the level of active DNA gyrase in the cell. In addition, strand separation is not efficiently extended through the region containing the nick site. These effects suggest a model in which MobC acts as a molecular wedge for the relaxosome-induced melting of oriT DNA. The effect of MobC on strand separation may be partially complemented by the helical distortion induced by supercoiling. However, MobC extends the melted region through the nick site, thus providing the single-stranded substrate required for cleavage by MobA. 45 matched cddid_all.tbl CDD pfam05714 pfam05714 428601 PFam54_60 Borrelia Bbcrasp-1 domain containing protein. This family contains lipoproteins from the Lyme disease spirochete Borrelia burgdorferi and related bacteria. This entry contains proteins from Paralogous family 54 (PFam54) and 60 and (PFam60). The first crystal structure of B. burgdorferi PFam54 member BBA68 revealed a previously unseen novel fold, which, according to the CATH protein domain classification, was named the Bbcrasp-1 fold because of the common name used for the protein BBA68. 184 matched cddid_all.tbl CDD pfam05715 pfam05715 461722 zf-piccolo Piccolo Zn-finger. This (predicted) Zinc finger is found in the bassoon and piccolo proteins. There are eight conserved cysteines, suggesting that it coordinates two zinc ligands. 60 matched cddid_all.tbl CDD pfam05716 pfam05716 428603 AKAP_110 A-kinase anchor protein 110 kDa (AKAP 110). This family consists of several mammalian protein kinase A anchoring protein 3 (PRKA3) or A-kinase anchor protein 110 kDa (AKAP 110) sequences. Agents that increase intracellular cAMP are potent stimulators of sperm motility. Anchoring inhibitor peptides, designed to disrupt the interaction of the cAMP-dependent protein kinase A (PKA) with A kinase-anchoring proteins (AKAPs), are potent inhibitors of sperm motility. PKA anchoring is a key biochemical mechanism controlling motility. AKAP110 shares compartments with both RI and RII isoforms of PKA and may function as a regulator of both motility- and head-associated functions such as capacitation and the acrosome reaction. 692 matched cddid_all.tbl CDD pfam05717 pfam05717 461723 TnpB_IS66 IS66 Orf2 like protein. This protein is found in insertion sequences related to IS66. The function of these proteins is uncertain, but they are probably essential for transposition. 96 matched cddid_all.tbl CDD pfam05718 pfam05718 283396 Pox_int_trans Poxvirus intermediate transcription factor. This family consists of several highly related Poxvirus sequences which are thought to be intermediate transcription factors. 382 matched cddid_all.tbl CDD pfam05719 pfam05719 428605 GPP34 Golgi phosphoprotein 3 (GPP34). This family consists of several eukaryotic GPP34 like proteins. GPP34 localizes to the Golgi complex and is conserved from yeast to humans. The cytosolic-ally exposed location of GPP34 predict a role for a novel coat protein in Golgi trafficking. 198 matched cddid_all.tbl CDD pfam05720 pfam05720 283398 Dicty_CAD Cell-cell adhesion domain. This family is based on a group of Dictyostelium discoideum proteins that are essential in early development. Swiss:P16642 and Swiss:P16643 are located on the cell surface and mediate cell-cell adhesion. 75 matched cddid_all.tbl CDD pfam05721 pfam05721 399029 PhyH Phytanoyl-CoA dioxygenase (PhyH). This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalysing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterized by the accumulation of phytanic acid in plasma and tissues. 213 matched cddid_all.tbl CDD pfam05722 pfam05722 114448 Ustilago_mating Ustilago B locus mating-type protein. This family consists of several Ustilago mating-type proteins. The b locus of the phytopathogenic fungus Ustilago maydis encodes a multiallelic recognition function that controls the ability of the fungus to form a dikaryon and complete the sexual stage of the life cycle. The b locus has at least 25 alleles and any combination of two different alleles, brought together by mating between haploid cells, allows the fungus to cause disease and undergo sexual development within the plant. 239 matched cddid_all.tbl CDD pfam05724 pfam05724 399030 TPMT Thiopurine S-methyltransferase (TPMT). This family consists of thiopurine S-methyltransferase proteins from both eukaryotes and prokaryotes. Thiopurine S-methyltransferase (TPMT) is a cytosolic enzyme that catalyzes S-methylation of aromatic and heterocyclic sulfhydryl compounds, including anticancer and immunosuppressive thiopurines. 218 matched cddid_all.tbl CDD pfam05725 pfam05725 191356 FNIP FNIP Repeat. This repeat is approximately 22 residues long and is only found in Dictyostelium discoideum. It appears to be related to pfam00560 (personal obs:C Yeats). The alignment consists of two tandem repeats. It is termed the FNIP repeat after the pattern of conserved residues. 44 matched cddid_all.tbl CDD pfam05726 pfam05726 399031 Pirin_C Pirin C-terminal cupin domain. This region is found the C-terminal half of the Pirin protein. 103 matched cddid_all.tbl CDD pfam05727 pfam05727 283402 UPF0228 Uncharacterized protein family (UPF0228). This small family of proteins is currently restricted Methanosarcina species. Members of this family are about 200 residues in length, except for Swiss:Q8TMK1 that has two copies of this region. Although the function of this region is unknown the pattern of conservation suggests that this may be an enzyme, including multiple conserved aspartate and glutamate residues (Bateman A. pers. obs.). The most conserved motif in these proteins is NEL/MEXNE/D, where X can be any amino acid, which is found at the C-terminus of these proteins. 124 matched cddid_all.tbl CDD pfam05728 pfam05728 283403 UPF0227 Uncharacterized protein family (UPF0227). Despite being classed as uncharacterized proteins, the members of this family are almost certainly enzymes that are distantly related to the pfam00561. 187 matched cddid_all.tbl CDD pfam05729 pfam05729 428606 NACHT NACHT domain. This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931. 166 matched cddid_all.tbl CDD pfam05730 pfam05730 399033 CFEM CFEM domain. This fungal specific cysteine rich domain is found in some proteins with proposed roles in fungal pathogenesis. The structure of the CFEM domain containing protein 'Surface antigen protein 2' from Candida albicans has been solved. 66 matched cddid_all.tbl CDD pfam05731 pfam05731 461724 TROVE TROVE domain. This presumed domain is found in TEP1 and Ro60 proteins, that are RNA-binding components of Telomerase, Ro and Vault RNPs. This domain has been named TROVE, (after Telomerase, Ro and Vault). This domain is probably RNA-binding. 361 matched cddid_all.tbl CDD pfam05732 pfam05732 428608 RepL Firmicute plasmid replication protein (RepL). This family consists of Firmicute RepL proteins which are involved in plasmid replication. 164 matched cddid_all.tbl CDD pfam05733 pfam05733 368585 Tenui_N Tenuivirus/Phlebovirus nucleocapsid protein. This family consists of several Tenuivirus and Phlebovirus nucleocapsid proteins. These are ssRNA viruses. In crystal structures the nucleocapsid protein from the Rift Valley fever virus (RVFV) displays a ring-shaped oligomeric assembly. Electron microscopy (EM) also demonstrates that, in complex with RNA, the RVFV nucleocapsid protein forms rings in solution. 224 matched cddid_all.tbl CDD pfam05734 pfam05734 283407 DUF832 Herpesvirus protein of unknown function (DUF832). This family consists of several herpesvirus proteins of unknown function. 228 matched cddid_all.tbl CDD pfam05735 pfam05735 461725 TSP_C Thrombospondin C-terminal region. This region is found at the C-terminus of thrombospondin and related proteins. 198 matched cddid_all.tbl CDD pfam05736 pfam05736 399036 OprF OprF membrane domain. This domain represents the presumed membrane spanning region of the OprF proteins. This region is involved in channel formation and is thought to form an 8-stranded beta-barrel. 156 matched cddid_all.tbl CDD pfam05737 pfam05737 283410 Collagen_bind Collagen binding domain. The domain fold is a jelly-roll, composed of two antiparallel beta-sheets and two short alpha-helices. A groove on beta-sheet I exhibited the best surface complementarity to the collagen. This site partially overlaps with the peptide sequence previously shown to be critical for collagen binding. Recombinant proteins containing single amino acid mutations designed to disrupt the surface of the putative binding site exhibited significantly lower affinities for collagen. 129 matched cddid_all.tbl CDD pfam05738 pfam05738 461726 Cna_B Cna protein B-type domain. This domain is found in Staphylococcus aureus collagen-binding surface protein. The structure of the repetitive B-region has been solved and forms a beta sandwich structure. 88 matched cddid_all.tbl CDD pfam05739 pfam05739 461727 SNARE SNARE domain. Most if not all vesicular membrane fusion events in eukaryotic cells are believed to be mediated by a conserved fusion machinery, the SNARE [soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptors] machinery. The SNARE domain is thought to act as a protein-protein interaction module in the assembly of a SNARE protein complex. 52 matched cddid_all.tbl CDD pfam05741 pfam05741 461728 zf-nanos Nanos RNA binding domain. This family consists of several conserved novel zinc finger domains found in the eukaryotic proteins Nanos and Xcat-2. In Drosophila melanogaster, Nanos functions as a localized determinant of posterior pattern. Nanos RNA is localized to the posterior pole of the maturing egg cell and encodes a protein that emanates from this localized source. Nanos acts as a translational repressor and thereby establishes a gradient of the morphogen Hunchback. Xcat-2 is found in the vegetal cortical region and is inherited by the vegetal blasomeres during development, and is degraded very early in development. The localized and maternally restricted expression of Xcat-2 RNA suggests a role for its protein in setting up regional differences in gene expression that occur early in development. 54 matched cddid_all.tbl CDD pfam05742 pfam05742 461729 TANGO2 Transport and Golgi organization 2. In eukaryotes this family is predicted to play a role in protein secretion and Golgi organization. In plants this family includes Swiss:A9X6Y0, which is involved in water permeability in the cuticles of fruit. Swiss:P54797 has been found to be expressed during early embryogenesis in mice. This protein contains a conserved NRDE motif. This gene has been characterized in Drosophila melanogaster and named as transport and Golgi organization 2, hence the name Tango2. 255 matched cddid_all.tbl CDD pfam05743 pfam05743 399041 UEV UEV domain. This family includes the eukaryotic tumour susceptibility gene 101 protein (TSG101). Altered transcripts of this gene have been detected in sporadic breast cancers and many other human malignancies. However, the involvement of this gene in neoplastic transformation and tumorigenesis is still elusive. TSG101 is required for normal cell function of embryonic and adult tissues but that this gene is not a tumour suppressor for sporadic forms of breast cancer. This family is related to the ubiquitin conjugating enzymes. 119 matched cddid_all.tbl CDD pfam05744 pfam05744 283416 Benyvirus_P25 Benyvirus P25/P26 protein. This family consists of P25 and P26 proteins from the beet necrotic yellow vein viruses. 240 matched cddid_all.tbl CDD pfam05745 pfam05745 368591 CRPA Chlamydia 15 kDa cysteine-rich outer membrane protein (CRPA). This family consists of several Chlamydia 15 kDa cysteine-rich outer membrane proteins which are associated with differentiation of reticulate bodies (RBs) into elementary bodies (EBs). 150 matched cddid_all.tbl CDD pfam05746 pfam05746 399042 DALR_1 DALR anticodon binding domain. This all alpha helical domain is the anticodon binding domain in Arginyl and glycyl tRNA synthetase. This domain is known as the DALR domain after characteriztic conserved amino acids. 117 matched cddid_all.tbl CDD pfam05748 pfam05748 283418 Rubella_E1 Rubella membrane glycoprotein E1. Rubella virus (RV), the sole member of the genus Rubivirus within the family Togaviridae, is a small enveloped, positive strand RNA virus. The nucleocapsid consists of 40S genomic RNA and a single species of capsid protein which is enveloped within a host-derived lipid bilayer containing two viral glycoproteins, E1 (58 kDa) and E2 (42-46 kDa). In virus infected cells, RV matures by budding either at the plasma membrane, or at the internal membranes depending on the cell type and enters adjacent uninfected cells by a membrane fusion process in the endosome, directed by E1-E2 heterodimers. The heterodimer formation is crucial for E1 transport out of the endoplasmic reticulum to the Golgi and plasma membrane. In RV E1, a cysteine at position 82 is crucial for the E1-E2 heterodimer formation and cell surface expression of the two proteins. The E1 has been shown to be a type 1 membrane protein, rich in cysteine residues with extensive intramolecular disulfide bonds. 496 matched cddid_all.tbl CDD pfam05749 pfam05749 283419 Rubella_E2 Rubella membrane glycoprotein E2. Rubella virus (RV), the sole member of the genus Rubivirus within the family Togaviridae, is a small enveloped, positive strand RNA virus. The nucleocapsid consists of 40S genomic RNA and a single species of capsid protein which is enveloped within a host-derived lipid bilayer containing two viral glycoproteins, E1 (58 kDa) and E2 (42-46 kDa). In virus infected cells, RV matures by budding either at the plasma membrane, or at the internal membranes depending on the cell type and enters adjacent uninfected cells by a membrane fusion process in the endosome, directed by E1-E2 heterodimers. The heterodimer formation is crucial for E1 transport out of the endoplasmic reticulum to the Golgi and plasma membrane. In RV E1, a cysteine at position 82 is crucial for the E1-E2 heterodimer formation and cell surface expression of the two proteins. 267 matched cddid_all.tbl CDD pfam05750 pfam05750 399043 Rubella_Capsid Rubella capsid protein. Rubella virus is an enveloped positive-strand RNA virus of the family Togaviridae. Virions are composed of three structural proteins: a capsid and two membrane-spanning glycoproteins, E2 and E1. During virus assembly, the capsid interacts with genomic RNA to form nucleocapsids. It has been discovered that capsid phosphorylation serves to negatively regulate binding of viral genomic RNA. This may delay the initiation of nucleocapsid assembly until sufficient amounts of virus glycoproteins accumulate at the budding site and/or prevent non-specific binding to cellular RNA when levels of genomic RNA are low. It follows that at a late stage in replication, the capsid may undergo dephosphorylation before nucleocapsid assembly occurs. 269 matched cddid_all.tbl CDD pfam05751 pfam05751 461730 FixH FixH. This family consists of several Rhizobium FixH like proteins. It has been suggested that suggested that the four proteins FixG, FixH, FixI, and FixS may participate in a membrane-bound complex coupling the FixI cation pump with a redox process catalyzed by FixG. 147 matched cddid_all.tbl CDD pfam05752 pfam05752 399045 Calici_MSP Calicivirus minor structural protein. This family consists of minor structural proteins largely from human calicivirus isolates. Human calicivirus causes gastroenteritis. The function of this family is unknown. 165 matched cddid_all.tbl CDD pfam05753 pfam05753 399046 TRAP_beta Translocon-associated protein beta (TRAPB). This family consists of several eukaryotic translocon-associated protein beta (TRAPB) or signal sequence receptor beta subunit (SSR-beta) proteins. The normal translocation of nascent polypeptides into the lumen of the endoplasmic reticulum (ER) is thought to be aided in part by a translocon-associated protein (TRAP) complex consisting of 4 protein subunits. The association of mature proteins with the ER and Golgi, or other intracellular locales, such as lysosomes, depends on the initial targeting of the nascent polypeptide to the ER membrane. A similar scenario must also exist for proteins destined for secretion. 178 matched cddid_all.tbl CDD pfam05754 pfam05754 428615 DUF834 Domain of unknown function (DUF834). This short presumed domain is found in a large number of hypothetical plant proteins. The domain is quite rich in conserved glycine residues. It occurs in some putative transposons but currently has no known function. 50 matched cddid_all.tbl CDD pfam05755 pfam05755 461731 REF Rubber elongation factor protein (REF). This family consists of the highly related rubber elongation factor (REF), small rubber particle protein (SRPP) and stress-related protein (SRP) sequences. REF and SRPP are released from the rubber particle membrane into the cytosol during osmotic lysis of the sedimentable organelles (lutoids). The exact function of this family is unknown. 206 matched cddid_all.tbl CDD pfam05756 pfam05756 399049 S-antigen S-antigen protein. This domain is found at the N terminus of S-antigen proteins from Plasmodium falciparum. S-antigens are heat stable proteins that are found in the blood of individuals infected with malaria. 92 matched cddid_all.tbl CDD pfam05757 pfam05757 399050 PsbQ Oxygen evolving enhancer protein 3 (PsbQ). This family consists of the plant specific oxygen evolving enhancer protein 3 (PsbQ). Photosystem II (PSII)1 is a pigment-protein complex, which consists of at least 25 different protein subunits, at present denoted PsbA-Z according to the genes that encode them. PsbQ plays an important role in the lumenal oxygen-evolving activity of PSII from higher plants and green algae. 198 matched cddid_all.tbl CDD pfam05758 pfam05758 368599 Ycf1 Ycf1. The chloroplast genomes of most higher plants contain two giant open reading frames designated ycf1 and ycf2. Although the function of Ycf1 is unknown, it is known to be an essential gene. 944 matched cddid_all.tbl CDD pfam05760 pfam05760 461732 IER Immediate early response protein (IER). This family consists of several eukaryotic immediate early response (IER) 2 and 5 proteins. The role of IER5 is unclear although it play an important role in mediating the cellular response to mitogenic signals. Again, little is known about the function of IER2 although it is thought to play a role in mediating the cellular responses to a variety of extracellular signals. 310 matched cddid_all.tbl CDD pfam05761 pfam05761 461733 5_nucleotid 5' nucleotidase family. This family of eukaryotic proteins includes 5' nucleotidase enzymes, such as purine 5'-nucleotidase EC:3.1.3.5. 445 matched cddid_all.tbl CDD pfam05762 pfam05762 399053 VWA_CoxE VWA domain containing CoxE-like protein. This family is annotated by SMART as containing a VWA (von Willebrand factor type A) domain. The exact function of this family is unknown. It is found as part of a CO oxidising (Cox) system operon is several bacteria. 221 matched cddid_all.tbl CDD pfam05763 pfam05763 428619 DUF835 Protein of unknown function (DUF835). The members of this archaebacterial protein family are around 250-300 amino acid residues in length. The function of these proteins is not known. 136 matched cddid_all.tbl CDD pfam05764 pfam05764 461734 YL1 YL1 nuclear protein. The proteins in this family are designated YL1. These proteins have been shown to be DNA-binding and may be a transcription factor. 245 matched cddid_all.tbl CDD pfam05766 pfam05766 428621 NinG Bacteriophage Lambda NinG protein. NinG or Rap is involved in recombination. Rap (recombination adept with plasmid) increases lambda-by-plasmid recombination catalyzed by Escherichia coli's RecBCD pathway. 195 matched cddid_all.tbl CDD pfam05767 pfam05767 283435 Pox_A14 Poxvirus virion envelope protein A14. This family consists of several Poxvirus virion envelope protein A14 like sequences. A14 is a component of the virion membrane and has been found to be an H1 phosphatase substrate in vivo and in vitro. A14 is hyperphosphorylated on serine residues in the absence of H1 expression. 93 matched cddid_all.tbl CDD pfam05768 pfam05768 399055 Glrx-like Glutaredoxin-like domain (DUF836). These proteins are related to the pfam00462 family. This entry includes several viral glutaredoxins and many related bacterial and eukaryotic proteins of unknown function. The best characterized member is G4L from Vaccinia virus (strain Western Reserve/WR) (VACV), which is necessary for virion morphogenesis and replication. This is a cytoplasmic protein which functions as a shuttle in a redox pathway between membrane-associated E10R and L1R or F9L. 80 matched cddid_all.tbl CDD pfam05769 pfam05769 461735 SIKE SIKE family. This family consists of several eukaryotic proteins. Suppressor of IKBKE 1 (SIKE) is a physiological suppressor of IKK-epsilon and TBK1, which are two IKK-related kinases involved in virus- and TLR3-triggered activation of interferon regulatory factor 3 (IRF-3). Other members of this family are circulating cathodic antigen (CCA), found in Schistosoma mansoni (Blood fluke), and FGFR1 oncogene partner 2, which may be involved in wound healing pathway. 180 matched cddid_all.tbl CDD pfam05770 pfam05770 368606 Ins134_P3_kin Inositol 1,3,4-trisphosphate 5/6-kinase ATP-grasp domain. This family consists of several inositol 1, 3, 4-trisphosphate 5/6-kinase proteins. Inositol 1,3,4-trisphosphate is at a branch point in inositol phosphate metabolism. It is dephosphorylated by specific phosphatases to either inositol 3,4-bisphosphate or inositol 1,3-bisphosphate. Alternatively, it is phosphorylated to inositol 1,3,4,6-tetrakisphosphate or inositol 1,3,4,5-tetrakisphosphate by inositol trisphosphate 5/6-kinase. This entry represents the ATP-grasp domain. 201 matched cddid_all.tbl CDD pfam05771 pfam05771 283438 Pox_A31 Poxvirus A31 protein. 113 matched cddid_all.tbl CDD pfam05772 pfam05772 428623 NinB NinB protein. The ninR region of phage lambda contains two recombination genes, orf (ninB) and rap (ninG), that have roles when the RecF and RecBCD recombination pathways of E. coli, respectively, operate on phage lambda. NinB binds to single-stranded DNA. 117 matched cddid_all.tbl CDD pfam05773 pfam05773 399058 RWD RWD domain. This domain was identified in WD40 repeat proteins and Ring finger domain proteins. The function of this domain is unknown. GCN2 is the alpha-subunit of the only translation initiation factor (eIF2 alpha) kinase that appears in all eukaryotes. Its function requires an interaction with GCN1 via the domain at its N-terminus, which is termed the RWD domain after three major RWD-containing proteins: RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases. The structure forms an alpha + beta sandwich fold consisting of two layers: a four-stranded antiparallel beta-sheet, and three side-by-side alpha-helices. 111 matched cddid_all.tbl CDD pfam05774 pfam05774 283441 Herpes_heli_pri Herpesvirus helicase-primase complex component. This family consists of several helicase-primase complex components from the Gammaherpesviruses. 127 matched cddid_all.tbl CDD pfam05775 pfam05775 461736 AfaD Enterobacteria AfaD invasin protein. This family consists of several AfaD and related proteins from Escherichia coli and Salmonella bacteria. The afa gene clusters encode an afimbrial adhesive sheath produced by Escherichia coli. The adhesive sheath is composed of two proteins, AfaD and AfaE, which are independently exposed at the bacterial cell surface. AfaE is required for bacterial adhesion to HeLa cells and AfaD for the uptake of adherent bacteria into these cells. 105 matched cddid_all.tbl CDD pfam05776 pfam05776 147756 Papilloma_E5A Papillomavirus E5A protein. Human papillomaviruses (HPVs) are epitheliotropic viruses, and their life cycle is intimately linked to the stratification and differentiation state of the host epithelial tissues. The kinetics of E5a protein expression during the complete viral life cycle has been studied and the highest level was found to be coincidental with the onset of virion morphogenesis. 91 matched cddid_all.tbl CDD pfam05777 pfam05777 283443 Acp26Ab Drosophila accessory gland-specific peptide 26Ab (Acp26Ab). This family consists of accessory gland-specific 26Ab peptides or male accessory gland secretory protein 355B from different Drosophila species. Drosophila males, like males of most other insects, transfer a group of specific proteins (Acp26Ab and Acp26Aa in Drosophila) to the females during mating. These proteins are produced primarily in the accessory gland and are likely to influence the female's reproduction. 90 matched cddid_all.tbl CDD pfam05778 pfam05778 461737 Apo-CIII Apolipoprotein CIII (Apo-CIII). This family consists of several mammalian apolipoprotein CIII (Apo-CIII) sequences. Apolipoprotein C-III is a 79-residue glycoprotein. It is synthesized in the intestine and liver as part of the very low density lipoprotein (VLDL) and the high density lipoprotein (HDL) particles. Owing to its positive correlation with plasma triglyceride (Tg) levels, Apo-CIII is suggested to play a role in Tg metabolism and is therefore of interest regarding atherosclerosis. However, unlike other apolipoproteins such as Apo-AI, Apo E or CII for which many naturally occurring mutations are known, the structure-function relationships of apo C-III remains a subject of debate. One possibility is that apo C-III inhibits lipoprotein lipase (LPL) activity, as shown by in vitro experiments. Another suggestion, is that elevated levels of Apo-CIII displace other apolipoproteins at the lipoprotein surface, modifying their clearance from plasma. 69 matched cddid_all.tbl CDD pfam05781 pfam05781 461738 MRVI1 MRVI1 protein. This family consists of mammalian MRVI1 proteins which are related to the lymphoid-restricted membrane protein (JAW1) and the IP3 receptor associated cGMP kinase substrates A and B (IRAGA and IRAGB). The function of MRVI1 is unknown although mutations in the Mrvi1 gene induces myeloid leukaemia by altering the expression of a gene important for myeloid cell growth and/or differentiation so it has been speculated that Mrvi1 is a tumour suppressor gene. IRAG is very similar in sequence to MRVI1 and is an essential NO/cGKI-dependent regulator of IP3-induced calcium release. Activation of cGKI decreases IP3-stimulated elevations in intracellular calcium, induces smooth muscle relaxation and contributes to the antiproliferative and pro-apoptotic effects of NO/cGMP. Jaw1 is a member of a class of proteins with COOH-terminal hydrophobic membrane anchors and is structurally similar to proteins involved in vesicle targeting and fusion. This suggests that the function and/or the structure of the ER in lymphocytes may be modified by lymphoid-restricted resident ER proteins. 521 matched cddid_all.tbl CDD pfam05782 pfam05782 461739 ECM1 Extracellular matrix protein 1 (ECM1). This family consists of several eukaryotic extracellular matrix protein 1 (ECM1) sequences. ECM1 has been shown to regulate endochondral bone formation, stimulate the proliferation of endothelial cells and induce angiogenesis. Mutations in the ECM1 gene can cause lipoid proteinosis, a disorder which causes generalized thickening of skin, mucosae and certain viscera. Classical features include beaded eyelid papules and laryngeal infiltration leading to hoarseness. 518 matched cddid_all.tbl CDD pfam05783 pfam05783 368612 DLIC Dynein light intermediate chain (DLIC). This family consists of several eukaryotic dynein light intermediate chain proteins. The light intermediate chains (LICs) of cytoplasmic dynein consist of multiple isoforms, which undergo post-translational modification to produce a large number of species. DLIC1 is known to be involved in assembly, organization, and function of centrosomes and mitotic spindles when bound to pericentrin. DLIC2 is a subunit of cytoplasmic dynein 2 that may play a role in maintaining Golgi organization by binding cytoplasmic dynein 2 to its Golgi-associated cargo. 468 matched cddid_all.tbl CDD pfam05784 pfam05784 283448 Herpes_UL82_83 Betaherpesvirus UL82/83 protein N terminus. This family represents the N terminal region of the Betaherpesvirus UL82 and UL83 proteins. As viruses are reliant upon their host cell to serve as proper environments for their replication, many have evolved mechanisms to alter intracellular conditions to suit their own needs. Human cytomegalovirus induces quiescent cells to enter the cell cycle and then arrests them in late G(1), before they enter the S phase, a cell cycle compartment that is presumably favourable for viral replication. The protein product of the human cytomegalovirus UL82 gene, pp71, can accelerate the movement of cells through the G(1) phase of the cell cycle. This activity would help infected cells reach the late G(1) arrest point sooner and thus may stimulate the infectious cycle. pp71 also induces DNA synthesis in quiescent cells, but a pp71 mutant protein that is unable to induce quiescent cells to enter the cell cycle still retains the ability to accelerate the G(1) phase. Thus, the mechanism through which pp71 accelerates G(1) cell cycle progression appears to be distinct from the one that it employs to induce quiescent cells to exit G(0) and subsequently enter the S phase. 343 matched cddid_all.tbl CDD pfam05785 pfam05785 283449 CNF1 Rho-activating domain of cytotoxic necrotizing factor. This family consists of several bacterial cytotoxic necrotizing factor proteins as well as related dermonecrotic toxin (DNT) from Bordetella species. Cytotoxic necrotizing factor 1 (CNF1) causes necrosis of rabbit skin and re-organization of the actin cytoskeleton in cultured cells. Bordetella dermonecrotic toxin (DNT) stimulates the assembly of actin stress fibres and focal adhesions by deamidating or polyaminating Gln63 of the small GTPase Rho. DNT is an A-B toxin which is composed of an N-terminal receptor-binding (B) domain and a C-terminal enzymatically active (A) domain. 286 matched cddid_all.tbl CDD pfam05786 pfam05786 428627 Cnd2 Condensin complex subunit 2. This family consists of several Barren protein homologs from several eukaryotic organizms. In Drosophila Barren (barr) is required for sister-chromatid segregation in mitosis. barr encodes a novel protein that is present in proliferating cells and has homologs in yeast and human. Mitotic defects in barr embryos become apparent during cycle 16, resulting in a loss of PNS and CNS neurons. Centromeres move apart at the metaphase-anaphase transition and Cyclin B is degraded, but sister chromatids remain connected, resulting in chromatin bridging. Barren protein localizes to chromatin throughout mitosis. Colocalization and biochemical experiments indicate that Barren associates with Topoisomerase II throughout mitosis and alters the activity of Topoisomerase II. It has been suggested that this association is required for proper chromosomal segregation by facilitating the decatenation of chromatids at anaphase. This family forms one of the three non-structural maintenance of chromosomes (SMC) subunits of the mitotic condensation complex along with Cnd1 and Cnd3. 750 matched cddid_all.tbl CDD pfam05787 pfam05787 399063 DUF839 Bacterial protein of unknown function (DUF839). This family consists of several bacterial proteins of unknown function that contain a predicted beta-propeller repeats. 504 matched cddid_all.tbl CDD pfam05788 pfam05788 461740 Orbi_VP1 Orbivirus RNA-dependent RNA polymerase (VP1). This family consists of the RNA-dependent RNA polymerase protein VP1 from the Orbiviruses. VP1 may have both enzymatic and structural roles in the virus life cycle. 1297 matched cddid_all.tbl CDD pfam05789 pfam05789 283452 Baculo_VP1054 Baculovirus VP1054 protein. This family consists of several VP1054 proteins from the Baculoviruses. VP1054 is a virus structural protein required for nucleocapsid assembly. 379 matched cddid_all.tbl CDD pfam05790 pfam05790 399065 C2-set Immunoglobulin C2-set domain. 80 matched cddid_all.tbl CDD pfam05791 pfam05791 461741 Bacillus_HBL Bacillus haemolytic enterotoxin (HBL). This family consists of several Bacillus haemolytic enterotoxins (HblC, HblD, HblA, NheA, and NheB) which can cause food poisoning in humans. 177 matched cddid_all.tbl CDD pfam05792 pfam05792 461742 Candida_ALS Candida agglutinin-like (ALS). This family consists of several agglutinin-like proteins from different Candida species. ALS genes of Candida albicans encode a family of cell-surface glycoproteins with a three-domain structure. Each Als protein has a relatively conserved N-terminal domain, a central domain consisting of a tandemly repeated motif of variable number, and a serine-threonine-rich C-terminal domain that is relatively variable across the family. The ALS family exhibits several types of variability that indicate the importance of considering strain and allelic differences when studying ALS genes and their encoded proteins. Fungal adhesins, which include sexual agglutinins, virulence factors, and flocculins, are surface proteins that mediate cell-cell and cell-environment interactions. It is possible that both the serine/threonine-rich domain and the cysteine residues in the C-terminal and DIPSY pfam11763 participate in anchoring the terminal domains inside the wall, so that only the inner part of Map4p, including the repeat region, is sticking out as a fold-back loop then able to act in adhesing. 33 matched cddid_all.tbl CDD pfam05793 pfam05793 310411 TFIIF_alpha Transcription initiation factor IIF, alpha subunit (TFIIF-alpha). Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) or RNA polymerase II-associating protein 74 (RAP74) is the large subunit of transcription factor IIF (TFIIF), which is essential for accurate initiation and stimulates elongation by RNA polymerase II. 528 matched cddid_all.tbl CDD pfam05794 pfam05794 461743 Tcp11 T-complex protein 11. This family consists of several eukaryotic T-complex protein 11 (Tcp11) related sequences. Tcp11 is only expressed in fertile adult mammalian testes and is thought to be important in sperm function and fertility. The family also contains the yeast Sok1 protein which is known to suppress cyclic AMP-dependent protein kinase mutants. 390 matched cddid_all.tbl CDD pfam05795 pfam05795 310413 Plasmodium_Vir Plasmodium vivax Vir protein. This family consists of several Vir proteins specific to Plasmodium vivax. The vir genes are present at about 600-1,000 copies per haploid genome and encode proteins that are immunovariant in natural infections, indicating that they may have a functional role in establishing chronic infection through antigenic variation. 371 matched cddid_all.tbl CDD pfam05796 pfam05796 283458 Chordopox_G2 Chordopoxvirus protein G2. This family consists of several Chordopoxvirus isatin-beta-thiosemicarbazone dependent protein (protein G2) sequences. Inactivation of the gene coding for this protein renders the virus dependent upon isatin-beta-thiosemicarbazone (IBT) for growth. 215 matched cddid_all.tbl CDD pfam05797 pfam05797 283459 Rep_4 Yeast trans-acting factor (REP1/REP2). This family consists of the yeast trans-acting factor B and C (REP1 and 2) proteins. The yeast plasmid stability system consists of two plasmid-coded proteins, Rep1 and Rep2, and a cis-acting locus, STB. The Rep proteins show both self- and cross-interactions in vivo and in vitro, and bind to the STB DNA with assistance from host factor(s). Within the yeast nucleus, the Rep1 and Rep2 proteins tightly associate with STB-containing plasmids into well organized plasmid foci that form a cohesive unit in partitioning. It is generally accepted that the protein-protein and DNA-protein interactions engendered by the Rep-STB system are central to plasmid partitioning. Point mutations in Rep1 that knock out interaction with Rep2 or with STB simultaneously block the ability of these Rep1 variants to support plasmid stability. 369 matched cddid_all.tbl CDD pfam05798 pfam05798 283460 Phage_FRD3 Bacteriophage FRD3 protein. This family consists of bacteriophage FRD3 proteins. 75 matched cddid_all.tbl CDD pfam05800 pfam05800 399068 GvpO Gas vesicle synthesis protein GvpO. This family consists of archaeal GvpO proteins which are required for gas vesicle synthesis. The family also contains two related sequences from Streptomyces coelicolor. 94 matched cddid_all.tbl CDD pfam05801 pfam05801 461744 DUF840 Lagovirus protein of unknown function (DUF840). This family consists of several Lagovirus sequences of unknown function, largely from rabbit hemorrhagic disease virus. 113 matched cddid_all.tbl CDD pfam05802 pfam05802 428629 EspB Enterobacterial EspB protein. EspB is a type-III-secreted pore-forming protein of enteropathogenic Escherichia coli (EPEC) which is essential for EPEC pathogenesis. EspB is also found in Citrobacter rodentium. 171 matched cddid_all.tbl CDD pfam05803 pfam05803 283464 Chordopox_L2 Chordopoxvirus L2 protein. This family consists of several Chordopoxvirus L2 proteins. 79 matched cddid_all.tbl CDD pfam05804 pfam05804 253396 KAP Kinesin-associated protein (KAP). This family consists of several eukaryotic kinesin-associated (KAP) proteins. Kinesins are intracellular multimeric transport motor proteins that move cellular cargo on microtubule tracks. It has been shown that the sea urchin KRP85/95 holoenzyme associates with a KAP115 non-motor protein, forming a heterotrimeric complex in vitro, called the Kinesin-II. It includes kinesin-associated protein 3 (KAP3, also known as SMAP). In human and mouse, KAP3 is involved in tethering the chromosomes to the spindle pole and in chromosome movement. It binds to the tail domain of the KIF3A/KIF3B heterodimer to form a heterotrimeric KIF3 complex and may regulate the membrane binding of this complex. 708 matched cddid_all.tbl CDD pfam05805 pfam05805 461745 L6_membrane L6 membrane protein. This family consists of several eukaryotic L6 membrane proteins. L6, IL-TMP, and TM4SF5 are cell surface proteins predicted to have four transmembrane domains. Previous sequence analysis led to their assignment as members of the tetraspanin superfamily it has now been found that that they are not significantly related to genuine tetraspanins, but instead constitute their own L6 family. Several members of this family have been implicated in human cancer. 192 matched cddid_all.tbl CDD pfam05806 pfam05806 399070 Noggin Noggin. This family consists of the eukaryotic Noggin proteins. Noggin is a glycoprotein that binds bone morphogenetic proteins (BMPs) selectively and, when added to osteoblasts, it opposes the effects of BMPs. It has been found that noggin arrests the differentiation of stromal cells, preventing cellular maturation. 215 matched cddid_all.tbl CDD pfam05808 pfam05808 461746 Podoplanin Podoplanin. This family consists of several mammalian podoplanin like proteins which are thought to control specifically the unique shape of podocytes. 135 matched cddid_all.tbl CDD pfam05810 pfam05810 399072 NinF NinF protein. This family consists of several bacteriophage NinF proteins as well as related sequences from E. coli. 57 matched cddid_all.tbl CDD pfam05811 pfam05811 461747 DUF842 Eukaryotic protein of unknown function (DUF842). This family consists of a number of conserved eukaryotic proteins of unknown function. The sequences carry three sets of CxxxC motifs, which might suggest a type of zinc-finger formation. 126 matched cddid_all.tbl CDD pfam05812 pfam05812 283470 Herpes_BLRF2 Herpesvirus BLRF2 protein. This family consists of several Herpesvirus BLRF2 proteins. 119 matched cddid_all.tbl CDD pfam05813 pfam05813 283471 Orthopox_F7 Orthopoxvirus F7 protein. 80 matched cddid_all.tbl CDD pfam05814 pfam05814 114536 Ac76 Orf76 (Ac76). This family consists mainly of baculovirus proteins. Family members include Autographa californica multiple nucleopolyhedrovirus (AcMNPV), protein AC76. Ac76 has been shown to be involved in intranuclear microvesicle formation. Functional studies suggest that ac76 is essential for both BV (budded virus) and ODV (occlusion-derived virus) development but is not required for viral DNA synthesis. 83 matched cddid_all.tbl CDD pfam05815 pfam05815 283472 AcMNPV_Orf101 Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf101. This family is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf101 (also known as Protein C42). It plays a role in host nuclear actin polymerization by recruiting p78/73 protein that is capable of activating an actin-related protein 2/3 complex to initiate nuclear actin polymerization. 377 matched cddid_all.tbl CDD pfam05816 pfam05816 461748 TelA Toxic anion resistance protein (TelA). This family consists of several prokaryotic TelA like proteins. TelA and KlA are associated with tellurite resistance and plasmid fertility inhibition. 330 matched cddid_all.tbl CDD pfam05817 pfam05817 461749 Ribophorin_II Oligosaccharyltransferase subunit Ribophorin II. This family contains eukaryotic Ribophorin II (RPN2) proteins. The mammalian oligosaccharyltransferase (OST) is a protein complex that effects the cotranslational N-glycosylation of newly synthesized polypeptides, and is composed of the following proteins: ribophorins I and II (RI and RII), OST48, and Dadl, N33/IAP, OST4, STT3. The family also includes the SWP1 protein from yeast. In yeast the oligosaccharyltransferase complex is composed 7 or 8 subunits, SWP1, being one of them. 624 matched cddid_all.tbl CDD pfam05818 pfam05818 428635 TraT Enterobacterial TraT complement resistance protein. The traT gene is one of the F factor transfer genes and encodes an outer membrane protein which is involved in interactions between an Escherichia coli and its surroundings. 214 matched cddid_all.tbl CDD pfam05819 pfam05819 428636 NolX NolX protein. This family consists of Rhizobium NolX and Xanthomonas HrpF proteins. The interaction between the plant pathogen Xanthomonas campestris pv. vesicatoria and its host plants is controlled by hrp genes (hypersensitive reaction and pathogenicity), which encode a type III protein secretion system. Among type III-secreted proteins are avirulence proteins, effectors involved in the induction of plant defence reactions. HrpF is dispensable for protein secretion but required for AvrBs3 recognition in planta, is thought to function as a translocator of effector proteins into the host cell. NolX, a soybean cultivar specificity protein, is secreted by a type III secretion system (TTSS) and shows homology to HrpF of the plant pathogen Xanthomonas campestris pv. vesicatoria. It is not known whether NolX functions at the bacterium-plant interface or acts inside the host cell. NolX is expressed in planta only during the early stages of nodule development. 435 matched cddid_all.tbl CDD pfam05820 pfam05820 399078 Ac81 Baculoviridae AC81. This family consists of several highly related Baculovirus proteins and includes Autographa californica multiple nucleopolyhedrovirus (AcMNPV) protein AC81, which is required for nucleocapsid envelopment. Ac81 contains a functional hydrophobic transmembrane (TM) domain, whose deletion resulted in a phenotype similar to that of Ac81 knockout. 178 matched cddid_all.tbl CDD pfam05821 pfam05821 428637 NDUF_B8 NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8). This family consists of several eukaryotic NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI) proteins. NADH:ubiquinone oxidoreductase (complex I) is an extremely complicated multiprotein complex located in the inner mitochondrial membrane. Its main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. Human complex I appears to consist of 41 subunits. 167 matched cddid_all.tbl CDD pfam05822 pfam05822 310424 UMPH-1 Pyrimidine 5'-nucleotidase (UMPH-1). This family consists of several eukaryotic pyrimidine 5'-nucleotidase proteins. P5'N-1, also known as uridine monophosphate hydrolase-1 (UMPH-1), is a member of a large functional group of enzymes, characterized by the ability to dephosphorylate nucleic acids. P5'N-1 catalyzes the dephosphorylation of pyrimidine nucleoside monophosphates to the corresponding nucleosides. Deficiencies in this proteins function can lead to several different disorders in humans. 246 matched cddid_all.tbl CDD pfam05823 pfam05823 399080 Gp-FAR-1 Nematode fatty acid retinoid binding protein (Gp-FAR-1). Parasitic nematodes produce at least two structurally novel classes of small helix-rich retinol- and fatty-acid-binding proteins that have no counterparts in their plant or animal hosts and thus represent potential targets for new nematicides. Gp-FAR-1 is a member of the nematode-specific fatty-acid- and retinol-binding (FAR) family of proteins but localizes to the surface of the organizm, placing it in a strategic position for interaction with the host. Gp-FAR-1 functions as a broad-spectrum retinol- and fatty-acid-binding protein, and it is thought that it is involved in the evasion of primary host plant defence systems. 142 matched cddid_all.tbl CDD pfam05824 pfam05824 461750 Pro-MCH Pro-melanin-concentrating hormone (Pro-MCH). This family consists of several mammalian pro-melanin-concentrating hormone (Pro-MCH) 1 and 2 proteins. Melanin-concentrating hormone (MCH) is a 19 amino acid cyclic peptide that was first isolated from the pituitary of teleost fish. It is produced from pro-MCH that encodes, in addition to MCH, NEI, and a putative peptide, NGE. In lower vertebrates, MCH acts to regulate skin colour by antagonising the melanin-dispersing actions of small alpha, Greek-melanocyte stimulating hormone (small alpha, Greek-MSH). In mammals, MCH serves as a neuropeptide and is found in many regions of the brain and especially the hypothalamus. It affects many types of behaviours such as appetite, sexual receptivity, aggression, and anxiety. MCH also stimulates the release of luteinising hormone. 86 matched cddid_all.tbl CDD pfam05825 pfam05825 283482 PSP94 Beta-microseminoprotein (PSP-94). This family consists of the mammalian specific protein beta-microseminoprotein. Prostatic secretory protein of 94 amino acids (PSP94), also called beta-microseminoprotein, is a small, nonglycosylated protein, rich in cysteine residues. It was first isolated as a major protein from human seminal plasma. The exact function of this protein is unknown. 94 matched cddid_all.tbl CDD pfam05826 pfam05826 461751 Phospholip_A2_2 Phospholipase A2. This family consists of several phospholipase A2 like proteins mostly from insects. 97 matched cddid_all.tbl CDD pfam05827 pfam05827 461752 VAS1_LD V-type proton ATPase subunit S1, luminal domain. This entry represents the luminal domain (LD) found in eukaryotic V-type proton ATPase subunit S1 involved in V-ATPase V0 assembly, including Ac45 subunit (ATP6AP1). This domain folds as a globular beta-prism structure which is structurally similar to LAMP1-3, thus, the LD domain of Ac45 is an evolutionarily conserved member of the LAMP family. Ac45 is an ER membrane protein that guides the V-type ATPase into specialized subcellular compartments and is critical for Vo complex assembly as it connects to multiple Vo subunits and phospholipids in the c-ring. Missense mutations in the X-linked ATP6AP1 gene cause immunodeficiency in males that leads to recurrent bacterial infection, hepatopathy, cognitive impairment, and abnormal protein glycosylation. 144 matched cddid_all.tbl CDD pfam05829 pfam05829 310429 Adeno_PX Adenovirus late L2 mu core protein (Protein X). This family consists of several Adenovirus late L2 mu core protein or Protein X sequences. 41 matched cddid_all.tbl CDD pfam05830 pfam05830 428641 NodZ Nodulation protein Z (NodZ). The nodulation genes of Rhizobia are regulated by the nodD gene product in response to host-produced flavonoids and appear to encode enzymes involved in the production of a lipo-chitose signal molecule required for infection and nodule formation. NodZ is required for the addition of a 2-O-methylfucose residue to the terminal reducing N-acetylglucosamine of the nodulation signal. This substitution is essential for the biological activity of this molecule. Mutations in nodZ result in defective nodulation. nodZ represents a unique nodulation gene that is not under the control of NodD and yet is essential for the synthesis of an active nodulation signal. 322 matched cddid_all.tbl CDD pfam05831 pfam05831 461753 GAGE GAGE protein. This family consists of several GAGE and XAGE proteins which are found exclusively in humans. The function of this family is unknown although they have been implicated in human cancers. 107 matched cddid_all.tbl CDD pfam05832 pfam05832 461754 DUF846 Eukaryotic protein of unknown function (DUF846). This family consists of several of unknown function from a variety of eukaryotic organizms. 139 matched cddid_all.tbl CDD pfam05833 pfam05833 428644 NFACT_N NFACT N-terminal and middle domains. This family contains the N-terminal and middle domains of NFACT (NEMF, FbpA, Caliban, and Tae2) proteins from eukaryotes, archaea and bacteria. Many members of this family act in ribosome quality control (RQC), including RqcH, which are involved in the addition of a poly-Ala tail to defective translated proteins to tag them for degradation. This process is analogous to the ssrA/tmRNA bacterial system. However, some other NFACT family members, such as bacterial proteins FbpA in Listeria or PavA in Streptococcus, are exported (despite lack of a classical signal peptide) and behave as fibronectin-binding adhesins associated with virulence. 451 matched cddid_all.tbl CDD pfam05834 pfam05834 310433 Lycopene_cycl Lycopene cyclase protein. This family consists of lycopene beta and epsilon cyclase proteins. Carotenoids with cyclic end groups are essential components of the photosynthetic membranes in all plants, algae, and cyanobacteria. These lipid-soluble compounds protect against photo-oxidation, harvest light for photosynthesis, and dissipate excess light energy absorbed by the antenna pigments. The cyclization of lycopene (psi, psi-carotene) is a key branch point in the pathway of carotenoid biosynthesis. Two types of cyclic end groups are found in higher plant carotenoids: the beta and epsilon rings. Carotenoids with two beta rings are ubiquitous, and those with one beta and one epsilon ring are common; however, carotenoids with two epsilon rings are rare. 380 matched cddid_all.tbl CDD pfam05835 pfam05835 461755 Synaphin Synaphin protein. This family consists of several eukaryotic synaphin 1 and 2 proteins. Synaphin/complexin is a cytosolic protein that preferentially binds to syntaxin within the SNARE complex. Synaphin promotes SNAREs to form precomplexes that oligomerise into higher order structures. A peptide from the central, syntaxin binding domain of synaphin competitively inhibits these two proteins from interacting and prevents SNARE complexes from oligomerising. It is thought that oligomerization of SNARE complexes into a higher order structure creates a SNARE scaffold for efficient, regulated fusion of synaptic vesicles. Synaphin promotes neuronal exocytosis by promoting interaction between the complementary syntaxin and synaptobrevin transmembrane regions that reside in opposing membranes prior to fusion. 142 matched cddid_all.tbl CDD pfam05836 pfam05836 283492 Chorion_S16 Chorion protein S16. This family consists of several examples of the fruit fly specific chorion protein S16. The chorion genes of Drosophila are amplified in response to developmental signals in the follicle cells of the ovary. 108 matched cddid_all.tbl CDD pfam05837 pfam05837 461756 CENP-H Centromere protein H (CENP-H). This family consists of several eukaryotic centromere protein H (CENP-H) sequences. Macromolecular centromere-kinetochore complex plays a critical role in sister chromatid separation, but its complete protein composition as well as its precise dynamic function during mitosis has not yet been clearly determined. CENP-H contains a coiled-coil structure and a nuclear localization signal. CENP-H is specifically and constitutively localized in kinetochores throughout the cell cycle. CENP-H may play a role in kinetochore organization and function throughout the cell cycle. This the C-terminus of the region, which is conserved from fungi to humans. 114 matched cddid_all.tbl CDD pfam05838 pfam05838 428646 Glyco_hydro_108 Glycosyl hydrolase 108. This family acts as a lysozyme (N-acetylmuramidase), EC:3.2.1.17. It contains a conserved EGGY motif near the N-terminus, the glutamic acid within this motif is essential for catalytic activity. In bacteria, it may activate the secretion of large proteins via the breaking and rearrangement of the peptidoglycan layer during secretion. It is frequently found at the N-terminus of proteins containing a C-terminal pfam09374 domain. 86 matched cddid_all.tbl CDD pfam05839 pfam05839 310437 Apc13p Apc13p protein. The anaphase-promoting complex (APC) is a conserved multi-subunit ubiquitin ligase required for the degradation of key cell cycle regulators Members of this family are components of the anaphase-promoting complex homologous to Apc13p. 89 matched cddid_all.tbl CDD pfam05840 pfam05840 336220 Phage_GPA Bacteriophage replication gene A protein (GPA). This family consists of a group of bacteriophage replication gene A protein (GPA) like sequences from both viruses and bacteria. The members of this family are likely to be endonucleases. 321 matched cddid_all.tbl CDD pfam05841 pfam05841 399091 Apc15p Apc15p protein. The anaphase-promoting complex (APC) is a conserved multi-subunit ubiquitin ligase required for the degradation of key cell cycle regulators Members of this family are components of the anaphase-promoting complex homologous to Apc15p. 118 matched cddid_all.tbl CDD pfam05842 pfam05842 191385 Euplotes_phero Euplotes octocarinatus mating pheromone protein. This family consists of several mating pheromone proteins from Euplotes octocarinatus. Cells of the ten mating types of the ciliate Euplotes octocarinatus communicate by pheromones before they enter conjugation. The pheromones induce homotypic pairing when applied to mating types that do not secrete the same pheromone(s). Heterotypic pairs (i.e., those between cells of different mating types) are formed only when both mating types in a mixture secrete a pheromone that the other does not. The genetics of mating types is based on four codominant mating type alleles, each allele determining production of a different pheromone. The pheromones not only induce pair formation but also attract cells. 135 matched cddid_all.tbl CDD pfam05843 pfam05843 428647 Suf Suppressor of forked protein (Suf). This family consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster Suppressor of forked [Su(f)] protein shares homology with the yeast RNA14 protein and the 77-kDa subunit of human cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilization and an important role of the GU-rich sequence for this regulation to occur. 291 matched cddid_all.tbl CDD pfam05844 pfam05844 283498 YopD YopD protein. This family consists of several bacterial YopD like proteins. Virulent Yersinia species harbour a common plasmid that encodes essential virulence determinants (Yersinia outer proteins [Yops]), which are regulated by the extracellular stimuli Ca2+ and temperature. YopD is thought to be a possible transmembrane protein and contains an amphipathic alpha-helix in its carboxy terminus. 292 matched cddid_all.tbl CDD pfam05845 pfam05845 428648 PhnH Bacterial phosphonate metabolism protein (PhnH). This family consists of several bacterial PhnH sequences which are known to be involved in phosphonate metabolism. 182 matched cddid_all.tbl CDD pfam05846 pfam05846 283500 Chordopox_A15 Chordopoxvirus A15 protein. This family consists of several Chordopoxvirus A15 like sequences. 90 matched cddid_all.tbl CDD pfam05847 pfam05847 461757 Baculo_LEF-3 Nucleopolyhedrovirus late expression factor 3 (LEF-3). This family consists of LEF-3 Nucleopolyhedrovirus late expression factor 3 (LEF-3) sequences which are known to be ssDNA-binding proteins. Alkaline nuclease (AN) and LEF-3 may participate in homologous recombination of the baculovirus genome in a manner similar to that of exonuclease (Redalpha) and DNA-binding protein (Redbeta) of the Red-mediated homologous recombination system of bacteriophage lambda. LEF-3 is essential for transporting the putative baculovirus helicase protein P143 into the nucleus where they function together during viral DNA replication. LEF-3 and other proteins have been shown to bind to closely linked sites on viral chromatin in vivo, suggesting that they may form part of the baculovirus replisome. 364 matched cddid_all.tbl CDD pfam05848 pfam05848 428649 CtsR CtsR N-terminal HTH domain. This family consists of several Firmicute transcriptional repressor of class III stress genes (CtsR) proteins. CtsR of L. monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon. This entry is the N-terminal HTH domain. 72 matched cddid_all.tbl CDD pfam05849 pfam05849 461758 L-fibroin Fibroin light chain (L-fibroin). This family consists of several moth fibroin light chain (L-fibroin) proteins. Fibroin of the silkworm, Bombyx mori, is secreted into the lumen of posterior silk gland (PSG) from the surrounding PSG cells as a molecular complex consisting of a heavy (H)-chain of approximately 350 kDa, a light (L)-chain of 25 kDa and a P25 of about 27 kDa. The H- and L-chains are disulfide-linked but P25 is associated with the H-L complex by non-covalent force. 239 matched cddid_all.tbl CDD pfam05851 pfam05851 147807 Lentivirus_VIF Lentivirus virion infectivity factor (VIF). This family consists of several feline specific Lentivirus virion infectivity factor (VIF) proteins. VIF is essential for productive FIV infection of host target cells in vitro. 250 matched cddid_all.tbl CDD pfam05852 pfam05852 283504 DUF848 Gammaherpesvirus protein of unknown function (DUF848). This family consists of several uncharacterized proteins from the Gammaherpesvirinae. 145 matched cddid_all.tbl CDD pfam05853 pfam05853 461759 BKACE beta-keto acid cleavage enzyme. BKACE, beta-keto acid cleavage enzyme plays, a role in lysine degradation. In certain instances it catalyzes the conversion of 3-keto-5-aminohexanoate and acetyl-CoA into acetoacetate and 3-aminobutyryl-CoA. The family is found to have at least 14 slightly different potential new enzymatic activities, all of which can therefore be designated as beta-keto acid cleavage enzymes. 274 matched cddid_all.tbl CDD pfam05854 pfam05854 399096 MC1 Non-histone chromosomal protein MC1. This family consists of archaeal chromosomal protein MC1 sequences which protect DNA against thermal denaturation. 90 matched cddid_all.tbl CDD pfam05856 pfam05856 461760 ARPC4 ARP2/3 complex 20 kDa subunit (ARPC4). This family consists of several eukaryotic ARP2/3 complex 20 kDa subunit (P20-ARC) proteins. The Arp2/3 protein complex has been implicated in the control of actin polymerization in cells. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3 it has been suggested that the complex promotes actin assembly in lamellipodia and may participate in lamellipodial protrusion. 166 matched cddid_all.tbl CDD pfam05857 pfam05857 399098 TraX TraX protein. This family consists of several bacterial TraX proteins. TraX is responsible for the amino-terminal acetylation of F-pilin subunits. 215 matched cddid_all.tbl CDD pfam05858 pfam05858 147812 BIV_Env Bovine immunodeficiency virus surface protein (SU). The bovine lentivirus also known as the bovine immunodeficiency-like virus (BIV) has conserved and hypervariable regions in the surface envelope gene. This family corresponds to the SU surface protein. 548 matched cddid_all.tbl CDD pfam05859 pfam05859 461761 Mis12 Mis12 protein. Kinetochores are the chromosomal sites for spindle interaction and play a vital role in chromosome segregation. Fission yeast kinetochore protein Mis12, is required for correct spindle morphogenesis, determining metaphase spindle length. Thirty-five to sixty percent extension of metaphase spindle length takes place in Mis12 mutants. It has been shown that Mis12 genetically interacts with Mal2, another inner centromere core complex protein in S. pombe. 140 matched cddid_all.tbl CDD pfam05860 pfam05860 461762 TPS TPS secretion domain. Filamentous hemagglutinin (FHA), the major 230-kDa adhesin of the whooping cough agent Bordetella pertussis, is one of the most efficiently secreted proteins in Gram-negative bacteria. FHA is secreted by means of the two-partner secretion (TPS) pathway. A TPS system is composed of two separate proteins, with TpsA the secreted protein and TpsB its associated specific outer-membrane transporter. All TPS-secreted proteins contain a distinctive N-proximal module essential for secretion, the TPS domain. The TPS domain folds into a beta-helix. This domain is found in a wide variety of secreted proteins from bacterial pathogens. 249 matched cddid_all.tbl CDD pfam05861 pfam05861 428653 PhnI Bacterial phosphonate metabolism protein (PhnI). This family consists of several Proteobacterial phosphonate metabolism protein (PhnI) sequences. Bacteria that use phosphonates as a phosphorus source must be able to break the stable carbon-phosphorus bond. In Escherichia coli phosphonates are broken down by a C-P lyase that has a broad substrate specificity. The genes for phosphonate uptake and degradation in E. coli are organized in an operon of 14 genes, named phnC to phnP. Three gene products (PhnC, PhnD and PhnE) comprise a binding protein-dependent phosphonate transporter, which also transports phosphate, phosphite, and certain phosphate esters such as phosphoserine; two gene products (PhnF and PhnO) may have a role in gene regulation; and nine gene products (PhnG, PhnH, PhnI, PhnJ, PhnK, PhnL, PhnM, PhnN, and PhnP) probably comprise a membrane-associated C-P lyase enzyme complex. 346 matched cddid_all.tbl CDD pfam05862 pfam05862 147815 IceA2 Helicobacter pylori IceA2 protein. This family consists of several Helicobacter pylori specific IceA2 proteins. The function of this family is unknown. 59 matched cddid_all.tbl CDD pfam05864 pfam05864 283512 Chordopox_RPO7 Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7). This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA. 63 matched cddid_all.tbl CDD pfam05865 pfam05865 310449 Cypo_polyhedrin Cypovirus polyhedrin protein. This family consists of several Cypovirus polyhedrin protein. Polyhedrin is known to form a crystalline matrix (polyhedra) in infected insect cells. 248 matched cddid_all.tbl CDD pfam05866 pfam05866 428654 RusA Endodeoxyribonuclease RusA. This family consists of several bacterial and phage Holliday junction resolvase (RusA) like proteins. The RusA protein of Escherichia coli is an endonuclease that can resolve Holliday intermediates and correct the defects in genetic recombination and DNA repair associated with inactivation of RuvAB or RuvC. 124 matched cddid_all.tbl CDD pfam05867 pfam05867 399103 DUF851 Protein of unknown function (DUF851). 241 matched cddid_all.tbl CDD pfam05868 pfam05868 114586 Rotavirus_VP7 Rotavirus major outer capsid protein VP7. This family consists of several Rotavirus major outer capsid protein VP7 sequences. The rotavirus capsid is composed of three concentric protein layers. Proteins VP4 and VP7 comprise the outer layer. VP4 forms spikes and is the viral attachment protein. VP7 is a glycoprotein and the major constituent of the outer protein layer. 249 matched cddid_all.tbl CDD pfam05869 pfam05869 428655 Dam DNA N-6-adenine-methyltransferase (Dam). This family consists of several bacterial and phage DNA N-6-adenine-methyltransferase (Dam) like sequences. 165 matched cddid_all.tbl CDD pfam05870 pfam05870 399105 PA_decarbox Phenolic acid decarboxylase (PAD). This family consists of several bacterial phenolic acid decarboxylase proteins. Phenolic acids, also called substituted cinnamic acids, are important lignin-related aromatic acids and natural constituents of plant cell walls. These acids (particularly ferulic, p-coumaric, and caffeic acids) bind the complex lignin polymer to the hemicellulose and cellulose in plants. The Phenolic acid decarboxylase (PAD) gene (pad) is transcriptionally regulated by p-coumaric, ferulic, or caffeic acid; these three acids are the three substrates of PAD. 158 matched cddid_all.tbl CDD pfam05871 pfam05871 461763 ESCRT-II ESCRT-II complex subunit. This family of conserved eukaryotic proteins are subunits of the endosome associated complex ESCRT-II which recruits transport machinery for protein sorting at the multivesicular body (MVB). This protein complex transiently associates with the endosomal membrane and thereby initiates the formation of ESCRT-III, a membrane-associated protein complex that functions immediately downstream of ESCRT-II during sorting of MVB cargo. ESCRT-II in turn functions downstream of ESCRT-I, a protein complex that binds to ubiquitinated endosomal cargo. 134 matched cddid_all.tbl CDD pfam05872 pfam05872 428657 HerA_C Helicase HerA-like C-terminal. HerA is a DNA helicase able to utilize either 3' or 5' single-stranded DNA extensions for loading and subsequent DNA duplex unwinding. It forms a complex with NurA nuclease, this complex has the 5'-3' DNA end resection activity and is essential for cell viability in the crenarchaeon Sulfolobus islandicus. This entry represents the C-terminal domain of HerA which seems to be involved in the conversion of ATP hydrolysis into DNA translocation. 503 matched cddid_all.tbl CDD pfam05873 pfam05873 461764 Mt_ATP-synt_D ATP synthase D chain, mitochondrial (ATP5H). This family consists of several ATP synthase D chain, mitochondrial (ATP5H) proteins. Subunit d has no extensive hydrophobic sequences, and is not apparently related to any subunit described in the simpler ATP synthases in bacteria and chloroplasts. 154 matched cddid_all.tbl CDD pfam05874 pfam05874 461765 PBAN Pheromone biosynthesis activating neuropeptide (PBAN). This family consists of several moth pheromone biosynthesis activating neuropeptide (PBAN) sequences. Female moths produce and release species specific sex pheromones to attract males for mating. Pheromone biosynthesis is hormonally regulated by the Pheromone Biosynthesis Activating Neuropeptide (PBAN) which is biosynthesized in the subesophageal ganglion (SOG). 184 matched cddid_all.tbl CDD pfam05875 pfam05875 461766 Ceramidase Ceramidase. This family consists of several ceramidases. Ceramidases are enzymes involved in regulating cellular levels of ceramides, sphingoid bases, and their phosphates, EC:3.5.1.23. This family belongs to the CREST superfamily, which are distantly related to the GPCRs. 259 matched cddid_all.tbl CDD pfam05876 pfam05876 461767 GpA_ATPase Phage terminase large subunit gpA, ATPase domain. This family consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, TerL (gpA), products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA during the DNA packaging process. TerL contains all the catalytic activities required for for DNA maturation and packaging. At the N-terminal (represented in this entry) reside the DNA translocase (packaging) and ATPase activities, while at the C-terminal resides the DNA maturation (nuclease/helicase) catalytic activity. 247 matched cddid_all.tbl CDD pfam05878 pfam05878 283523 Phyto_Pns9_10 Phytoreovirus nonstructural protein Pns9/Pns10. This family consists of the Phytoreovirus nonstructural proteins Pns9 and Pns10. The function of this family is unknown. 344 matched cddid_all.tbl CDD pfam05879 pfam05879 461768 RHD3_GTPase Root hair defective 3 GTP-binding protein (RHD3) GTPase domain. This is the GTPase domain of several eukaryotic root hair defective 3 (RHD3) like GTP-binding proteins, including RHD3 from Arabidopsis and Sey1 from yeast, which are involved in homotypic membrane fusion of the endoplasmic reticulum. This domain binds GTP and forms dimers with other molecule for membrane tethering. 243 matched cddid_all.tbl CDD pfam05880 pfam05880 283524 Fiji_64_capsid Fijivirus 64 kDa capsid protein. This family consists of several Fijivirus 64 kDa capsid proteins. 554 matched cddid_all.tbl CDD pfam05881 pfam05881 461769 CNPase 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase). This family consists of the eukaryotic protein 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP). 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP) is one of the earliest myelin-related proteins expressed in differentiating oligodendrocytes and Schwann cells. CNP is abundant in the central nervous system and in oligodendrocytes. This protein is also found in mammalian photoreceptor cells, testis and lymphocytes. Although the biological function of CNP is unknown, it is thought to play a significant role in the formation of the myelin sheath, where it comprises 4% of total protein. CNP selectively cleaves 2',3'-cyclic nucleotides to produce 2'-nucleotides in vitro. Although physiologically relevant substrates with 2',3'-cyclic termini are still unknown, numerous cyclic phosphate containing RNAs occur transiently within eukaryotic cells. Other known protein families capable of hydrolysing 2',3'-cyclic nucleotides include tRNA ligases and plant cyclic phosphodiesterases. The catalytic domains from all these proteins contain two tetra-peptide motifs H-X-T/S-X, where X is usually a hydrophobic residue. Mutation of either histidine in CNP abolishes enzymatic activity. CNPases belong to the 2H phosphoesterase superfamily. They share a common active site, characterized by two conserved histidines, with the bacterial tRNA-ligating enzyme LigT, vertebrate myelin-associated 2',3' phosphodiesterases, plant Arabidopsis thaliana CPDases and several several bacteria and virus proteins. 214 matched cddid_all.tbl CDD pfam05883 pfam05883 283526 Baculo_RING Baculovirus U-box/Ring-like domain. This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison. 138 matched cddid_all.tbl CDD pfam05884 pfam05884 368652 ZYG-11_interact Interactor of ZYG-11. This family of proteins represents the protein product of the gene W03D8.9 which has been identified as an interactor of ZYG-11. ZYG-11 is the substrate-recognition subunit for a CUL-2 based complex that regulates cell division and embryonic development. 295 matched cddid_all.tbl CDD pfam05886 pfam05886 283528 Orthopox_F8 Orthopoxvirus F8 protein. This family consists of several Orthopoxvirus F8 proteins. The function of this family is unknown. 65 matched cddid_all.tbl CDD pfam05887 pfam05887 368653 Trypan_PARP Procyclic acidic repetitive protein (PARP). This family consists of several Trypanosoma brucei procyclic acidic repetitive protein (PARP) like sequences. The procyclic acidic repetitive protein (parp) genes of Trypanosoma brucei encode a small family of abundant surface proteins whose expression is restricted to the procyclic form of the parasite. They are found at two unlinked loci, parpA and parpB; transcription of both loci is developmentally regulated. 134 matched cddid_all.tbl CDD pfam05889 pfam05889 399111 SepSecS O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS. Early annotation suggested this family, SepSecS, of several eukaryotic and archaeal proteins, was involved in antigen-antibodies responses in the liver and pancreas. Structural studies show that the family is O-phosphoseryl-tRNA(Sec) selenium transferase, an enzyme involved in the synthesis of the amino acid selenocysteine (Sec). Sec is the only amino acid whose biosynthesis occurs on its cognate transfer RNA (tRNA). SepSecS catalyzes the final step in the formation of the amino acid. The early observation that autoantibodies isolated from patients with type I autoimmune hepatitis targeted a ribonucleoprotein complex containing tRNASec led to the identification and characterization of the archaeal and the human SepSecS. SepSecS forms its own branch in the family of fold-type I pyridoxal phosphate (PLP) enzymes that goes back to the last universal common ancestor which explains why the archaeal sequences Swiss:Q8TXK0 and Swiss:Q8TYR3 are annotated as being pyridoxal phosphate-dependent enzymes. 389 matched cddid_all.tbl CDD pfam05890 pfam05890 461770 Ebp2 Eukaryotic rRNA processing protein EBP2. This family consists of several Eukaryotic rRNA processing protein EBP2 sequences. Ebp2p is required for the maturation of 25S rRNA and 60S subunit assembly. Ebp2p may be one of the target proteins of Rrs1p for executing the signal to regulate ribosome biogenesis. This family also plays a role in chromosome segregation. 245 matched cddid_all.tbl CDD pfam05891 pfam05891 461771 Methyltransf_PK AdoMet dependent proline di-methyltransferase. This protein is expressed in the tail neuron PVT and in uterine cells in C. elegans [worm-base]. In Saccharomyces cerevisiae this is AdoMet dependent proline di-methyltransferase. This enzyme catalyzes the di-methylation of ribosomal proteins Rpl12 and Rps25 at N-terminal proline residues. The methyltransferases described here specifically recognize the N-terminal X-Pro-Lys sequence motif, and they may account for nearly all previously described eukaryotic protein N-terminal methylation reactions. A number of other yeast and human proteins also share the recognition motif and may be similarly modified. As with other methyltransferases, this family carries the characteriztic GxGxG motif. 218 matched cddid_all.tbl CDD pfam05892 pfam05892 283531 Tricho_coat Trichovirus coat protein. This family consists of several coat proteins which are specific to the ssRNA positive-strand, no DNA stage viruses such as the Trichovirus and Vitivirus. 195 matched cddid_all.tbl CDD pfam05893 pfam05893 399113 LuxC Acyl-CoA reductase (LuxC). This family consists of several bacterial Acyl-CoA reductase (LuxC) proteins. The channelling of fatty acids into the fatty aldehyde substrate for the bacterial bioluminescence reaction is catalyzed by a fatty acid reductase multienzyme complex, which channels fatty acids through the thioesterase (LuxD), synthetase (LuxE) and reductase (LuxC) components. 401 matched cddid_all.tbl CDD pfam05894 pfam05894 461772 Podovirus_Gp16 Podovirus DNA encapsidation protein (Gp16). This family consists of several DNA encapsidation protein (Gp16) sequences from the phi-29-like viruses. Gene product 16 catalyzes the in vivo and in vitro genome-encapsidation reaction. 331 matched cddid_all.tbl CDD pfam05895 pfam05895 310464 DUF859 Siphovirus protein of unknown function (DUF859). This family consists of several uncharacterized proteins from the Siphoviruses as well as one bacterial sequence Swiss:Q8K6J6. Some of the members of this family are described as putative minor structural proteins. 626 matched cddid_all.tbl CDD pfam05896 pfam05896 461773 NQRA Na(+)-translocating NADH-quinone reductase subunit A (NQRA). This family consists of several bacterial Na(+)-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na(+)-translocating NADH: ubiquinone oxidoreductase (Na(+)-NQR) generates an electrochemical Na(+) potential driven by aerobic respiration. 257 matched cddid_all.tbl CDD pfam05899 pfam05899 399116 Cupin_3 EutQ-like cupin domain. This entry represents the cupin domain, with a conserved jelly roll-like beta-barrel fold capable of homodimerization found in bacteria, plant and fungi. It is present in EutQ family from the eut operon, involved in ethanolamine degradation. EutQ is essential during anoxic growth and has acetate kinase activity. The cupin domain from EutQ does not possess the His residues responsible for metal coordination in other classes of cupins. This domain is also found in (S)-ureidoglycine aminohydrolase (UGlyAH) from E.coli, which is involved in the anaerobic nitrogen utilization via the assimilation of allantoin. It catalyzes the deamination of allantoin to produce S-ureidoglycolate and ammonia from S-ureidoglycine. 74 matched cddid_all.tbl CDD pfam05901 pfam05901 428664 Excalibur Excalibur calcium-binding domain. Extracellular Ca2+-dependent nuclease YokF from Bacillus subtilis and several other surface-exposed proteins from diverse bacteria are encoded in the genomes in two paralogous forms that differ by a ~45 amino acid fragment, which comprises a novel conserved domain. Sequence analysis of this domain revealed a conserved DxDxDGxxCE motif, which is strikingly similar to the Ca2+-binding loop of the calmodulin-like EF-hand domains, suggesting an evolutionary relationship between them. Functions of many of the other proteins in which the novel domain, named Excalibur (extracellular calcium-binding region), is found, as well as a structural model of its conserved motif are consistent with the notion that the Excalibur domain binds calcium. This domain is but one more example of the diversity of structural contexts surrounding the EF-hand-like calcium-binding loop in bacteria. This loop is thus more widespread than hitherto recognized and the evolution of EF-hand-like domains is probably more complex than previously appreciated. 36 matched cddid_all.tbl CDD pfam05902 pfam05902 461774 4_1_CTD 4.1 protein C-terminal domain (CTD). At the C-terminus of all known 4.1 proteins is a sequence domain unique to these proteins, known as the C-terminal domain (CTD). Mammalian CTDs are associated with a growing number of protein-protein interactions, although such activities have yet to be associated with invertebrate CTDs. Mammalian CTDs are generally defined by sequence alignment as encoded by exons 18-21. Comparison of known vertebrate 4.1 proteins with invertebrate 4.1 proteins indicates that mammalian 4.1 exon 19 represents a vertebrate adaptation that extends the sequence of the CTD with a Ser/Thr-rich sequence. The CTD was first described as a 22/24-kDa domain by chymotryptic digestion of erythrocyte 4.1 (4.1R). CTD is thought to represent an independent folding structure which has gained function since the divergence of vertebrates from invertebrates. 107 matched cddid_all.tbl CDD pfam05903 pfam05903 461775 Peptidase_C97 PPPDE putative peptidase domain. The PPPDE superfamily (after Permuted Papain fold Peptidases of DsRNA viruses and Eukaryotes), consists of predicted thiol peptidases with a circularly permuted papain-like fold. The inference of the likely DUB function of the PPPDE superfamily proteins is based on the fusions of the catalytic domain to Ub-binding PUG (PUB)/UBA domains and a novel alpha-helical Ub-associated domain (the PUL domain, after PLAP, Ufd3p and Lub1p). 151 matched cddid_all.tbl CDD pfam05904 pfam05904 461776 DUF863 Plant protein of unknown function (DUF863). This family consists of a number of hypothetical proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown. 939 matched cddid_all.tbl CDD pfam05906 pfam05906 114618 DUF865 Herpesvirus-7 repeat of unknown function (DUF865). This family consists of a series of 12 repeats of 35 amino acids in length which are found exclusively in Herpesvirus-7. The function of this family is unknown. 35 matched cddid_all.tbl CDD pfam05907 pfam05907 461777 CXXC_Zn-b_euk CXXC motif containing zinc binding protein, eukaryotic. This family consists of a number of eukaryotic proteins including CXXC motif containing zinc binding protein (previously known as UPF0587 protein C1orf123). The crystal structure reveals that the protein binds a Zn2+ ion in a tetrahedral coordination with four Cys residues from two CxxC motifs. CXXC motif containing zinc binding protein was initially identified as an interaction partner for the heavy metal-associated (HMA) domain of CCS (copper chaperone for superoxide dismutase). However, it was shown that only misfolded mutant forms, lacking part of the zinc-binding sites, interact with CCS. 152 matched cddid_all.tbl CDD pfam05908 pfam05908 399122 Gamma_PGA_hydro Poly-gamma-glutamate hydrolase. This family consists of a number of bacterial and phage proteins that function as gamma-PGA hydrolase enzymes. Structurally the protein in this family adopted an open alpha/beta mixed core structure with a seven-stranded parallel/anti-parallel beta-sheet. This structure shows similarity to mammalian carboxypeptidase A and related enzymes. 191 matched cddid_all.tbl CDD pfam05910 pfam05910 428668 DUF868 Plant protein of unknown function (DUF868). This family consists of several hypothetical proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown. 266 matched cddid_all.tbl CDD pfam05911 pfam05911 461778 FPP Filament-like plant protein, long coiled-coil. FPP is a family of long coiled-coil plant proteins that are filament-like. It interacts with the nuclear envelope-associated protein, MAF1, the WPP family pfam13943. 859 matched cddid_all.tbl CDD pfam05912 pfam05912 399125 DUF870 Caenorhabditis elegans protein of unknown function (DUF870). This family consists of a number of hypothetical proteins which seem to be specific to Caenorhabditis elegans. The function of this family is unknown. 111 matched cddid_all.tbl CDD pfam05913 pfam05913 461779 MupG_C 6-phospho-N-acetylmuramidase, C-terminal. This entry represents the C-terminal domain of 6-phospho-N-acetylmuramidase (MupG) found in bacteria. It characterizes putative phospho sugar glycosidases found in Gram-negative and -positive species, but mainly in firmicutes. MupG from Staphylococcus aureus, specifically cleaves MurNAc 6P-GlcNAc, a product of cell wall turnover, into the sugars MurNAc 6P and GlcNAc, being involved in cell wall turnover and recycling. Since some species, for example Lactobacillus plantarum, possess several putative paralogs, the substrate specificity of these proteins may not be limited to cell wall sugars, but may include phosphorylated disaccharides in general. Most proteins containing this domain appear to consist of two structural subdomains, as it can be seen in the two available crystal structures of Enterococcus faecalis (PDB:2p0o) and Bacillus cereus (PDB:1X7F). The larger N-terminal domain constitutes a TIM-barrel like structure and the C-terminal domain (this entry) is similar to the cyclophilin family. It should be noted that some proteins lack this domain. 116 matched cddid_all.tbl CDD pfam05914 pfam05914 461780 RIB43A RIB43A. This family consists of several RIB43A-like eukaryotic proteins. Ciliary and flagellar microtubules contain a specialized set of protofilaments, termed ribbons, that are composed of tubulin and several associated proteins. RIB43A was first characterized in the unicellular biflagellate, Chlamydomonas reinhardtii although highly related sequences are present in several higher eukaryotes including humans. The function of this protein is unknown although the structure of RIB43A and its association with the specialized protofilament ribbons and with basal bodies is relevant to the proposed role of ribbons in forming and stabilising doublet and triplet microtubules and in organizing their three-dimensional structure. Human RIB43A homologs could represent a structural requirement in centriole replication in dividing cells. 372 matched cddid_all.tbl CDD pfam05915 pfam05915 399128 TMEM_230_134 Transmembrane proteins 230/134. This family consists of the eukaryotic transmembrane proteins 230 and 134 (TMEM230 and 134). TMEM134 function is unknown, but it has been shown to interact with E virus ORF2. TMEM 230 is involved in trafficking and recycling of synaptic vesicles. 115 matched cddid_all.tbl CDD pfam05916 pfam05916 399129 Sld5 GINS complex protein. The eukaryotic GINS complex is essential for the initiation and elongation phases of DNA replication. It consists of four paralogous protein subunits (Sld5, Psf1, Psf2 and Psf3), all of which are included in this family. The GINS complex is conserved from yeast to humans, and has been shown in human to bind directly to DNA primase. 105 matched cddid_all.tbl CDD pfam05917 pfam05917 283549 DUF874 Helicobacter pylori protein of unknown function (DUF874). This family consists of several hypothetical proteins specific to Helicobacter pylori. The function of this family is unknown. 398 matched cddid_all.tbl CDD pfam05918 pfam05918 428672 API5 Apoptosis inhibitory protein 5 (API5). This family consists of apoptosis inhibitory protein 5 (API5) sequences from several organizms. Apoptosis or programmed cell death is a physiological form of cell death that occurs in embryonic development and organ formation. It is characterized by biochemical and morphological changes such as DNA fragmentation and cell volume shrinkage. API5 is an anti apoptosis gene located in human chromosome 11, whose expression prevents the programmed cell death that occurs upon the deprivation of growth factors and is up-regulated in various cancer cells. This protein has an elongated all alpha-helical structure, in which the N-terminal half is similar to the HEAT repeat and the C-terminal half is similar to the ARM (Armadillo-like) repeat. This suggests that API5 is involved in protein-protein interactions and may act as a scaffold for multiprotein complexes. 532 matched cddid_all.tbl CDD pfam05919 pfam05919 253459 Mitovir_RNA_pol Mitovirus RNA-dependent RNA polymerase. This family consists of several Mitovirus RNA-dependent RNA polymerase proteins. The family also contains fragment matches in the mitochondria of Arabidopsis thaliana. 495 matched cddid_all.tbl CDD pfam05920 pfam05920 428673 Homeobox_KN Homeobox KN domain. This is a homeobox transcription factor KN domain conserved from fungi to human and plants. They were first identified as TALE homeobox genes in eukaryotes, (including KNOX and MEIS genes). They have been recently classified. 39 matched cddid_all.tbl CDD pfam05922 pfam05922 428674 Inhibitor_I9 Peptidase inhibitor I9. This family includes the proteinase B inhibitor from Saccharomyces cerevisiae and the activation peptides from peptidases of the subtilisin family. The subtilisin propeptides are known to function as molecular chaperones, assisting in the folding of the mature peptidase, but have also been shown to act as 'temporary inhibitors'. 82 matched cddid_all.tbl CDD pfam05923 pfam05923 461781 APC_r APC repeat. This short region is found repeated in the mid region of the adenomatous polyposis proteins (APCs). In the human protein many cancer-linked SNPs are found near the first three occurrences of the motif. These repeats bind beta-catenin. 24 matched cddid_all.tbl CDD pfam05924 pfam05924 461782 SAMP SAMP Motif. This short region is found repeated in the mid region of the adenomatous polyposis proteins (APCs). This motif binds axin. 22 matched cddid_all.tbl CDD pfam05925 pfam05925 283555 IpgD Enterobacterial virulence protein IpgD. This family consists of several enterobacterial IpgD like virulence factor proteins. In the Gram-negative pathogen Shigella flexneri, the virulence factor IpgD is translocated directly into eukaryotic cells and acts as a potent inositol 4-phosphatase that specifically dephosphorylates phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P(2)] into phosphatidylinositol 5-monophosphate [PtdIns(5)P] that then accumulates. Transformation of PtdIns(4,5)P(2) into PtdIns(5)P by IpgD is responsible for dramatic morphological changes of the host cell, leading to a decrease in membrane tether force associated with membrane blebbing and actin filament remodelling. 580 matched cddid_all.tbl CDD pfam05926 pfam05926 428676 Phage_GPL Phage head completion protein (GPL). This family consists of several phage head completion protein (GPL) as well as related bacterial sequences. Members of this family allow the completion of filled heads by rendering newly packaged DNA in the heads resistant to DNase. The protein is thought to bind to DNA filled capsids. 139 matched cddid_all.tbl CDD pfam05927 pfam05927 147854 Penaeidin Penaeidin. This family consists of several isoforms of the penaeidin protein which is specific to shrimps. Penaeidins, a unique family of antimicrobial peptides (AMPs) with both proline and cysteine-rich domains, were initially identified in the hemolymph of the Pacific white shrimp, Litopenaeus vannamei. 73 matched cddid_all.tbl CDD pfam05928 pfam05928 114639 Zea_mays_MuDR Zea mays MURB-like protein (MuDR). This family consists of several Zea mays specific MURB-like proteins. The transposition of Mu elements underlying Mutator activity in maize requires a transcriptionally active MuDR element. Despite variation in MuDR copy number and RNA levels in Mutator lines, transposition events are consistently late in plant development, and Mu excision frequencies are similar. 207 matched cddid_all.tbl CDD pfam05929 pfam05929 428677 Phage_GPO Phage capsid scaffolding protein (GPO) serine peptidase. This family consists of several bacteriophage capsid scaffolding proteins (GPO) and some related bacterial sequences. GPO is thought to function in both the assembly of proheads and the cleavage of GPN. The family is found to function as a serine peptidase, with a conserved Asp, His and Ser catalytic triad, as in subtilisin, and as represented in MEROPS:S73. The family includes SwissProt:P25478 from Enterobacteria phage P2 which cleaves itself and then becomes the scaffold protein upon which the bacteriophage prohead is built - a mechanism quite common amongst phages. 271 matched cddid_all.tbl CDD pfam05930 pfam05930 399137 Phage_AlpA Prophage CP4-57 regulatory protein (AlpA). This family consists of several short bacterial and phage proteins which are related to the E. coli protein AlpA. AlpA suppress two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light. Several of the sequences in this family are thought to be DNA-binding proteins. 51 matched cddid_all.tbl CDD pfam05931 pfam05931 368676 AgrD Staphylococcal AgrD protein. This family consists of several AgrD proteins from many Staphylococcus species. The agr locus was initially described in Staphylococcus aureus as an element controlling the production of exoproteins implicated in virulence. Its pattern of action has been shown to be complex, upregulating certain extracellular toxins and enzymes expressed post-exponentially and repressing some exponential-phase surface components. AgrD encodes the precursor of the autoinducing peptide (AIP).The AIP derived from AgrD by the action of AgrB interacts with AgrC in the membrane to activate AgrA, which upregulates transcription both from promoter P2, amplifying the response, and from P3, initiating the production of a novel effector: RNAIII. In S. aureus, delta-hemolysin is the only translation product of RNA III and is not involved in the regulatory functions of the transcript, which is therefore the primary agent for modulating the expression of other operons controlled by agr. 45 matched cddid_all.tbl CDD pfam05932 pfam05932 399138 CesT "Tir chaperone protein (CesT) family. This family consists of a number of bacterial sequences which are highly similar to the Tir chaperone protein in E. Coli. In many Gram-negative bacteria, a key indicator of pathogenic potential is the possession of a specialized type III secretion system, which is utilized to deliver virulence effector proteins directly into the host cell cytosol. Many of the proteins secreted from such systems require small cytosolic chaperones to maintain the secreted substrates in a secretion-competent state. CesT serves a chaperone function for the enteropathogenic Escherichia coli (EPEC) translocated intimin receptor (Tir) protein, which confers upon EPEC the ability to alter host cell morphology following intimate bacterial attachment. This family also contains several DspF and related sequences from several plant pathogenic bacteria. The ""disease-specific"" (dsp) region next to the hrp gene cluster of Erwinia amylovora is required for pathogenicity but not for elicitation of the hypersensitive reaction. DspF and AvrF are small (16 kDa and 14 kDa) and acidic with predicted amphipathic alpha helices in their C termini; they resemble chaperones for virulence factors secreted by type III secretion systems of animal pathogens." 119 matched cddid_all.tbl CDD pfam05933 pfam05933 283561 Fun_ATP-synt_8 Fungal ATP synthase protein 8 (A6L). This family consists of fungus specific ATP synthase protein 8 (EC:3.6.3.14). The family may be related to the ATP synthase protein 8 found in other eukaryotes pfam00895. 48 matched cddid_all.tbl CDD pfam05934 pfam05934 461783 MCLC Mid-1-related chloride channel (MCLC). This family consists of several mid-1-related chloride channels. mid-1-related chloride channel (MCLC) proteins function as a chloride channel when incorporated in the planar lipid bilayer. 549 matched cddid_all.tbl CDD pfam05935 pfam05935 399139 Arylsulfotrans Arylsulfotransferase (ASST). This family consists of several bacterial Arylsulfotransferase proteins. Arylsulfotransferase (ASST) transfers a sulfate group from phenolic sulfate esters to a phenolic acceptor substrate. 368 matched cddid_all.tbl CDD pfam05936 pfam05936 428679 T6SS_VasE Bacterial Type VI secretion, VC_A0110, EvfL, ImpJ, VasE. T6SS_VasE is a family of of bacterial proteins that are essential for the type VI pathogenic secretion system, although the exact function of this particular component of the system is still not known. 427 matched cddid_all.tbl CDD pfam05937 pfam05937 399141 EB1_binding EB-1 Binding Domain. This region, found at the C-terminus of the APC proteins, binds the microtubule-associating protein EB-1. At the C-terminus of the alignment is also a pfam00595 binding domain. A short motif in the middle of the region appears to be found in the APC2 proteins. 174 matched cddid_all.tbl CDD pfam05938 pfam05938 461784 Self-incomp_S1 Plant self-incompatibility protein S1. This family consists of a series of plant proteins which are related to the Papaver rhoeas S1 self-incompatibility protein. Self incompatibility (SI) is the single most important outbreeding device found in angiosperms and is a mechanism that regulates the acceptance or rejection of pollen. S1 is known to exhibit specific pollen-inhibitory properties. 89 matched cddid_all.tbl CDD pfam05939 pfam05939 428681 Phage_min_tail Phage minor tail protein. This family consists of a series of phage minor tail proteins and related sequences from several bacterial species. 107 matched cddid_all.tbl CDD pfam05940 pfam05940 428682 NnrS NnrS protein. This family consists of several bacterial NnrS like proteins. NnrS is a putative heme-Cu protein (NnrS) and a member of the short-chain dehydrogenase family. Expression of nnrS is dependent on the transcriptional regulator NnrR, which also regulates expression of genes required for the reduction of nitrite to nitrous oxide, including nirK and nor. NnrS is a haem- and copper-containing membrane protein. Genes encoding putative orthologues of NnrS are sometimes but not always found in bacteria encoding nitrite and/or nitric oxide reductase. NnrS contributes to nitrosative-stress tolerance in V. cholerae and protects the cellular iron pool from the formation of dinitrosyl iron complexes (DNICs), thus protecting critical metabolic pathways from inhibition. 368 matched cddid_all.tbl CDD pfam05941 pfam05941 283569 Chordopox_A20R Chordopoxvirus A20R protein. This family consists of several Chordopoxvirus A20R proteins. The A20R protein is required for DNA replication, is associated with the processive form of the viral DNA polymerase, and directly interacts with the viral proteins encoded by the D4R, D5R, and H5R open reading frames. A20R may contribute to the assembly or stability of the multiprotein DNA replication complex. 335 matched cddid_all.tbl CDD pfam05942 pfam05942 377572 PaREP1 Archaeal PaREP1/PaREP8 family. This family consists of several archaeal PaREP1 and PaREP8 proteins the function of this family is unknown. 115 matched cddid_all.tbl CDD pfam05943 pfam05943 428683 VipB EvpB/VC_A0108, tail sheath N-terminal domain. EvpB is a family of Gram-negative probable type VI secretion system components of the tail sheath. They have been known as COG:COG3517. These sheath-components, of which there are many copies in the sheath, are also variously referred to as VipA/VipB and TssB/TssC. On contact with another bacterial cell the sheath contracts and pushes the puncturing device and tube through the cell envelope and punches the target bacterial cell. 301 matched cddid_all.tbl CDD pfam05944 pfam05944 428684 Phage_term_smal Phage small terminase subunit. This family consists of several phage small terminase subunit proteins as well as some related bacterial sequences. 129 matched cddid_all.tbl CDD pfam05946 pfam05946 283573 TcpA Toxin-coregulated pilus subunit TcpA. This family consists of toxin-coregulated pilus subunit (TcpA) proteins from Vibrio cholerae and related sequences. The major virulence factors of toxigenic Vibrio cholerae are cholera toxin (CT), which is encoded by a lysogenic bacteriophage (CTXPhi), and toxin-coregulated pilus (TCP), an essential colonization factor which is also the receptor for CTXPhi. The genes for the biosynthesis of TCP are part of a larger genetic element known as the TCP pathogenicity island. 130 matched cddid_all.tbl CDD pfam05947 pfam05947 428685 T6SS_TssF Type VI secretion system, TssF. This is a family of Gram-negative bacterial proteins that form part of the type VI pathogenicity secretion system (T6SS), including TssF. TssF is homologs to phage tail proteins and is required for proper assembly of the Hcp tube (the T6SS inner tube) in bacteria. T6SSs are toxin delivery systems. It is a multiprotein complex requiring numerous core proteins (Tss proteins) including cytoplasmic, transmembrane, and outer membrane components. The needle or tube apparatus is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex. T6SSs contain 13 conserved components (TssA-TssM) which are thought to form the core apparatus and to enable effector proteins to be injected into target cells in a single cell-contact-dependent step. TssF one of the core components of T6SSs machinery, has been shown to be recruited by TssK into the membrane-associated T6SS complex, contributing to the dynamic mechanism of the system. Furthermore, it has been reported to interact with TssG proteins stabilizing each other while making contact with TssE, TssK and VgrG as well as with tube and sheath components. Bioinformatic analysis suggest that TssF and TssG share similarities with the J and I proteins of the bacteriophage P2 baseplate respectively. Further experimental studies show that functional TssF and TssK proteins assemble into static foci near the cell envelope. Moreover, biochemical and cytological approaches provide support to the role of TssE, TssF, TssG, TssK and VgrG as T6SS baseplate components and to a sequential recruitment hierarchy (membrane complex, baseplate, tail tube/sheath) during T6SS biogenesis. 606 matched cddid_all.tbl CDD pfam05949 pfam05949 461785 DUF881 Bacterial protein of unknown function (DUF881). This family consists of a series of hypothetical bacterial proteins. One of the family members Swiss:Q45543 from Bacillus subtilis is thought to be involved in cell division and sporulation. 141 matched cddid_all.tbl CDD pfam05950 pfam05950 283576 Orthopox_A36R Orthopoxvirus A36R protein. This family consists of several Orthopoxvirus A36R proteins. The A36R protein is predicted to be a type Ib membrane protein. 158 matched cddid_all.tbl CDD pfam05951 pfam05951 428687 Peptidase_M15_2 Bacterial protein of unknown function (DUF882). This family consists of a series of hypothetical bacterial proteins of unknown function. 152 matched cddid_all.tbl CDD pfam05952 pfam05952 368681 ComX Bacillus competence pheromone ComX. Natural genetic competence in Bacillus subtilis is controlled by quorum-sensing (QS). The ComP- ComA two-component system detects the signalling molecule ComX, and this signal is transduced by a conserved phosphotransfer mechanism. ComX is synthesized as an inactive precursor and is then cleaved and modified by ComQ before export to the extracellular environment. This family includes ComX phermones involved in quorum sensing. Amino acid sequence alignments between the two ComX precursor proteins in B. licheniformis, showed that their conservation is only restricted to the N-terminal ends. Moreover, high diversity in the amino acid sequence in C-terminus marked the pheromone-forming region, where, interestingly, the tryptophan residue is located. 55 matched cddid_all.tbl CDD pfam05953 pfam05953 428688 Allatostatin Allatostatin. This family consists of allatostatins, bombystatins, helicostatins, cydiastatins and schistostatin from several insect species. Allatostatins (ASTs) of the Tyr/Phe-Xaa-Phe-Gly Leu/Ile-NH2 family are a group of insect neuropeptides that inhibit juvenile hormone biosynthesis by the corpora allata. 11 matched cddid_all.tbl CDD pfam05954 pfam05954 428689 Phage_GPD Phage tail baseplate hub (GPD). This family includes a number of phage late expression gene D proteins and related bacterial sequences. This family also includes Bacteriophage Mu P proteins and related sequences. This protein forms the phage central baseplate hub. 302 matched cddid_all.tbl CDD pfam05955 pfam05955 368683 Herpes_gp2 Equine herpesvirus glycoprotein gp2. This family consists of a number of glycoprotein gp2 sequences from equine herpesviruses. 226 matched cddid_all.tbl CDD pfam05956 pfam05956 428690 APC_basic APC basic domain. This region of the APC family of proteins is known as the basic domain. It contains a high proportion of positively charged amino acids and interacts with microtubules. 336 matched cddid_all.tbl CDD pfam05957 pfam05957 461786 DUF883 DUF883 N-terminal domain. This family consists of several hypothetical bacterial proteins of unknown function. The N-terminal domain found in this entry is related to pfam05532. 53 matched cddid_all.tbl CDD pfam05958 pfam05958 428692 tRNA_U5-meth_tr tRNA (Uracil-5-)-methyltransferase. This family consists of (Uracil-5-)-methyltransferases EC:2.1.1.35 from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalyzed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity. 357 matched cddid_all.tbl CDD pfam05959 pfam05959 283584 DUF884 Nucleopolyhedrovirus protein of unknown function (DUF884). This family consists of several hypothetical Nucleopolyhedrovirus proteins of unknown function. 194 matched cddid_all.tbl CDD pfam05960 pfam05960 428693 DUF885 Bacterial protein of unknown function (DUF885). This family consists of several hypothetical bacterial proteins several of which are putative membrane proteins. 527 matched cddid_all.tbl CDD pfam05961 pfam05961 283586 Chordopox_A13L Chordopoxvirus A13L protein. This family consists of A13L proteins from the Chordopoxviruses. A13L or p8 is one of the three most abundant membrane proteins of the intracellular mature Vaccinia virus. 69 matched cddid_all.tbl CDD pfam05962 pfam05962 428694 HutD HutD. HutD from Pseudomonas fluorescens SBW25 is a component of the histidine uptake and utilization operon. HutD is operonic with the well characterized repressor protein HutC. Genetic analysis using transcriptional fusions (lacZ) and deletion mutants shows that hutD is necessary to maintain fitness in environments replete with histidine. Evidence outlined by Zhang & Rainey (2007) suggests that HutD functions as a governor that sets an upper bound on the level of hut operon transcription. The mechanistic basis is unknown, but in silico molecular docking studies based on the crystal structure of PA5104 (HutD from Pseudomonas aeruginosa) show that urocanate (the first breakdown product of histidine) docks with the active site of HutD. 180 matched cddid_all.tbl CDD pfam05963 pfam05963 283588 Cytomega_US3 Cytomegalovirus US3 protein. US3 of human cytomegalovirus is an endoplasmic reticulum resident transmembrane glycoprotein that binds to major histocompatibility complex class I molecules and prevents their departure. The endoplasmic reticulum retention signal of the US3 protein is contained in the luminal domain of the protein. 212 matched cddid_all.tbl CDD pfam05964 pfam05964 461787 FYRN F/Y-rich N-terminus. This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00541. 51 matched cddid_all.tbl CDD pfam05965 pfam05965 461788 FYRC F/Y rich C-terminus. This region is normally found in the trithorax/ALL1 family proteins. It is similar to SMART:SM00542. 83 matched cddid_all.tbl CDD pfam05966 pfam05966 283591 Chordopox_A33R Chordopoxvirus A33R protein. This family consists of several Chordopoxvirus A33R proteins. A33R plays a role in promoting Ab-resistant cell-to-cell spread of virus and interacts with A36R to incorporate the protein into the outer membrane of intracellular enveloped virions (IEV). 184 matched cddid_all.tbl CDD pfam05968 pfam05968 428697 Bacillus_PapR Bacillus PapR protein. This family consists of the Bacillus species specific PapR protein. The papR gene belongs to the PlcR regulon and is located 70 bp downstream from plcR. It encodes a 48-amino-acid peptide. Disruption of the papR gene abolishes expression of the PlcR regulon, resulting in a large decrease in haemolysis and virulence in insect larvae. A processed form of PapR activates the PlcR regulon by allowing PlcR to bind to its DNA target. This activating mechanism is strain specific. 48 matched cddid_all.tbl CDD pfam05969 pfam05969 461789 PSII_Ycf12 Photosystem II complex subunit Ycf12. Ycf12 has been identified as a core subunit in the photosystem II (PSII) complex. PsbZ has been shown to be required for the association of PsbK and Ycf12 with PSII. 32 matched cddid_all.tbl CDD pfam05970 pfam05970 428699 PIF1 PIF1-like helicase. This family includes homologs of the PIF1 helicase, which inhibits telomerase activity and is cell cycle regulated. This family includes a large number of largely uncharacterized plant proteins. This family includes a P-loop motif that is involved in nucleotide binding. 361 matched cddid_all.tbl CDD pfam05971 pfam05971 399160 Methyltransf_10 RNA methyltransferase. This family includes ribosomal RNA large subunit methyltransferase F, and related proteins, including methyltransferase-like protein 16 (METTL16). METTL16 is a conserved RNA methyltransferase which interacts specifically with the MALAT1 triple helix. METTL16 shows nuclear localization. Another functional study indicates that METTL16 regulates expression of human MAT2A, which encodes the SAM synthetase expressed in most cells. Furthermore, results indicate that METTL16 is the long-unknown methyltransferase for the U6 spliceosomal small nuclear RNA (snRNA) and it has evolved an additional function in vertebrates to control SAM homeostasis by post-transcriptionally regulating SAM synthetase gene expression. 291 matched cddid_all.tbl CDD pfam05972 pfam05972 461790 APC_15aa APC 15 residue motif. This motif, known as the 15 aa repeat, is found in the APC protein family. They are involved in binding beta-catenin along with the pfam05923 repeats. Many human cancer mutations map to the region around these motifs, and may be involved in disrupting their binding of beta-catenin. 15 matched cddid_all.tbl CDD pfam05973 pfam05973 461791 Gp49 Phage derived protein Gp49-like (DUF891). This family consists of hypothetical bacterial proteins of unknown function as well as phage Gp49 proteins. 90 matched cddid_all.tbl CDD pfam05974 pfam05974 428701 DUF892 Domain of unknown function (DUF892). This family consists of several hypothetical bacterial proteins of unknown function. 156 matched cddid_all.tbl CDD pfam05975 pfam05975 428702 EcsB Bacterial ABC transporter protein EcsB. This family consists of several bacterial ABC transporter proteins which are homologous to the EcsB protein of Bacillus subtilis. EcsB is thought to encode a hydrophobic protein with six membrane-spanning helices in a pattern found in other hydrophobic components of ABC transporters. 383 matched cddid_all.tbl CDD pfam05977 pfam05977 399164 MFS_3 Transmembrane secretion effector. This is a family of transport proteins. Members of this family include a protein responsible for the secretion of the ferric chelator, enterobactin, and a protein involved in antibiotic resistance. 523 matched cddid_all.tbl CDD pfam05978 pfam05978 461792 UNC-93 Ion channel regulatory protein UNC-93. The proteins in this family are represented by UNC-93 from Caenorhabditis elegans and also includes protein unc-93 homolog A (UNC93A), protein unc-93 homolog B1 (UNC93B1), and UNC93-like protein MFSD11 (also called major facilitator superfamily domain- containing protein 11 or protein ET). UNC-93 colocalizes with SUP-10 and SUP-9 within muscle cells. UNC-93 acts as a regulatory subunit of a multi-subunit potassium channel complex that may function in coordinating muscle contraction in C. elegans. UNC93B1 controls intracellular trafficking and transport of a subset of Toll-like receptors (TLRs), including TLR3, TLR7 and TLR9, from the endoplasmic reticulum to endolysosomes where they can engage pathogen nucleotides and activate signaling cascades. MFSD11 is ubiquitously expressed in the periphery and the central nervous system of mice, where it is expressed in excitatory and inhibitory mouse brain neurons. 379 matched cddid_all.tbl CDD pfam05979 pfam05979 428703 DUF896 Bacterial protein of unknown function (DUF896). In B. subtilis, one small SOS response operon under the control of LexA, the yneA operon, is comprised of three genes: yneA, yneB, and ynzC. This family consists of several short, hypothetical bacterial proteins of unknown function. These proteins are mainly found in gram-positive firmicutes. Structures show that the N-terminus is composed of two alpha helices forming a helix-loop-helix motif. The structure of ynzC from B. subtilis forms a trimeric complex. Structural modelling suggests this domain may bind nucleic acids. This family is also known as UPF0291. 62 matched cddid_all.tbl CDD pfam05980 pfam05980 368691 Toxin_7 Toxin 7. This family consists of several short spider neurotoxin proteins including many from the Funnel-web spider. 34 matched cddid_all.tbl CDD pfam05981 pfam05981 428704 CreA CreA protein. This family consists of several bacterial CreA proteins, the function of which is unknown. 118 matched cddid_all.tbl CDD pfam05982 pfam05982 461793 Sbt_1 Na+-dependent bicarbonate transporter superfamily. Family of bacterial proteins that are likely to be part of the Na(+)-dependent bicarbonate transporter (sbt) family. Members carry 10TMS in a 5+5 duplicated structure. The loop between helices 5 and 6 in Synechocystis PCC6803 is likely to be the location for regulatory mechanisms governing the activation of the transporter. 308 matched cddid_all.tbl CDD pfam05983 pfam05983 461794 Med7 MED7 protein. This family consists of several eukaryotic proteins which are homologs of the yeast MED7 protein. Activation of gene transcription in metazoans is a multi-step process that is triggered by factors that recognize transcriptional enhancer sites in DNA. These factors work with co-activators such as MED7 to direct transcriptional initiation by the RNA polymerase II apparatus. 180 matched cddid_all.tbl CDD pfam05984 pfam05984 283605 Cytomega_UL20A Cytomegalovirus UL20A protein. This family consists of several Cytomegalovirus UL20A proteins. UL20A is thought to be a glycoprotein. 103 matched cddid_all.tbl CDD pfam05985 pfam05985 461795 EutC Ethanolamine ammonia-lyase light chain (EutC). This family consists of several bacterial ethanolamine ammonia-lyase light chain (EutC) EC:4.3.1.7 sequences. Ethanolamine ammonia-lyase is a bacterial enzyme that catalyzes the adenosylcobalamin-dependent conversion of certain vicinal amino alcohols to oxo compounds and ammonia. 233 matched cddid_all.tbl CDD pfam05986 pfam05986 461796 ADAMTS_spacer1 ADAM-TS Spacer 1. This domain represents the Spacer-1 region from the ADAM-TS and ADAM-TS-like proteins. ADAM-TS (A Disintegrin and Metalloproteinase with Thrombospondin Motifs) is closely related to the ADAM family (A Disintegrin and Metalloproteinase) and is a subfamily of the metalloprotease family, sharing a high degree of sequence similarity and conserved domain organization among its members. Members of the ADAM-TS family have been implicated in a range of diseases. ADAM-TS-like proteins lack a metalloprotease domain. They resides in the ECM and have regulatory roles. Examples of ADAM-TS-like proteins are papilin and punctin. 115 matched cddid_all.tbl CDD pfam05987 pfam05987 428709 DUF898 Bacterial protein of unknown function (DUF898). This family consists of several bacterial proteins of unknown function. Some of the family members are described as putative membrane proteins. 334 matched cddid_all.tbl CDD pfam05988 pfam05988 428710 DUF899 Bacterial protein of unknown function (DUF899). This family consists of several uncharacterized bacterial proteins of unknown function. 216 matched cddid_all.tbl CDD pfam05989 pfam05989 283610 Chordopox_A35R Chordopoxvirus A35R protein. This family consists of several Chordopoxvirus sequences homologous to the Vaccinia virus A35R protein. The function of this family is unknown. 172 matched cddid_all.tbl CDD pfam05990 pfam05990 399172 DUF900 Alpha/beta hydrolase of unknown function (DUF900). This family consists of several hypothetical proteins of unknown function mostly found in Rhizobium species. Members of this family have an alpha/beta hydrolase fold. 236 matched cddid_all.tbl CDD pfam05991 pfam05991 428711 NYN_YacP YacP-like NYN domain. This family consists of bacterial proteins related to YacP. This family is uncharacterized functionally, but it has been suggested that these proteins are nucleases due to them containing a NYN domain. NYN (for N4BP1, YacP-like Nuclease) domains were discovered by Anantharaman and Aravind. Based on gene neighborhoods it was suggested that the bacterial YacP proteins interact with the Ribonuclease III and TrmH methylase in a processome complex that catalyzes the maturation of rRNA and tRNA. 165 matched cddid_all.tbl CDD pfam05992 pfam05992 461797 SbmA_BacA SbmA/BacA-like family. The Rhizobium meliloti bacA gene encodes a function that is essential for bacterial differentiation into bacteroids within plant cells in the symbiosis between R. meliloti and alfalfa. An Escherichia coli homolog of BacA, SbmA, is implicated in the uptake of microcins and bleomycin. This family is likely to be a subfamily of the ABC transporter family. 314 matched cddid_all.tbl CDD pfam05993 pfam05993 461798 Reovirus_M2 Reovirus major virion structural protein Mu-1/Mu-1C (M2). This family consists of several Reovirus major virion structural protein Mu-1/Mu-1C (M2) sequences. This family is family is thought to play a role in host cell membrane penetration. 639 matched cddid_all.tbl CDD pfam05994 pfam05994 461799 FragX_IP Cytoplasmic Fragile-X interacting family. This entry includes Cytoplasmic fragile X mental retardation interacting proteins 1/2 (CYFIP1/2) from humans and their homologs, such as Sra-1 (specifically Rac1-associated protein 1) from Drosophila and PIROGI from Arabidopsis. CYFIP1/2 interact with FMRP (fragile X mental retardation protein) which is responsible for pathologic manifestations in the Fragile X Syndrome. CYFIP1 interacts with the small GTPase Rac1. CYFIP1 represses cap-dependent translation of mRNA by interacting with the initiation factor eIF4E. CYFIP1 and CYFIP2 are part of the Wiskott-Aldrich syndrome protein-family verprolin-homologous protein (WAVE) complex that regulates actin polymerization at synapses. Drosophila Sra-1 interacts with the Kette and Wasp. It is required for neuronal and bristle development in Drosophila. PIROGI is part of a WAVE complex that activates the ARP2/3 complex and is Involved in regulation of actin organization. 842 matched cddid_all.tbl CDD pfam05995 pfam05995 428713 CDO_I Cysteine dioxygenase type I. Cysteine dioxygenase type I (EC:1.13.11.20) converts cysteine to cysteinesulphinic acid and is the rate-limiting step in sulphate production. 169 matched cddid_all.tbl CDD pfam05996 pfam05996 399177 Fe_bilin_red Ferredoxin-dependent bilin reductase. This family consists of several different but closely related proteins which include phycocyanobilin:ferredoxin oxidoreductase EC:1.3.7.5 (PcyA), 15,16-dihydrobiliverdin:ferredoxin oxidoreductase EC:1.3.7.2 (PebA) and phycoerythrobilin:ferredoxin oxidoreductase EC:1.3.7.3 (PebB). Phytobilins are linear tetrapyrrole precursors of the light-harvesting prosthetic groups of the phytochrome photoreceptors of plants and the phycobiliprotein photosynthetic antennae of cyanobacteria, red algae, and cryptomonads. It is known that that phytobilins are synthesized from heme via the intermediary of biliverdin IX alpha (BV), which is reduced subsequently by ferredoxin-dependent bilin reductases with different double-bond specificities. 228 matched cddid_all.tbl CDD pfam05997 pfam05997 461800 Nop52 Nucleolar protein,Nop52. Nop52 believed to be involved in the generation of 28S rRNA. 213 matched cddid_all.tbl CDD pfam05999 pfam05999 283619 Herpes_U5 Herpesvirus U5-like family. This family of Herpesvirus includes U4, U5 and UL27. 488 matched cddid_all.tbl CDD pfam06001 pfam06001 399179 RING_CBP-p300 CREB-binding protein/p300, atypical RING domain. CBP (CREB-binding protein) and p300 (also known as CREBBP or KAT3A and EP300 or KAT3B, respectively) are two histone acetyltransferases (HATs) that associate with and acetylate transcriptional regulators and chromatin. The catalytic core of animal CBP-p300 contains a bromodomain, a CH2 region containing a discontinuous PHD domain interrupted by this RING domain, and a HAT domain. Bromodomain-RING-PHD forms a compact module in which the RING domain is juxtaposed with the HAT substrate-binding site. This RING domain contains only a single zinc ion-binding cluster instead of two; instead of a second zinc atom, a network of hydrophobic interactions stabilizes the domain. The RING domain has an inhibitory role. Disease mutations that disrupt RING attachment lead to upregulation of HAT activity. HAT regulation may require repositioning of the RING domain to facilitate access to an otherwise partially occluded HAT active site. Plant CBP-p300 type HATs lack a bromodomain whose role in the animal animal CBP-p300's is to bind acetylated histones; it has been suggested that these plant proteins may utilize a different domain or another bromodomain protein to perform this function. This RING domain has also been referred to as DUF902. 40 matched cddid_all.tbl CDD pfam06002 pfam06002 428715 CST-I Alpha-2,3-sialyltransferase (CST-I). This family consists of several alpha-2,3-sialyltransferase (CST-I) proteins largely found in Campylobacter jejuni. 295 matched cddid_all.tbl CDD pfam06003 pfam06003 428716 SMN Survival motor neuron protein (SMN). This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs. 264 matched cddid_all.tbl CDD pfam06004 pfam06004 428717 DUF903 Bacterial protein of unknown function (DUF903). This family consists of several small bacterial proteins several of which are classified as putative lipoproteins. The function of this family is unknown. 49 matched cddid_all.tbl CDD pfam06005 pfam06005 428718 ZapB Cell division protein ZapB. ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. 71 matched cddid_all.tbl CDD pfam06006 pfam06006 368702 DUF905 Bacterial protein of unknown function (DUF905). This family consists of several short hypothetical Enterobacteria proteins of unknown function. Structural analysis of the surface features of the protein YvyC has revealed a single cluster of highly conserved residues on the surface. Additionally, these residues fall into two groups which lie within the two largest of the three cavities identified over the surface. The conclusion from this is that these two cavities with, Leu 58, Glu 75, Ile 82, and Glu 83 and Pro 86, conserved, are likely to be important for the molecular function and reflect the cavities found on the surface of the FlaG proteins in pfam03646. 70 matched cddid_all.tbl CDD pfam06007 pfam06007 428719 PhnJ Phosphonate metabolism protein PhnJ. This family consists of several bacterial phosphonate metabolism (PhnJ) sequences. The exact role that PhnJ plays in phosphonate utilization is unknown. 274 matched cddid_all.tbl CDD pfam06008 pfam06008 310534 Laminin_I Laminin Domain I. coiled-coil structure. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure. 258 matched cddid_all.tbl CDD pfam06009 pfam06009 368703 Laminin_II Laminin Domain II. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure. 138 matched cddid_all.tbl CDD pfam06011 pfam06011 428720 TRP Transient receptor potential (TRP) ion channel. This family of proteins are transient receptor potential (TRP) ion channels. They are essential for cellular viability and are involved in cell growth and cell wall synthesis. The genes for these proteins are homologous to polycystic kidney disease related ion channel genes. 424 matched cddid_all.tbl CDD pfam06012 pfam06012 428721 DUF908 Domain of Unknown Function (DUF908). 351 matched cddid_all.tbl CDD pfam06013 pfam06013 428722 WXG100 Proteins of 100 residues with WXG. ESAT-6 is a small protein appears to be of fundamental importance in virulence and protective immunity in Mycobacterium tuberculosis. homologs have been detected in other Gram-positive bacterial species. It may represent a novel secretion system potentially driven by the pfam01580 domains in the YukA-like proteins. 85 matched cddid_all.tbl CDD pfam06014 pfam06014 428723 DUF910 Bacterial protein of unknown function (DUF910). This family consists of several short bacterial proteins of unknown function. 61 matched cddid_all.tbl CDD pfam06015 pfam06015 283633 Chordopox_A30L Chordopoxvirus A30L protein. This family consists of several short Chordopoxvirus proteins which are homologous to the A30L protein of Vaccinia virus. The vaccinia virus A30L protein is required for the association of electron-dense, granular, proteinaceous material with the concave surfaces of crescent membranes, an early step in viral morphogenesis. A30L is known to interact with the G7L protein and it has been shown that the stability of each is dependent on its association with the other. 71 matched cddid_all.tbl CDD pfam06016 pfam06016 283634 Reovirus_L2 Reovirus core-spike protein lambda-2 (L2). This family consists of several Reovirus core-spike protein lambda-2 (L2) sequences. The reovirus L2 genome segment encodes the core spike protein lambda-2, which mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts. 1297 matched cddid_all.tbl CDD pfam06017 pfam06017 461801 Myosin_TH1 Unconventional myosin tail, actin- and lipid-binding. Unconventional myosins, ie those that are not found in muscle, have the common, classical-type head domain, sometimes a neck with the IQ calmodulin-binding motifs, and then non-standard tails. These tails determine the subcellular localization of the unconventional myosins and also help determine their individual functions. The family carries several different unconventional myosins, eg. Myo1f is expressed mainly in immune cells as well as in the inner ear where it can be associated with deafness, Myo1d has a lipid-binding module in their tail and is implicated in endosome vesicle recycling in epithelial cells. Myo1a, b, c and g from various eukaryotes are also found in this family. 196 matched cddid_all.tbl CDD pfam06018 pfam06018 399189 CodY CodY GAF-like domain. This domain is a GAF-like domain found at the N-terminus of several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. This domain is involved in GTP binding and also branched chain amino acids (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk. 177 matched cddid_all.tbl CDD pfam06019 pfam06019 147919 Phage_30_8 Phage GP30.8 protein. This family consists of several GP30.8 proteins from the T4-like phages. The function of this family is unknown. 124 matched cddid_all.tbl CDD pfam06020 pfam06020 310540 Roughex Drosophila roughex protein. This family consists of several roughex (RUX) proteins specific to Drosophila species. Roughex can influence the intracellular distribution of cyclin A and is therefore defined as a distinct and specialized cell cycle inhibitor for cyclin A-dependent kinase activity. Rux is though to regulate the metaphase to anaphase transition during development. 379 matched cddid_all.tbl CDD pfam06021 pfam06021 461802 Gly_acyl_tr_N Aralkyl acyl-CoA:amino acid N-acyltransferase. This family consists of several mammalian specific aralkyl acyl-CoA:amino acid N-acyltransferase (glycine N-acyltransferase) proteins EC:2.3.1.13. 203 matched cddid_all.tbl CDD pfam06022 pfam06022 399191 Cir_Bir_Yir Plasmodium variant antigen protein Cir/Yir/Bir. This family consists of several Cir, Yir and Bir proteins from the Plasmodium species P.chabaudi, P.yoelii and P.berghei. 253 matched cddid_all.tbl CDD pfam06023 pfam06023 283640 Csa1 CRISPR-associated exonuclease Csa1. CRISPR (clustered regularly interspaced short palindromic repeats) elements and cas (CRISPR-associated) genes are widespread in Bacteria and Archaea. The CRISPR/Cas system operates as a defense mechanism against mobile genetic elements (i.e., viruses or plasmids). Csa1 is part of the archaeal subtype I-A system. Cas1 has not yet been enzymatically characterized. 292 matched cddid_all.tbl CDD pfam06024 pfam06024 368709 Orf78 Orf78 (ac78). Family members include Autographa californica nuclear polyhedrosis virus (AcMNPV), AC78 or Orf78. AC78 is a late gene in the viral life cycle and encodes an envelope structural protein that plays an essential role in embedding the occlusion-derived virus (ODV) in the occlusion body. Although AC78 is not essential for budding virus formation or nucleocapsid assembly and ODV formation, number are significantly reduced if the gene is knocked-out. 101 matched cddid_all.tbl CDD pfam06025 pfam06025 461803 DUF913 Domain of Unknown Function (DUF913). Members of this family are found in various ubiquitin protein ligases. 369 matched cddid_all.tbl CDD pfam06026 pfam06026 461804 Rib_5-P_isom_A Ribose 5-phosphate isomerase A (phosphoriboisomerase A). This family consists of several ribose 5-phosphate isomerase A or phosphoriboisomerase A (EC:5.3.1.6) from bacteria, eukaryotes and archaea. 172 matched cddid_all.tbl CDD pfam06027 pfam06027 283644 SLC35F Solute carrier family 35. This is a family of putative solute carrier proteins from eukaryotes. 299 matched cddid_all.tbl CDD pfam06028 pfam06028 283645 DUF915 Alpha/beta hydrolase of unknown function (DUF915). This family consists of several bacterial proteins of unknown function. Members of this family have an alpha/beta hydrolase fold. 253 matched cddid_all.tbl CDD pfam06029 pfam06029 428728 AlkA_N AlkA N-terminal domain. 118 matched cddid_all.tbl CDD pfam06030 pfam06030 461805 DUF916 Bacterial protein of unknown function (DUF916). This family consists of several hypothetical bacterial proteins of unknown function. 120 matched cddid_all.tbl CDD pfam06031 pfam06031 461806 SERTA SERTA motif. This family consists of a novel motif designated as SERTA (for SEI-1, RBT1, and TARA), corresponding to the largest conserved region among TRIP-Br proteins. The function of this motif is uncertain, but the CDK4-interacting segment of p34SEI-1 (amino acid residues 44-161) includes most of the SERTA motif. 36 matched cddid_all.tbl CDD pfam06032 pfam06032 461807 DUF917 Protein of unknown function (DUF917). This family consists of hypothetical bacterial and archaeal proteins of unknown function. 350 matched cddid_all.tbl CDD pfam06033 pfam06033 461808 DUF918 Nucleopolyhedrovirus protein of unknown function (DUF918). This family consists of several Nucleopolyhedrovirus proteins with no known function. 152 matched cddid_all.tbl CDD pfam06034 pfam06034 114740 DUF919 Nucleopolyhedrovirus protein of unknown function (DUF919). This family consists of several short Nucleopolyhedrovirus proteins of unknown function. 62 matched cddid_all.tbl CDD pfam06035 pfam06035 428732 Peptidase_C93 Bacterial transglutaminase-like cysteine proteinase BTLCP. Members of this family are predicted to be bacterial transglutaminase-like cysteine proteinases. They contain a conserved Cys-His-Asp catalytic triad. Their structure is predicted to be similar to that of Salmonella typhimurium N-hydroxyarylamine O-acetyltransferase in pfam00797, however they lack the sub-domain which is important for arylamine recognition. 161 matched cddid_all.tbl CDD pfam06037 pfam06037 428733 DUF922 Bacterial protein of unknown function (DUF922). This family of proteins has a conserved HEXXH motif, suggesting they are putative peptidases of zincin fold. 159 matched cddid_all.tbl CDD pfam06039 pfam06039 461809 Mqo Malate:quinone oxidoreductase (Mqo). This family consists of several bacterial Malate:quinone oxidoreductase (Mqo) proteins (EC:1.1.99.16). Mqo takes part in the citric acid cycle. It oxidizes L-malate to oxaloacetate and donates electrons to ubiquinone-1 and other artificial acceptors or, via the electron transfer chain, to oxygen. NAD is not an acceptor and the natural direct acceptor for the enzyme is most likely a quinone. The enzyme is therefore called malate:quinone oxidoreductase, abbreviated to Mqo. Mqo is a peripheral membrane protein and can be released from the membrane by addition of chelators. 488 matched cddid_all.tbl CDD pfam06040 pfam06040 253527 Adeno_E3 Adenovirus E3 protein. This family consists of several Adenovirus E3 proteins. The E3 protein does not seem to be essential for virus replication in cultured cells suggesting that the protein may function in virus-host interactions. 126 matched cddid_all.tbl CDD pfam06041 pfam06041 428735 DUF924 Bacterial protein of unknown function (DUF924). This family consists of several hypothetical bacterial proteins of unknown function. Structurally, this family resembles TPR-like repeats. 185 matched cddid_all.tbl CDD pfam06042 pfam06042 461810 NTP_transf_6 Nucleotidyltransferase. This family consists of several hypothetical bacterial proteins of unknown function. This family was recently identified as belonging to the nucleotidyltransferase superfamily. 157 matched cddid_all.tbl CDD pfam06043 pfam06043 461811 Reo_P9 Reovirus P9-like family. 334 matched cddid_all.tbl CDD pfam06044 pfam06044 428737 DpnI Dam-replacing family. Dam-replacing protein (DRP) is an restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis. 182 matched cddid_all.tbl CDD pfam06045 pfam06045 283658 Rhamnogal_lyase Rhamnogalacturonate lyase family. Rhamnogalacturonate lyase (EC:4.2.2.-) degrades the rhamnogalacturonan I (RG-I) backbone of pectin. This family contains mainly members from plants, but also contains the plant pathogen Erwinia chrysanthemi. 211 matched cddid_all.tbl CDD pfam06046 pfam06046 428738 Sec6 Exocyst complex component Sec6. Sec6 is a component of the multiprotein exocyst complex. Sec6 interacts with Sec8, Sec10 and Exo70.These exocyst proteins localize to regions of active exocytosis-at the growing ends of interphase cells and in the medial region of cells undergoing cytokinesis-in an F-actin-dependent and exocytosis- independent manner. 570 matched cddid_all.tbl CDD pfam06047 pfam06047 461812 Nkap_C NF-kappa-B-activating protein C-terminal domain. This is the C-terminal domain found in NF-kappa-B-activating protein (Nkap) and a hypothetical open reading frame on chromosome 6, c6orf194. Functional studies in Nkap indicate that this domain is the HDAC3 binding domain and is required for transcriptional repression. Nkap functions as a transcriptional repressor on Notch target genes, and is required for T cell development and acquisition of functional competency. 102 matched cddid_all.tbl CDD pfam06048 pfam06048 428740 DUF927 Domain of unknown function (DUF927). This entry represents a domain found in bacterial proteins of unknown function. The crystal structure has been solved for a protein containing this domain SWISS:Q0WXP6. 286 matched cddid_all.tbl CDD pfam06049 pfam06049 461813 LSPR Coagulation Factor V LSPD Repeat. These repeats are found in coagulation factor V (five). The name LSPD derives from the conserved residues in the middle of the repeat.They occur in the B domain, which is cleaved prior to activation of the protein. It has been suggested that domain B bring domains A and C together for activation. 9 matched cddid_all.tbl CDD pfam06050 pfam06050 461814 HGD-D 2-hydroxyglutaryl-CoA dehydratase, D-component. Degradation of glutamate via the hydroxyglutarate pathway involves the syn-elimination of water from 2-hydroxyglutaryl-CoA. This anaerobic process is catalyzed by 2-hydroxyglutaryl-CoA dehydratase, an enzyme with two components (A and D) that reversibly associate during reaction cycles. This component contains one non-reducible [4Fe-4S]2+ cluster and a reduced riboflavin 5'-monophosphate. 339 matched cddid_all.tbl CDD pfam06051 pfam06051 428742 DUF928 Domain of Unknown Function (DUF928). Family of uncharacterized bacterial protein. 186 matched cddid_all.tbl CDD pfam06052 pfam06052 399210 3-HAO 3-hydroxyanthranilic acid dioxygenase. In eukaryotes 3-hydroxyanthranilic acid dioxygenase (EC:1.13.11.6) is part of the kynurenine pathway for the degradation of tryptophan and the biosynthesis of nicotinic acid.The prokaryotic homolog is involved in the 2-nitrobenzoate degradation pathway. 151 matched cddid_all.tbl CDD pfam06053 pfam06053 461815 DUF929 Domain of unknown function (DUF929). Family of proteins from the archaeon Sulfolobus, with undetermined function. According to structure prediction this protein has a thioredoxin fold. 205 matched cddid_all.tbl CDD pfam06054 pfam06054 283666 CoiA Competence protein CoiA-like family. Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterized protein. 377 matched cddid_all.tbl CDD pfam06055 pfam06055 428744 ExoD Exopolysaccharide synthesis, ExoD. Among the bacterial genes required for nodule invasion are the exo genes. These genes are involved in the production of an extracellular polysaccharide. Mutations in the exoD result in altered exopolysaccharide production and defects in nodule invasion. 179 matched cddid_all.tbl CDD pfam06056 pfam06056 428745 Terminase_5 Putative ATPase subunit of terminase (gpP-like). This family of proteins are annotated as ATPase subunits of phage terminase after. Terminases are viral proteins that are involved in packaging viral DNA into the capsid. 58 matched cddid_all.tbl CDD pfam06057 pfam06057 368724 VirJ Bacterial virulence protein (VirJ). This family consists of several bacterial VirJ virulence proteins. VirJ is thought to be involved in the type IV secretion system. It is thought that the substrate proteins localized to the periplasm may associate with the pilus in a manner that is mediated by VirJ, and suggest a two-step process for type IV secretion in Agrobacterium. 191 matched cddid_all.tbl CDD pfam06058 pfam06058 461816 DCP1 Dcp1-like decapping family. An essential step in mRNA turnover is decapping. In yeast, two proteins have been identified that are essential for decapping, Dcp1 (this family) and Dcp2 (pfam05026). The precise role of these proteins in the decapping reaction have not been established. Evidence suggests that the Dcp1 may enhance the function of Dcp2. 117 matched cddid_all.tbl CDD pfam06059 pfam06059 428747 DUF930 Domain of Unknown Function (DUF930). Family of bacterial proteins with undetermined function. All bacteria in this family are from the Rhizobiales order. 99 matched cddid_all.tbl CDD pfam06060 pfam06060 368727 Mesothelin Pre-pro-megakaryocyte potentiating factor precursor (Mesothelin). This family consists of several mammalian pre-pro-megakaryocyte potentiating factor precursor (MPF) or mesothelin proteins. Mesothelin is a glycosylphosphatidylinositol-linked glycoprotein highly expressed in mesothelial cells, mesotheliomas, and ovarian cancer, but the biological function of the protein is not known. 624 matched cddid_all.tbl CDD pfam06061 pfam06061 310566 Baculo_ME53 Baculoviridae ME53. ME53 is one of the major early-transcribed genes. The ME53 protein is reported to contain a putative zinc finger motif. 339 matched cddid_all.tbl CDD pfam06062 pfam06062 428748 UPF0231 Uncharacterized protein family (UPF0231). Family of uncharacterized Proteobacteria proteins. 121 matched cddid_all.tbl CDD pfam06064 pfam06064 399215 Gam Host-nuclease inhibitor protein Gam. The Gam protein inhibits RecBCD nuclease and is found in both bacteria and bacteriophage. 98 matched cddid_all.tbl CDD pfam06066 pfam06066 368729 SepZ SepZ. SepZ is a component of the type III secretion system use in bacteria. SepZ is a gene within the enterocyte effacement locus. SepZ mutants exhibit reduced invasion efficiency and lack of tyrosine phosphorylation of Hp90. 99 matched cddid_all.tbl CDD pfam06067 pfam06067 461817 DUF932 Domain of unknown function (DUF932). Family of prokaryotic proteins with unknown function. Contains a number of highly conserved polar residues that could suggest an enzymatic activity. 227 matched cddid_all.tbl CDD pfam06068 pfam06068 399217 TIP49 TIP49 P-loop domain. This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases. 347 matched cddid_all.tbl CDD pfam06069 pfam06069 310570 PerC PerC transcriptional activator. PerC is a transcriptional activator of EaeA/BfpA expression in enteropathogenic bacteria. 90 matched cddid_all.tbl CDD pfam06070 pfam06070 461818 Herpes_UL32 Herpesvirus large structural phosphoprotein UL32. The large phosphorylated protein (UL32-like) of herpes viruses is the polypeptide most frequently reactive in immuno-blotting analyses with antisera when compared with other viral proteins. 917 matched cddid_all.tbl CDD pfam06071 pfam06071 461819 YchF-GTPase_C Protein of unknown function (DUF933). This domain is found at the C terminus of the YchF GTP-binding protein and is possibly related to the ubiquitin-like and MoaD/ThiS superfamilies. 82 matched cddid_all.tbl CDD pfam06072 pfam06072 283682 Herpes_US9 Alphaherpesvirus tegument protein US9. This family consists of several US9 and related proteins from the Alphaherpesviruses. The function of the US9 protein is unknown although in Bovine herpesvirus 5 Us9 is essential for the anterograde spread of the virus from the olfactory mucosa to the bulb. 61 matched cddid_all.tbl CDD pfam06073 pfam06073 461820 DUF934 Bacterial protein of unknown function (DUF934). This family consists of several bacterial proteins of unknown function, however members have been suggested to be an accessory protein for sulfite reduction. This is based on the observation that they strongly cofit with various genes in the sulfate assimilation pathway in various Pseudomonas as well as in Marinobacter adhaerens HP15 and C. basilensis 4G11 (see Supplementary note 5 in.) 103 matched cddid_all.tbl CDD pfam06074 pfam06074 428752 DUF935 Protein of unknown function (DUF935). This family consists of several bacterial proteins of unknown function as well as the Bacteriophage Mu gp29 protein. 517 matched cddid_all.tbl CDD pfam06075 pfam06075 461821 DUF936 Plant protein of unknown function (DUF936). This family consists of several hypothetical proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown. 674 matched cddid_all.tbl CDD pfam06076 pfam06076 114778 Orthopox_F14 Orthopoxvirus F14 protein. This family consists of several short Orthopoxvirus F14 proteins. The function of this protein is unknown. 73 matched cddid_all.tbl CDD pfam06078 pfam06078 428754 DUF937 Bacterial protein of unknown function (DUF937). This family consists of several hypothetical bacterial proteins of unknown function. 134 matched cddid_all.tbl CDD pfam06079 pfam06079 461822 Apyrase Apyrase. This family consists of several eukaryotic apyrase proteins (EC:3.6.1.5). The salivary apyrases of blood-feeding arthropods are nucleotide hydrolysing enzymes implicated in the inhibition of host platelet aggregation through the hydrolysis of extracellular adenosine diphosphate.. 291 matched cddid_all.tbl CDD pfam06080 pfam06080 253548 DUF938 Protein of unknown function (DUF938). This family consists of several hypothetical proteins from both prokaryotes and eukaryotes. The function of this family is unknown. 201 matched cddid_all.tbl CDD pfam06081 pfam06081 428756 ArAE_1 Aromatic acid exporter family member 1. This family consists of bacterial proteins with three transmembrane regions that are purported to be aromatic acid exporters. 141 matched cddid_all.tbl CDD pfam06082 pfam06082 428757 YjbH Exopolysaccharide biosynthesis protein YbjH. YjbH is a family of Gram-negative beta-barrel outer-membrane lipoproteins that act as putative porins. YbjH is one of four gene-products expressed from an operon, yjbEFGH, which is regulated by the Rcs phosphorelay in a RcsA-dependent manner, similar to that of other exopolysaccharide biosynthetic pathways. It is highly possible that the yjbEFGH operon encodes a system involved in EPS secretion since none of the products is predicted to have enzymic activity, the products are all secreted and YbjH and F are predicted to be beta-barrel lipoproteins similar to porins. It may be that the operon products play some role in biofilm formation and/or matrix production. 661 matched cddid_all.tbl CDD pfam06083 pfam06083 461823 IL17 Interleukin-17. IL-17 is a potent proinflammatory cytokine produced by activated memory T cells. The IL-17 family is thought to represent a distinct signaling system that appears to have been highly conserved across vertebrate evolution. 81 matched cddid_all.tbl CDD pfam06084 pfam06084 399227 Cytomega_TRL10 Cytomegalovirus TRL10 protein. This family consists of several Cytomegalovirus TRL10 proteins. TRL10 represents a structural component of the virus particle and like the other HCMV envelope glycoproteins, is present in a disulfide-linked complex. 149 matched cddid_all.tbl CDD pfam06085 pfam06085 368737 Rz1 Lipoprotein Rz1 precursor. This family consists of several bacteria and phage lipoprotein Rz1 precursors. Rz1 is a proline-rich lipoprotein from bacteriophage lambda which is known to have fusogenic properties. Rz1-induced liposome fusion is thought to be mediated primarily by the generation of local perturbation in the bilayer lipid membrane and to a lesser extent by electrostatic forces. This family Rz1 and the Rz protein Rz (pfam03245) represent a unique example of two genes located in different reading frames in the same nucleotide sequence, which encode different proteins that are both required in the same physiological pathway. 41 matched cddid_all.tbl CDD pfam06086 pfam06086 399228 Pox_A30L_A26L Orthopoxvirus A26L/A30L protein. This family consists of several Orthopoxvirus A26L and A30L proteins. The Vaccinia A30L gene is regulated by a late promoter and encodes a protein of approximately 9 kDa. It is thought that the A30L protein is needed for vaccinia virus morphogenesis, specifically the association of the dense viroplasm with viral membranes. 219 matched cddid_all.tbl CDD pfam06087 pfam06087 461824 Tyr-DNA_phospho Tyrosyl-DNA phosphodiesterase. Covalent intermediates between topoisomerase I and DNA can become dead-end complexes that lead to cell death. Tyrosyl-DNA phosphodiesterase can hydrolyse the bond between topoisomerase I and DNA. 442 matched cddid_all.tbl CDD pfam06088 pfam06088 368739 TLP-20 Nucleopolyhedrovirus telokin-like protein-20 (TLP20). This family consists of several Nucleopolyhedrovirus telokin-like protein-20 (TLP20) sequences. The function of this family is unknown but TLP20 is known to shares some antigenic similarities to the smooth muscle protein telokin although the amino acid sequence shows no homologies to telokin. 164 matched cddid_all.tbl CDD pfam06089 pfam06089 461825 Asparaginase_II L-asparaginase II. This family consists of several bacterial L-asparaginase II proteins. L-asparaginase (EC:3.5.1.1) catalyzes the hydrolysis of L-asparagine to L-aspartate and ammonium. Rhizobium etli possesses two asparaginases: asparaginase I, which is thermostable and constitutive, and asparaginase II, which is thermolabile, induced by asparagine and repressed by the carbon source. 320 matched cddid_all.tbl CDD pfam06090 pfam06090 461826 Ins_P5_2-kin Inositol-pentakisphosphate 2-kinase. This is a family of inositol-pentakisphosphate 2-kinases (EC 2.7.1.158) (also known as inositol 1,3,4,5,6-pentakisphosphate 2-kinase, Ins(1,3,4,5,6)P5 2-kinase) and InsP5 2-kinase). This enzyme phosphorylates Ins(1,3,4,5,6)P5 to form Ins(1,2,3,4,5,6)P6 (also known as InsP6 or phytate). InsP6 is involved in many processes such as mRNA export, nonhomologous end-joining, endocytosis and ion channel regulation. 319 matched cddid_all.tbl CDD pfam06092 pfam06092 428762 DUF943 Enterobacterial putative membrane protein (DUF943). This family consists of several hypothetical putative membrane proteins from Escherichia coli, Yersinia pestis and Salmonella typhi. 151 matched cddid_all.tbl CDD pfam06093 pfam06093 399233 Spt4 Spt4/RpoE2 zinc finger. This family consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. Spt4 and Spt5 are tightly associated in a complex, while the physical association of the Spt4-Spt5 complex with Spt6 is considerably weaker. It has been demonstrated that Spt4, Spt5, and Spt6 play roles in transcription elongation in both yeast and humans including a role in activation by Tat. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. RpoE2 is one of 13 subunits in the archaeal RNA polymerase. These proteins contain a C4-type zinc finger, and the structure has been solved in. The structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4, and the complex binds to and travels along the elongating RNA polymerase. The Spt4-Spt5 complex is likely to be an ancient, core component of the transcription elongation machinery. 77 matched cddid_all.tbl CDD pfam06094 pfam06094 428763 GGACT Gamma-glutamyl cyclotransferase, AIG2-like. GGACT, gamma-glutamylamine cyclotransferase, is a ubiquitous enzyme found in bacteria, plants, and metazoans from Dictyostelium through to humans. It converts gamma-glutamylamines to free amines and 5-oxoproline. 118 matched cddid_all.tbl CDD pfam06096 pfam06096 368743 Baculo_8kDa Baculoviridae 8.2 KDa protein. Family of proteins from various Baculoviruses with undetermined function. 65 matched cddid_all.tbl CDD pfam06097 pfam06097 428764 DUF945 Bacterial protein of unknown function (DUF945). This family consists of several hypothetical bacterial proteins of unknown function. 458 matched cddid_all.tbl CDD pfam06098 pfam06098 461827 Radial_spoke_3 Radial spoke protein 3. This family consists of several radial spoke protein 3 (RSP3) sequences. Eukaryotic cilia and flagella present in diverse types of cells perform motile, sensory, and developmental functions in organizms from protists to humans. They are centred by precisely organized, microtubule-based structures, the axonemes. The axoneme consists of two central singlet microtubules, called the central pair, and nine outer doublet microtubules. These structures are well-conserved during evolution. The outer doublet microtubules, each composed of A and B sub-fibres, are connected to each other by nexin links, while the central pair is held at the centre of the axoneme by radial spokes. The radial spokes are T-shaped structures extending from the A-tubule of each outer doublet microtubule to the centre of the axoneme. Radial spoke protein 3 (RSP3), is present at the proximal end of the spoke stalk and helps in anchoring the radial spoke to the outer doublet. It is thought that radial spokes regulate the activity of inner arm dynein through protein phosphorylation and dephosphorylation. 286 matched cddid_all.tbl CDD pfam06099 pfam06099 428766 Phenol_hyd_sub Phenol hydroxylase subunit. This family consists of several bacterial phenol hydroxylase subunit proteins which are part of a multicomponent phenol hydroxylase. Some bacteria can utilize phenol or some of its methylated derivatives as their sole source of carbon and energy. The first step in this process is the conversion of phenol into catechol. Catechol is then further metabolized via the meta-cleavage pathway into TCA cycle intermediates. 56 matched cddid_all.tbl CDD pfam06100 pfam06100 428767 MCRA MCRA family. The MCRA (myosin-cross-reactive antigen) family of proteins were thought to have structural features in common with the beta chain of the class II antigens, as well as myosin, and may play an important role in the pathogenesis. More recent work shows that these proteins act as hydratase enzymes that convert linoleic acid and oleic acid to their respective 10-hydroxy derivatives. It has been suggested that MCRA proteins catalyze the first step in conjugated linoleic acid production. Proteins in this family act in an FAD dependent manner. The structure of a fatty acid double-bond hydratase from Lactobacillus acidophilus has been recently solved showing four structural domains. 492 matched cddid_all.tbl CDD pfam06101 pfam06101 461828 Vps62 Vacuolar protein sorting-associated protein 62. Vps62 is a vacuolar protein sorting (VPS) protein required for cytoplasm to vacuole targeting of proteins. 539 matched cddid_all.tbl CDD pfam06102 pfam06102 461829 RRP36 rRNA biogenesis protein RRP36. RRP36 is involved in the early processing steps of the pre-rRNA. 158 matched cddid_all.tbl CDD pfam06103 pfam06103 428770 DUF948 Bacterial protein of unknown function (DUF948). This family consists of bacterial sequences several of which are thought to be general stress proteins. 83 matched cddid_all.tbl CDD pfam06105 pfam06105 461830 Aph-1 Aph-1 protein. This family consists of several eukaryotic Aph-1 proteins.Gamma-secretase catalyzes the intramembrane proteolysis of Notch, beta-amyloid precursor protein, and other substrates as part of a new signaling paradigm and as a key step in the pathogenesis of Alzheimer's disease. It is thought that the presenilin heterodimer comprises the catalytic site and that a highly glycosylated form of nicastrin associates with it. Aph-1 and Pen-2, two membrane proteins genetically linked to gamma-secretase, associate directly with presenilin and nicastrin in the active protease complex. Co-expression of all four proteins leads to marked increases in presenilin heterodimers, full glycosylation of nicastrin, and enhanced gamma-secretase activity. APH-1 proteins have a similar but different set of motifs as compared to other families. Their four motifs are: QExxR, Fxxxx, Hxxxs and Hxxxs respectively. Given the inferred homology between APH-1 and other membrane proteases such as type II CAAX proteases and PrsW proteases, it is speculated that APH-1 may possess protease activity. 224 matched cddid_all.tbl CDD pfam06106 pfam06106 428772 SAUGI S. aureus uracil DNA glycosylase inhibitor. Uracil-DNA glycosylase inhibitors, are DNA mimic proteins that prevent the DNA binding sites of UDGs (Uracil DNA glycosylase) from interacting with their DNA substrate. SSP0047 (or SAUGI; for Staphylococcus aureus uracil-DNA glycosylase inhibitor) acts as a uracil-DNA glycosylase inhibitor that breaks the uracil-removing activity of S. aureus uracil-DNA glycosylase (SAUDG) pfam03167. The SAUGI/SAUDG complex has been determined, and shows that SAUGI binds to the SAUDG DNA binding region via several strong interactions, by using a hydrophobic pocket to hold SAUDG's protruding residue (i.e. SAUDG Leu184, E. coli UDG Leu191 and B. subtilis UDG Phe191). By binding to SAUDG in this way, SAUGI thus prevents SAUDG from binding to its DNA substrate and performing DNA repair activity. 112 matched cddid_all.tbl CDD pfam06107 pfam06107 461831 DUF951 Bacterial protein of unknown function (DUF951). This family consists of several short hypothetical bacterial proteins of unknown function. Structural modelling suggests this domain may bind nucleic acids. 55 matched cddid_all.tbl CDD pfam06108 pfam06108 428774 DUF952 Protein of unknown function (DUF952). This family consists of several hypothetical bacterial and plant proteins of unknown function. 84 matched cddid_all.tbl CDD pfam06109 pfam06109 399246 HlyE Haemolysin E (HlyE). This family consists of several enterobacterial haemolysin (HlyE) proteins.Hemolysin E (HlyE) is a novel pore-forming toxin of Escherichia coli, Salmonella typhi, and Shigella flexneri. HlyE is unrelated to the well characterized pore-forming E. coli hemolysins of the RTX family, haemolysin A (HlyA), and the enterohaemolysin encoded by the plasmid borne ehxA gene of E. coli 0157. However, it is evident that expression of HlyE in the absence of the RTX toxins is sufficient to give a hemolytic phenotype in E. coli. HlyE is a protein of 34 kDa that is expressed during anaerobic growth of E. coli. Anaerobic expression is controlled by the transcription factor, FNR, such that, upon ingestion and entry into the anaerobic mammalian intestine, HlyE is produced and may then contribute to the colonization of the host. 333 matched cddid_all.tbl CDD pfam06110 pfam06110 399247 DUF953 Eukaryotic protein of unknown function (DUF953). This family consists of several hypothetical eukaryotic proteins of unknown function. 119 matched cddid_all.tbl CDD pfam06112 pfam06112 428775 Herpes_capsid Gammaherpesvirus capsid protein. This family consists of several Gammaherpesvirus capsid proteins. The exact function of this family is unknown. 169 matched cddid_all.tbl CDD pfam06113 pfam06113 461832 BRE Brain and reproductive organ-expressed protein (BRE). This family consists of several eukaryotic brain and reproductive organ-expressed (BRE) proteins. BRE is a putative stress-modulating gene, found able to down-regulate TNF-alpha-induced-NF-kappaB activation upon over expression. A total of six isoforms are produced by alternative splicing predominantly at either end of the gene.Compared to normal cells, immortalized human cell lines uniformly express higher levels of BRE. Peripheral blood monocytes respond to LPS by down-regulating the expression of all the BRE isoforms.It is thought that the function of BRE and its isoforms is to regulate peroxisomal activities. 320 matched cddid_all.tbl CDD pfam06114 pfam06114 399250 Peptidase_M78 IrrE N-terminal-like domain. This entry includes the catalytic domain of the protein ImmA, which is a metallopeptidase containing an HEXXH zinc-binding motif from peptidase family M78. ImmA is encoded on a conjugative transposon. Conjugating bacteria are able to transfer conjugative transposons that can, for example, confer resistance to antibiotics. The transposon is integrated into the chromosome, but during conjugation excises itself and then moves to the recipient bacterium and re-integrate into its chromosome. Typically a conjugative tranposon encodes only the proteins required for this activity and the proteins that regulate it. During exponential growth, the ICEBs1 transposon of Bacillus subtilis is inactivated by the immunity repressor protein ImmR, which is encoded by the transposon and represses the genes for excision and transfer. Cleavage of ImmR relaxes repression and allows transfer of the transposon. ImmA has been shown to be essential for the cleavage of ImmR. This domain is also found in in metalloprotease IrrE, a central regulator of DNA damage repair in Deinococcaceae, HTH-type transcriptional regulators RamB and PrpC. 122 matched cddid_all.tbl CDD pfam06115 pfam06115 428777 DUF956 Domain of unknown function (DUF956). Family of bacterial sequences with undetermined function. 117 matched cddid_all.tbl CDD pfam06116 pfam06116 283718 RinB Transcriptional activator RinB. This family consists of several Staphylococcus aureus bacteriophage RinB proteins and related sequences from their host. The int gene of staphylococcal bacteriophage phi 11 is the only viral gene responsible for the integrative recombination of phi 11. rinA and rinB, are both required to activate expression of the int gene. 51 matched cddid_all.tbl CDD pfam06119 pfam06119 461833 NIDO Nidogen-like. This is a nidogen-like domain (NIDO) domain and is an extracellular domain found in nidogen and hypothetical proteins of unknown function. 90 matched cddid_all.tbl CDD pfam06120 pfam06120 428779 Phage_HK97_TLTM Tail length tape measure protein. This family consists of the tail length tape measure protein from bacteriophage HK97 and related sequences from Escherichia coli O157:H7. 295 matched cddid_all.tbl CDD pfam06121 pfam06121 399255 DUF959 Domain of Unknown Function (DUF959). This N-terminal domain is not expressed in the 'Short' isoform of Collagen A. 192 matched cddid_all.tbl CDD pfam06122 pfam06122 428780 TraH Conjugative relaxosome accessory transposon protein. The TraH protein is thought to be a relaxosome accessory component, also necessary for transfer but not for H-pilus synthesis within the conjugative transposon. 358 matched cddid_all.tbl CDD pfam06123 pfam06123 428781 CreD Inner membrane protein CreD. This family consists of several bacterial CreD or Cet inner membrane proteins. Dominant mutations of the cet gene of Escherichia coli result in tolerance to colicin E2 and increased amounts of an inner membrane protein with an Mr of 42,000. The cet gene is shown to be in the same operon as the phoM gene, which is required in a phoR background for expression of the structural gene for alkaline phosphatase, phoA. Although the Cet protein is not required for phoA expression, it has been suggested that the Cet protein has an enhancing effect on the transcription of phoA. 427 matched cddid_all.tbl CDD pfam06124 pfam06124 399258 DUF960 Staphylococcal protein of unknown function (DUF960). This family consists of several hypothetical proteins from several species of Staphylococcus. The function of this family is unknown. 94 matched cddid_all.tbl CDD pfam06125 pfam06125 461834 DUF961 Bacterial protein of unknown function (DUF961). This family consists of several hypothetical bacterial proteins of unknown function. 96 matched cddid_all.tbl CDD pfam06126 pfam06126 147993 Herpes_LAMP2 Herpesvirus Latent membrane protein 2. Family of Kaposi's sarcoma-associated herpesvirus (HHV8) latent membrane protein. 510 matched cddid_all.tbl CDD pfam06127 pfam06127 377609 Mpo1-like 2-hydroxy-palmitic acid dioxygenase Mpo1-like. Budding yeast Mpo1 is a dioxygenase that catalyzes the alpha-oxidation of a 2-hydroxy fatty acid in an Fe2+-dependent manner. This entry also includes Mpo1 homologs from bacteria, fungi and plants. Their function is not clear. 95 matched cddid_all.tbl CDD pfam06128 pfam06128 283728 Shigella_OspC Shigella flexneri OspC protein. This family consists of the Shigella flexneri specific protein OspC. The function of this family is unknown but it is thought that Osp proteins may be involved in post invasion events related to virulence. Since bacterial pathogens adapt to multiple environments during the course of infecting a host, it has been proposed that Shigella evolved a mechanism to take advantage of a unique intracellular cue, which is mediated through MxiE, to express proteins when the organizm reaches the eukaryotic cytosol. 292 matched cddid_all.tbl CDD pfam06129 pfam06129 283729 Chordopox_G3 Chordopoxvirus G3 protein. This family consists of several Chordopoxvirus specific G3 proteins. The function of this family is unknown. 108 matched cddid_all.tbl CDD pfam06130 pfam06130 461835 PTAC Phosphate propanoyltransferase. This family includes phosphotransacylases (PTACs) required for the degradation of 1,2-propanediol (1,2-PD). 67 matched cddid_all.tbl CDD pfam06131 pfam06131 283731 DUF963 Schizosaccharomyces pombe repeat of unknown function (DUF963). This family consists of a series of repeated sequences from one hypothetical protein found in Schizosaccharomyces pombe. The function of this family is unknown. 36 matched cddid_all.tbl CDD pfam06133 pfam06133 428784 Com_YlbF Control of competence regulator ComK, YlbF/YmcA. YlbF Is a family of short Gram-positive and archaeal proteins that includes both YlbF and YmcA which may interact synergistically. The family is necessary for correct biofilm formation, as null mutants of ymcA and ylbF fail to form pellicles at air-liquid interfaces and grow on solid media as smooth, undifferentiated colonies. During development, YmcA, YlbF and YaaT, family PSPI, pfam04468, interact directly with one another forming a stable ternary complex, in vitro. All three proteins are required for competence, sporulation and the formation of biofilms. The YmcA-YlbF-YaaT complex affects the phosphotransfer between Spo0F and Spo0B, thus accelerating the production of Spo0A~P. The three processes of biofilm formation, mature spore formation and competence all require the active, phosphorylated form of Spo0A, as Spo0A-P. 103 matched cddid_all.tbl CDD pfam06134 pfam06134 399262 RhaA L-rhamnose isomerase (RhaA). This family consists of several bacterial L-rhamnose isomerase proteins (EC:5.3.1.14). 417 matched cddid_all.tbl CDD pfam06135 pfam06135 428785 IreB IreB regulatory phosphoprotein. IreB is a cytosolic 10.5-kDa protein that is highly conserved among low-GC Gram-positive bacteria. Studies of E. faecalis mutants lacking ireB revealed that IreB acts downstream of IreK as a negative regulator of cephalosporin resistance in E. faecalis. IreB can be modified by phosphorylation in vivo, and mutations that prevent modification at the known sites of phosphorylation (T4 and T7) influence the ability of IreB to modulate cephalosporin resistance. Furthermore, mutations that impair dimerization abolish the regulation of cephalosporin resistance. 77 matched cddid_all.tbl CDD pfam06136 pfam06136 461836 SOK Protein SOSEKI, plant. This entry represents a group of plant proteins, including protein SOSEKI1-5 from Arabidopsis thaliana and Physcomitrium patens. SOK1-5 integrate apical-basal and radial organizmal axes to localize to polar cell edges and contain a DIX oligomerization domain that resembles that in the animal Dishevelled polarity regulator. 366 matched cddid_all.tbl CDD pfam06138 pfam06138 283736 Chordopox_E11 Chordopoxvirus E11 protein. This family consists of several Chordopoxvirus E11 proteins. The E11 gene of vaccinia virus encodes a 15-kDa polypeptide. Mutations in the E11 gene makes the virus temperature-sensitive due to either the fact that virus infectivity requires a threshold level of active E11 protein or that E11 function is conditionally essential. 126 matched cddid_all.tbl CDD pfam06139 pfam06139 399265 BphX BphX-like. Family of bacterial proteins located in the phenyl dioxygenase (bph) operon. The function of this family is unknown. 133 matched cddid_all.tbl CDD pfam06140 pfam06140 461837 Ifi-6-16 Interferon-induced 6-16 family. 79 matched cddid_all.tbl CDD pfam06141 pfam06141 399267 Phage_tail_U Phage minor tail protein U. Tail fibre component U of bacteriophage. 129 matched cddid_all.tbl CDD pfam06143 pfam06143 114838 Baculo_11_kDa Baculovirus 11 kDa family. Family of uncharacterized Baculovirus proteins that are all about 11 kDa in size. 84 matched cddid_all.tbl CDD pfam06144 pfam06144 428788 DNA_pol3_delta DNA polymerase III, delta subunit. DNA polymerase III, delta subunit (EC 2.7.7.7) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalyzed reaction. The delta subunit is also known as HolA. 174 matched cddid_all.tbl CDD pfam06145 pfam06145 148007 Corona_NS1 Coronavirus nonstructural protein NS1. Bovine coronavirus NS1 encodes a 4.9 kDa protein. 29 matched cddid_all.tbl CDD pfam06146 pfam06146 461838 PsiE Phosphate-starvation-inducible E family. This entry represents an integral membrane protein with 4 transmembrane helices. The second alpha helix contains a conserved glutamic acid residue and the third helix contains a conserved arginine residue. These two buried charged residues may interact. The type example for this family is the Phosphate-starvation-inducible E (PsiE) expression protein, which is under direct positive and negative control by PhoB and cAMP-CRP, respectively. The function of PsiE remains to be determined. This entry is sometimes found in proteins that contain other domains such as pfam11563. 122 matched cddid_all.tbl CDD pfam06147 pfam06147 461839 DUF968 Protein of unknown function (DUF968). Family of uncharacterized prophage proteins found in Gammaproteobacteria. These may be HNH-nucleases, as there are several conserved cysteines and histidines. 171 matched cddid_all.tbl CDD pfam06148 pfam06148 399271 COG2 COG (conserved oligomeric Golgi) complex component, COG2. The COG complex comprises eight proteins COG1-8. The COG complex plays critical roles in Golgi structure and function. The proposed function of the complex is to mediate the initial physical contact between transport vesicles and their membrane targets. A comparable role in tethering vesicles has been suggested for at least six additional large multisubunit complexes, including the exocyst, a complex that mediates trafficking to the plasma membrane. COG2 structure reveals a six-helix bundle with few conserved surface features but a general resemblance to recently determined crystal structures of four different exocyst subunits. These bundles inCOG2 may act as platforms for interaction with other trafficing proteins including SNAREs (soluble N-ethylmaleimide factor attachment protein receptors) and Rabs. 133 matched cddid_all.tbl CDD pfam06149 pfam06149 428791 DUF969 Protein of unknown function (DUF969). Family of uncharacterized bacterial membrane proteins. 216 matched cddid_all.tbl CDD pfam06150 pfam06150 428792 ChaB ChaB. This family of proteins contain a conserved 60 residue region. This protein is known as ChaB in E. coli and is found next to ChaA which is a cation transporter protein. ChaB may be regulate ChaA function in some way. 60 matched cddid_all.tbl CDD pfam06151 pfam06151 336318 Trehalose_recp Trehalose receptor. In Drosophila, taste is perceived by gustatory neurons located in sensilla distributed on several different appendages throughout the body of the animal. This family represents the taste receptor sensitive to trehalose. 411 matched cddid_all.tbl CDD pfam06152 pfam06152 428793 Phage_min_cap2 Phage minor capsid protein 2. Family of related phage minor capsid proteins. 366 matched cddid_all.tbl CDD pfam06153 pfam06153 283747 CdAMP_rec Cyclic-di-AMP receptor. CdAMP is a family of bacterial cyclic-di-AMP receptor proteins. Cyclic-di-AMP (c-di-AMP) is a bacterial secondary messenger involved in various processes, including sensing of DNA-integrity, cell wall metabolism and potassium transport. CdAMP_rec has a ferredoxin-like fold and is structurally related to Pii-signal transduction proteins. 109 matched cddid_all.tbl CDD pfam06154 pfam06154 399275 CbeA_antitoxin CbeA_antitoxin, type IV, cytoskeleton bundling-enhancing factor A. CbeA_antitoxin is a family of cognate antitoxins to the CbtA toxins that act by inhibiting the polymerization of cytoskeletal proteins, see pfam06755. These are classified as a type IV toxin-antitoxin system. The family includes three proteins from E. coli YagB, YeeU and YfjZ, which act not by forming a complex with CbtA but through acting as antagonists to the CbtA toxicity, by stabilising the CbtA target proteins. For example, YeeU binds directly to both MreB and FtsZ and enhances the bundling of their filaments in vitro. YeeU is also able to neutralize the toxicity caused by other MreB and FtsZ inhibitors, such as A22 [S-(3, 4-dichlorobenzyl)isothiourea] for MreB, and SulA and DicB for FtsZ. Thus CbeA, for cytoskeleton bundling-enhancing factor A, is proposed as a general name for all of these antitoxin proteins. 101 matched cddid_all.tbl CDD pfam06155 pfam06155 461840 GBBH-like_N Gamma-butyrobetaine hydroxylase-like, N-terminal. This domain is found in several proteins including gamma-butyrobetaine dioxygenase, Fe-S cluster assembly factor HCF101 and trimethyllysine dioxygenase proteins. Gamma-butyrobetaine hydroxylase (GBBH) is a alpha-ketoglutarate-dependent dioxygenase that catalyzes the biosynthesis of L-carnitine by hydroxylation of gamma-butyrobetaine (GBB). GBBH is a dimeric enzyme. The monomer consists of a catalytic double-stranded beta-helix domain and a smaller N-terminal domain. The N-terminal domain has a bound Zn ion, which is coordinated by three cysteines and one histidine. The N-terminal domain could facilitate dimer formation, but its precise function is not known. Other family members have been suggested to be involved in FeS cluster maintenance (see Supplementary note 5 in.) 87 matched cddid_all.tbl CDD pfam06156 pfam06156 428795 YabA Initiation control protein YabA. YabA is involved in initiation control of chromosome replication. It interacts with both DnaA and DnaN, acting as a bridge between these two proteins. 103 matched cddid_all.tbl CDD pfam06157 pfam06157 368769 DUF973 Protein of unknown function (DUF973). This family consists of several hypothetical archaeal proteins of unknown function. 309 matched cddid_all.tbl CDD pfam06159 pfam06159 461841 DUF974 Protein of unknown function (DUF974). Family of uncharacterized eukaryotic proteins. 244 matched cddid_all.tbl CDD pfam06160 pfam06160 428797 EzrA Septation ring formation regulator, EzrA. During the bacterial cell cycle, the tubulin-like cell-division protein FtsZ polymerizes into a ring structure that establishes the location of the nascent division site. EzrA modulates the frequency and position of FtsZ ring formation. The structure contains 5 spectrin like alpha helical repeats. 542 matched cddid_all.tbl CDD pfam06161 pfam06161 428798 DUF975 Protein of unknown function (DUF975). Family of uncharacterized bacterial proteins. 243 matched cddid_all.tbl CDD pfam06162 pfam06162 310625 PgaPase_1 Putative pyroglutamyl peptidase PgaPase_1. PgaPase_1 is a family of functionally diverse Caenorhabditis proteins. The family is homologous to the cysteine-peptidases, but lack of a strictly conserved Glu-Cys-His catalytic triad or pGlu binding site implies that it has other functions that could have resulted in a change in reaction-specificity or even of catalytic activity. 166 matched cddid_all.tbl CDD pfam06163 pfam06163 310626 DUF977 Bacterial protein of unknown function (DUF977). This family consists of several hypothetical bacterial proteins from Escherichia coli and Salmonella typhi. The function of this family is unknown. 134 matched cddid_all.tbl CDD pfam06165 pfam06165 461842 Glyco_transf_36 Glycosyltransferase family 36. The glycosyltransferase family 36 includes cellobiose phosphorylase (EC:2.4.1.20), cellodextrin phosphorylase (EC:2.4.1.49), chitobiose phosphorylase (EC:2.4.1.-). Many members of this family contain two copies of this domain. 247 matched cddid_all.tbl CDD pfam06166 pfam06166 428800 DUF979 Protein of unknown function (DUF979). This family consists of several putative bacterial membrane proteins. The function of this family is unclear. 308 matched cddid_all.tbl CDD pfam06167 pfam06167 428801 Peptidase_M90 Glucose-regulated metallo-peptidase M90. MtfA (earlier known as YeeI) is a transcription factor A that binds Mlc (make large colonies), itself a repressor of glucose and hence a protein important in regulation of the phosphoenolpyruvate:glucose-phosphotransferase (ptsG) system, the major glucose transporter in E.coli. Mlc is a repressor of ptsG, and MtfA is found to bind and inactivate Mlc with high affinity. The membrane-bound protein EIICBGlc encoded by the ptsG gene is the major glucose transporter in Escherichia coli. MtfA is found to be a glucose-regulated peptidase, whose activity is regulated by binding to Mlc available in the cytoplasm, which in turn has been released from EIICBGlc during times when no glucose is taken up. A physiologically relevant target for this peptidase is not yet known. 243 matched cddid_all.tbl CDD pfam06168 pfam06168 428802 DUF981 Protein of unknown function (DUF981). Family of uncharacterized proteins found in bacteria and archaea. 181 matched cddid_all.tbl CDD pfam06169 pfam06169 428803 DUF982 Protein of unknown function (DUF982). This family consists of several hypothetical proteins from Rhizobium meliloti, Rhizobium loti and Agrobacterium tumefaciens. The function of this family is unknown. Structural modelling suggests this domain may bind nucleic acids. 71 matched cddid_all.tbl CDD pfam06170 pfam06170 428804 DUF983 Protein of unknown function (DUF983). This family consists of several bacterial proteins of unknown function. 83 matched cddid_all.tbl CDD pfam06172 pfam06172 461843 Cupin_5 Cupin superfamily (DUF985). Family of uncharacterized proteins found in bacteria and eukaryotes that belongs to the Cupin superfamily. 139 matched cddid_all.tbl CDD pfam06173 pfam06173 428806 DUF986 Protein of unknown function (DUF986). This family consists of several bacterial putative membrane proteins of unknown function. 148 matched cddid_all.tbl CDD pfam06174 pfam06174 368775 DUF987 Protein of unknown function (DUF987). Family of bacterial proteins that are related to the hypothetical protein yeeT. 65 matched cddid_all.tbl CDD pfam06175 pfam06175 114868 MiaE tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE). This family consists of several bacterial tRNA-(MS(2)IO(6)A)-hydroxylase (MiaE) proteins. The modified nucleoside 2-methylthio-N-6-isopentenyl adenosine (ms2i6A) is present at position 37 (3' of the anticodon) of tRNAs that read codons beginning with U except tRNA(I,V Ser) in Escherichia coli. Salmonella typhimurium 2-methylthio-cis-ribozeatin (ms2io6A) is found in tRNA, probably in the corresponding species that have ms2i6A in E. coli. The miaE gene is absent in E. coli, a finding consistent with the absence of the hydroxylated derivative of ms2i6A in this species. 199 matched cddid_all.tbl CDD pfam06176 pfam06176 283765 WaaY Lipopolysaccharide core biosynthesis protein (WaaY). This family consists of several bacterial lipopolysaccharide core biosynthesis proteins (WaaY or RfaY). The waaY, waaQ, and waaP genes are located in the central operon of the waa (formerly rfa) locus on the chromosome of Escherichia coli. This locus contains genes whose products are involved in the assembly of the core region of the lipopolysaccharide molecule. WaaY is the enzyme that phosphorylates HepII in this system. 229 matched cddid_all.tbl CDD pfam06177 pfam06177 461844 QueT QueT transporter. This family includes the queT gene encoding a hypothetical integral membrane protein with 5 predicted transmembrane regions. The queT genes in Firmicutes are often preceded by the PreQ1 (7-aminomethyl-7-deazaguanine) riboswitches of two distinct classes, suggesting involvement of the QueT transporters in uptake of a queuosine biosynthetic intermediate. 140 matched cddid_all.tbl CDD pfam06178 pfam06178 399289 KdgM Oligogalacturonate-specific porin protein (KdgM). This family consists of several bacterial proteins which are homologous to the oligogalacturonate-specific porin protein KdgM from Erwinia chrysanthemi. The phytopathogenic Gram-negative bacteria Erwinia chrysanthemi secretes pectinases, which are able to degrade the pectic polymers of plant cell walls, and uses the degradation products as a carbon source for growth. KdgM is a major outer membrane protein, whose synthesis is strongly induced in the presence of pectic derivatives. KdgM behaves like a voltage-dependent porin that is slightly selective for anions and that exhibits fast block in the presence of trigalacturonate. In contrast to most porins, KdgM seems to be monomeric. 215 matched cddid_all.tbl CDD pfam06179 pfam06179 461845 Med22 Surfeit locus protein 5 subunit 22 of Mediator complex. This family consists of several eukaryotic Surfeit locus protein 5 (SURF5) sequences. The human Surfeit locus has been mapped on chromosome 9q34.1. The locus includes six tightly clustered housekeeping genes (Surf1-6), and the gene organization is similar in human, mouse and chicken Surfeit locus. The Med22 subunit of Mediator complex is part of the essential core head region. 101 matched cddid_all.tbl CDD pfam06180 pfam06180 399291 CbiK Cobalt chelatase (CbiK). This family consists of several bacterial cobalt chelatase (CbiK) proteins (EC:4.99.1.-). 261 matched cddid_all.tbl CDD pfam06181 pfam06181 428809 Urate_ox_N Urate oxidase N-terminal. Cytochrome c urate oxidase (Uox) PuuD is involved in purine degradation. In contrast with soluble Uox it is a membrane protein with an 8-helix transmembrane N-terminal domain and a C-terminal cytochrome c. 294 matched cddid_all.tbl CDD pfam06182 pfam06182 253605 ABC2_membrane_6 ABC-2 family transporter protein. This family acts as the transmembrane domain (TMD) of ABC transporters. The family includes proteins responsible for the transport of herbicides. 229 matched cddid_all.tbl CDD pfam06183 pfam06183 428810 DinI DinI-like family. This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity. The structure of DinI is known. 63 matched cddid_all.tbl CDD pfam06184 pfam06184 399294 Potex_coat Potexvirus coat protein. This family consists of several Potexvirus coat proteins. 153 matched cddid_all.tbl CDD pfam06185 pfam06185 428811 YecM YecM protein. This family consists of several bacterial YecM proteins of unknown function. 179 matched cddid_all.tbl CDD pfam06186 pfam06186 428812 DUF992 Protein of unknown function (DUF992). This family consists of several hypothetical bacterial proteins of unknown function. 143 matched cddid_all.tbl CDD pfam06187 pfam06187 428813 DUF993 Protein of unknown function (DUF993). This family consists of several hypothetical bacterial proteins of unknown function. 381 matched cddid_all.tbl CDD pfam06188 pfam06188 368784 HrpE HrpE/YscL/FliH and V-type ATPase subunit E. This is a prokaryotic family that contains proteins of the FliH and HrpE/YscL family. These proteins are involved in type III secretion, which is the process that drives flagellar biosynthesis and mediates bacterial-eukaryotic interactions. This family also V-type ATPase subunit E. This subunit appears to form a tight interaction with subunit G in the F0 complex. Subunits E and G may act together as stators to prevent certain subunits from rotating with the central rotary element. pfam01991 also contains V-type ATPase subunit E proteins. 187 matched cddid_all.tbl CDD pfam06189 pfam06189 461846 5-nucleotidase 5'-nucleotidase. This family consists of both eukaryotic and prokaryotic 5'-nucleotidase sequences (EC:3.1.3.5). 265 matched cddid_all.tbl CDD pfam06191 pfam06191 428815 DUF995 Protein of unknown function (DUF995). Family of uncharacterized Proteobacteria proteins. 140 matched cddid_all.tbl CDD pfam06193 pfam06193 283778 Orthopox_A5L Orthopoxvirus A5L protein-like. This family includes several Orthopoxvirus A5L proteins. The vaccinia virus WR A5L open reading frame (corresponding to open reading frame A4L in vaccinia virus Copenhagen) encodes an immunodominant late protein found in the core of the vaccinia virion. The A5 protein appears to be required for the immature virion to form the brick-shaped intracellular mature virion. 216 matched cddid_all.tbl CDD pfam06194 pfam06194 283779 Phage_Orf51 Phage Conserved Open Reading Frame 51. Family of conserved bacteriophage open reading frames. 80 matched cddid_all.tbl CDD pfam06195 pfam06195 428816 DUF996 Protein of unknown function (DUF996). Family of uncharacterized bacterial and archaeal proteins. 135 matched cddid_all.tbl CDD pfam06196 pfam06196 428817 DUF997 Protein of unknown function (DUF997). Family of predicted bacterial membrane protein with unknown function. 77 matched cddid_all.tbl CDD pfam06197 pfam06197 428818 DUF998 Protein of unknown function (DUF998). Family of conserved archaeal proteins. 185 matched cddid_all.tbl CDD pfam06198 pfam06198 114890 DUF999 Protein of unknown function (DUF999). Family of conserved Schizosaccharomyces pombe proteins with unknown function. 143 matched cddid_all.tbl CDD pfam06199 pfam06199 428819 Phage_tail_2 Phage tail tube protein. characterized members are major tail tube proteins from various phages, including lactococcal temperate bacteriophage TP901-1. 134 matched cddid_all.tbl CDD pfam06200 pfam06200 461847 tify tify domain. This short possible domain is found in a variety of plant transcription factors that contain GATA domains as well as other motifs. Although previously known as the Zim domain this is now called the tify domain after its most conserved amino acids. TIFY proteins can be further classified into two groups depending on the presence (group I) or absence (group II) of a C2C2-GATA domain. Functional annotation of these proteins is still poor, but several screens revealed a link between TIFY proteins of group II and jasmonic acid-related stress response. 33 matched cddid_all.tbl CDD pfam06201 pfam06201 461848 PITH PITH domain. This family was formerly known as DUF1000. The full-length, Txnl1, protein which is a probable component of the 26S proteasome, uses its C-terminal, PITH, domain to associate specifically with the 26S proteasome. PITH derives from proteasome-interacting thioredoxin domain. 148 matched cddid_all.tbl CDD pfam06202 pfam06202 428822 GDE_C Amylo-alpha-1,6-glucosidase. This family includes human glycogen branching enzyme Swiss:P35573. This enzyme contains a number of distinct catalytic activities. It has been shown for the yeast homolog Swiss:O93808 that mutations in this region disrupt the enzymes Amylo-alpha-1,6-glucosidase (EC:3.2.1.33). 370 matched cddid_all.tbl CDD pfam06203 pfam06203 461849 CCT CCT motif. This short motif is found in a number of plant proteins. It is rich in basic amino acids and has been called a CCT motif after Co, Col and Toc1. The CCT motif is about 45 amino acids long and contains a putative nuclear localization signal within the second half of the CCT motif. Toc1 mutants have been identified in this region. 44 matched cddid_all.tbl CDD pfam06206 pfam06206 428824 CpeT CpeT/CpcT family (DUF1001). This family consists of proteins of proteins belonging to the CpeT/CpcT family. These proteins are around 200 amino acids in length. The proteins contain a conserved motif PYR in the amino terminal half of the protein that may be functionally important. The species distribution of the family is interesting. So far it is restricted to cyanobacteria, cryptomonads and plants. It has been shown that CpcT encodes a bilin lyase responsible for attachment of phycocyanobilin to the beta subunit of phycocyanin. 179 matched cddid_all.tbl CDD pfam06207 pfam06207 461850 DUF1002 Protein of unknown function (DUF1002). This protein family has no known function. Its members are about 300 amino acids in length. It has so far been detected in Firmicute bacteria and some archaebacteria. 220 matched cddid_all.tbl CDD pfam06208 pfam06208 283790 BDV_G Borna disease virus G protein. This family consists of Borna disease virus G glycoprotein sequences. Borna disease virus (BDV) infection produces a variety of clinical diseases, from behavioural illnesses to classical fatal encephalitis. G protein is important for viral entry into the host cell. 503 matched cddid_all.tbl CDD pfam06209 pfam06209 461851 COBRA1 Cofactor of BRCA1 (COBRA1). This family consists of several cofactor of BRCA1 (COBRA1) like proteins. It is thought that COBRA1 along with BRCA1 is involved in chromatin unfolding. COBRA1 is recruited to the chromosome site by the first BRCT repeat of BRCA1, and is itself sufficient to induce chromatin unfolding. BRCA1 mutations that enhance chromatin unfolding also increase its affinity for, and recruitment of, COBRA1. It is thought that that reorganization of higher levels of chromatin structure is an important regulated step in BRCA1-mediated nuclear functions. 346 matched cddid_all.tbl CDD pfam06210 pfam06210 428827 DUF1003 Protein of unknown function (DUF1003). This family consists of several hypothetical bacterial proteins of unknown function. 101 matched cddid_all.tbl CDD pfam06211 pfam06211 283793 BAMBI BMP and activin membrane-bound inhibitor (BAMBI) N-terminal domain. This family consists of several eukaryotic BMP and activin membrane-bound inhibitor (BAMBI) proteins. Members of the transforming growth factor-beta (TGF-beta) superfamily, including TGF-beta, bone morphogenetic proteins (BMPs), activins and nodals, are vital for regulating growth and differentiation. BAMBI is related to TGF-beta-family type I receptors but lacks an intracellular kinase domain. BAMBI is co-expressed with the ventralising morphogen BMP4 during Xenopus embryogenesis and requires BMP signalling for its expression. The protein stably associates with TGF-beta-family receptors and inhibits BMP and activin as well as TGF-beta signalling. 107 matched cddid_all.tbl CDD pfam06212 pfam06212 461852 GRIM-19 GRIM-19 protein. This family consists of several eukaryotic gene associated with retinoic-interferon-induced mortality 19 (GRIM-19) proteins. GRIM-19, was reported to encode a small protein primarily distributed in the nucleus and was able to promote cell death induced by IFN-beta and RA. A bovine homolog of GRIM-19 was co-purified with mitochondrial NADH:ubiquinone oxidoreductase (complex I) in bovine heart. Therefore, its exact cellular localization and function are unclear. It has now been discovered that GRIM-19 is a specific interacting protein which negatively regulates Stat3 activity. 132 matched cddid_all.tbl CDD pfam06213 pfam06213 428829 CobT Cobalamin biosynthesis protein CobT. This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. 274 matched cddid_all.tbl CDD pfam06214 pfam06214 461853 SLAM Signaling lymphocytic activation molecule (SLAM) protein. This family consists of several mammalian signaling lymphocytic activation molecule (SLAM) proteins. Optimal T cell activation and expansion require engagement of the TCR plus co-stimulatory signals delivered through accessory molecules. SLAM, a 70-kDa co-stimulatory molecule belonging to the Ig superfamily, is defined as a human cell surface molecule that mediates CD28-independent proliferation of human T cells and IFN-gamma production by human Th1 and Th2 clones. SLAM has also been recognized as a receptor for measles virus. 125 matched cddid_all.tbl CDD pfam06215 pfam06215 368794 ISAV_HA Infectious salmon anaemia virus haemagglutinin. This family consists of several infectious salmon anaemia virus haemagglutinin proteins. Infectious salmon anaemia virus (ISAV), an orthomyxovirus-like virus, is an important fish pathogen in marine aquaculture. 380 matched cddid_all.tbl CDD pfam06216 pfam06216 283798 RTBV_P46 Rice tungro bacilliform virus P46 protein. This family consists of several Rice tungro bacilliform virus P46 proteins. The function of this family is unknown. 389 matched cddid_all.tbl CDD pfam06217 pfam06217 461854 GAGA_bind GAGA binding protein-like family. This family includes gbp a protein from Soybean that binds to GAGA element dinucleotide repeat DNA. It seems likely that the this domain mediates DNA binding. This putative domain contains several conserved cysteines and a histidine suggesting this may be a zinc-binding DNA interaction domain. 290 matched cddid_all.tbl CDD pfam06218 pfam06218 368796 NPR2 Nitrogen permease regulator 2. This family of regulators are involved in post-translational control of nitrogen permease. 439 matched cddid_all.tbl CDD pfam06219 pfam06219 461855 DUF1005 Protein of unknown function (DUF1005). Family of plant proteins with undetermined function. 430 matched cddid_all.tbl CDD pfam06220 pfam06220 368798 zf-U1 U1 zinc finger. This family consists of several U1 small nuclear ribonucleoprotein C (U1-C) proteins. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site (ss) at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' ss is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' ss. Binding of TIA-1 in the vicinity of a 5' ss helps to stabilize U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator. This domain is probably a zinc-binding. It is found in multiple copies in some members of the family. 38 matched cddid_all.tbl CDD pfam06221 pfam06221 428833 zf-C2HC5 Putative zinc finger motif, C2HC5-type. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. 54 matched cddid_all.tbl CDD pfam06222 pfam06222 368800 Phage_TAC_1 Phage tail assembly chaperone. 126 matched cddid_all.tbl CDD pfam06223 pfam06223 283804 Phage_tail_T Minor tail protein T. Minor tail protein T is located at the distal end and is involved in the assembly of the initiator complex for tail polymerization. 100 matched cddid_all.tbl CDD pfam06224 pfam06224 428834 HTH_42 Winged helix DNA-binding domain. This family contains two copies of a winged helix domain. 325 matched cddid_all.tbl CDD pfam06226 pfam06226 428835 DUF1007 Protein of unknown function (DUF1007). Family of conserved bacterial proteins with unknown function. 210 matched cddid_all.tbl CDD pfam06227 pfam06227 368802 Poxv_Bcl-2-like Poxvirus Bcl-2-like proteins. This family represents a group of Poxvirus Bcl-2-like proteins that function as immunomodulators to evade the host innate immune response through the inhibition of apoptosis or blocking the activation of pro-inflammatory transcription factors, such as interferon (IFN) regulatory factor-3 (IRF-3) and nuclear factor-kappaB (NF-kappaB). These proteins have low sequence identity but high structural similarity to the eukaryotic Bcl-2 protein family. They have a Bcl-2 fold which comprises a central hydrophobic alpha-helix that is surrounded by an additional layer of 6-7 amphipathic alpha-helices. Included in this family are proteins B14, A52, A46, C6, K7, N1, and N2. Protein N1 has the unusual dual ability of modulating apoptosis and inflammatory signalling. Protein K7, in addition to its anti-inflammatory activity, forms a complex with RNA helicase DDX3 and antagonizes interferon-beta promoter induction. 145 matched cddid_all.tbl CDD pfam06228 pfam06228 428836 ChuX_HutX Haem utilization ChuX/HutX. This family is found within haem utilization operons. It has a similar structure to that of pfam05171. pfam05171 usually occurs as a duplicated domain, but this domain occurs as a single domain and forms a dimer. The organization of the dimer is very similar to that of the duplicated pfam05171 domains. It binds haem via conserved histidines. 128 matched cddid_all.tbl CDD pfam06229 pfam06229 368803 FRG1 FRG1-like domain. The human FRG1 gene maps to human chromosome 4q35 and has been identified as a candidate for facioscapulohumeral muscular dystrophy. Currently, the function of FRG1 is unknown. 189 matched cddid_all.tbl CDD pfam06230 pfam06230 428837 LpxI_C LpxI C-terminal domain. This entry represents the catalytic C-terminal domain of the LpxI enzyme that is involved in biosynthesis of lipid A. Specifically it carried out the hydrolysis of UDP-2,3-diacyl- glucosamine. This step is either carried out by LpxI or LpxH. This domain comprises a five-stranded mixed beta-sheet bracketed by one alpha-helix on one side and three on the other. This domain is structurally related to a superfamily that includes cytosine deaminase. 131 matched cddid_all.tbl CDD pfam06231 pfam06231 283811 DUF1010 Protein of unknown function (DUF1010). Family of plasmid encoded proteins with unknown function. 81 matched cddid_all.tbl CDD pfam06232 pfam06232 399320 ATS3 Embryo-specific protein 3, (ATS3). This is a family of plant seed-specific proteins identified in Arabidopsis thaliana (Mouse-ear cress). ATS3 (Arabidopsis thaliana seed gene 3) is expressed in a pattern similar to the Arabidopsis seed storage protein genes. 125 matched cddid_all.tbl CDD pfam06233 pfam06233 428838 Usg Usg-like family. Family of bacterial proteins, referred to as Usg. Usg is found in the same operon as trpF, trpB, and trpA and is expressed in a coupled transcription-translation system. 80 matched cddid_all.tbl CDD pfam06234 pfam06234 428839 TmoB Toluene-4-monooxygenase system protein B (TmoB). This family consists of several Toluene-4-monooxygenase system protein B (TmoB) sequences. Pseudomonas mendocina KR1 metabolizes toluene as a carbon source. The initial step of the pathway is hydroxylation of toluene to form p-cresol by a multicomponent toluene-4-monooxygenase (T4MO) system. TmoB adopts a ubiquitin fold. Although TmoB is a component of the T4MO system, its precise role remains unclear. 78 matched cddid_all.tbl CDD pfam06235 pfam06235 368806 NAD4L NADH dehydrogenase subunit 4L (NAD4L). This family consists of NADH dehydrogenase subunit 4L (NAD4L) proteins from the mitochondria of several parasitic flatworms. 86 matched cddid_all.tbl CDD pfam06236 pfam06236 399323 MelC1 Tyrosinase co-factor MelC1. This family consists of several tyrosinase co-factor MELC1 proteins from a number of Streptomyces species. The melanin operon (melC) of Streptomyces antibioticus contains two genes, melC1 and melC2 (apotyrosinase). It is thought that MelC1 forms a transient binary complex with the downstream apotyrosinase MelC2 to facilitate the incorporation of copper ion and the secretion of tyrosinase indicating that MelC1 is a chaperone for the apotyrosinase MelC2. 113 matched cddid_all.tbl CDD pfam06237 pfam06237 461856 DUF1011 Protein of unknown function (DUF1011). Family of uncharacterized eukaryotic proteins. 99 matched cddid_all.tbl CDD pfam06239 pfam06239 461857 ECSIT Evolutionarily conserved signalling intermediate in Toll pathway. Activation of NF-kappaB as a consequence of signaling through the Toll and IL-1 receptors is a major element of innate immune responses. ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signaling pathways between TRAF-6 and MEKK-1. 191 matched cddid_all.tbl CDD pfam06240 pfam06240 399326 COXG Carbon monoxide dehydrogenase subunit G (CoxG). The CO dehydrogenase structural genes coxMSL are flanked by nine accessory genes arranged as the cox gene cluster. The cox genes are specifically and coordinately transcribed under chemolithoautotrophic conditions in the presence of CO as carbon and energy source. 140 matched cddid_all.tbl CDD pfam06241 pfam06241 428842 Castor_Poll_mid Castor and Pollux, part of voltage-gated ion channel. This family represents a short region in the middle of largely plant proteins that belong to the TCDB:1.A.1.23.2 family of the voltage-gated ion channel superfamily, eg UniProtKB:Q5H8A6, Q5H8A5 and Q4VY51. 99 matched cddid_all.tbl CDD pfam06242 pfam06242 428843 TrcR Transcriptional cell cycle regulator TrcR. This family represents a transcriptional cell cycle regulator (TrcR) found in Proteobacteria, mainly Alphaproteobacteria. It has been shown to associate with promoters and coding sequences in vivo in a rifampicin-dependent manner and to interact physically and genetically with RNA polymerase, resulting in the integration of cell cycle and antibiotic stress control with the general transcriptional machinery. 138 matched cddid_all.tbl CDD pfam06243 pfam06243 428844 PaaB Phenylacetic acid degradation B. Phenylacetic acid degradation protein B (PaaB) is thought to be part of a multicomponent oxygenase involved in phenylacetyl-CoA hydroxylation. 88 matched cddid_all.tbl CDD pfam06244 pfam06244 461858 Ccdc124 Coiled-coil domain-containing protein 124 /Oxs1. Oxs1 (oxidative stress transcription corepressor Oxs1) and Pap1 form a complex to regulate transcription when cells are exposed to diamide or Cd that causes disulfide stress. In fission yeast such as S. pombe, heterologous Oxs1-like proteins can enhance diamide stress tolerance. Furthermore, human and arabidopsis Oxs1 can interchangeably bind Pap1 or Pap1 homologs from human (cJun) and arabidopsis (bZIP10), suggesting that Oxs1 may be a component of an evolutionarily-conserved stress response pathway. Family members found in human such as Ccdc124 (Coiled-Coil Domain Containing Protein 124), were identified as a novel component of the centrosome during interphase and G2/M transition and is involved in cytokinesis. 84 matched cddid_all.tbl CDD pfam06245 pfam06245 461859 DUF1015 Protein of unknown function (DUF1015). Family of proteins with unknown function found in archaea and bacteria. 330 matched cddid_all.tbl CDD pfam06246 pfam06246 461860 Isy1 Isy1-like splicing family. Isy1 protein is important in the optimization of splicing. 247 matched cddid_all.tbl CDD pfam06247 pfam06247 399333 Plasmod_Pvs28 Pvs28 EGF domain. This family consists of several ookinete surface proteins (Pvs28) from several species of Plasmodium. Pvs25 and Pvs28 are expressed on the surface of ookinetes. These proteins are potential candidates for vaccine and induce antibodies that block the infectivity of Plasmodium vivax in immunized animals. The structure of this protein shows it is composed of four EGF domains. 35 matched cddid_all.tbl CDD pfam06248 pfam06248 461861 Zw10 Centromere/kinetochore Zw10. Zw10 and rough deal proteins are both required for correct metaphase check-pointing during mitosis. These proteins bind to the centromere/kinetochore. 509 matched cddid_all.tbl CDD pfam06249 pfam06249 114941 EutQ Ethanolamine utilization protein EutQ. The eut operon of Salmonella typhimurium encodes proteins involved in the cobalamin-dependent degradation of ethanolamine. The role of EutQ in this process is unclear. 152 matched cddid_all.tbl CDD pfam06250 pfam06250 428849 YhcG_C YhcG PDDEXK nuclease domain. This domain can be found in uncharacterized proteins in viruses, archaea and bacteria, most notably it is found in YhcG proteins found in E.coli. This entry represents the C-terminal PDDEXK domain belonging to the PD-(D/E)XK superfamily of nucleases involved in DNA recombination and repair. Profile HMM analysis identified a relationship between this C-terminal domain of YhcG and pfam01939, a family of NucS endonucleases. YHcG was identified in association with DNA processing enzymes, including the restriction complexes HsdMRS and McrABC, the integrases IntF and IntS, and the recombinase PinE. 155 matched cddid_all.tbl CDD pfam06251 pfam06251 461862 Caps_syn_GfcC_C Capsule biosynthesis GfcC C-terminal. Many bacteria are covered in a layer of surface-associated polysaccharide called the capsule. These capsules can be divided into four groups depending upon the organization of genes responsible for capsule assembly, the assembly pathway and regulation. This family plays a role in group 4 capsule biosynthesis. These proteins have a beta-grasp fold. Two beta-grasp domains, D2 and D3, are arranged in tandem. There is a C-terminal amphipathic helix which packs against D3. A helical hairpin insert in D2 binds to D3 and constrains its position, a conserved arginine residue at the end of this hairpin is essential for structural integrity. This is the C-terminal domain which covers D3 and D4 domains. 90 matched cddid_all.tbl CDD pfam06252 pfam06252 428851 GemA Bacteriophage Mu, GemA protein. This family consists of several bacterial and phage proteins, including GemA (also known as gp16) protein from Bacteriophage Mu. GemA is an early protein responsible for decreasing host DNA gyrase activity, that promotes DNA relaxation of bacterial host genome. Modulates the expression of various host genes probably controlled by supercoiling of their promoters. Host genes affected include DNA replication and cell division determinants. This family also includes the Mu-like prophage FluMu protein gp16 from Haemophilus influenzae. 118 matched cddid_all.tbl CDD pfam06253 pfam06253 428852 MTTB Trimethylamine methyltransferase (MTTB). This family consists of several trimethylamine methyltransferase (MTTB) (EC:2.1.1.-) proteins from numerous Rhizobium and Methanosarcina species. 502 matched cddid_all.tbl CDD pfam06254 pfam06254 368819 YdaT_toxin Putative bacterial toxin ydaT. YdaT_toxin is a family of putative bacterial toxins that are neutralized by the putative antitoxin YdaS, UniProtKB:P76063, family pfam144549. 88 matched cddid_all.tbl CDD pfam06255 pfam06255 283833 MafB Neisseria toxin MafB. MafB constitutes a family of secreted toxins in pathogenic Neisseria species, probably involved in interbacterial competition. Genes immediately downstream of mafB encode a specific immunity protein (MafI). MafB proteins exhibit a signal peptide sequence, a N-terminal conserved domain and a C-terminal variable region. Toxic domains identified at the C terminus include pfam15542, pfam14437, pfam15524, and pfam14436. 312 matched cddid_all.tbl CDD pfam06256 pfam06256 461863 Nucleo_LEF-12 Nucleopolyhedrovirus LEF-12 protein. This family consists of several Nucleopolyhedrovirus late expression factor-12 (LEF-12) proteins. The function of this family is unknown. 173 matched cddid_all.tbl CDD pfam06257 pfam06257 461864 VEG Biofilm formation stimulator VEG. VEG is a family that is highly conserved among Gram-positive bacteria. It stimulates biofilm formation through inducing transcription of the tapA-sipW-tasA operon. The products of this operon are resposible for production of the amyloid fibre (TasA) component of the biofilm. Veg or a Veg-induced protein acts as an antirepressor of SinR - part of the major overall biofilm transcriptional control system - to regulate and stimulate biofilm formation. Veg is transcribed at high levels during both exponential growth and sporulation. 61 matched cddid_all.tbl CDD pfam06258 pfam06258 428854 Mito_fiss_Elm1 Mitochondrial fission ELM1. In plants, this family is involved in mitochondrial fission. It binds to dynamin-related proteins and plays a role in their relocation from the cytosol to mitochondrial fission sites. Its function in bacteria is unknown. 302 matched cddid_all.tbl CDD pfam06259 pfam06259 283837 Abhydrolase_8 Alpha/beta hydrolase. Members of this family are predicted to have an alpha/beta hydrolase fold. They contain a predicted Ser-His-Asp catalytic triad, in which the serine is likely to act as a nucleophile. 178 matched cddid_all.tbl CDD pfam06260 pfam06260 283838 DUF1024 Protein of unknown function (DUF1024). This family consists of several hypothetical Staphylococcus aureus and Staphylococcus aureus phage phi proteins. The function of this family is unknown. 82 matched cddid_all.tbl CDD pfam06261 pfam06261 368820 LktC Actinobacillus actinomycetemcomitans leukotoxin activator LktC. This family consists of several Actinobacillus actinomycetemcomitans leukotoxin activator (LktC) proteins. Actinobacillus actinomycetemcomitans is a Gram-negative bacterium that has been implicated in the etiology of several forms of periodontitis, especially localized juvenile periodontitis. LktC along with LktB and LktD are thought to be required for activation and localization of the leukotoxin. 150 matched cddid_all.tbl CDD pfam06262 pfam06262 428855 Zincin_1 Zincin-like metallopeptidase. This family of proteins has a conserved HEXXH motif, suggesting they are putative peptidases of zincin fold. The structure of this family is a minimal version of the metalloprotease fold (PDB:3E11). 95 matched cddid_all.tbl CDD pfam06265 pfam06265 428856 YutD-like Putative antitoxin YutD-like. This family contains a group of uncharacterized bacterial proteins, including YutD from Bacillus subtilis (PDBe:2kl5), a probable antitoxin component of a putative type VII toxin-antitoxin (TA) system, that probably neutralizes cognate toxin YutE. 84 matched cddid_all.tbl CDD pfam06266 pfam06266 336357 HrpF HrpF protein. The species Pseudomonas syringae encompasses plant pathogens with differing host specificities and corresponding pathovar designations. P. syringae requires the Hrp (type III protein secretion) system, encoded by a 25-kb cluster of hrp and hrc genes, in order to elicit the hypersensitive response (HR) in nonhosts or to be pathogenic in hosts. The exact function of HrpF is unknown but the protein is needed for pathogenicity. 74 matched cddid_all.tbl CDD pfam06267 pfam06267 428857 DUF1028 Family of unknown function (DUF1028). Family of bacterial and archaeal proteins with unknown function. Some members are associated with a C-terminal peptidoglycan binding domain. So perhaps this could be an enzyme involved in peptidoglycan metabolism. 189 matched cddid_all.tbl CDD pfam06268 pfam06268 461865 Fascin Fascin domain. This family consists of several eukaryotic fascin or singed proteins. The fascins are a structurally unique and evolutionarily conserved group of actin cross-linking proteins. Fascins function in the organization of two major forms of actin-based structures: dynamic, cortical cell protrusions and cytoplasmic microfilament bundles. The cortical structures, which include filopodia, spikes, lamellipodial ribs, oocyte microvilli and the dendrites of dendritic cells, have roles in cell-matrix adhesion, cell interactions and cell migration, whereas the cytoplasmic actin bundles appear to participate in cell architecture. Dictyostelium hisactophilin, another actin-binding protein, is a submembranous pH sensor that signals slight changes of the H+ concentration to actin by inducing actin polymerization and binding to microfilaments only at pH values below seven. Members of this family are histidine rich, typically contain the repeated motif of HHXH. 111 matched cddid_all.tbl CDD pfam06269 pfam06269 283844 DUF1029 Protein of unknown function (DUF1029). This family consists of several short Chordopoxvirus proteins of unknown function. 53 matched cddid_all.tbl CDD pfam06270 pfam06270 114962 DUF1030 Protein of unknown function (DUF1030). This family consists of several short Circovirus proteins of unknown function. 53 matched cddid_all.tbl CDD pfam06271 pfam06271 428859 RDD RDD family. This family of proteins contain three highly conserved amino acids: one arginine and two aspartates, hence the name of RDD family. This region contains two predicted transmembrane regions. The arginine occurs at the N terminus of the first helix and the first aspartate occurs in the middle of this helix. The molecular function of this region is unknown. However this region may be involved in transport of an as yet unknown set of ligands (Bateman A pers. obs.). 134 matched cddid_all.tbl CDD pfam06273 pfam06273 310698 eIF-4B Plant specific eukaryotic initiation factor 4B. This family consists of several plant specific eukaryotic initiation factor 4B proteins. 502 matched cddid_all.tbl CDD pfam06275 pfam06275 114966 DUF1031 Protein of unknown function (DUF1031). This family consists of several Lactococcus lactis bacteriophage and Lactococcus lactis proteins of unknown function. 80 matched cddid_all.tbl CDD pfam06276 pfam06276 428860 FhuF Ferric iron reductase FhuF-like transporter. This family consists of several bacterial ferric iron reductase protein (FhuF) sequences. FhuF is involved in the reduction of ferric iron in cytoplasmic ferrioxamine B. This family also includes the IucA and IucC proteins. 163 matched cddid_all.tbl CDD pfam06277 pfam06277 377642 EutA Ethanolamine utilization protein EutA. This family consists of several bacterial EutA ethanolamine utilization proteins. The EutA protein is thought to protect the lyase (EutBC) from inhibition by CNB12. 475 matched cddid_all.tbl CDD pfam06278 pfam06278 461866 CNDH2_N Condensin II complex subunit CAP-H2 or CNDH2, N-terminal. CNDH2_N is the N-terminal domain of the H2 subunit of the condensing II complex, found in eukaryotes but not in fungi. Eukaryotes carry at least two condensin complexes, I and II, each made up of five subunits. The functions of the two complexes are collaborative but non-overlapping. CI appears to be functional in G2 phase in the cytoplasm beginning the process of chromosomal lateral compaction while the CII is concentrated in the nucleus, possibly to counteract the activity of cohesion at this stage. In prophase, CII contributes to axial shortening of chromatids while CI continues to bring about lateral chromatid compaction, during which time the sister chromatids are joined centrally by cohesins. There appears to be just one condensin complex in fungi. CI and CII each contain SMC2 and SMC4 (structural maintenance of chromosomes) subunits, then CI has non-SMC CAP-D2 (CND1), CAP-G (CND3), and CAP-H (CND2). CII has, in addition to the two SMCs, CAP-D3, CAPG2 and CAP-H2. All four of the CAP-D and CAP-G subunits have degenerate HEAT repeats, whereas the CAP-H are kleisins or SMC-interacting proteins (ie they bind directly to the SMC subunits in the complex). The SMC molecules are each long with a small hinge-like knob at the free end of a longish strand, articulating with each other at the hinge. Each strand ends in a knob-like head that binds to one or other end of the CAP-H subunit. The HEAT-repeat containing D and G subunits bind side-by-side between the ends of the H subunit. Activity of the various parts of the complex seem to be triggered by extensive phosphorylations, eg, entry of the complex, in Sch.pombe, into the nucleus during mitosis is promoted by Cdk1 phosphorylation of SMC4/Cut3; and it has been shown that Cdk1 phosphorylates CAP-D3 at Thr1415 in He-La cells thus promoting early stage chromosomal condensation by CII. 117 matched cddid_all.tbl CDD pfam06279 pfam06279 428862 DUF1033 Protein of unknown function (DUF1033). This family consists of several hypothetical bacterial proteins. Many of the sequences in this family are annotated as putative DNA binding proteins but the function of this family is unknown. 117 matched cddid_all.tbl CDD pfam06280 pfam06280 428863 fn3_5 Fn3-like domain. Fn3_5 is an fn3-like domain which is frequently found as the first of three on streptococcal C5a peptidase (SCP), a highly specific protease and adhesin/invasin. The family is found in conjunction with pfam00082, pfam02225 and pfam00746. 112 matched cddid_all.tbl CDD pfam06281 pfam06281 253656 VP1_VP3 Structural protein VP1/VP3. This family consists of Structural proteins VP1 and VP3 from Sulfolobus spindle-shape virus 1 (SSV1), two of the three structural proteins. 73 matched cddid_all.tbl CDD pfam06282 pfam06282 428864 DUF1036 Protein of unknown function (DUF1036). This family consists of several hypothetical bacterial proteins of unknown function. 111 matched cddid_all.tbl CDD pfam06283 pfam06283 461867 ThuA Trehalose utilization. This family consists of several bacterial ThuA-like proteins. ThuA appears to be involved in utilization of trehalose. The thuA and thuB genes form part of the trehalose/sucrose transport operon thuEFGKAB, which is located on the pSymB megaplasmid. The thuA and thuB genes are induced in vitro by trehalose but not by sucrose and the extent of its induction depends on the concentration of trehalose available in the medium. ThuA is involved in the conversion of of disaccharides to their respective 3-keto derivatives. 213 matched cddid_all.tbl CDD pfam06284 pfam06284 283854 Cytomega_UL84 Cytomegalovirus UL84 protein. This family consists of several Cytomegalovirus UL84 proteins. The open reading frame UL84 of human cytomegalovirus encodes a multifunctional regulatory protein which is required for viral DNA replication and binds with high affinity to the immediate-early transactivator IE2-p86. 586 matched cddid_all.tbl CDD pfam06286 pfam06286 253659 Coleoptericin Coleoptericin. This family consists of several insect Coleoptericin, Acaloleptin, Holotricin and Rhinocerosin proteins which are all known to be antibacterial proteins. 143 matched cddid_all.tbl CDD pfam06287 pfam06287 428866 DUF1039 Protein of unknown function (DUF1039). This family consists of several hypothetical bacterial proteins from Escherichia coli and Citrobacter rodentium. The function of this family is unknown. 65 matched cddid_all.tbl CDD pfam06288 pfam06288 428867 DUF1040 Protein of unknown function (DUF1040). This family consists of several bacterial YihD proteins of unknown function. 86 matched cddid_all.tbl CDD pfam06289 pfam06289 461868 FlbD Flagellar and Swarming motility proteins. This family consists of several bacterial FlbD flagellar proteins. Such as SwrD of Bacillus subtilis which is necessary for swarming because it increases flagellar torque. 59 matched cddid_all.tbl CDD pfam06290 pfam06290 428869 PsiB Plasmid SOS inhibition protein (PsiB). This family consists of several plasmid SOS inhibition protein (PsiB) sequences. 138 matched cddid_all.tbl CDD pfam06291 pfam06291 461869 Lambda_Bor Bor protein. This family consists of several Bacteriophage lambda Bor and Escherichia coli Iss proteins. Expression of bor significantly increases the survival of the Escherichia coli host cell in animal serum. This property is a well known bacterial virulence determinant indeed, bor and its adjacent sequences are highly homologous to the iss serum resistance locus of the plasmid ColV2-K94, which confers virulence in animals. It has been suggested that lysogeny may generally have a role in bacterial survival in animal hosts, and perhaps in pathogenesis. 77 matched cddid_all.tbl CDD pfam06292 pfam06292 461870 MUN MUN domain. This entry corresponds to the MUN domain found in Munc13 proteins. These constitute a family of three highly homologous molecules (Munc13-1, Munc13-2 and Munc13-3) with homology to Caenorhabditis elegans unc-13p. Munc13 proteins contain a phorbol ester-binding C1 domain and two C2 domains, which are Ca2+/phospholipid binding domains. Sequence analyses have uncovered two regions called Munc13 homology domains 1 (MHD1) and 2 (MHD2) that are arranged between two flanking C2 domains. MHD1 and MHD2 domains are present in a wide variety of proteins from Arabidopsis thaliana, C. elegans, Drosophila melanogaster, mouse, rat and human, some of which may function in a Munc13-like manner to regulate membrane trafficking. Structural studies have defined MHD1 and MHD2 to be part of the larger MUN domain which forms an elongated structure composed of any pairs of alpha helices. 473 matched cddid_all.tbl CDD pfam06293 pfam06293 428872 Kdo Lipopolysaccharide kinase (Kdo/WaaP) family. These lipopolysaccharide kinases are related to protein kinases pfam00069. This family includes waaP (rfaP) gene product is required for the addition of phosphate to O-4 of the first heptose residue of the lipopolysaccharide (LPS) inner core region. It has previously been shown that WaaP is necessary for resistance to hydrophobic and polycationic antimicrobials in E. coli and that it is required for virulence in invasive strains of S. enterica. 206 matched cddid_all.tbl CDD pfam06294 pfam06294 461871 CH_2 CH-like domain in sperm protein. Spef is a region of sperm flagellar proteins. It probably exerts a role in spermatogenesis in that the protein is expressed predominantly in adult tissue. It is present in the tails of developing and epididymal sperm internal to the fibrous sheath and around the dense outer fibres of the sperm flagellum. The amino-terminal domain (residues 1-110) shows a possible calponin homology (CH) domain; however Spef does not bind actin directly under in vitro conditions, so the function of the amino-terminal calponin-like domain is unclear. Transcription aberrations leading to a truncated protein result in immotile sperm. 91 matched cddid_all.tbl CDD pfam06295 pfam06295 428874 DUF1043 Protein of unknown function (DUF1043). This family consists of several hypothetical bacterial proteins of unknown function. 119 matched cddid_all.tbl CDD pfam06296 pfam06296 399359 RelE RelE toxin of RelE / RelB toxin-antitoxin system. RelE is a family of Gram-negative bacterial antitoxins of the RelE/RelB toxin-antitoxin system. Its cognate antitoxin is family RelB, pfam04221. 120 matched cddid_all.tbl CDD pfam06297 pfam06297 461872 PET PET Domain. This domain is suggested to be involved in protein-protein interactions. The family is found in conjunction with pfam00412. 85 matched cddid_all.tbl CDD pfam06298 pfam06298 428876 PsbY Photosystem II protein Y (PsbY). This family consists of several bacterial and plant photosystem II protein Y (PsbY) sequences. PsbY is a manganese-binding protein that has an L-arginine metabolising enzyme activity. 35 matched cddid_all.tbl CDD pfam06299 pfam06299 428877 DUF1045 Protein of unknown function (DUF1045). This family consists of several hypothetical proteins from Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown. 159 matched cddid_all.tbl CDD pfam06300 pfam06300 368834 Tsp45I Tsp45I type II restriction enzyme. This family consists of several type II restriction enzymes. 260 matched cddid_all.tbl CDD pfam06301 pfam06301 461873 Lambda_Kil Bacteriophage lambda Kil protein. This family consists of several Bacteriophage lambda Kil protein like sequences from both phages and bacteria. Induction of a lambda prophage causes the death of the host cell even in the absence of phage replication and lytic functions due to expression of the lambda kil gene. 42 matched cddid_all.tbl CDD pfam06303 pfam06303 428878 MatP MatP N-terminal domain. This family, many of whose members are YcbG, organizes the macrodomain Ter of the chromosome of bacteria such as E coli. In these bacteria, insulated macrodomains influence the segregation of sister chromatids and the mobility of chromosomal DNA. organization of the Terminus region (Ter) into a macrodomain relies on the presence of a 13 bp motif called matS repeated 23 times in the 800-kb-long domain. MatS sites are the main targets in the E. coli chromosome of YcbG or MatP (macrodomain Ter protein). MatP accumulates in the cell as a discrete focus that co-localizes with the Ter macrodomain. The effects of MatP inactivation reveal its role as the main organizer of the Ter macrodomain: in the absence of MatP, DNA is less compacted, the mobility of markers is increased, and segregation of the Ter macrodomain occurs early in the cell cycle. A specific organizational system is required in the Terminus region for bacterial chromosome management during the cell cycle. This entry represents the N-terminal domain of MatP. 84 matched cddid_all.tbl CDD pfam06304 pfam06304 428879 DUF1048 Protein of unknown function (DUF1048). This family includes LftS, a soluble globular cytoplasmic protein of unknown function. It is suggested that LftS acts in aurantimycin A sensing or in removal of LftR from its operator sites. 91 matched cddid_all.tbl CDD pfam06305 pfam06305 428880 LapA_dom Lipopolysaccharide assembly protein A domain. This family includes a domain found in lipopolysaccharide assembly protein A (LapA). LapA functions along with LapB in the assembly of lipopolysaccharide (LPS). Domains in this family are also found in some uncharacterized bacterial proteins. 64 matched cddid_all.tbl CDD pfam06306 pfam06306 114995 CgtA Beta-1,4-N-acetylgalactosaminyltransferase (CgtA). This family consists of several beta-1,4-N-acetylgalactosaminyltransferase proteins from Campylobacter jejuni. 347 matched cddid_all.tbl CDD pfam06307 pfam06307 253668 Herpes_IR6 Herpesvirus IR6 protein. This family consists of several Herpesvirus IR6 proteins. The equine herpesvirus 1 (EHV-1) IR6 protein forms typical rod-like structures in infected cells, influences virus growth at elevated temperatures, and determines the virulence of EHV-1 Rac strains. 214 matched cddid_all.tbl CDD pfam06308 pfam06308 368836 ErmC 23S rRNA methylastransferase leader peptide (ErmCL). This family consists of several very short bacterial 23S rRNA methylase leader peptide (ErmCL) sequences. ermC confers resistance to macrolide-lincosamide streptogramin B antibiotics by specifying a ribosomal RNA methylase, which results in decreased ribosomal affinity for these antibiotics. ermC expression is induced by exposure to erythromycin and is controlled by an uORF encoding the leader peptide ErmCL. It has been shown that the four C-terminal ErmCL residues I6F7V8I9 are crucial for ribosome stalling and that translation is arrested likely due to the PTC adopting an inactive conformation that prevents peptide bond formation with the incoming Ser-tRNASer at the 10th ermCL codon position. 31 matched cddid_all.tbl CDD pfam06309 pfam06309 399367 Torsin Torsin. This family consists of several eukaryotic torsin proteins. Torsion dystonia is an autosomal dominant movement disorder characterized by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of (pfam00004) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia. 120 matched cddid_all.tbl CDD pfam06311 pfam06311 461874 NumbF NUMB domain. This presumed domain is found in the Numb family of proteins adjacent to the PTB domain.. 95 matched cddid_all.tbl CDD pfam06312 pfam06312 428882 Neurexophilin Neurexophilin. This family consists of mammalian neurexophilin proteins. Mammalian brains contain four different neurexophilin proteins. Neurexophilins form a family of related glycoproteins that are proteolytically processed after synthesis and bind to alpha-neurexins. The structure and characteriztics of neurexophilins indicate that they function as neuropeptides that may signal via alpha-neurexins. 209 matched cddid_all.tbl CDD pfam06313 pfam06313 399369 ACP53EA Drosophila ACP53EA protein. This family consists of several Drosophila ACP53EA accessory gland (seminal) proteins. 90 matched cddid_all.tbl CDD pfam06314 pfam06314 428883 ADC Acetoacetate decarboxylase (ADC). This family consists of several acetoacetate decarboxylase (ADC) proteins (EC:4.1.1.4). 239 matched cddid_all.tbl CDD pfam06315 pfam06315 461875 AceK_kinase Isocitrate dehydrogenase kinase/phosphatase (AceK) kinase domain. This the C-terminal protein kinase domain of bacterial isocitrate dehydrogenase kinase/phosphatase (AceK) proteins (EC:2.7.1.116). It has a classic bi-lobe protein kinase fold with the ATP-binding cleft located at the interface between the two lobes. The N-terminal lobe comprises a twisted antiparallel beta-sheet of five strands and two alpha-helices. The C-terminal lobe is larger and mainly alpha-helical, with some stretches of antiparallel beta-strands. 256 matched cddid_all.tbl CDD pfam06316 pfam06316 115004 Ail_Lom Enterobacterial Ail/Lom protein. This family consists of several bacterial and phage Ail/Lom-like proteins. The Yersinia enterocolitica Ail protein is a known virulence factor. Proteins in this family are predicted to consist of eight transmembrane beta-sheets and four cell surface-exposed loops. It is thought that Ail directly promotes invasion and loop 2 contains an active site, perhaps a receptor-binding domain. The phage protein Lom is expressed during lysogeny, and encode host-cell envelope proteins. Lom is found in the bacterial outer membrane, and is homologous to virulence proteins of two other enterobacterial genera. It has been suggested that lysogeny may generally have a role in bacterial survival in animal hosts, and perhaps in pathogenesis. 199 matched cddid_all.tbl CDD pfam06317 pfam06317 399372 Arena_RNA_pol Arenavirus RNA polymerase. This family consists of several Arenavirus RNA polymerase proteins (EC:2.7.7.48). 2039 matched cddid_all.tbl CDD pfam06319 pfam06319 428885 MmcB-like DNA repair protein MmcB-like. This family includes Caulobacter MmcB (CCNA_03580), which is involved in DNA repair. It has been proposed to be an endonuclease that creates the substrate for translesion synthesis. 148 matched cddid_all.tbl CDD pfam06320 pfam06320 461876 GCN5L1 GCN5-like protein 1 (GCN5L1). This family consists of several eukaryotic GCN5-like protein 1 (GCN5L1) sequences. The function of this family is unknown. 113 matched cddid_all.tbl CDD pfam06321 pfam06321 399375 P_gingi_FimA Major fimbrial subunit protein (FimA). This family consists of several Porphyromonas gingivalis major fimbrial subunit protein (FimA) sequences. Fimbriae of Porphyromonas gingivalis, a periodontopathogen, play an important role in its adhesion to and invasion of host cells. The fimA genes encoding fimbrillin (FimA), a subunit protein of fimbriae, have been classified into five types, types I to V, based on nucleotide sequences. It has been found that type II FimA can bind to epithelial cells most efficiently through specific host receptors. Human dental plaque is a multispecies microbial biofilm that is associated with two common oral diseases, dental caries and periodontal disease. There is an inter-species contact-dependent communication system between P. gingivalis and S. cristatus that involces the Arc-A enzyme. 157 matched cddid_all.tbl CDD pfam06322 pfam06322 428886 Phage_NinH Phage NinH protein. This family consists of several phage NinH proteins. The function of this family is unknown. 60 matched cddid_all.tbl CDD pfam06323 pfam06323 428887 Phage_antiter_Q Phage antitermination protein Q. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 82 gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. 219 matched cddid_all.tbl CDD pfam06324 pfam06324 283885 Pigment_DH Pigment-dispersing hormone (PDH). This family consists of several eukaryotic pigment-dispersing hormone (PDH) proteins. The pigment-dispersing hormone (PDH) is produced in the eyestalks of Crustacea where it induces light-adapting movements of pigment in the compound eye and regulates the pigment dispersion in the chromatophores. 18 matched cddid_all.tbl CDD pfam06325 pfam06325 428888 PrmA Ribosomal protein L11 methyltransferase (PrmA). This family consists of several Ribosomal protein L11 methyltransferase (EC:2.1.1.-) sequences. 294 matched cddid_all.tbl CDD pfam06326 pfam06326 283887 Vesiculo_matrix Vesiculovirus matrix protein. This family consists of several Vesiculovirus matrix proteins. The matrix (M) protein of vesicular stomatitis virus (VSV) expressed in the absence of other viral components causes many of the cytopathic effects of VSV, including an inhibition of host gene expression and the induction of cell rounding. It has been shown that M protein also induces apoptosis in the absence of other viral components. It is thought that the activation of apoptotic pathways causes the inhibition of host gene expression and cell rounding by M protein. 240 matched cddid_all.tbl CDD pfam06327 pfam06327 461877 Adcy_cons_dom Adenylate cyclase, conserved domain. Adenylate cyclase (AC) enzyme uses ATP as its substrate to produce Cyclic AMP (cAMP), a ubiquitous signalling molecule that mediates many cellular processes by activating cAMP- dependent kinases and also inducing protein-protein interactions. Mammalian adenylate cyclase has nine closely related membrane-bound isoforms (AC1-9) showing significant sequence homology and sharing the same overall structure: two hydrophobic transmembrane domains, and two cytoplasmic domains that are responsible for the catalytic activity. These isoforms differ in both their tissue specificity and their regulation. This entry represents a region of unknown function found in many of these isoforms. It is part of the N-terminal cytoplasmic domain but its presence is not necessary for catalytic activity. 98 matched cddid_all.tbl CDD pfam06328 pfam06328 461878 Lep_receptor_Ig Ig-like C2-type domain. This domain is a ligand-binding immunoglobulin-like domain. The two cysteine residues form a disulphide bridge. 87 matched cddid_all.tbl CDD pfam06330 pfam06330 310730 TRI5 Trichodiene synthase (TRI5). This family consists of several fungal trichodiene synthase proteins (EC:4.2.3.6). TRI5 encodes the enzyme trichodiene synthase, which has been shown to catalyze the first step in the trichothecene pathways of Fusarium and Trichothecium species. 353 matched cddid_all.tbl CDD pfam06331 pfam06331 428891 Tfb5 Transcription factor TFIIH complex subunit Tfb5. This family is a component of the general transcription and DNA repair factor IIH. TFB5 has been shown to be required for efficient recruitment of TFIIH to a promoter. 67 matched cddid_all.tbl CDD pfam06333 pfam06333 461879 Med13_C Mediator complex subunit 13 C-terminal domain. Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med13 is part of the ancillary kinase module, together with Med12, CDK8 and CycC, which in yeast is implicated in transcriptional repression, though most of this activity is likely attributable to the CDK8 kinase. The large Med12 and Med13 proteins are required for specific developmental processes in Drosophila, zebrafish, and Caenorhabditis elegans but their biochemical functions are not understood. This domain is also identified as an RNaseH domain of the medPIWI PIWI/Argonaute module. medPIWI is the core domain found in the Med13 protein. The medPIWI module in Med13 is predicted to bind double-stranded nucleic acids, triggering the experimentally-observed conformational switch in the CDK8 subcomplex which regulates the Mediator complex. 322 matched cddid_all.tbl CDD pfam06334 pfam06334 283893 Orthopox_A47 Orthopoxvirus A47 protein. This family consists of several Orthopoxvirus A47 proteins. The function of this family is unknown. 244 matched cddid_all.tbl CDD pfam06335 pfam06335 428893 DUF1054 Protein of unknown function (DUF1054). This family consists of several hypothetical bacterial proteins of unknown function. 198 matched cddid_all.tbl CDD pfam06336 pfam06336 283895 Corona_5a Coronavirus 5a protein. This family consists of several Coronavirus 5a proteins. The function of this family is unknown. 64 matched cddid_all.tbl CDD pfam06337 pfam06337 399383 DUSP DUSP domain. The DUSP (domain present in ubiquitin-specific protease) domain is found at the N-terminus of Ubiquitin-specific proteases. The structure of this domain has been solved. Its tripod-like structure consists of a 3-fold alpha-helical bundle supporting a triple-stranded anti-parallel beta-sheet. 80 matched cddid_all.tbl CDD pfam06338 pfam06338 428894 ComK ComK protein. This family consists of several bacterial ComK proteins. The ComK protein of Bacillus subtilis positively regulates the transcription of several late competence genes as well as comK itself. It has been found that ClpX plays an important role in the regulation of ComK at the post-transcriptional level. 152 matched cddid_all.tbl CDD pfam06339 pfam06339 428895 Ectoine_synth Ectoine synthase. This family consists of several bacterial ectoine synthase proteins. The ectABC genes encode the diaminobutyric acid acetyltransferase (EctA), the diaminobutyric acid aminotransferase (EctB), and the ectoine synthase (EctC). Together these proteins constitute the ectoine biosynthetic pathway. 127 matched cddid_all.tbl CDD pfam06340 pfam06340 283899 TcpF Vibrio cholerae toxin co-regulated pilus biosynthesis protein F. This family consists of several Vibrio cholerae toxin co-regulated pilus biosynthesis protein F (TcpF) sequences. TcpF is known to be a secreted virulence protein but its exact function is unknown. 317 matched cddid_all.tbl CDD pfam06341 pfam06341 283900 DUF1056 Protein of unknown function (DUF1056). This family consists of several putative head-tail joining bacteriophage proteins. 63 matched cddid_all.tbl CDD pfam06342 pfam06342 115027 DUF1057 Alpha/beta hydrolase of unknown function (DUF1057). This family consists of several Caenorhabditis elegans specific proteins of unknown function. Members of this family have an alpha/beta hydrolase fold. 297 matched cddid_all.tbl CDD pfam06344 pfam06344 461880 Parecho_VpG Parechovirus Genome-linked protein. This family is of the Parechovirus genome-linked protein Vpg type P3B. 20 matched cddid_all.tbl CDD pfam06345 pfam06345 428896 Drf_DAD DRF Autoregulatory Domain. This motif is found in Diaphanous-related formins. It binds the N-terminal GTPase-binding domain; this link is broken when GTP-bound Rho binds to the GBD and activates the protein. The addition of DAD to mammalian cells induces actin filament formation, stabilizes microtubules, and activates serum-response mediated transcription. 15 matched cddid_all.tbl CDD pfam06346 pfam06346 461881 Drf_FH1 Formin Homology Region 1. This region is found in some of the Diaphanous related formins (Drfs). It consists of low complexity repeats of around 12 residues. 157 matched cddid_all.tbl CDD pfam06347 pfam06347 428898 SH3_4 Bacterial SH3 domain. SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues. They are found in a great variety of intracellular or membrane-associated proteins, in a variety of proteins with enzymatic activity, in adaptor proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteriztic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes. This family consists of several hypothetical bacterial proteins of unknown function, but that contain an SH-3 region. Family members include probable invasion-associated protein p60 that are conceptually translated from iap genes. The iap gene, which is regarded as a virulence-associated gene in L. monocytogenes, codes for a gene product that has murein-lytic activity and is involved in cell division. 56 matched cddid_all.tbl CDD pfam06348 pfam06348 399388 DUF1059 Protein of unknown function (DUF1059). This family consists of several short hypothetical archaeal proteins of unknown function. 56 matched cddid_all.tbl CDD pfam06350 pfam06350 461882 HSL_N Hormone-sensitive lipase (HSL) N-terminus. This family consists of several mammalian hormone-sensitive lipase (HSL) proteins (EC:3.1.1.-). Hormone-sensitive lipase, a key enzyme in fatty acid mobilization, overall energy homeostasis, and possibly steroidogenesis, is acutely controlled through reversible phosphorylation by catecholamines and insulin. 306 matched cddid_all.tbl CDD pfam06351 pfam06351 368854 Allene_ox_cyc Allene oxide cyclase. This family consists of several plant specific allene oxide cyclase proteins (EC:5.3.99.6). The allene oxide cyclase (AOC)-catalyzed step in jasmonate (JA) biosynthesis is important in the wound response of tomato. 175 matched cddid_all.tbl CDD pfam06353 pfam06353 461883 DUF1062 Protein of unknown function (DUF1062). This family consists of several hypothetical bacterial proteins of unknown function. 135 matched cddid_all.tbl CDD pfam06355 pfam06355 399391 Aegerolysin Aegerolysin. This family consists of several bacterial and fungal Aegerolysin-like proteins. It has been found that aegerolysin and ostreolysin are expressed during formation of primordia and fruiting bodies. It has been suggested that these haemolysins play an important role in initial phase of fungal fruiting. The bacterial members of this family are expressed during sporulation. Ostreolysin was found cytolytic to various erythrocytes and tumour cells. It forms transmembrane pores 4 nm in diameter. The activity is inhibited by total membrane lipids, and modulated by lysophosphatides. The potential use of aegerolysins is reviewed with special emphasis on their properties which would allow their use in therapeutics. Aegerolysin is part of the pleurotolysin pore-forming (Pleurotolysin) transporter superfamily. Member proteins assemble into a transmembrane pore complex. 131 matched cddid_all.tbl CDD pfam06356 pfam06356 428901 DUF1064 Protein of unknown function (DUF1064). This family consists of several phage and bacterial proteins of unknown function. 117 matched cddid_all.tbl CDD pfam06357 pfam06357 253691 Omega-toxin Omega-atracotoxin. This family consists of several Hadronyche versuta (Blue mountains funnel-web spider) specific omega-atracotoxin proteins. Omega-Atracotoxin-Hv1a is an insect-specific neurotoxin whose phylogenetic specificity derives from its ability to antagonize insect, but not vertebrate, voltage-gated calcium channels. Two spatially proximal residues, Asn(27) and Arg(35), form a contiguous molecular surface that is essential for toxin activity. It has been proposed that this surface of the beta-hairpin is a key site for interaction of the toxin with insect calcium channels. 37 matched cddid_all.tbl CDD pfam06358 pfam06358 283911 BNYVV_TGB3 Beet necrotic yellow vein virus, movement protein TGB3. This family is represented by Beet necrotic yellow vein virus movement protein TGB3 (also known as p15) which participates in the transport of viral RNA to the plasmodesmata. 111 matched cddid_all.tbl CDD pfam06360 pfam06360 399392 E_raikovi_mat Euplotes raikovi mating pheromone. This family consists of several Euplotes raikovi mating pheromone proteins. Diffusible polypeptide pheromones, which distinguish otherwise morphologically identical vegetative cell types from one another, are produced by some species of ciliates. In the marine sand-dwelling protozoan ciliate Euplotes raikovi, pheromone molecules promote the vegetative reproduction (mitogenic proliferation or growth) of the same cells from which they originate. As, understandably, such autocrine pheromone activity is primary to that of targeting and inducing a foreign cell to mate (paracrine functions), this finding provides an example of how the original function of a molecule can be obscured during evolution by the acquisition of a new one. 33 matched cddid_all.tbl CDD pfam06361 pfam06361 283912 RTBV_P12 Rice tungro bacilliform virus P12 protein. This family consists of several Rice tungro bacilliform virus P12 proteins. The function of this family is unknown. 110 matched cddid_all.tbl CDD pfam06362 pfam06362 115044 DUF1067 Protein of unknown function (DUF1067). This family consists of several hypothetical Mycobacterium leprae specific proteins. The function of this family is unknown. 97 matched cddid_all.tbl CDD pfam06363 pfam06363 368858 Picorna_P3A Picornaviridae P3A protein. This family consists of the P3A protein of picornaviridae. P3A has been identified as a genome-linked protein (VPg) and is involved in replication. 98 matched cddid_all.tbl CDD pfam06364 pfam06364 399393 DUF1068 Protein of unknown function (DUF1068). This family consists of several hypothetical plant proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown. 165 matched cddid_all.tbl CDD pfam06365 pfam06365 461884 CD34_antigen CD34/Podocalyxin family. This family consists of several mammalian CD34 antigen proteins. The CD34 antigen is a human leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. CD34 is a phosphoprotein. Activation of protein kinase C (PKC) has been found to enhance CD34 phosphorylation. This family contains several eukaryotic podocalyxin proteins. Podocalyxin is a major membrane protein of the glomerular epithelium and is thought to be involved in maintenance of the architecture of the foot processes and filtration slits characteriztic of this unique epithelium by virtue of its high negative charge. Podocalyxin functions as an anti-adhesin that maintains an open filtration pathway between neighbouring foot processes in the glomerular epithelium by charge repulsion. 211 matched cddid_all.tbl CDD pfam06366 pfam06366 428903 FlhE Flagellar protein FlhE. This family consists of several Enterobacterial FlhE flagellar proteins. The exact function of this family is unknown. 106 matched cddid_all.tbl CDD pfam06367 pfam06367 461885 Drf_FH3 Diaphanous FH3 Domain. This region is found in the Formin-like and and diaphanous proteins. 195 matched cddid_all.tbl CDD pfam06368 pfam06368 428905 Met_asp_mut_E Methylaspartate mutase E chain (MutE). This family consists of several methylaspartate mutase E chain proteins (EC:5.4.99.1). Glutamate mutase catalyzes the first step in the fermentation of glutamate by Clostridium tetanomorphum. This is an unusual isomerization in which L-glutamate is converted to threo-beta-methyl L-aspartate. 441 matched cddid_all.tbl CDD pfam06369 pfam06369 399397 Anemone_cytotox Sea anemone cytotoxic protein. Sea anemones are a rich source of cytotoxic proteins. Cytolysins comprise a group of more than 30 highly basic proteins with molecular masses of about 20 kDa. Cytolysins isolated from the sea anemone, Heteractis magnifica, include magnificalysin I (HMg I), magnificalysin II (HMg II) and Heteractis magnifica toxin (HMgtxn). These are highly homologous at their N-terminals. HMg I and II have molecular masses of approximately 19 kDa, and pI values of 9.4 and 10.0, respectively. Cytolysins isolated from other sea anemones Actinia tenebrosa (Tenebrosin-C, TN-C), Actinia equina (Equinatoxin, EqT) and Stichodactyla helianthus (ShC) exhibit pore-forming, haemolytic, cytotoxic, and heart stimulatory activities. 176 matched cddid_all.tbl CDD pfam06370 pfam06370 191504 DUF1069 Protein of unknown function (DUF1069). This family consists of several Maize streak virus 21.7 kDa proteins. The function of this family is unknown. 206 matched cddid_all.tbl CDD pfam06371 pfam06371 461886 Drf_GBD Diaphanous GTPase-binding Domain. This domain is bound to by GTP-attached Rho proteins, leading to activation of the Drf protein. 188 matched cddid_all.tbl CDD pfam06372 pfam06372 461887 Gemin6 Gemin6 Sm-like domain. This entry represents the N-terminal Sm-like domain from mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the pfam06003 complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles. 86 matched cddid_all.tbl CDD pfam06373 pfam06373 461888 CART Cocaine and amphetamine regulated transcript protein (CART). This family consists of several cocaine and amphetamine regulated transcript type I protein (CART) sequences. Cocaine and amphetamine regulated transcript (CART) peptide has been shown to be an anorectic peptide that inhibits both normal and starvation-induced feeding and completely blocks the feeding response induced by neuropeptide Y and regulated by leptin in the hypothalamus. The C-terminal part containing the three disulfide bridges is the biologically active part of the molecule affecting food intake. The solution structure of the active part of CART has a fold equivalent to other functionally distinct small proteins. CART consists mainly of turns and loops spanned by a compact framework composed by a few small stretches of antiparallel beta-sheet common to cystine knots. 70 matched cddid_all.tbl CDD pfam06374 pfam06374 428908 NDUF_C2 NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2). This family consists of several NADH-ubiquinone oxidoreductase subunit b14.5b proteins (EC:1.6.5.3). 109 matched cddid_all.tbl CDD pfam06375 pfam06375 461889 AP3D1 AP-3 complex subunit delta-1. AP-3 complex subunit delta-1 (AP3D1) is part of the AP-3 complex, an adaptor-related complex which is not clathrin- associated. The complex is associated with the Golgi region as well as more peripheral structures. AP3D1 is required for efficient transport of VSV-G (vesicular stomatitis virus glycoprotein) from the trans-Golgi network to the cell surface. 157 matched cddid_all.tbl CDD pfam06376 pfam06376 461890 AGP Arabinogalactan peptide. This entry represents the arabinogalactan peptide family found in plants. 35 matched cddid_all.tbl CDD pfam06377 pfam06377 428911 Adipokin_hormo Adipokinetic hormone. This family consists of several insect adipokinetic hormone as well as the related crustacean red pigment concentrating hormone. Flight activity of insects comprises one of the most intense biochemical processes known in nature, and therefore provides an attractive model system to study the hormonal regulation of metabolism during physical exercise. In long-distance flying insects, such as the migratory locust, both carbohydrate and lipid reserves are utilized as fuels for sustained flight activity. The mobilization of these energy stores in Locusta migratoria is mediated by three structurally related adipokinetic hormones (AKHs), which are all capable of stimulating the release of both carbohydrates and lipids from the fat body. 50 matched cddid_all.tbl CDD pfam06378 pfam06378 399403 DUF1071 Protein of unknown function (DUF1071). This family consists of several hypothetical bacterial and phage proteins of unknown function. 152 matched cddid_all.tbl CDD pfam06379 pfam06379 115061 RhaT L-rhamnose-proton symport protein (RhaT). This family consists of several bacterial L-rhamnose-proton symport protein (RhaT) sequences. 344 matched cddid_all.tbl CDD pfam06380 pfam06380 148156 DUF1072 Protein of unknown function (DUF1072). This family consists of several Barley yellow dwarf virus proteins of unknown function. 39 matched cddid_all.tbl CDD pfam06381 pfam06381 428912 DUF1073 Protein of unknown function (DUF1073). This family consists of several hypothetical bacterial proteins. The function of this family is unknown. 355 matched cddid_all.tbl CDD pfam06382 pfam06382 283927 Protamine_like Protamine and protamine like. This family consists of several insect proteins including protamine A (ProtA), protamine B (ProtB) and protamine-like protein 99C (Prtl99C) from Drosophila melanogaster. They contain a HMG-box and are involved in chromatin compaction during spermiogenesis. Prtl99C is a sperm chromatin-associated protein that is essential for male fertility. 125 matched cddid_all.tbl CDD pfam06384 pfam06384 399405 ICAT Beta-catenin-interacting protein ICAT. This family consists of several eukaryotic beta-catenin-interacting (ICAT) proteins. Beta-catenin is a multifunctional protein involved in both cell adhesion and transcriptional activation. Transcription mediated by the beta-catenin/Tcf complex is involved in embryological development and is upregulated in various cancers. ICAT selectively inhibits beta-catenin/Tcf binding in vivo, without disrupting beta-catenin/cadherin interactions. 76 matched cddid_all.tbl CDD pfam06385 pfam06385 283929 Baculo_LEF-11 Baculovirus LEF-11 protein. This family consists of several Baculovirus LEF-11 proteins. The exact function of this family is unknown although it has been shown that LEF-11 is required for viral DNA replication during the infection cycle. 93 matched cddid_all.tbl CDD pfam06386 pfam06386 461891 GvpL_GvpF Gas vesicle synthesis protein GvpL/GvpF. This family consists of several bacterial and archaeal gas vesicle synthesis protein (GvpL/GvpF) sequences. The exact function of this family is unknown. GvpL/GvpF qualify as possible candidates for nucleation proteins. Two hypothesized roles for these proteins are in initiation of gas vesicle synthesis and in determination of the curvature of the vesicle membrane. 243 matched cddid_all.tbl CDD pfam06387 pfam06387 461892 Calcyon D1 dopamine receptor-interacting protein (calcyon). This family consists of several D1 dopamine receptor-interacting (calcyon) proteins. D1/D5 dopamine receptors in the basal ganglia, hippocampus, and cerebral cortex modulate motor, reward, and cognitive behaviour. D1-like dopamine receptors likely modulate neocortical and hippocampal neuronal excitability and synaptic function via Ca(2+) as well as cAMP-dependent signaling. Defective calcyon proteins have been implicated in both attention-deficit/hyperactivity disorder (ADHD) and schizophrenia. 177 matched cddid_all.tbl CDD pfam06388 pfam06388 461893 DUF1075 Protein of unknown function (DUF1075). This family consists of several eukaryotic proteins of unknown function. 124 matched cddid_all.tbl CDD pfam06389 pfam06389 399409 Filo_VP24 Filovirus membrane-associated protein VP24. This family consists of several membrane-associated protein VP24 sequences from a variety of Ebola and Marburg viruses. The VP24 protein of Ebola virus is believed to be a secondary matrix protein and minor component of virions. VP24 possesses structural features commonly associated with viral matrix proteins and that VP24 may have a role in virus assembly and budding. 227 matched cddid_all.tbl CDD pfam06390 pfam06390 115071 NESP55 Neuroendocrine-specific golgi protein P55 (NESP55). This family consists of several mammalian neuroendocrine-specific golgi protein P55 (NESP55) sequences. NESP55 is a novel member of the chromogranin family and is a soluble, acidic, heat-stable secretory protein that is expressed exclusively in endocrine and nervous tissues, although less widely than chromogranins. 261 matched cddid_all.tbl CDD pfam06391 pfam06391 461894 MAT1 CDK-activating kinase assembly factor MAT1. MAT1 is an assembly/targeting factor for cyclin-dependent kinase-activating kinase (CAK), which interacts with the transcription factor TFIIH. The domain found to the N-terminal side of this domain is a C3HC4 RING finger. 202 matched cddid_all.tbl CDD pfam06392 pfam06392 368876 Asr Acid shock protein repeat. The Asr protein is synthesized as a precursor and the cleavage is essential for moderate to high acid tolerance. 22 matched cddid_all.tbl CDD pfam06393 pfam06393 428916 BID BH3 interacting domain (BID). BID is a member of the BCL-2 superfamily of proteins are key regulators of programmed cell death, hence this family is related to pfam00452. BID is a pro-apoptotic member of the Bcl-2 superfamily and as such posses the ability to target intracellular membranes and contains the BH3 death domain. The activity of BID is regulated by a Caspase 8-mediated cleavage event, exposing the BH3 domain and significantly changing the surface charge and hydrophobicity, which causes a change of cellular localization. 191 matched cddid_all.tbl CDD pfam06394 pfam06394 461895 Pepsin-I3 Pepsin inhibitor-3-like repeated domain. Pepsin inhibitor-3 consisting of two domains, each comprising an antiparallel beta-sheet flanked by an alpha-helix. In the enzyme-inhibitor complex, the N-terminal beta-strand of PI-3 pairs with one strand of the active site flap region of pepsin. The two domains are tandem repeats of sequence, and has therefore been termed repeated domain. 74 matched cddid_all.tbl CDD pfam06395 pfam06395 399412 CDC24 CDC24 Calponin. Is a calponin homology domain. 89 matched cddid_all.tbl CDD pfam06396 pfam06396 461896 AGTRAP Angiotensin II, type I receptor-associated protein (AGTRAP). This family consists of several angiotensin II, type I receptor-associated protein (AGTRAP) sequences. AGTRAP is known to interact specifically with the carboxyl-terminal cytoplasmic region of the angiotensin II type 1 (AT(1)) receptor to regulate different aspects of AT(1) receptor physiology. The function of this family is unclear. 148 matched cddid_all.tbl CDD pfam06397 pfam06397 283940 Desulfoferrod_N Desulfoferrodoxin, N-terminal domain. Most members of this family are small (approximately 36 amino acids) proteins that from homodimeric complexes. Each subunit contains a high-spin iron atom tetrahedrally bound to four cysteinyl sulphur atoms This family has a similar fold to the rubredoxin metal binding domain. It is also found as the N-terminal domain of desulfoferrodoxin, see (pfam01880). 36 matched cddid_all.tbl CDD pfam06398 pfam06398 399414 Pex24p Integral peroxisomal membrane peroxin. Peroxisomes play diverse roles in the cell, compartmentalising many activities related to lipid metabolism and functioning in the decomposition of toxic hydrogen peroxide. Sequence similarity was identified between two hypothetical proteins and the peroxin integral membrane protein Pex24p. 369 matched cddid_all.tbl CDD pfam06399 pfam06399 461897 GFRP GTP cyclohydrolase I feedback regulatory protein (GFRP). Tetrahydrobiopterin, the cofactor required for hydroxylation of aromatic amino acids regulates its own synthesis in via feedback inhibition of GTP cyclohydrolase I. This mechanism is mediated by the regulatory subunit called GTP cyclohydrolase I feedback regulatory protein (GFRP). 83 matched cddid_all.tbl CDD pfam06400 pfam06400 461898 Alpha-2-MRAP_N Alpha-2-macroglobulin RAP, N-terminal domain. The alpha-2-macroglobulin receptor-associated protein (RAP) is a intracellular glycoprotein that binds to the 2-macroglobulin receptor and other members of the low density lipoprotein receptor family. The protein inhibits binding of all currently known ligands of these receptors. The N-terminal domain is predominately alpha helical. Two different studies have provided conflicted domain boundaries. 123 matched cddid_all.tbl CDD pfam06401 pfam06401 461899 Alpha-2-MRAP_C Alpha-2-macroglobulin RAP, C-terminal domain. The alpha-2-macroglobulin receptor-associated protein (RAP) is a intracellular glycoprotein that binds to the 2-macroglobulin receptor and other members of the low density lipoprotein receptor family. The protein inhibits binding of all currently known ligands of these receptors. Two different studies have provided conflicted domain boundaries. 211 matched cddid_all.tbl CDD pfam06403 pfam06403 399418 Lamprin Lamprin. This family consists of several lamprin proteins from the Sea lamprey Petromyzon marinus. Lamprin, an insoluble non-collagen, non-elastin protein, is the major connective tissue component of the fibrillar extracellular matrix of lamprey annular cartilage. Although not generally homologous to any other protein, soluble lamprins contain a tandemly repeated peptide sequence (GGLGY) which is present in both silkmoth chorion proteins and spider dragline silk. Strong homologies to this repeat sequence are also present in several mammalian and avian elastins. It is thought that these proteins share a structural motif which promotes self-aggregation and fibril formation in proteins through interdigitation of hydrophobic side chains in beta-sheet/beta-turn structures, a motif that has been preserved in recognisable form over several hundred million years of evolution. 91 matched cddid_all.tbl CDD pfam06404 pfam06404 399419 PSK Phytosulfokine precursor protein (PSK). This family consists of several plant specific phytosulfokine precursor proteins. Phytosulfokines, are active as either a pentapeptide or a C-terminally truncated tetrapeptide. These compounds were first isolated because of their ability to stimulate cell division in somatic embryo cultures of Asparagus officinalis. 89 matched cddid_all.tbl CDD pfam06405 pfam06405 399420 RCC_reductase Red chlorophyll catabolite reductase (RCC reductase). This family consists of several red chlorophyll catabolite reductase (RCC reductase) proteins. Red chlorophyll catabolite (RCC) reductase (RCCR) and pheophorbide (Pheide) a oxygenase (PaO) catalyze the key reaction of chlorophyll catabolism, porphyrin macrocycle cleavage of Pheide a to a primary fluorescent catabolite (pFCC). 253 matched cddid_all.tbl CDD pfam06406 pfam06406 310773 StbA StbA protein. This family consists of several bacterial StbA plasmid stability proteins. 317 matched cddid_all.tbl CDD pfam06407 pfam06407 399421 BDV_P40 Borna disease virus P40 protein. This family consists of several Borna disease virus P40 proteins. Borna disease (BD) is a persistent viral infection of the central nervous system caused by the single-negative-strand, nonsegmented RNA Borna disease virus (BDV). P40 is known to be a nucleoprotein. 348 matched cddid_all.tbl CDD pfam06409 pfam06409 461900 NPIP Nuclear pore complex interacting protein (NPIP). This family consists of a series of primate specific nuclear pore complex interacting protein (NPIP) sequences. The function of this family is unknown but is well conserved from African apes to humans. 267 matched cddid_all.tbl CDD pfam06411 pfam06411 428923 HdeA HdeA/HdeB family. HdeA (hns-dependent expression protein A) is a single domain alpha-helical protein localized in the periplasmic space. HdeA is involved in acid resistance essential for infectivity of enteric bacterial pathogens. Functional studies demonstrate that HdeA is activated by a dimer-to-monomer transition at acidic pH, leading to suppression of aggregation by acid-denatured proteins. The gene encoding HdeA was initially identified as part of an operon regulated by the nucleoid protein H-NS. This family also contains HdeB. 92 matched cddid_all.tbl CDD pfam06412 pfam06412 428924 TraD Conjugal transfer protein TraD. This family contains bacterial TraD conjugal transfer proteins. Mutations in the TraD gene result in loss of transfer. 61 matched cddid_all.tbl CDD pfam06413 pfam06413 428925 Neugrin Neugrin. This family consists of several mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation. 218 matched cddid_all.tbl CDD pfam06414 pfam06414 428926 Zeta_toxin Zeta toxin. This family consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postregulational killing system in bacteria. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmids during cell division and kill cells that have lost the plasmid. 192 matched cddid_all.tbl CDD pfam06415 pfam06415 461901 iPGM_N BPG-independent PGAM N-terminus (iPGM_N). This family represents the N-terminal region of the 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (or phosphoglyceromutase or BPG-independent PGAM) protein (EC:5.4.2.1). The family is found in conjunction with pfam01676 (located in the C-terminal region of the protein). 217 matched cddid_all.tbl CDD pfam06416 pfam06416 368893 T3SS_NleG Effector protein NleG. Many bacterial pathogens deliver effector proteins into host cells via a type III secretion system. These effector proteins then alter the host cell's biology in ways that are advantageous to the pathogen. The NleG protein and its homologs form the largest family of effector proteins in the enterohemorrhagic Escherichia coli O157:H7, with 14 members identified in the Sakai strain alone. 113 matched cddid_all.tbl CDD pfam06417 pfam06417 461902 DUF1077 Protein of unknown function (DUF1077). This family consists of several hypothetical eukaryotic proteins of unknown function. 118 matched cddid_all.tbl CDD pfam06418 pfam06418 461903 CTP_synth_N CTP synthase N-terminus. This family consists of the N-terminal region of the CTP synthase protein (EC:6.3.4.2). This family is found in conjunction with pfam00117 located in the C-terminal region of the protein. CTP synthase catalyzes the synthesis of CTP from UTP by amination of the pyrimidine ring at the 4-position. 265 matched cddid_all.tbl CDD pfam06419 pfam06419 461904 COG6 Conserved oligomeric complex COG6. COG6 is a component of the conserved oligomeric golgi complex, which is composed of eight different subunits and is required for normal golgi morphology and localization. 611 matched cddid_all.tbl CDD pfam06420 pfam06420 428931 Mgm101p Mitochondrial genome maintenance MGM101. The mgm101 gene was identified as essential for maintenance of the mitochondrial genome in Saccharomyces cerevisiae. Based on its DNA-binding activity, and experimental work with a temperature-sensitive mgm101 mutant, it has been proposed that the mgm101 gene product performs an essential function in the repair of oxidatively damaged mitochondrial DNA. 170 matched cddid_all.tbl CDD pfam06421 pfam06421 461905 LepA_C GTP-binding protein LepA C-terminus. This family consists of the C-terminal region of several pro- and eukaryotic GTP-binding LepA proteins. 107 matched cddid_all.tbl CDD pfam06422 pfam06422 461906 PDR_CDR CDR ABC transporter. Corresponds to a region of the PDR/CDR subgroup of ABC transporters comprising extracellular loop 3, transmembrane segment 6 and linker region. 92 matched cddid_all.tbl CDD pfam06423 pfam06423 461907 GWT1 GWT1. Glycosylphosphatidylinositol (GPI) is a conserved post-translational modification to anchor cell surface proteins to plasma membrane in eukaryotes. GWT1 is involved in GPI anchor biosynthesis; it is required for inositol acylation in yeast. 138 matched cddid_all.tbl CDD pfam06424 pfam06424 461908 PRP1_N PRP1 splicing factor, N-terminal. This domain is specific to the N-terminal part of the prp1 splicing factor, which is involved in mRNA splicing (and possibly also poly(A)+ RNA nuclear export and cell cycle progression). This domain is specific to the N terminus of the RNA splicing factor encoded by prp1. It is involved in mRNA splicing and possibly also poly(A)and RNA nuclear export and cell cycle progression. 109 matched cddid_all.tbl CDD pfam06426 pfam06426 461909 SATase_N Serine acetyltransferase, N-terminal. The N-terminal domain of serine acetyltransferase has a sequence that is conserved in plants and bacteria. 104 matched cddid_all.tbl CDD pfam06427 pfam06427 461910 UDP-g_GGTase UDP-glucose:Glycoprotein Glucosyltransferase. This domain consists of 7 stranded beta-sandwiches found in UDP-glucose-glycoprotein glucosyltransferase-like proteins. UDP-g_GGTase is an important, central component of the QC system in the ER for checking that glycoproteins are folded correctly. This QC prevents incorrectly folded glycoproteins from leaving the ER. 109 matched cddid_all.tbl CDD pfam06428 pfam06428 428938 Sec2p GDP/GTP exchange factor Sec2p. In Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange factor for Sec4p, which is required for vesicular transport at the post-Golgi stage of yeast secretion. 92 matched cddid_all.tbl CDD pfam06429 pfam06429 428939 Flg_bbr_C Flagellar basal body rod FlgEFG protein C-terminal. This family consists of a number of C-terminal domains of unknown function. This domain seems to be specific to flagellar basal-body rod and flagellar hook proteins in which pfam00460 is often present at the extreme N terminus. 74 matched cddid_all.tbl CDD pfam06430 pfam06430 461911 L_lactis_RepB_C Lactococcus lactis RepB C-terminus. This family consists of the C-terminal region of RepB proteins from Lactococcus lactis (See pfam01051). 122 matched cddid_all.tbl CDD pfam06431 pfam06431 283968 Polyoma_lg_T_C Polyomavirus large T antigen C-terminus. 417 matched cddid_all.tbl CDD pfam06432 pfam06432 428940 GPI2 Phosphatidylinositol N-acetylglucosaminyltransferase. Glycosylphosphatidylinositol (GPI) represents an important anchoring molecule for cell surface proteins. The first step in its synthesis is the transfer of N-acetylglucosamine (GlcNAc) from UDP-N-acetylglucosamine to phosphatidylinositol (PI). This step involves products of three or four genes in both yeast (GPI1, GPI2 and GPI3) and mammals (GPI1, PIG A, PIG H and PIG C), respectively. 267 matched cddid_all.tbl CDD pfam06433 pfam06433 399440 Me-amine-dh_H Methylamine dehydrogenase heavy chain (MADH). Methylamine dehydrogenase (EC:1.4.99.3) a periplasmic quinoprotein found in several methyltrophic bacteria. Induced when grown on methylamine as a carbon source MADH catalyzes the oxidative deamination of amines to there corresponding aldehydes. MADH is a hetero- tetramer, comprised of two heavy chains (H) and two light chains (L). The H-chain forms a beta-propeller like structure. 343 matched cddid_all.tbl CDD pfam06434 pfam06434 461912 Aconitase_2_N Aconitate hydratase 2 N-terminus. This family represents the N-terminal region of several bacterial Aconitate hydratase 2 proteins and is found in conjunction with pfam00330. 204 matched cddid_all.tbl CDD pfam06435 pfam06435 283972 DUF1079 Repeat of unknown function (DUF1079). This family consists of several repeats of 31 residues in length and seems to be exclusive to Moraxella catarrhalis UspA proteins. The UspA1 and UspA2 proteins of Moraxella catarrhalis are structurally related and are exposed on the bacterial cell surface where can function adhesins. This family is commonly found with the pfam03895 family. 31 matched cddid_all.tbl CDD pfam06436 pfam06436 399442 Pneumovirus_M2 Pneumovirus matrix protein 2 (M2). This family consists of several Pneumovirus matrix glycoprotein M2 sequences. This family functions as a transcription processivity factor that is essential for virus replication. 155 matched cddid_all.tbl CDD pfam06437 pfam06437 428942 ISN1 IMP-specific 5'-nucleotidase. The Saccharomyces cerevisiae ISN1 (YOR155c) gene encodes an IMP-specific 5'-nucleotidase, which catalyzes degradation of IMP to inosine as part of the purine salvage pathway. 408 matched cddid_all.tbl CDD pfam06438 pfam06438 428943 HasA Heme-binding protein A (HasA). Free iron is limited in vertebrate hosts, thus an alternative to siderophores has been developed by pathogenic bacteria to access host iron bound in protein complexes. HasA is a secreted hemophore that has the ability to obtain iron from hemoglobin. Once bound to HasA, the heme is shuttled to the receptor HasR, which releases the heme into the bacterium. 194 matched cddid_all.tbl CDD pfam06439 pfam06439 399445 3keto-disac_hyd 3-keto-disaccharide hydrolase. This family has structural similarity to an endo-1,3-1,4-beta glucanase belonging to glycoside hydrolase family 16. A member containing this domain, BT2157 from B. thetaiotaomicron, hydrolyses 3-ketotrehalose during trehalose degradation that proceeds through a 3-keto-glycoside intermediate. Other members containing this domain are involved in disaccharide catabolism with 3-ketoglycoside intermediates. 182 matched cddid_all.tbl CDD pfam06440 pfam06440 428944 DNA_pol3_theta DNA polymerase III, theta subunit. DNA polymerase III (EC 2.7.7.7) is comprised of three tightly associated subunits, alpha, epsilon and theta. This family contains the theta subunit. The structure of the theta subunit shows that the N-terminal two thirds is comprised of three helices while the C-terminal third is disordered. The function of the theta subunit is poorly understood, but the interaction of the theta subunit with the epsilon subunit is thought to enhance the 3' to 5' exonucleolytic proofreading activity of epsilon. 70 matched cddid_all.tbl CDD pfam06441 pfam06441 461913 EHN Epoxide hydrolase N terminus. This family represents the N-terminal region of the eukaryotic epoxide hydrolase protein. Epoxide hydrolases (EC:3.3.2.3) comprise a group of functionally related enzymes that catalyze the addition of water to oxirane compounds (epoxides), thereby usually generating vicinal trans-diols. EHs have been found in all types of living organizms, including mammals, invertebrates, plants, fungi and bacteria. In animals, the major interest in EH is directed towards their detoxification capacity for epoxides since they are important safeguards against the cytotoxic and genotoxic potential of oxirane derivatives that are often reactive electrophiles because of the high tension of the three-membered ring system and the strong polarization of the C--O bonds. This is of significant relevance because epoxides are frequent intermediary metabolites which arise during the biotransformation of foreign compounds. This family is often found in conjunction with pfam00561. 106 matched cddid_all.tbl CDD pfam06442 pfam06442 368910 DHFR_2 R67 dihydrofolate reductase. R67 dihydrofolate reductase is a plasmid encoded enzyme that provides resistance to the antibacterial drug trimethoprim. The R67 dihydrofolate reductase does not share significant similarity to the chromosomal encoded dihydrofolate reductase. 78 matched cddid_all.tbl CDD pfam06443 pfam06443 115120 SEF14_adhesin SEF14-like adhesin. Family of enterotoxigenic bacterial adhesins. 165 matched cddid_all.tbl CDD pfam06444 pfam06444 461914 NADH_dehy_S2_C NADH dehydrogenase subunit 2 C-terminus. This family consists of the C-terminal region specific to the eukaryotic NADH dehydrogenase subunit 2 protein and is found in conjunction with pfam00361. 51 matched cddid_all.tbl CDD pfam06445 pfam06445 428947 GyrI-like GyrI-like small molecule binding domain. This family contains the small molecule binding domain of a number of different bacterial transcription activators. This family also contains DNA gyrase inhibitors. The GyrI superfamily contains a diad of the SHS2 module, adapted for small-molecule binding. The GyrI superfamily includes a family of secreted forms that is found only in animals and the bacterial pathogen Leptospira. 153 matched cddid_all.tbl CDD pfam06446 pfam06446 461915 Hepcidin Hepcidin. Hepcidin is a antibacterial and antifungal protein expressed in the liver and is also a signaling molecule in iron metabolism. The hepcidin protein is cysteine-rich and forms a distorted beta-sheet with an unusual disulphide bond found at the turn of the hairpin. 53 matched cddid_all.tbl CDD pfam06448 pfam06448 461916 DUF1081 Domain of Unknown Function (DUF1081). This region is found in Apolipophorin proteins. 112 matched cddid_all.tbl CDD pfam06449 pfam06449 368914 YMF19_C ATP synthase YMF19, C-terminal. This domain represents the C-terminal region of YMF19 of the F0 complex of mitochondrial F-ATPases from plants. This family is found in conjunction with pfam02326. 51 matched cddid_all.tbl CDD pfam06450 pfam06450 283984 NhaB Bacterial Na+/H+ antiporter B (NhaB). This family consists of several bacterial Na+/H+ antiporter B (NhaB) proteins. The exact function of this family is unknown. 515 matched cddid_all.tbl CDD pfam06451 pfam06451 368915 Moricin Moricin. Moricin is a antibacterial peptide that is highly basic. The structure of moricin reveals that it is comprised of a long alpha-helix. The N-terminus of the helix is amphipathic, and the C-terminus of the helix is predominately hydrophobic. The amphipathic N-terminal segment of the alpha- helix is mainly responsible for the increase in permeability of the bacterial membrane which kills the bacteria. 41 matched cddid_all.tbl CDD pfam06452 pfam06452 428950 CBM9_1 Carbohydrate family 9 binding domain-like. CBM9_1 is a C-terminal domain on bacterial xylanase proteins, and it is tandemly repeated in a number of family-members. The CBM9 module binds to amorphous and crystalline cellulose and a range of soluble di- and monosaccharides as well as to cello- and xylo- oligomers of different degrees of polymerization. Comparison of the glucose and cellobiose complexes during crystallization reveals surprising differences in binding of these two substrates by CBM9-2. Cellobiose was found to bind in a distinct orientation from glucose, while still maintaining optimal stacking and electrostatic interactions with the reducing end sugar. 180 matched cddid_all.tbl CDD pfam06453 pfam06453 115129 LT-IIB Type II heat-labile enterotoxin, B subunit (LT-IIB). Family of B subunits from the type II heat-labile enterotoxin. The B subunits form a pentameric ring, which interacts with one A subunit. Thus, the structural arrangement of type I and type II heat-labile enterotoxins are very similar. 122 matched cddid_all.tbl CDD pfam06454 pfam06454 399452 THH1_TOM1-3_dom THH1/TOM1/TOM3 domain. This domain is found in plant proteins including THH1/TOM1/TOM3 from Arabidopsis. TOM1 and TOM3 are transmembrane proteins necessary for the efficient multiplication of tobamoviruses. THH1 supports tobamovirus multiplication, but to a lesser extent than TOM1 and TOM3. Members containing this domain are part of the GPCR superfamily and involved in stress tolerance. 271 matched cddid_all.tbl CDD pfam06455 pfam06455 368917 NADH5_C NADH dehydrogenase subunit 5 C-terminus. This family represents the C-terminal region of several NADH dehydrogenase subunit 5 proteins and is found in conjunction with pfam00361 and pfam00662. 181 matched cddid_all.tbl CDD pfam06456 pfam06456 399453 Arfaptin Arfaptin-like domain. Arfaptin interacts with ARF1, a small GTPase involved in vesicle budding at the Golgi complex and immature secretory granules. The structure of arfaptin shows that upon binding to a small GTPase, arfaptin forms an elongated, crescent-shaped dimer of three-helix coiled-coils. The N-terminal region of ICA69 is similar to arfaptin. 207 matched cddid_all.tbl CDD pfam06457 pfam06457 115133 Ectatomin Ectatomin. Ectatomin is a toxic component from the Ectatomma tuberculatum ant venom. It is comprised of two subunits, A and B, which are homologous. The structure of ectatomin reveals that each subunit is comprised of two helices and a connecting hinge region, the forms a hairpin structure that is stabilized by disulphide bridges. The two hinges are connected by a disulphide bond. 34 matched cddid_all.tbl CDD pfam06458 pfam06458 461917 MucBP MucBP domain. The MucBP (MUCin-Binding Protein) domain is found in a wide variety of bacterial proteins, in several repeats. The domain is found in bacterial peptidoglycan bound proteins and is often found in conjunction with pfam00746 and pfam00560. 65 matched cddid_all.tbl CDD pfam06459 pfam06459 461918 RR_TM4-6 Ryanodine Receptor TM 4-6. This region covers TM regions 4-6 of the ryanodine receptor 1 family. 282 matched cddid_all.tbl CDD pfam06460 pfam06460 461919 CoV_Methyltr_2 Coronavirus 2'-O-methyltransferase. This domain covers the NSP16 region of the coronavirus polyprotein. The SARS-CoV RNA cap SAM-dependent (nucleoside-2'-O-)-methyltransferase (2'-O-MTase) is a heterodimer comprising SARS-CoV nsp10 and nsp16. When bound to nsp10, nsp16 is active as a type-0 RNA cap-dependent 2'-O-MTase, ie., active only when the cap guanine is methylated at its N7 position. Nsp10 binds to nsp16 through an activation surface area in nsp10, and the resulting complex exhibits RNA cap (nucleoside-2'-O)-methyltransferase activity. Nsp10 is a double zinc finger protein together with nsp4, nsp5, nsp12, nsp14, and nsp16, nsp10 has been found to be essential in the assembly of a functional replication/transcription complex. Nsp16 adopts a typical fold of the S-adenosylmethionine-dependent methyltransferase (SAM) family as defined initially for the catechol O-MTase but it lacks several elements of the canonical MTase fold, such as helices B and C. The nsp16 topology matches those of dengue virus NS5 N-terminal domain and of vaccinia virus VP39 MTases. 296 matched cddid_all.tbl CDD pfam06461 pfam06461 461920 CHDII_SANT-like CHD subfamily II, SANT-like domain. CHD proteins (name derived from the presence of a Chromodomain, SWI2/SNF2 ATPase/Helicase and a motif with sequence similarity to a DNA)binding domain) are ATP-dependent chromatin remodelers found in plant and animals. In eukaryotes, there are three subfamilies, I, II and III. This domain is found in members of subfamily II which play a role in repression of genes involved in developmental regulation, including Mi-2 from Drosophila melanogaster, CHD3/4/5 from animals and PICKLE (a CHD3/4-related protein) from Arabidopsis. Sequence analysis revealed that this domain has a considerable similarity to SANT domains suggesting that it fold into this type of domain and it is integral to the DNA binding domain of CHD remodelers in subfamily II. 137 matched cddid_all.tbl CDD pfam06462 pfam06462 461921 Hyd_WA Propeller. Tectonins I and II are two dominant proteins in the nuclei and nuclear matrix from plasmodia of Physarum polycephalum (Slime mold) and both proteins contain six tandem repeats that are each 33-37 amino acids in length. Homologous repeats are found in L-6, a bacterial lipopolysaccharide-binding lectin from horseshoe crab hemocytes. The repetitive sequences of the tectonins and L-6 are reminiscent of the WD repeats of the beta-subunit of G proteins, suggesting that they form beta-propeller domains. The tectonins may be lectins that function as part of a transmembrane signalling complex during phagocytosis. Tectonin beta-propeller repeat-containing protein 1 (TECPR1) has a critical function during autophagosome maturation and autophagosome-lysosome fusion. 30 matched cddid_all.tbl CDD pfam06463 pfam06463 428955 Mob_synth_C Molybdenum Cofactor Synthesis C. This region contains two iron-sulphur (3Fe-4S) binding sites. Mutations in this region of Swiss:O14940 cause MOCOD (Molybdenum Co-Factor Deficiency) type A. 127 matched cddid_all.tbl CDD pfam06464 pfam06464 368923 DMAP_binding DMAP1-binding Domain. This domain binds DMAP1, a transcriptional co-repressor. 104 matched cddid_all.tbl CDD pfam06465 pfam06465 461922 DUF1087 CHD subfamily II, DUF1087. This domain is found in chromatin remodelling factors (CHDs) from subfamily II including CHD3/4/5 from animals and PICKLE. from Arabidopsis. The exact function is, as yet, unknown. 60 matched cddid_all.tbl CDD pfam06466 pfam06466 461923 PCAF_N PCAF (P300/CBP-associated factor) N-terminal domain. This region is spliced out of Swiss:Q92830 isoform 2. It is predicted to be of a mixed alpha/beta fold - though predominantly helical. 249 matched cddid_all.tbl CDD pfam06467 pfam06467 428958 zf-FCS MYM-type Zinc finger with FCS sequence motif. MYM-type zinc fingers were identified in MYM family proteins. Human protein Swiss:Q14202 is involved in a chromosomal translocation and may be responsible for X-linked retardation in XQ13.1. Swiss:Q9UBW7 is also involved in disease. In myeloproliferative disorders it is fused to FGF receptor 1; in atypical myeloproliferative disorders it is rearranged. Members of the family generally are involved in development. This Zn-finger domain functions as a transcriptional trans-activator of late vaccinia viral genes, and orthologues are also found in all nucleocytoplasmic large DNA viruses, NCLDV. This domain is also found fused to the C termini of recombinases from certain prokaryotic transposons. 40 matched cddid_all.tbl CDD pfam06468 pfam06468 461924 Spond_N Spondin_N. This conserved region is found at the in the N-terminal half of several Spondin proteins. Spondins are involved in patterning axonal growth trajectory through either inhibiting or promoting adhesion of embryonic nerve cells. 192 matched cddid_all.tbl CDD pfam06469 pfam06469 461925 DUF1088 Neurobeachin-like, DUF1088. This domain is found in the neurobeachins (NBEAs) and BEACH domain containing proteins (BDCPs). NBEAS are localized near Golgi apparatus and is involved in vesicular trafficking, intracellular transport, membrane dynamics, endosomal recycling, and receptor signalling. BDCPs are associated with lysosome size, apoptosis, autophagy, granule size, or synapse formation. Mutations in this domain have been related to autosomal recessively inherited lipopolysaccharide-responsive beige-like anchor (LRBA) protein deficiency, responsible for common variable immunodeficiency (CVID) and autoimmune lymphoproliferative syndrome (ALPS). NBEAs deficiency may induce spine loss with defects in synaptic efficacy and plasticity, being associated with autism spectrum disorder (ASD) and ASD-related syndromes. 168 matched cddid_all.tbl CDD pfam06470 pfam06470 461926 SMC_hinge SMC proteins Flexible Hinge Domain. This family represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction. 116 matched cddid_all.tbl CDD pfam06471 pfam06471 399465 CoV_ExoN Coronavirus proofreading exoribonuclease. This region of coronavirus polyproteins encodes the NSP14 protein. Its N-terminal exoribonuclease (ExoN) domain plays a proofreading role for prevention of lethal mutagenesis, and the C-terminal domain functions as a (guanine-N7) methyl transferase (N7-MTase) for mRNA capping. NSP14 forms the nsp14-nsp10 complex involved in RNA viral proofreading. 515 matched cddid_all.tbl CDD pfam06472 pfam06472 399466 ABC_membrane_2 ABC transporter transmembrane region 2. This domain covers the transmembrane of a small family of ABC transporters and shares sequence similarity with pfam00664. Mutations in this domain in Swiss:P28288 are believed responsible for Zellweger Syndrome-2; mutations in Swiss:P33897 are responsible for recessive X-linked adrenoleukodystrophy. A Saccharomyces cerevisiae homolog is involved in the import of long-chain fatty acids. 269 matched cddid_all.tbl CDD pfam06473 pfam06473 461927 FGF-BP1 FGF binding protein 1 (FGF-BP1). This family consists of several mammalian FGF binding protein 1. Fibroblast growth factors (FGFs) play important roles during fetal and embryonic development. Fibroblast growth factor-binding protein (FGF-BP) 1 is a secreted protein that can bind fibroblast growth factors (FGFs) 1 and 2. 229 matched cddid_all.tbl CDD pfam06474 pfam06474 428963 MLTD_N MltD lipid attachment motif. This short motif is a lipid attachment site. 34 matched cddid_all.tbl CDD pfam06475 pfam06475 428964 Glycolipid_bind Putative glycolipid-binding. This family has a novel fold known as a spiral beta-roll, consisting of a 15-stranded beta sheet wrapped around a single alpha helix. It forms dimers. It has some structural similarity to the E. coli lipoprotein localization factors LolA and LolB. Its structure suggests that it may have a role in glycolipid binding. Its genomic context supports a role in glycolipid metabolism. 178 matched cddid_all.tbl CDD pfam06476 pfam06476 428965 DUF1090 Protein of unknown function (DUF1090). This family consists of several bacterial proteins of unknown function and is known as YqjC in E. coli. 109 matched cddid_all.tbl CDD pfam06477 pfam06477 461928 DUF1091 Protein of unknown function (DUF1091). This is a family of uncharacterized proteins. Based on its distant similarity to pfam02221 and conserved pattern of cysteine residues it is possible that these domains are also lipid binding. 83 matched cddid_all.tbl CDD pfam06478 pfam06478 461929 CoV_RPol_N Coronavirus RNA-dependent RNA polymerase, N-terminal. This family covers the N-terminal region of the coronavirus RNA-directed RNA Polymerase which corresponds to the nonstructural protein 12 (NSP12) produced by cleavage of ORF1b. NSP12 contains a polymerase domain that assumes a structure resembling a cupped 'right hand', similar to other polymerases, containing a fingers domain, a palm domain and a thumb domain. Coronavirus NSP12 also contains a nidovirus-unique N-terminal extension that possesses a kinase-like fold allowing the binding of NSP12 to NSP7 and NSP8. NSP12 possesses some minimal activity on its own, but the addition of the NSP7 and NSP8 co-factors greatly stimulates polymerase activity. 353 matched cddid_all.tbl CDD pfam06479 pfam06479 461930 Ribonuc_2-5A Ribonuclease 2-5A. This domain is a endoribonuclease. Specifically it cleaves an intron from Hac1 mRNA in humans, which causes it to be much more efficiently translated. 127 matched cddid_all.tbl CDD pfam06480 pfam06480 377663 FtsH_ext FtsH Extracellular. This domain is found in the FtsH family of proteins. FtsH is the only membrane-bound ATP-dependent protease universally conserved in prokaryotes. It only efficiently degrades proteins that have a low thermodynamic stability - e.g. it lacks robust unfoldase activity. This feature may be key and implies that this could be a criterion for degrading a protein. In Oenococcus oeni FtsH is involved in protection against environmental stress, and shows increased expression under heat or osmotic stress. These two lines of evidence suggest that it is a fundamental prokaryotic self-protection mechanism that checks if proteins are correctly folded (personal obs: Yeats C). The precise function of this N-terminal region is unclear. 103 matched cddid_all.tbl CDD pfam06481 pfam06481 428969 COX_ARM COX Aromatic Rich Motif. COX2 (Cytochrome O ubiquinol OXidase 2) is a major component of the respiratory complex during vegetative growth. It transfers electrons from a quinol to the binuclear centre of the catalytic subunit 1. The function of this region is not known. 46 matched cddid_all.tbl CDD pfam06482 pfam06482 461931 Endostatin Collagenase NC10 and Endostatin. NC10 stands for Non-helical region 10 and is taken from Swiss:P39059. A mutation in this region in Swiss:P39060 is associated with an increased risk of prostrate cancer. This domain is cleaved from the precursor and forms endostatin. Endostatin is a key tumour suppressor and has been used highly successfully to treat cancer. It is a potent angiogenesis inhibitor. Endostatin also binds a zinc ion near the N-terminus; this is likely to be of structural rather than functional importance according to. 169 matched cddid_all.tbl CDD pfam06483 pfam06483 368936 ChiC Chitinase C. This ~170 aa region is found at the C-terminus of pfam00704. 174 matched cddid_all.tbl CDD pfam06484 pfam06484 461932 Ten_N Teneurin Intracellular Region. This family is found in the intracellular N-terminal region of the Teneurin family of proteins. These proteins are 'pair-rule' genes and are involved in tissue patterning, specifically probably neural patterning. The intracellular domain is cleaved in response to homophilic interaction of the extracellular domain, and translocates to the nucleus. Here it probably carries out to some transcriptional regulatory activity. The length of this region and the conservation suggests that there may be two structural domains here (personal obs:C Yeats). 367 matched cddid_all.tbl CDD pfam06485 pfam06485 461933 Tab2-like_N RNA-binding protein Tab2/Atab2 N terminal. This is the N-terminal domain of proteins from photosynthetic organizms including plants and cyanobacteria, such as Tab2 proteins. Tab2 was first identified in Chlamydomonas reinhardtii as a RNA binding protein required for translation of the chloroplast PsaB photosystem I subunit. Later, the Tab2 homolog (ATAB2) from Arabidopsis was found involved in the signalling pathway of light-controlled synthesis of photosystem proteins during early plant development, presumably functioning as an activator of translation with targets at PSI and PSII. 55 matched cddid_all.tbl CDD pfam06486 pfam06486 428973 DUF1093 Protein of unknown function (DUF1093). This family consists of several hypothetical bacterial proteins of unknown function. 81 matched cddid_all.tbl CDD pfam06487 pfam06487 461934 SAP18 Sin3 associated polypeptide p18 (SAP18). This family consists of several eukaryotic Sin3 associated polypeptide p18 (SAP18) sequences. SAP18 is known to be a component of the Sin3-containing complex which is responsible for the repression of transcription via the modification of histone polypeptides. SAP18 is also present in the ASAP complex which is thought to be involved in the regulation of splicing during the execution of programmed cell death. 123 matched cddid_all.tbl CDD pfam06488 pfam06488 461935 L_lac_phage_MSP Phage tail tube protein. This is a family of Siphoviridae phage tail tube proteins including several from Lactococcus lactis. 218 matched cddid_all.tbl CDD pfam06489 pfam06489 399480 Orthopox_A49R Orthopoxvirus A49R protein. This family consists of several Orthopoxvirus A49R proteins. The function of this family is unknown. 150 matched cddid_all.tbl CDD pfam06490 pfam06490 428975 FleQ Flagellar regulatory protein FleQ. This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators that are involved in regulation of flagellar motility e.g. FleQ in Pseudomonas aeruginosa. It is clearly related to pfam00072, but lacks the conserved aspartate residue that undergoes phosphorylation in the classic two-component system response regulator (pfam00072). 108 matched cddid_all.tbl CDD pfam06491 pfam06491 428976 Disulph_isomer Disulphide isomerase. This family of proteins has disulphide isomerase activity, EC:5.3.4.1. It has a similar fold to thioredoxin, with an alpha-beta-alpha-beta-alpha-beta-beta-alpha topology. It has a conserved CGC motif in the loop immediately downstream of the first beta strand. This motif is essential for activity. 136 matched cddid_all.tbl CDD pfam06493 pfam06493 368941 DUF1096 Protein of unknown function (DUF1096). This family represents the N-terminal region of several proteins found in C. elegans. The family is often found with pfam02363. 52 matched cddid_all.tbl CDD pfam06495 pfam06495 253769 Transformer Fruit fly transformer protein. This family consists of transformer proteins from several Drosophila species and also from Ceratitis capitata (Mediterranean fruit fly). The transformer locus (tra) produces an RNA processing protein that alternatively splices the doublesex pre-mRNA in the sex determination hierarchy of Drosophila melanogaster. 182 matched cddid_all.tbl CDD pfam06496 pfam06496 428977 DUF1097 Protein of unknown function (DUF1097). This family consists of several bacterial putative membrane proteins. 140 matched cddid_all.tbl CDD pfam06497 pfam06497 284024 Baculo_Ac102 Baculovirus Ac102. This family of baculovirus proteins is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV) Ac102. Nuclear actin is critical for AcMNPV progeny production, and Ac102 plays an essential role in actin translocation to the nucleus. It plays a role in regulating nuclear actin polymerization as well as the morphogenesis and spatial distribution of viral capsid structures in the host nucleus. 99 matched cddid_all.tbl CDD pfam06500 pfam06500 428978 FrsA-like Esterase FrsA-like. The FrsA-like family includes FrsA, an esterase found to have the alpha/beta-hydrolase fold. t also includes the hydrolytic polyketide shortening protein Ayg1 from fungi, 2,6-dihydropseudooxynicotine hydrolase from Paenarthrobacter nicotinovorans and Fus2 from Gibberella species. The enzyme 2,6-dihydroxy-pseudo-oxynicotine hydrolase is involved in the nicotine-degradation pathway of Arthrobacter nicotinovorans. Fus2 is part of the gene cluster that mediates the biosynthesis of the mycotoxin fusarin C. Fus2 catalyzes closure of the 2-pyrrolidone ring of the intermediate 20-hydroxy-prefusarin to form another intermediate, 20-hydroxy-fusarin, which is then oxidized by Fus8. 414 matched cddid_all.tbl CDD pfam06501 pfam06501 253772 Herpes_U55 Human herpesvirus U55 protein. This family consists of several human herpesvirus U55 proteins. The function of this family is unknown. 432 matched cddid_all.tbl CDD pfam06502 pfam06502 115174 Equine_IAV_S2 Equine infectious anaemia virus S2 protein. This family consists of several equine infectious anaemia virus S2 proteins. The function of this family is unknown. 67 matched cddid_all.tbl CDD pfam06503 pfam06503 284026 DUF1101 Protein of unknown function (DUF1101). This family consists of several hypothetical Fijivirus proteins of unknown function. 360 matched cddid_all.tbl CDD pfam06504 pfam06504 399484 RepC Replication protein C (RepC). This family consists of several bacterial replication protein C (RepC) sequences. 273 matched cddid_all.tbl CDD pfam06505 pfam06505 428979 XylR_N Activator of aromatic catabolism. This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators in several proteobacteria, including activators of phenol degradation such as XylR. It is found adjacent to pfam02830. 100 matched cddid_all.tbl CDD pfam06506 pfam06506 428980 PrpR_N Propionate catabolism activator. This domain is found at the N terminus of several sigma54- dependent transcriptional activators including PrpR, which activates catabolism of propionate. 165 matched cddid_all.tbl CDD pfam06507 pfam06507 428981 Auxin_resp Auxin response factor. A conserved region of auxin-responsive transcription factors. 83 matched cddid_all.tbl CDD pfam06508 pfam06508 428982 QueC Queuosine biosynthesis protein QueC. This family of proteins participate in the biosynthesis of 7-carboxy-7-deazaguanine. They catalyze the conversion of 7-deaza-7-carboxyguanine to preQ0. 210 matched cddid_all.tbl CDD pfam06510 pfam06510 368946 DUF1102 Protein of unknown function (DUF1102). This family consists of several hypothetical archaeal proteins of unknown function. 141 matched cddid_all.tbl CDD pfam06511 pfam06511 399488 T3SS_TC Type III secretion systems tip complex components. This family consists of several invasion plasmid antigen IpaD proteins found in Shigella as well as homologs such as SipD from Salmonella and BipD from Burkholderia. Gram-negative bacteria use type III secretion systems (T3SSs) as protein transport devices for injecting virulence effector proteins into eukaryotic cells during infection. T3SSs consist of a needle complex (NC) and a tip complex (TC). In Shigella the TC is composed of two proteins, each essential to host cell sensing: IpaD and IpaB. IpaD is hydrophilic and required for tip recruitment of the hydrophobic proteins IpaB and IpaC, which later form the pore in host cell membranes. 355 matched cddid_all.tbl CDD pfam06512 pfam06512 461936 Na_trans_assoc Sodium ion transport-associated. Members of this family contain a region found exclusively in eukaryotic sodium channels or their subunits, many of which are voltage-gated. Members very often also contain between one and four copies of pfam00520 and, less often, one copy of pfam00612. 195 matched cddid_all.tbl CDD pfam06513 pfam06513 115185 DUF1103 Repeat of unknown function (DUF1103). This family consists of several repeats of around 30 residues in length which are found specifically in mature-parasite-infected erythrocyte surface antigen proteins from Plasmodium falciparum. This family often found in conjunction with pfam00226. 215 matched cddid_all.tbl CDD pfam06514 pfam06514 428984 PsbU Photosystem II 12 kDa extrinsic protein (PsbU). This family consists of several photosystem II 12 kDa extrinsic protein (PsbU) proteins from cyanobacteria and algae. PsbU is an extrinsic protein of the photosystem II complex of cyanobacteria and red algae. PsbU is known to stabilize the oxygen-evolving machinery of the photosystem II complex against heat-induced inactivation. This family appears to be related to the Helix-hairpin-helix domain. 93 matched cddid_all.tbl CDD pfam06515 pfam06515 115187 BDV_P10 Borna disease virus P10 protein. This family consists of several Borna disease virus P10 (or X) proteins. Borna disease virus (BDV) is unique among the non-segmented negative-strand RNA viruses of animals and man because it transcribes and replicates its genome in the nucleus of the infected cell. It has been suggested that the p10 protein plays a role in viral RNA synthesis or ribonucleoprotein transport. 87 matched cddid_all.tbl CDD pfam06516 pfam06516 428985 NUP Purine nucleoside permease (NUP). This family consists of several purine nucleoside permease from both bacteria and fungi. 304 matched cddid_all.tbl CDD pfam06517 pfam06517 284037 Orthopox_A43R Orthopoxvirus A43R protein. This family consists of several Orthopoxvirus A43R proteins. The function of this family is unknown. 195 matched cddid_all.tbl CDD pfam06518 pfam06518 428986 DUF1104 Protein of unknown function (DUF1104). This family consists of several hypothetical proteins of unknown function which appear to be found largely in Helicobacter pylori. The structure of HP0721 protein consists of a bundle of four alpha-helices connected by loops and stabilized by hydrophobic interactions. It has been suggested that this protein might represent a novel H. pylori. 83 matched cddid_all.tbl CDD pfam06519 pfam06519 399492 TolA TolA C-terminal. This family consists of several bacterial TolA proteins as well as two eukaryotic proteins of unknown function. Tol proteins are involved in the translocation of group A colicins. Colicins are bacterial protein toxins, which are active against Escherichia coli and other related species (See pfam01024). TolA is anchored to the cytoplasmic membrane by a single membrane spanning segment near the N-terminus, leaving most of the protein exposed to the periplasm. 94 matched cddid_all.tbl CDD pfam06521 pfam06521 399493 PAR1 PAR1 protein. This family consists of several plant specific PAR1 proteins from Nicotiana tabacum and Arabidopsis thaliana. The function of this family is unknown. 156 matched cddid_all.tbl CDD pfam06522 pfam06522 461937 B12D NADH-ubiquinone reductase complex 1 MLRQ subunit. The MLRQ subunit of mitochondrial NADH-ubiquinone reductase complex I is nuclear and is found in plants, insects, fungi and higher metazoans. It appears to act within the membrane and, in mammals, is highly expressed in muscle and neural tissue, indicative of a role in ATP generation. 69 matched cddid_all.tbl CDD pfam06523 pfam06523 115195 DUF1106 Protein of unknown function (DUF1106). This family consists of several hypothetical bacterial proteins found in Escherichia coli and Citrobacter rodentium. The function of this family is unknown. 91 matched cddid_all.tbl CDD pfam06524 pfam06524 368953 NOA36 NOA36 protein. This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown. 306 matched cddid_all.tbl CDD pfam06525 pfam06525 310845 SoxE Sulfocyanin (SoxE) domain. This family consists of several archaeal sulfocyanin (or blue copper protein) sequences from a number of Sulfolobus species. 149 matched cddid_all.tbl CDD pfam06526 pfam06526 428988 DUF1107 Protein of unknown function (DUF1107). This family consists of several short, hypothetical bacterial proteins of unknown function. 63 matched cddid_all.tbl CDD pfam06527 pfam06527 461938 TniQ TniQ. This family consists of several bacterial TniQ proteins. TniQ along with TniA and B is involved in the transposition of the mercury-resistance transposon Tn5053 which carries the mer operon. It has been suggested that the tni genes are involved in the dissemination of integrons. 143 matched cddid_all.tbl CDD pfam06528 pfam06528 428990 Phage_P2_GpE Phage P2 GpE. This family consists of several phage and bacterial proteins which are closely related to the GpE tail protein from Phage P2. 37 matched cddid_all.tbl CDD pfam06529 pfam06529 368956 Vert_IL3-reg_TF Vertebrate interleukin-3 regulated transcription factor. This family includes vertebrate transcription factors, some of which are regulated by IL-3/adenovirus E4 promoter binding protein. Others were found to strongly repress transcription in a DNA-binding-site-dependent manner. 332 matched cddid_all.tbl CDD pfam06530 pfam06530 428991 Phage_antitermQ Phage antitermination protein Q. This family consists of several phage antitermination protein Q and related bacterial sequences. Antiterminator proteins control gene expression by recognising control signals near the promoter and preventing transcriptional termination which would otherwise occur at sites that may be a long way downstream. 118 matched cddid_all.tbl CDD pfam06531 pfam06531 368958 DUF1108 Protein of unknown function (DUF1108). This family consists of several bacterial proteins from Staphylococcus aureus as well as a number of phage proteins. The function of this family is unknown. 84 matched cddid_all.tbl CDD pfam06532 pfam06532 428992 NrsF Negative regulator of sigma F. This family includes CC3252 (NrsF- Negative regulator of sigma F) from Caulobacter crescentus, which is proposed to be an anti-sigma factor. In particular, overexpression of NrsF prevents the induction of the sigF regulon after dichromate stress. Family members also include the anti-sigma factor OsrA (blr3039) from Bradyrhizobium japonicum, which is involved in sensing reactive oxygen species. There is evidence that OsrA binds an ECF-type sigma factor (EcfF) in vivo. Furthermore, the conserved cysteine residues 129 and 179 of OsrA are shown to be required for normal function. Family members have 6 predicted transmembrane regions. 204 matched cddid_all.tbl CDD pfam06533 pfam06533 399500 DUF1110 Protein of unknown function (DUF1110). This family consists of hypothetical proteins specific to Oryza sativa. One sequence appears to be tandemly repeated. 189 matched cddid_all.tbl CDD pfam06534 pfam06534 461939 RGM_C Repulsive guidance molecule (RGM) C-terminus. This family consists of several mammalian and one bird sequence from Gallus gallus (Chicken). This family represents the C-terminal region of several sequences but in others it represents the full protein. All of the mammalian proteins are hypothetical and have no known function but Swiss:Q8JG54 from the chicken is annotated as being a repulsive guidance molecule (RGM). RGM is a GPI-linked axon guidance molecule of the retinotectal system. RGM is repulsive for a subset of axons, those from the temporal half of the retina. Temporal retinal axons invade the anterior optic tectum in a superficial layer, and encounter RGM expressed in a gradient with increasing concentration along the anterior-posterior axis. Temporal axons are able to receive posterior-dependent information by sensing gradients or concentrations of guidance cues. Thus, RGM is likely to provide positional information for temporal axons invading the optic tectum in the stratum opticum. 171 matched cddid_all.tbl CDD pfam06535 pfam06535 461940 RGM_N Repulsive guidance molecule (RGM) N-terminus. This family consists of the N-terminal region of several mammalian and one bird sequence from Gallus gallus (Chicken). All of the mammalian proteins are hypothetical and have no known function but Swiss:Q8JG54 from the chicken is annotated as being a repulsive guidance molecule (RGM). RGM is a GPI-linked axon guidance molecule of the retinotectal system. RGM is repulsive for a subset of axons, those from the temporal half of the retina. Temporal retinal axons invade the anterior optic tectum in a superficial layer, and encounter RGM expressed in a gradient with increasing concentration along the anterior-posterior axis. Temporal axons are able to receive posterior-dependent information by sensing gradients or concentrations of guidance cues. Thus, RGM is likely to provide positional information for temporal axons invading the optic tectum in the stratum opticum. 165 matched cddid_all.tbl CDD pfam06536 pfam06536 368962 Av_adeno_fibre Avian adenovirus fibre, N-terminal. This family is the N-terminal region of avian adenovirus fibre proteins; the domain is frequently found repeated several times along the fibre. These fibres have been linked to variations in virulence. Avian adenoviruses possess penton capsomers that consist of a pentameric base associated with two fibres. 56 matched cddid_all.tbl CDD pfam06537 pfam06537 428995 DHOR Di-haem oxidoreductase, putative peroxidase. DHOR is a family of di-haem oxidoredictases. It carries the two characteriztic Cys-X-Y-Cys-His haem-binding motifs. The C-terminal high-potential site functions as an electron transfer centre, and the N-terminal low-potential site corresponds to the peroxidatic centre. Its probable function is as a peroxidase. 486 matched cddid_all.tbl CDD pfam06540 pfam06540 461941 GMAP Galanin message associated peptide (GMAP). This family consists of several galanin message associated peptides. In rat preprogalanin, galanin is C-terminally flanked by a 60 amino acid long peptide: galanin message-associated peptide (GMAP). GMAP sequences in different species show high degree of homology, but the biological function of this family is unknown. 61 matched cddid_all.tbl CDD pfam06541 pfam06541 461942 ABC_trans_CmpB Putative ABC-transporter type IV. CmpB is a family of membrane proteins that are likely to be part of a two-component type IV ABC-transporter system. Families can transport multiple drugs including ethidium and fluoroquinolones. UniProtKB:Q83XH0 is a member of TCDB family 3.A.1.121.4. 149 matched cddid_all.tbl CDD pfam06542 pfam06542 368965 PHA-1 Regulator protein PHA-1. This family represents the protein product of the gene pha-1 which coordinates with lin-35 Rb during animal development. The protein is expressed during embryonic development and functions in the cytoplasm. PHA-1 acts in a parallel pathway with UBC-18 to regulate the activity of a common cellular target. 403 matched cddid_all.tbl CDD pfam06543 pfam06543 284059 Lac_bphage_repr Lactococcus bacteriophage repressor. This family represents the C-terminus of Lactococcus bacteriophage repressor proteins. 49 matched cddid_all.tbl CDD pfam06544 pfam06544 461943 DUF1115 Protein of unknown function (DUF1115). This family represents the C-terminus of hypothetical eukaryotic proteins of unknown function. 135 matched cddid_all.tbl CDD pfam06545 pfam06545 428999 DUF1116 Protein of unknown function (DUF1116). This family contains hypothetical bacterial proteins of unknown function. 215 matched cddid_all.tbl CDD pfam06546 pfam06546 461944 Vert_HS_TF Vertebrate heat shock transcription factor. This family represents the C-terminal region of vertebrate heat shock transcription factors. Heat shock transcription factors regulate the expression of heat shock proteins - a set of proteins that protect the cell from damage caused by stress and aid the cell's recovery after the removal of stress. This C-terminal region is found with the N-terminal pfam00447, and may contain a three-stranded coiled-coil trimerization domain and a CE2 regulatory region, the latter of which is involved in sustained heat shock response. 275 matched cddid_all.tbl CDD pfam06547 pfam06547 399509 DUF1117 Protein of unknown function (DUF1117). This family represents the C-terminus of a number of hypothetical plant proteins. 110 matched cddid_all.tbl CDD pfam06549 pfam06549 368969 DUF1118 Protein of unknown function (DUF1118). This family consists of several hypothetical plant proteins of unknown function. 115 matched cddid_all.tbl CDD pfam06550 pfam06550 284066 SPP Signal-peptide peptidase, presenilin aspartyl protease. SPP is a family of signal-peptide aspartyl proteases. The family carries the characteriztic catalytic aspartate GXGD motif, and members are integral membrane peptidases of the presenilin-type with nine transmembrane regions. UniProtKB:Q18K19 is part of the TCDB family 1.A.54.3.4, the presenilin er Ca(2+) leak channel (presenilin). 283 matched cddid_all.tbl CDD pfam06551 pfam06551 368970 DUF1120 Protein of unknown function (DUF1120). This family consists of several hypothetical bacterial proteins of unknown function. 116 matched cddid_all.tbl CDD pfam06552 pfam06552 284068 TOM20_plant Plant specific mitochondrial import receptor subunit TOM20. This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins. Most mitochondrial proteins are encoded by the nuclear genome, and are synthesized in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria. 187 matched cddid_all.tbl CDD pfam06553 pfam06553 461945 BNIP3 BNIP3. This family consists of several mammalian specific BCL2/adenovirus E1B 19-kDa protein-interacting protein 3 or BNIP3 sequences. BNIP3 belongs to the Bcl-2 homology 3 (BH3)-only family, a Bcl-2-related family possessing an atypical Bcl-2 homology 3 (BH3) domain, which regulates PCD from mitochondrial sites by selective Bcl-2/Bcl-XL interactions. BNIP3 family members contain a C-terminal transmembrane domain that is required for their mitochondrial localization, homodimerization, as well as regulation of their pro-apoptotic activities. BNIP3-mediated apoptosis has been reported to be independent of caspase activation and cytochrome c release and is characterized by early plasma membrane and mitochondrial damage, prior to the appearance of chromatin condensation or DNA fragmentation. 181 matched cddid_all.tbl CDD pfam06554 pfam06554 399511 Olfactory_mark Olfactory marker protein. This family consists of several olfactory marker proteins. Expression of the olfactory marker protein (OMP) is highly restricted to mature olfactory receptor neurons in virtually all vertebrate species from fish to man. 149 matched cddid_all.tbl CDD pfam06556 pfam06556 461946 ASFV_p27 IAP-like protein p27 C-terminus. This family represents the C-terminal region of the African swine fever virus IAP-like protein p27. This family is found in conjunction with pfam00653. It has been suggested that the family may be a host range gene involved in aspects of infection in the arthropod host, ticks of the genus Ornithodoros. 131 matched cddid_all.tbl CDD pfam06557 pfam06557 399512 DUF1122 Protein of unknown function (DUF1122). This family consists of several hypothetical archaeal and bacterial proteins of unknown function. 162 matched cddid_all.tbl CDD pfam06558 pfam06558 429002 SecM Secretion monitor precursor protein (SecM). This family consists of several bacterial Secretion monitor precursor (SecM) proteins. SecM is known to regulate SecA expression. The eubacterial protein secretion machinery consists of a number of soluble and membrane associated components. One critical element is SecA ATPase, which acts as a molecular motor to promote protein secretion at translocation sites that consist of SecYE, the SecA receptor, and SecG and SecDFyajC proteins, which regulate SecA membrane cycling. 147 matched cddid_all.tbl CDD pfam06559 pfam06559 429003 DCD 2'-deoxycytidine 5'-triphosphate deaminase (DCD). This family consists of several bacterial 2'-deoxycytidine 5'-triphosphate deaminase proteins (EC:3.5.4.13). 361 matched cddid_all.tbl CDD pfam06560 pfam06560 284075 GPI Glucose-6-phosphate isomerase (GPI). This family consists of several bacterial and archaeal glucose-6-phosphate isomerase (GPI) proteins (EC:5.3.1.9). 177 matched cddid_all.tbl CDD pfam06563 pfam06563 461947 DUF1125 Protein of unknown function (DUF1125). This family consists of several short Lactococcus lactis and bacteriophage proteins. The function of this family is unknown. 55 matched cddid_all.tbl CDD pfam06564 pfam06564 429004 CBP_BcsQ "Cellulose biosynthesis protein BcsQ. This is a family of bacterial proteins involved in cellulose biosynthesis. (Roemling U. and Galperin M.Y. ""Bacterial cellulose biosynthesis. Diversity of operons and subunits"" (manuscript in preparation)). A second component of the extracellular matrix of the multicellular morphotype (rdar) of Salmonella typhimurium and Escherichia coli is cellulose. The family does contain a P-loop sequence motif suggesting a nucleotide binding function, but this has not been confirmed." 234 matched cddid_all.tbl CDD pfam06565 pfam06565 461948 DM10_dom DM10 domain. This entry represents the DM10 domain, which consists of approximately 105 residues whose function is unknown. It has been identified in nucleoside diphosphate kinases, namely Nucleoside diphosphate kinase 7 (NDK7), which contain a single copy of the DM10 domain, and in uncharacterized proteins including Rib72 from Chlamydomonas and EF-hand domain-containing protein 1/EF-hand domain-containing family member C2 (EFHC1/2) from mammals, which contain multiple copies of DM10 domains. In Chlamydomonas, and possibly mammals, DM10 domain-containing proteins are tightly bound to the flagellar doublet microtubules. This suggests that DM10 domains might act as flagellar NDK regulatory modules or as units specifically involved in axonemal targeting or assembly. This domain have a PH-like fold which includes seven beta strands, with a short 3-4 residue helix after the first strand, and a more extended alpha helical region at the C terminus. 104 matched cddid_all.tbl CDD pfam06566 pfam06566 368978 Chon_Sulph_att Chondroitin sulphate attachment domain. This family represents the chondroitin sulphate attachment domain of vertebrate neural transmembrane proteoglycans that contain EGF modules. Evidence has been accumulated to support the idea that neural proteoglycans are involved in various cellular events including mitogenesis, differentiation, axonal outgrowth and synaptogenesis. This domain contains several potential sites of chondroitin sulphate attachment, as well as potential sites of N-linked glycosylation. 249 matched cddid_all.tbl CDD pfam06567 pfam06567 461949 Neural_ProG_Cyt Neural chondroitin sulphate proteoglycan cytoplasmic domain. This family represents the C-terminal cytoplasmic domain of vertebrate neural chondroitin sulphate proteoglycans that contain EGF modules. Evidence has been accumulated to support the idea that neural proteoglycans are involved in various cellular events including mitogenesis, differentiation, axonal outgrowth and synaptogenesis. This domain contains a number of potential sites of phosphorylation by protein kinase C. 120 matched cddid_all.tbl CDD pfam06568 pfam06568 429007 DUF1127 Domain of unknown function (DUF1127). This family is found in several hypothetical bacterial proteins. In some cases it represents it represents the C-terminal region whereas in others it represents the whole sequence. 36 matched cddid_all.tbl CDD pfam06569 pfam06569 399518 DUF1128 Protein of unknown function (DUF1128). This family consists of several short, hypothetical bacterial proteins of unknown function. 71 matched cddid_all.tbl CDD pfam06570 pfam06570 429008 DUF1129 Protein of unknown function (DUF1129). This family consists of several hypothetical bacterial proteins of unknown function. 200 matched cddid_all.tbl CDD pfam06572 pfam06572 429009 DUF1131 Protein of unknown function (DUF1131). This family consists of several hypothetical bacterial proteins of unknown function. 169 matched cddid_all.tbl CDD pfam06573 pfam06573 461950 Churchill Churchill protein. This family consists of several eukaryotic Churchill proteins. This protein contains a novel zinc binding region that mediates FGF signaling during neural development (unpublished obs Sheng G and Stern C). 111 matched cddid_all.tbl CDD pfam06574 pfam06574 429011 FAD_syn FAD synthetase. This family corresponds to the N terminal domain of the bifunctional enzyme riboflavin kinase / FAD synthetase. These enzymes have both ATP:riboflavin 5'-phospho transferase and ATP:FMN-adenylyltransferase activity. They catalyze the 5'-phosphorylation of riboflavin to FMN and the adenylylation of FMN to FAD. This domain is thought to have the flavin mononucleotide (FMN) adenylyltransferase activity. 158 matched cddid_all.tbl CDD pfam06575 pfam06575 284087 DUF1132 Protein of unknown function (DUF1132). This family consists of several hypothetical proteins from Neisseria meningitidis. The function of this family is unknown. 101 matched cddid_all.tbl CDD pfam06576 pfam06576 148278 DUF1133 Protein of unknown function (DUF1133). This family consists of a number of hypothetical proteins from Escherichia coli O157:H7 and Salmonella typhi. The function of this family is unknown. 176 matched cddid_all.tbl CDD pfam06577 pfam06577 429012 EipA Envelope integrity protein A. This family includes envelope integrity protein A (EipA), a protein required for B. abortus envelope stress resistance and infection. It's gene expression is directly activated by CtrA which binds to the promoter region. eipA encodes a soluble periplasmic protein that adopts an unusual eight-stranded beta-barrel fold. 159 matched cddid_all.tbl CDD pfam06578 pfam06578 461951 YscK YOP proteins translocation protein K (YscK). This family consists of several YscK proteins. The function of this protein is unknown but it belongs to an operon involved in the secretion of Yop proteins across bacterial membranes. 209 matched cddid_all.tbl CDD pfam06579 pfam06579 399524 Ly-6_related Caenorhabditis elegans ly-6-related protein. This family consists of several Caenorhabditis elegans specific ly-6-related HOT and ODR proteins. These proteins are involved in the olfactory system. Odr-2 mutants are known to be defective in the ability to chemotax to odorants that are recognized by the two AWC olfactory neurons. Odr-2 encodes a membrane-associated protein related to the Ly-6 superfamily of GPI-linked signaling proteins. 125 matched cddid_all.tbl CDD pfam06580 pfam06580 461952 His_kinase Histidine kinase. This family represents a region within bacterial histidine kinase enzymes. Two-component signal transduction systems such as those mediated by histidine kinase are integral parts of bacterial cellular regulatory processes, and are used to regulate the expression of genes involved in virulence. Members of this family often contain pfam02518 and/or pfam00672. 79 matched cddid_all.tbl CDD pfam06581 pfam06581 461953 p31comet Mad1 and Cdc20-bound-Mad2 binding. This family is involved in the cell-cycle surveillance mechanism called the spindle checkpoint. This mechanism monitors the proper bipolar attachment of sister chromatids to spindle microtubules and ensures the fidelity of chromosome segregation during mitosis. A key player in mitosis is Mad2, and Mad2 exhibits an unusual two-state behaviour. A Mad1-Mad2 core complex recruits cytosolic Mad2 to kinetochores through Mad2 dimerization and converts Mad2 to a conformer amenable to Cdc20 binding. p31comet inactivates the checkpoint by binding to Mad1- or Cdc20-bound Mad2 in such a way as to stop Mad2 activation and to promote the dissociation of the Mad2-Cdc20 complex. 265 matched cddid_all.tbl CDD pfam06583 pfam06583 461954 Neogenin_C Neogenin C-terminus. This family represents the C-terminus of eukaryotic neogenin precursor proteins, which contains several potential phosphorylation sites. Neogenin is a member of the N-CAM family of cell adhesion molecules (and therefore contains multiple copies of pfam00047 and pfam00041) and is closely related to the DCC tumour suppressor gene product - these proteins may play an integral role in regulating differentiation programmes and/or cell migration events within many adult and embryonic tissues. 289 matched cddid_all.tbl CDD pfam06584 pfam06584 461955 DIRP DIRP. DIRP (Domain in Rb-related Pathway) is postulated to be involved in the Rb-related pathway, which is encoded by multiple eukaryotic genomes and is present in proteins including lin-9 of Caenorhabditis elegans, aly of fruit fly and mustard weed. Studies of lin-9 and aly of fruit fly proteins containing DIRP suggest that this domain might be involved in development. Aly, lin-9, act in parallel to, or downstream of, activation of MAPK by the RTK-Ras signalling pathway. 108 matched cddid_all.tbl CDD pfam06585 pfam06585 461956 JHBP Haemolymph juvenile hormone binding protein (JHBP). This family consists of several insect-specific haemolymph juvenile hormone binding proteins (JHBP). Juvenile hormone regulates embryogenesis, maintains the status quo of larval development and stimulates reproductive maturation in the adult insect. JH is transported from the sites of its synthesis to target tissues by a haemolymph carrier called juvenile hormone-binding protein (JHBP). JHBP protects the JH molecules from hydrolysis by non-specific esterases present in the insect haemolymph. The crystal structure of the JHBP from Galleria mellonella shows an unusual fold consisting of a long alpha-helix wrapped in a much curved antiparallel beta-sheet. The folding pattern for this structure closely resembles that found in some tandem-repeat mammalian lipid-binding and bactericidal permeability-increasing proteins, with a similar organization of the major cavity and a disulfide bond linking the long helix and the beta-sheet. It would appear that JHBP forms two cavities, only one of which, the one near the N- and C-termini, binds the hormone; binding induces a conformational change, of unknown significance. This family now includes DUF233, pfam03027. 239 matched cddid_all.tbl CDD pfam06586 pfam06586 429019 TraK TraK protein. This family consists of several TraK proteins from Escherichia coli, Salmonella typhi and Salmonella typhimurium. TraK is known to be essential for pilus assembly but its exact role in this process is unknown. 228 matched cddid_all.tbl CDD pfam06587 pfam06587 461957 DUF1137 Protein of unknown function (DUF1137). This family consists of several hypothetical proteins specific to Chlamydia species. The function of this family is unknown. 117 matched cddid_all.tbl CDD pfam06588 pfam06588 284099 Muskelin_N Muskelin N-terminus. This family represents the N-terminal region of muskelin and is found in conjunction with several pfam01344 repeats. Muskelin is an intracellular, kelch repeat protein that is needed in cell-spreading responses to the matrix adhesion molecule, thrombospondin-1. 197 matched cddid_all.tbl CDD pfam06589 pfam06589 399531 CRA Circumsporozoite-related antigen (CRA). This family consists of several circumsporozoite-related antigen (CRA) or exported protein-1 (EXP1) sequences found specifically in Plasmodium species. The function of this family is unknown. 123 matched cddid_all.tbl CDD pfam06590 pfam06590 115260 PerB PerB protein. This family consists of several PerB or BfpV proteins found specifically in Escherichia coli. PerB is thought to play a role in regulating the expression of BfpA. 129 matched cddid_all.tbl CDD pfam06591 pfam06591 148289 Phage_T4_Ndd T4-like phage nuclear disruption protein (Ndd). This family consists of several nuclear disruption (Ndd) proteins from T4-like phages. Early in a bacteriophage T4 infection, the phage ndd gene causes the rapid destruction of the structure of the Escherichia coli nucleoid. The targets of Ndd action may be the chromosomal sequences that determine the structure of the nucleoid. 154 matched cddid_all.tbl CDD pfam06592 pfam06592 429021 DUF1138 Protein of unknown function (DUF1138). This family consists of several hypothetical short plant proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown. 73 matched cddid_all.tbl CDD pfam06593 pfam06593 284102 RBDV_coat Raspberry bushy dwarf virus coat protein. This family consists of several Raspberry bushy dwarf virus coat proteins. 274 matched cddid_all.tbl CDD pfam06594 pfam06594 429022 HCBP_related Haemolysin-type calcium binding protein related domain. This family consists of a number of bacteria specific domains which are found in haemolysin-type calcium binding proteins. This family is found in conjunction with pfam00353 and is often found in multiple copies. 42 matched cddid_all.tbl CDD pfam06595 pfam06595 284104 BDV_P24 Borna disease virus P24 protein. This family consists of several Borna disease virus (BDV) P24 proteins. The function of this family is unknown. 201 matched cddid_all.tbl CDD pfam06596 pfam06596 429023 PsbX Photosystem II reaction centre X protein (PsbX). This family consists of several photosystem II reaction centre X protein (PsbX) sequences from both prokaryotes and eukaryotes. 37 matched cddid_all.tbl CDD pfam06597 pfam06597 429024 Clostridium_P47 Clostridium P-47 protein. This family consists of several P-47 proteins from various Clostridium species as well as two related sequences from Pseudomonas putida. The function of this family is unknown. 459 matched cddid_all.tbl CDD pfam06598 pfam06598 253815 Chlorovi_GP_rpt Chlorovirus glycoprotein repeat. This family consists of s number of repeats found in Chlorovirus glycoproteins. The function of this family is unknown. 34 matched cddid_all.tbl CDD pfam06599 pfam06599 115269 DUF1139 Protein of unknown function (DUF1139). This family consists of several hypothetical Fijivirus proteins of unknown function. 309 matched cddid_all.tbl CDD pfam06600 pfam06600 429025 DUF1140 Protein of unknown function (DUF1140). This family consists of several short, hypothetical phage and bacterial proteins. The function of this family is unknown. 99 matched cddid_all.tbl CDD pfam06601 pfam06601 284108 Orthopox_F6 Orthopoxvirus F6 protein. This family consists of several Orthopoxvirus F6L proteins the function of which are unknown. 72 matched cddid_all.tbl CDD pfam06602 pfam06602 461958 Myotub-related Myotubularin-like phosphatase domain. This family represents the phosphatase domain within eukaryotic myotubularin-related proteins. Myotubularin is a dual-specific lipid phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bi-phosphate. Mutations in gene encoding myotubularin-related proteins have been associated with disease. 332 matched cddid_all.tbl CDD pfam06603 pfam06603 429027 UpxZ UpxZ family of transcription anti-terminator antagonists. The UpxZ family of proteins acts to inhibit transcription of heterologous capsular polysaccharide loci in Bacteroides species by interfering with the action of the UpxY family of transcription anti-terminators. As antagonists of polysaccharide locus-specific UpxY transcription anti-terminators, the UpxZ proteins exert a hierarchical level of regulation, insuring that only one of the multiple phase-variable capsular polysaccharide loci per cell characteriztic of this genus is transcribed at a time. 104 matched cddid_all.tbl CDD pfam06605 pfam06605 429028 Prophage_tail Prophage endopeptidase tail. This family is of prophage tail proteins that are probably acting as endopeptidases. 253 matched cddid_all.tbl CDD pfam06607 pfam06607 148298 Prokineticin Prokineticin. This family consists of several prokineticin proteins and related BM8 sequences. The suprachiasmatic nucleus (SCN) controls the circadian rhythm of physiological and behavioural processes in mammals. It has been shown that prokineticin 2 (PK2), a cysteine-rich secreted protein, functions as an output molecule from the SCN circadian clock. PK2 messenger RNA is rhythmically expressed in the SCN, and the phase of PK2 rhythm is responsive to light entrainment. Molecular and genetic studies have revealed that PK2 is a gene that is controlled by a circadian clock. 97 matched cddid_all.tbl CDD pfam06608 pfam06608 461959 DUF1143 Protein of unknown function (DUF1143). This family consists of several hypothetical mammalian proteins (from mouse and human). The function of this family is unknown. 148 matched cddid_all.tbl CDD pfam06609 pfam06609 115279 TRI12 Fungal trichothecene efflux pump (TRI12). This family consists of several fungal specific trichothecene efflux pump proteins. Many of the genes involved in trichothecene toxin biosynthesis in Fusarium sporotrichioides are present within a gene cluster.It has been suggested that TRI12 may play a role in F. sporotrichioides self-protection against trichothecenes. 598 matched cddid_all.tbl CDD pfam06610 pfam06610 399538 AlaE L-alanine exporter. AlaE is a family of Gram-negative amino-acid transporters. It is not entirely clear why bacteria export metabolites but recent studies have shown that many excrete alanine. AlaE is likely to be the exporter protein for L-alanine. UniProtKB:A8ANM6, UniProt:G4R961 and UniProt:H5SVY7 are classified as putative alanine exporters. 141 matched cddid_all.tbl CDD pfam06611 pfam06611 429030 DUF1145 Protein of unknown function (DUF1145). This family consists of several hypothetical bacterial proteins of unknown function. 58 matched cddid_all.tbl CDD pfam06612 pfam06612 429031 DUF1146 Protein of unknown function (DUF1146). This family consists of several hypothetical bacterial proteins of unknown function. 48 matched cddid_all.tbl CDD pfam06613 pfam06613 461960 KorB_C KorB C-terminal beta-barrel domain. This family consists of several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon. This beta-barrel domain is found at the C-terminus of KorB. 58 matched cddid_all.tbl CDD pfam06614 pfam06614 461961 Neuromodulin Neuromodulin. This family consists of several neuromodulin (Axonal membrane protein GAP-43) sequences and is found in conjunction with pfam00612. GAP-43 is a neuronal calmodulin-binding phosphoprotein that is concentrated in growth cones and pre-synaptic terminals. 175 matched cddid_all.tbl CDD pfam06615 pfam06615 115285 Circovir2_Orf1 Circovirus 2, Orf1. This family consists of short Circovirus proteins of unknown function, including ORF1 (also known as Protein NS0) which may be involved in host modulation. 59 matched cddid_all.tbl CDD pfam06616 pfam06616 429034 BsuBI_PstI_RE BsuBI/PstI restriction endonuclease domain. This family represents the C-terminus of bacterial enzymes similar to type II restriction endonucleases BsuBI and PstI (EC:3.1.21.4). The enzymes of the BsuBI restriction/modification (R/M) system recognize the target sequence 5'CTGCAG and are functionally identical with those of the PstI R/M system. 153 matched cddid_all.tbl CDD pfam06617 pfam06617 461962 M-inducer_phosp M-phase inducer phosphatase. This family represents a region within eukaryotic M-phase inducer phosphatases (EC:3.1.3.48), which also contain the pfam00581 domain. These proteins are involved in the control of mitosis. 269 matched cddid_all.tbl CDD pfam06618 pfam06618 115288 DUF1148 Protein of unknown function (DUF1148). This family consists of several Maize streak virus proteins of unknown function. 114 matched cddid_all.tbl CDD pfam06619 pfam06619 429036 DUF1149 Protein of unknown function (DUF1149). This family consists of several hypothetical bacterial proteins of unknown function. 122 matched cddid_all.tbl CDD pfam06620 pfam06620 429037 DUF1150 Protein of unknown function (DUF1150). This family consists of several hypothetical bacterial proteins of unknown function. 71 matched cddid_all.tbl CDD pfam06621 pfam06621 461963 SIM_C Single-minded protein C-terminus. This family represents the C-terminal region of the eukaryotic single-minded (SIM) protein. Drosophila single-minded acts as a positive master gene regulator in central nervous system midline formation. There are two homologs in mammals: SIM1 and SIM2, which are members of the basic-helix-loop-helix PAS family of transcription factors. SIM1 and SIM2 are novel heterodimerization partners for ARNT in vitro, and they may function both as positive and negative transcriptional regulators in vivo, during embryogenesis and in the adult organizm. SIM2 is thought to contribute to some specific Down syndrome phenotypes. This family is found in conjunction with a pfam00989 domain and associated pfam00785 motif. 296 matched cddid_all.tbl CDD pfam06622 pfam06622 115292 SepQ SepQ protein. This family consists of several enterobacterial SepQ proteins from Escherichia coli and Citrobacter rodentium. The function of this family is unclear. 305 matched cddid_all.tbl CDD pfam06623 pfam06623 461964 MHC_I_C MHC_I C-terminus. This family represents the C-terminal region of the MHC class I antigen. The family is found in conjunction with pfam00129 and pfam00047. 28 matched cddid_all.tbl CDD pfam06624 pfam06624 461965 RAMP4 Ribosome associated membrane protein RAMP4. This family consists of several ribosome associated membrane protein RAMP4 (or SERP1) sequences. stabilization of membrane proteins in response to stress involves the concerted action of a rescue unit in the ER membrane comprised of SERP1/RAMP4, other components of the translocon, and molecular chaperones in the ER. 57 matched cddid_all.tbl CDD pfam06625 pfam06625 461966 DUF1151 Protein of unknown function (DUF1151). This family consists of several hypothetical eukaryotic proteins of unknown function. 111 matched cddid_all.tbl CDD pfam06626 pfam06626 399549 DUF1152 Protein of unknown function (DUF1152). This family consists of several hypothetical archaeal proteins of unknown function. 294 matched cddid_all.tbl CDD pfam06627 pfam06627 429042 DUF1153 Protein of unknown function (DUF1153). This family consists of several short, hypothetical bacterial proteins of unknown function. 87 matched cddid_all.tbl CDD pfam06628 pfam06628 461967 Catalase-rel Catalase-related immune-responsive. This family represents a small conserved region within catalase enzymes (EC:1.11.1.6). All members also contain the Catalase family, pfam00199 domain. Catalase decomposes hydrogen peroxide into water and oxygen, serving to protect cells from its toxic effects. This domain carries the immune-responsive amphipathic octa-peptide that is recognized by T cells. 65 matched cddid_all.tbl CDD pfam06629 pfam06629 461968 MipA MltA-interacting protein MipA. This family consists of several bacterial MltA-interacting protein (MipA) like sequences. As well as interacting with the membrane-bound lytic transglycosylase MltA, MipA is known to bind to PBP1B, a bifunctional murein transglycosylase/transpeptidase. MipA is considered to be a structural protein mediating the assembly of MltA to PBP1B into a complex. 221 matched cddid_all.tbl CDD pfam06630 pfam06630 284130 Exonuc_VIII Enterobacterial exodeoxyribonuclease VIII. This family consists of several Enterobacterial exodeoxyribonuclease VIII proteins. 203 matched cddid_all.tbl CDD pfam06631 pfam06631 461969 DUF1154 Protein of unknown function (DUF1154). This family represents a small conserved region of unknown function within eukaryotic phospholipase C (EC:3.1.4.3). All members also contain pfam00387 and pfam00388. 45 matched cddid_all.tbl CDD pfam06632 pfam06632 369011 XRCC4 DNA double-strand break repair and V(D)J recombination protein XRCC4. This family consists of several eukaryotic DNA double-strand break repair and V(D)J recombination protein XRCC4 sequences. In the non-homologous end joining pathway of DNA double-strand break repair, the ligation step is catalyzed by a complex of XRCC4 and DNA ligase IV. It is thought that XRCC4 and ligase IV are essential for alignment-based gap filling, as well as for final ligation of the breaks. 336 matched cddid_all.tbl CDD pfam06633 pfam06633 115303 DUF1155 Protein of unknown function (DUF1155). This family consists of several Cucumber mosaic virus ORF IIB proteins. The function of this family is unknown. 42 matched cddid_all.tbl CDD pfam06634 pfam06634 369012 DUF1156 Protein of unknown function (DUF1156). This family represents a conserved region within hypothetical prokaryotic and archaeal proteins of unknown function. Structural modelling suggests this domain may bind nucleic acids. 71 matched cddid_all.tbl CDD pfam06635 pfam06635 399554 T3SS_SCTL Type 3 secretion system stator protein. This family consists of Type 3 secretion system (T3SS) stator protein, previously known as nodulation protein NolV, from different Rhizobium species. The function of this family is unclear, however, it has been suggested that this protein is a component of the T3SS, which is used to inject bacterial effector proteins into eukaryotic host cells. 206 matched cddid_all.tbl CDD pfam06636 pfam06636 253836 DUF1157 Protein of unknown function (DUF1157). This family consists of several uncharacterized proteins from Melanoplus sanguinipes entomopoxvirus (MsEPV). The function of this family is unknown. 370 matched cddid_all.tbl CDD pfam06637 pfam06637 461970 PV-1 PV-1 protein (PLVAP). This family consists of several PV-1 (PLVAP) proteins which seem to be specific to mammals. PV-1 is a novel protein component of the endothelial fenestral and stomatal diaphragms. The function of this family is unknown. 439 matched cddid_all.tbl CDD pfam06638 pfam06638 461971 Strabismus Strabismus protein. This family consists of several strabismus (STB) or Van Gogh-like (VANGL) proteins 1 and 2. The exact function of this family is unknown. It is thought, however that STB1 gene and STB2 may be potent tumour suppressor gene candidates. 503 matched cddid_all.tbl CDD pfam06639 pfam06639 369015 BAP Basal layer antifungal peptide (BAP). This family consists of several basal layer antifungal peptide (BAP) sequences specific to Zea mays. The BAP2 peptide exhibits potent broad-range activity against a range of filamentous fungi, including several plant pathogens. 76 matched cddid_all.tbl CDD pfam06640 pfam06640 429048 P_C P protein C-terminus. This family represents the C-terminus of plant P proteins. The maize P gene is a transcriptional regulator of genes encoding enzymes for flavonoid biosynthesis in the pathway leading to the production of a red phlobaphene pigment, and P proteins are homologous to the DNA-binding domain of myb-like transcription factors. All members of this family contain the pfam00249 domain. 252 matched cddid_all.tbl CDD pfam06643 pfam06643 399557 DUF1158 Protein of unknown function (DUF1158). This family consists of several enterobacterial YbdJ proteins. The function of this family is unknown 78 matched cddid_all.tbl CDD pfam06644 pfam06644 461972 ATP11 ATP11 protein. This family consists of several eukaryotic ATP11 proteins. In Saccharomyces cerevisiae, expression of functional F1-ATPase requires two proteins encoded by the ATP11 and ATP12 genes. Atp11p is a molecular chaperone of the mitochondrial matrix that participates in the biogenesis pathway to form F1, the catalytic unit of the ATP synthase. 267 matched cddid_all.tbl CDD pfam06645 pfam06645 461973 SPC12 Microsomal signal peptidase 12 kDa subunit (SPC12). This family consists of several microsomal signal peptidase 12 kDa subunit proteins. Translocation of polypeptide chains across the endoplasmic reticulum (ER) membrane is triggered by signal sequences. Subsequently, signal recognition particle interacts with its membrane receptor and the ribosome-bound nascent chain is targeted to the ER where it is transferred into a protein-conducting channel. At some point, a second signal sequence recognition event takes place in the membrane and translocation of the nascent chain through the membrane occurs. The signal sequence of most secretory and membrane proteins is cleaved off at this stage. Cleavage occurs by the signal peptidase complex (SPC) as soon as the lumenal domain of the translocating polypeptide is large enough to expose its cleavage site to the enzyme. The signal peptidase complex is possibly also involved in proteolytic events in the ER membrane other than the processing of the signal sequence, for example the further digestion of the cleaved signal peptide or the degradation of membrane proteins. Mammalian signal peptidase is as a complex of five different polypeptide chains. This family represents the 12 kDa subunit (SPC12). 71 matched cddid_all.tbl CDD pfam06646 pfam06646 284141 CypI Extracytoplasmic thiamine-binding lipoprotein. Thiamine-binding lipoprotein (Cypl) and related proteins are specific to Mycoplasma species. Cypl, also known as p37, whose gene is part of an operon encoding two additional proteins, which are highly similar to components of the periplasmic binding-protein-dependent transport systems of Gram-negative bacteria. It has been suggested that p37 is part of a homologous, high-affinity transport system in Mycoplasma hyorhinis, a Gram-positive bacterium. Its structure indicates that it is a thiamine pyrophosphate-binding protein. The monomer is a mixed alpha/beta fold split into two globular domains (domains I and II) connected by two linker regions and the C-terminal helix. 330 matched cddid_all.tbl CDD pfam06648 pfam06648 148323 AcMNPV_Ac75 Autographa californica nuclear polyhedrosis virus (AcMNPV), Ac75. This family is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV) protein Ac75, which is required for the egress of nucleocapsids from the nucleus, formation of intranuclear microvesicles and subsequent budded virion formation, in addition to protein Ac93. Ac75 is not an integral membrane protein, but it interacts with integral membrane protein Ac76 and is associated with the nuclear membrane. 122 matched cddid_all.tbl CDD pfam06649 pfam06649 429051 DUF1161 Protein of unknown function (DUF1161). This family consists of several short, hypothetical bacterial proteins of unknown function. 52 matched cddid_all.tbl CDD pfam06650 pfam06650 461974 SHR-BD SHR-binding domain of vacuolar-sorting associated protein 13. SHR-BD is a family of eukaryotic proteins found on vacuolar-sorting associated proteins towards the C-terminus. In plants, the domain is found to be the region which interacts with SHR or the SHORT-ROOT transcription factor, a regulator of root-growth and asymmetric cell division that separates ground tissue into endodermis and cortex. The plant protein containing the SHR-BD is named SHRUBBY or SHBY, UniProtKB:Q9FT44. 275 matched cddid_all.tbl CDD pfam06651 pfam06651 284144 DUF1163 Protein of unknown function (DUF1163). This family represents the C-terminus of hypothetical Arabidopsis thaliana proteins of unknown function. 67 matched cddid_all.tbl CDD pfam06652 pfam06652 429053 Methuselah_N Methuselah N-terminus. This family represents the N-terminal region of the Drosophila specific Methuselah protein. Drosophila Methuselah (Mth) mutants have a 35% increase in average lifespan and increased resistance to several forms of stress, including heat, starvation, and oxidative damage. The protein affected by this mutation is related to G protein-coupled receptors of the secretin receptor family. Mth, like secretin receptor family members, has a large N-terminal ectodomain, which may constitute the ligand binding site. This family is found in conjunction with pfam00002. 179 matched cddid_all.tbl CDD pfam06653 pfam06653 399563 Claudin_3 Tight junction protein, Claudin-like. This is a family of probable membrane tight junction, Claudin-like, proteins. 164 matched cddid_all.tbl CDD pfam06656 pfam06656 461975 Tenui_PVC2 Tenuivirus PVC2 protein. This family consists of several Tenuivirus PVC2 proteins from Rice grassy stunt virus, Maize stripe virus and Rice hoja blanca virus. The function of this family is unknown. 784 matched cddid_all.tbl CDD pfam06657 pfam06657 461976 Cep57_MT_bd Centrosome microtubule-binding domain of Cep57. This C-terminal region of Cep57 binds, nucleates and bundles microtubules. The N-terminal part, family Cep57_CLD, pfam14073, is the centrosome localization domain Cep57. 77 matched cddid_all.tbl CDD pfam06658 pfam06658 461977 DUF1168 Protein of unknown function (DUF1168). This family consists of several hypothetical eukaryotic proteins of unknown function. 136 matched cddid_all.tbl CDD pfam06661 pfam06661 429056 VirE3 VirE3. This family represents a conserved region within Agrobacterium tumefaciens VirE3. Agrobacterium tumefaciens (a plant pathogen) has a tumour-inducing (Ti) plasmid of which part, the transfer (T)-region, is transferred to plant cells during the infection process. Vir proteins mediate the processing of the T-region and the transfer of a single-stranded (ss) DNA copy of this region, the T-strand, into the recipient cells. VirE3 is a translocated effector protein, but its specific role has not been established. 312 matched cddid_all.tbl CDD pfam06662 pfam06662 461978 C5-epim_C D-glucuronyl C5-epimerase C-terminus. This family represents the C-terminus of D-glucuronyl C5-epimerase (EC:5.1.3.-). Glucuronyl C5-epimerases catalyze the conversion of D-glucuronic acid (GlcUA) to L-iduronic acid (IdceA) units during the biosynthesis of glycosaminoglycans. 187 matched cddid_all.tbl CDD pfam06663 pfam06663 461979 CNK2_3_dom Connector enhancer of kinase suppressor of ras 2/3 domain. This family represents a conserved region of unknown function within Connector enhancer of kinase suppressor of ras 2 (CNK2, also known MAGUIN), Connector enhancer of kinase suppressor of ras 3 (CNK3) and CNK3/IPCEF1 fusion protein. This region is situated between the PDZ pfam00595 and PH pfam00169 domains in CNK2 and CNK3/IPCEF1, and after the PDZ domain in CNK3. All family members also contain an N-terminal pfam00536 domain. CNK2 is predominantly expressed in neural tissues, being critical for postsynaptic density morphology, implicated in X-linked intellectual disability (ID). CNK2 was first described as a regulator of Ras/MAPK signalling that lead to further studies concluding that it act as a scaffold for multiple signal cascades. It is able to direct the localization of regulatory proteins within the cell and influences the behaviour of important regulatory molecules. CNK3 regulates aldosterone-induced and epithelial sodium channel (ENaC)-mediated sodium transport through regulation of ENaC cell surface expression, acting as a scaffold protein that coordinates the assembly of an ENaC-regulatory complex (ERC). CNK3/IPCEF1 is required for hepatocyte growth factor (HGF)-dependent activation of Arf6 and HGF-stimulated cell migration. 214 matched cddid_all.tbl CDD pfam06664 pfam06664 461980 MIG-14_Wnt-bd Wnt-binding factor required for Wnt secretion. MIG-14 is a Wnt-binding factor. Newly synthesized EGL-20/Wnt binds to MIG-14 in the Golgi, targetting the Wnt to the cell membrane for secretion. AP-2-mediated endocytosis and retromer retrieval at the sorting endosome would recycle MIG-14 to the Golgi, where it can bind to EGL-20/Wnt for next cycle of secretion. 294 matched cddid_all.tbl CDD pfam06666 pfam06666 429059 DUF1173 Protein of unknown function (DUF1173). This family contains a group of hypothetical bacterial proteins that contain three conserved cysteine residues towards the N-terminal. The function of these proteins is unknown. 385 matched cddid_all.tbl CDD pfam06667 pfam06667 429060 PspB Phage shock protein B. This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages. Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one. 73 matched cddid_all.tbl CDD pfam06668 pfam06668 461981 ITI_HC_C Inter-alpha-trypsin inhibitor heavy chain C-terminus. This family represents the C-terminal region of inter-alpha-trypsin inhibitor heavy chains. Inter-alpha-trypsin inhibitors are glycoproteins with a high inhibitory activity against trypsin, built up from different combinations of four polypeptides: bikunin and the three heavy chains that belong to this family (HC1, HC2, HC3). The heavy chains do not have any protease inhibitory properties but have the capacity to interact in vitro and in vivo with hyaluronic acid, which promotes the stability of the extra-cellular matrix. All family members contain the pfam00092 domain. 189 matched cddid_all.tbl CDD pfam06670 pfam06670 115333 Etmic-2 Microneme protein Etmic-2. This family consists of several Microneme protein Etmic-2 sequences from Eimeria tenella. Etmic-2 is a 50 kDa acidic protein, which is found within the microneme organelles of Eimeria tenella sporozoites and merozoites. 379 matched cddid_all.tbl CDD pfam06671 pfam06671 429062 DUF1174 Repeat of unknown function (DUF1174). This family consists of a number of Caenorhabditis elegans specific repeats of around 36 residues in length which are found in two hypothetical proteins. This family is found in conjunction with pfam00024. 25 matched cddid_all.tbl CDD pfam06672 pfam06672 429063 DUF1175 Protein of unknown function (DUF1175). This family consists of several hypothetical bacterial proteins of around 210 residues in length. The function of this family is unknown. 225 matched cddid_all.tbl CDD pfam06673 pfam06673 115336 L_lactis_ph-MCP Lactococcus lactis bacteriophage major capsid protein. This family consists of several Lactococcus lactis bacteriophage major capsid proteins. 347 matched cddid_all.tbl CDD pfam06674 pfam06674 461982 DUF1176 Protein of unknown function (DUF1176). This family consists of several hypothetical bacterial proteins of around 340 residues in length. Members of this family contain six highly conserved cysteine residues. The function of this family is unknown. 319 matched cddid_all.tbl CDD pfam06675 pfam06675 399574 DUF1177 Protein of unknown function (DUF1177). This family consists of several hypothetical archaeal and and bacterial proteins of around 300 residues in length. The function of this family is unknown. 270 matched cddid_all.tbl CDD pfam06676 pfam06676 461983 DUF1178 Protein of unknown function (DUF1178). This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown. 149 matched cddid_all.tbl CDD pfam06677 pfam06677 461984 Auto_anti-p27 Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). This family consists of several Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) sequences. It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis. 38 matched cddid_all.tbl CDD pfam06678 pfam06678 369033 DUF1179 Protein of unknown function (DUF1179). This family consists of several hypothetical Caenorhabditis elegans proteins of around 106 residues in length. The function of the family is unknown. 107 matched cddid_all.tbl CDD pfam06679 pfam06679 429067 DUF1180 Protein of unknown function (DUF1180). This family consists of several hypothetical mammalian proteins of around 190 residues in length. The function of this family is unknown. 167 matched cddid_all.tbl CDD pfam06680 pfam06680 284166 DUF1181 Protein of unknown function (DUF1181). This family consists of several hypothetical proteins of around 120 residues in length which are found specifically in Trypanosoma brucei. The function of this family is unknown. 120 matched cddid_all.tbl CDD pfam06681 pfam06681 284167 DUF1182 Protein of unknown function (DUF1182). This family consists of several hypothetical proteins of around 360 residues in length and seems to be specific to Caenorhabditis elegans. The function of this family is unknown. It appears to carry seven TM regions. 208 matched cddid_all.tbl CDD pfam06682 pfam06682 461985 SARAF SOCE-associated regulatory factor of calcium homoeostasis. SARAF is as family of eukaryotic proteins embedded in the ER. SARAF is SOCE-associated regulatory factor, where SOCE is store operated calcium entry. ie a mechanism governing calcium homoeostasis in the cell and the mitochondria. SOCE involves the enabling of Ca2+ release-activated Ca2+ (CRAC) channels. SARAF is a single pass ER membrane protein whose systolic-facing domain is responsible for activity and whose luminary-facing domain carries out a regulatory function in conjunction with another membrane protein STIM, an ER single pass membrane protein that detects changes in ER Ca2+ levels through its EF-hand, conserved Ca2+ binding domain. STIM is the major target for SARAF regulation, and thus SARAF negatively regulates the SOCE entry of calcium into cells protecting them from overfilling. 322 matched cddid_all.tbl CDD pfam06683 pfam06683 310940 DUF1184 Protein of unknown function (DUF1184). This family contains a number of hypothetical proteins of unknown function from Arabidopsis thaliana. 203 matched cddid_all.tbl CDD pfam06684 pfam06684 461986 AA_synth Amino acid synthesis. This family of proteins is structurally similar to proteins with the Bacillus chorismate mutase-like (BCM-like) fold. This structure, combined with its genomic context, suggest that it has a role in amino acid synthesis. 175 matched cddid_all.tbl CDD pfam06685 pfam06685 429070 DUF1186 Protein of unknown function (DUF1186). This family consists of several hypothetical bacterial proteins of around 250 residues in length and is found in several Chlamydia and Anabaena species. The function of this family is unknown. 246 matched cddid_all.tbl CDD pfam06686 pfam06686 461987 SpoIIIAC Stage III sporulation protein AC/AD protein family. This family consists of several bacterial stage III sporulation protein AC (SpoIIIAC) and SpoIIIAD sequences. The exact function of this family is unknown. SpoIIIAD is the an uncharacterized protein which is part of the spoIIIA operon that acts at sporulation stage III as part of a cascade of events leading to endospore formation. The operon is regulated by sigmaG. 56 matched cddid_all.tbl CDD pfam06687 pfam06687 399580 SUR7 SUR7/PalI family. This family consists of several fungal-specific SUR7 proteins. Its activity regulates expression of RVS161, a homolog of human endophilin, suggesting a function for both in endocytosis. The protein carries four transmembrane domains and is thus likely to act as an anchoring protein for the eisosome to the plasma membrane. Eisosomes are the immobile protein complexes, that include the proteins Pil1 and Lsp1, which co-localize with sites of protein and lipid endocytosis at the plasma membrane. SUR7 protein may play a role in sporulation. This family also includes PalI which is part of a pH signal transduction cascade. Based on the similarity of PalI to the yeast Rim9 meiotic signal transduction component it has been suggested that PalI might be a membrane sensor for ambient pH. 201 matched cddid_all.tbl CDD pfam06688 pfam06688 115351 DUF1187 Protein of unknown function (DUF1187). This family consists of several short, hypothetical bacterial proteins of around 62 residues in length. Members of this family are found in Escherichia coli and Salmonella typhi. The function of this family is unknown. 61 matched cddid_all.tbl CDD pfam06689 pfam06689 461988 zf-C4_ClpX ClpX C4-type zinc finger. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type. This presumed zinc binding domain is found at the N-terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. The molecular function of this domain is now known. 39 matched cddid_all.tbl CDD pfam06690 pfam06690 399582 HcgC FeGP cofactor biosynthesis protein, methyltransferase HcgC. The iron guanylylpyridinol (FeGP) cofactor biosynthesis enzymes are encoded in a cluster of at least seven conserved genes (hcgA-G). This family represents the (SAM)-dependent methyltransferase HgcC, which covalently attaches the methyl group at the 3-position of the pyridinol ring. It is predominantly found as a monomer in solution, composed of a Rossmann-like coenzyme-binding-domain consisting of six parallel and one peripheral antiparallel strand flanked by six alpha-helices and a smaller alpha/beta domain. 248 matched cddid_all.tbl CDD pfam06691 pfam06691 429073 DUF1189 Protein of unknown function (DUF1189). This family consists of several hypothetical bacterial proteins of around 260 residues in length. The function of this family is unknown. 240 matched cddid_all.tbl CDD pfam06692 pfam06692 115355 MNSV_P7B Melon necrotic spot virus P7B protein. This family consists of several Melon necrotic spot virus (MNSV) P7B proteins. The function of this family is unknown. 61 matched cddid_all.tbl CDD pfam06693 pfam06693 429074 DUF1190 Protein of unknown function (DUF1190). This family consists of several hypothetical Enterobacterial proteins of around 212 residues in length and is known as YjfM in Escherichia coli. The function of this family is unknown. 158 matched cddid_all.tbl CDD pfam06694 pfam06694 369039 Plant_NMP1 Plant nuclear matrix protein 1 (NMP1). This family consists of several plant specific nuclear matrix protein 1 (NMP1) sequences. Nuclear Matrix Protein 1 is a ubiquitously expressed 36 kDa protein, which has no homologs in animals and fungi, but is highly conserved among flowering and non-flowering plants. NMP1 is located both in the cytoplasm and nucleus and that the nuclear fraction is associated with the nuclear matrix. NMP1 is a candidate for a plant-specific structural protein with a function both in the nucleus and cytoplasm. 318 matched cddid_all.tbl CDD pfam06695 pfam06695 429075 Sm_multidrug_ex Putative small multi-drug export protein. This family contains a small number of putative small multi-drug export proteins. 112 matched cddid_all.tbl CDD pfam06696 pfam06696 336475 Strep_SA_rep Streptococcal surface antigen repeat. This family consists of a number of ~25 residue long repeats found commonly in Streptococcal surface antigens although one copy is present in the HPSR2-heavy chain potential motor protein of Giardia lamblia. This family is often found in conjunction with pfam00746. 25 matched cddid_all.tbl CDD pfam06697 pfam06697 461989 DUF1191 Protein of unknown function (DUF1191). This family contains hypothetical plant proteins of unknown function. 182 matched cddid_all.tbl CDD pfam06698 pfam06698 429077 DUF1192 Protein of unknown function (DUF1192). This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown. 58 matched cddid_all.tbl CDD pfam06699 pfam06699 461990 PIG-F GPI biosynthesis protein family Pig-F. PIG-F is involved in glycosylphosphatidylinositol (GPI) anchor biosynthesis. 182 matched cddid_all.tbl CDD pfam06701 pfam06701 461991 MIB_HERC2 "Mib_herc2. Named ""mib/herc2 domain"" in. Usually the protein also contains an E3 ligase domain (either Ring or Hect)." 66 matched cddid_all.tbl CDD pfam06702 pfam06702 461992 Fam20C Golgi casein kinase, C-terminal, Fam20. Fam20C represents the C-terminus of eukaryotic secreted Golgi casein kinase proteins. Fam20C is the Golgi casein kinase that phosphorylates secretory pathway proteins within Ser-x-Glu/pSer motifs. Mutations in Fam20C cause Raine syndrome, an autosomal recessive osteosclerotic bone dysplasia. 218 matched cddid_all.tbl CDD pfam06703 pfam06703 461993 SPC25 Microsomal signal peptidase 25 kDa subunit (SPC25). This family consists of several microsomal signal peptidase 25 kDa subunit proteins. Translocation of polypeptide chains across the endoplasmic reticulum (ER) membrane is triggered by signal sequences. Subsequently, signal recognition particle interacts with its membrane receptor and the ribosome-bound nascent chain is targeted to the ER where it is transferred into a protein-conducting channel. At some point, a second signal sequence recognition event takes place in the membrane and translocation of the nascent chain through the membrane occurs. The signal sequence of most secretory and membrane proteins is cleaved off at this stage. Cleavage occurs by the signal peptidase complex (SPC) as soon as the lumenal domain of the translocating polypeptide is large enough to expose its cleavage site to the enzyme. The signal peptidase complex is possibly also involved in proteolytic events in the ER membrane other than the processing of the signal sequence, for example the further digestion of the cleaved signal peptide or the degradation of membrane proteins. Mammalian signal peptidase is as a complex of five different polypeptide chains. This family represents the 25 kDa subunit (SPC25). 153 matched cddid_all.tbl CDD pfam06705 pfam06705 284187 SF-assemblin SF-assemblin/beta giardin. This family consists of several eukaryotic SF-assemblin and related beta giardin proteins. During mitosis the SF-assemblin-based cytoskeleton is reorganized; it divides in prophase and is reduced to two dot-like structures at each spindle pole in metaphase. During anaphase, the two dots present at each pole are connected again. In telophase there is an asymmetrical outgrowth of new fibres. It has been suggested that SF-assemblin is involved in re-establishing the microtubular root system characteriztic of interphase cells after mitosis. 247 matched cddid_all.tbl CDD pfam06706 pfam06706 115368 CTV_P6 Citrus tristeza virus 6-kDa protein. This family consists of several Citrus tristeza virus (CTV) 6-kDa, 51 residue long hydrophobic (P6) proteins. The function of this family is unknown. 51 matched cddid_all.tbl CDD pfam06707 pfam06707 369046 DUF1194 Protein of unknown function (DUF1194). This family consists of several hypothetical Rhizobiales specific proteins of around 270 residues in length. The function of this family is unknown. 206 matched cddid_all.tbl CDD pfam06708 pfam06708 399592 DUF1195 Protein of unknown function (DUF1195). This family consists of several plant specific hypothetical proteins of around 160 residues in length. The function of this family is unknown. 147 matched cddid_all.tbl CDD pfam06711 pfam06711 429081 DUF1198 Protein of unknown function (DUF1198). This family consists of several bacterial proteins of around 150 residues in length which are specific to Escherichia coli, Salmonella species and Yersinia pestis. The function of this family is unknown. 143 matched cddid_all.tbl CDD pfam06712 pfam06712 115374 DUF1199 Protein of unknown function (DUF1199). This family consists of several hypothetical Feline immunodeficiency virus (FIV) proteins. Members of this family are typically around 67 residues long and are often annotated as ORF3 proteins. The function of this family is unknown. 52 matched cddid_all.tbl CDD pfam06713 pfam06713 369049 bPH_4 Bacterial PH domain. This family consists of several hypothetical proteins specific to Oceanobacillus and Bacillus species. Members of this family are typically around 130 residues in length. The function of this family is unknown. Members of this family have a PH domain like structure. 74 matched cddid_all.tbl CDD pfam06714 pfam06714 148361 Gp5_OB Gp5 N-terminal OB domain. This domain is found at the N terminus of the Gp5 baseplate protein of bacteriophage T4. This domain binds to the Gp27 protein. This domain has the common OB fold. 144 matched cddid_all.tbl CDD pfam06715 pfam06715 310962 Gp5_C Gp5 C-terminal repeat (3 copies). This repeat composes the C-terminal part of the bacteriophage T4 baseplate protein Gp5. This region of the protein forms a needle like projection from the baseplate that is presumed to puncture the bacterial cell membrane. Structurally three copies of the repeated region trimerize to form a beta solenoid type structure. This family also includes repeats from bacterial Vgr proteins. 24 matched cddid_all.tbl CDD pfam06716 pfam06716 284193 MP_p6 Movement protein p6. This entry represents the movement protein 6 (p6) from Beet yellows virus and related Closterovirus proteins. Movement proteins (MPs) encoded by many virus genera are specialized proteins essential for plant viral genomes or virions transport within and between cells. P6 is a small protein (6kDa) localized in the endoplasmic reticulum. It has a single-span N-terminal transmembrane domain and a C-terminal hydrophilic domain which faces the cytosol. It is involved, together with Hsp70h, CP, CPm, and P64, in cell to cell movement of the viral genome without any budding, being essential for this process. The mechanism of action of this protein is not clear. It is suggested that it also plays a role in virion formation. 54 matched cddid_all.tbl CDD pfam06717 pfam06717 284194 DUF1202 Protein of unknown function (DUF1202). This family consists of several hypothetical bacterial proteins of around 335 residues in length. Members of this family are found exclusively in Escherichia coli and Salmonella species and are often referred to as YggM proteins. The function of this family is unknown. 307 matched cddid_all.tbl CDD pfam06718 pfam06718 429082 DUF1203 Protein of unknown function (DUF1203). This family consists of several hypothetical bacterial proteins of around 155 residues in length. Family members are present in Rhizobium, Agrobacterium and Streptomyces species. 116 matched cddid_all.tbl CDD pfam06719 pfam06719 461994 AraC_N AraC-type transcriptional regulator N-terminus. This family represents the N-terminus of bacterial ARAC-type transcriptional regulators. In E. coli, these regulate the L-arabinose operon through sensing the presence of arabinose, and when the sugar is present, transmitting this information from the arabinose-binding domains to the protein's DNA-binding domains. This family might represent the N-terminal arm of the protein, which binds to the C-terminal DNA binding domains to hold them in a state where the protein prefers to loop and remain non-activating. All family members contain the pfam00165 domain. 152 matched cddid_all.tbl CDD pfam06720 pfam06720 336481 Phi-29_GP16_7 Bacteriophage phi-29 early protein GP16.7. This family consists of several bacteriophage phi-29 early protein GP16.7 sequences of around 130 residues in length. The function of this family is unknown. 130 matched cddid_all.tbl CDD pfam06721 pfam06721 284198 DUF1204 Protein of unknown function (DUF1204). This family represents the C-terminus of a number of Arabidopsis thaliana hypothetical proteins of unknown function. Family members contain a conserved DFD motif. 243 matched cddid_all.tbl CDD pfam06722 pfam06722 369050 DUF1205 Protein of unknown function (DUF1205). This family represents a conserved region of unknown function within bacterial glycosyl transferases. Many family members contain pfam03033. 95 matched cddid_all.tbl CDD pfam06723 pfam06723 399596 MreB_Mbl MreB/Mbl protein. This family consists of bacterial MreB and Mbl proteins as well as two related archaeal sequences. MreB is known to be a rod shape-determining protein in bacteria and goes to make up the bacterial cytoskeleton. Genes coding for MreB/Mbl are only found in elongated bacteria, not in coccoid forms. It has been speculated that constituents of the eukaryotic cytoskeleton (tubulin, actin) may have evolved from prokaryotic precursor proteins closely related to today's bacterial proteins FtsZ and MreB/Mbl. 327 matched cddid_all.tbl CDD pfam06724 pfam06724 461995 DUF1206 Domain of Unknown Function (DUF1206). This region consists of two a pair of transmembrane helices and occurs three times in each of the family member proteins. 70 matched cddid_all.tbl CDD pfam06725 pfam06725 399598 3D 3D domain. This short presumed domain contains three conserved aspartate residues, hence the name 3D. It has been shown to be part of the catalytic double psi beta barrel domain of MltA. 72 matched cddid_all.tbl CDD pfam06726 pfam06726 369052 BC10 Bladder cancer-related protein BC10. This family consists of a series of short proteins of around 90 residues in length. The human protein BC10 has been implicated in bladder cancer where the transcription of the gene coding for this protein is nearly completely abolished in highly invasive transitional cell carcinomas (TCCs). The protein is a small globular protein containing two transmembrane helices, and it is a multiply edited transcript. All the editing sites are found in either the 5'-UTR or the N-terminal section of the protein, which is predicted to be outside the membrane. The three coding edits are all non-synonymous and predicted to encode exposed residues. The function of this family is unknown. 65 matched cddid_all.tbl CDD pfam06727 pfam06727 310969 DUF1207 Protein of unknown function (DUF1207). This family consists of a number of hypothetical bacterial proteins of around 410 residues in length which seem to be specific to Chlamydia species. The function of this family is unknown. 337 matched cddid_all.tbl CDD pfam06728 pfam06728 429085 PIG-U GPI transamidase subunit PIG-U. Many eukaryotic proteins are anchored to the cell surface via glycosylphosphatidylinositol (GPI), which is posttranslationally attached to the carboxyl-terminus by GPI transamidase. The mammalian GPI transamidase is a complex of at least four subunits, GPI8, GAA1, PIG-S, and PIG-T. PIG-U is thought to represent a fifth subunit in this complex and may be involved in the recognition of either the GPI attachment signal or the lipid portion of GPI. 375 matched cddid_all.tbl CDD pfam06729 pfam06729 429086 CENP-R Kinetochore component, CENP-R. This family consists of mammalian kinetochore sub-complex proteins CENP-R, also referred to as nuclear receptor co-activator NRIF3 proteins. NRIF3 exhibits a distinct receptor specificity in interacting with and potentiating the activity of only TRs and RXRs but not other examined nuclear receptors. NRIF3 as a co-regulator that possesses both transactivation and transrepression domains and/or functions. Collectively, the NRIF3 family of co-regulators may play dual roles in mediating both positive and negative regulatory effects on gene expression. CENP-R is one of the 15 components that make up the constitutive centromere associated complex (CCAN) part of the kinetochore. A sub-complex of CCAN, consisting of CENP-P/O/R/Q/U self-assembles on kinetochores with varying stoichiometry and undergoes a pre-mitotic maturation step. Kinetochore assembly is a cell cycle regulated multi-step process. The initial step occurs during interphase and involves loading of the 15-subunit constitutive centromere associated complex (CCAN). Kinetochores are multi-protein megadalton assemblies that are required for attachment of microtubules to centromeres and, in turn, the segregation of chromosomes in mitosis. 138 matched cddid_all.tbl CDD pfam06730 pfam06730 284207 FAM92 FAM92 protein. This family of proteins has a role in embryogenesis. During embryogenesis it is essential for ectoderm and axial mesoderm development. It may regulate cell proliferation and apoptosis. 225 matched cddid_all.tbl CDD pfam06732 pfam06732 461996 Pescadillo_N Pescadillo N-terminus. This family represents the N-terminal region of Pescadillo. Pescadillo protein localizes to distinct substructures of the interphase nucleus including nucleoli, the site of ribosome biogenesis. During mitosis pescadillo closely associates with the periphery of metaphase chromosomes and by late anaphase is associated with nucleolus-derived foci and prenucleolar bodies. Blastomeres in mouse embryos lacking pescadillo arrest at morula stages of development, the nucleoli fail to differentiate and accumulation of ribosomes is inhibited. It has been proposed that in mammalian cells pescadillo is essential for ribosome biogenesis and nucleologenesis and that disruption to its function results in cell cycle arrest. This family is often found in conjunction with a pfam00533 domain. 269 matched cddid_all.tbl CDD pfam06733 pfam06733 399602 DEAD_2 DEAD_2. This represents a conserved region within a number of RAD3-like DNA-binding helicases that are seemingly ubiquitous - members include proteins of eukaryotic, bacterial and archaeal origin. RAD3 is involved in nucleotide excision repair, and forms part of the transcription factor TFIIH in yeast. 168 matched cddid_all.tbl CDD pfam06734 pfam06734 284210 UL97 UL97. This family represents a conserved region within viral UL97 phosphotransferases. UL97 participates in the phosphorylation of the nucleoside analog ganciclovir (GCV) to produce GCV-monophosphate. 187 matched cddid_all.tbl CDD pfam06736 pfam06736 429088 TMEM175 Endosomal/lysosomal potassium channel TMEM175. This family represents the conserved region of transmembrane protein 175 which is an organelle-specific potassium channel responsible for potassium conductance in endosomes and lysosomes. It forms a potassium-permeable leak-like channel, which regulates luminal pH stability and is required for autophagosome-lysosome fusion. TMEM175 is the major lysosomal potassium conductance. It is present in eukaryotes, where TMEM175 has two repeats of 6-transmembrane-spanning segments, and also in prokaryotes in which it has one copy. 88 matched cddid_all.tbl CDD pfam06737 pfam06737 399604 Transglycosylas Transglycosylase-like domain. This family of proteins are very likely to act as transglycosylase enzymes related to pfam00062 and pfam01464. These other families are weakly matched by this family, and include the known active site residues. 75 matched cddid_all.tbl CDD pfam06738 pfam06738 461997 ThrE Putative threonine/serine exporter. ThrE is a family of bacterial and Archaeal proteins that catalyze the export of L-threonine from the cell. UniProtKB:Q79VD1 has been characterized as being necessary for this export. The domain exhibits 10 putative TMs and catalyzes the proton-motive-force-dependent efflux of threonine and serine. 241 matched cddid_all.tbl CDD pfam06739 pfam06739 115400 SBBP Beta-propeller repeat. This family is related to pfam00400 and is likely to also form a beta-propeller. SBBP stands for Seven Bladed Beta Propeller. 38 matched cddid_all.tbl CDD pfam06740 pfam06740 429090 DUF1213 Protein of unknown function (DUF1213). This family represents a short conserved repeat within Drosophila melanogaster proteins of unknown function. Approximately 50 copies of this repeat are present in each protein. 32 matched cddid_all.tbl CDD pfam06741 pfam06741 461998 LsmAD LsmAD domain. This domain is found associated with Lsm domain. 65 matched cddid_all.tbl CDD pfam06742 pfam06742 429092 DUF1214 Protein of unknown function (DUF1214). This family represents the C-terminal region of several hypothetical proteins of unknown function. Family members are mostly bacterial, but a few are also found in eukaryotes and archaea. 110 matched cddid_all.tbl CDD pfam06743 pfam06743 461999 FAST_1 FAST kinase-like protein, subdomain 1. This family represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases (EC:2.7.1.-) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis. Note that many family members are hypothetical proteins. This region is often found immediately N-terminal to the FAST kinase-like protein, subdomain 2. 72 matched cddid_all.tbl CDD pfam06744 pfam06744 429094 IcmF_C Type VI secretion protein IcmF C2-like domain. IcmF_C family represents a conserved region situated towards the C-terminal end of IcmF-like proteins. It was thought to be involved in Vibrio cholerae cell surface reorganization that results in increased adherence to epithelial cells leading to an increased conjugation frequency. IcmF as a whole interacts with DotU whereby these bind tightly and form the docking area of the T6SS within the inner membrane. The exact function of this domain is not clear. 106 matched cddid_all.tbl CDD pfam06745 pfam06745 429095 ATPase KaiC. This family is in the P-loop NTPase superfamily and is found in archaea, bacteria and eukaryotes. More than one copy is sometimes found in each protein. This family includes KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria. 231 matched cddid_all.tbl CDD pfam06746 pfam06746 369060 DUF1216 Protein of unknown function (DUF1216). This family represents a conserved region, within Arabidopsis thaliana proteins, of unknown function. Family members sometimes contain more than one copy.It has been reported that this domain will be found in other Brassicaceae. 132 matched cddid_all.tbl CDD pfam06747 pfam06747 429096 CHCH CHCH domain. we have identified a conserved motif in the LOC118487 protein that we have called the CHCH motif. Alignment of this protein with related members showed the presence of three subgroups of proteins, which are called the S (Small), N (N-terminal extended) and C (C-terminal extended) subgroups. All three sub-groups of proteins have in common that they contain a predicted conserved [coiled coil 1]-[helix 1]-[coiled coil 2]-[helix 2] domain (CHCH domain). Within each helix of the CHCH domain, there are two cysteines present in a C-X9-C motif. The N-group contains an additional double helix domain, and each helix contains the C-X9-C motif. This family contains a number of characterized proteins: Cox19 protein - a nuclear gene of Saccharomyces cerevisiae, codes for an 11-kDa protein (Cox19p) required for expression of cytochrome oxidase. Because cox19 mutants are able to synthesize the mitochondrial and nuclear gene products of cytochrome oxidase, Cox19p probably functions post-translationally during assembly of the enzyme. Cox19p is present in the cytoplasm and mitochondria, where it exists as a soluble intermembrane protein. This dual location is similar to what was previously reported for Cox17p, a low molecular weight copper protein thought to be required for maturation of the CuA centre of subunit 2 of cytochrome oxidase. Cox19p have four conserved potential metal ligands, these are three cysteines and one histidine. Mrp10 - belongs to the class of yeast mitochondrial ribosomal proteins that are essential for translation. Eukaryotic NADH-ubiquinone oxidoreductase 19 kDa (NDUFA8) subunit. The CHCH domain was previously called DUF657. 35 matched cddid_all.tbl CDD pfam06748 pfam06748 429097 DUF1217 Protein of unknown function (DUF1217). This family represents a conserved region that is found within bacterial proteins, most of which are hypothetical. Some members contain multiple copies. 149 matched cddid_all.tbl CDD pfam06749 pfam06749 462000 DUF1218 Protein of unknown function (DUF1218). This family contains hypothetical plant proteins of unknown function. Family members contain a number of conserved cysteine residues. 95 matched cddid_all.tbl CDD pfam06750 pfam06750 462001 DiS_P_DiS Bacterial Peptidase A24 N-terminal domain. This family is found at the N-terminus of the pre-pilin peptidases (pfam01478). It's function has not been specifically determined; however some of the family have been characterized as bifunctional, and this domain may contain the N-methylation activity (EC:2.1.1.-). It consists of an intracellular region between a pair of transmembrane. This region contains an invariant proline and two almost fully conserved disulphide bridges - hence the name DiS-P-DiS. The cysteines have been shown to be essential to the overall function of the enzyme in, but their role was incorrectly ascribed. 84 matched cddid_all.tbl CDD pfam06751 pfam06751 429100 EutB Ethanolamine ammonia lyase large subunit (EutB). This family consists of several bacterial ethanolamine ammonia lyase large subunit (EutB) proteins (EC:4.3.1.7). Ethanolamine ammonia-lyase is a bacterial enzyme that catalyzes the adenosylcobalamin-dependent conversion of certain vicinal amino alcohols to oxo compounds and ammonia. The enzyme is a heterodimer composed of subunits of Mr approximately 55,000 (EutB) and 35,000 (EutC). 434 matched cddid_all.tbl CDD pfam06752 pfam06752 462002 E_Pc_C Enhancer of Polycomb C-terminus. This family represents the C-terminus of eukaryotic enhancer of polycomb proteins, which have roles in heterochromatin formation. This family contains several conserved motifs. 229 matched cddid_all.tbl CDD pfam06753 pfam06753 70231 Bradykinin Bradykinin. This family consists of several bradykinin sequences. The skins of anuran amphibians, in addition to mucus glands, contain highly specialized poison glands, which, in reaction to stress or attack, exude a complex noxious cocktail of biologically active molecules. These secretions often contain a plethora of peptides among which bradykinin or structural variants have been identified. 19 matched cddid_all.tbl CDD pfam06754 pfam06754 429102 PhnG Phosphonate metabolism protein PhnG. This family consists of several bacterial phosphonate metabolism protein PhnG sequences. In Escherichia coli, the phn operon encodes proteins responsible for the uptake and breakdown of phosphonates. The exact function of PhnG is unknown, however it is thought likely that along with six other proteins PhnG makes up the the C-P (carbon-phosphorus) lyase. 135 matched cddid_all.tbl CDD pfam06755 pfam06755 369065 CbtA_toxin CbtA_toxin of type IV toxin-antitoxin system. CbtA is a family of bacterial and archaeal toxins of type IV toxin-antitoxin system. Toxins from such systems in free-living bacteria inhibit cell growth by targeting essential functions of cellular metabolism. In this case the toxin inhibits cell-division leading to changes in morphology and finally lysis, by interacting with two essential cytoskeletal proteins, FtsZ and MreB. For FtsZ it inhibits its GTPase activity and GTP-dependent polymerization, and for MreB it inhibits its ATP-dependent polymerization. These actions of CbtA appear to occur simultaneously. he cognate antitoxin family is represented by pfam06154. 108 matched cddid_all.tbl CDD pfam06756 pfam06756 369066 S19 Chorion protein S19 C-terminal. This family represents the C-terminal region of eukaryotic chorion protein S19. In Drosophilidae, the S19 gene is known to form part of an autosomal cluster that also contains s16, s15 and s18. Note that members of this family contain a conserved PVA motif, and many contain pfam03964. 72 matched cddid_all.tbl CDD pfam06757 pfam06757 462003 Ins_allergen_rp Insect allergen related repeat, nitrile-specifier detoxification. This family exemplifies a case of novel gene evolution. The case in point is the arms-race between plants and their infective insective herbivores in the area of the glucosinolate-myrosinase system. Brassicas have developed the glucosinolate-myrosinase system as chemical defence mechanism against the insects, and consequently the insects have adapted to produce a detoxifying molecule, nitrile-specifier protein (NSP). NSP is present in the small white butterfly Pieris rapae. NSP is structurally different from and has no amino acid homology to any known detoxifying enzymes, and it appears to have arisen by a process of domain and gene duplication of a sequence of unknown function that is widespread in insect species and referred to as insect-allergen-repeat protein. Thus this family is found either as a single domain or as a multiple repeat-domain. 173 matched cddid_all.tbl CDD pfam06758 pfam06758 429104 Olduvai Olduvai domain. This domain formerly known as DUF1220 or NBPF domain has been renamed as the Olduvai domain. It is found highly duplicated in the human lineage. 68 matched cddid_all.tbl CDD pfam06760 pfam06760 429105 DUF1221 Protein of unknown function (DUF1221). This is a family of plant proteins, most of which are hypothetical and of unknown function. All members contain the pfam00069 domain, suggesting that they may possess kinase activity. 215 matched cddid_all.tbl CDD pfam06761 pfam06761 429106 IcmF-related Intracellular multiplication and human macrophage-killing. This family represents a conserved region within several bacterial proteins that resemble IcmF, which has been proposed to be involved in Vibrio cholerae cell surface reorganization, resulting in increased adherence to epithelial cells and increased conjugation frequency. Note that many family members are hypothetical proteins. 305 matched cddid_all.tbl CDD pfam06762 pfam06762 462004 LMF1 Lipase maturation factor. This family of transmembrane proteins includes the lipase maturation factor, LMF1. Lipoprotein lipase and hepatic lipase require LMF1 to fold into their active states. It acts as a chaperone required for maturation and transport of active lipoprotein lipase (LPL), through the secretory pathway. 419 matched cddid_all.tbl CDD pfam06763 pfam06763 284235 Minor_tail_Z Prophage minor tail protein Z (GPZ). This family consists of several prophage minor tail protein Z like sequences from Escherichia coli, Salmonella typhimurium and Lambda-like bacteriophages. 190 matched cddid_all.tbl CDD pfam06764 pfam06764 429108 DUF1223 Protein of unknown function (DUF1223). This family consists of several hypothetical proteins of around 250 residues in length which are found in both plants and bacteria. The function of this family is unknown. Structurally it lies in the Thioredoxin-like superfamily. 201 matched cddid_all.tbl CDD pfam06766 pfam06766 429109 Hydrophobin_2 Fungal hydrophobin. This is a family of fungal hydrophobins that seems to be restricted to ascomycetes. These are small, moderately hydrophobic extracellular proteins that have eight cysteine residues arranged in a strictly conserved motif. Hydrophobins are generally found on the outer surface of conidia and of the hyphal wall, and may be involved in mediating contact and communication between the fungus and its environment. Note that some family members contain multiple copies. 65 matched cddid_all.tbl CDD pfam06767 pfam06767 399625 Sif Sif protein. This family consists of several SifA and SifB and SseJ proteins which seem to be specific to the Salmonella species. SifA, SifB and SseJ have been demonstrated to localize to the Salmonella-containing vacuole (SCV) and to Salmonella-induced filaments (Sifs). Trafficking of SseJ and SifB away from the SCV requires the SPI-2 effector SifA. SseJ trafficking away from the SCV along Sifs is unnecessary for its virulence function. 336 matched cddid_all.tbl CDD pfam06769 pfam06769 284238 YoeB_toxin YoeB-like toxin of bacterial type II toxin-antitoxin system. YoeB_toxin is a family of bacterial toxins that forms one component of the type II toxin-antitoxin system in E. coli whose antitoxin is represented by YefM, found in pfam02604. The plasmid encoded Axe-Txe proteins in Enterococcus faecium act as an antitoxin-toxin pair. When the plasmid is lost, the antitoxin is degraded relatively quickly by host enzymes. This allows the toxin to interact with its intracellular target, thus killing the cell or impeding cell growth. These toxins are highly potent protein synthesis inhibitors, specifically blocking the initiation of translation. In the case of YoeB, it binds to the 50 S ribosomal subunit in 70 S ribosomes and interacts with the A site leading to mRNA cleavage at this site. As a result, the 3'-end portion of the mRNA is released from ribosomes, and translation initiation is effectively inhibited. 80 matched cddid_all.tbl CDD pfam06770 pfam06770 462005 Arif-1 Actin-rearrangement-inducing factor (Arif-1). This family consists of several Nucleopolyhedrovirus actin-rearrangement-inducing factor (Arif-1) proteins. In response to Autographa californica multicapsid nuclear polyhedrosis virus (AcMNPV) infection, a sequential rearrangement of the actin cytoskeleton occurs this is induced by Arif-1. Arif-1 is tyrosine phosphorylated and is located at the plasma membrane as a component of the actin rearrangement-inducing complex. 205 matched cddid_all.tbl CDD pfam06771 pfam06771 284240 Desmo_N Viral Desmoplakin N-terminus. This family represents the N-terminus of viral desmoplakin. Desmoplakin is a component of mature desmosomes, which are the main adhesive junctions in epithelia and cardiac muscle. Desmoplakin is also essential for the maturation of adherens junctions. Note that many family members are hypothetical. 97 matched cddid_all.tbl CDD pfam06772 pfam06772 462006 LtrA Bacterial low temperature requirement A protein (LtrA). This family consists of several bacteria specific low temperature requirement A (LtrA) protein sequences which have been found to be essential for growth at low temperatures in Listeria monocytogenes. 352 matched cddid_all.tbl CDD pfam06773 pfam06773 429111 Bim_N Bim protein N-terminus. This family represents the N-terminal region of several mammal specific Bim proteins. The Bim protein is one of the BH3-only proteins, members of the Bcl-2 family that have only one of the Bcl-2 homology regions, BH3. BH3-only proteins are essential initiators of apoptotic cell death. 40 matched cddid_all.tbl CDD pfam06775 pfam06775 462007 Seipin Putative adipose-regulatory protein (Seipin). Seipin is a protein of approximately 400 residues, in humans, which is the product of a gene homologous to the murine guanine nucleotide-binding protein (G protein) gamma-3 linked gene. This gene is implicated in the regulation of body fat distribution and insulin resistance and particularly in the auto-immune disease Berardinelli-Seip congenital lipodystrophy type 2. Seipin has no similarity with other known proteins or consensus motifs that might predict its function, but it is predicted to contain two transmembrane domains at residues 28-49 and 237-258, in human, and a third transmembrane domain might be present at residues 155-173. Seipin may also be implicated in Silver spastic paraplegia syndrome and distal hereditary motor neuropathy type V. 195 matched cddid_all.tbl CDD pfam06776 pfam06776 429113 IalB Invasion associated locus B (IalB) protein. This family consists of several invasion associated locus B (IalB) proteins and related sequences. IalB is known to be a major virulence factor in Bartonella bacilliformis where it was shown to have a direct role in human erythrocyte parasitism. IalB is upregulated in response to environmental cues signaling vector-to-host transmission. Such environmental cues would include, but not be limited to, temperature, pH, oxidative stress, and haemin limitation. It is also thought that IalB would aide B. bacilliformis survival under stress-inducing environmental conditions. The role of this protein in other bacterial species is unknown. 131 matched cddid_all.tbl CDD pfam06777 pfam06777 462008 HBB Helical and beta-bridge domain. HBB is the domain on DEAD-box eukaryotic DNA repair helicases (EC:3.6.1.-) that appears to be a unique fold. It's conformation is of alpha-helices 12-16 plus a short beta-bridge to the FeS-cluster domain at the N-terminal. The full-length XPD protein verifies the presence of damage to DNA and allows DNA repair to proceed. XPD is an assembly of several domains to form a doughnut-shaped molecule that is able to separate two DNA strands and scan the DNA for damage. HBB helps to form the overall DNA-clamping architecture. This family represents a conserved region within a number of eukaryotic DNA repair helicases (EC:3.6.1.-). 190 matched cddid_all.tbl CDD pfam06778 pfam06778 429114 Chlor_dismutase Chlorite dismutase. This family contains chlorite dismutase enzymes of bacterial and archaeal origin. This enzyme catalyzes the disproportionation of chlorite into chloride and oxygen. Note that many family members are hypothetical proteins. 191 matched cddid_all.tbl CDD pfam06779 pfam06779 399632 MFS_4 Uncharacterized MFS-type transporter YbfB. This family represents putative bacterial membrane proteins which may be sugar transporters. Members carry twelve transmembrane regions which are characteriztic of members of the major facilitator sugar-transporter superfamily. 365 matched cddid_all.tbl CDD pfam06780 pfam06780 311003 Erp_C Erp protein C-terminus. This family represents the C-terminus of bacterial Erp proteins that seem to be specific to Borrelia burgdorferi (a causative agent of Lyme disease). Borrelia Erp proteins are particularly heterogeneous, which might enable them to interact with a wide variety of host components. 140 matched cddid_all.tbl CDD pfam06781 pfam06781 429115 CrgA Cell division protein CrgA. CrgA is a trans-membrane (TM) protein, first described in Streptomyces as being required for sporulation through the coordination of several aspects of reproductive growth. In Mtb (Mycobacterium tuberculosis ) CrgA is a central component of the divisome, and consists of 93 residues with two predicted TM helices (TM1: residues 29-51; and TM2: residues 66-88). CrgA facilitates the recruitment of the proteins essential for peptidoglycan synthesis to the divisome and also stabilizes the divisome. Reduced production of CrgA results in elongated cells and reduced growth rate, and loss of CrgA impairs peptidoglycan synthesis. CrgA has homologs in other actinomycetes. 88 matched cddid_all.tbl CDD pfam06782 pfam06782 284250 UPF0236 Uncharacterized protein family (UPF0236). This is a family of unknown function found in Bacteria. Some family members are thought to be transposases. 479 matched cddid_all.tbl CDD pfam06783 pfam06783 399634 UPF0239 Uncharacterized protein family (UPF0239). 83 matched cddid_all.tbl CDD pfam06784 pfam06784 462009 UPF0240 Uncharacterized protein family (UPF0240). 171 matched cddid_all.tbl CDD pfam06785 pfam06785 429117 UPF0242 Uncharacterized protein family (UPF0242) N-terminus. This region includes an N-terminal transmembrane region and a C-terminal coiled-coil. 194 matched cddid_all.tbl CDD pfam06786 pfam06786 429118 UPF0253 Uncharacterized protein family (UPF0253). 65 matched cddid_all.tbl CDD pfam06787 pfam06787 399638 HcgF FeGP cofactor biosynthesis protein HcgF. This archaeal family includes the iron guanylylpyridinol (FeGP) cofactor biosynthesis protein HcgF which catalyzes the transesterification of AMP-GP to afford a Cys (HcgF)-S-GP thioester. 162 matched cddid_all.tbl CDD pfam06788 pfam06788 399639 UPF0257 Uncharacterized protein family (UPF0257). 235 matched cddid_all.tbl CDD pfam06789 pfam06789 462010 MINAR1_C MINAR1 C-terminal domain. Major intrinsically disordered Notch2-associated receptor 1 (MINAR1) is a Notch2-binding protein that has been shown to inhibit angiogenesis and breast cancer growth. This entry represents the C terminus of the MINAR1 protein. 148 matched cddid_all.tbl CDD pfam06790 pfam06790 284258 UPF0259 Uncharacterized protein family (UPF0259). 248 matched cddid_all.tbl CDD pfam06791 pfam06791 429120 TMP_2 Prophage tail length tape measure protein. This family represents a conserved region located towards the N-terminal end of prophage tail length tape measure protein (TMP). TMP is important for assembly of phage tails and involved in tail length determination. Mutated forms TMP cause tail fibres to be shortened. 205 matched cddid_all.tbl CDD pfam06792 pfam06792 429121 UPF0261 Uncharacterized protein family (UPF0261). 400 matched cddid_all.tbl CDD pfam06793 pfam06793 429122 UPF0262 Uncharacterized protein family (UPF0262). 152 matched cddid_all.tbl CDD pfam06794 pfam06794 429123 UPF0270 Uncharacterized protein family (UPF0270). 67 matched cddid_all.tbl CDD pfam06795 pfam06795 284263 Erythrovirus_X Erythrovirus X protein. This family consists of several Erythrovirus X proteins which seem to be found exclusively in human parvovirus and human erythrovirus. The function of this family is unknown. 81 matched cddid_all.tbl CDD pfam06796 pfam06796 429124 NapE Periplasmic nitrate reductase protein NapE. This family consists of several bacterial periplasmic nitrate reductase NapE proteins. Seven genes, napKEFDABC, encoding the periplasmic nitrate reductase system were cloned from the denitrifying phototrophic bacterium Rhodobacter sphaeroides f. sp. denitrificans IL106. NapE is thought to be a transmembrane protein. 53 matched cddid_all.tbl CDD pfam06797 pfam06797 369085 DUF1229 Protein of unknown function (DUF1229). This family consists of several hypothetical proteins of around 415 residues in length which seem to be specific to the bacterium Leptospira interrogans. 146 matched cddid_all.tbl CDD pfam06798 pfam06798 429125 PrkA PrkA serine protein kinase C-terminal domain. This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This family corresponds to the C-terminal domain. 251 matched cddid_all.tbl CDD pfam06799 pfam06799 429126 CGLD27-like Conserved in the green lineage and diatoms 27. This family consist of proteins found in plants and algal chloroplasts, and in cyanobacteria. It includes CGLD27 (Conserved in the green lineage and diatoms 27), which has been described as one out of 14 Fe-responsive orthologues in Chlamydomonas and Arabidopsis, indicating that it is an important component of the iron deficiency response of the plant lineage. 141 matched cddid_all.tbl CDD pfam06800 pfam06800 429127 Sugar_transport Sugar transport protein. This is a family of bacterial sugar transporters approximately 300 residues long. Members include glucose uptake proteins, ribose transport proteins, and several putative and hypothetical membrane proteins probably involved in sugar transport across bacterial membranes. These members are transmembrane proteins which are usually 5+5 duplications. This model recognizes a set of five TMs, 280 matched cddid_all.tbl CDD pfam06802 pfam06802 284269 DUF1231 Protein of unknown function (DUF1231). This family consists of several Orthopoxvirus specific proteins predominantly of around 340 residues in length. This family contains both B17 and B15 proteins, the function of which are unknown. 340 matched cddid_all.tbl CDD pfam06803 pfam06803 462011 DUF1232 Protein of unknown function (DUF1232). This family represents a conserved region of approximately 60 residues within a number of hypothetical bacterial and archaeal proteins of unknown function. 36 matched cddid_all.tbl CDD pfam06804 pfam06804 429129 Lipoprotein_18 NlpB/DapX lipoprotein. This family consists of a number of bacterial lipoproteins often known as NlpB or DapX. This lipoprotein is detected in outer membrane vesicles in Escherichia coli and appears to be nonessential. 297 matched cddid_all.tbl CDD pfam06805 pfam06805 284272 Lambda_tail_I Bacteriophage lambda tail assembly protein I. This family consists of tail assembly proteins from lambdoid and T1 phages and related prophages, e.g. the tail assembly protein I (TAPI). Members of this family contain a core ubiquitin fold domain. The exact function of TAPI is not clear but it is not incorporated into the mature tail. Gene neighborhoods reveal that TAPI co-occurs with genes encoding the host-specificity protein TapJ, and TapK, which contains a JAB metallopeptidase fused to an NlpC/P60 peptidase. It is proposed that the TAPI protein is processed by the peptidase domains of TapK. 82 matched cddid_all.tbl CDD pfam06806 pfam06806 399649 DUF1233 Putative excisionase (DUF1233). This family consists of several putative phage excisionase proteins of around 80 residues in length. 70 matched cddid_all.tbl CDD pfam06807 pfam06807 462012 Clp1 Pre-mRNA cleavage complex II protein Clp1. This family consists of several pre-mRNA cleavage complex II Clp1 (or HeaB) proteins. Six different protein factors are required in vitro for 3' end formation of mammalian pre-mRNAs by endonucleolytic cleavage and polyadenylation. Clp1 is a subunit of cleavage complex IIA, which is required for cleavage, but not for polyadenylation of pre-mRNA. 112 matched cddid_all.tbl CDD pfam06808 pfam06808 284275 DctM Tripartite ATP-independent periplasmic transporter, DctM component. This family contains a diverse range of predicted transporter proteins. Including the DctM subunit of the bacterial and archaeal TRAP C4-dicarboxylate transport (Dct) system permease. In general, C4-dicarboxylate transport systems allow C4-dicarboxylates like succinate, fumarate, and malate to be taken up. TRAP C4-dicarboxylate carriers are secondary carriers that use an electrochemical H+ gradient as the driving force for transport. DctM is an integral membrane protein that is one of the constituents of TRAP carriers. Note that many family members are hypothetical proteins. 413 matched cddid_all.tbl CDD pfam06809 pfam06809 284276 NPDC1 Neural proliferation differentiation control-1 protein (NPDC1). This family consists of several neural proliferation differentiation control-1 (NPDC1) proteins. NPDC1 plays a role in the control of neural cell proliferation and differentiation. It has been suggested that NPDC1 may be involved in the development of several secretion glands. This family also contains the C-terminal region of the C. elegans protein CAB-1 which is known to interact with AEX-3. 352 matched cddid_all.tbl CDD pfam06810 pfam06810 429131 Phage_GP20 Phage minor structural protein GP20. This family consists of several phage minor structural protein GP20 sequences of around 180 residues in length. The function of this family is unknown. 149 matched cddid_all.tbl CDD pfam06812 pfam06812 429132 ImpA_N ImpA, N-terminal, type VI secretion system. This family represents a conserved region located towards the N-terminal end of ImpA and related proteins. ImpA is an inner membrane protein, which has been suggested to be involved with proteins that are exported and associated with colony variations in Actinobacillus actinomycetemcomitans. The ImpA gene in Vibrio cholera and many other bacteria is expressed from the virulence factor operon which produces the pathogenic injection, type VI secretion system; although the exact function of this gene-product is not known it appears to be an essential component of the pathogenic effect. 115 matched cddid_all.tbl CDD pfam06813 pfam06813 284279 Nodulin-like Nodulin-like. This family represents a conserved region within plant nodulin-like proteins. 250 matched cddid_all.tbl CDD pfam06814 pfam06814 369089 Lung_7-TM_R Lung seven transmembrane receptor. This family represents a conserved region with eukaryotic lung seven transmembrane receptors and related proteins. 294 matched cddid_all.tbl CDD pfam06815 pfam06815 462013 RVT_connect Reverse transcriptase connection domain. This domain is known as the connection domain. This domain lies between the thumb and palm domains. 102 matched cddid_all.tbl CDD pfam06816 pfam06816 462014 NOD NOTCH protein. NOTCH signalling plays a fundamental role during a great number of developmental processes in multicellular animals. NOD and NODP represent a region present in many NOTCH proteins and NOTCH homologs in multiple species such as NOTCH2 and NOTCH3, LIN12, SC1 and TAN1. Role of NOD domain remains to be elucidated. 56 matched cddid_all.tbl CDD pfam06817 pfam06817 429135 RVT_thumb Reverse transcriptase thumb domain. This domain is known as the thumb domain. It is composed of a four helix bundle. 66 matched cddid_all.tbl CDD pfam06818 pfam06818 462015 Fez1 Fez1. This family represents the eukaryotic Fez1 protein. Fez1 contains a leucine-zipper region with similarity to the DNA-binding domain of the cAMP-responsive activating-transcription factor 5. There is evidence that Fez1 inhibits cancer cell growth through regulation of mitosis, and that its alterations result in abnormal cell growth. Note that some family members contain more than one copy of this region. 198 matched cddid_all.tbl CDD pfam06819 pfam06819 399657 Arc_PepC Archaeal Peptidase A24 C-terminal Domain. This region is of unknown function but is found in some archaeal pfam01478. It is predicted to be of mixed alpha/beta secondary structure by JPred. 112 matched cddid_all.tbl CDD pfam06820 pfam06820 148432 Phage_fiber_C Putative prophage tail fibre C-terminus. This family represents the C-terminus of a prophage tail fibre protein found mostly in E. coli. All family members contain a conserved RLGP motif. 64 matched cddid_all.tbl CDD pfam06821 pfam06821 399658 Ser_hydrolase Serine hydrolase. Members of this family have serine hydrolase activity. They contain a conserved serine hydrolase motif, GXSXG/A, where the serine is a putative nucleophile. This family has an alpha-beta hydrolase fold. Eukaryotic members of this family have a conserved LXCXE motif, which binds to retinoblastomas. This motif is absent from prokaryotic members of this family. 171 matched cddid_all.tbl CDD pfam06822 pfam06822 284287 DUF1235 Protein of unknown function (DUF1235). This family contains a number of viral proteins of unknown function. 261 matched cddid_all.tbl CDD pfam06823 pfam06823 429137 DUF1236 Protein of unknown function (DUF1236). This family contains a number of hypothetical bacterial proteins of unknown function. Some family members contain more than one copy of the region represented by this family. 64 matched cddid_all.tbl CDD pfam06824 pfam06824 429138 Glyco_hydro_125 Metal-independent alpha-mannosidase (GH125). This family, which contains bacterial and fungal glycoside hydrolases, is also known as GH125. They function as metal-independent alpha-mannosidases, with specificity for alpha-1,6-linked non-reducing terminal mannose residues. Structurally this family is part of the 6 hairpin glycosidase superfamily. 416 matched cddid_all.tbl CDD pfam06825 pfam06825 429139 HSBP1 Heat shock factor binding protein 1. Heat shock factor binding protein 1 (HSBP1) appears to be a negative regulator of the heat shock response. 51 matched cddid_all.tbl CDD pfam06826 pfam06826 284291 Asp-Al_Ex Predicted Permease Membrane Region. This family represents five transmembrane helices that are normally found flanking (five either side) a pair of pfam02080 domains. This suggests that the paired regions form a ten helical structure, probably forming the pore, whereas the pfam02080) binds a ligand for export or regulation of the pore. Swiss:Q8L3K8 is described as a aspartate-alanine antiporter. In conjunction with Swiss:Q8L3K9 it forms a 'proton motive metabolic cycle catalyzed by an aspartate-alanine exchange'. The general conservation of domain architecture in this family suggests that they are functional orthologues. 167 matched cddid_all.tbl CDD pfam06827 pfam06827 429140 zf-FPG_IleRS Zinc finger found in FPG and IleRS. This zinc binding domain is found at the C-terminus of isoleucyl tRNA synthetase and the enzyme Formamidopyrimidine-DNA glycosylase EC:3.2.2.23. 28 matched cddid_all.tbl CDD pfam06830 pfam06830 462016 Root_cap Root cap. The cells at the periphery of the root cap are continuously sloughed off from the root into the mucilage, and are thought to be programmed to die.This family represents a conserved region approximately 60 residues in length within plant root cap proteins, which may be involved in the process. 57 matched cddid_all.tbl CDD pfam06831 pfam06831 399664 H2TH Formamidopyrimidine-DNA glycosylase H2TH domain. Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. This family is the central domain containing the DNA-binding helix-two turn-helix domain. 89 matched cddid_all.tbl CDD pfam06832 pfam06832 429142 BiPBP_C Penicillin-Binding Protein C-terminus Family. This conserved region of approximately 90 residues is found in a sub-group of bacterial Penicillin-Binding Proteins (PBPs). A variable length loop region separates this region from the transpeptidase unit (pfam00905). It is predicted by PROF to be an all beta fold. 89 matched cddid_all.tbl CDD pfam06833 pfam06833 399666 MdcE Malonate decarboxylase gamma subunit (MdcE). This family consists of several bacterial malonate decarboxylase gamma subunit proteins. Malonate decarboxylase of Klebsiella pneumoniae consists of four different subunits and catalyzes the conversion of malonate plus H+ to acetate and CO2. The catalysis proceeds via acetyl and malonyl thioester residues with the phosphribosyl-dephospho-CoA prosthetic group of the acyl carrier protein (ACP) subunit. MdcD and E together probably function as malonyl-S-ACP decarboxylase. 232 matched cddid_all.tbl CDD pfam06834 pfam06834 429143 TraU TraU protein. This family consists of several bacterial TraU proteins. TraU appears to be more essential to conjugal DNA transfer than to assembly of pilus filaments. 306 matched cddid_all.tbl CDD pfam06835 pfam06835 429144 LptC Lipopolysaccharide-assembly, LptC-related. This family consists of several related groups of proteins one of which is the LptC family. LptC is involved in lipopolysaccharide-assembly on the outer membrane of Gram-negative organizms. The lipopolysaccharide component of the outer bacterial membrane is transported form its source of origin to the outer membrane by a set of proteins constituting a transport machinery that is made up of LptA, LptB, LptC, LptD, LptE. LptC is located on the inner membrane side of the intermembrane space. 175 matched cddid_all.tbl CDD pfam06836 pfam06836 429145 DUF1240 Protein of unknown function (DUF1240). This family consists of a number of hypothetical putative membrane proteins which seem to be specific to Photorhabdus and Yersinia species. The function of this family is unknown. 95 matched cddid_all.tbl CDD pfam06837 pfam06837 284300 Fijivirus_P9-2 Fijivirus P9-2 protein. This family consists of several Fijivirus specific P9-2 proteins from Rice black streaked dwarf virus (RBSDV) and Fiji disease virus. The function of this family is unknown. 207 matched cddid_all.tbl CDD pfam06838 pfam06838 429146 Met_gamma_lyase Methionine gamma-lyase. This is a putative pyridoxal 5'-phosphate-dependent methionine gamma-lyase enzyme involved in methionine catabolism. 405 matched cddid_all.tbl CDD pfam06839 pfam06839 462017 zf-GRF GRF zinc finger. This presumed zinc binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to pfam01396. 45 matched cddid_all.tbl CDD pfam06840 pfam06840 462018 DUF1241 Protein of unknown function (DUF1241). This family consists of several programmed cell death 10 protein (PDCD10 or TFAR15) sequences. The function of this family is unknown. 150 matched cddid_all.tbl CDD pfam06841 pfam06841 429149 Phage_T4_gp19 T4-like virus tail tube protein gp19. This family consists of several tail tube protein gp19 sequences from the T4-like viruses. This family also contains bacterial members which suggest lateral transfer of genes. 134 matched cddid_all.tbl CDD pfam06842 pfam06842 462019 DUF1242 Protein of unknown function (DUF1242). This family consists of a number of eukaryotic proteins of around 72 residues in length. The function of this family is unknown. 35 matched cddid_all.tbl CDD pfam06844 pfam06844 429151 DUF1244 Protein of unknown function (DUF1244). This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown. 65 matched cddid_all.tbl CDD pfam06847 pfam06847 429152 Arc_PepC_II Archaeal Peptidase A24 C-terminus Type II. This region is of unknown function but is found in some archaeal pfam01478. It is predicted to be of mixed alpha/beta secondary structure by Prof. 93 matched cddid_all.tbl CDD pfam06848 pfam06848 399675 Disaggr_repeat Disaggregatase related repeat. This family consists of several repeats which seem to be specific to the Methanosarcina archaea species and are often found in multiple copies in disaggregatase proteins. Members of this family are also found in single copies in several hypothetical proteins. This repeat is also known as DNRLRE repeat and is predicted form a mainly beta-strand structure with two alpha-helices [Adindla et al. Comparative and Functional Genomics 2004; 5:2-16]. It is found in some cell surface proteins. 179 matched cddid_all.tbl CDD pfam06849 pfam06849 429153 DUF1246 Protein of unknown function (DUF1246). This family represents the N-terminus of a number of hypothetical archaeal proteins of unknown function. This family is structurally related to the PreATP-grasp domain. 122 matched cddid_all.tbl CDD pfam06850 pfam06850 399677 PHB_depo_C PHB de-polymerase C-terminus. This family represents the C-terminus of bacterial poly(3-hydroxybutyrate) (PHB) de-polymerase. This degrades PHB granules to oligomers and monomers of 3-hydroxy-butyric acid. 203 matched cddid_all.tbl CDD pfam06851 pfam06851 462020 DUF1247 Protein of unknown function (DUF1247). This family contains a number of hypothetical viral proteins of unknown function approximately 200 residues long. 149 matched cddid_all.tbl CDD pfam06852 pfam06852 369108 DUF1248 Protein of unknown function (DUF1248). This family represents a conserved region within a number of proteins of unknown function that seem to be specific to C. elegans. Note that some family members contain more than one copy of this region. 181 matched cddid_all.tbl CDD pfam06853 pfam06853 429154 DUF1249 Protein of unknown function (DUF1249). This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown. 116 matched cddid_all.tbl CDD pfam06854 pfam06854 429155 Phage_Gp15 Bacteriophage Gp15 protein. This family consists of bacteriophage Gp15 proteins and related bacterial sequences. The function of this family is unknown 170 matched cddid_all.tbl CDD pfam06855 pfam06855 429156 YozE_SAM_like YozE SAM-like fold. YozE-like is a family of Firmicute proteins that carries a four-helix motif similar to sterile alpha motif (SAM) domains. The family is suggested to fall into two subfamilies, possibly with differing functions based on the different surface charges on the three structural representatives, YozE MW0776 and MW1311. What this function is is not yet known although it is likely to involve binding to DNA. 65 matched cddid_all.tbl CDD pfam06856 pfam06856 369111 AcMNPV_Orf17 Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf17. This family is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf17; it is a family of uncharacterized viral proteins. 121 matched cddid_all.tbl CDD pfam06857 pfam06857 429157 ACP Malonate decarboxylase delta subunit (MdcD). This family consists of several bacterial malonate decarboxylase delta subunit (MdcD) proteins. Malonate decarboxylase of Klebsiella pneumoniae consists of four different subunits and catalyzes the conversion of malonate plus H+ to acetate and CO2. The catalysis proceeds via acetyl and malonyl thioester residues with the phosphribosyl-dephospho-CoA prosthetic group of the acyl carrier protein (ACP) subunit. MdcC is the (apo) ACP subunit. The family also contains the CitD family of citrate lyase acyl carrier proteins. 83 matched cddid_all.tbl CDD pfam06858 pfam06858 462021 NOG1 Nucleolar GTP-binding protein 1 (NOG1). This family represents a conserved region of approximately 60 residues in length within nucleolar GTP-binding protein 1 (NOG1). In S. cerevisiae, the NOG1 gene has been shown to be essential for cell viability, suggesting that NOG1 may play an important role in nucleolar functions. Family members include eukaryotic, bacterial and archaeal proteins. 58 matched cddid_all.tbl CDD pfam06859 pfam06859 462022 Bin3 Bicoid-interacting protein 3 (Bin3). This family represents a conserved region of approximately 120 residues within eukaryotic Bicoid-interacting protein 3 (Bin3). Bin3, which shows similarity to a number of protein methyltransferases that modify RNA-binding proteins, interacts with Bicoid, which itself directs pattern formation in the early Drosophila embryo. The interaction might allow Bicoid to switch between its dual roles in transcription and translation. Note that family members contain a conserved HLN motif. 109 matched cddid_all.tbl CDD pfam06861 pfam06861 115513 BALF1 BALF1 protein. This family consists of several BALF1 proteins which seem to be specific to the Lymphocryptoviruses. BALF1, inhibits the antiapoptotic activity of EBV BHRF1 and of KSBcl-2. 184 matched cddid_all.tbl CDD pfam06862 pfam06862 369113 UTP25 Utp25, U3 small nucleolar RNA-associated SSU processome protein 25. UTP25 is a family of eukaryotic proteins. The family displays limited sequence similarity to DEAD-box RNA helicases, having alternative residues at the Walker A and DEAD-box sites, but conservation of structural and other key residues. The domain is required and sufficient for the interaction of Utp25 with Utp3. UTP25 interacts with nucleolar protein Nop19 in S. cerevisiae, and Nop19p is essential for the incorporation of Utp25p into pre-ribosomes. 471 matched cddid_all.tbl CDD pfam06863 pfam06863 429160 DUF1254 Protein of unknown function (DUF1254). This family represents a conserved region about 130 residues long within hypothetical proteins of unknown function. Family members include eukaryotic, bacterial and archaeal proteins. 131 matched cddid_all.tbl CDD pfam06864 pfam06864 429161 PAP_PilO Pilin accessory protein (PilO). This family consists of several enterobacterial PilO proteins. The function of PilO is unknown although it has been suggested that it is a cytoplasmic protein in the absence of other Pil proteins, but PilO protein is translocated to the outer membrane in the presence of other Pil proteins. Alternatively, PilO protein may form a complex with other Pil protein(s). PilO has been predicted to function as a component of the pilin transport apparatus and thin-pilus basal body. This family does not seem to be related to pfam04350. 412 matched cddid_all.tbl CDD pfam06865 pfam06865 462023 Ppnp Pyrimidine/purine nucleoside phosphorylase. This family consist of YaiE and related proteins. YaiE from E. coli catalyzes phosphorolysis of diverse nucleosides, yielding D-ribose 1-phosphate and free bases. 92 matched cddid_all.tbl CDD pfam06866 pfam06866 115518 DUF1256 Protein of unknown function (DUF1256). This family consists of several uncharacterized bacterial proteins which seem to be specific to the orders Clostridia and Bacillales. Family members are typically around 180 residues in length. The function of this family is unknown. These proteins are related to peptidase family M63 and so may be peptidases. 164 matched cddid_all.tbl CDD pfam06868 pfam06868 429163 DUF1257 Protein of unknown function (DUF1257). This family contains hypothetical proteins of unknown function that are approximately 120 residues long. Family members include eukaryotic and bacterial proteins. 103 matched cddid_all.tbl CDD pfam06869 pfam06869 429164 DUF1258 Protein of unknown function (DUF1258). This family represents a conserved region approximately 260 residues long within a number of hypothetical proteins of unknown function that seem to be specific to C. elegans. Note that this family contains a number of conserved cysteine and histidine residues.This family corresponds to the Mirage group of putative transposases and family members are relatively close homologs of Transposase_21 (pfam02992) proteins (1). 250 matched cddid_all.tbl CDD pfam06870 pfam06870 462024 RNA_pol_I_A49 A49-like RNA polymerase I associated factor. Saccharomyces cerevisiae A49 is a specific subunit associated with RNA polymerase I (Pol I) in eukaryotes. Pol I maintains transcription activities in A49 deletion mutants. However, such mutants are deficient in transcription activity at low temperatures. Deletion analysis of the fusion yeast homolog indicate that only the C-terminal two thirds are required for function. Transcript analysis has demonstrated that A49 is maximizing transcription of ribosomal DNA. 373 matched cddid_all.tbl CDD pfam06871 pfam06871 429166 TraH_2 TraH_2. This family consists of several TraH proteins which seem to be specific to Agrobacterium and Rhizobium species. This protein is thought to be involved in conjugal transfer but its function is unknown. This family does not appear to be related to pfam06122. 208 matched cddid_all.tbl CDD pfam06872 pfam06872 399689 EspG EspG protein. This family consists of several EspG like proteins from Citrobacter rodentium and Escherichia coli. EspG is secreted by the type III secretory system and is translocated into host epithelial cells. EspG is homologous with Shigella flexneri protein VirA and can rescue invasion in a Shigella virA mutant, indicating that these proteins are functionally equivalent in Shigella. EspG plays an accessory but as yet undefined role in EPEC virulence that may involve intestinal colonization. 351 matched cddid_all.tbl CDD pfam06873 pfam06873 284327 SerH Cell surface immobilization antigen SerH. This family consists of several cell surface immobilization antigen SerH proteins which seem to be specific to Tetrahymena thermophila. The SerH locus of Tetrahymena thermophila is one of several paralogous loci with genes encoding variants of the major cell surface protein known as the immobilization antigen (i-ag). 418 matched cddid_all.tbl CDD pfam06874 pfam06874 429167 FBPase_2 Firmicute fructose-1,6-bisphosphatase. This family consists of several bacterial fructose-1,6-bisphosphatase proteins (EC:3.1.3.11) which seem to be specific to phylum Firmicutes. Fructose-1,6-bisphosphatase (FBPase) is a well known enzyme involved in gluconeogenesis. This family does not seem to be structurally related to pfam00316. 639 matched cddid_all.tbl CDD pfam06875 pfam06875 115526 PRF Plethodontid receptivity factor PRF. This family consists of several plethodontid receptivity factor (PRF) proteins which seem to be specific to Plethodon jordani (Jordan's salamander). PRF is a courtship pheromone produced by males increase female receptivity. 214 matched cddid_all.tbl CDD pfam06876 pfam06876 369118 SCRL Plant self-incompatibility response (SCRL) protein. This family consists of several Plant self-incompatibility response (SCRL) proteins. The male component of the self-incompatibility response in Brassica has been shown to be encoded by the S locus cysteine-rich gene (SCR). SCR is related, at the sequence level, to the pollen coat protein (PCP) gene family whose members encode small, cysteine-rich proteins located in the proteo-lipidic surface layer (tryphine) of Brassica pollen grains. 67 matched cddid_all.tbl CDD pfam06877 pfam06877 429168 RraB Regulator of ribonuclease activity B. This family of proteins regulate mRNA abundance by binding to RNaseE and inhibiting its endonucleolytic activity. A subset of these proteins are predicted to function as immunity proteins. 98 matched cddid_all.tbl CDD pfam06878 pfam06878 399692 Pkip-1 Pkip-1 protein. This family consists of several Pkip-1 proteins which seem to be specific to Nucleopolyhedroviruses. The function of this family is unknown although it has been found that Pkip-1 is not essential for virus replication in cell culture or by in vivo intrahaemocoelic injection. 163 matched cddid_all.tbl CDD pfam06880 pfam06880 462025 DUF1262 Protein of unknown function (DUF1262). This family represents a conserved region within a number of proteins of unknown function that seem to be specific to Arabidopsis thaliana. Note that some family members contain more than one copy of this region. 101 matched cddid_all.tbl CDD pfam06881 pfam06881 462026 Elongin_A RNA polymerase II transcription factor SIII (Elongin) subunit A. This family represents a conserved region within RNA polymerase II transcription factor SIII (Elongin) subunit A. In mammals, the Elongin complex activates elongation by RNA polymerase II by suppressing transient pausing of the polymerase at many sites within transcription units. Elongin is a heterotrimer composed of A, B, and C subunits of 110, 18, and 15 kilodaltons, respectively. Subunit A has been shown to function as the transcriptionally active component of Elongin. 105 matched cddid_all.tbl CDD pfam06882 pfam06882 462027 DUF1263 Protein of unknown function (DUF1263). This family represents a conserved region located towards the C-terminus of a number proteins of unknown function that seem to be specific to Oryza sativa. 57 matched cddid_all.tbl CDD pfam06883 pfam06883 462028 RNA_pol_Rpa2_4 RNA polymerase I, Rpa2 specific domain. This domain is found between domain 3 (pfam04565) and domain 5 (pfam04565), but shows no homology to domain 4 of Rpb2. The external domains in multisubunit RNA polymerase (those most distant from the active site) are known to demonstrate more sequence variability. 58 matched cddid_all.tbl CDD pfam06884 pfam06884 429173 DUF1264 Protein of unknown function (DUF1264). This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 200 residues long. Some family members are annotated as putative lipoproteins. 168 matched cddid_all.tbl CDD pfam06886 pfam06886 462029 TPX2 Targeting protein for Xklp2 (TPX2) domain. This family represents a conserved region approximately 60 residues long within the eukaryotic targeting protein for Xklp2 (TPX2). Xklp2 is a kinesin-like protein localized on centrosomes throughout the cell cycle and on spindle pole microtubules during metaphase. In Xenopus, it has been shown that Xklp2 protein is required for centrosome separation and maintenance of spindle bi-polarity. TPX2 is a microtubule-associated protein that mediates the binding of the C-terminal domain of Xklp2 to microtubules. It is phosphorylated during mitosis in a microtubule-dependent way. The TPX domain appears to be truncated in fungal species. 77 matched cddid_all.tbl CDD pfam06887 pfam06887 462030 DUF1265 Protein of unknown function (DUF1265). This family represents a conserved region approximately 50 residues long within a number of proteins of unknown function that seem to be restricted to C. elegans. The GO annotation for this protein indicate that its a protein involved in nematode larval development and has a positive regulation on growth rate. 46 matched cddid_all.tbl CDD pfam06888 pfam06888 284339 Put_Phosphatase Putative Phosphatase. This family contains a number of putative eukaryotic acid phosphatases. Some family members represent the products of the PSI14 phosphatase family in Lycopersicon esculentum (Tomato). 234 matched cddid_all.tbl CDD pfam06889 pfam06889 462031 DUF1266 Protein of unknown function (DUF1266). This family consists of several hypothetical bacterial proteins of around 235 residues in length. Members of this family seem to be found exclusively in the Enterobacteria Salmonella typhimurium and Escherichia coli. The function of this family is unknown. 175 matched cddid_all.tbl CDD pfam06890 pfam06890 462032 Phage_Mu_Gp45 Bacteriophage Mu Gp45 spike protein. This family consists of Bacteriophage Mu Gp45 related proteins from both phages and bacteria. This protein forms the spike which punctures the cell membrane. 68 matched cddid_all.tbl CDD pfam06891 pfam06891 429177 P2_Phage_GpR P2 phage tail completion protein R (GpR). This family consists of P2 phage tail completion protein R (GpR) like sequences. GpR is thought to be a tail completion protein which is essential for stable head joining. 131 matched cddid_all.tbl CDD pfam06892 pfam06892 462033 Phage_CP76 Phage regulatory protein CII (CP76). This family consists of several phage regulatory protein CII (CP76) sequences which are thought to be DNA binding proteins which are involved in the establishment of lysogeny. 142 matched cddid_all.tbl CDD pfam06894 pfam06894 284344 Phage_TAC_2 Bacteriophage lambda tail assembly chaperone, TAC, protein G. This family consists of Bacteriophage lambda minor tail protein G and related sequences. The construction of phage tails involves a stage of tail-tube formation, and tail-tube polymerization requires two additional proteins, gpG and gpGT. The open reading frames, ORFs, for gpG and gpGT are overlapping and are related by a programmed translational frameshift. During virion morphogenesis, gpG is expressed in large amounts, and about 3.5% of the time, a -1 translational frameshift leads to the production of the larger fusion protein, gpGT. The correct ratio of gpG to gpGT, as determined by the frequency of frameshifting, is crucial for tail assembly. Since gpG accumulates to high levels during a lambda infection and yet is not found in mature phage particles it is believed to act as a chaperone. 126 matched cddid_all.tbl CDD pfam06896 pfam06896 311073 Phage_TAC_3 Phage tail assembly chaperone proteins, TAC. This is a family of phage tail tube assembly chaperone proteins from some Siphoviridae viruses. 115 matched cddid_all.tbl CDD pfam06897 pfam06897 429179 DUF1269 Protein of unknown function (DUF1269). This family consists of several bacterial and archaeal proteins of around 200 residues in length. The function of this family is unknown. The family carries a repeated glycine-zipper sequence- motif, GxxxGxxxG, where the x following the G is frequently found to be an alanine. As glycine-zippers occur in membrane proteins, this family is likely to be found spanning a membrane. 99 matched cddid_all.tbl CDD pfam06898 pfam06898 462034 YqfD Putative stage IV sporulation protein YqfD. This family consists of several putative bacterial stage IV sporulation (SpoIV) proteins. YqfD of Bacillus subtilis is known to be essential for efficient sporulation although its exact function is unknown. 379 matched cddid_all.tbl CDD pfam06899 pfam06899 429181 WzyE WzyE protein, O-antigen assembly polymerase. This family consists of several WzyE proteins which appear to be specific to Enterobacteria. Members of this family are described as putative ECA polymerases this has been found to be incorrect. The function of this family is unknown. The family is a transmembrane family with up to 11 TM regions, and is necessary for the assembly of O-antigen lipopolysaccharide. 447 matched cddid_all.tbl CDD pfam06900 pfam06900 284349 DUF1270 Protein of unknown function (DUF1270). This family consists of several hypothetical Staphylococcus aureus and phage proteins of 53 residues in length. The function of this family is unknown. 53 matched cddid_all.tbl CDD pfam06901 pfam06901 399706 FrpC RTX iron-regulated protein FrpC. This family consists of several RTX iron-regulated FrpC proteins which appear to be found exclusively in Neisseria meningitidis. FrpC has been shown to be related to the RTX family of bacterial cytotoxins. FrpC is found in the meningococcal outer membrane. The function of this family is unknown although it is thought to be a virulence factor. 228 matched cddid_all.tbl CDD pfam06902 pfam06902 399707 Fer4_19 Divergent 4Fe-4S mono-cluster. Members of this family contain three highly conserved cysteine residues. This family includes proteins containing divergent domains which are most likely to bind to iron-sulfur clusters. 64 matched cddid_all.tbl CDD pfam06903 pfam06903 429182 VirK VirK protein. This family consists of several bacterial VirK proteins of around 145 residues in length. The function of this family is unknown. 98 matched cddid_all.tbl CDD pfam06904 pfam06904 429183 Extensin-like_C Extensin-like protein C-terminus. This family represents the C-terminus (approx. 120 residues) of a number of bacterial extensin-like proteins. Extensins are cell wall glycoproteins normally associated with plants, where they strengthen the cell wall in response to mechanical stress. Note that many family members of this family are hypothetical. 176 matched cddid_all.tbl CDD pfam06905 pfam06905 462035 FAIM1 Fas apoptotic inhibitory molecule (FAIM1). This family consists of several fas apoptotic inhibitory molecule (FAIM1) proteins. FAIM expression is upregulated in B cells by anti-Ig treatment that induces Fas-resistance, and overexpression of FAIM diminishes sensitivity to Fas-mediated apoptosis of B and non-B cell lines. FAIM1 is highly evolutionarily conserved and is widely expressed in murine tissues, suggesting that FAIM plays an important role in cellular physiology. 172 matched cddid_all.tbl CDD pfam06906 pfam06906 429185 DUF1272 Protein of unknown function (DUF1272). This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown. 57 matched cddid_all.tbl CDD pfam06907 pfam06907 462036 Latexin Latexin. This family consists of several animal specific latexin proteins. Latexin is a carboxypeptidase A inhibitor and is expressed in a cell type-specific manner in both central and peripheral nervous systems in the rat. 217 matched cddid_all.tbl CDD pfam06908 pfam06908 429187 YpsA YspA SLOG family. Family in the SLOG superfamily showing fusions to NAD utilization and ADP-ribosylation domains including NUDIX, NADAR and MACRO. Members of this family are predicted to function as sensors of nucleotide, nucleotide-derived ligands, or nucleic acids, which are potentially processed/modified by the associating enzymes. 168 matched cddid_all.tbl CDD pfam06910 pfam06910 429188 MEA1 Male enhanced antigen 1 (MEA1). This family consists of several mammalian male enhanced antigen 1 (MEA1) proteins. The Mea-1 gene is found to be localized in primary and secondary spermatocytes and spermatids, but the protein products are detected only in spermatids. Intensive transcription of Mea-1 gene and specific localization of the gene product suggest that Mea-1 may play a important role in the late stage of spermatogenesis. 125 matched cddid_all.tbl CDD pfam06911 pfam06911 462037 Senescence Senescence domain. This is the AAA ATPase senescence domain (SC) found at the C-terminal of plant senescence-associated proteins and spartin. In Hemerocallis, petals a genetically based program that leads to senescence and cell death approximately 24 hours after the flower opens, and it is believed that senescence proteins produced around that time have a role in this program. This domain is also present at the C-terminal of Spartin, a protein from higher vertebrates associated with mitochondrial membranes and transportation along microtubules. Spartin functions presynaptically with endocytic adaptor Eps15 to regulate synaptic growth and function. Mutations in human spartin gene cause Troyer syndrome, a hereditary spastic paraplegia. This AAA ATPase domain, similar to other AAA proteins contain an alpha/beta nucleotide-binding domain (NBD) and a smaller four-helix bundle domain (HBD). Uniquely among AAA structures, spastin has two helices (N-terminal alpha1 and C-terminal alpha11) hat embrace the NBD. 186 matched cddid_all.tbl CDD pfam06912 pfam06912 462038 DUF1275 Protein of unknown function (DUF1275). This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown although most members have 6 TM regions, and may be putative permeases. 202 matched cddid_all.tbl CDD pfam06916 pfam06916 429191 FAM210A-B_dom FAM210A/B-like domain. This domain is found in mitochondrial proteins, including FAM210A and B, which contains a transmembrane peptide. Its function is not clear. FAM210A, a protein essential in maintaining skeletal muscle structure and strength, interacts with mitochondrial translation elongation factor EF-Tu and promotes mitochondrial protein expression. In FAM210A, this domain is responsible for binding EF-Tu. FAM210B plays a role in erythroid differentiation and is involved in cell proliferation and tumour cell growth suppression. 88 matched cddid_all.tbl CDD pfam06917 pfam06917 462039 Pectate_lyase_2 Periplasmic pectate lyase. This family consists of several Enterobacterial periplasmic pectate lyase proteins (EC:4.2.2.2). A major virulence determinant of the plant-pathogenic enterobacterium Erwinia chrysanthemi is the production of pectate lyase enzymes that degrade plant cell walls. 556 matched cddid_all.tbl CDD pfam06918 pfam06918 369136 DUF1280 Protein of unknown function (DUF1280). This family represents a conserved region approximately 200 residues long within a number of proteins of unknown function that seem to be specific to C. elegans. 219 matched cddid_all.tbl CDD pfam06919 pfam06919 284364 Phage_T4_Gp30_7 Phage Gp30.7 protein. This family consists of several phage Gp30.7 proteins of 121 residues in length. Family members seem to be exclusively from the T4-like viruses. The function of this family is unknown. 121 matched cddid_all.tbl CDD pfam06920 pfam06920 462040 DHR-2_Lobe_A DHR-2, Lobe A. This entry represents a conserved region within a number of eukaryotic dedicator of cytokinesis proteins (DOCK), which are guanine nucleotide exchange factors (GEFs), that activate some small GTPases by exchanging bound GDP for free GTP such as Rac. These proteins have a DOCK-homology region 1 (DHR-1, also known as DOCK-type C2 domain) at the N-terminus and a DHR-2 (also known as DOCKER domain) at the C-terminal. The DHR-2 is a GEF catalytic domain organized into three lobes, A, B and C, with the Rho-family binding site and catalytic centre generated entirely from lobes B and C. This entry represents Lobe A, formed from an antiparallel array of alpha helices that adopts a tetratricopeptide repeat-like fold, which through extensive contacts with lobe B, stabilizes DHR-2 domain. 154 matched cddid_all.tbl CDD pfam06922 pfam06922 115570 CTV_P13 Citrus tristeza virus P13 protein. This family consists of several Citrus tristeza virus (CTV) P13 13-kDa proteins. Citrus tristeza virus (CTV), a member of the closterovirus group, is one of the more complex single-stranded RNA viruses. The function of this family is unknown. 119 matched cddid_all.tbl CDD pfam06923 pfam06923 429193 GutM Glucitol operon activator protein (GutM). This family consists of several glucitol operon activator (GutM) proteins. Expression of the glucitol (gut) operon in Escherichia coli is regulated by an unusual, complex system which consists of an activator (encoded by the gutM gene) and a repressor (encoded by the gutR gene) in addition to the cAMP-CRP complex (CRP, cAMP receptor protein). Synthesis of the mRNA, which initiates at the promoter specific to the gutR gene, occurs within the gutM gene. Expressional control of the gut operon appears to occur as a consequence of the antagonistic action of the products of the autogenously regulated gutM and gutR genes. 105 matched cddid_all.tbl CDD pfam06924 pfam06924 462041 DUF1281 Protein of unknown function (DUF1281). This family consists of several hypothetical enterobacterial proteins of around 170 residues in length. Members of this family are found in Escherichia coli, Salmonella typhimurium and Shigella species. The function of this family is unknown. 179 matched cddid_all.tbl CDD pfam06925 pfam06925 284368 MGDG_synth Monogalactosyldiacylglycerol (MGDG) synthase. This family represents a conserved region of approximately 180 residues within plant and bacterial monogalactosyldiacylglycerol (MGDG) synthase (EC:2.4.1.46). In Arabidopsis, there are two types of MGDG synthase which differ in their N-terminal portion: type A and type B. 169 matched cddid_all.tbl CDD pfam06926 pfam06926 284369 Rep_Org_C Putative replisome organizer protein C-terminus. This family represents the C-terminus (approximately 100 residues) of a putative replisome organizer protein in Lactococcus bacteriophages. 95 matched cddid_all.tbl CDD pfam06929 pfam06929 399720 Rotavirus_VP3 Rotavirus VP3 protein. This family consists of several Rotavirus specific VP3 proteins. VP3 is known to be a viral guanylyltransferase and is thought to posses methyltransferase activity and therefore VP3 is a predicted multifunctional capping enzyme. 687 matched cddid_all.tbl CDD pfam06931 pfam06931 462042 Adeno_E4_ORF3 Mastadenovirus E4 ORF3 protein. This family consists of several Mastadenovirus E4 ORF3 proteins. Early proteins E4 ORF3 and E4 ORF6 have complementary functions during viral infection. Both proteins facilitate efficient viral DNA replication, late protein expression, and prevention of concatenation of viral genomes. A unique function of E4 ORF3 is the reorganization of nuclear structures known as PML oncogenic domains (PODs). The function of these domains is unclear, but PODs have been implicated in a number of important cellular processes, including transcriptional regulation, apoptosis, transformation, and response to interferon. 112 matched cddid_all.tbl CDD pfam06932 pfam06932 429195 DUF1283 Protein of unknown function (DUF1283). This family consists of several hypothetical proteins of around 115 residues in length which seem to be specific to Enterobacteria. The function of the family is unknown. 74 matched cddid_all.tbl CDD pfam06933 pfam06933 115579 SSP160 Special lobe-specific silk protein SSP160. This family consists of several special lobe-specific silk protein SSP160 sequences which appear to be specific to Chironomus (Midge) species. 758 matched cddid_all.tbl CDD pfam06934 pfam06934 429196 CTI Fatty acid cis/trans isomerase (CTI). This family consists of several fatty acid cis/trans isomerase proteins which appear to be found exclusively in bacteria of the orders Vibrionales and Pseudomonadales. Cis/trans isomerase (CTI) catalyzes the cis-trans isomerization of esterified unsaturated fatty acids in phospholipids, mainly palmitoleic acid (C16:1) and cis-vaccenic acid C(18:1), in response to toxic organic solvents, heat and osmotic stress, and heavy metals. The CTI protein is located in the periplasm and has been shown to be involved in solvent tolerance in Pseudomonas strains. 691 matched cddid_all.tbl CDD pfam06935 pfam06935 429197 DUF1284 Protein of unknown function (DUF1284). This family consists of several hypothetical bacterial and archaeal proteins of around 130 residues in length. The function of this family is unknown, although it is thought that they may be iron-sulphur binding proteins. 102 matched cddid_all.tbl CDD pfam06936 pfam06936 462043 Selenoprotein_S Selenoprotein S (SelS). This family consists of several mammalian selenoprotein S (SelS) sequences. SelS is a plasma membrane protein and is present in a variety of tissues and cell types. Selenoprotein S (SelS) is an intrinsically disordered protein. It formsa selenosulfide bond between cys 174 and Sec 188, that has a redox potential -234 mV. In vitro, SelS is an efficient reductase that depends on the presence of selenocysteine. Due to the high reactivity, SelS also has peroxidase activity that can catalyze the reduction of hydrogen peroxide. It is also resistant to inactivation by hydrogen peroxide which might provide evolutionary advantage compared to cysteine containing peroxidases. 192 matched cddid_all.tbl CDD pfam06937 pfam06937 284377 EURL EURL protein. This family consists of several animal EURL proteins. EURL is preferentially expressed in chick retinal precursor cells as well as in the anterior epithelial cells of the lens at early stages of development. EURL transcripts are found primarily in the peripheral dorsal retina, i.e., the most undifferentiated part of the dorsal retina. EURL transcripts are also detected in the lens at stage 18 and remain abundant in the proliferating epithelial cells of the lens until at least day 11. The distribution pattern of EURL in the developing retina and lens suggest a role before the events leading to cell determination and differentiation. 283 matched cddid_all.tbl CDD pfam06938 pfam06938 429199 DUF1285 Protein of unknown function (DUF1285). This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. The structures revealed a conserved core with domain duplication and a superficial similarity of the C-terminal domain to pleckstrin homology-like folds. The conservation of the domain- interface indicates a potential binding site that is likely to involve a nucleotide-based ligand, with genome-context and gene-fusion analyses additionally supporting a role for this family in signal transduction, possibly during oxidative stress. 144 matched cddid_all.tbl CDD pfam06939 pfam06939 311095 DUF1286 Protein of unknown function (DUF1286). This family consists of several hypothetical archaeal proteins of around 120 residues in length. All members of this family seem to be Sulfolobus species specific. The function of this family is unknown. 111 matched cddid_all.tbl CDD pfam06940 pfam06940 462044 DUF1287 Domain of unknown function (DUF1287). This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. This family is related to pfam00877. 163 matched cddid_all.tbl CDD pfam06941 pfam06941 284381 NT5C 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C). This family consists of several 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C (NT5C) proteins. 5'(3')-Deoxyribonucleotidase is a ubiquitous enzyme in mammalian cells whose physiological function is not known. 180 matched cddid_all.tbl CDD pfam06942 pfam06942 429201 GlpM GlpM protein. This family consists of several bacterial GlpM membrane proteins. GlpM is a hydrophobic protein containing 109 amino acids. It is thought that GlpM may play a role in alginate biosynthesis in Pseudomonas aeruginosa. 107 matched cddid_all.tbl CDD pfam06943 pfam06943 462045 zf-LSD1 LSD1 zinc finger. This family consists of several plant specific LSD1 zinc finger domains. Arabidopsis lsd1 mutants are hyper-responsive to cell death initiators and fail to limit the extent of cell death. Superoxide is a necessary and sufficient signal for cell death propagation. LSD1 monitors a superoxide-dependent signal and negatively regulates a plant cell death pathway. LSD1 protein contains three zinc finger domains, defined by CxxCxRxxLMYxxGASxVxCxxC. It has been suggested that LSD1 defines a zinc finger protein subclass and that LSD1 regulates transcription, via either repression of a pro-death pathway or activation of an anti-death pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. 23 matched cddid_all.tbl CDD pfam06945 pfam06945 462046 DUF1289 Protein of unknown function (DUF1289). This family consists of a number of hypothetical bacterial proteins. The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N-terminus. The function of this family is unknown. Structural modelling suggests this domain may bind nucleic acids. 47 matched cddid_all.tbl CDD pfam06946 pfam06946 311099 Phage_holin_5_1 Bacteriophage A118-like holin, Hol118. This family consists of several Listeria bacteriophage holin proteins and related bacterial sequences. Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis. It is thought that the temporal precision of holin-mediated lysis may occur through the build up of a holin oligomer which causes the lysis. 92 matched cddid_all.tbl CDD pfam06947 pfam06947 429204 DUF1290 Protein of unknown function (DUF1290). This family consists of several bacterial small basic proteins of around 100 residues in length. The function of this family is unknown. 86 matched cddid_all.tbl CDD pfam06949 pfam06949 462047 DUF1292 Protein of unknown function (DUF1292). This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown. 74 matched cddid_all.tbl CDD pfam06950 pfam06950 429206 DUF1293 Protein of unknown function (DUF1293). This family consists of several bacterial and phage proteins of around 115 residues in length. The function of this family is unknown. 115 matched cddid_all.tbl CDD pfam06951 pfam06951 399731 PLA2G12 Group XII secretory phospholipase A2 precursor (PLA2G12). This family consists of several group XII secretory phospholipase A2 precursor (PLA2G12) (EC:3.1.1.4) proteins. Group XII and group V PLA(2)s are thought to participate in helper T cell immune response through release of immediate second signals and generation of downstream eicosanoids. 186 matched cddid_all.tbl CDD pfam06952 pfam06952 429207 PsiA PsiA protein. This family consists of several Enterobacterial PsiA proteins. The function of PsiA is unknown although it is thought that it may affect the generation of an SOS signal in Escherichia coli. 237 matched cddid_all.tbl CDD pfam06953 pfam06953 462048 ArsD Arsenical resistance operon protein ArsD. ArsD was initially reported to be a trans-acting repressor of the arsRDABC operon, which confers resistance to arsenicals and antimonials in Escherichia coli. It has since been shown to be a metallochaperone that delivers As(III) to ArsA (the catalytic subunit of the ArsAB pump encoded by arsRDABC), increasing its affinity for As(III) allowing resistance to environmental concentrations of arsenic. ArsD has three conserved cysteines Cys(12), Cys(13), and Cys(18), which form a three sulfur-coordinated As(III) binding site that is essential for delivery of As(III) to, and activation of the ArsAB pump. This family also includes ArsD homologs which do not contain the conserved CCxxxxC required for function. 120 matched cddid_all.tbl CDD pfam06954 pfam06954 462049 Resistin Resistin. This family consists of several mammalian resistin proteins. Resistin is a 12.5-kDa cysteine-rich secreted polypeptide first reported from rodent adipocytes. It belongs to a multigene family termed RELMs or FIZZ proteins. Plasma resistin levels are significantly increased in both genetically susceptible and high-fat-diet-induced obese mice. Immunoneutralization of resistin improves hyperglycemia and insulin resistance in high-fat-diet-induced obese mice, while administration of recombinant resistin impairs glucose tolerance and insulin action in normal mice. It has been demonstrated that increases in circulating resistin levels markedly stimulate glucose production in the presence of fixed physiological insulin levels, whereas insulin suppressed resistin expression. It has been suggested that resistin could be a link between obesity and type 2 diabetes. 85 matched cddid_all.tbl CDD pfam06955 pfam06955 429210 XET_C Xyloglucan endo-transglycosylase (XET) C-terminus. This family represents the C-terminus (approximately 60 residues) of plant xyloglucan endo-transglycosylase (XET). Xyloglucan is the predominant hemicellulose in the cell walls of most dicotyledons. With cellulose, it forms a network that strengthens the cell wall. XET catalyzes the splitting of xyloglucan chains and the linking of the newly generated reducing end to the non-reducing end of another xyloglucan chain, thereby loosening the cell wall. Note that all family members contain the pfam00722 domain. 48 matched cddid_all.tbl CDD pfam06956 pfam06956 429211 RtcR Regulator of RNA terminal phosphate cyclase. RtcR is a sigma54-dependent enhancer binding protein that activates transcription of the rtcBA operon. The product of the rtcA gene is an RNA 3'-terminal phosphate cyclase. This domain is found at the N terminus of the RtcR sequence. RtcR, and other sigma54-dependent activators, contain pfam00158 in the central region of the protein sequence. 183 matched cddid_all.tbl CDD pfam06957 pfam06957 462050 COPI_C Coatomer (COPI) alpha subunit C-terminus. This family represents the C-terminus (approximately 500 residues) of the eukaryotic coatomer alpha subunit. Coatomer (COPI) is a large cytosolic protein complex which forms a coat around vesicles budding from the Golgi apparatus. Such coatomer-coated vesicles have been proposed to play a role in many distinct steps of intracellular transport. Note that many family members also contain the pfam04053 domain. 402 matched cddid_all.tbl CDD pfam06958 pfam06958 399737 Pyocin_S S-type Pyocin. This family represents a conserved region approximately 180 residues long within bacterial S-type pyocins. Pyocins are polypeptide toxins produced by, and active against, bacteria. S-type pyocins cause cell death by DNA breakdown due to endonuclease activity. 139 matched cddid_all.tbl CDD pfam06959 pfam06959 399738 RecQ5 RecQ helicase protein-like 5 (RecQ5). This family represents a conserved region approximately 200 residues long within eukaryotic RecQ helicase protein-like 5 (RecQ5). The RecQ helicases have been implicated in DNA repair and recombination, and RecQ5 may have an important role in DNA metabolism. 202 matched cddid_all.tbl CDD pfam06961 pfam06961 462051 DUF1294 Protein of unknown function (DUF1294). This family includes a number of hypothetical bacterial and archaeal proteins of unknown function. 55 matched cddid_all.tbl CDD pfam06962 pfam06962 429214 rRNA_methylase Putative rRNA methylase. This family contains a number of putative rRNA methylases. Note that many family members are hypothetical proteins. 137 matched cddid_all.tbl CDD pfam06963 pfam06963 462052 FPN1 Ferroportin1 (FPN1). This family represents a conserved region approximately 100 residues long within eukaryotic Ferroportin1 (FPN1), a protein that may play a role in iron export from the cell. This family may represent a number of transmembrane regions in Ferroportin1. 430 matched cddid_all.tbl CDD pfam06964 pfam06964 462053 Alpha-L-AF_C Alpha-L-arabinofuranosidase C-terminal domain. This family represents the C-terminus (approximately 200 residues) of bacterial and eukaryotic alpha-L-arabinofuranosidase (EC:3.2.1.55). This catalyzes the hydrolysis of nonreducing terminal alpha-L-arabinofuranosidic linkages in L-arabinose-containing polysaccharides. 192 matched cddid_all.tbl CDD pfam06965 pfam06965 429217 Na_H_antiport_1 Na+/H+ antiporter 1. This family contains a number of bacterial Na+/H+ antiporter 1 proteins. These are integral membrane proteins that catalyze the exchange of H+ for Na+ in a manner that is highly dependent on the pH. 378 matched cddid_all.tbl CDD pfam06966 pfam06966 399743 DUF1295 Protein of unknown function (DUF1295). This family contains a number of bacterial and eukaryotic proteins of unknown function that are approximately 300 residues long. 235 matched cddid_all.tbl CDD pfam06967 pfam06967 429218 Mo-nitro_C Mo-dependent nitrogenase C-terminus. This family represents the C-terminus (approximately 80 residues) of a number of bacterial Mo-dependent nitrogenases. These are involved in nitrogen fixation in cyanobacteria. Note that many family members are hypothetical proteins. 78 matched cddid_all.tbl CDD pfam06968 pfam06968 462054 BATS Biotin and Thiamin Synthesis associated domain. Biotin synthase (BioB), EC:2.8.1.6, catalyzes the last step of the biotin biosynthetic pathway. The reaction consists in the introduction of a sulphur atom into dethiobiotin. BioB functions as a homodimer. Thiamin synthesis if a complex process involving at least six gene products (ThiFSGH, ThiI and ThiJ). Two of the proteins required for the biosynthesis of the thiazole moiety of thiamine (vitamin B(1)) are ThiG and ThiH (this family) and form a heterodimer. Both of these reactions are thought of involve the binding of co-factors, and both function as dimers. This domain therefore may be involved in co-factor binding or dimerization (Finn, RD personal observation). 85 matched cddid_all.tbl CDD pfam06969 pfam06969 462055 HemN_C HemN C-terminal domain. Members of this family are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyzes the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX, one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain (pfam04055) suggest it may be a substrate binding domain. 66 matched cddid_all.tbl CDD pfam06970 pfam06970 429221 RepA_N Replication initiator protein A (RepA) N-terminus. This of family of predicted proteins represents the N-terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids. Most proteins in this family are bacterial, but archaeal and eukaryotic members are also included. 76 matched cddid_all.tbl CDD pfam06971 pfam06971 429222 Put_DNA-bind_N Putative DNA-binding protein N-terminus. This family represents the N-terminus (approximately 50 residues) of a number of putative bacterial DNA-binding proteins. 49 matched cddid_all.tbl CDD pfam06972 pfam06972 462056 GIP1_N GBF-interacting protein 1 N-terminal. This entry represents the N-terminal domain of GBF1-interacting protein 1 (GIP1, AT3G13222) from Arabidopsis. GIP1 may act as a coactivator that regulates transcription factors involved in lateral organ development of plants, such as bZIP transcription factors and LBD18. 60 matched cddid_all.tbl CDD pfam06973 pfam06973 429224 DUF1297 Domain of unknown function (DUF1297). This family represents the C-terminus (approximately 200 residues) of a number of archaeal proteins of unknown function. One member is annotated as being a possible carboligase enzyme. 188 matched cddid_all.tbl CDD pfam06974 pfam06974 462057 WS_DGAT_C WS/DGAT C-terminal domain. This domain is found at the C-terminus of wax ester synthases (WS)/diacylglycerol O-acyltransferases (DGAT). These enzymes are utilized for the in vivo production of biodiesel and other wax esters. 144 matched cddid_all.tbl CDD pfam06975 pfam06975 115620 DUF1299 Protein of unknown function (DUF1299). This family represents a conserved region approximately 50 residues long within a number of proteins of unknown function that seem to be specific to Arabidopsis thaliana. Note that many family members contain multiple copies of this region. 47 matched cddid_all.tbl CDD pfam06977 pfam06977 429226 SdiA-regulated SdiA-regulated. This family represents a conserved region approximately within a number of hypothetical bacterial proteins that may be regulated by SdiA, a member of the LuxR family of transcriptional regulators. Some family members contain the pfam01436 repeat. 249 matched cddid_all.tbl CDD pfam06978 pfam06978 429227 POP1 Ribonucleases P/MRP protein subunit POP1. This family represents a conserved region approximately 150 residues long located towards the N-terminus of the POP1 subunit that is common to both the RNase MRP and RNase P ribonucleoproteins (EC:3.1.26.5). These RNA-containing enzymes generate mature tRNA molecules by cleaving their 5' ends. 211 matched cddid_all.tbl CDD pfam06979 pfam06979 462058 TMEM70 TMEM70/TMEM186/TMEM223 protein family. This entry represents the TMEM70/TMEM186/TMEM223 protein family. TMEM70 is a family of proteins essential for assembly of the mitochondrial proton-transporting ATP synthase complex within the inner mitochondrial membrane. TMEM70 functions in the assembly of complexes I and V. 151 matched cddid_all.tbl CDD pfam06980 pfam06980 462059 DUF1302 Protein of unknown function (DUF1302). This entry represents a family of predicted outer membrane beta barrel proteins. These proteins remain uncharacterized. They are approximately 600 residues long. These proteins are likely part of an exporter system that includes an MMPL exporter, a DUF1329 protein pfam07044 family protein that likely acts as a LolA-like chaperone. 374 matched cddid_all.tbl CDD pfam06983 pfam06983 399756 3-dmu-9_3-mt 3-demethylubiquinone-9 3-methyltransferase. This family represents a conserved region approximately 100 residues long within a number of bacterial and archaeal 3-demethylubiquinone-9 3-methyltransferases (EC:2.1.1.64). Note that some family members contain more than one copy of this region, and that many members are hypothetical proteins. 116 matched cddid_all.tbl CDD pfam06984 pfam06984 369158 MRP-L47 Mitochondrial 39-S ribosomal protein L47 (MRP-L47). This family represents the N-terminal region (approximately 8 residues) of the eukaryotic mitochondrial 39-S ribosomal protein L47 (MRP-L47). Mitochondrial ribosomal proteins (MRPs) are the counterparts of the cytoplasmic ribosomal proteins, in that they fulfil similar functions in protein biosynthesis. However, they are distinct in number, features and primary structure. 86 matched cddid_all.tbl CDD pfam06985 pfam06985 369159 HET Heterokaryon incompatibility protein (HET). This family represents a conserved region approximately 150 residues long within various heterokaryon incompatibility proteins that seem to be restricted to ascomycete fungi. Genetic differences in specific het genes prevent a viable heterokaryotic fungal cell from being formed by the fusion of filaments from two different wild-type strains. Many family members also contain the pfam00400 repeat and the pfam05729 domain. 146 matched cddid_all.tbl CDD pfam06986 pfam06986 429230 TraN Type-1V conjugative transfer system mating pair stabilization. TraN is a large cysteine-rich outer membrane protein involved in the mating-pair stabilization (adhesin) component of the F-type conjugative plasmid transfer system. TraN is believed to interact with the core type IV secretion system apparatus through the TraV protein.3]. 240 matched cddid_all.tbl CDD pfam06988 pfam06988 429231 NifT NifT/FixU protein. This family consists of several NifT/FixU bacterial proteins. NifT/FixU is a very small, conserved protein that is found in nif clusters; however, its function is unknown. Although it is thought that the protein may be involved in biosynthesis of the FeMo cofactor of nitrogenase although perturbation of nifT expression in K. pneumoniae has only a limited effect on nitrogen fixation. 64 matched cddid_all.tbl CDD pfam06989 pfam06989 369161 BAALC_N BAALC N-terminus. This family represents the N-terminal region of the mammalian BAALC proteins. BAALC (brain and acute leukaemia, cytoplasmic), that is highly conserved among mammals but evidently absent from lower organizms. Two isoforms are specifically expressed in neuroectoderm-derived tissues, but not in tumours or cancer cell lines of non-neural tissue origin. It has been shown that blasts from a subset of patients with acute leukaemia greatly overexpress eight different BAALC transcripts, resulting in five protein isoforms. Among patients with acute myeloid leukaemia, those overexpressing BAALC show distinctly poor prognosis, pointing to a key role of the BAALC products in leukaemia. It has been suggested that BAALC is a gene implicated in both neuroectodermal and hematopoietic cell functions. 50 matched cddid_all.tbl CDD pfam06990 pfam06990 254007 Gal-3-0_sulfotr Galactose-3-O-sulfotransferase. This family consists of several mammalian galactose-3-O-sulfotransferase proteins. Gal-3-O-sulfotransferase is thought to play a critical role in 3'-sulfation of N-acetyllactosamine in both O- and N-glycans. 400 matched cddid_all.tbl CDD pfam06991 pfam06991 462060 MFAP1 Microfibril-associated/Pre-mRNA processing. MFAP1 was first named for proteins associated with microfibrils which are an important component of the extracellular matrix (ECM) of many tissues. For example, MFAP1 has been shown to be associated with elastin-like fibres at the base of Schlemm's canal endothelium cells, in the juxtacanalicular tissue, and in the uveal region. Based on its role in the ECM and the proximity of the MFAP1 gene to FBN1 it was hypothesized that mutations in MFAP1 contributed to heritable diseases affecting microfibrils, Marfan syndrome but this has now been shown not to be the case. MFAP1 has also been shown to interact directly with certain pre-mRNA processing factor proteins, Prps, which are also spliceosome components and is thus required for pre-mRNA processing. MAFP1 bound to Pr38 of yeast is necessary for cells in vivo to progress from G2 to M phase. 215 matched cddid_all.tbl CDD pfam06992 pfam06992 462061 Phage_lambda_P Replication protein P. This family consists of several Bacteriophage lambda replication protein P like proteins. The bacteriophage lambda P protein promoters replication of the phage chromosome by recruiting a key component of the cellular replication machinery to the viral origin. Specifically, P protein delivers one or more molecules of Escherichia coli DnaB helicase to a nucleoprotein structure formed by the lambda O initiator at the lambda replication origin. 162 matched cddid_all.tbl CDD pfam06993 pfam06993 429234 DUF1304 Protein of unknown function (DUF1304). This family consists of several hypothetical bacterial proteins of around 120 residues in length. The function of this family is unknown. 110 matched cddid_all.tbl CDD pfam06994 pfam06994 429235 Involucrin2 Involucrin. This family represents a conserved region approximately 60 residues long, multiple copies of which are found within eukaryotic involucrin, and which is rich in glutamine and glutamic acid residues. Involucrin forms part of the insoluble cornified cell envelope (a specialized protective barrier) of stratified squamous epithelia. Members of this family seem to be restricted to mammals. 41 matched cddid_all.tbl CDD pfam06995 pfam06995 429236 Phage_P2_GpU Phage P2 GpU. This family consists of several bacterial and phage proteins of around 130 residues in length which seem to be related to the bacteriophage P2 GpU protein which is thought to be involved in tail assembly. 119 matched cddid_all.tbl CDD pfam06996 pfam06996 429237 T6SS_TssG Type VI secretion, TssG. This is a family of Gram-negative bacterial proteins that form part of the type VI pathogenicity secretion system (T6SS), including TssG. TssG is homologs to phage tail proteins and is required for proper assembly of the Hcp tube in bacteria.One other member in this family, SciB (Q93IT4) from Salmonella enterica, is thought to be involved in virulence. 303 matched cddid_all.tbl CDD pfam06998 pfam06998 429238 DUF1307 Protein of unknown function (DUF1307). This family consists of several hypothetical bacterial proteins of around 150 residues in length. Some family members are described as putative lipoproteins but the function of the family is unknown. 114 matched cddid_all.tbl CDD pfam06999 pfam06999 462062 Suc_Fer-like Sucrase/ferredoxin-like. This family contains a number of bacterial and eukaryotic proteins approximately 400 residues long that resemble ferredoxin and appear to have sucrolytic activity. 217 matched cddid_all.tbl CDD pfam07000 pfam07000 399767 DUF1308 Protein of unknown function (DUF1308). This is a domain of unknown function found on the C-terminal of C7orf25 protein UPF0415. The C-terminal domain is homologous to the known PIN-like domains. The PIN-like domain is widespread among eukaryotes, including animals, plants, and fungi, but also present in some cyanobacteria, Deinococcus, and dsDNA viruses from the Mimiviridae family. The domain retains up to four potential catalytic residues, thus, depending on the protein is predicted to be an active or inactive nuclease and in a majority of the family members, the PIN-like domain is N-terminally fused with a potentially active PD-(D/E)XK-like domain pfam18474. 163 matched cddid_all.tbl CDD pfam07001 pfam07001 462063 BAT2_N BAT2 N-terminus. This family represents the N-terminus (approximately 200 residues) of the proline-rich protein BAT2. BAT2 is similar to other proteins with large proline-rich domains, such as some nuclear proteins, collagens, elastin, and synapsin. 190 matched cddid_all.tbl CDD pfam07002 pfam07002 462064 Copine Copine. This family represents a conserved region approximately 220 residues long within eukaryotic copines. Copines are Ca(2+)-dependent phospholipid-binding proteins that are thought to be involved in membrane-trafficking, and may also be involved in cell division and growth. 214 matched cddid_all.tbl CDD pfam07004 pfam07004 311141 SHIPPO-rpt Sperm-tail PG-rich repeat. This family represents a short conserved region carrying a PGP motif that is repeated in eukaryotic proteins of sperm-tails. Shippo orthologues from some species may include up to 40 Pro-Gly-Pro repeats. 33 matched cddid_all.tbl CDD pfam07005 pfam07005 462065 SBD_N Sugar-binding N-terminal domain. This is the N-terminal domain found in proteins in a range of Proteobacteria as well as the Gram-positive Oceanobacillus iheyensis. Structural analysis of the whole protein indicates the N- and C-termini act together to produce a surface into which a threonate-ADP complex is bound, demonstrating that a sugar binding site is on the N-terminal domain, and a nucleotide binding site is in the C-terminal domain. There is a critical motif, DDXTG, at approximately residues 22-25. Proteins containing this domain have been predicted as kinases. Some members are associated with PdxA2 by physical clustering and gene fusion with PdxA2. Some members that are fused with PdxA2 have been shown to be involved in L-4-hydroxythreonine (4HT) phosphorylation, part of the alternative pathway to make PLP (pyridoxal 5'-phosphate) out of a toxic metabolite, 4HT. However, 4HT phosphorylation might not be the main function of this group of proteins. Moreover, some members that are not associated with pdxA2, and even one that is associated with pdxA2, have lost 4HT kinase activity. Functional analysis demonstrate that family members include D-Threonate kinases (DtnK), D-Erythronate kinases (DenK) and 3-Oxo-tetronate kinases (OtnK). 229 matched cddid_all.tbl CDD pfam07006 pfam07006 429243 DUF1310 Protein of unknown function (DUF1310). This family consists of several hypothetical proteins of around 125 residues in length. Members of this family seem to be specific to Listeria and Streptococcus species. The function of this family is unknown. 116 matched cddid_all.tbl CDD pfam07007 pfam07007 429244 LprI Lysozyme inhibitor LprI. This family consists of several bacterial proteins of around 120 residues in length. Members of this family contain four highly conserved cysteine residues. Family members include lipoprotein LprI from Mycobacterium, which binds to and inhibits macrophage lysozyme, which may aid bacterial survival. 103 matched cddid_all.tbl CDD pfam07009 pfam07009 462066 NusG_II NusG domain II. This domain is found in some NusG proteins where it forms domain II. However most NusG proteins are missing this domain. In other cases this domain is found in isolation. The function of this domain is unknown. 107 matched cddid_all.tbl CDD pfam07010 pfam07010 429246 Endomucin Endomucin. This family consists of several mammalian endomucin proteins. Endomucin is an early endothelial-specific antigen that is also expressed on putative hematopoietic progenitor cells. 260 matched cddid_all.tbl CDD pfam07011 pfam07011 429247 Elf4 Early Flowering 4 domain. This domain forms an alpha-helical homodimer in ELF4 proteins. Protein EARLY FLOWERING 4 (Elf4) is a component of the central CCA1/LHY-TOC1 feedback loop in the circadian clock that promotes clock accuracy and is required for sustained rhythms in the absence of daily light/dark cycles. 83 matched cddid_all.tbl CDD pfam07012 pfam07012 429248 Curlin_rpt Curlin associated repeat. This family consists of several bacterial repeats of around 30 residues in length. These repeats are often found in multiple copies in the curlin proteins CsgA and CsgB. Curli fibres are thin aggregative surface fibres, connected with adhesion, which bind laminin, fibronectin, plasminogen, human contact phase proteins, and major histocompatibility complex (MHC) class I molecules. Curli fibres are coded for by the csg gene cluster, which is comprised of two divergently transcribed operons. One operon encodes the csgB, csgA, and csgC genes, while the other encodes csgD, csgE, csgF, and csgG. The assembly of the fibres is unique and involves extracellular self-assembly of the curlin subunit (CsgA), dependent on a specific nucleator protein (CsgB). CsgD is a transcriptional activator essential for expression of the two curli fibre operons, and CsgG is an outer membrane lipoprotein involved in extracellular stabilization of CsgA and CsgB. 34 matched cddid_all.tbl CDD pfam07013 pfam07013 284441 DUF1314 Protein of unknown function (DUF1314). This family consists of several Alphaherpesvirus proteins of around 200 residues in length. The function of this family is unknown. 197 matched cddid_all.tbl CDD pfam07014 pfam07014 399776 Hs1pro-1_C Hs1pro-1 protein C-terminus. This family represents the C-terminus (approximately 270 residues) of a number of plant Hs1pro-1 proteins, which are believed to confer nematode resistance. 258 matched cddid_all.tbl CDD pfam07015 pfam07015 148565 VirC1 VirC1 protein. This family consists of several bacterial VirC1 proteins. In Agrobacterium tumefaciens, a cis-active 24-base-pair sequence adjacent to the right border of the T-DNA, called overdrive, stimulates tumour formation by increasing the level of T-DNA processing. It is thought that the virC operon which enhances T-DNA processing probably does so because the VirC1 protein interacts with overdrive. It has now been shown that the virC1 gene product binds to overdrive but not to the right border of T-DNA. 231 matched cddid_all.tbl CDD pfam07016 pfam07016 284443 CRAM_rpt Cysteine-rich acidic integral membrane protein precursor. This family consists of several 24 residue repeats from the Trypanosoma brucei cysteine-rich, acidic integral membrane protein precursor (CRAM). CRAM is concentrated in the flagellar pocket, an invagination of the cell surface of the trypanosome where endocytosis has been documented. 22 matched cddid_all.tbl CDD pfam07017 pfam07017 429249 PagP Antimicrobial peptide resistance and lipid A acylation protein PagP. This family consists of several bacterial antimicrobial peptide resistance and lipid A acylation (PagP) proteins. The bacterial outer membrane enzyme PagP transfers a palmitate chain from a phospholipid to lipid A. In a number of pathogenic Gram-negative bacteria, PagP confers resistance to certain cationic antimicrobial peptides produced during the host innate immune response. 144 matched cddid_all.tbl CDD pfam07019 pfam07019 462067 EMC6 EMC6. This family consists of several Rab5-interacting proteins (RIP5 or Rab5ip) including ER membrane protein complex subunit 6 (EMC6) and RCAF1. The ras-related GTPase rab5 is rate-limiting for homotypic early endosome fusion. Rab5ip represents a novel rab5 interacting protein that may function on endocytic vesicles as a receptor for rab5-GDP and participate in the activation of rab5. EMC6 interacts with Rab5A and BECN1/Beclin 1 and regulates autophagosome formation. EMC6 is part of the EMC complex, required for efficient folding of proteins in the ER and for post-translational membrane insertion of tail-anchored (TA) proteins. 79 matched cddid_all.tbl CDD pfam07020 pfam07020 429251 Orthopox_C10L Orthopoxvirus C10L protein. This family consists of several Orthopoxvirus C10L proteins. C10L viral protein can play an important role in vaccinia virus evasion of the host immune system. It may consist in the blockade of IL-1 receptors by the C10L protein, a homolog of the IL-1 Ra. 83 matched cddid_all.tbl CDD pfam07021 pfam07021 399779 MetW Methionine biosynthesis protein MetW. This family consists of several bacterial and one archaeal methionine biosynthesis MetW proteins. Biosynthesis of methionine from homoserine in Pseudomonas putida takes place in three steps. The first step is the acylation of homoserine to yield an acyl-L-homoserine. This reaction is catalyzed by the products of the metXW genes and is equivalent to the first step in enterobacteria, gram-positive bacteria and fungi, except that in these microorganizms the reaction is catalyzed by a single polypeptide (the product of the metA gene in Escherichia coli and the met5 gene product in Neurospora crassa). In Pseudomonas putida, as in gram-positive bacteria and certain fungi, the second and third steps are a direct sulfhydrylation that converts the O-acyl-L-homoserine into homocysteine and further methylation to yield methionine. The latter reaction can be mediated by either of the two methionine synthetases present in the cells. 193 matched cddid_all.tbl CDD pfam07022 pfam07022 311152 Phage_CI_repr Bacteriophage CI repressor helix-turn-helix domain. This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic. 65 matched cddid_all.tbl CDD pfam07023 pfam07023 429252 DUF1315 Protein of unknown function (DUF1315). This family consists of several bacterial proteins of around 90 residues in length. The function of this family is unknown. 82 matched cddid_all.tbl CDD pfam07024 pfam07024 429253 ImpE ImpE protein. This family consists of several bacterial proteins including ImpE from Rhizobium leguminosarum. It has been suggested that the imp locus is involved in the secretion to the environment of proteins, including periplasmic RbsB protein, that cause blocking of infection specifically in pea plants. The exact function of this family is unknown. 122 matched cddid_all.tbl CDD pfam07026 pfam07026 284449 DUF1317 Protein of unknown function (DUF1317). This family consists of several hypothetical bacterial and phage proteins of around 60 residues in length. The function of this family is unknown. 60 matched cddid_all.tbl CDD pfam07027 pfam07027 462068 DUF1318 Protein of unknown function (DUF1318). This family consists of several bacterial proteins of around 100 residues in length and is often known as YdbL. The function of this family is unknown. 92 matched cddid_all.tbl CDD pfam07028 pfam07028 369174 DUF1319 Protein of unknown function (DUF1319). This family contains a number of viral proteins of unknown function approximately 200 residues long. Family members seem to be restricted to badnaviruses. 109 matched cddid_all.tbl CDD pfam07029 pfam07029 369175 CryBP1 CryBP1 protein. This family consists of several CryBP1 like proteins from Bacillus thuringiensis and Paenibacillus popilliae. Members of this family are thought to be involved in the overall toxicity of the bacteria to their hosts. 180 matched cddid_all.tbl CDD pfam07030 pfam07030 429255 Phage_Mu_Gp36 Bacteriophage Mu, Gp36. This family is represented by the Bacteriophage Mu, Gp36. The characteriztics of the protein distribution suggest prophage matches in addition to the phage matches. 109 matched cddid_all.tbl CDD pfam07032 pfam07032 369177 DUF1322 Protein of unknown function (DUF1322). This family consists of several hypothetical 9.4 kDa Borrelia burgdorferi (Lyme disease spirochete) proteins of around 78 residues in length. The function of this family is unknown. 73 matched cddid_all.tbl CDD pfam07033 pfam07033 462069 Orthopox_B11R Orthopoxvirus B11R protein. This family consists of several Orthopoxvirus B11R proteins of around 70 residues in length. The function of this family is unknown. 71 matched cddid_all.tbl CDD pfam07034 pfam07034 462070 ORC3_N Origin recognition complex (ORC) subunit 3 N-terminus. This family represents the N-terminus (approximately 300 residues) of subunit 3 of the eukaryotic origin recognition complex (ORC). Origin recognition complex (ORC) is composed of six subunits that are essential for cell viability. They collectively bind to the autonomously replicating sequence (ARS) in a sequence-specific manner and lead to the chromatin loading of other replication factors that are essential for initiation of DNA replication. This domain is predicted to contain an AAA+ fold but lack the residues important for ATP hydrolysis, thus, it is called AAA+ like. 330 matched cddid_all.tbl CDD pfam07035 pfam07035 429257 Mic1 Colon cancer-associated protein Mic1-like. This family represents the C-terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1. 157 matched cddid_all.tbl CDD pfam07037 pfam07037 399786 DUF1323 Putative transcription regulator (DUF1323). This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. This family appears to have an HTH domain and is therefore likely to act as a transcriptional regulator. 122 matched cddid_all.tbl CDD pfam07038 pfam07038 70500 Circovir2_Orf4 Circovirus 2, anti-apoptotic ORF4. This family represents the anti-apoptotic ORF4 protein from Circovirus 2, which antagonizes host cell apoptosis by interacting with host ferritin heavy chain (FHC). This protein physically binds host FHC, resulting in the reduction of FHC protein levels in host cells. The reduction of FHC concentration further inhibits the accumulation of reactive oxygen in host cells, leading to reduced apoptosis. 59 matched cddid_all.tbl CDD pfam07039 pfam07039 462071 DUF1325 SGF29 tudor-like domain. This domain is found in the yeast protein SAGA-associated factor 29. This domain is related to members of the Tudor domain superfamily such as pfam05641. The SAGA complex is involved in RNA polymerase II-dependent transcriptional regulation. The membership of the tudor domain superfamily suggests this domain may bind to RNA. 131 matched cddid_all.tbl CDD pfam07040 pfam07040 429259 DUF1326 Protein of unknown function (DUF1326). This family consists of several hypothetical bacterial proteins which seem to be found exclusively in Rhizobium and Ralstonia species. Members of this family are typically around 210 residues in length and contain 5 highly conserved cysteine residues at their N-terminus. The function of this family is unknown. 175 matched cddid_all.tbl CDD pfam07041 pfam07041 311164 DUF1327 Protein of unknown function (DUF1327). This family consists of several hypothetical bacterial proteins of around 115 residues in length which seem to be specific to Escherichia coli. The function of this family is unknown. 113 matched cddid_all.tbl CDD pfam07042 pfam07042 115680 TrfA TrfA protein. This family consists of several bacterial TrfA proteins. The trfA operon of broad-host-range IncP plasmids is essential to activate the origin of vegetative replication in diverse species. The trfA operon encodes two ORFs. The first ORF is highly conserved and encodes a putative single-stranded DNA binding protein (Ssb). The second, trfA, contains two translational starts as in the IncP alpha plasmids, generating related polypeptides of 406 (TrfA1) and 282 (TrfA2) amino acids. TrfA2 is very similar to the IncP alpha product, whereas the N-terminal region of TrfA1 shows very little similarity to the equivalent region of IncP alpha TrfA1. This region has been implicated in the ability of IncP alpha plasmids to replicate efficiently in Pseudomonas aeruginosa. 282 matched cddid_all.tbl CDD pfam07043 pfam07043 429260 DUF1328 Protein of unknown function (DUF1328). This family consists of several hypothetical bacterial proteins of around 50 residues in length. The function of this family is unknown. 38 matched cddid_all.tbl CDD pfam07044 pfam07044 429261 DUF1329 Protein of unknown function (DUF1329). This family consists of several hypothetical bacterial proteins of around 475 residues in length. The majority of family members are from Pseudomonas species but the family also contains sequences from Shewanella oneidensis and Thauera aromatica. 366 matched cddid_all.tbl CDD pfam07045 pfam07045 429262 DUF1330 Domain of unknown function (DUF1330). This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown. 94 matched cddid_all.tbl CDD pfam07046 pfam07046 336588 CRA_rpt Cytoplasmic repetitive antigen (CRA) like repeat. This family consists of several repeats of around 42 residues in length. These repeated sequences are found in multiple copies in Trypanosoma cruzi antigens, Swiss:Q26907 contains 23 copies of this repeat. 42 matched cddid_all.tbl CDD pfam07047 pfam07047 462072 OPA3 Optic atrophy 3 protein (OPA3). This family consists of several optic atrophy 3 (OPA3) proteins. OPA3 deficiency causes type III 3-methylglutaconic aciduria (MGA) in humans. This disease manifests with early bilateral optic atrophy, spasticity, extrapyramidal dysfunction, ataxia, and cognitive deficits, but normal longevity. 122 matched cddid_all.tbl CDD pfam07048 pfam07048 115686 DUF1331 Protein of unknown function (DUF1331). This family consists of several Circovirus proteins of around 35 residues in length. Members of this family are described as ORF-10 proteins and their function is unknown. 35 matched cddid_all.tbl CDD pfam07051 pfam07051 462073 OCIA Ovarian carcinoma immunoreactive antigen (OCIA). This family consists of several ovarian carcinoma immunoreactive antigen (OCIA) and related eukaryotic sequences. The function of this family is unknown. 87 matched cddid_all.tbl CDD pfam07052 pfam07052 462074 Hep_59 Hepatocellular carcinoma-associated antigen 59. This family represents a conserved region approximately 100 residues long within mammalian hepatocellular carcinoma-associated antigen 59 (HCA59). Family members are found in a variety of eukaryotes, such as fission yeast where telomere length and silencing protein 1 (Tls1) is required for telomeric heterochromatin assembly as well as telomere length control. Homologs in Arabidopsis are known as Cop1 suppressor 2 (CSU2). Csu2 inhibits constitutive photomorphogenic 1 (COP1) E3 ubiquitin ligase activity. Furthermore, CSU2 is required for primary root development under normal light growth condition. 102 matched cddid_all.tbl CDD pfam07054 pfam07054 429266 Pericardin_rpt Pericardin like repeat. This family consists of several repeated sequences of around 34 residues in length. This repeat is found in multiple copies in the Drosophila pericardin and other extracellular matrix proteins. 35 matched cddid_all.tbl CDD pfam07055 pfam07055 462075 Eno-Rase_FAD_bd Enoyl reductase FAD binding domain. This family carries the region of the enzyme trans-2-enoyl-CoA reductase, at the very C-terminus, that binds to FAD. The activity was characterized in Euglena where an unusual fatty acid synthesis path-way in mitochondria performs a malonyl-CoA independent synthesis of fatty acids leading to accumulation of wax esters, which serve as the sink for electrons stemming from glycolytic ATP synthesis and pyruvate oxidation. The full enzyme catalyzes the reduction of enoyl-CoA to acyl-CoA. The conserved region is seen as the motif FGFxxxxxDY. 64 matched cddid_all.tbl CDD pfam07056 pfam07056 399796 DUF1335 Protein of unknown function (DUF1335). This family represents a conserved region approximately 130 residues long within a number of proteins of unknown function that seem to be specific to the white spot syndrome virus (WSSV). 131 matched cddid_all.tbl CDD pfam07057 pfam07057 429268 TraI DNA helicase TraI. This family represents a conserved region approximately 130 residues long within the bacterial DNA helicase TraI (EC:3.6.1.-). TraI is a bifunctional protein that catalyzes the unwinding of duplex DNA as well as acts as a sequence-specific DNA trans-esterase, providing the site- and strand-specific nick required to initiate DNA transfer. 124 matched cddid_all.tbl CDD pfam07058 pfam07058 399798 MAP70 Microtubule-associated protein 70. This family represents a family of plant microtubule-associated proteins of size 70 kDa. The proteins contain four predicted coiled-coil domains, and truncation studies identify a central domain that targets the proteins to microtubules. It has no predicted trans-membrane domains, and the region between the coils from approximately residues 240-483 is the targetting region. 544 matched cddid_all.tbl CDD pfam07059 pfam07059 462076 EDR2_C Protein ENHANCED DISEASE RESISTANCE 2, C-terminal. This family represents the C-terminus (approximately 250 residues) of protein ENHANCED DISEASE RESISTANCE 2 (EDR2) from plants. EDR2 is a negative regulator of the salicylic acid (SA)-mediated resistance to pathogens, including the biotrophic powdery mildew pathogens Golovinomyces cichoracearum and Blumeria graminis, and the downy mildew pathogen Hyaloperonospora parasitica, probably by limiting the initiation of cell death and the establishment of the hypersensitive response (HR). 211 matched cddid_all.tbl CDD pfam07061 pfam07061 462077 Swi5 Swi5. Swi5 is involved in meiotic DNA repair synthesis and meiotic joint molecule formation.3]. It is known to interact with Swi2, Rhp51 and Swi6. 79 matched cddid_all.tbl CDD pfam07062 pfam07062 311178 Clc-like Clc-like. This family contains a number of Clc-like proteins that are approximately 250 residues long. 212 matched cddid_all.tbl CDD pfam07063 pfam07063 429271 DUF1338 Domain of unknown function (DUF1338). This domain is found in a variety of bacterial and fungal proteins. This entry represents proteins involved in D-lysine metabolism, which catalyze a successive decarboxylation and intramolecular hydroxylation of 2-oxoadipate forming 2-hydroxyglutarate in a Fe(II) and oxygen-dependent manner. The structure of this domain has been solved by structural genomics. The structure implies a zinc-binding function (information derived from TOPSAN for PDB:3iuz). 320 matched cddid_all.tbl CDD pfam07064 pfam07064 462078 RIC1 RIC1. RIC1 has been identified in yeast as a Golgi protein involved in retrograde transport to the cis-Golgi network. It forms a heterodimer with Rgp1 and functions as a guanyl-nucleotide exchange factor. 246 matched cddid_all.tbl CDD pfam07065 pfam07065 462079 D123 D123. This family contains a number of eukaryotic cell division cycle 123 (Cdc123, also known as D123) proteins approximately 330 residues long. It has been shown that mutated variants of D123 exhibit temperature-dependent differences in their degradation rate. D123 proteins are regulators of eIF2, the central regulator of translational initiation. Family members include ATP-grasp enzymes belonging to the R2K clade, wherein one of the absolutely-conserved lysine residues has migrated to the RAGYNA domain which is a part of the core ATP-grasp module. This family is found in eukaryotes as well as NCDLVs and diverse bacteria. In eukaryotes, the domain is found in both the CDC123 enzymes and a related clade of proteins found in amoeboid organizms, while in bacteria it is observed embedded in polymorphic toxin loci. 299 matched cddid_all.tbl CDD pfam07066 pfam07066 369194 DUF3882 Lactococcus phage M3 protein. This family consists of several Lactococcus phage middle-3 (M3) proteins of around 160 residues in length. The function of this family is unknown. 159 matched cddid_all.tbl CDD pfam07067 pfam07067 115703 DUF1340 Protein of unknown function (DUF1340). This family consists of several hypothetical Streptococcus thermophilus bacteriophage proteins of around 235 residues in length. The function of this family is unknown. 236 matched cddid_all.tbl CDD pfam07068 pfam07068 399804 Gp23 Major capsid protein Gp23. This family contains a number of major capsid Gp23 proteins approximately 500 residues long, from T4-like bacteriophages. 449 matched cddid_all.tbl CDD pfam07069 pfam07069 115705 PRRSV_2b Porcine reproductive and respiratory syndrome virus 2b. This family consists of several Porcine reproductive and respiratory syndrome virus (PRRSV) ORF2b proteins. The function of this family is unknown however it is known that large amounts of 2b protein are present in the virion and it is thought that this protein may be an integral component of the virion. 73 matched cddid_all.tbl CDD pfam07070 pfam07070 429274 Spo0M SpoOM protein. This family consists of several bacterial SpoOM proteins which are thought to control sporulation in Bacillus subtilis.Spo0M exerts certain negative effects on sporulation and its gene expression is controlled by sigmaH. 203 matched cddid_all.tbl CDD pfam07071 pfam07071 399806 KDGP_aldolase KDGP aldolase. DgaF is part of the dga operon required for wild-type growth of Salmonella Typhimurium with D-glucosaminate. It catalyzes the conversion of keto-3-deoxygluconate 6-phosphate (KDGP) to yield pyruvate and glyceraldehyde-3-phosphate. Orthologues of the dga genes are largely restricted to certain enteric bacteria and a few species in the phylum Firmicutes. 217 matched cddid_all.tbl CDD pfam07072 pfam07072 462080 ZapD Cell division protein. Cell division protein ZapD enhances FtsZ-ring assembly. It directly interacts with FtsZ and promotes bundling of FtsZ protofilaments, with a reduction in FtsZ GTPase activity. 210 matched cddid_all.tbl CDD pfam07073 pfam07073 429276 ROF Modulator of Rho-dependent transcription termination (ROF). This family consists of several bacterial modulator of Rho-dependent transcription termination (ROF) proteins. ROF binds transcription termination factor Rho and inhibits Rho-dependent termination in vivo. 80 matched cddid_all.tbl CDD pfam07074 pfam07074 399809 TRAP-gamma Translocon-associated protein, gamma subunit (TRAP-gamma). This family consists of several eukaryotic translocon-associated protein, gamma subunit (TRAP-gamma) sequences. The translocation site (translocon), at which nascent polypeptides pass through the endoplasmic reticulum membrane, contains a component previously called 'signal sequence receptor' that is now renamed as 'translocon-associated protein' (TRAP). The TRAP complex is comprised of four membrane proteins alpha, beta, gamma and delta which are present in a stoichiometric relation, and are genuine neighbours in intact microsomes. The gamma subunit is predicted to span the membrane four times. 170 matched cddid_all.tbl CDD pfam07075 pfam07075 462081 DUF1343 Protein of unknown function (DUF1343). This family consists of several hypothetical bacterial proteins of around 400 residues in length. The function of this family is unknown. 359 matched cddid_all.tbl CDD pfam07076 pfam07076 429278 DUF1344 Protein of unknown function (DUF1344). This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown. 59 matched cddid_all.tbl CDD pfam07077 pfam07077 429279 DUF1345 Protein of unknown function (DUF1345). This family consists of several hypothetical bacterial proteins of around 230 residues in length. The function of this family is unknown. 171 matched cddid_all.tbl CDD pfam07078 pfam07078 462082 FYTT Forty-two-three protein. This family consists of several mammalian proteins of around 320 residues in length called 40-2-3 proteins. The function of this family is unknown. 310 matched cddid_all.tbl CDD pfam07079 pfam07079 284489 DUF1347 Protein of unknown function (DUF1347). This family consists of several hypothetical bacterial proteins of around 610 residues in length. Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown. 548 matched cddid_all.tbl CDD pfam07080 pfam07080 462083 DUF1348 Protein of unknown function (DUF1348). This family consists of several highly conserved hypothetical proteins of around 150 residues in length. The function of this family is unknown. 130 matched cddid_all.tbl CDD pfam07081 pfam07081 462084 DUF1349 Protein of unknown function (DUF1349). This family consists of several hypothetical bacterial proteins but contains one sequence from Saccharomyces cerevisiae. Members of this family are typically around 200 residues in length. The function of this family is unknown. 168 matched cddid_all.tbl CDD pfam07082 pfam07082 115718 DUF1350 Protein of unknown function (DUF1350). This family consists of several hypothetical proteins from both cyanobacteria and plants. Members of this family are typically around 250 residues in length. The function of this family is unknown but the species distribution indicates that the family may be involved in photosynthesis. 250 matched cddid_all.tbl CDD pfam07083 pfam07083 429283 DUF1351 Protein of unknown function (DUF1351). This family consists of several bacterial and phage proteins of around 230 residues in length. The function of this family is unknown. 210 matched cddid_all.tbl CDD pfam07084 pfam07084 462085 Spot_14 Thyroid hormone-inducible hepatic protein Spot 14. This family consists of several thyroid hormone-inducible hepatic protein (Spot 14 or S14) sequences. Mainly expressed in tissues that synthesize triglycerides, the mRNA coding for Spot 14 has been shown to be increased in rat liver by insulin, dietary carbohydrates, glucose in hepatocyte culture medium, as well as thyroid hormone. In contrast, dietary fats and polyunsaturated fatty acids, have been shown to decrease the amount of Spot 14 mRNA, while an elevated level of cAMP acts as a dominant negative factor. In addition, liver-specific factors or chromatin organization of the gene have been shown to contribute to the regulation of its expression. Spot 14 protein is thought to be required for induction of hepatic lipogenesis. 151 matched cddid_all.tbl CDD pfam07085 pfam07085 429285 DRTGG DRTGG domain. This presumed domain is about 120 amino acids in length. It is found associated with CBS domains pfam00571, as well as the CbiA domain pfam01656. The function of this domain is unknown. It is named the DRTGG domain after some of the most conserved residues. This domain may be very distantly related to a pair of CBS domains. There are no significant sequence similarities, but its length and association with CBS domains supports this idea (Bateman A, pers. obs.). 105 matched cddid_all.tbl CDD pfam07086 pfam07086 462086 Jagunal Jagunal, ER re-organization during oogenesis. Jagunal is an endoplasmic-reticulum (ER)-membrane protein found in eukaryotes. It is involved in reorganizing the ER in cells that must increase exocytic membrane traffic during development, that is, in the oocyte during vitellogenesis. It facilitates vesicular traffic in the subcortex. 186 matched cddid_all.tbl CDD pfam07087 pfam07087 429287 DUF1353 Protein of unknown function (DUF1353). This family consists of several hypothetical bacterial proteins of around 100 residues in length. The function of this family is unknown. 91 matched cddid_all.tbl CDD pfam07088 pfam07088 462087 GvpD_P-loop GvpD gas vesicle protein, P-loop domain. This family consists of several archaeal GvpD gas vesicle regulatory proteins. GvpD is involved in the regulation of gas vesicle formation and functions as a repressor through the interaction and the breakdown induction of the transcriptional activator GvpE. This domain includes the P-loop and the basic region 1 (bR1, an arginine-rich region) which are essential for GvpD repressive function. 189 matched cddid_all.tbl CDD pfam07090 pfam07090 399821 GATase1_like Putative glutamine amidotransferase. This family consists of several hypothetical bacterial proteins of around 250 residues in length. The function of this family is unknown. The structure of this cytoplasmic domain was solved by the Midwest Center for Structural Genomics (MCSG). The structure has been classified as part of the Class-I Glutamine amidotransferase superfamily owing to similarity with other known structures. The monomer combines with itself to form a hexamer, and this hexamer exposes a potential catalytic surface rich in Glu, Asp, Tyr, Ser.Trp and His residues. 246 matched cddid_all.tbl CDD pfam07091 pfam07091 336604 FmrO Ribosomal RNA methyltransferase (FmrO). This family consists of several bacterial ribosomal RNA methyltransferase (aminoglycoside-resistance methyltransferase) proteins. 252 matched cddid_all.tbl CDD pfam07092 pfam07092 462088 DUF1356 Protein of unknown function (DUF1356). This family consists of several hypothetical mammalian proteins of around 250 residues in length. The function of this family is unknown. 232 matched cddid_all.tbl CDD pfam07093 pfam07093 462089 SGT1 SGT1 protein. This family consists of several eukaryotic SGT1 proteins. Human SGT1 or hSGT1 is known to suppress GCR2 and is highly expressed in the muscle and heart. The function of this family is unknown although it has been speculated that SGT1 may be functionally analogous to the Gcr2p protein of Saccharomyces cerevisiae which is known to be a regulatory factor of glycolytic gene expression. 586 matched cddid_all.tbl CDD pfam07094 pfam07094 284502 DUF1357 Protein of unknown function (DUF1357). This family consists of several hypothetical bacterial proteins of around 225 residues in length. Members of this family appear to be specific Borrelia burgdorferi (Lyme disease spirochete). The function of this family is unknown. 223 matched cddid_all.tbl CDD pfam07095 pfam07095 429290 IgaA Intracellular growth attenuator protein IgaA. This family consists of several bacterial intracellular growth attenuator (IgaA) proteins. IgaA is involved in negative control of bacterial proliferation within fibroblasts. IgaA is homologous to the E. coli YrfF and P. mirabilis UmoB proteins. Whereas the biological function of YrfF is currently unknown, UmoB has been shown elsewhere to act as a positive regulator of FlhDC, the master regulator of flagella and swarming. FlhDC has been shown to repress cell division during P. mirabilis swarming, suggesting that UmoB could repress cell division via FlhDC. This biological function, if maintained in S. enterica, could sustain a putative negative control of cell division and growth exerted by IgaA in intracellular bacteria. 696 matched cddid_all.tbl CDD pfam07096 pfam07096 429291 DUF1358 Protein of unknown function (DUF1358). This family consists of several hypothetical eukaryotic proteins of around 125 residues in length. The function of this family is unknown. 115 matched cddid_all.tbl CDD pfam07097 pfam07097 284505 DUF1359 Protein of unknown function (DUF1359). This family consists of several hypothetical bacterial and phage proteins of around 100 residues in length. Members of this family seem to be found exclusively in Lactococcus lactis and the bacteriophages that infect this species. The function of this family is unknown. 104 matched cddid_all.tbl CDD pfam07098 pfam07098 399825 DUF1360 Protein of unknown function (DUF1360). This family consists of several bacterial proteins of around 115 residues in length. Members of this family are found in Bacillus species and Streptomyces coelicolor, the function of the family is unknown. 102 matched cddid_all.tbl CDD pfam07099 pfam07099 429292 DUF1361 Protein of unknown function (DUF1361). This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown although some members are annotated as being putative integral membrane proteins. 167 matched cddid_all.tbl CDD pfam07100 pfam07100 399827 ASRT Anabaena sensory rhodopsin transducer. The family of bacterial Anabaena sensory rhodopsin transducers are likely to bind sugars or related metabolites. The entire protein is comprised of a single globular domain with an eight-stranded beta-sandwich fold. There are a few characteriztics which define this beta-sandwich fold as being distinct from other so-named folds, and these are: 1) a well conserved tryptophan, usually following a polar residue, present at the start of the first strand; this tryptophan appears to be central to a hydrophobic interaction required to hold the two beta-sheets of the sandwich together, and 2) a nearly absolutely conserved asparagine located at the end of the second beta-strand, that hydrogen bonds with the backbone carbonyls of the residues 2 and 4 positions downstream from it, thereby stabilising the characteriztic tight turn between strands 2 and 3 of the structure. 119 matched cddid_all.tbl CDD pfam07101 pfam07101 115736 DUF1363 Protein of unknown function (DUF1363). This family consists of several Trypanosoma brucei putative variant specific antigen proteins of around 80 residues in length. 124 matched cddid_all.tbl CDD pfam07102 pfam07102 429293 YbcO Putative nuclease YbcO. This family includes YbcO (pdbe:3G27), a putative nuclease from E. coli. Proteins in the entry have been predicted to have the His-Me finger nuclease domain and may act as a Recombinase that participates in DNA repair and replication. 91 matched cddid_all.tbl CDD pfam07103 pfam07103 462090 DUF1365 Protein of unknown function (DUF1365). This family consists of several bacterial and plant proteins of around 250 residues in length. The function of this family is unknown. 227 matched cddid_all.tbl CDD pfam07104 pfam07104 336610 DUF1366 Protein of unknown function (DUF1366). This family consists of several hypothetical Streptococcus thermophilus bacteriophage proteins of around 130 residues in length. One of the sequences in this family, from phage Sfi11 is known as Gp149. The function of this family is unknown. 116 matched cddid_all.tbl CDD pfam07105 pfam07105 429295 DUF1367 Protein of unknown function (DUF1367). This family consists of several highly conserved, hypothetical phage proteins of around 200 residues in length. The function of this family is unknown. Some proteins are annotated as IrsA (intracellular response to stress). 192 matched cddid_all.tbl CDD pfam07106 pfam07106 429296 TBPIP TBPIP/Hop2 winged helix domain. This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation. TBPIP was found to be an activator that specifically stimulates the homologous pairing catalyzed by DMC1. Family members also include yeast homologous-pairing protein 2 (Hop2) and its homologs from animals and plants. They are required for proper homologous pairing and efficient cross-over and intragenic recombination during meiosis. 62 matched cddid_all.tbl CDD pfam07107 pfam07107 429297 WI12 Wound-induced protein WI12. This family consists of several plant wound-induced protein sequences related to WI12 from Mesembryanthemum crystallinum. Wounding, methyl jasmonate, and pathogen infection is known to induce local WI12 expression. WI12 expression is also thought to be developmentally controlled in the placenta and developing seeds. WI12 preferentially accumulates in the cell wall and it has been suggested that it plays a role in the reinforcement of cell wall composition after wounding and during plant development. This family seems partly related to the NTF2-like superfamily. 104 matched cddid_all.tbl CDD pfam07108 pfam07108 369211 PipA PipA protein. This family consists of several Salmonella PipA (pathogenicity island-encoded protein A) and related phage sequences. PipA is thought to contribute to enteric but not to systemic salmonellosis. The family carries a highly conserved HEXXH sequence motif along with several highly conserved glutamic acid residues which might be indicative of the family being a metallo-peptidase. 200 matched cddid_all.tbl CDD pfam07109 pfam07109 462091 Mg-por_mtran_C Magnesium-protoporphyrin IX methyltransferase C-terminus. This family represents the C-terminus (approximately 100 residues) of bacterial and eukaryotic Magnesium-protoporphyrin IX methyltransferase (EC:2.1.1.11). This converts magnesium-protoporphyrin IX to magnesium-protoporphyrin IX methylester using S-adenosyl-L-methionine as a cofactor. 97 matched cddid_all.tbl CDD pfam07110 pfam07110 429298 EthD EthD domain. This family consists of several bacterial sequences which are related to the EthD protein of Rhodococcus ruber. In Rhodococcus ruber, EthD is thought to be involved in the degradation of ethyl tert-butyl ether (ETBE). EthD synthesis is induced by ETBE but it's exact function is unknown, it is however thought to be essential to the ETBE degradation system. 96 matched cddid_all.tbl CDD pfam07111 pfam07111 284517 HCR Alpha helical coiled-coil rod protein (HCR). This family consists of several mammalian alpha helical coiled-coil rod HCR proteins. The function of HCR is unknown but it has been implicated in psoriasis in humans and is thought to affect keratinocyte proliferation. 749 matched cddid_all.tbl CDD pfam07112 pfam07112 254061 DUF1368 Protein of unknown function (DUF1368). This family consists of several proteins with seem to be specific to red algae plasmids. Members of this family are typically around 415 residues in length. The function of this family is unknown. 404 matched cddid_all.tbl CDD pfam07114 pfam07114 462092 TMEM126 Transmembrane protein 126. This entry includes the transmembrane protein 126 A/B (TMEM126A/B) from animals. Human TMEM126B participates in constructing the membrane arm of mitochondrial respiratory complex I. 181 matched cddid_all.tbl CDD pfam07116 pfam07116 254062 DUF1372 Protein of unknown function (DUF1372). This family consists of several Streptococcus bacteriophage sequences and related proteins from Streptococcus species. Members of this family are typically around 100 residues in length and their function is unknown. 104 matched cddid_all.tbl CDD pfam07117 pfam07117 462093 DUF1373 Protein of unknown function (DUF1373). This family consists of several hypothetical proteins which seem to be specific to Oryzias latipes (Japanese ricefish). Members of this family are typically around 200 residues in length. The function of this family is unknown. 212 matched cddid_all.tbl CDD pfam07118 pfam07118 399833 DUF1374 Protein of unknown function (DUF1374). This family consists of several hypothetical Sulfolobus virus proteins of around 100 residues in length. The function of this family is unknown. 92 matched cddid_all.tbl CDD pfam07119 pfam07119 429301 DUF1375 Protein of unknown function (DUF1375). This family consists of several hypothetical, putative lipoproteins of around 80 residues in length. Members of this family seem to be specific to the Class Gammaproteobacteria. The function of this family is unknown. 53 matched cddid_all.tbl CDD pfam07120 pfam07120 462094 DUF1376 Protein of unknown function (DUF1376). This family consists of several hypothetical bacterial proteins of around 95 residues in length. The function of this family is unknown. 83 matched cddid_all.tbl CDD pfam07122 pfam07122 284524 VLPT Variable length PCR target protein (VLPT). This family consists of a number of 29 residue repeats which seem to be specific to the Ehrlichia chaffeensis variable length PCR target (VLPT) protein. Ehrlichia chaffeensis is a tick-transmitted rickettsial agent and is responsible for human monocytic ehrlichiosis (HME). The function of this family is unknown. 30 matched cddid_all.tbl CDD pfam07123 pfam07123 462095 PsbW Photosystem II reaction centre W protein (PsbW). This family consists of several plant specific photosystem II reaction centre W (PsbW) proteins. PsbW is a nuclear-encoded protein located in the thylakoid membrane of the chloroplast. PsbW is a core component of photosystem II but not photosystem I. This family does not appear to be related to pfam03912. 129 matched cddid_all.tbl CDD pfam07124 pfam07124 429304 Phytoreo_P8 Phytoreovirus outer capsid protein P8. This family consists of several Phytoreovirus outer capsid protein P8 sequences. 422 matched cddid_all.tbl CDD pfam07125 pfam07125 115758 DUF1378 Protein of unknown function (DUF1378). This family consists of hypothetical bacterial and phage proteins of around 59 residues in length. Bacterial members of this family seem to be specific to Enterobacteria. The function of this family is unknown. Structural modelling suggests this domain may bind nucleic acids. 59 matched cddid_all.tbl CDD pfam07126 pfam07126 429305 ZapC Cell-division protein ZapC. ZapC is one of four FtsZ-binding components of the Z ring in bacteria. Formation of the Z ring on the cytoplasmic surface of the membrane is the starting process for assembly of the cell-division apparatus. It binds directly to the Z ring, and although it is not essential for absolute cell division it contributes to it by enhancing the interactions between the FtsZ protofilaments (or polymers) which aggregate to form the ring conformation in the Z ring. 169 matched cddid_all.tbl CDD pfam07127 pfam07127 462096 Nodulin_late Late nodulin protein. This family consists of several plant specific late nodulin sequences which are homologous to the Pisum sativum (Garden pea) ENOD3 protein. ENOD3 is expressed in the late stages of root nodule formation and contains two pairs of cysteine residues towards the C-terminus which may be involved in metal-binding. 54 matched cddid_all.tbl CDD pfam07128 pfam07128 429307 DUF1380 Protein of unknown function (DUF1380). This family consists of several hypothetical bacterial proteins of around 140 residues in length. Members of this family seem to be specific to Enterobacteria. The function of this family is unknown. 137 matched cddid_all.tbl CDD pfam07129 pfam07129 462097 DUF1381 Protein of unknown function (DUF1381). This family consists of several hypothetical Staphylococcus aureus and Staphylococcus aureus bacteriophage proteins of around 65 residues in length. The function of this family is unknown. 44 matched cddid_all.tbl CDD pfam07130 pfam07130 429308 YebG YebG protein. This family consists of several bacterial YebG proteins of around 75 residues in length. The exact function of this protein is unknown but it is thought to be involved in the SOS response. The induction of the yebG gene occurs as cell enter into the stationary growth phase and is dependent on is dependent on cyclic AMP and H-NS. 72 matched cddid_all.tbl CDD pfam07131 pfam07131 429309 DUF1382 Protein of unknown function (DUF1382). This family consists of several hypothetical Escherichia coli and bacteriophage lambda-like proteins of around 60 residues in length. The function of this family is unknown. Structural modelling suggests this domain may bind nucleic acids. 60 matched cddid_all.tbl CDD pfam07133 pfam07133 429310 Merozoite_SPAM Merozoite surface protein (SPAM). This family consists of several Plasmodium falciparum SPAM (secreted polymorphic antigen associated with merozoites) proteins. Variation among SPAM alleles is the result of deletions and amino acid substitutions in non-repetitive sequences within and flanking the alanine heptad-repeat domain. Heptad repeats in which the a and d position contain hydrophobic residues generate amphipathic alpha-helices which give rise to helical bundles or coiled-coil structures in proteins. SPAM is an example of a P. falciparum antigen in which a repetitive sequence has features characteriztic of a well-defined structural element. 176 matched cddid_all.tbl CDD pfam07134 pfam07134 254068 AcMNPV_Orf18 Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf18. This family is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf18 (ac18); it is a family of uncharacterized viral proteins. 328 matched cddid_all.tbl CDD pfam07136 pfam07136 462098 DUF1385 Protein of unknown function (DUF1385). This family contains a number of hypothetical bacterial proteins of unknown function approximately 300 residues in length. Some family members are predicted to be metal-dependent. 231 matched cddid_all.tbl CDD pfam07137 pfam07137 462099 VDE VDE lipocalin domain. This family represents a conserved region approximately 150 residues long within plant violaxanthin de-epoxidase (VDE). In higher plants, violaxanthin de-epoxidase forms part of a conserved system that dissipates excess energy as heat in the light-harvesting complexes of photosystem II (PSII), thus protecting them from photo-inhibitory damage. 240 matched cddid_all.tbl CDD pfam07138 pfam07138 369226 AcMNPV_AC11 Baculovirus protein AC11. This family of baculovirus proteins is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV) protein AC11 (Orf11). ac11 is an early gene essential for budded-virus production and occlusion-derived-virus envelopment. 334 matched cddid_all.tbl CDD pfam07139 pfam07139 462100 DUF1387 Protein of unknown function (DUF1387). This family represents a conserved region approximately 300 residues long within a number of hypothetical proteins of unknown function that seem to be restricted to mammals. 311 matched cddid_all.tbl CDD pfam07140 pfam07140 284538 IFNGR1 Interferon gamma receptor (IFNGR1). This family consists of several eukaryotic and viral interferon gamma receptor proteins. Molecular interactions among cytokines and cytokine receptors in eukaryotes form the basis of many cell-signaling pathways relevant to immune function. Human interferon-gamma (IFN-gamma) signals through a multimeric receptor complex consisting of two different but structurally related transmembrane chains: the high-affinity receptor-binding subunit (IFN-gammaRalpha) and a species specific accessory factor (AF-1 or IFN-gammaRbeta). The vaccinia viral interferon gamma receptor has been shown to be secreted from infected cells during early infection. The structure has been halved such that the N-terminus of this family is now represented by Tissue_fac pfam01108. 133 matched cddid_all.tbl CDD pfam07141 pfam07141 369228 Phage_term_sma Putative bacteriophage terminase small subunit. This family consists of several putative Lactococcus bacteriophage terminase small subunit proteins. The exact function of this family is unknown. 174 matched cddid_all.tbl CDD pfam07142 pfam07142 429314 DUF1388 Repeat of unknown function (DUF1388). This family consists of several repeats of around 29 residues in length. Members of this family are found in the variable surface lipoproteins in Mycoplasma bovis and in mammalian neurofilament triplet H (NefH or NF-H) proteins. This repeat contains several Lys-Ser-Pro (KSP) motifs and in NefH these are thought to function as the main target for neurofilament directed protein kinases in vivo. 28 matched cddid_all.tbl CDD pfam07143 pfam07143 429315 CrtC CrtC N-terminal lipocalin domain. This family contains the members of the old Pfam family DUF2006. Structural characterization of family member Swiss:Q82US3 (from DUF2006 now merged into this family) has revealed a lipocalin-like fold with domain duplication. 175 matched cddid_all.tbl CDD pfam07145 pfam07145 429316 PAM2 Ataxin-2 C-terminal region. The PABP-interacting motif PAM2 has been identified in various eukaryotic proteins as an important binding site for pfam00658. It has been found in a wide range of eukaryotic proteins. Strikingly, this motif appears to occur solely outside of globular domains. 17 matched cddid_all.tbl CDD pfam07146 pfam07146 254076 DUF1389 Protein of unknown function (DUF1389). This family consists of several hypothetical bacterial proteins which seem to be specific to Chlamydia pneumoniae. Members of this family are typically around 400 residues in length. The function of this family is unknown. 311 matched cddid_all.tbl CDD pfam07147 pfam07147 462101 PDCD9 Mitochondrial 28S ribosomal protein S30 (PDCD9). This family consists of several eukaryotic mitochondrial 28S ribosomal protein S30 (or programmed cell death protein 9 PDCD9) sequences. The exact function of this family is unknown although it is known to be a component of the mitochondrial ribosome and a component in cellular apoptotic signaling pathways. 441 matched cddid_all.tbl CDD pfam07148 pfam07148 429318 MalM Maltose operon periplasmic protein precursor (MalM). This family consists of several maltose operon periplasmic protein precursor (MalM) sequences. The function of this family is unknown. 132 matched cddid_all.tbl CDD pfam07149 pfam07149 399850 Pes-10 Pes-10. This family consists of several Caenorhabditis elegans pes-10 and related proteins. Members of this family are typically around 400 residues in length. The function of this family is unknown. 397 matched cddid_all.tbl CDD pfam07150 pfam07150 284546 DUF1390 Protein of unknown function (DUF1390). This family consists of several Paramecium bursaria chlorella virus 1 (PBCV-1) proteins of around 250 residues in length. The function of this family is unknown. 226 matched cddid_all.tbl CDD pfam07151 pfam07151 462102 DUF1391 Protein of unknown function (DUF1391). This family consists of several Enterobacterial proteins of around 50 residues in length. Members of this family are found in Escherichia coli and Salmonella typhi where they are often known as YdfA. The function of this family is unknown. 48 matched cddid_all.tbl CDD pfam07152 pfam07152 462103 YaeQ YaeQ protein. This family consists of several hypothetical bacterial proteins of around 180 residues in length which are often known as YaeQ. YaeQ is homologous to RfaH, a specialized transcription elongation protein. YaeQ is known to compensate for loss of RfaH function. 172 matched cddid_all.tbl CDD pfam07153 pfam07153 369234 Marek_SORF3 Marek's disease-like virus SORF3 protein. This family consists of several SORF3 proteins from the Marek's disease-like viruses. Members of this family are around 350 residues in length. The function of this family is unknown. 290 matched cddid_all.tbl CDD pfam07154 pfam07154 284550 DUF1392 Protein of unknown function (DUF1392). This family consists of several hypothetical cyanobacterial proteins of around 150 residues in length which seem to be specific to Anabaena species. The function of this family is unknown. 150 matched cddid_all.tbl CDD pfam07155 pfam07155 429320 ECF-ribofla_trS ECF-type riboflavin transporter, S component. This family is the substrate-binding component (S component) of the energy coupling-factor (ECF)-type riboflavin transporter. It is a transmembrane protein which binds riboflavin, and is responsible for riboflavin-uptake by cells. 167 matched cddid_all.tbl CDD pfam07156 pfam07156 462104 Prenylcys_lyase Prenylcysteine lyase. This family contains prenylcysteine lyases (EC:1.8.3.5) that are approximately 500 residues long. Prenylcysteine lyase is a FAD-dependent thioether oxidase that degrades a variety of prenylcysteines, producing free cysteine, an isoprenoid aldehyde and hydrogen peroxide as products of the reaction. It has been noted that this enzyme has considerable homology with ClP55, a 55 kDa protein that is associated with chloride ion pumps. 364 matched cddid_all.tbl CDD pfam07157 pfam07157 462105 DNA_circ_N DNA circularization protein N-terminus. This family represents the N-terminus (approximately 100 residues) of a number of phage DNA circularization proteins. 88 matched cddid_all.tbl CDD pfam07158 pfam07158 115789 MatC_N Dicarboxylate carrier protein MatC N-terminus. This family represents the N-terminal region of the bacterial dicarboxylate carrier protein MatC. The MatC protein is an integral membrane protein that could function as a malonate carrier. 149 matched cddid_all.tbl CDD pfam07159 pfam07159 462106 CYRIA-B_Rac1-bd CYRIA/CYRIB Rac1 binding domain. This domain has been annotated as Rac1-binding domain. It can be found in human CYRIA/CYRIB and at the N terminus of CYFIP1/2. CYFIP proteins are known RAC1 effectors that stimulate actin polymerization. In mice, CYRIB (also known as CYRI or FAM49B) negatively regulates RAC1-driven cytoskeletal remodelling and plays a role in restricting infection mediated by Mycobacterium tuberculosis and Listeria monocytogenes. 301 matched cddid_all.tbl CDD pfam07160 pfam07160 462107 SKA1 Spindle and kinetochore-associated protein 1. Spindle and kinetochore-associated protein 1 (SKA1) is a component of the SKA1 complex (consists of Ska1, Ska2, and Ska3/Rama1), a microtubule-binding subcomplex of the outer kinetochore that is essential for proper chromosome segregation. 237 matched cddid_all.tbl CDD pfam07161 pfam07161 429325 LppX_LprAFG LppX_LprAFG lipoprotein. This entry consists of several lipoproteins mainly from Mycobacterium species, collectively known as the LppX_ LprAFG family. Proteins in this entry include LprG, LppX, LprF and lprA. 190 matched cddid_all.tbl CDD pfam07162 pfam07162 462108 B9-C2 Ciliary basal body-associated, B9 protein. The B9-C2 domain is found in proteins associated with the ciliary basal body. B9 domains were identified as a specific family of C2 domains. There are three sub-families represented by this family, notably, Mks1-Xbx7, Stumpy-Tza1 and Tza2 groups of proteins. Mutations in human Mks1 result in the developmental disorder Mechler-Gruber syndrome; mutations in mouse Stumpy lead to perinatal hydrocephalus and severe polycystic kidney disease. All the three distinct types of B9-C2 proteins cooperatively localize to the basal body or centrosome of cilia. 165 matched cddid_all.tbl CDD pfam07163 pfam07163 462109 Pex26 Pex26 protein. This family consists of Pex26 and related mammalian proteins. Pex26 is a type II peroxisomal membrane protein which recruits Pex6-Pex1 complexes to peroxisomes. Mutations in Pex26 can lead to human disorders. 301 matched cddid_all.tbl CDD pfam07165 pfam07165 429328 DUF1397 Protein of unknown function (DUF1397). This family consists of several insect specific proteins. Swiss:Q25513 is annotated as being a haemolymph glycoprotein precursor. The function of this family is unknown. 203 matched cddid_all.tbl CDD pfam07166 pfam07166 429329 DUF1398 Protein of unknown function (DUF1398). This family consists of several hypothetical Enterobacterial proteins of around 130 residues in length. Members of this family seem to be found exclusively in Escherichia coli and Salmonella species. The function of this family is unknown. 119 matched cddid_all.tbl CDD pfam07167 pfam07167 462110 PhaC_N Poly-beta-hydroxybutyrate polymerase (PhaC) N-terminus. This family represents the N-terminal region of the bacterial poly-beta-hydroxybutyrate polymerase (PhaC). Polyhydroxyalkanoic acids (PHAs) are carbon and energy reserve polymers produced in some bacteria when carbon sources are plentiful and another nutrient, such as nitrogen, phosphate, oxygen, or sulfur, becomes limiting. PHAs composed of monomeric units ranging from 3 to 14 carbons exist in nature. When the carbon source is exhausted, PHA is utilized by the bacterium. PhaC links D-(-)-3-hydroxybutyrl-CoA to an existing PHA molecule by the formation of an ester bond. This family appears to be a partial segment of an alpha/beta hydrolase domain. 173 matched cddid_all.tbl CDD pfam07168 pfam07168 462111 Ureide_permease Ureide permease. Heterocyclic nitrogen compounds may serve as nitrogen sources or nitrogen transport compounds in plants that are not able to fix nitrogen. This family represents ureide permease, a transporter of a wide spectrum of oxo derivatives of heterocyclic nitrogen compounds, including allantoin, uric acid and xanthine; it has 10 putative transmembrane domains with a large cytosolic central domain containing a 'Walker A' motif. Ureide permease is likely to transport other purine degradation products when nitrogen sources are low. Transport is dependent on glucose and a proton gradient. The family is found in bacteria, plants and yeast. These transporters are constituted of two sets of 5xTMs. 360 matched cddid_all.tbl CDD pfam07171 pfam07171 429332 MlrC_C MlrC C-terminus. This family represents the C-terminus (approximately 200 residues) of the product of a bacterial gene cluster that is involved in the degradation of the cyanobacterial toxin microcystin LR. Many members of this family are hypothetical proteins. 178 matched cddid_all.tbl CDD pfam07172 pfam07172 254089 GRP Glycine rich protein family. This family of proteins includes several glycine rich proteins as well as two nodulins 16 and 24. The family also contains proteins that are induced in response to various stresses. 91 matched cddid_all.tbl CDD pfam07173 pfam07173 429333 GRDP-like Glycine-rich domain-containing protein-like. This entry includes Arabidopsis Glycine-rich domain- containing protein 1 and 2 (GRDP1/2). They are involved in development and stress responses. 139 matched cddid_all.tbl CDD pfam07174 pfam07174 429334 FAP Fibronectin-attachment protein (FAP). This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix. 301 matched cddid_all.tbl CDD pfam07175 pfam07175 399867 Osteoregulin Osteoregulin. This family represents a conserved region approximately 180 residues long within osteoregulin, a bone-remodelling protein expressed highly in osteocytes within trabecular and cortical bone. A conserved RGD motif is found towards the C-terminal end of this region, and this is potentially involved in integrin recognition. 160 matched cddid_all.tbl CDD pfam07176 pfam07176 429335 DUF1400 Alpha/beta hydrolase of unknown function (DUF1400). This family contains a number of hypothetical proteins of unknown function that seem to be specific to cyanobacteria. Members of this family have an alpha/beta hydrolase fold. 127 matched cddid_all.tbl CDD pfam07177 pfam07177 462112 Neuralized Neuralized. This family contains a conserved region approximately 60 residues long within eukaryotic neuralized and neuralized-like proteins. Neuralized belongs to a group of ubiquitin ligases and is required in a subset of Notch pathway-mediated cell fate decisions during development of the Drosophila nervous system. Some family members contain multiple copies of this region. 149 matched cddid_all.tbl CDD pfam07178 pfam07178 429337 TraL TraL protein. This family consists of several bacterial TraL proteins. TraL is a predicted peripheral membrane protein which is thought to be involved in bacterial sex pilus assembly. The exact function of this family is unclear. 90 matched cddid_all.tbl CDD pfam07179 pfam07179 462113 SseB SseB protein N-terminal domain. This family consists of several SseB proteins which appear to be found exclusively in Enterobacteria. SseB is known to enhance serine-sensitivity in Escherichia coli and is part of the Salmonella pathogenicity island 2 (SPI-2) translocon. This entry contains the presumed N-terminal domain of SseB. 123 matched cddid_all.tbl CDD pfam07180 pfam07180 369250 CaiF_GrlA CaiF/GrlA transcriptional regulator. This is a family of transcriptional regulators. CaiF is involved in carnitine metabolism. GrlA is encoded within the LEE type III secretion system in the enteropathogenic E. coli O157:H. GrlR interacts with GrlA at its Helix-Turn-Helix (HTH) motif, preventing GrlA from binding to its target promoter DNA. 134 matched cddid_all.tbl CDD pfam07181 pfam07181 429339 VirC2 VirC2 protein. This family consists of several VirC2 proteins which seem to be found exclusively in Agrobacterium species and Rhizobium etli. VirC2 is known to be involved in virulence in Agrobacterium species but its exact function is unclear. 202 matched cddid_all.tbl CDD pfam07182 pfam07182 399872 DUF1402 Protein of unknown function (DUF1402). This family consists of several hypothetical bacterial proteins of around 310 residues in length. Members of this family seem to be found exclusively in Agrobacterium, Rhizobium and Brucella species. The function of this family is unknown. 300 matched cddid_all.tbl CDD pfam07183 pfam07183 399873 DUF1403 Protein of unknown function (DUF1403). This family consists of several hypothetical bacterial proteins of around 320 residues in length. Members of this family are mainly found in Rhizobium and Agrobacterium species. The function of this family is unknown. 320 matched cddid_all.tbl CDD pfam07184 pfam07184 115814 CTV_P33 Citrus tristeza virus P33 protein. This family consists of several Citrus tristeza virus (CTV) P33 proteins. The function of P33 is unclear although it is known that the protein is not needed for virion formation. 303 matched cddid_all.tbl CDD pfam07185 pfam07185 369252 DUF1404 Protein of unknown function (DUF1404). This family consists of several archaeal proteins of around 180 residues in length. Members of this family seem to be found exclusively in Sulfolobus tokodaii and Sulfolobus solfataricus. The function of this family is unknown. 169 matched cddid_all.tbl CDD pfam07187 pfam07187 429340 DUF1405 Protein of unknown function (DUF1405). This family consists of several bacterial and related archaeal protein of around 180 residues in length. The function of this family is unknown. 160 matched cddid_all.tbl CDD pfam07188 pfam07188 284577 KSHV_K8 Kaposi's sarcoma-associated herpesvirus (KSHV) K8 protein. This family consists of Kaposi's sarcoma-associated herpesvirus (KSHV) K8 proteins. KSHV is a human Gammaherpesvirus related to Epstein-Barr virus (EBV) and herpesvirus saimiri. KSHV open reading frame K8 encodes a basic region-leucine zipper protein of 237 aa that homodimerizes. K8 interacts and co-localizes with human pfam04855, a cellular chromatin-remodelling factor, both in vivo and in vitro. K8 is thought to function as a transcriptional activator under specific conditions and its transactivation activity requires its interaction with the cellular chromatin remodelling factor hSNF5. 238 matched cddid_all.tbl CDD pfam07189 pfam07189 462114 SF3b10 Splicing factor 3B subunit 10 (SF3b10). This family consists of several eukaryotic splicing factor 3B subunit 10 (SF3b10) proteins. SF3b10 is a 10 kDa subunit of the splicing factor SF3b. SF3b associates with the splicing factor SF3a and a 12S RNA unit to form the U2 small nuclear ribonucleoproteins complex. SF3b10 and SF3b14b are also thought to facilitate the interaction of U2 with the branch site. 75 matched cddid_all.tbl CDD pfam07190 pfam07190 148663 DUF1406 Protein of unknown function (DUF1406). This family consists of several Orthopoxvirus proteins of around 185 resides in length. Members of this family seem to be exclusive to Vaccinia, Camelpox and Cowpox viruses. Some family members are annotated as being C8 proteins but their function is unknown. 170 matched cddid_all.tbl CDD pfam07191 pfam07191 429341 zinc-ribbons_6 zinc-ribbons. This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family have 8 highly conserved cysteine residues, which form two zinc ribbon domains. 64 matched cddid_all.tbl CDD pfam07192 pfam07192 462115 SNURF SNURF/RPN4 protein. This family consists of several mammalian SNRPN upstream reading frame (SNURF) proteins. SNURF or RPF4 is a RING-finger protein and a coregulator of androgen receptor-dependent transcription. It has been suggested that SNURF is involved in the regulation of processes required for late steps of spermatid maturation. 69 matched cddid_all.tbl CDD pfam07193 pfam07193 284581 DUF1408 Protein of unknown function (DUF1408). This family consists of several hypothetical Lactococcus lactis and related phage proteins of around 75 residues in length. The function of this family is unknown. 71 matched cddid_all.tbl CDD pfam07194 pfam07194 462116 P2 P2 response regulator binding domain. The response regulators for CheA bind to the P2 domain, which is found between pfam01627 and pfam02895 as either one or two copies. Highly flexible linkers connect P2 to the rest of CheA and impart remarkable mobility to the P2 domain. This feature is thought to enhance the inter CheA dimer phosphotransfer reactions within the signalling complex, thereby amplifying the phosphorylation signal. 80 matched cddid_all.tbl CDD pfam07195 pfam07195 429344 FliD_C Flagellar hook-associated protein 2 C-terminus. The flagellar hook-associated protein 2 (HAP2 or FliD) forms the distal end of the flagella, and plays a role in mucin specific adhesion of the bacteria. This alignment covers the C-terminal region of this family of proteins. 230 matched cddid_all.tbl CDD pfam07196 pfam07196 399878 Flagellin_IN Flagellin hook IN motif. The function of this region is not clear, but it is found in many flagellar hook proteins, including FliD homologs. It is normally repeated, but is also apparently seen as a singleton. A conserved IN is seen at the centre of the motif. The diversity of these motifs makes it likely that some members of the family are not identified. 55 matched cddid_all.tbl CDD pfam07197 pfam07197 429345 DUF1409 Protein of unknown function (DUF1409). This family represents a short conserved region (approximately 50 residues long), sometimes repeated, within a number of hypothetical Oryza sativa proteins of unknown function. 48 matched cddid_all.tbl CDD pfam07198 pfam07198 429346 DUF1410 Protein of unknown function (DUF1410). This family represents a conserved domain approximately 100 residues long, multiple copies of which are found within hypothetical Ureaplasma parvum proteins of unknown function, as well as related species. 61 matched cddid_all.tbl CDD pfam07199 pfam07199 369258 DUF1411 Protein of unknown function (DUF1411). This family represents a conserved region approximately 150 residues long that is sometimes repeated within some Babesia bovis proteins of unknown function. 188 matched cddid_all.tbl CDD pfam07200 pfam07200 462117 Mod_r Modifier of rudimentary (Mod(r)) protein. This family represents a conserved region approximately 150 residues long within a number of eukaryotic proteins that show homology with Drosophila melanogaster Modifier of rudimentary (Mod(r)) proteins. The N-terminal half of Mod(r) proteins is acidic, whereas the C-terminal half is basic, and both of these regions are represented in this family. Members of this family include the Vps37 subunit of the endosomal sorting complex ESCRT-I, a complex involved in recruiting transport machinery for protein sorting at the multivesicular body (MVB). The yeast ESCRT-I complex consists of three proteins (Vps23, Vps28 and Vps37). The mammalian homolog of Vps37 interacts with Tsg101 (Pfam: PF05743) through its mod(r) domain and its function is essential for lysosomal sorting of EGF receptors. 146 matched cddid_all.tbl CDD pfam07201 pfam07201 399881 HrpJ HrpJ-like domain. This family represents a conserved region approximately 200 residues long within a number of bacterial hypersensitivity response secretion protein HrpJ and similar proteins. HrpJ forms part of a type III secretion system through which, in phytopathogenic bacterial species, virulence factors are thought to be delivered to plant cells. This family also includes the InvE invasion protein from Salmonella. This protein is involved in host parasite interactions and mutations in the InvE gene render Salmonella typhimurium non-invasive. InvE S. typhimurium mutants fail to elicit a rapid Ca2+ increase in cultured cells, an important event in the infection procedure and internalization of S. typhimurium into epithelial cells. This family includes bacterial SepL and SsaL proteins. SepL plays an essential role in the infection process of enterohemorrhagic Escherichia coli and is thought to be responsible for the secretion of EspA, EspD, and EspB. SsaL of Salmonella typhimurium is thought to be a component of the type III secretion system. 165 matched cddid_all.tbl CDD pfam07202 pfam07202 462118 Tcp10_C T-complex protein 10 C-terminus. This entry represents a repeating unit commonly found in the C terminus of the eukaryotic T-complex protein 10. The T-complex is involved in spermatogenesis in mice. The repeating unit is commonly found 3-4 times, but there is often a gap between the first and second repeats, which is big enough to accommodate another repeat unit. However, the score is insufficient to be included, and could be a degenerate repeat. 30 matched cddid_all.tbl CDD pfam07203 pfam07203 311262 DUF1412 Protein of unknown function (DUF1412). This family consists of several Caenorhabditis elegans proteins of around 70-75 residues in length. The function of this family is unknown. 53 matched cddid_all.tbl CDD pfam07204 pfam07204 115833 Orthoreo_P10 Orthoreovirus membrane fusion protein p10. This family consists of several Orthoreovirus membrane fusion protein p10 sequences. p10 is thought to be a multifunctional protein that plays a key role in virus-host interaction. 98 matched cddid_all.tbl CDD pfam07205 pfam07205 399883 DUF1413 Domain of unknown function (DUF1413). This family consists of several hypothetical bacterial proteins which seem to be specific to firmicute species. Members of this family are typically around 100 residues in length. The function of this family is unknown. 69 matched cddid_all.tbl CDD pfam07206 pfam07206 284592 Baculo_LEF-10 Baculovirus late expression factor 10 (LEF-10). This family consists of several Baculovirus specific late expression factor 10 (LEF-10) sequences. LEF-10 is thought to be a late expressed structural protein although its exact function is unknown. 71 matched cddid_all.tbl CDD pfam07207 pfam07207 399884 Lir1 Light regulated protein Lir1. This family consists of several plant specific light regulated Lir1 proteins. Lir1 mRNA accumulates in the light, reaching maximum and minimum steady-state levels at the end of the light and dark period, respectively. Plants germinated in the dark have very low levels of lir1 mRNA, whereas plants germinated in continuous light express lir1 at an intermediate but constant level. It is thought that lir1 expression is controlled by light and a circadian clock. The exact function of this family is unclear. 134 matched cddid_all.tbl CDD pfam07208 pfam07208 429349 DUF1414 Protein of unknown function (DUF1414). This family consists of several hypothetical bacterial proteins of around 70 residues in length. Members of this family are often referred to as YejL. The function of this family is unknown. 44 matched cddid_all.tbl CDD pfam07209 pfam07209 429350 DUF1415 Protein of unknown function (DUF1415). This family consists of several hypothetical bacterial proteins of around 180 residues in length. The function of this family is unknown. 171 matched cddid_all.tbl CDD pfam07210 pfam07210 429351 DUF1416 Protein of unknown function (DUF1416). This family consists of several hypothetical bacterial proteins of around 100 residues in length. Members of this family appear to be Actinomycete specific. The function of this family is unknown. 97 matched cddid_all.tbl CDD pfam07212 pfam07212 429352 Hyaluronidase_1 Hyaluronidase protein (HylP). This family consists of several phage associated hyaluronidase proteins (EC:3.2.1.35) which seem to be specific to Streptococcus pyogenes and Streptococcus pyogenes bacteriophages. The substrate of hyaluronidase is hyaluronic acid, a sugar polymer composed of alternating N-acetylglucosamine and glucuronic acid residues. Hyaluronic acid is found in the ground substance of human connective tissue and the vitreous of the eye and also is the sole component of the capsule of group A streptococci. The capsule has been shown to be an important virulence factor of this organizm by virtue of its ability to resist phagocytosis. Production by S. pyogenes of both a hyaluronic acid capsule and hyaluronidase enzymatic activity capable of destroying the capsule is an interesting, yet-unexplained, phenomenon. 273 matched cddid_all.tbl CDD pfam07213 pfam07213 284598 DAP10 DAP10 membrane protein. This family consists of several mammalian DAP10 membrane proteins. In activated mouse natural killer (NK) cells, the NKG2D receptor associates with two intracellular adaptors, DAP10 and DAP12, which trigger phosphatidyl inositol 3 kinase (PI3K) and Syk family protein tyrosine kinases, respectively. It has been suggested that the DAP10-PI3K pathway is sufficient to initiate NKG2D-mediated killing of target cells. 79 matched cddid_all.tbl CDD pfam07214 pfam07214 369264 DUF1418 Protein of unknown function (DUF1418). This family consists of several hypothetical Enterobacterial proteins of around 100 residues in length. Members of this family are often described as YbjC. In E. coli the ybjC gene is located downstream of nfsA (which encodes the major oxygen-insensitive nitroreductase). It is thought that nfsA and ybjC form an operon an its promoter is a class I SoxS-dependent promoter. The function of this family is unknown. 94 matched cddid_all.tbl CDD pfam07215 pfam07215 399888 DUF1419 Protein of unknown function (DUF1419). This family consists of several bacterial proteins of around 110 residues in length. Members of this family seem to be specific to Agrobacterium species and to Rhizobium loti. The function of this family is unknown. 112 matched cddid_all.tbl CDD pfam07216 pfam07216 284601 LcrG LcrG protein. This family consists of several bacterial LcrG proteins. Yersiniae are equipped with the Yop virulon, an apparatus that allows extracellular bacteria to deliver toxic Yop proteins inside the host cell cytosol in order to sabotage the communication networks of the host cell or even to cause cell death. LcrG is a component of the Yop virulon involved in the regulation of secretion of the Yops. 91 matched cddid_all.tbl CDD pfam07217 pfam07217 399889 Het-C Heterokaryon incompatibility protein Het-C. In filamentous fungi, het loci (for heterokaryon incompatibility) are believed to regulate self/nonself-recognition during vegetative growth. As filamentous fungi grow, hyphal fusion occurs within an individual colony to form a network. Hyphal fusion can occur also between different individuals to form a heterokaryon, in which genetically distinct nuclei occupy a common cytoplasm. However, heterokaryotic cells are viable only if the individuals involved have identical alleles at all het loci. 560 matched cddid_all.tbl CDD pfam07218 pfam07218 284603 RAP1 Rhoptry-associated protein 1 (RAP-1). This family consists of several rhoptry-associated protein 1 (RAP-1) sequences which appear to be specific to Plasmodium falciparum. 793 matched cddid_all.tbl CDD pfam07219 pfam07219 429353 HemY_N HemY protein N-terminus. This family represents the N-terminus (approximately 150 residues) of bacterial HemY porphyrin biosynthesis proteins. This is a membrane protein involved in a late step of protoheme IX synthesis. 104 matched cddid_all.tbl CDD pfam07220 pfam07220 115849 DUF1420 Protein of unknown function (DUF1420). This family consists of several hypothetical putative lipoproteins which seem to be found specifically in the bacterium Leptospira interrogans. Members of this family are typically around 670 resides in length and their function is unknown. 672 matched cddid_all.tbl CDD pfam07221 pfam07221 399891 GlcNAc_2-epim N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase). This family contains a number of eukaryotic and bacterial N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) enzymes (EC:5.1.3.8) approximately 500 residues long. This converts N-acyl-D-glucosamine to N-acyl-D-mannosamine. 347 matched cddid_all.tbl CDD pfam07222 pfam07222 429354 PBP_sp32 Proacrosin binding protein sp32. This family consists of several mammalian specific proacrosin binding protein sp32 sequences. sp32 is a sperm specific protein which is known to bind with with 55- and 53-kDa proacrosins and the 49-kDa acrosin intermediate. The exact function of sp32 is unclear, it is thought however that the binding of sp32 to proacrosin may be involved in packaging the acrosin zymogen into the acrosomal matrix. 243 matched cddid_all.tbl CDD pfam07223 pfam07223 399892 DUF1421 UBA-like domain (DUF1421). This domain represents a conserved region that has a UBA like fold. It is found in a number of plant proteins of unknown function. 45 matched cddid_all.tbl CDD pfam07224 pfam07224 254111 Chlorophyllase Chlorophyllase. This family consists of several plant specific Chlorophyllase proteins (EC:3.1.1.14). Chlorophyllase (Chlase) is the first enzyme involved in chlorophyll (Chl) degradation and catalyzes the hydrolysis of ester bond to yield chlorophyllide and phytol. 307 matched cddid_all.tbl CDD pfam07225 pfam07225 429355 NDUF_B4 NADH-ubiquinone oxidoreductase B15 subunit (NDUFB4). This family consists of several NADH-ubiquinone oxidoreductase B15 subunit proteins (EC:1.6.5.3). 124 matched cddid_all.tbl CDD pfam07226 pfam07226 429356 DUF1422 Protein of unknown function (DUF1422). This family consists of several hypothetical bacterial proteins of around 120 residues in length. The function of this family is unknown. 114 matched cddid_all.tbl CDD pfam07227 pfam07227 429357 PHD_Oberon PHD - plant homeodomain finger protein. PHD_oberon is a plant homeodomain finger domain of Oberon proteins from plants. Oberon is necessary for maintenance and/or establishment of both the shoot and root apical meristems in Arabidopsis. Oberon proteins are made up of a PHD finger domain and a coiled-coil domain. The PHD-finger domain is found in a wide variety of proteins involved in the regulation of chromatin structure. Oberon proteins mediate the TMO7 (the direct target of MP) expression through modification of, or binding to, chromatin at the TMO7 locus. TMO7 stands for the target of Monopteros 7 (MP) (or Auxin response factor 7). 130 matched cddid_all.tbl CDD pfam07228 pfam07228 462119 SpoIIE Stage II sporulation protein E (SpoIIE). This family contains a number of bacterial stage II sporulation E proteins (EC:3.1.3.16). These are required for formation of a normal polar septum during sporulation. The N-terminal region is hydrophobic and is expected to contain up to 12 membrane-spanning segments. 192 matched cddid_all.tbl CDD pfam07229 pfam07229 429359 VirE2 VirE2. This family consists of several VirE2 proteins which seem to be specific to Agrobacterium tumefaciens and Rhizobium etli. VirE2 is known to interact, via its C terminus, with VirD4. Agrobacterium tumefaciens transfers oncogenic DNA and effector proteins to plant cells during the course of infection. Substrate translocation across the bacterial cell envelope is mediated by a type IV secretion (TFS) system composed of the VirB proteins, as well as VirD4, a member of a large family of inner membrane proteins implicated in the coupling of DNA transfer intermediates to the secretion machine. VirE2 is therefore thought to be a protein substrate of a type IV secretion system which is recruited to a member of the coupling protein superfamily. 556 matched cddid_all.tbl CDD pfam07230 pfam07230 462120 Portal_Gp20 Bacteriophage T4-like portal protein (Gp20). This family consists of several bacteriophage T4-like capsid assembly (or portal) proteins. The exact mechanism by which the double-stranded (ds) DNA bacteriophages incorporate the portal protein at a unique vertex of the icosahedral capsid is unknown. In phage T4, there is evidence that this vertex, constituted by 12 subunits of gp20, acts as an initiator for the assembly of the major capsid protein and the scaffolding proteins into a prolate icosahedron of precise dimensions. The regulation of portal protein gene expression is an important regulator of prohead assembly in bacteriophage T4. 439 matched cddid_all.tbl CDD pfam07231 pfam07231 399899 Hs1pro-1_N Hs1pro-1 N-terminus. This family represents the N-terminus (approximately 180 residues) of plant Hs1pro-1, which is believed to confer resistance to nematodes. 195 matched cddid_all.tbl CDD pfam07232 pfam07232 115861 DUF1424 Putative rep protein (DUF1424). This family consists of several archaeal proteins of around 320 residues in length. Members of this family seem to be found exclusively in Halobacterium and Haloferax species. The function of this family is unknown. This protein is probably a rep protein due to conservation of functional motifs. 329 matched cddid_all.tbl CDD pfam07233 pfam07233 429361 DUF1425 Protein of unknown function (DUF1425). This family consists of several hypothetical bacterial proteins of around 125 residues in length. Several members of this family are described as putative lipoproteins and are often known as YcfL. The function of this family is unknown. 87 matched cddid_all.tbl CDD pfam07234 pfam07234 284616 Babuvirus_MP Movement and RNA silencing protein. This family consists of several Babuvirus proteins of around 120 residues in length. Proteins in this family include movement and RNA silencing protein (also known as MP) from Banana bunchy top virus. MP acts as a suppressor of RNA-mediated gene silencing, also known as post-transcriptional gene silencing (PTGS), a mechanism of plant viral defense that limits the accumulation of viral RNAs. It transports viral genome to neighbouring plant cells directly through plasmosdesmata, without any budding. The movement protein allows efficient cell to cell propagation, by bypassing the host cell wall barrier. 117 matched cddid_all.tbl CDD pfam07235 pfam07235 399901 DUF1427 Protein of unknown function (DUF1427). This family consists of several bacterial proteins of around 100 residues in length. The function of this family is unknown. 84 matched cddid_all.tbl CDD pfam07236 pfam07236 399902 Phytoreo_S7 Phytoreovirus S7 protein. This family consists of several Phytoreovirus S7 proteins which are thought to be viral core proteins. 505 matched cddid_all.tbl CDD pfam07237 pfam07237 429362 DUF1428 Protein of unknown function (DUF1428). This family consists of several hypothetical bacterial and one archaeal sequence of around 120 residues in length. The function of this family is unknown. The structure of this family shows it to be part of the Dimeric-alpha-beta-barrel superfamily. Many members are annotated as being RNA signal recognition particle 4.5S RNA, but this could not be verified. 102 matched cddid_all.tbl CDD pfam07238 pfam07238 399904 PilZ PilZ domain. PilZ is a c-di-GMP binding domain found in widespread cytoplasmic receptors, which is involved in regulation of motility, biofilm formation and virulence of many bacterial pathogens. This domain binds c-di-GMP through RXXXR and [D/N]hSXXG motifs, however, some PilZ domains lack these motifs and do not bind c-di-GMP. Proteins which contain PilZ are known to interact with the flagellar switch-complex proteins FliG and FliM. This interaction results in a reduction of torque generation and induces CCW motor bias. This is the canonical PilZ domain whose structure consists of six beta-strands that form a beta barrel, followed by a long C-terminal alpha-helix. 102 matched cddid_all.tbl CDD pfam07239 pfam07239 399905 OpcA Outer membrane protein OpcA. This family consists of several Neisseria species specific OpcA outer membrane proteins. Opc (formerly called 5C) is one of the major outer membrane proteins and has been shown to play an important role in meningococcal adhesion and invasion of both epithelial and endothelial cells. 250 matched cddid_all.tbl CDD pfam07240 pfam07240 399906 Turandot Stress-inducible humoral factor Turandot. This family consists of several Drosophila species specific Turandot proteins. The Turandot A (TotA) gene encodes a humoral factor, which is secreted from the fat body and accumulates in the body fluids. TotA is strongly induced upon bacterial challenge, as well as by other types of stress such as high temperature, mechanical pressure, dehydration, UV irradiation, and oxidative agents. It is also up-regulated during metamorphosis and at high age. Flies that over-express TotA show prolonged survival and retain normal activity at otherwise lethal temperatures. Although TotA is only induced by severe stress, it responds to a much wider range of stimuli than heat shock genes such as hsp70 or immune genes such as Cecropin A1. 81 matched cddid_all.tbl CDD pfam07242 pfam07242 369281 DUF1430 Protein of unknown function (DUF1430). This family represents the C-terminus (approximately 120 residues) of a number of hypothetical bacterial proteins of unknown function. These are possibly membrane proteins involved in immunity. 100 matched cddid_all.tbl CDD pfam07243 pfam07243 369282 Phlebovirus_G1 Phlebovirus glycoprotein G1. This family consists of several Phlebovirus glycoprotein G1 sequences. Members of the Bunyaviridae family acquire an envelope by budding through the lipid bilayer of the Golgi complex. The budding compartment is thought to be determined by the accumulation of the two heterodimeric membrane glycoproteins G1 and G2 in the Golgi. 527 matched cddid_all.tbl CDD pfam07244 pfam07244 462121 POTRA Surface antigen variable number repeat. This family is found primarily in bacterial surface antigens, normally as variable number repeats at the N-terminus. The C-terminus of these proteins is normally represented by pfam01103. The alignment centres on a -GY- or -GF- motif. Some members of this family are found in the mitochondria. It is predicted to have a mixed alpha/beta secondary structure. 78 matched cddid_all.tbl CDD pfam07245 pfam07245 462122 Phlebovirus_G2 Phlebovirus glycoprotein G2 fusion domain. This family consists of several Phlebovirus glycoprotein G2 sequences. Members of the Bunyaviridae family acquire an envelope by budding through the lipid bilayer of the Golgi complex. The budding compartment is thought to be determined by the accumulation of the two heterodimeric membrane glycoproteins G1 and G2 in the Golgi. 325 matched cddid_all.tbl CDD pfam07246 pfam07246 369285 Phlebovirus_NSM Phlebovirus nonstructural protein NS-M. This family consists of several Phlebovirus nonstructural NS-M proteins which represent the N-terminal region of the M polyprotein precursor. The function of this family is unknown. 228 matched cddid_all.tbl CDD pfam07247 pfam07247 369286 AATase Alcohol acetyltransferase. This family contains a number of alcohol acetyltransferase (EC:2.3.1.84) enzymes approximately 500 residues long found in both bacteria and metazoa. These catalyze the esterification of isoamyl alcohol by acetyl coenzyme A. 500 matched cddid_all.tbl CDD pfam07248 pfam07248 429365 DUF1431 Protein of unknown function (DUF1431). This family contains a number of Drosophila melanogaster proteins of unknown function. These contain several conserved cysteine residues. 155 matched cddid_all.tbl CDD pfam07249 pfam07249 369288 Cerato-platanin Cerato-platanin. This family contains a number of fungal cerato-platanin phytotoxic proteins approximately 150 residues long. Cerato-platanin contains four cysteine residues that form two disulphide bonds. 118 matched cddid_all.tbl CDD pfam07250 pfam07250 399910 Glyoxal_oxid_N Glyoxal oxidase N-terminus. This family represents the N-terminus (approximately 300 residues) of a number of plant and fungal glyoxal oxidase enzymes. Glyoxal oxidase catalyzes the oxidation of aldehydes to carboxylic acids, coupled with reduction of dioxygen to hydrogen peroxide. It is an essential component of the extracellular lignin degradation pathways of the wood-rot fungus Phanerochaete chrysosporium. 243 matched cddid_all.tbl CDD pfam07252 pfam07252 284628 DUF1433 Protein of unknown function (DUF1433). This family contains a number of hypothetical bacterial proteins of unknown function approximately 100 residues in length. 88 matched cddid_all.tbl CDD pfam07253 pfam07253 254125 Gypsy Gypsy protein. This family consists of several Gypsy/Env proteins from Drosophila and Ceratitis fruit fly species. Gypsy is an endogenous retrovirus of Drosophila melanogaster. Phylogenetic studies suggest that occasional horizontal transfer events of gypsy occur between Drosophila species. Gypsy possesses infective properties associated with the products of the envelope gene that might be at the origin of these interspecies transfers. This family contains many members with full-length matches; however, it also includes a number of very short sequences and short matches of sequences with other unrelated domains on them, which cannot be excluded. These matches may represent remnants of once-functional genes. 472 matched cddid_all.tbl CDD pfam07254 pfam07254 462123 Cpta_toxin Membrane-bound toxin component of toxin-antitoxin system. CptA is a family of bacterial proteins named for the member of this family, YGFX_ECOLI, Swissprot:Q46824. YgfX was previously thought to be the toxic part of a toxin-antitoxin module along with the antitoxin, pfam03937 Sdh5. However, studies have shown that, YgfX interferes with correct cell division and morphology. Furthermore, the function of YgfX-SdhE as a TA system could not be demonstrated in either E. coli or Serratia sp. ATCC 39006. YgfX is predicted to have a short N-terminal cytoplasmic domain followed by two transmembrane helices (TMHs) separated by a short periplasmic loop and finally, a larger C-terminal cytoplasmic domain. The TMHs of YgfX are required for activity, but the sequence of the cytoplasmic 13 N-terminal amino acids is not essential. Furthermore, the amino acids W34 and D117 are not required for localization but are necessary for YgfX multimerization, interaction with SdhE, and YgfX activity. It is proposed that the formation of YgfX multimeric membrane-bound proteins are required to enable the interaction with the cytoplasmic SDH assembly factor SdhE. Another study has demonstrated that sdhEygfX (bicistronic operon) affects pig biosynthesis, directly or indirectly, at the level of transcription of the biosynthetic operon (pigA-O). It has also been suggested that, in addition to indirect transcriptional activation of pigA-O, YgfX might facilitate the formation of a terminal pig biosynthetic complex consisting of PigB and PigC. 132 matched cddid_all.tbl CDD pfam07255 pfam07255 462124 Benyvirus_14KDa Benyvirus 14KDa protein. This family consists of several Benyvirus specific 14KDa proteins of around 125 residues in length. Members of this family contain 9 conserved cysteine residues. The function of this family is unknown. 123 matched cddid_all.tbl CDD pfam07256 pfam07256 429367 DUF1435 Protein of unknown function (DUF1435). This family consists of several hypothetical Enterobacterial proteins of around 80 residues in length. The function of this family is unknown. 75 matched cddid_all.tbl CDD pfam07258 pfam07258 462125 COMM_domain COMM domain. The leucine-rich, 70-85 amino acid long COMM domain is predicted to form a beta-sheet and an extreme C-terminal alpha- helix. The COMM domain containing proteins are about 200 residues in length and passed the C-terminal COMM domain. 64 matched cddid_all.tbl CDD pfam07259 pfam07259 462126 ProSAAS ProSAAS precursor. This family consists of several mammalian proSAAS precursor proteins. ProSAAS mRNA is expressed primarily in brain and other neuroendocrine tissues (pituitary, adrenal, pancreas); within brain, the mRNA is broadly distributed among neurons. ProSAAS is thought to be an endogenous inhibitor of prohormone convertase 1 may function as a neuropeptide. N-terminal fragments of proSAAS in intracellular Pick Bodies (PBs) may cause a functional disturbance of neurons in Pick's disease. 273 matched cddid_all.tbl CDD pfam07260 pfam07260 429370 ANKH Progressive ankylosis protein (ANKH). This family consists of several progressive ankylosis protein (ANK or ANKH) sequences. The ANK protein spans the outer cell membrane and shuttles inorganic pyrophosphate (PPi), a major inhibitor of physiologic and pathologic calcification, bone mineralization and bone resorption. Mutations in ANK are thought to give rise to Craniometaphyseal dysplasia (CMD) which is a rare skeletal disorder characterized by progressive thickening and increased mineral density of craniofacial bones and abnormally developed metaphyses in long bones. This family shows distant homology to the MOP (TCDB) superfamily of transporters. 344 matched cddid_all.tbl CDD pfam07261 pfam07261 462127 DnaB_2 Replication initiation and membrane attachment. This family consists of several bacterial replication initiation and membrane attachment (DnaB) proteins, as well as DnaD which is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication. DnaD has been merged into this family. This family also includes Ftn6, a cyanobacterial-specific divisome component possibly playing a role at the interface between DNA replication and cell division. Ftn6 possesses a conserved domain localized within the N-terminus of the proteins. This domain, named FND, exhibits sequence and structure similarities with the DnaD-like domains pfam04271 now merged into pfam07261. 70 matched cddid_all.tbl CDD pfam07262 pfam07262 399916 CdiI CDI immunity protein. CdiI immunity proteins function as part of the bacterial contact-dependent growth inhibition (CDI) system. CDI is mediated by the CdiB-CdiA two-partner secretion system. Each CdiA protein exhibits a distinct growth inhibition activity, which resides in the polymorphic C-terminal region (CdiA-CT). Cells with the CDI sytem also express a CdiI immunity protein that blocks the activity of cognate CdiA-CT, thereby protecting the cell from autoinhibition. In many CDI systems the cdiBAI genes are followed by orphan cdiA-CT/cdiI modules, suggesting that these modules are exchanged between the CDI systems of different bacteria. 155 matched cddid_all.tbl CDD pfam07263 pfam07263 462128 DMP1 Dentin matrix protein 1 (DMP1). This family consists of several mammalian dentin matrix protein 1 (DMP1) sequences. The dentin matrix acidic phosphoprotein 1 (DMP1) gene has been mapped to human chromosome 4q21. DMP1 is a bone and teeth specific protein initially identified from mineralized dentin. DMP1 is primarily localized in the nuclear compartment of undifferentiated osteoblasts. In the nucleus, DMP1 acts as a transcriptional component for activation of osteoblast-specific genes like osteocalcin. During the early phase of osteoblast maturation, Ca(2+) surges into the nucleus from the cytoplasm, triggering the phosphorylation of DMP1 by a nuclear isoform of casein kinase II. This phosphorylated DMP1 is then exported out into the extracellular matrix, where it regulates nucleation of hydroxyapatite. DMP1 is a unique molecule that initiates osteoblast differentiation by transcription in the nucleus and orchestrates mineralized matrix formation extracellularly, at later stages of osteoblast maturation. The DMP1 gene has been found to be ectopically expressed in lung cancer although the reason for this is unknown. 519 matched cddid_all.tbl CDD pfam07264 pfam07264 462129 EI24 Etoposide-induced protein 2.4 (EI24). This family contains a number of eukaryotic etoposide-induced 2.4 (EI24) proteins approximately 350 residues long as well as bacterial CysZ proteins (formerly known as DUF540). In cells treated with the cytotoxic drug etoposide, EI24 is induced by p53. It has been suggested to play an important role in negative cell growth control. 161 matched cddid_all.tbl CDD pfam07265 pfam07265 399919 TAP35_44 Tapetum specific protein TAP35/TAP44. This family consists of several plant tapetum specific proteins. Members of this family are found in Arabidopsis thaliana, Brassica napus and Sinapis alba. Members of this family may be involved in sporopollenin formation and/or deposition. 119 matched cddid_all.tbl CDD pfam07267 pfam07267 369296 Nucleo_P87 Nucleopolyhedrovirus capsid protein P87. This family consists of several Nucleopolyhedrovirus capsid protein P87 sequences. P87 is expressed late in infection and concentrated in infected cell nuclei. 623 matched cddid_all.tbl CDD pfam07268 pfam07268 284641 EppA_BapA Exported protein precursor (EppA/BapA). This family consists of a number of exported protein precursor (EppA and BapA) sequences which seem to be specific to Borrelia burgdorferi (Lyme disease spirochete). bapA gene sequences are quite stable but the encoded proteins do not provoke a strong immune response in most individuals. Conversely, EppA proteins are much more antigenic but are more variable in sequence. It is thought that BapA and EppA play important roles during the Borrelia burgdorferi infectious cycle. 138 matched cddid_all.tbl CDD pfam07270 pfam07270 284642 DUF1438 Protein of unknown function (DUF1438). This family consists of several hypothetical proteins of around 170 residues in length which appear to be mouse specific. The function of this family is unknown. 151 matched cddid_all.tbl CDD pfam07271 pfam07271 429374 Cytadhesin_P30 Cytadhesin P30/P32. This family consists of several Mycoplasma species specific Cytadhesin P32 and P30 proteins. P30 has been found to be membrane associated and localized on the tip organelle. It is thought that it is important in cytadherence and virulence. The N-terminus contains two predicted transmembrane helices followed by a long region of a short 6 residue proline rich repeat. 275 matched cddid_all.tbl CDD pfam07272 pfam07272 148716 Orthoreo_P17 Orthoreovirus P17 protein. This family consists of several Orthoreovirus P17 proteins. P17 is specified be ORF2 of the S1 gene and represents a nonstructural protein which associate with cell membranes. 146 matched cddid_all.tbl CDD pfam07273 pfam07273 429375 DUF1439 Protein of unknown function (DUF1439). This family consists of several hypothetical bacterial proteins of around 190 residues in length. Several members of this family are annotated as being putative lipoproteins and are often known as YceB. The function of this family is unknown. 152 matched cddid_all.tbl CDD pfam07274 pfam07274 429376 DUF1440 Protein of unknown function (DUF1440). This family contains a number of bacterial proteins of unknown function approximately 180 residues long. These are possibly integral membrane proteins. 133 matched cddid_all.tbl CDD pfam07275 pfam07275 462130 ArdA Antirestriction protein (ArdA). This family consists of several bacterial antirestriction (ArdA) proteins. ArdA functions in bacterial conjugation to allow an unmodified plasmid to evade restriction in the recipient bacterium and yet acquire cognate modification. 151 matched cddid_all.tbl CDD pfam07276 pfam07276 115901 PSGP Apopolysialoglycoprotein (PSGP). This family represents a series of 13 reside repeats found in the apopolysialoglycoprotein of Oncorhynchus mykiss (Rainbow trout) and Oncorhynchus masou (Cherry salmon). Polysialoglycoprotein (PSGP) of unfertilized eggs of rainbow trout consists of tandem repeats of a glycotridecapeptide, Asp-Asp-Ala-Thr*-Ser*-Glu-Ala-Ala-Thr*-Gly-Pro-Ser- Gly (* denotes the attachment site of a polysialoglycan chain). In response to egg activation, PSGP is discharged by exocytosis into the space between the vitelline envelope and the plasma membrane, i.e. the perivitelline space, where the 200-kDa PSGP molecules undergo rapid and dramatic depolymerization by proteolysis into glycotridecapeptides. 13 matched cddid_all.tbl CDD pfam07277 pfam07277 429378 SapC SapC. This family contains a number of bacterial SapC proteins approximately 250 residues long. In Campylobacter fetus, SapC forms part of a paracrystalline surface layer (S-layer) that confers serum resistance. 220 matched cddid_all.tbl CDD pfam07278 pfam07278 429379 DUF1441 Protein of unknown function (DUF1441). This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown. However, it appears to be distantly related to other HTH families so may act as a transcriptional regulator. 147 matched cddid_all.tbl CDD pfam07279 pfam07279 115904 DUF1442 Protein of unknown function (DUF1442). This family consists of several hypothetical Arabidopsis thaliana proteins of around 225 residues in length. The function of this family is unknown. 218 matched cddid_all.tbl CDD pfam07280 pfam07280 148722 Ac110_PIF Per os infectivity factor AC110. This family consists of several Baculovirus proteins of around 55 residues in length. Family members include Autographa californica nuclear polyhedrosis virus (AcMNPV) Per os infectivity factor AC110, which is required for oral infectivity. It may play a role after occlusion-derived virions pass through the host's peritrophic membrane. 43 matched cddid_all.tbl CDD pfam07281 pfam07281 462131 INSIG Insulin-induced protein (INSIG). This family contains a number of eukaryotic Insulin-induced proteins (INSIG-1 and INSIG-2) approximately 200 residues long. INSIG-1 and INSIG-2 are found in the endoplasmic reticulum and bind the sterol-sensing domain of SREBP cleavage-activating protein (SCAP), preventing it from escorting SREBPs to the Golgi. Their combined action permits feedback regulation of cholesterol synthesis over a wide range of sterol concentrations. 189 matched cddid_all.tbl CDD pfam07282 pfam07282 284650 OrfB_Zn_ribbon Putative transposase DNA-binding domain. This putative domain is found at the C-terminus of a large number of transposase proteins. This domain contains four conserved cysteines suggestive of a zinc binding domain. Given the need for transposases to bind DNA as well as the large number of DNA-binding zinc fingers we hypothesize this domain is DNA-binding. 69 matched cddid_all.tbl CDD pfam07283 pfam07283 429381 TrbH Conjugal transfer protein TrbH. This family contains TrbH, a bacterial conjugal transfer protein approximately 150 residues long. This contains a putative membrane lipoprotein lipid attachment site. 126 matched cddid_all.tbl CDD pfam07284 pfam07284 462132 BCHF 2-vinyl bacteriochlorophyllide hydratase (BCHF). This family contains the bacterial enzyme 2-vinyl bacteriochlorophyllide hydratase (EC:4.2.1.-) (approximately 150 residues long). This is involved in the light-independent bacteriochlorophyll biosynthesis pathway by adding water across the 2-vinyl group. 139 matched cddid_all.tbl CDD pfam07285 pfam07285 429383 DUF1444 Protein of unknown function (DUF1444). This family contains several hypothetical bacterial proteins of unknown function that are approximately 250 residues long. 264 matched cddid_all.tbl CDD pfam07286 pfam07286 462133 D-Glu_cyclase D-glutamate cyclase. This family includes mitochondrial D-glutamate cyclase which converts D-glutamate to 5-oxo-D-proline. This family also includes numerous uncharacterized proteins from bacteria. 143 matched cddid_all.tbl CDD pfam07287 pfam07287 462134 AtuA Acyclic terpene utilization family protein AtuA. This family consists of several bacterial and plant proteins of around 400 residues in length. One member of this family has been characterized in Pseudomonas citronellolis as AtuA, a member of a gene cluster that is essential for the acyclic terpene utilization (Atu) pathway. 348 matched cddid_all.tbl CDD pfam07288 pfam07288 462135 RpoY RNA polymerase epsilon subunit. RNA polymerase in bacteria is a multisubunit protein complex that is essential for gene expression. This entry represents the epsilon subunit encoded by the rpoY gene. The structure of epsilon shows simple beta sheet with an alpha helix running diagonally along the back of the structure forming a beta-beta-alpha-beta fold. 68 matched cddid_all.tbl CDD pfam07289 pfam07289 462136 BBL5 Bardet-Biedl syndrome 5 protein. BBS5 is part of the BBSome complex that may function as a coat complex required for sorting of specific membrane proteins to the primary cilia. Mutations in the BBS5 gene cause Bardet-Biedl syndrome 5. 334 matched cddid_all.tbl CDD pfam07290 pfam07290 429387 DUF1449 Protein of unknown function (DUF1449). This family consists of several bacterial proteins of around 210 residues in length. The function of this family is unknown. 199 matched cddid_all.tbl CDD pfam07291 pfam07291 399932 MauE Methylamine utilization protein MauE. This family consists of several bacterial methylamine utilization MauE proteins. Synthesis of enzymes involved in methylamine oxidation via methylamine dehydrogenase (MADH) is encoded by genes present in the mau cluster. MauE and MauD are specifically involved in the processing, transport, and/or maturation of the beta-subunit and that the absence of each of these proteins leads to production of a non-functional beta-subunit which becomes rapidly degraded. 184 matched cddid_all.tbl CDD pfam07292 pfam07292 462137 NID Nmi/IFP 35 domain (NID). This family represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi). This domain mediates Nmi-Nmi protein interactions and subcellular localization. 90 matched cddid_all.tbl CDD pfam07293 pfam07293 429389 DUF1450 Protein of unknown function (DUF1450). This family consists of several hypothetical bacterial proteins of around 80 residues in length. Members of this family contain four highly conserved cysteine residues. The function of this family is unknown. 75 matched cddid_all.tbl CDD pfam07294 pfam07294 284662 Fibroin_P25 Fibroin P25. This family consists of several insect fibroin P25 proteins. Silk fibroin produced by the silkworm Bombyx mori consists of a heavy chain, a light chain, and a glycoprotein, P25. The heavy and light chains are linked by a disulfide bond, and P25 associates with disulfide-linked heavy and light chains by non-covalent interactions. P25 is plays an important role in maintaining integrity of the complex. 196 matched cddid_all.tbl CDD pfam07295 pfam07295 429390 DUF1451 Zinc-ribbon containing domain. This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. 147 matched cddid_all.tbl CDD pfam07296 pfam07296 254144 TraP TraP protein. This family consists of several bacterial conjugative transfer TraP proteins from Escherichia coli and Salmonella typhimurium. TraP appears to play a minor role in conjugation and may interact with TraB, which varies in sequence along with TraP, in order to stabilize the proposed transmembrane complex formed by the tra operon products. 202 matched cddid_all.tbl CDD pfam07297 pfam07297 462138 DPM2 Dolichol phosphate-mannose biosynthesis regulatory protein (DPM2). This family consists of several eukaryotic dolichol phosphate-mannose biosynthesis regulatory (DPM2) proteins. Biosynthesis of glycosylphosphatidylinositol and N-glycan precursor is dependent upon a mannosyl donor, dolichol phosphate-mannose (DPM). DPM2, an 84 amino acid membrane protein expressed in the endoplasmic reticulum (ER), makes a complex with DPM1 that is essential for the ER localization and stable expression of DPM1. Moreover, DPM2 enhances binding of dolichol phosphate, a substrate of DPM synthase. Biosynthesis of DPM in mammalian cells is regulated by DPM2. 75 matched cddid_all.tbl CDD pfam07298 pfam07298 429392 NnrU NnrU protein. This family consists of several plant and bacterial NnrU proteins. NnrU is thought to be involved in the reduction of nitric oxide. The exact function of NnrU is unclear. It is thought however that NnrU and perhaps NnrT are required for expression of both nirK and nor. 193 matched cddid_all.tbl CDD pfam07299 pfam07299 462139 EF-G-binding_N Elongation factor G-binding protein, N-terminal. This domain can be found in the N terminus of the FusB, FusC, and FusD proteins from Staphylococcus aureus. They are elongation factor G (EF-G) binding proteins that are linked to the fusidic acid (FA) resistance in S. aureus. The FusB proteins are two-domain metalloproteins, and this N-terminal domain forms a four-helical bundle whose helices help to stabilize the conformation of the treble-clef zinc-finger in the C-terminal domain. FA is an antibiotic that binds to EF-G, preventing its release from the ribosome, thus stalling bacterial protein synthesis. The FusB proteins provide FA resistance by preventing formation or facilitating dissociation of the FA-locked EF-G-ribosome complex during elongation and ribosome recycling. 82 matched cddid_all.tbl CDD pfam07301 pfam07301 429394 DUF1453 CcdC protein. This family includes protein CcdC from Bacillus subtilis. The function of Ccdc is not known. 144 matched cddid_all.tbl CDD pfam07302 pfam07302 429395 AroM AroM protein. This family consists of several bacterial and archaeal AroM proteins. In Escherichia coli the aroM gene is cotranscribed with aroL. The function of this family is unknown. 218 matched cddid_all.tbl CDD pfam07303 pfam07303 462140 Occludin_ELL Occludin homology domain. This domain represents a conserved region approximately 100 residues long within eukaryotic occludin proteins and the RNA polymerase II elongation factor ELL. Occludin is an integral membrane protein that localizes to tight junctions, while ELL is an elongation factor that can increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by polymerase at multiple sites along the DNA. This shared domain is thought to mediate protein interactions. 101 matched cddid_all.tbl CDD pfam07304 pfam07304 429397 SRA1 Steroid receptor RNA activator (SRA1). This family consists of several hypothetical mammalian steroid receptor RNA activator proteins. SRA-RNAs likely to encode stable proteins are widely expressed in breast cancer cell lines. SRA-RNA is a steroid receptor co-activator which acts as a functional RNA and is classified as belonging to the growing family of functional non-coding RNAs. 147 matched cddid_all.tbl CDD pfam07305 pfam07305 429398 DUF1454 Protein of unknown function (DUF1454). This family consists of several Enterobacterial sequences of around 200 residues in length which are often known as YiiQ proteins. The function of this family is unknown. 187 matched cddid_all.tbl CDD pfam07306 pfam07306 284672 DUF1455 Protein of unknown function (DUF1455). This family consists of several hypothetical putative outer membrane proteins which appear to be specific to Anaplasma marginale and Anaplasma ovis. 130 matched cddid_all.tbl CDD pfam07307 pfam07307 399944 HEPPP_synt_1 Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1. This family contains subunit 1 of heptaprenyl diphosphate synthase (HEPPP synthase) (EC:2.5.1.30) (approximately 230 residues long) from Bacilli. The enzyme consists of two subunits, both of which are required for catalysis of heptaprenyl diphosphate synthesis. This family corresponds to the regulatory subunit. 210 matched cddid_all.tbl CDD pfam07308 pfam07308 462141 DUF1456 Protein of unknown function (DUF1456). This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown. 68 matched cddid_all.tbl CDD pfam07309 pfam07309 429400 FlaF Flagellar protein FlaF. This family consists of several bacterial FlaF flagellar proteins. FlaF and FlaG are trans-acting, regulatory factors that modulate flagellin synthesis during flagellum biogenesis. 112 matched cddid_all.tbl CDD pfam07310 pfam07310 399947 PAS_5 PAS domain. This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long. This region is is distantly similar to other PAS domains. 136 matched cddid_all.tbl CDD pfam07311 pfam07311 462142 Dodecin Dodecin. Dodecin is a flavin-binding protein,found in several bacteria and few archaea and represents a stand-alone version of the SHS2 domain. It most closely resembles the SHS2 domains of FtsA and Rpb7p, and represents a single domain small-molecule binding form. 62 matched cddid_all.tbl CDD pfam07312 pfam07312 462143 DUF1459 Protein of unknown function (DUF1459). This family consists of several hypothetical Caenorhabditis elegans proteins of around 85 residues in length. The function of this family is unknown. 81 matched cddid_all.tbl CDD pfam07313 pfam07313 429403 DUF1460 Protein of unknown function (DUF1460). This family consists of several hypothetical bacterial proteins of around 260 residues in length. The function of this family is unknown. 216 matched cddid_all.tbl CDD pfam07314 pfam07314 462144 DUF1461 Protein of unknown function (DUF1461). This family contains a number of hypothetical bacterial proteins of unknown function approximately 200 residues long. These are possibly integral membrane proteins. 175 matched cddid_all.tbl CDD pfam07315 pfam07315 429405 DUF1462 Protein of unknown function (DUF1462). This family consists of several hypothetical bacterial proteins of around 100 residues in length. The function of this family is unknown. 93 matched cddid_all.tbl CDD pfam07316 pfam07316 311332 DUF1463 Protein of unknown function (DUF1463). This family consists of several hypothetical bacterial proteins of around 140 residues in length. Members of this family seem to be found exclusively in Borrelia burgdorferi (Lyme disease spirochete). The function of this family is unknown. 137 matched cddid_all.tbl CDD pfam07317 pfam07317 429406 PilZN Flagellar regulator YcgR, PilZN domain. This domain is found N terminal to pfam07238, therefore named PilZN. Proteins which contain PilZN (also known as YcgR) are know to interact with the flagellar switch-complex proteins FliG and FliM. This interaction results in a reduction of torque generation and induces CCW motor bias. This domain exhibits a similar structur as PilZ domains comprising a beta-barrel fold but lack the C-terminal alpha-helix. 103 matched cddid_all.tbl CDD pfam07318 pfam07318 399952 DUF1464 Protein of unknown function (DUF1464). This family consists of several hypothetical archaeal proteins of around 350 residues in length. The function of this family is unknown. 327 matched cddid_all.tbl CDD pfam07319 pfam07319 429407 DnaI_N Primosomal protein DnaI N-terminus. This family represents the N-terminus (approximately 120 residues) of bacterial primosomal DnaI proteins, although one family member appears to be of viral origin. DnaI is one of the components of the Bacillus subtilis replication restart primosome, and is required for the DnaB75-dependent loading of the DnaC helicase. 90 matched cddid_all.tbl CDD pfam07321 pfam07321 399954 YscO Type III secretion protein YscO. This family contains the bacterial type III secretion protein YscO, which is approximately 150 residues long. YscO has been shown to be required for high-level expression and secretion of the anti-host proteins V antigen and Yops in Yersinia pestis. 148 matched cddid_all.tbl CDD pfam07322 pfam07322 284687 Seadorna_Vp10 Seadornavirus Vp10. This family consists of several Seadornavirus Vp10 proteins found in the Banna and Kadipiro viruses. Members of this family are typically around 240 residues in length. The function of this family is unknown. 241 matched cddid_all.tbl CDD pfam07323 pfam07323 429408 DUF1465 Protein of unknown function (DUF1465). This family consists of several hypothetical bacterial proteins of around 180 residues in length. The function of this family is unknown. 154 matched cddid_all.tbl CDD pfam07324 pfam07324 462145 DGCR6 DiGeorge syndrome critical region 6 (DGCR6) protein. This family contains DiGeorge syndrome critical region 6 (DGCR6) proteins (approximately 200 residues long) of a number of vertebrates. DGCR6 is a candidate for involvement in the DiGeorge syndrome pathology by playing a role in neural crest cell migration into the third and fourth pharyngeal pouches, the structures from which derive the organs affected in DiGeorge syndrome. Also found in this family is the Drosophila melanogaster gonadal protein gdl. 194 matched cddid_all.tbl CDD pfam07325 pfam07325 148753 Curto_V2 Curtovirus V2 protein. This family consists of several Curtovirus V2 proteins. The exact function of V2 is unclear but it is known that the protein is required for a successful host infection process. 126 matched cddid_all.tbl CDD pfam07326 pfam07326 462146 RCS1 Regulator of chromosome segregation 1. This family consists of several mammalian proteins of around 240 residues in length. Family members include regulator of chromosome segregation 1 (RCS1), also known as FAM64A, CATS or PIMREG (PICALM-interacting mitotic regulator). It is a substrate of APC/C. It may control the metaphase to anaphase transition. It is also a substrate of the Kinase Interacting Stathmin (KIS). RCS1 is highly expressed in cancer cell lines in a cell cycle dependent manner and is induced by mitogens. 232 matched cddid_all.tbl CDD pfam07327 pfam07327 115951 Neuroparsin Neuroparsin. This family consists of several locust specific neuroparsin proteins. Neuroparsins are produced by the A1 type of protocerebral median neurosecretory cells of the PI-CC system and display pleiotropic activities: inhibition of the effect of juvenile hormone, stimulation of fluid reabsorption of isolated recta, induction of an increase in hemolymph lipid and trehalose levels, and neurotrophic effects. 103 matched cddid_all.tbl CDD pfam07328 pfam07328 429411 VirD1 T-DNA border endonuclease VirD1. This family consists of several T-DNA border endonuclease VirD1 proteins which appear to be found exclusively in Agrobacterium species. Agrobacterium, a plant pathogen, is capable to stably transform the plant cell with a segment of its own DNA called T-DNA (transferred DNA). This process depends, among others, on the specialized bacterial virulence proteins VirD1 and VirD2 that excise the T-DNA from its adjacent sequences. VirD1 is thought to interact with VirD2 in this process. 142 matched cddid_all.tbl CDD pfam07330 pfam07330 429412 DUF1467 Protein of unknown function (DUF1467). This family consists of several bacterial proteins of around 90 residues in length. The function of this family is unknown. 82 matched cddid_all.tbl CDD pfam07331 pfam07331 462147 TctB Tripartite tricarboxylate transporter TctB family. This family consists of several hypothetical bacterial proteins of around 150 residues in length. This family was formerly known as DUF1468. 131 matched cddid_all.tbl CDD pfam07332 pfam07332 462148 Phage_holin_3_6 Putative Actinobacterial Holin-X, holin superfamily III. Phage_holin_3_6 is a family of small hydrophobic proteins with two or three transmembrane domains of the Hol-X family. Holin proteins are produced by double-stranded DNA bacteriophages that use an endolysin-holin strategy to achieve lysis of their hosts. The endolysins are peptidoglycan-degrading enzymes that are usually accumulated in the cytosol until access to the cell wall substrate is provided by the holin membrane lesion. 113 matched cddid_all.tbl CDD pfam07333 pfam07333 284695 SLR1-BP S locus-related glycoprotein 1 binding pollen coat protein (SLR1-BP). This family consists of a number of cysteine rich SLR1 binding pollen coat like proteins. Adhesion of pollen grains to the stigmatic surface is a critical step during sexual reproduction in plants. In Brassica, S locus-related glycoprotein 1 (SLR1), a stigma-specific protein belonging to the S gene family of proteins, has been shown to be involved in this step. SLR1-BP specifically binds SLR1 with high affinity. The SLR1-BP gene is specifically expressed in pollen at late stages of development and is a member of the class A pollen coat protein (PCP) family, which includes PCP-A1, an SLG (S locus glycoprotein)-binding protein. 56 matched cddid_all.tbl CDD pfam07334 pfam07334 284696 IFP_35_N Interferon-induced 35 kDa protein (IFP 35) N-terminus. This family represents the N-terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration. This family also includes N-myc-interactor (Nmi), a homologous interferon-induced protein. 76 matched cddid_all.tbl CDD pfam07335 pfam07335 429415 Glyco_hydro_75 Fungal chitosanase of glycosyl hydrolase group 75. This family consists of several fungal chitosanase proteins. Chitin, xylan, 6-O-sulphated chitosan and O-carboxymethyl chitin are indigestible by chitosanase. EC:3.2.1.132. The mechanism is likely to be inverting, and the probable catalytic neutrophile base is Asp, with the probable catalytic proton donor being Glu. (see the Chitosanase web-page from CAZY). 166 matched cddid_all.tbl CDD pfam07336 pfam07336 429416 ABATE Putative stress-induced transcription regulator. The structure of one member of the ABATE domain family consists of a two-domain organization, with the N-terminal domain presenting a new fold called the ABATE domain that may bind an as yet unknown ligand. The C-terminal domain forms a treble-clef zinc-finger that is likely to be involved in DNA binding. suggests a role as stress-induced transcriptional regulator. Further computational analyses sugeests a role as a stress-induced transcriptional regulator. Members of this family are found in Streptomyces, Rhizobium, Ralstonia, Agrobacterium and Bradyrhizobium species. 126 matched cddid_all.tbl CDD pfam07337 pfam07337 284699 CagY_M DC-EC Repeat. This repeat is found in the CagY proteins - part of the CAG pathogenicity island - and involved in delivery of the protein CagA into host cells. It forms part of a surface needle structure, and this repeat may form an alpha-helical rod structure. A conserved -DC- and -EC- can be seen in regularly spaced in the alignment. 32 matched cddid_all.tbl CDD pfam07338 pfam07338 429417 YdgH_BhsA-like YdgH/BhsA/McbA-like domain. This domain is found in several Enterobacterial proteins of around 90 residues in length, including E. coli YdgH, YhcN, BhsA and McbA, which play a role in stress response, biofilm formation and pathogenesis. BhsA (also known as ComC) reduces the permeability of the outer membrane to copper and may decrease biofilm formation by repressing cell-cell interaction and cell surface interaction. Members of this entry have one copy of this domain with the exception of YdgH, which has three copies. The function of this domain is unknown, however, it is suggested to be directly involved in host-pathogen interaction. 55 matched cddid_all.tbl CDD pfam07340 pfam07340 284701 Herpes_IE1 Cytomegalovirus IE1 protein. Expression from a human cytomegalovirus early promoter (E1.7) has been shown to be activated in trans by the IE2 gene product. Although the IE1 gene product alone had no effect on this early viral promoter, maximal early promoter activity was detected when both IE1 and IE2 gene products were present. The IE1 protein from cytomegalovirus is also known as UL123. 391 matched cddid_all.tbl CDD pfam07341 pfam07341 115964 DUF1473 Protein of unknown function (DUF1473). This family consists of several hypothetical bacterial proteins of around 150 residues in length. Members of this family seem to be found exclusively in Borrelia burgdorferi (Lyme disease spirochete). The function of this family is unknown. 163 matched cddid_all.tbl CDD pfam07342 pfam07342 369323 DUF1474 Protein of unknown function (DUF1474). This family consists of several bacterial proteins of around 100 residues in length. Members of this family seem to be found exclusively in Staphylococcus aureus. The function of this family is unknown. 100 matched cddid_all.tbl CDD pfam07343 pfam07343 399963 DUF1475 Protein of unknown function (DUF1475). This family consists of several hypothetical plant proteins of around 250 residues in length. Members of this family seem to be found exclusively in Arabidopsis thaliana. The function of this family is unknown. 236 matched cddid_all.tbl CDD pfam07344 pfam07344 399964 Amastin Amastin surface glycoprotein. This family contains the eukaryotic surface glycoprotein amastin (approximately 180 residues long).In Trypanosoma cruzi, amastin is particularly abundant during the amastigote stage. 156 matched cddid_all.tbl CDD pfam07345 pfam07345 429418 DUF1476 ATPase inhibitor subunit zeta. This entry represents zeta-subunits, which are found in alpha-proteobacterial F1F0-ATPase regulatory proteins. The zeta subunit is a potent inhibitor of the alpha-proteobacterial F1FO-ATPase. The inhibitory region resides in the first 14 N-terminal residues of the protein, which protrude from the 4-alpha-helix bundle structure of the isolated zeta subunit. 102 matched cddid_all.tbl CDD pfam07346 pfam07346 311348 DUF1477 Protein of unknown function (DUF1477). This family consists of several hypothetical Nucleopolyhedrovirus proteins of around 100 resides in length. The function of this family is unknown. 115 matched cddid_all.tbl CDD pfam07347 pfam07347 462149 CI-B14_5a NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a). This family contains the eukaryotic NADH:ubiquinone oxidoreductase subunit B14.5a (Complex I-B14.5a) (EC:1.6.5.3). This is approximately 100 residues long, and forms part of a multiprotein complex that resides on the inner mitochondrial membrane. The main function of the complex is the transport of electrons from NADH to ubiquinone, accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. 95 matched cddid_all.tbl CDD pfam07348 pfam07348 429420 Syd Syd protein (SUKH-2). This family contains a number of bacterial Syd proteins approximately 180 residues long. It has been suggested that Syd is loosely associated with the cytoplasmic surface of the cytoplasmic membrane, and that interaction with SecY may be involved in this membrane association. Operon analysis showed that Syd protein may function as immunity protein in bacterial toxin systems. 174 matched cddid_all.tbl CDD pfam07349 pfam07349 284709 DUF1478 Protein of unknown function (DUF1478). This family consists of several hypothetical Sapovirus proteins of around 165 residues in length. The function of this family is unknown. 161 matched cddid_all.tbl CDD pfam07350 pfam07350 399968 DUF1479 Protein of unknown function (DUF1479). This family consists of several hypothetical Enterobacterial proteins, of around 420 residues in length. Members of this family are often known as YbiU. The function of this family is unknown. 404 matched cddid_all.tbl CDD pfam07351 pfam07351 429421 DUF1480 Protein of unknown function (DUF1480). This family consists of several hypothetical Enterobacterial proteins of around 80 residues in length. The function of this family is unknown. 78 matched cddid_all.tbl CDD pfam07352 pfam07352 429422 Phage_Mu_Gam Bacteriophage Mu Gam like protein. This family consists of bacterial and phage Gam proteins. The gam gene of bacteriophage Mu encodes a protein which protects linear double stranded DNA from exonuclease degradation in vitro and in vivo. 146 matched cddid_all.tbl CDD pfam07353 pfam07353 462150 Uroplakin_II Uroplakin II. This family contains uroplakin II, which is approximately 180 residues long and seems to be restricted to mammals. Uroplakin II is an integral membrane protein, and is one of the components of the apical plaques of mammalian urothelium formed by the asymmetric unit membrane - this is believed to play a role in strengthening the urothelial apical surface to prevent the cells from rupturing during bladder distension. 165 matched cddid_all.tbl CDD pfam07354 pfam07354 336682 Sp38 Zona-pellucida-binding protein (Sp38). This family contains a number of zona-pellucida-binding proteins that seem to be restricted to mammals. These are sperm proteins that bind to the 90-kDa family of zona pellucida glycoproteins in a calcium-dependent manner. These represent some of the specific molecules that mediate the first steps of gamete interaction, allowing fertilization to occur. 177 matched cddid_all.tbl CDD pfam07355 pfam07355 429424 GRDB Glycine/sarcosine/betaine reductase selenoprotein B (GRDB). This family represents a conserved region approximately 350 residues long within the selenoprotein B component of the bacterial glycine, sarcosine and betaine reductase complexes. 347 matched cddid_all.tbl CDD pfam07356 pfam07356 429425 DUF1481 Protein of unknown function (DUF1481). This family consists of several hypothetical bacterial proteins of around 230 residues in length. Members of this family are often referred to as YjaH and are found in the Orders Vibrionales and Enterobacteriales. The function of this family is unknown. 186 matched cddid_all.tbl CDD pfam07357 pfam07357 429426 DRAT Dinitrogenase reductase ADP-ribosyltransferase (DRAT). This family consists of several bacterial dinitrogenase reductase ADP-ribosyltransferase (DRAT) proteins. Members of this family seem to be specific to Rhodospirillum, Rhodobacter and Azospirillum species. Dinitrogenase reductase ADP-ribosyl transferase (DRAT) carries out the transfer of the ADP-ribose from NAD to the Arg-101 residue of one subunit of the dinitrogenase reductase homodimer, resulting in inactivation of that enzyme. Dinitrogenase reductase-activating glycohydrolase (DRAG) removes the ADP-ribose group attached to dinitrogenase reductase, thus restoring nitrogenase activity. The DRAT-DRAG system negatively regulates nitrogenase activity in response to exogenous NH4+ or energy limitation in the form of a shift to darkness or to anaerobic conditions. 256 matched cddid_all.tbl CDD pfam07358 pfam07358 369331 DUF1482 Protein of unknown function (DUF1482). This family consists of several Enterobacterial proteins of around 60 residues in length. The function of this family is unknown. 57 matched cddid_all.tbl CDD pfam07359 pfam07359 284718 LEAP-2 Liver-expressed antimicrobial peptide 2 precursor (LEAP-2). This family consists of several mammalian liver-expressed antimicrobial peptide 2 (LEAP-2) sequences. LEAP-2 is a cysteine-rich, and cationic protein. LEAP-2 contains a core structure with two disulfide bonds formed by cysteine residues in relative 1-3 and 2-4 positions. LEAP-2 is synthesized as a 77-residue precursor, which is predominantly expressed in the liver and highly conserved among mammals. The largest native LEAP-2 form of 40 amino acid residues is generated from the precursor at a putative cleavage site for a furin-like endoprotease. In contrast to smaller LEAP-2 variants, this peptide exhibits dose-dependent antimicrobial activity against selected microbial model organizms. The exact function of this family is unclear. 77 matched cddid_all.tbl CDD pfam07361 pfam07361 429427 Cytochrom_B562 Cytochrome b562. This family contains the bacterial cytochrome b562. This forms a four-helix bundle that non-covalently binds a single heme prosthetic group.. 101 matched cddid_all.tbl CDD pfam07362 pfam07362 429428 CcdA Post-segregation antitoxin CcdA. This family consists of several Enterobacterial post-segregation antitoxin CcdA proteins. The F plasmid-carried bacterial toxin, the CcdB protein, is known to act on DNA gyrase in two different ways. CcdB poisons the gyrase-DNA complex, blocking the passage of polymerases and leading to double-strand breakage of the DNA. Alternatively, in cells that overexpress CcdB, the A subunit of DNA gyrase (GyrA) has been found as an inactive complex with CcdB. Both poisoning and inactivation can be prevented and reversed in the presence of the F plasmid-encoded antidote, the CcdA protein. 71 matched cddid_all.tbl CDD pfam07363 pfam07363 284721 DUF1484 Protein of unknown function (DUF1484). This family consists of several hypothetical bacterial proteins of around 110 residues in length. Members of this family appear to be found exclusively in Ralstonia solanacearum. The function of this family is unknown. 109 matched cddid_all.tbl CDD pfam07364 pfam07364 429429 DUF1485 Metallopeptidase family M81. This is a family of proteobacterial metallo-peptidases. 287 matched cddid_all.tbl CDD pfam07365 pfam07365 191732 Toxin_8 Alpha conotoxin precursor. This family consists of several alpha conotoxin precursor proteins from a number of Conus species. The alpha-conotoxins are small peptide neurotoxins from the venom of fish-hunting cone snails which block nicotinic acetylcholine receptors (nAChRs). 50 matched cddid_all.tbl CDD pfam07366 pfam07366 399975 SnoaL SnoaL-like polyketide cyclase. This family includes SnoaL a polyketide cyclase involved in nogalamycin biosynthesis. This family was formerly known as DUF1486. The proteins in this family adopt a distorted alpha-beta barrel fold. Structural data together with site-directed mutagenesis experiments have shown that SnoaL has a different mechanism to that of the classical aldolase for catalysing intramolecular aldol condensation. 126 matched cddid_all.tbl CDD pfam07367 pfam07367 429430 FB_lectin Fungal fruit body lectin. This family consists of several fungal fruit body lectin proteins. Fruit body lectins are thought to have insecticidal activity and may also function in capturing nematodes. 140 matched cddid_all.tbl CDD pfam07368 pfam07368 254173 DUF1487 Protein of unknown function (DUF1487). This family consists of several uncharacterized proteins from Drosophila melanogaster. The function of this family is unknown. 215 matched cddid_all.tbl CDD pfam07369 pfam07369 429431 DUF1488 Protein of unknown function (DUF1488). This family consists of several hypothetical bacterial proteins of around 85 residues in length. The function of this family is unknown. 82 matched cddid_all.tbl CDD pfam07370 pfam07370 429432 DUF1489 Protein of unknown function (DUF1489). This family consists of several hypothetical bacterial proteins of around 150 residues in length. Members of this family seem to be founds exclusively in the Class Alphaproteobacteria. The function of this family is unknown. 138 matched cddid_all.tbl CDD pfam07371 pfam07371 399979 DUF1490 Protein of unknown function (DUF1490). This family consists of several hypothetical bacterial proteins of around 90 residues in length. Members of the family seem to be found exclusively in Mycobacterium species. The function of this family is unknown. 88 matched cddid_all.tbl CDD pfam07372 pfam07372 429433 DUF1491 Protein of unknown function (DUF1491). This family consists of several bacterial proteins of around 115 residues in length. Members of this family seem to be found exclusively in the Class Alphaproteobacteria. The function of this family is unknown. 103 matched cddid_all.tbl CDD pfam07373 pfam07373 429434 CAMP_factor CAMP factor (Cfa). This family consists of several bacterial CAMP factor (Cfa) proteins which seem to be specific to Streptococcus species. The CAMP reaction is a synergistic lysis of erythrocytes by the interaction of an extracellular protein (CAMP factor) produced by some streptococcal species with the Staphylococcus aureus sphingomyelinase C (beta-toxin). 218 matched cddid_all.tbl CDD pfam07374 pfam07374 311366 DUF1492 Protein of unknown function (DUF1492). This family consists of several hypothetical, highly conserved Streptococcal and related phage proteins of around 100 residues in length. The function of this family is unknown. It appears to be distantly related to pfam08281. 100 matched cddid_all.tbl CDD pfam07376 pfam07376 284730 Prosystemin Prosystemin. This family consists of several plant specific prosystemin proteins. Prosystemin is the precursor protein of the 18 amino acid wound signal systemin which activates systemic defence in plant leaves against insect herbivores. 204 matched cddid_all.tbl CDD pfam07377 pfam07377 399982 DUF1493 Protein of unknown function (DUF1493). This family consists of several bacterial proteins of around 115 residues in length. Members of this family seem to be found exclusively in Salmonella and Yersinia species and several have been described as being putative cytoplasmic proteins. The function of this family is unknown. 111 matched cddid_all.tbl CDD pfam07378 pfam07378 429435 FlbT Flagellar protein FlbT. This family consists of several FlbT proteins. FlbT is a post-transcriptional regulator of flagellin. FlbT is associated with the 5' untranslated region (UTR) of fljK (25 kDa flagellin) mRNA and that this association requires a predicted loop structure in the transcript. Mutations within this loop abolish FlbT association and result in increased mRNA stability. It is therefore thought that FlbT promotes the degradation of flagellin mRNA by associating with the 5' UTR. 125 matched cddid_all.tbl CDD pfam07379 pfam07379 284733 DUF1494 Protein of unknown function (DUF1494). This family consists of several bacterial proteins of around 175 residues in length. Members of this family seem to be found exclusively in Chlamydia species. The function of this family is unknown. 179 matched cddid_all.tbl CDD pfam07380 pfam07380 284734 Pneumo_M2 Pneumovirus M2 protein. This family consists of several Pneumovirus M2 proteins. The M2-1 protein of respiratory syncytial virus (RSV) is a transcription processivity factor that is essential for virus replication. 89 matched cddid_all.tbl CDD pfam07381 pfam07381 369338 DUF1495 Winged helix DNA-binding domain (DUF1495). This family consists of several hypothetical archaeal proteins of around 110 residues in length. The structure of this domain possesses a winged helix DNA-binding domain suggesting these proteins are bacterial transcription factors. 90 matched cddid_all.tbl CDD pfam07382 pfam07382 369339 HC2 Histone H1-like nucleoprotein HC2. This family contains the bacterial histone H1-like nucleoprotein HC2 (approximately 200 residues long), which seems to be found mostly in Chlamydia. HC2 functions in DNA condensation, although it has been suggested that it also has other roles. 187 matched cddid_all.tbl CDD pfam07383 pfam07383 429436 DUF1496 Protein of unknown function (DUF1496). This family consists of several bacterial proteins of around 90 residues in length. Members of this family seem to be found exclusively in the Orders Vibrionales and Enterobacteriales. The function of this family is unknown. 51 matched cddid_all.tbl CDD pfam07384 pfam07384 284738 DUF1497 Protein of unknown function (DUF1497). This family consists of several phage and bacterial proteins of around 59 residues in length. Members of this family seem to be found exclusively in Lactococcus lactis and the bacteriophages that infect this organizm. The function of this family is unknown. 59 matched cddid_all.tbl CDD pfam07385 pfam07385 429437 Lyx_isomer D-lyxose isomerase. Members of this family of sugar isomerases belong to the cupin superfamily. The enzyme from Cohnella laevoribosii has been shown to be specific for D-lyxose, L-ribose, and D-mannose. E. coli sugar isomerase (EcSI) has been structurally and functionally characterized and shows a preference for D-lyxose and D-mannose. 223 matched cddid_all.tbl CDD pfam07386 pfam07386 462151 DUF1499 Protein of unknown function (DUF1499). This family consists of several hypothetical bacterial and plant proteins of around 125 residues in length. The function of this family is unknown. 114 matched cddid_all.tbl CDD pfam07387 pfam07387 254182 Seadorna_VP7 Seadornavirus VP7. This family consists of several Seadornavirus specific VP7 proteins of around 305 residues in length. The function of this family is unknown. However, it appears to be distantly related to protein kinases. 308 matched cddid_all.tbl CDD pfam07388 pfam07388 429439 A-2_8-polyST Alpha-2,8-polysialyltransferase (POLYST). This family contains the bacterial enzyme alpha-2,8-polysialyltransferase (EC:2.4.99.-) (approximately 500 residues long). This catalyzes the polycondensation of alpha-2,8-linked sialic acid required for the synthesis of polysialic acid (PSA). 321 matched cddid_all.tbl CDD pfam07389 pfam07389 462152 Pox_B6 Vaccinia B6 protein. This family consists of several Orthopoxvirus specific proteins, which include Vaccinia virus, B6 protein, of around 170 residues in length. The function of this family is unknown. 181 matched cddid_all.tbl CDD pfam07390 pfam07390 369342 P30 Mycoplasma P30 protein. This family consists of several P30 proteins which seem to be specific to Mycoplasma agalactiae. P30 is a 30-kDa immunodominant antigen and is known to be a transmembrane protein. 150 matched cddid_all.tbl CDD pfam07391 pfam07391 369343 NPR NPR nonapeptide repeat (2 copies). This nine residue repeat which I have called NPR after NonaPeptide Repeat. It is found in two malarial proteins and has the consensus EEhhEEhhP where h stands for a hydrophobic amino acid. 17 matched cddid_all.tbl CDD pfam07392 pfam07392 462153 P19Arf_N Cyclin-dependent kinase inhibitor 2a p19Arf N-terminus. This family represents the N-terminus (approximately 50 residues) of cyclin-dependent kinase inhibitor 2a p19Arf, which seems to be restricted to mammals. This is a tumour-suppressor protein that has been shown to inhibit the growth of human tumour cells lacking functional p53 by inducing a transient G2 arrest and subsequently apoptosis. 51 matched cddid_all.tbl CDD pfam07393 pfam07393 399988 Sec10 Exocyst complex component Sec10. This family contains the Sec10 component (approximately 650 residues long) of the eukaryotic exocyst complex, which specifically affects the synthesis and delivery of secretory and basolateral plasma membrane proteins. 704 matched cddid_all.tbl CDD pfam07394 pfam07394 429441 DUF1501 Protein of unknown function (DUF1501). This family contains a number of hypothetical bacterial proteins of unknown function approximately 400 residues long. 390 matched cddid_all.tbl CDD pfam07395 pfam07395 284747 Mig-14 Mig-14. This family contains a number of bacterial mig-14 proteins (approximately 270 residues long). In Salmonella, mig-14 contributes to resistance to antimicrobial peptides, although the mechanism is not fully understood. 264 matched cddid_all.tbl CDD pfam07396 pfam07396 429442 Porin_O_P Phosphate-selective porin O and P. This family represents a conserved region approximately 400 residues long within the bacterial phosphate-selective porins O and P. These are anion-specific porins, the binding site of which has a higher affinity for phosphate than chloride ions. Porin O has a higher affinity for polyphosphates, while porin P has a higher affinity for orthophosphate. In P. aeruginosa, porin O was found to be expressed only under phosphate-starvation conditions during the stationary growth phase. 371 matched cddid_all.tbl CDD pfam07397 pfam07397 116019 DUF1502 Repeat of unknown function (DUF1502). This family consists of a number of repeats of around 34 residues in length. Members of this family seem to be found exclusively in three hypothetical Murid herpesvirus 4 proteins. The function of this family is unknown. 34 matched cddid_all.tbl CDD pfam07398 pfam07398 429443 MDMPI_C MDMPI C-terminal domain. This domain is found at the C-terminus of the mycothiol maleylpyruvate isomerase enzyme (MDMPI). The structure of this protein has been solved. This domain appears weakly similar to pfam08608. 88 matched cddid_all.tbl CDD pfam07399 pfam07399 462154 Na_H_antiport_3 Putative Na+/H+ antiporter. This family consists of several hypothetical bacterial proteins of around 440 residues in length. The function of this family is unknown. Many members carry 11 or 12 transmembrane regions, suggesting that they might be transporters. One family member, UniProtKB:Q821X2 is classified by TCDB as being an NhaE type of Na+/H+ antiporter. 418 matched cddid_all.tbl CDD pfam07400 pfam07400 462155 IL11 Interleukin 11. This family contains interleukin 11 (approximately 200 residues long). This is a secreted protein that stimulates megakaryocytopoiesis, resulting in increased production of platelets, as well as activating osteoclasts, inhibiting epithelial cell proliferation and apoptosis, and inhibiting macrophage mediator production. These functions may be particularly important in mediating the hematopoietic, osseous and mucosal protective effects of interleukin 11. Family members seem to be restricted to mammals. 167 matched cddid_all.tbl CDD pfam07401 pfam07401 116023 Lenti_VIF_2 Bovine Lentivirus VIF protein. This family consists of several Lentivirus viral infectivity factor (VIF) proteins. VIF is known to be essential for ability of cell-free virus preparation to infect cells. Members of this family are specific to Bovine immunodeficiency virus (BIV) and Jembrana disease virus which also infects cattle. 198 matched cddid_all.tbl CDD pfam07402 pfam07402 284752 Herpes_U26 Human herpesvirus U26 protein. This family consists of several Human herpesvirus U26 proteins of around 300 residues in length. The function of this family is unknown. 293 matched cddid_all.tbl CDD pfam07403 pfam07403 369351 DUF1505 Protein of unknown function (DUF1505). This family consists of several uncharacterized Caenorhabditis elegans proteins of around 115 resides in length. Members of this family contain 6 highly conserved cysteine residues. The function of this family is unknown. 114 matched cddid_all.tbl CDD pfam07404 pfam07404 462156 TEBP_beta Telomere-binding protein beta subunit (TEBP beta). This domain represents the OB fold from several telomere-binding protein beta subunits which appear to be specific to the family Oxytrichidae. Telomeres are specialized protein-DNA complexes that compose the ends of eukaryotic chromosomes. Telomeres protect chromosome termini from degradation and recombination and act together with telomerase to ensure complete genome replication. TEBP beta forms a complex with TEBP alpha and this complex is able to recognize and bind ssDNA to form a sequence-specific, telomeric nucleoprotein complex that caps the very 3' ends of chromosomes. 140 matched cddid_all.tbl CDD pfam07405 pfam07405 284754 DUF1506 Protein of unknown function (DUF1506). This family consists of several bacterial proteins of around 130 residues in length. Members of this family seem to be specific to Borrelia burgdorferi (Lyme disease spirochete). The function of this family is unknown. 127 matched cddid_all.tbl CDD pfam07406 pfam07406 462157 NICE-3 NICE-3 protein. This family consists of several eukaryotic NICE-3 and related proteins. The gene coding for NICE-3 is part of the epidermal differentiation complex (EDC) which comprises a large number of genes that are of crucial importance for the maturation of the human epidermis. The function of NICE-3 is unknown. 182 matched cddid_all.tbl CDD pfam07407 pfam07407 284756 Seadorna_VP6 Seadornavirus VP6 protein. This family consists of several VP6 proteins from the Banna virus as well as a related protein VP5 from the Kadipiro virus. Members of this family are typically of around 420 residues in length. The function of this family is unknown. 420 matched cddid_all.tbl CDD pfam07408 pfam07408 429447 DUF1507 Protein of unknown function (DUF1507). This family consists of several hypothetical bacterial proteins of around 90 residues in length. The function of this family is unknown. 85 matched cddid_all.tbl CDD pfam07409 pfam07409 462158 GP46 Phage protein GP46. This family contains GP46 phage proteins (approximately 120 residues long). 104 matched cddid_all.tbl CDD pfam07410 pfam07410 429449 Phage_Gp111 Streptococcus thermophilus bacteriophage Gp111 protein. This family consists of several Streptococcus thermophilus bacteriophage Gp111 proteins of around 110 residues in length. The function of this family is unknown. 117 matched cddid_all.tbl CDD pfam07411 pfam07411 429450 DUF1508 Domain of unknown function (DUF1508). This family represents a series of bacterial domains of unknown function of around 50 residues in length. Members of this family are often found as tandem repeats and in some cases represent the whole protein. All member proteins are described as being hypothetical. 47 matched cddid_all.tbl CDD pfam07412 pfam07412 462159 Geminin Geminin. This family contains the eukaryotic protein geminin (approximately 200 residues long). Geminin inhibits DNA replication by preventing the incorporation of MCM complex into prereplication complex, and is degraded during the mitotic phase of the cell cycle. It has been proposed that geminin inhibits DNA replication during S, G2, and M phases and that geminin destruction at the metaphase-anaphase transition permits replication in the succeeding cell cycle. 194 matched cddid_all.tbl CDD pfam07413 pfam07413 284761 Herpes_UL37_2 Betaherpesvirus immediate-early glycoprotein UL37. This family consists of several Betaherpesvirus immediate-early glycoprotein UL37 sequences. The human cytomegalovirus (HCMV) UL37 immediate-early regulatory protein is a type I integral membrane N-glycoprotein which traffics through the ER and the Golgi network. 334 matched cddid_all.tbl CDD pfam07415 pfam07415 284762 Herpes_LMP2 Gammaherpesvirus latent membrane protein (LMP2) protein. This family consists of several Gammaherpesvirus latent membrane protein (LMP2) proteins. Epstein-Barr virus is a human Gammaherpesvirus that infects and establishes latency in B lymphocytes in vivo. The latent membrane protein 2 (LMP2) gene is expressed in latently infected B cells and encodes two protein isoforms, LMP2A and LMP2B, that are identical except for an additional N-terminal 119 aa cytoplasmic domain which is present in the LMP2A isoform. LMP2A is thought to play a key role in either the establishment or the maintenance of latency and/or the reactivation of productive infection from the latent state. The significance of LMP2B and its role in pathogenesis remain unclear. 497 matched cddid_all.tbl CDD pfam07416 pfam07416 284763 Crinivirus_P26 Crinivirus P26 protein. This family consists of several Crinivirus P26 proteins which seem to be found exclusively in the Lettuce infectious yellows virus. The function of this family is unknown. 227 matched cddid_all.tbl CDD pfam07417 pfam07417 462160 Crl Sigma factor-binding transcriptional regulator Crl. This family contains the bacterial Sigma factor-binding protein Crl (approximately 130 residues long). This is a transcriptional regulator of the csgA curlin subunit gene for curli fibres that are found on the surface of certain bacteria. These proteins bind to the sigma-S subunit of RNA polymerase, activating expression of sigma-S-regulated genes. It was initially suggested that Crl affects transcription initiation in vitro by other sigmas, such as sigma-70 and sigma-32. However, it is now established that Crl binds specifically to the alternative sigma factor S/RpoS and favors its association with the core RNAP (RNA polymerase), thereby increasing its activity, which in turn regulates general stress response that protects many Gram-negative bacteria from several harmful environmental conditions. Furthermore, sigma S factor/RpoS plays important roles in biofilm formation and virulence of the food-borne pathogen Salmonella enterica serovar Typhimurium. 127 matched cddid_all.tbl CDD pfam07418 pfam07418 400001 PCEMA1 Acidic phosphoprotein precursor PCEMA1. This family consists of several acidic phosphoprotein precursor PCEMA1 sequences which appear to be found exclusively in Plasmodium chabaudi. PCEMA1 is an antigen that is associated with the membrane of the infected erythrocyte throughout the entire intraerythrocytic cycle. The exact function of this family is unclear. 294 matched cddid_all.tbl CDD pfam07419 pfam07419 429453 PilM PilM. This family contains the bacterial protein PilM (approximately 150 residues long). PilM is an inner membrane protein that has been predicted to function as a component of the pilin transport apparatus and thin-pilus basal body. 135 matched cddid_all.tbl CDD pfam07420 pfam07420 284767 DUF1509 Protein of unknown function (DUF1509). This family consists of several uncharacterized viral proteins from the Marek's disease-like viruses. Members of this family are typically around 400 residues in length. The function of this family is unknown. 384 matched cddid_all.tbl CDD pfam07421 pfam07421 462161 Pro-NT_NN Neurotensin/neuromedin N precursor. This family contains the precursor of bacterial neurotensin/neuromedin N (approximately 170 residues long). This the common precursor of two biologically active related peptides, neurotensin and neuromedin N. It undergoes tissue-specific processing leading to the formation in some tissues and cancer cell lines of large peptides ending with the neurotensin or neuromedin N sequence. 161 matched cddid_all.tbl CDD pfam07422 pfam07422 429455 s48_45 Sexual stage antigen s48/45 domain. This family contains sexual stage s48/45 antigens from Plasmodium (approximately 450 residues long). These are surface proteins expressed by Plasmodium male and female gametes that have been shown to play a conserved and important role in fertilization. This domain contains 6 conserved cysteines suggesting 3 disulphide bridges. 109 matched cddid_all.tbl CDD pfam07423 pfam07423 429456 DUF1510 Domain of unknown function (DUF1510). This domain is found in hypothetical bacterial proteins of around 200 residues in length. The function of this domain is unknown. 93 matched cddid_all.tbl CDD pfam07424 pfam07424 429457 TrbM TrbM. This family contains the bacterial protein TrbM (approximately 180 residues long). In Comamonas testosteroni T-2, TrbM is derived from the IncP1beta plasmid pTSA, which encodes the widespread genes for p-toluenesulfonate (TSA) degradation. This family also includes MPFK and its functional homolog kikA, which are required for efficient conjugative transfer in IncP-9 plasmids. 153 matched cddid_all.tbl CDD pfam07425 pfam07425 116046 Pardaxin Pardaxin. This family consists of several Pardaxin proteins. Pardaxin, a 33-amino-acid pore-forming polypeptide toxin isolated from the Red Sea Moses sole Pardachirus marmoratus, has a helix-hinge-helix structure. This is a common structural motif found both in antibacterial peptides that can act selectively on bacterial membranes (e.g., cecropin), and in cytotoxic peptides that can lyse both mammalian and bacterial cells (e.g., melittin). Pardaxin possesses a high antibacterial activity with a significantly reduced haemolytic activity towards human red blood cells compared with melittin. Pardaxin has also been found to have a shark repellent action. 33 matched cddid_all.tbl CDD pfam07426 pfam07426 462162 Dynactin_p22 Dynactin subunit p22. This family contains p22, the smallest subunit of dynactin, a complex that binds to cytoplasmic dynein and is a required activator for cytoplasmic dynein-mediated vesicular transport. Dynactin localizes to the cleavage furrow and to the midbodies of dividing cells, suggesting that it may function in cytokinesis. Family members are approximately 170 residues long. 163 matched cddid_all.tbl CDD pfam07428 pfam07428 400006 Tri3 15-O-acetyltransferase Tri3. This family represents a conserved region approximately 400 residues long within 15-O-acetyltransferase (Tri3), which seems to be restricted to ascomycete fungi. In Fusarium sporotrichioides, this is required for acetylation of the C-15 hydroxyl group of trichothecenes in the biosynthesis of T-2 toxin. 416 matched cddid_all.tbl CDD pfam07429 pfam07429 429459 Glyco_transf_56 4-alpha-L-fucosyltransferase glycosyl transferase group 56. This family contains the bacterial enzyme 4-alpha-L-fucosyltransferase (Fuc4NAc transferase) (EC 2.4.1.-) (approximately 360 residues long). This catalyzes the synthesis of Fuc4NAc-ManNAcA-GlcNAc-PP-Und (lipid III) as part of the biosynthetic pathway of enterobacterial common antigen (ECA), a polysaccharide comprised of the trisaccharide repeat unit Fuc4NAc-ManNAcA-GlcNAc. 358 matched cddid_all.tbl CDD pfam07430 pfam07430 311397 PP1 Phloem filament protein PP1 cystatin-like domain. This domain represents a conserved region related to cystatins. Eight copies of which are found within the plant phloem filament protein PP1. This is one of the constituents of the proteinaceous filaments found in the sieve elements of Cucurbita phloem. 78 matched cddid_all.tbl CDD pfam07431 pfam07431 400008 DUF1512 Protein of unknown function (DUF1512). This family consists of several archaeal proteins of around 370 residues in length. The function of this family is unknown. 355 matched cddid_all.tbl CDD pfam07432 pfam07432 462163 Hc1 Histone H1-like protein Hc1. This family consists of several bacterial histone H1-like Hc1 proteins. In Chlamydia, Hc1 is expressed in the late stages of the life cycle, concomitant with the reorganization of chlamydial reticulate bodies into elementary bodies. This suggests that Hc1 protein plays a role in the condensation of chromatin during intracellular differentiation. 57 matched cddid_all.tbl CDD pfam07433 pfam07433 429460 DUF1513 Protein of unknown function (DUF1513). This entry represents bacterial proteins that are predicted to be the outer membrane component of an efeUOB-like ferrous iron, uptake system. 304 matched cddid_all.tbl CDD pfam07434 pfam07434 462164 CblD CblD like pilus biogenesis initiator. This family consists of several minor pilin proteins including CblD from Burkholderia cepacia which is known to CblD be the initiator of pilus biogenesis. The family also contains a variety of Enterobacterial minor pilin proteins. 295 matched cddid_all.tbl CDD pfam07435 pfam07435 400011 YycH YycH protein. This family contains the bacterial protein YycH which is approximately 450 residues long. YycH plays a role in signal transduction and is found immediately downstream of the essential histidine kinase YycG. YycG forms a two component system together with its cognate response regulator YycF. PhoA fusion studies have shown that YycH is transported across the cytoplasmic protein. It is postulated that YycH functions as an antagonist to YycG. The molecule is made up of three domains, and has a novel three-dimensional structure. The N-terminal domain features a calcium binding site and the central domain contains two conserved loop regions. 407 matched cddid_all.tbl CDD pfam07436 pfam07436 369364 Curto_V3 Curtovirus V3 protein. This family consists of several Curtovirus V3 proteins of around 90 residues in length. The function of this family is unknown. 87 matched cddid_all.tbl CDD pfam07437 pfam07437 284781 YfaZ YfaZ precursor. This family contains the precursor of the bacterial protein YfaZ (approximately 180 residues long). Many members of this family are hypothetical proteins. 180 matched cddid_all.tbl CDD pfam07438 pfam07438 369365 DUF1514 Protein of unknown function (DUF1514). This family consists of several Staphylococcus aureus and related bacteriophage proteins of around 65 residues in length. The function of this family is unknown. Structural modelling suggests this domain may bind nucleic acids. 62 matched cddid_all.tbl CDD pfam07439 pfam07439 400012 DUF1515 Protein of unknown function (DUF1515). This family consists of several hypothetical bacterial proteins of around 130 residues in length. Members of this family seem to be found exclusively in Rhizobium species. The function of this family is unknown. 113 matched cddid_all.tbl CDD pfam07440 pfam07440 116061 Caerin_1 Caerin 1 protein. This family consists of several caerin 1 proteins from Litoria species. The caerin 1 peptides are among the most powerful of the broad-spectrum antibiotic amphibian peptides. 24 matched cddid_all.tbl CDD pfam07441 pfam07441 462165 BofA SigmaK-factor processing regulatory protein BofA. This family contains the sigmaK-factor processing regulatory protein BofA (Bypass-of-forespore protein A) (approximately 80 residues long). During sporulation in Bacillus subtilis, transcription is controlled in the developing sporangium by a cascade of sporulation-specific transcription factors (sigma factors). Following engulfment, processing of sigmaK is inhibited by BofA. It has been suggested that this effect is exerted by alteration of the level of the SpoIVFA protein. 73 matched cddid_all.tbl CDD pfam07442 pfam07442 116063 Ponericin Ponericin. This family contains a number of ponericin peptides (approximately 30 residues long) from the venom of the predatory ant Pachycondyla goeldii. These peptides exhibit antibacterial and insecticidal properties, and may adopt an amphipathic alpha-helical structure in polar environments such as cell membranes. 29 matched cddid_all.tbl CDD pfam07443 pfam07443 462166 HARP HepA-related protein (HARP). This family represents a conserved region approximately 60 residues long within eukaryotic HepA-related protein (HARP). This exhibits single-stranded DNA-dependent ATPase activity, and is ubiquitously expressed in human and mouse tissues. Family members may contain more than one copy of this region. 55 matched cddid_all.tbl CDD pfam07444 pfam07444 429464 Ycf66_N Ycf66 protein N-terminus. This family represents the N-terminus (approximately 80 residues) of Ycf66, a protein that seems to be restricted to eukaryotes that contain chloroplasts and to cyanobacteria. 76 matched cddid_all.tbl CDD pfam07445 pfam07445 429465 PriC Primosomal replication protein priC. This family contains the bacterial primosomal replication protein priC. In Escherichia coli, this function in the assembly of the primosome. 174 matched cddid_all.tbl CDD pfam07447 pfam07447 400017 VP40 Matrix protein VP40. This family contains viral VP40 matrix proteins that seem to be restricted to the Filoviridae. These play an important role in the assembly process of virus particles by interacting with cellular factors, cellular membranes, and the ribonuclearprotein particle complex. It has been shown that the N-terminal region of VP40 folds into a mixture of hexameric and octameric states - these may have distinct roles. 292 matched cddid_all.tbl CDD pfam07448 pfam07448 429466 Spp-24 Secreted phosphoprotein 24 (Spp-24) cystatin-like domain. This family represents a conserved region approximately 60 residues long within secreted phosphoprotein 24 (Spp-24), which seems to be restricted to vertebrates. This is a non-collagenous protein found in bone that is related in sequence to the cystatin family of thiol protease inhibitors. This suggests that Spp-24 could function to modulate the thiol protease activities known to be involved in bone turnover. It is also possible that the intact form of Spp-24 found in bone could be a precursor to a biologically active peptide that coordinates an aspect of bone turnover. 64 matched cddid_all.tbl CDD pfam07449 pfam07449 400018 HyaE Hydrogenase-1 expression protein HyaE. This family contains bacterial hydrogenase-1 expression proteins approximately 120 residues long. This includes the E. coli protein HyaE, and the homologous proteins HoxO of R. eutropha and HupG of R. leguminosarum. Deletion of the hoxO gene in R. eutropha led to complete loss of the uptake [NiFe] hydrogenase activity, suggesting that it has a critical role in hydrogenase assembly. 108 matched cddid_all.tbl CDD pfam07450 pfam07450 429467 HycH Formate hydrogenlyase maturation protein HycH. This family contains the bacterial formate hydrogenlyase maturation protein HycH, which is approximately 140 residues long. This may be required for the conversion of a precursor form of the large subunit of hydrogenlyase 3 into a mature form. 129 matched cddid_all.tbl CDD pfam07451 pfam07451 400020 SpoVAD Stage V sporulation protein AD (SpoVAD). This family contains the bacterial stage V sporulation protein AD (SpoVAD), which is approximately 340 residues long. This is one of six proteins encoded by the spoVA operon, which is transcribed exclusively in the forespore at about the time of dipicolinic acid (DPA) synthesis in the mother cell. The functions of the proteins encoded by the spoVA operon are unknown, but it has been suggested they are involved in DPA transport during sporulation. 329 matched cddid_all.tbl CDD pfam07452 pfam07452 462167 CHRD CHRD domain. CHRD (after SWISS-PROT abbreviation for chordin) is a novel domain identified in chordin, an inhibitor of bone morphogenetic proteins. This family includes bacterial homologs. It is anticipated to have an immunoglobulin-like beta-barrel structure based on limited similarity to superoxide dismutases but, as yet, no clear functional prediction can be made. Its most conserved feature is a GE[I/L]RCG[V/I/L] motif towards its C-terminal end Most bacterial proteins in this family have only one CHRD domain, whereas it is found repeated in many eukaryotic proteins such as human chordin and Drosophila SOG.. 118 matched cddid_all.tbl CDD pfam07453 pfam07453 284793 NUMOD1 NUMOD1 domain. This domain probably represents a DNA-binding helix-turn-helix based on its similarity to other families (Bateman A pers obs). 37 matched cddid_all.tbl CDD pfam07454 pfam07454 462168 SpoIIP Stage II sporulation protein P (SpoIIP). This family contains the bacterial stage II sporulation protein P (SpoIIP) (approximately 350 residues long). It has been shown that a block in polar cytokinesis in Bacillus subtilis is mediated partly by transcription of spoIID, spoIIM and spoIIP. This inhibition of polar division is involved in the locking in of asymmetry after the formation of a polar septum during sporulation. Engulfment in Bacillus subtilis is mediated by two complementary systems: the first includes the proteins SpoIID, SpoIIM and SpoIIP (DMP) which carry out the engulfment, and the second includes the SpoIIQ-SpoIIIAGH (Q-AH) zipper, that recruits other proteins to the septum in a second-phase of the engulfment. The course of events follows as the incorporation firstly of SpoIIB into the septum during division to serve directly or indirectly as a landmark for localising SpoIIM and then SpoIIP and SpoIID to the septum. SpoIIP and SpoIID interact together to form part of the DMP complex. SpoIIP itself has been identified as an autolysin with peptidoglycan hydrolase activity. 263 matched cddid_all.tbl CDD pfam07455 pfam07455 429469 Psu Phage polarity suppression protein (Psu). This family contains a number of phage polarity suppression proteins (Psu) (approximately 190 residues long). The Psu protein of bacteriophage P4 causes suppression of transcriptional polarity in Escherichia coli by overcoming Rho termination factor activity. 182 matched cddid_all.tbl CDD pfam07456 pfam07456 429470 Hpre_diP_synt_I Heptaprenyl diphosphate synthase component I. This family contains component I of bacterial heptaprenyl diphosphate synthase (EC:2.5.1.30) (approximately 170 residues long). This is one of the two dissociable subunits that form the enzyme, both of which are required for the catalysis of the biosynthesis of the side chain of menaquinone-7. 147 matched cddid_all.tbl CDD pfam07457 pfam07457 429471 DUF1516 Protein of unknown function (DUF1516). This family contains a number of hypothetical bacterial proteins of unknown function approximately 120 residues long. 107 matched cddid_all.tbl CDD pfam07458 pfam07458 400025 SPAN-X Sperm protein associated with nucleus, mapped to X chromosome. This family contains human sperm proteins associated with the nucleus and mapped to the X chromosome (SPAN-X) (approximately 100 residues long). SPAN-X proteins are cancer-testis antigens (CTAs), and thus represent potential targets for cancer immunotherapy because they are widely distributed in tumours but not in normal tissues, except testes. They are highly insoluble, acidic, and polymorphic. 94 matched cddid_all.tbl CDD pfam07459 pfam07459 400026 CTX_RstB CTX phage RstB protein. This family contains a number of RstB proteins approximately 120 residues long, including RstB1 and RstB2, from the Vibrio cholerae phage CTX. Functional analyses indicate that rstB2 is required for integration of the CTXphi phage into the V. cholerae chromosome. 90 matched cddid_all.tbl CDD pfam07460 pfam07460 429472 NUMOD3 NUMOD3 motif. NUMOD3 is a DNA-binding motif found in homing endonucleases and related proteins. It occurs on its own or in tandem repeats in GIY-YIG (pfam01541) and HTH proteins. It constitutes a beta-turn-loop-helix subregion of the the DNA-binding domain of I-TevI homing endonuclease. 37 matched cddid_all.tbl CDD pfam07461 pfam07461 462169 NADase_NGA Nicotine adenine dinucleotide glycohydrolase (NADase). This family consists of several bacterial nicotine adenine dinucleotide glycohydrolase (NGA) proteins which appear to be specific to Streptococcus pyogenes. NAD glycohydrolase (NADase) is a potential virulence factor. Streptococcal NADase may contribute to virulence by its ability to cleave beta-NAD at the ribose-nicotinamide bond, depleting intracellular NAD pools and producing the potent vasoactive compound nicotinamide. 446 matched cddid_all.tbl CDD pfam07462 pfam07462 462170 MSP1_C Merozoite surface protein 1 (MSP1) C-terminus. This family represents the C-terminal region of merozoite surface protein 1 (MSP1) which are found in a number of Plasmodium species. MSP-1 is a 200-kDa protein expressed on the surface of the P. vivax merozoite. MSP-1 of Plasmodium species is synthesized as a high-molecular-weight precursor and then processed into several fragments. At the time of red cell invasion by the merozoite, only the 19-kDa C-terminal fragment (MSP-119), which contains two epidermal growth factor-like domains, remains on the surface. Antibodies against MSP-119 inhibit merozoite entry into red cells, and immunization with MSP-119 protects monkeys from challenging infections. Hence, MSP-119 is considered a promising vaccine candidate. 543 matched cddid_all.tbl CDD pfam07463 pfam07463 462171 NUMOD4 NUMOD4 motif. NUMOD4 is a putative DNA-binding motif found in homing endonucleases and related proteins. 52 matched cddid_all.tbl CDD pfam07464 pfam07464 462172 ApoLp-III Apolipophorin-III precursor (apoLp-III). This family consists of several insect apolipoprotein-III sequences. Exchangeable apolipoproteins constitute a functionally important family of proteins that play critical roles in lipid transport and lipoprotein metabolism. Apolipophorin III (apoLp-III) is a prototypical exchangeable apolipoprotein found in many insect species that functions in transport of diacylglycerol (DAG) from the fat body lipid storage depot to flight muscles in the adult life stage. 143 matched cddid_all.tbl CDD pfam07465 pfam07465 429475 PsaM Photosystem I protein M (PsaM). This family consists of several plant and cyanobacterial photosystem I protein M (PsaM) sequences. PsaM forms part of the photosystem I complex and its binding is stabilized by PsaI. 28 matched cddid_all.tbl CDD pfam07466 pfam07466 462173 DUF1517 Protein of unknown function (DUF1517). This family consists of several hypothetical glycine rich plant and bacterial proteins of around 300 residues in length. The function of this family is unknown. 182 matched cddid_all.tbl CDD pfam07467 pfam07467 400032 BLIP Beta-lactamase inhibitor (BLIP). The structure of BLIP reveals two structural domains, which form a polar, concave surface that docks onto a predominantly polar, convex protrusion on beta-lactamase. The ability of BLIP to adapt to a variety of class A beta-lactamases is thought to be due to flexibility between these two domains. 123 matched cddid_all.tbl CDD pfam07468 pfam07468 116089 Agglutinin Agglutinin domain. 141 matched cddid_all.tbl CDD pfam07469 pfam07469 462174 DUF1518 Nuclear receptor coactivator, DUF1518. This conserved domain of unknown function is usually found tandemly repeated in the nuclear receptor coactivator family (NCOA1/2/3, also known as the SRC/p160 nuclear receptor coactivator family, which are ligand-dependent transcription factors. 58 matched cddid_all.tbl CDD pfam07470 pfam07470 429478 Glyco_hydro_88 Glycosyl Hydrolase Family 88. Unsaturated glucuronyl hydrolase catalyzes the hydrolytic release of unsaturated glucuronic acids from oligosaccharides (EC:3.2.1.-) produced by the reactions of polysaccharide lyases. 345 matched cddid_all.tbl CDD pfam07471 pfam07471 369382 Phage_Nu1 Phage DNA packaging protein Nu1. Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA. 164 matched cddid_all.tbl CDD pfam07472 pfam07472 429479 PA-IIL Fucose-binding lectin II (PA-IIL). In Pseudomonas aeruginosa the fucose-binding lectin II (PA-IIL) contributes to the pathogenic virulence of the bacterium. PA-IIL functions as a tetramer when binding fucose. Each monomer is comprised of a nine-stranded, antiparallel beta-sandwich arrangement and contains two calcium cations that mediate the binding of fucose in a recognition mode unique among carbohydrate-protein interactions. 107 matched cddid_all.tbl CDD pfam07473 pfam07473 400036 Toxin_11 Spasmodic peptide gm9a; conotoxin from Conus species. This family consists of several spasmodic peptide gm9a sequences. Conotoxin gm9a is a putative 27-residue polypeptide encoded by Conus gloriamaris and is known to be a homolog of the 'spasmodic peptide', tx9a, isolated from the venom of the mollusc-hunting cone shell Conus textile. Upon injection of this venom component, normal mice are converted into behavioural phenocopies of a well-known mutant, the spasmodic mouse. 28 matched cddid_all.tbl CDD pfam07474 pfam07474 462175 G2F G2F domain. Nidogen, an invariant component of basement membranes, is a multifunctional protein that interacts with most other major basement membrane proteins. The G2 fragment or (G2F domain) contains binding sites for collagen IV and perlecan. The structure is composed of an 11-stranded beta-barrel with a central helix. This domain is structurally related to that of green fluorescent protein pfam01353. A large surface patch on the beta-barrel is conserved in all metazoan nidogens. 184 matched cddid_all.tbl CDD pfam07475 pfam07475 462176 Hpr_kinase_C HPr Serine kinase C-terminal domain. This family represents the C terminal kinase domain of Hpr Serine/threonine kinase PtsK. This kinase is the sensor in a multicomponent phosphorelay system in control of carbon catabolic repression in bacteria. This kinase in unusual in that it recognizes the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating enzymes. X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller. 171 matched cddid_all.tbl CDD pfam07476 pfam07476 284814 MAAL_C Methylaspartate ammonia-lyase C-terminus. Methylaspartate ammonia-lyase EC:4.3.1.2 catalyzes the second step of fermentation of glutamate. It is a homodimer. This family represents the C-terminal region of Methylaspartate ammonia-lyase and contains a TIM barrel fold similar to the pfam01188. This family represents the catalytic domain and contains a metal binding site. 247 matched cddid_all.tbl CDD pfam07477 pfam07477 462177 Glyco_hydro_67C Glycosyl hydrolase family 67 C-terminus. Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. This family represents the C terminal region of alpha-glucuronidase which is mainly alpha-helical. It wraps around the catalytic domain (pfam07488), making additional interactions both with the N-terminal domain (pfam03648) of its parent monomer and also forming the majority of the dimer-surface with the equivalent C-terminal domain of the other monomer of the dimer. 223 matched cddid_all.tbl CDD pfam07478 pfam07478 429483 Dala_Dala_lig_C D-ala D-ala ligase C-terminus. This family represents the C-terminal, catalytic domain of the D-alanine--D-alanine ligase enzyme EC:6.3.2.4. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF). 204 matched cddid_all.tbl CDD pfam07479 pfam07479 462178 NAD_Gly3P_dh_C NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus. NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the C-terminal substrate-binding domain. 142 matched cddid_all.tbl CDD pfam07481 pfam07481 369385 DUF1521 Domain of Unknown Function (DUF1521). This family of unknown function is found in a limited set of Bradyrhizobium proteins. There appears to be a periodic -DG- motif in it. 169 matched cddid_all.tbl CDD pfam07482 pfam07482 284819 DUF1522 Domain of Unknown Function (DUF1522). 110 matched cddid_all.tbl CDD pfam07483 pfam07483 400042 W_rich_C Tryptophan-rich Synechocystis species C-terminal domain. This domain is found at the C-terminus, normally between 2-3 copies, of a range of Synechocystis membrane proteins. This domain is fairly tryptophan rich as well. 105 matched cddid_all.tbl CDD pfam07484 pfam07484 429485 Collar Phage Tail Collar Domain. This region is occasionally found in conjunction with pfam03335. Most of the family appear to be phage tail proteins; however some appear to be involved in other processes. For instance Swiss:Q03314 from Rhizobium leguminosarum may be involved in plant-microbe interactions. A related protein Swiss:Q9L3N1 is involved in the pathogenicity of Microcystis aeruginosa. The finding of this family in a structural component of the phage tail fibre baseplate suggests that its function is structural rather than enzymatic. Structural studies show this region consists of a helix and a loop and three beta-strands. This alignment does not catch the third strand as it is separated from the rest of the structure by around 100 residues. This strand is conserved in homologs but the intervening sequence is not. Much of the function of Swiss:P10930 appears to reside in this intervening region. In the tertiary structure of the phage baseplate this domain forms part of the 'collar'. The domain may bind SO4, however the residues accredited with this vary between the PDB file and the Swiss-Prot entry. The long unconserved region maybe due to domain swapping in and out of a loop or reflective of rapid evolution. 57 matched cddid_all.tbl CDD pfam07485 pfam07485 429486 DUF1529 Domain of Unknown Function (DUF1259). This family is the lppY/lpqO homolog family. 120 matched cddid_all.tbl CDD pfam07486 pfam07486 462179 Hydrolase_2 Cell Wall Hydrolase. These enzymes have been implicated in cell wall hydrolysis, most extensively in Bacillus subtilis. For instance Swiss:P50739 is expressed during sporulation as an inactive form and then deposited on the cell outer cortex. During germination the the enzyme is activated and hydrolyses the cortex. A similar role is carried out by the partially redundant Swiss:P42249. It is not clear whether these enzymes are amidases or peptidases. 101 matched cddid_all.tbl CDD pfam07487 pfam07487 400046 SopE_GEF SopE GEF domain. This family represents the C-terminal guanine nucleotide exchange factor (GEF) domain of SopE. Salmonella typhimurium employs a type III secretion system to inject bacterial toxins into the host cell cytosol. These toxins transiently activate Rho family GTP-binding protein-dependent signaling cascades to induce cytoskeletal rearrangements. SopE, can activate Cdc42, an essential component of the host cellular signaling cascade, in a Dbl-like fashion despite its lack of sequence similarity to Dbl-like proteins, the Rho-specific eukaryotic guanine nucleotide exchange factors. 136 matched cddid_all.tbl CDD pfam07488 pfam07488 462180 Glyco_hydro_67M Glycosyl hydrolase family 67 middle domain. Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. This family represents the central catalytic domain of alpha-glucuronidase. 324 matched cddid_all.tbl CDD pfam07489 pfam07489 369388 Tir_receptor_C Translocated intimin receptor (Tir) C-terminus. Intimin and its translocated intimin receptor (Tir) are bacterial proteins that mediate adhesion between mammalian cells and attaching and effacing (A/E) pathogens. A unique and essential feature of A/E bacterial pathogens is the formation of actin-rich pedestals beneath the intimately adherent bacteria and localized destruction of the intestinal brush border. The bacterial outer membrane adhesin, intimin, is necessary for the production of the A/E lesion and diarrhoea. The A/E bacteria translocate their own receptor for intimin, Tir, into the membrane of mammalian cells using the type III secretion system. The translocated Tir triggers additional host signalling events and actin nucleation, which are essential for lesion formation. This family represents the Tir C-terminal domain which has been reported to bind uninfected host cells and beta-1 integrins although the role of intimin binding to integrins is unclear. This intimin C-terminal domain has also been shown to be sufficient for Tir recognition. 222 matched cddid_all.tbl CDD pfam07490 pfam07490 254231 Tir_receptor_N Translocated intimin receptor (Tir) N-terminus. Intimin and its translocated intimin receptor (Tir) are bacterial proteins that mediate adhesion between mammalian cells and attaching and effacing (A/E) pathogens. A unique and essential feature of A/E bacterial pathogens is the formation of actin-rich pedestals beneath the intimately adherent bacteria and localized destruction of the intestinal brush border. The bacterial outer membrane adhesin, intimin, is necessary for the production of the A/E lesion and diarrhoea. The A/E bacteria translocate their own receptor for intimin, Tir, into the membrane of mammalian cells using the type III secretion system. The translocated Tir triggers additional host signalling events and actin nucleation, which are essential for lesion formation. This family represents the Tir N-terminal domain which is involved in Tir stability and Tir secretion. 269 matched cddid_all.tbl CDD pfam07491 pfam07491 429489 PPI_Ypi1 Protein phosphatase inhibitor. These proteins include Ypi1,, a novel Saccharomyces cerevisiae type 1 protein phosphatase inhibitor and ppp1r11/hcgv, annotated as having protein phosphatase inhibitor activity. 57 matched cddid_all.tbl CDD pfam07492 pfam07492 429490 Trehalase_Ca-bi Neutral trehalase Ca2+ binding domain. Neutral trehalases mobilize trehalose accumulated by fungal cells as a protective and storage carbohydrate. This family represents a calcium-binding domain similar to EF hand. Residues 97 and 108 in Swiss:O42893 have been implicated in this interaction. It is thought that this domain may provide a general mechanism for regulating neutral trehalase activity in yeasts and filamentous fungi. 30 matched cddid_all.tbl CDD pfam07494 pfam07494 400050 Reg_prop Two component regulator propeller. A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats. These repeats show homology to pfam01011 and pfam00400 indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA. 24 matched cddid_all.tbl CDD pfam07495 pfam07495 400051 Y_Y_Y Y_Y_Y domain. This domain is mostly found at the end of the beta propellers (pfam07494) in a family of two component regulators. However they are also found tandemly repeated in Swiss:Q891H4 without other signal conduction domains being present. It's named after the conserved tyrosines found in the alignment. The exact function is not known. 65 matched cddid_all.tbl CDD pfam07496 pfam07496 462181 zf-CW "CW-type Zinc Finger. This domain appears to be a zinc finger. The alignment shows four conserved cysteine residues and a conserved tryptophan. It was first identified by, and is predicted to be a ""highly specialized mononuclear four-cysteine zinc finger...that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including...chromatin methylation status and early embryonic development."" Weak homology to pfam00628 further evidences these predictions (personal obs: C Yeats). Twelve different CW-domain-containing protein subfamilies are described, with different subfamilies being characteriztic of vertebrates, higher plants and other animals in which these domain is found." 46 matched cddid_all.tbl CDD pfam07497 pfam07497 462182 Rho_RNA_bind Rho termination factor, RNA-binding domain. The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers. 72 matched cddid_all.tbl CDD pfam07498 pfam07498 429493 Rho_N Rho termination factor, N-terminal domain. The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers. This domain is found to the N-terminus of the RNA binding domain (pfam07497). 43 matched cddid_all.tbl CDD pfam07499 pfam07499 462183 RuvA_C RuvA, C-terminal domain. Homologous recombination is a crucial process in all living organizms. In bacteria, this process the RuvA, RuvB, and RuvC proteins are involved. More specifically the proteins process the Holliday junction DNA. RuvA is comprised of three distinct domains. The domain represents the C-terminal domain and plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB. Within the Holliday junction, the C-terminal domain makes no interaction with DNA. 47 matched cddid_all.tbl CDD pfam07500 pfam07500 462184 TFIIS_M Transcription factor S-II (TFIIS), central domain. Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and pfam01096 are required for transcription activity. 112 matched cddid_all.tbl CDD pfam07501 pfam07501 462185 G5 G5 domain. This domain is found in a wide range of extracellular proteins. It is found tandemly repeated in up to 8 copies. It is found in the N-terminus of peptidases belonging to the M26 family which cleave human IgA. The domain is also found in proteins involved in metabolism of bacterial cell walls suggesting this domain may have an adhesive function. 75 matched cddid_all.tbl CDD pfam07502 pfam07502 462186 MANEC MANEC domain. This region of similarity, comprising 8 conserved cysteines, is found in the N-terminal region of several membrane-associated and extracellular proteins. Although formerly called MANSC (for motif at N terminus with seven cysteines) it has now been renamed by MANEC (motif at N terminus with eight cysteines) by Richard Mitter and Stephen Fitzgerald after the discovery of an eighth conserved cysteine. It is postulated that this domain may play a role in the formation of protein complexes involving various protease activators and inhibitors. 90 matched cddid_all.tbl CDD pfam07503 pfam07503 462187 zf-HYPF HypF finger. The HypF family of proteins are involved in the maturation and regulation of hydrogenase. In the N-terminus they appear to have two Zinc finger domains, as modelled by this family. 33 matched cddid_all.tbl CDD pfam07504 pfam07504 429499 FTP Fungalysin/Thermolysin Propeptide Motif. This motif is found in both the bacterial M4 peptidase propeptide and the fungal M36 propeptide. Its exact function is not clear, but it is likely to either inhibit the peptidase, so as to prevent its premature activation, or has a chaperone activity. Both of these roles have been ascribed to the M4 and M36 propeptides. 50 matched cddid_all.tbl CDD pfam07505 pfam07505 429500 DUF5131 Protein of unknown function (DUF5131). This is a family of bacterial and phage proteins of unknown function. There are three highly conserved cysteine residues in the disposition, Cx6Cxxc, amongst many highly conserved residues. 243 matched cddid_all.tbl CDD pfam07506 pfam07506 311449 RepB RepB plasmid partitioning protein. This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens. 185 matched cddid_all.tbl CDD pfam07507 pfam07507 429501 WavE WavE lipopolysaccharide synthesis. These proteins are encoded by putative wav gene clusters, which are responsible for the synthesis of the core oligosaccharide (OS) region of Vibrio cholerae lipopolysaccharide. 305 matched cddid_all.tbl CDD pfam07508 pfam07508 429502 Recombinase Recombinase. This domain is usually found associated with pfam00239 in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages. 102 matched cddid_all.tbl CDD pfam07509 pfam07509 429503 DUF1523 Protein of unknown function (DUF1523). 175 matched cddid_all.tbl CDD pfam07510 pfam07510 462188 DUF1524 Protein of unknown function (DUF1524). This family of uncharacterized proteins contain a conserved HXXP motif. A similar motif is seen in protein families in the His-Me finger endonuclease superfamily which suggests this family of proteins may also act as endonucleases. 141 matched cddid_all.tbl CDD pfam07511 pfam07511 429505 DUF1525 Protein of unknown function (DUF1525). 113 matched cddid_all.tbl CDD pfam07514 pfam07514 429506 TraI_2 Putative helicase. Some members of this family have been annotated as helicases. 326 matched cddid_all.tbl CDD pfam07515 pfam07515 429507 TraI_2_C Putative conjugal transfer nickase/helicase TraI C-term. 123 matched cddid_all.tbl CDD pfam07516 pfam07516 462189 SecA_SW SecA Wing and Scaffold domain. SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP dependent manner. This family is composed of two C-terminal alpha helical subdomains: the wing and scaffold subdomains. 213 matched cddid_all.tbl CDD pfam07517 pfam07517 462190 SecA_DEAD SecA DEAD-like domain. SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP dependent manner. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the pfam00270. 379 matched cddid_all.tbl CDD pfam07519 pfam07519 284851 Tannase Tannase and feruloyl esterase. This family includes fungal tannase and feruloyl esterase. It also includes several bacterial homologs of unknown function. 460 matched cddid_all.tbl CDD pfam07520 pfam07520 429510 SrfB Virulence factor SrfB. This family includes homologs of SsrAB is a two-component regulatory system encoded within the Salmonella pathogenicity island SPI-2. Among the products of genes activated by SsrAB within epithelial and macrophage cells is Swiss:Q9KIJ9. homologs are found in several other proteobacteria. 979 matched cddid_all.tbl CDD pfam07521 pfam07521 462191 RMMBL Zn-dependent metallo-hydrolase RNA specificity domain. The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. This, the fifth motif, appears to be specific to Zn-dependent metallohydrolases such as ribonuclease J 2 which are involved in the processing of mRNA. This domain adds essential structural elements to the CASP-domain and is unique to RNA/DNA-processing nucleases, showing that they are pre-mRNA 3'-end-processing endonucleases. 63 matched cddid_all.tbl CDD pfam07522 pfam07522 429512 DRMBL DNA repair metallo-beta-lactamase. The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair. 108 matched cddid_all.tbl CDD pfam07523 pfam07523 400072 Big_3 Bacterial Ig-like domain (group 3). This family consists of bacterial domains with an Ig-like fold. Members of this family are found in a variety of bacterial surface proteins. 67 matched cddid_all.tbl CDD pfam07524 pfam07524 400073 Bromo_TP Bromodomain associated. This domain is predicted to bind DNA and is often found associated with pfam00439 and in transcription factors. It has a histone-like fold. 77 matched cddid_all.tbl CDD pfam07525 pfam07525 462192 SOCS_box SOCS box. The SOCS box acts as a bridge between specific substrate- binding domains and more generic proteins that comprise a large family of E3 ubiquitin protein ligases. 39 matched cddid_all.tbl CDD pfam07526 pfam07526 429514 POX Associated with HOX. The function of this domain is unknown. It is often found in plant proteins associated with pfam00046. 139 matched cddid_all.tbl CDD pfam07527 pfam07527 462193 Hairy_orange Hairy Orange. The Orange domain is found in the Drosophila proteins Hesr-1, Hairy, and Enhancer of Split. The Orange domain is proposed to mediate specific protein-protein interaction between Hairy and Scute. 40 matched cddid_all.tbl CDD pfam07528 pfam07528 284860 DZF DZF domain. The function of this domain is unknown. It is often found associated with pfam00098 or pfam00035. This domain has been predicted to belong to the nucleotidyltransferase superfamily. 248 matched cddid_all.tbl CDD pfam07529 pfam07529 462194 HSA HSA domain. This domain is predicted to bind DNA and is often found associated with helicases. This region does not form a compact domain in the known structures. 67 matched cddid_all.tbl CDD pfam07530 pfam07530 148888 PRE_C2HC Associated with zinc fingers. This function of this domain is unknown and is often found associated with pfam00096. 68 matched cddid_all.tbl CDD pfam07531 pfam07531 462195 TAFH NHR1 homology to TAF. This corresponds to the region NHR1 that is conserved between the product of the nervy gene in Drosophila and the human mtg8b protein, which is hypothesized to be a transcription factor. 90 matched cddid_all.tbl CDD pfam07532 pfam07532 400079 Big_4 Bacterial Ig-like domain (group 4). This family consists of bacterial domains with an Ig-like fold. Members of this family are found in a variety of bacterial surface proteins. 59 matched cddid_all.tbl CDD pfam07533 pfam07533 462196 BRK BRK domain. The function of this domain is unknown. It is often found associated with helicases and transcription factors. 44 matched cddid_all.tbl CDD pfam07534 pfam07534 429519 TLD TLD. This domain is predicted to be an enzyme and is often found associated with pfam01476. It's structure consists of a beta-sandwich surrounded by two helices and two one-turn helices. 139 matched cddid_all.tbl CDD pfam07535 pfam07535 462197 zf-DBF DBF zinc finger. This domain is predicted to bind metal ions and is often found associated with pfam00533 and pfam02178. It was first identified in the Drosophila chiffon gene product, and is associated with initiation of DNA replication. 42 matched cddid_all.tbl CDD pfam07536 pfam07536 429521 HWE_HK HWE histidine kinase. Two-component systems, consisting of a histidine kinase and a cognate response regulator protein, represent the best-known apparatus for transducing external cues into a physiological response in bacteria. The HWE domain is found in a subset of two-component system kinases, belonging to the same superfamily as pfam00512 and pfam07568. The family was defined by the presence of a highly conserved H residue in the kinase domain and a WxE motif in a C-terminal ATPase domain that is related to pfam02518. It has been demonstrated to show structural and functional correlation with pfam07568. These proteins are found in a variety of alpha- and gamma- proteobacteria, with significant enrichment in the rhizobia. 83 matched cddid_all.tbl CDD pfam07537 pfam07537 429522 CamS CamS sex pheromone cAM373 precursor. This family includes CamS, from which Staphylococcus aureus sex pheromone staph-cAM373 is processed. 316 matched cddid_all.tbl CDD pfam07538 pfam07538 429523 ChW Clostridial hydrophobic W. A novel extracellular macromolecular system has been proposed based on the proteins containing ChW repeats. ChW stands for Clostridial hydrophobic with conserved W (tryptophan). This repeat was originally described in Clostridium acetobutylicum but is also found in other Gram-positive bacteria including Enterococcus faecalis, Streptococcus agalactiae and Streptomyces coelicolor. 35 matched cddid_all.tbl CDD pfam07539 pfam07539 462198 DRIM Down-regulated in metastasis. These eukaryotic proteins include DRIM (Down-Regulated In Metastasis), which is differentially expressed in metastatic and non-metastatic human breast carcinoma cells. It is believed to be involved in processing of non-coding RNA. 609 matched cddid_all.tbl CDD pfam07540 pfam07540 462199 NOC3p Nucleolar complex-associated protein. Nucleolar complex-associated protein (Noc3p) is conserved in eukaryotes and has essential roles in replication and rRNA processing in Saccharomyces cerevisiae. 92 matched cddid_all.tbl CDD pfam07541 pfam07541 462200 EIF_2_alpha Eukaryotic translation initiation factor 2 alpha subunit. These proteins share a region of similarity that falls towards the C terminus from pfam00575. 112 matched cddid_all.tbl CDD pfam07542 pfam07542 462201 ATP12 ATP12 chaperone protein. Mitochondrial F1-ATPase is an oligomeric enzyme composed of five distinct subunit polypeptides. The alpha and beta subunits make up the bulk of protein mass of F1. In Saccharomyces cerevisiae both subunits are synthesized as precursors with amino-terminal targeting signals that are removed upon translocation of the proteins to the matrix compartment. These proteins include examples from eukaryotes and bacteria and may have chaperone activity, being involved in F1 ATPase complex assembly. 121 matched cddid_all.tbl CDD pfam07543 pfam07543 369416 PGA2 Protein trafficking PGA2. A Saccharomyces cerevisiae member of this family (PGA2) is an ER protein which has been implicated in protein trafficking. 138 matched cddid_all.tbl CDD pfam07544 pfam07544 462202 Med9 RNA polymerase II transcription mediator complex subunit 9. This family of Med9 proteins is conserved in yeasts. It forms part of the middle region of Mediator. Med9 has two functional domains. The species-specific amino-terminal half (aa 1-63) plays a regulatory role in transcriptional regulation, whereas this well-conserved carboxy-terminal half (aa 64-149) has a more fundamental function involved in direct binding to the amino-terminal portions of Med4 and Med7 and the assembly of Med9 into the Middle module. Also, some unidentified factor(s) in med9 extracts may impact the binding of TFIID to the promoter. 80 matched cddid_all.tbl CDD pfam07545 pfam07545 462203 Vg_Tdu Vestigial/Tondu family. The mammalian TEF and the Drosophila scalloped genes belong to a conserved family of transcriptional factors that possesses a TEA/ATTS DNA-binding domain. Transcriptional activation by these proteins likely requires interactions with specific coactivators. In Drosophila, Scalloped (Sd) interacts with Vestigial (Vg) to form a complex, which binds DNA through the Sd TEA/ATTS domain. The Sd-Vg heterodimer is a key regulator of wing development, which directly controls several target genes and is able to induce wing outgrowth when ectopically expressed. This short conserved region is needed for interaction with Sd. 31 matched cddid_all.tbl CDD pfam07546 pfam07546 462204 EMI EMI domain. The Pfam alignment is truncated at the C-terminus and does not include the final cysteine defined in Callebaut et al. This is to stop the family overlapping with other domains. 69 matched cddid_all.tbl CDD pfam07547 pfam07547 400093 RSD-2 RSD-2 N-terminal domain. This domain is found in three copies in the N-terminus of the C. elegans RSD-2 protein. RSD-2 (RNAi spreading defective) is involved in systemic RNAi. Mutations in the rsd-2 gene do not effect somatic genes but only germline expressed genes. 83 matched cddid_all.tbl CDD pfam07548 pfam07548 311484 ChlamPMP_M Chlamydia polymorphic membrane protein middle domain. This family contains several Chlamydia polymorphic membrane proteins. Chlamydia pneumoniae is an obligate intracellular bacterium and a common human pathogen causing infection of the upper and lower respiratory tract. This domain is found between the beta-helical repeats (pfam02415) and the C-terminal pfam03797. This domain is excised subsequent to secretion. 170 matched cddid_all.tbl CDD pfam07549 pfam07549 462205 Sec_GG SecD/SecF GG Motif. This family consists of various prokaryotic SecD and SecF protein export membrane proteins. This SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC. SecD and SecF are required to maintain a proton motive force. This alignment encompasses a -GG- motif typically found in N-terminal half of the SecD/SecF proteins. 27 matched cddid_all.tbl CDD pfam07550 pfam07550 369421 DUF1533 Protein of unknown function (DUF1533). This family consists of several hypothetical bacterial proteins and is around 60 residues in length. It's function is not known. 59 matched cddid_all.tbl CDD pfam07552 pfam07552 284881 Coat_X Spore Coat Protein X and V domain. This family is found in the Bacilliales coat protein X as a tandem repeat and also in coat protein V. The proteins are found in the insoluble fraction. 54 matched cddid_all.tbl CDD pfam07553 pfam07553 462206 Lipoprotein_Ltp Host cell surface-exposed lipoprotein. This is a family of lipoproteins that is involved in superinfection exclusion. Proteins in this family have been shown to act at the stage of DNA release from the phage head into the cell. 48 matched cddid_all.tbl CDD pfam07554 pfam07554 400096 FIVAR FIVAR domain. This domain is found in a wide variety of contexts, but mostly occurring in cell wall associated proteins. A lack of conserved catalytic residues suggests that it is a binding domain. From context, possible substrates are hyaluronate or fibronectin (personal obs: C Yeats). This is further evidenced by. Possibly the exact substrate is N-acetyl glucosamine. Finding it in the same protein as pfam05089 further supports this proposal. It is found in the C-terminal part of Swiss:O82833, which is removed during maturation. Some of the proteins it is found in are involved in methicillin resistance. The name FIVAR derives from Found In Various Architectures. 69 matched cddid_all.tbl CDD pfam07555 pfam07555 429533 NAGidase beta-N-acetylglucosaminidase. This family has previously been described as a hyaluronidase. However, more recently it has been shown that this family has beta-N-acetylglucosaminidase activity. 293 matched cddid_all.tbl CDD pfam07556 pfam07556 429534 DUF1538 Protein of unknown function (DUF1538). This family contains several conserved glycines and phenylalanines. 209 matched cddid_all.tbl CDD pfam07557 pfam07557 462207 Shugoshin_C Shugoshin C terminus. Shugoshin-like proteins contain this conserved sequence at the C terminus, which is rich in basic amino-acids. Shugoshin (Sgo1) protects Rec8 at centromeres during anaphase I (during meiosis) so that sister chromatids remain tethered. Sgo2 is a paralogue of Sgo1 and is involved in correctly orienting sister-centromeres. 24 matched cddid_all.tbl CDD pfam07558 pfam07558 462208 Shugoshin_N Shugoshin N-terminal coiled-coil region. The Shugoshin protein is found to have this conserved N-terminal coiled-coil region and a highly conserved C-terminal basic region, family Shugoshin_C pfam07557. Shugoshin is a crucial target of Bub1 kinase function at kinetochores, necessary for both meiotic and mitotic localization of shugoshin to the kinetochore. Human shugoshin is diffusible and mediates kinetochore-driven formation of kinetochore-microtubules during bipolar spindle assembly. Further, the primary role of shugoshin is to ensure bipolar attachment of kinetochores, and its role in protecting cohesion has co-developed to facilitate this process. 45 matched cddid_all.tbl CDD pfam07559 pfam07559 429537 FlaE Flagellar basal body protein FlaE. This family consists of several bacterial FlaE flagellar proteins. These proteins are part of the flageller basal body rod complex. 94 matched cddid_all.tbl CDD pfam07560 pfam07560 116179 DUF1539 Domain of Unknown Function (DUF1539). 126 matched cddid_all.tbl CDD pfam07561 pfam07561 462209 DUF1540 Domain of Unknown Function (DUF1540). This family has four conserved cysteines, which is suggestive of a metal binding function. 40 matched cddid_all.tbl CDD pfam07562 pfam07562 462210 NCD3G Nine Cysteines Domain of family 3 GPCR. This conserved sequence contains several highly-conserved Cys residues that are predicted to form disulphide bridges. It is predicted to lie outside the cell membrane, tethered to the pfam00003 in several receptor proteins. 53 matched cddid_all.tbl CDD pfam07563 pfam07563 429540 DUF1541 Protein of unknown function (DUF1541). This family consists of several hypothetical bacterial and occurs as a tandem repeat. 52 matched cddid_all.tbl CDD pfam07564 pfam07564 429541 DUF1542 Domain of Unknown Function (DUF1542). This domain is found in several cell surface proteins, such as extracellular matrix-binding protein ebh. Some members are involved in antibiotic resistance (e.g Swiss:Q9RL69 and Swiss:Q9LCJ9) and/or cellular adhesion. In some proteins it is repeated more than fifteen times, being the most repeated domain in streptococci. This is a predominantly alpha-helical domain that form a long, thin, fibre-like structure and it has been proposed to function as a stalk that helps the adhesive non-repeat region (NRR) of proteins protrude beyond the cell surface. 77 matched cddid_all.tbl CDD pfam07565 pfam07565 429542 Band_3_cyto Band 3 cytoplasmic domain. This family contains the cytoplasmic domain of the Band 3 anion exchange proteins that exchange Cl-/HCO3-. Band 3 constitutes the most abundant polypeptide in the red blood cell membrane, comprising 25% of the total membrane protein. The cytoplasmic domain of band 3 functions primarily as an anchoring site for other membrane-associated proteins. Included among the protein ligands of cdb3 are ankyrin, protein 4.2, protein 4.1, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphofructokinase, aldolase, hemoglobin, hemichromes, and the protein tyrosine kinase (p72syk). 255 matched cddid_all.tbl CDD pfam07566 pfam07566 400107 DUF1543 Domain of Unknown Function (DUF1543). This domain is found as 1-2 copies in a small family of proteins of unknown function. 52 matched cddid_all.tbl CDD pfam07568 pfam07568 400108 HisKA_2 Histidine kinase. This is the dimerization and phosphoacceptor domain of a sub-family of histidine kinases. It shares sequence similarity with pfam00512 and pfam07536. It is usually found adjacent to a C-terminal ATPase domain (pfam02518). This domain is found in a wide range of Bacteria and also several Archaea. 76 matched cddid_all.tbl CDD pfam07569 pfam07569 462211 Hira TUP1-like enhancer of split. The Hira proteins are found in a range of eukaryotes and are implicated in the assembly of repressive chromatin. These proteins also contain pfam00400. 221 matched cddid_all.tbl CDD pfam07571 pfam07571 462212 TAF6_C TAF6 C-terminal HEAT repeat domain. TAF6_C is the C-terminal domain of the TAF6 subunit of the general transcription factor TFIID. The crystal structure reveals the presence of five conserved HEAT repeats. This region is necessary for the complexing together of the subunits TAF5, TAF6 and TAF9. 90 matched cddid_all.tbl CDD pfam07572 pfam07572 462213 BCNT Bucentaur or craniofacial development. Bucentaur or craniofacial development protein 1 (BCNT) in ruminents has a different domain architecture to that in mouse and human. For this reason it has been used as a model for molecular evolution. Both bovine and human BCNTs are phosphorylated by casein kinase II in vitro. 71 matched cddid_all.tbl CDD pfam07573 pfam07573 311502 AreA_N Nitrogen regulatory protein AreA N terminus. The AreA nitrogen regulatory protein proteins (which are GATA type transcription factors) share a highly conserved N terminus and pfam00320 at the C terminus. 94 matched cddid_all.tbl CDD pfam07574 pfam07574 462214 SMC_Nse1 Nse1 non-SMC component of SMC5-6 complex. S. cerevisiae Nse1 forms part of a complex with SMC5-SMC6. This non-structural maintenance of chromosomes (SMC) complex plays an essential role in genomic stability, being involved in DNA repair and DNA metabolism. It is conserved in eukaryotes from yeast to human. This domain lies immediately up-stream of the DNA-binding zinc-finger domain, zf-RING-like pfam08746. 196 matched cddid_all.tbl CDD pfam07575 pfam07575 400113 Nucleopor_Nup85 Nup85 Nucleoporin. A family of nucleoporins conserved from yeast to human. THe nuclear pore complex is a large assembly composed of two essential complexes: the heptameric Nup84 complex and the heteromeric Nic96-containing complex. The Nup84 complex is composed of one copy each of Nup84, Nup85, Nup120, Nup133, Nup145C, Sec13, and Seh1. The structure of a complex of Nup85 and Seh1 was solved. The N-terminus of Nup85 is inserted and forms a three-stranded blade that completes the Seh1 6-bladed beta-propeller in trans. Following its N-terminal insertion blade, Nup85 forms a compact cuboid structure composed of 20 helices, with two distinct modules, referred to as crown and trunk. 562 matched cddid_all.tbl CDD pfam07576 pfam07576 462215 BRAP2 BRCA1-associated protein 2. These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localization signals (NLSs) in vitro and in yeast two-hybrid screening. These proteins share a region of sequence similarity at their N terminus. They also have pfam02148 at the C terminus. 93 matched cddid_all.tbl CDD pfam07577 pfam07577 284902 DUF1547 Domain of Unknown Function (DUF1547). This domain appears to be found only in a small family of Chlamydia species. It is usually found repeated. This domain can be found in translocated actin-recruiting phosphoprotein (Tarp) from Chlamydia trachomatis serovar L2. Tarp appears to initiate or participate in signalling events that regulate the actin recruitment, which ultimately leads to internalization. 60 matched cddid_all.tbl CDD pfam07578 pfam07578 429547 LAB_N Lipid A Biosynthesis N-terminal domain. This family is found at the N-terminus of a group of Chlamydial Lipid A biosynthesis proteins. It is also found by itself in a family of proteins of unknown function. 68 matched cddid_all.tbl CDD pfam07579 pfam07579 311507 DUF1548 Domain of Unknown Function (DUF1548). This family appears to be found only in a small family of Chlamydia proteins. 135 matched cddid_all.tbl CDD pfam07580 pfam07580 462216 Peptidase_M26_C M26 IgA1-specific Metallo-endopeptidase C-terminal region. These peptidases, which cleave mammalian IgA, are found in Gram-positive bacteria. Often found associated with pfam00746, they may be attached to the cell wall. 733 matched cddid_all.tbl CDD pfam07581 pfam07581 429549 Glug The GLUG motif. This family is found in the IgA1 (M26) peptidases, which attached to the cell wall peptidoglycan by an amide bond. IgA1 protease selectively cleaves human IgA1 and is likely to be a pathogenicity factor in some pathogens. This family is also found in various other contexts, including with pfam05860. It is named GLUG after the mostly conserved G-L-any-G motif. 28 matched cddid_all.tbl CDD pfam07583 pfam07583 429550 PSCyt2 Protein of unknown function (DUF1549). A family of paralogues in the planctomyces. 208 matched cddid_all.tbl CDD pfam07584 pfam07584 429551 BatA Aerotolerance regulator N-terminal. These proteins share a highly-conserved sequence at their N-terminus. They include several proteins from Rhodopirellula baltica and also several from proteobacteria. The proteins are produced by the Batl operon which appears to be important in pathogenicity and aerotolerance. This family is the conserved N-terminus, but the full length proteins carry multiple membrane-spanning domains. BatA ensures bacterial survival in the early stages of the infection process, when the infected sites are aerobic, and is produced under conditions of oxidative stress. 76 matched cddid_all.tbl CDD pfam07585 pfam07585 377874 BBP7 Putative beta barrel porin-7 (BBP7). This is a family of putative beta barrel porin-7 BBP7 proteins identified initially in Rhodopirellula baltica. 350 matched cddid_all.tbl CDD pfam07586 pfam07586 429552 HXXSHH Protein of unknown function (DUF1552). A family of proteins identified in Rhodopirellula baltica. 302 matched cddid_all.tbl CDD pfam07587 pfam07587 429553 PSD1 Protein of unknown function (DUF1553). A family of proteins found in Rhodopirellula baltica. 213 matched cddid_all.tbl CDD pfam07588 pfam07588 369437 DUF1554 Protein of unknown function (DUF1554). A family of proteins identified in Leptospira interrogans. 136 matched cddid_all.tbl CDD pfam07589 pfam07589 377877 PEP-CTERM PEP-CTERM motif. This motif has been identified in a wide range of bacteria at their C-terminus. It has been suggested that this is a protein sorting signal. Based on phylogenetic profiling it has been suggested that the EpsH family of proteins mediate this function. 23 matched cddid_all.tbl CDD pfam07591 pfam07591 400120 PT-HINT Pretoxin HINT domain. A member of the HINT superfamily of proteases that is usually found N-terminal to the toxin module in polymorphic toxin systems. The domain is predicted to function in releasing the toxin domain by autoproteolysis. 136 matched cddid_all.tbl CDD pfam07592 pfam07592 462217 DDE_Tnp_ISAZ013 Rhodopirellula transposase DDE domain. These transposases are found in the planctomycete Rhodopirellula baltica, the cyanobacterium Nostoc, and the Gram-positive bacterium Streptomyces. 308 matched cddid_all.tbl CDD pfam07593 pfam07593 429555 UnbV_ASPIC ASPIC and UnbV. This conserved sequence is found associated with pfam00515 in several paralogous proteins in Rhodopirellula baltica. It is also found associated with pfam01839 in several eukaryotic integrin-like proteins (e.g. human ASPIC) and in several other bacterial proteins. 66 matched cddid_all.tbl CDD pfam07595 pfam07595 284918 Planc_extracel Planctomycete extracellular. This motif is conserved as the N terminus of several Rhodopirellula baltica proteins predicted to be extracellular. 24 matched cddid_all.tbl CDD pfam07596 pfam07596 284919 SBP_bac_10 Protein of unknown function (DUF1559). A large family of paralogous proteins apparently unique to planctomycetes. 268 matched cddid_all.tbl CDD pfam07598 pfam07598 284921 DUF1561 Protein of unknown function (DUF1561). A family of paralogous proteins in Leptospira interrogans. 625 matched cddid_all.tbl CDD pfam07599 pfam07599 203693 DUF1563 Protein of unknown function (DUF1563). A small family of short hypothetical proteins in Leptospira interrogans. 43 matched cddid_all.tbl CDD pfam07600 pfam07600 284922 DUF1564 Protein of unknown function (DUF1564). A family of paralogous proteins in Leptospira interrogans. Several have been annotated as possible CopG-like transcriptional regulators (see pfam01402). 167 matched cddid_all.tbl CDD pfam07602 pfam07602 284923 DUF1565 Protein of unknown function (DUF1565). These proteins share a region of homology in their N termini, and are found in several phylogenetically diverse bacteria and in the archaeon Methanosarcina acetivorans. Some of these proteins also contain characterized domains such as pfam00395 and pfam03422. 256 matched cddid_all.tbl CDD pfam07603 pfam07603 429556 DUF1566 Protein of unknown function (DUF1566). These proteins of unknown function are found in Leptospira interrogans and in several gamma proteobacteria. 117 matched cddid_all.tbl CDD pfam07606 pfam07606 429557 DUF1569 Protein of unknown function (DUF1569). A family of hypothetical proteins identified in Rhodopirellula baltica. 152 matched cddid_all.tbl CDD pfam07607 pfam07607 284926 DUF1570 Protein of unknown function (DUF1570). A family of hypothetical proteins in Rhodopirellula baltica. This family carries a highly conserved HExxH sequence motif characteriztic of members of the Peptidase clan MA. 129 matched cddid_all.tbl CDD pfam07608 pfam07608 400124 DUF1571 Protein of unknown function (DUF1571). A family of paralogous proteins in Rhodopirellula baltica. 208 matched cddid_all.tbl CDD pfam07609 pfam07609 429558 DUF1572 Protein of unknown function (DUF1572). These proteins, from several diverse bacteria, share a short conserved sequence towards their N termini. 163 matched cddid_all.tbl CDD pfam07610 pfam07610 429559 DUF1573 Protein of unknown function (DUF1573). These hypothetical proteins, from bacteria such as Rhodopirellula baltica, Bacteroides thetaiotaomicron, and Porphyromonas gingivalis, share a region of conserved sequence towards their N-termini. 98 matched cddid_all.tbl CDD pfam07611 pfam07611 369442 DUF1574 Protein of unknown function (DUF1574). A family of hypothetical proteins in Leptospira interrogans. 342 matched cddid_all.tbl CDD pfam07613 pfam07613 429560 DUF1576 Protein of unknown function (DUF1576). This small family is found in several undescribed proteins. The alignment is distinguished by the frequent occurrence of conserved glycine and aromatic residues. 176 matched cddid_all.tbl CDD pfam07614 pfam07614 369443 DUF1577 Protein of unknown function (DUF1577). A family of hypothetical proteins in Leptospira interrogans. 256 matched cddid_all.tbl CDD pfam07615 pfam07615 400128 Ykof YKOF-related Family. 81 matched cddid_all.tbl CDD pfam07617 pfam07617 429561 DUF1579 Protein of unknown function (DUF1579). A family of paralogous hypothetical proteins identified in Rhodopirellula baltica that also has members in Gloeobacter violaceus, Sinorhizobium meliloti and Agrobacterium tumefaciens. 155 matched cddid_all.tbl CDD pfam07618 pfam07618 284935 DUF1580 Protein of unknown function (DUF1580). A family of short hypothetical proteins found in Rhodopirellula baltica. 57 matched cddid_all.tbl CDD pfam07619 pfam07619 284936 DUF1581 Protein of unknown function (DUF1581). Several Rhodopirellula baltica proteins share this probable domain. Most of these proteins are predicted to be secreted or membrane-associated. 84 matched cddid_all.tbl CDD pfam07621 pfam07621 284937 DUF1582 Protein of unknown function (DUF1582). A family of hypothetical proteins in Rhodopirellula baltica. 29 matched cddid_all.tbl CDD pfam07622 pfam07622 462218 DUF1583 Protein of unknown function (DUF1583) C domain. Most of these Rhodopirellula baltica hypothetical proteins also match pfam07619. 256 matched cddid_all.tbl CDD pfam07624 pfam07624 429562 PSD2 Protein of unknown function (DUF1585). A conserved sequence region at the C terminus of several cytochrome-like proteins in Rhodopirellula baltica. 74 matched cddid_all.tbl CDD pfam07626 pfam07626 429563 PSD3 Protein of unknown function (DUF1587). A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also match pfam07624. 65 matched cddid_all.tbl CDD pfam07627 pfam07627 429564 PSCyt3 Protein of unknown function (DUF1588). A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also match pfam07626 and pfam07624. 98 matched cddid_all.tbl CDD pfam07628 pfam07628 284944 DUF1589 Protein of unknown function (DUF1589). A family of short hypothetical proteins in Rhodopirellula baltica. 164 matched cddid_all.tbl CDD pfam07631 pfam07631 429565 PSD4 Protein of unknown function (DUF1592). A region of similarity shared by several Rhodopirellula baltica cytochrome-like proteins that are predicted to be secreted. These proteins also match pfam07627, pfam07626, and pfam07624. 128 matched cddid_all.tbl CDD pfam07632 pfam07632 462219 DUF1593 Protein of unknown function (DUF1593). A family of proteins in Rhodopirellula baltica that are predicted to be secreted. Also, a member has been identified in Caulobacter crescentus. These proteins mat be related to pfam01156. 261 matched cddid_all.tbl CDD pfam07634 pfam07634 429567 RtxA RtxA repeat. This short repeat is found in the RtxA toxin family. 18 matched cddid_all.tbl CDD pfam07635 pfam07635 429568 PSCyt1 Planctomycete cytochrome C. These proteins share a region of homology at their N-terminus that contains the C-{CPWHF}-{CPWR}-C-H-{CFYW} motif typical of cytochromes C, or CxxCH. 59 matched cddid_all.tbl CDD pfam07636 pfam07636 148958 PSRT PSRT. This motif is found at the N terminus of several short hypothetical proteins in Rhodopirellula baltica and the predicted Arylsulfatase B (EC:3.1.6.12). 32 matched cddid_all.tbl CDD pfam07637 pfam07637 429569 PSD5 Protein of unknown function (DUF1595). A family of proteins in Rhodopirellula baltica, associated with pfam07635, pfam07626, pfam07631, pfam07627, and pfam07624. 62 matched cddid_all.tbl CDD pfam07638 pfam07638 254323 Sigma70_ECF ECF sigma factor. These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545. 185 matched cddid_all.tbl CDD pfam07639 pfam07639 377889 YTV YTV. These hypothetical proteins in Rhodopirellula baltica contain several repeats of a sequence whose core is the residues YTV. 40 matched cddid_all.tbl CDD pfam07642 pfam07642 429570 BBP2 Putative beta-barrel porin-2, OmpL-like. bbp2. BBP2 is a family of putative porin proteins that are likely to be outer membrane beta barrel proteins porins. 343 matched cddid_all.tbl CDD pfam07643 pfam07643 377890 DUF1598 Protein of unknown function (DUF1598). A family of Rhodopirellula baltica hypothetical proteins of about 500 amino acids in length. 84 matched cddid_all.tbl CDD pfam07645 pfam07645 429571 EGF_CA Calcium-binding EGF domain. 32 matched cddid_all.tbl CDD pfam07646 pfam07646 462220 Kelch_2 Kelch motif. The kelch motif was initially discovered in Kelch. In this protein there are six copies of the motif. It has been shown that Swiss:Q04652 is related to Galactose Oxidase for which a structure has been solved. The kelch motif forms a beta sheet. Several of these sheets associate to form a beta propeller structure as found in pfam00064, pfam00400 and pfam00415. 47 matched cddid_all.tbl CDD pfam07647 pfam07647 429573 SAM_2 SAM domain (Sterile alpha motif). 66 matched cddid_all.tbl CDD pfam07648 pfam07648 400135 Kazal_2 Kazal-type serine protease inhibitor domain. Usually indicative of serine protease inhibitors. However, kazal-like domains are also seen in the extracellular part of agrins, which are not known to be protease inhibitors. Kazal domains often occur in tandem arrays. Small alpha+beta fold containing three disulphides. 50 matched cddid_all.tbl CDD pfam07650 pfam07650 429574 KH_2 KH domain. 78 matched cddid_all.tbl CDD pfam07651 pfam07651 400137 ANTH ANTH domain. AP180 is an endocytotic accessory proteins that has been implicated in the formation of clathrin-coated pits. The domain is involved in phosphatidylinositol 4,5-bisphosphate binding and is a universal adaptor for nucleation of clathrin coats. 272 matched cddid_all.tbl CDD pfam07652 pfam07652 400138 Flavi_DEAD Flavivirus DEAD domain. 146 matched cddid_all.tbl CDD pfam07653 pfam07653 429575 SH3_2 Variant SH3 domain. SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organization. First described in the Src cytoplasmic tyrosine kinase. The structure is a partly opened beta barrel. 54 matched cddid_all.tbl CDD pfam07654 pfam07654 462221 C1-set Immunoglobulin C1-set domain. 85 matched cddid_all.tbl CDD pfam07655 pfam07655 429577 Secretin_N_2 Secretin N-terminal domain. This is a short domain found in bacterial type II/III secretory system proteins. The architecture of these proteins suggest that this family may be functionally analogous to pfam03958. 91 matched cddid_all.tbl CDD pfam07657 pfam07657 462222 MNNL N terminus of Notch ligand C2-like domain. This entry represents a region of conserved sequence at the N terminus of several Notch ligand proteins. The entry has been extended to correspond to the C2-like domain defined by the protein structure. 157 matched cddid_all.tbl CDD pfam07659 pfam07659 429579 DUF1599 Nucleotide modification associated domain 1. An alpha helical domain with conserved polar residues suggestive of enzymatic function. The domain is associated with the 5-hydroxymethyl uridine synthase and is predicted to play a role in modified base biosynthesis pathways. 61 matched cddid_all.tbl CDD pfam07660 pfam07660 429580 STN Secretin and TonB N terminus short domain. This is a short domain found at the N-terminus of the Secretins of the bacterial type II/III secretory system as well as the TonB-dependent receptor proteins. These proteins are involved in TonB-dependent active uptake of selective substrates. 51 matched cddid_all.tbl CDD pfam07661 pfam07661 429581 MORN_2 MORN repeat variant. This family represents an apparent variant of the pfam02493 repeat (personal obs:C Yeats). 22 matched cddid_all.tbl CDD pfam07662 pfam07662 462223 Nucleos_tra2_C Na+ dependent nucleoside transporter C-terminus. This family consists of nucleoside transport proteins. Swiss:Q62773 is a purine-specific Na+-nucleoside cotransporter localized to the bile canalicular membrane. Swiss:Q62674 is a a Na+-dependent nucleoside transporter selective for pyrimidine nucleosides and adenosine it also transports the anti-viral nucleoside analogues AZT and ddC. This alignment covers the C-terminus of this family of transporters. 205 matched cddid_all.tbl CDD pfam07663 pfam07663 429583 EIIBC-GUT_C Sorbitol phosphotransferase enzyme II C-terminus. 92 matched cddid_all.tbl CDD pfam07664 pfam07664 462224 FeoB_C Ferrous iron transport protein B C terminus. Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system. FeoB is a large 700-800 amino acid integral membrane protein. The N-terminus has been previously erroneously described as being ATP-binding. Recent work shows that it is similar to eukaryotic G-proteins and that it is a GTPase. 51 matched cddid_all.tbl CDD pfam07666 pfam07666 429585 MpPF26 M penetrans paralogue family 26. These proteins include those ascribed to M penetrans paralogue family 26 in. This family contains a region of transmembrane helices. 75 matched cddid_all.tbl CDD pfam07667 pfam07667 284973 DUF1600 Protein of unknown function (DUF1600). These proteins appear to be specific to Mycoplasma species. 109 matched cddid_all.tbl CDD pfam07668 pfam07668 284974 MpPF1 M penetrans paralogue family 1. This family of paralogous proteins identified in Mycoplasma penetrans includes homologs of p35. 313 matched cddid_all.tbl CDD pfam07669 pfam07669 369456 Eco57I Eco57I restriction-modification methylase. homologs of the Escherichia coli Eco57I restriction-modification methylase are found in several phylogenetically diverse bacteria. The structure of TaqI has been solved. 104 matched cddid_all.tbl CDD pfam07670 pfam07670 429586 Gate Nucleoside recognition. This region in the nucleoside transporter proteins are responsible for determining nucleoside specificity in the human CNT1 and CNT2 proteins. In the FeoB proteins, which are believed to be Fe2+ transporters, it includes the membrane pore region, so the function of this region is likely to be more general than just nucleoside specificity. This family may represent the pore and gate, with a wide potential range of specificity. Hence its name 'Gate'. 101 matched cddid_all.tbl CDD pfam07671 pfam07671 400147 DUF1601 Protein of unknown function (DUF1601). This repeat is found in a small number of proteins and is apparently limited to Coxiella and related species. 37 matched cddid_all.tbl CDD pfam07672 pfam07672 462225 MFS_Mycoplasma Mycoplasma MFS transporter. These proteins share some similarity with members of the Major Facilitator Superfamily (MFS). 297 matched cddid_all.tbl CDD pfam07675 pfam07675 284979 Cleaved_Adhesin Cleaved Adhesin Domain. This is a family of bacterial protein modules thought to function in various roles including cell adhesion, cell lysis and carbohydrate binding. A tandem repeat of these modules (either two or three repeats) constitute the haemagglutinin/adhesin (HA) regions of the gingipains, RgpA and Kgp, expressed by Porphyromonas gingivalis (Bacteroides gingivalis). They form components of the major extracellular virulence complex RgpA-Kgp - a mixture of proteinases and adhesin domains. The adhesin domains in this complex are found in proteinase-cleaved forms when isolated from the cell surface. Haemagglutinin genes of P. gingivalis (hagA1 HAGA1_PORGI - and hagA2 HAGA2_PORGI) suggest that such proteins are composed of eight to ten tandem repeats of these adhesin modules. Genomic data predicts that homologous protein modules are also expressed by a number of other bacteria and form part of putative multi-domain proteins, eg. Swiss:Q26BR9 and Swiss:B0VGL6. These domains may be acting in concert with other adhesion modules thought to be part of these multi-domain proteins such as fibronectin type III, pfam00041, and Meprin, A5, mu (MAM), pfam00629, domains. 166 matched cddid_all.tbl CDD pfam07676 pfam07676 429587 PD40 WD40-like Beta Propeller Repeat. This family appears to be related to the pfam00400 repeat. This repeat corresponds to the RIVW repeat identified in cell surface proteins [Adindla et al. Comparative and Functional Genomics 2004; 5:2-16]. 37 matched cddid_all.tbl CDD pfam07677 pfam07677 462226 A2M_recep A-macroglobulin receptor binding domain. This family includes the receptor binding domain region of the alpha-2-macroglobulin family. 92 matched cddid_all.tbl CDD pfam07678 pfam07678 462227 TED_complement A-macroglobulin TED domain. This entry corresponds to the TED domain of the complement components such as C3, C4 and C5. This domain contains a short highly conserved region of proteinase-binding alpha-macro-globulins contains the cysteine and a glutamine of a thiol-ester bond that is cleaved at the moment of proteinase binding, and mediates the covalent binding of the alpha-macro-globulin to the proteinase. The GCGEQ motif is highly conserved. 311 matched cddid_all.tbl CDD pfam07679 pfam07679 400151 I-set Immunoglobulin I-set domain. 90 matched cddid_all.tbl CDD pfam07680 pfam07680 429590 DoxA TQO small subunit DoxA. Thiosulphate:quinone oxidoreductase (TQO) is one of the early steps in elemental sulphur oxidation. A novel TQO enzyme was purified from the thermo-acidophilic archaeon Acidianus ambivalens and shown to consist of a large subunit (DoxD) and a smaller subunit (DoxA). The DoxD- and DoxA-like two subunits are fused together in a single polypeptide in Swiss:Q8AAF0. 131 matched cddid_all.tbl CDD pfam07681 pfam07681 429591 DoxX DoxX. These proteins appear to have some sequence similarity with pfam04173 but their function is unknown. 84 matched cddid_all.tbl CDD pfam07682 pfam07682 429592 SOR Sulphur oxygenase reductase. The sulphur oxygenase/reductase (SOR) of the thermo-acidophilic archaeon Acidianus ambivalens is an unusual enzyme consisting of 24 identical subunits arranged in a perfectly symmetrical hollow sphere and containing a mononuclear non-heme iron centre (personal communication: A. Kletzin). At 85 degrees C in vitro, elemental sulphur is oxidized to sulphite, thiosulphate and hydrogen sulphide with no external cofactors needed. The proposed equation is: 4S + O2 + 4 H2O ---> 2 HSO3- + 2 H2S + 2 H+. 302 matched cddid_all.tbl CDD pfam07683 pfam07683 462228 CobW_C Cobalamin synthesis protein cobW C-terminal domain. This is a large and diverse family of putative metal chaperones that can be separated into up to 15 subgroups. In addition to known roles in cobalamin biosynthesis and the activation of the Fe-type nitrile hydratase, this family is also known to be involved in the response to zinc limitation. The CobW subgroup involved in cobalamin synthesis represents only a small sub-fraction of the family. 93 matched cddid_all.tbl CDD pfam07684 pfam07684 462229 NODP NOTCH protein. NOTCH signalling plays a fundamental role during a great number of developmental processes in multicellular animals. NOD and NODP represent a region present in many NOTCH proteins and NOTCH homologs in multiple species such as NOTCH2 and NOTCH3, LIN12, SC1 and TAN1. The role of the NOD and NODP domains remains to be elucidated. 59 matched cddid_all.tbl CDD pfam07685 pfam07685 429595 GATase_3 CobB/CobQ-like glutamine amidotransferase domain. 189 matched cddid_all.tbl CDD pfam07686 pfam07686 462230 V-set Immunoglobulin V-set domain. This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others. 109 matched cddid_all.tbl CDD pfam07687 pfam07687 400158 M20_dimer Peptidase dimerization domain. This domain consists of 4 beta strands and two alpha helices which make up the dimerization surface of members of the M20 family of peptidases. This family includes a range of zinc metallopeptidases belonging to several families in the peptidase classification. Family M20 are Glutamate carboxypeptidases. Peptidase family M25 contains X-His dipeptidases. 107 matched cddid_all.tbl CDD pfam07688 pfam07688 429597 KaiA KaiA C-terminal domain. The cyanobacterial clock proteins KaiA and KaiB are proposed as regulators of the circadian rhythm in cyanobacteria. The overall fold of the KaiA C-terminal domain is that of a four-helix bundle, which forms a dimer in the known structure. 122 matched cddid_all.tbl CDD pfam07689 pfam07689 400160 KaiB KaiB domain. The cyanobacterial clock proteins KaiA and KaiB are proposed as regulators of the circadian rhythm in cyanobacteria. Mutations in both proteins have been reported to alter or abolish circadian rhythmicity. KaiB adopts an alpha-beta meander motif and is found to be a dimer. 82 matched cddid_all.tbl CDD pfam07690 pfam07690 429598 MFS_1 Major Facilitator Superfamily. 344 matched cddid_all.tbl CDD pfam07691 pfam07691 400161 PA14 PA14 domain. This domain forms an insert in bacterial beta-glucosidases and is found in other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins, including anthrax protective antigen (PA). The domain also occurs in a Dictyostelium prespore-cell-inducing factor Psi and in fibrocystin, the mammalian protein whose mutation leads to polycystic kidney and hepatic disease. The crystal structure of PA shows that this domain (named PA14 after its location in the PA20 pro-peptide) has a beta-barrel structure. The PA14 domain sequence suggests a binding function, rather than a catalytic role. The PA14 domain distribution is compatible with carbohydrate binding. 141 matched cddid_all.tbl CDD pfam07692 pfam07692 254362 Fea1 Low iron-inducible periplasmic protein. In Chlamydomonas reinhardtii, the gene encoding Swiss:Q9LD42 is induced by iron deficiency. In green algae, this protein is periplasmic. The two paralogues FEA1 and FEA2 are the major proteins secreted by iron-deficient Chlamydomonas reinhardtii, and both are up-regulated in response to iron deficiency. FEA1 but not FEA2 is up-regulated by high CO2 concentration. Both FEA1 and FEA2 are secreted into the periplasmic space and genetic evidence confirms that their association with the cell is required for growth in low iron. 359 matched cddid_all.tbl CDD pfam07693 pfam07693 462231 KAP_NTPase KAP family P-loop domain. The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side. 293 matched cddid_all.tbl CDD pfam07694 pfam07694 429599 5TM-5TMR_LYT 5TMR of 5TMR-LYT. This entry represents the transmembrane region of the 5TM-LYT (5TM Receptors of the LytS-YhcK type). 170 matched cddid_all.tbl CDD pfam07695 pfam07695 429600 7TMR-DISM_7TM 7TM diverse intracellular signalling. This entry represents the transmembrane region of the 7TM-DISM (7TM Receptors with Diverse Intracellular Signalling Modules). 207 matched cddid_all.tbl CDD pfam07696 pfam07696 429601 7TMR-DISMED2 7TMR-DISM extracellular 2. This entry represents one of two distinct types of extracellular domain found in the 7TM-DISM (7TM Receptors with Diverse Intracellular Signalling Modules) bacterial transmembrane proteins. It is possible that this domain adopts a jelly roll fold and acts as a receptor for carbohydrates and their derivatives. It can also recognize Ca(II) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 127 matched cddid_all.tbl CDD pfam07697 pfam07697 462232 7TMR-HDED 7TM-HD extracellular. This entry represents the extracellular domain of the 7TM-HD (7TM Receptors with HD hydrolase). 219 matched cddid_all.tbl CDD pfam07698 pfam07698 429603 7TM-7TMR_HD 7TM receptor with intracellular HD hydrolase. These bacterial 7TM receptor proteins have an intracellular pfam01966. This entry corresponds to the 7 helix transmembrane domain. These proteins also contain an N-terminal extracellular domain. 190 matched cddid_all.tbl CDD pfam07699 pfam07699 429604 Ephrin_rec_like Tyrosine-protein kinase ephrin type A/B receptor-like. This family has repeats of a region rich in cysteines. It is found in various ephrin type A and B receptors, which have tyrosine kinase activity. 48 matched cddid_all.tbl CDD pfam07700 pfam07700 462233 HNOB Haem-NO-binding. The HNOB (Haem NO Binding) domain, is a predominantly alpha-helical domain and binds heme via a covalent linkage to histidine. It is a haem protein sensor (SONO) that displays femtomolar affinity for nitrous oxide, NO. It is predicted to function as a haem-dependent sensor for gaseous ligands and to transduce diverse downstream signals in both bacteria and animals. 162 matched cddid_all.tbl CDD pfam07701 pfam07701 462234 HNOBA Heme NO binding associated. The HNOBA domain is found associated with the HNOB domain and pfam00211 in soluble cyclases and signalling proteins. The HNOB domain is predicted to function as a heme-dependent sensor for gaseous ligands, and transduce diverse downstream signals, in both bacteria and animals. 214 matched cddid_all.tbl CDD pfam07702 pfam07702 429607 UTRA UTRA domain. The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain that has a similar fold to pfam04345. It is believed to modulate activity of bacterial transcription factors in response to binding small molecules sugar phosphates and urocanate, Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 141 matched cddid_all.tbl CDD pfam07703 pfam07703 462235 A2M_BRD Alpha-2-macroglobulin bait region domain. Alpha-2-macroglobulins (A2Ms) are plasma proteins that trap and inhibit a broad range of proteases and are major components of the eukaryotic innate immune system. However, A2M-like proteins were identified in pathogenically invasive bacteria and species that colonize higher eukaryotes. This domain is found in eukaryotic and bacterial proteins. In human A2Ms, this domain encompasses macroglobulin-like domain MG5 and 6 including bait region. In Salmonella enterica ser A2Ms, this domain encompasses MG7 and MG8 including the bait region. The Bait region is cleaved by proteases, followed by a large conformational change that blocks the target protease within a cage-like complex. This model of protease entrapment is recognized as the Venus flytrap mechanism. 139 matched cddid_all.tbl CDD pfam07704 pfam07704 429609 PSK_trans_fac Rv0623-like transcription factor. This entry represents the Rv0623-like family of transcription factors associated with the PSK operon. 82 matched cddid_all.tbl CDD pfam07705 pfam07705 400172 CARDB CARDB. Cell adhesion related domain found in bacteria. 101 matched cddid_all.tbl CDD pfam07706 pfam07706 462236 TAT_ubiq Aminotransferase ubiquitination site. This segment contains a probable site of ubiquitination that ensures rapid degradation of tyrosine aminotransferase in rats. The half life of the enzyme in vivo is about 2-4 hours. In addition, unpublished information identifies at least 2 phosphorylation sites including CAPK at Ser29 and, at the other end of the protein, a casein kinase II site at S*QEECDK. This region of TAT is probably primarily related to regulatory events. Most other transaminases are much more stable and are not phosphorylated. 40 matched cddid_all.tbl CDD pfam07707 pfam07707 462237 BACK BTB And C-terminal Kelch. This domain is found associated with pfam00651 and pfam01344. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. This family appears to be closely related to the BTB domain (Finn RD, personal observation). 103 matched cddid_all.tbl CDD pfam07708 pfam07708 285010 Tash_PEST Tash protein PEST motif. This motif is found in the Tash AT-hook proteins of Theileria annulata. These proteins are transported to the hosts nucleus and are likely to be involved in pathogenesis. It is also often found in conjunction with pfam04385. It is suggested that they may be 'part of PEST motifs' (a signal for rapid proteolytic degradation) in, though this is not definite. This motif is also found in other T. annulata proteins, which have no other known domains in (unpublished data: C Yeats). 18 matched cddid_all.tbl CDD pfam07709 pfam07709 116323 SRR Seven Residue Repeat. Associated with pfam02969 in This repeat is found in some Plasmodium and Theileria proteins. 14 matched cddid_all.tbl CDD pfam07710 pfam07710 462238 P53_tetramer P53 tetramerization motif. 42 matched cddid_all.tbl CDD pfam07711 pfam07711 462239 RabGGT_insert Rab geranylgeranyl transferase alpha-subunit, insert domain. Rab geranylgeranyl transferase (RabGGT) catalyzes the addition of two geranylgeranyl groups to the C-terminal cysteine residues of Rab proteins, which is crucial for membrane association and function of these proteins in intracellular vesicular trafficking. This domain is inserted between pfam01239 repeats. This domain adopts an Ig-like fold and is thought to be involved in protein-protein interactions and might be involved in the recognition and binding of REP. 101 matched cddid_all.tbl CDD pfam07712 pfam07712 462240 SURNod19 Stress up-regulated Nod 19. 377 matched cddid_all.tbl CDD pfam07713 pfam07713 462241 DUF1604 Protein of unknown function (DUF1604). This family is found at the N-terminus of several eukaryotic RNA processing proteins. 84 matched cddid_all.tbl CDD pfam07714 pfam07714 462242 PK_Tyr_Ser-Thr Protein tyrosine and serine/threonine kinase. Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyze the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyze the reverse process. Protein kinases fall into three broad classes, characterized with respect to substrate specificity; Serine/threonine-protein kinases, tyrosine-protein kinases, and dual specificity protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins). This entry represents the catalytic domain found in a number of serine/threonine- and tyrosine-protein kinases. It does not include the catalytic domain of dual specificity kinases. 258 matched cddid_all.tbl CDD pfam07715 pfam07715 462243 Plug TonB-dependent Receptor Plug Domain. The Plug domain has been shown to be an independently folding subunit of the TonB-dependent receptors. It acts as the channel gate, blocking the pore until the channel is bound by ligand. At this point it under goes conformational changes opens the channel. 107 matched cddid_all.tbl CDD pfam07716 pfam07716 462244 bZIP_2 Basic region leucine zipper. 51 matched cddid_all.tbl CDD pfam07717 pfam07717 400182 OB_NTP_bind Oligonucleotide/oligosaccharide-binding (OB)-fold. This family is found towards the C-terminus of the DEAD-box helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. There do seem to be a couple of instances where it occurs by itself -. The structure PDB:3i4u adopts an OB-fold. helicases (pfam00270). In these helicases it is apparently always found in association with pfam04408. This C-terminal domain of the yeast helicase contains an oligonucleotide/oligosaccharide-binding (OB)-fold which seems to be placed at the entrance of the putative nucleic acid cavity. It also constitutes the binding site for the G-patch-containing domain of Pfa1p. When found on DEAH/RHA helicases, this domain is central to the regulation of the helicase activity through its binding of both RNA and G-patch domain proteins. 82 matched cddid_all.tbl CDD pfam07718 pfam07718 462245 Coatamer_beta_C Coatomer beta C-terminal region. This family is found at the C-terminus of the coatamer beta subunit proteins (Beta-coat proteins). This C-terminal domain probably adapts the function of the N-terminal pfam01602 domain. 138 matched cddid_all.tbl CDD pfam07719 pfam07719 429619 TPR_2 Tetratricopeptide repeat. This Pfam entry includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by pfam00515. 33 matched cddid_all.tbl CDD pfam07720 pfam07720 400185 TPR_3 Tetratricopeptide repeat. This Pfam entry includes tetratricopeptide-like repeats found in the LcrH/SycD-like chaperones. 34 matched cddid_all.tbl CDD pfam07721 pfam07721 311590 TPR_4 Tetratricopeptide repeat. This Pfam entry includes tetratricopeptide-like repeats not detected by the pfam00515, pfam07719 and pfam07720 models. 26 matched cddid_all.tbl CDD pfam07722 pfam07722 429620 Peptidase_C26 Peptidase C26. These peptidases have gamma-glutamyl hydrolase activity; that is they catalyze the cleavage of the gamma-glutamyl bond in poly-gamma-glutamyl substrates. They are structurally related to pfam00117, but contain extensions in four loops and at the C terminus. 219 matched cddid_all.tbl CDD pfam07723 pfam07723 336782 LRR_2 Leucine Rich Repeat. This Pfam entry includes some LRRs that fail to be detected with the pfam00560 model. 26 matched cddid_all.tbl CDD pfam07724 pfam07724 400187 AAA_2 AAA domain (Cdc48 subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. 168 matched cddid_all.tbl CDD pfam07725 pfam07725 429621 LRR_3 Leucine Rich Repeat. This Pfam entry includes some LRRs that fail to be detected by the pfam00560 model. 20 matched cddid_all.tbl CDD pfam07726 pfam07726 429622 AAA_3 ATPase family associated with various cellular activities (AAA). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. 131 matched cddid_all.tbl CDD pfam07727 pfam07727 400190 RVT_2 Reverse transcriptase (RNA-dependent DNA polymerase). A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. This Pfam entry includes reverse transcriptases not recognized by the pfam00078 model. 243 matched cddid_all.tbl CDD pfam07728 pfam07728 400191 AAA_5 AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model. 135 matched cddid_all.tbl CDD pfam07729 pfam07729 429623 FCD FCD domain. This domain is the C-terminal ligand binding domain of many members of the GntR family. This domain binds to a range of effector molecules, including Lactate, Zn(II), Ni(II), Ca(II), Mg(II), citrate, sugar acids, sialic acid and N-acetylglucosamine-6-P, that regulate the transcription of genes through the action of the N-terminal DNA-binding domain pfam00392 (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). This domain is found in Swiss:P45427 and Swiss:P31460 that are regulators of sugar biosynthesis operons. It is also in the known structure of FadR where it binds to acyl-coA, the domain is alpha helical. This family has been named as FCD for (FadR C-terminal Domain). 121 matched cddid_all.tbl CDD pfam07730 pfam07730 429624 HisKA_3 Histidine kinase. This is the dimerization and phosphoacceptor domain of a sub-family of histidine kinases. It shares sequence similarity with pfam00512 and pfam07536. 68 matched cddid_all.tbl CDD pfam07731 pfam07731 462246 Cu-oxidase_2 Multicopper oxidase. This entry contains many divergent copper oxidase-like domains that are not recognized by the pfam00394 model. 138 matched cddid_all.tbl CDD pfam07732 pfam07732 462247 Cu-oxidase_3 Multicopper oxidase. This entry contains many divergent copper oxidase-like domains that are not recognized by the pfam00394 model. 119 matched cddid_all.tbl CDD pfam07733 pfam07733 400196 DNA_pol3_alpha Bacterial DNA polymerase III alpha NTPase domain. 259 matched cddid_all.tbl CDD pfam07734 pfam07734 254394 FBA_1 F-box associated. Most of these proteins contain pfam00646 at the N terminus, suggesting that they are effectors linked with ubiquitination. 159 matched cddid_all.tbl CDD pfam07735 pfam07735 429626 FBA_2 F-box associated. Most of these proteins contain pfam00646 at the N terminus, suggesting that they are effectors linked with ubiquitination. 67 matched cddid_all.tbl CDD pfam07736 pfam07736 429627 CM_1 Chorismate mutase type I. Chorismate mutase (CM) EC:5.4.99.5 catalyzes the the conversion of chorismate to prephenate in the shikimate pathway of tyrosine and phenylalanine biosynthesis in bacteria, fungi and plants. The three types of CM are AroH class, AroQ class, prokaryotic type and AroQ class, eukaryotic type. Structurally CMs can be divided into two main groups: type I (AroH) class and type II (AroQ). Type I (AroH) CMs include CMs characterized by a trimeric pseudo alpha/beta barrel structure. The two types of the AroQ structural class (the Escherichia coli CM dimer and the yeast CM monomer) can be structurally superimposed, and the topology of the four-helix bundle forming the active site is conserved. CMs can be monofunctional or bifunctional (generally fused to another shikimate pathway member). Despite the structural differences, all CMs perform the same basic reaction. This entry represents chorismate mutases of the AroH class predominantly from Terrabacteria. 115 matched cddid_all.tbl CDD pfam07737 pfam07737 285037 ATLF Anthrax toxin lethal factor, N- and C-terminal domain. The C-terminal domain is the catalytically active domain whereas the N-terminal domain is likely to be inactive. 218 matched cddid_all.tbl CDD pfam07738 pfam07738 400199 Sad1_UNC Sad1 / UNC-like C-terminal. The C. elegans UNC-84 protein is a nuclear envelope protein that is involved in nuclear anchoring and migration during development. The S. pombe Sad1 protein localizes at the spindle pole body. UNC-84 and and Sad1 share a common C-terminal region, that is often termed the SUN (Sad1 and UNC) domain. In mammals, the SUN domain is present in two proteins, Sun1 and Sun2. The SUN domain of Sun2 has been demonstrated to be in the periplasm. 130 matched cddid_all.tbl CDD pfam07739 pfam07739 462248 TipAS TipAS antibiotic-recognition domain. This domain is found at the C-terminus of some MerR family transcription factors. The domain has an alpha-helical globin-like fold. The family includes Mta a central regulator of multidrug resistance in Bacillus subtilis. 117 matched cddid_all.tbl CDD pfam07740 pfam07740 462249 Toxin_12 Ion channel inhibitory toxin. This is a family of potent toxins that function as ion-channel inhibitors for several different ions. Omega-Grammotoxin SIA is a VSCC antagonist that inhibits neuronal N- and P-type VSCC responses. Huwentoxin-IV, from the Chinese bird spider, is a highly potent neurotoxin that specifically inhibits the neuronal tetrodotoxin-sensitive voltage-gated sodium channel in rat dorsal root ganglion neurons. Hainantoxin-4, from the venom of spider Selenocosmia hainana, adopts an inhibitor cystine knot structural motif like huwentoin-IV, and is a potent antagonist that acts at site 1 on tetrodotoxin-sensitive (TTX-S) sodium channels. Study of the molecular nature of toxin-receptor interactions has helped elucidate the functioning of many ion-channels. 29 matched cddid_all.tbl CDD pfam07741 pfam07741 462250 BRF1 Brf1-like TBP-binding domain. In budding yeasts, Brf1 forms the TFIIIB complex with TATA-binding protein (TBP) and Bdp1. The TFIIIB complex can be recruited to the Pol III promoters and form an exceptionally kinetically stable TFIIIB-DNA complex, which then recruits the Pol III enzymatic complex and helps maintain it for multiple transcription cycles in a process called facilitated recycling. This entry represents the TATA binding protein (TBP) binding domain of Brf1 that covers both the Brf homology II and III regions. 98 matched cddid_all.tbl CDD pfam07742 pfam07742 462251 BTG BTG family. 117 matched cddid_all.tbl CDD pfam07743 pfam07743 462252 HSCB_C HSCB C-terminal oligomerization domain. This domain is the HSCB C-terminal oligomerization domain and is found on co-chaperone proteins. 75 matched cddid_all.tbl CDD pfam07744 pfam07744 400205 SPOC SPOC domain. The SPOC (Spen paralogue and orthologue C-terminal) domain is involved in developmental signalling. 142 matched cddid_all.tbl CDD pfam07745 pfam07745 311610 Glyco_hydro_53 Glycosyl hydrolase family 53. This domain belongs to family 53 of the glycosyl hydrolase classification. These enzymes are enzymes are endo-1,4- beta-galactanases (EC:3.2.1.89). The structure of this domain is known and has a TIM barrel fold. 333 matched cddid_all.tbl CDD pfam07746 pfam07746 429632 LigA Aromatic-ring-opening dioxygenase LigAB, LigA subunit. This is a family of aromatic ring opening dioxygenases which catalyze the ring-opening reaction of protocatechuate and related compounds. 87 matched cddid_all.tbl CDD pfam07747 pfam07747 429633 MTH865 MTH865-like family. This domain has an EF-hand like fold. 70 matched cddid_all.tbl CDD pfam07748 pfam07748 400208 Glyco_hydro_38C Glycosyl hydrolases family 38 C-terminal domain. Glycosyl hydrolases are key enzymes of carbohydrate metabolism. 204 matched cddid_all.tbl CDD pfam07749 pfam07749 462253 ERp29 Endoplasmic reticulum protein ERp29, C-terminal domain. ERp29 is a ubiquitously expressed endoplasmic reticulum protein found in mammals. ERp29 is comprised of two domains. This domain, the C-terminal domain, has an all helical fold. ERp29 is thought to form part of the thyroglobulin folding complex. 95 matched cddid_all.tbl CDD pfam07750 pfam07750 400210 GcrA GcrA cell cycle regulator. GcrA is a master cell cycle regulator that, together with CtrA (see pfam00072 and pfam00486), is involved in controlling cell cycle progression and asymmetric polar morphogenesis. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery. 155 matched cddid_all.tbl CDD pfam07751 pfam07751 462254 Abi_2 Abi-like protein. This family, found in various bacterial species, contains sequences that are similar to the Abi group of proteins, which are involved in bacteriophage resistance mediated by abortive infection in Lactococcus species. The proteins are thought to have helix-turn-helix motifs, found in many DNA-binding proteins, allowing them to perform their function. 183 matched cddid_all.tbl CDD pfam07752 pfam07752 429636 S-layer S-layer protein. Archaeal S-layer proteins consist of two copies of this domain. 259 matched cddid_all.tbl CDD pfam07753 pfam07753 285051 DUF1609 Protein of unknown function (DUF1609). This region is found in a number of hypothetical proteins thought to be expressed by the eukaryote Encephalitozoon cuniculi, an obligate intracellular microsporidial parasite. It is approximately 200 residues long. 227 matched cddid_all.tbl CDD pfam07754 pfam07754 429637 HVO_2753_ZBP Small zinc finger protein HVO_2753-like, Zn-binding pocket. This domain is found in many archaeal proteins, including HVO_2753 (also known as Small CPxCG-related zinc finger protein) from Haloferax volcanii. NMR 3D structure analysis revealed the content of four C(P)XCG motifs, suggesting the presence of two zinc-binding pockets (ZBPs). However, only C(P)XCG motifs 2 and 4 (comprising Cys-32 to Cys-35 and Cys-50 to Cys-53) form a ZBP and binds one zinc atom, while C(P)XCG motifs 1 and 3 (comprising Cys-12 to Cys-15 and Cys-39 to Cys-42) form a four-Cys cluster that do not bind zinc. The four C(P)XCG motifs are critical for protein stability, folding and functionality. This domain can also be present in small zinc finger proteins from bacteria and eukaryotes. 46 matched cddid_all.tbl CDD pfam07755 pfam07755 429638 DUF1611 Domain of unknown function (DUF1611_C) P-loop domain. This region is found in a number of hypothetical bacterial and archaeal proteins. According to structure it has a P-loop structure. 198 matched cddid_all.tbl CDD pfam07756 pfam07756 429639 DUF1612 Protein of unknown function (DUF1612). This family includes sequences of largely unknown function but which share a number of features in common. They are expressed by bacterial species, and in many cases these bacteria are known to associate symbiotically with plants. Moreover, the majority are coded for by plasmids, which in many cases are known to confer on the organizm the ability to interact symbiotically with leguminous plants. An example of such a plasmid is NGR234, which encodes Y4CF, a protein of unknown function that is a member of this family. Other members of this family are expressed by organizms with a documented genomic similarity to plant symbionts. 127 matched cddid_all.tbl CDD pfam07757 pfam07757 462255 AdoMet_MTase Predicted AdoMet-dependent methyltransferase. Proteins in this family have been predicted to function as AdoMet-dependent methyltransferases. 115 matched cddid_all.tbl CDD pfam07758 pfam07758 429640 DUF1614 Protein of unknown function (DUF1614). This is a family of sequences coming from hypothetical proteins found in both bacterial and archaeal species. 170 matched cddid_all.tbl CDD pfam07759 pfam07759 429641 DUF1615 Protein of unknown function (DUF1615). This is a family of proteins of unknown function expressed by various bacterial species. Some members of this family are thought to be lipoproteins. Another member of this family is thought to be involved in photosynthesis. 320 matched cddid_all.tbl CDD pfam07760 pfam07760 429642 DUF1616 Protein of unknown function (DUF1616). This is a family of sequences from hypothetical archaeal proteins. The region in question is approximately 330 amino acid residues long. 301 matched cddid_all.tbl CDD pfam07761 pfam07761 429643 DUF1617 Protein of unknown function (DUF1617). This is a family of sequences from hypothetical bacterial and bacteriophage proteins. The region in question is approximately 150 residues long and is highly conserved throughout the family. 143 matched cddid_all.tbl CDD pfam07762 pfam07762 462256 DUF1618 Protein of unknown function (DUF1618). The members of this family are mainly hypothetical proteins expressed by Oryza sativa. 129 matched cddid_all.tbl CDD pfam07763 pfam07763 462257 FEZ FEZ-like protein. This is a family of eukaryotic proteins thought to be involved in axonal outgrowth and fasciculation. The N-terminal regions of these sequences are less conserved than the C-terminal regions, and are highly acidic. The C. elegans homolog, UNC-76, may play structural and signalling roles in the control of axonal extension and adhesion (particularly in the presence of adjacent neuronal cells) and these roles have also been postulated for other FEZ family proteins. Certain homologs have been definitively found to interact with the N-terminal variable region (V1) of PKC-zeta, and this interaction causes cytoplasmic translocation of the FEZ family protein in mammalian neuronal cells. The C-terminal region probably participates in the association with the regulatory domain of PKC-zeta. The members of this family are predicted to form coiled-coil structures, which may interact with members of the RhoA family of signalling proteins, but are not thought to contain other characteriztic protein motifs. Certain members of this family are expressed almost exclusively in the brain, whereas others (such as FEZ2) are expressed in other tissues, and are thought to perform similar but unknown functions in these tissues. 240 matched cddid_all.tbl CDD pfam07764 pfam07764 429646 Omega_Repress Omega Transcriptional Repressor. The omega transcriptional repressor regulates expression of involved in copy number control and stable maintenance of plasmids. The omega protein belongs to the structural superfamily of MetJ/Arc repressors featuring a ribbon-helix-helix DNA-binding motif with the beta-ribbon located in and recognising the major groove of operator DNA. 69 matched cddid_all.tbl CDD pfam07765 pfam07765 429647 KIP1 KIP1-like protein. This is a family of sequences found exclusively in plants. They are similar to kinase interacting protein 1 (KIP1), which has been found to interact with the kinase domain of PRK1, a receptor-like kinase. This particular region contains two coiled-coils, which are described as motifs involved in protein-protein interactions. It has also been suggested that the protein's coiled- coils allow it to dimerize in vivo. 74 matched cddid_all.tbl CDD pfam07766 pfam07766 462258 LETM1_RBD LETM1-like, RBD. Members of this entry are inner mitochondrial membrane proteins which play a role in potassium and hydrogen ion exchange. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans. This entry represents the ribosome-binding domain (RBD) of LETM1/MDM38 proteins. 229 matched cddid_all.tbl CDD pfam07767 pfam07767 462259 Nop53 Nop53 (60S ribosomal biogenesis). This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins. 353 matched cddid_all.tbl CDD pfam07768 pfam07768 285065 PVL_ORF50 PVL ORF-50-like family. This is a family of sequences found in both bacteria and bacteriophages. This region is approximately 130 residues long and in some cases is found as part of the PVL (Panton-Valentine leukocidin) group of genes, which encode a member of the leukocidin group of bacterial toxins that kill leukocytes by creation of pores in the cell membrane. PVL appears to be a virulence factor associated with a number of human diseases. 116 matched cddid_all.tbl CDD pfam07769 pfam07769 429650 PsiF_repeat psiF repeat. This region is approximately 35 residues long. It is found repeated in a number of putative phosphate starvation- inducible proteins expressed by various bacterial species. psiF is known to be an example of such phosphate starvation-inducible proteins. 34 matched cddid_all.tbl CDD pfam07771 pfam07771 369508 TSGP1 Tick salivary peptide group 1. This contains a group of peptides derived from a salivary gland cDNA library of the tick Ixodes scapularis. Also present are peptides from a related tick species, Ixodes ricinus. They are characterized by a putative signal peptide indicative of secretion and conserved cysteine residues. 120 matched cddid_all.tbl CDD pfam07773 pfam07773 462260 TCTN_DUF1619 Tectonic domain DUF1619. This is a conserved domain found in tectonic proteins (TCTN1/2/3) which contains a Cys rich N-terminal region. Although its function is currently unknown (this domain is also known as DUF1619), studies in TCTN2 suggest that it is indispensable for normal functions. These proteins form a complex required for hedgehog signalling transduction. 315 matched cddid_all.tbl CDD pfam07774 pfam07774 462261 EMC1_C ER membrane protein complex subunit 1, C-terminal. This is the C-terminal domain of ER membrane protein complex subunit 1. ER membrane protein complex subunit 1 is a component of the ER membrane protein complex (EMC, composed of EMC1, EMC2, EMC3, EMC4, EMC5 and EMC6). In Saccharomyces cerevisiae, the EMC seems to be required for efficient folding of proteins in the endoplasmic reticulum (ER). 214 matched cddid_all.tbl CDD pfam07775 pfam07775 285070 PaRep2b PaRep2b protein. This is a family of proteins, expressed in the crenarchaeon Pyrobaculum aerophilum, whose members are variable in length and level of conservation. The presence of numerous frameshifts and internal stop codons in multiple alignments are thought to indicate that most family members are no longer functional. 512 matched cddid_all.tbl CDD pfam07776 pfam07776 462262 zf-AD Zinc-finger associated domain (zf-AD). The zf-AD domain, also known as ZAD, forms an atypical treble-cleft-like zinc co-ordinating fold. The zf-AD domain is thought to be involved in mediating dimer formation, but does not bind to DNA. 75 matched cddid_all.tbl CDD pfam07777 pfam07777 400228 MFMR G-box binding protein MFMR. This region is found to the N-terminus of the pfam00170 transcription factor domain. It is between 150 and 200 amino acids in length. The N-terminal half is rather rich in proline residues and has been termed the PRD (proline rich domain), whereas the C-terminal half is more polar and has been called the MFMR (multifunctional mosaic region). It has been suggested that this family is composed of three sub-families called A, B and C, classified according to motif composition. It has been suggested that some of these motifs may be involved in mediating protein-protein interactions. The MFMR region contains a nuclear localization signal in bZIP opaque and GBF-2. The MFMR also contains a transregulatory activity in TAF-1. The MFMR in CPRF-2 contains cytoplasmic retention signals. 96 matched cddid_all.tbl CDD pfam07778 pfam07778 429654 CENP-I Mis6. Mis6 is an essential centromere connector protein acting during G1-S phase of the cell cycle. Mis6 is thought to be required for recruiting CENP-A, the centromere- specific histone H3 variant, an important event for centromere function and chromosome segregation during mitosis. 515 matched cddid_all.tbl CDD pfam07779 pfam07779 462263 Cas1_AcylT 10 TM Acyl Transferase domain found in Cas1p. Cas1p protein of Cryptococcus neoformans is required for the synthesis of O-acetylated glucuronoxylomannans, a consitutent of the capsule, and is critical for its virulence. The multi TM domain of the Cas1p was unified with the 10 TM Sugar Acyltransferase superfamily. This superfamily is comprised of members from the OatA, MdoC, OpgC, NolL and GumG families in addition to the Cas1p family. The Cas1p protein has a N terminal PC-Esterase domain with the opposing Acyl esterase activity. 483 matched cddid_all.tbl CDD pfam07780 pfam07780 462264 Spb1_C Spb1 C-terminal domain. This presumed domain is found at the C-terminus of a family of FtsJ-like methyltransferases. Members of this family are involved in 60S ribosomal biogenesis, for example Swiss:P25582. 209 matched cddid_all.tbl CDD pfam07781 pfam07781 369516 Reovirus_Mu2 Reovirus minor core protein Mu-2. This family represents the Reovirus core protein Mu-2. Mu-2 is a microtubule associated protein and is thought to play a key role in the formation and structural organization of reovirus inclusion bodies. 727 matched cddid_all.tbl CDD pfam07782 pfam07782 462265 DC_STAMP DC-STAMP-like protein. This is a family of sequences which are similar to a region of the dendritic cell-specific transmembrane protein (DC-STAMP). This is thought to be a novel receptor protein that shares no identity with other multimembrane-spanning proteins. It is thought to have seven putative transmembrane regions, two of which are found in the region featured in this family. DC-STAMP is also described as having potential N-linked glycosylation sites and a potential phosphorylation site for PKC, but these are not conserved throughout the family. 191 matched cddid_all.tbl CDD pfam07784 pfam07784 462266 DUF1622 Protein of unknown function (DUF1622). This is a family of 14 highly conserved sequences, from hypothetical proteins expressed by both bacterial and archaeal species. 77 matched cddid_all.tbl CDD pfam07785 pfam07785 400233 DUF1623 Protein of unknown function (DUF1623). The members of this family are all derived from relatively short hypothetical proteins thought to be expressed by various Nucleopolyhedroviruses. 90 matched cddid_all.tbl CDD pfam07786 pfam07786 377915 HGSNAT_cat Heparan-alpha-glucosaminide N-acetyltransferase, catalytic. This entry includes the catalytic domain of HGSNAT (Heparan-alpha-glucosaminide N-acetyltransferase). It contains the conserved histidine in the active site (His269), thought to hold the acetyl group during the transfer across the membrane and required for its enzymatic activity. HGSNAT transfers an acetyl group from cytoplasmically derived acetyl-CoA to terminal N-glucosamine residues of heparan sulfate within the lysosomes. 222 matched cddid_all.tbl CDD pfam07787 pfam07787 462267 TMEM43 Transmembrane protein 43. This entry represents the transmembrane protein 43 family of proteins, which may function as tetraspanin-like membrane organizers. 249 matched cddid_all.tbl CDD pfam07788 pfam07788 369519 PDDEXK_10 PD-(D/E)XK nuclease superfamily. This family is found to carry modified motifs characteriztic of PD-(D/E)XK endonuclease superfamily. These are the conserved Glu of motif I, the Asp surreounded by hydrophobics of motif II, EIKS of motif III, and the lysine of mmotif IV has migrated to an alpha-helix following the third core beta-strand. The conserved patch of positively charged lysine and arginine residues in the motif IV apha-helix might be involved in substrate-binding or be contributing to active site formation. Members with an additional N-terminal coi9led-coil domain, are annotated as tropomyosin, coiled-coil or microtubule binding proteins. 74 matched cddid_all.tbl CDD pfam07789 pfam07789 429660 DUF1627 Protein of unknown function (DUF1627). This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of bacterial species. The region in question is approximately 150 amino acid residues long. 155 matched cddid_all.tbl CDD pfam07790 pfam07790 400235 Pilin_N Archaeal Type IV pilin, N-terminal. This entry represents the N-terminal domain of archaeal pilins, which play important roles in surface adhesion and twitching motility. This domain contains an conserved N- terminal hydrophobic motif. 78 matched cddid_all.tbl CDD pfam07791 pfam07791 369521 DUF1629 Protein of unknown function (DUF1629). This family consists of sequences from hypothetical proteins thought to be expressed by two members of the Xanthomonas genus. The region in question is 125 amino acid residues long. 123 matched cddid_all.tbl CDD pfam07792 pfam07792 400236 Afi1 Docking domain of Afi1 for Arf3 in vesicle trafficking. This domain occurs at the N-terminal of Afi1, an Arf3p-interacting protein, is a protein necessary for vesicle trafficking in yeast. This domain is the interacting region of the protein which binds to Arf3, the highly conserved small GTPases (ADP-ribosylation factors). Afi1 is distributed asymmetrically at the plasma membrane and is required for polarized distribution of Arf3 but not of an Arf3 guanine nucleotide-exchange factor, Yel1p. However, Afi1 is not required for targeting of Arf3 or Yel1p to the plasma membrane. Afi1 functions as an Arf3 polarization-specific adapter and participates in development of polarity. Although Arf3 is the homolog of human Arf6 it does not function in the same way, not being necessary for endocytosis or for mating factor receptor internalization. In the S phase, however, it is concentrated at the plasma membrane of the emerging bud. Because of its polarized localization and its critical function in the normal budding pattern of yeast, Arf3 is probably a regulator of vesicle trafficking, which is important for polarized growth. 119 matched cddid_all.tbl CDD pfam07793 pfam07793 429661 DUF1631 Protein of unknown function (DUF1631). The members of this family are sequences derived from a group of hypothetical proteins expressed by certain bacterial species. The region concerned is approximately 440 amino acid residues in length. 742 matched cddid_all.tbl CDD pfam07794 pfam07794 116408 DUF1633 Protein of unknown function (DUF1633). This family contains sequences derived from a group of hypothetical proteins expressed by Arabidopsis thaliana. These sequences are highly similar and the region concerned is about 100 residues long. 698 matched cddid_all.tbl CDD pfam07795 pfam07795 400238 DUF1635 Protein of unknown function (DUF1635). The members of this family include sequences that are parts of hypothetical proteins expressed by plant species. The region in question is about 170 amino acids long. 223 matched cddid_all.tbl CDD pfam07796 pfam07796 429662 DUF1638 Protein of unknown function (DUF1638). This family contains sequences covering an approximately 270 amino acid stretch of a group of hypothetical proteins. These proteins are expressed by archaeal species of the Methanosarcina genus. 160 matched cddid_all.tbl CDD pfam07797 pfam07797 400240 DUF1639 Protein of unknown function (DUF1639). This approximately 50 residue region is found in a number of sequences derived from hypothetical plant proteins. This region features a highly basic 5 amino-acid stretch towards its centre. 50 matched cddid_all.tbl CDD pfam07798 pfam07798 462268 CCDC90-like Coiled-coil domain-containing protein 90-like. This entry includes coiled-coil domain-containing proteins 90 (CCDC90) and related proteins. CCDC90A is a key regulator of the mitochondrial calcium uniporter (MCU) and hence was renamed MCUR1. A study in mammals and in yeast homolog fmp32 has reported that MCUR1 is a cytochrome c oxidase assembly factor and that it has an indirect role as a regulator of MCU, however, subsequent publications confirmed the function of MCUR1 as a regulator of MCU. The role of CCDC90B proteins is still not known. 175 matched cddid_all.tbl CDD pfam07799 pfam07799 429664 DUF1643 Protein of unknown function (DUF1643). The members of this family are all sequences found within hypothetical proteins expressed by various bacterial species. The region concerned is approximately 150 residues long. 133 matched cddid_all.tbl CDD pfam07800 pfam07800 462269 DUF1644 Protein of unknown function (DUF1644). This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, and is probably a zinc-binding domain. 164 matched cddid_all.tbl CDD pfam07801 pfam07801 369527 DUF1647 Protein of unknown function (DUF1647). The sequences making up this family are all derived from hypothetical proteins expressed by C. elegans. The region in question is approximately 160 amino acids long. The GO annotation for this protein indicates the protein to be involved in nematode larval development and to have a positive regulation on growth rate. 141 matched cddid_all.tbl CDD pfam07802 pfam07802 429666 GCK GCK domain. This domain is found in proteins carrying other domains known to be involved in intracellular signalling pathways (such as pfam00071) indicating that it might also be involved in these pathways. It has 4 highly conserved cysteine residues, suggesting that it can bind zinc ions. Moreover, it is found repeated in some members of this family; this may indicate that these domains are able to interact with one another, raising the possibility that this domain mediates heterodimerization. 74 matched cddid_all.tbl CDD pfam07803 pfam07803 462270 GSG-1 GSG1-like protein. This family contains sequences bearing similarity to a region of GSG1, a protein specifically expressed in testicular germ cells. It is possible that overexpression of the human homolog may be involved in tumourigenesis of human testicular germ cell tumours. The region in question has four highly-conserved cysteine residues. 109 matched cddid_all.tbl CDD pfam07804 pfam07804 462271 HipA_C HipA-like C-terminal domain. The members of this family are similar to a region close to the C-terminus of the HipA protein expressed by various bacterial species (for example Swiss:P23874). This protein is known to be involved in high-frequency persistence to the lethal effects of inhibition of either DNA or peptidoglycan synthesis. When expressed alone, it is toxic to bacterial cells, but it is usually tightly associated with HipB, and the HipA-HipB complex may be involved in autoregulation of the hip operon. The hip proteins may be involved in cell division control and may interact with cell division genes or their products. 224 matched cddid_all.tbl CDD pfam07806 pfam07806 116420 Nod_GRP Nodule-specific GRP repeat. The region featured in this family is found repeated in a number of plant proteins, some of which are expressed specifically in nodules formed during symbiotic interactions with certain bacterial species. Some of these proteins are also termed glycine-rich proteins (GRPs), due to the presence of a glycine-rich C-terminal region in their structures. Bacterial infection is required for the induction of nodule-specific GRP genes, and it is thought that nodule-specific GRPs may play non-redundant roles required at specific stages of nodule development. Members of this group of proteins may be cytosolic, whereas others are thought to be membrane-associated. 38 matched cddid_all.tbl CDD pfam07807 pfam07807 462272 RED_C RED-like protein C-terminal region. This family contains sequences that are similar to the C-terminal region of Red protein. This and related proteins are thought to be localized to the nucleus, and contain a RED repeat which consists of a number of RE and RD sequence elements. The region in question has several conserved NLS sequences. The function of Red protein is unknown, but efficient sequestration to nuclear bodies suggests that its expression may be tightly regulated or that the protein self-aggregates extremely efficiently. 112 matched cddid_all.tbl CDD pfam07808 pfam07808 462273 RED_N RED-like protein N-terminal region. This family contains sequences that are similar to the N-terminal region of Red protein. This and related proteins contain a RED repeat which consists of a number of RE and RD sequence elements. The region in question has several conserved NLS sequences and a putative trimeric coiled-coil region, suggesting that these proteins are expressed in the nucleus. The function of Red protein is unknown, but efficient sequestration to nuclear bodies suggests that its expression may be tightly regulated of that the protein self-aggregates extremely efficiently. 227 matched cddid_all.tbl CDD pfam07809 pfam07809 462274 RTP801_C RTP801 C-terminal region. The members of this family are sequences similar to the C-terminal region of RTP801, the protein product of a hypoxia-inducible factor 1 (HIF-1)- responsive gene. Two members of this family expressed by Drosophila melanogaster, Scylla and Charybde, are designated by the GenBank as Hox targets. RTP801 is thought to be involved in various cellular processes. Its overexpression caused the apoptosis- resistant phenotype in cycling cells, and apoptosis sensitivity in growth arrested cells. Moreover, the protein product of the mouse homolog of RTP801 (dig2) is thought to be induced by diverse apoptotic signals, and also by dexamethasone treatment. 116 matched cddid_all.tbl CDD pfam07810 pfam07810 462275 TMC TMC domain. These sequences are similar to a region conserved amongst various protein products of the transmembrane channel-like (TMC) gene family, such as Transmembrane channel-like protein 3 and EVIN2 - this region is termed the TMC domain. Mutations in these genes are implicated in a number of human conditions, such as deafness and epidermodysplasia verruciformis. TMC proteins are thought to have important cellular roles, and may be modifiers of ion channels or transporters. 111 matched cddid_all.tbl CDD pfam07811 pfam07811 462276 TadE TadE-like protein. The members of this family are similar to a region of the protein product of the bacterial tadE locus. In various bacterial species, the tad locus is closely linked to flp-like genes, which encode proteins required for the production of pili involved in adherence to surfaces. It is thought that the tad loci encode proteins that act to assemble or export an Flp pilus in various bacteria. All tad loci but TadA have putative transmembrane regions, and in fact the region in question is this family has a high proportion of hydrophobic amino acid residues. 43 matched cddid_all.tbl CDD pfam07812 pfam07812 462277 TfuA TfuA-like protein. This family consists of a group of sequences that are similar to a region of TfuA protein. This protein is involved in the production of trifolitoxin (TFX), an gene-encoded, post-translationally modified peptide antibiotic. The role of TfuA in TFX synthesis is unknown, and it may be involved in other cellular processes. 120 matched cddid_all.tbl CDD pfam07813 pfam07813 429675 LTXXQ LTXXQ motif family protein. This protein family includes two copies of a five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP. This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH. Another member of this family, Spy is also a periplasmic protein that may be involved in the response to stress. The homology between CpxP and Spy may indicate that these two proteins are functionally related. 97 matched cddid_all.tbl CDD pfam07814 pfam07814 462278 WAPL Wings apart-like protein regulation of heterochromatin. This family contains sequences expressed in eukaryotic organizms bearing high similarity to the WAPL conserved region of D. melanogaster wings apart-like protein. This protein is involved in the regulation of heterochromatin structure. hWAPL, the human homolog, is found to play a role in the development of cervical carcinogenesis, and is thought to have similar functions to Drosophila wapl protein. Malfunction of the hWAPL pathway is thought to activate an apoptotic pathway that consequently leads to cell death. 344 matched cddid_all.tbl CDD pfam07815 pfam07815 462279 Abi_HHR Abl-interactor HHR. The region featured in this family is found towards the N-terminus of a number of adaptor proteins that interact with Abl-family tyrosine kinases. More specifically, it is termed the homeo-domain homologous region (HHR), as it is similar to the DNA-binding region of homeo-domain proteins. Other homeo-domain proteins have been implicated in specifying positional information during embryonic development, and in the regulation of the expression of cell-type specific genes. The Abl-interactor proteins are thought to coordinate the cytoplasmic and nuclear functions of the Abl-family kinases, and seem to be involved in cytoskeletal reorganization, but their precise role remains unclear. 64 matched cddid_all.tbl CDD pfam07816 pfam07816 429678 DUF1645 Protein of unknown function (DUF1645). These sequences are derived from a number of hypothetical plant proteins. The region in question is approximately 270 amino acids long. Some members of this family are annotated as yeast pheromone receptor proteins AR781 but no literature was found to support this. 193 matched cddid_all.tbl CDD pfam07817 pfam07817 462280 GLE1 GLE1-like protein. The members of this family are sequences that are similar to the human protein GLE1. This protein is localized at the nuclear pore complexes and functions in poly(A)+ RNA export to the cytoplasm. 234 matched cddid_all.tbl CDD pfam07818 pfam07818 462281 HCNGP HCNGP-like protein. This family comprises sequences bearing significant similarity to the mouse transcriptional regulator protein HCNGP. This protein is localized to the nucleus and is thought to be involved in the regulation of beta-2-microglobulin genes. 91 matched cddid_all.tbl CDD pfam07819 pfam07819 369540 PGAP1 PGAP1-like protein. The sequences found in this family are similar to PGAP1. This is an endoplasmic reticulum membrane protein with a catalytic serine containing motif that is conserved in a number of lipases. PGAP1 functions as a GPI inositol-deacylase; this deacylation is important for the efficient transport of GPI-anchored proteins from the endoplasmic reticulum to the Golgi body. This entry also includes Tgl2, a mitochondria protein that serves as a triacylglycerol lipase in budding yeasts. 233 matched cddid_all.tbl CDD pfam07820 pfam07820 429681 TraC TraC-like protein. The members of this family are sequences that are similar to TraC. The gene encoding this protein is one of a group of genes found on plasmid p42a of Rhizobium etli CFN42 that are thought to be involved in the process of plasmid self-transmission. mobilization of plasmid p42a is of importance as it is required for transfer of plasmid p42a, which is also known as plasmid pSym as it carries most of the genes required for nodulation and nitrogen fixation by the symbiotic bacterium. The predicted protein products of p42a are similar to known transfer proteins of Agrobacterium tumefaciens plasmid pTiC58. 88 matched cddid_all.tbl CDD pfam07821 pfam07821 400259 Alpha-amyl_C2 Alpha-amylase C-terminal beta-sheet domain. This domain is organized as a five-stranded anti-parallel beta-sheet. It is the probable result of a decay of the common-fold. 59 matched cddid_all.tbl CDD pfam07822 pfam07822 400260 Toxin_13 Neurotoxin B-IV-like protein. The members of this family resemble neurotoxin B-IV, which is a crustacean-selective neurotoxin produced by the marine worm Cerebratulus lacteus. This highly cationic peptide is approximately 55 residues and is arranged to form two antiparallel helices connected by a well-defined loop in a hairpin structure. The branches of the hairpin are linked by four disulphide bonds. Three residues identified as being important for activity, namely Arg-17, -25 and -34, are found on the same face of the molecule, while another residue important for activity, Trp30, is on the opposite side. The protein's mode of action is not entirely understood, but it may act on voltage-gated sodium channels, possibly by binding to an as yet uncharacterized site on these proteins. Its site of interaction may also be less specific, for example it may interact with negatively charged membrane lipids. 55 matched cddid_all.tbl CDD pfam07823 pfam07823 311669 CPDase Cyclic phosphodiesterase-like protein. Cyclic phosphodiesterase (CPDase) is involved in the tRNA splicing pathway. This protein exhibits a bilobal arrangement of two alpha-beta modules. Two antiparallel helices are found on the outer side of each lobe and frame an antiparallel beta-sheet that is wrapped around an accessible cleft. Moreover, the beta-strands of each lobe interact with the other lobe. The central water-filled cavity houses the enzyme's active site. 199 matched cddid_all.tbl CDD pfam07824 pfam07824 429682 Chaperone_III Type III secretion chaperone domain. Type III secretion chaperones are involved in delivering virulence effector proteins from bacterial pathogens directly into eukaryotic cells. The chaperones may prevent aggregation and degradation of their substrates, may target the effector to the secretion apparatus, and may ensure a secretion-component unfolded confirmation of their specific substrate. One member of this family, SigE forms homodimers in crystal. The monomers have a novel fold with an alpha-beta(3)-alpha-beta(2)-alpha topology. 110 matched cddid_all.tbl CDD pfam07825 pfam07825 116439 Exc Excisionase-like protein. The phage-encoded excisionase protein (Xis) is involved in excisive recombination by regulating the assembly of the excisive intasome and by inhibiting viral integration. It adopts an unusual 'winged'-helix structure in which two alpha helices are packed against two extended strands. Also present in the structure is a two-stranded anti-parallel beta-sheet, whose strands are connected by a four-residue 'wing'. During interaction with DNA, helix alpha2 is thought to insert into the major groove, while the wing contacts the adjacent minor groove or phosphodiester backbone. The C-terminal region of Xis is involved in interaction with phage-encoded integrase (Int), and a putative C-terminal alpha helix may fold upon interaction with Int and/or DNA. 72 matched cddid_all.tbl CDD pfam07826 pfam07826 429683 IMP_cyclohyd IMP cyclohydrolase-like protein. This enzyme is may catalyze the cyclization of 5-formylamidoimidazole-4-carboxamide ribonucleotide to inosine monophosphate (IMP), a reaction which is important in de novo purine biosynthesis in archaeal species. This single domain protein is arranged to form an overall fold that consists of a four-layered alpha-beta-beta-alpha core structure. The two antiparallel beta-sheets pack against each other and are covered by alpha-helices on one face of the molecule. The protein is structurally similar to members of the N-terminal nucleophile (NTN) hydrolase superfamily. A deep pocket was in fact found on the surface of IMP cyclohydrolase in a position equivalent to that of active sites of NTN-hydrolases, but an N-terminal nucleophile could not be found. Therefore, it is thought that this enzyme is structurally but not functionally similar to members of the NTN-hydrolase family. 191 matched cddid_all.tbl CDD pfam07827 pfam07827 285116 KNTase_C KNTase C-terminal domain. Kanamycin nucleotidyltransferase (KNTase) is involved in conferring resistance to aminoglycoside antibiotics and catalyzes the transfer of a nucleoside monophosphate group from a nucleotide to kanamycin. This enzyme is dimeric with each subunit being composed of two domains. The C-terminal domain contains five alpha helices, four of which are organized into an up-and-down alpha helical bundle. Residues found in this domain may contribute to this enzyme's active site. 132 matched cddid_all.tbl CDD pfam07828 pfam07828 369543 PA-IL PA-IL-like protein. The members of this family are similar to the galactophilic lectin-1 expressed by P. aeruginosa (PA-IL). Lectins recognising specific carbohydrates found on the surface of host cells are known to be involved in the initiation of infections by this organizm. The protein is thought to be organized into an extensive network of beta-sheets, as is the case with many other lectins. 121 matched cddid_all.tbl CDD pfam07829 pfam07829 311671 Toxin_14 "Alpha-A conotoxin PIVA-like protein. Alpha-A conotoxin PIVA is the major paralytic toxin found in the venom produced by the piscivorous snail Conus purpurascens. This peptide acts by blocking the acetylcholine binding site of the nicotinic acetylcholine receptor at the neuromuscular junction. The overall shape of the peptide is described as an ""iron"" with a highly charged hydrophilic loop of 15S-19R forming the ""handle"" domain that is exposed to the exterior of the protein. The stability of the conotoxin is primarily governed by three disulphide bonds. A triangular structural motif formed by residues 19R, 12H and 6Y is thought to constitute a ""binding core"" that is important in binding to the acetylcholine receptor." 26 matched cddid_all.tbl CDD pfam07830 pfam07830 429684 PP2C_C Protein serine/threonine phosphatase 2C, C-terminal domain. Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It consists of two domains: an N-terminal catalytic domain and a C-terminal domain characteriztic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain. 79 matched cddid_all.tbl CDD pfam07831 pfam07831 429685 PYNP_C Pyrimidine nucleoside phosphorylase C-terminal domain. This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP) there is an added three-stranded anti-parallel beta sheet as compared to other members of the family, such as E. coli thymidine phosphorylase (TP). The domain contains an alpha/ beta hammerhead fold and residues in this domain seem to be important in formation of the homodimer. 74 matched cddid_all.tbl CDD pfam07832 pfam07832 400264 Bse634I Cfr10I/Bse634I restriction endonuclease. Cfr10I and Bse634I are two Type II restriction endonucleases. They exhibit a conserved tetrameric architecture that is of functional importance, wherein two dimers are arranged 'back-to-back' with their putative DNA-binding clefts facing opposite directions. These clefts are formed between two monomers that interact, mainly via hydrophobic interactions supported by a few hydrogen bonds, to form a U-shaped dimer. Each monomer is folded to form a compact alpha-beta structure, whose core is made up of a five-stranded mixed beta-sheet.The monomer may be split into separate N-terminal and C-terminal subdomains at a hinge located in helix alpha3. 281 matched cddid_all.tbl CDD pfam07833 pfam07833 400265 Cu_amine_oxidN1 Copper amine oxidase N-terminal domain. Copper amine oxidases catalyze the oxidative deamination of primary amines to the corresponding aldehydes, while reducing molecular oxygen to hydrogen peroxide. These enzymes are dimers of identical subunits, each comprising four domains. The N-terminal domain, which is absent in some amine oxidases, consists of a five-stranded antiparallel beta sheet twisted around an alpha helix. The D1 domains from the two subunits comprise the 'stalk' of the mushroom-shaped dimer, and interact with each other but do not pack tightly against each other. 93 matched cddid_all.tbl CDD pfam07834 pfam07834 462282 RanGAP1_C RanGAP1 C-terminal domain. Ran-GTPase activating protein 1 (RanGAP1) is a GTPase activator for the nuclear Ras-related regulatory protein Ran, converting it to the putatively inactive GDP-bound state. Its C-terminal domain is required for RanGAP1 localization at the vertebrate nuclear pore complex, and is sumoylated by the small ubiquitin-related modifier protein (SUMO-1). This domain is composed almost entirely of helical substructures that are organized into an alpha-alpha superhelix fold, with the exception of the peptide containing the lysine residue required for SUMO-1 conjugation. 177 matched cddid_all.tbl CDD pfam07835 pfam07835 429687 COX4_pro_2 Bacterial aa3 type cytochrome c oxidase subunit IV. Bacterial cytochrome c oxidase is found bound to the to the cell membrane, where it is involved in the generation of the transmembrane proton electrochemical gradient. It is composed of four subunits. Subunit IV consists of one transmembrane helix that does not interact directly with the other subunits, but maintains its position by indirect contacts via phospholipid molecules found in the structure. The function of subunit IV is as yet unknown. 46 matched cddid_all.tbl CDD pfam07836 pfam07836 429688 DmpG_comm DmpG-like communication domain. This domain is found towards the C-terminal region of various aldolase enzymes. It consists of five alpha-helices, four of which form an antiparallel helical bundle that plugs the C-terminus of the N-terminal TIM barrel domain. The communication domain is thought to play an important role in the heterodimerization of the enzyme. 63 matched cddid_all.tbl CDD pfam07837 pfam07837 462283 FTCD_N Formiminotransferase domain, N-terminal subdomain. The formiminotransferase (FT) domain of formiminotransferase- cyclodeaminase (FTCD) forms a homodimer, and each protomer comprises two subdomains. The N-terminal subdomain is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This, in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to form a number of contacts with residues found in both the N-terminal and C-terminal subdomains. 176 matched cddid_all.tbl CDD pfam07839 pfam07839 462284 CaM_binding Plant calmodulin-binding domain. The sequences featured in this family are found repeated in a number of plant calmodulin-binding proteins, and are thought to constitute the calmodulin-binding domains. Binding of the proteins to calmodulin depends on the presence of calcium ions. These proteins are thought to be involved in various processes, such as plant defence responses and stolonization or tuberization. 118 matched cddid_all.tbl CDD pfam07840 pfam07840 429691 FadR_C FadR C-terminal domain. This family contains sequences that are similar to the fatty acid metabolism regulator protein (FadR). This functions as a dimer, with each monomer being composed of an N-terminal DNA-binding domain and a regulatory C-terminal domain. A linker comprising two short alpha helices joins the two domains. In the C-terminal domain, an antiparallel array of six alpha helices forms a barrel-like structure, while a seventh alpha helix forms a 'lid' at the end closest to the N-terminal domain. This structure was found to be similar to that of the C-terminal domain of the Tet repressor. Long-chain acyl-CoA thioesters interact directly and reversibly with the C-terminal domain, and this interaction affects the structure and therefore the DNA binding properties of the N-terminal domain. 163 matched cddid_all.tbl CDD pfam07841 pfam07841 462285 DM4_12 DM4/DM12 family. This family contains sequences derived from hypothetical proteins expressed by two insect species, D. melanogaster and A. gambiae. The region in question is approximately 115 amino acid residues long and contains four highly- conserved cysteine residues. 86 matched cddid_all.tbl CDD pfam07842 pfam07842 400273 GCFC GC-rich sequence DNA-binding factor-like protein. This entry describes a domain found in a number of GC-rich sequence DNA-binding factor proteins and homologs, as well as in a number of other proteins including Tuftelin-interacting protein 11. While the function of the domain is unknown, some of the proteins it is found in are reported to be involved in pre-mRNA splicing. This domain is also found in Sip1, a septin interacting protein. 275 matched cddid_all.tbl CDD pfam07843 pfam07843 429693 DUF1634 Protein of unknown function (DUF1634). This family contains many hypothetical bacterial and archaeal proteins. A few members of this family are annotated as being putative transmembrane proteins, and the region in question in fact contains many hydrophobic residues. 102 matched cddid_all.tbl CDD pfam07845 pfam07845 429694 DUF1636 Protein of unknown function (DUF1636). The sequences featured in this family are derived from a number of hypothetical prokaryotic proteins. The region in question is approximately 130 amino acids long. 117 matched cddid_all.tbl CDD pfam07846 pfam07846 285130 Metallothio_Cad Metallothionein family. The sequences making up Metallothio_Cad are found repeated in metallothionein proteins expressed by several different Tetrahymena species. Metallothioneins are low molecular mass, cysteine-rich metal-binding proteins that are thought to be involved in the regulation of levels of trace metals, and detoxification of these metals when present in excess. Some of the metallothioneins found in this family (for example, Swiss:Q8T6B3) are known to be induced by cadmium and are thought to be involved in the cellular sequestration of toxic metal ions. The high proportion of cysteine residues allows the metal ions to be bound by the formation of clusters of metal-thiolate complexes. Tetrahymena spp. metallothioneins differ from other eukaryotic metallothioneins mainly in the length of their sequences and in the cysteine-containing motifs they exhibit. 20 matched cddid_all.tbl CDD pfam07847 pfam07847 462286 PCO_ADO PCO_ADO. This entry includes cysteine oxidases (PCOs) from plants and 2-aminoethanethiol dioxygenases (ADOs) from animals. 201 matched cddid_all.tbl CDD pfam07848 pfam07848 285132 PaaX PaaX-like protein. This family contains proteins that are similar to the product of the paaX gene of Escherichia coli. This protein is involved in the regulation of expression of a group of proteins known to participate in the metabolism of phenylacetic acid. In fact, some members of this family are annotated by InterPro as containing a winged helix DNA-binding domain (Interpro:IPR009058). 70 matched cddid_all.tbl CDD pfam07849 pfam07849 400277 DUF1641 Protein of unknown function (DUF1641). Archaeal and bacterial hypothetical proteins are found in this family, with the region in question being approximately 40 residues long. 39 matched cddid_all.tbl CDD pfam07850 pfam07850 462287 Renin_r Renin receptor-like protein. The sequences featured in this family are similar to a region of the human renin receptor that bears a putative transmembrane spanning segment. The renin receptor is involved in intracellular signal transduction by the activation of the ERK1/ERK2 pathway, and it also serves to increase the efficiency of angiotensinogen cleavage by receptor-bound renin, therefore facilitating angiotensin II generation and action on a cell surface. 97 matched cddid_all.tbl CDD pfam07851 pfam07851 462288 TMPIT TMPIT-like protein. A number of members of this family are annotated as being transmembrane proteins induced by tumour necrosis factor alpha, but no literature was found to support this. 324 matched cddid_all.tbl CDD pfam07852 pfam07852 369557 DUF1642 Protein of unknown function (DUF1642). The sequences making up this family are derived from various hypothetical phage and prophage proteins. The region in question is approximately 140 amino acids long. 136 matched cddid_all.tbl CDD pfam07853 pfam07853 462289 DUF1648 Domain of unknown function (DUF1648). This domain is found in proteins expressed by bacterial or archaeal species. Some of these are annotated as being transmembrane proteins, and in fact many of these sequences contain a high proportion of hydrophobic residues. One protein containing this domain is immunity protein SdpI (swiss:O32241) from Bacillus subtilis, which provides protection for the cell against the toxic effects of its own SdpC killing factor, and also functions as a receptor/signal transduction protein. 49 matched cddid_all.tbl CDD pfam07854 pfam07854 285138 DUF1646 Protein of unknown function (DUF1646). Some of the members of this family are hypothetical bacterial and archaeal proteins, but others are annotated as being cation transporters expressed by the archaebacterium Methanosarcina mazei (Swiss:Q8PXG5, Swiss:Q8PXG7 and Swiss:Q8PXG8). 347 matched cddid_all.tbl CDD pfam07855 pfam07855 462290 ATG101 Autophagy-related protein 101. Atg101 is a critical autophagy factor that functions together with ULK, Atg13 and FIP200. Atg101 has been shown to be a HORMA (Hop1, Rev7 and MAD2) domain protein with an open conformation. 149 matched cddid_all.tbl CDD pfam07856 pfam07856 462291 Orai-1 Mediator of CRAC channel activity. ORAI-1 is a protein homolog of Drosophila Orai and human Orai1, Orai2 and Orai3. ORAI-1 GFP reporters are co- expressed with STIM-1 (ER CA(2+) sensors) in the gonad and intestine. The protein has four predicted transmembrane domains with a highly conserved region between TM2 ad TM3. This conserved domain is thought to function in channel regulation. ORAI1- related proteins are required for the production of the calcium channel, CRAC, along with STIM1-related proteins. 168 matched cddid_all.tbl CDD pfam07857 pfam07857 285141 TMEM144 Transmembrane family, TMEM144 of transporters. Members of this family fall in to the drug/metabolite transporter (dmt) superfamily. They carry 10xTM domains arranged as 5+5. Although these two sets may originally have arisen by gene-duplication the divergence now is such that the two halves are no longer homologous. 333 matched cddid_all.tbl CDD pfam07858 pfam07858 400283 LEH Limonene-1,2-epoxide hydrolase catalytic domain. Epoxide hydrolases catalyze the hydrolysis of epoxides to corresponding diols, which is important in detoxification, synthesis of signal molecules, or metabolism. Limonene-1,2- epoxide hydrolase (LEH) differs from many other epoxide hydrolases in its structure and its novel one-step catalytic mechanism. Its main fold consists of a six-stranded mixed beta-sheet, with three N-terminal alpha helices packed to one side to create a pocket that extends into the protein core. A fourth helix lies in such a way that it acts as a rim to this pocket. Although mainly lined by hydrophobic residues, this pocket features a cluster of polar groups that lie at its deepest point and constitute the enzyme's active site. 125 matched cddid_all.tbl CDD pfam07859 pfam07859 400284 Abhydrolase_3 alpha/beta hydrolase fold. This catalytic domain is found in a very wide range of enzymes. 208 matched cddid_all.tbl CDD pfam07860 pfam07860 462292 CCD WisP family C-Terminal Region. This family is found at the C-terminus of the Tropheryma whipplei WisP family proteins. 130 matched cddid_all.tbl CDD pfam07861 pfam07861 311693 WND WisP family N-Terminal Region. This family is found at the N-terminus of the Tropheryma whipplei WisP family proteins. 239 matched cddid_all.tbl CDD pfam07862 pfam07862 462293 Nif11 Nif11 domain. This domain is found mainly in the Cyanobacteria and in Proteobacteria such as the nitrogen-fixing bacterium Azotobacter vinelandii. It is found in Nif11, a protein described in Azotobacter as linked to nitrogen fixation. It also constitutes a leader peptide in Nif11-derived peptides (N11P), which are thought to be post-translationally modified microcins derived from a putative nitrogen-fixing protein. N11P sequences have a classic leader peptide cleavage motif, usually Gly-Gly, which marks the end of family-wide similarity area and the beginning of a low-complexity region rich in Cys, Gly and Ser. 47 matched cddid_all.tbl CDD pfam07863 pfam07863 400286 CtnDOT_TraJ homologs of TraJ from Bacteroides conjugative transposon. Members of this family have been implicated in as being involved in an unusual form of DNA transfer (conjugation) in Bacteroides. The family has been named CtnDOT_TraJ to avoid confusion with other conjugative transfer systems. 66 matched cddid_all.tbl CDD pfam07864 pfam07864 400287 DUF1651 Protein of unknown function (DUF1651). This is a family containing bacterial proteins of unknown function. 73 matched cddid_all.tbl CDD pfam07865 pfam07865 429701 DUF1652 Protein of unknown function (DUF1652). This is a family containing hypothetical bacterial proteins. 67 matched cddid_all.tbl CDD pfam07866 pfam07866 462294 DUF1653 Protein of unknown function (DUF1653). This is a family of hypothetical bacterial proteins of unknown function. 61 matched cddid_all.tbl CDD pfam07867 pfam07867 429703 DUF1654 Protein of unknown function (DUF1654). This family consists of proteins from the Pseudomonadaceae. 67 matched cddid_all.tbl CDD pfam07868 pfam07868 285151 DUF1655 Protein of unknown function (DUF1655). This protein is found in some prophages found in Lactobacillales lactis. 55 matched cddid_all.tbl CDD pfam07869 pfam07869 429704 DUF1656 Protein of unknown function (DUF1656). This entry represents a putative component of efflux pumps that comprise MFP and FUSC proteins. Several members are in an operon with and have similar mutants phenotypes as an RND efflux pump and a fusaric acid resistance-like protein. This system is involved in transporting diverse substrates including 4-hydroxybenzoate and octanoate. 56 matched cddid_all.tbl CDD pfam07870 pfam07870 462295 DUF1657 Protein of unknown function (DUF1657). This domain appears to be restricted to the Bacillales. 49 matched cddid_all.tbl CDD pfam07872 pfam07872 462296 DUF1659 Protein of unknown function (DUF1659). This family consists of hypothetical bacterial proteins of unknown function. 43 matched cddid_all.tbl CDD pfam07873 pfam07873 462297 YabP YabP family. This family of proteins is involved in spore coat assembly during the process of sporulation. 64 matched cddid_all.tbl CDD pfam07874 pfam07874 369565 DUF1660 Prophage protein (DUF1660). This protein is found in Lactobacillae prophages. 64 matched cddid_all.tbl CDD pfam07875 pfam07875 462298 Coat_F Coat F domain. The Coat F proteins, which contribute to the Bacillales spore coat. It occurs multiple times in the genomes it is found in. 63 matched cddid_all.tbl CDD pfam07876 pfam07876 400293 Dabb Stress responsive A/B Barrel Domain. The function of this family is unknown, but it is upregulated in response to salt stress in Populus balsamifera. It is also found at the C-terminus of an fructose 1,6-bisphosphate aldolase from Hydrogenophilus thermoluteolus. Swiss:Q93NG5 is found in the pA01 plasmid, which encodes genes for molybdopterin uptake and degradation of plant alkaloid nicotine. The structure of one has been solved and the domain forms an a/b barrel dimer. Although there is a clear duplication within the domain it is not obviously detectable in the sequence. 96 matched cddid_all.tbl CDD pfam07877 pfam07877 285160 DUF1661 Protein of unknown function (DUF1661). This is a family containing bacterial proteins of unknown function. Many of the proteins in this family are hypothetical. 31 matched cddid_all.tbl CDD pfam07878 pfam07878 429709 RHH_5 CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5. This family contains bacterial proteins that form a ribbon-helix-helix fold. This fold occurs in many examples of bacterial antitoxins. 43 matched cddid_all.tbl CDD pfam07879 pfam07879 429710 PHB_acc_N PHB/PHA accumulation regulator DNA-binding domain. This domain is found at the N-terminus of the Polyhydroxyalkanoate (PHA) synthesis regulators. These regulators have been shown to directly bind DNA and PHA. The invariant nature of this domain compared to the C-terminal pfam05233 domain(s) suggests that it contains the DNA-binding function. 61 matched cddid_all.tbl CDD pfam07880 pfam07880 400296 T4_gp9_10 Bacteriophage T4 gp9/10-like protein. The members of this family are similar to gene products 9 (gp9) and 10 (gp10) of bacteriophage T4. Both proteins are components of the viral baseplate. Gp9 connects the long tail fibres of the virus to the baseplate and triggers tail contraction after viral attachment to a host cell. The protein is active as a trimer, with each monomer being composed of three domains. The N-terminal domain consists of an extended polypeptide chain and two alpha helices. The alpha1 helix from each of the three monomers in the trimer interacts with its counterparts to form a coiled-coil structure. The middle domain is a seven-stranded beta-sandwich that is thought to be a novel protein fold. The C-terminal domain is thought to be essential for gp9 trimerization and is organized into an eight- stranded antiparallel beta-barrel, which was found to resemble the 'jelly roll' fold found in many viral capsid proteins. The long flexible region between the N-terminal and middle domains may be required for the function of gp9 to transmit signals from the long tail fibres. Together with gp11, gp10 initiates the assembly of wedges that then go on to associate with a hub to form the viral baseplate. 285 matched cddid_all.tbl CDD pfam07881 pfam07881 462299 Fucose_iso_N1 L-fucose isomerase, first N-terminal domain. The members of this family are similar to L-fucose isomerase expressed by E. coli (EC:5.3.1.3). This enzyme corresponds to glucose-6-phosphate isomerase in glycolysis, and converts an aldo-hexose to a ketose to prepare it for aldol cleavage. The enzyme is a hexamer, with each subunit being wedge-shaped and composed of three domains. Both domains 1 and 2 contain central parallel beta-sheets with surrounding alpha helices. Domain 1 demonstrates the beta-alpha-beta-alpha- beta Rossman fold. The active centre is shared between pairs of subunits related along the molecular three-fold axis, with domains 2 and 3 from one subunit providing most of the substrate-contacting residues, and domain 1 from the adjacent subunit contributing some other residues. 169 matched cddid_all.tbl CDD pfam07882 pfam07882 429712 Fucose_iso_N2 L-fucose isomerase, second N-terminal domain. The members of this family are similar to L-fucose isomerase expressed by E. coli (EC:5.3.1.3). This enzyme corresponds to glucose-6-phosphate isomerase in glycolysis, and converts an aldo-hexose to a ketose to prepare it for aldol cleavage. The enzyme is a hexamer, with each subunit being wedge-shaped and composed of three domains. Both domains 1 and 2 contain central parallel beta- sheets with surrounding alpha helices. The active centre is shared between pairs of subunits related along the molecular three-fold axis, with domains 2 and 3 from one subunit providing most of the substrate-contacting residues. 180 matched cddid_all.tbl CDD pfam07883 pfam07883 462300 Cupin_2 Cupin domain. This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). 71 matched cddid_all.tbl CDD pfam07884 pfam07884 429714 VKOR Vitamin K epoxide reductase family. Vitamin K epoxide reductase (VKOR) recycles reduced vitamin K, which is used subsequently as a co-factor in the gamma-carboxylation of glutamic acid residues in blood coagulation enzymes. VKORC1 is a member of a large family of predicted enzymes that are present in vertebrates, Drosophila, plants, bacteria and archaea. Four cysteine residues and one residue, which is either serine or threonine, are identified as likely active-site residues. In some plant and bacterial homologs the VKORC1 homologous domain is fused with domains of the thioredoxin family of oxidoreductases. 132 matched cddid_all.tbl CDD pfam07885 pfam07885 462301 Ion_trans_2 Ion channel. This family includes the two membrane helix type ion channels found in bacteria. 78 matched cddid_all.tbl CDD pfam07886 pfam07886 429716 BA14K BA14K-like protein. The sequences found in this family are similar to the BA14K proteins expressed by Brucella abortus and by Brucella suis. BA14K was found to be strongly immunoreactive; it induces both humoral and cellular responses in hosts throughout the infective process. 30 matched cddid_all.tbl CDD pfam07887 pfam07887 462302 Calmodulin_bind Calmodulin binding protein-like N-terminal domain. The members of this family are putative or actual calmodulin binding proteins expressed by various plant species. Some members (for example, Swiss:Q8H6T7), are known to be involved in the induction of plant defence responses. However, their precise function in this regards is as yet unknown. 147 matched cddid_all.tbl CDD pfam07888 pfam07888 462303 CALCOCO1 Calcium binding and coiled-coil domain (CALCOCO1) like. Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein coexpressed by Mus musculus (CoCoA/CALCOCO1). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1, and thus enhances transcriptional activation by a number of nuclear receptors. CALCOCO1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region. 488 matched cddid_all.tbl CDD pfam07889 pfam07889 462304 DUF1664 Protein of unknown function (DUF1664). The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long. 122 matched cddid_all.tbl CDD pfam07890 pfam07890 462305 Rrp15p Rrp15p. Rrp15p is required for the formation of 60S ribosomal subunits. 126 matched cddid_all.tbl CDD pfam07891 pfam07891 462306 DUF1666 Protein of unknown function (DUF1666). These sequences are derived from hypothetical plant proteins of unknown function. The region in question is approximately 250 residues long. 246 matched cddid_all.tbl CDD pfam07892 pfam07892 462307 DUF1667 Protein of unknown function (DUF1667). Hypothetical archaeal and bacterial proteins make up this family. A few proteins are annotated as being potential metal-binding proteins, and in fact the members of this family have four highly conserved cysteine residues, but no further literature evidence was found in this regard. 82 matched cddid_all.tbl CDD pfam07893 pfam07893 369579 DUF1668 Protein of unknown function (DUF1668). The hypothetical proteins found in this family are expressed by Oryza sativa and are of unknown function. 330 matched cddid_all.tbl CDD pfam07894 pfam07894 462308 FAM83 FAM83 A-H. The FAM83 family members include FAM83A-H. They are oncogenes that function as intermediaries in EGFR/RAS signaling. 276 matched cddid_all.tbl CDD pfam07895 pfam07895 400310 DUF1673 Protein of unknown function (DUF1673). This family contains hypothetical proteins of unknown function expressed by two archaeal species. 207 matched cddid_all.tbl CDD pfam07896 pfam07896 429724 DUF1674 Protein of unknown function (DUF1674). The members of this family are sequences derived from hypothetical eukaryotic and bacterial proteins. The region in question is approximately 60 residues long. 50 matched cddid_all.tbl CDD pfam07897 pfam07897 462309 EAR Ethylene-responsive binding factor-associated repression. The EAR motif is the ethylene-responsive element binding factor-associated amphiphilic repression motif. This motif binds to the Groucho/Tup1-type co-repressor TOPLESS (TPL) and TPL-related proteins. The motif is frequently to be find at the N-terminus of NINJA, or Novel INteractor of JAZ, proteins. The EAR motif, defined by the consensus sequence patterns of either LxLxL or DLN xxP, is the most predominant form of transcriptional repression motif so far identified in plants. It is highly conserved in transcriptional regulators that are known to function as negative regulators in a broad range of developmental and physiological processes across evolutionarily diverse plant species. This family is closely related to family AUX_IAA Pam:PF02309 which also has an LxLxL signature. 35 matched cddid_all.tbl CDD pfam07898 pfam07898 462310 DUF1676 Protein of unknown function (DUF1676). This family contains sequences derived from proteins of unknown function expressed by Drosophila melanogaster and Anopheles gambiae. 172 matched cddid_all.tbl CDD pfam07899 pfam07899 462311 Frigida Frigida-like protein. This family is composed of plant proteins that are similar to FRIGIDA protein expressed by Arabidopsis thaliana. This protein is probably nuclear and is required for the regulation of flowering time in the late-flowering phenotype. It is known to increase RNA levels of flowering locus C. Allelic variation at the FRIGIDA locus is a major determinant of natural variation in flowering time. 290 matched cddid_all.tbl CDD pfam07900 pfam07900 369585 DUF1670 Protein of unknown function (DUF1670). The hypothetical eukaryotic proteins found in this family are of unknown function. 218 matched cddid_all.tbl CDD pfam07901 pfam07901 285184 DUF1672 Protein of unknown function (DUF1672). This family is composed of hypothetical bacterial proteins of unknown function. 271 matched cddid_all.tbl CDD pfam07902 pfam07902 369586 Gp58 gp58-like protein. Sequences found in this family are derived from a number of bacteriophage and prophage proteins. They are similar to gp58, a minor structural protein of Lactococcus delbrueckii bacteriophage LL-H. 594 matched cddid_all.tbl CDD pfam07903 pfam07903 285186 PaRep2a PaRep2a protein. This is a family of proteins expressed by the crenarchaeon Pyrobaculum aerophilum. The members are highly variable in length and level of conservation. The presence of numerous frameshifts and internal stop codons in multiple alignments are thought to indicate that most family members are no longer functional. 122 matched cddid_all.tbl CDD pfam07904 pfam07904 429728 Eaf7 Chromatin modification-related protein EAF7. The S. cerevisiae member of this family Swiss:P53911 is part of NuA4, the only essential histone acetyltransferase complex in Saccharomyces cerevisiae involved in global histone acetylation. 97 matched cddid_all.tbl CDD pfam07905 pfam07905 462312 PucR Purine catabolism regulatory protein-like family. The bacterial proteins found in this family are similar to the purine catabolism regulatory protein expressed by Bacillus subtilis (PucR). PucR is thought to be a transcriptional activator involved in the induction of the purine degradation pathway, and may contain a LysR-like DNA-binding domain. It is similar to LysR-type regulators in that it represses its own expression. The other members of this family are also annotated as being putative regulatory proteins. 117 matched cddid_all.tbl CDD pfam07906 pfam07906 369588 Toxin_15 ShET2 enterotoxin, N-terminal region. The members of this family are are sequences that are similar to the N-terminal half of the ShET2 enterotoxin produced by Shigella flexneri and Escherichia coli. This protein was found to confer toxigenicity in the Ussing chamber, and the N-terminal region was found to be important for the protein's enterotoxic effect. It is thought to be a hydrophobic protein that forms inclusion bodies within the bacterial cell, and may be secreted by the Mxi system. Most members of this family are annotated as putative enterotoxins, but one member is a regulator of acetyl CoA synthetase, and another two members (Swiss:P76205 and Swiss:P23325) are annotated as ankyrin-like regulatory proteins and contain Ank repeats (pfam00023). 278 matched cddid_all.tbl CDD pfam07907 pfam07907 462313 YibE_F YibE/F-like protein. The sequences featured in this family are similar to two proteins expressed by Lactococcus lactis, YibE and YibF. Most of the members of this family are annotated as being putative membrane proteins, and in fact the sequences contain a high proportion of hydrophobic residues. 241 matched cddid_all.tbl CDD pfam07909 pfam07909 116521 DUF1663 Protein of unknown function (DUF1663). The members of this family are hypothetical proteins expressed by Trypanosoma cruzi, a eukaryotic parasite that causes Chagas' disease in humans. This region is found as multiple copies per protein. 514 matched cddid_all.tbl CDD pfam07910 pfam07910 400318 Peptidase_C78 Peptidase family C78. This family formerly known as DUF1671 has been shown to be a cysteine peptidase called (Ufm1)-specific protease. 199 matched cddid_all.tbl CDD pfam07911 pfam07911 462314 DUF1677 Protein of unknown function (DUF1677). The sequences found in this family are all derived from hypothetical plant proteins of unknown function. The region features a number of highly conserved cysteine residues. 89 matched cddid_all.tbl CDD pfam07912 pfam07912 400320 ERp29_N ERp29, N-terminal domain. ERp29 is a ubiquitously expressed endoplasmic reticulum protein, and is involved in the processes of protein maturation and protein secretion in this organelle. The protein exists as a homodimer, with each monomer being composed of two domains. The N-terminal domain featured in this family is organized into a thioredoxin-like fold that resembles the a domain of human protein disulphide isomerase (PDI). However, this domain lacks the C-X-X-C motif required for the redox function of PDI; it is therefore thought that ERp29's function is similar to the chaperone function of PDI. The N-terminal domain is exclusively responsible for the homodimerization of the protein, without covalent linkages or additional contacts with other domains. 126 matched cddid_all.tbl CDD pfam07913 pfam07913 285193 DUF1678 Protein of unknown function (DUF1678). This family is composed of uncharacterized proteins expressed by Methanopyrus kandleri, a hyperthermophilic archaebacterium. 196 matched cddid_all.tbl CDD pfam07914 pfam07914 369592 DUF1679 Uncharacterized oxidoreductase dhs-27. The region featured in this family is found in a number of C. elegans proteins, in one case as a repeat. In many of the family members, this region is associated with the CHK region described by SMART as being found in ZnF_C4 and HLH domain-containing kinases. In fact, one member of this family is annotated as being a member of the nuclear hormone receptor family, and contains regions typical of such proteins (Interpro:IPR000536, Interpro:IPR008946, and Interpro:IPR001628). 413 matched cddid_all.tbl CDD pfam07915 pfam07915 400321 PRKCSH Glucosidase II beta subunit-like protein. The sequences found in this family are similar to a region found in the beta-subunit of glucosidase II, which is also known as protein kinase C substrate 80K-H (PRKCSH). The enzyme catalyzes the sequential removal of two alpha-1,3-linked glucose residues in the second step of N-linked oligosaccharide processing. The beta subunit is required for the solubility and stability of the heterodimeric enzyme, and is involved in retaining the enzyme within the endoplasmic reticulum. Mutations in the gene coding for PRKCSH have been found to be involved in the development of autosomal dominant polycystic liver disease (ADPLD), but the precise role the protein has in the pathogenesis of this disease is unknown. This family also includes an ER sensor for misfolded glycoproteins and is therefore likely to be a generic sugar binding domain. 72 matched cddid_all.tbl CDD pfam07916 pfam07916 429732 TraG_N TraG-like protein, N-terminal region. The bacterial sequences found in this family are similar to the N-terminal region of the TraG protein. This is a membrane-spanning protein, with three predicted transmembrane segments and two periplasmic regions. TraG protein is known to be essential for DNA transfer in the process of conjugation, with the N-terminal portion being required for F pilus assembly. The protein is thought to interact with the periplasmic domain of TraN to stabilize mating-cell interactions. 390 matched cddid_all.tbl CDD pfam07918 pfam07918 462315 CAP160 CAP160 repeat. This region featured in this family is repeated in spinach cold acclimation protein CAP160 CAP160 is induced during periods of drought stress; its precise function is unknown but it has been implicated in the stabilization of membranes, cytoskeletal elements, and ribosomes. By acting as a compatible solute, it may reduce the toxic effects of cellular solutes that accumulate at high concentration during dehydration; it may also function as an enzyme that produces such a solute. Other members of this family are also induced by water stress, abscisic acid, and/or low temperature, such as desiccation-responsive protein 29B and CDet11-24 protein. 27 matched cddid_all.tbl CDD pfam07919 pfam07919 429734 Gryzun Gryzun, putative trafficking through Golgi. The proteins featured in this family are all eukaryotic, and many of them are annotated as being Gryzun. Gryzun is distantly related to, but distinct from, the Trs130 subunit of the TRAPP complex but is absent from S. cerevisiae. RNAi of human Gryzun blocks Golgi exit. Thus the family is likely to be involved with trafficking of proteins through membranes, perhaps as part of the TRAPP complex. 590 matched cddid_all.tbl CDD pfam07920 pfam07920 429735 DUF1684 Protein of unknown function (DUF1684). The sequences featured in this family are found in hypothetical archaeal and bacterial proteins of unknown function. The region in question is approximately 200 amino acids long. 141 matched cddid_all.tbl CDD pfam07921 pfam07921 254516 Fibritin_C Fibritin C-terminal region. This family features sequences bearing similarity to the C-terminal portion of the bacteriophage T4 protein fibritin. This protein is responsible for attachment of long tail fibres to virus particle, and forms the 'whiskers' or fibres on the neck of the virion. The region seen in this family contains an N-terminal coiled-coil portion and the C-terminal globular foldon domain (residues 457-486), which is essential for fibritin trimerization and folding. This domain consists of a beta-hairpin; three such hairpins come together in a beta-propeller-like arrangement in the trimer, which is stabilized by hydrogen bonds, salt bridges and hydrophobic interactions. 93 matched cddid_all.tbl CDD pfam07922 pfam07922 429736 Glyco_transf_52 Glycosyltransferase family 52. This family features glycosyltransferases belonging to glycosyltransferase family 52, which have alpha-2,3- sialyltransferase (EC:4.2.99.4) and alpha-glucosyltransferase (EC 2.4.1.-) activity. For example, beta-galactoside alpha-2,3- sialyltransferase expressed by Neisseria meningitidis is a member of this family and is involved in a step of lipooligosaccharide biosynthesis requiring sialic acid transfer; these lipooligosaccharides are thought to be important in the process of pathogenesis. This family includes several bacterial lipooligosaccharide sialyltransferases similar to the Haemophilus ducreyi LST protein. Haemophilus ducreyi is the cause of the sexually transmitted disease chancroid and produces a lipooligosaccharide (LOS) containing a terminal sialyl N-acetyllactosamine trisaccharide. 271 matched cddid_all.tbl CDD pfam07923 pfam07923 429737 N1221 N1221-like protein. The sequences featured in this family are similar to a hypothetical protein product of ORF N1221 in the CPT1-SPC98 intergenic region of the yeast genome. This encodes an acidic polypeptide with several possible transmembrane regions. 282 matched cddid_all.tbl CDD pfam07924 pfam07924 429738 NuiA Nuclease A inhibitor-like protein. This family consists of protein sequences that are similar to the nuclease A inhibitor expressed by bacteria of the genus Anabaena (NuiA). This sequence is organized to form an alpha-beta-alpha sandwich fold, which is similar to the PR-1-like fold. NuiA interacts with nuclease A by means of residues located at one end of the molecule, including residues making up the loop between helices III and IV and the loop between strands C and D. The mechanism of inhibition of nuclease A by NuiA is as yet incompletely understood. 130 matched cddid_all.tbl CDD pfam07925 pfam07925 369599 RdRP_5 Reovirus RNA-dependent RNA polymerase lambda 3. The sequences in this family are similar to the reoviral minor core protein lambda 3, which functions as a RNA-dependent RNA polymerase within the protein capsid. It is organized into 3 domains. N- and C-terminal domains create a 'cage' that encloses a conserved central catalytic domain within a hollow centre; this catalytic domain is arranged to form 'fingers', 'palm' and 'thumb' subdomains. Unlike other RNA polymerases, like HIV reverse transcriptase and T7 RNA polymerase, lambda 3 protein binds template and substrate with only localized rearrangements, and catalytic activity can occur with little structural change. However, the structure of the catalytic complex is similar to that of other polymerase catalytic complexes with known structure. 1271 matched cddid_all.tbl CDD pfam07926 pfam07926 462316 TPR_MLP1_2 TPR/MLP1/MLP2-like protein. The sequences featured in this family are similar to a region of human TPR protein and to yeast myosin-like proteins 1 (MLP1) and 2 (MLP2). These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores. TPR is thought to be a component of nuclear pore complex- attached intra-nuclear filaments, and is implicated in nuclear protein import. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerization of kinase domains or by targeting these kinases to the nuclear pore complex. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity. 129 matched cddid_all.tbl CDD pfam07927 pfam07927 462317 HicA_toxin HicA toxin of bacterial toxin-antitoxin,. HicA_toxin is a bacterial family of toxins that act as mRNA interferases. The antitoxin that neutralizes this is family HicB, pfam15919. 56 matched cddid_all.tbl CDD pfam07928 pfam07928 462318 Vps54 Vps54-like protein. This family contains various proteins that are homologs of the yeast Vps54 protein, such as the rat homolog, the human homolog, and the mouse homolog. In yeast, Vps54 associates with Vps52 and Vps53 proteins to form a trimolecular complex that is involved in protein transport between Golgi, endosomal, and vacuolar compartments. All Vps54 homologs contain a coiled coil region (not found in the region featured in this family) and multiple dileucine motifs. 131 matched cddid_all.tbl CDD pfam07929 pfam07929 462319 PRiA4_ORF3 Plasmid pRiA4b ORF-3-like protein. Members of this family are similar to the protein product of ORF-3 found on plasmid pRiA4 in the bacterium Agrobacterium rhizogenes. This plasmid is responsible for tumourigenesis at wound sites of plants infected by this bacterium, but the ORF-3 product does not seem to be involved in the pathogenetic process. Other proteins found in this family are annotated as being putative TnpR resolvases (Swiss:Q9LCU7, Swiss:Q50439), but no further evidence was found to back this. Moreover, another member of this family is described as a probable lexA repressor and in fact carries a LexA DNA binding domain (pfam01726), but no references were found to expand on this. 165 matched cddid_all.tbl CDD pfam07930 pfam07930 400333 DAP_B D-aminopeptidase, domain B. D-aminopeptidase is a dimeric enzyme with each monomer being composed of three domains. Domain B is organized to form a beta barrel made up of eight antiparallel beta strands. It is connected to domain A, the catalytic domain, by an eight-residue sequence, and also interacts with both domains A and C via non-covalent bonds. Domain B probably functions in maintaining domain C in a good position to interact with domain A. 181 matched cddid_all.tbl CDD pfam07931 pfam07931 400334 CPT Chloramphenicol phosphotransferase-like protein. The members of this family are all similar to chloramphenicol 3-O phosphotransferase (CPT) expressed by Streptomyces venezuelae. Chloramphenicol (Cm) is a metabolite produced by this bacterium that can inhibit ribosomal peptidyl transferase activity and therefore protein production. By transferring a phosphate group to the C-3 hydroxyl group of Cm, CPT inactivates this potentially lethal metabolite. 172 matched cddid_all.tbl CDD pfam07933 pfam07933 462320 DUF1681 Protein of unknown function (DUF1681). This family is composed of sequences derived from a number of hypothetical eukaryotic proteins of unknown function. 157 matched cddid_all.tbl CDD pfam07934 pfam07934 429744 OGG_N 8-oxoguanine DNA glycosylase, N-terminal domain. The presence of 8-oxoguanine residues in DNA can give rise to G-C to T-A transversion mutations. This enzyme is found in archaeal, bacterial and eukaryotic species, and is specifically responsible for the process which leads to the removal of 8-oxoguanine residues. It has DNA glycosylase activity (EC:3.2.2.23) and DNA lyase activity (EC:4.2.99.18). The region featured in this family is the N-terminal domain, which is organized into a single copy of a TBP-like fold. The domain contributes residues to the 8-oxoguanine binding pocket. 115 matched cddid_all.tbl CDD pfam07935 pfam07935 311750 SSV1_ORF_D-335 ORF D-335-like protein. The sequences featured in this family are similar to a probable integrase expressed by the SSV1 virus of the archaebacterium Sulfolobus shibatae. This protein may be necessary for the integration of the virus into the host genome by a process of site-specific recombination. 63 matched cddid_all.tbl CDD pfam07936 pfam07936 254527 Defensin_4 Potassium-channel blocking toxin. This family features the antihypertensive and antiviral proteins BDS-I and BDS-II expressed by Anemonia sulcata. BDS-I is organized into a triple-stranded antiparallel beta-sheet, with an additional small antiparallel beta-sheet at the N-terminus. Both peptides are known to specifically block the Kv3.4 potassium channel, and thus bring about a decrease in blood pressure. Moreover, they inhibit the cytopathic effects of mouse hepatitis virus strain MHV-A59 on mouse liver cells, by an unknown mechanism. 34 matched cddid_all.tbl CDD pfam07937 pfam07937 285213 DUF1686 Protein of unknown function (DUF1686). The members of this family are all hypothetical proteins of unknown function expressed by the eukaryotic parasite Encephalitozoon cuniculi GB-M1. The region in question is approximately 250 amino acids long. 182 matched cddid_all.tbl CDD pfam07938 pfam07938 429745 Fungal_lectin Fungal fucose-specific lectin. Lectins are involved in many recognition events at the molecular or cellular level. These fungal lectins, such as Aleuria aurantia lectin (AAL), specifically recognize fucosylated glycans. AAL is a dimeric protein, with each monomer being organized into a six-bladed beta-propeller fold and a small antiparallel two-stranded beta-sheet. The beta-propeller fold is important in fucose recognition; five binding pockets are found between the propeller blades. The small beta-sheet, on the other hand, is involved in the dimerization process. 299 matched cddid_all.tbl CDD pfam07939 pfam07939 462321 DUF1685 Protein of unknown function (DUF1685). The members of this family are hypothetical eukaryotic proteins of unknown function. The region in question is approximately 100 amino acid residues long. 59 matched cddid_all.tbl CDD pfam07940 pfam07940 429747 Hepar_II_III Heparinase II/III-like protein. This family features sequences that are similar to a region of the Flavobacterium heparinum proteins heparinase II and heparinase III. The former is known to degrade heparin and heparin sulphate, whereas the latter predominantly degrades heparin sulphate. Both are secreted into the periplasmic space upon induction with heparin. 237 matched cddid_all.tbl CDD pfam07941 pfam07941 429748 K_channel_TID Potassium channel Kv1.4 tandem inactivation domain. This family features the tandem inactivation domain found at the N-terminus of the Kv1.4 potassium channel. It is composed of two subdomains. Inactivation domain 1 (ID1, residues 1-38) consists of a flexible N-terminus anchored at a 5-turn helix, and is thought to work by occluding the ion pathway, as is the case with a classical ball domain. Inactivation domain 2 (ID2, residues 40-50) is a 2.5 turn helix with a high proportion of hydrophobic residues that probably serves to attach ID1 to the cytoplasmic face of the channel. In this way, it can promote rapid access of ID1 to the receptor site in the open channel. ID1 and ID2 function together to being about fast inactivation of the Kv1.4 channel, which is important for the channel's role in short-term plasticity. 71 matched cddid_all.tbl CDD pfam07942 pfam07942 400340 CARME Carnosine N-methyltransferase. This family includes Carnosine N-methyltransferase (E.C:2.1.1.22), conserved from yeast to human, that catalyzes the formation of anserine (beta-alanyl-N(Pi)-methyl-L-histidine) from carnosine. Anserine, a methylated derivative of carnosine (beta-alanyl-L-histidine), is an abundant constituent of vertebrate skeletal muscles. It also methylates other L-histidine-containing di- and tripeptides such as Gly-Gly-His, Gly-His and homocarnosine (GABA-His). 268 matched cddid_all.tbl CDD pfam07943 pfam07943 429749 PBP5_C Penicillin-binding protein 5, C-terminal domain. Penicillin-binding protein 5 expressed by E. coli functions as a D-alanyl-D-alanine carboxypeptidase. It is composed of two domains that are oriented at approximately right angles to each other. The N-terminal domain (pfam00768) is the catalytic domain. The C-terminal domain featured in this family is organized into a sandwich of two anti-parallel beta-sheets, and has a relatively hydrophobic surface as compared to the N-terminal domain. Its precise function is unknown; it may mediate interactions with other cell wall-synthesising enzymes, thus allowing the protein to be recruited to areas of active cell wall synthesis. It may also function as a linker domain that positions the active site in the catalytic domain closer to the peptidoglycan layer, to allow it to interact with cell wall peptides. 91 matched cddid_all.tbl CDD pfam07944 pfam07944 400342 Glyco_hydro_127 Beta-L-arabinofuranosidase, GH127. One member of this family, from Bidobacterium longicum, UniProtKB:E8MGH8, has been characterized as an unusual beta-L-arabinofuranosidase enzyme, EC:3.2.1.185. It rleases l-arabinose from the l-arabinofuranose (Araf)-beta1,2-Araf disaccharide and also transglycosylates 1-alkanols with retention of the anomeric configuration. Terminal beta-l-arabinofuranosyl residues have been found in arabinogalactan proteins from a mumber of different plantt species. beta-l-Arabinofuranosyl linkages with 1-4 arabinofuranosides are also found in the sugar chains of extensin and solanaceous lectins, hydroxyproline (Hyp)2-rich glycoproteins that are widely observed in plant cell wall fractions. The critical residue for catalytic activity is Glu-338, in a ET/SCAS sequence context. 503 matched cddid_all.tbl CDD pfam07945 pfam07945 116555 Toxin_16 Janus-atracotoxin. This family includes three peptides secreted by the spider Hadronyche versuta (Swiss:P82226, Swiss:P82227, Swiss:P82228). These are insect-selective, excitatory neurotoxins that may function by antagonising muscle acetylcholine receptors, or acetylcholine receptor subtypes present in other invertebrate neurons. Janus atracotoxin-Hv1c (J-ACTX-Hv1c) is organized into a disulphide-rich globular core (residues 3-19) and a beta-hairpin (residues 20-34). There are 4 disulphide bridges, one of which is a vicinal disulphide bridge; this is known to be unimportant in the maintenance of structure but critical for insecticidal activity. 36 matched cddid_all.tbl CDD pfam07946 pfam07946 462322 CCDC47 PAT complex subunit CCDC47. This family represents CCDC47 proteins which are a component of the PAT complex, an endoplasmic reticulum (ER)-resident membrane multiprotein complex that facilitates multi-pass membrane proteins insertion into membranes. The PAT complex, formed by CCDC47 and Asterix proteins, acts as an intramembrane chaperone by directly interacting with nascent transmembrane domains (TMDs), releasing its substrates upon correct folding, and is needed for optimal biogenesis of multi-pass membrane proteins. CCDC47 is required to maintain the stability of Asterix. CCDC47 is associated with various membrane-associated processes and is component of a ribosome-associated ER translocon complex involved in multi-pass membrane protein transport into the ER membrane and biogenesis. It is also involved in the regulation of calcium ion homeostasis in the ER, being also required for proper protein degradation via the ERAD (ER-associated degradation) pathway. 323 matched cddid_all.tbl CDD pfam07947 pfam07947 429751 YhhN YhhN family. The members of this family are similar to the hypothetical protein yhhN expressed by E. coli. Many are annotated as possible transmembrane proteins, and in fact they all have a high proportion of hydrophobic residues. A human member of this family, formerly known as TMEM86B, is a lysoplasmalogenase that catalyzes the hydrolysis of the vinyl ether bond of lysoplasmalogen. Putative conserved active site residues have been proposed for the YhhN family. 182 matched cddid_all.tbl CDD pfam07948 pfam07948 285223 Nairovirus_M Nairovirus M polyprotein-like. The sequences in this family are similar to the Dugbe virus M polyprotein precursor, which includes glycoproteins G1 and G2. Both are thought to be inserted in the membrane of the Golgi complex of the infected host cell, and G1 is known to have a role in infection of vertebrate hosts. 657 matched cddid_all.tbl CDD pfam07949 pfam07949 400345 YbbR YbbR-like protein. The members of this family are are all hypothetical bacterial proteins of unknown function, and are similar to the YbbR protein expressed by Bacillus subtilis (Swiss:O34659, Swiss:O87088). One member is annotated as an uncharacterized secreted protein, whereas another member is described as a hypothetical protein in the 5'region of the def gene of Thermus thermophilus, which encodes a deformylase, but no further information was found in either case. This region is found repeated up to four times in many members of this family. 80 matched cddid_all.tbl CDD pfam07950 pfam07950 400346 MCP1_TM MDM10-complementing protein 1, transmembrane domain. This entry represents the transmembrane domains found in MDM10-complementing protein 1 from yeast, a mitochondrial protein involved in in mitochondrial lipid homeostasis. 105 matched cddid_all.tbl CDD pfam07951 pfam07951 285226 Toxin_R_bind_C Clostridium neurotoxin, C-terminal receptor binding. The Clostridium neurotoxin family is composed of tetanus neurotoxins and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (pfam01742), the central translocation domains and two receptor binding domains. This domains is the C-terminal receptor binding domain, which adopts a modified beta-trefoil fold with a six stranded beta-barrel and a beta-hairpin triplet capping the domain. The first step in the intoxication process is a binding event between this domains and the pre-synaptic nerve ending. 217 matched cddid_all.tbl CDD pfam07952 pfam07952 400347 Toxin_trans Clostridium neurotoxin, Translocation domain. The Clostridium neurotoxin family is composed of tetanus neurotoxin and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (pfam01742), the central translocation domains and two receptor binding domains. Subsequent to cell surface binding and receptor mediated endocytosis of the neurotoxin, an acid induced conformational change in the neurotoxin translocation domain is believed to allow the domain to penetrate the endosome and from a pore, thereby facilitating the passage of the catalytic domain across the membrane into the cytosol. The structure of the translocation reveals a pair of helices that are 105 Angstroms long and is structurally distinct from other pore forming toxins. 323 matched cddid_all.tbl CDD pfam07953 pfam07953 400348 Toxin_R_bind_N Clostridium neurotoxin, N-terminal receptor binding. The Clostridium neurotoxin family is composed of tetanus neurotoxin and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein. The N-terminal catalytic domain (pfam01742), the central translocation domains and two receptor binding domains. This domains is the N-terminal receptor binding domain,which is comprised of two seven-stranded beta-sheets sandwiched together to form a jelly role motif. The role of this domain in receptor binding appears to be indirect. 192 matched cddid_all.tbl CDD pfam07954 pfam07954 369614 DUF1689 Protein of unknown function (DUF1689). Family of fungal proteins with unknown function. A member of this family has been found to localize in the mitochondria. 143 matched cddid_all.tbl CDD pfam07955 pfam07955 400349 DUF1687 Protein of unknown function (DUF1687). This is a putative redox protein which is predicted to have a thioredoxin fold containing a single active cysteine. 124 matched cddid_all.tbl CDD pfam07956 pfam07956 429752 DUF1690 Protein of Unknown function (DUF1690). Family of uncharacterized fungal proteins. 138 matched cddid_all.tbl CDD pfam07957 pfam07957 400351 DUF3294 Protein of unknown function (DUF3294). This family was annotated as mitochondrial Ribosomal protein MRP8, based on the presumed similarity of the S.cerevisiae protein to an E.coli mitochondrial ribosomal protein; however, this similarity is spurious, and the function is not known [Wood, V]. 213 matched cddid_all.tbl CDD pfam07958 pfam07958 429753 DUF1688 Protein of unknown function (DUF1688). A family of uncharacterized proteins. 420 matched cddid_all.tbl CDD pfam07959 pfam07959 462323 Fucokinase L-fucokinase. In the salvage pathway of GDP-L-fucose, free cytosolic fucose is phosphorylated by L-fucokinase to form L-fucose-L-phosphate, which is then further converted to GDP-L-fucose in the reaction catalyzed by GDP-L-fucose pyrophosphorylase. 405 matched cddid_all.tbl CDD pfam07960 pfam07960 369619 CBP4 CBP4. The CBP4 in S. cerevisiae is essential for the expression and activity of ubiquinol-cytochrome c reductase. This family describes fungal and human proteins.. 125 matched cddid_all.tbl CDD pfam07961 pfam07961 254545 MBA1 MBA1-like protein. Mba1 is an inner membrane protein that is part of the mitochondrial protein export machinery. It binds to the large subunit of mitochondrial ribosomes and cooperates with the C-terminal ribosome-binding domain of Oxa1, which is a central component of the insertion machinery of the inner membrane. In the absence of both Mba1 and the C-terminus of Oxa1, mitochondrial translation products fail to be properly inserted into the inner membrane and serve as substrates of the matrix chaperone Hsp70. It is proposed that Mba1 functions as a ribosome receptor that cooperates with Oxa1 in the positioning of the ribosome exit site to the insertion machinery of the inner membrane. 235 matched cddid_all.tbl CDD pfam07962 pfam07962 462324 Swi3 Replication Fork Protection Component Swi3. Replication fork pausing is required to initiate a recombination events. More specifically, Swi1 is required for recombination near the mat1 locus. Swi3 has been found to co-purify with Swi1 Swi3, together with Swi1, define a fork protection complex that coordinates leading- and lagging-strand synthesis and stabilizes stalled replication forks. The Swi1-Swi3 complex is required for accurate replication, fork protection and replication checkpoint signalling 83 matched cddid_all.tbl CDD pfam07963 pfam07963 429756 N_methyl Prokaryotic N-terminal methylation motif. This short motif directs methylation of the conserved phenylalanine residue. It is most often found at the N-terminus of pilins and other proteins involved in secretion, see pfam00114, pfam05946, pfam02501 and pfam07596. 27 matched cddid_all.tbl CDD pfam07964 pfam07964 369621 Red1 Rec10 / Red1. Rec10 / Red1 is involved in meiotic recombination and chromosome segregation during homologous chromosome formation. This protein localizes to the synaptonemal complex in S. cerevisiae and the analogous structures (linear elements) in S. pombe. This family is currently only found in fungi. 748 matched cddid_all.tbl CDD pfam07965 pfam07965 462325 Integrin_B_tail Integrin beta tail domain. This is the beta tail domain of the Integrin protein. Integrins are receptors which are involved in cell-cell and cell-extracellular matrix interactions. 84 matched cddid_all.tbl CDD pfam07966 pfam07966 462326 A1_Propeptide A1 Propeptide. Most eukaryotic endopeptidases (Merops Family A1) are synthesized with signal and propeptides. The animal pepsin-like endopeptidase propeptides form a distinct family of propeptides, which contain a conserved motif approximately 30 residues long. In pepsinogen A, the first 11 residues of the mature pepsin sequence are displaced by residues of the propeptide. The propeptide contains two helices that block the active site cleft, in particular the conserved Asp11 residue, in pepsin, hydrogen bonds to a conserved Arg residues in the propeptide. This hydrogen bond stabilizes the propeptide conformation and is probably responsible for triggering the conversion of pepsinogen to pepsin under acidic conditions. 27 matched cddid_all.tbl CDD pfam07967 pfam07967 429759 zf-C3HC C3HC zinc finger-like. This zinc-finger like domain is distributed throughout the eukaryotic kingdom in NIPA (Nuclear interacting partner of ALK) proteins. NIPA is implicate to perform some sort of antiapoptotic role in nucleophosmin-anaplastic lymphoma kinase (ALK) mediated signaling events. The domain is often repeated, with the second domain usually containing a large insert (approximately 90 residues) after the first three cysteine residues. The Schizosaccharomyces pombe the protein containing this domain is involved in mRNA export from the nucleus. 132 matched cddid_all.tbl CDD pfam07968 pfam07968 429760 Leukocidin Leukocidin/Hemolysin toxin family. 253 matched cddid_all.tbl CDD pfam07969 pfam07969 400360 Amidohydro_3 Amidohydrolase family. 464 matched cddid_all.tbl CDD pfam07970 pfam07970 462327 COPIIcoated_ERV Endoplasmic reticulum vesicle transporter. This family is conserved from plants and fungi to humans. Erv46 works in close conjunction with Erv41 and together they form a complex which cycles between the endoplasmic reticulum and Golgi complex. Erv46-41 interacts strongly with the endoplasmic reticulum glucosidase II. Mammalian glucosidase II comprises a catalytic alpha-subunit and a 58 kDa beta subunit, which is required for ER localization. All proteins identified biochemically as Erv41p-Erv46p interactors are localized to the early secretory pathway and are involved in protein maturation and processing in the ER and/or sorting into COPII vesicles for transport to the Golgi. 225 matched cddid_all.tbl CDD pfam07971 pfam07971 429762 Glyco_hydro_92 Glycosyl hydrolase family 92. Members of this family are alpha-1,2-mannosidases, enzymes which remove alpha-1,2-linked mannose residues from Man(9)(GlcNAc)(2) by hydrolysis. They are critical for the maturation of N-linked oligosaccharides and ER-associated degradation. 465 matched cddid_all.tbl CDD pfam07972 pfam07972 429763 Flavodoxin_NdrI NrdI Flavodoxin like. 119 matched cddid_all.tbl CDD pfam07973 pfam07973 429764 tRNA_SAD Threonyl and Alanyl tRNA synthetase second additional domain. The catalytically active from of threonyl/alanyl tRNA synthetase is a dimer. Within the tRNA synthetase class II dimer, the bound tRNA interacts with both monomers making specific interactions with the catalytic domain, the C-terminal domain, and this domain (the second additional domain). The second additional domain is comprised of a pair of perpendicularly orientated antiparallel beta sheets, of four and three strands, respectively, that surround a central alpha helix that forms the core of the domain. 43 matched cddid_all.tbl CDD pfam07974 pfam07974 400365 EGF_2 EGF-like domain. This family contains EGF domains found in a variety of extracellular proteins. 26 matched cddid_all.tbl CDD pfam07975 pfam07975 336887 C1_4 TFIIH C1-like domain. The carboxyl-terminal region of TFIIH is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterized by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C (pfam00130). 55 matched cddid_all.tbl CDD pfam07976 pfam07976 429765 Phe_hydrox_dim Phenol hydroxylase, C-terminal dimerization domain. Phenol hydroxylase acts a homodimer, to hydroxylates phenol to catechol or similar product. The enzyme is comprised of three domains. The first two domains from the active site. The third domain, this domain, is involved in forming the dimerization interface. The domain adopts a thioredoxin-like fold. 166 matched cddid_all.tbl CDD pfam07977 pfam07977 429766 FabA FabA-like domain. This enzyme domain has a HotDog fold. 132 matched cddid_all.tbl CDD pfam07978 pfam07978 429767 NIPSNAP NIPSNAP. Members of this family include many hypothetical proteins. It also includes members of the NIPSNAP family which have putative roles in vesicular transport. This domain is often found in duplicate. 102 matched cddid_all.tbl CDD pfam07979 pfam07979 311782 Intimin_C Intimin C-type lectin domain. This domain is found at the C-terminus of intimin. Its structure has been solved and shown to have a C-lectin type of structure. Intimin is a bacterial adhesion molecule involved in intimate attachment of enteropathogenic and enterohemorrhagic Escherichia coli to mammalian host cells. Intimin targets the translocated intimin receptor (Tir), which is exported by the bacteria and integrated into the host cell plasma membrane. 101 matched cddid_all.tbl CDD pfam07980 pfam07980 429768 SusD_RagB SusD family. This domain is found in bacterial cell surface proteins such SusD and SusD-like proteins as well RagB, outer membrane surface receptor antigen. Bacteroidetes, one of the two dominant bacterial phyla in the human gut, are Gram-negative saccharolytic microorganizms that utilize a diverse array of glycans. Hence, they express starch-utilization system (Sus) for glycan uptake. SusD has 551 amino acids, and is almost entirely alpha-helical, with 22 alpha-helices, eight of which form 4 tetra-trico peptide repeats (TPRs: helix-turn-helix motifs involved in protein-protein interactions). The four TPRs pack together to create a right-handed super-helix. This is predicted to mediate the formation of SusD and SusC porin complex at the cell surface. The interaction between SusC and TPR1/TPR2 region of SusD is predicted to be of functional importance since it allows SusD to be in position for oligosaccharide capture from other Sus lipoproteins and delivery of these glycans to the SusC porin. The non-TPR containing portion of SusD is where starch binding occurs. The binding site is a shallow surface cavity located on top of TPR1. SusD homologs such as SusD-like proteins have a critical role in carbohydrate acquisition. Both SusD and its homologs, contain 15-20 residues at the N-terminus that might be a flexible linker region, anchoring the protein to the membrane and the glycan-binding domain. Other homologs to SusD have been examined in Porphyromonas gingivalis such as RagB, an immunodominant outer-membrane surface receptor antigen. Structural characterization of RagB shows substantial similarity with Bacteroides thetaiotaomicron SusD (i.e alpha-helices and TPR regions). Based on this structural similarity, functional studies suggest that, RagB binding of glycans occurs at pockets on the molecular surface that are distinct from those of SusD. 294 matched cddid_all.tbl CDD pfam07981 pfam07981 400370 Plasmod_MYXSPDY Plasmodium repeat_MYXSPDY. This repeat is found in two hypothetical Plasmodium proteins. 17 matched cddid_all.tbl CDD pfam07982 pfam07982 462328 Herpes_UL74 Herpes UL74 glycoproteins. Members of this family are viral glycoproteins that form part of an envelope complex. 418 matched cddid_all.tbl CDD pfam07983 pfam07983 400371 X8 X8 domain. The X8 domain domain contains at least 6 conserved cysteine residues that presumably form three disulphide bridges. The domain is found in an Olive pollen allergen as well as at the C-terminus of several families of glycosyl hydrolases. This domain may be involved in carbohydrate binding. This domain is characteriztic of GPI-anchored domains. 76 matched cddid_all.tbl CDD pfam07984 pfam07984 462329 NTP_transf_7 Nucleotidyltransferase. This family contains many hypothetical proteins. It also includes four nematode prion-like proteins. This domain has been identified as part of the nucleotidyltransferase superfamily. 320 matched cddid_all.tbl CDD pfam07985 pfam07985 462330 SRR1 SRR1 domain. SRR1 proteins are signalling proteins involved in regulating the circadian clock in Arabidopsis. This presumed domain has a Rossmann-like fold and structural models suggest it may have a methyltransferase function. 170 matched cddid_all.tbl CDD pfam07986 pfam07986 462331 TBCC Tubulin binding cofactor C. Members of this family are involved in the folding pathway of tubulins and form a beta helix structure. 119 matched cddid_all.tbl CDD pfam07987 pfam07987 429772 DUF1775 Domain of unkown function (DUF1775). Domain found in bacteria with undetermined function. Its structure has been determined and is an immunoglobulin-like fold. 146 matched cddid_all.tbl CDD pfam07988 pfam07988 462332 LMSTEN LMSTEN motif. This region of Myb proteins has previously been described as the transcriptional activation domain present in the vertebrate c-Myb and A-Myb, but neither vertebrate B-Myb proteins nor Myb proteins of invertebrates. Because vertebrate B-Myb (but neither A-Myb nor c-Myb) can partially complement Drosophila Myb null mutants, this region appears to have been a relatively recent insertion. 47 matched cddid_all.tbl CDD pfam07989 pfam07989 462333 Cnn_1N Centrosomin N-terminal motif 1. This domain has been identified in two microtubule associated proteins in Schizosaccharomyces pombe, Mto1 and Pcp1. Mto1 has been identified in association with spindle pole body and non-spindle pole body microtubules. The pericentrin homolog Pcp1 is also associated with the fungal centrosome or spindle pole body (SPB). Members of this family have been named centrosomins, and are an essential mitotic centrosome component required for assembly of all other known pericentriolar matrix proteins in order to achieve microtubule-organizing activity in fission yeast. Cnn_1N is a short conserved motif towards the N-terminus. Motif 1 is found to be necessary for proper recruitment of gamma-tubulin, D-TACC (the homolog of vertebrate transforming acidic coiled-coil proteins [TACC]), and Minispindles (Msps) to embryonic centrosomes but is not required for assembly of other centrosome components including Aurora A kinase and CP60 in Drosophila. 69 matched cddid_all.tbl CDD pfam07990 pfam07990 400378 NABP Nucleic acid binding protein NABP. Many members of this family are putative nucleic acid binding proteins. One member of this family has been partially characterized and contains two putative phosphorylation sites and a possible dimerization / leucine zipper domain. 387 matched cddid_all.tbl CDD pfam07991 pfam07991 285265 IlvN Acetohydroxy acid isomeroreductase, NADPH-binding domain. Acetohydroxy acid isomeroreductase catalyzes the conversion of acetohydroxy acids into dihydroxy valerates. This reaction is the second in the synthetic pathway of the essential branched side chain amino acids valine and isoleucine. This N-terminal region of the enzyme carries the binding-site for NADPH. The active-site for enzymatic activity lies in the C-terminal part, IlvC, pfam01450. 165 matched cddid_all.tbl CDD pfam07992 pfam07992 400379 Pyr_redox_2 Pyridine nucleotide-disulphide oxidoreductase. This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain. 301 matched cddid_all.tbl CDD pfam07993 pfam07993 462334 NAD_binding_4 Male sterility protein. This family represents the C-terminal region of the male sterility protein in a number of arabidopsis and drosophila. A sequence-related jojoba acyl CoA reductase is also included. 257 matched cddid_all.tbl CDD pfam07994 pfam07994 462335 NAD_binding_5 Myo-inositol-1-phosphate synthase. This is a family of myo-inositol-1-phosphate synthases. Inositol-1-phosphate catalyzes the conversion of glucose-6- phosphate to inositol-1-phosphate, which is then dephosphorylated to inositol. Inositol phosphates play an important role in signal transduction. 435 matched cddid_all.tbl CDD pfam07995 pfam07995 429776 GSDH Glucose / Sorbosone dehydrogenase. Members of this family are glucose/sorbosone dehydrogenases that possess a beta-propeller fold. 327 matched cddid_all.tbl CDD pfam07996 pfam07996 429777 T4SS Type IV secretion system proteins. Members of this family are components of the type IV secretion system. They mediate intracellular transfer of macromolecules via a mechanism ancestrally related to that of bacterial conjugation machineries. 189 matched cddid_all.tbl CDD pfam07997 pfam07997 429778 DUF1694 Protein of unknown function (DUF1694). This family contains many hypothetical proteins. 117 matched cddid_all.tbl CDD pfam07998 pfam07998 191923 Peptidase_M54 Peptidase family M54. This is a family of metallopeptidases. Two human proteins have been reported to degrade synthetic substrates and peptides. 176 matched cddid_all.tbl CDD pfam07999 pfam07999 462336 RHSP Retrotransposon hot spot protein, P-loop domain. Members of this entry are retrotransposon hot spot proteins (RHSPs). They are associated with polymorphic subtelomeric regions in Trypanosoma. These proteins contain a P-loop (ATP/GTP-binding) motif, represented in this entry, at the C-terminal of the conserved box 1. This domain also includes the retrotransposon insertion site. 312 matched cddid_all.tbl CDD pfam08000 pfam08000 462337 bPH_1 Bacterial PH domain. This family contains many bacterial hypothetical proteins. The structures of Swiss:A1SD03, PDB:3hsa, and Swiss:A3QB43, PDB:3dcx, show similarities to the PH or pleckstrin homology domain. First evidence of PH-like domains in bacteria suggests role in cell envelope stress response. 122 matched cddid_all.tbl CDD pfam08001 pfam08001 285273 CMV_US CMV US. This is a family of unique short (US) cytoplasmic glycoproteins which are expressed in cytomegalovirus. 245 matched cddid_all.tbl CDD pfam08002 pfam08002 462338 DUF1697 Protein of unknown function (DUF1697). This family contains many hypothetical bacterial proteins. 131 matched cddid_all.tbl CDD pfam08003 pfam08003 429781 Methyltransf_9 Protein of unknown function (DUF1698). This family contains many hypothetical proteins. It also includes two putative methyltransferase proteins, Swiss:Q8EEE6 and Swiss:Q88MX8. 315 matched cddid_all.tbl CDD pfam08004 pfam08004 429782 DUF1699 Protein of unknown function (DUF1699). This family contains many archaeal proteins which have very conserved sequences. 130 matched cddid_all.tbl CDD pfam08005 pfam08005 462339 PHR PHR domain. This domain is called PHR as it was original found in the proteins PAM, highwire and RPM. This domain can be duplicated in the highwire, PFAM and PRM sequence. The C-terminal region of the protein BTBD1 includes the PHR domain and is known to interact with Topoisomerase I, an enzyme which relaxes DNA supercoils. 150 matched cddid_all.tbl CDD pfam08006 pfam08006 285278 DUF1700 Protein of unknown function (DUF1700). This family contains many hypothetical bacterial proteins and putative membrane proteins. 181 matched cddid_all.tbl CDD pfam08007 pfam08007 462340 JmjC_2 JmjC domain. This entry includes proteins with a JmjC domain that belong to the cupin superfamily, including Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66, Ribosomal oxygenase 1/2, and 50S ribosomal protein L16 3-hydroxylase from Escherichia coli. Proteins are bifunctional, acting as histone lysine demethylases and ribosomal histidine hydroxylases. 116 matched cddid_all.tbl CDD pfam08008 pfam08008 285280 Viral_cys_rich Viral cysteine rich. Members of this family are polydna viral proteins that contain a cysteine rich motif. Some members of this family have multiple copies of this domain. 83 matched cddid_all.tbl CDD pfam08009 pfam08009 429784 CDP-OH_P_tran_2 CDP-alcohol phosphatidyltransferase 2. This domain is found on CDP-alcohol phosphatidyltransferases. These enzymes catalyze the displacement of CMP from a CDP-alcohol by a second alcohol with formation of a phosphodiester bond and concomitant breaking of a phosphoride anhydride bond. 37 matched cddid_all.tbl CDD pfam08010 pfam08010 285282 Phage_30_3 Bacteriophage protein GP30.3. Proteins in this family are bacteriophage GP30.3 proteins. Their function is poorly characterized. 138 matched cddid_all.tbl CDD pfam08011 pfam08011 400391 PDDEXK_9 PD-(D/E)XK nuclease superfamily. This family contains many hypothetical bacterial proteins. It has been identified as a member of the PD-(D/E)XK nuclease superfamily through transitive meta profile searches. DUF1703 has the predicted secondary structure pattern of the restriction endonuclease-like fold core and contains an additional beta-strand at the C-terminus. 104 matched cddid_all.tbl CDD pfam08012 pfam08012 400392 DUF1702 Protein of unknown function (DUF1702). This family of proteins contains many bacterial proteins that are encoded by the UnbL gene. The function of these proteins is unknown. 319 matched cddid_all.tbl CDD pfam08013 pfam08013 429785 GatZ_KbaZ-like D-tagatose-1,6-bisphosphate aldolase subunit GatZ/KbaZ-like. Escherichia coli and other enteric bacteria contain two closely related D-tagatose 1,6-bisphosphate (TagBP)-specific aldolases involved in catabolism of galactitol (genes gatY gatZ) and of N-acetyl-galactosamine and D-galactosamine (genes kbaY, kbaZ, also called agaY, agaZ). The catalytic subunits GatY/KbaY alone are sufficient to show aldolase activity and contain most or all of the residues that have been identified as essential in substrate/product recognition and catalysis for class II aldolases. However, these aldolases differ from other Class II aldolases (which are homodimeric enzymes) in that they require subunits GatZ/KbaZ for full activity and for good in vivo and in vitro stability. The Z subunits alone do not show any aldolase activity. This entry represents GatZ and KbaZ subunits. This entry also includes the D-tagatose 6-phosphate 4-epimerase Atu3167 from Agrobacterium fabrum which catalyzes the epimerization of D-tagatose 6-phosphate to D-fructose 6-phosphate. It should be noted that the previous suggestion of a tagatose 6P-kinase function for other members of this family has been debated. 420 matched cddid_all.tbl CDD pfam08014 pfam08014 429786 DUF1704 Domain of unknown function (DUF1704). This family contains many hypothetical proteins. 365 matched cddid_all.tbl CDD pfam08015 pfam08015 369652 Pheromone Fungal mating-type pheromone. This family corresponds to mating-type pheromone proteins. The homobasidiomycetes, or mushroom fungi, have arguably the most complex mating system of all known organizms. Many species possess a mating system known as bifactorial incompatibility, where two unlinked loci control the mating -type of an individual incompatibility loci (the A and B mating-type loci). Each A mating-type sublocus encodes a pair of divergently transcribed homeodomain transcription factors while the genes responsible for B mating-type activity encode lipopeptide pheromones and G-protein -coupled pheromone receptors. 67 matched cddid_all.tbl CDD pfam08016 pfam08016 462341 PKD_channel Polycystin cation channel. This family contains the cation channel region from group II of Transient receptor potential (TRP) channels, the TRPP subfamily, including PKD1, PKD2, PKD2L and mucolipin proteins. 225 matched cddid_all.tbl CDD pfam08017 pfam08017 311808 Fibrinogen_BP Fibrinogen binding protein. Proteins in this family bind to fibrinogen. Members of this family includes the fibrinogen receptor, FbsA, which mediates platelet aggregation. 393 matched cddid_all.tbl CDD pfam08018 pfam08018 429787 Antimicrobial_1 Frog antimicrobial peptide. This family includes antimicrobial peptides secreted from skins of frogs. The secretion of antimicrobial peptides from the skins of frogs plays an important role in the self defense of these frogs. Structural characterization of these peptides showed that they belonged to four known families: the brevinin-1 family, the esculentin-2 family, the ranatuerin-2 family and the temporin family. 23 matched cddid_all.tbl CDD pfam08019 pfam08019 429788 EptA_B_N Phosphoethanolamine transferase EptA/EptB. This entry represents a domain found in a group of bacterial phosphoethanolamine transferases, including eptA from Helicobacter pylori and eptB from Escherichia coli EC:2.7.8.42. This domain is found immediately N-terminal to the sulphatase domain in many sulphatases. 151 matched cddid_all.tbl CDD pfam08020 pfam08020 429789 DUF1706 Protein of unknown function (DUF1706). This family contains many hypothetical proteins from bacteria and yeast. 162 matched cddid_all.tbl CDD pfam08021 pfam08021 311811 FAD_binding_9 Siderophore-interacting FAD-binding domain. 118 matched cddid_all.tbl CDD pfam08022 pfam08022 285293 FAD_binding_8 FAD-binding domain. 108 matched cddid_all.tbl CDD pfam08023 pfam08023 400398 Antimicrobial_2 Frog antimicrobial peptide. This family consists of the major classes of antimicrobial peptides secreted from the skin of frogs that protect the frogs against invading microbes. They are typically between 10-50 amino acids long and are derived from proteolytic cleavage of larger precursors. Major classes of peptides such esculentin, gaegurin, brevinin, rugosin and ranatuerin are included in this family. 31 matched cddid_all.tbl CDD pfam08024 pfam08024 116634 Antimicrobial_4 Ant antimicrobial peptide. This family consists of the ponericin family of antimicrobial peptides isolated from predatory ant Pachycondyla goeldii. The ponericin peptides may adopt amphipathic alpha-helical structure in polar environments. In the ant colony, these peptides exhibit a defensive role against microbial pathogens arising from prey introduction and/or ingestion. 24 matched cddid_all.tbl CDD pfam08025 pfam08025 116635 Antimicrobial_3 Spider antimicrobial peptide. This family includes antimicrobial peptides isolated from the crude venom of the wolf spider Oxyopes kitabensis. These peptides, known as oxyopinins, are the largest linear cationic amphipathic peptides chemically characterized and exhibit disrupting activities towards biological membranes. 37 matched cddid_all.tbl CDD pfam08026 pfam08026 369654 Antimicrobial_5 Bee antimicrobial peptide. This family consists of antimicrobial peptides produced by bees. These peptides have strong antimicrobial and some anti-fungal activity and has homology to abaecin which is the largest proline-rich antimicrobial peptide isolated from European bumblebee Bombus pascuorum. 31 matched cddid_all.tbl CDD pfam08027 pfam08027 369655 Albumin_I Albumin I chain b. The albumin I protein, a hormone-like peptide, stimulates kinase activity upon binding a membrane bound 43 kDa receptor. The structure of this domain (chain b) reveals a knottin like fold, comprise of three beta strands. 35 matched cddid_all.tbl CDD pfam08028 pfam08028 429790 Acyl-CoA_dh_2 Acyl-CoA dehydrogenase, C-terminal domain. 133 matched cddid_all.tbl CDD pfam08029 pfam08029 462342 HisG_C HisG, C-terminal domain. 73 matched cddid_all.tbl CDD pfam08030 pfam08030 429792 NAD_binding_6 Ferric reductase NAD binding domain. 149 matched cddid_all.tbl CDD pfam08031 pfam08031 369658 BBE Berberine and berberine like. This domain is found in the berberine bridge and berberine bridge- like enzymes which are involved in the biosynthesis of numerous isoquinoline alkaloids. They catalyze the transformation of the N-methyl group of (S)-reticuline into the C-8 berberine bridge carbon of (S)-scoulerine. 45 matched cddid_all.tbl CDD pfam08032 pfam08032 429793 SpoU_sub_bind RNA 2'-O ribose methyltransferase substrate binding. This domain is a RNA 2'-O ribose methyltransferase substrate binding domain. 74 matched cddid_all.tbl CDD pfam08033 pfam08033 429794 Sec23_BS Sec23/Sec24 beta-sandwich domain. 86 matched cddid_all.tbl CDD pfam08034 pfam08034 400403 TES Trematode eggshell synthesis protein. This domain has been identified in a number of distantly related species of trematodes. This protein domain is crucial for eggshell synthesis in trematodes (Ebersberger I). 66 matched cddid_all.tbl CDD pfam08035 pfam08035 462343 Op_neuropeptide Opioids neuropeptide. This family corresponds to the conserved YGG motif that is found in a wide variety of opioid neuropeptides such as enkephalin. 30 matched cddid_all.tbl CDD pfam08036 pfam08036 285304 Antimicrobial_6 Diapausin family of antimicrobial peptide. This family consists of diapausin-related antimicrobial peptides. Diapause during periods of environmental adversity is an essential part of the life cycle of many organizms with the molecular basis being different among animals. Diapause-specific peptides provide anti-fungal activity and act as N-type voltage-gated calcium channel blocker. 39 matched cddid_all.tbl CDD pfam08037 pfam08037 311820 Attractin Attractin family. This family consists of the attractin family of water-borne pheromone. Mate attraction in Aplysia involves a long-distance water-borne signal in the form of the attractin peptide, that is released during egg laying. These peptides contain 6 conserved cysteines and are folded into 2 antiparallel helices. The second helix contains the IEECKTS sequence conserved in Aplysia attractins. 55 matched cddid_all.tbl CDD pfam08038 pfam08038 462344 Tom7 TOM7 family. This family consists of TOM7 family of mitochondrial import receptors. TOM7 forms part of the translocase of the outer mitochondrial membrane (TOM) complex and it appears to function as a modulator of the dynamics of the mitochondrial protein transport machinery by promoting the dissociation of subunits of the outer membrane translocase. 41 matched cddid_all.tbl CDD pfam08039 pfam08039 429796 Mit_proteolip Mitochondrial proteolipid. This family consists of proteins with similarity to the mitochondrial proteolipids. Mitochondrial proteolipid consists of about 60 amino acids residues and is about 6.8 kDa in size. 60 matched cddid_all.tbl CDD pfam08040 pfam08040 462345 NADH_oxidored MNLL subunit. This family consists of the MNLL subunits of NADH-ubiquinone oxidoreductase complex. NADH-ubiquinone oxidoreductase is involved in the transfer of electrons from NADH to the electron transport chain. This oxidation of NADH is coupled to proton transfer across the membrane, generating a proton motive force that is utilized for the synthesis of ATP. MNLL subunit is one of the many subunits found in the complex and it contains a mitochondrial import sequence. However, the role of MNLL subunit is unclear. 56 matched cddid_all.tbl CDD pfam08041 pfam08041 429798 PetM PetM family of cytochrome b6f complex subunit 7. This family consists of the PetM family of cytochrome b6f complex subunit IV. The cytochrome b6f complex consists of 7 subunits and contains 2 beta hemes and 1 chlorophyll alpha per cytochrome f. It is highly active in transferring electrons from decylplastoquinol to oxidized plastocyanin. 29 matched cddid_all.tbl CDD pfam08042 pfam08042 429799 PqqA PqqA family. This family consists of proteins belonging to the coenzyme Pyrroloquinoline quinone A (pqqA) family. PQQ is the non-covalently bounded prosthetic group of many quinoproteins catalysing reactions in the periplasm of Gram-negative bacteria. PQQ is formed by the fusion of glutamate and tyrosine and synthesis of PQQ require the proteins encoded by the pqqABCDEF operon but details of the biosynthetic pathway are unclear. 19 matched cddid_all.tbl CDD pfam08043 pfam08043 462346 Xin Xin repeat. The repeat has the consensus sequence GDV(K/Q/R)(T/S/G)X(R/K/T) WLFETXPLD. This repeat motif is typically found in the N-terminus of the proteins, with a copy number between 2 and 28 repeats. Direct evidence for binding to and stabilising F-actin has been found in the human protein Swiss:Q702N9. The homologs in mouse and chicken localize in the adherens junction complex of the intercalated disc in cardiac muscle and in the myotendon junction of skeletal muscle. mXin may co-localize with Vinculin which is known to attach the actin to the cytoplasmic membrane. It has been shown that the amino-terminus of human xin (CMYA1) binds the EVH1 domain of Mena/VASP/EVL, and the carboxy-terminus binds the, for the filamin family unique, domain 20 of filaminC. This confirms the proposed role of xin repeat containing proteins as F-actin-binding adapter proteins. 16 matched cddid_all.tbl CDD pfam08044 pfam08044 462347 DUF1707 Domain of unknown function (DUF1707). This domain is found in a variety of Actinomycetales proteins. All of the proteins containing this domain are hypothetical and probably membrane bound or associated. Currently, it is unclear to the function of this domain. 53 matched cddid_all.tbl CDD pfam08045 pfam08045 429802 CDC14 Cell division control protein 14, SIN component. Cdc14 is a component of the septation initiation network (SIN) and is required for the localization and activity of Sid1. Sid1 is a protein kinase that localizes asymmetrically to one spindle pole body (SPB) in anaphase disappears prior to cell separation. 284 matched cddid_all.tbl CDD pfam08046 pfam08046 429803 IlvGEDA_leader IlvGEDA operon leader peptide. This family consists of the leader peptides of ilvGEDA operon. The expression of the ilvGEDA operon of E coli K-12 is multivalently controlled by the three branched -chain amino acids. Regulation is thought to occur by attenuation of transcription in response to the changing levels of the cognate tRNAs. Transcription of this operon is usually terminated at the end of the leader (regulatory) region. 32 matched cddid_all.tbl CDD pfam08047 pfam08047 285314 His_leader Histidine operon leader peptide. This family consists of the leader peptide of the histidine (his) operon. The his operon contains all the genes necessary for histidine biosynthesis. The region corresponding to the untranslated 5' end of the transcript, named the his leader region, displays the typical features of the T box transcriptional attenuation mechanism which is involved in the regulation of many amino acid biosynthetic operons. 16 matched cddid_all.tbl CDD pfam08048 pfam08048 116658 RepA1_leader Tap RepA1 leader peptide. This family consists of the RepA1 leader peptides. The frequency of replication of IncFII plasmid NR1 during the cell division cycle is regulated by the control of the synthesis of the plasmid-specific replication initiation protein (RepA1). When RepA1 is synthesized, it binds to the plasmid replication origin (ori) and effects the assembly of a replication complex composed of host proteins that mediate the replication of the plasmid. The tap gene encodes a 24-amino acids protein. The translation of tap is required for translation of repA. 25 matched cddid_all.tbl CDD pfam08049 pfam08049 429804 IlvB_leader IlvB leader peptide. This family consists of the leader peptides of the ilvB operon. This region encodes a potential leader polypeptide containing 32 amino acids, 12 of which are the regulatory amino acids valine and leucine. A model for the multivalent regulation of this operon by valyl- and leucyl-tRNA is proposed on the basis of the mutually exclusive formation of five strong stem-and-loop structures in the leader mRNA. 32 matched cddid_all.tbl CDD pfam08050 pfam08050 254601 Tet_res_leader Tetracycline resistance leader peptide. This family consists of the tetracycline resistance leader peptide. The presence of 3 inverted repeats which can form 2 different conformations of mRNA suggests that the tetracycline resistance (TcR) region is regulated by a translational attenuation mechanism. A Rho-independent transcriptional terminator structure is present immediately after the translational stop codon of the TET protein. 20 matched cddid_all.tbl CDD pfam08051 pfam08051 369670 Ery_res_leader1 Erythromycin resistance leader peptide. This family consists of erythromycin resistance gene leader peptides. These leader peptides are involved in the translational attenuation of erythromycin resistance genes. Interestingly, the consensus sequence of peptides conferring erythromycin resistance is similar to that of the leader peptides, thus indicating that a similar type of interaction between the nascent peptide and antibiotics can occur in both cases. This family also includes a small number of regions from within larger proteins from actinomycetes. 15 matched cddid_all.tbl CDD pfam08052 pfam08052 285317 PyrBI_leader PyrBI operon leader peptide. This family consists of the pyrBI operon leader peptides. The expression of the pyrBI operon, which encodes the subunits of the pyrimidine biosynthetic enzyme aspartate transcarbamylase. is regulated primarily through a UTP-sensitive transcriptional attenuation control mechanism. In this mechanism, the concentration of UTP determines the extent of coupling between transcription and translation within the pyrBI leader region, hence determining the level of rho-independent transcriptional termination at an attenuator preceding the pyrB gene. 44 matched cddid_all.tbl CDD pfam08053 pfam08053 369671 Tna_leader Tryptophanase operon leader peptide. This family consists of the tryptophanase (tna) operon leader peptide. Tna catalyzes the degradation of L-tryptophan to indole, pyruvate and ammonia, enabling the bacteria to utilize tryptophan as a source of carbon, nitrogen and energy. The tna operon of E. coli contains two major structural genes, tnaA and tnaB. Preceding tnaA in the tna operon is a 319 -nucleotide transcribed regulatory region that contains the coding region for a 24-residue leader peptide, TnaC. The RNA sequence in the vicinity of the tnaC stop codon is rich in Cytidylate residues which is required for efficient Rho -dependent termination in the leader region of the tna operon. 23 matched cddid_all.tbl CDD pfam08054 pfam08054 429805 Leu_leader Leucine operon leader peptide. This family consists of the leucine operon leader peptide. The leucine operon is involved in the control of the biosynthesis of leucine. Four adjacent leucine codons within the leucine leader RNA are critically important in transcription attenuation-mediated control of leucine operon expression in bacteria. The leader RNA contains translational start and stop signals, a cluster of four leucine codons and overlapping regions of dyad symmetry that are capable of forming stem-and-loop structures. 28 matched cddid_all.tbl CDD pfam08055 pfam08055 116663 Trp_leader1 Tryptophan leader peptide. This family consists of the tryptophan (trp) leader peptides. Tryptophan accumulation is the principal event resulting in downregulation of transcription of the structural genes of the trp operon. The leader peptide of the trp operon forms mutually exclusive secondary structures that would either result in the termination of transcription of the trp operon when tryptophan is in plentiful supply or vice versa. 18 matched cddid_all.tbl CDD pfam08056 pfam08056 429806 Trp_leader2 Tryptophan operon leader peptide. This family consists of the tryptophan operon leader peptides. The tryptophan operon is regulated by transcription attenuation in response to changes in the level of tryptophan. The transcript of the leader peptide can adopt alternative mutually-exclusive secondary structures that would either result in termination of transcription of the tryptophan structural genes or in transcription of the entire operon. 41 matched cddid_all.tbl CDD pfam08057 pfam08057 71493 Ery_res_leader2 Erythromycin resistance leader peptide. This family consists of erythromycin resistance gene leader peptides. These leader peptides are involved in the transcriptional attenuation control of the synthesis of the macrolide-lincosamide -streptogramin B resistance protein. It acts as a transcriptional attenuator, in contrast to other inducible erm genes. The mRNA leader sequence can fold in either of two mutually exclusive conformations, one of which is postulated to form in the absence of induction, and to contain two rho factor-independent terminators.. 14 matched cddid_all.tbl CDD pfam08058 pfam08058 400412 NPCC Nuclear pore complex component. Proteins containing this domain are components of the nuclear pore complex. One member of this family is Nucleoporin POM34, which is thought to have a role in anchoring peripheral Nups into the pore and mediating pore formation. 134 matched cddid_all.tbl CDD pfam08059 pfam08059 462348 SEP SEP domain. The SEP domain is named after Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47. In p47, the SEP domain has been shown to bind to and inhibit the cysteine protease cathepsin L. Most SEP domains are succeeded closely by a UBX domain. 75 matched cddid_all.tbl CDD pfam08061 pfam08061 429808 P68HR P68HR (NUC004) repeat. This short region is found in two copies in p68-like RNA helicases. 35 matched cddid_all.tbl CDD pfam08062 pfam08062 285324 P120R P120R (NUC006) repeat. This characteriztic repeat of proliferating cell nuclear antigen P120 is found in three copies. 22 matched cddid_all.tbl CDD pfam08063 pfam08063 462349 PADR1 PADR1 (NUC008) domain. This domain is found in poly(ADP-ribose)-synthetases. The function of this domain is unknown. 53 matched cddid_all.tbl CDD pfam08064 pfam08064 462350 UME UME (NUC010) domain. This domain is characteriztic of UVSB PI-3 kinase, MEI-41 and ESR1. 102 matched cddid_all.tbl CDD pfam08065 pfam08065 462351 KI67R KI67R (NUC007) repeat. This family represents the KI67/Chmadrin repeat. The function of this repeat is unknown. 112 matched cddid_all.tbl CDD pfam08066 pfam08066 462352 PMC2NT PMC2NT (NUC016) domain. This domain is found at the N-terminus of 3'-5' exonucleases with HRDC domains, and also in putative exosome components. 89 matched cddid_all.tbl CDD pfam08067 pfam08067 429813 ROKNT ROKNT (NUC014) domain. This presumed domain is found at the N-terminus of RNP K-like proteins that also contains KH domains pfam00013. 39 matched cddid_all.tbl CDD pfam08068 pfam08068 462353 DKCLD DKCLD (NUC011) domain. This is a TruB_N/PUA domain associated N-terminal domain of Dyskerin-like proteins. 58 matched cddid_all.tbl CDD pfam08069 pfam08069 462354 Ribosomal_S13_N Ribosomal S13/S15 N-terminal domain. This domain is found at the N-terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021. 57 matched cddid_all.tbl CDD pfam08070 pfam08070 462355 DTHCT DTHCT (NUC029) region. The DTCHT region is the C-terminal part of DNA gyrases B / topoisomerase IV / HATPase proteins. This region is composed of quite low complexity sequence. 97 matched cddid_all.tbl CDD pfam08071 pfam08071 429817 RS4NT RS4NT (NUC023) domain. This is the N-terminal domain of Ribosomal S4 / S4e proteins. This domain is associated with S4 and KOW domains. 37 matched cddid_all.tbl CDD pfam08072 pfam08072 462356 BDHCT BDHCT (NUC031) domain. This is a C-terminal domain in Bloom's syndrome DEAD helicase subfamily. 41 matched cddid_all.tbl CDD pfam08073 pfam08073 462357 CHDNT CHDNT (NUC034) domain. The CHDNT domain is found in PHD/RING finger and chromo domain-associated helicases. 54 matched cddid_all.tbl CDD pfam08074 pfam08074 462358 CHDCT2 CHDCT2 (NUC038) domain. The CHDCT2 C-terminal domain is found in PHD/RING finger and chromo domain-associated CHD-like helicases. 145 matched cddid_all.tbl CDD pfam08075 pfam08075 462359 NOPS NOPS (NUC059) domain. This domain is found at the C-terminus of NONA and PSP1 proteins adjacent to 1 or 2 pfam00076 domains. 52 matched cddid_all.tbl CDD pfam08076 pfam08076 285338 TetM_leader Tetracycline resistance determinant leader peptide. This family consists of the tetracycline resistance determinant tet(M) leader peptides. A short open reading frame corresponding to a 28 amino acid peptide which contain a number of inverted repeat sequences was found immediately upstream of the tet(M). Transcriptional analyses has found that expression of tet(M) resulted from an extension of a small transcript representing the upstream leader region into the resistance determinant. Thus this leader sequence is responsible for transcriptional attenuation and thus regulation of the transcription of tet(M). 28 matched cddid_all.tbl CDD pfam08077 pfam08077 71513 Cm_res_leader Chloramphenicol resistance gene leader peptide. This family consists of chloramphenicol (Cm) resistance gene leader peptides. Inducible resistance to Cm in both Gram positive and Gram negative bacteria is controlled by translation attenuation. In translation attenuation, the ribosome-binding-site (RBS) for the resistance determinant is sequestered in a secondary structure domain within the mRNA. Preceding the secondary structure is a short, translated ORF termed the leader. Ribosome stalling in the leader causes the destabilization of the downstream secondary structure, allowing initiation of translation of the Cm resistance gene. 17 matched cddid_all.tbl CDD pfam08078 pfam08078 369686 PsaX PsaX family. This family consists of the PsaX family of photosystem I (PSI) protein subunits. PSI is a large multi-subunit pigment protein complex embedded in the thylakoid membranes of green plants and cyanobacteria. PsaX is one of the 12 protein subunits found in PSI and these subunits are arranged as monomers or trimers within the membrane as shown by the structure of the trimeric complex from Synechococcus elongatus. 35 matched cddid_all.tbl CDD pfam08079 pfam08079 462360 Ribosomal_L30_N Ribosomal L30 N-terminal domain. This presumed domain is found at the N-terminus of Ribosomal L30 proteins and has been termed RL30NT or NUC018. 72 matched cddid_all.tbl CDD pfam08080 pfam08080 429823 zf-RNPHF RNPHF zinc finger. This domain is a putative zinc-binding domain (CHHC motif) in RNP H and F. The domain is often associated with pfam00076. 36 matched cddid_all.tbl CDD pfam08081 pfam08081 400429 RBM1CTR RBM1CTR (NUC064) family. This C-terminal region is found in RBM1-like RNA binding hnRNPs. 45 matched cddid_all.tbl CDD pfam08082 pfam08082 462361 PRO8NT PRO8NT (NUC069), PrP8 N-terminal domain. The PRO8NT domain is found at the N-terminus of pre-mRNA splicing factors of PRO8 family. The NLS or nuclear localization signal for these spliceosome proteins begins at the start and runs for 60 residues. N-terminal to this domain is a highly variable proline-rich region. 152 matched cddid_all.tbl CDD pfam08083 pfam08083 400431 PROCN PROCN (NUC071) domain. The PROCN domain is the central domain in pre-mRNA splicing factors of PRO8 family. 402 matched cddid_all.tbl CDD pfam08084 pfam08084 462362 PROCT PROCT (NUC072) domain. The PROCT domain is the C-terminal domain in pre-mRNA splicing factors of PRO8 family. 111 matched cddid_all.tbl CDD pfam08085 pfam08085 429826 Entericidin Entericidin EcnA/B family. This family consists of the entericidin antidote/toxin peptides. The entericidin locus is activated in stationary phase under high osmolarity conditions by rho-S and simultaneously repressed by the osmoregulatory EnvZ/OmpR signal transduction pathway. The entericidin locus encodes tandem paralogous genes (ecnAB) and directs the synthesis of two small cell-envelope lipoproteins which can maintain plasmids in bacterial population by means of post-segregational killing. 20 matched cddid_all.tbl CDD pfam08086 pfam08086 116691 Toxin_17 Ergtoxin family. This family consists of ergtoxin peptides which are toxins secreted by the scorpions. The ergtoxins are capable of blocking the function of K+ channels. More than 100 ergtoxins have been found from scorpion venoms and they have been classified into three subfamilies according to their primary structures. 41 matched cddid_all.tbl CDD pfam08087 pfam08087 191941 Toxin_18 Conotoxin O-superfamily. This family consists of members of the conotoxin O-superfamily. The O-superfamily of conotoxins consists of 3 groups of Conus peptides that belong to the same structural group. These 3 groups differ in their pharmacological properties: the w-conotoxins which inhibit calcium channels, the delta-conotoxins which slow down the inactivation rate of voltage -sensitive sodium channels and the muO-conotoxins block the voltage sensitive sodium currents. 31 matched cddid_all.tbl CDD pfam08088 pfam08088 400434 Toxin_19 Conotoxin I-superfamily. This family consists of the I-superfamily of conotoxins. This is a new class of peptides in the venom of some Conus species. These toxins are characterized by four disulfide bridges and inhibit of modify ion channels of nerve cells. The I-superfamily conotoxins is found in five or six major clades of cone snails and could possible be found in many more species. 40 matched cddid_all.tbl CDD pfam08089 pfam08089 400435 Toxin_20 Huwentoxin-II family. This family consists of the huwentoxin-II (HWTX-II) family of toxins secreted by spiders. These toxins are found in venom that secreted from the bird spider Selenocosmia huwena Wang. The HWTX-II adopts a novel scaffold different from the ICK motif that is found in other huwentoxins. HWTX-II consists of 37 amino acids residues including six cysteines involved in three disulfide bridges. 39 matched cddid_all.tbl CDD pfam08090 pfam08090 116695 Enterotoxin_HS1 Heat stable E.coli enterotoxin 1. Heat-stable toxin 1 of entero-aggregative E.coli (EAST1) is a small toxin. It is not, however, solely associated with entero-aggregative E.coli but also with many other diarrhoaeic E. coli families. Some studies have established the role of EAST1 in some human outbreaks of diarrhoea. Isolates from farm animals have been shown to carry the astA gene coding for EAST1. However, the relation between the presence of EAST1 and disease is not conclusive. 36 matched cddid_all.tbl CDD pfam08091 pfam08091 400436 Toxin_21 Spider insecticidal peptide. This family consists of insecticidal peptides isolated from venom of spiders of Aptostichus schlingeri and Calisoga sp. Nine insecticidal peptides were isolated from the venom of the Aptostichus schlingeri spider and seven of these toxins cause flaccid paralysis to insect larvae within 10 min of injection. However, all nine peptides were lethal within 24 hours. The structure of Aps III was solved and shown to be an atypical knottin peptide with four disulphide bridges. 40 matched cddid_all.tbl CDD pfam08092 pfam08092 149265 Toxin_22 Magi peptide toxin family. This family consists of Magi peptide toxins (Magi 1, 2 and 5) isolated from the venom of Hexathelidae spider. These insecticidal peptide toxins bind to sodium channels and induce flaccid paralysis when injected into lepidopteran larvae. However, these peptides are not toxic to mice when injected intracranially at 20 pmol/g. 38 matched cddid_all.tbl CDD pfam08093 pfam08093 116698 Toxin_23 Magi 5 toxic peptide family. This family consists of toxic peptides (Magi 5) found in the venom of the Hexathelidae spider. Magi 5 is the first spider toxin with binding affinity to site 4 of a mammalian sodium channel and the toxin has an insecticidal effect on larvae, causing paralysis when injected into the larvae. 30 matched cddid_all.tbl CDD pfam08094 pfam08094 311850 Toxin_24 Conotoxin TVIIA/GS family. This family consists of conotoxins isolated from the venom of cone snail Conus tulipa and Conus geographus. Conotoxin TVIIA, isolated from Conus tulipa displays little sequence homology with other well-characterized pharmacological classes of peptides, but displays similarity with conotoxin GS, a peptide from Conus geographus. Both these peptides block skeletal muscle sodium channels and also share several biochemical features and represent a distinct subgroup of the four-loop conotoxins. 33 matched cddid_all.tbl CDD pfam08095 pfam08095 71530 Toxin_25 Hefutoxin family. This family consists of the hefutoxins that are found in the venom of the scorpion Heterometrus fulvipes. These toxins, kappa-hefutoxin1 and kappa-hefutoxin2, exhibit no homology to any known toxins. The hefutoxins are potassium channel toxins. 22 matched cddid_all.tbl CDD pfam08096 pfam08096 71531 Bombolitin Bombolitin family. This family consists of the bombolitin peptides that are found in the venom of the bumblebee Megabombus pennsylvanicus. Bombolitins are structurally and functionally very similar. They lyse erythrocytes and liposomes, release histamine from rat peritoneal mast cells, and stimulate phospholipase A2 from different sources. 17 matched cddid_all.tbl CDD pfam08097 pfam08097 71532 Toxin_26 Conotoxin T-superfamily. This family consists of the T-superfamily of conotoxins. Eight different T-superfamily peptides from five Conus species were identified. These peptides share a consensus signal sequence, and a conserved arrangement of cysteine residues. T-superfamily peptides were found expressed in venom ducts of all major feeding types of Conus, suggesting that the T-superfamily is a large and diverse group of peptides, widely distributed in the 500 different Conus species. 11 matched cddid_all.tbl CDD pfam08098 pfam08098 462363 ATX_III Anemonia sulcata toxin III family. This family consists of the Anemonia sulcata toxin III (ATX III) neurotoxin family. ATX III is a neurotoxin that is produced by sea anemone; it adopts a compact structure containing four reverse turns and two other chain reversals, but no regular alpha-helix or beta-sheet. A hydrophobic patch found on the surface of the peptide may constitute part of the sodium channel binding surface. 27 matched cddid_all.tbl CDD pfam08099 pfam08099 400438 Toxin_27 Scorpion calcine family. This family consists of the calcine family of scorpion toxins. The calcine family consists of Maurocalcine and Imperatoxin. These toxins have been shown to be potent effector of ryanodyne-sensitive calcium channel from skeletal muscles. These toxins are thus useful for dihydropyridine receptor/ryanodyne receptor interaction studies. 33 matched cddid_all.tbl CDD pfam08100 pfam08100 400439 dimerization dimerization domain. This domain is found at the N-terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerization of these proteins. 50 matched cddid_all.tbl CDD pfam08101 pfam08101 429827 Msb1-Mug8_dom Meiotically up-regulated protein Msb1/Mug8 domain. This domain of unknown function is found in fungal proteins including Mug8 from Schizosaccharomyces pombe which may have a role in meiosis and septation. Saccharomyces cerevisiae homolog MSB1 (swiss:P21339) may be involved in positive regulation of 1,3-beta-glucan synthesis and the Pkc1p-MAPK pathway. 423 matched cddid_all.tbl CDD pfam08102 pfam08102 116704 Antimicrobial_7 Scorpion antimicrobial peptide. This family consists of antimicrobial peptides secreted by scorpions. Novel antimicrobial peptides have been isolated from scorpions, namely the opistoporin and the pandinin. These peptides form essentially helical structures and demonstrate high antimicrobial activity against Gram-negative and Gram-positive bacteria respectively. 43 matched cddid_all.tbl CDD pfam08103 pfam08103 116705 Antimicrobial_8 Uperin family. This family consists of the uperin family of antimicrobial peptides. Uperin is a wide-spectrum antibiotic peptide isolated from the Australian toadlet, Uperoleia mjobergii. Being only 17 amino acid residues long, it is smaller than most other wide-spectrum antibiotic peptides isolated from amphibians. Uperin adopts a well-defined amphipathic alpha-helix with distinct hydrophilic and hydrophobic faces. 17 matched cddid_all.tbl CDD pfam08104 pfam08104 71539 Antimicrobial_9 Ponericin L family. This family consists of the ponericin L family of antimicrobial peptides that are isolated from the venom of the predatory ant Pachycondyla goeldii. Ponericin L family shares similarities with dermaseptins. Ponericin L may adopt an amphipathic alpha-helical structure in polar environments and these peptides exhibit a defensive role against microbial pathogens arising from prey introduction and/or ingestion. 24 matched cddid_all.tbl CDD pfam08105 pfam08105 311854 Antimicrobial10 Metchnikowin family. This family consists of the metchnikowin family of antimicrobial peptides from Drosophila. metchnikowin is a proline-rich peptide whose expression is immune-inducible. Induction of the metchnikowin gene expression can be mediated either by the TOLL pathway or by the imd gene product. The metchnikowin peptide is unique among the Drosophila antimicrobial peptides in that it is active against both bacteria and fungi. 50 matched cddid_all.tbl CDD pfam08106 pfam08106 71541 Antimicrobial11 Formaecin family. This family consists of the formaecin family of antimicrobial peptides isolated from the bulldog ant Myrmecia gulosa in response to bacterial infection. Formaecins are inducible peptide antibiotics and are active against growing Escherichia coli but were inactive against other Gram-negative and Gram-positive bacteria. Formaecin peptides are 16 amino acids long, are rich in proline and have N-acetylgalactosamine O-linked to a conserved threonine. 16 matched cddid_all.tbl CDD pfam08107 pfam08107 116706 Antimicrobial12 Pleurocidin family. This family consists of the pleurocidin family of antimicrobial peptides. Pleurocidins are found in the skin mucous secretions of the winter flounder (Pleuronectes americanus) and these peptides exhibit antimicrobial activity against Escherichia coli. Pleurocidin is predicted to assume an amphipathic alpha-helical conformation similar to other linear antimicrobial peptides and may play a role in innate host defense. 42 matched cddid_all.tbl CDD pfam08108 pfam08108 71543 Antimicrobial13 Halocidin family. This family consists of the halocidin family of antimicrobial peptides. Halocidins are isolated from the haemocytes of the tunicate, Halocynthia aurantium. They are dimeric in structures which are found via a disulfide linkage between cysteines of two different- sized monomers. Halocidins have been shown to have strong antimicrobial activities against a wide variety of pathogenic bacteria and could be ideal candidates as peptide antibiotics against multidrug-resistant bacteria. 15 matched cddid_all.tbl CDD pfam08109 pfam08109 71544 Antimicrobial14 Lactocin 705 family. This family consists of lactocin 705 which is a bacteriocin produced by Lactobacillus casei CRL 705. Lactocin 705 is a class IIb bacteriocin, whose activity depends upon the complementation of two peptides (705-alpha and 705-beta) of 33 amino acid residues each. Lactocin 705 is active against several Gram-positive bacteria, including food-borne pathogens and is a good candidate to be used for biopreservation of fermented meats. 31 matched cddid_all.tbl CDD pfam08110 pfam08110 149268 Antimicrobial15 Ocellatin family. This family consists of the ocellatin family of antimicrobial peptides. Ocellatins are produced from the electrical-stimulated skin secretions of the South American frog, Leptodactylus ocellatus. The family consists of three structurally related peptides, ocellatin 1, ocellatin 2 and ocellatin 3. These peptides present hemolytic activity against human erythrocytes and are also active against Escherichia coli. 19 matched cddid_all.tbl CDD pfam08111 pfam08111 71546 Pea-VEAacid Pea-VEAacid family. This family consists of the PEA-VEAacid neuropeptides family. These neuropeptides are isolated from the abdominal perisympathetic organs of the American cockroach. These peptides are found together with Pea-YLS-amide and Pea-SKNacid, giving a unique neuropeptide pattern in abdominal perisympathetic organs. The functions of these neuropeptides are unknown. 15 matched cddid_all.tbl CDD pfam08112 pfam08112 116708 ATP-synt_E_2 ATP synthase epsilon subunit. This family consists of epsilon subunits of the ATP synthase. The ATP synthase complex is composed of an oligomeric transmembrane sector (CF0), and a catalytic core (CF1). CF1 is composed of 5 subunits, of which the epsilon subunit functions as a potent inhibitor of ATPase activity in both soluble and bound CF1. Only when the epsilon inhibition is disabled is high ATPase activity detected in ATPase 56 matched cddid_all.tbl CDD pfam08113 pfam08113 285350 CoxIIa Cytochrome c oxidase subunit IIa family. This family consists of the cytochrome c oxidase subunit IIa family. The bax-type cytochrome c oxidase from Thermus thermophilus is known as a two subunit enzyme. From its crystal structure, it was discovered that an additional transmembrane helix 'subunit IIa' spans the membrane. This subunit consists of 34 residues forming one helix across the membrane. The presence of this subunit seems to be important for the function of cytochrome c oxidases. 33 matched cddid_all.tbl CDD pfam08114 pfam08114 285351 PMP1_2 ATPase proteolipid family. This family consists of small proteolipids associated with the plasma membrane H+ ATPase. Two proteolipids (PMP1 and PMP2) are associated with the ATPase and both genes are similarly expressed in the wild-type strain of yeast with no modification of the level of transcription of one PMP gene is detected in a strain deleted of the other. Though both proteolipids show similarity with other small proteolipids associated with other cation -transporting ATPases, their functions remain unclear. 43 matched cddid_all.tbl CDD pfam08115 pfam08115 285352 Toxin_28 SFI toxin family. This family consists of the SFI family of spider toxins. This family of toxins might share structural, evolutionary and functional relationships with other small, highly structurally constrained spider neurotoxins. These toxins are highly selective agonists/antagonists of different voltage-dependent calcium channels and are extremely valuable reagents in the analysis of neuromuscular function. 35 matched cddid_all.tbl CDD pfam08116 pfam08116 149271 Toxin_29 PhTx neurotoxin family. This family consists of PhTx insecticidal neurotoxins that are found in the venom of Brazilian, Phoneutria nigriventer. The venom of the Phoneutria nigrivente contains numerous neurotoxic polypeptides of 30-140 amino acids which exert a range of biological effects. While some of these neurotoxins are lethal to mice after intracerebroventricular injections, others are extremely toxic to insects of the orders Diptera and Dictyoptera but had much weaker toxic effects on mice. 31 matched cddid_all.tbl CDD pfam08117 pfam08117 400441 Toxin_30 Ptu family. This family consists of toxic peptides that are isolated from the saliva of assassin bugs. The saliva contains a complex mixture of proteins that are used by the bug either to immobilize the prey or to digest it. One of the proteins (Ptu1) has been purified and shown to block reversibly the N-type calcium channels and to be less specific for the L- and P/Q- type calcium channels expressed in BHK cells. 36 matched cddid_all.tbl CDD pfam08118 pfam08118 429828 MDM31_MDM32 Yeast mitochondrial distribution and morphology (MDM) proteins. Proteins in this family are yeast mitochondrial inner membrane proteins MDM31 and MDM32. These proteins are required for the maintenance of mitochondrial morphology, and the stability of mitochondrial DNA. 519 matched cddid_all.tbl CDD pfam08119 pfam08119 71554 Toxin_31 Scorpion acidic alpha-KTx toxin family. This family consists of acidic alpha-KTx short chain scorpion toxins. These toxins named parabutoxins, block voltage-gated K channels and have extremely low pI values. Furthermore, they lack the crucial pore-plugging lysine. In addition, the second important residue of the dyad, the hydrophobic residue (Phe or Tyr) is also missing. 37 matched cddid_all.tbl CDD pfam08120 pfam08120 71555 Toxin_32 Tamulustoxin family. This family consists of the tamulustoxins which are found in the venom of the Indian red scorpion (Mesobuthus tamulus). Tamulustoxin shares no similarity with other scorpion venom toxins, although the positions of its six cysteine residues suggest that it shares the same structural scaffold. Tamulustoxin acts as a potassium channel blocker. 35 matched cddid_all.tbl CDD pfam08121 pfam08121 71556 Toxin_33 Waglerin family. This family consists of the lethal peptides (waglerins) that are found in the venom of Trimeresurus wagleri. Waglerins are 22-24 residue lethal peptides and are competitive antagonist of the muscle nicotinic receptor (nAChR). Waglerin-1 possesses a distinctive selectivity for the alpha-epsilon interface binding site of the mouse nAChR. 22 matched cddid_all.tbl CDD pfam08122 pfam08122 462364 NDUF_B12 NADH-ubiquinone oxidoreductase B12 subunit family. This family consists of the NADH-ubiquinone oxidoreductase B12 subunit proteins. NADH is the central source of electrons in the mitochondrial and bacterial respiration. NADH-ubiquinone oxidoreductase is involved in the transfer of electrons from NADH to the electron transport chain. This oxidation of NADH is coupled to proton transfer across the membrane, generating a proton motive force that is utilized for the synthesis of ATP. The function of this subunit is unclear. 55 matched cddid_all.tbl CDD pfam08123 pfam08123 149273 DOT1 Histone methylation protein DOT1. The DOT1 domain regulates gene expression by methylating histone H3. H3 methylation by DOT1 has been shown to be required for the DNA damage checkpoint in yeast. 205 matched cddid_all.tbl CDD pfam08124 pfam08124 429830 Lyase_8_N Polysaccharide lyase family 8, N terminal alpha-helical domain. This family consists of a group of secreted bacterial lyase enzymes EC:4.2.2.1 capable of acting on hyaluronan and chondroitin in the extracellular matrix of host tissues, contributing to the invasive capacity of the pathogen. 323 matched cddid_all.tbl CDD pfam08125 pfam08125 369700 Mannitol_dh_C Mannitol dehydrogenase C-terminal domain. 246 matched cddid_all.tbl CDD pfam08126 pfam08126 285357 Propeptide_C25 Propeptide_C25. This is found at the N terminal end of some of the members of the C25 peptidase family (PF01364). Little is known about the function of this motif. 205 matched cddid_all.tbl CDD pfam08127 pfam08127 462365 Propeptide_C1 Peptidase family C1 propeptide. This motif is found at the N terminal of some members of the Peptidase_C1 family (pfam00112) and is involved in activation of this peptidase. 40 matched cddid_all.tbl CDD pfam08129 pfam08129 71564 Antimicrobial17 Alpha/beta enterocin family. This family consists of the alpha and beta enterocins and lactococcin G peptides. These peptides have some antimicrobial properties; they inhibit the growth of Enterococcus spp. and a few other gram-positive bacteria. These peptides act as pore- forming toxins that create cell membrane channels through a barrel-stave mechanism and thus produce an ionic imbalance in the cell. These family of antimicrobial peptides belong to the class II group of bacteriocin. 57 matched cddid_all.tbl CDD pfam08130 pfam08130 116721 Antimicrobial18 Type A lantibiotic family. This family consists of the type A lantibiotic peptides. Both Pep5 and epicidin-280 are ribosomally-synthesized antimicrobial peptides produced by Gram-positive bacteria that are characterized by the presence of lanthionine and/or methyllanthionine residues. The lantibiotics family has a highly specific activity against multi- drug resistant bacteria and has potential to be utilized in a wide range of medical applications. 60 matched cddid_all.tbl CDD pfam08131 pfam08131 400446 Defensin_3 Defensin-like peptide family. This family consists of the defensin-like peptides (DLPs) isolated from platypus venom. These DLPs show similar three-dimensional fold to that of beta-defensin-12 and sodium-channel neurotoxin Shl. However the side chains known to be functionally important to beta-defensin-12 and Shl are not conserved in DLPs. This suggests a different biological function. Consistent with this contention, DLPs have been shown to possess no anti-microbial properties and have no observable activity on rat dorsal-root-ganglion sodium-channel currents. 39 matched cddid_all.tbl CDD pfam08132 pfam08132 462366 AdoMetDC_leader S-adenosyl-l-methionine decarboxylase leader peptide. This family consists of the S-adenosyl-l-methionine decarboxylase (AdoMetDC) leader peptides. AdoMetDC is a key regulatory enzymes in the biosynthesis of polyamines. All expressed plant AdoMetDC mRNA 5' leader sequences contain a highly conserved pair of overlapping upstream ORFs (uORFs) that overlap by one base. Sequences of the small uORFs are highly conserved between monocot, dicot and gymnosperm AdoMetDC mRNA species, suggesting a translational regulatory mechanism. 51 matched cddid_all.tbl CDD pfam08133 pfam08133 285360 Nuclease_act Anticodon nuclease activator family. This family consists of the anticodon nuclease activator proteins. Pre-existing host tRNAs are reprocessed during bacteriophage T4 infection of certain Escherichia coli strains. In this pathway, tRNA(Lys) is cleaved 5' by the anticodon nuclease to the wobble base and is later restored in polynucleotide kinase and RNA ligase reactions. 26 matched cddid_all.tbl CDD pfam08134 pfam08134 400447 cIII cIII protein family. This family consists of the cIII family of regulatory proteins. The lambda CIII protein has 54 amino acids and it forms an amphipathic helix within its amino acid sequence. Lambda cIII stabilizes the lambda cII protein and the host sigma factor 32, responsible for transcribing genes of the heat shock regulon. 37 matched cddid_all.tbl CDD pfam08135 pfam08135 285362 EPV_E5 Major transforming protein E5 family. This family consists of the major transforming proteins (E5) of the bovine papilloma virus (BPV). The equine sarcoid is one of the most common dermatological lesion in equids. It is a benign, locally invasive dermal fibroblastic lesion and studies have shown an association of the lesions with BPV. E5 is a short hydrophobic membrane protein localising to the Golgi apparatus and other intracellular membranes. It binds to and constitutively activates the platelet-derived growth factor-beta in transformed cells. This stimulation activates a receptor signaling cascade which results in an intracellular growth stimulatory signal. 43 matched cddid_all.tbl CDD pfam08136 pfam08136 311863 Ribosomal_S22 30S ribosomal protein subunit S22 family. This family consists of the 30S ribosomal proteins subunit S22 polypeptides. This polypeptide is 47 amino acids in length and has a molecular weight of about 5 kDa. The S22 subunit is a component of the stationary-phase-specific ribosomal protein and is assembled in the ribosomal particles in the stationary phase. This subunit along with other stationary-phase-specific ribosomal proteins result in compositional changes of ribosomes during the stationary phase. The significance of this change is not clear as yet. 44 matched cddid_all.tbl CDD pfam08137 pfam08137 462367 DVL DVL family. This family consists of the DVL family of proteins. In a gain-of-function genetic screen for genes that influence fruit development in Arabidopsis, DEVIL (DVL) gene was identified. DVL is a small protein and overexpression of the protein results in pleiotropic phenotypes featured by shortened stature, rounder rosette leaves, clustered inflorescences, shortened pedicles, and siliques with pronged tips. DVL family is a novel class of small polypeptides and the overexpression phenotypes suggest that these polypeptides may have a role in plant development. 19 matched cddid_all.tbl CDD pfam08138 pfam08138 285365 Sex_peptide Sex peptide (SP) family. This family consists of Sex Peptides (SP) that are found in Drosophila. On mating, Drosophila females decreases her remating rate and increases her egg-laying rate due, in part, to the transfer of SP from the male to the female. SP are found in seminal fluids transferred from the male to the female during mating. The male seminal fluid proteins are referred to as accessory gland proteins (Acps). The SP is one of the most interesting Acps and plays an important role in reproduction. 55 matched cddid_all.tbl CDD pfam08139 pfam08139 429834 LPAM_1 Prokaryotic membrane lipoprotein lipid attachment site. In prokaryotes, membrane lipoproteins are synthesized with a precursor signal peptide, which is cleaved by a specific lipoprotein signal peptidase (signal peptidase II). The peptidase recognizes a conserved sequence and cuts upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached. Analysis of lipoprotein and non-lipoprotein signal peptides reveals that the two classes differ significantly only in the region close to the signal peptidase cleavage site. This region is apolar and has the consensus sequence LA(G,A) 1C in the lipoproteins, but is polar and has small, uncharged residues in positions - 3 and - 1 in the non-lipoproteins. specialized signal peptide containing a lipobox motif in the carboxyl region of the signal peptide carries a cysteine residue which is the invariable target for lipidation by lipoprotein diacylglyceryl transferase (Lgt). Lipidation at this residue serves to anchor the lipoprotein to the membrane. Lipidation has been considered to be a prerequisite for the action of lipoprotein signal peptidase (Lsp), which removes the signal peptide and leaves the cysteine of the lipobox as the new amino-terminal residue of the mature lipoprotein. 18 matched cddid_all.tbl CDD pfam08140 pfam08140 369707 Cuticle_1 Crustacean cuticle protein repeat. This family consists of the cuticle proteins from the Cancer pagurus and the Homarus americanus. These proteins are isolated from the calcified regions of the crustacean and they contain two copies of an 18 residue sequence motif, which thus far has been found only in crustacean calcified exoskeletons. 40 matched cddid_all.tbl CDD pfam08141 pfam08141 462368 SspH Small acid-soluble spore protein H family. This family consists of the small acid-soluble spore proteins (SASP) of the H type (sspH). SspH are unique to spores of Bacillus subtilis and are expressed only in the forespore compartment during sporulation of this organizm. The sspH genes are monocistronic and are recognized by the forespore-specific sigma factor for RNA polymerase - sigma-G. The specific role of this protein is unclear but is thought to play a role in sporulation under conditions different from that of the common laboratory tests of spore properties. 58 matched cddid_all.tbl CDD pfam08142 pfam08142 462369 AARP2CN AARP2CN (NUC121) domain. This domain is the central domain of AARP2. It is weakly similar to the GTP-binding domain of elongation factor TU. 86 matched cddid_all.tbl CDD pfam08143 pfam08143 311868 CBFNT CBFNT (NUC161) domain. This N terminal domain is found in proteins of CARG-binding factor A-like proteins. 60 matched cddid_all.tbl CDD pfam08144 pfam08144 462370 CPL CPL (NUC119) domain. This C-terminal domain is found in Penguin-like proteins associated with Pumilio like repeats. 140 matched cddid_all.tbl CDD pfam08145 pfam08145 462371 BOP1NT BOP1NT (NUC169) domain. This N terminal domain is found in BOP1-like WD40 proteins. 259 matched cddid_all.tbl CDD pfam08146 pfam08146 462372 BP28CT BP28CT (NUC211) domain. This C terminal domain is found in BAP28-like nucleolar proteins. 148 matched cddid_all.tbl CDD pfam08147 pfam08147 462373 DBP10CT DBP10CT (NUC160) domain. This C terminal domain is found in the Dbp10p subfamily of hypothetical RNA helicases. 66 matched cddid_all.tbl CDD pfam08148 pfam08148 462374 DSHCT DSHCT (NUC185) domain. This C terminal domain is found in DOB1/SK12/helY-like DEAD box helicases. 154 matched cddid_all.tbl CDD pfam08149 pfam08149 462375 BING4CT BING4CT (NUC141) domain. This C terminal domain is found in the BING4 family of nucleolar WD40 repeat proteins. 79 matched cddid_all.tbl CDD pfam08150 pfam08150 462376 FerB FerB (NUC096) domain. This is central domain B in proteins of the Ferlin family. 76 matched cddid_all.tbl CDD pfam08151 pfam08151 462377 FerI FerI (NUC094) domain. This domain is present in proteins of the Ferlin family. It is often located between two C2 domains. 52 matched cddid_all.tbl CDD pfam08152 pfam08152 462378 GUCT GUCT (NUC152) domain. This is the C terminal domain found in the RNA helicase II / Gu protein family. 96 matched cddid_all.tbl CDD pfam08153 pfam08153 462379 NGP1NT NGP1NT (NUC091) domain. This N terminal domain is found in a subfamily of hypothetical nucleolar GTP-binding proteins similar to human NGP1. 129 matched cddid_all.tbl CDD pfam08154 pfam08154 462380 NLE NLE (NUC135) domain. This domain is located N terminal to WD40 repeats. It is found in the microtubule-associated protein Swiss:Q12024. 66 matched cddid_all.tbl CDD pfam08155 pfam08155 462381 NOGCT NOGCT (NUC087) domain. This C terminal domain is found in the NOG subfamily of nucleolar GTP-binding proteins. 51 matched cddid_all.tbl CDD pfam08156 pfam08156 462382 NOP5NT NOP5NT (NUC127) domain. This N terminal domain is found in RNA-binding proteins of the NOP5 family. 66 matched cddid_all.tbl CDD pfam08157 pfam08157 462383 NUC129 NUC129 domain. This C terminal domain is found in a novel family of hypothetical nucleolar proteins. 62 matched cddid_all.tbl CDD pfam08158 pfam08158 462384 NUC130_3NT NUC130/3NT domain. This N terminal domain is found in a novel nucleolar protein family. 50 matched cddid_all.tbl CDD pfam08159 pfam08159 462385 NUC153 NUC153 domain. This small domain is found in a a novel nucleolar family. 29 matched cddid_all.tbl CDD pfam08161 pfam08161 462386 NUC173 NUC173 domain. This is the central domain of of novel family of hypothetical nucleolar proteins. 202 matched cddid_all.tbl CDD pfam08163 pfam08163 462387 DNAPKcs_CC3 DNA-dependent protein kinase catalytic subunit, CC3. DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is involved in DNA nonhomologous end joining (NHEJ), which is recruited by Ku70/80 heterodimer to DNA ends and required for double-strand breaks (DSBs) repair. DNA-PKcs phosphorylates a number of protein substrates, including the heat shock protein 90 (HSP90), the transcription factors p53, specificity protein 1 (Sp1), among others. It folds into three well-defined large structural units, consisting of a N-terminal region (arranged in four supersecondary alpha-helical structures, N1-N4), the Circular Cradle (consisting of five supersecondary alpha-helical structures CC1-CC5), and the C-terminal Head (comprising FAT, FRB, kinase, and FATC). The CCs form a curved elliptical ring that serves as a scaffold to maintain the integrity of the whole complex. This domain represents a region of the Circular Cradle segment (CC) from DNA-PKcs that covers the complete CC3 and part of CC4. This domain contains the Ku-binding site A and a the highly conserved region (HCR) II. 387 matched cddid_all.tbl CDD pfam08164 pfam08164 462388 TRAUB Apoptosis-antagonizing transcription factor, C-terminal. This C terminal domain is found in traube proteins. This is the domain of the AATF proteins that interacts with BLOS2 or Ceap, that functions as an adaptor in processes such as protein and vesicle processing and transport, and perhaps transcription. 81 matched cddid_all.tbl CDD pfam08165 pfam08165 462389 FerA FerA (NUC095) domain. This is central domain A in proteins of the Ferlin family. 65 matched cddid_all.tbl CDD pfam08166 pfam08166 149302 NUC202 NUC202 domain. This domain is found in a novel family of nucleolar proteins. 61 matched cddid_all.tbl CDD pfam08167 pfam08167 429855 RIX1 rRNA processing/ribosome biogenesis. Rix1 is a nucleoplasmic particle involved in rRNA processing/ribosome assembly. It associates with two other proteins, Ipi1 and Ipi3, to form the RIX1 complex that allows Rea1 - the AAA ATPase - to associate with the 60S ribosomal subunit. More than 170 assembly factors are involved in the construction and maturation of yeast ribosomes, and after these factors have completed their function they need to be released from the pre-ribosomes. Rea1 induces the release of the assembly protein complex in a mechanical fashion. This family is usually associated with NUC202, pfam08166. 183 matched cddid_all.tbl CDD pfam08168 pfam08168 429856 NUC205 NUC205 domain. This domain is found in a novel family of nucleolar proteins. 44 matched cddid_all.tbl CDD pfam08169 pfam08169 462390 RBB1NT RBB1NT (NUC162) domain. This domain is found N terminal to the ARID/BRIGHT domain in DNA-binding proteins of the Retinoblastoma-binding protein 1 family. 93 matched cddid_all.tbl CDD pfam08170 pfam08170 462391 POPLD POPLD (NUC188) domain. This domain is found in POP1-like nucleolar proteins. 92 matched cddid_all.tbl CDD pfam08171 pfam08171 400476 Mad3_BUB1_II Mad3/BUB1 homology region 2. This domain is found in checkpoint proteins which are involved in cell division. This region has been shown to be necessary and sufficient for the binding of MAD3 to BUB3 in Saccharomyces cerevisiae. This domain is present in BUB1 which also binds BUB3. 65 matched cddid_all.tbl CDD pfam08172 pfam08172 462392 CASP_C CASP C terminal. This domain is the C-terminal region of the CASP family of proteins. It is a Golgi membrane protein which is thought to have a role in vesicle transport. 247 matched cddid_all.tbl CDD pfam08173 pfam08173 429860 YbgT_YccB Membrane bound YbgT-like protein. This family contains a set of membrane proteins, typically 33 amino acids long. The family has no known function, but the protein is found in the operon CydAB in E. coli. Members have a consensus motif (MWYFXW) which is rich in aromatic residues. The protein forms a single membrane-spanning helix. This family seems to be restricted to Proteobacteria. 26 matched cddid_all.tbl CDD pfam08174 pfam08174 462393 Anillin Cell division protein anillin. Anillin is a protein involved in septin organization during cell division. It is an actin binding protein that is localized to the cleavage furrow, and it maintains the localization of active myosin, which ensures the spatial control of concerted contraction during cytokinesis. 139 matched cddid_all.tbl CDD pfam08175 pfam08175 369735 SspO Small acid-soluble spore protein O family. This family consists of the small acid-soluble spore proteins (SASP) O type (sspO). SspO (originally cotK) are unique to the spores of Bacillus subtilis and are expressed only in the forespore compartment of sporulating cells of this organizm. The sspO is the first gene in a likely operon with sspP and transcription of this gene is primarily by RNA polymerase with the forespore-specific sigma factor, sigma-G. Mutation deleting sspO causes the loss of the SspO from the forespore but had no discernible effect on sporulation, spore properties or spore germination. 50 matched cddid_all.tbl CDD pfam08176 pfam08176 285399 SspK Small acid-soluble spore protein K family. This family consists of the small acid-soluble spore proteins (SASP) belonging to the K type (sspK). The sspK are unique to the spores of Bacillus subtilis and are expressed only in the forespore compartment of sporulating cells of this organizm. The sspK gene is monocistronic and transcription is primarily by the RNA polymerase with the forespore-specific sigma factor, sigma-G. Mutation deleting sspK results in loss of SspK from the spore but had no discernible effect on sporulation, spore properties or spore germination. 47 matched cddid_all.tbl CDD pfam08177 pfam08177 285400 SspN Small acid-soluble spore protein N family. This family consists of the small acid-soluble spore protein (SASP) N type (sspN). SspN is a 48 residues protein that is expressed only in the forespore compartment of sporulating Bacillus subtilis. The sspN gene is recognized equally by both sigma-G and sigma-F. The role of SspN is still not well-defined. 46 matched cddid_all.tbl CDD pfam08178 pfam08178 285401 GnsAB_toxin GnsA/GnsB toxin of bacterial toxin-antitoxin system. This family consists of the GnsA/GnsB family. GnsA and GnsB are multicopy suppressors of the secG null mutation. These proteins participate in the synthesis of phospholipids, suggesting the functional relationship between SecG and membrane phospholipids. Over-expression of gnsA and gnsB causes a remarkable increase in the unsaturated fatty acid content. However, the gnsA-gnsB double null mutant exhibits no effect. Both proteins are predicted to possess a helix-turn-helix structure. GnsAB is a family of putative bacterial toxins (both GnsA and GnsB) that, are neutralized by the antitoxin YmcE, pfam15939. 54 matched cddid_all.tbl CDD pfam08179 pfam08179 400480 SspP Small acid-soluble spore protein P family. This family consists of the small acid-soluble spore proteins (SASP) P type (sspP). sspP is expressed only in the forespore compartment of the sporulating cell. sspP is also expressed under sigma-G control from the same promoter as sspO. Mutations deleting sspP causes no discernible effect on sporulation, spore properties or spore germination. 44 matched cddid_all.tbl CDD pfam08180 pfam08180 400481 BAGE B melanoma antigen family. This family consists of the B melanoma antigen (BAGE) peptides. The BAGE gene encodes a human tumour antigen that is recognized by a cytolytic T lymphocyte. BAGE genes are expressed in melanomas, bladder and lung carcinomas and in a few tumours of other histological types. 28 matched cddid_all.tbl CDD pfam08181 pfam08181 285404 DegQ DegQ (SacQ) family. This family consists of the DegQ (formerly sacQ) regulatory peptides. The DegQ family of peptides control the rates of synthesis of a class of both secreted and intracellular degradative enzymes in Bacillus subtilis. DegQ is 46 amino acids long and activates the synthesis of degradative enzymes. The expression of this peptide was shown to be subjected both to catabolite repression and DegS-DegU-mediated control. Thus allowing an increase in the rate of synthesis of degQ under conditions of nitrogen starvation. 46 matched cddid_all.tbl CDD pfam08182 pfam08182 400482 Pedibin Pedibin/Hym-346 family. This family consists of the pedibin and Hym-346 signalling peptides. These two peptides have been isolated from Hydra vulgaris and Hydra magnipapillata. Experiments have indicated that both cause a reduction in the positional value gradient, the principle patterning process governing the maintenance of form in the adult hydra. The peptides cause an increase in the rate of foot regeneration following bisection of the body column. Thus both play important signalling roles in patterning processes in cnidaria and maybe in more complex metazoans. 35 matched cddid_all.tbl CDD pfam08183 pfam08183 369736 SpoV Stage V sporulation protein family. This family consists of the stage V sporulation (SpoV) proteins of Bacillus subtilis which includes SpoVM. SpoVM is an small, 26 residue-long protein that is produced in the mother cell chamber of the sporangium during the process of sporulation in B. subtilis. SpoVM forms an amphipathic alpha-helix and is recruited to the polar septum shortly after the sporangium undergoes asymmetric division. The function of SpoVM depends on proper subcellular localization. 25 matched cddid_all.tbl CDD pfam08184 pfam08184 116772 Cuticle_2 Cuticle protein 7 isoform family. This family consists of cuticle protein 7 isoforms that are isolated from the carapace cuticle of a juvenile horseshoe crab, Limulus polyphemus. There are 3 isoforms of cuticle protein 7. The 3 isoforms are N-terminally blocked but could be deblocked by treatment with pyroglutaminase, showing that the N-terminal residue is a pyroglutamine residue. 59 matched cddid_all.tbl CDD pfam08186 pfam08186 369737 Wound_ind Wound-inducible basic protein family. This family consists of the wound-inducible basic proteins from plants. The metabolic activities of plants are dramatically altered upon mechanical injury or pathogen attack. A large number of proteins accumulates at wound or infection sites, such as the wound-inducible basic proteins. These proteins are small, 47 amino acids in length, has no signal peptides and are hydrophilic and basic. 44 matched cddid_all.tbl CDD pfam08187 pfam08187 71621 Tetradecapep Myoactive tetradecapeptides family. This family consists of myoactive tetradecapeptides that are isolated from the gut of earthworms, Eisenia foetida and Pheretima vitata. These peptides were termed ETP and PTP respectively. Both peptides showed a potent excitatory action on spontaneous contractions of the anterior gut. These peptides show similarity to Molluscan tetradecapeptides and arthropodan tridecapeptides. 14 matched cddid_all.tbl CDD pfam08188 pfam08188 71622 Protamine_3 Spermatozal protamine family. This family consists of the spermatozal protamines. Spermatozal protamines play an important role in remodelling of the sperm chromatin during mammalian spermiogenesis. Nuclear elongation and chromatin condensation are concomitant with modifications in the basic protein complement associated with DNA. Somatic histones are initially replaced by testis -specific histone variants, then by transitional proteins, and ultimately by protamines. 48 matched cddid_all.tbl CDD pfam08189 pfam08189 400483 Meleagrin Meleagrin/Cygnin family. This family consists of meleagrin and cygnin basic peptides that are isolated from turkey and black swan respectively. Both peptides are low in molecular weight and contains three disulphide bonds with high concentrations of aromatic residues. These peptides show similarity to transferrins and probably play some vital role in avian eggs but the exact function is still unknown. 38 matched cddid_all.tbl CDD pfam08190 pfam08190 369738 PIH1 PIH1 N-terminal domain. This domain is involved in pre-rRNA processing. It has has been shown to be required either for nucleolar retention or correct assembly of the box C/D snoRNP in Saccharomyces cerevisiae. 166 matched cddid_all.tbl CDD pfam08191 pfam08191 369739 LRR_adjacent LRR adjacent. These are small, all beta strand domains, structurally described for the protein Internalin (InlA) and related proteins InlB, InlE, InlH from the pathogenic bacterium Listeria monocytogenes. Their function appears to be mainly structural: They are fused to the C-terminal end of leucine-rich repeats (LRR), significantly stabilising the LRR, and forming a common rigid entity with the LRR. They are themselves not involved in protein-protein-interactions but help to present the adjacent LRR-domain for this purpose. These domains belong to the family of Ig-like domains in that they consist of two sandwiched beta sheets that follow the classical connectivity of Ig-domains. The beta strands in one of the sheets is, however, much smaller than in most standard Ig-like domains, making it somewhat of an outlier. 57 matched cddid_all.tbl CDD pfam08192 pfam08192 369740 Peptidase_S64 Peptidase family S64. This family of fungal proteins is involved in the processing of membrane bound transcription factor Stp1. The processing causes the signalling domain of Stp1 to be passed to the nucleus where several permease genes are induced. The permeases are important for uptake of amino acids, and processing of tp1 only occurs in an amino acid-rich environment. This family is predicted to be distantly related to the trypsin family (MEROPS:S1) and to have a typical trypsin-like catalytic triad. 684 matched cddid_all.tbl CDD pfam08193 pfam08193 429862 INO80_Ies4 INO80 complex subunit Ies4. The INO80 ATPase is a member of the SNF2 family of ATPases and functions as an integral component of a multisubunit ATP-dependent chromatin remodelling complex. This family of proteins corresponds to the fungal Ies4 subunit of INO80. 230 matched cddid_all.tbl CDD pfam08194 pfam08194 400485 DIM DIM protein. Drosophila immune-induced molecules (DIMs) are short proteins induced during the immune response of Drosophila. This family includes DIMs 1 to 4 that have masses below 5 kDa. 36 matched cddid_all.tbl CDD pfam08195 pfam08195 369743 TRI9 TRI9 protein. Putative gene of 129 bp in the Trichothecene gene cluster of Fusarium sporotrichioides and F. graminearum. Encoding a predicted protein of 43 amino acids which function is unknown. 43 matched cddid_all.tbl CDD pfam08196 pfam08196 285414 UL2 UL2 protein. Orf UL2 of Human cytomegalovirus (HCMV) which is a short protein of unknown function 59 matched cddid_all.tbl CDD pfam08197 pfam08197 285415 TT_ORF2a pORF2a truncated protein. Most isolated ORF2 of TT virus (TTV) encode a 49 amino acids protein (pORF2a) because of an in-frame stop codon. ORF2s isolated from G1 TTV encode 202 amino acids protein (pORF2ab). 49 matched cddid_all.tbl CDD pfam08198 pfam08198 400486 Thymopoietin Thymopoietin protein. Short protein of 49 amino acid isolated from bovine spleen cells. Thymopoietins (TMPOs) are a group of ubiquitously expressed nuclear proteins. They are suggested to play an important role in nuclear envelope organization and cell cycle control. 48 matched cddid_all.tbl CDD pfam08199 pfam08199 285417 E2 Bacteriophage E2-like protein. Short conseved protein described in Lactococcus Bacteriophage c2 of 37 amino acids. 37 matched cddid_all.tbl CDD pfam08200 pfam08200 369745 Phage_1_1 Bacteriophage 1.1 Protein. Gene 1.1 in Bacteriophage T7 encodes a 42 amino acid protein, rich in basic amino acids suggesting its interaction with nucleic acids. Many homologs are present in different T7 and T3-like bacteriophage. 45 matched cddid_all.tbl CDD pfam08201 pfam08201 369746 BssC_TutF BssC/TutF protein. BssC short protein (57 amino acids) has been described as the gamma-subunit of benzylsuccinate synthase from Thauera aromatica strain K172. TutF has been identified and described as highly similar to BssC in T.aromatica strain T1. 56 matched cddid_all.tbl CDD pfam08202 pfam08202 369747 MIS13 Mis12-Mtw1 protein family. Mis12-Mtw1 is a eukaryotic conserved kinetochore protein that is involved in chromosome segregation. 288 matched cddid_all.tbl CDD pfam08203 pfam08203 462394 RNA_polI_A14 Yeast RNA polymerase I subunit RPA14. This is a family of yeast proteins. A14 is one of the final two subunits of Saccharomyces cerevisiae RNA polymerase I and is proposed to play a role in the recruitment of pol I to the promoter. 115 matched cddid_all.tbl CDD pfam08204 pfam08204 400488 V-set_CD47 CD47 immunoglobulin-like domain. This family represents the CD47 leukocyte antigen V-set like Ig domain. 93 matched cddid_all.tbl CDD pfam08205 pfam08205 400489 C2-set_2 CD80-like C2-set immunoglobulin domain. These domains belong to the immunoglobulin superfamily. 89 matched cddid_all.tbl CDD pfam08206 pfam08206 429863 OB_RNB Ribonuclease B OB domain. This family includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies. 58 matched cddid_all.tbl CDD pfam08207 pfam08207 429864 EFP_N Elongation factor P (EF-P) KOW-like domain. 58 matched cddid_all.tbl CDD pfam08208 pfam08208 462395 RNA_polI_A34 DNA-directed RNA polymerase I subunit RPA34.5. This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription. 205 matched cddid_all.tbl CDD pfam08209 pfam08209 369754 Sgf11 Sgf11 (transcriptional regulation protein). The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae. The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation. 33 matched cddid_all.tbl CDD pfam08210 pfam08210 462396 APOBEC_N APOBEC-like N-terminal domain. A mechanism of generating protein diversity is mRNA editing. Members of this family are C-to-U editing enzymes. The N-terminal domain of APOBEC-1 like proteins is the catalytic domain, while the C-terminal domain is a pseudocatalyitc domain. More specifically, the catalytic domain is a zinc dependent deaminases domain and is essential for cytidine deamination.APOBEC-3 like members contain two copies of this domain. RNA editing by APOBEC-1 requires homodimerization and this complex interacts with RNA binding proteins to from the editosome (and references therein). This family also includes the functionally homologous activation induced deaminase (AID), which is essential for the development of antibody diversity in B lymphocytes, and the sea lamprey PmCDA1 and PmCDA2, which are predicted to play an AID-like role in the adaptive immune response of jawless vertebrates. Divergent members of this family are present in various eukaryotes such as Nematostella, C. elegans, Micromonas and Emiliania, and prokaryotes such as Wolbachia and Pseudomonas brassicacearum. 170 matched cddid_all.tbl CDD pfam08211 pfam08211 429867 dCMP_cyt_deam_2 Cytidine and deoxycytidylate deaminase zinc-binding region. 122 matched cddid_all.tbl CDD pfam08212 pfam08212 400495 Lipocalin_2 Lipocalin-like domain. Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The structure is an eight-stranded beta barrel. 143 matched cddid_all.tbl CDD pfam08213 pfam08213 429868 COX24_C Mitochondrial mRNA-processing protein COX24, C-terminal. This domain of unknown function is found at the C terminal end of Mitochondrial small ribosomal subunit protein mS38, also known as Mitochondrial mRNA-processing protein COX24 in yeast which is involved in the splicing of the COX1 mRNA. COX24 is a component of the mitochondrial ribosome (mitoribosome), responsible for the synthesis of mitochondrial genome-encoded proteins, including at least some of the essential transmembrane subunits of the mitochondrial respiratory chain. The mitoribosomes are attached to the mitochondrial inner membrane and translation products are cotranslationally integrated into the membrane. This domain is also found in COX24 mammalian homolog Aurora kinase A-interacting protein. This entry also includes uncharacterized proteins from bacteria. 31 matched cddid_all.tbl CDD pfam08214 pfam08214 400497 HAT_KAT11 Histone acetylation protein. Histone acetylation is required in many cellular processes including transcription, DNA repair, and chromatin assembly. This family contains the fungal KAT11 protein (previously known as RTT109) which is required for H3K56 acetylation. Loss of KAT11 results in the loss of H3K56 acetylation, both on bulk histone and on chromatin. KAT11 and H3K56 acetylation appear to correlate with actively transcribed genes and associate with the elongating form of Pol II in yeast. This family also incorporates the p300/CBP histone acetyltransferase domain which has different catalytic properties and cofactor regulation to KAT11. 348 matched cddid_all.tbl CDD pfam08216 pfam08216 462397 CTNNBL Catenin-beta-like, Arm-motif containing nuclear. CTNNBL is a family of eukaryotic nuclear proteins of the catenin-beta-like 1 type that contain an armadillo motif. A human nuclear protein with this domain is thought to have a role in apoptosis. The interaction of CTNNBL1 with its known partners (the Prp19-CDC5L complex and AID) is mediated by recognition of NLS (nuclear localization signal) motifs. The RNA-splicing factor Prp31 is also an interactor, with recognition also occurring through the NLS. CTNNBL1 uses its central armadillo (ARM) domain to bind NLS-containing partners. 473 matched cddid_all.tbl CDD pfam08218 pfam08218 429870 Citrate_ly_lig Citrate lyase ligase C-terminal domain. This family is composed of the C-terminal domain of citrate lyase ligase EC:6.2.1.22. 182 matched cddid_all.tbl CDD pfam08219 pfam08219 400499 TOM13 Outer membrane protein TOM13. The TOM13 family of proteins are mitochondrial outer membrane proteins that mediate the assembly of beta-barrel proteins. 82 matched cddid_all.tbl CDD pfam08220 pfam08220 285436 HTH_DeoR DeoR-like helix-turn-helix domain. 57 matched cddid_all.tbl CDD pfam08221 pfam08221 400500 HTH_9 RNA polymerase III subunit RPC82 helix-turn-helix domain. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 160 to about 10 kDa. This region is a probably DNA-binding helix-turn-helix. 62 matched cddid_all.tbl CDD pfam08222 pfam08222 429871 HTH_CodY CodY helix-turn-helix domain. This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk. 61 matched cddid_all.tbl CDD pfam08223 pfam08223 429872 PaaX_C PaaX-like protein C-terminal domain. This family contains proteins that are similar to the product of the paaX gene of Escherichia coli. This protein is involved in the regulation of expression of a group of proteins known to participate in the metabolism of phenylacetic acid. 99 matched cddid_all.tbl CDD pfam08224 pfam08224 462398 DUF1719 Domain of unknown function (DUF1719). This is a domain of unknown function. It may have a role in ATPase activation. 231 matched cddid_all.tbl CDD pfam08225 pfam08225 400502 Antimicrobial19 Pseudin antimicrobial peptide. Pseudins are a subfamily of the FSAP family (Frog Secreted Active Peptides) extracted from the skin of the paradoxical frog Pseudis paradoxa (Pseudidae). The pseudins belong to the class of cationic, amphipathic-helical antimicrobial peptides. 23 matched cddid_all.tbl CDD pfam08226 pfam08226 369766 DUF1720 Domain of unknown function (DUF1720). This domain is found in different combinations with cortical patch components EF hand, SH3 and ENTH and is therefore likely to be involved in cytoskeletal processes. This family contains many hypothetical proteins. 75 matched cddid_all.tbl CDD pfam08227 pfam08227 429874 DASH_Hsk3 DASH complex subunit Hsk3 like. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro. This family also includes several higher eukaryotic proteins. However, other DASH subunits do not appear to be conserved in higher eukaryotes. 45 matched cddid_all.tbl CDD pfam08228 pfam08228 400504 RNase_P_pop3 RNase P subunit Pop3. This family of fungal proteins form a subunit of RNase P, the ribonucleoprotein enzyme that cleaves the leader sequence of precursor tRNAs to generate mature tRNAs. The structure of Pop3 has been assigned the L7Ae/L30e fold. This RNA-binding fold is also present in human RNase P subunit Rpp38, raising the possibility that Pop3p and Rpp38 are functional homologs. 158 matched cddid_all.tbl CDD pfam08229 pfam08229 369769 SHR3_chaperone ER membrane protein SH3. This family of proteins are membrane localized chaperones that are required for correct plasma membrane localization of amino acid permeases (AAPs). SH3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of SH3, AAPs are retained in the ER. 185 matched cddid_all.tbl CDD pfam08230 pfam08230 462399 CW_7 CW_7 repeat. This domain was originally found in the C-terminal moiety of the Cpl-7 lysozyme encoded by the Streptococcus pneumoniae bacteriophage Cp-7. It is also found in the cell wall hydrolases of human and life-stock pathogens. CW_7 repeats make up a cell wall binding motif. 40 matched cddid_all.tbl CDD pfam08231 pfam08231 462400 SYF2 SYF2 splicing factor. Proteins in this family are involved in cell cycle progression and pre-mRNA splicing. 152 matched cddid_all.tbl CDD pfam08232 pfam08232 462401 Striatin Striatin family. Striatin is an intracellular protein which has a caveolin-binding motif, a coiled-coil structure, a calmodulin-binding site, and a WD (pfam00400) repeat domain. It acts as a scaffold protein and is involved in signalling pathways. 85 matched cddid_all.tbl CDD pfam08234 pfam08234 462402 Spindle_Spc25 Chromosome segregation protein Spc25. This is a family of chromosome segregation proteins. It contains Spc25, which is a conserved eukaryotic kinetochore protein involved in cell division. In fungi the Spc25 protein is a subunit of the Nuf2-Ndc80 complex, and in vertebrates it forms part of the Ndc80 complex. 71 matched cddid_all.tbl CDD pfam08235 pfam08235 462403 LNS2 LNS2 (Lipin/Ned1/Smp2). This domain is found in Saccharomyces cerevisiae protein SMP2, proteins with an N-terminal lipin domain (Pfam: PF04571). SMP2 (also known as PAH1) is involved in plasmid maintenance and respiration, and has been identified as a Mg2+-dependent phosphatidate phosphatase (EC:3.1.3.4) that contains a haloacid dehalogenase (HAD)-like domain. Lipin proteins are involved in adipose tissue development and insulin resistance. 226 matched cddid_all.tbl CDD pfam08236 pfam08236 462404 SRI SRI (Set2 Rpb1 interacting) domain. The SRI (Set2 Rpb1 interacting) domain mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation. This domain is conserved from yeast to humans. Members of this family form a compact, closed three-helix bundle, with an up-down-up topology. The first and second helices are antiparallel to each other and are of similar length; the third helix, which is packed across helices alpha1 and alpha2 is slightly shorter, consisting of only 15 amino acids. Most conserved hydrophobic residues are largely buried in the interior of the structure and form an extensive and contiguous hydrophobic core that stabilizes the packing of the three-helix bundle. This domain mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation. 83 matched cddid_all.tbl CDD pfam08237 pfam08237 369775 PE-PPE PE-PPE domain. This domain is found C terminal to the PE (pfam00934) and PPE (pfam00823) domains. The secondary structure of this domain is predicted to be a mixture of alpha helices and beta strands. 227 matched cddid_all.tbl CDD pfam08238 pfam08238 429881 Sel1 Sel1 repeat. This short repeat is found in the Sel1 protein. It is related to TPR repeats. 35 matched cddid_all.tbl CDD pfam08239 pfam08239 462405 SH3_3 Bacterial SH3 domain. 54 matched cddid_all.tbl CDD pfam08240 pfam08240 400513 ADH_N Alcohol dehydrogenase GroES-like domain. This is the catalytic domain of alcohol dehydrogenases. Many of them contain an inserted zinc binding domain. This domain has a GroES-like structure. 106 matched cddid_all.tbl CDD pfam08241 pfam08241 462406 Methyltransf_11 Methyltransferase domain. Members of this family are SAM dependent methyltransferases. 94 matched cddid_all.tbl CDD pfam08242 pfam08242 400515 Methyltransf_12 Methyltransferase domain. Members of this family are SAM dependent methyltransferases. 98 matched cddid_all.tbl CDD pfam08243 pfam08243 462407 SPT2 SPT2 chromatin protein. This family includes the Saccharomyces cerevisiae protein SPT2 which is a chromatin protein involved in transcriptional regulation. 106 matched cddid_all.tbl CDD pfam08244 pfam08244 462408 Glyco_hydro_32C Glycosyl hydrolases family 32 C terminal. This domain corresponds to the C terminal domain of glycosyl hydrolase family 32. It forms a beta sandwich module. 162 matched cddid_all.tbl CDD pfam08245 pfam08245 462409 Mur_ligase_M Mur ligase middle domain. 199 matched cddid_all.tbl CDD pfam08246 pfam08246 462410 Inhibitor_I29 Cathepsin propeptide inhibitor domain (I29). This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide. There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin Swiss:Q70SU8. This family is classified as I29 by MEROPS. 58 matched cddid_all.tbl CDD pfam08247 pfam08247 116832 ENOD40 ENOD40 protein. Rohrig et al. reported the in vitro translation of two peptides of 12 and 24 amino acids from the short, overlapping ORFs of soybean ENOD40 mRNA. The putative role of the enod40 genes has been in favour of organogenesis, such as induction of the cortical cell divisions that lead to initiation of nodule primordia, in developing lateral roots and embryonic tissues. This supports the hypothesis for a role of enod40 in lateral organ development. 12 matched cddid_all.tbl CDD pfam08248 pfam08248 116833 Tryp_FSAP Tryptophyllin-3 skin active peptide. PdT-3 or Tryptophyllin-3 peptide is a subfamily of the family Tryptophyllin and of the superfamily FSAP (Frog Skin Active Peptide). Originally identified in skin extracts of Neotropical leaf frogs, Phyllomedusa sp. This subfamily has an average length of 13 amino acids. The pharmacological activity of the tryptophyllins remains to be established but it seems that these peptides possess an action on liver protein synthesis and body weight. 12 matched cddid_all.tbl CDD pfam08249 pfam08249 116834 Mastoparan Mastoparan protein. Mastoparans are a family of tetradecapeptides from wasp venom, that have been shown to directly activate GTP-binding regulatory proteins. These peptides show selectivity among G proteins: they strongly activate Go and Gi but not Gs or Gt. The peptide of this family are composed by 14 amino acids but they can assume different structures. 14 matched cddid_all.tbl CDD pfam08250 pfam08250 116835 Sperm_act_pep Sperm-activating peptides. The sperm-activating peptides (SAPs) are isolated in egg-conditioned media (egg jelly) of sea urchins. SAPs have several effects on sea urchin spermatozoa: stimulate sperm respiration and motility through intracellular alkalinization, transient elevation of cAMP, cGMP and Ca++levels in sperm cells. 10 matched cddid_all.tbl CDD pfam08251 pfam08251 116836 Mastoparan_2 Mastoparan peptide. Mastoparan (MP) peptides I II and III are extracted from the venom gland of the Neotropical social wasp Protopolybia exigua(Saussure) They are tetradecapeptides presenting from seven to ten hydrophobic amino acid residues and from two to four lysine residues in their primary sequences. These peptide cause the degranulation of mast cells. Protopolybia-MP-I also act causing hemolysis in erythrocytes. 14 matched cddid_all.tbl CDD pfam08252 pfam08252 285459 Leader_CPA1 arg-2/CPA1 leader peptide. In this family there are Leaders Peptides involved in the regulation the glutaminase subunit (small subunit) of arginine-specific carbamoyl phosphate synthetase. In Neurospora crassa it is a small upstream ORF of 24 codon above the arg-2 locus. In yeast it is the leader peptide of the CPA1 gene. The 5' region of CPA1 mRNA contains a 25 codon upstream open reading frame. The leader peptide, the product of the upstream open reading frame, plays an essential, negative role in the specific repression of CPA1 by arginine. 23 matched cddid_all.tbl CDD pfam08253 pfam08253 285460 Leader_Erm Erm Leader peptide. These short proteins are Leader peptides (15-19 amino acids) of erm genes that code for resistance determinants in Staphylococcus aureus. 19 matched cddid_all.tbl CDD pfam08254 pfam08254 285461 Leader_Thr Threonine leader peptide. Threonine leader peptide of the Threonine operon thrA1A2BC. It as been sequenced in different bacteria: E. coli, Serratia marcescens, Salmonella typhi. 22 matched cddid_all.tbl CDD pfam08255 pfam08255 285462 Leader_Trp Trp-operon Leader Peptide. The tryptophan operon regulatory region of C. freundii's (leader transcript) encodes a 14-residue peptide containing characteriztic tandem tryptophan residues. It is about 10 nucleotides shorter than those of E. coli and S. typhimurium. 14 matched cddid_all.tbl CDD pfam08256 pfam08256 116841 Antimicrobial20 Aurein-like antibiotic peptide. This family of antibacterial peptides are secreted from the granular dorsal glands of the Green and Golden Bell Frog Litoria aurea, Southern Bell Frog L. raniformis, Blue Mountains tree-frog Litoria citropa (genus Litoria) and frogs from genus Uperoleia. They are a part of the FSAP peptide family. Amongst the more active of these are aurein 1.2, aurein 2.2 and aurein 3.1; caerin 1.1, maculatin 1.1, uperin 3.6; citropin 1.1, citropin 1.2, citropin 1.3 and a minor peptide are wide-spectrum antibacterial peptides. 13 matched cddid_all.tbl CDD pfam08257 pfam08257 400520 Sulfakinin Sulfakinin family. The sulfakinin (SK) family of neuropeptides have only been identified in crustaceans and insects. For most species there is the potential for producing two sulfakinin peptides one have a short sulfakinin sequence The function of the sulfakinins is difficult to assess. For the American cockroach, various forms of the endogenous sulfakinins have been shown to be active on the hindgut, and also on the heart. In C. vomitoria the peptides act as neurotransmitters or neuromodulators, linking the brain with all thoracic and abdominal ganglia. In adults of P. monodon they appear to be restricted to a few neurones in the brain with a neural pathway extending along to the ventral thoracic and abdominal ganglia. 9 matched cddid_all.tbl CDD pfam08258 pfam08258 116843 WWamide WWamide peptide. This family contain neuropeptides, isolated from ganglia of the African giant snail, Achatina fulica. Each peptide has a Trp residue at both the N- and C-termini. Purified WWamide-1, -2 and -3 showed an inhibitory effect on the phasic contractions of the anterior byssus retractor muscle (ABRM). 7 matched cddid_all.tbl CDD pfam08259 pfam08259 400521 Periviscerokin Periviscerokinin family. Abdominal Perisympathetic organs of insects contain Periviscerokinins neuropeptides of about 11 amino acids. 11 matched cddid_all.tbl CDD pfam08260 pfam08260 116845 Kinin Insect kinin peptide. These neuropeptides are the first members of the insect kinin-family isolated from the American cockroach. Their occurrence in the retrocerebral complex suggests a physiological role as a neurohormone. The C-terminal sequence Phe-X-Ser-Trp-Gly-NH2 characterized the peptides as members of the insect kinin family. Data suggest a possible involvement of insect kinins in water-balance by regulating the osmoregulation. These peptides have length from 6 to 14 amino acids. 8 matched cddid_all.tbl CDD pfam08261 pfam08261 87473 Carcinustatin Carcinustatin peptide. A total of 20 peptides of the superfamily allostatin were isolated from the shore crab Carcinus maenas. They are named carcinustatin 1 to 20 and their length ranges from 5 to 27 amino acids. This family includes carcinustatin 8,9,15 and 16. 8 matched cddid_all.tbl CDD pfam08262 pfam08262 116846 Lem_TRP Leucophaea maderae tachykinin-related peptide. These peptides are designated Leucophaea maderae tachykinin-related peptides (Lem TRPs). Some were isolated from the midgut of L. maderae, whereas others appear to be brain specific. The Lem TRPs of the brain are myotropic and induce increases in the amplitude and frequency of spontaneous contractions and tonus of hindgut muscle in L. maderae. They were also isolated from brain-corpora, cardiaca-corpora, allata-suboesophageal ganglion extracts of the Locusta migratoria. They stimulate visceral muscle contractions of the oviduct and the foregut of Locusta migratoria. 10 matched cddid_all.tbl CDD pfam08263 pfam08263 462411 LRRNT_2 Leucine rich repeat N-terminal domain. Leucine Rich Repeats pfam00560 are short sequence motifs present in a number of proteins with diverse functions and cellular locations. Leucine Rich Repeats are often flanked by cysteine rich domains. This domain is often found at the N-terminus of tandem leucine rich repeats. 41 matched cddid_all.tbl CDD pfam08264 pfam08264 400523 Anticodon_1 Anticodon-binding domain of tRNA ligase. This domain is found mainly hydrophobic tRNA synthetases. The domain binds to the anticodon of the tRNA ligase. 141 matched cddid_all.tbl CDD pfam08265 pfam08265 462412 YL1_C YL1 nuclear protein C-terminal domain. This domain is found in proteins of the YL1 family. These proteins have been shown to be DNA-binding and may be a transcription factor. This domain is found in proteins that are not YL1 proteins. 29 matched cddid_all.tbl CDD pfam08266 pfam08266 462413 Cadherin_2 Cadherin-like. This cadherin domain is usually the most N-terminal copy of the domain. 83 matched cddid_all.tbl CDD pfam08267 pfam08267 400526 Meth_synt_1 Cobalamin-independent synthase, N-terminal domain. The N-terminal domain and C-terminal domains of cobalamin-independent synthases together define a catalytic cleft in the enzyme. The N-terminal domain is thought to bind the substrate, in particular, the negatively charged polyglutamate chain. The N-terminal domain is also thought to stabilize a loop from the C-terminal domain. 310 matched cddid_all.tbl CDD pfam08268 pfam08268 285468 FBA_3 F-box associated domain. 125 matched cddid_all.tbl CDD pfam08269 pfam08269 462414 dCache_2 Cache domain. Double Cache domain 2 (dCache_2) may be a result of single Cache domain 2 (sCache_2) duplication. 298 matched cddid_all.tbl CDD pfam08270 pfam08270 429889 PRD_Mga M protein trans-acting positive regulator (MGA) PRD domain. Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions. This corresponds to the PRD like region. 219 matched cddid_all.tbl CDD pfam08271 pfam08271 400527 TF_Zn_Ribbon TFIIB zinc-binding. The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure. 43 matched cddid_all.tbl CDD pfam08272 pfam08272 462415 Topo_Zn_Ribbon Topoisomerase I zinc-ribbon-like. Some Proteobacteria topoisomerase I contain two zinc-ribbon-like domains at the C-terminus that structurally homologous to pfam01396. However, this domain no longer bind zinc. Indeed, only one of the four cysteine residues remains. 39 matched cddid_all.tbl CDD pfam08273 pfam08273 400529 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. 37 matched cddid_all.tbl CDD pfam08274 pfam08274 429891 YjdM_Zn_Ribbon PhnA Zinc-Ribbon. 30 matched cddid_all.tbl CDD pfam08275 pfam08275 429892 Toprim_N DNA primase catalytic core, N-terminal domain. 128 matched cddid_all.tbl CDD pfam08276 pfam08276 429893 PAN_2 PAN-like domain. 67 matched cddid_all.tbl CDD pfam08277 pfam08277 429894 PAN_3 PAN-like domain. 71 matched cddid_all.tbl CDD pfam08278 pfam08278 429895 DnaG_DnaB_bind DNA primase DnaG DnaB-binding. Eubacterial DnaG primases interact with several factors to from the replisome. One of these factors in DnaB, a helicase. This domain has been demonstrated to be responsible for the interaction between DnaG and DnaB. 122 matched cddid_all.tbl CDD pfam08279 pfam08279 429896 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins. 52 matched cddid_all.tbl CDD pfam08280 pfam08280 311953 HTH_Mga M protein trans-acting positive regulator (MGA) HTH domain. Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions. 59 matched cddid_all.tbl CDD pfam08281 pfam08281 400535 Sigma70_r4_2 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. 54 matched cddid_all.tbl CDD pfam08282 pfam08282 429897 Hydrolase_3 haloacid dehalogenase-like hydrolase. This family contains haloacid dehalogenase-like hydrolase enzymes. 255 matched cddid_all.tbl CDD pfam08283 pfam08283 285483 Gemini_AL1_M Geminivirus rep protein central domain. This is the cetral domain of the geminivirus rep proteins. 107 matched cddid_all.tbl CDD pfam08284 pfam08284 400537 RVP_2 Retroviral aspartyl protease. Single domain aspartyl proteases from retroviruses, retrotransposons, and badnaviruses (plant dsDNA viruses). These proteases are generally part of a larger polyprotein; usually pol, more rarely gag. Retroviral proteases appear to be homologous to a single domain of the two-domain eukaryotic aspartyl proteases. 134 matched cddid_all.tbl CDD pfam08285 pfam08285 462416 DPM3 Dolichol-phosphate mannosyltransferase subunit 3 (DPM3). This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex. 89 matched cddid_all.tbl CDD pfam08286 pfam08286 429899 Spc24 Spc24 subunit of Ndc80. Spc24 is a component of the evolutionarily conserved kinetochore-associated Ndc80 complex and is involved in chromosome segregation 107 matched cddid_all.tbl CDD pfam08287 pfam08287 429900 DASH_Spc19 Spc19. Spc19 is a component of the DASH complex. The DASH complex associates with the spindle pole body and is important for spindle and kinetochore integrity during cell division. 148 matched cddid_all.tbl CDD pfam08288 pfam08288 400541 PIGA PIGA (GPI anchor biosynthesis). This domain is found on phosphatidylinositol n-acetylglucosaminyltransferase proteins. These proteins are involved in GPI anchor biosynthesis and are associated with disease the paroxysmal nocturnal haemoglobinuria. 90 matched cddid_all.tbl CDD pfam08289 pfam08289 429901 Flu_M1_C Influenza Matrix protein (M1) C-terminal domain. This region is thought to be a second domain of the M1 matrix protein. 95 matched cddid_all.tbl CDD pfam08290 pfam08290 429902 Hep_core_N Hepatitis core protein, putative zinc finger. This short region is found at the N-terminus of some hepatitis core proteins. Its conservation of four cys and his suggests a zinc binding domain. 27 matched cddid_all.tbl CDD pfam08291 pfam08291 429903 Peptidase_M15_3 Peptidase M15. 109 matched cddid_all.tbl CDD pfam08292 pfam08292 400543 RNA_pol_Rbc25 RNA polymerase III subunit Rpc25. Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III. 121 matched cddid_all.tbl CDD pfam08293 pfam08293 462417 MRP-S33 Mitochondrial ribosomal subunit S27. This family of proteins corresponds to mitochondrial ribosomal subunit S27 in prokaryotes and to subunit S33 in humans. It is a small 106 residue protein.The evolutionary history of the mitoribosomal proteome that is encoded by a diverse subset of eukaryotic genomes, reveals an ancestral ribosome of alpha-proteobacterial descent that more than doubled its protein content in most eukaryotic lineages. Several new MRPs have originated via duplication of existing MRPs as well as by recruitment from outside of the mitoribosomal proteome. 87 matched cddid_all.tbl CDD pfam08294 pfam08294 311963 TIM21 TIM21. TIM21 interacts with the outer mitochondrial TOM complex and promotes the insertion of proteins into the inner mitochondrial membrane. 145 matched cddid_all.tbl CDD pfam08295 pfam08295 462418 Sin3_corepress Sin3 family co-repressor. This domain is found on transcriptional regulators. It forms interactions with histone deacetylases. 97 matched cddid_all.tbl CDD pfam08297 pfam08297 400546 U3_snoRNA_assoc U3 snoRNA associated. This family of proteins is associated with U3 snoRNA. U3 snoRNA is required for nucleolar processing of pre-18S ribosomal RNA. 88 matched cddid_all.tbl CDD pfam08298 pfam08298 116881 AAA_PrkA PrkA AAA domain. This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain. 358 matched cddid_all.tbl CDD pfam08299 pfam08299 462419 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix. 69 matched cddid_all.tbl CDD pfam08300 pfam08300 369801 HCV_NS5a_1a Hepatitis C virus non-structural 5a zinc finger domain. The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. This domain corresponds to the N-terminal zinc binding domain. 62 matched cddid_all.tbl CDD pfam08301 pfam08301 149382 HCV_NS5a_1b Hepatitis C virus non-structural 5a domain 1b. The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. This region corresponds to the 1b domain. 102 matched cddid_all.tbl CDD pfam08302 pfam08302 400548 tRNA_lig_CPD Fungal tRNA ligase phosphodiesterase domain. This domain is found in fungal tRNA ligases and has cyclic phosphodiesterase activity. tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns. 253 matched cddid_all.tbl CDD pfam08303 pfam08303 400549 tRNA_lig_kinase tRNA ligase kinase domain. This domain is found in fungal tRNA ligases and has kinase activity. tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns. This family contains a P-loop motif. 168 matched cddid_all.tbl CDD pfam08305 pfam08305 429907 NPCBM NPCBM/NEW2 domain. This novel putative carbohydrate binding module (NPCBM) domain is found at the N-terminus of glycosyl hydrolase family 98 proteins. This domain has also been called the NEW2 domain (Naumoff DG. Phylogenetic analysis of alpha-galactosidases of the GH27 family. Molecular Biology (Engl Transl). (2004)38:388-399.) 137 matched cddid_all.tbl CDD pfam08306 pfam08306 400551 Glyco_hydro_98M Glycosyl hydrolase family 98. This domain is the putative catalytic domain of glycosyl hydrolase family 98 proteins. 328 matched cddid_all.tbl CDD pfam08307 pfam08307 285502 Glyco_hydro_98C Glycosyl hydrolase family 98 C-terminal domain. This putative domain is found at the C-terminus of glycosyl hydrolase family 98 proteins. This domain is not expected to form part of the catalytic activity. 270 matched cddid_all.tbl CDD pfam08308 pfam08308 429908 PEGA PEGA domain. This domain is found in both archaea and bacteria and has similarity to S-layer (surface layer) proteins. It is named after the characteriztic PEGA sequence motif found in this domain. The secondary structure of this domain is predicted to be beta-strands [Adindla et al. Comparative and Functional Genomics 2004; 5:2-16]. 71 matched cddid_all.tbl CDD pfam08309 pfam08309 285504 LVIVD LVIVD repeat. This repeat is found in bacterial and archaeal cell surface proteins, many of which are hypothetical. The secondary structure corresponding to this repeat is predicted to comprise from 1-7 of 4-beta-strands which may associate to form a beta-propeller. The repeat copy number varies from 3-29. This repeat is sometimes found with the PKD domain pfam00801. 42 matched cddid_all.tbl CDD pfam08310 pfam08310 429909 LGFP LGFP repeat. This 54 amino acid repeat is found in many hypothetical proteins. Several hypothetical proteins from C.glutamicum and C.efficiens along with PS1 protein contain this repeat region. The N-terminus region of PS1 contains an esterase domain which transfers corynomycolic acid. The C-terminus region consists of 4 tandem LGFP repeats. It is hypothesized that the PS1 proteins in Corynebacterium, when associated with the cell wall, may be anchored via the LGFP tandem repeats that may be important for maintaining cell wall integrity [Adindla et al. Comparative and Functional Genomics 2004; 5:2-16]. Deletion of Swiss:Q01377 protein results in a 10-fold increase in the cell volume of the organizm and infers the corresponding proteins involvement in the cell shape formation. The secondary structure of each repeat is predicted to comprise two beta-strands and one alpha-helix [Adindla et al. 2004]. 53 matched cddid_all.tbl CDD pfam08311 pfam08311 462420 Mad3_BUB1_I Mad3/BUB1 homology region 1. Proteins containing this domain are checkpoint proteins involved in cell division. This region has been shown to be essential for the binding of the binding of BUB1 and MAD3 to CDC20p. 123 matched cddid_all.tbl CDD pfam08312 pfam08312 462421 cwf21 cwf21 domain. The cwf21 family is involved in mRNA splicing. It has been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe. The function of the cwf21 domain is to bind directly to the spliceosomal protein Prp8. Mutations in the cwf21 domain prevent Prp8 from binding. The structure of this domain has recently been solved which shows this domain to be composed of two alpha helices. 44 matched cddid_all.tbl CDD pfam08313 pfam08313 462422 SCA7 SCA7, zinc-binding domain. This domain is found in the protein Sgf73/Sca7 which is a component of the multihistone acetyltransferase complexes SAGA and SILK. This domain is also found in Ataxin-7, a human protein which in its polyglutamine expanded pathological form, is responsible for the neurodegenerative disease spinocerebellar ataxia 7 (SCA7). Ataxin-7 is an integral component of the mammalian SAGA-like complexes, the TATA-binding protein-free TAF-containing complex (TFTC) and the SPT3/TAF9/GCN5 acetyltransferase complex (STAGA). This domain is a minimal domain in ataxin-7-like proteins that is required for interaction with TFTC/STAGA subunits and is conserved highly through evolution. The domain contains a conserved Cys(3)His motif that binds zinc, thus indicating this to be a new zinc-binding domain. 61 matched cddid_all.tbl CDD pfam08314 pfam08314 429913 Sec39 Secretory pathway protein Sec39. Mnaimneh et al identified Sec39p as a protein involved in ER-Golgi transport in a large scale promoter shut down analysis of essential yeast genes. Kraynack et al. (2005) showed that Sec39p (Dsl3p) is required for Golgi-ER retrograde transport and is part of a very stable protein complex that also includes Dsl1p (in mammals ZW10), Tip20p (Rint-1) and the ER localized Q-SNARE proteins Ufe1p (syntaxin-18), Sec20p and Use1p. This was confirmed in a genome-wide analysis of protein complexes by Gavin et al (2006). 725 matched cddid_all.tbl CDD pfam08315 pfam08315 462423 cwf18 cwf18 pre-mRNA splicing factor. The cwf18 family is involved in mRNA splicing. It has been isolated as a subcomplex of the splicosome in Schizosaccharomyces pombe. 135 matched cddid_all.tbl CDD pfam08316 pfam08316 400558 Pal1 Pal1 cell morphology protein. Pal1 is a membrane associated protein that is involved in the maintenance of cylindrical cellular morphology. It localizes to sites of active growth. Pal1 physically interacts and displays overlapping localization with the Huntingtin-interacting-protein (Hip1)-related protein Sla2p/End4p. 135 matched cddid_all.tbl CDD pfam08317 pfam08317 462424 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association. 196 matched cddid_all.tbl CDD pfam08318 pfam08318 462425 COG4 COG4 transport protein. This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi an intra Golgi transport. 326 matched cddid_all.tbl CDD pfam08320 pfam08320 462426 PIG-X PIG-X / PBN1. Mammalian PIG-X and yeast PBN1 are essential components of glycosylphosphatidylinositol-mannosyltransferase I. These enzymes are involved in the transfer of sugar molecules. 207 matched cddid_all.tbl CDD pfam08321 pfam08321 462427 PPP5 PPP5 TPR repeat region. This region is specific to the PPP5 subfamily of serine/threonine phosphatases and contains TPR repeats. 92 matched cddid_all.tbl CDD pfam08323 pfam08323 400563 Glyco_transf_5 Starch synthase catalytic domain. 239 matched cddid_all.tbl CDD pfam08324 pfam08324 462428 PUL PUL domain. The PUL (PLAP, Ufd3p and Lub1p) domain is a novel alpha-helical Ub-associated domain. It directly binds to Cdc48, a chaperone-like AAA ATPase that collects ubiquitylated substrates. 261 matched cddid_all.tbl CDD pfam08325 pfam08325 311984 WLM WLM domain. This is a predicted metallopeptidase domain called WLM (Wss1p-like metalloproteases). These are linked to the Ub-system by virtue of fusions with the UB-binding PUG (PUB), Ub-like, and Little Finger domains. More specifically, genetic evidence implicates the WLM family in de-SUMOylation. 190 matched cddid_all.tbl CDD pfam08326 pfam08326 462429 ACC_central Acetyl-CoA carboxylase, central region. The region featured in this family is found in various eukaryotic acetyl-CoA carboxylases, N-terminal to the catalytic domain (pfam01039). This enzyme (EC:6.4.1.2) is involved in the synthesis of long-chain fatty acids, as it catalyzes the rate-limiting step in this process. 718 matched cddid_all.tbl CDD pfam08327 pfam08327 429921 AHSA1 Activator of Hsp90 ATPase homolog 1-like protein. This family includes eukaryotic, prokaryotic and archaeal proteins that bear similarity to a C-terminal region of human activator of 90 kDa heat shock protein ATPase homolog 1 (AHSA1/p38). This protein is known to interact with the middle domain of Hsp90, and stimulate its ATPase activity. It is probably a general upregulator of Hsp90 function, particularly contributing to its efficiency in conditions of increased stress. p38 is also known to interact with the cytoplasmic domain of the VSV G protein, and may thus be involved in protein transport. It has also been reported as being underexpressed in Down's syndrome. This region is found repeated in two members of this family (Swiss:Q8XY04 and Swiss:Q6MH87). The structure of YndB from Bacillus subtilis showed the helix-grip fold consisting of a beta-sheet with two small and one long alpha-helix which form a hydrophobic cavity that preferentially binds lipid-like molecules. This structure confirms its similarity with the eukaryote protein Aha1 and its classification as a member of the AHSA1 family). 125 matched cddid_all.tbl CDD pfam08328 pfam08328 462430 ASL_C Adenylosuccinate lyase C-terminal. This domain is found at the C-terminus of adenylosuccinate lyase(ASL; PurB in E. coli). It has been identified in bacteria, eukaryotes and archaea and is found together with the lyase domain pfam00206. ASL catalyzes the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate. 115 matched cddid_all.tbl CDD pfam08329 pfam08329 400568 ChitinaseA_N Chitinase A, N-terminal domain. This domain is found in a number of bacterial chitinases and similar viral proteins. It is organized into a fibronectin III module domain-like fold, comprising only beta strands. Its function is not known, but it may be involved in interaction with the enzyme substrate, chitin. It is separated by a hinge region from the catalytic domain (pfam00704); this hinge region is probably mobile, allowing the N-terminal domain to have different relative positions in solution. 130 matched cddid_all.tbl CDD pfam08331 pfam08331 462431 QueG_DUF1730 Epoxyqueuosine reductase QueG, DUF1730. This domain of unknown function occurs in Epoxyqueuosine reductase QueG, an iron-sulfur cluster-binding protein, together with the 4Fe-4S binding domain (pfam00037). QueG catalyzes the conversion of epoxyqueuosine (oQ) to queuosine (Q), which is a hypermodified base found in the wobble positions of tRNA(Asp), tRNA(Asn), tRNA(His) and tRNA(Tyr). 77 matched cddid_all.tbl CDD pfam08332 pfam08332 285524 CaMKII_AD Calcium/calmodulin dependent protein kinase II association domain. This domain is found at the C-terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (pfam00069) at their N-terminus. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers. 128 matched cddid_all.tbl CDD pfam08333 pfam08333 429924 DUF1725 Protein of unknown function (DUF1725). This family include many eukaryotic and one bacterial sequence. Many of its members are annotated as being putative L1 retrotransposons or LINE-1 reverse transcriptase homologs. The region in question is found repeated in some family members. 18 matched cddid_all.tbl CDD pfam08334 pfam08334 429925 T2SSG Type II secretion system (T2SS), protein G. The Type II secretion system, also called Secretion-dependent pathway (SDP), is responsible for the transport of proteins across the outer membrane first exported to the periplasm by the Sec or Tat translocon in Gram-negative (diderm) bacteria. The T2SG family includes proteins such as EpsG (P45773) in Vibrio cholera, XcpT also called PddA (Q00514) in Pseudomonas aeruginosa or PulG (P15746)in Klebsiella pneumoniae. The PulG is thought to be anchored in the inner membrane with its C-terminus directed towards the periplasme. Together with other members of the Type II secretion machinery, it is thought to assemble into a pilus-like structure that may function as a dynamic mechanism to push secreted proteins out of the cell. The polypeptide is organized into a long N-terminal alpha-helix followed by a loop region that separates it from a C-terminal anti-parallel beta-sheet. 106 matched cddid_all.tbl CDD pfam08335 pfam08335 462432 GlnD_UR_UTase GlnD PII-uridylyltransferase. This is a family of bifunctional uridylyl-removing enzymes/uridylyltransferases (UR/UTases, GlnD) that are responsible for the modification (EC:2.7.7.59) of the regulatory protein P-II, or GlnB (pfam00543). In response to nitrogen limitation, these transferases catalyze the uridylylation of the PII protein, which in turn stimulates deadenylylation of glutamine synthetase (GlnA). Deadenylylated glutamine synthetase is the more active form of the enzyme. Moreover, uridylylated PII can act together with NtrB and NtrC to increase transcription of genes in the sigma54 regulon, which include glnA and other nitrogen-level controlled genes. It has also been suggested that the product of the glnD gene is involved in other physiological functions such as control of iron metabolism in certain species. The region described in this family is found in many of its members to be C-terminal to a nucleotidyltransferase domain (pfam01909), and N-terminal to an HD domain (pfam01966) and two ACT domains (pfam01842). 140 matched cddid_all.tbl CDD pfam08336 pfam08336 462433 P4Ha_N Prolyl 4-Hydroxylase alpha-subunit, N-terminal region. The members of this family are eukaryotic proteins, and include all three isoforms of the prolyl 4-hydroxylase alpha subunit. This enzyme (EC:1.14.11.2) is important in the post-translational modification of collagen, as it catalyzes the formation of 4-hydroxyproline. In vertebrates, the complete enzyme is an alpha2-beta2 tetramer; the beta-subunit is identical to protein disulphide isomerase. The function of the N-terminal region featured in this family does not seem to be known. 135 matched cddid_all.tbl CDD pfam08337 pfam08337 462434 Plexin_cytopl Plexin cytoplasmic RasGAP domain. This family features the C-terminal regions of various plexins. Plexins are receptors for semaphorins, and plexin signalling is important in path finding and patterning of both neurons and developing blood vessels. The cytoplasmic region, which has been called a SEX domain in some members of this family, is involved in downstream signalling pathways, by interaction with proteins such as Rac1, RhoD, Rnd1 and other plexins. This domain acts as a RasGAP domain. 500 matched cddid_all.tbl CDD pfam08338 pfam08338 462435 DUF1731 Domain of unknown function (DUF1731). This domain of unknown function appears towards the C-terminus of proteins of the NAD dependent epimerase/dehydratase family (pfam01370) in bacteria, eukaryotes and archaea. Many of the proteins in which it is found are involved in cell-division inhibition. 46 matched cddid_all.tbl CDD pfam08339 pfam08339 429930 RTX_C RTX C-terminal domain. This family describes the C-terminal region of various bacterial haemolysins and leukotoxins, which belong to the RTX family of toxins. These are produced by various Gram negative bacteria, such as E. coli and Actinobacillus pleuropneumoniae. RTX toxins may interact with lipopolysaccharide (LPS) to functionally impair and eventually kill leukocytes. This region is found in association with the RTX N-terminal domain (pfam02382) and multiple hemolysin-type calcium-binding repeats (pfam00353). 131 matched cddid_all.tbl CDD pfam08340 pfam08340 462436 DUF1732 Domain of unknown function (DUF1732). This domain of unknown function is often found at the C-terminus of bacterial proteins, many of which are hypothetical, including proteins of the YicC family which have pfam03755 at the N-terminus. These include a protein important in the stationary phase of growth, and required for growth at high temperature. Structural modelling suggests this domain may bind nucleic acids. 85 matched cddid_all.tbl CDD pfam08341 pfam08341 462437 TED Thioester domain. This domain is found near the N-terminus of a variety of bacterial surface proteins and pili. This domain contains an unusual covalent ester bond between a conserved cysteine and glutamine residue. 105 matched cddid_all.tbl CDD pfam08343 pfam08343 429933 RNR_N Ribonucleotide reductase N-terminal. This domain is found at the N-terminus of bacterial ribonucleoside-diphosphate reductases (ribonucleotide reductases, RNRs) which catalyze the formation of deoxyribonucleotides. It occurs together with the RNR all-alpha domain (pfam00317) and the RNR barrel domain (pfam02867). 82 matched cddid_all.tbl CDD pfam08344 pfam08344 462438 TRP_2 Transient receptor ion channel II. This domain is found in the transient receptor ion channel (Trp) family of proteins. There is strong evidence that Trp proteins are structural elements of calcium-ion entry channels activated by G protein-coupled receptors. This domain does not tend to appear with the TRP domain (pfam06011) but is often found to the C-terminus of Ankyrin repeats (pfam00023). 60 matched cddid_all.tbl CDD pfam08345 pfam08345 462439 YscJ_FliF_C Flagellar M-ring protein C-terminal. This domain is found in bacterial flagellar M-ring (FliF) proteins together with the YscJ/FliF domain (pfam01514). 156 matched cddid_all.tbl CDD pfam08346 pfam08346 429936 AntA AntA/AntB antirepressor. In E. coli the two proteins AntA and AntB have 62% amino acid identities near their N termini. AntA appears to be encoded by a truncated and divergent copy of AntB. The two proteins are homologous to putative antirepressors found in numerous bacteriophages, such as the hypothetical antirepressor protein encoded by the gene LO142 of the bacteriophage 933W. 68 matched cddid_all.tbl CDD pfam08347 pfam08347 462440 CTNNB1_binding N-terminal CTNNB1 binding. This region tends to appear at the N-terminus of proteins also containing DNA-binding HMG (high mobility group) boxes (pfam00505) and appears to bind the armadillo repeat of CTNNB1 (beta-catenin), forming a stable complex. Signaling by Wnt through TCF/LCF is involved in developmental patterning, induction of neural tissues, cell fate decisions and stem cell differentiation. Isoforms of HMG T-cell factors lacking the N-terminal CTNNB1-binding domain cannot fulfill their role as transcriptional activators in T-cell differentiation. 207 matched cddid_all.tbl CDD pfam08348 pfam08348 429938 PAS_6 YheO-like PAS domain. This family contains various hypothetical bacterial proteins that are similar to the E. coli protein YheO. Their function is unknown, but are likely to be involved in signalling based on the presence of this PAS domain. 115 matched cddid_all.tbl CDD pfam08349 pfam08349 429939 DUF1722 Protein of unknown function (DUF1722). This domain of unknown function is found in bacteria and archaea and is homologous to the hypothetical protein ybgA from E. coli. 115 matched cddid_all.tbl CDD pfam08350 pfam08350 429940 FilR1_middle Methanogenesis regulatory protein FilR1, middle domain. This archaeal domain of unknown function has been found at the middle of Methanogenesis regulatory protein FilR1 and at the C-terminus of archaeal proteins, including several transcriptional regulators of the ArsR family (see pfam01022). FilR1 is a member of the two-component regulatory system FilI/FilRs which is involved in the regulation of methanogenesis. 62 matched cddid_all.tbl CDD pfam08351 pfam08351 462441 TmcA_N tRNA(Met) cytidine acetyltransferase TmcA, N-terminal. This domain of unknown function is often found at the N-terminus of the bacterial tRNA(Met) cytidine acetyltransferase TmcA. TmcA catalyzes the formation of N(4)-acetylcytidine (ac4C) at the wobble position of tRNA(Met) by using acetyl-CoA as an acetyl donor and either ATP or GTP. This modification is thought to ensure precise recognition of the AUG codon by strengthening C-G base-pair interaction and also prevent misrecognition of the near cognate AUA codon. This domain is also found in mammalian N-acetyltransferase 10 (NAT10) and fungal protein Kre33. Kre33 and NAT10 are RNA cytosine acetyltransferases with specificity toward both 18S rRNA and tRNAs and contain additional putative nuclear and nucleolar localization signals (NLS and NoLS respectively). 178 matched cddid_all.tbl CDD pfam08352 pfam08352 400588 oligo_HPY Oligopeptide/dipeptide transporter, C-terminal region. This family features a region found towards the C-terminus of oligopeptide ABC transporter ATP binding proteins, immediately following the ATP-binding domain (pfam00005). All characterized members appear able to be involved in the transport of oligopeptides or dipeptides. Some are important for sporulation or antibiotic resistance. Some dipeptide transporters also act on the heme precursor delta-aminolevulinic acid. 65 matched cddid_all.tbl CDD pfam08353 pfam08353 462442 MurT_C MurT ligase C-terminal. This entry represents the C-terminal domain of MurT ligase from Gram-positive bacteria. MurT is part of the bi-enzymatic complex MurT-GatD involved in the amidation of the alpha-carboxyl group of the D-isoglutamate residue in Lipid II in the peptidoglycan layer to produce D-isoglutamine. This domain contains an aspartate at position 349, the third residue in the catalytic triad GatD-C94, GatD-H189, MurT-D349. This C-terminal domain is built around a central six-stranded, predominantly parallel beta-sheet that is sandwiched between four alpha-helices on one side and two alpha-helices on the other. The MurT-GatD heterodimer adopts a boomerang-shaped conformation, with GatD packing against the C-terminal domain of MurT. 110 matched cddid_all.tbl CDD pfam08354 pfam08354 369827 DUF1729 Domain of unknown function (DUF1729). This domain of unknown function is found in fatty acid synthase beta subunits together with the MaoC-like domain (pfam01575) and the Acyltransferase domain (pfam00698). The domain has been identified in fungi and bacteria. 353 matched cddid_all.tbl CDD pfam08355 pfam08355 462443 EF_assoc_1 EF hand associated. This region typically appears on the C-terminus of EF hands in GTP-binding proteins such as Arht/Rhot (may be involved in mitochondrial homeostasis and apoptosis). The EF hand associated region is found in yeast, vertebrates and plants. 70 matched cddid_all.tbl CDD pfam08356 pfam08356 462444 EF_assoc_2 EF hand associated. This region predominantly appears near EF-hands (pfam00036) in GTP-binding proteins. It is found in all three eukaryotic kingdoms. 85 matched cddid_all.tbl CDD pfam08357 pfam08357 254756 SEFIR SEFIR domain. This family comprises IL17 receptors (IL17Rs) and SEF proteins. The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (pfam01582), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways. 150 matched cddid_all.tbl CDD pfam08358 pfam08358 149427 Flexi_CP_N Carlavirus coat. This domain is found together with the viral coat protein domain (pfam00286) in coat/capsid proteins of Carlaviruses infecting plants. 52 matched cddid_all.tbl CDD pfam08359 pfam08359 285548 TetR_C_4 YsiA-like protein, C-terminal region. The members of this family are thought to be TetR-type transcriptional regulators that bear particular similarity to YsiA, a hypothetical protein expressed by B. subtilis. 133 matched cddid_all.tbl CDD pfam08360 pfam08360 400592 TetR_C_5 QacR-like protein, C-terminal region. This family features the C-terminal region of a number of proteins that bear similarity to the QacR protein, a transcriptional regulator of the TetR family. QacR is able to bind various environmental agents, which include a number of cationic lipophilic compounds, and thus regulate the transcription of QacA, a multidrug efflux pump. The C-terminal region contains the multifaceted, expansive drug-binding pocket, which is composed of several separate, but linked, binding sites. 131 matched cddid_all.tbl CDD pfam08361 pfam08361 429945 TetR_C_2 MAATS-type transcriptional repressor, C-terminal region. This domain is named after the various transcriptional regulatory proteins that it contains, including MtrR, AcrR, ArpR, TtgR and SmeT. These are members of the TetR family of transcriptional repressors, that are involved in the control of expression of multidrug resistance proteins. This domain binds multiple drugs, antibiotics, flavonoids and indole (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 121 matched cddid_all.tbl CDD pfam08362 pfam08362 429946 TetR_C_3 YcdC-like protein, C-terminal region. This family comprises proteins that belong to the TetR family of transcriptional regulators. They bear particular similarity to YcdC, a putative HTH-containing protein. This family features the C-terminal region of these sequences, which does not include the helix-turn-helix. 143 matched cddid_all.tbl CDD pfam08363 pfam08363 400594 GbpC Glucan-binding protein C. This domain is found in the Streptococcus Glucan-binding protein C (GbpC) and also in surface protein antigen (Spa)-family proteins which show sequence similarity to GbpC. 260 matched cddid_all.tbl CDD pfam08364 pfam08364 429947 IF2_assoc Bacterial translation initiation factor IF-2 associated region. Most of the sequences in this alignment come from bacterial translation initiation factors (IF-2, also pfam04760), but the domain is also found in the eukaryotic translation initiation factor 4 gamma in yeast and in a hypothetical Euglenozoa protein of unknown function. 39 matched cddid_all.tbl CDD pfam08365 pfam08365 462445 IGF2_C Insulin-like growth factor II E-peptide. This domain is found at the C-terminal domain of the insulin-like growth factor II (IGF-2, also see pfam00049) in vertebrates and seems to represent the E-peptide. 56 matched cddid_all.tbl CDD pfam08366 pfam08366 462446 LLGL LLGL2. This domain is found in lethal giant larvae homolog 2 (LLGL2) proteins and syntaxin-binding proteins like tomosyn. It has been identified in eukaryotes and tends to be found together with WD repeats (pfam00400). 103 matched cddid_all.tbl CDD pfam08367 pfam08367 462447 M16C_assoc Peptidase M16C associated. This domain appears in eukaryotes as well as bacteria and tends to be found near the C-terminus of the metalloprotease M16C (pfam05193). 248 matched cddid_all.tbl CDD pfam08368 pfam08368 462448 FAST_2 FAST kinase-like protein, subdomain 2. This family represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases (EC:2.7.1.-) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis. Note that many family members are hypothetical proteins. This subdomain is often found associated with the FAST kinase-like protein, subdomain 2. 89 matched cddid_all.tbl CDD pfam08369 pfam08369 462449 PCP_red Proto-chlorophyllide reductase 57 kD subunit. This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of Nitrogenase component 1 type Oxidoreductases (pfam00148) and sometimes independently in bacterial proteins such as the Proto-chlorophyllide reductase 57 kD subunit of the Cyanobacterium Synechocystis. 45 matched cddid_all.tbl CDD pfam08370 pfam08370 462450 PDR_assoc Plant PDR ABC transporter associated. This domain is found on the C-terminus of ABC-2 type transporter domains (pfam01061). It seems to be associated with the plant pleiotropic drug resistance (PDR) protein family of ABC transporters. Like in yeast, plant PDR ABC transporters may also play a role in the transport of antifungal agents [also pfam06422]. The PDR family is characterized by a configuration in which the ABC domain is nearer the N-terminus of the protein than the transmembrane domain. 65 matched cddid_all.tbl CDD pfam08372 pfam08372 337028 PRT_C Plant phosphoribosyltransferase C-terminal. This domain is found at the C-terminus of phosphoribosyltransferases and phosphoribosyltransferase-like proteins. It contains putative transmembrane regions. It often appears together with calcium-ion dependent C2 domains (pfam00168). 156 matched cddid_all.tbl CDD pfam08373 pfam08373 429953 RAP RAP domain. This domain is found in various eukaryotic species, where it is found in proteins that are important in various parasite-host cell interactions. It is thought to be an RNA-binding domain. The domain is involved in plant defence in response to bacterial infection. 58 matched cddid_all.tbl CDD pfam08374 pfam08374 462451 Protocadherin Protocadherin. The structure of protocadherins is similar to that of classic cadherins (pfam00028), but particularly on the cytoplasmic domains they also have some unique features. They are expressed in a variety of organizms and are found in high concentrations in the brain where they seem to be localized mainly at cell-cell contact sites. Their expression seems to be developmentally regulated. 217 matched cddid_all.tbl CDD pfam08375 pfam08375 462452 Rpn3_C Proteasome regulatory subunit C-terminal. This eukaryotic domain is found at the C-terminus of 26S proteasome regulatory subunits such as the non-ATPase Rpn3 subunit which is essential for proteasomal function. It occurs together with the PCI/PINT domain (pfam01399). 57 matched cddid_all.tbl CDD pfam08376 pfam08376 462453 NIT Nitrate and nitrite sensing. The nitrate- and nitrite sensing domain (NIT) is found in receptor components of signal transducing pathways in bacteria which control gene expression, cellular motility and enzyme activity in response to nitrate and nitrite concentrations. The NIT domain is predicted to be all alpha-helical in structure. 227 matched cddid_all.tbl CDD pfam08377 pfam08377 429957 MAP2_projctn MAP2/Tau projection domain. This domain is found in the MAP2/Tau family of proteins which includes MAP2, MAP4, Tau, and their homologs. All isoforms contain a conserved C-terminal domain containing tubulin-binding repeats (pfam00418), and a N-terminal projection domain of varying size. This domain has a net negative charge and exerts a long-range repulsive force. This provides a mechanism that can regulate microtubule spacing which might facilitate efficient organelle transport. 1134 matched cddid_all.tbl CDD pfam08378 pfam08378 462454 NERD Nuclease-related domain. The nuclease-related domain (NERD) is found in a range of bacterial as well as archaeal and plant proteins. It has distant similarity to endonucleases (hence its name) and its predicted secondary structure is helix - sheet - sheet - sheet - sheet - weak sheet/long loop - helix - sheet - sheet. The majority of NERD-containing proteins are single-domain, but in several cases proteins containing NERD have additional domains which in 75% of cases are involved in DNA processing. 108 matched cddid_all.tbl CDD pfam08379 pfam08379 462455 Bact_transglu_N Bacterial transglutaminase-like N-terminal region. This region is found towards the N-terminus of various archaeal and bacterial hypothetical proteins. Some of these are annotated as being transglutaminase-like proteins, and in fact contain a transglutaminase-like superfamily domain (pfam01841). 80 matched cddid_all.tbl CDD pfam08381 pfam08381 429960 BRX Transcription factor regulating root and shoot growth via Pin3. The BREVIS RADIX (BRX) domain was characterized as being a transcription factor in plants regulating the extent of cell proliferation and elongation in the growth zone of the root. BRX is rate limiting for auxin-responsive gene-expression by mediating cross-talk with the brassino-steroid pathway. BRX has a ubiquitous, although quantitatively variable role in modulating the growth rate in both the root and the shoot. The family features a short region of alpha-helix, approximately 60 residues in length, which is found repeated up to three times. BRX is expressed in the vasculature and is rate-limiting for transcriptional auxin action. 56 matched cddid_all.tbl CDD pfam08383 pfam08383 462456 Maf_N Maf N-terminal region. This region is found in various leucine zipper transcription factors of the Maf family. These are implicated in the regulation of insulin gene expression, in erythroid differentiation, and in differentiation of the neuroretina. 34 matched cddid_all.tbl CDD pfam08384 pfam08384 429962 NPP Pro-opiomelanocortin, N-terminal region. This family features the N-terminal peptide of pro-opiomelanocortin (NPP). It is thought to represent an important pituitary peptide, given its high yield from pituitary glands, and exhibits a potent in vitro aldosterone-stimulating activity. 43 matched cddid_all.tbl CDD pfam08385 pfam08385 462457 DHC_N1 Dynein heavy chain, N-terminal region 1. Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit. The region featured in this family includes the sequences implicated in mediating these interactions. It is thought to be flexible and not to adopt a rigid conformation. 560 matched cddid_all.tbl CDD pfam08386 pfam08386 429964 Abhydrolase_4 TAP-like protein. This is a family of putative bacterial peptidases and hydrolases that bear similarity to a tripeptidyl aminopeptidase isolated from Streptomyces lividans. A member of this family is thought to be involved in the C-terminal processing of propionicin F, a bacteriocidin characterized from Propionibacterium freudenreichii. 98 matched cddid_all.tbl CDD pfam08387 pfam08387 462458 FBD FBD. This region is found in F-box (pfam00646) and other domain containing plant proteins; it is repeated in two family members. Its precise function is unknown, but it is thought to be associated with nuclear processes. In fact, several family members are annotated as being similar to transcription factors. 45 matched cddid_all.tbl CDD pfam08388 pfam08388 429966 GIIM Group II intron, maturase-specific domain. This region is found mainly in various bacterial and archaeal species, but a few members of this family are expressed by fungal and chlamydomonal species. It has been implicated in the binding of intron RNA during reverse transcription and splicing. 80 matched cddid_all.tbl CDD pfam08389 pfam08389 462459 Xpo1 Exportin 1-like protein. The sequences featured in this family are similar to a region close to the N-terminus of yeast exportin 1 (Xpo1, Crm1). This region is found just C-terminal to an importin-beta N-terminal domain (pfam03810) in many members of this family. Exportin 1 is a nuclear export receptor that interacts with leucine-rich nuclear export signal (NES) sequences, and Ran-GTP, and is involved in translocation of proteins out of the nucleus. 147 matched cddid_all.tbl CDD pfam08390 pfam08390 462460 TRAM1 TRAM1-like protein. This family comprises sequences that are similar to human TRAM1. This is a transmembrane protein of the endoplasmic reticulum, thought to be involved in the membrane transfer of secretory proteins. The region featured in this family is found N-terminal to the longevity-assurance protein region (pfam03798). 63 matched cddid_all.tbl CDD pfam08391 pfam08391 462461 Ly49 Ly49-like protein, N-terminal region. The sequences making up this family are annotated as, or are similar to, Ly49 receptors. These are type II transmembrane receptors expressed by mouse natural killer (NK) cells. They are classified as being activating (e.g.Ly49D and H) or inhibitory (e.g. Ly49A and G), depending on their effect on NK cell function. They are members of the C-type lectin receptor superfamily, and in fact in many family members this region is found immediately N-terminal to a lectin C-type domain (pfam00059). 119 matched cddid_all.tbl CDD pfam08392 pfam08392 429970 FAE1_CUT1_RppA FAE1/Type III polyketide synthase-like protein. The members of this family are described as 3-ketoacyl-CoA synthases, type III polyketide synthases, fatty acid elongases and fatty acid condensing enzymes, and are found in both prokaryotic and eukaryotic (mainly plant) species. The region featured in this family contains the active site residues, as well as motifs involved in substrate binding. 290 matched cddid_all.tbl CDD pfam08393 pfam08393 462462 DHC_N2 Dynein heavy chain, N-terminal region 2. Dyneins are described as motor proteins of eukaryotic cells, as they can convert energy derived from the hydrolysis of ATP to force and movement along cytoskeletal polymers, such as microtubules. This region is found C-terminal to the dynein heavy chain N-terminal region 1 (pfam08385) in many members of this family. No functions seem to have been attributed specifically to this region. 402 matched cddid_all.tbl CDD pfam08394 pfam08394 285580 Arc_trans_TRASH Archaeal TRASH domain. This region is found in the C-terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module. 37 matched cddid_all.tbl CDD pfam08395 pfam08395 462463 7tm_7 7tm Chemosensory receptor. This family includes a number of gustatory and odorant receptors mainly from insect species such as A. gambiae and D. melanogaster. They are classified as G-protein-coupled receptors (GPCRs), or seven-transmembrane receptors. They show high sequence divergence, consistent with an ancient origin for the family. 370 matched cddid_all.tbl CDD pfam08396 pfam08396 254775 Toxin_34 Spider toxin omega agatoxin/Tx1 family. The Tx1 family lethal spider neurotoxin induces excitatory symptoms in mice. 75 matched cddid_all.tbl CDD pfam08397 pfam08397 429972 IMD IRSp53/MIM homology domain. The N-terminal predicted helical stretch of the insulin receptor tyrosine kinase substrate p53 (IRSp53) is an evolutionary conserved F-actin bundling domain involved in filopodium formation. The domain has been named IMD after the IRSp53 and missing in metastasis (MIM) proteins in which it occurs. Filopodium-inducing IMD activity is regulated by Cdc42 and Rac1 and is SH3-independent. 218 matched cddid_all.tbl CDD pfam08398 pfam08398 429973 Phospholip_A2_4 Phospholipase A2-like domain. This entry represents a domain that is likely to be a phospholipase A2-like enzyme. It is found in a variety of contexts across the tree of life. The family includes he N-terminal region of the Parvovirus VP1 coat protein. 80 matched cddid_all.tbl CDD pfam08399 pfam08399 462464 VWA_N VWA N-terminal. This domain is found at the N-terminus of proteins containing von Willebrand factor type A (VWA, pfam00092) and Cache (pfam02743) domains. It has been found in vertebrates, Drosophila and C. elegans but has not yet been identified in other eukaryotes. It is probably involved in the function of some voltage-dependent calcium channel subunits. 122 matched cddid_all.tbl CDD pfam08400 pfam08400 285585 phage_tail_N Prophage tail fibre N-terminal. This domain is found at the N-terminus of prophage tail fibre proteins. 134 matched cddid_all.tbl CDD pfam08401 pfam08401 429975 ArdcN N-terminal domain of anti-restriction factor ArdC. This is the ssDNA binding domain of anti-restriction factor ArdC deployed by plasmids and phages in polyvalent proteins related to the BHD domains of XPC/Rad4 and the Tc-38 domain found in kinetoplastid minicircle binding proteins. The structure of this domain is composed of three alpha-helices and a three-stranded beta-sheet that supports a long and protuberant beta-hairpin. This domain is also found in the N-terminal region of the RP4 TraC1 primase, together with the Toprim domain (pfam01751, pfam13362 and pfam13662). 127 matched cddid_all.tbl CDD pfam08402 pfam08402 462465 TOBE_2 TOBE domain. The TOBE domain (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum and sulphate. Found in ABC transporters immediately after the ATPase domain. In this family a strong RPE motif is found at the presumed N-terminus of the domain. 73 matched cddid_all.tbl CDD pfam08403 pfam08403 429977 AA_permease_N Amino acid permease N-terminal. This domain is found to the N-terminus of the amino acid permease domain (pfam00324) in metazoan Na-K-Cl cotransporters. 70 matched cddid_all.tbl CDD pfam08404 pfam08404 285589 Baculo_p74_N Baculoviridae P74 N-terminal. This domain is found at the N-terminus of P74 occlusion-derived virus (ODV) envelope proteins which are required for oral infectivity. The envelope proteins are found in baculoviruses which are insect pathogens. The C-terminus of P74 is anchored to the membrane whereas the N-terminus is exposed to the virion surface. Furthermore P74 is unusual for a virus envelope protein as it lacks an N-terminal localization signal sequence. Also see pfam04583. 300 matched cddid_all.tbl CDD pfam08405 pfam08405 462466 Calici_PP_N Viral polyprotein N-terminal. This domain is found at the N-terminus of non-structural viral polyproteins of the Caliciviridae subfamily. 358 matched cddid_all.tbl CDD pfam08406 pfam08406 429978 CbbQ_C CbbQ/NirQ/NorQ C-terminal. This domain is found at the C-terminus of proteins of the CbbQ/NirQ/NorQ family of proteins which play a role in the post-translational activation of Rubisco. It is also found in the Thauera aromatica TutH protein which is similar to the CbbQ/NirQ/NorQ family, as well as in putative chaperones. The ATPase family associated with various cellular activities (AAA) pfam07728 is found in the same bacterial and archaeal proteins as the domain described here. 85 matched cddid_all.tbl CDD pfam08407 pfam08407 462467 Chitin_synth_1N Chitin synthase N-terminal. This is the N-terminal domain of Chitin synthase (pfam01644). 70 matched cddid_all.tbl CDD pfam08408 pfam08408 369858 DNA_pol_B_3 DNA polymerase family B viral insert. This viral domain is found between the exonuclease domain of the DNA polymerase family B (pfam03104) and the pfam00136 domain, connecting the two. 128 matched cddid_all.tbl CDD pfam08409 pfam08409 462468 TMTC_DUF1736 Protein O-mannosyl-transferase TMTC, DUF1736. This domain of unknown function is found in O-mannosyl -transferases TMTC1-4, and constitutes a loop between TM7 and TM8 located in the ER lumen that contains a small hydrophobic, but not membrane-embedded helix. This loop is critical for catalysis and binding of ligands, especially the lipid-linked sugar moiety. TMTCs transfers mannosyl residues to the hydroxyl group of serine or threonine residues. The 4 members of the TMTC family are O-mannosyl-transferases acting primarily on the cadherin superfamily; each member has distinct roles in decorating the cadherin domains with O-linked mannose glycans at specific regions. These proteins also act as O-mannosyl-transferase on other proteins such as PDIA3. 75 matched cddid_all.tbl CDD pfam08410 pfam08410 429981 DUF1737 Domain of unknown function (DUF1737). This domain of unknown function is found at the N-terminus of bacterial and viral hypothetical proteins. 51 matched cddid_all.tbl CDD pfam08411 pfam08411 429982 Exonuc_X-T_C Exonuclease C-terminal. This bacterial domain is found at the C-terminus of Exodeoxyribonuclease I/Exonuclease I (pfam00929), which is a single-strand specific DNA nuclease affecting recombination and expression pathways. The exonuclease I protein in E. coli is associated with DNA deoxyribophosphodiesterase (dRPase). 267 matched cddid_all.tbl CDD pfam08412 pfam08412 400630 Ion_trans_N Ion transport protein N-terminal. This metazoan domain is found to the N-terminus of pfam00520 in voltage- and cyclic nucleotide-gated K/Na ion channels. 43 matched cddid_all.tbl CDD pfam08414 pfam08414 462469 NADPH_Ox Respiratory burst NADPH oxidase. This domain is found in plant proteins such as respiratory burst NADPH oxidase proteins which produce reactive oxygen species as a defence mechanism. It tends to occur to the N-terminus of an EF-hand (pfam00036), which suggests a direct regulatory effect of Ca2+ on the activity of the NADPH oxidase in plants. 100 matched cddid_all.tbl CDD pfam08416 pfam08416 429984 PTB Phosphotyrosine-binding domain. The phosphotyrosine-binding domain (PTB, also phosphotyrosine-interaction or PI domain) in the protein tensin tends to be found at the C-terminus. Tensin is a multi-domain protein that binds to actin filaments and functions as a focal-adhesion molecule (focal adhesions are regions of plasma membrane through which cells attach to the extracellular matrix). Human tensin has actin-binding sites, an SH2 (pfam00017) domain and a region similar to the tumour suppressor PTEN. The PTB domain interacts with the cytoplasmic tails of beta integrin by binding to an NPXY motif. 131 matched cddid_all.tbl CDD pfam08417 pfam08417 429985 PaO Pheophorbide a oxygenase. This domain is found in bacterial and plant proteins to the C-terminus of a Rieske 2Fe-2S domain (pfam00355). One of the proteins the domain is found in is Pheophorbide a oxygenase (PaO) which seems to be a key regulator of chlorophyll catabolism. Arabidopsis PaO (AtPaO) is a Rieske-type 2Fe-2S enzyme that is identical to Arabidopsis accelerated cell death 1 and homologous to lethal leaf spot 1 (LLS1) of maize, in which the domain described here is also found. 89 matched cddid_all.tbl CDD pfam08418 pfam08418 462470 Pol_alpha_B_N DNA polymerase alpha subunit B N-terminal. This is the eukaryotic DNA polymerase alpha subunit B N-terminal domain which is involved in complex formation. This domain adopts an OB fold. 240 matched cddid_all.tbl CDD pfam08421 pfam08421 429987 Methyltransf_13 Putative zinc binding domain. This domain is found at the N-terminus of bacterial methyltransferases and contains four conserved cysteines suggesting a potential zinc binding domain. 62 matched cddid_all.tbl CDD pfam08423 pfam08423 462471 Rad51 Rad51. Rad51 is a DNA repair and recombination protein and is a homolog of the bacterial ATPase RecA protein. 255 matched cddid_all.tbl CDD pfam08424 pfam08424 462472 NRDE-2 NRDE-2, necessary for RNA interference. This is a family of eukaryotic proteins. Eukaryotic cells express a wide variety of endogenous small regulatory RNAs that regulate heterochromatin formation, developmental timing, defence against parasitic nucleic acids, and genome rearrangement. Many small regulatory RNAs are thought to function in nuclei, and in plants and fungi small interfering (si)RNAs associate with nascent transcripts and direct chromatin and/or DNA modifications. This family protein, NRDE-2, is required for small interfering (si)RNA-mediated silencing in nuclei. NRDE-2 associates with the Argonaute protein NRDE-3 within nuclei and is recruited by NRDE-3/siRNA complexes to nascent transcripts that have been targeted by RNA interference, RNAi, the process whereby double-stranded RNA (dsRNA) directs the sequence-specific degradation of mRNA. 316 matched cddid_all.tbl CDD pfam08426 pfam08426 429989 ICE2 ICE2. ICE2 is a fungal ER protein which has been shown to play an important role in forming/maintaining the cortical ER. It has also bee identified as a protein which is necessary for nuclear inner membrane targeting. 402 matched cddid_all.tbl CDD pfam08427 pfam08427 462473 ARMH3_C Armadillo-like helical domain-containing protein 3, C-terminal. This is the C-terminal domain of Armadillo-like helical domain- containing protein 3 (ARMH3), the previously uncharacterized peripheral Golgi protein C10orf76. ARMH3 interacts with and is involved in GBF1 recruitment, Golgi maintenance and protein secretion. The function of this domain is unknown. 231 matched cddid_all.tbl CDD pfam08428 pfam08428 462474 Rib Rib domain. The region featured in this family is found repeated in a number of bacterial surface proteins, such as Rib and alpha. These are expressed by group B streptococci, and Rib is thought to confer protective immunity. 76 matched cddid_all.tbl CDD pfam08429 pfam08429 462475 PLU-1 PLU-1-like protein. Sequences in this family bear similarity to the central region of PLU-1. This is a nuclear protein that may have a role in DNA-binding and transcription, and is closely associated with the malignant phenotype of breast cancer. This region is found in various other Jumonji/ARID domain-containing proteins (see pfam02373, pfam01388). 336 matched cddid_all.tbl CDD pfam08430 pfam08430 369872 Forkhead_N Forkhead N-terminal region. The region described in this family is found towards the N-terminus of various eukaryotic forkhead/HNF-3-related transcription factors (which contain the pfam00250 domain). These proteins play key roles in embryogenesis, maintenance of differentiated cell states, and tumourigenesis. 139 matched cddid_all.tbl CDD pfam08432 pfam08432 429993 Vfa1 AAA-ATPase Vps4-associated protein 1. Vps Four-Associated 1, Vfa1, in yeast, is an endosomal protein that interacts with the AAA-ATPase Vps4. It would seem to be involved in regulating the trafficking of other proteins to the endocytic vacuole. There is a CCCH zinc finger at the N-terminus. 179 matched cddid_all.tbl CDD pfam08433 pfam08433 400643 KTI12 Chromatin associated protein KTI12. This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II. The Elongator complex has histone acetyltransferase activity. 269 matched cddid_all.tbl CDD pfam08434 pfam08434 462476 CLCA Calcium-activated chloride channel N terminal. The CLCA family of calcium-activated chloride channels has been identified in many epithelial and endothelial cell types as well as in smooth muscle cells and has four or five putative transmembrane regions. Additionally to their role as chloride channels some CLCA proteins function as adhesion molecules and may also have roles as tumour suppressors. This protein cleaves itself into an N-terminal portion and a C-terminal portion. The N-terminus contains an HEXXHXXXGXXDE motif which is essential for proteolytic cleavage. 266 matched cddid_all.tbl CDD pfam08435 pfam08435 429995 Calici_coat_C Calicivirus coat protein C-terminal. This is the calicivirus coat protein (pfam00915) C-terminal region. 224 matched cddid_all.tbl CDD pfam08436 pfam08436 462477 DXP_redisom_C 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain. This domain is found to the C-terminus of pfam02670 domains in bacterial and plant 1-deoxy-D-xylulose 5-phosphate reductoisomerases which catalyze the formation of 2-C-methyl-D-erythritol 4-phosphate from 1-deoxy-D-xylulose-5-phosphate in the presence of NADPH. 84 matched cddid_all.tbl CDD pfam08437 pfam08437 429997 Glyco_transf_8C Glycosyl transferase family 8 C-terminal. This domain is found at the C-terminus of the Pfam: PF01501 domain in bacterial glucosyltransferase and galactosyltransferase proteins. 54 matched cddid_all.tbl CDD pfam08438 pfam08438 429998 MMR_HSR1_C GTPase of unknown function C-terminal. This domain is found at the C-terminus of pfam01926 in archaeal and eukaryotic GTP-binding proteins. The C-terminal domain of the GTP-binding proteins is necessary for the complete activity of the protein of interacting with the 50S ribosome and binding of both adenine and guanine nucleotides, with a preference for guanine nucleotides. 109 matched cddid_all.tbl CDD pfam08439 pfam08439 429999 Peptidase_M3_N Oligopeptidase F. This domain is found to the N-terminus of the pfam01432 domain in bacterial and archaeal proteins including Oligoendopeptidase F. An example of this protein is Lactococcus lactis PepF. 70 matched cddid_all.tbl CDD pfam08440 pfam08440 285618 Poty_PP Potyviridae polyprotein. This domain is found in polyproteins of the viral Potyviridae taxon. 277 matched cddid_all.tbl CDD pfam08441 pfam08441 462478 Integrin_alpha2 Integrin alpha. This domain is found in integrin alpha and integrin alpha precursors to the C terminus of a number of pfam01839 repeats and to the N-terminus of the pfam00357 cytoplasmic region. This region is composed of three immunoglobulin-like domains. 449 matched cddid_all.tbl CDD pfam08442 pfam08442 400651 ATP-grasp_2 ATP-grasp domain. 202 matched cddid_all.tbl CDD pfam08443 pfam08443 369879 RimK RimK-like ATP-grasp domain. This ATP-grasp domain is found in the ribosomal S6 modification enzyme RimK. 188 matched cddid_all.tbl CDD pfam08444 pfam08444 117021 Gly_acyl_tr_C Aralkyl acyl-CoA:amino acid N-acyltransferase, C-terminal region. This family features the C-terminal region of several mammalian specific aralkyl acyl-CoA:amino acid N-acyltransferase (glycine N-acyltransferase) proteins EC:2.3.1.13. 89 matched cddid_all.tbl CDD pfam08445 pfam08445 117022 FR47 FR47-like protein. The members of this family are similar to the C-terminal region of the D. melanogaster hypothetical protein FR47. This protein has been found to consist of two N-acyltransferase-like domains swapped with the C-terminal strands. 86 matched cddid_all.tbl CDD pfam08446 pfam08446 400652 PAS_2 PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. 107 matched cddid_all.tbl CDD pfam08447 pfam08447 430001 PAS_3 PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. 89 matched cddid_all.tbl CDD pfam08448 pfam08448 312075 PAS_4 PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. This domain is associated to signalling systems and works as a signal sensor domain. It recognizes differently substituted aromatic hydrocarbons, oxygen, different dodecanoic acids, autoinducers, 3,5-dimethyl-pyrazin-2-ol and N-alanyl-aminoacetone (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 110 matched cddid_all.tbl CDD pfam08449 pfam08449 462479 UAA UAA transporter family. This family includes transporters with a specificity for UDP-N-acetylglucosamine. 307 matched cddid_all.tbl CDD pfam08450 pfam08450 462480 SGL SMP-30/Gluconolactonase/LRE-like region. This family describes a region that is found in proteins expressed by a variety of eukaryotic and prokaryotic species. These proteins include various enzymes, such as senescence marker protein 30 (SMP-30), gluconolactonase and luciferin-regenerating enzyme (LRE). SMP-30 is known to hydrolyse diisopropyl phosphorofluoridate in the liver, and has been noted as having sequence similarity, in the region described in this family, with PON1 and LRE. 246 matched cddid_all.tbl CDD pfam08451 pfam08451 462481 A_deaminase_N Adenosine/AMP deaminase N-terminal. This domain is found to the N-terminus of the Adenosine/AMP deaminase domain (pfam00962) in metazoan proteins such as the Cat eye syndrome critical region protein 1 and its homologs. 95 matched cddid_all.tbl CDD pfam08452 pfam08452 369884 DNAP_B_exo_N DNA polymerase family B exonuclease domain, N-terminal. This domain is found in viral DNA polymerases to the N-terminus of DNA polymerase family B exonuclease domains (pfam03104). 21 matched cddid_all.tbl CDD pfam08453 pfam08453 430004 Peptidase_M9_N Peptidase family M9 N-terminal. This domain is found in microbial collagenase metalloproteases to the N-terminus of pfam01752. 183 matched cddid_all.tbl CDD pfam08454 pfam08454 462482 RIH_assoc RyR and IP3R Homology associated. This eukaryotic domain is found in ryanodine receptors (RyR) and inositol 1,4,5-trisphosphate receptors (IP3R) which together form a superfamily of homotetrameric ligand-gated intracellular Ca2+ channels. There seems to be no known function for this domain. Also see the IP3-binding domain pfam01365 and pfam02815. 98 matched cddid_all.tbl CDD pfam08455 pfam08455 462483 SNF2_assoc Bacterial SNF2 helicase associated. This domain is found in bacterial proteins of the SWF/SNF/SWI helicase family to the N-terminus of the SNF2 family N-terminal domain (pfam00176) and together with the Helicase conserved C-terminal domain (pfam00271). The function of the domain is not clear. 370 matched cddid_all.tbl CDD pfam08456 pfam08456 285632 Vmethyltransf_C Viral methyltransferase C-terminal. This domain is found to the C-terminus of the viral methyltransferase domain (pfam01660) in single-stranded-RNA positive-strand viruses with no DNA stage in the Virgaviridae family. 230 matched cddid_all.tbl CDD pfam08457 pfam08457 430007 Sfi1 Sfi1 spindle body protein. This is a family of fungal spindle pole body proteins that play a role in spindle body duplication. They contain binding sites for calmodulin-like proteins called centrins which are present in microtubule-organizing centres. 570 matched cddid_all.tbl CDD pfam08458 pfam08458 430008 PH_2 Plant pleckstrin homology-like region. This family describes a pleckstrin homology (PH)-like region found in several plant proteins of unknown function. 104 matched cddid_all.tbl CDD pfam08459 pfam08459 462484 UvrC_RNaseH_dom UvrC RNAse H endonuclease domain. This domain is found in the C subunits of the bacterial and archaeal UvrABC system which catalyzes nucleotide excision repair in a multi-step process. UvrC catalyzes the first incision on the fourth or fifth phosphodiester bond 3' and on the eighth phosphodiester bond 5' from the damage that is to be excised. The domain described here represents the RNAse H endonuclease domain, located at the C-terminal, between the UvrBC and the (HhH)2 domains, nearby the N-terminal of the HhH. Despite the lack of sequence homology, the endonuclease domain has an RNase H-like fold, which is characteriztic of enzymes with nuclease or polynucleotide transferase activities. RNase H-related enzymes typically contain a highly conserved carboxylate triad, usually DDE, in their catalytic centre. However, instead of a third carboxylate, UvrC of Thermotoga maritima was found to contain a highly conserved histidine (H488) on helix-4 in close proximity to two aspartates. 150 matched cddid_all.tbl CDD pfam08460 pfam08460 430010 SH3_5 Bacterial SH3 domain. 68 matched cddid_all.tbl CDD pfam08461 pfam08461 285637 HTH_12 Ribonuclease R winged-helix domain. This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaebacteria. 66 matched cddid_all.tbl CDD pfam08462 pfam08462 117039 Carmo_coat_C Carmovirus coat protein. This domain is found to the C-terminus of the pfam00729 domain in Carmoviruses. 99 matched cddid_all.tbl CDD pfam08463 pfam08463 462485 EcoEI_R_C EcoEI R protein C-terminal. The restriction enzyme EcoEI recognizes 5'-GAGN(7)ATGC-3' and is composed of the three proteins R, M, and S. The domain described here is found at the C-terminus of the R protein (HsdR) which is required for both nuclease and ATPase activity. 159 matched cddid_all.tbl CDD pfam08464 pfam08464 369889 Gemini_AC4_5_2 Geminivirus AC4/5 conserved region. This domain is found in replication initiator (Rep) associated proteins such as AC5 in the Geminivirus/Begomovirus. 43 matched cddid_all.tbl CDD pfam08465 pfam08465 285639 Herpes_TK_C Thymidine kinase from Herpesvirus C-terminal. This domain is found towards the C terminus in Herpesvirus Thymidine kinases. 33 matched cddid_all.tbl CDD pfam08466 pfam08466 462486 IRK_N Inward rectifier potassium channel N-terminal. This metazoan domain is found to the N-terminus of the pfam01007 domain in Inward rectifier potassium channels (KIR2 or IRK2). 45 matched cddid_all.tbl CDD pfam08467 pfam08467 285641 Luteo_P1-P2 Luteovirus RNA polymerase P1-P2/replicase. This domain is found in RNA-dependent RNA polymerase P1-P2 fusion/replicase proteins in plant Luteoviruses. 339 matched cddid_all.tbl CDD pfam08468 pfam08468 430013 MTS_N Methyltransferase small domain N-terminal. This domain is found to the N-terminus of the methyltransferase small domain (pfam05175) in bacterial proteins. 157 matched cddid_all.tbl CDD pfam08469 pfam08469 400664 NPHI_C Nucleoside triphosphatase I C-terminal. This viral domain is found to the C-terminus of Poxvirus nucleoside triphosphatase phosphohydrolase I (NPH I) together with the helicase conserved C-terminal domain (pfam00271). 148 matched cddid_all.tbl CDD pfam08470 pfam08470 400665 NTNH_C Nontoxic nonhaemagglutinin C-terminal. Bacteria of the Clostridium genus produce protein neurotoxins, which are complexes consisting of neurotoxin (NT), haemagglutinin (HA), nontoxic nonhaemagglutinin (NTNH), and RNA. The domain described here is found at the C-terminus of the NTNH component. 162 matched cddid_all.tbl CDD pfam08471 pfam08471 430014 Ribonuc_red_2_N Class II vitamin B12-dependent ribonucleotide reductase. This domain is found to the N-terminus of the ribonucleotide reductase barrel domain (pfam02867). It occurs in bacterial class II ribonucleotide reductase proteins which depend upon coenzyme B12 (deoxyadenosylcobalamine). 99 matched cddid_all.tbl CDD pfam08472 pfam08472 462487 S6PP_C Sucrose-6-phosphate phosphohydrolase C-terminal. This is the Sucrose-6-phosphate phosphohydrolase (S6PP or SPP) C-terminal domain as found in in plant sucrose phosphatases. These enzymes irreversibly catalyze the last step in sucrose synthesis following the formation of Sucrose-6-Phosphate via sucrose-phosphate synthase (SPS). 133 matched cddid_all.tbl CDD pfam08473 pfam08473 462488 VGCC_alpha2 Neuronal voltage-dependent calcium channel alpha 2acd. This eukaryotic domain has been found in the neuronal voltage-dependent calcium channel (VGCC) alpha 2a, 2c, and 2d subunits. It is also found in other calcium channel alpha-2 delta subunits to the C-terminus of a Cache domain (pfam02743). 432 matched cddid_all.tbl CDD pfam08474 pfam08474 462489 MYT1 Myelin transcription factor 1. This domain is found in the myelin transcription factor 1 (MYT1) of chordates. MYT1 contains C2HC zinc finger domains (pfam01530) and is expressed in developing neurons of the central nervous system where it is involved in the selection of neuronal precursor cells. 237 matched cddid_all.tbl CDD pfam08475 pfam08475 285649 Baculo_VP91_N Viral capsid protein 91 N-terminal. This domain is found in Baculoviridae including the nucleopolyhedrovirus at the N-terminus of the viral capsid protein 91 (VP91). 192 matched cddid_all.tbl CDD pfam08476 pfam08476 285650 VD10_N Viral D10 N-terminal. This domain is found on the N-terminus of the viral protein D10 (VD10) and the related MutT motif proteins. The VD10 protein is probably essential for virus replication and is often found to the N-terminus of a pfam00293 domain. 41 matched cddid_all.tbl CDD pfam08477 pfam08477 462490 Roc Ras of Complex, Roc, domain of DAPkinase. Roc, or Ras of Complex, proteins are mitochondrial Rho proteins (Miro-1, and Miro-2) and atypical Rho GTPases. Full-length proteins have a unique domain organization, with tandem GTP-binding domains and two EF hand domains (pfam00036) that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis. 114 matched cddid_all.tbl CDD pfam08478 pfam08478 430019 POTRA_1 POTRA domain, FtsQ-type. FtsQ/DivIB bacterial division proteins (pfam03799) contain an N-terminal POTRA domain (for polypeptide-transport-associated domain). This is found in different types of proteins, usually associated with a transmembrane beta-barrel. FtsQ/DivIB may have chaperone-like roles, which has also been postulated for the POTRA domain in other contexts. 69 matched cddid_all.tbl CDD pfam08479 pfam08479 430020 POTRA_2 POTRA domain, ShlB-type. The POTRA domain (for polypeptide-transport-associated domain) is found towards the N-terminus of ShlB family proteins (pfam03865). ShlB is important in the secretion and activation of the haemolysin ShlA. It has been postulated that the POTRA domain has a chaperone-like function over ShlA; it may fold back into the C-terminal beta-barrel channel. 73 matched cddid_all.tbl CDD pfam08480 pfam08480 285654 Disaggr_assoc Disaggregatase related. This domain is found in disaggregatases and several hypothetical proteins of the archaeal genus Methanosarcina. Disaggregatases cause aggregates to separate into single cells and contain parallel beta-helix repeats. Also see pfam06848. 194 matched cddid_all.tbl CDD pfam08481 pfam08481 400671 GBS_Bsp-like GBS Bsp-like repeat. This domain is found as a repeat in a number of Streptococcus proteins including some hypothetical proteins and Bsp. Bsp is a protein of group B Streptococcus (GBS) which might control cell morphology. 89 matched cddid_all.tbl CDD pfam08482 pfam08482 430021 HrpB_C ATP-dependent helicase C-terminal. This domain is found near the C-terminus of bacterial ATP-dependent helicases such as HrpB. 126 matched cddid_all.tbl CDD pfam08484 pfam08484 430022 Methyltransf_14 C-methyltransferase C-terminal domain. This domain is found in bacterial C-methyltransferase proteins. This domain is found C-terminal to methyltransferase domains such as pfam08241 or pfam08242. But this domain is not a methyltransferase. 160 matched cddid_all.tbl CDD pfam08485 pfam08485 430023 Polysacc_syn_2C Polysaccharide biosynthesis protein C-terminal. This domain is found to the C-terminus of the pfam02719 domain in bacterial polysaccharide biosynthesis enzymes including the capsule protein CapD and several putative epimerases/dehydratases. 48 matched cddid_all.tbl CDD pfam08486 pfam08486 462491 SpoIID Stage II sporulation protein. This domain is found in the stage II sporulation protein SpoIID. SpoIID is necessary for membrane migration as well as for some of the earlier steps in engulfment during bacterial endospore formation. The domain is also found in amidase enhancer proteins. Amidases, like SpoIID, are cell wall hydrolases. 100 matched cddid_all.tbl CDD pfam08487 pfam08487 462492 VIT Vault protein inter-alpha-trypsin domain. Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains. ITIs play a role in extracellular matrix (ECM) stabilization and tumour metastasis as well as in plasma protease inhibition. The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N-terminus of a von Willebrand factor type A domain (pfam00092) in ITI heavy chains (ITIHs) and their precursors. 111 matched cddid_all.tbl CDD pfam08488 pfam08488 254827 WAK Wall-associated kinase. This domain is found together with the eukaryotic protein kinase domain pfam00069 in plant wall-associated kinases (WAKs) and related proteins. WAKs are serine-threonine kinases which might be involved in signalling to the cytoplasm and are required for cell expansion. 103 matched cddid_all.tbl CDD pfam08489 pfam08489 430026 DUF1743 Domain of unknown function (DUF1743). This domain of unknown function is found in tRNA(Ile2) 2-agmatinylcytidine synthetase TiaS. TiaS is an archaeal ATP-dependent agmatine transferase that catalyzes the formation of 2-agmatinylcytidine (agm2C) at the wobble position (C34) of tRNA(Ile2). This modified base specifically recognizes AUA codons. 116 matched cddid_all.tbl CDD pfam08490 pfam08490 462493 DUF1744 Domain of unknown function (DUF1744). This domain is found at the C-terminal of the epsilon catalytic subunit of DNA polymerase. It is found C terminal to pfam03104 and pfam00136. 400 matched cddid_all.tbl CDD pfam08491 pfam08491 400679 SE Squalene epoxidase. This domain is found in squalene epoxidase (SE) and related proteins which are found in taxonomically diverse groups of eukaryotes and also in bacteria. SE was first cloned from Saccharomyces cerevisiae where it was named ERG1. It contains a putative FAD binding site and is a key enzyme in the sterol biosynthetic pathway. Putative transmembrane regions are found to the protein's C-terminus. 276 matched cddid_all.tbl CDD pfam08492 pfam08492 462494 SRP72 SRP72 RNA-binding domain. This region has been identified as the binding site of the SRP72 protein to SRP RNA. 53 matched cddid_all.tbl CDD pfam08493 pfam08493 430029 AflR Aflatoxin regulatory protein. This domain is found in the aflatoxin regulatory protein (AflR) which is involved in the regulation of the biosynthesis of aflatoxin in the fungal genus Aspergillus. It occurs together with the fungal Zn(2)-Cys(6) binuclear cluster domain (pfam00172). 99 matched cddid_all.tbl CDD pfam08494 pfam08494 430030 DEAD_assoc DEAD/H associated. This domain is found in ATP-dependent helicases as well as a number of hypothetical proteins together with the helicase conserved C-terminal domain (pfam00270) and the pfam00271 domain. 182 matched cddid_all.tbl CDD pfam08495 pfam08495 462495 FIST FIST N domain. The FIST N domain is a novel sensory domain, which is present in signal transduction proteins from Bacteria, Archaea and Eukarya. Chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids. 126 matched cddid_all.tbl CDD pfam08496 pfam08496 430032 Peptidase_S49_N Peptidase family S49 N-terminal. This domain is found to the N-terminus of bacterial signal peptidases of the S49 family (pfam01343). 147 matched cddid_all.tbl CDD pfam08497 pfam08497 462496 Radical_SAM_N Radical SAM N-terminal. This domain tends to occur to the N-terminus of the pfam04055 domain in hypothetical bacterial proteins. 299 matched cddid_all.tbl CDD pfam08498 pfam08498 430034 Sterol_MT_C Sterol methyltransferase C-terminal. This domain is found to the C-terminus of a methyltransferase domain (pfam08241) in fungal and plant sterol methyltransferases. 66 matched cddid_all.tbl CDD pfam08499 pfam08499 462497 PDEase_I_N 3'5'-cyclic nucleotide phosphodiesterase N-terminal. This domain is found to the N-terminus of the calcium/calmodulin-dependent 3'5'-cyclic nucleotide phosphodiesterase domain (pfam00233). 61 matched cddid_all.tbl CDD pfam08500 pfam08500 149522 Tombus_P33 Tombusvirus p33. Tombusviruses, which replicate in a wide range of plant hosts, replicate with the help of viral replicase protein including the overlapping p33 and p92 proteins which contain the domain described here. 142 matched cddid_all.tbl CDD pfam08501 pfam08501 400688 Shikimate_dh_N Shikimate dehydrogenase substrate binding domain. This domain is the substrate binding domain of shikimate dehydrogenase. 83 matched cddid_all.tbl CDD pfam08502 pfam08502 400689 LeuA_dimer LeuA allosteric (dimerization) domain. This is the C-terminal regulatory (R) domain of alpha-isopropylmalate synthase, which catalyzes the first committed step in the leucine biosynthetic pathway. This domain, is an internally duplicated structure with a novel fold. It comprises two similar units that are arranged such that the two -helices pack together in the centre, crossing at an angle of 34 degrees, sandwiched between the two three-stranded, antiparallel beta-sheets. The overall domain is thus constructed as a beta-alpha-beta three-layer sandwich. 112 matched cddid_all.tbl CDD pfam08503 pfam08503 430036 DapH_N Tetrahydrodipicolinate succinyltransferase N-terminal. This domain is found at the N-terminus of tetrahydrodipicolinate N-succinyltransferase (DapH) which catalyzes the acylation of L-2-amino-6-oxopimelate to 2-N-succinyl-6-oxopimelate in the meso-diaminopimelate/lysine biosynthetic pathway of bacteria, blue-green algae, and plants. The N-terminal domain as defined here contains three alpha-helices and two twisted hairpin loops. 83 matched cddid_all.tbl CDD pfam08504 pfam08504 430037 RunxI Runx inhibition domain. This domain lies to the C-terminus of Runx-related transcription factors and homologous proteins (AML, CBF-alpha, PEBP2). Its function might be to interact with functional cofactors. 98 matched cddid_all.tbl CDD pfam08505 pfam08505 400692 MMR1 Mitochondrial Myo2 receptor-related protein. Myo2p, a class V myosin, is essential for mitochondrial distribution, class V being vital for organelle distribution in S. cerevisiae. It is the myosin essential for mitochondrial distribution. The established mechanism for distribution of cellular components by class V myosins is that they interact with the cargo at the C-terminal tail domain and transport it along the actin cytoskeleton using the N-terminal motor domain. Cargo-specific myosin receptors act as the link between the myosin tail and cargo. Myo2 binds with MMR1 (mitochondrial Myo2p receptor-related 1), the receptor on cargo, via the C-terminal domain. 267 matched cddid_all.tbl CDD pfam08506 pfam08506 430038 Cse1 Cse1. This domain is present in Cse1 nuclear export receptor proteins. Cse1 mediates the nuclear export of importin alpha. This domain contains HEAT repeats. 370 matched cddid_all.tbl CDD pfam08507 pfam08507 400693 COPI_assoc COPI associated protein. Proteins in this family colocalize with COPI vesicle coat proteins. 130 matched cddid_all.tbl CDD pfam08508 pfam08508 430039 DUF1746 Fungal domain of unknown function (DUF1746). This is a fungal domain of unknown function. This domain can be found in DSC E3 ubiquitin ligase complex subunit 4 (Dsc4) from S. pombe, a component of the DSC E3 ubiquitin ligase complex required for the sre1 transcriptional activator proteolytic cleavage to release the soluble transcription factor from the membrane in low oxygen or sterol conditions. The complex plays also an important role in the multivesicular body (MVB) pathway and functions in a post-endoplasmic reticulum pathway for protein degradation. This domain is also found in GLD1 from S. cerevisiae, also a component of the DSC E3 ubiquitin ligase complex involved in the targeting of the DSC complex to the Golgi apparatus and endosome membranes via the AP3 pathway to ubiquitinate Golgi/endosome membrane proteins. 116 matched cddid_all.tbl CDD pfam08509 pfam08509 430040 Ad_cyc_g-alpha Adenylate cyclase G-alpha binding domain. This fungal domain is found in adenylate cyclase and interacts with the alpha subunit of heterotrimeric G proteins. 48 matched cddid_all.tbl CDD pfam08510 pfam08510 462498 PIG-P PIG-P. PIG-P (phosphatidylinositol N-acetylglucosaminyltransferase subunit P) is an enzyme involved in GPI anchor biosynthesis. 121 matched cddid_all.tbl CDD pfam08511 pfam08511 462499 COQ9 COQ9. COQ9 is an enzyme that is required for the biosynthesis of coenzyme Q. It may either catalyze a reaction in the coenzyme Q biosynthetic pathway or have a regulatory role. 73 matched cddid_all.tbl CDD pfam08512 pfam08512 462500 Rtt106 Histone chaperone Rttp106-like. This family includes Rttp106, a histone chaperone involved in heterochromatin-mediated silencing. This domain belongs to the Pleckstrin homology domain superfamily. 84 matched cddid_all.tbl CDD pfam08513 pfam08513 462501 LisH LisH. The LisH (lis homology) domain mediates protein dimerization and tetramerization. The LisH domain is found in Sif2, a component of the Set3 complex which is responsible for repressing meiotic genes. It has been shown that the LisH domain helps mediate interaction with components of the Set3 complex. 25 matched cddid_all.tbl CDD pfam08514 pfam08514 462502 STAG STAG domain. STAG domain proteins are subunits of cohesin complex - a protein complex required for sister chromatid cohesion in eukaryotes. The STAG domain is present in Schizosaccharomyces pombe mitotic cohesin Psc3, and the meiosis specific cohesin Rec11. Many organizms express a meiosis-specific STAG protein, for example, mice and humans have a meiosis specific variant called STAG3, although budding yeast does not have a meiosis specific version. 113 matched cddid_all.tbl CDD pfam08515 pfam08515 462503 TGF_beta_GS Transforming growth factor beta type I GS-motif. This motif is found in the transforming growth factor beta (TGF-beta) type I which regulates cell growth and differentiation. The name of the GS motif comes from its highly conserved GSGSGLP signature in the cytoplasmic juxtamembrane region immediately preceding the protein's kinase domain. Point mutations in the GS motif modify the signaling ability of the type I receptor. 28 matched cddid_all.tbl CDD pfam08516 pfam08516 462504 ADAM_CR ADAM cysteine-rich. ADAMs are membrane-anchored proteases that proteolytically modify cell surface and extracellular matrix (ECM) in order to alter cell behaviour. It has been shown that the cysteine-rich domain of ADAM13 regulates the protein's metalloprotease activity. 105 matched cddid_all.tbl CDD pfam08517 pfam08517 462505 AXH Ataxin-1 and HBP1 module (AXH). AXH is a protein-protein and RNA binding motif found in Ataxin-1 (ATX1). ATX1 is responsible for the autosomal-dominant neurodegenerative disorder Spinocerebellar ataxia type-1 (SCA1) in humans. The AXH module has also been identified in the apparently unrelated transcription factor HBP1 which is thought to be involved in the architectural regulation of chromatin and in specific gene expression. 111 matched cddid_all.tbl CDD pfam08518 pfam08518 462506 GIT_SHD Spa2 homology domain (SHD) of GIT. GIT proteins are signaling integrators with GTPase-activating function which may be involved in the organization of the cytoskeletal matrix assembled at active zones (CAZ). The function of the CAZ might be to define sites of neurotransmitter release. Mutations in the Spa2 homology domain (SHD) domain of GIT1 described here interfere with the association of GIT1 with Piccolo, beta-PIX, and focal adhesion kinase. 29 matched cddid_all.tbl CDD pfam08519 pfam08519 462507 RFC1 Replication factor RFC1 C terminal domain. This is the C terminal domain of replication factor C, RFC1. RFC complexes hydrolyse ATP and load sliding clamps such as PCNA (proliferating cell nuclear antigen) onto double-stranded DNA. RFC1 is essential for RFC function in vivo. 158 matched cddid_all.tbl CDD pfam08520 pfam08520 430050 DUF1748 Fungal protein of unknown function (DUF1748). This is a family of fungal proteins of unknown function. 69 matched cddid_all.tbl CDD pfam08521 pfam08521 430051 2CSK_N Two-component sensor kinase N-terminal. This domain is found in bacterial two-component sensor kinases towards the N-terminus. It recognizes Autoinducer 3 (AI-3), epinephrine, norepineprhine and Fe(III) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 142 matched cddid_all.tbl CDD pfam08522 pfam08522 430052 DUF1735 Domain of unknown function (DUF1735). This domain of unknown function is found in a number of bacterial proteins including acylhydrolases. The structure of this domain has a beta-sandwich fold. 120 matched cddid_all.tbl CDD pfam08523 pfam08523 462508 MBF1 Multiprotein bridging factor 1. This domain is found in the multiprotein bridging factor 1 (MBF1) which forms a heterodimer with MBF2. It has been shown to make direct contact with the TATA-box binding protein (TBP) and interacts with Ftz-F1, stabilising the Ftz-F1-DNA complex. It is also found in the endothelial differentiation-related factor (EDF-1). Human EDF-1 is involved in the repression of endothelial differentiation, interacts with CaM and is phosphorylated by PKC. The domain is found in a wide range of eukaryotic proteins including metazoans, fungi and plants. A helix-turn-helix motif (pfam01381) is found to its C-terminus. 68 matched cddid_all.tbl CDD pfam08524 pfam08524 400708 rRNA_processing rRNA processing. This is a family of proteins that are involved in rRNA processing. In a localization study they were found to localize to the nucleus and nucleolus. The family also includes other metazoa members from plants to mammals where the protein has been named BR22 and is associated with TTF-1, thyroid transcription factor 1. In the lungs, the family binds TTF-1 to form a complex which influences the expression of the key lung surfactant protein-B (SP-B) and -C (SP-C), the small hydrophobic surfactant proteins that maintain surface tension in alveoli. 142 matched cddid_all.tbl CDD pfam08525 pfam08525 430054 OapA_N Opacity-associated protein A N-terminal motif. This family includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation. This motif occurs at the N-terminus of these proteins. It contains a conserved histidine followed by a run of hydrophobic residues. 27 matched cddid_all.tbl CDD pfam08526 pfam08526 462509 PAD_N Protein-arginine deiminase (PAD) N-terminal domain. This family represents the N-terminal non-catalytic domain of protein-arginine deiminase. This domain has a cupredoxin-like fold. 113 matched cddid_all.tbl CDD pfam08527 pfam08527 462510 PAD_M Protein-arginine deiminase (PAD) middle domain. This family represents the central non-catalytic domain of protein-arginine deiminase. This domain has an immunoglobulin-like fold. 159 matched cddid_all.tbl CDD pfam08528 pfam08528 462511 Whi5 Whi5 like. In metazoans, cyclin-dependent kinase(CDK) dependent phosphorylation of the retinoblastoma Tudor suppressor protein (Rb) alleviates repression of E2F and thereby activates G1/S transcription. The cell size regulator Whi5 appears to be an analogous target of CDK activity during G1 phase. 25 matched cddid_all.tbl CDD pfam08529 pfam08529 462512 NusA_N NusA N-terminal domain. This domain represents the RNA polymerase binding domain of NusA. 120 matched cddid_all.tbl CDD pfam08530 pfam08530 400714 PepX_C X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain. This domain contains a beta sandwich domain. 216 matched cddid_all.tbl CDD pfam08531 pfam08531 400715 Bac_rhamnosid_N Alpha-L-rhamnosidase N-terminal domain. This family consists of bacterial rhamnosidase A and B enzymes. This domain is probably involved in substrate recognition. 172 matched cddid_all.tbl CDD pfam08532 pfam08532 369931 Glyco_hydro_42M Beta-galactosidase trimerization domain. This is non catalytic domain B of beta-galactosidase enzymes belong to the glycosyl hydrolase 42 family. This domain is related to glutamine amidotransferase enzymes, but the catalytic residues are replaced by non functional amino acids. This domain is involved in trimerization. 207 matched cddid_all.tbl CDD pfam08533 pfam08533 400716 Glyco_hydro_42C Beta-galactosidase C-terminal domain. This domain is found at the C-terminus of beta-galactosidase enzymes that belong to the glycosyl hydrolase 42 family. 58 matched cddid_all.tbl CDD pfam08534 pfam08534 400717 Redoxin Redoxin. This family of redoxins includes peroxiredoxin, thioredoxin and glutaredoxin proteins. 148 matched cddid_all.tbl CDD pfam08535 pfam08535 400718 KorB KorB domain. This family consists of several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon. This domain includes the DNA-binding HTH motif. 88 matched cddid_all.tbl CDD pfam08536 pfam08536 400719 Whirly Whirly transcription factor. This family contains the plant whirly transcription factors. 136 matched cddid_all.tbl CDD pfam08537 pfam08537 400720 NBP1 Fungal Nap binding protein NBP1. NBP1 is a nuclear protein which has been shown in Saccharomyces cerevisiae to be essential for the G2/M transition of the cell cycle. 332 matched cddid_all.tbl CDD pfam08538 pfam08538 369936 DUF1749 Protein of unknown function (DUF1749). This is a plant and fungal family of unknown function. This family contains many hypothetical proteins. 299 matched cddid_all.tbl CDD pfam08539 pfam08539 430059 HbrB HbrB-like. HbrB is involved hyphal growth and polarity. 159 matched cddid_all.tbl CDD pfam08540 pfam08540 400722 HMG_CoA_synt_C Hydroxymethylglutaryl-coenzyme A synthase C terminal. 280 matched cddid_all.tbl CDD pfam08541 pfam08541 430060 ACP_syn_III_C 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal. This domain is found on 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III EC:2.3.1.41, the enzyme responsible for initiating the chain of reactions of the fatty acid synthase in plants and bacteria. 90 matched cddid_all.tbl CDD pfam08542 pfam08542 462513 Rep_fac_C Replication factor C C-terminal domain. This is the C-terminal domain of RFC (replication factor-C) protein of the clamp loader complex which binds to the DNA sliding clamp (proliferating cell nuclear antigen, PCNA). The five modules of RFC assemble into a right-handed spiral, which results in only three of the five RFC subunits (RFC-A, RFC-B and RFC-C) making contact with PCNA, leaving a wedge-shaped gap between RFC-E and the PCNA clamp-loader complex. The C-terminal is vital for the correct orientation of RFC-E with respect to RFC-A. 87 matched cddid_all.tbl CDD pfam08543 pfam08543 430062 Phos_pyr_kin Phosphomethylpyrimidine kinase. This enzyme EC:2.7.4.7 is part of the Thiamine pyrophosphate (TPP) synthesis pathway, TPP is an essential cofactor for many enzymes. 246 matched cddid_all.tbl CDD pfam08544 pfam08544 430063 GHMP_kinases_C GHMP kinases C terminal. This family includes homoserine kinases, galactokinases and mevalonate kinases. 85 matched cddid_all.tbl CDD pfam08545 pfam08545 430064 ACP_syn_III 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III. This domain is found on 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III EC:2.3.1.180, the enzyme responsible for initiating the chain of reactions of the fatty acid synthase in plants and bacteria. 80 matched cddid_all.tbl CDD pfam08546 pfam08546 462514 ApbA_C Ketopantoate reductase PanE/ApbA C terminal. This is a family of 2-dehydropantoate 2-reductases also known as ketopantoate reductases, EC:1.1.1.169. The reaction catalyzed by this enzyme is: (R)-pantoate + NADP(+) <=> 2-dehydropantoate + NADPH. AbpA catalyzes the NADPH reduction of ketopantoic acid to pantoic acid in the alternative pyrimidine biosynthetic (APB) pathway. ApbA and PanE are allelic. ApbA, the ketopantoate reductase enzyme is required for the synthesis of thiamine via the APB biosynthetic pathway. 125 matched cddid_all.tbl CDD pfam08547 pfam08547 462515 CIA30 Complex I intermediate-associated protein 30 (CIA30). This protein is associated with mitochondrial Complex I intermediate-associated protein 30 (CIA30) in human and mouse. The family is also present in Schizosaccharomyces pombe which does not contain the NADH dehydrogenase component of complex I, or many of the other essential subunits. This means it is possible that this family of protein may not be directly involved in oxidative phosphorylation. 156 matched cddid_all.tbl CDD pfam08548 pfam08548 430067 Peptidase_M10_C Peptidase M10 serralysin C terminal. Serralysins are peptidases related to mammalian matrix metallopeptidases (MMPs). The peptidase unit is found at the N terminal while this domain at the C terminal forms a corkscrew and is thought to be important for secretion of the protein through the bacterial cell wall. This domain contains the calcium ion binding domain pfam00353. 222 matched cddid_all.tbl CDD pfam08549 pfam08549 462516 SWI-SNF_Ssr4_N SWI/SNF and RSC complexes subunit Ssr4 N-terminal. This entry represents the N-terminal domain of SWI/SNF and RSC complexes subunit Ssr4 from S. pombe, a essential member of the chromatin structure remodelling complex (RSC) and the SWI/SNF complex. The structure of this domain revealed that it has a novel fold comprising an antiparallel beta-sheet of seven strands with alpha-helices on one side and random coil on the other. It contains the highly conserved motif WxxxxxPxxGxxxxxxxxxxxxxxxDG. RSC is involved in transcription regulation and nucleosome positioning which controls, particularly, membrane and organelle development genes. The ATP-dependent chromatin remodelling complex SWI/SNF is required for the positive and negative regulation of gene expression of a large number of genes through the regulation of nucleosome remodelling. 217 matched cddid_all.tbl CDD pfam08550 pfam08550 430068 DUF1752 Fungal protein of unknown function (DUF1752). This is a family of fungal proteins of unknown function. This short section domain is bounded by two highly conserved tryptophans. The family contains Swiss:P34072 that is thought to be a negative regulator of RAS-cAMP pathway in S.cerevisiae. the Sch.pombe member is a GAF1 transcription factor Swiss:Q10280 that is also associated with the zinc finger family GATA pfam00320. 28 matched cddid_all.tbl CDD pfam08551 pfam08551 369945 DUF1751 Eukaryotic integral membrane protein (DUF1751). This domain is found in eukaryotic integral membrane proteins. Swiss:Q12239, a Saccharomyces cerervisiae protein, has been shown to localize COP II vesicles. 99 matched cddid_all.tbl CDD pfam08552 pfam08552 430069 Kei1 Inositolphosphorylceramide synthase subunit Kei1. Kei1 is a subunit of Saccharomyces cerevisiae inositol phosphorylceramide (IPC) synthase. It is localized to the Golgi and is cleaved by the late Golgi processing endopeptidase Kex2. Kei1 is essential for both the activity and the Golgi localization of IPC synthase. 181 matched cddid_all.tbl CDD pfam08553 pfam08553 430070 VID27 VID27 C-terminal WD40-like domain. This is a family of fungal and plant proteins and contains many hypothetical proteins. VID27 is a cytoplasmic protein that plays a potential role in vacuolar protein degradation. This region is predicted to contain a WD40 repeat domain. 356 matched cddid_all.tbl CDD pfam08555 pfam08555 369948 FAM32A FAM32A. FAM32A, also known as OTAG12, has been linked to ovarian tumour in humans and mice. 91 matched cddid_all.tbl CDD pfam08557 pfam08557 462517 Lipid_DES Sphingolipid Delta4-desaturase (DES). Sphingolipids are important membrane signalling molecules involved in many different cellular functions in eukaryotes. Sphingolipid delta 4-desaturase catalyzes the formation of (E)-sphing-4-enine. Some proteins in this family have bifunctional delta 4-desaturase/C-4-hydroxylase activity. Delta 4-desaturated sphingolipids may play a role in early signalling required for entry into meiotic and spermatid differentiation pathways during Drosophila spermatogenesis. This small domain associates with FA_desaturase pfam00487 and appears to be specific to sphingolipid delta 4-desaturase. 37 matched cddid_all.tbl CDD pfam08558 pfam08558 400735 TRF Telomere repeat binding factor (TRF). Telomere repeat binding factor (TRF) family proteins are important for the regulation of telomere stability. The two related human TRF proteins hTRF1 and hTRF2 form homodimers and bind directly to telomeric TTAGGG repeats via the myb DNA binding domain pfam00249 at the carboxy terminus. TRF1 is implicated in telomere length regulation and TRF2 in telomere protection. Other telomere complex associated proteins are recruited through their interaction with either TRF1 or TRF2. The fission yeast protein Taz1p (telomere-associated in Schizosaccharomyces pombe) has similarity to both hTRF1 and hTRF2 and may perform the dual functions of TRF1 and TRF2 at fission yeast telomeres. This domain is composed of multiple alpha helices arranged in a solenoid conformation similar to TPR repeats. The fungal members have now also been found to carry two double strand telomeric repeat binding factors. 212 matched cddid_all.tbl CDD pfam08559 pfam08559 462518 Cut8 Cut8, nuclear proteasome tether protein. In Schizosaccharomyces pombe, Cut8 is a nuclear envelope protein that physically interacts with and tethers 26S proteasome in the nucleus resulting in the nuclear accumulation of proteasome. Cut8 comprises three functional domains. An N-terminal lysine-rich segment which binds to the proteasome when ubiquitinated, a central dimerization domain and a C-terminal nine-helix, pdb:3q5w, bundle which shows structural similarity to 14-3-3 phosphoprotein-binding domains. The helical bundle is necessary for liposome and cholesterol binding. Cut8 is a proteasome substrate and the N-terminal segment is polyubiquitinated and functions as a degron tag. Ubiquitination of the amino N-terminal segment is essential for the function of Cut8. Lysine residues in the N-terminal segment of Cut8 are required for physical interaction with proteasome. In fission yeast the function of Cut8 has been demonstrated to be regulated by ubiquitin-conjugating Rhp6/Ubc2/Rad6 and ligating enzymes Ubr1. Cut8 homologs have been identified in Drosophila melanogaster, Anopheles gambiae and Dictyostelium discoideum. 203 matched cddid_all.tbl CDD pfam08560 pfam08560 430073 DUF1757 Protein of unknown function (DUF1757). This family of proteins are about 150 amino acids in length and have no known function. 148 matched cddid_all.tbl CDD pfam08561 pfam08561 430074 Ribosomal_L37 Mitochondrial ribosomal protein L37. This family includes yeast MRPL37 a mitochondrial ribosomal protein. 88 matched cddid_all.tbl CDD pfam08562 pfam08562 462519 Crisp Crisp. This domain is found on Crisp proteins which contain pfam00188 and has been termed the Crisp domain. It is found in the mammalian reproductive tract and the venom of reptiles, and has been shown to regulate ryanodine receptor Ca2+ signalling. It contains 10 conserved cysteines which are all involved in disulphide bonds and is structurally related to the ion channel inhibitor toxins BgK and ShK. 55 matched cddid_all.tbl CDD pfam08563 pfam08563 462520 P53_TAD P53 transactivation motif. The binding of the p53 transactivation domain by regulatory proteins regulates p53 transcription activation. This motif is comprised of a single amphipathic alpha helix and contains a highly conserved sequence. 25 matched cddid_all.tbl CDD pfam08564 pfam08564 430077 CDC37_C Cdc37 C terminal domain. Cdc37 is a protein required for the activity of numerous eukaryotic protein kinases. This domains corresponds to the C terminal domain whose function is unclear. It is found C terminal to the Hsp90 chaperone (Heat shocked protein 90) binding domain pfam08565 and the N terminal kinase binding domain of Cdc37 pfam03234. 87 matched cddid_all.tbl CDD pfam08565 pfam08565 430078 CDC37_M Cdc37 Hsp90 binding domain. Cdc37 is a molecular chaperone required for the activity of numerous eukaryotic protein kinases. This domains corresponds to the Hsp90 chaperone (Heat shocked protein 90) binding domain of Cdc37. It is found between the N terminal Cdc37 domain pfam03234, which is predominantly involved in kinase binding, and the C terminal domain of Cdc37 pfam08564 whose function is unclear. 113 matched cddid_all.tbl CDD pfam08566 pfam08566 400743 Pam17 Mitochondrial import protein Pam17. The presequence translocase-associated motor (PAM) drives the completion of preprotein translocation into the mitochondrial matrix. The Pam17 subunit is required for formation of a stable complex between cochaperones Pam16 and Pam18 and promotes the association of Pam16-Pam18 with the presequence translocase. Mitochondria lacking Pam17 are selectively impaired in the import of matrix proteins. 165 matched cddid_all.tbl CDD pfam08567 pfam08567 462521 PH_TFIIH TFIIH p62 subunit, N-terminal domain. The N-terminal domain of the TFIIH basal transcription factor complex p62 subunit (BTF2-p62) forms an interaction with the 3' endonuclease XPG, which is essential for activity. The 3' endonuclease XPG is a major component of the nucleotide excision repair machinery. The structure of the N-terminal domain reveals that it adopts a pleckstrin homology (PH) fold. This PH-type domain has been shown to bind to a mono-phosphorylated inositide. 88 matched cddid_all.tbl CDD pfam08568 pfam08568 400745 Kinetochor_Ybp2 Uncharacterized protein family, YAP/Alf4/glomulin. This entry contains a number of protein families with apparently unrelated functions. These include the YAP binding proteins of yeasts. These are stress response and redox homeostasis proteins, induced by hydrogen peroxide or induced in response to alkylating agent methyl methanesulphonate (MMS). The family includes Aberrant root formation protein 4 (Alf4) of Arabidopsis thaliana (Mouse-ear cress), which is required for the initiation of lateral roots independent from auxin signalling. It may also function in maintaining the pericycle in the mitotically competent state needed for lateral root formation. The family includes glomulin (FAP68), which is essential for normal development of the vasculature and may represent a naturally occurring ligand of the immunophilins FKBP59 and FKBP12. 624 matched cddid_all.tbl CDD pfam08569 pfam08569 462522 Mo25 Mo25-like. Mo25-like proteins are involved in both polarised growth and cytokinesis. In fission yeast Mo25 is localized alternately to the spindle pole body and to the site cell division in a cell cycle dependent manner. 331 matched cddid_all.tbl CDD pfam08570 pfam08570 430081 DUF1761 Protein of unknown function (DUF1761). Family of conserved fungal and bacterial membrane proteins with unknown function. 122 matched cddid_all.tbl CDD pfam08571 pfam08571 462523 Yos1 Yos1-like. In yeast, Yos1 is a subunit of the Yip1p-Yif1p complex and is required for transport between the endoplasmic reticulum and the Golgi complex. Yos1 appears to be conserved in eukaryotes. 81 matched cddid_all.tbl CDD pfam08572 pfam08572 462524 PRP3 pre-mRNA processing factor 3 (PRP3). Pre-mRNA processing factor 3 (PRP3) is a U4/U6-associated splicing factor. The human PRP3 has been implicated in autosomal retinitis pigmentosa. 219 matched cddid_all.tbl CDD pfam08573 pfam08573 462525 SAE2 DNA endonuclease activator SAE2/CtIP C-terminus. SAE2 is a protein involved in repairing meiotic and mitotic double-strand breaks in DNA. It has been shown to negatively regulate DNA damage checkpoint signalling. SAE2 is homologous to the CtIP proteins in mammals and an homologous protein in plants. Crucial sequence motifs that are highly conserved are the CxxC and the RHR motifs in this C-terminal part of the protein. In budding yeast, genetic evidence suggests that the SAE2 protein is essential for the processing of hairpin DNA intermediates and meiotic double-strand breaks by Mre11/Rad50 complexes. SAE2 binds DNA and exhibits endonuclease activity on single-stranded DNA independently of Mre11/Rad50 complexes, but hairpin DNA structures are cleaved cooperatively in the presence of Mre11/Rad50 or Mre11/Rad50/Xrs2. Hairpin structures are not processed at the tip by SAE2 but rather at single-stranded DNA regions adjacent to the hairpin. The catalytic activities of SAE2 are important for its biological functions. Although proteins containing this domain were described as endonucleases, it is now known that they actually function as endonuclease activators. This domain contains highly conserved residues at its 15-residue extreme that are indispensable for MRN (Mre11-Rad50-Nbs1) complex activation, through the stimulation of Mre11 endonuclease activity. 108 matched cddid_all.tbl CDD pfam08574 pfam08574 430085 Iwr1 Transcription factor Iwr1. Iwr1 is involved in transcription from polymerase II promoters; it interacts with with most of the polymerase II subunits. Deletion of this protein results in hypersensitivity to the K1 killer toxin. 72 matched cddid_all.tbl CDD pfam08576 pfam08576 400752 DUF1764 Eukaryotic protein of unknown function (DUF1764). This is a family of eukaryotic proteins of unknown function. This family contains many hypothetical proteins. 99 matched cddid_all.tbl CDD pfam08577 pfam08577 430086 PI31_Prot_C PI31 proteasome regulator. PI31 is a cellular regulator of proteasome formation and of proteasome-mediated antigen processing. 80 matched cddid_all.tbl CDD pfam08578 pfam08578 430087 DUF1765 Protein of unknown function (DUF1765). This region represents a conserved region found in hypothetical proteins from fungi, mycetozoa and entamoebidae. 125 matched cddid_all.tbl CDD pfam08579 pfam08579 369970 RPM2 Mitochondrial ribonuclease P subunit (RPM2). Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends. RPM2 is a protein subunit of the yeast mitochondrial RNase P. It has the ability to act as transcriptional activator in the nucleus where it plays a role in defining the steady-state levels of mRNAs for some nucleus-encoded mitochondrial components. 119 matched cddid_all.tbl CDD pfam08580 pfam08580 430088 KAR9 Yeast cortical protein KAR9. The KAR9 protein in Saccharomyces cerevisiae is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules. KAR9 localizes at the shmoo tip in mating cells and at the tip of the growing bud in anaphase. 684 matched cddid_all.tbl CDD pfam08581 pfam08581 400755 Tup_N Tup N-terminal. The N-terminal domain of the Tup protein has been shown to interact with the Ssn6 transcriptional co-repressor. 77 matched cddid_all.tbl CDD pfam08583 pfam08583 400756 Cmc1 Cytochrome c oxidase biogenesis protein Cmc1 like. Cmc1 is a metallo-chaperone like protein which is known to localize to the inner mitochondrial membrane in Saccharomyces cerevisiae. It is essential for full expression of cytochrome c oxidase and respiration. Cmc1 contains two Cx9C motifs and is able to bind copper(I). Cmc1 is thought to play a role in mitochondrial copper trafficking and transfer to cytochrome c oxidase. 70 matched cddid_all.tbl CDD pfam08584 pfam08584 462526 Ribonuc_P_40 Ribonuclease P 40kDa (Rpp40) subunit. The tRNA processing enzyme ribonuclease P (RNase P) consists of an RNA molecule and at least eight protein subunits. Subunits hpop1, Rpp21, Rpp29, Rpp30, Rpp38, and Rpp40 (this entry) are involved in extensive, but weak, protein-protein interactions in the holoenzyme complex. 277 matched cddid_all.tbl CDD pfam08585 pfam08585 462527 RMI1_N RecQ mediated genome instability protein. RMI1_N is an N-terminal family of eukaryotic proteins. The domain probably carries an oligo-nucleotide-binding domain or OB-fold, and forms a stable complex with Bloom syndrome protein BLM and DNA topoisomerase 3-alpha. 194 matched cddid_all.tbl CDD pfam08586 pfam08586 400759 Rsc14 RSC complex, Rsc14/Ldb7 subunit. RSC is an ATP-dependent chromatin remodelling complex found in yeast. The RSC components Rsc7/Npl6 and Rsc14/Ldb7 interact physically and/or functionally with Rsc3, Rsc30, and Htl1 to form a module important for a broad range of RSC functions. 99 matched cddid_all.tbl CDD pfam08587 pfam08587 430091 UBA_2 Ubiquitin associated domain (UBA). This is a UBA (ubiquitin associated) domain. Ubiquitin is involved in intracellular proteolysis. 45 matched cddid_all.tbl CDD pfam08588 pfam08588 430092 DUF1769 Protein of unknown function (DUF1769). Family of fungal protein with unknown function. 209 matched cddid_all.tbl CDD pfam08589 pfam08589 430093 ATG43 Autophagy receptor ATG43. This family represents the autophagy receptor ATG43 from fungi. It is a mitochondrial outer membrane protein which serves as a mitophagy receptor to promote the selective degradation of mitochondria. 98 matched cddid_all.tbl CDD pfam08590 pfam08590 462528 DUF1771 Domain of unknown function (DUF1771). This domain is highly charged and may represent a small helical extension of the Smr domain (pfam01713), known as N-ext, whose function is not yet clear. 62 matched cddid_all.tbl CDD pfam08591 pfam08591 430095 RNR_inhib Ribonucleotide reductase inhibitor. This family includes S. pombe Spd1. Spd1p inhibits fission yeast RNR activity by interacting with the Cdc22p. 101 matched cddid_all.tbl CDD pfam08592 pfam08592 462529 Anthrone_oxy Anthrone oxygenase. This family consists of anthrone oxygenases found in bacteria and fungi, and involved in the synthesis of different products. GedH from Aspergillus terreus is part of the gene cluster that mediates the biosynthesis of geodin, EncC from Neosartorya fumigata is involved in the biosynthesis of endocrocin, and MdpH from Aspergillus nidulans in the biosynthesis of monodictyphenone. 107 matched cddid_all.tbl CDD pfam08593 pfam08593 400766 DUF1773 Domain of unknown function. This is the C-terminal part of some meiotically up-regulated gene products from fission yeast. The actual function is not yet known but the proteins are likely to be cell-surface glycoproteins. 58 matched cddid_all.tbl CDD pfam08594 pfam08594 369983 UPF0300 Uncharacterized protein family (UPF0300). This family of proteins appear to be specific to S. pombe. 212 matched cddid_all.tbl CDD pfam08595 pfam08595 430097 RXT2_N RXT2-like, N-terminal. The family represents the N-terminal region of RXT2-like proteins. In S. cerevisiae, RXT2 has been demonstrated to be involved in conjugation with cellular fusion (mating) and invasive growth. A high throughput localization study has localized RXT2 to the nucleus. 139 matched cddid_all.tbl CDD pfam08596 pfam08596 400768 Lgl_C Lethal giant larvae(Lgl) like, C-terminal. The Lethal giant larvae (Lgl) tumour suppressor family is conserved from yeast to mammals. The Lgl family functions in cell polarity, at least in part, by regulating SNARE-mediated membrane delivery events at the cell surface. The N-terminal half of Lgl members contains WD40 repeats (see pfam00400), while the C-terminal half appears specific to the family. 393 matched cddid_all.tbl CDD pfam08597 pfam08597 462530 eIF3_subunit Translation initiation factor eIF3 subunit. This is a family of proteins which are subunits of the eukaryotic translation initiation factor 3 (eIF3). In yeast it is called Hcr1. The Saccharomyces cerevisiae protein Swiss:Q05775 has been shown to be required for processing of 20S pre-rRNA and binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p. 239 matched cddid_all.tbl CDD pfam08598 pfam08598 430099 Sds3 Sds3-like. Repression of gene transcription is mediated by histone deacetylases containing repressor-co-repressor complexes, which are recruited to promoters of target genes via interactions with sequence-specific transcription factors. The co-repressor complex contains a core of at least seven proteins. This family represents the conserved region found in Sds3, Dep1 and BRMS1-homolog p40 proteins. 218 matched cddid_all.tbl CDD pfam08599 pfam08599 462531 Nbs1_C DNA damage repair protein Nbs1. This C terminal region of the DNA damage repair protein Nbs1 has been identified to be necessary for the binding of Mre11 and Tel1. 62 matched cddid_all.tbl CDD pfam08600 pfam08600 369989 Rsm1 Rsm1-like. Rsm1 is a protein involved in mRNA export from the nucleus 97 matched cddid_all.tbl CDD pfam08601 pfam08601 369990 PAP1 Transcription factor PAP1. The transcription factor Pap1 regulates antioxidant-gene transcription in response to H2O2. This region is cysteine rich. Alkylation of cysteine residues following treatment with a cysteine alkylating agent can mask the accessibility of the nuclear exporter Crm1, triggering nuclear accumulation and Pap1 dependent transcriptional expression. 363 matched cddid_all.tbl CDD pfam08602 pfam08602 369991 Mgr1 Mgr1-like, i-AAA protease complex subunit. The S. cerevisiae Mgr1 protein has been shown to be required for mitochondrial viability in yeast lacking mitochondrial DNA. It is a mitochondrial inner membrane protein, which interacts with Yme1 and is a new subunit of the i-AAA protease complex. 374 matched cddid_all.tbl CDD pfam08603 pfam08603 462532 CAP_C Adenylate cyclase associated (CAP) C terminal. 157 matched cddid_all.tbl CDD pfam08604 pfam08604 462533 Nup153 Nucleoporin Nup153-like. This family contains both the nucleoporin Nup153 from human and Nup154 from fission yeast. These have been demonstrated to be functionally equivalent. 507 matched cddid_all.tbl CDD pfam08605 pfam08605 369994 Rad9_Rad53_bind Fungal Rad9-like Rad53-binding. In Saccharomyces cerevisiae the Rad9 a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via Rad53 pfam00498 domains. This region is structurally composed of a pair of TUDOR domains. 129 matched cddid_all.tbl CDD pfam08606 pfam08606 400774 Prp19 Prp19/Pso4-like. This regions is found specifically in PRP19-like protein. The region represented by this family covers the sequence implicated in self-interaction and a coiled-coiled motif. PRP19-like proteins form an oligomer that is necessary for spliceosome assembly. 65 matched cddid_all.tbl CDD pfam08608 pfam08608 400775 Wyosine_form Wyosine base formation. Some proteins in this family appear to be important in wyosine base formation in a subset of phenylalanine specific tRNAs. It has been proposed that they participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW. 63 matched cddid_all.tbl CDD pfam08609 pfam08609 462534 Fes1 Nucleotide exchange factor Fes1. Fes1 is a cytosolic homolog of Sls1, an ER protein which has nucleotide exchange factor activity. Fes1 in yeast has been shown to bind to the molecular chaperone Hsp70 and has adenyl-nucleotide exchange factor activity. 89 matched cddid_all.tbl CDD pfam08610 pfam08610 462535 Pex16 Peroxisomal membrane protein (Pex16). Pex16 is a peripheral protein located at the matrix face of the peroxisomal membrane. 347 matched cddid_all.tbl CDD pfam08611 pfam08611 430105 DUF1774 Fungal protein of unknown function (DUF1774). This is a fungal family of unknown function. 95 matched cddid_all.tbl CDD pfam08612 pfam08612 400779 Med20 TATA-binding related factor (TRF) of subunit 20 of Mediator complex. This family of proteins is related to TATA-binding protein (TBP). TBP is a highly conserved RNA polymerase II general transcription factor that binds to the core promoter and initiates assembly of the preinitiation complex. Human TRF has been shown to associate with an RNA polymerase II-SRB complex. This Med20 subunit of Mediator is found in the non-essential part of the head. 200 matched cddid_all.tbl CDD pfam08613 pfam08613 400780 Cyclin Cyclin. This family includes many different cyclin proteins. Members include the G1/S-specific cyclin pas1, and the phosphate system cyclin PHO80/PHO85. 149 matched cddid_all.tbl CDD pfam08614 pfam08614 462536 ATG16 Autophagy protein 16 (ATG16). Autophagy is a ubiquitous intracellular degradation system for eukaryotic cells. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. ATG16 (also known as Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway. 176 matched cddid_all.tbl CDD pfam08615 pfam08615 400782 RNase_H2_suC Ribonuclease H2 non-catalytic subunit (Ylr154p-like). This entry represents the non-catalytic subunit of RNase H2, which in S. cerevisiae is Ylr154p/Rnh203p. Whereas bacterial and archaeal RNases H2 are active as single polypeptides, the Saccharomyces cerevisiae homolog, Rnh2Ap, when expressed in Escherichia coli, fails to produce an active RNase H2. For RNase H2 activity three proteins are required [Rnh2Ap (Rnh201p), Ydr279p (Rnh202p) and Ylr154p (Rnh203p)]. Deletion of any one of the proteins or mutations in the catalytic site in Rnh2A leads to loss of RNase H2 activity. RNase H2 ia an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. It participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication. 133 matched cddid_all.tbl CDD pfam08616 pfam08616 400783 SPA Stabilization of polarity axis. Swiss:Q99222 has been shown to interact with the outer plaque of the spindle pole body. In Aspergillus nidulans the protein member is necessary for stabilization of the polarity axes during septation. and in S. cerevisiae it functions as a polarization-specific docking factor. 113 matched cddid_all.tbl CDD pfam08617 pfam08617 462537 CGI-121 Kinase binding protein CGI-121. CGI-121 has been shown to bind to the p53-related protein kinase (PRPK). PRPK is a novel protein kinase which binds to and induces phosphorylation of the tumour suppressor protein p53. CGI-121 is part of a conserved protein complex, KEOPS. The KEOPS complex is involved in telomere uncapping and telomere elongation. Interestingly this family also include archaeal homologs, formerly in the DUF509 family. A structure for these proteins has been solved by structural genomics. 160 matched cddid_all.tbl CDD pfam08618 pfam08618 370005 Opi1 Transcription factor Opi1. Opi1 is a leucine zipper containing yeast transcription factor that negatively regulates phospholipid biosynthesis. It represses the expression of several UAS(INO) cis acting element containing genes and its activity is mediated by phosphorylations catalyzed by protein kinase A, protein kinase C and casein kinase II. 416 matched cddid_all.tbl CDD pfam08619 pfam08619 400785 Nha1_C Alkali metal cation/H+ antiporter Nha1 C terminus. The C terminus of the plasma membrane Nha1 antiporter plays an important role in the immediate cell response to hypo-osmotic shock which prevents an execessive loss of ions and water. This domain is found with pfam00999. 323 matched cddid_all.tbl CDD pfam08620 pfam08620 462538 RPAP1_C RPAP1-like, C-terminal. Inhibition of RPAP1 synthesis in Saccharomyces cerevisiae results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11. This entry represents the C-terminal region that contains the motif GLHHH. This region is conserved from yeast to humans. 69 matched cddid_all.tbl CDD pfam08621 pfam08621 462539 RPAP1_N RPAP1-like, N-terminal. Inhibition of RPAP1 synthesis in Saccharomyces cerevisiae results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11. This entry represents the N-terminal region of RPAP-1 that is conserved from yeast to humans. 46 matched cddid_all.tbl CDD pfam08622 pfam08622 430110 Svf1 Svf1-like N-terminal lipocalin domain. Family of proteins that are involved in survival during oxidative stress. This entry corresponds to the N-terminal lipocalin domain of a pair. 162 matched cddid_all.tbl CDD pfam08623 pfam08623 430111 TIP120 TATA-binding protein interacting (TIP20). TIP120 (also known as cullin-associated and neddylation-dissociated protein 1) is a TATA binding protein interacting protein that enhances transcription. 165 matched cddid_all.tbl CDD pfam08624 pfam08624 430112 CRC_subunit Chromatin remodelling complex Rsc7/Swp82 subunit. This family has been identified as a subunit of chromatin remodelling complexes. Saccharomyces cerevisiae Swiss:P32832 and its paralogue Swiss:P43554 have been identified as subunits of the RSC chromatin remodelling complex, and SWI/SNF chromatin remodelling complex respectively. 134 matched cddid_all.tbl CDD pfam08625 pfam08625 462540 Utp13 Utp13 specific WD40 associated domain. Utp13 is a component of the five protein Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome. Pwp2 is capable of interacting directly with the 35 S pre-rRNA 5' end. 139 matched cddid_all.tbl CDD pfam08626 pfam08626 430114 TRAPPC9-Trs120 Transport protein Trs120 or TRAPPC9, TRAPP II complex subunit. This region is found at the N terminal of Saccharomyces cerevisiae Trs120 protein. Trs120 is a subunit of the multiprotein complex TRAPP (transport particle protein) which functions in ER to Golgi traffic. Trs120 is specific to the larger TRAPP complex, TRAPP II, along with Trs65p and Trs130p(TRAPPC10). It is suggested that Trs120p is required for the stability of the Trs130p subunit, suggesting that these two proteins might interact in some way. It is likely that there is a complex function for TRAPP II in multiple pathways. 1221 matched cddid_all.tbl CDD pfam08627 pfam08627 400793 CRT-like CRT-like, chloroquine-resistance transporter-like. This family represents the Plasmodium falciparum chloroquine resistance transporter (CRT) and homologous proteins. CRT regulates other transporters, like Na-H antiporter or nonselective cation transporters. The Arabidopsis homologs are involved in thiol transport from the plastid to the cytosol, playing a significant role in regulating GSH levels and the redox potential of the cytosol. homologs from Dictyostelium discoideum are also included in this family. 331 matched cddid_all.tbl CDD pfam08628 pfam08628 462541 Nexin_C Sorting nexin C terminal. This region is found a the C terminal of proteins belonging to the sorting nexin family. It is found on proteins which also contain pfam00787. 111 matched cddid_all.tbl CDD pfam08629 pfam08629 400795 PDE8 PDE8 phosphodiesterase. This region is found in members of the PDE8 phosphodiesterase family. It is found with pfam00233. 52 matched cddid_all.tbl CDD pfam08630 pfam08630 430116 Dfp1_Him1_M Dfp1/Him1, central region. This is the middle regions described by Ogino et al. This region, together with the C-terminal zinc finger (pfam07535) is essential for the mitotic and kinase activation functions of Dfp1/Him1. 128 matched cddid_all.tbl CDD pfam08631 pfam08631 462542 SPO22 Meiosis protein SPO22/ZIP4 like. SPO22/ZIP4 in yeast is a meiosis specific protein involved in sporulation. It has been shown to regulate crossover distribution by promoting synaptonemal complex formation. 273 matched cddid_all.tbl CDD pfam08632 pfam08632 370018 Zds_C Activator of mitotic machinery Cdc14 phosphatase activation C-term. This region of the Zds1 protein is critical for sporulation and has also been shown to suppress the calcium sensitivity of Zds1 deletions. The C-terminal motif is common to both Zds1 and Zds2 proteins, both of which are putative interactors of Cdc55 and are required for the completion of mitotic exit and cytokinesis. They both contribute to timely Cdc14 activation during mitotic exit and are required downstream of separase to facilitate nucleolar Cdc14 release. 49 matched cddid_all.tbl CDD pfam08633 pfam08633 430118 Rox3 Rox3 mediator complex subunit. The mediator complex is part of the RNA polymerase II holoenzyme. Rox3 is a subunit of the mediator complex. 167 matched cddid_all.tbl CDD pfam08634 pfam08634 430119 Pet127 Mitochondrial protein Pet127. Pet127 has been implicated in mitochondrial RNA stability and/or processing and is localized to the mitochondrial membrane. The Pet127 family is part of the PD-(D/E)XK nuclease superfamily including a full set of active site residues. 275 matched cddid_all.tbl CDD pfam08635 pfam08635 117208 ox_reductase_C Putative oxidoreductase C terminal domain. This is the C-terminal domain of a family of putative oxidoreductases. 142 matched cddid_all.tbl CDD pfam08636 pfam08636 430120 Pkr1 ER protein Pkr1. Pkr1 has been identified as an ER protein of unknown function. 69 matched cddid_all.tbl CDD pfam08637 pfam08637 430121 NCA2 ATP synthase regulation protein NCA2. NCA2 has been shown to be required for the regulation of ATP synthase subunits Atp6p and Atp8p in Saccharomyces cerevisiae. 288 matched cddid_all.tbl CDD pfam08638 pfam08638 462543 Med14 Mediator complex subunit MED14. Saccharomyces cerevisiae RGR1 mediator complex subunit affects chromatin structure, transcriptional regulation of diverse genes and sporulation, required for glucose repression, HO repression, RME1 repression and sporulation. This subunit is also found in higher eukaryotes and Med14 is the agreed unified nomenclature for this subunit. Med14 is found in the tail region of Mediator. 192 matched cddid_all.tbl CDD pfam08639 pfam08639 400803 SLD3 DNA replication regulator SLD3. The SLD3 DNA replication regulator is required for loading and maintenance of Cdc45 on chromatin during DNA replication. 534 matched cddid_all.tbl CDD pfam08640 pfam08640 462544 U3_assoc_6 U3 small nucleolar RNA-associated protein 6. This is a family of U3 nucleolar RNA-associated proteins which are involved in nucleolar processing of pre-18S ribosomal RNA. 86 matched cddid_all.tbl CDD pfam08641 pfam08641 430124 Mis14 Kinetochore protein Mis14 like. Mis14 is a kinetochore protein which is known to be recruited to kinetochores independently of CENP-A. 136 matched cddid_all.tbl CDD pfam08642 pfam08642 430125 Rxt3 Histone deacetylation protein Rxt3. Rxt3 has been shown in yeast to be required for histone deacetylation. 113 matched cddid_all.tbl CDD pfam08643 pfam08643 370028 DUF1776 Fungal family of unknown function (DUF1776). This is a fungal family of unknown function. One of the proteins in this family Swiss:P32792 has been localized to the mitochondria. 295 matched cddid_all.tbl CDD pfam08644 pfam08644 462545 SPT16 FACT complex subunit (SPT16/CDC68). Proteins in this family are subunits the FACT complex. The FACT complex plays a role in transcription initiation and promotes binding of TATA-binding protein (TBP) to a TATA box in chromatin. 151 matched cddid_all.tbl CDD pfam08645 pfam08645 370030 PNK3P Polynucleotide kinase 3 phosphatase. Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin. 161 matched cddid_all.tbl CDD pfam08646 pfam08646 462546 Rep_fac-A_C Replication factor-A C terminal domain. This domain is found at the C terminal of replication factor A. Replication factor A (RPA) binds single-stranded DNA and is involved in replication, repair, and recombination of DNA. 146 matched cddid_all.tbl CDD pfam08647 pfam08647 462547 BRE1 BRE1 E3 ubiquitin ligase. BRE1 is an E3 ubiquitin ligase that has been shown to act as a transcriptional activator through direct activator interactions. 95 matched cddid_all.tbl CDD pfam08648 pfam08648 462548 SNRNP27 U4/U6.U5 small nuclear ribonucleoproteins. This is a family of eukaryotic proteins including U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein may play a role in mRNA splicing. 56 matched cddid_all.tbl CDD pfam08649 pfam08649 430129 DASH_Dad1 DASH complex subunit Dad1. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules. Throughout the cell cycle Dad1 remains bound to kinetochores throughout the cell cycle and its association is dependent on the Mis6 and Mal2. 55 matched cddid_all.tbl CDD pfam08650 pfam08650 430130 DASH_Dad4 DASH complex subunit Dad4. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro. 71 matched cddid_all.tbl CDD pfam08651 pfam08651 462549 DASH_Duo1 DASH complex subunit Duo1. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro. 72 matched cddid_all.tbl CDD pfam08652 pfam08652 462550 RAI1 RAI1 like PD-(D/E)XK nuclease. RAI1 is homologous to Caenorhabditis elegans DOM-3 and human DOM3Z and binds to a nuclear exoribonuclease. It is required for 5.8S rRNA processing. Profile-profile comparison tools demonstrate this to be a PD-(D/E)XK nuclease, with a full set of canonical active site signature motifs characteriztic to the PD-(D/E)XK nuclease superfamily. 69 matched cddid_all.tbl CDD pfam08653 pfam08653 430133 DASH_Dam1 DASH complex subunit Dam1. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules. 56 matched cddid_all.tbl CDD pfam08654 pfam08654 430134 DASH_Dad2 DASH complex subunit Dad2. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro. 99 matched cddid_all.tbl CDD pfam08655 pfam08655 430135 DASH_Ask1 DASH complex subunit Ask1. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules. 64 matched cddid_all.tbl CDD pfam08656 pfam08656 430136 DASH_Dad3 DASH complex subunit Dad3. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro. 75 matched cddid_all.tbl CDD pfam08657 pfam08657 400819 DASH_Spc34 DASH complex subunit Spc34. The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis. In Saccharomyces cerevisiae DASH forms both rings and spiral structures on microtubules in vitro. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules. 279 matched cddid_all.tbl CDD pfam08658 pfam08658 430137 Rad54_N Rad54 N terminal. This is the N terminal of the DNA repair protein Rad54. 180 matched cddid_all.tbl CDD pfam08659 pfam08659 430138 KR KR domain. This enzymatic domain is part of bacterial polyketide synthases and catalyzes the first step in the reductive modification of the beta-carbonyl centres in the growing polyketide chain. It uses NADPH to reduce the keto group to a hydroxy group. 180 matched cddid_all.tbl CDD pfam08660 pfam08660 370045 Alg14 Oligosaccharide biosynthesis protein Alg14 like. Alg14 is involved dolichol-linked oligosaccharide biosynthesis and anchors the catalytic subunit Alg13 to the ER membrane. 171 matched cddid_all.tbl CDD pfam08661 pfam08661 462551 Rep_fac-A_3 Replication factor A protein 3. Replication factor A is involved in eukaryotic DNA replication, recombination and repair. 105 matched cddid_all.tbl CDD pfam08662 pfam08662 462552 eIF2A Eukaryotic translation initiation factor eIF2A. This is a family of eukaryotic translation initiation factors. 194 matched cddid_all.tbl CDD pfam08663 pfam08663 400823 HalX HalX domain. HalX is a domain of unknown function, previously (mis)annotated as HoxA-like transcriptional regulator. 68 matched cddid_all.tbl CDD pfam08664 pfam08664 462553 YcbB YcbB domain. YcbB is a DNA-binding domain. 136 matched cddid_all.tbl CDD pfam08665 pfam08665 430139 PglZ PglZ domain. This family is a member of the Alkaline phosphatase clan. 176 matched cddid_all.tbl CDD pfam08666 pfam08666 430140 SAF SAF domain. This domain family includes a range of different proteins. Such as antifreeze proteins and flagellar FlgA proteins, and CpaB pilus proteins. 63 matched cddid_all.tbl CDD pfam08667 pfam08667 400827 BetR BetR domain. This family includes an N-terminal helix-turn-helix domain. 148 matched cddid_all.tbl CDD pfam08668 pfam08668 430141 HDOD HDOD domain. 196 matched cddid_all.tbl CDD pfam08669 pfam08669 462554 GCV_T_C Glycine cleavage T-protein C-terminal barrel domain. This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyzes the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase. 80 matched cddid_all.tbl CDD pfam08670 pfam08670 462555 MEKHLA MEKHLA domain. The MEKHLA domain shares similarity with the PAS domain and is found in the 3' end of plant HD-ZIP III homeobox genes, and bacterial proteins. 144 matched cddid_all.tbl CDD pfam08671 pfam08671 400831 SinI Anti-repressor SinI. SinR is a pleiotropic regulator of several late growth processes. It is a tetrameric DNA binding protein whose activity is down-regulated thorough the formation of a SinI:SinR protein complex. When complexed with SinI, the SinR tetramer is disrupted such that is no longer able to bind DNA. 28 matched cddid_all.tbl CDD pfam08672 pfam08672 462556 ANAPC2 Anaphase promoting complex (APC) subunit 2. The anaphase promoting complex or cyclosome (APC2) is an E3 ubiquitin ligase which is part of the SCF family of ubiquitin ligases. Ubiquitin ligases catalyze the transfer of ubiquitin from the ubiquitin conjugating enzyme (E2), to the substrate protein. 60 matched cddid_all.tbl CDD pfam08673 pfam08673 430145 RsbU_N Phosphoserine phosphatase RsbU, N-terminal domain. RsbU is a phosphoserine phosphatase which acts as a positive regulator of the general stress-response factor of gram positive organizms, sigma-B. The phosphatase activity of RsbU is stimulated by association with the RsbT kinase. Deletions in the N terminal domain are deleterious to the activity of RsbU. 75 matched cddid_all.tbl CDD pfam08674 pfam08674 430146 AChE_tetra Acetylcholinesterase tetramerization domain. The acetylcholinesterase tetramerization domain is found at the C terminus and forms a left handed superhelix. 35 matched cddid_all.tbl CDD pfam08675 pfam08675 400835 RNA_bind RNA binding domain. This domain corresponds to the RNA binding domain of Poly(A)-specific ribonuclease (PARN). 75 matched cddid_all.tbl CDD pfam08676 pfam08676 430147 MutL_C MutL C terminal dimerization domain. MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognizes mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerization. 145 matched cddid_all.tbl CDD pfam08677 pfam08677 400837 GP11 GP11 baseplate wedge protein. GP11 is a viral structural protein that connects short tail fibres to the baseplate. The tail region is responsible for attachment to the host bacteria during infection. 252 matched cddid_all.tbl CDD pfam08678 pfam08678 400838 Rsbr_N Rsbr N terminal. Rsbr is a regulator of the RNA polymerase sigma factor subunit sigma(B). The structure of the N terminal domain belongs to the globin fold superfamily. 130 matched cddid_all.tbl CDD pfam08679 pfam08679 430148 DsrD Dissimilatory sulfite reductase D (DsrD). The structure of the DsrD protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins. The structure suggests a possible role for DsrD in transcription of translation of genes which catalyze dissimilatory sulfite reduction. 65 matched cddid_all.tbl CDD pfam08680 pfam08680 400839 DUF1779 TATA-box binding. TATA-box_bdg is a family of bacterial proteins. YwmB from Bacillus subtilis contains a circularly permuted TATA-box binding protein-like fold. Jian-Xiang Liu, Qi Xie, Jun Lin. Protein Structural Data Mining and Evolutionary Bioinformatic Analysis on Domains of TATA-box Binding Protein-like Fold. Life Science Journal 2014; 11(2): 298-302 (not yet in PubMed 27-02-2014). 184 matched cddid_all.tbl CDD pfam08681 pfam08681 462557 DUF1778 Protein of unknown function (DUF1778). This is a family of uncharacterized proteins. The structure of one of the hypothetical proteins in this family has been solved and it forms a helix structure which may form interactions with DNA. 75 matched cddid_all.tbl CDD pfam08682 pfam08682 430150 DUF1780 Putative endonuclease, protein of unknown function (DUF1780). This is a family of uncharacterized proteins. The structure of a hypothetical protein from Pseudomonas aeruginosa has shown it to adopt an alpha/beta fold, placing it in the Endonuclease superfamily/clan of restriction endonucleases. 208 matched cddid_all.tbl CDD pfam08683 pfam08683 462558 CAMSAP_CKK Microtubule-binding calmodulin-regulated spectrin-associated. This is the C-terminal domain of a family of eumetazoan proteins collectively defined as calmodulin-regulated spectrin-associated, or CAMSAP, proteins. CAMSAP proteins carry an N-terminal region that includes the CH domain, a central region including a predicted coiled-coil and this C-terminal, or CKK, domain - defined as being present in CAMSAP, KIAA1078 and KIAA1543, The C-terminal domain is the part of the CAMSAP proteins that binds to microtubules. The domain appears to act by producing inhibition of neurite extension, probably by blocking microtubule function. CKK represents a domain that has evolved with the metazoa. The structure of a murine hypothetical protein from RIKEN cDNA has shown the domain to adopt a mainly beta barrel structure with an associated alpha-helical hairpin. 119 matched cddid_all.tbl CDD pfam08684 pfam08684 430152 ocr DNA mimic ocr. The structure of an ocr protein from bacteriophage T7 has shown that this protein mimics the size and shape of a bent DNA molecule. ocr has also been shown to be an inhibitor of the complex type I DNA restriction enzymes. 101 matched cddid_all.tbl CDD pfam08685 pfam08685 462559 GON GON domain. The GON domain is found in the ADAMTS (a disintegrin and metalloproteinase domain with thrombospondin type-1 modules) family of proteins. It contains several conserved cysteine residues. 200 matched cddid_all.tbl CDD pfam08686 pfam08686 462560 PLAC PLAC (protease and lacunin) domain. The PLAC (protease and lacunin) domain is a short six-cysteine region that is usually found at the C terminal of proteins. It is found in a range of proteins including PACE4 (paired basic amino acid cleaving enzyme 4) and the extracellular matrix protein lacunin. 31 matched cddid_all.tbl CDD pfam08687 pfam08687 462561 ASD2 Apx/Shroom domain ASD2. This region is found in the actin binding protein Shroom which mediates apical contriction in epithelial cells and is required for neural tube closure. 290 matched cddid_all.tbl CDD pfam08688 pfam08688 462562 ASD1 Apx/Shroom domain ASD1. This region is found in the actin binding protein Shroom which mediates apical contriction in epithelial cells and is required for neural tube closure. ASD1 has been implicated directly in F-actin binding. 179 matched cddid_all.tbl CDD pfam08689 pfam08689 370064 Med5 Mediator complex subunit Med5. The mediator complex is required for the expression of nearly all RNA pol II dependent genes in Saccharomyces cerevisiae. Deletion of the MED5 gene leads to increased transcription of nuclear genes encoding components of the oxidative phosphorylation machinery, and decreased transcription of mitochondrial genes encoding components of the same machinery. There is no orthologue from pombe, and this subunit appears to be fungal specific. 1082 matched cddid_all.tbl CDD pfam08690 pfam08690 400847 GET2 GET complex subunit GET2. This family corresponds to the GET complex subunit GET2. The GET complex is involved in the retrieval of ER resident proteins from the Golgi. It forms a complex with GET1 and constitutes the ER membrane receptor for GET3. It facilitates the release of tail- anchored (TA) proteins from GET3 and mediates the subsequent entry into the ER membrane. 308 matched cddid_all.tbl CDD pfam08691 pfam08691 462563 Nse5 DNA repair proteins Nse5 and Nse6. Nse5 and Nse6 are non essential nuclear proteins that are critical for chromosome segregation in fission yeast. Nse5 forms a dimer with Nse6 and facilitates DNA repair as part of the Smc5-Smc6 holocomplex. 503 matched cddid_all.tbl CDD pfam08692 pfam08692 400848 Pet20 Mitochondrial protein Pet20. Pet20 is a mitochondrial protein which is thought to play a role in the correct assembly/maintenance of mitochondrial components. 134 matched cddid_all.tbl CDD pfam08693 pfam08693 462564 SKG6 SKG6 family. SKG6/Axl2 are membrane proteins that show polarised intracellular localization. SKG6_Tmem is the highly conserved transmembrane alpha-helical domain of SKG6 and Axl2 proteins,. The full-length fungal protein has a negative regulatory function in cytokinesis. 663 matched cddid_all.tbl CDD pfam08694 pfam08694 400850 UFC1 Ubiquitin-fold modifier-conjugating enzyme 1. Ubiquitin-like (UBL) post-translational modifiers are covalently linked to most, if not all, target protein(s) through an enzymatic cascade analogous to ubiquitylation, consisting of E1 (activating), E2 (conjugating), and E3 (ligating) enzymes. Ubiquitin-fold modifier 1 (Ufm1) a ubiquitin-like protein is activated by a novel E1-like enzyme, Uba5, by forming a high-energy thioester bond. Activated Ufm1 is then transferred to its cognate E2-like enzyme, Ufc1, in a similar thioester linkage. This family represents the E2-like enzyme. 155 matched cddid_all.tbl CDD pfam08695 pfam08695 430157 Coa1 Cytochrome oxidase complex assembly protein 1. Coa1 is an inner mitochondrial membrane protein that associates with Shy1 and is required for cytochrome oxidase complex IV assembly. It contains a conserved hydrophobic segment (amino acids 74-92) with the potential to form a membrane-spanning helix. The N-terminus of Coa1 is rich in positively charged amino acids and could form an amphipathic alpha helix, characteriztic of a mitochondrial presequence. A cleavage site for the mitochondrial processing peptidase is predicted adjacent to the presequence. Upon in vitro import into mitochondria, Coa1 is processed to a mature form, indicating that it possesses a cleavable presequence. The eukaryotic cytochrome oxidase complex consists of 12-13 subunits, with three mitochondrial encoded subunits, Cox1-Cox3, forming the core enzyme. Translation of the Cox1 transcript requires the two promoters, Pet309 and Mss51, and the latter has an additional role in translational elongation. Coa1 is necessary for linking the activity of Mss51 to Cox1 insertion into the assembly complex. 117 matched cddid_all.tbl CDD pfam08696 pfam08696 462565 Dna2 DNA replication factor Dna2. Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, ( 5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways. 203 matched cddid_all.tbl CDD pfam08698 pfam08698 462566 Fcf2 Fcf2 pre-rRNA processing. This is a family of eukaryotic nucleolar proteins that are involved in pre-rRNA processing. 93 matched cddid_all.tbl CDD pfam08699 pfam08699 462567 ArgoL1 Argonaute linker 1 domain. ArgoL1 is a region found in argonaute proteins. It normally co-occurs with pfam02179 and pfam02171. It is a linker region between the N-terminal and the PAZ domains. It contains an alpha-helix packed against a three-stranded antiparallel beta-sheet with two long beta-strands (beta8 and beta9) of the sheet spanning one face of the adjacent N and PAZ domains. L1 together with linker 2, L2, PAZ and ArgoN forms a compact global fold. 52 matched cddid_all.tbl CDD pfam08700 pfam08700 462568 Vps51 Vps51/Vps67. This family includes a presumed domain found in a number of components of vesicular transport. The VFT tethering complex (also known as GARP complex, Golgi associated retrograde protein complex, Vps53 tethering complex) is a conserved eukaryotic docking complex which is involved recycling of proteins from endosomes to the late Golgi. Vps51 (also known as Vps67) is a subunit of VFT and interacts with the SNARE Tlg1. Cog1_N is the N-terminus of the Cog1 subunit of the eight-unit Conserved Oligomeric Golgi (COG) complex that participates in retrograde vesicular transport and is required to maintain normal Golgi structure and function. The subunits are located in two lobes and Cog1 serves to bind the two lobes together probably via the highly conserved N-terminal domain of approximately 85 residues. 86 matched cddid_all.tbl CDD pfam08701 pfam08701 462569 GN3L_Grn1 GNL3L/Grn1 putative GTPase. Grn1 (yeast) and GNL3L (human) are putative GTPases which are required for growth and play a role in processing of nucleolar pre-rRNA. This family contains a potential nuclear localization signal. 77 matched cddid_all.tbl CDD pfam08702 pfam08702 462570 Fib_alpha Fibrinogen alpha/beta chain family. Fibrinogen is a protein involved in platelet aggregation and is essential for the coagulation of blood. This domain forms part of the central coiled coiled region of the protein which is formed from two sets of three non-identical chains (alpha, beta and gamma). 143 matched cddid_all.tbl CDD pfam08703 pfam08703 462571 PLC-beta_C PLC-beta C terminal. This domain corresponds to the alpha helical C terminal domain of phospholipase C beta. 176 matched cddid_all.tbl CDD pfam08704 pfam08704 312288 GCD14 tRNA methyltransferase complex GCD14 subunit. GCD14 is a subunit of the tRNA methyltransferase complex and is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA. 242 matched cddid_all.tbl CDD pfam08705 pfam08705 312289 Gag_p6 Gag protein p6. HIV protein p6 contains two late-budding domains (L domains) which are short sequence motifs essential for viral particle release. p6 interacts with the endosomal sorting complex and represents a docking site for several cellular and binding factors. The PTAP motif interacts with the cellular budding factor TSG101. This domain is also found in some chimpanzee immunodeficiency virus (SIV-cpz) proteins. 37 matched cddid_all.tbl CDD pfam08706 pfam08706 378029 D5_N D5 N terminal like. This domain is found in D5 proteins of DNA viruses and bacteriophage P4 DNA primases phages. 145 matched cddid_all.tbl CDD pfam08707 pfam08707 430165 PriCT_2 Primase C terminal 2 (PriCT-2). This alpha helical domain is found at the C terminal of primases. 76 matched cddid_all.tbl CDD pfam08708 pfam08708 430166 PriCT_1 Primase C terminal 1 (PriCT-1). This alpha helical domain is found at the C terminal of primases. 64 matched cddid_all.tbl CDD pfam08709 pfam08709 462572 Ins145_P3_rec Inositol 1,4,5-trisphosphate/ryanodine receptor. This domain corresponds to the ligand binding region on inositol 1,4,5-trisphosphate receptor, and the N terminal region of the ryanodine receptor. Both receptors are involved in Ca2+ release. They can couple to the activation of neurotransmitter-gated receptors and voltage-gated Ca2+ channels on the plasma membrane, thus allowing the endoplasmic reticulum discriminate between different types of neuronal activity. 212 matched cddid_all.tbl CDD pfam08710 pfam08710 285872 CoV_NSP9 Coronavirus replicase NSP9. Nsp9 is a single-stranded RNA-binding viral protein involved in RNA synthesis. Several crystallographic structures of nsp9 have shown that it is composed of seven beta strands and a single alpha helix. Nsp9 proteins have N-finger motifs and highly conserved GXXXG motifs that both play critical roles in dimerization. The conserved helix-helix dimer interface containing a GXXXG protein-protein interaction motif is biologically relevant to SARS-CoV replication. 111 matched cddid_all.tbl CDD pfam08711 pfam08711 462573 Med26 TFIIS helical bundle-like domain. Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. Notably, the 'small' and 'large' Mediator complexes differ in their subunit composition: the Med26 subunit preferentially associates with the small, active complex, whereas cdk8, cyclin C, Med12 and Med13 associate with the large Mediator complex. This family includesthe C terminal region of a number of eukaryotic hypothetical proteins which are homologous to the Saccharomyces cerevisiae protein IWS1. IWS1 is known to be an Pol II transcription elongation factor and interacts with Spt6 and Spt5. 52 matched cddid_all.tbl CDD pfam08712 pfam08712 462574 Nfu_N Scaffold protein Nfu/NifU N terminal. This domain is found at the N terminus of NifU and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the the assembly of iron-sulphur clusters. 81 matched cddid_all.tbl CDD pfam08713 pfam08713 378033 DNA_alkylation DNA alkylation repair enzyme. Proteins in this family are predicted to be DNA alkylation repair enzymes. The structure of a hypothetical protein in this family shows it to adopt a supercoiled alpha helical structure. 212 matched cddid_all.tbl CDD pfam08714 pfam08714 430170 Fae Formaldehyde-activating enzyme (Fae). Formaldehyde-activating enzyme is an enzyme required for energy metabolism and formaldehyde detoxification. It catalyzes the condensation of formaldehyde and tetrahydromethanopterin to methylene tetrahydromethanopterin. 158 matched cddid_all.tbl CDD pfam08715 pfam08715 430171 CoV_peptidase Coronavirus papain-like peptidase. This entry contains coronavirus cysteine endopeptidases that belong to MEROPS peptidase family C16 and are required for proteolytic processing of the replicase polyprotein. All coronaviruses encode between one and two accessory cysteine proteinases that recognize and process one or two sites in the amino-terminal half of the replicase polyprotein during assembly of the viral replication complex. HCoV and TGEV encode two accessory proteinases, called coronavirus papain-like proteinase 1 and 2 (PL1-PRO and PL2-PRO). IBV and SARS encodes only one called PL-PRO. The structure of this protein has shown it adopts a fold similar that of de-ubiquitinating enzymes. The peptidase family C16 domain is about 260 amino acids in length. This domain is predicted to have an alpha-beta structural organization known as the papain-like fold. It consists of three alpha-helices and three strands of antiparallel beta-sheet. 318 matched cddid_all.tbl CDD pfam08716 pfam08716 285878 CoV_NSP7 Coronavirus replicase NSP7. NSP7 (non structural protein 7) has been implicated in viral RNA replication and is predominantly alpha helical in structure. It forms a hexadecameric supercomplex with NSP8 that adopts a hollow cylinder-like structure. The dimensions of the central channel and positive electrostatic properties of the cylinder imply that it confers processivity on RNA-dependent RNA polymerase. NSP7 and NSP8 heterodimers play a role in the stabilization of NSP12 regions involved in RNA binding and are essential for a highly active NSP12 polymerase complex. 83 matched cddid_all.tbl CDD pfam08717 pfam08717 400866 CoV_NSP8 Coronavirus replicase NSP8. Viral NSP8 (non structural protein 8) forms a hexadecameric supercomplex with NSP7 that adopts a hollow cylinder-like structure. The dimensions of the central channel and positive electrostatic properties of the cylinder imply that it confers processivity on RNA-dependent RNA polymerase. NSP7 and NSP8 heterodimers play a role in the stabilization of NSP12 regions involved in RNA binding and are essential for a highly active NSP12 polymerase complex. It has been demonstrated that NSP8 acts as an oligo(U)-templated polyadenylyltransferase but also has robust (mono/oligo) adenylate transferase activities. NSP8 has N- and C-terminal D/ExD/E conserved motifs, being the N-terminal motif critical for RNA polymerase activity as these residues are part of the Mg2-binding active site. 197 matched cddid_all.tbl CDD pfam08718 pfam08718 462575 GLTP Glycolipid transfer protein (GLTP). GLTP is a cytosolic protein that catalyzes the intermembrane transfer of glycolipids. 140 matched cddid_all.tbl CDD pfam08719 pfam08719 462576 NADAR NADAR domain. This is a domain of unknown function, it has been named been named the NADAR (NAD and ADP-ribose) domain. 156 matched cddid_all.tbl CDD pfam08720 pfam08720 462577 Hema_stalk Influenza C hemagglutinin stalk. This domain corresponds to the stalk segment of hemagglutinin in influenza C virus. It forms a coiled coil structure. 175 matched cddid_all.tbl CDD pfam08721 pfam08721 462578 Tn7_Tnp_TnsA_C TnsA endonuclease C terminal. The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5' end of the transposon is carried out by TnsA, and breakage and joining at the 3' end is carried out by TnsB. The C terminal domain of TnsA binds DNA. 83 matched cddid_all.tbl CDD pfam08722 pfam08722 462579 Tn7_TnsA-like_N TnsA-like endonuclease N terminal. The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5' end of the transposon is carried out by TnsA, and breakage and joining at the 3' end is carried out by TnsB. The N terminal domain of TnsA is catalytic. This domain is also found in Bacteriophage T4 gp4-like head completion protein whose nuclease activity is required for packaging. This domain contains the catalytic triad of one basic and two acidic residues that form a restriction endonuclease-like active site and conserved between TnsA with gp4 proteins. 83 matched cddid_all.tbl CDD pfam08723 pfam08723 72147 Gag_p15 Gag protein p15. Gag p15 is a viral membrane-binding matrix protein which is alpha helical in structure. 123 matched cddid_all.tbl CDD pfam08724 pfam08724 312303 Rep_N Rep protein catalytic domain like. Adeno-associated virus (AAV) Replication (Rep) protein is essential for viral replication and integration. The catalytic domain has DNA binding and endonuclease activity. 187 matched cddid_all.tbl CDD pfam08725 pfam08725 462580 Integrin_b_cyt Integrin beta cytoplasmic domain. Integrins are a group of transmembrane proteins which function as extracellular matrix receptors and in cell adhesion. Integrins are ubiquitously expressed and are heterodimeric, each composed of an alpha and beta subunit. Several variations of the the alpha and beta subunits exist, and association of different alpha and beta subunits can have different a different binding specificity. This domain corresponds to the cytoplasmic domain of the beta subunit. 41 matched cddid_all.tbl CDD pfam08726 pfam08726 430177 EFhand_Ca_insen Ca2+ insensitive EF hand. EF hands are helix-loop-helix binding motifs involved in the regulation of many cellular processes. EF hands usually bind to Ca2+ ions which causes a major conformational change that allows the protein to interact with its designated targets. This domain corresponds to an EF hand which has partially or entirely lost its calcium-binding properties. The calcium insensitive EF hand is still able to mediate protein-protein recognition. 69 matched cddid_all.tbl CDD pfam08727 pfam08727 400873 P3A Poliovirus 3A protein like. This domain is found in positive-strand RNA viruses. The 3A protein is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. 59 matched cddid_all.tbl CDD pfam08728 pfam08728 400874 CRT10 CRT10. CRT10 is a transcriptional regulator of ribonucleotide reductase (RNR) genes. RNR catalyzes the rate limiting step in dNTP synthesis. Mutations in CRT10 have been shown to enhance hydroxyurea resistance. 618 matched cddid_all.tbl CDD pfam08729 pfam08729 462581 HUN HPC2 and ubinuclein domain. HPC2 (Histone promoter control 2) is required for cell-cycle regulation of histone transcription. It regulates transcription of the histone genes during the S-phase of the cell cycle by repressing transcription at other cell cycle stages. HPC2 mutants display synthetic interactions with FACT complex which allows RNA Pol II to elongate through nucleosomes. Hpc2 is one of the proteins of one of the multi-subunit complexes that mediate replication- independent nucleosome assembly, along with histone chaperone proteins. the Hip4 sequence from SCH. pombe is an integral component of this complex that is required for transcriptional silencing at multiple loci. HPC2, ubinuclein/yemanuclein, and the cell cycle regulator FLJ25778 share a conserved domain that is predicted to bind histone tails. This domain is also referred to as the HRD or Hpc2-related domain. 52 matched cddid_all.tbl CDD pfam08730 pfam08730 400876 Rad33 Rad33. Rad33 is involved in nucleotide excision repair (NER). NER is the main pathway for repairing DNA lesions induced by UV. Cells deleted for RAD33 display intermediate UV sensitivity that is epistatic with NER. 165 matched cddid_all.tbl CDD pfam08731 pfam08731 400877 AFT Transcription factor AFT. AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This family includes the paralogous pair of transcription factors AFT1 and AFT2. 91 matched cddid_all.tbl CDD pfam08732 pfam08732 400878 HIM1 HIM1. HIM1 (high induction of mutagenesis protein 1) plays a role in the control of spontaneous and induced mutagenesis. It is thought to participate in the control of processing of mutational intermediates appearing during error-prone bypass of DNA damage. 169 matched cddid_all.tbl CDD pfam08733 pfam08733 400879 PalH PalH/RIM21. PalH (also known as RIM21) is a transmembrane protein required for proteolytic cleavage of Rim101/PacC transcription factors which are activated by C terminal proteolytic processing. Rim101/PacC family proteins play a key role in pH-dependent responses and PalH has been implicated as a pH sensor. 335 matched cddid_all.tbl CDD pfam08734 pfam08734 430178 GYD GYD domain. This protein is found in a range of bacteria. It is usually less than 100 amino acids in length. The function of the protein is unknown. It may belong to the dimeric alpha/beta barrel superfamily. 89 matched cddid_all.tbl CDD pfam08735 pfam08735 430179 DUF1786 Putative pyruvate format-lyase activating enzyme (DUF1786). This family is annotated as pyruvate formate-lyase activating enzyme (EC:1.97.1.4) in UniProt. It is not clear where this annotation comes from. 253 matched cddid_all.tbl CDD pfam08736 pfam08736 462582 FA FERM adjacent (FA). This region is found adjacent to Band 4.1 / FERM domains (pfam00373) in a subset of FERM containing protein. The region has been hypothesized to play a role in regulatory adaptation, based on similarity to other protein kinase substrates. 44 matched cddid_all.tbl CDD pfam08737 pfam08737 430181 Rgp1 Rgp1. Rgp1 forms heterodimer with Ric1 (pfam07064) which associates with Golgi membranes and functions as a guanyl-nucleotide exchange factor. 414 matched cddid_all.tbl CDD pfam08738 pfam08738 370092 Gon7 Gon7 family. In S. cerevisiae Gon7 is a member of the KEOPS protein complex. A protein complex proposed to be involved in transcription and promoting telomere uncapping and telomere elongation. 105 matched cddid_all.tbl CDD pfam08740 pfam08740 462583 BCS1_N BCS1 N terminal. This domain is found at the N terminal of the mitochondrial ATPase BSC1. It encodes the import and intramitochondrial sorting for the protein. 178 matched cddid_all.tbl CDD pfam08741 pfam08741 430183 YwhD YwhD family. This family of proteins are currently uncharacterized. They are around 170 amino acids in length. 162 matched cddid_all.tbl CDD pfam08742 pfam08742 462584 C8 C8 domain. This domain contains 8 conserved cysteine residues, but this family only contains 7 of them to overlaps with other domains. It is found in disease-related proteins including von Willebrand factor, Alpha tectorin, Zonadhesin and Mucin. It is often found on proteins containing pfam00094 and pfam01826. 68 matched cddid_all.tbl CDD pfam08743 pfam08743 462585 Nse4_C Nse4 C-terminal. Nse4 is the kleisin component of the Smc5/6 DNA repair complex. It bridges the heads of Smc5 and Smc6. This is the C-terminal domain of Nse4 that interacts with the head domain of Smc5. 89 matched cddid_all.tbl CDD pfam08744 pfam08744 285901 NOZZLE Plant transcription factor NOZZLE. NOZZLE is a transcription factor that plays a role in patterning the proximal-distal and adaxial-abaxial axes. 335 matched cddid_all.tbl CDD pfam08745 pfam08745 462586 PIN_5 PINc domain ribonuclease. This is a family of bacterial and archaeal PINc domains. PIN domains are characterized by the conservation of three acidic residues, possibly four, an Asp at residue 13, a Glu at 63, and then Asps at 172 and 194 in UniProtKB:Q58360. Family members include Homologs of Aquifex RNase P (HARP) proteins. 210 matched cddid_all.tbl CDD pfam08746 pfam08746 430187 zf-RING-like RING-like domain. This is a zinc finger domain that is related to the C3HC4 RING finger domain (pfam00097). 43 matched cddid_all.tbl CDD pfam08747 pfam08747 430188 BrxB BREX protein BrxB. This family includes BREX protein BrxB from Bacillus cereus, which is part of a type 1 BREX (bacteriophage exclusion) system, a system that provides immunity against bacteriophage, which allows phage adsorption but prevents phage DNA replication, without degradation of the phage DNA. The exact function of BrxB is not clear. 119 matched cddid_all.tbl CDD pfam08748 pfam08748 370098 Phage_TAC_4 Phage tail assembly chaperone. This is a family of phage tail assembly chaperone proteins largely from phage T1 Gp40. 124 matched cddid_all.tbl CDD pfam08750 pfam08750 462587 CNP1 CNP1-like family. This family of proteins are likely to be lipoproteins. CNP1 (cryptic neisserial protein) has been expressed in E. coli and shown to be localized periplasmicly. 135 matched cddid_all.tbl CDD pfam08751 pfam08751 430190 TrwC TrwC relaxase. Relaxases are DNA strand transferases which function during the conjugative cell to cell DNA transfer. TrwC binds to the origin of transfer (oriT) and melts the double helix. 279 matched cddid_all.tbl CDD pfam08752 pfam08752 462588 COP-gamma_platf Coatomer gamma subunit appendage platform subdomain. COPI-coated vesicles function in retrograde transport from the Golgi to the ER, and in intra-Golgi transport. This is the platform subdomain of the coatomer gamma subunit appendage domain. It carries a protein-protein interaction site at UniProt:P53620, residue W776, which in yeast binds to the ARFGAP Glo3p, and in mammalian gamma-COP binds to a Glo3p orthologue, ARFGAP2. 149 matched cddid_all.tbl CDD pfam08753 pfam08753 462589 NikR_C NikR C terminal nickel binding domain. NikR is a transcription factor that regulates nickel uptake. It consists of two dimeric DNA binding domains separated by a tetrameric regulatory domain that binds nickel. This domain corresponds to the C terminal regulatory domain which contains four nickel binding sites at the tetramer interface. 75 matched cddid_all.tbl CDD pfam08755 pfam08755 430193 YccV-like Hemimethylated DNA-binding protein YccV like. YccV is a hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression. The structure of one of the hypothetical proteins in this family has been solved and it forms a beta sheet structure with a terminating alpha helix. 96 matched cddid_all.tbl CDD pfam08756 pfam08756 430194 YfkB YfkB-like domain. This protein is adjacent to YfkA in B. subtilis. In other bacterial species it is fused to this protein. As YfkA contains a Radical SAM domain it suggests this domain is interacts with them. 149 matched cddid_all.tbl CDD pfam08757 pfam08757 430195 CotH CotH kinase protein. Members of this family include the spore coat protein H (cotH). This protein is an atypical protein kinase that phosphorylates CotB and CotG. 318 matched cddid_all.tbl CDD pfam08758 pfam08758 462590 Cadherin_pro Cadherin prodomain like. Cadherins are a family of proteins that mediate calcium dependent cell-cell adhesion. They are activated through cleavage of a prosequence in the late Golgi. This domain corresponds to the folded region of the prosequence, and is termed the prodomain. The prodomain shows structural resemblance to the cadherin domain, but lacks all the features known to be important for cadherin-cadherin interactions. 90 matched cddid_all.tbl CDD pfam08759 pfam08759 430197 GT-D Glycosyltransferase GT-D fold. This domain is found at the C terminus of proteins such as the probable glycosyltransferase Gly that also contain the glycosyl transferase domain at the N terminus. It is also found N-terminal in numerous putative glycosyltransferases such as GalT1. GalT1 has been shown to catalyze the third step of Fap1 glycosylation. This domain is structurally distinct from all known GT folds of glycosyltransferases and contains a metal binding site. This new glycosyltransferase fold has been named GT-D. 223 matched cddid_all.tbl CDD pfam08760 pfam08760 430198 DUF1793 Domain of unknown function (DUF1793). This presumed domain is found at the C-terminus of a glutaminase protein from fungi. This domain is also found as a single domain protein in Bacteroides thetaiotaomicron. 169 matched cddid_all.tbl CDD pfam08761 pfam08761 430199 dUTPase_2 dUTPase. 2-Deoxyuridine 5-triphosphate nucleotidohydrolase (dUTPase) catalyzes the hydrolysis of dUTP to dUMP and pyrophosphate (EC:3.6.1.23). Members of this family have a novel all-alpha fold and are unrelated to the all-beta fold found in dUTPases of the majority of organizms. This family contains both dUTPase homologs of dUTPase including dCTPase of phage T4. 162 matched cddid_all.tbl CDD pfam08762 pfam08762 370104 CRPV_capsid CRPV capsid protein like. This is a family of capsid proteins found in positive stranded ssRNA viruses such as cricket paralysis virus (CRPV). It forms an all beta sheet structure. 198 matched cddid_all.tbl CDD pfam08763 pfam08763 462591 Ca_chan_IQ Voltage gated calcium channel IQ domain. Voltage gated calcium channels control cellular calcium entry in response to changes in membrane potential. The isoleucine-glutamine (IQ) motif in the voltage gated calcium channel IQ domain interacts with hydrophobic pockets of Ca2+/calmodulin. The interaction regulates two self-regulatory calcium dependent feedback mechanism, calcium dependent inactivation (CDI), and calcium-dependent facilitation (CDF). 77 matched cddid_all.tbl CDD pfam08764 pfam08764 312335 Coagulase Staphylococcus aureus coagulase. Staphylococcus aureus secretes a cofactor called coagulase. Coagulase is an extracellular protein that forms a complex with human prothrombin, and activates it without the usual proteolytic cleavages. The resulting complex directly initiates blood clotting. 279 matched cddid_all.tbl CDD pfam08765 pfam08765 400902 Mor Mor transcription activator family. Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N terminal region of Mor is the dimerization region, and the C terminal contains a helix-turn-helix motif which binds DNA. 107 matched cddid_all.tbl CDD pfam08766 pfam08766 462592 DEK_C DEK C terminal domain. DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C terminal of DEK and is of clinical importance since it can reverse the characteriztic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family. This domain is also found in chitin synthase proteins like Swiss:Q8TF96, and in protein phosphatases such as Swiss:Q6NN85. 54 matched cddid_all.tbl CDD pfam08767 pfam08767 430202 CRM1_C CRM1 C terminal. CRM1 (also known as Exportin1) mediates the nuclear export of proteins bearing a leucine-rich nuclear export signal (NES). CRM1 forms a complex with the NES containing protein and the small GTPase Ran. This region forms an alpha helical structure formed by six helical hairpin motifs that are structurally similar to the HEAT repeat, but share little sequence similarity to the HEAT repeat. 323 matched cddid_all.tbl CDD pfam08768 pfam08768 462593 THAP4_heme-bd THAP4-like, heme-binding beta-barrel domain. This domain can be found in THAP4 from mammals and At1g79260 from Arabidopsis. THAP4 catalyzes the heme-based conversion of peroxynitrite into nitrate-NO3- in vitro. At1g79260 is a nitrophorin-like heme-binding protein that may reversibly bind nitric oxide (NO) and be involved in NO transport. This entry also includes the beta-barrel domain of Caenorhabditis elegans protein male abnormal 7 (Mab-7) which plays an important role in determining body shape and sensory ray morphology. Nitrobindins (Nbs), constituting a heme-protein family spanning from bacteria to Homo sapiens, display an all-beta-barrel structural organization. Proteins containing this domain are putatively related to fatty acid-binding proteins (FABPs). 151 matched cddid_all.tbl CDD pfam08769 pfam08769 462594 Spo0A_C Sporulation initiation factor Spo0A C terminal. The response regulator Spo0A is comprised of a phophoacceptor domain and a transcription activation domain. This domain corresponds to the transcription activation domain and forms an alpha helical structure comprising of 6 alpha helices. The structure contains a helix-turn-helix and binds DNA. 104 matched cddid_all.tbl CDD pfam08770 pfam08770 462595 SoxZ Sulphur oxidation protein SoxZ. SoxZ forms an anti parallel beta structure and forms a complex with SoxY. Sulphur oxidation occurs at the thiol of a conserved cysteine residue of the SoxY subunit. 94 matched cddid_all.tbl CDD pfam08771 pfam08771 462596 FRB_dom FKBP12-rapamycin binding domain. The macrolide antibiotic rapamycin and the cytosol protein FKBP12 can form a complex which specifically inhibits the TORC1 complex, leading to growth arrest. The FKBP12-rapamycin complex interferes with TORC1 function by binding to the FKBP12-rapamycin binding domain (FRB) of the TOR proteins. This entry represents the FRB domain. 98 matched cddid_all.tbl CDD pfam08772 pfam08772 462597 NOB1_Zn_bind Nin one binding (NOB1) Zn-ribbon like. This domain corresponds to a zinc ribbon and is found on the RNA binding protein NOB1 (Nin one binding). 72 matched cddid_all.tbl CDD pfam08773 pfam08773 462598 CathepsinC_exc Cathepsin C exclusion domain. Cathepsin C (dipeptidyl peptidase I) is the physiological activator of a group of serine proteases. This domain corresponds to the exclusion domain whose structure excludes the approach of a polypeptide apart from its termini. It forms an enclosed beta barrel structure composed from 8 anti-parallel beta strands. Based on a structural comparison and interaction data, it is suggested that the exclusion domain originates from a metallo-protease inhibitor. 118 matched cddid_all.tbl CDD pfam08774 pfam08774 430209 VRR_NUC VRR-NUC domain. 115 matched cddid_all.tbl CDD pfam08775 pfam08775 430210 ParB ParB family. ParB is a component of the par system which mediates accurate DNA partition during cell division. It recognizes A-box and B-box DNA motifs. ParB forms an asymmetric dimer with 2 extended helix-turn-helix (HTH) motifs that bind to A-boxes. The HTH motifs emanate from a beta sheet coiled coil DNA binding module. Both DNA binding elements are free to rotate around a flexible linker, this enables them to bind to complex arrays of A- and B-box elements on adjacent DNA arms of the looped partition site. 125 matched cddid_all.tbl CDD pfam08776 pfam08776 462599 VASP_tetra VASP tetramerization domain. Vasodilator-stimulated phosphoprotein (VASP) is an actin cytoskeletal regulatory protein. This region corresponds to the tetramerization domain which forms a right handed alpha helical coiled coil structure. 35 matched cddid_all.tbl CDD pfam08777 pfam08777 400913 RRM_3 RNA binding motif. This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif. 102 matched cddid_all.tbl CDD pfam08778 pfam08778 430212 HIF-1a_CTAD HIF-1 alpha C terminal transactivation domain. Hypoxia inducible factor-1 alpha (HIF-1 alpha) is the regulatory subunit of the heterodimeric transcription factor HIF-1. It plays a key role in cellular response to low oxygen tension. This region corresponds to the C terminal transactivation domain. 37 matched cddid_all.tbl CDD pfam08779 pfam08779 462600 bCoV_NS7A Betacoronavirus NS7A protein. This entry corresponds to the Human SARS virus NS7A protein (also known as 7a, accessory protein 7a, X4 and U122). The structure of this protein shows similarities to the immunoglobulin like fold and a known member of the immunoglobulin (Ig) domain superfamily, which suggests a binding activity to integrin I domains. In SARS-CoV-infected cells, the NS7A protein is expressed and retained intra-cellularly within the Golgi network. NS7A has been implicated to function during the replication cycle of SARS-CoV. 107 matched cddid_all.tbl CDD pfam08780 pfam08780 430213 NTase_sub_bind Nucleotidyltransferase substrate binding protein like. Nucleotidyltransferases (EC 2.7.7) comprise a large enzyme family with diverse roles in polynucleotide synthesis and modification. This domain is structurally related to kanamycin nucleotidyltransferase (KNTase) and forms a complex with HI0073, a sequence homolog of the nucleotide-binding domain of this nucleotidyltransferase superfamily. 126 matched cddid_all.tbl CDD pfam08781 pfam08781 462601 DP Transcription factor DP. DP forms a heterodimer with E2F and regulates genes involved in cell cycle progression. The transcriptional activity of E2F is inhibited by the retinoblastoma protein which binds to the E2F-DP heterodimer and negatively regulates the G1-S transition. 138 matched cddid_all.tbl CDD pfam08782 pfam08782 462602 c-SKI_SMAD_bind c-SKI Smad4 binding domain. c-SKI is an oncoprotein that inhibits TGF-beta signaling through interaction with Smad proteins. This domain binds to Smad4 94 matched cddid_all.tbl CDD pfam08783 pfam08783 462603 DWNN DWNN domain. DWNN is a ubiquitin like domain found at the N terminus of the RBBP6 family of splicing-associated proteins. The DWNN domain is independently expressed in higher vertebrates so it may function as a novel ubiquitin-like modifier of other proteins. 74 matched cddid_all.tbl CDD pfam08784 pfam08784 400920 RPA_C Replication protein A C terminal. This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. 106 matched cddid_all.tbl CDD pfam08785 pfam08785 462604 Ku_PK_bind Ku C terminal domain like. The non-homologous end joining (NHEJ) pathway is one method by which double stranded breaks in chromosomal DNA are repaired. Ku is a component of a multi-protein complex that is involved in the NHEJ. Ku has affinity for DNA ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). This domain is found at the C terminal of Ku which binds to DNA-PKcs. 117 matched cddid_all.tbl CDD pfam08786 pfam08786 430218 DcrB DcrB. DcrB is a bacterial protein required for phages C1 and C6 adsorption. It may be involved in the opening or formation of diffusion channels in the outer membrane. Structurally, it consist of an antiparallel beta sheet with some alpha helical regions. 127 matched cddid_all.tbl CDD pfam08787 pfam08787 400923 Alginate_lyase2 Alginate lyase. Alginate lyases are enzymes that degrade the linear polysaccharide alignate. They cleave the glycosidic linkage of alignate through a beta-elimination reaction. This family forms an all beta fold and is different to all alpha fold of pfam05426. 222 matched cddid_all.tbl CDD pfam08788 pfam08788 430219 NHR2 NHR2 domain like. The NHR2 (Nervy homology 2) domain is found in the ETO protein where it mediates oligomerization and protein-protein interactions. It forms an alpha-helical tetramer. 67 matched cddid_all.tbl CDD pfam08789 pfam08789 285942 PBCV_basic_adap PBCV-specific basic adaptor domain. The small PBCV-specific basic adaptor domain is found fused to S/T protein kinases and the 2-Cysteine domain. 38 matched cddid_all.tbl CDD pfam08790 pfam08790 462605 zf-LYAR LYAR-type C2HC zinc finger. This C2HC zinc finger is found in LYAR proteins such as Swiss:Q08288 which are involved in cell growth regulation. 28 matched cddid_all.tbl CDD pfam08792 pfam08792 285944 A2L_zn_ribbon A2L zinc ribbon domain. This zinc ribbon domain is found associated with some viral A2L transcription factors. 33 matched cddid_all.tbl CDD pfam08793 pfam08793 285945 2C_adapt 2-cysteine adaptor domain. The virus-specific 2-cysteine adaptor domain is found fused to OTU/A20-like peptidases and S/T protein kinases. The domain associations of these proteins indicate that they might function as viral adaptors connecting the kinases and OTU/A20 peptidases to specific targets. 35 matched cddid_all.tbl CDD pfam08794 pfam08794 400925 Lipoprot_C Lipoprotein GNA1870 C terminal like. GNA1870 is a surface exposed lipoprotein in Neisseria meningitidis that and is a potent antigen of Meningococcus. The structure of the C terminal domain consists of an anti-parallel beta barrel overlaid by a short alpha helical region. 155 matched cddid_all.tbl CDD pfam08795 pfam08795 430221 DUF1796 Putative papain-like cysteine peptidase (DUF1796). 161 matched cddid_all.tbl CDD pfam08796 pfam08796 430222 DUF1797 Protein of unknown function (DUF1797). This is a domain of unknown function. It forms a central anti-parallel beta sheet with flanking alpha helical regions. 67 matched cddid_all.tbl CDD pfam08797 pfam08797 400928 HIRAN HIRAN domain. The HIRAN domain (HIP116, Rad5p N-terminal) is found in the N-terminal regions of the SWI2/SNF2 proteins typified by HIP116 and Rad5p. The HIRAN domain is found as a standalone protein in several bacteria and prophages, or fused to other catalytic domains, such as a nuclease of the restriction endonuclease fold and TDP1-like DNA phosphoesterases, in the eukaryotes. It has been predicted that this domain functions as a DNA-binding domain that probably recognizes features associated with damaged DNA or stalled replication forks 96 matched cddid_all.tbl CDD pfam08798 pfam08798 430223 CRISPR_assoc CRISPR associated protein. This domain forms an anti-parallel beta strand structure with flanking alpha helical regions. 210 matched cddid_all.tbl CDD pfam08799 pfam08799 462606 PRP4 pre-mRNA processing factor 4 (PRP4) like. This small domain is found on PRP4 ribonuleoproteins. PRP4 is a U4/U6 small nuclear ribonucleoprotein that is involved in pre-mRNA processing. 29 matched cddid_all.tbl CDD pfam08800 pfam08800 430225 VirE_N VirE N-terminal domain. This presumed domain is found at the N-terminus of VirE proteins. 133 matched cddid_all.tbl CDD pfam08801 pfam08801 400932 Nucleoporin_N Nup133 N terminal like. Nup133 is a nucleoporin that is crucial for nuclear pore complex (NPC) biogenesis. The N terminal forms a seven-bladed beta propeller structure. This family now contains other sized nucleoporins, including Nup155, Nup8, Nuo132, Nup15 and Nup170. 426 matched cddid_all.tbl CDD pfam08803 pfam08803 400933 ydhR Putative mono-oxygenase ydhR. ydhR is a homodimeric protein that comprises of a central four-stranded beta sheet and four surrounding alpha helices. It shows structural homology to the ActVA-Orf6 and YgiN proteins which indicates it could be a mono-oxygenase. 96 matched cddid_all.tbl CDD pfam08804 pfam08804 430226 gp32 gp32 DNA binding protein like. gp32 is a single stranded (ss) DNA binding protein in bacteriophage T4 that is essential for DNA replication, recombination and repair. The ssDNA binding cleft of gp32 comprises regions from three structural subdomains. 201 matched cddid_all.tbl CDD pfam08805 pfam08805 430227 PilS PilS N terminal. Type IV pili are bacterial virulence-associated adhesins that promote bacterial attachment to host cells. In Salmonella typhi, the structural pilin protein PilS interacts with the cystic fibrosis transmembrane conductance regulator. Mutagenesis studies suggest that residues on an alpha-beta loop and the C terminal disulphide-bonded region of PilS might be involved in binding specificity of the pilus. 138 matched cddid_all.tbl CDD pfam08806 pfam08806 462607 Sep15_SelM Sep15/SelM redox domain. Sep15 and SelM are eukaryotic selenoproteins that have a thioredoxin-like domain and a surface accessible active site redox motif. This suggests that they function as thiol-disulphide isomerases involved in disulphide bond formation in the endoplasmic reticulum. Structurally it resembles the thioredoxin-fold. 75 matched cddid_all.tbl CDD pfam08807 pfam08807 400936 DUF1798 Bacterial domain of unknown function (DUF1798). This domain is found in many hypothetical proteins. The structure of one of the proteins in this family has been solved and it adopts an all alpha helical fold. 108 matched cddid_all.tbl CDD pfam08808 pfam08808 400937 RES RES domain. This presumed domain contains 3 highly conserved polar groups that could form an active site. These are an arginine, glutamate and serine, hence the RES domain. The domain is found widely distributed in bacteria. The domain is about 150 residues in length. 154 matched cddid_all.tbl CDD pfam08809 pfam08809 400938 DUF1799 Phage related hypothetical protein (DUF1799). Members of this family are about 100 amino acids in length and are uncharacterized. 75 matched cddid_all.tbl CDD pfam08810 pfam08810 430229 KapB Kinase associated protein B. This bacterial protein forms an anti-parallel beta sheet with an extending alpha helical region. 111 matched cddid_all.tbl CDD pfam08811 pfam08811 430230 DUF1800 Protein of unknown function (DUF1800). This is a family of large bacterial proteins of unknown function. 438 matched cddid_all.tbl CDD pfam08812 pfam08812 430231 YtxC YtxC-like family. This family includes proteins similar to B. subtilis YtxC an uncharacterized protein. 215 matched cddid_all.tbl CDD pfam08813 pfam08813 370135 Phage_tail_3 Phage tail tube protein, TTP. This is a family of phage tail tube proteins. A few members have an associated bacterial Ig-like domain, pfam02368, at their C-terminus. 165 matched cddid_all.tbl CDD pfam08814 pfam08814 430232 XisH XisH protein. The fdxN element, along with two other DNA elements, is excised from the chromosome during heterocyst differentiation in cyanobacteria. The xisH as well as the xisF and xisI genes are required. 133 matched cddid_all.tbl CDD pfam08815 pfam08815 462608 Nuc_rec_co-act Nuclear receptor coactivator. This region is found on eukaryotic nuclear receptor coactivators and forms an alpha helical structure. 47 matched cddid_all.tbl CDD pfam08816 pfam08816 430234 Ivy Inhibitor of vertebrate lysozyme (Ivy). This bacterial family is a strong inhibitor of vertebrate lysozyme. 117 matched cddid_all.tbl CDD pfam08817 pfam08817 430235 YukD WXG100 protein secretion system (Wss), protein YukD. The YukD protein family members participate in the formation of a translocon required for the secretion of WXG100 proteins (pfam06013) in monoderm bacteria, with the WXG100 protein secretion system (Wss). Like the cytoplasmic protein EsaC in Staphylococcus aureus, YukD was hypothesized to play a role of a chaperone. YukD adopts a ubiquitin-like fold. Usually, ubiquitin covalently binds to protein and flags them for protein degradation, however conjugation assays have indicated that the classical YukD lacks the capacity for covalent bond formation with other proteins. In contrast to the situation in firmicutes, YukD-like proteins in actinobacteria are often fused to a transporter involved in the ESAT-6/ESX/Wss secretion pathway. Members of the YukD family are also associated in gene neighborhoods with other enzymatic members of the ubiquitin signaling and degradation pathway such as the E1, E2 and E3 trienzyme complex that catalyze ubiquitin transfer to substrates, and the JAB family metallopeptidases that are involved in its release. This suggests that a subset of the YukD family in bacteria are conjugated and released from proteins as in the eukaryotic ubiquitin-mediated signaling and degradation pathway. 77 matched cddid_all.tbl CDD pfam08818 pfam08818 430236 DUF1801 Domain of unknown function (DU1801). This domain is found in the Intracellular iron chaperone frataxin YdhG and the uncharacterized protein YdeI from Bacillus subtilis. 94 matched cddid_all.tbl CDD pfam08819 pfam08819 430237 DUF1802 Domain of unknown function (DUF1802). The function of this family is unknown. This region is found associated with a pfam04471 suggesting they could be part of a restriction modification system.. 175 matched cddid_all.tbl CDD pfam08820 pfam08820 430238 DUF1803 Domain of unknown function (DUF1803). This small domain is found in one or two copies in proteins from bacteria. The function of this domain is unknown. 91 matched cddid_all.tbl CDD pfam08821 pfam08821 462609 CGGC CGGC domain. This putative domain contains a quite highly conserved sequence of CGGC in its central region. The domain has many conserved cysteines and histidines suggestive of a zinc binding function. 105 matched cddid_all.tbl CDD pfam08822 pfam08822 400949 DUF1804 Protein of unknown function (DUF1804). This family of bacterial protein is uncharacterized. 164 matched cddid_all.tbl CDD pfam08823 pfam08823 430240 PG_binding_2 Putative peptidoglycan binding domain. This family may be a peptidoglycan binding domain. 74 matched cddid_all.tbl CDD pfam08824 pfam08824 462610 Serine_rich Serine rich protein interaction domain. This is a serine rich domain that is found in the docking protein p130(cas) (Crk-associated substrate). This domain folds into a four helix bundle which is associated with protein-protein interactions. 157 matched cddid_all.tbl CDD pfam08825 pfam08825 462611 E2_bind E2 binding domain. E1 and E2 enzymes play a central role in ubiquitin and ubiquitin-like protein transfer cascades. This is an E2 binding domain that is found on NEDD8 activating E1 enzyme. The domain resembles ubiquitin, and recruits the catalytic core of the E2 enzyme Ubc12 in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains. 81 matched cddid_all.tbl CDD pfam08826 pfam08826 117396 DMPK_coil DMPK coiled coil domain like. This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure. It plays a role in dimerization. 61 matched cddid_all.tbl CDD pfam08827 pfam08827 430243 DUF1805 Domain of unknown function (DUF1805). This domain is found in bacteria and archaea and has an N terminal tetramerization region that is composed of beta sheets. 62 matched cddid_all.tbl CDD pfam08828 pfam08828 462612 DSX_dimer Doublesex dimerization domain. Doublesex (DSX) is a transcription factor that regulates somatic sexual differences in Drosophila. The structure of this domain has revealed a novel dimeric arrangement of ubiquitin-associated folds that has not previously been identified in a transcription factor. 49 matched cddid_all.tbl CDD pfam08829 pfam08829 462613 AlphaC_N Alpha C protein N terminal. The alpha C protein (ACP) is found in Streptococcus and acts as an invasin which plays a role in the internalization and translocation of the organizm across human epithelial surfaces. Group B Streptococcus is the leading cause of diseases including bacterial pneumonia, sepsis and meningitis. The N terminal of ACP is associated with virulence and forms a beta sandwich and a three helix bundle. ACP consists of an N-terminal domain (170 amino acids) followed by a variable number of tandem repeats (82 amino acids each) and a C-terminal domain (45 amino acids) containing an LPXTG peptidoglycan-anchoring motif. This entry is the N-terminal domain of ACP (NtACP). NtACP can be further divided into two structurally distinct domains, D1 and D2. D1, the more distal (amino-terminal) portion, consists of a beta sandwich with strong structural homology to fibronectin's integrin-binding region (FnIII10). D2 consists of three antiparallel alpha helix coils containing a portion of the glycosaminoglycan (GAG)-binding domain adjacent to the repeat region. NtACP binds to heparin and GAGs only when it is covalently associated with the adjacent repeat region. NtACP's D1 region contains a K144- T145-D146 (KTD) motif, located within a loop region that is structurally analogous to the loop containing the RGD integrin-binding motif in FnIII10. Single mutation within the KTD motif (D146A), present in the D1 domain, reduces NtACP binding to a1b integrion. The a1b1-integrin is one of four collagen-binding I-domain-containing integrins. Structural analysis of the D1 domain, in particular the region containing the putative integrin-binding loop and KTD motif, shares a strong structural homology with the FnIII10's integrin-binding region. Amino acid sequence alignment of Alps indicates that KTD is highly conserved. 106 matched cddid_all.tbl CDD pfam08830 pfam08830 430245 DUF1806 Protein of unknown function (DUF1806). This is a bacterial family of uncharacterized proteins. The structure of one of the proteins in this family has been solved and it adopts a beta barrel-like structure. 112 matched cddid_all.tbl CDD pfam08831 pfam08831 462614 MHCassoc_trimer Class II MHC-associated invariant chain trimerization domain. The class II associated invariant chain peptide is required for folding and localization of MHC class II heterodimers. This domain is involved in trimerization of the ectoderm and interferes with DM/class II binding. The trimeric protein forms a cylindrical shape which is thought to be important for interactions between the invariant chain and class II molecules. 69 matched cddid_all.tbl CDD pfam08832 pfam08832 462615 SRC-1 Steroid receptor coactivator. This domain is found in steroid/nuclear receptor coactivators and contains two LXXLL motifs that are involved in receptor binding. The family includes SRC-1/NcoA-1, NcoA-2/TIF2, pCIP/ACTR/GRIP-1/AIB1. 87 matched cddid_all.tbl CDD pfam08833 pfam08833 462616 Axin_b-cat_bind Axin beta-catenin binding motif. This motif is found on the scaffolding protein Axin which is a component of the beta-catenin destruction complex. It competes with the tumour suppressor adenomatous polyposis coli protein (APC) for binding to beta-catenin. 35 matched cddid_all.tbl CDD pfam08837 pfam08837 462617 DUF1810 Protein of unknown function (DUF1810). This is a family of uncharacterized proteins. The structure of one of the members in this family has been solved and it adopts a mainly alpha helical structure. 136 matched cddid_all.tbl CDD pfam08838 pfam08838 430250 DUF1811 Protein of unknown function (DUF1811). This is a bacterial family of uncharacterized proteins. Some of the proteins are annotated as being transcriptional regulators (see Swiss:Q4MQL7, Swiss:Q65MA2). The structure of one of the proteins in this family has revealed a beta-barrel like structure with helix-turn-helix like motif. 100 matched cddid_all.tbl CDD pfam08839 pfam08839 462618 CDT1 DNA replication factor CDT1 like. CDT1 is a component of the replication licensing system and promotes the loading of the mini-chromosome maintenance complex onto chromatin. Geminin is an inhibitor of CDT1 and prevents inappropriate re-initiation of replication on an already fired origin. This region of CDT1 binds to Geminin. 172 matched cddid_all.tbl CDD pfam08840 pfam08840 430252 BAAT_C BAAT / Acyl-CoA thioester hydrolase C terminal. This catalytic domain is found at the C terminal of acyl-CoA thioester hydrolases and bile acid-CoA:amino acid N-acetyltransferases (BAAT). 211 matched cddid_all.tbl CDD pfam08841 pfam08841 430253 DDR Diol dehydratase reactivase ATPase-like domain. Diol dehydratase (DDH, EC:4.2.1.28) and its isofunctional homolog glycerol dehydratase (GDH, EC.4.2.1.30) are enzymes which catalyze the conversion of glycerol 1,2-propanediol, and 1,2-ethanediol to aldehydes. These reactions require coenzyme B12. Cleavage of the Co-C bond of coenzyme B12 by substrates or coenzyme analogues results in inactivation during which coenzyme B12 remains tightly bound to the apoenzyme. This family comprises of the large subunit of the diol dehydratase and glycerol dehydratase reactivating factors whose function is to reactivate the holoenzyme by exchange of a damaged cofactor for intact coenzyme. 328 matched cddid_all.tbl CDD pfam08842 pfam08842 400962 Mfa2 Fimbrillin-A associated anchor proteins Mfa1 and Mfa2. This family of proteins may be lipoproteins principally from bacilli. They are between 300 and 400 residues. Many Bacteroides-like bacterial species, including Porphyromonas gingivalis, the causal agent of periodontal infection, carry at least two types of fimbriae, namely FimA and Mfa1 fimbriae, following the names of their major subunit proteins. Normally, FimA fimbriae are long filaments that are easily detached from cells, whereas Mfa1 fimbriae are short filaments that are tightly bound to cells; however, in the absence of Mfa2 protein, the Mfa1 fimbriae are also very long and are not attached. Mfa2 and Mfa1 are associated with each other in whole P. gingivalis cells to the extent that Mfa2 is located on the cell surface and probably associated with Mfa1 fimbriae in such a way that it anchors the Mfa1 fimbriae to the cell surface and regulates Mfa1 filament length. 276 matched cddid_all.tbl CDD pfam08843 pfam08843 430254 AbiEii Nucleotidyl transferase AbiEii toxin, Type IV TA system. This family was recently identified as belonging to the nucleotidyltransferase superfamily. AbiEii is the cognate toxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is pfam13338. 239 matched cddid_all.tbl CDD pfam08844 pfam08844 400964 DUF1815 Domain of unknown function (DUF1815). This presumed domain is about 100 amino acids in length and is functionally uncharacterized. 98 matched cddid_all.tbl CDD pfam08845 pfam08845 370150 SymE_toxin Toxin SymE, type I toxin-antitoxin system. SymE (SOS-induced yjiW gene with similarity to MazE ) is an SOS-induced toxin. It inhibits cell growth, decreases protein synthesis and increases RNA degradation. It may play a role in the recycling of RNAs damaged under SOS response-inducing conditions. It is predicted to have an AbrB fold, similar to that of the antitoxin MazE. Its translation is repressed by the antisense RNA SymR, which acts as an antitoxin. 54 matched cddid_all.tbl CDD pfam08846 pfam08846 430255 DUF1816 Domain of unknown function (DUF1816). Swiss:Q4C9H3 is associated with the pfam01383 domain suggesting this presumed domain could have a role in phycobilisomes. 64 matched cddid_all.tbl CDD pfam08847 pfam08847 430256 Crr6 Chlororespiratory reduction 6. Chlororespiratory reduction 6 (Crr6) is a factor required for the assembly or stabilization of the chloroplast NAD(P)H dehydrogenase complex in Arabidopsis. 150 matched cddid_all.tbl CDD pfam08848 pfam08848 430257 DUF1818 Domain of unknown function (DUF1818). This presumed domain is found in a small family of cyanobacterial protein. These proteins are functionally uncharacterized. 113 matched cddid_all.tbl CDD pfam08849 pfam08849 462619 BrxA BrxA. BrxA is part of the phage resistance system BREX (Bacteriophage Exclusion). It shares structural homology with the RNA-binding antitermination protein NusB. 181 matched cddid_all.tbl CDD pfam08850 pfam08850 430259 DUF1820 Domain of unknown function (DUF1820). This family includes small functionally uncharacterized proteins around 100 amino acids in length. 97 matched cddid_all.tbl CDD pfam08852 pfam08852 370155 DUF1822 Protein of unknown function (DUF1822). This family of proteins are functionally uncharacterized. 370 matched cddid_all.tbl CDD pfam08853 pfam08853 430260 DUF1823 Domain of unknown function (DUF1823). This presumed domain is functionally uncharacterized. 111 matched cddid_all.tbl CDD pfam08854 pfam08854 430261 DUF1824 Domain of unknown function (DUF1824). This uncharacterized family of proteins are principally found in cyanobacteria. 124 matched cddid_all.tbl CDD pfam08855 pfam08855 430262 DUF1825 Domain of unknown function (DUF1825). This uncharacterized family of proteins are principally found in cyanobacteria. 103 matched cddid_all.tbl CDD pfam08856 pfam08856 430263 DUF1826 Protein of unknown function (DUF1826). These proteins are functionally uncharacterized. 198 matched cddid_all.tbl CDD pfam08857 pfam08857 430264 ParBc_2 Putative ParB-like nuclease. This domain is probably distantly related to pfam02195. Suggesting these uncharacterized proteins have a nuclease function. 159 matched cddid_all.tbl CDD pfam08858 pfam08858 430265 IDEAL IDEAL domain. This short domain is found at the C-terminus of proteins in the UPF0302 family. The domain is named after the sequence of the most conserved region in some members. The function of this domain is unknown. 36 matched cddid_all.tbl CDD pfam08859 pfam08859 430266 DGC DGC domain. This domain appears to be a zinc binding domain from the conservation of four potential chelating cysteines. The domain is named after a conserved central motif. The function of this domain is unknown. 103 matched cddid_all.tbl CDD pfam08860 pfam08860 430267 DUF1827 Domain of unknown function (DUF1827). This presumed domain has no known function. 91 matched cddid_all.tbl CDD pfam08861 pfam08861 430268 DUF1828 Domain of unknown function DUF1828. This presumed domain is functionally uncharacterized. 90 matched cddid_all.tbl CDD pfam08862 pfam08862 462620 DUF1829 Domain of unknown function DUF1829. This short domain is usually associated with pfam08861. 87 matched cddid_all.tbl CDD pfam08863 pfam08863 430270 YolD YolD-like protein. Members of this family are functionally uncharacterized. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from gram-negative bacteria. This family has been shown to belong to the WYL-like superfamily. 94 matched cddid_all.tbl CDD pfam08864 pfam08864 430271 UPF0302 UPF0302 domain. This family is known as UPF0302. It is currently uncharacterized. 105 matched cddid_all.tbl CDD pfam08865 pfam08865 430272 DUF1830 Domain of unknown function (DUF1830). This family of short proteins is functionally uncharacterized. 66 matched cddid_all.tbl CDD pfam08866 pfam08866 430273 DUF1831 Putative amino acid metabolism. Solution of the structure of the Lactobacillus plantarum protein from this family has indicated a potential new fold with remote similarities to TBP-like (TATA-binding protein) structures. This similarity, in combination with genomic context analysis, leads us to propose an involvement in amino-acid metabolism. The potentially novel fold is an alpha + beta fold comprising two beta sheets packed against a single helix. The enzyme is present in the cytosol. 110 matched cddid_all.tbl CDD pfam08867 pfam08867 430274 FRG FRG domain. This presumed domain contains a conserved N-terminal (F/Y)RG motif. It is functionally uncharacterized. 93 matched cddid_all.tbl CDD pfam08868 pfam08868 370164 YugN YugN-like family. This family of proteins related to B. subtilis YugN are functionally uncharacterized. 130 matched cddid_all.tbl CDD pfam08869 pfam08869 430275 XisI XisI protein. The fdxN element, along with two other DNA elements, is excised from the chromosome during heterocyst differentiation in cyanobacteria. The xisH as well as the xisF and xisI genes are required. 103 matched cddid_all.tbl CDD pfam08870 pfam08870 430276 DndE DNA sulphur modification protein DndE. DndE is a small protein of 126 residues. It is a putative carboxylase homologous to NCAIR synthetase. It is encoded by an operon that is associated with a sulphur-based modification to DNA. 110 matched cddid_all.tbl CDD pfam08872 pfam08872 430277 KGK KGK domain. This presumed domain is found in one or two copies in cyanobacterial proteins. It is named after a short sequence motif. 115 matched cddid_all.tbl CDD pfam08873 pfam08873 370167 Phage_Mu_Gp37 Bacteriophage Mu, Gp37. This family is represented by Bacteriophage Mu, Gp37 (also known as Probable tail terminator protein) which may stop tail tube polymerization by capping the rapidly polymerizing tail tube once it has reached its requisite length and prevent its depolymerization. This family also has prophages matches, such as the Gp37 protein from the FluMu prophage. 204 matched cddid_all.tbl CDD pfam08874 pfam08874 430278 DUF1835 Domain of unknown function (DUF1835). This family of proteins are functionally uncharacterized. 122 matched cddid_all.tbl CDD pfam08875 pfam08875 286019 DUF1833 Domain of unknown function (DUF1833). This family of proteins are functionally uncharacterized and are predicted to adopt an all-beta fold. They are often found in gene neighborhoods containing genes for an NlpC peptidase and a Ubiquitin domain predicted to be involved in tail assembly. 150 matched cddid_all.tbl CDD pfam08876 pfam08876 430279 DUF1836 Domain of unknown function (DUF1836). This family of proteins are functionally uncharacterized. 102 matched cddid_all.tbl CDD pfam08877 pfam08877 430280 MepB-like MepB-like. In Staphylococcus aureus MepB is encoded by the MepRAB operon. This operon has been shown to play a role in drug resistance and, although the functions of MepR and MapA are known, there is still little information regarding MepB's function. Structural studies have shown that this protein is structural similar to the PD-(D/E)XK family of endonucleases, although PD-(D/E)XK's catalytic active site residues are not conserved in MepB. MepB binds DNA and RNA, with a higher affinity for RNA and single stranded DNA than for double stranded DNA. The association of MepB with this drug resistance operon suggests that this protein is involved in antimicrobial response, role which is believed to be carried out through its interactions with nucleic acids. 122 matched cddid_all.tbl CDD pfam08878 pfam08878 378078 HamA HamA. Hachiman antiphage defense system has been described in Ralstonia solanacearum species complex (RSSC), and is composed of two genes, hamAB, which encode a protein of unknown function HamA, represented in this entry, and an helicase (HamB). Only one strain (KACC10722) from phylotype IV shows this system complete and both genes are organized in an operon. 230 matched cddid_all.tbl CDD pfam08879 pfam08879 462621 WRC WRC. The WRC domain, named after the conserved Trp-Arg-Cys motif, contains two distinctive features: a putative nuclear localization signal and a zinc-finger motif (C3H). It is suggested that the WRC domain functions in DNA binding. 42 matched cddid_all.tbl CDD pfam08880 pfam08880 462622 QLQ QLQ. The QLQ domain is named after the conserved Gln, Leu, Gln motif. The QLQ domain is found at the N-terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. This domain has thus been postulated to be involved in mediating protein interactions. 35 matched cddid_all.tbl CDD pfam08881 pfam08881 430283 CVNH CVNH domain. CyanoVirin-N Homology domains are found in the sugar-binding antiviral protein cyanovirin-N (CVN) as well as filamentous ascomycetes and in the fern Ceratopteris richardii. 101 matched cddid_all.tbl CDD pfam08882 pfam08882 430284 Acetone_carb_G Acetone carboxylase gamma subunit. Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO(2) to form acetoacetate. 114 matched cddid_all.tbl CDD pfam08883 pfam08883 430285 DOPA_dioxygen Dopa 4,5-dioxygenase family. This family of proteins are related to Swiss:P87064, a DOPA 4,5-dioxygenase that is involved in synthesis of betalain. DOPA-dioxygenase is the key enzyme involved in betalain biosynthesis. It converts 3,4-dihydroxyphenylalanine to betalamic acid, a yellow chromophore. 105 matched cddid_all.tbl CDD pfam08884 pfam08884 400994 Flagellin_D3 Flagellin D3 domain. This domain is found in the central portion bacterial flagellin FliC. The domain contains a structural motif called a beta-folium fold. Although no specific function is assigned to this domain its deletion leads to a reduction in filament stability. 88 matched cddid_all.tbl CDD pfam08885 pfam08885 430286 GSCFA GSCFA family. This family of proteins are functionally uncharacterized. They have been named GSCFA after a highly conserved N-terminal motif in the alignment. Distant similarity to the pfam00657 lipases suggests these proteins are likely to be enzymes. 237 matched cddid_all.tbl CDD pfam08886 pfam08886 462623 GshA Glutamate-cysteine ligase. This is a rare family of glutamate--cysteine ligases, EC:6.3.2.2, demonstrated first in Thiobacillus ferrooxidans and present in a few other Proteobacteria. It is the first of two enzymes for glutathione biosynthesis. It is also called gamma-glutamylcysteine synthetase. The structure of this family has been solved, and is similar to that of human glutathione synthetase and very different to gamma-glutamylcysteine synthetase from Escherichia coli. 402 matched cddid_all.tbl CDD pfam08887 pfam08887 400997 GAD-like GAD-like domain. This domain is functionally uncharacterized, but it appears to be distantly related to the GAD domain pfam02938. 102 matched cddid_all.tbl CDD pfam08888 pfam08888 430288 HopJ HopJ type III effector protein. Pathovars of Pseudomonas syringae interact with their plant hosts via the action of Hrp outer protein (Hop) effector proteins, injected into plant cells by the type III secretion system. The proteins in this family are called HopJ after the original member HopPmaJ. 109 matched cddid_all.tbl CDD pfam08889 pfam08889 430289 WbqC WbqC-like protein family. This family of proteins are functionally uncharacterized. However it is found in an O-antigen gene cluster in E. coli and other bacteria suggesting a role in O-antigen production. Feng et al. suggest that wbnG may code for a glycine transferase. 217 matched cddid_all.tbl CDD pfam08890 pfam08890 462624 Phage_TAC_5 Phage XkdN-like tail assembly chaperone protein, TAC. This is a family of phage tail assembly chaperone proteins, TACs, from Gram-positive bacteriophages, in particular PBSX from Firmicutes. 136 matched cddid_all.tbl CDD pfam08891 pfam08891 430291 YfcL YfcL protein. This family of proteins are functionally uncharacterized. THey are related to the short YfcL protein from E. coli. 83 matched cddid_all.tbl CDD pfam08892 pfam08892 430292 YqcI_YcgG YqcI/YcgG family. This family of proteins are functionally uncharacterized. The family include YqcI and YcgG from B. subtilis. The alignment contains a conserved FPC motif at the N-terminus and CPF at the C-terminus. 211 matched cddid_all.tbl CDD pfam08893 pfam08893 430293 DUF1839 Domain of unknown function (DUF1839). This family of proteins are functionally uncharacterized. 311 matched cddid_all.tbl CDD pfam08894 pfam08894 430294 DUF1838 Protein of unknown function (DUF1838). This family of proteins are functionally uncharacterized. 231 matched cddid_all.tbl CDD pfam08895 pfam08895 462625 DUF1840 Domain of unknown function (DUF1840). This family of proteins are functionally uncharacterized. 107 matched cddid_all.tbl CDD pfam08896 pfam08896 430296 DUF1842 Domain of unknown function (DUF1842). This domain is found at the N-terminus of proteins that are functionally uncharacterized. 110 matched cddid_all.tbl CDD pfam08897 pfam08897 462626 DUF1841 Domain of unknown function (DUF1841). This family of proteins are functionally uncharacterized. 135 matched cddid_all.tbl CDD pfam08898 pfam08898 430298 DUF1843 Domain of unknown function (DUF1843). This domain is found at the C-terminus of a family of proteins that are functionally uncharacterized. The presumed domain is about 60 amino acid residues in length and is found independently in some proteins. 52 matched cddid_all.tbl CDD pfam08899 pfam08899 430299 DUF1844 Domain of unknown function (DUF1844). This family of proteins are functionally uncharacterized. 76 matched cddid_all.tbl CDD pfam08900 pfam08900 430300 AcaB Transcriptional regulator AcaB. This family of proteins is found in the IncC family of broad-host-range plasmids which enables the spread of antibiotic resistance genes among human enteric pathogens. Recently, AcaB member has been characterized as a transcriptional regulator that plays a crucial role in the regulation of IncC conjugation. It is a DNA binding protein which binds upstream of the acaDB promoter to increase its transcription and, in turn, acaDB activates the transcription of IncC conjugation genes. Structurally, AcaB consists of two helical hairpins in tandem which assemble into an anti-parallel four-helix bundle to form a two-stranded antiparallel beta-sheet positioned parallel to the helices. This is structurally similar to bacterial transcription factors from the ribbon-helix-helix (RHH) superfamily. 214 matched cddid_all.tbl CDD pfam08901 pfam08901 430301 DUF1847 Protein of unknown function (DUF1847). This family of proteins are functionally uncharacterized. THey contain 4 N-terminal cysteines that may form a zinc binding domain. 157 matched cddid_all.tbl CDD pfam08902 pfam08902 430302 DUF1848 Domain of unknown function (DUF1848). This family of proteins are functionally uncharacterized. The C-terminus contains a cluster of cysteines that are similar to the iron-sulfur cluster found at the N-terminus of pfam04055. 262 matched cddid_all.tbl CDD pfam08903 pfam08903 430303 DUF1846 Domain of unknown function (DUF1846). This family of proteins are functionally uncharacterized. Some members of the family are annotated as ATP-dependent peptidases. However, we can find no support for this annotation. 489 matched cddid_all.tbl CDD pfam08904 pfam08904 430304 EipB_like EipB-like. This entry includes a group of bacterial proteins, including EipB from Brucella. EipB is a periplasmic protein that functions as part of a system required for cell envelope homeostasis. It adopts a beta-spiral fold, consisting of 14 beta-strands and 2 alpha-helices. 249 matched cddid_all.tbl CDD pfam08905 pfam08905 430305 DUF1850 Domain of unknown function (DUF1850). This family of proteins are functionally uncharacterized. Some members of this family appear to be misannotated as RocC an amino acid transporter from B. subtilis. 87 matched cddid_all.tbl CDD pfam08906 pfam08906 401014 DUF1851 Domain of unknown function (DUF1851). This domain is found at the C-terminus of a variety of proteins that are functionally uncharacterized. 72 matched cddid_all.tbl CDD pfam08907 pfam08907 430306 DUF1853 Domain of unknown function (DUF1853). This family of proteins are functionally uncharacterized. 283 matched cddid_all.tbl CDD pfam08908 pfam08908 430307 MesX Putative oxygenase MesX. This family represents MesX, the putative oxygenase component of an oxygen-dependent methionine synthase MesD. It is required for MesD for activity. 321 matched cddid_all.tbl CDD pfam08909 pfam08909 462627 DUF1854 Domain of unknown function (DUF1854). This potential domain is functionally uncharacterized. It is found at the C-terminus of a number of ATP transporter proteins suggesting this domain may be involved in ligand binding. 126 matched cddid_all.tbl CDD pfam08910 pfam08910 462628 Aida_N Aida N-terminus. This is the N-terminal domain of the axin interactor, dorsalization-associated protein family. 103 matched cddid_all.tbl CDD pfam08911 pfam08911 462629 NUP50 NUP50 (Nucleoporin 50 kDa). Nucleoporin 50 kDa (NUP50) acts as a cofactor for the importin-alpha:importin-beta heterodimer, which in turn allows for transportation of many nuclear-targeted proteins through nuclear pore complexes. The C terminus of NUP50 binds importin-beta through RAN-GTP, the N terminus binds the C terminus of importin-alpha, while a central domain binds importin-beta. NUP50:importin-alpha:importin-beta then binds cargo and can stimulate nuclear import. The N-terminal domain of NUP50 is also able to actively displace nuclear localization signals from importin-alpha. 71 matched cddid_all.tbl CDD pfam08912 pfam08912 462630 Rho_Binding Rho Binding. Rho Binding Domain is responsible for the recognition and binding of Rho binding domain-containing proteins (such as ROCK) to Rho, resulting in activation of the GTPase which in turn modulates the phosphorylation of various signalling proteins. This domain is within an amphipathic alpha-helical coiled-coil and interacts with Rho through predominantly hydrophobic interactions. 68 matched cddid_all.tbl CDD pfam08913 pfam08913 430312 VBS Vinculin Binding Site. Vinculin binding sites are predominantly found in talin and talin-like molecules, enabling binding of vinculin to talin, stabilising integrin-mediated cell-matrix junctions. Talin, in turn, links integrins to the actin cytoskeleton. The consensus sequence for Vinculin binding sites is LxxAAxxVAxxVxxLIxxA, with a secondary structure prediction of four amphipathic helices. The hydrophobic residues that define the VBS are themselves 'masked' and are buried in the core of a series of helical bundles that make up the talin rod. 125 matched cddid_all.tbl CDD pfam08914 pfam08914 286058 Myb_DNA-bind_2 Rap1 Myb domain. The Rap1 Myb domain adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function of this domain is unclear: it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions. 65 matched cddid_all.tbl CDD pfam08915 pfam08915 430313 tRNA-Thr_ED Archaea-specific editing domain of threonyl-tRNA synthetase. Archaea-specific editing domain of threonyl-tRNA synthetase, with marked structural similarity to D-amino acids deacylases found in eubacteria and eukaryotes. This domain can bind D-amino acids, and ensures high fidelity during translation. It is especially responsible for removing incorrectly attached serine from tRNA-Thr. The domain forms a fold that can be be defined as two layers of beta-sheets (a three-stranded sheet and a five-stranded sheet), with two alpha-helices located adjacent to the five-stranded sheet. 137 matched cddid_all.tbl CDD pfam08916 pfam08916 462631 Phe_ZIP Phenylalanine zipper. The phenylalanine zipper consists of aromatic side chains from ten phenylalanine residues that are stacked within a hydrophobic core. This zipper mediates dimerization of various proteins, such as APS and SH2-B/Lnk. 57 matched cddid_all.tbl CDD pfam08917 pfam08917 462632 ecTbetaR2 Transforming growth factor beta receptor 2 ectodomain. The Transforming growth factor beta receptor 2 ectodomain is a compact fold consisting of nine beta-strands and a single helix stabilized by a network of six intra strand disulphide bonds. The folding topology includes a central five-stranded antiparallel beta-sheet, eight-residues long at its centre, covered by a second layer consisting of two segments of two-stranded antiparallel beta-sheets (beta1-beta4, beta3-beta9). 103 matched cddid_all.tbl CDD pfam08918 pfam08918 430316 PhoQ_Sensor PhoQ Sensor. The PhoQ Sensor is required for the virulence of various Gram-negative bacteria by allowing interaction of PhoPQ with the intracellular membrane, resulting in remodelling of the bacterial cell surface and subsequent bacterial resistance to host antimicrobial peptides. The domain contains a major flat acidic surface, which binds to at least 3 calcium ions, neutralising the domain's negative charge and allowing interaction with the negatively charged membrane. This domain recognizes divalent metal cations, and antimicrobial cationic peptides (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 179 matched cddid_all.tbl CDD pfam08919 pfam08919 462633 F_actin_bind F-actin binding. The F-actin binding domain forms a compact bundle of four antiparallel alpha-helices, which are arranged in a left-handed topology. Binding of F-actin to the F-actin binding domain may result in cytoplasmic retention and subcellular distribution of the protein, as well as possible inhibition of protein function. 108 matched cddid_all.tbl CDD pfam08920 pfam08920 462634 SF3b1 Splicing factor 3B subunit 1. This family consists of several eukaryotic splicing factor 3B subunit 1 proteins, which associate with p14 through a C-terminus beta-strand that interacts with beta-3 of the p14 RNA recognition motif (RRM) beta-sheet, which is in turn connected to an alpha-helix by a loop that makes extensive contacts with both the shorter C-terminal helix and RRM of p14. This subunit is required for 'A' splicing complex assembly (formed by the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA) and 'E' splicing complex assembly. 114 matched cddid_all.tbl CDD pfam08921 pfam08921 430319 DUF1904 Domain of unknown function (DUF1904). This domain is found in a set of hypothetical bacterial proteins. 107 matched cddid_all.tbl CDD pfam08922 pfam08922 430320 DUF1905 Domain of unknown function (DUF1905). This domain is found in a set of hypothetical bacterial proteins. 78 matched cddid_all.tbl CDD pfam08923 pfam08923 462635 MAPKK1_Int Mitogen-activated protein kinase kinase 1 interacting. Mitogen-activated protein kinase kinase 1 interacting protein is a small subcellular adaptor protein required for MAPK signaling and ERK1/2 activation. The overall topology of this domain has a central five-stranded beta-sheet sandwiched between a two alpha-helix and a one alpha-helix layer. 119 matched cddid_all.tbl CDD pfam08924 pfam08924 430322 DUF1906 Domain of unknown function (DUF1906). This domain is found in a set of uncharacterized hypothetical bacterial proteins. 179 matched cddid_all.tbl CDD pfam08925 pfam08925 462636 DUF1907 Domain of Unknown Function (DUF1907). The structure of this domain displays an alpha-beta-beta-alpha four layer topology, with an HxHxxxxxxxxxH motif that coordinates a zinc ion, and an acetate anion at a site that likely supports the enzymatic activity of an ester hydrolase. 281 matched cddid_all.tbl CDD pfam08926 pfam08926 462637 DUF1908 Domain of unknown function (DUF1908). This domain is found in a set of hypothetical/structural eukaryotic proteins. 281 matched cddid_all.tbl CDD pfam08928 pfam08928 430325 DUF1910 Domain of unknown function (DUF1910). This domain is found in a set of hypothetical bacterial proteins. 117 matched cddid_all.tbl CDD pfam08929 pfam08929 462638 DUF1911 Domain of unknown function (DUF1911). This domain is found in a set of hypothetical bacterial proteins. 105 matched cddid_all.tbl CDD pfam08930 pfam08930 430327 DUF1912 Domain of unknown function (DUF1912). This domain has no known function. It is found in various Streptococcal proteins. 84 matched cddid_all.tbl CDD pfam08931 pfam08931 286074 Caudo_bapla_RBP Receptor-binding protein of phage tail base-plate Siphoviridae, head. Caudo_bapla_RBP is a family of proteins expressed from ORF18 of the Lactococcus P2-like phage. This is one of three protein species, shoulders, neck, and head, that form the phage tail base-plate. In the overall structure this head domain exists as six trimers, and is necessary for specific recognition of the receptors at the host cell surface. Siphoviridae are the P2-like Caudovirales of Lactococcus. This family now includes DUF1914. Family Baseplate, pfam16774, is the ORF15 or shoulder component of the base-plate complex. 262 matched cddid_all.tbl CDD pfam08933 pfam08933 255115 DUF1864 Domain of unknown function (DUF1864). This domain has no known function. It is found in various hypothetical and conserved domain proteins. 387 matched cddid_all.tbl CDD pfam08934 pfam08934 462639 Rb_C Rb C-terminal domain. The Rb C-terminal domain is required for high-affinity binding to E2F-DP complexes and for maximal repression of E2F-responsive promoters, thereby acting as a growth suppressor by blocking the G1-S transition of the cell cycle. This domain has a strand-loop-helix structure, which directly interacts with both E2F1 and DP1, followed by a tail segment that lacks regular secondary structure. 152 matched cddid_all.tbl CDD pfam08935 pfam08935 462640 VP4_2 Viral protein VP4 subunit. This domain is predominantly found in viral proteins from the family Picornaviridae. It is VP4 of the viral polyprotein which, in poliovirus, is part of the capsid that consists of 60 copies each of four proteins VP1, VP2, VP3, and VP4 arranged on an icosahedral lattice. VP4 is on the inside and differs from the others in being small, myristoylated and having an extended structure. Productive infection involves the externalization of the VP4, which is cleaved from the rest, along with the N-terminus of VP1. There thus seem to be three stages of the virus, ie a multi-step process for cell entry involving RNA translocation through a membrane channel formed by the externalized N termini of VP1. 84 matched cddid_all.tbl CDD pfam08936 pfam08936 462641 CsoSCA Carboxysome Shell Carbonic Anhydrase. Carboxysome Shell Carbonic Anhydrase is a bacterial carbonic anhydrase localized in the carboxysome, where it converts bicarbonate ions to carbon dioxide for use in carbon fixation. It contains three domains, these being: (1) an N-terminal domain composed primarily of four alpha-helices; (2) a catalytic domain containing a tightly bound zinc ion and (3) a C-terminal domain with weak structural similarity to the catalytic domain. 455 matched cddid_all.tbl CDD pfam08937 pfam08937 430330 DUF1863 MTH538 TIR-like domain (DUF1863). This domain adopts the flavodoxin fold, that is, five parallel beta-strands and four helical segments. The structure is a three-layer sandwich with alpha-1 and alpha-4 on one side of the beta-sheet, and alpha-2 and alpha-3 on the other side. Probable role in signal transduction as a phosphorylation-independent conformational switch protein. This domain is similar to the TIR domain. 127 matched cddid_all.tbl CDD pfam08938 pfam08938 462642 HBS1_N HBS1 N-terminus. This domain is found at the N-terminus of HBS1 proteins. It interacts with the ribosomal protein rpS3 at the mRNA entry site. 76 matched cddid_all.tbl CDD pfam08939 pfam08939 401038 DUF1917 Domain of unknown function (DUF1917). This domain is found in various hypothetical and basophilic leukaemia proteins. It has no known function. 258 matched cddid_all.tbl CDD pfam08940 pfam08940 430332 DUF1918 Domain of unknown function (DUF1918). This domain, found in various hypothetical bacterial proteins, has no known function. 58 matched cddid_all.tbl CDD pfam08941 pfam08941 430333 USP8_interact USP8 interacting. This domain interacts with the UBP deubiquitinating enzyme USP8. 179 matched cddid_all.tbl CDD pfam08942 pfam08942 430334 DUF1919 Domain of unknown function (DUF1919). This domain has no known function. It is found in various hypothetical and putative bacterial proteins. 191 matched cddid_all.tbl CDD pfam08943 pfam08943 430335 CsiD CsiD. This family consists of various bacterial proteins pertaining to the non-haem Fe(II)-dependent oxygenase family. Exact function is unknown, but a putative role includes involvement in the control of utilization of gamma-aminobutyric acid. 294 matched cddid_all.tbl CDD pfam08944 pfam08944 430336 p47_phox_C NADPH oxidase subunit p47Phox, C terminal domain. The C terminal domain of the phagocyte NADPH oxidase subunit p47Phox contains conserved PxxP motifs that allow binding to SH3 domains, with subsequent activation of the NADPH oxidase, and generation of superoxide, which plays a crucial role in host defence against microbial infection. 32 matched cddid_all.tbl CDD pfam08945 pfam08945 462643 Bclx_interact Bcl-x interacting, BH3 domain. This domain is a long alpha helix, required for interaction with Bcl-x. It is found in BAM, Bim and Bcl2-like protein 11. This domain is also known as the BH3 domain between residues 146 and 161. 38 matched cddid_all.tbl CDD pfam08946 pfam08946 430338 Osmo_CC Osmosensory transporter coiled coil. The osmosensory transporter coiled coil is a C-terminal domain found in various bacterial osmoprotective transporters, such as ProP, Proline/betaine transporter, Proline permease 2 and the citrate proton symporters. It adopts an antiparallel coiled-coil structure, and is essential for osmosensory and osmoprotectant transporter function. 45 matched cddid_all.tbl CDD pfam08947 pfam08947 462644 BPS BPS (Between PH and SH2). The BPS (Between PH and SH2) domain, comprised of 2 beta strands and a C-terminal helix, is an approximately 45 residue region found in the adaptor proteins Grb7/10/14 that mediates inhibition of the tyrosine kinase domain of the insulin receptor by binding of the N-terminal portion of the BPS domain to the substrate peptide groove of the kinase, acting as a pseudosubstrate inhibitor. 46 matched cddid_all.tbl CDD pfam08948 pfam08948 401047 PRD1_P5_spike_N Bacteriophage PRD1, P5, spike N-terminal. The spike structure of bacteriophage PRD1 is comprised of proteins P2, P5, and P31. P5 is an elongated multidomain trimer. This domain is found at the N-terminal of bacteriophage PRD1 spike protein P5 and mediates the interaction with protein P31. The C-terminal domain appears to contain the residues responsible for the trimerization of the protein. 126 matched cddid_all.tbl CDD pfam08949 pfam08949 401048 PRD1_P5_C Bacteriophage PRD1, spike protein P5, C-terminal. This domain is found at the C-terminal of bacteriophage PRD1 spike protein P5.. The spike structure of bacteriophage PRD1 is comprised of proteins P2, P5, and P31. P5 is an elongated multidomain trimer. This C-terminal domain appears to contain the residues responsible for the trimerization of the protein. 219 matched cddid_all.tbl CDD pfam08950 pfam08950 401049 DUF1861 Protein of unknown function (DUF1861). This hypothetical protein, found in bacteria and in the eukaryote Leishmania, has no known function. 295 matched cddid_all.tbl CDD pfam08951 pfam08951 430340 EntA_Immun Enterocin A Immunity. Gram-positive lactobacilli produce bacteriocins to kill closely-related competitor species. To protect themselves from the bacteriocidal activity of this molecule they co-express an immunity protein (for discussion of this operon see Bacteriocin_IIc pfam10439). The immunity protein structure is a soluble, cytoplasmic, antiparallel four alpha-helical globular bundle with a fifth, more flexible and more divergent C-terminal helical hair-pin. The C-terminal hair-pin recognizes the C-terminus of the producer bacteriocin and this interaction is sufficient to dis-orient the bacteriocin within the membrane and close up the permeabilising pore that on its own the bacteriocin creates. These immunity proteins interact in the same way with other bacteriocins, family Bacteriocin_II, pfam01721. Since many enterococci can produce more than one bacteriocin it seems likely that the whole operon can be carried on transferable plasmids. 68 matched cddid_all.tbl CDD pfam08952 pfam08952 286093 DUF1866 Domain of unknown function (DUF1866). This domain, found in Synaptojanin, has no known function. 146 matched cddid_all.tbl CDD pfam08953 pfam08953 462645 DUF1899 Domain of unknown function (DUF1899). This set of domains is found in various eukaryotic proteins. Function is unknown. 66 matched cddid_all.tbl CDD pfam08954 pfam08954 462646 Trimer_CC trimerization motif. This domain is predominantly found in the structural protein coronin, and is duplicated in some sequences. It appears to have the function of stabilising the topology of short coiled-coils in proteins. 52 matched cddid_all.tbl CDD pfam08955 pfam08955 401053 BofC_C BofC C-terminal domain. The C-terminal domain of the bacterial protein 'bypass of forespore C' contains a three-stranded beta-sheet and three alpha-helices. Its exact function is, as yet, unknown. 74 matched cddid_all.tbl CDD pfam08956 pfam08956 430343 DUF1869 Domain of unknown function (DUF1869). This domain is found in a set of hypothetical bacterial proteins. 56 matched cddid_all.tbl CDD pfam08958 pfam08958 401055 DUF1871 Domain of unknown function (DUF1871). This set of hypothetical proteins is produced by prokaryotes pertaining to the Bacillus genus. 77 matched cddid_all.tbl CDD pfam08960 pfam08960 430344 STIV_B116-like STIV B116-like. The sulfolobus turreted icosahedral virus (STIV) infects Sulfolobus species found in the hot springs of Yellowstone National Park. It has 37 ORFs including B116, whose function is unknown. The structure of B116 reveals a fold consisting of a five-stranded beta-sheet flanked on one side by three alpha helices. Two subunits come together to form a homodimer with a 10-stranded mixed beta-sheet, where the topology of the central strands resembles an unclosed beta-barrel. 100 matched cddid_all.tbl CDD pfam08961 pfam08961 430345 NRBF2 Nuclear receptor-binding factor 2, autophagy regulator. NRBF2 plays an essential role in autophagy, the cellular pathway that degrades long-lived proteins and other cytoplasmic contents through lysosomes. NRBF2 binds Atg14L - a Beclin-binding protein - directly via the MIT domain and enhances Atg14L-linked Vps34 kinase (a class III phosphatidylinositol-3 kinase) activity and autophagy induction. 200 matched cddid_all.tbl CDD pfam08962 pfam08962 430346 Rv2632c-like Rv2632c-like. This entry includes a set of Actinobacterial proteins, including Rv2632c from Mycobacterium tuberculosis that is strongly implicated in the onset of non-replicating persistence, and thereby latent tuberculosis. Rv2632c contains a dsRBD-like (2 layers alpha/beta) fold (PDBe:2fgg). It shares remarkable similarity with bacterial hibernation factors, despite very low sequence similarity. Based on this structure it was predicted that Rv1738, highly up-regulated in conditions that mimic the onset of persistence, helps trigger dormancy by association with the bacterial ribosome. 82 matched cddid_all.tbl CDD pfam08963 pfam08963 401059 DUF1878 Protein of unknown function (DUF1878). This domain is found in a set of hypothetical bacterial proteins. 110 matched cddid_all.tbl CDD pfam08964 pfam08964 401060 Crystall_3 Beta/Gamma crystallin. This family of beta/gamma crystallins includes the N-terminal domain of Dictyostelium discoideum Calcium-dependent cell adhesion molecule 1, which mediates cell-cell adhesion through homophilic interactions. 86 matched cddid_all.tbl CDD pfam08965 pfam08965 401061 DUF1870 Domain of unknown function (DUF1870). This domain is found in a set of hypothetical bacterial proteins. It contains a helix-turn-helix domain so may be a DNA-binding protein. 117 matched cddid_all.tbl CDD pfam08966 pfam08966 430347 DUF1882 Domain of unknown function (DUF1882). This domain is found in a set of hypothetical bacterial proteins. 72 matched cddid_all.tbl CDD pfam08967 pfam08967 370216 DUF1884 Domain of unknown function (DUF1884). This domain is found in a set of hypothetical bacterial proteins. It shows similarity to the N-terminus of ATP-synthase. 92 matched cddid_all.tbl CDD pfam08968 pfam08968 370217 DUF1885 Domain of unknown function (DUF1885). This domain is found in a set of hypothetical proteins produced by bacteria of the Bacillus genus. 131 matched cddid_all.tbl CDD pfam08969 pfam08969 462647 USP8_dimer USP8 dimerization domain. This domain is predominantly found in the amino terminal region of Ubiquitin carboxyl-terminal hydrolase 8 (USP8). It forms a five helical bundle that dimerizes. 113 matched cddid_all.tbl CDD pfam08970 pfam08970 370219 Sda Sporulation inhibitor A. Members of this protein family contain two antiparallel alpha helices that are linked by a highly structured inter-helix loop to form a helical hairpin; the structure is stabilized by numerous hydrophobic and electrostatic interactions. These sporulation inhibitors are antikinases that bind to the histidine kinase KinA phosphotransfer domain and act as a molecular barricade that inhibit productive interaction between the ATP binding site and the phosphorylatable KinA His residue. This results in the inhibition of sporulation (by preventing phosphorylation of spo0A). 45 matched cddid_all.tbl CDD pfam08971 pfam08971 401064 GlgS Glycogen synthesis protein. Members of this family are involved in glycogen synthesis in Enterobacteria. The structure of the polypeptide chain comprises a bundle of two parallel amphipathic helices, alpha-1 and alpha-3, and a short hydrophobic helix alpha-2 sandwiched between them. 66 matched cddid_all.tbl CDD pfam08972 pfam08972 312506 DUF1902 Domain of unknown function (DUF1902). Members of this family of prokaryotic proteins adopt a fold consisting of one alpha-helix and four beta-strands. Their function has not, as yet, been elucidated. 75 matched cddid_all.tbl CDD pfam08973 pfam08973 430349 TM1506 Domain of unknown function (DUF1893). A member of the deaminase fold that binds an unknown ligand in the crystal structure. The protein is ADP-ribosylated at a conserved aspartate. Contextual analysis suggests that the domain is likely to bind NAD or ADP ribose either to sense redox states or to function as a regulatory ADP ribosyltransferase. 126 matched cddid_all.tbl CDD pfam08974 pfam08974 430350 DUF1877 Domain of unknown function (DUF1877). This domain is found in a set of hypothetical bacterial proteins. 163 matched cddid_all.tbl CDD pfam08975 pfam08975 430351 2H-phosphodiest Domain of unknown function (DUF1868). This group of 2H-phosphodiesterases comprises a single family typified by the protein mlr3352 from M.loti. Members are also present in various alpha-proteobacteria, Synechocystis, Streptococcus and Chilo iridescent virus. The presence of a member of this predominantly bacterial group in a large eukaryotic DNA virus represents a potential case of horizontal transfer from a bacterial source into a virus. Several proteins of bacterial origin have been noticed in the insect viruses (L.M.Iyer, E.V.Koonin and L.Aravind, unpublished observations and these appear to have been acquired from endo-symbiotic or parasitic bacteria that share the same host cells with the viruses. Presence of 2H proteins in the proteomes of large DNA viruses (e.g. T4 57B protein and the Fowl-pox virus FPV025) may point to some role for these proteins in regulating the viral tRNA metabolism. Each member of this family contains an internal duplication, each of which contains an HXTX motif that defines the family. 116 matched cddid_all.tbl CDD pfam08976 pfam08976 401068 EF-hand_11 EF-hand domain. This domain is found predominantly in DJ binding proteins. 105 matched cddid_all.tbl CDD pfam08977 pfam08977 286116 BOFC_N Bypass of Forespore C, N terminal. The N-terminal domain of 'bypass of forespore C' is composed of a four-stranded beta-sheet covered by an alpha-helix. The beta-sheet has a beta2-beta1-beta4-beta3 topology, where strands beta1 and beta2 and strands beta3 and beta4 are connected by beta-turns, whereas strands beta2 and beta3 are joined by an alpha-helix that runs across one face of the beta-sheet. This domain is similar to the third immunoglobulin G-binding domain of protein G from Streptococcus, the latter belonging to a large and diverse group of cell surface-associated proteins that bind to immunoglobulins. It has been hypothesized that this domain may be a mediator of protein-protein interactions involved in proteolytic events at the cell surface. 49 matched cddid_all.tbl CDD pfam08978 pfam08978 401069 Reoviridae_Vp9 Reoviridae VP9. This domain is found in various VP9 viral outer-coat proteins. It has no known function. 280 matched cddid_all.tbl CDD pfam08979 pfam08979 430352 DUF1894 Domain of unknown function (DUF1894). Members of this family have an important role in methanogenesis. They assume an alpha-beta globular structure consisting of six beta-strands and three alpha-helices forming the secondary structural topological arrangement of alpha1-beta1-alpha2-beta2-beta3-beta4-beta5-beta6-alpha3. 85 matched cddid_all.tbl CDD pfam08980 pfam08980 430353 DUF1883 Domain of unknown function (DUF1883). Predicted ligand-binding domain of the PPC-like beta-sandwich fold. Observed in conserved gene neighbourhoods with diverse nucleotide-activated effector and related conflict systems, potentially recognizes invasive molecules and initiates system responses or directly triggers directly-associated effector domains. 86 matched cddid_all.tbl CDD pfam08982 pfam08982 430354 AtaL Acetylaranotin biosynthesis cluster protein L. This entry includes acetylaranotin biosynthesis cluster protein L (AtaL) from Aspergillus terreus, which is a non-ribosomal peptide synthetase. It is required for the biosynthesis of the toxin acetylaranotin, which is a disulfide bridged cyclic dipeptide. There are a number of steps in the biosyntheis of this epipolythiodioxopiperazine toxin from two phenylananines, but the specific function of AtaL has yet to be determined. homologs are also known from bacteria. 146 matched cddid_all.tbl CDD pfam08983 pfam08983 430355 V1R_C Vasopressin V1 receptor, C-terminal. This is the conserved C-terminal domain of Vasopressin V1a/b receptors (V1R), which is involved in receptor trafficking and facilitates the interaction between the intracellular loops of the receptor, the G proteins and coupling to phospholipase C. This domain is unstructured and may reflect its conformational plasticity that may be necessary for proper function of V1R. 48 matched cddid_all.tbl CDD pfam08984 pfam08984 462648 DUF1858 Domain of unknown function (DUF1858). This domain has no known function. It is found in various hypothetical bacterial proteins. 57 matched cddid_all.tbl CDD pfam08985 pfam08985 430357 DP-EP DP-EP family. The DP-EP family of proteins, formerly known as DUF1888 have been shown to catalyze a cleavage of an internal peptide bond. 120 matched cddid_all.tbl CDD pfam08986 pfam08986 462649 DUF1889 Domain of unknown function (DUF1889). This domain is found in a set of hypothetical bacterial proteins. They are probably cytoplasmic proteins. 96 matched cddid_all.tbl CDD pfam08987 pfam08987 370227 DUF1892 Protein of unknown function (DUF1892). Members of this family, that are synthesized by Saccharomycetes, adopt a structure consisting of a four-stranded beta-sheet, with strand order beta2-beta1-beta4-beta3, and two alpha-helices, with an overall topology of beta-beta-alpha-beta-beta-alpha. They have no known function. 107 matched cddid_all.tbl CDD pfam08988 pfam08988 430358 T3SS_needle_E Type III secretion system, cytoplasmic E component of needle. T3SS_needle_E is a family of proteins from the operon that builds and controls the needle of the injection system of type III secretion. The YscE protein, produced by the pathogen Yersinia, assumes a secondary structure composed of two anti-parallel alpha-helices separated by a flexible loop. The family is cytoplasmic and may help to stabilize and prevent early polymerization of the needle-protein F. 66 matched cddid_all.tbl CDD pfam08989 pfam08989 401076 DUF1896 Domain of unknown function (DUF1896). This domain is found in a set of hypothetical bacterial proteins. 142 matched cddid_all.tbl CDD pfam08990 pfam08990 462650 Docking Erythronolide synthase docking domain. Polyketide synthase (PKS) catalyzes the biosynthesis of polyketides, which are structurally and functionally diverse natural products in microorganizms and plants. Type I modular PKSs are the large, multifunctional enzymes responsible for the production of a diverse family of structurally rich and often biologically active natural products. The efficiency of acyl transfer at the interfaces of the individual PKS proteins is thought to be governed by helical regions, termed docking domains (dd). Two such N-terminal domains dimerize to form amphipathic parallel alpha-helical coiled coils: dimerization is essential for protein function. 29 matched cddid_all.tbl CDD pfam08991 pfam08991 430360 MTCP1 Mature-T-Cell Proliferation I type. Members of this family adopt a coiled coil structure, with two antiparallel alpha-helices that are tightly strapped together by two disulfide bridges at each end. The protein sequence shows a cysteine motif, required for the stabilization of the coiled-coil-like structure. Additional inter-helix hydrophobic contacts impart stability to this scaffold. The precise function of this eukaryotic domain is, as yet, unknown. MTCP1 is found in mitochondria. Mature-T-Cell Proliferation) is the first gene unequivocally identified in the group of uncommon leukemias with a mature phenotype. 58 matched cddid_all.tbl CDD pfam08992 pfam08992 401079 QH-AmDH_gamma Quinohemoprotein amine dehydrogenase, gamma subunit. Members of this family contain a cross-linked, proteinous quinone cofactor, cysteine tryptophylquinone, which is required for catalysis of the oxidative deamination of a wide range of aliphatic and aromatic amines. The domain assumes a globular secondary structure, with two short alpha-helices having many turns and bends. 75 matched cddid_all.tbl CDD pfam08993 pfam08993 401080 T4_Gp59_N T4 gene Gp59 loader of gp41 DNA helicase. Bacteriophage T4 gene-59 helicase assembly protein is required for recombination-dependent DNA replication, which is the predominant mode of DNA replication in the late stage of T4 infection. T4 gene-59 helicase assembly protein accelerates the loading of the T4 gene-41 helicase during DNA synthesis by the T4 replication system in vitro. T4 gene-59 helicase assembly protein binds to both T4 gene-41 helicase and T4 gene-32 single-stranded DNA binding protein, and to single and double-stranded DNA. The structure of T4 gene-59 helicase assembly protein reveals a novel alpha-helical bundle fold with two domains of similar size, this being the N-terminal domain that consists of six alpha-helices linked by loop segments and short turns. The surface of the domain contains large regions of exposed hydrophobic residues and clusters of acidic and basic residues. This domain has structural similarity to members of the high-mobility-group (HMG) family of DNA minor groove binding proteins including rat HMG1A and lymphoid enhancer-binding factor, and is required for binding of the helicase to the DNA minor groove. 93 matched cddid_all.tbl CDD pfam08994 pfam08994 401081 T4_Gp59_C T4 gene Gp59 loader of gp41 DNA helicase C-term. Bacteriophage T4 gene-59 helicase assembly protein is required for recombination-dependent DNA replication, which is the predominant mode of DNA replication in the late stage of T4 infection. T4 gene-59 helicase assembly protein accelerates the loading of the T4 gene-41 helicase during DNA synthesis by the T4 replication system in vitro. T4 gene-59 helicase assembly protein binds to both T4 gene-41 helicase and T4 gene-32 single-stranded DNA binding protein, and to single and double-stranded DNA. The structure of T4 gene-59 helicase assembly protein reveals a novel alpha-helical bundle fold with two domains of similar size, this being the C-terminal domain that consists of seven alpha-helices with short intervening loops and turns. The surface of the domain contains large regions of exposed hydrophobic residues and clusters of acidic and basic residues. The hydrophobic region on the 'bottom' surface of the domain near the C-terminal helix binds the leading strand DNA, whilst the hydrophobic region on the 'top' surface of the domain lies between the two arms of the fork DNA, allowing for T4 gene 41 helicase binding and assembly into a hexameric complex around the lagging strand. 109 matched cddid_all.tbl CDD pfam08995 pfam08995 117561 NIP_1 Necrosis inducing protein-1. Necrosis inducing protein-1, a fungal avirulence protein produced by plants, consists of two parts containing beta-sheets of two and three anti-parallel strands, respectively. Five intramolecular disulfide bonds, stabilize these parts and their position with respect to each other, providing a high level of stability. 82 matched cddid_all.tbl CDD pfam08996 pfam08996 462651 zf-DNA_Pol DNA Polymerase alpha zinc finger. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. Function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain. 184 matched cddid_all.tbl CDD pfam08997 pfam08997 462652 UCR_6-4kD Ubiquinol-cytochrome C reductase complex, 6.4kD protein. The ubiquinol-cytochrome C reductase complex (cytochrome bc1 complex) is an essential component of the mitochondrial cellular respiratory chain. This family represents the 6.4kD protein, which may be closely linked to the iron-sulphur protein in the complex and function as an iron-sulphur protein binding factor. 51 matched cddid_all.tbl CDD pfam08998 pfam08998 370234 Epsilon_antitox Bacterial epsilon antitoxin. The epsilon antitoxin, produced by various prokaryotes, forms part of a postsegregational killing system which is involved in the initiation of programmed cell death of plasmid-free cells. The protein is folded into a three-helix bundle that directly interacts with the zeta toxin, inactivating it. 89 matched cddid_all.tbl CDD pfam08999 pfam08999 286135 SP_C-Propep Surfactant protein C, N terminal propeptide. The N-terminal propeptide of surfactant protein C adopts an alpha-helical structure, with turn and extended regions. It's main function is the stabilization of metastable surfactant protein C (SP-C), since the latter can irreversibly transform from its native alpha-helical structure to beta-sheet aggregates and form amyloid-like fibrils. The correct intracellular trafficking of proSP-C has also been reported to depend on the propeptide. 96 matched cddid_all.tbl CDD pfam09000 pfam09000 401084 Cytotoxic Cytotoxic. The cytotoxic domain confers cytotoxic activity to proteins, enabling the formation of nucleolytic breaks in 16S ribosomal RNA. The structure of the domain reveals a highly twisted central beta-sheet elaborated with a short N-terminal alpha-helix. 82 matched cddid_all.tbl CDD pfam09001 pfam09001 430363 DUF1890 Domain of unknown function (DUF1890). This domain is found in a set of hypothetical archaeal proteins. 139 matched cddid_all.tbl CDD pfam09002 pfam09002 430364 DUF1887 Domain of unknown function (DUF1887). This domain is found in a set of hypothetical bacterial proteins. 386 matched cddid_all.tbl CDD pfam09003 pfam09003 430365 Arm-DNA-bind_1 Bacteriophage lambda integrase, Arm DNA-binding domain. The amino terminal domain of bacteriophage lambda integrase folds into a three-stranded, antiparallel beta-sheet that packs against a C-terminal alpha-helix, adopting a fold that is structurally related to the three-stranded beta-sheet family of DNA-binding domains (which includes the GCC-box DNA-binding domain and the N-terminal domain of Tn916 integrase). This domain is responsible for high-affinity binding to each of the five DNA arm-type sites and is also a context-sensitive modulator of DNA cleavage. 73 matched cddid_all.tbl CDD pfam09004 pfam09004 117570 ALKBH8_N Alkylated DNA repair protein alkB homolog 8, N-terminal. This domain is the N-terminal domain of Alkylated DNA repair protein alkB homolog 8 (ALKBH8) and its homologs. This domain corresponds to the basic alpha-helix located at the N-terminal of the RRM domain, which enhances its RNA binding affinity. 38 matched cddid_all.tbl CDD pfam09005 pfam09005 462653 DUF1897 Domain of unknown function (DUF1897). This domain is found in Psi proteins produced by Drosophila, and in various eukaryotic hypothetical proteins. It has no known function. 36 matched cddid_all.tbl CDD pfam09006 pfam09006 286141 Surfac_D-trimer Lung surfactant protein D coiled-coil trimerization. This domain, predominantly found in lung surfactant protein D, forms a triple-helical parallel coiled coil, and mediates trimerization of the protein. 46 matched cddid_all.tbl CDD pfam09007 pfam09007 462654 EBP50_C EBP50, C-terminal. This C terminal domain allows interaction of EBP50 with FERM (four-point one ERM) domains, resulting in the activation of Ezrin-radixin-moesin (ERM), with subsequent cytoskeletal modulation and cellular growth control. It includes a disordered section between two reasonably well conserved hydrophobic regions. 127 matched cddid_all.tbl CDD pfam09008 pfam09008 401088 Head_binding Head binding. The head binding domain found in the Phage P22 tailspike protein contains two regular beta-sheets, A and B, oriented nearly perpendicular to each other and composed of five and three strands respectively. The topology of the strands is exclusively antiparallel. The tailspike protein trimerizes through this domain, and the direction of the strands with respect to the molecular triad is almost parallel for beta-sheet A, whereas beta-sheet B is perpendicular to the triad, forming a dome-like structure. This domain is dispensable for thermostability and SDS resistance of the intact protein, and its deletion has only minor effects on tailspike folding kinetics. 103 matched cddid_all.tbl CDD pfam09009 pfam09009 430368 Exotox-A_cataly Exotoxin A catalytic. Members of this family, which are found in prokaryotic exotoxin A, catalyze the transfer of ADP ribose from nicotinamide adenine dinucleotide (NAD) to elongation factor-2 in eukaryotic cells, with subsequent inhibition of protein synthesis. 177 matched cddid_all.tbl CDD pfam09010 pfam09010 401090 AsiA Anti-Sigma Factor A. Anti-sigma factor A is a transcriptional inhibitor that inhibits sigma 70-directed transcription by weakening its interaction with the core of the host's RNA polymerase. It is an all-helical protein, composed of six helical segments and intervening loops and turns, as well as a helix-turn-helix DNA binding motif, although neither free anti-sigma factor nor anti-sigma factor bound to sigma-70 has been shown to interact directly with DNA. In solution, the protein forms a symmetric dimer of small (10.59 kDa) protomers, which are composed of helix and coil regions and are devoid of beta-strand/sheet secondary structural elements. 85 matched cddid_all.tbl CDD pfam09011 pfam09011 430369 HMG_box_2 HMG-box domain. This short 71 residue domain is an HMG-box domain. HMG-box domains mediate re-modelling of chromatin-structure. Mammalian HMG-box proteins are of two types: those that are non-sequence-specific DNA-binding proteins with two HMG-box domains and a long highly acidic C-tail; and a diverse group of sequence-specific transcription factor-proteins with either a single HMG-box or up to six copies, and no acidic C-tail. 72 matched cddid_all.tbl CDD pfam09012 pfam09012 462655 FeoC FeoC like transcriptional regulator. This family contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependant transcriptional repressor. 69 matched cddid_all.tbl CDD pfam09013 pfam09013 401093 YopH_N YopH, N-terminal. The N-terminal domain of YopH is a compact structure composed of four alpha-helices and two beta-hairpins. Helices alpha-1 and alpha-3 are parallel to each other and antiparallel to helices alpha-2 and alpha-4. This domain targets YopH for secretion from the bacterium and translocation into eukaryotic cells, and has phosphotyrosyl peptide-binding activity, allowing for recognition of p130Cas and paxillin. 123 matched cddid_all.tbl CDD pfam09014 pfam09014 430371 Sushi_2 Beta-2-glycoprotein-1 fifth domain. The fifth domain of beta-2-glycoprotein-1 (b2GP-1) is composed of four well-defined anti-parallel beta-strands and two short alpha-helices, as well as a long highly flexible loop. It plays an important role in the binding of b2GP-1 to negatively charged compounds and subsequent capture for binding of anti-b2GP-1 antibodies. 88 matched cddid_all.tbl CDD pfam09015 pfam09015 401095 NgoMIV_restric NgoMIV restriction enzyme. Members of this family are prokaryotic DNA restriction enzymes, exhibiting an alpha/beta structure, with a central region comprising a mixed six-stranded beta-sheet with alpha-helices on each side. A long 'arm' protrudes out of the core of the domain between strands beta2 and beta3 and is mainly involved in the tetramerization interface of the protein. These restriction enzymes recognize the double-stranded sequence GCCGGC and cleave after G-1. 275 matched cddid_all.tbl CDD pfam09016 pfam09016 430372 Pas_Saposin Pas factor saposin fold. Members of this family adopt a compact structure comprising five alpha helices. Charged and polar residues are exposed mostly on the surface, while most of the hydrophobic residues are buried inside the hydrophobic core of the helical bundle. The precise function of this domain is unknown, but it is has been shown to induce secretion of periplasmic proteins, especially collagenase. 73 matched cddid_all.tbl CDD pfam09017 pfam09017 117583 Transglut_prok Microbial transglutaminase. Microbial transglutaminase (MTG) catalyzes an acyl transfer reaction by means of a Cys-Asp diad mechanism, in which the gamma-carboxyamide groups of peptide-bound glutamine residues act as the acyl donors. The MTG molecule forms a single, compact domain belonging to the alpha+beta folding class, containing 11 alpha-helices and 8 beta-strands. The alpha-helices and the beta-strands are concentrated mainly at the amino and carboxyl ends of the polypeptide, respectively. These secondary structures are arranged so that a beta-sheet is surrounded by alpha-helices, which are clustered into three regions. 414 matched cddid_all.tbl CDD pfam09018 pfam09018 312535 Phage_Capsid_P3 P3 major capsid protein. The P3 major capsid protein adopts a 'double-barrel' structure comprising two eight-stranded viral beta-barrels or jelly rolls, each of which contains a 12-residue alpha-helix. This protein then trimerizes through a 'trimerization loop' sequence, and is incorporated within the viral capsid. 394 matched cddid_all.tbl CDD pfam09019 pfam09019 401096 EcoRII-C EcoRII C terminal. The C-terminal catalytic domain of the Restriction Endonuclease EcoRII has a restriction endonuclease-like fold with a central five-stranded mixed beta-sheet surrounded on both sides by alpha-helices. It cleaves DNA specifically at single 5' CCWGG sites. 165 matched cddid_all.tbl CDD pfam09020 pfam09020 286154 YopE_N YopE, N terminal. The N terminal YopE domain targets YopE for secretion from the bacterium and translocation into eukaryotic cells. 126 matched cddid_all.tbl CDD pfam09021 pfam09021 430373 HutP HutP. The HutP protein family regulates the expression of Bacillus 'hut' structural genes by an anti-termination complex, which recognizes three UAG triplet units, separated by four non-conserved nucleotides on the RNA terminator region. L-histidine and Mg2+ ions are also required. These proteins exhibit the structural elements of alpha/beta proteins, arranged in the order: alpha-alpha-beta-alpha-alpha-beta-beta-beta in the primary structure, and the four antiparallel beta-strands form a beta-sheet in the order beta1-beta2-beta3-beta4, with two alpha-helices each on the front (alpha1 and alpha2) and at the back (alpha3 and alpha4) of the beta-sheet. 128 matched cddid_all.tbl CDD pfam09022 pfam09022 286156 Staphostatin_A Staphostatin A. The staphostatin A polypeptide chain folds into a slightly deformed, eight-stranded beta-barrel, with strands beta-4 through beta-8 forming an antiparallel sheet while the N-terminus forms a a psi-loop motif. Members of this family constitute a class of cysteine protease inhibitors distinct in the fold and the mechanism of action from any known inhibitors of these enzymes. 105 matched cddid_all.tbl CDD pfam09023 pfam09023 462656 Staphostatin_B Staphostatin B. Staphostatin B inhibits the cysteine protease Staphopain B, produced by Staphylococcus aureus, by blocking the active site of the enzyme. The domain adopts an eight-stranded mixed beta-barrel structure, with a deviation from the up-down topology of canonical beta-barrels in the amino-terminal part of the molecule. 105 matched cddid_all.tbl CDD pfam09025 pfam09025 286158 T3SS_needle_reg YopR, type III needle-polymerization regulator. The YopR core domain, predominantly found in the Gammaproteobacteria virulence factor YopR, is composed of five alpha-helices, four of which are arranged in an antiparallel bundle. Little is known about this domain, though it may contribute to the virulence of the protein YopR. YopR controls the selective access of early (YscF, YscI and YscP) substrates to the type III secretion machines of yersiniae and other Gammaproteobacteriae. YopR is a mobile regulatory component thought to function as a checkpoints probing the completion of discrete intermediary stages in the assembly of the type III injection pathway. The location of secreted YopR (into the medium) is directly controlling the secretion of YscF, the polymerized needle protein pfam09392, thereby impacting the assembly of type III machines. 145 matched cddid_all.tbl CDD pfam09026 pfam09026 462657 CENP-B_dimeriz Centromere protein B dimerization domain. The centromere protein B (CENP-B) dimerization domain is composed of two alpha-helices, which are folded into an antiparallel configuration. dimerization of CENP-B is mediated by this domain, in which monomers dimerize to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation. 100 matched cddid_all.tbl CDD pfam09027 pfam09027 430374 GTPase_binding GTPase binding. The GTPase binding domain binds to the G protein Cdc42, inhibiting both its intrinsic and stimulated GTPase activity. The domain is largely unstructured in the absence of Cdc42. 66 matched cddid_all.tbl CDD pfam09028 pfam09028 430375 Mac-1 Mac 1. The bacterial protein Mac 1 adopts an alpha/beta fold, with 14 beta strands and 9 alpha helices. The N-terminal domain is made up predominantly of alpha helices, whereas the C-terminal domain consists predominantly of beta sheets. Mac 1 blocks polymorphonuclear opsonophagocytosis, inhibits the production of reactive oxygen species and contains IgG endopeptidase activity. 353 matched cddid_all.tbl CDD pfam09029 pfam09029 462658 Preseq_ALAS 5-aminolevulinate synthase presequence. The N terminal presequence domain found in 5-aminolevulinate synthase exists as an amphipathic helix, with a positively charged surface provided by lysine residues and no stable helix at the N-terminus. The domain is essential for the import process by which ALAS is transported into the mitochondria: translocase of the outer membrane (Tom) and translocase of the inner membrane protein complexes appear responsible for recognition and import through the mitochondrial membrane. The protein Tom20 is anchored to the mitochondrial outer membrane, and its interaction with presequences is thought to be the recognition step which allows subsequent import. 114 matched cddid_all.tbl CDD pfam09030 pfam09030 462659 Creb_binding Creb binding. The Creb binding domain assumes a structure comprising of three alpha-helices which pack in a bundle, exposing a hydrophobic groove between alpha-1 and alpha-3 within which complimentary domains found in the protein 'activator for thyroid hormone and retinoid receptors' (ACTR) can dock. Docking of these domains is required for the recruitment of RNA polymerase II and the basal transcription machinery. 111 matched cddid_all.tbl CDD pfam09032 pfam09032 462660 Siah-Interact_N Siah interacting protein, N terminal. The N terminal domain of Siah interacting protein (SIP) adopts a helical hairpin structure with a hydrophobic core stabilized by a classic knobs-and-holes arrangement of side chains contributed by the two amphipathic helices. Little is known about this domain's function, except that it is crucial for interactions with Siah. It has also been hypothesized that SIP can dimerize through this N terminal domain. 77 matched cddid_all.tbl CDD pfam09033 pfam09033 462661 DFF-C DNA Fragmentation factor 45kDa, C terminal domain. The C terminal domain of DNA Fragmentation factor 45kDa (DFF-C) consists of four alpha-helices, which are folded in a helix-packing arrangement, with alpha-2 and alpha-3 packing against a long C-terminal helix (alpha-4). The main function of this domain is the inhibition of DFF40 by binding to its C-terminal catalytic domain through ionic interactions, thereby inhibiting the fragmentation of DNA in the apoptotic process. In addition to blocking the DNase activity of DFF40, the C-terminal region of DFF45 is also important for the DFF40-specific folding chaperone activity, as demonstrated by the ability of DFF45 to refold DFF40. 164 matched cddid_all.tbl CDD pfam09034 pfam09034 430379 TRADD_N TRADD, N-terminal domain. The N terminal domain of 'Tumour necrosis factor receptor type 1 associated death domain protein' (TRADD) folds into an alpha-beta sandwich with a four-stranded beta sheet and six alpha helices, each forming one layer of the structure. The domain allows docking of TRADD onto 'tumour necrosis factor receptor-associated factor' (TRAF): the binding is at the beta-sandwich domain, away from the coiled-coil domain. Binding ensures the recruitment of cIAPs to the signaling complex, which may be important for direct caspase-8 inhibition and the immediate suppression of apoptosis at the apical point of the cascade. 112 matched cddid_all.tbl CDD pfam09035 pfam09035 286167 Tn916-Xis Excisionase from transposon Tn916. The phage-encoded excisionase protein Tn916-Xis adopts a winged-helix structure that consists of a three-stranded anti-parallel beta-sheet that packs against a helix-turn-helix (HTH) motif and a third C-terminal alpha-helix. It is encoded for by Tn916, which also codes for the integrase Tn916-Int. The protein interacts with DNA by the insertion of helix alpha-2 into the major groove and the contact of the hairpin that connects strands beta-2 and beta-3 with the adjacent phosphodiester backbone and/or minor groove. Tn916-Xis stimulates phage excision and inhibits viral integration by stabilising distorted DNA structures. 62 matched cddid_all.tbl CDD pfam09036 pfam09036 430380 Bcr-Abl_Oligo Bcr-Abl oncoprotein oligomerization domain. The Bcr-Abl oncoprotein oligomerization domain consists of a short N-terminal helix (alpha-1), a flexible loop and a long C-terminal helix (alpha-2). Together these form an N-shaped structure, with the loop allowing the two helices to assume a parallel orientation. The monomeric domains associate into a dimer through the formation of an antiparallel coiled coil between the alpha-2 helices and domain swapping of two alpha-1 helices, where one alpha-1 helix swings back and packs against the alpha-2 helix from the second monomer. Two dimers then associate into a tetramer. The oligomerization domain is essential for the oncogenicity of the Bcr-Abl protein. 73 matched cddid_all.tbl CDD pfam09037 pfam09037 430381 Sulphotransf Stf0 sulphotransferase. Members of this family are essential for the biosynthesis of sulpholipid-1 in prokaryotes. They adopt a structure that belongs to the sulphotransferase superfamily, consisting of a single domain with a core four-stranded parallel beta-sheet flanked by alpha-helices. 244 matched cddid_all.tbl CDD pfam09038 pfam09038 430382 53-BP1_Tudor Tumour suppressor p53-binding protein-1 Tudor. Members of this family consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. This domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3. 118 matched cddid_all.tbl CDD pfam09039 pfam09039 370256 HTH_Tnp_Mu_2 Mu DNA binding, I gamma subdomain. Members of this family are responsible for binding the DNA attachment sites at each end of the Mu genome. They adopt a secondary structure comprising a four helix bundle tightly packed around a hydrophobic core consisting of aliphatic and aromatic amino acid residues. Helices 1 and 2 are oriented antiparallel to each other. Helix 3 crosses helices 1 and 2 at angles of 60 and 120 degrees, respectively. Excluding the C-terminal helix 4, the fold of the I-gamma subdomain is remarkably similar to that of the homeodomain family of helix-turn-helix DNA-binding proteins, although their amino acid sequences are completely unrelated. 109 matched cddid_all.tbl CDD pfam09040 pfam09040 312544 H-K_ATPase_N Gastric H+/K+-ATPase, N terminal domain. Members of this family adopt an alpha-helical conformation under hydrophobic conditions. The domain contains tyrosine residues, phosphorylation of which regulates the function of the ATPase. Additionally, the domain also interacts with various structural proteins, including the spectrin-binding domain of ankyrin III. 43 matched cddid_all.tbl CDD pfam09041 pfam09041 430383 Aurora-A_bind Aurora-A binding. The Aurora-A binding domain binds to two distinct sites on the Aurora kinase: the upstream residues bind at the N-terminal lobe, whilst the downstream residues bind in an alpha-helical conformation between the N- and C-terminal lobes. The two Aurora-A binding motifs are connected by a flexible linker that is variable in length and sequence across species. Binding of the domain results strong activation of Aurora-A and protection from deactivating dephosphorylation by phosphatase PP1. 68 matched cddid_all.tbl CDD pfam09042 pfam09042 462662 Titin_Z Titin Z. The titin Z domain, that recognizes and binds to the C-terminal calmodulin-like domain of alpha-actinin-2 (Act-EF34), adopts a helical structure, and binds in a groove formed by the two planes between the helix pairs of Act-EF34. This interaction is essential for sarcomere assembly. 43 matched cddid_all.tbl CDD pfam09043 pfam09043 401110 Lys-AminoMut_A D-Lysine 5,6-aminomutase TIM-barrel domain of alpha subunit. Members of his family are involved in the 1,2 rearrangement of the terminal amino group of DL-lysine and of L-beta-lysine, using adenosylcobalamin (AdoCbl) and pyridoxal-5'-phosphate as co-factors. The structure is predominantly a PLP-binding TIM barrel domain, with several additional alpha-helices and beta-strands at the N and C termini. These helices and strands form an intertwined accessory clamp structure that wraps around the sides of the TIM barrel and extends up toward the Ado ligand of the Cbl co-factor, providing most of the interactions observed between the protein and the Ado ligand of the Cbl, suggesting that its role is mainly in stabilising AdoCbl in the precatalytic resting state. This is a TIM-barrel domain. 508 matched cddid_all.tbl CDD pfam09044 pfam09044 370259 Kp4 Kp4. Members of this fungal family of toxins specifically inhibit voltage-gated calcium channels in mammalian cells. They adopt an alpha/beta-sandwich structure, comprising a five-stranded antiparallel beta-sheet with two antiparallel alpha-helices lying at approximately 45 degrees to these strands. 123 matched cddid_all.tbl CDD pfam09045 pfam09045 312549 L27_2 L27_2. The L27_2 domain is a protein-protein interaction domain capable of organizing scaffold proteins into supramolecular assemblies by formation of heteromeric L27_2 domain complexes. L27_2 domain-mediated protein assemblies have been shown to play essential roles in cellular processes including asymmetric cell division, establishment and maintenance of cell polarity, and clustering of receptors and ion channels. Members of this family form specific heterotetrameric complexes, in which each domain contains three alpha-helices. The two N-terminal helices of each L27_2 domain pack together to form a tight, four-helix bundle in the heterodimer, whilst the third helix of each L27_2 domain forms another four-helix bundle that assembles the two units of the heterodimer into a tetramer. 58 matched cddid_all.tbl CDD pfam09046 pfam09046 401111 AvrPtoB-E3_ubiq AvrPtoB E3 ubiquitin ligase. The E3 ubiquitin ligase domain found in the bacterial protein AvrPtoB inhibits immunity-associated programmed cell death (PCD) when translocated into plant cells, probably by recruiting E2 enzymes and transferring ubiquitin molecules to cellular proteins involved in regulation of PCD and targeting them for degradation. The structure of this domain reveals a globular fold centred on a four-stranded beta-sheet that packs against two helices on one face and has three very extended loops connecting the elements of secondary structure, with remarkable homology to the RING-finger and U-box families of proteins involved in ubiquitin ligase complexes in eukaryotes. 118 matched cddid_all.tbl CDD pfam09047 pfam09047 370261 MEF2_binding MEF2 binding. The myocyte enhancer factor-2 (MEF2) binding domain, predominantly found in the calcineurin-binding protein CABIN 1, adopts an amphipathic alpha-helical structure, which allows it to bind a hydrophobic groove on the MEF2S domain, forming a triple-helical interaction. Interaction of this domain with MEF2 causes repression of transcription. 35 matched cddid_all.tbl CDD pfam09048 pfam09048 430385 Cro Cro. Members of this family are involved in the repression of transcription by binding as a homodimer to palindromic DNA operator sites in phage lambda: they repress genes expressed in early phage development and are necessary for the late stage of lytic growth. These proteins have a secondary structure consisting of three alpha-helices and three beta-sheets, and dimerize through interactions between the two antiparallel beta-strands. 59 matched cddid_all.tbl CDD pfam09049 pfam09049 401113 SNN_transmemb Stannin transmembrane. Members of this family consist of a single highly hydrophobic transmembrane helix that transverses the lipid bilayer at a 20 degree angle with respect to the membrane normal. They contain a conserved cysteine residue (Cys32) that, together with Cys34 found in the stannin unstructured linker domain, constitutes the putative trimethyltin-binding site that resides at the end of the transmembrane domain close to the lipid/solvent interface. 32 matched cddid_all.tbl CDD pfam09050 pfam09050 370263 SNN_linker Stannin unstructured linker. Members of this family are unstructured, acting as connectors of the stannin helical domains. They contain a conserved CXC metal-binding motif and a putative 14-3-3-zeta binding domain. Upon coordinating dimethytin, considerable structural or dynamic changes in the flexible loop region of SNN may take place, recruiting other binding partners such as 14-3-3-zeta, and thereby initiating the apoptotic cascade. 26 matched cddid_all.tbl CDD pfam09051 pfam09051 401114 SNN_cytoplasm Stannin cytoplasmic. Members of this family consist of a distorted cytoplasmic helix that is partially absorbed into the plane of the lipid bilayer with a tilt angle of approximately 80 degrees from the membrane normal. They interact with the surface of the lipid bilayer, and contribute to the initiation of the apoptotic cascade on binding of the unstructured linker domain to dimethyltin. 26 matched cddid_all.tbl CDD pfam09052 pfam09052 401115 SipA SipA N-terminal domain. Salmonella invasion protein A is an actin-binding protein that contributes to host cytoskeletal rearrangements by stimulating actin polymerization and counteracting F-actin destabilising proteins. Members of this family possess an all-helical fold consisting of eight alpha-helices arranged so that six long, amphipathic helices form a compact fold that surrounds a final, predominantly hydrophobic helix in the middle of the molecule. 213 matched cddid_all.tbl CDD pfam09053 pfam09053 462663 CagZ CagZ. CagZ is a 23 kDa protein consisting of a single compact L-shaped domain, composed of seven alpha-helices that run antiparallel to each other. 70% of the residues are in alpha-helix conformation and no beta-sheet is present. CagZ is essential for the translocation of the pathogenic protein CagA into host cells. 198 matched cddid_all.tbl CDD pfam09055 pfam09055 430386 Sod_Ni Nickel-containing superoxide dismutase. Nickel containing superoxide dismutase (NiSOD) is a metalloenzyme containing a hexameric assembly of right-handed 4-helix bundles of up-down-up-down topology with an N-terminal His-Cys-X-X-Pro-Cys-Gly-X-Tyr motif that chelates the active site Ni ions. NiSOD catalyzes the disproportionation of superoxide to peroxide and molecular oxygen through alternate oxidation and reduction of Ni, protecting cells from the toxic products of aerobic metabolism. 127 matched cddid_all.tbl CDD pfam09056 pfam09056 430387 Phospholip_A2_3 Prokaryotic phospholipase A2. The prokaryotic phospholipase A2 domain is predominantly found in bacterial and fungal phospholipases, as well as various hypothetical and putative proteins. It enables the liberation of fatty acids and lysophospholipid by hydrolysing the 2-ester bond of 1,2-diacyl-3-sn-phosphoglycerides. The domain adopts an alpha-helical secondary structure, consisting of five alpha-helices and two helical segments. 102 matched cddid_all.tbl CDD pfam09057 pfam09057 462664 Smac_DIABLO Second Mitochondria-derived Activator of Caspases. Second Mitochondria-derived Activator of Caspases promotes apoptosis by activating caspases in the cytochrome c/Apaf-1/caspase-9 pathway, and by opposing the inhibitory activity of inhibitor of apoptosis proteins (XIAP-BIR3). The protein assumes an elongated three-helix bundle structure, and forms a dimer in solution. 231 matched cddid_all.tbl CDD pfam09058 pfam09058 462665 L27_1 L27_1. The L27 domain is a protein interaction module that exists in a large family of scaffold proteins, functioning as an organization centre of large protein assemblies required for the establishment and maintenance of cell polarity. L27 domains form specific heterotetrameric complexes, in which each domain contains three alpha-helices. 59 matched cddid_all.tbl CDD pfam09059 pfam09059 401121 TyeA TyeA. Members of this family are composed of two pairs of parallel alpha-helices, and interact with the bacterial protein YopN via hydrophobic residues located on the helices. Association of TyeA with the C terminus of YopN is accompanied by conformational changes in both polypeptides that create order out of disorder: the resulting structure then serves as an impediment to type III secretion of YopN. 81 matched cddid_all.tbl CDD pfam09060 pfam09060 462666 L27_N L27_N. The L27_N domain plays a role in the biogenesis of tight junctions and in the establishment of cell polarity in epithelial cells. Each L27_N domain consists of three alpha-helices, the first two of which form an antiparallel coiled-coil. Two L27 domains come together to form a four-helical bundle with the antiparallel coiled-coils formed by the first two helices. The third helix of each domain forms another coiled-coil packing at one end of the four-helix bundle, creating a large hydrophobic interface: the hydrophobic interactions are the major force that drives heterodimer formation. 48 matched cddid_all.tbl CDD pfam09061 pfam09061 401123 Stirrup Stirrup. The Stirrup domain, found in the prokaryotic protein ribonucleotide reductase, has a molecular mass of 9 kDa and is folded into an alpha/beta structure. It allows for binding of the reductase to DNA via electrostatic interactions, since it has a predominance of positive charges distributed on its surface. 79 matched cddid_all.tbl CDD pfam09062 pfam09062 401124 Endonuc_subdom PI-PfuI Endonuclease subdomain. The endonuclease subdomain, found in the prokaryotic protein ribonucleotide reductase, assumes an alpha-beta-beta-alpha-beta-beta-alpha-alpha topology. The four stranded beta-sheet forms a saddle-shaped surface and assembles together through an interface made of alpha-helices. The presence of 14 basic residues on the surface of the beta-sheets suggests that this large groove may be involved in DNA binding. 98 matched cddid_all.tbl CDD pfam09063 pfam09063 401125 Phage_coat Phage PP7 coat protein. Members of this family form the capsid of P. aeruginosa phage PP7. They adopt a secondary structure consisting of a six stranded beta sheet and an alpha helix. 127 matched cddid_all.tbl CDD pfam09064 pfam09064 312559 Tme5_EGF_like Thrombomodulin like fifth domain, EGF-like. Members of this family adopt a fold similar to other EGF domains, with a flat major and a twisted minor beta sheet. Disulphide pairing, however, is not of the usual 1-3, 2-4, 5-6 type; rather 1-2, 3-4, 5-6 pairing is found. Its extended major sheet (strands beta-2 and beta-3 and the connecting loop) projects into thrombin's active site groove. This domain is required for interaction of thrombomodulin with thrombin, and subsequent activation of protein-C. 34 matched cddid_all.tbl CDD pfam09065 pfam09065 72483 Haemadin Haemadin. Members of this family adopt a secondary structure consisting of five short beta-strands (beta1-beta5), which are arranged in two antiparallel distorted sheets formed by strands beta1-beta4-beta5 and beta2-beta3 facing each other. This beta-sandwich is stabilized by six enclosed cysteines arranged in a [1-2, 3-5, 4-6] disulphide pairing resulting in a disulphide-rich hydrophobic core that is largely inaccessible to bulk solvent. The close proximity of disulfide bonds [3-5] and [4-6] organizes haemadin into four distinct loops. The N-terminal segment of this domain binds to the active site of thrombin, inhibiting it. 27 matched cddid_all.tbl CDD pfam09066 pfam09066 462667 B2-adapt-app_C Beta2-adaptin appendage, C-terminal sub-domain. Members of this family adopt a structure consisting of a 5 stranded beta-sheet, flanked by one alpha helix on the outer side, and by two alpha helices on the inner side. This domain is required for binding to clathrin, and its subsequent polymerization. Furthermore, a hydrophobic patch present in the domain also binds to a subset of D-phi-F/W motif-containing proteins that are bound by the alpha-adaptin appendage domain (epsin, AP180, eps15). 111 matched cddid_all.tbl CDD pfam09067 pfam09067 401127 EpoR_lig-bind Erythropoietin receptor, ligand binding. Members of this family interact with erythropoietin (EPO), with subsequent initiation of the downstream chain of events associated with binding of EPO to the receptor, including EPO-induced erythroblast proliferation and differentiation through induction of the JAK2/STAT5 signaling cascade. The domain adopts a secondary structure composed of a short amino-terminal helix, followed by two beta-sandwich regions. 104 matched cddid_all.tbl CDD pfam09068 pfam09068 462668 EF-hand_2 EF hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilization of the WW domain (pfam00397), enhancing dystroglycan binding. 123 matched cddid_all.tbl CDD pfam09069 pfam09069 462669 EF-hand_3 EF-hand. Members of this family adopt a helix-loop-helix motif, as per other EF hand domains. However, since they do not contain the canonical pattern of calcium binding residues found in many EF hand domains, they do not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilization of the WW domain (pfam00397), enhancing dystroglycan binding. 90 matched cddid_all.tbl CDD pfam09070 pfam09070 462670 PFU PFU (PLAA family ubiquitin binding). This domain is found N terminal to pfam08324 and binds to ubiquitin. 111 matched cddid_all.tbl CDD pfam09071 pfam09071 286197 Alpha-amyl_C Alpha-amylase, C terminal. Members of this family, which are found in the prokaryotic protein glycosyltrehalose trehalohydrolase, assume a gamma-crystallin-type fold with a five-stranded anti-parallel beta-sheet that packs against the C-terminal side of a beta-alpha barrel. This domain is common to family 13 glycosidases and typically contains a five to ten strand beta-sheet, however its precise fold varies. 67 matched cddid_all.tbl CDD pfam09072 pfam09072 462671 TMA7 Translation machinery associated TMA7. TMA7 plays a role in protein translation. Deletions of the TMA7 gene results in altered protein synthesis rates. 62 matched cddid_all.tbl CDD pfam09073 pfam09073 401132 BUD22 BUD22. BUD22 has been shown in yeast to be a nuclear protein involved in bud-site selection. It plays a role in positioning the proximal bud pole signal. More recently it has been shown to be involved in ribosome biogenesis. 426 matched cddid_all.tbl CDD pfam09074 pfam09074 401133 Mer2 Mer2. Mer2 (Rec107) forms part of a complex that is required for meiotic double strand DNA break formation. Mer2 increases in abundance and is phosphorylated during the prophase phase of cell division. Blocking double strand break formation results in delayed dephosphorylation and dissociation of Mer2 from the chromosome. 193 matched cddid_all.tbl CDD pfam09075 pfam09075 401134 STb_secrete Heat-stable enterotoxin B, secretory. Members of this family assume a helical secondary structure, with two alpha helices forming a disulphide crosslinked alpha-helical hairpin. The disulphide bonds are crucial for the toxic activity of the protein, and are required for maintenance of the tertiary structure, and subsequent interaction with the particulate form of guanylate cyclase, increasing cyclic GMP levels within the host intestinal epithelial cells. 48 matched cddid_all.tbl CDD pfam09076 pfam09076 370280 Crystall_2 Beta/Gamma crystallin. Members of this family assume a beta-gamma-crystallin fold, wherein nine beta-strands are connected by loop, and are separated into two sheets, each sheet forming the Greek key motif. The two Greek key motifs face each other in the global topology. The three-dimensional structure of the molecule is a 'sandwich'-shaped beta-barrel structure: hydrophobic side-chains are packed in the large interface area of the beta-sheets. In Streptomyces killer toxin-like protein domain confers a cytocidal effect to the toxin, causing cell death in both budding and fission yeasts, and morphological changes in yeasts and filamentous fungi. This family also includes chitin-biding antifungal proteins. 69 matched cddid_all.tbl CDD pfam09077 pfam09077 401135 Phage-MuB_C Mu B transposition protein, C terminal. The C terminal domain of the B transposition protein from Bacteriophage Mu comprises four alpha-helices arranged in a loosely packed bundle, where helix alpha1 runs parallel to alpha3, and anti-parallel to helices alpha2 and alpha4. The domain allows for non-specific binding of Mu to double-stranded DNA, allowing for integration into the bacterial genome, and mediates dimerization of the protein. 78 matched cddid_all.tbl CDD pfam09078 pfam09078 430396 CheY-binding CheY binding. Members of this family adopt a secondary structure consisting of an open-face beta/alpha sandwich, with four antiparallel beta-strands and two alpha-helices. They bind to a corresponding domain on CheY, with subsequent phosphorylation of the CheY Asp57 residue, and activation of CheY, which then affects flagellar rotation. 63 matched cddid_all.tbl CDD pfam09079 pfam09079 462672 Cdc6_C CDC6, C terminal winged helix domain. The C terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localization factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity. 84 matched cddid_all.tbl CDD pfam09080 pfam09080 401138 K-cyclin_vir_C K cyclin, C terminal. Members of this family adopt a secondary structure consisting of a five alpha-helix cyclin fold. Interaction with cyclin dependent kinases (CDKs) at a PSTAIRE sequence motif within the catalytic cleft of CDK results in the regulation of CDK activity. 104 matched cddid_all.tbl CDD pfam09081 pfam09081 462673 AMT4_dom_C Glucan 1,4-alpha-maltotetraohydrolase, domain C. This entry represents Domain C from Glucan 1,4-alpha- maltotetraohydrolase, which consists of five antiparallel beta-strands. 64 matched cddid_all.tbl CDD pfam09082 pfam09082 401140 DUF1922 Domain of unknown function (DUF1922). Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C-terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown. 65 matched cddid_all.tbl CDD pfam09083 pfam09083 462674 DUF1923 Domain of unknown function (DUF1923). Members of this family are found in maltosyltransferases, and adopt a secondary structure consisting of eight antiparallel beta-strands, which form an open-sided 'jelly roll' Greek key beta-barrel. Their exact function is, as yet, unknown. 64 matched cddid_all.tbl CDD pfam09084 pfam09084 430398 NMT1 NMT1/THI5 like. This family contains the NMT1 and THI5 proteins. These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine.3]. They are regulated by thiamine. The protein adopts a fold related to the periplasmic binding protein (PBP) family. Both pyridoxal-5'-phosphate (PLP) and an iron atom are bound to the protein suggesting numerous residues of the active site necessary for HMP-P biosynthesis. The yeast protein is a dimer and, although exceptionally using PLP as a substrate, has notable similarities with enzymes dependent on this molecule as a cofactor. 216 matched cddid_all.tbl CDD pfam09085 pfam09085 430399 Adhes-Ig_like Adhesion molecule, immunoglobulin-like. Members of this family are found in a set of mucosal cellular adhesion proteins and adopt an immunoglobulin-like beta-sandwich structure, with seven strands arranged in two beta-sheets in a Greek-key topology. They are essential for recruitment of lymphocytes to specific tissues. 110 matched cddid_all.tbl CDD pfam09086 pfam09086 430400 DUF1924 Domain of unknown function (DUF1924). This domain is found in a set of bacterial proteins, including Cytochrome c-type protein. It is functionally uncharacterized. 91 matched cddid_all.tbl CDD pfam09087 pfam09087 430401 Cyc-maltodext_N Cyclomaltodextrinase, N-terminal. Members of this family assume a beta-sandwich structure composed of the eight antiparallel beta-strands. A ten residue linker is also present at the C-terminal end, which connects the N terminal domain to a distal domain in the protein. This domain participates in oligomerization of the protein, wherein the N-terminal domain of one subunit contacts the active centre of the other subunit, and is also required for binding of cyclodextrin to substrate. 88 matched cddid_all.tbl CDD pfam09088 pfam09088 370287 MIF4G_like MIF4G like. Members of this family are involved in mediating U snRNA export from the nucleus. They adopt a highly helical structure, wherein the polypeptide chain forms a right-handed solenoid. At the tertiary level, the domain is composed of a superhelical arrangement of successive antiparallel pairs of helices. 191 matched cddid_all.tbl CDD pfam09089 pfam09089 430402 gp12-short_mid Phage short tail fibre protein gp12, middle domain. Members of this family adopt a right-handed triple-stranded beta-helix fold, and are found in the middle of the phage short tail fibre protein gp12. 81 matched cddid_all.tbl CDD pfam09090 pfam09090 462675 MIF4G_like_2 MIF4G like. Members of this family are involved in mediating U snRNA export from the nucleus. They adopt a highly helical structure, wherein the polypeptide chain forms a right-handed solenoid. At the tertiary level, the domain is composed of a superhelical arrangement of successive antiparallel pairs of helices. 262 matched cddid_all.tbl CDD pfam09092 pfam09092 430404 Lyase_N Lyase, N terminal. Members of this family are predominantly found in chondroitin ABC lyase I, and adopt a jelly-roll fold topology consisting of a two-layered bent beta-sheet sandwich with one short alpha-helix. The convex beta sheet is composed of five antiparallel strands, whilst the concave beta-sheet contains five antiparallel beta-strands with a loop between two consecutive strands folding back onto the concave surface. This domain is required for binding of the protein to long glycosaminoglycan chains. 166 matched cddid_all.tbl CDD pfam09093 pfam09093 430405 Lyase_catalyt Lyase, catalytic. Members of this family are predominantly found in chondroitin ABC lyase I, and adopt a helical structure, with fifteen alpha-helices which are at least two turns long and several short helical turns. The bulk of the domain is formed by ten alpha-helices forming five hairpin-like pairs and arranged into an incomplete toroid, the (alpha/alpha)5 fold. Additionally, two long and two short alpha-helices at the N terminus of the domain wrap around the toroid. At the C-terminal end of the toroid there is one additional short alpha-helix. This domain is required for degradation of polysaccharides containing 1,4-beta-D-hexosaminyl and 1,3-beta-D-glucoronosyl or 1,3-alpha-L-iduronosyl linkages to disaccharides containing 4-deoxy-beta-D-gluc-4-enuronosyl groups. 357 matched cddid_all.tbl CDD pfam09094 pfam09094 430406 AmyA-A_glucT_m Alpha-amylase/4-alpha-glucanotransferase, middle domain. This entry represents a domain found in prokaryotic alpha-amylase and 4-alpha-glucanotransferase. It is adjacent to the C-terminal domain (pfam09095). This domain adopts an immunoglobulin/ albumin-binding domain-like fold, with a bundle of three alpha-helices. Their function is, as yet, unknown. 78 matched cddid_all.tbl CDD pfam09095 pfam09095 430407 AmyA-gluTrfs_C Alpha-amylase/4-alpha-glucanotransferase, C-terminal. This entry represents a domain found in prokaryotic alpha-amylase and 4-alpha-glucanotransferase. It adopts a beta-sandwich fold, in which two layers of anti-parallel beta-sheets are arranged in a nearly parallel fashion. The exact function of this family is, as yet, unknown, however it has been proposed that they may play a role in transglycosylation reactions. 277 matched cddid_all.tbl CDD pfam09096 pfam09096 462676 Phage-tail_2 Baseplate structural protein, domain 2. Members of this family adopt a beta barrel structure with a Greek key topology, which is topologically similar to the FMN-binding split barrel. They are structural component of the viral baseplate, predominantly found in the structural protein gp27. 173 matched cddid_all.tbl CDD pfam09097 pfam09097 462677 Phage-tail_1 Baseplate structural protein, domain 1. Members of this family adopt a beta barrel structure with a Greek key topology, which is topologically similar to the FMN-binding split barrel. They are structural component of the viral baseplate, predominantly found in the structural protein gp27. 196 matched cddid_all.tbl CDD pfam09098 pfam09098 401149 Dehyd-heme_bind Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding. Members of this family are predominantly found in the prokaryotic protein quinohemoprotein amine dehydrogenase. They have a predominantly alpha-helical structure and can be divided into two subdomains, each binding a haem C group via a conserved CXXCH motif. 164 matched cddid_all.tbl CDD pfam09099 pfam09099 430408 Qn_am_d_aIII Quinohemoprotein amine dehydrogenase, alpha subunit domain III. Members of this family, which are predominantly found in the prokaryotic protein quinohemoprotein amine dehydrogenase, adopt an immunoglobulin-like beta-sandwich fold, with seven strands arranged into two beta sheets; the fold is possibly related to the immunoglobulin and/or fibronectin type III superfamilies. The precise function of this domain has not, as yet, been defined. 82 matched cddid_all.tbl CDD pfam09100 pfam09100 430409 Qn_am_d_aIV Quinohemoprotein amine dehydrogenase, alpha subunit domain IV. Members of this family, which are predominantly found in the prokaryotic protein quinohemoprotein amine dehydrogenase, adopt an immunoglobulin-like beta-sandwich fold, with seven strands arranged into two beta sheets; the fold is possibly related to the immunoglobulin and/or fibronectin type III superfamilies. The precise function of this domain has not, as yet, been defined. 133 matched cddid_all.tbl CDD pfam09101 pfam09101 286224 Exotox-A_bind Exotoxin A binding. Members of this family are found in Pseudomonas aeruginosa exotoxin A, and are responsible for binding of the toxin to the alpha-2-macroglobulin receptor, with subsequent internalization into endosomes. The domain adopts a thirteen-strand antiparallel beta jelly roll topology, which belongs to the Concanavalin A-like lectins/glucanases fold superfamily. 274 matched cddid_all.tbl CDD pfam09102 pfam09102 401151 Exotox-A_target Exotoxin A, targeting. Members of this family are found in Pseudomonas aeruginosa exotoxin A, and are responsible for transmembrane targeting of the toxin, as well as transmembrane translocation of the catalytic domain into the cytoplasmic compartment. A furin cleavage site is present within the domain: cleavage generates a 37 kDa carboxy-terminal fragment, which includes the enzymatic domain, which is then is translocated into the cytoplasm. The domain adopts a helical structure, with six alpha-helices forming a bundle. 142 matched cddid_all.tbl CDD pfam09103 pfam09103 462678 BRCA-2_OB1 BRCA2, oligonucleotide/oligosaccharide-binding, domain 1. Members of this family assume an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB1 has a shallow groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for weak single strand DNA binding. The domain also binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome. 123 matched cddid_all.tbl CDD pfam09104 pfam09104 462679 BRCA-2_OB3 BRCA2, oligonucleotide/oligosaccharide-binding, domain 3. Members of this family assume an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding. 139 matched cddid_all.tbl CDD pfam09105 pfam09105 462680 SelB-wing_1 Elongation factor SelB, winged helix. Members of this family adopt a winged-helix fold, with an alpha/beta structure consisting of three alpha-helices and a twisted three-stranded antiparallel beta-sheet, with an alpha-beta-alpha-alpha-beta-beta connectivity. They are involved in both DNA and RNA binding. 61 matched cddid_all.tbl CDD pfam09106 pfam09106 430412 SelB-wing_2 Elongation factor SelB, winged helix. Members of this family adopt a winged-helix fold, with an alpha/beta structure consisting of three alpha-helices and a twisted three-stranded antiparallel beta-sheet, with an alpha-beta-alpha-alpha-beta-beta connectivity. They are involved in both DNA and RNA binding. 57 matched cddid_all.tbl CDD pfam09107 pfam09107 430413 SelB-wing_3 Elongation factor SelB, winged helix. Members of this family adopt a winged-helix fold, with an alpha/beta structure consisting of three alpha-helices and a twisted three-stranded antiparallel beta-sheet, with an alpha-beta-alpha-alpha-beta-beta connectivity. They are involved in both DNA and RNA binding. 46 matched cddid_all.tbl CDD pfam09108 pfam09108 401156 Xol-1_N Switch protein XOL-1, N-terminal. Members of this family, which are required for the formation of the active site of the sex-determining protein Xol-1, adopt a secondary structure consisting of five alpha helices and six antiparallel beta sheets, in a beta-alpha-beta-beta-beta-alpha-beta-alpha-alpha-alpha-beta arrangement. The fold of this family is similar to that found in ribosomal protein S5 domain 2-like. 160 matched cddid_all.tbl CDD pfam09109 pfam09109 401157 Xol-1_GHMP-like Switch protein XOL-1, GHMP-like. Members of this family, which are required for the formation of the active site of the sex-determining protein Xol-1, adopt a secondary structure consisting of five alpha helices and seven antiparallel beta sheets, in a beta-alpha-beta-alpha-alpha-alpha-beta-beta-alpha-beta-beta-beta arrangement. The fold of this family is structurally similar to that found in the C-terminal domain of GHMP Kinase. 196 matched cddid_all.tbl CDD pfam09110 pfam09110 430414 HAND HAND. The HAND domain adopts a secondary structure consisting of four alpha helices, three of which (H2, H3, H4) form an L-like configuration. Helix H2 runs antiparallel to helices H3 and H4, packing closely against helix H4, whilst helix H1 reposes in the concave surface formed by these three helices and runs perpendicular to them. The domain confers DNA and nucleosome binding properties to the protein. 110 matched cddid_all.tbl CDD pfam09111 pfam09111 462681 SLIDE SLIDE. The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (pfam00249) repeats or homeodomains. 116 matched cddid_all.tbl CDD pfam09112 pfam09112 430416 N-glycanase_N Peptide-N-glycosidase F, N terminal. Members of this family adopt an eight-stranded antiparallel beta jelly roll configuration, with the beta strands arranged into two sheets. They are similar in topology to many viral capsid proteins, as well as lectins and several glucanases. The domain allows the protein to bind sugars and catalyzes the complete removal of N-linked oligosaccharide chains from glycoproteins. 147 matched cddid_all.tbl CDD pfam09113 pfam09113 462682 N-glycanase_C Peptide-N-glycosidase F, C terminal. Members of this family adopt an eight-stranded antiparallel beta jelly roll configuration, with the beta strands arranged into two sheets. They are similar in topology to many viral capsid proteins, as well as lectins and several glucanases. The domain allows the protein to bind sugars and catalyzes the complete removal of N-linked oligosaccharide chains from glycoproteins. 137 matched cddid_all.tbl CDD pfam09114 pfam09114 312591 MotA_activ Transcription factor MotA, activation domain. Members of this family of viral protein domains are implicated in transcriptional activation. They are almost completely alpha-helical, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2. 95 matched cddid_all.tbl CDD pfam09115 pfam09115 430418 DNApol3-delta_C DNA polymerase III, delta subunit, C terminal. Members of this family, which are predominantly found in prokaryotic DNA polymerase III, assume an alpha helical structure, with a core of five alpha helices, and an additional small helix. They are essential for the formation of the polymerase clamp loader. 112 matched cddid_all.tbl CDD pfam09116 pfam09116 401163 gp45-slide_C gp45 sliding clamp, C terminal. Members of this family are essential for the interaction of the gp45 sliding clamp with the corresponding polymerase. They adopt a DNA clamp fold, consisting of two alpha helices and two beta sheets - the fold is duplicated and has internal pseudo two-fold symmetry. 105 matched cddid_all.tbl CDD pfam09117 pfam09117 370303 MiAMP1 MiAMP1. MiAMP1 is a highly basic protein from the nut kernel of Macadamia integrifolia which inhibits the growth of several microbial plant pathogens in vitro while having no effect on mammalian or plant cells. It consists of eight beta-strands which are arranged in two Greek key motifs. These Greek key motifs then associate to form a Greek key beta-barrel. 76 matched cddid_all.tbl CDD pfam09118 pfam09118 462683 GO-like_E_set Galactose oxidase-like, Early set domain. E or 'early' set domains are associated with the catalytic domain of galactose oxidase at the C-terminal end. Galactose oxidase is an extracellular monomeric enzyme which catalyzes the stereospecific oxidation of a broad range of primary alcohol substrates, and possesses a unique mononuclear copper site essential for catalysing a two-electron transfer reaction during the oxidation of primary alcohols to corresponding aldehydes. The second redox active centre necessary for the reaction was found to be situated at a tyrosine residue. The C-terminal domain of galactose oxidase may be related to the immunoglobulin and/or fibronectin type III superfamilies. These domains are associated with different types of catalytic domains at either the N-terminal or C-terminal end, and may be involved in homodimeric/tetrameric/dodecameric interactions. Members of this family adopt a secondary structure consisting of a bundle of seven, mostly antiparallel, beta-strands surrounding a hydrophobic core. The 7 strands are arranged in 2 sheets, in a Greek-key topology. This domain is found in sugar-utilizing enzymes, such as galactose oxidase or chitinase. 91 matched cddid_all.tbl CDD pfam09119 pfam09119 401165 SicP-binding SicP binding. Members of this family bind the chaperone SicP, which is required both to maintain the stability of SptP, as well as to ensure the eventual secretion of the protein. The domain is found in the Salmonella effector protein SptP, which interacts with SicP chaperone dimers mainly through four regions of its chaperone-binding domain. The structure of the SptP-SicP complex contains four molecules of SicP, aligned in a linear fashion and arranged in two sets of tightly bound homodimers that bind two SptP molecules. The SicP homodimers do not interact with each other, but are held together by a molecular interface formed between two SptP molecules. Each SptP molecule is wrapped around by three SicP chaperones (two chaperones from one homodimer and a third one from the opposite homodimer pair). 84 matched cddid_all.tbl CDD pfam09121 pfam09121 462684 Tower Tower. Members of this family adopt a secondary structure consisting of a pair of long, antiparallel alpha-helices (the stem) that support a three-helix bundle (3HB) at their end. The 3HB contains a helix-turn-helix motif and is similar to the DNA binding domains of the bacterial site-specific recombinases, and of eukaryotic Myb and homeodomain transcription factors. The Tower domain has an important role in the tumour suppressor function of BRCA2, and is essential for appropriate binding of BRCA2 to DNA. 42 matched cddid_all.tbl CDD pfam09122 pfam09122 401167 DUF1930 Domain of unknown function (DUF1930). Members of this family are found in 3-mercaptopyruvate sulfurtransferase, and have no known function. They adopt a structure consisting of a four-stranded antiparallel beta-sheet and an alpha-helix, arranged in a beta(2)-alpha-beta(2) fashion, and bearing a remarkable structural similarity to the FK506-binding protein class of peptidylprolyl cis/trans-isomerase. 67 matched cddid_all.tbl CDD pfam09123 pfam09123 430421 DUF1931 Domain of unknown function (DUF1931). Members of this family, which are found in a set of hypothetical bacterial proteins, contain a core of six alpha-helices, where one central helix is surrounded by the other five. The exact function of this family has not, as yet, been determined. The known structure shows this domain contains two copies of the histone fold. 138 matched cddid_all.tbl CDD pfam09124 pfam09124 401169 Endonuc-dimeriz T4 recombination endonuclease VII, dimerization. Members of this family, which are predominantly found in Bacteriophage T4 recombination endonuclease VII, adopt a helical secondary structure, with three alpha helices oriented parallel to each other. They mediate dimerization of the protein, as well as binding to the DNA major groove. 54 matched cddid_all.tbl CDD pfam09125 pfam09125 462685 COX2-transmemb Cytochrome C oxidase subunit II, transmembrane. Members of this family adopt a tertiary structure consisting of two antiparallel transmembrane helices, in a transmembrane helix hairpin fold. 38 matched cddid_all.tbl CDD pfam09126 pfam09126 401170 NaeI Restriction endonuclease NaeI. Members of this family adopt a secondary structure consisting of nine alpha-helices, six 3-10 helices and 13 beta-strands. They bind two GCC-CGG recognition sequences to cleave DNA into blunt-ended products. 288 matched cddid_all.tbl CDD pfam09127 pfam09127 462686 Leuk-A4-hydro_C Leukotriene A4 hydrolase, C-terminal. Members of this family adopt a structure consisting of two layers of parallel alpha-helices, five in the inner layer and four in the outer, arranged in an antiparallel manner, with perpendicular loops containing short helical segments on top. They are required for the formation of a deep cleft harbouring the catalytic Zn2+ site in Leukotriene A4 hydrolase. 112 matched cddid_all.tbl CDD pfam09128 pfam09128 462687 RGS-like Regulator of G protein signalling-like domain. Members of this family adopt a structure consisting of twelve helices that fold into a compact domain that contains the overall structural scaffold observed in other RGS proteins and three additional helical elements that pack closely to it. Helices 1-9 comprise the RGS (pfam00615) fold, in which helices 4-7 form a classic antiparallel bundle adjacent to the other helices. Like other RGS structures, helices 7 and 8 span the length of the folded domain and form essentially one continuous helix with a kink in the middle. Helices 10-12 form an apparently stable C-terminal extension of the structural domain, and although other RGS proteins lack this structure, these elements are intimately associated with the rest of the structural framework by hydrophobic interactions. Members of the family bind to active G-alpha proteins, promoting GTP hydrolysis by the alpha subunit of heterotrimeric G proteins, thereby inactivating the G protein and rapidly switching off G protein-coupled receptor signalling pathways. 191 matched cddid_all.tbl CDD pfam09129 pfam09129 401173 Chol_subst-bind Cholesterol oxidase, substrate-binding. The substrate-binding domain found in Cholesterol oxidase is composed of an eight-stranded mixed beta-pleated sheet and six alpha-helices. This domain is positioned over the isoalloxazine ring system of the FAD cofactor bound by FAD_binding_4 (PF:PF01565) and forms the roof of the active site cavity, allowing for catalysis of oxidation and isomerization of cholesterol to cholest-4-en-3-one. 321 matched cddid_all.tbl CDD pfam09130 pfam09130 430423 DUF1932 Domain of unknown function (DUF1932). This domain is found in a set of hypothetical prokaryotic proteins. Its exact function has not, as yet, been described. 70 matched cddid_all.tbl CDD pfam09131 pfam09131 117687 Endotoxin_mid Bacillus thuringiensis delta-Endotoxin, middle domain. Members of this family adopt a structure consisting of three four-stranded beta-sheets, each with a Greek key fold, with internal pseudo threefold symmetry. Thus they act as a receptor binding beta-prism, binding to insect-specific receptors of gut epithelial cells. 206 matched cddid_all.tbl CDD pfam09132 pfam09132 462688 BmKX BmKX. Members of this family assume a structure adopted by most short-chain scorpion toxins, consisting of a cysteine-stabilized alpha/beta scaffold consisting of a short 3-10-helix and a two-stranded antiparallel beta-sheet. They are predominantly found in short-chain scorpion toxins, and their biological method of action has not, as yet, been defined. 30 matched cddid_all.tbl CDD pfam09133 pfam09133 462689 SANTA SANTA (SANT Associated). The SANTA domain (SANT Associated domain) is approximately 90 amino acids in length and is conserved in Eukaryota. It is sometimes found in association with the SANT domain (pfam00249, also known as Myb-like DNA-binding domain) implying a putative function in regulating chromatin remodelling. Sequence analysis has showed that the SANTA domain is likely to form four central beta-sheets with three flanking alpha- helixes. Many conserved hydrophobic residues are present which implying a possible role in protein-protein interactions. 87 matched cddid_all.tbl CDD pfam09134 pfam09134 430426 Invasin_D3 Invasin, domain 3. Members of this family adopt a structure consisting of an immunoglobulin-like beta-sandwich, with seven strands in two beta-sheets, arranged in a Greek-key topology. It forms part of the extracellular region of the protein, which can be expressed as a soluble protein (Inv497) that binds integrins and promotes subsequent uptake by cells when attached to bacteria. 98 matched cddid_all.tbl CDD pfam09135 pfam09135 430427 Alb1 Alb1. Alb1 is a nuclear shuttling factor involved in ribosome biogenesis. 105 matched cddid_all.tbl CDD pfam09136 pfam09136 430428 Glucodextran_B Glucodextranase, domain B. Members of this family adopt a structure consisting of seven/eight-strand antiparallel beta-sheets, in a Greek-key topology, similar to the immunoglobulin beta-sandwich fold. They act as cell wall anchors, where they interact with the S-layer present in the cell wall of Gram-positive bacteria by hydrophobic interactions. In glucodextranase, Domain B is buried in the S-layer, and a flexible linker located between domain B and the catalytic unit confers motion to the catalytic unit, which is capable of efficient hydrolysis of the substrates located close to the cell surface. 83 matched cddid_all.tbl CDD pfam09137 pfam09137 430429 Glucodextran_N Glucodextranase, domain N. Members of this family, which are uniquely found in bacterial and archaeal glucoamylases and glucodextranases, adopt a structure consisting of 17 antiparallel beta-strands. These beta-strands are divided into two beta-sheets, and one of the beta-sheets is wrapped by an extended polypeptide, which appears to stabilize the domain. Members of this family are mainly concerned with catalytic activity, hydrolysing alpha-1,6-glucosidic linkages of dextran to release beta-D-glucose from the non-reducing end via an inverting reaction mechanism. 263 matched cddid_all.tbl CDD pfam09138 pfam09138 370315 Urm1 Urm1 (Ubiquitin related modifier). Urm1 is a ubiquitin related protein that modifies proteins in the yeast ubiquitin-like pathway urmylation. Structural comparisons and phylogenetic analysis of the ubiquitin superfamily has indicated that Urm1 has the most conserved structural and sequence features of the common ancestor of the entire superfamily. 96 matched cddid_all.tbl CDD pfam09139 pfam09139 462690 Tam41_Mmp37 Phosphatidate cytidylyltransferase, mitochondrial. Tam41 also known as MMp37 is a mitochondrial phosphatidate cytidylyltransferase (CDP-DAG synthase)(EC:2.7.7.41) that catalyzes the formation of CDP-diacylglycerol (CDP-DAG) from phosphatidic acid (PA) in the mitochondrial inner membrane. It is required for the biosynthesis of the dimeric phospholipid cardiolipin, which stabilizes supercomplexes of the mitochondrial respiratory chain in the mitochondrial inner membrane. It is suggested that the N-terminal portion of Tam41 may possess the NTase (Nucleotide Transferase) fold, which is consistent with the CDP-DAG synthase function of Tam41. Furthermore, it has been shown that Tam41/MMP37 proteins possess the NTase fold but they have only one active site carboxylate and thus probably are not able to carry out enzymatic reaction. These potentially non-active members of NTase fold superfamily may bind ATP, hydrolysis of which is necessary for the translocation of proteins through the membrane. 322 matched cddid_all.tbl CDD pfam09140 pfam09140 401181 MipZ ATPase MipZ. MipZ is an ATPase that forms a complex with the chromosome partitioning protein ParB near the chromosomal origin of replication. It is responsible for the temporal and spatial regulation of FtsZ ring formation. 262 matched cddid_all.tbl CDD pfam09141 pfam09141 462691 Talin_middle Talin, middle domain. Members of this family adopt a structure consisting of five alpha helices that fold into a bundle. They contain a Vinculin binding site (VBS) composed of a hydrophobic surface spanning five turns of helix four. Activation of the VBS causes subsequent recruitment of Vinculin, which enables maturation of small integrin/talin complexes into more stable adhesions. Formation of the complex between VBS and Vinculin requires prior unfolding of this middle domain: once released from the talin hydrophobic core, the VBS helix is then available to induce the 'bundle conversion' conformational change within the vinculin head domain thereby displacing the intramolecular interaction with the vinculin tail, allowing vinculin to bind actin. 161 matched cddid_all.tbl CDD pfam09142 pfam09142 430432 TruB_C tRNA Pseudouridine synthase II, C terminal. The C terminal domain of tRNA Pseudouridine synthase II adopts a PUA (pfam01472) fold, with a four-stranded mixed beta-sheet flanked by one alpha-helix on each side. It allows for binding of the enzyme to RNA, as well as stabilization of the RNA molecule. 56 matched cddid_all.tbl CDD pfam09143 pfam09143 401183 AvrPphF-ORF-2 AvrPphF-ORF-2. Members of this family of plant pathogenic proteins adopt an elongated structure somewhat reminiscent of a mushroom that can be divided into 'stalk' and 'head' subdomains. The stalk subdomain is composed of the N-terminal helix (alpha1) and beta strands beta3-beta4. An antiparallel beta sheet (beta5, beta7-beta8) forms the base of the head subdomain that interacts with the stalk. A pair of twisted antiparallel beta sheets (beta1 and beta6; beta2 and beta9/9') supported by alpha2 form the dome of the head. The head subdomain possesses weak structural similarity with the catalytic portion of a number of ADP-ribosyltransferase toxins. 175 matched cddid_all.tbl CDD pfam09144 pfam09144 72561 YpM Yersinia pseudo-tuberculosis mitogen. Members of this family of Yersinia pseudo-tuberculosis mitogens adopt a sandwich structure consisting of nine strands in two beta sheets, in a jelly-roll topology. As with other super-antigens, they are able to excessively activate T cells by binding to the T cell receptor. 117 matched cddid_all.tbl CDD pfam09145 pfam09145 401184 Ubiq-assoc Ubiquitin-associated. Ubiquitin associated domains contain approximately 40 residues and bind ubiquitin non-covalently. They adopt a secondary structure consisting of three alpha-helices, and have been identified in various modular proteins involved in protein trafficking, clathrin assembly/disassembly, DNA repair, proteasomal degradation, and cell cycle regulation. 44 matched cddid_all.tbl CDD pfam09147 pfam09147 462692 CarA_N Carbapenam-3-carboxylate synthase, N-terminal. This domain is found in the N-terminal of carbapenam-3-carboxylate synthase (carA), and is composed of two antiparallel six-stranded beta-sheets that form a sandwich, flanked on each side by two alpha-helices. carA is involved in the biosynthesis of carbapenam-3-carboxylate, a beta-lactam antibiotic of the carbapenem class. It catalyzes the ATP-dependent formation of (3S,5S)-carbapenam-3-carboxylate from (2S,5S)-5-carboxymethylproline. 199 matched cddid_all.tbl CDD pfam09148 pfam09148 462693 DUF1934 Domain of unknown function (DUF1934). Members of this family are found in a set of hypothetical bacterial proteins. Their precise function has not, as yet, been defined. 123 matched cddid_all.tbl CDD pfam09149 pfam09149 401186 DUF1935 Domain of unknown function (DUF1935). Members of this family are found in various bacterial and eukaryotic hypothetical proteins, as well as in the cysteine protease calpain. Their exact function has not, as yet, been defined. 100 matched cddid_all.tbl CDD pfam09150 pfam09150 430435 Carot_N Orange carotenoid protein, N-terminal. Members of this family adopt an alpha-helical structure consisting of two four-helix bundles. They are predominantly found in prokaryotic orange carotenoid protein, and carotenoid binding proteins. 149 matched cddid_all.tbl CDD pfam09151 pfam09151 401188 DUF1936 Domain of unknown function (DUF1936). This domain is found in a set of hypothetical Archaeal proteins. Its exact function has not, as yet, been defined. It possesses a zinc ribbon fold. 34 matched cddid_all.tbl CDD pfam09152 pfam09152 430436 DUF1937 Domain of unknown function (DUF1937). This domain is found in a set of hypothetical bacterial proteins. Their exact function has not, as yet, been described. 111 matched cddid_all.tbl CDD pfam09153 pfam09153 401189 MGMT_N Methylated DNA-protein cysteine methyltransferase, N-terminal. This domain is found in the archaeal protein O6-alkylguanine-DNA alkyltransferase (also known as Methylated DNA-protein cysteine methyltransferase MGMT), adopt a secondary structure consisting of a three stranded antiparallel beta-sheet and three alpha helices. This entry represents the N-terminal ribonuclease H-like domain, associated with 6-O-methylguanine DNA methyltransferase activity. The exact function has not, as yet, been defined, though it has been postulated that they confer thermostability to the archaeal protein. 90 matched cddid_all.tbl CDD pfam09154 pfam09154 401190 Alpha-amy_C_pro Alpha-amylase C-terminal. This entry represents a C-terminal domain associated with prokaryotic alpha-amylases, which adopt a secondary structure consisting of an eight-stranded antiparallel beta-sheet containing a Greek key motif. Their exact function has not, as yet, been determined. 57 matched cddid_all.tbl CDD pfam09155 pfam09155 312612 DUF1940 Domain of unknown function (DUF1940). Members of this family adopt a secondary structure consisting of six alpha helices, with four long helices (alpha1, alpha2, alpha5, alpha6) form a left-handed, antiparallel alpha helical bundle. The function of this family of Archaeal hypothetical proteins has not, as yet, been defined. 143 matched cddid_all.tbl CDD pfam09156 pfam09156 462694 Anthrax-tox_M Anthrax toxin lethal factor, middle domain. Members of this family, which are predominantly found in anthrax toxin lethal factor, adopt a structure consisting of a core of antiparallel beta sheets and alpha helices. They form a long deep groove within the protein that anchors the 16-residue N-terminal tail of MAPKK-2 before cleavage. It has been noted that this domain resembles the ADP-ribosylating toxin from Bacillus cereus, but the active site has been modified to augment substrate recognition. 286 matched cddid_all.tbl CDD pfam09157 pfam09157 462695 TruB-C_2 Pseudouridine synthase II TruB, C-terminal. Members of this family adopt a secondary structure consisting of a four-stranded beta sheet and one alpha helix. They are predominantly RNA-binding domains, mostly found in Pseudouridine synthase II TruB. 57 matched cddid_all.tbl CDD pfam09158 pfam09158 286268 MotCF Bacteriophage T4 MotA, C-terminal. Members of this family adopt a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. The beta-strands form a single anti-parallel beta-sheet and the three alpha-helices pack side-by-side onto one surface of the beta-sheet. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. The domain is a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end. 103 matched cddid_all.tbl CDD pfam09159 pfam09159 401193 Ydc2-catalyt Mitochondrial resolvase Ydc2 / RNA splicing MRS1. Members of this family adopt a secondary structure consisting of two beta sheets and one alpha helix, arranged as a beta-alpha-beta motif. Each beta sheet has five strands, arranged in a 32145 order, with the second strand being antiparallel to the rest. Mitochondrial resolvase Ydc2 is capable of resolving Holliday junctions and cleaves DNA after 5'-CT-3' and 5'-TT-3' sequences. This family also contains the mitochondrial RNA-splicing protein MRS1 which is involved in the excision of group I introns. 251 matched cddid_all.tbl CDD pfam09160 pfam09160 430438 FimH_man-bind FimH, mannose binding. Members of this family adopt a secondary structure consisting of a beta sandwich, with nine strands arranged in two sheets in a Greek key topology. They are predominantly found in bacterial mannose-specific adhesins, since they are capable of binding to D-mannose. 145 matched cddid_all.tbl CDD pfam09162 pfam09162 462696 Tap-RNA_bind Tap, RNA-binding. Members of this family adopt a structure consisting of an alpha+beta sandwich with an antiparallel beta-sheet, arranged in a 2(beta-alpha-beta) motif. They are mainly found in mRNA export factors, and mediate the sequence nonspecific nuclear export of cellular mRNAs as well as the sequence-specific export of retroviral mRNAs bearing the constitutive transport element. 80 matched cddid_all.tbl CDD pfam09163 pfam09163 430440 Form-deh_trans Formate dehydrogenase N, transmembrane. Members of this family are predominantly found in the beta subunit of formate dehydrogenase, and consist of a single transmembrane helix. They act as a transmembrane anchor, and allow for conduction of electrons within the protein. 43 matched cddid_all.tbl CDD pfam09164 pfam09164 462697 VitD-bind_III Vitamin D binding protein, domain III. Members of this family are predominantly found in Vitamin D binding protein, and adopt a multi-helical structure. They are required for formation of an actin 'clamp', allowing the protein to bind to actin. 65 matched cddid_all.tbl CDD pfam09165 pfam09165 462698 Ubiq-Cytc-red_N Ubiquinol-cytochrome c reductase 8 kDa, N-terminal. Members of this family adopt a structure consisting of many antiparallel beta sheets, with few alpha helices, in a non-globular arrangement. They are required for proper functioning of the respiratory chain. 75 matched cddid_all.tbl CDD pfam09166 pfam09166 462699 Biliv-reduc_cat Biliverdin reductase, catalytic. Members of this family adopt a structure consisting of four alpha helices and six beta sheets, in an alpha-beta-alpha-alpha-alpha-beta-beta-beta-beta-beta arrangement. They contain a catalytic active site, capable of reducing the gamma-methene bridge of the open tetrapyrrole, biliverdin IX alpha, to bilirubin with the concomitant oxidation of a NADH or NADPH cofactor. 113 matched cddid_all.tbl CDD pfam09167 pfam09167 430444 DUF1942 Domain of unknown function (DUF1942). Members of this family of bacterial proteins assume a beta-sandwich structure consisting of two antiparallel beta-sheets similar to an immunoglobulin-like fold, with an additional small, antiparallel beta-sheet. The longer-stranded beta-sheet is made up of four antiparallel beta-strands. The shorter-stranded beta-sheet consists of five beta-strands, four of these beta-strands form an antiparallel beta-sheet. The exact function of this family of proteins is unknown, though a putative role includes involvement in host-bacterial interactions involved in endocytosis or phagocytosis, possibly during bacterial internalization. 123 matched cddid_all.tbl CDD pfam09168 pfam09168 430445 PepX_N X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal. Members of this family adopt a secondary structure consisting of a helical bundle of eight alpha helices and three beta strands, the last alpha helix connecting to the first strand of the catalytic domain. The first strand of the N-terminus also forms a small parallel beta sheet with strand 5' of catalytic domain. The domain mediates dimerization of the protein, with two proline residues present in the domain being critical for interaction. 157 matched cddid_all.tbl CDD pfam09169 pfam09169 462700 BRCA-2_helical BRCA2, helical. Members of this family adopt a helical structure, consisting of a four-helix cluster core (alpha 1, alpha 8, alpha 9, alpha 10) and two successive beta-hairpins (beta 1 to beta 4). An approx. 50-amino acid segment that contains four short helices (alpha 2 to alpha 4), meanders around the surface of the core structure. In BRCA2, the alpha 9 and alpha 10 helices pack with BRCA-2_OB1 (pfam09103) through van der Waals contacts involving hydrophobic and aromatic residues, and also through side-chain and backbone hydrogen bonds. The domain binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome. 187 matched cddid_all.tbl CDD pfam09170 pfam09170 462701 STN1_2 CST, complex subunit STN1, C terminal. STN1 is a component of the CST complex, a complex that binds to single-stranded DNA and is required for protecting telomeres from DNA degradation. The CST complex binds single-stranded DNA with high affinity in a sequence-independent manner, while isolated subunits bind DNA with low affinity on their own. In addition to telomere protection, the CST complex probably has a more general role in DNA metabolism at non-telomeric sites. This entry represents the C-terminal region of Stn1 which has two winged helix-turn-helix (wHTH) motifs, wHTH1 and wHTH2. wHTH1 is structurally similar to that in RPA32 with a large insertion between helices alpha2 and alpha3, unique to Stn1, that may allow interaction with a different set of proteins that function at telomeres such as Ctc1. wHTH2 is most similar to the DNA-binding wHTH motifs of the pur operon repressor and RepE replication initiator, but it does not bind double-stranded DNA. 167 matched cddid_all.tbl CDD pfam09171 pfam09171 401203 AGOG N-glycosylase/DNA lyase. This domain is predominantly found in the Archaeal protein N-glycosylase/DNA lyase. 248 matched cddid_all.tbl CDD pfam09172 pfam09172 462702 Vit_open_b-sht Vitellinogen, open beta-sheet. This entry represents the open beta-sheet domain found in vitellinogen, which generally corresponds to a domain within the lipovitellin-1 peptide product. This domain adopts a structure consisting of several large open beta-sheets. 300 matched cddid_all.tbl CDD pfam09173 pfam09173 462703 eIF2_C Initiation factor eIF2 gamma, C terminal. Members of this family, which are found in the initiation factors eIF2 and EF-Tu, adopt a structure consisting of a beta barrel with Greek key topology. They are required for formation of the ternary complex with GTP and initiator tRNA. 86 matched cddid_all.tbl CDD pfam09174 pfam09174 462704 Maf1 Maf1 regulator. Maf1 is a negative regulator of RNA polymerase III. It targets the initiation factor TFIIIB. 174 matched cddid_all.tbl CDD pfam09175 pfam09175 462705 Vit_b-sht_shell Vitellinogen, beta-sheet shell. This entry represents the beta-sheet shell domain found in vitellinogen, which generally corresponds to the lipovitellin-2 peptide product. This domain consists of several large open beta-sheets. 167 matched cddid_all.tbl CDD pfam09176 pfam09176 430452 Mpt_N Methylene-tetrahydromethanopterin dehydrogenase, N-terminal. Members of this family adopt a alpha-beta structure, with a core comprising three alpha/beta/alpha layers, in which each sheet contains four strands. They are predominantly found in prokaryotic methylene-tetrahydromethanopterin dehydrogenase, which catalyzes the dehydrogenation of methylene-tetrahydromethanopterin and the reversible dehydrogenation of methylene-H(4)F. 81 matched cddid_all.tbl CDD pfam09177 pfam09177 462706 Syntaxin-6_N Syntaxin 6, N-terminal. Members of this family, which are found in the amino terminus of various SNARE proteins, adopt a structure consisting of an antiparallel three-helix bundle. Their exact function has not been determined, though it is known that they regulate the SNARE motif, as well as mediate various protein-protein interactions involved in membrane-transport. 99 matched cddid_all.tbl CDD pfam09178 pfam09178 462707 MGTA_C 4-alpha-glucanotransferase, C-terminal. Members of this family, which are predominantly found in prokaryotic 4-alpha-glucanotransferase, adopt a structure composed of six antiparallel beta-strands, four of which form a beta-sheet and another two form a type I' beta-hairpin. The role of this family of domains, has not, as yet, been defined. 50 matched cddid_all.tbl CDD pfam09179 pfam09179 462708 TilS TilS substrate binding domain. This domain is found in the tRNA(Ile) lysidine synthetase (TilS) protein. 66 matched cddid_all.tbl CDD pfam09180 pfam09180 462709 ProRS-C_1 Prolyl-tRNA synthetase, C-terminal. Members of this family are predominantly found in prokaryotic prolyl-tRNA synthetase. They contain a zinc binding site, and adopt a structure consisting of alpha helices and antiparallel beta sheets arranged in 2 layers, in a beta-alpha-beta-alpha-beta motif. 67 matched cddid_all.tbl CDD pfam09181 pfam09181 401212 ProRS-C_2 Prolyl-tRNA synthetase, C-terminal. Members of this family are predominantly found in prokaryotic prolyl-tRNA synthetase. They contain a zinc binding site, and adopt a structure consisting of alpha helices and antiparallel beta sheets arranged in 2 layers, in a beta-alpha-beta-alpha-beta motif. 66 matched cddid_all.tbl CDD pfam09182 pfam09182 430456 PuR_N Bacterial purine repressor, N-terminal. The N-terminal domain of the bacterial purine repressor PuR is a winged-helix domain, a subdivision of the HTH structural family. It consists of a canonical arrangement of secondary structures: a1-b1-a2-T-a3-b2-W-b3, where a2-T-a3 is the HTH motif, a3 is the recognition helix, and W is the wing. The domain allows for recognition of a conserved CGAA sequence in the centre of a DNA PurBox, resulting in binding to the major groove of DNA. 70 matched cddid_all.tbl CDD pfam09183 pfam09183 401214 DUF1947 Domain of unknown function (DUF1947). Members of this family are found in a set of hypothetical Archaeal proteins. Their exact function has not, as yet, been defined. 63 matched cddid_all.tbl CDD pfam09184 pfam09184 462710 PPP4R2 PPP4R2. PPP4R2 (protein phosphatase 4 core regulatory subunit R2) is the regulatory subunit of the histone H2A phosphatase complex. It has been shown to confer resistance to the anticancer drug cisplatin in yeast, and may confer resistance in higher eukaryotes. 256 matched cddid_all.tbl CDD pfam09185 pfam09185 401216 DUF1948 Domain of unknown function (DUF1948). Members of this family of Mycoplasma hypothetical proteins adopt a helical structure, with one central alpha-helix surrounded by five others, in a NusB-like fold. Their function has not, as yet, been determined. 140 matched cddid_all.tbl CDD pfam09186 pfam09186 430458 DUF1949 Domain of unknown function (DUF1949). Members of this family pertain to a set of functionally uncharacterized hypothetical bacterial proteins. They adopt a ferredoxin-like fold, with a beta-alpha-beta-beta-alpha-beta arrangement. 56 matched cddid_all.tbl CDD pfam09187 pfam09187 401218 RdDM_RDM1 RNA-directed DNA methylation 1. This family of plant proteins includes RDM1 from Arabidopsis, which is a component of the RNA-directed DNA methylation (RdDM) effector complex and may have a role in linking siRNA production with pre-existing or de novo cytosine methylation. As part of the DDR complex with two other RdDM components, it has been shown to facilitate association of PolV to chromatin. 119 matched cddid_all.tbl CDD pfam09188 pfam09188 286297 DUF1951 Domain of unknown function (DUF1951). Members of this family of Mycoplasma hypothetical proteins adopt a helical structure, with a buried central helix. Their function has not, as yet, been determined. 137 matched cddid_all.tbl CDD pfam09189 pfam09189 401219 DUF1952 Domain of unknown function (DUF1952). Members of this family are found in various Thermus thermophilus proteins. Their exact function has not, as yet, been determined. 73 matched cddid_all.tbl CDD pfam09190 pfam09190 462711 DALR_2 DALR domain. This DALR domain is found in cysteinyl-tRNA-synthetases. 63 matched cddid_all.tbl CDD pfam09191 pfam09191 462712 CD4-extracel CD4, extracellular. Members of this family adopt an immunoglobulin-like beta-sandwich, with seven strands in 2 beta sheets, in a Greek key topology. They are predominantly found in the extracellular portion of CD4 proteins, where they enable interaction with major histocompatibility complex class II antigens. 106 matched cddid_all.tbl CDD pfam09192 pfam09192 370352 Act-Frag_cataly Actin-fragmin kinase, catalytic. Members of this family assume a secondary structure consisting of eight beta strands and 11 alpha-helices, organized in two lobes. They are predominantly found in actin-fragmin kinase, where they act as a catalytic domain that mediates the phosphorylation of actin. 278 matched cddid_all.tbl CDD pfam09193 pfam09193 462713 CholecysA-Rec_N Cholecystokinin A receptor, N-terminal. Members of this family are found in the extracellular region of the cholecystokinin A receptor, where they adopt a tertiary structure consisting of a few helical turns and a disulphide-crosslinked loop. They are required for interaction of the cholecystokinin A receptor with it's corresponding hormonal ligand. 47 matched cddid_all.tbl CDD pfam09194 pfam09194 430461 Endonuc-BsobI Restriction endonuclease BsobI. Members of this family of prokaryotic restriction endonucleases recognize the double-stranded sequence CYCGRG (where Y = T/C, and R = A/G) and cleave after C-1. They catalyze the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. 314 matched cddid_all.tbl CDD pfam09195 pfam09195 430462 Endonuc-BglII Restriction endonuclease BglII. Members of this family are predominantly found in prokaryotic restriction endonuclease BglII, and adopt a structure consisting of an alpha/beta core containing a six-stranded beta-sheet surrounded by five alpha-helices, two of which are involved in homodimerization of the endonuclease. They recognize the double-stranded DNA sequence AGATCT and cleave after A-1, resulting in specific double-stranded fragments with terminal 5'-phosphates. 163 matched cddid_all.tbl CDD pfam09196 pfam09196 462714 DUF1953 Domain of unknown function (DUF1953). This domain is found in the Archaeal protein maltooligosyl trehalose synthase produced by Sulfolobus spp. Its function has not, as yet, been defined. 63 matched cddid_all.tbl CDD pfam09197 pfam09197 401223 Rap1-DNA-bind Rap1, DNA-binding. Members of this family, which are predominantly found in the yeast protein rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACACC region in the 3' region of the DNA-binding site. 108 matched cddid_all.tbl CDD pfam09198 pfam09198 72614 T4-Gluco-transf Bacteriophage T4 beta-glucosyltransferase. Members of this family are DNA-modifying enzymes encoded by bacteriophage T4 that transfer glucose from uridine diphosphoglucose to 5-hydroxymethyl cytosine bases of phage T4 DNA. 38 matched cddid_all.tbl CDD pfam09199 pfam09199 401224 SSL_OB Staphylococcal superantigen-like OB-fold domain. This OB-fold domain folds into a five-stranded beta-barrel. Members of this family are found in various staphylococcal toxins described as staphylococcal superantigen-like (SSL) proteins that are related to the staphylococcal enterotoxins (SEs) or superantigens. These SSL proteins of which 11 have so far been characterized have a typical SE tertiary structure consisting of a distinct oligonucleotide/oligosaccharide binding (OB-fold), this domain, linked to a beta-grasp domain, family Stap_Strp_tox_C, pfam02876. SSLs do not bind to T-cell receptors or major histocompatibility complex class II molecules and do not stimulate T cells. SSLs target components of innate immunity, such as complement, Fc receptors, and myeloid cells 2,3,4,5,6,7,8]. SSL protein 7 (SSL7) is the best characterized of the SSLs and binds complement factor C5 and IgA with high affinity and inhibits the end stage of complement activation and IgA binding to FcalphaR. 84 matched cddid_all.tbl CDD pfam09200 pfam09200 312644 Monellin Monellin. Monellin, a protein produced by the West African plant Dioscoreophyllum cumminsii, is approximately 70,000 times sweeter than sucrose on a molar basis. The protein adopts an alpha-beta structure, with a cystatin-like fold, where each helix packs against a coiled antiparallel beta-sheet. 40 matched cddid_all.tbl CDD pfam09201 pfam09201 370358 SRX SRX, signal recognition particle receptor alpha subunit. Members of this family, which are predominantly found in eukaryotic signal recognition particle receptor alpha, consist of a central six-stranded anti-parallel beta-sheet sandwiched by helix alpha1 on one side and helices alpha2-alpha4 on the other. They interact with the small GTPase SR-beta, forming a complex that matches a class of small G protein-effector complexes, including Rap-Raf, Ras-PI3K(gamma), Ras-RalGDS, and Arl2-PDE(delta). Structurally the alpha subunit is SNARE-like. 148 matched cddid_all.tbl CDD pfam09202 pfam09202 462715 Rio2_N Rio2, N-terminal. Members of this family are found in Rio2, and are structurally homologous to the winged helix (wHTH) domain. They adopt a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains. 82 matched cddid_all.tbl CDD pfam09203 pfam09203 430464 MspA MspA. MspA is a membrane porin produced by Mycobacteria, allowing hydrophilic nutrients to enter the bacterium. The protein forms a tightly interconnected octamer with eightfold rotation symmetry that resembles a goblet and contains a central channel. Each subunit fold contains a beta-sandwich of Ig-like topology and a beta-ribbon arm that forms an oligomeric transmembrane barrel. 176 matched cddid_all.tbl CDD pfam09204 pfam09204 401227 Colicin_immun Bacterial self-protective colicin-like immunity. Colicin D, which is synthesized by various prokaryotes, adopts an antiparallel four helical bundle fold: the helices are tightly packed, forming a compact cylindrical molecule. The protein specifically cleaves the anticodon loop of all four tRNA-Arg isoacceptors, thereby inactivating prokaryotic protein synthesis and leading to cell death. This family also contains immunity proteins to klebicins and microcins. Many bacteria produce proteins that destroy their competitors. Colicin D is one such. The immunity proteins are expressed on the same operon as their cognate bacteriocins and protect the expressing bacterium from the effects of its own bacteriocin. 84 matched cddid_all.tbl CDD pfam09205 pfam09205 401228 DUF1955 Domain of unknown function (DUF1955). Members of this family are found in hypothetical proteins synthesized by the Archaeal organizm Sulfolobus. Their exact function has not, as yet, been determined. 159 matched cddid_all.tbl CDD pfam09206 pfam09206 430465 ArabFuran-catal Alpha-L-arabinofuranosidase B, catalytic. Members of this family, which are present in fungal alpha-L-arabinofuranosidase B, adopt a beta-sandwich fold similar to that of Concanavalin A-like lectins/glucanase. The beta-sandwich fold consists of two anti-parallel beta-sheets with seven and and six strands, respectively. In addition, there are four helices outside of the beta-strands. The beta-sandwich strands are closely packed and curved with a jelly roll topology, creating a small catalytic pocket. The domain catalyzes the hydrolysis of alpha-1,2-, alpha-1,3- and alpha-1,5-L-arabinofuranosidic bonds in L-arabinose-containing hemicelluloses such as arabinoxylan and L-arabinan. 315 matched cddid_all.tbl CDD pfam09207 pfam09207 430466 Yeast-kill-tox Yeast killer toxin. Members of this family, which are produced by Williopsis fungi, adopt a secondary structure consisting of eight strands in two beta sheets, in a Greek-key topology. 87 matched cddid_all.tbl CDD pfam09208 pfam09208 401230 Endonuc-MspI Restriction endonuclease MspI. Members of this family of prokaryotic restriction endonucleases recognize the palindromic tetranucleotide sequence 5'-CCGG and cleave between the first and second nucleotides, leaving 2 base 5' overhangs. They fold into an alpha/beta architecture, with a five-stranded mixed beta-sheet sandwiched on both sides by alpha-helices. 258 matched cddid_all.tbl CDD pfam09209 pfam09209 430467 CecR_C HTH-type transcriptional dual regulator CecR, C-terminal domain. This entry represents the C-terminal domain found in CecR (regulator of cefoperazone and chloramphenicol sensitivity), previously known as YbiH. CecR has been shown to control sensitivity to cefoperazone and chloramphenicol through regulating the transcription of the cecR-ybhGFSR operon and the rhlE gene. 125 matched cddid_all.tbl CDD pfam09210 pfam09210 430468 BE_C 1,4-alpha-glucan branching enzyme, C-terminal. This entry represents the C-terminal domain found in bacterial 1,4-alpha-glucan branching enzymes, such as TTHA1902 from Thermus thermophilus and TK1436 from Thermococcus kodakarensis, which belong to the glycoside hydrolase family 57 (GH57). These enzymes catalyze the formation of branch points in alpha-glucans by cleavage of an alpha-1,4 glycosidic bond and subsequent transfer of the cleaved-off oligosaccharide to a new alpha-1,6 position. This is an alpha-helical domain composed of a four alpha-helical bundle. It plays a role in the formation of the active-site cleft, being essential for substrate binding and catalysis. 98 matched cddid_all.tbl CDD pfam09211 pfam09211 401233 DUF1958 Domain of unknown function (DUF1958). Members of this functionally uncharacterized family are found in prokaryotic penicillin-binding protein 4. 63 matched cddid_all.tbl CDD pfam09212 pfam09212 117765 CBM27 Carbohydrate binding module 27. Members of this family are carbohydrate binding modules that bind to beta-1, 4-manno-oligosaccharides, carob galactomannan, and konjac glucomannan, but not to cellulose (insoluble and soluble) or soluble birchwood xylan. They adopt a beta sandwich structure comprising 13 beta strands with a single, small alpha-helix and a single metal atom. 173 matched cddid_all.tbl CDD pfam09213 pfam09213 117766 M3 M3. Members of this family of viral chemokine binding proteins adopt a structure consisting of two different beta-sandwich domains of partial topological similarity to immunoglobulin-like folds. They bind with the CC-chemokine MCP-1, acting as cytokine decoy receptors. 367 matched cddid_all.tbl CDD pfam09214 pfam09214 401234 Prd1-P2 Bacteriophage Prd1, adsorption protein P2. Members of this family form a set of bacteriophage adsorption proteins, composed mainly of beta-strands whose complicated topology forms an elongated seahorse-shaped molecule with a distinct head, containing a pseudo-beta propeller structure with approximate 6-fold symmetry, and tail. They are required for the attachment of the phage to the host conjugative DNA transfer complex. This is a poorly understood large transmembrane complex of unknown architecture, with at least 11 different proteins. 554 matched cddid_all.tbl CDD pfam09215 pfam09215 401235 Phage-Gp8 Bacteriophage T4, Gp8. Members of this family of viral baseplate structural proteins adopt a structure consisting of a three-layer beta-sandwich with two finger-like loops containing an alpha-helix at the opposite sides of the sandwich. The two peripheral, five-stranded, antiparallel beta-sheets are stacked against the middle, four-stranded, antiparallel beta-sheet. Attachment of this family of proteins to the baseplate during assembly creates a binding site for subsequent attachment of Gp6. 337 matched cddid_all.tbl CDD pfam09216 pfam09216 401236 Pfg27 Pfg27. Members of this family are essential for gametocytogenesis in Plasmodium falciparum. They contain a fold composed of two pseudo dyad-related repeats of the helix-turn-helix motif, serving as a platform for RNA and Src homology-3 (SH3) binding. 176 matched cddid_all.tbl CDD pfam09217 pfam09217 430469 EcoRII-N Restriction endonuclease EcoRII, N-terminal. The N-terminal effector-binding domain of the Restriction Endonuclease EcoRII has a DNA recognition fold, allowing for binding to 5'-CCWGG sequences. It assumes a structure composed of an eight-stranded beta-sheet with the strands in the order of b2, b5, b4, b3, b7, b6, b1 and b8. They are mostly antiparallel to each other except that b3 is parallel to b7. Alternatively, it may also be viewed as consisting of two mini beta-sheets of four antiparallel beta-strands, sheet I from beta-strands b2, b5, b4, b3 and sheet II from strands b7, b6, b1, b8, folded into an open mixed beta-barrel with a novel topology. Sheet I has a simple Greek key motif while sheet II does not. 148 matched cddid_all.tbl CDD pfam09218 pfam09218 401238 DUF1959 Domain of unknown function (DUF1959). This domain is found in a set of uncharacterized Archaeal hypothetical proteins. Its function has not, as yet, been described. 116 matched cddid_all.tbl CDD pfam09220 pfam09220 401239 LA-virus_coat L-A virus, major coat protein. Members of this family form the major coat protein of the Saccharomyces cerevisiae L-A virus. 439 matched cddid_all.tbl CDD pfam09221 pfam09221 401240 Bacteriocin_IId Bacteriocin class IId cyclical uberolysin-like. Members of this family are membrane-interacting peptides, produced by Firmicutes that display a broad anti-microbial spectrum against Gram-positive and Gram-negative bacteria. They adopt a helical structure, with four or five alpha helices forming a Saposin-like fold. The structure has been found to be cyclical. It should be pointed out that one reference implies that both circularin A and gassericin A are class V or IIc-type bacteriocins; however we find that these two proteins fall into different Pfam families families, this one and BacteriocIIc_cy, pfam12173. 67 matched cddid_all.tbl CDD pfam09222 pfam09222 370370 Fim-adh_lectin Fimbrial adhesin F17-AG, lectin domain. Members of this family are carbohydrate-specific lectin domains found in bacterial fimbrial adhesins. They adopt a compact, elongated structure consisting of a beta-sandwich with two major sheets: one consisting of five long strands in mixed orientations, and a front sheet with four antiparallel strands, forming an immunoglobin-like fold. 171 matched cddid_all.tbl CDD pfam09223 pfam09223 430470 ZinT ZinT (YodA) periplasmic lipocalin-like zinc-recruitment. ZinT plays a critical role in recruiting periplasmic zinc to the bacterial zinc-uptake complex ZnuABC, consisting of families pfam01297,pfam00950, pfam00005, regulated by the transcription-regulator FUR, pfam01475. ZinT acts as a Zn2+-buffering protein that delivers Zn2+ to ZnuA (TroA), pfam01297. Members of this family of prokaryotic domains were first identified as part of the response of bacteria to a challenge with the toxic heavy metal cadmium. They are able to bind to cadmium, and ensure its subsequent elimination. 181 matched cddid_all.tbl CDD pfam09224 pfam09224 401242 DUF1961 Domain of unknown function (DUF1961). Members of this family are found in a set of hypothetical bacterial proteins. Their exact function has not, as yet, been determined. 214 matched cddid_all.tbl CDD pfam09225 pfam09225 430471 Endonuc-PvuII Restriction endonuclease PvuII. Members of this family are predominantly found in prokaryotic restriction endonuclease PvuII. They recognize the double-stranded DNA sequence 5'-CAGCTG-3' and cleave after G-3, resulting in specific double-stranded fragments with terminal 5'-phosphates. 155 matched cddid_all.tbl CDD pfam09226 pfam09226 312659 Endonuc-HincII Restriction endonuclease HincII. Members of this family of prokaryotic restriction endonucleases recognize the double-stranded sequence 5'-GTYRAC-3' and cleave after Y-3. They catalyze the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. 247 matched cddid_all.tbl CDD pfam09227 pfam09227 286330 Bubble Bubble protein. Members of this family of fungal domains are functionally uncharacterized. They may act as toxins. 64 matched cddid_all.tbl CDD pfam09228 pfam09228 401243 Prok-TraM Prokaryotic Transcriptional repressor TraM. Members of this family of transcriptional repressors adopt a T-shaped structure, with a core composed of two antiparallel alpha-helices. These proteins can be divided into two parts, a 'globular head' and an 'elongated tail', and they negatively regulate conjugation and the expression of tra genes by antagonising traR/AAI-dependent activation. 102 matched cddid_all.tbl CDD pfam09229 pfam09229 462716 Aha1_N Activator of Hsp90 ATPase, N-terminal. Members of this family, which are predominantly found in the protein 'Activator of Hsp90 ATPase' adopt a secondary structure consisting of an N-terminal alpha-helix leading into a four-stranded meandering antiparallel beta-sheet, followed by a C-terminal alpha-helix. The two helices are packed together, with the beta-sheet curving around them. They bind to the molecular chaperone HSP82 and stimulate its ATPase activity. 134 matched cddid_all.tbl CDD pfam09230 pfam09230 462717 DFF40 DNA fragmentation factor 40 kDa. Members of this family of eukaryotic apoptotic proteins induce DNA fragmentation and chromatin condensation during apoptosis. 226 matched cddid_all.tbl CDD pfam09231 pfam09231 286334 RDV-p3 Rice dwarf virus p3. Members of this family are core structural proteins found in the double-stranded RNA virus Phytoreovirus. They are large proteins without apparent domain division, with a number of all-alpha regions and one all beta domain near the C-terminal end. 963 matched cddid_all.tbl CDD pfam09232 pfam09232 370376 Caenor_Her-1 Caenorhabditis elegans Her-1. Her-1 adopts an all-helical structure with two subdomains: residues 19-80 comprise a left-handed three-helix bundle with an overhand connection between the second and third helices, whilst residues 81-164 comprise a left-handed anti-parallel four-helix bundle in which the first helix consists of four consecutive turns of 3-10-helix. Fourteen Cys are conserved in all known HER-1 sequences and form seven disulfide bonds. The protein dictates male development in Caenorhabditis elegans, probably by playing a direct role in cell signaling during C. elegans sex determination. It also inhibits the function of tra-2a. 131 matched cddid_all.tbl CDD pfam09233 pfam09233 430474 Endonuc-EcoRV Restriction endonuclease EcoRV. Members of this family of prokaryotic restriction endonucleases recognize the double-stranded sequence 5'-GATATC-3' and cleave after T-3. They catalyze the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. 244 matched cddid_all.tbl CDD pfam09234 pfam09234 430475 DUF1963 Domain of unknown function (DUF1963). This domain is found in a set of hypothetical bacterial proteins. Its exact function has not, as yet, been described. 178 matched cddid_all.tbl CDD pfam09235 pfam09235 401248 SAM_Ste50p Ste50p, sterile alpha motif. The fungal Ste50p SAM domain consists of five helices, which form a compact, globular fold. It is required for mediation of homodimerization and heterodimerization (and in some cases oligomerization) of the protein. 75 matched cddid_all.tbl CDD pfam09236 pfam09236 462718 AHSP Alpha-haemoglobin stabilising protein. Alpha-haemoglobin stabilising protein (AHSP) acts a molecular chaperone for free alpha-haemoglobin, preventing the harmful aggregation of alpha-haemoglobin during normal erythroid cell development: it specifically protects free alpha-haemoglobin from precipitation. AHSP adopts a helical secondary structure consisting of an elongated antiparallel three alpha-helix bundle. 87 matched cddid_all.tbl CDD pfam09237 pfam09237 462719 GAGA GAGA factor. Members of this family bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognizes the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognizes the A in the fourth position of the consensus sequence. 54 matched cddid_all.tbl CDD pfam09238 pfam09238 462720 IL4Ra_N Interleukin-4 receptor alpha chain, N-terminal. Members of this family are related in overall topology to fibronectin type III modules and fold into a sandwich comprising seven antiparallel beta sheets arranged in a three-strand and a four-strand beta-pleated sheet. They are required for binding of interleukin-4 to the receptor alpha chain, which is a crucial event for the generation of a Th2-dominated early immune response. 94 matched cddid_all.tbl CDD pfam09239 pfam09239 430478 Topo-VIb_trans Topoisomerase VI B subunit, transducer. Members of this family adopt a structure consisting of a four-stranded beta-sheet backed by three alpha-helices, the last of which is over 50 amino acids long and extends from the body of the protein by several turns. This domain has been proposed to mediate intersubunit communication by structurally transducing signals from the ATP binding and hydrolysis domains to the DNA binding and cleavage domains of the gyrase holoenzyme. 157 matched cddid_all.tbl CDD pfam09240 pfam09240 401252 IL6Ra-bind Interleukin-6 receptor alpha chain, binding. Members of this family adopt a structure consisting of an immunoglobulin-like beta-sandwich, with seven strands in two beta-sheets, in a Greek-key topology. They are required for binding to the cytokine Interleukin-6. 96 matched cddid_all.tbl CDD pfam09241 pfam09241 462721 Herp-Cyclin Herpesviridae viral cyclin. Members of this family of viral cyclins adopt a helical structure consisting of five alpha-helices, with one helix surrounded by the others. They specifically activate CDK6 of host cells to a very high degree. 106 matched cddid_all.tbl CDD pfam09242 pfam09242 462722 FCSD-flav_bind Flavocytochrome c sulphide dehydrogenase, flavin-binding. Members of this family adopt a structure consisting of a beta(3,4)-alpha(3) core, and an alpha+beta sandwich. They are required for binding to flavin, and subsequent electron transfer. 69 matched cddid_all.tbl CDD pfam09243 pfam09243 401254 Rsm22 Mitochondrial small ribosomal subunit Rsm22. Rsm22 has been identified as a mitochondrial small ribosomal subunit and is a methyltransferase. In Schizosaccharomyces pombe, Rsm22 is tandemly fused to Cox11 (a factor required for copper insertion into cytochrome oxidase) and the two proteins are proteolytically cleaved after import into the mitochondria. 275 matched cddid_all.tbl CDD pfam09244 pfam09244 401255 DUF1964 Domain of unknown function (DUF1964). Members of this family of bacterial domains adopt a beta-sandwich fold, with Greek-key topology. They are C-terminal to the catalytic sucrose phosphorylase beta/alpha barrel domain, and are functionally uncharacterized. 67 matched cddid_all.tbl CDD pfam09245 pfam09245 312671 MA-Mit Mycoplasma arthritidis-derived mitogen. Mycoplasma arthritidis-derived mitogen (MA-Mit) adopts a completely alpha-helical structure consisting of ten alpha helices. It is a superantigen that can activate large fractions of T cells bearing particular TCR V-beta elements. Two MA-Mit molecules form an asymmetric dimer and cross-link two MHC antigens to form a dimerized MA-Mit-MHC complex. 213 matched cddid_all.tbl CDD pfam09246 pfam09246 430480 PHAT PHAT. The PHAT (pseudo-HEAT analogous topology) domain assumes a structure consisting of a layer of three parallel helices packed against a layer of two antiparallel helices, into a cylindrical shaped five-helix bundle. It is found in the RNA-binding protein Smaug, where it is essential for high-affinity RNA binding. 110 matched cddid_all.tbl CDD pfam09247 pfam09247 462723 TBP-binding TATA box-binding protein binding. Members of this family adopt a structure consisting of three alpha helices and a beta-hairpin. They bind to TATA box-binding protein (TBP), inhibiting TBP interaction with the TATA element, thereby resulting in shutting down of gene transcription. 59 matched cddid_all.tbl CDD pfam09248 pfam09248 430482 DUF1965 Domain of unknown function (DUF1965). Members of this family of fungal domains adopt a structure that consists of an alpha/beta motif. Their exact function has not, as yet, been determined. 68 matched cddid_all.tbl CDD pfam09249 pfam09249 430483 tRNA_NucTransf2 tRNA nucleotidyltransferase, second domain. Members of this family adopt a structure consisting of a five helical bundle core. They are predominantly found in Archaeal tRNA nucleotidyltransferase, following the catalytic nucleotidyltransferase domain. 111 matched cddid_all.tbl CDD pfam09250 pfam09250 430484 Prim-Pol Bifunctional DNA primase/polymerase, N-terminal. Members of this family adopt a structure consisting of a core of antiparallel beta sheets. They are found in various bacterial hypothetical proteins, and have been shown to harbour both primase and polymerase activities. 158 matched cddid_all.tbl CDD pfam09251 pfam09251 312676 PhageP22-tail Salmonella phage P22 tail-spike. Members of this family of viral domains adopt a structure consisting of a single-stranded right-handed beta-helix, which in turn is made of parallel beta-strands and short turns. They are required for recognition of the 0-antigenic repeating units of the cell surface, and for subsequent infection of the bacterial cell. 550 matched cddid_all.tbl CDD pfam09252 pfam09252 462724 Feld-I_B Allergen Fel d I-B chain. Members of this family of cat allergens adopt a helical structure consisting of eight alpha helices, in a Uteroglobin-like fold. They are one of the most important causes of allergic asthma worldwide. 67 matched cddid_all.tbl CDD pfam09253 pfam09253 401260 Ole_e_6 Pollen allergen Ole e 6. Members of this family consist of two nearly antiparallel alpha-helices, that are connected by a short loop and followed by a long, unstructured C-terminal tail. They are highly allergenic, primarily mediating olive allergy. 39 matched cddid_all.tbl CDD pfam09254 pfam09254 401261 FokI_cleav_dom FokI, cleavage domain. Members of this family are predominantly found in prokaryotic restriction endonuclease FokI, and adopt a structure consisting of an alpha/beta/alpha core containing a five-stranded beta-sheet. They recognize the double-stranded DNA sequence 5'-GGATG-3' and cleave DNA phosphodiester groups 9 base pairs away on this strand and 13 base pairs away on the complementary strand. This entry represents the C-terminal cleavage domain of FokI. 188 matched cddid_all.tbl CDD pfam09255 pfam09255 462725 Antig_Caf1 Caf1 Capsule antigen. Members of this family are predominantly found in the F1 capsule antigen Caf1 synthesized by Yersinia bacteria. They adopt a structure consisting of a seven strands arranged in two beta-sheets, in a Greek-key topology, and mediate targeting of the bacterium to sites of infection. 136 matched cddid_all.tbl CDD pfam09256 pfam09256 462726 BaffR-Tall_bind BAFF-R, TALL-1 binding. Members of this family, which are predominantly found in the tumour necrosis factor receptor superfamily member 13c, BAFF-R, are required for binding to tumour necrosis factor ligand TALL-1. 30 matched cddid_all.tbl CDD pfam09257 pfam09257 462727 BCMA-Tall_bind BCMA, TALL-1 binding. Members of this family, which are predominantly found in the tumour necrosis factor receptor superfamily member 17, BCMA, are required for binding to tumour necrosis factor ligand TALL-1. 37 matched cddid_all.tbl CDD pfam09258 pfam09258 430488 Glyco_transf_64 Glycosyl transferase family 64 domain. Members of this family catalyze the transfer reaction of N-acetylglucosamine and N-acetylgalactosamine from the respective UDP-sugars to the non-reducing end of [glucuronic acid]beta 1-3[galactose]beta 1-O-naphthalenemethanol, an acceptor substrate analog of the natural common linker of various glycosylaminoglycans. They are also required for the biosynthesis of heparan-sulphate. 241 matched cddid_all.tbl CDD pfam09259 pfam09259 401265 Fve Fungal immunomodulatory protein Fve. Fve is a major fruiting body protein from Flammulina velutipes, a mushroom possessing immunomodulatory activity. It stimulates lymphocyte mitogenesis, suppresses systemic anaphylaxis reactions and oedema, enhances transcription of IL-2, IFN-gamma and TNF-alpha, and haemagglutinates red blood cells. It appears to be a lectin with specificity for complex cell-surface carbohydrates. Fve adopts a tertiary structure consisting of an immunoglobulin-like beta-sandwich, with seven strands arranged in two beta sheets, in a Greek-key topology. It forms a non-covalently linked homodimer containing no Cys, His or Met residues; dimerization occurs by 3-D domain swapping of the N-terminal helices and is stabilized predominantly by hydrophobic interactions. 111 matched cddid_all.tbl CDD pfam09260 pfam09260 370390 A_amylase_dom_C Alpha-amylase, domain C. This domain is found at the C-terminal of various fungal alpha-amylase proteins. It has been identified as a secondary binding site, which might be part of a starch interaction site. It has a beta- sandwich fold comprising an antiparallel beta-sheet with eight strands. 90 matched cddid_all.tbl CDD pfam09261 pfam09261 462728 Alpha-mann_mid Alpha mannosidase middle domain. Members of this family adopt a structure consisting of three alpha helices, in an immunoglobulin/albumin-binding domain-like fold. They are predominantly found in the enzyme alpha-mannosidase. 98 matched cddid_all.tbl CDD pfam09262 pfam09262 462729 PEX-1N Peroxisome biogenesis factor 1, N-terminal. Members of this family adopt a double psi beta-barrel fold, similar in structure to the Cdc48 N-terminal domain. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation. 77 matched cddid_all.tbl CDD pfam09263 pfam09263 462730 PEX-2N Peroxisome biogenesis factor 1, N-terminal. Members of this family adopt a Cdc48 domain 2-like fold, with a beta-alpha-beta(3) arrangement. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation. 83 matched cddid_all.tbl CDD pfam09264 pfam09264 401269 Sial-lect-inser Vibrio cholerae sialidase, lectin insertion. Members of this family are predominantly found in Vibrio cholerae sialidase, and adopt a beta sandwich structure consisting of 12-14 strands arranged in two beta-sheets. They bind to lectins with high affinity helping to target the protein to sialic acid-rich environments, thereby enhancing the catalytic efficiency of the enzyme. 198 matched cddid_all.tbl CDD pfam09265 pfam09265 462731 Cytokin-bind Cytokinin dehydrogenase 1, FAD and cytokinin binding. Members of this family adopt an alpha+beta sandwich structure with an antiparallel beta-sheet, in a ferredoxin-like fold. They are predominantly found in plant cytokinin dehydrogenase 1, where they are capable of binding both FAD and cytokinin substrates. The substrate displays a 'plug-into-socket' binding mode that seals the catalytic site and precisely positions the carbon atom undergoing oxidation in close contact with the reactive locus of the flavin. 278 matched cddid_all.tbl CDD pfam09266 pfam09266 286365 VirDNA-topo-I_N Viral DNA topoisomerase I, N-terminal. Members of this family are predominantly found in viral DNA topoisomerase, and assume a beta(2)-alpha-beta-alpha-beta(2) fold, with a left-handed crossover between strands beta2 and beta3. 58 matched cddid_all.tbl CDD pfam09267 pfam09267 370396 Dict-STAT-coil Dictyostelium STAT, coiled coil. Members of this family are found in Dictyostelium STAT proteins and adopt a structure consisting of four long alpha-helices, folded into a coiled coil. They are responsible for nuclear export of the protein. 114 matched cddid_all.tbl CDD pfam09268 pfam09268 462732 Clathrin-link Clathrin, heavy-chain linker. Members of this family adopt a structure consisting of alpha-alpha superhelix. They are predominantly found in clathrin, where they act as a heavy-chain linker domain. 24 matched cddid_all.tbl CDD pfam09269 pfam09269 462733 DUF1967 Domain of unknown function (DUF1967). Members of this family contain a four-stranded beta sheet and three alpha helices flanked by an additional beta strand. They are predominantly found in the bacterial GTP-binding protein Obg, and are still functionally uncharacterized. 67 matched cddid_all.tbl CDD pfam09270 pfam09270 462734 BTD Beta-trefoil DNA-binding domain. Members of this family of DNA binding domains adopt a beta-trefoil fold, that is, a capped beta-barrel with internal pseudo threefold symmetry. In the DNA-binding protein LAG-1, it also is the site of mutually exclusive interactions with NotchIC (and the viral protein EBNA2) and co-repressors (SMRT/N-Cor and CIR). 123 matched cddid_all.tbl CDD pfam09271 pfam09271 462735 LAG1-DNAbind LAG1, DNA binding. Members of this family are found in various eukaryotic hypothetical proteins and in the DNA-binding protein LAG-1. They adopt a beta sandwich structure, with nine strands in two beta-sheets, in a Greek-key topology, and allow for DNA binding. This domain is also known as RHR-N (Rel-homology region) as it related to Rel domain proteins. 148 matched cddid_all.tbl CDD pfam09272 pfam09272 462736 Hepsin-SRCR Hepsin, SRCR domain. Members of this family form an extracellular domain of the serine protease hepsin. They are formed primarily by three elements of regular secondary structure: a 12-residue alpha helix, a twisted five-stranded antiparallel beta sheet, and a second, two-stranded, antiparallel sheet. The two beta-sheets lie at roughly right angles to each other, with the helix nestled between the two, adopting an SRCR fold. The exact function of this domain has not been identified, though it probably may serve to orient the protease domain or place it in the vicinity of its substrate. 110 matched cddid_all.tbl CDD pfam09273 pfam09273 462737 Rubis-subs-bind Rubisco LSMT substrate-binding. Members of this family adopt a multihelical structure, with an irregular array of long and short alpha-helices. They allow binding of the protein to substrate, such as the N-terminal tails of histones H3 and H4 and the large subunit of the Rubisco holoenzyme complex. 130 matched cddid_all.tbl CDD pfam09274 pfam09274 117819 ParG ParG. Members of this family of plasmid partition proteins adopt a ribbon-helix-helix fold, with a core of four alpha-helices. They are an essential component of the DNA partition complex of the multidrug resistance plasmid TP228. 76 matched cddid_all.tbl CDD pfam09275 pfam09275 286372 Pertus-S4-tox Pertussis toxin S4 subunit. Members of this family of Bordetella pertussis toxins adopt a structure consisting of an OB fold, with a closed or partly opened beta-barrel in a Greek-key topology. 110 matched cddid_all.tbl CDD pfam09276 pfam09276 462738 Pertus-S5-tox Pertussis toxin S5 subunit. Members of this family of Bordetella pertussis toxins adopt a structure consisting of an OB fold, with a closed or partly opened beta-barrel in a Greek-key topology. 97 matched cddid_all.tbl CDD pfam09277 pfam09277 401277 Erythro-docking Erythronolide synthase, docking. Members of this family of docking domains are found in prokaryotic erythronolide synthase. They adopt a structure consisting of a bundle of four alpha-helices, and mediate homodimerization of the protein, stabilising the resulting complex. 58 matched cddid_all.tbl CDD pfam09278 pfam09278 462739 MerR-DNA-bind MerR, DNA binding. Members of this family of DNA-binding domains are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold. 65 matched cddid_all.tbl CDD pfam09279 pfam09279 401279 EF-hand_like Phosphoinositide-specific phospholipase C, efhand-like. Members of this family are predominantly found in phosphoinositide-specific phospholipase C. They adopt a structure consisting of a core of four alpha helices, in an EF like fold, and are required for functioning of the enzyme. 85 matched cddid_all.tbl CDD pfam09280 pfam09280 462740 XPC-binding XPC-binding domain. Members of this family adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair. 57 matched cddid_all.tbl CDD pfam09281 pfam09281 430500 Taq-exonuc Taq polymerase, exonuclease. Members of this family are found in prokaryotic Taq DNA polymerase, where they assume a ribonuclease H-like motif. The domain confers 5'-3' exonuclease activity to the polymerase. 129 matched cddid_all.tbl CDD pfam09282 pfam09282 462741 Mago-bind Mago binding. Members of this family adopt a structure consisting of a small globular all-beta-domain, with a three-stranded beta-sheet and a contiguous beta-hairpin. They bind to Mago alpha-helices via extensive electrostatic interactions and at a beta2-beta3 loop via hydrophobic interactions. 27 matched cddid_all.tbl CDD pfam09284 pfam09284 462742 RhgB_N Rhamnogalacturonan lyase B, N-terminal. Members of this family are found in both fungi, bacteria and wood-eating arthropods. The domain is found at the N-terminus of rhamnogalacturonase B, a member of the polysaccharide lyase family 4. The domain adopts a structure consisting of a beta super-sandwich, with eighteen strands in two beta-sheets. The three domains of the whole protein rhamnogalacturonan lyase (RGL4), are involved in the degradation of rhamnogalacturonan-I, RG-I, an important pectic plant cell-wall polysaccharide. The active-site residues are a lysine at position 169 in UniProtKB:Q00019 and a histidine at 229, Lys169 is likely to be a proton abstractor, His229 a proton donor in the mechanism. The substrate is a disaccharide, and RGL4, in contrast to other rhamnogalacturonan hydrolases, cleaves the alpha-1,4 linkages of RG-I between Rha and GalUA through a beta-elimination resulting in a double bond in the nonreducing GalUA residue, and is thus classified as a polysaccharide lyase (PL). 249 matched cddid_all.tbl CDD pfam09285 pfam09285 430503 Elong-fact-P_C Elongation factor P, C-terminal. Members of this family of nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology. 56 matched cddid_all.tbl CDD pfam09286 pfam09286 401284 Pro-kuma_activ Pro-kumamolisin, activation domain. Members of this family are found in various subtilase propeptides, and adopt a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptide. 142 matched cddid_all.tbl CDD pfam09287 pfam09287 401285 CEP1-DNA_bind CEP-1, DNA binding. Members of this family of DNA-binding domains are found the transcription factor CEP-1. They adopt a beta sandwich structure, with nine strands in two beta-sheets, in a Greek-key topology. 198 matched cddid_all.tbl CDD pfam09288 pfam09288 117832 UBA_3 Fungal ubiquitin-associated domain. Members of this family of ubiquitin binding domains adopt a structure consisting of a three alpha-helix bundle. They are predominantly found in fungal ubiquitin-protein ligases. 55 matched cddid_all.tbl CDD pfam09289 pfam09289 462743 FOLN Follistatin/Osteonectin-like EGF domain. Members of this family are predominantly found in osteonectin and follistatin and adopt an EGF-like fold. 22 matched cddid_all.tbl CDD pfam09290 pfam09290 430505 AcetDehyd-dimer Prokaryotic acetaldehyde dehydrogenase, dimerization. Members of this family are found in prokaryotic acetaldehyde dehydrogenase (acylating), and adopt a structure consisting of an alpha-beta-alpha-beta(3) core. They mediate dimerization of the protein. 138 matched cddid_all.tbl CDD pfam09291 pfam09291 462744 DUF1968 Domain of unknown function (DUF1968). Members of this family are found in mammalian T-cell antigen receptor, and adopt an immunoglobulin-like beta-sandwich fold, with seven strands in two beta-sheets in a Greek-key topology. Their exact function has not, as yet, been determined. 80 matched cddid_all.tbl CDD pfam09292 pfam09292 462745 Neil1-DNA_bind Endonuclease VIII-like 1, DNA bind. Members of this family are predominantly found in Endonuclease VIII-like 1 and adopt a glucocorticoid receptor-like fold. They allow for DNA binding. 39 matched cddid_all.tbl CDD pfam09293 pfam09293 401290 RNaseH_C T4 RNase H, C terminal. Members of this family are found in T4 RNaseH ribonuclease, and adopt a SAM domain-like fold, consisting of a bundle of four/five helices. These residues may have a role in providing a docking site for other proteins or enzymes in the replication fork. 124 matched cddid_all.tbl CDD pfam09294 pfam09294 462746 Interfer-bind Interferon-alpha/beta receptor, fibronectin type III. Members of this family adopt a secondary structure consisting of seven beta-strands arranged in an immunoglobulin-like beta-sandwich, in a Greek-key topology. They are required for binding to interferon-alpha. 103 matched cddid_all.tbl CDD pfam09295 pfam09295 401292 ChAPs ChAPs (Chs5p-Arf1p-binding proteins). ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialized cargo from the Golgi. They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they form also interactions with each other. 395 matched cddid_all.tbl CDD pfam09296 pfam09296 462747 NUDIX-like NADH pyrophosphatase-like rudimentary NUDIX domain. The N-terminal domain in NADH pyrophosphatase, which has a rudiment Nudix fold according to SCOP. 96 matched cddid_all.tbl CDD pfam09297 pfam09297 430510 zf-NADH-PPase NADH pyrophosphatase zinc ribbon domain. This domain is found in between two duplicated NUDIX domains. It has a zinc ribbon structure. 32 matched cddid_all.tbl CDD pfam09298 pfam09298 462748 FAA_hydrolase_N Fumarylacetoacetase N-terminal. The N-terminal domain of fumarylacetoacetate hydrolase is functionally uncharacterized, and adopts a structure consisting of an SH3-like barrel. 104 matched cddid_all.tbl CDD pfam09299 pfam09299 430512 Mu-transpos_C Mu transposase, C-terminal. Members of this family are found in various prokaryotic integrases and transposases. They adopt a beta-barrel structure with Greek-key topology. 61 matched cddid_all.tbl CDD pfam09300 pfam09300 286393 Tecti-min-caps Tectiviridae, minor capsid. Members of this family form the minor capsid protein of various Tectiviridae. 83 matched cddid_all.tbl CDD pfam09301 pfam09301 401297 DUF1970 Domain of unknown function (DUF1970). Members of this family consist of various uncharacterized viral hypothetical proteins. 118 matched cddid_all.tbl CDD pfam09302 pfam09302 462749 XLF XLF-Cernunnos, XRcc4-like factor, NHEJ component. XLF (also called Cernunnos) is Xrcc4-like-factor, and interacts with the XRCC4-DNA ligase IV complex to promote DNA non-homologous end-joining. It directly interacts with the XRCC4-Ligase IV complex and siRNA-mediated down-regulation of XLF in human cell lines leads to radio-sensitivity and impaired DNA non-homologous end-joining. This family contains Nej1 (non-homologous end-joining factor), and Lif1, ligase-interacting factor. XLF forms one of the components of the NHEJ machinery for DNA non-homologous end-joining. 180 matched cddid_all.tbl CDD pfam09303 pfam09303 401299 KcnmB2_inactiv KCNMB2, ball and chain domain. Members of this family are found in the cytoplasmic N-terminus of KCNMB2, the beta-2 subunit of large conductance calcium and voltage-activated potassium channels. They are responsible for the fast inactivation of these channels. 30 matched cddid_all.tbl CDD pfam09304 pfam09304 312712 Cortex-I_coil Cortexillin I, coiled coil. Members of this family are predominantly found in the actin-bundling protein Cortexillin I from Dictyostelium discoideum. They adopt a structure consisting of an 18-heptad-repeat alpha-helical coiled-coil, and are a prerequisite for the assembly of Cortexillin I. 107 matched cddid_all.tbl CDD pfam09305 pfam09305 370419 TACI-CRD2 TACI, cysteine-rich domain. Members of this family are predominantly found in tumour necrosis factor receptor superfamily, member 13b (TACI), and are required for binding to the ligands APRIL and BAFF. 39 matched cddid_all.tbl CDD pfam09306 pfam09306 286399 Phage-scaffold Bacteriophage, scaffolding protein. Members of this family of scaffolding proteins are produced by various bacteriophages. 303 matched cddid_all.tbl CDD pfam09307 pfam09307 462750 MHC2-interact CLIP, MHC2 interacting. Members of this family are found in class II invariant chain-associated peptide (CLIP), and are required for association with class II major histocompatibility complex (MHC) in the MHC class II processing pathway. 109 matched cddid_all.tbl CDD pfam09308 pfam09308 430514 LuxQ-periplasm LuxQ, periplasmic. Members of this family constitute the periplasmic sensor domain of the prokaryotic protein LuxQ, and assume a structure consisting of two tandem Per/ARNT/Simple-minded (PAS) folds. 239 matched cddid_all.tbl CDD pfam09309 pfam09309 462751 FCP1_C FCP1, C-terminal. The C-terminal domain of FCP-1 is required for interaction with the carboxy terminal domain of RAP74. Interaction relies extensively on van der Waals contacts between hydrophobic residues situated within alpha-helices in both domains. 254 matched cddid_all.tbl CDD pfam09310 pfam09310 430516 PD-C2-AF1 POU domain, class 2, associating factor 1. Members of this family are transcriptional coactivators that specifically associate with either OCT1 or OCT2, through recognition of their POU domains. They are essential for the response of B-cells to antigens and required for the formation of germinal centres. 249 matched cddid_all.tbl CDD pfam09311 pfam09311 462752 Rab5-bind Rabaptin-like protein. Members of this family are predominantly found in Rabaptin and allow for binding to the GTPase Rab5. This interaction is necessary and sufficient for Rab5-dependent recruitment of Rabaptin5 to early endosomal membranes. 307 matched cddid_all.tbl CDD pfam09312 pfam09312 430518 SurA_N SurA N-terminal domain. This domain is found at the N-terminus of the chaperone SurA. It is a helical domain of unknown function. The C-terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. 118 matched cddid_all.tbl CDD pfam09313 pfam09313 430519 DUF1971 Domain of unknown function (DUF1971). Members of this family of functionally uncharacterized domains are predominantly found in bacterial Tellurite resistance protein. 80 matched cddid_all.tbl CDD pfam09314 pfam09314 430520 DUF1972 Domain of unknown function (DUF1972). Members of this family of functionally uncharacterized domains are found in bacterial glycosyltransferases and rhamnosyltransferases. 186 matched cddid_all.tbl CDD pfam09316 pfam09316 462753 Cmyb_C C-myb, C-terminal. Members of this family are predominantly found in the proto-oncogene c-myb and the viral transforming protein myb. Truncation of the domain results in 'activation' of c-myb and subsequent tumourigenesis. 157 matched cddid_all.tbl CDD pfam09317 pfam09317 430522 ACDH_C Acyl-CoA dehydrogenase, C-terminal, bacterial type. This C-terminal domain is functionally uncharacterized and is predominantly found in various prokaryotic acyl-coenzyme A dehydrogenases and seems to be essential for its function. 284 matched cddid_all.tbl CDD pfam09318 pfam09318 370428 Glyco_trans_A_1 Glycosyl transferase 1 domain A. Glyco_trans_A_1 is family of found predominantly at the N-terminus of various prokaryotic alpha-glucosyltransferases. According to whether the domain exists as a whole molecule or as a half molecule determines the number of sugar residues that the molecule transfers. Two-domain proteins are processive in that they transfer more than one sugar residue, processively; single domain proteins transfer just one sugar moiety. 199 matched cddid_all.tbl CDD pfam09320 pfam09320 462754 DUF1977 Domain of unknown function (DUF1977). Members of this family of functionally uncharacterized domains are predominantly found in dnaj-like proteins. 108 matched cddid_all.tbl CDD pfam09321 pfam09321 312723 DUF1978 Domain of unknown function (DUF1978). Members of this family are found in various hypothetical proteins produced by the bacterium Chlamydia pneumoniae. Their exact function has not, as yet, been identified. 244 matched cddid_all.tbl CDD pfam09322 pfam09322 430524 DUF1979 Domain of unknown function (DUF1979). Members of this family of functionally uncharacterized domains are found in various Oryza sativa mutator-like transposases. 58 matched cddid_all.tbl CDD pfam09323 pfam09323 462755 DUF1980 Domain of unknown function (DUF1980). Members of this family are found in a set of prokaryotic hypothetical proteins. Their exact function, has not, as yet, been defined. 180 matched cddid_all.tbl CDD pfam09324 pfam09324 462756 DUF1981 Domain of unknown function (DUF1981). Members of this family of functionally uncharacterized domains are found in various plant and yeast protein transport proteins. 84 matched cddid_all.tbl CDD pfam09325 pfam09325 430527 Vps5 Vps5 C terminal like. Vps5 is a sorting nexin that functions in membrane trafficking. This is the C terminal dimerization domain. 236 matched cddid_all.tbl CDD pfam09326 pfam09326 462757 NADH_dhqG_C NADH-ubiquinone oxidoreductase subunit G, C-terminal. Members of this family of are found at the C-terminus of NADH dehydrogenases subunit G or NADH-ubiquinone oxidoreductase subunit G. EC:1.6.99.5. 41 matched cddid_all.tbl CDD pfam09327 pfam09327 430529 DUF1983 Domain of unknown function (DUF1983). Members of this family of functionally uncharacterized domains are found in various bacteriophage host specificity proteins. 75 matched cddid_all.tbl CDD pfam09328 pfam09328 401316 Phytochelatin_C Domain of unknown function (DUF1984). Members of this family of functionally uncharacterized domains are found at the C-terminus of plant phytochelatin synthases. 252 matched cddid_all.tbl CDD pfam09329 pfam09329 462758 zf-primase Primase zinc finger. This zinc finger is found in yeast Mcm10 proteins and DnaG-type primases. 46 matched cddid_all.tbl CDD pfam09330 pfam09330 430531 Lact-deh-memb D-lactate dehydrogenase, membrane binding. Members of this family are predominantly found in prokaryotic D-lactate dehydrogenase, forming the cap-membrane-binding domain, which consists of a large seven-stranded antiparallel beta-sheet flanked on both sides by alpha-helices. They allow for membrane association. 290 matched cddid_all.tbl CDD pfam09331 pfam09331 462759 DUF1985 Domain of unknown function (DUF1985). Members of this family of functionally uncharacterized domains are found in a set of Arabidopsis thaliana hypothetical proteins. 133 matched cddid_all.tbl CDD pfam09332 pfam09332 462760 Mcm10 Mcm10 replication factor. Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha. 349 matched cddid_all.tbl CDD pfam09333 pfam09333 462761 ATG_C Autophagy-related protein C terminal domain. ATG2 (also known as Apg2) is a peripheral membrane protein. It functions in both cytoplasm-to-vacuole targeting and in autophagy. 96 matched cddid_all.tbl CDD pfam09334 pfam09334 401322 tRNA-synt_1g tRNA synthetases class I (M). This family includes methionyl tRNA synthetases. 387 matched cddid_all.tbl CDD pfam09335 pfam09335 430535 SNARE_assoc SNARE associated Golgi protein. This is a family of SNARE associated Golgi proteins. The yeast member of this family localizes with the t-SNARE Tlg2. 120 matched cddid_all.tbl CDD pfam09336 pfam09336 462762 Vps4_C Vps4 C terminal oligomerization domain. This domain is found at the C terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerization. 61 matched cddid_all.tbl CDD pfam09337 pfam09337 430537 zf-H2C2 H2C2 zinc finger. This domain binds to histone upstream activating sequence (UAS) elements that are found in histone gene promoters. 39 matched cddid_all.tbl CDD pfam09338 pfam09338 430538 Gly_reductase Glycine/sarcosine/betaine reductase component B subunits. This is a family of glycine reductase, sarcosine reductase and betaine reductases. These enzymes catalyze the following reactions. sarcosine reductase: Acetyl phosphate + methylamine + thioredoxin disulphide = N-methylglycine + phosphate + thioredoxin Acetyl phosphate + NH(3) + thioredoxin disulphide = glycine + phosphate + thioredoxin. betaine reductase: Acetyl phosphate + trimethylamine + thioredoxin disulphide = N,N,N-trimethylglycine + phosphate + thioredoxin. 426 matched cddid_all.tbl CDD pfam09339 pfam09339 430539 HTH_IclR IclR helix-turn-helix domain. 52 matched cddid_all.tbl CDD pfam09340 pfam09340 462763 NuA4 Histone acetyltransferase subunit NuA4. The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast. NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control. 78 matched cddid_all.tbl CDD pfam09341 pfam09341 462764 Pcc1 Transcription factor Pcc1. Pcc1 is a transcription factor that functions in regulating genes involved in cell cycle progression and polarised growth. 75 matched cddid_all.tbl CDD pfam09342 pfam09342 286432 DUF1986 Domain of unknown function (DUF1986). This domain is found in serine proteases and is predicted to contain disulphide bonds. 116 matched cddid_all.tbl CDD pfam09343 pfam09343 430542 DUF2460 Conserved hypothetical protein 2217 (DUF2460). This model represents a family of conserved hypothetical proteins. It is usually (but not always) found in apparent phage-derived regions of bacterial chromosomes. 204 matched cddid_all.tbl CDD pfam09344 pfam09344 430543 Cas_CT1975 CT1975-like protein. CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family is represented by CT1975 of Chlorobium tepidum. 352 matched cddid_all.tbl CDD pfam09345 pfam09345 430544 SiaC SiaC family regulatory phosphoprotein. This entry represents the SiaC family regulatory phosphoprotein which undergoes a regulatory phosphorylation at Thr-68 of founder protein PA0170 from Pseudomonas aeruginosa, but in more distant homologs, T can be S. Also, it is part of motif NTSS, so may contain more than one phosphorylation site. Phosphorylation causes regulatory change to protein-protein interaction, in a pathway that seems broadly distributed, involves a diguanylate cyclase, and in the case of Pseudomonas aeruginosa affects aggregation and biofilm formation responses. 121 matched cddid_all.tbl CDD pfam09346 pfam09346 430545 SMI1_KNR4 SMI1 / KNR4 family (SUKH-1). Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation. Genome contextual information showed that SMI1 are primary immunity proteins in bacterial toxin systems. 120 matched cddid_all.tbl CDD pfam09347 pfam09347 430546 DUF1989 Domain of unknown function (DUF1989). This family of proteins are functionally uncharacterized. 165 matched cddid_all.tbl CDD pfam09348 pfam09348 430547 DUF1990 Domain of unknown function (DUF1990). This family of proteins are functionally uncharacterized. 152 matched cddid_all.tbl CDD pfam09349 pfam09349 462765 OHCU_decarbox OHCU decarboxylase. The proteins in this family are OHCU decarboxylase - enzymes of the purine catabolism that catalyze the conversion of OHCU into S(+)-allantoin. This is the third step of the conversion of uric acid (a purine derivative) to allantoin. Step one is catalyzed by urate oxidase (pfam01014) and step two is catalyzed by HIUases (pfam00576). 156 matched cddid_all.tbl CDD pfam09350 pfam09350 462766 DJC28_CD DnaJ homolog, subfamily C, member 28, conserved domain. This domain is found in proteins that may have a role in protein folding or as a chaperone, including DnaJ homolog subfamily C member 28. DnaJ is a member of the J-protein family (also known as HSP40), which are defined by the presence of a J domain that regulate the activity of 70kDa heat-shock proteins. The function of this domain is not yet known. 72 matched cddid_all.tbl CDD pfam09351 pfam09351 462767 DUF1993 Domain of unknown function (DUF1993). This family of proteins are functionally uncharacterized. 161 matched cddid_all.tbl CDD pfam09353 pfam09353 430551 DUF1995 Domain of unknown function (DUF1995). This family of proteins are functionally uncharacterized. 201 matched cddid_all.tbl CDD pfam09354 pfam09354 430552 HNF_C HNF3 C-terminal domain. This presumed domain is found in the C-terminal region of Hepatocyte Nuclear Factor 3 alpha and beta chains. Its specific function is uncertain. The N-terminal region of this presumed domain contains an EH1 (engrailed homology 1) motif, that is characterized by the FxIxxIL sequence. 67 matched cddid_all.tbl CDD pfam09355 pfam09355 430553 Phage_Gp19 Phage protein Gp19/Gp15/Gp42. This family of proteins are functionally uncharacterized. They are found in a variety of bacteriophage. 116 matched cddid_all.tbl CDD pfam09356 pfam09356 430554 Phage_BR0599 Phage conserved hypothetical protein BR0599. This entry describes a family of proteins found almost exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus gene transfer agent, which packages DNA. An apparent exception is Wolbachia pipientis wMel, a bacterial endosymbiont of the fruit fly, which has several candidate phage-related genes physically separate from obvious prophage regions. 80 matched cddid_all.tbl CDD pfam09357 pfam09357 430555 RteC RteC protein. Human colonic Bacteroides species harbor a family of large conjugative transposons, called tetracycline resistance (Tcr) elements. Activities of these elements are enhanced by pregrowth of bacteria in medium containing tetracycline, indicating that at least some Tcr element genes are regulated by tetracycline. An insertional disruption in the rteC gene abolished self-transfer of the Tcr element to Bacteroides recipients, indicating that the gene was essential for self-transfer. 218 matched cddid_all.tbl CDD pfam09358 pfam09358 462768 E1_UFD Ubiquitin fold domain. The ubiquitin fold domain is found at the C-terminus of ubiquitin-activating E1 family enzymes. This domain binds to E2 enzymes. 93 matched cddid_all.tbl CDD pfam09359 pfam09359 401343 VTC VTC domain. This presumed domain is found in the yeast vacuolar transport chaperone proteins VTC2, VTC3 and VTC4. This domain is also found in a variety of bacterial proteins. 235 matched cddid_all.tbl CDD pfam09360 pfam09360 462769 zf-CDGSH Iron-binding zinc finger CDGSH type. The CDGSH-type zinc finger domain binds iron rather than zinc as a redox-active pH-labile 2Fe-2S cluster. The conserved sequence C-X-C-X2-(S/T)-X3-P-X-C-D-G-(S/A/T)-H is a defining feature of this family. The domain is oriented towards the cytoplasm and is tethered to the mitochondrial membrane by a more N-terminal domain found in higher vertebrates, MitoNEET_N, pfam10660. The domain forms a uniquely folded homo-dimer and spans the outer mitochondrial membrane, orienting the iron-binding residues towards the cytoplasm. 41 matched cddid_all.tbl CDD pfam09361 pfam09361 462770 Phasin_2 Phasin protein. This entry describes a group of small proteins found associated with inclusions in bacterial cells. Most associate with polyhydroxyalkanoate (PHA) inclusions, the most common of which consist of polyhydroxybutyrate (PHB). These are designated granule-associate proteins or phasins. 90 matched cddid_all.tbl CDD pfam09362 pfam09362 462771 DUF1996 Domain of unknown function (DUF1996). This family of proteins are functionally uncharacterized. 234 matched cddid_all.tbl CDD pfam09363 pfam09363 462772 XFP_C XFP C-terminal domain. Bacterial enzyme splits fructose-6-P and/or xylulose-5-P with the aid of inorganic phosphate into either acetyl-P and erythrose-4-P and/or acetyl-P and glyeraldehyde-3-P EC:4.1.2.9, EC:4.1.2.22. 200 matched cddid_all.tbl CDD pfam09364 pfam09364 401348 XFP_N XFP N-terminal domain. Bacterial enzyme splits fructose-6-P and/or xylulose-5-P with the aid of inorganic phosphate into either acetyl-P and erythrose-4-P and/or acetyl-P and glyeraldehyde-3-P EC:4.1.2.9, EC:4.1.2.22. This family is distantly related to transketolases e.g. pfam02779. 364 matched cddid_all.tbl CDD pfam09365 pfam09365 462773 DUF2461 Conserved hypothetical protein (DUF2461). Members of this family are widely (though sparsely) distributed bacterial proteins, about 230 residues in length. All members have a motif RxxRDxRFxxx[DN]KxxY. The function of this protein family is unknown. 207 matched cddid_all.tbl CDD pfam09366 pfam09366 462774 DUF1997 Protein of unknown function (DUF1997). This family of proteins are functionally uncharacterized. 153 matched cddid_all.tbl CDD pfam09367 pfam09367 430563 CpeS CpeS-like protein. This family, that includes CpeS proteins, is functionally uncharacterized. 168 matched cddid_all.tbl CDD pfam09368 pfam09368 462775 Sas10 Sas10 C-terminal domain. Sas10 is an Essential subunit of U3-containing Small Subunit (SSU) processome complex involved in the production of the 18S rRNA and assembly of the small ribosomal subunit. 74 matched cddid_all.tbl CDD pfam09369 pfam09369 462776 MZB MrfA Zn-binding domain. This is the C-terminal MrfA Zn+2-binding domain (MZB, also referred to as DUF1998) which contains a conserved four-cysteine signature motif. These four Cys reside in a short coil between two alpha-helices and form a metal ion-binding site. This domain is frequently found at the C-terminal of ndNTPases, however, it is also found encoded in a standalone gene, downstream of putative helicase domain-encoding genes associated with bacterial anti-phage defense system DISARM. MrfA (Mitomycin repair factor A, also known as YprA in Bacillus subtilis) is a DNA helicase that supports repair of mitomycin C-induced DNA damage. MrfA homologs are widely distributed in bacteria and are also present in archaea, fungi and plants. The MrfA-homolog in yeast, Hrq1, also reduces mitomycin C sensitivity. Hrq1 has high similarity to human RecQ4 and was therefore assigned to the RecQ-like helicase family. MrfA homologs appear to be missing in Enterobacteria, however, certain pathogenic Escherichia coli and Salmonella strains harbour Z5898-like helicases with this domain. 78 matched cddid_all.tbl CDD pfam09370 pfam09370 430566 PEP_hydrolase Phosphoenolpyruvate hydrolase-like. This domain has a TIM barrel fold related to IGPS and to phosphoenolpyruvate mutase/aldolase/carboxylase. 266 matched cddid_all.tbl CDD pfam09371 pfam09371 462777 Tex_N Tex-like protein N-terminal domain. This presumed domain is found at the N-terminus of Swiss:Q45388. This protein defines a novel family of prokaryotic transcriptional accessory factors. 183 matched cddid_all.tbl CDD pfam09372 pfam09372 286461 PRANC PRANC domain. This presumed domain is found at the C-terminus of a variety of Pox virus proteins. The PRANC (Pox proteins Repeats of ANkyrin - C terminal) domain is also found on its own in some proteins. The function of this domain is unknown, but it appears to be related to the F-box domain and may play a similar role. 95 matched cddid_all.tbl CDD pfam09373 pfam09373 117915 PMBR Pseudomurein-binding repeat. Methanothermobacter thermautotrophicus is a methanogenic Gram-positive microorganizm with a cell wall consisting of pseudomurein. This repeat specifically binds to pseudomurein. This repeat is found at the N terminus of PeiW and PeiP which are pseudomurein binding phage proteins. 33 matched cddid_all.tbl CDD pfam09374 pfam09374 401356 PG_binding_3 Predicted Peptidoglycan domain. This family contains a potential peptidoglycan binding domain. 76 matched cddid_all.tbl CDD pfam09375 pfam09375 430568 Peptidase_M75 Imelysin. The imelysin peptidase was first identified in Pseudomonas aeruginosa. The active site residues have not been identified. However, His201 and Glu204 are completely conserved in the family and occur in an HXXE motif that is also found in family M14. 289 matched cddid_all.tbl CDD pfam09376 pfam09376 401358 NurA NurA domain. This family includes NurA a nuclease exhibiting both single-stranded endonuclease activity and 5'-3' exonuclease activity on single-stranded and double-stranded DNA from the hyperthermophilic archaeon Sulfolobus acidocaldarius. 252 matched cddid_all.tbl CDD pfam09377 pfam09377 462778 SBDS_domain_II SBDS protein, domain II. Members containing this domain are highly conserved in species ranging from archaea to vertebrates and plants, including several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. These proteins play a role in RNA metabolism. In yeast Sdo1 is involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes. SBDS protein is composed of three domains. The N-terminal (pfam01172) (FYSH) domain (domain I) is the most frequent target for disease mutations and contains a novel mixed alpha/beta-fold, the central domain (domain II) represented in this entry consists of a three-helical bundle and the C-terminal domain that has a ferredoxin-like fold. 62 matched cddid_all.tbl CDD pfam09378 pfam09378 401360 HAS-barrel HAS barrel domain. The HAS barrel is named after HerA-ATP Synthase. In ATP synthases, this domain is implicated in the assembly of the catalytic toroid and docking of accessory subunits, such as the subunit of the ATP synthase complex. Similar roles in docking of the functional partner, the NurA nuclease, and assembly of the HerA toroid complex appear likely for the HAS-barrel of the HerA family. 91 matched cddid_all.tbl CDD pfam09379 pfam09379 430570 FERM_N FERM N-terminal domain. This domain is the N-terminal ubiquitin-like structural domain of the FERM domain. 63 matched cddid_all.tbl CDD pfam09380 pfam09380 462779 FERM_C FERM C-terminal PH-like domain. 85 matched cddid_all.tbl CDD pfam09381 pfam09381 401363 Porin_OmpG Outer membrane protein G (OmpG). Porins are channel proteins in the outer membrane of gram negative bacteria which mediate the uptake of molecules required for growth and survival. Escherichia coli OmpG forms a 14 stranded beta-barrel and in contrast to most porins, appears to function as a monomer. The central pore of OmpG is wider than other E. coli porins and it is speculated that it may form a non-specific channel for the transport of larger oligosaccharides. 285 matched cddid_all.tbl CDD pfam09382 pfam09382 462780 RQC RQC domain. This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure. The RQC domain, found only in RecQ family enzymes, is a high affinity G4 DNA binding domain. 108 matched cddid_all.tbl CDD pfam09383 pfam09383 462781 NIL NIL domain. This domain is found at the C-terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family. 73 matched cddid_all.tbl CDD pfam09384 pfam09384 462782 UTP15_C UTP15 C terminal. U3 snoRNA is ubiquitous in eukaryotes and is required for nucleolar processing of pre-18S ribosomal RNA. It is a component of the ribosomal small subunit (SSU) processome. UTP15 is needed for optimal pre-ribosomal RNA transcription by RNA polymerase I, together with a subset of U3 proteins required for transcription (t-UTPs). This entry represents the C terminal of UTP15, and is found adjacent to WD40 repeats (pfam00400). 146 matched cddid_all.tbl CDD pfam09385 pfam09385 286473 HisK_N Histidine kinase N terminal. This domain is found at the N terminal of sensor histidine kinase proteins. 129 matched cddid_all.tbl CDD pfam09386 pfam09386 430575 ParD Antitoxin ParD. ParD is a plasmid anti-toxin than forms a ribbon-helix-helix DNA binding structure. It stabilizes plasmids by inhibiting ParE toxicity in cells that express ParD and ParE. ParD forms a dimer and also regulates its own promoter (parDE). 80 matched cddid_all.tbl CDD pfam09387 pfam09387 430576 MRP Mitochondrial RNA binding protein MRP. MRP1 and MRP2 are mitochondrial RNA binding proteins that form a heteromeric complex. The MRP1/MRP2 heterotetrameric complex binds to guide RNAs and stabilizes them in an unfolded conformation suitable for RNA-RNA hybridization. Each MRP subunit adopts a 'whirly' transcription factor fold. 192 matched cddid_all.tbl CDD pfam09388 pfam09388 462783 SpoOE-like Spo0E like sporulation regulatory protein. Spore formation is an extreme response to starvation and can also be a component of disease transmission. Sporulation is controlled by an expanded two-component system where starvation signals result in sensor kinase activation and phosphorylation of the master sporulation response regulator Spo0A. Phosphatases such as Spo0E dephosphorylate Spo0A thereby inhibiting sporulation. This is a family of Spo0E-like phosphatases. The structure of a Bacillus anthracis member of this family has revealed an anti-parallel alpha-helical structure. 42 matched cddid_all.tbl CDD pfam09390 pfam09390 370462 DUF1999 Protein of unknown function (DUF1999). This family contains a putative Fe-S binding reductase whose structure adopts an alpha and beta fold. 151 matched cddid_all.tbl CDD pfam09391 pfam09391 462784 DUF2000 Protein of unknown function (DUF2000). This is a family of proteins of unknown function. The structure of one of the proteins in this family has been shown to adopt an alpha beta fold. 133 matched cddid_all.tbl CDD pfam09392 pfam09392 430579 T3SS_needle_F Type III secretion needle MxiH, YscF, SsaG, EprI, PscF, EscF. Type III secretion systems are essential virulence determinants for many gram-negative bacterial pathogens. MxiH is an extracellular alpha helical needle that is required for translocation of effector proteins into host cells. Once inside, the effector proteins subvert normal cell function to aid infection. The needle protein F, polymerizes to form a shaft. 67 matched cddid_all.tbl CDD pfam09393 pfam09393 430580 DUF2001 Phage tail tube protein. This is a family of phage tail tube proteins including protein XkdM from phage-like element PBSX protein whose structure adopts a beta barrel flanked with alpha helical regions. 138 matched cddid_all.tbl CDD pfam09394 pfam09394 462785 Inhibitor_I42 Chagasin family peptidase inhibitor I42. Chagasin is a cysteine peptidase inhibitor which forms a beta barrel structure. 90 matched cddid_all.tbl CDD pfam09396 pfam09396 430582 Thrombin_light Thrombin light chain. Thrombin is an enzyme that cleaves bonds after Arg and Lys, converts fibrinogen to fibrin and activates factors V, VII, VIII. Prothrombin is activated on the surface of a phospholipid membrane where factor Xa removes the activation peptide and cleaves the remaining part into light and heavy chains. This domain corresponds to the light chain of thrombin. 48 matched cddid_all.tbl CDD pfam09397 pfam09397 462786 FtsK_gamma Ftsk gamma domain. This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding. 63 matched cddid_all.tbl CDD pfam09398 pfam09398 312785 FOP_dimer FOP N terminal dimerization domain. Fibroblast growth factor receptor 1 (FGFR1) oncogene partner (FOP) is a centrosomal protein that is involved in anchoring microtubules to subcellular structures. This domain includes a Lis-homology motif. It forms an alpha helical bundle and is involved in dimerization. 81 matched cddid_all.tbl CDD pfam09399 pfam09399 462787 bCoV_lipid_BD Betacoronavirus lipid binding protein. This is a family of proteins found in SARS and SARS-like coronaviruses. It includes Protein 9b from SARS coronavirus 2 (SARS-CoV-2), human SARS coronavirus (SARS-CoV) and bat coronaviruses. Protein 9B is one of 8 accessory proteins in SARS-CoV. The gene (ORF 9b, also known as ORF 13) that encodes this protein is included within the nucleocapsid (N) gene (alternative ORF). Data suggest that protein 9b is a structural component of SARS-CoV virions and functions as an unusual lipid binding protein. SARS-CoV ORF-9b has been shown to localize to the outer mitochondrial membrane and to target mitochondrial antiviral signalling proteins (MAVS), suppressing innate immunity. Protein 9b from SARS CoV comprises 98 amino acids. It's structure has a novel fold which forms a dimeric tent-like beta structure with an amphipathic surface, and a central hydrophobic cavity that binds lipid molecules. This cavity is likely to be involved in membrane attachment. 98 matched cddid_all.tbl CDD pfam09400 pfam09400 430585 DUF2002 Protein of unknown function (DUF2002). This is a family of putative cytoplasmic proteins. The structure of these proteins form an antiparallel beta and sheet and contain some alpha helical regions. 110 matched cddid_all.tbl CDD pfam09401 pfam09401 462788 CoV_NSP10 Coronavirus RNA synthesis protein NSP10. Non-structural protein 10 (NSP10) is involved in RNA synthesis. It is synthesized as a polyprotein whose cleavage generates many non-structural proteins. NSP10 contains two zinc binding motifs and forms two anti-parallel helices which are stacked against an irregular beta sheet. A cluster of basic residues on the protein surface suggests a nucleic acid-binding function. NSP10 interacts with NSP14 and NSP16 and regulates their respective ExoN and 2-O-MTase activities. When binding to the N-terminal of NSP14, nsp10 allows the ExoN active site to adopt a stably closed conformation and is an allosteric regulator that stabilizes NSP16. The residue Tyr-96 plays a crucial role in the NSP10-NSP16/NSP14 interaction. This residue is specific for SARS-CoV NSP10 and is a phenylalanine in most other Coronavirus homologs. 119 matched cddid_all.tbl CDD pfam09402 pfam09402 430586 MSC Man1-Src1p-C-terminal domain. MAN1 is an integral protein of the inner nuclear membrane which binds to chromatin associated proteins and plays a role in nuclear organization. The C terminal nucleoplasmic region forms a DNA binding winged helix and binds to Smad. This C-terminal tail is also found in S. cerevisiae and is thought to consist of three conserved helices followed by two downstream strands. 333 matched cddid_all.tbl CDD pfam09403 pfam09403 430587 FadA Adhesion protein FadA. FadA (Fusobacterium adhesin A) is an adhesin which forms two alpha helices that form an intra-molecular coiled-coil arrangement. 99 matched cddid_all.tbl CDD pfam09404 pfam09404 401380 C12orf66_like KICSTOR complex C12orf66 like. This entry includes C12orf66-like proteins. Human C12orf66 is part of the KICSTOR complex that functions in the amino acid-sensing branch of the TORC1 signaling pathway. 440 matched cddid_all.tbl CDD pfam09405 pfam09405 430588 Btz CASC3/Barentsz eIF4AIII binding. This domain is found on CASC3 (cancer susceptibility candidate gene 3 protein) which is also known as Barentsz (Btz). CASC3 is a component of the EJC (exon junction complex) which is a complex that is involved in post-transcriptional regulation of mRNA in metazoa. The complex is formed by the association of four proteins (eIF4AIII, Barentsz, Mago, and Y14), mRNA, and ATP. This domain wraps around eIF4AIII and stacks against the 5' nucleotide. 121 matched cddid_all.tbl CDD pfam09406 pfam09406 430589 DUF2004 Protein of unknown function (DUF2004). This is a family of proteins with unknown function. The structure of one of the proteins in this family has revealed a novel alpha-beta fold. 107 matched cddid_all.tbl CDD pfam09407 pfam09407 430590 AbiEi_1 AbiEi antitoxin C-terminal domain. AbiEi_1 is the cognate antitoxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is pfam13338. 142 matched cddid_all.tbl CDD pfam09408 pfam09408 462789 bCoV_S1_RBD Betacoronavirus spike glycoprotein S1, receptor binding. This entry represents the receptor binding domain (S1 RBD) of the betacoronavirus spike glycoprotein. The spike glycoprotein is arranged in trimers on the surface of the viral membrane and is essential for viral entry. The spike protein is translated as a large polypeptide that is subsequently cleaved to the distal S1, responsible for receptor binding, and the membrane-anchored S2 responsible for membrane fusion. The coronavirus (SARS-CoV) S1 subunit is composed of two distinct domains: an N-terminal domain (S1 NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Each of these domains have been implicated in binding to host receptors. However, most coronaviruses are not known to utilize both the S1 NTD and S1 RBD for viral entry. SARS-CoV makes use of its S1 RBD to bind to the human angiotensin-converting enzyme 2 (ACE2) as its host receptor. 156 matched cddid_all.tbl CDD pfam09409 pfam09409 462790 PUB PUB domain. The PUB (also known as PUG) domain is found in peptide N-glycanase where it functions as a AAA ATPase binding domain. This domain is also found on other proteins linked to the ubiquitin-proteasome system. 80 matched cddid_all.tbl CDD pfam09411 pfam09411 462791 PagL Lipid A 3-O-deacylase (PagL). PagL is an outer membrane protein with lipid A 3-O-deacylase activity. It forms an 8 stranded beta barrel structure. 129 matched cddid_all.tbl CDD pfam09412 pfam09412 462792 XendoU Endoribonuclease XendoU. This is a family of endoribonucleases involved in RNA biosynthesis which has been named XendoU in Xenopus laevis. XendoU is a U-specific metal dependent enzyme that produces products with a 2'-3' cyclic phosphate termini. 262 matched cddid_all.tbl CDD pfam09413 pfam09413 430595 DUF2007 Putative prokaryotic signal transducing protein. This is a family of putative prokaryotic signal transducing proteins of Pii-type. 66 matched cddid_all.tbl CDD pfam09414 pfam09414 430596 RNA_ligase RNA ligase. This is a family of RNA ligases. The enzyme repairs RNA strand breaks in nicked DNA:RNA and RNA:RNA but not in DNA:DNA duplexes. 120 matched cddid_all.tbl CDD pfam09415 pfam09415 462793 CENP-X CENP-S associating Centromere protein X. The centromere, essential for faithful chromosome segregation during mitosis, has a network of constitutive centromere-associated (CCAN) proteins associating with it during mitosis. So far in vertebrates at least 15 centromere proteins have been identified, which are divided into several subclasses based on functional and biochemical analyses. These provide a platform for the formation of a functional kinetochore during mitosis. CENP-S is one that does not associate with the CENP-H-containing complex but rather interacts with CENP-X to form a stable assembly of outer kinetochore proteins that functions downstream of other components of the CCAN. This complex may directly allow efficient and stable formation of the outer kinetochore on the CCAN platform. 72 matched cddid_all.tbl CDD pfam09416 pfam09416 401391 UPF1_Zn_bind RNA helicase (UPF2 interacting domain). UPF1 is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD). 152 matched cddid_all.tbl CDD pfam09418 pfam09418 401392 DUF2009 Protein of unknown function (DUF2009). This is a eukaryotic family of proteins with unknown function. 454 matched cddid_all.tbl CDD pfam09419 pfam09419 430598 PGP_phosphatase Mitochondrial PGP phosphatase. This is a family of proteins that acts as a mitochondrial phosphatase in cardiolipin biosynthesis. Cardiolipin is a unique dimeric phosphoglycerolipid predominantly present in mitochondrial membranes. The inverted phosphatase motif includes the highly conserved DKD triad. 168 matched cddid_all.tbl CDD pfam09420 pfam09420 430599 Nop16 Ribosome biogenesis protein Nop16. Nop16 is a protein involved in ribosome biogenesis. 209 matched cddid_all.tbl CDD pfam09421 pfam09421 401394 FRQ Frequency clock protein. The frequency clock protein, is the central component of the frq-based circadian negative feedback loop, regulates various aspects of the circadian clock in Neurospora crassa. This protein has been shown to interact with itself via a coiled-coil. 982 matched cddid_all.tbl CDD pfam09422 pfam09422 462794 WTX WTX protein. The WTX protein is found to be inactivated in one third of Wilms tumours. The WTX protein is functionally uncharacterized. 467 matched cddid_all.tbl CDD pfam09423 pfam09423 430601 PhoD PhoD-like phosphatase. 345 matched cddid_all.tbl CDD pfam09424 pfam09424 430602 YqeY Yqey-like protein. The function of this domain found in the YqeY protein is uncertain. 143 matched cddid_all.tbl CDD pfam09425 pfam09425 430603 Jas_motif Jas motif. This entry represents the Jas motif. The Jas motif can bind to jasmonate as a partially unwound helix. It can also bind to Myc proteins which are key mediators of josmonate signalling in plants. 25 matched cddid_all.tbl CDD pfam09426 pfam09426 401399 Nyv1_longin Vacuolar R-SNARE Nyv1, longin domain. This domain corresponds to the N terminal longin domain of vacuolar R-SNARE Nyv1 which contains YXXomega-like sorting motif (Y31GTI34), responsible for the AP3-dependent vacuolar localization of Nyv1. 138 matched cddid_all.tbl CDD pfam09427 pfam09427 430604 DUF2014 Domain of unknown function (DUF2014). This domain is found at the C terminal of a family of ER membrane bound transcription factors called sterol regulatory element binding proteins (SREBP). 262 matched cddid_all.tbl CDD pfam09428 pfam09428 430605 DUF2011 Fungal protein of unknown function (DUF2011). This is a family of fungal proteins whose function is unknown. 90 matched cddid_all.tbl CDD pfam09429 pfam09429 462795 Wbp11 WW domain binding protein 11. The WW domain is a small protein module with a triple-stranded beta-sheet fold. This is a family of WW domain binding proteins. 76 matched cddid_all.tbl CDD pfam09430 pfam09430 430607 EMC7_beta-sandw ER membrane protein complex subunit 7, beta-sandwich domain. This is the beta-sandwich domain found in ER membrane protein complex subunit 7 (EMC7), which is an integral membrane component of the EMC. EMC is widely conserved and involved in membrane protein biogenesis. It mediates the insertion into endoplasmic reticulum membranes of newly synthesized membrane proteins in an energy-independent manner, both post-translational insertions of tail-anchored proteins and co-translational insertion of multipass membrane proteins. This entry includes UPF0620 protein C83.10 from S. pombe, an orthologue of animal EMC7. This domain is also found in nodal modulators, which have been identified as part of a protein complex that participates in the nodal signalling pathway during vertebrate development. 121 matched cddid_all.tbl CDD pfam09431 pfam09431 462796 SPIN90_LRD SPIN90/Ldb17, leucine-rich domain. This is the conserved leucine-rich domain (LRD) within the C-terminal domain of SPIN90 (also known as NCK interacting protein with SH3 domain (NCKIPSD)) from animals, Ldb17 from budding yeasts and Dip1 from fission yeasts. Ldb17 is involved in the regulation of endocytosis in yeast. SPIN90 is an F-actin binding protein that regulates actin polymerization and endocytosis. It associates with and activates the Arp2/3 complex, without requiring a preformed actin filament. This LRD, within the C-terminal armadillo repeat (ARM) domain of SPIN90, is important for activation of Arp2/3 complex. 135 matched cddid_all.tbl CDD pfam09432 pfam09432 401405 THP2 Tho complex subunit THP2. The THO complex plays a role in coupling transcription elongation to mRNA export. It is composed of subunits THP2, HPR1, THO2 and MFT1. 129 matched cddid_all.tbl CDD pfam09435 pfam09435 401406 DUF2015 Fungal protein of unknown function (DUF2015). This is a fungal family of uncharacterized proteins. 110 matched cddid_all.tbl CDD pfam09436 pfam09436 430609 DUF2016 Domain of unknown function (DUF2016). A predicted alpha+beta domain that is usually fused N-terminal to the JAB metallopeptidase. This protein in turn is found in conserved gene neighborhoods that include genes encoding the bacterial homologs of the ubiquitin modification system such as the E1, E2 and Ub proteins. The domain is also known as the JAB-N domain. 72 matched cddid_all.tbl CDD pfam09437 pfam09437 117976 Pombe_5TM Pombe specific 5TM protein. 219 matched cddid_all.tbl CDD pfam09438 pfam09438 430610 DUF2017 Domain of unknown function (DUF2017). This is an alpha-helical domain found in gene neighborhoods that contain genes encoding ubiquitin, cysteine synthases and JAB peptidases. 175 matched cddid_all.tbl CDD pfam09439 pfam09439 462797 SRPRB Signal recognition particle receptor beta subunit. The beta subunit of the signal recognition particle receptor (SRP) is a transmembrane GTPase which anchors the alpha subunit to the endoplasmic reticulum membrane. 181 matched cddid_all.tbl CDD pfam09440 pfam09440 462798 eIF3_N eIF3 subunit 6 N terminal domain. This is the N terminal domain of subunit 6 translation initiation factor eIF3. 132 matched cddid_all.tbl CDD pfam09441 pfam09441 462799 Abp2 ARS binding protein 2. This DNA-binding protein binds to the autonomously replicating sequence (ARS) binding element. It may play a role in regulating the cell cycle response to stress signals. 171 matched cddid_all.tbl CDD pfam09442 pfam09442 430614 DUF2018 Domain of unknown function (DUF2018). Acid-adaptive protein possibly of physiological significance when H.pylori colonizes the human stomach, which adopts a unique four alpha-helical triangular conformations. The biologically active form is thought to be a tetramer. The protein is expressed along with six other proteins, some of which are related to iron storage and haem biosynthesis. 83 matched cddid_all.tbl CDD pfam09443 pfam09443 462800 CFC Cripto_Frl-1_Cryptic (CFC). CFC domain is one half of the membrane protein Cripto, a protein overexpressed in many tumours and structurally similar to the C-terminal extracellular portions of Jagged 1 and Jagged 2. CFC is approx 40-residues long, compacted by three internal disulphide bridges, and binds Alk4 via a hydrophobic patch. CFC is structurally homologous to the VWFC-like domain. 35 matched cddid_all.tbl CDD pfam09444 pfam09444 430616 MRC1 MRC1-like domain. This putative domain is found to be the most conserved region in mediator of replication checkpoint protein 1. 141 matched cddid_all.tbl CDD pfam09445 pfam09445 370496 Methyltransf_15 RNA cap guanine-N2 methyltransferase. RNA cap guanine-N2 methyltransferases such as Schizosaccharomyces pombe Tgs1 and Giardia lamblia Tgs2 catalyze methylation of the exocyclic N2 amine of 7-methylguanosine. 165 matched cddid_all.tbl CDD pfam09446 pfam09446 462801 VMA21 VMA21-like domain. This presumed short domain appears to contain two potential transmembrane helices. VMA21 is localized in the ER where it is needed as an accessory factor for assembly of the V0 component of the vacuolar ATPase. 64 matched cddid_all.tbl CDD pfam09447 pfam09447 430618 Cnl2_NKP2 Cnl2/NKP2 family protein. This family includes the Cnl2 kinetochore protein. 65 matched cddid_all.tbl CDD pfam09448 pfam09448 430619 MmlI Methylmuconolactone methyl-isomerase. MmlI is a short, approx 115 residue, protein of two alpha helices and four beta strands. It is involved in the catabolism of methyl-substituted aromatics via a modified oxo-adipate pathway in bacteria. The enzyme appears to be monomeric in some species and tetrameric in others. The known structure shows two copies of the protein form a dimeric alpha beta barrel. 109 matched cddid_all.tbl CDD pfam09449 pfam09449 430620 DUF2020 Domain of unknown function (DUF2020). Protein of unknown function found in bacteria. 144 matched cddid_all.tbl CDD pfam09450 pfam09450 430621 DUF2019 Domain of unknown function (DUF2019). Protein of unknown function found in bacteria. 105 matched cddid_all.tbl CDD pfam09451 pfam09451 430622 ATG27 Autophagy-related protein 27. 261 matched cddid_all.tbl CDD pfam09452 pfam09452 370502 Mvb12 ESCRT-I subunit Mvb12. The endosomal sorting complex required for transport (ESCRT) complexes play a critical role in receptor down-regulation and retroviral budding. A new component of the ESCRT-I complex was identified, multivesicular body sorting factor of 12 kD (Mvb12), which binds to the coiled-coil domain of the ESCRT-I subunit vacuolar protein sorting 23 (Vps23). 90 matched cddid_all.tbl CDD pfam09453 pfam09453 462802 HIRA_B HIRA B motif. The HirA B (Histone regulatory homolog A binding) motif is the essential binding interface between HIRA pfam07569 and ASF1a, of approx. 40 residues. It forms an antiparallel beta-hairpin that binds perpendicular to the strands of the beta-sandwich of ASF1a N-terminal core domain, via beta-sheet, salt bridge and van der Waals interactions. The two histone chaperone proteins, HIRA and ASF1a, form a heterodimer with histones H3 and H4. HIRA is the human orthologue of Hir proteins known to silence histone gene expression and create transcriptionally silent heterochromatin in yeast, flies, plants and humans. The yeast CAF1B proteins which bind H3 also carry this motif at their very C-terminus. 22 matched cddid_all.tbl CDD pfam09454 pfam09454 462803 Vps23_core Vps23 core domain. ESCRT complexes form the main machinery driving protein sorting from endosomes to lysosomes. The core domain of the Vps23 subunit of the heterotrimeric ESCRT-I complex is a helical hairpin sandwiched in a fan-like formation between two other helical hairpins from Vps28 (pfam03997) and Vps37. Vps23 gives ESCRT-I complex its stability. 60 matched cddid_all.tbl CDD pfam09455 pfam09455 401419 Cas_DxTHG CRISPR-associated (Cas) DxTHG family. CRISPR is a term for Clustered Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. The family describes Cas proteins of about 400 residues that include the motif [VIL]-D-x-[ST]-H-[GS]. The CRISPR and associated proteins are thought to be involved in the evolution of host resistance. The exact molecular function of this family is currently unknown. 313 matched cddid_all.tbl CDD pfam09456 pfam09456 462804 RcsC RcsC Alpha-Beta-Loop (ABL). This domain is found in the C-terminus of the phospho-relay kinase RcsC between pfam00512 and pfam00072, and forms a discrete alpha/beta/loop structure. 91 matched cddid_all.tbl CDD pfam09457 pfam09457 462805 RBD-FIP FIP domain. The FIP domain is the Rab11-binding domain (RBD) at the C-terminus of a family of Rab11-interacting proteins (FIPs). The Rab proteins constitute the largest family of small GTPases (>60 members in mammals). Among them Rab11 is a well characterized regulator of endocytic and recycling pathways. Rab11 associates with a broad range of post-Golgi organelles, including recycling endosomes. 41 matched cddid_all.tbl CDD pfam09458 pfam09458 462806 H_lectin H-type lectin domain. The H-type lectin domain is a unit of six beta chains, combined into a homo-hexamer. It is involved in self/non-self recognition of cells, through binding with carbohydrates. It is sometimes found in association with the F5_F8_type_C domain pfam00754. 67 matched cddid_all.tbl CDD pfam09459 pfam09459 430627 EB_dh Ethylbenzene dehydrogenase. Eythylbenzene dehydrogenase is a heterotrimer of three subunits that catalyzes the anaerobic degradation of hydrocarbons. The alpha subunit contains the catalytic centre as a Molybdenum cofactor-complex. This removes an electron-pair from the hydrocarbon and passes it along an electron transport system involving iron-sulphur complexes held in the beta subunit and a Haem b molecule contained in the gamma subunit. The electron-pair is then subsequently passed to an as yet unknown receiver. The enzyme is found in a variety of different bacteria. 192 matched cddid_all.tbl CDD pfam09460 pfam09460 462807 Saf-Nte_pilin Saf-pilin pilus formation protein. This domain consists of the adjacent Saf-Nte and Saf-pilin chains of the pilus-forming complex. Pilus assembly in Gram-negative bacteria involves a Donor-strand exchange mechanism between the C- and the N-termini of this domain. The C-terminal subunit forms an incomplete Ig-fold which is then complemented by the 10-18 residue N-terminus of another, incoming, pilus subunit which is not involved in the Ig-fold. The N-terminus sequences contain a motif of alternating hydrophobic residues that occupy the P2 to P5 binding pockets in the groove of the first pilus subunit. 144 matched cddid_all.tbl CDD pfam09461 pfam09461 370510 PcF Phytotoxin PcF protein. PcF is a 52 residue protein factor of two alpha helices, containing a 4-hydroxyproline and three cysteine bridges. The presence of the hydroxyproline is unique in relation to other fungal phytotoxic proteins. The protein has a high content of acidic side-chains implying a lack of binding with lipid-rich components of membranes and appears to be an extracellular phytotoxin that causes leaf necrosis in strawberries. 43 matched cddid_all.tbl CDD pfam09462 pfam09462 370511 Mus7 Mus7/MMS22 family. This family includes a conserved region from the Mus7 protein. Mus7 is involved in the repair of replication-associated DNA damage in the fission yeast Schizosaccharomyces pombe. Mus7 functions in the same pathway as Mus81, a subunit of the Mus81-Eme1 structure-specific endonuclease, which has been implicated in the repair of the replication-associated DNA damage. The MMS22 proteins are involved in repairing double-stranded DNA breaks created by the cleavage reaction of topoisomerase II. 610 matched cddid_all.tbl CDD pfam09463 pfam09463 430628 Opy2 Opy2 protein. Opy2p acts as a membrane anchor in the HOG signalling pathway. 35 matched cddid_all.tbl CDD pfam09465 pfam09465 462808 LBR_tudor Lamin-B receptor of TUDOR domain. The Lamin-B receptor, found on the TUDOR domain pfam00567, is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner Nuclear Envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with Importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the NE. 55 matched cddid_all.tbl CDD pfam09466 pfam09466 312837 Yqai Hypothetical protein Yqai. This hypothetical protein is expressed in bacteria, particularly Bacillus subtilis. It forms a homo-dimer, with each monomer containing an alpha helix and four beta strands. 66 matched cddid_all.tbl CDD pfam09467 pfam09467 462809 Yopt Hypothetical protein Yopt. This hypothetical protein is expressed in bacteria, particularly Bacillus subtilis. It forms homo-dimers, with each monomer consisting of one alpha helix and three beta strands. 71 matched cddid_all.tbl CDD pfam09468 pfam09468 401427 RNase_H2-Ydr279 Ydr279p protein family (RNase H2 complex component) wHTH domain. RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organizms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologs of Ydr279p. It is not known whether non yeast proteins in this family fulfil the same function. 157 matched cddid_all.tbl CDD pfam09469 pfam09469 462810 Cobl Cordon-bleu ubiquitin-like domain. The Cordon-bleu protein domain is highly conserved among vertebrates. The sequence contains three repeated lysine, arginine, and proline-rich regions, the KKRAP motif. The exact function of the protein is unknown but it is thought to be involved in mid-brain neural tube closure. It is expressed specifically in the node. This domain has a ubiquitin-like fold. 79 matched cddid_all.tbl CDD pfam09470 pfam09470 462811 Telethonin Telethonin protein. Telethonin is a 167-residue protein which complexes with the large muscle protein, titin. The very N-terminus of titin, composed of two immunoglobulin-like (Ig) domains, referred to as Z1 and Z2, interacts with the N-terminal region (residues 1-53) of telethonin, mediating the antiparallel assembly of two Z1Z2 domains. The C-terminus of the telethonin appears to induce dimerization of this 2:1 titin/telethonin structure which thus forms a complex necessary for myofibril assembly and maintenance of the intact Z-disk of skeletal and cardiac muscles. 150 matched cddid_all.tbl CDD pfam09471 pfam09471 430630 Peptidase_M64 IgA Peptidase M64. This is a family of highly selective metallo-endopeptidases. The primary structure of the Clostridium ramosum IgA proteinase shows no significant overall similarity to any other known metallo-endopeptidase. 259 matched cddid_all.tbl CDD pfam09472 pfam09472 430631 MtrF Tetrahydromethanopterin S-methyltransferase, F subunit (MtrF). Many archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This domain is mostly found in MtrF, where it covers the entire length of the protein. This polypeptide is one of eight subunits of the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase complex found in methanogenic archaea. This is a membrane-associated enzyme complex that uses methyl-transfer reactions to drive a sodium-ion pump. MtrF itself is involved in the transfer of the methyl group from N5-methyltetrahydromethanopterin to coenzyme M. Subsequently, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase. In some organizms this domain is found at the C terminal region of what appears to be a fusion of the MtrA and MtrF proteins. The function of these proteins is unknown, though it is likely that they are involved in C1 metabolism. 62 matched cddid_all.tbl CDD pfam09474 pfam09474 462812 Type_III_YscX Type III secretion system YscX (type_III_YscX). Members of this family are encoded within bacterial type III secretion gene clusters. Among all species with type III secretion, those with this protein are found among those that target animal rather than plant cells. The member of this family in Yersinia was shown by mutation to be required for type III secretion of Yops effector proteins and therefore is believed to be part of the secretion machinery. 119 matched cddid_all.tbl CDD pfam09475 pfam09475 430632 Dot_icm_IcmQ Dot/Icm secretion system protein (dot_icm_IcmQ). Proteins in this entry are the IcmQ component of Dot/Icm secretion systems, as found in the obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii. While this system resembles type IV secretion systems and has been called a form of type IV, the literature now seems to favour calling this the Dot/Icm system. This protein was shown to be essential for translocation. 178 matched cddid_all.tbl CDD pfam09476 pfam09476 430633 Pilus_CpaD Pilus biogenesis CpaD protein (pilus_cpaD). Proteins in this entry consist of a pilus biogenesis protein, CpaD, from Caulobacter, and homologs in other bacteria, including three in the root nodule bacterium Bradyrhizobium japonicum. The molecular function of the homologs is not known. 200 matched cddid_all.tbl CDD pfam09477 pfam09477 401433 Type_III_YscG Bacterial type II secretion system chaperone protein (type_III_yscG). YscG is a molecular chaperone for YscE, where both are part of the type III secretion system that in Yersinia is designated Ysc (Yersinia secretion). The secretion system delivers effector proteins, designated Yops (Yersinia outer proteins), in Yersinia. This entry consists of YscG from Yersinia and functionally equivalent type III secretion proteins in other species: e.g. AscG in Aeromonas and LscG in Photorhabdus luminescens. 116 matched cddid_all.tbl CDD pfam09478 pfam09478 286553 CBM49 Carbohydrate binding domain CBM49. This domain is found at the C terminal of cellulases and in vitro binding studies have shown it to binds to crystalline cellulose. 80 matched cddid_all.tbl CDD pfam09479 pfam09479 462813 Flg_new Listeria-Bacteroides repeat domain (List_Bact_rpt). This model describes a conserved core region of about 43 residues which occurs in more than 400 mostly secreted or cell surface-located proteins from over 300 eubacterial and few archaeal species. These proteins contain between one and 34 copies of the domain that often occur in tandem arrays with up to more than 20 copies. 65 matched cddid_all.tbl CDD pfam09480 pfam09480 430635 PrgH Type III secretion system protein PrgH-EprH (PrgH). In Salmonella, the gene encoding this protein is part of a four-gene operon PrgHIJK, while in other organizms it is found in type III secretion operons. PrgH has been shown to be required for type III secretion and is a structural component of the needle complex, which is the core component of type III secretion systems. 373 matched cddid_all.tbl CDD pfam09481 pfam09481 462814 CRISPR_Cse1 CRISPR-associated protein Cse1 (CRISPR_cse1). Clusters of short DNA repeats with non-homologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry, represented by CT1972 from Chlorobaculum tepidum, is found in the CRISPR/Cas subtype Ecoli regions of many bacteria (most of which are mesophiles), and not in Archaea. It is designated Cse1. 467 matched cddid_all.tbl CDD pfam09482 pfam09482 430637 OrgA_MxiK Bacterial type III secretion apparatus protein (OrgA_MxiK). This protein is encoded by genes which are found in type III secretion operons, and has been shown to be essential for the invasion phenotype in Salmonella and a component of the secretion apparatus. The protein is known as OrgA in Salmonella due to its oxygen-dependent expression pattern in which low-oxygen levels up-regulate the gene. In Shigella the gene is called MxiK and has been shown to be essential for the proper assembly of the needle complex, which is the core component of type III secretion systems. 181 matched cddid_all.tbl CDD pfam09483 pfam09483 430638 HpaP Type III secretion protein (HpaP). This entry represents C-terminal domain of proteins encoded by genes which are always found in type III secretion operons, although their function in the processes of secretion and virulence is unclear. Hpa stands for Hrp-associated gene, where Hrp stands for hypersensitivity response and virulence. see also PMID:18584024 90 matched cddid_all.tbl CDD pfam09484 pfam09484 430639 Cas_TM1802 CRISPR-associated protein TM1802 (cas_TM1802). Clusters of short DNA repeats with non-homologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This minor cas protein is found in at least five prokaryotic genomes: Methanosarcina mazei, Sulfurihydrogenibium azorense, Thermotoga maritima, Carboxydothermus hydrogenoformans, and Dictyoglomus thermophilum, the first of which is archaeal while the rest are bacterial. 588 matched cddid_all.tbl CDD pfam09485 pfam09485 462815 CRISPR_Cse2 CRISPR-associated protein Cse2 (CRISPR_cse2). Clusters of short DNA repeats with non-homologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family of proteins, represented by CT1973 from Chlorobaculum tepidum, is encoded by genes found in the CRISPR/Cas subtype Ecoli regions of many bacteria (most of which are mesophiles), and not in Archaea. It is designated Cse2. 145 matched cddid_all.tbl CDD pfam09486 pfam09486 370523 HrpB7 Bacterial type III secretion protein (HrpB7). This entry represents proteins encoded by genes which are found in type III secretion operons in a narrow range of species including Xanthomonas, Burkholderia and Ralstonia. 157 matched cddid_all.tbl CDD pfam09487 pfam09487 370524 HrpB2 Bacterial type III secretion protein (HrpB2). This entry represents proteins encoded by genes which are found in type III secretion operons in a narrow group of species including Xanthomonas, Burkholderia and Ralstonia. 114 matched cddid_all.tbl CDD pfam09488 pfam09488 401440 Osmo_MPGsynth Mannosyl-3-phosphoglycerate synthase (osmo_MPGsynth). This family consists of examples of mannosyl-3-phosphoglycerate synthase (MPGS), which together with mannosyl-3-phosphoglycerate phosphatase (MPGP) EC:2.4.1.217, comprises a two-step pathway for mannosylglycerate biosynthesis. Mannosylglycerate is a compatible solute that tends to be restricted to extreme thermophiles of archaea and bacteria. Note that in Rhodothermus marinus, this pathway is one of two; the other is condensation of GDP-mannose with D-glycerate by mannosylglycerate synthase. 380 matched cddid_all.tbl CDD pfam09489 pfam09489 430641 CbtB Probable cobalt transporter subunit (CbtB). This entry represents a family of proteins which have been proposed to act as cobalt transporters acting in concert with vitamin B12 biosynthesis systems. Evidence for this assignment includes 1) prediction of a single transmembrane segment and a C-terminal histidine-rich motif likely to be a metal-binding site, 2) positional gene linkage with known B12 biosynthesis genes, 3) upstream proximity of B12 transcriptional regulatory sites, 4) the absence of other known cobalt import systems and 5) the obligate co-localization with a protein (CbtA) predicted to have five additional transmembrane segments. 50 matched cddid_all.tbl CDD pfam09490 pfam09490 430642 CbtA Probable cobalt transporter subunit (CbtA). This entry represents a family of proteins which have been proposed to act as cobalt transporters acting in concert with vitamin B12 biosynthesis systems. Evidence for this assignment includes 1) prediction of five transmembrane segments, 2) positional gene linkage with known B12 biosynthesis genes, 3) upstream proximity of B12 transcriptional regulatory sites, 4) the absence of other known cobalt import systems and 5) the obligate co-localization with a small protein (CbtB) having a single additional transmembrane segment and a C-terminal histidine-rich motif likely to be a metal-binding site. 240 matched cddid_all.tbl CDD pfam09491 pfam09491 401443 RE_AlwI AlwI restriction endonuclease. This family includes the AlwI (recognizes GGATC), Bsp6I (recognizes GC^NGC), BstNBI (recognizes GASTC), PleI(recognizes GAGTC) and MlyI (recognizes GAGTC) restriction endonucleases. 441 matched cddid_all.tbl CDD pfam09492 pfam09492 401444 Pec_lyase Pectic acid lyase. Members of this family are isozymes of pectate lyase (EC:4.2.2.2), also called polygalacturonic transeliminase and alpha-1,4-D-endopolygalacturonic acid lyase. 289 matched cddid_all.tbl CDD pfam09493 pfam09493 462816 DUF2389 Tryptophan-rich protein (DUF2389). Members of this family are small hypothetical proteins of 60 to 100 residues from Cyanobacteria and some Proteobacteria. Prochlorococcus marinus strains have two members, other species one only. Interestingly, of the eight most conserved residues, four are aromatic and three are invariant tryptophans. It appears all species that encode this protein can synthesize tryptophan de novo. 61 matched cddid_all.tbl CDD pfam09494 pfam09494 430644 Slx4 Slx4 endonuclease. The Slx4 protein is a heteromeric structure-specific endonuclease found from fungi to mammals. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates. 60 matched cddid_all.tbl CDD pfam09495 pfam09495 462817 DUF2462 Protein of unknown function (DUF2462). This protein is highly conserved, but its function is unknown. It can be isolated from HeLa cell nucleoli and is found to be homologous with Leydig cell tumour protein whose function is unknown. 77 matched cddid_all.tbl CDD pfam09496 pfam09496 430646 CENP-O Cenp-O kinetochore centromere component. This eukaryotic protein is a component of the inner kinetochore subcomplex of the centromere. It has been shown to be involved in chromosome segregation via regulation of the spindle in both yeast and human. 202 matched cddid_all.tbl CDD pfam09497 pfam09497 462818 Med12 Transcription mediator complex subunit Med12. Med12 is a negative regulator of the Gli3-dependent sonic hedgehog signalling pathway via its interaction with Gli3 within the RNA polymerase II transcriptional Mediator. A complex is formed between Med12, Med13, CDK8 and CycC which is responsible for suppression of transcription. This subunit forms part of the Kinase section of Mediator. 63 matched cddid_all.tbl CDD pfam09498 pfam09498 430648 DUF2388 Protein of unknown function (DUF2388). This family consists of small hypothetical proteins, about 100 amino acids in length. The family includes five members (three in tandem) in Pseudomonas aeruginosa PAO1 and in Pseudomonas putida (strain KT2440), four in Pseudomonas syringae DC3000, and single members in several other Proteobacteria. The function is unknown. 70 matched cddid_all.tbl CDD pfam09499 pfam09499 286574 RE_ApaLI ApaLI-like restriction endonuclease. This family includes R.ApaLI and R.XbaI restriction endonucleases. ApaLI recognizes and cleaves the sequence GTGCAC. 189 matched cddid_all.tbl CDD pfam09500 pfam09500 430649 YiiD_C Putative thioesterase (yiiD_Cterm). This entry consists of a broadly distributed uncharacterized domain often found as a standalone protein. The member from Shewanella oneidensis is described from crystallography work as a putative thioesterase because it belongs to the HotDog clan of enzymes. About half of the members of this family are fused to an Acetyltransf_1 domain pfam00583. 144 matched cddid_all.tbl CDD pfam09501 pfam09501 312864 Bac_small_YrzI Probable sporulation protein (Bac_small_yrzI). Members of this family are very small proteins, about 47 residues each, in the genus Bacillus. Single members are found in Bacillus subtilis and Bacillus halodurans, while arrays of six members in tandem are found in Bacillus cereus and Bacillus anthracis. An EIxxE motif present in most members of this family resembles cleavage sites by the germination protease GPR in a number of small acid-soluble spore proteins (SASP). A role in sporulation is possible. 45 matched cddid_all.tbl CDD pfam09502 pfam09502 401452 HrpB4 Bacterial type III secretion protein (HrpB4). This entry represents proteins encoded by genes which are found in type III secretion operons in a narrow range of species including Xanthomonas, Burkholderia and Ralstonia. 217 matched cddid_all.tbl CDD pfam09504 pfam09504 401453 RE_Bsp6I Bsp6I restriction endonuclease. This family includes the Bsp6I (recognizes and cleaves GC^NGC) restriction endonucleases. 179 matched cddid_all.tbl CDD pfam09505 pfam09505 370535 Dimeth_Pyl Dimethylamine methyltransferase (Dimeth_PyL). This family consists of dimethylamine methyltransferases from the genus Methanosarcina. It is found in three nearly identical copies in each of Methanosarcina acetivorans, Methanosarcina barkeri, and Methanosarcina mazei. It is one of a suite of three non-homologous enzymes with a critical UAG-encoded pyrrolysine residue in these species (along with trimethylamine methyltransferase and monomethylamine methyltransferase). It demethylates dimethylamine, leaving monomethylamine, and methylates the prosthetic group of the small corrinoid protein MtbC. The methyl group is then transferred by methylcorrinoid:coenzyme M methyltransferase to coenzyme M. Note that the pyrrolysine residue is variously translated as K or X, or as a stop codon that truncates the sequence. 462 matched cddid_all.tbl CDD pfam09506 pfam09506 430650 Salt_tol_Pase Glucosylglycerol-phosphate phosphatase (Salt_tol_Pase). Proteins in this family are glucosylglycerol-phosphate phosphatases, with the gene symbol stpA (Salt Tolerance Protein A). A motif characteriztic of acid phosphatases is found, but otherwise this family shows little sequence similarity to other phosphatases. This enzyme acts on the glucosylglycerol phosphate, product of glucosylglycerol phosphate synthase and immediate precursor of the osmoprotectant glucosylglycerol. 391 matched cddid_all.tbl CDD pfam09507 pfam09507 462819 CDC27 DNA polymerase subunit Cdc27. This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterized by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif. 427 matched cddid_all.tbl CDD pfam09508 pfam09508 462820 Lact_bio_phlase Lacto-N-biose phosphorylase N-terminal TIM barrel domain. The gene which codes for this protein in gut-bacteria is located in a novel putative operon for galactose metabolism. The protein appears to be a carbohydrate-processing phosphorolytic enzyme (EC:2.4.1.211), unlike either glycoside hydrolases or glycoside lyase. Intestinal colonization by bifidobacteria is important for human health, especially in pediatrics, because colonization seems to prevent infection by some pathogenic bacteria that cause diarrhoea or other illnesses. The operon seems to be involved in intestinal colonization by bifidobacteria mediated by metabolism of mucin sugars. In addition, it may also resolve the question of the nature of the bifidus factor in human milk as the lacto-N-biose structure found in milk oligosaccharides. 434 matched cddid_all.tbl CDD pfam09509 pfam09509 430653 Hypoth_Ymh Protein of unknown function (Hypoth_ymh). This entry consists of a relatively rare prokaryotic protein family (about 8 occurrences per 200 genomes). Genes for members of this family appear to be associated variously with phage and plasmid regions, restriction system loci, transposons, and housekeeping genes. Their function is unknown. 119 matched cddid_all.tbl CDD pfam09510 pfam09510 430654 Rtt102p Rtt102p-like transcription regulator protein. This protein is found in fungi. The family includes Rtt102p, a transcription regulator protein which appears to be integrally associated with both the Swi-Snf and the RSC chromatin remodelling complexes,. 131 matched cddid_all.tbl CDD pfam09511 pfam09511 462821 RNA_lig_T4_1 RNA ligase. Members of this family include T4 phage proteins with ATP-dependent RNA ligase activity. Host defence to phage may include cleavage and inactivation of specific tRNA molecules; members of this family act to reverse this RNA damage. The enzyme is adenylated, transiently, on a Lys residue in a motif KXDGSL. This family also includes fungal tRNA ligases that have adenylyltransferase activity. tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns.i 221 matched cddid_all.tbl CDD pfam09512 pfam09512 430656 ThiW Thiamine-precursor transporter protein (ThiW). Levels of thiamine pyrophosphate (TPP) or thiamine regulate transcription or translation of a number of thiamine biosynthesis, salvage, or transport genes in a wide range of prokaryotes. The mechanism involves direct binding, with no protein involved, to a structural element called THI found in the untranslated upstream region of thiamine metabolism gene operons. This element is called a riboswitch and is seen also for other metabolites such as FMN and glycine. This protein family consists of proteins identified in operons controlled by the THI riboswitch and designated ThiW. The hydrophobic nature of this protein and reconstructed metabolic background suggests that this protein acts in transport of a thiazole precursor of thiamine. 150 matched cddid_all.tbl CDD pfam09514 pfam09514 430657 SSXRD SSXRD motif. SSX1 can repress transcription, and this has been attributed to a putative Kruppel associated box (KRAB) repression domain at the N-terminus. However, from the analysis of these deletion constructs further repression activity was found at the C-terminus of SSX1. Which has been called the SSXRD (SSX Repression Domain). The potent repression exerted by full-length SSX1 appears to localize to this region. 31 matched cddid_all.tbl CDD pfam09515 pfam09515 430658 Thia_YuaJ Thiamine transporter protein (Thia_YuaJ). Members of this protein family have been assigned as thiamine transporters by a phylogenetic analysis of families of genes regulated by the THI element, a broadly conserved RNA secondary structure element through which thiamine pyrophosphate (TPP) levels can regulate transcription of many genes related to thiamine transport, salvage, and de novo biosynthesis. Species with this protein always lack the ThiBPQ ABC transporter. In some species (e.g. Streptococcus mutans and Streptococcus pyogenes), yuaJ is the only THI-regulated gene. Evidence from Bacillus cereus indicates thiamine uptake is coupled to proton translocation. 177 matched cddid_all.tbl CDD pfam09516 pfam09516 401462 RE_CfrBI CfrBI restriction endonuclease. This family includes the CfrBI (recognizes and cleaves C^CWWGG) restriction endonuclease. 257 matched cddid_all.tbl CDD pfam09517 pfam09517 370543 RE_Eco29kI Eco29kI restriction endonuclease. This family includes the Eco29kI (recognizes and cleaves CCGC^GG ) restriction endonuclease. 161 matched cddid_all.tbl CDD pfam09518 pfam09518 286590 RE_HindIII HindIII restriction endonuclease. This family includes the HindIII (recognizes and cleaves A^AGCTT) restriction endonuclease. 284 matched cddid_all.tbl CDD pfam09519 pfam09519 462822 RE_HindVP HindVP restriction endonuclease. This family includes the HindVP (recognizes GRCGYC bu the cleavage site is unknown) restriction endonucleases. 324 matched cddid_all.tbl CDD pfam09520 pfam09520 430660 RE_TdeIII Type II restriction endonuclease, TdeIII. This family includes many TdeIII restriction endonucleases that recognize and cleave at GGNCC sites. TdeIII cleave unmethylated double-stranded DNA. 239 matched cddid_all.tbl CDD pfam09521 pfam09521 430661 RE_NgoPII NgoPII restriction endonuclease. This family includes the NgoPII (recognizes and cleaves GG^CC) restriction endonuclease. 262 matched cddid_all.tbl CDD pfam09522 pfam09522 337439 RE_R_Pab1 R.Pab1 restriction endonuclease. 119 matched cddid_all.tbl CDD pfam09523 pfam09523 430662 DUF2390 Protein of unknown function (DUF2390). Members of this family are bacterial hypothetical proteins, about 160 amino acids in length, found in various proteobacteria, including members of the genera Pseudomonas and Vibrio. The C-terminal region is poorly conserved and is not included in the model. 103 matched cddid_all.tbl CDD pfam09524 pfam09524 430663 Phg_2220_C Conserved phage C-terminus (Phg_2220_C). This entry represents the conserved C-terminal domain of a family of proteins found exclusively in bacteriophage and in bacterial prophage regions. The functions of this domain and the proteins containing it are unknown. 73 matched cddid_all.tbl CDD pfam09526 pfam09526 430664 DUF2387 Probable metal-binding protein (DUF2387). Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria. 72 matched cddid_all.tbl CDD pfam09527 pfam09527 462823 ATPase_gene1 Putative F0F1-ATPase subunit Ca2+/Mg2+ transporter. This model represents a protein found encoded in F1F0-ATPase operons in several genomes, including Methanosarcina barkeri (archaeal) and Chlorobium tepidum (bacterial). It is a small protein (about 100 amino acids) with long hydrophobic stretches and is presumed to be a subunit of the enzyme. It carries two transmembrane helices and is a magnesium or calcium uniporter. The atp operon of alkaliphilic Bacillus pseudofirmus OF4, as in most prokaryotes, contains the eight structural genes for the F-ATPase (ATP synthase), which are preceded by an atpI gene that encodes a membrane protein with 2 TMSs. A tenth gene, atpZ, has been found in this operon, which is upstream of and overlapping with atpI. 54 matched cddid_all.tbl CDD pfam09528 pfam09528 312885 Ehrlichia_rpt Ehrlichia tandem repeat (Ehrlichia_rpt). This entry represents 30 amino acid tandem repeat, found in a variable number of copies in an immunodominant outer membrane protein of Ehrlichia chaffeensis, a tick-borne obligate intracellular pathogen. These short tandem-repeats elicit a strong antibody response in the hosts. 36 matched cddid_all.tbl CDD pfam09529 pfam09529 430666 Intg_mem_TP0381 Integral membrane protein (intg_mem_TP0381). This entry represents a family of hydrophobic proteins with seven predicted transmembrane alpha helices. Members are found in Bacillus subtilis (ywaF), TP0381 from Treponema pallidum (TP0381), Streptococcus pyogenes, Rhodococcus erythropolis, etc. 210 matched cddid_all.tbl CDD pfam09531 pfam09531 462824 Ndc1_Nup Nucleoporin protein Ndc1-Nup. Ndc1 is a nucleoporin protein that is a component of the Nuclear Pore Complex, and, in fungi, also of the Spindle Pole Body. It consists of six transmembrane segments, three lumenal loops, both concentrated at the N-terminus and cytoplasmic domains largely at the C-terminus, all of which are well conserved. 522 matched cddid_all.tbl CDD pfam09532 pfam09532 430668 FDF FDF domain. The FDF domain, so called because of the conserved FDF at its N termini, is an entirely alpha-helical domain with multiple exposed hydrophilic loops. It is found at the C terminus of Scd6p-like SM domains. It is also found with other divergent Sm domains and in proteins such as Dcp3p and FLJ21128, where it is found N terminal to the YjeF-N domain, a novel Rossmann fold domain. 104 matched cddid_all.tbl CDD pfam09533 pfam09533 430669 DUF2380 Predicted lipoprotein of unknown function (DUF2380). This family consists of at least 9 paralogs in Myxococcus xanthus, a member of the Deltaproteobacteria. One appears truncated toward the N-terminus; the others are predicted lipoproteins. The function is unknown. 189 matched cddid_all.tbl CDD pfam09534 pfam09534 430670 Trp_oprn_chp Tryptophan-associated transmembrane protein (Trp_oprn_chp). Members of this family are predicted transmembrane proteins with four membrane-spanning helices. Members are found in the Actinobacteria (Mycobacterium, Corynebacterium, Streptomyces), always associated with genes for tryptophan biosynthesis. 180 matched cddid_all.tbl CDD pfam09535 pfam09535 430671 Gmx_para_CXXCG Protein of unknown function (Gmx_para_CXXCG). This entry consists of at least 10 paralogous proteins from Myxococcus xanthus and that lack detectable sequence similarity to any other protein family. An imperfectly conserved CXXCG motif, a probable binding site, appears twice in the multiple sequence alignment. 235 matched cddid_all.tbl CDD pfam09536 pfam09536 430672 DUF2378 Protein of unknown function (DUF2378). This family consists of a set of at least 17 paralogous proteins in Myxococcus xanthus DK 1622 and and 12 in Stigmatella aurantiaca DW4/3-1. Members are about 200 amino acids in length. The function is unknown. 177 matched cddid_all.tbl CDD pfam09537 pfam09537 430673 DUF2383 Domain of unknown function (DUF2383). Members of this protein family are found mostly in the Proteobacteria, although one member is found in the the marine planctomycete Pirellula sp. strain 1. The function is unknown. 106 matched cddid_all.tbl CDD pfam09538 pfam09538 430674 FYDLN_acid Protein of unknown function (FYDLN_acid). Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown. 108 matched cddid_all.tbl CDD pfam09539 pfam09539 430675 DUF2385 Protein of unknown function (DUF2385). Members of this uncharacterized protein family are found in a number of alphaproteobacteria, including root nodule bacteria, Brucella suis, Caulobacter crescentus, and Rhodopseudomonas palustris. Conserved residues include two well-separated cysteines, suggesting a disulfide bond. The function is unknown. 96 matched cddid_all.tbl CDD pfam09543 pfam09543 430676 DUF2379 Protein of unknown function (DUF2379). This family consists of at least 7 paralogs in Myxococcus xanthus and 6 in Stigmatella aurantiaca, both members of the Deltaproteobacteria. The function is unknown. 119 matched cddid_all.tbl CDD pfam09544 pfam09544 430677 DUF2381 Protein of unknown function (DUF2381). This family consists of at least 8 paralogs in Myxococcus xanthus, a member of the Deltaproteobacteria. The function is unknown. 287 matched cddid_all.tbl CDD pfam09545 pfam09545 286611 RE_AccI AccI restriction endonuclease. This family includes the AccI (recognizes and cleaves GT^MKAC) restriction endonuclease. 366 matched cddid_all.tbl CDD pfam09546 pfam09546 462825 Spore_III_AE Stage III sporulation protein AE (spore_III_AE). This represents the stage III sporulation protein AE, which is encoded in a spore formation operon spoIIIAABCDEFGH under the control of sigma G. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. 321 matched cddid_all.tbl CDD pfam09547 pfam09547 462826 SpoIVA_ATPase Stage IV sporulation protein A, ATPase domain. SpoIVA is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. This protein assembles into static polymers driven by ATP hydrolysis and is anchored to the outer forespore membrane through its C-terminal domain. This entry represents the ATPase domain located at the N-terminal of SpoIVA. It contains a conserved 'sensor' threonine residue that is involved in coordinating a Mg+2 ion. 237 matched cddid_all.tbl CDD pfam09548 pfam09548 462827 Spore_III_AB Stage III sporulation protein AB (spore_III_AB). SpoIIIAB represents the stage III sporulation protein AB, which is encoded in a spore formation operon: spoIIIAABCDEFGH that is under sigma G regulation. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. 169 matched cddid_all.tbl CDD pfam09549 pfam09549 430681 RE_Bpu10I Bpu10I restriction endonuclease. This family includes the Bpu10I (recognizes and cleaves CCTNAGC (-5/-2)) restriction endonucleases. 220 matched cddid_all.tbl CDD pfam09550 pfam09550 430682 Phage_TAC_6 Phage tail assembly chaperone protein, TAC. This is a family of phage tail assembly chaperone proteins largely derived from the Rhodobacter species viral agent GTA (gene transfer agent) gp10. 58 matched cddid_all.tbl CDD pfam09551 pfam09551 462828 Spore_II_R Stage II sporulation protein R (spore_II_R). SpoIIR is designated stage II sporulation protein R. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. SpoIIR is a signalling protein that links the activation of sigma E to the transcriptional activity of sigma F during sporulation. 125 matched cddid_all.tbl CDD pfam09552 pfam09552 286618 RE_BstXI BstXI restriction endonuclease. This family includes the BstXI (recognizes and cleaves CCANNNNN^NTGG) restriction endonuclease. 290 matched cddid_all.tbl CDD pfam09553 pfam09553 430684 RE_Eco47II Eco47II restriction endonuclease. This family includes the Eco47II (which recognizes GGNCC, but the cleavage site unknown) restriction endonuclease. 202 matched cddid_all.tbl CDD pfam09554 pfam09554 370557 RE_HaeII HaeII restriction endonuclease. This family includes the HaeII (recognizes and cleaves RGCGC^Y) restriction endonuclease. 338 matched cddid_all.tbl CDD pfam09556 pfam09556 401481 RE_HaeIII HaeIII restriction endonuclease. This family includes the HaeIII (recognizes and cleaves GG^CC) restriction endonuclease. 298 matched cddid_all.tbl CDD pfam09557 pfam09557 430685 DUF2382 Domain of unknown function (DUF2382). This entry describes an uncharacterized domain, sometimes found in association with a PRC-barrel domain pfam05239 which is also found in rRNA processing protein RimM and in a photosynthetic reaction centre complex protein). This domain is found in proteins from Bacillus subtilis, Deinococcus radiodurans, Nostoc sp. PCC 7120, Myxococcus xanthus, and several other species. The function is not known. 111 matched cddid_all.tbl CDD pfam09558 pfam09558 430686 DUF2375 Protein of unknown function (DUF2375). Two members of this family are found in Colwellia psychrerythraea (strain 34H / ATCC BAA-681) and one each in various other species of Colwellia and Shewanella. One member from C. psychrerythraea is of special interest because it is preceded by the same cis-regulatory site as a number of genes that have the PEP-CTERM domain described by PEP_anchor (IPR013424). 69 matched cddid_all.tbl CDD pfam09559 pfam09559 430687 Cas6 Cas6 Crispr. The Cas6 Crispr family of proteins averaging 140 residues are characterized by having a GhGxxxxxGhG motif, where h indicates a hydrophobic residue, at the C-terminus. The CRISPR-Cas system is possibly a mechanism of defence against invading pathogens and plasmids that functions analogously to the RNA interference (RNAi) systems in eukaryotes. 190 matched cddid_all.tbl CDD pfam09560 pfam09560 430688 Spore_YunB Sporulation protein YunB (Spo_YunB). Spo_YunB is the sporulation protein YunB. In Bacillus subtilis its expression is controlled by sigmaE.The gene YunB seems to code for a protein involved, at least indirectly, in the pathway leading to the activation of sigmaK. Inactivation of YunB delays sigmaK activation and results in reduced sporulation efficiency. 91 matched cddid_all.tbl CDD pfam09561 pfam09561 430689 RE_HpaII HpaII restriction endonuclease. This family includes the HpaII (recognizes and cleaves C^CGG) restriction endonuclease. 352 matched cddid_all.tbl CDD pfam09562 pfam09562 401486 RE_LlaMI LlaMI restriction endonuclease. This family includes the LlaMI (recognizes and cleaves CC^NGG) restriction endonuclease. 242 matched cddid_all.tbl CDD pfam09563 pfam09563 370562 RE_LlaJI LlaJI restriction endonuclease. This family includes the LlaJI (recognizes GACGC) restriction endonucleases. 365 matched cddid_all.tbl CDD pfam09564 pfam09564 401487 RE_NgoBV NgoBV restriction endonuclease. This family includes the NgoBV (recognizes GGNNCC but cleavage site is unknown) restriction endonuclease. 238 matched cddid_all.tbl CDD pfam09565 pfam09565 401488 RE_NgoFVII NgoFVII restriction endonuclease. This family includes the NgoFVII (recognizes GCSGC but cleavage site unknown) restriction endonuclease. 293 matched cddid_all.tbl CDD pfam09566 pfam09566 430690 RE_SacI SacI restriction endonuclease. This family includes the SacI (recognizes and cleaves GAGCT^C) restriction endonuclease. 270 matched cddid_all.tbl CDD pfam09567 pfam09567 430691 RE_MamI MamI restriction endonuclease. This family includes the MamI (recognizes and cleaves GATNN^NNATC) restriction endonuclease. 183 matched cddid_all.tbl CDD pfam09568 pfam09568 430692 RE_MjaI MjaI restriction endonuclease. This family includes the MjaI (recognizes CTAG but cleavage site unknown) restriction endonuclease. 170 matched cddid_all.tbl CDD pfam09569 pfam09569 401492 RE_ScaI ScaI restriction endonuclease. This family includes the ScaI (recognizes and cleaves AGT^ACT) restriction endonuclease. 192 matched cddid_all.tbl CDD pfam09570 pfam09570 312916 RE_SinI SinI restriction endonuclease. This family includes the SinI (recognizes and cleaves G^GWCC) restriction endonuclease. 218 matched cddid_all.tbl CDD pfam09571 pfam09571 286631 RE_XcyI XcyI restriction endonuclease. This family includes the XcyI (recognizes and cleaves C^CCGGG) restriction endonucleases. 305 matched cddid_all.tbl CDD pfam09572 pfam09572 401493 RE_XamI XamI restriction endonuclease. This family includes the XamI (recognizes GTCGAC but cleavage site unknown) restriction endonuclease. 254 matched cddid_all.tbl CDD pfam09573 pfam09573 401494 RE_TaqI TaqI restriction endonuclease. This family includes the TaqI (recognizes and cleaves T^CGA) restriction endonuclease. 229 matched cddid_all.tbl CDD pfam09574 pfam09574 430693 DUF2374 Protein of unknown function (Duf2374). This very small protein (about 46 amino acids) consists largely of a single predicted membrane-spanning region. It is found in Photobacterium profundum SS9 and in three species of Vibrio, always near periplasmic nitrate reductase genes, but far from the periplasmic nitrate reductase genes in Aeromonas hydrophila ATCC 7966. 42 matched cddid_all.tbl CDD pfam09575 pfam09575 286635 Spore_SspJ Small spore protein J (Spore_SspJ). Spore_SspJ represents a group of small acid-soluble proteins (SASP) from Bacillus sp., which are present in spores but not in growing cells. The sspJ gene is transcribed in the forespore compartment by RNA polymerase with the forespore-specific sigmaG. Loss of SspJ causes a slight decrease in the rate of spore outgrowth in an otherwise wild-type background. 46 matched cddid_all.tbl CDD pfam09577 pfam09577 312918 Spore_YpjB Sporulation protein YpjB (SpoYpjB). These proteins are found in the endospore-forming bacteria which include Bacillus species. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon. Sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect, but this gene is not, however, a part of the endospore formation minimal gene set. 223 matched cddid_all.tbl CDD pfam09578 pfam09578 462829 Spore_YabQ Spore cortex protein YabQ (Spore_YabQ). This protein is predicted to span the membrane several times. It is only found in genomes of species that perform sporulation, such as Bacillus subtilis, Clostridium tetani, and other members of the Firmicutes (low-GC Gram-positive bacteria). Mutation of this sigmaE-dependent gene blocks development of the spore cortex. The length of the C-terminal region, which includes some hydrophobic regions, is variable. 75 matched cddid_all.tbl CDD pfam09579 pfam09579 462830 Spore_YtfJ Sporulation protein YtfJ (Spore_YtfJ). Proteins in this family are encoded by bacterial genomes if, and only if, the species is capable of endospore formation. YtfJ was confirmed in spores of B. subtilis; it appears to be expressed in the forespore under control of SigF. 81 matched cddid_all.tbl CDD pfam09580 pfam09580 401497 Spore_YhcN_YlaJ Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ). This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain. 157 matched cddid_all.tbl CDD pfam09581 pfam09581 462831 Spore_III_AF Stage III sporulation protein AF (Spore_III_AF). This family represents the stage III sporulation protein AF (Spore_III_AF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of these proteins is poorly conserved. 184 matched cddid_all.tbl CDD pfam09582 pfam09582 462832 AnfO_nitrog Iron only nitrogenase protein AnfO (AnfO_nitrog). Proteins in this entry include Anf1 from Rhodobacter capsulatus (Rhodopseudomonas capsulata) and AnfO from Azotobacter vinelandii. They are found exclusively in species which contain the iron-only nitrogenase, and are encoded immediately downstream of the structural genes for the nitrogenase enzyme in these species. 190 matched cddid_all.tbl CDD pfam09583 pfam09583 430698 Phageshock_PspG Phage shock protein G (Phageshock_PspG). This protein was previously designated as YjbO in Escherichia coli. It is found only in genomes that have the phage shock operon (psp), but it is only rarely encoded near other psp genes. The psp regulon is upregulated in response to a number of stress conditions, including ethanol, expression of the filamentous phage secretin protein IV and other secretins and heat shock. 63 matched cddid_all.tbl CDD pfam09584 pfam09584 430699 Phageshock_PspD Phage shock protein PspD (Phageshock_PspD). Members of this family are phage shock protein PspD, found in a minority of bacteria that carry the defining genes of the phage shock regulon (pspA, pspB, pspC, and pspF). It is found in Escherichia coli, Yersinia pestis, and closely related species, where it is part of the phage shock operon. It is known to be expressed but its function is unknown. 61 matched cddid_all.tbl CDD pfam09585 pfam09585 401502 Lin0512_fam Conserved hypothetical protein (Lin0512_fam). This family consists of few members, broadly distributed. It occurs so far in several Firmicutes (twice in Oceanobacillus), one Cyanobacterium, one alpha Proteobacterium, and (with a long prefix) in plants. The function is unknown. The alignment includes a well conserved motif GxGxDxHG near the N-terminus. 114 matched cddid_all.tbl CDD pfam09586 pfam09586 430700 YfhO Bacterial membrane protein YfhO. This protein is a conserved membrane protein. The yfhO gene is transcribed in Difco sporulation medium and the transcription is affected by the YvrGHb two-component system. Some members of this family have been annotated as glycosyl transferases of the PMT family. 839 matched cddid_all.tbl CDD pfam09587 pfam09587 430701 PGA_cap Bacterial capsule synthesis protein PGA_cap. This protein is a putative poly-gamma-glutamate capsule biosynthesis protein found in bacteria. Poly-gamma-glutamate is a natural polymer that may be involved in virulence and may help bacteria survive in high salt concentrations. It is a surface-associated protein. 246 matched cddid_all.tbl CDD pfam09588 pfam09588 430702 YqaJ YqaJ-like viral recombinase domain. This protein family is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit. 142 matched cddid_all.tbl CDD pfam09589 pfam09589 370573 HrpA_pilin HrpA pilus formation protein. HrpA is an essential component of the type III secretion system (TTSS) which pathogens use to inject virulence factors directly into their host cells, and to cause disease. The TTSS has an Hrp pilus appendage for channelling effector proteins through the plant cell wall and this pilus elongates by the addition of HrpA pilin subunits at the distal end. 96 matched cddid_all.tbl CDD pfam09590 pfam09590 150302 Env-gp36 Lentivirus surface glycoprotein. This protein is found in feline immunodeficiency retrovirus. It represents the surface glycoprotein which is found in the polyprotein C-terminal to the Env protein. 591 matched cddid_all.tbl CDD pfam09591 pfam09591 286649 DUF2463 Protein of unknown function (DUF2463). This protein is found in eukaryotic, parasitic microsporidia. Its function is unknown. 210 matched cddid_all.tbl CDD pfam09592 pfam09592 401506 DUF2031 Protein of unknown function (DUF2031). This protein is expressed in Plasmodium; its function is unknown. It may be the product of gene family pyst-b. 227 matched cddid_all.tbl CDD pfam09593 pfam09593 401507 Pathogen_betaC1 Beta-satellite pathogenicity beta C1 protein. Cotton leaf-curl disease - CLCuD - is of major economic importance in cotton-growing areas of the far-east. The infectious agent appears to be a single-stranded DNA molecule of approx 1350 nucleotides in length, which, when inoculated with the Begomovirus into cotton, induces symptoms typical of CLCuD. This molecule requires the Begomovirus for replication and encapsidation. DNA beta encodes a single protein, betaC1. The intracellular distribution of betaC1 is consistent with the hypothesis that it has a role in transporting the DNA A of Begomovirus from the nuclear site of replication to the plasmodesmatal exit sites of the infected cell. The DNA beta-encoded protein, betaC1, is the determinant of both pathogenicity and suppression of gene silencing. 117 matched cddid_all.tbl CDD pfam09594 pfam09594 430703 GT87 Glycosyltransferase family 87. The enzymes in this family are glycosyltransferases. PimE is involved in phosphatidylinositol mannoside (PIM) synthesis, a major class of glycolipids in all mycobacteria. PimE is a polyprenol-phosphate-mannose-dependent mannosyltransferase that transfers the fifth mannose of PIM. The family also includes alpha(1-->3) arabinofuranosyltransferase, invloved in the synthesis of of mycobacterial arabinogalactan. 237 matched cddid_all.tbl CDD pfam09595 pfam09595 462833 Metaviral_G Metaviral_G glycoprotein. This is a viral attachment glycoprotein from region G of metaviruses. It is high in serine and threonine suggesting it is highly glycosylated. 183 matched cddid_all.tbl CDD pfam09596 pfam09596 462834 MamL-1 MamL-1 domain. The MamL-1 domain is a polypeptide of up to 70 residues, numbers 15-67 of which adopt an elongated kinked helix that wraps around ANK and CSL forming one of the complexes in the build-up of the Notch transcriptional complex for recruiting general transcription factors.. 58 matched cddid_all.tbl CDD pfam09597 pfam09597 462835 IGR IGR protein motif. This domain is found in fungal proteins and contains a conserved IGR motif. Its function is unknown. 55 matched cddid_all.tbl CDD pfam09598 pfam09598 430706 Stm1_N Stm1. This region is found at the N terminal of the Stm1 protein. Stm1 is a G4 quadraplex and purine motif triplex nucleic acid-binding protein. It has been implicated in many biological processes including apoptosis and telomere biosynthesis. Stm1 is known to interact with CDC13, and is known to associate with ribosomes and nuclear telomere cap complexes. 64 matched cddid_all.tbl CDD pfam09599 pfam09599 286655 IpaC_SipC Salmonella-Shigella invasin protein C (IpaC_SipC). This entry represents a family of proteins associated with bacterial type III secretion systems, which are injection machines for virulence factors into host cell cytoplasm. Characterized members of this protein family are known to be secreted and are described as invasins, including IpaC from Shigella flexneri and SipC from Salmonella typhimurium. Members may be referred to as invasins, pathogenicity island effectors, and cell invasion proteins. 334 matched cddid_all.tbl CDD pfam09600 pfam09600 430707 Cyd_oper_YbgE Cyd operon protein YbgE (Cyd_oper_YbgE). This entry describes a small protein of unknown function, about 100 amino acids in length, essentially always found in an operon with CydAB, subunits of the cytochrome d terminal oxidase. It appears to be an integral membrane protein. It is found so far only in the Proteobacteria. 76 matched cddid_all.tbl CDD pfam09601 pfam09601 430708 DUF2459 Protein of unknown function (DUF2459). This conserved hypothetical protein of unknown function is found in several Proteobacteria. Its function is unknown and its genome context is not well-conserved. It is found amid urease genes in at least one species. 171 matched cddid_all.tbl CDD pfam09602 pfam09602 370578 PhaP_Bmeg Polyhydroxyalkanoic acid inclusion protein (PhaP_Bmeg). This entry describes a protein found in polyhydroxyalkanoic acid (PHA) gene regions and incorporated into PHA inclusions in Bacillus cereus and Bacillus megaterium. The role of the protein may include amino acid storage. 168 matched cddid_all.tbl CDD pfam09603 pfam09603 462836 Fib_succ_major Fibrobacter succinogenes major domain (Fib_succ_major). This domain of about 175 to 200 amino acids is found, in from one to five copies, in over 50 proteins in Fibrobacter succinogenes S85, an obligate anaerobe of the rumen. Many members of this family have an apparent lipoprotein signal sequence. Conserved cysteine residues, suggestive of disulfide bond formation, are also consistent with an extracytoplasmic location for this domain. This domain can also be found in small numbers of proteins in Chlorobium tepidum and Bacteroides thetaiotaomicron. 171 matched cddid_all.tbl CDD pfam09604 pfam09604 462837 Potass_KdpF F subunit of K+-transporting ATPase (Potass_KdpF). This entry describes a very small integral membrane peptide KdpF, a subunit of the K(+)-translocating Kdp complex. It is found upstream of the KdpA subunit (IPR004623). Because of its very small size and highly hydrophobic character, it is sometimes missed in genome annotation. 22 matched cddid_all.tbl CDD pfam09605 pfam09605 430711 Trep_Strep Hypothetical bacterial integral membrane protein (Trep_Strep). This family consists of strongly hydrophobic proteins about 190 amino acids in length with a strongly basic motif near the C-terminus. It is found in rather few species, but in paralogous families of 12 members in the oral pathogenic spirochaete Treponema denticola and 2 in Streptococcus pneumoniae R6. 185 matched cddid_all.tbl CDD pfam09606 pfam09606 312941 Med15 ARC105 or Med15 subunit of Mediator complex non-fungal. The approx. 70 residue Med15 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, Med15 is a critical transducer of gene activation signals that control early metazoan development. 732 matched cddid_all.tbl CDD pfam09607 pfam09607 462838 BrkDBD Brinker DNA-binding domain. This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway. 58 matched cddid_all.tbl CDD pfam09608 pfam09608 430712 Alph_Pro_TM Putative transmembrane protein (Alph_Pro_TM). This family consists of predicted transmembrane proteins of about 270 amino acids. Members are found, so far, only among the Alphaproteobacteria and only once in each genome. 227 matched cddid_all.tbl CDD pfam09609 pfam09609 312943 Cas_GSU0054 CRISPR-associated protein, GSU0054 family (Cas_GSU0054). This entry represents a rare CRISPR-associated protein. So far, members are found in Geobacter sulfurreducens and in two unpublished genomes: Gemmata obscuriglobus and Actinomyces naeslundii. CRISPR-associated proteins typically are found near CRISPR repeats and other CRISPR-associated proteins, have low levels of sequence identify, have sequence relationships that suggest lateral transfer, and show some sequence similarity to DNA-active proteins such as helicases and repair proteins. 552 matched cddid_all.tbl CDD pfam09610 pfam09610 462839 Myco_arth_vir_N Mycoplasma virulence signal region (Myco_arth_vir_N). This entry represents the N-terminal region of a family of large, virulence-associated proteins in Mycoplasma arthritidis and smaller proteins in Mycoplasma capricolum. It includes a probable signal sequence or signal anchor, which, in most instances, has four consecutive Lys residues before the hydrophobic stretch. 32 matched cddid_all.tbl CDD pfam09611 pfam09611 430713 Cas_Csy1 CRISPR-associated protein (Cas_Csy1). CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This entry, typified by YPO2465 of Yersinia pestis, is a CRISPR-associated (Cas) entry strictly associated with the Ypest subtype of CRISPR/Cas locus. It is designated Csy1, for CRISPR/Cas Subtype Ypest protein 1. 376 matched cddid_all.tbl CDD pfam09612 pfam09612 401521 HtrL_YibB Bacterial protein of unknown function (HtrL_YibB). The protein from this rare, uncharacterized protein family is designated HtrL or YibB in E. coli, where its gene is found in a region of LPS core biosynthesis genes. homologs are found in Shigella flexneri, Campylobacter jejuni, and Caenorhabditis elegans only. The htrL gene may represent an insertion to the LPS core biosynthesis region, rather than an LPS biosynthetic protein. 267 matched cddid_all.tbl CDD pfam09613 pfam09613 312947 HrpB1_HrpK Bacterial type III secretion protein (HrpB1_HrpK). This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia. 126 matched cddid_all.tbl CDD pfam09614 pfam09614 430714 Cas_Csy2 CRISPR-associated protein (Cas_Csy2). CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This entry, typified by YPO2464 of Yersinia pestis, is a CRISPR-associated (Cas) entry strictly associated with the Ypest subtype of CRISPR/Cas locus. It is designated Csy2, for CRISPR/Cas Subtype Ypest protein 2. 295 matched cddid_all.tbl CDD pfam09615 pfam09615 430715 Cas_Csy3 CRISPR-associated protein (Cas_Csy3). CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This entry, typified by YPO2463 of Yersinia pestis, is a CRISPR-associated (Cas) entry strictly associated with the Ypest subtype of CRISPR/Cas locus. It is designated Csy3, for CRISPR/Cas Subtype Ypest protein 3. 328 matched cddid_all.tbl CDD pfam09617 pfam09617 401524 Cas_GSU0053 CRISPR-associated protein GSU0053 (Cas_GSU0053). This entry is found in CRISPR-associated (cas) proteins in the genomes of Geobacter sulfurreducens PCA and Desulfotalea psychrophila LSv54 (both Desulfobacterales from the Deltaproteobacteria), Gemmata obscuriglobus (a Planctomycete), and Actinomyces naeslundii MG1 (Actinobacteria). 170 matched cddid_all.tbl CDD pfam09618 pfam09618 430716 Cas_Csy4 CRISPR-associated protein (Cas_Csy4). CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family, typified by YPO2462 of Yersinia pestis, is a CRISPR-associated (Cas) family strictly associated with the Ypest subtype of CRISPR/Cas locus. It is designated Csy4, for CRISPR/Cas Subtype Ypest protein 4. 181 matched cddid_all.tbl CDD pfam09619 pfam09619 430717 YscW Type III secretion system lipoprotein chaperone (YscW). This entry is encoded within type III secretion operons. The protein has been characterized as a chaperone for the outer membrane pore component YscC. YscW is a lipoprotein which is itself localized to the outer membrane and, it is believed, facilitates the oligomerization and localization of YscC. 105 matched cddid_all.tbl CDD pfam09620 pfam09620 430718 Cas_csx3 CRISPR-associated protein (Cas_csx3). This entry is encoded in CRISPR-associated (cas) gene clusters, near CRISPR repeats, in the genomes of several different thermophiles: Archaeoglobus fulgidus (archaeal), Aquifex aeolicus (Aquificae), Dictyoglomus thermophilum (Dictyoglomi), and a thermophilic Synechococcus (Cyanobacteria). It is not yet assigned to a specific CRISPR/cas subtype (hence the x designation csx3). 79 matched cddid_all.tbl CDD pfam09621 pfam09621 286674 LcrR Type III secretion system regulator (LcrR). This family of proteins are encoded within type III secretion operons and have been characterized in Yersinia as a regulator of the Low-Calcium Response (LCR). 138 matched cddid_all.tbl CDD pfam09622 pfam09622 430719 DUF2391 Putative integral membrane protein (DUF2391). This entry is found in Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Rhizobium meliloti, and Gloeobacter violaceus in a conserved two-gene neighbourhood. Proteins containing this entry appear to span the membrane seven times. 267 matched cddid_all.tbl CDD pfam09623 pfam09623 430720 Cas_NE0113 CRISPR-associated protein NE0113 (Cas_NE0113). Members of this minor CRISPR-associated (Cas) protein family are encoded in cas gene clusters in Vibrio vulnificus YJ016, Nitrosomonas europaea ATCC 19718, Mannheimia succiniciproducens MBEL55E, and Verrucomicrobium spinosum. 209 matched cddid_all.tbl CDD pfam09624 pfam09624 430721 DUF2393 Protein of unknown function (DUF2393). The function of this protein is unknown. It is always found as part of a two-gene operon with IPR013416, a protein that appears to span the membrane seven times. It has so far been found in the bacteria Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Rhizobium meliloti, and Gloeobacter violaceus. 142 matched cddid_all.tbl CDD pfam09625 pfam09625 462840 VP9 VP9 protein. VP9 is a protein containing a ferredoxin fold. Two dimers come together to form one asymmetric unit which possesses a DNA recognition fold and specific metal binding sites possibly for zinc. It is postulated that being a non-structural protein VP9 is involved in the transcriptional regulation of the White spot syndrome virus, WSSV, from which it comes. WSSV is the major viral pathogen in shrimp aquaculture. VP9 is found N-terminal to the pfam07056 domain. 73 matched cddid_all.tbl CDD pfam09626 pfam09626 430723 DHC Dihaem cytochrome c. Dihaem cytochrome c (DHC) is a soluble c-type cytochrome that folds into two distinct domains, each binding a single haem group and connected by a small linker region. Despite little sequence similarity, the N-terminal domain (residues 12-75) is a class I type cytochrome c, that binds one of the haems, but the domain surrounding the other haem is structurally unique. DHC binds electrostatically to an oxygen-binding protein, sphaeroides haem protein (SHP), as a component of a conserved electron transfer pathway. DHC acts as the physiological electron donor for SHP during phototrophic growth. In certain species DHC is found upstream of pfam01292. 111 matched cddid_all.tbl CDD pfam09627 pfam09627 462841 PrgU PrgU-like protein. PrgU is a protein of plasmid in origin expressed mainly in Enterococcus bacteria. It forms a six beta-strand barrel with three accompanying alpha helices and is probably a homo-dimer in the cell. PrgU probably acts as a RNA-binding regulator that mitigates toxicity accompanying overproduction of PrgB-like adhesins, which are involved in conjugative transfer. 105 matched cddid_all.tbl CDD pfam09628 pfam09628 462842 YvfG YvfG protein. Yvfg is a hypothetical protein of 71 residues expressed in some bacteria. The monomer consists of two parallel alpha helices, and the protein crystallizes as a homo-dimer. 67 matched cddid_all.tbl CDD pfam09629 pfam09629 462843 YorP YorP protein. YorP is a 71 residue protein found in bacteria. As it is also found in a bacteriophage it might be of viral origin. The structure is of an alpha helix between two of five beta strands. The function is unknown. 71 matched cddid_all.tbl CDD pfam09630 pfam09630 430725 DUF2024 Domain of unknown function (DUF2024). This protein of 86 residues is expressed in bacteria. It consists of four alpha helices and two beta strands. Its function is unknown. One UniProt entry gives the gene name as Traf5. 81 matched cddid_all.tbl CDD pfam09631 pfam09631 462844 Sen15 Sen15 protein. The Sen15 subunit of the tRNA intron-splicing endonuclease is one of the two structural subunits of this hetero-tetrameric enzyme. Residues 36-157 of this subunit possess a novel homodimeric fold. Each monomer consists of three alpha-helices and a mixed antiparallel/parallel beta-sheet. Two monomers of Sen15 fold with two monomers of Sen34, one of the two catalytic subunits, to form an alpha2-beta2 tetramer as part of the functional endonuclease assembly. 101 matched cddid_all.tbl CDD pfam09632 pfam09632 401535 Rac1 Rac1-binding domain. The Rac1-binding domain is the C-terminal portion of YpkA from Yersinia. It is an all-helical molecule consisting of two distinct subdomains connected by a linker. the N-terminal end, residues 434-615, consists of six helices organized into two three-helix bundles packed against each other. This region is involved with binding to GTPases. The C-terminal end, residues 705-732. is a novel and elongated fold consisting of four helices clustered into two pairs, and this fold carries the helix implicated in actin activation. Rac1-binding domain mimics host guanidine nucleotide dissociation inhibitors (GDIs) of the Rho GTPases, thereby inhibiting nucleotide exchange in Rac1 and causing cytoskeletal disruption in the host. It is usually found downstream of pfam00069. 293 matched cddid_all.tbl CDD pfam09633 pfam09633 430727 DUF2023 Protein of unknown function (DUF2023). This protein of approx.120 residues consists of three beta strands and five alpha helices, thought to fold into a homo-dimer. It is expressed in bacteria. 99 matched cddid_all.tbl CDD pfam09634 pfam09634 430728 DUF2025 Protein of unknown function (DUF2025). This protein is produced from gene PA1123 in Pseudomonas. It contains three alpha helices and six beta strands and is thought to be monomeric. It appears to be present in the biofilm layer and may be a lipoprotein. 105 matched cddid_all.tbl CDD pfam09635 pfam09635 401537 MetRS-N MetRS-N binding domain. The MetRS-N domain binds an Arc1-P domain in a tetrameric complex resembling a classical GST homo-dimer. Domain-swapping between symmetrically related MetRS-N and Arc1p-N domains generates a 2:2 tetramer held together by van der Waals forces. This domain is necessary for formation of the aminoacyl-tRNA synthetase complex necessary for tRNA nuclear export and shuttling as part of the translational apparatus. The domain is associated with pfam09334. 121 matched cddid_all.tbl CDD pfam09636 pfam09636 401538 XkdW XkdW protein. This protein of approx. 100 residues contains two alpha helices and two beta strands and is probably monomeric. It is expressed in bacteria but is probably viral in origin. Its function is unknown. 106 matched cddid_all.tbl CDD pfam09637 pfam09637 462845 Med18 Med18 protein. Med18 is one subunit of Mediator, a head-module multiprotein complex, that stimulates basal RNA polymerase II (Pol II) transcription. Med18 consists of an eight-stranded beta-barrel with a central pore and three flanking helices. It complexes with Med8 and Med20 proteins by forming a heterodimer of two-fold symmetry with Med20 and binding the C-terminal alpha-helix region of Med8 across the top of its barrel. This complex creates a multipartite TBP-binding site that can be modulated by transcriptional activators. 230 matched cddid_all.tbl CDD pfam09638 pfam09638 286688 Ph1570 Ph1570 protein. This is a hypothetical protein from Pyroccous horikoshii of unknown function. It contains six alpha helices and eight beta strands and is thought to be monomeric. 156 matched cddid_all.tbl CDD pfam09639 pfam09639 401540 YjcQ YjcQ protein. YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is expressed in bacteria and also in viruses. It appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown. However, it is thought to be a prophage head protein in viruses. 94 matched cddid_all.tbl CDD pfam09640 pfam09640 430729 DUF2027 Domain of unknown function (DUF2027). This protein domain is of unknown function. though putatively involved in DNA mismatch repair. It is associated with pfam01713. 154 matched cddid_all.tbl CDD pfam09641 pfam09641 378228 DUF2026 Protein of unknown function (DUF2026). This protein of approx. 100 residues is found in bacteria. It contains up to five alpha helices and up to seven beta strands and is probably monomeric. Its function is unknown. It is cited as a major prophage head protein, so might generally be of viral origin. 205 matched cddid_all.tbl CDD pfam09642 pfam09642 401542 YonK YonK protein. YonK protein is expressed by the bacterial prophage SPbetaC. It is a 63 residue protein that associates into a homo-octamer in the form of a beta-stranded barrel with four outer helical features at points of the compass. Its function is unknown. 58 matched cddid_all.tbl CDD pfam09643 pfam09643 430730 YopX YopX protein. YopX is a protein that is largely helical, with three identical chains probably complexing into a twelve-chain structure. 127 matched cddid_all.tbl CDD pfam09644 pfam09644 401544 Mg296 Mg296 protein. This protein of 129 residues is expressed in bacteria. It consists of three identical chains of five alpha helices. Two copies of each chain associate into a complex of six units of possible biological significance but of unknown function. 126 matched cddid_all.tbl CDD pfam09645 pfam09645 401545 F-112 F-112 protein. F-112 protein is of 70-110 residues and is found in viruses. Its winged-helix structure suggests a DNA-binding function. 71 matched cddid_all.tbl CDD pfam09646 pfam09646 430731 Gp37 Gp37 protein. This protein of 154 residues consists of a unit of helices and beta sheets that crystallizes into a beautiful asymmetrical dodecameric barrel-structure, of two six-membered rings one on top of the other. It is expressed in bacteria but is of viral origin as it is found in phage BcepMu and is probably a pathogenesis factor. 134 matched cddid_all.tbl CDD pfam09648 pfam09648 430732 YycI YycI protein. This domain is exclusively found in YycI proteins in the low GC content Gram positive species. These two domains share the same structural fold with domains two and three of YycH pfam07435. Both, YycH and YycI are always found in pair on the chromosome, downstream of the essential histidine kinase YycG. Additionally, both proteins share a function in regulating the YycG kinase with which they appear to form a ternary complex. Lastly, the two proteins always contain an N-terminal transmembrane helix and are localized to the periplasmic space as shown by PhoA fusion studies. 231 matched cddid_all.tbl CDD pfam09649 pfam09649 462846 CHZ Histone chaperone domain CHZ. This domain is highly conserved from yeasts to humans and is part of the chaperone protein HIRIP3 in vertebrates which interacts with the H3.3 chaperone HIRA, implicated in histone replacement during transcription. N- and C- termini of Chz family members are relatively divergent but do contain similar acidic stretches rich in Glu/Asp residues, characteriztic of all histone chaperones. 34 matched cddid_all.tbl CDD pfam09650 pfam09650 430734 PHA_gran_rgn Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn). Proteins in this entry are encoded by genes involved in either polyhydroxyalkanoic acid (PHA) biosynthesis or utilization, including proteins found at the surface of PHA granules. These proteins have so far been found in the Pseudomonadales, Xanthomonadales, and Vibrionales, all of which belong to the Gammaproteobacteria. 79 matched cddid_all.tbl CDD pfam09651 pfam09651 401550 Cas_APE2256 CRISPR-associated protein (Cas_APE2256). This entry represents a conserved region of about 150 amino acids found in at least five archaeal and three bacterial species. These species all contain CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats). In six of eight species, the protein is encoded the vicinity of a CRISPR/Cas locus. 136 matched cddid_all.tbl CDD pfam09652 pfam09652 430735 Cas_VVA1548 Putative CRISPR-associated protein (Cas_VVA1548). This entry represents a conserved region of about 95 amino acids found exclusively in species with CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats). In all bacterial species that contain this entry, the genes encoding the proteins are in the midst of a cluster of cas (CRISPR-associated) genes. 91 matched cddid_all.tbl CDD pfam09654 pfam09654 430736 DUF2396 Protein of unknown function (DUF2396). These conserved hypothetical proteins have so far been found only in the Cyanobacteria. They are about 170 amino acids long and contain a CxxCx(14)CxxH motif near the N-terminus. 159 matched cddid_all.tbl CDD pfam09655 pfam09655 430737 Nitr_red_assoc Conserved nitrate reductase-associated protein (Nitr_red_assoc). Proteins in this entry are found in the Cyanobacteria, and are mostly encoded near nitrate reductase and molybdopterin biosynthesis genes. Molybdopterin guanine dinucleotide is a cofactor for nitrate reductase. These proteins are sometimes annotated as nitrate reductase-associated proteins, though their function is unknown. 144 matched cddid_all.tbl CDD pfam09656 pfam09656 430738 PGPGW Putative transmembrane protein (PGPGW). Proteins in this entry are putative Actinobacterial proteins of about 150 amino acids in length, with three predicted transmembrane helices and an unusual motif with consensus sequence PGPGW. 53 matched cddid_all.tbl CDD pfam09657 pfam09657 286705 Cas_Csx8 CRISPR-associated protein Csx8 (Cas_Csx8). Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry describes proteins of unknown function which are encoded in the midst of a cas gene operon. 493 matched cddid_all.tbl CDD pfam09658 pfam09658 462847 Cas_Csx9 CRISPR-associated protein (Cas_Csx9). Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry describes archaeal proteins encoded in cas gene regions. 377 matched cddid_all.tbl CDD pfam09659 pfam09659 462848 Cas_Csm6 CRISPR-associated protein (Cas_Csm6). Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. 373 matched cddid_all.tbl CDD pfam09660 pfam09660 430739 DUF2397 Protein of unknown function (DUF2397). Proteins in this entry are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). 483 matched cddid_all.tbl CDD pfam09661 pfam09661 430740 DUF2398 Protein of unknown function (DUF2398). Proteins in this entry are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Betaproteobacteria). 362 matched cddid_all.tbl CDD pfam09662 pfam09662 286710 Phenyl_P_gamma Phenylphosphate carboxylase gamma subunit (Phenyl_P_gamma). Members of this protein family are the gamma subunit of phenylphosphate carboxylase. Phenol (methyl-benzene) is converted to phenylphosphate, then para-carboxylated by this four-subunit enzyme, with the release of phosphate, to 4-hydroxybenzoate. The enzyme contains neither biotin nor thiamin pyrophosphate. The gamma subunit has no known homologs. 83 matched cddid_all.tbl CDD pfam09663 pfam09663 401557 Amido_AtzD_TrzD Amidohydrolase ring-opening protein (Amido_AtzD_TrzD). Members of this family are ring-opening amidohydrolases, including cyanuric acid amidohydrolase (CAH) (EC:3.5.2.15) (AtzD and TrzD) and barbituric acid hydrolase (BAH). Note that barbiturase does not act as defined for EC:3.5.2.1 (barbiturate + water = malonate + urea) but rather catalyzes the ring opening of barbiturase acid to ureidomalonic acid. Cyanuric acid hydrolases (AtzD) and barbiturases are homologous and found almost exclusively in bacteria. CAH is a homotetramer, the monomer of which possesses a fold that is dubbed the Toblerone fold. Although not obvious from the protein sequence, each CAH monomer possesses 3-fold rotational symmetry, for which the repeated structural motif is structurally similar to that of the YjgF superfamily of proteins (two alpha helices and a four-strand antiparallel beta-sheet), despite having low sequence similarity. This suggests that the Toblerone fold evolved from concatenated YjgF family proteins. The 3-fold symmetry of each CAH monomer extends to the active site, which contains three Arg-Lys-Ser triads, which bind the substrate via an extensive hydrogen bonding network. 361 matched cddid_all.tbl CDD pfam09664 pfam09664 401558 DUF2399 Protein of unknown function C-terminus (DUF2399). Proteins in this entry are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Beta-proteobacteria). Just the C-terminal region is ioncluded here. 152 matched cddid_all.tbl CDD pfam09665 pfam09665 430741 RE_Alw26IDE Type II restriction endonuclease (RE_Alw26IDE). Members of this entry are type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family. characterized specificities of the three members are GGTCTC, CGTCTC and the shared subsequence GTCTC. 508 matched cddid_all.tbl CDD pfam09666 pfam09666 401560 Sororin Sororin protein. Sororin is an essential, cell cycle-dependent mediator of sister chromatid cohesion. The protein is nuclear in interphase cells, dispersed from the chromatin in mitosis, and interacts with the cohesin complex. 155 matched cddid_all.tbl CDD pfam09667 pfam09667 430742 DUF2028 Domain of unknown function (DUF2028). This region of similarity is found in the vertebrate homologs of the drosophila Bobby Sox. 180 matched cddid_all.tbl CDD pfam09668 pfam09668 312981 Asp_protease Aspartyl protease. This family of eukaryotic aspartyl proteases have a fold similar to retroviral proteases which implies they function proteolytically during regulated protein turnover. 124 matched cddid_all.tbl CDD pfam09669 pfam09669 462849 Phage_pRha Phage regulatory protein Rha (Phage_pRha). Members of this protein family are found in temperate phage and bacterial prophage regions. Members include the product of the rha gene of the lambdoid phage phi-80, a late operon gene. The presence of this gene interferes with infection of bacterial strains that lack integration host factor (IHF), which regulates the rha gene. It is suggested that Rha is a phage regulatory protein. 91 matched cddid_all.tbl CDD pfam09670 pfam09670 401562 Cas_Cas02710 CRISPR-associated protein (Cas_Cas02710). Members of this family are found, exclusively in the vicinity of CRISPR repeats and other CRISPR-associated (cas) genes, in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum), Thermus thermophilus (Deinococcus-Thermus), Chloroflexus aurantiacus (Chloroflexi), and Thermomicrobium roseum (Thermomicrobia). 377 matched cddid_all.tbl CDD pfam09671 pfam09671 401563 Spore_GerQ Spore coat protein (Spore_GerQ). Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria). This protein is cross-linked by a spore coat-associated transglutaminase. 76 matched cddid_all.tbl CDD pfam09673 pfam09673 430744 TrbC_Ftype Type-F conjugative transfer system pilin assembly protein. This entry represents TrbC, a protein that is an essential component of the F-type conjugative pilus assembly system for the transfer of plasmid DNA. The N-terminal portion of these proteins is heterogeneous. 112 matched cddid_all.tbl CDD pfam09674 pfam09674 430745 DUF2400 Protein of unknown function (DUF2400). Members of this uncharacterized protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighbourhoods show little conservation. 228 matched cddid_all.tbl CDD pfam09675 pfam09675 286721 Chlamy_scaf Chlamydia-phage Chp2 scaffold (Chlamy_scaf). Members of this entry are encoded by genes in chlamydia-phage such as Chp2. These viruses have around eight genes and obligately infect intracellular bacterial pathogens of the genus Chlamydia. This protein is annotated as VP3 or structural protein (as if a protein of mature viral particles), however, it is displaced from procapsids as DNA is packaged, and therefore is more correctly described as a scaffolding protein. 109 matched cddid_all.tbl CDD pfam09676 pfam09676 430746 TraV Type IV conjugative transfer system lipoprotein (TraV). This entry includes TraV, which is a component of conjugative type IV secretion system. TraV is an outer membrane lipoprotein that is believed to interact with the secretin TraK. The alignment contains three conserved cysteines in the N-terminal half. 128 matched cddid_all.tbl CDD pfam09677 pfam09677 430747 TrbI_Ftype Type-F conjugative transfer system protein (TrbI_Ftype). This entry represents TrbI, an essential component of the F-type conjugative transfer system for plasmid DNA transfer that has been shown to be localized to the periplasm. 106 matched cddid_all.tbl CDD pfam09678 pfam09678 430748 Caa3_CtaG Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG). Members of this family are the CtaG protein required for assembly of active cytochrome c oxidase of the caa3 type, as found in Bacillus subtilis. 239 matched cddid_all.tbl CDD pfam09679 pfam09679 370613 TraQ Type-F conjugative transfer system pilin chaperone (TraQ). This entry represents TraQ, a protein that makes a specific interaction with pilin (TraA) to aid its transfer through the inner membrane during the process of F-type conjugative pilus assembly. 85 matched cddid_all.tbl CDD pfam09680 pfam09680 401569 YjcZ_2 Family of unknown function. This is a family of unknown function. However, family members such as yjcZ has been shown to be sporulation specific and transcribed by the SigK RNA polymerase beginning at t4 of sporulation. 24 matched cddid_all.tbl CDD pfam09681 pfam09681 430749 Phage_rep_org_N N-terminal phage replisome organizer (Phage_rep_org_N). This entry represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region is N-terminal to the low-complexity region. 121 matched cddid_all.tbl CDD pfam09682 pfam09682 401571 Phage_holin_6_1 Bacteriophage holin of superfamily 6 (Holin_LLH). Phage_holin_6_1 or Holin_LLH identifies a family of phage holins from a number of phage and prophage regions of Gram-positive bacteria. Like other holins, it is large for holins (about 100-160 amino acids) with stretches of hydrophobic sequence and is encoded adjacent to lytic enzymes. Holin LLH family is found in phage of Firmicutes and have an N-terminal transmembrane segment. 100 matched cddid_all.tbl CDD pfam09683 pfam09683 430750 Lactococcin_972 Bacteriocin (Lactococcin_972). These sequences represent bacteriocins related to lactococcin. Members tend to be found in association with a seven transmembrane putative immunity protein. 62 matched cddid_all.tbl CDD pfam09684 pfam09684 430751 Tail_P2_I Phage tail protein (Tail_P2_I). These sequences represent the family of phage P2 protein I and related tail proteins from a number of temperate phage of Gram-negative bacteria. 132 matched cddid_all.tbl CDD pfam09685 pfam09685 430752 DUF4870 Domain of unknown function (DUF4870). 107 matched cddid_all.tbl CDD pfam09686 pfam09686 430753 Plasmid_RAQPRD Plasmid protein of unknown function (Plasmid_RAQPRD). This entry identifies a family of proteins, which are about 100 amino acids in length, including a predicted signal sequence and a perfectly conserved motif RAQPRD towards the C terminus. Members are found in the Pseudomonas putida TOL plasmid pWW0 and in cryptic plasmid regions of Salmonella enterica subsp. enterica serovar Typhi and Pseudomonas syringae DC3000. The function of these proteins are unknown. 75 matched cddid_all.tbl CDD pfam09687 pfam09687 430754 PRESAN Plasmodium RESA N-terminal. The short, four-helical domain first identified in the Plasmodium export proteins PHISTa and PHISTc has been extended to become this six-helical PRESAN domain identified in the P. falciparum-specific RESA-type (Ring-infected erythrocyte surface antigen) proteins in association with the DnaJ domain. Overall, at least 67 proteins have been detected in P. falciparum with complete copies of the PRESAN domain. No versions of this domain were detected in other apicomplexan genera, suggesting that the domain was 'invented' after the divergence of the lineage leading to the genus Plasmodium undergoing a dramatic proliferation only in P. falciparum. A secondary structure-prediction derived from the multiple alignment of the PRESAN family reveals that it is composed of an all-helical fold with six conserved helical segments. There is some evidence it might localize to membranes. 125 matched cddid_all.tbl CDD pfam09688 pfam09688 401577 Wx5_PLAF3D7 Protein of unknown function (Wx5_PLAF3D7). This set of protein sequences represent a family of at least four proteins in Plasmodium falciparum (isolate 3D7). An interesting feature is five perfectly conserved Trp residues. 144 matched cddid_all.tbl CDD pfam09689 pfam09689 401578 PY_rept_46 Plasmodium yoelii repeat (PY_rept_46). This repeat is found in the products of only 2 genes in Plasmodium species. It is found in no other organizms. 51 matched cddid_all.tbl CDD pfam09690 pfam09690 401579 PYST-C1 Plasmodium yoelii subtelomeric region (PYST-C1). This group of sequences are defined by the N-terminal domain of a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes. There are no obvious homologs to these genes in any other organizm. The C-terminal portions of the genes that contain this domain are divergent and some contain other yoelii-specific paralogous domains such as PYST-C2 (IPR006491). 55 matched cddid_all.tbl CDD pfam09691 pfam09691 401580 T2SS_PulS_OutS Type II secretion system pilotin lipoprotein (PulS_OutS). This family comprises lipoproteins from four gamma proteobacterial species: PulS protein of Klebsiella pneumoniae (P20440), the OutS protein of Erwinia chrysanthemi (Q01567) and Pectobacterium chrysanthemi, and the functionally uncharacterized E. coli protein EtpO. PulS and OutS have been shown to interact with and facilitate insertion of secretins into the outer membrane, suggesting a chaperone-like, or piloting function for members of this family. In the pilotin from this four-helix protein from enterohemorrhagic Escherichia coli, the straight helix alpha2, the curved helix alpha3 and the bent helix alpha4 surround the central N-terminal helix alpha1. These helices create a prominent groove, mainly formed by side chains of helices 1,2 and 3 suggesting this groove is important as a binding site. 96 matched cddid_all.tbl CDD pfam09692 pfam09692 430755 Arb1 Argonaute siRNA chaperone (ARC) complex subunit Arb1. Arb1 is required for histone H3 Lys9 (H3-K9) methylation, heterochromatin, assembly and siRNA generation in fission yeast. 404 matched cddid_all.tbl CDD pfam09693 pfam09693 462850 Phage_XkdX Phage uncharacterized protein (Phage_XkdX). This entry identifies a family of small (about 50 amino acid) phage proteins, found in at least 12 different phage and prophage regions of Gram-positive bacteria. In a number of these phage, the gene for this protein is found near the holin and endolysin genes. 40 matched cddid_all.tbl CDD pfam09694 pfam09694 286740 Gcw_chp Bacterial protein of unknown function (Gcw_chp). This entry represents a conserved hypothetical protein about 240 residues in length found so far in Proteobacteria including Shewanella oneidensis and Ralstonia solanacearum, usually as part of a paralogous family. The function is unknown. 228 matched cddid_all.tbl CDD pfam09695 pfam09695 430757 YtfJ_HI0045 Bacterial protein of unknown function (YtfJ_HI0045). These are sequences from gamma proteobacteria that are related to the E. coli protein, YtfJ. 159 matched cddid_all.tbl CDD pfam09696 pfam09696 430758 Ctf8 Ctf8. Ctf8 (chromosome transmissions fidelity 8) is a component of the Ctf18 RFC-like complex which is a DNA clamp loader involved in sister chromatid cohesion. 129 matched cddid_all.tbl CDD pfam09697 pfam09697 430759 Porph_ging Protein of unknown function (Porph_ging). This family of proteins of unknown function is found in Porphyromonas gingivalis (Bacteroides gingivalis). 81 matched cddid_all.tbl CDD pfam09698 pfam09698 286744 GSu_C4xC__C2xCH Geobacter CxxxxCH...CXXCH motif (GSu_C4xC__C2xCH). This motif occurs from three to eight times in eight different proteins of Geobacter sulfurreducens. The final CXXCH motif matches the cytochrome c family haem-binding site signature, suggesting that the sequence may be involved in haem-binding. 36 matched cddid_all.tbl CDD pfam09699 pfam09699 462851 Paired_CXXCH_1 Doubled CXXCH motif (Paired_CXXCH_1). This entry represents a domain of about 41 amino acids that contains, among other motifs, two copies of the motif CXXCH associated with haem binding. This domain is predicted to be a high molecular weight c-type cytochrome and is often found in multiple copies. Members are found mostly in species of Shewanella, Geobacter, and Vibrio. 41 matched cddid_all.tbl CDD pfam09700 pfam09700 430761 Cas_Cmr3 CRISPR-associated protein (Cas_Cmr3). CRISPR is a term for Clustered Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR associated) proteins. This highly divergent family, found in at least ten different archaeal and bacterial species, is represented by TM1793 from Thermotoga maritima. 366 matched cddid_all.tbl CDD pfam09701 pfam09701 430762 Cas_Cmr5 CRISPR-associated protein (Cas_Cmr5). CRISPR is a term for Clustered, Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family, represented by TM1791.1 of Thermotoga maritima, is found in both archaeal and bacterial species. 119 matched cddid_all.tbl CDD pfam09702 pfam09702 430763 Cas_Csa5 CRISPR-associated protein (Cas_Csa5). CRISPR is a term for Clustered, Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry represents a minor family of Cas proteins found in various species of Sulfolobus and Pyrococcus (all archaeal). It is found with two different CRISPR loci in Sulfolobus solfataricus. 102 matched cddid_all.tbl CDD pfam09703 pfam09703 286749 Cas_Csa4 CRISPR-associated protein (Cas_Csa4). CRISPR loci appear to be mobile elements with a wide host range. This entry represents a protein that tends to be found near CRISPR repeats. The species range for this species, so far, is exclusively archaeal. It is found so far in only four different species, and includes two tandem genes in Pyrococcus furiosus DSM 3638. CRISPR is a term for Clustered, Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. 355 matched cddid_all.tbl CDD pfam09704 pfam09704 430764 Cas_Cas5d CRISPR-associated protein (Cas_Cas5). CRISPR is a term for Clustered, Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This small Cas family is represented by CT1134 of Chlorobium tepidum. 215 matched cddid_all.tbl CDD pfam09706 pfam09706 401591 Cas_CXXC_CXXC CRISPR-associated protein (Cas_CXXC_CXXC). CRISPR is a term for Clustered, Regularly Interspaced Short Palindromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This entry describes a conserved region of about 65 amino acids from an otherwise highly divergent protein found in a minority of CRISPR-associated protein regions. This region features two motifs of CXXC. 69 matched cddid_all.tbl CDD pfam09707 pfam09707 430765 Cas_Cas2CT1978 CRISPR-associated protein (Cas_Cas2CT1978). This entry represents a minor branch of the Cas2 family of CRISPR-associated protein which are found in IPR003799. Cas proteins are found adjacent to a characteriztic short, palindromic repeat cluster termed CRISPR, a probable mobile DNA element. 86 matched cddid_all.tbl CDD pfam09709 pfam09709 430766 Cas_Csd1 CRISPR-associated protein (Cas_Csd1). CRISPR loci appear to be mobile elements with a wide host range. This entry represents proteins that tend to be found near CRISPR repeats. The species range, so far, is exclusively bacterial and mesophilic, although CRISPR loci are particularly common among the archaea and thermophilic bacteria. Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. 562 matched cddid_all.tbl CDD pfam09710 pfam09710 286754 Trep_dent_lipo Treponema clustered lipoprotein (Trep_dent_lipo). This entry represents a family of six predicted lipoproteins from a region of about 20 tandemly arranged genes in the Treponema denticola genome. Two other neighbouring genes share the lipoprotein signal peptide region but do not show more extensive homology. The function of this locus is unknown. 397 matched cddid_all.tbl CDD pfam09711 pfam09711 430767 Cas_Csn2 CRISPR-associated protein (Cas_Csn2). CRISPR loci appear to be mobile elements with a wide host range. This entry represents proteins found only in CRISPR-containing species, near other CRISPR-associated proteins (cas). The species range so far for these proteins is pathogenic bacteria only. Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). 181 matched cddid_all.tbl CDD pfam09712 pfam09712 370627 PHA_synth_III_E Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E). This entry represents the PhaE subunit of the heterodimeric class (class III) of polymerase for poly(R)-hydroxyalkanoic acids (PHAs), carbon and energy storage polymers of many bacteria. The most common PHA is polyhydroxybutyrate but about 150 different constituent hydroxyalkanoic acids (HAs) have been identified in various species. 314 matched cddid_all.tbl CDD pfam09713 pfam09713 401595 A_thal_3526 Plant protein 1589 of unknown function (A_thal_3526). This plant-specific family of proteins is defined by an uncharacterized region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana and Oryza sativa. The function of the proteins are unknown. 51 matched cddid_all.tbl CDD pfam09715 pfam09715 401596 Plasmod_dom_1 Plasmodium protein of unknown function (Plasmod_dom_1). These sequences represent an uncharacterized family consisting of a small number of hypothetical proteins of the malaria parasite Plasmodium falciparum (isolate 3D7). 66 matched cddid_all.tbl CDD pfam09716 pfam09716 430768 ETRAMP Malarial early transcribed membrane protein (ETRAMP). These sequences represent a family of proteins from the malaria parasite Plasmodium falciparum, several of which have been shown to be expressed specifically in the ring stage as well as the rodent parasite Plasmodium yoelii. A homolog from Plasmodium chabaudi was localized to the parasitophorous vacuole membrane. Members have an initial hydrophobic, Phe/Tyr-rich, stretch long enough to span the membrane, a highly charged region rich in Lys, a second putative transmembrane region and a second highly charged, low complexity sequence region. Some members have up to 100 residues of additional C-terminal sequence. These genes have been shown to be found in the sub-telomeric regions of both Plasmodium falciparum and P. yoelii chromosomes. 81 matched cddid_all.tbl CDD pfam09717 pfam09717 462852 CPW_WPC Plasmodium falciparum domain of unknown function (CPW_WPC). This group of sequences is defined by a domain of about 61 residues in length with six well-conserved cysteine residues and six well-conserved aromatic sites. The domain can be found in tandem repeats, and is known so far only in Plasmodium falciparum. It is named for motifs of CPxxW and (less well conserved) WPC. Its function is unknown. 59 matched cddid_all.tbl CDD pfam09718 pfam09718 430770 Tape_meas_lam_C Lambda phage tail tape-measure protein (Tape_meas_lam_C). This represents a relatively well-conserved region near the C terminus of the tape measure protein of a lambda and related phage. The protein, which controls phage tail length, is typically about 1000 residues in length. Both low-complexity sequence and insertion/deletion events appear common in this family. Mutational studies suggest a ruler or template role in the determination of phage tail length. Similar behaviour is attributed to proteins from distantly related or unrelated families in other phage. 76 matched cddid_all.tbl CDD pfam09719 pfam09719 462853 C_GCAxxG_C_C Putative redox-active protein (C_GCAxxG_C_C). This entry represents a putative redox-active protein of about 140 residues, with four perfectly conserved Cys residues. It includes a CGAXXG motif. Most members are found within one or two loci of transporter or oxidoreductase genes. A member from Geobacter sulfurreducens, located in a molybdenum transporter operon, has a TAT (twin-arginine translocation) signal sequence for Sec-independent transport across the plasma membrane, a hallmark of bound prosthetic groups such as FeS clusters. 115 matched cddid_all.tbl CDD pfam09720 pfam09720 462854 Unstab_antitox Putative addiction module component. This entry defines several short bacterial proteins, typically about 75 amino acids long, which are always found as part of a pair (at least) of small genes. The other protein in the pair always belongs to a family of plasmid stabilization proteins (IPR007712). It is likely that this protein and its partner comprise some form of addiction module - a pair of genes consisting of a stable toxin and an unstable antitoxin which mediate programmed cell death - although these gene-pairs are usually found on the bacterial main chromosome. 54 matched cddid_all.tbl CDD pfam09721 pfam09721 430773 Exosortase_EpsH Transmembrane exosortase (Exosortase_EpsH). Members of this family are designated exosortase, analogous to sortase in cell wall sorting mediated by LPXTG domains in Gram-positive bacteria. The phylogenetic distribution of the proteins in this entry is nearly perfectly correlated with the distribution of the proteins having the PEP-CTERM anchor motif, IPR013424. Members of this entry are integral membrane proteins with eight predicted transmembrane helices in common. Some members of this family have long trailing sequences past the region described by this model. This model does not include the region of the first predicted transmembrane region. The best characterized member is EpsH of Methylobacillus sp. 12S, where it is part of a locus associated with biosynthesis of the exopolysaccharide methanol-an. 250 matched cddid_all.tbl CDD pfam09722 pfam09722 462855 Xre_MbcA_ParS_C Antitoxin Xre/MbcA/ParS C-terminal toxin-binding domain. This entry represents the C-terminal domain of antitoxin components of a type II toxin-antitoxin (TA) system, including Xre from Pseudomonas putida, MbcA from Mycobacterium sp. and ParS from Sphingobium sp.. This domain interacts with the toxin component and sterically blocks its active site, neutralising its effect. These antitoxins also have a HTH domain at the N-terminal. 51 matched cddid_all.tbl CDD pfam09723 pfam09723 462856 Zn-ribbon_8 Zinc ribbon domain. This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence. 41 matched cddid_all.tbl CDD pfam09724 pfam09724 462857 Dcc1 Sister chromatid cohesion protein Dcc1. Sister chromatid cohesion protein Dcc1 is a component of the Ctf18-RFC complex. This complex is required for the efficient establishment of chromosome cohesion during S-phase and for loading the replication clamp Pol30/PCNA, which functions in DNA replication and repair. Ctf18-RFC loads PCNA onto DNA in an ATP-dependent manner. It may also have PCNA-unloading activity. 317 matched cddid_all.tbl CDD pfam09725 pfam09725 462858 Fra10Ac1 Folate-sensitive fragile site protein Fra10Ac1. This entry represents the full-length proteins in which, in higher eukaryotes, the nested domain EDSLL lies. Fra10Ac1 is a highly conserved protein, of unknown function that is nuclear and highly expressed in brain. 117 matched cddid_all.tbl CDD pfam09726 pfam09726 462859 Macoilin Macoilin family. The Macoilin proteins has an N-terminal portion that is composed of 5 trasnmembrane helices, followed by a C-terminal coiled-coil region. Macoilin is a highly conserved protein present in eukaryotes. Macoilin appears to be found in the ER and be involved in the function of neurons. 670 matched cddid_all.tbl CDD pfam09727 pfam09727 462860 CortBP2 Cortactin-binding protein-2. This entry is the first approximately 250 residues of cortactin-binding protein 2. In addition to being a positional candidate for autism this protein is expressed at highest levels in the brain in humans. The human protein has six associated ankyrin repeat domains pfam00023 towards the C-terminus which act as protein-protein interaction domains. 187 matched cddid_all.tbl CDD pfam09728 pfam09728 462861 Taxilin Myosin-like coiled-coil protein. Taxilin contains an extraordinarily long coiled-coil domain in its C-terminal half and is ubiquitously expressed. It is a novel binding partner of several syntaxin family members and is possibly involved in Ca2+-dependent exocytosis in neuroendocrine cells. Gamma-taxilin, described as leucine zipper protein Factor Inhibiting ATF4-mediated Transcription (FIAT), localizes to the nucleus in osteoblasts and dimerizes with ATF4 to form inactive dimers, thus inhibiting ATF4-mediated transcription. 302 matched cddid_all.tbl CDD pfam09729 pfam09729 462862 Gti1_Pac2 Gti1/Pac2 family. In S. pombe the gti1 protein promotes the onset of gluconate uptake upon glucose starvation. In S. pombe the Pac2 protein controls the onset of sexual development, by inhibiting the expression of ste11, in a pathway that is independent of the cAMP cascade. 112 matched cddid_all.tbl CDD pfam09730 pfam09730 462863 BicD Microtubule-associated protein Bicaudal-D. BicD proteins consist of three coiled-coiled domains and are involved in dynein-mediated minus end-directed transport from the Golgi apparatus to the endoplasmic reticulum (ER). For full functioning they bind with GSK-3beta pfam05350 to maintain the anchoring of microtubules to the centromere. It appears that amino-acid residues 437-617 of BicD and the kinase activity of GSK-3 are necessary for the formation of a complex between BicD and GSK-3beta in intact cells. 717 matched cddid_all.tbl CDD pfam09731 pfam09731 430783 Mitofilin Mitochondrial inner membrane protein. Mitofilin controls mitochondrial cristae morphology. Mitofilin is enriched in the narrow space between the inner boundary and the outer membranes, where it forms a homotypic interaction and assembles into a large multimeric protein complex. The first 78 amino acids contain a typical amino-terminal-cleavable mitochondrial presequence rich in positive-charged and hydroxylated residues and a membrane anchor domain. In addition, it has three centrally located coiled coil domains. 618 matched cddid_all.tbl CDD pfam09732 pfam09732 401611 CactinC_cactus Cactus-binding C-terminus of cactin protein. CactinC_cactus is the C-terminal 200 residues of the cactin protein which are necessary for the association of cactin with IkappaB-cactus as one of the intracellular members of the Rel complex. The Rel (NF-kappaB) pathway is conserved in invertebrates and vertebrates. In mammals, it controls the activities of the immune and inflammatory response genes as well as viral genes, and is critical for cell growth and survival. In Drosophila, the Rel pathway functions in the innate cellular and humoral immune response, in muscle development, and in the establishment of dorsal-ventral polarity in the early embryo. Most members of the family also have a Cactin_mid domain pfam10312 further upstream. 125 matched cddid_all.tbl CDD pfam09733 pfam09733 462864 VEFS-Box VEFS-Box of polycomb protein. The VEFS-Box (VRN2-EMF2-FIS2-Su(z)12) box is the C-terminal region of these proteins, characterized by an acidic cluster and a tryptophan/methionine-rich sequence, the acidic-W/M domain. Some of these sequences are associated with a zinc-finger domain about 100 residues towards the N-terminus. This protein is one of the polycomb cluster of proteins which control HOX gene transcription as it functions in heterochromatin-mediated repression. 137 matched cddid_all.tbl CDD pfam09734 pfam09734 462865 Tau95 RNA polymerase III transcription factor (TF)IIIC subunit HTH domain. TFIIIC1 is a multisubunit DNA binding factor that serves as a dynamic platform for assembly of pre-initiation complexes on class III genes. This entry represents the tau 95 subunit which holds a key position in TFIIIC, exerting both upstream and downstream influence on the TFIIIC-DNA complex by rendering the complex more stable. Once bound to tDNA-intragenic promoter elements, TFIIIC directs the assembly of TFIIIB on the DNA, which in turn recruits the RNA polymerase III (pol III) and activates multiple rounds of transcription. 151 matched cddid_all.tbl CDD pfam09735 pfam09735 462866 Nckap1 Nck-associated protein 1. Nck-associated protein 1 is part of lamellipodial complex that controls Rac-dependent actin remodeling. It associates preferentially with the first SH3 domain of Nck and is a component of the WAVE2 complex composed of ABI1, CYFIP1/SRA1, NCKAP1/NAP1 and WASF2/WAVE2. It is also a component of the WAVE1 complex composed of ABI2, CYFIP2, C3orf10/HSPC300, NCKAP1 and WASF1/WAVE1. CYFIP2 binds to activated RAC1 which causes the complex to dissociate, releasing activated WASF1. The complex can also be activated by NCK1. Expression of this protein was found to be markedly reduced in patients with Alzheimer's disease. 1114 matched cddid_all.tbl CDD pfam09736 pfam09736 462867 Bud13 Pre-mRNA-splicing factor of RES complex. This entry is characterized by proteins with alternating conserved and low-complexity regions. Bud13 together with Snu17p and a newly identified factor, Pml1p/Ylr016c, form a novel trimeric complex. called The RES complex, pre-mRNA retention and splicing complex. Subunits of this complex are not essential for viability of yeasts but they are required for efficient splicing in vitro and in vivo. Furthermore, inactivation of this complex causes pre-mRNA leakage from the nucleus. Bud13 contains a unique, phylogenetically conserved C-terminal region of unknown function. 144 matched cddid_all.tbl CDD pfam09737 pfam09737 462868 Det1 De-etiolated protein 1 Det1. This is the C-terminal conserved 400 residues of Det1 proteins of approximately 550 amino acids. Det1 (de-etiolated-1) is an essential negative regulator of plant light responses, and it is a component of the Arabidopsis CDD complex containing DDB1 and COP10 ubiquitin E2 variant. Mammalian Det1 forms stable DDD-E2 complexes, consisting of DDB1, DDA1 (DET1, DDB1 Associated 1), and a member of the UBE2E group of canonical ubiquitin conjugating enzymes and modulates Cul4A function. 412 matched cddid_all.tbl CDD pfam09738 pfam09738 462869 LRRFIP LRRFIP family. LRRFIP1 is a transcriptional repressor which preferentially binds to the GC-rich consensus sequence (5'- AGCCCCCGGCG-3') and may regulate expression of TNF, EGFR and PDGFA. LRRFIP2 may function as activator of the canonical Wnt signalling pathway, in association with DVL3, upstream of CTNNB1/beta-catenin. 303 matched cddid_all.tbl CDD pfam09739 pfam09739 462870 MCM_bind Mini-chromosome maintenance replisome factor. This entry is of proteins of approximately 600 residues in length containing alternating regions of conservation and low complexity. The Arabidopsis protein is a replisome factor found to bind with the mini-chromosome maintenance, MCM-binding, complex and is crucial for efficient DNA replication. The family now spans the full-length proteins. 572 matched cddid_all.tbl CDD pfam09740 pfam09740 462871 DUF2043 Uncharacterized conserved protein (DUF2043). This is a 100 residue conserved region of a family of proteins found from fungi to humans. This region contains three conserved Cysteines and a motif of {CP}{y/l}{HG}. 106 matched cddid_all.tbl CDD pfam09741 pfam09741 462872 DUF2045 Uncharacterized conserved protein (DUF2045). This entry is the conserved 250 residues of proteins of approximately 450 amino acids. It contains several highly conserved motifs including a CVxLxxxD motif.The function is unknown. 223 matched cddid_all.tbl CDD pfam09742 pfam09742 462873 Dymeclin Dyggve-Melchior-Clausen syndrome protein. Dymeclin (Dyggve-Melchior-Clausen syndrome protein) contains a large number of leucine and isoleucine residues and a total of 17 repeated dileucine motifs. It is characteriztically about 700 residues long and present in plants and animals. Mutations in the gene coding for this protein in humans give rise to the disorder Dyggve-Melchior-Clausen syndrome (DMC, MIM 223800) which is an autosomal-recessive disorder characterized by the association of a spondylo-epi-metaphyseal dysplasia and mental retardation. DYM transcripts are widely expressed throughout human development and Dymeclin is not an integral membrane protein of the ER, but rather a peripheral membrane protein dynamically associated with the Golgi apparatus. 645 matched cddid_all.tbl CDD pfam09743 pfam09743 462874 E3_UFM1_ligase E3 UFM1-protein ligase 1. The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organizms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme. 272 matched cddid_all.tbl CDD pfam09744 pfam09744 462875 Jnk-SapK_ap_N JNK_SAPK-associated protein-1. This is the N-terminal 200 residues of a set of proteins conserved from yeasts to humans. Most of the proteins in this entry have an RhoGEF pfam00621 domain at their C-terminal end. 150 matched cddid_all.tbl CDD pfam09745 pfam09745 462876 NSRP1_N Nuclear speckle splicing regulatory protein 1, N-terminal. This domain is found at the N-terminal of Nuclear speckle splicing regulatory protein 1 (NRP1, also known as Nuclear speckle-related protein 70 and Coiled-coil domain-containing protein 55) and contains a coiled-coil domain that plays a critical role in NRP1 alternative splicing activity and self-oligomerization. NRP1 is a RNA-binding protein that mediates pre-mRNA alternative splicing regulation. 121 matched cddid_all.tbl CDD pfam09746 pfam09746 462877 Membralin Tumour-associated protein. Membralin is evolutionarily highly conserved; though it seems to represent a unique protein family. The protein appears to contain several transmembrane regions. In humans it is expressed in certain cancers, particularly ovarian cancers. Membralin-like gene homologs have been identified in plants including grape, cotton and tomato. 390 matched cddid_all.tbl CDD pfam09747 pfam09747 462878 CCD97-like_C Coiled-coil domain containing protein 97-like, C-terminal. This domain is found at the C-terminal of CCD97. In some proteins, this domain is found as two conserved domains separated by a region of low complexity, spanning some 200 residues. The function is unknown. 194 matched cddid_all.tbl CDD pfam09748 pfam09748 462879 Med10 Transcription factor subunit Med10 of Mediator complex. Med10 is one of the protein subunits of the Mediator complex, tethered to Rgr1 protein. The Mediator complex is required for the transcription of most RNA polymerase II (Pol II)-transcribed genes. Med10 specifically mediates basal-level HIS4 transcription via Gcn4, and, additionally, there is a putative requirement for Med10 in Bas2-mediated transcription. Med10 is part of the middle region of Mediator. 119 matched cddid_all.tbl CDD pfam09749 pfam09749 462880 HVSL Uncharacterized conserved protein. This entry is of proteins of approximately 300 residues conserved from plants to humans. It contains two conserved motifs, HxSL and FHVSL. The function is unknown. 238 matched cddid_all.tbl CDD pfam09750 pfam09750 462881 DRY_EERY Alternative splicing regulator. This entry represents the conserved N-terminal region of SWAP (suppressor-of-white-apricot protein) proteins. This region contains two highly conserved motifs, viz: DRY and EERY, which appear to be the sites for alternative splicing of exons 2 and 3 of the SWAP mRNA. These proteins are thus thought to be involved in auto-regulation of pre-mRNA splicing. Most family members are associated with two Surp domains pfam01805 and an Arginine- serine-rich binding region towards the C-terminus. 129 matched cddid_all.tbl CDD pfam09751 pfam09751 430802 Es2 Nuclear protein Es2. This entry is of a family of proteins of approximately 500 residues with alternating regions of low complexity and conservation where the domain similarities are strong. Apart from a predicted coiled-coil domain, no other known functional domains have been characterized. The protein appears to be expressed in the nucleus and particularly highly in the pons sub-region of the brain. The protein is clearly necessary for normal development of the nervous system. 420 matched cddid_all.tbl CDD pfam09752 pfam09752 370661 ABHD18 Alpha/beta hydrolase domain containing 18. This entry represents alpha/beta hydrolase domain-containing protein 18 (ABHD18). Its function is not clear. 352 matched cddid_all.tbl CDD pfam09753 pfam09753 462882 Use1 Membrane fusion protein Use1. This entry is of a family of proteins all approximately 300 residues in length. The proteins have a single C-terminal trans-membrane domain and a SNARE [soluble NSF (N-ethylmaleimide-sensitive fusion protein) attachment protein receptor] domain of approximately 60 residues. The SNARE domains are essential for membrane fusion and are conserved from yeasts to humans. Use1 is one of the three protein subunits that make up the SNARE complex and it is specifically required for Golgi-endoplasmic reticulum retrograde transport. 245 matched cddid_all.tbl CDD pfam09754 pfam09754 462883 PAC2 PAC2 family. This PAC2 (Proteasome assembly chaperone) family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 247 and 307 amino acids in length. These proteins function as a chaperone for the 26S proteasome. The 26S proteasome mediates ubiquitin-dependent proteolysis in eukaryotic cells. A number of studies including very recent ones have revealed that assembly of its 20S catalytic core particle is an ordered process that involves several conserved proteasome assembly chaperones (PACs). Two heterodimeric chaperones, PAC1-PAC2 and PAC3-PAC4, promote the assembly of rings composed of seven alpha subunits. 175 matched cddid_all.tbl CDD pfam09755 pfam09755 401633 DUF2046 Uncharacterized conserved protein H4 (DUF2046). This is the conserved N-terminal 350 residues of a family of proteins of unknown function possibly containing a coiled-coil domain. 304 matched cddid_all.tbl CDD pfam09756 pfam09756 370664 DDRGK DDRGK domain. This is a family of proteins of approximately 300 residues, found in plants and vertebrates. They contain a highly conserved DDRGK motif. 188 matched cddid_all.tbl CDD pfam09757 pfam09757 401634 Arb2 Arb2 domain. This domain is found at the C-terminal of Clr3 (Cryptic loci regulator 3) also known as histone deacetylase clr3 (EC:3.5.1.98). Structure analysis reveals that the Arb2 domain has clear homology to alpha/beta-hydrolases but that it is lacking the catalytic triad of these enzymes. Functional studies show that the Arb2 domain is necessary for centromeric heterochromatin silencing suggesting a model where the Arb2 domain, through residues N562 and Y563, acts as an anchor that connects the HDAC activity of Clr3 to the SHREC complex. SHREC (Snf2/Hdac Repressive) complex in fission yeast drives transcriptional gene silencing in heterochromatin. 252 matched cddid_all.tbl CDD pfam09758 pfam09758 462884 FPL Uncharacterized conserved protein. This entry represents an N-terminal region of approximately 150 residues of a family of proteins of unknown function. It contains a highly conserved FPL motif. 148 matched cddid_all.tbl CDD pfam09759 pfam09759 462885 Atx10homo_assoc Spinocerebellar ataxia type 10 protein domain. This is the conserved C-terminal 100 residues of Ataxin-10. Ataxin-10 belongs to the family of armadillo repeat proteins and in solution it tends to form homotrimeric complexes, which associate via a tip-to-tip association in a horseshoe-shaped contact with the concave sides of the molecules facing each other. This domain may represent the homo-association site since that is located near the C-terminus of Ataxin-10. The protein does not contain a signal sequence for secretion or any subcellular compartment confirming its cytoplasmic localization, specifically to the olivocerebellar region. 99 matched cddid_all.tbl CDD pfam09762 pfam09762 462886 CCDC93_CC CCDC93, coiled-coil domain. This is a coiled-coil domain found in CCDC93. Human CCDC93 is part of the COMMD/CCDC22/CCDC93 (CCC) complex that interacts with the multisubunit WASH complex, which is required for endosomal deposition of F-actin and cargo trafficking in conjunction with the retromer. The CCC complex controls Notch activation by modulating its intracellular trafficking. 173 matched cddid_all.tbl CDD pfam09763 pfam09763 401638 Sec3_C Exocyst complex component Sec3. This entry is the conserved middle and C-terminus of the Sec3 protein. Sec3 binds to the C-terminal cytoplasmic domain of GLYT1 (glycine transporter protein 1). Sec3 is the exocyst component that is closest to the plasma membrane docking site and it serves as a spatial landmark in the plasma membrane for incoming secretory vesicles. Sec3 is recruited to the sites of polarised membrane growth through its interaction with Rho1p, a small GTP-binding protein. 696 matched cddid_all.tbl CDD pfam09764 pfam09764 462887 Nt_Gln_amidase N-terminal glutamine amidase. This protein is conserved from plants to humans. It represents a family of N terminal glutamine amidases. The enzyme removes the NH2 group from a Gln, at the N-terminal, rendering it a Glu. 180 matched cddid_all.tbl CDD pfam09765 pfam09765 462888 FANCL_d1 FANCL UBC-like domain 1. This entry represents the first of three UBC-like domain found in the FANCL protein, which is the catalytic E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits of the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2. 89 matched cddid_all.tbl CDD pfam09766 pfam09766 462889 FmiP_Thoc5 Fms-interacting protein/Thoc5. This entry carries part of the crucial 144 N-terminal residues of the FmiP (Fms interacting protein). A member of the THO (suppressors of the transcriptional defects of hpr1delta by overexpression) complex which is a subcomplex of the transcription/export (TREX) complex. It is essential for the binding of the protein to the cytoplasmic domain of activated Fms-molecules in M-CSF induced haematopoietic differentiation of macrophages. Fmip is also known as THOC5 (THO complex subunit 5) a 683 amino acids long protein which contains a nuclear localization sequence (NLS), a leucine zipper and a PEST like sequence (aa. 303-319) that carries three ataxia-telangiectasia mutated (ATM) kinase specific phosphorylation sites. The C-terminus contains a THOC1 binding site. The level of FMIP/Thoc5 expression might form a threshold that determines whether cells differentiate into macrophages or into granulocytes. 347 matched cddid_all.tbl CDD pfam09767 pfam09767 462890 DUF2053 Predicted membrane protein (DUF2053). This entry is of the conserved N-terminal 150 residues of proteins conserved from plants to humans. The function is unknown although some annotation suggests it to be a transmembrane protein. 157 matched cddid_all.tbl CDD pfam09768 pfam09768 430811 Peptidase_M76 Peptidase M76 family. This is a family of metalloproteases. Proteins in this family are also annotated as Ku70-binding proteins. 168 matched cddid_all.tbl CDD pfam09769 pfam09769 462891 ApoO Apolipoprotein O. Members of this family promote cholesterol efflux from macrophage cells. They are present in various lipoprotein complexes, including HDL, LDL and VLDL. The apoprotein is secreted by a microsomal triglyceride transfer protein (MTTP)-dependent mechanism, probably as a VLDL-associated protein that is subsequently transferred to HDL. 131 matched cddid_all.tbl CDD pfam09770 pfam09770 401645 PAT1 Topoisomerase II-associated protein PAT1. Members of this family are necessary for accurate chromosome transmission during cell division. 846 matched cddid_all.tbl CDD pfam09771 pfam09771 401646 Tmemb_18A Transmembrane protein 188. The function of this family of transmembrane proteins has not, as yet, been determined. 118 matched cddid_all.tbl CDD pfam09772 pfam09772 430813 Tmem26 Transmembrane protein 26. The function of this family of transmembrane proteins has not, as yet, been determined. 285 matched cddid_all.tbl CDD pfam09773 pfam09773 462892 Meckelin Meckelin (Transmembrane protein 67). Members of this family are thought to be related to the ciliary basal body. Defects result in Meckel syndrome type 3, [MIM:607361], an autosomal recessive disorder characterized by a combination of renal cysts and variably associated features including developmental anomalies of the central nervous system (typically encephalocele), hepatic ductal dysplasia and cysts, and polydactyly. Joubert syndrome type 6 [MIM:610688] is also a manifestation of certain mutations; it is an autosomal recessive congenital malformation of the cerebellar vermis and brainstem with abnormalities of axonal decussation (crossing in the brain) affecting the corticospinal tract and superior cerebellar peduncles. Individuals with Joubert syndrome have motor and behavioral abnormalities, including an inability to walk due to severe clumsiness and 'mirror' movements, and cognitive and behavioural disturbances. 821 matched cddid_all.tbl CDD pfam09774 pfam09774 430815 MIX23 Intermembrane space protein MIX23. Intermembrane space protein MIX23 regulates or stabilizes the mitochondrial protein import machinery and is specifically up-regulated under stress conditions. It is critical for the efficient import of proteins into the mitochondrial matrix, particularly if the function of the translocase of the inner membrane 23 is compromised. MIX23, also known as Caffeine-induced death protein 2 (Cid2), is evolutionarily conserved and a homolog of the human protein CCDC58. 156 matched cddid_all.tbl CDD pfam09775 pfam09775 401649 Keratin_assoc Keratinocyte-associated protein 2. Members of this family comprise various keratinocyte-associated proteins. Their exact function has not, as yet, been determined. 129 matched cddid_all.tbl CDD pfam09776 pfam09776 462893 Mitoc_L55 Mitochondrial ribosomal protein L55. Members of this family are involved in mitochondrial biogenesis and G2/M phase cell cycle progression. They form a component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins. 115 matched cddid_all.tbl CDD pfam09777 pfam09777 430817 OSTMP1 Osteopetrosis-associated transmembrane protein 1 precursor. Members of this family of proteins are required for osteoclast and melanocyte maturation and function. Mutations give rise to autosomal recessive osteopetrosis [MIM:259700]; also called autosomal recessive Albers-Schonberg disease. 231 matched cddid_all.tbl CDD pfam09778 pfam09778 462894 Guanylate_cyc_2 Guanylylate cyclase. Members of this family of proteins catalyze the conversion of guanosine triphosphate (GTP) to 3',5'-cyclic guanosine monophosphate (cGMP) and pyrophosphate. 212 matched cddid_all.tbl CDD pfam09779 pfam09779 462895 Ima1_N Ima1 N-terminal domain. This domain occurs at the N-terminus of the Schizosaccharomyces pombe inner nuclear membrane (INM) protein, Ima1. Ima1 interacts with other inner nuclear membrane proteins. 131 matched cddid_all.tbl CDD pfam09781 pfam09781 430820 NDUF_B5 NADH:ubiquinone oxidoreductase, NDUFB5/SGDH subunit. Members of this family mediate the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone, the reaction that occurs being: NADH + ubiquinone = NAD(+) + ubiquinol. 186 matched cddid_all.tbl CDD pfam09782 pfam09782 462896 NDUF_B6 NADH:ubiquinone oxidoreductase, NDUFB6/B17 subunit. Members of this family mediate the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone, the reaction that occurs being: NADH + ubiquinone = NAD(+) + ubiquinol. 126 matched cddid_all.tbl CDD pfam09783 pfam09783 462897 Vac_ImportDeg Vacuolar import and degradation protein. Members of this family are involved in the negative regulation of gluconeogenesis. They are required for both proteosome-dependent and vacuolar catabolite degradation of fructose-1,6-bisphosphatase (FBPase), where they probably regulate FBPase targeting from the FBPase-containing vesicles to the vacuole. 162 matched cddid_all.tbl CDD pfam09784 pfam09784 401656 L31 Mitochondrial ribosomal protein L31. This is a family of mitochondrial ribosomal proteins. L31 is essential for mitochondrial function in yeast. 102 matched cddid_all.tbl CDD pfam09785 pfam09785 462898 Prp31_C Prp31 C terminal domain. This is the C terminal domain of the pre-mRNA processing factor Prp31. Prp31 is required for U4/U6.U5 tri-snRNP formation. In humans this protein has been linked to autosomal dominant retinitis pigmentosa. 121 matched cddid_all.tbl CDD pfam09786 pfam09786 462899 CytochromB561_N Cytochrome B561, N terminal. Members of this family are found in the N terminal region of cytochrome B561, as well as in various other putative uncharacterized proteins. 579 matched cddid_all.tbl CDD pfam09787 pfam09787 462900 Golgin_A5 Golgin subfamily A member 5. Members of this family of proteins are involved in maintaining Golgi structure. They stimulate the formation of Golgi stacks and ribbons, and are involved in intra-Golgi retrograde transport. Two main interactions have been characterized: one with RAB1A that has been activated by GTP-binding and another with isoform CASP of CUTL1. 305 matched cddid_all.tbl CDD pfam09788 pfam09788 462901 Tmemb_55A Transmembrane protein 55A. Members of this family catalyze the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate. 248 matched cddid_all.tbl CDD pfam09789 pfam09789 462902 CC149 Coiled-coil domain-containing protein 149-A. Members of this family have been annotated as being coiled-coil domain-containing protein 149, however they currently have no known function. 314 matched cddid_all.tbl CDD pfam09790 pfam09790 462903 Hyccin Hyccin. Members of this family of proteins may have a role in the beta-catenin-Tcf/Lef signaling pathway, as well as in the process of myelination of the central and peripheral nervous system. Defects in Hyccin are the cause of hypomyelination with congenital cataracts [MIM:610532]. This disorder is characterized by congenital cataracts, progressive neurologic impairment, and diffuse myelin deficiency. Affected individuals experience progressive pyramidal and cerebellar dysfunction, muscle weakness and wasting prevailing in the lower limbs. 323 matched cddid_all.tbl CDD pfam09791 pfam09791 462904 Oxidored-like Oxidoreductase-like protein, N-terminal. Members of this family are found in the N terminal region of various oxidoreductase like proteins. Their exact function is, as yet, unknown. 45 matched cddid_all.tbl CDD pfam09792 pfam09792 430830 But2 Ubiquitin 3 binding protein But2 C-terminal domain. This family is of proteins conserved in yeasts. It binds to Uba3 and is involved in the NEDD8 signalling pathway. This family represents a presumed C-terminal domain. 138 matched cddid_all.tbl CDD pfam09793 pfam09793 462905 AD Anticodon-binding domain. This domain of approximately 100 residues is conserved from plants to humans. It is frequently found in association with Lsm domain-containing proteins. It is an anticodon-binding domain of a prolyl-tRNA synthetase, whose PDB structure is available under the identifier 1h4q. 90 matched cddid_all.tbl CDD pfam09794 pfam09794 430832 Avl9 Transport protein Avl9. Avl9 is a protein involved in exocytic transport from the Golgi. It has been speculated that Avl9 could play a role in deforming membranes for vesicle fission and/or in recruiting cargo. 379 matched cddid_all.tbl CDD pfam09795 pfam09795 401667 ATG31 Autophagy-related protein 31. Autophagy is an intracellular degradation system that responds to nutrient starvation. Cis1/Atg31 has been shown to be required for autophagosome formation in Saccharomyces cerevisiae. It interacts with Atg17. 154 matched cddid_all.tbl CDD pfam09796 pfam09796 430833 QCR10 Ubiquinol-cytochrome-c reductase complex subunit (QCR10). The QCR10 family of proteins are a component of the ubiquinol-cytochrome c reductase complex (also known as complex III or cytochrome b-c1 complex). This complex is located on the inner mitochondrial membrane and it couples electron transfer from ubiquinol to cytochrome. This subunit (QCR10) is required for stable association of the iron-sulfur protein with the complex. 62 matched cddid_all.tbl CDD pfam09797 pfam09797 430834 NatB_MDM20 N-acetyltransferase B complex (NatB) non catalytic subunit. This is the non-catalytic subunit of the N-terminal acetyltransferase B complex (NatB). The NatB complex catalyzes the acetylation of the amino-terminal methionine residue of all proteins beginning with Met-Asp or Met-Glu and of some proteins beginning with Met-Asn or Met-Met. In Saccharomyces cerevisiae this subunit is called MDM20 and in Schizosaccharomyces pombe it is called Arm1. NatB acetylates the Tpm1 protein and regulates and tropomyocin-actin interactions. This subunit is required by the NatB complex for the N-terminal acetylation of Tpm1. 368 matched cddid_all.tbl CDD pfam09798 pfam09798 462906 LCD1 DNA damage checkpoint protein. This is a family of proteins which regulate checkpoint kinases. In Schizosaccharomyces pombe this protein is called Rad26 and in Saccharomyces cerevisiae it is called LCD1. 615 matched cddid_all.tbl CDD pfam09799 pfam09799 462907 Transmemb_17 Predicted membrane protein. This is a 100 amino acid region of a family of proteins conserved from nematodes to humans. It is predicted to be a transmembrane region but its function is not known. 107 matched cddid_all.tbl CDD pfam09801 pfam09801 370705 SYS1 Integral membrane protein S linking to the trans Golgi network. Members of this family are integral membrane proteins involved in protein trafficking between the late Golgi and endosome. They may also serve as a receptor for ADP-ribosylation factor-related protein 1 (ARFRP1). Sys1p is a small integral membrane protein with four predicted transmembrane domains that localizes to the Trans Golgi network TGN in yeast and human cells. 144 matched cddid_all.tbl CDD pfam09802 pfam09802 430836 Sec66 Preprotein translocase subunit Sec66. Members of this family of proteins are a component of the heterotetrameric Sec62/63 complex composed of SEC62, SEC63, SEC66 and SEC72. The Sec62/63 complex associates with the Sec61 complex to form the Sec complex. Sec 66 is involved in SRP-independent post-translational translocation across the endoplasmic reticulum and functions together with the Sec61 complex and KAR2 in a channel-forming translocon complex. Furthermore, Sec66 is also required for growth at elevated temperatures. 176 matched cddid_all.tbl CDD pfam09803 pfam09803 462908 Pet100 Pet100. Pet100 is a chaperone required for the assembly of cytochrome c oxidase. The human Pet100 homolog (also known as C19orf79) has been shown to be located in the mitochondrial inner membrane and forms a ~300 kDa subcomplex with mitochondrial complex IV subunits. 63 matched cddid_all.tbl CDD pfam09804 pfam09804 430838 DENND11 DENN domain-containing protein 11. DENN domain-containing protein 11 (also known as LCHN) is thought to play a role in neuritogenesis, as well as in neuronal recovery and/or restructuring in the hippocampus following transient cerebral ischemia. 283 matched cddid_all.tbl CDD pfam09805 pfam09805 430839 Nop25 Nucleolar protein 12 (25kDa). Members of this family of proteins are part of the yeast nuclear pore complex-associated pre-60S ribosomal subunit. The family functions as a highly conserved exonuclease that is required for the 5'-end maturation of 5.8S and 25S rRNAs, demonstrating that 5'-end processing also has a redundant pathway. Nop25 binds late pre-60S ribosomes, accompanying them from the nucleolus to the nuclear periphery; and there is evidence for both physical and functional links between late 60S subunit processing and export. 134 matched cddid_all.tbl CDD pfam09806 pfam09806 430840 CDK2AP Cyclin-dependent kinase 2-associated protein. Members of this family of proteins are cell-growth suppressors, associating with and influencing the biological activities of important cell cycle regulators in the S phase including monomeric non-phosphorylated cyclin-dependent kinase 2 (CDK2) and DNA polymerase alpha/primase. An association between mutations in the gene coding for this protein and oral cancer has been described. 211 matched cddid_all.tbl CDD pfam09807 pfam09807 462909 ELP6 Elongation complex protein 6. ELP6 is a subunit of the RNA polymerase II elongator complex. The Elongator complex promotes RNA-polymerase II transcript elongation through histone acetylation in the nucleus and tRNA modification in the cytoplasm. ELP5 and ELP6 play a major role in the migration, invasion and tumorigenicity of melanoma cells, as integral subunits of Elongator 252 matched cddid_all.tbl CDD pfam09808 pfam09808 430842 SNAPC1 Small nuclear RNA activating complex (SNAPc), subunit 1. Members of this family are part of the SNAPc complex (SNAPC1) required for the transcription of both RNA polymerase II and III small-nuclear RNA genes. They bind to the proximal sequence element (PSE), a non-TATA-box basal promoter element common to these 2 types of genes. Furthermore, they also recruit TBP and BRF2 to the U6 snRNA TATA box. 189 matched cddid_all.tbl CDD pfam09809 pfam09809 286847 MRP-L27 Mitochondrial ribosomal protein L27. Members of this family of proteins are components of the mitochondrial ribosome large subunit. They are also involved in apoptosis and cell cycle regulation. 97 matched cddid_all.tbl CDD pfam09810 pfam09810 430843 Exo5 Exonuclease V - a 5' deoxyribonuclease. Exonuclease V is a monomeric 5' deoxyribonuclease that is localized in the nucleus. It degrades single-stranded, but not double-stranded, DNA from the 5'-end, and the products are dinucleotides, except the 3'-terminal tri- and tetranucleotides, which are not degraded. The initial hydrolytic cut of exonuclease V on the dephosphorylated substrate produces a mixture of dinucleoside monophosphates and trinucleoside diphosphates. The enzyme is processive in action. Exo5 is specific for single-stranded DNA and does not hydrolyze RNA. However, Exo5 has the capacity to slide across 5' double-stranded DNA or 5' RNA sequences and resume cutting two nucleotides downstream of the double-stranded-to-single-stranded junction or RNA-to-DNA junction, respectively. 363 matched cddid_all.tbl CDD pfam09811 pfam09811 430844 Yae1_N Essential protein Yae1, N terminal. Members of this family are found in the N terminal region of the essential protein Yae1. Their exact function has not, as yet, been determined. The family DUF1715, pfam08215 has now been merged into this family. 39 matched cddid_all.tbl CDD pfam09812 pfam09812 430845 MRP-L28 Mitochondrial ribosomal protein L28. Members of this family are components of the mitochondrial large ribosomal subunit. Mature mitochondrial ribosomes consist of a small (37S) and a large (54S) subunit. The 37S subunit contains at least 33 different proteins and 1 molecule of RNA (15S). The 54S subunit contains at least 45 different proteins and 1 molecule of RNA (21S). 157 matched cddid_all.tbl CDD pfam09813 pfam09813 462910 Coa3_cc Cytochrome c oxidase assembly factor 3. This entry represents a coiled-coil domain found in cytochrome c oxidase assembly factor 3 and homologs. Cytochrome c oxidase assembly factor 3, previously known as coiled coil domain-containing protein 56 (CCDC56), plays a critical role in the biogenesis and activity of cytochrome c oxidase (COX). 49 matched cddid_all.tbl CDD pfam09814 pfam09814 462911 HECT_2 HECT-like Ubiquitin-conjugating enzyme (E2)-binding. HECT_2 is a family of UbcH10-binding proteins. 362 matched cddid_all.tbl CDD pfam09815 pfam09815 462912 XK-related XK-related protein. Members of this family comprise various XK-related proteins, that are involved in sodium-dependent transport of neutral amino acids or oligopeptides. These proteins are responsible for the Kx blood group system - defects results in McLeod syndrome [MIM:314850], an X-linked multi-system disorder characterized by late onset abnormalities in the neuromuscular and hematopoietic systems. 332 matched cddid_all.tbl CDD pfam09816 pfam09816 462913 EAF RNA polymerase II transcription elongation factor. Members of this family act as transcriptional transactivators of ELL and ELL2 elongation activities.3]. Eaf proteins form a stable heterodimer complex with ELL proteins to facilitate the binding of RNA polymerase II to activate transcription elongation. The N-terminus of approx 120 residues is globular and highly conserved. 101 matched cddid_all.tbl CDD pfam09817 pfam09817 401684 Zwilch RZZ complex, subunit zwilch. The protein Zwilch is an essential component of the mitotic checkpoint, which prevents cells from prematurely exiting mitosis. It is required for the assembly of the dynein-dynactin, Mad2 complexes and spindly/CG15415 onto kinetochores. 573 matched cddid_all.tbl CDD pfam09818 pfam09818 462914 ABC_ATPase ATPase of the ABC class. This is the C-terminal ATPase domain from bacterial ABC class ATPases. This entry also includes MRB1590 from Trypanosoma brucei brucei has a central ATPase domain homologous to this domain. 282 matched cddid_all.tbl CDD pfam09819 pfam09819 430850 ABC_cobalt ABC-type cobalt transport system, permease component. Members of this family of prokaryotic proteins include various hypothetical proteins as well as ABC-type cobalt transport systems. 121 matched cddid_all.tbl CDD pfam09820 pfam09820 430851 AAA-ATPase_like Predicted AAA-ATPase. This family contains many hypothetical bacterial proteins. This family was previously the N-terminal part of the Pfam DUF1703 (pfam08011) family before it was split into two. This region is predicted to be an AAA-ATPase domain. 278 matched cddid_all.tbl CDD pfam09821 pfam09821 430852 AAA_assoc_C C-terminal AAA-associated domain. This had been thought to be an ATPase domain of ABC-transporter proteins. However, only one member has any trans-membrane regions. It is associated with an upstream ATP-binding cassette family, pfam00005. 117 matched cddid_all.tbl CDD pfam09822 pfam09822 430853 ABC_transp_aux ABC-type uncharacterized transport system. This domain is found in various eukaryotic and prokaryotic intra-flagellar transport proteins involved in gliding motility, as well as in several hypothetical proteins. 264 matched cddid_all.tbl CDD pfam09823 pfam09823 430854 DUF2357 Domain of unknown function (DUF2357). This entry was previously the N terminal portion of DUF524 (pfam04411) before it was split into two. This domain has no known function. It is predicted to adopt an all beta secondary structure pattern followed by mainly alpha-helical structures. 248 matched cddid_all.tbl CDD pfam09824 pfam09824 430855 ArsR ArsR transcriptional regulator. Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family. 159 matched cddid_all.tbl CDD pfam09825 pfam09825 462915 BPL_N Biotin-protein ligase, N terminal. The function of this structural domain is unknown. It is found to the N terminus of the biotin protein ligase (BPL) catalytic domain. This domain is essential in BPL activity. 277 matched cddid_all.tbl CDD pfam09826 pfam09826 430857 Beta_propel Beta propeller domain. Members of this family comprise secreted bacterial proteins containing C-terminal beta-propeller domain distantly related to WD-40 repeats. Jpred secondary-structure prediction shows family to be a series of 4 short beta-strands, characteriztic of beta-propeller families. 504 matched cddid_all.tbl CDD pfam09827 pfam09827 462916 CRISPR_Cas2 CRISPR associated protein Cas2. This entry represents members of the family of Cas2, one of the first four protein families found to be associated with prokaryotic genomes containing multiple CRISPR elements. CRISPR systems protect against invasive nucleic acid sequences, including phage. Cas2 proteins have been characterized as either endoribonuclease (for ssRNA) or endodeoxyribonuclease (for dsDNA), depending on the system to which the Cas2 belongs. The cas genes usually are found near the palindromic repeats. The structural subunit of Cas2, belongs to the VapD family of interferases. The interferase catalytic site is intact in the majority of the Cas2 proteins but is disrupted in some, and is not required for spacer acquisition. This entry also includes the endoribonuclease VapD. 72 matched cddid_all.tbl CDD pfam09828 pfam09828 430859 Chrome_Resist Chromate resistance exported protein. Members of this family of bacterial proteins, are involved in the reduction of chromate accumulation and are essential for chromate resistance. 131 matched cddid_all.tbl CDD pfam09829 pfam09829 430860 DUF2057 Uncharacterized protein conserved in bacteria (DUF2057). This domain, found in various prokaryotic proteins, has no known function. 192 matched cddid_all.tbl CDD pfam09830 pfam09830 430861 ATP_transf ATP adenylyltransferase C-terminal domain. Members of this family of proteins catabolize Ap4N nucleotides (where N is A,C,G or U). Additionally they catalyze the conversion of adenosine-5-phosphosulfate (AMPs) plus Pi to ADP plus sulphate, the exchange of NDP and phosphate and the synthesis of Ap4A from AMPs plus ATP. 103 matched cddid_all.tbl CDD pfam09831 pfam09831 430862 DUF2058 Uncharacterized protein conserved in bacteria (DUF2058). This domain, found in various prokaryotic proteins, has no known function. 174 matched cddid_all.tbl CDD pfam09832 pfam09832 430863 DUF2059 Uncharacterized protein conserved in bacteria (DUF2059). This domain, found in various prokaryotic proteins, has no known function. 59 matched cddid_all.tbl CDD pfam09834 pfam09834 430864 DUF2061 Predicted membrane protein (DUF2061). This domain, found in various prokaryotic proteins, has no known function. 51 matched cddid_all.tbl CDD pfam09835 pfam09835 430865 DUF2062 Uncharacterized protein conserved in bacteria (DUF2062). This domain, found in various prokaryotic proteins, has no known function. 139 matched cddid_all.tbl CDD pfam09836 pfam09836 430866 DUF2063 Putative DNA-binding domain. This family represents the N-terminal part of a Neisseria protein, UniProtKB:Q5F5I0, PDB:3dee. It runs from residues 31-117 as a helical bundle with 4 main helices. \From genomic context and the fold of the C-terminal part, it is suggested that this protein is involved in transcriptional regulation. 86 matched cddid_all.tbl CDD pfam09837 pfam09837 462917 DUF2064 Uncharacterized protein conserved in bacteria (DUF2064). This family has structural similarity to proteins in the nucleotide-diphospho-sugar transferases superfamily. The similarity suggests that it is an enzyme with a sugar substrate. 120 matched cddid_all.tbl CDD pfam09838 pfam09838 430868 DUF2065 Uncharacterized protein conserved in bacteria (DUF2065). This domain, found in various prokaryotic proteins, has no known function. 56 matched cddid_all.tbl CDD pfam09839 pfam09839 430869 DUF2066 Uncharacterized protein conserved in bacteria (DUF2066). This domain, found in various prokaryotic proteins, has no known function. 230 matched cddid_all.tbl CDD pfam09840 pfam09840 378268 DUF2067 Uncharacterized protein conserved in archaea (DUF2067). This domain, found in various archaeal proteins, has no known function. 186 matched cddid_all.tbl CDD pfam09842 pfam09842 462918 DUF2069 Predicted membrane protein (DUF2069). This domain, found in various prokaryotes, has no known function. 101 matched cddid_all.tbl CDD pfam09843 pfam09843 430871 DUF2070 Predicted membrane protein (DUF2070). This is a family of Archaeal 7-TM proteins. There are 6 closely assembled TM-regions at the N-terminus followed by a long intracellular, from residues 220-590, highly conserved region, of unknown function, terminating with one more TM-region. The short 25 residue section between TMs 5 and 6 might lie on the outer surface of the membrane and be acting as a receptor (from TMHMM). 561 matched cddid_all.tbl CDD pfam09844 pfam09844 430872 DUF2071 Uncharacterized conserved protein (COG2071). This conserved protein (similar to YgjF), found in various prokaryotes, has no known function. 211 matched cddid_all.tbl CDD pfam09845 pfam09845 430873 DUF2072 Zn-ribbon containing protein. This archaeal protein has no known function. 134 matched cddid_all.tbl CDD pfam09846 pfam09846 430874 DUF2073 Uncharacterized protein conserved in archaea (DUF2073). This archaeal protein has no known function. 105 matched cddid_all.tbl CDD pfam09847 pfam09847 286883 12TM_1 Membrane protein of 12 TMs. This family carries twelve transmembrane regions. It does not have any characteriztic nucleotide-binding-domains of the GxSGSGKST type. so it may not be an ATP-binding cassette transporter. However, it may well be a transporter of some description. ABC transporters always have two nucleotide binding domains; this has two unusual conserved sequence-motifs: 'KDhKxhhR' and 'LxxLP'. 448 matched cddid_all.tbl CDD pfam09848 pfam09848 430875 DUF2075 Schlafen group 3, DNA/RNA helicase domain. This domain is found in at the C terminus of group 3 Schlafen proteins from mammals, and represents the DNA/RNA helicase domain. Schlafen proteins are involved in the control of cell proliferation, induction of immune responses, and in the regulation of viral replication. These proteins inhibit DNA replication and promote cell death in response to DNA damage. They play a role in genome surveillance to kill cells with defective replication. This domain is also found in various uncharacterized prokaryotic proteins fused to a DNA helicase, GIY-YIG or PD-(D/E)XK catalytic domain or HsdR-N(terminal) domain, which are similar to AAA DNA helicase, Type III restriction enzyme ATPase, RecD and RuvB helicase. 355 matched cddid_all.tbl CDD pfam09849 pfam09849 430876 DUF2076 Uncharacterized protein conserved in bacteria (DUF2076). This domain, found in various hypothetical prokaryotic proteins, has no known function. The domain, however, is found in various periplasmic ligand-binding sensor proteins. 263 matched cddid_all.tbl CDD pfam09850 pfam09850 430877 DotU Type VI secretion system protein DotU. DotU is a family of Gram-negative bacterial proteins that form part of the membrane-joining complex of the type VI secretion system. DotU binds tightly to IcmF and together they are tethered to the inner membrane at one end and the peptidoglycan layer at the other; they interact with Lip1 which then tethers the peptidoglycan layer to the outer membrane. 205 matched cddid_all.tbl CDD pfam09851 pfam09851 430878 SHOCT Short C-terminal domain. 28 matched cddid_all.tbl CDD pfam09852 pfam09852 430879 DUF2079 Predicted membrane protein (DUF2079). This domain, found in various hypothetical prokaryotic proteins, has no known function. 457 matched cddid_all.tbl CDD pfam09853 pfam09853 430880 DUF2080 Putative transposon-encoded protein (DUF2080). This domain, found in various hypothetical archaeal proteins, has no known function. 50 matched cddid_all.tbl CDD pfam09855 pfam09855 430881 zinc_ribbon_13 Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082). This domain, found in various hypothetical prokaryotic proteins, as well as some Zn-ribbon nucleic-acid-binding proteins has no known function. 63 matched cddid_all.tbl CDD pfam09856 pfam09856 430882 ScfRs Short-chain fatty acyl coenzyme A regulators. This family includes short-chain fatty acid regulators such as RAMB (regulator of acetate metabolism B), PCCR (Propionyl-CoA carboxylase regulator), PrpR (Propionate regulator). RamB is a negative transcriptional regulator of genes involved in acetate metabolism of C. glutamicum. It is responsible for expression control of the AK, PTA, ICL, and MS genes and, thus, for the proper adaptation to acetate as carbon and energy source. Nucleotide sequence analysis indicate the RamB protein consists of 469 aa with a putative HTH motif at the N terminus. PCCR prevents the accumulation of propionyl-CoA by controlling expression of the gene encoding propionyl-CoA carboxylase, which is responsible for propionyl-CoA consumption by Rhodobacter sphaeroides. Many other Proteobacteria and Actinomycetales contain one or several PccR homologs that group into distinct clades on the basis of the pathway of acyl-CoA metabolism that they control. PrpR is a transcriptional activator controlling prpDBC2 operon which encodes enzymes 2-methylcitrate dehydratase (PrpD2), 2-methylisocitrate lyase (PrpB2) and 2-methylcitrate synthase (PrpC2). They are essential for growth with propionate as carbon source. The regulatory protein belongs to the HTH_XRE regulator family. It has a length of 441 amino acids and an N-terminal lamda repressor-like DNA-binding domain. 157 matched cddid_all.tbl CDD pfam09857 pfam09857 430883 YjhX_toxin Putative toxin of bacterial toxin-antitoxin pair. YjhX_toxin is a putative toxin of a bacterial toxin-antitoxin pair, which is neutralized by the proteins YjhQ in family pfam00583. 85 matched cddid_all.tbl CDD pfam09858 pfam09858 430884 DUF2085 Predicted membrane protein (DUF2085). This domain, found in various hypothetical prokaryotic proteins, has no known function. 90 matched cddid_all.tbl CDD pfam09859 pfam09859 430885 Oxygenase-NA Oxygenase, catalysing oxidative methylation of damaged DNA. This family of bacterial sequences is predicted to catalyze oxidative de-methylation of damaged bases in DNA. 172 matched cddid_all.tbl CDD pfam09860 pfam09860 462919 DUF2087 Uncharacterized protein conserved in bacteria (DUF2087). This domain, found in various hypothetical prokaryotic proteins and transcriptional activators, has no known function. Structural modelling suggests this domain may bind nucleic acids. 67 matched cddid_all.tbl CDD pfam09861 pfam09861 401722 Lar_N Lactate racemase N-terminal domain. This is the N-terminal domain found in Lactate racemase enzymes EC:5.1.2.1. LarA is a nickel-dependent lactate racemase from the larA-E operon of Lactobacillus plantarum, whereas LarB, LarC and LarE are accessory proteins required for the incorporation of Ni in the lactate racemase apoprotein. LarA contains 18 beta-strands and 16 alpha-helices arranged in a novel fold composed of two domains of similar size. This entry represents the N-terminal domain of LarA and related proteins. 204 matched cddid_all.tbl CDD pfam09862 pfam09862 462920 DUF2089 Protein of unknown function (DUF2089). This domain, found in various hypothetical prokaryotic proteins, has no known function. This domain is a zinc-ribbon. 113 matched cddid_all.tbl CDD pfam09863 pfam09863 430888 DUF2090 Uncharacterized protein conserved in bacteria (DUF2090). This domain, found in various prokaryotic carbohydrate kinases, has no known function. 310 matched cddid_all.tbl CDD pfam09864 pfam09864 462921 MliC Membrane-bound lysozyme-inhibitor of c-type lysozyme. Lysozymes are ancient and important components of the innate immune system of animals that hydrolyse peptidoglycan, the major bacterial cell wall polymer. Various mechanisms have evolved by which bacteria can evade this bactericidal enzyme, one being the production of lysozyme inhibitors. MliC (membrane bound lysozyme inhibitor of c-type lysozyme) of E. coli and Pseudomonas aeruginosa, possess lysozyme inhibitory activity and confer increased lysozyme tolerance upon expression in E. coli. Structural analyses show that the invariant loop of MliC plays a crucial role in the inhibition of the lysozyme by its insertion into the active site cleft of the lysozyme, where the loop forms hydrogen and ionic bonds with the catalytic residues. 68 matched cddid_all.tbl CDD pfam09865 pfam09865 430890 DUF2092 Predicted periplasmic protein (DUF2092). This domain, found in various hypothetical prokaryotic proteins, has no known function. 209 matched cddid_all.tbl CDD pfam09866 pfam09866 430891 DUF2093 Uncharacterized protein conserved in bacteria (DUF2093). This domain, found in various hypothetical prokaryotic proteins, has no known function. 41 matched cddid_all.tbl CDD pfam09867 pfam09867 430892 TagF_N TagF N-terminal domain, Type VI secretion system-associated. This is the N-terminal domain of the T6S-associated protein, TagF. A post-translational repressor of the hemolysin co-regulated secretion island I (HSI-I)-encoded type VI secretion system (H1-T6SS) found in Pseudomonas aeruginosa. The type VI secretion system (T6SS) is found broadly among the Proteobacteria and is implicated in diverse processes including host-cell interactions, biofilm formation and gene regulation. Furthermore, studies indicate that the T6SS plays a critical role in interbacterial interactions. TagF has been shown to regulate the activity of the H1-T6SS in a manner that does not require phosphorylated-Fha1, PpkA, or other Tag proteins. Additionally TagF is found to associate as a homodimer with nearly identical monomers composed of alpha and beta elements assembled as a three-layer sandwich (alpha-beta-alpha). 135 matched cddid_all.tbl CDD pfam09868 pfam09868 370731 DUF2095 Uncharacterized protein conserved in archaea (DUF2095). This domain, found in various hypothetical prokaryotic proteins, has no known function. 129 matched cddid_all.tbl CDD pfam09869 pfam09869 401729 DUF2096 Uncharacterized protein conserved in archaea (DUF2096). This domain, found in various hypothetical prokaryotic proteins, has no known function. 168 matched cddid_all.tbl CDD pfam09870 pfam09870 401730 DUF2097 Uncharacterized protein conserved in archaea (DUF2097). This domain, found in various hypothetical prokaryotic proteins, has no known function. 83 matched cddid_all.tbl CDD pfam09871 pfam09871 430893 DUF2098 Uncharacterized protein conserved in archaea (DUF2098). This domain, found in various hypothetical prokaryotic proteins, has no known function. 94 matched cddid_all.tbl CDD pfam09872 pfam09872 430894 DUF2099 Uncharacterized protein conserved in archaea (DUF2099). This domain, found in various hypothetical prokaryotic proteins, has no known function. 257 matched cddid_all.tbl CDD pfam09873 pfam09873 401733 DUF2100 Uncharacterized protein conserved in archaea (DUF2100). This domain, found in various hypothetical archaeal proteins, has no known function. 210 matched cddid_all.tbl CDD pfam09874 pfam09874 255617 DUF2101 Predicted membrane protein (DUF2101). This domain, found in various archaeal and bacterial proteins, has no known function. 206 matched cddid_all.tbl CDD pfam09875 pfam09875 430895 DUF2102 Uncharacterized protein conserved in archaea (DUF2102). This domain, found in various hypothetical archaeal proteins, has no known function. 102 matched cddid_all.tbl CDD pfam09876 pfam09876 430896 DUF2103 Predicted metal-binding protein (DUF2103). This domain, found in various putative metal binding prokaryotic proteins, has no known function. 98 matched cddid_all.tbl CDD pfam09877 pfam09877 401736 EhaL Energy-converting hydrogenase subunit EhaL. This family of archaeal proteins represents the Energy-converting hydrogenase subunit EhaL. Eha is the essential conduit of electrons from H2 and supports methanogenesis. 99 matched cddid_all.tbl CDD pfam09878 pfam09878 401737 DUF2105 Predicted membrane protein (DUF2105). This domain, found in various hypothetical archaeal proteins, has no known function. 200 matched cddid_all.tbl CDD pfam09879 pfam09879 430897 DUF2106 Predicted membrane protein (DUF2106). This domain, found in various hypothetical archaeal proteins, has no known function. 151 matched cddid_all.tbl CDD pfam09880 pfam09880 430898 DUF2107 Predicted membrane protein (DUF2107). This domain, found in various hypothetical archaeal proteins, has no known function. 73 matched cddid_all.tbl CDD pfam09881 pfam09881 430899 DUF2108 Predicted membrane protein (DUF2108). This domain, found in various hypothetical archaeal proteins, has no known function. 70 matched cddid_all.tbl CDD pfam09882 pfam09882 430900 DUF2109 Predicted membrane protein (DUF2109). This domain, found in various hypothetical archaeal proteins, has no known function. 76 matched cddid_all.tbl CDD pfam09883 pfam09883 430901 DUF2110 Uncharacterized protein conserved in archaea (DUF2110). This domain, found in various hypothetical archaeal proteins, has no known function. 223 matched cddid_all.tbl CDD pfam09884 pfam09884 430902 DUF2111 Uncharacterized protein conserved in archaea (DUF2111). This domain, found in various hypothetical archaeal proteins, has no known function. 83 matched cddid_all.tbl CDD pfam09885 pfam09885 430903 DUF2112 Uncharacterized protein conserved in archaea (DUF2112). This domain, found in various hypothetical archaeal proteins, has no known function. 143 matched cddid_all.tbl CDD pfam09886 pfam09886 430904 DUF2113 Uncharacterized protein conserved in archaea (DUF2113). This domain, found in various hypothetical archaeal proteins, has no known function. 182 matched cddid_all.tbl CDD pfam09887 pfam09887 430905 DUF2114 Uncharacterized protein conserved in archaea (DUF2114). This domain, found in various hypothetical archaeal proteins, has no known function. 449 matched cddid_all.tbl CDD pfam09888 pfam09888 430906 DUF2115 Uncharacterized protein conserved in archaea (DUF2115). This domain, found in various hypothetical archaeal proteins, has no known function. 163 matched cddid_all.tbl CDD pfam09889 pfam09889 401748 DUF2116 Uncharacterized protein containing a Zn-ribbon (DUF2116). This domain, found in various hypothetical archaeal proteins, has no known function. Structural modelling suggests this domain may bind nucleic acids. 59 matched cddid_all.tbl CDD pfam09890 pfam09890 462922 DUF2117 Uncharacterized protein conserved in archaea (DUF2117). This domain, found in various hypothetical archaeal proteins, has no known function. 326 matched cddid_all.tbl CDD pfam09891 pfam09891 378294 DUF2118 Uncharacterized protein conserved in archaea (DUF2118). This domain, found in various hypothetical archaeal proteins, has no known function. 149 matched cddid_all.tbl CDD pfam09892 pfam09892 430908 DUF2119 Uncharacterized protein conserved in archaea (DUF2119). This domain, found in various hypothetical archaeal proteins, has no known function. 186 matched cddid_all.tbl CDD pfam09893 pfam09893 401751 DUF2120 Uncharacterized protein conserved in archaea (DUF2120). This domain, found in various hypothetical archaeal proteins, has no known function. 136 matched cddid_all.tbl CDD pfam09894 pfam09894 462923 DUF2121 Uncharacterized protein conserved in archaea (DUF2121). This domain, found in various hypothetical archaeal proteins, has no known function. 196 matched cddid_all.tbl CDD pfam09895 pfam09895 378295 DUF2122 RecB-family nuclease (DUF2122). This domain, found in various hypothetical archaeal proteins, has no known function. 106 matched cddid_all.tbl CDD pfam09897 pfam09897 430909 DUF2124 Uncharacterized protein conserved in archaea (DUF2124). This domain, found in various hypothetical archaeal proteins, has no known function. 141 matched cddid_all.tbl CDD pfam09898 pfam09898 430910 DUF2125 Uncharacterized protein conserved in bacteria (DUF2125). This domain, found in various hypothetical prokaryotic proteins, has no known function. 311 matched cddid_all.tbl CDD pfam09899 pfam09899 462924 DUF2126 Putative amidoligase enzyme (DUF2126). Members of this family of bacterial domains are predominantly found in transglutaminase and transglutaminase-like proteins. Their exact function is, as yet, unknown, but they are likely to act as amidoligase enzymes Protein in this family are found in conserved gene neighborhoods encoding a glutamine amidotransferase-like thiol peptidase (in proteobacteria) or an Aig2 family cyclotransferase protein (in firmicutes). 822 matched cddid_all.tbl CDD pfam09900 pfam09900 430912 DUF2127 Predicted membrane protein (DUF2127). This domain, found in various hypothetical prokaryotic and archaeal proteins, has no known function. 140 matched cddid_all.tbl CDD pfam09902 pfam09902 430913 DUF2129 Uncharacterized protein conserved in bacteria (DUF2129). This domain, found in various hypothetical prokaryotic proteins, has no known function. Structural modelling suggests this domain may bind nucleic acids. 70 matched cddid_all.tbl CDD pfam09903 pfam09903 430914 DUF2130 Uncharacterized protein conserved in bacteria (DUF2130). This domain, found in various hypothetical prokaryotic proteins, has no known function. 248 matched cddid_all.tbl CDD pfam09904 pfam09904 430915 HTH_43 Winged helix-turn helix. This family, found in various hypothetical prokaryotic proteins, is a probable winged helix DNA-binding domain. 89 matched cddid_all.tbl CDD pfam09905 pfam09905 430916 VF530 DNA-binding protein VF530. VF530 contains a unique four-helix motif that shows some similarity to the C-terminal double-stranded DNA (dsDNA) binding domain of RecA, as well as other nucleic acid binding domains. 63 matched cddid_all.tbl CDD pfam09906 pfam09906 430917 DUF2135 Uncharacterized protein conserved in bacteria (DUF2135). This domain, found in various hypothetical prokaryotic proteins, has no known function. 48 matched cddid_all.tbl CDD pfam09907 pfam09907 462925 HigB_toxin HigB_toxin, RelE-like toxic component of a toxin-antitoxin system. HigB_toxin is a family of RelE-like prokaryotic proteins that function as mRNA interferases. HigB cleaves translated mRNA only, and cleavage depended on translation of the target RNAs. HigB belongs to the RelE super-family of RNases. The toxin-antitoxin gene-pair is induced by environmental stress factors. 73 matched cddid_all.tbl CDD pfam09909 pfam09909 430919 DUF2138 Uncharacterized protein conserved in bacteria (DUF2138). This domain, found in various hypothetical prokaryotic proteins, has no known function. 555 matched cddid_all.tbl CDD pfam09910 pfam09910 401762 DUF2139 Uncharacterized protein conserved in archaea (DUF2139). This domain, found in various hypothetical archaeal proteins, has no known function. 340 matched cddid_all.tbl CDD pfam09911 pfam09911 430920 DUF2140 Uncharacterized protein conserved in bacteria (DUF2140). This domain, found in various hypothetical prokaryotic proteins, has no known function. 186 matched cddid_all.tbl CDD pfam09912 pfam09912 462926 DUF2141 Uncharacterized protein conserved in bacteria (DUF2141). This domain, found in various hypothetical prokaryotic proteins, has no known function. 112 matched cddid_all.tbl CDD pfam09913 pfam09913 430922 DUF2142 Predicted membrane protein (DUF2142). This domain, found in various hypothetical prokaryotic proteins, has no known function. 393 matched cddid_all.tbl CDD pfam09916 pfam09916 430923 DUF2145 Uncharacterized protein conserved in bacteria (DUF2145). This domain, found in various hypothetical prokaryotic proteins, has no known function. 200 matched cddid_all.tbl CDD pfam09917 pfam09917 462927 DUF2147 Uncharacterized protein conserved in bacteria (DUF2147). This domain, found in various hypothetical prokaryotic proteins, has no known function. 112 matched cddid_all.tbl CDD pfam09918 pfam09918 430925 DUF2148 Uncharacterized protein containing a ferredoxin domain (DUF2148). This domain, found in various hypothetical bacterial proteins containing a ferredoxin domain, has no known function. 65 matched cddid_all.tbl CDD pfam09919 pfam09919 430926 DUF2149 Uncharacterized conserved protein (DUF2149). This domain, found in various hypothetical prokaryotic proteins, has no known function. 92 matched cddid_all.tbl CDD pfam09920 pfam09920 430927 DUF2150 Uncharacterized protein conserved in archaea (DUF2150). This domain, found in various hypothetical archaeal proteins, has no known function. 189 matched cddid_all.tbl CDD pfam09921 pfam09921 378308 DUF2153 Uncharacterized protein conserved in archaea (DUF2153). This domain, found in various hypothetical archaeal proteins, has no known function. 123 matched cddid_all.tbl CDD pfam09922 pfam09922 430928 DUF2154 Cell wall-active antibiotics response 4TMS YvqF. This domain is found in various prokaryotic proteins, including cell wall-active antibiotic response proteins. This entry includes protein product of the yvqF gene, located immediately upstream of vraS. It is associated with glycopeptide resistance in Staphylococcus aureus. 114 matched cddid_all.tbl CDD pfam09923 pfam09923 430929 DUF2155 Uncharacterized protein conserved in bacteria (DUF2155). This domain, found in various hypothetical prokaryotic proteins, has no known function. 88 matched cddid_all.tbl CDD pfam09924 pfam09924 430930 LPG_synthase_C Phosphatidylglycerol lysyltransferase, C-terminal. This domain can be found in the C-terminal region of phosphatidylglycerol lysyltransferase mprF, which catalyzes the transfer of a lysyl group from L-lysyl-tRNA(Lys) to to membrane-bound phosphatidylglycerol (PG), which produces lysylphosphatidylglycerol (LPG). This domain can also be found in lysylphosphatidylglycerol biosynthesis bifunctional protein LysX, which is the two-domain lysyl-transferase (mprF)-lysyl-tRNA synthetase (lysU) protein is responsible for LPG production. 297 matched cddid_all.tbl CDD pfam09925 pfam09925 430931 DUF2157 Predicted membrane protein (DUF2157). This domain, found in various hypothetical prokaryotic proteins, has no known function. 141 matched cddid_all.tbl CDD pfam09926 pfam09926 430932 DUF2158 Uncharacterized small protein (DUF2158). Members of this family of prokaryotic proteins have no known function. 52 matched cddid_all.tbl CDD pfam09928 pfam09928 430933 DUF2160 Predicted small integral membrane protein (DUF2160). The members of this family of hypothetical prokaryotic proteins have no known function. It is thought that they are transmembrane proteins, but their function has not been inferred yet. 88 matched cddid_all.tbl CDD pfam09929 pfam09929 430934 DUF2161 Putative PD-(D/E)XK phosphodiesterase (DUF2161). This family of proteins is functionally uncharacterized. This family of proteins is found in prokaryotes. Advanced homology-detection methods supported with superfamily-wide domain architecture and horizontal gene transfer analyses s have established this family to be a member of the PD-(D/E)XK superfamily. 111 matched cddid_all.tbl CDD pfam09930 pfam09930 430935 DUF2162 Predicted transporter (DUF2162). Members of this family of bacterial proteins are thought to be membrane transporters, but their exact function has not, as yet, been elucidated. 223 matched cddid_all.tbl CDD pfam09931 pfam09931 430936 DUF2163 Uncharacterized conserved protein (DUF2163). This domain, found in various hypothetical prokaryotic proteins, has no known function. 159 matched cddid_all.tbl CDD pfam09932 pfam09932 462928 DUF2164 Uncharacterized conserved protein (DUF2164). This domain, found in various hypothetical prokaryotic proteins, has no known function. 74 matched cddid_all.tbl CDD pfam09933 pfam09933 430938 DUF2165 Predicted small integral membrane protein (DUF2165). This domain, found in various hypothetical prokaryotic proteins, has no known function. 157 matched cddid_all.tbl CDD pfam09935 pfam09935 430939 DUF2167 Protein of unknown function (DUF2167). This domain, found in various hypothetical membrane-anchored prokaryotic proteins, has no known function. 235 matched cddid_all.tbl CDD pfam09936 pfam09936 430940 Methyltrn_RNA_4 SAM-dependent RNA methyltransferase. This family has a Rossmanoid fold, with a deep trefoil knot in its C-terminal region. It has structural similarity to RNA methyltransferases, and is likely to function as an S-adenosyl-L-methionine (SAM)-dependent RNA 2'-O methyltransferase. 181 matched cddid_all.tbl CDD pfam09937 pfam09937 430941 DUF2169 Uncharacterized protein conserved in bacteria (DUF2169). This domain, found in various hypothetical prokaryotic proteins, has no known function. 294 matched cddid_all.tbl CDD pfam09938 pfam09938 430942 DUF2170 Uncharacterized protein conserved in bacteria (DUF2170). This domain, found in various hypothetical prokaryotic proteins, has no known function. 137 matched cddid_all.tbl CDD pfam09939 pfam09939 430943 DUF2171 Uncharacterized protein conserved in bacteria (DUF2171). This domain, found in various hypothetical prokaryotic proteins, has no known function. 63 matched cddid_all.tbl CDD pfam09940 pfam09940 430944 DUF2172 Domain of unknown function (DUF2172). This domain, found in various hypothetical prokaryotic proteins, has no known function. An aminopeptidase domain is conserved within the family, but its relevance has not been established yet. Rebuilding from PDB:3kt9 shows this is an inserted (nested domain within the amino-peptidase). The function of this small domain is not known. 91 matched cddid_all.tbl CDD pfam09941 pfam09941 370757 DUF2173 Uncharacterized conserved protein (DUF2173). This domain, found in various hypothetical prokaryotic proteins, has no known function. 104 matched cddid_all.tbl CDD pfam09943 pfam09943 370758 DUF2175 Uncharacterized protein conserved in archaea (DUF2175). This domain, found in various hypothetical archaeal proteins, has no known function. 98 matched cddid_all.tbl CDD pfam09945 pfam09945 462929 DUF2177 Predicted membrane protein (DUF2177). This domain, found in various hypothetical bacterial proteins, has no known function. 124 matched cddid_all.tbl CDD pfam09946 pfam09946 401789 DUF2178 Predicted membrane protein (DUF2178). This domain, found in various hypothetical archaeal proteins, has no known function. 106 matched cddid_all.tbl CDD pfam09947 pfam09947 401790 DUF2180 Uncharacterized protein conserved in archaea (DUF2180). This domain, found in various hypothetical archaeal proteins, has no known function. A few of the family members contain a zinc finger domain. 68 matched cddid_all.tbl CDD pfam09948 pfam09948 430946 DUF2182 Predicted metal-binding integral membrane protein (DUF2182). This domain, found in various hypothetical bacterial membrane proteins having predicted metal-binding properties, has no known function. 188 matched cddid_all.tbl CDD pfam09949 pfam09949 462930 APP1_cat Phosphatidate phosphatase APP1, catalytic domain. This entry represents a conserved region found in Phosphatidate phosphatase APP1 from yeast, which contains the catalytic motif DXDX(T/V), present in other Mg+2-dependent phosphatases. This domain has a weak sequence similarity to the haloacid dehalogenase-like domain. APP1 catalyzes the dephosphorylation of phosphatidate to yield diacylglycerol and may play a role in vesicular trafficking through its phosphatidate phosphatase activity at cortical actin patches. 153 matched cddid_all.tbl CDD pfam09950 pfam09950 462931 DUF2184 Uncharacterized protein conserved in bacteria (DUF2184). This domain, found in various hypothetical bacterial proteins, has no known function. 251 matched cddid_all.tbl CDD pfam09951 pfam09951 462932 DUF2185 Protein of unknown function (DUF2185). This domain, found in various hypothetical bacterial proteins, has no known function. 85 matched cddid_all.tbl CDD pfam09952 pfam09952 370761 AbiEi_2 Transcriptional regulator, AbiEi antitoxin, Type IV TA system. AbiEi_2 is the cognate antitoxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is pfam13338. 142 matched cddid_all.tbl CDD pfam09953 pfam09953 401795 DUF2187 Uncharacterized protein conserved in bacteria (DUF2187). This domain, found in various hypothetical bacterial proteins, has no known function. 60 matched cddid_all.tbl CDD pfam09954 pfam09954 378323 DUF2188 Uncharacterized protein conserved in bacteria (DUF2188). This domain represents a ribosome-associating protein predicted to mediate translation inhibition alongside repair of DNA damage or restriction in conflict contexts. A subset of this family contains a conserved histidine residue, raising the possibility that it directly acts as a RNase or in RNA end-processing. 62 matched cddid_all.tbl CDD pfam09955 pfam09955 430949 DUF2189 Predicted integral membrane protein (DUF2189). Members of this family are found in various hypothetical prokaryotic proteins, as well as putative cytochrome c oxidases. Their exact function has not, as yet, been established. 126 matched cddid_all.tbl CDD pfam09956 pfam09956 430950 DUF2190 Uncharacterized conserved protein (DUF2190). This domain, found in various hypothetical prokaryotic proteins has no known function. 103 matched cddid_all.tbl CDD pfam09957 pfam09957 462933 VapB_antitoxin Bacterial antitoxin of type II TA system, VapB. VapB is the antitoxin of a bacterial toxin-antitoxin gene pair. The cognate toxin is VapC, pfam05016. The family contains several related antitoxins from Cyanobacteria and Actinobacterial families. Antitoxins of this class carry an N-terminal ribbon-helix-helix domain, RHH, that is highly conserved across all type II bacterial antitoxins, which dimerizes with the RHH domain of a second VapB molecule. A hinge section follows the RHH, with an additional pair of flexible alpha helices at the C-terminus. This C-terminus is the Toxin-binding region of the dimer, and so is specific to the cognate toxin, whereas the RHH domain has the specific function of lying across the RNA-binding groove of the toxin dimer and inactivating the active-site - a more general function of all antitoxins. 43 matched cddid_all.tbl CDD pfam09958 pfam09958 378325 DUF2192 Uncharacterized protein conserved in archaea (DUF2192). This domain, found in various hypothetical archaeal proteins, has no known function. 229 matched cddid_all.tbl CDD pfam09959 pfam09959 430951 DUF2193 Uncharacterized protein conserved in archaea (DUF2193). This domain, found in various hypothetical archaeal proteins, has no known function. 498 matched cddid_all.tbl CDD pfam09960 pfam09960 401800 DUF2194 Uncharacterized protein conserved in bacteria (DUF2194). This domain, found in various hypothetical bacterial proteins, has no known function. 586 matched cddid_all.tbl CDD pfam09961 pfam09961 430952 DUF2195 Uncharacterized protein conserved in bacteria (DUF2195). This domain, found in various hypothetical bacterial proteins, has no known function. 117 matched cddid_all.tbl CDD pfam09962 pfam09962 430953 DUF2196 Uncharacterized conserved protein (DUF2196). This domain, found in various hypothetical bacterial proteins, has no known function. 59 matched cddid_all.tbl CDD pfam09963 pfam09963 430954 DUF2197 Uncharacterized protein conserved in bacteria (DUF2197). This domain, found in various hypothetical bacterial proteins, has no known function. 56 matched cddid_all.tbl CDD pfam09964 pfam09964 401803 DUF2198 Uncharacterized protein conserved in bacteria (DUF2198). This domain, found in various hypothetical bacterial proteins, has no known function. 72 matched cddid_all.tbl CDD pfam09965 pfam09965 430955 DUF2199 Uncharacterized protein conserved in bacteria (DUF2199). This domain, found in various hypothetical bacterial proteins, has no known function. 145 matched cddid_all.tbl CDD pfam09966 pfam09966 430956 DUF2200 Uncharacterized protein conserved in bacteria (DUF2200). This domain, found in various hypothetical bacterial proteins, has no known function. 110 matched cddid_all.tbl CDD pfam09967 pfam09967 401806 DUF2201 VWA-like domain (DUF2201). This domain, found in various hypothetical bacterial proteins, has no known function. However, it is clearly related to the VWA domain. 123 matched cddid_all.tbl CDD pfam09968 pfam09968 401807 DUF2202 Uncharacterized protein domain (DUF2202). This domain, found in various hypothetical archaeal proteins, has no known function. 162 matched cddid_all.tbl CDD pfam09969 pfam09969 430957 DUF2203 Uncharacterized conserved protein (DUF2203). This domain, found in various hypothetical bacterial proteins, has no known function. 121 matched cddid_all.tbl CDD pfam09970 pfam09970 378331 DUF2204 Nucleotidyl transferase of unknown function (DUF2204). This domain, found in various hypothetical archaeal proteins, has no known function. However, this family was identified as belonging to the nucleotidyltransferase superfamily. 181 matched cddid_all.tbl CDD pfam09971 pfam09971 401809 DUF2206 Predicted membrane protein (DUF2206). This domain, found in various hypothetical archaeal proteins, has no known function. 380 matched cddid_all.tbl CDD pfam09972 pfam09972 430958 DUF2207 Predicted membrane protein (DUF2207). This domain, found in various hypothetical bacterial proteins, has no known function. 390 matched cddid_all.tbl CDD pfam09973 pfam09973 378334 DUF2208 Predicted membrane protein (DUF2208). This domain, found in various hypothetical archaeal proteins, has no known function. 231 matched cddid_all.tbl CDD pfam09974 pfam09974 401811 DUF2209 Uncharacterized protein conserved in archaea (DUF2209). This domain, found in various hypothetical archaeal proteins, has no known function. 121 matched cddid_all.tbl CDD pfam09976 pfam09976 430959 TPR_21 Tetratricopeptide repeat-like domain. This family resembles a single unit of a TPR repeat. 194 matched cddid_all.tbl CDD pfam09977 pfam09977 430960 Tad_C Putative Tad-like Flp pilus-assembly. This domain, found in various hypothetical prokaryotic proteins, is likely to be involved in Flp lius biogenesis. 93 matched cddid_all.tbl CDD pfam09979 pfam09979 430961 DUF2213 Uncharacterized protein conserved in bacteria (DUF2213). Members of this family of bacterial proteins comprise various hypothetical and phage-related proteins. The exact function of these proteins has not, as yet, been determined. 166 matched cddid_all.tbl CDD pfam09980 pfam09980 430962 DUF2214 Predicted membrane protein (DUF2214). This domain, found in various hypothetical bacterial proteins, has no known function. 147 matched cddid_all.tbl CDD pfam09981 pfam09981 430963 DUF2218 Uncharacterized protein conserved in bacteria (DUF2218). This domain, found in various hypothetical bacterial proteins, has no known function. 88 matched cddid_all.tbl CDD pfam09982 pfam09982 430964 DUF2219 Uncharacterized protein conserved in bacteria (DUF2219). This domain, found in various hypothetical bacterial proteins, has no known function. 294 matched cddid_all.tbl CDD pfam09983 pfam09983 462934 DUF2220 Uncharacterized protein conserved in bacteria C-term(DUF2220). This domain, found in various hypothetical bacterial proteins, has no known function. The family represents just the C-terminus. 180 matched cddid_all.tbl CDD pfam09984 pfam09984 430966 sCache_4 Single cache domain 4. Members of this family of domains are found in various BarA-like signal transduction histidine kinases, which are involved in the regulation of carbon metabolism via the csrA/csrB regulatory system. The role of this domain has not, as yet, been established. 146 matched cddid_all.tbl CDD pfam09985 pfam09985 401820 Glucodextran_C C-terminal binding-module, SLH-like, of glucodextranase. Glucodextran_C is the C-terminal domain of glucodextranase-like proteins found in various prokaryotic membrane-anchored proteins. It shows homology to the carbohydrate-binding unit of some glycosidases. 228 matched cddid_all.tbl CDD pfam09986 pfam09986 430967 DUF2225 Uncharacterized protein conserved in bacteria (DUF2225). This domain, found in various hypothetical bacterial proteins, has no known function. 213 matched cddid_all.tbl CDD pfam09987 pfam09987 255677 DUF2226 Uncharacterized protein conserved in archaea (DUF2226). This domain, found in various hypothetical archaeal proteins, has no known function. 252 matched cddid_all.tbl CDD pfam09988 pfam09988 430968 DUF2227 Uncharacterized metal-binding protein (DUF2227). Members of this family of hypothetical bacterial proteins possess metal binding properties; however, their exact function has not, as yet, been determined. 166 matched cddid_all.tbl CDD pfam09989 pfam09989 462935 DUF2229 CoA enzyme activase uncharacterized domain (DUF2229). Members of this family include various bacterial hypothetical proteins, as well as CoA enzyme activases. The exact function of this domain has not, as yet, been defined. 213 matched cddid_all.tbl CDD pfam09990 pfam09990 462936 DUF2231 Predicted membrane protein (DUF2231). This domain, found in various hypothetical bacterial proteins, has no known function. It has similarity to pfam01292 suggesting it is a haem-binding cytochrome. 139 matched cddid_all.tbl CDD pfam09991 pfam09991 370773 DUF2232 Predicted membrane protein (DUF2232). This family of bacterial proteins are multi-pass membrane proteins with up to 10 (2 x 4/5) transmembrane regions. The exact function of this potential pore molecule is not known, but in many instances it is associated with ABC-transporter-like domains, implying that it is part of a secretion system that uses energy. 290 matched cddid_all.tbl CDD pfam09992 pfam09992 430971 NAGPA Phosphodiester glycosidase. This is a family conserved from bacteria to humans. The structure of a member from Bacteroides has been crystallized and modelled onto the luminal region of the human member of the family, the transmembrane glycoprotein N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase. There is some conservation of potentially functional residues, implying that in the bacterial members this family acts in some way as a phosphodiester glycosidase. The human protein is also present, so the eukaryotic members are likely to be catalysing the second step in the formation of the mannose 6-phosphate targeting signal on lysosomal enzyme oligosaccharides. 169 matched cddid_all.tbl CDD pfam09994 pfam09994 462937 DUF2235 Uncharacterized alpha/beta hydrolase domain (DUF2235). This domain, found in various hypothetical bacterial proteins, has no known function. 284 matched cddid_all.tbl CDD pfam09995 pfam09995 462938 MPAB_Lcp_cat ER-bound oxygenase mpaB/B'/Rubber oxygenase, catalytic domain. This is the catalytic domain found in the endoplasmic reticulum (ER) -bound oxygenases mpaB' (MPAB2) and mpaB (MPAB) from Penicillium roqueforti and Penicillium brevicompactum and in the rubber oxygenase (Lcp) from Streptomyces sp., which contains highly conserved arginine and histidine residues. Structural analysis from Lcp revealed that Arg164, Thr168 and His198 are crucial active site residues. The mpaB and mpaB' are part of the gene cluster that mediates the biosynthesis of mycophenolic acid (MPA). Lcp (Latex clearing proteins) is a rubber oxygenase that catalyzes the extracellular cleavage of poly (cis-1,4-isoprene). This domain is also present in uncharacterized proteins from Mycobacterium sp. and hypothetical proteins, mainly from bacteria and fungi. 223 matched cddid_all.tbl CDD pfam09996 pfam09996 462939 DUF2237 Uncharacterized protein conserved in bacteria (DUF2237). This domain, found in various hypothetical bacterial proteins, has no known function. 108 matched cddid_all.tbl CDD pfam09997 pfam09997 430975 DUF2238 Predicted membrane protein (DUF2238). This domain, found in various hypothetical bacterial proteins, has no known function. 140 matched cddid_all.tbl CDD pfam09998 pfam09998 430976 DUF2239 Uncharacterized protein conserved in bacteria (DUF2239). This domain, found in various hypothetical bacterial proteins, has no known function. 181 matched cddid_all.tbl CDD pfam09999 pfam09999 401831 DUF2240 Uncharacterized protein conserved in archaea (DUF2240). This domain, found in various hypothetical archaeal proteins, has no known function. 144 matched cddid_all.tbl CDD pfam10000 pfam10000 430977 ACT_3 ACT domain. This domain, found in various hypothetical bacterial proteins, has no known function. However, its structure is similar to the ACT domain which suggests that it binds to amino acids and regulates other protein activity. This family was formerly known as DUF2241. 69 matched cddid_all.tbl CDD pfam10001 pfam10001 430978 DUF2242 Uncharacterized protein conserved in bacteria (DUF2242). This domain is found in various hypothetical bacterial proteins, and has no known function. 121 matched cddid_all.tbl CDD pfam10002 pfam10002 430979 DUF2243 Predicted membrane protein (DUF2243). This domain, found in various hypothetical bacterial proteins, has no known function. 139 matched cddid_all.tbl CDD pfam10003 pfam10003 462940 DUF2244 Integral membrane protein (DUF2244). This domain, found in various bacterial hypothetical and putative membrane proteins, has no known function. 136 matched cddid_all.tbl CDD pfam10004 pfam10004 430981 DUF2247 Uncharacterized protein conserved in bacteria (DUF2247). This domain, found in various hypothetical bacterial proteins, has no known function. 158 matched cddid_all.tbl CDD pfam10005 pfam10005 430982 zinc-ribbon_6 zinc-ribbon domain. This family appears to be a true zinc-ribbon, with two sets of putative zinc-binding domains in tandem. 93 matched cddid_all.tbl CDD pfam10006 pfam10006 430983 DUF2249 Uncharacterized conserved protein (DUF2249). Members of this family of hypothetical bacterial proteins have no known function. 70 matched cddid_all.tbl CDD pfam10007 pfam10007 401839 DUF2250 Uncharacterized protein conserved in archaea (DUF2250). Members of this family of hypothetical archaeal proteins have no known function. 93 matched cddid_all.tbl CDD pfam10008 pfam10008 430984 DUF2251 Uncharacterized protein conserved in bacteria (DUF2251). Members of this family of hypothetical bacterial proteins have no known function. 89 matched cddid_all.tbl CDD pfam10009 pfam10009 462941 DUF2252 Uncharacterized protein conserved in bacteria (DUF2252). This domain, found in various hypothetical bacterial proteins, has no known function. 383 matched cddid_all.tbl CDD pfam10011 pfam10011 430986 DUF2254 Predicted membrane protein (DUF2254). Members of this family of bacterial proteins comprises various hypothetical and putative membrane proteins. Their exact function, has not, as yet, been defined. 370 matched cddid_all.tbl CDD pfam10012 pfam10012 430987 DUF2255 Uncharacterized protein conserved in bacteria (DUF2255). Members of this family of hypothetical bacterial proteins have no known function. 113 matched cddid_all.tbl CDD pfam10013 pfam10013 462942 DUF2256 Uncharacterized protein conserved in bacteria (DUF2256). Members of this family of hypothetical bacterial proteins have no known function. 40 matched cddid_all.tbl CDD pfam10014 pfam10014 462943 2OG-Fe_Oxy_2 2OG-Fe dioxygenase. This family contains 2-oxoglutarate (2OG) and Fe-dependent dioxygenases. It includes L-isoleucine dioxygenase (IDO). 191 matched cddid_all.tbl CDD pfam10015 pfam10015 401846 DUF2258 Uncharacterized protein conserved in archaea (DUF2258). Members of this family of hypothetical bacterial archaeal have no known function. Structural modelling suggests this domain may bind nucleic acids. 78 matched cddid_all.tbl CDD pfam10016 pfam10016 430990 DUF2259 Predicted secreted protein (DUF2259). Members of this family of hypothetical bacterial proteins have no known function. 188 matched cddid_all.tbl CDD pfam10017 pfam10017 462944 Methyltransf_33 Histidine-specific methyltransferase, SAM-dependent. The mycobacterial members of this family are expressed from part of the ergothioneine biosynthetic gene cluster. EGTD is the histidine methyltransferase that transfers three methyl groups to the alpha-amino moiety of histidine, in the first stage of the production of this histidine betaine derivative that carries a thiol group attached to the C2 atom of an imidazole ring. 304 matched cddid_all.tbl CDD pfam10018 pfam10018 401849 Med4 Vitamin-D-receptor interacting Mediator subunit 4. Members of this family function as part of the Mediator (Med) complex, which links DNA-bound transcriptional regulators and the general transcription machinery, particularly the RNA polymerase II enzyme. They play a role in basal transcription by mediating activation or repression according to the specific complement of transcriptional regulators bound to the promoter. 184 matched cddid_all.tbl CDD pfam10020 pfam10020 430992 DUF2262 Uncharacterized protein conserved in bacteria (DUF2262). This domain, found in various hypothetical bacterial proteins, has no known function. 141 matched cddid_all.tbl CDD pfam10021 pfam10021 430993 DUF2263 Uncharacterized protein conserved in bacteria (DUF2263). This domain, found in various hypothetical bacterial and eukaryotic proteins, has no known function. 136 matched cddid_all.tbl CDD pfam10022 pfam10022 430994 DUF2264 Uncharacterized protein conserved in bacteria (DUF2264). Members of this family of hypothetical bacterial proteins have no known function. 352 matched cddid_all.tbl CDD pfam10023 pfam10023 430995 Aminopep Putative aminopeptidase. This family of bacterial proteins has a conserved HEXXH motif, suggesting that members are putative peptidases of zincin fold. 322 matched cddid_all.tbl CDD pfam10025 pfam10025 430996 DUF2267 Uncharacterized conserved protein (DUF2267). This domain, found in various hypothetical bacterial proteins, has no known function. 122 matched cddid_all.tbl CDD pfam10026 pfam10026 430997 DUF2268 Predicted Zn-dependent protease (DUF2268). This domain, found in various hypothetical bacterial proteins, as well as predicted zinc dependent proteases, has no known function. 195 matched cddid_all.tbl CDD pfam10027 pfam10027 430998 DUF2269 Predicted integral membrane protein (DUF2269). Members of this family of bacterial hypothetical integral membrane proteins have no known function. 150 matched cddid_all.tbl CDD pfam10028 pfam10028 430999 DUF2270 Predicted integral membrane protein (DUF2270). This domain, found in various hypothetical bacterial proteins, has no known function. 182 matched cddid_all.tbl CDD pfam10029 pfam10029 431000 DUF2271 Predicted periplasmic protein (DUF2271). This domain, found in various hypothetical bacterial proteins and misannotated lysozyme proteins, it has no known function. This domain contains a [S/T]GA[S/T] conserved motif and serves as a flavinylation substrate for ApbE, and is likely to be involved in extracytosolic redox activities. 136 matched cddid_all.tbl CDD pfam10030 pfam10030 370785 DUF2272 Uncharacterized protein conserved in bacteria (DUF2272). Members of this family of hypothetical bacterial proteins have no known function. However, given its similarity to the CHAP domain it seems likely that this is an enzyme involved in cleaving peptidoglycan. 191 matched cddid_all.tbl CDD pfam10031 pfam10031 431001 DUF2273 Small integral membrane protein (DUF2273). Members of this family of hypothetical bacterial proteins have no known function. 46 matched cddid_all.tbl CDD pfam10032 pfam10032 431002 Pho88 Phosphate transport (Pho88). Members of this family of proteins are involved in regulating inorganic phosphate transport, as well as telomere length regulation and maintenance. Family members such as SND3 (SRP-independent targeting protein 3, encoded by PHO88, also known as YBR106W) is localized to the endoplasmic reticulum (ER). SND3 works together with SND1 and SND2; these proteins function in parallel with the SRP and GET pathways to target a broad range of substrates to the ER. The SND proteins constitute an alternative targeting route to the ER. SND3/PHO88 was first identified as a Saccharomyces cerevisiae protein involved in inorganic phosphate transport. Functional analysis revealed that Loss of SND3 has been shown to affect secretion of the yeast acid phosphatase. 175 matched cddid_all.tbl CDD pfam10033 pfam10033 431003 ATG13 Autophagy-related protein 13. Members of this family of phosphoproteins are involved in cytoplasm to vacuole transport (Cvt), and more specifically in Cvt vesicle formation. They are probably involved in the switching machinery regulating the conversion between the Cvt pathway and autophagy. Finally, ATG13 is also required for glycogen storage.3]. 228 matched cddid_all.tbl CDD pfam10034 pfam10034 462945 Dpy19 Q-cell neuroblast polarization. Dyp-19, formerly known as DUF2211, is a transmembrane domain family that is required to orient the neuroblast cells, QR and QL accurately on the anterior-posterior axis: QL and QR are born in the same anterior-posterior position, but polarise and migrate left-right asymmetrically, QL migrating towards the posterior and QR migrating towards the anterior. It is also required, with unc-40, to express mab-5 correctly in the Q cell descendants. The Dpy-19 protein derives from the C. elegans DUMPY mutant, Swiss:P34413. 646 matched cddid_all.tbl CDD pfam10035 pfam10035 462946 DUF2179 Uncharacterized protein conserved in bacteria (DUF2179). This domain, found in various hypothetical bacterial proteins, has no known function. 55 matched cddid_all.tbl CDD pfam10036 pfam10036 401864 RLL RNA transcription, translation and transport factor protein. This entry represents RNA transcription, translation and transport factor protein (RTRAF, also known as hCLE/C14orf166) from eukaryotes. It is part of the DDX1-HSPC117-FAM98B complex that shuttles between the nucleus and the cytoplasm transporting RNAs. It is also a component of the tRNA-splicing ligase complex and is required for tRNA ligation. Human RTRAF works as a positive modulator of the RNA polymerase II activity. It also interacts with influenza virus polymerase subunit PA and plays an important role in influenza virus replication. Family members carry a characteriztic RLL sequence-motif. 243 matched cddid_all.tbl CDD pfam10037 pfam10037 462947 MRP-S27 Mitochondrial 28S ribosomal protein S27. Members of this family of small ribosomal proteins possess one of three conserved blocks of sequence found in proteins that stimulate the dissociation of guanine nucleotides from G-proteins, leaving open the possibility that MRP-S27 might be a functional partner of GTP-binding ribosomal proteins. 395 matched cddid_all.tbl CDD pfam10038 pfam10038 431007 DUF2274 Protein of unknown function (DUF2274). Members of this family of hypothetical bacterial proteins have no known function. 69 matched cddid_all.tbl CDD pfam10039 pfam10039 401867 DUF2275 Predicted integral membrane protein (DUF2275). This domain, found in various hypothetical bacterial proteins and in the RNA polymerase sigma factor, has no known function. 201 matched cddid_all.tbl CDD pfam10040 pfam10040 462948 CRISPR_Cas6 CRISPR-associated endoribonuclease Cas6. Cas6 is a member of the RAMP (repeat-associated mysterious protein) superfamily. It is among the most widely distributed Cas proteins and is found in both bacteria and archaea. Cas6 functions in the generation of CRISPR-derived guide RNAs for invader defense in prokaryotes. 65 matched cddid_all.tbl CDD pfam10041 pfam10041 431009 DUF2277 Uncharacterized conserved protein (DUF2277). Members of this family of hypothetical bacterial proteins have no known function. 74 matched cddid_all.tbl CDD pfam10042 pfam10042 462949 DUF2278 Uncharacterized conserved protein (DUF2278). Members of this family of hypothetical bacterial proteins have no known function. 205 matched cddid_all.tbl CDD pfam10043 pfam10043 431011 DUF2279 Predicted periplasmic lipoprotein (DUF2279). This domain, found in various hypothetical bacterial proteins, has no known function. 91 matched cddid_all.tbl CDD pfam10044 pfam10044 462950 LIN52 Retinal tissue protein. LIN52 is a family of proteins of approximately 112 amino acids in length which is conserved from nematodes to humans. The proposed tertiary structure is of almost entirely alpha helix interrupted only by loops located at proline residues. Three sites in the protein sequence reveal two types of possible post-translation modification. A serine residue, at position 41, is a candidate for protein kinase C phosphorylation. Glycine residues at position 69 and 91 are probable sites for acetylation by covalent amide linkage of myristate via N-myristoyl transferase. LIN52 is differentially expressed in the trout retina between parr and smolt developmental stages (smoltification). It is likely to be a house-keeping protein. LIN52 forms a complex (LINC) required for transcriptional activation of G2/M genes. The LINC core complex consists of at least five subunits including the chromatin-associated LIN-9 and RbAp48 proteins. LINC associates with a large number of E2F-regulated promoters in quiescent cells. Family members are required for spermatogenesis by repressing testis-specific gene expression. 92 matched cddid_all.tbl CDD pfam10045 pfam10045 431012 DUF2280 Uncharacterized conserved protein (DUF2280). Members of this family of hypothetical bacterial proteins have no known function. 103 matched cddid_all.tbl CDD pfam10046 pfam10046 462951 BLOC1_2 Biogenesis of lysosome-related organelles complex-1 subunit 2. Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system. 96 matched cddid_all.tbl CDD pfam10047 pfam10047 462952 DUF2281 Protein of unknown function (DUF2281). Members of this family of hypothetical bacterial proteins have no known function. 64 matched cddid_all.tbl CDD pfam10048 pfam10048 431015 DUF2282 Predicted integral membrane protein (DUF2282). Members of this family of hypothetical bacterial proteins and putative signal peptide proteins have no known function. 52 matched cddid_all.tbl CDD pfam10049 pfam10049 431016 DUF2283 Protein of unknown function (DUF2283). Members of this family of hypothetical bacterial proteins have no known function. 49 matched cddid_all.tbl CDD pfam10050 pfam10050 431017 DUF2284 Predicted metal-binding protein (DUF2284). Members of this family of metal-binding hypothetical bacterial proteins have no known function. 161 matched cddid_all.tbl CDD pfam10051 pfam10051 378369 DUF2286 Uncharacterized protein conserved in archaea (DUF2286). Members of this family of hypothetical archaeal proteins have no known function. 138 matched cddid_all.tbl CDD pfam10052 pfam10052 431018 DUF2288 Protein of unknown function (DUF2288). Members of this family of hypothetical bacterial proteins have no known function. 91 matched cddid_all.tbl CDD pfam10053 pfam10053 370798 DUF2290 Uncharacterized conserved protein (DUF2290). Members of this family of hypothetical bacterial proteins have no known function. 195 matched cddid_all.tbl CDD pfam10054 pfam10054 431019 DUF2291 Predicted periplasmic lipoprotein (DUF2291). Members of this family of hypothetical bacterial proteins have no known function. 200 matched cddid_all.tbl CDD pfam10055 pfam10055 431020 DUF2292 Uncharacterized small protein (DUF2292). Members of this family of hypothetical bacterial proteins have no known function. 37 matched cddid_all.tbl CDD pfam10056 pfam10056 431021 DUF2293 Uncharacterized conserved protein (DUF2293). This domain, found in various hypothetical bacterial proteins, has no known function. 85 matched cddid_all.tbl CDD pfam10057 pfam10057 431022 MpsC Na+-translocating membrane potential-generating system (MpsC). This entry corresponds to the Na+-translocating membrane potential-generating system subunit MpsC. 111 matched cddid_all.tbl CDD pfam10058 pfam10058 401882 zinc_ribbon_10 Predicted integral membrane zinc-ribbon metal-binding protein. This domain, found in various hypothetical bacterial and eukaryotic metal-binding proteins is a probably zinc-ribbon. 51 matched cddid_all.tbl CDD pfam10060 pfam10060 431023 DUF2298 Uncharacterized membrane protein (DUF2298). This domain, found in various hypothetical bacterial proteins, has no known function. 484 matched cddid_all.tbl CDD pfam10061 pfam10061 401884 DUF2299 Uncharacterized conserved protein (DUF2299). Members of this family of hypothetical bacterial proteins have no known function. 137 matched cddid_all.tbl CDD pfam10062 pfam10062 431024 DUF2300 Predicted secreted protein (DUF2300). This domain, found in various bacterial hypothetical and putative signal peptide proteins, has no known function. 122 matched cddid_all.tbl CDD pfam10063 pfam10063 431025 DUF2301 Uncharacterized integral membrane protein (DUF2301). This domain, found in various hypothetical bacterial proteins, has no known function. 133 matched cddid_all.tbl CDD pfam10065 pfam10065 431026 DUF2303 Uncharacterized conserved protein (DUF2303). Members of this family of hypothetical bacterial proteins have no known function. 268 matched cddid_all.tbl CDD pfam10066 pfam10066 462953 DUF2304 Uncharacterized conserved protein (DUF2304). Members of this family of hypothetical archaeal proteins have no known function. 106 matched cddid_all.tbl CDD pfam10067 pfam10067 431028 DUF2306 Predicted membrane protein (DUF2306). Members of this family of hypothetical bacterial proteins have no known function. 147 matched cddid_all.tbl CDD pfam10069 pfam10069 431029 DICT Sensory domain in DIguanylate Cyclases and Two-component system. DICT is a sensory domain found associated with GGDEF, EAL, HD-GYP, STAS, and two component systems (histidine-kinase type). It assumes an alpha+beta fold with a 4-stranded beta-sheet and might have a role in light response (Natural history of sensor domains in bacterial signaling systems by Aravind L, LM Iyer, Anantharaman V, from 'Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition.' Caister Academic Press. 2010) - see (http://de.scribd.com/doc/28576661/Bacterial-Signaling-Chapter) 126 matched cddid_all.tbl CDD pfam10070 pfam10070 431030 DabA Probable inorganic carbon transporter subunit DabA. This entry represents the probable inorganic carbon transporter subunit DabA, which is part of an energy-coupled inorganic carbon pump together with DabB subunit in DAB operons (DAB1 and DAB2), found in a wide range of bacteria and archaea. Members of this family were previously known as UPF0753. DAB operon is required for CO2 concentrating mechanisms. The substrate of this subunit may be CO2 rather than carbonate ions based on kinetic calculations and in experimental assays in which E.coli was deleted of its carbonic anhydrase genes and expression of DAB2 operon restores its growth. Structural homology modelling suggests that DabA contains a domain that is distantly homologous to a type II beta-carbonic anhydrase (CA). 759 matched cddid_all.tbl CDD pfam10071 pfam10071 431031 DUF2310 Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310). Members of this family of proteobacterial zinc ribbon proteins are thought to bind to nucleic acids, however their exact function has not as yet been defined. 255 matched cddid_all.tbl CDD pfam10073 pfam10073 431032 DUF2312 Uncharacterized protein conserved in bacteria (DUF2312). Members of this family of hypothetical bacterial proteins have no known function. Structural modelling suggests this domain may bind nucleic acids. 72 matched cddid_all.tbl CDD pfam10074 pfam10074 431033 DUF2285 Uncharacterized conserved protein (DUF2285). This domain, found in various hypothetical bacterial proteins, has no known function. 102 matched cddid_all.tbl CDD pfam10075 pfam10075 462954 CSN8_PSD8_EIF3K CSN8/PSMD8/EIF3K family. This domain is conserved from plants to humans. It is a signature protein motif found in components of CSN (COP9 signalosome) where it functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development. It is found in Eukaryotic translation initiation factor 3 subunit K, a component of the eukaryotic translation initiation factor 3 (eIF-3) complex required for the initiation of protein synthesis. It is also found in 26S proteasome non-ATPase regulatory subunit 8 (PSMD8), a regulatory subunit of the 26S proteasome. 137 matched cddid_all.tbl CDD pfam10076 pfam10076 431034 Phage_Mu_Gp48 Bacteriophage Mu-like, Gp48. Members of this family of proteins comprise various hypothetical and putative bacteriophage tail proteins, including Gp48 from Bacteriophage Mu and other Mu-like prophages such as FluMu. 150 matched cddid_all.tbl CDD pfam10077 pfam10077 431035 DUF2314 Uncharacterized protein conserved in bacteria (DUF2314). This domain is found in various bacterial hypothetical proteins, as well as putative ankyrin repeat proteins. The exact function of the domains comprising this family has not, as yet, been determined. 135 matched cddid_all.tbl CDD pfam10078 pfam10078 401896 DUF2316 Uncharacterized protein conserved in bacteria (DUF2316). Members of this family of hypothetical bacterial proteins have no known function. 89 matched cddid_all.tbl CDD pfam10079 pfam10079 462955 BshC Bacillithiol biosynthesis BshC. Members of this protein family include BshC, which is an enzyme required for bacillithiol biosynthesis and described as a cysteine-adding enzyme. 540 matched cddid_all.tbl CDD pfam10080 pfam10080 401898 FtrD-like Membrane iron-sulfur containing protein FtrD-like. Members of this family are bacterial membrane proteins associated with the FTR1 protein, an homologous to FtrC in the FtrABCD complex. This complex is a ferric iron transporter in which the ferric iron is generated by ferrous oxidation that requires the electron transfer by iron-sulfur cluster-containing FrtD. Proteins in this family are part of the iron-sulfur-containing Rieske superfamily and are likely to have an analogous function to FtrD in iron transport. 98 matched cddid_all.tbl CDD pfam10081 pfam10081 431037 Abhydrolase_9 Alpha/beta-hydrolase family. This is a family of alpha/beta hydrolases which may function as lipases. This domain is the catalytic domain and includes the catalytic triad and the GXSXG sequence motif which is a characteriztic of these enzymes. 282 matched cddid_all.tbl CDD pfam10082 pfam10082 431038 BBP2_2 Putative beta-barrel porin 2. This domain is a putative beta-barrel porin type 2. 378 matched cddid_all.tbl CDD pfam10083 pfam10083 431039 DUF2321 Uncharacterized protein conserved in bacteria (DUF2321). Members of this family of hypothetical bacterial proteins have no known function. 156 matched cddid_all.tbl CDD pfam10084 pfam10084 431040 DUF2322 Uncharacterized protein conserved in bacteria (DUF2322). Members of this family of hypothetical bacterial proteins have no known function. 99 matched cddid_all.tbl CDD pfam10086 pfam10086 431041 YhfC YhfC intramembrane metalloprotease. This family includes proteins that are mainly from Firmicutes and Proteobacteria. Family members bear the consensus signature of 'EExxR' the second motif 'HxxxE' and the third motif 'H/Qxxxs'. The fourth motif, 'HxxxB', is shared by the PrsW proteases pfam13367 and the CPBP pfam02517, and APH-1 families. There are currently no experimental functional data for members of this group, however, they are predicted to be integral membrane proteins with several transmembrane segments and hypothesized metalloprotease function. YhfC intramembrane metalloprotease, CPBP family (type II CAAX Proteases and Bacteriocin Processing enzymes), PrsW proteases and APH-1 are distantly related. They share four predicted core transmembrane segments and possess similar, yet distinct sets of sequence motifs. 223 matched cddid_all.tbl CDD pfam10087 pfam10087 431042 DUF2325 Uncharacterized protein conserved in bacteria (DUF2325). Members of this family of hypothetical bacterial proteins have no known function. 94 matched cddid_all.tbl CDD pfam10088 pfam10088 431043 DUF2326 Uncharacterized protein conserved in bacteria (DUF2326). This domain, found in various hypothetical bacterial proteins, has no known function. 139 matched cddid_all.tbl CDD pfam10090 pfam10090 431044 HPTransfase Histidine phosphotransferase C-terminal domain. HPTransfase is a family of essential histidine phosphotransferases. It controls the activity of the master bacterial cell-cycle regulator CtrA through phosphorylation. It behaves as a homodimer by adopting the domain architecture of the intracellular part of class I histidine kinases. Each subunit consists of two distinct domains: an N-terminal helical hairpin domain and a C-terminal [alpha]/[beta] domain. The two N-terminal domains are adjacent within the dimer, forming a four-helix bundle. The C-terminal domain adopts an atypical Bergerat ATP-binding fold. 123 matched cddid_all.tbl CDD pfam10091 pfam10091 431045 Glycoamylase Putative glucoamylase. The structure of UniProt:Q5LIB7 has an alpha/alpha toroid fold and is similar structurally to a number of glucoamylases. Most of these structural homologs are glucoamylases, involved in breaking down complex sugars (e.g. starch). The biologically relevant state is likely to be monomeric. The putative active site is located at the centre of the toroid with a well defined large cavity. 218 matched cddid_all.tbl CDD pfam10092 pfam10092 431046 DUF2330 Uncharacterized protein conserved in bacteria (DUF2330). Members of this family of hypothetical bacterial proteins have no known function. 275 matched cddid_all.tbl CDD pfam10093 pfam10093 462956 EarP Elongation-Factor P (EF-P) rhamnosyltransferase EarP. This entry includes family members such as EarP enzymes which are essential for post-translational activation of elongation factor P(EF-P). It was identified as EF-P arginine R32 specific rhamnosyl transferase in Shewanella oneidensis using dTDP-beta-L-rhamnose as donor substrate. This was further confirmed for Pseudomonas aeruginosa, Pseudomonas putida and Neisseria meningitidis. As for S. oneidensis and P. aeruginosa, EarP enzyme acts as an inverting glycosyltransferase, thus mediating the formation of an alpha-L-rhamnosidic linkage. Structural analysis show that EarP is composed of two opposing domains with Rossmann folds, thus constituting a B pattern-type glycosyltransferase (GT-B) and provide basis for arginine glycosylation by EarP. Mutational analysis of efp and earP genes, resulted in a substantial decrease in the production of rhamnolipids and pyocyanin (important factors for colonization and invasion during infection) of P. aeruginosa. Collectively this indicates that EarP and EF-P are essential for P. aeruginosa pathogenicity.The protein family is also annotated in the CaZy Database as GT104. 373 matched cddid_all.tbl CDD pfam10094 pfam10094 431048 DUF2332 Uncharacterized protein conserved in bacteria (DUF2332). Members of this family of hypothetical bacterial proteins have no known function. 335 matched cddid_all.tbl CDD pfam10095 pfam10095 431049 DUF2333 Uncharacterized protein conserved in bacteria (DUF2333). Members of this family of hypothetical bacterial proteins have no known function. 330 matched cddid_all.tbl CDD pfam10096 pfam10096 462957 DUF2334 Uncharacterized protein conserved in bacteria (DUF2334). This domain, found in various hypothetical bacterial proteins, has no known function. 208 matched cddid_all.tbl CDD pfam10097 pfam10097 431051 DUF2335 Predicted membrane protein (DUF2335). Members of this family of hypothetical bacterial proteins have no known function. 50 matched cddid_all.tbl CDD pfam10098 pfam10098 431052 DUF2336 Uncharacterized protein conserved in bacteria (DUF2336). Members of this family of hypothetical bacterial proteins have no known function. 258 matched cddid_all.tbl CDD pfam10099 pfam10099 431053 RskA Anti-sigma-K factor rskA. This domain, formerly known as DUF2337, is the anti-sigma-K factor, RskA. In Mycobacterium tuberculosis the protein positively regulates expression of the antigenic proteins MPB70 and MPB83. 180 matched cddid_all.tbl CDD pfam10100 pfam10100 401915 Staph_opine_DH Staphylopine dehydrogenase. A member of this family has been identified in Staphylococcus aureus as a dehydrogenase involved in the synthesis of a new metallophore,named staphylopine. It is encoded as part of an operon that also includes an histidine racemase and an enzyme distantly related to nicotianamine synthase. Staphylopine is involved in metal acquisition, chelating nickel, cobalt, zinc, copper or iron, depending on the growing conditions. Metal acquisition is vital for bacteria growing in metal-scarce environments, such as inside a host in the case of pathogens. 423 matched cddid_all.tbl CDD pfam10101 pfam10101 431054 DUF2339 Predicted membrane protein (DUF2339). This domain, found in various hypothetical bacterial proteins, has no known function. 680 matched cddid_all.tbl CDD pfam10102 pfam10102 431055 DUF2341 Domain of unknown function (DUF2341). Members of this family are found in various bacterial proteins, including MotA/TolQ/ExbB proton channels and other transport proteins. The exact function of this set of domains has not, as yet, been determined. 84 matched cddid_all.tbl CDD pfam10103 pfam10103 431056 Zincin_2 Zincin-like metallopeptidase. This family of proteins has a conserved HEXXH motif, suggesting they are putative peptidases of zincin fold. The structure of this family has similarity to Peptidase_M1 (pfam01433, PDB:3CMN). 340 matched cddid_all.tbl CDD pfam10104 pfam10104 431057 Brr6_like_C_C Di-sulfide bridge nucleocytoplasmic transport domain. Brr6_like_C_C is the highly conserved C-terminal region of a group of proteins found in fungi. It carries four highly conserved cysteine residues. It is suggested that members of the family interact with each other via di-sulfide bridges to form a complex which is involved in nucleocytoplasmic transport. Brr6 in yeast is an essential integral membrane protein of the NE-ER, wit two predicted transmembrane domains, and is a dosage suppressor of Apq12, pfam12716. 133 matched cddid_all.tbl CDD pfam10105 pfam10105 431058 DUF2344 Uncharacterized protein conserved in bacteria (DUF2344). This domain, found in various hypothetical bacterial proteins and Radical Sam domain proteins, has no known function. This domain is distantly related to tRNA pseudouridine synthases, suggesting this family may carry out a function related to RNA modification. But this family appears to lack the catalytic aspartate found in pseudouridine synthases. 179 matched cddid_all.tbl CDD pfam10106 pfam10106 431059 DUF2345 Uncharacterized protein conserved in bacteria (DUF2345). Members of this family are found in various bacterial hypothetical proteins, as well as Rhs element Vgr proteins. 151 matched cddid_all.tbl CDD pfam10107 pfam10107 401922 Endonuc_Holl Endonuclease related to archaeal Holliday junction resolvase. This domain is found in various predicted bacterial endonucleases which are distantly related to archaeal Holliday junction resolvases. 159 matched cddid_all.tbl CDD pfam10108 pfam10108 462958 DNA_pol_B_exo2 Predicted 3'-5' exonuclease related to the exonuclease domain of PolB. This domain is found in various prokaryotic 3'-5' exonucleases and hypothetical proteins. 210 matched cddid_all.tbl CDD pfam10109 pfam10109 431061 Phage_TAC_7 Phage tail assembly chaperone proteins, E, or 41 or 14. This is family of various Myoviridae bacteriophage tail assembly chaperone, or TAC, proteins. 79 matched cddid_all.tbl CDD pfam10110 pfam10110 431062 GPDPase_memb Membrane domain of glycerophosphoryl diester phosphodiesterase. Members of this family comprise the membrane domain of the prokaryotic enzyme glycerophosphoryl diester phosphodiesterase. 321 matched cddid_all.tbl CDD pfam10111 pfam10111 313356 Glyco_tranf_2_2 Glycosyltransferase like family 2. Members of this family of prokaryotic proteins include putative glucosyltransferase, which are involved in bacterial capsule biosynthesis. 276 matched cddid_all.tbl CDD pfam10112 pfam10112 431063 Halogen_Hydrol 5-bromo-4-chloroindolyl phosphate hydrolysis protein. Members of this family of prokaryotic proteins mediate the hydrolysis of 5-bromo-4-chloroindolyl phosphate bonds. 191 matched cddid_all.tbl CDD pfam10113 pfam10113 401927 Fibrillarin_2 FeGP cofactor biosynthesis protein, fibrillarin family. Members of this family of proteins include archaeal fibrillarin homologs also known as HcgG which is involved in biosynthesis of Iron-guanylylpyridinol (FeGP) cofactor. 500 matched cddid_all.tbl CDD pfam10114 pfam10114 462959 PocR Sensory domain found in PocR. PocR, a ligand binding domain, has a novel variant of the PAS-like Fold. Evidence suggests that it binds small hydrocarbon derivatives such as 1,3-propanediol. In (Natural history of sensor domains in bacterial signaling systems by Aravind L, LM Iyer, Anantharaman V, from 'Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition.' Caister Academic Press. 2010) - see (http://de.scribd.com/doc/28576661/Bacterial-Signaling-Chapter) 155 matched cddid_all.tbl CDD pfam10115 pfam10115 431065 HlyU Transcriptional activator HlyU. This domain, found in various hypothetical prokaryotic proteins, has no known function. One of the sequences in this family corresponds to the transcriptional activator HlyU, indicating a possible similar role in other members. 91 matched cddid_all.tbl CDD pfam10116 pfam10116 431066 Host_attach Protein required for attachment to host cells. Members of this family of bacterial proteins are required for the attachment of the bacterium to host cells. Furthermore, it has been reported that this family includes bacterial family of the archaeo-eukaryotic release factor superfamily, lacks fusions to N-terminal codon recognition domain and C-terminal Pelota domain. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome. 136 matched cddid_all.tbl CDD pfam10117 pfam10117 431067 McrBC McrBC 5-methylcytosine restriction system component. Members of this family of bacterial proteins modify the specificity of mcrB restriction by expanding the range of modified sequences restricted. 320 matched cddid_all.tbl CDD pfam10118 pfam10118 431068 Metal_hydrol Predicted metal-dependent hydrolase. Members of this family of proteins comprise various bacterial transition metal-dependent hydrolases. 249 matched cddid_all.tbl CDD pfam10119 pfam10119 431069 MethyTransf_Reg Predicted methyltransferase regulatory domain. Members of this family of domains are found in various prokaryotic methyltransferases, where they regulate the activity of the methyltransferase domain. 84 matched cddid_all.tbl CDD pfam10120 pfam10120 431070 ThiP_synth Thiamine-phosphate synthase. This family is thiamine-phosphate synthase, and it belongs to the SCOP phosphomethylpyrimidine kinase C-terminal domain-like family. Vitamin B1 (thiamine pyrophosphate) is involved in several microbial metabolic functions. Thiamine biosynthesis is accomplished by joining two intermediate molecules that are synthesized separately, HMP-PP and HET-P. In the archaeon Natrialba magadii, ThiE and ThiN, are known to join HMP-PP ( hydroxymethylpyrimidine pyrophosphate) and HET-P (hydroxyethylthiazole phosphate) to generate thiamine phosphate. Whereas ThiE in Natrialba magadii is a mono-functional protein, ThiN exists as a C-terminal domain in a ThiDN fusion protein - examples of all three forms, from various prokaryotes, are found in this family. 164 matched cddid_all.tbl CDD pfam10122 pfam10122 287133 Mu-like_Com Mu-like prophage protein Com. Members of this family of proteins comprise the translational regulator of mom. 52 matched cddid_all.tbl CDD pfam10123 pfam10123 431071 Mu-like_Pro Mu-like prophage I protein. Members of this family of proteins comprise various viral Mu-like prophage I proteins. 328 matched cddid_all.tbl CDD pfam10124 pfam10124 431072 Mu-like_gpT Mu-like prophage major head subunit gpT. Members of this family of proteins comprise various caudoviral prophage proteins, including the Mu-like prophage major head subunit gpT. 289 matched cddid_all.tbl CDD pfam10125 pfam10125 401936 NADHdeh_related NADH dehydrogenase I, subunit N related protein. This family comprises a set of NADH dehydrogenase I, subunit N related proteins found in archaea. Their exact function, has not, as yet, been determined. 218 matched cddid_all.tbl CDD pfam10126 pfam10126 401937 Nit_Regul_Hom Uncharacterized protein, homolog of nitrogen regulatory protein PII. This domain, found in various hypothetical archaeal proteins, has no known function. It is distantly similar to the nitrogen regulatory protein PII. 107 matched cddid_all.tbl CDD pfam10127 pfam10127 431073 RlaP RNA repair pathway DNA polymerase beta family. Family of the DNA polymerase beta superfamily, with closest affinities to the Minimal Nucleotide Transferase clade (MNT). Observed in diverse RNA repair genome contexts centered on both RtcB and Rnl-type (ATP-grasp fold) repair ligases. Members of this family of bacterial proteins catalyze the transfer of nucleotide residues from nucleoside diphosphates or triphosphates into dimer or polymer forms. 245 matched cddid_all.tbl CDD pfam10128 pfam10128 462960 OpcA_G6PD_assem Glucose-6-phosphate dehydrogenase subunit N-terminal domain. Members of this family are found in various prokaryotic OpcA and glucose-6-phosphate dehydrogenase proteins. This entry represents the N-terminal Rossmann like domain. 117 matched cddid_all.tbl CDD pfam10129 pfam10129 431075 OpgC_C OpgC protein. This domain, found in various hypothetical and OpgC prokaryotic proteins. It is likely to act as an acyltransferase enzyme. 358 matched cddid_all.tbl CDD pfam10130 pfam10130 370825 PIN_2 PIN domain. Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases). 132 matched cddid_all.tbl CDD pfam10131 pfam10131 401941 PTPS_related 6-pyruvoyl-tetrahydropterin synthase related domain; membrane protein. This domain is found in various bacterial hypothetical membrane proteins, as well as in tetratricopeptide TPR_2 repeat protein. The exact function of the domain has not, as yet, been established. 621 matched cddid_all.tbl CDD pfam10133 pfam10133 431076 CooT CO dehydrogenase accessory protein CooT. CooT is an accessory protein required for maturation of Carbon Monoxide Dehydrogenase (CODH). It is a member of a Ni(ii)-binding protein family, linked to anaerobic metabolism in bacteria and archaea, and in most cases to the presence of CODH. Structure analysis indicates that it is a homodimer featuring a fold that resembles an Sm-like domain. 59 matched cddid_all.tbl CDD pfam10134 pfam10134 431077 RPA Replication initiator protein A. Members of this family of bacterial proteins are single-stranded DNA binding proteins that are involved in DNA replication, repair and recombination. 229 matched cddid_all.tbl CDD pfam10135 pfam10135 431078 Rod-binding Rod binding protein. Members of this family are involved in the assembly of the prokaryotic flagellar rod. 50 matched cddid_all.tbl CDD pfam10136 pfam10136 431079 SpecificRecomb Site-specific recombinase. Members of this family are uncharacterized bacterial proteins which are thought to be putative site-specific recombinase, although there is no evidence supporting this and may be misannotated. Sequence analysis predict helical transmembrane domains and seem to be distantly related to formate/nitrate transporters, with structural similarity to aquaporins. This may suggest that, actually, they are associated with transporter activity. 640 matched cddid_all.tbl CDD pfam10137 pfam10137 431080 TIR-like Predicted nucleotide-binding protein containing TIR-like domain. Members of this family of bacterial nucleotide-binding proteins contain a TIR-like domain. Their exact function has not, as yet, been defined. 120 matched cddid_all.tbl CDD pfam10138 pfam10138 401947 vWA-TerF-like vWA found in TerF C terminus. vWA domain fused to TerD domain typified by the TerF protein. Some times found as solos. 200 matched cddid_all.tbl CDD pfam10139 pfam10139 431081 Virul_Fac Putative bacterial virulence factor. Members of this family of prokaryotic proteins include various putative virulence factor effector proteins. Their exact function is, as yet, unknown. 878 matched cddid_all.tbl CDD pfam10140 pfam10140 431082 YukC WXG100 protein secretion system (Wss), protein YukC. Members of this family of proteins include predicted membrane proteins homologous to YukC in B. subtilis. The YukC protein family would participate to the formation of a translocon required for the secretion of WXG100 proteins (pfam06013) in monoderm bacteria, the WXG100 protein secretion system (Wss). This family includes EssB in Staphylococcus aureus. 357 matched cddid_all.tbl CDD pfam10141 pfam10141 431083 ssDNA-exonuc_C Single-strand DNA-specific exonuclease, C terminal domain. Members of this set of prokaryotic domains are found in a set of single-strand DNA-specific exonucleases, including RecJ. Their exact function has not, as yet, been determined. 202 matched cddid_all.tbl CDD pfam10142 pfam10142 401951 PhoPQ_related PhoPQ-activated pathogenicity-related protein. Members of this family of bacterial proteins are involved in the virulence of some pathogenic proteobacteria. 366 matched cddid_all.tbl CDD pfam10143 pfam10143 462961 PhosphMutase 2,3-bisphosphoglycerate-independent phosphoglycerate mutase. This family represents 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGAM), a metalloenzyme found particularly in archaea and some eubacteria, which catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate in the reaction: [(2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate] (EC 5.4.2.12). 171 matched cddid_all.tbl CDD pfam10144 pfam10144 431085 SMP_2 Bacterial virulence factor haemolysin. Members of this family of bacterial proteins are membrane proteins that effect the expression of haemolysin under anaerobic conditions. 159 matched cddid_all.tbl CDD pfam10145 pfam10145 462962 PhageMin_Tail Phage-related minor tail protein. Members of this family are found in putative phage tail tape measure proteins. 201 matched cddid_all.tbl CDD pfam10146 pfam10146 462963 zf-C4H2 Zinc finger-containing protein. This is a family of proteins which appears to have a highly conserved zinc finger domain at the C terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members are annotated as being tumour-associated antigen HCA127 in humans but this could not confirmed. 213 matched cddid_all.tbl CDD pfam10147 pfam10147 431088 CR6_interact Growth arrest and DNA-damage-inducible proteins-interacting protein 1. Members of this family of proteins act as negative regulators of G1 to S cell cycle phase progression by inhibiting cyclin-dependent kinases. Inhibitory effects are additive with GADD45 proteins but occur also in the absence of GADD45 proteins. Furthermore, they act as a repressor of the orphan nuclear receptor NR4A1 by inhibiting AB domain-mediated transcriptional activity. 204 matched cddid_all.tbl CDD pfam10148 pfam10148 431089 SCHIP-1 Schwannomin-interacting protein 1. Members of this family are coiled coil protein involved in linking membrane proteins to the cytoskeleton. 233 matched cddid_all.tbl CDD pfam10149 pfam10149 462964 TM231 Transmembrane protein 231. This is a family of transmembrane proteins, given the number 231, of unknown function. It is conserved in eukaryotes. 300 matched cddid_all.tbl CDD pfam10150 pfam10150 462965 RNase_E_G Ribonuclease E/G family. Ribonuclease E and Ribonuclease G are related enzymes that cleave a wide variety of RNAs. 267 matched cddid_all.tbl CDD pfam10151 pfam10151 462966 TMEM214 TMEM214, C-terminal, caspase 4 activator. This is the N-terminal domain of transmembrane family 214, from eukaryotes. The family is localized on the endoplasmic reticulum where it recruits procaspase 4 to the ER and subsequently allows this to be cleaved to caspase 4 so leading to apoptosis. 661 matched cddid_all.tbl CDD pfam10152 pfam10152 462967 CCDC53 Subunit CCDC53 of WASH complex. CCDC53 is a component of the WASH complex, which plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting. 146 matched cddid_all.tbl CDD pfam10153 pfam10153 462968 Efg1 rRNA-processing protein Efg1. Efg1 is involved in rRNA processing. 114 matched cddid_all.tbl CDD pfam10154 pfam10154 431095 DUF2362 Uncharacterized conserved protein (DUF2362). This is a family of proteins conserved from nematodes to humans. The function is not known. 500 matched cddid_all.tbl CDD pfam10155 pfam10155 401964 CNOT11 CCR4-NOT transcription complex subunit 11. This is a family of unknown function found in eukaryotes. Family members include CNOT 11 a subunit of the CCR4-NOT. CNOT11 was shown to interact with the first amino acids of CNOT1 and with CNOT10 and to be required for the association of CNOT10 with the CCR4-NOT complex. 124 matched cddid_all.tbl CDD pfam10156 pfam10156 401965 Med17 Subunit 17 of Mediator complex. This Mediator complex subunit was formerly known as Srb4 in yeasts or Trap80 in Drosophila and human. The Med17 subunit is located within the head domain and is essential for cell viability to the extent that a mutant strain of cerevisiae lacking it shows all RNA polymerase II-dependent transcription ceasing at non-permissive temperatures. 441 matched cddid_all.tbl CDD pfam10157 pfam10157 462969 BORCS6 BLOC-1-related complex sub-unit 6 C-terminal helix. This is a family of conserved proteins found from nematodes to humans. Family members include BORCS6 (BLOC-1-related complex sub-unit 6) also known as Lyspersin (lysosome-dispersing protein) or C17orf59. It constitutes sub-unit 6 of the BORC complex (BLOC-one-related complex). BORC is a multisubunit complex that regulates the positioning of lysosomes at the cell periphery, and consequently affects cell migration. BORC associates with the lysosomal membrane, where it functions to recruit the small GTPase Arl8. This initiates a series of interactions that promote the microtubule-guided transport of lysosomes toward the cell periphery. this entry represents a C-terminal alpha helix according to structure predictions. 101 matched cddid_all.tbl CDD pfam10158 pfam10158 287167 LOH1CR12 Tumour suppressor protein. This is a region of 130 amino acids that is the most conserved region of hypothetical proteins involved in loss of heterozygosity and thus tumour suppression. The exact function of family members is not known. This region is also found in subunit 5 of the BLOC-1-related complex, which is also found in the BORC complex. BLOC-1 is important for the biogenesis of lysosome-related organelles, and BORC is important for the positioning of the lysosome in the cytoplasm. The BORC complex associates with the lysosomal membrane where it recruits the small GTPase Arl8, which leads in turn to the kinesin-dependent movement of lysosomes toward the plus ends of microtubules in the peripheral cytoplasm. 131 matched cddid_all.tbl CDD pfam10159 pfam10159 431097 MMtag Multiple myeloma tumor-associated. This is a glycine-rich domain that is the most highly conserved region of a family of proteins that in vertebrates are associated with tumours in multiple myelomas. The region may contain nuclear localization signals, so it might act as a signal molecule in the nucleus. 78 matched cddid_all.tbl CDD pfam10160 pfam10160 462970 Tmemb_40 Predicted membrane protein. This is a region of 280 amino acids from a group of proteins conserved from plants to humans. It is predicted to be a membrane protein but its function is otherwise unknown. 251 matched cddid_all.tbl CDD pfam10161 pfam10161 431099 DDDD Putative mitochondrial precursor protein. This is a family of small conserved proteins found from nematodes to humans. The C-terminal region is rich in asparagine. Members are putatively assigned to be mitochondrial precursor proteins but this could not be confirmed. 76 matched cddid_all.tbl CDD pfam10162 pfam10162 462971 G8 G8 domain. This domain is found in disease proteins PKHD1 and KIAA1199 and is named G8 after its 8 conserved glycines. It is predicted to contain 10 beta strands and an alpha helix. 121 matched cddid_all.tbl CDD pfam10163 pfam10163 462972 EnY2 Transcription factor e(y)2. EnY2 is a small transcription factor which is combined in a complex with the TAFII40 protein. The protein is conserved from paramecium to humans. 78 matched cddid_all.tbl CDD pfam10164 pfam10164 431102 BRI3 Brain protein I3. This is a highly conserved family of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N-terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein I3 (Bri3). Their function is unknown but they appear to play a role in TNF-induced cell death. 104 matched cddid_all.tbl CDD pfam10165 pfam10165 462973 Ric8 Guanine nucleotide exchange factor synembryn. Ric8 is involved in the EGL-30 neurotransmitter signalling pathway. It is a guanine nucleotide exchange factor that regulates neurotransmitter secretion. 412 matched cddid_all.tbl CDD pfam10166 pfam10166 431104 DUF2368 Uncharacterized conserved protein (DUF2368). This family is conserved from nematodes to humans. The function is not known. 134 matched cddid_all.tbl CDD pfam10167 pfam10167 462974 BORCS8 BLOC-1-related complex sub-unit 8. This is the N-terminal 80 residues of a family of proteins conserved from plants to humans. It contains a characteriztic NEP sequence motif. Family members include BORCS8 (BLOC-1-related complex sub-unit 8) also known as MEF2BNB. It constitutes sub-unit 8 of the BORC complex (BLOC-one-related complex). BORC is a multisubunit complex that regulates the positioning of lysosomes at the cell periphery, and consequently affects cell migration. BORC associates with the lysosomal membrane, where it functions to recruit the small GTPase Arl8. This initiates a series of interactions that promote the microtubule-guided transport of lysosomes toward the cell periphery. 107 matched cddid_all.tbl CDD pfam10168 pfam10168 462975 Nup88 Nuclear pore component. Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumour cells. 713 matched cddid_all.tbl CDD pfam10169 pfam10169 462976 Laps Learning-associated protein. This is a family of 121-amino acid secretory proteins. Laps functions in the regulation of neuronal cell adhesion and/or movement and synapse attachment. Laps binds to the ApC/EBP (Aplysia CCAAT/enhancer binding protein) promoter and activates the transcription of ApC/EBP mRNA. 124 matched cddid_all.tbl CDD pfam10170 pfam10170 431108 C6_DPF Cysteine-rich domain. This is the N-terminal approximately 100 amino acids of a family of proteins found from nematodes to humans. It contains between six and eight highly conserved cysteine residues and a characteriztic DPF sequence motif. One member is putatively named as receptor for egg jelly protein but this could not confirmed. 94 matched cddid_all.tbl CDD pfam10171 pfam10171 462977 Tim29 Translocase of the Inner Mitochondrial membrane 29. This is a family of proteins conserved from nematodes to humans. The function is not known. However, family members such as the import inner membrane translocase sub-unit Tim29 (C19orf52) found in human, is shown to be required for the stability of the TIM22 complex. TIM22 complex imports and inserts multi-pass trans-membrane proteins into the mitochondrial inner membrane by formation of a twin-pore translocase with components in the outer and inner membranes. TIM29 is integrated into the inner member with the C terminus exposed to the inter-membrane space and able to contact the translocase of the outer membrane. It is required for complex stability and for the addition of the TIMM22 protein to the complex. 163 matched cddid_all.tbl CDD pfam10172 pfam10172 401980 DDA1 Det1 complexing ubiquitin ligase. DDA1 (De-etiolated 1, Damaged DNA binding protein 1 associated 1) protein binds strongly with DDB1 and Det1 forming a DDD complex which is part of the ubiquitin conjugation system. 66 matched cddid_all.tbl CDD pfam10173 pfam10173 431110 Mit_KHE1 Mitochondrial K+-H+ exchange-related. The members of this family function as mitochondrial potassium-hydrogen exchange transporters. The family is part of a large mitochondrial KHE protein complex. 191 matched cddid_all.tbl CDD pfam10174 pfam10174 431111 Cast RIM-binding protein of the cytomatrix active zone. This is a family of proteins that form part of the CAZ (cytomatrix at the active zone) complex which is involved in determining the site of synaptic vesicle fusion. The C-terminus is a PDZ-binding motif that binds directly to RIM (a small G protein Rab-3A effector). The family also contains four coiled-coil domains. 766 matched cddid_all.tbl CDD pfam10175 pfam10175 462978 MPP6 M-phase phosphoprotein 6. This family represents the M-phase phosphoprotein 6 (MPP6) which is involved in the generation of the 3' end of the 5.8S rRNA precursor. MPP6 is required for the integrity maintenance of the rRNA processing complex as it mediates the interaction between MTR4 (RNA helicase) and RRP6 (an 3'-5' exonuclease), and the recruitment of Nuclear VCP-like 2 (NVL2) to the nuclear exosome. 131 matched cddid_all.tbl CDD pfam10176 pfam10176 401984 DUF2370 Protein of unknown function (DUF2370). This family is conserved from fungi to humans. The human member is annotated as a Golgi-associated protein-Nedd4 WW domain-binding protein but this could not be confirmed. 215 matched cddid_all.tbl CDD pfam10177 pfam10177 462979 DUF2371 Uncharacterized conserved protein (DUF2371). This is a family of proteins conserved from nematodes to humans. The function is not known. 141 matched cddid_all.tbl CDD pfam10178 pfam10178 462980 PAC3 Proteasome assembly chaperone 3. PAC3 is a family of eukaryotic proteasome assembly chaperone 3 proteins conserved from fungi to plants to humans. PAC3 plays a crucial part in the assembly of the 20S core proteasome unit, in conjunction with PAC4. 87 matched cddid_all.tbl CDD pfam10179 pfam10179 462981 NDNF Neuron-derived neurotrophic factor, first Fn(III) domain. This domain is found towards the N-terminal of Neuron-derived neurotrophic factor (NDNF) which contains the first fibronectin type III domain and one of the predicted N-linked glycosylation sites. NDNF is a glycosylated and disulfide-bonded secreted protein expressed in brain and spinal cord that promotes migration and neurite growth. It also promotes endothelial cell survival, vessel formation and plays an important role in the process of revascularization. 127 matched cddid_all.tbl CDD pfam10180 pfam10180 462982 WKF WKF domain. This is the C-terminal conserved region of a family of proteins found from fungi to humans. The domain is named WKF after a conserved sequence motif. This domain has been shown to bind RNA. This domain was previously known as DUF2373. 62 matched cddid_all.tbl CDD pfam10181 pfam10181 462983 PIG-H GPI-GlcNAc transferase complex, PIG-H component. PIG-H is a family of conserved proteins that complexes with three other proteins to form the GPI-GnT (glycosylphosphatidylinositol anchor biosynthesis transferase) complex. It appears to be a peripheral membrane protein facing the cytoplasm involved in the first step in GPI anchor formation. 67 matched cddid_all.tbl CDD pfam10182 pfam10182 401990 Flo11 Flo11 domain. This presumed domain is found at the N-terminus of the S. cerevisiae Flo11 protein. Flo11 is required for diploid pseudohyphal formation and haploid invasive growth. It belongs to a family of proteins involved in invasive growth, cell-cell adhesion, and mating, many of which can substitute for each other under abnormal conditions. 151 matched cddid_all.tbl CDD pfam10183 pfam10183 462984 ESSS ESSS subunit of NADH:ubiquinone oxidoreductase (complex I). This subunit is part of the mitochondrial NADH:ubiquinone oxidoreductase (complex I). It carries mitochondrial import sequences. 115 matched cddid_all.tbl CDD pfam10184 pfam10184 370865 DUF2358 Uncharacterized conserved protein (DUF2358). DUF2358 is a family of conserved proteins found from plants to humans. The function is unknown. 113 matched cddid_all.tbl CDD pfam10185 pfam10185 462985 Mesd Chaperone for wingless signalling and trafficking of LDL receptor. Mesd is a family of highly conserved proteins found from nematodes to humans. The final C-terminal residues, KEDL, are the endoplasmic reticulum retention sequence as it is an ER protein specifically required for the intracellular trafficking of members of the low-density lipoprotein family of receptors (LDLRs). The N- and C-terminal sequences are predicted to adopt a random coil conformation, with the exception of an isolated predicted helix within the N-terminal region, The central folded domain flanked by natively unstructured regions is the necessary structure for facilitating maturation of LRP6 (Low-Density Lipoprotein Receptor-Related Protein 6 Maturation). 155 matched cddid_all.tbl CDD pfam10186 pfam10186 462986 ATG14 Vacuolar sorting 38 and autophagy-related subunit 14. The Atg14 or Apg14 proteins are hydrophilic proteins with a predicted molecular mass of 40.5 kDa, and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole. Subcellular fractionation indicate that Apg14p and Apg6p are peripherally associated with a membrane structure(s). Apg14p was co-immunoprecipitated with Apg6p, suggesting that they form a stable protein complex. These results imply that Apg6/Vps30p has two distinct functions: in the autophagic process and in the vacuolar protein sorting pathway. Apg14p may be a component specifically required for the function of Apg6/Vps30p through the autophagic pathway. There are 17 auto-phagosomal component proteins which are categorized into six functional units, one of which is the AS-PI3K complex (Vps30/Atg6 and Atg14). The AS-PI3K complex and the Atg2-Atg18 complex are essential for nucleation, and the specific function of the AS-PI3K apparently is to produce phosphatidylinositol 3-phosphate (PtdIns(3)P) at the pre-autophagosomal structure (PAS). The localization of this complex at the PAS is controlled by Atg14. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. This effect seems to be mediated through direct interaction of the human Atg14 with Beclin 1 in the human phosphatidylinositol 3-kinase class III complex. 347 matched cddid_all.tbl CDD pfam10187 pfam10187 462987 FAM192A_Fyv6_N FAM192A/Fyv6, N-terminal domain. This is a the N-terminal domain of the mammalian PIP30/FAM192A protein and the fungal Fyv6 protein. PIP30/FAM192A acts as a regulator PA28-gamma, a nuclear activator of the 20S proteasome. PIP30 favors PA28-gamma interaction with the 20S proteasome while inhibiting its association with coilin, a central component of nuclear Cajal bodies. Fyv6 is involved in telomere length regulation and required for survival upon exposure to K1 killer toxin. It promotes fully efficient non-homologous end-joining (NHEJ) by a mechanism activated in postdiauxic/stationary phase. 102 matched cddid_all.tbl CDD pfam10188 pfam10188 431122 Oscp1 Organic solute transport protein 1. Oscp1 is a family of proteins conserved from plants to humans. It is called organic solute transport protein or oxido-red- nitro domain-containing protein 1, however no reference could be find to confirm the function of the protein. 173 matched cddid_all.tbl CDD pfam10189 pfam10189 431123 Ints3_N Integrator complex subunit 3 N-terminal. The Integrator complex is involved in small nuclear RNA (snRNA) U1 and U2 transcription, and in their 3'-box-dependent processing. This complex associates with the C-terminal domain of RNA polymerase II largest subunit and is recruited to the U1 and U2 snRNAs genes. This entry represents the N-terminal domain of the Integrator complex subunit 3 (Ints3), also known as SOSS complex subunit A (SOSSA). It is a component of the sensor of single-stranded DNA complex (SOSS), which associates with single-stranded DNA, important for DNA repair and efficient homologous recombination. This subunit serves as a central adaptor for SOSS complex assembly and stability, and facilitates the accumulation of the complex to the sites of DNA damage. This region acts as a scaffold for SOSSB1 and SOSSC interaction and it is not essential for ssDNA binding. 409 matched cddid_all.tbl CDD pfam10190 pfam10190 462988 Tmemb_170 Putative transmembrane protein 170. Tmem170 is a family of putative transmembrane proteins conserved from fungi to nematodes to humans. The protein is only of approximately 130 amino acids in length. The function is unknown. 106 matched cddid_all.tbl CDD pfam10191 pfam10191 431125 COG7 Golgi complex component 7 (COG7). COG7 is a component of the conserved oligomeric Golgi complex which is required for normal Golgi morphology and localization. Mutation in COG7 causes a congenital disorder of glycosylation. 772 matched cddid_all.tbl CDD pfam10192 pfam10192 462989 GpcrRhopsn4 Rhodopsin-like GPCR transmembrane domain. This region of 270 amino acids is the seven transmembrane alpha-helical domains included within five GPCRRHODOPSN4 motifs of a G-protein-coupled-receptor (GPCR) protein, conserved from nematodes to humans. GPCRs are integral membrane receptors whose intracellular actions are mediated by signalling pathways involving G proteins and downstream secondary messengers. 257 matched cddid_all.tbl CDD pfam10193 pfam10193 462990 Telomere_reg-2 Telomere length regulation protein. This family is the central conserved 110 amino acid region of a group of proteins called telomere-length regulation or clock abnormal protein-2 which are conserved from plants to humans. The full-length protein regulates telomere length and contributes to silencing of sub-telomeric regions. In vitro the protein binds to telomeric DNA repeats. 112 matched cddid_all.tbl CDD pfam10195 pfam10195 462991 Phospho_p8 DNA-binding nuclear phosphoprotein p8. P8 is a short 80-82 amino acid protein that is conserved from nematodes to humans. It carries at least one protein kinase C domain suggesting a possible role in signal transduction and it is thought to be a phosphoprotein, but the sites of phosphorylation and the kinases involved remain to be determined. 58 matched cddid_all.tbl CDD pfam10197 pfam10197 462992 Cir_N N-terminal domain of CBF1 interacting co-repressor CIR. This is a 45 residue conserved region at the N-terminal end of a family of proteins referred to as CIRs (CBF1-interacting co-repressors). CBF1 (centromere-binding factor 1) acts as a transcription factor that causes repression by binding specifically to GTGGGAA motifs in responsive promoters, and it requires CIR as a co-repressor. CIR binds to histone deacetylase and to SAP30 and serves as a linker between CBF1 and the histone deacetylase complex. 37 matched cddid_all.tbl CDD pfam10198 pfam10198 462993 Ada3 Histone acetyltransferases subunit 3. Ada3 is a family of proteins conserved from yeasts to humans. It is an essential component of the Ada transcriptional coactivator (alteration/deficiency in activation) complex. Ada3 plays a key role in linking histone acetyltransferase-containing complexes to p53 (tumour suppressor protein) thereby regulating p53 acetylation, stability and transcriptional activation following DNA damage. 123 matched cddid_all.tbl CDD pfam10199 pfam10199 462994 Adaptin_binding Alpha and gamma adaptin binding protein p34. p34 is a protein involved in membrane trafficking. It is known to interact with both alpha and gamma adaptin. It has been speculated that p34 may play a chaperone role such as preventing the soluble adaptors from co-assembling with soluble clathrin, or helping to remove the adaptors from the coated vesicle. Another possible function is in aiding the recruitment of soluble adaptors onto the membrane. 96 matched cddid_all.tbl CDD pfam10200 pfam10200 431131 Ndufs5 NADH:ubiquinone oxidoreductase, NDUFS5-15kDa. This is a family of short, approximately 105 amino acid residue, proteins which form part of NADH:ubiquinone oxidoreductase complex I. Complex I is the first multisubunit inner membrane protein complex of the mitochondrial electron transport chain and it transfers two electrons from NADH to ubiquinone. The protein carries four highly conserved cysteine residues but these do not appear to be in a configuration which would favour metal binding so the exact function of the protein is uncertain. 96 matched cddid_all.tbl CDD pfam10203 pfam10203 402002 Pet191_N Cytochrome c oxidase assembly protein PET191. Pet191_N is the conserved N-terminal of a family of conserved proteins found from nematodes to humans. It carries six highly conserved cysteine residues. Pet191 is required for the assembly of active cytochrome c oxidase but does not form part of the final assembled complex. 67 matched cddid_all.tbl CDD pfam10204 pfam10204 462995 DuoxA Dual oxidase maturation factor. DuoxA (Dual oxidase maturation factor) is the essential protein necessary for the final release of DUOX2 (an NADPH:O2 oxidoreductase flavoprotein) from the endoplasmic reticulum. Dual oxidases (DUOX1 and DUOX2) constitute the catalytic core of the hydrogen peroxide generator, which generates H2O2 at the apical membrane of thyroid follicular cells, essential for iodination of thyroglobulin by thyroid peroxidases. DuoxA carries five membrane-integral regions including a reverse signal-anchor with external N-terminus (type III) and two N-glycosylation sites. It is conserved from nematodes to humans. 277 matched cddid_all.tbl CDD pfam10205 pfam10205 462996 KLRAQ Predicted coiled-coil domain-containing protein. This is the N-terminal 100 amino acid domain of a family of proteins conserved from nematodes to humans. It carries a characteriztic KLRAQ sequence-motif. The function is not known. 105 matched cddid_all.tbl CDD pfam10206 pfam10206 431134 WRW Mitochondrial F1F0-ATP synthase, subunit f. This is a family of small proteins of approximately 110 amino acids, which are highly conserved from nematodes to humans. Some members of the family have been annotated in Swiss-Prot as being the f subunit of mitochondrial F1F0-ATP synthase but this could not be confirmed. The sequence has a well-conserved WRW motif. The exact function of the protein is not known. 102 matched cddid_all.tbl CDD pfam10208 pfam10208 462997 ARMET_C ARMET, C-terminal. This is the C-terminal domain of ARMET (also known as mesencephalic astrocyte-derived neurotrophic factor (MANF) or arginine-rich protein). This domain is well conserved among Armet family proteins whose structure is composed of a basic-helix-loop-helix (bHLH) motif. ARMET is a small protein of approximately 170 residues. It is soluble protein resident in the endoplasmic reticulum and induced by ER stress. It appears to be involved with dealing with mis-folded proteins in the ER, thus in quality control of ER stress. 43 matched cddid_all.tbl CDD pfam10209 pfam10209 462998 DUF2340 Uncharacterized conserved protein (DUF2340). This is a family of small proteins of approximately 150 amino acids of unknown function. 120 matched cddid_all.tbl CDD pfam10210 pfam10210 462999 MRP-S32 Mitochondrial 28S ribosomal protein S32. This entry is of a family of short, approximately 100 amino acid residues, proteins which are mitochondrial 28S ribosomal proteins named as MRP-S32. Their exact function could not be confirmed. 91 matched cddid_all.tbl CDD pfam10211 pfam10211 463000 Ax_dynein_light Axonemal dynein light chain. Axonemal dynein light chain proteins play a dynamic role in flagellar and cilia motility. Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organizms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains. 187 matched cddid_all.tbl CDD pfam10212 pfam10212 463001 TTKRSYEDQ Predicted coiled-coil domain-containing protein. This is the C-terminal 500 amino acids of a family of proteins with a predicted coiled-coil domain conserved from nematodes to humans. It carries a characteriztic TTKRSYEDQ sequence-motif. The function is not known. 523 matched cddid_all.tbl CDD pfam10213 pfam10213 463002 MRP-S28 Mitochondrial ribosomal subunit protein. This is a conserved region of approx. 125 residues of one of the proteins that makes up the small subunit of the mitochondrial ribosome. In Saccharomyces cerevisiae the protein is MRP-S24 whereas in humans it is MRP-S28. The human mitochondrial ribosome has 29 distinct proteins in the small subunit and these have homologs in, for example, Drosophila melanogaster, Caenorhabditis elegans, and in the genomes of several fungi. 126 matched cddid_all.tbl CDD pfam10214 pfam10214 431141 Rrn6 RNA polymerase I-specific transcription-initiation factor. RNA polymerase I-specific transcription-initiation factor Rrn6 and Rrn7 represent components of a multisubunit transcription factor essential for the initiation of rDNA transcription by Pol I. These proteins are found in fungi. 846 matched cddid_all.tbl CDD pfam10215 pfam10215 431142 Ost4 Oligosaccaryltransferase. Ost4 is a very short, approximately 30 residues, enzyme found from fungi to vertebrates. It is a member of the ER oligosaccaryltansferase complex, EC 2.4.1.119, that catalyzes the asparagine-linked glycosylation of proteins. It appears to be an integral membrane protein that mediates the en bloc transfer of a preassembled high-mannose oligosaccharide onto asparagine residues of nascent polypeptides as they enter the lumen of the rough endoplasmic reticulum (RER). 34 matched cddid_all.tbl CDD pfam10216 pfam10216 431143 ChpXY CO2 hydration protein (ChpXY). This small family of proteins includes paralogues ChpX and ChpY in Synechococcus sp. PCC7942 and other cyanobacteria, associated with distinct NAD(P)H dehydrogenase complexes. These proteins collectively enable light-dependent CO2 hydration and CO2 uptake; loss of both blocks growth at low CO2 concentrations. 352 matched cddid_all.tbl CDD pfam10217 pfam10217 463003 DUF2039 Uncharacterized conserved protein (DUF2039). This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown. 89 matched cddid_all.tbl CDD pfam10218 pfam10218 463004 SPRING1 SREBP regulating gene protein. SPRING1 is a glycosylated Golgi-resident membrane protein involved in SREBP signaling and cholesterol metabolism. It modulates the proper localization of SCAP (SREBP cleavage-activating protein) to the endoplasmic reticulum, thereby controlling the level of functional SCAP. 128 matched cddid_all.tbl CDD pfam10220 pfam10220 463005 Smg8_Smg9 Smg8_Smg9. Smg8 and Smg9 are two subunits of the Smg-1 complex. They suppress Smg-1 kinase activity in the isolated Smg-1 complex, and are involved in nonsense-mediated mRNA decay (NMD) in both mammals and nematodes. 883 matched cddid_all.tbl CDD pfam10221 pfam10221 463006 Mat89Bb Cell cycle and development regulator Mat89Bb. This is entry represents the cell cycle regulator Mat89b (also known as protein asunder), which plays an evolutionarily conserved role as a crucial regulator of both cell cycle and development. It is a component of INT (Integrator) complex, being involved in the 3'-end processing of the U7 snRNA, and also the spliceosomal snRNAs U1 and U5. Mat89Bb is also required for the correct dynein-dynactin perinuclear localization. Mat89Bb is a PNG kinase substrate, that is essential for S-M cycles of early Drosophila embryogenesis, Xenopus embryonic cell cycles and morphogenesis, and cell division in cultured mammalian cells. 683 matched cddid_all.tbl CDD pfam10222 pfam10222 431148 DUF2152 Uncharacterized conserved protein (DUF2152). This is a family of proteins conserved from worms to humans. Its function is unknown. 593 matched cddid_all.tbl CDD pfam10223 pfam10223 463007 DUF2181 Uncharacterized conserved protein (DUF2181). This is region of approximately 250 residues conserved from worms to humans. Its function is unknown. 241 matched cddid_all.tbl CDD pfam10224 pfam10224 431150 DUF2205 Short coiled-coil protein. This entry represents a highly conserved 100 residue coiled-coil region which is found in short coiled-coil protein (SCOC) in human and UNC-69 in Caenorhabditis elegans. In human, SCOC is required for autophagosome formation during amino acid starvation. It forms a starvation-sensitive trimeric complex with UVRAG (UV radiation resistance associated gene) and FEZ1 and may regulate ULK1 and Beclin 1 complex activities. In C. elegans, this small, evolutionarily conserved coiled-coil domain-containing protein, UNC-69, acts as a binding partner of UNC-76. Together they participate in a common genetic pathway necessary for axon extension and cooperate to regulate the size and position of synaptic vesicles in axons. Moreover, both proteins colocalize as puncta in neuronal processes and mutations in UNC-69 preferentially disrupt membrane traffic within axons. 71 matched cddid_all.tbl CDD pfam10225 pfam10225 463008 NEMP NEMP family. This entry includes a group of nuclear envelope integral membrane proteins from animals and plants, including NEMP1 from Xenopus laevis. NEMP1 is a RanGTP-binding protein and is involved in eye development. 249 matched cddid_all.tbl CDD pfam10226 pfam10226 463009 CCDC85 CCDC85 family. This entry includes human CCDC85A/B/C and C. elegans Picc-1 protein. Picc-1 serves as a linker protein which helps to recruit the Rho GTPase-activating protein, pac-1, to adherens junctions. Human CCDC85B suppresses the beta-catenin activity in a p53-dependent manner. 192 matched cddid_all.tbl CDD pfam10228 pfam10228 463010 DUF2228 Uncharacterized conserved protein (DUF2228). This is a family of conserved proteins of approximately 700 residues found from worms to humans. 251 matched cddid_all.tbl CDD pfam10229 pfam10229 431154 MMADHC Methylmalonic aciduria and homocystinuria type D protein. This entry represents methylmalonic aciduria and homocystinuria type D protein and homologs. These proteins are involved in cobalamin (vitamin B12) metabolism. 272 matched cddid_all.tbl CDD pfam10230 pfam10230 370901 LIDHydrolase Lipid-droplet associated hydrolase. This family of proteins is conserved from plants to humans. The function is as a lipid-droplet hydrolase. Human LDAH plays a role in cholesterol homeostasis. 261 matched cddid_all.tbl CDD pfam10231 pfam10231 463011 COA8 Cytochrome c oxidase assembly factor 8. Apoptogenic protein 1 (Apop1, also known as cytochrome c oxidase assembly factor 8), previously thought to induce apoptosis through the Cyclophilin-D-dependent pathway, is required for cytochrome c oxidase (COX) assembly and function. Apop1 is controlled by the ubiquitination-proteasome system (UPS). In Drosophila melanogaster, Apop1 is also involved in neurological impairment, COX enzymatic activity, and resistance to oxidative stress conditions. 119 matched cddid_all.tbl CDD pfam10232 pfam10232 463012 Med8 Mediator of RNA polymerase II transcription complex subunit 8. Arc32, or Med8, is one of the subunits of the Mediator complex of RNA polymerase II. The region conserved contains two alpha helices putatively necessary for binding to other subunits within the core of the Mediator complex. The N-terminus of Med8 binds to the essential core Head part of Mediator and the C-terminus hinges to Med18 on the non-essential part of the Head that also includes Med20. 230 matched cddid_all.tbl CDD pfam10233 pfam10233 431157 Cg6151-P Uncharacterized conserved protein CG6151-P. This is a family of small, less than 200 residue long, proteins which are named as CG6151-P proteins that are conserved from fungi to humans. The function is unknown. The fungal members have a characteriztic ICP sequence motif. Some members are annotated as putative clathrin-coated vesicle protein but this could not be defined. 113 matched cddid_all.tbl CDD pfam10234 pfam10234 463013 Cluap1 Clusterin-associated protein-1. This protein is conserved from worms to humans. The protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell. 268 matched cddid_all.tbl CDD pfam10235 pfam10235 431159 Cript Microtubule-associated protein CRIPT. The CRIPT protein is a cytoskeletal protein involved in microtubule production. The C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners. SAP90 is concentrated in the post synaptic density of glutamatergic neurons. 87 matched cddid_all.tbl CDD pfam10236 pfam10236 431160 DAP3 Mitochondrial ribosomal death-associated protein 3. This is a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29). 310 matched cddid_all.tbl CDD pfam10237 pfam10237 463014 N6-adenineMlase Probable N6-adenine methyltransferase. This is a protein of approximately 200 residues which is conserved from plants to humans. It contains a highly conserved QFW motif close to the N-terminus and a DPPF motif in the centre. The DPPF motif is characteriztic of N-6 adenine-specific DNA methylases, and this family is found in eukaryotes. 118 matched cddid_all.tbl CDD pfam10238 pfam10238 463015 Eapp_C E2F-associated phosphoprotein. This entry represents the conserved C-terminal portion of an E2F binding protein. E2F transcription factors play an essential role in cell proliferation and apoptosis and their activity is frequently deregulated in human cancers. E2F activity is regulated by a variety of mechanisms, frequently mediated by proteins binding to individual members or a subgroup of the family. EAPP interacts with a subset of E2F factors and influences E2F-dependent promoter activity. EAPP is present throughout the cell cycle but disappears during mitosis. 133 matched cddid_all.tbl CDD pfam10239 pfam10239 463016 DUF2465 Protein of unknown function (DUF2465). FAM98A and B proteins are found from worms to humans but their function is unknown. This entry is of a family of proteins that is rich in glycines. 302 matched cddid_all.tbl CDD pfam10240 pfam10240 463017 DUF2464 Multivesicular body subunit 12. MVB12A (also known as CFBP) and MVB12B are subunits of the ESCRT-I complex, which mediates the sorting of ubiquitinated cargo protein from the plasma membrane to the endosomal vesicle. MVB12A plays a key role in the ligand-mediated internalization and down-regulation of the EGF receptor. 255 matched cddid_all.tbl CDD pfam10241 pfam10241 463018 KxDL Uncharacterized conserved protein. This is a family of short proteins which are conserved over a region of 80 residues. There is a characteriztic KxDL motif towards the C-terminus. The function is unknown. 80 matched cddid_all.tbl CDD pfam10242 pfam10242 463019 L_HMGIC_fpl Lipoma HMGIC fusion partner-like protein. This is a group of proteins expressed from a series of genes referred to as Lipoma HMGIC fusion partner-like. The proteins carry four highly conserved transmembrane domains in this entry. In certain instances, eg in LHFPL5, mutations cause deafness in humans and hypospadias, and LHFPL1 is transcribed in six liver tumour cell lines. 176 matched cddid_all.tbl CDD pfam10243 pfam10243 463020 MIP-T3 Microtubule-binding protein MIP-T3 CH-like domain. This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. 113 matched cddid_all.tbl CDD pfam10244 pfam10244 463021 MRP-L51 Mitochondrial ribosomal subunit. MRP-L51 is a family of small proteins from the intact 55 S mitochondrial ribosome. It has otherwise been referred to as bMRP-64. The exact function of this family is not known. 93 matched cddid_all.tbl CDD pfam10245 pfam10245 431167 MRP-S22 Mitochondrial 28S ribosomal protein S22. This is the conserved N-terminus and central portion of the mitochondrial small subunit 28S ribosomal protein S22. Mammalian mitochondria carry out the synthesis of 13 polypeptides that are essential for oxidative phosphorylation and, hence, for the synthesis of the majority of the ATP used by eukaryotic organizms. The number of proteins produced by prokaryotes is smaller, reflected in the lower number of ribosomal proteins present in them. 241 matched cddid_all.tbl CDD pfam10246 pfam10246 402037 MRP-S35 Mitochondrial ribosomal protein MRP-S35. This is a family of short mitochondrial ribosomal proteins, less than 200 amino acids long. that are highly conserved from worms to humans. The structure has previously been referred to as MRP-S18 but the current numbering fits the preferred nomenclature from these authors. 105 matched cddid_all.tbl CDD pfam10247 pfam10247 431168 Romo1 Reactive mitochondrial oxygen species modulator 1. This is a family of small, approximately 100 amino acid, proteins found from yeasts to humans. The majority of endogenous reactive oxygen species (ROS) in cells are produced by the mitochondrial respiratory chain. An increase or imbalance in ROS alters the intracellular redox homeostasis, triggers DNA damage, and may contribute to cancer development and progression. Members of this family are mitochondrial reactive oxygen species modulator 1 (Romo1) proteins that are responsible for increasing the level of ROS in cells. Increased Romo1 expression can have a number of other effects including: inducing premature senescence of cultured human fibroblasts.and increased resistance to 5-fluorouracil. 66 matched cddid_all.tbl CDD pfam10248 pfam10248 463022 Mlf1IP Myelodysplasia-myeloid leukemia factor 1-interacting protein. This entry is the conserved central region of a group of proteins that are putative transcriptional repressors. The structure contains a putative 14-3-3 binding motif involved in the subcellular localization of various regulatory molecules, and it may be that interaction with the transcription factor DREF could be regulated through this motif. DREF regulates proliferation-related genes in Drosophila. Mlf1IP is expressed in both the nuclei and the cytoplasm and thus may have multi-functions. 174 matched cddid_all.tbl CDD pfam10249 pfam10249 431170 NDUFB10 NADH-ubiquinone oxidoreductase subunit 10. NDUFB10 is a family of conserved proteins of up to 180 residues. It is one of the 41 protein subunits within the hydrophobic fraction of the NADH:ubiquinone oxidoreductase (complex I), a multiprotein complex located in the inner mitochondrial membrane whose main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. NDUFB10 is encoded in the nucleus. 126 matched cddid_all.tbl CDD pfam10250 pfam10250 463023 O-FucT GDP-fucose protein O-fucosyltransferase. This is a family of conserved proteins representing the enzyme responsible for adding O-fucose to EGF (epidermal growth factor-like) repeats. Six highly conserved cysteines are present in O-FucT-1 as well as a DXD-like motif (ERD), conserved in mammals, Drosophila, and C. elegans. Both features are characteriztic of several glycosyltransferase families. The enzyme is a membrane-bound protein released by proteolysis and, as for most glycosyltransferases, is strongly activated by manganese. 247 matched cddid_all.tbl CDD pfam10251 pfam10251 463024 PEN-2 Presenilin enhancer-2 subunit of gamma secretase. This entry is a short 101 peptide protein which is the smallest subunit of the gamma-secretase aspartyl protease complex that catalyzes the intramembrane cleavage of a subset of type I transmembrane proteins. The other active constituents of the complex are presenilin (PS) nicastrin and anterior pharynx defective-1 (APH-1) protein. PEN-2 adopts a hairpin orientation in the membrane with its N- and C-terminal domains facing the luminal/extracellular space, and the C-terminal domain maintains PS stability within the complex. 93 matched cddid_all.tbl CDD pfam10252 pfam10252 463025 PP28 Casein kinase substrate phosphoprotein PP28. This domain is a region of 70 residues conserved in proteins from plants to humans and contains a serine/arginine rich motif. In rats the full protein is a casein kinase substrate, and this region contains phosphorylation sites for both cAMP-dependent protein kinase and casein kinase II. 80 matched cddid_all.tbl CDD pfam10253 pfam10253 463026 PRCC Mitotic checkpoint regulator, MAD2B-interacting. This family constitutes the major, conserved, portion of PRCC proteins. In humans this family interacts with MAD2B, the mitotic checkpoint protein. In Schizosaccharomyces pombe this protein is part of the Cwf-complex that is known to be involved in pre-mRNA splicing. 205 matched cddid_all.tbl CDD pfam10254 pfam10254 463027 Pacs-1 PACS-1 cytosolic sorting protein. PACS-1 is a cytosolic sorting protein that directs the localization of membrane proteins in the trans-Golgi network (TGN)/endosomal system. PACS-1 connects the clathrin adaptor AP-1 to acidic cluster sorting motifs contained in the cytoplasmic domain of cargo proteins such as furin, the cation-independent mannose-6-phosphate receptor and in viral proteins such as human immunodeficiency virus type 1 Nef. 416 matched cddid_all.tbl CDD pfam10255 pfam10255 463028 Paf67 RNA polymerase I-associated factor PAF67. RNA polymerase I is a multisubunit enzyme and its transcription competence is dependent on the presence of PAF67. This family of proteins is conserved from worms to humans. 399 matched cddid_all.tbl CDD pfam10256 pfam10256 463029 Erf4 Golgin subfamily A member 7/ERF4 family. This family of proteins includes Golgin subfamily A member 7 proteins as well as Ras modification protein ERF4. 116 matched cddid_all.tbl CDD pfam10257 pfam10257 370927 RAI16-like Retinoic acid induced 16-like protein. This is the conserved N-terminal 450 residues of a family of proteins described as retinoic acid-induced protein 16-like proteins. The exact function is not known. The proteins are found from worms to humans. 357 matched cddid_all.tbl CDD pfam10258 pfam10258 463030 PHAX_RNA-bd Phosphorylated adapter RNA export protein, RNA-binding domain. The phosphorylated adaptor for RNA export (PHAX) protein transports U3 snoRNA from the nucleus after transcription. This entry represents the highly conserved U3 snoRNA-binding domain of PHAX, which is characterized by having two pairs of adjacent glycines with the sequence motif GGx12GG. This domain adopts a novel helical fold and binds non-specific single-stranded RNA and comprises five alpha-helices linked by short loops containing 1 to 4 residues, apart from helices alpha3 and 4 that are linked by 13 residues. The fold is unique to this kind of RNA binding domains which show no structural homology with other RNA-binding domains. 84 matched cddid_all.tbl CDD pfam10259 pfam10259 463031 Rogdi_lz Rogdi leucine zipper containing protein. This is a family of conserved proteins which have been suggested as containing leucine-zipper domains. A leucine zipper domain is a region of 30 amino acids with leucines repeating every seven or eight residues; these proteins do have many such leucines. The protein in Drosophila comes from the gene ROGDI. 290 matched cddid_all.tbl CDD pfam10260 pfam10260 431179 SAYSvFN Uncharacterized conserved domain (SAYSvFN). This domain of approximately 75 residues contains a highly conserved SATSv/iFN motif. The function is unknown but the domain is conserved from plants to humans. 70 matched cddid_all.tbl CDD pfam10261 pfam10261 402051 Scs3p Inositol phospholipid synthesis and fat-storage-inducing TM. This is a family of transmembrane proteins which are variously annotated as possibly being inositol phospholipid synthesis protein and fat-storage-inducing. The members are conserved from yeasts to humans and are localized to the endoplasmic reticulum where they are involved in triglyceride lipid droplet formation. 242 matched cddid_all.tbl CDD pfam10262 pfam10262 463032 Rdx Rdx family. This entry is an approximately 100 residue region of selenoprotein-T, conserved from plants to humans. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins, including selenoprotein T. However, despite its binding to UGTR and that its mRNA is up-regulated in extended asphyxia, the function of the protein and hence of this region of it is unknown. Selenoprotein W contains selenium as selenocysteine in the primary protein structure and levels of this selenoprotein are affected by selenium. 74 matched cddid_all.tbl CDD pfam10263 pfam10263 463033 SprT-like SprT-like family. This family represents a domain found in eukaryotes and prokaryotes. The domain contains a characteriztic motif of the zinc metallopeptidases. This family includes the bacterial SprT protein. 106 matched cddid_all.tbl CDD pfam10264 pfam10264 431182 Stork_head Winged helix Storkhead-box1 domain. This is the conserved N-terminal winged helix domain of Storkhead-box1 protein which is likely to be a DNA binding domain. In humans the full-length protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia. 79 matched cddid_all.tbl CDD pfam10265 pfam10265 463034 Miga Mitoguardin. Mitoguardin (Miga) was first identified in flies as a mitochondrial outer-membrane protein that promotes mitochondrial fusion. Later, the mammalian Miga homologs, Miga1 and Miga2, were identified. They are found to promote mitochondrial fusion by regulating mitochondrial phospholipid metabolism via MitoPLD. 532 matched cddid_all.tbl CDD pfam10266 pfam10266 463035 Strumpellin Hereditary spastic paraplegia protein strumpellin. This is a family of proteins conserved from plants to humans, in which two closely situated point mutations in the human protein lead to the condition of hereditary spastic paraplegia. Strumpellin contains one known domain called a spectrin repeat that consists of three alpha-helices of a characteriztic length wrapped in a left-handed coiled coil. The spectrin proteins have multiple copies of this repeat, which can then form multimers in the cell. Spectrin associates with the cell membrane via spectrin repeats in the ankyrin protein. The spectrin repeat is a structural platform for cytoskeletal protein assemblies. 1082 matched cddid_all.tbl CDD pfam10267 pfam10267 463036 Tmemb_cc2 Predicted transmembrane and coiled-coil 2 protein. This family of transmembrane coiled-coil containing proteins is conserved from worms to humans. Its function is unknown. 401 matched cddid_all.tbl CDD pfam10268 pfam10268 463037 Tmemb_161AB Predicted transmembrane protein 161AB. Transmemb_161AB is a family of conserved proteins found from worms to humans. Members are putative transmembrane proteins but otherwise the function is not known. 469 matched cddid_all.tbl CDD pfam10269 pfam10269 402059 Tmemb_185A Transmembrane Fragile-X-F protein. This is a family of conserved transmembrane proteins that appear in humans to be expressed from a region upstream of the FragileXF site and to be intimately linked with the Fragile-X syndrome. Absence of TMEM185A does not necessarily lead to developmental delay, but might in combination with other, yet unknown, factors. Otherwise, the lack of the TMEM185A protein is either disposable (redundant) or its function can be complemented by the highly similar chromosome 2 retro-pseudogene product, TMEM185B. 245 matched cddid_all.tbl CDD pfam10270 pfam10270 431186 MMgT Membrane magnesium transporter. This entry represents a novel family of membrane magnesium transporters (MMgT). The proteins, MMgT1 and MMgT2, are localized to the Golgi complex and post-Golgi vesicles, including the early endosomes, suggesting that they may provide regulated pathways for Mg(2+) transport in the Golgi and post-Golgi organelles of epithelium-derived cells. 117 matched cddid_all.tbl CDD pfam10271 pfam10271 463038 Tmp39 Putative transmembrane protein. This is a family of conserved proteins found from worms to humans. They are putative transmembrane proteins but the function is unknown. 426 matched cddid_all.tbl CDD pfam10272 pfam10272 463039 Tmpp129 Putative transmembrane protein precursor. This is a family of proteins conserved from worms to humans. The proteins are purported to be transmembrane protein-precursors but the function is unknown. 350 matched cddid_all.tbl CDD pfam10273 pfam10273 463040 WGG Pre-rRNA-processing protein TSR2. This entry represents the central conserved section of a family of proteins described as pre-rRNA-processing protein TSR2. The region has a distinctive WGG motif but the function is unknown. 80 matched cddid_all.tbl CDD pfam10274 pfam10274 431190 ParcG Parkin co-regulated protein. This family of proteins is transcribed anti-sense along the DNA to the Parkin gene product and the two appear to be transcribed under the same promoter. The protein has predicted alpha-helical and beta-sheet domains which suggest its function is in the ubiquitin/proteasome system. Mutations in parkin are the genetic cause of early-onset and autosomal recessive juvenile parkinsonism. 183 matched cddid_all.tbl CDD pfam10275 pfam10275 431191 Peptidase_C65 Peptidase C65 Otubain. This family of proteins conserved from plants to humans is a highly specific ubiquitin iso-peptidase that removes ubiquitin from proteins. The modification of cellular proteins by ubiquitin (Ub) is an important event that underlies protein stability and function in eukaryote being a dynamic and reversible process. Otubain carries several key conserved domains: (i) the OTU (ovarian tumour domain) in which there is an active cysteine protease triad (ii) a nuclear localization signal, (iii) a Ub interaction motif (UIM)-like motif phi-xx-A-xxxs-xx-Ac (where phi indicates an aromatic amino acid, x indicates any amino acid and Ac indicates an acidic amino acid), (iv) a Ub-associated (UBA)-like domain and (v) the LxxLL motif. 240 matched cddid_all.tbl CDD pfam10276 pfam10276 463041 zf-CHCC Zinc-finger domain. This is a short zinc-finger domain conserved from fungi to humans. It is Cx8Hx14Cx2C. 37 matched cddid_all.tbl CDD pfam10277 pfam10277 431193 Frag1 Frag1/DRAM/Sfk1 family. This family includes Frag1, DRAM and Sfk1 proteins. Frag1 (FGF receptor activating protein 1) is a protein that is conserved from fungi to humans. There are four potential iso-prenylation sites throughout the peptide, viz CILW, CIIW and CIGL. Frag1 is a membrane-spanning protein that is ubiquitously expressed in adult tissues suggesting an important cellular function. Dram is a family of proteins conserved from nematodes to humans with six hydrophobic transmembrane regions and an Endoplasmic Reticulum signal peptide. It is a lysosomal protein that induces macro-autophagy as an effector of p53-mediated death, where p53 is the tumour-suppressor gene that is frequently mutated in cancer. Expression of Dram is stress-induced. This region is also part of a family of small plasma membrane proteins, referred to as Sfk1, that may act together with or upstream of Stt4p to generate normal levels of the essential phospholipid PI4P, thus allowing proper localization of Stt4p to the actin cytoskeleton. 220 matched cddid_all.tbl CDD pfam10278 pfam10278 287279 Med19 Mediator of RNA pol II transcription subunit 19. Med19 represents a family of conserved proteins which are members of the multi-protein co-activator Mediator complex. Mediator is required for activation of RNA polymerase II transcription by DNA binding transactivators. 178 matched cddid_all.tbl CDD pfam10279 pfam10279 192511 Latarcin Latarcin precursor. This family represents the precursor proteins for a number of short antimicrobial peptides called Latarcins. Latarcins were discovered in the venom of the spider Lachesana tarabaevi. Latarcins are likely to adopt amphipathic alpha-helical structure in the plasma membrane. 64 matched cddid_all.tbl CDD pfam10280 pfam10280 463042 Med11 Mediator complex protein. Mediator is a large, modular protein complex that is conserved from yeast to human and conveys regulatory signals from DNA-binding transcription factors to RNA polymerase II. Not only are the polypeptides conserved but the structural organization is also largely conserved. One or two subunits are either fungal or vertebral specific but Med11 is one of the subunits that is conserved from fungi to humans. Med11 appears to be necessary for the full and successful assembly of the core head sub-region. 119 matched cddid_all.tbl CDD pfam10281 pfam10281 431195 Ish1 Putative nuclear envelope organization protein. This entry represents a repeat found in the fungal protein Ish1, a protein which has a role in nuclear membrane organization. 37 matched cddid_all.tbl CDD pfam10282 pfam10282 431196 Lactonase Lactonase, 7-bladed beta-propeller. This entry contains bacterial 6-phosphogluconolactonases (6PGL)YbhE-type (EC:3.1.1.31) which hydrolyse 6-phosphogluconolactone to 6-phosphogluconate. The entry also contains the fungal muconate lactonising enzyme carboxy-cis,cis-muconate cyclase (EC:5.5.1.5) and muconate cycloisomerase (EC:5.5.1.1), which convert cis,cis-muconates to muconolactones and vice versa as part of the microbial beta-ketoadipate pathway. Structures of proteins in this family have revealed a 7-bladed beta-propeller fold. 340 matched cddid_all.tbl CDD pfam10283 pfam10283 463043 zf-CCHH PBZ domain. This domain is a zinc-finger motif that in humans is part of the APLF, aprataxin- and PNK-like forkhead association domain-containing protein. The ZnF is highly conserved both in primary sequence and in the spacing between the putative zinc coordinating residues and is configured CX5CX6HX5H. Many of the proteins containing the APLF-like ZnF are involved in DNA strand break repair and/or contain domains implicated in DNA metabolism. 25 matched cddid_all.tbl CDD pfam10284 pfam10284 118808 Luciferase_3H Luciferase helical bundle domain. This domain is found associated with the the catalytic domain of dinoflagellate luciferase. Luciferase is involved in catalysing the light emitting reaction in bioluminescence. The structure of this domain has been solved. This domain has a three helix bundle structure that holds four important histidines that are thought to play a role in the pH regulation of the enzyme. 66 matched cddid_all.tbl CDD pfam10285 pfam10285 118809 Luciferase_cat Luciferase catalytic domain. This domain is the catalytic domain of dinoflagellate luciferase. Luciferase is involved in catalysing the light emitting reaction in bioluminescence. The structure of this domain has been solved. The core part of the domain is a 10 stranded beta barrel that is structurally similar to lipocalins and FABP. 296 matched cddid_all.tbl CDD pfam10287 pfam10287 431198 YJL171C_Tos1_C Cell wall protein YJL171C/Tos1, C-terminal. This entry represents a domain found in a group of fungal cell wall proteins, including Tos1 and YJL171C from budding yeasts. They contain 5 highly conserved cysteines, two of which form a characteriztic CGC sequence motif. Their function is not clear. It has been shown that these proteins are related to known glycosyl hydrolases. 224 matched cddid_all.tbl CDD pfam10288 pfam10288 463044 CTU2 Cytoplasmic tRNA 2-thiolation protein 2. CTU2 is a family of proteins necessary for the formation of the wobble nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces cerevisiae. The family is conserved from plants to humans ]1]. It plays a central role in the 2-thiolation of 5-methoxycarbonylmethyl-2-thiouridine, or the wobble nucleoside. This wobble modification in tRNAs, 5-methoxycarbonylmethyl-2-thiouridine (mcm(5)s(2)U), is required for the proper decoding of NNR codons in eukaryotes. The 2-thio group gives rigidity by largely fixing the C3'-endo ribose puckering, ensuring stable and accurate codon-anticodon pairing. 106 matched cddid_all.tbl CDD pfam10290 pfam10290 463045 YJL171C_Tos1_N Cell wall protein YJL171C/Tos1, N-terminal. This domain is found in the N-terminal region of cell wall proteins, including Tos1 and YJL171C from budding yeasts. The function of this glycine-rich region is unknown. 59 matched cddid_all.tbl CDD pfam10291 pfam10291 463046 muHD Muniscin C-terminal mu homology domain. The muniscins are a family of endocytic adaptors that is conserved from yeast to humans.This C-terminal domain is structurally similar to mu homology domains, and is the region of the muniscin proteins involved in the interactions with the endocytic adaptor-scaffold proteins Ede1-eps15. This interaction influences muniscin localization. The muniscins provide a combined adaptor-membrane-tubulation activity that is important for regulating endocytosis. 255 matched cddid_all.tbl CDD pfam10292 pfam10292 370953 7TM_GPCR_Srab Serpentine type 7TM GPCR receptor class ab chemoreceptor. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srab is part of the Sra superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The expression pattern of the srab genes is biologically intriguing. Of the six promoters successfully expressed in transgenic organizms, one was exclusively expressed in the tail phasmid neurons, two were exclusively expressed in a head amphid neuron, and two were expressed both in the head and tail neurons as well as a limited number of other cells. 324 matched cddid_all.tbl CDD pfam10293 pfam10293 431201 DUF2405 Domain of unknown function (DUF2405). This is a conserved region of a family of proteins conserved in fungi. The function is unknown. 152 matched cddid_all.tbl CDD pfam10294 pfam10294 313513 Methyltransf_16 Lysine methyltransferase. Methyltrans_16 is a lysine methyltransferase. characterized members of this family are protein methyltransferases targetting Lys residues in specific proteins, including calmodulin, VCP, Kin17 and Hsp70 proteins. 172 matched cddid_all.tbl CDD pfam10295 pfam10295 402077 DUF2406 Uncharacterized protein (DUF2406). This is a family of small proteins conserved in fungi. The function is not known. 58 matched cddid_all.tbl CDD pfam10296 pfam10296 431202 MMM1 Maintenance of mitochondrial morphology protein 1. MMM1 is conserved from plants to humans. MMM1 is an integral ER protein. It is N-glycosylated, and forms a complex with Mdm10, Mdm12and Mdm34 to tether the mitochondria to the endoplasmic reticulum. 312 matched cddid_all.tbl CDD pfam10297 pfam10297 402079 Hap4_Hap_bind Minimal binding motif of Hap4 for binding to Hap2/3/5. In Saccharomyces cerevisiae, the haem-activated protein complex Hap2/3/4/5 plays a major role in the transcription of genes involved in respiration. Hap4_Hap_bind is the essential domain of Hap4 which allows it to associate with Hap2, Hap3 and Hap5 to form the Hap complex. 17 matched cddid_all.tbl CDD pfam10298 pfam10298 431203 WhiA_N WhiA N-terminal LAGLIDADG-like domain. This domain is found at the N terminal of sporulation factor WhiA. This domain is related to the LAGLIDADG Homing endonuclease domain while the C terminal domain of WhiA is predicted to be a DNA binding helix-turn-helix domain. 86 matched cddid_all.tbl CDD pfam10300 pfam10300 463047 Iml2-TPR_39 Iml2/Tetratricopeptide repeat protein 39. This is a family of proteins conserved from fungi to humans, including fungal Inclusion body clearance protein Iml2 protein, animal tetratricopeptide repeat protein 39A/B/C (TT39A/B/C) and some uncharacterized proteins. Members of this family carry a tetratricopeptide repeat pfam07719 at their C terminus. This entry includes Iml2 and its paralogue-YKR018C from S. cerevisiae; Iml2 localizes to the cytoplasm and nucleus, and its expression is increased in response to DNA replication stress. It is found to be involved in lipid droplet-mediated inclusion body clearing after protein folding stress. In humans, TTC39A (also known as DEME6) is expressed in primary breast carcinomas but not in normal breast tissue, and has a putative eukaryotic RNP-1 RNA binding region and a candidate anchoring transmembrane domain. It is coordinately regulated with oestrogen receptor, but is not necessarily oestradiol-responsive. TTC39B has been linked to lipid metabolism. 469 matched cddid_all.tbl CDD pfam10302 pfam10302 370959 Dsc3_N DSC E3 ubiquitin ligase complex subunit 3, ubiquitin-like domain. This is the N-terminal ubiquitin-like domain of DSC E3 ubiquitin ligase complex subunit 3 (Dsc3). Dsc3 is a component of the DSC E3 ubiquitin ligase complex (a Golgi-specific protein ubiquitination system) that functions in protein homeostasis under non-stress conditions, playing a role in protein quality control through endosome and Golgi-associated degradation pathway (EGAD). Yeast DSC E3 ubiquitin ligase complex is the homolog of Hrd1 E3 ligase complex from mammals, in which Dsc1, Dsc2 and Dsc3 corresponds to Hrd1, Der1 and Usa1, respectively. Dsc3 is a Herp-like protein that acts as a bridge between Dsc1 and Dsc2 for their interaction. 101 matched cddid_all.tbl CDD pfam10303 pfam10303 431205 DUF2408 Protein of unknown function (DUF2408). This is a family of proteins conserved in fungi. The function is unknown. 130 matched cddid_all.tbl CDD pfam10304 pfam10304 431206 RTP1_C2 Required for nuclear transport of RNA pol II C-terminus 2. This domain is found towards the C-terminus of required for the nuclear transport of RNA pol II protein (RTP1). RTP1 is required for the nuclear localization of RNA polymerase II. This family is found in association with pfam10363. 34 matched cddid_all.tbl CDD pfam10305 pfam10305 431207 Fmp27_SW RNA pol II promoter Fmp27 protein domain. Fmp27_SW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteriztic SW and GKG sequence motifs. 101 matched cddid_all.tbl CDD pfam10306 pfam10306 431208 FLILHELTA Hypothetical protein FLILHELTA. This is a family of conserved proteins found in fungi. It contains a characteriztic FL(I)LHE(L)TA sequence motif, where the bracketed residues are I, L or V. The function is not known. 82 matched cddid_all.tbl CDD pfam10307 pfam10307 431209 HAD_SAK_1 HAD domain family 1 in Swiss Army Knife RNA repair proteins. Family of HAD domain phophoesterases observed in large eukaryotic proteins with predicted role in RNA repair, the so-called 'Swiss Army Knife' repair proteins. May be involved in phosphate group removal during RNA re-ligation.There are two characteriztic sequence motifs, GGWW and TGR. 198 matched cddid_all.tbl CDD pfam10309 pfam10309 463048 NCBP3 Nuclear cap-binding protein subunit 3. NCBP3 and NCBP1 form an alternative cap-binding complex in higher eukaryotes. NCBP3 binds mRNA, associates with components of the mRNA processing machinery and contributes to polyA RNA export. 59 matched cddid_all.tbl CDD pfam10310 pfam10310 431211 DUF5427 Family of unknown function (DUF5427). This is a domain of unknown function. Family members found in Saccharomyces cerevisiae, are synthetic lethal with genes involved in maintenance of telomere capping. However, experimental evidence is yet to verify the exact function of family members and the domain. 456 matched cddid_all.tbl CDD pfam10311 pfam10311 431212 Ilm1 Increased loss of mitochondrial DNA protein 1. This is a family of proteins of approximately 200 residues that are conserved in fungi. Ilm1 is part of the peroxisome, a complex that is the sole site of beta-oxidation in Saccharomyces cerevisiae and known to be required for optimal growth in the presence of fatty acid. Ilm1 may participate in the control of the C16/C18 ratio since it interacts strongly with Mga2p, a transcription factor that controls expression of Ole1, the sole fatty acyl desaturase in S. cerevisiae responsible for conversion of the saturated fatty acids stearate (C18) and palmitate (C16) to oleate and palmitoleate, respectively. 160 matched cddid_all.tbl CDD pfam10312 pfam10312 463049 Cactin_mid Conserved mid region of cactin. This is the conserved middle region of a family of proteins referred to as cactins. The region contains two of three predicted coiled-coil domains. Most members of this family have a CactinC_cactus pfam09732 domain at the C-terminal end. Upstream of Mid_cactin in Drosophila members are a serine-rich region, some non-typical RD motifs and three predicted bipartite nuclear localization signals, none of which are well-conserved. Cactin associates with IkappaB-cactus as one of the intracellular members of the Rel (NF-kappaB) pathway which is conserved in invertebrates and vertebrates. In mammals, this pathway controls the activities of the immune and inflammatory response genes as well as viral genes, and is critical for cell growth and survival. In Drosophila, the Rel pathway functions in the innate cellular and humoral immune response, in muscle development, and in the establishment of dorsal-ventral polarity in the early embryo. 186 matched cddid_all.tbl CDD pfam10313 pfam10313 402091 DUF2415 Uncharacterized protein domain (DUF2415). This is a short, 30 residue domain, from a family of proteins conserved in fungi. The function is unknown. There is a characteriztic DLL sequence motif. 43 matched cddid_all.tbl CDD pfam10315 pfam10315 402092 Aim19 Altered inheritance of mitochondria protein 19. This is a family of conserved proteins found in fungi. The function is not known. 111 matched cddid_all.tbl CDD pfam10316 pfam10316 402093 7TM_GPCR_Srbc Serpentine type 7TM GPCR chemoreceptor Srbc. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srbc is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. 273 matched cddid_all.tbl CDD pfam10317 pfam10317 402094 7TM_GPCR_Srd Serpentine type 7TM GPCR chemoreceptor Srd. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srd is part of the larger Str superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. 292 matched cddid_all.tbl CDD pfam10318 pfam10318 402095 7TM_GPCR_Srh Serpentine type 7TM GPCR chemoreceptor Srh. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srh is part of the Str superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. 302 matched cddid_all.tbl CDD pfam10319 pfam10319 370974 7TM_GPCR_Srj Serpentine type 7TM GPCR chemoreceptor Srj. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srj is part of the Str superfamily of chemoreceptors. The srj family is designated as the out-group based on its location in preliminary phylogenetic analyses of the entire superfamily. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. 310 matched cddid_all.tbl CDD pfam10320 pfam10320 255903 7TM_GPCR_Srsx Serpentine type 7TM GPCR chemoreceptor Srsx. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. 257 matched cddid_all.tbl CDD pfam10321 pfam10321 402096 7TM_GPCR_Srt Serpentine type 7TM GPCR chemoreceptor Srt. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srt is a member of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. 313 matched cddid_all.tbl CDD pfam10322 pfam10322 370976 7TM_GPCR_Sru Serpentine type 7TM GPCR chemoreceptor Sru. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Sru is a member of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. 304 matched cddid_all.tbl CDD pfam10323 pfam10323 370977 7TM_GPCR_Srv Serpentine type 7TM GPCR chemoreceptor Srv. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srv is a member of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. 283 matched cddid_all.tbl CDD pfam10324 pfam10324 402097 7TM_GPCR_Srw Serpentine type 7TM GPCR chemoreceptor Srw. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srw is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srw do not appear to be under as strong an adaptive evolutionary pressure as those of Srz. 318 matched cddid_all.tbl CDD pfam10325 pfam10325 431214 7TM_GPCR_Srz Serpentine type 7TM GPCR chemoreceptor Srz. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srz is a solo families amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. The genes encoding Srz appear to be under strong adaptive evolutionary pressure. 264 matched cddid_all.tbl CDD pfam10326 pfam10326 402099 7TM_GPCR_Str Serpentine type 7TM GPCR chemoreceptor Str. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Str is a member of the Str superfamily of chemoreceptors. Almost a quarter (22.5%) of str and srj family genes and pseudogenes in C. elegans appear to have been newly formed by gene duplications since the species split. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. 307 matched cddid_all.tbl CDD pfam10327 pfam10327 313539 7TM_GPCR_Sri Serpentine type 7TM GPCR chemoreceptor Sri. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Sri is part of the Str superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. 303 matched cddid_all.tbl CDD pfam10328 pfam10328 431215 7TM_GPCR_Srx Serpentine type 7TM GPCR chemoreceptor Srx. Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srx is part of the Srg superfamily of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'. 262 matched cddid_all.tbl CDD pfam10329 pfam10329 431216 DUF2417 Region of unknown function (DUF2417). This is a region of a family of proteins conserved in fungi some of whose members also have the Abhydrolase_1, pfam00561, domain in their sequence. The function of this region is not known. 234 matched cddid_all.tbl CDD pfam10330 pfam10330 402102 Stb3 Putative Sin3 binding protein. This is a family of the conserved N-terminal end of a group of proteins conserved in fungi. It is likely to be a Sin3 binding protein. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex. Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 is a DNA-binding protein. 79 matched cddid_all.tbl CDD pfam10332 pfam10332 431217 DUF2418 Protein of unknown function (DUF2418). This is a conserved 100 residue central region of a family of proteins found in fungi. It carries a characteriztic EYD sequence motif. The function is not known. 96 matched cddid_all.tbl CDD pfam10333 pfam10333 370985 Pga1 GPI-Mannosyltransferase II co-activator. Pga1 is found only in yeasts and not in mammals. It localizes in the ER as a glycosylated integral membrane protein. It binds to the GPI-mannosyltransferase II subunit of the GPI and it is responsible for the second mannose addition to GPI precursors. The GPI-anchoring complex is a glycolipid that functions as a membrane anchor for many cell-surface proteins. 174 matched cddid_all.tbl CDD pfam10334 pfam10334 370986 ArAE_2 Aromatic acid exporter family member 2. This is a family of proteins conserved in fungi. The function is not known. 228 matched cddid_all.tbl CDD pfam10335 pfam10335 463050 DUF294_C Putative nucleotidyltransferase substrate binding domain. This domain is found associated with presumed nucleotidyltransferase domains and seems to be distantly related to other helical substrate binding domains. 144 matched cddid_all.tbl CDD pfam10336 pfam10336 402105 DUF2420 Protein of unknown function (DUF2420). This is a family of proteins conserved in fungi. The function is not known. 107 matched cddid_all.tbl CDD pfam10337 pfam10337 370988 ArAE_2_N Putative ER transporter, 6TM, N-terminal. This is a family of proteins conserved in fungi. The function is not known. This family is the C-terminal half of some member proteins which contain the DUF2421 pfam10334 domain at their N-terminus. These proteins are putative endoplasmic reticulum tranpsorters, with a total of 12 TMs. 470 matched cddid_all.tbl CDD pfam10338 pfam10338 431219 DUF2423 Protein of unknown function (DUF2423). This is a family of proteins conserved in fungi. The function is not known. 44 matched cddid_all.tbl CDD pfam10339 pfam10339 402107 Vel1p Yeast-specific zinc responsive. This is a small family of proteins from Saccharomyces and related species. The function is not known but member proteins are highly induced in zinc-depleted conditions and have increased expression in NAP1-deletion mutants. The S. cerevisiae genes are named VEL by association with Velum formation in the wine making process http://www.ajevonline.org/content/48/1/55.abstract 202 matched cddid_all.tbl CDD pfam10340 pfam10340 313549 Say1_Mug180 Steryl acetyl hydrolase. This entry includes budding yeast steryl acetyl hydrolase 1 (Say1) and fission yeast Mug180. Say1 is a a membrane-anchored deacetylase required for the deacetylation of acetylated sterols. It is involved in the resistance to eugenol and pregnenolone toxicity. Mug180 has a role in meiosis. 374 matched cddid_all.tbl CDD pfam10341 pfam10341 431220 TPP1 Shelterin complex subunit, TPP1/ACD. TPP1 is a component of the telomerase holoenzyme, involved in telomere replication. It has been demonstrated that TPP1 dimerizes and binds to DNA and RNA. Furthermore, TPP1 stimulates the dissociation of RNA/DNA hetero-duplexes. Yeast telomerase protein TPP1 (Est3 in yeast) is a novel type of GTPase. The key residues in Swiss:Q03096 are an Asp at residue 86 and the Arg at residue 110. The Asp is totally conserved in the family, whereas the Arg is not so well conserved. The N-terminal of TPP1 is likely to be the binding surface for TINF2, whereas the C-terminus probably binds to POT1, thereby tethering POT1 to the shelterin complex. The complex bound to telomeric DNA increases the activity and processivity of the human telomerase core enzyme, thus helping to maintain the length of the telomeres. This domain is conserved from fungi to mammals, hence family Telomere_Pot1 has been merged into the family. The human shelterin complex includes six proteins: telomere repeat binding factor 1 (TRF1), TRF2, repressor/activator protein 1 (RAP1), TRF1-interacting nuclear protein 2 (TIN2), TIN2-interacting protein 1 (TPP1) and protection of telomeres 1 (POT1). 107 matched cddid_all.tbl CDD pfam10342 pfam10342 463051 Kre9_KNH Kre9/KNH-like N-terminal Ig-like domain. This entry represents the N-terminal Ig-like domain found in a family of serine- threonine-rich membrane-anchored proteins, anchored by glycosyl-phosphatidylinositol. This family includes Kre9. In A. fumigatus these proteins play a role in fungal cell wall organization. In Lentinula edodes this family is involved in fruiting body formation, and may have a more general role in signalling in other organizms as it interacts with MAPK. The family is also found in archaea and bacteria. 94 matched cddid_all.tbl CDD pfam10343 pfam10343 463052 Q_salvage Potential Queuosine, Q, salvage protein family. Q_salvage proteins occur in most Eukarya as well as in a few bacteria possible via horizontal gene-transfer. Queuosine (Q) is a chemical modification found at the wobble position of tRNAs that have GUN anticodons. Most bacteria synthesize queuosine de novo, whereas eukaryotes rely solely on salvaging this essential component from the environment or the gut flora. The exact enzymatic function of the domain has yet to be determined, but structural similarity with DNA glycosidases suggests a ribonucleoside hydrolase role. 285 matched cddid_all.tbl CDD pfam10344 pfam10344 431223 Fmp27 Mitochondrial protein from FMP27. This family contains mitochondrial FMP27 proteins which in yeasts together with SEN1 are long genes that exist in a looped conformation, effectively bringing together their promoter and terminator regions. Pol-II is located at both ends of FMP27 when this gene is transcribed from a GAL1 promoter under induced and non-induced conditions. The exact function of the Fmp27 protein is not certain. 865 matched cddid_all.tbl CDD pfam10345 pfam10345 463053 Cohesin_load Cohesin loading factor. Cohesin_load is a common cohesin loading factor protein that is conserved in fungi. It is associated with the cohesin complex and is required in G1 for cohesin binding to chromosomes but dispensable in G2 when cohesion has been established. It is referred to as both Ssl3, in pombe, and Scc4, in S.cerevisiae. It complexes with Mis4. 585 matched cddid_all.tbl CDD pfam10346 pfam10346 431224 Con-6 Conidiation protein 6. Con-6 is the conserved N-terminal region of a family of small proteins found in fungi. It is expressed at approximately 6 hours after the induction of development and is induced just prior to major constriction-chain growth. 33 matched cddid_all.tbl CDD pfam10347 pfam10347 402113 Fmp27_GFWDK RNA pol II promoter Fmp27 protein domain. Fmp27_GFWDK is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteriztic GFWDK sequence motifs. Some members are associated with domain Fmp27_SW (pfam10305) towards the N terminus. 155 matched cddid_all.tbl CDD pfam10348 pfam10348 402114 DUF2427 Domain of unknown function (DUF2427). This is the N-terminal region of a family of proteins conserved in fungi. Several members are annotated as being Ftp1 but this could not be confirmed. The function is not known. 105 matched cddid_all.tbl CDD pfam10350 pfam10350 463054 DUF2428 THADA/TRM732, DUF2428. This conserved domain is found in Thyroid adenoma-associated proteins (THADA) and the yeast homolog, TRM732. Trm732 forms a complex with the methyltransferase Trm7 to 2'- O-methylate tRNA residue 32 (Nm32), being required for Trm7 methylation activity. In humans, mutations of the Trm7 homolog FTSJ1, which interacts with THADA, impair Nm32 modifications, associated with non-syndromic X-linked intellectual disability. It has been suggested that these proteins may play a role in additional biological processes not related to translation. This domain contains a RRSAGLP conserved motif that is required for tRNA modification activity (Funk HM et.al., Preprint from bioRxiv, 03 Jun 2021 DOI: 10.1101/2021.06.03.446962). 260 matched cddid_all.tbl CDD pfam10351 pfam10351 463055 Apt1 Golgi-body localization protein domain. This is the C-terminus of a family of proteins conserved from plants to humans. The plant members are localized to the Golgi proteins and appear to regulate membrane trafficking, as they are required for rapid vesicle accumulation at the tip of the pollen tube. The C-terminus probably contains the Golgi localization signal and it is well-conserved. 466 matched cddid_all.tbl CDD pfam10353 pfam10353 118874 DUF2430 Protein of unknown function (DUF2430). This is a family of short, 111 residue, proteins found in S. pombe. The function is not known. 107 matched cddid_all.tbl CDD pfam10354 pfam10354 463056 BMT5-like rRNA (uridine-N3-)-methyltransferase BTM5-like. This is the N-terminal domain found in proteins from plants, yeast and humans, including 25S rRNA (uridine-N(3))-methyltransferase BMT5 from S. cerevisiae and the poorly characterized Ferredoxin-fold anticodon-binding domain-containing protein 1 from human and Heavy metal-associated isoprenylated plant protein 41 from Arabidopsis. This domain has a characteriztic Rossmann-like fold of S-adenosyl-L-methionine (SAM) binding domains. BTM5 is a SAM-dependent methyltransferase that specifically methylates the N3 position of uridine in 25S rRNA. 162 matched cddid_all.tbl CDD pfam10355 pfam10355 431228 Ytp1 Protein of unknown function (Ytp1). This is a family of proteins found in fungi. The region appears to contain regions similar to mitochondrial electron transport proteins. The C-terminal domain is hydrophobic and negatively charged. There are consensus sites for both N-linked glycosylation and cAMP-dependent protein kinase phosphorylation. 275 matched cddid_all.tbl CDD pfam10356 pfam10356 287343 DUF2034 Protein of unknown function (DUF2034). This protein is expressed in fungi but its function is unknown. 185 matched cddid_all.tbl CDD pfam10357 pfam10357 463057 Kin17_mid Domain of Kin17 curved DNA-binding protein. Kin17_mid is the conserved central 169 residue region of a family of Kin17 proteins. Towards the N-terminal end there is a zinc-finger domain, and in human and mouse members there is a RecA-like domain further downstream. The Kin17 protein in humans forms intra-nuclear foci during cell proliferation and is re-distributed in the nucleoplasm during the cell cycle. 123 matched cddid_all.tbl CDD pfam10358 pfam10358 463058 NT-C2 N-terminal C2 in EEIG1 and EHBP1 proteins. This version of the C2 domain was initally identified in the vertebrate estrogen early-induced gene 1 (EEIG1), and its Drosophila ortholog required for uptake of dsRNA via the endocytotic machinery to induce RNAi silencing. It is also in C.elegans ortholog Sym-3 (SYnthetic lethal with Mec-3) and the mammalian protein EHBP1 (EH domain Binding Protein-1) that regulates endocytotic recycling and two plant proteins, RPG that regulates Rhizobium-directed polar growth and PMI1 (Plastid Movement Impaired 1) that is essential for intracellular movement of chloroplasts in response to blue light. 143 matched cddid_all.tbl CDD pfam10359 pfam10359 431231 Fmp27_WPPW RNA pol II promoter Fmp27 protein domain. Fmp27_WPPW is a conserved domain of a family of proteins involved in RNA polymerase II transcription initiation. It contains characteriztic HQR and WPPW sequence motifs. and is towards the C-terminal in members which contain Fmp27_SW pfam10305. 480 matched cddid_all.tbl CDD pfam10360 pfam10360 402122 DUF2433 Protein of unknown function (DUF2433). This is a conserved 120 residue region of a family of proteins found in fungi. The function is not known. 95 matched cddid_all.tbl CDD pfam10361 pfam10361 431232 DUF2434 Protein of unknown function (DUF2434). This is a family of proteins conserved in fungi. The function is not known. 294 matched cddid_all.tbl CDD pfam10363 pfam10363 463059 RTP1_C1 Required for nuclear transport of RNA pol II C-terminus 1. This domain is found towards the C-terminus of required for the nuclear transport of RNA pol II protein (RTP1). RTP1 is required for the nuclear localization of RNA polymerase II. This family is found in association with pfam10304. 112 matched cddid_all.tbl CDD pfam10364 pfam10364 431234 NKWYS Putative capsular polysaccharide synthesis protein. Found only in Vibrio species, pombe and one other fungi, this is a the N-terminal 150 residues of a family of proteins of unknown function. There is a characteriztic NKWYS sequence motif. 132 matched cddid_all.tbl CDD pfam10365 pfam10365 287351 DUF2436 Domain of unknown function (DUF2436). This domain is found on peptidase C25 proteins and has no known function. 164 matched cddid_all.tbl CDD pfam10366 pfam10366 371008 Vps39_1 Vacuolar sorting protein 39 domain 1. This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex. Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole. In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange. The precise function of this domain has not been characterized. 108 matched cddid_all.tbl CDD pfam10367 pfam10367 402126 Vps39_2 Vacuolar sorting protein 39 domain 2. This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex. Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole. In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange. This domain is involved in localization and in mediating the interactions of Vps39 with Vps11. 109 matched cddid_all.tbl CDD pfam10368 pfam10368 431235 YkyA Putative cell-wall binding lipoprotein. YkyA is a family of proteins containing a lipoprotein signal and a hydrolase domain. It is similar to cell wall binding proteins and might also be recognisable by a host immune defence system. It is thus likely to belong to pathways important for pathogenicity. 185 matched cddid_all.tbl CDD pfam10369 pfam10369 463060 ALS_ss_C Small subunit of acetolactate synthase. ALS_ss_C is the C-terminal half of a family of proteins which are the small subunits of acetolactate synthase. Acetolactate synthase is a tetrameric enzyme, containing probably two large and two small subunits, which catalyzes the first step in branched-chain amino acid biosynthesis. This reaction is sensitive to certain herbicides. 73 matched cddid_all.tbl CDD pfam10370 pfam10370 463061 DUF2437 Domain of unknown function (DUF2437). This is the N-terminal 50 amino acids of a group of bacterial proteins annotated as fumarylacetoacetate hydrolase-containing enzymes. In most cases members are associated with FAA_hydrolase pfam01557 further towards the C-terminus. 50 matched cddid_all.tbl CDD pfam10371 pfam10371 431238 EKR Domain of unknown function. EKR is a short, 33 residue, domain found in bacterial and some lower eukaryotic species which lies between a POR (pyruvate ferredoxin/flavodoxin oxidoreductase) pfam01558 and the 4Fe-4S binding domain Fer4 pfam00037. It contains a characteriztic EKR sequence motif. The exact function of this domain is not known. 54 matched cddid_all.tbl CDD pfam10372 pfam10372 402131 YojJ Bacterial membrane-spanning protein N-terminus. YojJ is the N-terminus of a family of bacterial proteins some of which are associated with DUF147 pfam02457 towards the C-terminus. It is a putative membrane-spanning protein. 69 matched cddid_all.tbl CDD pfam10373 pfam10373 431239 EST1_DNA_bind Est1 DNA/RNA binding domain. Est1 is a protein which recruits or activates telomerase at the site of polymerization. This is the DNA/RNA binding domain of EST1. 279 matched cddid_all.tbl CDD pfam10374 pfam10374 463062 EST1 Telomerase activating protein Est1. Est1 is a protein which recruits or activates telomerase at the site of polymerization. Structurally it resembles a TPR-like repeat. 98 matched cddid_all.tbl CDD pfam10375 pfam10375 431241 GRAB GRAB domain. The GRAB (GRIP-related Arf-binding) domain is towards the C-terminus of Rud3 type proteins. This domain is related to the GRIP domain, but the conserved tyrosine residue found at position 4 in all GRIP domains is replaced by a leucine residue. The Arf small GTPase is localized to the cis-Golgi where it recruits proteins via their GRAB domain, as part of the transport of cargo from the endoplasmic reticulum to the plasma membrane. 49 matched cddid_all.tbl CDD pfam10376 pfam10376 431242 Mei5 Double-strand recombination repair protein. Mei5 is one of a pair of meiosis-specific proteins which facilitate the loading of Dmc1 on to Rad51 on DNA at double-strand breaks during recombination. Recombination is carried out by a large protein complex based around the two RecA homologs, Rad51 and Dmc1. This complex may play both a catalytic and a structural role in the interaction between homologous chromosomes during meiosis. Mei5 is seen to contain a coiled-coli region. 207 matched cddid_all.tbl CDD pfam10377 pfam10377 463063 ATG11 Autophagy-related protein 11. The function of this family is conflicting. In the fission yeast, Schizosaccharomyces pombe, this protein has been shown to interact with the telomere cap complex and it is also required for dimerization and kinase activation of Atg1. However, in budding yeast, Saccharomyces cerevisiae, this protein is called ATG11 and is shown to be involved in autophagy. 130 matched cddid_all.tbl CDD pfam10378 pfam10378 402136 RRM Putative RRM domain. This is a putative RRM, RNA-binding, domain found only in fungi. It occurs in proteins annotated as Nrd1 yeast proteins, which are known to carry RRM domains. It is not homologous with any of the other RRM domains, eg RRM_1 pfam00076. 46 matched cddid_all.tbl CDD pfam10379 pfam10379 463064 nec1 Virulence protein nec1. This is a family of virulence proteins that are found in pathogenic Streptomyces species. 184 matched cddid_all.tbl CDD pfam10380 pfam10380 371017 CRF1 Transcription factor CRF1. CRF1 is a transcription factor that co-represses ribosomal genes with FHL1 via the TOR signalling pathway and protein kinase A. 122 matched cddid_all.tbl CDD pfam10382 pfam10382 463065 DUF2439 Protein of unknown function (DUF2439). This domain can be found in proteins that have been implicated in telomere maintenance in Saccharomyces cerevisiae and in meiotic chromosome segregation in Schizosaccharomyces pombe. It can also be found in Mte1 (Mph1-associated telomere maintenance protein 1), human zinc finger protein ZGRF1 (C4ORF21) and fission yeast Dbl2. Mte1 is a D-loop-binding protein that interacts and stimulates the helicase and fork regression activities of Mph1 while inhibiting the ability of Mph1 to dissociate recombination intermediates. Mph1 and Mte1 interdependently colocalize at DNA damage-induced foci and dysfunctional telomeres. Mte1 is indicated to play a role in regulation of crossover recombination, response to replication stress, and telomere maintenance. The fission yeast, Dbl2 is needed for cellular resistance to the topoisomerase I poison camptothecin, forms DNA damage-induced foci, and is needed for the optimal recruitment of Fml1 to DNA damage, while the human ZGRF1 protein has been linked to DNA cross-link repair and mutations of it have been found in a variety of human tumors. ZGRF1 is a 5'-to-3'helicase that interacts with RAD51 and stimulates homologous recombination and, thus, promotes the repair of replication-blocking DNA lesions. Having said that, there is no evidence to suggest that this domain is implicated in DNA damage resistance or for nuclear focus formation. 74 matched cddid_all.tbl CDD pfam10383 pfam10383 402139 Clr2 Transcription-silencing protein Clr2. Clr2 is a chromatin silencing protein, one of a quartet of proteins forming the core of SHREC, a multienzyme effector complex that mediates hetero-chromatic transcriptional gene silencing in fission yeast. Clr2 does not have any obvious well-conserved domains but, along with the other core proteins, binds to the histone deacetylase Clr3, and on its own might also have a role in chromatin organization at the cnt domain, the site of kinetochore assembly. 138 matched cddid_all.tbl CDD pfam10384 pfam10384 463066 Scm3 Centromere protein Scm3. Scm3 is a centromere protein that has been shown in Saccharomyces cerevisiae to be required for G2/M progression and Cse4 localization. The C terminal region of Scm3 proteins is variable in size and sometimes consists of DNA binding motifs. 54 matched cddid_all.tbl CDD pfam10385 pfam10385 463067 RNA_pol_Rpb2_45 RNA polymerase beta subunit external 1 domain. RNA polymerases catalyze the DNA-dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region. 66 matched cddid_all.tbl CDD pfam10386 pfam10386 402142 DUF2441 Protein of unknown function (DUF2441). This is a family of highly conserved, predicted, proteins from Bacillus species. The structure forms a homo-dimer. The function is unknown. 141 matched cddid_all.tbl CDD pfam10387 pfam10387 431248 DUF2442 Protein of unknown function (DUF2442). This family of bacterial and fungal proteins has several members annotated as being putative molybdopterin-guanine dinucleotide biosynthesis protein A; however this could not be verified. Hence the function is not known. This family also includes the DUF3532 that was found to be related and was merged into this family. Members of this family also fall into the NE0471 N-terminal domain-like superfamily, a family of proteins with a unique fold in SCOP:143880. 72 matched cddid_all.tbl CDD pfam10388 pfam10388 402144 YkuI_C EAL-domain associated signalling protein domain. In Bacillus species this highly conserved region of the YkuI protein lies immediately downstream of the EAL (diguanylate cyclase/phosphodiesterase domain 2) pfam00563 domain so that together they form a monomer which dimerizes for its enzymatic action. The region contains three alpha helices and five beta strands and is the C-terminal half of the structure. 166 matched cddid_all.tbl CDD pfam10390 pfam10390 463068 ELL RNA polymerase II elongation factor ELL. ELL is a family of RNA polymerase II elongation factors. It is bound stably to elongation-associated factors 1 and 2, EAFs, and together these act as a strong regulator of transcription activity. by direct interaction with Pol II. ELL binds to pol II on its own but the affinity is greatly increased by the cooperation of EAF. Some members carry an Occludin domain pfam07303 just downstream. There is no S. cerevisiae member. 281 matched cddid_all.tbl CDD pfam10391 pfam10391 463069 DNA_pol_lambd_f Fingers domain of DNA polymerase lambda. DNA polymerases catalyze the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone. 51 matched cddid_all.tbl CDD pfam10392 pfam10392 192566 COG5 Golgi transport complex subunit 5. The COG complex, the peripheral membrane oligomeric protein complex involved in intra-Golgi protein trafficking, consists of eight subunits arranged in two lobes bridged by Cog1. Cog5 is in the smaller, B lobe, bound in with Cog6-8, and is itself bound to Cog1 as well as, strongly, to Cog7. 132 matched cddid_all.tbl CDD pfam10393 pfam10393 463070 Matrilin_ccoil Trimeric coiled-coil oligomerization domain of matrilin. This short domain is a coiled coil structure and has a single cysteine residue at the start which is likely to form a di-sulfide bridge with a corresponding cysteine in an upstream EGF (pfam00008) domain thereby spanning a VWA (pfam00092) domain. All three domains can be associated together as in the cartilage matrix protein matrilin, where this domain is likely to be responsible for oligomerization. 43 matched cddid_all.tbl CDD pfam10394 pfam10394 463071 Hat1_N Histone acetyl transferase HAT1 N-terminus. This domain is the N-terminal half of the structure of histone acetyl transferase HAT1. It is often found in association with the C-terminal part of the GNAT Acetyltransf_1 (pfam00583) domain. It seems to be motifs C and D of the structure. Histone acetyltransferases (HATs) catalyze the transfer of an acetyl group from acetyl-CoA to the lysine E-amino groups on the N-terminal tails of histones. HATs are involved in transcription since histones tend to be hyper-acetylated in actively transcribed regions of chromatin, whereas in transcriptionally silent regions histones are hypo-acetylated. 158 matched cddid_all.tbl CDD pfam10395 pfam10395 402149 Utp8 Utp8 family. Utp8 is an essential component of the nuclear tRNA export machinery in Saccharomyces cerevisiae. It is a tRNA binding protein that acts at a step between tRNA maturation /aminoacylation, and translocation of the tRNA across the nuclear pore complex. 690 matched cddid_all.tbl CDD pfam10396 pfam10396 463072 TrmE_N GTP-binding protein TrmE N-terminus. This family represents the shorter, B, chain of the homo-dimeric structure which is a guanine nucleotide-binding protein that binds and hydrolyses GTP. TrmE is homologous to the tetrahydrofolate-binding domain of N,N-dimethylglycine oxidase and indeed binds formyl-tetrahydrofolate. TrmE actively participates in the formylation reaction of uridine and regulates the ensuing hydrogenation reaction of a Schiff's base intermediate. This B chain is the N-terminal portion of the protein consisting of five beta-strands and three alpha helices and is necessary for mediating dimer formation within the protein. 117 matched cddid_all.tbl CDD pfam10397 pfam10397 463073 ADSL_C Adenylosuccinate lyase C-terminus. This is the C-terminal seven alpha helices of the structure whose full length represents the enzyme adenylosuccinate lyase. This sequence lies C-terminal to the conserved motif necessary for beta-elimination reactions, Adenylosuccinate lyase catalyzes two steps in the synthesis of purine nucleotides: the conversion of succinylaminoimidazole-carboxamide ribotide into aminoimidazole-carboxamide ribotide, the eighth step of the de novo pathway, and the formation of adenosine monophosphate (AMP) from adenylosuccinate, the second step in the conversion of inosine monophosphate into AMP. 78 matched cddid_all.tbl CDD pfam10398 pfam10398 431255 DUF2443 Protein of unknown function (DUF2443). This is a small family of highly conserved proteins from bacteria, in particular Helicobacter species, The structure is a bundle of alpha helices. The function is not known. 79 matched cddid_all.tbl CDD pfam10399 pfam10399 463074 UCR_Fe-S_N Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal. This is the N-terminal region of the E or R chain, Ubiquitinol-cytochrome C reductase Fe-S subunit, of the hetero-hexameric cytochrome bc1 complex. This region is a TAT-signal region. The cytochrome bc1 complex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. The enzyme couples the transfer of electrons from ubiquinol to cytochrome c with the the generation of a protein gradient across the membrane. The motif is also associated with Rieske (pfam00355), UCR_TM (pfam02921) and Ubiq-Cytc-red_N (pfam09165). 41 matched cddid_all.tbl CDD pfam10400 pfam10400 463075 Vir_act_alpha_C Virulence activator alpha C-term. This structure is homo-dimeric, and the domain here is the C-terminal half of the structure, often associated with PadR upstream, (pfam03551), which is a transcriptional regulator. 82 matched cddid_all.tbl CDD pfam10401 pfam10401 463076 IRF-3 Interferon-regulatory factor 3. This is the interferon-regulatory factor 3 chain of the hetero-dimeric structure which also contains the shorter chain CREB-binding protein. These two subunits make up the DRAF1 (double-stranded RNA-activated factor 1). Viral dsRNA produced during viral transcription or replication leads to the activation of DRAF1. The DNA-binding specificity of DRAF1 correlates with transcriptional induction of ISG (interferon-alpha,beta-stimulated gene). IRF-3 preexists in the cytoplasm of uninfected cells and translocates to the nucleus following viral infection. Translocation of IRF-3 is accompanied by an increase in serine and threonine phosphorylation, and association with the CREB coactivator occurs only after infection. 180 matched cddid_all.tbl CDD pfam10403 pfam10403 463077 BHD_1 Rad4 beta-hairpin domain 1. This short domain is found in the Rad4 protein. This domain binds to DNA. 54 matched cddid_all.tbl CDD pfam10404 pfam10404 463078 BHD_2 Rad4 beta-hairpin domain 2. This short domain is found in the Rad4 protein. This domain binds to DNA. 63 matched cddid_all.tbl CDD pfam10405 pfam10405 463079 BHD_3 Rad4 beta-hairpin domain 3. This short domain is found in the Rad4 protein. This domain binds to DNA. 73 matched cddid_all.tbl CDD pfam10406 pfam10406 431262 TAF8_C Transcription factor TFIID complex subunit 8 C-term. This is the C-terminal, Delta, part of the TAF8 protein. The N-terminal is generally the histone fold domain, Bromo_TP (pfam07524). TAF8 is one of the key subunits of the transcription factor for pol II, TFIID. TAF8 is one of the several general cofactors which are typically involved in gene activation to bring about the communication between gene-specific transcription factors and components of the general transcription machinery. 49 matched cddid_all.tbl CDD pfam10407 pfam10407 431263 Cytokin_check_N Cdc14 phosphatase binding protein N-terminus. Cytokinesis in yeasts involves a family of proteins whose essential function is to bind Cdc14-family phosphatase and prevent this from being sequestered and inhibited in the nucleolus. This is the highly conserved N-terminus of a family of proteins which act as cytokinesis checkpoint controls by allowing cells to cope with cytokinesis defects. These proteins are required for rDNA silencing and mini-chromosome maintenance. 71 matched cddid_all.tbl CDD pfam10408 pfam10408 463080 Ufd2P_core Ubiquitin elongating factor core. This is the most conserved part of the core region of Ufd2P ubiquitin elongating factor or E4, running from helix alpha-11 to alpha-38. It consists of 31 helices of variable length connected by loops of variable size forming a compact unit; the helical packing pattern of the compact unit consists of five structural repeats that resemble tandem Armadillo (ARM) repeats. This domain is involved in ubiquitination as it binds Cdc48p and escorts ubiquitinated proteins from Cdc48p to the proteasome for degradation. The core is structurally similar to the nuclear transporter protein importin-alpha. The core is associated with the U-box at the C-terminus, pfam04564, which has ligase activity. 594 matched cddid_all.tbl CDD pfam10409 pfam10409 463081 PTEN_C2 C2 domain of PTEN tumour-suppressor protein. This is the C2 domain-like domain, in greek key form, of the PTEN protein, phosphatidyl-inositol triphosphate phosphatase, and it is the C-terminus. This domain may well include a CBR3 loop which means it plays a central role in membrane binding. This domain associates across an extensive interface with the N-terminal phosphatase domain DSPc (pfam00782) suggesting that the C2 domain productively positions the catalytic part of the protein onto the membrane. 133 matched cddid_all.tbl CDD pfam10410 pfam10410 463082 DnaB_bind DnaB-helicase binding domain of primase. This domain is the C-terminal region three-helical domain of primase. Primases synthesize short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases, and this domain is the region of the primase which binds DnaB-helicase. It is associated with the Toprim domain (pfam01751) which is the central catalytic core. 54 matched cddid_all.tbl CDD pfam10411 pfam10411 431267 DsbC_N Disulfide bond isomerase protein N-terminus. This is the N-terminal domain of the disulfide bond isomerase DsbC. The whole molecule is V-shaped, where each arm is a DsbC monomer of two domains linked by a hinge; and the N-termini of each monomer join to form the dimer interface at the base of the V, so are vital for dimerization. DsbC is required for disulfide bond formation and functions as a disulfide bond isomerase during oxidative protein-folding in bacterial periplasm. It also has chaperone activity. 54 matched cddid_all.tbl CDD pfam10412 pfam10412 431268 TrwB_AAD_bind Type IV secretion-system coupling protein DNA-binding domain. The plasmid conjugative coupling protein TrwB forms hexamers from six structurally very similar protomers. This hexamer contains a central channel running from the cytosolic pole (made up by the AADs) to the membrane pole ending at the transmembrane pore shaped by 12 transmembrane helices, rendering an overall mushroom-like structure. The TrwB_AAD (all-alpha domain) domain appears to be the DNA-binding domain of the structure. TrwB, a basic integral inner-membrane nucleoside-triphosphate-binding protein, is the structural prototype for the type IV secretion system coupling proteins, a family of proteins essential for macromolecular transport between cells and export. 386 matched cddid_all.tbl CDD pfam10413 pfam10413 313611 Rhodopsin_N Amino terminal of the G-protein receptor rhodopsin. Rhodopsin is the archetypal G-protein-coupled receptor. Such receptors participate in virtually all physiological processes, as signalling molecules. They utilize heterotrimeric guanosine triphosphate (GTP)-binding proteins to transduce extracellular signals to intracellular events. Rhodopsin is important because of the pivotal role it plays in visual signal transduction. Rhodopsin is a dimeric transmembrane protein and its intradiskal surface consists of this amino terminal domain and three loops connecting six of the seven transmembrane helices. The N-terminus is a compact domain of alpha-helical regions with breaks and bends at proline residues outside the membrane. The transmembrane part of rhodopsin is represented by 7tm_1 (pfam00001). The N-terminal domain is extracellular is and is necessary for successful dimerization and molecular stability. 35 matched cddid_all.tbl CDD pfam10414 pfam10414 431269 CysG_dimerizer Sirohaem synthase dimerization region. Bacterial sulfur metabolism depends on the iron-containing porphinoid sirohaem. CysG, S-adenosyl-L-methionine (SAM)-dependent bis-methyltransferase, dehydrogenase and ferrochelatase, synthesizes sirohaem from uroporphyrinogen III via reactions which encompass two branchpoint intermediates in tetrapyrrole biosynthesis, diverting flux first from protoporphyrin IX biosynthesis and then from cobalamin (vitamin B12) biosynthesis. CysG is a dimer of two structurally similar protomers held together asymmetrically through a number of salt-bridges across complementary residues in the CysG_dimerizer region to produce a series of active sites, accounting for CysG's multifunctionality, catalysing four diverse reactions: two SAM-dependent methylations, NAD+-dependent tetrapyrrole dehydrogenation and metal chelation. The CysG_dimerizer region holding the two protomers together is of 74 residues. 56 matched cddid_all.tbl CDD pfam10415 pfam10415 463083 FumaraseC_C Fumarase C C-terminus. Fumarase C catalyzes the stereo-specific interconversion of fumarate to L-malate as part of the Kreb's cycle. The full-length protein forms a tetramer with visible globular shape. FumaraseC_C is the C-terminal 65 residues referred to as domain 3. The core of the molecule consists of a bundle of 20 alpha-helices from the five-helix bundle of domain 2. The projections from the core of the tetramer are generated from domains 1 and 3 of each subunit. FumaraseC_C does not appear to be part of either the active site or the activation site but is helical in structure forming a little bundle. 52 matched cddid_all.tbl CDD pfam10416 pfam10416 402166 IBD Transcription-initiator DNA-binding domain IBD. In Trichomonas vaginalis, thought to be the earliest extant eukaryote, the sole initiator element for control of the start of transcription is Inr, and this is recognized by the initiator binding protein IBP39. IBP39 contains an N-terminal Inr binding domain, IBD, connected via a flexible, proteolytically sensitive, linker (residues 127-145) to a C-terminal domain. The IBD structure reveals a winged-helix-wing conformation with each element binding to DNA, the central helix-turn-helix contributing the majority of the specificity-determining contacts with the Inr core motif TCAPy(T/A). The binding of IBP39 to the Inr directly recruits RNA polymerase II and in this way initiates transcription. 125 matched cddid_all.tbl CDD pfam10417 pfam10417 431271 1-cysPrx_C C-terminal domain of 1-Cys peroxiredoxin. This is the C-terminal domain of 1-Cys peroxiredoxin (1-cysPrx), a member of the peroxiredoxin superfamily which protect cells against membrane oxidation through glutathione (GSH)-dependent reduction of phospholipid hydroperoxides to corresponding alcohols. The C-terminal domain is crucial for providing the extra cysteine necessary for dimerization of the whole molecule. Loss of the enzyme's peroxidase activity is associated with oxidation of the catalytic cysteine, upstream of this domain; and glutathionylation, presumably through its disruption of protein structure, facilitates access for GSH, resulting in spontaneous reduction of the mixed disulfide to the sulfhydryl and consequent activation of the enzyme. The domain is associated with family AhpC-TSA, pfam00578, which carries the catalytic cysteine. 40 matched cddid_all.tbl CDD pfam10418 pfam10418 463084 DHODB_Fe-S_bind Iron-sulfur cluster binding domain of dihydroorotate dehydrogenase B. Lactococcus lactis is one of the few organizms with two dihydroorotate dehydrogenases, DHODs, A and B. The B enzyme is a prototype for DHODs in Gram-positive bacteria that use NAD+ as the second substrate. DHODB is a hetero-tetramer composed of a central homodimer of PyrDB subunits resembling the DHODA structure and two PyrK subunits along with three different cofactors: FMN, FAD, and a [2Fe-2S] cluster. The [2Fe-2S] iron-sulfur cluster binds to this C-terminal domain of the PyrK subunit, which is at the interface between the flavin and NAD binding domains and contains three beta-strands. The four cysteine residues at the N-terminal part of this domain are the ones that bind, in pairs, to the iron-sulfur cluster. The conformation of the whole molecule means that the iron-sulfur cluster is localized in a well-ordered part of this domain close to the FAD binding site. The FAD and and NAD binding domains are FAD_binding_6, pfam00970 and NAD_binding_1, pfam00175. 40 matched cddid_all.tbl CDD pfam10419 pfam10419 463085 TFIIIC_sub6 TFIIIC subunit triple barrel domain. This is a family of proteins subunits of TFIIIC. TFIIIC in yeast and humans is required for transcription of tRNA and 5 S RNA genes by RNA polymerase III. Yeast members of this family are fused to phosphoglycerate mutase domain. 91 matched cddid_all.tbl CDD pfam10420 pfam10420 463086 IL12p40_C Cytokine interleukin-12p40 C-terminus. IL12p40_C is the largely beta stranded C-terminal, D3, domain of interleukin-12p40 or interleukin-12B. This interleukin is produced on stimulation by macrophage-engulfed micro-organizms and other stimuli, when it dimerizes with interleukin-12p35 to form a heterodimer which then binds to receptors on natural killer cells to activate them to destroy the micro-organizms. This domain contains two disulfide bridges, one of which serves to bind p40 to p35 and the other to hold the beta strands within the domain together. The cupped shape of the p35 binding interface matches the elbow-like bend between D2 and D3 in p40. The domain is often associated with family fn3, pfam00041. 80 matched cddid_all.tbl CDD pfam10421 pfam10421 463087 OAS1_C 2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus. This is the largely alpha-helical, C-terminal half of 2'-5'-oligoadenylate synthetase 1, being described as domain 2 of the enzyme and homologous to a tandem ubiquitin repeat. It carries the region of enzymic activity between 320 and 344 at the extreme C-terminal end. Oligoadenylate synthetases are antiviral enzymes that counteract vial attack by degrading viral RNA. The enzyme uses ATP in 2'-specific nucleotidyl transfer reactions to synthesize 2'.5'-oligoadenylates, which activate latent ribonuclease, resulting in degradation of viral RNA and inhibition of virus replication. This domain is often associated with NTP_transf_2 pfam01909. 188 matched cddid_all.tbl CDD pfam10422 pfam10422 255978 LRS4 Monopolin complex subunit LRS4. Monopolin is a protein complex, originally identified in Saccharomyces cerevisiae, that is required for the segregation of homologous centromeres to opposite poles of a dividing cell during meiosis I. The orthologous complex in Schizosaccharomyces pombe is not required for meiosis I chromosome segregation, but is proposed to play a similar physiological role in clamping microtubule binding sites. In S.cerevisiae this subunit is called LRS4, and in S. pombe it is known as Mde4. 211 matched cddid_all.tbl CDD pfam10423 pfam10423 431276 AMNp_N Bacterial AMP nucleoside phosphorylase N-terminus. This is the N-terminal domain of bacterial AMP nucleoside phosphorylase (AMNp). The N- and C-termini form distinct domains which intertwine with each other to form a stable monomer which associates with five other monomers to yield the active hexamer. The N-terminus consists of a long helix and a four-stranded sheet with a novel topology. The C-terminus binds the nucleoside whereas the N-terminus acts as the enzymatic regulatory domain. AMNp (EC:3.2.2.4) catalyzes the hydrolysis of AMP to form adenine and ribose 5-phosphate. thereby regulating intracellular AMP levels. 155 matched cddid_all.tbl CDD pfam10425 pfam10425 431277 SdrG_C_C "C-terminus of bacterial fibrinogen-binding adhesin. This is the C-terminal half of a bacterial fibrinogen-binding adhesin SdrG. SdrG is a Gram-positive cell-wall-anchored adhesin that allows attachment of the bacterium to host tissues via specific binding to the beta-chain of human fibrinogen (Fg). SdrG binds to its ligand with a dynamic ""dock, lock, and latch"" mechanism which represents a general mode of ligand-binding for structurally related cell wall-anchored proteins in most Gram-positive bacteria. The C-terminal part of SdrG(276-596) is integral to the folding of the immunoglobulin-like whole to create the docking grooves necessary for Fg binding. The domain is associated with families of Cna_B, pfam05738." 156 matched cddid_all.tbl CDD pfam10426 pfam10426 431278 zf-RAG1 Recombination-activating protein 1 zinc-finger domain. This is a C2-H2 zinc-finger domain closely resembling the classical TFIIIA-type zinc-finger, CX3FX5LX2-3H, despite having a valine and a tyrosine at the core instead of a phenylalanine and a leucine, hence CX3VX1LX2YX2H. The structure, nevertheless, contains the characteriztic two-stranded beta-sheet and alpha-helix of a classical zinc-finger. The domain binds one zinc and, in complex with the zinc-RING-finger domain, helps to stabilize the whole of the dimerization region of recombination activating protein 1 (RAG1). The function of the whole is to bind double-stranded DNA. 30 matched cddid_all.tbl CDD pfam10427 pfam10427 463088 Ago_hook Argonaute hook. This region has been called the argonaute hook. It has been shown to bind to the Piwi domain pfam02171 of Argnonaute proteins. 148 matched cddid_all.tbl CDD pfam10428 pfam10428 431280 SOG2 RAM signalling pathway protein. SOG2 proteins in Saccharomyces cerevisiae are involved in cell separation and cytokinesis. 476 matched cddid_all.tbl CDD pfam10429 pfam10429 402175 Mtr2 Nuclear pore RNA shuttling protein Mtr2. Mtr2 is a monomeric, dual-action, RNA-shuttle protein found in yeasts. Transport across the nuclear-cytoplasmic membrane is via the macro-molecular membrane-spanning nuclear pore complex, NPC. The pore is lined by a subset of NPC members called nucleoporins that present FG (Phe-Gly) receptors, characteriztically GLFG and FXFG motifs, for shuttling RNAs and proteins. RNA cargo is bound to soluble transport proteins (nuclear export factors) such as Mex67 in yeasts, and TAP in metazoa, which pass along the pore by binding to successive FG receptors. Mtr2 when bound to Mex67 maximizes this FG-binding. Mtr2 also acts independently of Mex67 in transporting the large ribosomal RNA subunit through the pore. 164 matched cddid_all.tbl CDD pfam10430 pfam10430 463089 Ig_Tie2_1 Tie-2 Ig-like domain 1. 95 matched cddid_all.tbl CDD pfam10431 pfam10431 463090 ClpB_D2-small C-terminal, D2-small domain, of ClpB protein. This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, pfam00004) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerization, forming a tight interface with the D2-large domain of a neighbouring subunit and thereby providing enough binding energy to stabilize the functional assembly. The domain is associated with two Clp_N, pfam02861, at the N-terminus as well as AAA, pfam00004 and AAA_2, pfam07724. 81 matched cddid_all.tbl CDD pfam10432 pfam10432 431283 bact-PGI_C Bacterial phospho-glucose isomerase C-terminal SIS domain. This is the C-terminal SIS domain of a bacterial phospho-glucose isomerase EC:5.3.1.9 protein which is similar to eukaryote homologs to the extent that the sequence includes the cluster of threonines and serines that forms the sugar phosphate-binding site in conventional PGI. This domain contributes a good proportion of the active catalytic site residues. This PGI uses the same catalytic mechanisms for both glucose ring-opening and isomerization for the interconversion of glucose 6-phosphate to fructose 6-phosphate. It is associated with family SIS, pfam01380. 147 matched cddid_all.tbl CDD pfam10433 pfam10433 463091 MMS1_N Mono-functional DNA-alkylating methyl methanesulfonate N-term. MMS1 is a protein that protects against replication-dependent DNA damage in Saccharomyces cerevisiae. MMS1 belongs to the DDB1 family of cullin 4 adaptors and the two proteins are homologous. MMS1 bridges the interaction of MMS22 and Crt10 with Cul8/Rtt101. Cul8/Rtt101 is a cullin protein involved in the regulation of DNA replication subsequent to DNA damage. The N-terminal region of MMS1 and the C-terminal of MMS22 are required for the the MMS1-MMS22 interaction. The human HIV-1 virion-associated protein Vpr assembles with DDB1 through interaction with DCAF1 (chromatin assembly factor) to form an E3 ubiquitin ligase that targets cellular substrates for proteasome-mediated degradation and subsequent G2 arrest. 486 matched cddid_all.tbl CDD pfam10434 pfam10434 371048 MAM1 Monopolin complex protein MAM1. Monopolin is a protein complex, originally identified in Saccharomyces cerevisiae, that is required for the segregation of homologous centromeres to opposite poles of a dividing cell during meiosis I. MAM1 is required in S. cerevisiae for monopolar attachment. 255 matched cddid_all.tbl CDD pfam10435 pfam10435 463092 BetaGal_dom2 Beta-galactosidase, domain 2. This is the second domain of the five-domain beta-galactosidase enzyme that altogether catalyzes the hydrolysis of beta(1-3) and beta(1-4) galactosyl bonds in oligosaccharides as well as the inverse reaction of enzymatic condensation and trans-glycosylation. This domain is made up of 16 antiparallel beta-strands and an alpha-helix at its C terminus. The fold of this domain appears to be unique. In addition, the last seven strands of the domain form a subdomain with an immunoglobulin-like (I-type Ig) fold in which the first strand is divided between the two beta-sheets. In penicillin spp this strand is interrupted by a 12-residue insertion which forms an additional edge-strand to the second beta-sheet of the sub-domain. The remainder of the second domain forms a series of beta-hairpins at its N terminus, four strands of which are contiguous with part of the Ig-like sub-domain, forming in total a seven-stranded antiparallel beta-sheet. This domain is associated with family Glyco_hydro_35, pfam01301, which is N-terminal to it, but itself has no metazoan members. 180 matched cddid_all.tbl CDD pfam10436 pfam10436 463093 BCDHK_Adom3 Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase. Catabolism and synthesis of leucine, isoleucine and valine are finely balanced, allowing the body to make the most of dietary input but removing excesses to prevent toxic build-up of their corresponding keto-acids. This is the butyryl-CoA dehydrogenase, subunit A domain 3, a largely alpha-helical bundle of the enzyme BCDHK. This enzyme is the regulator of the dehydrogenase complex that breaks branched-chain amino-acids down, by phosphorylating and thereby inactivating it when synthesis is required. The domain is associated with family HATPase_c pfam02518 which is towards the C-terminal. 158 matched cddid_all.tbl CDD pfam10437 pfam10437 431286 Lip_prot_lig_C Bacterial lipoate protein ligase C-terminus. This is the C-terminal domain of a bacterial lipoate protein ligase. There is no conservation between this C-terminus and that of vertebrate lipoate protein ligase C-termini, but both are associated with the domain BPL_LipA_LipB pfam03099, further upstream. This domain is required for adenylation of lipoic acid by lipoate protein ligases. The domain is not required for transfer of lipoic acid from the adenylate to the lipoyl domain. Upon adenylation, this domain rotates 180 degrees away from the active site cleft. Therefore, the domain does not interact with the lipoyl domain during transfer. 85 matched cddid_all.tbl CDD pfam10438 pfam10438 431287 Cyc-maltodext_C Cyclo-malto-dextrinase C-terminal domain. This domain is at the very C-terminus of cyclo-malto-dextrinase proteins and consists of 8 beta strands, is largely globular and appears to help stabilize the acitve sites created by upstream domains, Cyc-maltodext_N pfam09087, and Alpha-amylase pfam00128. Cyclo-malto-dextrinases hydrolyse cyclodextrans to maltose and glucose and catalyze trans-glycosylation of oligosaccharides to the C3-, C4- or C6-hydroxyl groups of various acceptor sugar molecules. 76 matched cddid_all.tbl CDD pfam10439 pfam10439 402184 Bacteriocin_IIc Bacteriocin class II with double-glycine leader peptide. This is a family of bacteriocidal bacteriocins secreted by Streptococcal species in order to kill off closely-related competitor Gram-positives. The sequence includes the peptide precursor, this being cleaved off proteolytically at the double-glycine. The family does not carry the YGNGVXC motif characteriztic of pediocin-like Bacteriocins, Bacteriocin_II pfam01721. The producer bacteria are protected from the effects of their own bacteriocins by production of a specific immunity protein which is co-transcribed with the genes encoding the bacteriocins, eg family EntA_Immun pfam08951. The bacteriocins are structurally more specific than their immunity-protein counterparts. Typically, production of the bacteriocin gene is from within an operon carrying up to 6 genes including a typical two-component regulatory system (R and H), a small peptide pheromone (C), and a dedicated ABC transporter (A and -B) as well as an immunity protein. The ABC transporter is thought to recognize the N termini of both the pheromone and the bacteriocins and to transport these peptides across the cytoplasmic membrane, concurrent with cleavage at the conserved double-glycine motif. Cleaved extracellular C can then bind to the sensor kinase, H, resulting in activation of R and up-regulation of the entire gene cluster via binding to consensus sequences within each promoter. It seems likely that this whole regulon is carried on a transmissible plasmid which is passed between closely related Firmicute species since many clinical isolates from different Firmicutes can produce at least two bacteriocins. and the same bacteriocins can be produced by different species. 58 matched cddid_all.tbl CDD pfam10440 pfam10440 431288 WIYLD Ubiquitin-binding WIYLD domain. This presumed domain has been predicted to contain three alpha helices. The domain was named the WIYLD domain based on the pattern of most conserved residues. It binds ubiquitin. In the Arabidopsis thaliana histone-lysine N-methyltransferase SUVR4, binding of ubiquitin to this domain stimulates enzymatic activity and converts its activity from a strict dimethylase to a di/trimethylase. 58 matched cddid_all.tbl CDD pfam10441 pfam10441 431289 Urb2 Urb2/Npa2 family. This family includes the Urb2 protein from yeast that are involved in ribosome biogenesis. 213 matched cddid_all.tbl CDD pfam10442 pfam10442 463094 FIST_C FIST C domain. The FIST C domain is a novel sensory domain, which is present in signal transduction proteins from Bacteria, Archaea and Eukarya. Chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids. 135 matched cddid_all.tbl CDD pfam10443 pfam10443 371055 RNA12 RNA12 protein. This family includes RNA12 from S. cerevisiae. That protein contains an RRM domain. This region is C-terminal to that and includes a P-loop motif suggesting this region binds to NTP. The RNA12 proteins is involved in pre-rRNA maturation. 429 matched cddid_all.tbl CDD pfam10444 pfam10444 463095 Nbl1_Borealin_N Nbl1 / Borealin N terminal. Nbl1 is a subunit of the conserved CPC, the chromosomal passenger complex, which regulates mitotic chromosome segregation. In Fungi and Animalia, this complex consists of the kinase Aurora B/AIR-2/Ipl1p, INCENP/ICP-1/Sli15p, and Survivin/BIR-1/Bir1p. In Animalia, a fourth subunit (Borealin/Dasra/CSC-1) is required for targeting CPC to centromeres and central spindles. Nbl1 has been shown in budding yeast to be essential for viability, and for CPC localization, stability, integrity, and function. The N terminus of Borealin is homologous to Nbl1. This family contains both Nbl1, and the N terminal region of Borealin. 57 matched cddid_all.tbl CDD pfam10445 pfam10445 402189 DUF2456 Protein of unknown function (DUF2456). This is a family of uncharacterized proteins. 94 matched cddid_all.tbl CDD pfam10446 pfam10446 431292 DUF2457 Protein of unknown function (DUF2457). This is a family of uncharacterized proteins. 459 matched cddid_all.tbl CDD pfam10447 pfam10447 402191 EXOSC1 Exosome component EXOSC1/CSL4. This family of proteins are components of the exosome 3'->5' exoribonuclease complex. The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions. 112 matched cddid_all.tbl CDD pfam10448 pfam10448 402192 POC3_POC4 20S proteasome chaperone assembly proteins 3 and 4. This family contains chaperones of the 20S proteasome which function in early 20S proteasome assembly. The structures of two of the proteins in this family (POC3 and POC4) have been solved, and they closely resemble those of the mammalian proteasome assembling chaperone PAC3, although there is little sequence similarity between them. 136 matched cddid_all.tbl CDD pfam10450 pfam10450 402193 POC1 POC1 chaperone. In yeast, POC1 is a chaperone of the 20S proteasome which functions in early 20S proteasome assembly. 223 matched cddid_all.tbl CDD pfam10451 pfam10451 371062 Stn1 Telomere regulation protein Stn1. The budding yeast protein Stn1 is a DNA-binding protein which has specificity for telomeric DNA. Structural profiling has predicted an OB-fold. This domain is the N-terminal part of the molecule, which adopts the OB fold. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution. 252 matched cddid_all.tbl CDD pfam10452 pfam10452 371063 TCO89 TORC1 subunit TCO89. TC089 is a component of the TORC1 complex. TORC1 is responsible for a wide range of rapamycin-sensitive cellular activities. 546 matched cddid_all.tbl CDD pfam10453 pfam10453 463096 NUFIP1 Nuclear fragile X mental retardation-interacting protein 1 (NUFIP1). Proteins in this family have been implicated in the assembly of the large subunit of the ribosome and in telomere maintenance. Some proteins in this family contain a CCCH zinc finger. This family contains a protein called human fragile X mental retardation-interacting protein 1, which is known to bind RNA and is phosphorylated upon DNA damage. 53 matched cddid_all.tbl CDD pfam10454 pfam10454 431294 DUF2458 Protein of unknown function (DUF2458). This a is family of uncharacterized proteins. 172 matched cddid_all.tbl CDD pfam10455 pfam10455 402196 BAR_2 Bin/amphiphysin/Rvs domain for vesicular trafficking. This Pfam entry includes proteins that are not matched by pfam03114. 286 matched cddid_all.tbl CDD pfam10456 pfam10456 313646 BAR_3_WASP_bdg WASP-binding domain of Sorting nexin protein. The C-terminal region of the Sorting nexin group of proteins appears to carry a BAR-like (Bin/amphiphysin/Rvs) domain. This domain is very diverse and the similarities with other BAR domains are few. In the Sorting nexins it is associated with family PX, pfam00787.13, and in combination with PX appears to be necessary to bind WASP along with p85 to form a multimeric signalling complex. 236 matched cddid_all.tbl CDD pfam10457 pfam10457 463097 MENTAL Cholesterol-capturing domain. Human meta-static lymph node (MLN) 64 is a late endosomal membrane protein, and carries this MENTAL (MLN64N-terminal) domain at its N-terminus. The domain is composed of four trans-membrane helices with three short intervening loops. The function of the domain is to capture cholesterol and pass it to the associated START domain pfam01852 for transfer to a cytosolic acceptor protein or membrane. In mammals, the MENTAL domain is involved in the localization of MLN64 and MENTHO in late endosomes, and also in homo-and of hetero-interactions of these two proteins. 177 matched cddid_all.tbl CDD pfam10458 pfam10458 431296 Val_tRNA-synt_C Valyl tRNA synthetase tRNA binding arm. This domain is found at the C-terminus of Valyl tRNA synthetases. 66 matched cddid_all.tbl CDD pfam10459 pfam10459 431297 Peptidase_S46 Peptidase S46. Dipeptidyl-peptidase 7 (DPP-7) is the best characterized member of this family. It is a serine peptidase that is located on the cell surface and is predicted to have two N-terminal transmembrane domains. 695 matched cddid_all.tbl CDD pfam10460 pfam10460 431298 Peptidase_M30 Peptidase M30. This family contains the metallopeptidase hyicolysin. Hyicolysin has a zinc ion which is liganded by two histidine and one glutamate residue. 369 matched cddid_all.tbl CDD pfam10461 pfam10461 463098 Peptidase_S68 Peptidase S68. This family of serine peptidases contains PIDD proteins. PIDD forms a complex with RAIDD and procaspase-2 that is known as the 'PIDDosome'. The PIDDosome forms when DNA damage occurs and either activates NF-kappaB, leading to cell survival, or caspase-2, which leads to apoptosis. 34 matched cddid_all.tbl CDD pfam10462 pfam10462 287440 Peptidase_M66 Peptidase M66. This family of metallopeptidases contains StcE, a virulence factor found in Shiga toxigenic Escherichia coli organizms. StcE peptidase cleaves C1 esterase inhibitor. 306 matched cddid_all.tbl CDD pfam10463 pfam10463 402201 Peptidase_U49 Peptidase U49. This family contains Lit peptidase from Escherichia coli. Lit protease functions in bacterial cell death in response to infection by bacteriophage T4. Following binding of Gol peptide to domains II and III of elongation factor Tu, the Lit peptidase cleaves domain I of the elongation factor. This prevents binding of guanine nucleotides, shuts down translation and leads to cell death. 198 matched cddid_all.tbl CDD pfam10464 pfam10464 463099 Peptidase_U40 Peptidase U40. This family contains P5 murein endopeptidase from bacteriophage phi-6. P5 murein endopeptidase has lytic activity against several gram-negative bacteria. It is thought that the enzyme cleaves the cell wall peptide bridge formed by meso-2,6-diaminopimelic acid and D-Ala 212 matched cddid_all.tbl CDD pfam10465 pfam10465 463100 Inhibitor_I24 PinA peptidase inhibitor. PinA inhibits the endopeptidase La. It binds to the La homotetramer but does not interfere with the ATP binding site or the active site of La. 140 matched cddid_all.tbl CDD pfam10466 pfam10466 402202 Inhibitor_I34 Saccharopepsin inhibitor I34. The saccharopepsin inhibitor is highly specific for the aspartic peptidase saccharopepsin. It is largely unstructured in the absence of saccharopepsin, but in the presence, the inhibitor undergoes a conformation change forming an almost perfect alpha-helix from Asn2 to Met32 in the active site cleft of the peptidase. 69 matched cddid_all.tbl CDD pfam10467 pfam10467 313652 Inhibitor_I48 Peptidase inhibitor clitocypin. Clitocypin binds and inhibits cysteine proteinases. It has no similarity to any other known cysteine proteinase inhibitors but bears some similarity to a lectin-like family of proteins from mushrooms. 142 matched cddid_all.tbl CDD pfam10468 pfam10468 402203 Inhibitor_I68 Carboxypeptidase inhibitor I68. This is a family of tick carboxypetidase inhibitors. 74 matched cddid_all.tbl CDD pfam10469 pfam10469 402204 AKAP7_NLS AKAP7 2'5' RNA ligase-like domain. AKAP7_NLS is the N-terminal domain of the cyclic AMP-dependent protein kinase A, PKA, anchor protein AKAP7. This protein anchors PKA for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes. AKAP7_NLS carries the nuclear localization signal (NLS) KKRKK, that indicates the cellular destiny of this anchor protein. Binding to the regulatory subunits RI and RII of PKA is mediated via the family AKAP7_RIRII_bdg. at the C-terminus. This family represents a region that contains two 2'5' RNA ligase like domains pfam02834. Presumably this domain carried out some as yet unknown enzymatic function. 207 matched cddid_all.tbl CDD pfam10470 pfam10470 463101 AKAP7_RIRII_bdg PKA-RI-RII subunit binding domain of A-kinase anchor protein. AKAP7_RIRII_bdg is the C-terminal domain of the cyclic AMP-dependent protein kinase A, PKA, anchor protein AKAP7. This protein anchors PKA, for its role in regulating PKA-mediated gene transcription in both somatic cells and oocytes, by binding to its regulatory subunits, RI and RII, hence being known as a dual-specific AKAP. The 25 crucial amino acids of RII-binding domains in general form structurally conserved amphipathic helices with unrelated sequences; hydrophobic amino acid residues form the backbone of the interaction and hydrogen bond- and salt-bridge-forming amino acid residues increase the affinity of the interaction. The N-terminus, of family AKAP7_NLS, carries the nuclear localization signal. 56 matched cddid_all.tbl CDD pfam10471 pfam10471 402205 ANAPC_CDC26 Anaphase-promoting complex APC subunit CDC26. The anaphase-promoting complex (APC) or cyclosome is a cell cycle-regulated ubiquitin-protein ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins thereby targeting them for proteolysis by the 26S proteasome. CDC26 is one of the nine or so subunits identified within APC but its exact function is not known. The APC/C becomes active at the metaphase/anaphase transition and remains active during G1 phase. One mechanism linked to activation of the APC/C is phosphorylation. The yeast APC/C is composed of at least 13 subunits, but the function of many of the subunits is unknown. Hcn1 is the smallest subunit of the S. pombe APC/C, and is found to be essential for cell viability, APC/C integrity, and proper APC/C regulation. In addition, Hcn1 phosphorylation indicates a specific role for the phosphorylation of this subunit late in the cell cycle. 65 matched cddid_all.tbl CDD pfam10472 pfam10472 371074 CReP_N eIF2-alpha phosphatase phosphorylation constitutive repressor. This is the conserved N-terminal domain of CReP, constitutive repressor of eIF2-alpha phosphorylation/protein phosphatase 1, catalytic subunit. It functions in the dephosphorylation of eIF2-alpha under basal conditions in the absence of stress. In response to translation inhibition, there is reduced synthesis of the labile CReP that contributes to elevated levels of eIF2-alpha phosphorylation. The C-terminus, family PP1c, is shared with the apoptosis-associated protein Gadd34 and herpes simplex virus. 411 matched cddid_all.tbl CDD pfam10473 pfam10473 463102 CENP-F_leu_zip Leucine-rich repeats of kinetochore protein Cenp-F/LEK1. Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway. There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance. 140 matched cddid_all.tbl CDD pfam10474 pfam10474 463103 DUF2451 Protein of unknown function C-terminus (DUF2451). This protein is found in eukaryotes but its function is not known. The C-terminal part of some members is DUF2450. 229 matched cddid_all.tbl CDD pfam10475 pfam10475 431303 Vps54_N Vacuolar-sorting protein 54, of GARP complex. This is a family of vacuolar-sorting proteins 54, from eukaryotes. Along with VPS52 and VPS53 this forms the Golgi-associated retrograde protein complex GARP. VPS54 is separated into N- and C-terminal regions each of which has a different function. This N-terminal family of is important for GARP complex assembly and stability, whereas the C-terminal domain, pfam07928, brings about localization to an early endocytic compartment. 291 matched cddid_all.tbl CDD pfam10476 pfam10476 463104 DUF2448 Protein of unknown function C-terminus (DUF2448). The family DUF2349 is the N-terminal part of this family. This protein is found in eukaryotes but its function is not known. 201 matched cddid_all.tbl CDD pfam10477 pfam10477 371079 EIF4E-T Nucleocytoplasmic shuttling protein for mRNA cap-binding EIF4E. EIF4E-T is the transporter protein for shuttling the mRNA cap-binding protein EIF4E protein, targeting it for nuclear import. EIF4E-T contains several key binding domains including two functional leucine-rich NESs (nuclear export signals) between residues 438-447 and 613-638 in the human protein. The other two binding domains are an EIF4E-binding site, between residues 27-42 in Q9EST3, and a bipartite NLS (nuclear localization signals) between 194-211, and these lie in family EIF4E-T_N. EIF4E is the eukaryotic translation initiation factor 4E that is the rate-limiting factor for cap-dependent translation initiation. 646 matched cddid_all.tbl CDD pfam10479 pfam10479 463105 FSA_C Fragile site-associated protein C-terminus. This is the conserved C-terminal half of the protein KIAA1109 which is the fragile site-associated protein FSA. Genome-wide-association studies showed this protein to linked to the susceptibility to coeliac disease. The protein may also be associated with polycystic kidney disease. 701 matched cddid_all.tbl CDD pfam10480 pfam10480 119000 ICAP-1_inte_bdg Beta-1 integrin binding protein. ICAP-1 is a serine/threonine-rich protein that binds to the cytoplasmic domains of beta-1 integrins in a highly specific manner, binding to a NPXY sequence motif on the beta-1 integrin. The cytoplasmic domains of integrins are essential for cell adhesion, and the fact that phosphorylation of ICAP-1 by interaction with the cell-matrix implies an important role of ICAP-1 during integrin-dependent cell adhesion. Overexpression of ICAP-1 strongly reduces the integrin-mediated cell spreading on extracellular matrix and inhibits both Cdc42 and Rac1. In addition, ICAP-1 induces release of Cdc42 from cellular membranes and prevents the dissociation of GDP from this GTPase. An additional function of ICAP-1 is to promote differentiation of osteoprogenitors by supporting their condensation through modulating the integrin high affinity state, 200 matched cddid_all.tbl CDD pfam10481 pfam10481 463106 CENP-F_N Cenp-F N-terminal domain. Mitosin or centromere-associated protein-F (Cenp-F) is found bound across the centromere as one of the proteins of the outer layer of the kinetochore. Most of the kinetochore/centromere functions appear to depend upon binding of the C-terminal par to f the molecule, whereas the N-terminal part, here, may be a cytoplasmic player in controlling the function of microtubules and dynein. 304 matched cddid_all.tbl CDD pfam10482 pfam10482 463107 CtIP_N Tumour-suppressor protein CtIP N-terminal domain. CtIP is predominantly a nuclear protein that complexes with both BRCA1 and the BRCA1-associated RING domain protein (BARD1). At the protein level, CtIP expression varies with cell cycle progression in a pattern identical to that of BRCA1. Thus, the steady-state levels of CtIP polypeptides, which remain low in resting cells and G1 cycling cells, increase dramatically as Dividing cells traverse the G1/S boundary. CtIP can potentially modulate the functions ascribed to BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control. This N-terminal domain carries a coiled-coil region and is essential for homodimerization of the protein. The C-terminal domain is family pfam08573. 120 matched cddid_all.tbl CDD pfam10483 pfam10483 431307 Elong_Iki1 Elongator subunit Iki1. This family is a component of the RNA polymerase II elongator complex. This complex is involved in elongation of RNA polymerase II transcription and in modification of wobble nucleosides in tRNA. 282 matched cddid_all.tbl CDD pfam10484 pfam10484 463108 MRP-S23 Mitochondrial ribosomal protein S23. MRP-S23 is one of the proteins that makes up the 55S ribosome in eukaryotes from nematodes to humans. It does not appear to carry any common motifs, either RNA binding or ribosomal protein motifs. All of the mammalian MRPs are encoded in nuclear genes that are evolving more rapidly than those encoding cytoplasmic ribosomal proteins. The MRPs are imported into mitochondria where they assemble coordinately with mitochondrially transcribed rRNAs into ribosomes that are responsible for translating the 13 mRNAs for essential proteins of the oxidative phosphorylation system. MRP-S23 is significantly up-regulated in uterine cancer cells. 128 matched cddid_all.tbl CDD pfam10486 pfam10486 463109 PI3K_1B_p101 Phosphoinositide 3-kinase gamma adapter protein p101 subunit. Class I PI3Ks are dual-specific lipid and protein kinases involved in numerous intracellular signaling pathways. Class IB PI3K, p110gamma, is mainly activated by seven-transmembrane G-protein-coupled receptors (GPCRs), through its regulatory subunit p101 and G-protein beta-gamma subunits. 860 matched cddid_all.tbl CDD pfam10487 pfam10487 463110 Nup188 Nucleoporin subcomplex protein binding to Pom34. This is one of the many peptides that make up the nucleoporin complex (NPC), and is found across eukaryotes. The Nup188 subcomplex (Nic96p-Nup188p-Nup192p-Pom152p) is one of at least six that make up the NPC, and as such is symmetrically localized on both faces of the NPC at the nuclear end, being integrally bound to the C-terminus of Pom34p. 925 matched cddid_all.tbl CDD pfam10488 pfam10488 431311 PP1c_bdg Phosphatase-1 catalytic subunit binding region. This conserved C-terminus appears to be a protein phosphatase-1 catalytic subunit (PP1C) binding region, which may in some circumstances also be retroviral in origin since it is found in both herpes simplex virus and in mouse and man. This domain is found in Gadd-34 apoptosis-associated proteins as well as the constitutive repressor of eIF2-alpha phosphorylation/protein phosphatase 1, regulatory (inhibitor) subunit 15b, otherwise known as CReP. Diverse stressful conditions are associated with phosphorylation of the {alpha} subunit of eukaryotic translation initiation factor 2 (eIF2{alpha}) on serine 51. This signaling event, which is conserved from yeast to mammals, negatively regulates the guanine nucleotide exchange factor, eIF2-B and inhibits the recycling of eIF2 to its active GTP bound form. In mammalian cells eIF2{alpha} phosphorylation emerges as an important event in stress signaling that impacts on gene expression at both the translational and transcriptional levels. 287 matched cddid_all.tbl CDD pfam10490 pfam10490 463111 CENP-F_C_Rb_bdg Rb-binding domain of kinetochore protein Cenp-F/LEK1. Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway. This domain is at the very C-terminus of the C-terminal coiled-coil, and is one of the key Rb-binding domains. 47 matched cddid_all.tbl CDD pfam10491 pfam10491 463112 Nrf1_DNA-bind NLS-binding and DNA-binding and dimerization domains of Nrf1. In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human. Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates. The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila. The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein, Swiss-Prot:Q8C4C0, there is also an NLS domain at 88-116, and a DNA binding and dimerization domain at 127-282. Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity. 213 matched cddid_all.tbl CDD pfam10492 pfam10492 463113 Nrf1_activ_bdg Nrf1 activator activation site binding domain. In Drosophila, the erect wing (ewg) protein is required for proper development of the central nervous system and the indirect flight muscles. The fly ewg gene encodes a novel DNA-binding domain that is also found in four genes previously identified in sea urchin, chicken, zebrafish, and human. Nuclear respiratory factor-1 is a transcriptional activator that has been implicated in the nuclear control of respiratory chain expression in vertebrates. The first 26 amino acids of nuclear respiratory factor-1 are required for the binding of dynein light chain. The interaction with dynein light chain is observed for both ewg and Nrf-1, transcription factors that are structurally and functionally similar between humans and Drosophila. The highest level of expression of both ewg and Nrf-1 was found in the central nervous system, somites, first branchial arch, optic vesicle, and otic vesicle. In the mouse Nrf-1 protein there is an activation domain at 303-469, the most conserved part of which is this domain 446-469. Ewg is a site-specific transcriptional activator, and evolutionarily conserved regions of ewg contribute both positively and negatively to transcriptional activity. The family Nrf1_DNA-bind is associated with this domain towards the N-terminal, as is the N terminal of the activation domain. 82 matched cddid_all.tbl CDD pfam10493 pfam10493 463114 Rod_C Rough deal protein C-terminal region. Rod, the Rough deal protein, displays a dynamic intracellular staining pattern, localising first to kinetochores in pro-metaphase, but moving to kinetochore microtubules at metaphase. Early in anaphase the protein is once again restricted to the kinetochores, where it persists until the end of telophase. This behaviour is in all respects similar to that described for ZW10, and indeed the two proteins function together, localization of each depending upon the other. These two proteins are found at the kinetochore in complex with a third, Zwilch, in both flies and humans. The C-terminus is the most conserved part of the protein. During pro-metaphase, the ZW10-Rod complex, dynein/dynactin, and Mad2 all accumulate on unattached kinetochores; microtubule capture leads to Mad2 depletion as it is carried off by dynein/dynactin; ZW10-Rod complex accumulation continues, replenishing kinetochore dynein. The continuing recruitment of the ZW10-Rod complex during metaphase may serve to maintain adequate dynein/dynactin complex on kinetochores for assisting chromatid movement during anaphase. The ZW10-Rod complex acts as a bridge whose association with Zwint-1 links Mad1 and Mad2, components that are directly responsible for generating the diffusible 'wait anaphase' signal, to a structural, inner kinetochore complex containing Mis12 and KNL-1AF15q14, the last of which has been proved to be essential for kinetochore assembly in C. elegans. Removal of ZW10 or Rod inactivates the mitotic checkpoint. 551 matched cddid_all.tbl CDD pfam10494 pfam10494 431315 Stk19 Serine-threonine protein kinase 19. This serine-threonine protein kinase number 19 is expressed from the MHC and predominantly in the nucleus. Protein kinases are involved in signal transduction pathways and play fundamental roles in the regulation of cell functions. This is a novel Ser/Thr protein kinase, that has Mn2+-dependent protein kinase activity that phosphorylates alpha -casein at Ser/Thr residues and histone at Ser residues. It can be covalently modified by the reactive ATP analogue 5'-p-fluorosulfonylbenzoyladenosine in the absence of ATP, and this modification is prevented in the presence of 1 mM ATP, indicating that the kinase domain of is capable of binding ATP. 262 matched cddid_all.tbl CDD pfam10495 pfam10495 463115 PACT_coil_coil Pericentrin-AKAP-450 domain of centrosomal targeting protein. This domain is a coiled-coil region close to the C-terminus of centrosomal proteins that is directly responsible for recruiting AKAP-450 and pericentrin to the centrosome. Hence the suggested name for this region is a PACT domain (pericentrin-AKAP-450 centrosomal targeting). This domain is also present at the C-terminus of coiled-coil proteins from Drosophila and S. pombe, and that from the Drosophila protein is sufficient for targeting to the centrosome in mammalian cells. The function of these proteins is unknown but they seem good candidates for having a centrosomal or spindle pole body location. The final 22 residues of this domain in AKAP-450 appear specifically to be a calmodulin-binding domain indicating that this member at least is likely to contribute to centrosome assembly. 77 matched cddid_all.tbl CDD pfam10496 pfam10496 463116 Syntaxin-18_N SNARE-complex protein Syntaxin-18 N-terminus. This is the conserved N-terminal of Syntaxin-18. Syntaxin-18 is found in the SNARE complex of the endoplasmic reticulum and functions in the trafficking between the ER intermediate compartment and the cis-Golgi vesicle. In particular, the N-terminal region is important for the formation of ER aggregates. More specifically, syntaxin-18 is involved in endoplasmic reticulum-mediated phagocytosis, presumably by regulating the specific and direct fusion of the ER with the plasma or phagosomal membranes. 87 matched cddid_all.tbl CDD pfam10497 pfam10497 463117 zf-4CXXC_R1 Zinc-finger domain of monoamine-oxidase A repressor R1. R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type. 99 matched cddid_all.tbl CDD pfam10498 pfam10498 463118 IFT57 Intra-flagellar transport protein 57. Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organizms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans. 360 matched cddid_all.tbl CDD pfam10500 pfam10500 463119 SR-25 Nuclear RNA-splicing-associated protein. SR-25, otherwise known as ADP-ribosylation factor-like factor 6-interacting protein 4, is expressed in virtually all tissues. At the N-terminus there is a repeat of serine-arginine (SR repeat), and towards the middle of the protein there are clusters of both serines and of basic amino acids. The presence of many nuclear localization signals strongly implies that this is a nuclear protein that may contribute to RNA splicing. SR-25 is also implicated, along with heat-shock-protein-27, as a mediator in the Rac1 (GTPase ras-related C3 botulinum toxin substrate 1) signalling pathway. 226 matched cddid_all.tbl CDD pfam10501 pfam10501 402226 Ribosomal_L50 Ribosomal subunit 39S. The 39S ribosomal protein appears to be a subunit of one of the larger mitochondrial 66S or 70S units. Under conditions of ethanol-stress in rats the larger subunit is largely dissociated into its smaller components. In E. coli, in the absence of the enzyme pseudouridine synthase (RluD) synthase, there is an accumulation of 50S and 30S subunits and the appearance of abnormal particles (62S and 39S), with concomitant loss of 70S ribosomes. 109 matched cddid_all.tbl CDD pfam10502 pfam10502 431321 Peptidase_S26 Signal peptidase, peptidase S26. This is a family of membrane signal serine endopeptidases which function in the processing of newly-synthesized secreted proteins. Peptidase S26 removes the hydrophobic, N-terminal, signal peptides as proteins are translocated across membranes. The active site residues take the form of a catalytic dyad that is Ser, Lys in subfamily S26A; the Ser is the nucleophile in catalysis, and the Lys is the general base. 162 matched cddid_all.tbl CDD pfam10503 pfam10503 431322 Esterase_PHB Esterase PHB depolymerase. This family of proteins include acetyl xylan esterases (AXE), feruloyl esterases (FAE), and poly(3-hydroxybutyrate) (PHB) depolymerases. 222 matched cddid_all.tbl CDD pfam10504 pfam10504 463120 DUF2452 Protein of unknown function (DUF2452). This protein is found in eukaryotes but its function is unknown. 156 matched cddid_all.tbl CDD pfam10505 pfam10505 463121 NARG2_C NMDA receptor-regulated gene protein 2 C-terminus. The transition of neuronal cells from pre-cursor to mature state is regulated by the N-methyl-d-aspartate (NMDA) receptor, a glutamate-gated ion channel that is permeable to Ca2+. NMDA receptors probably mediate this activity by permitting expression of NARG2. NARG2 is transiently expressed, being a regulatory protein that is present in the nucleus of dividing cells and then down-regulated as progenitors exit the cell cycle and begin to differentiate. NARG2 contains repeats of (S/T)PXX, (11 in mouse, six in human), a putative DNA-binding motif that is found in many gene-regulatory proteins including Kruppel, Hunchback and Antennapedi. 208 matched cddid_all.tbl CDD pfam10506 pfam10506 463122 MCC-bdg_PDZ PDZ domain of MCC-2 bdg protein for Usher syndrome. The protein has a high homology to the tumour suppressor MCC (mutated in colon cancer; or MCC1 hereafter) and was named MCC2. MCC2 protein binds the first PDZ domain of AIE-75 with its C-terminal amino acids -DTFL. A possible role of MCC2 as a tumor suppressor has been put forward. The carboxyl terminus of the predicted protein was DTFL which matched the consensus motif X-S/T-X-phi (phi: hydrophobic amino acid residue) for binding to the PDZ domain of AIE-75. 65 matched cddid_all.tbl CDD pfam10507 pfam10507 463123 TMEM65 Transmembrane protein 65. MEM65 is an intercalated disc protein that interacts with with connexin 43 (Cx43) and is required for correct localization of Cx43 to the intercalated disc. It is essential for cardiac function in zebrafish. 108 matched cddid_all.tbl CDD pfam10508 pfam10508 463124 Proteasom_PSMB Proteasome non-ATPase 26S subunit. The 26S proteasome, a eukaryotic ATP-dependent, dumb-bell shaped, protease complex with a molecular mass of approx 20kDa consists of a central 20S proteasome,functioning as a catalytic machine, and two large V-shaped terminal modules, having possible regulatory roles,composed of multiple subunits of 25- 110 kDa attached to the central portion in opposite orientations. It is responsible for degradation of abnormal intracellular proteins, including oxidatively damaged proteins, and may play a role as a component of a cellular anti-oxidative system. Expression of catalytic core subunits including PSMB5 and peptidase activities of the proteasome were elevated following incubation with 3-methylcholanthrene. The 20S proteasome comprises a cylindrical stack of four rings, two outer rings formed by seven alpha-subunits (alpha1-alpha7) and two inner rings of seven beta-subunits (beta1-beta7). Two outer rings of alpha subunits maintain structure, while the central beta rings contain the proteolytic active core subunits beta1 (PSMB6), beta2 (PSMB7), and beta5 (PSMB5). Expression of PSMB5 can be altered by chemical reactants, such as 3-methylcholanthrene. 499 matched cddid_all.tbl CDD pfam10509 pfam10509 463125 GalKase_gal_bdg Galactokinase galactose-binding signature. This is the highly conserved galactokinase signature sequence which appears to be present in all galactokinases irrespective of how many other ATP binding sites, etc that they carry. The function of this domain appears to be to bind galactose, and the domain is normally at the N-terminus of the enzymes, EC:2.7.1.6. This domain is associated with the families GHMP_kinases_C, pfam08544 and GHMP_kinases_N, pfam00288. 50 matched cddid_all.tbl CDD pfam10510 pfam10510 463126 PIG-S Phosphatidylinositol-glycan biosynthesis class S protein. PIG-S is one of several key, core, components of the glycosylphosphatidylinositol (GPI) trans-amidase complex that mediates GPI anchoring in the endoplasmic reticulum. Anchoring occurs when a protein's C-terminal GPI attachment signal peptide is replaced with a pre-assembled GPI. Mammalian GPITransamidase consists of at least five components: Gaa1, Gpi8, PIG-S, PIG-T, and PIG-U, all five of which are required for function. It is possible that Gaa1, Gpi8, PIG-S, and PIG-T form a tightly associated core that is only weakly associated with PIG-U. The exact function of PIG-S is unclear. 502 matched cddid_all.tbl CDD pfam10511 pfam10511 371104 Cementoin Trappin protein transglutaminase binding domain. Trappin-2, itself a protease inhibitor, has this unique N-terminal domain that enables it to become cross-linked to extracellular matrix proteins by transglutaminase. This domain contains several repeated motifs with the the consensus sequence Gly-Gln-Asp-Pro-Val-Lys, and these together can anchor the whole molecule to extracellular matrix proteins, such as laminin, fibronectin, beta-crystallin, collagen IV, fibrinogen, and elastin, by transglutaminase-catalyzed cross-links. The whole domain is rich in glutamine and lysine, thus allowing and transglutaminase(s) to catalyze the formation of an intermolecular epsilon-(gamma-glutamyl)lysine isopeptide bond. Cementoin is associated with the WAP family, pfam00095, at the C-terminus. 17 matched cddid_all.tbl CDD pfam10512 pfam10512 463127 Borealin Cell division cycle-associated protein 8. The chromosomal passenger complex of Aurora B kinase, INCENP, and Survivin has essential regulatory roles at centromeres and the central spindle in mitosis. Borealin is also a member of the complex. Approximately half of Aurora B in mitotic cells is complexed with INCENP, Borealin, and Survivin. Depletion of Borealin by RNA interference delays mitotic progression and results in kinetochore-spindle mis-attachments and an increase in bipolar spindles associated with ectopic asters. 120 matched cddid_all.tbl CDD pfam10513 pfam10513 463128 EPL1 Enhancer of polycomb-like. This is a family of EPL1 (Enhancer of polycomb-like) proteins. The EPL1 protein is a member of a histone acetyltransferase complex which is involved in transcriptional activation of selected genes. 168 matched cddid_all.tbl CDD pfam10514 pfam10514 402236 Bcl-2_BAD Pro-apoptotic Bcl-2 protein, BAD. BAD is a Bcl-2 homology domain 3 (BH3)-only pro-apoptotic member of the Bcl-2 protein family that is regulated by phosphorylation in response to survival factors. Binding of BAD to mitochondria is thought to be exclusively mediated by its BH3 domain. Membrane localization of BAD mediates membrane translocation of Bcl-XL. The C-terminal part of BAD is sufficient for membrane binding. There are two segments with differing lipid-binding preferences, LBD1 and LBD2, that are responsible for this binding: (i) LBD1 located in the proximity of the BH3 domain (amino acids 122-131) and (ii) LBD2, the putative C-terminal alpha-helix-5. Phosphorylation-regulated 14-3-3 protein binding may expose the cholesterol-preferring LBD1 and bury the LBD2, thereby mediating translocation of BAD to raft-like micro-domains. 166 matched cddid_all.tbl CDD pfam10515 pfam10515 463129 APP_amyloid Beta-amyloid precursor protein C-terminus. This is the amyloid, C-terminal, protein of the beta-Amyloid precursor protein (APP) which is a conserved and ubiquitous transmembrane glycoprotein strongly implicated in the pathogenesis of Alzheimer's disease but whose normal biological function is unknown. The C-terminal 100 residues are released and aggregate into amyloid deposits which are strongly implicated in the pathology of Alzheimer's disease plaque-formation. The domain is associated with family A4_EXTRA, pfam02177, further towards the N-terminus. 52 matched cddid_all.tbl CDD pfam10516 pfam10516 402238 SHNi-TPR SHNi-TPR. SHNi-TPR family members contain a reiterated sequence motif that is an interrupted form of TPR repeat. 38 matched cddid_all.tbl CDD pfam10517 pfam10517 463130 DM13 Electron transfer DM13. The DM13 domain is a component of a novel electron-transfer system potentially involved in oxidative modification of animal cell-surface proteins. It contains a nearly absolutely conserved cysteine, which could be involved in a redox reaction, either as a naked thiol group or through binding a prosthetic group like heme. 105 matched cddid_all.tbl CDD pfam10518 pfam10518 463131 TAT_signal TAT (twin-arginine translocation) pathway signal sequence. 26 matched cddid_all.tbl CDD pfam10520 pfam10520 463132 Lipid_desat Lipid desaturase domain. This entry represents a family of lipid desaturase domains. The TMEM189 protein is a plasmanylethanolamine desaturase enzyme. The domain is also found on fatty acid saturase FAD4 in Arabidopsis. 174 matched cddid_all.tbl CDD pfam10521 pfam10521 431336 Tti2 Tti2 family. Budding yeast Tti2 is a subunit of the ASTRA complex, which is involved in chromatin remodelling. Tti2 homolog from humans, TELO2-interacting protein 2, is part of the TTT complex that is involved in the cellular resistance to DNA damage stresses. 282 matched cddid_all.tbl CDD pfam10522 pfam10522 371112 RII_binding_1 RII binding domain. This domain is found is a wide variety of AKAPs (A kinase anchoring proteins). The domain is also found on micro-tubule-associated proteins. 19 matched cddid_all.tbl CDD pfam10523 pfam10523 463133 BEN BEN domain. The BEN domain is found in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Computational analysis suggests that the BEN domain mediates protein-DNA and protein-protein interactions during chromatin organization and transcription. The BEN domain-containing protein 3 (BEND3) is shown to interact (via BEN domains 1 and 3) with ERCC6L (via N-terminal TPR repeat and SNF2 HeliC region of ERCC6L) which stimulates the ERCC6L translocase and ATPase activities. 76 matched cddid_all.tbl CDD pfam10524 pfam10524 463134 NfI_DNAbd_pre-N Nuclear factor I protein pre-N-terminus. The Nuclear factor I (NFI) family of site-specific DNA-binding proteins (also known as CTF or CAAT box transcription factor) functions both in viral DNA replication and in the regulation of gene expression in higher organizms. The N-terminal 200 residues contains the DNA-binding and dimerization domain, but also has an 8-47 residue highly conserved region 5' of this, whose function is not known. Deletion of the N-terminal 200 amino acids removes the DNA-binding activity, dimerization-ability and the stimulation of adenovirus DNA replication. 41 matched cddid_all.tbl CDD pfam10525 pfam10525 431338 Engrail_1_C_sig Engrailed homeobox C-terminal signature domain. Engrailed homeobox proteins are characterized by the presence of a conserved region of some 20 amino-acid residues located at the C-terminal of the 'homeobox' domain. This domain of approximately 20 residues forms a kind of a signature pattern for this subfamily of proteins. 31 matched cddid_all.tbl CDD pfam10528 pfam10528 463135 GLEYA GLEYA domain. The GLEYA domain is related to lectin-like binding domains found in the S. cerevisiae Flo proteins and the C. glabrata Epa proteins. It is a carbohydrate-binding domain that is found in fungal adhesins (also referred to as agglutinins or flocculins). Adhesins with a GLEYA domain possess a typical N-terminal signal peptide and a domain of conserved sequence repeats, but lack glycosylphosphatidylinositol (GPI) anchor attachment signals. They contain a conserved motif G(M/L)(E/A/N/Q)YA, hence the name GLEYA. Based on sequence homology, it is suggested that the GLEYA domain would predominantly contain beta sheets. The GLEYA domain is also found in S. pombe protein Swiss:Q92344, thought to be a kinetochore portein (Sim4 complex subunit), however no direct evidence for kinetochore association has been found. Furthermore, a global protein localization study in S. pombe identified it as a secreted protein localized to the Golgi complex. 91 matched cddid_all.tbl CDD pfam10529 pfam10529 402246 Hist_rich_Ca-bd Histidine-rich Calcium-binding repeat region. This is a histidine-rich calcium binding repeat which appears in proteins called histidine-rich-calcium binding proteins (HRC). HRC is a high capacity, low affinity Ca2+-binding protein, residing in the lumen of the sarcoplasmic reticulum. HRC binds directly to triadin. This binding interaction occurs between the histidine-rich region of HRC and multiple clusters of charged amino acids, named as the KEKE motifs, in the lumenal domain of triadin. The region in which this repeat is found in many copies is long and variable but is the acidic region of the protein. There is also a cysteine-rich region further towards the C-terminus. HRC may regulate sarcoplasmic reticular calcium transport and play a critical role in maintaining calcium homeostasis and function in the heart. HRC as a candidate regulator of sarcoplasmic reticular calcium uptake. 15 matched cddid_all.tbl CDD pfam10530 pfam10530 287498 Toxin_35 Toxin with inhibitor cystine knot ICK or Knottin scaffold. Spider toxins of the CSTX family are ion channel toxins containing an inhibitor cystine knot (ICK) structural motif or Knottin scaffold. The four disulfide bonds present in the CSTX spider toxin family are arranged in the following pattern: 1-4, 2-5, 3-8 and 6-7. CSTX-1 is the most important component of C. salei venom in terms of relative abundance and toxicity and therefore is likely to contribute significantly to the overall toxicity of the whole venom. CSTX-1 blocked rat neuronal L-type, but no other types of HVA Cav channels. Interestingly, the omega-toxins from Phoneutria nigriventer venom (another South American species also belonging to the Ctenidae family) are included as they carry the same disulfide bond arrangement. suggestive that CSTX-1 may interact with Cav channels. Calcium ion voltage channel heteromultimer containing an L-type pore-forming alpha1-subunit is the most probable candidate for the molecular target of CSTX-1 and these toxins. 61 matched cddid_all.tbl CDD pfam10531 pfam10531 463136 SLBB SLBB domain. 56 matched cddid_all.tbl CDD pfam10532 pfam10532 119052 Plant_all_beta Plant specific N-all beta domain. This domain was identified by Babu and colleagues. It is found associated with the WRKY domain pfam03106. 114 matched cddid_all.tbl CDD pfam10533 pfam10533 463137 Plant_zn_clust Plant zinc cluster domain. This zinc binding domain was identified by Babu and colleagues and found associated with the WRKY domain pfam03106. 42 matched cddid_all.tbl CDD pfam10534 pfam10534 463138 CRIC_ras_sig Connector enhancer of kinase suppressor of ras. The CRIC - Connector enhancer of kinase suppressor of ras - domain functions as a scaffold in several signal cascades and acts on proliferation, differentiation and apoptosis. 93 matched cddid_all.tbl CDD pfam10536 pfam10536 463139 PMD Plant mobile domain. This domain was identified by Babu and colleagues in a variety of transposases. 354 matched cddid_all.tbl CDD pfam10537 pfam10537 463140 WAC_Acf1_DNA_bd ATP-utilizing chromatin assembly and remodelling N-terminal. ACF (for ATP-utilizing chromatin assembly and remodelling factor) is a chromatin-remodelling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. The WAC (WSTF/Acf1/cbp146) domain is an approximately 110-residue module present at the N-termini of Acf1-related proteins in a variety of organizms. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. 101 matched cddid_all.tbl CDD pfam10538 pfam10538 431345 ITAM_Cys-rich Hantavirus ITAM motif. This entry represents an ITAM motif found in Hantavirus glycoprotein N. 38 matched cddid_all.tbl CDD pfam10539 pfam10539 463141 Dev_Cell_Death Development and cell death domain. The DCD domain is found in plant proteins involved in development and cell death. The DCD domain is an approximately 130 amino acid long stretch that contains several mostly invariable motifs. These include a FGLP and a LFL motif at the N-terminus and a PAQV and a PLxE motif towards the C-terminus of the domain. The DCD domain is present in proteins with different architectures. Some of these proteins contain additional recognisable motifs, like the KELCH repeats or the ParB domain. 126 matched cddid_all.tbl CDD pfam10541 pfam10541 463142 KASH Nuclear envelope localization domain. The KASH (for Klarsicht/ANC-1/Syne-1 homology) or KLS domain is a highly hydrophobic nuclear envelope localization domain of approximately 60 amino acids comprising a 20-amino-acid transmembrane region and a 30-35-residue C-terminal region that lies between the inner and the outer nuclear membranes. During meiotic prophase, telomeres cluster to form a bouquet arrangement of chromosomes. SUN and KASH domain proteins form complexes that span both membranes of the nuclear envelope. The KASH domain links the dynein motor complex of the microtubules, through the outer nuclear membrane to the Sad1 domain in the inner nuclear membrane which then interacts with the bouquet proteins Bqt1 and Bqt2 that are complexed with Bqt4, Rap1 and Taz1 and attached to the telomere. SUN domain-containing proteins are essential for recruiting KASH domain proteins at the outer nuclear membrane, and KASH domains provide a generic NE tethering device for functionally distinct proteins whose cytoplasmic domains mediate nuclear positioning, maintain physical connections with other cellular organelles, and possibly even influence chromosome dynamics. 58 matched cddid_all.tbl CDD pfam10542 pfam10542 371125 Vitelline_membr Vitelline membrane cysteine-rich region. In Drosophila melanogaster the vitelline membrane (VM) is the first layer of the eggshell produced by the follicular epithelium. It is composed of at least four different proteins. VM proteins are similarly organized with a central highly conserved 38-amino acid domain which is flanked by unrelated regions. The domain contains three highly conserved cysteines. 37 matched cddid_all.tbl CDD pfam10543 pfam10543 431348 ORF6N ORF6N domain. This domain was identified by Iyer and colleagues. 84 matched cddid_all.tbl CDD pfam10544 pfam10544 463143 T5orf172 T5orf172 domain. This domain was identified by Iyer and colleagues. 99 matched cddid_all.tbl CDD pfam10545 pfam10545 463144 MADF_DNA_bdg Alcohol dehydrogenase transcription factor Myb/SANT-like. The myb/SANT-like domain in Adf-1 (MADF) is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. 84 matched cddid_all.tbl CDD pfam10546 pfam10546 402259 P63C P63C domain. This domain was identified by Iyer and colleagues. 93 matched cddid_all.tbl CDD pfam10547 pfam10547 431351 P22_AR_N P22_AR N-terminal domain. This domain was identified by Iyer and colleagues. 110 matched cddid_all.tbl CDD pfam10548 pfam10548 402261 P22_AR_C P22AR C-terminal domain. This domain was identified by Iyer and colleagues. It is found associated with pfam10547. 73 matched cddid_all.tbl CDD pfam10549 pfam10549 287514 ORF11CD3 ORF11CD3 domain. This domain was identified by Iyer and colleagues. 52 matched cddid_all.tbl CDD pfam10550 pfam10550 402262 Toxin_36 Conantokin toxin. The conantokins are a family of neuroactive peptides found in the venoms of fish-hunting cone snails. They possess a high content of gamma-carboxyglutamic acid (Gla) (4-5 residues), a non-standard amino-acid made by the post-translational modification of glutamate (Glu) residue. Conantokins are the only natural biochemically characterized peptides known to be N-methyl-D-aspartate (NMDA) receptor antagonists. 17 matched cddid_all.tbl CDD pfam10551 pfam10551 463145 MULE MULE transposase domain. This domain was identified by Babu and colleagues. 98 matched cddid_all.tbl CDD pfam10552 pfam10552 431353 ORF6C ORF6C domain. This domain was identified by Iyer and colleagues. 114 matched cddid_all.tbl CDD pfam10553 pfam10553 287517 MSV199 MSV199 domain. This domain was identified by Iyer and colleagues. 132 matched cddid_all.tbl CDD pfam10554 pfam10554 431354 Phage_ASH Ash protein family. This family was identified by Iyer and colleagues. It includes the Ash protein from bacteriophage P4. 105 matched cddid_all.tbl CDD pfam10555 pfam10555 431355 MraY_sig1 Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1. Phospho-N-acetylmuramoyl-pentapeptide-transferase (EC 2.7.8.13) (mraY) is a bacterial enzyme responsible for the formation of the first lipid intermediate of the cell wall peptidoglycan synthesis. It catalyzes the formation of undecaprenyl-pyrophosphoryl-N-acetylmuramoyl-pentapeptide from UDP-MurNAc-pentapeptide and undecaprenyl-phosphate. It is an integral membrane protein with probably ten transmembrane domains. This domain is located at the end of the first cytoplasmic loop and the beginning of the second transmembrane domain. 13 matched cddid_all.tbl CDD pfam10557 pfam10557 463146 Cullin_Nedd8 Cullin protein neddylation domain. This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognizes and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae, and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue. 63 matched cddid_all.tbl CDD pfam10558 pfam10558 431357 MTP18 Mitochondrial 18 KDa protein (MTP18). This family of proteins are mitochondrial 18KDa proteins that are often misannotated as carbonic anhydrases. It was shown that knockdown of MTP18 protein results in a cytochrome c release from mitochondria and consequently leads to apoptosis. Overexpression studies suggest that MTP18 is required for mitochondrial fission. 169 matched cddid_all.tbl CDD pfam10559 pfam10559 431358 Plug_translocon Plug domain of Sec61p. The Sec61/SecY translocon mediates translocation of proteins across the membrane and integration of membrane proteins into the lipid bilayer. The structure of the translocon revealed a plug domain blocking the pore on the lumenal side.The plug is unlikely to be important for sealing the translocation pore in yeast but it plays a role in stabilising Sec61p during translocon formation. The domain runs from residues 52-74. 33 matched cddid_all.tbl CDD pfam10561 pfam10561 463147 C2orf69 C2orf69. This family includes C2orf69 from human, previously known as UPF0565, which is an important regulator of human mitochondrial function and may also influence other metabolic pathways. 296 matched cddid_all.tbl CDD pfam10562 pfam10562 402271 CaM_bdg_C0 Calmodulin-binding domain C0 of NMDA receptor NR1 subunit. This is a very short highly conserved domain that is C-terminal to the cytosolic transmembrane region IV of the NMDA-receptor 1. It has been shown to bind Calmodulin-Calcium with high affinity. The ionotropic N-methyl-D-aspartate receptor (NMDAR) is a major source of calcium flux into neurons in the brain and plays a critical role in learning, memory, neural development, and synaptic plasticity. Calmodulin (CaM) regulates NMDARs by binding tightly to the C0 and C1 regions of their NR1 subunit. The conserved tryptophan is considered to be the anchor residue. 29 matched cddid_all.tbl CDD pfam10563 pfam10563 431360 CA_like Delta carbonic anhydrase. Delta carbonic anhydrases are one of the at least five independently evolved families of carbonic anhydrases. Their activities, low CO2-induction, and localizations have been well studied in diatoms. The catalytic mechanism of delta CAs is currently unknown. Proteins of this family are also common in bacteria, but due to more distant relationship (identities less than 30% to the diatom delta CAs) and to the lack of experimental data the carbonic anhydrase activity is only putative in prokaryotic delta CAs. 180 matched cddid_all.tbl CDD pfam10564 pfam10564 402273 MAR_sialic_bdg Sialic-acid binding micronemal adhesive repeat. This domain is a novel carbohydrate-binding domain found on micronemal proteins. Micronemal proteins (MICs) are released onto the parasite surface just before invasion of host cells and play important roles in host cell recognition, attachment and penetration. Toxoplasma gondii can infect and replicate within all nucleated cells. This domain interacts with sialylated oligosaccharides; the protein in Toxoplasma gondii is a monomer but several MAR domains are carried on the protein. Each MAR domain contains one central sialic acid-binding pocket. 94 matched cddid_all.tbl CDD pfam10565 pfam10565 463148 NMDAR2_C N-methyl D-aspartate receptor 2B3 C-terminus. This domain is found at the C-terminus of many NMDA-receptor proteins, many of which also carry the Ligated ion-channel family pfam00060 further upstream as well as the ANF_receptor family pfam01094. This region is predicted to be a large extra-cellular domain of the NMDA receptor proteins, being highly hydrophilic, and is thought to be integrally involved in the function of the receptor. The region also carries a number of potential N-glycosylation sites. 634 matched cddid_all.tbl CDD pfam10566 pfam10566 463149 Glyco_hydro_97 Glycoside hydrolase 97. This domain is the catalytic region of the bacterial glycosyl-hydrolase family 97. This central part of the GH97 family protein sequences represents a typical and complete (beta/alpha)8-barrel or catalytic TIM-barrel type domain. The N- and C-terminal parts of the sequences, mainly consisting of beta-strands, form two additional non-catalytic domains. In all known glycosidases with the (beta-alpha)8-barrel fold, the amino acid residues at the active site are located on the C-termini of the beta-strands. 279 matched cddid_all.tbl CDD pfam10567 pfam10567 431363 Nab6_mRNP_bdg RNA-recognition motif. This conserved domain is found in fungal proteins and appears to be involved in RNA-processing. It binds to poly-adenylated RNA, interacts genetically with mRNA 3'-end processing factors, copurifies with the nuclear cap-binding protein Cbp20p, and is found in complexes containing other translation factors, such as EIF4G as in Swiss:P39935 and Swiss:P39936. 309 matched cddid_all.tbl CDD pfam10568 pfam10568 463150 Tom37 Outer mitochondrial membrane transport complex protein. The TOM37 protein is one of the outer membrane proteins that make up the TOM complex for guiding cytosolic mitochondrial beta-barrel proteins from the cytosol across the outer mitochondrial membrane into the intra-membrane space. In conjunction with TOM70 it guides peptides without an MTS into TOM40, the protein that forms the passage through the outer membrane. It has homology with Metaxin-1, also part of the outer mitochondrial membrane beta-barrel protein transport complex. 126 matched cddid_all.tbl CDD pfam10570 pfam10570 287532 Myelin-PO_C Myelin-PO cytoplasmic C-term p65 binding region. Myelin protein zero is the major myelin protein in the peripheral central nervous system and is essential for normal myelination. The family is a single-pass transmembrane molecule containing one Ig-like loop in the extracellular domain and this highly basic 69 residue C-terminal cytoplasmic domain which is the region that interacts with protein p65. 65 matched cddid_all.tbl CDD pfam10571 pfam10571 402278 UPF0547 Uncharacterized protein family UPF0547. This domain contains a zinc-ribbon motif. 26 matched cddid_all.tbl CDD pfam10572 pfam10572 463151 UPF0556 UPF0556 domain. This putative domain has no known function. It is found in a variety of eukaryotic species often as a single domain protein but also found at the C-terminus of a few other protein contains other domains. 125 matched cddid_all.tbl CDD pfam10573 pfam10573 287535 UPF0561 Uncharacterized protein family UPF0561. This family of proteins has no known function. 120 matched cddid_all.tbl CDD pfam10574 pfam10574 463152 UPF0552 Arp2/3-interacting proteins Arpin. This family includes proteins such as Arp2/3-interacting proteins (Arpin). Arpin regulates actin polymerization by inhibiting the actin-nucleating activity of the Arp2/3 complex. It induces cell turning by pausing cell migration. 224 matched cddid_all.tbl CDD pfam10576 pfam10576 463153 EndIII_4Fe-2S Iron-sulfur binding domain of endonuclease III. Escherichia coli endonuclease III (EC 4.2.99.18) is a DNA repair enzyme that acts both as a DNA N-glycosylase, removing oxidized pyrimidines from DNA, and as an apurinic/apyrimidinic (AP) endonuclease, introducing a single-strand nick at the site from which the damaged base was removed. Endonuclease III is an iron-sulfur protein that binds a single 4Fe-4S cluster. The 4Fe-4S cluster does not seem to be important for catalytic activity, but is probably involved in the proper positioning of the enzyme along the DNA strand. The 4Fe-4S cluster is bound by four cysteines which are all located in a 17 amino acid region at the C-terminal end of endonuclease III. A similar region is also present in the central section of mutY and in the C-terminus of ORF-10 and of the Micro-coccus UV endonuclease. 17 matched cddid_all.tbl CDD pfam10577 pfam10577 463154 UPF0560 Uncharacterized protein family UPF0560. This family of proteins has no known function. 811 matched cddid_all.tbl CDD pfam10578 pfam10578 371146 SVS_QK Seminal vesicle protein repeat. 12 matched cddid_all.tbl CDD pfam10579 pfam10579 431369 Rapsyn_N Rapsyn N-terminal myristoylation and linker region. Neuromuscular junction formation relies upon the clustering of acetylcholine receptors and other proteins in the muscle membrane. Rapsyn is a peripheral membrane protein that is selectively concentrated at the neuromuscular junction and is essential for the formation of synaptic acetylcholine receptor aggregates. Acetylcholine receptors fail to aggregate beneath nerve terminals in mice where rapsyn has been knocked out. The N-terminal six amino acids of rapsyn are its myristoylation site, and myristoylation is necessary for the targeting of the protein to the membrane. 80 matched cddid_all.tbl CDD pfam10580 pfam10580 431370 Neuromodulin_N Gap junction protein N-terminal region. 31 matched cddid_all.tbl CDD pfam10581 pfam10581 463155 Synapsin_N Synapsin N-terminal. This highly conserved domain of synapsin proteins has a serine at position 9 or 10 which is a phosphorylation site. The domain appears to be the part of the molecule that binds to calmodulin. 32 matched cddid_all.tbl CDD pfam10583 pfam10583 431372 Involucrin_N Involucrin of squamous epithelia N-terminus. This is the N-terminal three beta strands of involucrin, a protein present in keratinocytes of epidermis and other stratified squamous epithelia. Involucrin first appears in the cell cytosol, but ultimately becomes cross-linked to membrane proteins by transglutaminase thus helping in the formation of an insoluble envelope beneath the plasma membrane. Apigenin is a plant-derived flavanoid that has significant promise as a skin cancer chemopreventive agent. It has been found that apigenin regulates normal human keratinocyte differentiation by suppressing it and this is associated with reduced cell proliferation without apoptosis. The downstream part of the protein is represented by the family Involucrin, pfam00904. 69 matched cddid_all.tbl CDD pfam10584 pfam10584 463156 Proteasome_A_N Proteasome subunit A N-terminal signature. This domain is conserved in the A subunits of the proteasome complex proteins. 23 matched cddid_all.tbl CDD pfam10585 pfam10585 463157 UBA_E1_SCCH Ubiquitin-activating enzyme, SCCH domain. Ubiquitin-activating enzyme (E1 enzyme) activates ubiquitin by first adenylating with ATP its C-terminal glycine residue and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding an ubiquitin-E1 thiolester and free AMP. Later the ubiquitin moiety is transferred to a cysteine residue on one of the many forms of ubiquitin-conjugating enzymes (E2). This domain carries the last of five conserved cysteines that is part of the active site of the enzyme, responsible for ubiquitin thiolester complex formation, the active site being represented by the sequence motif PICTLKNFP. The catalytic cysteine domain contains the E1 active site cysteine, and is divided in two half-domains, FCCH and SCCH, for 'first' and 'second' catalytic cysteine half-domain, respectively. This is the SCCH domain in which resides the catalytic cysteine. 254 matched cddid_all.tbl CDD pfam10587 pfam10587 463158 EF-1_beta_acid Eukaryotic elongation factor 1 beta central acidic region. 28 matched cddid_all.tbl CDD pfam10588 pfam10588 463159 NADH-G_4Fe-4S_3 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region. 40 matched cddid_all.tbl CDD pfam10589 pfam10589 463160 NADH_4Fe-4S NADH-ubiquinone oxidoreductase-F iron-sulfur binding region. 85 matched cddid_all.tbl CDD pfam10590 pfam10590 463161 PNP_phzG_C Pyridoxine 5'-phosphate oxidase C-terminal dimerization region. This domain represents one of the two dimerization regions of the protein, located at the edge of the dimer interface, at the C-terminus, being the last three beta strands, S6, S7, and S8 along with the last three residues to the end. In Swiss:P21159, S6 runs from residues 178-192, S7 from 200-206 and S8 from 211-215. the extended loop, of residues 167-177 may well be involved in the pocket formed between the two dimers that positions the FMN molecule.To date, the only time functional oxidase or phenazine biosynthesis activities have been experimentally demonstrated is when the sequences contain both pfam01243 and pfam10590. It is unknown the role performed by each domain in bringing about molecular functions of either oxidase or phenazine activity. 42 matched cddid_all.tbl CDD pfam10591 pfam10591 463162 SPARC_Ca_bdg Secreted protein acidic and rich in cysteine Ca binding region. The SPARC_Ca_bdg domain of Secreted Protein Acidic and Rich in Cysteine is responsible for the anti-spreading activity of human urothelial cells. It is rich in alpha-helices. This extracellular calcium-binding domain contains two EF-hands that each coordinates one Ca2+ ion, forming a helix-loop-helix structure that not only drives the conformation of the protein but is also necessary for biological activity. The anti-spreading activity was dependent on the coordination of Ca2+ by a Glu residue at the Z position of EF-hand 2. 111 matched cddid_all.tbl CDD pfam10592 pfam10592 431380 AIPR AIPR protein. This family of proteins was identified in as an abortive infection phage resistance protein often found in restriction modification system operons. 296 matched cddid_all.tbl CDD pfam10593 pfam10593 431381 Z1 Z1 domain. This uncharacterized domain was identified by Iyer and colleagues. It is found associated with a helicase domain of superfamily type II. 215 matched cddid_all.tbl CDD pfam10595 pfam10595 431382 UPF0564 Uncharacterized protein family UPF0564. This family of proteins has no known function. However, one of the members, Swiss:Q22CP8, is annotated as an EF-hand family protein. 364 matched cddid_all.tbl CDD pfam10596 pfam10596 431383 U6-snRNA_bdg U6-snRNA interacting domain of PrP8. This domain incorporates the interacting site for the U6-snRNA as part of the U4/U6.U5 tri-snRNPs complex of the spliceosome, and is the prime candidate for the role of cofactor for the spliceosome's RNA core. The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor. 159 matched cddid_all.tbl CDD pfam10597 pfam10597 402297 U5_2-snRNA_bdg U5-snRNA binding site 2 of PrP8. The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor. 134 matched cddid_all.tbl CDD pfam10598 pfam10598 463163 RRM_4 RNA recognition motif of the spliceosomal PrP8. The large RNA-protein complex of the spliceosome catalyzes pre-mRNA splicing. One of the most conserved core proteins is PrP8 which occupies a central position in the catalytic core of the spliceosome, and has been implicated in several crucial molecular rearrangements that occur there, and has recently come under the spotlight for its role in the inherited human disease, Retinitis Pigmentosa. The RNA-recognition motif of PrP8 is highly conserved and provides a possible RNA binding centre for the 5-prime SS, BP, or 3-prime SS of pre-mRNA which are known to contact with Prp8. The most conserved regions of an RRM are defined as the RNP1 and RNP2 sequences. Recognition of RNA targets can also be modulated by a number of other factors, most notably the two loops beta1-alpha1, beta2-beta3 and the amino acid residues C-terminal to the RNP2 domain. 92 matched cddid_all.tbl CDD pfam10599 pfam10599 371156 Nup_retrotrp_bd Retro-transposon transporting motif. This is the highly conserved C-terminal motif GRKIxxxxxRRKx of nucleoporins that plays a critical and unique role in the nuclear import of retro-transposons in both yeasts and higher organizms. It would appear that the arginine residues at positions 2 and 9-10 constitute a bipartite nuclear localization signal, with two basic peptide motifs separated by an interchangeable spacer sequence, that is crucial for the retro-transposon activity. 86 matched cddid_all.tbl CDD pfam10600 pfam10600 463164 PDZ_assoc PDZ-associated domain of NMDA receptors. This domain is found in higher eukaryotes between the second and third PDZ domains, pfam00595, of glutamate receptor like proteins. Its exact function is not known. 67 matched cddid_all.tbl CDD pfam10601 pfam10601 463165 zf-LITAF-like LITAF-like zinc ribbon domain. Members of this family display a conserved zinc ribbon structure with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure. 68 matched cddid_all.tbl CDD pfam10602 pfam10602 431387 RPN7 26S proteasome subunit RPN7. RPN7 (known as the non ATPase regulatory subunit 6 in higher eukaryotes) is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae to be required for structural integrity. The 26S proteasome is is involved in the ATP-dependent degradation of ubiquitinated proteins. 174 matched cddid_all.tbl CDD pfam10604 pfam10604 431388 Polyketide_cyc2 Polyketide cyclase / dehydrase and lipid transport. This family contains polyketide cylcases/dehydrases which are enzymes involved in polyketide synthesis. It also includes other proteins of the START superfamily. 139 matched cddid_all.tbl CDD pfam10605 pfam10605 431389 3HBOH 3HB-oligomer hydrolase (3HBOH). D-(-)-3-hydroxybutyrate oligomer hydrolase (also known as 3HB-oligomer hydrolase) functions in the degradation of poly-3-hydroxybutyrate (PHB). It catalyzes the hydrolysis of D(-)-3-hydroxybutyrate oligomers (3HB-oligomers) into 3HB-monomers. 689 matched cddid_all.tbl CDD pfam10606 pfam10606 431390 GluR_Homer-bdg "Homer-binding domain of metabotropic glutamate receptor. This is the proline-rich region of metabotropic glutamate receptor proteins that binds Homer-related synaptic proteins. The Homer proteins form a physical tether linking mGluRs with the inositol trisphosphate receptors (IP3R) that appears to be due to the proline-rich ""Homer ligand"" (PPXXFr). Activation of PI turnover triggers intracellular calcium release. MGluR function is altered in the mouse model of human Fragile X syndrome mental retardation, a disorder caused by loss of function mutations in the Fragile X mental retardation gene Fmr1. Homer 3 (and to a lesser extent Homer 1b/c) has been shown to form a multimeric complex with mGlu1a and the IP3 receptor, indicating that Homers may play a role in the localization of receptors to their signalling partners." 51 matched cddid_all.tbl CDD pfam10607 pfam10607 402305 CTLH CTLH/CRA C-terminal to LisH motif domain. RanBPM is a scaffolding protein and is important in regulating cellular function in both the immune system and the nervous system. This domain is at the C-terminus of the proteins and is the binding domain for the CRA motif (for CT11-RanBPM), which is comprised of approximately 100 amino acids at the C terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined. This region contains CTLH and CRA domains annotated by SMART; however, these may be a single domain, and it is refereed to as a C-terminal to LisH motif. 143 matched cddid_all.tbl CDD pfam10608 pfam10608 431391 MAGUK_N_PEST Polyubiquitination (PEST) N-terminal domain of MAGUK. The residues upstream of this domain are the probable palmitoylation sites, particularly two cysteines. The domain has a putative PEST site at the very start that seems to be responsible for poly-ubiquitination. PEST domains are polypeptide sequences enriched in proline (P), glutamic acid (E), serine (S) and threonine (T) that target proteins for rapid destruction. The whole domain, in conjunction with a C-terminal domain of the longer protein, is necessary for dimerization of the whole protein. 85 matched cddid_all.tbl CDD pfam10609 pfam10609 431392 ParA NUBPL iron-transfer P-loop NTPase. This family contains ATPases involved in plasmid partitioning. It also contains the cytosolic Fe-S cluster assembling factor NBP35 which is required for biogenesis and export of both ribosomal subunits. 246 matched cddid_all.tbl CDD pfam10610 pfam10610 313764 Tafi-CsgC Thin aggregative fimbriae synthesis protein. Fimbriae are cell-surface protein polymers, of eg. E coli and Salmonella spp, that mediate interactions important for host and environmental persistence, development of biofilms, motility, colonization and invasion of cells, and conjugation. Four general assembly pathways for different fimbriae have been proposed, one of which is extracellular nucleation-precipitation (ENP), that differs from the others in that fibre-growth occurs extracellularly. Thin aggregative fimbriae (Tafi) are the only fimbriae dependent on the ENP pathway. Tafi were first identified in Salmonella spp and the controlling operon termed agf; however subsequent isolation of the homologous operon in E coli led to its being called csg. Tafi are known as curli because, in the absence of extracellular polysaccharides, their morphology appears curled; however, when expressed with such polysaccharides their morphology appears as a tangled amorphous matrix. The gene agfC is found to be transcribed at low levels, localized to the periplasm in a mature form, and in combination with AgfE is important for AgfA extracellular assembly, which facilitates the synthesis of Tafi. The genes involved in Tafi production are organized into two adjacent divergently transcribed operons, agfBAC and agfDEFG, both of which are required for biosynthesis and assembly. 98 matched cddid_all.tbl CDD pfam10611 pfam10611 431393 DUF2469 Protein of unknown function (DUF2469). Member proteins often found in Actinomycetes clustered with signal peptidase and/or RNAse-HII. 100 matched cddid_all.tbl CDD pfam10612 pfam10612 402308 Spore-coat_CotZ Spore coat protein Z. This family has members annotated as Spore coat protein Z, otherwise known as CotZ, It is a cysteine-rich spore coat family, and along with CotY is necessary for assembly of intact exosporium. 157 matched cddid_all.tbl CDD pfam10613 pfam10613 463166 Lig_chan-Glu_bd Ligated ion channel L-glutamate- and glycine-binding site. This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine. It is found in association with Lig_chan, pfam00060. 111 matched cddid_all.tbl CDD pfam10614 pfam10614 431395 CsgF Type VIII secretion system (T8SS), CsgF protein. The extracellular nucleation-precipitation (ENP) pathway or Type VIII secretion system (T8SS) in Gram-negative (diderm) bacteria is responsible for the secretion and assembly of prepilins for fimbiae biogenesis, the prototypical curli. Besides the T2SS that can be involved in the assembly of prototypical Type 4 pilus, the T4SS that can be involved in the biogenesis of the prototypical pilus T, the T3SS involved in the assembly of the injectisome and the T7SS involved in the formation of the prototypical Type 1 pilus, the T8SS differs in that fibre-growth occurs extracellularly. The curli, also called thin aggregative fimbriae (Tafi), are the only fimbriae dependent on the T8SS. Tafi were first identified in Salmonella spp and the controlling operon termed agf; however subsequent isolation of the homologous operon in E coli led to its being called csg. In the absence of extracellular polysaccharides Tafi appear curled, although when expressed with such polysaccharides their morphology appears as a tangled amorphous matrix. CsgF is one of three putative curli assembly factors appearing to act as a nucleator protein. Unlike eukaryotic amyloid formation, curli biogenesis is a productive pathway requiring a specific assembly machinery. 132 matched cddid_all.tbl CDD pfam10615 pfam10615 431396 DUF2470 Domain of unknown function (DUF2470). This domain is found in a group of putative heme-iron utilization proteins, such as HugZ. It can also be found in C-terminal of the glutamyl-tRNA reductase-binding (GluTRBP) protein from Arabidopsis. GluTRBP is involved in the regulation of glutamyl-tRNA reductase (GluTR) which is important for the synthesis and distribution of 5-aminolevulinate, a precursor in heme and chlorophyll biosynthesis. GluTRBP is necessary for efficient photosynthetic electron transport in chloroplasts. 73 matched cddid_all.tbl CDD pfam10616 pfam10616 402312 DUF2471 Protein of unknown function (DUF2471). The function of this family is unknown. Members all come from Burkholderia spp. Swiss:A2WH83 is annotated as Serine/threonine-protein kinase, but this could not be confirmed. 118 matched cddid_all.tbl CDD pfam10617 pfam10617 431397 DUF2474 Protein of unknown function (DUF2474). This family of short proteins has no known function. 39 matched cddid_all.tbl CDD pfam10618 pfam10618 431398 Tail_tube Phage tail tube protein. This bacterial family of proteins contains phage tail tube proteins related to the Mu phage protein Swiss:P79679. Bacteriophage Mu has an eicosahedral head and contractile tail. The tail is composed of an outer sheath and an inner tube. 117 matched cddid_all.tbl CDD pfam10620 pfam10620 431399 MdcG Phosphoribosyl-dephospho-CoA transferase MdcG. MdcG is a phosphoribosyl-dephospho-CoA transferase that is involved in the biosynthesis of the prosthetic group of malonate decarboxylase. Malonate decarboxylase from Klebsiella pneumoniae contains an acyl carrier protein (MdcC) to which a 2'-(5' '-phosphoribosyl)-3'-dephospho-CoA prosthetic group is attached via phosphodiester linkage. MdcG catalyzes the following reaction: 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA + apo-[acyl-carrier-protein] = holo-[acyl-carrier-protein] + diphosphate. 196 matched cddid_all.tbl CDD pfam10621 pfam10621 431400 FpoO F420H2 dehydrogenase subunit FpoO. This is the FpoO subunit of F420H2 dehydrogenase, an enzyme which oxidizes reduced coenzyme F420. Reduced coenzyme F420 is a universal electron carrier in methanogens. 110 matched cddid_all.tbl CDD pfam10622 pfam10622 402316 Ehbp Energy-converting hydrogenase B subunit P (EhbP). Ehb (energy-converting hydrogenase B) is an methanogenic archaeal enzyme that functions in one of the metabolic pathways involved in methanol reduction to methane. This family contains subunit P of Ehb. 77 matched cddid_all.tbl CDD pfam10623 pfam10623 151143 PilI Plasmid conjugative transfer protein PilI. The thin pilus of plasmid R64 belongs to the type IV family and is required for liquid matings. pilI is one of 14 genes that have been identified as being involved in biogenesis of the R64 thin pilus. 83 matched cddid_all.tbl CDD pfam10624 pfam10624 463167 TraS Plasmid conjugative transfer entry exclusion protein TraS. Entry exclusion (Eex) is a process which prevents redundant transfer of DNA between donor cells. TraS is a protein involved in Eex. It blocks redundant conjugative DNA synthesis and transport between donor cells, and it is suggested that TraS interferes with a signalling pathway that is required to trigger DNA transfer. TraS on the recipient cell is known to form an interaction with TraG on the donor cell. 162 matched cddid_all.tbl CDD pfam10625 pfam10625 431401 UspB Universal stress protein B (UspB). UspB in Escherichia coli is a 14kDa protein which is predicted to be an integral membrane protein. Overexpression of UspB results in cell death in stationary phase, and mutants of uspB are sensitive to ethanol exposure during stationary phase. 107 matched cddid_all.tbl CDD pfam10626 pfam10626 431402 TraO Conjugative transposon protein TraO. This is a family of conjugative transposon proteins. 168 matched cddid_all.tbl CDD pfam10627 pfam10627 431403 CsgE Curli assembly protein CsgE. Curli are a class highly aggregated surface fibres that are part of a complex extracellular matrix. They promote biofilm formation in addition to other activities. CsgE is a non-structural protein involved in curli biogenesis. CsgE forms an outer membrane complex with the curli assembly proteins CsgG and CsgF. 105 matched cddid_all.tbl CDD pfam10628 pfam10628 402319 CotE Outer spore coat protein E (CotE). CotE is a morphogenic protein that is required for the assembly of the outer coat of the endospore and spore resistance to lysozyme. CotE also regulates the expression of cotA, cotB, cotC and other genes encoding spore outer coat proteins. The timing of cotE expression has been shown in Bacillus subtilis to affect spore coat morphology but not lysozyme resistance. 177 matched cddid_all.tbl CDD pfam10629 pfam10629 431404 DUF2475 Protein of unknown function (DUF2475). This family of proteins has no known function. 67 matched cddid_all.tbl CDD pfam10630 pfam10630 463168 DUF2476 Protein of unknown function (DUF2476). This is a family of proteins of unknown function. The family is rich in proline residues. 258 matched cddid_all.tbl CDD pfam10631 pfam10631 463169 DUF2477 Protein of unknown function (DUF2477). This is a family of proteins with no known function. The family is rich in proline residues. 142 matched cddid_all.tbl CDD pfam10633 pfam10633 431406 NPCBM_assoc NPCBM-associated, NEW3 domain of alpha-galactosidase. The English-language version of the first reference can be found on pages 388-399 of the above. This domain has been named NEW3 but its actual function is not known. It is found on proteins which are bacterial galactosidases. The domain is associated with the NPCBM family, pfam08305, a novel putative carbohydrate binding module found at the N-terminus of glycosyl hydrolases. 78 matched cddid_all.tbl CDD pfam10634 pfam10634 431407 Iron_transport Fe2+ transport protein. This is a bacterial family of periplasmic proteins that are thought to function in high-affinity Fe2+ transport. 150 matched cddid_all.tbl CDD pfam10635 pfam10635 431408 DisA-linker DisA bacterial checkpoint controller linker region. The DisA protein is a bacterial checkpoint protein that dimerizes into an octameric complex. The protein consists of three distinct domains. the first, N-terminal region, from 1-145 is globular and is represented by family DisA_N, pfam02457; the next 146-289 residues is this domain that consists of an elongated bundle of three alpha helices (alpha-6, alpha-10, and alpha-11), one side of which carries an additional three helices (alpha7-9), thus forming a spine like-linker between domains 1 and 3. The C-terminal residues of domain 3 are family HHH, pfam00633, the specific DNA-binding domain. The octameric complex thus has structurally linked nucleotide-binding and DNA-binding HhH domains and the nucleotide-binding domains are bound to a cyclic di-adenosine phosphate such that DisA is a specific di-adenylate cyclase. The di-adenylate cyclase activity is strongly suppressed by binding to branched DNA, but not to duplex or single-stranded DNA, suggesting a role for DisA as a monitor of the presence of stalled replication forks or recombination intermediates via DNA structure-modulated c-di-AMP synthesis. 141 matched cddid_all.tbl CDD pfam10636 pfam10636 431409 hemP Hemin uptake protein hemP. This is a bacterial family of proteins that are involved in the uptake of the iron source hemin. 37 matched cddid_all.tbl CDD pfam10637 pfam10637 402326 Ofd1_CTDD Oxoglutarate and iron-dependent oxygenase degradation C-term. Ofd1 is a prolyl 4-hydroxylase-like 2-oxoglutarate-Fe(II) dioxygenase that accelerates the degradation of Sre1N in the presence of oxygen. The domain is conserved from yeasts to humans. Yeast Sre1 is the orthologue of mammalian sterol regulatory element binding protein (SREBP), and it responds to changes in oxygen-dependent sterol synthesis as an indirect measure of oxygen availability. However, unlike the prolyl 4-hydroxylases that regulate mammalian hypoxia-inducible factor, Ofd1 uses multiple domains to regulate Sre1N degradation by oxygen; the Ofd1 N-terminal dioxygenase domain is required for oxygen sensing and this Ofd1 C-terminal domain accelerates Sre1N degradation in yeasts. 255 matched cddid_all.tbl CDD pfam10638 pfam10638 402327 Sfi1_C Spindle body associated protein C-terminus. This C-terminal domain of spindle-body-associated protein Sfi1 has an important role to play in the bridge-splitting during bi-polar spindle assembly, and this separation event possibly requires interaction with integral components of the nuclear envelope, such as the Mps2-Bbp1 complex. Centrally to this domain is a region carrying centrin-binding repeats with repeating units containing tryptophan, family Sfi1_central, pfam08457. 100 matched cddid_all.tbl CDD pfam10639 pfam10639 371174 TMEM234 Putative transmembrane family 234. TMEM234 is a family of putative inner membrane proteins. Many bacterial members are annotated as putative L-Ara4N-phosphoundecaprenol flippase subunit ArnE, and as inner membrane proteins. They may be transporters of the multi-drug-resistant superfamily. 113 matched cddid_all.tbl CDD pfam10640 pfam10640 287595 Pox_ATPase-GT mRNA capping enzyme N-terminal, ATPase and guanylyltransferase. This domain is the N-terminus of the large subunit viral mRNA capping enzyme, and carries both the ATPase and the guanylyltransferase activities of the enzyme. The guanylyltransferase enzymatic region runs from residues 242 (leucine)-273(arginine), the core of the acitve site being the lysine residue at 260. The ATPase activity is at the very N-terminal part of the domain. 311 matched cddid_all.tbl CDD pfam10642 pfam10642 431410 Tom5 Mitochondrial import receptor subunit or translocase. This protein family is very short and is only found in yeasts. Tom5 is one of three very small translocases of the mitochondrial outer membrane. Tom5 links mitochondrial preprotein receptors to the general import pore. Deletion of the C-terminal transmembrane domain of Tom5 interfered with phosphatidylserine (PS) transfer to mitochondria and disrupted mitochondrial function. 47 matched cddid_all.tbl CDD pfam10643 pfam10643 463170 Cytochrome-c551 Photosystem P840 reaction-centre cytochrome c-551. A photosynthetic reaction-centre complex is found in certain green sulphur bacteria such as Chlorobium vibrioforme which are anaerobic photo-auto-trophic organizms. The primary electron donor is P840, a probable B-Chl a dimer, and the primary electron acceptor is a B-Chl monomer. Also on the donor side c-type cytochromes are known to function as electron donors to photo-oxidized P840. This family is thus the secondary endogenous donor of the photosynthetic reaction-centre complex and is a membrane-bound cytochrome containing a single haem group. 216 matched cddid_all.tbl CDD pfam10644 pfam10644 431412 Misat_Tub_SegII Misato Segment II tubulin-like domain. The misato protein contains three distinct, conserved domains, segments I, II and III. Segments I and III are common to Tubulins pfam00091, but segment II aligns with myosin heavy chain sequences from D. melanogaster (PIR C35815), rabbit (SP P04460), and human (PIR S12458). Segment II of misato is a major contributor to its greater length compared with the various tubulins. The most significant sequence similarities to this 54-amino acid region are from a motif found in the heavy chains of myosins from different organizms. A comparison of segment II with the vertebrate myosin heavy chains reveals that it is homologous to a myosin peptide in the hinge region linking the S2 and LMM domains. Segment II also contains heptad repeats which are characteriztic of the myosin tail alpha-helical coiled-coils. This myosin-like homology may be due only to the fact that both myosin and Misato carry coiled-coils, which appear similar but are not necessarily homologous (Wood V, personal communication). 115 matched cddid_all.tbl CDD pfam10645 pfam10645 431413 Carb_bind Carbohydrate binding. This is a carbohydrate binding domain which has been shown in Schizosaccharomyces pombe to be required for septum localization. 49 matched cddid_all.tbl CDD pfam10646 pfam10646 463171 Germane Sporulation and spore germination. The GerMN domain is a region of approximately 100 residues that is found, duplicated, in the Bacillus GerM protein and is implicated in both sporulation and spore germination. The domain is found in a number of different bacterial species both alone and in association with other domains such as Amidase_3 pfam01520, Gmad1 and Gmad2. It is predicted to have a novel alpha-beta fold. 112 matched cddid_all.tbl CDD pfam10647 pfam10647 431415 Gmad1 Lipoprotein LpqB beta-propeller domain. The Gmad1 domain is found associated with the GerMN family, pfam10646, in bacterial spore formation. It is predicted to have a beta-propeller fold and to have a passive binding role rather than a catalytic function owing to the low number of conserved hydrophilic residues. 255 matched cddid_all.tbl CDD pfam10648 pfam10648 431416 Gmad2 Immunoglobulin-like domain of bacterial spore germination. This domain is found linked to the GerMN domain pfam10646 in some bacterial proteins. It is predicted to contain an immunoglobulin-like all-beta fold. 86 matched cddid_all.tbl CDD pfam10649 pfam10649 431417 DUF2478 Protein of unknown function (DUF2478). This is a family of hypothetical bacterial proteins found in the vicinity of Molybdenum ABC transporter ATP-binding gene-products MobA MobB and MobC. However the function could not be confirmed. This family appears to belong to the P-loop superfamily by alignment to pfam03266. However, the characteriztic P-loop sequence motif appears to have diverged beyond recognition in this family. 159 matched cddid_all.tbl CDD pfam10650 pfam10650 431418 zf-C3H1 Putative zinc-finger domain. This domain is conserved in fungi and might be a zinc-finger domain as it contains three conserved Cs and an H in the C-x8-C-x5-C-x3-H conformation typical of a zinc-finger. 22 matched cddid_all.tbl CDD pfam10651 pfam10651 431419 BppU_N BppU N-terminal domain. This is the N-terminal domain of baseplate upper proteins (BppU, also known as ORF48) which is found in phage from a number of different bacteria. The N-terminal domain exhibits a beta-sandwich immunoglobulin fold. 141 matched cddid_all.tbl CDD pfam10652 pfam10652 431420 DUF2480 Protein of unknown function (DUF2480). All the members of this family are uncharacterized proteins, but the environment in which they are found on the bacterial genome suggests a function as a glucose-6-phosphate isomerase (EC 5.3.1.9). This could not, however, be confirmed. 165 matched cddid_all.tbl CDD pfam10653 pfam10653 287607 Phage-A118_gp45 Protein gp45 of Bacteriophage A118. This domain is found in bacteriophage and is thought to have a gp45 function within the phage tail-fibre system. 62 matched cddid_all.tbl CDD pfam10654 pfam10654 463172 DUF2481 Protein of unknown function (DUF2481). This is a hypothetical protein family homologous to Lmo2305 in Bacteriophage A118 systems. 126 matched cddid_all.tbl CDD pfam10655 pfam10655 463173 DUF2482 Hypothetical protein of unknown function (DUF2482). All the members of this very small, very short family are derived from bacteriophages, of the SA bacteriophages 11, Mu50B, system, and from the Staphylococcal_phi-Mu50B-like_prophages subsystem. All members are hypothetical proteins. 97 matched cddid_all.tbl CDD pfam10656 pfam10656 371183 DUF2483 Hypothetical protein of unknown function (DUF2483). This is a family of proteins found in bacteriophage particularly of the SA bacteriophages 11, Mu50B, family, homologous to phi-ETA orf16. 72 matched cddid_all.tbl CDD pfam10657 pfam10657 463174 RC-P840_PscD Photosystem P840 reaction centre protein PscD. The photosynthetic reaction centres (RCs) of aerotolerant organizms contain a heterodimeric core, built up of two strongly homologous polypeptides each of which contributes five transmembrane peptide helices to hold a pseudo-symmetric double set of redox components. Two molecules of PscD are housed within a subunit. PscD may be involved in stabilising the PscB component since it is found to co-precipitate with FMO (Fenna-Mathews-Olson BChl a-protein) and PscB. It may also be involved in the interaction with ferredoxin. 144 matched cddid_all.tbl CDD pfam10658 pfam10658 402340 DUF2484 Protein of unknown function (DUF2484). A role of this family in UDP-N-acetylenolpyruvoylglucosamine reductase, as MurB, could not be confirmed. 76 matched cddid_all.tbl CDD pfam10659 pfam10659 287612 Trypan_glycop_C Trypanosome variant surface glycoprotein C-terminal domain. The trypanosome parasite expresses these proteins to evade the immune response. 104 matched cddid_all.tbl CDD pfam10660 pfam10660 313801 MitoNEET_N Iron-containing outer mitochondrial membrane protein N-terminus. MitoNEET_N is the N-terminal region of the MitoNEET and Miner-type proteins that carry a zf-CDGSH, pfam09360, redox-active 2Fe-2S cluster. The whole protein regulates oxidative capacity. The domain is an anchor sequence that tethers the protein to the outer membrane. 64 matched cddid_all.tbl CDD pfam10661 pfam10661 287614 EssA WXG100 protein secretion system (Wss), protein EssA. The WXG100 protein secretion system (Wss) is responsible for the secretion of WXG100 proteins (pfam06013) such as ESAT-6 and CFP-10 in Mycobacterium tuberculosis or EsxA and EsxB in Staphylococcus aureus. In S. aureus, the Wss seems to be encoded by a locus of eight CDS, called ess (eSAT-6 secretion system). This locus encodes, amongst several other proteins, EssA, a protein predicted to possess one transmembrane domain. Due to its predicted membrane location and its absolute requirement for WXG100 protein secretion, it has been speculated that EssA could form a secretion apparatus in conjunction with the polytopic membrane protein EsaA, YukC (pfam10140) and YukAB, which is a membrane-bound ATPase containing Ftsk/SpoIIIE domains (pfam01580) called EssC in S. aureus and Snm1/Snm2 in Mycobacterium tuberculosis. Proteins homologous to EssA, YukC, EsaA and YukD seem absent from mycobacteria. 148 matched cddid_all.tbl CDD pfam10662 pfam10662 402341 PduV-EutP Ethanolamine utilization - propanediol utilization. Members of this family function in ethanolamine and propanediol degradation pathways. PduV may be involved in the association of the bacterial microcompartments (BMCs) to filaments. 137 matched cddid_all.tbl CDD pfam10664 pfam10664 431422 NdhM Cyanobacterial and plastid NDH-1 subunit M. The proton-pumping NADH:ubiquinone oxidoreductase catalyzes the electron transfer from NADH to ubiquinone linked with proton translocation across the membrane. It is the largest, most complex and least understood of the respiratory chain enzymes and is referred to as Complex I. The subunit composition of the enzyme varies between groups of organizms. Complex I originating from mammalian mitochondria contains 45 different proteins, whereas in bacteria, the corresponding complex NDH-1 consists of 14 different polypeptides. homologs of these 14 proteins are found among subunits of the mitochondrial complex I, and therefore bacterial NDH-1 might be considered a model proton-pumping NADH dehydrogenase with a minimal set of subunits. Escherichia coli NDH-1 readily disintegrates into 3 sub-complexes: a water-soluble NADH dehydrogenase fragment (NuoE, -F, and -G),the connecting fragment (NuoB, -C, -D, and -I), and the membrane fragment (NuoA, -H, -J, -K, -L, -M, -N). In cyanobacteria and their descendants, the chloroplasts of green plants, the subunit composition of NDH-1 remains obscure. The genes for eleven subunits NdhA-NdhK, homologous to the NuoA-NuoD and NuoH-NuoN of the E. coli complex, have been found in the genome of Synechocystis sp. PCC 6803 which has a family of 6 ndhD genes and a family of 3 ndhF genes. Two reported multisubunit complexes, NDH-1L and NDH-1M, represent distinct NDH-1 complexes in the thylakoid membrane of Synechocystis 6803 -cyanobacterium. NDH-1L was shown to be essential for photoheterotrophic cell growth, whereas expression of NDH-1M was a prerequisite for CO2 uptake and played an important role in growth of cells at low CO2. Here we report the subunit composition of these two complexes. Fifteen proteins were discovered in NDH-1L including NdhL, a new component of the membrane fragment, and Ssl1690 (designated as NdhO), a novel peripheral subunit. The cyanobacterial NDH-1 complex contains additional subunits, NdhM and NdhN, compared with the minimal set of the bacterial enzyme and these seem to be specific for thylakoid-located NDH-1 of photosynthetic organizms. The three subunits of NDH-1, NdhM, NdhN and NdhO are essential for effecting cyclic electron flow around photosystem I, by supplying extra-ATP for photosynthesis in both plastids and cyanobacteria. 107 matched cddid_all.tbl CDD pfam10665 pfam10665 431423 Minor_capsid_1 Minor capsid protein. This is a putative tail-knob or minor capsid protein from bacteriophages. 104 matched cddid_all.tbl CDD pfam10666 pfam10666 402344 Phage_TAC_8 Phage tail assembly chaperone protein Gp14 ()A118. This phage protein family is expressed from within a cluster of tail- and base plate-producing genes. It is a family of tail assembly chaperone proteins. 140 matched cddid_all.tbl CDD pfam10667 pfam10667 402345 DUF2486 Protein of unknown function (DUF2486). This family is made up of members from various Burkholderia spp. The function is unknown. 251 matched cddid_all.tbl CDD pfam10668 pfam10668 402346 Phage_terminase Phage terminase small subunit. This family of small highly conserved proteins come from a subset of Firmicute species. Its putative function is as a phage terminase small subunit. 67 matched cddid_all.tbl CDD pfam10669 pfam10669 402347 Phage_Gp23 Protein gp23 (Bacteriophage A118). This is the highly conserved family of the major tail subunit protein. 120 matched cddid_all.tbl CDD pfam10670 pfam10670 463175 DUF4198 Domain of unknown function (DUF4198). This family was previously missannotated in Pfam as NikM. 207 matched cddid_all.tbl CDD pfam10671 pfam10671 431425 TcpQ Toxin co-regulated pilus biosynthesis protein Q. The toxin-coregulated pilus (TCP) of Vibrio cholerae and the soluble TcpF protein that is secreted via the TCP biogenesis apparatus are essential for intestinal colonization in the disease of cholera. TcpQ is part of an outer membrane complex of the TCP biogenesis apparatus, comprised of TcpC and TcpQ, and the TcpQ is required for proper localization of TcpC to the outer membrane. The domain is found in other Proteobacterial species apart from Vibrio. 80 matched cddid_all.tbl CDD pfam10672 pfam10672 287624 Methyltrans_SAM S-adenosylmethionine-dependent methyltransferase. Members of this family are S-adenosylmethionine-dependent methyltransferases from gamma-proteobacterial species. The diversity in the roles of methylation is matched by the almost bewildering number of methyltransferase enzymes that catalyze the methylation reaction. Although several classes of methyltransferase enzymes are known, the great majority of methylation reactions are catalyzed by the S-adenosylmethionine-dependent methyltransferases. 286 matched cddid_all.tbl CDD pfam10673 pfam10673 431426 DUF2487 Protein of unknown function (DUF2487). This is a bacterial family of uncharacterized proteins. 142 matched cddid_all.tbl CDD pfam10674 pfam10674 431427 Ycf54 Protein of unknown function (DUF2488). This protein is conserved in the green lineage and located in the chloroplast. 91 matched cddid_all.tbl CDD pfam10675 pfam10675 431428 DUF2489 Protein of unknown function (DUF2489). This is a bacterial family of uncharacterized proteins. 130 matched cddid_all.tbl CDD pfam10676 pfam10676 371190 gerPA Spore germination protein gerPA/gerPF. This is a bacterial family of proteins that are required for the formation of functionally normal spores. Proteins in this family may be involved in establishing normal coat structure and/or permeability which could control the access of germinants to their receptor. 69 matched cddid_all.tbl CDD pfam10677 pfam10677 431429 DUF2490 Protein of unknown function (DUF2490). This is a bacterial family of uncharacterized proteins. They appear to belong to the outer membrane beta barrel superfamily. 180 matched cddid_all.tbl CDD pfam10678 pfam10678 431430 DUF2492 Protein of unknown function (DUF2492). This is a bacterial family of uncharacterized proteins. 77 matched cddid_all.tbl CDD pfam10679 pfam10679 431431 DUF2491 Protein of unknown function (DUF2491). This is a bacterial family of uncharacterized proteins. 211 matched cddid_all.tbl CDD pfam10680 pfam10680 463176 RRN9 RNA polymerase I specific transcription initiation factor. Initiation of transcription of ribosomal DNA (rDNA) in yeast involves an interaction of upstream activation factor (UAF) with the upstream element of the promoter, to form a stable UAF-template complex. UAF, together with the TATA-binding transcription initiation factor protein TBP, then recruits an essential core factor to the promoter, to form a stable preinitiation complex. This Rrn9 domain, which seems to be constrained to fungi, is the two highly conserved regions of proteins which form one of the subunits of UAF and appears to be the region responsible for the interaction with TBP. The family includes the S.pombe Arc1 protein, which is found to be essential for the accumulation of condensin at kinetochores. 65 matched cddid_all.tbl CDD pfam10681 pfam10681 431433 Rot1 Chaperone for protein-folding within the ER, fungal. This conserved fungal family is an essential molecular chaperone in the endoplasmic reticulum. Molecular chaperones transiently interact with unfolded proteins to inhibit their self-aggregation and to support their folding and/or assembly. Rot1 is a general chaperone with some substrate specificity, its substrates being the structurally unrelated Kre5 Kre6 Big1 Atg22, which are type I, type II, and polytopic membrane proteins. The dependencies of each for Rot1 do not share similarities. However, their folding does require BiP, and one of these proteins was simultaneously associated with both Rot1 and BiP. In addition, Rot1 may cooperate with BiP/Kar2 in the folding of Kre6. 209 matched cddid_all.tbl CDD pfam10682 pfam10682 463177 UL40 Glycoprotein of human cytomegalovirus HHV-5. This is glycoprotein UL40 from human cytomegalovirus or herpesvirus 5. The signal sequence of the UL40 polypeptide contains an HLA-E ligand identical with HLA-Cw*0304. The first 37 residues of UL40, including this ligand, are predicted to encode a signal peptide. The virus thus prevents the lysis by NK (natural killer) cells of the cell it has invaded. 214 matched cddid_all.tbl CDD pfam10683 pfam10683 402358 DBD_Tnp_Hermes Hermes transposase DNA-binding domain. This domain confers specific DNA-binding on Hermes transposase. 67 matched cddid_all.tbl CDD pfam10684 pfam10684 313818 BDM Putative biofilm-dependent modulation protein. This is a family of tightly conserved proteins from Enterobacteriaceae which are annotated as being biofilm-dependent modulation protein homologs. 71 matched cddid_all.tbl CDD pfam10685 pfam10685 431434 KGG Stress-induced bacterial acidophilic repeat motif. This repeat is found in proteins which are expressed under conditions of stress in bacteria. The repeat contains a highly conserved, characteriztic sequence motif,KGG, that is also recognized by plants and lower eukaryotes and repeated in their LEA (late embryogenesis abundant) family of proteins, thereby rendering those proteins bacteriostatic. An example of such an LEA family is LEA_5, pfam00477. Further downstream from this motif is a Walker A, nucleotide binding, motif GXXXXGK(S,T), that in YciG of E coli, eg Swiss:Q8X7B4, is QSGGNKSGKS. YciG is expressed as part of a three-gene operon, yciGFE, and this operon is induced by stress and is regulated by RpoS, which controls the general stress-response in E coli. YciG was shown to be important for stationary-phase resistance to thermal stress and in particular to acid stress. 22 matched cddid_all.tbl CDD pfam10686 pfam10686 431435 YAcAr YspA, cpYpsA-related SLOG family. Family in the SLOG superfamily, related to YspA and cpYpsA families and shows associations with NAD utilization and ADP-ribosylation domains including NUDIX, NADAR and MACRO. Members of this family are predicted to function as sensors of nucleotide, nucleotide-derived ligands, or nucleic acids, which are potentially processed/modified by associating effectors. Also associates in a distinct system with a phosphoribosyltransferase (PRTase) domain. 66 matched cddid_all.tbl CDD pfam10688 pfam10688 431436 Imp-YgjV Bacterial inner membrane protein. This is a family of inner membrane proteins. Many of the members are YgjV protein. 155 matched cddid_all.tbl CDD pfam10689 pfam10689 431437 DUF2496 Protein of unknown function (DUF2496). This family consists of proteins from Gammaproteobacteria spp. Many members are annotated as being like the E coli protein YbaM. 43 matched cddid_all.tbl CDD pfam10690 pfam10690 151186 Myticin-prepro Myticin pre-proprotein from the mussel. Myticin is a cysteine-rich peptide produced in three isoforms, A, B and C, by Mytilus galloprovincialis, the Mediterranean mussel. Some isoforms show antibacterial activity against gram-positive bacteria, while others are additionally active against the fungus Fusarium oxysporum and a gram-negative bacterium, Escherichia coli D31. Myticin-prepro is the precursor peptide. The mature molecule, named myticin, consists of 40 residues, with four intramolecular disulfide bridges and a cysteine array in the primary structure different from that of previously characterized cysteine-rich antimicrobial peptides. The first 20 amino acids are a putative signal peptide, and the antimicrobial peptide sequence is a 36-residue C-terminal extension. Such a structure suggests that myticins are synthesized as prepro-proteins that are then processed by various proteolytic events before storage in the haemocytes as the active peptide. Myticin precursors are expressed mainly in the haemocytes. The family Mytilin has been merged into this family. 98 matched cddid_all.tbl CDD pfam10691 pfam10691 431438 DUF2497 Protein of unknown function (DUF2497). Members of this family belong to the Alphaproteobacteria. The function of the family is not known. 70 matched cddid_all.tbl CDD pfam10692 pfam10692 431439 DUF2498 Protein of unknown function (DUF2498). Members of this family are Gammaproteobacteria. Many are annotated as like E coli protein YciN. The function is not known. 79 matched cddid_all.tbl CDD pfam10693 pfam10693 463178 DUF2499 Protein of unknown function (DUF2499). Members of this family are found in plants, lower eukaryotes, and bacteria and the chloroplast where it is annotated as Ycf49 or Ycf49-like. The function is not known though several members are annotated as putative membrane proteins. 87 matched cddid_all.tbl CDD pfam10694 pfam10694 431441 DUF2500 Protein of unknown function (DUF2500). The members of this family are largely confined to the Gammaproteobacteria. The function is not known. 100 matched cddid_all.tbl CDD pfam10696 pfam10696 431442 DUF2501 Protein of unknown function (DUF2501). Members of this family are all Proteobacteria. Several are annotated as being YjjA or YjjA-like, but this protein is uncharacterized. 77 matched cddid_all.tbl CDD pfam10697 pfam10697 431443 DUF2502 Protein of unknown function (DUF2502). Members of this family are all Gammaproteobacteria. The function is not known. 90 matched cddid_all.tbl CDD pfam10698 pfam10698 431444 DUF2505 Protein of unknown function (DUF2505). Members of this family are all Actinobacteria. The function is not known. 151 matched cddid_all.tbl CDD pfam10699 pfam10699 431445 HAP2-GCS1 Male gamete fusion factor. The gene encoding Arabidopsis HAP2 is allelic with GCS1 (Generative cell-specific protein 1). HAP2 is expressed only in the haploid sperm and is required for efficient guidance of the pollen tube to the ovules. In Arabidopsis the protein is a predicted membrane protein with an N-terminal secretion signal, a single transmembrane domain and a C-terminal histidine-rich domain. HAP2-GCS1 is found from plants to lower eukaryotes and is necessary for the fusion of the gametes in fertilization. Studies in the green alga Chlamydomonas and the malaria organizm Plasmodium showed that it is involved in a novel mechanism for gamete fusion where a first species-specific protein binds male and female gamete membranes together after which a second, broadly conserved protein, either directly or indirectly, causes fusion of the two membranes together. The broadly conserved protein is represented by this HAP2-GCS1 domain, conserved from plants to lower eukaryotes. In Plasmodium berghei the protein is expressed only in male gametocytes and gametes, having a male-specific function during the interaction with female gametes, and being indispensable for parasite fertilization. The gene in plants and eukaryotes might well have originated from acquisition of plastids from red algae. 475 matched cddid_all.tbl CDD pfam10702 pfam10702 431446 DUF2507 Protein of unknown function (DUF2507). This family is conserved in Firmicutes. The function is not known. 123 matched cddid_all.tbl CDD pfam10703 pfam10703 431447 MoaF MoaF N-terminal domain. MoaF protein is essential for the production of the monoamine-inducible 30kDa protein in Klebsiella. It is necessary for reconstituting organoautotrophic growth in Ralstonia eutropha. It is conserved in Proteobacteria and some lower eukaryotes. The operon regulating the Moa genes is responsible for molybdenum cofactor biosynthesis. This entry corresponds to the N-terminal domain. 108 matched cddid_all.tbl CDD pfam10704 pfam10704 431448 DUF2508 Protein of unknown function (DUF2508). This family is conserved in Firmicutes. Several members are annotated as being the protein YaaL. The function is not known. 71 matched cddid_all.tbl CDD pfam10705 pfam10705 463179 Ycf15 Chloroplast protein precursor Ycf15 putative. In some species of plants the ycf15 gene is probably not a protein-coding gene because the protein in these species has premature stop codons. Most of the members of the family are hypothetical or uncharacterized. 86 matched cddid_all.tbl CDD pfam10706 pfam10706 402373 Aminoglyc_resit Aminoglycoside-2''-adenylyltransferase. This family is conserved in Bacteria. It confers resistance to kanamycin, gentamicin, and tobramycin. The protein is also produced by plasmids in various bacterial species and confers resistance to essentially all clinically available aminoglycosides except streptomycin, and it eliminates the synergism between aminoglycosides and cell-wall active agents. 174 matched cddid_all.tbl CDD pfam10707 pfam10707 402374 YrbL-PhoP_reg PhoP regulatory network protein YrbL. This is a family of proteins that are activated by PhoP. PhoP protein controls the expression of a large number of genes that mediate adaptation to low Mg2+ environments and/or virulence in several bacterial species. YbrL is proposed to be acting in a loop activity with PhoP and PrmA analogous to the multicomponent loop in Salmonella where the PhoP-dependent PmrD protein activates the regulatory protein PmrA, and the activated PmrA then represses transcription from the PmrD promoter which harbours binding sites for both the PhoP and PmrA proteins. Expression of YrbL is induced in low Mg2+ in a PhoP-dependent fashion and repressed by Fe3+ in a PmrA-dependent manner. 185 matched cddid_all.tbl CDD pfam10708 pfam10708 431450 DUF2510 Protein of unknown function (DUF2510). This is family of proteins conserved in Actinobacteria. Many members are annotated as putative membrane proteins but this could not be confirmed. 35 matched cddid_all.tbl CDD pfam10709 pfam10709 431451 DUF2511 Protein of unknown function (DUF2511). This family is conserved in bacteria. The function is not known. 87 matched cddid_all.tbl CDD pfam10710 pfam10710 371204 DUF2512 Protein of unknown function (DUF2512). Proteins in this family are predicted to be integral membrane proteins, and many of them are annotated as being YndM protein. They are all found in Firmicutes. The true function is not known. 136 matched cddid_all.tbl CDD pfam10711 pfam10711 431452 DUF2513 Hypothetical protein (DUF2513). This family is found in bacteria. The function is not known. 100 matched cddid_all.tbl CDD pfam10712 pfam10712 402378 NAD-GH NAD-specific glutamate dehydrogenase. The members of this are annotated as being NAD-specific glutamate dehydrogenase encoded in antisense gene pair with DnaK-J. 576 matched cddid_all.tbl CDD pfam10713 pfam10713 431453 DUF2509 Protein of unknown function (DUF2509). This family is conserved in Proteobacteria. The function is not known but many of the members are annotated as protein YgdB. 131 matched cddid_all.tbl CDD pfam10714 pfam10714 371207 LEA_6 Late embryogenesis abundant protein 18. This is a family of late embryogenesis-abundant proteins There is high accumulation of this protein in dry seeds, and in the roots of full-grown plants in response to dehydration and ABA (abscisic acid application) treatments. This LEA protein disappears after germination. It accumulates in growing regions of well irrigated hypocotyls and meristems suggesting a role in seedling growth resumption on rehydration. As a group the LEA proteins are highly hydrophilic, contain a high percentage of glycine residues, lack Cys and Trp residues and do not coagulate upon exposure to high temperature, and for these reasons are considered to be members of a group of proteins called hydrophilins. Expression of the protein is negatively regulated during etiolating growth, particularly in roots, in contrast to its expression patterns during normal growth. 75 matched cddid_all.tbl CDD pfam10715 pfam10715 463180 REGB_T4 T4-page Endoribonuclease RegB. The RegB endoribonuclease encoded by bacteriophage T4 is a unique sequence-specific nuclease that cleaves in the middle of GGAG or, in a few cases, GGAU tetranucleotides, preferentially those found in the Shine-Dalgarno regions of early phage mRNAs. Phage RB49 in addition to RegB utilizes Escherichia coli endoribonuclease E for the degradation of its transcripts for gene regB. The deduced primary structure of RegB proteins of 32 phages studied is almost identical to that of T4, while the sequences of RegB encoded by phages RB69, TuIa and RB49 show substantial divergence from their T4 counterpart. Rebuilding from the PDB:2hx6 structure, this family does not fall into the Lysozyme-like family, but rather is a new member of the RelE/YoeB structural and functional family of ribonucleases specialising in mRNA inactivation within the ribosome. 150 matched cddid_all.tbl CDD pfam10716 pfam10716 402381 NdhL NADH dehydrogenase transmembrane subunit. The NdhL family is a component of the NDH-1L complex that is one of the proton-pumping NADH:ubiquinone oxidoreductases that catalyze the electron transfer from NADH to ubiquinone linked with proton translocation across the membrane. NDH-1L is essential for photoheterotrophic cell growth. NdhL appears to contain two transmembrane helices and it is necessary for the functioning of though not the correct assembly of the NDH-1 complex in Synechocystis 6803. The conservation between cyanobacteria and green plants suggests that chloroplast NDH-1 complexes contain related subunits. 76 matched cddid_all.tbl CDD pfam10717 pfam10717 287662 ODV-E18 Occlusion-derived virus envelope protein ODV-E18. This family of occlusion-derived viral envelope proteins are detected in viral-induced intranuclear microvesicles and are not detected in the plasma membrane, cytoplasmic membranes, or the nuclear envelope. The ODV-E18 protein is encoded by baculovirus late genes with transcription initiating from a TAAG motif. It exists as a dimer in the ODV envelope and contains a hydrophobic domain which is putatively acting as a target or retention signal for intranuclear microvesicles. 87 matched cddid_all.tbl CDD pfam10718 pfam10718 402382 Ycf34 Hypothetical chloroplast protein Ycf34. This family is of proteins annotated as hypothetical chloroplast protein YCF34. The function is not known. 78 matched cddid_all.tbl CDD pfam10719 pfam10719 463181 ComFB Late competence development protein ComFB. This family is conserved in bacteria. Some members, with three conserved cysteines, are annotated as late competence development protein ComFB. 79 matched cddid_all.tbl CDD pfam10720 pfam10720 371209 DUF2515 Protein of unknown function (DUF2515). This family is conserved in Firmicutes. Several members are annotated as YppC. The function is not known. 303 matched cddid_all.tbl CDD pfam10721 pfam10721 431455 DUF2514 Protein of unknown function (DUF2514). This family is conserved in bacteria and some viruses. The function is not known. 161 matched cddid_all.tbl CDD pfam10722 pfam10722 431456 YbjN Putative bacterial sensory transduction regulator. YbjN is a putative sensory transduction regulator protein found in Proteobacteria. As it is a multi-copy suppressor of the coenzyme A-associated temperature sensitivity in temperature-sensitive mutant strains of Escherichia coli the suggestion is that it both helps CoA-A1 and possibly works as a general stabilizer for some other unstable proteins. This family was expanded to subsume other related families: DUF1790, DUF1821 and DUF2596. 126 matched cddid_all.tbl CDD pfam10723 pfam10723 287668 RepB-RCR_reg Replication regulatory protein RepB. This is a family of proteins which regulate replication of rolling circle replication (RCR) plasmids that have a double-strand replication origin (dso). Regulation of replication of RCR plasmids occurs mainly at initiation of leading strand synthesis at the dso, such that Rep protein concentration controls plasmid replication. 81 matched cddid_all.tbl CDD pfam10724 pfam10724 431457 DUF2516 Protein of unknown function (DUF2516). This family is conserved in Actinobacteria. The function is not known. 91 matched cddid_all.tbl CDD pfam10725 pfam10725 431458 DUF2517 Protein of unknown function (DUF2517). This family is conserved in Proteobacteria. Several members are annotated as being protein YbfA. The function is not known. 61 matched cddid_all.tbl CDD pfam10726 pfam10726 431459 DUF2518 Protein of function (DUF2518). This family is conserved in Cyanobacteria. Several members are annotated as the protein Ycf51. The function is not known. 142 matched cddid_all.tbl CDD pfam10727 pfam10727 287672 Rossmann-like Rossmann-like domain. This family of proteins contain a Rossmann-like domain. 127 matched cddid_all.tbl CDD pfam10728 pfam10728 463182 DUF2520 Domain of unknown function (DUF2520). This presumed domain is found C-terminal to a Rossmann-like domain suggesting that these proteins are oxidoreductases. 126 matched cddid_all.tbl CDD pfam10729 pfam10729 313850 CedA Cell division activator CedA. CedA is made up of four antiparallel beta-strands and an alpha-helix. It activates cell division by inhibiting chromosome over-replication. This is mediated by binding to dsDNA via the beta-sheet.. 75 matched cddid_all.tbl CDD pfam10730 pfam10730 371213 DUF2521 Protein of unknown function (DUF2521). Family of unknown function specific to Bacillus. 146 matched cddid_all.tbl CDD pfam10731 pfam10731 287676 Anophelin Thrombin inhibitor from mosquito. Members of this family are all inhibitors of thrombin, the peptidase that is at the end of the blood coagulation cascade and which creates the clot by cleaving fibrinogen. The interaction between thrombin and fibrinogen involves two different areas of contact - via the thrombin active site and via a second substrate-binding site known as an exosite. The inhibitor acts by blocking the exosite, rather than by interacting with the active site. The inhibitors are from mosquitoes that feed on human blood and which, by inhibiting thrombin, prevent the blood from clotting and keep it flowing. 65 matched cddid_all.tbl CDD pfam10732 pfam10732 287677 DUF2524 Protein of unknown function (DUF2524). This family of proteins with unknown function appears to be restricted to Bacillaceae bacteria. 84 matched cddid_all.tbl CDD pfam10733 pfam10733 431461 DUF2525 Protein of unknown function (DUF2525). This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. The family has a highly conserved sequence. 60 matched cddid_all.tbl CDD pfam10734 pfam10734 431462 DUF2523 Protein of unknown function (DUF2523). This is a family of phage related proteins whose function is uncharacterized. 80 matched cddid_all.tbl CDD pfam10735 pfam10735 402390 DUF2526 Protein of unknown function (DUF2526). This family of proteins with unknown function is restricted to Enterobacteriaceae. The family has a highly conserved sequence. 76 matched cddid_all.tbl CDD pfam10736 pfam10736 119256 DUF2527 Protein of unknown function (DUF2627). This family of proteins with unknown function appears to be restricted to a family of Enterobacterial proteins. It has a highly conserved sequence. 38 matched cddid_all.tbl CDD pfam10737 pfam10737 371215 GerPC Spore germination protein GerPC. GerPC is required for the formation of functionally normal spores. The gerP locus encodes a number of proteins which are thought to be involved in the establishment of normal spore coat structure and/or permeability, which allows the access of germinants to their receptor. 173 matched cddid_all.tbl CDD pfam10738 pfam10738 431463 Lpp-LpqN Probable lipoprotein LpqN. This family is conserved in Mycobacteriaceae and is likely to be a lipoprotein. 171 matched cddid_all.tbl CDD pfam10739 pfam10739 431464 DUF2550 Protein of unknown function (DUF2550). This family is conserved in Corynebacterineae. The function is not known though most members are annotated as either secreted, or membrane, proteins. 127 matched cddid_all.tbl CDD pfam10740 pfam10740 431465 DUF2529 Domain of unknown function (DUF2529). This domain is conserved in the Bacillales. The function is not known, but given this domains relationship to the SIS domain it may carry out a sugar isomerase reaction. Several members are annotated as being YWJG, a protein expressed downstream of pyrG, a gene encoding for cytidine triphosphate synthetase. 169 matched cddid_all.tbl CDD pfam10741 pfam10741 431466 T2SSM_b Type II secretion system (T2SS), protein M subtype b. The T2SMb family is conserved in Proteobacteria and Actinobacteria, and differs from the T2SM proteins in Vibrio spp. (pfam04612). 111 matched cddid_all.tbl CDD pfam10742 pfam10742 431467 DUF2555 Protein of unknown function (DUF2555). This family is conserved in Cyanobacteria. The function is not known. 55 matched cddid_all.tbl CDD pfam10743 pfam10743 431468 Phage_Cox Regulatory phage protein cox. This family of phage Cox proteins is expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes. 87 matched cddid_all.tbl CDD pfam10744 pfam10744 463183 Med1 Mediator of RNA polymerase II transcription subunit 1. Mediator complexes are basic necessities for linking transcriptional regulators to RNA polymerase II. This domain, Med1, is conserved from plants to fungi to humans and forms part of the Med9 submodule of the Srb/Med complex. it is one of three subunits essential for viability of the whole organizm via its role in environmentally-directed cell-fate decisions. Med1 is part of the tail region of the Mediator complex. 386 matched cddid_all.tbl CDD pfam10745 pfam10745 431470 DUF2530 Protein of unknown function (DUF2530). This family of proteins with unknown function appears to be restricted to mycobacteria. 73 matched cddid_all.tbl CDD pfam10746 pfam10746 431471 Phage_holin_2_2 Phage holin T7 family, holin superfamily II. Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis. 60 matched cddid_all.tbl CDD pfam10747 pfam10747 402398 SirA Sporulation inhibitor of replication protein SirA. This entry represents the Sporulation inhibitor of replication (sirA) family of proteins from Bacillus sp. Induction of sporulation in rapidly growing cells inhibits replication; this is thought to be through the action of SirA protein and independent of phosphorylated Spo0A; however SirA protein synthesis is induced by Spo0A. 140 matched cddid_all.tbl CDD pfam10748 pfam10748 402399 HofP DNA utilization proteins HofP. This family includes the Escherischia coli protein HofP, one of eight genes shown to be required for the utilization of extracellular DNA as a nutrient source in starving conditions, allowing DNA to be the sole source for carbon and energy. Proteins in this entry appear are found only in Enterobacteriaceae. 132 matched cddid_all.tbl CDD pfam10749 pfam10749 402400 DUF2534 Protein of unknown function (DUF2534). This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. 80 matched cddid_all.tbl CDD pfam10750 pfam10750 371221 DUF2536 Protein of unknown function (DUF2536). This family of proteins with unknown function appears to be restricted to Bacillus spp. Structural modelling suggests this domain may bind nucleic acids. 68 matched cddid_all.tbl CDD pfam10751 pfam10751 313866 DUF2535 Protein of unknown function (DUF2535). This family of proteins with unknown function appears to be restricted to Bacillus spp. 83 matched cddid_all.tbl CDD pfam10752 pfam10752 313867 DUF2533 Protein of unknown function (DUF2533). This family of proteins with unknown function appears to be restricted to Bacillus spp. 83 matched cddid_all.tbl CDD pfam10753 pfam10753 431472 Toxin_GhoT_OrtT Toxin GhoT_OrtT. GhoT is part of the GhoT-GhoS type V toxin-antitoxin (TA) system. OrtT is homologous to GhoT, but it is not part of a TA pair. In this case, it acts as an independent toxin to reduce growth during stress related to amino acid and DNA synthesis. 55 matched cddid_all.tbl CDD pfam10754 pfam10754 431473 DUF2569 Protein of unknown function (DUF2569). This family is conserved in bacteria. The function is not known, but several members are annotated as being YdgK or a homolog thereof. 143 matched cddid_all.tbl CDD pfam10755 pfam10755 431474 DUF2585 Protein of unknown function (DUF2585). This family is conserved in Proteobacteria. The function is not known. 164 matched cddid_all.tbl CDD pfam10756 pfam10756 431475 bPH_6 Bacterial PH domain. This domain has a bacterial type PH domain structure. This domain was previously known as DUF2581. This family is conserved in the Actinomycetales. Although several members are annotated as RbiX homologs, RbiX being a putative regulator of riboflavin biosynthesis, the function could not be confirmed. 73 matched cddid_all.tbl CDD pfam10757 pfam10757 431476 YbaJ Biofilm formation regulator YbaJ. YbaJ regulates biofilm formation. It also has an important role in the regulation of motility in the biofilm. YbaJ functions in increasing conjugation, aggregation and decreasing the motility, resulting in an increase of biofilm 118 matched cddid_all.tbl CDD pfam10758 pfam10758 463184 DUF2586 Protein of unknown function (DUF2586). This bacterial family of proteins is a component of a contractile injection system related to phage sheath proteins. 391 matched cddid_all.tbl CDD pfam10759 pfam10759 431478 BPA Bacterial proteasome activator. This is a family of bacterial proteasome cofactors. The family member from Mycobacterium tuberculosis, protein Rv3780, was shown to form rings and cap proteasome core particles. It enhanced peptide and protein degradation by proteasomes in an adenosine triphosphate (ATP)-independent manner, promoting degradation of the heat shock protein repressor HspR. 160 matched cddid_all.tbl CDD pfam10761 pfam10761 431479 DUF2590 Protein of unknown function (DUF2590). This family of proteins has no known function. 98 matched cddid_all.tbl CDD pfam10762 pfam10762 431480 DUF2583 Protein of unknown function (DUF2583). Some members in this family of proteins are annotated as YchH however currently no function is known. 86 matched cddid_all.tbl CDD pfam10763 pfam10763 402408 DUF2584 Protein of unknown function (DUF2584). This bacterial family of proteins have no known function. 77 matched cddid_all.tbl CDD pfam10764 pfam10764 463185 Gin Inhibitor of sigma-G Gin. Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB. 44 matched cddid_all.tbl CDD pfam10765 pfam10765 431481 Phage_P22_NinX Bacteriophage P22, NinX. This family is represented by Bacteriophage P22, NinX. The characteriztics of the protein distribution suggest prophage matches in addition to the phage matches. 106 matched cddid_all.tbl CDD pfam10766 pfam10766 431482 AcrZ Multidrug efflux pump-associated protein AcrZ. AcrZ is associated with the AcrA-TolC multidrug efflux pump, it may enhance the ability of the pump to recognize and export certain substrates. 48 matched cddid_all.tbl CDD pfam10767 pfam10767 431483 DUF2593 Protein of unknown function (DUF2593). This family of proteins appear to be restricted to Enterobacteriaceae. Some members in the family are annotated as YbjO however currently there is no known function. 141 matched cddid_all.tbl CDD pfam10768 pfam10768 431484 FliX Class II flagellar assembly regulator. The FliX protein is possibly a transient component of the flagellum that is required for the assembly process. FliX may contribute to the targeting or assembly of the P- and L-ring protein monomers at the cell pole. The family carries a potential N-terminal signal sequence and at least one transmembrane domain indicating that it might function either in or in association with the cell membrane. 135 matched cddid_all.tbl CDD pfam10769 pfam10769 431485 DUF2594 Protein of unknown function (DUF2594). This family of proteins with unknown function appear to be restricted to Enterobacteriaceae. 74 matched cddid_all.tbl CDD pfam10771 pfam10771 431486 DUF2582 Winged helix-turn-helix domain (DUF2582). This family is conserved in bacteria and archaea. The function is not known. The structure of two proteins in this family were solved using NMR and shown to adopt a winged helix-turn-helix fold. Structural analysis shows that these proteins form an unusual dimeric conformation. This dimer was shown to be similar to that found in the FadR and TubR wHTH domains. It was suggested that these proteins are not very likely to bind to DNA. 65 matched cddid_all.tbl CDD pfam10772 pfam10772 431487 Phage_HP1_Orf24 Bacteriophage HP1, Orf24. This family is represented by Bacteriophage HP1, Orf24, whose function is unknown. The characteriztics of the protein distribution suggest prophage matches in addition to the phage matches. 134 matched cddid_all.tbl CDD pfam10774 pfam10774 402415 DUF4226 Domain of unknown function (DUF4226). This family of mycobacterial proteins are uncharacterized. This family has partial similarity to EspA related proteins. 115 matched cddid_all.tbl CDD pfam10775 pfam10775 431488 ATP_sub_h ATP synthase complex subunit h. Subunit h is a component of the yeast mitochondrial F1-F0 ATP synthase. It is essential for the correct assembly and functioning of this enzyme. Subunit h occupies a central place in the peripheral stalk between the F1 sector and the membrane. 67 matched cddid_all.tbl CDD pfam10776 pfam10776 431489 DUF2600 Protein of unknown function (DUF2600). This is a bacterial family of proteins. Some members in the family are annotated as YtpB however currently no function is known. 328 matched cddid_all.tbl CDD pfam10777 pfam10777 431490 YlaC Inner membrane protein YlaC. Members of this family include proteins annotated as inner membrane protein YlaC in E. coli and Salmonella. The function of this family is unknown. 154 matched cddid_all.tbl CDD pfam10778 pfam10778 402418 DehI Halocarboxylic acid dehydrogenase DehI. Haloacid dehalogenases catalyze the removal of halides from organic haloacids. DehI can process both L- and D-substrates. A crucial aspartate residue is predicted to activate a water molecule for nucleophilic attack of the substrate chiral centre resulting in an inversion of the configuration of either L- or D-substrates in contrast to D-only enzymes. 148 matched cddid_all.tbl CDD pfam10779 pfam10779 402419 XhlA Haemolysin XhlA. XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes. This family has had DUF1267, pfam06895, merged into it. 67 matched cddid_all.tbl CDD pfam10780 pfam10780 463186 MRP_L53 39S ribosomal protein L53/MRP-L53. MRP-L53 is also known as Mrp144. It is part of the 39S ribosome. 54 matched cddid_all.tbl CDD pfam10781 pfam10781 431492 DSRB Dextransucrase DSRB. DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose. 61 matched cddid_all.tbl CDD pfam10782 pfam10782 402422 zf-C2HCIx2C Zinc-finger. This bacterial family of proteins is a zinc-finger domain of the C2HC type with an additional cysteine. 58 matched cddid_all.tbl CDD pfam10783 pfam10783 431493 DUF2599 Protein of unknown function (DUF2599). This family is conserved in Actinobacteria. The function is not known. 94 matched cddid_all.tbl CDD pfam10784 pfam10784 119304 Plasmid_stab_B Plasmid stability protein. This family is conserved in the Enterobacteriales. It is a putative plasmid stability protein in that it is expressed from the operon involved in stability, but its actual function has not yet been characterized. 72 matched cddid_all.tbl CDD pfam10785 pfam10785 463187 NADH-u_ox-rdase NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit. This family is the N-terminal domain of NADH-ubiquinone oxidoreductase 21 kDa subunits from fungi, lower metazoa and plants. 85 matched cddid_all.tbl CDD pfam10786 pfam10786 431495 G6PD_bact Glucose-6-phosphate 1-dehydrogenase (EC 1.1.1.49). This family is conserved in Firmicutes and Proteobacteria. Several members are annotated as being glucose-6-phosphate 1-dehydrogenase (EC:1.1.1.49) but this could not be confirmed. 213 matched cddid_all.tbl CDD pfam10787 pfam10787 402426 YfmQ Uncharacterized protein from bacillus cereus group. This family is conserved in the Bacillus cereus group. Several members are called YfmQ but the function is not known. 141 matched cddid_all.tbl CDD pfam10788 pfam10788 431496 DUF2603 Protein of unknown function (DUF2603). This family is conserved in Epsilon-proteobacteria. The function is not known. 137 matched cddid_all.tbl CDD pfam10789 pfam10789 256166 Phage_RpbA Phage RNA polymerase binding, RpbA. Upon infection the RpbA encode phage protein binds to the ADP-ribosylated core RNA polymerase and modulates function to preferentially bind T4 promoters. This is a non-essential protein to the phage life cycle. 108 matched cddid_all.tbl CDD pfam10790 pfam10790 463188 DUF2604 Protein of Unknown function (DUF2604). Family of bacterial proteins with undetermined function. 85 matched cddid_all.tbl CDD pfam10791 pfam10791 431498 F1F0-ATPsyn_F Mitochondrial F1-F0 ATP synthase subunit F of fungi. The membrane bound F1-FO-type H+ ATP synthase of mitochondria catalyzes the terminal step in oxidative respiration converting the generation of the electrochemical gradient into ATP for cellular biosynthesis. The general structure and the core subunits of the enzyme are highly conserved in both prokaryotic and eukaryotic organizms. 87 matched cddid_all.tbl CDD pfam10792 pfam10792 431499 DUF2605 Protein of unknown function (DUF2605). This family is conserved in Cyanobacteria. The function is not known. 96 matched cddid_all.tbl CDD pfam10793 pfam10793 371249 Gloverin Gloverin-like protein. This family of proteins are Gloverin-like. Gloverin is a 13.8kDa inducible antibacterial insect protein which inhibits the synthesis of vital outer membrane proteins leading to a permeable outer membrane. Gloverin contains a large number of glycine residues. 161 matched cddid_all.tbl CDD pfam10794 pfam10794 287732 DUF2606 Protein of unknown function (DUF2606). Family of bacterial proteins with unknown function. These proteins have been classified as membrane proteins 134 matched cddid_all.tbl CDD pfam10795 pfam10795 431500 DUF2607 Protein of unknown function (DUF2607). This family is conserved in Gammaproteobacteria. The function is not known. 95 matched cddid_all.tbl CDD pfam10796 pfam10796 431501 Anti-adapt_IraP Sigma-S stabilization anti-adaptor protein. This family is conserved in Enterobacteriaceae. It is one of a series of proteins, expressed by these bacteria in response to stress, that help to regulate Sigma-S, the stationary phase sigma factor of Escherichia coli and Salmonella. IraP is essential for Sigma-S stabilization in some but not all starvation conditions. 86 matched cddid_all.tbl CDD pfam10797 pfam10797 431502 YhfT Protein of unknown function. This family is conserved in Firmicutes and Proteobacteria. The function is not known but several members are annotated as being homologs of E coli YhfT, a protein thought to be involved in fatty acid oxidation. 422 matched cddid_all.tbl CDD pfam10798 pfam10798 431503 YmgB Biofilm development protein YmgB/AriR. YmgB is part of the three gene cluster ymgABC which has a role in biofilm development and stability. YmgB represses biofilm formation in rich medium containing glucose, decreases cellular motility and also protects the cell from acid which indicates that YmgB has an important function in acid-resistance. YmgB binds as a dimer to genes which are important for biofilm formation via a ligand. Due to its important function in acid resistance it is also known as AriR (regulator of acid resistance influenced by indole). 59 matched cddid_all.tbl CDD pfam10799 pfam10799 313902 YliH Biofilm formation protein (YliH/bssR). YliH is induced in biofilms and is involved in repression of motility in the biofilms. YliH is also known as bssR (regulator of biofilm through signal secreton). 126 matched cddid_all.tbl CDD pfam10800 pfam10800 402435 DUF2528 Protein of unknown function (DUF2528). This family of proteins has no known function. Some of the sequences are annotated as ea10 however the function of this protein is unknown. 103 matched cddid_all.tbl CDD pfam10801 pfam10801 431504 DUF2537 Protein of unknown function (DUF2537). This bacterial family of proteins has no known function. 75 matched cddid_all.tbl CDD pfam10802 pfam10802 402437 DUF2540 Protein of unknown function (DUF2540). This family of proteins with unknown function appears to be restricted to Methanococcus. 75 matched cddid_all.tbl CDD pfam10803 pfam10803 313906 GerPB Spore germination GerPB. Members of this family are required for formation of functionally normal spores. They may be involved in the establishment of spore coat structure or permeability. 52 matched cddid_all.tbl CDD pfam10804 pfam10804 402438 DUF2538 Protein of unknown function (DUF2538). This family of proteins has no known function. 155 matched cddid_all.tbl CDD pfam10805 pfam10805 402439 DUF2730 Protein of unknown function (DUF2730). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. 101 matched cddid_all.tbl CDD pfam10806 pfam10806 402440 SAM35 SAM35, subunit of SAM coomplex. SAM35 is a family of fungal proteins found in the peripheral mitochondrial outer membrane. It is essential for cell viability. It forms a subunit of the SAM (sorting and assembly machinery) complex and is crucial for the assembly of the precursors of Tom40 and porin, the outer membrane beta-barrel proteins involved in mitochondrial biogenesis. SAM35 is required in order for the Sam50 subunit of the SAM complex to bind outer membrane substrate proteins. 125 matched cddid_all.tbl CDD pfam10807 pfam10807 287745 DUF2541 Protein of unknown function (DUF2541). This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. All proteins are annotated as YaaI precursor however currently no function is known. 130 matched cddid_all.tbl CDD pfam10808 pfam10808 151258 DUF2542 Protein of unknown function (DUF2542). This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. The family has a highly conserved sequence. 79 matched cddid_all.tbl CDD pfam10809 pfam10809 431505 DUF2732 Protein of unknown function (DUF2732). This family of proteins has no known function. 74 matched cddid_all.tbl CDD pfam10810 pfam10810 431506 DUF2545 Protein of unknown function (DUF2545). This family of proteins with unknown function is restricted to Enterobacteriaceae. The sequence is highly conserved. 80 matched cddid_all.tbl CDD pfam10811 pfam10811 287748 DUF2532 Protein of unknown function (DUF2532). This bacterial family of proteins has no known function. 158 matched cddid_all.tbl CDD pfam10812 pfam10812 402442 DUF2561 Protein of unknown function (DUF2561). This family of proteins with unknown function appears to be restricted to Mycobacterium spp. 204 matched cddid_all.tbl CDD pfam10813 pfam10813 287750 Herpesvir_UL11 Herpesvirus UL11 homolog. This entry contains viral proteins that are involved in virion envelopment and egress. It includes Epstein-Barr virus (EBV) BBLF1 protein (also known as cytoplasmic envelopment protein 3), which is present in the tegument layer of EBV and is involved in virion maturation. BBLF1 also participates in viral entry at the fusion step probably by regulating the core fusion machinery. BBLF1 has been shown to localize to the trans-Golgi network along with gp350/220, a site where final envelopment of EBV particles takes place. BBLF1 shares 13 to 15% amino acid sequence identity with the herpes simplex virus 1 UL11 and cytomegalovirus UL99 tegument proteins, and like these it is a myristoylated and palmitoylated protein. 32 matched cddid_all.tbl CDD pfam10814 pfam10814 431507 CwsA Cell wall synthesis protein CwsA. Cell wall synthesis protein CwsA is required for cell division, cell wall synthesis and cell shape maintenance. 133 matched cddid_all.tbl CDD pfam10815 pfam10815 313911 ComZ ComZ. ComZ is part of a two gene operon. It affects competence regulation by negatively affecting the transcription of the ComG operon. ComZ contains a leucine zipper motif. 55 matched cddid_all.tbl CDD pfam10816 pfam10816 431508 DUF2760 Domain of unknown function (DUF2760). This is a bacterial family of uncharacterized proteins. 123 matched cddid_all.tbl CDD pfam10817 pfam10817 287754 DUF2563 Protein of unknown function (DUF2563). This family of proteins with unknown function appears to be restricted to Mycobacterium. 104 matched cddid_all.tbl CDD pfam10818 pfam10818 431509 SecM_small secA translation cis-regulator SecM, small type. In E. coli, SecM encodes a presecretory protein that regulates secA expression at the translational level. SecM contains a C-terminal sequence motif that induces a transient translation arrest. SecM signal peptide plays an essential role in this regulatory process by acting as a molecular timer that coordinates secM membrane targeting with the synthesis of the arrest motif. 96 matched cddid_all.tbl CDD pfam10819 pfam10819 287756 DUF2564 Protein of unknown function (DUF2564). This family of proteins with unknown function appears to be restricted to Bacillus spp. 78 matched cddid_all.tbl CDD pfam10820 pfam10820 431510 DUF2543 Protein of unknown function (DUF2543). This family of proteins with unknown function appear to be restricted to Enterobacteriaceae. The family has a highly conserved sequence. 81 matched cddid_all.tbl CDD pfam10821 pfam10821 431511 DUF2567 Protein of unknown function (DUF2567). This is a bacterial family of proteins with unknown function. 166 matched cddid_all.tbl CDD pfam10823 pfam10823 431512 DUF2568 Protein of unknown function (DUF2568). One member in this family is annotated as yrdB which is part of a four gene operon however currently no function is known. 92 matched cddid_all.tbl CDD pfam10824 pfam10824 371259 T7SS_ESX_EspC Excreted virulence factor EspC, type VII ESX diderm. T7SS_ESX-EspC is a family of exported virulence proteins from largely Acinetobacteria and a few Fimicutes, Gram-positive bacteria. It is exported in conjunction with EspA as an interacting pair.ED F8ADQ6.1/227-313; F8ADQ6.1/227-313; 100 matched cddid_all.tbl CDD pfam10825 pfam10825 431513 DUF2752 Protein of unknown function (DUF2752). This family is conserved in bacteria. Many members are annotated as being putative membrane proteins. 49 matched cddid_all.tbl CDD pfam10826 pfam10826 431514 DUF2551 Protein of unknown function (DUF2551). This Archaeal family of proteins has no known function. 83 matched cddid_all.tbl CDD pfam10827 pfam10827 371260 DUF2552 Protein of unknown function (DUF2552). This bacterial family of proteins has no known function. 79 matched cddid_all.tbl CDD pfam10828 pfam10828 402451 DUF2570 Protein of unknown function (DUF2570). This is a family of proteins with unknown function. 108 matched cddid_all.tbl CDD pfam10829 pfam10829 313921 DUF2554 Protein of unknown function (DUF2554). This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. 76 matched cddid_all.tbl CDD pfam10830 pfam10830 371262 DUF2553 Protein of unknown function (DUF2553). This family of bacterial proteins has no known function. 75 matched cddid_all.tbl CDD pfam10831 pfam10831 431515 DUF2556 Protein of unknown function (DUF2556). This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. 53 matched cddid_all.tbl CDD pfam10832 pfam10832 431516 DUF2559 Protein of unknown function (DUF2559). This family of proteins appear to be restricted to Enterobacteriaceae. The sequences are annotated as yhfG however currently no function is known. 54 matched cddid_all.tbl CDD pfam10833 pfam10833 431517 DUF2572 Protein of unknown function (DUF2572). This bacterial family of proteins has no known function. 219 matched cddid_all.tbl CDD pfam10834 pfam10834 287770 DUF2560 Protein of unknown function (DUF2560). This family of proteins has no known function. 72 matched cddid_all.tbl CDD pfam10835 pfam10835 313925 DUF2573 Protein of unknown function (DUF2573). Some members in this bacterial family of proteins are annotated as YusU however no function is currently known. This family of proteins appears to be restricted to Bacillus spp. 75 matched cddid_all.tbl CDD pfam10836 pfam10836 287772 DUF2574 Protein of unknown function (DUF2574). This family of proteins appears to be restricted to Enterobacteriaceae. Members of the family are annotated as yehE however currently no function is known. 93 matched cddid_all.tbl CDD pfam10838 pfam10838 313926 DUF2677 Protein of unknown function (DUF2677). Members in this family of proteins are annotated as UL121 however currently no function is known. 166 matched cddid_all.tbl CDD pfam10839 pfam10839 287774 DUF2647 Protein of unknown function (DUF2647). This eukaryotic family of proteins are annotated as ycf68 but have no known function. 70 matched cddid_all.tbl CDD pfam10840 pfam10840 431518 DUF2645 Protein of unknown function (DUF2645). This family of proteins appear to be restricted to Enterobacteriaceae. Some members in the family are annotated as YjeO however no function for this protein is currently known. 98 matched cddid_all.tbl CDD pfam10841 pfam10841 402455 DUF2644 Protein of unknown function (DUF2644). This family of proteins with unknown function appear to be restricted to Pasteurellaceae. 59 matched cddid_all.tbl CDD pfam10842 pfam10842 402456 DUF2642 Protein of unknown function (DUF2642). This family of proteins with unknown function appear to be restricted to Bacillus spp. 61 matched cddid_all.tbl CDD pfam10843 pfam10843 371266 RGI1 Respiratory growth induced protein 1. This family of fungal proteins includes RGI1, standing for respiratory growth induced 1. RGI1 is involved in aerobic energetic metabolism. 194 matched cddid_all.tbl CDD pfam10844 pfam10844 463189 DUF2577 Protein of unknown function (DUF2577). This family of proteins has no known function 107 matched cddid_all.tbl CDD pfam10845 pfam10845 313931 DUF2576 Protein of unknown function (DUF2576). The function of this viral family of proteins is unknown. 48 matched cddid_all.tbl CDD pfam10846 pfam10846 371267 DUF2722 Protein of unknown function (DUF2722). This eukaryotic family of proteins has no known function. 369 matched cddid_all.tbl CDD pfam10847 pfam10847 431520 DUF2656 Protein of unknown function (DUF2656). This bacterial family of proteins has no known function. 141 matched cddid_all.tbl CDD pfam10849 pfam10849 287783 DUF2654 Protein of unknown function (DUF2654). Some members in this family of proteins are annotated as a-gt.4 however currently no function is known. 70 matched cddid_all.tbl CDD pfam10850 pfam10850 313933 DUF2653 Protein of unknown function (DUF2653). This family of proteins with unknown function appears to be restricted to Bacillus spp. 88 matched cddid_all.tbl CDD pfam10851 pfam10851 431521 DUF2652 Protein of unknown function (DUF2652). This family of proteins has no known function. 118 matched cddid_all.tbl CDD pfam10852 pfam10852 371270 DUF2651 Protein of unknown function (DUF2651). This family of proteins with unknown function appears to be restricted to Bacillus spp. 73 matched cddid_all.tbl CDD pfam10853 pfam10853 463190 DUF2650 Protein of unknown function (DUF2650). This family of proteins with unknown function appear to be restricted to Caenorhabditis elegans. 35 matched cddid_all.tbl CDD pfam10854 pfam10854 287788 DUF2649 Protein of unknown function (DUF2649). Members in this family of proteins are annotated as Plectrovirus orf 10 transmembrane proteins however currently no function is known. 67 matched cddid_all.tbl CDD pfam10856 pfam10856 463191 DUF2678 Protein of unknown function (DUF2678). This family of proteins has no known function. 118 matched cddid_all.tbl CDD pfam10857 pfam10857 287791 DUF2701 Protein of unknown function (DUF2701). This viral family of proteins has no known function. 63 matched cddid_all.tbl CDD pfam10858 pfam10858 463192 DUF2659 Protein of unknown function (DUF2659). This bacterial family of proteins has no known function. 224 matched cddid_all.tbl CDD pfam10859 pfam10859 313938 DUF2660 Protein of unknown function (DUF2660). This is a family of proteins with unknown function. 91 matched cddid_all.tbl CDD pfam10860 pfam10860 287794 DUF2661 Protein of unknown function (DUF2661). This viral family of proteins have no known function. 113 matched cddid_all.tbl CDD pfam10861 pfam10861 431525 DUF2784 Protein of Unknown function (DUF2784). This is a family of uncharacterized protein. The function is not known however it is conserved in Bacteria. 109 matched cddid_all.tbl CDD pfam10862 pfam10862 431526 FcoT FcoT-like thioesterase domain. Proteins in this family have a HotDog fold. This family was formerly known as domain of unknown function 2662 (DUF2662). The structure of Rv0098 from M. tuberculosis suggested a thioesterase function. Assays showed that this protein was a thioesterase with a preference for long chain fatty acyl groups. The maximal Kcat was observed for palmitoyl-CoA although longer and shorter molecules were also cleaved. In solution this protein forms a homo-hexameric complex. 150 matched cddid_all.tbl CDD pfam10863 pfam10863 402465 NOP19 Nucleolar protein 19. Nucleolar protein 19 plays an essential role in 40S ribosomal subunit biogenesis. 140 matched cddid_all.tbl CDD pfam10864 pfam10864 371275 DUF2663 Protein of unknown function (DUF2663). Some members in this family of proteins are annotated as YpbF however currently no function is known. 130 matched cddid_all.tbl CDD pfam10865 pfam10865 431527 DUF2703 Domain of unknown function (DUF2703). This family of protein has no known function, but it may be distantly related to the thioredoxin fold. It contains the CXXC motif that is characteriztic of thioredoxins. 120 matched cddid_all.tbl CDD pfam10866 pfam10866 313944 DUF2704 Protein of unknown function (DUF2704). This viral family of proteins has no known function. 167 matched cddid_all.tbl CDD pfam10867 pfam10867 287800 DUF2664 Protein of unknown function (DUF2664). This family of proteins is a viral family, annotated as UL96. Currently no function is known. 89 matched cddid_all.tbl CDD pfam10868 pfam10868 402467 Defensin_like Cysteine-rich antifungal protein 2, defensin-like. This is a family of plant antifungal proteins. It has insecticidal and antifungal activity against certain plant pathogens. 50 matched cddid_all.tbl CDD pfam10869 pfam10869 402468 DUF2666 Protein of unknown function (DUF2666). This Archaeal family of proteins has no known function. 135 matched cddid_all.tbl CDD pfam10870 pfam10870 287802 DUF2729 Protein of unknown function (DUF2729). This viral family of proteins has no known function. 57 matched cddid_all.tbl CDD pfam10871 pfam10871 402469 DUF2748 Protein of unknown function (DUF2748). This is a bacterial family of proteins with unknown function. 439 matched cddid_all.tbl CDD pfam10872 pfam10872 287804 DUF2740 Protein of unknown function (DUF2740). This family of proteins with unknown function has a highly conserved sequence. 48 matched cddid_all.tbl CDD pfam10873 pfam10873 313948 CYYR1 Cysteine and tyrosine-rich protein 1. Members in this family of proteins are annotated as Cysteine and tyrosine-rich protein 1, however currently no function is known. 149 matched cddid_all.tbl CDD pfam10874 pfam10874 371279 DUF2746 Protein of unknown function (DUF2746). This family of proteins has no known function. 101 matched cddid_all.tbl CDD pfam10875 pfam10875 287807 DUF2670 Protein of unknown function (DUF2670). This bacterial family of proteins has no known function. 145 matched cddid_all.tbl CDD pfam10876 pfam10876 337861 Phage_TAC_9 Phage tail assembly chaperone protein, TAC. This is a family of putative phage tail assembly chaperone proteins largely from Haemophilus and Xylella species. 133 matched cddid_all.tbl CDD pfam10877 pfam10877 402470 DUF2671 Protein of unknown function (DUF2671). This family of proteins with unknown function appears to be restricted to Rickettsia spp. 89 matched cddid_all.tbl CDD pfam10878 pfam10878 313952 DUF2672 Protein of unknown function (DUF2672). This family of proteins with unknown function appear to be restricted to Rickettsiae. 67 matched cddid_all.tbl CDD pfam10879 pfam10879 463193 DUF2674 Protein of unknown function (DUF2674). This family of proteins with unknown function appears to be conserved to Rickettsia spp. 63 matched cddid_all.tbl CDD pfam10880 pfam10880 313953 DUF2673 Protein of unknown function (DUF2673). This family of proteins with unknown function appears to be restricted to Rickettsiae spp. 82 matched cddid_all.tbl CDD pfam10881 pfam10881 431528 DUF2726 Protein of unknown function (DUF2726). This bacterial family of proteins has no known function. 126 matched cddid_all.tbl CDD pfam10882 pfam10882 378504 bPH_5 Bacterial PH domain. This family of proteins with unknown function appear to be related to bacterial PH domains. This family was formerly known as DUF2679. 100 matched cddid_all.tbl CDD pfam10883 pfam10883 402472 DUF2681 Protein of unknown function (DUF2681). This family of proteins is found in bacteria. Proteins in this family are typically between 81 and 117 amino acids in length. 87 matched cddid_all.tbl CDD pfam10884 pfam10884 287815 DUF2683 Protein of unknown function (DUF2683). This family of proteins with unknown function appears to be restricted to Methanosarcinaceae. 78 matched cddid_all.tbl CDD pfam10886 pfam10886 287817 DUF2685 Protein of unknown function (DUF2685). Members in this family of proteins are annotated as uvdY.-2 which is an open reading frame within uvsY. However currently there is no known function. 55 matched cddid_all.tbl CDD pfam10887 pfam10887 287818 DUF2686 Protein of unknown function (DUF2686). Some members in this family of proteins are annotated as yjfZ however currently no function is known. 285 matched cddid_all.tbl CDD pfam10888 pfam10888 371285 DUF2742 Protein of unknown function (DUF2742). Members in this family of phage proteins are the product of the gene phiRv1, however no function is known. 97 matched cddid_all.tbl CDD pfam10890 pfam10890 371286 Cyt_b-c1_8 Cytochrome b-c1 complex subunit 8. This entry represents subunit 8 of the Cytochrome b-c1 complex. 72 matched cddid_all.tbl CDD pfam10891 pfam10891 151339 DUF2719 Protein of unknown function (DUF2719). This family of proteins with unknown function appears to be restricted to Nucleopolyhedrovirus. 81 matched cddid_all.tbl CDD pfam10892 pfam10892 371287 DUF2688 Protein of unknown function (DUF2688). Members in this family of proteins are annotated as KleB however currently no function is known. 56 matched cddid_all.tbl CDD pfam10893 pfam10893 463194 Phage_186_Fil Bacteriophage 186, Fil. This family is represented by Bacteriophage 186, Fil, a protein that causes filamentation. The characteriztics of the protein distribution suggest prophage matches in addition to the phage matches. 56 matched cddid_all.tbl CDD pfam10894 pfam10894 313958 DUF2689 Protein of unknown function (DUF2689). Members in this family of proteins are annotated as TrbD however currently no function is known. 57 matched cddid_all.tbl CDD pfam10895 pfam10895 371289 DUF2715 Domain of unknown function (DUF2715). This family of proteins with unknown function appears to be largely found in spirochaete bacteria. It is related to membrane beta barrel proteins. 153 matched cddid_all.tbl CDD pfam10896 pfam10896 402473 DUF2714 Protein of unknown function (DUF2714). This family of proteins with unknown function appears to be restricted to Mycoplasmataceae. 143 matched cddid_all.tbl CDD pfam10897 pfam10897 313960 DUF2713 Protein of unknown function (DUF2713). This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. 235 matched cddid_all.tbl CDD pfam10898 pfam10898 371291 DUF2716 Protein of unknown function (DUF2716). This bacterial family of proteins has no known function. 140 matched cddid_all.tbl CDD pfam10899 pfam10899 431530 AbiGi Putative abortive phage resistance protein AbiGi, antitoxin. This is a bacterial family of proteins with unknown function. AbiGi is a family of putative type IV toxin-antitoxin system antitoxins. The AbiG abortive phage resistance system affects lactococcal bacteriophages phiP335 and phiQ30 but not the other P335 phage species. AbiGii toxin appears to confer resistance to phages by a mechanism of abortive infection that acts by interfering with phage RNA synthesis. The cognate toxin is found in pfam16873. 185 matched cddid_all.tbl CDD pfam10901 pfam10901 402475 DUF2690 Protein of unknown function (DUF2690). This bacterial family of proteins has no known function. 86 matched cddid_all.tbl CDD pfam10902 pfam10902 431531 WYL_2 WYL_2, Sm-like SH3 beta-barrel fold. WYL_2 is a family of Sm-like SH3 beta-barrel fold containing domains. WYL is named for three conserved amino acids found in a subset of domains of this superfamily. These residues are not strongly conserved throughout the family. Rather, the conservation pattern includes four basic residues and a position often occupied by a cysteine, which are predicted to line a ligand-binding groove typical of the Sm-like SH3 beta-barrels. It is predicted to be a ligand-sensing domain that could bind negatively charged ligands, such as nucleotides or nucleic acid fragments, to regulate CRISPR-Cas and other defense systems such as the abortive infection AbiG system 74 matched cddid_all.tbl CDD pfam10903 pfam10903 371294 DUF2691 Protein of unknown function (DUF2691). This bacterial family of proteins has no known function. 152 matched cddid_all.tbl CDD pfam10904 pfam10904 287827 DUF2694 Protein of unknown function (DUF2694). This family of proteins with unknown function appears to be restricted to Mycobacterium spp. 97 matched cddid_all.tbl CDD pfam10905 pfam10905 402477 DUF2695 Protein of unknown function (DUF2695). This bacterial family of proteins has no known function. 53 matched cddid_all.tbl CDD pfam10906 pfam10906 371295 Mrx7 MIOREX complex component 7. This entry includes budding yeast MIOREX complex component 7 (Mrx7), which associates with mitochondrial ribosome. Its function is not clear. 66 matched cddid_all.tbl CDD pfam10907 pfam10907 431532 DUF2749 Protein of unknown function (DUF2749). This bacterial family of proteins appear to come from the Trb operon however currently no function is known. 72 matched cddid_all.tbl CDD pfam10908 pfam10908 431533 DUF2778 Protein of unknown function (DUF2778). This is a bacterial family of uncharacterized proteins. 120 matched cddid_all.tbl CDD pfam10909 pfam10909 463195 DUF2682 Protein of unknown function (DUF2682). This viral family of proteins has no known function. 88 matched cddid_all.tbl CDD pfam10910 pfam10910 287830 DUF2744 Protein of unknown function (DUF2744). This is a viral family of proteins with unknown function. 119 matched cddid_all.tbl CDD pfam10911 pfam10911 151358 T7-like_Y65 Bacteriophage T7-like gene 6.5. Members in this family of proteins are annotated as gene 6.5 protein, however, currently there is no known function. 77 matched cddid_all.tbl CDD pfam10912 pfam10912 371296 DUF2700 Protein of unknown function (DUF2700). This family of proteins with unknown function appears to be restricted to Caenorhabditis elegans. 136 matched cddid_all.tbl CDD pfam10913 pfam10913 313971 DUF2706 Protein of unknown function (DUF2706). This family of proteins with unknown function appears to be restricted to Rickettsia spp. 59 matched cddid_all.tbl CDD pfam10915 pfam10915 402479 DUF2709 Protein of unknown function (DUF2709). This bacterial family of proteins has no known function. 237 matched cddid_all.tbl CDD pfam10916 pfam10916 463196 DUF2712 Protein of unknown function (DUF2712). This family of proteins with unknown function appear to be restricted to Bacillales. 111 matched cddid_all.tbl CDD pfam10917 pfam10917 371300 Fungus-induced Fungus-induced protein. This entry represents fungus-induced proteins which may have role in hypoxia response. 49 matched cddid_all.tbl CDD pfam10918 pfam10918 313975 DUF2718 Protein of unknown function (DUF2718). This viral family of proteins has no known function. 129 matched cddid_all.tbl CDD pfam10920 pfam10920 402481 DUF2705 Protein of unknown function (DUF2705). This bacterial family of transmembrane proteins is related to ABC2 membrane transporter proteins. 226 matched cddid_all.tbl CDD pfam10921 pfam10921 287837 DUF2710 Protein of unknown function (DUF2710). This family of proteins with unknown function appears to be restricted to Mycobacteriaceae. 104 matched cddid_all.tbl CDD pfam10922 pfam10922 313976 T7-like_gp12 Bacteriophage T7-like, gene 1.2. The T7-like bacteriophage gene 1.2 protein is an inhibitor of the Escherichia coli dGTP triphosphohydrolase (dGTPase) and is implicated in DNA replication. 85 matched cddid_all.tbl CDD pfam10923 pfam10923 431535 BrxC_BrxD BREX system ATP-binding protein BrxC/D. This is the ATP-binding domain found in proteins that are associated with Bacteriophage Exclusion (BREX) system, a defense system that allows bacteriophage adsorption but blocks phage DNA replication. This domain is found in the ATP-binding proteins BrxC/pglY (due to its homology with pglY from Pgl system) and BrxD. 412 matched cddid_all.tbl CDD pfam10924 pfam10924 402483 DUF2711 Protein of unknown function (DUF2711). Some members in this family of proteins are annotated as ywbB however currently there is no known function. 216 matched cddid_all.tbl CDD pfam10925 pfam10925 431536 DUF2680 Protein of unknown function (DUF2680). Members in this family of proteins are annotated as yckD however currently no function is known. 57 matched cddid_all.tbl CDD pfam10926 pfam10926 431537 DUF2800 Protein of unknown function (DUF2800). This is a family of uncharacterized proteins found in bacteria and viruses. Some members of this family are annotated as being Phi APSE P51-like proteins. 366 matched cddid_all.tbl CDD pfam10927 pfam10927 287842 DUF2738 Protein of unknown function (DUF2738). This is a viral family of proteins with unknown function. 236 matched cddid_all.tbl CDD pfam10928 pfam10928 431538 DUF2810 Protein of unknown function (DUF2810). This is a bacterial family of uncharacterized proteins. 53 matched cddid_all.tbl CDD pfam10929 pfam10929 431539 DUF2811 Protein of unknown function (DUF2811). This is a bacterial family of uncharacterized proteins. 57 matched cddid_all.tbl CDD pfam10930 pfam10930 402487 DUF2737 Protein of unknown function (DUF2737). This family of proteins has no known function. 53 matched cddid_all.tbl CDD pfam10931 pfam10931 431540 DUF2735 Protein of unknown function (DUF2735). Some members in this family of proteins are annotated as glutamine synthetase translation inhibitor however this function can not be confirmed. 52 matched cddid_all.tbl CDD pfam10932 pfam10932 431541 DUF2783 Protein of unknown function (DUF2783). This is a bacterial family of uncharacterized protein. 59 matched cddid_all.tbl CDD pfam10933 pfam10933 431542 DUF2827 Protein of unknown function (DUF2827). This is a family of uncharacterized proteins found in Burkholderia. 362 matched cddid_all.tbl CDD pfam10934 pfam10934 463197 DUF2634 Protein of unknown function (DUF2634). Some members in this family of proteins are annotated as phage related, xkdS however currently there is no known function. 104 matched cddid_all.tbl CDD pfam10935 pfam10935 431544 DUF2637 Protein of unknown function (DUF2637). This family of proteins has no known function. 161 matched cddid_all.tbl CDD pfam10936 pfam10936 431545 DUF2617 Protein of unknown function DUF2617. This bacterial family of proteins has no known function. 156 matched cddid_all.tbl CDD pfam10937 pfam10937 402493 S36_mt Ribosomal protein S36, mitochondrial. This entry is represented by a mitochondrial ribosomal protein of the small subunit, which has similarity to human mitochondrial ribosomal protein MRP-S36. 116 matched cddid_all.tbl CDD pfam10938 pfam10938 431546 YfdX YfdX protein. YfdX is a protein found in Proteobacteria of unknown function. The protein coding for this gene is regulated by EvgA in E. coli. 148 matched cddid_all.tbl CDD pfam10939 pfam10939 431547 DUF2631 Protein of unknown function (DUF2631). This is s bacterial family of proteins with unknown function. 63 matched cddid_all.tbl CDD pfam10940 pfam10940 287855 SpeFL Leader peptide SpeFL. SpeFL is a small protein (arrest peptide) encoded upstream of inducible ornithine carboxylase gene (speF) that controls expression of downstream genes (speF and patE) by nascent chain-translational arrest and transcriptional attenuation. Ornithine capture by a translating ribosome controls bacterial polyamine synthesis, inducing the expression of ornithine decarboxylase SpeF4, in a mechanism involving ribosome stalling and transcription antitermination 40 matched cddid_all.tbl CDD pfam10941 pfam10941 431548 DUF2620 Protein of unknown function DUF2620. This is a bacterial family of proteins with unknown function. 116 matched cddid_all.tbl CDD pfam10942 pfam10942 431549 DUF2619 Protein of unknown function (DUF2619). This bacterial family of proteins has no known function. 69 matched cddid_all.tbl CDD pfam10943 pfam10943 287858 DUF2632 Protein of unknown function (DUF2632). This is a family of membrane proteins with unknown function. 233 matched cddid_all.tbl CDD pfam10944 pfam10944 431550 DUF2630 Protein of unknown function (DUF2630). This bacterial family of proteins have no known function. 80 matched cddid_all.tbl CDD pfam10945 pfam10945 431551 CBP_BcsR "Cellulose biosynthesis protein BcsR. CBP_BcsR is a family of bacterial cellulose biosynthesis proteins. Cellulose is necessary for biofilm formation in bacteria. Roemling U. and Galperin M.Y. ""Bacterial cellulose biosynthesis. Diversity of operons and subunits"" (manuscript in preparation)." 42 matched cddid_all.tbl CDD pfam10946 pfam10946 402500 DUF2625 Protein of unknown function DUF2625. Some members in this family of proteins are annotated as ybfG however currently no function is known. 207 matched cddid_all.tbl CDD pfam10947 pfam10947 431552 DUF2628 Protein of unknown function (DUF2628). Some members in this family of proteins are annotated as yigF however currently no function is known. 78 matched cddid_all.tbl CDD pfam10948 pfam10948 431553 DUF2635 Protein of unknown function (DUF2635). This is a family of phage proteins with unknown function. 46 matched cddid_all.tbl CDD pfam10949 pfam10949 371311 DUF2777 Protein of unknown function (DUF2777). This family of proteins with unknown function appears to be restricted to Bacillus cereus. 181 matched cddid_all.tbl CDD pfam10950 pfam10950 402502 Organ_specific Organ specific protein. This eukaryotic family includes a number of plant organ-specific proteins. The predicted amino acid sequence suggests that these proteins could be exported and glycosylated. Family members consist of an N-terminal region with no repeats and a C-terminal region which carries multiple tandem repeats. The N-terminal region ends before the repeats region and is defined as the area that extends from the end of the signal peptide to the start of the tandem repeat region. Its length varies considerably, ranging from 30 to 80 amino acids. Generally, these proteins vary in size where it is suggested that thirty-six percent of the sequences had fewer than 150 amino acids; 41% ranged from 150 to 250, and 23% had more than 250 amino acids. Accordingly, these proteins belong to category II of proteins having repeats in tandem; that is, those with the repeats ranging in length from 20 to 40 residues. The second region (C-terminal) in the mature protein is the tandem repeat oligopeptide area. The repeats start with a common hexapeptide (E/D)FEPRP and end with X4Y i.e. (D/E)FEPRPX4Y. Full-length sequences revealed considerable variability in the number of repeats, ranging from 2 to 17. The length of the repeats also varied, ranging from 12 amino acids to 34 amino acids. 117 matched cddid_all.tbl CDD pfam10951 pfam10951 431554 DUF2776 Protein of unknown function (DUF2776). This bacterial family of proteins has no known function. 348 matched cddid_all.tbl CDD pfam10952 pfam10952 431555 DUF2753 Protein of unknown function (DUF2753). This bacterial family of proteins has no known function. 140 matched cddid_all.tbl CDD pfam10953 pfam10953 402504 DUF2754 Protein of unknown function (DUF2754). This family of proteins with unknown function appear to be restricted to Enterobacteriaceae. 70 matched cddid_all.tbl CDD pfam10954 pfam10954 402505 DUF2755 Protein of unknown function (DUF2755). Some members in this family of proteins are annotated as YaiY however no function is known. The family appears to be restricted to Enterobacteriaceae. 100 matched cddid_all.tbl CDD pfam10955 pfam10955 402506 Fin Anti-sigma-F factor Fin. Fin (formerly known as YabK) is a small protein required for efficient switching from sigma(F)- to sigma(G)-directed gene expression during sporulation in Bacillus subtilis. Fin has been proposed to be an anti-sigma(F) factor which, by disabling sigma(F), promotes the switch to late developmental gene expression in the forespore. 73 matched cddid_all.tbl CDD pfam10956 pfam10956 402507 DUF2756 Protein of unknown function (DUF2756). Some members in this family of proteins are annotated yhhA however currently no function is known. The family appears to be restricted to Enterobacteriaceae. 104 matched cddid_all.tbl CDD pfam10957 pfam10957 337871 Spore_Cse60 Sporulation protein Cse60. Cse60 is expressed during sporulation in Bacillus subtilis. Transcription commences around 2h after the start of sporulation and had an absolute requirement for the transcription factor sigmaE. Cse60 is an acidic product of only 60 residues, whose function is not known. 60 matched cddid_all.tbl CDD pfam10958 pfam10958 431556 DUF2759 Protein of unknown function (DUF2759). This family of proteins with unknown function appear to be restricted to Bacillaceae. 50 matched cddid_all.tbl CDD pfam10959 pfam10959 371315 DUF2761 Protein of unknown function (DUF2761). Members in this family of proteins are annotated as KleF however no function is known. 94 matched cddid_all.tbl CDD pfam10960 pfam10960 431557 Holin_BhlA BhlA holin family. The Phage_holin_BhlA family is a family of holin-like proteins from both bacteriophages and bacterial chromosomes. In bacteriophage, holins are small membrane proteins that accumulate and oligomerise to form non-specific lesions in the cytoplasmic membrane allowing the release of the second protein, endolysins, to access the peptidoglycan. Most holins share common structural features: two or three transmembrane domains separated by a beta-turn, a short hydrophilic N-terminus, a highly charged C-terminus and a dual translational start motif. The BhlA holin of Bacillus is found to be toxic to the host cell where the site of action of is on the cell membrane and causes bacterial death by cell membrane disruption. 66 matched cddid_all.tbl CDD pfam10961 pfam10961 463198 SelK_SelG Selenoprotein SelK_SelG. This entry inclues a group of eukaryotic selenoproteins, such as SelK and SelG. SelK seems to play an important role in protecting cells from endoplasmic reticulum stress induced apoptosis. SelG may be involved in regulating the redox state of the cell. 84 matched cddid_all.tbl CDD pfam10962 pfam10962 431559 DUF2764 Protein of unknown function (DUF2764). This bacterial family of proteins has no known function. 271 matched cddid_all.tbl CDD pfam10963 pfam10963 431560 Phage_TAC_10 Phage tail assembly chaperone. This is a family of phage tail assembly chaperone proteins. 82 matched cddid_all.tbl CDD pfam10964 pfam10964 431561 DUF2766 Protein of unknown function (DUF2766). This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. 79 matched cddid_all.tbl CDD pfam10965 pfam10965 431562 DUF2767 Protein of unknown function (DUF2767). This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. 67 matched cddid_all.tbl CDD pfam10966 pfam10966 431563 DUF2768 Protein of unknown function (DUF2768). This family of proteins with unknown function appear to be restricted to Bacillus spp. 58 matched cddid_all.tbl CDD pfam10967 pfam10967 431564 DUF2769 Protein of unknown function (DUF2769). This family of proteins have no known function. 57 matched cddid_all.tbl CDD pfam10968 pfam10968 431565 DUF2770 Protein of unknown function (DUF2770). Members in this family of proteins are annotated as yceO however currently no function is known. 36 matched cddid_all.tbl CDD pfam10969 pfam10969 431566 DUF2771 Protein of unknown function (DUF2771). This bacterial family of proteins has no known function. 128 matched cddid_all.tbl CDD pfam10970 pfam10970 287884 GerPE Spore germination protein GerPE. GerPE is required for the formation of functionally normal spores. It could be involved in the establishment of a normal spore coat structure and (or) permeability, which allows the access of germinants to their receptor. 123 matched cddid_all.tbl CDD pfam10971 pfam10971 287885 DUF2773 Protein of unknown function (DUF2773). This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. 81 matched cddid_all.tbl CDD pfam10972 pfam10972 431567 CsiV Peptidoglycan-binding protein, CsiV. CsiV, a small periplasmic protein (cell-shape integrity in Vibrio), is essential for growth of Vibrio cholerae in the presence of DAA, non-canonical amino-acids, the typical components of peptidoglycan side-chains in Vibrio cholerae. CsiV interacts with LpoA, the lipoprotein activator of penicillin-binding-protein1A that is necessary for mediating the assembly of peptidoglycan. CsiV acts through LpoA to promote peptidoglycan biogenesis in V. cholerae and other vibrio species as well as in the other genera where this protein is found. 207 matched cddid_all.tbl CDD pfam10973 pfam10973 431568 DUF2799 Protein of unknown function (DUF2799). Some members in this family of proteins are annotated as yfiL which has no known function. 86 matched cddid_all.tbl CDD pfam10974 pfam10974 431569 DUF2804 Protein of unknown function (DUF2804). This is a family of proteins with unknown function. 321 matched cddid_all.tbl CDD pfam10975 pfam10975 431570 DUF2802 Protein of unknown function (DUF2802). This bacterial family of proteins has no known function. 63 matched cddid_all.tbl CDD pfam10976 pfam10976 431571 DUF2790 Protein of unknown function (DUF2790). This family of proteins with unknown function appear to be restricted to Pseudomonadaceae. 77 matched cddid_all.tbl CDD pfam10977 pfam10977 431572 DUF2797 Protein of unknown function (DUF2797). This family of proteins has no known function. 227 matched cddid_all.tbl CDD pfam10978 pfam10978 431573 DUF2785 Protein of unknown function (DUF2785). Some members in this family are annotated as hypothetical membrane spanning proteins however this cannot be confirmed. The family has no known function. 174 matched cddid_all.tbl CDD pfam10979 pfam10979 431574 DUF2786 Protein of unknown function (DUF2786). This family of proteins has no known function. 40 matched cddid_all.tbl CDD pfam10980 pfam10980 431575 DUF2787 Protein of unknown function (DUF2787). This bacterial family of proteins has no known function. 128 matched cddid_all.tbl CDD pfam10981 pfam10981 431576 DUF2788 Protein of unknown function (DUF2788). This bacterial family of proteins have no known function. 50 matched cddid_all.tbl CDD pfam10982 pfam10982 431577 DUF2789 Protein of unknown function (DUF2789). This bacterial family of proteins has no known function. 74 matched cddid_all.tbl CDD pfam10983 pfam10983 431578 DUF2793 Protein of unknown function (DUF2793). This is a bacterial family of proteins with unknown function. 86 matched cddid_all.tbl CDD pfam10984 pfam10984 431579 DUF2794 Protein of unknown function (DUF2794). This is a bacterial family of proteins with unknown function. 84 matched cddid_all.tbl CDD pfam10985 pfam10985 463199 DUF2805 Protein of unknown function (DUF2805). This is a bacterial family of proteins with unknown function. 71 matched cddid_all.tbl CDD pfam10986 pfam10986 463200 DUF2796 Protein of unknown function (DUF2796). This bacterial family of proteins has no known function. 162 matched cddid_all.tbl CDD pfam10987 pfam10987 463201 DUF2806 Protein of unknown function (DUF2806). This bacterial family of proteins has no known function. 221 matched cddid_all.tbl CDD pfam10988 pfam10988 431583 DUF2807 Putative auto-transporter adhesin, head GIN domain. This bacterial family of proteins shows structural similarity to other pectin lyase families. Although structures from this family align with acetyl-transferases, there is no conservation of catalytic residues found. It is likely that the function is one of cell-adhesion. In PDB:3jx8, it is interesting to note that the sequence of contains several well defined sequence repeats, centred around GSG motifs defining the tight beta turn between the two sheets of the super-helix; there are 8 such repeats in the C-terminal half of the protein, which could be grouped into 4 repeats of two. It seems likely that this family belongs to the superfamily of trimeric auto-transporter adhesins (TAAs), which are important virulence factors in Gram-negative pathogens. In the case of Parabacteroides distasonis, which is a component of the normal distal human gut microbiota, TAA-like complexes probably modulate adherence to the host (information derived from TOPSAN). 181 matched cddid_all.tbl CDD pfam10989 pfam10989 431584 DUF2808 Protein of unknown function (DUF2808). This family of proteins with unknown function appears to be restricted to Cyanobacteria. 144 matched cddid_all.tbl CDD pfam10990 pfam10990 431585 DUF2809 Protein of unknown function (DUF2809). Some members in this family of proteins are annotated as yjgA however currently no function for the protein is known. 86 matched cddid_all.tbl CDD pfam10991 pfam10991 431586 DUF2815 Protein of unknown function (DUF2815). This is a phage related family of proteins with unknown function. 167 matched cddid_all.tbl CDD pfam10992 pfam10992 402535 Epiplasmin Epiplasmin protein. This entries covers epiplasmins, a multigene family in Paramecium. They make up a scale structure called the epiplasm under the cell membrane. 83 matched cddid_all.tbl CDD pfam10993 pfam10993 431587 DUF2818 Protein of unknown function (DUF2818). This bacterial family of proteins has no known function. 93 matched cddid_all.tbl CDD pfam10994 pfam10994 431588 DUF2817 Protein of unknown function (DUF2817). This family of proteins has no known function. 340 matched cddid_all.tbl CDD pfam10995 pfam10995 463202 CBP_GIL Cellulose biosynthesis GIL. This family of proteins includes members involved in cellulose biosynthesis such as BcsE proteins found in Salmonella typhimurium. Family members carry a GIL domain on the C-temrinal. The GIL domain, for GGDEF I-site like domain, is a c-di-GMP binding domain on the BcsE proteins of enterobacteria. It is not essentail for cellulose synthesis but is critical for maximal cellulose production. Cellulose production in enterobacteria is controlled by a two-tiered c-di-GMP-dependent system involving BcsE and the PilZ domain containing glycosyltransferase BcsA. The RxGD motif of the GIL domain is required for c-di-GMP binding. 513 matched cddid_all.tbl CDD pfam10996 pfam10996 463203 Beta-Casp Beta-Casp domain. The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains. 109 matched cddid_all.tbl CDD pfam10997 pfam10997 431591 Amj Alternate to MurJ. This bacterial family of proteins has no known function. However, family members include lipid II flippase Amj, which is required for bacterial cell wall synthesis. It transports lipid-linked peptidoglycan precursors from the inner to the outer surface of the cytoplasmic membrane. 253 matched cddid_all.tbl CDD pfam10998 pfam10998 463204 DUF2838 Protein of unknown function (DUF2838). This bacterial family of proteins has no known function. 108 matched cddid_all.tbl CDD pfam10999 pfam10999 431592 DUF2839 Protein of unknown function (DUF2839). This bacterial family of unknown function appear to be restricted to Cyanobacteria. 67 matched cddid_all.tbl CDD pfam11000 pfam11000 431593 DUF2840 Protein of unknown function (DUF2840). This bacterial family of proteins have no known function. 148 matched cddid_all.tbl CDD pfam11001 pfam11001 431594 DUF2841 Protein of unknown function (DUF2841). This family of proteins with unknown function are all present in yeast. 122 matched cddid_all.tbl CDD pfam11002 pfam11002 463205 RDM RFPL defining motif (RDM). The RDM domain is found on RFPL (Ret finger protein like) proteins. In humans, RFPL transcripts can be detected at the onset of neurogenesis in differentiating human embryonic stem cells, and in the developing human neocortex. The RDM domain is thought to have emerged from a neofunctionalization event. It is found N terminal to the SPRY domain (pfam00622). 42 matched cddid_all.tbl CDD pfam11003 pfam11003 431596 DUF2842 Protein of unknown function (DUF2842). This bacterial family of proteins have no known function. 61 matched cddid_all.tbl CDD pfam11004 pfam11004 431597 Kdo_hydroxy 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) hydroxylase. This is a family of 3-deoxy-D-manno-oct-2-ulosonic acid 3-hydroxylases, which catalyze the conversion of 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) to D-glycero-D-talo-oct-2-ulosonic acid (Ko). It contains a potential iron-binding motif, HXDX(n)H (n>40). Hydroxylation activity is iron-dependent. 273 matched cddid_all.tbl CDD pfam11005 pfam11005 431598 DUF2844 Protein of unknown function (DUF2844). This bacterial family of proteins has no known function. 129 matched cddid_all.tbl CDD pfam11006 pfam11006 431599 DUF2845 Protein of unknown function (DUF2845). This bacterial family of proteins has no known function. 78 matched cddid_all.tbl CDD pfam11007 pfam11007 463206 CotJA Spore coat associated protein JA (CotJA). CotJA is part of the CotJ operon which contains CotJA and CotJC. The operon encodes spore coat proteins. Interaction of CotJA with CotJC is required for the assembly of both CotJA and CotJC into the spore coat. 35 matched cddid_all.tbl CDD pfam11008 pfam11008 431601 DUF2846 Protein of unknown function (DUF2846). Some members in this family of proteins with unknown function are annotated as lipoproteins however this cannot be confirmed. 91 matched cddid_all.tbl CDD pfam11009 pfam11009 431602 DUF2847 Protein of unknown function (DUF2847). Some members in this bacterial family of proteins with unknown function are annotated as YtxJ, a putative general stress protein. This cannot be confirmed. 103 matched cddid_all.tbl CDD pfam11010 pfam11010 431603 DUF2848 Protein of unknown function (DUF2848). This bacterial family of proteins has no known function. 193 matched cddid_all.tbl CDD pfam11011 pfam11011 431604 DUF2849 Protein of unknown function (DUF2849). This bacterial family of proteins has been suggested to be an electron source for sulfite reductase. This family is usually found upstream of cysI, the beta subunit of this enzyme. This family was also found fused to cysI in Pseudomonas putida GB-1. 86 matched cddid_all.tbl CDD pfam11012 pfam11012 431605 DUF2850 Protein of unknown function (DUF2850). This family of proteins with unknown function appear to be restricted to Vibrionaceae. 79 matched cddid_all.tbl CDD pfam11013 pfam11013 431606 DUF2851 Protein of unknown function (DUF2851). This bacterial family of proteins has no known function. 369 matched cddid_all.tbl CDD pfam11014 pfam11014 431607 DUF2852 Protein of unknown function (DUF2852). This bacterial family of proteins has no known function. 116 matched cddid_all.tbl CDD pfam11015 pfam11015 431608 DUF2853 Protein of unknown function (DUF2853). This bacterial family of proteins has no known function. 101 matched cddid_all.tbl CDD pfam11016 pfam11016 431609 DUF2854 Protein of unknown function (DUF2854). This family of proteins has no known function. 145 matched cddid_all.tbl CDD pfam11017 pfam11017 431610 DUF2855 Protein of unknown function (DUF2855). This family of proteins has no known function. 339 matched cddid_all.tbl CDD pfam11018 pfam11018 431611 Cuticle_3 Pupal cuticle protein C1. Insect cuticles are composite structures whose mechanical properties are optimized for biological function. The major components are the chitin filament system and the cuticular proteins, and the cuticle's properties are determined largely by the interactions between these two sets of molecules. The proteins can be ordered by species. 182 matched cddid_all.tbl CDD pfam11019 pfam11019 431612 DUF2608 Protein of unknown function (DUF2608). This family is conserved in Bacteria. The function is not known. 240 matched cddid_all.tbl CDD pfam11020 pfam11020 371344 DUF2610 Domain of unknown function (DUF2610). This family is conserved in Proteobacteria. One member is annotated as being elongation factor P but this could not be confirmed. This domain is related to the Ribbon-helix-helix superfamily so may be a DNA-binding protein. 78 matched cddid_all.tbl CDD pfam11021 pfam11021 431613 DUF2613 Protein of unknown function (DUF2613). This is a family of putative small secreted proteins expressed by Actinobacteria. The function is not known. 55 matched cddid_all.tbl CDD pfam11022 pfam11022 431614 ATP19 ATP synthase subunit K. This entry represents ATP synthase subunit K (Atp19) from fungi. Atp19 is the subunit k of the mitochondrial F1F0 ATP synthase, which produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. 64 matched cddid_all.tbl CDD pfam11023 pfam11023 431615 DUF2614 Zinc-ribbon containing domain. This is a family of proteins conserved in the Bacillaceae family. Some members are annotated as being protein YgzB. The function is not known. 111 matched cddid_all.tbl CDD pfam11024 pfam11024 337892 DGF-1_4 Dispersed gene family protein 1 of Trypanosoma cruzi region 4. This protein is likely to be highly expressed, and is expressed from the sub-telomeric region. However, the function is not known. Other domains on this protein include DGF-1_N, DGF-1_2, and DGF-1_5. This domain is just downstream from the C-terminus, but not the C-terminus of proteins, also annotated as being DGF-1, that constitute family DGF-1_C. 70 matched cddid_all.tbl CDD pfam11025 pfam11025 314067 GP40 Glycoprotein GP40 of Cryptosporidium. This family is highly conserved in Cryptosporidium spp. Many members are annotated as being a 60 kDa glycoprotein. 164 matched cddid_all.tbl CDD pfam11026 pfam11026 463207 DUF2721 Protein of unknown function (DUF2721). This family is conserved in bacteria. The function is not known. 127 matched cddid_all.tbl CDD pfam11027 pfam11027 402563 DUF2615 Protein of unknown function (DUF2615). This small. approximately 100 residue, family is conserved from worms to humans. It is cysteine-rich with a characteriztic FDxCEC sequence motif. The function is not known. 102 matched cddid_all.tbl CDD pfam11028 pfam11028 463208 DUF2723 Protein of unknown function (DUF2723). This family is conserved in bacteria. The function is not known. 179 matched cddid_all.tbl CDD pfam11029 pfam11029 402565 DAZAP2 DAZ associated protein 2 (DAZAP2). DAZ associated protein 2 has a highly conserved sequence throughout evolution including a conserved polyproline region and several SH2/SH3 binding sites. It occurs as a single copy gene with a four-exon organization and is located on chromosome 12. It encodes a ubiquitously expressed protein and binds to DAZ and DAZL1 through DAZ repeats. 129 matched cddid_all.tbl CDD pfam11030 pfam11030 287944 Nucleocapsid-N Nucleocapsid protein N. This is the N protein of the nucleocapsid. The nucleocapsid functions to protect the RNA against nuclease degradation and to promote it's reverse transcription. The NC protein promotes viral RNA dimerization and encapsidation and initiates reverse transcription by activating the annealing of the primer tRNA to the initiation site. 167 matched cddid_all.tbl CDD pfam11031 pfam11031 287945 Phage_holin_T Bacteriophage T holin. Bacteriophage effects host lysis with T holin along with an endolysin. T disrupts the membrane allowing sequential events which lead to the attack of the peptidoglycan. T has an usual periplasmic domain which transduces environmental information for the real-time control of lysis timing. 233 matched cddid_all.tbl CDD pfam11032 pfam11032 463209 ApoM ApoM domain. ApoM is a 25 kDa plasma protein associated with high-density lipoproteins (HDLs). ApoM is important in the formation of pre-ss-HDL and also in increasing cholesterol efflux from macrophage foam cells. Lipoproteins consist of lipids solubilized by apolipoproteins. ApoM lacks an external amphipathic motif and is uniquely secreted to plasma without cleavage of its terminal signal peptide. 188 matched cddid_all.tbl CDD pfam11033 pfam11033 402567 ComJ Competence protein J (ComJ). ComJ is a competence specific protein. 122 matched cddid_all.tbl CDD pfam11034 pfam11034 431619 Grg1 Glucose-repressible protein Grg1. This fungal protein increases during glucose deprivation. Its function is unknown. 65 matched cddid_all.tbl CDD pfam11035 pfam11035 463210 SNAPC2 Small nuclear RNA activating complex (SNAPc), subunit 2. This family of proteins is snRNA-activating protein complex subunit 2 (SNAPc subunit 2). The SNAPc complex allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element, the TATA box. The family functions both to specifically recognize the proximal sequence element present in the core promoters of human snRNA genes and to stimulate TBP recognition of the neighbouring TATA box present in human U6 snRNA promoters. 320 matched cddid_all.tbl CDD pfam11036 pfam11036 151483 YqgB Virulence promoting factor. YqgB encodes adaptive factors that acts in synergy with vqfZ, enabling the bacteria to cope with the physical environment in vivo, facilitating colonization of the host. 43 matched cddid_all.tbl CDD pfam11037 pfam11037 463211 Musclin Insulin-resistance promoting peptide in skeletal muscle. Musclin is a muscle derived secretory peptide which induces insulin resistance in vitro. It encodes a 130 amino acid sequence including a NH(2) terminal 30 amino acid signal sequence. Musclin expression level is tightly regulated by nutritional changes. 133 matched cddid_all.tbl CDD pfam11038 pfam11038 287951 DGF-1_5 Dispersed gene family protein 1 of Trypanosoma cruzi region 5. This protein is likely to be highly expressed, and is expressed from the sub-telomeric region. However, the function is not known. Other domains on this protein include DGF-1_N, DGF-1_2, and DGF-1_4. This domain is just downstream from the C-terminus, but not the C-terminus of proteins, also annotated as being DGF-1, that constitute family DGF-1_C. 278 matched cddid_all.tbl CDD pfam11039 pfam11039 371353 DUF2824 Protein of unknown function (DUF2824). This family of proteins has no known function. Some members in the family are annotated as the P22 head assembly protein gp14 however this cannot be confirmed. 151 matched cddid_all.tbl CDD pfam11040 pfam11040 337895 DGF-1_C Dispersed gene family protein 1 of Trypanosoma cruzi C-terminus. This protein is likely to be highly expressed, and is expressed from the sub-telomeric region. However, the function is not known. This is the very C-terminal part of the protein. 87 matched cddid_all.tbl CDD pfam11041 pfam11041 431622 DUF2612 Protein of unknown function (DUF2612). This is a phage protein family expressed from a range of Proteobacteria species. The function is not known. 181 matched cddid_all.tbl CDD pfam11042 pfam11042 431623 DUF2750 Protein of unknown function (DUF2750). This family is conserved in Proteobacteria. The function is not known. 102 matched cddid_all.tbl CDD pfam11043 pfam11043 287956 Anti-RecBCD_p2 Bacteriophage P22, anti-RecBCD protein 2. This phage protein modulates the activity of the host recBCD nuclease promoting phage growth and recombination, and protects the linear double stranded DNA from exonuclease degradation. 97 matched cddid_all.tbl CDD pfam11044 pfam11044 431624 TMEMspv1-c74-12 Plectrovirus spv1-c74 ORF 12 transmembrane protein. This is a family of proteins expressed by Plectroviruses. The plectroviruses are single-stranded DNA viruses belonging to the Inoviridae. Except that it is a putative transmembrane protein the function is not known. 49 matched cddid_all.tbl CDD pfam11045 pfam11045 431625 YbjM Putative inner membrane protein of Enterobacteriaceae. This family is conserved in the Enterobacteriaceae. It is a putative inner membrane protein, named YbjM, but the function is not known. 116 matched cddid_all.tbl CDD pfam11046 pfam11046 431626 HycA_repressor Transcriptional repressor of hyc and hyp operons. This family is conserved in Proteobacteria. It is likely to be the transcriptional repressor molecule for the hyc and hyp operons, which express, amongst others, the protein HycA. This protein may be harnessed for the reduction of technetium oxide, an unwelcome product of radio-nucleotide bioaccumulation. HycA produces formate hydrogenlyase, one of the key proteins necessary for metal compound reduction. 140 matched cddid_all.tbl CDD pfam11047 pfam11047 287960 SopD Salmonella outer protein D. SopD is a type III virulence effector protein whose structure consists of 38% alpha-helix and 26% beta-strand. 319 matched cddid_all.tbl CDD pfam11049 pfam11049 287961 KSHV_K1 Glycoprotein K1 of Kaposi's sarcoma-associated herpes virus. This is a highly glycosylated cytoplasmic and membrane protein similar to the immunoglobulin receptor family that is expressed as an inducible early-lytic-cycle gene product in primary effusion lymphoma cell-lines. This domain would appear to be the cytoplasmic region of the protein. 71 matched cddid_all.tbl CDD pfam11050 pfam11050 287962 Viral_env_E26 Virus envelope protein E26. E26 is a multifunctional protein. One form of E26 associates with viral DNA or DNA binding proteins, while a second form associates with intracellular membranes. 225 matched cddid_all.tbl CDD pfam11051 pfam11051 402574 Mannosyl_trans3 Mannosyltransferase putative. This family is conserved in fungi. Several members are annotated as being alpha-1,3-mannosyltransferase but this could not be confirmed. 273 matched cddid_all.tbl CDD pfam11052 pfam11052 337898 Tr-sialidase_C Trans-sialidase of Trypanosoma hydrophobic C-terminal. This is a highly conserved sequence motif that is the very C-terminus of a number of more diverse proteins from Trypanosoma cruzi. All members of the family are annotated putatively as being trans-sialidase but this appears to be a diverse group. 23 matched cddid_all.tbl CDD pfam11053 pfam11053 287965 DNA_Packaging Terminase DNA packaging enzyme. Phage T4 terminase functions in packaging concatemeric DNA. The T4 terminase is composed of a large subunit, gp17 ad a small subunit, gp16. The role of gp16 is not well characterized however it is known that it binds to double-stranded DNA but not single stranded DNA. 157 matched cddid_all.tbl CDD pfam11054 pfam11054 402575 Surface_antigen Sporozoite TA4 surface antigen. This family of proteins is a Eukaryotic family of surface antigens. One of the better characterized members of the family is the sporulated TA4 antigen. The TA4 gene encodes a single polypeptide of 25 kDa which contains a 17 and a 8 kD polypeptide. 209 matched cddid_all.tbl CDD pfam11055 pfam11055 402576 Gsf2 Glucose signalling factor 2. Gsf2 is localized to the ER and functions to promote the secretion of certain hexose transporters. 371 matched cddid_all.tbl CDD pfam11056 pfam11056 463212 UvsY Recombination, repair and ssDNA binding protein UvsY. UvsY protein enhances the rate of single-stranded-DNA-dependant ATP hydrolysis by UvsX protein. The enhancement of ATP hydrolysis by UvsY protein is shown to result from the ability of UvsY protein to increase the affinity of UvsX protein for single-stranded DNA. 128 matched cddid_all.tbl CDD pfam11057 pfam11057 314086 Cortexin Cortexin of kidney. In the middle of cortexin protein there is a single membrane-spanning domain which indicates that this protein may be a membrane protein involved in intracellular or extracellular signalling of the kidney or brain, since it is expressed specifically in the kidneys and brain only. The protein is highly conserved among species. Cortexin is also thought to be important to neurons of both the developing and adult cerebral cortex. 73 matched cddid_all.tbl CDD pfam11058 pfam11058 287970 Ral Antirestriction protein Ral. Ral alleviates restriction and enhances modification by the E.Coli restriction and modification system. 66 matched cddid_all.tbl CDD pfam11059 pfam11059 431627 DUF2860 Protein of unknown function (DUF2860). This bacterial family of proteins has no known function. 297 matched cddid_all.tbl CDD pfam11060 pfam11060 431628 DUF2861 Protein of unknown function (DUF2861). This bacterial family of proteins has no known function. 260 matched cddid_all.tbl CDD pfam11061 pfam11061 431629 DUF2862 Protein of unknown function (DUF2862). This family of proteins has no known function. 60 matched cddid_all.tbl CDD pfam11062 pfam11062 463213 DUF2863 Protein of unknown function (DUF2863). This bacterial family of proteins have no known function. 398 matched cddid_all.tbl CDD pfam11064 pfam11064 431631 DUF2865 Protein of unknown function (DUF2865). This bacterial family of proteins has no known function. 114 matched cddid_all.tbl CDD pfam11065 pfam11065 431632 DUF2866 Protein of unknown function (DUF2866). This bacterial family of proteins have no known function. 64 matched cddid_all.tbl CDD pfam11066 pfam11066 431633 DUF2867 Protein of unknown function (DUF2867). This bacterial family of proteins have no known function. 143 matched cddid_all.tbl CDD pfam11067 pfam11067 431634 DUF2868 Protein of unknown function (DUF2868). Some members in this family of proteins with unknown function are annotated as putative membrane proteins. However, this cannot be confirmed. 306 matched cddid_all.tbl CDD pfam11068 pfam11068 431635 YlqD YlqD protein. The structure of a representative of this family has been solved (pdb:4dci) and found to form a tetrameric structure of prefoldin-like architecture with the beta-barrel core and helical coiled coil tentacles. This suggests that this family may act as molecular chaperones. 131 matched cddid_all.tbl CDD pfam11069 pfam11069 463214 CFAP298 Cilia- and flagella-associated protein 298. This is a eukaryotic family of proteins which includes a group of cilia- and flagella-associated protein, including Kur from zebrafish and C21orf59 from humans. Kur has been shown to play a dual role in cilia motility and polarization. Primary ciliary dyskinesia (PCD) is caused when defects of motile cilia lead to chronic airway infections, male infertility, and situs abnormalities. Mutations in the C21orf59 gene cause ciliary dyskinesia, primary, 26 (CILD26). 95 matched cddid_all.tbl CDD pfam11070 pfam11070 431637 DUF2871 Protein of unknown function (DUF2871). This family of proteins has no known function. 133 matched cddid_all.tbl CDD pfam11071 pfam11071 431638 Nuc_deoxyri_tr3 Nucleoside 2-deoxyribosyltransferase YtoQ. 140 matched cddid_all.tbl CDD pfam11072 pfam11072 431639 DUF2859 Protein of unknown function (DUF2859). This is a bacterial family of uncharacterized proteins. 147 matched cddid_all.tbl CDD pfam11073 pfam11073 463215 NSs Rift valley fever virus non structural protein (NSs) like. This family contains several Phlebovirus non structural proteins which act as a major determinant of virulence by antagonising interferon beta gene expression. 242 matched cddid_all.tbl CDD pfam11074 pfam11074 431641 DUF2779 Domain of unknown function(DUF2779). This domain is conserved in bacteria. The function is not known. 126 matched cddid_all.tbl CDD pfam11075 pfam11075 431642 DUF2780 Protein of unknown function VcgC/VcgE (DUF2780). This is a bacterial family of uncharacterized proteins. 175 matched cddid_all.tbl CDD pfam11076 pfam11076 431643 YbhQ Putative inner membrane protein YbhQ. This family is conserved in Proteobacteria. The function is not known but most members are annotated as being inner membrane protein YbhQ. 132 matched cddid_all.tbl CDD pfam11077 pfam11077 371366 DUF2616 Protein of unknown function (DUF2616). This cysteine-rich family is expressed by the double-stranded Nucleopolyhedrovirus, a member of the Baculoviridae family of dsDNA viruses. The function is not known. 172 matched cddid_all.tbl CDD pfam11078 pfam11078 337907 Optomotor-blind Optomotor-blind protein N-terminal region. This family is conserved in Drosophila spp. Optomotor-blind is one of the essential toolkit proteins for coordinating development in diverse animal taxa, and in Drosophila it plays a key role in establishing the abdominal pigmentation pattern, in development of the central nervous system and leg and wing imaginal disc-formation of Drosophila melanogaster. This is the N-terminal region of the protein and does not include the T-box-containing transcription factor that plays a part in DNA-binding. 79 matched cddid_all.tbl CDD pfam11079 pfam11079 402594 YqhG Bacterial protein YqhG of unknown function. This family of putative proteins is conserved in the Bacillaceae family of the Firmicutes. The function is not known. 258 matched cddid_all.tbl CDD pfam11080 pfam11080 431644 GhoS Endoribonuclease GhoS. GhoS is part of the GhoT-GhoS type V toxin-antitoxin (TA) system. GhoT is inhibited by antitoxin GhoS, which specifically cleaves its mRNA. 87 matched cddid_all.tbl CDD pfam11081 pfam11081 314108 Adeno_L433K_22K Adenovirus L4-33K/L4-22K. Adenoviruses express up to 20 distinct mRNAs from five major late transcription unit (MLTU) regions, L1 to L5. The L4 region expresses L4-33K and a related protein, L4-22K. L4-22K and L4-33K have complementary but not redundant functions that provide the normal pattern of mRNA production during the late phase of infection. L4-33K is an alternative RNA splicing factor that up-regulates several MLTU splice acceptor sites as the late phase progresses. L4-22K plays a role in genome packaging via its binding, in association with IVa2, to the A2 sequence within the packaging signal. Additionally, L4-22K plays an important role in the temporal switch from the early to late phase of infection by regulating both early and late gene expression. 168 matched cddid_all.tbl CDD pfam11082 pfam11082 287992 DUF2880 Protein of unknown function (DUF2880). This bacterial family of proteins has no known function. 79 matched cddid_all.tbl CDD pfam11083 pfam11083 431645 Streptin-Immun Lantibiotic streptin immunity protein. Streptococcal species produce a lantibiotic, streptin, in a similar manner to the production of nisin and subtilin by other lactic acid bacteria, in order to compete against competing bacteria within the environment. The immunity protein protects the bacterium from destruction by its own lantibiotic. In general, there is little homology between the immunity proteins of different genera of bacteria. 93 matched cddid_all.tbl CDD pfam11084 pfam11084 431646 DUF2621 Protein of unknown function (DUF2621). This family is conserved in the Bacillaceae family. Several members are named as YneK. The function is not known. 139 matched cddid_all.tbl CDD pfam11085 pfam11085 314111 YqhR Conserved membrane protein YqhR. This family is conserved in the Bacillaceae family of the Firmicutes. The function is not known. 165 matched cddid_all.tbl CDD pfam11086 pfam11086 463216 DUF2878 Protein of unknown function (DUF2878). This bacterial family of proteins has no known function. Some members annotate the proteins as the permease component of a Mn2+/Zn2+ transport system however this cannot be confirmed. 150 matched cddid_all.tbl CDD pfam11087 pfam11087 151532 PRD1_DD PRD1 phage membrane DNA delivery. This small family of phage proteins are bound in the viral membrane and assist, along with P11 and P18 in the delivery of DNA. 54 matched cddid_all.tbl CDD pfam11088 pfam11088 287997 RL11D Glycoprotein encoding membrane proteins RL5A and RL6. RL5A and RL6 are part of the RL11 family which are predicted to encode membrane glycoproteins. Two adjacent open reading frames potentially encode a domain that is the hallmark of proteins encoded by the RL11 family. 99 matched cddid_all.tbl CDD pfam11089 pfam11089 431648 SyrA Exopolysaccharide production repressor. SyrA is a small protein located in the cytoplasmic membrane that lacks an apparent DNA binding domain. SyrA mediates the transcriptional up-regulation of exo genes involved in the biosynthesis of the symbiotic exopolysaccharide succinoglycan. It does this through a mechanism which requires a two component system. 38 matched cddid_all.tbl CDD pfam11090 pfam11090 151535 Phage_T7_Gp13 Bacteriophage T7, probable scaffold protein Gp13. This family represents Bacteriophage T7 Gp13, which may act as an organizer for the correct association of several proteins in the surrounding of the head-tail connector protein gp8. 86 matched cddid_all.tbl CDD pfam11091 pfam11091 463217 T4_tail_cap Tail-tube assembly protein. This tail tube protein is also referred to as Gp48. It is required for the assembly and length regulation of the tail tube of bacteriophage T4. 342 matched cddid_all.tbl CDD pfam11092 pfam11092 463218 Alveol-reg_P311 Neuronal protein 3.1 (p311). P311 has several PEST-like motifs and is found in neuron and muscle cells. P311 could have some function in myo-fibroblast transformation and prevention of fibrosis. It has also been identified as a potential regulator of alveolar generation. 67 matched cddid_all.tbl CDD pfam11093 pfam11093 402600 Mitochondr_Som1 Mitochondrial export protein Som1. Som1 is a component of the mitochondrial protein export system. The various Som1 proteins exhibit a highly conserved region and a pattern of cysteine residues. stabilization of Som1 occurs through an interaction between Som1 and Imp1, a peptidase required for proteolytic processing of certain proteins during their transport across the mitochondrial membrane. This suggests that Som1 represents a third subunit of the Imp1 peptidase complex 81 matched cddid_all.tbl CDD pfam11094 pfam11094 288002 UL11 Membrane-associated tegument protein. The UL11 gene product of herpes simplex virus is a membrane-associated tegument protein that is incorporated into the HSV virion and functions in viral envelopment. UL11 is acylated which is crucial for lipid raft association. 39 matched cddid_all.tbl CDD pfam11095 pfam11095 463219 Gemin7 Gem-associated protein 7 (Gemin7). Gemin7 is a novel component of the survival of motor neuron complex which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE. 76 matched cddid_all.tbl CDD pfam11097 pfam11097 288004 DUF2883 Protein of unknown function (DUF2883). This family of proteins have no known function but appear to be restricted to phage. 75 matched cddid_all.tbl CDD pfam11098 pfam11098 463220 Chlorosome_CsmC Chlorosome envelope protein C. Chlorosomes are light-harvesting antennae found in green bacteria. CsmC is one of the proteins that exists in the chlorosome envelope. CsmC has been shown to exist as a homomultimer with CsmD in the chlorosome envelope. CsmC is thought to be important in chlorosome elongation and shape. 139 matched cddid_all.tbl CDD pfam11099 pfam11099 463221 M11L Apoptosis regulator M11L like. Apoptosis regulators function to modulate the apoptotic cascades and thereby favour productive viral replication. M11L inhibits mitochondrial-dependant apoptosis by mimicking and competing with host proteins for the binding and blocking of Bak and Bax, two executioner proteins. 160 matched cddid_all.tbl CDD pfam11100 pfam11100 314118 TrbE Conjugal transfer protein TrbE. TrbE is essential for conjugation and phage adsorption. It contains four common motifs and one conserved domain. 66 matched cddid_all.tbl CDD pfam11101 pfam11101 431653 DUF2884 Protein of unknown function (DUF2884). Some members in this bacterial family of proteins are annotated as YggN which currently has no known function. 228 matched cddid_all.tbl CDD pfam11102 pfam11102 431654 YjbF Group 4 capsule polysaccharide lipoprotein gfcB, YjbF. This family includes lipoprotein GfcB (YmcC), involved in group 4 capsule polysaccharide formation. YjbF is a family of Gram-negative bacterial outer-membrane lipoproteins, predicted to be a beta-barrel and possibly a porin that is one of four gene-products expressed from an operon, yjbEFGH, which is regulated by the Rcs phosphorelay in a RcsA-dependent manner, similar to that of other exopolysaccharide biosynthetic pathways. It is highly possible that the yjbEFGH operon encodes a system involved in EPS secretion since none of the products is predicted to have enzymic activity, the products are all secreted and YbjF and H are predicted to be beta-barrel lipoproteins similar to porins. It may be that the operon products play some role in biofilm formation and/or matrix production. 189 matched cddid_all.tbl CDD pfam11103 pfam11103 431655 DUF2887 Protein of unknown function (DUF2887). This bacterial family of proteins has no known function. These proteins may be distantly related to the PD(D/E)XK superfamily. 200 matched cddid_all.tbl CDD pfam11104 pfam11104 431656 PilM_2 Type IV pilus assembly protein PilM;. The type IV pilus assembly protein PilM is required for competency and pilus biogenesis. It binds to PilN and ATP. 340 matched cddid_all.tbl CDD pfam11105 pfam11105 314123 CCAP Arthropod cardioacceleratory peptide 2a. CCAP exerts a reversible and dose-dependant cardio-stimulatory effect on the semi-isolated heart of experimental beetles. CCAP also increases free hemolymph sugar concentration in young larvae and adults of the meal-worm beetle. 128 matched cddid_all.tbl CDD pfam11106 pfam11106 431657 YjbE Exopolysaccharide production protein YjbE. YjbE is part of a four gene operon which is involved in exopolysaccharide production. The expression of YjbE is higher than the rest of the operon yjbEFGH. It appears to be restricted to Enterobacteriaceae. YbjE is one of four gene-products expressed from an operon, yjbEFGH, which is regulated by the Rcs phosphorelay in a RcsA-dependent manner, similar to that of other exopolysaccharide biosynthetic pathways. It is highly possible that the yjbEFGH operon encodes a system involved in EPS secretion since none of the products is predicted to have enzymic activity, the products are all secreted and YbjH and F are predicted to be beta-barrel lipoproteins similar to porins. It may be that the operon products play some role in biofilm formation and/or matrix production. 79 matched cddid_all.tbl CDD pfam11107 pfam11107 463222 FANCF Fanconi anemia group F protein (FANCF). FANCF regulates its own expression by methylation at both mRNA and protein levels. Methylation-induced inactivation of FANCF has an important role on the occurrence of ovarian cancers by disrupting the FA-BRCA pathway. 345 matched cddid_all.tbl CDD pfam11108 pfam11108 463223 Phage_glycop_gL Viral glycoprotein L. GL forms a complex with gH, a glycoprotein known to be essential for entry of HSV-1 into cells and virus-induced cell fusion. It is a hetero-oligomer of gH and gL which is incorporated into virions and transported to the cell surface which acts during entry of virus into cells 98 matched cddid_all.tbl CDD pfam11109 pfam11109 431659 RFamide_26RFa Orexigenic neuropeptide Qrfp/P518. Qrfp/P518 has a direct role in maintaining bone mineral density. Qrfp has also found to be important in energy homeostasis by regulating appetite and energy expenditure in mice. The c-terminal 28 residues are the functional 26RFa. 131 matched cddid_all.tbl CDD pfam11110 pfam11110 314127 Phage_hub_GP28 Baseplate hub distal subunit. These baseplate proteins are also referred to as Gp28. Gp28 is the structural component of the central part of the bacteriophage T4 baseplate, which possesses a hydrophobic region and is membrane bound. Gp28 forms a complex with gp27 which is another structural component of the baseplate. 154 matched cddid_all.tbl CDD pfam11111 pfam11111 463224 CENP-M Centromere protein M (CENP-M). The prime candidate for specifying centromere identity is the array of nucleosomes assembles with CENP-A. CENP-A recruits a nucleosome associated complex (NAC) comprised of CENP-M along with two other proteins. Assembly of the CENP-A NAC at centromeres is partly dependant on CENP-M. The CENP-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival. 173 matched cddid_all.tbl CDD pfam11112 pfam11112 431661 PyocinActivator Pyocin activator protein PrtN. PrtN is a transcriptional activator for pyocin synthesis genes. It activates the expression of various pyocin genes by interaction with the DNA sequences conserved in the 5' noncoding regions of the pyocin genes. 74 matched cddid_all.tbl CDD pfam11113 pfam11113 371381 Phage_head_chap Head assembly gene product. This head assembly protein is also refereed to as gene product 40 (Gp40). A specific gp20-gp40 membrane insertion structure constitutes the T4 prohead assembly initiation complex. This protein in T4 stimulates head formation. 56 matched cddid_all.tbl CDD pfam11114 pfam11114 431662 Minor_capsid_2 Minor capsid protein. Most of the members of this family are annotated as being minor capsid proteins. The genomes carrying the genes usually have three similar proteins adjacent to each other, hence this one being named as No.2. 105 matched cddid_all.tbl CDD pfam11115 pfam11115 431663 DUF2623 Protein of unknown function (DUF2623). This family is conserved in the Enterobacteriaceae family. Several members are named as YghW. The function is not known. 93 matched cddid_all.tbl CDD pfam11116 pfam11116 402612 DUF2624 Protein of unknown function (DUF2624). This family is conserved in the Bacillaceae family. Several members are named as YqfT. The function is not known. 83 matched cddid_all.tbl CDD pfam11117 pfam11117 431664 DUF2626 Protein of unknown function (DUF2626). This family is conserved in the Bacillaceae family. Several members are named as YqgY. The function is not known. 73 matched cddid_all.tbl CDD pfam11118 pfam11118 431665 DUF2627 Protein of unknown function (DUF2627). This family is conserved in the Bacillaceae family. Several members are named as YqzF. The function is not known. 72 matched cddid_all.tbl CDD pfam11119 pfam11119 463225 DUF2633 Protein of unknown function (DUF2633). This family is conserved largely in Gammaproteobacteria. Several members are named as YfgG. The function is not known. 43 matched cddid_all.tbl CDD pfam11120 pfam11120 431667 CBP_BcsF "Cellulose biosynthesis protein BcsF. CBP_BcsF is a family of bacterial cellulose biosynthesis proteins. Cellulose is necessary for biofilm formation in bacteria. (Roemling U. and Galperin M.Y. ""Bacterial cellulose biosynthesis. Diversity of operons and subunits"" (manuscript in preparation))." 60 matched cddid_all.tbl CDD pfam11121 pfam11121 288026 DUF2639 Protein of unknown function (DUF2639). This family is conserved in the Bacillaceae family. Several members are named as being YflJ, but the function is not known. 37 matched cddid_all.tbl CDD pfam11122 pfam11122 371387 Spore-coat_CotD Inner spore coat protein D. This family is conserved in the Enterobacteriaceae family. CotD is an inner spore coat protein that is expressed in the middle phase of mother cell gene expression. Along with CotD, CotH, CotS and CotT it is assumed to assemble into the loose skeleton of the matrix, between the shells of SpoIVA and CotE. Coat proteins do not share much sequence similarity between species, but this does not imply they do not share secondary, tertiary, or quaternary features. 86 matched cddid_all.tbl CDD pfam11123 pfam11123 402615 DNA_Packaging_2 DNA packaging protein. This DNA packaging protein is also referred to as gene 18 product (gp18). This protein is required for DNA packaging and functions in a complex with gp19. 82 matched cddid_all.tbl CDD pfam11124 pfam11124 463226 Pho86 Inorganic phosphate transporter chaperone Pho86. Pho86p is an ER chaperone required for chaperoning multi-pass membrane proteins through the ER membrane compartment. It is essential for growth when phosphate levels are limiting, being involved in the regulation of Pho84p, a high-affinity phosphate transporter which is localized to the endoplasmic reticulum (ER) in low phosphate medium. When the level of phosphate increases Pho84p is transported to the vacuole. Pho86p is required for packaging of Pho84p in to COPII vesicles. This entry also includes the Uncharacterized protein C12B10.02c from S. pombe, which is thought to be an orthologue of S. cerevisiae Pho86. 288 matched cddid_all.tbl CDD pfam11125 pfam11125 288030 Phage_MS2_lysis Bacteriophage MS2, lysis protein. This entry represents putative lysis proteins from Bacteriophage MS2 and Bacteriophage BZ13. The bacteriophage MS2 lysin protein swiss:C0M1L5 was identified as an overlapping cistron in the bacteriophage MS2 RNA. This proteins induces the formation of specific membrane adhesion sites between the inner and outer membranes, apparently leading to host cell lysis. Lysis may be performed via activation of host murein hydrolases. 54 matched cddid_all.tbl CDD pfam11126 pfam11126 288031 Phage_DsbA Transcriptional regulator DsbA. DsbA is a double stranded binding protein found in bacteriophage T4 which is involved in transcriptional regulation. DsbA, along with other viral proteins, interacts with the host RNA polymerase core enzyme enabling initiation of transcription. DsbA acts as an enhancer protein of late genes in vitro. The protein consists of mainly alpha helices. 67 matched cddid_all.tbl CDD pfam11127 pfam11127 463227 DUF2892 Protein of unknown function (DUF2892). This family is conserved in bacteria. The function is not known. 66 matched cddid_all.tbl CDD pfam11128 pfam11128 371390 Nucleocap_ssRNA Plant viral coat protein nucleocapsid. This family of nucleocapsid proteins is from ssRNA negative-strand viruses of plant origin. 179 matched cddid_all.tbl CDD pfam11129 pfam11129 151573 EIAV_Rev Rev protein of equine infectious anaemia virus. The sequence of this family is highly conserved and carries a nuclear export signal from residues 31-55, and RNA binding/nuclear localization signals of RRDR at residue 76 and KRRRK at residue 159. Rev is an essential regulatory protein required for nucleocytoplasmic transport of incompletely spliced viral mRNAs that encode structural proteins. Rev has been shown to down-regulate the expression of viral late genes and alter sensitivity to Gag-specific cytotoxic-T-lymphocytes (CTL). Equine infectious anaemia virus (EIAV) exhibits a high rate of genetic variation in vivo, and results in a clinically variable disease in infected horses. 134 matched cddid_all.tbl CDD pfam11130 pfam11130 431669 TraC_F_IV TraC protein. This family of TraC proteins is conserved in Proteobacteria. TraC is a cytoplasmic, peripheral membrane protein and is one of the proteins encoded by the F transfer region of the conjugative plasmid that is required for the assembly of F pilin into the mature F pilus structure. F pili are filamentous appendages that help establish the physical contact between donor and recipient cells involved in the conjugation process. 232 matched cddid_all.tbl CDD pfam11131 pfam11131 288035 PhrC_PhrF Rap-phr extracellular signalling. PhrC and PhrF stimulate ComA-dependent gene expression to different levels and are both required for full expression of genes activated by ComA, which activates the expression of genes involved in competence development and the production of several secreted products. 38 matched cddid_all.tbl CDD pfam11132 pfam11132 371391 SplA Transcriptional regulator protein (SplA). The SplA protein functions in trans as a negative regulator of the level of splB-lacZ expression in the developing forespore. 73 matched cddid_all.tbl CDD pfam11133 pfam11133 431670 Phage_head_fibr Head fiber protein. This head fiber protein is also refereed to as Gp8.5. Gp8.5 is a structural protein in phage. It is a dispensable head protein. 277 matched cddid_all.tbl CDD pfam11134 pfam11134 288037 Phage_stabilize Phage stabilization protein. Members of this family are phage proteins that are probably involved with stabilising the condensed DNA within the capsid. 469 matched cddid_all.tbl CDD pfam11135 pfam11135 288038 DUF2888 Protein of unknown function (DUF2888). Some members in this family of proteins with unknown function are annotated as immediate early protein ICP-18 however this cannot be confirmed. 144 matched cddid_all.tbl CDD pfam11136 pfam11136 463228 DUF2889 Protein of unknown function (DUF2889). This bacterial family of proteins has no known function. 123 matched cddid_all.tbl CDD pfam11137 pfam11137 463229 DUF2909 Protein of unknown function (DUF2909). This is a family of proteins conserved in Proteobacteria of unknown function. 60 matched cddid_all.tbl CDD pfam11138 pfam11138 431673 DUF2911 Protein of unknown function (DUF2911). This bacterial family of proteins has no known function. 141 matched cddid_all.tbl CDD pfam11139 pfam11139 431674 SfLAP Sap, sulfolipid-1-addressing protein. SAP is a transmembrane transport protein with six predicted transmembrane helices, with a hydrophilic domain between helices 3 and 4. This hyrodphobic region is highly variable among identified Gap-like (GPL, peptidoglycolipid, addressing protein) proteins and may be involved in substrate recognition. SAP also belongs to the LysE protein superfamily (pfam01810), whose members have been implicated in small molecule transport in bacteria. Other Gap proteins export metabolites across the cell membrane so it is possible that Sap specifically may be involved in transport of sulfolipid-1 across the membrane. 213 matched cddid_all.tbl CDD pfam11140 pfam11140 431675 DUF2913 Protein of unknown function (DUF2913). This family of proteins with unknown function appear to be restricted to Gammaproteobacteria. 207 matched cddid_all.tbl CDD pfam11141 pfam11141 431676 DUF2914 Protein of unknown function (DUF2914). This bacterial family of proteins has no known function. 61 matched cddid_all.tbl CDD pfam11142 pfam11142 431677 DUF2917 Protein of unknown function (DUF2917). This bacterial family of proteins appears to be restricted to Proteobacteria. 59 matched cddid_all.tbl CDD pfam11143 pfam11143 431678 DUF2919 Protein of unknown function (DUF2919). This bacterial family of proteins has no known function. Some members are annotated as YfeZ however this cannot be confirmed. 146 matched cddid_all.tbl CDD pfam11144 pfam11144 314148 DUF2920 Protein of unknown function (DUF2920). This bacterial family of proteins has no known function. 394 matched cddid_all.tbl CDD pfam11145 pfam11145 431679 DUF2921 Protein of unknown function (DUF2921). This eukaryotic family of proteins has no known function. 886 matched cddid_all.tbl CDD pfam11146 pfam11146 431680 DUF2905 Protein of unknown function (DUF2905). This is a family of bacterial proteins conserved of unknown function. 64 matched cddid_all.tbl CDD pfam11148 pfam11148 463230 DUF2922 Protein of unknown function (DUF2922). This bacterial family of proteins has no known function. 63 matched cddid_all.tbl CDD pfam11149 pfam11149 431682 DUF2924 Protein of unknown function (DUF2924). This bacterial family of proteins has no known function. 134 matched cddid_all.tbl CDD pfam11150 pfam11150 431683 DUF2927 Protein of unknown function (DUF2927). This family is conserved in Proteobacteria. Several members are described as being putative lipoproteins, but otherwise the function is not known. 205 matched cddid_all.tbl CDD pfam11151 pfam11151 431684 DUF2929 Protein of unknown function (DUF2929). This family of proteins with unknown function appears to be restricted to Firmicutes. 56 matched cddid_all.tbl CDD pfam11152 pfam11152 431685 CCB2_CCB4 Cofactor assembly of complex C subunit B, CCB2/CCB4. Cofactor maturation pathways such as the CCB system (system IV) for cytochrome c-heme attachment are conserved in all organizms performing oxygenic photosynthesis. The CCB system consists of four proteins: CCB1-4. CCB2 and CCB4 are paralogues derived from a unique cyanobacterial ancestor. Orthologues are conserved in higher plants. 192 matched cddid_all.tbl CDD pfam11153 pfam11153 431686 DUF2931 Protein of unknown function (DUF2931). This entry represents a set of lipoproteins that contain an N-terminal lipoprotein attachment site. 190 matched cddid_all.tbl CDD pfam11154 pfam11154 463231 DUF2934 Protein of unknown function (DUF2934). This bacterial family of proteins has no known function. 37 matched cddid_all.tbl CDD pfam11155 pfam11155 463232 DUF2935 Domain of unknown function (DUF2935). This family of proteins with unknown function appears to be restricted to Firmicutes. The structure of this protein has been solved and each domain is composed of four alpha helices. A metal cluster composed of iron and magnesium lies between the two domains. 121 matched cddid_all.tbl CDD pfam11157 pfam11157 431688 DUF2937 Protein of unknown function (DUF2937). This family of proteins with unknown function appears to be restricted to Proteobacteria. 162 matched cddid_all.tbl CDD pfam11158 pfam11158 431689 DUF2938 Protein of unknown function (DUF2938). This bacterial family of proteins has no known function. Some members are thought to be membrane proteins however this cannot be confirmed. 150 matched cddid_all.tbl CDD pfam11159 pfam11159 431690 DUF2939 Protein of unknown function (DUF2939). This bacterial family of proteins has no known function. 92 matched cddid_all.tbl CDD pfam11160 pfam11160 431691 Hva1_TUDOR Hypervirulence associated proteins TUDOR domain. Family members include HVA1 (hypervirulence-associated protein 1) whose absence is associated with a hypervirulent phenotype in mice. Metabolomics analysis suggests that when HVA1 is absent there is a block in the citric acid cycle, while structural analysis of the Hva1 protein suggests a potential interaction with NADPH. The structural architecture of Hva1 bears similarity with Tudor domains. 59 matched cddid_all.tbl CDD pfam11161 pfam11161 463233 DUF2944 Protein of unknown function (DUF2946). This family of proteins with unknown function appear to be restricted to Proteobacteria. 184 matched cddid_all.tbl CDD pfam11162 pfam11162 431693 DUF2946 Protein of unknown function (DUF2946). This family of proteins has no known function. 116 matched cddid_all.tbl CDD pfam11163 pfam11163 431694 DUF2947 Protein of unknown function (DUF2947). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. 151 matched cddid_all.tbl CDD pfam11164 pfam11164 431695 DUF2948 Protein of unknown function (DUF2948). This family of proteins with unknown function appear to be restricted to Proteobacteria. 136 matched cddid_all.tbl CDD pfam11165 pfam11165 431696 DUF2949 Protein of unknown function (DUF2949). This family of proteins with unknown function appear to be restricted to Cyanobacteria. 56 matched cddid_all.tbl CDD pfam11166 pfam11166 288067 DUF2951 Protein of unknown function (DUF2951). This family of proteins has no known function. It has a highly conserved sequence. 98 matched cddid_all.tbl CDD pfam11167 pfam11167 378578 DUF2953 Protein of unknown function (DUF2953). This family of proteins has no known function. 53 matched cddid_all.tbl CDD pfam11168 pfam11168 431697 DUF2955 Protein of unknown function (DUF2955). Some members in this family of proteins with unknown function annotate the proteins as membrane protein. However, this cannot be confirmed. 140 matched cddid_all.tbl CDD pfam11169 pfam11169 431698 DUF2956 Protein of unknown function (DUF2956). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. 101 matched cddid_all.tbl CDD pfam11170 pfam11170 431699 DUF2957 Protein of unknown function (DUF2957). Some members annotate the proteins to be putative lipoproteins however this cannot be confirmed. Currently no function is known for this family of proteins. 298 matched cddid_all.tbl CDD pfam11171 pfam11171 431700 DUF2958 Protein of unknown function (DUF2958). Some members are annotated as lipoproteins however this cannot be confirmed. This family of proteins has no known function. 111 matched cddid_all.tbl CDD pfam11172 pfam11172 431701 DUF2959 Protein of unknown function (DUF2959). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. 189 matched cddid_all.tbl CDD pfam11173 pfam11173 431702 DUF2960 Protein of unknown function (DUF2960). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. 79 matched cddid_all.tbl CDD pfam11174 pfam11174 463234 DUF2970 Protein of unknown function (DUF2970). This short family is conserved in Proteobacteria. The function is not known. 56 matched cddid_all.tbl CDD pfam11175 pfam11175 463235 DUF2961 Protein of unknown function (DUF2961). This family of proteins has no known function. 234 matched cddid_all.tbl CDD pfam11176 pfam11176 463236 Tma16 Translation machinery-associated protein 16. Proteins in this family localize to the nucleus. Their function is not clear. 146 matched cddid_all.tbl CDD pfam11177 pfam11177 431706 DUF2964 Protein of unknown function (DUF2964). This family of proteins with unknown function appears to be restricted to Proteobacteria. 62 matched cddid_all.tbl CDD pfam11178 pfam11178 314179 DUF2963 Protein of unknown function (DUF2963). This family of proteins with unknown function appears to be restricted to Mollicutes. 51 matched cddid_all.tbl CDD pfam11179 pfam11179 402654 DUF2967 Protein of unknown function (DUF2967). This family of proteins with unknown function appears to be restricted to Drosophila. 954 matched cddid_all.tbl CDD pfam11180 pfam11180 431707 DUF2968 Protein of unknown function (DUF2968). This family of proteins has no known function. 180 matched cddid_all.tbl CDD pfam11181 pfam11181 463237 YflT Heat induced stress protein YflT domain. YflT is a heat induced protein. According to AlphaFold this domain is composed of a core of four beta strands that form a central beta sheet with alpha helices packed on both side. This family shows sequence similarity to pfam11821 which includes the ActD protein which forms an accessory component of the Alternative complex III which catalyzes the oxidation of membrane-bound quinol and the reduction of cytochrome c or an equivalent electron carrier. This suggests that members of this family may also be involved in forming larger redox complexes. 99 matched cddid_all.tbl CDD pfam11182 pfam11182 402657 AlgF Alginate O-acetyl transferase AlgF. AlgF is essential for the addition of O-acetyl groups to alginate, an extracellular polysaccharide. The presence of O-acetyl groups plays an important role in the ability of the polymer to act as a virulence factor. 164 matched cddid_all.tbl CDD pfam11183 pfam11183 402658 PmrD Polymyxin resistance protein PmrD. PmrB forms a two-component system (TCS) with PmrA that allows Gram-negative bacteria to survive the cationic antimicrobial peptide polymyxin G. The TCS is linked to another one via the polymyxin resistance protein PmrD. PmrD is the first protein identified to mediate the connectivity between the two TCSs. It binds to the N terminal domain of the PmrA response regulator which prevents its dephosphorylation, thereby promoting the the transcription of genes involved in polymyxin resistance. 81 matched cddid_all.tbl CDD pfam11184 pfam11184 431709 DUF2969 Protein of unknown function (DUF2969). This family of proteins with unknown function appears to be restricted to Lactobacillales. 71 matched cddid_all.tbl CDD pfam11185 pfam11185 463238 DUF2971 Protein of unknown function (DUF2971). This bacterial family of proteins has no known function. 89 matched cddid_all.tbl CDD pfam11186 pfam11186 288086 DUF2972 Protein of unknown function (DUF2972). Some members in this family of proteins with unknown function are annotated as sugar transferase proteins, however this cannot be confirmed. 198 matched cddid_all.tbl CDD pfam11187 pfam11187 402661 Mbeg1-like "Mbeg1-like. This family includes a group of uncharacterized proteins from bacteria. Recently, a member from Gemella sanguinis M325, Mbeg1 (for ""microbiome bacteria effector gene"") has been identified as the first example of this protein family being associated with a potential effector function in the human microbiome." 224 matched cddid_all.tbl CDD pfam11188 pfam11188 463239 DUF2975 Protein of unknown function (DUF2975). This family of bacterial proteins have no known function. These proteins are likely to be integral membrane proteins. The proteins contain a highly conserved glutamic acid close to their C-terminus. 130 matched cddid_all.tbl CDD pfam11189 pfam11189 431712 DUF2973 Protein of unknown function (DUF2973). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently they have no known function. 68 matched cddid_all.tbl CDD pfam11190 pfam11190 431713 DUF2976 Protein of unknown function (DUF2976). This family of proteins has no known function. Some members are annotated as membrane proteins however this cannot be confirmed. 86 matched cddid_all.tbl CDD pfam11191 pfam11191 431714 DUF2782 Protein of unknown function (DUF2782). This is a bacterial family of proteins whose function is unknown. 88 matched cddid_all.tbl CDD pfam11192 pfam11192 288092 DUF2977 Protein of unknown function (DUF2977). This family of proteins has no known function. 61 matched cddid_all.tbl CDD pfam11193 pfam11193 431715 DUF2812 Protein of unknown function (DUF2812). This is a bacterial family of uncharacterized proteins, however some members of this family are annotated as membrane proteins. 108 matched cddid_all.tbl CDD pfam11195 pfam11195 431716 DUF2829 Protein of unknown function (DUF2829). This is a uncharacterized family of proteins found in bacteria and bacteriphages. 71 matched cddid_all.tbl CDD pfam11196 pfam11196 431717 DUF2834 Protein of unknown function DUF2834. The function of DUF2834 is not clear. 96 matched cddid_all.tbl CDD pfam11197 pfam11197 431718 DUF2835 Protein of unknown function (DUF2835). This is a bacterial family of uncharacterized proteins. One member of this family is annotated as the A subunit of Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV). 71 matched cddid_all.tbl CDD pfam11198 pfam11198 431719 DUF2857 Protein of unknown function (DUF2857). This is a bacterial family of uncharacterized proteins. 174 matched cddid_all.tbl CDD pfam11199 pfam11199 431720 DUF2891 Protein of unknown function (DUF2891). This is a bacterial family of uncharacterized proteins. 324 matched cddid_all.tbl CDD pfam11200 pfam11200 431721 DUF2981 Protein of unknown function (DUF2981). This eukaryotic family of proteins has no known function. 331 matched cddid_all.tbl CDD pfam11201 pfam11201 431722 DUF2982 Protein of unknown function (DUF2982). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. 151 matched cddid_all.tbl CDD pfam11202 pfam11202 431723 StiP-like tellurite-like stress resistance cysteine protease StiP and similar proteins. StiP is a cysteine protease involved in surviving common types of physiological stress, which can be mimicked by tellurite in laboratory settings. The family is fused to a C-terminal RNA binding Pelota domain, pfam01248. These genes are found in the biosynthetic operon associated with the Ter stress response operon and are predicted to be involved in the biosynthesis of a ribo-nucleoside involved in stress response. 246 matched cddid_all.tbl CDD pfam11203 pfam11203 431724 EccE Putative type VII ESX secretion system translocon, EccE. EccE is a family of largely Gram-positive bacterial transmembrane componenets of the type VII secretion system characterized in Mycobacterium tuberculosis, systems ESX1-5. Translocation of virulent peptides through the membranes is thought to be mediated via a complex that includes EccB, EccC, EccD, EccE, and MycP. EccB, EccC, EccD, and EccE form a stable complex in the mycobacterial cell envelope. 97 matched cddid_all.tbl CDD pfam11204 pfam11204 431725 DUF2985 Protein of unknown function (DUF2985). This eukaryotic family of proteins has no known function. 78 matched cddid_all.tbl CDD pfam11205 pfam11205 431726 DUF2987 Protein of unknown function (DUF2987). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. 145 matched cddid_all.tbl CDD pfam11207 pfam11207 431727 DUF2989 Protein of unknown function (DUF2989). Some members in this bacterial family of proteins are annotated as lipoproteins however this cannot be confirmed. 201 matched cddid_all.tbl CDD pfam11208 pfam11208 402678 DUF2992 Protein of unknown function (DUF2992). This bacterial family of proteins has no known function. However, the cis-regulatory yjdF motif, just upstream from the gene encoding the proteins for this family, is a small non-coding RNA, Rfam:RF01764. The yjdF motif is found in many Firmicutes, including Bacillus subtilis. In most cases, it resides in potential 5' UTRs of homologs of the yjdF gene whose function is unknown. However, in Streptococcus thermophilus, a yjdF RNA motif is associated with an operon whose protein products synthesize nicotinamide adenine dinucleotide (NAD+). Also, the S. thermophilus yjdF RNA lacks typical yjdF motif consensus features downstream of and including the P4 stem. Thus, if yjdF RNAs are riboswitch aptamers, the S. thermophilus RNAs might sense a distinct compound that structurally resembles the ligand bound by other yjdF RNAs. On the ohter hand, perhaps these RNAs have an alternative solution forming a similar binding site, as is observed with some SAM riboswitches. 132 matched cddid_all.tbl CDD pfam11209 pfam11209 431728 LmeA LmeA-like phospholipid-binding. LmeA is a conserved cell-envelope protein critical for controlling the mannan chain length of lipomannan/lipoarabinomannan. 220 matched cddid_all.tbl CDD pfam11210 pfam11210 431729 DUF2996 Protein of unknown function (DUF2996). This family of proteins has no known function. 120 matched cddid_all.tbl CDD pfam11211 pfam11211 431730 DUF2997 Protein of unknown function (DUF2997). This family of proteins has no known function. 47 matched cddid_all.tbl CDD pfam11212 pfam11212 431731 DUF2999 Protein of unknown function (DUF2999). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. 82 matched cddid_all.tbl CDD pfam11213 pfam11213 463240 DUF3006 Protein of unknown function (DUF3006). This family of proteins has no known function. 67 matched cddid_all.tbl CDD pfam11214 pfam11214 402683 Med2 Mediator complex subunit 2. This family of mediator complex subunit 2 proteins is conserved in fungi. Cyclin-dependent kinase CDK8 or Srb10 interacts with and phosphorylates Med2. Post-translational modifications of Mediator subunits are important for regulation of gene expression. 100 matched cddid_all.tbl CDD pfam11215 pfam11215 431733 DUF3010 Protein of unknown function (DUF3010). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. 137 matched cddid_all.tbl CDD pfam11216 pfam11216 431734 DUF3012 Protein of unknown function (DUF3012). This family of proteins with unknown function is restricted to Gammaproteobacteria. 32 matched cddid_all.tbl CDD pfam11217 pfam11217 431735 DUF3013 Protein of unknown function (DUF3013). This bacterial family of proteins with unknown function appear to be restricted to Firmicutes. 159 matched cddid_all.tbl CDD pfam11218 pfam11218 402687 DUF3011 Protein of unknown function (DUF3011). This bacterial family of proteins has no known function. Most members belong to Proteobacteria. 197 matched cddid_all.tbl CDD pfam11219 pfam11219 431736 DUF3014 Protein of unknown function (DUF3014). This family of proteins with unknown function appears to be restricted to Proteobacteria. 156 matched cddid_all.tbl CDD pfam11220 pfam11220 431737 DUF3015 Protein of unknown function (DUF3015). This bacterial family of proteins has no known function. 137 matched cddid_all.tbl CDD pfam11221 pfam11221 463241 Med21 Subunit 21 of Mediator complex. Med21 has been known as Srb7 in yeasts, hSrb7 in humans and Trap 19 in Drosophila. The heterodimer of the two subunits Med7 and Med21 appears to act as a hinge between the middle and the tail regions of Mediator. 134 matched cddid_all.tbl CDD pfam11222 pfam11222 431739 DUF3017 Protein of unknown function (DUF3017). This bacterial family of proteins with unknown function appear to be restricted to Actinobacteria. 74 matched cddid_all.tbl CDD pfam11223 pfam11223 402691 DUF3020 SPP41, DUF3020. This domain is found in the conserved fungal proteins SPP41 (suppressor of PrP4, there are four members, 1 to 4). In S. cerevisiae it is conserved towards the C-terminus of HMG domains. The function is not known. However, it has been shown that SPP41 is involved in negative regulation of expression of spliceosome components PRP4 and PRP3 and that it relocalizes to the cytosol in response to hypoxia. 49 matched cddid_all.tbl CDD pfam11224 pfam11224 288122 DUF3023 Protein of unknown function (DUF3023). This bacterial family of proteins with unknown function appear to be restricted to Alphaproteobacteria. 130 matched cddid_all.tbl CDD pfam11225 pfam11225 431740 DUF3024 Protein of unknown function (DUF3024). This family of proteins has no known function. 56 matched cddid_all.tbl CDD pfam11226 pfam11226 431741 DUF3022 Protein of unknown function (DUF3022). This family of proteins with unknown function appears to be restricted to Proteobacteria. 105 matched cddid_all.tbl CDD pfam11227 pfam11227 431742 DUF3025 Protein of unknown function (DUF3025). Some members in this bacterial family of proteins are annotated as transmembrane proteins however this cannot be confirmed. Currently this family of proteins has no known function. 210 matched cddid_all.tbl CDD pfam11228 pfam11228 431743 DUF3027 Protein of unknown function (DUF3027). This family of proteins with unknown function appears to be restricted to Actinobacteria. 193 matched cddid_all.tbl CDD pfam11229 pfam11229 463242 Focadhesin Focadhesin. Focadhesin (FOCAD) is focal adhesion protein with potential tumour suppressor function in gliomas. The structure prediction indicates that it consists in repetitive alpha hairpins that adopt an armadillo-like fold. 589 matched cddid_all.tbl CDD pfam11230 pfam11230 431745 DUF3029 Protein of unknown function (DUF3029). Some members in this family of proteins are annotated as ykkI. Currently no function is known. 485 matched cddid_all.tbl CDD pfam11231 pfam11231 431746 DUF3034 Protein of unknown function (DUF3034). This family of proteins with unknown function appears to be restricted to Proteobacteria. 255 matched cddid_all.tbl CDD pfam11232 pfam11232 463243 Med25 Mediator complex subunit 25 PTOV activation and synapsin 2. Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-active part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This family is the combined PTOV and SD2 domains. the PTOV domain being the domain through which Med25 co-operates with the histone acetyltransferase CBP, but the function of the SD2 domain is unclear. 154 matched cddid_all.tbl CDD pfam11233 pfam11233 402700 DUF3035 Protein of unknown function (DUF3035). This family of proteins with unknown function appear to be restricted to Alphaproteobacteria. 140 matched cddid_all.tbl CDD pfam11235 pfam11235 463244 Med25_SD1 Mediator complex subunit 25 synapsin 1. The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA, domain, this SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This The function of the SD domains is unclear. 157 matched cddid_all.tbl CDD pfam11236 pfam11236 431749 DUF3037 Protein of unknown function (DUF3037). This bacterial family of proteins has no known function. 118 matched cddid_all.tbl CDD pfam11237 pfam11237 431750 DUF3038 Protein of unknown function (DUF3038). This family of proteins with unknown function appear to be restricted to Cyanobacteria. 169 matched cddid_all.tbl CDD pfam11238 pfam11238 431751 DUF3039 Protein of unknown function (DUF3039). This family of proteins with unknown function appears to be restricted to Actinobacteria. 55 matched cddid_all.tbl CDD pfam11239 pfam11239 431752 DUF3040 Protein of unknown function (DUF3040). Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed. 82 matched cddid_all.tbl CDD pfam11240 pfam11240 463245 DUF3042 Protein of unknown function (DUF3042). This family of proteins with unknown function appears to be restricted to Firmicutes. 54 matched cddid_all.tbl CDD pfam11241 pfam11241 431754 DUF3043 Protein of unknown function (DUF3043). Some members in this family of proteins with unknown function are annotated as membrane proteins. This cannot be confirmed. 171 matched cddid_all.tbl CDD pfam11242 pfam11242 402708 DUF2774 Protein of unknown function (DUF2774). This is a viral family of proteins with unknown function. 63 matched cddid_all.tbl CDD pfam11243 pfam11243 288140 DUF3045 Protein of unknown function (DUF3045). Members in this family of proteins are annotated as gene protein 30.1. Currently no function is known. 88 matched cddid_all.tbl CDD pfam11244 pfam11244 463246 Med25_NR-box Mediator complex subunit 25 C-terminal NR box-containing. The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA, domain, an SD1 - synapsin 1 - domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and this C-terminal NR box-containing domain (646-650) from C69-747. The NR box of MED25 is critical for its recruitment to the promoter, probably through an interaction with pre bound RAR. 89 matched cddid_all.tbl CDD pfam11245 pfam11245 288142 DUF2544 Protein of unknown function (DUF2544). This is a bacterial family of proteins with unknown function. 246 matched cddid_all.tbl CDD pfam11246 pfam11246 402710 Phage_gp53 Base plate wedge protein 53. The baseplate of bacteriophage T4 controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. The structure of the baseplate suggests a mechanism of baseplate structural transition during the initial stages of T4 infection. The baseplate is assembled from six identical wedges that surround the central hub. Gp53, along with other T4 gene products, combine sequentially to assemble a wedge. 200 matched cddid_all.tbl CDD pfam11247 pfam11247 314235 Phage_T7_55 Bacteriophage T7, gene 5.5. This family of phage proteins include Bacteriophage T7 gene 5.5 (also known as Protein suppressor of silencing) which plays a role in the inhibition of gene silencing by the host nucleoid-associated protein H-NS/hns. It disrupts higher-order H-NS-DNA complexes. 99 matched cddid_all.tbl CDD pfam11248 pfam11248 431756 DUF3046 Protein of unknown function (DUF3046). This family of proteins with unknown function appears to be restricted to Actinobacteria. 62 matched cddid_all.tbl CDD pfam11249 pfam11249 463247 DUF3047 Protein of unknown function (DUF3047). This bacterial family of proteins has no known function. 198 matched cddid_all.tbl CDD pfam11250 pfam11250 463248 FAF Fantastic Four meristem regulator. FAF is a family of plant proteins that regulate the size of the shoot meristem by modulating the CLV3-WUS feedback loop. The proteins are expressed in the centre of the shoot meristem, overlapping with the site of WUS - the homeodomain transcription factor WUSCHEL- expression. FAF proteins are capable of modulating shoot growth by repressing WUS in the organizing centre of the shoot meristem. The ability of plants to form new organs throughout their life cycle requires tight control of the meristems to avoid unregulated growth. Plants have evolved an elaborate genetic network that controls meristem size and maintenance. WUS and the CLAVATA (CLV) ligand-receptor system are at the core of the network that regulates the size of the stem cell population in the shoot meristem. 56 matched cddid_all.tbl CDD pfam11251 pfam11251 431759 DUF3050 Protein of unknown function (DUF3050). This bacterial family of proteins has no known function. 232 matched cddid_all.tbl CDD pfam11252 pfam11252 151694 DUF3051 Protein of unknown function (DUF3051). This viral family of proteins has no known function. 189 matched cddid_all.tbl CDD pfam11253 pfam11253 431760 DUF3052 Protein of unknown function (DUF3052). This family of proteins with unknown function appears to be restricted to Actinobacteria. 123 matched cddid_all.tbl CDD pfam11254 pfam11254 431761 DUF3053 Protein of unknown function (DUF3053). Some members in this family of proteins are annotated as the membrane protein YiaF. No function is currently known. 220 matched cddid_all.tbl CDD pfam11255 pfam11255 431762 DUF3054 Protein of unknown function (DUF3054). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known. 110 matched cddid_all.tbl CDD pfam11256 pfam11256 431763 DUF3055 Protein of unknown function (DUF3055). This family of proteins with unknown function appear to be restricted to Firmicutes. 80 matched cddid_all.tbl CDD pfam11258 pfam11258 463249 DUF3048 Protein of unknown function (DUF3048) N-terminal domain. Some members in this bacterial family of proteins are annotated as YerB. However currently no function is known. This entry represents the N-terminal domain. 143 matched cddid_all.tbl CDD pfam11259 pfam11259 431765 DUF3060 Protein of unknown function (DUF3060). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. 58 matched cddid_all.tbl CDD pfam11260 pfam11260 371436 Spidroin_MaSp Major ampullate spidroin 1 and 2. Dragline silk is composed of two proteins, major ampullate spidroin 1 (MaSp1) and major ampullate spidroin 2 (MaSp2). MaSp1 contains five alpha-helices. Only the C-terminus of the proteins are shown. 85 matched cddid_all.tbl CDD pfam11261 pfam11261 463250 IRF-2BP1_2 Interferon regulatory factor 2-binding protein zinc finger. IRF-2BP1 and IRF-2BP2 are nuclear transcriptional repressor proteins and can inhibit both enhancer-activated and basal transcription. They both contain N-terminal zinc finger represented in this family and C-terminal RING finger domains. 52 matched cddid_all.tbl CDD pfam11262 pfam11262 463251 Tho2 Transcription factor/nuclear export subunit protein 2. THO and TREX form a eukaryotic complex which functions in messenger ribonucleoprotein metabolism and plays a role in preventing the transcription-associated genetic instability. Tho2, along with four other subunits forms THO 304 matched cddid_all.tbl CDD pfam11263 pfam11263 463252 Attachment_P66 Borrelia burgdorferi attachment protein P66. P66 is an outer membrane protein in Borrelia burgdorferi, the agent of Lyme disease. P66 has a role in the attachment of Borrelia burgdorferi to human cell-surface receptors. 253 matched cddid_all.tbl CDD pfam11264 pfam11264 431769 ThylakoidFormat Thylakoid formation protein. THF1 is localized to the outer plastid membrane and the stroma. THF1 has a role in sugar signalling. THF1 is also thought to have a role in chloroplast and leaf development. THF1 has been shown to play a crucial role in vesicle-mediated thylakoid membrane biogenesis. 216 matched cddid_all.tbl CDD pfam11265 pfam11265 463253 Med25_VWA Mediator complex subunit 25 von Willebrand factor type A. The overall function of the full-length Med25 is efficiently to coordinate the transcriptional activation of RAR/RXR (retinoic acid receptor/retinoic X receptor) in higher eukaryotic cells. Human Med25 consists of several domains with different binding properties, the N-terminal, VWA domain which is this one, an SD2 domain from residues 229-381, a PTOV(B) or ACID domain from 395-545, an SD2 domain from residues 564-645 and a C-terminal NR box-containing domain (646-650) from 646-747. This VWA or von Willebrand factor type A domain when bound to RAR and the histone acetyltransferase CBP is responsible for recruiting Med1 to the rest of the Mediator complex. 213 matched cddid_all.tbl CDD pfam11266 pfam11266 402726 Ald_deCOase Long-chain fatty aldehyde decarbonylase. This cyanobacterial family of fatty aldehyde decarbonylases acts on mainly C16 and C18 substrates to form hydrocarbons and carbon monoxide. Note that the corresponding EC number (EC:4.1.99.5) dating from 1989 refers to a nonorthologous Pisum sativum enzyme that acts on C18 and longer chains and attaches the overly narrow narrow name octadecanal decarbonylase. 215 matched cddid_all.tbl CDD pfam11267 pfam11267 431770 DUF3067 Domain of unknown function (DUF3067). This family of proteins found in plants and cyanobacteria has no known function. The structure of this domain has been solved by NMR for the alr2454 protein. The structure was determined to be a novel fold composed of four alpha helices and a sheet of three anti-parallel beta-strands. 90 matched cddid_all.tbl CDD pfam11268 pfam11268 431771 DUF3071 Protein of unknown function (DUF3071). Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known. 165 matched cddid_all.tbl CDD pfam11269 pfam11269 431772 DUF3069 Protein of unknown function (DUF3069). This family of proteins with unknown function appear to be restricted to Gammaproteobacteria. 118 matched cddid_all.tbl CDD pfam11270 pfam11270 288164 DUF3070 Protein of unknown function (DUF3070). This eukaryotic family of proteins has no known function. 23 matched cddid_all.tbl CDD pfam11271 pfam11271 431773 PorA Porin PorA. Members of this family include PorA, a channel-forming protein found mostly in Gram-positive bacteria. 295 matched cddid_all.tbl CDD pfam11272 pfam11272 402730 DUF3072 Protein of unknown function (DUF3072). This bacterial family of proteins has no known function. 56 matched cddid_all.tbl CDD pfam11273 pfam11273 431774 DUF3073 Protein of unknown function (DUF3073). This family of proteins with unknown function appears to be restricted to Actinobacteria. 63 matched cddid_all.tbl CDD pfam11274 pfam11274 431775 DUF3074 Protein of unknown function (DUF3074). This eukaryotic family of proteins has no known function but appears to be part of the START superfamily. 181 matched cddid_all.tbl CDD pfam11275 pfam11275 371447 DUF3077 Protein of unknown function (DUF3077). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. 77 matched cddid_all.tbl CDD pfam11276 pfam11276 431776 DUF3078 Protein of unknown function (DUF3078). This bacterial family of proteins has no known function. 90 matched cddid_all.tbl CDD pfam11277 pfam11277 463254 Med24_N Mediator complex subunit 24 N-terminal. This subunit of the Mediator complex appears to be conserved only from insects to humans. It is essential for correct retinal development in fish. Subunit composition of the mediator contributes to the control of differentiation in the vertebrate CNS as there are divergent functions of the mediator subunits Crsp34/Med27, Trap100/Med24, and Crsp150/Med14. 989 matched cddid_all.tbl CDD pfam11278 pfam11278 431777 DUF3079 Protein of unknown function (DUF3079). This family of proteins with unknown function appears to be restricted to Proteobacteria. 49 matched cddid_all.tbl CDD pfam11279 pfam11279 431778 DUF3080 Protein of unknown function (DUF3080). Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed. Currently this family has no known function. 314 matched cddid_all.tbl CDD pfam11280 pfam11280 431779 DUF3081 Protein of unknown function (DUF3081). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. 77 matched cddid_all.tbl CDD pfam11281 pfam11281 431780 DUF3083 Protein of unknown function (DUF3083). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. 314 matched cddid_all.tbl CDD pfam11282 pfam11282 431781 DUF3082 Protein of unknown function (DUF3082). This family of proteins has no known function. 80 matched cddid_all.tbl CDD pfam11283 pfam11283 431782 DUF3084 Protein of unknown function (DUF3084). This bacterial family of proteins has no known function. 77 matched cddid_all.tbl CDD pfam11284 pfam11284 402739 DUF3085 Protein of unknown function (DUF3085). This family of proteins with unknown function appears to be restricted to Proteobacteria. 89 matched cddid_all.tbl CDD pfam11285 pfam11285 431783 DUF3086 Protein of unknown function (DUF3086). This family of proteins with unknown function appears to be restricted to Cyanobacteria. 276 matched cddid_all.tbl CDD pfam11286 pfam11286 431784 DUF3087 Protein of unknown function (DUF3087). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. 165 matched cddid_all.tbl CDD pfam11287 pfam11287 431785 DUF3088 Protein of unknown function (DUF3088). This family of proteins with unknown function appears to be restricted to Proteobacteria. 110 matched cddid_all.tbl CDD pfam11288 pfam11288 431786 DUF3089 Protein of unknown function (DUF3089). This family of proteins has no known function but appears to have an alpha/beta hydrolase domain and so is likely to be enzymatic. 207 matched cddid_all.tbl CDD pfam11289 pfam11289 463255 bCoV_viroporin Betacoronavirus viroporin. This entry represents protein 3a encoded by Orf3/3a, also known as X1, which forms homotetrameric potassium, sodium or calcium sensitive ion channels (viroporin) that causes ER-stress in host cells and may modulate virus release. This is a pro-apoptosis-inducing protein that localizes to the endoplasmic reticulum (ER)-Golgi compartment. SARS-CoV causes apoptosis of infected cells through NLRP3 inflammasome activation. Protein 3a also promotes the ubiquitination of apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) mediated by its interaction with TNF receptor-associated factor 3 (TRAF3). This protein induces NF-kappa B activation and upregulates fibrinogen secretion with high cytokine production. Through the activation of the PERK pathway of unfolded protein response (UPR), this protein causes phosphorylation of eIF2-alpha leading to reduced translation of cellular proteins and as the activation of pro-apoptotic downstream effectors (i.e ATF4, CHOP). 273 matched cddid_all.tbl CDD pfam11290 pfam11290 431788 DUF3090 Protein of unknown function (DUF3090). This family of proteins with unknown function appears to be restricted to Actinobacteria. 170 matched cddid_all.tbl CDD pfam11291 pfam11291 151732 DUF3091 Protein of unknown function (DUF3091). This eukaryotic family of proteins has no known function. 100 matched cddid_all.tbl CDD pfam11292 pfam11292 431789 DUF3093 Protein of unknown function (DUF3093). This family of proteins with unknown function appears to be restricted to Actinobacteria. Some members are annotated as alanine rich membrane proteins however this cannot be confirmed. 141 matched cddid_all.tbl CDD pfam11293 pfam11293 431790 DUF3094 Protein of unknown function (DUF3094). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. 55 matched cddid_all.tbl CDD pfam11294 pfam11294 431791 DUF3095 Protein of unknown function (DUF3095). Some members in this bacterial family of proteins are annotated as adenylyl cyclase however this cannot be confirmed. Currently no function is known. 377 matched cddid_all.tbl CDD pfam11295 pfam11295 431792 DUF3096 Protein of unknown function (DUF3096). This family of proteins with unknown function appears to be restricted to Proteobacteria. 37 matched cddid_all.tbl CDD pfam11296 pfam11296 431793 DUF3097 Protein of unknown function (DUF3097). This family of proteins with unknown function appears to be restricted to Actinobacteria. 267 matched cddid_all.tbl CDD pfam11297 pfam11297 431794 DUF3098 Protein of unknown function (DUF3098). This bacterial family of proteins has no known function. 67 matched cddid_all.tbl CDD pfam11298 pfam11298 431795 DUF3099 Protein of unknown function (DUF3099). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known. 72 matched cddid_all.tbl CDD pfam11299 pfam11299 431796 DUF3100 Protein of unknown function (DUF3100). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known. 235 matched cddid_all.tbl CDD pfam11300 pfam11300 402753 DUF3102 Protein of unknown function (DUF3102). This family of proteins has no known function. 129 matched cddid_all.tbl CDD pfam11301 pfam11301 431797 DUF3103 Protein of unknown function (DUF3103). This family of proteins with unknown function appear to be restricted to Proteobacteria. 351 matched cddid_all.tbl CDD pfam11302 pfam11302 402755 DUF3104 Protein of unknown function (DUF3104). This family of proteins with unknown function appears to be restricted to Cyanobacteria. 69 matched cddid_all.tbl CDD pfam11303 pfam11303 463256 DUF3105 Protein of unknown function (DUF3105). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known. 130 matched cddid_all.tbl CDD pfam11304 pfam11304 463257 DUF3106 Protein of unknown function (DUF3106). Some members in this family of proteins are annotated as transmembrane proteins however this cannot be confirmed. Currently no function is known. 104 matched cddid_all.tbl CDD pfam11305 pfam11305 431800 DUF3107 Protein of unknown function (DUF3107). Some members in this family of proteins are annotated as ATP-binding proteins however this cannot be confirmed. Currently no function is known. 73 matched cddid_all.tbl CDD pfam11306 pfam11306 431801 DUF3108 Protein of unknown function (DUF3108). This is a bacterial family of putative lipoproteins. The structure for Swiss:Q64U78, PDB:3fzx, the first structural template for this large family including several homologs in the human gut microbiome and in metagenomic datasets, folds into a beta barrel that topologically looks like a small-scale porin (such as FepA). Swiss:Q64U78 is a putative exported protein, and this fold is of the YmcC-like type, with a predicted signal peptide SpI cleavage site AGAMA|QNQDC, and a Phobius server prediction of non-cytoplasmic localization for amino acids 21-236. The possibility of it being a membrane protein can be ruled out by the hydrophilic nature of the solvent exposed surface outside the barrels. Analysis of sequence conservation suggests that an area near Glu172/Trp206 is potentially interesting. These two residues are also conserved in Dali hit PDB:2in5, a hypothetical lipoprotein classified as a new YmcC-like fold in SCOP (SCOP:159271, with a 12-stranded meander beta-sheet folded into a deformed beta-barrel) despite large structural differences between the two structures, suggesting similarity in function. 225 matched cddid_all.tbl CDD pfam11307 pfam11307 463258 DUF3109 Protein of unknown function (DUF3109). This bacterial family of proteins has no known function. 181 matched cddid_all.tbl CDD pfam11308 pfam11308 402761 Glyco_hydro_129 Glycosyl hydrolases related to GH101 family, GH129. This family of bacterial and lower eukaryote glycosyl hydrolases is related to CAZy family GH129,and distantly to GH101, and is made up of sub-families GHL1-GHL3. In the example Swiss:C02A26, the substrate-binding Asp is residue 596, the nucleophilic Asp is residue 706, and the proton donor Glu is residue 747. 324 matched cddid_all.tbl CDD pfam11309 pfam11309 402762 DUF3112 Protein of unknown function (DUF3112). This eukaryotic family of proteins has no known function. 217 matched cddid_all.tbl CDD pfam11310 pfam11310 288203 DUF3113 Protein of unknown function (DUF3113). This family of proteins has no known function. It has a highly conserved sequence. 60 matched cddid_all.tbl CDD pfam11311 pfam11311 431803 DUF3114 Protein of unknown function (DUF3114). Some members in this family of proteins with unknown function are annotated as cytosolic proteins. This cannot be confirmed. 266 matched cddid_all.tbl CDD pfam11312 pfam11312 431804 Methyltransf_34 Putative SAM-dependent methyltransferase. This family of largely fungal proteins are likely to be a methyltransferase. This was determined through multiple motif screening in yeast. 293 matched cddid_all.tbl CDD pfam11313 pfam11313 402765 DUF3116 Protein of unknown function (DUF3116). This family of proteins with unknown function appears to be restricted to Bacillales. 84 matched cddid_all.tbl CDD pfam11314 pfam11314 431805 DUF3117 Protein of unknown function (DUF3117). This family of proteins with unknown function appears to be restricted to Actinobacteria. 50 matched cddid_all.tbl CDD pfam11315 pfam11315 463259 Med30 Mediator complex subunit 30. Med30 is a metazoan-specific subunit of Mediator, having no homologs in yeasts. 147 matched cddid_all.tbl CDD pfam11316 pfam11316 431807 Rhamno_transf Putative rhamnosyl transferase. Most members of this family are uncharacterized, but one is a putative side-chain-rhamnosyl transferase. 235 matched cddid_all.tbl CDD pfam11317 pfam11317 431808 DUF3119 Protein of unknown function (DUF3119). This family of proteins has no known function. 108 matched cddid_all.tbl CDD pfam11318 pfam11318 431809 DUF3120 Protein of unknown function (DUF3120). This family of proteins with unknown function appears to be restricted to Cyanobacteria. 199 matched cddid_all.tbl CDD pfam11319 pfam11319 431810 VasI Type VI secretion system VasI, EvfG, VC_A0118. VasI is a family of Gram-negative proteins that form part of the pathogenicity apparatus for bacteria-to-bacteria attack. The exact function of this component is not known. 182 matched cddid_all.tbl CDD pfam11320 pfam11320 431811 DUF3122 Protein of unknown function (DUF3122). This family of proteins with unknown function appear to be restricted to Cyanobacteria. 134 matched cddid_all.tbl CDD pfam11321 pfam11321 463260 DUF3123 Protein of unknown function (DUF3123). This eukaryotic family of proteins has no known function. 62 matched cddid_all.tbl CDD pfam11322 pfam11322 431813 DUF3124 Protein of unknown function (DUF3124). This bacterial family of proteins has no known function. 123 matched cddid_all.tbl CDD pfam11324 pfam11324 431814 DUF3126 Protein of unknown function (DUF3126). This family of proteins with unknown function appear to be restricted to Alphaproteobacteria. 63 matched cddid_all.tbl CDD pfam11325 pfam11325 431815 DUF3127 Domain of unknown function (DUF3127). This bacterial family of proteins has no known function. However, it does show distant similarity to pfam00436, with proteins such as Swiss:D1W984 being similar to both families. This suggests that this family may have a DNA-binding function. 84 matched cddid_all.tbl CDD pfam11326 pfam11326 463261 DUF3128 Protein of unknown function (DUF3128). This eukaryotic family of proteins has no known function. 80 matched cddid_all.tbl CDD pfam11327 pfam11327 431817 Egh16-like Egh16-like virulence factor. This eukaryotic family of proteins includes a group of fungal proteins, including Egh16 from Erysiphe graminis f.sp. hordei and its homologs. They are found in pathogenic fungi and may play important roles during the early infection stage in fungal pathogens. 183 matched cddid_all.tbl CDD pfam11328 pfam11328 288220 DUF3130 Protein of unknown function (DUF3130. This bacterial family of proteins has no known function. 89 matched cddid_all.tbl CDD pfam11329 pfam11329 431818 DUF3131 Protein of unknown function (DUF3131). This bacterial family of proteins has no known function. 367 matched cddid_all.tbl CDD pfam11330 pfam11330 371472 30K_MP_C_Ter C-Terminal of 30K viral movement proteins. This entry represents the C-terminal region found in viral movement proteins (MP) of the 30K type. This region has been suggested to be conserved in secondary structure in Ophioviruses Mps. It contains two parts, (i) a long segment with the potential to form an alpha-helix (alphaB), rich in charged residues, and (ii) a region highly variable in sequence downstream of alphaB. The C-terminal region corresponds to a protease domain which contains a strictly conserved DTG tripeptide also found in related aspartic retroviral proteases. This protease is required for autocleavage of the Movement Protein of ophioviruses in an N-terminal part that supports movement of viral particles through the plant, and this C-terminal part which retains protease activity. Mutations in the aspartate residue in the core domain pfam17644 had an impact on cell to cell movement. 242 matched cddid_all.tbl CDD pfam11331 pfam11331 431819 zinc_ribbon_12 Probable zinc-ribbon domain. This eukaryotic family of proteins has no known function. 45 matched cddid_all.tbl CDD pfam11332 pfam11332 431820 DUF3134 Protein of unknown function (DUF3134). This family of proteins with unknown function appears to be restricted to Cyanobacteria. 68 matched cddid_all.tbl CDD pfam11333 pfam11333 431821 DUF3135 Protein of unknown function (DUF3135). This family of proteins with unkown function appears to be restricted to Proteobacteria. 81 matched cddid_all.tbl CDD pfam11334 pfam11334 402781 DUF3136 Protein of unknown function (DUF3136). This family of proteins with unknown function appear to be restricted to Cyanobacteria. 64 matched cddid_all.tbl CDD pfam11335 pfam11335 431822 DUF3137 Protein of unknown function (DUF3137). This bacterial family of proteins has no known function. 140 matched cddid_all.tbl CDD pfam11336 pfam11336 402783 DUF3138 Protein of unknown function (DUF3138). This family of proteins with unknown function appear to be restricted to Proteobacteria. 525 matched cddid_all.tbl CDD pfam11337 pfam11337 431823 DUF3139 Protein of unknown function (DUF3139). This family of proteins with unknown function appears to be restricted to Firmicutes. 77 matched cddid_all.tbl CDD pfam11338 pfam11338 431824 DUF3140 Protein of unknown function (DUF3140). Some members in this family of proteins are annotated as DNA binding proteins. No function is currently known. 92 matched cddid_all.tbl CDD pfam11339 pfam11339 431825 DUF3141 Protein of unknown function (DUF3141). This family of proteins with unknown function appears to be restricted to Proteobacteria. 582 matched cddid_all.tbl CDD pfam11340 pfam11340 431826 DUF3142 Protein of unknown function (DUF3142). This bacterial family of proteins has no known function. 223 matched cddid_all.tbl CDD pfam11341 pfam11341 463262 DUF3143 Protein of unknown function (DUF3143). This family of proteins has no known function. 65 matched cddid_all.tbl CDD pfam11342 pfam11342 431828 DUF3144 Protein of unknown function (DUF3144). This family of proteins with unknown function appears to be restricted to Proteobacteria. 77 matched cddid_all.tbl CDD pfam11343 pfam11343 431829 DUF3145 Protein of unknown function (DUF3145). This family of proteins with unknown function appear to be restricted to Actinobacteria. 156 matched cddid_all.tbl CDD pfam11344 pfam11344 402790 DUF3146 Protein of unknown function (DUF3146). This family of proteins with unknown function appear to be restricted to Cyanobacteria. 80 matched cddid_all.tbl CDD pfam11345 pfam11345 288237 DUF3147 Protein of unknown function (DUF3147). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known. 111 matched cddid_all.tbl CDD pfam11346 pfam11346 431830 DUF3149 Protein of unknown function (DUF3149). This bacterial family of proteins has no known function. 37 matched cddid_all.tbl CDD pfam11347 pfam11347 431831 DUF3148 Protein of unknown function (DUF3148). This family of proteins has no known function. 61 matched cddid_all.tbl CDD pfam11348 pfam11348 431832 DUF3150 Protein of unknown function (DUF3150). This bacterial family of proteins with unknown function appears to be restricted to Proteobacteria. 256 matched cddid_all.tbl CDD pfam11349 pfam11349 431833 DUF3151 Protein of unknown function (DUF3151). This family of proteins with unknown function appears to be restricted to Actinobacteria. 126 matched cddid_all.tbl CDD pfam11350 pfam11350 431834 DUF3152 Protein of unknown function (DUF3152). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function. 206 matched cddid_all.tbl CDD pfam11351 pfam11351 402795 GTA_holin_3TM Holin of 3TMs, for gene-transfer release. This is a family of bacterial 3TM holins. In Rhodobacter capsulatus the protein is expressed just overlapping and downstream of a putative N-acetylmuramidase lysozyme (an endolysin) thought to be responsible for lysing a phage particle, RcGTA - a gene-transfer agent. A holin would be necessary for such an endolysin to access the peptidoglycan. Gene-transfer agents are bacteriophage-like genetic elements with the sole known function of horizontal gene transfer, serving an important role in microbial evolution. In order to be released from the cell these require the combined action of an endolysin and this holin. 123 matched cddid_all.tbl CDD pfam11352 pfam11352 402796 DUF3155 Protein of unknown function (DUF3155). This family of proteins with unknown function appears to be restricted to Cyanobacteria. 88 matched cddid_all.tbl CDD pfam11353 pfam11353 402797 DUF3153 Protein of unknown function (DUF3153). This family of proteins with unknown function appear to be restricted to Cyanobacteria. Some members are annotated as membrane proteins however this cannot be confirmed. 191 matched cddid_all.tbl CDD pfam11354 pfam11354 431835 DUF3156 Protein of unknown function (DUF3156). This family of proteins with unknown function appears to be restricted to Proteobacteria. 154 matched cddid_all.tbl CDD pfam11355 pfam11355 431836 DUF3157 Protein of unknown function (DUF3157). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. 199 matched cddid_all.tbl CDD pfam11356 pfam11356 431837 T2SSC Type II secretion system protein C. This is the greater N-terminal region of GspC-type proteins. GspC proteins form part of the sophisticated transport mechanism of Gram-negative pathogens for injecting divers proteins into their hosts, a type-II secretion system - T2SS. The region is made up of a short N-terminal cytoplasmic domain that is followed by the single transmembrane helix, a Pro-rich linker, and the so-called homology region domain in the periplasm. This inner membrane GspC interacts with the outer membrane secretin GspD via periplasmic domains, an interaction which is critical for the effectiveness of type II secretion. 142 matched cddid_all.tbl CDD pfam11357 pfam11357 463263 Spy1 Cell cycle regulatory protein. Speedy (Spy1) is a cell cycle regulatory protein which activates CDK2, the major kinase that allows progression through G1/S phase and further replication events. Spy1 expression overcomes a p27-induced cell cycle arrest to allow for DNA synthesis, so cell cycle progression occurs due to an interaction between Spy1 and p27. Spy1 is also known as Ringo protein A. 131 matched cddid_all.tbl CDD pfam11358 pfam11358 431839 DUF3158 Protein of unknown function (DUF3158). Some members in this family of proteins are annotated as integrase regulator R however this cannot be confirmed. This family of proteins with unknown function appear to be restricted to Proteobacteria. 156 matched cddid_all.tbl CDD pfam11359 pfam11359 288251 gpUL132 Glycoprotein UL132. Glycoprotein UL132 is a low-abundance structural component of Human cytomegalovirus (HCMV). The function of this protein is not fully understood. 238 matched cddid_all.tbl CDD pfam11360 pfam11360 431840 DUF3110 Protein of unknown function (DUF3110). This family of proteins has no known function. 84 matched cddid_all.tbl CDD pfam11361 pfam11361 431841 DUF3159 Protein of unknown function (DUF3159). Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed. Currently this family of proteins has no known function. 188 matched cddid_all.tbl CDD pfam11362 pfam11362 402803 DUF3161 Protein of unknown function (DUF3161). This eukaryotic family of proteins has no known function. 83 matched cddid_all.tbl CDD pfam11363 pfam11363 431842 DUF3164 Protein of unknown function (DUF3164). This family of proteins has no known function. 194 matched cddid_all.tbl CDD pfam11364 pfam11364 431843 DUF3165 Protein of unknown function (DUF3165). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function. 79 matched cddid_all.tbl CDD pfam11365 pfam11365 463264 SOGA Protein SOGA. The SOGA (suppressor of glucose by autophagy) family consists of proteins SOGA1, SOGA2, and SOGA3. SOGA1 regulates autophagy by playing a role in the reduction of glucose production in an adiponectin and insulin dependent manner. 95 matched cddid_all.tbl CDD pfam11367 pfam11367 431845 DUF3168 Protein of unknown function (DUF3168). This family of proteins has no known function but is likely to be a component of bacteriophage. 117 matched cddid_all.tbl CDD pfam11368 pfam11368 463265 DUF3169 Protein of unknown function (DUF3169). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function. 248 matched cddid_all.tbl CDD pfam11369 pfam11369 431847 DUF3160 Protein of unknown function (DUF3160). This family of proteins has no known function. 608 matched cddid_all.tbl CDD pfam11371 pfam11371 431848 DUF3172 Protein of unknown function (DUF3172). This family of proteins has no known function. 139 matched cddid_all.tbl CDD pfam11372 pfam11372 402810 DUF3173 Domain of unknown function (DUF3173). This family of proteins with unknown function appears to be restricted to Firmicutes. These proteins appear to be distantly related to HHH domains and are therefore likely to be DNA-binding. Genomic environment-visualization confirms the likely function as being DNA-binding, as this short protein lies very closely between an integrase and a replication protein (http://www.microbesonline.org/). 58 matched cddid_all.tbl CDD pfam11373 pfam11373 431849 DUF3175 Protein of unknown function (DUF3175). This family of proteins with unknown function appears to be restricted to Proteobacteria. 84 matched cddid_all.tbl CDD pfam11374 pfam11374 463266 DUF3176 Protein of unknown function (DUF3176). This eukaryotic family of proteins has no known function. 107 matched cddid_all.tbl CDD pfam11375 pfam11375 431851 DUF3177 Protein of unknown function (DUF3177). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function. 189 matched cddid_all.tbl CDD pfam11376 pfam11376 431852 DUF3179 Protein of unknown function (DUF3179). This family of proteins has no known function. 289 matched cddid_all.tbl CDD pfam11377 pfam11377 431853 DUF3180 Protein of unknown function (DUF3180). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function. 136 matched cddid_all.tbl CDD pfam11378 pfam11378 431854 DUF3181 Protein of unknown function (DUF3181). This family of proteins has no known function. 88 matched cddid_all.tbl CDD pfam11379 pfam11379 431855 DUF3182 Protein of unknown function (DUF3182). This family of proteins with unknown function appears to be restricted to Proteobacteria. 353 matched cddid_all.tbl CDD pfam11380 pfam11380 463267 Stealth_CR2 Stealth protein CR2, conserved region 2. Stealth_CR2 is the second of several highly conserved regions on stealth proteins in metazoa and bacteria. There are up to four CR regions on all member proteins. CR2 carries a well-conserved NDD sequence-motif. The domain is found in tandem with CR1, CR3 and CR4 on both potential metazoan hosts and pathogenic eubacterial species that are capsular polysaccharide phosphotransferases. The CR domains appear on eukaryotic proteins such as GNPTAB, N-acetylglucosamine-1-phosphotransferase subunits alpha/beta. Horizontal gene-transfer seems to have occurred between host and bacteria of these sequence-regions in order for the bacteria to evade detection by the host innate immune system. 108 matched cddid_all.tbl CDD pfam11381 pfam11381 431857 DUF3185 Protein of unknown function (DUF3185). Some members in this bacterial family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known. 56 matched cddid_all.tbl CDD pfam11382 pfam11382 431858 MctB Copper transport outer membrane protein, MctB. Outer membrane channel protein MctB in Mycobacterium tuberculosis is part of a Cu resistance mechanism that ensures low intracellular Cu levels in the bacterium. Human resisitance to bacteria, mediated via IFN-gamma-mediated activation of macrophages, may involve the use of reactive Cu(1) in the presence of hyrodgen peroxide, since acitivated Cu is toxic to bacteria. IFN-gamma stimulates the trafficking of the Cu transporter ATP7a to the vesicles that fuse with phagosomes and these phagosomes are found to have a high Cu content and an increaseed bactericidal activity against E.coli. Using MctB, Mycobacterium tuberculosis may limit the amount of excess Cu within it whole in the host. 298 matched cddid_all.tbl CDD pfam11383 pfam11383 402821 DUF3187 Protein of unknown function (DUF3187). This family of proteins with unknown function appear to be restricted to Proteobacteria. These proteins are likely to be outer membrane proteins. 320 matched cddid_all.tbl CDD pfam11384 pfam11384 431859 DUF3188 Protein of unknown function (DUF3188). This bacterial family of proteins has no known function. 50 matched cddid_all.tbl CDD pfam11385 pfam11385 402823 DUF3189 Protein of unknown function (DUF3189). This family of proteins with unknown function appears to be restricted to Firmicutes 147 matched cddid_all.tbl CDD pfam11386 pfam11386 371502 VERL Vitelline envelope receptor for lysin. VERL, the egg vitelline envelope (VE) receptor for lysin, is a giant unbranched glycoprotein comprising 30% of the vitelline envelope. Lysin binds to VERL and creates a hole as VERL molecules lose cohesion and splay apart. These proteins are important in the mediation of fertilization 78 matched cddid_all.tbl CDD pfam11387 pfam11387 431860 DUF2795 Protein of unknown function (DUF2795). This family of proteins has no known function. 44 matched cddid_all.tbl CDD pfam11388 pfam11388 431861 DotA Phagosome trafficking protein DotA. DotA is essential for intracellular growth in Legionella. DotA is thought to play an important role in regulating initial phagosome trafficking decisions either upon or immediately after macrophage uptake. 105 matched cddid_all.tbl CDD pfam11389 pfam11389 371504 Porin_OmpL1 Leptospira porin protein OmpL1. OmpL1 is a member of the outer membrane (OM) proteins in the mammalian pathogen Leptospira. Specifically, it is a porin. 272 matched cddid_all.tbl CDD pfam11390 pfam11390 431862 FdsD NADH-dependant formate dehydrogenase delta subunit FdsD. FdsD is the delta subunit of the enzyme formate dehydrogenase. This subunit may play a role in maintaining the quaternary structure by means of electrostatic interactions with the other subunits. The delta subunit is not involved in the active centre of the enzyme. 60 matched cddid_all.tbl CDD pfam11391 pfam11391 463268 DUF2798 Protein of unknown function (DUF2798). This family of proteins has no known function. 59 matched cddid_all.tbl CDD pfam11392 pfam11392 431864 DUF2877 Protein of unknown function (DUF2877). This bacterial family of proteins are putative carboxylase proteins however this cannot be confirmed. 109 matched cddid_all.tbl CDD pfam11393 pfam11393 431865 T4BSS_DotI_IcmL Type-IV b secretion system, inner-membrane complex component. IcmL contains two amphipathic beta-sheet regions, required for the pore-forming ability which may be related to the transfer of this protein into a host cell membrane. The icmL gene shows significant similarity to plasmid genes involved in conjugation however IcmL is thought to be required for macrophage killing. It is unknown whether conjugation plays a role in macrophage killing. This is a family of DotI/IcmL proteins of type IVb secretion systems, that reside in the inner-membrane. It carries a single transmembrane helix in the N-terminal conserved region, has an extra-periplasmic domain, and is conserved in all T4BSSs including I-type conjugation systems (TraM). DotI/IcmL (and DotJ) may form an inner membrane complex that associates with the core complex. 180 matched cddid_all.tbl CDD pfam11394 pfam11394 288282 DUF2875 Protein of unknown function (DUF2875). This family of proteins with unknown function appear to be restricted to Proteobacteria. 462 matched cddid_all.tbl CDD pfam11395 pfam11395 431866 bCoV_NS7B Betacoronavirus NS7B protein. This entry corresponds to Human SARS coronavirus (SARS-CoV) and similar betacoronaviruses NS7B protein (also known as accessory protein 7b, NS7B, ORF7b and 7b). It was found to be a structural component of SARS-CoV virions and an integral membrane protein. Its transmembrane domain is essential for Golgi compartment localization. 43 matched cddid_all.tbl CDD pfam11396 pfam11396 431867 PepSY_like Putative beta-lactamase-inhibitor-like, PepSY-like. This family of bacterial proteins is probably periplasmic. Members are found predominantly in microbes of the human gut and oral cavity. Structurally, one member of this family is found to show similarity to the beta-lactamase-inhibitor PepSY proteins, so the overall function may be inhibitory. There are tandem repeats of the domain on many family members. 83 matched cddid_all.tbl CDD pfam11397 pfam11397 371506 GlcNAc Glycosyltransferase (GlcNAc). GlcNAc is an enzyme that carries out the first glycosylation step of hydroxylated Skp1, a ubiquitous eukaryotic protein, in the cytoplasm. 351 matched cddid_all.tbl CDD pfam11398 pfam11398 431868 DUF2813 Protein of unknown function (DUF2813). This entry contains YjbD from Escherichia coli, which is annotated as a nucleotide triphosphate hydrolase. 372 matched cddid_all.tbl CDD pfam11399 pfam11399 431869 DUF3192 Protein of unknown function (DUF3192). Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed. 101 matched cddid_all.tbl CDD pfam11401 pfam11401 402833 Tetrabrachion Tetrabrachion. Tetrabrachion forms a parallel right-handed coiled coil structure with hydrophobic interactions and salt bridges forming a thermostable tetrameric structure. It contains large hydrophobic cavities. No function is known for this family of proteins. 49 matched cddid_all.tbl CDD pfam11402 pfam11402 402834 Antifungal_prot Antifungal protein. Antifungal protein consists of five antiparallel beta strands which are highly twisted creating a beta barrel stabilized by four internal disulphide bridges. A cationic site adjacent to a hydrophobic stretch on the protein surface may constitute a phospholipid binding site. 50 matched cddid_all.tbl CDD pfam11403 pfam11403 463269 Yeast_MT Yeast metallothionein. Metallothioneins are characterized by an abundance of cysteine residues and a lack of generic secondary structure motifs. This protein functions in primary metal storage, transport and detoxification. For the first 40 residues in the protein the polypeptide wraps around the metal by forming two large parallel loops separated by a deep cleft containing the metal cluster. 39 matched cddid_all.tbl CDD pfam11404 pfam11404 431870 Potassium_chann Potassium voltage-gated channel. Fast inactivation of voltage-dependant potassium channels occurs by a 'ball-and-chain'-type mechanism. It controls membrane excitability and signal propagation in central neurons. Inactivation is regulated by protein phosphorylation where phosphorylation of serine residues leads to a reduction of the fast inactivation. 29 matched cddid_all.tbl CDD pfam11405 pfam11405 402837 Inhibitor_I67 Bromelain inhibitor VI. Bromelain inhibitor VI is a double-chain inhibitor consisting of a 11-residue and a 41-residue chain. This protein is the 41-residue heavy chain which is joined to the 11-residue chain by disulphide bonds. The inhibitor acts to inhibit the cysteine proteinase bromelain. 41 matched cddid_all.tbl CDD pfam11406 pfam11406 371512 Tachystatin_A Antimicrobial peptide tachystatin A. Tachystatin A contains a cysteine-stabilized triple-stranded beta-sheet and shows features common to membrane-interactive peptides. Tachystatin A is thought to have an antimicrobial activity similar to defensins.Tachystatin A is also a chitin-binding peptide. 44 matched cddid_all.tbl CDD pfam11407 pfam11407 402838 RestrictionMunI Type II restriction enzyme MunI. Type II restriction enzyme MunI recognizes the palindromic sequence C/AATTG. It makes contact with the DNA via the major groove. 202 matched cddid_all.tbl CDD pfam11408 pfam11408 463270 Helicase_Sgs1 Sgs1 RecQ helicase. RecQ helicases unwind DNA in an ATP-dependent manner. Sgs1 has a HRDC (helicase and RNaseD C-terminal) domain which modulates the helicase function via auxiliary contacts to DNA. 80 matched cddid_all.tbl CDD pfam11409 pfam11409 463271 SARA Smad anchor for receptor activation (SARA). Smad proteins mediate transforming growth factor-beta (TGF-beta) signaling from the transmembrane serine-threonine receptor kinases to the nucleus. SARA recruits Smad2 to the TGF-beta receptors for phosphorylation. 37 matched cddid_all.tbl CDD pfam11410 pfam11410 371514 Antifungal_pept Antifungal peptide. This peptide has six cysteines involved in three disulphide bonds. It contains a global fold which involves a cysteine-knotted three-stranded antiparallel beta-sheet along with a flexible loop and four beta-reverse turns. It also has an amphiphilic character which is the main structural basis of its biological function. 33 matched cddid_all.tbl CDD pfam11411 pfam11411 463272 DNA_ligase_IV DNA ligase IV. DNA ligase IV along with Xrcc4 functions in DNA non-homologous end joining. This process is required to mend double-strand breaks. Upon ligase binding to an Xrcc4 dimer, the helical tails unwind leading to a flat interaction surface. 34 matched cddid_all.tbl CDD pfam11412 pfam11412 463273 DsbC Disulphide bond corrector protein DsbC. This entry represents the N-terminal domain of DsbD, a transmembrane electron transporter. DsbD binds to a DsbC dimer and selectively activates it using electrons from the cytoplasm. The N-terminal domain of DsbD (DsbDN) is capable of forming disulfides with oxidized DsbC, DsbE, or DsbG as well as with reduced DsbD. 115 matched cddid_all.tbl CDD pfam11413 pfam11413 463274 HIF-1 Hypoxia-inducible factor-1. HIF-1 is a transcriptional complex and controls cellular systemic homeostatic responses to oxygen availability. In the presence of oxygen HIF-1 alpha is targeted for proteasomal degradation by pHVL, a ubiquitination complex. 32 matched cddid_all.tbl CDD pfam11414 pfam11414 463275 Suppressor_APC Adenomatous polyposis coli tumour suppressor protein. The tumour suppressor protein, APC, has a nuclear export activity as well as many different intracellular functions. The structure consists of three alpha-helices forming two separate antiparallel coiled coils. 82 matched cddid_all.tbl CDD pfam11415 pfam11415 151854 Toxin_37 Antifungal peptide termicin. Termicin is a cysteine-rich antifungal peptide which exhibits antibacterial activity. A cysteine stabilized alpha beta motif is formed due to an alpha-helical segment and a two-stranded antiparallel beta-sheet. 35 matched cddid_all.tbl CDD pfam11416 pfam11416 463276 Syntaxin-5_N Syntaxin-5 N-terminal, Sly1p-binding domain. Syntaxin-5_N is the Sed5 N-terminal and the N-terminus of Syntaxin-5-like proteins. It is the region of Syntaxin that interacts with Sly1p, a positive regulator of intracellular membrane fusion, allowing SM (cytosolic Sec1/munc18-like) proteins to stay associated with the assembling fusion machinery. This allows the SM proteins to participate in late fusion steps. 23 matched cddid_all.tbl CDD pfam11417 pfam11417 402845 Inhibitor_G39P Loader and inhibitor of phage G40P. G39P inhibits the initiation of DNA replication by blocking G40P replicative helicase. G39P has a bipartite stricture consisting of a folded N-terminal domain and an unfolded C-terminal domain. The C terminal is essential for helicase interaction. 66 matched cddid_all.tbl CDD pfam11418 pfam11418 431877 Scaffolding_pro Phi29 scaffolding protein. This protein is also referred to as gp7. The protein contains a DNA-binding function and may halve a role in mediating the structural transition from prohead to mature virus and also scaffold release.Gp7 is arranged within the capsid as a series of concentric shells. 100 matched cddid_all.tbl CDD pfam11419 pfam11419 402847 DUF3194 Protein of unknown function (DUF3194). This family of proteins has no known function however the structure has been determined. The protein consists of two alpha-helices packed on the same side of a central beta-hairpin. 83 matched cddid_all.tbl CDD pfam11420 pfam11420 431878 Subtilosin_A Bacteriocin subtilosin A. Subtilosin A is a bacteriocin from Bacillus subtilis.The protein has a cyclized peptide backbone and forms three cross-liks between the sulphurs of Cys13, Cys7 and Cys4 and the alpha-positions of Phe22,Thr28 and Phe31. 35 matched cddid_all.tbl CDD pfam11421 pfam11421 463277 Synthase_beta ATP synthase F1 beta subunit. The NMR solution structure of the protein in SDS micelles was found to contain two helices, an N-terminal amphipathic alpha-helix and a C-terminal alpha-helix separated by a large unstructured internal domain. The N-terminal alpha-helix is the Tom20 receptor binding site whereas the C-terminal alpha-helix is located upstream of the mitochondrial processing peptidase cleavage site. 47 matched cddid_all.tbl CDD pfam11422 pfam11422 402849 IBP39 Initiator binding protein 39 kDa. IBP39 recognizes the initiator which is solely responsible for transcription start site selection. IBP39 contains an N-terminal Inr binding domain connected to a C-terminal domain. The C domain structure indicates that it interacts with the T. vaginalis RNAP II large subunit C-terminal domain. Binding of IBP39 to Inr recruits RNAP II and initiates transcription. 179 matched cddid_all.tbl CDD pfam11423 pfam11423 402850 Repressor_Mnt Regulatory protein Mnt. Mnt is a repressor which is involved in the genetic switch between lysogenic and lytic growth in bacteriophage P22. The C-terminal domain of the protein consists of a dimer of two antiparallel coiled coils with a right handed twist, which is both stronger and has closer inter-helical separation compared with those found in left-handed coiled coils. 25 matched cddid_all.tbl CDD pfam11424 pfam11424 402851 DUF3195 Protein of unknown function (DUF3195). This archaeal family of proteins has no known function. 85 matched cddid_all.tbl CDD pfam11426 pfam11426 371524 Tn7_TnsC_Int Tn7 transposition regulator TnsC. TnsC is a molecular switch that regulates transposition and interacts with TnsA which is a component of the transposase. The two proteins interact via the residues 504-555 on TnsC. The TnsA/TnsC interaction is very important in Tn7 transposition. 47 matched cddid_all.tbl CDD pfam11427 pfam11427 192757 HTH_Tnp_Tc3_1 Tc3 transposase. Tc3 is transposase with a specific DNA-binding domain which contains three alpha-helices, two of which form a helix-turn-helix motif which makes four base-specific contacts with the major groove. The N-terminus makes contacts with the minor groove. There is a base specific recognition between Tc3 and the transposon DNA. The DNA binding domain forms a dimer in which each monomer binds a separate transposon end. This implicates that the dimer has a role in synapsis and is necessary for the simultaneous cleavage of both transposon termini. 50 matched cddid_all.tbl CDD pfam11428 pfam11428 402852 DUF3196 Protein of unknown function (DUF3196). This proteins is the product of the gene MPN330 and is thought to involved in a cellular function that has yet to be characterized. The proteins has 11 helices and a novel fold. No function is currently known for this protein. 264 matched cddid_all.tbl CDD pfam11429 pfam11429 463278 Colicin_D Colicin D. Colicin D is a tRNase which kills sensitive E.coli cells via a specific tRNA cleavage. It targets the four isoaccepting tRNAs for Arg and cleaves the phosphodiester bond between positions 38 and 39 at the 3' junction of the anticodon stem and the loop. 85 matched cddid_all.tbl CDD pfam11430 pfam11430 402854 EGL-1 Programmed cell death activator EGL-1. Initiation of programmed cell death in C.elegans occurs by the binding of EGL-1 to CED-9 which disrupts a complex involving CED-4/CED-9 and allows CED-4 to activate CED-3, a caspase. It is the C terminal domain of EGL-1 which is involved in the formation of the complex with CED-9. The formation of the complex induces structural rearrangements in CED-9 and EGL-1 adopts an extended alpha-helical conformation. 20 matched cddid_all.tbl CDD pfam11431 pfam11431 402855 Transport_MerF Membrane transport protein MerF. The mercury transport membrane protein, MerF has a core helix-loop-helix domain. It has two vicinal pairs of cysteine residues which are involved in the transport of Hg(II) across the membrane and are exposed to the cytoplasm. 45 matched cddid_all.tbl CDD pfam11432 pfam11432 463279 DUF3197 Protein of unknown function (DUF3197). This bacterial family of proteins has no known function. 113 matched cddid_all.tbl CDD pfam11433 pfam11433 371530 DUF3198 Protein of unknown function (DUF3198). Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently, this archaeal family has no known function. 49 matched cddid_all.tbl CDD pfam11434 pfam11434 371531 CHIPS Chemotaxis-inhibiting protein CHIPS. The chemotaxis inhibitory protein, CHIPS, is an excreted virulence factor which acts by binding to C5a and formylated peptide receptor (FPR), blocking phagocyte responses. A fragment of CHIPS, which contains residues 31-121 comprises of an alpha helix packed onto a four stranded anti-parallel beta-sheet. Most of the conserved residues of CHIPS are present in the alpha-helix. 91 matched cddid_all.tbl CDD pfam11435 pfam11435 402856 She2p RNA binding protein She2p. She2p is a RNA binding protein which binds to RNA via a helical hairpin. The protein is required for the actin dependent transport of ASH1 mRNA in yeast, a form of mRNP translocation. ASH1 mRNP requires recognition of zip code elements by the RNA binding protein She2p. She2p contains a globular domain consisting of a bundle of five alpha-helices. 199 matched cddid_all.tbl CDD pfam11436 pfam11436 402857 DUF3199 Protein of unknown function (DUF3199). Some members in this family of proteins with unknown function are annotated as YqbG however this cannot be confirmed. Currently the proteins has no known function. 123 matched cddid_all.tbl CDD pfam11437 pfam11437 371534 Vanabin-2 Vanadium-binding protein 2. The Vanadium binding protein, Vanabin2, contains four alpha-helices connected by nine disulphide bonds. Vanadium accumulates in Ascidians however the biological reason remains unclear. 93 matched cddid_all.tbl CDD pfam11438 pfam11438 288317 N36 36-mer N-terminal peptide of the N protein (N36). The arginine-rich motif of the N protein is involved in transcriptional antitermination of phage lambda. N36 forms a complex with boxB RNA by binding tightly to the major groove of the boxB hairpin via hydrophobic and electrostatic interactions forming a bent alpha helix. 35 matched cddid_all.tbl CDD pfam11439 pfam11439 371535 T3SchapCesA Type III secretion system filament chaperone CesA. This family represents a chaperone protein for the type III secretion system - TTSS - translocon protein EspA, to prevent the latter's self-polymerization. The TTSS is a highly specialized bacterial protein secretory pathway, similar in many ways to the flagellar system, that is essential for the pathogenesis of many Gram-negative bacteria. The twenty or so proteins making up the TTSS apparatus, referred to as the needle complex, allow the injection of virulence proteins (known as effectors) directly into the cytoplasm of the eukaryotic host cells they infect; however, the injection process itself is mediated by a subset of extracellular proteins that are secreted by the needle complex to the bacterial surface and assembled into the type III translocon - EspA. EspB and EspD. EspA polymerizes into an extracellular filament, and, as with other fibrous proteins, is apt to undergo massive polymerization when overexpressed. CesA is the secretion chaperone protein that binds to EspA. CesA is dimeric and helical, and it traps EspA in a monomeric state and inhibits its polymerization. 95 matched cddid_all.tbl CDD pfam11440 pfam11440 288318 AGT DNA alpha-glucosyltransferase. The T4 bacteriophage of E.coli protects its DNA via two glycosyltransferases which glucosylate 5-hydroxymethyl cytosines (5-HMC) using UDP-glucose. These two proteins are the retaining alpha-glucosyltransferase (AGT) and the inverting beta-glucosyltransferase (BGT). The proteins in this family are AGT. AGT adopts the GT-B fold and binds both the sugar donor and acceptor to the C-terminal domain. There is evidence for a role of AGT in the base-flipping mechanism and for its specific recognition of the acceptor base. 355 matched cddid_all.tbl CDD pfam11441 pfam11441 288319 MxiM Pilot protein MxiM. MxiM, a Shigella pilot protein, is essential for the assembly and membrane association of the Shigella secretin MxiD. MxiM contains an orthologous secretin component and has a specific binding domain for the acyl chains of bacterial lipids. The C terminal domain of MxiD hinders lipid binding to MxiM. 115 matched cddid_all.tbl CDD pfam11442 pfam11442 288320 DUF2826 Protein of unknown function (DUF2826). This is a family of uncharacterized proteins that is highly conserved in Trypanosoma cruzi. 158 matched cddid_all.tbl CDD pfam11443 pfam11443 431881 DUF2828 Domain of unknown function (DUF2828). This is a uncharacterized domain found in eukaryotes and viruses. 615 matched cddid_all.tbl CDD pfam11444 pfam11444 431882 DUF2895 Protein of unknown function (DUF2895). This is a bacterial family of uncharacterized proteins. 189 matched cddid_all.tbl CDD pfam11445 pfam11445 431883 DUF2894 Protein of unknown function (DUF2894). This is a bacterial family of uncharacterized proteins. 181 matched cddid_all.tbl CDD pfam11446 pfam11446 431884 DUF2897 Protein of unknown function (DUF2897). This is a bacterial family of uncharacterized proteins. 52 matched cddid_all.tbl CDD pfam11447 pfam11447 402862 DUF3201 Protein of unknown function (DUF3201). This archaeal family of proteins has no known function. 153 matched cddid_all.tbl CDD pfam11448 pfam11448 431885 DUF3005 Protein of unknown function (DUF3005). This is a bacterial family of uncharacterized proteins. 109 matched cddid_all.tbl CDD pfam11449 pfam11449 431886 ArsP_2 Putative, 10TM heavy-metal exporter. This is a family of putative manganese transporters with 9-11 TMs. Members carry two well-conserved characteriztic sequence- motifs of 'PGCG'. 363 matched cddid_all.tbl CDD pfam11450 pfam11450 431887 DUF3008 Protein of unknwon function (DUF3008). This is a bacterial family of uncharacterized proteins. 57 matched cddid_all.tbl CDD pfam11452 pfam11452 431888 DUF3000 Protein of unknown function (DUF3000). This is a bacterial family of uncharacterized proteins. 173 matched cddid_all.tbl CDD pfam11453 pfam11453 431889 DUF2950 Protein of unknown function (DUF2950). This is a bacterial family of uncharacterized proteins. 274 matched cddid_all.tbl CDD pfam11454 pfam11454 431890 DUF3016 Protein of unknown function (DUF3016). This is a bacterial family of uncharacterized proteins. 139 matched cddid_all.tbl CDD pfam11455 pfam11455 463280 MazE-like Antitoxin MazE-like. This entry includes MazE from Mycobacterium smegmatis. MazE is an antitoxin component of a type II toxin-antitoxin (TA) system. 64 matched cddid_all.tbl CDD pfam11456 pfam11456 431892 DUF3019 Protein of unknown function (DUF3019). This is a bacterial family of uncharacterized proteins. 102 matched cddid_all.tbl CDD pfam11457 pfam11457 402870 DUF3021 Protein of unknown function (DUF3021). This is a bacterial family of uncharacterized proteins. 130 matched cddid_all.tbl CDD pfam11458 pfam11458 402871 Mistic Membrane-integrating protein Mistic. Mistic is an integral membrane protein that folds autonomously into the membrane.The protein forms a helical bundle with a polar lipid-facing surface. Mistic can be used for high-level production of other membrane proteins in their native conformations. 74 matched cddid_all.tbl CDD pfam11459 pfam11459 463281 AbiEi_3 Transcriptional regulator, AbiEi antitoxin, Type IV TA system. AbiEi_3 is the cognate antitoxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is pfam13338. 157 matched cddid_all.tbl CDD pfam11460 pfam11460 431894 DUF3007 Protein of unknown function (DUF3007). This is a family of uncharacterized proteins found in bacteria and eukaryotes. 95 matched cddid_all.tbl CDD pfam11461 pfam11461 463282 RILP Rab interacting lysosomal protein. RILP contains a domain which contains two coiled-coil regions and is found mainly in the cytosol. RILP is recruited onto late endosomal and lysosomal membranes by Rab7 and acts as a downstream effector of Rab7. This recruitment process is important for phagosome maturation and fusion with late endosomes and lysosomes. 69 matched cddid_all.tbl CDD pfam11462 pfam11462 431896 DUF3203 Protein of unknown function (DUF3203). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. 74 matched cddid_all.tbl CDD pfam11463 pfam11463 431897 R-HINP1I R.HinP1I restriction endonuclease. Hinp1I is a type II restriction endonuclease, recognising and cleaving a palindromic tetranucleotide sequence (G/CGC) resulting in 2 nt 5' overhanging ends. HINP1I has a conserved catalytic core domain containing an active site motif SDC18QXK and a DNA-binding domain. 205 matched cddid_all.tbl CDD pfam11464 pfam11464 463283 Rbsn Rabenosyn Rab binding domain. Rabenosyn-5 (Rbsn) is a multivalent effector with interacts with the Rab family.Rsbn contains distinct Rab4 and Rab5 binding sites within residues 264-500 and 627-784 respectively. Rab proteins are GTPases involved in the regulation of all stages of membrane trafficking. 39 matched cddid_all.tbl CDD pfam11465 pfam11465 288342 Receptor_2B4 Natural killer cell receptor 2B4. 2B4 is a transmembrane receptor which is expressed primarily on natural killer cells. It plays a role in activating NK-mediated cytotoxicity through its interaction with CD48 on target cells in a subset of CD8 T cells. The structure of 2B4 consists of an immunoglobulin variable domain fold and contains two beta-sheets. One of the beta-sheets, the six-stranded sheet, contains structural features that may have a role in ligand recognition and receptor function. 108 matched cddid_all.tbl CDD pfam11466 pfam11466 402876 Doppel Prion-like protein Doppel. Dpl is a homolog related to the prion protein (PrP). Dpl is toxic to neurons and is expressed in the brains of mice that do not express PrP. In DHPC and SDS micelles, Dpl shoes about 40% alpha-helical structure however in aqueous solution it consists of a random coil. The alpha helical segment can adopt a transmembrane localization also in a membrane. The unprocessed Dpl protein is thought to posses a possible channel formation mechanism which may be related to toxicity through direct interaction with cell membranes and damage to the cell membrane. It is suggested that the peptide is neither in an entirely random coil nor in a completely alpha-helical conformation, possible continuously interchanging between the two conformations. 30 matched cddid_all.tbl CDD pfam11467 pfam11467 463284 LEDGF Lens epithelium-derived growth factor (LEDGF). LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure. 120 matched cddid_all.tbl CDD pfam11468 pfam11468 371546 PTase_Orf2 Aromatic prenyltransferase Orf2. In vivo Orf2 attaches a geranyl group to a 1,3,6,8-tetrahydroxynaphthalene-derived polyketide during naphterpin biosynthesis. In vitro, Orf2 catalyzes carbon-carbon based and carbon-oxygen based prenylation of hydroxyl-containing aromatic acceptors of synthetic, microbial and plant origin. 287 matched cddid_all.tbl CDD pfam11469 pfam11469 402878 Ribonucleas_3_2 Ribonuclease III. This is a family of archaeal ribonuclease_III proteins. 119 matched cddid_all.tbl CDD pfam11470 pfam11470 463285 TUG-UBL1 TUG ubiquitin-like domain. TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly. TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site. This domain is also found at the N-terminus of yeast UBX4. 65 matched cddid_all.tbl CDD pfam11471 pfam11471 431901 Sugarporin_N Maltoporin periplasmic N-terminal extension. This domain would appear to be the periplasmic, N-terminal extension of the outer membrane maltoporins, pfam02264, LamB. 31 matched cddid_all.tbl CDD pfam11472 pfam11472 431902 DUF3206 Protein of unknown function (DUF3206). This bacterial family of proteins has no known function. 128 matched cddid_all.tbl CDD pfam11473 pfam11473 314404 B2 RNA binding protein B2. B2 is expressed by the insect Flock House virus (FHV) as a counter-defense mechanism against antiviral RNA silencing during infection. In vitro, B2 binds to dsRNA as a dimer and inhibits the cleavage of it by Dicer. B2 blocks cleavage of the FHV genome by Dicer and also the incorporation of FHV small interfering RNAs into the RNA-induced silencing complex. 72 matched cddid_all.tbl CDD pfam11474 pfam11474 431903 N-Term_TEN Telomerase reverse transcriptase TEN domain. This is the N terminal domain of the protein telomerase reverse transcriptase called TEN. The TEN domain is able to bind both RNA and telomeric DNA and contributes towards telomerase catalysis. The TEN domain has a structure that consists of a core beta sheet surrounded by seven alpha helices and a short beta hairpin. 188 matched cddid_all.tbl CDD pfam11475 pfam11475 288349 VP_N-CPKC Virion protein N terminal domain. This is the N terminal domain of a family of virion proteins which contains a zinc finger domain. Currently no function is known. 32 matched cddid_all.tbl CDD pfam11476 pfam11476 402882 TgMIC1 Toxoplasma gondii micronemal protein 1 TgMIC1. TgMIC1 is released as part of a complex by Toxoplasma gondii prior to invasion. The complex which consists of TgMIC4-MIC1-MIC6 participates in host cell attachment and penetration and is critical in invasion. This is the C terminal domain of TgMIC1 which has a Galectin-like fold which interacts with and stabilizes TgMIC6 providing a mechanism for an exit from the early secretory compartments and trafficking of the complex to micronemes. 137 matched cddid_all.tbl CDD pfam11477 pfam11477 402883 PM0188 Sialyltransferase PMO188. PMO188 is a sialyltransferase from P.multocida. It transfers sialic acid from cytidine 5'-monophosphonuraminic acid to an acceptor sugar. It has important catalytic residues such as Asp141, His311, Glu338, Ser355 and Ser356. 385 matched cddid_all.tbl CDD pfam11478 pfam11478 314405 Tachystatin_B Antimicrobial chitin binding protein tachystatin B. Tachystatin B is an antimicrobial chitin binding peptide and consists of two isotopes B1 and B2.Both structures contain a short antiparallel beta sheet with an inhibitory cysteine knot motif. Tyr(14) and Arg(17) are thought to be the essential residues for chitin binding. 42 matched cddid_all.tbl CDD pfam11479 pfam11479 371552 Suppressor_P21 RNA silencing suppressor P21 C-terminal domain. P21 is produced by Beet yellows virus to suppress the antiviral silencing response mounted by the host. P21 acts by binding directly to siRNA which is a mediator in the process. P21 has an octameric ring structure with a large central cavity. This is the C-terminal domain. The N-terminal domain is pfam11757. 80 matched cddid_all.tbl CDD pfam11480 pfam11480 431904 ImmE5 Colicin-E5 Imm protein. Imms bind specifically to cognate colicins in order to protect their host cells. Imm-E5 is a specific inhibitor protein of colicin E5. It binds to E5 C-terminal ribonuclease domain (CRD) to prevent cell death. The binding mode of E5-CRD and Imm-E5 mimics that of mRNA and tRNA suggesting an evolutionary pathway from the RNA-RNA interaction through the RNA-protein interaction of tRNA/E5-CRD. 82 matched cddid_all.tbl CDD pfam11482 pfam11482 431905 DUF3208 Protein of unknown function (DUF3208). This bacterial family of proteins has no known function. 108 matched cddid_all.tbl CDD pfam11483 pfam11483 402885 DUF3209 Protein of unknown function (DUF3209). This family of proteins has no known function. 123 matched cddid_all.tbl CDD pfam11485 pfam11485 402886 DUF3211 Protein of unknown function (DUF3211). This archaeal family of proteins has no known function. 136 matched cddid_all.tbl CDD pfam11486 pfam11486 288356 DUF3212 Protein of unknown function (DUF3212). Members in this family of proteins are annotated as YfmB however currently no function for this protein is known. 119 matched cddid_all.tbl CDD pfam11487 pfam11487 431906 RestrictionSfiI Type II restriction enzyme SfiI. SfiI is a restriction enzyme that can cleave two DNA sites simultaneously to leave 3-base 3' overhangs. It acts as a homo-tetramer and recognizes a specific eight base-paid palindromic DNA sequence. After binding two copies of its recognition sequence, SfiI becomes activated leading to cleavage of all four DNA strands. The structure of SfiI consists of a central twisted beta-sheet surrounded by alpha-helices. 215 matched cddid_all.tbl CDD pfam11488 pfam11488 431907 Lge1 Transcriptional regulatory protein LGE1. This family of proteins is conserved from fungi to human. In yeasts it is involved in the ubiquitination of histones H2A and H2B. This ubiquitination step is a vital one in the regulation of the transcriptional activity of RNA polymerase II. In S. cerevisiae, Rad6 and Bre1 are present in a complex, also containing Lge1, that is required for H2B ubiquitination. Bre1 is the H2B ubiquitin ligase that interacts with acidic activators, such as Gal4, and recruits Rad6 and its binding partner Lge1 to target promoters. In S. pombe the equivalent protein to Lge1 appears to be Shf1. In human, periphilin acts a transcriptional co-repressor and regulates cell cycle progression. 64 matched cddid_all.tbl CDD pfam11489 pfam11489 371558 Aim21 Altered inheritance of mitochondria protein 21. This is a family of proteins conserved in yeasts. Saccharomyces cerevisiae Aim21 may be involved in mitochondrial migration along actin filament. It may also interact with ribosomes. 677 matched cddid_all.tbl CDD pfam11490 pfam11490 431908 DNA_pol3_a_NII DNA polymerase III polC-type N-terminus II. This is the second N-terminal domain, NII domain, of the DNA polymerase III polC subunit A that is found only in Firmicutes. DNA polymerase polC-type III enzyme functions as the 'replicase' in low G + C Gram-positive bacteria. Purine asymmetry is a characteriztic of organizms with a heterodimeric DNA polymerase III alpha-subunit constituted by polC which probably plays a direct role in the maintenance of strand-biased gene distribution; since, among prokaryotic genomes, the distribution of genes on the leading and lagging strands of the replication fork is known to be biased. It has been predicted that the N-terminus of polC folds into two globular domains, NI and NII. A predicted hydrophobic surface patch suggests this domain may be involved in protein binding. This domain is associated with DNA_pol3_alpha pfam07733 and DNA_pol3_a_NI pfam14480. 117 matched cddid_all.tbl CDD pfam11491 pfam11491 402890 DUF3213 Protein of unknown function (DUF3213). The backbone structure of this family of proteins has been determined however the function remains unknown. The protein has an alpha and beta structure with a ferredoxin-like fold. 85 matched cddid_all.tbl CDD pfam11492 pfam11492 288362 Dicistro_VP4 Cricket paralysis virus, VP4. This is a family of minor capsid proteins, known as VP4, from the dicistroviridae. The dicistroviridae is a group of small, RNA-containing viruses that are closely structurally related to the picornaviridae. VP4 is a short, extended polypeptide chain found within the viral capsid, at the interface between the external protein shell and packaged RNA genome. 53 matched cddid_all.tbl CDD pfam11493 pfam11493 431909 TSP9 Thylakoid soluble phosphoprotein TSP9. The plant-specific protein, TSP9 is phosphorylated and released in response to changing light conditions from the photosynthetic membrane. The protein resembles the characteriztics of transcription/translation regulatory factors. The structure of the protein is predicted to consist of a random coil. 79 matched cddid_all.tbl CDD pfam11494 pfam11494 402892 Ta0938 Ta0938. Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. 92 matched cddid_all.tbl CDD pfam11495 pfam11495 402893 Regulator_TrmB Archaeal transcriptional regulator TrmB. TrmB is an alpha-glucoside sensing transcriptional regulator. The protein is the transcriptional repressor for gene cluster encoding trehalose/maltose ABC transporter in T.litoralis and P.furiosus. TrmB has lost its DNA binding domain but retained its sugar recognition site. A nonreducing glucosyl residue is shared by all substrates bound to TrmB which suggests that its a common recognition motif. 233 matched cddid_all.tbl CDD pfam11496 pfam11496 402894 HDA2-3 Class II histone deacetylase complex subunits 2 and 3. This family of class II histone deacetylase complex subunits HDA2 and HDA3 is found in fungi, The member from S. pombe is referred to as Ccq1 in Swiss:Q10432. These proteins associate with HDA1 to generate the activity of the HDA1 histone deacetylase complex. HDA1 interacts with itself and with the HDA2-HDA3 subcomplex to form a probable tetramer and these interactions are necessary for catalytic activity. The HDA1 histone deacetylase complex is responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. HDA2 and HDA3 have a conserved coiled-coil domain towards their C-terminus. 281 matched cddid_all.tbl CDD pfam11497 pfam11497 431910 NADH_Oxid_Nqo15 NADH-quinone oxidoreductase chain 15. This protein, Nqo15, is a part of respiratory complex 1 which is a complex that plays a central role in cellular energy production in both bacteria and mitochondria. Nqo15 has a similar fold to Frataxin, the mitochondrial iron chaperone. This protein may have a role in iron-sulphur cluster regeneration in the complex. This domain represents more than half the molecular mass of the entire complex. 123 matched cddid_all.tbl CDD pfam11498 pfam11498 151935 Activator_LAG-3 Transcriptional activator LAG-3. The C.elegans Notch pathway, involved in the control of growth, differentiation and patterning in animal development, relies on either of the receptors GLP-1 or LIN-12. Both these receptors promote signalling by the recruitment of LAG-3 to target promoters, where it then acts as a transcriptional activator. LAG-3 works as a ternary complex together with the DNA binding protein, LAG-1. Its N-terminal region adopts an elongated kinked helix that is required for complex assembly. 476 matched cddid_all.tbl CDD pfam11500 pfam11500 402896 Cut12 Cut12 conserved domain. This is the central coiled-coil region of the spindle pole body-associated protein cut12 also found in other fungi, barring S. cerevisiae. The full protein has two predicted coiled-coil regions, and one consensus phosphorylation site for p34cdc2 and two for MAP kinase. During fission yeast mitosis, the duplicated spindle pole bodies (SPBs) nucleate microtubule arrays that interdigitate to form the mitotic spindle. Cut12 is localized to the SPB throughout the cell cycle, predominantly around the inner face of the interphase SPB, adjacent to the nucleus. Cut12 associates with Fin1 and is important in this context for the activity of Plo1. 149 matched cddid_all.tbl CDD pfam11501 pfam11501 431911 bCoV_NSP1 Betacoronavirus replicase NSP1. This entry represents the non structural protein NSP1 from Betacoronavirus NSP1 is the N-terminal cleavage product from the viral replicase that mediates RNA replication and processing. Structurally, the protein consists of a mixed parallel/antiparallel 6-stranded beta barrel with an alpha helix covering one end of the barrel and another helix alongside the barrel. NSP1 binds to the 40S ribosomal subunit and inhibits translation, and it also induces a template-dependent endonucleolytic cleavage of host mRNAs. NSP1 also suppresses the host innate immune functions by inhibiting type I interferon expression and host antiviral signalling pathways. 138 matched cddid_all.tbl CDD pfam11502 pfam11502 431912 BCL9 B-cell lymphoma 9 protein. The Wnt pathway plays a role in embryonic development, stem cell growth and tumorigenesis. BCL9 associates with beta-catenin and Tcf in the nucleus when the Wnt pathway is stimulated leading to the transactivation of Wnt target genes. 37 matched cddid_all.tbl CDD pfam11503 pfam11503 371567 DUF3215 Protein of unknown function (DUF3215). This family of proteins with unknown function appears to be restricted to Saccharomycetaceae. 72 matched cddid_all.tbl CDD pfam11504 pfam11504 314418 Colicin_Ia Colicin Ia. Colicins are toxic molecules secreted to kill other bacteria in times of stress. Colicin Ia kills susceptible E.coli cells by binding to the colicin I receptor leading to the formation of a voltage-dependant ion channel. The protein can be divided into three domains, a translocation domain, a receptor binding domain and a channel forming domain. 72 matched cddid_all.tbl CDD pfam11505 pfam11505 402898 DUF3216 Protein of unknown function (DUF3216). This family of archaeal proteins with unknown function appears to be restricted ton Thermococcaceae. 91 matched cddid_all.tbl CDD pfam11506 pfam11506 402899 DUF3217 Protein of unknown function (DUF3217). This family of proteins with unknown function appears to be restricted to Mycoplasma. Some members in this family of proteins are annotated as MG376 however this cannot be confirmed. 104 matched cddid_all.tbl CDD pfam11507 pfam11507 402900 Transcript_VP30 Ebola virus-specific transcription factor VP30. VP30 is a nucleocapsid-associated Ebola virus-specific transcription factor. It acts by stabilising nascent mRNA in Ebola virus replication. The C terminal domain of VP30 folds into a dimeric helical assembly. VP30 assembles into hexamers in solution by an N-terminal oligomerization domain which activates the transcription function of the protein. The oligomerization is mediated by hydrophobic amino acids at 94-112. 131 matched cddid_all.tbl CDD pfam11508 pfam11508 402901 DUF3218 Protein of unknown function (DUF3218). This family of proteins with unknown function appears to be restricted to Pseudomonas. 213 matched cddid_all.tbl CDD pfam11510 pfam11510 288377 FA_FANCE Fanconi Anaemia group E protein FANCE. Fanconi Anaemia (FA) is a cancer predisposition disorder. In response to DNA damage, the FA core complex monoubiquitinates the downatream FANCD2 protein. The protein FANCE has an important role in DNA repair as it is the FANCD2-binding protein in the FA core complex so it represents the link between the FA core complex and FANCD2. The sequence shown is the C terminal domain of the protein which consists predominantly of helices and does not contain any beta-strand. The fold of the polypeptide is a continuous right-handed solenoidal pattern from the N terminal to the C terminal end. 262 matched cddid_all.tbl CDD pfam11511 pfam11511 314420 RhodobacterPufX Intrinsic membrane protein PufX. PufX organizes RC-LH1, the photosynthesis reaction centre-light harvesting complex 1 core complex of Rhodobacter sphaeroides. It also facilitates the exchange of quinol for quinone between the reaction centre and cytochrome bc(1) complexes. In organic solvent, PufX contains two hydrophobic helices which are flanked by unstructured regions and connected by a helical bend. 67 matched cddid_all.tbl CDD pfam11512 pfam11512 431913 Atu4866 Agrobacterium tumefaciens protein Atu4866. Atu4866 is a protein with unknown function from Agrobacterium tumefaciens however the structure has been determined. Atu4866 adopts a streptavidin-like fold and has a beta-barrel/sandwich which is formed by eight antiparallel beta-strands. Atu4866 has a potential ligand-binding site where is has a stretch of conserved residues on the surface. 75 matched cddid_all.tbl CDD pfam11513 pfam11513 314422 TA0956 Thermoplasma acidophilum protein TA0956. TA0956 is a protein from Thermoplasma acidophilum which currently has no known function however the structure has been determined. The protein has a two-layered alpha/beta-sandwich topology and is a putative Elongation factor 1-alpha binding motif. 110 matched cddid_all.tbl CDD pfam11514 pfam11514 402902 DUF3219 Protein of unknown function (DUF3219). This family of proteins with unknown function appears to be restricted to Bacillaceae. Some members in this family of proteins are annotated as YkvR however this cannot be confirmed. 94 matched cddid_all.tbl CDD pfam11515 pfam11515 463286 Cul7 Mouse development and cellular proliferation protein Cullin-7. The Cullin Ring Ligase family member, Cul7, is required for normal mouse development and cellular proliferation. Cul7 has a CPH domain which is a p53 interaction domain. The CPH domain interaction surface of P53 is present in the tetramerization domain. 78 matched cddid_all.tbl CDD pfam11516 pfam11516 151953 DUF3220 Protein of unknown function (DUF3120). This family of proteins with unknown function appears to be restricted to Bordetella. 106 matched cddid_all.tbl CDD pfam11517 pfam11517 402904 Nab2 Nuclear abundant poly(A) RNA-bind protein 2 (Nab2). Nab2 is a yeast heterogeneous nuclear ribonucleoprotein that modulates poly(A) tail length and mRNA. This is the N terminal domain of the protein which mediates interactions with the C-terminal globular domain, Myosin-like protein 1 and the mRNA export factor, Gfd1.The N-terminal domain of Nab2 shows a structure of a helical fold. The N terminal domain of Nab2 is thought to mediate protein protein interactions that facilitate the nuclear export of mRNA. An essential hydrophobic Phe73 patch on the N terminal domain is thought to be a important component of the interface between Nab2 and Mlp1. 101 matched cddid_all.tbl CDD pfam11518 pfam11518 431915 DUF3221 Protein of unknown function (DUF3221). This family of proteins with unknown function appears to be restricted to Bacillus. Some members in this family of proteins are annotated as YobA however this cannot be confirmed. YobA is a protein with unknown function. 82 matched cddid_all.tbl CDD pfam11519 pfam11519 402906 DUF3222 Protein of unknown function (DUF3222). This family of proteins with unknown function appears to be restricted to Rhodopseudomonas. 75 matched cddid_all.tbl CDD pfam11520 pfam11520 402907 Cren7 Chromatin protein Cren7. Cren7 is a chromatin protein found in Crenarchaeota and has a higher affinity for double-stranded DNA than for single-stranded DNA. The protein contains negative DNA supercoils and is associated with genomic DNA in vivo.Cren7 interacts with duplex DNA through a beta-sheet and a long flexible loop. The function has not been completely determined but it is thought that the protein may have a role similar to that of archaeal proteins in Euryarchaea. 55 matched cddid_all.tbl CDD pfam11521 pfam11521 463287 TFIIE-A_C C-terminal general transcription factor TFIIE alpha. TFIIE is compiled of two subunits, alpha and beta. This family of proteins are the C terminal domain of the alpha subunit of the protein which is the largest subunit and contains several functional domains which are important for basal transcription and cell growth. The C terminal end of the protein binds directly to the amino-terminal PH domain of p62/Tfb1 (of IIH) which is involved in the recruitment of the general transcription factor IIH to the transcription preinitiation complex. P53 competes for the same binding site as TFIIE alpha which shows their structural similarity. Like p53, TFIIE alpha 336-439 can activate transcription in vivo. 85 matched cddid_all.tbl CDD pfam11522 pfam11522 402909 Pik1 Yeast phosphatidylinositol-4-OH kinase Pik1. Pik1 is a regulator of membrane traffic and participates in the mating-pheromone signal-transduction cascade. The protein is localized to the nucleus and cytoplasm in the Golgi. Pik1 is thought to have an actin-independent role in membrane transport. 50 matched cddid_all.tbl CDD pfam11523 pfam11523 431917 DUF3223 Protein of unknown function (DUF3223). This family of proteins has no known function. 75 matched cddid_all.tbl CDD pfam11524 pfam11524 314430 SeleniumBinding Selenium binding protein. Selenium is an important nutrient that needs to be regulated since lack of the nutrient leads to cell abnormalities and high concentrations are toxic. SeBP regulates the level of free selenium in the cell by sequestering the nutrient during transport. SeBP acts as a pentamer and delivers the selenium to the selenophosphate synthetase enzyme. Each subunit is composed of an alpha helix on top of a four stranded twisted ss sheet, stabilized by hydrogen bonds. 82 matched cddid_all.tbl CDD pfam11525 pfam11525 431918 CopK Copper resistance protein K. CopK is a periplasmic dimeric protein which is strongly up-regulated in the presence of copper, leading to a high periplasmic accumulation. CopK has two different binding sites for Cu(I), each with a different affinity for the metal. Binding of the first Cu(I) ion induces a conformational change of CopK which involves dissociation of the dimeric apo-protein. Binding of a second Cu(I) further increases the plasticity of the protein. CopK has features that are common with functionally related proteins such as a structure consisting of an all-beta fold and a methionine-rich Cu(I) binding site. 70 matched cddid_all.tbl CDD pfam11526 pfam11526 431919 CFIA_Pcf11 Subunit of cleavage factor IA Pcf11. Pcf11 is a subunit of an essential polyadenylation factor in Saccharomyces cerevisiae, CFIA. Pcf11 binds to Clp1, another subunit of CFIA whose interaction is responsible for maintaining a tight coupling between the Clp1 nucleotide binding subunit and the other components of the polyadenylation machinery. 83 matched cddid_all.tbl CDD pfam11527 pfam11527 463288 ARL2_Bind_BART The ARF-like 2 binding protein BART. BART binds specifically to ARL2.GTP with a high affinity however it does not bind to ARL2.GDP. It is thought that this specific interaction is due to BART being the first identified ARL2-specific effector. The function is not completely characterized. BART is predominantly cytosolic but can also be found to be associated with mitochondria. BART is also involved in binding to the adenine nucleotide transporter ANT1. 115 matched cddid_all.tbl CDD pfam11528 pfam11528 431921 DUF3224 Protein of unknown function (DUF3224). This bacterial family of proteins has no known function. 124 matched cddid_all.tbl CDD pfam11529 pfam11529 151966 AvrL567-A Melampsora lini avirulence protein AvrL567-A. AvrL567-A is a protein from the fungal pathogen flax which induces plant disease resistance in flax plants. The protein has a novel fold. 127 matched cddid_all.tbl CDD pfam11530 pfam11530 288394 Pilin_PilX Minor type IV pilin, PilX. PilX is a protein from Neisseria meningitidis which is crucial for the formation of bacterial aggregates and adhesion to human cells. The structure of PilX is similar to all pilins as it has the common alpha/beta roll fold. PilX subunits have surface-exposed motifs which are thought to stabilize bacterial aggregates against pilus retraction. It also illustrates how a minor pilus component can modulate the virulence properties of pili which have a simple composition and structure. 127 matched cddid_all.tbl CDD pfam11531 pfam11531 402914 CARM1 Coactivator-associated arginine methyltransferase 1 N terminal. CARM1 is an arginine methyltransferase which methylates a variety of different proteins and plays a role in gene expression. This is the N terminal domain of the protein which has a PH domain, normally present to regulate protein-protein interactions.A molecular switch is also present on the N terminal domain. 105 matched cddid_all.tbl CDD pfam11532 pfam11532 463289 HnRNP_M_NLS HnRNP M nuclear localization signal. This entry represents the nuclear localization signal of HnRNP M a splicing regulatory factor. 30 matched cddid_all.tbl CDD pfam11533 pfam11533 431923 DUF3225 Protein of unknown function (DUF3225). This bacterial family of proteins has no known function. 126 matched cddid_all.tbl CDD pfam11534 pfam11534 431924 HTHP Hexameric tyrosine-coordinated heme protein (HTHP). HTHP is from the marine bacterium Silicibacter pomeroyi and has peroxidase and catalase activity. HTHP consists of six monomers which each binds a solvent accessible heme group and is stabilized by the interaction of three neighbouring monomers. The heme iron is penta-coordinated with a tyrosine residue as proximal ligand. 71 matched cddid_all.tbl CDD pfam11535 pfam11535 402918 Calci_bind_CcbP Calcium binding. CcbP is a Ca(2+) binding protein which, in Anabaena, is thought to bind Ca(2+) by protein surface charge. When bound to Ca(2+), the protein becomes more compact and the level of free calcium decreases. The free Ca(2+) concentration which is regulated by CcbP is critical for the differentiation process. Calcium signalling is widespread in bacterial species, and prokaryotic cells like eukaryotes are equipped with all the elements to maintain Ca2+ homeostasis. 105 matched cddid_all.tbl CDD pfam11536 pfam11536 463290 DUF3226 Protein of unknown function (DUF3226). This archaeal family of proteins has no known function. 212 matched cddid_all.tbl CDD pfam11537 pfam11537 371589 NitrOD5 Nitrosopumilus output domain 5. NitrOD5 (Nitrosopumilus output domain 5) is found in thaumarchaea, either in stand-alone form or in combination with the Response_reg pfam00072 domain (Galperin et al., 2018, Phyletic distribution and lineage-specific domain architectures of archaeal two-component signal transduction systems). 93 matched cddid_all.tbl CDD pfam11538 pfam11538 402920 Snurportin1 Snurportin1. Snurportin1 is a novel nuclear import receptor which contains an N-terminal importin beta binding domain which is essential for its function of a snRNP-specific nuclear import receptor. Snurportin1 interacts with m3G-cap where it enhances the m3G-cap dependent nuclear import of U snRNPs in Xenopus laevis oocytes and digitonin-permeabilized HeLa cells. 40 matched cddid_all.tbl CDD pfam11539 pfam11539 402921 DUF3228 Protein of unknown function (DUF3228). This family of proteins has no known function. 192 matched cddid_all.tbl CDD pfam11540 pfam11540 463291 Dynein_IC2 Cytoplasmic dynein 1 intermediate chain 2. Intermediate chain IC 2 forms part of the complex cytoplasmic dynein 1 along with a heavy chain (HC), two light intermediate chains (LICs) and three light chains (LCs). The complex is responsible for hydrolysing ATP to generate force toward the minus end of microtubules. IC binds to the HC via the N terminal binding domain on the HC and ICs contain binding sites for the LCs. The ICs are responsible for binding to kinetochores and the Golgi apparatus through an interaction with the p150Glued subunit of dynactin which is another complex. 31 matched cddid_all.tbl CDD pfam11542 pfam11542 402923 Mdv1 Mitochondrial division protein 1. Mdv1 is a component of the mitochondrial fission machinery in Saccharomyces cerevisiae. The protein is also involved in peroxisome proliferation. Mdv1 along with Fis1 is also involved in controlling Dnm-1 dependant devision, a GTPase involved in the mediation of mitochondrial division. In this role, Mdv1 is the linker between Fis1 and Dnm1. Mdv1 plays a key role in the regulation of Dnm1 self-assembly. 49 matched cddid_all.tbl CDD pfam11543 pfam11543 431926 UN_NPL4 Nuclear pore localization protein NPL4. Npl4 is part of the heterodimer UN along with Ufd1 which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert. 80 matched cddid_all.tbl CDD pfam11544 pfam11544 402925 Spc42p Spindle pole body component Spc42p. Spc42p is a 42-kD component of the S.cerevisiae spindle body that localizes to the electron dense central region of the SPB.Spc42p is a phosphoprotein which forms a polymeric layer at the periphery of the SPB central plaque. This functions during SPB duplication and also facilitates the attachment of the SPB to the nuclear membrane. 72 matched cddid_all.tbl CDD pfam11545 pfam11545 463292 HemeBinding_Shp Cell surface heme-binding protein Shp. Shp is part of a complex which functions in heme uptake in Streptococcus pyogenes. During which, Shp transfers its heme to HtsA which is a component of an ABC transporter. The heme binding region of Shp contains an immunoglobulin-like beta-sandwich fold and has a unique heme-iron coordination with the axial ligands being two methionine residues from the same Shp molecule. Surrounding the heme pocket, there is a negative surface which may serve as a docking interface for heme transfer. 148 matched cddid_all.tbl CDD pfam11546 pfam11546 371594 CompInhib_SCIN Staphylococcal complement inhibitor SCIN. SCIN is released by Staphylococcus aureus to counteract the host immune defense. The protein binds to and inhibits C3 convertases on the bacterial surface, reducing phagocytosis and blocking downstream effector functions by C3b deposition on its surface. An 18 residue stretch 31-48 is crucial for SCIN activity. 114 matched cddid_all.tbl CDD pfam11547 pfam11547 431928 E3_UbLigase_EDD E3 ubiquitin ligase EDD. EDD, the ER ubiquitin ligase from the HECT ligases, contains an N-terminal ubiquitin-associated domain which binds ubiquitin. Ubiquitin is recognized by helices alpha-1 and -3 in in the UBA domain. EDD is involved in DNA damage repair pathways and binds to mono-ubiquitinated proteins. 52 matched cddid_all.tbl CDD pfam11548 pfam11548 463293 Receptor_IA-2 Protein-tyrosine phosphatase receptor IA-2. IA-2 is a protein-tyrosine phosphatase receptor that upon exocytosis, the cytoplasmic domain is cleaved and moves to the nucleus where it enhances transcription of the insulin gene. The mature exodomain of IA-2 participates in adhesion to the extracellular matrix and is self-proteolyzed in vitro by reactive oxygen species which may be a new shedding mechanism. 89 matched cddid_all.tbl CDD pfam11549 pfam11549 431930 Sec31 Protein transport protein SEC31. Sec31 is involved in COPII coat formation as it forms through the sequential binding of three cytoplasmic proteins: Sar1, Sec23/24 and Sec13/31. Sec13/31 is recruited by the pre-budding complex and polymerization of Sec13/31 occurs to form an octahedral cage that is the outer shell of the COPII coat. Sec13/31 is a hetero-tetramer which is organized as a linear array of alpha-solenoid and beta-propeller domains to form a rod in which twenty-four copies assemble to form the COPII cub-octahedron. 50 matched cddid_all.tbl CDD pfam11550 pfam11550 402929 IglC Intracellular growth locus C protein. IglC protein is involved in the escape of F.tularensis live vaccine strain. It has been shown that the expression of IglC is essential for F.tularensis to induce macrophage apoptosis. IglC adopts a beta-sandwich conformation that has no similarity to any known protein structure. 210 matched cddid_all.tbl CDD pfam11551 pfam11551 431931 Omp28 Outer membrane protein Omp28. Omp28 is a 28-kDa outer membrane protein from Porphyromonas gingivalis. Omp28 is thought to be a surface adhesion/receptor protein. Omp28 is expressed in a wide distribution of P.gingivalis strains. 171 matched cddid_all.tbl CDD pfam11553 pfam11553 402931 DUF3231 Protein of unknown function (DUF3231). This bacterial family of proteins has no known function. 161 matched cddid_all.tbl CDD pfam11554 pfam11554 402932 DUF3232 Protein of unknown function (DUF3232). This bacterial family of proteins has no known function. 151 matched cddid_all.tbl CDD pfam11555 pfam11555 463294 Inhibitor_Mig-6 EGFR receptor inhibitor Mig-6. When the kinase domain of EGFR binds to segment one of Mitogen induced gene 6 (Mig-6), EGFR becomes inactive due to the conformation it adopts which is Src/CDK like. The binding of the two proteins prevents EGFR acting as a cyclin-like activator for other kinase domains.The structure of Mig-6(1) consists of alpha helices-G and -H with a polar surface and hydrophobic residues for interactions with EGFR. A critical step for the activation of EGFR is the formation of an asymmetric dimer involving the kinase domains of the protein. Since Mig-6 binds to the kinase domain it blocks this process and EGFR becomes inactive. 74 matched cddid_all.tbl CDD pfam11556 pfam11556 431933 EBA-175_VI Erythrocyte binding antigen 175. EBA-175 is involved in the formation of a tight junction, a necessary step in invasion. This family represents the region VI which is a cysteine rich domain essential for EBA-175 trafficking. The structure is a homodimer that contains a five-alpha-helical core stabilized by four disulphide bridges. 81 matched cddid_all.tbl CDD pfam11557 pfam11557 371601 Omp_AT Solitary outer membrane autotransporter beta-barrel domain. Omp_AT is a family of Gram-negative Gamma-proteobacteria outer membrane autotransporter beta-barrel proteins. Secondary structure prediction indicates a beta-barrel domain of 12 beta-strands. with an N terminal helix running along the central barrel axis perpendicular to the 12 antiparallel strands that form the barrel. Autotransporter translocation units defined by a beta-barrel of 12 to 14 antiparallel strands with an N terminal helix perpendicular to the barrel. 327 matched cddid_all.tbl CDD pfam11558 pfam11558 402935 HET-s_218-289 Het-s 218-289. This family of proteins is residues 218-289 of Het-s, a protein of Podospora anserina. Het-s plays a role in heterokaryon incompatibility which prevents different forms of parasitism. This region of the protein is the C-terminal end and is unstructured in solution but forms infectious fibrils in vitro which has a structure consisting of a left-handed beta solenoid which contains two windings per molecule. 61 matched cddid_all.tbl CDD pfam11559 pfam11559 463295 ADIP Afadin- and alpha -actinin-Binding. This family is found in mammals where it is localized at cell-cell adherens junctions, and in Sch. pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins localized at Cell-Cell Adherens Junctions. 151 matched cddid_all.tbl CDD pfam11560 pfam11560 371604 LAP2alpha Lamina-associated polypeptide 2 alpha. LAPs are components of the nuclear lamina which supports the nuclear envelope.LAP2alpha is a non-membrane-associated member of the LAP family which is unique. This family of proteins is the C terminal domain of LAP2alpha which consists of residues 459-693 and constitutes a dimeric structure with an antiparallel coiled coil. LAP2alpha is involved in cell-cycle regulation and chromatin organization and preferentially binds to lamin A/C. 234 matched cddid_all.tbl CDD pfam11561 pfam11561 371605 Saw1 Single strand annealing-weakened 1. This family of yeast proteins is involved in single-strand-annealing, or SSA. SSA entails multiple steps: end resection and ssDNA formation; annealing of complementary ssDNAs; removal of 3' single-stranded non-homologous tails; gap fill-in synthesis; and ligation. Saw1 in combination with Slx4 catalyzes the 3' non-homologous tail removal during recombination. Saw1 interacts physically with Rad1/Rad10, Msh2/Msh3, and Rad52 proteins, and works by targeting Rad1/Rad10 to Rad52-coated recombination intermediates. 244 matched cddid_all.tbl CDD pfam11563 pfam11563 431935 Protoglobin Protoglobin. This family includes protoglobin from Methanosarcina acetivorans C2A. It is also found near the N-terminus of the Haem-based aerotactic transducer HemAT in Bacillus subtilis. It is part of the haemoglobin superfamily. Protoglobin has specific loops and an amino-terminal extension which leads to the burying of the haem within the matrix of the protein. Protoglobin-specific apolar tunnels allow the access of O2, CO and NO to the haem distal site. In HemAT it acts as an oxygen sensor domain. It can also recognize cyanide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 149 matched cddid_all.tbl CDD pfam11564 pfam11564 402938 BpuJI_N Restriction endonuclease BpuJI - N terminal. BpuJI is a restriction endonuclease which recognizes the asymmetric sequence 5'-CCCGT and cuts at multiple sites in the surrounding area of the target sequence. This family of proteins is the N terminal domain of BpuJI which has DNA recognition functions. The recognition domain has two subdomains D1 and D2. The recognition of the target sequence occurs through major groove contacts of amino acids on the helix-turn-helix region and the N-terminal arm. 278 matched cddid_all.tbl CDD pfam11565 pfam11565 288422 PorB Alpha helical Porin B. Porin B is a porin from Corynebacterium glutamicum which allows the exchange of material across the mycolic acid layer which is the protective nonpolar barrier. Porin B has an alpha helical core structure consisting of four alpha-helices surrounding a nonpolar interior. There is a disulphide bridge between helices 1 and 4 to form a stable covalently bound ring. The channel of PorB is oligomeric. 99 matched cddid_all.tbl CDD pfam11566 pfam11566 463296 PI31_Prot_N PI31 proteasome regulator N-terminal. PI31 is a regulatory subunit of the immuno-proteasome which is an inhibitor of the 20 S proteasome in vitro.PI31 is also an F-box protein Fbxo7.Skp1 binding partner which requires an N terminal FP domain in both proteins for the interaction to occur via the FP beta sheets. The structure of PI31 FP domain contains a novel alpha/beta-fold and two intermolecular contact surfaces. This is the N-terminal domain of the members. 156 matched cddid_all.tbl CDD pfam11567 pfam11567 402940 PfUIS3 Plasmodium falciparum UIS3 membrane protein. UIS3 is a membrane protein essential for sporozoite development in infected hepatocytes. This family is 130-229 of the Plasmodium falciparum UIS3 protein which is compact and has an all alpha-helical structure.PfUIS3(130-229) interacts with lipids, phospholipid lysosomes, the human liver fatty acid-binding protein and with the lipid phosphatidylethanolamine. The interaction with liver fatty acid-binding protein provides the parasite with a method to import essential fatty acids/lipids during rapid growth phases of sporozoites. 101 matched cddid_all.tbl CDD pfam11568 pfam11568 431937 Med29 Mediator complex subunit 29. Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-active part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med29, along with Med11 and Med28, in mammals, is part of the core head-region of the complex. Med29 is the apparent orthologue of the Drosophila melanogaster Intersex protein, which interacts directly with, and functions as a transcriptional coactivator for, the DNA-binding transcription factor Doublesex, so it is likely that mammalian Med29 serves as a target for one or more DNA-binding transcriptional activators. 138 matched cddid_all.tbl CDD pfam11569 pfam11569 463297 Homez Homeodomain leucine-zipper encoding, Homez. Homez contains two leucine zipper-like motifs and an acidic domain and belongs to the superfamily of homeobox-containing proteins. The presence of leucine zippers suggests that Homez can function as a homo or heterodimer in the nucleus. It is thought that the first leucine zipper and homeodomain 1 (HD1)of Homez is responsible for dimerization and HD2 has a specific DNA-binding activity. Homez is also thought to function as a transcriptional repressor due to the acidic region in its C-terminal domain. Homez is involved in a complex regulatory network. 57 matched cddid_all.tbl CDD pfam11570 pfam11570 314459 E2R135 Coiled-coil receptor-binding R-domain of colicin E2. E2 is a DNase which utilizes the outer membrane receptor BtuB to bind to and enter the cell. This family of proteins is E2R135 (residues 321-443) which is the part of E2 which is responsible for binding to BtuB in a coiled coil formation. 136 matched cddid_all.tbl CDD pfam11571 pfam11571 463298 Med27 Mediator complex subunit 27. Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells. 85 matched cddid_all.tbl CDD pfam11572 pfam11572 402943 DUF3234 Protein of unknown function (DUF3234). This bacterial family of proteins has no known function. Some members in this family of proteins are annotated as TTHA0547 however this cannot be confirmed. 95 matched cddid_all.tbl CDD pfam11573 pfam11573 463299 Med23 Mediator complex subunit 23. Med23 is one of the subunits of the Tail portion of the Mediator complex that regulates RNA polymerase II activity. Med23 is required for heat-shock-specific gene expression, and has been shown to mediate transcriptional activation of E1A in mice. 1301 matched cddid_all.tbl CDD pfam11574 pfam11574 431940 Rpf1_C Resuscitation-promoting factor Rpf1, C-terminal. This is the C-terminal domain of Resuscitation-promoting factor Rpf1 from Corynebacterium glutamicum, which is adjacent the RPF domain (pfam06737). The function of this domain is not yet known. Rpf1 has peptidoglycan hydrolytic activity and stimulates resuscitation of dormant cells. 83 matched cddid_all.tbl CDD pfam11575 pfam11575 431941 FhuF_C FhuF 2Fe-2S C-terminal domain. This family consists of several bacterial ferric iron reductase protein (FhuF) sequences. FhuF is involved in the reduction of ferric iron in cytoplasmic ferrioxamine B. This domain is the C-terminal domain that contains 4 conserved cysteine residues that are found to be part of a 2Fe-2S cluster. 21 matched cddid_all.tbl CDD pfam11576 pfam11576 402947 HcgB FeGP cofactor biosynthesis protein HcgB, guanylyltransferase. This entry represents the guanylyltransferase component of the Iron-guanylylpyridinol (FeGP) cofactor biosynthesis protein HcgB. This family of proteins with unknown function appears to be restricted to Methanobacteria. 152 matched cddid_all.tbl CDD pfam11577 pfam11577 431942 NEMO NF-kappa-B essential modulator NEMO. NEMO is a regulatory protein which is part of the IKK complex along with the catalytic IKKalpha and beta kinases. The IKK complex phosphorylates IkappaB targeting it for degradation which results in the release of NF-kappaB which initiates the inflammatory response, cell proliferation or cell differentiation. NEMO activates the IKK complex's activity by associating with the unphosphorylated IKK kinase C termini.The core domain of NEMO is a dimer which binds to two fragments of IKK. 67 matched cddid_all.tbl CDD pfam11578 pfam11578 463300 DUF3237 Protein of unknown function (DUF3237). This family of proteins has no known function 149 matched cddid_all.tbl CDD pfam11579 pfam11579 314467 DUF3238 Protein of unknown function (DUF3238). This family of proteins with unknown function appears to be restricted to Bacillus cereus. 192 matched cddid_all.tbl CDD pfam11580 pfam11580 431944 DUF3239 Protein of unknown function (DUF3239). This bacterial family of proteins may be membrane proteins however this cannot be confirmed. Currently there is no known function. 125 matched cddid_all.tbl CDD pfam11581 pfam11581 371613 Argos Antagonist of EGFR signalling, Argos. Argos is a natural secreted antagonist of EGFR signalling which functions by binding growth factor ligands that activate EGFR by forming a clamp like structure using three disulphide-bonded beta-sheet domains. 129 matched cddid_all.tbl CDD pfam11582 pfam11582 431945 DUF3240 Protein of unknown function (DUF3240). This family of proteins with unknown function appears to be restricted to Proteobacteria. 102 matched cddid_all.tbl CDD pfam11583 pfam11583 431946 AurF P-aminobenzoate N-oxygenase AurF. This family is a metalloenzyme which is involved in the biosynthesis of antibiotic aureothin by catalysing the formation of p-nitrobenzoic acid from p-aminobenzoic acid. AurF is a non-heme di-iron monooxygenase which creates nitroarenes via the sequential oxidation of aminoarenes. 279 matched cddid_all.tbl CDD pfam11584 pfam11584 402951 Toxin_ToxA Proteinaceous host-selective toxin ToxA. ToxA is produced by particular Pyrenophora tritici-repentis races and is a proteinaceous host-selective toxin. It is necessary and sufficient to cause cell death in sensitive wheat cultivars.ToxA adopts a single-domain, beta-sandwich fold which has novel topology. The protein is directly involved in recognition events required for ToxA action. It is thought to be distantly related to FnIII proteins, gaining entry to the host via an integrin-like receptor. 117 matched cddid_all.tbl CDD pfam11585 pfam11585 431947 Stomoxyn Insect antimicrobial peptide, stomoxyn. Stomoxyn, localized in the gut epithelium, is an insect antimicrobial peptide which functions in killing a range of microorganizms, parasites and some viruses. Stomoxyn has a structure consisting of a random coil in water however in TFE it adopts a stable helical structure. Stomoxyn is thought to have a similar function to cecropin A from Hyalophora cecropia due to structural similarities. 40 matched cddid_all.tbl CDD pfam11586 pfam11586 402952 DUF3242 Protein of unknown function (DUF3242). This protein from Thermotoga maritima is a hypothetical ORFan protein, TM1622, whose structure has been determined. The protein is composed of seven beta strands and three alpha helices. 125 matched cddid_all.tbl CDD pfam11587 pfam11587 463301 Prion_bPrPp Major prion protein bPrPp - N terminal. This family represents the N-terminal domain (1-30) of the bovine prion protein (bPrPp). The proteins structure consists of mainly alpha helices. BPrPp forms a stable helix which inserts in a transmembrane location in the bilayer, with the N -terminal (1-30) functioning as a cell-penetrating peptide. 30 matched cddid_all.tbl CDD pfam11588 pfam11588 431948 DUF3243 Protein of unknown function (DUF3243). This family of proteins with unknown function appears to be restricted to Firmicutes. 79 matched cddid_all.tbl CDD pfam11589 pfam11589 431949 DUF3244 Domain of unknown function (DUF3244). This domain adopts an immunoglobulin-like beta-sandwich fold and structurally is most similar to fibronectin. 100 matched cddid_all.tbl CDD pfam11590 pfam11590 314473 DNAPolymera_Pol DNA polymerase catalytic subunit Pol. This family of proteins represents the catalytic subunit, Pol, of the Herpes simplex virus DNA polymerase. Pol binds UL42, making up the DNA polymerase. UL42 is a processivity subunit which binds to the C-terminal of Pol in a similar way that the cell cycle regulator p21 binds to PCNA. 36 matched cddid_all.tbl CDD pfam11591 pfam11591 152027 2Fe-2S_Ferredox Ferredoxin chloroplastic transit peptide. The structure of chloroplast ferredoxin in water is unstructured however in a 30:70 molar-ratio mixture of 2,2,2-trifluoroethanol, residues 3 to 13 form an alpha-helix. The rest of the peptide remains unstructured. This family is the N-terminal of the [2Fe-2S] ferredoxin from C.reinhardtii. This protein catalyzes the final reaction in a pathway which allows the production of H(2) from water in the chloroplast. 34 matched cddid_all.tbl CDD pfam11592 pfam11592 288446 AvrPto Central core of the bacterial effector protein AvrPto. This family of proteins represents the bacterial effector protein AvrPto from Pseudomonas syringae. This is the central core region of the protein which consists of a three-helix bundle motif. AvrPto is part of a type III secretion system from P.syringae which is involved in the bacterial speck disease of tomato. In resistant plants, AvrPto interacts with the host Pto kinase, which elicits an antibacterial defense response. In plants lacking resistance, the Pto kinase is not present and AvrPto acts as a virulence factor, promoting bacterial growth. 105 matched cddid_all.tbl CDD pfam11593 pfam11593 402954 Med3 Mediator complex subunit 3 fungal. Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Mediator subunit Hrs1/Med3 is a physical target for Cyc8-Tup1, a yeast transcriptional co-repressor. 398 matched cddid_all.tbl CDD pfam11594 pfam11594 463302 Med28 Mediator complex subunit 28. Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours. 101 matched cddid_all.tbl CDD pfam11595 pfam11595 371618 DUF3245 Protein of unknown function (DUF3245). This is a family of proteins conserved in fungi. The function is not known, and there is no S. cerevisiae member. 148 matched cddid_all.tbl CDD pfam11596 pfam11596 371619 DUF3246 Protein of unknown function (DUF3246). This is a small family of fungal proteins one of whose members, Swiss:A3LUS4 from Pichia stipitis is described as being an extremely serine rich protein-mucin-like protein. 241 matched cddid_all.tbl CDD pfam11597 pfam11597 463303 Med13_N Mediator complex subunit 13 N-terminal. Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med13 is part of the ancillary kinase module, together with Med12, CDK8 and CycC, which in yeast is implicated in transcriptional repression, though most of this activity is likely attributable to the CDK8 kinase. The large Med12 and Med13 proteins are required for specific developmental processes in Drosophila, zebrafish, and Caenorhabditis elegans but their biochemical functions are not understood. 314 matched cddid_all.tbl CDD pfam11598 pfam11598 463304 COMP Cartilage oligomeric matrix protein. This family of proteins represents the five-stranded coiled-coil domain of cartilage oligomeric matrix protein (COMP). This region has a binding site between two internal rings formed by Leu37 and Thr40 43 matched cddid_all.tbl CDD pfam11599 pfam11599 431953 AviRa RRNA methyltransferase AviRa. This family of proteins represents the methyltransferase AviRa from Streptomyces viridochromogenes. This protein mediates the resistance to the antibiotic avilamycin. AviRa methylates a specific guanine base within the peptidyl-transferase loop of the 23S ribosomal RNA. 232 matched cddid_all.tbl CDD pfam11600 pfam11600 402959 CAF-1_p150 Chromatin assembly factor 1 complex p150 subunit, N-terminal. CAF-1_p150 is a polypeptide subunit of CAF-1, which functions in depositing newly synthesized and acetylated histones H3/H4 into chromatin during DNA replication and repair. CAF-1_p150 includes the HP1 interaction site, the PEST, KER and ED interacting sites. CAF-1_p150 interacts directly with newly synthesized and acetylated histones through the acidic KER and ED domains. The PEST domain is associated with proteins that undergo rapid proteolysis. 164 matched cddid_all.tbl CDD pfam11601 pfam11601 463305 Shal-type Shal-type voltage-gated potassium channels, N-terminal. This family represents the short N-terminal helical domain of Shal-type voltage-gated potassium channels. The domain interacts with Kv channel-interacting proteins to modulate cell surface expression and the function of Kv4 channels. The interaction of the N-terminus of Shal-type protein Kv4.2 and the Kv interacting protein KChiP1 forms a structure which is like the structure between calmodulin and its target peptides when they interact. Interactions of an N terminal alpha helix in Kv4.2 and a C terminal alpha helix in KChIP1 are essential for the modulation of Kv4.2 by KChIPs. 28 matched cddid_all.tbl CDD pfam11602 pfam11602 402961 NTPase_P4 ATPase P4 of dsRNA bacteriophage phi-12. P4 is a packaging motor which is involved in the packaging of phi-12 genome into preformed capsids using ATP. P4 is located at the vertices of the icosahedral capsid. ATP drives RNA translocation through cooperative conformational changes. 320 matched cddid_all.tbl CDD pfam11603 pfam11603 431955 Sir1 Sir1, ORC-binding domain. This entry represents the ORC-binding domain of Sir1. Sir1 interacts with the BAH domain of the Orc1 subunit of the origin recognition complex (ORC) resulting in the establishment of silent chromatin at HMR and HML in S.cerevisiae. The amino acids from the ORC interaction region of Sir1 are presented on a conserved, convex surface that forms a complementary interface with the Orc1 BAH domain, critical for transcriptional silencing. Proteins containing this domain also include Y' element ATP-dependent helicase protein 1, which catalyzes DNA unwinding and is involved in telomerase-independent telomere maintenance. 120 matched cddid_all.tbl CDD pfam11604 pfam11604 463306 CusF_Ec Copper binding periplasmic protein CusF. CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein. 68 matched cddid_all.tbl CDD pfam11605 pfam11605 402964 Vps36_ESCRT-II Vacuolar protein sorting protein 36 Vps36. Vps36 is a subunit of ESCRT-II, a protein involved in driving protein sorting from endosomes to lysosomes. The GLUE domain of Vps36 allows for a tight interaction to occur between the protein and Vps28, a subunit of ESCRT-I. This interaction is critical for ubiquitinated cargo progression from early to late endosomes. 92 matched cddid_all.tbl CDD pfam11606 pfam11606 152042 AlcCBM31 Family 31 carbohydrate binding protein. This family of proteins represents the family 31 carbohydrate-binding module of beta-1,2-xylanase. This protein is from Alcaligenes sp. strain XY-234. The AlcCBM31 module makes a beta-sandwich structure with an immunoglobulin fold and contains two intra-molecular disulfide bonds. AlcCBM31 shows affinity with only beta-1,3-xylan. 93 matched cddid_all.tbl CDD pfam11607 pfam11607 402965 DUF3247 Protein of unknown function (DUF3247). This family of proteins is the protein product of the gene XC5848 from Xanthomonas campestris. The protein has no known function however its structure has been determined. The protein adopts a Lsm fold however differences with the fold were observed at the N-terminal and internal regions. 92 matched cddid_all.tbl CDD pfam11608 pfam11608 463307 MARF1_RRM1 MARF1, RNA recognition motif 1. MARF1 (also known as Limkain-b1) is an essential protein for controlling meiosis and retrotransposon surveillance in mouse oocytes, first described as a human autoantigen localized to a subset of ABCD3 and PXF marked peroxisomes. It may function both as an adaptor to recruit specific RNA targets and an effector to catalyze the specific cleavages of target RNAs. MARF1 contains an N-terminal NYN domain, two central RRMs, and C-terminal OST-HTH/LOTUS domains. This domain represents the RNA recognition motif 1 (RRM1) of MARF1. 89 matched cddid_all.tbl CDD pfam11609 pfam11609 431957 DUF3248 Protein of unknown function (DUF3248). This family of proteins is thought to be the product of the gene TT1592 from Thermus thermophilus however this cannot be confirmed. Currently there is no known function. 62 matched cddid_all.tbl CDD pfam11610 pfam11610 402967 Ste5 Scaffold protein Ste5, Fus3-binding region. This family of proteins represents the Fus3 binding region of Ste5. Ste5 functions in the yeast mating pathway and is required for signalling through the mating response MAPK pathway. Ste5 has separate binding sites for each member of the MAPK cascade. This region of Ste5 allosterically activates autophosphroylation of Fus3, a mitogen-activated protein kinase. Auto-activated Fus3 has a negative regulatory role, and promotes Ste5 phosphorylation which leads to a decrease in pathway transcriptional output. 30 matched cddid_all.tbl CDD pfam11611 pfam11611 431958 DUF4352 Domain of unknown function (DUF4352). Members of these family are putative lipoproteins that fall into the Antigen MPT63/MPB63 (immunoprotective extracellular protein) superfamily. 125 matched cddid_all.tbl CDD pfam11612 pfam11612 431959 T2SSJ Type II secretion system (T2SS), protein J. The T2SJ proteins are pseudopilins, which are targeted to the membrane in E. Coli. T2SJ forms a complex with T2SI (pfam02501) and T2SK (pfam03934) which is part of the Type II secretion apparatus involved in the translocation of proteins across the outer membrane in E.coli. The T2SK-I-J complex has quasihelical characteriztics. 137 matched cddid_all.tbl CDD pfam11614 pfam11614 431960 FixG_C IG-like fold at C-terminal of FixG, putative oxidoreductase. This domain is part of a transmembrane protein, FixG, itself part of the FixGHIS operon closely associated with the FixNOPQ operon that is the symbiotically essential cbb3-type haem-copper oxidase complex. FixG expression is induced by oxygen-deprivation. This C-terminal domain adopts an E-set Ig-like fold. 116 matched cddid_all.tbl CDD pfam11615 pfam11615 402971 Caf4 CCR4-associated factor 4. Caf4 is a WD40 repeats containing protein involved in mitochondrial fission. It displays physical interactions with CCR4-NOT complex. It has a paralogue, Mdv1. Both Caf4 and Mdv1 act as adapter proteins, binding to Fis1 on the mitochondrial outer membrane and recruiting the dynamin-like GTPase Dnm1 to form mitochondrial fission complexes. However, Fis1 and Caf4, but not Mdv1, determine the polar localization of Dnm1 clusters on the mitochondrial surface. 60 matched cddid_all.tbl CDD pfam11616 pfam11616 463308 EZH2_WD-Binding WD repeat binding protein EZH2. This family of proteins represents Enhancer of zest homolog 2, (EZH2) a 30 residue peptide which binds to a WD-repeat domain of EED by residues 39-68. EED is a component of PRC2 complex which is involved in gene expression. This interaction is required for the HMTase activity of PCR2. 30 matched cddid_all.tbl CDD pfam11617 pfam11617 463309 Cu-binding_MopE Putative metal-binding motif. The seqeunce of structure 2vov is not matched in any other sequence either in UniProt or in NCBI (Sep2014). The model is of a short repeat not found on the G1UBC6 - 2vov - protein. The presence of conserved cysteine residues and the lack of hydrophobic residues suggests that this repeat might be a metal-binding site, perhaps for zinc or calcium ions. 28 matched cddid_all.tbl CDD pfam11618 pfam11618 463310 C2-C2_1 First C2 domain of RPGR-interacting protein 1. This domain is the first, more N-terminal, C2 domain on X-linked retinitis pigmentosa GTPase regulator-interacting proteins, or RPGR-interacting proteins. 143 matched cddid_all.tbl CDD pfam11619 pfam11619 314489 P53_C Transcription factor P53 - C terminal domain. This family of proteins is the C terminal domain of the transcription factor P53. While the rest of the protein is quite conserved between the different transcription factors such as p53 and p73, the C terminal domain is highly divergent. The DM-p53 structure is characterized by an additional N-terminal beta-strand and a C-terminal helix. 67 matched cddid_all.tbl CDD pfam11620 pfam11620 463311 GABP-alpha GA-binding protein alpha chain. This family of proteins represents the transcription factor GABP alpha. This alpha domain is a five-stranded beta-sheet crossed by a distorted helix termed an OST domain. The surface of the GABP alpha OST domain contains two clusters of negatively-charged residues suggesting there are positively-charged partner proteins. The OST domain binds to the CH1 and CH3 domains of the co-activator histone acetyltransferase CBP/p300, a direct link between GABP and transcriptional machinery has been made. 81 matched cddid_all.tbl CDD pfam11621 pfam11621 288473 Sbi-IV C3 binding domain 4 of IgG-bind protein SBI. This family of proteins represents Sbi domain IV which binds the central complement protein C3. Sbi-IV interacts with Sbi-III to induce a consumption of complement via alternative pathway activation. When not interacting with Sbi-III, Sbi-IV inhibits the alternative pathway without complement consumption. The structure of Sbi-IV consists of a three-helix bundle fold. 69 matched cddid_all.tbl CDD pfam11622 pfam11622 402976 DUF3251 Protein of unknown function (DUF3251). This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. This domain is found in a group of bacterial lipoproteins such as YajI from E.coli and SadB from Salmonella typhimurium. SadB is required for proper surface expression of the autotransporter adhesin SadA. 156 matched cddid_all.tbl CDD pfam11623 pfam11623 431964 NdhS NAD(P)H dehydrogenase subunit S. This family is found in Bacteria and Streptophyta includes members such as NdhS (NAD(P)H-quinone oxidoreductase subunit S). NdhS, also known as CRR31 (chlororespiratory reduction 31), is a subunit of the chloroplast NADH dehydrogenase-like (NDH) complex. It is also a subunit of the cyanobacterial NDH-1 complex. NAD(P)H-oxidizing subunits have not been found in chloroplasts or cyanobacteria, where ferredoxin is probably the electron donor. NdhS contributes to the formation of a ferredoxin binding site of NDH and is necessary for high affinity binding of ferredoxin. The cyanobacterial NDH-1 complex, also known as NADPH:plastoquinone oxidoreductase or type I NAD(P)H dehydrogenase, is involved in plastoquinone reduction and cyclic electron transfer (CET) around photosystem I. The chloroplast NDH is more similar to cyanobacterial NDH-1, which is believed to be the origin of chloroplast NDH, than to mitochondrial NADH dehydrogenase present in the same species. The NDH complexes of chloroplasts, however, contain many subunits that are absent from cyanobacterial NDH-1 complexes. 52 matched cddid_all.tbl CDD pfam11624 pfam11624 402978 M157 MHC class I-like protein M157. This family of proteins represents M157,a divergent form of MHC class I-like proteins which is the protein product of the mouse cytomegalovirus. This protein is unique in its ability to engage both activating (Ly49H) and inhibitory (Ly49I) natural killer cell receptors. M157 is involved in intra- and intermolecular interacts within and between its domains to form a compact MHC-like molecule. 247 matched cddid_all.tbl CDD pfam11625 pfam11625 431965 DUF3253 Protein of unknown function (DUF3253). This bacterial family of proteins has no known function. 80 matched cddid_all.tbl CDD pfam11626 pfam11626 431966 Rap1_C TRF2-interacting telomeric protein/Rap1 - C terminal domain. This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C terminal domain. Rap1 is otherwise known as TRF2-interacting protein, as it is one of the six subunit components of the Shelterin complex. Shelterin protects telomere ends from attack by DNA-repair mechanisms. Model doesn't capture Sch. pombe as it cuts this sequence into two. 82 matched cddid_all.tbl CDD pfam11627 pfam11627 463312 HnRNPA1 Nuclear factor hnRNPA1. This family of proteins represents hnRNPA1, a nuclear factor that binds to Pol II transcripts. The family of hnRNP proteins are involved in numerous RNA-related activities. 38 matched cddid_all.tbl CDD pfam11628 pfam11628 463313 TCR_zetazeta T-cell surface glycoprotein CD3 zeta chain. The incorporation of the zetazeta signalling module requires one basic TCR alpha and two zetazeta aspartic acid TM residues. The structure of the zetazeta(TM) dimer consists of a left-handed coiled coil with polar contacts. Two aspartic acids are critical for zetazeta dimerization and assembly with TCR. 31 matched cddid_all.tbl CDD pfam11629 pfam11629 463314 Mst1_SARAH C terminal SARAH domain of Mst1. This family of proteins represents the C terminal SARAH domain of Mst1. SARAH controls apoptosis and cell cycle arrest via the Ras, RASSF, MST pathway. The Mst1 SARAH domain interacts with Rassf1 and Rassf5 by forming a heterodimer which mediates the apoptosis process. 48 matched cddid_all.tbl CDD pfam11630 pfam11630 152066 Anti-LPS-SCYG Anti-lipopolysaccharide factor/Scygonadin. Anti-lipopolysaccharide factor binds to bacterial LPS and may specifically inhibit the LPS-mediated activation of the hemolymph coagulation. It has a strong antibacterial effect, especially on the growth of Gram-negative bacteria. This entry also includes the antibacterial protein Scygonadin, which has antibacterial activity against the Gram-positive bacterium Micrococcus luteus. 97 matched cddid_all.tbl CDD pfam11631 pfam11631 288482 DUF3255 Protein of unknown function (DUF3255). Members in this family of proteins are annotated as YxeF however no function is currently known. The family appears to be restricted to Bacillus. 123 matched cddid_all.tbl CDD pfam11632 pfam11632 402984 LcnG-beta Lactococcin G-beta. This family of proteins is LcnG-beta, which with LcnG-alpha constitute the two-peptide bacteriocin lactococcin G (LcnG). This family of proteins represents the N terminal domain which has an alpha-helical structure and is amphiphilic. Both peptides have a GxxxG motif which they use for interaction through a helix-helix structure. 61 matched cddid_all.tbl CDD pfam11633 pfam11633 431970 bCoV_SUD_M Betacoronavirus single-stranded poly(A) binding domain. This domain identifies non-structural protein NSP3, the product of ORF1a in group 2 coronavirus. It is found in human SARS coronavirus polyprotein 1a and 1ab, and in related coronavirus polyproteins. NSP3 binds to viral RNA, nucleocapsid protein, as well as other viral proteins, and participates in polyprotein processing. The domain exhibits a macrodomain fold containing the nsp3 residues 528 to 648, with a flexibly extended N-terminal tail from residues 513 to 527 and a C-terminal flexible tail of residues 649 to 651. SUD-M(527-651) binds single-stranded poly(A); the contact area with this RNA on the protein surface, and the electrophoretic mobility shift assays confirm that SUD-M has higher affinity for purine bases than for pyrimidine bases. 126 matched cddid_all.tbl CDD pfam11634 pfam11634 288483 IPI_T4 Nuclease inhibitor from bacteriophage T4. This family of proteins represents IPI from bacteriophage T4. This protein is a nuclease inhibitor which is injected by T4 to protect its DNA from gmrS/gmrD CT of pathogenic Escherichia coli into the infected host. The structure of this protein consists of two small beta-sheets flanked by N and C termini by alpha-helices. The protein has a gmrS/gmrD hydrophobic binding site. 76 matched cddid_all.tbl CDD pfam11635 pfam11635 371639 Med16 Mediator complex subunit 16. Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med16 is one of the subunits of the Tail portion of the Mediator complex and is required for lipopolysaccharide gene-expression. Several members including the human protein, Swiss:Q9Y2X0, have one or more WD40 domains on them, pfam00400. 755 matched cddid_all.tbl CDD pfam11636 pfam11636 463315 Troponin-I_N Troponin I residues 1-32. This family of proteins represents the cardiac N-extension of troponin I. This region of the protein (1-32) interacts with the N-lobe of cTnC and modulates myofilament calcium(2) sensitivity. 32 matched cddid_all.tbl CDD pfam11637 pfam11637 402985 UvsW-1 UvsW.1 domain. This domain represents the UvsW.1 domain that is typically encoded by the gene adjacent to that of phage UvsW-like SF2 helicases. UvsW.1 features a trihelical bundle fold that is related to other nucleic acid binding domains such as the HRDC domain of the RecQ helicases. 56 matched cddid_all.tbl CDD pfam11638 pfam11638 463316 DnaA_N DnaA N-terminal domain. This family of proteins represents the N-terminal domain of DnaA, a protein involved in the initiation of bacterial chromosomal replication. The structure of this domain is known. It is also found in three copies in some proteins. The exact function of this domain is uncertain but it has been suggested to play a role in oligomerization. 65 matched cddid_all.tbl CDD pfam11639 pfam11639 402987 HapK REDY-like protein HapK. This family of proteins represents HapK, a protein of unknown function, with two homologs PigK and RedY. The monomer structure of the protein contains a four-stranded anti parallel beta-sheet, three alpha-helices and a short C terminal tail which it uses for dimer formation. The surface of HapK has a deep cavity with consists of a kinked helix and a beta-four strand. HapK could be involved in prodigiosin biosynthesis, specifically the binding of a bipyrrole intermediate such as HBM or MBM. 103 matched cddid_all.tbl CDD pfam11640 pfam11640 463317 TAN Telomere-length maintenance and DNA damage repair. ATM is a large protein kinase, in humans, critical for responding to DNA double-strand breaks (DSBs). Tel1, the orthologue from budding yeast, also regulates responses to DSBs. Tel1 is important for maintaining viability and for phosphorylation of the DNA damage signal transducer kinase Rad53 (an orthologue of mammalian CHK2). In addition to functioning in the response to DSBs, numerous findings indicate that Tel1/ATM regulates telomeres. The overall domain structure of Tel1/ATM is shared by proteins of the phosphatidylinositol 3-kinase (PI3K)-related kinase (PIKK) family, but this family carries a unique and functionally important TAN sequence motif, near its N-terminal, LxxxKxxE/DRxxxL. which is conserved specifically in the Tel1/ATM subclass of the PIKKs. The TAN motif is essential for both telomere length maintenance and Tel1 action in response to DNA damage. It is classified as an EC:2.7.11.1. 150 matched cddid_all.tbl CDD pfam11641 pfam11641 152077 Antigen_Bd37 Glycosylphosphatidylinositol-anchored merozoite surface protein. This family of proteins represents the core region of Bd37, a surface antigen of B.divergens which is GPI-anchored at the surface of the merozoite. The structure of the protein consists of mainly alpha folds and has three sub domains. 224 matched cddid_all.tbl CDD pfam11642 pfam11642 402989 Blo-t-5 Mite allergen Blo t 5. This family of proteins is Blo t 5, an allergen protein from Blomia tropicalis mites. This protein shoes strong reactivity with IgE in asthmatic and rhinitis patients. The structure of the protein contains three alpha helices which form a coiled-coil. 118 matched cddid_all.tbl CDD pfam11644 pfam11644 431974 DUF3256 Protein of unknown function (DUF3256). This family of proteins with unknown function appears to be restricted to Bacteroidales. 195 matched cddid_all.tbl CDD pfam11645 pfam11645 431975 PDDEXK_5 PD-(D/E)XK endonuclease. This family of endonucleases includes a group I intron-encoded endonuclease. This family belongs to the PD-(D/E)XK superfamily. 136 matched cddid_all.tbl CDD pfam11646 pfam11646 431976 DUF3258 Protein of unknown function DUF3258. This viral family are possible phage integrase proteins however this cannot be confirmed. 115 matched cddid_all.tbl CDD pfam11647 pfam11647 431977 MLD Membrane Localization Domain. This is a membrane localization domain found in multiple families of bacterial toxins including all of the clostridial glucosyltransferase toxins and various MARTX toxins (multifunctional-autoprocessing RTX toxins). In the Pasteurella multocida toxin (PMT) C-terminal fragment, structural analysis have indicated that the C1 domain possesses a signal that leads the toxin to the cell membrane. Furthermore, the C1 domain was found to structurally resemble the phospholipid-binding domain of C. difficile toxin B. Functional studies in Vibrio cholera indicate that the subdomain at the N terminus of RID (Rho-inactivation domain), homologous to the membrane targeting C1 domain of Pasteurella multocida toxin, is a conserved membrane localization domain essential for proper localization. The Rho-inactivation domain (RID) of MARTX (Multifunctional Autoprocessing RTX toxin) is responsible for inactivating the Rho-family of small GTPases in Vibrio cholerae. It is a bacterial toxin that self-process by a cysteine peptidase mechanism. The Vibrio cholerae RTX toxin is an autoprocessing cysteine protease whose activity is stimulated by the intracellular environment. This cysteine peptidase belongs to MEROPS peptidase family G6. 81 matched cddid_all.tbl CDD pfam11648 pfam11648 463318 RIG-I_C-RD C-terminal domain of RIG-I. This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependant dimerization. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity. 117 matched cddid_all.tbl CDD pfam11649 pfam11649 288494 T4_neck-protein Virus neck protein. This family of protein represents gene product 14, a major component of the neck in T4-like viruses along with gene product 13. Gene product 14 is rich is beta-sheets. The formation of the neck to the head of the bacteriophage is crucial for the tail attachment. 254 matched cddid_all.tbl CDD pfam11650 pfam11650 402995 P22_Tail-4 P22 tail accessory factor. This tail accessory factor of the P22 virus is also referred to as gene product 4 (Gp4). The proteins structure consists of 60% alpha helices. Gp4 is the first tail accessory factor to be added to newly DNA-filled capsids during P22-morphogenesis. In solution, the protein acts as a monomer and has low structural stability. The interaction of gp4 with the portal protein involves the binding of two non-equivalent sets of six gp4 proteins. Gp4 acts as a structural adaptor for gp10 and gp26, the other tail accessory factors. 148 matched cddid_all.tbl CDD pfam11651 pfam11651 431979 P22_CoatProtein P22 coat protein - gene protein 5. This family of proteins represents gene product 5 from bacteriophage P22. This protein is involved in the formation of the pro-capsid shells in the bacteriophage. In total, there are 415 molecules of the coat protein which are arranged in an icosahedral shell. 417 matched cddid_all.tbl CDD pfam11652 pfam11652 463319 FAM167 FAM167. This entry describes a eukaryotic protein family of unknown function designated FAM167. 84 matched cddid_all.tbl CDD pfam11653 pfam11653 314509 VirionAssem_T7 Bacteriophage T7 virion assembly protein. This family of proteins represents the gene product 7.3 from T7 bacteriophage. The protein is localized to the tail and is thought to be important in virion assembly. Particles assembled in the absence of the protein fail to adsorb to cells. 99 matched cddid_all.tbl CDD pfam11654 pfam11654 402998 NCE101 Non-classical export protein 1. This entry represents the non classical export protein 1 family. Family members are Involved in a novel pathway of export of proteins that lack a cleavable signal sequence. 45 matched cddid_all.tbl CDD pfam11655 pfam11655 431981 DUF2589 Protein of unknown function (DUF2589). This family of proteins has no known function. 159 matched cddid_all.tbl CDD pfam11656 pfam11656 431982 DUF3811 YjbD family (DUF3811). This is a family of proteobacteria proteins of unknown function. This family is unrelated to pfam03960 which contains a set of transcription factors that are also named YjbD. 88 matched cddid_all.tbl CDD pfam11657 pfam11657 431983 Activator-TraM Transcriptional activator TraM. TraM is required for quorum dependence. It binds to and in-activates TraR which controls the replication of the tumour-inducing virulence plasmid. TraM interacts in a two-step process with DNA-TraR to form a large, stable anti-activation complex. 142 matched cddid_all.tbl CDD pfam11658 pfam11658 463320 CBP_BcsG "Cellulose biosynthesis protein BcsG. CBP_BcsG is a family of bacterial cellulose biosynthesis proteins. Cellulose is necessary for biofilm formation in bacteria. (Roemling U. and Galperin M.Y. ""Bacterial cellulose biosynthesis. Diversity of operons and subunits"" (manuscript in preparation))." 516 matched cddid_all.tbl CDD pfam11659 pfam11659 431985 DUF3261 Protein of unknown function (DUF3261). This family of proteins with unknown function appears to be restricted to Proteobacteria. The family is related to the LolB family suggesting a role in lipoprotein insertion in the outer membrane. 140 matched cddid_all.tbl CDD pfam11660 pfam11660 431986 DUF3262 Protein of unknown function (DUF3262). This family of proteins with unknown function appears to be restricted to Proteobacteria. 75 matched cddid_all.tbl CDD pfam11661 pfam11661 431987 DUF2986 Protein of unknown function (DUF2986). This family of proteins has no known function. 43 matched cddid_all.tbl CDD pfam11662 pfam11662 431988 DUF3263 Protein of unknown function (DUF3263). This family of proteins with unknown function appears to be restricted to Actinobacteria. 74 matched cddid_all.tbl CDD pfam11663 pfam11663 431989 Toxin_YhaV Toxin with endonuclease activity, of toxin-antitoxin system. YhaV causes reversible bacteriostasis and is part of a toxin-antitoxin system in Escherichia coli along with PrlF. The toxicity of YhaV is counteracted by PrlF by the formation of a tight complex which binds to the promoter of the prlF-yhaV operon. In vitro, YhaV also has endonuclease activity. 138 matched cddid_all.tbl CDD pfam11665 pfam11665 431990 DUF3265 Protein of unknown function (DUF3265). This family of proteins with unknown function appear to be restricted to Vibrio. 28 matched cddid_all.tbl CDD pfam11666 pfam11666 431991 DUF2933 Protein of unknown function (DUF2933). This bacterial family of proteins has no known function. 50 matched cddid_all.tbl CDD pfam11667 pfam11667 431992 DUF3267 Putative zincin peptidase. This family of proteins has a conserved HEXXH motif, suggesting the members are putative peptidases of zincin fold. 106 matched cddid_all.tbl CDD pfam11668 pfam11668 288512 Gp_UL130 HCMV glycoprotein pUL130. This family of proteins represents pUL130 from Human cytomegalovirus, a glycoprotein secreted from infected cells that is incorporated into the virion envelope as a Golgi-matured form. The protein promotes endothelial cell infection through a producer cell modification of the virion. 159 matched cddid_all.tbl CDD pfam11669 pfam11669 463321 WBP-1 WW domain-binding protein 1. This family of proteins represents WBP-1, a ligand of the WW domain of Yes-associated protein. This protein has a proline-rich domain. WBP-1 does not bind to the SH3 domain. 102 matched cddid_all.tbl CDD pfam11670 pfam11670 371661 MSP1a Major surface protein 1a (MSP1a). MSP1a is part of the A.marginale major surface protein 1 (MSP1) complex and exists as a heterodimer with MSP1b. The complex has adhesive functions in bovine erythrocytes invasion. 252 matched cddid_all.tbl CDD pfam11671 pfam11671 152107 Apis_Csd Complementary sex determiner protein. This family of proteins represents the complementary sex determiner in the honeybee. In the honeybee, the mechanism of sex determination depends on the csd gene which produces an SR-type protein. Males are homozygous while females are homozygous for the csd gene. Heterozygosity generates an active protein which initiates female development. 146 matched cddid_all.tbl CDD pfam11672 pfam11672 431994 DUF3268 zinc-finger-containing domain. This is a family of bacterial and plasmid sequences that carry at least one zinc-finger towards the N-terminus and a possible second at the C-terminus. 117 matched cddid_all.tbl CDD pfam11673 pfam11673 288515 DUF3269 Protein of unknown function (DUF3269). This family of proteins has no known function. 73 matched cddid_all.tbl CDD pfam11674 pfam11674 431995 DUF3270 Protein of unknown function (DUF3270). This family of proteins with unknown function appears to be restricted to Streptococcus. 88 matched cddid_all.tbl CDD pfam11675 pfam11675 403011 DUF3271 Protein of unknown function (DUF3271). This family of proteins with unknown function appears to be restricted to Plasmodium. 248 matched cddid_all.tbl CDD pfam11676 pfam11676 431996 DUF3272 Protein of unknown function (DUF3272). This family of proteins with unknown function appears to be restricted to Streptococcus. 61 matched cddid_all.tbl CDD pfam11677 pfam11677 403013 DUF3273 Protein of unknown function (DUF3273). Some members in this family of proteins are annotated as multi-transmembrane proteins however this cannot be confirmed. Currently this family has no known function. 265 matched cddid_all.tbl CDD pfam11678 pfam11678 371665 DUF3274 Protein of unknown function (DUF3274). This bacterial family of proteins has no known function. 286 matched cddid_all.tbl CDD pfam11679 pfam11679 431997 DUF3275 Protein of unknown function (DUF3275). This family of proteins with unknown function appear to be restricted to Proteobacteria. 207 matched cddid_all.tbl CDD pfam11680 pfam11680 431998 DUF3276 Protein of unknown function (DUF3276). This bacterial family of proteins has no known function. 128 matched cddid_all.tbl CDD pfam11681 pfam11681 431999 KPP10_Orf10 Bacteriophage KPP10, Structural protein ORF10. This family is represented by Bacteriophage KPP10, Structural protein ORF10, whose function is unknown. The characteriztics of the protein distribution suggest prophage matches in addition to the phage matches. 144 matched cddid_all.tbl CDD pfam11682 pfam11682 288524 zinc_ribbon_11 Probable zinc-ribbon. This family of proteins with unknown function appears to be restricted to Enterobacteriaceae. It is a probably zinc-ribbon. 127 matched cddid_all.tbl CDD pfam11683 pfam11683 371668 DUF3278 Protein of unknown function (DUF3278). This bacterial family of proteins has no known function. 127 matched cddid_all.tbl CDD pfam11684 pfam11684 432000 DUF3280 Protein of unknown function (DUF2380). This family of proteins with unknown function appears to be restricted to Proteobacteria. 133 matched cddid_all.tbl CDD pfam11685 pfam11685 314533 DUF3281 Protein of unknown function (DUF3281). This family of bacterial proteins has no known function. 267 matched cddid_all.tbl CDD pfam11686 pfam11686 432001 DUF3283 Protein of unknown function (DUF3283). This family of proteins with unknown function appears to be restricted to Proteobacteria. 61 matched cddid_all.tbl CDD pfam11687 pfam11687 463322 DUF3284 Domain of unknown function (DUF3284). This family of proteins with unknown function appears to be restricted to Firmicutes. 115 matched cddid_all.tbl CDD pfam11688 pfam11688 432003 DUF3285 Protein of unknown function (DUF3285). This family of proteins with unknown function appears to be restricted to Cyanobacteria. 44 matched cddid_all.tbl CDD pfam11690 pfam11690 314536 DUF3287 Protein of unknown function (DUF3287). This eukaryotic family of proteins has no known function. 121 matched cddid_all.tbl CDD pfam11691 pfam11691 432004 DUF3288 Protein of unknown function (DUF3288). This family of proteins with unknown function appears to be restricted to Cyanobacteria. 88 matched cddid_all.tbl CDD pfam11692 pfam11692 432005 DUF3289 Protein of unknown function (DUF3289). This family of proteins with unknown function appears to be restricted to Proteobacteria. 272 matched cddid_all.tbl CDD pfam11693 pfam11693 403022 DUF2990 Protein of unknown function (DUF2990). This family of proteins represents a fungal protein with unknown function. 62 matched cddid_all.tbl CDD pfam11694 pfam11694 432006 DUF3290 Protein of unknown function (DUF3290). This family of proteins with unknown function appears to be restricted to Firmicutes. 144 matched cddid_all.tbl CDD pfam11695 pfam11695 432007 DUF3291 Domain of unknown function (DUF3291). This bacterial family of proteins has no known function. 136 matched cddid_all.tbl CDD pfam11696 pfam11696 432008 DUF3292 Protein of unknown function (DUF3292). This eukaryotic family of proteins has no known function. 648 matched cddid_all.tbl CDD pfam11697 pfam11697 432009 DUF3293 Protein of unknown function (DUF3293). This bacterial family of proteins has no known function. 73 matched cddid_all.tbl CDD pfam11698 pfam11698 432010 V-ATPase_H_C V-ATPase subunit H. The yeast Saccharomyces cerevisiae vacuolar H+-ATPase (V-ATPase) is a multisubunit complex responsible for acidifying organelles. It functions as an ATP dependent proton pump that transports protons across a lipid bilayer. This domain corresponds to the C terminal domain of the H subunit of V-ATPase. The N-terminal domain is required for the activation of the complex whereas the C-terminal domain is required for coupling ATP hydrolysis to proton translocation. 117 matched cddid_all.tbl CDD pfam11699 pfam11699 403028 CENP-C_C Mif2/CENP-C like. CENP-C_C is a C-terminal family of fungal and eukaryote proteins necessary for centromere formation. CENP-C is the inner-kinetochore centromere (CEN) binding protein. In the budding-yeast, Mif2, the yeast homolog, binds in the CDEIII region of the centromere, and has been shown to recruit a substantial subset of all inner and outer kinetochore proteins. Mif2 adopts a cupin fold and is extremely similar both in polypeptide chain conformation and in dimer geometry to the dimerization domain of a bacterial transcription factor. The Mif2 dimer appears to be part of an enhanceosome-like structure that nucleates kinetochore assembly in budding yeast. This C-terminal domain is the region via which CENP-C localizes to centromeres throughout the cell cycle 2,3]. 85 matched cddid_all.tbl CDD pfam11700 pfam11700 371676 ATG22 Vacuole effluxer Atg22 like. Autophagy is a major survival survival mechanism in which eukaryotes recycle cellular nutrients during stress conditions. Atg22, Avt3 and Avt4 are partially redundant vacuolar effluxes, which mediate the efflux of leucine and other amino acids resulting from autophagy. This family also includes other transporter proteins. 479 matched cddid_all.tbl CDD pfam11701 pfam11701 432011 UNC45-central Myosin-binding striated muscle assembly central. The UNC-45 or small muscle protein 1 of C.elegans is expressed in two forms from different genomic positions in mammals, as a general tissue protein UNC-45a and a specific form Unc-45b expressed only in striated and skeletal muscle. All members carry up to three amino-terminal tetratricopeptide repeat (TPR) domains towards their N-terminal, a UCS domain at the C-terminal that contains a number of Arm repeats pfam00514 and this central region of approximately 400 residues. Both the general form and the muscle form of UNC-45 function in myotube formation through cell fusion. Myofibril formation requires both GC and SM UNC-45, consistent with the fact that the cytoskeleton is necessary for the development and maintenance of organized myofibrils. The S. pombe Rng3p, is crucial for cell shape, normal actin cytoskeleton, and contractile ring assembly, and is essential for assembly of the myosin II-containing progenitors of the contractile ring. Widespread defects in the cytoskeleton are found in null mutants of all three fungal proteins. Mammalian Unc45 is found to act as a specific chaperone during the folding of myosin and the assembly of striated muscle by forming a stable complex with the general chaperone Hsp90. The exact function of this central region is not known. 151 matched cddid_all.tbl CDD pfam11702 pfam11702 403030 DUF3295 Protein of unknown function (DUF3295). This family is conserved in fungi but the function is not known. 489 matched cddid_all.tbl CDD pfam11703 pfam11703 403031 UPF0506 UPF0506. This uncharacterized family is found in Schistosoma genomes. Although uncharacterized it appears to belong to the knottin fold. The sequence is composed of two repeats of a 6 cysteine motif. 59 matched cddid_all.tbl CDD pfam11704 pfam11704 463323 Folliculin Vesicle coat protein involved in Golgi to plasma membrane transport. In yeast cells this family functions in the regulated delivery of Gap1p (a general amino acid permease) to the cell surface, perhaps as a component of a post-Golgi secretory-vesicle coat complex. Birt-Hogg-Dube (BHD)4 syndrome is an autosomal dominant disorder characterized by hamartomas of skin follicles, lung cysts, spontaneous pneumothorax, and renal cell carcinoma. Folliculin is the protein from the BHD4 gene and is found to have no significant homology to any other human proteins. It is expressed in most tissues. These same symptoms also occur in TSC or tuberous sclerosis complex, suggesting that the same pathway is involved, and it is likely that the target is the down-stream Tor2 - an essential gene. Folliculin appears to bind Tor2, and down-regulation of Tor2 activity leads to up-regulation of nitrogen responsive genes including membrane transporters and amino acid permeases. 163 matched cddid_all.tbl CDD pfam11705 pfam11705 463324 RNA_pol_3_Rpc31 DNA-directed RNA polymerase III subunit Rpc31. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA pol III-specific, and form the functionally distinct groups (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in S.cerevisiae and H.sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain. 213 matched cddid_all.tbl CDD pfam11706 pfam11706 432014 zf-CGNR CGNR zinc finger. This family consists of a C-terminal zinc finger domain. It seems likely to be DNA-binding given the conservation of many positively charged residues. The domain is named after a highly conserved motif found in many members of the family. 44 matched cddid_all.tbl CDD pfam11707 pfam11707 463325 Npa1 Ribosome 60S biogenesis N-terminal. Npa1p is required for ribosome biogenesis and operates in the same functional environment as Rsa3p and Dbp6p during early maturation of 60S ribosomal subunits. The protein partners of Npa1p include eight putative helicases as well as the novel Npa2p factor. Npa1p can also associate with a subset of H/ACA and C/D small nucleolar RNPs (snoRNPs) involved in the chemical modification of residues in the vicinity of the peptidyl transferase centre. The protein has also been referred to as Urb1, and this domain at the N-terminal is one of several conserved regions along the length. 332 matched cddid_all.tbl CDD pfam11708 pfam11708 463326 Slu7 Pre-mRNA splicing Prp18-interacting factor. The spliceosome, an assembly of snRNAs (U1, U2, U4/U6, and U5) and proteins, catalyzes the excision of introns from pre-mRNAs in two successive trans-esterification reactions. Step 2 depends upon integral spliceosome constituents such as U5 snRNA and Prp8 and non-spliceosomal proteins Prp16, Slu7, Prp18, and Prp22. ATP hydrolysis by the DEAH-box enzyme Prp16 promotes a conformational change in the spliceosome that leads to protection of the 3'ss from targeted RNase H cleavage. This change, which probably reflects binding of the 3'ss PyAG in the catalytic centre of the spliceosome, requires the ordered recruitment of Slu7, Prp18, and Prp22 to the spliceosome. There is a close functional relationship between Prp8, Prp18, and Slu7, and Prp18 interacts with Slu7, so that together they recruit Prp22 to the spliceosome. Most members of the family carry a zinc-finger of the CCHC-type upstream of this domain. 258 matched cddid_all.tbl CDD pfam11709 pfam11709 463327 Mit_ribos_Mrp51 Mitochondrial ribosomal protein subunit. This family is the mitochondrial ribosomal small-subunit protein Mrp51. Its function is not entirely clear, but deletion of the MRP51 gene completely blocked mitochondrial gene expression. 358 matched cddid_all.tbl CDD pfam11710 pfam11710 371685 Git3 G protein-coupled glucose receptor regulating Gpa2. Git3 is one of six proteins required for glucose-triggered adenylate cyclase activation, and is a G protein-coupled receptor responsible for the activation of adenylate cyclase through Gpa2 - heterotrimeric G protein alpha subunit, part of the glucose-detection pathway. Git3 contains seven predicted transmembrane domains, a third cytoplasmic loop and a cytoplasmic tail. This is the conserved N-terminus of these proteins, and the C-terminal conserved region is now in family Git3_C. 201 matched cddid_all.tbl CDD pfam11711 pfam11711 463328 Tim54 Inner membrane protein import complex subunit Tim54. Mitochondrial function depends on the import of hundreds of different proteins synthesized in the cytosol. Protein import is a multi-step pathway which includes the binding of precursor proteins to surface receptors, translocation of the precursor across one or both mitochondrial membranes, and folding and assembly of the imported protein inside the mitochondrion. Most precursor proteins carry amino-terminal targeting signals, called pre-sequences, and are imported into mitochondria via import complexes located in both the outer and the inner membrane (IM). The IM complex, TIM, is made up of at least two proteins which mediate translocation of proteins into the matrix by removing their signal peptide and another pair of proteins, Tim54 and Tim22, that insert the polytopic proteins, that carry internal targetting information, into the inner membrane. 374 matched cddid_all.tbl CDD pfam11712 pfam11712 463329 Vma12 Endoplasmic reticulum-based factor for assembly of V-ATPase. The yeast vacuolar proton-translocating ATPase (V-ATPase) is the best characterized member of the V-ATPase family. A total of thirteen genes are required for encoding the subunits of the enzyme complex itself and an additional three for providing factors necessary for the assembly of the whole. Vma12 is one of these latter, all three of which are localized to the endoplasmic reticulum. 139 matched cddid_all.tbl CDD pfam11713 pfam11713 288550 Peptidase_C80 Peptidase C80 family. This family belongs to cysteine peptidase family C80. 152 matched cddid_all.tbl CDD pfam11714 pfam11714 152150 Inhibitor_I53 Thrombin inhibitor Madanin. Members of this family are the peptidase inhibitor madanin proteins. These proteins were isolated from tick saliva. 78 matched cddid_all.tbl CDD pfam11715 pfam11715 432020 Nup160 Nucleoporin Nup120/160. Nup120 is conserved from fungi to plants to humans, and is homologous with the Nup160 of vertebrates. The nuclear core complex, or NPC, mediates macromolecular transport across the nuclear envelope. Deletion of the NUP120 gene causes clustering of NPCs at one side of the nuclear envelope, moderate nucleolar fragmentation and slower cell growth. The vertebrate NPC is estimated to contain between 30 and 60 different proteins. most of which are not known. Two important ones in creating the nucleoporin basket are Nup98 and Nup153, and Nup120, in conjunction with Nup 133, interacts with these two and itself plays a role in mRNA export. Nup160, Nup133, Nup96, and Nup107 are all targets of phosphorylation. The phosphorylation sites are clustered mainly at the N-terminal regions of these proteins, which are predicted to be natively disordered. The entire Nup107-160 sub-complex is stable throughout the cell cycle, thus it seems unlikely that phosphorylation affects interactions within the Nup107-160 sub-complex, but rather that it regulates the association of the sub-complex with the NPC and other proteins. 540 matched cddid_all.tbl CDD pfam11716 pfam11716 432021 MDMPI_N Mycothiol maleylpyruvate isomerase N-terminal domain. 139 matched cddid_all.tbl CDD pfam11717 pfam11717 432022 Tudor-knot RNA binding activity-knot of a chromodomain. This is a novel knotted tudor domain which is required for binding to RNA. The know influences the loop conformation of the helical turn Ht2 - residues 61-6 3- that is located at the side opposite the knot in the tudor domain-chromodomain; stabilization of Ht2 is essential for RNA binding. 55 matched cddid_all.tbl CDD pfam11718 pfam11718 463330 CPSF73-100_C Pre-mRNA 3'-end-processing endonuclease polyadenylation factor C-term. This is the C-terminal conserved region of the pre-mRNA 3'-end-processing of the polyadenylation factor CPSF-73/CPSF-100 proteins. The exact function of this domain is not known. 204 matched cddid_all.tbl CDD pfam11719 pfam11719 371692 Drc1-Sld2 DNA replication and checkpoint protein. Genome duplication is precisely regulated by cyclin-dependent kinases CDKs, which bring about the onset of S phase by activating replication origins and then prevent re-licensing of origins until mitosis is completed. The optimum sequence motif for CDK phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found to have at least 11 potential phosphorylation sites. Drc1 is required for DNA synthesis and S-M replication checkpoint control. Drc1 associates with Cdc2 and is phosphorylated at the onset of S phase when Cdc2 is activated. Thus Cdc2 promotes DNA replication by phosphorylating Drc1 and regulating its association with Cut5. Sld2 and Sld3 represent the minimal set of S-CDK substrates required for DNA replication. 391 matched cddid_all.tbl CDD pfam11720 pfam11720 288556 Inhibitor_I78 Peptidase inhibitor I78 family. This family includes Aspergillus elastase inhibitor and belongs to MEROPS peptidase inhibitor family I78. 65 matched cddid_all.tbl CDD pfam11721 pfam11721 432024 Malectin "Malectin domain. Malectin is a membrane-anchored protein of the endoplasmic reticulum that recognizes and binds Glc2-N-glycan. It carries a signal peptide from residues 1-26, a C-terminal transmembrane helix from residues 255-274, and a highly conserved central part of approximately 190 residues followed by an acidic, glutamate-rich region. Carbohydrate-binding is mediated by the four aromatic residues, Y67, Y89, Y116, and F117 and the aspartate at D186. NMR-based ligand-screening studies has shown binding of the protein to maltose and related oligosaccharides, on the basis of which the protein has been designated ""malectin"", and its endogenous ligand is found to be Glc2-high-mannose N-glycan." 165 matched cddid_all.tbl CDD pfam11722 pfam11722 463331 zf-TRM13_CCCH CCCH zinc finger in TRM13 protein. This domain is found at the N-terminus of TRM13 methyltransferase proteins. It is presumed to be a zinc binding domain. 29 matched cddid_all.tbl CDD pfam11723 pfam11723 403045 Aromatic_hydrox Homotrimeric ring hydroxylase. This domain is found on aromatic hydroxylating enzymes such as 2-oxo-1,2-dihydroquinoline 8-monooxygenase from Pseudomonas putida and carbazole 1,9a-dioxygenase from Janthinobacterium. These enzymes are homotrimers and are distantly related to the typical oxygenase. This domain is found C terminal to the Rieske domain which binds an iron-sulphur cluster. 241 matched cddid_all.tbl CDD pfam11724 pfam11724 432026 YvbH_ext YvbH-like oligomerization region. This region is found at the C-terminus of a group of bacterial PH domains. This region is composed of a helical hairpin that appears to mediate oligomerization based on the known structure. This elaboration of the bacterial PH domain is only found in Bacillales. 61 matched cddid_all.tbl CDD pfam11725 pfam11725 463332 AvrE_T3Es AvrE-family Type-III effector proteins (T3Es). This family is secreted by gram-negative Gammaproteobacteria such as Pseudomonas syringae of tomato and the fire blight plant pathogen Erwinia amylovora, amongst others. It is an essential pathogenicity factor of approximately 198 kDa. Its injection into the host-plant is dependent upon the bacterial type III or Hrp secretion system. The family is long and carries a number of predicted functional regions, including in Erwinia stewartii an ERMS or endoplasmic reticulum membrane retention signal at both the C- and the N-termini, a leucine-zipper motif from residues 539-560, and a nuclear localization signal at 1358-1361. this conserved AvrE-family of effectors is among the few that are required for full virulence of many phytopathogenic pseudomonads, erwinias and pantoeas. A double beta-propeller structure is found towards the N-terminus. Furthermore, AvrE1, an AvrE-family T3E from Pseudomonas syringae pv. tomato strain DC3000, associates with specific PP2A B- subunit proteins from its susceptible host Arabidopsis. In a similar fashion, the WtsE (AvrE-family T3E from the maize pathogen Pantoea stewartii subsp. Stewartii) has been shown to target maize protein phosphatase 2A (PP2A) heterotrimeric enzyme complexes via direct interaction with B- regulatory subunits. Taken together, it has been indicated that that sub-component specific PP2A complexes are targeted by bacterial T3Es, including direct targeting by members of the widely conserved AvrE-family. Additionally, DspE, a type-III effector encoded by the broad-host-range bacterial soft-rot pathogen Pectobacterium carotovorum subsp. carotovorum (Pcc), has been indicated to be required and sufficient for disease-associated cell death in host plants. 1483 matched cddid_all.tbl CDD pfam11726 pfam11726 432027 Inovirus_Gp2 Inovirus Gp2. Isoform G2P plays an essential role in viral DNA replication; it binds to the origin of replication and cleaves the dsDNA replicative form I (RFI) and becomes covalently bound to it via phosphotyrosine bond, generating the dsDNA replicative form II (RFII). 179 matched cddid_all.tbl CDD pfam11727 pfam11727 403047 ISG65-75 Invariant surface glycoprotein. This family is found in Trypanosome species, and appears to be one of two invariant surface glycoproteins, ISG65 and ISG75. that are found in the mammalian stage of the parasitic protozoan. the sequence suggests the two families are polypeptides with N-terminal signal sequences, hydrophilic extracellular domains, single trans-membrane alpha-helices and short cytoplasmic domains. they are both expressed in the bloodstream form but not in the midgut stage. Both polypeptides are distributed over the entire surface of the parasite. 280 matched cddid_all.tbl CDD pfam11728 pfam11728 432028 ArAE_1_C Putative aromatic acid exporter C-terminal domain. This region is a presumed intracellular domain found in a set of bacterial presumed transporter proteins. The region is about 160 amino acids in length. 161 matched cddid_all.tbl CDD pfam11729 pfam11729 288565 Capsid-VNN nodavirus capsid protein. The capsid or coat protein of this family is expressed in Nodaviridae, that are ssRNA positive-strand viruses, with no DNA stage. These viruses are the causative agents of viral nervous necrosis in marine fish. 340 matched cddid_all.tbl CDD pfam11730 pfam11730 432029 DUF3297 Protein of unknown function (DUF3297). This family is expressed in Proteobacteria and Actinobacteria. The function is not known. 71 matched cddid_all.tbl CDD pfam11731 pfam11731 463333 Cdd1 Pathogenicity locus. Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed. 82 matched cddid_all.tbl CDD pfam11732 pfam11732 463334 Thoc2 Transcription- and export-related complex subunit. The THO/TREX complex is the transcription- and export-related complex associated with spliceosomes that preferentially deal with spliced mRNAs as opposed to unspliced mRNAs. Thoc2 plays a role in RNA polymerase II (RNA pol II)-dependent transcription and is required for the stability of DNA repeats. In humans, the TRE complex is comprised of the exon-junction-associated proteins Aly/REF and UAP56 together with the THO proteins THOC1 (hHpr1/p84), Thoc2 (hRlr1), THOC3 (hTex1), THOC5 (fSAP79), THOC6 (fSAP35), and THOC7 (fSAP24). Although much evidence indicates that the function of the TREX complex as an adaptor between the mRNA and components of the export machinery is conserved among eukaryotes, in Drosophila the majority of mRNAs can be exported from the nucleus independently of the THO complex. 75 matched cddid_all.tbl CDD pfam11733 pfam11733 314574 NP1-WLL Non-capsid protein NP1. This family is the non-capsid protein NP1 of the ssDNA, Parvovirinae virus Bocavirus of cattle and humans. 213 matched cddid_all.tbl CDD pfam11734 pfam11734 463335 TilS_C TilS substrate C-terminal domain. This domain is found in the tRNA(Ile) lysidine synthetase (TilS) protein. 73 matched cddid_all.tbl CDD pfam11735 pfam11735 432033 CAP59_mtransfer Cryptococcal mannosyltransferase 1. The capsule of pathogenic fungi is a complex polysaccharide whose formation is determined by a number of enzymes including, most importantly, alpha-1,3-mannosyltransferase 1, EC:2.4.1.-. 225 matched cddid_all.tbl CDD pfam11736 pfam11736 432034 DUF3299 Protein of unknown function (DUF3299). This is a family of bacterial proteins of unknown function. 106 matched cddid_all.tbl CDD pfam11737 pfam11737 463336 DUF3300 Protein of unknown function (DUF3300). This hypothetical bacterial gene product has a long hydrophobic segment and is thus likely to be a membrane protein. 229 matched cddid_all.tbl CDD pfam11738 pfam11738 463337 DUF3298 Protein of unknown function (DUF3298). This family of bacterial protein C-terminal regions is highly conserved but the function is not known. Several members are annotated as being endo-1,4-beta-xylanase-like, but this could not be confirmed, and the structure can be defined as a heat-shock cognate 70kd protein 44kd ATPase. 81 matched cddid_all.tbl CDD pfam11739 pfam11739 432037 DctA-YdbH Dicarboxylate transport. In certain bacterial families this protein is expressed from the ydbH gene, and there is a suggestion that this is a form of DctA or dicarboxylate transport protein. Dicarboxylate transport proteins are found in aerobic bacteria which grow on succinate or other C4-dicarboxylates. 198 matched cddid_all.tbl CDD pfam11740 pfam11740 432038 KfrA_N Plasmid replication region DNA-binding N-term. The broad host-range plasmid RK2 is able to replicate in and be inherited in a stable manner in diverse Gram-negative bacterial species. It encodes a number of co-ordinately regulated operons including a central control korF1 operon that represses the kfrA operon. The KfrA polypeptide is a site-specific DNA-binding protein whose operator overlaps the kfrA promoter. The N-terminus, containing an helix-turn-helix motif, is essential for function. Downstream from this family is an extended coiled-coil domain containing a heptad repeat segment which is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning. 117 matched cddid_all.tbl CDD pfam11741 pfam11741 463338 AMIN AMIN domain. This N-terminal domain of various bacterial protein families is crucial for the targetting of periplasmic or extracellular proteins to specific regions of the bacterial envelope. AMIN is derived from the N-terminal domain of AmiC, an N-acetylmuramoyl-l-alanine amidase of Escherichia coli which localizes to the septal ring during division and plays a key role in the separation of daughter cells. The AMIN domain is present in several protein families besides amidases suggesting that AMIN may represent a general targetting determinant involved in the localization of periplasmic protein complexes. 96 matched cddid_all.tbl CDD pfam11742 pfam11742 432040 DUF3302 Protein of unknown function (DUF3302). This family of unknown function is expressed by proteobacteria. 77 matched cddid_all.tbl CDD pfam11743 pfam11743 432041 DUF3301 Protein of unknown function (DUF3301). This family is conserved in Proteobacteria, but the function is not known. 93 matched cddid_all.tbl CDD pfam11744 pfam11744 432042 ALMT Aluminium activated malate transporter. 408 matched cddid_all.tbl CDD pfam11745 pfam11745 463339 DUF3304 Protein of unknown function (DUF3304). This is a family of bacterial proteins of unknown function. 103 matched cddid_all.tbl CDD pfam11746 pfam11746 463340 DUF3303 Domain of unknown function (DUF3303). Several members are annotated as being LysM domain-like proteins, but these did not match any LysM domains reported in the literature. 92 matched cddid_all.tbl CDD pfam11747 pfam11747 432045 RebB Killing trait. RebB is one of three proteins necessary for the production of R- bodies, refractile inclusion bodies produced by a small number of bacterial species, essential for the expression of the killing trait of the endosymbiont bacteria that produce them for attack upon the host Paramecium. R-bodies are highly insoluble protein ribbons which coil into cylindrical structures in the cell and the genes for their synthesis and assembly are encoded on a plasmid. One of these three proteins is RebB. 68 matched cddid_all.tbl CDD pfam11748 pfam11748 432046 DUF3306 Protein of unknown function (DUF3306). This family of proteobacterial species proteins has no known function. 120 matched cddid_all.tbl CDD pfam11749 pfam11749 463341 DUF3305 Protein of unknown function (DUF3305). Several members of this family are annotated as being molybdopterin-guanine dinucleotide biosynthesis protein A; however, this could not be confirmed. The family is found in proteobacteria. 141 matched cddid_all.tbl CDD pfam11750 pfam11750 432048 DUF3307 Protein of unknown function (DUF3307). This family of bacterial proteins has no known function. 126 matched cddid_all.tbl CDD pfam11751 pfam11751 403066 PorP_SprF Type IX secretion system membrane protein PorP/SprF. This entry describes a protein family unique to, and greatly expanded in, the Bacteriodetes. Species in this lineage include several, such as Cytophaga hutchinsonii and Cytophaga johnsonae (Flavobacterium johnsoniae), that exhibit a poorly understood rapid gliding phenotype. Several members of this protein family are found in operons with other genes whose loss leads to a loss of the rapid gliding phenotype. 274 matched cddid_all.tbl CDD pfam11752 pfam11752 432049 DUF3309 Protein of unknown function (DUF3309). This family is conserved in bacteria but its function is not known. 49 matched cddid_all.tbl CDD pfam11753 pfam11753 432050 DUF3310 Protein of unknwon function (DUF3310). This is a family of conserved bacteriophage proteins of unknown function. 59 matched cddid_all.tbl CDD pfam11754 pfam11754 463342 Velvet Velvet factor. The velvet factor is conserved in many fungal species and is found to have gained different roles depending on the organizm's need, expanding the conserved role in developmental programmes. The velvet factor orthologues can be adapted to the fungal-specific life cycle and may be involved in diverse functions such as sclerotia formation and toxin production, as in A. parasiticus, nutrition-dependent sporulation, as in A. fumigatus, or the microconidia-to-macroconidia ratio and cell wall formation, as in the heterothallic fungus Fusarium verticilloides. 238 matched cddid_all.tbl CDD pfam11755 pfam11755 432052 DUF3311 Protein of unknown function (DUF3311). This is a family of short bacterial proteins of unknown function. 59 matched cddid_all.tbl CDD pfam11756 pfam11756 432053 YgbA_NO Nitrous oxide-stimulated promoter. The function of ygaB is not known but it is a promoter that is stimulated by the presence of nitrous oxide. It is regulated by the gene-product of the bacterial nsrR gene. 106 matched cddid_all.tbl CDD pfam11757 pfam11757 403072 RSS_P20 Suppressor of RNA silencing P21-like N-terminal domain. This domain can be found at the N-terminal region of is a large family of putative suppressors of RNA silencing proteins, P20-P25, from ssRNA positive-strand viruses such as Closterovirus, Potyvirus and Cucumovirus families. RNA silencing is one of the major mechanisms of defence against viruses, and, in response, some viruses have evolved or acquired functions for suppression of RNA silencing. These counter-defencive viral proteins with RNA silencing suppressor (RSS) activity were originally discovered in the members of plant virus genera Potyvirus and Cucumovirus. Each of the conserved blocks of amino acids found in P21-like proteins corresponds to a computer-predicted alpha-helix, with the most C-terminal element being 42 residues long. This suggests conservation of the predominantly alpha-helical secondary structure in the P21-like proteins. C-terminal domain entry found under pfam11479. 94 matched cddid_all.tbl CDD pfam11758 pfam11758 403073 Bacteriocin_IIi Aureocin-like type II bacteriocin. This is a small family of type II bacteriocins usually encoded on a plasmid. characteriztically the members are small, cationic, rich in Lys and Try, and bring about a generalized membrane permeabilization leading to leakage of ions. The family includes aureocin A, lacticins Q and Z, and BhtB as well as an archaeal member. 51 matched cddid_all.tbl CDD pfam11759 pfam11759 314599 KRTAP Keratin-associated matrix. The major structural proteins of mammalian hair are the hair keratin intermediate filaments (KIFs) and the keratin-associated proteins (KRTAPs). In the hair cortex, hair keratins are embedded in an inter-filamentous matrix consisting of KRTAPs which are essential for the formation of a rigid and resistant hair shaft as a result of disulfide bonds between cysteine residues. There are essentially three groups of KRTAPs, viz: the high-sulfur (HS) and ultra-high-sulfur (UHS) KRTAPs (cysteine content: 16-30 and >30 mol%, respectively) and the high-glycine/tyrosine (HGT: 35-60 mol% glycine and tyrosine) KRTAPs. 59 matched cddid_all.tbl CDD pfam11760 pfam11760 463343 CbiG_N Cobalamin synthesis G N-terminal. Members of this family are involved in cobalamin synthesis. The gene refered to by Swiss:P72862 has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyze adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyzes a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process. Within the cobalamin synthesis pathway CbiG catalyzes the both the opening of the lactone ring and the extrusion of the two-carbon fragment of cobalt-precorrin-5A from C-20 and its associated methyl group (deacylation) to give cobalt-precorrin-5B. The N-terminal of the enzyme is conserved in this family, and the C-terminal and the mid-sections are conserved independently in other families, CbiG_C and CbiG_mid, although the distinct function of each region is unclear. 79 matched cddid_all.tbl CDD pfam11761 pfam11761 432055 CbiG_mid Cobalamin biosynthesis central region. Members of this family are involved in cobalamin synthesis. The gene refered to by Swiss:P72862 has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyze adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyzes a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process. 88 matched cddid_all.tbl CDD pfam11762 pfam11762 432056 Arabinose_Iso_C L-arabinose isomerase C-terminal domain. This is a family of L-arabinose isomerases, AraA, EC:5.3.1.4. These enzymes catalyze the reaction: L-arabinose <=> L-ribulose. This reaction is the first step in the pathway of L-arabinose utilization as a carbon source after entering the cell L-arabinose is converted into L-ribulose by the L-arabinose isomerases enzyme. This is a C-terminal non catalytic domain. 114 matched cddid_all.tbl CDD pfam11763 pfam11763 403077 DIPSY Cell-wall adhesin ligand-binding C-terminal. The DIPSY domain is characterized by the distinctive D*I*PSY motif at the very C-terminus of yeast cell-wall glycoproteins. It appears not to be conserved in any other species, however. In fungi, cell adhesion is required for flocculation, mating and virulence, and is mediated by covalently bound cell wall proteins termed adhesins. Map4, an adhesin required for mating in Schizosaccharomyces pombe, is N-glycosylated and O-glycosylated, and is an endogenous substrate for the mannosyl transferase Oma4p. Map4 has a modular structure with an N-terminal signal peptide, a serine and threonine (S/T)-rich domain that includes nine repeats of 36 amino acids (rich in serine and threonine residues, but lacking glutamines), and a C-terminal DIPSY domain with no glycosyl-phosphatidyl inositol (GPI)-anchor signal. The N-terminal S/T-rich regions, are required for cell wall attachment, but the C-terminal DIPSY domain is required for agglutination and mating in liquid and solid media. 122 matched cddid_all.tbl CDD pfam11764 pfam11764 463344 N-SET COMPASS (Complex proteins associated with Set1p) component N. The n-SET or N-SET domain is a component of the COMPASS complex, associated with SET1, conserved in yeasts and in other eukaryotes up to humans. The COMPASS complex functions to methylate the fourth lysine of Histone 3 and for the silencing of genes close to the telomeres of chromosomes. This domain promotes trimethylation in conjunction with an RRM domain and is necessary for binding of the Spp1 component of COMPASS into the complex. 172 matched cddid_all.tbl CDD pfam11765 pfam11765 403079 Hyphal_reg_CWP Hyphally regulated cell wall protein N-terminal. The proteins in this family are all fungal and largely annotated as being hyphally regulated cell wall proteins, and several are listed as the enzyme EC:3.2.1.18. This enzyme is acetylneuraminyl hydrolase or exo-alpha-sialidase, that hydrolyses glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates. 322 matched cddid_all.tbl CDD pfam11766 pfam11766 403080 Candida_ALS_N Cell-wall agglutinin N-terminal ligand-sugar binding. This is likely to be the sugar or ligand binding domain of the yeast alpha-agglutinins. 241 matched cddid_all.tbl CDD pfam11767 pfam11767 432058 SET_assoc Histone lysine methyltransferase SET associated. SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. A subset of SET domains have been called PR domains. The SET domain consists of two regions known as N-SET and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure. This domain is found in fungi associated with SET and N-SET domains. 65 matched cddid_all.tbl CDD pfam11768 pfam11768 432059 Frtz WD repeat-containing and planar cell polarity effector protein Fritz. Fritz is a probable effector of the planar cell polarity signaling pathway which regulates the septin cytoskeleton in both ciliogenesis and collective cell movements. In Drosophila melanogaster, fritz regulates both the location and the number of wing cell prehair initiation sites. 544 matched cddid_all.tbl CDD pfam11769 pfam11769 432060 DUF3313 Protein of unknown function (DUF3313). This a bacterial family of proteins which are annotated as putative lipoproteins. 186 matched cddid_all.tbl CDD pfam11770 pfam11770 463345 GAPT GRB2-binding adapter (GAPT). This is a family of transmembrane proteins which bind the growth factor receptor-bound protein 2 (GRB2) in B cells. In contrast to other transmembrane adaptor proteins, GAPT is not phosphorylated upon BCR ligation. It associates with GRB2 constitutively through its proline-rich region. 144 matched cddid_all.tbl CDD pfam11771 pfam11771 463346 DUF3314 Protein of unknown function (DUF3314). This small family contains human, mouse and fish members but the function is not known. 162 matched cddid_all.tbl CDD pfam11772 pfam11772 432063 EpuA DNA-directed RNA polymerase subunit beta. This short 60-residue long bacterial family is the beta subunit of the DNA-directed RNA polymerase, likely to be EC:2.7.7.6. It is membrane-bound and is referred to by the name EpuA. 46 matched cddid_all.tbl CDD pfam11773 pfam11773 432064 PulG Type II secretory pathway pseudopilin. The secreton (type II secretion) and type IV pilus biogenesis branches of the general secretory pathway in Gram-negative bacteria share many features that suggest a common evolutionary origin. Five components of the secreton, the pseudopilins, are similar to subunits of type IV pili. Pseudopilin PulG is one of the secreton pseudopilins, and is found to assemble into pilus-like bundles. PulG interacts with proteins H, I and J within the multi-protein complex as well as blocking extracellular secretion and reducing the amount of PulE protein as well as the amounts of PulL, PulM, PulC and PulD when G is over-expressed. In Klebsiella the pilus-like structure is composed largely of PulG. 82 matched cddid_all.tbl CDD pfam11774 pfam11774 432065 Lsr2 Lsr2. Lsr2 is a small, basic DNA-bridging protein present in Mycobacterium and related actinomycetes. It is a functional homolog of the H-NS-like proteins. H-NS proteins play a role in nucleoid organization and also function as a pleiotropic regulator of gene expression. 109 matched cddid_all.tbl CDD pfam11775 pfam11775 288608 CobT_C Cobalamin biosynthesis protein CobT VWA domain. This family consists of several bacterial cobalamin biosynthesis (CobT) proteins. CobT is involved in the transformation of precorrin-3 into cobyrinic acid. 220 matched cddid_all.tbl CDD pfam11776 pfam11776 432066 RcnB Nickel/cobalt transporter regulator. RcnB is a family of Proteobacteria proteins. RcnB is required for maintaining metal ion homeostasis, in conjunction with the efflux pump RcnA, family NicO, pfam03824. 51 matched cddid_all.tbl CDD pfam11777 pfam11777 432067 DUF3316 Protein of unknown function (DUF3316). This family of bacterial proteins has no known function. Several members are, however, annotated as being putative acyl-CoA synthetase, but this could not be confirmed. 142 matched cddid_all.tbl CDD pfam11778 pfam11778 403090 SID Septation initiation. This family is required for activation of the spg1 GTPase signalling cascade which leads to the initiation of septation and the subsequent termination of mitosis. It may act as a scaffold at the spindle pole body to which other components of the spg1 signalling cascade attach in pombe. In S.cerevisiae it is both required for the proper formation of the spindle pole body outer plaque and may also connect the outer plaque to the central plaque embedded in the nuclear envelope. 135 matched cddid_all.tbl CDD pfam11779 pfam11779 463347 SPT_ssu-like Small subunit of serine palmitoyltransferase-like. Serine palmitoyltransferase (SPT) catalyzes the first committed step in sphingolipid biosynthesis. In mammals, two small subunits of serine palmitoyltransferase, ssSPTa and ssSPTb, substantially enhance the activity of SPT, conferring full enzyme activity upon it. The 2 ssSPT isoforms share a conserved hydrophobic central domain, which is predicted to reside in the membrane. 54 matched cddid_all.tbl CDD pfam11780 pfam11780 432069 DUF3318 Protein of unknown function (DUF3318). This is a bacterial family of uncharacterized proteins. 141 matched cddid_all.tbl CDD pfam11781 pfam11781 463348 zf-RRN7 Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7. This is the zinc-finger at the start of transcription-binding factor that associates strongly with both Rrn6 and Rrn7 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter. 32 matched cddid_all.tbl CDD pfam11782 pfam11782 432071 DUF3319 Protein of unknown function (DUF3319). This is a family of short bacterial proteins, a few of which are annotated as being minor tail protein. Otherwise the function is unknown. 89 matched cddid_all.tbl CDD pfam11783 pfam11783 432072 Cytochrome_cB Cytochrome c bacterial. This is a family of long bacterial cytochrome c proteins, found in Proteobacteria and Chlorobi families. 173 matched cddid_all.tbl CDD pfam11784 pfam11784 432073 DUF3320 Protein of unknown function (DUF3320). This family is conserved in Proteobacteria and Chlorobi families. Many members are annotated as being putative DNA helicase-related proteins. 50 matched cddid_all.tbl CDD pfam11785 pfam11785 403096 Aft1_OSA Aft1 osmotic stress response (OSM) domain. This domain is found in the transcription factor Aft1 which is required for a wide range of stress responses. The OSM domain has been shown to be involved in the osmotic stress response. 57 matched cddid_all.tbl CDD pfam11786 pfam11786 371723 Aft1_HRA Aft1 HRA domain. This domain is found in the transcription factor Aft1 which is required for a wide range of stress responses. The HRA domain is involved in meiotic recombination. It has been shown to be necessary and sufficient to activate recombination. 76 matched cddid_all.tbl CDD pfam11787 pfam11787 403097 Aft1_HRR Aft1 HRR domain. This domain is found in the transcription factor Aft1 which is required for a wide range of stress responses. The HRR domain is involved in meiotic recombination. It has been shown to be necessary and sufficient to repress recombination. 68 matched cddid_all.tbl CDD pfam11788 pfam11788 432074 MRP-L46 39S mitochondrial ribosomal protein L46. This is the L46 subunit of the mammalian mitochondrial ribosome, conserved from plants and fungi. 120 matched cddid_all.tbl CDD pfam11789 pfam11789 403098 zf-Nse Zinc-finger of the MIZ type in Nse subunit. Nse1 and Nse2 are novel non-SMC subunits of the fission yeast Smc5-6 DNA repair complex. This family is the zinc-finger domain similar to the MIZ type of zinc-finger. 57 matched cddid_all.tbl CDD pfam11790 pfam11790 432075 Glyco_hydro_cc Glycosyl hydrolase catalytic core. This family is probably a glycosyl hydrolase, and is conserved in fungi and some Proteobacteria. The pombe member is annotated as being from IPR013781. 231 matched cddid_all.tbl CDD pfam11791 pfam11791 463349 Aconitase_B_N Aconitate B N-terminal domain. This family represents the N-terminal domain of Aconitase B. 151 matched cddid_all.tbl CDD pfam11792 pfam11792 288625 Baculo_LEF5_C Baculoviridae late expression factor 5 C-terminal domain. This C-terminal domain is likely to be a zinc-binding domain. 42 matched cddid_all.tbl CDD pfam11793 pfam11793 463350 FANCL_C FANCL C-terminal domain. This domain is found at the C-terminus of the Fancl protein in humans which is the putative E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits of the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2. 69 matched cddid_all.tbl CDD pfam11794 pfam11794 463351 HpaB_N 4-hydroxyphenylacetate 3-hydroxylase N terminal. HpaB encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli. HpaB is part of a heterodimeric enzyme that also requires HpaC. The enzyme is NADH-dependent and uses FAD as the redox chromophore. This family also includes PvcC, which may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis. 266 matched cddid_all.tbl CDD pfam11795 pfam11795 463352 DUF3322 Uncharacterized protein conserved in bacteria N-term (DUF3322). This domain, found in various hypothetical bacterial proteins, has no known function. The family represents just the N-terminus. 189 matched cddid_all.tbl CDD pfam11796 pfam11796 403103 DUF3323 Protein of unknown function N-terminus (DUF3323). Proteins in this entry are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Beta-proteobacteria). 209 matched cddid_all.tbl CDD pfam11797 pfam11797 463353 DUF3324 Protein of unknown function C-terminal (DUF3324). This family consists of several hypothetical bacterial proteins of unknown function. 138 matched cddid_all.tbl CDD pfam11798 pfam11798 432081 IMS_HHH IMS family HHH motif. These proteins are involved in UV protection, eg. 32 matched cddid_all.tbl CDD pfam11799 pfam11799 463354 IMS_C impB/mucB/samB family C-terminal domain. These proteins are involved in UV protection (Swiss). 104 matched cddid_all.tbl CDD pfam11800 pfam11800 432083 RP-C_C Replication protein C C-terminal region. Replication protein C is involved in the early stages of viral DNA replication. 102 matched cddid_all.tbl CDD pfam11801 pfam11801 432084 Tom37_C Tom37 C-terminal domain. The TOM37 protein is one of the outer membrane proteins that make up the TOM complex for guiding cytosolic mitochondrial beta-barrel proteins from the cytosol across the outer mitochondrial membrane into the intra-membrane space. In conjunction with TOM70 it guides peptides without an MTS into TOM40, the protein that forms the passage through the outer membrane. It has homology with Metaxin-1, also part of the outer mitochondrial membrane beta-barrel protein transport complex. 145 matched cddid_all.tbl CDD pfam11802 pfam11802 463355 CENP-K Centromere-associated protein K. CENP-K is one of seven new CENP-A-nucleosome distal (CAD) centromere components (the others being CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S) that are identified as assembling on the CENP-A nucleosome associated complex, NAC. The CENP-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival despite continued centromere-derived mitotic checkpoint signalling. CENP-K is centromere-associated through its interaction with one or more components of the CENP-A NAC. 263 matched cddid_all.tbl CDD pfam11803 pfam11803 463356 UXS1_N UDP-glucuronate decarboxylase N-terminal. The N-terminus of the UDP-glucuronate decarboxylases may be involved in localization to the perinuclear Golgi membrane. 75 matched cddid_all.tbl CDD pfam11804 pfam11804 432087 DUF3325 Protein of unknown function (DUF3325). This family of short proteins are functionally uncharacterized. This family is restricted to Alpha-, Beta- and Gamma-proteobacteria. 101 matched cddid_all.tbl CDD pfam11805 pfam11805 432088 DUF3326 Protein of unknown function (DUF3326). This protein is functionally uncharacterized. It is about 300-500 amino acids in length. This family is found in plants and bacteria. 336 matched cddid_all.tbl CDD pfam11806 pfam11806 432089 Enterochelin_N Enterochelin esterase, N-terminal. This entry represents the N-terminal domain of enterochelin esterase. The activity of the enzyme has been characterized. Fes catalyzes the hydrolysis of the 2,3-dihydroxy-N- benzoyl-L-serine trimer, enterochelin, forming 2,3- dihydroxybenzoylserine. It also catalyzes hydrolysis of free enterobactin and ferric enterobactin. Upon hydrolysis of ferric enterobactin by Fes, released iron is probably reduced by a second enzyme. Enterochelin esterase represents a family of non-peptidase homologs belonging to the MEROPS peptidase family S9, clan SC. 121 matched cddid_all.tbl CDD pfam11807 pfam11807 403112 UstYa Mycotoxin biosynthesis protein UstYa. Oxidase ustYa is involved in the production of ustiloxins, toxic cyclic peptides, in fungi. Ustiloxins were found to be the first example of cyclic peptidyl secondary metabolites that are ribosomally synthesized in filamentous fungi. The homologous genes ustYa and ustYb (which are found in the gene cluster for ustiloxins) have been shown to be involved in cyclization of the peptide. 220 matched cddid_all.tbl CDD pfam11808 pfam11808 432090 PhoR Phosphate regulon sensor protein PhoR. This family is only found in bacteria. Family members include PhoR. A member of the two-component regulatory system PhoR/PhoB involved in the phosphate regulon genes expression. PhoR is the bifunctional histidine autokinase/phospho-PhoB phosphatase that donates a phosphoryl group to PhoB when environmental Pi is limiting and removes the phosphoryl group from phosphorylated PhoB (PhoB-P) when environmental Pi is abundant. 84 matched cddid_all.tbl CDD pfam11809 pfam11809 288642 DUF3330 Domain of unknown function (DUF3330). This family of proteins are functionally uncharacterized. This family is only found in bacteria. 69 matched cddid_all.tbl CDD pfam11810 pfam11810 432091 DUF3332 Domain of unknown function (DUF3332). This family of proteins are functionally uncharacterized. This family is only found in bacteria. 160 matched cddid_all.tbl CDD pfam11811 pfam11811 432092 DUF3331 Domain of unknown function (DUF3331). This family of proteins are functionally uncharacterized. This family is only found in bacteria. Proteins in this family vary in length from 96 to 160 amino acids. 91 matched cddid_all.tbl CDD pfam11812 pfam11812 463357 DUF3333 Domain of unknown function (DUF3333). This family of proteins are functionally uncharacterized. This family is only found in bacteria. This presumed domain is typically between 116 to 159 amino acids in length. 150 matched cddid_all.tbl CDD pfam11813 pfam11813 432094 DUF3334 Protein of unknown function (DUF3334). This family of proteins are functionally uncharacterized. This family is only found in bacteria. Proteins in this family are typically between 227 to 238 amino acids in length. 226 matched cddid_all.tbl CDD pfam11814 pfam11814 432095 DUF3335 Peptidase_C39 like family. 206 matched cddid_all.tbl CDD pfam11815 pfam11815 432096 DUF3336 Domain of unknown function (DUF3336). This family of proteins are functionally uncharacterized. This family is found in bacteria and eukaryotes. This presumed domain is typically between 143 to 227 amino acids in length. 139 matched cddid_all.tbl CDD pfam11816 pfam11816 463358 DUF3337 Domain of unknown function (DUF3337). This family of proteins are functionally uncharacterized. This family is only found in eukaryotes. This presumed domain is typically between 285 to 342 amino acids in length. 171 matched cddid_all.tbl CDD pfam11817 pfam11817 463359 Foie-gras_1 Foie gras liver health family 1. Mutating the gene foie gras in zebrafish has been shown to affect development; the mutants develop large, lipid-filled hepatocytes in the liver, resembling those in individuals with fatty liver disease. Foie-gras protein is long and has several well-defined domains though none of them has a known function. We have annotated this one as the first. The C-terminus of this region contains TPR repeats. 248 matched cddid_all.tbl CDD pfam11818 pfam11818 432098 DUF3340 C-terminal domain of tail specific protease (DUF3340). This presumed domain is found at the C-terminus of tail specific proteases. Its function is unknown. This family is found in bacteria and eukaryotes. This presumed domain is typically between 88 to 187 amino acids in length. 150 matched cddid_all.tbl CDD pfam11819 pfam11819 463360 CUPID Cytohesin Ubiquitin Protein Inducing Domain. C1ORF106 also known as INAVA (Innate Immune Activator), is identified as a risk factor for the chronic inflammatory bowel diseases (IBD). Mice lacking the protein show defects in intestinal barrier integrity at steady state and greater susceptibility to mucosal infection. INAVA carries CUPID (Cytohesin Ubiquitin Protein Inducing Domain). Three other human proteins contain CUPID: FRMD4A, FRMD4B, and CCDC120- proteins implicated in neurite outgrowth, and in human cancer, Alzheimer's, celiac, and heart disease. All appear to bind the ARF-GEF (guanine nucleotide-exchange factors) cytohesin family members, such as proteins (ARF 1-4), which regulate cell membrane and F-actin dynamics. INAVA-CUPID binds cytohesin 2 (also known as ARNO), targets the molecule to lateral membranes of epithelial monolayers, and enables ARNO to affect F-actin assembly that underlies cell-cell junctions and barrier function. In the case of inflammatory signalling, ARNO can coordinate CUPID function by binding and inhibiting CUPID activity of acting as an enhancer of TRAF6 dependent polyubiquitination. In other words, ARNO acts as a negative-regulator of inflammatory responses. In summary, INAVA-CUPID exhibits dual functions, coordinated directly by ARNO, that bridge epithelial barrier function with extracellular signals and inflammation. 136 matched cddid_all.tbl CDD pfam11820 pfam11820 463361 DUF3339 Protein of unknown function (DUF3339). This family of proteins are functionally uncharacterized. This family is found in eukaryotes. Proteins in this family are about 70 amino acids in length. 66 matched cddid_all.tbl CDD pfam11821 pfam11821 432101 ActD Alternative complex III, ActD subunit. Alternative complex III (ACIII) is a multisubunit quinol:electron acceptor oxidoreductase that couples quinol oxidation with transmembrane proton translocation similar to bc1 complex (or complex III). It is a key component of the respiratory and photosynthetic electron transport chains in many bacteria. It has six subunits (ActA-F), ActD subunit represented in this entry. The transmembrane regions of this subunit form part of the TM arm of the complex. Although the function of this subunit is not clear, it may play a role in stabilizing the TM region of ACIII which contributes to a stable menaquinol binding pocket and proton translocation passage. 168 matched cddid_all.tbl CDD pfam11822 pfam11822 432102 SANBR_BTB SANT and BTB domain regulator of CSR, BTB domain. Class switch recombination (CSR) is the process by which B cells switch production from IgM/IgD to other immunoglobulin isotypes in the immune response process. This entry represents the BTB domain found at the N-terminal half of the protein SANT and BTB domain regulator of class switch recombination (SANBR, previously known as KIAA1841). This domain is responsible for the negative regulation of CSR. 97 matched cddid_all.tbl CDD pfam11823 pfam11823 463362 Se_S_carrier Putative Se/S carrier protein-like. This family of proteins are functionally uncharacterized. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length. It has been suggested that this family of proteins may be chaperones involved in Se or S trafficking in the cell. 63 matched cddid_all.tbl CDD pfam11824 pfam11824 432104 DUF3344 Protein of unknown function (DUF3344). This family of proteins are functionally uncharacterized. This protein is found in bacteria and archaea. Proteins in this family are typically between 367 to 1857 amino acids in length. 272 matched cddid_all.tbl CDD pfam11825 pfam11825 463363 Nuc_recep-AF1 Nuclear/hormone receptor activator site AF-1. Nuclear receptors (NRs) are a family of ligand-inducible transcription factors, and, like other transcription factors, they contain a distinct DNA binding domain that allows for target gene recognition and several activation domains that possess the ability to activate transcription. One of these activation domains is at the N-terminal, although there are two distinct motifs within this domain, between residues 20-36 and between 74 and the end of this domain, which are the binding regions. One of the co-activators is TIF1beta, which appears to bind at the first motif. 113 matched cddid_all.tbl CDD pfam11826 pfam11826 288659 DUF3346 Protein of unknown function (DUF3346). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 231 to 659 amino acids in length. 225 matched cddid_all.tbl CDD pfam11827 pfam11827 432106 DUF3347 Protein of unknown function (DUF3347). This entry represents a functionally uncharacterized domain found in bacterial proteins. 93 matched cddid_all.tbl CDD pfam11828 pfam11828 432107 DUF3348 Protein of unknown function (DUF3348). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 244 to 323 amino acids in length. 246 matched cddid_all.tbl CDD pfam11829 pfam11829 463364 DUF3349 Protein of unknown function (DUF3349). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. 94 matched cddid_all.tbl CDD pfam11830 pfam11830 463365 DUF3350 Domain of unknown function (DUF3350). This domain is functionally uncharacterized and is found in eukaryotic proteins, such as TBC1 domain family members 1 and 4. This presumed domain is typically between 50 to 64 amino acids in length. TBC domain proteins may act as GTPase-activating proteins for RAB2A, RAB8A, RAB10 and RAB14. 63 matched cddid_all.tbl CDD pfam11831 pfam11831 463366 Myb_Cef pre-mRNA splicing factor component. This family is a region of the Myb-Related Cdc5p/Cef1 proteins, in fungi, and is part of the pre-mRNA splicing factor complex. 227 matched cddid_all.tbl CDD pfam11832 pfam11832 432111 DUF3352 Protein of unknown function (DUF3352). This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 538 to 575 amino acids in length. 529 matched cddid_all.tbl CDD pfam11833 pfam11833 432112 CPP1-like Protein CHAPERONE-LIKE PROTEIN OF POR1-like. This entry includes proteins from bacteria and eukaryotes. The plant member, CHAPERONE-LIKE PROTEIN OF POR1 (CPP1), is an essential protein for chloroplast development, plays a role in the regulation of POR (light-dependent protochlorophyllide oxidoreductase) stability and function. 194 matched cddid_all.tbl CDD pfam11834 pfam11834 463367 KHA KHA, dimerization domain of potassium ion channel. KHA is the tetramerization domain of eukaryotic voltage-dependent potassium ion-channel proteins. In plants the domain lies at the C-terminus whereas in many chordates it lies at the N-terminus. 65 matched cddid_all.tbl CDD pfam11835 pfam11835 432114 RRM_8 RRM-like domain. This domain is related to the RRM domains suggesting it may have an RNA-binding function. 89 matched cddid_all.tbl CDD pfam11836 pfam11836 432115 Phage_TAC_11 Phage tail tube protein, GTA-gp10. This is a family of phage tail tube proteins. 97 matched cddid_all.tbl CDD pfam11837 pfam11837 432116 INV_N Beta-fructofuranosidase, N-terminal domain. This entry represents the N-terminal domain of beta-fructofuranosidase, which is involved in the hydrolysis of terminal non-reducing beta-D-fructofuranoside residues in beta-D-fructofuranosides. 108 matched cddid_all.tbl CDD pfam11838 pfam11838 463368 ERAP1_C ERAP1-like C-terminal domain. This large domain is composed of 16 alpha helices organized as 8 HEAT-like repeats. This domain forms a concave face that faces towards the active site of the peptidase. 316 matched cddid_all.tbl CDD pfam11839 pfam11839 432118 Alanine_zipper Alanine-zipper, major outer membrane lipoprotein. This is a family of a major outer membrane lipoprotein, OprL that is an alanine-zipper. Zipper motifs are a seven-repeat motif where the first and fourth positions are occupied by an aliphatic residue, usually a leucine. These residues are positioned on the outside of the coil such as to bind firmly to one or more monomers of the protein to create a triple or five-helical coiled-coil that probably forms a seam in a membrane. 69 matched cddid_all.tbl CDD pfam11840 pfam11840 403138 DUF3360 Protein of unknown function (DUF3360). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 489 to 517 amino acids in length. 485 matched cddid_all.tbl CDD pfam11841 pfam11841 463369 ELMO_ARM ELMO, armadillo-like helical domain. This domain is found in eukaryotes and predominantly in ELMO (Elongation and Cell motility) proteins and corresponds to the armadillo repeats domain (ARR). It may play an important role in defining the functions of the ELMO family members and may be functionally linked to the ELMO domain in these proteins, being involved in protein-protein interactions. 154 matched cddid_all.tbl CDD pfam11842 pfam11842 432120 DUF3362 Domain of unknown function (DUF3362). This domain is functionally uncharacterized. This domain is found in bacteria and archaea. This presumed domain is typically between 117 to 158 amino acids in length. 148 matched cddid_all.tbl CDD pfam11843 pfam11843 463370 DUF3363 Protein of unknown function (DUF3363). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 323 to 658 amino acids in length. 375 matched cddid_all.tbl CDD pfam11844 pfam11844 432122 DUF3364 Domain of unknown function (DUF3364). This domain is functionally uncharacterized. This domain is found in bacteria. This presumed domain is about 60 amino acids in length. 56 matched cddid_all.tbl CDD pfam11845 pfam11845 432123 DUF3365 Protein of unknown function (DUF3365). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 198 to 657 amino acids in length. 167 matched cddid_all.tbl CDD pfam11846 pfam11846 432124 Wzy_C_2 Virulence factor membrane-bound polymerase, C-terminal. Wzy is a membrane-bound polymerase of 12 TMs, found in Gram-positive bacteria such as Streptococcus pnuemoniae. It forms part of the EPS or exopolysaccharide system. This family is the 6xTMs at the C-terminal end of the molecule. Wzy functions in polymerizing the oligosaccharide repeat subunits to form high-molecular-weight capsular polysaccharides. A contiguous emebrane-bound flippase, Wzx, pfam01943, transports the repeat units to the external surface of the membrane. These polysaccharides form the capsule and their differing compositions contribute to the multidudinous pneumococcal capsular serotypes, all being structurally and antigenically different. 186 matched cddid_all.tbl CDD pfam11847 pfam11847 432125 DUF3367 Alpha-(1->3)-arabinofuranosyltransferase. Family members include alpha-(1->3)-arabinofuranosyltransferase (AftD, EC:2.4.2.47) which is involved in the biosynthesis of the arabinogalactan (AG) region of the mycolylarabinogalactan-peptidoglycan (mAGP) complex, an essential component of the mycobacterial cell wall. It catalyzes the addition of an arabinofuranosyl (Araf) residue from the sugar donor decaprenyl-phospho-arabinose (DPA) on the C-3 of an alpha-(1->5)-linked Araf from the arabinan backbone of AG. 641 matched cddid_all.tbl CDD pfam11848 pfam11848 463371 DUF3368 Domain of unknown function (DUF3368). This domain is functionally uncharacterized. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length. 46 matched cddid_all.tbl CDD pfam11849 pfam11849 432127 DUF3369 Domain of unknown function (DUF3369). This domain is functionally uncharacterized. This domain is found in bacteria. This presumed domain is about 170 amino acids in length. The domain appears to be related to the GAF domain. 168 matched cddid_all.tbl CDD pfam11850 pfam11850 432128 DUF3370 Protein of unknown function (DUF3370). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 452 to 532 amino acids in length. 422 matched cddid_all.tbl CDD pfam11851 pfam11851 463372 DUF3371 Domain of unknown function (DUF3371). This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 125 to 142 amino acids in length. 128 matched cddid_all.tbl CDD pfam11852 pfam11852 432130 Pullul_strch_C Alpha-1,6-glucosidases, pullulanase-type, C-terminal. This entry represents the uncharacterized C-terminal domain of secreted (or membrane-anchored) pullulanases of Gram-negative bacteria and pullulanase-type starch debranching enzymes of plants. Both enzymes hydrolyse alpha-1,6 glycosidic linkages. Pullulan is an unusual, industrially important polysaccharide in which short alpha-1,4 chains (maltotriose) are connected in alpha-1,6 linkages. Enzymes that cleave alpha-1,6 linkages in pullulan and release maltotriose are called pullulanases although pullulan itself may not be the natural substrate. 167 matched cddid_all.tbl CDD pfam11853 pfam11853 432131 DUF3373 Protein of unknown function (DUF3373). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length. 401 matched cddid_all.tbl CDD pfam11854 pfam11854 432132 MtrB_PioB Putative outer membrane beta-barrel porin, MtrB/PioB. MtrB-PioB is a family of bacterial putative outer membrane porins. This family, is secreted as part of the pio (phototrophic iron oxidation) operon that has been found to couple the oxidation of ferrous iron [Fe(II)] to reductive CO2 fixation using light energy. PioABC is found in Rhodopseudomonas palustris and MtrB-PioB is likely to be a beta-barrel porin. Similar to other outer membrane porins, PioB and MtrB are predicted to have long loops protruding into the extracellular space and short turns on the periplasmic side. 632 matched cddid_all.tbl CDD pfam11855 pfam11855 463373 DUF3375 Protein of unknown function (DUF3375). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 479 to 499 amino acids in length. 469 matched cddid_all.tbl CDD pfam11856 pfam11856 371765 DUF3376 Protein of unknown function (DUF3376). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 770 to 1142 amino acids in length. 521 matched cddid_all.tbl CDD pfam11857 pfam11857 463374 DUF3377 Domain of unknown function (DUF3377). This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is about 70 amino acids in length. 72 matched cddid_all.tbl CDD pfam11858 pfam11858 432135 DUF3378 Domain of unknown function (DUF3378). This domain is functionally uncharacterized. This domain is found in bacteria. This presumed domain is about 80 amino acids in length. 76 matched cddid_all.tbl CDD pfam11859 pfam11859 432136 DUF3379 Protein of unknown function (DUF3379). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 234 to 251 amino acids in length. 235 matched cddid_all.tbl CDD pfam11860 pfam11860 432137 Muramidase N-acetylmuramidase. Endolysins are bacteriophage encoded proteins synthesized at the end of the lytic infection cycle. They degrade the peptidoglycan (PG) of the host bacterium to allow viral progeny release. This domain family is found in bacteria and viruses. It is also found associated with pfam01471. One of the family members is the modular Gp110 endolysin found in the Salmonella phage. This domain represents the catalytic region found in the C-terminal of Gp110. It has been demonstrated to have N-acetylmuramidase (lysozyme) activity cleaving the beta-(1,4) glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine residues in the sugar backbone of the PG. Furthermore, sequence alignments containing this domain show that the Gp110 E101 residue is conserved (suggesting that is is the catalytic residue), and followed by serine (a common feature in lysozymes). The structure of endolysins varies depending on their origin. In general, most of the endolysins from phages infecting Gram-positive bacteria have a modular structure consisting of one or two N-terminal enzymatic active domains (EADs) and a C-terminal cell wall binding domain (CBD) separated by a short linker. In silico analysis indicate that this endolysin has a modular structure harboring this EAD family at the C terminus and a PG_binding_1 CBD at the N terminus. 173 matched cddid_all.tbl CDD pfam11861 pfam11861 463375 DUF3381 Domain of unknown function (DUF3381). This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 156 to 174 amino acids in length. This domain is found associated with pfam07780, pfam01728. 150 matched cddid_all.tbl CDD pfam11862 pfam11862 432139 DUF3382 Domain of unknown function (DUF3382). This domain is functionally uncharacterized. This domain is found in bacteria. This presumed domain is about 100 amino acids in length. This domain is found associated with pfam02653. 98 matched cddid_all.tbl CDD pfam11863 pfam11863 432140 DUF3383 Protein of unknown function (DUF3383). This family of proteins are functionally uncharacterized. This protein is found in bacteria and viruses. Proteins in this family are typically between 356 to 501 amino acids in length. 493 matched cddid_all.tbl CDD pfam11864 pfam11864 463376 DUF3384 Domain of unknown function (DUF3384). This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 422 to 486 amino acids in length. This domain is found associated with pfam02145. 407 matched cddid_all.tbl CDD pfam11865 pfam11865 463377 DUF3385 Domain of unknown function (DUF3385). This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 160 to 172 amino acids in length. This domain is found associated with pfam00454, pfam02260, pfam02985, pfam02259 and pfam08771. 160 matched cddid_all.tbl CDD pfam11866 pfam11866 432143 DUF3386 Protein of unknown function (DUF3386). This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are about 220 amino acids in length. 211 matched cddid_all.tbl CDD pfam11867 pfam11867 432144 DUF3387 Domain of unknown function (DUF3387). This domain is functionally uncharacterized. This domain is found in bacteria and archaea. This presumed domain is typically between 255 to 340 amino acids in length. This domain is found associated with pfam04851, pfam04313. 331 matched cddid_all.tbl CDD pfam11868 pfam11868 432145 DUF3388 Protein of unknown function (DUF3388). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 261 to 275 amino acids in length. This protein is found associated with pfam01842. 190 matched cddid_all.tbl CDD pfam11869 pfam11869 432146 DUF3389 Protein of unknown function (DUF3389). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are about 80 amino acids in length. 75 matched cddid_all.tbl CDD pfam11870 pfam11870 432147 LutB_C Lactate utilization protein B, C-terminal. This domain is functionally uncharacterized. This domain is found at the C-terminal of a family of 4Fe-4S, iron-sulphur cluster binding proteins, including Lactate utilization protein B (LutB). These proteins have a perfect 4Fe-4S binding motif C-x(2)-C-x(2)-C-x(3)-CP followed by either a perfect or imperfect (the first Cys replaced by Ser) second copy. Members probably bind two 4Fe-4S iron-sulphur clusters. This domain is found in LutB proteins in association with the LUD domain (pfam02589) and usually Fer4_8 (pfam13183). The LutABC operon is involved in lactate-utilization and is essential. 86 matched cddid_all.tbl CDD pfam11871 pfam11871 432148 DUF3391 Domain of unknown function (DUF3391). This functionally uncharacterized, N-terminal domain is found in a number of bacterial proteins, including Cyclic di-GMP phosphodiesterase PA4108. It is often found associated with the HD domain pfam13328. 136 matched cddid_all.tbl CDD pfam11872 pfam11872 432149 DUF3392 Protein of unknown function (DUF3392). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are about 110 amino acids in length. 104 matched cddid_all.tbl CDD pfam11873 pfam11873 432150 Mltc_N Membrane-bound lytic murein transglycosylase C, N-terminal domain. This domain is found associated with pfam01464. It is the N-terminal structural domain of MltC (Membrane-bound lytic murein transglycosylase C), one of the seven lytic transglycosylases found in the genome of the Gram-negative bacterium Escherichia coli. The role of the N-terminal domain is suggested to be important not as a mere structural extension of the active site beyond what is seen in other lytic transglycosylases but one that creates a peptide-binding site at position +2. 161 matched cddid_all.tbl CDD pfam11874 pfam11874 432151 DUF3394 Domain of unknown function (DUF3394). This domain is functionally uncharacterized. This domain is found in bacteria. This presumed domain is about 190 amino acids in length. This domain is found associated with pfam06808. 179 matched cddid_all.tbl CDD pfam11875 pfam11875 463378 DnaJ-like_C11_C DnaJ-like protein C11, C-terminal. This is the C-terminal domain found in DnaJ-like proteins, including DnaJ homolog subfamily C member 11 (DNAJC11) from mammals and Chaperone protein dnaJ 13 from Arabidopsis. DNAJC11 is a mitochondrial outer membrane protein involved in mitochondrial biogenesis and in the response to microenvironment changes and requirements. The J-domain is mediated its mitochondrial localization, while this domain is critical for protein-protein interactions. 144 matched cddid_all.tbl CDD pfam11876 pfam11876 463379 DUF3396 Protein of unknown function (DUF3396). This family of proteins are functionally uncharacterized. This protein is found in bacteria and viruses. Proteins in this family are typically between 302 to 382 amino acids in length. 205 matched cddid_all.tbl CDD pfam11877 pfam11877 432154 DUF3397 Protein of unknown function (DUF3397). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 114 to 128 amino acids in length. 112 matched cddid_all.tbl CDD pfam11878 pfam11878 463380 DOCK_C-D_N Dedicator of cytokinesis C/D, N terminal. This entry represents the N-terminal domain of the DOCK-C subfamily (DOCK 6, 7, 8) and DOCK-D subfamily (DOCK 9, 10, 11). DOCK family members are evolutionarily conserved guanine nucleotide exchange factors (GEFs) for Rho-family GTPases, required during several cellular processes, such as cell motility and phagocytosis. DOCK proteins are categorized into four subfamilies based on their sequence homology: DOCK-A (DOCK1/180, 2, 5), DOCK-B subfamily (DOCK3, 4), DOCK-C subfamily (DOCK6, 7, 8), DOCK-D subfamily (DOCK9, 10, 11). 112 matched cddid_all.tbl CDD pfam11879 pfam11879 463381 DUF3399 Domain of unknown function (DUF3399). This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is about 100 amino acids in length. This domain is found associated with pfam02214, pfam00520. 76 matched cddid_all.tbl CDD pfam11880 pfam11880 463382 DUF3400 Domain of unknown function (DUF3400). This domain is functionally uncharacterized. This domain is found in bacteria. This presumed domain is about 50 amino acids in length. This domain is found associated with pfam02754, pfam02913, pfam01565. 45 matched cddid_all.tbl CDD pfam11881 pfam11881 463383 SPAR_C C-terminal domain of SPAR protein. This domain is found st the C-terminus of many spine-associated Rap GTPase-activating - SPAR - proteins in eukaryotes. This domain is found associated with pfam02145, pfam00595. The exact function is not known. 242 matched cddid_all.tbl CDD pfam11882 pfam11882 463384 DUF3402 Domain of unknown function (DUF3402). This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 350 to 473 amino acids in length. This domain is found associated with pfam07923. 432 matched cddid_all.tbl CDD pfam11883 pfam11883 463385 DUF3403 Domain of unknown function (DUF3403). This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is about 50 amino acids in length. This domain is found associated with pfam00069, pfam08276, pfam00954, pfam01453. 47 matched cddid_all.tbl CDD pfam11884 pfam11884 432161 DUF3404 Domain of unknown function (DUF3404). This domain is functionally uncharacterized. This domain is found in bacteria. This presumed domain is about 260 amino acids in length. This domain is found associated with pfam02518, pfam00512. 259 matched cddid_all.tbl CDD pfam11885 pfam11885 432162 DUF3405 Protein of unknown function (DUF3405). This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 636 to 810 amino acids in length. 493 matched cddid_all.tbl CDD pfam11886 pfam11886 432163 TOC159_MAD Translocase of chloroplast 159/132, membrane anchor domain. This is the membrane-anchor domain of translocase of chloroplast 159, TOC159/132. This domain is present in plants at the C-terminus of the GTPase, AIG1, pfam04548, and anchors the GTPas region to the outer membrane of the chloroplast. The domain may carry a very C-terminal sequence motif that resembles a transit peptide. 267 matched cddid_all.tbl CDD pfam11887 pfam11887 432164 Mce4_CUP1 Cholesterol uptake porter CUP1 of Mce4, putative. Mce4_CUP1 is a family of putative Mce4 transporters of cholesterol. The domain is found associated with pfam02470. The full TCDB classification for this family in conjunction with PF02470 is TC:3.A.1.27.4. 222 matched cddid_all.tbl CDD pfam11888 pfam11888 432165 DUF3408 Protein of unknown function (DUF3408). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 amino acids in length. 136 matched cddid_all.tbl CDD pfam11889 pfam11889 288721 Capsid_pestivir Capsid protein C, pestivirus. This domain is found in the genome polyprotein from Pestivirus. It covers part of the capsid protein C region in the polyprotein. 56 matched cddid_all.tbl CDD pfam11890 pfam11890 432166 DUF3410 Domain of unknown function (DUF3410). This domain is functionally uncharacterized. This domain is found in bacteria. This presumed domain is about 90 amino acids in length. This domain is found associated with pfam02826, pfam00389. This domain has a conserved RRE sequence motif. 81 matched cddid_all.tbl CDD pfam11891 pfam11891 432167 RETICULATA-like Protein RETICULATA-related. This entry represents RETICULATA and related proteins from plants. Arabidopsis RETICULATA protein is involved in differential development of bundle sheath and mesophyll cell chloroplasts. 177 matched cddid_all.tbl CDD pfam11892 pfam11892 463386 DUF3412 Domain of unknown function (DUF3412). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 120 amino acids in length. This domain is found associated with pfam03641. 121 matched cddid_all.tbl CDD pfam11893 pfam11893 432169 DUF3413 Domain of unknown function (DUF3413). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 250 amino acids in length. This domain is found associated with pfam00884. 246 matched cddid_all.tbl CDD pfam11894 pfam11894 463387 Nup192 Nuclear pore complex scaffold, nucleoporins 186/192/205. This is a family of eukaryotic nucleoporins of several different sizes. All of them are long and form the scaffold of the nuclear pore complex. Nup192 in particular modulates the permeability of the central channel of the NPC central or nuclear pore complex. 1484 matched cddid_all.tbl CDD pfam11895 pfam11895 403189 Peroxidase_ext Fungal peroxidase extension region. This region is found as an extension to a haem peroxidase domain in some fungi. This region is about 80 amino acids in length and forms an extended structure on the surface of the peroxidase domain pfam00141. 72 matched cddid_all.tbl CDD pfam11896 pfam11896 463388 GlgE_dom_N_S Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S. This entry represents domain N and S of GlgE. GlgE is a homodimer and a member of the GH13_3 CAZy subfamily. Each subunit of GlgE is composed of five domains, domain A is a (beta/alpha)8 barrel, typical of the catalytic domain of this family of enzymes, that forms part of the dimer interface. Domain B corresponds to an insertion after the third beta-strand of domain A. In GlgE, domain B is fairly typical for a GH13 enzyme in having a pair of anti-parallel strands and one short helix. The C-terminal domain C has a beta-sandwich fold. The N-terminal domain N, which also consists of a beta-sandwich fold, forms the core of the dimer interface. The final domain arises from an insertion within domain N and forms a four-helix bundle where the last helix is discontinuous and slightly kinked. This domain, which will henceforth be referred to as domain S, participates in the dimer interface and interacts directly with domain B of the neighbouring subunit. 185 matched cddid_all.tbl CDD pfam11897 pfam11897 432172 DUF3417 Protein of unknown function (DUF3417). This family of proteins are functionally uncharacterized. This protein is found in bacteria and archaea. Proteins in this family are typically between 145 to 860 amino acids in length. This protein is found associated with pfam00343. This protein has a conserved AYF sequence motif. 109 matched cddid_all.tbl CDD pfam11898 pfam11898 463389 DUF3418 Domain of unknown function (DUF3418). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is typically between 582 to 594 amino acids in length. This domain is found associated with pfam07717, pfam00271, pfam04408. 587 matched cddid_all.tbl CDD pfam11899 pfam11899 432174 DUF3419 Protein of unknown function (DUF3419). This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 398 to 802 amino acids in length. 382 matched cddid_all.tbl CDD pfam11900 pfam11900 314729 DUF3420 Domain of unknown function (DUF3420). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 50 amino acids in length. This domain is found associated with pfam00023. 47 matched cddid_all.tbl CDD pfam11901 pfam11901 463390 DUF3421 Protein of unknown function (DUF3421). This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 119 to 296 amino acids in length. 114 matched cddid_all.tbl CDD pfam11902 pfam11902 432176 DUF3422 Protein of unknown function (DUF3422). This family of proteins are functionally uncharacterized. This protein is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 426 to 444 amino acids in length. 415 matched cddid_all.tbl CDD pfam11903 pfam11903 432177 ParD_like ParD-like antitoxin of type II bacterial toxin-antitoxin system. ParD-like antitoxin is a family of archaeal and bacterial proteins of a type II bacterial toxin-antitoxin system. Many of the cognate toxins for these molecules fall into family ParE-like_toxin, pfam15781. Gene-pairs are expressed from the same operon, the toxin of the pair being expressed first, eg, for UniProtKB:Q3AQ93 and UniProtKB:Q3AQ94. 73 matched cddid_all.tbl CDD pfam11904 pfam11904 463391 GPCR_chapero_1 GPCR-chaperone. This domain, and the associated ANK family repeat pfam00023 domain, together act as a chaperone for biogenesis and folding of the DP receptor for prostaglandin D2. 298 matched cddid_all.tbl CDD pfam11905 pfam11905 403197 DUF3425 Domain of unknown function (DUF3425). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 120 to 143 amino acids in length. 128 matched cddid_all.tbl CDD pfam11906 pfam11906 432179 DUF3426 Protein of unknown function (DUF3426). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 262 to 463 amino acids in length. 147 matched cddid_all.tbl CDD pfam11907 pfam11907 463392 DUF3427 Domain of unknown function (DUF3427). This presumed domain is functionally uncharacterized. This domain is found in bacteria and archaea. This domain is typically between 243 to 275 amino acids in length. This domain is found associated with pfam04851, pfam00271. 278 matched cddid_all.tbl CDD pfam11909 pfam11909 432181 NdhN NADH-quinone oxidoreductase cyanobacterial subunit N. The proton-pumping NADH:ubiquinone oxidoreductase catalyzes the electron transfer from NADH to ubiquinone linked with proton translocation across the membrane. It is the largest, most complex and least understood of the respiratory chain enzymes and is referred to as Complex I. The subunit composition of the enzyme varies between groups of organizms. Complex I originating from mammalian mitochondria contains 45 different proteins, whereas in bacteria, the corresponding complex NDH-1 consists of 14 different polypeptides. homologs of these 14 proteins are found among subunits of the mitochondrial complex I, and therefore bacterial NDH-1 might be considered a model proton-pumping NADH dehydrogenase with a minimal set of subunits. Escherichia coli NDH-1 readily disintegrates into 3 subcomplexes: a water-soluble NADH dehydrogenase fragment (NuoE, -F, and -G),the connecting fragment (NuoB, -C, -D, and -I), and the membrane fragment (NuoA, -H, -J, -K, -L, -M, -N). In cyanobacteria and their descendants, the chloroplasts of green plants, the subunit composition of NDH-1 remains obscure. The genes for eleven subunits NdhA-NdhK, homologous to the NuoA-NuoD and NuoH-NuoN of the E. coli complex, have been found in the genome of Synechocystis sp. PCC 6803 which has a family of 6 ndhD genes and a family of 3 ndhF genes. Two reported multisubunit complexes, NDH-1L and NDH-1M, represent distinct NDH-1 complexes in the thylakoid membrane of Synechocystis 6803 -cyanobacterium. NDH-1L was shown to be essential for photoheterotrophic cell growth, whereas expression of NDH-1M was a prerequisite for CO2 uptake and played an important role in growth of cells at low CO2. Here we report the subunit composition of these two complexes. Fifteen proteins were discovered in NDH-1L including NdhL, a new component of the membrane fragment, and Ssl1690 (designated as NdhO), a novel peripheral subunit. The cyanobacterial NDH-1 complex contains additional subunits, NdhM and NdhN, compared with the minimal set of the bacterial enzyme and these seem to be specific for thylakoid-located NDH-1 of photosynthetic organizms. 150 matched cddid_all.tbl CDD pfam11910 pfam11910 432182 NdhO Cyanobacterial and plant NDH-1 subunit O. The proton-pumping NADH:ubiquinone oxidoreductase catalyzes the electron transfer from NADH to ubiquinone linked with proton translocation across the membrane. It is the largest, most complex and least understood of the respiratory chain enzymes and is referred to as Complex I. The subunit composition of the enzyme varies between groups of organizms. Complex I originating from mammalian mitochondria contains 45 different proteins, whereas in bacteria, the corresponding complex NDH-1 consists of 14 different polypeptides. homologs of these 14 proteins are found among subunits of the mitochondrial complex I, and therefore bacterial NDH-1 might be considered a model proton-pumping NADH dehydrogenase with a minimal set of subunits. Escherichia coli NDH-1 readily disintegrates into 3 subcomplexes: a water-soluble NADH dehydrogenase fragment (NuoE, -F, and -G),the connecting fragment (NuoB, -C, -D, and -I), and the membrane fragment (NuoA, -H, -J, -K, -L, -M, -N). In cyanobacteria and their descendants, the chloroplasts of green plants, the subunit composition of NDH-1 remains obscure. The genes for eleven subunits NdhA-NdhK, homologous to the NuoA-NuoD and NuoH-NuoN of the E. coli complex, have been found in the genome of Synechocystis sp. PCC 6803 which has a family of 6 ndhD genes and a family of 3 ndhF genes. Two reported multisubunit complexes, NDH-1L and NDH-1M, represent distinct NDH-1 complexes in the thylakoid membrane of Synechocystis 6803 -cyanobacterium. NDH-1L was shown to be essential for photoheterotrophic cell growth, whereas expression of NDH-1M was a prerequisite for CO2 uptake and played an important role in growth of cells at low CO2. Here we report the subunit composition of these two complexes. Fifteen proteins were discovered in NDH-1L including NdhL, a new component of the membrane fragment, and Ssl1690 (designated as NdhO), a novel peripheral subunit. The three nuclear-encoded subunits NdhM,NdhN and NdhO are vital for the functional integrity of the plastidial complex. 65 matched cddid_all.tbl CDD pfam11911 pfam11911 463393 DUF3429 Protein of unknown function (DUF3429). This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 147 to 245 amino acids in length. 141 matched cddid_all.tbl CDD pfam11912 pfam11912 256719 CfaA_B_C Counting factor-associated protein A/B/C. Developing Dictyostelium (Slime mold) cells form large aggregation streams that break up into groups of cells. Each group then becomes a fruiting body. Cells sense if there are too many cells in a stream by sensing the concentration of counting factor (CF), a protein complex secreted by the aggregating cells. This entry includes counting factor-associated protein A/B/C from Slime mold. 204 matched cddid_all.tbl CDD pfam11913 pfam11913 432184 DUF3431 Protein of unknown function (DUF3431). This family of proteins are functionally uncharacterized. This protein is found in eukaryotes. Proteins in this family are typically between 291 to 390 amino acids in length. This protein has a conserved NLRC sequence motif. 211 matched cddid_all.tbl CDD pfam11914 pfam11914 403204 DUF3432 Domain of unknown function (DUF3432). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 100 amino acids in length. This domain is found associated with pfam00096. This domain has two conserved sequence motifs: YPSPV and PSP. 98 matched cddid_all.tbl CDD pfam11915 pfam11915 463394 DUF3433 Protein of unknown function (DUF3433). This is a family of functionally uncharacterized proteins. The family is found in eukaryotes, and represents the conserved central region of the member proteins. 91 matched cddid_all.tbl CDD pfam11916 pfam11916 463395 Vac14_Fig4_bd Vacuolar protein 14 C-terminal Fig4p binding. Vac14 is a scaffold for the Fab1 kinase complex, a complex that allows for the dynamic interconversion of PI3P and PI(3,5)P2p (phosphoinositide phosphate (PIP) lipids, that are generated transiently on the cytoplasmic face of selected intracellular membranes). This interconversion is regulated by at least five proteins in yeast: the lipid kinase Fab1p, lipid phosphatase Fig4p, the Fab1p activator Vac7p, the Fab1p inhibitor Atg18p, and Vac14p, a protein required for the activity of both Fab1p and Fig4p. The C-terminal region of Vac14 binds to Fig4p. The full length Vac14 in yeasts is likely to be a protein carrying a succession of HEAT repeats, most of which have now degenerated. This regulatory system is crucial for the proper functioning of the mammalian nervous system. 179 matched cddid_all.tbl CDD pfam11917 pfam11917 371796 DUF3435 Protein of unknown function (DUF3435). This family of proteins are functionally uncharacterized. This protein is found in eukaryotes. Proteins in this family are typically between 435 to 791 amino acids in length. This family is related to pfam00589 suggesting it may be an integrase enzyme. 418 matched cddid_all.tbl CDD pfam11918 pfam11918 463396 Peptidase_S41_N N-terminal domain of Peptidase_S41 in eukaryotic IRBP. Peptidase_S41_N is a family found at the N-terminus of the functional unit of interphotoreceptor retinoid binding proteins 3, IRBP, in eukaryotes. From the structure of PDB:1j7x, the domain forms the N-terminal end of the module which is characterized as a serine-peptidase, pfam03572. Peptidase_S41_N forms a three-helix bundle followed by a small beta strand and is termed domain A. Part of the peptidase domain folds back over domain A to create a largely hydrophobic cleft between the two domains. On binding of ligand domain A is structurally rearranged with respect to domain B. 129 matched cddid_all.tbl CDD pfam11919 pfam11919 463397 DUF3437 Domain of unknown function (DUF3437). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 142 to 163 amino acids in length. 86 matched cddid_all.tbl CDD pfam11920 pfam11920 432189 DUF3438 Protein of unknown function (DUF3438). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 276 to 307 amino acids in length. 288 matched cddid_all.tbl CDD pfam11921 pfam11921 288750 DUF3439 Domain of unknown function (DUF3439). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 46 to 94 amino acids in length. This domain is found associated with pfam01462, pfam00560. 122 matched cddid_all.tbl CDD pfam11922 pfam11922 432190 DUF3440 Domain of unknown function (DUF3440). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is typically between 53 to 190 amino acids in length. This domain is found associated with pfam01507. This domain has a conserved KND sequence motif. 181 matched cddid_all.tbl CDD pfam11923 pfam11923 432191 NFACT-C NFACT protein C-terminal domain. This is the C-terminal domain of the NFACT (NEMF, FbpA, Caliban, and Tae2) proteins involved in the ribosomal quality control pathway. This context is conserved in archaea and eukaryotes, but NFACT proteins in bacteria lack the NFACT-C domain. 104 matched cddid_all.tbl CDD pfam11924 pfam11924 432192 IAT_beta Inverse autotransporter, beta-domain. This is a family of beta-barrel porin-like outer membrane proteins from enteropathogenic Gram-negative bacteria. Intimins and invasins are virulence factors produced by pathogenic Gram-negative bacteria. They carry C-terminal extracellular passenger domains that are involved in adhesion to host cells and N-terminal beta domains that are embedded in the outer membrane. This family represents the beta-barrel porin-like domain in the outer membrane that can be found in intimins, invasins and some inverse autotransporters. 279 matched cddid_all.tbl CDD pfam11925 pfam11925 432193 DUF3443 Protein of unknown function (DUF3443). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 400 to 434 amino acids in length. This protein has two conserved sequence motifs: NPV and DNNG. 365 matched cddid_all.tbl CDD pfam11926 pfam11926 463398 DUF3444 Domain of unknown function (DUF3444). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 210 amino acids in length. This domain is found associated with pfam00226. This domain has two conserved sequence motifs: FSH and FSH. 210 matched cddid_all.tbl CDD pfam11927 pfam11927 463399 DUF3445 Protein of unknown function (DUF3445). This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 264 to 418 amino acids in length. This protein has a conserved RLP sequence motif. This protein has two completely conserved R residues that may be functionally important. 231 matched cddid_all.tbl CDD pfam11928 pfam11928 463400 DUF3446 Early growth response N-terminal domain. Proteins containing this domain include early growth response protein 1/2/3 (EGR1/2/3). EGR1 is a transcriptional regulator that binds specifically to 9-bp target sequences containing two CpG sites that can potentially be methylated at four cytosine bases. EGR2, also known as Krox20, is an E3 ligase that sumoylates its Nab coregulators. This domain has a single completely conserved residue P that may be functionally important. Furthermore, it is found associated with pfam00096. 104 matched cddid_all.tbl CDD pfam11929 pfam11929 371804 DUF3447 Domain of unknown function (DUF3447). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 80 amino acids in length. This domain is found associated with pfam00023. This domain has a conserved SHN sequence motif. It seems likely that this region represents divergent Ankyrin repeats. 76 matched cddid_all.tbl CDD pfam11931 pfam11931 432197 SF3a60_Prp9_C SF3a60/Prp9 C-terminal. This domain corresponds to the C-terminal region of SF3a60 subunit (Prp9 in yeast counterpart) from the highly conserved heterotrimeric complex SF3a found in eukaryotes. It is essential for pre-mRNA splicing that functions in spliceosome assembly within the mature U2 snRNP (small ribonucleoprotein particle). This domain has two conserved sequence motifs: PIP and CEICG. It contains a zinc-finger domain of the C2H2-type which might be important for RNA binding and protein-protein interactions with components of the SF3b complex. 120 matched cddid_all.tbl CDD pfam11932 pfam11932 432198 DUF3450 Protein of unknown function (DUF3450). This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are about 260 amino acids in length. 238 matched cddid_all.tbl CDD pfam11933 pfam11933 463401 Na_trans_cytopl Cytoplasmic domain of voltage-gated Na+ ion channel. This is a large cytoplasmic domain towards the start of voltage-dependent sodium ion channel proteins in eukaryotes. It is found closely associated with pfam06512 and pfam00520. 163 matched cddid_all.tbl CDD pfam11934 pfam11934 463402 DUF3452 Domain of unknown function (DUF3452). This presumed domain is functionally uncharacterized. This domain is found in bacteria and eukaryotes. This domain is typically between 124 to 150 amino acids in length. This domain is found associated with pfam01858, pfam01857. This domain has a single completely conserved residue W that may be functionally important. 134 matched cddid_all.tbl CDD pfam11935 pfam11935 463403 SYMPK_PTA1_N Symplekin/PTA1 N-terminal. This is the N-terminal domain found in the symplekin protein from animals and PTA1 protein from budding yeasts and is typically between 239 to 261 amino acids in length. Symplekin is a scaffold protein that functions as a component of a multimolecular complex involved in histone mRNA 3'-end processing. PTA1 is involved in pre-tRNA processing. PTA1 is a subunit of the cleavage and polyadenylation factor (CPF), which plays a key role in polyadenylation-dependent pre-mRNA 3'-end formation and cooperates with cleavage factors including the CFIA complex and NAB4/CFIB. This domain has the ARM or HEAT fold, with seven pairs of antiparallel alpha-helices arranged in the shape of an arc. It is important for interaction with Ssu72 and stimulates Ssu72 C-terminal domain phosphatase activity in vitro. 218 matched cddid_all.tbl CDD pfam11937 pfam11937 314761 DUF3455 Protein of unknown function (DUF3455). This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 174 to 251 amino acids in length. 142 matched cddid_all.tbl CDD pfam11938 pfam11938 463404 DUF3456 TLR4 regulator and MIR-interacting MSAP. This family of proteins, found from plants to humans, is PRAT4 (A and B), a Protein Associated with Toll-like receptor 4. The Toll family of receptors - TLRs - plays an essential role in innate recognition of microbial products, the first line of defence against bacterial infection. PRAT4A influences the subcellular distribution and the strength of TLR responses and alters the relative activity of each TLR. PRAT4B regulates TLR4 trafficking to the cell surface and the extent of its expression there. TLR4 recognizes lipopolysaccharide (LPS), one of the most immuno-stimulatory glycolipids constituting the outer membrane of the Gram-negative bacteria. This family has also been described as a SAP-like MIR-interacting protein family. 151 matched cddid_all.tbl CDD pfam11939 pfam11939 432203 NiFe-hyd_HybE [NiFe]-hydrogenase assembly, chaperone, HybE. Members of this family are chaperones for the assembly of [NiFe] hydrogenases, in the family of HybE, which is specific for hydrogenase-2 of Escherichia coli. Members often have an additional N-terminal rubredoxin domain. 151 matched cddid_all.tbl CDD pfam11940 pfam11940 463405 DUF3458 Domain of unknown function (DUF3458) Ig-like fold. This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. The domain has an Ig-like fold. This domain is found associated with pfam01433. 95 matched cddid_all.tbl CDD pfam11941 pfam11941 432205 DUF3459 Domain of unknown function (DUF3459). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 110 amino acids in length. This domain is found associated with pfam00128, pfam02922. 92 matched cddid_all.tbl CDD pfam11942 pfam11942 463406 Spt5_N Spt5 transcription elongation factor, acidic N-terminal. This is the very acidic N-terminal region of the early transcription elongation factor Spt5. The Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The actual function of this N-terminal domain is not known although it is dispensable for binding to Spt4. 97 matched cddid_all.tbl CDD pfam11943 pfam11943 463407 DUF3460 Protein of unknown function (DUF3460). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are about 70 amino acids in length. This protein has a conserved WDK sequence motif. 58 matched cddid_all.tbl CDD pfam11944 pfam11944 432208 DUF3461 Protein of unknown function (DUF3461). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are about 130 amino acids in length. This protein has two conserved sequence motifs: KFK and HLE. 124 matched cddid_all.tbl CDD pfam11945 pfam11945 463408 WASH_WAHD WAHD domain of WASH complex. This domain forms part of the WASH-complex of domains and proteins that activates the Arp2/3 complex, see pfam04062. The Arp2/3 complex regulates endocytosis, sorting, and trafficking within the cell. The WAHD domain attaches to the FAM21 proteins via its N-terminal residues and to the microtubules via its C-terminal residues. 286 matched cddid_all.tbl CDD pfam11946 pfam11946 432210 DUF3463 Domain of unknown function (DUF3463). This presumed domain is functionally uncharacterized. This domain is found in bacteria and archaea. This domain is about 140 amino acids in length. This domain is found associated with pfam04055. This domain has two conserved sequence motifs: CTPWG and PCYL, plus a highly conserved CxxCxxHC motif. 134 matched cddid_all.tbl CDD pfam11947 pfam11947 432211 DUF3464 Photosynthesis affected mutant 68. This entry includes chloroplastic protein PAM68 and the Sll0933 homolog from Cyanobacteria (blue-green algae). PAM68 is involved in early steps in photosystem II (PSII) biogenesis and in maturation and stability of newly synthesized psbA protein. 150 matched cddid_all.tbl CDD pfam11948 pfam11948 432212 DUF3465 Protein of unknown function (DUF3465). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif. 124 matched cddid_all.tbl CDD pfam11949 pfam11949 432213 DUF3466 Protein of unknown function (DUF3466). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 564 to 612 amino acids in length. 605 matched cddid_all.tbl CDD pfam11950 pfam11950 432214 DUF3467 Protein of unknown function (DUF3467). This family of proteins are functionally uncharacterized. This protein is found in bacteria, archaea and viruses. Proteins in this family are typically between 101 to 118 amino acids in length. 92 matched cddid_all.tbl CDD pfam11951 pfam11951 403235 Fungal_trans_2 Fungal specific transcription factor domain. This family of are likely to be transcription factors. This protein is found in fungi. Proteins in this family are typically between 454 to 826 amino acids in length. This protein is found associated with pfam00172. 384 matched cddid_all.tbl CDD pfam11952 pfam11952 463409 XTBD XRN-Two Binding Domain, XTBD. XTBD is a family of eukaryotic proteins that act as an XRN2-binding module. XRN2 is an essential exoribonuclease in eukaryotes that processes and degrades a number of different substrates. XTBD is found on a number of different proteins to link them to XRN, such as PAXT-1. 85 matched cddid_all.tbl CDD pfam11953 pfam11953 463410 DUF3470 Domain of unknown function (DUF3470). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 50 amino acids in length. This domain is found associated with pfam00037. This domain has a single completely conserved residue N that may be functionally important. 42 matched cddid_all.tbl CDD pfam11954 pfam11954 432217 DUF3471 Domain of unknown function (DUF3471). This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 98 to 114 amino acids in length. This domain is found associated with pfam00144. 95 matched cddid_all.tbl CDD pfam11955 pfam11955 432218 PORR Plant organelle RNA recognition domain. This family, which was previously known as DUF860, has been shown to be a component of group II intron ribonucleoprotein particles in maize chloroplasts. The domain is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. All of the members are predicted to localize to mitochondria or chloroplasts. It seems likely that most PORR proteins function in organellar RNA metabolism. 328 matched cddid_all.tbl CDD pfam11956 pfam11956 463411 KCNQC3-Ank-G_bd Ankyrin-G binding motif of KCNQ2-3. Interactions with ankyrin-G are crucial to the localization of voltage-gated sodium channels (VGSCs) at the axon initial segment and for neurons to initiate action potentials. This conserved 9-amino acid motif ((V/A)P(I/L)AXXE(S/D)D) is required for ankyrin-G binding and functions to localize sodium channels to a variety of 'excitable' membrane domains both inside and outside of the nervous system. This motif has also been identified in the potassium channel 6TM proteins KCNQ2 and KCNQ3, that correspond to the M channels that exert a crucial influence over neuronal excitability. KCNQ2/KCNQ3 channels are preferentially localized to the surface of axons both at the axonal initial segment and more distally, and this axonal initial segment targeting of surface KCNQ channels is mediated by these ankyrin-G binding motifs of KCNQ2 and KCNQ3. KCNQ3 is a major determinant of M channel localization to the AIS, rather than KCNQ2. Phylogenetic analysis reveals that anchor motifs evolved sequentially in chordates (NaV channel) and jawed vertebrates (KCNQ2/3). 101 matched cddid_all.tbl CDD pfam11957 pfam11957 463412 efThoc1 THO complex subunit 1 transcription elongation factor. The THO complex plays a role in coupling transcription elongation to mRNA export. It is composed of subunits THP2, HPR1, THO2 and MFT1. The THO complex is a nuclear complex that is required for transcription elongation through genes containing tandemly repeated DNA sequences. The THO complex is also part of the TREX (TRanscription EXport) complex that is involved in coupling transcription to export of mRNAs to the cytoplasm. 464 matched cddid_all.tbl CDD pfam11958 pfam11958 432221 DUF3472 Domain of unknown function (DUF3472). This presumed domain is functionally uncharacterized. This domain is found in bacteria, eukaryotes and viruses. This domain is typically between 174 to 190 amino acids in length. This domain has a single completely conserved residue G that may be functionally important. 173 matched cddid_all.tbl CDD pfam11959 pfam11959 432222 DUF3473 Domain of unknown function (DUF3473). This presumed domain is functionally uncharacterized. This domain is found in bacteria and archaea. This domain is about 130 amino acids in length. This domain is found associated with pfam01522. This domain has two completely conserved residues (P and H) that may be functionally important. 130 matched cddid_all.tbl CDD pfam11960 pfam11960 403244 DUF3474 Domain of unknown function (DUF3474). This presumed domain is functionally uncharacterized. This domain is found in bacteria and eukaryotes. This domain is typically between 126 to 140 amino acids in length. This domain is found associated with pfam00487. 127 matched cddid_all.tbl CDD pfam11961 pfam11961 432223 DUF3475 Domain of unknown function (DUF3475). This entry represents the N-terminal domain of PSI proteins from Arabidopsis. This domain is found associated with pfam05003. PSI1 was identified as a gene that is co-expressed with the phytosulfokine (PSK) receptor genes PSKR1 and PSKR2 in Arabidopsis thaliana. PSI proteins are plant-specific and promote growth. 57 matched cddid_all.tbl CDD pfam11962 pfam11962 371823 Peptidase_G2 Peptidase_G2, IMC autoproteolytic cleavage domain. This domain is found at the very C-terminus of bacteriophage parallel beta-helical tailspike proteins. It carries the enzymic residues that induce autoproteolytic cleavage to bring about maturation of the folding process of the helix in a chaperone-like manner. The domain thus mediates the assembly of a large tailspike protein and then releases itself after maturation. These C-terminal regions that autoproteolytically release themselves after maturation are exchangeable between functionally unrelated N-terminal proteins and have been identified in a number of bacteriophage tailspike proteins. 221 matched cddid_all.tbl CDD pfam11963 pfam11963 152398 B-CoV_A_NSP1 Betacoronavirus, lineage A, NSP1. This family the N-terminal region of the Betacoronavirus polyprotein which contains non-structural protein 1 (Nsp1) from Betacoronavirus lineage A. This protein is important for viral replication and pathogenesis. It suppresses the host innate immune functions by inhibiting type I interferon expression and host antiviral signalling pathways. 355 matched cddid_all.tbl CDD pfam11964 pfam11964 432224 SpoIIAA-like SpoIIAA-like. These proteins adopt an alpha/beta SpoIIAA-like fold, similar to that found in STAT (pfam01740). They adopt open and closed conformations arising from different arrangements of their alpha-2 and alpha-3 helices. They may be membrane associated and may function as carriers of non-polar compounds. 105 matched cddid_all.tbl CDD pfam11965 pfam11965 463413 DUF3479 Domain of unknown function (DUF3479). This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. This domain is about 160 amino acids in length. This domain is found associated with pfam02514. 159 matched cddid_all.tbl CDD pfam11966 pfam11966 432226 SSURE SSURE domain. Streptococcal surface repeat domain - SSURE - is a protein fragment found to bind to extracellular matrix protein fibronectin but not to collagen or submaxillary mucin in Streptococci. Anti-SSURE antibodies recognized the corresponding protein on the surface of streptococcal cells. The full-length proteins are thus fibronectin-binding surface adhesins. The structure was predicted to be composed of two subdomains. 149 matched cddid_all.tbl CDD pfam11967 pfam11967 463414 RecO_N Recombination protein O N terminal. Recombination protein O (RecO) is involved in DNA repair and pfam00470 pathway recombination. This domain forms a beta barrel structure. 80 matched cddid_all.tbl CDD pfam11968 pfam11968 371825 Bmt2 25S rRNA (adenine(2142)-N(1))-methyltransferase, Bmt2. This entry represents Bmt2 and its homogues. In Saccharomyces cerevisiae, Bmt2 is a nucleolar S-adenosylmethionine-dependent rRNA methyltransferase that is responsible for the N-1-methyl-adenosine base modification of 25S rRNA.It specifically methylates the N1 position of adenine 2142 in 25S rRNA. 221 matched cddid_all.tbl CDD pfam11969 pfam11969 463415 DcpS_C Scavenger mRNA decapping enzyme C-term binding. This family consists of several scavenger mRNA decapping enzymes (DcpS) and is the C-terminal region. DcpS is a scavenger pyrophosphatase that hydrolyses the residual cap structure following 3' to 5' decay of an mRNA. The association of DcpS with 3' to 5' exonuclease exosome components suggests that these two activities are linked and there is a coupled exonucleolytic decay-dependent decapping pathway. The C-terminal domain contains a histidine triad (HIT) sequence with three histidines separated by hydrophobic residues. The central histidine within the DcpS HIT motif is critical for decapping activity and defines the HIT motif as a new mRNA decapping domain, making DcpS the first member of the HIT family of proteins with a defined biological function. 114 matched cddid_all.tbl CDD pfam11970 pfam11970 371826 GPR_Gpa2_C G protein-coupled glucose receptor regulating Gpa2 C-term. GPR1 is one of six proteins required for glucose-triggered adenylate cyclase activation, and is a G protein-coupled receptor responsible for the activation of adenylate cyclase through Gpa2 - heterotrimeric G protein alpha subunit, part of the glucose-detection pathway. The protein contains seven predicted transmembrane domains, a third cytoplasmic loop and a cytoplasmic tail. This family is the conserved C-terminal domain of the member proteins. 76 matched cddid_all.tbl CDD pfam11971 pfam11971 432229 CAMSAP_CH CAMSAP CH domain. This domain is the N-terminal CH domain from the CAMSAP proteins. 85 matched cddid_all.tbl CDD pfam11972 pfam11972 432230 HTH_13 HTH DNA binding domain. This is a helix-turn-helix DNA binding domain. 54 matched cddid_all.tbl CDD pfam11973 pfam11973 463416 NQRA_SLBB NQRA C-terminal domain. This family consists of the C-terminal domain of several bacterial Na(+)-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na(+)-translocating NADH: ubiquinone oxidoreductase (Na(+)-NQR) generates an electrochemical Na(+) potential driven by aerobic respiration. 51 matched cddid_all.tbl CDD pfam11974 pfam11974 432232 bMG3 Bacterial alpha-2-macroglobulin MG3 domain. This is the MG3 domain from bacterial alpha2-macroglobulins. 102 matched cddid_all.tbl CDD pfam11975 pfam11975 463417 Glyco_hydro_4C Family 4 glycosyl hydrolase C-terminal domain. 158 matched cddid_all.tbl CDD pfam11976 pfam11976 403255 Rad60-SLD Ubiquitin-2 like Rad60 SUMO-like. The small ubiquitin-related modifier SUMO-1 is a Ub/Ubl family member, and although SUMO-1 shares structural similarity to Ub, SUMO's cellular functions remain distinct insomuch as SUMO modification alters protein function through changes in activity, cellular localization, or by protecting substrates from ubiquitination. Rad60 family members contain functionally enigmatic, integral SUMO-like domains (SLDs). Despite their divergence from SUMO, each Rad60 SLD interacts with a subset of SUMO pathway enzymes: SLD2 specifically binds the SUMO E2 conjugating enzyme (Ubc9)), whereas SLD1 binds the SUMO E1 (Fub2, also called Uba2) activating and E3 (Pli1, also called Siz1 and Siz2) specificity enzymes. Structural analysis of PDB:2uyz reveals a mechanistic basis for the near-synonymous roles of Rad60 and SUMO in survival of genotoxic stress and suggest unprecedented DNA-damage-response functions for SLDs in regulating SUMOylation. The Rad60 branch of this family is also known as RENi (Rad60-Esc2-Nip45), and biologically it should be two distinct families SUMO and RENi (Rad60-Esc2-Nip45). 72 matched cddid_all.tbl CDD pfam11977 pfam11977 403256 RNase_Zc3h12a Zc3h12a-like Ribonuclease NYN domain. This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes. It has been suggested that this domain belongs to the PIN domain superfamily. This domain has also been identified as part of the NYN domain family. 154 matched cddid_all.tbl CDD pfam11978 pfam11978 463418 MVP_shoulder Shoulder domain. This domain is found in the Major Vault Protein and has been called the shoulder domain. This family includes two bacterial proteins Swiss:A6FXE2 and Swiss:A1ZGE7. This suggests that some bacteria may possess vault particles. 118 matched cddid_all.tbl CDD pfam11979 pfam11979 463419 DUF3480 Domain of unknown function (DUF3480). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 350 to 362 amino acids in length. This domain is found associated with pfam01363. 353 matched cddid_all.tbl CDD pfam11980 pfam11980 403259 DUF3481 C-terminal domain of neuropilin glycoprotein. This domain is found in eukaryotes at the C-terminus of neuropilins. It represents the transmembrane region of these transmembrane glycoproteins, that are predominantly co-receptors for another class of proteins known as semaphorins. The domain is found associated with pfam00754, pfam00431, pfam00629. 82 matched cddid_all.tbl CDD pfam11981 pfam11981 432236 DUF3482 Domain of unknown function (DUF3482). This presumed domain is functionally uncharacterized. This domain is found in bacteria and eukaryotes. This domain is typically between 289 to 301 amino acids in length. This domain is found associated with pfam01926. The central region of these proteins contains a hydrophobic region that is similar to pfam05433. 291 matched cddid_all.tbl CDD pfam11982 pfam11982 432237 DUF3483 Domain of unknown function (DUF3483). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 230 amino acids in length. This domain is found associated with pfam02754. 217 matched cddid_all.tbl CDD pfam11983 pfam11983 432238 FtsA_C Cell division protein FtsA, C-terminal. This family is the C-terminal region of essential streptococcal FtsA proteins and their homologs. It acts as an intra-molecular switch, triggered by ATP, to promote polymerization of the whole protein and to attach it to the membrane. FtsA is essential for the formation of the septum that divides fully-grown cells into two daughter cells at cell-division. FtsA anchors the constricting FtsZ ring to the membrane. 65 matched cddid_all.tbl CDD pfam11984 pfam11984 432239 DUF3485 Protein of unknown function (DUF3485). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 223 to 526 amino acids in length. This protein is found associated with pfam09721. 194 matched cddid_all.tbl CDD pfam11985 pfam11985 463420 Phage_Mu_Gp27 Bacteriophage Mu, Gp27. This family is represented by Bacteriophage Mu, Gp27. It is probably the small subunit of terminase, which recognizes viral DNA, binding to the packaging initiation site (pac) and regulates the ATPase activity of the terminase large subunit. The characteriztics of the protein distribution suggest prophage matches in addition to the phage matches. 170 matched cddid_all.tbl CDD pfam11986 pfam11986 288812 PB1-F2 Influenza A Proapoptotic protein. PB1-F2 is a protein found in almost all known strains of Influenza A virus - a negative sense ssRNA Orthomyxovirus. It originates from translation of the viral polymerase gene in an alternative reading frame. PB1-F2 consists of two independent structural domains, two closely neighboring short helices at the N terminus, and an extended C-terminal helix. Although the protein has originally been described to induce apoptosis, it has now been shown that PB1-F2 more likely acts as an apoptosis promoter in concert with other apoptosis-inducing agents. PB1-F2 promotes apoptosis by localising to the mitochondria where it destabilizes the membrane. This will cause release of cytochrome C which activates the caspase cascade of apoptosis through the endogenous pathway. In this way it acts like the Bcl-2 protein family which are physiological apoptotic regulators in cells. 87 matched cddid_all.tbl CDD pfam11987 pfam11987 463421 IF-2 Translation-initiation factor 2. IF-2 is a translation initiator in each of the three main phylogenetic domains (Eukaryotes, Bacteria and Archaea). IF2 interacts with formylmethionine-tRNA, GTP, IF1, IF3 and both ribosomal subunits. Through these interactions, IF2 promotes the binding of the initiator tRNA to the A site in the smaller ribosomal subunit and catalyzes the hydrolysis of GTP following initiation-complex formation. 116 matched cddid_all.tbl CDD pfam11988 pfam11988 403266 Dsl1_N Retrograde transport protein Dsl1 N terminal. Dsl1 is a peripheral membrane protein required for transport between the Golgi and the endoplasmic reticulum. It is localized to the ER membrane, and in vitro it specifically binds to coatomer, the major component of the protein coat of COPI vesicles. It is comprised primarily of alpha helical bundles. It complexes with another subunit of the Dsl1p complex called Tip20 which forms heterodimers by pairing the N termini of each protein. A central disorganized region between the N and C termini of Dsl1 contains binding sites for coatomer. The C terminus of Dsl1 contains a binding site to the Sec39 subunit of the Dsl1p complex. 350 matched cddid_all.tbl CDD pfam11989 pfam11989 432242 Dsl1_C Retrograde transport protein Dsl1 C terminal. Dsl1 is a peripheral membrane protein required for transport between the Golgi and the endoplasmic reticulum. It is localized to the ER membrane, and in vitro it specifically binds to coatomer, the major component of the protein coat of COPI vesicles. Binding sites for coatomer are found on a disorganized region between the C and N termini of Dsl1. The C terminal domain is involved in binding to the Sec39 subunit of the Dsl1p complex. The N terminal complexes with another subunit of the Dsl1p complex called Tip20 which forms heterodimers by pairing the N termini of each protein. 194 matched cddid_all.tbl CDD pfam11990 pfam11990 432243 DUF3487 Protein of unknown function (DUF3487). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 121 to 136 amino acids in length. This protein has a conserved RLN sequence motif. 115 matched cddid_all.tbl CDD pfam11991 pfam11991 463422 Trp_DMAT Tryptophan dimethylallyltransferase. This family of proteins represents tryptophan dimethylallyltransferase (EC:2.5.1.34), which catalyzes the first step of ergot alkaloid biosynthesis. Ergot alkaloids, which are produced by endophyte fungi, can enhance plant host fitness, but also cause livestock toxicosis to host plants. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 390 to 465 amino acids in length. 356 matched cddid_all.tbl CDD pfam11992 pfam11992 463423 TgpA_N TgpA N-terminal domain. This domain can be found at the N terminus of TgpA from Pseudomonas aeruginosa. TgpA is a transglutaminase that plays a critical role in the viability of Pseudomonas aeruginosa. This domain is composed of 5 transmembrane helices. 336 matched cddid_all.tbl CDD pfam11993 pfam11993 432246 Ribosomal_S4Pg Ribosomal S4P (gammaproteobacterial). This family of proteins are ribosomal SSU S4 p proteins. This protein is found in gamma-proteobacteria. Proteins in this family are typically between 162 to 178 amino acids in length. 158 matched cddid_all.tbl CDD pfam11994 pfam11994 432247 DUF3489 Protein of unknown function (DUF3489). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important. 68 matched cddid_all.tbl CDD pfam11995 pfam11995 463424 DUF3490 Domain of unknown function (DUF3490). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 160 amino acids in length. This domain is found associated with pfam00225. This domain is found associated with pfam00225. This domain has two conserved sequence motifs: EVE and ESA. 161 matched cddid_all.tbl CDD pfam11996 pfam11996 314813 DUF3491 Protein of unknown function (DUF3491). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 286 to 3225 amino acids in length. This protein is found associated with pfam04488. This protein is found associated with pfam04488. 946 matched cddid_all.tbl CDD pfam11997 pfam11997 432249 DUF3492 Domain of unknown function (DUF3492). This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 259 to 282 amino acids in length. This domain is found associated with pfam00534. This domain has two conserved sequence motifs: GGVS and EHGIY. 268 matched cddid_all.tbl CDD pfam11998 pfam11998 432250 DUF3493 Low psii accumulation1 / Rep27. This family includes members such as low psii accumulation1 (lpa1) from plants as well as Rep27 proteins found in unicellular green alga Chlamydomonas reinhardtii. The Arabidopsis LPA1 is a chaperone required for efficient photosystem II (PSII) assembly. It binds to psbA during de novo biogenesis of PSII. Other studies show that REP27 in Chlamydomonas reinhardtii chloroplast thylakoids, plays a dual role in the regulation of D1 protein turnover by facilitating cotranslational biosynthesis insertion (C-terminal domain) and activation (tetratricopeptide repeat [TPR] motifs) of the nascent D1 during the PSII repair process. 73 matched cddid_all.tbl CDD pfam11999 pfam11999 432251 Ice_binding Ice-binding-like. This family includes members found in bacteria, fungi and archaea, many of which are ice-binding proteins (IBPs). In Antarctic bacterium Flavobacterium frigoris PS1, FfIBP is an ice-binding protein that inhibits ice growth through direct interaction with ice crystals to permit the survival of polar organizms in extremely cold environments. In arctic yeast Leucosporidium sp, LeIBP, an ice-binding protein, can lower the freezing point below the melting point once it binds to ice. Family members also have a single completely conserved glycine residue that may be functionally important. 205 matched cddid_all.tbl CDD pfam12000 pfam12000 432252 Glyco_trans_4_3 Glycosyl transferase family 4 group. This domain is found associated with pfam00534. 168 matched cddid_all.tbl CDD pfam12001 pfam12001 463425 DUF3496 Domain of unknown function (DUF3496). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 110 amino acids in length. 109 matched cddid_all.tbl CDD pfam12002 pfam12002 463426 MgsA_C MgsA AAA+ ATPase C terminal. The MgsA protein possesses DNA-dependent ATPase and ssDNA annealing activities. MgsA contributes to the recovery of stalled replication forks and therefore prevents genomic instability caused by aberrant DNA replication. Additionally, MgsA may play a role in chromosomal segregation. This is consistent with a report that MgsA co-localizes with the replisome and affects chromosome segregation. This domain represents the C terminal region of MgsA. 158 matched cddid_all.tbl CDD pfam12004 pfam12004 463427 DUF3498 Domain of unknown function (DUF3498). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 433 to 538 amino acids in length. This domain is found associated with pfam00616, pfam00168. This domain has two conserved sequence motifs: DLQ and PLSFQNP. 511 matched cddid_all.tbl CDD pfam12005 pfam12005 432256 DUF3499 Protein of unknown function (DUF3499). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 125 to 163 amino acids in length. 119 matched cddid_all.tbl CDD pfam12006 pfam12006 432257 DUF3500 Protein of unknown function (DUF3500). This family of proteins is functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 335 to 438 amino acids in length. This protein has a conserved GHH sequence motif. This protein has two completely conserved G residues that may be functionally important. 294 matched cddid_all.tbl CDD pfam12007 pfam12007 432258 DUF3501 Protein of unknown function (DUF3501). This family of proteins is functionally uncharacterized. This protein is found in bacteria and archaea. Proteins in this family are about 200 amino acids in length. The structure of protein Swiss:Q63J81 from B. pseudomallei has been solved. This protein contains two domains, domain I (1:31, 46:81) is a helical domain, domain II (32:45,82-193) is a mainly beta protein with a beta barrel. According to crystal contacts the proteins probably functions as a dimer. The gene neighbourhood analysis suggests that this protein may be functionally related to rubrerythrin and ferredoxin. The wedge surface between the two domains might be functionally important. The fold of this protein could best be described as a circularly permuted C2-like fold (details derived from TOPSAN). 187 matched cddid_all.tbl CDD pfam12008 pfam12008 432259 EcoR124_C Type I restriction and modification enzyme - subunit R C terminal. This enzyme has been characterized and shown to belong to a new family of the type I class of restriction and modification enzymes. This family is involved in bacterial defence by making double strand breaks in specific double stranded DNA sequences, e.g. that of invading bacteriophages. EcoR124 is made up of three subunits, HsdR, HsdS and HsdM. The R subunit has ATPase and restriction endonuclease activity. This domain is the C terminal of the R subunit. 232 matched cddid_all.tbl CDD pfam12009 pfam12009 463428 Telomerase_RBD Telomerase ribonucleoprotein complex - RNA binding domain. Telomeres in most organizms are comprised of tandem simple sequence repeats. The total length of telomeric repeat sequence at each chromosome end is determined in a balance of sequence loss and sequence addition. One major influence on telomere length is the enzyme telomerase. It is a reverse transcriptase that adds these simple sequence repeats to chromosome ends by copying a template sequence within the RNA component of the enzyme. The RNA binding domain of telomerase - TRBD - is made up of twelve alpha helices and two short beta sheets. How telomerase and associated regulatory factors physically interact and function with each other to maintain appropriate telomere length is poorly understood. It is known however that TRBD is involved in formation of the holoenzyme (which performs the telomere extension) in addition to recognition and binding of RNA. 133 matched cddid_all.tbl CDD pfam12010 pfam12010 463429 DUF3502 Domain of unknown function (DUF3502). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 140 amino acids in length. This domain is found associated with pfam01547. 131 matched cddid_all.tbl CDD pfam12011 pfam12011 288834 NPH-II RNA helicase NPH-II. RNA helicase NPH-II or I8 is found in Poxviridae. It is essential for viral replication and plays an important role during transcription of early mRNAs, presumably by preventing R-loop formation behind the elongating RNA polymerase. It acts as NTP-dependent helicase that catalyzes unidirectional unwinding of 3'tailed duplex RNAs. It might also play a role in the export of newly synthesized mRNA chains out of the core into the cytoplasm and is required for propagation of viral particles. 168 matched cddid_all.tbl CDD pfam12012 pfam12012 463430 DUF3504 Domain of unknown function (DUF3504). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 156 to 173 amino acids in length. 162 matched cddid_all.tbl CDD pfam12013 pfam12013 371847 OrsD Orsellinic acid/F9775 biosynthesis cluster protein D. This family of proteins is functionally uncharacterized. This protein is found in eukaryotes. Proteins in this family are typically between 247 to 1018 amino acids in length. Family members include orsellinic acid/F9775 biosynthesis cluster protein D (orsD) from Emericella nidulans. The orsD gene is part of the cluster that encodes components for the biosynthesis of orsellinic acid, as well as biosynthesis of the cathepsin K inhibitors F9775 A and F9775 B, but the function of orsD is unknown. OrsD contains two segments that are likely to be C2H2 zinc binding domains. 114 matched cddid_all.tbl CDD pfam12014 pfam12014 463431 Cyclin_D1_bind Cyclin D1 binding domain. Ubiquitin-dependent proteolysis of cyclin D1 is associated with normal and tumour cell proliferation and survival. The best characterized member of this family is the SCF FBXO31 (Skp1-Cul1-Rbx1-FBXO31) ubiquitin ligase complex mediates genotoxic stress-induced cyclin D1 degradation. FBXO31 possesses a unique substrate-binding beta barrel domain, whereas cyclin D1 binds to FBXO31 by tucking its free C-terminal carboxylate tail into an open cavity of the C-terminal FBXO31 beta-barrel. Biophysical and functional studies demonstrated that SCFFBXO31 is capable of recruiting and ubiquitinating cyclin D1 in a phosphorylation-independent manner. 147 matched cddid_all.tbl CDD pfam12015 pfam12015 403288 Bud3_N Bud3, N-terminal. This domain is found in the N-terminal of the yeast Bud3 protein. Bud3 is involved in bud-site selection in budding yeasts. This domain has a conserved ENL sequence motif. 182 matched cddid_all.tbl CDD pfam12016 pfam12016 403289 Stonin2_N Stonin 2. Stonin 2 is involved in clathrin mediated endocytosis. It binds to Eps15 by its highly conserved NPF motif. The complex formed has been shown to directly associate with the clathrin adaptor complex AP-2, and to localize to clathrin-coated pits (CCPs). In addition, stonin2 was recently identified as a specific sorting adaptor for synaptotagmin, and may thus regulate synaptic vesicle recycling. 338 matched cddid_all.tbl CDD pfam12017 pfam12017 288840 Tnp_P_element Transposase protein. Protein in this family are transposases found in insects. This region is about 230 amino acids in length and is found associated with pfam05485. 219 matched cddid_all.tbl CDD pfam12018 pfam12018 463432 FAP206 Domain of unknown function. This domain of about 280 residues is found in eukaryotes. There are two conserved sequence motifs: GFC and GLL. This family is also known as UPF0704. This domain is found in FAP206, a protein associated with cilia and flagella. In the ciliate Tetrahymena, the cilium has radial spokes, each of which is a macromolecular complex essential for motility. A triplet of three radial spokes, RS1, RS2, and RS3, is repeated every 96 nm along the doublet microtubule. Each spoke has a distinct base that docks to the doublet and is linked to different inner dynein arms. Knockout of the FAP206 gene results in slow cell motility and the 96-nm repeats lack RS2 and dynein c. FAP206 is probably part of the front prong and docks RS2 and dynein c to the microtubule. 273 matched cddid_all.tbl CDD pfam12019 pfam12019 463433 GspH Type II transport protein GspH. GspH is involved in bacterial type II export systems. Like all pilins, GspH has an N terminus alpha helix. This helix is followed by nine beta strands forming two beta sheets, one of five antiparallel strands and one of four antiparallel strands. GspH is a minor pseudopilin; it is expressed much less than other pseudopilins in the type II secretion pilus (major pilins). The function and localization of minor pseudo-pilins are still to be fully unraveled. It has been suggested that some minor pseudopilins may assemble either into the base or the tip of pili, or both. They function as initiators or regulators of pilus biogenesis and dynamics, and/or as adaptors between various pseudopilin component and other members of the T2SS. 108 matched cddid_all.tbl CDD pfam12020 pfam12020 432266 TAFA TAFA family. This family of secreted proteins are brain specific and thought to be chemokines. These proteins are found in vertebrates. Proteins in this family are typically between 94 to 133 amino acids in length and contain a number of conserved cysteines. 89 matched cddid_all.tbl CDD pfam12021 pfam12021 432267 DUF3509 Protein of unknown function (DUF3509). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 92 to 110 amino acids in length. This protein has two completely conserved residues (G and R) that may be functionally important. 87 matched cddid_all.tbl CDD pfam12022 pfam12022 463434 COG2_C COG complex component, COG2, C-terminal. The COG complex comprises eight proteins (COG1-8) and plays critical roles in Golgi structure and function. It is necessary for retrograde trafficking in the Golgi apparatus and for protein glycosylation. This uncharacterized domain is found in the C-terminal of COG complex subunit 2 proteins. In Arabidopsis, COG2 forms a complex with FPP3/VETH1 and FPP2/VETH2 and ensures the correct secondary cell wall (SCW) deposition pattern by recruiting exocyst components to cortical microtubules in xylem cells during secondary cell wall deposition. 129 matched cddid_all.tbl CDD pfam12023 pfam12023 463435 DUF3511 Domain of unknown function (DUF3511). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 50 amino acids in length. This domain has two completely conserved residues (Y and K) that may be functionally important. 45 matched cddid_all.tbl CDD pfam12024 pfam12024 463436 DUF3512 Domain of unknown function (DUF3512). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 231 to 249 amino acids in length. This domain is found associated with pfam00439. 186 matched cddid_all.tbl CDD pfam12025 pfam12025 288848 Phage_C Phage protein C. This family of phage proteins is functionally uncharacterized. Proteins in this family are typically between 68 to 86 amino acids in length. 68 matched cddid_all.tbl CDD pfam12026 pfam12026 463437 CAS_C Crk-Associated Substrate C-terminal domain. This is a C-terminal domain found in CAS family members. The CAS (Crk-Associated Substrate) protein family is a group of scaffolding proteins that play important modulatory roles in both normal and pathological cell growth regulation. They contain an N-terminal Src homology 3 (SH3) domain pfam00018 and a substrate domain (SD). The SD contains a large number of YxxP motifs, which when phosphorylated by Src-family kinases provide canonical binding sites for proteins containing SH2 domains such as Crk, Crk-L, CRKII presumed domain is functionally uncharacterized. 202 matched cddid_all.tbl CDD pfam12027 pfam12027 314839 DUF3514 Protein of unknown function (DUF3514). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 368 to 823 amino acids in length. 256 matched cddid_all.tbl CDD pfam12028 pfam12028 432272 DUF3515 Protein of unknown function (DUF3515). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 166 to 214 amino acids in length. This protein has a conserved RCG sequence motif. 159 matched cddid_all.tbl CDD pfam12029 pfam12029 432273 DUF3516 Domain of unknown function (DUF3516). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is typically between 460 to 473 amino acids in length. This domain is found associated with pfam00270, pfam00271. 460 matched cddid_all.tbl CDD pfam12030 pfam12030 463438 DUF3517 Domain of unknown function (DUF3517). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 340 amino acids in length. This domain is found associated with pfam00443. 407 matched cddid_all.tbl CDD pfam12031 pfam12031 463439 BAF250_C SWI/SNF-like complex subunit BAF250/Osa. This entry represents the mammalian BAF250a/b and its homolog osa from fruit flies. They are part of the SWI/SNF-like ATP-dependent chromatin remodelling complex that regulates gene expression through regulating nucleosome remodelling. In humans there are two BAF250 isoforms, BAF250a/ARID1a and BAF250b/ARID1b. BAF250a/b may be E3 ubiquitin ligases that target histone H2B. 257 matched cddid_all.tbl CDD pfam12032 pfam12032 463440 CLIP Regulatory CLIP domain of proteinases. CLIP is a regulatory domain which controls the proteinase action of various proteins of the trypsin family, e.g. easter and pap2. The CLIP domain remains linked to the protease domain after cleavage of a conserved residue which retains the protein in zymogen form. It is named CLIP because it can be drawn in the shape of a paper clip. It has many disulphide bonds and highly conserved cysteine residues, and so it folds extensively. 54 matched cddid_all.tbl CDD pfam12033 pfam12033 152468 DUF3519 Protein of unknown function (DUF3519). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 117 to 1154 amino acids in length. This protein has a single completely conserved residue Q that may be functionally important. 104 matched cddid_all.tbl CDD pfam12034 pfam12034 432277 DUF3520 Domain of unknown function (DUF3520). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 180 amino acids in length. This domain is found associated with pfam00092. 182 matched cddid_all.tbl CDD pfam12036 pfam12036 463441 DUF3522 Protein of unknown function (DUF3522). This family of proteins is functionally uncharacterized. This protein is found in eukaryotes. Proteins in this family are typically between 220 to 787 amino acids in length. This family belongs to the CREST superfamily, which are distant members of the GPCR superfamily. 183 matched cddid_all.tbl CDD pfam12037 pfam12037 463442 ATAD3_N ATPase family AAA domain-containing protein 3, N-terminal. This is the conserved N-terminal domain of ATPase family AAA domain-containing protein 3 (ATAD3) which is involved in dimerization and interacts with the inner surface of the outer mitochondrial membrane. This domain is found associated with the AAA ATPase domain (pfam00004). ATAD3 is essential for mitochondrial network organization, mitochondrial metabolism and cell growth at organizm and cellular level. It may also play an important role in mitochondrial protein synthesis. 264 matched cddid_all.tbl CDD pfam12038 pfam12038 432280 DUF3524 Domain of unknown function (DUF3524). This presumed domain is functionally uncharacterized. This domain is found in bacteria and eukaryotes. This domain is about 170 amino acids in length. This domain is found associated with pfam00534. This domain has two conserved sequence motifs: HENQ and FNS. This domain has a single completely conserved residue S that may be functionally important. 165 matched cddid_all.tbl CDD pfam12039 pfam12039 152474 DUF3525 Protein of unknown function (DUF3525). This family of proteins is functionally uncharacterized. This protein is found in viruses. Proteins in this family are about 360 amino acids in length. 404 matched cddid_all.tbl CDD pfam12040 pfam12040 432281 DUF3526 Domain of unknown function (DUF3526). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is typically between 149 to 170 amino acids in length. This domain has a single completely conserved residue P that may be functionally important. 140 matched cddid_all.tbl CDD pfam12041 pfam12041 403308 DELLA Transcriptional regulator DELLA protein N terminal. Gibberellins are plant hormones which have great impact on growth signalling. DELLA proteins are transcriptional regulators of growth related proteins which are downregulated when gibberellins bind to their receptor GID1. GID1 forms a complex with DELLA proteins and signals them towards 26S proteasome. The N terminal of DELLA proteins contains conserved DELLA and VHYNP motifs which are important for GID1 binding and proteolysis of the DELLA proteins. 68 matched cddid_all.tbl CDD pfam12042 pfam12042 314852 RP1-2 Tubuliform egg casing silk strands structural domain. Spiders use fibroins to make silk strands. This family includes tubuliform silk fibroins which are used to protect egg cases. This domain is a structural domain which is found in repeats of up to 20 in many individuals (although this is not necessarily the case). RP1 makes up structural domains in the N terminal while RP2 makes up structural domains in the C terminal. 167 matched cddid_all.tbl CDD pfam12043 pfam12043 463443 DUF3527 Domain of unknown function (DUF3527). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 120 amino acids in length. This domain has a conserved CDCGGWD sequence motif. 350 matched cddid_all.tbl CDD pfam12044 pfam12044 432283 Metallopep Putative peptidase family. This family of proteins is functionally uncharacterized. However, it does contain an HEXXH motif characteriztic of metallopeptidases. This protein is found mainly in fungi. Proteins in this family are typically between 625 to 773 amino acids in length. 426 matched cddid_all.tbl CDD pfam12045 pfam12045 432284 DUF3528 Protein of unknown function (DUF3528). This family of proteins is functionally uncharacterized. This protein is found in eukaryotes. Proteins in this family are typically between 185 to 298 amino acids in length. This protein is found associated with pfam00046. 127 matched cddid_all.tbl CDD pfam12046 pfam12046 432285 CCB1 Cofactor assembly of complex C subunit B. Cofactor maturation pathways such as the CCB system (system IV) for cytochrome c-heme attachment are conserved in all organizms performing oxygenic photosynthesis. The CCB system consists of four protein, CCB1-4. The four CCBs are well conserved between green algae and plants. 166 matched cddid_all.tbl CDD pfam12047 pfam12047 463444 DNMT1-RFD Cytosine specific DNA methyltransferase replication foci domain. This domain is part of a cytosine specific DNA methyltransferase enzyme. It functions non-catalytically to target the protein towards replication foci. This allows the DNMT1 protein to methylate the correct residues. This domain targets DMAP1 and HDAC2 to the replication foci during the S phase of mitosis. They are thought to have some importance in conversion of critical histone lysine moieties. 143 matched cddid_all.tbl CDD pfam12048 pfam12048 432287 DUF3530 Protein of unknown function (DUF3530). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 272 to 336 amino acids in length. These proteins are distantly related to alpa/beta hydrolases so they may act as enzymes. 308 matched cddid_all.tbl CDD pfam12049 pfam12049 432288 DUF3531 Protein of unknown function (DUF3531). This family of proteins is functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 149 to 199 amino acids in length. 139 matched cddid_all.tbl CDD pfam12051 pfam12051 432289 DUF3533 Protein of unknown function (DUF3533). This family of transmembrane proteins is functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 393 to 772 amino acids in length. 381 matched cddid_all.tbl CDD pfam12052 pfam12052 463445 VGCC_beta4Aa_N Voltage gated calcium channel subunit beta domain 4Aa N terminal. The beta subunit of voltage gated calcium channels is coded for by four genes 1-4. Gene 4 can produce two types of beta4A domain (beta4Aa and beta4Ab) according to how the gene splicing is carried out. This family is part of the beta4Aa N terminal domain. It is made up of an alpha helix and a beta strand. It is thought to regulate the channel properties through protein-protein interactions with non Ca channel proteins. 42 matched cddid_all.tbl CDD pfam12053 pfam12053 463446 Par3_HAL_N_term N-terminal of Par3 and HAL proteins. This domain is about 150 amino acids in length found associated with pfam00595 in eukaryotes. It has a conserved GILD sequence motif. Family members have been found to be essential for cell polarity establishment and maintenance such as Par3 (partitioning defective) and involved in conversion of histidine into ammonia (a crucial step for forming histamine in humans) such as Histidine ammonia lyase (HAL). This N-terminal domain is found to mediate oligomerization critical for the membrane localization of Par-3. It is also found to possess a self-association capacity via a front-to-back mode in Par-3 and HAL proteins. However, unlike the Par-3 N-terminal domain which self-assembles into a left-handed helical filament, the HAL N-terminal domain does not tend to form a helical filament but rather self-assembles into circular oligomeric particles. This has been suggested to be likely due to the absence of equivalent charged residues that are essential for the longitudinal packing of the Par-3 N-terminal domain filament. 82 matched cddid_all.tbl CDD pfam12054 pfam12054 463447 DUF3535 Domain of unknown function (DUF3535). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 439 to 459 amino acids in length. This domain is found associated with pfam00271, pfam02985, pfam00176. This domain has two completely conserved residues (P and K) that may be functionally important. 445 matched cddid_all.tbl CDD pfam12055 pfam12055 432293 DUF3536 Domain of unknown function (DUF3536). This presumed domain is functionally uncharacterized. This domain is found in bacteria and archaea. This domain is typically between 274 to 285 amino acids in length. This domain is found associated with pfam03065. 284 matched cddid_all.tbl CDD pfam12056 pfam12056 463448 DUF3537 Protein of unknown function (DUF3537). This family of transmembrane proteins are functionally uncharacterized. This protein is found in eukaryotes. Proteins in this family are typically between 427 to 453 amino acids in length. 392 matched cddid_all.tbl CDD pfam12057 pfam12057 463449 BAG6 BCL2-associated athanogene 6. This domain is found in large proline-rich protein BAG6 protein. It has a conserved SDL sequence motif. Human BAG6 is an ATP-independent molecular chaperone preventing the aggregation of misfolded and hydrophobic patches-containing proteins. It functions as part of a cytosolic protein quality control complex, the BAG6/BAT3 complex, which maintains these client proteins in a soluble state and participates to their proper delivery to the endoplasmic reticulum or alternatively can promote their sorting to the proteasome where they undergo degradation. 115 matched cddid_all.tbl CDD pfam12058 pfam12058 432296 DUF3539 Protein of unknown function (DUF3539). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are about 90 amino acids in length. This protein has a conserved NHP sequence motif. 86 matched cddid_all.tbl CDD pfam12059 pfam12059 432297 DUF3540 Protein of unknown function (DUF3540). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 212 to 238 amino acids in length. This protein has a conserved SCL sequence motif. 197 matched cddid_all.tbl CDD pfam12060 pfam12060 432298 DUF3541 Domain of unknown function (DUF3541). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 230 amino acids in length. 225 matched cddid_all.tbl CDD pfam12061 pfam12061 403325 NB-LRR Late blight resistance protein R1. R1 is a gene for resistance to late blight, the most destructive disease in potato cultivation worldwide. The R1 gene belongs to the class of plant genes for pathogen resistance that have a leucine zipper motif, a putative nucleotide binding domain and a leucine-rich repeat domain. This protein is found associated with pfam00931. 297 matched cddid_all.tbl CDD pfam12062 pfam12062 463450 HSNSD heparan sulfate-N-deacetylase. This family of proteins is are heparan sulfate N-deacetylase enzymes. This protein is found in eukaryotes. This proteinenzyme is often found associated with pfam00685. 429 matched cddid_all.tbl CDD pfam12063 pfam12063 463451 DUF3543 Domain of unknown function (DUF3543). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is typically between 217 to 291 amino acids in length. This domain is found associated with pfam00069. This domain has a single completely conserved residue A that may be functionally important. 251 matched cddid_all.tbl CDD pfam12064 pfam12064 463452 DUF3544 Protein kinase C-binding protein 1. This is a domain found predominantly in eukaryotes and associated with pfam00628 pfam01753 pfam00439 pfam00855. Family members include protein kinase C-binding protein 1 (also known as ZMYND8) which acts as a transcriptional corepressor of the H3K4 demethylase JARID1D. ZMYND8 (zinc finger and MYND [myeloid, Nervy, and DEAF-1] domain containing 8) binds acetylated damaged chromatin, including actively transcribed regions, as a means of recruiting the nucleosome remodeling and histone deacetylation (NuRD) chromatin remodeling complex for transcriptional repression and DNA double-strand break (DSB) repair by homologous recombination (HR). 195 matched cddid_all.tbl CDD pfam12065 pfam12065 432302 DUF3545 Protein of unknown function (DUF3545). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 60 to 77 amino acids in length. This protein has two completely conserved residues (R and L) that may be functionally important. 59 matched cddid_all.tbl CDD pfam12066 pfam12066 463453 SERRATE_Ars2_N SERRATE/Ars2, N-terminal domain. This domain can be found in the N terminus of the SERRATE (SE) from plants and its homolog, Ars2, from animals. They play a role in nuclear RNA metabolism. They interact with the nuclear cap-binding complex (CBC) and mediates interactions with diverse RNA processing and transport machineries in a transcript-dependent manner. Interestingly, the plant SERRATE does not have the RNA recognition motif (RRM) domain found in metazoans and S. pombe. This domain has two completely conserved Y residues that may be functionally important. 110 matched cddid_all.tbl CDD pfam12067 pfam12067 463454 Sox17_18_mid Sox 17/18 central domain. This is the central region of eukaryotic SOX17 and 18 transcription factor proteins. It lies just downstream of the HMG-box family, pfam00505, and is followed by a C-terminal domain. 49 matched cddid_all.tbl CDD pfam12068 pfam12068 432305 PH_RBD Rab-binding domain (RBD). This domain has been called the Rab-binding domain (RBD). The domain adopts a Ph-like fold. This domain is found associated with pfam00566. 149 matched cddid_all.tbl CDD pfam12069 pfam12069 432306 DUF3549 Protein of unknown function (DUF3549). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are about 340 amino acids in length. This protein has a conserved LDE sequence motif. 340 matched cddid_all.tbl CDD pfam12070 pfam12070 463455 SCAI Protein SCAI. SCAI is a transcriptional cofactor and tumour suppressor that suppresses MKL1-induced SRF transcriptional activity. It may function in the RHOA-DIAPH1 signal transduction pathway and regulate cell migration through transcriptional regulation of ITGB1. 521 matched cddid_all.tbl CDD pfam12071 pfam12071 371883 DUF3551 Protein of unknown function (DUF3551). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 79 to 104 amino acids in length. This protein has a single completely conserved residue C that may be functionally important. 77 matched cddid_all.tbl CDD pfam12072 pfam12072 463456 RNase_Y_N RNase Y N-terminal region. 201 matched cddid_all.tbl CDD pfam12073 pfam12073 432309 DUF3553 Protein of unknown function (DUF3553). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are about 60 amino acids in length. This protein has two conserved sequence motifs: GQVQS and TVNF. 48 matched cddid_all.tbl CDD pfam12074 pfam12074 463457 Gcn1_N Generalcontrol nonderepressible 1 (Gcn1) N-terminal. This domain is found in the N-terminal region of Gcn1 protein, which acts as a translation activator that mediates translational control by regulating Gcn2 kinase activity. 350 matched cddid_all.tbl CDD pfam12075 pfam12075 432311 KN_motif KN motif. This small motif is found at the N-terminus of Kank proteins and has been called the KN (for Kank N-terminal) motif. This protein is found in eukaryotes. Proteins in this family are typically between 413 to 1202 amino acids in length. This protein is found associated with pfam00023. This protein has two conserved sequence motifs: TPYG and LDLDF. Kank1 was obtained by positional cloning of a tumor suppressor gene in renal cell carcinoma, while the other members were found by homology search. The family is involved in the regulation of actin polymerization and cell motility through signaling pathways containing PI3K/Akt and/or unidentified modulators/effectors. 39 matched cddid_all.tbl CDD pfam12076 pfam12076 463458 Wax2_C WAX2 C-terminal domain. This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 170 amino acids in length. This domain is found associated with pfam04116. This domain has a conserved LEGW sequence motif. This region has similarity to short chain dehydrogenases. 164 matched cddid_all.tbl CDD pfam12077 pfam12077 432313 DUF3556 Transmembrane protein of unknown function (DUF3556). This family of transmembrane proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 576 to 592 amino acids in length. 572 matched cddid_all.tbl CDD pfam12078 pfam12078 371889 DUF3557 Domain of unknown function (DUF3557). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 150 amino acids in length. 154 matched cddid_all.tbl CDD pfam12079 pfam12079 432314 DUF3558 Protein of unknown function (DUF3558). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 177 to 195 amino acids in length. 173 matched cddid_all.tbl CDD pfam12080 pfam12080 432315 GldM_C GldM C-terminal domain. This domain is found in bacteria at the C-terminus of the GldM protein. This domain is typically between 169 to 182 amino acids in length. This domain has two completely conserved residues (Y and N) that may be functionally important. GldM, is named for the member from Cytophaga johnsonae (Flavobacterium johnsoniae), which is required for a type of rapid gliding motility found in certain members of the Bacteriodetes. 177 matched cddid_all.tbl CDD pfam12081 pfam12081 432316 GldM_N GldM N-terminal domain. This domain is found in bacteria at the N-terminus of the GldM protein. This domain is typically between 169 to 182 amino acids in length. This domain has two completely conserved residues (Y and N) that may be functionally important. GldM, is named for the member from Cytophaga johnsonae (Flavobacterium johnsoniae), which is required for a type of rapid gliding motility found in certain members of the Bacteriodetes. 186 matched cddid_all.tbl CDD pfam12083 pfam12083 432317 DUF3560 Domain of unknown function (DUF3560). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 120 amino acids in length. This domain has a conserved GHHSE sequence motif. 124 matched cddid_all.tbl CDD pfam12084 pfam12084 432318 DUF3561 Protein of unknown function (DUF3561). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are about 110 amino acids in length. 107 matched cddid_all.tbl CDD pfam12085 pfam12085 432319 DUF3562 Protein of unknown function (DUF3562). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important. 60 matched cddid_all.tbl CDD pfam12086 pfam12086 432320 DUF3563 Protein of unknown function (DUF3563). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are about 50 amino acids in length. This protein has conserved AYL and DLE sequence motifs. 61 matched cddid_all.tbl CDD pfam12087 pfam12087 432321 DUF3564 Protein of unknown function (DUF3564). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 118 to 142 amino acids in length. This protein has a conserved WSRE sequence motif. 120 matched cddid_all.tbl CDD pfam12088 pfam12088 432322 DUF3565 Protein of unknown function (DUF3565). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 30 to 78 amino acids in length. This protein has two conserved sequence motifs: WVA and CGH. 56 matched cddid_all.tbl CDD pfam12089 pfam12089 432323 DUF3566 Transmembrane domain of unknown function (DUF3566). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 136 to 304 amino acids in length. This region represents a transmembrane region found at the C-terminus of the proteins. 118 matched cddid_all.tbl CDD pfam12090 pfam12090 463459 Spt20 Spt20 family. This presumed domain is found in the Spt20 proteins from both human and yeast. The Spt20 protein is part of the SAGA complex which is a large complex mediating histone deacetylation. Yeast Spt20 has been shown to play a role in structural integrity of the SAGA complex as as no intact SAGA could be purified in spt20 deletion strains. 176 matched cddid_all.tbl CDD pfam12091 pfam12091 432325 DUF3567 Protein of unknown function (DUF3567). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are about 90 amino acids in length. This protein has a conserved EIVDK sequence motif. 85 matched cddid_all.tbl CDD pfam12092 pfam12092 403350 DUF3568 Protein of unknown function (DUF3568). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are about 130 amino acids in length. 124 matched cddid_all.tbl CDD pfam12093 pfam12093 152528 bCoV_NS8 Betacoronavirus NS8 protein. This family of proteins includes the accessory proteins encoded by the ORF8 in coronaviruses, also known as accessory protein 8, or non-structural protein 8 (NS8). This is distinct from NSP8, which is encoded on the replicase polyprotein. Proteins in this family are typically between 39 to 121 amino acids in length. This protein has two conserved sequence motifs: EDPCP and INCQ. It may modulate viral pathogenicity or replication in favour of human adaptation. ORF8 was suggested as one of the relevant genes in the study of human adaptation of the virus. This entry includes the NS8a and NS8b proteins from human SARS coronavirus (SARS-CoV). Recently, the the structure of SARS-CoV-2 ORF has been determined and revealed a core of approximately 60 residues similar to SARS-CoV ORF7a, the Ig-like fold, with the addition of two dimerization interfaces unique to SARS-CoV-2 ORF8. It forms a covalent disulfide-linker dimer through an N-terminal sequence specific to SARS-CoV-2 and a separate non-covalent interface is formed by another SARS-CoV-2 specific sequence. The presence of these interfaces shows that SARS-CoV-2 ORF8 can form unique large-scale assemblies not possible for SARS-CoV, potentially mediating unique immune suppression and evasion activities. 126 matched cddid_all.tbl CDD pfam12094 pfam12094 432326 DUF3570 Protein of unknown function (DUF3570). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 396 to 444 amino acids in length. Proteins in this family contain the [S/T]GA[S/T] motif and thus, is flavinylated by ApbE. This suggests that they may be involved in extracytosolic redox activities. 413 matched cddid_all.tbl CDD pfam12095 pfam12095 432327 CRR7 Protein CHLORORESPIRATORY REDUCTION 7. This entry includes protein from blue-green algae and plants, including CRR7 protein from Arabidopsis. CRR7 is part of the chloroplastic NAD(P)H dehydrogenase complex (NDH Complex) involved in respiration, photosystem I (PSI) cyclic electron transport and CO2 uptake. It is essential for the stable formation of the NDH Complex. 81 matched cddid_all.tbl CDD pfam12096 pfam12096 432328 DUF3572 Protein of unknown function (DUF3572). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are about 100 amino acids in length. 84 matched cddid_all.tbl CDD pfam12097 pfam12097 288914 DUF3573 Protein of unknown function (DUF3573). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 372 to 530 amino acids in length. 383 matched cddid_all.tbl CDD pfam12098 pfam12098 432329 DUF3574 Protein of unknown function (DUF3574). This family of proteins is functionally uncharacterized. This protein is found in bacteria and viruses. Proteins in this family are typically between 144 to 163 amino acids in length. This protein has a conserved TPRF sequence motif. 103 matched cddid_all.tbl CDD pfam12099 pfam12099 432330 DUF3575 Protein of unknown function (DUF3575). This family of proteins are functionally uncharacterized. This family is only found in bacteria. Proteins in this family are typically between 187 to 236 amino acids in length. 177 matched cddid_all.tbl CDD pfam12100 pfam12100 432331 DUF3576 Domain of unknown function (DUF3576). This presumed domain is functionally uncharacterized. This domain is found in bacteria. This domain is about 100 amino acids in length. This domain has a single completely conserved residue G that may be functionally important. 101 matched cddid_all.tbl CDD pfam12101 pfam12101 432332 DUF3577 Protein of unknown function (DUF3577). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 143 to 307 amino acids in length. 133 matched cddid_all.tbl CDD pfam12102 pfam12102 432333 MrcB_N MrcB-like, N-terminal domain. This model describes the N-terminal domain of a group of mostly uncharacterized proteins, including 5-methylcytosine-specific restriction enzyme B (also known as MrcB) from E. coli. MrcB recognizes N4- and C5-methylcytosine (and 5-hydroxy-methylcytosines) produced by a broad range of DNA methylases and appears to act against 5-methylcytosine preceded by a purine residue. The N-terminal domain of MrcB has been shown to be a DNA-binding domain, and the crystal structure has been solved. 183 matched cddid_all.tbl CDD pfam12103 pfam12103 403358 Lipl32 Surface lipoprotein of Spirochaetales order. Lipl32 is an outer membrane surface lipoprotein of Leptospira like bacteria. 178 matched cddid_all.tbl CDD pfam12104 pfam12104 403359 Tcell_CD4_C T cell CD4 receptor C terminal region. This domain is the C terminal domain of the CD4 T cell receptor. The C terminal domain is the cytoplasmic domain which relays the signal for T cell activation. This process involves co-receptor internalization. This domain is involved in binding to the N terminal of Lck co-receptor in a Zn2+ clasp structure. 28 matched cddid_all.tbl CDD pfam12105 pfam12105 463460 SpoU_methylas_C SpoU, rRNA methylase, C-terminal. This domain is found in bacteria. This domain is about 60 amino acids in length. This domain is found in association with pfam00588. This domain has a conserved LFE sequence motif. Some members of the Pfam family SpoU_methylase, pfam00588, carry this very distinctive sequence region at their extreme C-terminus. The exact function of this region is not known. 54 matched cddid_all.tbl CDD pfam12106 pfam12106 432335 Colicin_E5 Colicin E5 ribonuclease domain. Colicin is a protein produced by bacteria with Col plasmids. Its function is to attack E. coli through actions on its inner membrane ion channels or through ribonuclease or deoxyribonuclease actions. The C terminal domain is the ribonuclease domain. It specifically cleaves tRNA anticodons which recognize codons in the form NAY (N:any nucleotide, A:adenosine, Y:pyrimidine) which corresponds to Tyrosine, Histidine, Asparagine and Aspartic Acid. E5-CRD can be referred to as an RNA restriction enzyme that specifically recognizes and cleaves single-stranded GU sequences. 88 matched cddid_all.tbl CDD pfam12107 pfam12107 152542 VEK-30 Plasminogen (Pg) ligand in fibrinolytic pathway. Pg is an important mediator of angiostatin production in the fibrinolytic pathway. Pg is made up of five subunit kringle molecules (Pg-K1 to Pg-K5), of which the first three make the protein angiostatin. VEK-30 is a domain of the group A streptococcal protein PAM. It binds to Pg-K2 of angiostatin and activates the molecule to mediate its anti-angiogenic effects. VEK-30 binds to angiostatin via a C terminal lysine with argininyl and glutamyl side chain residues known as a 'through space isostere'. 17 matched cddid_all.tbl CDD pfam12108 pfam12108 463461 SF3a60_bindingd Splicing factor SF3a60 binding domain. This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription. 27 matched cddid_all.tbl CDD pfam12109 pfam12109 432337 CXCR4_N CXCR4 Chemokine receptor N terminal. CXCR4 and its ligand stromal cell-derived factor-1 (a.k.a. CXCL12) are essential for proper fetal development. CXCR4 is also the major coreceptor for T-tropic strains of human immunodeficiency virus 1 (HIV-1), and SDF-1 inhibits HIV-1 infection. Additionally, SDF-1 and CXCR4 mediate cancer cell migration and metastasis. The N terminal domain of most chemokine receptors is the ligand binding domain and so the N terminal domain of CXCR4 is the binding site for SDF-1. 33 matched cddid_all.tbl CDD pfam12110 pfam12110 463462 Nup96 Nuclear protein 96. Nup96 (often known by the name of its yeast homolog Nup145C) is part of the Nup84 heptameric complex in the nuclear pore complex. Nup96 complexes with Sec13 in the middle of the heptamer. The function of the heptamer is to coat the curvature of the nuclear pore complex between the inner and outer nuclear membranes. Nup96 is predicted to be an alpha helical solenoid. The interaction between Nup96 and Sec13 is the point of curvature in the heptameric complex. 287 matched cddid_all.tbl CDD pfam12111 pfam12111 432339 PNPase_C Polyribonucleotide phosphorylase C terminal. PNPase regulates the expression of small non-coding RNAs that control expression of outer-membrane proteins. The enzyme also affects complex processes, such as the tissue-invasive virulence of Salmonella enterica and the regulation of a virulence-factor secretion system in Yersinia. In Escherichia coli, PNPase is involved in the quality control of ribosomal RNA precursors and is required for growth following cold shock. This family contains the C terminal protomer domain of the PNPase core. The function of the C terminal protomer is to catalyze phosphorolysis through its two active sites. 37 matched cddid_all.tbl CDD pfam12112 pfam12112 463463 DUF3579 Protein of unknown function (DUF3579). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 98 to 126 amino acids in length. This protein has a conserved FRP sequence motif. 87 matched cddid_all.tbl CDD pfam12113 pfam12113 288929 SVM_signal SVM protein signal sequence. This region is presumed to be a signal peptide sequence found in Sequence-variable mosaic (SVM) proteins. This domain is found in phytoplasmas. This presumed signal sequence is about 30 amino acids in length. 33 matched cddid_all.tbl CDD pfam12114 pfam12114 463464 Period_C Period protein 2/3C-terminal region. This domain is found in eukaryotes. This domain is typically between 164 to 200 amino acids in length. This domain is found associated with pfam08447. 171 matched cddid_all.tbl CDD pfam12115 pfam12115 314916 Salp15 Salivary protein of 15kDa inhibits CD4+ T cell activation. This is a family of 15kDa salivary proteins from Acari Arachnids that is induced on feeding and assists the parasite to remain attached to its arthropod host. By repressing calcium fluxes triggered by TCR engagement, Salp15 inhibits CD4+ T cell activation. Salp15 shows weak similarity to Inhibin A, a member of the TGF-beta superfamily that inhibits the production of cytokines and the proliferation of T cells. 112 matched cddid_all.tbl CDD pfam12116 pfam12116 403367 SpoIIID Stage III sporulation protein D. This stage III sporulation protein is a small DNA-binding family that is essential for gene expression of the mother-cell compartment during sporulation. The domain is found in bacteria and viruses, and is about 40 amino acids in length. It has a conserved RGG sequence motif. 82 matched cddid_all.tbl CDD pfam12117 pfam12117 288933 NS1_C Parvovirus non-structural protein 1, C-terminal. This domain is the transactivation domain of the Parvovirus NS1 protein, located immediately C-terminal to the helicase. Parvovirus are some of the smallest viruses containing linear, non-segmented single-stranded DNA genomes, with an average genome size of 5000 nucleotides. They infect a wide range of invertebrates and vertebrates and are well known for causing enteric disease in mammals. Genomes contain two large ORFs: NS1 and VP1; other ORFs are found in some sub-types and different gene products can arise from splice variants and the use of different start codons. NS1 protein is essential for viral life cycle stages, including DNA replication, trans-regulation of the two viral promoters and modulation of heterologous promoters. It exhibits DNA binding, endonuclease and helicase activities and is the major contributor to the toxic effect on host cells. 121 matched cddid_all.tbl CDD pfam12118 pfam12118 432342 SprA-related SprA-related family. This family of bacterial proteins has a conserved HEXXH motif, suggesting they are putative peptidases of zincin fold. Proteins in this family are typically between 234 to 465 amino acids in length. Most members are annotated as being SprA-related. 335 matched cddid_all.tbl CDD pfam12119 pfam12119 432343 DUF3581 Protein of unknown function (DUF3581). This protein is found in bacteria. Proteins in this family are about 240 amino acids in length. 217 matched cddid_all.tbl CDD pfam12120 pfam12120 432344 Arr-ms Rifampin ADP-ribosyl transferase. This protein is found in bacteria. Proteins in this family are typically between 136 to 150 amino acids in length. The opportunistic pathogen Mycobacterium smegmatis is resistant to rifampin because of the presence of a chromosomally encoded rifampin ADP-ribosyltransferase (Arr-ms). Arr-ms is a small enzyme whose activity thus renders rifamycin antibiotics ineffective. 99 matched cddid_all.tbl CDD pfam12121 pfam12121 403370 DD_K Dermaseptin. This protein is found in eukaryotes. Proteins in this family are typically between 30 to 76 amino acids in length. This protein is found associated with pfam03032. This domain is part of a dermaseptin protein which is used as an antimicrobial agent. The full protein is almost completely defined in an alpha helical domain. It creates high levels of disorder at the level of the phospholipid head group of bacterial membranes suggesting that it partitions into the bilayer where it severely disrupts membrane packing. 23 matched cddid_all.tbl CDD pfam12122 pfam12122 432345 Rhomboid_N Cytoplasmic N-terminal domain of rhomboid serine protease. Rhomboid_N is the N-terminal cytoplasmic domain of the rhomboid intra-membraneous serine protease, otherwise known as Peptidase_S54, pfam01694. This N-terminal domain has similarity to other GlnB-like domains, some of which appear to have a binding role, eg to peptidoglycan. It is not clear exactly what the function of this domain is in the protease, but its presence is critical for maintaining a catalytically competent state for the protein. 86 matched cddid_all.tbl CDD pfam12123 pfam12123 338253 CBD_PlyG PlyG Cell wall binding domain. This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is thought to be a cell wall binding domain. 44 matched cddid_all.tbl CDD pfam12124 pfam12124 288939 bCoV_SUD_C Betacoronavirus SUD-C domain. This domain is found in betacoronavirus non-structural protein NSP3, and is about 65 amino acids in length. It was originally thought to exist only in SARS-coronaviruses, and so was termed the SARS-unique domain (SUD), however this has since been shown to be incorrect. The domain is also known as DPUP (domain preceding Ubl2 and PL2pro). NSP3 is the product of ORF1a, proteolytically released from the pp1a/1ab polyprotein. The SUD domain has three globular domains, SUD-N (N-terminal), SUD-M (middle region of SUD), and SUD-C (C-terminal). SUD-C adopts a fold consisting of seven beta-strands arranged in an anti-parallel beta-sheet, and two alpha-helices which are packed against the same side of the beta-sheet. It adopts a frataxin like fold with structural similarities to DNA-binding domains. It has been shown that SUD-C binds to single-stranded RNA and recognizes purine bases more strongly than pyrimidine bases, but these interactions are stabilized in the presence of SUD-M. The function of this domain is not clear but studies of structural homologs of SUD-C suggest that it could be related to metal, adenylate and nucleic acid binding. 66 matched cddid_all.tbl CDD pfam12125 pfam12125 463465 Beta-TrCP_D D domain of beta-TrCP. This domain is found in eukaryotes, and is approximately 40 amino acids in length. It is found associated with pfam00646, pfam00400. The protein that contains this domain functions as a ubiquitin ligase. Ubiquitination is required to direct proteins towards the proteasome for degradation. This protein is part of the WD40 class of F box proteins. The D domain of these F box proteins is involved in mediating the dimerization of the protein. dimerization is necessary to polyubiquitinate substrates so this D domain is vital in directing substrates towards the proteasome for degradation. 39 matched cddid_all.tbl CDD pfam12126 pfam12126 432347 DUF3583 Protein of unknown function (DUF3583). This domain is found in eukaryotes, and is typically between 302 and 338 amino acids in length. It is found in association with pfam00097 and pfam00643. Most members are promyelocytic leukemia proteins, and this family lies towards the C-terminus. 329 matched cddid_all.tbl CDD pfam12127 pfam12127 432348 FloA Flotillin-like protein FloA. This entry represents flotillin-like protein FloA from bacteria. Bacterial flotillin-like proteins are found in membrane microdomains that may be equivalent to eukaryotic membrane rafts. Similarly to eukaryotic flotillin proteins, flotillins in bacteria play an essential role in organizing and maintaining the correct architecture of the functional membrane microdomains. Bacillus subtilis has two flotillin paralogs, FloT and FloA. The absence of one of the flotillins has only minor effects, but the absence of both proteins has very severe effects: loss of proper cell shape, a defect in cell division. 314 matched cddid_all.tbl CDD pfam12128 pfam12128 432349 DUF3584 Protein of unknown function (DUF3584). This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. This family contains a P-loop motif suggesting it is a nucleotide binding protein. It may be involved in replication. 1191 matched cddid_all.tbl CDD pfam12129 pfam12129 463466 PHTF1-2_N Homeodomain containing protein PHTF1/2, N-terminal. This domain is found in a group of homeodomain containing proteins from animals, including PHTF1/2,eukaryotes, and is typically between 101 and 140 amino acids in length. PHTF proteins do not display any sequence similarity to known or predicted proteins, but their conservation among species suggests an essential function. The 84 kDa PHTF1 protein is an integral membrane protein, anchored to a cell membrane by six to eight trans-membrane domains, that is associated with a domain of the endoplasmic reticulum (ER) juxtaposed to the Golgi apparatus. It is present during meiosis and spermiogenesis, and, by the end of spermiogenesis, is released from the mature spermatozoon within the residual bodies. PHTF1 enhances the binding of FEM1B -feminization homolog 1B - to cell membranes. Fem-1 was initially identified in the signaling pathway for sex determination, as well as being implicated in apoptosis, but its biochemical role is still unclear, and neither FEM1B nor PHTF1 is directly implicated in apoptosis in spermatogenesis. It is the ANK domain of FEM1B that is necessary for the interaction with the N-terminal region of PHTF1. 156 matched cddid_all.tbl CDD pfam12130 pfam12130 463467 bMERB_dom Bivalent Mical/EHBP Rab binding domain. A variety of different effector proteins interact specifically with GTP-bound Rab proteins and mediate their versatile roles in membrane trafficking, including budding of vesicles from a donor membrane, directed transport through the cell and finally tethering and fusion with a target membrane. The 'bivalent Mical/EHBP Rab binding' (bMERB) domain is a Rab effector domain that is present in proteins of the Mical and EHBP families, both known to act in endosomal trafficking. The bMERB domain displays a preference for Rab8 family proteins (Rab8, 10, 13 and 15) and at least some of the bMERB domains contain two separate binding sites for Rab-proteins, allowing Micals and EHBPs to bind two Rabs simultaneously. The strong similarity between the two binding sites within one bMRB domain strongly suggests an evolutionarily development via duplication of a common ancestor supersecondary structure element. The bMERB domain has a completely alpha-helical fold consisting of a central helix and N- and C-terminal helices folding back on this central helix. 131 matched cddid_all.tbl CDD pfam12131 pfam12131 403378 DUF3586 Protein of unknown function (DUF3586). This domain is found in eukaryotes. This domain is about 80 amino acids in length and is found associated with pfam08246, and pfam00112. 75 matched cddid_all.tbl CDD pfam12132 pfam12132 371912 DUF3587 Protein of unknown function (DUF3587). This protein is found in viruses. Proteins in this family are typically between 209 and 248 amino acids in length. 201 matched cddid_all.tbl CDD pfam12133 pfam12133 463468 bCoV_NS6 Betacoronavirus NS6 protein. This entry represents non-structural protein NS6 (also known as non-structural protein 6, accessory protein 6, or X3 protein), which is highly conserved among SARS-related coronaviruses. (This is distinct from NSP6 which is encoded on the replicase polyprotein). Proteins in this family are typically between 42 to 63 amino acids in length. NS6 is located in the endoplasmic reticulum. It has been reported that NS6 can increase the cellular gene synthesis and it can also induce apoptosis through Jun N-terminal kinase and Caspase-3 mediated stress. This protein can modulate host antiviral responses by inhibiting synthesis and signalling of IFN-beta, via NS6 interaction with host N-Myc (and STAT) interactor (Nmi) protein and suppressing the translocation of signal transducer and activator of transcription 1 (STAT1). 62 matched cddid_all.tbl CDD pfam12134 pfam12134 432353 PRP8_domainIV PRP8 domain IV core. This domain is found in eukaryotes, and is about 20 amino acids in length. It is found associated with pfam10597, pfam10596, pfam10598, pfam08083, pfam08082, pfam01398, pfam08084. There is a conserved LILR sequence motif. The domain is a selenomethionine domain in a subunit of the spliceosome. The function of PRP8 domain IV is believed to be interaction with the splicosomal core. 230 matched cddid_all.tbl CDD pfam12135 pfam12135 403381 Plasmo_rep Plasmodium repeat family. This repeat is found in plasmodia. This entry contains two copies of the repeat. The function of these proteins is unknown. 25 matched cddid_all.tbl CDD pfam12136 pfam12136 152571 RNA_pol_Rpo13 RNA polymerase Rpo13 subunit HTH domain. This domain is found in archaea, and is about 40 amino acids in length. It has a single completely conserved residue E that may be functionally important. It is found in the archaeal DNA dependent RNA polymerase. The domain is a 'helix-turn-helix' (HTH) domain in the Rpo13 subunit of the RNA polymerase. This domain is involved in downstream DNA binding, and the entire subunit has also been implicated in contacting transcription factor II B. 40 matched cddid_all.tbl CDD pfam12137 pfam12137 432354 RapA_C RNA polymerase recycling family C-terminal. This domain is found in bacteria. This domain is about 360 amino acids in length. This domain is found associated with pfam00271, pfam00176. The function of this domain is not known, but structurally it forms an alpha-beta fold in nature with a central beta-sheet flanked by helices and loops, the beta-sheet being mainly antiparallel and flanked by four alpha helices, among which the two longer helices exhibit a coiled-coil arrangement. 359 matched cddid_all.tbl CDD pfam12138 pfam12138 432355 Spherulin4 Spherulation-specific family 4. This protein is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 250 and 398 amino acids in length. There is a conserved NPG sequence motif and there are two completely conserved G residues that may be functionally important. Starvation will often induce spherulation - the production of spores - and this process may involve DNA-methylation. Changes in the methylation of spherulin4 are associated with the formation of spherules, but these changes are probably transient. Methylation of the gene accompanies its transcriptional activation, and spherulin4 mRNA is only detectable in late spherulating cultures and mature spherules. It is a spherulation-specific protein. 238 matched cddid_all.tbl CDD pfam12139 pfam12139 432356 APS-reductase_C Adenosine-5'-phosphosulfate reductase beta subunit. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 112 to 142 amino acids in length. This family is found in association with pfam00037, and has a conserved FPIRTT sequence motif. The whole beta subunit has the enzymic properties of EC:1.8.99.2. 82 matched cddid_all.tbl CDD pfam12140 pfam12140 463469 SLED SLED domain. The SLED (Scm-Like Embedded Domain) domain is a double-stranded DNA binding domain found in Scml2 which is a member of the Polycomb group of proteins involved in epigenetic gene silencing. 112 matched cddid_all.tbl CDD pfam12141 pfam12141 403385 BMT Beta-mannosyltransferases. This entry represents a group of fungal beta-mannosyltransferase that are involved in cell wall biosynthesis. For example, in Candida albicans, BMT1-4 enzymes act stepwise to add beta-mannoses on to cell-wall phosphopeptidomannan (PPM). While Bmt5 and Bmt6 are involved in the addition of the first and third beta-mans to phospholipomannan (PLM), respectively. Furthermore, in Saccharomyces cerevisiae, BMT5 and BMT6 are responsible for methylation of uridine residues in the 25S rRNA. 485 matched cddid_all.tbl CDD pfam12142 pfam12142 463470 PPO1_DWL Polyphenol oxidase middle domain. This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length, and the family is found in association with pfam00264. Most members are annotated as being polyphenol oxidases, and many are from plants or plastids. There is a conserved DWL sequence motif which gives the family its name. 52 matched cddid_all.tbl CDD pfam12143 pfam12143 371919 PPO1_KFDV Protein of unknown function (DUF_B2219). This domain family is found in eukaryotes, and is typically between 138 and 152 amino acids in length. and the family is found in association with pfam00264. Many members are plant or plastid polyphenol oxidases, and there is a highly conserved sequence motif: KFDV, from which the name derives. This is the C-terminal domain of these oxidases. 130 matched cddid_all.tbl CDD pfam12144 pfam12144 463471 Med12-PQL Eukaryotic Mediator 12 catenin-binding domain. This domain is found in eukaryotes, and is typically between 325 and 354 amino acids in length. Both development and carcinogenesis are driven by signal transduction within the canonical Wnt/beta-catenin pathway through both programmed and unprogrammed changes in gene transcription. Beta-catenin physically and functionally targets this PQL (proline-, glutamine-, leucine-rich) region of the Med12 subunit of Mediator to activate transcription. The beta-catenin transactivation domain binds directly to isolated Med12 and intact Mediator both in vitro and in vivo, and Mediator is recruited to Wnt-responsive genes in a beta-catenin-dependent manner. 210 matched cddid_all.tbl CDD pfam12145 pfam12145 463472 Med12-LCEWAV Eukaryotic Mediator 12 subunit domain. This domain is found in eukaryotes, and is typically between 325 and 354 amino acids in length. The function of this particular region of the Mediator subunit Med12 is not known, but there is a conserved sequence motif: LCEWAV, from which the name derives. 471 matched cddid_all.tbl CDD pfam12146 pfam12146 463473 Hydrolase_4 Serine aminopeptidase, S33. This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. It is found in association with pfam00561. The majority of the members in this family carry the exopeptidase active-site residues of Ser-122, Asp-239 and His-269 as in UniProtKB:Q7ZWC2. 238 matched cddid_all.tbl CDD pfam12147 pfam12147 432362 Methyltransf_20 Putative methyltransferase. This domain is found in bacteria and eukaryotes and is approximately 110 amino acids in length. It is found in association with pfam00561. The family shows homology to methyltransferases. 309 matched cddid_all.tbl CDD pfam12148 pfam12148 463474 TTD Tandem tudor domain within UHRF1. TTD, tandem tudor domain within UHRF1 preferentially binds H3 histone tails trimethylated at Lys-9. It specifically recognizes H3 tail peptides with the heterochromatin-associated modification state of trimethylated lysine 9 and unmodified lysine 4 (H3K4me0/K9me3). This domain is found in eukaryotes and is found in association with pfam00097, pfam02182, pfam00628, pfam00240. 155 matched cddid_all.tbl CDD pfam12149 pfam12149 403392 HSV_VP16_C Herpes simplex virus virion protein 16 C terminal. This domain is found in viruses, and is about 30 amino acids in length. It is found in association with pfam02232. This domain is the C terminal of the HSV virion protein 16. This protein is a transcription promoter. The C terminal domain is the carboxyl subdomain of the acidic transcriptional activation domain. The protein binds to DNA binding proteins to carry out its function. Such proteins include TATA binding protein, CBP, TBP-binding protein, etc. 26 matched cddid_all.tbl CDD pfam12150 pfam12150 403393 MFP2b Cytosolic motility protein. This domain family is found in eukaryotes, and is approximately 50 amino acids in length. These proteins are found in nematodes. They complex with MSP (major sperm protein) to allow motility. Their action is quite similar to the action of bacterial actin molecules. 343 matched cddid_all.tbl CDD pfam12151 pfam12151 432364 MVL Mannan-binding protein. This domain family is found in bacteria, and is approximately 40 amino acids in length, There is a single completely conserved residue G that may be functionally important. The domain occurs in two types of proteins. In mannan binding proteins, it forms a homodimeric molecule which complexes into a homo-octamer. In thiamidases it occurs without repeats but in the presence of other domains. MVL is distinct amongst other oligomannoside binding proteins in that it exhibits specificity for certain tetrasaccharides. Each molecule of MVL has four distinct carbohydrate binding sites. 36 matched cddid_all.tbl CDD pfam12152 pfam12152 432365 eIF_4G1 Eukaryotic translation initiation factor 4G1. This domain is found in eukaryotes, and is about 80 amino acids in length. It is found in association with pfam02854. This domain is part of the protein eIF_4G. It binds to eIF_4E by wrapping around its N terminal to form the eIF_4F complex. This complex binds various eIF_4E-BPs (binding proteins) to regulate initiation of translation. 60 matched cddid_all.tbl CDD pfam12153 pfam12153 403395 CAP18_C LPS binding domain of CAP18 (C terminal). This domain family is found in eukaryotes, and is approximately 30 amino acids in length, and the family is found in association with pfam00666. CAP18 is a protein which is derived from rabbit granulocytes. It has two domains, an N terminal DUF and a C terminal Gram negative LPS binding domain. This domain is the C terminal domain. 27 matched cddid_all.tbl CDD pfam12154 pfam12154 152589 HCMVantigenic_N Glycoprotein B N-terminal antigenic domain of HCMV. This domain is found in viruses, and is approximately 40 amino acids in length. The domain is found in association with pfam00606. There are two conserved sequence motifs: SVS and TSS. This family is the amino-terminal antigenic domain of glycoprotein B of human cytomegalovirus. 36 matched cddid_all.tbl CDD pfam12155 pfam12155 152590 NADHdh-2_N NADH dehydrogenase subunit 2 N-terminal. This domain is found in eukaryotes, and is approximately 90 amino acids in length. It is found associated with pfam00361. All members are annotated as being NADH dehydrogenase subunit 2, and this region is the N-terminus. 88 matched cddid_all.tbl CDD pfam12156 pfam12156 463475 ATPase-cat_bd Putative metal-binding domain of cation transport ATPase. This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with pfam00403, pfam00122, pfam00702. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases. 86 matched cddid_all.tbl CDD pfam12157 pfam12157 463476 DUF3591 Protein of unknown function (DUF3591). This domain is found in eukaryotes and is typically between 445 to 462 amino acids in length. Most members are annotated as being transcription initiation factor TFIID subunit 1, and this region is the conserved central portion of these proteins. 456 matched cddid_all.tbl CDD pfam12158 pfam12158 432368 DUF3592 Protein of unknown function (DUF3592). This family of proteins is functionally uncharacterized.This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 150 and 242 amino acids in length. 136 matched cddid_all.tbl CDD pfam12159 pfam12159 463477 DUF3593 Protein of unknown function (DUF3593). This family of proteins is functionally uncharacterized.This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 98 and 228 amino acids in length. There is a conserved LHG sequence motif. 88 matched cddid_all.tbl CDD pfam12160 pfam12160 432370 Fibrinogen_aC Fibrinogen alpha C domain. This domain family is found in eukaryotes, and is approximately 70 amino acids in length, and the family is found in association with pfam08702. This domain is the C terminal domain of fibrinogen in mammals. The domain lies in the C terminal half of the alpha C region in these proteins. The function of the domain is that of intramolecular and intermolecular interactions to form fibrin. 68 matched cddid_all.tbl CDD pfam12161 pfam12161 463478 HsdM_N HsdM N-terminal domain. This domain is found at the N-terminus of the methylase subunit of Type I DNA methyltransferases. This domain family is found in bacteria and archaea, and is typically between 123 and 138 amino acids in length. The family is found in association with pfam02384. Mutations in this region of EcoKI methyltransferase abolish the normally strong preference of this system for methylating hemimethylated substrate. The structure of this domain has been shown to be all alpha-helical. 123 matched cddid_all.tbl CDD pfam12162 pfam12162 432372 STAT1_TAZ2bind STAT1 TAZ2 binding domain. This domain family is found in eukaryotes, and is approximately 20 amino acids in length, and the family is found in association with pfam02865, pfam00017, pfam01017, pfam02864. This domain is the C terminal domain of STAT1. This domain binds selectively to the TAZ2 domain of CRB (CREB-binding protein). In this process it becomes a transcriptional activator and can initiate transcription of certain genes. 23 matched cddid_all.tbl CDD pfam12163 pfam12163 432373 HobA DNA replication regulator. This family of proteins is found exclusively in epsilon-proteobacteria. Proteins in this family are approximately 180 amino acids in length. The structure of HobA is a modified Rossmann fold consisting of a five-stranded parallel beta-sheet (beta1-5) flanked on one side by alpha-2, alpha-3 and alpha-6 helices and alpha-4 and alpha-5 on the other. The alpha-1 helix is extended away from and has minimal interaction with the globular part of the protein. Four monomers interact to form a tetrameric molecule. Four calcium atoms bind to the tetramer and these binding sites may have functional relevance. The function of HobA is to regulate DNA replication and its does this by binding to DNA-A, but the exact mechanism of how this regulation occurs is purely speculative 180 matched cddid_all.tbl CDD pfam12164 pfam12164 463479 SporV_AA Stage V sporulation protein AA. This domain family is found in bacteria - primarily Firmicutes, and is approximately 90 amino acids in length. There is a single completely conserved residue G that may be functionally important. Most annotation associated with this domain suggests that it is involved in the fifth stage of sporulation, however there is little publication to back this up. 89 matched cddid_all.tbl CDD pfam12165 pfam12165 463480 Alfin Alfin. The Alfin family includes PHD finger protein Alfin1 and Alfin1-like proteins. Alfin1 is a histone-binding component that specifically recognizes H3 tails trimethylated on 'Lys-4' (H3K4me3), which marks transcription start sites of virtually all active genes. 126 matched cddid_all.tbl CDD pfam12166 pfam12166 463481 Piezo_RRas_bdg Piezo non-specific cation channel, R-Ras-binding domain. This is an extracellular domain at the C-terminus of Piezo, or FAM38 mechanosensitive non-specific cation channel proteins. It seems likely that this region of the Piezo proteins may be responsible for R-Ras recruitment because this region is capable of relocalising R-Ras to the ER in eukaryotes. 415 matched cddid_all.tbl CDD pfam12167 pfam12167 432377 Arm-DNA-bind_2 Arm DNA-binding domain. This domain is found at the N-terminus of various phage integrases. The domain binds to DNA. 65 matched cddid_all.tbl CDD pfam12168 pfam12168 432378 DNA_pol3_tau_4 DNA polymerase III subunits tau domain IV DnaB-binding. This domain family is found in bacteria, and is approximately 80 amino acids in length. The family is found in association with pfam00004. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. 82 matched cddid_all.tbl CDD pfam12169 pfam12169 432379 DNA_pol3_gamma3 DNA polymerase III subunits gamma and tau domain III. This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with pfam00004. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. 143 matched cddid_all.tbl CDD pfam12170 pfam12170 432380 DNA_pol3_tau_5 DNA polymerase III tau subunit V interacting with alpha. This domain family is found in bacteria, and is approximately 140 amino acids in length. The family is found in association with pfam00004. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. The extreme C-terminal region of this domain 5 is the part which interacts with the alpha subunit of the DNA polymerase III holoenzyme. 142 matched cddid_all.tbl CDD pfam12171 pfam12171 432381 zf-C2H2_jaz Zinc-finger double-stranded RNA-binding. This domain family is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localize in the nucleus, particularly the nucleolus. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localization. 27 matched cddid_all.tbl CDD pfam12172 pfam12172 463482 DUF35_N Rubredoxin-like zinc ribbon domain (DUF35_N). This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in Swiss:O53566. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. 37 matched cddid_all.tbl CDD pfam12173 pfam12173 152608 BacteriocIIc_cy Bacteriocin class IIc cyclic gassericin A-like. This class of bacteriocins was previously described as class V. The members include gassericin A, acidocin B and butyrovibriocin AR10, all of which are hydrophobic cyclical structures. The N- and C-termini are covalently linked, and the circular molecule is resistant to several proteases and peptidases. The immunity protein that protects Lactobacillus gasseri from the toxic effects of its bacteriocin, gassericin A, has been identified. It is found to be a small positively-charged hydrophobic peptide of 53 amino acids containing a putative transmembrane segment - a structure unlike that of the more common immunity proteins as found in pfam08951. 91 matched cddid_all.tbl CDD pfam12174 pfam12174 432383 RST RCD1-SRO-TAF4 (RST) plant domain. This domain is found in plant RCD1, SRO and TAF4 proteins, hence its name of RST. It is required for interaction with multiple plant transcription factors. Radical-Induced Cell Death1 (RCD1) is an important regulator of stress and hormonal and developmental responses in Arabidopsis thaliana, as is its closest homolog, SRO1 - Similar To RCD-One1. TBP-Associated Factor 4 (TAF4) and TAF4-b are components of the transcription initiation factor complex TFIID. 67 matched cddid_all.tbl CDD pfam12175 pfam12175 403413 WSS_VP White spot syndrome virus structural envelope protein VP. This family of proteins is found in viruses. Proteins in this family are approximately 210 amino acids in length. There is a conserved NNT sequence motif. These proteins are structural envelope proteins in viruses. This is the beta barrel C terminal domain. There is a protruding N terminal domain which completes the proteins. Three of four envelope proteins in white spot syndrome virus share sequence homology with each other and are present in this family - VP24, VP26 and VP28. VP19 is the other major envelope protein but shares no sequence homology with the other proteins. These proteins are essential for entry into cells of the crustacean host. 201 matched cddid_all.tbl CDD pfam12176 pfam12176 432384 MtaB Methanol-cobalamin methyltransferase B subunit. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 460 amino acids in length. MtaB folds as a TIM barrel and contains a novel zinc-binding motif. Zinc(II) lies at the bottom of a funnel formed at the C-terminal beta-barrel end and ligates to two cysteinyl sulfurs (Cys-220 and Cys-269) and one carboxylate oxygen (Glu-164). The function of this protein is to catalyze the cleavage of the C O bond in methanol by an SN2 mechanism. It complexes with MtaA and MtaC to perform this function. 459 matched cddid_all.tbl CDD pfam12177 pfam12177 463483 Proho_convert Prohormone convertase enzyme. This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam01483, pfam00082. There are two completely conserved residues (Y and D) that may be functionally important. This protein is the C terminal domain of a prohormone convertase enzyme which targets hormones in dense core secretory granules. This C terminal tail domain is the domain responsible for targeting these dense core secretory granules. The domain adopts an alpha helical structure. 39 matched cddid_all.tbl CDD pfam12178 pfam12178 463484 INCENP_N Chromosome passenger complex (CPC) protein INCENP N terminal. This domain family is found in eukaryotes, and is approximately 40 amino acids in length. INCENP is a regulatory protein in the chromosome passenger complex. It is involved in regulation of the catalytic protein Aurora B. It performs this function in association with two other proteins - Survivin and Borealin. These proteins form a tight three-helical bundle. The N terminal domain is the domain involved in formation of this three helical bundle. 36 matched cddid_all.tbl CDD pfam12179 pfam12179 463485 IKKbetaNEMObind I-kappa-kinase-beta NEMO binding domain. This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam00069. These proteins are involved in inflammatory reactions. They cause release of NF-kappa-B into the nucleus of inflammatory cells and upregulation of transcription of proinflammatory cytokines. They perform this function by phosphorylating I-kappa-B proteins which are targeted for degradation to release NF-kappa-B. This kinase (I-kappa-kinase-beta) is found in association with IKK-alpha and NEMO (NF-kappa-B essential modulator). This domain is the binding site of IKK-beta for NEMO. 37 matched cddid_all.tbl CDD pfam12180 pfam12180 463486 EABR TSG101 and ALIX binding domain of CEP55. This domain family is found in eukaryotes, and is approximately 40 amino acids in length. This domain is the active domain of CEP55. CEP55 is a protein involved in cytokinesis, specifically in abscission of the plasma membrane at the midbody. To perform this function, CEP55 complexes with ESCRT-I (by a Proline rich sequence in its TSG101 domain) and ALIX. This is the domain on CEP55 which binds to both TSG101 and ALIX. It also acts as a hinge between the N and C termini. This domain is called EABR. 34 matched cddid_all.tbl CDD pfam12181 pfam12181 403419 MogR_DNAbind DNA binding domain of the motility gene repressor (MogR). This domain family is found in bacteria, and is approximately 150 amino acids in length. MogR is involved in repression of transcription of the flagellar gene in Listeria bacteria. This allows a phenotypical switch from an extracellular bacterium to an intracellular pathogen. MogR binds AT rich flagellar gene promoter regions upstream of the flagellar gene. These regions follow the pattern 5'-TTTTNNNNNAAAA-3'. This domain is the DNA binding domain of MogR. 151 matched cddid_all.tbl CDD pfam12182 pfam12182 403420 DUF3642 Bacterial lipoprotein. This domain family is found in bacteria, and is approximately 60 amino acids in length. There is a single completely conserved Y residue that may be functionally important. This domain is from a bacterial lipoprotein, a major virulence factor in Gram negative bacteria. 83 matched cddid_all.tbl CDD pfam12183 pfam12183 463487 NotI Restriction endonuclease NotI. This family of proteins is found in bacteria. Proteins in this family are typically between 270 and 341 amino acids in length. There is a conserved CPF sequence motif. The type IIP restriction enzyme, NotI, is a homodimer that recognizes the 8 bp DNA sequence 5'-GC/GGCCGC-3' and cleaves both strands of DNA to create 5', 4 base cohesive overhangs. 232 matched cddid_all.tbl CDD pfam12185 pfam12185 463488 IR1-M Nup358/RanBP2 E3 ligase domain. This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The family is found in association with pfam00638, pfam00641, pfam00160. There are two conserved sequence motifs: TFFC and EDF. Nup358/RanBP2 is a nucleoporin involved in ubiquitination of many different protein targets from various cellular pathways. It complexes with Ubc9, SUMO-1 and RanGAP1 to perform this function. This is the ligase domain which binds to Ubc9. 60 matched cddid_all.tbl CDD pfam12186 pfam12186 403423 AcylCoA_dehyd_C Acyl-CoA dehydrogenase C terminal. This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with pfam02770, pfam00441, pfam02771. There is a conserved ARRL sequence motif. The C terminal domain is an alpha helical domain. The flavin ring of Acyl-CoA dehydrogenase is buried in the crevice between the two alpha helical domains and the beta-sheet domain of one subunit, and the adenosine pyrophosphate moiety is stretched into the subunit junction of a neighbouring subunit, composed of two C terminal domains. 111 matched cddid_all.tbl CDD pfam12187 pfam12187 288997 VirArc_Nuclease Viral/Archaeal nuclease. This family of proteins is found in archaea and viruses. Proteins in this family are typically between 211 and 244 amino acids in length. These proteins are nucleases from fusseloviruses and sulfolobus archaea. 149 matched cddid_all.tbl CDD pfam12188 pfam12188 432390 STAT2_C Signal transducer and activator of transcription 2 C terminal. This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The family is found in association with pfam02865, pfam00017, pfam01017, pfam02864. There is a conserved DLP sequence motif. STATs are involved in transcriptional regulation and are the only regulators known to be modulated by tyrosine phosphorylation. STAT2 forms a trimeric complex with STAT1 and IRF-9 (Interferon Regulatory Factor 9), on activation of the cell by interferon, which is called ISGF3 (Interferon-stimulated gene factor 3). The C terminal domain of STAT2 contains a nuclear export signal (NES) which allows export of STAT2 into the cytoplasm along with any complexed molecules. 55 matched cddid_all.tbl CDD pfam12189 pfam12189 432391 VirE1 Single-strand DNA-binding protein. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved IELE sequence motif. VirE1 is an acidic chaperone protein which binds to VirE2, a ssDNA binding protein. These proteins are virulence factors of the plant pathogens Agrobacteria. VirE1 competes for the ssDNA binding site of VirE2. 63 matched cddid_all.tbl CDD pfam12190 pfam12190 371952 amfpi-1 Fungal protease inhibitor. This protein family is found in eukaryotes, and is approximately 50 amino acids in length. These proteins are fungal protease inhibitors. 91 matched cddid_all.tbl CDD pfam12191 pfam12191 403424 stn_TNFRSF12A Tumour necrosis factor receptor stn_TNFRSF12A_TNFR domain. This family of proteins is found in eukaryotes. Proteins in this family are typically between 129 and 184 amino acids in length. This is the stn_TNFRSF12A_TNFR domain from the tumour necrosis factor receptor. The function of this domain is unknown. 129 matched cddid_all.tbl CDD pfam12192 pfam12192 371954 CBP Fungal calcium binding protein. This domain is found in eukaryotes, and is approximately 60 amino acids in length. There is a single completely conserved residue C that may be functionally important. This is a calcium binding domain from the fungal protein CBP (calcium binding protein). This protein is a virulence factor with unknown virulence mechanisms. CBP complexes as a highly intertwined homodimer. Each monomer is comprised of four alpha helices which adopt the saposin fold, characteriztic of a protein family that binds to membranes and lipids. 76 matched cddid_all.tbl CDD pfam12193 pfam12193 432392 Sulf_coat_C Sulfolobus virus coat protein C terminal. This domain family is found in viruses, and is approximately 70 amino acids in length. It is the C terminal of a coat protein in sulfolobus viruses. 134 matched cddid_all.tbl CDD pfam12194 pfam12194 403425 Ste5_C Protein kinase Fus3-binding. This domain family is found in eukaryotes, and is approximately 190 amino acids in length. This domain is the penultimate C terminal domain from the protein ste5 which co-catalyzes the phosphorylation of fus3 by ste7. It is involved in the MAPK pathways. This domain is the minimal scaffold domain of ste5. It binds to the mitogen activated protein kinase fus3 before it is phosphorylated. 189 matched cddid_all.tbl CDD pfam12195 pfam12195 152630 End_beta_barrel Beta barrel domain of bacteriophage endosialidase. This domain family is found in bacteria and viruses, and is approximately 80 amino acids in length.This domain is the beta barrel domain of bacteriophage endosialidase which represents the one of the two sialic acid binding sites of the enzyme. The domain is nested in the beta propeller domain of the endosialidase enzyme. The endosialidase protein complexes to form homotrimeric molecules. 83 matched cddid_all.tbl CDD pfam12196 pfam12196 463489 hNIFK_binding FHA Ki67 binding domain of hNIFK. This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam00076. There are two conserved sequence motifs: TPVCTP and LERRKS. This domain is found on the human nucleolar protein hNIFK. It binds to the fork-head-associated domain of human Ki67. High-affinity binding requires sequential phosphorylation by two kinases, CDK1 and GSK3, yielding pThr238, pThr234 and pSer230. This interaction is involved in cell cycle regulation. 40 matched cddid_all.tbl CDD pfam12197 pfam12197 314977 lci Bacillus cereus group antimicrobial protein. This domain is found in bacteria, and is approximately 40 amino acids in length. This domain is found in bacillus cereus group bacteria. It is an antimicrobial protein. 42 matched cddid_all.tbl CDD pfam12198 pfam12198 432394 Tuberculin Tuberculin-active protein. This entry represents the tuberculin-active protein from Mycobacterium tuberculosis. 83 matched cddid_all.tbl CDD pfam12199 pfam12199 289007 efb-c Extracellular fibrinogen binding protein C terminal. This domain family is found in bacteria, and is approximately 70 amino acids in length. There is a conserved VLK sequence motif. It is the C terminal domain of bacterial extracellular fibrinogen binding protein. It contains a helical motif involved in complement regulation. This motif binds to complement and changes its conformation to a form which cannot activate downstream components of the complement cascade. 65 matched cddid_all.tbl CDD pfam12200 pfam12200 463490 DUF3597 Domain of unknown function (DUF3597). This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 126 and 281 amino acids in length. The function of this domain is unknown. The structure of this domain has been found to contain five helices with a long flexible loop between helices one and two. 127 matched cddid_all.tbl CDD pfam12201 pfam12201 432396 bcl-2I13 Bcl2-interacting killer, BH3-domain containing. This is a family of pro-apoptotic Bcl-x proteins, B cell leukaemia/lymphoma 2, or BIKs. BIK proteins rely for their activity upon an intact BH3 domain lying between residues 48 and 80, as in UniProt:Q13323. 156 matched cddid_all.tbl CDD pfam12202 pfam12202 463491 OSR1_C Oxidative-stress-responsive kinase 1 C-terminal domain. This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam00069. There is a single completely conserved residue F that may be functionally important. OSR1 is involved in the signalling cascade which activates Na/K/2Cl cotransporter during osmotic stress. This domain is the C terminal domain of OSR1 which recognizes a motif (Arg-Phe-Xaa-Val) on the OSR1-activating protein WNK1. 62 matched cddid_all.tbl CDD pfam12203 pfam12203 403429 HDAC4_Gln Glutamine rich N terminal domain of histone deacetylase 4. This domain is found in eukaryotes, and is approximately 90 amino acids in length. The family is found in association with pfam00850. The domain forms an alpha helix which complexes to form a tetramer. The glutamine rich domains have many intra- and inter-helical interactions which are thought to be involved in reversible assembly and disassembly of proteins. The domain is part of histone deacetylase 4 (HDAC4) which removes acetyl groups from histones. This restores their positive charge to allow stronger DNA binding thus restricting transcriptional activity. 91 matched cddid_all.tbl CDD pfam12204 pfam12204 432398 DUF3598 Domain of unknown function (DUF3598). This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 230 and 398 amino acids in length. These proteins are formed entirely from B sheets which form a barrel structure similar to those seen in the lipocalin superfamily. 264 matched cddid_all.tbl CDD pfam12205 pfam12205 463492 GIT1_C G protein-coupled receptor kinase-interacting protein 1 C term. This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with pfam01412, pfam00023, pfam08518. GIT1 plays an important role in cell adhesion, motility, cytoskeletal remodelling and membrane trafficking. To perform this function, it localizes p21-activated kinase (PAK) and PAK-interactive exchange factor to focal adhesions. Its activation is regulated by interaction between its paxillin-binding C terminal and the LD motifs of paxillin. The C terminal folds into a four helix bundle. 110 matched cddid_all.tbl CDD pfam12206 pfam12206 403432 DUF3599 Domain of unknown function (DUF3599). This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. This domain is the phage-like element pbsx protein xkdh. 115 matched cddid_all.tbl CDD pfam12207 pfam12207 403433 DUF3600 Domain of unknown function (DUF3600). This family of proteins is found in bacteria. Proteins in this family are approximately 230 amino acids in length. This domain is the C terminal of the putative ecf-type sigma factor negative effector. 157 matched cddid_all.tbl CDD pfam12208 pfam12208 432400 DUF3601 Domain of unknown function (DUF3601). This domain family is found in bacteria, and is approximately 80 amino acids in length. 79 matched cddid_all.tbl CDD pfam12209 pfam12209 432401 SAC3 Leucine permease transcriptional regulator helical domain. This domain family is found in eukaryotes, and is approximately 80 amino acids in length. The family is found in association with pfam03399. This domain is a helical domain in the middle of leucine permease transcriptional regulator. 77 matched cddid_all.tbl CDD pfam12210 pfam12210 463493 Hrs_helical Hepatocyte growth factor-regulated tyrosine kinase substrate. This domain family is found in eukaryotes, and is approximately 100 amino acids in length. The family is found in association with pfam00790, pfam01363, pfam02809. This domain is the helical region of Hrs which forms the core complex of ESCRT with STAM. 95 matched cddid_all.tbl CDD pfam12211 pfam12211 314987 LMWSLP_N Low molecular weight S layer protein N terminal. This family of proteins is found in bacteria. Proteins in this family are typically between 328 and 381 amino acids in length. There is a conserved LGDG sequence motif. Clostridial species have a layer of surface proteins surrounding their membrane. This layer is comprised of a high molecular weight protein and a low molecular weight protein. This domain is the N terminal domain of the low molecular weight protein. It is a structural domain. 258 matched cddid_all.tbl CDD pfam12212 pfam12212 314988 PAZ_2 PAZ domain. This entry corresponds to the PAZ domain found in some archaeal argonaute proteins. It is an siRNA binding domain. 127 matched cddid_all.tbl CDD pfam12213 pfam12213 463494 Dpoe2NT DNA polymerases epsilon N terminal. This domain is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with pfam04042. There is a single completely conserved residue F that may be functionally important. This domain is the N terminal domain of DNA polymerase epsilon subunit B. It forms a primarily alpha helical structure in which four helices are arranged in two hairpins with connecting loops containing beta strands which form a short parallel sheet. DNA polymerase epsilon is required in DNA replication for synthesis of the leading strand. This domain has close structural relation to AAA+ protein C terminal domains. 73 matched cddid_all.tbl CDD pfam12214 pfam12214 463495 TPX2_importin Cell cycle regulated microtubule associated protein. This domain is found in eukaryotes. This domain is typically between 127 to 182 amino acids in length. This domain is found associated with pfam06886. This domain is found in the protein TPX2 (a.k.a p100) which is involved in cell cycling. It is only expressed between the start of the S phase and completion of cytokinesis. The microtubule-associated protein TPX2 has been reported to be crucial for mitotic spindle formation. This domain is close to the C terminal of TPX2. The protein importin alpha regulates the activity of TPX2 by binding to the nuclear localization signal in this domain. 129 matched cddid_all.tbl CDD pfam12215 pfam12215 463496 Glyco_hydr_116N beta-glucosidase 2, glycosyl-hydrolase family 116 N-term. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 320 to 354 amino acids in length. This domain is found associated with pfam04685. It is found just after the extreme N terminus. The N-terminal is thought to be the luminal domain while the C terminal is the cytosolic domain. The catalytic domain of GBA-2 is unknown. The primary catabolic pathway for glucosylceramide is catalysis by the lysosomal enzyme glucocerebrosidase. In higher eukaryotes, glucosylceramide is the precursor of glycosphingolipids, a complex group of ubiquitous membrane lipids. Mutations in the human protein cause motor-neurone defects in hereditary spastic paraplegia. The catalytic nucleophile, identified in UniProtKB:Q97YG8_SULSO, is a glutamine-335 in the downstream family pfam04685. 309 matched cddid_all.tbl CDD pfam12216 pfam12216 371968 m04gp34like Immune evasion protein. This protein is found in archaea and viruses. Proteins in this family are typically between 265 to 342 amino acids in length. The proteins in this family are or are related to the m04 encoded protein gp34 of pathogenic microorganizms such as murine cytomegalovirus. m06 and m152 genes are expressed earlier in the intracellular replication phases of these microorganizm' life cycles. They function to inhibit MHC-1 loading and export. gp34 is theorized to prevent immune reactions from NK cells which would ordinarily recognize and attack cells lacking MHC. 267 matched cddid_all.tbl CDD pfam12217 pfam12217 152652 End_beta_propel Catalytic beta propeller domain of bacteriophage endosialidase. This domain family is found in bacteria and viruses, and is typically between 443 and 460 amino acids in length. This domain is the highly conserved beta propeller of bacteriophage endosialidase which represents the catalytically active part of the enzymes. This core domain forms stable SDS-resistant trimers. There is a nested beta barrel domain in this domain (pfam12195). The endosialidase protein complexes to form a homotrimeric molecule. 449 matched cddid_all.tbl CDD pfam12218 pfam12218 314993 End_N_terminal N terminal extension of bacteriophage endosialidase. This domain family is found in bacteria and viruses, and is approximately 70 amino acids in length. This domain is found in the bacteriophage protein endosialidase. The two N-terminal domains (this domain and the beta propeller) assemble in the compact 'cap' whereas the C-terminal domain forms an extended tail-like structure. The very N-terminal part of the 'cap' region (residues 246 to 312) holds the only alpha-helix of the protein and is presumably the residual part of the deleted N-terminal head-binding domain. The endosialidase protein complexes to form homotrimeric molecules. 67 matched cddid_all.tbl CDD pfam12219 pfam12219 152654 End_tail_spike Catalytic domain of bacteriophage endosialidase. This domain family is found in bacteria and viruses, and is approximately 160 amino acids in length. There are two conserved sequence motifs: VSR and YGA. This domain is the C terminal domain of the bacteriophage protein endosialidase. The endosialidase protein forms homotrimeric molecules and this domain complexes into a tail-spike stalk. The stalk region folds in a triple beta-helix that is interrupted by a small triple beta-prism domain. The tail-spike is a multifunctional protein device used by the phage to fulfill the following functions: (i) to adsorb to the bacterial polySia capsule (ii) to de-polymerize the capsule to gain access to the outer bacterial membrane, and finally (iii) to mediate tight adhesion to the membrane, a prerequisite for the initiation of the infection cycle. 160 matched cddid_all.tbl CDD pfam12220 pfam12220 432406 U1snRNP70_N U1 small nuclear ribonucleoprotein of 70kDa MW N terminal. This domain is found in eukaryotes. This domain is about 90 amino acids in length. This domain is found associated with pfam00076. This domain is part of U1 snRNP, which is the pre-mRNA binding protein of the penta-snRNP spliceosome complex. It extends over a distance of 180 A from its RNA binding domain, wraps around the core domain of U1 snRNP consisting of the seven Sm proteins and finally contacts U1-C, which is crucial for 5'-splice-site recognition. 91 matched cddid_all.tbl CDD pfam12221 pfam12221 463497 HflK_N Bacterial membrane protein N terminal. This domain is found in bacteria. This domain is typically between 65 to 81 amino acids in length. This domain is found associated with pfam01145. This domain is the N terminal of the bacterial membrane protein HflK. HflK complexes with HflC to form a membrane protease which is modulated by the GTPase HflX. The N terminal domain of HflK is the membrane spanning region which anchors the protein in the bacterial membrane. 43 matched cddid_all.tbl CDD pfam12222 pfam12222 403439 PNGaseA Peptide N-acetyl-beta-D-glucosaminyl asparaginase amidase A. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 558 and 775 amino acids in length. There is a conserved TGG sequence motif. PNGase A is a protein which cleaves glycopeptides. 434 matched cddid_all.tbl CDD pfam12223 pfam12223 432408 DUF3602 Protein of unknown function (DUF3602). This domain family is found in eukaryotes, and is typically between 78 and 89 amino acids in length. 80 matched cddid_all.tbl CDD pfam12224 pfam12224 432409 Amidoligase_2 Putative amidoligase enzyme. This family of proteins are likely to act as amidoligase enzymes Protein in this family are found in conserved gene neighborhoods encoding a glutamine amidotransferase-like thiol peptidase (in proteobacteria) or an Aig2 family cyclotransferase protein (in firmicutes). 235 matched cddid_all.tbl CDD pfam12225 pfam12225 463498 DUF5981 Methylene-tetrahydrofolate reductase C terminal. This family is found in bacteria and archaea, and is approximately 100 amino acids in length. There is a conserved NGPCGG sequence motif. This family is the C terminal of methylene-tetrahydrofolate reductase. This protein reduces FAD using the reducing equivalents from reduced FAD, subsequently reduces tetrahydrofolate. The C terminal of MTHFR contains the FAD binding site and is the catalytic portion of the enzyme. 89 matched cddid_all.tbl CDD pfam12226 pfam12226 371974 Astro_capsid_p Turkey astrovirus capsid protein. This family of proteins is found in viruses. Proteins in this family are typically between 241 and 261 amino acids in length. These proteins are capsid proteins from various astrovirus strains. 361 matched cddid_all.tbl CDD pfam12227 pfam12227 371975 DUF3603 Protein of unknown function (DUF3603). This protein is found in bacteria and eukaryotes. Proteins in this family are about 250 amino acids in length. 214 matched cddid_all.tbl CDD pfam12228 pfam12228 371976 DUF3604 Protein of unknown function (DUF3604). This family of proteins is found in bacteria. Proteins in this family are typically between 621 and 693 amino acids in length. 591 matched cddid_all.tbl CDD pfam12229 pfam12229 403443 PG_binding_4 Putative peptidoglycan binding domain. This domain is found associated with the L,D-transpeptidase domain pfam03734. The structure of this domain has been solved and shows a mixed alpha-beta fold composed of nine beta strands and four alpha helices. This domain is usually found to be duplicated. Therefore, it seems likely that this domain acts to bind the two unlinked peptidoglycan chains and bring them into close association so they can be cross linked by the transpeptidase domain (Bateman A pers. observation). 117 matched cddid_all.tbl CDD pfam12230 pfam12230 403444 PRP21_like_P Pre-mRNA splicing factor PRP21 like protein. This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with pfam01805. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. 213 matched cddid_all.tbl CDD pfam12231 pfam12231 463499 Rif1_N Rap1-interacting factor 1 N terminal. This domain family is found in eukaryotes, and is typically between 135 and 146 amino acids in length. Rif1 is a protein which interacts with Rap1 to regulate telomere length. Interaction with telomeres limits their length. The N terminal region contains many HEAT- and ARMADILLO- type repeats. These are helical folds which form extended curved proteins or RNA interface surfaces. 363 matched cddid_all.tbl CDD pfam12232 pfam12232 463500 Myf5 Myogenic determination factor 5. This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with pfam00010, pfam01586. There is a conserved CSD sequence motif. Myf5 is responsible for directing cells to the skeletal myocyte lineage during development. Myf5 is likely to act in a similar way to the other MRF4 proteins such as MyoD which perform the same function. These are histone acetyltransferases and histone deacetylases which activate and repress genes involved in the myocyte lineage. 71 matched cddid_all.tbl CDD pfam12233 pfam12233 289037 p12I Human adult T cell leukemia/lymphoma virus protein. This family of proteins is found in viruses. Proteins in this family are approximately 100 amino acids in length. p12I binds to the immature beta and gamma-c chains of the interleukin-2 receptor retarding their translocation to the plasma membrane. p12I forms dimers which bind to these chains. 99 matched cddid_all.tbl CDD pfam12234 pfam12234 432413 Rav1p_C RAVE protein 1 C terminal. This domain family is found in eukaryotes, and is typically between 621 and 644 amino acids in length. This family is the C terminal region of the protein RAVE (regulator of the ATPase of vacuolar and endosomal membranes). Rav1p is involved in regulating the glucose dependent assembly and disassembly of vacuolar ATPase V1 and V0 subunits. 637 matched cddid_all.tbl CDD pfam12235 pfam12235 463501 FXMRP1_C_core Fragile X-related 1 protein core C terminal. This domain family is found in eukaryotes, and is typically between 126 and 160 amino acids in length. The family is found in association with pfam05641, pfam00013. This family is the core C terminal region of the fragile X related 1 proteins FXR1P, FXR2 and FMR1. These different proteins have different regions at their very C-terminus. The Glutamine-arginine rich region facilitates protein interactions. This family contains two blocks of RGG repeats that bind to G-quartet sequences in a wide variety of mRNAs. 129 matched cddid_all.tbl CDD pfam12236 pfam12236 432415 Head-tail_con Bacteriophage head to tail connecting protein. This family of head-tail connector proteins is found in bacteria and viruses. Proteins in this family are typically between 516 and 555 amino acids in length. This protein is found in Phage T7 and T3 among others. 478 matched cddid_all.tbl CDD pfam12237 pfam12237 463502 PCIF1_WW Phosphorylated CTD interacting factor 1 WW domain. This domain family is found in bacteria and eukaryotes, and is approximately 180 amino acids in length. This domain is the WW domain of PCIF1. PCIF1 interacts with phosphorylated RNA polymerase II carboxy-terminal domain (CTD). The WW domain of PCIF1 can directly and preferentially bind to the phosphorylated CTD compared to the unphosphorylated CTD. PCIF1 binds to the hyperphosphorylated RNAP II (RNAP IIO) in vitro and in vivo. Double immunofluorescence labeling in HeLa cells demonstrated that PCIF1 and endogenous RNAP IIO are co-localized in the cell nucleus. Thus, PCIF1 may play a role in mRNA synthesis by modulating RNAP IIO activity. 172 matched cddid_all.tbl CDD pfam12238 pfam12238 289042 MSA-2c Merozoite surface antigen 2c. This family of proteins is found in eukaryotes. Proteins in this family are typically between 263 and 318 amino acids in length. There is a conserved SFT sequence motif. MSA-2 is a plasma membrane glycoprotein which can be found in Babesia bovis species. 216 matched cddid_all.tbl CDD pfam12239 pfam12239 432417 DUF3605 Protein of unknown function (DUF3605). This family of proteins is found in eukaryotes and viruses. Proteins in this family are typically between 161 and 256 amino acids in length. 155 matched cddid_all.tbl CDD pfam12240 pfam12240 463503 Angiomotin_C Angiomotin C terminal. This domain family is found in eukaryotes, and is typically between 197 and 211 amino acids in length. This family is the C terminal region of angiomotin. Angiomotin regulates the action of angiogenesis inhibitor angiostatin. The C terminal region of angiomotin appears to be involved in directing the protein chemotactically. 200 matched cddid_all.tbl CDD pfam12241 pfam12241 463504 Enoyl_reductase Trans-2-enoyl-CoA reductase catalytic region. This family of trans-2-enoyl-CoA reductases, EC:1.3.1.44, carries the the catalytic sites of the enzyme, characterized by the conserved sequence motifs: YNThhhFxK, and YShAPxR. In Euglena where the enzyme has been characterized it catalyzes the reduction of enoyl-CoA to acyl-CoA in an unusual fatty acid pathway in mitochondria. the whole path performs a malonyl-CoA independent synthesis of fatty acids leading to accumulation of wax esters, which serve as the sink for electrons stemming from glycolytic ATP synthesis and pyruvate oxidation. 236 matched cddid_all.tbl CDD pfam12242 pfam12242 432420 Eno-Rase_NADH_b NAD(P)H binding domain of trans-2-enoyl-CoA reductase. This family carries the region of the enzyme trans-2-enoyl-CoA reductase, EC:1.3.1.44, which binds NAD(P)H. The activity of the enzyme was characterized in Euglena where an unusual fatty acid synthesis path-way in the mitochondria performs a malonyl-CoA independent synthesis of fatty acids leading to accumulation of wax esters, which serve as the sink for electrons stemming from glycolytic ATP synthesis and pyruvate oxidation. The full enzyme catalyzes the reduction of enoyl-CoA to acyl-CoA. The binding site is conserved as GA/CSpGYG, where p is any polar residue. 78 matched cddid_all.tbl CDD pfam12243 pfam12243 403455 CTK3 CTD kinase subunit gamma CTK3. The C-terminal domain kinase (CTDK-1), is a three-subunit complex comprised of Ctk1, Ctk2, and Ctk3, that plays a key role in regulation of transcription and translation and in coordinating these two processes. Both Ctk2 and Ctk3 are regulated at the level of protein turnover, and are unstable proteins processed through a ubiquitin-proteasome pathway. Their physical interaction is required to protect both subunits from degradation, and both Ctk2 and Ctk3 are required for Ctk1 CTD kinase activation. The mammalian P-TEFb is mirrored by the combined complexes in yeast of the CTDK1 and the Bur1/2. 123 matched cddid_all.tbl CDD pfam12244 pfam12244 432421 DUF3606 Protein of unknown function (DUF3606). This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important. 53 matched cddid_all.tbl CDD pfam12245 pfam12245 403457 Big_3_2 Bacterial Ig-like domain. This family consists of bacterial domains with an Ig-like fold. Members of this family are found in a variety of bacterial surface proteins. 122 matched cddid_all.tbl CDD pfam12246 pfam12246 432422 MKT1_C Temperature dependent protein affecting M2 dsRNA replication. This domain family is found in eukaryotes, and is typically between 231 and 255 amino acids in length. There is a single completely conserved residue P that may be functionally important. MKT1 is required for maintenance of K2 toxin above 30 degrees C in strains with the L-A-HN variant of the L-A double-stranded RNA virus of Saccharomyces cerevisiae. MKT1 is a 93 kDa protein with serine-rich regions and the retroviral protease signature, DTG. This family is the C terminal region of MKT1. 242 matched cddid_all.tbl CDD pfam12247 pfam12247 432423 MKT1_N Temperature dependent protein affecting M2 dsRNA replication. This domain family is found in eukaryotes, and is typically between 231 and 255 amino acids in length. There is a single completely conserved residue P that may be functionally important. MKT1 is required for maintenance of K2 toxin above 30 degrees C in strains with the L-A-HN variant of the L-A double-stranded RNA virus of Saccharomyces cerevisiae. MKT1 is a 93 kDa protein with serine-rich regions and the retroviral protease signature, DTG. This family is the N terminal region of MKT1. 84 matched cddid_all.tbl CDD pfam12248 pfam12248 463505 Methyltransf_FA Farnesoic acid 0-methyl transferase. This domain family is found in bacteria and eukaryotes, and is approximately 110 amino acids in length.Farnesoic acid O-methyl transferase (FAMeT) is the enzyme that catalyzes the formation of methyl farnesoate (MF) from farnesoic acid (FA) in the biosynthetic pathway of juvenile hormone (JH). 104 matched cddid_all.tbl CDD pfam12249 pfam12249 432425 AftA_C Arabinofuranosyltransferase A C terminal. This domain family is found in bacteria, and is typically between 179 and 190 amino acids in length. This family is the C terminal region of AftA. The enzyme catalyzes the addition of the first key arabinofuranosyl residue from the sugar donor beta-D-arabinofuranosyl-1-monophosphoryldecaprenol to the galactan domain of the cell wall, thus priming the galactan for further elaboration by the arabinofuranosyltransferases. The C terminal region is predicted to be directed towards the periplasm. 177 matched cddid_all.tbl CDD pfam12250 pfam12250 432426 AftA_N Arabinofuranosyltransferase N terminal. This domain family is found in bacteria, and is typically between 430 and 441 amino acids in length. This family is the N terminal region of AftA. The enzyme catalyzes the addition of the first key arabinofuranosyl residue from the sugar donor beta-D-arabinofuranosyl-1-monophosphoryldecaprenol to the galactan domain of the cell wall, thus priming the galactan for further elaboration by the arabinofuranosyltransferases. The N terminal region has been predicted to span 11 transmembrane regions. 421 matched cddid_all.tbl CDD pfam12251 pfam12251 463506 SNAPC3 snRNA-activating protein complex (SNAPc), subunit 3. This entry represents the C-terminal part of the SNAPC3 protein found in eukaryotes. This protein is part of the snRNA-activating protein complex which activates RNA polymerases II and III. There is a cysteine-histidine cluster which contains two possible zinc finger motifs. 191 matched cddid_all.tbl CDD pfam12252 pfam12252 432428 SidE_PDE SidE phosphodiesterase (PDE) domain. This entry represents the phosphodiesterase (PDE) domain found in the bacterial ubiquitinating enzymes, which belong to the SidE family. This domain catalyzes the conjugation of ADP-ribosylated ubiquitin (ADPR-Ub), previously synthesized by the mono-ADP-ribosyltransferase (mART) domain, to a serine residue on substrates to generate a protein-phosphoribosyl-Ub (PR-Ub) product. These pathogen proteins are secreted bacterial effector proteins, which are translocated inside the host cell using the Dot/Icm secretion system. The SidE family of enzymes carry out ubiquitination of host cell proteins in an E1/E2-independent manner. 225 matched cddid_all.tbl CDD pfam12253 pfam12253 463507 CAF1A Chromatin assembly factor 1 subunit A. The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A. The A domain is uniquely required for the progression of S phase in mouse cells, independent of its ability to promote histone deposition but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints. 75 matched cddid_all.tbl CDD pfam12254 pfam12254 463508 DNA_pol_alpha_N DNA polymerase alpha subunit p180 N terminal. This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with pfam00136, pfam08996, pfam03104. This family is the N terminal of DNA polymerase alpha subunit p180 protein. The N terminal contains the catalytic region of the alpha subunit. 65 matched cddid_all.tbl CDD pfam12255 pfam12255 463509 TcdB_toxin_midC Insecticide toxin TcdB middle/C-terminal region. This domain family is found in bacteria, and is approximately 150 amino acids in length. The family is found in association with pfam03534. This family is the C-terminal-sided middle region of the bacterial insecticide toxin TcdB. 141 matched cddid_all.tbl CDD pfam12256 pfam12256 403467 TcdB_toxin_midN Insecticide toxin TcdB middle/N-terminal region. This domain family is found in bacteria and archaea, and is typically between 164 and 180 amino acids in length. The family is found in association with pfam05593. This family is the N-terminal-sided middle region of the bacterial insecticide toxin TcdB. This region appears related to the FG-GAP repeat pfam01839. 181 matched cddid_all.tbl CDD pfam12257 pfam12257 463510 IML1 Vacuolar membrane-associated protein Iml1. Proteins in this family contain a DEP domain, which is a globular domain of about 80 residues. This entry includes vacuolar membrane-associated protein Iml1 and DEP domain-containing protein 5/DDB_G0279099. In Saccharomyces cerevisiae, Iml1 is a subunit of both the SEA (Seh1-associated) and Iml1 complexes (Iml1-Npr2-Npr3). SEA complex is associates dynamically with the vacuole and is involved in autophagy. Iml1 complex is required for non-nitrogen-starvation (NNS)-induced autophagy. 278 matched cddid_all.tbl CDD pfam12258 pfam12258 463511 Microcephalin Microcephalin protein. This family of proteins is found in eukaryotes. Proteins in this family are typically between 384 and 835 amino acids in length. Microcephalin is involved in determining the size of the brain in animals. It is a protein, which if expressed homozygously causes the organizm to have the condition microcephaly. organizms expressing the mutated form of this protein in a homozygous manner develop a condition called microcephaly - a drastically reduced brain mass and volume. Microcephalin is predicted to contain three BRCA1 C-terminal domains, the first of which is the probable microcephaly mutation site. 390 matched cddid_all.tbl CDD pfam12259 pfam12259 371998 Baculo_F Baculovirus F protein. This protein is found in a variety of baculoviruses. It is known as the F protein. Matches to this family are additionally found in some presumed transposons. 606 matched cddid_all.tbl CDD pfam12260 pfam12260 463512 PIP49_C Protein-kinase domain of FAM69. This is the C-terminal region of a family of FAM69 proteins from Metazoa and Viridiplantae that are active protein-kinases. The family members have a short transmembrane helix close to the N-terminus, and thereafter are highly enriched with cysteines. FAM69 proteins are localized to the endoplasmic reticulum. Many members also have a short EF-hand, calcium-binding, domain just upstream of the kinase domain. The exact function of the more N-terminal family is uncertain. 188 matched cddid_all.tbl CDD pfam12261 pfam12261 432434 T_hemolysin Thermostable hemolysin. This family of proteins is found in bacteria. Proteins in this family are typically between 200 and 228 amino acids in length. T_hemolysin is a pore-forming toxin of bacteria, able to lyse erythrocytes from a number of mammalian species. 171 matched cddid_all.tbl CDD pfam12262 pfam12262 432435 Lipase_bact_N Bacterial virulence factor lipase N-terminal. This domain family is found in bacteria, and is typically between 258 and 271 amino acids in length. There are two conserved sequence motifs: DGT and DGWST. This family is the N-terminal region of bacterial virulence factor lipase. The N-terminal region contains a potential signalling sequence. 237 matched cddid_all.tbl CDD pfam12263 pfam12263 432436 DUF3611 Protein of unknown function (DUF3611). This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 180 and 205 amino acids in length. There are two completely conserved residues (W and G) that may be functionally important. 176 matched cddid_all.tbl CDD pfam12264 pfam12264 152699 Waikav_capsid_1 Waikavirus capsid protein 1. The rice tungro spherical waikavirus polyprotein is cleaved into 7 proteins, including three capsid proteins, by the tungro spherical virus-type peptidase pfam12381. This family represents the capsid protein 1. 197 matched cddid_all.tbl CDD pfam12265 pfam12265 463513 CAF1C_H4-bd Histone-binding protein RBBP4 or subunit C of CAF1 complex. The CAF-1 complex is a conserved heterotrimeric protein complex that promotes histone H3 and H4 deposition onto newly synthesized DNA during replication or DNA repair; specifically it facilitates replication-dependent nucleosome assembly with the major histone H3 (H3.1). This domain is an alpha helix which sits just upstream of the WD40 seven-bladed beta-propeller in the human RbAp46 protein. RbAp46 folds into the beta-propeller and binds histone H4 in a groove formed between this N-terminal helix and an extended loop inserted into blade six. 69 matched cddid_all.tbl CDD pfam12266 pfam12266 432438 DUF3613 Protein of unknown function (DUF3613). This family of proteins is found in bacteria. Proteins in this family are typically between 94 and 126 amino acids in length. 66 matched cddid_all.tbl CDD pfam12267 pfam12267 152702 DUF3614 Protein of unknown function (DUF3614). This family of proteins is found in viruses. Proteins in this family are typically between 162 and 495 amino acids in length. 173 matched cddid_all.tbl CDD pfam12268 pfam12268 432439 DUF3612 Protein of unknown function (DUF3612). This domain family is found in bacteria, and is approximately 180 amino acids in length. The family is found in association with pfam01381. 176 matched cddid_all.tbl CDD pfam12269 pfam12269 463514 CpG_bind_C CpG binding protein C-terminal domain. CpG-binding protein is a transcriptional activator that exhibits a DNA binding specificity for unmethylated CpG motifs. CpG is made of a PHD1, an acidic, a basic, a coiled-coil, and a PHD2 domains. This protein contains three cysteine-rich domains identified at the N-terminal, central region and C-terminal of the protein, where the central cysteine-rich domain is located within the DNA-binding domain, found between PHD1 and the acidic domains. This domain is found in eukaryotes, and is approximately 240 amino acids in length. It is found at the C-terminal of the CpG-binding protein containing the coiled-coil and PHD2 domains. 235 matched cddid_all.tbl CDD pfam12270 pfam12270 432441 Cyt_c_ox_IV Cytochrome c oxidase subunit IV. This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. This family is the fourth subunit of the cytochrome c oxidase complex. This subunit does not have a catalytic capacity but instead, is required for assembly and/or stability of the complex. 132 matched cddid_all.tbl CDD pfam12271 pfam12271 432442 Chs7 Chitin synthase export chaperone. This family of proteins is found in eukaryotes, and are typically between 288 and 332 amino acids in length. Family members include the Saccharomyces cerevisiae Chs7, an integral membrane protein located in the ER which is directly involved in chitin synthesis through the regulation of chitin synthase III (CSIII) activity. In the absence of CHS7 gene product, Chs3p, but not other secreted proteins, is retained in the ER, leading to a severe defect in CSIII activity and consequently, to a reduced rate of chitin synthesis. In addition, chs7 null mutants show the yeast phenotypes associated with a lack of chitin: reduced mating efficiency and lack of the chitosan ascospore layer, clear indications of Chs7p function throughout the S. cerevisiae biological cycle. Hence, Chs7 is involved in the regulation of CSIII activity by controlling Chs3p export from the ER. 283 matched cddid_all.tbl CDD pfam12273 pfam12273 432443 RCR Chitin synthesis regulation, resistance to Congo red. RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5. 113 matched cddid_all.tbl CDD pfam12274 pfam12274 463515 DUF3615 Protein of unknown function (DUF3615). This domain family is found in bacteria and eukaryotes, and is typically between 86 and 97 amino acids in length. There is a conserved FAE sequence motif. There is a single completely conserved residue F that may be functionally important. 94 matched cddid_all.tbl CDD pfam12275 pfam12275 432445 DUF3616 Protein of unknown function (DUF3616). This family of proteins is found in bacteria. Proteins in this family are typically between 335 and 392 amino acids in length. There is a conserved GLRGPV sequence motif. 328 matched cddid_all.tbl CDD pfam12276 pfam12276 463516 DUF3617 Protein of unknown function (DUF3617). This family of proteins is found in bacteria. Proteins in this family are typically between 155 and 179 amino acids in length. There is a single completely conserved residue C that may be functionally important. 110 matched cddid_all.tbl CDD pfam12277 pfam12277 432447 DUF3618 Protein of unknown function (DUF3618). This domain family is found in bacteria, and is approximately 50 amino acids in length. 47 matched cddid_all.tbl CDD pfam12278 pfam12278 463517 SDP_N Sex determination protein N terminal. This family of proteins is found in eukaryotes. Proteins in this family are typically between 168 and 410 amino acids in length. This family is the N terminal end of the sex determination protein of many different animals. It plays a role in the gender determination of around 20% of all animals. 139 matched cddid_all.tbl CDD pfam12279 pfam12279 463518 DUF3619 Protein of unknown function (DUF3619). This protein is found in bacteria. Proteins in this family are about 140 amino acids in length. This protein has two conserved sequence motifs: AAR and DDLP. 127 matched cddid_all.tbl CDD pfam12280 pfam12280 463519 BSMAP Brain specific membrane anchored protein. This family of proteins is found in eukaryotes. Proteins in this family are typically between 285 and 331 amino acids in length. BSMAP has a putative transmembrane domain and is predicted to be a type I membrane glycoprotein. 197 matched cddid_all.tbl CDD pfam12281 pfam12281 463520 NTP_transf_8 Nucleotidyltransferase. This is a family of bacterial proteins that have a nucleotidyltransferase fold. The fold-prediction is backed up by conservation of three highly characteriztic sequence motifs found in all other nucleotidyl transferases: i) pDhDhhh(h/p), where p is a polar residue and h is a hydrophobic residue; ii) upstream of the first, a GG/S; iii) a conserved D/E in a hydrophobic surround. In the classification of nucleotidyltransferases proposed in this is a group XVIII NTP-transferase. Many of these sequences were classified in the COG database as COG5397. The exact function is not known. 209 matched cddid_all.tbl CDD pfam12282 pfam12282 432452 PdtaS_GAF Histidine kinase PdtaS, GAF domain. This entry represents the GAF domain of the sensor region in the cytosolic histidine kinase (HK), PdtaS, from Mycobacterium tuberculosis. The N-terminal region of this protein is comprised of closely linked GAF and PAS domains, both are ubiquitous and form dimeric interfaces. GAF domains are known to bind heme (as can PAS domains), to be involved in redox responses and even to function as catalytic domains. 140 matched cddid_all.tbl CDD pfam12283 pfam12283 289084 Protein_K Bacteriophage protein K. This family of proteins is found in viruses. Proteins in this family are approximately 60 amino acids in length. This family is a protein expressed by bacteriophages which has an unknown function. There is evidence that it is non-essential for in vivo production of a mature phage. 56 matched cddid_all.tbl CDD pfam12284 pfam12284 463521 HoxA13_N Hox protein A13 N terminal. This family of proteins is found in eukaryotes. Proteins in this family are typically between 149 and 306 amino acids in length. The family is found in association with pfam00046. This family is the N terminal of the Hox gene protein involved in formation of the digital arch of the hands and feet as well as in correct genital formation. Mutation of the protein is associated with hand-foot-genital syndrome. 122 matched cddid_all.tbl CDD pfam12285 pfam12285 432454 Astrovir_pp_1 Astroviridae polyprotein 1. This family of proteins is found in non-structural polyprotein 1 A/AB from Astroviridae. They are typically between 49 and 62 amino acids in length. There are two conserved sequence motifs: QPLDLS and EQQ. 171 matched cddid_all.tbl CDD pfam12286 pfam12286 432455 DUF3622 Protein of unknown function (DUF3622). This family of proteins is found in bacteria. Proteins in this family are typically between 72 and 107 amino acids in length. There is a conserved VSK sequence motif. 71 matched cddid_all.tbl CDD pfam12287 pfam12287 463522 Caprin-1_C Cytoplasmic activation/proliferation-associated protein-1 C term. This family of proteins is found in eukaryotes. Proteins in this family are typically between 343 and 708 amino acids in length. This family is the C terminal region of caprin-1. Caprin-1 is a protein involved in regulating cellular proliferation. In mutated phenotypes, the G1 phase of the cell cycle is greatly lengthened, impairing normal proliferation. The C terminal region of caprin-1 contains RGG motifs which are characteriztic of RNA binding domains. It is possible that caprin-1 functions through an RNA binding mechanism. 320 matched cddid_all.tbl CDD pfam12288 pfam12288 403489 CsoS2_M Carboxysome shell peptide mid-region. This domain family is found in bacteria and eukaryotes, and is approximately 430 amino acids in length. This family is annotated frequently as a carboxysome shell peptide, however there is little publication to confirm this. 420 matched cddid_all.tbl CDD pfam12289 pfam12289 403490 Rotavirus_VP1 Rotavirus VP1 C-terminal domain. This domain is the C-terminal bracelet domain of the rotavirus VP1 RNA-directed RNA polymerase. It surrounds the exit tunnel for dsRNA produced by replication and for the RNA template for transcription. 312 matched cddid_all.tbl CDD pfam12290 pfam12290 432457 DUF3802 Protein of unknown function (DUF3802). This family of proteins is found in bacteria. Proteins in this family are typically between 114 and 143 amino acids in length. There is a conserved KNLFD sequence motif. 111 matched cddid_all.tbl CDD pfam12291 pfam12291 403491 DUF3623 Protein of unknown function (DUF3623). This family of proteins is found in bacteria. Proteins in this family are typically between 261 and 345 amino acids in length. 255 matched cddid_all.tbl CDD pfam12292 pfam12292 432458 DUF3624 Protein of unknown function (DUF3624). This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There is a conserved GRC sequence motif. 74 matched cddid_all.tbl CDD pfam12293 pfam12293 432459 T4BSS_DotH_IcmK Putative outer membrane core complex of type IVb secretion. T4BSS_DotH_IcmK is a family of bacterial transporter proteins from Proteobacteria. DotH is an integral outer membrane component and it may form an outer membrane complex along with DotD and DotC functionally equivalent to secretins. DotH is the strongest candidate for the VirB9 counterpart of other T4BSS systems. 238 matched cddid_all.tbl CDD pfam12294 pfam12294 403494 DUF3626 Protein of unknown function (DUF3626). This family of proteins is found in bacteria. Proteins in this family are typically between 294 and 374 amino acids in length. 301 matched cddid_all.tbl CDD pfam12295 pfam12295 463523 Symplekin_C Symplekin tight junction protein C terminal. This domain family is found in eukaryotes, and is approximately 180 amino acids in length. There is a single completely conserved residue P that may be functionally important. Symplekn has been localized, by light and electron microscopy, to the plaque associated with the cytoplasmic face of the tight junction-containing zone (zonula occludens) of polar epithelial cells and of Sertoli cells of testis. However, both the mRNA and the protein can also be detected in a wide range of cell types that do not form tight junctions. Careful analyses have revealed that the protein occurs in all these diverse cells in the nucleoplasm, and only in those cells forming tight junctions is it recruited, partly but specifically, to the plaque structure of the zonula occludens. 185 matched cddid_all.tbl CDD pfam12296 pfam12296 463524 HsbA Hydrophobic surface binding protein A. This protein is found in eukaryotes. Proteins in this family are typically between 171 to 275 amino acids in length. Although the HsbA amino acid sequence suggests that HsbA may be hydrophilic, HsbA adsorbed to hydrophobic PBSA (Polybutylene succinate-co-adipate) surfaces in the presence of NaCl or CaCl2. When HsbA was adsorbed on the hydrophobic PBSA surfaces, it promoted PBSA degradation via the CutL1 polyesterase. CutL1 interacts directly with HsbA attached to the hydrophobic QCM electrode surface. These results suggest that when HsbA is adsorbed onto the PBSA surface, it recruits CutL1, and that when CutL1 is accumulated on the PBSA surface, it stimulates PBSA degradation. 123 matched cddid_all.tbl CDD pfam12297 pfam12297 463525 EVC2_like Ellis van Creveld protein 2 like protein. This family of proteins is found in eukaryotes. Proteins in this family are typically between 571 and 1310 amino acids in length. There are two conserved sequence motifs: LPA and ELH. EVC2 is implicated in Ellis van Creveld chondrodysplastic dwarfism in humans. Mutations in this protein can give rise to this congenital condition. LIMBIN is a protein which shares around 80% sequence homology with EVC2 and it is implicated in a similar condition in bovine chondrodysplastic dwarfism. 428 matched cddid_all.tbl CDD pfam12298 pfam12298 403498 Bot1p Eukaryotic mitochondrial regulator protein. This family of proteins is found in eukaryotes. Proteins in this family are typically between 168 and 381 amino acids in length. Bot1p localizes to the mitochondria in live cells and cofractionates with purified mitochondrial ribosomes. Bot1p has a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery. Observations also indicate that in fission yeast, alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms. 172 matched cddid_all.tbl CDD pfam12299 pfam12299 372024 DUF3627 Protein of unknown function (DUF3627). This domain family is found in bacteria and viruses, and is approximately 90 amino acids in length. The family is found in association with pfam02498. 93 matched cddid_all.tbl CDD pfam12300 pfam12300 372025 RhlB ATP-dependent RNA helicase RhlB. Proteins in this entry are DEAD Box RhlB RNA Helicases found in Xanthomonadaceae bacteria. 181 matched cddid_all.tbl CDD pfam12301 pfam12301 463526 CD99L2 CD99 antigen like protein 2. This family of proteins is found in eukaryotes. Proteins in this family are typically between 165 and 237 amino acids in length. CD99L2 and CD99 are involved in trans-endothelial migration of neutrophils in vitro and in the recruitment of neutrophils into inflamed peritoneum. 162 matched cddid_all.tbl CDD pfam12302 pfam12302 372027 DUF3629 Protein of unknown function (DUF3629). This family of proteins is found in eukaryotes. Proteins in this family are typically between 256 and 292 amino acids in length. 218 matched cddid_all.tbl CDD pfam12304 pfam12304 463527 BCLP Beta-casein like protein. This protein is found in eukaryotes. Proteins in this family are typically between 216 to 240 amino acids in length. This protein has two conserved sequence motifs: VLR and TRIY. BCLP is associated with cell morphology and a regulation of growth pattern of tumor. It is found in adenocarcinomas of uterine cervical tissues. 184 matched cddid_all.tbl CDD pfam12305 pfam12305 432465 DUF3630 Protein of unknown function (DUF3630). This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. There is a single completely conserved residue D that may be functionally important. 91 matched cddid_all.tbl CDD pfam12306 pfam12306 432466 PixA Inclusion body protein. This family of proteins is found in bacteria. Proteins in this family are typically between 173 and 191 amino acids in length. PixA is thought to be specifically produced in Xenorhabdus nematophila. It is an inclusion body protein. 168 matched cddid_all.tbl CDD pfam12307 pfam12307 432467 DUF3631 Protein of unknown function (DUF3631). This protein is found in bacteria. Proteins in this family are typically between 180 to 701 amino acids in length. 185 matched cddid_all.tbl CDD pfam12308 pfam12308 432468 Noelin-1 Neurogenesis glycoprotein. This domain family is found in eukaryotes, and is approximately 100 amino acids in length. The family is found in association with pfam02191. There are two conserved sequence motifs: SAQ and VQN. Noelin-1 is a glycoprotein which is secreted mainly by postmitotic neurogenic tissues in the developing central and peripheral nervous systems, first appearing after neural tube closure. It is likely that it forms large multimeric complexes.It has a divergent function in neurogenesis. In animal caps neuralized by expression of noggin, co-expression of Noelin-1 causes expression of neuronal differentiation markers several stages before neurogenesis normally occurs in this tissue. Finally, only secreted forms of the protein can activate sensory marker expression, while all forms of the protein can induce early neurogenesis. 100 matched cddid_all.tbl CDD pfam12309 pfam12309 463528 KBP_C KIF-1 binding protein C terminal. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 365 and 621 amino acids in length. There is a conserved LLP sequence motif. KBP is a binding partner for KIF1Balpha that is a regulator of its transport function and thus represents a type of kinesin interacting protein. 362 matched cddid_all.tbl CDD pfam12310 pfam12310 463529 Elf-1_N Transcription factor protein N terminal. This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with pfam00178. There is a conserved PAVIVE sequence motif. Elf-1 is an immune cell specific transcription factor. It is found in T cells, B cells, megakaryocytes,and mast cells and is involved in the control of transcription for various immune proteins. These include IL-2, GM-CSF, IL-5, IL-2 receptor alpha chain, and CD4 in T cells, IgH, blk, and lyn in B cells, TdT in T and B cells, IL-3 in megakaryocytes, and SCL and Fc-epsilon-RI alpha chain in mast cells. 109 matched cddid_all.tbl CDD pfam12311 pfam12311 432471 DUF3632 Protein of unknown function (DUF3632). This domain family is found in eukaryotes, and is approximately 170 amino acids in length. There is a conserved ALE sequence motif. 183 matched cddid_all.tbl CDD pfam12312 pfam12312 372036 NeA_P2 Nepovirus subgroup A polyprotein. This family of proteins is found in viruses. Proteins in this family are typically between 259 and 1110 amino acids in length. The family is found in association with pfam03688, pfam03689, pfam03391. This family is one of the polyproteins expressed by Nepoviruses in subgroup A. 175 matched cddid_all.tbl CDD pfam12313 pfam12313 372037 NPR1_like_C NPR1/NIM1 like defence protein C terminal. This family of proteins is found in eukaryotes. Proteins in this family are typically between 251 and 588 amino acids in length. The family is found in association with pfam00023, pfam00651. There are two conserved sequence motifs: LENRV and DLN. NPR1 (NIM1) is a defence protein in many plant species. 204 matched cddid_all.tbl CDD pfam12314 pfam12314 403508 IMCp Inner membrane complex protein. This domain is found in bacteria and eukaryotes. This domain is about 120 amino acids in length. This family is the inner membrane complex of parasitic organizms. This is a cytoskeletal structure associated with the pellicle of these parasites. 87 matched cddid_all.tbl CDD pfam12315 pfam12315 463530 DA1-like Protein DA1. Proteins in this family include protein DA1 and its homologs. In Arabidopsis thaliana, DA1 is an ubiquitin receptor that limits final seed and organ size by restricting the period of cell proliferation. It may act maternally to control seed mass. 214 matched cddid_all.tbl CDD pfam12316 pfam12316 463531 Dsh_C Segment polarity protein dishevelled (Dsh) C terminal. This domain family is found in eukaryotes, and is typically between 177 and 207 amino acids in length. The family is found in association with pfam00778, pfam02377, pfam00610, pfam00595. The segment polarity gene dishevelled (dsh) is required for pattern formation of the embryonic segments. It is involved in the determination of body organization through the Wingless pathway (analogous to the Wnt-1 pathway). 209 matched cddid_all.tbl CDD pfam12317 pfam12317 463532 IFT46_B_C Intraflagellar transport complex B protein 46 C terminal. This family of proteins is found in eukaryotes. Proteins in this family are typically between 298 and 416 amino acids in length. IFT46 is a flagellar protein of complex B. Like all IFT proteins, it is required for transport of IFT particles into the flagella. 203 matched cddid_all.tbl CDD pfam12318 pfam12318 432475 FAD-SLDH Membrane bound FAD containing D-sorbitol dehydrogenase. This family of proteins is found in bacteria. Proteins in this family are typically between 168 and 189 amino acids in length. There is a conserved ALM sequence motif. This family is a membrane protein (FAD-SLDH) involved in oxidation of D-sorbitol to L-sorbose. 160 matched cddid_all.tbl CDD pfam12319 pfam12319 432476 TryThrA_C Tryptophan-Threonine-rich plasmodium antigen C terminal. This protein is found in eukaryotes. Proteins in this family are typically between 254 to 536 amino acids in length. This family is the C terminal of a surface antigen of malarial Plasmodium species. It is currently being targeted for use as part of a subunit vaccine against Plasmodium falciparum, the main species involved in causing human malaria. 214 matched cddid_all.tbl CDD pfam12320 pfam12320 463533 SbcD_C Type 5 capsule protein repressor C-terminal domain. This domain is found in bacteria and archaea. This domain is about 90 amino acids in length. This domain is found associated with pfam00149. SbcD works in complex with SbdC (SbcDC) which is a transcription regulator. It down-regulates transcription of arl and mgr to inhibit type 5 capsule protein production. It acts as part of the SOS pathway of bacteria. 100 matched cddid_all.tbl CDD pfam12321 pfam12321 432478 DUF3634 Protein of unknown function (DUF3634). This family of proteins is found in bacteria. Proteins in this family are typically between 103 and 114 amino acids in length. 98 matched cddid_all.tbl CDD pfam12322 pfam12322 289120 T4_baseplate T4 bacteriophage base plate protein. This protein is found in viruses. Proteins in this family are typically between 208 to 249 amino acids in length. This protein has a single completely conserved residue S that may be functionally important. This family includes the two base plate proteins in T4 bacteriophages. These are gp51 and gp26, encoded by late genes. 132 matched cddid_all.tbl CDD pfam12323 pfam12323 432479 HTH_OrfB_IS605 Helix-turn-helix domain. This is the N terminal helix-turn-helix domain of Transposase_2 pfam01385. 47 matched cddid_all.tbl CDD pfam12324 pfam12324 432480 HTH_15 Helix-turn-helix domain of alkylmercury lyase. Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This is the N terminal helix-turn-helix domain associated with pfam03243. 74 matched cddid_all.tbl CDD pfam12325 pfam12325 432481 TMF_TATA_bd TATA element modulatory factor 1 TATA binding. This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organization in animal and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family. 115 matched cddid_all.tbl CDD pfam12326 pfam12326 432482 EOS1 N-glycosylation protein. This family is not required for survival of S.cerevisiae, but its deletion leads to heightened sensitivity to oxidative stress. It appears to be involved in N-glycosylation, and resides in the endoplasmic reticulum. 160 matched cddid_all.tbl CDD pfam12327 pfam12327 463534 FtsZ_C FtsZ family, C-terminal domain. This family includes the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ is a GTPase, like tubulin. FtsZ can polymerize into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea. 95 matched cddid_all.tbl CDD pfam12328 pfam12328 372048 Rpp20 Rpp20 subunit of nuclear RNase MRP and P. The nuclear RNase P of Saccharomyces cerevisiae is made up of at least nine protein subunits; Pop1, Pop3, Pop4, Pop5, Pop6, Pop7, Pop8, Rpr2 and Rpp1. Many of these subunits seem to be present also in the RNase MRP, with the exception of Rpr2 (Rpp21) which is unique to RNase P. Human nuclear RNase P and MRP appear to contain at least 10 protein subunits, Rpp14, Rpp20, Rpp21, Rpp25, Rpp29, Rpp30, Rpp38, Rpp40, hPop1 and hPop5, although there is recent evidence that not all of these subunits are shared between P and MRP. Archaeal RNase P has at least four protein subunits homologous to eukaryotic RNase P/MRP proteins. In the yeast RNase P, Pop6 and Pop7 (the Rpp20 homolog) interact with each other and they are both interaction partners of Pop4; in the human MRP Rpp25 and Rpp20 interact with each other and Rpp25 binds to Rpp29 (Pop4). 118 matched cddid_all.tbl CDD pfam12329 pfam12329 372049 TMF_DNA_bd TATA element modulatory factor 1 DNA binding. This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures.. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organization in animal and plant cells. 74 matched cddid_all.tbl CDD pfam12330 pfam12330 432484 Haspin_kinase Haspin like kinase domain. This family represents the haspin-like kinase domains. 369 matched cddid_all.tbl CDD pfam12331 pfam12331 432485 DUF3636 Protein of unknown function (DUF3636). This domain family is found in eukaryotes, and is approximately 160 amino acids in length. 148 matched cddid_all.tbl CDD pfam12333 pfam12333 463535 Ipi1_N Rix1 complex component involved in 60S ribosome maturation. This domain family is found in eukaryotes, and is typically between 91 and 105 amino acids in length. This family is the N terminal of Ipi1, a component of the Rix1 complex which works in conjunction with Rea1 to mature the 60S ribosome. 101 matched cddid_all.tbl CDD pfam12334 pfam12334 372053 rOmpB Rickettsia outer membrane protein B. This domain family is found in bacteria, and is approximately 220 amino acids in length. The family is found in association with pfam03797. This family is the middle region of one of the outer membrane proteins of Rickettsia which is involved in adhesion to eukaryotic cells for uptake. 223 matched cddid_all.tbl CDD pfam12335 pfam12335 463536 SBF2 Myotubularin protein. This domain family is found in eukaryotes, and is approximately 220 amino acids in length. The family is found in association with pfam02141, pfam03456, pfam03455. This family is the middle region of SBF2, a member of the myotubularin family. Myotubularin-related proteins have been suggested to work in phosphoinositide-mediated signalling events that may also convey control of myelination. Mutations of SBF2 are implicated in Charcot-Marie-Tooth disease. 227 matched cddid_all.tbl CDD pfam12336 pfam12336 463537 SOXp SOX transcription factor. This domain family is found in eukaryotes, and is approximately 80 amino acids in length. The family is found in association with pfam00505. There are two conserved sequence motifs: KKDK and LPG. This family is made up of SOX transcription factors. These are involved in upregulation of nestin, a neural promoter. 89 matched cddid_all.tbl CDD pfam12337 pfam12337 289134 DUF3637 Protein of unknown function (DUF3637). This domain family is found in viruses, and is approximately 70 amino acids in length. The family is found in association with pfam00073, pfam08935. 67 matched cddid_all.tbl CDD pfam12338 pfam12338 403524 RbcS Ribulose-1,5-bisphosphate carboxylase small subunit. This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam00101. There is a conserved APF sequence motif. There are two completely conserved residues (L and P) that may be functionally important. This family is the small subunit of ribulose-1,5-bisphosphate. 45 matched cddid_all.tbl CDD pfam12339 pfam12339 432489 DNAJ_related DNA-J related protein. This domain family is found in bacteria, and is approximately 130 amino acids in length. The family is found in association with pfam00226. There is a conserved YYLD sequence motif. Mostof the sequences in this family are annotated as DNA-J related proteins but there is little publication to back this up. 120 matched cddid_all.tbl CDD pfam12340 pfam12340 463538 DUF3638 Protein of unknown function (DUF3638). This domain family is found in eukaryotes, and is approximately 230 amino acids in length. There are two conserved sequence motifs: LLE and NMG. 225 matched cddid_all.tbl CDD pfam12341 pfam12341 463539 Mcl1_mid Minichromosome loss protein, Mcl1, middle region. Mcl1_mid, or the middle domain of minichromosome loss protein 1, is the domain that lies between a 7-bladed beta-propeller at the N-terminus, family WD40 pfam00400 etc, and a Homeobox (HMG) domain, pfam00505, at the C-terminus. The full length proteins with all three domains are referred to as DNA polymerase alpha accessory factor Mcl1, but the exact function of this domain is not known. 288 matched cddid_all.tbl CDD pfam12342 pfam12342 152777 DUF3640 Protein of unknown function (DUF3640). This family of proteins is found in viruses. Proteins in this family are typically between 25 and 211 amino acids in length. 26 matched cddid_all.tbl CDD pfam12343 pfam12343 432492 DeaD_C DeaD helicase C-terminal disordered region. This region family is found at the C-terminus of the DeaD helicase, which are involved in various cellular processes such as transcription, translation and DNA recombination. This region contains several repeats which contain an ERRE sequence motif. 61 matched cddid_all.tbl CDD pfam12344 pfam12344 463540 UvrB Ultra-violet resistance protein B. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam00271, pfam02151, pfam04851. There are two conserved sequence motifs: YAD and RRR. This family is the C terminal region of the UvrB protein which conveys mutational resistance against UV light to various different species. 43 matched cddid_all.tbl CDD pfam12345 pfam12345 463541 DUF3641 Protein of unknown function (DUF3641). This domain family is found in bacteria and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with pfam04055. This family consists of proteins which are commonly annotated as Radical SAM domains but there is little annotation to back this up. 134 matched cddid_all.tbl CDD pfam12346 pfam12346 463542 HJURP_mid Holliday junction recognition protein-associated repeat. Vertebral Holliday junction recognition proteins carry an SCM3 domain at their N-terminus as do the eukaryotic fungi, but they also carry this central, conserved region. The function of this family is not known. Further downstream there is also a repeated domain, also of unknown function. Investigation of Scm3 and associated proteins is likely to be directly relevant to understanding the mechanism of HJURP-mediated CENP-A chromatin assembly at human centromeres. 115 matched cddid_all.tbl CDD pfam12347 pfam12347 463543 HJURP_C Holliday junction regulator protein family C-terminal repeat. Although this family is conserved in the Holliday junction regulator, HJURP, proteins in higher eukaryotes, alongside an Scm3, pfam10384, family, its exact function is not known. The C-terminal region of Scm3 proteins has been evolving rapidly, and this short repeat at the C-terminal end can be present in up to two copies in the higher eukaryotes. 63 matched cddid_all.tbl CDD pfam12348 pfam12348 432496 CLASP_N CLASP N terminal. This region is found at the N terminal of CLIP-associated proteins (CLASPs). CLASPs are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules. In yeast, Drosophila, and Xenopus, a single CLASP orthologue is present. In mammals, a second paralogue (CLASP2) exists which has some functional overlap with CLASP1. 227 matched cddid_all.tbl CDD pfam12349 pfam12349 463544 Sterol-sensing Sterol-sensing domain of SREBP cleavage-activation. Sterol regulatory element-binding proteins (SREBPs) are membrane-bound transcription factors that promote lipid synthesis in animal cells. They are embedded in the membranes of the endoplasmic reticulum (ER) in a helical hairpin orientation and are released from the ER by a two-step proteolytic process. Proteolysis begins when the SREBPs are cleaved at Site-1, which is located at a leucine residue in the middle of the hydrophobic loop in the lumen of the ER. Upon proteolytic processing SREBP can activate the expression of genes involved in cholesterol biosynthesis and uptake. SCAP stimulates cleavage of SREBPs via fusion of the their two C-termini. This domain is the transmembrane region that traverses the membrane eight times and is the sterol-sensing domain of the cleavage protein. WD40 domains are found towards the C-terminus. 153 matched cddid_all.tbl CDD pfam12350 pfam12350 432498 CTK3_C CTD kinase subunit gamma CTK3 C-terminus. The C-terminal domain kinase (CTDK-1), is a three-subunit complex comprised of Ctk1, Ctk2, and Ctk3, that plays a key role in regulation of transcription and translation and in coordinating these two processes. Both Ctk2 and Ctk3 are regulated at the level of protein turnover, and are unstable proteins processed through a ubiquitin-proteasome pathway. Their physical interaction is required to protect both subunits from degradation, and both Ctk2 and Ctk3 are required for Ctk1 CTD kinase activation. The mammalian P-TEFb is mirrored by the combined complexes in yeast of the CTDK1 and the Bur1/2. It is not clear what independent function this C-terminal domain has. 59 matched cddid_all.tbl CDD pfam12351 pfam12351 372065 Fig1 Ca2+ regulator and membrane fusion protein Fig1. During the mating process of yeast cells, two Ca2+ influx pathways become activated. The resulting elevation of cytosolic free Ca2+ activates downstream signaling factors that promote long term survival of unmated cells. Fig1 is a regulator of the low affinity Ca2+ influx system (LACS), and is also required for efficient membrane fusion during yeast mating. 181 matched cddid_all.tbl CDD pfam12352 pfam12352 289148 V-SNARE_C Snare region anchored in the vesicle membrane C-terminus. Within the SNARE proteins interactions in the C-terminal half of the SNARE helix are critical to the driving of membrane fusion; whereas interactions in the N-terminal half of the SNARE domain are important for promoting priming or docking of the vesicle pfam05008. 66 matched cddid_all.tbl CDD pfam12353 pfam12353 463545 eIF3g Eukaryotic translation initiation factor 3 subunit G. This domain family is found in eukaryotes, and is approximately 130 amino acids in length. The family is found in association with pfam00076. This family is subunit G of the eukaryotic translation initiation factor 3. Subunit G is required for eIF3 integrity. 126 matched cddid_all.tbl CDD pfam12354 pfam12354 289150 Internalin_N Bacterial adhesion/invasion protein N terminal. This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with pfam00560, pfam08191, pfam09479. There are two completely conserved residues (I and F) that may be functionally important. Internalin mediates bacterial adhesion and invasion of epithelial cells in the human intestine through specific interaction with its host cell receptor E-cadherin. This family is the N terminal of internalin, the cap domain of the protein. The cap domain is conserved between different internalin types. The cap domain does not interact with E cadherin, therefore its function is presumably structural: capping the hydrophobic core. 50 matched cddid_all.tbl CDD pfam12355 pfam12355 463546 Dscam_C Down syndrome cell adhesion molecule C terminal. This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with pfam00047, pfam07679, pfam00041. The Down syndrome cell adhesion molecule (Dscam) belongs to a family of cell membrane molecules involved in the differentiation of the nervous system. This is the C terminal cytoplasmic tail region of Dscam. 118 matched cddid_all.tbl CDD pfam12356 pfam12356 463547 BIRC6 Baculoviral IAP repeat-containing protein 6. BIRC6 is an anti-apoptotic protein which can regulate cell death by controlling caspases and by acting as an E3 ubiquitin-protein ligase. 161 matched cddid_all.tbl CDD pfam12357 pfam12357 463548 PLD_C Phospholipase D C terminal. This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with pfam00168, pfam00614. There is a conserved FPD sequence motif. This family is the C terminal of phospholipase D. PLD is a major plant lipid-degrading enzyme which is involved in signal transduction. 69 matched cddid_all.tbl CDD pfam12358 pfam12358 463549 DUF3644 Protein of unknown function (DUF3644). This domain family is found in bacteria, and is typically between 65 and 80 amino acids in length. 71 matched cddid_all.tbl CDD pfam12359 pfam12359 463550 DUF3645 Protein of unknown function (DUF3645). This domain family is found in eukaryotes, and is approximately 40 amino acids in length. There is a conserved HPD sequence motif. 33 matched cddid_all.tbl CDD pfam12360 pfam12360 403540 Pax7 Paired box protein 7. This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam00046, pfam00292. Pax7 belongs to a family of genes that encode paired-box-containing transcription factors involved in the control of developmental processes. Pax7 has a distinct role in the specification of myogenic satellite cells. 45 matched cddid_all.tbl CDD pfam12361 pfam12361 432505 DBP Duffy-antigen binding protein. This family of proteins is found in eukaryotes. Proteins in this family are typically between 449 and 1061 amino acids in length. The family is found in association with pfam05424. There are two conserved sequence motifs: NKNGG and QKHDF. This family is part of the Duffy-antigen binding protein of Plasmodium spp. This protein is an antigen on these parasites which enable them to invade erythrocytes. 304 matched cddid_all.tbl CDD pfam12362 pfam12362 432506 DUF3646 DNA polymerase III gamma and tau subunits C terminal. This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with pfam00004. The proteins in this family are frequently annotated as the gamma and tau subunits of DNA polymerase III, however there is little accompanying literature to back this up. 114 matched cddid_all.tbl CDD pfam12363 pfam12363 372073 Phage_TAC_12 Phage tail assembly chaperone protein, TAC. This is a family of phage tail assembly chaperone proteins from Siphoviridae phages. 111 matched cddid_all.tbl CDD pfam12364 pfam12364 372074 DUF3648 Protein of unknown function (DUF3648). This family of proteins is found in eukaryotes and viruses. Proteins in this family are typically between 53 and 3115 amino acids in length. There are two completely conserved residues (A and F) that may be functionally important. 141 matched cddid_all.tbl CDD pfam12365 pfam12365 432507 DUF3649 Protein of unknown function (DUF3649). This domain family is found in bacteria and eukaryotes, and is approximately 30 amino acids in length. 27 matched cddid_all.tbl CDD pfam12366 pfam12366 432508 Casc1_C Cancer susceptibility candidate 1 C-terminal. This is the C-terminal domain of Cancer susceptibility candidate 1 (Casc1) which has many SNPs associated with cancer susceptibility. 222 matched cddid_all.tbl CDD pfam12367 pfam12367 463551 PFO_beta_C Pyruvate ferredoxin oxidoreductase beta subunit C terminal. This domain family is found in bacteria and archaea, and is approximately 70 amino acids in length. The family is found in association with pfam02775. There are two completely conserved residues (A and G) that may be functionally important. PFO is involved in carbon dioxide fixation via a reductive TCA cycle. It forms a heterodimer (alpha/beta). The beta subunit has binding motifs for Fe-S clusters and thiamine pyrophosphate. 62 matched cddid_all.tbl CDD pfam12368 pfam12368 463552 Rhodanese_C Rhodanase C-terminal. Rhodanase_C is found as the domain-extension to Rhodanase enzyme in some members of the Rhodanase family. Rhodanase is pfam00581. 66 matched cddid_all.tbl CDD pfam12369 pfam12369 432511 GnHR_trans Gonadotropin hormone receptor transmembrane region. This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with pfam00560, pfam00001. There are two completely conserved C residues that may be functionally important. This family contains the transmembrane region of Follicular stimulating hormone and leutenizing hormone - the two major gonadotropin hormone receptors. These receptors are G protein coupled receptors involved in development and maturation of germ cells in both fecund genders. The transmembrane region is conserved between the two different receptors while the extracellular ligand binding domains are less well conserved. 68 matched cddid_all.tbl CDD pfam12371 pfam12371 463553 TMEM131_like_N Transmembrane protein 131-like N-terminal. TMEM131_like is a family of bacterial, plant and other metazoa transmembrane proteins. Many of the members are multi-pass transmembrane proteins. This domain represents the N-terminal region which contains a conserved homology domain (CHD1). 84 matched cddid_all.tbl CDD pfam12372 pfam12372 463554 DUF3652 Huntingtin protein region. This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam02985. This family is in the middle region of the Huntingtin protein associated with Huntington's disease. The protein is of unknown function, however it is known that a polyglutamine (CAG) repeat in the gene coding for it results in the development of Huntington's disease. 41 matched cddid_all.tbl CDD pfam12373 pfam12373 372080 Msg2_C Major surface glycoprotein 2 C terminal. This domain family is found in eukaryotes, and is approximately 30 amino acids in length. The family is found in association with pfam02349. This family is the C terminal of major surface glycoprotein 2 of virulent bacteria. It is a virulence factor antigen. 30 matched cddid_all.tbl CDD pfam12374 pfam12374 463555 Dmrt1 Double-sex mab3 related transcription factor 1. This domain family is found in eukaryotes, and is typically between 61 and 73 amino acids in length. The family is found in association with pfam00751. This family is a transcription factor involved in sex determination. The proteins in this family contain a zinc finger-like DNA-binding motif, DM domain. 71 matched cddid_all.tbl CDD pfam12375 pfam12375 432514 DUF3653 Phage protein. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 112 and 194 amino acids in length. 66 matched cddid_all.tbl CDD pfam12376 pfam12376 289169 DUF3654 Protein of unknown function (DUF3654). This family of proteins is found in eukaryotes. Proteins in this family are typically between 193 and 612 amino acids in length. 138 matched cddid_all.tbl CDD pfam12377 pfam12377 432515 DuffyBP_N Duffy binding protein N terminal. This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The family is found in association with pfam05424. This family contains the N terminus of the Duffy receptor binding domain. 65 matched cddid_all.tbl CDD pfam12378 pfam12378 463556 P1_N Mycoplasma adhesin P1, N-terminal. This entry represents the N-terminal domain cytadhesin P1 from Mycoplasma. Cytadhesins are virulence factor proteins which mediate attachment of bacterial cells to host cells for invasion. P1 forms a transmembrane complex with P40/P90 called the 'Nap', which mediates motility and infectivity. Structure of P1, revealed that it consists of a large N-terminal domain consisting of seven consecutive beta-sheets each with four antiparallel beta-strands, except for the seventh which has two strands, and adopts a beta-propeller topology. Those two strands correspond to the cytoadherence epitope which has important immune properties. The N-terminal domain is highly variable and described as a structured core surrounded by a fuzzy surface. 286 matched cddid_all.tbl CDD pfam12379 pfam12379 432517 bCoV_NSP3_N Betacoronavirus replicase NSP3, N-terminal. This domain family corresponds to the N-terminal domain of NSP3 (non-structural protein 3, also known as nsp3) found in Betacoronavirus, which is encoded on the replicase polyprotein. This family includes the NSP3a domain which has the ubiquitin-like 1 (UB1) and glutamic acid-rich acidic (AC) hypervariable domains. NSP3a interacts with numerous other proteins involved in replication and transcription and may serve as a scaffolding protein for these processes. The N-terminal NSP3a domain interacts with N (nucleocapsid) protein to colocalize genomic RNA with the nascent replicase-transcriptase complex at the earliest stages of infection, essential for the virus. The C-terminal Glu-rich subdomain is best described as a flexible tail attached to the globular UB1 subdomain. The family is found in association with pfam08716, pfam01661, pfam05409, pfam06471, pfam08717, pfam06478, pfam09401, pfam06460, pfam08715, pfam08710. 149 matched cddid_all.tbl CDD pfam12380 pfam12380 289173 Peptidase_C62 Gill-associated viral 3C-like peptidase. a positive-stranded RNA virus of prawns, that has been called yellow head virus protease and gill-associated virus 3C-like peptidase. The GAV cysteine protease is predicted to be the key enzyme in the processing of the GAV replicase polyprotein precursors, pp1a and pp1ab. This protease employs a Cys(2968)-His(2879) catalytic dyad. 284 matched cddid_all.tbl CDD pfam12381 pfam12381 152816 Peptidase_C3G Tungro spherical virus-type peptidase. This is the protease for self-cleavage of the positive single-stranded polyproteins of a number of plant viral genomes. The protease activity of the polyprotein is at the C-terminal end, adjacent to the putative RNA polymerase. 231 matched cddid_all.tbl CDD pfam12382 pfam12382 152817 Peptidase_A2_2 Retrotransposon peptidase. This is a small family of fungal retroviral aspartyl peptidases. 137 matched cddid_all.tbl CDD pfam12383 pfam12383 289174 SARS_3b Severe acute respiratory syndrome coronavirus 3b protein. This family of proteins is found in viruses. Proteins in this family are typically between 32 and 154 amino acids in length. This family contains the SARS coronavirus 3b protein which is predominantly localized in the nucleolus, and induces G0/G1 arrest and apoptosis in transfected cells. 153 matched cddid_all.tbl CDD pfam12384 pfam12384 152819 Peptidase_A2B Ty3 transposon peptidase. Ty3 is a gypsy-type, retrovirus-like, element found in the budding yeast. The Ty3 aspartyl protease is required for processing of the viral polyprotein into its mature species. 177 matched cddid_all.tbl CDD pfam12385 pfam12385 403550 Peptidase_C70 Papain-like cysteine protease AvrRpt2. This is a family of cysteine proteases, found in actinobacteria, protobacteria and firmicutes. Papain-like cysteine proteases play a crucial role in plant-pathogen/pest interactions. On entering the host they act on non-self substrates, thereby manipulating the host to evade proteolysis. AvrRpt2 from Pseudomonas syringae pv. tomato DC3000 triggers resistance to P. syringae-2-dependent defence responses, including hypersensitive cell death, by cleaving the Arabidopsis RIN4 protein which is monitored by the cognate resistance protein RPS2. 143 matched cddid_all.tbl CDD pfam12386 pfam12386 403551 Peptidase_C71 Pseudomurein endo-isopeptidase Pei. This peptidase has the catalytic triad C-H-D at the C-terminal end, a triad similar to that in thiol proteases and animal transglutaminases. It catalyzes the in vitro lysis of M. marburgensis cells under reducing conditions and exhibits characteriztics of metal-activated peptidases. 149 matched cddid_all.tbl CDD pfam12387 pfam12387 289175 Peptidase_C74 Pestivirus NS2 peptidase. The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the bovine viral diarrhea virus polyprotein, a cleavage that is correlated with cytopathogenicity. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. 200 matched cddid_all.tbl CDD pfam12388 pfam12388 432518 Peptidase_M57 Dual-action HEIGH metallo-peptidase. The catalytic triad for this family of proteases is HE-H-H, which in many members is in the sequence motif HEIGH. 212 matched cddid_all.tbl CDD pfam12389 pfam12389 372085 Peptidase_M73 Camelysin metallo-endopeptidase. 196 matched cddid_all.tbl CDD pfam12390 pfam12390 432519 Se-cys_synth_N Selenocysteine synthase N terminal. This domain family is found in bacteria, and is approximately 40 amino acids in length. The family is found in association with pfam03841. There is a single completely conserved residue P that may be functionally important. This family is the N terminal region of selenocysteine synthase which catalyzes the conversion of seryl-tRNA(Sec) into selenocysteyl-tRNA(Sec). 40 matched cddid_all.tbl CDD pfam12391 pfam12391 432520 PCDO_beta_N Protocatechuate 3,4-dioxygenase beta subunit N terminal. This domain family is found in bacteria, and is approximately 40 amino acids in length. The family is found in association with pfam00775. There are two completely conserved residues (Y and R) that may be functionally important. This family is the N terminal region of the beta subunit of protocatechuate 3,4-dioxidase. This enzyme utilizes a mononuclear, non-heme Fe3+ centre to catalyze metabolic cellular reactions. 32 matched cddid_all.tbl CDD pfam12392 pfam12392 463557 DUF3656 Collagenase. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 120 amino acids in length. The family is found in association with pfam01136. 67 matched cddid_all.tbl CDD pfam12393 pfam12393 152828 Dr_adhesin Dr family adhesin. This domain family is found in bacteria, and is approximately 20 amino acids in length. The family is found in association with pfam04619. This family is the Dr-family adhesin expressed by uropathogenic E. coli. 21 matched cddid_all.tbl CDD pfam12394 pfam12394 463558 DUF3657 Protein FAM135. This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The family is found in association with pfam05057. 64 matched cddid_all.tbl CDD pfam12395 pfam12395 432523 DUF3658 Protein of unknown function. This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with pfam08874. There are two completely conserved residues (D and R) that may be functionally important. 107 matched cddid_all.tbl CDD pfam12396 pfam12396 432524 DUF3659 Protein of unknown function (DUF3659). This domain family is found in bacteria and eukaryotes, and is approximately 70 amino acids in length. 60 matched cddid_all.tbl CDD pfam12397 pfam12397 463559 U3snoRNP10 U3 small nucleolar RNA-associated protein 10. This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with pfam08146. This family is the protein associated with U3 snoRNA which is involved in the processing of pre-rRNA. 116 matched cddid_all.tbl CDD pfam12398 pfam12398 432526 DUF3660 Receptor serine/threonine kinase. This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam00954, pfam01453, pfam00069, pfam08276. There is a conserved ELPL sequence motif. 39 matched cddid_all.tbl CDD pfam12399 pfam12399 463560 BCA_ABC_TP_C Branched-chain amino acid ATP-binding cassette transporter. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 30 amino acids in length. The family is found in association with pfam00005. There is a conserved AYLG sequence motif. This family is the C terminal of an ATP dependent branched-chain amino acid transporter. This domain is essential for LPS transport, through critical interactions with Walker A and switch helix domains. 25 matched cddid_all.tbl CDD pfam12400 pfam12400 463561 STIMATE STIMATE family. STIMATE is a ER-resident multi-transmembrane protein that serves as a positive regulator of Ca(2+) influx in vertebrates. It interacts with ER-resident Ca2+ sensor protein STIM1 to promote STIM1 conformational switch. This entry also includes budding yeast YPL162C. 124 matched cddid_all.tbl CDD pfam12401 pfam12401 463562 FhaA_N FhaA, N-terminal domain. This domain can be found at the N terminus of FHA domain-containing protein Fha from Mycobacterium tuberculosis. The FHA (Fork Head Associated) domain is a phosphopeptide- specific binding domain that enables the protein to specifically bind to sequences containing phosphothreonine. FhaA is one of the major substrates of Ser/Thr protein kinases (STPK) and plays a role in the regulation of cell growth and peptidoglycan synthesis by binding to MviN. It may inhibit the late stages of peptidoglycan synthesis. 115 matched cddid_all.tbl CDD pfam12402 pfam12402 403564 nlz1 NocA-like zinc-finger protein 1. This domain family is found in eukaryotes, and is typically between 42 and 57 amino acids in length. There is a conserved GAY sequence motif. There is a single completely conserved residue G that may be functionally important. Nlz1 self-associated via its C terminus, interacted with Nlz2, and bound to histone deacetylases. 58 matched cddid_all.tbl CDD pfam12403 pfam12403 463563 Pax2_C Paired-box protein 2 C terminal. This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with pfam00292. This family is the C terminal of the paired-box protein 2 which is a transcription factor involved in embryonic development and organogenesis. 113 matched cddid_all.tbl CDD pfam12404 pfam12404 432531 DUF3663 Peptidase. This domain family is found in bacteria, and is approximately 80 amino acids in length. The family is found in association with pfam00883. There is a conserved WAF sequence motif. 77 matched cddid_all.tbl CDD pfam12406 pfam12406 289191 DUF3664 Surface protein. This family of proteins is found in eukaryotes. Proteins in this family are typically between 131 and 312 amino acids in length. 99 matched cddid_all.tbl CDD pfam12407 pfam12407 403567 Abdominal-A Homeobox protein. This domain family is found in eukaryotes, and is approximately 30 amino acids in length. The family is found in association with pfam00046. This family is a homeobox protein involved in differentiation of embryonic cells to form the abdominal region. 24 matched cddid_all.tbl CDD pfam12408 pfam12408 463564 DUF3666 Ribose-5-phosphate isomerase. This domain family is found in bacteria, and is approximately 50 amino acids in length. The family is found in association with pfam02502. There are two completely conserved residues (D and F) that may be functionally important. 47 matched cddid_all.tbl CDD pfam12409 pfam12409 463565 P5-ATPase P5-type ATPase cation transporter. This domain family is found in eukaryotes, and is typically between 110 and 126 amino acids in length. The family is found in association with pfam00122, pfam00702. P-type ATPases comprise a large superfamily of proteins, present in both prokaryotes and eukaryotes, that transport inorganic cations and other substrates across cell membranes. 123 matched cddid_all.tbl CDD pfam12410 pfam12410 289195 rpo30_N Poxvirus DNA dependent RNA polymerase 30kDa subunit. This family of proteins is found in viruses. Proteins in this family are typically between 193 and 259 amino acids in length. The family is found in association with pfam01096. There are two conserved sequence motifs: GIEYSKD and LRY. This family is N terminal of the 30 kDa subunit of poxvirus DNA-d-RNA-pol. It has structural similarity to the eukaryotic transcriptional elongation factor SII. 135 matched cddid_all.tbl CDD pfam12411 pfam12411 463566 Choline_sulf_C Choline sulfatase enzyme C terminal. This domain family is found in bacteria, eukaryotes and viruses, and is approximately 60 amino acids in length. The family is found in association with pfam00884. There are two completely conserved residues (R and W) that may be functionally important. This family is the C terminal of choline sulfatase, the enzyme responsible for catalysing the conversion of choline-O-sulfate and, at a lower rate, phosphorylcholine, into choline. 53 matched cddid_all.tbl CDD pfam12412 pfam12412 432535 DUF3667 Protein of unknown function (DUF3667). This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. There is a single completely conserved residue P that may be functionally important. 45 matched cddid_all.tbl CDD pfam12413 pfam12413 463567 DLL_N Homeobox protein distal-less-like N terminal. This domain family is found in eukaryotes, and is approximately 80 amino acids in length. The family is found in association with pfam00046. This family is the N terminal of a homeobox protein involved in embryonic development and adult neural regeneration. 83 matched cddid_all.tbl CDD pfam12414 pfam12414 463568 Fox-1_C Calcitonin gene-related peptide regulator C terminal. This domain family is found in eukaryotes, and is typically between 69 and 99 amino acids in length. The family is found in association with pfam00076. This family is the C terminal of Fox-1, a protein involved in the regulation of calcitonin gene-related peptide to mediate the neuron-specific splicing pattern. Fox-1, with Fox-2, functions to repress exon 4 inclusion. 94 matched cddid_all.tbl CDD pfam12415 pfam12415 289200 rpo132 Poxvirus DNA dependent RNA polymerase. This domain family is found in viruses, and is approximately 30 amino acids in length. The family is found in association with pfam04566, pfam00562, pfam04567, pfam04560, pfam04565. This family is the second largest subunit of the poxvirus DNA dependent RNA polymerase. It has structural similarity to the second-largest RNA polymerase subunits of eubacteria, archaebacteria, and eukaryotes. 32 matched cddid_all.tbl CDD pfam12416 pfam12416 463569 DUF3668 Cep120 protein. This family includes the Cep120 protein which is associated with centriole structure and function. 226 matched cddid_all.tbl CDD pfam12417 pfam12417 463570 DUF3669 Zinc finger protein. This domain family is found in eukaryotes, and is typically between 64 and 80 amino acids in length. 66 matched cddid_all.tbl CDD pfam12418 pfam12418 463571 AcylCoA_DH_N Acyl-CoA dehydrogenase N terminal. This domain family is found in bacteria and eukaryotes, and is approximately 30 amino acids in length. The family is found in association with pfam02770, pfam00441, pfam02771. This family is one of the enzymes involved in AcylCoA interaction in beta-oxidation. 32 matched cddid_all.tbl CDD pfam12419 pfam12419 463572 DUF3670 SNF2 Helicase protein. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with pfam00271, pfam00176. Most of the proteins in this family are annotated as SNF2 helicases but there is little accompanying literature to confirm this. 136 matched cddid_all.tbl CDD pfam12420 pfam12420 432542 DUF3671 Protein of unknown function. This domain family is found in eukaryotes, and is typically between 96 and 116 amino acids in length. 115 matched cddid_all.tbl CDD pfam12421 pfam12421 289206 DUF3672 Fibronectin type III protein. This domain family is found in bacteria and viruses, and is typically between 126 and 146 amino acids in length. The family is found in association with pfam09327, pfam00041. There are two completely conserved G residues that may be functionally important. Many of the proteins in this family are annotated as fibronectin type III however there is little accompanying literature to confirm this. 133 matched cddid_all.tbl CDD pfam12422 pfam12422 463573 Condensin2nSMC Condensin II non structural maintenance of chromosomes subunit. This domain family is found in eukaryotes, and is approximately 150 amino acids in length. This family is part of a non-SMC subunit of condensin II which is involved in maintenance of the structural integrity of chromosomes. Condensin II is made up of SMC (structural maintenance of chromosomes) and non-SMC subunits. The non-SMC subunits bind to the catalytic ends of the SMC subunit dimer. The condensin holocomplex is able to introduce superhelical tension into DNA in an ATP hydrolysis- dependent manner, resulting in the formation of positive supercoils in the presence of topoisomerase I and of positive knots in the presence of topoisomerase II. 149 matched cddid_all.tbl CDD pfam12423 pfam12423 463574 KIF1B Kinesin protein 1B. This domain family is found in eukaryotes, and is approximately 50 amino acids in length. The family is found in association with pfam00225, pfam00498. KIF1B is an anterograde motor for transport of mitochondria in axons of neuronal cells. 43 matched cddid_all.tbl CDD pfam12424 pfam12424 463575 ATP_Ca_trans_C Plasma membrane calcium transporter ATPase C terminal. This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The family is found in association with pfam00689, pfam00122, pfam00702, pfam00690. There is a conserved QTQ sequence motif. This family is the C terminal of a calcium transporting ATPase located in the plasma membrane. 47 matched cddid_all.tbl CDD pfam12425 pfam12425 432546 DUF3673 Protein of unknown function (DUF3673). This domain family is found in eukaryotes, and is approximately 50 amino acids in length. 53 matched cddid_all.tbl CDD pfam12426 pfam12426 289211 DUF3674 RNA dependent RNA polymerase. This domain family is found in viruses, and is approximately 40 amino acids in length. There is a conserved MFNLKF sequence motif. There are two completely conserved residues (E and P) that may be functionally important. 41 matched cddid_all.tbl CDD pfam12428 pfam12428 463576 DUF3675 Protein of unknown function (DUF3675). This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with pfam00097. There are two completely conserved residues (R and L) that may be functionally important. 119 matched cddid_all.tbl CDD pfam12429 pfam12429 338349 DUF3676 Protein of unknown function (DUF3676). This domain family is found in eukaryotes, and is approximately 230 amino acids in length. 230 matched cddid_all.tbl CDD pfam12430 pfam12430 463577 ABA_GPCR Abscisic acid G-protein coupled receptor. This domain family is found in eukaryotes, and is typically between 177 and 216 amino acids in length. This family is part of the abscisic acid (ABA) G-protein coupled receptor. ABA is a stress hormone in plants. 186 matched cddid_all.tbl CDD pfam12431 pfam12431 432549 CitT Transcriptional regulator. This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with pfam00072. There is a single completely conserved residue G that may be functionally important. CitT is a transcriptional regulator which allows transcription of the citM gene which codes for the secondary transporter in the Mg-citrate transport complex. 30 matched cddid_all.tbl CDD pfam12432 pfam12432 463578 DUF3677 Protein of unknown function (DUF3677). This domain family is found in eukaryotes, and is approximately 80 amino acids in length. 81 matched cddid_all.tbl CDD pfam12433 pfam12433 403585 PV_NSP1 Parvovirus non-structural protein 1. This family of proteins is found in viruses. Proteins in this family are typically between 109 and 668 amino acids in length. Parvoviral NSPs regulate host gene expression through histone acetylation. 71 matched cddid_all.tbl CDD pfam12434 pfam12434 463579 Malate_DH Malate dehydrogenase enzyme. This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with pfam00390, pfam03949, pfam01515. There is a conserved AAL sequence motif. There is a single completely conserved residue R that may be functionally important. Malate dehydrogenase is one of the enzymes involved in the citric acid cycle in mitochondria. It converts malate to oxaloacetate using NAD as a cofactor. 32 matched cddid_all.tbl CDD pfam12435 pfam12435 432550 DUF3678 Protein of unknown function (DUF3678). This domain family is found in eukaryotes, and is approximately 40 amino acids in length. 35 matched cddid_all.tbl CDD pfam12436 pfam12436 463580 USP7_ICP0_bdg ICP0-binding domain of Ubiquitin-specific protease 7. This domain is one of two C-terminal domains on the much longer ubiquitin-specific proteases. This particular one is found to interact with the herpesvirus 1 trans-acting transcriptional protein ICP0/VMW110. 239 matched cddid_all.tbl CDD pfam12437 pfam12437 463581 GSIII_N Glutamine synthetase type III N terminal. This domain family is found in bacteria and eukaryotes, and is approximately 160 amino acids in length. The family is found in association with pfam00120. This family is the N terminal region of glutamine synthetase type III which is one of the enzymes responsible for generation of glutamine through conversion glutamate to glutamine by the incorporation of ammonia (NH3). 160 matched cddid_all.tbl CDD pfam12438 pfam12438 315165 DUF3679 Protein of unknown function (DUF3679). This domain family is found in bacteria, and is approximately 60 amino acids in length. 56 matched cddid_all.tbl CDD pfam12439 pfam12439 432553 GDE_N Glycogen debranching enzyme N terminal. This domain family is found in bacteria and archaea, and is typically between 218 and 229 amino acids in length. The family is found in association with pfam06202. Glycogen debranching enzyme catalyzes the debranching of amylopectin in glycogen. This is done by transferring three glucose subunits of glycogen from one parallel chain to another. This has the effect of enabling the glucose residues to become more accessible for glycolysis. 209 matched cddid_all.tbl CDD pfam12440 pfam12440 463582 MAGE_N Melanoma associated antigen family N terminal. This domain family is found in eukaryotes, and is typically between 82 and 96 amino acids in length. The family is found in association with pfam01454. This family is the N terminal of various melanoma associated antigens. These are tumour rejection antigens which are expressed on HLA-A1 of tumour cells and they are recognized by cytotoxic T lymphocytes (CTLs). 92 matched cddid_all.tbl CDD pfam12441 pfam12441 463583 CopG_antitoxin CopG antitoxin of type II toxin-antitoxin system. CopG antitoxin is a member of a type II toxin-antitoxin system family found in bacteria and archaea. Most antitoxins encoded by the relBE and parDE loci belong to the MetJ/Arc/CopG family of dimeric proteins which bind DNA through N-terminal ribbon-helix-helix (RHH) motifs. The toxin for CopG proteins falls into the family BrnT_toxin, pfam04365. 79 matched cddid_all.tbl CDD pfam12442 pfam12442 463584 DUF3681 Protein of unknown function (DUF3681). This family of proteins is found in eukaryotes. Proteins in this family are typically between 112 and 212 amino acids in length. There is a single completely conserved residue G that may be functionally important. 95 matched cddid_all.tbl CDD pfam12443 pfam12443 463585 AKNA AT-hook-containing transcription factor. This domain family is found in eukaryotes, and is approximately 110 amino acids in length. This family contains a transcription factor which regulates the expression of the costimulatory molecules on lymphocytes. 95 matched cddid_all.tbl CDD pfam12444 pfam12444 463586 Sox_N Sox developmental protein N terminal. This domain family is found in eukaryotes, and is typically between 69 and 88 amino acids in length. The family is found in association with pfam00505. There are two conserved sequence motifs: YDW and PVR. This family contains Sox8, Sox9 and Sox10 proteins which have structural similarity. Sox proteins are involved in developmental processes. 76 matched cddid_all.tbl CDD pfam12445 pfam12445 372114 FliC Flagellin protein. This domain family is found in bacteria, and is typically between 125 and 147 amino acids in length. The family is found in association with pfam00669, pfam00700. There are two completely conserved G residues that may be functionally important. This family is the flagellin motor protein which confers motility to bacterial cells. 127 matched cddid_all.tbl CDD pfam12446 pfam12446 289231 DUF3682 Protein of unknown function (DUF3682). This domain family is found in eukaryotes, and is typically between 125 and 136 amino acids in length. 129 matched cddid_all.tbl CDD pfam12447 pfam12447 463587 DUF3683 Protein of unknown function (DUF3683). This domain family is found in bacteria, and is approximately 120 amino acids in length. The family is found in association with pfam02754, pfam01565, pfam02913. 114 matched cddid_all.tbl CDD pfam12448 pfam12448 463588 Milton Kinesin associated protein. This domain family is found in eukaryotes, and is typically between 143 and 173 amino acids in length. The family is found in association with pfam04849. This family is a region of the protein milton. Milton recruits the heavy chain of kinesin to mitochondria to allow the motor movement function of kinesin. 171 matched cddid_all.tbl CDD pfam12449 pfam12449 463589 DUF3684 Protein of unknown function (DUF3684). This domain family is found in eukaryotes, and is typically between 1072 and 1090 amino acids in length. 1096 matched cddid_all.tbl CDD pfam12450 pfam12450 432562 vWF_A von Willebrand factor. This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with pfam00092. There are two conserved sequence motifs: STF and DVD. There are two completely conserved residues (E and N) that may be functionally important. In hemostasis, platelet adhesion to the damaged vessel wall is mediated by several proteins, including von Willebrand factor. In solution vWF becomes immobilized via its A3 domain on the fibrillar collagen of the vessel wall and acts as an intermediary between collagen and the platelet receptor glycoprotein Ibalpha (GPIbalpha), which is the only platelet receptor that does not require prior activation for bond formation. 94 matched cddid_all.tbl CDD pfam12451 pfam12451 463590 VPS11_C Vacuolar protein sorting protein 11 C terminal. This domain family is found in eukaryotes, and is approximately 50 amino acids in length. Vps 11 is one of the evolutionarily conserved class C vacuolar protein sorting genes (c-vps: vps11, vps16, vps18, and vps33), whose products physically associate to form the c-vps protein complex required for vesicle docking and fusion. 44 matched cddid_all.tbl CDD pfam12452 pfam12452 432564 DUF3685 Protein of unknown function (DUF3685). This domain family is found in bacteria and eukaryotes, and is approximately 190 amino acids in length. There are two completely conserved residues (L and D) that may be functionally important. 192 matched cddid_all.tbl CDD pfam12453 pfam12453 403599 PTP_N Protein tyrosine phosphatase N terminal. This domain family is found in eukaryotes, and is approximately 30 amino acids in length. The family is found in association with pfam00041. There is a single completely conserved residue L that may be functionally important. This family consists of various protein tyrosine phosphatase haematopoietic receptors, e.g. CD45, which dephosphorylate growth stimulating proteins. This limits growth signalling in haematopoietic cells. 26 matched cddid_all.tbl CDD pfam12454 pfam12454 372120 Ecm33 GPI-anchored cell wall organization protein. This domain family is found in eukaryotes, and is approximately 40 amino acids in length. Ecm33 is an essential cell wall component and is important for cell wall integrity. 40 matched cddid_all.tbl CDD pfam12455 pfam12455 463591 Dynactin Dynein associated protein. This domain family is found in eukaryotes, and is approximately 280 amino acids in length. The family is found in association with pfam01302. There is a single completely conserved residue E that may be functionally important. Dynactin has been associated with Dynein, a kinesin protein which is involved in organelle transport, mitotic spindle assembly and chromosome segregation. Dynactin anchors Dynein to specific subcellular structures. 287 matched cddid_all.tbl CDD pfam12456 pfam12456 463592 hSac2 Inositol phosphatase. This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with pfam02383. hSac2 functions as an inositol polyphosphate 5-phosphatase. 115 matched cddid_all.tbl CDD pfam12457 pfam12457 463593 TIP_N Tuftelin interacting protein N terminal. This domain family is found in eukaryotes, and is typically between 99 and 114 amino acids in length. The family is found in association with pfam08697, pfam01585. There are two completely conserved residues (G and F) that may be functionally important. TIP is involved in enamel assembly by interacting with one of the major proteins responsible for biomineralization of enamel - tuftelin. 94 matched cddid_all.tbl CDD pfam12458 pfam12458 432568 DUF3686 ATPase involved in DNA repair. This domain family is found in bacteria, and is approximately 450 amino acids in length. There are two conserved sequence motifs: DVF and SPNGED. 446 matched cddid_all.tbl CDD pfam12459 pfam12459 432569 DUF3687 D-Ala-teichoic acid biosynthesis protein. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. There are two completely conserved residues (L and Y) that may be functionally important. 43 matched cddid_all.tbl CDD pfam12460 pfam12460 463594 MMS19_C RNAPII transcription regulator C-terminal. MMS19 is required for both nucleotide excision repair (NER) and RNA polymerase II (RNAP II) transcription. This C-terminal domain, along with the N-terminal, MMS19_N, form part of a silencing complex in fission yeast that contains Dos2, Rik1, Mms19 and Cdc20 (the catalytic subunit of DNA polymerase-epsilon). This complex regulates RNA polymerase II (RNA Pol II) activity in heterochromatin and is required for DNA replication and heterochromatin assembly. This domain has a HEAT-like repeat structure. 426 matched cddid_all.tbl CDD pfam12461 pfam12461 432571 DUF3688 Spiroplasma phage ORF1-like family. This entry includes the ORF1 protein from spiroplasma phages. 709 matched cddid_all.tbl CDD pfam12462 pfam12462 432572 Helicase_IV_N DNA helicase IV / RNA helicase N terminal. This domain family is found in bacteria, and is approximately 170 amino acids in length. This family is found in bacterial DNA helicase IV, at the N-terminus of pfam00580. 162 matched cddid_all.tbl CDD pfam12463 pfam12463 463595 DUF3689 Protein of unknown function (DUF3689). This family of proteins is found in eukaryotes. Proteins in this family are typically between 399 and 797 amino acids in length. 311 matched cddid_all.tbl CDD pfam12464 pfam12464 463596 Mac Maltose acetyltransferase. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with pfam00132. Mac uses acetyl-CoA as acetyl donor to acetylated cytoplasmic maltose. 52 matched cddid_all.tbl CDD pfam12465 pfam12465 463597 Pr_beta_C Proteasome beta subunits C terminal. This domain family is found in eukaryotes, and is approximately 40 amino acids in length. The family is found in association with pfam00227. There is a conserved GTT sequence motif. There is a single completely conserved residue Y that may be functionally important. This family includes the C terminal of the beta-type subunits of the proteasome, a multimeric complex that degrades proteins into peptides as part of the MHC class I-mediated Ag-presenting pathway. 36 matched cddid_all.tbl CDD pfam12466 pfam12466 372129 GDH_N Glutamate dehydrogenase N terminal. This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with pfam05088. There is a conserved ALR sequence motif. Glutamate dehydrogenase (GDH) is a homohexameric, mitochondrial enzyme that reversibly catalyzes the oxidative deamination of L-glutamate to 2-oxoglutarate using either NADP(H) or NAD(H) with comparable efficacy. 95 matched cddid_all.tbl CDD pfam12467 pfam12467 289250 CMV_1a Cucumber mosaic virus 1a protein family. This domain family is found in viruses, and is typically between 156 and 171 amino acids in length. The family is found in association with pfam01443, pfam01660. 1a protein is the major virulence factor of the cucumber mosaic virus (CMV). The Ns strain of CMV causes necrotic lesions to Nicotiana spp. while other strains cause systemic mosaic. The determinant of the pathogenesis of these different strains is the specific amino acid residue at the 461 residue of the 1a protein. 184 matched cddid_all.tbl CDD pfam12468 pfam12468 432576 TTSSLRR Type III secretion system leucine rich repeat protein. This domain family is found in bacteria, and is approximately 50 amino acids in length. There are two completely conserved residues (Y and W) that may be functionally important. This family consists of leucine-rich repeat proteins involved in type III secretion. 54 matched cddid_all.tbl CDD pfam12469 pfam12469 432577 Cmr2_N CRISPR-associated protein Cmr2, N-terminal. This domain family is typically between 101 and 138 amino acids in length and it is found in subunit Crm2 of the CRISPR RNA-Cas protein complex (Cmr complex). 112 matched cddid_all.tbl CDD pfam12470 pfam12470 463598 SUFU_C Suppressor of Fused Gli/Ci N terminal binding domain. This domain family is found in eukaryotes, and is typically between 192 and 219 amino acids in length. The family is found in association with pfam05076. There is a conserved HGRHFT sequence motif. This family is the C terminal domain of the Suppressor of Fused protein (Su(fu)). Su(fu) is a repressor of the Gli and Ci transcription factors of the Hedgehog signalling cascade. It functions by binding these proteins and preventing their translocation to the nucleus. The C terminal domain is only found in eukaryotic Su(fu) proteins; it is not present in bacterial homologs. The C terminal domain binds to the N terminal of Gli/Ci while the N terminal of Su(fu) binds to the C terminal of Gli/Ci. This dual binding mechanism is likely an evolutionary advancement in this signalling cascade which is not present in bacterial homologs. 200 matched cddid_all.tbl CDD pfam12471 pfam12471 432579 GTP_CH_N GTP cyclohydrolase N terminal. This domain family is found in bacteria and eukaryotes, and is approximately 190 amino acids in length. This family is the N terminal of GTP cyclohydrolase, the rate limiting enzyme in the synthesis of tetrahydrobiopterin. 193 matched cddid_all.tbl CDD pfam12472 pfam12472 432580 DUF3693 Phage related protein. This domain family is found in bacteria and viruses, and is approximately 60 amino acids in length. 60 matched cddid_all.tbl CDD pfam12473 pfam12473 463599 DUF3694 Kinesin protein. This domain family is found in eukaryotes, and is typically between 131 and 151 amino acids in length. The family is found in association with pfam00225, pfam00498. There is a single completely conserved residue W that may be functionally important. 149 matched cddid_all.tbl CDD pfam12474 pfam12474 463600 PKK Polo kinase kinase. This domain family is found in eukaryotes, and is approximately 140 amino acids in length. The family is found in association with pfam00069. Polo-like kinase 1 (Plx1) is essential during mitosis for the activation of Cdc25C, for spindle assembly, and for cyclin B degradation. This family is Polo kinase kinase (PKK) which phosphorylates Polo kinase and Polo-like kinase to activate them. PKK is a serine/threonine kinase. 139 matched cddid_all.tbl CDD pfam12475 pfam12475 289258 Amdo_NSP Amdovirus non-structural protein. This domain family is found in viruses, and is approximately 50 amino acids in length. This family contains proteins of each of the four types of Amdovirus non-structural protein. 54 matched cddid_all.tbl CDD pfam12476 pfam12476 432583 DUF3696 Protein of unknown function (DUF3696). This domain family is found in bacteria and archaea, and is approximately 50 amino acids in length. 53 matched cddid_all.tbl CDD pfam12477 pfam12477 432584 TraW_N Sex factor F TraW protein N terminal. This domain family is found in bacteria, and is approximately 30 amino acids in length. There is a single completely conserved residue G that may be functionally important. The traW gene of the E. coli K-12 sex factor, F, encodes one of the numerous proteins required for conjugative transfer of this plasmid. 30 matched cddid_all.tbl CDD pfam12478 pfam12478 372135 DUF3697 Ubiquitin-associated protein 2. This domain family is found in eukaryotes, and is approximately 30 amino acids in length. The family is found in association with pfam00627. There are two conserved sequence motifs: AVEMPG and QFG. 32 matched cddid_all.tbl CDD pfam12479 pfam12479 372136 DUF3698 Protein of unknown function (DUF3698). This domain family is found in eukaryotes, and is typically between 89 and 105 amino acids in length. 101 matched cddid_all.tbl CDD pfam12480 pfam12480 463601 DUF3699 Protein of unknown function (DUF3699). This domain family is found in eukaryotes, and is approximately 80 amino acids in length. 71 matched cddid_all.tbl CDD pfam12481 pfam12481 403619 DUF3700 Aluminium induced protein. This domain family is found in eukaryotes, and is approximately 120 amino acids in length. There are two conserved sequence motifs: YGL and LRDR. This family is related to GATase enzyme domains. 228 matched cddid_all.tbl CDD pfam12482 pfam12482 432586 DUF3701 Phage integrase protein. This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with pfam00589. 88 matched cddid_all.tbl CDD pfam12483 pfam12483 403620 GIDE E3 Ubiquitin ligase. This domain family is found in bacteria, archaea and eukaryotes, and is typically between 150 and 163 amino acids in length. There is a single completely conserved residue E that may be functionally important. GIDE is an E3 ubiquitin ligase which is involved in inducing apoptosis. 160 matched cddid_all.tbl CDD pfam12484 pfam12484 372141 PPE-SVP PPE-SVP subfamily C-terminal region. This domain family is found in bacteria, and is approximately 90 amino acids in length. The family is found to the C-terminus of pfam00823. There is a conserved SVP sequence motif which is diagnostic of this subfamily. There is a single completely conserved residue W that may be functionally important. The proteins in this family are PPE proteins implicated in immunostimulation and virulence. 80 matched cddid_all.tbl CDD pfam12485 pfam12485 463602 SLY Lymphocyte signaling adaptor protein. This domain family is found in eukaryotes, and is typically between 144 and 156 amino acids in length. The family is found in association with pfam07647, pfam07653. There is a conserved LGKK sequence motif. SLY contains a Src homology 3 domain and a sterile alpha motif, suggesting that it functions as a signaling adaptor protein in lymphocytes. 156 matched cddid_all.tbl CDD pfam12486 pfam12486 463603 VasL Type VI secretion system, EvfB, or VasL. EvfB or VasL is a domain found on many Gram-negative proteins with an ImpA_N domain at the N-terminus. These proteins are expressed from the pathogenicity locus that forms the bacterial type VI secretion system. The exact function of VasL is not known. One E.coli member is annotated as being EvfB, though the E.coli equivalent of ImpA would be expected to be EvfG. It is possible that in many bacteria what is a single protein in one species, eg E.coli, is a fusion of two genes in others, which would explain an ImpA at the N-terminus and a VasL at the C-terminus. 147 matched cddid_all.tbl CDD pfam12487 pfam12487 432589 DUF3703 Protein of unknown function (DUF3703). This family of proteins is found in bacteria. Proteins in this family are typically between 113 and 135 amino acids in length. 109 matched cddid_all.tbl CDD pfam12488 pfam12488 403624 DUF3704 Protein of unknown function (DUF3704). This domain family is found in eukaryotes, and is approximately 30 amino acids in length. 27 matched cddid_all.tbl CDD pfam12489 pfam12489 463604 ARA70 Nuclear coactivator. This domain family is found in eukaryotes, and is typically between 127 and 138 amino acids in length. This family is ARA70, a nuclear coactivator which interacts with peroxisome proliferator-activated receptor gamma (PPARgamma) to regulate transcription and the addition of the PPARgamma ligand (prostaglandin J2) enhances this interaction. 135 matched cddid_all.tbl CDD pfam12490 pfam12490 463605 BCAS3 Breast carcinoma amplified sequence 3. This domain family is found in eukaryotes, and is typically between 229 and 245 amino acids in length. The proteins in this family have been shown to be proto-oncogenes implicated in the development of breast cancer. 234 matched cddid_all.tbl CDD pfam12491 pfam12491 463606 ApoB100_C Apolipoprotein B100 C terminal. This domain family is found in eukaryotes, and is approximately 60 amino acids in length. There are two conserved sequence motifs: QLS and LIDL. ApoB100 has an essential role in the assembly and secretion of triglyceride-rich lipoproteins and lipids transport. 57 matched cddid_all.tbl CDD pfam12493 pfam12493 289275 DUF3709 Protein of unknown function (DUF3709). This domain family is found in bacteria, and is approximately 30 amino acids in length. There are two conserved sequence motifs: RCLMK and LIEL. 33 matched cddid_all.tbl CDD pfam12494 pfam12494 463607 DUF3695 Protein of unknown function (DUF3695). This family of proteins is found in eukaryotes. Proteins in this family are typically between 157 and 192 amino acids in length. There is a single completely conserved residue D that may be functionally important. 95 matched cddid_all.tbl CDD pfam12495 pfam12495 463608 Vip3A_N Vegetative insecticide protein 3A N terminal. This family of proteins is found in bacteria. Proteins in this family are typically between 170 and 789 amino acids in length. The family is found in association with pfam02018. Vip3A represents a novel class of proteins insecticidal to lepidopteran insect larvae. 177 matched cddid_all.tbl CDD pfam12496 pfam12496 463609 BNIP2 Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2. This domain family is found in eukaryotes, and is typically between 119 and 133 amino acids in length. There is a conserved HGGY sequence motif. This family is Bcl2-/adenovirus E1B nineteen kDa-interacting protein 2. It interacts with pro- and anti- apoptotic molecules in the cell. 135 matched cddid_all.tbl CDD pfam12497 pfam12497 463610 ERbeta_N Estrogen receptor beta. This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with pfam00104, pfam00105. There is a conserved IPS sequence motif. There are two completely conserved residues (Y and W) that may be functionally important. ERbeta binds estrogens with an affinity similar to that of ERalpha, and activates expression of reporter genes containing estrogen response elements in an estrogen-dependent manner. ERbeta acts as a transcription factor once bound to its ligand and it can dimerize with ERalpha. 114 matched cddid_all.tbl CDD pfam12498 pfam12498 403631 bZIP_C Basic leucine-zipper C terminal. This family of proteins is found in eukaryotes. Proteins in this family are typically between 174 and 411 amino acids in length. The family is found in association with pfam00170. There is a conserved KVK sequence motif. There is a single completely conserved residue K that may be functionally important. Various bZIP proteins have been found and shown to play a role in seed-specific gene expression. bZIP binds to the alpha-globulin gene promoter, but not to promoters of other major storage genes such as glutelin, prolamin and albumin. 122 matched cddid_all.tbl CDD pfam12499 pfam12499 463611 DUF3707 Pherophorin. This domain family is found in eukaryotes, and is typically between 147 and 160 amino acids in length. The proteins in this family are frequently annotated as pherophorins however there is little accompanying literature to confirm this. 139 matched cddid_all.tbl CDD pfam12500 pfam12500 463612 TRSP TRSP domain C terminus to PRTase_2. This domain occurs C-terminal to PRTase_2 and has highly conserved GXXE and TRSP signatures. It is found in bacteria. These genes are found in the biosynthetic operon associated with the Ter stress response operon and are predicted to be involved in the biosynthesis of a ribo-nucleoside involved in stress response. 128 matched cddid_all.tbl CDD pfam12501 pfam12501 432598 DUF3708 Phosphate ATP-binding cassette transporter. This domain family is found in bacteria, and is typically between 143 and 173 amino acids in length. The family is found in association with pfam00528. There is a single completely conserved residue P that may be functionally important. 165 matched cddid_all.tbl CDD pfam12502 pfam12502 432599 DUF3710 Protein of unknown function (DUF3710). This family of proteins is found in bacteria. Proteins in this family are typically between 237 and 284 amino acids in length. There are two conserved sequence motifs: DLG and DGPRW. 177 matched cddid_all.tbl CDD pfam12503 pfam12503 289285 CMV_1a_C Cucumber mosaic virus 1a protein C terminal. This domain family is found in viruses, and is approximately 90 amino acids in length. The family is found in association with pfam01443, pfam01660. There is a conserved GLG sequence motif. 1a protein is the major virulence factor of the cucumber mosaic virus (CMV). The Ns strain of CMV causes necrotic lesions to Nicotiana spp. while other strains cause systemic mosaic. The determinant of the pathogenesis of these different strains is the specific amino acid residue at the 461 residue of the 1a protein. 84 matched cddid_all.tbl CDD pfam12505 pfam12505 403636 DUF3712 Protein of unknown function (DUF3712). This domain family is found in eukaryotes, and is approximately 130 amino acids in length. 125 matched cddid_all.tbl CDD pfam12506 pfam12506 289287 DUF3713 Protein of unknown function (DUF3713). This family of proteins is found in bacteria. Proteins in this family are typically between 92 and 1225 amino acids in length. There is a single completely conserved residue S that may be functionally important. 115 matched cddid_all.tbl CDD pfam12507 pfam12507 403637 HCMV_UL139 Human Cytomegalovirus UL139 protein. This family of proteins is found in eukaryotes and viruses. Proteins in this family are approximately 140 amino acids in length. UL139 product shared sequence homology with human CD24, a signal transducer modulating B-cell activation responses, and the sequences in the G1c variant of UL139 contained a specific attachment site of prokaryotic membrane lipoprotein lipid. 100 matched cddid_all.tbl CDD pfam12508 pfam12508 432600 Transposon_TraM Conjugative transposon, TraM. Proteins in this entry are designated TraM and are found in a proposed transfer region of a class of conjugative transposon found in the Bacteroides lineage. 194 matched cddid_all.tbl CDD pfam12509 pfam12509 463613 DUF3715 Protein of unknown function (DUF3715). This domain family is found in eukaryotes, and is approximately 170 amino acids in length. 150 matched cddid_all.tbl CDD pfam12510 pfam12510 463614 Smoothelin Smoothelin cytoskeleton protein. This domain family is found in eukaryotes, and is approximately 50 amino acids in length. The family is found in association with pfam00307. Smoothelin is a cytoskeletal protein specifically expressed in differentiated smooth muscle cells and has been shown to co-localize with smooth muscle alpha actin. 50 matched cddid_all.tbl CDD pfam12511 pfam12511 403641 DUF3716 Protein of unknown function (DUF3716). This domain family is found in eukaryotes, and is approximately 60 amino acids in length. 59 matched cddid_all.tbl CDD pfam12512 pfam12512 463615 DUF3717 Protein of unknown function (DUF3717). This family of proteins is found in bacteria. Proteins in this family are typically between 75 and 117 amino acids in length. There is a conserved AIN sequence motif. There are two completely conserved residues (L and Y) that may be functionally important. 65 matched cddid_all.tbl CDD pfam12513 pfam12513 463616 SUV3_C Mitochondrial degradasome RNA helicase subunit C terminal. This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with pfam00271. The yeast mitochondrial degradosome (mtEXO) is an NTP-dependent exoribonuclease involved in mitochondrial RNA metabolism. mtEXO is made up of two subunits: an RNase (DSS1) and an RNA helicase (SUV3). These co-purify with mitochondrial ribosomes. 47 matched cddid_all.tbl CDD pfam12514 pfam12514 432605 DUF3718 Protein of unknown function (DUF3718). This domain family is found in bacteria and viruses, and is approximately 70 amino acids in length. There is a single completely conserved residue C that may be functionally important. 66 matched cddid_all.tbl CDD pfam12515 pfam12515 432606 CaATP_NAI Ca2+-ATPase N terminal autoinhibitory domain. This domain family is found in eukaryotes, and is approximately 50 amino acids in length. The family is found in association with pfam00689, pfam00122, pfam00702, pfam00690. There is a conserved RRFR sequence motif. There are two completely conserved residues (F and W) that may be functionally important. This family is the N terminal autoinhibitory domain of an endosomal Ca2+-ATPase. 45 matched cddid_all.tbl CDD pfam12516 pfam12516 463617 DUF3719 Protein of unknown function (DUF3719). This domain family is found in eukaryotes, and is approximately 70 amino acids in length. There is a conserved HLR sequence motif. There are two completely conserved residues (W and H) that may be functionally important. 66 matched cddid_all.tbl CDD pfam12517 pfam12517 338388 DUF3720 Protein of unknown function (DUF3720). This domain family is found in eukaryotes, and is approximately 100 amino acids in length. There are two completely conserved A residues that may be functionally important. 99 matched cddid_all.tbl CDD pfam12518 pfam12518 403646 DUF3721 Protein of unknown function. This domain family is found in bacteria and eukaryotes, and is approximately 30 amino acids in length. There is a conserved WMPC sequence motif. There are two completely conserved residues (A and C) that may be functionally important. 33 matched cddid_all.tbl CDD pfam12519 pfam12519 432608 MDM10 Mitochondrial distribution and morphology protein 10. MDM10 is a family of eukaryotic proteins that forms a subunit of the SAM complex for biogenesis of beta-barrel proteins, though not porins, into the outer mitochondrial membrane. 431 matched cddid_all.tbl CDD pfam12520 pfam12520 372162 DUF3723 Protein of unknown function (DUF3723). This family of proteins is found in eukaryotes. Proteins in this family are typically between 374 and 1069 amino acids in length. There is a conserved LGF sequence motif. 504 matched cddid_all.tbl CDD pfam12521 pfam12521 152955 DUF3724 Protein of unknown function (DUF3724). This domain family is found in viruses, and is approximately 20 amino acids in length. The family is found in association with pfam00073. There is a single completely conserved residue Y that may be functionally important. 23 matched cddid_all.tbl CDD pfam12522 pfam12522 315236 UL73_N Cytomegalovirus glycoprotein N terminal. This domain family is found in viruses, and is approximately 30 amino acids in length. The family is found in association with pfam03554. This family is an envelope glycoprotein of human cytomegalovirus (HCMV). 27 matched cddid_all.tbl CDD pfam12523 pfam12523 152957 DUF3725 Protein of unknown function (DUF3725). This domain family is found in viruses, and is approximately 70 amino acids in length. The family is found in association with pfam01577. There is a conserved FLE sequence motif. 74 matched cddid_all.tbl CDD pfam12524 pfam12524 315237 GlyL_C dsDNA virus glycoprotein L C terminal. This domain family is found in viruses, and is typically between 55 and 80 amino acids in length. The family is found in association with pfam05259. This family is the C terminal of glycoprotein L from various types of double stranded DNA viruses (dsDNA). 65 matched cddid_all.tbl CDD pfam12525 pfam12525 432609 DUF3726 Protein of unknown function (DUF3726). This domain family is found in bacteria and eukaryotes, and is approximately 80 amino acids in length. There is a single completely conserved residue E that may be functionally important. 74 matched cddid_all.tbl CDD pfam12526 pfam12526 372164 DUF3729 Protein of unknown function (DUF3729). This family of proteins is found in viruses. Proteins in this family are typically between 145 and 1707 amino acids in length. The family is found in association with pfam01443, pfam01661, pfam05417, pfam01660, pfam00978. There is a single completely conserved residue L that may be functionally important. 115 matched cddid_all.tbl CDD pfam12527 pfam12527 432610 DUF3727 Protein of unknown function (DUF3727). This domain family is found in bacteria and eukaryotes, and is approximately 100 amino acids in length. 97 matched cddid_all.tbl CDD pfam12528 pfam12528 432611 T2SSppdC Type II secretion prepilin peptidase dependent protein C. 80 matched cddid_all.tbl CDD pfam12529 pfam12529 463618 Xylo_C Xylosyltransferase C terminal. This domain family is found in eukaryotes, and is typically between 169 and 183 amino acids in length. The family is found in association with pfam02485. There is a single completely conserved residue G that may be functionally important. Xylosyltransferases are enzymes involved in the biosynthesis of the glycosaminoglycan linker region in proteoglycans. 180 matched cddid_all.tbl CDD pfam12530 pfam12530 463619 DUF3730 Focadhesin/RST1, DUF3730. This domain of unknown function is found in Focadhesin from animals and RST1 (RESURRECTION 1) from plants. Focadhesin (FOCAD) is a focal adhesion protein with potential tumour suppressor function in gliomas. RST1 was originally identified in a genetic screen for factors involved in the biosynthesis of epicuticular waxes. Later, RST1 and RST1 INTERACTING PROTEIN (RIPR) have been shown to act as cofactors of the cytoplasmic exosome and the Ski complex in plants. It is involved in the suppression of siRNA-mediated silencing of transgenes and certain endogenous transcripts. Structure predictions suggest that this is an alpha-helical domain with and armadillo-like fold. 227 matched cddid_all.tbl CDD pfam12531 pfam12531 432614 DUF3731 DNA-K related protein. This domain family is found in bacteria, and is approximately 250 amino acids in length. There are two conserved sequence motifs: RPG and WRR. The proteins in this family are frequently annotated as DNA-K related proteins however there is little accompanying literature to confirm this. 247 matched cddid_all.tbl CDD pfam12532 pfam12532 463620 DUF3732 Protein of unknown function (DUF3732). This domain family is found in bacteria and eukaryotes, and is typically between 180 and 198 amino acids in length. There is a conserved DQP sequence motif. 182 matched cddid_all.tbl CDD pfam12533 pfam12533 463621 Neuro_bHLH Neuronal helix-loop-helix transcription factor. This domain family is found in eukaryotes, and is approximately 80 amino acids in length. The family is found C-terminal to pfam00010. There is a single completely conserved residue W that may be functionally important. Neuronal basic helix-loop-helix (bHLH) transcription factors such as neuroD and neurogenin have been shown to play important roles in neuronal development. 122 matched cddid_all.tbl CDD pfam12534 pfam12534 463622 Pannexin_like Pannexin-like TM region of LRRC8. Pannexin_like is a family of the four transmembrane domains of metazoan leucine-rich-repeat-containing 8 proteins. These four TMs associate into hexamers resulting in homo- or heteromeric channels that connect the cytosol to the extracellular space. The family is found in association with pfam00560. 345 matched cddid_all.tbl CDD pfam12535 pfam12535 432618 Nudix_N Hydrolase of X-linked nucleoside diphosphate N terminal. This family of proteins is found in eukaryotes. Proteins in this family are typically between 847 and 5344 amino acids in length. These enzymes hydrolyse the molecular motif of a nucleoside diphosphate linked to some other moiety, X. 54 matched cddid_all.tbl CDD pfam12536 pfam12536 432619 DUF3734 Patatin phospholipase. This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with pfam01734. There are two completely conserved residues (F and G) that may be functionally important. The proteins in this family are frequently annotated as patatin family phospholipases however there is little accompanying literature to confirm this. 106 matched cddid_all.tbl CDD pfam12537 pfam12537 463623 GPHR_N The Golgi pH Regulator (GPHR) Family N-terminal. GPHR_N is the N-terminal 5TM region of the Golgi pH regulator proteins in eukaryotes. It plays vital roles in the transport of newly synthesized proteins from the Golgi to the plasma membrane, in the glycosylation of proteins along the exocytic pathway and the structural organization of the Golgi apparatus. 68 matched cddid_all.tbl CDD pfam12538 pfam12538 372173 FtsK_SpoIIIE_N DNA transporter. This domain family is found in bacteria, and is typically between 107 and 121 amino acids in length. The family is found in association with pfam01580. The FtsK/SpoIIIE family of DNA transporters are responsible for translocating missegregated chromosomes after the completion of cell division. 115 matched cddid_all.tbl CDD pfam12539 pfam12539 432621 Csm1 Chromosome segregation protein Csm1/Pcs1. Saccharomyces cerevisiae Csm1 is part of the monopolin complex. Csm1 forms a complex with Mde4 and promotes monoorientation during meiosis. Csm1 also plays a mitotic role in DNA replication. This family also contains the Schizosaccharomyces pombe homolog to Csm1, Pcs1. Pcs1 forms a complex with Mde4 and acts in the central kinetochore domain to clamp microtubule binding sites together. The two complexes (Csm1/Lrs4 and Pcs1/Mde4) contribute to the prevention of merotelic attachment. 84 matched cddid_all.tbl CDD pfam12540 pfam12540 463624 DUF3736 Protein of unknown function (DUF3736). This domain family is found in eukaryotes, and is typically between 135 and 160 amino acids in length. 135 matched cddid_all.tbl CDD pfam12541 pfam12541 463625 DUF3737 Protein of unknown function (DUF3737). This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 281 and 297 amino acids in length. 274 matched cddid_all.tbl CDD pfam12542 pfam12542 463626 CWC25 Pre-mRNA splicing factor. This domain family is found in eukaryotes, and is approximately 100 amino acids in length. The family is found in association with pfam10197. There is a single completely conserved residue Y that may be functionally important. Cwc25 has been identified to associate with pre-mRNA splicing factor Cef1/Ntc85, a component of the Prp19-associated complex (NTC) involved in spliceosome activation. Cwc25 is neither tightly associated with NTC nor required for spliceosome activation, but is required for the first catalytic reaction. 97 matched cddid_all.tbl CDD pfam12543 pfam12543 403664 DUF3738 Protein of unknown function (DUF3738). This family of proteins is found in bacteria. Proteins in this family are typically between 251 and 457 amino acids in length. 188 matched cddid_all.tbl CDD pfam12544 pfam12544 378876 LAM_C Lysine-2,3-aminomutase. This domain family is found in bacteria, archaea and eukaryotes, and is typically between 111 and 127 amino acids in length. The family is found in association with pfam04055. LAM catalyzes the interconversion of L-alpha-lysine and L-beta-lysine, which proceeds by migration of the amino group from C2 to C3 concomitant with cross-migration of the 3-pro-R hydrogen of L-alpha-lysine to the 2-pro-R position of L-beta-lysine. 127 matched cddid_all.tbl CDD pfam12545 pfam12545 432625 DUF3739 Filamentous haemagglutinin family outer membrane protein. This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with pfam05860. 111 matched cddid_all.tbl CDD pfam12546 pfam12546 403665 Cryptochrome_C Blue/Ultraviolet sensing protein C terminal. This domain family is found in eukaryotes, and is typically between 113 and 125 amino acids in length. The family is found in association with pfam03441, pfam00875. Cryptochromes are blue/ultraviolet-A light sensing photoreceptors involved in regulating various growth and developmental responses in plants. 121 matched cddid_all.tbl CDD pfam12547 pfam12547 463627 ATXN-1_C Ataxin-1 like family. This entry represents the N-terminal and central region of the Ataxin-1 protein. 531 matched cddid_all.tbl CDD pfam12548 pfam12548 463628 DUF3740 Sulfatase protein. This domain family is found in eukaryotes, and is typically between 144 and 173 amino acids in length. The family is found in association with pfam00884. 142 matched cddid_all.tbl CDD pfam12549 pfam12549 403668 TOH_N Tyrosine hydroxylase N terminal. This domain family is found in eukaryotes, and is approximately 30 amino acids in length. There is a single completely conserved residue G that may be functionally important. Tyrosine hydroxylase converts L-tyrosine to L-DOPA in the catecholamine synthesis pathway. 25 matched cddid_all.tbl CDD pfam12550 pfam12550 432628 GCR1_C Transcriptional activator of glycolytic enzymes. This domain family is found in eukaryotes, and is approximately 80 amino acids in length. This family is activates the transcription of glycolytic enzymes. 80 matched cddid_all.tbl CDD pfam12551 pfam12551 432629 PHBC_N Poly-beta-hydroxybutyrate polymerase N terminal. This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with pfam07167, pfam00561. There is a single completely conserved residue W that may be functionally important. PHBC is the third enzyme of the poly-beta-hydroxybutyrate biosynthetic pathway. 41 matched cddid_all.tbl CDD pfam12552 pfam12552 432630 DUF3741 Protein of unknown function (DUF3741). This domain family is found in eukaryotes, and is approximately 50 amino acids in length. 45 matched cddid_all.tbl CDD pfam12553 pfam12553 372185 DUF3742 Protein of unknown function (DUF3742). This domain family is found in bacteria, and is approximately 50 amino acids in length. There is a single completely conserved residue Y that may be functionally important. 114 matched cddid_all.tbl CDD pfam12554 pfam12554 432631 MOZART1 Mitotic-spindle organizing gamma-tubulin ring associated. The name MOZART is derived from letters of 'mitotic-spindle organizing proteins associated with a ring of gamma-tubulin'. This family operates as part of the gamma-tubulin ring complex, gamma-TuRC, one of the complexes necessary for chromosome segregation. This complex is located at centrosomes and mediates the formation of bipolar spindles in mitosis; it consists of six subunits. However, unlike the other four known subunits, this family does not carry the conserved 'Spc97-Spc98' GCP domain, so the TUBCGP nomenclature cannot be used for it. MOZART1 is required for gamma-TuRC recruitment to centrosomes. 43 matched cddid_all.tbl CDD pfam12555 pfam12555 432632 TPPK_C Thiamine pyrophosphokinase C terminal. This domain family is found in bacteria, and is approximately 50 amino acids in length. The proteins in this family catalyzes the pyrophosphorylation of thiamine in yeast and synthesizes thiamine pyrophosphate (TPP), a thiamine coenzyme. 50 matched cddid_all.tbl CDD pfam12556 pfam12556 432633 CobS_N Cobaltochelatase CobS subunit N terminal. This domain family is found in bacteria, and is approximately 40 amino acids in length. The family is found in association with pfam07728. There are two completely conserved residues (P and F) that may be functionally important. This family is the N terminal of the CobS subunit of cobaltochelatase. Cobaltochelatase belongs to the AAA+ superfamily of proteins. CobS and CobT form a chaperone like complex. 34 matched cddid_all.tbl CDD pfam12557 pfam12557 432634 Co_AT_N Cob(I)alamin adenosyltransferase N terminal. This domain family is found in bacteria and eukaryotes, and is approximately 20 amino acids in length. The family is found in association with pfam02572. Cob(I)alamin adenosyltransferase adenosylates Co(I) in an ATP-dependent manner in the conversion of aquacobalamin to its coenzyme form. This is the third step in this process, after two steps involved in the reduction of Co(III) to Co(I). 25 matched cddid_all.tbl CDD pfam12558 pfam12558 432635 DUF3744 ATP-binding cassette cobalt transporter. This domain family is found in bacteria, and is approximately 70 amino acids in length. The family is found in association with pfam00005. There is a conserved REP sequence motif. There is a single completely conserved residue P that may be functionally important. The proteins in this family are frequently annotated as ABC Cobalt transporters however there is little accompanying literature to confirm this. 72 matched cddid_all.tbl CDD pfam12559 pfam12559 372187 Inhibitor_I10 Serine endopeptidase inhibitors. This family includes both microviridins and marinostatins. It seems likely that in both cases it is the C-terminus which becomes the active inhibitor after post-translational modifications of the full length, pre-peptide. it is the ester linkages within the key, 12-residue. region that circularise the molecule giving it its inhibitory conformation. 64 matched cddid_all.tbl CDD pfam12560 pfam12560 463629 RAG1_imp_bd RAG1 importin binding. This region of RAG1 is responsible for binding to importin alpha. 287 matched cddid_all.tbl CDD pfam12561 pfam12561 432637 TagA ToxR activated gene A lipoprotein domain. This domain family is found in bacteria, and is approximately 140 amino acids in length. The family is found in association with pfam10462. 99 matched cddid_all.tbl CDD pfam12562 pfam12562 289339 DUF3746 Protein of unknown function (DUF3746). This domain family is found in viruses, and is approximately 40 amino acids in length. The family is found in association with pfam04595. 37 matched cddid_all.tbl CDD pfam12563 pfam12563 403679 Hemolysin_N Hemolytic toxin N terminal. This domain family is found in bacteria, and is approximately 190 amino acids in length. The family is found in association with pfam07968, pfam00652. This family is a bacterial virulence factor - hemolysin - which forms pores in erythrocytes and causes them to lyse. 192 matched cddid_all.tbl CDD pfam12564 pfam12564 432638 TypeIII_RM_meth Type III restriction/modification enzyme methylation subunit. This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with pfam01555. There are two completely conserved residues (F and S) that may be functionally important. This family is a bacterial phage resistance protein. It functions in a type III restriction/modification enzyme complex. It is part of the methylation subunit of the complex. It binds DNA and methylates it. 56 matched cddid_all.tbl CDD pfam12565 pfam12565 432639 DUF3747 Protein of unknown function (DUF3747). This family of proteins is found in bacteria. Proteins in this family are typically between 215 and 413 amino acids in length. There is a conserved DSNGYS sequence motif. 171 matched cddid_all.tbl CDD pfam12566 pfam12566 432640 DUF3748 Protein of unknown function (DUF3748). This domain family is found in bacteria and eukaryotes, and is approximately 120 amino acids in length. It is likely to contain 2 to 3 copies of a PD40-like repeat. 119 matched cddid_all.tbl CDD pfam12567 pfam12567 432641 CD45 Leukocyte receptor CD45. This family of proteins is found in eukaryotes. Proteins in this family are typically between 77 and 1130 amino acids in length. The family is found in association with pfam00041. CD45 plays a critical role in T-cell receptor (TCR)-mediated signaling. CD45 interacts with SKAP55 which is a transcriptional activator of IL-2. 59 matched cddid_all.tbl CDD pfam12568 pfam12568 432642 PanZ Acetyltransferase (GNAT) domain, PanZ. This domain family is found in bacteria, and is approximately 40 amino acids in length. The proteins in this family are members of the acetyltransferases of the GNAT family. Family members such as PanZ has been shown to be involved in the biosynthesis of Coenzyme A (CoA). CoA is a ubiquitous and essential cofactor, synthesized from the precursor pantothenate. In all organizms, the final step in pantothenate biosynthesis relies on the presence of beta-alanine, which comes from different sources in bacteria, yeast, and plants. In bacteria, beta-alanine is derived by the action of alpha-decarboxylase (ADC) enzyme. PanZ promotes the activation of the zymogen, PanD, to form aspartate alpha-decarboxylase (ADC) in a CoA-dependent manner. Thereby, playing an essential role in the biosynthetic pathway to pantothenate and the regulation of CoA biosynthesis. Structure and function studies show that direct interaction of PanD with the PanZ Arg43-Leu46 loop promotes PanD to adopt a reactive conformation, which leads to activation. 128 matched cddid_all.tbl CDD pfam12569 pfam12569 463630 NatA_aux_su N-terminal acetyltransferase A, auxiliary subunit. This entry represents N-terminal acetyltransferase A (NatA) auxiliary subunit (also known as NMDA receptor-regulated protein 1), which is a non-catalytic component of the NatA N-terminal acetyltransferase that catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala. N-terminal acetylation plays a role in normal eukaryotic translation and processing, protecting against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome, and may present the N terminus of nascent polypeptides for acetylation. 514 matched cddid_all.tbl CDD pfam12570 pfam12570 432644 DUF3750 Protein of unknown function (DUF3750). This family of proteins is found in bacteria. Proteins in this family are typically between 175 and 265 amino acids in length. 128 matched cddid_all.tbl CDD pfam12571 pfam12571 463631 DUF3751 Phage tail-collar fibre protein. This domain family is found in bacteria and viruses, and is approximately 160 amino acids in length. There are two completely conserved residues (K and W) that may be functionally important. The members are annotated as being putative phage tail or tail-collar proteins. 149 matched cddid_all.tbl CDD pfam12572 pfam12572 463632 DUF3752 Protein of unknown function (DUF3752). This domain family is found in eukaryotes, and is typically between 140 and 163 amino acids in length. 150 matched cddid_all.tbl CDD pfam12573 pfam12573 432647 OxoDH_E1alpha_N 2-oxoisovalerate dehydrogenase E1 alpha subunit N terminal. This domain family is found in bacteria, and is approximately 40 amino acids in length. The family is found in association with pfam00676. There are two conserved sequence motifs: VPEP and RPG. This family is the alpha subunit of the E1 component of 2-oxoisovalerate dehydrogenase. This is the enzyme complex responsible for metabolism of pyruvate, 2-oxoglutarate, branched chain 2-oxo acids and acetoin. The E1 component is a heterotetramer of alpha2beta2. The homodimerized beta subunits are flanked by two alpha subunits in a 'vise' structure. 41 matched cddid_all.tbl CDD pfam12574 pfam12574 403690 120_Rick_ant 120 KDa Rickettsia surface antigen. This domain family is found in bacteria, and is approximately 40 amino acids in length. This family is a Rickettsia surface antigen of 120 KDa which may be used as an antigen for immune response against the bacterial species. 238 matched cddid_all.tbl CDD pfam12575 pfam12575 289352 Pox_EPC_I2-L1 Poxvirus entry protein complex L1 and I2. Pox_EPC_I2-L1 family of proteins is found in poxviruses. Proteins in this family are approximately 70 amino acids in length. There is a conserved YLK sequence motif. 71 matched cddid_all.tbl CDD pfam12576 pfam12576 403691 DUF3754 Protein of unknown function (DUF3754). This domain family is found in bacteria, archaea and eukaryotes, and is typically between 135 and 166 amino acids in length. There is a single completely conserved residue P that may be functionally important. 136 matched cddid_all.tbl CDD pfam12577 pfam12577 463633 PPARgamma_N PPAR gamma N-terminal region. Peroxisome proliferator-activated receptors (PPAR) are nuclear hormone receptors that control the expression of genes involved in lipid homeostasis in mammals. This sequence region is found at the N-terminus of these proteins. The family is found in association with pfam00104, pfam00105. It is not clear if this region is a separate protein domain. 78 matched cddid_all.tbl CDD pfam12578 pfam12578 463634 3-PAP Myotubularin-associated protein. This domain family is found in eukaryotes, and is typically between 115 and 138 amino acids in length. Myotubularin is a dual-specific phosphatase that dephosphorylates phosphatidylinositol 3-phosphate and phosphatidylinositol (3,5)-bisphosphate. 3-PAP is a catalytically inactive member of the myotubularin gene family, which coprecipitates lipid phosphatidylinositol 3-phosphate-3-phosphatase activity from lysates of human platelets. 132 matched cddid_all.tbl CDD pfam12579 pfam12579 463635 DUF3755 Protein of unknown function (DUF3755). This domain family is found in eukaryotes, and is approximately 40 amino acids in length. There is a single completely conserved residue N that may be functionally important. 34 matched cddid_all.tbl CDD pfam12580 pfam12580 463636 TPPII Tripeptidyl peptidase II. This domain family is found in bacteria and eukaryotes, and is approximately 190 amino acids in length. The family is found in association with pfam00082. Tripeptidyl peptidase II (TPPII) is a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides. 187 matched cddid_all.tbl CDD pfam12581 pfam12581 315289 DUF3756 Protein of unknown function (DUF3756). This domain family is found in viruses, and is approximately 40 amino acids in length. 41 matched cddid_all.tbl CDD pfam12582 pfam12582 432652 DUF3757 Protein of unknown function (DUF3757). This family of proteins is found in bacteria. Proteins in this family are typically between 94 and 154 amino acids in length. 125 matched cddid_all.tbl CDD pfam12583 pfam12583 403697 TPPII_N Tripeptidyl peptidase II N terminal. This domain family is found in bacteria and eukaryotes, and is approximately 190 amino acids in length. The family is found in association with pfam00082. Tripeptidyl peptidase II (TPPII) is a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides. 136 matched cddid_all.tbl CDD pfam12584 pfam12584 403698 TRAPPC10 Trafficking protein particle complex subunit 10, TRAPPC10. This domain forms part of the TRAPP complex for mediating vesicle docking and fusion in the Golgi apparatus. The fungal version is referred to as Trs130, and an alternative vertebrate alias is TMEM1. 147 matched cddid_all.tbl CDD pfam12585 pfam12585 432653 DUF3759 Protein of unknown function (DUF3759). This family of proteins is found in eukaryotes. Proteins in this family are typically between 107 and 132 amino acids in length. There is a single completely conserved residue H that may be functionally important. 91 matched cddid_all.tbl CDD pfam12586 pfam12586 315294 DUF3760 Protein of unknown function (DUF3760). This domain family is found in eukaryotes, and is typically between 46 and 64 amino acids in length. 44 matched cddid_all.tbl CDD pfam12587 pfam12587 432654 DUF3761 Protein of unknown function (DUF3761). This family of proteins is found in bacteria. Proteins in this family are typically between 100 and 157 amino acids in length. 88 matched cddid_all.tbl CDD pfam12588 pfam12588 463637 PSDC Phophatidylserine decarboxylase. This domain family is found in bacteria and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with pfam02666. Phosphatidylserine decarboxylase (PSD) is an important enzyme in the synthesis of phosphatidylethanolamine in both prokaryotes and eukaryotes. 138 matched cddid_all.tbl CDD pfam12589 pfam12589 432656 WBS_methylT Methyltransferase involved in Williams-Beuren syndrome. This domain family is found in eukaryotes, and is typically between 72 and 83 amino acids in length. The family is found in association with pfam08241. This family is made up of S-adenosylmethionine-dependent methyltransferases. The proteins are deleted in Williams-Beuren syndrome (WBS), a complex developmental disorder with multisystemic manifestations including supravalvular aortic stenosis (SVAS) and a specific cognitive phenotype. 81 matched cddid_all.tbl CDD pfam12590 pfam12590 403703 Acyl-thio_N Acyl-ATP thioesterase. This domain family is found in bacteria and eukaryotes, and is typically between 120 and 131 amino acids in length. The family is found in association with pfam01643. The plant acyl-acyl carrier protein (ACP) thioesterases (TEs) have roles in fatty acid synthesis. 131 matched cddid_all.tbl CDD pfam12591 pfam12591 153025 DUF3762 Protein of unknown function (DUF3762). This domain family is found in viruses, and is approximately 80 amino acids in length. The family is found in association with pfam05533. 80 matched cddid_all.tbl CDD pfam12592 pfam12592 432657 ATPase_RavA_C ATPase, RavA, C-terminal. This domain is found at the C-terminal of bacterial regulatory ATPase RavA (Regulatory ATPase variant A) and is the second subdomain that forms the discontinuous triple helical domain. RavA forms an hexamer in which the triple helical domain mediates the lateral interactions between neighbouring RavA monomers. 55 matched cddid_all.tbl CDD pfam12593 pfam12593 289369 McyA_C Microcystin synthetase C terminal. This domain family is found in bacteria, and is approximately 40 amino acids in length. The family is found in association with pfam08242, pfam00501. There is a conserved YAN sequence motif. Microcystins form a large family of small cyclic heptapeptides harbouring extensive modifications in amino acid residue composition and functional group chemistry. These peptide hepatotoxins contain a range of non-proteinogenic amino acids and unusual peptide bonds, and are typically N-methylated. They are synthesized on large enzyme complexes consisting of non-ribosomal peptide synthetases and polyketide synthases. This family is made up of the C terminal of microcystin synthetase, one of the proteins involved in this synthesis pathway. 43 matched cddid_all.tbl CDD pfam12594 pfam12594 463638 DUF3764 Protein of unknown function (DUF3764). This family of proteins is found in bacteria. Proteins in this family are typically between 89 and 101 amino acids in length. 89 matched cddid_all.tbl CDD pfam12595 pfam12595 463639 Rhomboid_SP Rhomboid serine protease. This domain family is found in eukaryotes, and is approximately 210 amino acids in length. The family is found in association with pfam01694. Rhomboid is a seven-transmembrane spanning protein that resides in the Golgi and acts as a serine protease to cleave Spitz. 193 matched cddid_all.tbl CDD pfam12596 pfam12596 257152 Tnp_P_element_C 87kDa Transposase. This domain family is found in eukaryotes, and is typically between 78 and 110 amino acids in length. The family is found in association with pfam05485. There are two completely conserved residues (D and G) that may be functionally important. This family is an 87kDa transposase protein which catalyzes both the precise and imprecise excision of a nonautonomous P transposable element. 107 matched cddid_all.tbl CDD pfam12597 pfam12597 403707 Cox20 Cytochrome c oxidase assembly protein COX20. Complex IV (CIV) is a copper-heme oxidase that couples electron transfer from cytochrome c to oxygen with proton extrusion across the inner membrane to contribute to the proton gradient required for ATP generation. This entry includes fungal mitochondrial complex IV assembly factor Cox20 and its homologs (also known as FAM36A in metazoa. Human CIV is formed by three catalytic core subunits (COX1/2/3). COX20 has been found to form a complex with SCO1, SCO2, and newly synthesized COX2. It may act as a chaperone in the early steps of COX2 maturation. 101 matched cddid_all.tbl CDD pfam12598 pfam12598 432659 TBX T-box transcription factor. This domain family is found in eukaryotes, and is typically between 77 and 89 amino acids in length. The family is found in association with pfam00907. There are two completely conserved residues (S and P) that may be functionally important. T-box genes encode transcription factors involved in morphogenesis and organogenesis of vertebrates and invertebrates 81 matched cddid_all.tbl CDD pfam12599 pfam12599 432660 DUF3768 Protein of unknown function (DUF3768). This family of proteins is found in bacteria. Proteins in this family are typically between 108 and 129 amino acids in length. There are two conserved sequence motifs: NDP and RVLT. 83 matched cddid_all.tbl CDD pfam12600 pfam12600 432661 DUF3769 Protein of unknown function (DUF3769). This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 560 and 931 amino acids in length. 443 matched cddid_all.tbl CDD pfam12601 pfam12601 289375 Rubi_NSP_C Rubivirus non-structural protein. This domain family is found in viruses, and is approximately 70 amino acids in length. The family is found in association with pfam05407. The rubella virus (RUB) nonstructural (NS) protein (NSP) ORF encodes a protease that cleaves the NSP precursor (240 kDa) at a single site to produce two products. 66 matched cddid_all.tbl CDD pfam12602 pfam12602 315304 FinO_N Fertility inhibition protein N terminal. This domain family is found in bacteria, and is typically between 62 and 102 amino acids in length. The family is found in association with pfam04352. The FinOP (fertility inhibition) system of F-like plasmids consists of an antisense RNA (FinP) and a 22 kDa protein (FinO) which act in concert to prevent the translation of TraJ, the positive regulator of the transfer operon. 62 matched cddid_all.tbl CDD pfam12603 pfam12603 289377 DUF3770 Protein of unknown function (DUF3770). This domain family is found in viruses, and is approximately 250 amino acids in length. The family is found in association with pfam04196. 235 matched cddid_all.tbl CDD pfam12604 pfam12604 432662 gp37_C Tail fibre protein gp37 C terminal. This domain family is found in bacteria and viruses, and is typically between 49 and 166 amino acids in length. The family is found in association with pfam03906. In T-even phages, gp37 and gp38 are components of the tail Faber that are critical for phage-host interaction. 157 matched cddid_all.tbl CDD pfam12605 pfam12605 463640 CK1gamma_C Casein kinase 1 gamma C terminal. This domain family is found in eukaryotes, and is typically between 54 and 99 amino acids in length. The family is found in association with pfam00069. CK1gamma is a membrane-bound member of the CK1 family. Gain-of-function and loss-of-function experiments show that CK1gamma is both necessary and sufficient to transduce LRP6 signalling in vertebrates and Drosophila cells. 99 matched cddid_all.tbl CDD pfam12606 pfam12606 403713 RELT Tumour necrosis factor receptor superfamily member 19. This family of proteins is found in eukaryotes. Proteins in this family are typically between 49 and 288 amino acids in length. There are two completely conserved residues (K and Y) that may be functionally important. The members of tumor necrosis factor receptor (TNFR) superfamily have been designated as the 'guardians of the immune system' due to their roles in immune cell proliferation, differentiation, activation, and death (apoptosis). The messenger RNA of RELT is especially abundant in hematologic tissues such as spleen, lymph node, and peripheral blood leukocytes as well as in leukemias and lymphomas. RELT is able to activate the NF-kappaB pathway and selectively binds tumor necrosis factor receptor-associated factor 1. RELT is a TNF receptor family member that is expressed in hematological tissues and can stimulate the proliferation of T-cells, the p38 and JNK MAPK pathways, and serves as a substrate for the closely related kinases OSR1 and SPAK. Furthermore, family members include the homologs RELL1 and RELL2 (RELT-like protein 1 and 2 respectively). RELT, RELL1 and RELL2 bind to each other in vitro and co-localize with one another at the plasma membrane. Functional studies of the role of RELT, show that overexpression of RELT in epithelial cells induces cell death by promoting cell rounding and DNA fragmentation. 42 matched cddid_all.tbl CDD pfam12607 pfam12607 432664 DUF3772 Protein of unknown function (DUF3772). This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with pfam00924. 63 matched cddid_all.tbl CDD pfam12608 pfam12608 432665 T4bSS_IcmS Type IVb secretion, IcmS, effector-recruitment. This is a family of Gram-negative bacterial proteins involved in the Dot/Icm type IVb transport system. Members are small acidic cytoplasmic proteins required for Dot/Icm-dependent activities. Binary complexes of IcmW-IcmS and of IcmS-LvgA have been consistently reported, suggestive of the binary WXG100 system. The IcmW-IcmS complex may play a role in recruitment of effector proteins to the transport apparatus. 93 matched cddid_all.tbl CDD pfam12609 pfam12609 463641 DUF3774 Wound-induced protein. This family of proteins is found in eukaryotes. Proteins in this family are typically between 81 and 97 amino acids in length. The proteins in the family are often annotated as wound-induced proteins however there is little accompanying literature to confirm this. 77 matched cddid_all.tbl CDD pfam12610 pfam12610 432667 SOCS Suppressor of cytokine signalling. This domain family is found in bacteria and eukaryotes, and is approximately 60 amino acids in length. The family is found in association with pfam07525, pfam00017. The suppressors of cytokine signaling (SOCS) family play important roles in regulating a variety of signal transduction pathways that are involved in immunity, growth and development of organizms. 57 matched cddid_all.tbl CDD pfam12611 pfam12611 463642 Flagellar_put Putative flagellar. Proteins in this entry are encoded in a subset of bacterial flagellar operons, generally between genes designated flgD and flgE, in species as diverse as Bacillus halodurans and various other Firmicutes, Geobacter sulfurreducens, and Bdellovibrio bacteriovorus. 24 matched cddid_all.tbl CDD pfam12612 pfam12612 463643 TFCD_C Tubulin folding cofactor D C terminal. This domain family is found in eukaryotes, and is typically between 182 and 199 amino acids in length. The family is found in association with pfam02985. There is a single completely conserved residue R that may be functionally important. Tubulin folding cofactor D does not co-polymerize with microtubules either in vivo or in vitro, but instead modulates microtubule dynamics by sequestering beta-tubulin from GTP-bound alphabeta-heterodimers in microtubules. 187 matched cddid_all.tbl CDD pfam12613 pfam12613 403719 FliC_SP Flagellin structural protein. This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with pfam00669, pfam00700. This family is the bacterial flagellin structural protein. It is involved with cell motility. 53 matched cddid_all.tbl CDD pfam12614 pfam12614 432670 RRF_GI Ribosome recycling factor. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 130 amino acids in length. There are two conserved sequence motifs: LPS and LKR. Overproduction of ribosome recycling factor (RRF) reduces tna operon expression and increases the rate of cleavage of TnaC-tRNA(2)(Pro), relieving the growth inhibition associated with plasmid-mediated tnaC overexpression. 126 matched cddid_all.tbl CDD pfam12615 pfam12615 432671 TraD_N F sex factor protein N terminal. This domain family is found in bacteria, and is typically between 96 and 107 amino acids in length. The family is found in association with pfam10412. TraD is a cytoplasmic membrane protein with possible DNA binding domains. It is part of the bacterial F sex factor complex. 97 matched cddid_all.tbl CDD pfam12616 pfam12616 432672 DUF3775 Protein of unknown function (DUF3775). This domain family is found in bacteria, and is approximately 80 amino acids in length. There is a single completely conserved residue G that may be functionally important. 69 matched cddid_all.tbl CDD pfam12617 pfam12617 463644 LdpA_C Iron-Sulfur binding protein C terminal. This domain family is found in bacteria and eukaryotes, and is typically between 179 and 201 amino acids in length. The family is found in association with pfam00037. LdpA (light-dependent period) plays a role in controlling the redox state in cyanobacteria to modulate its. circadian clock. LdpA is a protein with Iron-Sulfur cluster-binding motifs. 183 matched cddid_all.tbl CDD pfam12618 pfam12618 463645 DUF3776 Protein of unknown function (DUF3776). This domain family is found in eukaryotes, and is approximately 100 amino acids in length. 110 matched cddid_all.tbl CDD pfam12619 pfam12619 403724 MCM2_N Mini-chromosome maintenance protein 2. This domain family is found in eukaryotes, and is typically between 138 and 153 amino acids in length. The family is found in association with pfam00493. Mini-chromosome maintenance (MCM) proteins are essential for DNA replication. These proteins use ATPase activity to perform this function. 148 matched cddid_all.tbl CDD pfam12620 pfam12620 432675 DUF3778 Protein of unknown function (DUF3778). This domain family is found in eukaryotes, and is typically between 48 and 61 amino acids in length. There is a conserved LRF sequence motif. 52 matched cddid_all.tbl CDD pfam12621 pfam12621 432676 PHM7_ext Extracellular tail, of 10TM putative phosphate transporter. This PHM7_ext family is found in plants and fungi. It represents the C-terminal extracellular domain of the putative phosphate transporter, PHM7. The three N-terminal TMS are found in family RSN1_TM, pfam02714; the cytoplssmic domain is pfam14703, and the remaining 7TM region is in pfam02714. 84 matched cddid_all.tbl CDD pfam12622 pfam12622 403727 NpwBP mRNA biogenesis factor. The full-length Wbp11 proteins carry several copies of a PPGPPP motif throughout their length. This motif is thought to be necessary for folding of the molecule as it helps to bind the WW domain, Wbp11, pfam09429. This domain together with Wbp11 may function as components of an mRNA factory in the nucleus. 47 matched cddid_all.tbl CDD pfam12623 pfam12623 432677 Hen1_L RNA repair, ligase-Pnkp-associating, region of Hen1. This domain is the N-terminal region of the bacterial Hen1 protein. This protein forms stable hetero-tetramer with Pnkp. The hetero-tetramer was able to repair transfer RNAs cleaved by ribotoxins in vitro. This domain provides the ligase activity of the hetero-tetramer. 230 matched cddid_all.tbl CDD pfam12624 pfam12624 463646 Chorein_N N-terminal region of Chorein or VPS13. Although mutations in the full-length vacuolar protein sorting 13A (VPS13A) protein in vertebrates lead to the disease of chorea-acanthocytosis, the exact function of any of the regions within the protein is not yet known. This region is the proposed leucine zipper at the N-terminus. The full-length protein is a transmembrane protein with a presumed role in vesicle-mediated sorting and intracellular protein transport. 116 matched cddid_all.tbl CDD pfam12625 pfam12625 432679 Arabinose_bd Arabinose-binding domain of AraC transcription regulator, N-term. AraC is a bacterial transcriptional regulatory protein with a DNA-binding domain at the C-terminus, HTH_AraC, pfam00165, and this dimerization domain which harbours the arabinose-binding pocket at the N-terminus. AraC positively and negatively regulates expression of the proteins required for the uptake and catabolism of the sugar L-arabinose 1,2,3]. 185 matched cddid_all.tbl CDD pfam12626 pfam12626 463647 PolyA_pol_arg_C Polymerase A arginine-rich C-terminus. The C-terminus of polymerase A in E coli is arginine-rich and is necessary for full functioning of the enzyme. 116 matched cddid_all.tbl CDD pfam12627 pfam12627 463648 PolyA_pol_RNAbd Probable RNA and SrmB- binding site of polymerase A. This region encompasses much of the RNA and SrmB binding motifs on polymerase A. 64 matched cddid_all.tbl CDD pfam12628 pfam12628 403733 Inhibitor_I71 Falstatin, cysteine peptidase inhibitor. This family of peptidase inhibitors is expressed from plasmodial protozoal species. Falstatin is found to be a potent reversible inhibitor of the P. falciparum cysteine proteases falcipain-2 and falcipain-3, as well as other parasite- and non-parasite-derived cysteine proteases, but is only a relatively weak inhibitor of the P. falciparum cysteine proteases falcipain-1 and dipeptidyl aminopeptidase 1. Thus, P. falciparum requires expression of falstatin to limit proteolysis by certain host or parasite cysteine proteases during erythrocyte invasion. 173 matched cddid_all.tbl CDD pfam12629 pfam12629 289401 Pox_polyA_pol_C Poxvirus poly(A) polymerase C-terminal domain. This domain is found at the C-terminus of the pox virus PolyA polymerase protein. 199 matched cddid_all.tbl CDD pfam12630 pfam12630 403734 Pox_polyA_pol_N Poxvirus poly(A) polymerase N-terminal domain. This domain is found at the N-terminus of the pox virus Poly(A) polymerase protein. According to SCOP this domain contains a helix-hairpin-helix motif. 108 matched cddid_all.tbl CDD pfam12631 pfam12631 463649 MnmE_helical MnmE helical domain. The tRNA modification GTPase MnmE consists of three domains. An N-terminal domain, a helical domain and a GTPase domain which is nested within the helical domain. This family represents the helical domain. 326 matched cddid_all.tbl CDD pfam12632 pfam12632 463650 Vezatin Mysoin-binding motif of peroxisomes. Vezatin is a peroxisome transmembrane receptor that is involved in membrane-membrane and cell-cell adhesions. In the movement of peroxisomes it binds to class V and class VIIa myosins to guide the organelle through the microtubules and allow pathogens to internalize themselves into host cells. Vezatin is crucial for spermatozoan production. In mouse cells it interacts with the cadherin-catenin complex bridging it to the C-terminal FERM domain of myosin VIIA. 282 matched cddid_all.tbl CDD pfam12633 pfam12633 432684 Adenyl_cycl_N Adenylate cyclase NT domain. 198 matched cddid_all.tbl CDD pfam12634 pfam12634 432685 Inp1 Inheritance of peroxisomes protein 1. Inp1 is a family of peripheral membrane proteins of peroxisomes. Inp1p binds Pex25p, Pex30p, and Vps1p, all of which are involved in controlling peroxisome division. The levels of Inp1p vary with the cell cycle, and Inp1 acts as a factor that retains peroxisomes in cells and controls peroxisome division. Inp1p promotes the retention of peroxisomes in mother cells and buds of budding yeast by attaching peroxisomes to as-yet-unidentified cortical structures. 137 matched cddid_all.tbl CDD pfam12635 pfam12635 403738 DUF3780 Protein of unknown function (DUF3780). This family of proteins is functionally uncharacterized.This family of proteins is found in bacteria. Proteins in this family are typically between 189 and 206 amino acids in length. There are two conserved sequence motifs: PEERWWL and GWR. This family is found in a very sporadic set of bacterial species, suggesting that it may have been horizontally transferred. One protein is annotated as plasmid borne. 184 matched cddid_all.tbl CDD pfam12636 pfam12636 432686 DUF3781 Protein of unknown function (DUF3781). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 82 and 98 amino acids in length. There are two conserved sequence motifs: GKNWY and ITA. 72 matched cddid_all.tbl CDD pfam12637 pfam12637 463651 TSCPD TSCPD domain. This family of proteins is found in bacteria, archaea and viruses. The domain is found in isolation in many proteins where it has a conserved C-terminal motif TSCPD after which the domain is named. Most copies of the domain possess 4 conserved cysteines that may be part of an Iron-sulfur cluster. This domain is found at the C-terminus of some ribonucleoside-diphosphate reductase enzymes. 74 matched cddid_all.tbl CDD pfam12638 pfam12638 403741 Staygreen Staygreen protein. This family of proteins have been implicated in chlorophyll degradation. Intriguingly members of this family are also found in non-photosynthetic bacteria. 147 matched cddid_all.tbl CDD pfam12639 pfam12639 432688 Colicin-DNase DNase/tRNase domain of colicin-like bacteriocin. Colicin-like bacteriocins are complex structures with an N-terminal beta-barrel translocation domain (pfam09000), a long double-alpha-helical receptor-binding domain (pfam11570) and this C-terminal RNAse/DNase domain with endonuclease activity. Their competitor bacteriocidal action is by a process that involves binding to a surface receptor, entering the cell, and, finally, killing it. The lethal action of colicin E3 is a specific cleavage in the ribosomal decoding A site. The crystal structure of colicin E3 reveals a Y-shaped molecule with the receptor binding domain forming a 100 Angstrom long stalk and the two globular heads of the translocation domain and this catalytic domain comprising the two arms. 96 matched cddid_all.tbl CDD pfam12640 pfam12640 432689 UPF0489 UPF0489 domain. This family is probably an enzyme which is related to the Arginase family. 177 matched cddid_all.tbl CDD pfam12641 pfam12641 432690 Flavodoxin_3 Flavodoxin domain. This family represents a flavodoxin domain. 159 matched cddid_all.tbl CDD pfam12642 pfam12642 463652 TpcC Conjugative transposon protein TcpC. This family of proteins are annotated as conjugative transposon protein TcpC. The transfer clostridial plasmid (tcp) locus is part of some conjugative antibiotic resistance and virulence plasmids. TcpC was one of five genes whose products had low-level sequence identity to Tn916 proteins, having similarity to ORF13 homologs from Tn916, Tn5397, and CW459tet. This family of proteins is found in bacteria. Proteins in this family are typically between 302 and 351 amino acids in length. 230 matched cddid_all.tbl CDD pfam12643 pfam12643 463653 MazG-like MazG-like family. This family of short proteins are distantly related to the MazG enzyme. This suggests that these proteins are enzymes that catalyze a related reaction. 85 matched cddid_all.tbl CDD pfam12644 pfam12644 372238 DUF3782 Protein of unknown function (DUF3782). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 91 and 186 amino acids in length. 78 matched cddid_all.tbl CDD pfam12645 pfam12645 463654 HTH_16 Helix-turn-helix domain. This domain appears to be a helix-turn-helix domain suggesting that this might be a transcriptional regulatory protein. Some members of this family are annotated as conjugative transposon domains. 65 matched cddid_all.tbl CDD pfam12646 pfam12646 432694 DUF3783 Domain of unknown function (DUF3783). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 60 amino acids in length. 56 matched cddid_all.tbl CDD pfam12647 pfam12647 432695 RNHCP RNHCP domain. This family of proteins is found in bacteria. Proteins in this family are typically between 94 and 143 amino acids in length. There is a conserved RNHCP sequence motif. 85 matched cddid_all.tbl CDD pfam12648 pfam12648 432696 TcpE TcpE family. This family of proteins includes TcpE a conjugative transposon membrane protein.This family of proteins is found in bacteria. Proteins in this family are typically between 122 and 168 amino acids in length. 106 matched cddid_all.tbl CDD pfam12650 pfam12650 463655 DUF3784 Domain of unknown function (DUF3784). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 96 and 110 amino acids in length. 94 matched cddid_all.tbl CDD pfam12651 pfam12651 289422 RHH_3 Ribbon-helix-helix domain. This short bacterial protein contains a ribbon-helix-helix domain that is likely to be DNA-binding. 44 matched cddid_all.tbl CDD pfam12652 pfam12652 463656 CotJB CotJB protein. CotJ is a sigma E-controlled operon involved in the spore coat of Bacillus subtilis. This protein has been identified as a spore coat protein. 76 matched cddid_all.tbl CDD pfam12653 pfam12653 463657 DUF3785 Protein of unknown function (DUF3785). This family of proteins is functionally uncharacterized.This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. These proteins share two CXXC motifs suggesting these are zinc binding proteins. This protein is found in clostridia in an operon with three signalling proteins, suggesting this protein may be a DNA-binding transcription regulator downstream of an as yet unknown signalling pathway (Bateman A pers obs). 136 matched cddid_all.tbl CDD pfam12654 pfam12654 432699 DUF3786 Domain of unknown function (DUF3786). This presumed domain is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 201 and 257 amino acids in length. Some proteins also contains an iron-sulfur cluster. 176 matched cddid_all.tbl CDD pfam12655 pfam12655 403755 DUF3787 Domain of unknown function (DUF3787). This family of proteins is functionally uncharacterized. This family of proteins is found in Clostridia. Proteins in this family are approximately 60 amino acids in length. There is a conserved TAAW sequence motif that may be functionally important. 52 matched cddid_all.tbl CDD pfam12656 pfam12656 432700 G-patch_2 G-patch domain. Yeast Spp2, a G-patch protein and spliceosome component, interacts with the ATP-dependent DExH-box splicing factor Prp2. As this interaction involves the G-patch sequence in Spp2 and is required for the recruitment of Prp2 to the spliceosome before the first catalytic step of splicing, it is proposed that Spp2 might be an accessory factor that confers spliceosome specificity on Prp2. 61 matched cddid_all.tbl CDD pfam12657 pfam12657 463658 TFIIIC_delta Transcription factor IIIC subunit delta N-term. In humans there are six subunits of transcription factor IIIC, and this one is the 90 kDa subunit; whereas in fungi the complex resolves into nine different subunits and this is No. 9 in yeasts. The whole subunit is involved in RNA polymerase III-mediated transcription. It is possible that this N-terminal domain interacts with TFIIIC subunit 8. 176 matched cddid_all.tbl CDD pfam12658 pfam12658 403757 Ten1 Telomere capping, CST complex subunit. Stn1 and Ten1 are DNA-binding proteins with specificity for telomeric DNA substrates and both protect chromosome termini from unregulated resection and regulate telomere length. Stn1 complexes with Ten1 and Cdc13 to function as a telomere-specific replication protein A (RPA)-like complex. These three interacting proteins associate with the telomeric overhang in budding yeast, whereas a single protein known as Pot1 (protection of telomeres-1) performs this function in fission yeast, and a two-subunit complex consisting of POT1 and TPP1 associates with telomeric ssDNA in humans. S.pombe has Stn1- and Ten1-like proteins that are essential for chromosome end protection. Stn1 orthologues exist in all species that have Pot1, whereas Ten1-like proteins can be found in all fungi. Fission yeast Stn1 and Ten1 localize at telomeres in a manner that correlates with the length of the ssDNA overhang, suggesting that they specifically associate with the telomeric ssDNA. Two separate protein complexes are required for chromosome end protection in fission yeast. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution. Ten1 is one of the three components of the CST complex, which, in conjunction with the Shelterin complex helps protect telomeres from attack by DNA-repair mechanisms. 115 matched cddid_all.tbl CDD pfam12659 pfam12659 463659 Stn1_C Telomere capping C-terminal wHTH. This domain consists of tandem winged helix-turn-helix motifs. Stn1 and Ten1 are DNA-binding proteins with specificity for telomeric DNA substrates and both protect chromosome termini from unregulated resection and regulate telomere length. Stn1 complexes with Ten1 and Cdc13 to function as a telomere-specific replication protein A (RPA)-like complex. These three interacting proteins associate with the telomeric overhang in budding yeast, whereas a single protein known as Pot1 (protection of telomeres-1) performs this function in fission yeast, and a two-subunit complex consisting of POT1 and TPP1 associates with telomeric ssDNA in humans. S.pombe has Stn1- and Ten1-like proteins that are essential for chromosome end protection. Stn1 orthologues exist in all species that have Pot1, whereas Ten1-like proteins can be found in all fungi. Fission yeast Stn1 and Ten1 localize at telomeres in a manner that correlates with the length of the ssDNA overhang, suggesting that they specifically associate with the telomeric ssDNA. Two separate protein complexes are required for chromosome end protection in fission yeast. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution. 164 matched cddid_all.tbl CDD pfam12660 pfam12660 372246 zf-TFIIIC Putative zinc-finger of transcription factor IIIC complex. This zinc-finger domain is at the very C-terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions. 87 matched cddid_all.tbl CDD pfam12661 pfam12661 463660 hEGF Human growth factor-like EGF. hEGF, or human growth factor-like EGF, domains have six conserved residues disulfide-bonded into the characteriztic 'ababcc' pattern. They are involved in growth and proliferation of cells, in proteins of the Notch/Delta pathway, neurogulin and selectins. hEGFs are also found in mosaic proteins with four-disulfide laminin EGFs such as aggrecan and perlecan. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal Cys residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In hEGFs the C-terminal thiol resides in the beta-turn, resulting in shorter loop-lengths between the Cys residues of disulfide 'c', typically C[8-9]XC. These shorter loop-lengths are also typical of the four-disulfide EGF domains, laminin ad integrin. Tandem hEGF domains have six linking residues between terminal cysteines of adjacent domains. hEGF domains may or may not bind calcium in the linker region. hEGF domains with the consensus motif CXD4X[F,Y]XCXC are hydroxylated exclusively in the Asp residue. 22 matched cddid_all.tbl CDD pfam12662 pfam12662 463661 cEGF Complement Clr-like EGF-like. cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteriztic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue. 22 matched cddid_all.tbl CDD pfam12663 pfam12663 432705 DUF3788 Protein of unknown function (DUF3788). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 137 and 149 amino acids in length. This family may be distantly related to RelE proteins. 131 matched cddid_all.tbl CDD pfam12664 pfam12664 432706 DUF3789 Protein of unknown function (DUF3789). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There are two completely conserved residues (V and C) that may be functionally important. 32 matched cddid_all.tbl CDD pfam12666 pfam12666 432707 PrgI PrgI family protein. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 116 and 146 amino acids in length. This protein is found in an operon that is part of a Type IV secretion system. 91 matched cddid_all.tbl CDD pfam12667 pfam12667 432708 NigD_N NigD-like N-terminal OB domain. This family of proteins is functionally uncharacterized. This family of proteins is found in Bacteroides species. Proteins in this family are typically between 234 and 260 amino acids in length. These proteins possess an N-terminal lipoprotein attachment site. The family includes NigD a protein found in the Nig operon that encodes a bacteriocin called nigrescin. It has been suggested that NigD may be the immunity protein for nigrescin (NigC) because it is directly downstream. This domain has an OB fold. 66 matched cddid_all.tbl CDD pfam12668 pfam12668 463662 DUF3791 Protein of unknown function (DUF3791). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 71 and 125 amino acids in length. 60 matched cddid_all.tbl CDD pfam12669 pfam12669 463663 FeoB_associated FeoB-associated Cys-rich membrane protein. Members of this family typically are small proteins encoded next to FeoB, part of a ferrous iron uptake system. They consist of a highly hydrophobic predicted membrane segment, followed by a short, Cys-rich region, for an average length of less than sixty amino acids. In some cases, member proteins are fusion proteins, with the region described by this family occurring as a C-terminal extension to FeoB. 45 matched cddid_all.tbl CDD pfam12670 pfam12670 463664 DUF3792 Protein of unknown function (DUF3792). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. These proteins are integral membrane proteins. 110 matched cddid_all.tbl CDD pfam12671 pfam12671 403767 Amidase_6 Putative amidase domain. 161 matched cddid_all.tbl CDD pfam12672 pfam12672 463665 DUF3793 Protein of unknown function (DUF3793). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 187 and 211 amino acids in length. There are two conserved sequence motifs: PHE and LGYP. 171 matched cddid_all.tbl CDD pfam12673 pfam12673 463666 DUF3794 Domain of unknown function (DUF3794). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 90 amino acids in length. The family is found in association with pfam01476. 80 matched cddid_all.tbl CDD pfam12674 pfam12674 463667 Zn_ribbon_2 Putative zinc ribbon domain. This domain appears to be a zinc binding DNA-binding domain. 82 matched cddid_all.tbl CDD pfam12675 pfam12675 463668 DUF3795 Protein of unknown function (DUF3795). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 99 and 171 amino acids in length. This protein is likely to be zinc binding given the conserved cysteines. 81 matched cddid_all.tbl CDD pfam12676 pfam12676 403772 DUF3796 Protein of unknown function (DUF3796). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. 112 matched cddid_all.tbl CDD pfam12677 pfam12677 289447 DUF3797 Domain of unknown function (DUF3797). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif. 48 matched cddid_all.tbl CDD pfam12678 pfam12678 463669 zf-rbx1 RING-H2 zinc finger domain. There are 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding. The protein, of which this domain is the conserved region, participates in diverse functions relevant to chromosome metabolism and cell cycle control. 55 matched cddid_all.tbl CDD pfam12679 pfam12679 403774 ABC2_membrane_2 ABC-2 family transporter protein. This family is related to the ABC-2 membrane transporter family. 281 matched cddid_all.tbl CDD pfam12680 pfam12680 432716 SnoaL_2 SnoaL-like domain. This family contains a large number of proteins that share the SnoaL fold. 100 matched cddid_all.tbl CDD pfam12681 pfam12681 403776 Glyoxalase_2 Glyoxalase-like domain. This domain is related to the Glyoxalase domain pfam00903. 118 matched cddid_all.tbl CDD pfam12682 pfam12682 403777 Flavodoxin_4 Flavodoxin. This is a family of flavodoxins. Flavodoxins are electron transfer proteins that carry a molecule of non-covalently bound FMN. 155 matched cddid_all.tbl CDD pfam12683 pfam12683 403778 DUF3798 Protein of unknown function (DUF3798). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 247 and 417 amino acids in length. Most of the proteins in this family have an N-terminal lipoprotein attachment site. These proteins have distant similarity to periplasmic ligand binding families such as pfam02608, which suggests that this family have a similar role. 271 matched cddid_all.tbl CDD pfam12684 pfam12684 432717 DUF3799 PDDEXK-like domain of unknown function (DUF3799). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 265 and 420 amino acids in length. It appears that these proteins are distantly related to the PDDEXK superfamily and so these domains are likely to be nucleases. This family has a C-terminal cysteine cluster similar to that found in pfam01930. 231 matched cddid_all.tbl CDD pfam12685 pfam12685 463670 SpoIIIAH SpoIIIAH-like protein. Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling. This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function that in sporulation. Proteins in this family are typically between 174 and 223 amino acids in length. 197 matched cddid_all.tbl CDD pfam12686 pfam12686 463671 DUF3800 Protein of unknown function (DUF3800). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 215 and 302 amino acids in length. There is a DE motif at the N-terminus and a QXXD motif at the C-terminus that may be functionally important. 112 matched cddid_all.tbl CDD pfam12687 pfam12687 432720 DUF3801 Protein of unknown function (DUF3801). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 158 and 187 amino acids in length. This family includes the PcfB protein. 132 matched cddid_all.tbl CDD pfam12688 pfam12688 403783 TPR_5 Tetratrico peptide repeat. BH0479 of Bacillus halodurans is a hypothetical protein which contains a tetratrico peptide repeat (TPR) structural motif. The TPR motif is often involved in mediating protein-protein interactions. This protein is likely to function as a dimer. The first 48 amino acids are not present in the clone construct. This Pfam entry includes tetratricopeptide-like repeats not detected by the pfam00515, pfam07719, pfam07720 and pfam07221 models. 119 matched cddid_all.tbl CDD pfam12689 pfam12689 372256 Acid_PPase Acid Phosphatase. This family contains phosphatase enzymes and other proteins of the HAD superfamily. It includes MDP-1 which is a eukaryotic magnesium-dependent acid phosphatase. 169 matched cddid_all.tbl CDD pfam12690 pfam12690 432721 BsuPI Intracellular proteinase inhibitor. This is a bacterial domain which has been named BsuPI in Bacillus subtilis. This domain is found in Swiss:P39804, where it has been suggested to regulate the major intracellular proteinase (ISP-1) activity in vivo. The structure of proteins in this family adopt an Ig-like fold. 100 matched cddid_all.tbl CDD pfam12691 pfam12691 432722 Minor_capsid_3 Bacteriophage minor capsid protein. This family is from one of three adjacent genes, all of which are involved in formation of the minor phage capsid. 117 matched cddid_all.tbl CDD pfam12692 pfam12692 432723 Methyltransf_17 S-adenosyl-L-methionine methyltransferase. This domain is found in bacterial proteins. The structure of the proteins in this family suggest that they function as a methyltransferase. 160 matched cddid_all.tbl CDD pfam12693 pfam12693 432724 GspL_C GspL periplasmic domain. This domain is the periplasmic domain of the GspL/EpsL family proteins. These proteins are involved in type II secretion systems. 158 matched cddid_all.tbl CDD pfam12694 pfam12694 463672 cpYpsA Circularly permutated YpsA SLOG family. The structure of proteins in this family contain central beta strands with flanking alpha helices. The structure is similar to that of a molybdenum cofactor carrier protein.This family belongs in the SLOG superfamily, circularly-permuted version of YspA famiy showing fusions to NAD utilization and ADP-ribosylation domains including NUDIX, NADAR and MACRO. Members of this family are predicted to function as sensors of nucleotide, nucleotide-derived ligands, or nucleic acids, which are potentially processed/modified by associating effectors. 146 matched cddid_all.tbl CDD pfam12695 pfam12695 315383 Abhydrolase_5 Alpha/beta hydrolase family. This family contains a diverse range of alpha/beta hydrolase enzymes. 164 matched cddid_all.tbl CDD pfam12696 pfam12696 432726 TraG-D_C TraM recognition site of TraD and TraG. This family includes both TraG and TraD as well as VirD4 proteins. TraG is essential for DNA transfer in bacterial conjugation. These proteins are thought to mediate interactions between the DNA-processing (Dtr) and the mating pair formation (Mpf) systems. This domain interacts with the relaxosome component TraM via the latter's tetramerization domain. TraD is a hexameric ring ATPase that forms the cytoplasmic face of the conjugative pore. 125 matched cddid_all.tbl CDD pfam12697 pfam12697 463673 Abhydrolase_6 Alpha/beta hydrolase family. This family contains alpha/beta hydrolase enzymes of diverse specificity. 211 matched cddid_all.tbl CDD pfam12698 pfam12698 463674 ABC2_membrane_3 ABC-2 family transporter protein. This family is related to the ABC-2 membrane transporter family pfam01061. 345 matched cddid_all.tbl CDD pfam12699 pfam12699 403791 phiKZ_IP phiKZ-like phage internal head proteins. Phage internal head proteins (IP) are proteins that are encoded by a bacteriophage and assembled into the mature virion inside the capsid head. The most analogous characterized IP proteins are those of bacteriophage T4, which are known to be proteolytically processed during phage maturation, and then subsequently injected into the host cell during infection. The phiKZ_IP family consists of internal head proteins encoded by phiKZ-like phages. Each phage encodes three to six members of this family. Members of the family reside in the head and are cleaved during phage maturation to separate an N-terminal propeptide from a C-terminal domain. The C-terminal domain remains in the mature capsid. The N-terminal propeptide domain is either mostly or completely removed from the mature capsid. In one case, an unrelated polypeptide is embedded in the propeptide and also remains in the mature capsid. The phiKZ-like IP proteins are not discernibly homologous to the T4 IP proteins, and it is not known if the phiKZ-like IP proteins are injected into the host cell, or have some other function within the head. The alignment and HMM model exclude most of the propeptide region, but include the cleavage sites. The first 100 residues, including the cleavage sites, constitute the most conservative part of the seed alignment. 323 matched cddid_all.tbl CDD pfam12700 pfam12700 403792 HlyD_2 HlyD family secretion protein. This family is related to pfam00529. 413 matched cddid_all.tbl CDD pfam12701 pfam12701 463675 LSM14 Scd6-like Sm domain. The Scd6-like Sm domain is found in Scd6p from S. cerevisiae, Rap55 from the newt Pleurodeles walt, and its orthologs from fungi, animals, plants and apicomplexans. The domain is also found in Dcp3p and the human EDC3/FLJ21128 protein where it is fused to the the Rossmanoid YjeF-N domain. In addition both EDC3 and Scd6p are found fused to the FDF domain. 75 matched cddid_all.tbl CDD pfam12702 pfam12702 432729 Lipocalin_3 Lipocalin-like. This is a family of proteins of 115 residues on average. The family has two highly conserved tryptophan residues. The fold is very similar to the lipocalin-like fold from several comparable structures. 92 matched cddid_all.tbl CDD pfam12703 pfam12703 403795 ptaRNA1_toxin Toxin of toxin-antitoxin type 1 system. This family is the toxin of a type 1 toxin-antitoxin system which is found in a relatively widespread range of bacterial species. The species distribution suggests frequent horizontal gene transfer. In a type 1 system, as characterized for the plasmid-encoded E coli hok/sok system, the toxin-encoding stable mRNA encodes a protein which rapidly leads to cell death unless the translation is suppressed by a short-lived small RNA. The plasmid-encoded module prevents the growth of plasmid-free offspring, thus ensuring the persistence of the plasmid in the population. Plasmid-free cells arising after cell-division will be killed because the stable mRNA toxin is present while the comparably unstable anti-toxin is rapidly degraded. Where the system is transcribed chromosomally, the mechanism is poorly understood. 73 matched cddid_all.tbl CDD pfam12704 pfam12704 463676 MacB_PCD MacB-like periplasmic core domain. This family represents the periplasmic core domain found in a variety of ABC transporters. The structure of this family has been solved for the MacB protein. Some structural similarity was found to the periplasmic domain of the AcrB multidrug efflux transporter. 211 matched cddid_all.tbl CDD pfam12705 pfam12705 432731 PDDEXK_1 PD-(D/E)XK nuclease superfamily. Members of this family belong to the PD-(D/E)XK nuclease superfamily 250 matched cddid_all.tbl CDD pfam12706 pfam12706 432732 Lactamase_B_2 Beta-lactamase superfamily domain. This family is part of the beta-lactamase superfamily and is related to pfam00753. 196 matched cddid_all.tbl CDD pfam12707 pfam12707 403799 DUF3804 Protein of unknown function (DUF3804). This family is approximately 130 residues. Dali search indicates this protein carries a NTF2-fold with a hydrophobic cavity as a structural homolog to 1JB2, 2R4I, 3FSD and 2UX0. In this hydrophobic cavity, Arg 118 provides the H-bonding force to hold a PEG molecule from crystallization. The interface interaction suggests that the biomolecule of Swiss:Q46KI2 is a dimer. Two members of the family are annotated as putative EF-Tu domain 2 but there is no match to this family so this is likely to be a false assignment. There are two highly conserved tryptophan residues towards the C-terminal end of the family. 128 matched cddid_all.tbl CDD pfam12708 pfam12708 403800 Pectate_lyase_3 Pectate lyase superfamily protein. This family of proteins possesses a beta helical structure like Pectate lyase. This family is most closely related to glycosyl hydrolase family 28. 213 matched cddid_all.tbl CDD pfam12709 pfam12709 403801 Fungal_TACC Fungal Transforming acidic coiled-coil (TACC) proteins. TACC proteins are present in different organizms, ranging from yeasts to mammals. Schizosaccharomyces pombe has one TACC protein, known as Alp7 or Mia1p. Alp7/TACC consists of two domains: the N-terminal half that contains the nuclear localization signal (NLS) and has no homology to the other TACC members, and the C-terminal half, which consists of the conserved coiled-coil TACC domain. Alp7/TACC forms a complex with Alp14/TOG and localizes to microtubules, SPBs and kinetochores. This complex is necessary for mitotic and meiotic spindle assembly and proper chromosome segregation. The homolog from S. cerevisiae, Slk19, also has a role in spindle assembly and stability, and it is required for proper chromosome segregation. 77 matched cddid_all.tbl CDD pfam12710 pfam12710 432733 HAD haloacid dehalogenase-like hydrolase. 188 matched cddid_all.tbl CDD pfam12712 pfam12712 432734 DUF3805 Domain of unknown function (DUF3805). This family represent the N-terminal domain of the structure. In two related Bacteroides species the gene lies immediately upstream from a putative ATP binding component of an ATP transporter and a putative histidinol phosphatase. The structure of this domain is strikingly similar to the N-terminal structure of 1tui, also of unknown function. The domain carries four conserved tryptophan residues. 152 matched cddid_all.tbl CDD pfam12713 pfam12713 432735 DUF3806 Domain of unknown function (DUF3806). This family represent the C-terminal domain of the structure. In two related Bacteroides species the gene lies immediately upstream from a putative ATP binding component of an ATP transporter and a putative histidinol phosphatase. The structure of this domain is strikingly similar to the N-terminal structure of 1ma7 whose C-terminal domain is a phage integrase, pfam00589. 86 matched cddid_all.tbl CDD pfam12714 pfam12714 432736 TILa TILa domain. This cysteine rich domain occurs along side the TIL pfam01826 domain and is likely to be a distantly related relative. 54 matched cddid_all.tbl CDD pfam12715 pfam12715 403805 Abhydrolase_7 Abhydrolase family. This is a family of probable bacterial abhydrolases. 387 matched cddid_all.tbl CDD pfam12716 pfam12716 432737 Apq12 Nuclear pore assembly and biogenesis. This is a family of conserved fungal proteins involved in nuclear pore assembly. Apq12 is an integral membrane protein of the nuclear envelope (NE) and endoplasmic reticulum. Its absence leads to a partial block in mRNA export and cold-sensitive defects in the growth and localization of a subset of nucleoporins, particularly those asymmetrically localized to the cytoplasmic fibrils. The defects in nuclear pore assembly appear to be due to defects in regulating membrane fluidity. 53 matched cddid_all.tbl CDD pfam12717 pfam12717 463677 Cnd1 non-SMC mitotic condensation complex subunit 1. The three non-SMC (structural maintenance of chromosomes) subunits of the mitotic condensation complex are Cnd1-3. The whole complex is essential for viability and the condensing of chromosomes in mitosis. 162 matched cddid_all.tbl CDD pfam12718 pfam12718 403808 Tropomyosin_1 Tropomyosin like. This family is a set of eukaryotic tropomyosins. Within the yeast Tpm1 and Tpm2, biochemical and sequence analyses indicate that Tpm2p spans four actin monomers along a filament, whereas Tpm1p spans five. Despite its shorter length, Tpm2p can compete with Tpm1p for binding to F-actin. Over-expression of Tpm2p in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1p. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis. The family also contains higher eukaryote Tpm3 members. 142 matched cddid_all.tbl CDD pfam12719 pfam12719 463678 Cnd3 Nuclear condensing complex subunits, C-term domain. The Cnd1-3 proteins are the three non-SMC (structural maintenance of chromosomes) proteins that go to make up the mitotic condensation complex along with the two SMC protein families, XCAP-C and XCAP-E, (or in the case of fission yeast, Cut3 and Cut14). The five-member complex seems to be conserved from yeasts to vertebrates. This domain is the C-terminal, cysteine-rich domain of Cnd3. The complex shuttles between the nucleus, during mitosis, and the cytoplasm during the rest of the cycle. Thus this family is made up of the C-termini of XCAP-Gs, Ycg1 and Ycs5 members. 286 matched cddid_all.tbl CDD pfam12720 pfam12720 432740 DUF3807 Protein of unknown function (DUF3807). This is a family of conserved fungal proteins of unknown function. 179 matched cddid_all.tbl CDD pfam12721 pfam12721 463679 RHIM RIP homotypic interaction motif. RIP proteins are receptor-interacting serine/threonine-protein kinases or cell death proteins. This interacting domain is involved in virus recognition. The RHIM domain is necessary for the recruitment of RIP and RIP3 by the IFN-inducible protein DNA-dependent activator of IRFs (DAI), also known as DLM-1 or Z-DNA binding protein (ZBP1). Both the RIP kinases contribute to DAI-induced NF-kappaB activation. RIP3 undergoes auto phosphorylation on binding to DAI. 21 matched cddid_all.tbl CDD pfam12722 pfam12722 463680 Hid1 High-temperature-induced dauer-formation protein. Hid1 (high-temperature-induced dauer-formation protein 1) represents proteins of approximately 800 residues long and is conserved from fungi to humans. Functionally it might be involved in vesicle secretion or be an inter-cellular signalling protein or be a novel insulin receptor. It was previously thought to contain up to seven potential transmembrane domains separated by regions of low complexity. However, biochemical membrane fraction analysis demonstrate that HID-1 is a peripheral membrane protein tightly associated with the Golgi apparatus but not a transmembrane protein predicted by the bioinformatic programs. Furthermore, it contains a conserved N-terminal myristoylation site was required for HID-1 binding to the Golgi apparatus. 804 matched cddid_all.tbl CDD pfam12723 pfam12723 432743 DUF3809 Protein of unknown function (DUF3809). This family of proteins is functionally uncharacterized. This family of proteins is found in Deinococci bacteria. Proteins in this family are typically between 117 and 157 amino acids in length. 136 matched cddid_all.tbl CDD pfam12724 pfam12724 463681 Flavodoxin_5 Flavodoxin domain. This is a family of flavodoxins. Flavodoxins are electron transfer proteins that carry a molecule of non-covalently bound FMN. 144 matched cddid_all.tbl CDD pfam12725 pfam12725 463682 DUF3810 Protein of unknown function (DUF3810). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 333 and 377 amino acids in length. There is a conserved HEXXH sequence motif that is characteriztic of metallopeptidases. This family may therefore belong to an as yet uncharacterized family of peptidase enzymes. 318 matched cddid_all.tbl CDD pfam12726 pfam12726 432746 SEN1_N SEN1 N terminal. This domain is found at the N terminal of the helicase SEN1. SEN1 is a Pol II termination factor for noncoding RNA genes. The N terminal of SEN1, unlike the C terminal, is not required for growth. 744 matched cddid_all.tbl CDD pfam12727 pfam12727 463683 PBP_like PBP superfamily domain. This family belongs to the periplasmic binding domain superfamily. It is often associated with a helix-turn-helix domain. 192 matched cddid_all.tbl CDD pfam12728 pfam12728 463684 HTH_17 Helix-turn-helix domain. This domain is a DNA-binding helix-turn-helix domain. 51 matched cddid_all.tbl CDD pfam12729 pfam12729 432749 4HB_MCP_1 Four helix bundle sensory module for signal transduction. This family is a four helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterized in E coli chemoreceptors. This domain recognizes citrate and TCA cycle intermediates, cis-aconitate, boric acid, Phenanthrene, pyrene and benzopyrene (Matilla et el., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 181 matched cddid_all.tbl CDD pfam12730 pfam12730 403819 ABC2_membrane_4 ABC-2 family transporter protein. This family is related to the ABC-2 membrane transporter family pfam01061. 179 matched cddid_all.tbl CDD pfam12731 pfam12731 372275 Mating_N Mating-type protein beta 1. This domain is found in some fungi and is the C-terminus of a homeodomain-containing transcription factor protein involved in mating. 95 matched cddid_all.tbl CDD pfam12732 pfam12732 432750 YtxH YtxH-like protein. This family of proteins is found in bacteria. Proteins in this family are typically between 100 and 143 amino acids in length. The N-terminal region is the most conserved. Proteins is this family are functionally uncharacterized. 71 matched cddid_all.tbl CDD pfam12733 pfam12733 403821 Cadherin-like Cadherin-like beta sandwich domain. This domain is found in several bacterial, metazoan and chlorophyte algal proteins. A profile-profile comparison recovered the cadherin domain and a comparison of the predicted structure of this domain with the crystal structure of the cadherin showed a congruent seven stranded secondary structure. The domain is widespread in bacteria and seen in the firmicutes, actinobacteria, certain proteobacteria, bacteroides and chlamydiae with an expansion in Clostridium. In contrast, it is limited in its distribution in eukaryotes suggesting that it was derived through lateral transfer from bacteria. In prokaryotes, this domain is widely fused to other domains such as FNIII (Fibronectin Type III), TIG, SLH (S-layer homology), discoidin, cell-wall-binding repeat domain and alpha-amylase-like glycohydrolases. These associations are suggestive of a carbohydrate-binding function for this cadherin-like domain. In animal proteins it is associated with an ATP-grasp domain. 89 matched cddid_all.tbl CDD pfam12734 pfam12734 403822 CYSTM Cysteine-rich TM module stress tolerance. The members of this family are short cysteine-rich membrane proteins that most probably dimerize together to form a transmembrane sulfhydryl-lined pore. The CYSTM module is always present at the extreme C-terminus of the protein in which it is present. Furthermore, like the yeast prototypes, the majority of the proteins also possess a proline/glutamine-rich segment upstream of the CYSTM module that is likely to form a polar, disordered head in the cytoplasm. The presence of an atypical well-conserved acidic residue at the C-terminal end of the TM helix suggests that this might interact with a positively charged moiety in the lipid head group. Consistently across the eukaryotes, the different versions of the CYSTM module appear to have roles in stress-response or stress-tolerance, and, more specifically, in resistance to deleterious substances, implying that these might be general functions of the whole family. 37 matched cddid_all.tbl CDD pfam12735 pfam12735 463685 Trs65 TRAPP trafficking subunit Trs65. This family is one of the subunits of the TRAPP Golgi trafficking complex. TRAPP subunits are found in two different sized complexes, TRAPP I and TRAPP II. While both complexes contain the same seven subunits, Bet3p, Bet5p, Trs20p, Trs23p, Trs31p, Trs33p and Trs85p, with TRAPPC human equivalents, TRAPP II has the additional three subunits,Trs65p, Trs120p and Trs130p. While it has been implicated in cell wall biogenesis and stress response, the role of Trs65 in TRAPP II is supported by the findings that the protein co-localizes with Trs130p, and deletion of TRS65 in yeast leads to a conditional lethal phenotype if either one of the other TRAPP II-specific subunits is modified. Furthermore, the trs65 mutant has reduced Ypt31/32p guanine nucleotide exchange, GEF, activity. 311 matched cddid_all.tbl CDD pfam12736 pfam12736 463686 CABIT Cell-cycle sustaining, positive selection,. The 'CABIT' domain (for 'cysteine-containing, all- in Themis') is found in a newly identified gene family that has three mammalian homologs (Themis, Icb1 and 9130404H23Rik) that encode proteins with two CABIT domains and a highly conserved proline-rich region. In contrast, Fam59A, Fam59B and related proteins from mammals to cnidarians, including the insect Serrano proteins, have a single copy of the CABIT domain, a proline-rich region and often a C-terminal SAM (sterile-motif) domain. Multiple-sequence alignment has predicted that the CABIT domain adopts an all-strand structure with at least 12 strands, ie a dyad of six-stranded beta-barrel units. The CABIT domain contains a nearly absolutely conserved cysteine residue which is likely to be central to its function. CABIT domain proteins function downstream of tyrosine kinase signalling and interact with GRB2. 261 matched cddid_all.tbl CDD pfam12737 pfam12737 372279 Mating_C C-terminal domain of homeodomain 1. Mating in fungi is controlled by the loci that determine the mating type of an individual, and only individuals with differing mating types can mate. Basidiomycete fungi have evolved a unique mating system, termed tetrapolar or bifactorial incompatibility, in which mating type is determined by two unlinked loci; compatibility at both loci is required for mating to occur. The multi-allelic tetrapolar mating system is considered to be a novel innovation that could have only evolved once, and is thus unique to the mushroom fungi. This domain is C-terminal to the homeodomain transcription factor region. 412 matched cddid_all.tbl CDD pfam12738 pfam12738 463687 PTCB-BRCT twin BRCT domain. This is a BRCT domain that appears in duplicate in most member sequences. BRCT domains are peptide- and phosphopeptide-binding modules. BRCT domains are present in a number of proteins involved in DNA checkpoint controls and DNA repair. 63 matched cddid_all.tbl CDD pfam12739 pfam12739 463688 TRAPPC-Trs85 ER-Golgi trafficking TRAPP I complex 85 kDa subunit. This family is one of the subunits of the TRAPP Golgi trafficking complex. TRAPP subunits are found in two different sized complexes, TRAPP I and TRAPP II, and this Trs85 is in the smaller complex. TRAPP I, but Not TRAPP II, functions in ER-Golgi transport. Trs85p was reported to function in the cytosol-to-vacuole targeting pathway, suggesting a role for this subunit in autophagy as well as in secretion. The overall architecture of TRAPP I shows the other components to be Bet3p (TRAPPC3), Bet5p (TRAPPC1), Trs20p (TRAPPC2), Trs23p (TRAPPC4), Trs31p (TRAPPC5), Trs33p (TRAPPC6a and b) and Trs85p. 350 matched cddid_all.tbl CDD pfam12740 pfam12740 432755 Chlorophyllase2 Chlorophyllase enzyme. This family consists of several chlorophyllase and chlorophyllase-2 (EC:3.1.1.14) enzymes. Chlorophyllase (Chlase) is the first enzyme involved in chlorophyll (Chl) degradation and catalyzes the hydrolysis of an ester bond to yield chlorophyllide and phytol. The family includes both plant and Amphioxus members. 254 matched cddid_all.tbl CDD pfam12741 pfam12741 432756 SusD-like Susd and RagB outer membrane lipoprotein. This is a family of SusD-like proteins, one member of which, BT1043, is an outer membrane lipoprotein involved in host glycan metabolism. The structures of this and SusD-homologs in the family are dominated by tetratrico peptide repeats that may facilitate association with outer membrane beta-barrel transporters required for glycan uptake. The structure of BT1043 complexed with N-acetyllactosamine reveals that recognition is mediated via hydrogen bonding interactions with the reducing end of beta-N-acetylglucosamine, suggesting a role in binding glycans liberated from the mucin polypeptide. Mammalian distal gut bacteria have an expanded capacity to utilize glycans. In the absence of dietary sources, some species rely on host-derived mucosal glycans. The ability of Bacteroides thetaiotaomicron, a prominent human gut symbiont, to forage host glycans contributes to both its ability to persist within an individual host and its ability to be transmitted naturally to new hosts at birth. 495 matched cddid_all.tbl CDD pfam12742 pfam12742 403829 Gryzun-like Gryzun, putative Golgi trafficking. Members of this family are involved in Golgi trafficking. 56 matched cddid_all.tbl CDD pfam12743 pfam12743 432757 ESR1_C Oestrogen-type nuclear receptor final C-terminal. This is the very C-terminal region of a subfamily of nuclear receptors that includes oestrogen receptors and other subfamily 3 group A members. The actual function of this region is not known, but the domain is absent from all the other types of nuclear receptors. Oestrogen receptors modulate AP-1-dependent transcription through two distinct mechanisms: via protein-protein interactions on DNA; and via non-genomic actions. The mechanism used depends on the cellular localization of the receptor. In addition to the more extensively studied cross-talk on DNA, additional non-genomic actions might be very important in target tissues in which membrane-associated ERs are found. These non-genomic actions probably contribute to the overall physiological responses mediated by ligand-bound ERs and might possibly be mediated via this C-terminal domain. 44 matched cddid_all.tbl CDD pfam12744 pfam12744 403831 ATG19 Autophagy protein Atg19, Atg8-binding. Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. In contrast to autophagy, however, the Cvt pathway is a highly selective process that involves the sequestration of at least two specific cargos that are resident vacuolar hydrolases, aminopeptidase I (Ape1) and alpha-mannosidase (Ams1). These proteins are sequestered within a double-membrane vesicle, termed a Cvt vesicle. The Cvt vesicle is fairly consistent in size, and is much smaller than the autophagosome, being 140-160 nm in diameter. The prApe1 is sequestered within either Cvt vesicles or autophagosomes, depending on the nutrient conditions, and delivered to the vacuole. Autophagy and the Cvt pathway are topologically and mechanistically similar and share most of the same machinery. The Ape1 complex is ultimately enwrapped within either Cvt vesicles or autophagosomes at the perivacuolar PAS. The receptor protein Atg19 binds to the Ape1 complex through the prApe1 propeptide to form the Cvt complex in the cytosol. In the absence of Atg19, prApe1 can form an Ape1 complex, but does not localize at the PAS. Atg19 is a peripheral membrane protein with differing binding sites for both Ape1 and Ams1. The Atg8-binding region in the yeast proteins is this very C-terminal residues. 246 matched cddid_all.tbl CDD pfam12745 pfam12745 432758 HGTP_anticodon2 Anticodon binding domain of tRNAs. This is an HGTP_anticodon binding domain, found largely on Gcn2 proteins which bind tRNA to down regulate translation in certain stress situations. 259 matched cddid_all.tbl CDD pfam12746 pfam12746 403833 GNAT_acetyltran GNAT acetyltransferase. Many of the members are annotated s being Zwittermicin A resistance proteins, whereas others are listed as being GNAT acetyltransferases. The family has similarities to the GNAT acetyltransferase family. 239 matched cddid_all.tbl CDD pfam12747 pfam12747 372287 DdrB DdrB-like protein. This family includes the Deinococcus DdrB protein which is a ssDNA binding protein. This family also includes some possibly distantly related cyanobacterial proteins. However, these are not strongly supported. The structure of DdrB is known. 126 matched cddid_all.tbl CDD pfam12749 pfam12749 315429 Metallothio_Euk Eukaryotic metallothionein. This is a family of eukaryotic metallothioneins. 66 matched cddid_all.tbl CDD pfam12750 pfam12750 432759 Maff2 Maff2 family. This family of short membrane proteins are related to the protein Maff2. Maff2 lies just outside the direct repeats of a tetracycline resistance transposable element. This protein may contain transmembrane helices. 70 matched cddid_all.tbl CDD pfam12751 pfam12751 432760 Vac7 Vacuolar segregation subunit 7. Vac7 is localized at the vacuole membrane, a location which is consistent with its involvement in vacuole morphology and inheritance. Vac7 has been shown to function as an upstream regulator of the Fab1 lipid kinase pathway. The Fab1 lipid p[pathway is important for correct regulation of membrane trafficking events. 384 matched cddid_all.tbl CDD pfam12752 pfam12752 463689 SUZ SUZ domain. The SUZ domain is a conserved RNA-binding domain found in eukaryotes and enriched in positively charged amino acids. It was first characterized in the C.elegans protein Szy-20 where it has been shown to bind RNA and allow their localization to the centrosome. Warning- the domain has a compositionally biased character. 56 matched cddid_all.tbl CDD pfam12753 pfam12753 403837 Nro1 Nuclear pore complex subunit Nro1. In fission yeast, this protein is a positive regulator of the stability of Sre1N, the sterol regulatory element-binding protein which is an ER membrane-bound transcription factor that controls adaptation to low oxygen-growth. In addition, the fission yeast Nro1 is a direct inhibitor of a protein that inhibits SreN1 degradation, Ofd1 (an oxoglutamate deoxygenase). The outcome of this reactivity is that Ofd1 acts as an oxygen sensor that regulates the binding of Nro1 to Ofd1 to control the stability of Sre1N. Solution of the structure of Nro1 reveals it to be made up of a number of TPR coils. TPR proteins are composed of three to 16 tandem peptide repeat motifs of 34 amino acids with degenerate sequence. The helical pairs adopt a helix-turn-helix anti-parallel arrangement with interacting helices. In general, TPR motifs are stacked together so that helix A from TPRn is packed between helix B from TPRn and helix A from TPRn+1. In Nro1, the 12 alpha helices forming the six TPR motifs are organized as follows from N terminus to C terminus - TPR1A, TPR1B, TPR2A, TPR2B, TPR3A, TPR3B, TPR4A, TPR4B, TPR5A, TPR5B, TPR6A, and TPR6B with the C-terminal helix (hC) running above the sixth TPR motif with an angle of approx 45 degrees with TPR6A and TPR6B. The corresponding TPRs structural motifs are longer (50 residues) than are canonical ones (34 amino acids) and are organized into two subdomains - Nro1-N (residues 55-225) and Nro1-C (residues 226-393). The Nro1/Etti protein plays a role in nuclear import suggesting that it is residues 4-19 that are interacting with Ofd1. 414 matched cddid_all.tbl CDD pfam12754 pfam12754 372291 Blt1 Blt1 N-terminal domain. During size-dependent cell cycle transitions controlled by the ubiquitous cyclin-dependent kinase Cdk1, Blt1 has been shown to co-localize with Cdr2 in the medial interphase nodes, as well as with Mid1 which was previously shown to localize to similar interphase structures. Physical interactions between Blt1-Mid1, Blt1-Cdr2 and Cdr2-Mid1 were detected, indicating that medial cortical nodes are formed by the ordered, Cdr2-dependent assembly of multiple interacting proteins during interphase. This domain show similarity to ubiquitin family proteins. 150 matched cddid_all.tbl CDD pfam12755 pfam12755 403838 Vac14_Fab1_bd Vacuolar 14 Fab1-binding region. Vac14 is a scaffold for the Fab1 kinase complex, a complex that allows for the dynamic interconversion of PI3P and PI(3,5)P2p (phosphoinositide phosphate (PIP) lipids, that are generated transiently on the cytoplasmic face of selected intracellular membranes). This interconversion is regulated by at least five proteins in yeast: the lipid kinase Fab1p, lipid phosphatase Fig4p, the Fab1p activator Vac7p, the Fab1p inhibitor Atg18p, and Vac14p, a protein required for the activity of both Fab1p and Fig4p. This domain appears to be the one responsible for binding to Fab1. The full length Vac14 in yeasts is likely to be a protein carrying a succession of HEAT repeats, most of which have now degenerated. This regulatory system is crucial for the proper functioning of the mammalian nervous system. 97 matched cddid_all.tbl CDD pfam12756 pfam12756 463690 zf-C2H2_2 C2H2 type zinc-finger (2 copies). This family contains two copies of a C2H2-like zinc finger domain. 98 matched cddid_all.tbl CDD pfam12757 pfam12757 432763 Eisosome1 Eisosome protein 1. Eisosome protein 1 is required for normal formation of eisosomes, large cytoplasmic protein assemblies that localize to specialized domains on plasma membrane and mark the site of endocytosis. 125 matched cddid_all.tbl CDD pfam12758 pfam12758 372295 DUF3813 Protein of unknown function (DUF3813). This is an uncharacterized family of Bacillus proteins. 60 matched cddid_all.tbl CDD pfam12759 pfam12759 289525 HTH_Tnp_IS1 InsA C-terminal domain. This short domain is found at the C-terminus of the InsA protein. This domain contains a helix-turn-helix domain. 46 matched cddid_all.tbl CDD pfam12760 pfam12760 432764 Zn_Tnp_IS1595 Transposase zinc-ribbon domain. This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It is likely a zinc-binding beta ribbon domain that could bind the DNA. 46 matched cddid_all.tbl CDD pfam12761 pfam12761 432765 End3 Actin cytoskeleton-regulatory complex protein END3. Endocytosis is accomplished through the sequential recruitment at endocytic sites of proteins that drive cargo sorting, membrane invagination and vesicle release. End3p is part of the coat module protein complex Pan1, along with Pan1p, Sla1p, and Sla2p. The proteins in this complex are regulated by phosphorylation events. End3p also regulates the cortical actin cytoskeleton. The subunits of the Pan1 complex are homologous to mammalian intersectin. 200 matched cddid_all.tbl CDD pfam12762 pfam12762 432766 DDE_Tnp_IS1595 ISXO2-like transposase domain. This domain probably functions as an integrase that is found in a wide variety of transposases, including ISXO2. 154 matched cddid_all.tbl CDD pfam12763 pfam12763 289529 EF-hand_4 Cytoskeletal-regulatory complex EF hand. This is an efhand family from the N-terminal of actin cytoskeleton-regulatory complex END3 and similar proteins from fungi and closely related species. 104 matched cddid_all.tbl CDD pfam12764 pfam12764 463691 Gly-rich_Ago1 Glycine-rich region of argonaut. This domain is often found at the very N-terminal of argonaut-like proteins. 103 matched cddid_all.tbl CDD pfam12765 pfam12765 403845 Cohesin_HEAT HEAT repeat associated with sister chromatid cohesion. This HEAT repeat is found most frequently in sister chromatid cohesion proteins such as Nipped-B. HEAT repeats are found tandemly repeated in many proteins, and they appear to serve as flexible scaffolding on which other components can assemble. 42 matched cddid_all.tbl CDD pfam12766 pfam12766 432768 Pyridox_oxase_2 Pyridoxamine 5'-phosphate oxidase. Pyridoxamine 5'-phosphate oxidase catalyzes the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP), the terminal step in the de novo biosynthesis of PLP in Escherichia coli and part of the salvage pathway of this coenzyme in both E. coli and mammalian cells. This region is the flavoprotein FMN-binding domain. 99 matched cddid_all.tbl CDD pfam12767 pfam12767 463692 SAGA-Tad1 Transcriptional regulator of RNA polII, SAGA, subunit. The yeast SAGA complex is a multifunctional coactivator that regulates transcription by RNA polymerase II. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA. The complex can also be conceived of as consisting of two histone-fold-containing core subunits, and this family is one of these. As a family it is likely to carry binding regions for interactions with a number of the other components of the complex. 135 matched cddid_all.tbl CDD pfam12768 pfam12768 463693 Rax2 Cortical protein marker for cell polarity. Diploid yeast cells repeatedly polarise and bud from their poles, due probably to the presence of highly stable membrane markers, and Rax2 is one such marker. It is inherited immutably at the cell cortex for multiple generations, and has a half-life exceeding several generations. The persistent inheritance of cortical protein markers would provide a means of coupling a cell's history with the future development of a precise morphogenetic form. Both Rax1 and Rax2 localize to the distal pole as well as to the division site and they interact both with each other and with Bud8p and Bud9p in the establishment and/or maintenance of the cortical markers for bipolar budding. thus Rax2 is likely to control cell polarity during vegetative growth, and in fission yeast this is done by regulating the localization of for3p. 148 matched cddid_all.tbl CDD pfam12769 pfam12769 463694 PNTB_4TM 4TM region of pyridine nucleotide transhydrogenase, mitoch. PNTB_4TM is the region upstream of family PNTB, pfam02233, that carries four of this transporters transmembrane regions. PNTB is the beta-subunit of pyridine nucleotide transhydrogenase. This family forms part of the Proton-translocating Transhydrogenase (PTH) Family. 84 matched cddid_all.tbl CDD pfam12770 pfam12770 432771 CHAT CHAT domain. These proteins appear to be related to peptidases in peptidase clan CD that includes the caspases. This domain has been termed the CHAT domain for Caspase HetF Associated with Tprs. This family has been identified as a sister group to the separins. 287 matched cddid_all.tbl CDD pfam12771 pfam12771 463695 SusD-like_2 Starch-binding associating with outer membrane. SusD is a secreted starch-binding protein with an N-terminal lipid tail that allows it to associate with the outer membrane. 415 matched cddid_all.tbl CDD pfam12772 pfam12772 463696 GHBP Growth hormone receptor binding. Growth hormone receptor binding protein is produced either by proteolysis of the GHR (growth hormone receptor) at the cell surface thereby releasing its extracellular domain, the GHBP (growth hormone-binding protein), or, in rodents, by alternative processing of the GHR transcript. The sheddase proteolytic enzyme responsible for the cleavage is TACE (tumour necrosis factor-alpha-converting enzyme). Growth hormone (GH) binding to GH receptor (GHR) is the initial step that leads to the physiological functions of the hormone. The biological effects of GHBP are determined by the serum levels of growth hormone (GH), which can vary. Low levels of GH can result in a dwarf phenotype and have been positively correlated with an increased life expectancy. High levels of GH can lead to gigantism or a clinical syndrome termed acromegaly and have been implicated in diabetic eye and kidney damage. 303 matched cddid_all.tbl CDD pfam12773 pfam12773 432773 DZR Double zinc ribbon. This family consists of a pair of zinc ribbon domains. 45 matched cddid_all.tbl CDD pfam12774 pfam12774 463697 AAA_6 Hydrolytic ATP binding site of dynein motor region. This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities: AAA1-AAA6). This is the first site (out of four nucleotide binding sites in the dynein motor) where the movement depends on ATP hydrolysis. When this site is nucleotide free or bound to ADP, the microtubule binding domain (MTBD) binds to the microtubule and the linker adopts the straight post-power-stroke conformation. Upon ATP binding and hydrolysis, the MTBD detaches from the microtubule and the linker is primed into the pre-power-stroke conformation. Dynein's AAA+ domains are each divided into an alpha/beta large subdomain designated with an L and and alpha small subdomains designated with an S. This is the AAA1 large (AAA1L) subdomain with the accompanying small subdomain (AAA1S). AAA1L, AAA1S and AAA2L enclose ADP.vanadate (ADP.Vi, ATP-hydrolysis transition state analogue). The AAA1L sensor-I loop, which varies in position depending on dynein's nucleotide state, swings in to contact AAA2L forming the important AAA1 nucleotide-binding site. 327 matched cddid_all.tbl CDD pfam12775 pfam12775 463698 AAA_7 P-loop containing dynein motor region. This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities (AAA1-AAA6). This is the third nucleotide binding sites in the dynein motor. However, AAA3 has lost the catalytic residues necessary for ATP hydrolysis (the Walker B glutamate, the arginine finger, sensor-I and sensor-II motifs). 179 matched cddid_all.tbl CDD pfam12776 pfam12776 432776 Myb_DNA-bind_3 Myb/SANT-like DNA-binding domain. This presumed domain appears to be related to other Myb/SANT like DNA binding domains. In particular pfam10545 seems most related. This family is greatly expanded in plants and appears in several proteins annotated as transposon proteins. 96 matched cddid_all.tbl CDD pfam12777 pfam12777 463699 MT Microtubule-binding stalk of dynein motor. the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component. 344 matched cddid_all.tbl CDD pfam12778 pfam12778 432777 PXPV PXPV repeat (3 copies). This short repeat is found in multiple copies in a variety of Burkholderia proteins. The function of this region is unknown. 22 matched cddid_all.tbl CDD pfam12779 pfam12779 463700 WXXGXW WXXGXW repeat (2 copies). This short repeat contains the motif WXXGXW where X can be any amino acid. It is generally found in 2-5 copies in short secreted bacterial proteins. Its precise function is as yet unknown, but evidence suggests that members of this family are important for the function of specific sub-types of two-partner secretion systems. 26 matched cddid_all.tbl CDD pfam12780 pfam12780 463701 AAA_8 P-loop containing dynein motor region D4. The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor. 259 matched cddid_all.tbl CDD pfam12781 pfam12781 463702 AAA_9 ATP-binding dynein motor region. This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities (AAA1-AAA6). This is the fifth AAA+ domain subdomain AAA5S. Structural analysis reveal that it is the coiled-coil buttress interface. The relative movement of AAA5S together with the stalk (AAA4S), is coupled to rearrangements in the AAA+ ring. Closure of the AAA1 site and the rigid body movement of AAA2-AAA4 force the AAA4/AAA5 interface to close and the AAA6L subdomain to rotate towards the ring centre. The AAA5S subdomain rotates as a unit together with AAA6L, and this movement pulls the buttress relative to the stalk. 222 matched cddid_all.tbl CDD pfam12782 pfam12782 432781 Innate_immun Invertebrate innate immunity transcript family. The immune response of the purple sea urchin appears to be more complex than previously believed in that it uses immune-related gene families homologous to vertebrate Toll-like and NOD/NALP-like receptor families as well as C-type lectins and a rudimentary complement system. In addition, the species also produces this unusual family of mRNAs, also known as 185/333, which is strongly upregulated in response to pathogen challenge. 291 matched cddid_all.tbl CDD pfam12783 pfam12783 463703 Sec7_N Guanine nucleotide exchange factor in Golgi transport N-terminal. The full-length Sec7 functions proximally in the secretory pathway as a protein binding scaffold for the coat protein complexes COPII-COPI. The COPII-COPI-protein switch is necessary for maturation of the vesicular-tubular cluster, VTC, intermediate compartments for Golgi compartment biogenesis. This N-terminal domain however does not appear to be binding either of the COP or the ARF. 154 matched cddid_all.tbl CDD pfam12784 pfam12784 432783 PDDEXK_2 PD-(D/E)XK nuclease family transposase. Members of this family belong to the PD-(D/E)XK nuclease superfamily. These proteins are transposase proteins. 228 matched cddid_all.tbl CDD pfam12785 pfam12785 463704 VESA1_N Variant erythrocyte surface antigen-1. This family represents the N-terminal of the variant erythrocyte surface antigen 1, versions a and b, of Babesia. Babesia bovis is a tick-borne, intra-erythrocytic, protozoal parasite of cattle that shares many lifestyle parallels with the most virulent of the human malarial parasites, Plasmodium falciparum. Babesia uses antigenic variation to establish consistent infections of long duration. The two variants of VESA1, a and b, are expressed from different but closely related genes, and variation is achieved through the involvement of a segmental gene conversion mechanism and low-frequency epigenetic in situ switching of transcriptional activity from the VESA1 gene-pair to a possible other gene pair. 461 matched cddid_all.tbl CDD pfam12786 pfam12786 193262 GBV-C_env GB virus C genotype envelope. This the envelope protein from the ssRNA GB virus genotype C. 413 matched cddid_all.tbl CDD pfam12787 pfam12787 463705 EcsC EcsC protein family. Proteins in this family are related to EcsC from B. subtilis. This protein is found in an operon with EcsA and EcsB which are components of an ABC transport system. The function of this protein is unknown. 245 matched cddid_all.tbl CDD pfam12788 pfam12788 463706 YmaF YmaF family. This family of proteins contain 6 HXH motifs and is named after the B. subtilis YmaF protein. It seems likely that these are involved in metal binding. The function of this protein is unknown. 97 matched cddid_all.tbl CDD pfam12789 pfam12789 463707 PTR Phage tail repeat like. This family largely contains proteins from the eukaryote Trichomonas vaginalis. These proteins contain multiple HXH repeats. Some proteins in this family are annotated as having phage tail repeats. The function of this family is unknown. 60 matched cddid_all.tbl CDD pfam12790 pfam12790 432786 T6SS-SciN Type VI secretion lipoprotein, VasD, EvfM, TssJ, VC_A0113. One of the virulence mechanisms of E coli is the production of toxins which it produces from dedicated machineries called secretion systems. Seven secretion systems have been described, which assemble from 3 to up to more than 20 subunits. These secretion systems derive from or have co-evolved with bacterial organelles such as ABC transporters (type I), type IV pili (type 2), flagella (type 3), or conjugative machines (type IV). The type VI secretion system (T6SS) is present in most pathogens that have contact with animals, plants, or humans. SciN is a lipoprotein tethered to the outer membrane and expressed in the periplasm of E coli and is essential for T6S-dependent secretion of the Hcp-like SciD protein and for biofilm formation. 120 matched cddid_all.tbl CDD pfam12791 pfam12791 463708 RsgI_N Anti-sigma factor N-terminus. The heat shock genes in B. subtilis can be classified into several groups according to their regulation, and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes. Regulation of sigma factor I is carried out by RsgI from the same operon, and this N-terminal cytoplasmic portion of RsgI ('upstream' of the single transmembrane helix) has been shown to interact directly with Sigma-I. 53 matched cddid_all.tbl CDD pfam12792 pfam12792 463709 CSS-motif CSS motif domain associated with EAL. This family with its characteriztic highly conserved CSS sequence motif is found N-terminal to the EAL, pfam00563, domain in many cyclic diguanylate phosphodiesterases. 209 matched cddid_all.tbl CDD pfam12793 pfam12793 432788 SgrR_N Sugar transport-related sRNA regulator N-term. Small, non-coding RNA molecules play important regulatory roles in a variety of physiological processes in bacteria. SgrR_N is the N-terminus of a family of proteins which regulate the transcription of these sRNAs, in particular SgrS. SgrR_N contains a helix-turn-helix motif characteriztic of winged-helix DNA-binding transcriptional regulators. SgrS is a small RNA required for recovery from glucose-phosphate stress in bacteria. In examining the regulation of sgrR expression it was found that SgrR negatively auto-regulates its own transcription in the presence and absence of stress, and thus SgrR coordinates the response to glucose-phosphate stress by binding specifically to sgrS promoter DNA. 115 matched cddid_all.tbl CDD pfam12794 pfam12794 432789 MscS_TM Mechanosensitive ion channel inner membrane domain 1. The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this domain is one of the inner membrane domains. 332 matched cddid_all.tbl CDD pfam12795 pfam12795 432790 MscS_porin Mechanosensitive ion channel porin domain. The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this MscS_porin is towards the N-terminal of the molecules. The high concentration of negative charges at the extracellular entrance of the pore helps select the cations for efflux. 238 matched cddid_all.tbl CDD pfam12796 pfam12796 463710 Ank_2 Ankyrin repeats (3 copies). 91 matched cddid_all.tbl CDD pfam12797 pfam12797 463711 Fer4_2 4Fe-4S binding domain. This superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. 22 matched cddid_all.tbl CDD pfam12798 pfam12798 463712 Fer4_3 4Fe-4S binding domain. This superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. 15 matched cddid_all.tbl CDD pfam12799 pfam12799 463713 LRR_4 Leucine Rich repeats (2 copies). Leucine rich repeats are short sequence motifs present in a number of proteins with diverse functions and cellular locations. These repeats are usually involved in protein-protein interactions. Each Leucine Rich Repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine Rich Repeats are often flanked by cysteine rich domains. 44 matched cddid_all.tbl CDD pfam12800 pfam12800 463714 Fer4_4 4Fe-4S binding domain. This superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. 17 matched cddid_all.tbl CDD pfam12801 pfam12801 432796 Fer4_5 4Fe-4S binding domain. Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. 48 matched cddid_all.tbl CDD pfam12802 pfam12802 432797 MarR_2 MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif. 60 matched cddid_all.tbl CDD pfam12803 pfam12803 289567 G-7-MTase mRNA (guanine-7-)methyltransferase (G-7-MTase). The Sendai virus RNA-dependent RNA polymerase complex, which consists of L and P proteins, participates in the synthesis of viral mRNAs that possess a methylated cap structure. The N-terminal of the L protein acts as the RNA-dependent RNA polymerase part of the molecule, family Paramyx_RNA_pol, pfam00946. This domain is the C-terminal part of the L protein and it catalyzes cap methylation through its mRNA (guanine-7-)methyltransferase (G-7-MTase) activity. 317 matched cddid_all.tbl CDD pfam12804 pfam12804 463715 NTP_transf_3 MobA-like NTP transferase domain. This family includes the MobA protein (Molybdopterin-guanine dinucleotide biosynthesis protein A). The family also includes a wide range of other NTP transferase domain. 159 matched cddid_all.tbl CDD pfam12805 pfam12805 432799 FUSC-like FUSC-like inner membrane protein yccS. This family has similarities to the fusaric acid resistance protein family. The proteins are lodged in the inner membrane. 284 matched cddid_all.tbl CDD pfam12806 pfam12806 463716 Acyl-CoA_dh_C Acetyl-CoA dehydrogenase C-terminal like. this domain would appear to be the very C-terminal region of many bacterial acetyl-CoA dehydrogenases. 126 matched cddid_all.tbl CDD pfam12807 pfam12807 463717 eIF3_p135 Translation initiation factor eIF3 subunit 135. Translation initiation factor eIF3 is a multi-subunit protein complex required for initiation of protein biosynthesis in eukaryotic cells. The complex promotes ribosome dissociation, the binding of the initiator methionyl-tRNA to the 40 S ribosomal subunit, and mRNA recruitment to the ribosome. The protein product from TIF31 genes in yeast is p135 which associates with the eIF3 but does not seem to be necessary for protein translation initiation. 168 matched cddid_all.tbl CDD pfam12808 pfam12808 315477 Mto2_bdg Micro-tubular organizer Mto1 C-term Mto2-binding region. The C-terminal region of the micro-tubular organizer protein 1 (mto1) is the binding domain for attachment to Mto2p.The full-length Mto1 protein is required for microtubule nucleation from non-spindle pole body MTOCs in fission yeast. The interaction of Mto2p with this region of Mto1 is critical for anchoring the cytokinetic actin ring to the medial region of the cell and for proper coordination of mitosis with cytokinesis. 52 matched cddid_all.tbl CDD pfam12809 pfam12809 403881 Metallothi_Euk2 Eukaryotic metallothionein. This is a family of eukaryotic metallothioneins. 69 matched cddid_all.tbl CDD pfam12810 pfam12810 403882 Gly_rich Glycine rich protein. This family of proteins is greatly expanded in Trichomonas vaginalis. The proteins are composed of several glycine rich motifs interspersed through the sequence. Although many proteins have been annotated by similarity in the family these annotations given the biased composition of the sequences these are unlikely to be functionally relevant. 257 matched cddid_all.tbl CDD pfam12811 pfam12811 432802 BaxI_1 Bax inhibitor 1 like. The Bax-inhibitor-1 region of the receptor molecules is conserved from bacteria to humans. 234 matched cddid_all.tbl CDD pfam12812 pfam12812 372324 PDZ_1 PDZ-like domain. PDZ domains are found in diverse signalling proteins in bacteria, yeasts, plants, insects and vertebrates. this is a family of PDZ-like domains from bacteria, plants and fungi. 78 matched cddid_all.tbl CDD pfam12813 pfam12813 432803 XPG_I_2 XPG domain containing. This family is largely of fungal proteins and is related to the XP-G protein family. 249 matched cddid_all.tbl CDD pfam12814 pfam12814 403884 Mcp5_PH Meiotic cell cortex C-terminal pleckstrin homology. The PH domain of these largely fungal proteins is necessary for the cortical localization of the protein during meiosis, since the overall function of the protein is to anchor dynein at the cell cortex during the horsetail phase. During prophase I of fission yeast, horsetail nuclear movement occurs, and this starts when all the telomeres become bundled at the spindle pole body - SPB. Subsequent to this, the nucleus undergoes a dynamic oscillation, resulting in elongated nuclear morphology. Horsetail nuclear movement is thought to be predominantly due to the pulling of astral microtubules that link the SPB to cortical microtubule-attachment sites at the opposite end of the cell; the pulling force is believed to be provided by cytoplasmic dynein and dynactin. 119 matched cddid_all.tbl CDD pfam12815 pfam12815 372327 CTD Spt5 C-terminal nonapeptide repeat binding Spt4. The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteriztic TPA motif. 71 matched cddid_all.tbl CDD pfam12816 pfam12816 463718 Vps8 Golgi CORVET complex core vacuolar protein 8. Vps8 is one of the Golgi complex components necessary for vacuolar sorting. Eukaryotic cells contain a highly dynamic endo-membrane system, in which individual organelles keep their identity despite continuous vesicle generation and fusion. Vesicles that bud from a donor membrane are targeted and delivered to each individual organelle, where they release their cargo after fusion with the acceptor membrane. Vps8 is the core component of the endosomal tethering complex CORVET (class C core vacuole/endosome tethering). Vps8 co-operates with Vps21-GTP to mediate endosomal clustering in a reaction that is dependent on Vps3. Vps8 is the only CORVET subunit that is enriched on late endosomes, suggesting that it is a marker for the maturation of late endosomes. Late endosomes form intralumenal vesicles, and the resulting multivesicular bodies fuse with the vacuole to release their cargoes. 194 matched cddid_all.tbl CDD pfam12818 pfam12818 289579 Tegument_dsDNA dsDNA viral tegument protein. This is a family of tegument proteins from double-stranded DNA herpesvirus and related viral species. 277 matched cddid_all.tbl CDD pfam12819 pfam12819 432805 Malectin_like Malectin-like domain. Malectin is a membrane-anchored protein of the endoplasmic reticulum that recognizes and binds Glc2-N-glycan. The domain is found on a number of plant receptor kinases and is distantly related to malectin domains. 330 matched cddid_all.tbl CDD pfam12820 pfam12820 463719 BRCT_assoc Serine-rich domain associated with BRCT. This domain is found on BRCA1 proteins. 164 matched cddid_all.tbl CDD pfam12821 pfam12821 432807 ThrE_2 Threonine/Serine exporter, ThrE. ThrE_2 is a family of membrane proteins involved in the export of threonine and serine. L-threonine, L-serine are both substrates for the exporter. The exporter exhibits nine-ten predicted transmembrane-spanning helices with long charged C and N termini and an amphipathic helix present within the N terminus. L-Threonine can be made by the amino acid-producing bacterium Corynebacterium glutamicum, but the potential for amino acid formation can be considerably improved by reducing its intracellular degradation into glycine and increasing its export by this exporter. Members of the family are found in Bacteria, Archaea, and the fungal kingdoms, and the family can exist either as a single long polypeptide chain or as two short polypeptides. All family members show an extended hydrophilic N-terminal domain with weak sequence similarity to portions of hydrolases (proteases, peptidases, and glycosidases); this suggests that since this region is cytoplasmic to the membrane it may be generating the transport substrate, so may imply that threonine may not be the primary substrate and the ThrE has a subsidiary function. 129 matched cddid_all.tbl CDD pfam12822 pfam12822 432808 ECF_trnsprt ECF transporter, substrate-specific component. Energy-coupling factor (ECF) transporters consist of a substrate-specific component (known as the S component), and an energy-coupling module. The substrate-binding component is a small integral membrane protein which captures specific substrates and forms an active transporter in the presence of the energy-coupling AT module. 157 matched cddid_all.tbl CDD pfam12823 pfam12823 432809 DUF3817 Domain of unknown function (DUF3817). This domain is of unknown function. It is sometimes found adjacent to pfam07690 and pfam03176 which are both transporter domains. 89 matched cddid_all.tbl CDD pfam12824 pfam12824 432810 MRP-L20 Mitochondrial ribosomal protein subunit L20. This family is the essential mitochondrial ribosomal protein subunit L20 of fungi. 161 matched cddid_all.tbl CDD pfam12825 pfam12825 463720 DUF3818 Domain of unknown function in PX-proteins (DUF3818). This domain is found on proteins carrying a PX domain. Its function is unknown. 333 matched cddid_all.tbl CDD pfam12826 pfam12826 432812 HHH_2 Helix-hairpin-helix motif. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain. 64 matched cddid_all.tbl CDD pfam12827 pfam12827 403894 Peroxin-22 Peroxisomal biogenesis protein family. Peroxin-22 is a integral peroxisomal membrane protein family. The N-terminus is in the matrix and the C-terminus is in the cytosol. The N-terminus carries a 25-amino acid peroxisome membrane-targeting signal. It interacts with the ubiquitin-conjugating peripheral peroxisomal membrane enzyme Pex4p anchoring it at the peroxisomal membrane. Both Pex proteins are involved at the same stage of peroxisome biogenesis. 109 matched cddid_all.tbl CDD pfam12828 pfam12828 432813 PXB PX-associated. This domain is associated with the PX domain. 131 matched cddid_all.tbl CDD pfam12829 pfam12829 463721 Mhr1 Transcriptional regulation of mitochondrial recombination. This family is involved in the transcriptional regulation of recombination in the mitochondria, 83 matched cddid_all.tbl CDD pfam12830 pfam12830 463722 Nipped-B_C Sister chromatid cohesion C-terminus. This domain lies towards the C-terminus of nipped-B or sister chromatid cohesion proteins. 180 matched cddid_all.tbl CDD pfam12831 pfam12831 432816 FAD_oxidored FAD dependent oxidoreductase. This family of proteins contains FAD dependent oxidoreductases and related proteins. 420 matched cddid_all.tbl CDD pfam12832 pfam12832 432817 MFS_1_like MFS_1 like family. This family contains proteins related to the MFS superfamily. 362 matched cddid_all.tbl CDD pfam12833 pfam12833 432818 HTH_18 Helix-turn-helix domain. 81 matched cddid_all.tbl CDD pfam12834 pfam12834 432819 Phage_int_SAM_2 Phage integrase, N-terminal. This is a family of DNA-binding prophage integrases. It is found largely in Proteobacteria. 91 matched cddid_all.tbl CDD pfam12835 pfam12835 432820 Integrase_1 Integrase. This is a family of DNA-binding prophage integrases found in Proteobacteria. 149 matched cddid_all.tbl CDD pfam12836 pfam12836 463723 HHH_3 Helix-hairpin-helix motif. The HhH domain is a short DNA-binding domain. 62 matched cddid_all.tbl CDD pfam12837 pfam12837 432822 Fer4_6 4Fe-4S binding domain. This superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. 24 matched cddid_all.tbl CDD pfam12838 pfam12838 463724 Fer4_7 4Fe-4S dicluster domain. Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters. 51 matched cddid_all.tbl CDD pfam12840 pfam12840 432824 HTH_20 Helix-turn-helix domain. This domain represents a DNA-binding Helix-turn-helix domain found in transcriptional regulatory proteins. 61 matched cddid_all.tbl CDD pfam12841 pfam12841 463725 YvrJ YvrJ protein family. This family of short proteins are related to B. subtilis YvrJ protein. None of the members of this family have been functionally characterized. 35 matched cddid_all.tbl CDD pfam12842 pfam12842 463726 DUF3819 CCR4-Not complex, Not1 subunit, domain of unknown function DUF3819. This is an uncharacterized domain that is found on the CCR4-Not complex component Not1. Not1 is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID. 143 matched cddid_all.tbl CDD pfam12843 pfam12843 463727 QSregVF_b Putative quorum-sensing-regulated virulence factor. QSregVF_b is a family of short Pseudomonas proteins that are potential virulence factors. The structure of UniProtKB:Q9HY15 a secreted protein has been solved and deposited as PDB:3npd, from pfam13652. It is predicted that these two adjacent proteins form a single transcriptional unit based on the prediction that together they interact with their adjacent protein PotD, which is the putrescine-binding periplasmic protein in the polyamine uptake system comprising PotABCD. These two adjacent proteins are predicted to be quroum-sensing-regulated virulence factors. 66 matched cddid_all.tbl CDD pfam12844 pfam12844 463728 HTH_19 Helix-turn-helix domain. Members of this family contains a DNA-binding helix-turn-helix domain. This family contains many example antitoxins from bacterial toxin-antitoxin systems. These antitoxins are likely to be DNA-binding domains. 64 matched cddid_all.tbl CDD pfam12845 pfam12845 463729 TBD TBD domain. The Tbk1/Ikki binding domain (TBD) is a 40 amino acid domain able to bind kinases, has been found to be essential for poly(I:C)-induced IRF activation. The domain is found in SINTBAD, TANK and NAP1 protein. This domain is predicted to form an a-helix with residues essential for kinase binding clustering on one side. 56 matched cddid_all.tbl CDD pfam12846 pfam12846 315512 AAA_10 AAA-like domain. This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins, including VirB4 components of the Type IV secretory pathway and conjugal transfer protein TrbE. This entry includes the arcaheal Vir4/HerA homolog CedB, a membrane-bound protein that is highly induced upon UV treatment and essential for DNA transfer between Sulfolobus cells. 362 matched cddid_all.tbl CDD pfam12847 pfam12847 463730 Methyltransf_18 Methyltransferase domain. Protein in this family function as methyltransferases. 151 matched cddid_all.tbl CDD pfam12848 pfam12848 463731 ABC_tran_Xtn ABC transporter. This domain is an extension of some members of pfam00005 and other ABC-transporter families. 85 matched cddid_all.tbl CDD pfam12849 pfam12849 432831 PBP_like_2 PBP superfamily domain. This domain belongs to the periplasmic binding protein superfamily. 267 matched cddid_all.tbl CDD pfam12850 pfam12850 432832 Metallophos_2 Calcineurin-like phosphoesterase superfamily domain. Members of this family are part of the Calcineurin-like phosphoesterase superfamily. 150 matched cddid_all.tbl CDD pfam12851 pfam12851 372343 Tet_JBP Oxygenase domain of the 2OGFeDO superfamily. A double-stranded beta helix (DSBH) fold domain of the 2-oxoglutarate (2OG)-Fe(II)-dependent dioxygenase (2OGFeDO) superfamily found in various eukaryotes, bacteria and bacteriophages. Members of this family catalyze nucleic acid modifications, such as thymidine hydroxylation during base J synthesis in kinetoplastids, and the conversion of 5 methyl-cytosine (5-mC) to 5-hydroxymethyl-cytosine (hmC), or further oxidation to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Metazoan TET proteins contain a cysteine-rich region inserted into the core of the DSBH fold. Vertebrate TET proteins are oncogenes that are mutated in various myeloid cancers. Fungal and algal versions of this family are linked to a predicted transposase and show lineage-specific expansions. 166 matched cddid_all.tbl CDD pfam12852 pfam12852 432833 Cupin_6 Cupin. This is a family of bacterial and eukaryotic proteins that belong to the Cupin superfamily. Some of the proteins in this family are annotated as being members of the AraC family of transcription factors, in which case this domain corresponds to the ligand binding domain. 184 matched cddid_all.tbl CDD pfam12853 pfam12853 372344 NADH_u_ox_C C-terminal of NADH-ubiquinone oxidoreductase 21 kDa subunit. This family is the C-terminal domain of NADH-ubiquinone oxidoreductase 21 kDa subunits from fungi. 89 matched cddid_all.tbl CDD pfam12854 pfam12854 403914 PPR_1 PPR repeat. This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. The exact function is not known. 34 matched cddid_all.tbl CDD pfam12855 pfam12855 432834 Ecl1 ECL1/2/3 zinc binding proteins. This family is involved in the chronological life-span of S. cerevisiae. Over-expression leads to an extended viability of wild-type strains, indicating a role in regulation. There are four cysteine residues conserved in the N-terminal region involved in zinc binding and have been shown to be essential for protein functions. Ecl1-family proteins are essential for sexual development caused by zinc depletion in S. pombe. They are also important for cellular response to zinc limitation. 172 matched cddid_all.tbl CDD pfam12856 pfam12856 403916 ANAPC9 Anaphase-promoting complex subunit 9. Apc9 is one of the subunits of the anaphase-promoting complex, or cyclosome, which is essential for regulating entry into anaphase and exit from mitosis. The APC is a ubiquitin-protein ligase complex. All APC subunits are members of the cullin family proteins, which bind to a ring-finger subunit via a conserved cullin domain. The APC is made up of four parts, the third of which is a tetratricopeptide repeat arm (TPR) that contains Apc9. 112 matched cddid_all.tbl CDD pfam12857 pfam12857 432835 TOBE_3 TOBE-like domain. The TOBE domain (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum and sulfate. Found in ABC transporters immediately after the ATPase domain. 59 matched cddid_all.tbl CDD pfam12859 pfam12859 463732 ANAPC1 Anaphase-promoting complex subunit 1 WD40 beta-propeller domain. Apc1 is the largest of the subunits of the anaphase-promoting complex or cyclosome. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes. Infection of human fibroblasts with human cytomegalovirus (HCMV) leads to cell cycle dysregulation, which is associated with the inactivation of the anaphase-promoting complex. Apc1 consists of a N-terminal WD40 beta-propeller domain, a middle domain (Mid-N), a PC domain and a C-terminal domain (Mid-C) that coalesces with Mid-N to form Apc1Mid which connects Apc1-WD40 with Apc1-PC and comprises an alpha-solenoid capped by a beta-sandwich. The N-terminal domain is essential for APC/C catalytic activity as it mediates the coactivator-induced conformational change of the APC/C which promotes UbcH10 binding. 295 matched cddid_all.tbl CDD pfam12860 pfam12860 432837 PAS_7 PAS fold. The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs. The PAS fold appears in archaea, eubacteria and eukarya. 115 matched cddid_all.tbl CDD pfam12861 pfam12861 403920 zf-ANAPC11 Anaphase-promoting complex subunit 11 RING-H2 finger. Apc11 is one of the subunits of the anaphase-promoting complex or cyclosome. The APC subunits are cullin family proteins with ubiquitin ligase activity. Polyubiquitination marks proteins for degradation by the 26S proteasome and is carried out by a cascade of enzymes that includes ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and is responsible for recruiting E2s to the APC and for mediating the subsequent transfer of ubiquitin to APC substrates in vivo. In Saccharomyces cerevisiae this RING-H2 finger protein defines the minimal ubiquitin ligase activity of the APC, and the integrity of the RING-H2 finger is essential for budding yeast cell viability. 85 matched cddid_all.tbl CDD pfam12862 pfam12862 432838 ANAPC5 Anaphase-promoting complex subunit 5. Apc5 is a subunit of the anaphase-promoting complex/cyclosome (APC/C) which is a multi-subunit ubiquitin ligase that mediates the proteolysis of cell cycle proteins in mitosis and G1. Apc5, although it does not harbour a classical RNA binding domain, Apc5 binds the poly(A) binding protein (PABP), which directly binds the internal ribosome entry site (IRES) of growth factor 2 mRNA. PABP was found to enhance IRES-mediated translation, whereas Apc5 over-expression counteracted this effect. In addition to its association with the APC/C complex, Apc5 binds much heavier complexes and co-sediments with the ribosomal fraction. The N-terminus of Afi1 serves to stabilize the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC. This region of the Apc5 member proteins carries a TPR-like motif. 91 matched cddid_all.tbl CDD pfam12863 pfam12863 403922 DUF3821 Domain of unknown function (DUF3821). This is a domain largely confined to sequences from Methanomicrobiales found on putative lipases. The function is not known. 202 matched cddid_all.tbl CDD pfam12864 pfam12864 432839 DUF3822 Protein of unknown function (DUF3822). This is a family of uncharacterized bacterial proteins. However, structural-similarity searches indicate the family takes on an actin-like ATPase fold. 241 matched cddid_all.tbl CDD pfam12866 pfam12866 432840 DUF3823 Protein of unknown function (DUF3823) N-terminal domain. This is a family of uncharacterized proteins from Bacteroidetes. This domain has a beta-sandwich prealbumin-like fold. 92 matched cddid_all.tbl CDD pfam12867 pfam12867 463733 DinB_2 DinB superfamily. The DinB family are an uncharacterized family of potential enzymes. The structure of these proteins is composed of a four helix bundle. 128 matched cddid_all.tbl CDD pfam12868 pfam12868 372351 DUF3824 Domain of unknwon function (DUF3824). This is a repeating domain found in fungal proteins. It is proline-rich, and the function is not known. 145 matched cddid_all.tbl CDD pfam12869 pfam12869 378982 tRNA_anti-like tRNA_anti-like. This is a family of bacterial, archeael and viral proteins that is related to the tRNA_anti family pfam01336. The major characteriztic of families like tRNA_anti is their OB-fold, and many of them bind DNA. 162 matched cddid_all.tbl CDD pfam12870 pfam12870 432842 DUF4878 Domain of unknown function (DUF4878). This is a family of putative lipoproteins from bacteria. The family is probably related to the NTF2-like transpeptidase family. 111 matched cddid_all.tbl CDD pfam12871 pfam12871 463734 PRP38_assoc Pre-mRNA-splicing factor 38-associated hydrophilic C-term. This domain is a hydrophilic region found at the C-terminus of plant and metazoan pre-mRNA-splicing factor 38 proteins. The function is not known. 98 matched cddid_all.tbl CDD pfam12872 pfam12872 463735 OST-HTH OST-HTH/LOTUS domain. A predicted RNA-binding domain found in insect Oskar and vertebrate TDRD5/TDRD7 proteins that nucleate or organize structurally related ribonucleoprotein (RNP) complexes, the polar granule and nuage, is poorly understood. The domain adopts the winged helix-turn- helix fold and bind RNA with a potential specificity for dsRNA.In eukaryotes this domain is often combined in the same polypeptide with protein-protein- or lipid- interaction domains that might play a role in anchoring these proteins to specific cytoskeletal structures. Thus, proteins with this domain might have a key role in the recognition and localization of dsRNA, including miRNAs, rasiRNAs and piRNAs hybridized to their targets. In other cases, this domain is fused to ubiquitin-binding, E3 ligase and ubiquitin-like domains indicating a previously under-appreciated role for ubiquitination in regulating the assembly and stability of nuage-like RNP complexes. Both bacteria and eukaryotes encode a conserved family of proteins that combines this predicted RNA-binding domain with a previously uncharacterized RNase domain belonging to the superfamily that includes the 5'->3' nucleases, PIN and NYN domains. 64 matched cddid_all.tbl CDD pfam12873 pfam12873 432844 DUF3825 Domain of unknown function (DUF3825). Potential uncharacterized enzymatic domain associated with bacterial pfam12872 domains. Has conserved residues suggestive of an enzymatic role probably related to RNA metabolism. 233 matched cddid_all.tbl CDD pfam12874 pfam12874 463736 zf-met Zinc-finger of C2H2 type. This is a zinc-finger domain with the CxxCx(12)Hx(6)H motif, found in multiple copies in a wide range of proteins from plants to metazoans. Some member proteins, particularly those from plants, are annotated as being RNA-binding. 25 matched cddid_all.tbl CDD pfam12875 pfam12875 432846 DUF3826 Protein of unknown function (DUF3826). This is a putative sugar-binding family. 185 matched cddid_all.tbl CDD pfam12876 pfam12876 372355 Cellulase-like Sugar-binding cellulase-like. This is a putative cellulase family. The structure is a TIM-barrel. 355 matched cddid_all.tbl CDD pfam12877 pfam12877 463737 DUF3827 Domain of unknown function (DUF3827). This family contains the Swiss:Q9HCM3 protein which has been found to be fused fused to BRAF gene in many cases of pilocytic astrocytomas. The fusion is due mainly to a tandem duplication of 2 Mb at 7q34. Although nothing is known about the function of Swiss:Q9HCM3 protein, the BRAF protein is a well characterized oncoprotein. It is a serine/threonine protein kinase which is implicated in MAP/ERK signalling, a critical pathway for the regulation of cell division, differentiation and secretion. 677 matched cddid_all.tbl CDD pfam12878 pfam12878 432848 SICA_beta SICA extracellular beta domain. The SICA (schizont-infected cell agglutination) proteins of P. knowlesi, one of the variant antigen gene families, are associated with parasitic virulence. These proteins are comprised of multiple domains, with the extracellular domains occurring at different frequencies. There can be between 1 and 10 copies of this cysteine-rich domain. 174 matched cddid_all.tbl CDD pfam12879 pfam12879 432849 SICA_C SICA C-terminal inner membrane domain. The SICA (schizont-infected cell agglutination) proteins of P. knowlesi, one of the variant antigen gene families, are associated with parasitic virulence. These proteins are comprised of multiple domains, with the extracellular domains occurring at different frequencies. The C-terminal domain is thought to remain in the erythrocyte, found juxtaposition to the single transmembrane domain. To date, all full length proteins contain a single copy of this domain. 145 matched cddid_all.tbl CDD pfam12881 pfam12881 432850 NUT NUT protein. This family includes the NUT protein. The gene encoding for NUT protein (Nuclear Testis protein) is found fused to BRD3 or BRD4 genes, in some aggressive types of carcinoma, due to chromosomal translocations. Proteins of the BRD family contain two bromodomains that bind transcriptionally active chromatin through associations with acetylated histones H3 and H4. Such proteins are crucial for the regulation of cell cycle progression. On the other hand, little is known about NUT protein. NUT is known to have a Nuclear Export Sequence (NES) as well as a Nuclear localization Signal (NLS), both located towards the C-terminal end of the protein. A fused NUT-GFP protein showed either cytoplasmic or nuclear localization, suggesting that it is subject to nuclear/cytoplasmic shuttling. Consistent with this possibility, treatment with leptomycin B an inhibitor of CRM1-dependent nuclear export resulted in re-distribution of NUT-GFP to the nucleus. Inspection of NUT revealed a C-terminal sequence similar to known nuclear export sequences (NES) which are often regulated by phosphorylation. This family carries some natively unstructured sequence. 717 matched cddid_all.tbl CDD pfam12883 pfam12883 403935 DUF3828 Protein of unknown function (DUF3828). This is a family of bacterial proteins of unknown function. 122 matched cddid_all.tbl CDD pfam12884 pfam12884 463738 TORC_N Transducer of regulated CREB activity, N terminus. This family includes the N terminal region of TORC proteins. TORC (Transducer of regulated CREB activity) is a protein family of coactivators that enhances the activity of CRE-depended transcription via a phosphorylation-independent interaction with the bZIP DNA binding/dimerization domain of CREB (cAMP Response Element-Binding). The proteins display a highly conserved predicted N-terminal coiled-coil domain and an invariant sequence matching a protein kinase A (PKA) phosphorylation consensus sequence (RKXS). The coiled-coil structure interacts with the bZIP domain of CREB. This interaction may occur via ionic bonds because it is disrupted under high-salt conditions. In addition to CREB-binding, the N-terminal region plays a role in the tetramer formation of TORCs, but the physiological function of the multimeric complex has not been clarified yet. 63 matched cddid_all.tbl CDD pfam12885 pfam12885 463739 TORC_M Transducer of regulated CREB activity middle domain. This family includes the region between the N and C terminus of TORC proteins. TORC (Transducer of regulated CREB activity) is a protein family of coactivators that enhances the activity of CRE-depended transcription via a phosphorylation-independent interaction with the bZIP DNA binding/dimerization domain of CREB (cAMP Response Element-Binding). Although the C- and N- terminal domains of these proteins have been well characterized, no functional role has been assigned to the central region, yet. 154 matched cddid_all.tbl CDD pfam12886 pfam12886 463740 TORC_C Transducer of regulated CREB activity, C terminus. This family includes the C terminal region of TORC proteins. TORC (Transducer of regulated CREB activity) is a protein family of coactivators that enhances the activity of CRE-depended transcription via a phosphorylation-independent interaction with the bZIP DNA binding/dimerization domain of CREB (cAMP Response Element-Binding). The C terminus region is negatively charged, resembling the transcription activation domains. When this domain, from all three human TORC proteins, was expressed as fusion proteins with the DNA-binding domain of GAL4 (GAL4-BD), and tested for induction of a minimal promoter linked to GAL4-binding sites (UAS-GAL4), UAS-GAL4 was potently induced by GAL4-BD fusions containing the C-terminal portion of all three human TORCs. 75 matched cddid_all.tbl CDD pfam12887 pfam12887 432854 SICA_alpha SICA extracellular alpha domain. The SICA (schizont-infected cell agglutination) proteins of P. knowlesi, one of the variant antigen gene families, are associated with parasitic virulence. These proteins are comprised of multiple domains, with the extracellular domains occurring at different frequencies. This domain is typically found at the N-terminus, with 1 or 2 copies per protein. The domain is cysteine-rich domain and similar to pfam12878. 185 matched cddid_all.tbl CDD pfam12888 pfam12888 463741 Lipid_bd Lipid-binding putative hydrolase. This is a small family of lipid-binding proteins found in Bacteroidetes. 140 matched cddid_all.tbl CDD pfam12889 pfam12889 432856 DUF3829 Protein of unknown function (DUF3829). This is a small family of proteins from several bacterial species, whose function is not known. It may, however, be related to the GvpL_GvpF family of proteins, pfam06386. 283 matched cddid_all.tbl CDD pfam12890 pfam12890 315550 DHOase Dihydro-orotase-like. This is a small family of dihydro-orotase-like proteins from various bacteria. 142 matched cddid_all.tbl CDD pfam12891 pfam12891 432857 Glyco_hydro_44 Glycoside hydrolase family 44. This is a family of bacterial glycoside hydrolases formerly known as cellulase family J, and now known as Cel44A. It is one of the major enzymatic components of the cellulosome of Clostridium thermocellum strain F1 and of many other Firmicutes. 234 matched cddid_all.tbl CDD pfam12892 pfam12892 463742 FctA Spy0128-like isopeptide containing domain. The FCT and equivalent region genes of Streptococcus pyogenes and other related bacteria encode surface proteins that include fibronectin- and collagen-binding proteins and the serological markers known as T antigens. Some of these proteins give rise to pilus-like appendages. The FctA family is found in many Firmicutes and related bacteria. In S. pyogenes, the pili have a role in bacterial adherence and colonization of human tissues. Members of this family have a conserved N-terminal lysine and C-terminal asparagine that can form a covalent isopeptide bond. 107 matched cddid_all.tbl CDD pfam12893 pfam12893 432859 Lumazine_bd_2 Putative lumazine-binding. This is a family of uncharacterized proteins. However, the family belongs to the NTF2-like superfamily of various enzymes, and some of the members of the family are putative dehydrogenases. 116 matched cddid_all.tbl CDD pfam12894 pfam12894 403945 ANAPC4_WD40 Anaphase-promoting complex subunit 4 WD40 domain. Apc4 contains an N-terminal propeller-shaped WD40 domain.The N-terminus of Afi1 serves to stabilize the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC, 91 matched cddid_all.tbl CDD pfam12895 pfam12895 463743 ANAPC3 Anaphase-promoting complex, cyclosome, subunit 3. Apc3, otherwise known as Cdc27, is one of the subunits of the anaphase-promoting complex or cyclosome. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes. The protein members of this family contain TPR repeats just as those of Apc7 do, and it appears that these TPR units bind the C-termini of the APC co-activators CDH1 and CDC20. 82 matched cddid_all.tbl CDD pfam12896 pfam12896 463744 ANAPC4 Anaphase-promoting complex, cyclosome, subunit 4. Apc4 is one of the larger of the subunits of the anaphase-promoting complex or cyclosome. This family represents the long domain downstream of the WD40 repeat/s that are present on the Apc4 subunits. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes. Results in C.elegans show that the primary essential role of the spindle assembly checkpoint is not in the chromosome segregation process itself but rather in delaying anaphase onset until all chromosomes are properly attached to the spindle. the APC/C is likely to be required for all metaphase-to-anaphase transitions in a multicellular organizm. 203 matched cddid_all.tbl CDD pfam12897 pfam12897 403948 Asp_aminotransf Aspartate amino-transferase. These proteins catalyze the reversible transfer of an amino group from the amino acid substrate to an acceptor alpha-keto acid. They require pyridoxal 5'-phosphate (PLP) as a cofactor to catalyze this reaction. Trans-amination reactions are of central importance in amino acid metabolism and in links to carbohydrate and fat metabolism. This class of amino-transferases acts as dimers in a head-to-tail configuration. It has been demonstrated that these proteins are aspartate amino-transferases from Bacteria (Jansen, R.S. et al. Nat Commun 11, 1960 (2020)). 419 matched cddid_all.tbl CDD pfam12898 pfam12898 432862 Stc1 Stc1 domain. The domain contains 8 conserved cysteines that may bind to zinc. In S. pombe this protein acts as a protein linker which links the chromatin modifying CLRC complex to RNAi by tethering it to the RITS complex. The region is reported as a LIM domain here, but has a slightly different arrangement of its CxxC pairs from the Pfam LIM domain pfam00412, hence why it is not part of that family. The tandem zinc-finger structure could mediate protein-protein interactions. 78 matched cddid_all.tbl CDD pfam12899 pfam12899 432863 Glyco_hydro_100 Alkaline and neutral invertase. This is a family of bacterial and plant alkaline and neutral invertases, EC:3.2.1.26, previously known as Invertase_neut pfam04853. 429 matched cddid_all.tbl CDD pfam12900 pfam12900 432864 Pyridox_ox_2 Pyridoxamine 5'-phosphate oxidase. Pyridoxamine 5'-phosphate oxidase is a FMN flavoprotein that catalyzes the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP). This entry contains several pyridoxamine 5'-phosphate oxidases, and related proteins. 143 matched cddid_all.tbl CDD pfam12901 pfam12901 463745 SUZ-C SUZ-C motif. The SUZ-C domain is a conserved motif found in one or more copies in several RNA-binding proteins. It is always found at the C-terminus of the protein and appear to be required for localization of the protein to specific subcellular structures. It was first characterized in the C.elegans protein Szy-20 which localizes to the centrosome. It is widely distributed in eukaryotes. 33 matched cddid_all.tbl CDD pfam12902 pfam12902 403953 Ferritin-like Ferritin-like. This is a family of bacterial ferritin-like substances that also includes a C-terminal domain of VioB, polyketide synthase enzymes, that make up one of the key components of the violacein biosynthesis pathway. Violacein is a purple-coloured, broad-spectrum antibacterial pigment. 222 matched cddid_all.tbl CDD pfam12903 pfam12903 432866 DUF3830 Protein of unknown function (DUF3830). This is a family of bacterial and archaeal proteins, the structure for one of whose members has been characterized. PDB:3kop from Swiss:A0JVT3 probably adopts a new hexameric form compared to previous structures. The putative active is near the domain interface. 3kop is most closely related, structurally to PDB:1zx8, where the potential active site is located near residues E51 and Y53 (conserved in 1zx8). Beyond the two residues above, the other residues are not conserved. Also the shape of the active site differs from that of 1zx8. PDB:1zx8 belongs to family DUF369. pfam04126, which is part of the cyclophilin-like clan. 144 matched cddid_all.tbl CDD pfam12904 pfam12904 463746 Collagen_bind_2 Putative collagen-binding domain of a collagenase. This domain is likely to be the collagen-binding domain of a family of bacterial collagenase enzymes. It is the C-terminal part of the PDB:3kzs structure determined from Swiss:Q8A905 (information derived from TOPSAN). 92 matched cddid_all.tbl CDD pfam12905 pfam12905 432868 Glyco_hydro_101 Endo-alpha-N-acetylgalactosaminidase. Virulence of pathogenic organizms such as the Gram-positive Streptococcus pneumoniae is largely determined by the ability to degrade host glycoproteins and to metabolize the resultant carbohydrates. This family is the enzymatic region, EC:3.2.1.97, of the cell surface proteins that specifically cleave Gal-beta-1,3-GalNAc-alpha-Ser/Thr (T-antigen, galacto-N-biose), the core 1 type O-linked glycan common to mucin glycoproteins. This reaction is exemplified by the S. pneumoniae protein Swiss:B2DRU5, where Asp764 is the catalytic nucleophile-base and Glu796 the catalytic proton donor. 273 matched cddid_all.tbl CDD pfam12906 pfam12906 403957 RINGv RING-variant domain. 47 matched cddid_all.tbl CDD pfam12907 pfam12907 403958 zf-met2 Zinc-binding. This is small family of metazoan zinc-binding proteins. 38 matched cddid_all.tbl CDD pfam12910 pfam12910 403959 PHD_like Antitoxin of toxin-antitoxin, RelE / RelB, TA system. This domain appears to be the N-terminus of the RelB antitoxin of toxin-antitoxin stability system or prevent-host death system. Together RelE toxin and the RelB antitoxin form a non-toxic complex. Although toxin-antitoxin gene cassettes were first found in plasmids, it is clear that these loci are abundant in free-living prokaryotes, including many pathogenic bacteria, and these toxin-antitoxin loci provide a control mechanism that helps free-living prokaryotes cope with nutritional stress. 139 matched cddid_all.tbl CDD pfam12911 pfam12911 463747 OppC_N N-terminal TM domain of oligopeptide transport permease C. Oligopeptide permeases (Opp) have been identified in numerous gram-negative and -positive bacteria. These transport systems belong to the superfamily of highly conserved ATP-binding cassette transporters. Typically, Opp importers comprise a complex of five proteins. The oligopeptide-binding protein OppA is responsible for the capture of peptides from the external medium. Two integral highly hydrophobic membrane spanning proteins, OppB and OppC, form a channel through the membrane used for peptide translocation. This N-terminal domain appears to be the first TM domain of the molecule. 53 matched cddid_all.tbl CDD pfam12912 pfam12912 432870 N_NLPC_P60 NLPC_P60 stabilising domain, N term. This domain, at the N-terminus, appears to be the stabilising domain for the structure from Swiss:Q72DN3, PDB:3m1u, which is a four-domain protein. The next domain is an SH3b1, the third an SH3b2 and the last, the C-terminal region, the catalytic domain of the cysteine-peptidase type, ie family NLPC_P60, pfam00877 (details derived from TOPSAN). 107 matched cddid_all.tbl CDD pfam12913 pfam12913 432871 SH3_6 SH3 domain (SH3b1 type). This domain appears to be an SH3 domain of the SH3b1-type, and is just C-terminal to an N-terminal domain that is probably the stabilising domain for the structure from Swiss:Q72DN3, PDB:3m1u, which is a four-domain protein. The next domain is an SH3b2 and the last, the C-terminal region, is the catalytic domain of the cysteine-peptidase type, ie family NLPC_P60, pfam00877 (details derived from TOPSAN). 53 matched cddid_all.tbl CDD pfam12914 pfam12914 432872 SH3_7 SH3 domain of SH3b2 type. This domain appears to be an SH3 domain of the SH3b2-type, and is the second SH3 domain to be found, downstream of an N-terminal domain that is probably the stabilising domain, for the structure from Swiss:Q72DN3, PDB:3m1u, which is a four-domain protein. The last, the C-terminal region, is the catalytic domain of the cysteine-peptidase type, ie family NLPC_P60, pfam00877 (details derived from TOPSAN). 47 matched cddid_all.tbl CDD pfam12915 pfam12915 463748 DUF3833 Protein of unknown function (DUF3833). This is a family of uncharacterized proteins found in Proteobacteria. 163 matched cddid_all.tbl CDD pfam12916 pfam12916 315571 DUF3834 Protein of unknown function (DUF3834). This family is likely to be related to solute-binding lipo-proteins. 201 matched cddid_all.tbl CDD pfam12917 pfam12917 432874 YfbR-like 5'-deoxynucleotidase YfbR-like. This entry contains Escherichia coli (strain K12) YfbR. It a 5'-deoxynucleotidase that functions as a dCMP phosphohydrolase in a salvage pathway for the synthesis of dUMP in a dcd/deoA mutant. YfbR contains a conserved HD domain. YfbR has phosphatase activity with deoxyribonucleoside 5'-monophosphates and does not hydrolyze ribonucleotides or deoxyribonucloside 3'-monophosphates. Crystal structures of YfbR have been solved, it was suggested that the biological unit is a dimer. This family also includes phage HD domain-containing hydrolase-like enzymes, such as A0A2H5BHG9 and A0A2L0V156 from Acinetobacter phage SH-Ab15497, which are associated with PurZ, an enzyme that catalyzes the synthesis of diaminopurine (Z), a DNA modification that gives phages an advantage for evading host restriction enzymes activity. They have 2'-deoxyadenine 5'-triphosphate triphosphohydrolase (dATPase) activity and catalyze the hydrolysis of 2'-deoxyadenine 5'-triphosphate dATP to 2'-deoxyadenine (dA) and triphosphate. These enzymes are highly specific for dATP and also catalyze the hydrolysis of dADP and dAMP into dA, releasing pyrophosphate and phosphate, respectively. Thus, these dATPases facilitate the synthesis of Z-genome synthesis removing dATP and dADP from the nucleotide pool of the host. 182 matched cddid_all.tbl CDD pfam12918 pfam12918 403966 TcdB_N TcdB toxin N-terminal helical domain. This is a short helical bundle domain found associated with the catalytic domain of the TcdB toxin from C. difficile. The function of this domain is unknown, but it may be involved in substrate recognition. 66 matched cddid_all.tbl CDD pfam12919 pfam12919 372382 TcdA_TcdB TcdA/TcdB catalytic glycosyltransferase domain. This domain represents the N-terminal glycosyltransferase from a set of toxins found in some bacteria. This domain in TcdB glycosylates the host RhoA protein. 382 matched cddid_all.tbl CDD pfam12920 pfam12920 463749 TcdA_TcdB_pore TcdA/TcdB pore forming domain. This family represents the most conserved region within the C. difficile Toxin A and Toxin B pore forming region. 626 matched cddid_all.tbl CDD pfam12921 pfam12921 372384 ATP13 Mitochondrial ATPase expression. ATP13 is necessary for the expression of subunit 9 of mitochondrial ATPase. The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria. 114 matched cddid_all.tbl CDD pfam12922 pfam12922 463750 Cnd1_N non-SMC mitotic condensation complex subunit 1, N-term. The three non-SMC (structural maintenance of chromosomes) subunits of the mitotic condensation complex are Cnd1-3. The whole complex is essential for viability and the condensing of chromosomes in mitosis. This is the conserved N-terminus of the subunit 1. 164 matched cddid_all.tbl CDD pfam12923 pfam12923 432877 RRP7 Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain. RRP7 is an essential protein in yeast that is involved in pre-rRNA processing and ribosome assembly. It is speculated to be required for correct assembly of rpS27 into the pre-ribosomal particle. 119 matched cddid_all.tbl CDD pfam12924 pfam12924 463751 APP_Cu_bd Copper-binding of amyloid precursor, CuBD. This short domain, part of the extra-cellular N-terminus of the amyloid precursor protein, APP, can bind both copper and zinc, CuBD. The structure of Cu2+-bound CuBD reveals that the metal ligands are His147, His151, Tyr168 and two water molecules, which are arranged in a square pyramidal geometry. The structure of Cu+-bound CuBD is almost identical to the Cu2+-bound structure except for the loss of one of the water ligands. The geometry of the site is unfavourable for Cu+, thus providing a mechanism by which CuBD could readily transfer Cu ions to other proteins. 56 matched cddid_all.tbl CDD pfam12925 pfam12925 463752 APP_E2 E2 domain of amyloid precursor protein. The E2 domain is the largest of the conserved domains of the amyloid precursor protein. The structure of E2 consists of two coiled-coil sub-structures connected through a continuous helix, and bears an unexpected resemblance to the spectrin family of protein structures.E 2 can reversibly dimerize in solution, and the dimerization occurs along the longest dimension of the molecule in an antiparallel orientation, which enables the N-terminal substructure of one monomer to pack against the C-terminal substructure of a second monomer. The high degree of conservation of residues at the putative dimer interface suggests that the E2 dimer observed in the crystal could be physiologically relevant. Heparin sulfate proteoglycans, the putative ligands for the precursor present in extracellular matrix, bind to E2 at a conserved and positively charged site near the dimer interface. 190 matched cddid_all.tbl CDD pfam12926 pfam12926 432879 MOZART2 Mitotic-spindle organizing gamma-tubulin ring associated. FAM128A and FAM128B proteins have been re-named MOZART2A and B. The name MOZART is derived from letters of 'mitotic-spindle organizing proteins associated with a ring of gamma-tubulin'. This family operates as part of the gamma-tubulin ring complex, gamma-TuRC, one of the complexes necessary for chromosome segregation. This complex is located at centrosomes and mediates the formation of bipolar spindles in mitosis; it consists of six subunits. However, unlike the other four known subunits, the MOZART proteins, both 1 and 2, do not carry the conserved 'Spc97-Spc98' GCP domain, so the TUBCGP nomenclature cannot be used for it. The exact function of MOZART2 is not clear. 90 matched cddid_all.tbl CDD pfam12927 pfam12927 463753 DUF3835 Domain of unknown function (DUF3835). This is a C-terminal domain conserved in fungi. 73 matched cddid_all.tbl CDD pfam12928 pfam12928 463754 tRNA_int_end_N2 tRNA-splicing endonuclease subunit sen54 N-term. This is an N-terminal family of archaeal and metazoan sen54 proteins that forms one of the tRNA-splicing endonuclease subunits. 69 matched cddid_all.tbl CDD pfam12929 pfam12929 432882 Mid1 Stretch-activated Ca2+-permeable channel component. MID1 is a yeast Saccharomyces cerevisiae gene encoding a plasma membrane protein required for Ca2+ influx induced by the mating pheromone, alpha-factor. Mid1 protein plays a crucial role in supplying Ca2+ during the mating process. Mid1 is composed of 548-amino-acid residues with four hydrophobic regions named H1, H2, H3 and H4, and two cysteine-rich regions (C1 and C2) at the C-terminal. This family contains the H3, H4, C1 and C2 regions. suggesting that H1 is a signal sequence responsible for the alpha-factor-induced Mid1 delivery to the plasma membrane. The region from H1 to H3 is required for the localization of Mid1 in the plasma and ER membranes. Trafficking of Mid1-GFP to the plasma membrane is dependent on the N-glycosylation of Mid1 and the transporter protein Sec12. This findings suggests that the trafficking of Mid1-GFP to the plasma membrane requires a Sec12-dependent pathway from the ER to the Golgi, and that Mid1 is recruited via a Sec6- and Sec7-independent pathway from the Golgi to the plasma membrane. 429 matched cddid_all.tbl CDD pfam12930 pfam12930 432883 DUF3836 Family of unknown function (DUF3836). Family of uncharacterized proteins found in Bacteroidales species. 121 matched cddid_all.tbl CDD pfam12931 pfam12931 432884 Sec16_C Sec23-binding domain of Sec16. Sec16 is a multi-domain vesicle coat protein. The C-terminal region is the part that binds to Sec23, a COPII vesicle coat protein. This association is part of the transport vesicle coat structure. 279 matched cddid_all.tbl CDD pfam12932 pfam12932 432885 Sec16 Vesicle coat trafficking protein Sec16 mid-region. Sec16 is a multi-domain vesicle coat protein. This central region is the functional part of the molecules and thus is vital for the family's role in mediating the movement of protein-cargo between the organelles of the secretory pathway. 119 matched cddid_all.tbl CDD pfam12933 pfam12933 463755 FTO_NTD FTO catalytic domain. This domain is the catalytic AlkB-like domain from the FTO protein. This domain catalyzes a demethylase activity with a preference for 3-methylthymidine. 275 matched cddid_all.tbl CDD pfam12934 pfam12934 432887 FTO_CTD FTO C-terminal domain. This domain is found at the C-terminus of the FTO protein which was shown to be associated with increased BMI and obesity risk in humans. The N-terminal domain of this protein is a DNA demethylase and this domain is found to associate with the N-terminal domain in the crystal structure. This domain is alpha helical with three helices that form a bundle. 170 matched cddid_all.tbl CDD pfam12935 pfam12935 315590 Sec16_N Vesicle coat trafficking protein Sec16 N-terminus. Sec16 is a multi-domain vesicle coat protein. The overall function of Sec16 is in mediating the movement of protein-cargo between the organelles of the secretory pathway. Over-expression of truncated mutants of only the N-terminus are lethal, and this portion does not appear to be essential for function so may act as a stabilising region. 236 matched cddid_all.tbl CDD pfam12936 pfam12936 463756 Kri1_C KRI1-like family C-terminal. The yeast member of this family (Kri1p) is found to be required for 40S ribosome biogenesis in the nucleolus. This is the C-terminal domain of the family. 89 matched cddid_all.tbl CDD pfam12937 pfam12937 463757 F-box-like F-box-like. This is an F-box-like family. 45 matched cddid_all.tbl CDD pfam12938 pfam12938 432890 M_domain M domain of GW182. 243 matched cddid_all.tbl CDD pfam12939 pfam12939 432891 DUF3837 Domain of unknown function (DUF3837). A small, compact all-alpha helical domain of unknown function. This domain is currently only found in Clostridiales species. 92 matched cddid_all.tbl CDD pfam12940 pfam12940 315595 RAG1 Recombination-activation protein 1 (RAG1), recombinase. This family is one of the two different components of the RAG1-RAG2 V(D)J recombinase complex. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS). Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerizes with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerization and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008. 653 matched cddid_all.tbl CDD pfam12941 pfam12941 289693 HCV_NS5a_C HCV NS5a protein C-terminal region. This is a family of proteins found in the hepatitis C virus. This family contains the C-terminal region of the NS5A protein. CC The molecular function of the non-structural 5a protein is uncertain. The NS5a protein is phosphorylated when expressed in mammalian cells. It is thought to interact with the ds RNA dependent (interferon inducible) kinase PKR. 242 matched cddid_all.tbl CDD pfam12942 pfam12942 289694 Archaeal_AmoA Archaeal ammonia monooxygenase subunit A (AmoA). This is an archeael family that contains ammonia monooxygenase subunit A. Ammonia monooxygenase is an enzyme that oxidizes ammonia to nitrite and nitrate, thus playing a significant role in the nitrogen cycle. Ammonia-oxidising archaea (AOA) are widespread in marine environments. 183 matched cddid_all.tbl CDD pfam12943 pfam12943 372401 DUF3839 Protein of unknown function (DUF3839). This is a family of uncharacterized proteins that are found in Trichomonas. 242 matched cddid_all.tbl CDD pfam12944 pfam12944 403983 HAV_VP Hepatitis A virus viral protein VP. This is a family of the viral protein found in hepatitis A viruses. HAV is unique among picornaviruses in targeting the liver. 169 matched cddid_all.tbl CDD pfam12945 pfam12945 463758 PilZNR Flagellar protein YcgR. This domain is found N terminal to pfam07238. Proteins which contain YcgR domains are known to interact with the flagellar switch-complex proteins FliG and FliM. This interaction results in a reduction of torque generation and induces CCW motor bias. This family contains members not captured by pfam07317. This domain has a beta-barrel fold PilZ domains and lack the C-terminal alpha- helix. 81 matched cddid_all.tbl CDD pfam12946 pfam12946 403985 EGF_MSP1_1 MSP1 EGF domain 1. This EGF-like domain is found at the C-terminus of the malaria parasite MSP1 protein. MSP1 is the merozoite surface protein 1. This domain is part of the C-terminal fragment that is proteolytically processed from the the rest of the protein and is left attached to the surface of the invading parasite. 37 matched cddid_all.tbl CDD pfam12947 pfam12947 463759 EGF_3 EGF domain. This family includes a variety of EGF-like domain homologs. This family includes the C-terminal domain of the malaria parasite MSP1 protein. 36 matched cddid_all.tbl CDD pfam12948 pfam12948 403987 MSP7_C MSP7-like protein C-terminal domain. MSP7 is a protein family the malaria parasite that has been found to be associated with processed fragments from the MSP1 protein in a complex involved in red blood cell invasion. 125 matched cddid_all.tbl CDD pfam12949 pfam12949 403988 HeH HeH/LEM domain. This is a HeH domain. HeH domains form helix-extended loop-helix (HeH) structures. It was demonstrated that the DNA-binding activity of the HEH/LEM domain assists the association of proteins with the centromeric region. This domain is closely related to pfam03020 and pfam02037. 35 matched cddid_all.tbl CDD pfam12950 pfam12950 403989 TaqI_C TaqI-like C-terminal specificity domain. This domain is found at the C-terminus of the TaqI protein and is involved in DNA-binding and substrate recognition. 119 matched cddid_all.tbl CDD pfam12951 pfam12951 463760 PATR Passenger-associated-transport-repeat. This Autotransporter-associated beta strand repeat model represents a core 32-residue region of a class of bacterial protein repeat found in one to 30 copies per protein. Most proteins with a copy of this repeat have domains associated with membrane autotransporters (pfam03797). The repeats occur with a periodicity of 60 to 100 residues. A pattern of sequence conservation is that every second residue is well-conserved across most of the domain. These repeats as likely to have a beta-helical structure. This repeat plays a role in the efficient transport of autotransporter virulence factors to the bacterial surface during growth and infection. The repeat is always associated with the passenger domain of the autotransporter. For these reasons it has been coined the Passenger-associated Transport Repeat (PATR). The mechanism by which the PATR motif promotes transport is uncertain but it is likely that the conserved glycines (see HMM Logo) are required for flexibility of folding and that this folding drives secretion. Autotransporters that contain PATR(s) associate with distinct virulence traits such as subtilisin (S8) type protease domains and polymorphic outer-membrane protein repeats, whilst SPATE (S6) type protease and lipase-like autotransporters do not tend to contain PATR motifs. 28 matched cddid_all.tbl CDD pfam12952 pfam12952 432895 DUF3841 Domain of unknown function (DUF3841). This presumed domain is around 190 amino acids in length. As yet no function has been given to any member of the family. 178 matched cddid_all.tbl CDD pfam12953 pfam12953 432896 DUF3842 Domain of unknown function (DUF3842). This short protein is found mainly in firmicute bacteria. It is functionally uncharacterized. 130 matched cddid_all.tbl CDD pfam12954 pfam12954 432897 DUF3843 Protein of unknown function (DUF3843). A family of uncharacterized proteins found by clustering human gut metagenomic sequences. 411 matched cddid_all.tbl CDD pfam12955 pfam12955 432898 DUF3844 Domain of unknown function (DUF3844). This presumed domain is found in fungal species. It contains 8 largely conserved cysteine residues. This domain is found in proteins that are thought to be found in the endoplasmic reticulum. 104 matched cddid_all.tbl CDD pfam12956 pfam12956 403995 DUF3845 Domain of Unknown Function with PDB structure. Member PDB:3GF6 has statistically significant similarity to TNF-like jelly roll fold may indicate an immunomodulatory function or a bioadhesion role 221 matched cddid_all.tbl CDD pfam12957 pfam12957 432899 DUF3846 Domain of unknown function (DUF3846). A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This domain is found associated with an pfam07275 like domain. This suggests that this family may also be involved in evading host restriction. 92 matched cddid_all.tbl CDD pfam12958 pfam12958 432900 DUF3847 Protein of unknown function (DUF3847). A family of uncharacterized proteins found by clustering human gut metagenomic sequences. 81 matched cddid_all.tbl CDD pfam12959 pfam12959 403998 DUF3848 Protein of unknown function (DUF3848). A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This domain frequently seen with DUF3849. 93 matched cddid_all.tbl CDD pfam12960 pfam12960 432901 DUF3849 Protein of unknown function (DUF3849). A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This domain frequently seen with DUF3848. 123 matched cddid_all.tbl CDD pfam12961 pfam12961 432902 DUF3850 Domain of unknown function (DUF3850). The search results from NCBI sequence alignment indicates a conserved domain belonging to ASCH superfamily. Dali searching results show that the protein is a structurally similar to the PUA domain, suggesting it may be involved in RNA recognition. It has been reported that the deletion of PUA genes results in impaired growth (RluD) and competitive disadvantage (TruB) in Escherichia coli. Suggestions have been put forward that, apart from their usual catalytic role, certain PUS enzymes (e.g. TruB) may also act as chaperones for RNA folding. The interface interaction indicates that the biomolecule of protein NP_809782.1 should be a dimer. 77 matched cddid_all.tbl CDD pfam12962 pfam12962 289714 DUF3851 Protein of unknown function (DUF3851). A family of uncharacterized proteins found by clustering human gut metagenomic sequences. 126 matched cddid_all.tbl CDD pfam12963 pfam12963 404001 DUF3852 Protein of unknown function (DUF3852). A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This domain frequently seen with DUF3848. 107 matched cddid_all.tbl CDD pfam12964 pfam12964 432903 DUF3853 Protein of unknown function (DUF3853). A family of uncharacterized proteins found by clustering human gut metagenomic sequences. 97 matched cddid_all.tbl CDD pfam12965 pfam12965 432904 DUF3854 Domain of unknown function (DUF3854). A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This domain is likely to be related to the Toprim domain. 124 matched cddid_all.tbl CDD pfam12966 pfam12966 432905 AtpR N-ATPase, AtpR subunit. Membrane protein with three predicted transmembrane segments, two of which contain conserved Arg residues. AtpR genes are found in the N-ATPase (archaeal-type F1-Fo-ATPase) operons and are predicted to interact with the conserved Glu/Asp residues in the c subunits, regulating the assembly and/or function of the membrane-embedded ring of 'c' (proteolipid) subunits (pfam00137). 86 matched cddid_all.tbl CDD pfam12967 pfam12967 404004 DUF3855 Domain of Unknown Function with PDB structure (DUF3855). Family based on orphan protein (TM0875) from Thermotoga maritima that has been structurally determined as PDB:1022. The TM0875 gene of Thermotoga maritima encodes a hypothetical protein NP_228683 of unknown function. Analysis of TM0875 genomic context reveals the presence of MMT1 (a predicted Co/Zn/Cd cation transporter) and an inactive homolog of metal-dependent proteases. 1O22 shows weak structural similarity with the phosphoribosylformylglycinamidine synthase 1t4a (Dali Z-scr=4.6), the yggU protein (PDB structure:1n91; with DALI Z-scr=3), and with the thioesterase superfamily member (PDB structure 2cy9 - found using FATCAT), even though they have very low sequence identity. 157 matched cddid_all.tbl CDD pfam12968 pfam12968 463761 DUF3856 Domain of Unknown Function (DUF3856). TPR-like protein. The 2hr2 structure belongs to the SCOP all alpha class, TPR-like superfamily, CT2138-like family. A DALI search gives hits with the putative peptidyl-prolyl isomerase 2fbn (Z=16), the SGTA protein (Z=16), the PLCR protein 2qfc (Z=16), a putative FK506-binding protein (PDB:1qz2-A; DALI Z-score 15.3; RMSD 2.9; 16% sequence identity within 132 superimposed residues), and with the tetratricopeptide repeats of the protein phosphatase 5 (PDB:2bug; DALI Z-score 15.1; RMSD 2.5; 19% sequence identity within 117 superimposed residues). 142 matched cddid_all.tbl CDD pfam12969 pfam12969 432907 DUF3857 Domain of Unknown Function with PDB structure (DUF3857). This family is based on the first domain of the PDB structure PDB:3KD4(residues 1-228). It is structurally similar to domains in other hydrolases, eg. M1 family aminopeptidase (3ebi, Z=10, rmsd 3.6A for 152 CA, seq id 12%), despite lack of any significant sequence similarity. 131 matched cddid_all.tbl CDD pfam12970 pfam12970 404007 DUF3858 Domain of Unknown Function with PDB structure (DUF3858). This family is based on the third domain of the PDB structure 3KD4(residues 410-525). It is structurally similar to part of neuropilin-2 (Z=4.6, rmsd 3.6A for 83 CA, 7% seq id). This domain and the second domain appears to be part of peptide-n-glycanase (1x3w, 2g9f). 116 matched cddid_all.tbl CDD pfam12971 pfam12971 463762 NAGLU_N Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain. Alpha-N-acetylglucosaminidase, a lysosomal enzyme required for the stepwise degradation of heparan sulfate. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterized by neurological dysfunction but relatively mild somatic manifestations. The structure shows that the enzyme is composed of three domains. This N-terminal domain has an alpha-beta fold. 81 matched cddid_all.tbl CDD pfam12972 pfam12972 463763 NAGLU_C Alpha-N-acetylglucosaminidase (NAGLU) C-terminal domain. Alpha-N-acetylglucosaminidase, a lysosomal enzyme required for the stepwise degradation of heparan sulfate. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterized by neurological dysfunction but relatively mild somatic manifestations. The structure shows that the enzyme is composed of three domains. This C-terminal domain has an all alpha helical fold. 258 matched cddid_all.tbl CDD pfam12973 pfam12973 463764 Cupin_7 ChrR Cupin-like domain. Members of this family are part of the cupin superfamily. This family includes the transcriptional activator ChrR. 91 matched cddid_all.tbl CDD pfam12974 pfam12974 432911 Phosphonate-bd ABC transporter, phosphonate, periplasmic substrate-binding protein. This is a family of periplasmic proteins which are part of the transport system for alkylphosphonate uptake. 243 matched cddid_all.tbl CDD pfam12975 pfam12975 432912 DUF3859 Domain of unknown function (DUF3859). This short domain is functionally uncharacterized. 127 matched cddid_all.tbl CDD pfam12976 pfam12976 315622 DUF3860 Domain of Unknown Function with PDB structure (DUF3860). A protein family created to cover PDB:2OD5. 2OD5 is a hypothetical protein (JCVI_PEP_1096688149193) from an environmental metagenome (unidentified marine microbe). 92 matched cddid_all.tbl CDD pfam12977 pfam12977 432913 DUF3861 Domain of Unknown Function with PDB structure (DUF3861). The 3cjl structure is likely a representative of a new fold with some resemblance to 3-helical bundle folds such as the serum albumin-like fold of SCOP. No significant hits reported by a Dali search. This protein is the first structural representative of a small (about 60 proteins) family of proteins that are found among proteo- and enterobacteria (REF http://www.topsan.org/Proteins/JCSG/3CJL). 90 matched cddid_all.tbl CDD pfam12978 pfam12978 432914 DUF3862 Domain of Unknown Function with PDB structure (DUF3862). PDB:3D4E shared structural similarity to beta-lactamase inhibitory proteins (BLIP) which already include 1XXM, 1S0W, 1JTG, 2G2U, 2G2W, 2B5R, and 3due. All of structures are involved in beta-lactamase inhibitor complex. (REF http://www.topsan.org/Proteins/JCSG/3d4e) 159 matched cddid_all.tbl CDD pfam12979 pfam12979 432915 DUF3863 Domain of Unknown Function with PDB structure (DUF3863). Domain based on 1-364 domain of PDB:3LM3 which is encoded by the BDI_3119 gene from Parabacteroides distasonis atcc 8503. 349 matched cddid_all.tbl CDD pfam12980 pfam12980 289731 DUF3864 Domain of Unknown Function with PDB structure (DUF3864). Domain based on 366-449 domain of PDB:3LM3 which is encoded by the BDI_3119 gene from Parabacteroides distasonis atcc 8503. 80 matched cddid_all.tbl CDD pfam12981 pfam12981 432916 DUF3865 Domain of Unknown Function with PDB structure (DUF3865). Family based of PDB:3B5P encoded by ZP_00108531 from nitrogen-fixing cyanobacterium Nostoc punctiforme pcc 73102 is a CADD-like protein of unknown function. Superposition between protein structures encoded by CT610 from Chlamydia trachomatis (PDB code 1rwc), pyrroloquinolinquinone synthase C (PqqC, PDB code 1otv) and ZP_00108531 revealed that putative active sites in CT610 and ZP_00108531 are identical. ( REF: http://www.topsan.org/Proteins/JCSG/3B5P). 224 matched cddid_all.tbl CDD pfam12982 pfam12982 432917 DUF3866 Protein of unknown function (DUF3866). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 352 and 374 amino acids in length. 317 matched cddid_all.tbl CDD pfam12983 pfam12983 404015 DUF3867 Protein of unknown function (DUF3867). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 190 amino acids in length. 185 matched cddid_all.tbl CDD pfam12984 pfam12984 432918 DUF3868 Domain of unknown function, B. Theta Gene description (DUF3868). Based on Bacteroides thetaiotaomicron gene BT_1065, a putative uncharacterized protein As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), It appears to be upregulated in the presence of host or other bacterial species vs when in culture. 109 matched cddid_all.tbl CDD pfam12985 pfam12985 432919 DUF3869 Domain of unknown function (DUF3869). A family based on the N-terminal domain of 3KOG, which shows weak but consistent remote homology with adhesive families such as immunoglobulins and cadherins, suggesting it might form an attachment module. 101 matched cddid_all.tbl CDD pfam12986 pfam12986 432920 DUF3870 Domain of unknown function (DUF3870). A family based on the C-terminal domain of 3KOG which shows structural similarity to pore-forming proteins, suggesting it may have a lytic function. 94 matched cddid_all.tbl CDD pfam12987 pfam12987 432921 DUF3871 Domain of unknown function, B. Theta Gene description (DUF3871). Based on Bacteroides thetaiotaomicron gene BT_2984, a putative uncharacterized protein As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231). It appears to be upregulated in the presence of host or other bacterial species vs when in culture. 318 matched cddid_all.tbl CDD pfam12988 pfam12988 432922 TraQ_transposon TraQ conjugal transfer protein. TraQ is a conjugative transposon lipoprotein. It is a component of the type IV secretion system. TraQ belongs to the immunoglobulin superfamily and shares structural similarity to other proteins involved in pili production for bacterial cell attachment. It appears to be upregulated in the presence of host or other bacterial species vs when in culture. 115 matched cddid_all.tbl CDD pfam12989 pfam12989 432923 DUF3873 Domain of unknown function, B. Theta Gene description (DUF3873). Based on Bacteroides thetaiotaomicron gene BT_2286, a putative uncharacterized protein. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or other bacterial species vs when in culture. 68 matched cddid_all.tbl CDD pfam12990 pfam12990 432924 DUF3874 Domain of unknonw function from B. Theta Gene description (DUF3874). Based on Bacteroides thetaiotaomicron gene BT_4228, a putative uncharacterized protein As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), It appears to be upregulated in the presence of host or other bacterial species vs when in culture. 71 matched cddid_all.tbl CDD pfam12991 pfam12991 432925 DUF3875 Domain of unknown function, B. Theta Gene description (DUF3875). Based on Bacteroides thetaiotaomicron gene BT_4769, a conserved protein found in a conjugate transposon. As seem in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231). It appears to be upregulated in the presence of host or other bacterial species vs when in culture. 50 matched cddid_all.tbl CDD pfam12992 pfam12992 432926 DUF3876 Domain of unknown function, B. Theta Gene description (DUF3876). Based on Bacteroides thetaiotaomicron gene BT_0092, a conserved protein found in a conjugate transposon. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or other bacterial species vs when in culture. 91 matched cddid_all.tbl CDD pfam12993 pfam12993 463765 DUF3877 Domain of unknown function, E. rectale Gene description (DUF3877). Based on Eubacterium rectale gene EUBREC_0237. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14737), it appears to be upregulated in the presence of Bacteroides thetaiotaomicron vs when isolated in culture. 173 matched cddid_all.tbl CDD pfam12994 pfam12994 404025 DUF3878 Domain of unknown function, E. rectale Gene description (DUF3878). Based on Eubacterium rectale gene EUBREC_0973. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14737). it appears to be upregulated in the presence of Bacteroides thetaiotaomicron vs when isolated in culture. 300 matched cddid_all.tbl CDD pfam12995 pfam12995 289746 DUF3879 Domain of unknown function, E. rectale Gene description (DUF3879). Based on Eubacterium rectale gene EUBREC_1343. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14737), it appears to be upregulated in the presence of Bacteroides thetaiotaomicron vs when isolated in culture. 179 matched cddid_all.tbl CDD pfam12996 pfam12996 463766 DUF3880 DUF based on E. rectale Gene description (DUF3880). Based on Eubacterium rectale gene EUBREC_3218. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14737), It appears to be upregulated in the presence of Bacteroides thetaiotaomicron vs when isolated in culture. 77 matched cddid_all.tbl CDD pfam12997 pfam12997 463767 DUF3881 Domain of unknown function, E. rectale Gene description (DUF3881). Based on Eubacterium rectale gene EUBREC_3695. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE14737), it appears to be upregulated in the presence of Bacteroides thetaiotaomicron vs when isolated in culture. 283 matched cddid_all.tbl CDD pfam12998 pfam12998 463768 ING Inhibitor of growth proteins N-terminal histone-binding. Histones undergo numerous post-translational modifications, including acetylation and methylation, at residues which are then probable docking sites for various chromatin remodelling complexes. Inhibitor of growth proteins (INGs) specifically bind to residues that have been thus modified. INGs carry a well-characterized C-terminal PHD-type zinc-finger domain, binding with lysine 4-tri-methylated histone H3 (H3K4me3), as well as this N-terminal domain that binds unmodified H3 tails. Although these two regions can bind histones independently, together they increase the apparent association of the ING for the H3 tail. 100 matched cddid_all.tbl CDD pfam12999 pfam12999 372423 PRKCSH-like Glucosidase II beta subunit-like. The sequences found in this family are similar to a region found in the beta-subunit of glucosidase II, which is also known as protein kinase C substrate 80K-H (PRKCSH). The enzyme catalyzes the sequential removal of two alpha-1,3-linked glucose residues in the second step of N-linked oligosaccharide processing. The beta subunit is required for the solubility and stability of the heterodimeric enzyme, and is involved in retaining the enzyme within the endoplasmic reticulum. 176 matched cddid_all.tbl CDD pfam13000 pfam13000 372424 Acatn Acetyl-coenzyme A transporter 1. The mouse Acatn is a 61 kDa hydrophobic protein with six to 10 transmembrane domains. It appears to promote 9-O-acetylation in gangliosides. 543 matched cddid_all.tbl CDD pfam13001 pfam13001 463769 Ecm29 Proteasome stabilizer. The proteasome consists of two subunits, and the capacity of the proteasome to degrade protein depends crucially on the interaction between these two subunits. This interaction is affected by a wide range of factors including metabolites, such as ATP, and proteasome-associated proteins such as Ecm29. Ecm29 stabilizes the interaction between the two subunits. 496 matched cddid_all.tbl CDD pfam13002 pfam13002 404030 LDB19 Arrestin_N terminal like. This is a family of proteins related to the Arrestin_N terminal family. 183 matched cddid_all.tbl CDD pfam13004 pfam13004 432932 BACON Putative binding domain, N-terminal. The BACON (Bacteroidetes-Associated Carbohydrate-binding Often N-terminal) domain is an all-beta domain found in diverse architectures, principally in combination with carbohydrate-active enzymes and proteases. These architectures suggest a carbohydrate-binding function which is also supported by the nature of BACON's few conserved amino-acids. The phyletic distribution of BACON and other data tentatively suggest that it may frequently function to bind mucin. Further work with the characterized structure of a member of glycoside hydrolase family 5 enzyme, PDB:3ZMR, has found no evidence for carbohydrate-binding for this domain. 61 matched cddid_all.tbl CDD pfam13005 pfam13005 463770 zf-IS66 zinc-finger binding domain of transposase IS66. This is a zinc-finger region of the N-terminus of the insertion element IS66 transposase. 46 matched cddid_all.tbl CDD pfam13006 pfam13006 432934 Nterm_IS4 Insertion element 4 transposase N-terminal. This family represents the N-terminal region of proteins carrying the transposase enzyme, DDE_Tnp_1 (that was Transposase_11), pfam01609, at the C-terminus. The full-length members are Insertion Element 4, IS4. Within the collection of E.coli strains, ECOR, the number of IS4 elements varies from zero to 14, with an average of 5 copies/strain. 95 matched cddid_all.tbl CDD pfam13007 pfam13007 463771 LZ_Tnp_IS66 Transposase C of IS166 homeodomain. This is a leucine-zipper-like or homeodomain-like region of transposase TnpC of insertion element IS66. 67 matched cddid_all.tbl CDD pfam13008 pfam13008 372427 zf-Paramyx-P Zinc-binding domain of Paramyxoviridae V protein. The Paramyxoviridae, which include such respiroviruses as para-influenzae and measles, produce phosphoproteins - protein P - that are integral to the polymerase transcription-replication complex. Protein P consists of two functionally distinct moieties, an N-terminal PNT, and a C-terminal PCT. The P gene region transcribes proteins from all three ORFs, and the V protein consists of the PNT moiety and a more C-terminal 2-zinc-binding domain. This conserved region consists of the two-zinc-binding section sandwiched between beta sheets 6 and 7 of the overall V protein. It is the binding of this core domain of V protein with the DDB1 protein (part of the ubiquitin-ligase complex) of eukaryotes which represents the key element of the virus-host protein interaction. In the Henipavirus family which includes Nipah and Hendra viruses, the V protein is able to block IFN (interferon) signalling by preventing IFN-induced STAT phosphorylation and nuclear translocation. The P gene of morbillivirus is co-transcriptionally edited leading to a V protein being produced. 45 matched cddid_all.tbl CDD pfam13009 pfam13009 432936 Integrase_2 Putative integrase. This family represents putative integrases found in association with IS elements. 329 matched cddid_all.tbl CDD pfam13010 pfam13010 289758 pRN1_helical Primase helical domain. This alpha helical domain is found in a set of bacterial plasmid replication proteins. The domain is found to the C-terminus of the primase/polymerase domain. Mutants of this domain are defective in template binding, dinucleotide formation and conformation change prior to DNA extension. 138 matched cddid_all.tbl CDD pfam13011 pfam13011 289759 LZ_Tnp_IS481 leucine-zipper of insertion element IS481. This is the upstream region of the conjoined ORF AB of insertion element 481. The significance of IS481 in the detection of Bordetella pertussis is discussed in. The B portion of the ORF AB carries the transposase activity in family rve, pfam00665. 85 matched cddid_all.tbl CDD pfam13012 pfam13012 463772 MitMem_reg Maintenance of mitochondrial structure and function. This is C-terminal to the Mov24 region of the yeast proteasomal subunit Rpn11 and seems likely to regulate the mitochondrial fission and tubulation processes, ie the outer mitochondrial membrane proteins. This function appears to be unrelated to the proteasome activity of the N-terminal region. 72 matched cddid_all.tbl CDD pfam13013 pfam13013 404037 F-box-like_2 F-box-like domain. The F-box domain has a role in mediating protein-protein interactions in a variety of contexts, such as polyubiquitination, transcription elongation, centromere binding and translational repression. 107 matched cddid_all.tbl CDD pfam13015 pfam13015 404038 PRKCSH_1 Glucosidase II beta subunit-like protein. The sequences found in this family are similar to a region found in the beta-subunit of glucosidase II, which is also known as protein kinase C substrate 80K-H (PRKCSH). The enzyme catalyzes the sequential removal of two alpha-1,3-linked glucose residues in the second step of N-linked oligosaccharide processing. The beta subunit is required for the solubility and stability of the heterodimeric enzyme, and is involved in retaining the enzyme within the endoplasmic reticulum. The beta-subunit confers substrate specificity for di- and monoglucosylated glycans on the glucose-trimming activity of the alpha-subunit. 154 matched cddid_all.tbl CDD pfam13016 pfam13016 404039 Gliadin Cys-rich Gliadin N-terminal. This is a cysteine-rich N-terminal region of gliadin and avenin plant proteins. The exact function is not known. 75 matched cddid_all.tbl CDD pfam13017 pfam13017 404040 Maelstrom "piRNA pathway germ-plasm component. Maelstrom is a germ-plasm component protein, that is shown to be functionally involved in the piRNA pathway. It is conserved throughout Eukaryota, though it appears to have been lost from all examined teleost fish species. The domain architecture shows that it is coupled with several DNA- and RNA- related domains such as HMG box, SR-25-like and HDAC_interact domains. Sequence analysis and fold recognition have found a distant similarity between Maelstrom domain and the DnaQ 3'-5' exonuclease family with the RNase H fold (Exonuc_X-T, pfam00929); notably, that the Maelstrom domains from basal eukaryotes contain the conserved 3'-5' exonuclease active site residues (Asp-Glu-Asp-His-Asp, DEDHD). However, the animal and some amoeba maelstrom contain another set of conserved residues (Glu-His-His-Cys-His-Cys, EHHCHC). This evolutionary link together with structural examinations leads to the hypothesis that Maelstrom domains may have a potential nuclease-transposase activity or RNA-binding ability that may be implicated in piRNA biogenesis. A protein function evolution mode, namely ""active site switch"", has been proposed, in which the amoeba Maelstrom domains are the possible evolutionary intermediates due to their harbouring of the specific characteriztics of both 3'-5' exonuclease and Maelstrom domains." 212 matched cddid_all.tbl CDD pfam13018 pfam13018 463773 ESPR Extended Signal Peptide of Type V secretion system. This conserved domain is called ESPR for Extended Signal Peptide Region. It is present at the N-terminus of the signal peptides of proteins belonging to the Type V secretion systems, including the autotransporters (T5aSS), TpsA exoproteins of the two-partner system (T5bSS) and trimeric autotransporters (TAAs). So far, the ESPR is present only in Gram-negative bacterial proteins originating from the classes Beta- and Gamma-proteobacteria. ESPR severely impairs inner membrane translocation, suggesting that it adopts a particular conformation or it interacts with a cytoplasmic or inner membrane co-factor, prior to exportation. Deletion of ESPR causes mis-folding of the TAAs passenger domain in the periplasm, substantially impairing its translocation across the outer membrane. 50 matched cddid_all.tbl CDD pfam13019 pfam13019 372432 Sde2_N_Ubi Silencing defective 2 N-terminal ubiquitin domain. Sde2 (silencing defective 2) is a ubiquitin-fold-containing splicing regulator that supports splicing of selected pre-mRNAs in an intron-specific manner in Schizosaccharomyces pombe. Both fission yeast and human Sde2 are translated as inactive precursor proteins harbouring the ubiquitin-fold domain linked through an invariant GGKGG motif to a C-terminal domain. The Sde2 protein has a ubiquitin-fold at its N-terminus, which must be cleaved by the ubiquitin-specific proteases (USPs) Ubp5 and Ubp15. After cleavage, the C-terminal domain of Sde2, which starts with a lysine, gets incorporated into the spliceosome. This entry represents the ubiquitin fold N-terminal domain found in Sde2 proteins. 165 matched cddid_all.tbl CDD pfam13020 pfam13020 463774 NOV_C Protein NO VEIN, C-terminal. This domain of unknown function is found at the C-terminal of Protein NO VEIN from Arabidopsis, a protein essential for cell fate determination during embryogenesis. It mediates this process through an auxin-dependent pathway. This domain is also found in some restriction endonucleases. 91 matched cddid_all.tbl CDD pfam13021 pfam13021 404043 DUF3885 Domain of unknown function (DUF3885). A putative Rac prophage DNA binding protein. This domain family is found in bacteria, and is approximately 40 amino acids in length. There is a conserved YDDRG sequence motif. There is a single completely conserved residue D that may be functionally important. 38 matched cddid_all.tbl CDD pfam13022 pfam13022 404044 HTH_Tnp_1_2 Helix-turn-helix of insertion element transposase. This is a family of largely phage proteins which are likely to be a helix-turn-helix insertion elements. 122 matched cddid_all.tbl CDD pfam13023 pfam13023 432939 HD_3 HD domain. HD domains are metal dependent phosphohydrolases. 163 matched cddid_all.tbl CDD pfam13024 pfam13024 338588 DUF3884 Protein of unknown function (DUF3884). This family of proteins is functionally uncharacterized. However several proteins are annotated as Tagatose 1,6-diphosphate aldolase, but evidence to support this could not be found. This family of proteins is found in bacteria. Proteins in this family are typically between 61 and 106 amino acids in length. There are two completely conserved residues (Y and F) that may be functionally important. 73 matched cddid_all.tbl CDD pfam13025 pfam13025 315655 DUF3886 Protein of unknown function (DUF3886). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two completely conserved L residues that may be functionally important. 68 matched cddid_all.tbl CDD pfam13026 pfam13026 432940 DUF3887 Protein of unknown function (DUF3887). This domain family is found in bacteria and archaea, and is approximately 90 amino acids in length. 91 matched cddid_all.tbl CDD pfam13027 pfam13027 463775 DUF3888 Protein of unknown function (DUF3888). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 111 and 149 amino acids in length. 87 matched cddid_all.tbl CDD pfam13028 pfam13028 404048 DUF3889 Protein of unknown function (DUF3889). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. There are two completely conserved residues (A and Y) that may be functionally important. 84 matched cddid_all.tbl CDD pfam13029 pfam13029 289775 DUF3890 Domain of unknown function (DUF3890). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 70 amino acids in length. 84 matched cddid_all.tbl CDD pfam13030 pfam13030 432941 DUF3891 Protein of unknown function (DUF3891). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 250 amino acids in length. 215 matched cddid_all.tbl CDD pfam13031 pfam13031 463776 DUF3892 Protein of unknown function (DUF3892). DUF3892 is related to the truncated RNaseH fold-containing ribosome hibernation factors. Predicted to function as a possible conflict effector domain at the ribosome, based on comparable genome contextual associations with DUF2188, including repeated association with nucleotide-activated effector conflict systems. 70 matched cddid_all.tbl CDD pfam13032 pfam13032 432943 RNaseH_pPIWI_RE RNaseH domain of pPIWI_RE. RNaseH domain of the pPIWI_RE PIWI/Argonaute module. pPIWI_RE is found in a conserved three-gene island that also contains a DinG-type helicase and an REase nuclease. This three gene island is predicted to form a conflict system which targets R-loop formation of invasive plasmids during plasmid replication. 281 matched cddid_all.tbl CDD pfam13033 pfam13033 372437 DUF3894 Protein of unknown function (DUF3894). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 66 and 79 amino acids in length. There are two conserved sequence motifs: FNIC and MALLNLT. 54 matched cddid_all.tbl CDD pfam13034 pfam13034 372438 DUF3895 Protein of unknown function (DUF3895). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. There are two completely conserved residues (Y and L) that may be functionally important. 76 matched cddid_all.tbl CDD pfam13035 pfam13035 315663 DUF3896 Protein of unknown function (DUF3896). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. 61 matched cddid_all.tbl CDD pfam13036 pfam13036 463777 LpoB Peptidoglycan-synthase activator LpoB. This is a family of Gram-negative bacterial outer membrane lipoproteins. LpoB is required for the function of the major peptidoglycan synthase enzyme PBP1B. It interacts with PBP1B protein via the UvrB-like non-catalytic domain on that protein. LpoB has a 54-aa-long flexible N-terminal stretch followed by a globular domain with similarity to the N-terminal domain of the prevalent periplasmic protein TolB. The long, flexible N-terminal region of LpoB enables it to span the periplasm and reach its docking site in PBP1B. Peptidoglycan is the essential polymer within the sacculus that surrounds the cytoplasmic membrane of bacteria. 147 matched cddid_all.tbl CDD pfam13037 pfam13037 404053 DUF3898 Domain of unknown function (DUF3898). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 90 amino acids in length. There are two conserved sequence motifs: DFG and FEKG. 89 matched cddid_all.tbl CDD pfam13038 pfam13038 432945 DUF3899 Domain of unknown function (DUF3899). Putative Tryptophanyl-tRNA synthetase. 84 matched cddid_all.tbl CDD pfam13039 pfam13039 372442 DUF3900 Protein of unknown function (DUF3900). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 360 amino acids in length. 249 matched cddid_all.tbl CDD pfam13040 pfam13040 379027 Fur_reg_FbpB Fur-regulated basic protein B. This family of proteins is regulated by the ferric uptake regulator protein Fur. This family represses expression of the lutABC operon encoding iron sulfur-containing enzymes necessary for growth on lactate. 39 matched cddid_all.tbl CDD pfam13041 pfam13041 463778 PPR_2 PPR repeat family. This repeat has no known function. It is about 35 amino acids long and is found in up to 18 copies in some proteins. The family appears to be greatly expanded in plants and fungi. The repeat has been called PPR. 50 matched cddid_all.tbl CDD pfam13042 pfam13042 289787 DUF3902 Protein of unknown function (DUF3902). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 170 amino acids in length. There is a conserved LGI sequence motif. 161 matched cddid_all.tbl CDD pfam13043 pfam13043 432947 DUF3903 Domain of unknown function (DUF3903). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 40 amino acids in length. 40 matched cddid_all.tbl CDD pfam13044 pfam13044 289789 Fusion_F0 Fusion glycoprotein F0, Isavirus. Fusion between viral and cellular membranes is mediated by viral membrane fusion glycoproteins. This entry represents fusion glycoprotein F0 from the infectious salmon anemia virus (ISAV). The precursor protein F0 is proteolytically cleaved to F1 and F2, which are held together by disulphide bridges. 436 matched cddid_all.tbl CDD pfam13045 pfam13045 315671 DUF3905 Protein of unknown function (DUF3905). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. 84 matched cddid_all.tbl CDD pfam13046 pfam13046 289791 DUF3906 Protein of unknown function (DUF3906). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved EKK sequence motif. 64 matched cddid_all.tbl CDD pfam13047 pfam13047 379028 DUF3907 Protein of unknown function (DUF3907). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 160 amino acids in length. There is a conserved AYTG sequence motif. 146 matched cddid_all.tbl CDD pfam13048 pfam13048 315673 DUF3908 Protein of unknown function (DUF3908). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 140 amino acids in length. There is a single completely conserved residue Y that may be functionally important. 134 matched cddid_all.tbl CDD pfam13049 pfam13049 432948 DUF3910 Protein of unknown function (DUF3910). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. 95 matched cddid_all.tbl CDD pfam13050 pfam13050 432949 DUF3911 Protein of unknown function (DUF3911). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 78 matched cddid_all.tbl CDD pfam13051 pfam13051 404059 DUF3912 Protein of unknown function (DUF3912). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 92 matched cddid_all.tbl CDD pfam13052 pfam13052 315677 DUF3913 Protein of unknown function (DUF3913). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. 57 matched cddid_all.tbl CDD pfam13053 pfam13053 372448 DUF3914 Protein of unknown function (DUF3914). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. There are two conserved sequence motifs: KFDIR and DLW. 89 matched cddid_all.tbl CDD pfam13054 pfam13054 315678 DUF3915 Protein of unknown function (DUF3915). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. 126 matched cddid_all.tbl CDD pfam13055 pfam13055 432950 DUF3917 Protein of unknown function (DUF3917). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. 71 matched cddid_all.tbl CDD pfam13056 pfam13056 289801 DUF3918 Protein of unknown function (DUF3918). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There are two completely conserved residues (G and R) that may be functionally important. 43 matched cddid_all.tbl CDD pfam13057 pfam13057 432951 DUF3919 Protein of unknown function (DUF3919). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 251 and 262 amino acids in length. There is a conserved YLNG sequence motif. 232 matched cddid_all.tbl CDD pfam13058 pfam13058 372451 DUF3920 Protein of unknown function (DUF3920). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. 126 matched cddid_all.tbl CDD pfam13059 pfam13059 404062 DUF3922 Protein of unknown function (DUF3992). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 87 and 98 amino acids in length. 79 matched cddid_all.tbl CDD pfam13060 pfam13060 289805 DUF3921 Protein of unknown function (DUF3921). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. 58 matched cddid_all.tbl CDD pfam13061 pfam13061 404063 DUF3923 Protein of unknown function (DUF3923). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 65 matched cddid_all.tbl CDD pfam13062 pfam13062 289807 DUF3924 Protein of unknown function (DUF3924). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. 62 matched cddid_all.tbl CDD pfam13063 pfam13063 432952 DUF3925 Protein of unknown function (DUF3925). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. 65 matched cddid_all.tbl CDD pfam13064 pfam13064 372454 DUF3927 Protein of unknown function (DUF3927). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 50 amino acids in length. There is a conserved SVL sequence motif. There is a single completely conserved residue D that may be functionally important. 53 matched cddid_all.tbl CDD pfam13065 pfam13065 432953 DUF3928 Protein of unknown function (DUF3928). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. 95 matched cddid_all.tbl CDD pfam13066 pfam13066 372456 DUF3929 Protein of unknown function (DUF3929). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. 64 matched cddid_all.tbl CDD pfam13067 pfam13067 432954 DUF3930 Protein of unknown function (DUF3930). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 51 and 67 amino acids in length. 51 matched cddid_all.tbl CDD pfam13068 pfam13068 432955 DUF3932 Protein of unknown function (DUF3932). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 81 matched cddid_all.tbl CDD pfam13069 pfam13069 432956 DUF3933 Protein of unknown function (DUF3933). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. 52 matched cddid_all.tbl CDD pfam13070 pfam13070 289815 DUF3934 Protein of unknown function (DUF3934). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There are two conserved sequence motifs: GTG and SKG. 40 matched cddid_all.tbl CDD pfam13071 pfam13071 372460 DUF3935 Protein of unknown function (DUF3935). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two conserved sequence motifs: FVF and LGV. 70 matched cddid_all.tbl CDD pfam13072 pfam13072 289817 MciZ Mother cell inhibitor of FtsZ. This family of proteins is found in bacteria. Family members are approximately 40 amino acids in length. There is a conserved GKAW sequence motif. There is a single completely conserved residue G that may be functionally important. Family members include the Bacillus subtilis cell-division inhibitor, MciZ (mother cell inhibitor of FtsZ) which blocks the assembly of FtsZ. FtsZ (filamentation temperature-sensitive Z) is the bacterial homolog of tubulin. Crystal structure reveals that MciZ binds to the C-terminal polymerization interface of FtsZ, the equivalent of the minus end of tubulin, causing shortening of protofilaments and blocking the assembly of higher-order FtsZ structures. Hence, MciZ provides a capping-based regulatory mechanism for FtsZ. 37 matched cddid_all.tbl CDD pfam13073 pfam13073 372461 DUF3937 Protein of unknown function (DUF3937). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 72 matched cddid_all.tbl CDD pfam13074 pfam13074 432957 DUF3938 Protein of unknown function (DUF3938). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. 98 matched cddid_all.tbl CDD pfam13075 pfam13075 432958 DUF3939 Protein of unknown function (DUF3939). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 150 amino acids in length. 134 matched cddid_all.tbl CDD pfam13076 pfam13076 315692 Fur_reg_FbpA Fur-regulated basic protein A. This family of proteins is regulated by the ferric uptake regulator protein Fur. This family does not regulate the lutABC operon encoding iron sulfur-containing enzymes necessary for growth on lactate. 36 matched cddid_all.tbl CDD pfam13077 pfam13077 432959 DUF3909 Protein of unknown function (DUF3909). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. 108 matched cddid_all.tbl CDD pfam13078 pfam13078 289823 DUF3942 Protein of unknown function (DUF3942). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. 137 matched cddid_all.tbl CDD pfam13079 pfam13079 404067 DUF3916 Protein of unknown function (DUF3916). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 170 amino acids in length. There is a single completely conserved residue S that may be functionally important. 147 matched cddid_all.tbl CDD pfam13080 pfam13080 404068 DUF3926 Protein of unknown function (DUF3926). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 46 and 63 amino acids in length. There is a single completely conserved residue P that may be functionally important. 43 matched cddid_all.tbl CDD pfam13081 pfam13081 289826 DUF3941 Domain of unknown function (DUF3941). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 30 amino acids in length. There is a conserved YSK sequence motif. 24 matched cddid_all.tbl CDD pfam13082 pfam13082 432960 DUF3931 Protein of unknown function (DUF3931). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 66 matched cddid_all.tbl CDD pfam13083 pfam13083 463779 KH_4 KH domain. 73 matched cddid_all.tbl CDD pfam13084 pfam13084 432962 DUF3943 Domain of unknown function (DUF3943). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 110 amino acids in length. 108 matched cddid_all.tbl CDD pfam13085 pfam13085 432963 Fer2_3 2Fe-2S iron-sulfur cluster binding domain. The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which abeta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. 107 matched cddid_all.tbl CDD pfam13086 pfam13086 404072 AAA_11 AAA domain. This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. 248 matched cddid_all.tbl CDD pfam13087 pfam13087 463780 AAA_12 AAA domain. This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. 196 matched cddid_all.tbl CDD pfam13088 pfam13088 463781 BNR_2 BNR repeat-like domain. This family of proteins contains BNR-like repeats suggesting these proteins may act as sialidases. 280 matched cddid_all.tbl CDD pfam13089 pfam13089 463782 PP_kinase_N Polyphosphate kinase N-terminal domain. Polyphosphate kinase (Ppk) catalyzes the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. 106 matched cddid_all.tbl CDD pfam13090 pfam13090 463783 PP_kinase_C Polyphosphate kinase C-terminal domain 2. Polyphosphate kinase (Ppk) catalyzes the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. This C2-terminal domain has a structure similar to phospholipase D. It is one of two closely related carboxy-terminal domains (C1 and C2 domains). Both the C1 and C2 domains (residues 322-502 and 503-687, respectively) consist of a sevenstranded mixed beta-sheet flanked by five alpha-helices. However, the structural topology and relative orientations of the helices to the beta-sheet in these two domains are different. The C1 and C2 domains are highly conserved in the PPK family. Some of the residues previously shown to be crucial for the enzyme catalytic activity are located in these two domains. 172 matched cddid_all.tbl CDD pfam13091 pfam13091 463784 PLDc_2 PLD-like domain. 132 matched cddid_all.tbl CDD pfam13092 pfam13092 432969 CENP-L Kinetochore complex Sim4 subunit Fta1. CENP-L is one of the components that assembles onto the CENP-A-nucleosome distal (CAD) centromere. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-A, the centromere-specific histone H3 variant, assembles an array of nucleosomes and it is this that seems to be the prime candidate for specifying centromere identity. CENP-A nucleosomes directly recruit a proximal CENP-A nucleosome associated complex (NAC) comprised of CENP-M, CENP-N and CENP-T, CENP-U(50), CENP-C and CENP-H. Assembly of the CENP-A NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Additionally, there are seven other subunits which make up the CENP-A-nucleosome distal (CAD) centromere, CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S, also assembling on the CENP-A NAC. Fta1 is the equivalent component of the fission yeast Sim4 complex. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. 158 matched cddid_all.tbl CDD pfam13093 pfam13093 404079 FTA4 Kinetochore complex Fta4 of Sim4 subunit, or CENP-50. Fission yeast has three kinetochore protein complexes. Two complexes, Sim4 and Ndc80-MIND-Spc7 (NMS), are constitutive components, whereas the third complex, DASH, is transiently associated with kinetochores only in mitosis and is required for precise chromosome segregation. The Sim4 complex functions as a loading dock for the DASH complex. Sim4 consists of a number of different proteins including Ftas 1-7 and Dad1. 199 matched cddid_all.tbl CDD pfam13094 pfam13094 432970 CENP-Q CENP-Q, a CENPA-CAD centromere complex subunit. CENP-Q is one of the components that assembles onto the CENPA-nucleosome distal (CAD) centromere. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-A, the centromere-specific histone H3 variant, assembles an array of nucleosomes and it is this that seems to be the prime candidate for specifying centromere identity. CENPA nucleosomes directly recruit a proximal CENPA-nucleosome-associated complex (NAC) comprised of CENP-M, CENP-N and CENP-T, CENP-U(50), CENP-C and CENP-H. Assembly of the CENPA NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Additionally, there are seven other subunits which make up the CENPA-nucleosome distal (CAD) centromere, CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S, also assembling on the CENP-A NAC. Fta7 is the equivalent component of the fission yeast Sim4 complex. 159 matched cddid_all.tbl CDD pfam13095 pfam13095 432971 FTA2 Kinetochore Sim4 complex subunit FTA2. Fission yeast has three kinetochore protein complexes. Two complexes, Sim4 and Ndc80-MIND-Spc7 (NMS), are constitutive components, whereas the third complex, DASH, is transiently associated with kinetochores only in mitosis and is required for precise chromosome segregation. The Sim4 complex functions as a loading dock for the DASH complex. Sim4 consists of a number of different proteins including Ftas 1-7 and Dad1. The equivalent higher eukaryotic protein is CENP-P. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-A, the centromere-specific histone H3 variant, assembles an array of nucleosomes and it is this that seems to be the prime candidate for specifying centromere identity. CENP-A nucleosomes directly recruit a proximal CENP-A nucleosome associated complex (NAC) comprised of CENP-M, CENP-N and CENP-T, CENP-U(50), CENP-C and CENP-H. Assembly of the CENP-A NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Additionally, there are seven other subunits which make up the CENP-A-nucleosome distal (CAD) centromere, CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S, also assembling on the CENP-A NAC. 204 matched cddid_all.tbl CDD pfam13096 pfam13096 289841 CENP-P CENP-A-nucleosome distal (CAD) centromere subunit, CENP-P. CENP-P is one of the components that assembles onto the CENP-A-nucleosome distal (CAD) centromere. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-A, the centromere-specific histone H3 variant, assembles an array of nucleosomes and it is this that seems to be the prime candidate for specifying centromere identity. CENP-A nucleosomes directly recruit a proximal CENP-A nucleosome associated complex (NAC) comprised of CENP-M, CENP-N and CENP-T, CENP-U(50), CENP-C and CENP-H. Assembly of the CENP-A NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Additionally, there are seven other subunits which make up the CENP-A-nucleosome distal (CAD) centromere, CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S, also assembling on the CENP-A NAC. Fta7 is the equivalent component of the fission yeast Sim4 complex. 177 matched cddid_all.tbl CDD pfam13097 pfam13097 463785 CENP-U CENP-A nucleosome associated complex (NAC) subunit. CENP-U is one of the components that assembles onto the CENP-A-nucleosome associated complex (NAC). The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-A, the centromere-specific histone H3 variant, assembles an array of nucleosomes and it is this that seems to be the prime candidate for specifying centromere identity. CENP-A nucleosomes directly recruit a proximal CENP-A nucleosome associated complex (NAC) comprised of CENP-M, CENP-N and CENP-T, CENP-U(50), CENP-C and CENP-H. Assembly of the CENP-A NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Additionally, there are seven other subunits which make up the CENP-A-nucleosome distal (CAD) centromere, CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S, also assembling on the CENP-A NAC. FTA4 is the equivalent component of the fission yeast Sim4 complex. 180 matched cddid_all.tbl CDD pfam13098 pfam13098 379034 Thioredoxin_2 Thioredoxin-like domain. 103 matched cddid_all.tbl CDD pfam13099 pfam13099 289844 DUF3944 Domain of unknown function (DUF3944). This short domain is sometimes found N terminal to pfam03981. 35 matched cddid_all.tbl CDD pfam13100 pfam13100 404083 OstA_2 OstA-like protein. This is a family of OstA-like proteins that are related to pfam03968. 158 matched cddid_all.tbl CDD pfam13101 pfam13101 463786 DUF3945 Protein of unknown function (DUF3945). A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This is a C-terminal repeated region. 59 matched cddid_all.tbl CDD pfam13102 pfam13102 463787 Phage_int_SAM_5 Phage integrase SAM-like domain. A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This family appears related to the N-terminal domain of phage integrases. 99 matched cddid_all.tbl CDD pfam13103 pfam13103 463788 TonB_2 TonB C terminal. This family contains TonB members that are not captured by pfam03544. 85 matched cddid_all.tbl CDD pfam13104 pfam13104 289849 DUF3956 Protein of unknown function (DUF3956). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. 45 matched cddid_all.tbl CDD pfam13105 pfam13105 432976 DUF3959 Protein of unknown function (DUF3959). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 260 amino acids in length. 238 matched cddid_all.tbl CDD pfam13106 pfam13106 432977 DUF3961 Domain of unknown function (DUF3961). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and viruses, and is approximately 40 amino acids in length. 39 matched cddid_all.tbl CDD pfam13107 pfam13107 289852 DUF3964 Protein of unknown function (DUF3964). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. There are two conserved sequence motifs: FYF and AFW. 109 matched cddid_all.tbl CDD pfam13108 pfam13108 404088 DUF3969 Protein of unknown function (DUF3969). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. 102 matched cddid_all.tbl CDD pfam13109 pfam13109 432978 AsmA_1 AsmA-like C-terminal region. This family is similar to the C-terminal of the AsmA protein of E. coli. 214 matched cddid_all.tbl CDD pfam13110 pfam13110 404090 DUF3966 Protein of unknown function (DUF3966). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 86 amino acids in length. 42 matched cddid_all.tbl CDD pfam13111 pfam13111 432979 pPIWI_RE_X pPIWI_RE module N-terminal domain. Domain observed N-terminal to the pPIWI_RE domain module. PIWI/Argonaute modules are typically N-terminally fused to the PTND1 and PTND2 domains, pPIWI_RE_X may represent an ancestral version of these domains or represent a N-terminal innovation predating the emergence of PTND1 and PTND2. 398 matched cddid_all.tbl CDD pfam13112 pfam13112 289857 DUF3965 Protein of unknown function (DUF3965). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 380 amino acids in length. 291 matched cddid_all.tbl CDD pfam13113 pfam13113 372483 DUF3970 Protein of unknown function (DUF3970). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved NPKY sequence motif. 55 matched cddid_all.tbl CDD pfam13114 pfam13114 432980 RecO_N_2 RecO N terminal. This entry contains members that are not captured by pfam11967. 71 matched cddid_all.tbl CDD pfam13115 pfam13115 432981 YtkA YtkA-like. 86 matched cddid_all.tbl CDD pfam13116 pfam13116 432982 DUF3971 Protein of unknown function. Some members of this family are related to the AsmA family proteins. 288 matched cddid_all.tbl CDD pfam13117 pfam13117 432983 Cag12 Cag pathogenicity island protein Cag12. This is a Proteobacterial family of Cag pathogenicity island proteins. 96 matched cddid_all.tbl CDD pfam13118 pfam13118 372487 DUF3972 Protein of unknown function (DUF3972). This is a Proteobacterial family of unknown function. Some of the proteins in this family are annotated as being kinesin-like proteins. 125 matched cddid_all.tbl CDD pfam13119 pfam13119 432984 DUF3973 Domain of unknown function (DUF3973). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 40 amino acids in length. There is a conserved YCI sequence motif. 40 matched cddid_all.tbl CDD pfam13120 pfam13120 432985 DUF3974 Domain of unknown function (DUF3974). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 130 amino acids in length. 126 matched cddid_all.tbl CDD pfam13121 pfam13121 404097 DUF3976 Domain of unknown function (DUF3976). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 40 amino acids in length. 40 matched cddid_all.tbl CDD pfam13122 pfam13122 289867 DUF3977 Protein of unknown function (DUF3977). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 77 matched cddid_all.tbl CDD pfam13123 pfam13123 372491 DUF3978 Protein of unknown function (DUF3978). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 150 amino acids in length. 144 matched cddid_all.tbl CDD pfam13124 pfam13124 289869 DUF3963 Protein of unknown function (DUF3963). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 42 and 85 amino acids in length. There is a conserved DIQKW sequence motif. 40 matched cddid_all.tbl CDD pfam13125 pfam13125 432986 DUF3958 Protein of unknown function (DUF3958). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. There are two conserved sequence motifs: RLF and TWH. 107 matched cddid_all.tbl CDD pfam13126 pfam13126 315729 DUF3975 Protein of unknown function (DUF3975). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. 80 matched cddid_all.tbl CDD pfam13127 pfam13127 432987 DUF3955 Protein of unknown function (DUF3955). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 68 and 87 amino acids in length. There are two completely conserved residues (G and E) that may be functionally important. 59 matched cddid_all.tbl CDD pfam13128 pfam13128 315731 DUF3954 Protein of unknown function (DUF3954). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 60 amino acids in length. 49 matched cddid_all.tbl CDD pfam13129 pfam13129 404100 DUF3953 Protein of unknown function (DUF3953). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 47 and 76 amino acids in length. 40 matched cddid_all.tbl CDD pfam13130 pfam13130 315733 DUF3952 Domain of unknown function (DUF3952). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 110 amino acids in length. There is a conserved VMSAS sequence motif. 101 matched cddid_all.tbl CDD pfam13131 pfam13131 315734 DUF3951 Protein of unknown function (DUF3951). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 56 and 71 amino acids in length. There is a conserved YTP sequence motif. 52 matched cddid_all.tbl CDD pfam13132 pfam13132 404101 DUF3950 Domain of unknown function (DUF3950). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and viruses, and is approximately 30 amino acids in length. There is a conserved NFS sequence motif. 30 matched cddid_all.tbl CDD pfam13133 pfam13133 315735 DUF3949 Protein of unknown function (DUF3949). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 69 and 87 amino acids in length. 60 matched cddid_all.tbl CDD pfam13134 pfam13134 315736 DUF3948 Protein of unknown function (DUF3948). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. 35 matched cddid_all.tbl CDD pfam13135 pfam13135 289880 DUF3947 Protein of unknown function (DUF3947). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 91 matched cddid_all.tbl CDD pfam13136 pfam13136 432988 DUF3984 Protein of unknown function (DUF3984). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 393 and 442 amino acids in length. 324 matched cddid_all.tbl CDD pfam13137 pfam13137 289882 DUF3983 Protein of unknown function (DUF3983). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 40 amino acids in length. There is a conserved AWRN sequence motif. 34 matched cddid_all.tbl CDD pfam13138 pfam13138 432989 DUF3982 Protein of unknown function (DUF3982). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 47 and 73 amino acids in length. There are two conserved sequence motifs: EKL and EIP. 35 matched cddid_all.tbl CDD pfam13139 pfam13139 372494 DUF3981 Domain of unknown function (DUF3981). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 110 amino acids in length. 115 matched cddid_all.tbl CDD pfam13140 pfam13140 289885 DUF3980 Domain of unknown function (DUF3980). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 90 amino acids in length. 87 matched cddid_all.tbl CDD pfam13141 pfam13141 432990 DUF3979 Protein of unknown function (DUF3979). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. 115 matched cddid_all.tbl CDD pfam13142 pfam13142 372496 DUF3960 Domain of unknown function (DUF3960). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is typically between 72 and 89 amino acids in length. 89 matched cddid_all.tbl CDD pfam13143 pfam13143 404104 DUF3986 Protein of unknown function (DUF3986). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. 87 matched cddid_all.tbl CDD pfam13144 pfam13144 432991 ChapFlgA Chaperone for flagella basal body P-ring formation. ChapFlgA is a family similar to the SAF family, and includes chaperones for flagellar basal-body proteins and pilus-assembly proteins, FlgA, RcpB and CpaB. ChapFlgA is necessary for the formation of the P-ring of the flagellum, FlgI, which sits in the peptidoglycan layer of the outer membrane of the bacterium. FlgA plays an auxiliary role in P-ring assembly. 122 matched cddid_all.tbl CDD pfam13145 pfam13145 432992 Rotamase_2 PPIC-type PPIASE domain. 121 matched cddid_all.tbl CDD pfam13146 pfam13146 432993 TRL TRL-like protein family. This family includes the TRL protein that is found in a locus that includes several tRNAs. The function of this protein is not known. The proteins in this family usually have a lipoprotein attachment site at their N-terminus. 77 matched cddid_all.tbl CDD pfam13148 pfam13148 432994 DUF3987 Protein of unknown function (DUF3987). A family of uncharacterized proteins found by clustering human gut metagenomic sequences. 365 matched cddid_all.tbl CDD pfam13149 pfam13149 463789 Mfa_like_1 Fimbrillin-like. A family of putative fimbrillin proteins found by clustering human gut metagenomic sequences. Analysis of structural comparisons shows this family to be part of the FimbA (CL0450) superfamily of adhesin components or fimbrillins. 244 matched cddid_all.tbl CDD pfam13150 pfam13150 463790 TraL_transposon Conjugative transposon protein TraL. This family contains conjugal transfer protein TraL. 86 matched cddid_all.tbl CDD pfam13151 pfam13151 463791 DUF3990 Protein of unknown function (DUF3990). A family of uncharacterized proteins found by clustering human gut metagenomic sequences. 151 matched cddid_all.tbl CDD pfam13152 pfam13152 289896 DUF3967 Protein of unknown function (DUF3967). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 173 and 249 amino acids in length. 35 matched cddid_all.tbl CDD pfam13153 pfam13153 463792 DUF3985 Protein of unknown function (DUF3985). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. 44 matched cddid_all.tbl CDD pfam13154 pfam13154 432999 DUF3991 Protein of unknown function (DUF3991). This family of proteins is often associated with family Toprim, pfam01751. 74 matched cddid_all.tbl CDD pfam13155 pfam13155 463793 Toprim_2 Toprim-like. This is a family or Toprim-like proteins. 88 matched cddid_all.tbl CDD pfam13156 pfam13156 433001 Mrr_cat_2 Restriction endonuclease. Prokaryotic family found in type II restriction enzymes containing the hallmark (D/E)-(D/E)XK active site. Presence of catalytic residues implicates this region in the enzymatic cleavage of DNA 127 matched cddid_all.tbl CDD pfam13157 pfam13157 463794 Enas Endospore appendages. The surface of Bacillus and Clostridium endospores is decorated with long filamentous endospores appendages that resemble pili from Gram- negative and Gram-positive bacteria. They show two morphologies, the main or Staggered-type (S-Ena) which accounts for 90% of the fibres, and the Ladder-like (L-Ena) which is smaller and less abundant. They are a novel class of Gram-positive pili, consisting in single domain subunits with a jellyroll topology comprised by two juxtaposed beta-sheets. This domain represents the S-Ena core. Disulfide bonding through the N-terminal connector peptide that precedes this domain stabilizes longitudinally the fibres, bridging the helical turns. This results in flexible pili, highly resistant to environmental harsh such as heat, drought, and chemical damage. 111 matched cddid_all.tbl CDD pfam13158 pfam13158 372503 DUF3993 Protein of unknown function (DUF3993). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 160 amino acids in length. 118 matched cddid_all.tbl CDD pfam13159 pfam13159 372504 DUF3994 Domain of unknown function (DUF3994). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is typically between 97 and 111 amino acids in length. 99 matched cddid_all.tbl CDD pfam13160 pfam13160 433002 DUF3995 Protein of unknown function (DUF3995). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 138 and 149 amino acids in length. There are two completely conserved residues (W and P) that may be functionally important. 125 matched cddid_all.tbl CDD pfam13161 pfam13161 315755 DUF3996 Protein of unknown function (DUF3996). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 172 and 203 amino acids in length. 154 matched cddid_all.tbl CDD pfam13162 pfam13162 404117 DUF3997 Protein of unknown function (DUF3997). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. 107 matched cddid_all.tbl CDD pfam13163 pfam13163 433003 DUF3999 Protein of unknown function (DUF3999). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 440 and 470 amino acids in length. There is a single completely conserved residue D that may be functionally important. 422 matched cddid_all.tbl CDD pfam13164 pfam13164 463795 Diedel Diedel. Diedel (die) was identified as an insect immune response protein. It is up-regulated after a septic injury and may act as a negative regulator of the JAK/STAT signalling pathway. Its homologs can be found in Drosophila and Acyrtosiphon pisum. Interestingly, the orthologues of the die gene are present in the genome of insect DNA viruses of the Baculoviridae and Ascoviridae families. The viral homologs suppress the immune deficiency (IMD) pathway in Drosophila. 75 matched cddid_all.tbl CDD pfam13165 pfam13165 433005 SCIFF Six-cysteine peptide SCIFF. Members of this protein family are essentially universal in the class Clostidia and therefore highly abundant in the human gut microbiome. This short peptide is designated SCIFF, for Six Cysteines in Forty-Five residues. It is a presumed ribosomal natural product precursor, always found associated with a yet-uncharacterized radical SAM protein that resembles other peptide modification radical SAM enzymes and is designated SCIFF radical SAM maturase. 43 matched cddid_all.tbl CDD pfam13166 pfam13166 463796 AAA_13 AAA domain. This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease. 712 matched cddid_all.tbl CDD pfam13167 pfam13167 463797 GTP-bdg_N GTP-binding GTPase N-terminal. This is the N-terminal region of GTP-binding HflX-like proteins. The full-length members bind and interact with the 50S ribosome and are GTPases, hydrolysing GTP/GDP/ATP/ADP. This N-terminal region is necessary for stability of the whole protein. 87 matched cddid_all.tbl CDD pfam13168 pfam13168 289912 Poxvirus_B22R_C Poxvirus B22R protein C-terminal. This is the highly conserved C-terminal region of poxvirus proteins from eg, Fowlpox virus, Myxoma virus, Lumpy skin disease, Variola virus and other members of the Poxviridae family of double-stranded, no-RNA stage poxviruses. 195 matched cddid_all.tbl CDD pfam13169 pfam13169 289913 Poxvirus_B22R_N Poxvirus B22R protein N-terminal. This is the highly conserved N-terminal region of poxvirus proteins from eg, Fowlpox virus, Myxoma virus, Lumpy skin disease, Variola virus and other members of the Poxviridae family of double-stranded, no-RNA stage poxviruses. 88 matched cddid_all.tbl CDD pfam13170 pfam13170 433008 DUF4003 Protein of unknown function (DUF4003). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 327 and 345 amino acids in length. 296 matched cddid_all.tbl CDD pfam13171 pfam13171 463798 DUF4004 Protein of unknown function (DUF4004). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 210 amino acids in length. 196 matched cddid_all.tbl CDD pfam13173 pfam13173 463799 AAA_14 AAA domain. This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. 128 matched cddid_all.tbl CDD pfam13174 pfam13174 463800 TPR_6 Tetratricopeptide repeat. 33 matched cddid_all.tbl CDD pfam13175 pfam13175 433011 AAA_15 AAA ATPase domain. This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. 392 matched cddid_all.tbl CDD pfam13176 pfam13176 433012 TPR_7 Tetratricopeptide repeat. 36 matched cddid_all.tbl CDD pfam13177 pfam13177 433013 DNA_pol3_delta2 DNA polymerase III, delta subunit. DNA polymerase III, delta subunit (EC 2.7.7.7) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalyzed reaction. The delta subunit is also known as HolA. 161 matched cddid_all.tbl CDD pfam13178 pfam13178 404128 DUF4005 Protein of unknown function (DUF4005). This is a C-terminal region of plant IQ-containing putative calmodulin-binding proteins. 97 matched cddid_all.tbl CDD pfam13179 pfam13179 433014 DUF4006 Family of unknown function (DUF4006). This is a family of short, approx 65 residue-long, bacterial proteins of unknown function. 63 matched cddid_all.tbl CDD pfam13180 pfam13180 433015 PDZ_2 PDZ domain. 74 matched cddid_all.tbl CDD pfam13181 pfam13181 404131 TPR_8 Tetratricopeptide repeat. 33 matched cddid_all.tbl CDD pfam13182 pfam13182 433016 DUF4007 Protein of unknown function (DUF4007). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 284 and 326 amino acids in length. This domain is found associated with pfam01507 in some proteins, suggesting a functional link. 287 matched cddid_all.tbl CDD pfam13183 pfam13183 433017 Fer4_8 4Fe-4S dicluster domain. Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters. 64 matched cddid_all.tbl CDD pfam13184 pfam13184 433018 KH_5 NusA-like KH domain. 69 matched cddid_all.tbl CDD pfam13185 pfam13185 433019 GAF_2 GAF domain. The GAF domain is named after some of the proteins it is found in, including cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA. It is also found in guanylyl cyclases and phytochromes. The structure of a GAF domain shows that the domain shares a similar fold with the PAS domain. This domain can bind O2, CO and NO (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 137 matched cddid_all.tbl CDD pfam13186 pfam13186 433020 SPASM Iron-sulfur cluster-binding domain. This domain occurs as an additional C-terminal iron-sulfur cluster binding domain in many radical SAM domain, pfam04055 proteins. The domain occurs in a number of proteins that modify a protein to become an active enzyme, or a peptide to become a ribosomal natural product. The domain is named SPASM because it occurs in the maturases of Subilitosin, PQQ, Anaerobic Sulfatases, and Mycofactocin. 66 matched cddid_all.tbl CDD pfam13187 pfam13187 463801 Fer4_9 4Fe-4S dicluster domain. 50 matched cddid_all.tbl CDD pfam13188 pfam13188 463802 PAS_8 PAS domain. PAS domains are involved in many signalling proteins where they are used as a signal sensor domain. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Heme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. This domain recognizes oxygen and CO (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 65 matched cddid_all.tbl CDD pfam13189 pfam13189 433023 Cytidylate_kin2 Cytidylate kinase-like family. This family includes enzymes related to cytidylate kinase. 176 matched cddid_all.tbl CDD pfam13190 pfam13190 463803 PDGLE PDGLE domain. This short presumed domain is usually found on its own. However, it is also found associated with pfam01891 suggesting it may have a role in cobalt uptake. The domain is named after a short motif found within many members of the family. 101 matched cddid_all.tbl CDD pfam13191 pfam13191 433025 AAA_16 AAA ATPase domain. This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. 167 matched cddid_all.tbl CDD pfam13192 pfam13192 433026 Thioredoxin_3 Thioredoxin domain. 71 matched cddid_all.tbl CDD pfam13193 pfam13193 463804 AMP-binding_C AMP-binding enzyme C-terminal domain. This is a small domain that is found C terminal to pfam00501. It has a central beta sheet core that is flanked by alpha helices. 76 matched cddid_all.tbl CDD pfam13194 pfam13194 463805 DUF4010 Domain of unknown function (DUF4010). This is a family of putative membrane proteins found in archaea and bacteria. It is sometimes found C terminal to pfam02308. 209 matched cddid_all.tbl CDD pfam13195 pfam13195 463806 DUF4011 Protein of unknown function (DUF4011). This family of proteins is found in archaea and bacteria. Many members are annotated as being putative DNA helicase-related proteins. 163 matched cddid_all.tbl CDD pfam13196 pfam13196 433030 DUF4012 Protein of unknown function (DUF4012). This is a family of uncharacterized proteins found in archaea and bacteria. 144 matched cddid_all.tbl CDD pfam13197 pfam13197 433031 DUF4013 Protein of unknown function (DUF4013). This is a family of uncharacterized proteins that is found in archaea and bacteria. 167 matched cddid_all.tbl CDD pfam13198 pfam13198 338629 DUF4014 Protein of unknown function (DUF4014). This is a bacterial and viral family of uncharacterized proteins. 72 matched cddid_all.tbl CDD pfam13199 pfam13199 463807 Glyco_hydro_66 Glycosyl hydrolase family 66. This family is a set of glycosyl hydrolase enzymes including cycloisomaltooligosaccharide glucanotransferase (EC:2.4.1.-) and dextranase (EC:3.2.1.11) activities. 557 matched cddid_all.tbl CDD pfam13200 pfam13200 433033 DUF4015 Putative glycosyl hydrolase domain. This domain is related to other known glycosyl hydrolases suggesting this domain is also involved in carbohydrate break down. 313 matched cddid_all.tbl CDD pfam13201 pfam13201 433034 PCMD Putative carbohydrate metabolism domain. This domain has been suggested to participate in carbohydrate metabolism. Structural evidence indicates that it might be a carbohydrate binding domain, with or without enzymatic activity. In particular, it has been hypothesized that it might act as a glycoside hydrolase. 238 matched cddid_all.tbl CDD pfam13202 pfam13202 433035 EF-hand_5 EF hand. 25 matched cddid_all.tbl CDD pfam13203 pfam13203 404152 DUF2201_N Putative metallopeptidase domain. This domain, found in various hypothetical bacterial proteins, has no known function. However, it is related to pfam01435. 271 matched cddid_all.tbl CDD pfam13204 pfam13204 463808 DUF4038 Protein of unknown function (DUF4038). A family of putative cellulases. 320 matched cddid_all.tbl CDD pfam13205 pfam13205 463809 Big_5 Bacterial Ig-like domain. 105 matched cddid_all.tbl CDD pfam13206 pfam13206 404155 VSG_B Trypanosomal VSG domain. This family represents the B-type variant surface glycoproteins from trypanosomal parasites. This family is related to pfam00913. 354 matched cddid_all.tbl CDD pfam13207 pfam13207 463810 AAA_17 AAA domain. 136 matched cddid_all.tbl CDD pfam13208 pfam13208 433039 TerB_N TerB N-terminal domain. The TerB_N domain is found N-terminal to TerB, and TerB_C containing proteins. It has a predominantly alpha-helical structure and contains an absolutely conserved glutamate. The presence of a conserved acidic residue suggests that it might chelate metal like TerB. These proteins occur in a two-gene operon containing an AAA+ ATPase and SF-II DNA helicase suggesting a role in stress-response or phage defence. 204 matched cddid_all.tbl CDD pfam13209 pfam13209 289952 DUF4017 Protein of unknown function (DUF4017). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. 60 matched cddid_all.tbl CDD pfam13210 pfam13210 404158 DUF4018 Domain of unknown function (DUF4018). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 190 amino acids in length. 198 matched cddid_all.tbl CDD pfam13211 pfam13211 433040 DUF4019 Protein of unknown function (DUF4019). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 130 and 183 amino acids in length. There is a single completely conserved residue E that may be functionally important. 104 matched cddid_all.tbl CDD pfam13212 pfam13212 372518 DUF4020 Domain of unknown function (DUF4020). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is typically between 176 and 195 amino acids in length. 174 matched cddid_all.tbl CDD pfam13213 pfam13213 289956 DUF4021 Protein of unknown function (DUF4021). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved YGM sequence motif. 46 matched cddid_all.tbl CDD pfam13214 pfam13214 289957 DUF4022 Protein of unknown function (DUF4022). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 73 and 85 amino acids in length. 77 matched cddid_all.tbl CDD pfam13215 pfam13215 372519 DUF4023 Protein of unknown function (DUF4023). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There is a conserved KLP sequence motif. 35 matched cddid_all.tbl CDD pfam13216 pfam13216 315802 DUF4024 Protein of unknown function (DUF4024). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There is a conserved RDE sequence motif. 35 matched cddid_all.tbl CDD pfam13217 pfam13217 315803 DUF4025 Protein of unknown function (DUF4025). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved EGT sequence motif. 50 matched cddid_all.tbl CDD pfam13218 pfam13218 433041 DUF4026 Protein of unknown function (DUF4026). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 450 amino acids in length. The family is found in association with pfam10077. 323 matched cddid_all.tbl CDD pfam13219 pfam13219 404161 DUF4027 Protein of unknown function (DUF4027). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There is a conserved CLGGF sequence motif. 36 matched cddid_all.tbl CDD pfam13220 pfam13220 289962 DUF4028 Protein of unknown function (DUF4028). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 67 and 93 amino acids in length. There are two conserved sequence motifs: IVKI and YVKKWF. 65 matched cddid_all.tbl CDD pfam13221 pfam13221 372521 DUF4029 Protein of unknown function (DUF4029). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 95 and 119 amino acids in length. 96 matched cddid_all.tbl CDD pfam13222 pfam13222 289964 DUF4030 Protein of unknown function (DUF4030). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 164 and 197 amino acids in length. 142 matched cddid_all.tbl CDD pfam13223 pfam13223 433042 DUF4031 Protein of unknown function (DUF4031). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 91 and 130 amino acids in length. There is a conserved HYD sequence motif. 76 matched cddid_all.tbl CDD pfam13224 pfam13224 433043 DUF4032 Domain of unknown function (DUF4032). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 170 amino acids in length. The family is found in association with pfam06293. 163 matched cddid_all.tbl CDD pfam13225 pfam13225 404164 D27-like_C Beta-carotene isomerase D27-like, C-terminal. This is the C-terminal domain of Beta-carotene isomerase D27 that may contain an iron binding domain. Beta-carotene isomerase D27 (also known as Protein DWARF-27) from plants is involved in strigolactones biosynthesis. It is a beta-carotene isomerase that converts all-trans-beta-carotene into 9-cis-beta-carotene, which is cleaved by CCD7 into a 9-cis-configured aldehyde. This is an iron-containing protein that localizes in chloroplasts and is expressed mainly in vascular cells of shoots and roots. 88 matched cddid_all.tbl CDD pfam13226 pfam13226 404165 DUF4034 Domain of unknown function (DUF4034). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 280 amino acids in length. There is a conserved PRW sequence motif. 274 matched cddid_all.tbl CDD pfam13227 pfam13227 433044 DUF4035 Protein of unknown function (DUF4035). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 67 and 93 amino acids in length. 55 matched cddid_all.tbl CDD pfam13228 pfam13228 433045 DUF4037 Domain of unknown function (DUF4037). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and eukaryotes, and is approximately 100 amino acids in length. There is a single completely conserved residue P that may be functionally important. 101 matched cddid_all.tbl CDD pfam13229 pfam13229 463811 Beta_helix Right handed beta helix region. This region contains a parallel beta helix region that shares some similarity with Pectate lyases. 158 matched cddid_all.tbl CDD pfam13230 pfam13230 433047 GATase_4 Glutamine amidotransferases class-II. This family captures members that are not found in pfam00310. 272 matched cddid_all.tbl CDD pfam13231 pfam13231 433048 PMT_2 Dolichyl-phosphate-mannose-protein mannosyltransferase. This family contains members that are not captured by pfam02366. 160 matched cddid_all.tbl CDD pfam13232 pfam13232 315815 Complex1_LYR_1 Complex1_LYR-like. This is a family of proteins carrying the LYR motif of family Complex1_LYR, pfam05347, likely to be involved in Fe-S cluster biogenesis in mitochondria. 99 matched cddid_all.tbl CDD pfam13233 pfam13233 463812 Complex1_LYR_2 Complex1_LYR-like. This is a family of proteins carrying the LYR motif of family Complex1_LYR, pfam05347, likely to be involved in Fe-S cluster biogenesis in mitochondria. 79 matched cddid_all.tbl CDD pfam13234 pfam13234 463813 rRNA_proc-arch rRNA-processing arch domain. Mtr4 is the essential RNA helicase, and is an exosome-activating cofactor. This arch domain is carried in Mtr4 and Ski2 (the cytosolic homolog of Mtr4). The arch domain is required for proper 5.8S rRNA processing, and appears to function independently of canonical helicase activity. 267 matched cddid_all.tbl CDD pfam13236 pfam13236 463814 CLU Clustered mitochondria. The CLU domain (CLUstered mitochondria) is a eukaryotic domain found in proteins from fungi, protozoa, plants to humans. It is required for correct functioning of the mitochondria and mitochondrial transport although the exact function of the domain is unknown. In Dictyostelium the full-length protein is required for a very late step in fission of the outer mitochondrial membrane suggesting that mitochondria are transported along microtubules, as in mammalian cells, rather than along actin filaments, as in budding yeast. Disruption of the protein-impaired cytokinesis and caused mitochondria to cluster at the cell centre. It is likely that CLU functions in a novel pathway that positions mitochondria within the cell based on their physiological state. Disruption of the CLU pathway may enhance oxidative damage, alter gene expression, cause mitochondria to cluster at microtubule plus ends, and lead eventually to mitochondrial failure. 225 matched cddid_all.tbl CDD pfam13237 pfam13237 404174 Fer4_10 4Fe-4S dicluster domain. This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich. 56 matched cddid_all.tbl CDD pfam13238 pfam13238 433052 AAA_18 AAA domain. 128 matched cddid_all.tbl CDD pfam13239 pfam13239 463815 2TM 2TM domain. This short region contains two transmembrane alpha helices that are found associated with a wide range of other domains. This domain may be involved in cell lysis or peptidoglycan turnover. 80 matched cddid_all.tbl CDD pfam13240 pfam13240 433054 zinc_ribbon_2 zinc-ribbon domain. This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR. pfam12773. 21 matched cddid_all.tbl CDD pfam13241 pfam13241 433055 NAD_binding_7 Putative NAD(P)-binding. This domain is found in fungi, plants, archaea and bacteria. 104 matched cddid_all.tbl CDD pfam13242 pfam13242 433056 Hydrolase_like HAD-hyrolase-like. 75 matched cddid_all.tbl CDD pfam13243 pfam13243 433057 SQHop_cyclase_C Squalene-hopene cyclase C-terminal domain. Squalene-hopene cyclase, EC:5.4.99.17, catalyzes the cyclization of squalene into hopene in bacteria. This reaction is part of a cationic cyclization cascade, which is homologous to a key step in cholesterol biosynthesis. This family is the C-terminal half of the molecule. 319 matched cddid_all.tbl CDD pfam13244 pfam13244 463816 MbhD MBH, subunit D. Hydrogen gas-evolving membrane-bound hydrogenase (MBH) is a respiratory complex homologous to the quinone-reducing Complex I. Like Complex I, MBH has peripheral and membrane arms. MBH is made of 14 subunits (MbhA-N). MbhJ, K, L, N and M form the Membrane-anchored hydrogenase module. MbhJ, K, L, N are predicted to be exposed to the cytoplasm and form the peripheral arm. The remaining 10 subunits are predicted to be integral membrane proteins forming the membrane arm, made of 44 transmembrane helices (TMH). MbhA, B, C and F form the Sodium translocation module. MbhD, E, G and H form the Proton translocation module. MbhI is the linker between the hydrogenase module and the proton-translocating membrane module. It anchors the discontinuous TMH7 of MbhH via its middle lateral helix and the C-terminal of TMH2, found in MbhE. MbhD and MbhE together are equivalent to Nqo10 of Complex I. MbhD has three TM helices. 67 matched cddid_all.tbl CDD pfam13245 pfam13245 433059 AAA_19 AAA domain. 136 matched cddid_all.tbl CDD pfam13246 pfam13246 463817 Cation_ATPase Cation transport ATPase (P-type). This domain is found in cation transport ATPases, including phospholipid-transporting ATPases, calcium-transporting ATPases, and sodium-potassium ATPases. 91 matched cddid_all.tbl CDD pfam13247 pfam13247 404184 Fer4_11 4Fe-4S dicluster domain. Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters. 99 matched cddid_all.tbl CDD pfam13248 pfam13248 404185 zf-ribbon_3 zinc-ribbon domain. This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR. pfam12773. 25 matched cddid_all.tbl CDD pfam13249 pfam13249 433061 SQHop_cyclase_N Squalene-hopene cyclase N-terminal domain. Squalene-hopene cyclase, EC:5.4.99.17, catalyzes the cyclization of squalene into hopene in bacteria. This reaction is part of a cationic cyclization cascade, which is homologous to a key step in cholesterol biosynthesis. This family is the N-terminal domain. 290 matched cddid_all.tbl CDD pfam13250 pfam13250 433062 DUF4041 Domain of unknown function (DUF4041). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, archaea and viruses, and is approximately 60 amino acids in length. The family is found in association with pfam10544. 55 matched cddid_all.tbl CDD pfam13251 pfam13251 463818 DUF4042 Domain of unknown function (DUF4042). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is approximately 180 amino acids in length. 182 matched cddid_all.tbl CDD pfam13252 pfam13252 463819 DUF4043 Protein of unknown function (DUF4043). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 369 and 424 amino acids in length. There is a single completely conserved residue G that may be functionally important. 382 matched cddid_all.tbl CDD pfam13253 pfam13253 433065 DUF4044 Protein of unknown function (DUF4044). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 42 and 56 amino acids in length. There is a single completely conserved residue M that may be functionally important. 33 matched cddid_all.tbl CDD pfam13254 pfam13254 433066 DUF4045 Domain of unknown function (DUF4045). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and eukaryotes, and is typically between 384 and 430 amino acids in length. 415 matched cddid_all.tbl CDD pfam13255 pfam13255 404192 DUF4046 Protein of unknown function (DUF4046). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 64 and 331 amino acids in length. 90 matched cddid_all.tbl CDD pfam13256 pfam13256 315838 DUF4047 Domain of unknown function (DUF4047). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 130 amino acids in length. There are two conserved sequence motifs: TEA and FPKT. 125 matched cddid_all.tbl CDD pfam13257 pfam13257 372535 DUF4048 Domain of unknown function (DUF4048). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 228 and 257 amino acids in length. 252 matched cddid_all.tbl CDD pfam13258 pfam13258 289998 DUF4049 Domain of unknown function (DUF4049). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is typically between 310 and 324 amino acids in length. 333 matched cddid_all.tbl CDD pfam13259 pfam13259 463820 DUF4050 Protein of unknown function (DUF4050). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 109 and 173 amino acids in length. There are two conserved sequence motifs: IPL and FLVD. 124 matched cddid_all.tbl CDD pfam13261 pfam13261 315842 DUF4052 Protein of unknown function (DUF4052). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 220 amino acids in length. 217 matched cddid_all.tbl CDD pfam13262 pfam13262 463821 DUF4054 Protein of unknown function (DUF4054). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 120 and 152 amino acids in length. 105 matched cddid_all.tbl CDD pfam13263 pfam13263 433069 PHP_C PHP-associated. This is a subunit, probably the alpha, of bacterial and eukaryotic DNA polymerase III, associated with the PHP domain, pfam02811. 56 matched cddid_all.tbl CDD pfam13264 pfam13264 433070 DUF4055 Domain of unknown function (DUF4055). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and viruses, and is approximately 140 amino acids in length. 135 matched cddid_all.tbl CDD pfam13265 pfam13265 372540 DUF4056 Protein of unknown function (DUF4056). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 355 and 380 amino acids in length. 266 matched cddid_all.tbl CDD pfam13266 pfam13266 404197 DUF4057 Protein of unknown function (DUF4057). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 279 and 322 amino acids in length. 299 matched cddid_all.tbl CDD pfam13267 pfam13267 433071 DUF4058 Protein of unknown function (DUF4058). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 244 and 264 amino acids in length. 252 matched cddid_all.tbl CDD pfam13268 pfam13268 404198 DUF4059 Protein of unknown function (DUF4059). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved DKT sequence motif. 72 matched cddid_all.tbl CDD pfam13269 pfam13269 433072 DUF4060 Protein of unknown function (DUF4060). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. There are two conserved sequence motifs: VEVV and SYVAT. 74 matched cddid_all.tbl CDD pfam13270 pfam13270 463822 CCDC28 Coiled-coil domain-containing protein 28. This entry includes CCDC28A and CCDC28B. CCDC28B modulates mTORC2 complex assembly and function, possibly enhances AKT1 phosphorylation. 88 matched cddid_all.tbl CDD pfam13271 pfam13271 463823 DUF4062 Domain of unknown function (DUF4062). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 80 amino acids in length. There is a conserved SST sequence motif. 78 matched cddid_all.tbl CDD pfam13272 pfam13272 433075 Holin_2-3 Putative 2/3 transmembrane domain holin. Holin_2-3 is a putative holins with 2 or 3 transmembrane segments. It consists of many proteobacterial proteins ranging in size from about 70 aas to 120 aas. They have 2 or 3 predicted TMSs. Although some are annotated as phage proteins or holins, none appears to be functionally characterized. 106 matched cddid_all.tbl CDD pfam13273 pfam13273 433076 DUF4064 Protein of unknown function (DUF4064). 102 matched cddid_all.tbl CDD pfam13274 pfam13274 433077 DUF4065 Protein of unknown function (DUF4065). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea and viruses. Proteins in this family are typically between 155 and 202 amino acids in length. 108 matched cddid_all.tbl CDD pfam13275 pfam13275 433078 S4_2 S4 domain. The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4. 65 matched cddid_all.tbl CDD pfam13276 pfam13276 463824 HTH_21 HTH-like domain. This domain contains a predicted helix-turn-helix suggesting a DNA-binding function. 60 matched cddid_all.tbl CDD pfam13277 pfam13277 463825 YmdB YmdB-like protein. This family of putative phosphoesterases contains the B. subtilis protein YmdB. 252 matched cddid_all.tbl CDD pfam13279 pfam13279 463826 4HBT_2 Thioesterase-like superfamily. This family contains a wide variety of enzymes, principally thioesterases. These enzymes are part of the Hotdog fold superfamily. 121 matched cddid_all.tbl CDD pfam13280 pfam13280 433082 WYL WYL domain. WYL is a Sm-like SH3 beta-barrel fold containing domain. It is a member of the WYL-like superfamily, named for three conserved amino acids found in a subset of the superfamily. However, these residues are not strongly conserved throughout the family. Rather, the conservation pattern includes four basic residues and a position often occupied by a cysteine, which are predicted to line a ligand-binding groove typical of the Sm-like SH3 beta-barrels. A WYL domain protein (sll7009) is a negative regulator of the I-D CRISPR-Cas system in Synechocystis sp. It is predicted to be a ligand-sensing domain that could bind negatively charged ligands, such as nucleotides or nucleic acid fragments, to regulate CRISPR-Cas and other defense systems such as the abortive infection AbiG system. 172 matched cddid_all.tbl CDD pfam13281 pfam13281 463827 MAP3K_TRAF_bd MAP3K TRAFs-binding domain. This entry corresponds to the TNF receptor-associated factors (TRAFs)-binding domain found at the N-terminus of some MAP3Ks, like Apoptosis signal-regulating kinases (ASK). This domain is flanked by a thioredoxin-binding domain and a PH-like domain. It includes seven tetratricopeptide repeats (TPRs) and, together with the PH-like domain, constitutes the central regulatory domain of ASK1. 370 matched cddid_all.tbl CDD pfam13282 pfam13282 463828 DUF4070 Domain of unknown function (DUF4070). This is a bacterial domain often found at the C-terminus of Radical_SAM methylases. 142 matched cddid_all.tbl CDD pfam13283 pfam13283 433085 NfrA_C Bacteriophage N adsorption protein A C-term. The function of this domain is unknown but it is found at the C-terminus of bacteriophage N4 adsorption protein A, in association with an N-terminal region of TPR repeats. 173 matched cddid_all.tbl CDD pfam13284 pfam13284 433086 DUF4072 Domain of unknown function (DUF4072). This short domain is normally found at the very N-terminus of Hyrdrolases pfam00702. 46 matched cddid_all.tbl CDD pfam13285 pfam13285 290024 DUF4073 Domain of unknown function (DUF4073). This family is frequently found at the C-terminus of bacterial proteins carrying the family, Metallophos pfam00149. 157 matched cddid_all.tbl CDD pfam13286 pfam13286 433087 HD_assoc Phosphohydrolase-associated domain. This domain is found on bacterial and archaeal metal-dependent phosphohydrolases. 91 matched cddid_all.tbl CDD pfam13287 pfam13287 463829 Fn3_assoc Fn3 associated. 59 matched cddid_all.tbl CDD pfam13288 pfam13288 463830 DXPR_C DXP reductoisomerase C-terminal domain. This is the C-terminal domain of the 1-deoxy-D-xylulose-5-phosphate reductoisomerase enzyme. This domain forms a left handed super-helix. 116 matched cddid_all.tbl CDD pfam13289 pfam13289 433090 SIR2_2 SIR2-like domain. This family of proteins are related to the sirtuins. 141 matched cddid_all.tbl CDD pfam13290 pfam13290 433091 CHB_HEX_C_1 Chitobiase/beta-hexosaminidase C-terminal domain. 67 matched cddid_all.tbl CDD pfam13291 pfam13291 463831 ACT_4 ACT domain. ACT domains bind to amino acids and regulate associated enzyme domains. These ACT domains are found at the C-terminus of the RelA protein. 79 matched cddid_all.tbl CDD pfam13292 pfam13292 463832 DXP_synthase_N 1-deoxy-D-xylulose-5-phosphate synthase. This family contains 1-deoxyxylulose-5-phosphate synthase (DXP synthase), an enzyme which catalyzes the thiamine pyrophosphoate-dependent acyloin condensation reaction between carbon atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate, to yield 1-deoxy-D- xylulose-5-phosphate, a precursor in the biosynthetic pathway to isoprenoids, thiamine (vitamin B1), and pyridoxol (vitamin B6). 274 matched cddid_all.tbl CDD pfam13293 pfam13293 463833 DUF4074 Domain of unknown function (DUF4074). This family is found at the C-terminal of Homeobox proteins in Metazoa. 63 matched cddid_all.tbl CDD pfam13294 pfam13294 372549 DUF4075 Domain of unknown function (DUF4075). The members of this family are putative mature parasite-infected erythrocyte surface antigen protein from Bacillus spp. 79 matched cddid_all.tbl CDD pfam13295 pfam13295 290034 DUF4077 Domain of unknown function (DUF4077). This is the N-terminal region of methyl-accepting chemotaxis proteins from Bacillus spp. The function is not known. 176 matched cddid_all.tbl CDD pfam13296 pfam13296 463834 T6SS_Vgr Putative type VI secretion system Rhs element Vgr. This is a family of putative type VI secretion system Rhs element Vgr proteins from Proteobacteria. 108 matched cddid_all.tbl CDD pfam13297 pfam13297 463835 SDE2_2C Replication stress response SDE2 C-terminal. This domain represents the C-terminal region of the Replication stress response SDE2, a genome surveillance factor. It contains the DNA-binding SAP domain, frequently found in proteins involved in DNA repair. SDE2 C-terminal domain must be cleaved from its N-terminal at a diglycine motif within the ubiquitin-like fold, after Proliferating cell nuclear antigen (PCNA) interaction. This generates a functional protein that negatively regulates damage-inducible PCNA monoubiquitination, which then is proteolytically degraded to allow S phase progression and replication fork recovery in response to DNA damage. 80 matched cddid_all.tbl CDD pfam13298 pfam13298 433097 LigD_N DNA polymerase Ligase (LigD). This is the N terminal region of ATP dependant DNA ligase. 103 matched cddid_all.tbl CDD pfam13299 pfam13299 463836 CPSF100_C Cleavage and polyadenylation factor 2 C-terminal. This family lies at the C-terminus of many fungal and plant cleavage and polyadenylation specificity factor subunit 2 proteins. The exact function of the domain is not known, but is likely to function as a binding domain for the protein within the overall CPSF complex. 162 matched cddid_all.tbl CDD pfam13300 pfam13300 463837 DUF4078 Domain of unknown function (DUF4078). This family is found from fungi to humans, but its exact function is not known. 86 matched cddid_all.tbl CDD pfam13301 pfam13301 433100 DUF4079 Protein of unknown function (DUF4079). This is an uncharacterized family of proteins. 141 matched cddid_all.tbl CDD pfam13302 pfam13302 379112 Acetyltransf_3 Acetyltransferase (GNAT) domain. This domain catalyzes N-acetyltransferase reactions. 139 matched cddid_all.tbl CDD pfam13303 pfam13303 433101 PTS_EIIC_2 Phosphotransferase system, EIIC. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. The sugar-specific permease of the PTS consists of three domains (IIA, IIB and IIC). The IIC domain catalyzes the transfer of a phosphoryl group from IIB to the sugar substrate. 327 matched cddid_all.tbl CDD pfam13304 pfam13304 433102 AAA_21 AAA domain, putative AbiEii toxin, Type IV TA system. Several members are annotated as being of the abortive phage resistance system, in which case the family would be acting as the toxin for a type IV toxin-antitoxin resistance system. 303 matched cddid_all.tbl CDD pfam13305 pfam13305 463838 TetR_C_33 Tetracyclin repressor-like, C-terminal domain. This domain is around 80 amino acids in length. It is found to the C-terminus of a DNA-binding helix-turn-helix domain. This domain may be involved transcriptional regulation predicted to belong to the TetR family. This domain contains three conserved residues (WHG) near the C-terminus. 104 matched cddid_all.tbl CDD pfam13306 pfam13306 463839 LRR_5 BspA type Leucine rich repeat region (6 copies). This family includes a number of leucine rich repeats. This family contains a large number of BSPA-like surface antigens from Trichomonas vaginalis. 127 matched cddid_all.tbl CDD pfam13307 pfam13307 463840 Helicase_C_2 Helicase C-terminal domain. This domain is found at the C-terminus of DEAD-box helicases. 168 matched cddid_all.tbl CDD pfam13308 pfam13308 433105 YARHG YARHG domain. This presumed extracellular domain is about 70 amino acids in length. It is named YARHG after a conserved motif in the sequence. This domain is associated with peptidases and bacterial kinase proteins. Its molecular function is unknown. 84 matched cddid_all.tbl CDD pfam13309 pfam13309 463841 HTH_22 HTH domain. This domain is a helix-turn-helix domain that is likely to act as a DNA-binding domain. 63 matched cddid_all.tbl CDD pfam13310 pfam13310 463842 Virulence_RhuM Virulence protein RhuM family. There are currently no experimental data for members of this group or their homologs. However, these proteins are implicated in virulence/pathogenicity because RhuM is encoded in the SPI-3 pathogenicity island in Salmonella typhimurium. 252 matched cddid_all.tbl CDD pfam13311 pfam13311 404233 DUF4080 Protein of unknown function (DUF4080). A family of uncharacterized proteins found by clustering human gut metagenomic sequences. 188 matched cddid_all.tbl CDD pfam13312 pfam13312 433108 DUF4081 Domain of unknown function (DUF4081). This domain is often found N-terminal to the GNAT acetyltransferase domain, pfam00583 and FR47, pfam08445. 105 matched cddid_all.tbl CDD pfam13313 pfam13313 433109 DUF4082 Domain of unknown function (DUF4082). This domain is distantly related to the PHR domain pfam08005. This domain is often found between successive bacterial Ig domains, pfam13205. 143 matched cddid_all.tbl CDD pfam13314 pfam13314 372557 DUF4083 Domain of unknown function (DUF4083). This is a family of very short, approximately 60 residue, proteins from Firmicutes, that are all putatively annotated as being MutT/Nudix. However, the characteriztic Nudix motif of GX(5)EX(7)REUXEE is absent. 57 matched cddid_all.tbl CDD pfam13315 pfam13315 372558 DUF4085 Protein of unknown function (DUF4085). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 101 and 269 amino acids in length. 206 matched cddid_all.tbl CDD pfam13316 pfam13316 433110 DUF4087 Protein of unknown function (DUF4087). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 140 and 280 amino acids in length. There is a conserved RCGW sequence motif. 95 matched cddid_all.tbl CDD pfam13317 pfam13317 433111 DUF4088 Protein of unknown function (DUF4088). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 258 and 300 amino acids in length. 226 matched cddid_all.tbl CDD pfam13318 pfam13318 433112 AtzG-like 1-carboxybiuret hydrolase subunit AtzG-like. AtzG is essential for the production of soluble, active AtzE, which is a 1-carboxybiuret hydrolase. 50 matched cddid_all.tbl CDD pfam13319 pfam13319 433113 DUF4090 Protein of unknown function (DUF4090). This family of proteins is functionally uncharacterized. This family of proteins is found in cyanobacteria. Proteins in this family are approximately 90 amino acids in length. A member of this family, the ssr1528 gene was found to be regulated by an sRNA NsiR4. In addition the expression of that gene was repressed under conditions of nitrogen depletion suggesting it may have a role related to cellular nitrogen status. 84 matched cddid_all.tbl CDD pfam13320 pfam13320 463843 DUF4091 Domain of unknown function (DUF4091). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 70 amino acids in length. There is a single completely conserved residue G that may be functionally important. 66 matched cddid_all.tbl CDD pfam13321 pfam13321 372562 DUF4084 Domain of unknown function (DUF4084). This family of Firmicute proteins is frequently associated with the EAL, GGDEF and PAS families, pfam00563, pfam00990, and pfam00989. The exact function is not known. 304 matched cddid_all.tbl CDD pfam13322 pfam13322 290061 DUF4092 Domain of unknown function (DUF4092). This family is found in Proteobacteria. The function is not known. 176 matched cddid_all.tbl CDD pfam13323 pfam13323 404239 HPIH N-terminal domain with HPIH motif. This family is found in fungi on proteins carrying the PAS, pfam00989, domain. There is a well-conserved characteriztic HPIH motif, but the function is not known. 152 matched cddid_all.tbl CDD pfam13324 pfam13324 463844 GCIP Grap2 and cyclin-D-interacting. GCIP, or Grap2 and cyclin-D-interacting protein, is found in eukaryotes, and in the protein Swiss:O95273, residues 149-190 constitute a helix-loop-helix domain, residues 190-240 an acidic region, and 240-261 a leucine zipper domain. GCIP interacts with full-length Grap2 protein and with the COOH-terminal unique and SH3 domains (designated QC domain) of Grap2. It is potentially involved in the regulation of cell differentiation and proliferation through Grap2 and cyclin D-mediated signalling pathways. In mice, it is involved in G1/S-phase progression of hepatocytes, which in older animals is associated with the development of liver tumours. In vitro it acts as an inhibitory HLH protein, for example, blocking transcription of the HNF-4 promoter. In its function as a cyclin D1-binding protein it is able to reduce CDK4-mediated phosphorylation of the retinoblastoma protein and to inhibit E2F-mediated transcriptional activity. GCIP has also been shown to have interact physically with Rad (Ras associated with diabetes), Rad being important in regulating cellular senescence. 261 matched cddid_all.tbl CDD pfam13325 pfam13325 463845 MCRS_N N-terminal region of micro-spherule protein. This domain is found in plants and higher eukaryotes, and is the N-terminal region of micro-spherule proteins which repress the transactivation activities of Nrf1 (p45 nuclear factor-erythroid 2 (p45 NF-E2)-related factor 1). In conjunction with DIPA the full-length protein acts as a transcription repressor. The exact function of the region is not known. 199 matched cddid_all.tbl CDD pfam13326 pfam13326 433117 PSII_Pbs27 Photosystem II Pbs27. This family of proteins contains Pbs27, a highly conserved component of photosystem II. Pbs27 is comprised of four helices arranged in a right handed up-down-up-down fold, with a less ordered region located at the N-terminus. 140 matched cddid_all.tbl CDD pfam13327 pfam13327 433118 T3SS_LEE_assoc Type III secretion system subunit. This is a family of bacterial putative type III secretion apparatus proteins associated with the locus of enterocyte effacement (LEE). 162 matched cddid_all.tbl CDD pfam13328 pfam13328 433119 HD_4 HD domain. HD domains are metal dependent phosphohydrolases. 157 matched cddid_all.tbl CDD pfam13329 pfam13329 433120 ATG2_CAD Autophagy-related protein 2 CAD motif. The Atg2 protein, an integral membrane protein, is required for a range of functions including the regulation of autophagy in conjunction with the Atg1-Atg13 complex. Atg2 binds Atg9. The precise function of this region, with its characteriztic highly conserved CAD sequence motif, is not known. 155 matched cddid_all.tbl CDD pfam13330 pfam13330 463846 Mucin2_WxxW Mucin-2 protein WxxW repeating region. This family is repeating region found on mucins 2 and 5. The function is not known, but the repeat can be present in up to 32 copies, as in Swiss:C3Y5K5, from Branchiostoma floridae. The region carries a highly conserved WxxW sequence motif and also has at least six well conserved cysteine residues. 85 matched cddid_all.tbl CDD pfam13331 pfam13331 433122 DUF4093 Domain of unknown function (DUF4093). This domain lies at the C-terminus of primase proteins carrying the TOPRIM, pfam01751, domain. The exact function of the domain is not known. 85 matched cddid_all.tbl CDD pfam13332 pfam13332 433123 Fil_haemagg_2 Hemagglutinin repeat. 169 matched cddid_all.tbl CDD pfam13333 pfam13333 372570 rve_2 Integrase core domain. 52 matched cddid_all.tbl CDD pfam13334 pfam13334 463847 DUF4094 Domain of unknown function (DUF4094). This domain is found in plant proteins that often carry a galactosyltransferase domain, pfam01762, at their C-terminus. 91 matched cddid_all.tbl CDD pfam13335 pfam13335 433125 Mg_chelatase_C Magnesium chelatase, subunit ChlI C-terminal. This is a family of the C-terminal of putative bacterial magnesium chelatase subunit ChlI proteins. Most members have the associated pfam01078. 93 matched cddid_all.tbl CDD pfam13336 pfam13336 433126 AcetylCoA_hyd_C Acetyl-CoA hydrolase/transferase C-terminal domain. This family contains several enzymes which take part in pathways involving acetyl-CoA. Acetyl-CoA hydrolase EC:3.1.2.1 catalyzes the formation of acetate from acetyl-CoA, CoA transferase (CAT1) EC:2.8.3.- produces succinyl-CoA, and acetate-CoA transferase EC:2.8.3.8 utilizes acyl-CoA and acetate to form acetyl-CoA. 154 matched cddid_all.tbl CDD pfam13337 pfam13337 463848 BrxL_ATPase Lon-like protease BrxL-like, ATPase domain. This entry represents the ATPase domain found in BREX system Lon protease-like protein BrxL from Bacillus cereus and similar proteins. BrxL is part of a type 1 BREX system which contains a C-terminal Lon-like protease domain (pfam05362. BREX systems (bacteriophage exclusion) provide immunity against bacteriophage, a system that allows phage adsorption but prevents phage DNA replication, without degradation of the phage DNA. Methylation of bacterial DNA by PglX probably guides self/non-self discrimination. This entry also includes a few uncharacterized viral sequences. 313 matched cddid_all.tbl CDD pfam13338 pfam13338 463849 AbiEi_4 Transcriptional regulator, AbiEi antitoxin. AbiEi_4 is the cognate antitoxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is pfam13338. 49 matched cddid_all.tbl CDD pfam13339 pfam13339 463850 AATF-Che1 Apoptosis antagonizing transcription factor. The N-terminal and leucine-zipper region of the apoptosis antagonizing transcription factor-Che1. 136 matched cddid_all.tbl CDD pfam13340 pfam13340 433130 DUF4096 Putative transposase of IS4/5 family (DUF4096). 76 matched cddid_all.tbl CDD pfam13341 pfam13341 404256 RAG2_PHD RAG2 PHD domain. This domain is found at the C-terminus of the RAG2 protein. The structure of this domain has been shown bound to histone H3 trimethylated at lysine 4 (H3K4me3). 78 matched cddid_all.tbl CDD pfam13342 pfam13342 463851 Toprim_Crpt C-terminal repeat of topoisomerase. 60 matched cddid_all.tbl CDD pfam13343 pfam13343 463852 SBP_bac_6 Bacterial extracellular solute-binding protein. This family includes bacterial extracellular solute-binding proteins. 247 matched cddid_all.tbl CDD pfam13344 pfam13344 433132 Hydrolase_6 Haloacid dehalogenase-like hydrolase. This family is part of the HAD superfamily. 101 matched cddid_all.tbl CDD pfam13346 pfam13346 433133 ABC2_membrane_5 ABC-2 family transporter protein. This family is related to the ABC-2 membrane transporter family pfam01061. 206 matched cddid_all.tbl CDD pfam13347 pfam13347 433134 MFS_2 MFS/sugar transport protein. This family is part of the major facilitator superfamily of membrane transport proteins. 427 matched cddid_all.tbl CDD pfam13349 pfam13349 433135 DUF4097 Putative adhesin. This has a putative all-beta structure with a twenty-residue repeat with a highly conserved repeating GD, gly-asp, motif. It may form part of a bacterial adhesin. 246 matched cddid_all.tbl CDD pfam13350 pfam13350 463853 Y_phosphatase3 Tyrosine phosphatase family. This family is closely related to the pfam00102 and pfam00782 families. 243 matched cddid_all.tbl CDD pfam13351 pfam13351 433137 DUF4099 Protein of unknown function (DUF4099). A family of uncharacterized proteins found by clustering human gut metagenomic sequences. The C-terminal repeat region of this family is DUF4098, pfam13345. 80 matched cddid_all.tbl CDD pfam13352 pfam13352 372575 DUF4100 Protein of unknown function (DUF4100). This is a family of uncharacterized proteins found in Physcomitrella. 207 matched cddid_all.tbl CDD pfam13353 pfam13353 433138 Fer4_12 4Fe-4S single cluster domain. This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich. 137 matched cddid_all.tbl CDD pfam13354 pfam13354 463854 Beta-lactamase2 Beta-lactamase enzyme family. This is the catalytic domain of class A beta-lactamases. It is closely related to Beta-lactamase, pfam00144, the serine beta-lactamase-like superfamily, which contains the distantly related pfam00905 and PF00768 D-alanyl-D-alanine carboxypeptidase. 215 matched cddid_all.tbl CDD pfam13355 pfam13355 433140 ARC6-like_IMS ARC6-like, IMS domain. This domain corresponds to the C-terminal intermembrane space (IMS) region from protein accumulation and replication of chloroplasts 6 (ARC6) and its paralogue PARC6. ARC6 and PARC6 are components of the plastid division machinery which are essential for the chloroplast replication process, which implies the assembly and constriction of the tubulin-like FtsZ ring on the stromal surface of the inner envelope membrane (IEM) and the dynamin-like ARC5 ring on the cytosolic surface of the outer envelope membrane (OEM). ARC6 is evolutionarily related to the cyanobacterial cell division protein Ftn2/ZipN, having similar structures. This domain from ARC6 and PARC6 interacts with PDV2 and PDV1 respectively. PDV proteins recruit dynamin-like ARC5 ring to the chloroplast surface and mediates its constriction. ARC6/PARC6 are key to connect and coordinate Fst and ARC5 rings during fission. 117 matched cddid_all.tbl CDD pfam13356 pfam13356 433141 Arm-DNA-bind_3 Arm DNA-binding domain. This DNA-binding domain is found at the N-terminus of a wide variety of phage integrase proteins. 78 matched cddid_all.tbl CDD pfam13358 pfam13358 433142 DDE_3 DDE superfamily endonuclease. This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. 146 matched cddid_all.tbl CDD pfam13359 pfam13359 463855 DDE_Tnp_4 DDE superfamily endonuclease. This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. 158 matched cddid_all.tbl CDD pfam13360 pfam13360 433144 PQQ_2 PQQ-like domain. This domain contains several repeats of the PQQ repeat. 233 matched cddid_all.tbl CDD pfam13361 pfam13361 433145 UvrD_C UvrD-like helicase C-terminal domain. This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold. 377 matched cddid_all.tbl CDD pfam13362 pfam13362 433146 Toprim_3 Toprim domain. The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation. 97 matched cddid_all.tbl CDD pfam13363 pfam13363 463856 BetaGal_dom3 Beta-galactosidase, domain 3. This is the third domain of the five-domain beta-galactosidase enzyme that altogether catalyzes the hydrolysis of beta(1-3) and beta(1-4) galactosyl bonds in oligosaccharides as well as the inverse reaction of enzymatic condensation and trans-glycosylation. This domain has an Ig-like fold. 65 matched cddid_all.tbl CDD pfam13364 pfam13364 463857 BetaGal_dom4_5 Beta-galactosidase jelly roll domain. This domain is found in beta galactosidase enzymes. It has a jelly roll fold. 111 matched cddid_all.tbl CDD pfam13365 pfam13365 433149 Trypsin_2 Trypsin-like peptidase domain. This family includes trypsin-like peptidase domains. 142 matched cddid_all.tbl CDD pfam13366 pfam13366 463858 PDDEXK_3 PD-(D/E)XK nuclease superfamily. Members of this family belong to the PD-(D/E)XK nuclease superfamily 117 matched cddid_all.tbl CDD pfam13367 pfam13367 433150 PrsW-protease PrsW family intramembrane metalloprotease. This family includes members such as the experimentally characterized PrsW protease from Bacillus subtilis. PrsW mediates site-1 cleavage of anti-sigma factor RsiW, and it senses antimicrobial peptides that damage the cell membrane and other agents that cause cell envelope stress. PrsW proteases, CPBP family (type II CAAX Proteases and Bacteriocin Processing enzymes), YhfC intramembrane metalloprotease, and APH-1 are distantly related. They share four predicted core transmembrane segments and possess similar, yet distinct sets of sequence motifs. The first N-terminal motif in PrsW bears the consensus signature of 'EExxK' the second motif 'FxxxE' and the third motif possess a conserved histidine. The fourth motif, 'HxxxB', is shared by the PrsW proteases and the CPBP, APH-1 and the YhfC families. Site-directed mutagenesis indicates that either double point mutation of the two conserved glutamates in the first motif (E75A/E76A), or a single mutation of the conserved histidine in the fourth motif (H175A), are of functional importance. 195 matched cddid_all.tbl CDD pfam13368 pfam13368 433151 Toprim_C_rpt Topoisomerase C-terminal repeat. This domain is repeated up to five times to form the C-terminal region of bacterial topoisomerase immediately downstream of the zinc-finger motif. 51 matched cddid_all.tbl CDD pfam13369 pfam13369 463859 Transglut_core2 Transglutaminase-like superfamily. 155 matched cddid_all.tbl CDD pfam13370 pfam13370 433153 Fer4_13 4Fe-4S single cluster domain of Ferredoxin I. Fer4_13 is a ferredoxin I from sulfate-reducing bacteria. Chemical sequence analysis suggests that this characteriztic [4Fe-4S] cluster sulfur environment is widely distributed among ferredoxins. 58 matched cddid_all.tbl CDD pfam13371 pfam13371 463860 TPR_9 Tetratricopeptide repeat. 73 matched cddid_all.tbl CDD pfam13372 pfam13372 433155 Alginate_exp Alginate export. This domain forms an 18-stranded beta-barrel pore which is likely to act as an alginate export channel. 394 matched cddid_all.tbl CDD pfam13373 pfam13373 404283 Dsc3_C DSC E3 ubiquitin ligase complex subunit 3, C-terminal domain. This is the C-terminal domain of DSC E3 ubiquitin ligase complex subunit 3 (Dsc3), which contains two transmembrane helices and a characteriztic GFDRL sequence motif. Dsc3 is a component of the DSC E3 ubiquitin ligase complex (a Golgi-specific protein ubiquitination system) that functions in protein homeostasis under non-stress conditions, playing a role in protein quality control. Yeast DSC E3 ubiquitin ligase complex is the homolog of Hrd1 E3 ligase complex from mammals, in which Dsc1, Dsc2 and Dsc3 corresponds to Hrd1, Der1, and Usa1, respectively. Dsc3 is a Herp-like protein that acts as a bridge between Dsc1 and Dsc2 for their interaction. 141 matched cddid_all.tbl CDD pfam13374 pfam13374 463861 TPR_10 Tetratricopeptide repeat. 42 matched cddid_all.tbl CDD pfam13375 pfam13375 433157 RnfC_N RnfC Barrel sandwich hybrid domain. This domain is part of the barrel sandwich hybrid superfamily. It is found at the N-terminus of the RnfC Electron transport complex protein. It appears to be most related to the N-terminal NQRA domain (pfam05896). 101 matched cddid_all.tbl CDD pfam13376 pfam13376 433158 OmdA Bacteriocin-protection, YdeI or OmpD-Associated. This is a family of archaeal and bacterial proteins predicted to be periplasmic. YdeI is important for resistance to polymyxin B in broth and for bacterial survival in mice upon oral, but not intraperitoneal inoculation, suggesting a role for YdeI in the gastrointestinal tract of mice. Production of the ydeI gene is regulated by the Rcs (regulator of capsule synthesis) phospho-relay system pathway independently of RcsA, and additionally transcription of the protein is regulated by the stationary-phase sigma factor, RpoS (sigma-S). YdeI confers protection against cationic AMPs (Antimicrobial peptides) or bacteriocins in conjunction with the general porin Omp, thus justifying its name of OmdA, for OmpD-Associated protein. 60 matched cddid_all.tbl CDD pfam13377 pfam13377 433159 Peripla_BP_3 Periplasmic binding protein-like domain. This domain is found in a variety of transcriptional regulatory proteins. It is related to bacterial periplasmic binding proteins, although this domain is unlikely to be found in the periplasm. This domain acts as a sensor binding small molecule ligands that the DNA-binding domain responds to. This domain recognizes Sugars, sugar phosphates, sugar acids and purines (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 160 matched cddid_all.tbl CDD pfam13378 pfam13378 463862 MR_MLE_C Enolase C-terminal domain-like. This domain appears at the C-terminus of many of the proteins that carry the MR_MLE_N pfam02746 domain. EC:4.2.1.40. 217 matched cddid_all.tbl CDD pfam13379 pfam13379 463863 NMT1_2 NMT1-like family. This family is closely related to the pfam09084 family. 254 matched cddid_all.tbl CDD pfam13380 pfam13380 433162 CoA_binding_2 CoA binding domain. This domain has a Rossmann fold and is found in a number of proteins including succinyl CoA synthetases, malate and ATP-citrate ligases. 116 matched cddid_all.tbl CDD pfam13382 pfam13382 463864 Adenine_deam_C Adenine deaminase C-terminal domain. This family represents a C-terminal region of the adenine deaminase enzyme. 168 matched cddid_all.tbl CDD pfam13383 pfam13383 372586 Methyltransf_22 Methyltransferase domain. This family appears to be a methyltransferase domain. 252 matched cddid_all.tbl CDD pfam13384 pfam13384 433164 HTH_23 Homeodomain-like domain. 50 matched cddid_all.tbl CDD pfam13385 pfam13385 463865 Laminin_G_3 Concanavalin A-like lectin/glucanases superfamily. This domain belongs to the Concanavalin A-like lectin/glucanases superfamily. 151 matched cddid_all.tbl CDD pfam13386 pfam13386 463866 DsbD_2 Cytochrome C biogenesis protein transmembrane region. 199 matched cddid_all.tbl CDD pfam13387 pfam13387 433167 DUF4105 Domain of unknown function (DUF4105). This is a family of uncharacterized bacterial proteins. There is a highly conserved histidine residue and a well-conserved NCT motif. 167 matched cddid_all.tbl CDD pfam13388 pfam13388 404296 DUF4106 Protein of unknown function (DUF4106). This family of proteins are found in large numbers in the Trichomonas vaginalis proteome. The function of this protein is unknown. 431 matched cddid_all.tbl CDD pfam13389 pfam13389 372588 DUF4107 Protein of unknown function (DUF4107). This family of putative proteins are found in Trichomonas vaginalis in large numbers. The function of this protein is unknown. 167 matched cddid_all.tbl CDD pfam13390 pfam13390 290126 DUF4108 Protein of unknown function (DUF4108). This family of putative proteins are found in Trichomonas vaginalis in large numbers. The function of this protein is unknown. 145 matched cddid_all.tbl CDD pfam13391 pfam13391 433168 HNH_2 HNH endonuclease. 66 matched cddid_all.tbl CDD pfam13392 pfam13392 433169 HNH_3 HNH endonuclease. This is a zinc-binding loop of Fold group 7 as found in endo-deoxy-ribonucleases and HNH nucleases. 46 matched cddid_all.tbl CDD pfam13393 pfam13393 433170 tRNA-synt_His Histidyl-tRNA synthetase. This is a family of class II aminoacyl-tRNA synthetase-like and ATP phosphoribosyltransferase regulatory subunits. 309 matched cddid_all.tbl CDD pfam13394 pfam13394 433171 Fer4_14 4Fe-4S single cluster domain. 115 matched cddid_all.tbl CDD pfam13395 pfam13395 433172 HNH_4 HNH endonuclease. This HNH nuclease domain is found in CRISPR-related proteins. 55 matched cddid_all.tbl CDD pfam13396 pfam13396 463867 PLDc_N Phospholipase_D-nuclease N-terminal. This family is often found at the very N-terminus of proteins from the phospholipase_D-nuclease family, PLDc, pfam00614. However, a large number of members are full-length within this family. 43 matched cddid_all.tbl CDD pfam13397 pfam13397 433174 RbpA RNA polymerase-binding protein. RbpA is a family bacterial RNA polymerase-binding proteins. RbpA acts as a transcription factor by binding to the sigma subunit of RNA polymerase. 104 matched cddid_all.tbl CDD pfam13398 pfam13398 433175 Peptidase_M50B Peptidase M50B-like. This is a family of bacterial and plant peptidases in the same family as MEROPS:M50B. 194 matched cddid_all.tbl CDD pfam13399 pfam13399 463868 LytR_C LytR cell envelope-related transcriptional attenuator. This family appears at the C-terminus of members of the LytR_cpsA_psr, pfam03816, family 87 matched cddid_all.tbl CDD pfam13400 pfam13400 433177 Tad Putative Flp pilus-assembly TadE/G-like. This is an N-terminal domain on a family of putative Flp pilus-assembly proteins. The exact function is not known. The Flp-pilus biogenesis genes include the Tad genes, and some members of this family are putatively assigned as being TadG. 47 matched cddid_all.tbl CDD pfam13401 pfam13401 379165 AAA_22 AAA domain. 129 matched cddid_all.tbl CDD pfam13402 pfam13402 433178 Peptidase_M60 Peptidase M60, enhancin and enhancin-like. This family of peptidases contains a zinc metallopeptidase motif (HEXXHX(8,28)E) and possesses mucinase activity. It includes the viral enhancins as well as enhancin-like peptidases from bacterial species. Enhancins are a class of metalloproteases found in some baculoviruses that enhance viral infection by degrading the peritrophic membrane (PM) of the insect midgut. Bacterial enhancins are found to be cytotoxic when compared to viral enhancin, however, suggesting that the bacterial enhancins do not enhance infection in the same way as viral enhancin. Bacterial enhancins may have evolved a distinct biochemical function. These bacterial domains are peptidases targetting host glycoproteins and thus probably play an important role in successful colonization of both vertebrate mucosal surfaces and the invertebrate digestive tract by both mutualistic and pathogenic microbes. This family has been augmented by a merge with the sequences in the Enhancin Pfam family. 268 matched cddid_all.tbl CDD pfam13403 pfam13403 433179 Hint_2 Hint domain. This domain is found in inteins. 147 matched cddid_all.tbl CDD pfam13404 pfam13404 433180 HTH_AsnC-type AsnC-type helix-turn-helix domain. 41 matched cddid_all.tbl CDD pfam13405 pfam13405 463869 EF-hand_6 EF-hand domain. 30 matched cddid_all.tbl CDD pfam13406 pfam13406 404311 SLT_2 Transglycosylase SLT domain. This family is related to the SLT domain pfam01464. 292 matched cddid_all.tbl CDD pfam13407 pfam13407 433182 Peripla_BP_4 Periplasmic binding protein domain. This domain is found in a variety of bacterial periplasmic binding proteins. This domain recognizes fructose (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 259 matched cddid_all.tbl CDD pfam13408 pfam13408 433183 Zn_ribbon_recom Recombinase zinc beta ribbon domain. This short bacterial protein contains a zinc ribbon domain that is likely to be DNA-binding. This domain is found in site specific recombinase proteins. This family appears most closely related to pfam04606. 58 matched cddid_all.tbl CDD pfam13409 pfam13409 433184 GST_N_2 Glutathione S-transferase, N-terminal domain. This family is closely related to pfam02798. 68 matched cddid_all.tbl CDD pfam13410 pfam13410 433185 GST_C_2 Glutathione S-transferase, C-terminal domain. This domain is closely related to pfam00043. 67 matched cddid_all.tbl CDD pfam13411 pfam13411 463870 MerR_1 MerR HTH family regulatory protein. 66 matched cddid_all.tbl CDD pfam13412 pfam13412 404317 HTH_24 Winged helix-turn-helix DNA-binding. 45 matched cddid_all.tbl CDD pfam13413 pfam13413 433187 HTH_25 Helix-turn-helix domain. This domain is a helix-turn-helix domain that probably binds to DNA. 62 matched cddid_all.tbl CDD pfam13414 pfam13414 315977 TPR_11 TPR repeat. 42 matched cddid_all.tbl CDD pfam13415 pfam13415 433188 Kelch_3 Galactose oxidase, central domain. 49 matched cddid_all.tbl CDD pfam13416 pfam13416 433189 SBP_bac_8 Bacterial extracellular solute-binding protein. This family includes bacterial extracellular solute-binding proteins. 281 matched cddid_all.tbl CDD pfam13417 pfam13417 433190 GST_N_3 Glutathione S-transferase, N-terminal domain. 75 matched cddid_all.tbl CDD pfam13418 pfam13418 433191 Kelch_4 Galactose oxidase, central domain. 49 matched cddid_all.tbl CDD pfam13419 pfam13419 404323 HAD_2 Haloacid dehalogenase-like hydrolase. 178 matched cddid_all.tbl CDD pfam13420 pfam13420 433192 Acetyltransf_4 Acetyltransferase (GNAT) domain. 153 matched cddid_all.tbl CDD pfam13421 pfam13421 433193 Band_7_1 SPFH domain-Band 7 family. 211 matched cddid_all.tbl CDD pfam13422 pfam13422 463871 DUF4110 Domain of unknown function (DUF4110). This is a family that is found predominantly at the C-terminus of Kelch-containing proteins. However, the exact function of this region is not known. 95 matched cddid_all.tbl CDD pfam13423 pfam13423 463872 UCH_1 Ubiquitin carboxyl-terminal hydrolase. 305 matched cddid_all.tbl CDD pfam13424 pfam13424 315987 TPR_12 Tetratricopeptide repeat. 77 matched cddid_all.tbl CDD pfam13425 pfam13425 404328 O-antigen_lig O-antigen ligase like membrane protein. 461 matched cddid_all.tbl CDD pfam13426 pfam13426 463873 PAS_9 PAS domain. This domain is found in many signalling proteins in which it functions as a sensor domain. It recognizes FMN, Zn(II), FAD and riboflavin (MAtilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 93 matched cddid_all.tbl CDD pfam13427 pfam13427 433197 DUF4111 Domain of unknown function (DUF4111). Although the exact function of this domain is not known it frequently appears downstream of the family Nucleotidyltransferase, pfam01909. It is also found in species associated with methicillin-resistant bacteria. 102 matched cddid_all.tbl CDD pfam13428 pfam13428 463874 TPR_14 Tetratricopeptide repeat. 44 matched cddid_all.tbl CDD pfam13429 pfam13429 433199 TPR_15 Tetratricopeptide repeat. 279 matched cddid_all.tbl CDD pfam13430 pfam13430 433200 DUF4112 Domain of unknown function (DUF4112). This family has several highly conserved GD sequence-motifs of unknown function. The family is found in bacteria, archaea and fungi. 104 matched cddid_all.tbl CDD pfam13431 pfam13431 433201 TPR_17 Tetratricopeptide repeat. 34 matched cddid_all.tbl CDD pfam13432 pfam13432 433202 TPR_16 Tetratricopeptide repeat. This family is found predominantly at the C-terminus of transglutaminase enzyme core regions. 68 matched cddid_all.tbl CDD pfam13433 pfam13433 463875 Peripla_BP_5 Periplasmic binding protein domain. This domain is found in a variety of bacterial periplasmic binding proteins. 363 matched cddid_all.tbl CDD pfam13434 pfam13434 433204 Lys_Orn_oxgnase L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase. This is a family of Rossmann fold oxidoreductases that catalyze NADPH-dependent hydroxylation and are involved in siderophore biosynthesis. This family includes L-ornithine 5-monooxygenase, which catalyzes the hydroxylation of L-ornithine at the N5 position, and L-lysine 6-monooxygenase, which catalyzes the hydroxylation of lysine at the N6 position (EC:1.14.13.59). 338 matched cddid_all.tbl CDD pfam13435 pfam13435 372604 Cytochrome_C554 Cytochrome c554 and c-prime. This family is a tetra-haem cytochrome involved in the oxidation of ammonia. It is found in both phototrophic and denitrifying bacteria. 84 matched cddid_all.tbl CDD pfam13436 pfam13436 433205 Gly-zipper_OmpA Glycine-zipper domain. 44 matched cddid_all.tbl CDD pfam13437 pfam13437 433206 HlyD_3 HlyD family secretion protein. This is a family of largely bacterial haemolysin translocator HlyD proteins. 104 matched cddid_all.tbl CDD pfam13438 pfam13438 463876 DUF4113 Domain of unknown function (DUF4113). Although the function is not known this domain occurs almost invariably at the very C-terminus of the IMS family DNA-polymerase repair proteins, IMS, pfam00817. 49 matched cddid_all.tbl CDD pfam13439 pfam13439 463877 Glyco_transf_4 Glycosyltransferase Family 4. 169 matched cddid_all.tbl CDD pfam13440 pfam13440 404342 Polysacc_synt_3 Polysaccharide biosynthesis protein. 293 matched cddid_all.tbl CDD pfam13441 pfam13441 463878 Gly-zipper_YMGG YMGG-like Gly-zipper. 45 matched cddid_all.tbl CDD pfam13442 pfam13442 463879 Cytochrome_CBB3 Cytochrome C oxidase, cbb3-type, subunit III. 67 matched cddid_all.tbl CDD pfam13443 pfam13443 433211 HTH_26 Cro/C1-type HTH DNA-binding domain. This is a helix-turn-helix domain that probably binds to DNA. 63 matched cddid_all.tbl CDD pfam13444 pfam13444 463880 Acetyltransf_5 Acetyltransferase (GNAT) domain. This family contains proteins with N-acetyltransferase functions. 102 matched cddid_all.tbl CDD pfam13445 pfam13445 463881 zf-RING_UBOX RING-type zinc-finger. This zinc-finger is a typical RING-type of plant ubiquitin ligases. 38 matched cddid_all.tbl CDD pfam13446 pfam13446 463882 RPT A repeated domain in UCH-protein. This is a repeated domain found in de-ubiquitinating proteins. It's exact function is not known although it is likely to be involved in the binding of the Ubps in the complex with Rsp5 and Rup1. 59 matched cddid_all.tbl CDD pfam13447 pfam13447 433215 Multi-haem_cyto Seven times multi-haem cytochrome CxxCH. This domain carries up to seven CxxCH repeated sequence motifs, characteriztic of multi-haem cytochromes. 269 matched cddid_all.tbl CDD pfam13448 pfam13448 433216 DUF4114 Domain of unknown function (DUF4114). This is a repeated domain that is found towards the C-terminal of many different types of bacterial proteins. There are highly conserved glutamate and aspartate residues suggesting that this domain might carry enzymic activity. 81 matched cddid_all.tbl CDD pfam13449 pfam13449 433217 Phytase-like Esterase-like activity of phytase. This is a repeated domain that carries several highly conserved Glu and Asp residues indicating the likelihood that the domain incorporates the enzymic activity of the PLC-like phospho-diesterase part of the proteins. 284 matched cddid_all.tbl CDD pfam13450 pfam13450 433218 NAD_binding_8 NAD(P)-binding Rossmann-like domain. 67 matched cddid_all.tbl CDD pfam13451 pfam13451 463883 zf-trcl Probable zinc-ribbon domain. This is a probable zinc-binding domain with two CxxC sequence motifs, found in various families of bacteria. 48 matched cddid_all.tbl CDD pfam13452 pfam13452 433220 MaoC_dehydrat_N N-terminal half of MaoC dehydratase. It is clear from the structures of bacterial members of MaoC dehydratase, pfam01575, that the full-length functional dehydratase enzyme is made up of two structures that dimerize to form a whole. Divergence of the N- and C- monomers in higher eukaryotes has led to two distinct domains, this one and MaoC_dehydratas. However, in order to function as an enzyme both are required together. 132 matched cddid_all.tbl CDD pfam13453 pfam13453 433221 zf-TFIIB Transcription factor zinc-finger. 41 matched cddid_all.tbl CDD pfam13454 pfam13454 433222 NAD_binding_9 FAD-NAD(P)-binding. 155 matched cddid_all.tbl CDD pfam13455 pfam13455 372608 MUG113 Meiotically up-regulated gene 113. This is a family of fungal proteins found to be up-regulated in meiosis. 73 matched cddid_all.tbl CDD pfam13456 pfam13456 433223 RVT_3 Reverse transcriptase-like. This domain is found in plants and appears to be part of a retrotransposon. 123 matched cddid_all.tbl CDD pfam13457 pfam13457 463884 GW GW (Gly-Tryp) dipeptide domain. This is a GW domain found in the C-terminal of InlB proteins which belong to the extended family of internalin proteins found in Listeria. These 80 residue GW domains are unique to InlB among the internalins but are present in other proteins of Gram-positive bacteria. GW domains (named after a GlyTryp dipeptide) are structurally and evolutionary related to SH3 domains. Despite of this, GW domains are unlikely to act as functional mimics of SH3 domains since their potential proline-binding sites are blocked or destroyed. They are highly basic and interact with poly-anions. The GW domains are responsible for the non-covalent attachment to the bacterial cell surface through binding to lipoteichoic acid. The GW domains alone do not stimulate uptake, but they synergize with the Met-binding internalin domain. 74 matched cddid_all.tbl CDD pfam13458 pfam13458 433225 Peripla_BP_6 Periplasmic binding protein. This family includes a diverse range of periplasmic binding proteins. 342 matched cddid_all.tbl CDD pfam13459 pfam13459 404359 Fer4_15 4Fe-4S single cluster domain. 66 matched cddid_all.tbl CDD pfam13460 pfam13460 463885 NAD_binding_10 NAD(P)H-binding. 183 matched cddid_all.tbl CDD pfam13462 pfam13462 433227 Thioredoxin_4 Thioredoxin. 164 matched cddid_all.tbl CDD pfam13463 pfam13463 433228 HTH_27 Winged helix DNA-binding domain. 68 matched cddid_all.tbl CDD pfam13464 pfam13464 433229 DUF4115 Domain of unknown function (DUF4115). This short domain is often found at the C-terminus of proteins containing a helix-turn-helix domain. The function of this domain is unknown. 67 matched cddid_all.tbl CDD pfam13465 pfam13465 463886 zf-H2C2_2 Zinc-finger double domain. 26 matched cddid_all.tbl CDD pfam13466 pfam13466 433231 STAS_2 STAS domain. The STAS (after Sulphate Transporter and AntiSigma factor antagonist) domain is found in the C-terminal region of Sulphate transporters and bacterial antisigma factor antagonists. It has been suggested that this domain may have a general NTP binding function. 80 matched cddid_all.tbl CDD pfam13467 pfam13467 433232 RHH_4 Ribbon-helix-helix domain. This short bacterial protein contains a ribbon-helix-helix domain that is likely to be DNA-binding. 65 matched cddid_all.tbl CDD pfam13468 pfam13468 433233 Glyoxalase_3 Glyoxalase-like domain. This domain is related to the Glyoxalase domain pfam00903. 175 matched cddid_all.tbl CDD pfam13469 pfam13469 463887 Sulfotransfer_3 Sulfotransferase family. 173 matched cddid_all.tbl CDD pfam13470 pfam13470 463888 PIN_3 PIN domain. Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases). 115 matched cddid_all.tbl CDD pfam13471 pfam13471 433236 Transglut_core3 Transglutaminase-like superfamily. This family includes uncharacterized proteins that are related to the transglutaminase like domain pfam01841. 117 matched cddid_all.tbl CDD pfam13472 pfam13472 463889 Lipase_GDSL_2 GDSL-like Lipase/Acylhydrolase family. This family of presumed lipases and related enzymes are similar to pfam00657. 176 matched cddid_all.tbl CDD pfam13473 pfam13473 379208 Cupredoxin_1 Cupredoxin-like domain. The cupredoxin-like fold consists of a beta-sandwich with 7 strands in 2 beta-sheets, which is arranged in a Greek-key beta-barrel. 104 matched cddid_all.tbl CDD pfam13474 pfam13474 433238 SnoaL_3 SnoaL-like domain. This family contains a large number of proteins that share the SnoaL fold. 121 matched cddid_all.tbl CDD pfam13475 pfam13475 433239 DUF4116 Domain of unknown function (DUF4116). 49 matched cddid_all.tbl CDD pfam13476 pfam13476 463890 AAA_23 AAA domain. 190 matched cddid_all.tbl CDD pfam13477 pfam13477 433241 Glyco_trans_4_2 Glycosyl transferase 4-like. 139 matched cddid_all.tbl CDD pfam13478 pfam13478 463891 XdhC_C XdhC Rossmann domain. This entry is the rossmann domain found in the Xanthine dehydrogenase accessory protein. 143 matched cddid_all.tbl CDD pfam13479 pfam13479 433243 AAA_24 AAA domain. This AAA domain is found in a wide variety of presumed phage proteins. 199 matched cddid_all.tbl CDD pfam13480 pfam13480 433244 Acetyltransf_6 Acetyltransferase (GNAT) domain. This family contains proteins with N-acetyltransferase functions. 143 matched cddid_all.tbl CDD pfam13481 pfam13481 463892 AAA_25 AAA domain. This AAA domain is found in a wide variety of presumed DNA repair proteins. 193 matched cddid_all.tbl CDD pfam13482 pfam13482 433246 RNase_H_2 RNase_H superfamily. 163 matched cddid_all.tbl CDD pfam13483 pfam13483 433247 Lactamase_B_3 Beta-lactamase superfamily domain. This family is part of the beta-lactamase superfamily and is related to pfam00753. 160 matched cddid_all.tbl CDD pfam13484 pfam13484 463893 Fer4_16 4Fe-4S double cluster binding domain. 65 matched cddid_all.tbl CDD pfam13485 pfam13485 290220 Peptidase_MA_2 Peptidase MA superfamily. 247 matched cddid_all.tbl CDD pfam13486 pfam13486 372615 Dehalogenase Reductive dehalogenase subunit. This family is most frequently associated with a Fer4 iron-sulfur cluster towards the C-terminal region. 288 matched cddid_all.tbl CDD pfam13487 pfam13487 433249 HD_5 HD domain. HD domains are metal dependent phosphohydrolases. 64 matched cddid_all.tbl CDD pfam13488 pfam13488 463894 Gly-zipper_Omp Glycine zipper. 46 matched cddid_all.tbl CDD pfam13489 pfam13489 404385 Methyltransf_23 Methyltransferase domain. This family appears to be a methyltransferase domain. 162 matched cddid_all.tbl CDD pfam13490 pfam13490 463895 zf-HC2 Putative zinc-finger. This is a putative zinc-finger found in some anti-sigma factor proteins. 35 matched cddid_all.tbl CDD pfam13491 pfam13491 463896 FtsK_4TM 4TM region of DNA translocase FtsK/SpoIIIE. 4TM_FtsK is the integral membrane domain of the FtsK DNA tranlocases. During sporulation in Bacillus subtilis, the SpoIIIE protein is believed to form a translocation pore at the leading edge of the nearly closed septum. The E. coli FtsK protein is homologous to SpoIIIE, and can free chromosomes trapped in vegetative septa. 171 matched cddid_all.tbl CDD pfam13492 pfam13492 433253 GAF_3 GAF domain. 129 matched cddid_all.tbl CDD pfam13493 pfam13493 463897 DUF4118 Domain of unknown function (DUF4118). This domain is found in a wide variety of bacterial signalling proteins. It is likely to be a transmembrane domain involved in ligand sensing. 107 matched cddid_all.tbl CDD pfam13494 pfam13494 433255 DUF4119 Domain of unknown function, B. Theta Gene description (DUF4119). Based on Bacteroides thetaiotaomicron gene BT_0594, a putative uncharacterized protein. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or vs when in culture 87 matched cddid_all.tbl CDD pfam13495 pfam13495 463898 Phage_int_SAM_4 Phage integrase, N-terminal SAM-like domain. 83 matched cddid_all.tbl CDD pfam13496 pfam13496 463899 DUF4120 Domain of unknown function (DUF4120). Based on Bacteroides thetaiotaomicron gene BT_2585, a putative uncharacterized protein. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or vs when in culture. 96 matched cddid_all.tbl CDD pfam13497 pfam13497 433257 DUF4121 Domain of unknown function (DUF4121). Based on Bacteroides thetaiotaomicron gene BT_2588, a putative uncharacterized protein. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or vs when in culture. 264 matched cddid_all.tbl CDD pfam13498 pfam13498 404393 DUF4122 Domain of unknown function (DUF4122). Based on Bacteroides thetaiotaomicron gene BT_2607, a putative uncharacterized protein. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or vs when in culture. 220 matched cddid_all.tbl CDD pfam13499 pfam13499 463900 EF-hand_7 EF-hand domain pair. 67 matched cddid_all.tbl CDD pfam13500 pfam13500 433259 AAA_26 AAA domain. This domain is found in a number of proteins involved in cofactor biosynthesis such as dethiobiotin synthase and cobyric acid synthase. This domain contains a P-loop motif. 198 matched cddid_all.tbl CDD pfam13501 pfam13501 463901 SoxY Sulfur oxidation protein SoxY. This domain is found in the sulfur oxidation protein SoxY. It is closely related to the Desulfoferrodoxin family pfam01880. Dissimilatory oxidation of thiosulfate is carried out by the ubiquitous sulfur-oxidizing (Sox) multi-enzyme system. In this system, SoxY plays a key role, functioning as the sulfur substrate-binding protein that offers its sulfur substrate, which is covalently bound to a conserved C-terminal cysteine, to another oxidizing Sox enzyme. The structure of this domain shows an Ig-like fold. 109 matched cddid_all.tbl CDD pfam13502 pfam13502 463902 AsmA_2 AsmA-like C-terminal region. This family is similar to the C-terminal of the AsmA protein of E. coli. 226 matched cddid_all.tbl CDD pfam13503 pfam13503 433262 DUF4123 Domain of unknown function (DUF4123). This presumed domain is functionally uncharacterized. It is about 120 amino acids in length and contains several conserved motifs that may be functionally important. This domain is sometimes associated with the FHA domain. 128 matched cddid_all.tbl CDD pfam13505 pfam13505 463903 OMP_b-brl Outer membrane protein beta-barrel domain. This domain is found in a wide range of outer membrane proteins. This domain assumes a membrane bound beta-barrel fold. 175 matched cddid_all.tbl CDD pfam13506 pfam13506 433264 Glyco_transf_21 Glycosyl transferase family 21. This is a family of ceramide beta-glucosyltransferases - EC:2.4.1.80. 173 matched cddid_all.tbl CDD pfam13507 pfam13507 463904 GATase_5 CobB/CobQ-like glutamine amidotransferase domain. This family captures members that are not found in pfam00310, pfam07685 and pfam13230. 260 matched cddid_all.tbl CDD pfam13508 pfam13508 463905 Acetyltransf_7 Acetyltransferase (GNAT) domain. This domain catalyzes N-acetyltransferase reactions. 84 matched cddid_all.tbl CDD pfam13509 pfam13509 433267 S1_2 S1 domain. The S1 domain was originally identified as a repeat motif in the ribosomal S1 protein. It was later identified in a wide range of proteins. The S1 domain has an OB-fold structure. The S1 domain is involved in nucleic acid binding. 61 matched cddid_all.tbl CDD pfam13510 pfam13510 433268 Fer2_4 2Fe-2S iron-sulfur cluster binding domain. The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This cluster appears within sarcosine oxidase proteins. 82 matched cddid_all.tbl CDD pfam13511 pfam13511 433269 DUF4124 Domain of unknown function (DUF4124). This presumed domain is found in a variety of bacterial proteins. It is found associated at the N-terminus associated with other domains such as the SLT domain and glutaredoxin domains in some proteins. The function of this domain is unknown, but it may have an Ig-like fold. 53 matched cddid_all.tbl CDD pfam13512 pfam13512 433270 TPR_18 Tetratricopeptide repeat. 145 matched cddid_all.tbl CDD pfam13513 pfam13513 463906 HEAT_EZ HEAT-like repeat. The HEAT repeat family is related to armadillo/beta-catenin-like repeats (see pfam00514). These EZ repeats are found in subunits of cyanobacterial phycocyanin lyase and other proteins and probably carry out a scaffolding role. 55 matched cddid_all.tbl CDD pfam13514 pfam13514 433272 AAA_27 AAA domain. This domain is found in a number of double-strand DNA break proteins. This domain contains a P-loop motif. 207 matched cddid_all.tbl CDD pfam13515 pfam13515 433273 FUSC_2 Fusaric acid resistance protein-like. 126 matched cddid_all.tbl CDD pfam13516 pfam13516 463907 LRR_6 Leucine Rich repeat. 24 matched cddid_all.tbl CDD pfam13517 pfam13517 433275 FG-GAP_3 FG-GAP-like repeat. This entry represents a repeat found in alpha integrins and related proteins in which form a 7-fold repeat that adopts a beta-propeller fold. This repeat contains a putative calcium-binding site. These repeats are found in multiple proteins from eukaryotes and bacteria and mediate diverse biological processes at both molecular and cellular levels, such as cell-cell interactions, host-pathogen recognition or innate immune responses. 61 matched cddid_all.tbl CDD pfam13518 pfam13518 463908 HTH_28 Helix-turn-helix domain. This helix-turn-helix domain is often found in transposases and is likely to be DNA-binding. 52 matched cddid_all.tbl CDD pfam13519 pfam13519 463909 VWA_2 von Willebrand factor type A domain. 103 matched cddid_all.tbl CDD pfam13520 pfam13520 404414 AA_permease_2 Amino acid permease. 427 matched cddid_all.tbl CDD pfam13521 pfam13521 433278 AAA_28 AAA domain. 164 matched cddid_all.tbl CDD pfam13522 pfam13522 433279 GATase_6 Glutamine amidotransferase domain. This domain is a class-II glutamine amidotransferase domain found in a variety of enzymes, such as asparagine synthetase and glutamine--fructose-6-phosphate transaminase. 130 matched cddid_all.tbl CDD pfam13523 pfam13523 433280 Acetyltransf_8 Acetyltransferase (GNAT) domain. This domain catalyzes N-acetyltransferase reactions. 145 matched cddid_all.tbl CDD pfam13524 pfam13524 433281 Glyco_trans_1_2 Glycosyl transferases group 1. 93 matched cddid_all.tbl CDD pfam13525 pfam13525 433282 YfiO Outer membrane lipoprotein. This outer membrane lipoprotein carries a TPR-like region towards its N-terminal. YfiO in E.coli is one of three outer membrane lipoproteins that form a multicomponent YaeT complex in the outer membrane of Gram-negative bacteria that is involved in the targeting and folding of beta-barrel outer membrane proteins. YfiO is the only essential lipoprotein component of the complex. It is required for the proper assembly and/or targeting of outer membrane proteins to the outer membrane. Through its interactions with NlpB it maintains the functional integrity of the YaeT complex. 200 matched cddid_all.tbl CDD pfam13526 pfam13526 404420 DUF4125 Protein of unknown function (DUF4125). 197 matched cddid_all.tbl CDD pfam13527 pfam13527 404421 Acetyltransf_9 Acetyltransferase (GNAT) domain. This domain catalyzes N-acetyltransferase reactions. 124 matched cddid_all.tbl CDD pfam13528 pfam13528 404422 Glyco_trans_1_3 Glycosyl transferase family 1. 321 matched cddid_all.tbl CDD pfam13529 pfam13529 379241 Peptidase_C39_2 Peptidase_C39 like family. 139 matched cddid_all.tbl CDD pfam13530 pfam13530 463910 SCP2_2 Sterol carrier protein domain. 105 matched cddid_all.tbl CDD pfam13531 pfam13531 463911 SBP_bac_11 Bacterial extracellular solute-binding protein. This family includes bacterial extracellular solute-binding proteins. 225 matched cddid_all.tbl CDD pfam13532 pfam13532 433285 2OG-FeII_Oxy_2 2OG-Fe(II) oxygenase superfamily. 191 matched cddid_all.tbl CDD pfam13533 pfam13533 433286 Biotin_lipoyl_2 Biotin-lipoyl like. 50 matched cddid_all.tbl CDD pfam13534 pfam13534 433287 Fer4_17 4Fe-4S dicluster domain. This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich. 61 matched cddid_all.tbl CDD pfam13535 pfam13535 316093 ATP-grasp_4 ATP-grasp domain. This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity. 160 matched cddid_all.tbl CDD pfam13536 pfam13536 463912 EmrE Putative multidrug resistance efflux transporter. This is a membrane protein family whose members are purported to be related to the DMT or Drug/Metabolite Transporter (DMT) Superfamily. Members are all uncharacterized. 259 matched cddid_all.tbl CDD pfam13537 pfam13537 433289 GATase_7 Glutamine amidotransferase domain. This domain is a class-II glutamine amidotransferase domain found in a variety of enzymes such as asparagine synthetase and glutamine-fructose-6-phosphate transaminase. 123 matched cddid_all.tbl CDD pfam13538 pfam13538 463913 UvrD_C_2 UvrD-like helicase C-terminal domain. This domain is found at the C-terminus of a wide variety of helicase enzymes. This domain has a AAA-like structural fold. 52 matched cddid_all.tbl CDD pfam13539 pfam13539 433291 Peptidase_M15_4 D-alanyl-D-alanine carboxypeptidase. This family resembles VanY, pfam02557, which is part of the peptidase M15 family. 67 matched cddid_all.tbl CDD pfam13540 pfam13540 463914 RCC1_2 Regulator of chromosome condensation (RCC1) repeat. 30 matched cddid_all.tbl CDD pfam13541 pfam13541 433293 ChlI Subunit ChlI of Mg-chelatase. 121 matched cddid_all.tbl CDD pfam13542 pfam13542 463915 HTH_Tnp_ISL3 Helix-turn-helix domain of transposase family ISL3. 51 matched cddid_all.tbl CDD pfam13543 pfam13543 463916 SAM_KSR1 SAM like domain present in kinase suppressor RAS 1. 70 matched cddid_all.tbl CDD pfam13545 pfam13545 463917 HTH_Crp_2 Crp-like helix-turn-helix domain. This family represents a crp-like helix-turn-helix domain that is likely to bind DNA. 68 matched cddid_all.tbl CDD pfam13546 pfam13546 433296 DDE_5 DDE superfamily endonuclease. This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. 271 matched cddid_all.tbl CDD pfam13547 pfam13547 433297 GTA_TIM GTA TIM-barrel-like domain. This domain is found in the gene transfer agent protein. An unusual system of genetic exchange exists in the purple nonsulfur bacterium Rhodobacter capsulatus. DNA transmission is mediated by a small bacteriophage-like particle called the gene transfer agent (GTA) that transfers random 4.5-kb segments of the producing cell's genome to recipient cells, where allelic replacement occurs. The genes involved in this process appear to be found widely in bacteria. According to the SUPERFAMILY database this domain has a TIM barrel fold. 298 matched cddid_all.tbl CDD pfam13548 pfam13548 433298 DUF4126 Domain of unknown function (DUF4126). 174 matched cddid_all.tbl CDD pfam13549 pfam13549 463918 ATP-grasp_5 ATP-grasp domain. This family includes a diverse set of enzymes that possess ATP-dependent carboxylate-amine ligase activity. 221 matched cddid_all.tbl CDD pfam13550 pfam13550 433300 Phage-tail_3 Putative phage tail protein. This putative domain is found in the large gene transfer agent protein. These produce defective phage like particles. This domain is similar to other phage-tail protein families. 163 matched cddid_all.tbl CDD pfam13551 pfam13551 433301 HTH_29 Winged helix-turn helix. This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding. 64 matched cddid_all.tbl CDD pfam13552 pfam13552 404442 DUF4127 Protein of unknown function (DUF4127). This family of uncharacterized bacterial proteins are about 500 amino acids in length. 493 matched cddid_all.tbl CDD pfam13553 pfam13553 463919 FIIND "Function to find. The function to find (FIIND) was initially discovered in two proteins, NLRP1 (aka NALP1, CARD7, NAC, DEFCAP) and CARD8 (aka TUCAN, Cardinal). NLRP1 is a member of the Nod-like receptor (NLR) protein superfamily and is involved in apoptosis and inflammation. To date, it is the only NLR protein known to have a FIIND domain. The FIIND domain is also present in the CARD8 protein where, like in NLRP1, it is followed by a C-terminal CARD domain. Both proteins are described to form an ""inflammasome"", a macro-molecular complex able to process caspase 1 and activate pro-IL1beta. The FIIND domain is present in only a very small subset of the kingdom of life, comprising primates, rodents (mouse, rat), carnivores (dog) and a few more, such as horse. The function of this domain is yet to be determined. Publications describing the newly discovered NLRP1 protein failed to identify it as a separate domain; for example, it was taken as part of the adjacent leucine rich repeat domain (LRR). Upon discovery of CARD8 it was noted that the N-terminal region shared significant sequence identity with an undescribed region in NLRP1. Before getting its final name, FIIND, this domain was termed NALP1-associated domain (NAD)." 252 matched cddid_all.tbl CDD pfam13554 pfam13554 433303 DUF4128 Bacteriophage related domain of unknown function. The three-dimensional structure of NP_888769.1, PDB:2L25, reveals a tail terminator protein gpU fold, which suggests that the protein could have a bacteriophage origin. 128 matched cddid_all.tbl CDD pfam13555 pfam13555 433304 AAA_29 P-loop containing region of AAA domain. 61 matched cddid_all.tbl CDD pfam13556 pfam13556 433305 HTH_30 PucR C-terminal helix-turn-helix domain. This helix-turn-helix domain is often found at the C-terminus of PucR-like transcriptional regulators such as Swiss:O32138 and is likely to be DNA-binding. 56 matched cddid_all.tbl CDD pfam13557 pfam13557 463920 Phenol_MetA_deg Putative MetA-pathway of phenol degradation. 237 matched cddid_all.tbl CDD pfam13558 pfam13558 463921 SbcC_Walker_B SbcC/RAD50-like, Walker B motif. This entry represents the Walker B domain of RAD50 from eukaryotes and the prokaryotic homolog SbcCD complex subunit C. RAD50-ATPase forms a complex with Mre11-nuclease that detects and processes diverse and obstructed DNA ends. This domain is separated of the Walker A domain by a long coiled-coil domain and forms the nucleotide-binding domain (NBD) when the coiled coils fold back on themselves and bring together Walker A and B domains. Two RAD50-NBDs forms heterotetramers with a Mre11 nuclease dimer that assemble as catalytic head module that binds and cleaves DNA in an ATP-dependent reaction. Through secondary structural analysis, it has been suggested that there is a wide structural conservation in the Rad50/SMC protein family as seen in structural similarities between RAD50's hook and ABC-ATPase MukB's elbow region. 90 matched cddid_all.tbl CDD pfam13559 pfam13559 433308 DUF4129 Domain of unknown function (DUF4129). This presumed domain is found at the C-terminus of proteins that contain a transglutaminase core domain. The function of this domain is unknown. The domain has a conserved TXXE motif. 70 matched cddid_all.tbl CDD pfam13560 pfam13560 433309 HTH_31 Helix-turn-helix domain. This domain is a helix-turn-helix domain that probably binds to DNA. 64 matched cddid_all.tbl CDD pfam13561 pfam13561 433310 adh_short_C2 Enoyl-(Acyl carrier protein) reductase. This domain is found in Enoyl-(Acyl carrier protein) reductases. 236 matched cddid_all.tbl CDD pfam13562 pfam13562 463922 NTP_transf_4 Sugar nucleotidyl transferase. This is a probable sugar nucleotidyl transferase family. 146 matched cddid_all.tbl CDD pfam13563 pfam13563 433312 2_5_RNA_ligase2 2'-5' RNA ligase superfamily. This family contains proteins related to pfam02834. These proteins are likely to be enzymes, but they may not share the RNA ligase activity. 152 matched cddid_all.tbl CDD pfam13564 pfam13564 433313 DoxX_2 DoxX-like family. This family of uncharacterized proteins are related to DoxX pfam07681. 103 matched cddid_all.tbl CDD pfam13565 pfam13565 463923 HTH_32 Homeodomain-like domain. 73 matched cddid_all.tbl CDD pfam13566 pfam13566 463924 DUF4130 Domain of unknown function (DUF4130. 157 matched cddid_all.tbl CDD pfam13567 pfam13567 379269 DUF4131 Domain of unknown function (DUF4131). This domain is frequently found to the N-terminus of the Competence domain, pfam03772. 165 matched cddid_all.tbl CDD pfam13568 pfam13568 433316 OMP_b-brl_2 Outer membrane protein beta-barrel domain. This domain is found in a wide range of outer membrane proteins. This domain assumes a membrane bound beta-barrel fold. 175 matched cddid_all.tbl CDD pfam13569 pfam13569 433317 DUF4132 Domain of unknown function (DUF4132). This domain might be involved in the biosynthesis of the molybdopterin cofactor in E.coli. 179 matched cddid_all.tbl CDD pfam13570 pfam13570 463925 PQQ_3 PQQ-like domain. 36 matched cddid_all.tbl CDD pfam13571 pfam13571 433319 DUF4133 Domain of unknown function (DUF4133). Based on Bacteroides thetaiotaomicron gene BT_0094, a putative uncharacterized protein as seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), It appears to be upregulated in the presence of host or vs when in culture. 91 matched cddid_all.tbl CDD pfam13572 pfam13572 433320 DUF4134 Domain of unknown function (DUF4134). Based on Bacteroides thetaiotaomicron gene BT_0095, a putative uncharacterized protein As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), It appears to be upregulated in the presence of host or vs when in culture. 92 matched cddid_all.tbl CDD pfam13573 pfam13573 404462 SprB SprB repeat. This repeat occurs several times in SprB, a cell surface protein involved in gliding motility in the bacterium Flavobacterium johnsoniae. 37 matched cddid_all.tbl CDD pfam13574 pfam13574 372637 Reprolysin_2 Metallo-peptidase family M12B Reprolysin-like. This zinc-binding metallo-peptidase has the characteriztic binding motif HExxGHxxGxxH of Reprolysin-like peptidases of family M12B. 193 matched cddid_all.tbl CDD pfam13575 pfam13575 433321 DUF4135 Domain of unknown function (DUF4135). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and archaea, and is approximately 380 amino acids in length. The family is found in association with pfam05147. This domain may be involved in synthesis of a lantibiotic compound. 374 matched cddid_all.tbl CDD pfam13576 pfam13576 433322 Pentapeptide_3 Pentapeptide repeats (9 copies). 48 matched cddid_all.tbl CDD pfam13577 pfam13577 433323 SnoaL_4 SnoaL-like domain. This family contains a large number of proteins that share the SnoaL fold. 125 matched cddid_all.tbl CDD pfam13578 pfam13578 433324 Methyltransf_24 Methyltransferase domain. This family appears to be a methyltransferase domain. 106 matched cddid_all.tbl CDD pfam13579 pfam13579 433325 Glyco_trans_4_4 Glycosyl transferase 4-like domain. 158 matched cddid_all.tbl CDD pfam13580 pfam13580 433326 SIS_2 SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars. 138 matched cddid_all.tbl CDD pfam13581 pfam13581 433327 HATPase_c_2 Histidine kinase-like ATPase domain. 127 matched cddid_all.tbl CDD pfam13582 pfam13582 463926 Reprolysin_3 Metallo-peptidase family M12B Reprolysin-like. This zinc-binding metallo-peptidase has the characteriztic binding motif HExxGHxxGxxH of Reprolysin-like peptidases of family M12B. 122 matched cddid_all.tbl CDD pfam13583 pfam13583 404471 Reprolysin_4 Metallo-peptidase family M12B Reprolysin-like. This zinc-binding metallo-peptidase has the characteriztic binding motif HExxGHxxGxxH of Reprolysin-like peptidases of family M12B. 203 matched cddid_all.tbl CDD pfam13584 pfam13584 463927 BatD BatD DUF11 like domain. This domain that probably has an Ig-like fold is found in three copies in BatD proteins that are involved in tolerance to oxygen in in Bacteroides spp. 93 matched cddid_all.tbl CDD pfam13585 pfam13585 404473 CHU_C CHU_C Type IX secretion signal domain. This domain was initially identified from proteins from C. hutchinsonii giving rise to the CHU name. This domain adopts an immunoglobulin like domain that is foundat the C-terminus of various bacterial cell surface proteins. This domain was shown to be essential for localization of the CHU_3220 protein. It is likely that this domain target the proteins containing it to the type IX secretion system. This domain is cleaved off the protein which is then anchored to the outer membrane. 85 matched cddid_all.tbl CDD pfam13586 pfam13586 463928 DDE_Tnp_1_2 Transposase DDE domain. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. 90 matched cddid_all.tbl CDD pfam13588 pfam13588 433331 HSDR_N_2 Type I restriction enzyme R protein N terminus (HSDR_N). This family consists of a number of N terminal regions found in type I restriction enzyme R (HSDR) proteins. Restriction and modification (R/M) systems are found in a wide variety of prokaryotes and are thought to protect the host bacterium from the uptake of foreign DNA. Type I restriction and modification systems are encoded by three genes: hsdR, hsdM, and hsdS. The three polypeptides, HsdR, HsdM, and HsdS, often assemble to give an enzyme (R2M2S1) that modifies hemimethylated DNA and restricts unmethylated DNA. 110 matched cddid_all.tbl CDD pfam13589 pfam13589 433332 HATPase_c_3 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase. This family represents, additionally, the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90. 135 matched cddid_all.tbl CDD pfam13590 pfam13590 463929 DUF4136 Domain of unknown function (DUF4136). This domain is found in bacterial lipoproteins. The function is not known. 148 matched cddid_all.tbl CDD pfam13591 pfam13591 433334 MerR_2 MerR HTH family regulatory protein. 84 matched cddid_all.tbl CDD pfam13592 pfam13592 433335 HTH_33 Winged helix-turn helix. This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding. 60 matched cddid_all.tbl CDD pfam13593 pfam13593 433336 SBF_like SBF-like CPA transporter family (DUF4137). These family members are 7TM putative membrane transporter proteins. The family is similar to the SBF family of bile-acid symporters, pfam01758. 313 matched cddid_all.tbl CDD pfam13595 pfam13595 404481 DUF4138 Domain of unknown function (DUF4138). Based on Bacteroides thetaiotaomicron gene BT_4780, a putative uncharacterized protein. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or vs when in culture. 244 matched cddid_all.tbl CDD pfam13596 pfam13596 404482 PAS_10 PAS domain. This is a sensor domain that recognizes O2, CO and NO (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 106 matched cddid_all.tbl CDD pfam13597 pfam13597 463930 NRDD Anaerobic ribonucleoside-triphosphate reductase. 554 matched cddid_all.tbl CDD pfam13598 pfam13598 433338 DUF4139 Domain of unknown function (DUF4139). This family is usually found at the C-terminus of proteins. 317 matched cddid_all.tbl CDD pfam13599 pfam13599 433339 Pentapeptide_4 Pentapeptide repeats (9 copies). 78 matched cddid_all.tbl CDD pfam13600 pfam13600 463931 DUF4140 N-terminal domain of unknown function (DUF4140). This family is often found at the N-terminus of its member proteins, with DUF4139, pfam13598, at the C-terminus. 99 matched cddid_all.tbl CDD pfam13601 pfam13601 463932 HTH_34 Winged helix DNA-binding domain. 80 matched cddid_all.tbl CDD pfam13602 pfam13602 433341 ADH_zinc_N_2 Zinc-binding dehydrogenase. 131 matched cddid_all.tbl CDD pfam13603 pfam13603 433342 tRNA-synt_1_2 Leucyl-tRNA synthetase, Domain 2. This is a family of the conserved region of Leucine-tRNA ligase or Leucyl-tRNA synthetase, EC:6.1.1.4. 185 matched cddid_all.tbl CDD pfam13604 pfam13604 433343 AAA_30 AAA domain. This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B. 191 matched cddid_all.tbl CDD pfam13605 pfam13605 433344 DUF4141 Domain of unknown function (DUF4141). Based on Bacteroides thetaiotaomicron gene BT_4772, a putative uncharacterized protein. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or vs when in culture. 53 matched cddid_all.tbl CDD pfam13606 pfam13606 463933 Ank_3 Ankyrin repeat. Ankyrins are multifunctional adaptors that link specific proteins to the membrane-associated, spectrin- actin cytoskeleton. This repeat-domain is a 'membrane-binding' domain of up to 24 repeated units, and it mediates most of the protein's binding activities. 30 matched cddid_all.tbl CDD pfam13607 pfam13607 433345 Succ_CoA_lig Succinyl-CoA ligase like flavodoxin domain. This domain contains the catalytic domain from Succinyl-CoA ligase alpha subunit and other related enzymes. A conserved histidine is involved in phosphoryl transfer. 138 matched cddid_all.tbl CDD pfam13608 pfam13608 290339 Potyvirid-P3 Protein P3 of Potyviral polyprotein. This is the P3 protein section of the Potyviridae polyproteins. The function is not known except that the protein is essential to viral survival. 452 matched cddid_all.tbl CDD pfam13609 pfam13609 433346 Porin_4 Gram-negative porin. 311 matched cddid_all.tbl CDD pfam13610 pfam13610 433347 DDE_Tnp_IS240 DDE domain. This DDE domain is found in a wide variety of transposases including those found in IS240, IS26, IS6100 and IS26. 138 matched cddid_all.tbl CDD pfam13611 pfam13611 372647 Peptidase_S76 Serine peptidase of plant viral polyprotein, P1. This family is the P1 protein of the Potyviridae polyproteins that is a serine peptidase at the N-terminus. The catalytic triad in Swiss:Q65730, the ssRNA positive-strand Brome streak mosaic rymovirus, is His-311, Asp-322 and Ser-355. 119 matched cddid_all.tbl CDD pfam13612 pfam13612 433348 DDE_Tnp_1_3 Transposase DDE domain. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contains three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction. 154 matched cddid_all.tbl CDD pfam13613 pfam13613 463934 HTH_Tnp_4 Helix-turn-helix of DDE superfamily endonuclease. This domain is the probable DNA-binding region of transposase enzymes, necessary for efficient DNA transposition. Most of the members derive from the IS superfamily IS5 and rather fewer from IS4. 53 matched cddid_all.tbl CDD pfam13614 pfam13614 433350 AAA_31 AAA domain. This family includes a wide variety of AAA domains including some that have lost essential nucleotide binding residues in the P-loop. 177 matched cddid_all.tbl CDD pfam13616 pfam13616 404499 Rotamase_3 PPIC-type PPIASE domain. Rotamases increase the rate of protein folding by catalysing the interconversion of cis-proline and trans-proline. 116 matched cddid_all.tbl CDD pfam13617 pfam13617 463935 Lipoprotein_19 YnbE-like lipoprotein. This family includes lipoproteins similar to E. coli YnbE. Protein in this family are typically 60 amino acids in length and contain an N-terminal lipid attachment site, which has been included in the alignment to increase sensitivity. The specific function of these proteins is unknown. 34 matched cddid_all.tbl CDD pfam13618 pfam13618 433352 Gluconate_2-dh3 Gluconate 2-dehydrogenase subunit 3. This family corresponds to subunit 3 of the Gluconate 2-dehydrogenase enzyme that catalyzes the conversion of gluconate to 2-dehydro-D-gluconate EC:1.1.99.3. 134 matched cddid_all.tbl CDD pfam13619 pfam13619 433353 KTSC KTSC domain. This short domain is named after Lysine tRNA synthetase C-terminal domain. It is found at the C-terminus of some Lysyl tRNA synthetases as well as a single domain in bacterial proteins. The domain is about 60 amino acids in length and contains a reasonably conserved YXY motif in the centre of the sequence. The function of this domain is unknown but it could be an RNA binding domain. 58 matched cddid_all.tbl CDD pfam13620 pfam13620 433354 CarboxypepD_reg Carboxypeptidase regulatory-like domain. 81 matched cddid_all.tbl CDD pfam13621 pfam13621 463936 Cupin_8 Cupin-like domain. This cupin like domain shares similarity to the JmjC domain. 251 matched cddid_all.tbl CDD pfam13622 pfam13622 463937 4HBT_3 Thioesterase-like superfamily. This family contains a wide variety of enzymes, principally thioesterases. These enzymes are part of the Hotdog fold superfamily. 246 matched cddid_all.tbl CDD pfam13623 pfam13623 463938 SurA_N_2 SurA N-terminal domain. This domain is found at the N-terminus of the chaperone SurA. It is a helical domain of unknown function. The C-terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. 145 matched cddid_all.tbl CDD pfam13624 pfam13624 433358 SurA_N_3 SurA N-terminal domain. This domain is found at the N-terminus of the chaperone SurA. It is a helical domain of unknown function. The C-terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. 162 matched cddid_all.tbl CDD pfam13625 pfam13625 463939 Helicase_C_3 Helicase conserved C-terminal domain. This domain family is found in a wide variety of helicases and helicase-related proteins. 121 matched cddid_all.tbl CDD pfam13627 pfam13627 433360 LPAM_2 Prokaryotic lipoprotein-attachment site. In prokaryotes, membrane lipoproteins are synthesized with a precursor signal peptide, which is cleaved by a specific lipoprotein signal peptidase (signal peptidase II). The peptidase recognizes a conserved sequence and cuts upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached. 22 matched cddid_all.tbl CDD pfam13628 pfam13628 433361 DUF4142 Domain of unknown function (DUF4142). This is a bacterial family of unknown function. 138 matched cddid_all.tbl CDD pfam13629 pfam13629 433362 T2SS-T3SS_pil_N Pilus formation protein N terminal region. 72 matched cddid_all.tbl CDD pfam13630 pfam13630 463940 SdpI SdpI/YfhL protein family. This family of proteins includes the SdpI and YfhL proteins from B. subtilis. The SdpI protein is a multipass integral membrane protein that protects toxin-producing cells from being killed. Killing is mediated by the exported toxic protein SdpC an extracellular protein that induces the synthesis of an immunity protein. 71 matched cddid_all.tbl CDD pfam13631 pfam13631 433364 Cytochrom_B_N_2 Cytochrome b(N-terminal)/b6/petB. 169 matched cddid_all.tbl CDD pfam13632 pfam13632 433365 Glyco_trans_2_3 Glycosyl transferase family group 2. Members of this family of prokaryotic proteins include putative glucosyltransferases, which are involved in bacterial capsule biosynthesis. 192 matched cddid_all.tbl CDD pfam13634 pfam13634 463941 Nucleoporin_FG Nucleoporin FG repeat region. This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145. 90 matched cddid_all.tbl CDD pfam13635 pfam13635 463942 DUF4143 Domain of unknown function (DUF4143). This domain is almost always found C-terminal to an ATPase core family. 159 matched cddid_all.tbl CDD pfam13636 pfam13636 433368 Methyltranf_PUA RNA-binding PUA-like domain of methyltransferase RsmF. Methyltranf_PUA is the second of two C-terminal domains found on bacterial methyltransferase RsmF that modifies the 16S ribosomal RNA. It has some structural similarity to the RNA-binding PUA domains suggesting that it is involved in RNA recognition. It lies downstream of the catalytic centre of this methyltransferase, family pfam01189. 50 matched cddid_all.tbl CDD pfam13637 pfam13637 372654 Ank_4 Ankyrin repeats (many copies). 54 matched cddid_all.tbl CDD pfam13638 pfam13638 433369 PIN_4 PIN domain. Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases). 131 matched cddid_all.tbl CDD pfam13639 pfam13639 433370 zf-RING_2 Ring finger domain. 44 matched cddid_all.tbl CDD pfam13640 pfam13640 463943 2OG-FeII_Oxy_3 2OG-Fe(II) oxygenase superfamily. This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily. 94 matched cddid_all.tbl CDD pfam13641 pfam13641 433372 Glyco_tranf_2_3 Glycosyltransferase like family 2. Members of this family of prokaryotic proteins include putative glucosyltransferase, which are involved in bacterial capsule biosynthesis. 230 matched cddid_all.tbl CDD pfam13642 pfam13642 433373 DUF4144 protein structure with unknown function. A family based on the three-dimensional structure of YP_926445.1 (PDB:2L6O) 95 matched cddid_all.tbl CDD pfam13643 pfam13643 433374 DUF4145 Domain of unknown function (DUF4145). This domain is found in a variety of restriction endonuclease enzymes. The exact function of this domain is uncertain. 88 matched cddid_all.tbl CDD pfam13644 pfam13644 404523 DKNYY DKNYY family. This family represents a group of proteins found enriched in fusobacteria. These proteins contain many repeats of a DKNXXYY motif. The repeats are spaced at about 35 amino acid residues intervals. These proteins are likely to be associated with the membrane. The specific function of these proteins is unknown. 150 matched cddid_all.tbl CDD pfam13645 pfam13645 463944 YkuD_2 L,D-transpeptidase catalytic domain. This family is related to pfam03734. 167 matched cddid_all.tbl CDD pfam13646 pfam13646 433376 HEAT_2 HEAT repeats. This family includes multiple HEAT repeats. 88 matched cddid_all.tbl CDD pfam13647 pfam13647 404526 Glyco_hydro_80 Glycosyl hydrolase family 80 of chitosanase A. This is a small family of bacterial chitosanases. These have lysozyme-like activity. 307 matched cddid_all.tbl CDD pfam13648 pfam13648 404527 Lipocalin_4 Lipocalin-like domain. 89 matched cddid_all.tbl CDD pfam13649 pfam13649 463945 Methyltransf_25 Methyltransferase domain. This family appears to be a methyltransferase domain. 96 matched cddid_all.tbl CDD pfam13650 pfam13650 433378 Asp_protease_2 Aspartyl protease. This family consists of predicted aspartic proteases, typically from 180 to 230 amino acids in length, in MEROPS clan AA. This model describes the well-conserved 121-residue C-terminal region. The poorly conserved, variable length N-terminal region usually contains a predicted transmembrane helix. 90 matched cddid_all.tbl CDD pfam13651 pfam13651 404530 EcoRI_methylase Adenine-specific methyltransferase EcoRI. This methylase recognizes the double-stranded sequence GAATTC, causes specific methylation on A-3 on both strands, and protects the DNA from cleavage by the EcoRI endonuclease. 343 matched cddid_all.tbl CDD pfam13652 pfam13652 433379 QSregVF Putative quorum-sensing-regulated virulence factor. This is a family of short ~14 kDa proteins from Psuedomonas. The structure of UniProtKB:Q9HY15 a secreted protein has been solved and deposited as PDB:3npd. It comprises one structural domain with five beta-strands and five alpha-helices. Various comparative structural prediction methods plus its genomic location point to the protein forming a functional dimer with its adjacent genomic partner, UniProtKB:Q9HY14, in pfam12843. Together these might be regulated by the other product from the PotABCD operon, namely the putrescine-binding periplasmic protein UniProtKB:Q9HY16. which has been implicated in quorum-sensing. QSregVF is certainly up-regulated in quorum-sensing, and is predicted to be a virulence factor. 112 matched cddid_all.tbl CDD pfam13653 pfam13653 433380 GDPD_2 Glycerophosphoryl diester phosphodiesterase family. This family also includes glycerophosphoryl diester phosphodiesterases as well as agrocinopine synthase, the similarity to GDPD has been noted. This family appears to have weak but not significant matches to mammalian phospholipase C pfam00388, which suggests that this family may adopt a TIM barrel fold. 30 matched cddid_all.tbl CDD pfam13654 pfam13654 463946 AAA_32 LonB-like, AAA domain. This entry includes a wide variety of AAA domains, including some that have lost essential nucleotide binding residues in the P-loop. This domain is found in Lon proteases from archaea and bacteria. 133 matched cddid_all.tbl CDD pfam13655 pfam13655 433382 RVT_N N-terminal domain of reverse transcriptase. This domain is found at the N-terminus of bacterial reverse transcriptases. 83 matched cddid_all.tbl CDD pfam13656 pfam13656 463947 RNA_pol_L_2 RNA polymerase Rpb3/Rpb11 dimerization domain. The two eukaryotic subunits Rpb3 and Rpb11 dimerize to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerization domain of the alpha subunit/Rpb3 is interrupted by an insert domain (pfam01000). Some of the alpha subunits also contain iron-sulphur binding domains (pfam00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Many of the members of this family carry only the N-terminal region of Rpb11. 75 matched cddid_all.tbl CDD pfam13657 pfam13657 433384 Couple_hipA HipA N-terminal domain. This domain is found to the N-terminus of HipA-like proteins. It is also found in isolation in some proteins. 95 matched cddid_all.tbl CDD pfam13660 pfam13660 463948 DUF4147 Domain of unknown function (DUF4147). This domain is frequently found at the N-terminus of proteins carrying the glycerate kinase-like domain MOFRL, pfam05161. 230 matched cddid_all.tbl CDD pfam13661 pfam13661 433386 2OG-FeII_Oxy_4 2OG-Fe(II) oxygenase superfamily. This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily. 98 matched cddid_all.tbl CDD pfam13662 pfam13662 433387 Toprim_4 Toprim domain. The toprim domain is found in a wide variety of enzymes involved in nucleic acid manipulation. 85 matched cddid_all.tbl CDD pfam13663 pfam13663 433388 DUF4148 Domain of unknown function (DUF4148). 62 matched cddid_all.tbl CDD pfam13664 pfam13664 463949 DUF4149 Domain of unknown function (DUF4149). 102 matched cddid_all.tbl CDD pfam13665 pfam13665 433390 Tox-PAAR-like Toxin PAAR-like domain. This domain is found at the N-terminal of bacterial toxin systems, including Tse7 (type IV secretion exported 7) from Pseudomonas aeruginosa, a type VI secretion exported toxin with DNase activity that induces growth arrest and ultimately DNA degradation within target cell. The structure of this domain has a PAAR-like organization necessary for interaction with T6SS VgrG tip and correct toxin delivery. 108 matched cddid_all.tbl CDD pfam13667 pfam13667 463950 ThiC-associated ThiC-associated domain. This domain is most frequently found at the N-terminus of the ThiC family of proteins, pfam01964. The function is not known. 71 matched cddid_all.tbl CDD pfam13668 pfam13668 433392 Ferritin_2 Ferritin-like domain. This family contains ferritins and other ferritin-like proteins such as members of the DPS family and bacterioferritins. 138 matched cddid_all.tbl CDD pfam13669 pfam13669 463951 Glyoxalase_4 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily. 109 matched cddid_all.tbl CDD pfam13670 pfam13670 433394 PepSY_2 Peptidase propeptide and YPEB domain. This region is likely to have a protease inhibitory function (personal obs:C Yeats). The name is derived from Peptidase & Bacillus subtilis YPEB. 83 matched cddid_all.tbl CDD pfam13671 pfam13671 463952 AAA_33 AAA domain. This family of domains contain only a P-loop motif, that is characteriztic of the AAA superfamily. Many of the proteins in this family are just short fragments so there is no Walker B motif. 143 matched cddid_all.tbl CDD pfam13672 pfam13672 404547 PP2C_2 Protein phosphatase 2C. Protein phosphatase 2C is a Mn++ or Mg++ dependent protein serine/threonine phosphatase. 209 matched cddid_all.tbl CDD pfam13673 pfam13673 463953 Acetyltransf_10 Acetyltransferase (GNAT) domain. This family contains proteins with N-acetyltransferase functions such as Elp3-related proteins. 128 matched cddid_all.tbl CDD pfam13675 pfam13675 433397 PilJ Type IV pili methyl-accepting chemotaxis transducer N-term. This domain is found on many type IV pili methyl-accepting chemotaxis transducer proteins where there is also a HAMP signature towards the C-terminus. It is a monomodular four-helix bundle and recognizes nitrate and nitrite (Matilla et al. FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 112 matched cddid_all.tbl CDD pfam13676 pfam13676 463954 TIR_2 TIR domain. This is a family of Toll-like receptors. 118 matched cddid_all.tbl CDD pfam13677 pfam13677 463955 MotB_plug Membrane MotB of proton-channel complex MotA/MotB. This is the MotB member of the E.coli MotA/MotB proton-channel complex that forms the stator of the bacterial membrane flagellar motor. Key residues act as a plug to prevent premature proton flow. The plug is in the periplasm just C-terminal to the MotB TM, consisting of an amphipathic alpha helix flanked by Pro-52 and Pro-65, eg in Swiss:D3V2T1. In addition to the Pro residues, Ile-58, Tyr-61, and Phe 62 are also essential for plug function. 57 matched cddid_all.tbl CDD pfam13678 pfam13678 372668 Peptidase_M85 NFkB-p65-degrading zinc protease. This family of bacterial metallo-peptidases is thought to compromise the inflammatory response by degrading p65 thereby down-regulating the NF-kappaB signalling pathway. NF-kappa-B is a pleiotropic transcription factor which is present in almost all cell types and is involved in many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis. NF-kappa-B is a homo- or heterodimeric complex formed by the Rel-like domain-containing proteins RELA/p65, RELB, NFKB1/p105, NFKB1/p50, REL and NFKB2/p52; and the heterodimeric p65-p50 complex appears to be most abundant one. 251 matched cddid_all.tbl CDD pfam13679 pfam13679 379330 Methyltransf_32 Methyltransferase domain. This family appears to be a methyltransferase domain. 138 matched cddid_all.tbl CDD pfam13680 pfam13680 404552 DUF4152 Protein of unknown function (DUF4152). This family of proteins is functionally uncharacterized. This family of proteins is found in archaea. Proteins in this family are approximately 230 amino acids in length. The structure of PF2046 from pyrococcus furiosus has been solved. It shows an RNaseH like fold that conserves critical catalytic residues. This suggests that these proteins may cleave nucleic acid. 224 matched cddid_all.tbl CDD pfam13681 pfam13681 433400 PilX Type IV pilus assembly protein PilX C-term. This family is likely to be the C-terminal region of type IV pilus assembly PilX or PilW proteins. 93 matched cddid_all.tbl CDD pfam13682 pfam13682 433401 CZB Chemoreceptor zinc-binding domain. The chemoreceptor zinc-binding domain (CZB) is found in bacterial signal transduction proteins - most frequently receptors involved in chemotaxis and motility, but also in c-di-GMP signalling and nitrate/nitrite-sensing. Originally discovered in the cytoplasmic chemoreceptor TlpD from Helicobacter pylori, it is often found C-terminal to the MCPsignal domain in cytoplasmic chemoreceptor proteins. The CZB domain contains a core sequence motif, Hxx[WFYL]x21-28Cx[LFMVI]Gx[WFLVI]x18-27HxxxH. The highly-conserved H-C-H-H residues of this motif are believed to coordinate zinc; mutating the latter two histidines of the motif to alanines abolishes Zn binding. This domain binds zinc with high affinity, with a Kd in the femtomolar range. This domain has been shown in E. coli to be a zinc sensor that regulates the catalytic activity of pfam00990. This domain also binds the chemoattractant HOCl at a site very close to that of zinc. It has been shown that zinc participates in HOCl sensing by forming a redox 'Cys-Zn switch' that reacts towards HOCl (Matilla et. al.,FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 64 matched cddid_all.tbl CDD pfam13683 pfam13683 433402 rve_3 Integrase core domain. 67 matched cddid_all.tbl CDD pfam13684 pfam13684 433403 Dak1_2 Dihydroxyacetone kinase family. This is the kinase domain of the dihydroxyacetone kinase family. 313 matched cddid_all.tbl CDD pfam13685 pfam13685 404557 Fe-ADH_2 Iron-containing alcohol dehydrogenase. 251 matched cddid_all.tbl CDD pfam13686 pfam13686 433404 DrsE_2 DsrE/DsrF/DrsH-like family. DsrE is a small soluble protein involved in intracellular sulfur reduction. The family also includes YrkE proteins. 156 matched cddid_all.tbl CDD pfam13687 pfam13687 463956 DUF4153 Domain of unknown function (DUF4153). Members of this family are annotated as putative inner membrane proteins. 371 matched cddid_all.tbl CDD pfam13688 pfam13688 372673 Reprolysin_5 Metallo-peptidase family M12. 191 matched cddid_all.tbl CDD pfam13689 pfam13689 433405 DUF4154 YfiR/HmsC-like. This family of proteins is found in bacteria and includes YfiR from E. coli. YfiR has been shown to regulate YfiN, a diguanylate cyclase and a bifunctional protein that produces c-di-GMP in response to reductive stress and then dynamically relocates to the division site to arrest cell division in response to envelope stress in Escherichia coli. YfiR may serve as a periplasmic redox sensor that regulates YfiN activity in response to reducing conditions. HmsC in Yersinia Pestis is the orthologue of YfiR from E. coli. HmsC is a periplasmic protein that interacts directly with the periplasmic domain (PD) of HmsD and causes proteolytic degradation of HmsD, which in turn negatively regulates Y. pestis biofilm formation. 140 matched cddid_all.tbl CDD pfam13690 pfam13690 433406 CheX Chemotaxis phosphatase CheX. CheX is very closely related to the CheC chemotaxis phosphatase, but it dimerizes in a different way, via a continuous beta sheet between the subunits. CheC and CheX both dephosphorylate CheY, although CheC requires binding of CheD to achieve the activity of CheX. The ability of bacteria to modulate their swimming behaviour in the presence of external chemicals (nutrients and repellents) is one of the most rudimentary behavioural responses known, but the the individual components are very sensitively tuned. 94 matched cddid_all.tbl CDD pfam13691 pfam13691 404562 Lactamase_B_4 tRNase Z endonuclease. This is family of tRNase Z enzymes, that are closely related structurally to the Lactamase_B family members. tRNase Z is the endonuclease that is involved in tRNA 3'-end maturation through removal of the 3'-trailer sequences from tRNA precursors. The fission yeast Schizosaccharomyces pombe contains two candidate tRNase Zs encoded by two essential genes. The first, Swiss:Q10155, is targeted to the nucleus and has an SV40 nuclear localization signal at its N-terminus, consisting of four consecutive arginine and lysine residues between residues 208 and 211 (KKRK) that is critical for the NLS function. The second, Swiss:P87168, is targeted to the mitochondria, with an N-terminal mitochondrial targeting signal within the first 38 residues. 63 matched cddid_all.tbl CDD pfam13692 pfam13692 463957 Glyco_trans_1_4 Glycosyl transferases group 1. 138 matched cddid_all.tbl CDD pfam13693 pfam13693 433408 HTH_35 Winged helix-turn-helix DNA-binding. 70 matched cddid_all.tbl CDD pfam13694 pfam13694 404565 Hph Sec63/Sec62 complex-interacting family. This is a family of closely related Hph proteins that are integral endoplasmic reticulum (ER) membrane proteins required for yeast survival under environmental stress conditions. They interact with several subunits of the Sec63/Sec62 complex that mediates post-translational translocation of proteins into the ER. Cells with mutant Hph1 and Hph2 proteins revealed phenotypes resembling those of mutants defective for vacuolar proton ATPase (V-ATPase) activity. The yeast V-ATPase is a multisubunit complex whose function, structure, and assembly have been well characterized. Cells with impaired V-ATPase activity fail to acidify the vacuole, cannot grow at alkaline pH, and are sensitive to high concentrations of extracellular calcium. 187 matched cddid_all.tbl CDD pfam13695 pfam13695 463958 zf-3CxxC Zinc-binding domain. This is a family with several pairs of CxxC motifs possibly representing a multiple zinc-binding region. Only one pair of cysteines is associated with a highly conserved histidine residue. 96 matched cddid_all.tbl CDD pfam13696 pfam13696 463959 zf-CCHC_2 Zinc knuckle. This is a zinc-binding domain of the form CxxCxxxGHxxxxC from a variety of different species. 21 matched cddid_all.tbl CDD pfam13698 pfam13698 433411 DUF4156 Domain of unknown function (DUF4156). The function of this family is unknown but members are annotated as putative lipoprotein outer membrane proteins. 88 matched cddid_all.tbl CDD pfam13699 pfam13699 433412 DUF4157 Domain of unknown function (DUF4157). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 80 amino acids in length. This domain contains an HEXXH motif that is characteriztic of many families of metallopeptidases. However, no peptidase activity has been shown for this domain. 79 matched cddid_all.tbl CDD pfam13700 pfam13700 433413 DUF4158 Domain of unknown function (DUF4158). The exact function of this domain is not clear, but it frequently occurs as an N-terminal region of transposase 3 or IS3 family of insertion elements. 165 matched cddid_all.tbl CDD pfam13701 pfam13701 433414 DDE_Tnp_1_4 Transposase DDE domain group 1. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. 433 matched cddid_all.tbl CDD pfam13702 pfam13702 433415 Lysozyme_like Lysozyme-like. 165 matched cddid_all.tbl CDD pfam13704 pfam13704 433416 Glyco_tranf_2_4 Glycosyl transferase family 2. Members of this family of prokaryotic proteins include putative glucosyltransferases, 97 matched cddid_all.tbl CDD pfam13705 pfam13705 463960 TRC8_N TRC8 N-terminal domain. This region is found at the N-terminus of the TRC8 protein. TRC8 is an E3 ubiquitin-protein ligase also known as RNF139. This region contains 12 transmembrane domains. This region has been suggested to contain a sterol sensing domain. It has been found that TRC8 protein levels are sterol responsive and that it binds and stimulates ubiquitylation of the endoplasmic reticulum anchor protein INSIG. 489 matched cddid_all.tbl CDD pfam13707 pfam13707 463961 RloB RloB-like protein. This family includes the RloB protein that is found within a bacterial restriction modification operon. This family includes the AbiLii protein that is found as part of a plasmid encoded phage abortive infection mechanism. Deletion within abiLii abolished the phage resistance. The family includes some proteins annotated as CRISPR Csm2 proteins. 158 matched cddid_all.tbl CDD pfam13708 pfam13708 433419 DUF4942 Domain of unknown function (DUF4942). The function of this family is not known. 184 matched cddid_all.tbl CDD pfam13709 pfam13709 433420 DUF4159 Domain of unknown function (DUF4159). Members of this family are hypothetical proteins. 191 matched cddid_all.tbl CDD pfam13710 pfam13710 463962 ACT_5 ACT domain. ACT domains bind to amino acids and regulate associated enzyme domains. These ACT domains are found at the C-terminus of the RelA protein. 62 matched cddid_all.tbl CDD pfam13711 pfam13711 463963 DUF4160 Domain of unknown function (DUF4160). 61 matched cddid_all.tbl CDD pfam13712 pfam13712 463964 Glyco_tranf_2_5 Glycosyltransferase like family. Members of this family of prokaryotic proteins include putative glucosyltransferases, which are involved in bacterial capsule biosynthesis. 210 matched cddid_all.tbl CDD pfam13713 pfam13713 404581 BRX_N Transcription factor BRX N-terminal domain. The BREVIS RADIX (BRX) domain was characterized as being a transcription factor in plants regulating the extent of cell proliferation and elongation in the growth zone of the root. BRX is rate limiting for auxin-responsive gene-expression by mediating cross-talk with the brassino-steroid pathway. BRX has a ubiquitous, although quantitatively variable role in modulating the growth rate in both the root and the shoot. This family features a short region, also alpha-helical, N-terminal to the repeated alpha-helices of family BRX, pfam08381. BRX is expressed in the vasculature and is rate-limiting for transcriptional auxin action. 37 matched cddid_all.tbl CDD pfam13714 pfam13714 433424 PEP_mutase Phosphoenolpyruvate phosphomutase. This domain includes the enzyme Phosphoenolpyruvate phosphomutase (EC:5.4.2.9). This protein Swiss:O86937 has been characterized as catalysing the formation of a carbon-phosphorus bond by converting phosphoenolpyruvate (PEP) to phosphonopyruvate (P-Pyr). This enzyme has a TIM barrel fold. 241 matched cddid_all.tbl CDD pfam13715 pfam13715 433425 CarbopepD_reg_2 CarboxypepD_reg-like domain. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 90 amino acids in length. The family is found in association with pfam07715 and pfam00593. 88 matched cddid_all.tbl CDD pfam13716 pfam13716 463965 CRAL_TRIO_2 Divergent CRAL/TRIO domain. This family includes divergent members of the CRAL-TRIO domain family. This family includes ECM25 that contains a divergent CRAL-TRIO domain identified by Gallego and colleagues. 140 matched cddid_all.tbl CDD pfam13717 pfam13717 433426 zinc_ribbon_4 zinc-ribbon domain. This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR, pfam12773. 36 matched cddid_all.tbl CDD pfam13718 pfam13718 463966 GNAT_acetyltr_2 GNAT acetyltransferase 2. This domain has N-acetyltransferase activity. It has a GCN5-related N-acetyltransferase (GNAT) fold. 227 matched cddid_all.tbl CDD pfam13719 pfam13719 316258 zinc_ribbon_5 zinc-ribbon domain. This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR, pfam12773. 37 matched cddid_all.tbl CDD pfam13720 pfam13720 463967 Acetyltransf_11 Udp N-acetylglucosamine O-acyltransferase; Domain 2. This is domain 2, or the C-terminal domain, of Udp N-acetylglucosamine O-acyltransferase. This enzyme is a zinc-dependent enzyme that catalyzes the deacetylation of UDP-3-O-((R)-3-hydroxymyristoyl)-N-acetylglucosamine to form UDP-3-O-(R-hydroxymyristoyl)glucosamine and acetate. 82 matched cddid_all.tbl CDD pfam13721 pfam13721 463968 SecD-TM1 SecD export protein N-terminal TM region. This domain appears to be the fist transmembrane region of the SecD export protein. SecD is directly involved in protein secretion and important for the release of proteins that have been translocated across the cytoplasmic membrane. 103 matched cddid_all.tbl CDD pfam13722 pfam13722 433430 CstA_5TM 5TM C-terminal transporter carbon starvation CstA. CstA_5TM is the last five transmembrane regions of the peptide transporter carbon starvation family CstA. 118 matched cddid_all.tbl CDD pfam13723 pfam13723 433431 Ketoacyl-synt_2 Beta-ketoacyl synthase, N-terminal domain. 226 matched cddid_all.tbl CDD pfam13724 pfam13724 433432 DNA_binding_2 DNA-binding domain. This domain, often found on ovate proteins, binds to single-stranded and double-stranded DNA. Binding to DNA is not sequence-specific. 48 matched cddid_all.tbl CDD pfam13725 pfam13725 463969 tRNA_bind_2 Possible tRNA binding domain. This domain, found at the C-terminus of tRNA(Met) cytidine acetyltransferase, may be involved in tRNA-binding. 231 matched cddid_all.tbl CDD pfam13726 pfam13726 433434 Na_H_antiport_2 Na+-H+ antiporter family. This family includes integral membrane proteins, some of which are NA+-H+ antiporters. 88 matched cddid_all.tbl CDD pfam13727 pfam13727 433435 CoA_binding_3 CoA-binding domain. 175 matched cddid_all.tbl CDD pfam13728 pfam13728 433436 TraF F plasmid transfer operon protein. TraF protein undergoes proteolytic processing associated with export. The 19 amino acids at the amino terminus of the polypeptides appear to constitute a typical membrane leader peptide - not included in this family, while the remainder of the molecule is predicted to be primarily hydrophilic in character. F plasmid TraF and TraH are required for F pilus assembly and F plasmid transfer, and they are both localized to the outer membrane in the presence of the complete F transfer region, especially TraV, the putative anchor. 224 matched cddid_all.tbl CDD pfam13729 pfam13729 433437 TraF_2 F plasmid transfer operon, TraF, protein. 269 matched cddid_all.tbl CDD pfam13730 pfam13730 463970 HTH_36 Helix-turn-helix domain. 55 matched cddid_all.tbl CDD pfam13731 pfam13731 433439 WxL WxL domain surface cell wall-binding. The WxL motif appears in two or three copies in these bacterial proteins and confers a cell surface localization function. It seems likely that this region is the cell wall-binding domain of gram-positive bacteria, and may interact with the peptidoglycan. 205 matched cddid_all.tbl CDD pfam13732 pfam13732 463971 DUF4162 Domain of unknown function (DUF4162). This domain is found at the C-terminus of bacterial ABC transporter proteins. The function is not known. 82 matched cddid_all.tbl CDD pfam13733 pfam13733 463972 Glyco_transf_7N N-terminal region of glycosyl transferase group 7. This is the N-terminal half of a family of galactosyltransferases from a wide range of Metazoa with three related galactosyltransferases activities, all three of which are possessed by one sequence in some cases. EC:2.4.1.90, N-acetyllactosamine synthase; EC:2.4.1.38, Beta-N-acetylglucosaminyl-glycopeptide beta-1,4- galactosyltransferase; and EC:2.4.1.22 Lactose synthase. Note that N-acetyllactosamine synthase is a component of Lactose synthase along with alpha-lactalbumin, in the absence of alpha-lactalbumin EC:2.4.1.90 is the catalyzed reaction. 125 matched cddid_all.tbl CDD pfam13734 pfam13734 433442 Inhibitor_I69 Spi protease inhibitor. This family includes the inhibitor Spi and the pro-peptides of streptopain (SpeB). SpeB is produced as a 43 kDa pre-pro-protein, which is secreted via the recently described Sec secretory pathway Exportal. There is tight coupling between this inhibitor and its associated protease: the gene for the inhibitor Spi is located directly downstream from the gene for the streptococcal cysteine protease SpeB, and the sequence of the inhibitor is very similar to that of the SpeB propeptide. This is an example of an inhibitor molecule that is a structural homolog of the cognate propeptide, and is genetically linked to the protease gene. 98 matched cddid_all.tbl CDD pfam13735 pfam13735 433443 tRNA_NucTran2_2 tRNA nucleotidyltransferase domain 2 putative. 149 matched cddid_all.tbl CDD pfam13737 pfam13737 433444 DDE_Tnp_1_5 Transposase DDE domain. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. 112 matched cddid_all.tbl CDD pfam13738 pfam13738 404603 Pyr_redox_3 Pyridine nucleotide-disulphide oxidoreductase. 296 matched cddid_all.tbl CDD pfam13739 pfam13739 463973 PdaC Deacetylase PdaC. This domain forms an alpha-beta-two layer sandwich. It is found in the Bacillus subtilis proteins anti-sigma-V factor RsiV, which downregulates SigV activity, and peptidoglycan-N-acetylmuramic acid deacetylase PdaC, which catalyzes the deacetylation of N-acetylmuramic acid which makes the peptidoglycan resistant to lysosyme. It is found in association with Heat-shock cognate 70kd protein 44kd ATPase, pfam11738. 94 matched cddid_all.tbl CDD pfam13740 pfam13740 433446 ACT_6 ACT domain. ACT domains bind to amino acids and regulate associated enzyme domains. 76 matched cddid_all.tbl CDD pfam13741 pfam13741 433447 MRP-S25 Mitochondrial ribosomal protein S25. This is the family of fungal 37S mitochondrial ribosomal S25 proteins. 221 matched cddid_all.tbl CDD pfam13742 pfam13742 463974 tRNA_anti_2 OB-fold nucleic acid binding domain. This family contains OB-fold domains that bind to nucleic acids. 95 matched cddid_all.tbl CDD pfam13743 pfam13743 404608 Thioredoxin_5 Thioredoxin. 176 matched cddid_all.tbl CDD pfam13744 pfam13744 433449 HTH_37 Helix-turn-helix domain. Members of this family contains a DNA-binding helix-turn-helix domain. 80 matched cddid_all.tbl CDD pfam13746 pfam13746 404610 Fer4_18 4Fe-4S dicluster domain. This family includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. The structure of the domain is an alpha-antiparallel beta sandwich. 114 matched cddid_all.tbl CDD pfam13747 pfam13747 433450 DUF4164 Domain of unknown function (DUF4164). This is a family of short, approx 100 residue-long, bacterial proteins of unknown function. There is several conserved LE/LD sequence pairs. 89 matched cddid_all.tbl CDD pfam13748 pfam13748 433451 ABC_membrane_3 ABC transporter transmembrane region. This family represents a unit of six transmembrane helices. 235 matched cddid_all.tbl CDD pfam13749 pfam13749 463975 HATPase_c_4 Putative ATP-dependent DNA helicase recG C-terminal. This domain may well interact selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. 88 matched cddid_all.tbl CDD pfam13750 pfam13750 404614 Big_3_3 Bacterial Ig-like domain (group 3). This family consists of bacterial domains with an Ig-like fold. Members of this family are found in a variety of bacterial surface proteins. 157 matched cddid_all.tbl CDD pfam13751 pfam13751 433453 DDE_Tnp_1_6 Transposase DDE domain. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. 125 matched cddid_all.tbl CDD pfam13752 pfam13752 433454 DUF4165 Domain of unknown function (DUF4165). 121 matched cddid_all.tbl CDD pfam13753 pfam13753 404617 SWM_repeat Putative flagellar system-associated repeat. This family appears to be a repeated unit that can occur up to 29 times in these outer membrane proteins. It is putatively associated with a novel flagellar system. 87 matched cddid_all.tbl CDD pfam13754 pfam13754 404618 Big_3_4 Domain of unknown function. This is a family of uncharacterized Clostridiales proteins. 105 matched cddid_all.tbl CDD pfam13755 pfam13755 404619 Sensor_TM1 Sensor N-terminal transmembrane domain. This domain is found at the N-terminus of the sensor component of the two-component regulatory system. It includes a transmembrane region and part of the periplasmic region, which is likely to be involved in stimulus sensing. 68 matched cddid_all.tbl CDD pfam13756 pfam13756 433455 Stimulus_sens_1 Stimulus-sensing domain. This domain is found in the periplasmic region of the sensor component of the two-component regulatory system. The periplasmic region is likely to be involved in stimulus sensing. 110 matched cddid_all.tbl CDD pfam13757 pfam13757 404621 VIT_2 Vault protein inter-alpha-trypsin domain. Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains. ITIs play a role in extracellular matrix (ECM) stabilization and tumour metastasis as well as in plasma protease inhibition. The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N-terminus of a von Willebrand factor type A domain (pfam00092) in ITI heavy chains (ITIHs) and their precursors. 78 matched cddid_all.tbl CDD pfam13758 pfam13758 372710 Prefoldin_3 Prefoldin subunit. This family includes prefoldin subunits that are not detected by pfam02996. 99 matched cddid_all.tbl CDD pfam13759 pfam13759 433456 2OG-FeII_Oxy_5 Putative 2OG-Fe(II) oxygenase. This family has structural similarity to the 2OG-Fe(II) oxygenase superfamily. 101 matched cddid_all.tbl CDD pfam13761 pfam13761 433457 DUF4166 Domain of unknown function (DUF4166). This domain is often found at the C-terminus of proteins containing pfam03435. 181 matched cddid_all.tbl CDD pfam13762 pfam13762 372712 MNE1 Mitochondrial splicing apparatus component. MNE1 is a novel component of the mitochondrial splicing apparatus responsible for the processing of a COX1 group I intron in yeast. Yeast cells lacking MNE1 are deficient in intron splicing in the gene encoding the Cox1 subunit of cytochrome oxidase but do contain wild-type levels of the bc1 complex. 141 matched cddid_all.tbl CDD pfam13763 pfam13763 433458 DUF4167 Domain of unknown function (DUF4167). 75 matched cddid_all.tbl CDD pfam13764 pfam13764 433459 E3_UbLigase_R4 E3 ubiquitin-protein ligase UBR4. This is a family of E3 ubiquitin ligase enzymes. 807 matched cddid_all.tbl CDD pfam13765 pfam13765 463976 PRY SPRY-associated domain. PRY is a 50-60 amino acids domain associated with SPRY domains, adjacent to its N-terminal. PRY and SPRY domains are structurally very similar and consist of a beta sandwich fold. Distant homologs are domains in butyrophilin/marenostrin/pyrin, evolutionarily more ancient than SPRY/B30.2 counterpart. 49 matched cddid_all.tbl CDD pfam13767 pfam13767 433461 DUF4168 Domain of unknown function (DUF4168). 78 matched cddid_all.tbl CDD pfam13768 pfam13768 372716 VWA_3 von Willebrand factor type A domain. 155 matched cddid_all.tbl CDD pfam13769 pfam13769 433462 Virulence_fact Virulence factor. This domain is found in conserved virulence factors. It is often found in association with pfam02985 and pfam08712. 81 matched cddid_all.tbl CDD pfam13770 pfam13770 433463 DUF4169 Domain of unknown function (DUF4169). 55 matched cddid_all.tbl CDD pfam13771 pfam13771 463977 zf-HC5HC2H PHD-like zinc-binding domain. The members of this family are annotated as containing PHD domain, but the zinc-binding region here is not typical of PHD domains. The conformation here is a well-conserved cysteine-histidine rich region spanning 90 residues, where the Cys and His are arranged as HxxC(31)CxxC(6)CxxCxxxxCxxxxHxxC (21)CxxH. 88 matched cddid_all.tbl CDD pfam13772 pfam13772 433465 AIG2_2 AIG2-like family. This family is found in bacteria and metazoa. 83 matched cddid_all.tbl CDD pfam13773 pfam13773 433466 DUF4170 Domain of unknown function (DUF4170). 68 matched cddid_all.tbl CDD pfam13774 pfam13774 463978 Longin Regulated-SNARE-like domain. Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex. Longins are the only R-SNAREs that are common to all eukaryotes, and they are characterized by a conserved N-terminal domain with a profilin-like fold called a longin domain. 81 matched cddid_all.tbl CDD pfam13775 pfam13775 463979 DUF4171 Domain of unknown function (DUF4171). This short family is frequently found at the N-terminus of Homeobox proteins. 125 matched cddid_all.tbl CDD pfam13776 pfam13776 433469 DUF4172 Domain of unknown function (DUF4172). The family is often found in association with pfam02661. 82 matched cddid_all.tbl CDD pfam13777 pfam13777 433470 DUF4173 Domain of unknown function (DUF4173). This domain of unknown function contains multiple predicted transmembrane domains. 188 matched cddid_all.tbl CDD pfam13778 pfam13778 463980 DUF4174 Domain of unknown function (DUF4174). This domain of unknown function is found in a putative tumour suppressor gene and in a ligand for the the urokinase-type plasminogen activator receptor, which plays a role in cellular migration and adhesion. 120 matched cddid_all.tbl CDD pfam13779 pfam13779 463981 DUF4175 Domain of unknown function (DUF4175). 833 matched cddid_all.tbl CDD pfam13780 pfam13780 433473 DUF4176 Domain of unknown function (DUF4176). 74 matched cddid_all.tbl CDD pfam13781 pfam13781 463982 DoxX_3 DoxX-like family. This family of uncharacterized proteins are related to DoxX pfam07681. 101 matched cddid_all.tbl CDD pfam13782 pfam13782 463983 SpoVAB Stage V sporulation protein AB. This family of proteins is required for sporulation. 109 matched cddid_all.tbl CDD pfam13783 pfam13783 433476 DUF4177 Domain of unknown function (DUF4177). 65 matched cddid_all.tbl CDD pfam13784 pfam13784 463984 Fic_N Fic/DOC family N-terminal. This domain is found at the N-terminus of the Fic/DOC family, pfam02661. 79 matched cddid_all.tbl CDD pfam13785 pfam13785 433478 DUF4178 Domain of unknown function (DUF4178). 143 matched cddid_all.tbl CDD pfam13786 pfam13786 463985 DUF4179 Domain of unknown function (DUF4179). 93 matched cddid_all.tbl CDD pfam13787 pfam13787 433480 HXXEE Protein of unknown function with HXXEE motif. This domain contains an HXXEE motif, another conserved histidine and a YXPG motif. Its function is unknown. 100 matched cddid_all.tbl CDD pfam13788 pfam13788 433481 DUF4180 Domain of unknown function (DUF4180). 111 matched cddid_all.tbl CDD pfam13789 pfam13789 372726 DUF4181 Domain of unknown function (DUF4181). 108 matched cddid_all.tbl CDD pfam13790 pfam13790 372727 SR1P SR1 protein. This family of proteins is encoded by the dual function SR1 RNA. SR1 is a sRNA which regulates arginine metabolism, it also encodes a short protein that binds to glyceraldehyde-3-phosphate dehydrogenase (GapA) and stabilizes the gapA operon mRNAs. 37 matched cddid_all.tbl CDD pfam13791 pfam13791 433482 Sigma_reg_C Sigma factor regulator C-terminal. This family is the C-terminal domain of a sigma factor regulator, this may represent a sensory domain. 157 matched cddid_all.tbl CDD pfam13793 pfam13793 433483 Pribosyltran_N N-terminal domain of ribose phosphate pyrophosphokinase. This family is frequently found N-terminal to the Pribosyltran, pfam00156. 117 matched cddid_all.tbl CDD pfam13794 pfam13794 205967 MiaE_2 tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)-like. 185 matched cddid_all.tbl CDD pfam13795 pfam13795 433484 HupE_UreJ_2 HupE / UreJ protein. These proteins contain many conserved histidines that may be involved in nickel binding. 154 matched cddid_all.tbl CDD pfam13796 pfam13796 433485 Sensor Putative sensor. This family is often found at the N-terminus of proteins containing pfam07730 and pfam02518. The N-termini of proteins containing these two domains often function in stimulus sensing. 180 matched cddid_all.tbl CDD pfam13797 pfam13797 404651 Post_transc_reg Post-transcriptional regulator. This family includes post-transcriptional regulators. 83 matched cddid_all.tbl CDD pfam13798 pfam13798 433486 PCYCGC Protein of unknown function with PCYCGC motif. This domain contains a PCYCGC motif and four other conserved cysteines. Its function is unknown. 154 matched cddid_all.tbl CDD pfam13799 pfam13799 404653 DUF4183 Domain of unknown function (DUF4183). This domain of unknown function contains a highly conserved ING motif. 74 matched cddid_all.tbl CDD pfam13800 pfam13800 463986 Sigma_reg_N Sigma factor regulator N-terminal. This domain is found near the N-terminus of a sigma factor regulator. The N-terminus is responsible for interaction with the sigma factor. 89 matched cddid_all.tbl CDD pfam13801 pfam13801 433488 Metal_resist Heavy-metal resistance. This is a metal-binding protein which is involved in resistance to heavy-metal ions. The protein forms a four-helix hooked hairpin, consisting of two long alpha helices each flanked by a shorter alpha helix. It binds a metal ion in a type-2 like centre. It contains two copies of an LTXXQ motif. 119 matched cddid_all.tbl CDD pfam13802 pfam13802 463987 Gal_mutarotas_2 Galactose mutarotase-like. This family is found N-terminal to glycosyl-hydrolase domains, and appears to be similar to the galactose mutarotase superfamily. 67 matched cddid_all.tbl CDD pfam13803 pfam13803 433490 DUF4184 Domain of unknown function (DUF4184). This domain of unknown function contains several highly conserved histidines. 236 matched cddid_all.tbl CDD pfam13804 pfam13804 290518 HERV-K_env_2 Retro-transcribing viruses envelope glycoprotein. This family comes from human endogenous retrovirus K envelope glycoproteins. 169 matched cddid_all.tbl CDD pfam13805 pfam13805 404658 Pil1 Eisosome component PIL1. In the budding yeast, S. cerevisiae, Pil1 and another cytoplasmic protein, Lsp1, together form large immobile assemblies at the plasma membrane that mark sites for endocytosis, called eisosomes. Endocytosis functions to recycle plasma membrane components, to regulate cell-surface expression of signalling receptors and to internalize nutrients in all eukaryotic cells. 265 matched cddid_all.tbl CDD pfam13806 pfam13806 433491 Rieske_2 Rieske-like [2Fe-2S] domain. 103 matched cddid_all.tbl CDD pfam13807 pfam13807 433492 GNVR G-rich domain on putative tyrosine kinase. This domain is found between two families, Wzz, pfam02706 and CbiA pfam01656. There is a highly conserved GNVR sequence motif which characterizes this domain. The function is not known. 82 matched cddid_all.tbl CDD pfam13808 pfam13808 433493 DDE_Tnp_1_assoc DDE_Tnp_1-associated. This domain is frequently found N-terminal to the transposase, IS family DDE_Tnp_1, pfam01609 and its relatives. 88 matched cddid_all.tbl CDD pfam13809 pfam13809 433494 Tubulin_2 Tubulin like. Many of the residues conserved in Tubulin, pfam00091, are also highly conserved in this family. 339 matched cddid_all.tbl CDD pfam13810 pfam13810 433495 DUF4185 Domain of unknown function (DUF4185). 309 matched cddid_all.tbl CDD pfam13811 pfam13811 433496 DUF4186 Domain of unknown function (DUF4186). 109 matched cddid_all.tbl CDD pfam13812 pfam13812 316342 PPR_3 Pentatricopeptide repeat domain. This family matches additional variants of the PPR repeat that were not captured by the model for pfam01535. In the case of the Arabidopsis protein UniProtKB:Q66GI4, the repeated helices in this N-terminal region, of protein-only RNase P (PRORP) enzymes, form the pentatricopeptide repeat (PPR) domain which enhances pre-tRNA binding affinity. PROPRP enzymes process precursor tRNAs in human mitochondria and in all tRNA-using compartments of Arabidopsis thaliana. 63 matched cddid_all.tbl CDD pfam13813 pfam13813 372734 MBOAT_2 Membrane bound O-acyl transferase family. 84 matched cddid_all.tbl CDD pfam13814 pfam13814 433497 Replic_Relax Replication-relaxation. This family includes proteins which are essential for plasmid replication and plasmid DNA relaxation. 190 matched cddid_all.tbl CDD pfam13815 pfam13815 433498 Dzip-like_N Iguana/Dzip1-like DAZ-interacting protein N-terminal. The DAZ gene-product - Deleted in Azoospermia - and a closely related sequence are required early in germ-cell development in order to maintain germ-cell populations. This family is the N-terminal region that is the only part of the protein in some fungi and lower metazoa. 118 matched cddid_all.tbl CDD pfam13816 pfam13816 433499 Dehydratase_hem Haem-containing dehydratase. This family includes aldoxime dehydratase, EC:4.99.1.5. This is a haem-containing enzyme, which catalyzes the dehydration of aldoximes to their corresponding nitrile. It also includes phenylacetaldoxime dehydratase, EC:4.99.1.7. This haem-containing enzyme catalyzes the dehydration of Z-phenylacetaldoxime to phenylacetonitrile. The enzyme forms an elliptic beta barrel, composed of eight beta-strands, flanked by alpha-helices. 308 matched cddid_all.tbl CDD pfam13817 pfam13817 433500 DDE_Tnp_IS66_C IS66 C-terminal element. 39 matched cddid_all.tbl CDD pfam13820 pfam13820 463988 Nucleic_acid_bd Putative nucleic acid-binding region. This is a family of putative nucleic acid-binding proteins. Several members are annotated as being nuclear receptor coactivator 6 proteins but this could not be confirmed. 143 matched cddid_all.tbl CDD pfam13821 pfam13821 463989 DUF4187 Domain of unknown function (DUF4187). This family is found at the very C-terminus of proteins that carry a G-patch domain, pfam01585. The domain is short and cysteine-rich. 50 matched cddid_all.tbl CDD pfam13822 pfam13822 433503 ACC_epsilon Acyl-CoA carboxylase epsilon subunit. This family includes the epsilon subunits of propionyl-CoA carboxylase, EC:6.4.1.3, and acetyl-CoA carboxylase, EC:6.4.1.2. These enzymes are involved in the biosynthesis of long-chain fatty acids. The epsilon subunit is necessary for an efficient interaction between the alpha and beta subunits of these enzymes. 60 matched cddid_all.tbl CDD pfam13823 pfam13823 433504 ADH_N_assoc Alcohol dehydrogenase GroES-associated. This short domain is frequently found at the N-terminus of the alcohol dehydrogenase GroES-like domain, Pfam: PF08240. 23 matched cddid_all.tbl CDD pfam13824 pfam13824 433505 zf-Mss51 Zinc-finger of mitochondrial splicing suppressor 51. Mss51 regulates the expression of cytochrome oxidase, so this domain is probably DNA-binding. 54 matched cddid_all.tbl CDD pfam13825 pfam13825 372740 Paramyxo_P_V_N Paramyxovirus structural protein V/P N-terminus. This family consists of several Paramyxoviridae structural protein P and V sequences. From a structural point of view, P is the best-characterized protein of the replicative complex. P is organized into two moieties that are functionally and structurally distinct: a C-terminal moiety (PCT) and an N-terminal moiety (PNT). PCT is the most conserved in sequence and contains all regions required for virus transcription, whereas PNT, which is poorly conserved, provides several additional functions required for replication. P protein plays a crucial role in the enzyme by positioning L onto the N/RNA template through an interaction with the C-terminal domain of N. Without P, L is not functional. The N, P, and L proteins of SeV and measles and mumps viruses are functionally equivalent. However, sequence identity between proteins from these viruses is limited, and the viruses have been placed in different genera (Respirovirus, Morbilivirus, and Rubulavirus, respectively). SeV P protein (568 aa) is a modular protein with distinct functional domains. The N-terminal part of P (PNT) is a chaperone for N and prevents it from binding to non-viral RNA in the infected cell. 309 matched cddid_all.tbl CDD pfam13826 pfam13826 433506 DUF4188 Domain of unknown function (DUF4188). 118 matched cddid_all.tbl CDD pfam13827 pfam13827 433507 DUF4189 Domain of unknown function (DUF4189). This domain of unknown function contains six well-conserved cysteine residues. 97 matched cddid_all.tbl CDD pfam13828 pfam13828 433508 DUF4190 Domain of unknown function (DUF4190). This integral membrane domain is functionally uncharacterized. One of the membrane helices contains two GXXG motifs that are usually associated with dimerization. 61 matched cddid_all.tbl CDD pfam13829 pfam13829 433509 DUF4191 Domain of unknown function (DUF4191). 219 matched cddid_all.tbl CDD pfam13830 pfam13830 433510 DUF4192 Domain of unknown function (DUF4192). 317 matched cddid_all.tbl CDD pfam13831 pfam13831 463990 PHD_2 PHD-finger. PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3. 35 matched cddid_all.tbl CDD pfam13832 pfam13832 463991 zf-HC5HC2H_2 PHD-zinc-finger like domain. 109 matched cddid_all.tbl CDD pfam13833 pfam13833 404678 EF-hand_8 EF-hand domain pair. 54 matched cddid_all.tbl CDD pfam13834 pfam13834 433513 DUF4193 Domain of unknown function (DUF4193). This domain of unknown function contains four conserved cysteines and a conserved histidine, including a CXXXXH motif. 98 matched cddid_all.tbl CDD pfam13835 pfam13835 463992 DUF4194 Domain of unknown function (DUF4194). 165 matched cddid_all.tbl CDD pfam13836 pfam13836 463993 DUF4195 Domain of unknown function (DUF4195). This family is found at the N-terminus of metazoan proteins that carry PHD-like zinc-finger domains. The function is not known. 184 matched cddid_all.tbl CDD pfam13837 pfam13837 463994 Myb_DNA-bind_4 Myb/SANT-like DNA-binding domain. This presumed domain appears to be related to other Myb/SANT-like DNA binding domains. In particular pfam10545 seems most related. This family is greatly expanded in plants and appears in several proteins annotated as transposon proteins. 84 matched cddid_all.tbl CDD pfam13838 pfam13838 463995 Clathrin_H_link Clathrin-H-link. This short domain is found on clathrins, and often appears on proteins directly downstream from the Clathrin-link domain pfam09268. 66 matched cddid_all.tbl CDD pfam13839 pfam13839 463996 PC-Esterase GDSL/SGNH-like Acyl-Esterase family found in Pmr5 and Cas1p. The PC-Esterase family is comprised of Cas1p, the Homo sapiens C7orf58, Arabidopsis thaliana PMR5 and a group of plant freezing resistance/cold acclimatization proteins typified by Arabidopsis thaliana ESKIMO1, animal FAM55D proteins, and animal FAM113 proteins. The PC-Esterase family has features that are both similar and different from the canonical GDSL/SGNH superfamily. The members of this family are predicted to have Acyl esterase activity and predicted to modify cell-surface biopolymers such as glycans and glycoproteins. The Cas1p protein has a Cas1_AcylT domain, in addition, with the opposing acyltransferase activity. The C7orf58 family has a ATP-Grasp domain fused to the PC-Esterase and is the first identified secreted tubulin-tyrosine ligase like enzyme in eukaryotes. The plant family with PMR5, ESK1, TBL3 etc have a N-terminal C rich potential sugar binding domain followed by PC-Esterase domain. 281 matched cddid_all.tbl CDD pfam13840 pfam13840 433519 ACT_7 ACT domain. The ACT domain is a structural motif of 70-90 amino acids that functions in the control of metabolism, solute transport and signal transduction. They are thus found in a variety of different proteins in a variety of different arrangements. In mammalian phenylalanine hydroxylase the domain forms no contacts but promotes an allosteric effect despite the apparent lack of ligand binding. 65 matched cddid_all.tbl CDD pfam13841 pfam13841 463997 Defensin_beta_2 Beta defensin. The beta defensins are antimicrobial peptides implicated in the resistance of epithelial surfaces to microbial colonization. 30 matched cddid_all.tbl CDD pfam13842 pfam13842 404687 Tnp_zf-ribbon_2 DDE_Tnp_1-like zinc-ribbon. This zinc-ribbon domain is frequently found at the C-terminal of proteins derived from transposable elements. 31 matched cddid_all.tbl CDD pfam13843 pfam13843 433521 DDE_Tnp_1_7 Transposase IS4. 349 matched cddid_all.tbl CDD pfam13844 pfam13844 404688 Glyco_transf_41 Glycosyl transferase family 41. This family of glycosyltransferases includes O-linked beta-N-acetylglucosamine (O-GlcNAc) transferase, an enzyme which catalyzes the addition of O-GlcNAc to serine and threonine residues. In addition to its function as an O-GlcNAc transferase, human OGT, also appears to proteolytically cleave the epigenetic cell-cycle regulator HCF-1. 543 matched cddid_all.tbl CDD pfam13845 pfam13845 433522 Septum_form Septum formation. This domain is found in a protein which is predicted to play a role in septum formation during cell division. 227 matched cddid_all.tbl CDD pfam13846 pfam13846 433523 DUF4196 Domain of unknown function (DUF4196). This is a short region of ccdc82_homologs that is conserved from Schizo. pombe up to humans. The function is not known. 112 matched cddid_all.tbl CDD pfam13847 pfam13847 463998 Methyltransf_31 Methyltransferase domain. This family appears to have methyltransferase activity. 150 matched cddid_all.tbl CDD pfam13848 pfam13848 463999 Thioredoxin_6 Thioredoxin-like domain. 184 matched cddid_all.tbl CDD pfam13850 pfam13850 464000 ERGIC_N Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC). This family is the N-terminal of ERGIC proteins, ER-Golgi intermediate compartment clusters, otherwise known as Ervs, and is associated with family COPIIcoated_ERV, pfam07970. 91 matched cddid_all.tbl CDD pfam13851 pfam13851 464001 GAS Growth-arrest specific micro-tubule binding. This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells. 200 matched cddid_all.tbl CDD pfam13852 pfam13852 433527 DUF4197 Protein of unknown function (DUF4197). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 228 and 249 amino acids in length. 199 matched cddid_all.tbl CDD pfam13853 pfam13853 404695 7tm_4 Olfactory receptor. The members of this family are transmembrane olfactory receptors. 278 matched cddid_all.tbl CDD pfam13854 pfam13854 433528 Kelch_5 Kelch motif. The kelch motif was initially discovered in Kelch. In this protein there are six copies of the motif. It has been shown that Swiss:Q04652 is related to Galactose Oxidase for which a structure has been solved. The kelch motif forms a beta sheet. Several of these sheets associate to form a beta propeller structure as found in pfam00064, pfam00400 and pfam00415. 41 matched cddid_all.tbl CDD pfam13855 pfam13855 404697 LRR_8 Leucine rich repeat. 61 matched cddid_all.tbl CDD pfam13856 pfam13856 433529 Gifsy-2 ATP-binding sugar transporter from pro-phage. Members of this short family are putative ATP-binding sugar transporter-like protein. 98 matched cddid_all.tbl CDD pfam13857 pfam13857 433530 Ank_5 Ankyrin repeats (many copies). 56 matched cddid_all.tbl CDD pfam13858 pfam13858 433531 DUF4199 Protein of unknown function (DUF4199). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 167 and 182 amino acids in length. 156 matched cddid_all.tbl CDD pfam13859 pfam13859 372760 BNR_3 BNR repeat-like domain. This family of proteins contains BNR-like repeats suggesting these proteins may act as sialidases. 302 matched cddid_all.tbl CDD pfam13860 pfam13860 433532 FlgD_ig FlgD Ig-like domain. This domains has an immunoglobulin like beta sandwich fold. It is found in the FlgD protein the flagellar hook capping protein. THe structure for this domain shows that it is inserted within a TUDOR like beta barrel domain. 78 matched cddid_all.tbl CDD pfam13861 pfam13861 433533 FLgD_tudor FlgD Tudor-like domain. This domain has a tudor domain-like beta barrel fold. It is found in the FlgD protein the flagellar hook capping protein. The structure for this domain shows that it contains a nested Ig-like domain within it. However in some firmicute proteins this inserted domain is absent such as Q67K21. 136 matched cddid_all.tbl CDD pfam13862 pfam13862 464002 BCCIP BCCIP. This family of proteins includes BRCA2 and CDKN1A-interacting protein (BCCIP) and BCP1. In fungi, BCP1 is involved in nuclear export, actin cytoskeleton organization and vesicular transport. Its homolog in human and mouse, BCCIP, may promote cell cycle arrest by enhancing the inhibition of CDK2 activity by CDKN1A/p21 and may be required for repair of DNA damage by homologous recombination in conjunction with BRCA2. 199 matched cddid_all.tbl CDD pfam13863 pfam13863 464003 DUF4200 Domain of unknown function (DUF4200). This family is found in eukaryotes. It is a coiled-coil domain of unknwon function. 119 matched cddid_all.tbl CDD pfam13864 pfam13864 464004 Enkurin Calmodulin-binding. This is a family of apparent calmodulin-binding proteins found at high levels in the testis and vomeronasal organ and at lower levels in certain other tissues. Enkurin is a scaffold protein that binds PI3 kinase to sperm transient receptor potential (canonical) (TRPC) channels. The mammalian transient receptor potential (canonical) channels are the primary candidates for the Ca(2+) entry pathway activated by the hormones, growth factors, and neurotransmitters that exert their effect through activation of PLC. Calmodulin binds to the C-terminus of all TRPC channels, and dissociation of calmodulin from TRPC4 results in profound activation of the channel. 92 matched cddid_all.tbl CDD pfam13865 pfam13865 464005 FoP_duplication C-terminal duplication domain of Friend of PRMT1. Fop, or Friend of Prmt1, proteins are conserved from fungi and plants to vertebrates. There is little that is actually conserved except for this C-terminal LDXXLDAYM region where X is any amino acid). The Fop proteins themselves are nuclear proteins localized to regions with low levels of DAPI, with a punctate/speckle-like distribution. Fop is a chromatin-associated protein and it co-localizes with facultative heterochromatin. It is is critical for oestrogen-dependent gene activation. 81 matched cddid_all.tbl CDD pfam13866 pfam13866 404707 zf-SAP30 SAP30 zinc-finger. SAP30 is a subunit of the histone deacetylase complex, and this domain is a zinc-finger. Solution of the structure shows a novel fold comprising two beta-strands and two alpha-helices with the zinc organizing centre showing remote resemblance to the treble clef motif. In silico analysis of the structure revealed a highly conserved surface dominated by basic residues. NMR-based analysis of potential ligands for the SAP30 zn-finger motif indicated a strong preference for nucleic acid substrates. The zinc-finger of SAP3 probably functions as a double-stranded DNA-binding motif, thereby expanding the known functions of both SAP30 and the mammalian Sin3 co-repressor complex. 72 matched cddid_all.tbl CDD pfam13867 pfam13867 464006 SAP30_Sin3_bdg Sin3 binding region of histone deacetylase complex subunit SAP30. This C-terminal domain of the SAP30 proteins appears to be the binding region for Sin3. 53 matched cddid_all.tbl CDD pfam13868 pfam13868 464007 TPH Trichohyalin-plectin-homology domain. This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain. 341 matched cddid_all.tbl CDD pfam13869 pfam13869 433540 NUDIX_2 Nucleotide hydrolase. Nudix hydrolases are found in all classes of organizm and hydrolyse a wide range of organic pyrophosphates, including nucleoside di- and triphosphates, di-nucleoside and diphospho-inositol polyphosphates, nucleotide sugars and RNA caps, with varying degrees of substrate specificity. 188 matched cddid_all.tbl CDD pfam13870 pfam13870 464008 DUF4201 Domain of unknown function (DUF4201). This is a family of coiled-coil proteins from eukaryotes. The function is not known. 177 matched cddid_all.tbl CDD pfam13871 pfam13871 464009 Helicase_C_4 C-terminal domain on Strawberry notch homolog. Strawberry notch proteins carry DExD/H-box groups upstream of this domain. The function of this domain is not known. These proteins promote the expression of diverse targets, potentially through interactions with transcriptional activator or repressor complexes. 269 matched cddid_all.tbl CDD pfam13872 pfam13872 464010 AAA_34 P-loop containing NTP hydrolase pore-1. 300 matched cddid_all.tbl CDD pfam13873 pfam13873 433544 Myb_DNA-bind_5 Myb/SANT-like DNA-binding domain. This presumed domain appears to be related to other Myb/SANT like DNA binding domains. This family is greatly expanded in arthropods and higher eukaryotes. 78 matched cddid_all.tbl CDD pfam13874 pfam13874 464011 Nup54 Nucleoporin complex subunit 54. This is the human Nup54 subunit of the nucleoporin complex, equivalent to Nup57 of yeast. Nup54, Nup58 and Nup62 all have similar affinities for importin-beta. It seems likely that they are the only FG-repeat nucleoporins of the central channel, and as such they would form a zone of equal affinity spanning the central channel. The diffusion of importin-beta import complexes through the central channel may be a stochastic process as the affinities are similar, whereas movement from cytoplasmic fibrils to the central channel and from the central channel to the nuclear basket would be facilitated by the subtle differences in affinity between them. 139 matched cddid_all.tbl CDD pfam13875 pfam13875 433546 DUF4202 Domain of unknown function (DUF4202). This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 187 and 205 amino acids in length. There are two conserved sequence motifs: LED and KMS. The function of these proteins is unknown, although many are incorrectly annotated as glutamyl tRNA synthetases. 184 matched cddid_all.tbl CDD pfam13876 pfam13876 433547 Phage_gp49_66 Phage protein (N4 Gp49/phage Sf6 gene 66) family. This family of phage proteins is functionally uncharacterized. The family includes bacteriophage Sf6 gene 66 as well as phage N4 GP49 protein. Proteins in this family are typically between 87 and 154 amino acids in length. There is a conserved NGF sequence motif. 79 matched cddid_all.tbl CDD pfam13877 pfam13877 464012 RPAP3_C Potential Monad-binding region of RPAP3. This domain is found at the C-terminus of RNA-polymerase II-associated proteins. These proteins bind to Monad and are involved in regulating apoptosis. They contain TPR-repeats towards the N_terminus. 91 matched cddid_all.tbl CDD pfam13878 pfam13878 464013 zf-C2H2_3 zinc-finger of acetyl-transferase ESCO. 40 matched cddid_all.tbl CDD pfam13879 pfam13879 464014 Hmw_CFAP97 Hemingway/CFA97. Drosophila Hemingway (Hmw) is required for motile cilia function and sperm flagella assembly. The human orthologue, known as cilia- and flagella-associated protein 97 (CFAP97) or KIAA1430, localizes to the primary cilium. Another member of this family is the uncharacterized protein CFAP97D1/2 (CFAP97 domain-containing protein 1/2). 100 matched cddid_all.tbl CDD pfam13880 pfam13880 464015 Acetyltransf_13 ESCO1/2 acetyl-transferase. 69 matched cddid_all.tbl CDD pfam13881 pfam13881 372780 Rad60-SLD_2 Ubiquitin-2 like Rad60 SUMO-like. 111 matched cddid_all.tbl CDD pfam13882 pfam13882 464016 Bravo_FIGEY Bravo-like intracellular region. This is the very C-terminal intracellular region of neural adhesion molecule L1 proteins that are also known as Bravo or NrCAM. It lies upstream of the IG and Fn3 domains and has the highly conserved motif FIGEY. The function is not known. 88 matched cddid_all.tbl CDD pfam13883 pfam13883 404723 Pyrid_oxidase_2 Pyridoxamine 5'-phosphate oxidase. 167 matched cddid_all.tbl CDD pfam13884 pfam13884 404724 Peptidase_S74 Chaperone of endosialidase. This is the very C-terminal, chaperone, domain of the bacteriophage protein endosialidase. It releases itself, via the serine-lysine dyad at the N-terminus, from the remainder of the end-tail-spike. Cleavage occurs after the threonine which is the final residue of the End-tail-spike family, pfam12219. The endosialidase protein forms homotrimeric molecules in bacteriophages. The catalytic dyad allows this portion of the molecule to be cleaved from the more N-terminal region such that the latter can fold and bind to polysialic acid in the bacterial outer envelope. 56 matched cddid_all.tbl CDD pfam13885 pfam13885 464017 Keratin_B2_2 Keratin, high sulfur B2 protein. 45 matched cddid_all.tbl CDD pfam13886 pfam13886 464018 DUF4203 Domain of unknown function (DUF4203). This is the N-terminal region of 7tm proteins. The function is not known. 201 matched cddid_all.tbl CDD pfam13887 pfam13887 464019 MYRF_ICA Myelin regulatory factor ICA domain. This domain corresponds to the Intramolecular Chaperone Auto-processing (ICA) domain of myelin regulatory factor (Myrf) located at its C-terminal and belongs to the Peptidase S74 family. It forms a homo-trimer and carries out the auto-cleavage of Myrf releasing the Myrf N-terminal homo-trimer from the ER membrane. This allows its entry to the nucleus to function as a homo-trimer transcription factor. 36 matched cddid_all.tbl CDD pfam13888 pfam13888 464020 MRF_C2 Myelin gene regulatory factor C-terminal domain 2. This domain is found further downstream of Peptidase_S74, pfam13884, and MRF_C1, pfam13887. The function is not known. 139 matched cddid_all.tbl CDD pfam13889 pfam13889 464021 Chromosome_seg Chromosome segregation during meiosis. The proteins come from eukaryotes, plants and animals, and are necessary for chromosome segregation during meiosis. 55 matched cddid_all.tbl CDD pfam13890 pfam13890 464022 Rab3-GTPase_cat Rab3 GTPase-activating protein catalytic subunit. This family is the probable catalytic subunit of the GTPase activating protein that has specificity for Rab3 subfamily (RAB3A, RAB3B, RAB3C and RAB3D). It is likely to convert active Rab3-GTP to the inactive form Rab3-GDP. Rab3 proteins are involved in regulated exocytosis of neurotransmitters and hormones. The Rab3 GTPase-activating complex is a heterodimer composed of RAB3GAP and RAB3-GAP150. This complex interacts with DMXL2. 158 matched cddid_all.tbl CDD pfam13891 pfam13891 464023 zf-C3Hc3H Potential DNA-binding domain. This domain is likely to be the DNA-binding domain of chromatin re-modelling proteins and helicases. 62 matched cddid_all.tbl CDD pfam13892 pfam13892 464024 DBINO DNA-binding domain. DBINO is a DNA-binding domain found on global transcription activator SNF2L1 proteins and chromatin re-modelling proteins. 134 matched cddid_all.tbl CDD pfam13893 pfam13893 433561 RRM_5 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. 125 matched cddid_all.tbl CDD pfam13894 pfam13894 464025 zf-C2H2_4 C2H2-type zinc finger. This family contains a number of divergent C2H2 type zinc fingers. 24 matched cddid_all.tbl CDD pfam13895 pfam13895 464026 Ig_2 Immunoglobulin domain. This domain contains immunoglobulin-like domains. 79 matched cddid_all.tbl CDD pfam13896 pfam13896 464027 Glyco_transf_49 Glycosyl-transferase for dystroglycan. This glycosyl-transferase brings about the glycosylation of the alpha-dystroglycan subunit. Dystroglycan is an integral member of the skeletal muscular dystrophin glycoprotein complex, which links dystrophin to proteins in the extracellular matrix. 327 matched cddid_all.tbl CDD pfam13897 pfam13897 464028 GOLD_2 Golgi-dynamics membrane-trafficking. Sec14-like Golgi-trafficking domain The GOLD domain is always found combined with lipid- or membrane-association domains. 133 matched cddid_all.tbl CDD pfam13898 pfam13898 464029 MINDY-3_4_CD Deubiquitinating enzyme MINDY-3/4, conserved domain. Deubiquitinating enzymes (DUBs) remove ubiquitin (Ub) from Ub-conjugated substrates to regulate the functional outcome of ubiquitination. This entry includes MINDY-3/4. They belong to the MINDY (motif interacting with Ub-containing novel DUB) family (peptidase family C121), whose members are deubiquitinating enzymes releasing Lys48-linked ubiquitin. This is a conserved domain found in deubiquitinating enzymes, MINDY-3 and MINDY-4. 345 matched cddid_all.tbl CDD pfam13899 pfam13899 433567 Thioredoxin_7 Thioredoxin-like. Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. 84 matched cddid_all.tbl CDD pfam13901 pfam13901 464030 zf-RING_9 Putative zinc-RING and/or ribbon. This is a family of cysteine-rich proteins. Many members also carry a pleckstrin-homology domain, pfam00169 205 matched cddid_all.tbl CDD pfam13902 pfam13902 464031 R3H-assoc R3H-associated N-terminal domain. This family is found at the N-terminus of R3H, pfam01424, domain-containing proteins. The function is not known. 127 matched cddid_all.tbl CDD pfam13903 pfam13903 372799 Claudin_2 PMP-22/EMP/MP20/Claudin tight junction. Members of this family are claudins, that form tight junctions between cells. 191 matched cddid_all.tbl CDD pfam13904 pfam13904 464032 CCDC34 Coiled-coil domain-containing protein 3. This family is found in eukaryotes; it has several conserved tryptophan residues. The function is not known. 221 matched cddid_all.tbl CDD pfam13905 pfam13905 464033 Thioredoxin_8 Thioredoxin-like. Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond. 95 matched cddid_all.tbl CDD pfam13906 pfam13906 464034 AA_permease_C C-terminus of AA_permease. This is the C-terminus of AA-permease enzymes that is not captured by the models pfam00324 and pfam13520. 51 matched cddid_all.tbl CDD pfam13907 pfam13907 464035 DUF4208 Domain of unknown function (DUF4208). This domain is found at the C-terminus of chromodomain-helicase-DNA-binding proteins. The exact function of the domain is undetermined. 93 matched cddid_all.tbl CDD pfam13908 pfam13908 464036 Shisa Wnt and FGF inhibitory regulator. Shisa is a transcription factor-type molecule that physically interacts with immature forms of the Wnt receptor Frizzled and the FGF receptor within the endoplasmic reticulum to inhibit their post-translational maturation and trafficking to the cell surface. 187 matched cddid_all.tbl CDD pfam13909 pfam13909 404746 zf-H2C2_5 C2H2-type zinc-finger domain. 25 matched cddid_all.tbl CDD pfam13910 pfam13910 433574 DUF4209 Domain of unknown function (DUF4209). This short domain is found in bacteria and eukaryotes, though not in yeasts or Archaea. It carries a highly conserved RNxxxHG sequence motif. 89 matched cddid_all.tbl CDD pfam13911 pfam13911 433575 AhpC-TSA_2 AhpC/TSA antioxidant enzyme. This family contains proteins related to alkyl hydro-peroxide reductase (AhpC) and thiol specific antioxidant (TSA). 114 matched cddid_all.tbl CDD pfam13912 pfam13912 433576 zf-C2H2_6 C2H2-type zinc finger. 27 matched cddid_all.tbl CDD pfam13913 pfam13913 464037 zf-C2HC_2 zinc-finger of a C2HC-type. This family contains a number of divergent C2H2 type zinc fingers. 25 matched cddid_all.tbl CDD pfam13914 pfam13914 464038 Phostensin Phostensin PP1-binding and SH3-binding region. Phostensin has been identified as a PP1 regulatory protein binding PP1 at the KISF motif. The domain also appears to carry an incomplete incomplete SH3-binding domain PxRxP further upstream. It is likely that Phostensin targets PP1 to the F-actin cytoskeleton. Phostensin binds to actin and decreases the elongation and depolymerization rates of actin filament pointed ends. 138 matched cddid_all.tbl CDD pfam13915 pfam13915 404751 DUF4210 Domain of unknown function (DUF4210). This short domain is found in fungi, plants and animals, and the proteins appear to be necessary for chromosome segregation during meiosis. 66 matched cddid_all.tbl CDD pfam13916 pfam13916 464039 Phostensin_N PP1-regulatory protein, Phostensin N-terminal. Phostensin has been identified as a PP1 regulatory protein binding protein. This domain is N-terminal to the PP1- and SH3-binding regions though may carry an additional SH3-binding motif. It is likely that Phostensin targets PP1 to the F-actin cytoskeleton. Phostensin binds to actin and decreases the elongation and depolymerization rates of actin filament pointed ends. 84 matched cddid_all.tbl CDD pfam13917 pfam13917 404753 zf-CCHC_3 Zinc knuckle. The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger. 41 matched cddid_all.tbl CDD pfam13918 pfam13918 464040 PLDc_3 PLD-like domain. 180 matched cddid_all.tbl CDD pfam13919 pfam13919 464041 ASXH Asx homology domain. A conserved alpha helical domain with a characteriztic LXXLL motif. The LXXLL motif is detected in diverse transcription factors, coactivators and corepressors and is implicated in mediating interactions between them. The ASXH domain is found in animals, fungi and plants and is predicted to play a role in mediating contact between transcription factors and chromatin-associated complexes. In Drosophila Asx and Human ASXL1, the ASXH domain is predicted to mediate interactions with the Calypso and BAP1 deubiquitinases (DUBs) which further belong to the UCHL5/UCH37 clade of DUBs. 129 matched cddid_all.tbl CDD pfam13920 pfam13920 464042 zf-C3HC4_3 Zinc finger, C3HC4 type (RING finger). 50 matched cddid_all.tbl CDD pfam13921 pfam13921 372817 Myb_DNA-bind_6 Myb-like DNA-binding domain. This family contains the DNA binding domains from Myb proteins, as well as the SANT domain family. 60 matched cddid_all.tbl CDD pfam13922 pfam13922 316444 PHD_3 PHD domain of transcriptional enhancer, Asx. This is the DNA-binding domain on the additional sex combs-like 1 proteins. The Asx protein acts as an enhancer of trithorax and polycomb in displaying bidirectional homoeotic phenotypes in Drosophila, suggesting that it is required for maintenance of both activation and silencing of Hox genes. Asx is required for normal adult haematopoiesis and its function depends on its cellular context. 68 matched cddid_all.tbl CDD pfam13923 pfam13923 404756 zf-C3HC4_2 Zinc finger, C3HC4 type (RING finger). 40 matched cddid_all.tbl CDD pfam13924 pfam13924 464043 Lipocalin_5 Lipocalin-like domain. This family includes domains distantly related to lipocalins. However, they do contain the important GXW motif in the first strand. The protein in this family include aln5, which is involved in biosynthesis of alnumycin. The family also includes the ZFK protein from Trypanosoma brucei which is a protein kinase. This domain is at the C-terminus of that protein. The domain is also found as the C-terminal domain in StiJ a protein involved in producing stigmatellin. This domain has been assumed to catalyze a final cyclization reaction. 140 matched cddid_all.tbl CDD pfam13925 pfam13925 464044 Katanin_con80 con80 domain of Katanin. The con80 domain of katanin is the C-terminal region of the protein that binds to the N-terminal domain of katanin-p60, the catalytic ATPase. The complex associates with a specific subregion of the mitotic spindle leading to increased microtubule disassembly and targeting of p60 to the spindle poles. The assembly and function of the mitotic spindle requires the activity of a number of microtubule-binding proteins. Katanin, a heterodimeric microtubule-severing ATPase, is found localized at mitotic spindle poles. A proposed model is that katanin is targeted to spindle poles through a combination of direct microtubule binding by the p60 subunit and through interactions between the WD40 domain and an unknown protein. 160 matched cddid_all.tbl CDD pfam13926 pfam13926 464045 DUF4211 Domain of unknown function (DUF4211). 138 matched cddid_all.tbl CDD pfam13927 pfam13927 464046 Ig_3 Immunoglobulin domain. This family contains immunoglobulin-like domains. 78 matched cddid_all.tbl CDD pfam13928 pfam13928 464047 Flocculin_t3 Flocculin type 3 repeat. This repeat is found in the Flocculation protein FLO9 close to its C-terminus. 44 matched cddid_all.tbl CDD pfam13929 pfam13929 433586 mRNA_stabil mRNA stabilization. This domain is an mRNA stabilization factor. 286 matched cddid_all.tbl CDD pfam13930 pfam13930 433587 Endonuclea_NS_2 DNA/RNA non-specific endonuclease. 133 matched cddid_all.tbl CDD pfam13931 pfam13931 464048 Microtub_bind Kinesin-associated microtubule-binding. This domain binds to micotubules. 139 matched cddid_all.tbl CDD pfam13932 pfam13932 464049 GIDA_C tRNA modifying enzyme MnmG/GidA C-terminal domain. The GidA associated domain is a domain that has been identified at the C-terminus of protein GidA. It consists of several helices, the last three being rather short and forming small bundle. GidA is an tRNA modification enzyme found in bacteria and mitochondrial. Based on mutational analysis this domain has been suggested to be implicated in binding of the D-stem of tRNA and to be responsible for the interaction with protein MnmE. Structures of GidA in complex with either tRNA or MnmE are missing. Reported to bind to Pfam family MnmE, pfam12631. 214 matched cddid_all.tbl CDD pfam13933 pfam13933 404766 HRXXH Putative peptidase family. This family of putative peptidases are closely related to the M35 family pfam02102. In this family the metal binding HEXXH motif is replaced with HRXXH. The exact function of these proteins is unknown. Members of this family are found to be fungal allergens. 244 matched cddid_all.tbl CDD pfam13934 pfam13934 464050 ELYS Nuclear pore complex assembly. ELYS (embryonic large molecule derived from yolk sac) is conserved from fungi such Aspergillus nidulans and Schizosaccharomyces pombe to human. It is important for the assembly of the nuclear pore complex. 219 matched cddid_all.tbl CDD pfam13935 pfam13935 379401 Ead_Ea22 Ead/Ea22-like protein. This family contains phage proteins and bacterial proteins that are likely to represent integrated phage proteins. This family includes the Lambda phage Ea22 early protein as well as the Bacteriophage P22 Ead protein. 139 matched cddid_all.tbl CDD pfam13936 pfam13936 433591 HTH_38 Helix-turn-helix domain. This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding. 44 matched cddid_all.tbl CDD pfam13937 pfam13937 433592 DUF4212 Domain of unknown function (DUF4212). This family includes several putative integral membrane proteins which have been predicted as the putative subunit of transporters for D-alanine or lactate. 77 matched cddid_all.tbl CDD pfam13938 pfam13938 464051 DUF4213 Putative heavy-metal chelation. This domain of unknown function has an enolase N-terminal domain-like fold. Its genomic context suggests that it may have a role in anaerobic vitamin B12 biosynthesis. This domain is often found at the N-terminus of proteins containing DUF364, pfam04016. The structure of UnioProtKB:B8FUJ5, PDB:3l5o, suggests that the whole protein has this enolase N-terminal-like fold and an Rossmann-like C-terminal domain. Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The protein may be playing a role in heavy-metal chelation. 73 matched cddid_all.tbl CDD pfam13939 pfam13939 404771 TisB_toxin Toxin TisB, type I toxin-antitoxin system. TisB (toxicity-induced by SOS B) is an SOS-induced toxic peptide. It is a hydrophobic membrane-spanning protein which inhibits cell growth. Its expression is inhibited by the antisense RNA IstR-1, which acts as an antitoxin. 28 matched cddid_all.tbl CDD pfam13940 pfam13940 404772 Ldr_toxin Toxin Ldr, type I toxin-antitoxin system. This family includes the Ldr (long direct repeat) toxins. In Escherichia coli there are four Ldr toxins, LdrA, LdrB, LdrC and LdrD. These toxins inhibit cell growth, decrease cell viability and cause nucleoid condensation. LdrD expression is inhibited by the antisense RNA RdlD, which functions as an antitoxin. 35 matched cddid_all.tbl CDD pfam13941 pfam13941 433594 MutL MutL protein. This small family includes, GlmL/MutL from Clostridium tetanomorphum and Clostridium cochlearium. GlmL is located between the genes for the two subunits, epsilon (GlmE) and sigma (GlmS), of the coenzyme-B12-dependent glutamate mutase (methylaspartate mutase), the first enzyme in a pathway of glutamate fermentation. Members shows significant sequence similarity to the hydantoinase branch of the hydantoinase/oxoprolinase family. 448 matched cddid_all.tbl CDD pfam13942 pfam13942 433595 Lipoprotein_20 YfhG lipoprotein. This family includes the YfhG protein from E. coli. Members of this family have an N-terminal lipoprotein attachment site. The members of this family are functionally uncharacterized. 175 matched cddid_all.tbl CDD pfam13943 pfam13943 433596 WPP WPP domain. 101 matched cddid_all.tbl CDD pfam13944 pfam13944 433597 Calycin_like Calycin-like beta-barrel domain. 121 matched cddid_all.tbl CDD pfam13945 pfam13945 372833 NST1 Salt tolerance down-regulator. NST1 is a family of proteins that seem to be involved, directly or indirectly, in the salt sensitivity of some cellular functions in yeast. It does this without affecting sodium accumulation. It negatively affects salt-tolerance through an interaction with the splicing factor Msl1p. This interaction stresses the importance of efficient RNA processing under salt stress conditions. 186 matched cddid_all.tbl CDD pfam13946 pfam13946 433598 DUF4214 Domain of unknown function (DUF4214). This domain is found on a variety of different proteins including transferases, and allergen V5/Tpx-1 related proteins. 72 matched cddid_all.tbl CDD pfam13947 pfam13947 464052 GUB_WAK_bind Wall-associated receptor kinase galacturonan-binding. This cysteine-rich GUB_WAK_bind domain is the extracellular part of this serine/threonine kinase that binds to the cell-wall pectins. 64 matched cddid_all.tbl CDD pfam13948 pfam13948 290659 DUF4215 Domain of unknown function (DUF4215). The function of this family is unknown. 47 matched cddid_all.tbl CDD pfam13949 pfam13949 464053 ALIX_LYPXL_bnd ALIX V-shaped domain binding to HIV. The binding of the LYPxL motif of late HIV p6Gag and EIAV p9Gag to this domain is necessary for viral budding.This domain is generally central between an N-terminal Bro1 domain, pfam03097 and a C-terminal proline-rich domain. The retroviruses thus used this domain to hijack the ESCRT system of the cell. 294 matched cddid_all.tbl CDD pfam13952 pfam13952 464054 DUF4216 Domain of unknown function (DUF4216). This DUF is sometimes found at the C-terminal end of proteins carrying a Transposase_21 domain, pfam02992. 72 matched cddid_all.tbl CDD pfam13953 pfam13953 464055 PapC_C PapC C-terminal domain. The PapC C-terminal domain is a structural domain found at the C-terminus of the E. coli PapC protein. Pili are assembled using the chaperone usher system. In E.coli this is composed of the chaperone PapD and the usher PapC. This domain represents the C-terminal domain from PapC and its homologs. This domain has a beta-sandwich structure similar to the plug domain of PapC. 66 matched cddid_all.tbl CDD pfam13954 pfam13954 433603 PapC_N PapC N-terminal domain. The PapC N-terminal domain is a structural domain found at the N-terminus of the E. coli PapC protein. Pili are assembled using the chaperone usher system. In E.coli this is composed of the chaperone PapD and the usher PapC. This domain represents the N-terminal domain from PapC and its homologs. This domain is involved in substrate binding. 146 matched cddid_all.tbl CDD pfam13955 pfam13955 372839 Fst_toxin Toxin Fst, type I toxin-antitoxin system. Fst (faecalis plasmid stabilization toxin), also known as RNA I, is a toxic peptide. Its N-terminus forms a transmembrane alpha helix, its C terminus is disordered and is likely to be cytosolic. Its translation is inhibited by the antisense RNA, RNA II, which acts as an antitoxin. 21 matched cddid_all.tbl CDD pfam13956 pfam13956 206126 Ibs_toxin Toxin Ibs, type I toxin-antitoxin system. The Ibs (induction brings stasis) proteins are a family of toxic peptides. Their expression is inhibited by the Sib antisense RNAs, which act as antitoxins. 19 matched cddid_all.tbl CDD pfam13957 pfam13957 433604 YafO_toxin Toxin YafO, type II toxin-antitoxin system. YafO is a toxin which inhibits protein synthesis. It acts as a ribosome-dependent mRNA interferase. It forms part of a type II toxin-antitoxin system, where the YafN protein acts as an antitoxin. This domain forms complexes with yafN antitoxins containing pfam02604. 101 matched cddid_all.tbl CDD pfam13958 pfam13958 433605 ToxN_toxin Toxin ToxN, type III toxin-antitoxin system. ToxN acts as a toxin, it is part of a type III toxin-antitoxin system. It acts as a ribosome independent endoribonuclease. It interacts with, and is inhibited by, the RNA antitoxin, ToxI. Three ToxN monomers bind to three ToxI monomers to create a trimeric ToxN-ToxI complex. 155 matched cddid_all.tbl CDD pfam13959 pfam13959 464056 DUF4217 Domain of unknown function (DUF4217). This short domain is found at the C-terminus of many helicase proteins. 59 matched cddid_all.tbl CDD pfam13960 pfam13960 433607 DUF4218 Domain of unknown function (DUF4218). 112 matched cddid_all.tbl CDD pfam13961 pfam13961 433608 DUF4219 Domain of unknown function (DUF4219). This domain is very short and is found at the N-terminal of many Gag-pol polyprotein and related proteins. There is a highly conserved YxxWxxxM sequence motif. 27 matched cddid_all.tbl CDD pfam13962 pfam13962 433609 PGG Domain of unknown function. The PGG domain is named for the highly conserved sequence motif found at the startt of the domain. The function is not known. 114 matched cddid_all.tbl CDD pfam13963 pfam13963 433610 Transpos_assoc Transposase-associated domain. 74 matched cddid_all.tbl CDD pfam13964 pfam13964 404790 Kelch_6 Kelch motif. 50 matched cddid_all.tbl CDD pfam13965 pfam13965 464057 SID-1_RNA_chan dsRNA-gated channel SID-1. This is a family of proteins that are transmembrane dsRNA-gated channels. They passively transport dsRNA into cells and do not act as ATP-dependent pumps. They are required for systemic RNA interference. This family of proteins belong to the CREST superfamily, which are distantly related to GPCRs. 599 matched cddid_all.tbl CDD pfam13966 pfam13966 433612 zf-RVT zinc-binding in reverse transcriptase. This domain would appear to be a zinc-binding region of a putative reverse transcriptase. 84 matched cddid_all.tbl CDD pfam13967 pfam13967 433613 RSN1_TM Late exocytosis, associated with Golgi transport. This family represents the first three transmembrane regions of 11-TM proteins involved in vesicle transport. In S. cerevisiae these proteins are members of the yeast facilitator superfamily and are integral membrane proteins localized to the cell periphery, in particular to the bud-neck region. The distribution is consistent with a role in late exocytosis which is in agreement with the proteins' ability to substitute for the function of Sro7p, required for the sorting of the protein Enap1 into Golgi-derived vesicles destined for the cell surface. 158 matched cddid_all.tbl CDD pfam13968 pfam13968 464058 DUF4220 Domain of unknown function (DUF4220). This family is found in plants and is often associated with DUF294, pfam04578. 316 matched cddid_all.tbl CDD pfam13969 pfam13969 372852 Pab87_oct Pab87 octamerization domain. This domain was first characterized as the C-terminal domain of Pab87 serine protease from Pyrococcus abyssi. The domain is reported to play a crucial role in Pab87 octamerization and active site compartmentalization. Its up-and-down 8-stranded beta-barrel 3D structure is reminiscent of the one found in lipocalins. 96 matched cddid_all.tbl CDD pfam13970 pfam13970 404795 DUF4221 Domain of unknown function (DUF4221). This family of bacterial lipoproteins contain a beta propeller structure. 310 matched cddid_all.tbl CDD pfam13971 pfam13971 464059 Mei4 Meiosis-specific protein Mei4. This family of meiosis specific proteins is required for correct meiotic chromosome segregation and recombination. It is required for meiotic DNA double-strand break (DSB) formation. 340 matched cddid_all.tbl CDD pfam13972 pfam13972 433616 TetR Bacterial transcriptional repressor. This family of bacterial transcriptional repressors is characterized by the short approximately 50 amino acid stretch of residues constituting the helix-turn-helix DNA binding motif, around the YRFhY motif. The target proteins that are repressed are involved in the transcriptional control of multi-drug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The regulatory network in which TetR itself is involved is in being released in the presence of tetracycline, binding to the target operator, and repressing tetA transcription. 143 matched cddid_all.tbl CDD pfam13973 pfam13973 372855 DUF4222 Domain of unknown function (DUF4222). This short protein is likely to be of phage origin. For example it is found in the Enterobacteria phage YYZ-2008. It is largely found in enteric bacteria. The molecular function of this protein is unknown. 53 matched cddid_all.tbl CDD pfam13974 pfam13974 433617 YebO YebO-like protein. This short protein is uncharacterized. It seems likely to be of phage origin as it is found in Swiss:Q9MCU2 and Swiss:Q9MCS4. The protein is also found in a variety of enteric bacteria. 78 matched cddid_all.tbl CDD pfam13975 pfam13975 464060 gag-asp_proteas gag-polyprotein putative aspartyl protease. This family of putative aspartyl proteases is found pre-dominantly in retroviral proteins. 92 matched cddid_all.tbl CDD pfam13976 pfam13976 372857 gag_pre-integrs GAG-pre-integrase domain. This domain is found associated with retroviral insertion elements and lies just upstream of the integrase region on the polyproteins. 67 matched cddid_all.tbl CDD pfam13977 pfam13977 433619 TetR_C_6 BetI-type transcriptional repressor, C-terminal. This family comprises the C-terminal portion of proteins that belong to the TetR family of transcriptional regulators. The C terminus represents the regulatory region, and does not include the DNA binding helix-turn-helix domain. The target proteins that are repressed are involved in the transcriptional control of multi-drug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. One of the target proteins is BetI, an osmoprotectant which controls the choline-glycine betaine pathway in E.coli. 112 matched cddid_all.tbl CDD pfam13978 pfam13978 433620 DUF4223 Protein of unknown function (DUF4223). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. These proteins are likely to be lipoproteins (attachment site currently included in alignment). 54 matched cddid_all.tbl CDD pfam13979 pfam13979 464061 SopA_C SopA-like catalytic domain. This domain is found in the E. coli Type III secretion effector proteins SopA and NleL. These proteins have been shown to act as E3 ubiquitin ligase enzymes. This domain contains the active site cysteine residue. 166 matched cddid_all.tbl CDD pfam13980 pfam13980 433622 UPF0370 Uncharacterized protein family (UPF0370). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved DWP sequence motif. 61 matched cddid_all.tbl CDD pfam13981 pfam13981 433623 SopA SopA-like central domain. This domain is found in the E. coli Type III secretion effector proteins SopA and NleL. These proteins have been shown to act as E3 ubiquitin ligase enzymes. 126 matched cddid_all.tbl CDD pfam13982 pfam13982 433624 YbfN YbfN-like lipoprotein. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. Members of this family are lipoproteins. 88 matched cddid_all.tbl CDD pfam13983 pfam13983 404804 YsaB YsaB-like lipoprotein. This family of proteins is functionally uncharacterized. These proteins are related to E.coli YsaB. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. These proteins are lipoproteins. 75 matched cddid_all.tbl CDD pfam13984 pfam13984 433625 MsyB MsyB protein. The MsyB protein has been found to be able to restore protein export defects caused by a temperature-sensitive secY or secA mutation. However, its exact molecular function is still unknown, but it may play a role in protein export. Proteins in this family are approximately 120 amino acids in length. This family of proteins is found in bacteria. 120 matched cddid_all.tbl CDD pfam13985 pfam13985 464062 YbgS YbgS-like protein. This family of proteins is functionally uncharacterized. The family includes the YbgS protein from E. coli. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. Some members of this family are annotated as homeobox protein, but this annotation cannot be verified. 120 matched cddid_all.tbl CDD pfam13986 pfam13986 433627 DUF4224 Domain of unknown function (DUF4224). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. The protein is likely to be of phage origin and is found as protein Gp02 in the Xylella phage Xfas53. 45 matched cddid_all.tbl CDD pfam13987 pfam13987 433628 YedD YedD-like protein. This family of proteins related to the YedD protein is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. These proteins are lipoproteins. 106 matched cddid_all.tbl CDD pfam13988 pfam13988 433629 DUF4225 Protein of unknown function (DUF4225). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 182 and 282 amino acids in length. 163 matched cddid_all.tbl CDD pfam13989 pfam13989 433630 YejG YejG-like protein. The YejG protein family is a group of functionally uncharacterized proteins related to Swiss:P0AD21. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. 104 matched cddid_all.tbl CDD pfam13990 pfam13990 404811 YjcZ YjcZ-like protein. This family of proteins is functionally uncharacterized. The family includes the YjcZ protein from E. coli. This family of proteins is found in enteric bacteria. Proteins in this family are approximately 300 amino acids in length. There are two conserved sequence motifs: FGD and MPR. 272 matched cddid_all.tbl CDD pfam13991 pfam13991 433631 BssS BssS protein family. The BssS protein family is a group of proteins that are involved in regulation of biofilm formation. Proteins in this family are approximately 80 amino acids in length. 72 matched cddid_all.tbl CDD pfam13992 pfam13992 404813 YecR YecR-like lipoprotein. The YecR-like family of lipoproteins includes the YecR protein from E. coli. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 110 amino acids in length. 73 matched cddid_all.tbl CDD pfam13993 pfam13993 433632 YccJ YccJ-like protein. The YccJ-like family of proteins includes the E. coli YccJ protein which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 67 matched cddid_all.tbl CDD pfam13994 pfam13994 433633 PgaD PgaD-like protein. This family includes the PgaD protein from E. coli. The homopolymer poly-beta-1,6-N-acetyl-D-glucosamine (beta-1,6-GlcNAc; PGA) serves as an adhesin for the maintenance of biofilm structural stability in eubacteria. The pgaABCD operon is required for its synthesis and export. It has been shown that PgaD is essential for this process. 148 matched cddid_all.tbl CDD pfam13995 pfam13995 433634 YebF YebF-like protein. The YebF-like protein family appears to be a group of colicin immunity proteins. As well as YebF the family includes cmi, the colicin M immunity protein. This domain family is found in bacteria, and is approximately 80 amino acids in length. The alignment contains two conserved cysteine residues that form a disulphide bond in the solved structure. 89 matched cddid_all.tbl CDD pfam13996 pfam13996 433635 YobH YobH-like protein. The YobH-like protein family includes the YobH protein from E. coli, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. There are two conserved sequence motifs: GYG and GLGL. 70 matched cddid_all.tbl CDD pfam13997 pfam13997 464063 YqjK YqjK-like protein. The YqjK-like protein family includes the E. coli YqjK protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. There is a single completely conserved residue R that may be functionally important. 72 matched cddid_all.tbl CDD pfam13998 pfam13998 404818 MgrB MgrB protein. The MgrB protein is a short lipoprotein. The mgrB gene has a mg2+ responsive promoter. Deletion of mgrB results in a potent increase in PhoP-regulated transcription. The PhoQ/PhoP signaling system responds to low magnesium and the presence of certain cationic antimicrobial peptides. Over-expression of mgrB decreased transcription at both high and low concentrations of magnesium. Localization and bacterial two-hybrid studies suggest that MgrB resides in the inner-membrane and interacts directly with PhoQ. This domain family is found in bacteria, and is approximately 40 amino acids in length. There are two conserved sequence motifs: CDQ and GIC. 29 matched cddid_all.tbl CDD pfam13999 pfam13999 404819 MarB MarB protein. The MarB protein is found in the multiple antibiotic resistance (mar) locus in Escherichia coli. The MarB protein is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved GSDKSD sequence motif. 63 matched cddid_all.tbl CDD pfam14000 pfam14000 290707 Packaging_FI DNA packaging protein FI. This family includes the lambda phage DNA-packaging protein FI. Proteins in this family are typically between 124 and 140 amino acids in length. There is a conserved EEE sequence motif. 131 matched cddid_all.tbl CDD pfam14001 pfam14001 404820 YdfZ YdfZ protein. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved YDRNRN sequence motif. The E. coli protein has been shown to bind selenium. 64 matched cddid_all.tbl CDD pfam14002 pfam14002 433637 YniB YniB-like protein. The YniB-like protein family includes the E. coli YniB protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 180 amino acids in length. This family of proteins are integral membrane proteins. 166 matched cddid_all.tbl CDD pfam14003 pfam14003 404822 YlbE YlbE-like protein. The YlbE-like protein family includes the B. subtilis protein YlbE, which is functionally uncharacterized. This family of cytosolic proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. There is a conserved WYR sequence motif. 61 matched cddid_all.tbl CDD pfam14004 pfam14004 372877 DUF4227 Protein of unknown function (DUF4227). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 71 matched cddid_all.tbl CDD pfam14005 pfam14005 404823 YpjP YpjP-like protein. The YpjP-like protein family includes the B. subtilis YpjP protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 200 amino acids in length. 133 matched cddid_all.tbl CDD pfam14006 pfam14006 379412 YqzL YqzL-like protein. The YqzL-like protein family includes the B. subtilis YqzL protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. 40 matched cddid_all.tbl CDD pfam14007 pfam14007 433638 YtpI YtpI-like protein. The YtpI-like protein family includes the B. subtilis YtpI protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 73 and 101 amino acids in length. 87 matched cddid_all.tbl CDD pfam14008 pfam14008 464064 Metallophos_C Iron/zinc purple acid phosphatase-like protein C. This domain is found at the C-terminus of Purple acid phosphatase proteins. 60 matched cddid_all.tbl CDD pfam14009 pfam14009 464065 PADRE PADRE domain. This entry represents the Pathogen and abiotic stress response, cadmium tolerance, disordered region-containing (PADRE) domain, which is specifically found in plants. PADRE typically occurs in small single-domain proteins with a bipartite architecture. PADRE contains conserved sequence motifs at the N-terminal, and its C-terminal includes an intrinsically disordered region with multiple phosphorylation sites. This domain is associated with plant defense upon diverse stress stimulus and has a role in disease resistance to fungi. 146 matched cddid_all.tbl CDD pfam14010 pfam14010 404826 PEPcase_2 Phosphoenolpyruvate carboxylase. This family of phosphoenolpyruvate carboxylases is based on seqeunces not picked up by the model for PEPcase, PF00311. Most of the family members are from Archaea. 496 matched cddid_all.tbl CDD pfam14011 pfam14011 433641 ESX-1_EspG EspG family. This family of proteins contains the the EspG1, EspG2 and EspG3 proteins from M. tuberculosis. These proteins are involved in the ESAT-6 secretion system 1 (ESX-1) of Mycobacterium tuberculosis which is important for virulence and intercellular spread. Proteins in this family are typically between 254 and 295 amino acids in length. 242 matched cddid_all.tbl CDD pfam14012 pfam14012 433642 DUF4229 Protein of unknown function (DUF4229). This family of integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 95 and 122 amino acids in length. 67 matched cddid_all.tbl CDD pfam14013 pfam14013 433643 MT0933_antitox MT0933-like antitoxin protein. This family of proteins contains the MT0933 protein, which has been identified as an antitoxin to /protein MT0934. This family of proteins is found in bacteria. Proteins in this family are typically between 61 and 90 amino acids in length. 49 matched cddid_all.tbl CDD pfam14014 pfam14014 433644 DUF4230 Protein of unknown function (DUF4230). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 203 and 228 amino acids in length. 134 matched cddid_all.tbl CDD pfam14015 pfam14015 464066 DUF4231 Protein of unknown function (DUF4231). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 148 and 288 amino acids in length. 105 matched cddid_all.tbl CDD pfam14016 pfam14016 433646 DUF4232 Protein of unknown function (DUF4232). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 177 and 242 amino acids in length. Many members of this family are lipoproteins. 130 matched cddid_all.tbl CDD pfam14017 pfam14017 433647 DUF4233 Protein of unknown function (DUF4233). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 122 and 147 amino acids in length. Proteins in this family are integral membrane proteins. 106 matched cddid_all.tbl CDD pfam14018 pfam14018 404834 DUF4234 Domain of unknown function (DUF4234). This presumed integral membrane protein domain is functionally uncharacterized. This domain family is found in bacteria and archaea, and is approximately 70 amino acids in length. 69 matched cddid_all.tbl CDD pfam14019 pfam14019 433648 DUF4235 Protein of unknown function (DUF4235). This family of integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 88 and 119 amino acids in length. 77 matched cddid_all.tbl CDD pfam14020 pfam14020 433649 DUF4236 Protein of unknown function (DUF4236). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 69 and 402 amino acids in length. 55 matched cddid_all.tbl CDD pfam14021 pfam14021 433650 TNT Tuberculosis necrotizing toxin. This is the C-terminal domain secreted by Mycobacterium tuberculosis (Mtb). It induces necrosis of infected cells to evade immune responses. Mtb utilizes the protein CpnT to kill human macrophages by secreting its C-terminal domain (CTD), named tuberculosis necrotizing toxin (TNT) that induces necrosis. It acts as a NAD+ glycohydrolase which hydrolyzes the essential cellular coenzyme NAD+ in the cytosol of infected macrophages resulting in necrotic cell death. CpnT transports its toxic CTD from the cell surface of M. tuberculosis by proteolytic cleavage, where the toxin is cleaved to induce host cell death. Structural analysis determined that the TNT core contains only six beta-strands as opposed to seven found in all known NAD+-utilizing toxins, and is significantly smaller, with only two short alpha-helices and two 3/10 helices. Furthermore, the putative NAD+ binding pocket identified Q822, Y765 and R757 as residues possibly involved in NAD+-binding and hydrolysis based on similar positions of catalytic amino acids of ADP-ribosylating toxins. While glutamine 822 residue was detected to be highly conserved among TNT homologs. 84 matched cddid_all.tbl CDD pfam14022 pfam14022 464067 DUF4238 Protein of unknown function (DUF4238). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 274 and 374 amino acids in length. 284 matched cddid_all.tbl CDD pfam14023 pfam14023 464068 DUF4239 Protein of unknown function (DUF4239). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 254 and 270 amino acids in length. 215 matched cddid_all.tbl CDD pfam14024 pfam14024 433652 DUF4240 Protein of unknown function (DUF4240). This presumed domain is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 169 and 263 amino acids in length. This domain is often associated with the WGR domain pfam05406. 128 matched cddid_all.tbl CDD pfam14025 pfam14025 433653 DUF4241 Protein of unknown function (DUF4241). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 205 and 315 amino acids in length. There is a conserved GDG sequence motif at the C-terminus. 140 matched cddid_all.tbl CDD pfam14026 pfam14026 433654 DUF4242 Protein of unknown function (DUF4242). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 90 and 170 amino acids in length. There is a single completely conserved residue C that may be functionally important. 74 matched cddid_all.tbl CDD pfam14027 pfam14027 464069 Questin_oxidase Questin oxidase-like. This family consists of oxidoreductases involved in the synthesis of different polyketides and derivatives. Questin oxidase GedK from Aspergillus terreus catalyzes the ring cleavage of the anthraquinone questin to form benzophenone desmethylsulochrin. It is part of the gene cluster that mediates the biosynthesis of geodin, an intermediate in the biosynthesis of other natural products. MdpL from Emericella nidulans is part of the gene cluster that mediates the biosynthesis of monodictyphenone. 336 matched cddid_all.tbl CDD pfam14028 pfam14028 433656 Lant_dehydr_C Lantibiotic biosynthesis dehydratase C-term. Lant_dehydr_C is the C-terminal domain of a family of dehydratases that are involved in the biosynthesis of lantibiotics. While the extensive N-terminal domain, pfam04738, is involved in the serine-threonine glutamylation step of the synthetic process, this C-terminal domain, once thought to be a separate domain from the dehydratase enzymic activity, is necessary for the final glutamate-elimination step in the generation of the lantibiotic. Lantibiotics are a class of peptide antibiotic that contains one or more thioether bonds. 278 matched cddid_all.tbl CDD pfam14029 pfam14029 433657 DUF4244 Protein of unknown function (DUF4244). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 66 and 95 amino acids in length. There is a conserved EYA sequence motif. 50 matched cddid_all.tbl CDD pfam14030 pfam14030 433658 DUF4245 Protein of unknown function (DUF4245). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 188 and 235 amino acids in length. 156 matched cddid_all.tbl CDD pfam14031 pfam14031 433659 D-ser_dehydrat Putative serine dehydratase domain. This domain is found at the C-terminus of yeast D-serine dehydratase. Structures have been solved for two bacterial members of this family. The yeast protein has been shown to be a zinc dependant enzyme. 96 matched cddid_all.tbl CDD pfam14032 pfam14032 433660 PknH_C PknH-like extracellular domain. This domain is functionally uncharacterized. It is found as the periplasmic domain of the bacterial protein kinase PknH. The domain is also found in isolation in numerous proteins, for example the lipoproteins lpqQ, lprH, lppH and lpqA from M. tuberculosis. This family of proteins is found in bacteria. Proteins in this family are typically between 214 and 268 amino acids in length. There are two completely conserved C residues that are likely to form a disulphide bond. A second pair of cysteines are less well conserved probably form a second disulphide bond. It seems likely that this domain functions to bind some as yet unknown ligand. 188 matched cddid_all.tbl CDD pfam14033 pfam14033 433661 DUF4246 Protein of unknown function (DUF4246). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and fungi. Proteins in this family are typically between 392 and 644 amino acids in length. 421 matched cddid_all.tbl CDD pfam14034 pfam14034 433662 Spore_YtrH Sporulation protein YtrH. This family of proteins is involved in sporulation. It may contribute to the formation and stability of the thick peptidoglycan layer between the two membranes of the spore, known as the cortex. In Bacillus subtilis its expression is regulated by sigma-E. 99 matched cddid_all.tbl CDD pfam14035 pfam14035 433663 YlzJ YlzJ-like protein. The YlzJ-like protein family includes the B. subtilis YlzJ protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 61 and 72 amino acids in length. There are two completely conserved residues (L and G) that may be functionally important. 65 matched cddid_all.tbl CDD pfam14036 pfam14036 433664 YlaH YlaH-like protein. The YlaH-like protein family includes the B. subtilis YlaH protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. There is a conserved LGFA sequence motif. 75 matched cddid_all.tbl CDD pfam14037 pfam14037 372886 YoqO YoqO-like protein. The YoqO-like protein family includes the B. subtilis YoqO protein, which is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 120 amino acids in length. There are two completely conserved residues (I and Y) that may be functionally important. 116 matched cddid_all.tbl CDD pfam14038 pfam14038 372887 YqzE YqzE-like protein. The YqzE-like protein family includes the B. subtilis YqzE protein, which is functionally uncharacterized. It is a part of the ComG operon, which is regulated by the competence transcription factor ComK. This family of proteins is found in bacteria. Proteins in this family are typically between 49 and 66 amino acids in length. 53 matched cddid_all.tbl CDD pfam14039 pfam14039 433665 YusW YusW-like protein. The YusW-like protein family includes the B. subtilis YusW protein, which is functionally uncharacterized. This family of proteins is found in bacteria, and is approximately 90 amino acids in length. 91 matched cddid_all.tbl CDD pfam14040 pfam14040 404851 DNase_NucA_NucB Deoxyribonuclease NucA/NucB. NucB is a non-specific endonuclease, which can hydrolyse both single- and double-stranded DNA substrates, in a divalent cation-dependent manner and to be expressed in late stage II of sporulation. NucB and NucA show structural similarity with other His-Me finger nucleases which are characterized by a common beta-beta-alpha motif. The beta-beta-alpha motif contains a central pair of anti-parallel beta-strands flanked by a conserved distal alpha-helix that sits in the major groove of DNA; the loop connecting the two beta-strands is variable in length and conformation. Direct magnesium co-ordination are highly conserved in NucB sequences in DRDE and DNRG (DD) motifs. The conserved Glu94 in B.subtilis NucB, corresponds to the conserved His in the His-Me finger family. Mutation of individual amino acids in these motifs in B. subtilis-NucB (Asp93 and Glu94 from motif 1, and Asn117 from motif 2) abrogates enzyme activity completely. 113 matched cddid_all.tbl CDD pfam14041 pfam14041 433666 Lipoprotein_21 LppP/LprE lipoprotein. The family includes putative lipoproteins LppP and LprE from species of Mycobacterium. LppP is required for optimal growth of M. tuberculosis. 86 matched cddid_all.tbl CDD pfam14042 pfam14042 433667 DUF4247 Domain of unknown function (DUF4247). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 143 and 271 amino acids in length. 122 matched cddid_all.tbl CDD pfam14043 pfam14043 433668 WVELL WVELL protein. This family includes the B. subtilis YfjH protein, which is functionally uncharacterized. This is not a homolog of E. coli YfjH, a synonym for IscX, which belongs to pfam04384. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length and contain a highly conserved WVELL motif. 74 matched cddid_all.tbl CDD pfam14044 pfam14044 433669 NETI NETI protein. This family includes the B. subtilis YebG protein, which is functionally uncharacterized. This is not a homolog of E. coli YebG, which belongs to pfam07130. This family of proteins is found in bacteria. Proteins in this family are typically between 42 and 66 amino acids in length and contain a conserved NETI motif. 56 matched cddid_all.tbl CDD pfam14045 pfam14045 433670 YIEGIA YIEGIA protein. This family includes the B. subtilis YphB protein, which is functionally uncharacterized. Its expression is regulated by the sporulation transcription factor sigma-F, however it is not essential for sporulation or germination. This is not a homolog of E. coli YphB, which belongs to pfam01263. This family of proteins is found in bacteria. Proteins in this family are typically between 276 and 300 amino acids in length and contain a conserved YIEGIA motif. 282 matched cddid_all.tbl CDD pfam14046 pfam14046 464070 NR_Repeat Nuclear receptor repeat. This is a repeat domain involved in dimerization of nuclear receptors proteins and in transcriptional regulation in general. It contains a Leu-Xaa-Xaa-Leu-Leu motif which has been characterized for the orphan nuclear receptor Dax-1, which represses the constitutively expressed protein Ad4BP/SF-1. The LXXLL motif plays in important role in binding of Dax-1 to Ad4BP/SF-1. The domain is subject to structure determination by the Joint Center of Structural Genomics. 47 matched cddid_all.tbl CDD pfam14047 pfam14047 464071 DCR Dppa2/4 conserved region. This domain has been characterized in the finding of a developmental pluripotency associated gene (Dppa) in the lower vertebrate Xenopus laevis. Previous to this discovery, Dppa genes were known only in higher vertebrates. The domain is subject to structure determination by the Joint Center of Structural Genomics. 67 matched cddid_all.tbl CDD pfam14048 pfam14048 464072 MBD_C C-terminal domain of methyl-CpG binding protein 2 and 3. CpG-methylation is a frequently occurring epigenetic modification of vertebrate genomes resulting in transcriptional repression. This domain was found at the C-terminus of the methyl-CpG-binding domain (MBD) containing proteins MBD2 and MBD3, the latter was shown to not bind directly to methyl-CpG DNA but rather interact with components of the NuRD/Mi2 complex, an abundant deacetylase complex. The domain is subject to structure determination by the Joint Center of Structural Genomics. 94 matched cddid_all.tbl CDD pfam14049 pfam14049 433674 Dppa2_A Dppa2/4 conserved region in higher vertebrates. Developmental pluripotency associated genes (Dppa) in lower vertebrates have remained undetected until the discovery of a Dppa homolog in Xenopus laevis, reporting a new domain termed Dppa2/4 conserved region (DCR). In higher vertebrate Dppa proteins the DCR domain is located next to the here-reported domain. The domain is subject to structure determination by the Joint Center of Structural Genomics. 85 matched cddid_all.tbl CDD pfam14050 pfam14050 464073 Nudc_N N-terminal conserved domain of Nudc. The N-terminus of nuclear distribution gene C homolog (NUDC) proteins contains a highly conserved region consisting of a predicted three helix bundle. In the human homolog this segment has been targeted for structure determination by the Joint Center for Structural Genomics. NUDC forms a complex with other NUD proteins and is involved in several cellular division activities. Recently it was shown that NUDC regulates platelet-activating factor (PAF) acetylhydrolase with PAF being a pro-inflammatory secondary lipidic messenger. 60 matched cddid_all.tbl CDD pfam14051 pfam14051 464074 DPF1-3_N DPF1-3, N-terminal. This putative domain has been detected on requiem/DPF family proteins. It was identified as an adaptor molecule that links nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kappa-B) dimer RelB/p52 and switch/sucrose-nonfermentable (SWI/SNF) chromatin remodelling factor. 67 matched cddid_all.tbl CDD pfam14052 pfam14052 433677 Caps_assemb_Wzi Capsule assembly protein Wzi. Many bacteria are covered in a layer of surface-associated polysaccharide called the capsule. These capsules can be divided into four groups depending upon the organization of genes responsible for capsule assembly, the assembly pathway and regulation. This family plays a role in group 1 capsule biosynthesis. It is likely to be involved in the later stages of capsule assembly. It is likely to consist of a beta-barrel structure. 391 matched cddid_all.tbl CDD pfam14053 pfam14053 433678 DUF4248 Domain of unknown function (DUF4248). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 73 and 86 amino acids in length. 66 matched cddid_all.tbl CDD pfam14054 pfam14054 433679 DUF4249 Domain of unknown function (DUF4249). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 279 and 365 amino acids in length and contain an lipoprotein attachment site at their N-terminus. 255 matched cddid_all.tbl CDD pfam14055 pfam14055 404865 NVEALA NVEALA protein. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 75 and 92 amino acids in length. There is a conserved NVEALA sequence motif. 64 matched cddid_all.tbl CDD pfam14056 pfam14056 464075 DUF4250 Domain of unknown function (DUF4250). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There are two completely conserved residues (N and R) that may be functionally important. 54 matched cddid_all.tbl CDD pfam14057 pfam14057 433681 GGGtGRT GGGtGRT protein. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 330 amino acids in length and contain many highly conserved residues including a GGGtGRT motif. 326 matched cddid_all.tbl CDD pfam14058 pfam14058 464076 PcfK PcfK-like protein. The PcfK-like protein family includes the Enterococcus faecalis PcfK protein, which is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 137 and 257 amino acids in length. There are two completely conserved residues (D and L) that may be functionally important. 139 matched cddid_all.tbl CDD pfam14059 pfam14059 433683 DUF4251 Domain of unknown function (DUF4251). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 164 and 196 amino acids in length. 130 matched cddid_all.tbl CDD pfam14060 pfam14060 433684 DUF4252 Domain of unknown function (DUF4252). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 154 and 182 amino acids in length. 123 matched cddid_all.tbl CDD pfam14061 pfam14061 464077 Mtf2_C Polycomb-like MTF2 factor 2. Mammalian Polycomb-like gene MTF2/PCL2 forms a complex with Polycomb repressive complex-2 (PRC2) and collaborates with PRC1 to achieve repression of Hox gene expression. The human MTF2 gene is expressed in three splicing variants, each of them contains the short C-terminal domain defined here. The domain is subject to structure determination by the Joint Center of Structural Genomics. 48 matched cddid_all.tbl CDD pfam14062 pfam14062 433686 DUF4253 Domain of unknown function (DUF4253). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 110 amino acids in length. 109 matched cddid_all.tbl CDD pfam14063 pfam14063 433687 DUF4254 Protein of unknown function (DUF4254). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 195 and 207 amino acids in length. 144 matched cddid_all.tbl CDD pfam14064 pfam14064 464078 HmuY HmuY protein. HmuY is a novel heme-binding protein that recruits heme from host carriers and delivers it to its cognate outer-membrane transporter, the TonB-dependent receptor HmuR. This family of proteins is found in bacteria. Proteins in this family are typically between 214 and 278 amino acids in length. 155 matched cddid_all.tbl CDD pfam14065 pfam14065 433689 Pvc16_N Pvc16 N-terminal domain. This protein forms part of a contractile injection system. Photorhabdus virulence cassette (PVC) represents one group of extracellular CISs that are present in both bacteria and archaea. This entry include Pvc16. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 190 and 320 amino acids in length. This domain alone in Pvc16 is able to produce PVC particles with normal length but without the outer sheath, indicating the main function of this N-terminal domain in terminating the tube growth. 176 matched cddid_all.tbl CDD pfam14066 pfam14066 433690 DUF4256 Protein of unknown function (DUF4256). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 190 amino acids in length. 173 matched cddid_all.tbl CDD pfam14067 pfam14067 433691 LssY_C LssY C-terminus. This domain is found at the C-terminus of Legionella LssY proteins, which may be a part of the type I secretion system. This domain is functionally uncharacterized. This domain is found in bacteria, and is typically between 182 and 195 amino acids in length. It is often found in association with pfam09335 and PF01569. There are two completely conserved residues (P and W) that may be functionally important. 188 matched cddid_all.tbl CDD pfam14068 pfam14068 433692 YuiB Putative membrane protein. This family of bacterial proteins is functionally uncharacterized. Proteins in this family are approximately 100 amino acids in length. There is a conserved FGIGF sequence motif, and many members are putative membrane proteins. 101 matched cddid_all.tbl CDD pfam14069 pfam14069 404879 SpoVIF Stage VI sporulation protein F. The sporulation-specific SpoVIF (YjcC) protein of Bacillus subtilis is essential for the development of heat-resistant spores. Its expression is governed by SigK. 72 matched cddid_all.tbl CDD pfam14070 pfam14070 464079 YjfB_motility Putative motility protein. This family of proteins is regulated in B. subtilis by SigD, and is likely to be involved in motility or flagellin production, Proteins in this family are approximately 60 amino acids in length, and contain two highly conserved asparagine residues. 57 matched cddid_all.tbl CDD pfam14071 pfam14071 404881 YlbD_coat Putative coat protein. This is a family of putative bacterial coat proteins. Proteins in this family are approximately 140 amino acids in length. 127 matched cddid_all.tbl CDD pfam14072 pfam14072 433694 DndB DNA-sulfur modification-associated. This is family of bacterial proteins likely to be necessary for binding to DNA and recognising the modification sites. Members are found in bacteria, archaea and on viral plasmids, and are typically between 354 and 474 amino acids in length. There is a conserved DGQHR sequence motif. 337 matched cddid_all.tbl CDD pfam14073 pfam14073 464080 Cep57_CLD Centrosome localization domain of Cep57. The CLD or centrosome localization domain of Cep57 is found at the N-terminus, and lies approximately between residues 58 and 239. This region lies within the first alpha-helical coiled-coil segment of Cep57, and localizes to the centrosome internally to gamma-tubulin, suggesting that it is either on both centrioles or on a centromatrix component. This N-terminal region can also multimerize with the N-terminus of other Cep57 molecules. The C-terminal part, Family Cep57_MT_bd, pfam06657, is the microtubule-binding region of Cep57. 178 matched cddid_all.tbl CDD pfam14074 pfam14074 372902 DUF4257 Protein of unknown function (DUF4257). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. 80 matched cddid_all.tbl CDD pfam14075 pfam14075 464081 UBN_AB Ubinuclein conserved middle domain. Ubinuclein 1 and 2 (UBN1, UBN2) are members of a histone chaperone complex involved in the formation of a certain type of facultative heterochromatin, called senescence-associated heterochromatin foci (SAHF). The domain described here is conserved in many eukaryotes such as human, rat, drosophila, and zebra-fish and has been targeted for protein structure determination by the Joint Center for Structural Genomics. 212 matched cddid_all.tbl CDD pfam14076 pfam14076 464082 DUF4258 Domain of unknown function (DUF4258). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 95 and 124 amino acids in length. Structural models show this family adopts a structure found in bacterial toxins, suggesting this family are the toxins in a toxin-antitoxin system. 70 matched cddid_all.tbl CDD pfam14077 pfam14077 433698 WD40_alt Alternative WD40 repeat motif. WD repeats are short subdomains of about 40 amino acids and fold into 4 antiparallel beta hairpins. This domain here has been detected on the C-terminus of WD repeat-containing protein 18 during target selection by the Joint Center for Structural Genomics. 48 matched cddid_all.tbl CDD pfam14078 pfam14078 433699 DUF4259 Domain of unknown function (DUF4259). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 118 and 145 amino acids in length. 130 matched cddid_all.tbl CDD pfam14079 pfam14079 433700 DUF4260 Domain of unknown function (DUF4260). This family of integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 114 and 126 amino acids in length. There is a conserved GLK sequence motif. 112 matched cddid_all.tbl CDD pfam14080 pfam14080 464083 DUF4261 Domain of unknown function (DUF4261). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 80 amino acids in length. 77 matched cddid_all.tbl CDD pfam14081 pfam14081 433702 DUF4262 Domain of unknown function (DUF4262). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 147 and 227 amino acids in length. Swiss:Q50763 is incorrectly annotated as the KatG protein. 127 matched cddid_all.tbl CDD pfam14082 pfam14082 433703 DUF4263 Domain of unknown function (DUF4263). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 244 and 403 amino acids in length. 165 matched cddid_all.tbl CDD pfam14083 pfam14083 433704 PGDYG PGDYG protein. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 150 amino acids in length. There is a conserved PGDYG motif. 101 matched cddid_all.tbl CDD pfam14084 pfam14084 433705 DUF4264 Protein of unknown function (DUF4264). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. 52 matched cddid_all.tbl CDD pfam14085 pfam14085 433706 DUF4265 Domain of unknown function (DUF4265). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 139 and 168 amino acids in length. 111 matched cddid_all.tbl CDD pfam14086 pfam14086 433707 DUF4266 Domain of unknown function (DUF4266). This presumed lipoprotein domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 50 amino acids in length. 50 matched cddid_all.tbl CDD pfam14087 pfam14087 433708 DUF4267 Domain of unknown function (DUF4267). This family of integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 126 and 142 amino acids in length. 110 matched cddid_all.tbl CDD pfam14088 pfam14088 404896 DUF4268 Domain of unknown function (DUF4268). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 151 and 387 amino acids in length. 138 matched cddid_all.tbl CDD pfam14089 pfam14089 433709 KbaA KinB-signalling pathway activation in sporulation. This family of small proteins is found in the membrane and is necessary for kinase KinB signalling during sporulation. There is a conserved GFF sequence motif. The initiation of sporulation in Bacillus subtilis is dependent on the phosphorylation of the Spo0A transcription factor mediated by the phospho-relay and by two major kinases, KinA and KinB. 179 matched cddid_all.tbl CDD pfam14090 pfam14090 433710 HTH_39 Helix-turn-helix domain. This helix-turn-helix domain is often found in phage proteins and is likely to be DNA-binding. 70 matched cddid_all.tbl CDD pfam14091 pfam14091 404898 DUF4269 Domain of unknown function (DUF4269). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 176 and 187 amino acids in length. There is a conserved KTE sequence motif. 151 matched cddid_all.tbl CDD pfam14092 pfam14092 433711 DUF4270 Domain of unknown function (DUF4270). This family of lipoproteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 444 and 534 amino acids in length. 439 matched cddid_all.tbl CDD pfam14093 pfam14093 433712 DUF4271 Domain of unknown function (DUF4271). This family of integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 221 and 326 amino acids in length. 207 matched cddid_all.tbl CDD pfam14094 pfam14094 433713 DUF4272 Domain of unknown function (DUF4272). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 221 and 399 amino acids in length. 207 matched cddid_all.tbl CDD pfam14096 pfam14096 404902 DUF4274 Domain of unknown function (DUF4274). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 80 amino acids in length. 76 matched cddid_all.tbl CDD pfam14097 pfam14097 404903 SpoVAE Stage V sporulation protein AE1. Members of this family are all described as putative stage V sporulation protein AE, although this could not be confirmed. Proteins in this family are approximately 190 amino acids in length. 179 matched cddid_all.tbl CDD pfam14098 pfam14098 404904 SSPI Small, acid-soluble spore protein I. This family of proteins is putatively assigned as a small, acid-soluble spore protein 1. Proteins in this family are approximately 70 amino acids in length. There is a conserved LPGLGV sequence motif. 65 matched cddid_all.tbl CDD pfam14099 pfam14099 433714 Polysacc_lyase Polysaccharide lyase. This family includes heparin lyase I, EC:4.2.2.7. Heparin lyase I depolymerizes heparin by cleaving the glycosidic linkage next to an iduronic acid moiety. The structure of heparin lyase I consists of a beta-jelly roll domain with a long, deep substrate-binding groove and an unusual thumb domain containing many basic residues extending from the main body of the enzyme. This family also includes glucuronan lyase, EC:4.2.2.14. The structure glucuronan lyase is a beta-jelly roll. 212 matched cddid_all.tbl CDD pfam14100 pfam14100 433715 DUF6807 Family of unknown function (DUF6807). This family includes bacterial proteins of unknown function. 275 matched cddid_all.tbl CDD pfam14101 pfam14101 316612 DUF4275 Domain of unknown function (DUF4275). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. 139 matched cddid_all.tbl CDD pfam14102 pfam14102 464084 Caps_synth_CapC Capsule biosynthesis CapC. This family of proteins play a role in capsule biosynthesis. They are essential for gamma-polyglutamic acid (PGA) production. 119 matched cddid_all.tbl CDD pfam14103 pfam14103 433717 DUF4276 Domain of unknown function (DUF4276). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 190 and 224 amino acids in length. There is a single completely conserved residue E that may be functionally important. 187 matched cddid_all.tbl CDD pfam14104 pfam14104 433718 DUF4277 Domain of unknown function (DUF4277). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and archaea, and is approximately 110 amino acids in length. There is a conserved NGLGF sequence motif. 109 matched cddid_all.tbl CDD pfam14105 pfam14105 433719 DUF4278 Domain of unknown function (DUF4278). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 58 and 136 amino acids in length. There is a single completely conserved residue R that may be functionally important. 55 matched cddid_all.tbl CDD pfam14106 pfam14106 433720 DUF4279 Domain of unknown function (DUF4279). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 134 and 145 amino acids in length. 116 matched cddid_all.tbl CDD pfam14107 pfam14107 433721 DUF4280 Domain of unknown function (DUF4280). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 129 and 456 amino acids in length. There is a single completely conserved residue C that may be functionally important. 109 matched cddid_all.tbl CDD pfam14108 pfam14108 433722 ABA4-like ABA DEFICIENT 4-like. This family of proteins is found in bacteria and plants. It includes abscisic acid (ABA)-deficient 4 protein (ABA4) from Arabidopsis thaliana, which has a role in neoxanthin synthesis and may be important for the de novo ABA synthesis specifically during dehydration. 127 matched cddid_all.tbl CDD pfam14109 pfam14109 433723 GldH_lipo GldH lipoprotein. Members of this protein family are predicted lipoproteins, exclusive to the Bacteroidetes phylum. Proteins in this family are typically between 155 and 167 amino acids in length. Members include GldH, a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Not all Bacteroidetes with members of this protein family may have gliding motility. 129 matched cddid_all.tbl CDD pfam14110 pfam14110 464085 DUF4282 Domain of unknown function (DUF4282). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 93 and 155 amino acids in length. There is a single completely conserved residue E that may be functionally important. 86 matched cddid_all.tbl CDD pfam14111 pfam14111 464086 DUF4283 Domain of unknown function (DUF4283). This domain family is found in plants, and is approximately 100 amino acids in length. Considering the very diverse range of other domains it is associated with it is possible that this domain is a binding/guiding region. There are two highly conserved tryptophan residues. 145 matched cddid_all.tbl CDD pfam14112 pfam14112 433726 DUF4284 Immunity protein 22. A predicted immunity protein with an alpha+beta fold and conserved tryptophan,tyrosine and an acidic residues. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, which usually contains toxin domains of the ColD/E5, Tox-REase-4, Ntox49 or Ntox14 families. The domain is also found in heterogeneous polyimmunity loci. 117 matched cddid_all.tbl CDD pfam14113 pfam14113 433727 Tae4 Type VI secretion system (T6SS), amidase effector protein 4. Tae4 is a new form of toxin-antitoxin system protein for a type VI secretion system, T6SS. T6SS has roles in interspecies interactions, as well as higher order host-infection, by injecting effector proteins into the periplasmic compartment of the recipient cells of closely related species. Pseudomonas aeruginosa produces at least three effector proteins to other cells and thus has three specific cognate immunity proteins to protect itself. Tae4, or type VI amidase effector 4, in Enterobacter cloacae has a cognate Tai4 or type VI amidase immunity 4 protein. The immunity protein is Tai4, pfam16695. 115 matched cddid_all.tbl CDD pfam14114 pfam14114 464087 DUF4286 Domain of unknown function (DUF4286). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 100 and 112 amino acids in length. 100 matched cddid_all.tbl CDD pfam14115 pfam14115 316626 YuzL YuzL-like protein. The YuzL-like protein family includes the B. subtilis YuzL protein, which is functionally uncharacterized. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. 41 matched cddid_all.tbl CDD pfam14116 pfam14116 433729 YyzF YyzF-like protein. The YyzF-like protein family includes the B. subtilis YyzF protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. 48 matched cddid_all.tbl CDD pfam14117 pfam14117 433730 DUF4287 Domain of unknown function (DUF4287). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 70 and 180 amino acids in length. 60 matched cddid_all.tbl CDD pfam14118 pfam14118 290824 YfzA YfzA-like protein. The YfzA-like protein family includes the B. subtilis YfzA protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. 90 matched cddid_all.tbl CDD pfam14119 pfam14119 379479 DUF4288 Domain of unknown function (DUF4288). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. 84 matched cddid_all.tbl CDD pfam14120 pfam14120 433731 YhzD YhzD-like protein. The YhzD-like protein family includes the B. subtilis YhzD protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved GKL sequence motif. 61 matched cddid_all.tbl CDD pfam14121 pfam14121 433732 Porin_10 Putative porin. This family of membrane bet-barrel proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 655 and 722 amino acids in length. Swiss:Q2S343 is identified by Gene3D as a membrane bound beta-barrel. These sequences are putative porins. 602 matched cddid_all.tbl CDD pfam14122 pfam14122 316632 YokU YokU-like protein, putative antitoxin. The YokU-like protein family includes the B. subtilis YokU protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two conserved CXXC sequence motifs. This is likely to be a family of bacterial antitoxins, as the sequence bears remote homology to the RelE fold family. 87 matched cddid_all.tbl CDD pfam14123 pfam14123 433733 DUF4290 Domain of unknown function (DUF4290). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 200 and 221 amino acids in length. There are two conserved sequence motifs: EYGR and KLWD. 172 matched cddid_all.tbl CDD pfam14124 pfam14124 433734 DUF4291 Domain of unknown function (DUF4291). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 190 and 214 amino acids in length. There are two conserved sequence motifs: VYQAY and RMTW. 180 matched cddid_all.tbl CDD pfam14125 pfam14125 464088 DUF4292 Domain of unknown function (DUF4292). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 243 and 287 amino acids in length. 208 matched cddid_all.tbl CDD pfam14126 pfam14126 464089 DUF4293 Domain of unknown function (DUF4293). This family of integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 136 and 154 amino acids in length. 153 matched cddid_all.tbl CDD pfam14127 pfam14127 433737 DUF4294 Domain of unknown function (DUF4294). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 192 and 226 amino acids in length. 149 matched cddid_all.tbl CDD pfam14128 pfam14128 433738 DUF4295 Domain of unknown function (DUF4295). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. There are two completely conserved residues (K and Y) that may be functionally important. 47 matched cddid_all.tbl CDD pfam14129 pfam14129 433739 DUF4296 Domain of unknown function (DUF4296). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 90 amino acids in length. 87 matched cddid_all.tbl CDD pfam14130 pfam14130 433740 Cap4_nuclease Cap4 dsDNA endonuclease. This domain family corresponds to the N-terminal of CD-NTase associated protein 4 (Cap4) from bacteria and archaea. CD-NTase-associated protein 4 (Cap4) is a nucleotide second messenger sensor that functions is CBASS immunity. This is the effector domain which has dsDNA nuclease activity, sharing structural homology with type II restriction endonucleases and it has the putative active-site conserved residues required for divalent metal coordination. This domain is inactive as a monomer; after Cap4 signal recognition through its C-terminal SAVED domain, it oligomerises to closely locate two nuclease effector domains. This domain does not participates in ligand specificity and it has a promiscuous DNA cleavage response. 212 matched cddid_all.tbl CDD pfam14131 pfam14131 433741 DUF4298 Domain of unknown function (DUF4298). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 94 and 105 amino acids in length. There are two completely conserved residues (Y and D) that may be functionally important. 87 matched cddid_all.tbl CDD pfam14132 pfam14132 404932 DUF4299 Domain of unknown function (DUF4299). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 275 and 313 amino acids in length. There are two conserved sequence motifs: RGF and DAY. There are two completely conserved residues (P and D) that may be functionally important. 301 matched cddid_all.tbl CDD pfam14133 pfam14133 464090 DUF4300 Domain of unknown function (DUF4300). This family of lipoproteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 281 and 303 amino acids in length. There are two conserved sequence motifs: NCR and PYQ. 252 matched cddid_all.tbl CDD pfam14134 pfam14134 433742 DUF4301 Domain of unknown function (DUF4301). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 505 and 516 amino acids in length. 508 matched cddid_all.tbl CDD pfam14135 pfam14135 433743 DUF4302 Domain of unknown function (DUF4302). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 344 and 443 amino acids in length. There are two completely conserved residues (R and L) that may be functionally important. 232 matched cddid_all.tbl CDD pfam14136 pfam14136 404936 DUF4303 Domain of unknown function (DUF4303). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 169 and 192 amino acids in length. 153 matched cddid_all.tbl CDD pfam14137 pfam14137 433744 DUF4304 Domain of unknown function (DUF4304). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 154 and 223 amino acids in length. 66 matched cddid_all.tbl CDD pfam14138 pfam14138 464091 COX16 Cytochrome c oxidase assembly protein COX16. This family represents homologs of COX16 which has been shown to be involved in assembly of cytochrome oxidase. Protein in this family are typically between 106 and 134 amino acids in length. 79 matched cddid_all.tbl CDD pfam14139 pfam14139 404939 YpzG YpzG-like protein. The YpzG-like protein family includes the B. subtilis YpzG protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. There is a conserved QVNG sequence motif. 49 matched cddid_all.tbl CDD pfam14140 pfam14140 290845 YpzI YpzI-like protein. The YpzI-like protein family includes the B. subtilis YpzI protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. 42 matched cddid_all.tbl CDD pfam14141 pfam14141 433746 YqzM YqzM-like protein. The YqzM-like protein family includes the B. subtilis YqzM protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. 40 matched cddid_all.tbl CDD pfam14142 pfam14142 290847 YrzO YrzO-like protein. The YrzO-like protein family includes the B. subtilis YrzO protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. 46 matched cddid_all.tbl CDD pfam14143 pfam14143 372926 YrhC YrhC-like protein. The YrhC-like protein family includes the B. subtilis YrhC protein, which is functionally uncharacterized. YrhC is on the same operon as the MccA and MccB genes, which are involved in the conversion of methionine to cysteine. Expression of this operon is repressed in the presence of sulphate or cysteine. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 72 matched cddid_all.tbl CDD pfam14144 pfam14144 464092 DOG1 Seed dormancy control. This family of plant proteins appears to be a highly specific controller seed dormancy. 76 matched cddid_all.tbl CDD pfam14145 pfam14145 464093 YrhK YrhK-like protein. The YrhK-like protein family includes the B. subtilis YrhK protein, which is functionally uncharacterized. Its expression is under the control of the motility sigma factor sigma-D. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 60 amino acids in length. 57 matched cddid_all.tbl CDD pfam14146 pfam14146 433749 DUF4305 Domain of unknown function (DUF4305). This family includes the B. subtilis YdiK protein, which is functionally uncharacterized. This is not a homolog of E. coli YdiK, which belongs to pfam01594. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. 37 matched cddid_all.tbl CDD pfam14147 pfam14147 290852 Spore_YhaL Sporulation protein YhaL. This family of proteins is involved in sporulation. In B. subtilis its expression is regulated by the early mother-cell-specific transcription factor sigma-E. 52 matched cddid_all.tbl CDD pfam14148 pfam14148 290853 YhdB YhdB-like protein. The YhdB-like protein family includes the B. subtilis YhdB protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 57 and 82 amino acids in length. There are two conserved sequence motifs: LMVRT and FLHAY. 71 matched cddid_all.tbl CDD pfam14149 pfam14149 433750 YhfH YhfH-like protein. The YhfH-like protein family includes the B. subtilis YhfH protein, which is functionally uncharacterized. Its expression is repressed by the Spx paralogue MgsR, which regulates genes involved in stress response. This family of proteins is found in bacteria. Proteins in this family are typically between 42 and 53 amino acids in length. 37 matched cddid_all.tbl CDD pfam14150 pfam14150 372929 YesK YesK-like protein. The YesK-like protein family includes the B. subtilis YesK protein, which is functionally uncharacterized. Its expression is regulated by the sporulation-specific sigma factor sigma-E. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. 81 matched cddid_all.tbl CDD pfam14151 pfam14151 372930 YfhD YfhD-like protein. The YfhD-like protein family includes the B. subtilis YfhD protein, which is functionally uncharacterized. Its expression is regulated by the sporulation-specific sigma factor sigma-F. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. There is a single completely conserved residue E that may be functionally important. 59 matched cddid_all.tbl CDD pfam14152 pfam14152 372931 YfhE YfhE-like protein. The YfhE-like protein family includes the B. subtilis YfhE protein, which is functionally uncharacterized. Its expression may be regulated by the sigma factor sigma-B, which regulates the expression of stress-response proteins. This family of proteins is found in bacteria. Proteins in this family are approximately 40 amino acids in length. There is a conserved QEV sequence motif. 36 matched cddid_all.tbl CDD pfam14153 pfam14153 372932 Spore_coat_CotO Spore coat protein CotO. Bacillus spores are protected by a protein shell consisting of over 50 different polypeptides, known as the coat. This family of proteins has an important morphogenetic role in coat assembly, it is involved in the assembly of at least 5 different coat proteins including CotB, CotG, CotS, CotSA and CotW. It is likely to act at a late stage of coat assembly. 180 matched cddid_all.tbl CDD pfam14154 pfam14154 316659 DUF4306 Domain of unknown function (DUF4306). This family includes the B. subtilis YjdJ protein, which is functionally uncharacterized. This is not a homolog of E. coli YjdJ, which belongs to pfam00583. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 95 and 152 amino acids in length. 88 matched cddid_all.tbl CDD pfam14155 pfam14155 433751 DUF4307 Domain of unknown function (DUF4307). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 132 and 153 amino acids in length. There is a single completely conserved residue C that may be functionally important. 111 matched cddid_all.tbl CDD pfam14156 pfam14156 404944 AbbA_antirepres Antirepressor AbbA. This family inactivates the repressor AbrB, which represses genes switched on during the transition from the exponential to the stationary phase of growth. It binds to AbrB and prevents it from binding to DNA. 63 matched cddid_all.tbl CDD pfam14157 pfam14157 404945 YmzC YmzC-like protein. The YmzC-like protein family includes the B. subtilis YmzC protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 91 amino acids in length. There is a conserved ELR sequence motif. 58 matched cddid_all.tbl CDD pfam14158 pfam14158 404946 YndJ YndJ-like protein. The YndJ-like protein family includes the B. subtilis YndJ protein, which is functionally uncharacterized. This family is found in bacteria and archaea, and is typically between 222 and 269 amino acids in length. There are two completely conserved G residues that may be functionally important. 260 matched cddid_all.tbl CDD pfam14159 pfam14159 433752 CAAD CAAD domains of cyanobacterial aminoacyl-tRNA synthetase. This domain is present in aminoacyl-tRNA synthetases (aaRSs), enzymes that couple tRNAs to their cognate amino acids. aaRSs from cyanobacteria containing the CAAD (for cyanobacterial aminoacyl-tRNA synthetases appended domain) protein domains are localized in the thylakoid membrane. The domain bears two putative transmembrane helices and is present in glutamyl-, isoleucyl-, leucyl-, and valyl-tRNA synthetases, the latter of which has probably recruited the domain more than once during evolution. 85 matched cddid_all.tbl CDD pfam14160 pfam14160 464094 FAM110_C Centrosome-associated C terminus. This is the C-terminus of a family of proteins that colocalize with the centrosome/microtubule organization centre in interphase and at the spindle poles in mitosis. 113 matched cddid_all.tbl CDD pfam14161 pfam14161 464095 FAM110_N Centrosome-associated N terminus. This is the N-terminus of a family of proteins that colocalize with the centrosome/microtubule organization centre in interphase and at the spindle poles in mitosis. 107 matched cddid_all.tbl CDD pfam14162 pfam14162 464096 YozD YozD-like protein. The YozD-like protein family includes the B. subtilis YozD protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. 56 matched cddid_all.tbl CDD pfam14163 pfam14163 433755 SieB Super-infection exclusion protein B. This family includes superinfection exclusion proteins. These proteins prevent the growth of superinfecting phage which are insensitive to repression. It aborts lytic development of superinfecting phage. 147 matched cddid_all.tbl CDD pfam14164 pfam14164 372939 YqzH YqzH-like protein. The YqzH-like protein family includes the B. subtilis YqzH protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. 64 matched cddid_all.tbl CDD pfam14165 pfam14165 316669 YtzH YtzH-like protein. The YtzH-like protein family includes the B. subtilis YtzH protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There is a conserved DIL sequence motif. 86 matched cddid_all.tbl CDD pfam14166 pfam14166 372940 YueH YueH-like protein. The YueH-like protein family includes the B. subtilis YueH protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 79 matched cddid_all.tbl CDD pfam14167 pfam14167 372941 YfkD YfkD-like protein. The YfkD-like protein family includes the B. subtilis YfkD protein, which is functionally uncharacterized. Its expression is regulated by the sigma factor sigma-B, which regulates the expression of stress-response proteins, and by the forespore-specific sigma factor sigma-G. This family of proteins is found in bacteria. Proteins in this family are typically between 254 and 265 amino acids in length. 232 matched cddid_all.tbl CDD pfam14168 pfam14168 404951 YjzC YjzC-like protein. The YjzC-like protein family includes the B. subtilis YjzC protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. 55 matched cddid_all.tbl CDD pfam14169 pfam14169 372943 YdjO Cold-inducible protein YdjO. This family includes the B. subtilis YdjO protein, which is functionally uncharacterized. This is not a homolog of E. coli YdjO. B. subtilis YdjO is cold-inducible. Its expression is induced by the extracytoplasmic function sigma factor sigma-W. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. 59 matched cddid_all.tbl CDD pfam14171 pfam14171 404952 SpoIISA_toxin Toxin SpoIISA, type II toxin-antitoxin system. SpoIISA is a toxin which causes lysis of vegetatively growing cells. It forms part of a type II toxin-antitoxin system, where the SpoIISB protein, pfam14185, acts as an antitoxin. It is a transmembrane protein, with a cytoplasmic domain accounting for approximately two-thirds of the protein. The structure of the cytoplasmic domain resembles that of the GAF domains, Pfam: PF01590. SpoIISB binds to the cytoplasmic domain of SpoIISA with high affinity. 236 matched cddid_all.tbl CDD pfam14172 pfam14172 464097 DUF4309 Domain of unknown function (DUF4309). This family includes the B. subtilis YjgB protein, which is functionally uncharacterized. This is not a homolog of E. coli YjgB. Expression of B. subtilis YjgB is regulated by the alternative transcription factor sigma-B. This family is found in bacteria, and is approximately 140 amino acids in length. 130 matched cddid_all.tbl CDD pfam14173 pfam14173 372946 ComGG ComG operon protein 7. This family is required for DNA-binding during transformation of competent bacterial cells. 95 matched cddid_all.tbl CDD pfam14174 pfam14174 433756 YycC YycC-like protein. The YycC-like protein family includes the B. subtilis YycC protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. There is a conserved HIL sequence motif. 50 matched cddid_all.tbl CDD pfam14175 pfam14175 404954 YaaC YaaC-like Protein. The YaaC-like protein family includes the B. subtilis YaaC protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 320 and 333 amino acids in length. 313 matched cddid_all.tbl CDD pfam14176 pfam14176 404955 YxiJ YxiJ-like protein. The YxiJ-like protein family includes the B. subtilis YxiJ protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. 110 matched cddid_all.tbl CDD pfam14177 pfam14177 464098 YkyB YkyB-like protein. The YkyB-like protein family includes the B. subtilis YkyB protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 150 amino acids in length. There are two conserved sequence motifs: NRHAKTA and HLG. 116 matched cddid_all.tbl CDD pfam14178 pfam14178 290882 YppF YppF-like protein. The YppF-like protein family includes the B. subtilis YppF protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved LLDF sequence motif. 59 matched cddid_all.tbl CDD pfam14179 pfam14179 372950 YppG YppG-like protein. The YppG-like protein family includes the B. subtilis YppG protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 115 and 181 amino acids in length. There are two completely conserved residues (F and G) that may be functionally important. 101 matched cddid_all.tbl CDD pfam14181 pfam14181 404956 YqfQ YqfQ-like protein. The YqfQ-like protein family includes the B. subtilis YqfQ protein, also known as VrrA, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 237 amino acids in length. There are two conserved sequence motifs: QYGP and PKLY. 166 matched cddid_all.tbl CDD pfam14182 pfam14182 372951 YgaB YgaB-like protein. The YgaB-like protein family includes the B. subtilis YgaB protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. 76 matched cddid_all.tbl CDD pfam14183 pfam14183 433757 YwpF YwpF-like protein. The YwpF-like protein family includes the B. subtilis YwpF protein, which is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 167 amino acids in length. There is a conserved IIN sequence motif. 133 matched cddid_all.tbl CDD pfam14184 pfam14184 433758 YrvL Regulatory protein YrvL. YrvL prevents expression and activity of the YrvI sigma factor. It may function as an anti-sigma factor 121 matched cddid_all.tbl CDD pfam14185 pfam14185 290888 SpoIISB_antitox Antitoxin SpoIISB, type II toxin-antitoxin system. Members of this family act as antitoxins. They bind to the SpoIISA toxin, pfam14171. They are disordered proteins which adopt structure only when bound to SpoIISA. 55 matched cddid_all.tbl CDD pfam14186 pfam14186 464099 Aida_C2 Axin interactor dorsalization-associated protein, C-terminal. This is the C-terminal domain of the axin-interacting protein family, and is a distinct version of the C2 domain. This domain is critical for interactions with cytoskeletal in the context of cellular adhesion points, thus it is combined with diverse domains related to cytoskeletal functions. This domain has predominantly a beta-strand globular fold composed of an antiparallel beta-sandwich with two beta-sheets, and three short alpha-helices to stabilize the conformation. 140 matched cddid_all.tbl CDD pfam14187 pfam14187 404960 DUF4310 Domain of unknown function (DUF4310). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 214 and 231 amino acids in length. 208 matched cddid_all.tbl CDD pfam14188 pfam14188 433759 DUF4311 Domain of unknown function (DUF4311). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 260 amino acids in length. 212 matched cddid_all.tbl CDD pfam14189 pfam14189 433760 DUF4312 Domain of unknown function (DUF4312). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 99 and 118 amino acids in length. 84 matched cddid_all.tbl CDD pfam14190 pfam14190 404963 DUF4313 Domain of unknown function (DUF4313). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 136 and 171 amino acids in length. 103 matched cddid_all.tbl CDD pfam14191 pfam14191 433761 YodL YodL-like. The YodL-like protein family includes the B. subtilis YodL protein, which is functionally uncharacterized. This domain family is found in bacteria, and is approximately 100 amino acids in length. There are two completely conserved residues (Y and D) that may be functionally important. 100 matched cddid_all.tbl CDD pfam14192 pfam14192 433762 DUF4314 Domain of unknown function (DUF4314). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is typically between 56 and 93 amino acids in length. 69 matched cddid_all.tbl CDD pfam14193 pfam14193 433763 DUF4315 Domain of unknown function (DUF4315). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. 79 matched cddid_all.tbl CDD pfam14194 pfam14194 433764 Cys_rich_VLP Cysteine-rich VLP. This presumed domain is functionally uncharacterized. This domain family is found in bacteria and eukaryotes, and is approximately 60 amino acids in length. It contains 6 conserved cysteines and a conserved VLP sequence motif. 57 matched cddid_all.tbl CDD pfam14195 pfam14195 433765 DUF4316 Domain of unknown function (DUF4316). This domain is functionally uncharacterized. This domain is found in bacteria, and is typically between 56 and 95 amino acids in length. 44 matched cddid_all.tbl CDD pfam14196 pfam14196 464100 ATC_hydrolase L-2-amino-thiazoline-4-carboxylic acid hydrolase. This family of enzymes catalyzes the conversion of L-2-amino-delta2-thiazoline-4-carboxylic acid (L-ATC) to N-carbamoyl-L-cysteine. It cleaves the carbon-sulphur bond in the ring structure of L-ATC to produce N-carbamoyl-L-cysteine. 145 matched cddid_all.tbl CDD pfam14197 pfam14197 372959 Cep57_CLD_2 Centrosome localization domain of PPC89. The N-terminal region of the fission yeast spindle pole body protein PPC89 has low similarity to the human Cep57 protein. The CLD or centrosome localization domain of Cep57 and PPC89 is found at the N-terminus. This region localizes to the centrosome internally to gamma-tubulin, suggesting that it is either on both centrioles or on a centromatrix component. This N-terminal region can also multimerize with the N-terminus of other Cep57 molecules. The C-terminal part, Family Cep57_MT_bd, pfam06657, is the microtubule-binding region of Cep57 and PPC89. 67 matched cddid_all.tbl CDD pfam14198 pfam14198 433767 TnpV Transposon-encoded protein TnpV. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 114 and 125 amino acids in length. 112 matched cddid_all.tbl CDD pfam14199 pfam14199 464101 DUF4317 Domain of unknown function (DUF4317). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 225 and 451 amino acids in length. There is a single completely conserved residue P that may be functionally important. 370 matched cddid_all.tbl CDD pfam14200 pfam14200 464102 RicinB_lectin_2 Ricin-type beta-trefoil lectin domain-like. 89 matched cddid_all.tbl CDD pfam14201 pfam14201 404973 DUF4318 Domain of unknown function (DUF4318). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. There is a single completely conserved residue F that may be functionally important. 75 matched cddid_all.tbl CDD pfam14202 pfam14202 433770 TnpW Transposon-encoded protein TnpW. This family of proteins is found in bacteria. Proteins in this family are typically between 54 and 75 amino acids in length. There is a single completely conserved residue G that may be functionally important. 34 matched cddid_all.tbl CDD pfam14203 pfam14203 433771 TTRAP Putative transposon-transfer assisting protein. TTRAP is a family of small bacterial proteins largely from Clostrium difficile. From comparative and other structural studies of the PDB:2L7K, UniProtKB:Q18AW3, it has been suggested that this family is required for interacting with other proteins in order to facilitate the transfer of the transposon CTn4 between different bacterial species. PDB:2L7K comprises an alpha-helical fold of four alpha-helices leading to the production of two clefts, the larger of which displays two highly conserved residues in close proximity, Glu-8 and Lys-48. The gene concerned is part of an operon within transposon CTn4, and is expressed alongside a putative DNA primase, a DNA topoisomerase and conjugal transfer proteins. 62 matched cddid_all.tbl CDD pfam14204 pfam14204 464103 Ribosomal_L18_c Ribosomal L18 C-terminal region. This domain is the C-terminal end of ribosomal L18/L5 proteins. 55 matched cddid_all.tbl CDD pfam14205 pfam14205 404977 Cys_rich_KTR Cysteine-rich KTR. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 60 amino acids in length. There are 4 conserved cysteines and a conserved KTR sequence motif. 54 matched cddid_all.tbl CDD pfam14206 pfam14206 433773 Cys_rich_CPCC Cysteine-rich CPCC. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 68 and 104 amino acids in length. There are six conserved cysteines and a conserved CPCC sequence motif. 75 matched cddid_all.tbl CDD pfam14207 pfam14207 433774 DpnD-PcfM DpnD/PcfM-like protein. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 57 and 153 amino acids in length. There are two completely conserved residues (E and A) that may be functionally important. 46 matched cddid_all.tbl CDD pfam14208 pfam14208 404980 DUF4320 Domain of unknown function (DUF4320). This family of proteins is found in bacteria. Proteins in this family are typically between 120 and 131 amino acids in length. There are two completely conserved residues (G and Y) that may be functionally important. 117 matched cddid_all.tbl CDD pfam14209 pfam14209 464104 DUF4321 Domain of unknown function (DUF4321). This family of proteins is functionally uncharacterized. It is found in bacteria, and is approximately 50 amino acids in length. 48 matched cddid_all.tbl CDD pfam14210 pfam14210 290912 DUF4322 Domain of unknown function (DUF4322). This presumed domain is functionally uncharacterized. This domain family is found in archaea, and is approximately 60 amino acids in length. There is a conserved QTV sequence motif. 66 matched cddid_all.tbl CDD pfam14213 pfam14213 433776 DUF4325 STAS-like domain of unknown function (DUF4325). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 99 and 341 amino acids in length. This domain is distantly related to the STAS domain. 63 matched cddid_all.tbl CDD pfam14214 pfam14214 464105 Helitron_like_N Helitron helicase-like domain at N-terminus. This family is found in Helitrons, recently recognized eukaryotic transposons that are predicted to amplify by a rolling-circle mechanism. In many instances a protein-coding gene is disrupted by their insertion. 199 matched cddid_all.tbl CDD pfam14215 pfam14215 464106 bHLH-MYC_N bHLH-MYC and R2R3-MYB transcription factors N-terminal. This is the N-terminal region of a family of MYB and MYC transcription factors. The DNA-binding HLH domain is further downstream, pfam00010. Members of the MYB and MYC family regulate the biosynthesis of phenylpropanoids in several plant species (DOI:10.1007/s11295-009-0232-y). 121 matched cddid_all.tbl CDD pfam14216 pfam14216 433779 DUF4326 Domain of unknown function (DUF4326). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 100 and 162 amino acids in length. There are two completely conserved residues (P and C) that may be functionally important. 80 matched cddid_all.tbl CDD pfam14217 pfam14217 433780 DUF4327 Domain of unknown function (DUF4327). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 67 matched cddid_all.tbl CDD pfam14218 pfam14218 433781 COP23 Circadian oscillating protein COP23. This family includes the circadian oscillating protein COP23 from Cyanothece sp. (strain PCC 8801). The levels of this peripheral membrane protein display a circadian oscillation. 138 matched cddid_all.tbl CDD pfam14219 pfam14219 433782 DUF4328 Domain of unknown function (DUF4328). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 218 and 342 amino acids in length. 166 matched cddid_all.tbl CDD pfam14220 pfam14220 433783 DUF4329 Domain of unknown function (DUF4329). This domain is functionally uncharacterized. It is found in bacteria and eukaryotes, and is approximately 130 amino acids in length. It is often found in association with pfam05593 and pfam03527. There is a single completely conserved residue D and a highly conserved HTH motif which may be functionally important. 114 matched cddid_all.tbl CDD pfam14221 pfam14221 433784 DUF4330 Domain of unknown function (DUF4330). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 165 and 177 amino acids in length. There is a single completely conserved residue G that may be functionally important. 167 matched cddid_all.tbl CDD pfam14222 pfam14222 464107 MOR2-PAG1_N Cell morphogenesis N-terminal. This family is the conserved N-terminal region of proteins that are involved in cell morphogenesis. 554 matched cddid_all.tbl CDD pfam14223 pfam14223 464108 Retrotran_gag_2 gag-polypeptide of LTR copia-type. This family is found in Plants and fungi, and contains LTR-polyproteins, or retrotransposons of the copia-type. 130 matched cddid_all.tbl CDD pfam14224 pfam14224 433787 DUF4331 Domain of unknown function (DUF4331). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 223 and 526 amino acids in length. There is a conserved FPY sequence motif. 416 matched cddid_all.tbl CDD pfam14225 pfam14225 464109 MOR2-PAG1_C Cell morphogenesis C-terminal. This family is the conserved C-terminal region of proteins that are involved in cell morphogenesis. 252 matched cddid_all.tbl CDD pfam14226 pfam14226 464110 DIOX_N non-haem dioxygenase in morphine synthesis N-terminal. This is the highly conserved N-terminal region of proteins with 2-oxoglutarate/Fe(II)-dependent dioxygenase activity. 116 matched cddid_all.tbl CDD pfam14228 pfam14228 433790 MOR2-PAG1_mid Cell morphogenesis central region. This family is the conserved central region of proteins that are involved in cell morphogenesis. 1113 matched cddid_all.tbl CDD pfam14229 pfam14229 464111 DUF4332 Domain of unknown function (DUF4332). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 134 and 356 amino acids in length. This domain contains helix-hairpin-helix motifs. 122 matched cddid_all.tbl CDD pfam14230 pfam14230 433792 DUF4333 Domain of unknown function (DUF4333). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 140 and 255 amino acids in length. There are two completely conserved C residues that may be functionally important. 76 matched cddid_all.tbl CDD pfam14231 pfam14231 433793 GXWXG GXWXG protein. This domain is found in bacteria and eukaryotes, and is approximately 60 amino acids in length. There is a conserved GXWXG motif. This domain is frequently found at the N-terminus of pfam14232. 59 matched cddid_all.tbl CDD pfam14232 pfam14232 433794 DUF4334 Domain of unknown function (DUF4334). This domain family is found in bacteria and eukaryotes, and is approximately 60 amino acids in length. This domain is frequently found at the C-terminus of pfam14231. 58 matched cddid_all.tbl CDD pfam14233 pfam14233 433795 DUF4335 Domain of unknown function (DUF4335). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 204 and 480 amino acids in length. There are two completely conserved residues (G and D) that may be functionally important. 184 matched cddid_all.tbl CDD pfam14234 pfam14234 433796 DUF4336 Domain of unknown function (DUF4336). 321 matched cddid_all.tbl CDD pfam14235 pfam14235 433797 DUF4337 Domain of unknown function (DUF4337). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 187 and 201 amino acids in length. There is a single completely conserved residue Q that may be functionally important. 155 matched cddid_all.tbl CDD pfam14236 pfam14236 433798 DUF4338 Domain of unknown function (DUF4338). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 206 and 475 amino acids in length. 229 matched cddid_all.tbl CDD pfam14237 pfam14237 464112 GYF_2 GYF domain 2. This domain is found in bacteria, archaea and eukaryotes, and is approximately 50 amino acids in length. It contains an evolutionary conserved signature W-X-Y-X6-11-GPF-X4-M-X2-W-X3-GYF, the site of interaction with proline-rich peptides. Family members include RME-8 (Required for receptor-mediated endocytosis 8), a DNAJC13 protein. RME-8 was first identified as a protein that is required for endocytosis in Caenorhabditis elegans. It coordinates the activity of the WASH complex with the function of the retromer SNX dimer to control endosomal tubulation. Family members found in Arabidopsis include Arabidopsis trithorax-related3 (Atxr3), also known as set domain group 2 (Sdg2). It is the major enzyme responsible for H3K4me3 in Arabidopsis and SDG2-dependent H3K4m3 is critical for regulating gene expression and plant development. Another family member found in Arabidopsis is Tic56. It is an essential subunit of a 1-MDa protein complex at the inner chloroplast envelope membrane. Furthermore, Tic56 is important for rRNA processing and chloroplast ribosome assembly. 50 matched cddid_all.tbl CDD pfam14238 pfam14238 433800 DUF4340 Domain of unknown function (DUF4340). This domain is found in bacteria, and is typically between 183 and 196 amino acids in length. 183 matched cddid_all.tbl CDD pfam14239 pfam14239 433801 RRXRR RRXRR protein. This domain is found in bacteria, eukaryotes and viruses, and is approximately 180 amino acids in length. It contains a conserved RRXRR motif. It is often found in association with pfam01844. 173 matched cddid_all.tbl CDD pfam14240 pfam14240 433802 YHYH YHYH protein. This domain family is found in bacteria, eukaryotes and viruses, and is typically between 141 and 198 amino acids in length. There is a conserved YHYH sequence motif. 188 matched cddid_all.tbl CDD pfam14242 pfam14242 464113 DUF4342 Domain of unknown function (DUF4342). This family of proteins is found in bacteria. Proteins in this family are typically between 97 and 206 amino acids in length. There is a single completely conserved residue P that may be functionally important. 79 matched cddid_all.tbl CDD pfam14243 pfam14243 433804 R2K_3 ATP-grasp domain, R2K clade family 3. Family of ATP-grasp enzymes belonging to the R2K clade, wherein one of the absolutely-conserved lysine residues has migrated to the RAGYNA domain which is a part of the core ATP-grasp module. This family is predicted to catalyze peptide ligation reactions on protein substrates in biological conflict contexts, probably between bacteriophages and their hosts. 172 matched cddid_all.tbl CDD pfam14244 pfam14244 464114 Retrotran_gag_3 gag-polypeptide of LTR copia-type. This family is found in Plants and fungi, and contains pol polyprotein-like retroelements or retrotransposons of the copia-type. It is a short domain at the very start of these polypeptides. 48 matched cddid_all.tbl CDD pfam14245 pfam14245 433806 Pilin_PilA Type IV pilin PilA. This family consists of proteins which form type IV pili. In M. xanthus these pili are required for social motility. 136 matched cddid_all.tbl CDD pfam14246 pfam14246 433807 TetR_C_7 AefR-like transcriptional repressor, C-terminal domain. This family comprises the C-terminal domain of transcriptional regulators of the TetR family. It includes the AefR transcriptional regulator from P. syringae. It is found in association with pfam00440. 119 matched cddid_all.tbl CDD pfam14247 pfam14247 433808 DUF4344 Putative metallopeptidase. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 247 and 291 amino acids in length. There is a conserved EED sequence motif. This is a putative metallopeptidase. 214 matched cddid_all.tbl CDD pfam14248 pfam14248 433809 DUF4345 Domain of unknown function (DUF4345). This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 125 and 141 amino acids in length. There is a single completely conserved residue E that may be functionally important. 119 matched cddid_all.tbl CDD pfam14249 pfam14249 464115 Tocopherol_cycl Tocopherol cyclase. This family contains tocopherol cyclases. These enzymes are involved in the synthesis of tocopherols and tocotrienols (vitamin E). 335 matched cddid_all.tbl CDD pfam14250 pfam14250 405013 AbrB-like AbrB-like transcriptional regulator. This family of DNA-binding proteins is likely to act as a transcriptional regulator. This family does not include E.coli AbrB, which belongs to pfam05145. 67 matched cddid_all.tbl CDD pfam14251 pfam14251 405014 DUF4346 Domain of unknown function (DUF4346). This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 127 and 502 amino acids in length. There are two conserved sequence motifs: LDP and DHA. Many members of this family have been annotated as dihydropteroate synthases, however no experimental evidence can be found for this and Swiss:Q57571 has been shown not to possess dihydropteroate synthase activity. 118 matched cddid_all.tbl CDD pfam14252 pfam14252 433811 DUF4347 Domain of unknown function (DUF4347). This domain family is found in bacteria and eukaryotes, and is approximately 160 amino acids in length. There are two completely conserved residues (C and G) that may be functionally important. 164 matched cddid_all.tbl CDD pfam14253 pfam14253 433812 AbiH Bacteriophage abortive infection AbiH. This family of proteins confers resistance to bacteriophage. 248 matched cddid_all.tbl CDD pfam14254 pfam14254 405017 DUF4348 Domain of unknown function (DUF4348). Two structures have been solved form this DUF, PDB:4mjf and PDB:3sbu. TOPSAN records that both proteins are the only structural representatives of Pfam PF14254, DUF4348. There are no other significant hits in FFAS. DUF4348 has ~200 proteins, all from Bacteroidetes, and all with a single domain architecture with just one DUF4348 domain. There appears to be a possible gene duplication in the protein as the N-terminal domain (approx residues 25-174) and C-terminal domain (approx residues 175-286) superimpose quite well with ~1.9A r.m.s.d. and ~30% sequence identity. 230 matched cddid_all.tbl CDD pfam14255 pfam14255 464116 Cys_rich_CPXG Cysteine-rich CPXCG. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There are 5 conserved cysteines which occur in a CPXCG motif and a DCXXCCXP motif. 49 matched cddid_all.tbl CDD pfam14256 pfam14256 433814 YwiC YwiC-like protein. The YwiC-like protein family includes the B. subtilis YwiC protein, which is functionally uncharacterized. This domain family is found in bacteria, and is approximately 130 amino acids in length. There is a single completely conserved residue G that may be functionally important. 124 matched cddid_all.tbl CDD pfam14257 pfam14257 464117 DUF4349 Domain of unknown function (DUF4349). This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 282 and 353 amino acids in length. There is a single completely conserved residue D that may be functionally important. The N-terminus contains a lipoprotein signal peptide sequence. 213 matched cddid_all.tbl CDD pfam14258 pfam14258 464118 DUF4350 Domain of unknown function (DUF4350). This domain family is found in bacteria, archaea, and is approximately 170 to 200 amino acids in length. This domain is part of the glutaminase superfamily, suggesting it may have an enzymatic function. The domain is founded between two transmembrane helix domains giving it a membrane localization. 181 matched cddid_all.tbl CDD pfam14260 pfam14260 464119 zf-C4pol C4-type zinc-finger of DNA polymerase delta. In fission yeast this zinc-finger domain appears is the region of Pol3 that binds directly to the B-subunit, Cdc1. Pol delta is a hetero-tetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1. 68 matched cddid_all.tbl CDD pfam14261 pfam14261 433818 DUF4351 Domain of unknown function (DUF4351). This domain is found in bacteria, and is approximately 60 amino acids in length. 59 matched cddid_all.tbl CDD pfam14262 pfam14262 433819 Cthe_2159 Carbohydrate-binding domain-containing protein Cthe_2159. Cthe_2159 from Clostridium thermocellum is the first representative of a novel family of cellulose and/or acid-sugar binding beta-helix proteins that share structural similarities with polysaccharide lyases. 264 matched cddid_all.tbl CDD pfam14263 pfam14263 433820 DUF4354 Domain of unknown function (DUF4354). Several members of this family are annotated as being ATP/GTP-binding site motif A (P-loop) proteins, but this could not be confirmed. The one PDB:3NRF structure solved for this family exhibits an immunoglobin-like beta-sandwich fold. Crystal packing suggests that a tetramer is a significant oligomerization state, and a disulfide bridge is formed between Cys 125 at the C-terminal end of the monomer, and Cys 69. 125 matched cddid_all.tbl CDD pfam14264 pfam14264 433821 Glucos_trans_II Glucosyl transferase GtrII. This family includes glucosyl transferase II from the Shigella phage SfII, which mediates seroconversion of S. flexneri when the phage is integrated into the host chromosome. 306 matched cddid_all.tbl CDD pfam14265 pfam14265 405026 DUF4355 Domain of unknown function (DUF4355). This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 180 and 214 amino acids in length. 119 matched cddid_all.tbl CDD pfam14266 pfam14266 433822 YceG_bac Putative component of 'biosynthetic module'. YceG is a family of proteins found in bacteria. Proteins in this family are approximately 540 amino acids in length. YceG is an additional gene-product encoded in the Ter operon and might thus be part of a 'biosynthetic module' encoding certain enzymes. 480 matched cddid_all.tbl CDD pfam14267 pfam14267 433823 DUF4357 Domain of unknown function (DUF4357). This domain family is found in bacteria and archaea, and is approximately 60 amino acids in length. There are two completely conserved residues (G and W) that may be functionally important. 54 matched cddid_all.tbl CDD pfam14268 pfam14268 433824 YoaP YoaP-like. The YoaP-like domain is found at the C-terminus of the B. subtilis YoaP protein. It is found in bacteria and archaea, and is approximately 40 amino acids in length. The family is found in association with pfam00583. There is a single completely conserved residue A that may be functionally important. 44 matched cddid_all.tbl CDD pfam14269 pfam14269 372989 Arylsulfotran_2 Arylsulfotransferase (ASST). 301 matched cddid_all.tbl CDD pfam14270 pfam14270 433825 DUF4358 Domain of unknown function (DUF4358). This domain family is found in bacteria, and is approximately 110 amino acids in length. 97 matched cddid_all.tbl CDD pfam14271 pfam14271 433826 DUF4359 Domain of unknown function (DUF4359). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. There are two completely conserved residues (P and S) that may be functionally important. 103 matched cddid_all.tbl CDD pfam14272 pfam14272 405032 Gly_rich_SFCGS Glycine-rich SFCGS. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. There are a number of highly conserved motifs including an SFCGSGGAGA motif. 113 matched cddid_all.tbl CDD pfam14273 pfam14273 433827 DUF4360 Domain of unknown function (DUF4360). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 200 and 228 amino acids in length. There is a conserved GCP sequence motif near the N-terminus. 178 matched cddid_all.tbl CDD pfam14274 pfam14274 433828 DUF4361 Domain of unknown function (DUF4361). 142 matched cddid_all.tbl CDD pfam14275 pfam14275 464120 DUF4362 Domain of unknown function (DUF4362). This family of proteins is found in bacteria. Proteins in this family are typically between 93 and 146 amino acids in length. There is a conserved IRIV sequence motif. 91 matched cddid_all.tbl CDD pfam14276 pfam14276 464121 DUF4363 Domain of unknown function (DUF4363). This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. 107 matched cddid_all.tbl CDD pfam14277 pfam14277 464122 DUF4364 Domain of unknown function (DUF4364). This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 180 amino acids in length. 162 matched cddid_all.tbl CDD pfam14278 pfam14278 464123 TetR_C_8 Transcriptional regulator C-terminal region. This domain is a tetracycline repressor, domain 2, or C-terminus. 103 matched cddid_all.tbl CDD pfam14279 pfam14279 464124 HNH_5 HNH endonuclease. This domain is related to other HNH domain families such as pfam01844. Suggesting that these proteins have a nucleic acid cleaving function. 56 matched cddid_all.tbl CDD pfam14280 pfam14280 433834 DUF4365 Domain of unknown function (DUF4365). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 182 and 530 amino acids in length. There is a single completely conserved residue D that may be functionally important. 141 matched cddid_all.tbl CDD pfam14281 pfam14281 433835 PDDEXK_4 PD-(D/E)XK nuclease superfamily. Members of this family belong to the PD-(D/E)XK nuclease superfamily. 181 matched cddid_all.tbl CDD pfam14282 pfam14282 433836 FlxA FlxA-like protein. This family includes FlxA from E. coli. The expression of FlxA is regulated by the FliA sigma factor, a transcription factor specific for class 3 flagellar operons. However FlxA is not required for flagellar function or formation. 101 matched cddid_all.tbl CDD pfam14283 pfam14283 433837 DUF4366 Domain of unknown function (DUF4366). This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 227 and 387 amino acids in length. 158 matched cddid_all.tbl CDD pfam14284 pfam14284 464125 PcfJ PcfJ-like protein. The PcfJ-like protein family includes the E. faecalis PcfJ protein, which is functionally uncharacterized. It is found in bacteria and viruses, and is typically between 159 and 170 amino acids in length. There is a conserved HCV sequence motif. 147 matched cddid_all.tbl CDD pfam14285 pfam14285 433839 DUF4367 Domain of unknown function (DUF4367). This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 229 and 435 amino acids in length. 110 matched cddid_all.tbl CDD pfam14286 pfam14286 405044 DHHW DHHW protein. This family of proteins is found in bacteria. Proteins in this family are typically between 366 and 404 amino acids in length. There is a conserved DHHW motif. There is some distant homology to the Lipase_GDSL_2 family. 385 matched cddid_all.tbl CDD pfam14287 pfam14287 433840 DUF4368 Domain of unknown function (DUF4368). This domain family is found in bacteria, and is approximately 70 amino acids in length. The family is found in association with pfam00239 and pfam07508. There is a single completely conserved residue G that may be functionally important. 64 matched cddid_all.tbl CDD pfam14288 pfam14288 464126 FKS1_dom1 1,3-beta-glucan synthase subunit FKS1, domain-1. The FKS1_dom1 domain is likely to be the 'Class I' region just N-terminal to the first set of transmembrane helices that is involved in 1,3-beta-glucan synthesis itself. This family is found on proteins with family Glucan_synthase, pfam02364. 112 matched cddid_all.tbl CDD pfam14289 pfam14289 433842 DUF4369 Domain of unknown function (DUF4369). This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with pfam00578. LPAM signal peptide sequence is found in some family members. 92 matched cddid_all.tbl CDD pfam14290 pfam14290 372997 SDH5_plant Succinate dehydrogenase subunit 5, mitochondrial. Complex II [succinate dehydrogenase (succinate-ubiquinone oxidoreductase); SDH] is the only enzyme shared by both the electron transport chain and the tricarboxylic acid (TCA) cycle in mitochondria. In plants, this complex is considered unusual because it has accessory subunits (SDH5-SDH8), in addition to the catalytic subunits of SDH found in all eukaryotes (SDH1- SDH4). This family represents the accessory complex II subunit Succinate dehydrogenase subunit 5 mitochondrial, from plants. 237 matched cddid_all.tbl CDD pfam14291 pfam14291 405048 DUF4371 Domain of unknown function (DUF4371). 236 matched cddid_all.tbl CDD pfam14292 pfam14292 433843 SusE SusE outer membrane protein. This family includes the SusE outer membrane protein from Bacteroides thetaiotaomicron. This protein has a role in starch utilization, but is not essential for growth on starch. 106 matched cddid_all.tbl CDD pfam14293 pfam14293 464127 YWFCY YWFCY protein. This entry is found in bacteria, and is approximately 140 amino acids in length. It represents an integral membrane region found in many Type IV secretion protein. There is a conserved YWFCY motif. It is often found in association with pfam02534. 144 matched cddid_all.tbl CDD pfam14294 pfam14294 433845 DUF4372 Domain of unknown function (DUF4372). This domain family is found in bacteria, and is approximately 80 amino acids in length. The family is found in association with pfam01609. There is a single completely conserved residue G that may be functionally important. 74 matched cddid_all.tbl CDD pfam14295 pfam14295 433846 PAN_4 PAN domain. 51 matched cddid_all.tbl CDD pfam14296 pfam14296 433847 O-ag_pol_Wzy O-antigen polysaccharide polymerase Wzy. This family includes O-antigen polysaccharide polymerases. These enzymes link O-units via a glycosidic linkage to form a long O-antigen. These enzymes vary in specificity and sequence. 468 matched cddid_all.tbl CDD pfam14297 pfam14297 433848 DUF4373 Domain of unknown function (DUF4373). This domain is found in bacteria, eukaryotes and viruses, and is approximately 90 amino acids in length. 88 matched cddid_all.tbl CDD pfam14298 pfam14298 433849 DUF4374 Domain of unknown function (DUF4374). This family of proteins is found in bacteria. Proteins in this family are typically between 406 and 466 amino acids in length. 429 matched cddid_all.tbl CDD pfam14299 pfam14299 464128 PP2 Phloem protein 2. Phloem protein 2 (PP2) is one of the most abundant and enigmatic proteins in the phloem sap. PP2 is translocated in the assimilate stream where its lectin activity or RNA-binding properties can exert effects over long distances. 151 matched cddid_all.tbl CDD pfam14300 pfam14300 433851 DUF4375 Domain of unknown function (DUF4375). This family of proteins is found in bacteria. Proteins in this family are typically between 156 and 204 amino acids in length. There is a single completely conserved residue G that may be functionally important. 116 matched cddid_all.tbl CDD pfam14301 pfam14301 433852 DUF4376 Domain of unknown function (DUF4376). This domain family is found in bacteria and viruses, and is approximately 110 amino acids in length. 102 matched cddid_all.tbl CDD pfam14302 pfam14302 433853 DUF4377 Domain of unknown function (DUF4377). This domain family is found in bacteria and archaea, and is approximately 80 amino acids in length. 76 matched cddid_all.tbl CDD pfam14303 pfam14303 464129 NAM-associated No apical meristem-associated C-terminal domain. This domain is found in a number of different types of plant proteins including NAM-like proteins. 142 matched cddid_all.tbl CDD pfam14304 pfam14304 464130 CSTF_C Transcription termination and cleavage factor C-terminal. The C-terminal section of CSTF proteins is a discreet structure is crucial for mRNA 3'-end processing. This domain interacts with Pcf11 and possibly PC4, thus linking CstF2 to transcription, transcriptional termination, and cell growth. 41 matched cddid_all.tbl CDD pfam14305 pfam14305 291003 ATPgrasp_TupA TupA-like ATPgrasp. A member of the ATP-grasp fold predicted to be involved in the biosynthesis of cell surface polysaccharides such as the O-antigen in proteobacteria, the capsule in firmicutes and the polyglutamate chain of teichuronopeptide. 241 matched cddid_all.tbl CDD pfam14306 pfam14306 464131 PUA_2 PUA-like domain. This PUA like domain is found at the N-terminus of ATP-sulfurylase enzymes. 159 matched cddid_all.tbl CDD pfam14307 pfam14307 464132 Glyco_tran_WbsX Glycosyltransferase WbsX. Members of this family are found in within O-antigen biosynthesis clusters in Gram negative bacteria, where they are predicted to function as glycosyltransferases. 311 matched cddid_all.tbl CDD pfam14308 pfam14308 433858 DnaJ-X X-domain of DnaJ-containing. IN certain plant and yeast proteins, the DnaJ-1 proteins have a three-domain structure. The x-domain lies between the N-terminal DnaJ and the C-terminal Z domains. The exact function is not known. 205 matched cddid_all.tbl CDD pfam14309 pfam14309 464133 DUF4378 Domain of unknown function (DUF4378). 157 matched cddid_all.tbl CDD pfam14310 pfam14310 433860 Fn3-like Fibronectin type III-like domain. This domain has a fibronectin type III-like structure. It is often found in association with pfam00933 and pfam01915. Its function is unknown. 70 matched cddid_all.tbl CDD pfam14311 pfam14311 433861 DUF4379 Probable Zinc-ribbon domain. This domain is found in bacteria, eukaryotes and viruses, and is approximately 60 amino acids in length. It contains a CXXCXH motif and a CPXC motif. 54 matched cddid_all.tbl CDD pfam14312 pfam14312 316802 FG-GAP_2 FG-GAP repeat. 49 matched cddid_all.tbl CDD pfam14313 pfam14313 316803 Soyouz_module N-terminal region of Paramyxovirinae phosphoprotein (P). The soyouz module moiety is the N-terminal region of the phosphoprotein (P) from the subfamily Paramyxovirinae of the family Paramyxoviridae viruses. The main genera in this subfamily include the Rubulaviruses, avulaviruses, respiroviruses, henipaviruses, and morbilliviruses, all of which are enveloped viruses with a non-segmented, negative, single-stranded RNA genome encapsidated by the nucleoprotein (N) within a helical nucleocapsid. 58 matched cddid_all.tbl CDD pfam14314 pfam14314 316804 Methyltrans_Mon Virus-capping methyltransferase. This is the methyltransferase region of the Mononegavirales single-stranded RNA viral RNA polymerase enzymes. This region is involved in the mRNA-capping of the virion particles. 685 matched cddid_all.tbl CDD pfam14315 pfam14315 373010 DUF4380 Domain of unknown function (DUF4380). This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 288 and 372 amino acids in length. There are two completely conserved residues (G and E) that may be functionally important. 295 matched cddid_all.tbl CDD pfam14316 pfam14316 433862 DUF4381 Domain of unknown function (DUF4381). This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 158 and 180 amino acids in length. 145 matched cddid_all.tbl CDD pfam14317 pfam14317 433863 YcxB YcxB-like protein. The YcxB-like protein family includes the B. subtilis YcxB protein, which is a functionally uncharacterized transmembrane protein. This family of proteins is found in bacteria, and is approximately 60 amino acids in length. 61 matched cddid_all.tbl CDD pfam14318 pfam14318 405070 Mononeg_mRNAcap Mononegavirales mRNA-capping region V. This V domain of L RNA-polymerase carries a new motif, GxxTx(n)HR, that is essential for mRNA cap formation. Nonsegmented negative-sense (NNS) RNA viruses, Mononegavirales, cap their mRNA by an unconventional mechanism. Specifically, 5'-monophosphate mRNA is transferred to GDP derived from GTP through a reaction that involves a covalent intermediate between the large polymerase protein L and mRNA. The V region is essential for this process. 241 matched cddid_all.tbl CDD pfam14319 pfam14319 464134 Zn_Tnp_IS91 Transposase zinc-binding domain. This domain is likely to be a zinc-binding domain. It is found at the N-terminus of transposases belonging to the IS91 family. 90 matched cddid_all.tbl CDD pfam14320 pfam14320 291018 Paramyxo_PNT Phosphoprotein P region PNT disordered. The N-terminal half of the phosphoprotein P of the Paramyxovirinae viruses. The very first 60 residues have been built as the family Soyouz-module, pfam14313. The remaining part of the region, here, is disordered, and is liable to induced folding under the right physiological conditions. The region undergoes an unstructured-to-structured transition upon binding to Measles virus tail, C, unstructured region. 311 matched cddid_all.tbl CDD pfam14321 pfam14321 433865 DUF4382 Domain of unknown function (DUF4382). This family is found in bacteria and archaea, and is typically between 142 and 161 amino acids in length. 149 matched cddid_all.tbl CDD pfam14322 pfam14322 405073 SusD-like_3 Starch-binding associating with outer membrane. SusD is a secreted polysaccharide-binding protein with an N-terminal lipid moiety that allows it to associate with the outer membrane. SusD probably mediates xyloglucan-binding prior to xyloglucan transport in the periplasm for degradation. This domain is found N-terminal to pfam07980. 185 matched cddid_all.tbl CDD pfam14323 pfam14323 464135 GxGYxYP_C GxGYxYP putative glycoside hydrolase C-terminal domain. This family carries a characteriztic sequence motif, GxGYxYP, and is a putative glycoside hydrolase. This domain is found in association with pfam16216. Associated families are sugar-processing domains. 226 matched cddid_all.tbl CDD pfam14324 pfam14324 464136 PINIT PINIT domain. The PINIT domain is a protein domain that is found in PIAS proteins. The PINIT domain is about 180 amino acids in length. 137 matched cddid_all.tbl CDD pfam14325 pfam14325 433867 DUF4383 Domain of unknown function (DUF4383). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 137 and 164 amino acids in length. 125 matched cddid_all.tbl CDD pfam14326 pfam14326 433868 DUF4384 Domain of unknown function (DUF4384). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and archaea, and is approximately 80 amino acids in length. 81 matched cddid_all.tbl CDD pfam14327 pfam14327 433869 CSTF2_hinge Hinge domain of cleavage stimulation factor subunit 2. The hinge domain of cleavage stimulation factor subunit 2 proteins, CSTF2, is necessary for binding to the subunit CstF-77 within the polyadenylation complex and subsequent nuclear localization. This suggests that nuclear import of a pre-formed CSTF complex is an essential step in polyadenylation. Accurate and efficient polyadenylation is essential for transcriptional termination, nuclear export, translation, and stability of eukaryotic mRNAs. CSTF2 is an important regulatory subunit of the polyadenylation complex. 81 matched cddid_all.tbl CDD pfam14328 pfam14328 433870 DUF4385 Domain of unknown function (DUF4385). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 149 and 163 amino acids in length. 143 matched cddid_all.tbl CDD pfam14329 pfam14329 433871 DUF4386 Domain of unknown function (DUF4386). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 214 and 245 amino acids in length. 210 matched cddid_all.tbl CDD pfam14330 pfam14330 464137 DUF4387 Domain of unknown function (DUF4387). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are approximately 110 amino acids in length. There is a conserved RSKN sequence motif. 98 matched cddid_all.tbl CDD pfam14331 pfam14331 433873 IcmF-related_N IcmF-related N-terminal domain. This domain is found in bacterial IcmF (intracellular multiplication and human macrophage-killing) proteins. It is found to the N-terminus of the IcmF-related domain, pfam06761. 258 matched cddid_all.tbl CDD pfam14332 pfam14332 433874 DUF4388 Domain of unknown function (DUF4388). This domain family is found in bacteria, and is typically between 102 and 135 amino acids in length. 105 matched cddid_all.tbl CDD pfam14333 pfam14333 433875 DUF4389 Domain of unknown function (DUF4389). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 104 and 223 amino acids in length. There is a single completely conserved residue R that may be functionally important. 76 matched cddid_all.tbl CDD pfam14334 pfam14334 464138 DUF4390 Domain of unknown function (DUF4390). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 192 and 203 amino acids in length. 158 matched cddid_all.tbl CDD pfam14335 pfam14335 464139 DUF4391 Domain of unknown function (DUF4391). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 220 and 257 amino acids in length. 221 matched cddid_all.tbl CDD pfam14336 pfam14336 464140 DUF4392 Domain of unknown function (DUF4392). This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 282 and 585 amino acids in length. There are two completely conserved G residues that may be functionally important. 291 matched cddid_all.tbl CDD pfam14337 pfam14337 433879 Abi_alpha Abortive infection alpha. Enterococci such as Enterococcus faecalis and Enterococcus faecium are part of the normal human gut microbiota. However they can also be a source of nosocomial infections specially in immunocompromised patients. Virulent bacteriophages, i.e., viruses that infect and obligatorily lyse bacteria might provide alternative options for combating them. Yet, bacterial resistance to phage is taking place in similar fashion to antibiotic resistance. This might be, in part due to temperate phages that are stably associated with their host. They compete for their bacterial host, in addition to repressor-dependent immunity against similar phages, some phage express genes conferring resistance to infection by more or less unrelated phages. They can encode abortive infection (Abi) mechanisms that cause an interruption of invasive phage development and a premature death of the infected bacteria. For instance, E. faecalis V583 prophage 6 confers resistance to the virulent phage Idefix infection mainly due to Abia-alpha protein. This Pfam family corresponds to Abi-alpha protein sequences which is mostly found in prophages, arguing that it is essentially a temperate phage weapon to fight against other phages. 192 matched cddid_all.tbl CDD pfam14338 pfam14338 433880 Mrr_N Mrr N-terminal domain. This domain is found at the N-terminus of the Mrr restriction endonuclease catalytic domain, pfam04471. Fold recognition analysis predicts that it is a diverged member of the winged helix variant of helix turn helix proteins. It may play a role in DNA sequence recognition. 82 matched cddid_all.tbl CDD pfam14339 pfam14339 433881 DUF4394 Domain of unknown function (DUF4394). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 262 and 476 amino acids in length. 227 matched cddid_all.tbl CDD pfam14340 pfam14340 433882 DUF4395 Domain of unknown function (DUF4395). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 142 and 168 amino acids in length. There are two completely conserved C residues that may be functionally important. 130 matched cddid_all.tbl CDD pfam14341 pfam14341 464141 PilX_N PilX N-terminal. This domain is found at the N-terminus of the PilX prepilin-like proteins which are involved in type 4 fimbrial biogenesis. 51 matched cddid_all.tbl CDD pfam14342 pfam14342 433884 DUF4396 Domain of unknown function (DUF4396). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 167 and 310 amino acids in length. 141 matched cddid_all.tbl CDD pfam14343 pfam14343 464142 PrcB_C PrcB C-terminal. This domain is found at the C-terminus of Treponema denticola PrcB. PrcB interacts with the PrtP protease (dentilisin) and is required for the stability of the protease complex. 56 matched cddid_all.tbl CDD pfam14344 pfam14344 464143 DUF4397 Domain of unknown function (DUF4397). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 120 amino acids in length. 115 matched cddid_all.tbl CDD pfam14345 pfam14345 433887 GDYXXLXY GDYXXLXY protein. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 171 and 199 amino acids in length. It contains a conserved GDYXXLXY motif. 159 matched cddid_all.tbl CDD pfam14346 pfam14346 464144 DUF4398 Domain of unknown function (DUF4398). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 127 and 269 amino acids in length. 78 matched cddid_all.tbl CDD pfam14347 pfam14347 433889 DUF4399 Domain of unknown function (DUF4399). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 135 and 1079 amino acids in length. 91 matched cddid_all.tbl CDD pfam14348 pfam14348 433890 DUF4400 Domain of unknown function (DUF4400). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 209 and 249 amino acids in length. There is a single completely conserved residue P that may be functionally important. 204 matched cddid_all.tbl CDD pfam14349 pfam14349 433891 SprA_N Motility related/secretion protein. This domain is found repeated three times in the N-terminal half of the gliding motility-related SprA proteins. The role of this domain in motility is uncertain. It is also found in proteins required for secretion. 509 matched cddid_all.tbl CDD pfam14350 pfam14350 433892 Beta_protein Beta protein. This family includes the beta protein from Bacteriophage T4. Beta protein prevents the gop protein from killing the bacterial host cell. 343 matched cddid_all.tbl CDD pfam14351 pfam14351 433893 DUF4401 Domain of unknown function (DUF4401). This family of proteins is found in bacteria. Proteins in this family are typically between 357 and 735 amino acids in length. The family is found in association with pfam09925. There is a single completely conserved residue K that may be functionally important. 308 matched cddid_all.tbl CDD pfam14352 pfam14352 433894 DUF4402 Domain of unknown function (DUF4402). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 155 and 182 amino acids in length. 129 matched cddid_all.tbl CDD pfam14353 pfam14353 433895 CpXC CpXC protein. This presumed domain is functionally uncharacterized. This domain is found in bacteria and archaea, and is typically between 122 and 134 amino acids in length. It contains four conserved cysteines forming two CpXC motifs. 121 matched cddid_all.tbl CDD pfam14354 pfam14354 464145 Lar_restr_allev Restriction alleviation protein Lar. This family includes the restriction alleviation protein Lar encoded by the Rac prophage of Escherichia coli. This protein modulates the activity of the Escherichia coli restriction and modification system. 59 matched cddid_all.tbl CDD pfam14355 pfam14355 433897 Abi_C Abortive infection C-terminus. This domain is found at the C-terminus of the Lactococcus lactis abortive infection protein Abi-859. This protein confers bacteriophage resistance. 82 matched cddid_all.tbl CDD pfam14356 pfam14356 464146 DUF4403 Domain of unknown function (DUF4403). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 455 and 518 amino acids in length. There is a single completely conserved residue W that may be functionally important. 424 matched cddid_all.tbl CDD pfam14357 pfam14357 464147 DUF4404 Domain of unknown function (DUF4404). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There are two completely conserved residues (P and G) that may be functionally important. 83 matched cddid_all.tbl CDD pfam14358 pfam14358 464148 DUF4405 Domain of unknown function (DUF4405). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and archaea, and is approximately 50 amino acids in length. There are two conserved histidines that may be functionally important. This family is N-terminally truncated compared to other members of the clan. 66 matched cddid_all.tbl CDD pfam14359 pfam14359 464149 DUF4406 Domain of unknown function (DUF4406). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 98 and 145 amino acids in length. 91 matched cddid_all.tbl CDD pfam14360 pfam14360 464150 PAP2_C PAP2 superfamily C-terminal. This family is closely related to the C-terminal a region of PAP2. 74 matched cddid_all.tbl CDD pfam14361 pfam14361 433903 RsbRD_N RsbT co-antagonist protein rsbRD N-terminal domain. This domain is found at the N-terminus of a number of anti-sigma-factor antagonist proteins including B. subtilis RsbRD. These proteins are negative regulators of the general stress transcription factor sigma(B). It is found in association with pfam01740. 104 matched cddid_all.tbl CDD pfam14362 pfam14362 464151 DUF4407 Domain of unknown function (DUF4407). This family of proteins is found in bacteria. Proteins in this family are typically between 366 and 597 amino acids in length. There is a single completely conserved residue R that may be functionally important. 295 matched cddid_all.tbl CDD pfam14363 pfam14363 464152 AAA_assoc Domain associated at C-terminal with AAA. This domain is found in association with the AAA family, pfam00004. 95 matched cddid_all.tbl CDD pfam14364 pfam14364 405114 DUF4408 Domain of unknown function (DUF4408). This domain is found at the N-terminus of member of the DUF761 family pfam05553. Many members are plant proteins. 33 matched cddid_all.tbl CDD pfam14365 pfam14365 464153 Neprosin_AP Neprosin activation peptide. Pitcher plants are insectivorous and secrete a digestive fluid into the pitcher. This fluid contains a mixture of enzymes including peptidases. One of these is neprosin, characterized from the pitcher plant Nepenthes ventrata. This peptidase is of unknown catalytic type and is unaffected by standard peptidase inhibitors. Unusually, activity is directed towards prolyl bonds, but unlike most peptidase that cleave after proline, there is no restriction on sequence length or position of the proline residue. The peptidase is secreted and is presumed to possess an N-terminal activation peptide. This domain corresponds to the presumed activation peptide. 119 matched cddid_all.tbl CDD pfam14366 pfam14366 433907 DUF4410 Domain of unknown function (DUF4410). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 187 and 238 amino acids in length. 118 matched cddid_all.tbl CDD pfam14367 pfam14367 433908 DUF4411 Domain of unknown function (DUF4411). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 153 and 170 amino acids in length. There is a single completely conserved residue D that may be functionally important. 159 matched cddid_all.tbl CDD pfam14368 pfam14368 433909 LTP_2 Probable lipid transfer. The members of this family are probably involved in lipid transfer. The family has several highly conserved cysteines, paired in various ways. 100 matched cddid_all.tbl CDD pfam14369 pfam14369 433910 zinc_ribbon_9 zinc-ribbon. 35 matched cddid_all.tbl CDD pfam14370 pfam14370 464154 Topo_C_assoc C-terminal topoisomerase domain. This domain is found at the C-terminal of topoisomerase and other similar enzymes. 68 matched cddid_all.tbl CDD pfam14371 pfam14371 464155 DUF4412 Domain of unknown function (DUF4412). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, archaea and eukaryotes, and is typically between 75 and 104 amino acids in length. 191 matched cddid_all.tbl CDD pfam14372 pfam14372 433913 DUF4413 Domain of unknown function (DUF4413). This domain is part of an RNase-H fold section of longer proteins some of which are transposable elements possibly of the Pong type, since some members are putative Tam3 transposases. 100 matched cddid_all.tbl CDD pfam14373 pfam14373 464156 Imm_superinfect Superinfection immunity protein. This family includes the E. coli bacteriophage T4 superinfection immunity (imm) protein. When E. coli is sequentially infected with two T-even type bacteriophage the DNA of the superinfecting phage is excluded from the host, into the periplasmic space. The immunity protein plays a role in this process. 42 matched cddid_all.tbl CDD pfam14374 pfam14374 464157 Ribos_L4_asso_C 60S ribosomal protein L4 C-terminal domain. This family is found at the very C-terminal of 60 ribosomal L4 proteins. 74 matched cddid_all.tbl CDD pfam14375 pfam14375 433916 Cys_rich_CWC Cysteine-rich CWC. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 74 and 102 amino acids in length. It contains eight conserved cysteines, including a conserved CWC sequence motif. 49 matched cddid_all.tbl CDD pfam14376 pfam14376 464158 Haem_bd Haem-binding domain. This domain contains a potential haem-binding motif, CXXCH. This family is found in association with pfam00034 and pfam03150. 133 matched cddid_all.tbl CDD pfam14377 pfam14377 464159 UBM Ubiquitin binding region. This family contains repetitive element (RE) from a subgroup of HECT E3 ubiquitin ligases and the Y-family translesion polymerases, including human HUWE1 and Arabidopsis UPL1. Each of these repetitive elements are approximately 20 amino acids in length and contain two predicted helical segments separated by a Leu-Pro motif. The REs from the Y-family polymerases were shown to bind ubiquitin and were the basis for a novel ubiquitin-binding domain called the ubiquitin-binding motif (UBM). 34 matched cddid_all.tbl CDD pfam14378 pfam14378 433919 PAP2_3 PAP2 superfamily. 190 matched cddid_all.tbl CDD pfam14379 pfam14379 464160 Myb_CC_LHEQLE MYB-CC type transfactor, LHEQLE motif. This family is found towards the C-terminus of Myb-CC type transcription factors, and carries a highly conserved LHEQLE sequence motif. 47 matched cddid_all.tbl CDD pfam14380 pfam14380 464161 WAK_assoc Wall-associated receptor kinase C-terminal. This WAK_assoc domain is cysteine-rich and lies C-terminal to the binding domain, GUB_WAK_bind, pfam13947. 96 matched cddid_all.tbl CDD pfam14381 pfam14381 433922 EDR1 Ethylene-responsive protein kinase Le-CTR1. EDR1 regulates disease resistance and ethylene-induced senescence, and is also involved in stress response signalling and cell death regulation. 198 matched cddid_all.tbl CDD pfam14382 pfam14382 464162 ECR1_N Exosome complex exonuclease RRP4 N-terminal region. ECR1_N is an N-terminal region of the exosome complex exonuclease RRP proteins. It is a G-rich domain which structurally is a rudimentary single hybrid fold with a permuted topology. 38 matched cddid_all.tbl CDD pfam14383 pfam14383 405132 VARLMGL DUF761-associated sequence motif. This family is found frequently at the N-terminus of family DUF3741, pfam12552. 32 matched cddid_all.tbl CDD pfam14384 pfam14384 433924 BrnA_antitoxin BrnA antitoxin of type II toxin-antitoxin system. BrnA is family of antitoxins that neutralizes the toxin BrnT, pfam04365. It consists of 3 alpha-helices and a C-terminal ribbon-helix-helix DNA binding domain. As in other toxin-antitoxin systems, BrnA negatively autoregulates the brnTA operon and has higher affinity for the DNA operator when complexed with BrnT. It dimerizes with two molecules of its toxin BrnT. 67 matched cddid_all.tbl CDD pfam14385 pfam14385 433925 DUF4416 Domain of unknown function (DUF4416). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 176 and 187 amino acids in length. There is a conserved DPG sequence motif. 162 matched cddid_all.tbl CDD pfam14386 pfam14386 405135 DUF4417 Domain of unknown function (DUF4417). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 220 and 340 amino acids in length. There is a single completely conserved residue G that may be functionally important. 182 matched cddid_all.tbl CDD pfam14387 pfam14387 405136 DUF4418 Domain of unknown function (DUF4418). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 132 and 150 amino acids in length. 118 matched cddid_all.tbl CDD pfam14388 pfam14388 433926 DUF4419 Domain of unknown function (DUF4419). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 348 and 454 amino acids in length. 302 matched cddid_all.tbl CDD pfam14389 pfam14389 464163 Lzipper-MIP1 Leucine-zipper of ternary complex factor MIP1. This leucine-zipper is towards the N-terminus of MIP1 proteins. These proteins, here largely from plants, are subunits of the TORC2 (rictor-mTOR) protein complex controlling cell growth and proliferation. The leucine-zipper is likely to be the region that interacts with plant MADS-box factors, 82 matched cddid_all.tbl CDD pfam14390 pfam14390 433928 DUF4420 Putative PD-(D/E)XK family member, (DUF4420). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 310 and 334 amino acids in length. Advanced homology-detection methods supported with superfamily-wide domain architecture and horizontal gene transfer analyses have established this family to be a member of the PD-(D/E)XK superfamily. 311 matched cddid_all.tbl CDD pfam14391 pfam14391 433929 DUF4421 Domain of unknown function (DUF4421). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 336 and 370 amino acids in length. 298 matched cddid_all.tbl CDD pfam14392 pfam14392 433930 zf-CCHC_4 Zinc knuckle. The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. This particular family is found in plant proteins. 49 matched cddid_all.tbl CDD pfam14393 pfam14393 433931 DUF4422 Domain of unknown function (DUF4422). This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 255 and 371 amino acids in length. 219 matched cddid_all.tbl CDD pfam14394 pfam14394 405143 DUF4423 Domain of unknown function (DUF4423). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 170 amino acids in length. 168 matched cddid_all.tbl CDD pfam14395 pfam14395 373045 COOH-NH2_lig Phage phiEco32-like COOH.NH2 ligase-type 2. A family of COOH-NH2 ligases/GCS superfamily found in the neighborhood of YheC/D-like ATP-grasp and the CotE family of proteins in the firmicutes. Contextual analysis suggests that it might be involved in cell wall modification and spore coat biosynthesis. 253 matched cddid_all.tbl CDD pfam14396 pfam14396 464164 CFTR_R Cystic fibrosis TM conductance regulator (CFTR), regulator domain. 213 matched cddid_all.tbl CDD pfam14397 pfam14397 405145 ATPgrasp_ST Sugar-transfer associated ATP-grasp. A member of the ATP-grasp fold predicted to be involved in the biosynthesis of cell surface polysaccharides. 278 matched cddid_all.tbl CDD pfam14398 pfam14398 405146 ATPgrasp_YheCD YheC/D like ATP-grasp. A member of the ATP-grasp fold predicted to be involved in the modification/biosynthesis of spore-wall and capsular proteins. 256 matched cddid_all.tbl CDD pfam14399 pfam14399 433933 BtrH_N Butirosin biosynthesis protein H, N-terminal. BtrH_N is the N-terminus of the acyl carrier protein:aminoglycoside acyltransferase BtrH. Alternatively it can be referred to as butirosin biosynthesis protein H. BtrH transfers the unique (S)-4-amino-2-hydroxybutyrate (AHBA) side chain, which protects the antibiotic butirosin from several common resistance mechanisms. Butirosin, an aminoglycoside antibiotic produced by Bacillus circulans, exhibits improved antibiotic properties over its parent molecule and retains bactericidal activity toward many aminoglycoside-resistant strains. Butirosin is unique in carrying the AHBA side-chain. BtrH transfers the AHBA from the acyl carrier protein BtrI to the parent aminoglycoside ribostamycin as a gamma-glutamylated dipeptide. 134 matched cddid_all.tbl CDD pfam14400 pfam14400 433934 Transglut_i_TM Inactive transglutaminase fused to 7 transmembrane helices. A family of inactive transglutaminases fused to seven transmembrane helices. The transglutaminase domain is predicted to be extracellularly located. Members of this family are associated in gene neighbourhoods with a pepsin-like peptidase and an ATP-grasp of the RimK-family. The ATP-grasp is predicted to modify the 7TM protein or a cofactor that interacts with it. 161 matched cddid_all.tbl CDD pfam14401 pfam14401 433935 RLAN RimK-like ATPgrasp N-terminal domain. An uncharacterized alpha+beta fold domain that is mostly fused to a RimK-like ATP-grasp and is found in bacteria and euryarchaea. Members of this family are almost always associated in gene neighborhoods with a GNAT-like acetyltransferase fused to a papain-like petidase. Additionally M20-like peptidases, GCS2, 4Fe-4S Ferredoxins, a distinct metal-sulfur cluster protein and ribosomal proteins are found in the gene neighborhoods. Contextual analysis suggests a role for these in peptide biosynthesis. 150 matched cddid_all.tbl CDD pfam14402 pfam14402 433936 7TM_transglut 7 transmembrane helices usually fused to an inactive transglutaminase. A family of seven transmembrane helices fused to an inactive transglutaminase domain. The transglutaminase domain is predicted to be extracellularly located. Members of this family are associated in gene neighborhoods with a pepsin-like peptidase and an ATP-grasp of the RimK-family. The ATP-grasp is predicted to modify the 7TM protein or a cofactor that interacts with it. 248 matched cddid_all.tbl CDD pfam14403 pfam14403 464165 CP_ATPgrasp_2 Circularly permuted ATP-grasp type 2. Circularly permuted ATP-grasp prototyped by Roseiflexus RoseRS_2616 that is associated in gene neighborhoods with a GCS2-like COOH-NH2 ligase, alpha/beta hydrolase fold peptidase, GAT-II -like amidohydrolase, and M20 peptidase. Members of this family are predicted to be involved in the biosynthesis of small peptides. 378 matched cddid_all.tbl CDD pfam14404 pfam14404 405152 Strep_pep Ribosomally synthesized peptide in Streptomyces species. A ribosomally synthesized peptide related to microviridin and marinostatin, usually in the gene neighborhood of one or more RimK-like ATP-grasp. The gene-context suggests that it is further modified by the ATP-grasp. The peptide is predicted to function in a defensive or developmental role, or as an antibiotic. 63 matched cddid_all.tbl CDD pfam14406 pfam14406 405153 Bacteroid_pep Ribosomally synthesized peptide in Bacteroidetes. Ribosomally synthesized peptide that is usually in the gene neighborhood of a RimK-like ATP-grasp, and an ABC ATPase fused to a papain-like domain. It is often present in multiple tandem gene copies. The gene contexts suggest that it is modified by the ATP-grasp as in the biosynthesis of microviridin and marinostatin. They might function in defense or development or as peptide antibiotics. 52 matched cddid_all.tbl CDD pfam14407 pfam14407 373050 Frankia_peptide Ribosomally synthesized peptide prototyped by Frankia Franean1_4349. Ribosomally synthesized peptide linked to cyclases in chloroflexi. It may have a link to cyclic nucleotide signaling. 62 matched cddid_all.tbl CDD pfam14408 pfam14408 433938 Actino_peptide Ribosomally synthesized peptide in actinomycetes. Ribosomally synthesized peptide that is usually in the gene neighbourhood of a RimK-like ATP-grasp and an aspartyl-O-methylase. Gene contexts suggest that it is further modified by the ATP-grasp and the methylase. It might function in defence or development, or as a peptide antibiotic. 58 matched cddid_all.tbl CDD pfam14409 pfam14409 291106 Herpeto_peptide Ribosomally synthesized peptide in Herpetosiphon. Ribosomally synthesized peptide that is usually in the gene neighbourhood of a RimK-like ATP-grasp, and an ABC ATPase fused to a papain-like domain. It is often present in multiple tandem gene copies. Gene contexts suggest that it is modified by the ATP=grasp. It might function in defence or development, or as a peptide antibiotic. 56 matched cddid_all.tbl CDD pfam14410 pfam14410 433939 GH-E HNH/ENDO VII superfamily nuclease with conserved GHE residues. A predicted nuclease of the HNH/EndoVII superfamily of the treble clef fold which is closely related to the NucA-like family. The name is derived from the conserved G, H and E residues. It is found in several bacterial polymorphic toxin systems. Some GH-E members preserve the conserved cysteines of the treble-clef suggesting that they might represent potential evolutionary intermediates from a classical HNH domain to the derived NucA-like form. 72 matched cddid_all.tbl CDD pfam14411 pfam14411 433940 LHH A nuclease of the HNH/ENDO VII superfamily with conserved LHH. LHH is a predicted nuclease of the HNH/ENDO VII superfamily of the treble clef fold. The name is derived from the conserved motif, LHH. It is found in bacterial polymorphic toxin systems and functions as a toxin module. Like WHH and AHH, LHH nuclease contain 4 conserved histidines of which, the first one is predicted to bind metal-ion and other three ones are involved in activation of water molecule for hydrolysis. 76 matched cddid_all.tbl CDD pfam14412 pfam14412 464166 AHH A nuclease family of the HNH/ENDO VII superfamily with conserved AHH. AHH is a predicted nuclease of the HNH/ENDO VII superfamily of the treble clef fold. The name is derived from the conserved motif, AHH. It is found in bacterial polymorphic toxin systems and functions as a toxin module. Like WHH and LHH, the AHH nuclease contains 4 conserved histidines of which, the first one is predicted to bind a metal-ion and the other three ones are involved in activation of a water molecule for hydrolysis. 112 matched cddid_all.tbl CDD pfam14413 pfam14413 464167 Thg1C Thg1 C terminal domain. Thg1 polymerases contain an additional region of conservation C-terminal to the core palm domain that comprise of 5 helices and two strands. This region has several well-conserved charged residues including a basic residue found towards the end of the first helix of this unit might contribute to the Thg1-specific active site. This C-terminal module of Thg1 is predicted to form a helical bundle that functions equivalently to the fingers of the other nucleic acid polymerases, probably in interacting with the template HtRNA. 116 matched cddid_all.tbl CDD pfam14414 pfam14414 433943 WHH A nuclease of the HNH/ENDO VII superfamily with conserved WHH. WHH is a predicted nuclease of the HNH/ENDO VII superfamily of the treble clef fold. The name is derived from the conserved motif WHH. It is found in bacterial polymorphic toxin systems and functions as a toxin module. WHH is the shortest version of HNH nuclease families. Like AHH and LHH, the WHH nuclease contains 4 conserved histidines of which the first one is predicted to bind a metal-ion and other three ones are involved in activation of water molecule for hydrolysis. 43 matched cddid_all.tbl CDD pfam14415 pfam14415 433944 DUF4424 Domain of unknown function (DUF4424). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 310 and 361 amino acids in length. 300 matched cddid_all.tbl CDD pfam14416 pfam14416 464168 PMR5N PMR5 N terminal Domain. The plant family with PMR5, ESK1, TBL3 etc have a N-terminal C rich predicted sugar binding domain followed by the PC-Esterase (acyl esterase) domain. 54 matched cddid_all.tbl CDD pfam14417 pfam14417 433946 MEDS MEDS: MEthanogen/methylotroph, DcmR Sensory domain. MEDS is prototyped by DcmR and is likely to function with the PocR domain in certain organizms in sensing hydrocarbon derivatives. The MEDS domain occurs fused to Histidine Kinase and as stand-alone version. Sequence analysis shows that it is a catalytically inactive version of the P-loop NTPase domain of the RecA superfamily. 160 matched cddid_all.tbl CDD pfam14418 pfam14418 405163 OHA OST-HTH Associated domain. OHA occurs with OST-HTH. 74 matched cddid_all.tbl CDD pfam14419 pfam14419 405164 SPOUT_MTase_2 AF2226-like SPOUT RNA Methylase fused to THUMP. SPOUT superfamily RNA methylase fused to RNA binding THUMP domain. 173 matched cddid_all.tbl CDD pfam14420 pfam14420 464169 Clr5 Clr5 domain. This domain is found at the N-terminus of the Clr5 protein which has been shown to be involved in silencing in fission yeast. This domain has been found to often be associated with proteins that contain ankyrin repeats and large regions of disordered sequence. 54 matched cddid_all.tbl CDD pfam14421 pfam14421 405166 LmjF365940-deam A distinct subfamily of CDD/CDA-like deaminases. A distinct branch of the CDD/CDA-like deaminases prototyped by Leishmania LmjF36.5940. Members of this family are widely distributed across several microbial eukaryotes such as kinetoplastids, chlorophyte algae, stramenopiles and the alveolate Perkinsus. Domain architectures suggest that these proteins might possess mRNA editing or DNA mutagenizing activity. 197 matched cddid_all.tbl CDD pfam14423 pfam14423 405167 Imm5 Immunity protein Imm5. A predicted Immunity protein, with an all-alpha fold, present in bacterial polymorphic toxin systems as an immediate neighbor of the toxin. 186 matched cddid_all.tbl CDD pfam14424 pfam14424 464170 Toxin-deaminase The BURPS668_1122 family of deaminases. A member of the nucleic acid/nucleotide deaminase superfamily prototyped by Burkholderia BURPS668_1122. Members of this family are found as toxins in polymorphic toxin systems in a wide range of bacteria and in the eukaryote Perkinsus. Members of this family typically possess a DxE catalytic motif in Helix-2 of the core fold instead of the more common C[H]xE motif. The Perkinsus versions are predicted to be inactive. 142 matched cddid_all.tbl CDD pfam14425 pfam14425 373060 Imm3 Immunity protein Imm3. A predicted Immunity protein, with a mostly all-alpha fold, present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene. 119 matched cddid_all.tbl CDD pfam14426 pfam14426 339223 Imm2 Immunity protein Imm2. A predicted Immunity protein, with a mostly all-alpha fold, present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene. 60 matched cddid_all.tbl CDD pfam14427 pfam14427 373061 Pput2613-deam Pput_2613-like deaminase. A member of the nucleic acid/nucleotide deaminase superfamily prototyped by Pseudomonas Pput_2613. Members of this family are predicted to function as toxins in bacterial polymorphic toxin systems. 118 matched cddid_all.tbl CDD pfam14428 pfam14428 433948 DddA-like Double-stranded DNA deaminase toxin A. Members of this family are predicted to function as toxins in bacterial polymorphic toxin systems, including DddA from Burkholderia cenocepacia. DddA is part of the cellular contact- dependent growth inhibition (CDI) system that allows bacteria to communicate with and inhibit the growth of closely related neighbouring bacteria in a contact-dependent fashion. Its deaminase domain has double-stranded DNA cytidine deaminase activity and can be used for CRISPR-free mitochondrial base editing. 136 matched cddid_all.tbl CDD pfam14429 pfam14429 464171 DOCK-C2 C2 domain in Dock180 and Zizimin proteins. The Dock180/Dock1 and Zizimin proteins are atypical GTP/GDP exchange factors for the small GTPases Rac and Cdc42 and are implicated cell-migration and phagocytosis. Across all Dock180 proteins, two regions are conserved: C-terminus termed CZH2 or DHR2 (or the Dedicator of cytokinesis) whereas CZH1/DHR1 contain a new family of the C2 domain. 185 matched cddid_all.tbl CDD pfam14430 pfam14430 405170 Imm1 Immunity protein Imm1. A predicted immunity protein, with an alpha+beta fold and a conserved C-terminal tryptophan residue. The protein is present in a wide range of bacteria in polymorphic toxin systems as an immediate gene neighbour of the toxin gene. 125 matched cddid_all.tbl CDD pfam14431 pfam14431 373065 YwqJ-deaminase YwqJ-like deaminase. A member of the nucleic acid/nucleotide deaminase superfamily prototyped by Bacillus YwqJ. Members of this family are present in a wide phyletic range of bacteria and a few basidiomycetes. Bacterial versions are predicted to function as toxins in bacterial polymorphic toxin systems. 134 matched cddid_all.tbl CDD pfam14432 pfam14432 464172 DYW_deaminase DYW family of nucleic acid deaminases. This is the DYW domain found in nucleic acid deaminases prototyped by the plant PPR DYW proteins that are implicated in chloroplast and mitochondrial RNA transcript maturation by numerous C to U editing events. The name derives from the DYW motif present at the C-terminus of the classical plant PPR DYW deaminases. Members containing this domain are present in bacteria, plants, Naegleria, and fungi. Plants and Naegleria show lineage-specific expansions of this family. This domain contains a characteriztic zinc-binding motif (CXXC, HXE) which has been shown to bind zinc ions. This domain is often fused to PPR repeats. Ascomycete versions, which are independent lateral transfers, contain a large insert within the domain and are often fused to ankyrin repeats. Bacterial versions are predicted to function as toxins in polymorphic toxin systems. 93 matched cddid_all.tbl CDD pfam14433 pfam14433 405171 SUKH-3 SUKH-3 immunity protein. This family belongs to the SUKH superfamily and functions as immunity proteins in bacterial toxin systems. 140 matched cddid_all.tbl CDD pfam14434 pfam14434 433950 Imm6 Immunity protein Imm6. A predicted immunity protein, with an alpha+beta fold (mostly alpha helices). The protein is present in polymorphic toxin systems as an immediate gene neighbor of the toxin gene. 121 matched cddid_all.tbl CDD pfam14435 pfam14435 433951 SUKH-4 SUKH-4 immunity protein. This family belongs to the SUKH superfamily and functions as immunity proteins in bacterial toxin systems. 140 matched cddid_all.tbl CDD pfam14436 pfam14436 433952 EndoU_bacteria Bacterial EndoU nuclease. This is a bacterial virion of EndoU nuclease. It is found at C-terminal region of polymorphic toxin proteins. 131 matched cddid_all.tbl CDD pfam14437 pfam14437 433953 MafB19-deam MafB19-like deaminase. A member of the nucleic acid/nucleotide deaminase superfamily prototyped by Neisseria MafB19. Members of this family are present in a wide phyletic range of bacteria and are predicted to function as toxins in bacterial polymorphic toxin systems. 144 matched cddid_all.tbl CDD pfam14438 pfam14438 464173 SM-ATX Ataxin 2 SM domain. This SM domain is found in Ataxin-2. 78 matched cddid_all.tbl CDD pfam14439 pfam14439 405177 Bd3614-deam Bd3614-like deaminase. A member of the nucleic acid/nucleotide deaminase superfamily prototyped by Bdellovibrio Bd3614. They are typified by a distinct N-terminal globular domain. The Bdellovibrio version occurs in a predicted operon with a 23S rRNA G2445-modifying methylase suggesting that it might be involved in RNA editing. 113 matched cddid_all.tbl CDD pfam14440 pfam14440 405178 XOO_2897-deam Xanthomonas XOO_2897-like deaminase. A member of the nucleic acid/nucleotide deaminase superfamily prototyped by Xanthomonas XOO_2897. Members of this family are present in a wide phyletic range of bacteria and are predicted to function as toxins in bacterial polymorphic toxin systems. The Xanthomonas XOO_2897 lack an immunity protein and is predicted to be deployed against its eukaryotic host. 101 matched cddid_all.tbl CDD pfam14441 pfam14441 464174 OTT_1508_deam OTT_1508-like deaminase. A member of the nucleic acid/nucleotide deaminase superfamily prototyped by Orientia OTT_1508. Members of this family are present in a wide phyletic range of bacteria,including several intracellular parasites and eukaryotes such as fungi, Leishmania, Selaginella, and some apicomplexa. In bacteria, these deaminases are predicted to function as toxins in bacterial polymorphic toxin systems. Versions in intracellular bacteria lack immunity proteins and are likely to be deployed against their eukaryotic hosts. Eukaryotic versions are predicted to function as nucleic acid (either DNA or RNA) deaminases. Among eukaryotes, some fungi show lineage-specific expansions of this family. Many fungal versions are fused to a distinct N-terminal globular domain. Various fungal versions are fused to domains involved in chromatin function. Apicomplexan versions are fused to tRNA guanine transglycosylase domain. 66 matched cddid_all.tbl CDD pfam14442 pfam14442 405180 Bd3614_N Bd3614-like deaminase N-terminal. This is a globular domain that occurs N-terminal to the Bd3614-like deaminases, which are predicted to be involved in RNA editing. 92 matched cddid_all.tbl CDD pfam14443 pfam14443 464175 DBC1 DBC1. DBC1 and it homologs from diverse eukaryotes are a catalytically inactive version of the Nudix hydrolase (MutT) domain. DBC1 is predicted to bind NAD metabolites and regulate the activity of SIRT1 or related deacetylases by sensing the soluble products or substrates of the NAD-dependent deacetylation reaction. 123 matched cddid_all.tbl CDD pfam14444 pfam14444 464176 S1-like S1-like. S1-like RNA binding domain found in DBC1 58 matched cddid_all.tbl CDD pfam14445 pfam14445 379611 Prok-RING_2 Prokaryotic RING finger family 2. RING finger family found sporadically in bacteria and archaea, and associated with other components of the ubiquitin-based signaling and degradation system, including ubiquitin and the E1 and E2 proteins. The bacterial versions contain transmembrane helices. 56 matched cddid_all.tbl CDD pfam14446 pfam14446 433958 Prok-RING_1 Prokaryotic RING finger family 1. RING finger family found sporadically in bacteria and archaea, and associated in gene neighborhoods with other components of the ubiquitin-based signaling and degradation system, including ubiquitin, the E1 and E2 proteins and the JAB-like metallopeptidase. The bacterial versions contain transmembrane helices. 52 matched cddid_all.tbl CDD pfam14447 pfam14447 433959 Prok-RING_4 Prokaryotic RING finger family 4. RING finger family domain found sporadically in bacteria. The finger is fused to an N-terminal alpha-helical domain, ROT/Trove-like repeats and a C-terminal TerD domain. The architecture suggests a possible role in an RNA-processing complex. 46 matched cddid_all.tbl CDD pfam14448 pfam14448 373075 Nuc_N Nuclease N terminal. This is a conserved short region that is found in many bacterial polymorphic toxin proteins. It is often located before C-terminal nuclease domains. 58 matched cddid_all.tbl CDD pfam14449 pfam14449 433960 PT-TG Pre-toxin TG. PT-TG is a conserved region found in many bacterial toxin proteins. It could function as a linker that links N-terminal secretion-related domain and C-terminal toxin domain. It contains a TG motif. 68 matched cddid_all.tbl CDD pfam14450 pfam14450 464177 FtsA Cell division protein FtsA. FtsA is essential for bacterial cell division, and co-localizes to the septal ring with FtsZ. It has been suggested that the interaction of FtsA-FtsZ has arisen through coevolution in different bacterial strains. The FtsA protein contains two structurally related actin-like ATPase domains which are also structurally related to the ATPase domains of HSP70 (see PF00012). FtsA has a SHS2 domain PF02491 inserted in to the RnaseH fold PF02491. 167 matched cddid_all.tbl CDD pfam14451 pfam14451 433962 Ub-Mut7C Mut7-C ubiquitin. This member of the ubiquitin superfamily is found at the N-terminus of Mut7-C like RNAses, suggestive of an RNA-binding role. 81 matched cddid_all.tbl CDD pfam14452 pfam14452 433963 Multi_ubiq Multiubiquitin. A ubiquitin superfamily domain that is often present in multiple tandem copies in the same polypeptide. Members of this family are associated in gene neighborhoods, or on occasions fused to, bacterial homologs of components of ubiquitin-dependent modification system such as the E1, E2 and JAB metallopeptidase enzymes and a distinct metal-binding domain. The E2/UBC fold domain appears to be inactive. The JAB domain in these operons is usually fused to the E1 domain. 69 matched cddid_all.tbl CDD pfam14453 pfam14453 464178 ThiS-like ThiS-like ubiquitin. A member of the ubiquitin superfamily that is often fused to the ThiF-like (E1)- ubiquitin activating enzyme and is present in gene neighborhoods with components of the thiamine biosynthesis pathway. 57 matched cddid_all.tbl CDD pfam14454 pfam14454 433964 Prok_Ub Prokaryotic Ubiquitin. A Ubiquitin-superfamily protein that is present across several bacterial lineages, and found in gene neighborhoods with components of the ubiquitin modification system such as the E1, E2 and JAB proteins, and a novel alpha-helical protein, which is predicted to be enzymatic. 63 matched cddid_all.tbl CDD pfam14455 pfam14455 433965 Metal_CEHH Predicted metal binding domain. A predicted metal-binding domain that is found in gene-neighborhood associations with genes encoding components of the bacterial homologs of the ubiquitin modification pathway including the E1, E2, JAB metallopeptidase and ubiquitin proteins. The domain is characterized by a conserved motif with a CxxxxxEYHxxxxH signature. 176 matched cddid_all.tbl CDD pfam14456 pfam14456 433966 alpha-hel2 Alpha-helical domain 2. An alpha-helical domain found in gene neighborhoods encoding genes containing bacterial homologs of components of the ubiquitin modification pathway such as the E1, E2, Ub and JAB peptidase proteins. 303 matched cddid_all.tbl CDD pfam14457 pfam14457 433967 Prok-E2_A Prokaryotic E2 family A. A member of the E2/UBC superfamily of proteins found in several bacteria. The active site residues are very similar to the eukaryotic E2 proteins. Members of this family are usually fused to E1 and JAB domains C-terminal to the E2 domain. The protein is usually in the gene neighborhood of a gene encoding a distinct metallobetalactamase family protein. 163 matched cddid_all.tbl CDD pfam14459 pfam14459 433968 Prok-E2_C Prokaryotic E2 family C. A divergent member of the E2/UBC superfamily of proteins found in bacteria. Members of the family contain a conserved cysteine in place of the histidine of the classical E2/UBC proteins. Members of this family are usually fused to an E1 domain at their C-terminus. The protein is usually in the gene neighborhood of a gene encoding a JAB peptidase and another encoding a predicted metal binding domain. 129 matched cddid_all.tbl CDD pfam14460 pfam14460 433969 Prok-E2_D Prokaryotic E2 family D. A member of the E2/UBC superfamily of proteins found in several bacteria. Members of this family lack the conserved histidine of the classical E2-fold. However, they have an absolutely conserved histidine carboxyl-terminal to the conserved cysteine. Members of this family are usually present in a conserved gene neighborhood with genes encoding members of the Ub modification pathway such as the E1, Ub and JAB proteins. These neighborhoods also contain a gene encoding a rapidly diverging alpha-helical protein. 169 matched cddid_all.tbl CDD pfam14461 pfam14461 433970 Prok-E2_B Prokaryotic E2 family B. A member of the E2/UBC superfamily of proteins found in several bacteria. The active site residues are similar to the eukaryotic E2 proteins but lack the conserved asparagine. Members of this family are usually fused to an E1 domain at the C-terminus. The protein is usually in the gene neighborhood of a gene encoding a member of the pol-beta nucleotidyltransferase superfamily. Many of the operons in this family are in ICE-like mobile elements and plasmids. 134 matched cddid_all.tbl CDD pfam14462 pfam14462 433971 Prok-E2_E Prokaryotic E2 family E. A member of the E2/UBC superfamily of proteins found in diverse bacteria. Analysis of the active site residues suggest that members of this family are inactive as they lack the characteriztic catalytic residues of the E2 enzymes. They are usually fused to or in the neighborhood of a multi/poly ubiquitin domain protein. Other proteins of the ubiquitin modification pathway such as the E1 and JAB proteins are also found in its gene neighborhood along with a distinct predicted metal-binding protein. 119 matched cddid_all.tbl CDD pfam14463 pfam14463 405196 E1-N E1 N-terminal domain. An uncharacterized alpha/beta domain fused to E1 proteins. This protein is usually present in gene neighbourhoods with genes encoding a JAB protein and a predicted metal-binding protein. In related E1 proteins, the E1-N domain is replaced by an E2/UBC superfamily domain. 151 matched cddid_all.tbl CDD pfam14464 pfam14464 464179 Prok-JAB Prokaryotic homologs of the JAB domain. These are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based signaling and protein turnover pathways in eukaryotes. Prokaryotic JAB domains are predicted to have a similar role in their cognates of the ubiquitin modification pathway. The domain is widely found in bacteria, archaea and phages where they are present in several gene contexts in addition to those that correspond to the prokaryotic cognates of the eukaryotic Ub pathway. Other contexts in which JAB domains are present include gene neighbor associations with ubiquitin fold domains in cysteine and siderophore biosynthesis, and phage tail morphogenesis, where they are shown or predicted to process the associated ubiquitin. A distinct family, the RadC-like JAB domains are widespread in bacteria and are predicted to function as nucleases. In halophilic archaea the JAB domain shows strong gene-neighborhood associations with a nucleotidyltransferase suggesting a role in nucleotide metabolism. 113 matched cddid_all.tbl CDD pfam14465 pfam14465 433973 NFRKB_winged NFRKB Winged Helix-like. This domain covers regions 370-495 of human nuclear factor related to kappaB binding (NFRKB) protein. 103 matched cddid_all.tbl CDD pfam14466 pfam14466 405199 PLCC PLAT/LH2 and C2-like Ca2+-binding lipoprotein. A small family of bacterial proteins, found in several Bacteroides species. Structure determination (NMR and Xray) shows an immunoglobulin beta-barrel fold. Multiple homologs have been found in human gut metagenomics data sets. Structural experimentation shows it to share features with two well-established protein architectures in the SCOP database, ie, C2 (calcium/lipid-binding domain) of the Pfam PF00168 and PLAT/LH2 (lipase/lipooxigenase domain) of the Pfam PF01477. The C2 and PLAT/LH2 domains bind Ca2+ in their functions of targeting proteins to cell-membranes; this domain is also shown to bind Ca2+ as well as to be a novel fold. 128 matched cddid_all.tbl CDD pfam14467 pfam14467 433974 DUF4426 Domain of unknown function (DUF4426). Members of this entry are found mostly in g-proteobacteria, especially in Vibrio. Strangely enough, there seems to be one eukaryotic homolog in Nematostella vectensis (NEMVEDRAFT_v1g226006), where the PA0388-like domain is fused with a domain homogous to the Methionine biosynthesis protein MetW (see below). In several Pseudomonas species, but also in Vibrio vulnificus and Azotobacter vinelandii PA0388 homologs are genomic neighbors of Nucleoside 5-triphosphatase RdgB (dHAPTP, dITP, XTP-specific) (EC 3.6.1.15) and Methionine biosynthesis protein MetW. On the other hand, in most Vibrio species it appears as a part of a conserved operon involved in possible response to stress. 120 matched cddid_all.tbl CDD pfam14468 pfam14468 291157 DUF4427 Protein of unknown function (DUF4427). This domain is often found at the C-terminal of proteins with pfam10899 domain, for instance in STY1911 protein from a multiple drug resistant Salmonella enterica serovar Typhi CT18. 132 matched cddid_all.tbl CDD pfam14469 pfam14469 464180 AKAP28 28 kDa A-kinase anchor. 28 kDa AKAP (AKAP28) is highly enriched in human airway axonemes. The mRNA for AKAP28 is up-regulated as primary airway cells differentiate and is specifically expressed in tissues containing cilia and/or flagella. Homologs of AKAP28 are present in all animals and in some, including mice the AKAP28-like domain are preceded by another uncharacterized domain 121 matched cddid_all.tbl CDD pfam14470 pfam14470 464181 bPH_3 Bacterial PH domain. Proteins in this family are distantly related to PH domains. 94 matched cddid_all.tbl CDD pfam14471 pfam14471 464182 DUF4428 Domain of unknown function (DUF4428). This putative zinc finger domain is found in uncharacterized bacterial proteins. 51 matched cddid_all.tbl CDD pfam14472 pfam14472 405204 DUF4429 Domain of unknown function (DUF4429). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, archaea and viruses, and is approximately 90 amino acids in length. This domain is often found in two tandem copies. 95 matched cddid_all.tbl CDD pfam14473 pfam14473 464183 RD3 RD3 protein. RD3 is a human protein that is found preferentially expressed in the retina. Mutations in RD3 causes Leber Congenital Amaurosis type 12. 129 matched cddid_all.tbl CDD pfam14474 pfam14474 464184 RTC4 "RTC4-like domain. This presumed domain is found in the RTC4 protein from yeasts. In Saccharomyces cerevisiae, Cdc13 binds telomeric DNA to recruit telomerase and to ""cap"" chromosome ends. RTC4 was identified in a screen to identify novel proteins and pathways that cap telomeres, or that respond to uncapped telomeres. This domain is also found in proteins that contain a DNA-binding myb domain." 121 matched cddid_all.tbl CDD pfam14475 pfam14475 433978 Mso1_Sec1_bdg Sec1-binding region of Mso1. Mso1p is a component of the secretory vesicle docking complex whose function is closely associated with that of Sec1p. It is a small hydrophilic protein that is enriched in the microsomal membrane fraction, and this binding domain is towards the N-terminus of Mso1. The yeast Sec1p protein functions in the docking of secretory transport vesicles to the plasma membrane. Mso1p and Sec1p interact at sites of exocytosis and the Mso1p-Sec1p interaction site depends on a functional Rab GTPase Sec4p and its GEF Sec2p. The C-terminal region of Mso1 (not built) assists in targetting Sec1 to the sites of polarised membrane transport. 40 matched cddid_all.tbl CDD pfam14476 pfam14476 405208 Chloroplast_duf Petal formation-expressed. The members of this plant family from Arabidopsis thaliana appear to be proteins found in the chloroplast, expressed in the pollen tube during the petal differentiation and expansion stage. The function is not known. 319 matched cddid_all.tbl CDD pfam14477 pfam14477 316951 Mso1_C Membrane-polarising domain of Mso1. Mso1p is a component of the secretory vesicle docking complex whose function is closely associated with that of Sec1p. It is a small hydrophilic protein that is enriched in the microsomal membrane fraction. The yeast Sec1p protein functions in the docking of secretory transport vesicles to the plasma membrane. Mso1p and Sec1p interact at sites of exocytosis and the Mso1p-Sec1p interaction site depends on a functional Rab GTPase Sec4p and its GEF Sec2p. This C-terminal region of Mso1 assists in targeting Sec1 to the sites of polarised membrane transport, the SNARES and Sec4. 54 matched cddid_all.tbl CDD pfam14478 pfam14478 433979 DUF4430 Domain of unknown function (DUF4430). Although this family has overlaps with SLBB, the majority of its sequences are unique. Several family members, eg UniProtKB:A0RGA8, that do not overlap have an LPXTG-cell wall anchor at their C-terminus, a SSF_Family 10_polysaccharide_lyase or Glycosyltransferase structure associated with them in the middle region, as shown by InterPro, as well as this domain at the N-terminus. 72 matched cddid_all.tbl CDD pfam14479 pfam14479 433980 HeLo Prion-inhibition and propagation. This N-terminal region, HeLo, has a prion-inhibitory effect in cis on its own prion-forming domain (PFD) and in trans on HET-s prion propagation. The domain is found exclusively in the fungal kingdom. Its structure, as it occurs in the HET-s/HET-S proteins, consists of two bundles of alpha-helices that pack into a single globular domain. The domain boundary determined from its structure and from protease-resistance experiments overlaps with the C-terminal prion-forming domain of HET-s (PF11558. The HeLo domains of HET-s and HET-S are very similar and their few differences (and not the prion-forming domains) determine the compatibility-phenotype of the fungi in which the proteins are expressed. The mechanism of the HeLo domain-function in heterokaryon-incompatibility is still under investigation, however the HeLo domain is found in similar protein architectures as other cell death and apoptosis-inducing domains. The only other HeLo protein to which a function has been associated is LopB from L. maculans. Although its specific role in L. maculans is unknown, LopB- mutants have impaired ability to form lesions on oilseed rape. The HeLo domain is not related to the HET domain (PF06985) which is another domain involved in heterokaryon incompatibility. 166 matched cddid_all.tbl CDD pfam14480 pfam14480 433981 DNA_pol3_a_NI DNA polymerase III polC-type N-terminus I. This is the first N-terminal domain, NI domain, of the DNA polymerase III polC subunit A that is found only in Firmicutes. DNA polymerase polC-type III enzyme functions as the 'replicase' in low G + C Gram-positive bacteria. Purine asymmetry is a characteriztic of organizms with a heterodimeric DNA polymerase III alpha-subunit constituted by polC which probably plays a direct role in the maintenance of strand-biased gene distribution; since, among prokaryotic genomes, the distribution of genes on the leading and lagging strands of the replication fork is known to be biased. It has been predicted that the N-terminus of polC folds into two globular domains, NI and NII. A predicted patch of elecrostatic potential at the surface of this domain suggests a possible involvement in nucleic acid binding. This domain is associated with DNA_pol3_alpha pfam07733 and DNA_pol3_a_NI pfam11490. 72 matched cddid_all.tbl CDD pfam14481 pfam14481 373090 Fimbrial_PilY2 Type 4 fimbrial biogenesis protein PilY2. Members of this family were experimentally shown to be involved in fimbrial biogenesis, but its exact role appears to be unknown. 105 matched cddid_all.tbl CDD pfam14484 pfam14484 464185 FISNA Fish-specific NACHT associated domain. This domain is frequently found associated with the NACHT domain (pfam05729) in fish and other vertebrates. 72 matched cddid_all.tbl CDD pfam14485 pfam14485 373092 DUF4431 Domain of unknown function (DUF4431). 48 matched cddid_all.tbl CDD pfam14486 pfam14486 433983 DUF4432 Domain of unknown function (DUF4432). 302 matched cddid_all.tbl CDD pfam14487 pfam14487 433984 DarT ssDNA thymidine ADP-ribosyltransferase, DarT. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 201 and 230 amino acids in length. There is a single completely conserved residue E that may be functionally important. This family is distantly similar to pfam01885. Studies in search for novel ADP-ribosylation systems in bacterial genomes have identified an operon that encodes a conserved protein containing a distinct type of macrodomain associated with this family. This led to the identification of a toxin-antitoxin (TA) system, with DarT acting as the toxin. It is an enzyme that specifically modifies thymidines on single-stranded DNA in a sequence-specific manner by a nucleotide-type modification called ADP-ribosylation. This modification in turn can be removed by DarG, the antitoxin macrodomain protein. In addition, it was illustrated that substitution of the single completely conserved glutamate residue resulted in attenuation of function where DarT was non-toxic. 201 matched cddid_all.tbl CDD pfam14488 pfam14488 433985 DUF4434 Domain of unknown function (DUF4434). 169 matched cddid_all.tbl CDD pfam14489 pfam14489 464186 QueF QueF-like protein. This protein is involved in the biosynthesis of queuosine. In some proteins this domain appears to be fused to pfam06508. 81 matched cddid_all.tbl CDD pfam14490 pfam14490 464187 HHH_4 Helix-hairpin-helix containing domain. This presumed domain contains at least one helix-hairpin-helix motif. This domain is often found in RecD helicases. 91 matched cddid_all.tbl CDD pfam14491 pfam14491 433988 DUF4435 Protein of unknown function (DUF4435). This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 285 and 362 amino acids in length. This domain is sometimes associated with AAA domains. 233 matched cddid_all.tbl CDD pfam14492 pfam14492 464188 EFG_III Elongation Factor G, domain III. This domain is found in Elongation Factor G. It shares a similar structure with domain V (pfam00679). Structural studies in drosophila indicate this is domain 3. 75 matched cddid_all.tbl CDD pfam14493 pfam14493 464189 HTH_40 Helix-turn-helix domain. This presumed domain is found at the C-terminus of a large number of helicase proteins. 89 matched cddid_all.tbl CDD pfam14494 pfam14494 433990 DUF4436 Domain of unknown function (DUF4436). This is a family of membrane and transmembrane proteins from mycobacterial and related species. The function is not known. 255 matched cddid_all.tbl CDD pfam14495 pfam14495 433991 Cytochrom_C550 Cytochrome c-550 domain. This domain is a heme binding cytochrome known as cytochrome c550, or cytochrome c549, or PsbV. 136 matched cddid_all.tbl CDD pfam14496 pfam14496 433992 NEL C-terminal novel E3 ligase, LRR-interacting. This NEL or novel E3 ligase domain is found at the C-terminus of bacterial virulence factors. Its sequence is different from those of the eukaryotic HECT and RING-finger E3 ligases, and it subverts the host ubiquitination process. At the N-terminus of the family-members there is a series of LRR repeats, and the NEL domain interacts with the most N-terminal repeat. The key residue for the ligation step is the cysteine, eg found at position 386 in UniProtKB:E7K2H2. The LRR section sequesters this active site until invasion has occurred. 216 matched cddid_all.tbl CDD pfam14497 pfam14497 464190 GST_C_3 Glutathione S-transferase, C-terminal domain. This domain is closely related to pfam00043. 104 matched cddid_all.tbl CDD pfam14498 pfam14498 405224 Glyco_hyd_65N_2 Glycosyl hydrolase family 65, N-terminal domain. This domain represents a domain found to the N-terminus of the glycosyl hydrolase 65 family catalytic domain. 233 matched cddid_all.tbl CDD pfam14499 pfam14499 433994 DUF4437 Domain of unknown function (DUF4437). This family of proteins is found in bacteria. Proteins in this family are typically between 152 and 283 amino acids in length. 250 matched cddid_all.tbl CDD pfam14500 pfam14500 433995 MMS19_N Dos2-interacting transcription regulator of RNA-Pol-II. This domain, along with the C-terminal part, pfam12460, is an essential component of a silencing complex in fission yeast that contains Dos2, Rik1, Mms19 and Cdc20 (the catalytic subunit of DNA polymerase-epsilon). This complex regulates RNA polymerase II (RNA Pol II) activity in heterochromatin and is required for DNA replication and heterochromatin assembly. 258 matched cddid_all.tbl CDD pfam14501 pfam14501 433996 HATPase_c_5 GHKL domain. This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90. 102 matched cddid_all.tbl CDD pfam14502 pfam14502 433997 HTH_41 Helix-turn-helix domain. 48 matched cddid_all.tbl CDD pfam14503 pfam14503 433998 YhfZ_C YhfZ C-terminal domain. This domain is often found in association with the helix-turn-helix domain HTH_41 (pfam14502). It includes YhfZ proteins from Escherichia coli and Shigella flexneri. 236 matched cddid_all.tbl CDD pfam14504 pfam14504 433999 CAP_assoc_N CAP-associated N-terminal. The function of this domain is unknown, but it is found towards the N-terminus of bacterial proteins carrying the CAP domain, pfam00188. All members that do not otherwise carry an additional Cu_amine_oxidN1, pfam07833, domain are likely to be extracellular as they start with a signal-peptide. Most other non-bacterial proteins with the CAP domain are allergenic. 140 matched cddid_all.tbl CDD pfam14505 pfam14505 464191 DUF4438 Domain of unknown function (DUF4438). 256 matched cddid_all.tbl CDD pfam14506 pfam14506 434001 CppA_N CppA N-terminal. This is the N-terminal domain of the CppA protein found in species of Streptococcus. CppA is a putative C3-glycoprotein degrading proteinase, involved in pathogenicity. It is often found associated with pfam14507. 123 matched cddid_all.tbl CDD pfam14507 pfam14507 434002 CppA_C CppA C-terminal. This is the C-terminal domain of the CppA protein found in species of Streptococcus. CppA is a putative C3-glycoprotein degrading proteinase, involved in pathogenicity. It is often found associated with pfam14506. 102 matched cddid_all.tbl CDD pfam14508 pfam14508 464192 GH97_N Glycosyl-hydrolase 97 N-terminal. This N-terminal domain of glycosyl-hydrolase-97 contributes part of the active site pocket. It is also important for contact with the catalytic and C-terminal domains of the whole. 234 matched cddid_all.tbl CDD pfam14509 pfam14509 464193 GH97_C Glycosyl-hydrolase 97 C-terminal, oligomerization. Glycosyl-hydrolase-97 is made up of three tightly linked and highly conserved globular domains. The C-terminal domain is found to be necessary for oligomerization of the whole molecule in order to create the active-site pocket and the Ca++-binding site. 97 matched cddid_all.tbl CDD pfam14510 pfam14510 464194 ABC_trans_N ABC-transporter N-terminal. This domain is found at the N-terminus of ABC-transporter proteins from fungi, plants to higher eukaryotes. It is predicted to be an intracellular domain. 80 matched cddid_all.tbl CDD pfam14511 pfam14511 464195 RE_EcoO109I Type II restriction endonuclease EcoO109I. This is a family of Type II restriction endonucleases. 191 matched cddid_all.tbl CDD pfam14512 pfam14512 405236 TM1586_NiRdase Putative TM nitroreductase. Compared with the more traditional NADH oxidase/flavin reductase family, this family is a duplication, consisting of two similar domains arranged as the subunits of the dimeric NADH oxidase/flavin reductase with one conserved active site. 214 matched cddid_all.tbl CDD pfam14513 pfam14513 464196 DAG_kinase_N Diacylglycerol kinase N-terminus. This domain is found at the N-terminus of diacylglycerol kinases. 135 matched cddid_all.tbl CDD pfam14514 pfam14514 405238 TetR_C_9 Tetracyclin repressor-like, C-terminal domain. This family comprises proteins that belong to the TetR family of transcriptional regulators. This family features the C-terminal region of these sequences, which does not include the N-terminal helix-turn-helix. 130 matched cddid_all.tbl CDD pfam14515 pfam14515 405239 HOASN Haem-oxygenase-associated N-terminal helices. This domain represents a pair of alpha helices, which are found at the N-terminus of some Haem-oxygenase globular domain. 92 matched cddid_all.tbl CDD pfam14516 pfam14516 373105 AAA_35 AAA-like domain. This family of proteins are part of the AAA superfamily. 331 matched cddid_all.tbl CDD pfam14517 pfam14517 464197 Tachylectin Tachylectin. This family of lectins binds N-acetylglucosamine and N-acetylgalactosamine and may be involved in innate immunity. It has a five-bladed beta-propeller structure with five carbohydrate-binding sites, one per beta sheet. 228 matched cddid_all.tbl CDD pfam14518 pfam14518 434009 Haem_oxygenas_2 Iron-containing redox enzyme. The CADD, Chlamydia protein associating with death domains, crystal structure reveals a dimer of seven-helical bundles. Each bundle contains a di-iron centre adjacent to an internal cavity that forms an active site similar to that of methane mono-oxygenase hydrolase. 178 matched cddid_all.tbl CDD pfam14519 pfam14519 405242 Macro_2 Macro-like domain. This domain is an ADP-ribose binding module. It is found in a number of yeast proteins. 290 matched cddid_all.tbl CDD pfam14520 pfam14520 434010 HHH_5 Helix-hairpin-helix domain. 57 matched cddid_all.tbl CDD pfam14521 pfam14521 464198 Aspzincin_M35 Lysine-specific metallo-endopeptidase. This is the catalytic region of aspzincins, a group of lysine-specific metallo-endopeptidases in the MEROPS:M35 family. They exhibit the following active-site architecture. The active site is composed of two helices and a loop region and includes the HExxH and GTxDxxYG motifs. In UniProt:P81054, His117, His121 and Asp130 coordinate to the catalytic zinc ligands. An electrostatically negative region composed of Asp154 and Glu157 attracts a positively charged Lys side chain of a substrate in a specific manner. 138 matched cddid_all.tbl CDD pfam14522 pfam14522 434012 Cytochrome_C7 Cytochrome c7 and related cytochrome c. This family includes cytochromes c7 and c7-type. In cytochromes c7 all three haems are bis-His co-ordinated, while in c7-type the last haem is His-Met co-ordinated. Desulfuromonas acetoxidans and Geobacter metallireducens cytochrome c7 participate in the anaerobic iron respiration, but Geobacter metallireducens cytochrome c7 hasn't a Fe(III) reductase activity. This entry also includes cytochrome c nitrite reductase subunit NrfH from Desulfovibrio vulgaris which forms a complex with cytochrome c nitrite reductase NrfA. 62 matched cddid_all.tbl CDD pfam14523 pfam14523 464199 Syntaxin_2 Syntaxin-like protein. This domain includes syntaxin-like domains including from the Vam3p protein. 101 matched cddid_all.tbl CDD pfam14524 pfam14524 464200 Wzt_C Wzt C-terminal domain. This domain is found at the C-terminus of the Wzt protein. The crystal structure of C-Wzt(O9a) reveals a beta sandwich with an immunoglobulin-like topology that contains the O-antigenic polysaccharide binding pocket. This domain is often associated with the ABC-transporter domain. 141 matched cddid_all.tbl CDD pfam14525 pfam14525 434015 AraC_binding_2 AraC-binding-like domain. This domain is related to the AraC ligand binding domain pfam02311. 173 matched cddid_all.tbl CDD pfam14526 pfam14526 434016 Cass2 Integron-associated effector binding protein. This family contains Cass2 from Vibrio cholerae, an integron-associated protein that has been shown to bind cationic drug compounds with submicromolar affinity. Cass2 has been proposed to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and other closely-related species. 149 matched cddid_all.tbl CDD pfam14527 pfam14527 434017 LAGLIDADG_WhiA WhiA LAGLIDADG-like domain. This domain is found within the sporulation regulator WhiA. It is a LAGLIDADG superfamily like domain. 93 matched cddid_all.tbl CDD pfam14528 pfam14528 434018 LAGLIDADG_3 LAGLIDADG-like domain. This domain is part of the LAGLIDADG superfamily. 82 matched cddid_all.tbl CDD pfam14529 pfam14529 434019 Exo_endo_phos_2 Endonuclease-reverse transcriptase. This domain represents the endonuclease region of retrotransposons from a range of bacteria, archaea and eukaryotes. These are enzymes largely from class EC:2.7.7.49. 118 matched cddid_all.tbl CDD pfam14530 pfam14530 434020 DUF4439 Domain of unknown function (DUF4439). This domain has a ferritin-like fold. 132 matched cddid_all.tbl CDD pfam14531 pfam14531 405254 Kinase-like Kinase-like. This family includes the pseudokinases ROP2 and ROP8 from Toxoplasma gondii. These proteins have a typical bilobed protein kinase fold, but lack catalytic actvity. 288 matched cddid_all.tbl CDD pfam14532 pfam14532 434021 Sigma54_activ_2 Sigma-54 interaction domain. 138 matched cddid_all.tbl CDD pfam14533 pfam14533 464201 USP7_C2 Ubiquitin-specific protease C-terminal. This C-terminal domain on many long ubiquitin-specific proteases has no known function. 204 matched cddid_all.tbl CDD pfam14534 pfam14534 434023 DUF4440 Domain of unknown function (DUF4440). 107 matched cddid_all.tbl CDD pfam14535 pfam14535 434024 AMP-binding_C_2 AMP-binding enzyme C-terminal domain. This is a small domain that is found C terminal to pfam00501. It has a central beta sheet core that is flanked by alpha helices. 96 matched cddid_all.tbl CDD pfam14536 pfam14536 405258 DUF4441 Domain of unknown function (DUF4441). This family is largely made up of uncharacterized proteins from the Ciliophora. The function is not known. 114 matched cddid_all.tbl CDD pfam14537 pfam14537 434025 Cytochrom_c3_2 Cytochrome c3. 79 matched cddid_all.tbl CDD pfam14538 pfam14538 464202 Raptor_N Raptor N-terminal CASPase like domain. This domain is found at the N-terminus of the Raptor protein. It has been identified to have a CASPase like structure. It conserves the characteriztic cys/his dyad of the caspases suggesting it may have a peptidase activity. 152 matched cddid_all.tbl CDD pfam14539 pfam14539 434027 DUF4442 Domain of unknown function (DUF4442). This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 139 and 165 amino acids in length. There is a conserved PYF sequence motif. There is a single completely conserved residue N that may be functionally important. 131 matched cddid_all.tbl CDD pfam14540 pfam14540 434028 NTF-like Nucleotidyltransferase-like. Structural comparisons with PDB:1kny indicate that this N-terminal domain resembles a nucleotidyltransferase fold. 118 matched cddid_all.tbl CDD pfam14541 pfam14541 434029 TAXi_C Xylanase inhibitor C-terminal. The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylasnase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival. 160 matched cddid_all.tbl CDD pfam14542 pfam14542 434030 Acetyltransf_CG GCN5-related N-acetyl-transferase. This family of GCN5-related N-acetyl-transferases bind both CoA and acetyl-CoA. They are characterized by highly conserved glycine, a cysteine residue in the acetyl-CoA binding site near the acetyl group, their small size compared with other GNATs and a lack of of an obvious substrate-binding site. It is proposed that they transfer an acetyl group from acetyl-CoA to one or more unidentified aliphatic amines via an acetyl (cysteine) enzyme intermediate. The substrate might be another macromolecule. 79 matched cddid_all.tbl CDD pfam14543 pfam14543 464203 TAXi_N Xylanase inhibitor N-terminal. The N- and C-termini of the members of this family are jointly necessary for creating the catalytic pocket necessary for cleaving xylanase. Phytopathogens produce xylanase that destroys plant cells, so its destruction through proteolysis is vital for plant-survival. 172 matched cddid_all.tbl CDD pfam14544 pfam14544 464204 DUF4443 Domain of unknown function (DUF4443). This is a family of archaeal proteins. The domain is a putative gyrase domain. 100 matched cddid_all.tbl CDD pfam14545 pfam14545 464205 DBB Dof, BCAP, and BANK (DBB) motif,. The DBB domain is named from the Drosophila (Downstream of FGFR - Dof, also known as Heartbroken or Stumps) protein, the BANKS and BCAP, both signalling in B-cell pathway, proteins. This domain defines a minimal region required for mediating Dof dimerization. Since this domain can interact both with itself and with a region in the C-terminal part of the molecule, it may mediate either intermolecular or intramolecular interactions. Mutants lacking this domain disrupt FGFR signal transduction and fibroblast growth-factor signalling. The DBB domain of BCAP mediates BCAP TIR dimerization and negatively regulates TLR signalling. 139 matched cddid_all.tbl CDD pfam14547 pfam14547 434033 Hydrophob_seed Hydrophobic seed protein. This domain has a four-helix bundle structure. It contains four disulfide bonds, of which three function to keep the C- and N-terminal parts of the molecule in place. 85 matched cddid_all.tbl CDD pfam14549 pfam14549 405268 P22_Cro DNA-binding transcriptional regulator Cro. Bacteriophage P22 Cro protein represses genes normally expressed in early phage development and is necessary for the late stage of lytic growth. It does this by binding to the OL and OR operator-regions normally used by the repressor protein for lysogenic maintenance. 60 matched cddid_all.tbl CDD pfam14550 pfam14550 405269 Peptidase_S78_2 Putative phage serine protease XkdF. This domain is largely found on phage proteins. In a number of cases the domain is associated with a SAM-dependent methyltransferase. Members are serine peptidases. 120 matched cddid_all.tbl CDD pfam14551 pfam14551 464206 MCM_N MCM N-terminal domain. This family contains the N-terminal domain of MCM proteins. 95 matched cddid_all.tbl CDD pfam14552 pfam14552 434035 Tautomerase_2 Tautomerase enzyme. 82 matched cddid_all.tbl CDD pfam14553 pfam14553 405272 YqbF YqbF, hypothetical protein domain. This N-terminal domain is found in Bacillus and related spp. The function is not known. 43 matched cddid_all.tbl CDD pfam14554 pfam14554 405273 VEGF_C VEGF heparin-binding domain. This short domain is found at the C-terminus of VEGF. It has been shown to have heparin binding activity. 49 matched cddid_all.tbl CDD pfam14555 pfam14555 464207 UBA_4 UBA-like domain. 43 matched cddid_all.tbl CDD pfam14556 pfam14556 373128 AF2331-like AF2331-like. AF2331-like is a 11-kDa orphan protein of unknown function from Archaeoglobus fulgidus. The structure consists of an alpha + beta fold formed by an unusual homodimer, where the two core beta-sheets are interdigitated, containing strands alternating from both subunits. AF2331 contains multiple negatively charged surface clusters and is located on the same operon as the basic protein AF2330. It is suggested that AF2331 and AF2330 may form a charge-stabilized complex in vivo, though the role of the negatively charged surface clusters is not clear. 90 matched cddid_all.tbl CDD pfam14557 pfam14557 317018 AphA_like Putative AphA-like transcriptional regulator. Members of this family are putative transcriptional regulators that appear to be related to the pfam03551 family. This family includes AphA-like members. 174 matched cddid_all.tbl CDD pfam14558 pfam14558 434037 TRP_N ML-like domain. This domain is distantly similar to pfam02221 and conserves its pattern of conserved cysteines. This suggests that this domain may be involved in lipid binding. 137 matched cddid_all.tbl CDD pfam14559 pfam14559 434038 TPR_19 Tetratricopeptide repeat. 65 matched cddid_all.tbl CDD pfam14560 pfam14560 405277 Ubiquitin_2 Ubiquitin-like domain. This entry contains ubiquitin-like domains. 83 matched cddid_all.tbl CDD pfam14561 pfam14561 434039 TPR_20 Tetratricopeptide repeat. 90 matched cddid_all.tbl CDD pfam14562 pfam14562 373131 Endonuc_BglI Restriction endonuclease BglI. This restriction endonuclease binds DNA as a dimer. BglI recognizes and cleaves the interrupted DNA sequence GCCNNNNNGGC and cleaves between the fourth and fifth unspecified base pair to produce 3' overhanging ends. 285 matched cddid_all.tbl CDD pfam14563 pfam14563 405279 DUF4444 Domain of unknown function (DUF4444). This domain family is found in bacteria, and is approximately 40 amino acids in length. There is a conserved LIPL sequence motif. There are two completely conserved G residues that may be functionally important. 41 matched cddid_all.tbl CDD pfam14564 pfam14564 434040 Membrane_bind Membrane binding. This family includes the C-terminal domain of Dictyostelium discoideum Calcium-dependent cell adhesion molecule 1, which has an immunoglobulin-like fold. It tethers the protein to the cell membrane. 110 matched cddid_all.tbl CDD pfam14565 pfam14565 405281 IL22 Interleukin 22 IL-10-related T-cell-derived-inducible factor. Interleukin-22 is distantly related to interleukin (IL)-10, and is produced by activated T cells. IL-22 is a ligand for CRF2-4, a member of the class II cytokine receptor family. 139 matched cddid_all.tbl CDD pfam14566 pfam14566 464208 PTPlike_phytase Inositol hexakisphosphate. Inositol hexakisphosphate, often called phytate, is found in abundance in seeds and acting as an inorganic phosphate reservoir. Phytases are phosphatases that hydrolyze phytate to less-phosphorylated myo-inositol derivatives and inorganic phosphate. The active-site sequence (HCXXGXGR) of the phytase identified from the gut micro-organizm Selenomonas ruminantium forms a loop (P loop) at the base of a substrate binding pocket that is characteriztic of protein tyrosine phosphatases (PTPs). The depth of this pocket is an important determinant of the substrate specificity of PTPs. In humans this enzyme is thought to aid bone mineralization and salvage the inositol moiety prior to apoptosis. 157 matched cddid_all.tbl CDD pfam14567 pfam14567 434042 SUKH_5 SMI1-KNR4 cell-wall. Members of this family are related to the SMI1/KNR4-like or SUKH superfamily of proteins. 133 matched cddid_all.tbl CDD pfam14568 pfam14568 434043 SUKH_6 SMI1-KNR4 cell-wall. Members of this family are related to the SMI1/KNR4-like or SUKH superfamily of proteins. 120 matched cddid_all.tbl CDD pfam14569 pfam14569 464209 zf-UDP Zinc-binding RING-finger. This RING/U-box type zinc-binding domain is frequently found in the catalytic subunit (irx3) of cellulose synthase. The enzymic class is EC:2.4.1.12, whereby the synthase removes the glucose from UDP-glucose and adds it to the growing cellulose, thereby releasing UDP. The domain-structure is treble-clef like (PDB:1weo). 75 matched cddid_all.tbl CDD pfam14570 pfam14570 405286 zf-RING_4 RING/Ubox like zinc-binding domain. 47 matched cddid_all.tbl CDD pfam14571 pfam14571 434045 Di19_C Stress-induced protein Di19, C-terminal. C-terminal domain of Di19, a protein that increases the sensitivity of plants to environmental stress, such as salinity, drought, osmotic stress and cold. the protein is also induced by an increased supply of stress-related hormones such as abscisic acid ABA and ethylene. There is a zinc-finger at the N-terminus, zf-Di19, pfam05605. 102 matched cddid_all.tbl CDD pfam14572 pfam14572 434046 Pribosyl_synth Phosphoribosyl synthetase-associated domain. This family includes several examples of enzymes from class EC:2.7.6.1, phosphoribosyl-pyrophosphate transferase. 184 matched cddid_all.tbl CDD pfam14573 pfam14573 373139 PP-binding_2 Acyl-carrier. 96 matched cddid_all.tbl CDD pfam14574 pfam14574 464210 RACo_C_ter C-terminal domain of RACo the ASKHA domain. This family includes reductive activator of CoFeSP (RACo) proteins. Structure analysis of RACo indicate that it contains 4 regions: N-terminal region pfam00111 (residues 3-94) binding the [2Fe-2S] cluster, a linker region (residues 95-125), the middle region (residues 126-206), and the large C-terminal domain (residues 207-630). This entry is specific for the C-terminal domain which harbors the ATP-binding site. Structural studies show that the C-terminal domain contains the conserved beta-beta-beta-alpha-beta-alpha-beta-alpha topology characteriztic of the ASKHA (acetate and sugar kinases/heat shock protein 70/actin). Despite the low-sequence identity shared between members of the ASKHA super family, they show a common central fold. Members of the ASKHA include proteins that catalyze phosphoryl transfers or hydrolysis of ATP in a variety of biological contexts. Asp, Asn, Glu, and Gln residues are well conserved in the core of the ASKHA proteins, where they interact with the phosphates of ATP and the bound Mg2+ ions. 261 matched cddid_all.tbl CDD pfam14575 pfam14575 464211 EphA2_TM Ephrin type-A receptor 2 transmembrane domain. Epha2_TM represents the left-handed dimer transmembrane domain of of EphA2 receptor. This domain oligomerises and is important for the active signalling process. 72 matched cddid_all.tbl CDD pfam14576 pfam14576 464212 SEO_N Sieve element occlusion N-terminus. Sieve element occlusion (SEO) proteins, or forisomes, are phloem proteins which accumulate during sieve element differentiation. This domain represents the N-terminus of SEO proteins. 287 matched cddid_all.tbl CDD pfam14577 pfam14577 405292 SEO_C Sieve element occlusion C-terminus. Sieve element occlusion (SEO) proteins, or forisomes, are phloem proteins which accumulate during sieve element differentiation. This domain represents the C-terminus of SEO proteins. 232 matched cddid_all.tbl CDD pfam14578 pfam14578 405293 GTP_EFTU_D4 Elongation factor Tu domain 4. Elongation factor Tu consists of several structural domains, and this is usually the fourth. 86 matched cddid_all.tbl CDD pfam14579 pfam14579 434050 HHH_6 Helix-hairpin-helix motif. The HHH domain is a short DNA-binding domain. 88 matched cddid_all.tbl CDD pfam14580 pfam14580 405295 LRR_9 Leucine-rich repeat. 175 matched cddid_all.tbl CDD pfam14581 pfam14581 434051 SseB_C SseB protein C-terminal domain. This family consists of several SseB proteins which appear to be found exclusively in Enterobacteria. SseB is known to enhance serine-sensitivity in Escherichia coli and is part of the Salmonella pathogenicity island 2 (SPI-2) translocon. This presumed domain is found at the C-terminus of SseB proteins. 105 matched cddid_all.tbl CDD pfam14582 pfam14582 405297 Metallophos_3 Metallophosphoesterase, calcineurin superfamily. Members of this family are part of the Calcineurin-like phosphoesterase superfamily. 259 matched cddid_all.tbl CDD pfam14583 pfam14583 434052 Pectate_lyase22 Oligogalacturonate lyase. This is a family of oligogalacturonate lyases, referred to more generally as pectate lyase family 22. These proteins fold into 7-bladed beta-propellers. 386 matched cddid_all.tbl CDD pfam14584 pfam14584 464213 DUF4446 Protein of unknown function (DUF4446). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 165 and 176 amino acids in length. 150 matched cddid_all.tbl CDD pfam14585 pfam14585 405299 CagY_I CagY type 1 repeat. This repeat is found at the N-terminus of the CagY proteins - part of the CAG pathogenicity island - and involved in delivery of the protein CagA into host cells. 65 matched cddid_all.tbl CDD pfam14586 pfam14586 291265 MHC_I_2 Class I Histocompatibility antigen, NKG2D ligand, domains 1 and 2. Members of this family are known as retinoic-acid-inducible proteins. They are ligands for the activating immunoreceptor NKG2D, which is widely expressed on natural killer cells, T cells, and macrophages. 174 matched cddid_all.tbl CDD pfam14587 pfam14587 434054 Glyco_hydr_30_2 O-Glycosyl hydrolase family 30. 364 matched cddid_all.tbl CDD pfam14588 pfam14588 405301 YjgF_endoribonc YjgF/chorismate_mutase-like, putative endoribonuclease. YjgF_Endoribonuc is a putative endoribonuclease. The structure is of beta-alpha-beta-alpha-beta(2) domains common both to bacterial chorismate mutase and to members of the YjgF family. These proteins form trimers with a three-fold symmetry with three closely-packed beta-sheets. The YjgF family is a large, widely distributed family of proteins of unknown biochemical function that are highly conserved among eubacteria, archaea and eukaryotes. 148 matched cddid_all.tbl CDD pfam14589 pfam14589 373147 NrfD_2 Polysulfide reductase. Bacterial polysulfide reductase is an integral membrane protein complex responsible for quinone-coupled reduction of polysulfide, a process important in extreme environments such as deep-sea vents and hot springs. Polysulfides are a class of compounds composed of chains of sulfur atoms, which in their simplest form are present as an anion with general formula Sn(2-). In nature, polysulfides are found in particularly high concentrations in extreme volcanic or geothermically active environments. Here, the reduction and oxidation of polysulfides are vital processes for many bacteria and are essential steps in the global sulfur cycle. In particular, the reduction of polysulfide to hydrogen sulfide in these environments is usually linked to energy-generating respiratory processes, supporting growth of many microorganizms, particularly hyperthermophiles. 281 matched cddid_all.tbl CDD pfam14590 pfam14590 434055 DUF4447 Domain of unknown function (DUF4447). This family of proteins is found in bacteria. Proteins in this family are approximately 170 amino acids in length. 166 matched cddid_all.tbl CDD pfam14591 pfam14591 373148 AF0941-like AF0941-like. Members of this family are of unknown function. 113 matched cddid_all.tbl CDD pfam14592 pfam14592 434056 Chondroitinas_B Chondroitinase B. This family includes chondroitinases. These enzymes cleave the glycosaminoglycan dermatan sulfate. 426 matched cddid_all.tbl CDD pfam14593 pfam14593 434057 PH_3 PH domain. 103 matched cddid_all.tbl CDD pfam14594 pfam14594 434058 Sipho_Gp37 Siphovirus ReqiPepy6 Gp37-like protein. This family includes numerous phage proteins from Siphoviruses. The function of this protein is uncertain, but it is related to pfam06605. In Rhodococcus phage ReqiPepy6 this protein is called Gp37. 336 matched cddid_all.tbl CDD pfam14595 pfam14595 434059 Thioredoxin_9 Thioredoxin. 129 matched cddid_all.tbl CDD pfam14596 pfam14596 291272 STAT6_C STAT6 C-terminal. This family represents the C-terminus of mammalian STAT6 (Signal transducer and activator of transcription 6), it contains an LXXLL motif which binds to NCOA1 (Nuclear receptor coactivator 1). 193 matched cddid_all.tbl CDD pfam14597 pfam14597 373150 Lactamase_B_5 Metallo-beta-lactamase superfamily. This is a small family of putative metal-dependent hydrolases. 199 matched cddid_all.tbl CDD pfam14598 pfam14598 464214 PAS_11 PAS domain. This family includes the PAS-B domain of NCOA1 (Nuclear receptor coactivator 1), which binds to an LXXLL motif in the C-terminal region of STAT6 (Signal transducer and activator of transcription 6). 110 matched cddid_all.tbl CDD pfam14599 pfam14599 464215 zinc_ribbon_6 Zinc-ribbon. This is a typical zinc-ribbon finger, with each pair of zinc-ligands coming from more-or-less either side of two knuckles. It is found in eukaryotes. 59 matched cddid_all.tbl CDD pfam14600 pfam14600 434062 CBM_5_12_2 Cellulose-binding domain. This C-terminal domain belongs to the CAZy family of carbohydrate-binding domains that are associated with glycosyl-hydrolases. It is suggested to bind cellulose. 62 matched cddid_all.tbl CDD pfam14601 pfam14601 434063 TFX_C DNA_binding protein, TFX, C-term. This is the C-terminal region of TFX-like DNA-binding proteins. 83 matched cddid_all.tbl CDD pfam14602 pfam14602 434064 Hexapep_2 Hexapeptide repeat of succinyl-transferase. 33 matched cddid_all.tbl CDD pfam14603 pfam14603 464216 hSH3 Helically-extended SH3 domain. This domain is the 70 C-terminal residues of ADAP - Adhesion and de-granulation promoting adapter protein. It shows homology to SH3 domains; however, conserved residues of the fold are absent. It thus represents an altered SH3 domain fold. An N-terminal, amphipathic, helix makes extensive contacts to residues of the regular SH3 domain fold thereby creating a composite surface with unusual surface properties. The domain can no longer bind conventional proline-rich peptides. There are key phosphorylation sites within the two hSH3 domains and it would appear that binding at these sites does not materially affect the folding of these regions although the equilibrium towards the unfolded state may be slightly altered. The binding partners of the hSH3 domains are still unknown. 89 matched cddid_all.tbl CDD pfam14604 pfam14604 434066 SH3_9 Variant SH3 domain. 49 matched cddid_all.tbl CDD pfam14605 pfam14605 373156 Nup35_RRM_2 Nup53/35/40-type RNA recognition motif. 53 matched cddid_all.tbl CDD pfam14606 pfam14606 434067 Lipase_GDSL_3 GDSL-like Lipase/Acylhydrolase family. 181 matched cddid_all.tbl CDD pfam14607 pfam14607 434068 GxDLY N-terminus of Esterase_SGNH_hydro-type. This domain lies upstream of SGNH hydrolase, but its function is not known. There is a highly conserved GxDLY sequence-motif. 146 matched cddid_all.tbl CDD pfam14608 pfam14608 464217 zf-CCCH_2 RNA-binding, Nab2-type zinc finger. This is an unusual zinc-finger family, and is represented by fingers 5-7 of Nab2. Nab2 ZnF5-7 are zinc-fingers of the type C-x8-C-x5-C-x3-H. Nab2 ZnFs function in the generation of export-competent mRNPs. Mab2 is a conserved polyadenosine-RNA-binding Zn finger protein required for both mRNA export and polyadenylation regulation and becomes attached to the mRNP after splicing and during or immediately after polyadenylation. The three ZnFs, 5-7, have almost identical folds and, most unusually, associate with one another to form a single coherent structural unit. ZnF5-7 bind to eight consecutive adenines, and chemical shift perturbations identify residues on each finger that interact with RNA. 19 matched cddid_all.tbl CDD pfam14609 pfam14609 405315 GCP5-Mod21 gamma-Tubulin ring complex non-core subunit mod21. GCP5-Mod21 is a non-core subunit of the larger gamma-tubulin ring complex that effects microtubule nucleation from both centrosomal and non-centrosomal sites. This subunit, unlike GCP2 and and GCP3 and others, is not thought to be essential for viability in the fission yeast, and may not be expressed in very high concentrations. Fission yeast can form a large gamma-Tubulin complex C similar to that found in higher eukaryotes and this complex is important for maintaining normal levels of microtubule nucleation in vivo. 676 matched cddid_all.tbl CDD pfam14610 pfam14610 464218 Psg1 Ykl077w/Psg1 (Pma1 Stabilization in Golgi). Ykl077w/Psg1 (Pma1 Stabilization in the Golgi) physically interacts with Exp1 (for ER eXport of Pma1). Psg1 can be found in the Golgi and coat protein I (COPI) vesicles but does not directly bind Pma1. Loss of Psg1 causes enhanced degradation of Pma1 in the vacuole. Psg1 is 392aa protein with a predicted signal sequence at its N-terminus and a single TMD near the C-terminus. The short cytosolic region bears 2 putative retrieval motifs KRR and KKxxKxx. It was previously shown to be cleaved by the Ca+ dependent serine protease, Kex2. 185 matched cddid_all.tbl CDD pfam14611 pfam14611 434070 SLS Mitochondrial inner-membrane-bound regulator. SLS is a fungal domain found bound to the mitochondrial inner-membrane. It reacts physically with fungal Kar2p to promote translocation across the endoplasmic-reticulum membrane. This action appeared to be mediated via the promotion of the Sec63p-mediated activation of Kar2p's ATPase activity. This indicates that the Sls1p protein is a GrpE-like protein in the endoplasmic reticulum. In S.cerevisiae the SLS1 gene (ScSLS1) is not essential but is also involved in ERAD and folding. 198 matched cddid_all.tbl CDD pfam14612 pfam14612 405318 Ino80_Iec3 IEC3 subunit of the Ino80 complex, chromatin re-modelling. This is a family of fungal chromatin re-modelling proteins found in one of the chromatin-central complexes, Ino80. The function was identified in Schizosaccharomyces pombe but there is no orthologue in S. cerevisiae. 231 matched cddid_all.tbl CDD pfam14613 pfam14613 434071 DUF4449 Protein of unknown function (DUF4449). This is a fungal DUF of unknown function. A member of this family designated HAM-13 is thought to associate with MAPKs and to be required for proper cell communication but it is also possible to be involved in other processes such as cell signalling or trafficking. 156 matched cddid_all.tbl CDD pfam14614 pfam14614 405320 DUF4450 Domain of unknown function (DUF4450). This is a family of bacterial proteins of unknown function. 213 matched cddid_all.tbl CDD pfam14615 pfam14615 434072 Rsa3 Ribosome-assembly protein 3. This is a family of 60S ribosome-assembly proteins, from fungi. 46 matched cddid_all.tbl CDD pfam14616 pfam14616 405322 Rua1_C Transcription regulator Rua1, C-terminal. This entry represents a domain that can be found at the C terminus f fungal proteins such as meiotic expression up-regulated protein 26 from Schizosaccharomyces pombe, Ecm8 from Saccharomyces cerevisiae and Rua1 from Ustilago maydis. Rua1 is a transcription factor and part of the gene cluster that mediates the biosynthesis of the glycolipid biosurfactant ustilagic acid (UA). 120 matched cddid_all.tbl CDD pfam14617 pfam14617 373164 CMS1 U3-containing 90S pre-ribosomal complex subunit. This is a family of fungal and plant CMS1-like proteins. The family has similarity to the DEAD-box helicases. 250 matched cddid_all.tbl CDD pfam14618 pfam14618 405323 DUF4452 Domain of unknown function (DUF4452). This fungal family has no known function. However, it is rich in paired, as CXXC, cysteines and histidines, but these do not fall in the conformation that might suggest zinc-binding. 169 matched cddid_all.tbl CDD pfam14619 pfam14619 464219 SnAC Snf2-ATP coupling, chromatin remodelling complex. This domain appears to play a crucial role in chromatin remodelling for yeast SWI/SNF. It binds histones. It is required for mobilising nucleosomes and lies within the catalytic subunit of the yeast SWI/SNF. It is found to be universally conserved. 69 matched cddid_all.tbl CDD pfam14620 pfam14620 405325 YPEB YpeB sporulation. YPEB is a protein that is necessary for the functioning of SleB during spore-cortex hydrolysis. 361 matched cddid_all.tbl CDD pfam14621 pfam14621 464220 RFX5_DNA_bdg RFX5 DNA-binding domain. RFX5 and RFXAP reveals molecular details associated with MHCII gene expression. 219 matched cddid_all.tbl CDD pfam14622 pfam14622 434075 Ribonucleas_3_3 Ribonuclease-III-like. Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3. 127 matched cddid_all.tbl CDD pfam14623 pfam14623 434076 Vint Hint-domain. This short domain is a conserved region of intein-containing proteins from lower eukaryotes. 166 matched cddid_all.tbl CDD pfam14624 pfam14624 464221 Vwaint VWA / Hh protein intein-like. VWA-Hint proteins carry this conserved domain of around 300 residues, now named the Vwaint domain. Such proteins do not seem to have a signal peptide for secretion. Generally, this domain lies between the N-terminal VWA domain and the more C-terminal 'Vint'-type Hint domain. The exact function of this domain is not known. 70 matched cddid_all.tbl CDD pfam14625 pfam14625 464222 Lustrin_cystein Lustrin, cysteine-rich repeated domain. This repeated domain is found in proteins from lower eukaryotes in lustrin, perlucin, pearl nacre, and other similar protein-types. Each repeat lies between Kunitz-BPTI repeats, in certain species, which are also cysteine-rich. The cysteines may form the disulfide bonds observed for other members of this superfamily. 46 matched cddid_all.tbl CDD pfam14626 pfam14626 405331 RNase_Zc3h12a_2 Zc3h12a-like Ribonuclease NYN domain. This family is found to be a divergent form of the NYN-domain- containing RNAse family. 122 matched cddid_all.tbl CDD pfam14627 pfam14627 405332 DUF4453 Domain of unknown function (DUF4453). This short domain is found only on a small subgroup of proteins from Gram-negative Proteobacteria that also carry a YARHG domain, pfam13308. They carry three conserved tryptophan and three conserved cysteine residues. 107 matched cddid_all.tbl CDD pfam14628 pfam14628 434079 DUF4454 Domain of unknown function (DUF4454). This C-terminal domain is found only on a small subgroup of proteins from Gram-positive Clostridiales that also carry a YARHG domain, pfam13308. 210 matched cddid_all.tbl CDD pfam14629 pfam14629 464223 ORC4_C Origin recognition complex (ORC) subunit 4 C-terminus. This entry represents the C-terminus of origin recognition complex subunit 4. 212 matched cddid_all.tbl CDD pfam14630 pfam14630 464224 ORC5_C Origin recognition complex (ORC) subunit 5 C-terminus. This entry represents the C-terminus of origin recognition complex subunit 5. 267 matched cddid_all.tbl CDD pfam14631 pfam14631 464225 FancD2 Fanconi anaemia protein FancD2 nuclease. The Fanconi anaemia protein FancD2 is a nuclease necessary for the repair of DNA interstrand-crosslinks. 1346 matched cddid_all.tbl CDD pfam14632 pfam14632 464226 SPT6_acidic Acidic N-terminal SPT6. The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a transcription regulator, but the exact function of this acidic region is not certain. 89 matched cddid_all.tbl CDD pfam14633 pfam14633 464227 SH2_2 SH2 domain. 206 matched cddid_all.tbl CDD pfam14634 pfam14634 434085 zf-RING_5 zinc-RING finger domain. 43 matched cddid_all.tbl CDD pfam14635 pfam14635 291309 HHH_7 Helix-hairpin-helix motif. 104 matched cddid_all.tbl CDD pfam14636 pfam14636 464228 FNIP_N Folliculin-interacting protein N-terminus. This is the N-terminus of folliculin-interacting proteins. 125 matched cddid_all.tbl CDD pfam14637 pfam14637 434087 FNIP_M Folliculin-interacting protein middle domain. This is the middle domain of folliculin-interacting proteins. 226 matched cddid_all.tbl CDD pfam14638 pfam14638 464229 FNIP_C Folliculin-interacting protein C-terminus. This is the C-terminus of folliculin-interacting proteins. This region is responsible for binding to folliculin. 189 matched cddid_all.tbl CDD pfam14639 pfam14639 258777 YqgF Holliday-junction resolvase-like of SPT6. The YqgF domain of SPT6 proteins is homologous to the E.coli RuvC but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage 150 matched cddid_all.tbl CDD pfam14641 pfam14641 464230 HTH_44 Helix-turn-helix DNA-binding domain of SPT6. This helix-turn-helix represents the first of two DNA-binding domains on the SPT6 proteins. 115 matched cddid_all.tbl CDD pfam14642 pfam14642 405345 FAM47 FAM47 family. The function of this Chordate family of proteins is not known. 257 matched cddid_all.tbl CDD pfam14643 pfam14643 464231 DUF4455 Domain of unknown function (DUF4455). This domain family is found in bacteria and eukaryotes, and is approximately 480 amino acids in length. There are two completely conserved residues (W and P) that may be functionally important. 469 matched cddid_all.tbl CDD pfam14644 pfam14644 464232 DUF4456 Domain of unknown function (DUF4456). This domain family is found in bacteria and eukaryotes, and is approximately 210 amino acids in length. There is a single completely conserved residue E that may be functionally important. 209 matched cddid_all.tbl CDD pfam14645 pfam14645 464233 Chibby Chibby family. This family includes the eukaryotic chibby proteins. These proteins inhibit the wingless/Wnt pathway by binding to beta-catenin and inhibiting beta-catenin-mediated transcriptional activation. Chibby is Japanese for small, and is named after the RNAi phenotype seen in Drosophila. 113 matched cddid_all.tbl CDD pfam14646 pfam14646 464234 MYCBPAP MYCBP-associated protein family. This family of eukaryotic proteins includes the mammalian MYCBP-associated proteins. These proteins may be synaptic processes and may have a role in spermatogenesis. 432 matched cddid_all.tbl CDD pfam14647 pfam14647 434094 FAM91_N FAM91 N-terminus. 307 matched cddid_all.tbl CDD pfam14648 pfam14648 464235 FAM91_C FAM91 C-terminus. 428 matched cddid_all.tbl CDD pfam14649 pfam14649 464236 Spatacsin_C Spatacsin C-terminus. This family includes the C-terminus of spatacsin. 294 matched cddid_all.tbl CDD pfam14650 pfam14650 464237 FAM75 FAM75 family. 382 matched cddid_all.tbl CDD pfam14651 pfam14651 405354 Lipocalin_7 Lipocalin / cytosolic fatty-acid binding protein family. Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). 128 matched cddid_all.tbl CDD pfam14652 pfam14652 464238 DUF4457 Domain of unknown function (DUF4457). This family of proteins is found in eukaryotes. It is found repeated several times in the vertebrate KIAA0556 proteins. 323 matched cddid_all.tbl CDD pfam14653 pfam14653 464239 IGFL Insulin growth factor-like family. This family includes the insulin growth factor-like proteins. These proteins are potential ligands for the IGFLR1 cell membrane receptor. 83 matched cddid_all.tbl CDD pfam14654 pfam14654 434100 Epiglycanin_C Mucin, catalytic, TM and cytoplasmic tail region. This family represents the non-tandem repeat domain including cleavage site, the transmembrane helix domain, and the cytoplasmic tail of epiglycanin and related mucins. 91 matched cddid_all.tbl CDD pfam14655 pfam14655 464240 RAB3GAP2_N Rab3 GTPase-activating protein regulatory subunit N-terminus. This family includes the N-terminus of the Rab3 GTPase-activating protein non-catalytic subunit. Rab3 GTPase-activating protein is a GTPase activating protein with specificity for Rab3 subfamily. 416 matched cddid_all.tbl CDD pfam14656 pfam14656 464241 RAB3GAP2_C Rab3 GTPase-activating protein regulatory subunit C-terminus. This family includes the N-terminus of the Rab3 GTPase-activating protein non-catalytic subunit. Rab3 GTPase-activating protein is a GTPase activating protein with specificity for Rab3 subfamily. 594 matched cddid_all.tbl CDD pfam14657 pfam14657 464242 Arm-DNA-bind_4 Arm DNA-binding domain. This family includes AP2-like domains found in a variety of phage integrase proteins. These domains bind to Arm DNA sites. 44 matched cddid_all.tbl CDD pfam14658 pfam14658 405361 EF-hand_9 EF-hand domain. 66 matched cddid_all.tbl CDD pfam14659 pfam14659 464243 Phage_int_SAM_3 Phage integrase, N-terminal SAM-like domain. This domain is found in a variety of phage integrase proteins. 55 matched cddid_all.tbl CDD pfam14660 pfam14660 434105 DUF4458 Domain of unknown function (DUF4458). this domain is found in tandem repeats on the N-terminus of secreted LRR proteins from human associated Bacteroidetes domain boundaries are based on the JCSG solved 3D structure of JCSG target SP16667A (BT_0210) 114 matched cddid_all.tbl CDD pfam14661 pfam14661 464244 HAUS6_N HAUS augmin-like complex subunit 6 N-terminus. This family includes the N-terminus of HAUS augmin-like complex subunit 6. The HAUS augmin-like complex contributes to mitotic spindle assembly, maintenance of chromosome integrity and completion of cytokinesis. 233 matched cddid_all.tbl CDD pfam14662 pfam14662 405365 KASH_CCD Coiled-coil region of CCDC155 or KASH. This coiled-coil region is found in the central part of KASH or Klarsicht/ANC-1/Syne/homology proteins. KASH are a meiosis-specific proteins that localize at telomeres and interact with SUN1, thus being implicated in meiotic chromosome dynamics and homolog pairing. 191 matched cddid_all.tbl CDD pfam14663 pfam14663 464245 RasGEF_N_2 Rapamycin-insensitive companion of mTOR RasGEF_N domain. Rictor appears to serve as a scaffolding protein that is important for maintaining mTORC2 integrity. The mammalian target of rapamycin (mTOR) is a conserved Ser/Thr kinase that forms two functionally distinct complexes, mTROC1 and mTORC2, important for nutrient and growth-factor signalling. This region is the more conserved central section that may include several individual domains. Rictor can be inhibited in the short-term by rapamycin. 107 matched cddid_all.tbl CDD pfam14664 pfam14664 464246 RICTOR_N Rapamycin-insensitive companion of mTOR, N-term. Rictor appears to serve as a scaffolding protein that is important for maintaining mTORC2 integrity. The mammalian target of rapamycin (mTOR) is a conserved Ser/Thr kinase that forms two functionally distinct complexes, mTROC1 and mTORC2, important for nutrient and growth-factor signalling. This region is the N-terminal conserved section that may include several individual domains. Rictor can be inhibited in the short-term by rapamycin. 372 matched cddid_all.tbl CDD pfam14665 pfam14665 464247 RICTOR_phospho Rapamycin-insensitive companion of mTOR, phosphorylation-site. Rictor appears to serve as a scaffolding protein that is important for maintaining mTORC2 integrity. The mammalian target of rapamycin (mTOR) is a conserved Ser/Thr kinase that forms two functionally distinct complexes, mTROC1 and mTORC2, important for nutrient- and growth-factor signalling. This short region is the phoshorylation site. Rictor does interact with 14-3-3 in a Thr1135-dependent manner. Rictor can be inhibited by short-term rapamycin treatment showing that Thr1135 is an mTORC1-regulated site. 108 matched cddid_all.tbl CDD pfam14666 pfam14666 464248 RICTOR_M Rapamycin-insensitive companion of mTOR, middle domain. Rictor appears to serve as a scaffolding protein that is important for maintaining mTORC2 integrity. The mammalian target of rapamycin (mTOR) is a conserved Ser/Thr kinase that forms two functionally distinct complexes, mTROC1 and mTORC2, important for nutrient and growth-factor signalling. This region is the more conserved central section that may include several individual domains. Rictor can be inhibited in the short-term by rapamycin. 104 matched cddid_all.tbl CDD pfam14667 pfam14667 434111 Polysacc_synt_C Polysaccharide biosynthesis C-terminal domain. This family represents the C-terminal integral membrane region of polysaccharide biosynthesis proteins. 141 matched cddid_all.tbl CDD pfam14668 pfam14668 464249 RICTOR_V Rapamycin-insensitive companion of mTOR, domain 5. Rictor appears to serve as a scaffolding protein that is important for maintaining mTORC2 integrity. The mammalian target of rapamycin (mTOR) is a conserved Ser/Thr kinase that forms two functionally distinct complexes, mTROC1 and mTORC2, important for nutrient and growth-factor signalling. These long eukaryotic proteins carry several well-conserved domains, and this is No.5. 71 matched cddid_all.tbl CDD pfam14669 pfam14669 464250 Asp_Glu_race_2 Putative aspartate racemase. This is a small family of vertebrate putative aspartate racemases. The family lies on TOPAZ 1 proteins. 176 matched cddid_all.tbl CDD pfam14670 pfam14670 464251 FXa_inhibition Coagulation Factor Xa inhibitory site. This short domain on coagulation enzyme factor Xa is found to be the target for a potent inhibitor of coagulation, TAK-442. 36 matched cddid_all.tbl CDD pfam14671 pfam14671 464252 DSPn Dual specificity protein phosphatase, N-terminal half. The active core of the dual specificity protein phosphatase is made up of two globular domains both with the DSP-like fold. This family represents the N-terminal half of the core. These domains are arranged in tandem, and are associated via an extensive interface to form a single globular whole. The conserved PTP signature motif (Cys-[X]5-Arg) that defines the catalytic centre of all PTP-family members is located within the C-terminal domain, family DSPc, pfam00782. Although the centre of the catalytic site is formed from DSPc, two loops from the N-terminal domain, DSPn, also contribute to the catalytic site, facilitating peptide substrate specificity. 140 matched cddid_all.tbl CDD pfam14672 pfam14672 464253 LCE Late cornified envelope. This is a family of late cornified envelope proteins that are expressed in skin. 94 matched cddid_all.tbl CDD pfam14673 pfam14673 405375 DUF4459 Domain of unknown function (DUF4459). This family appears only on sequences from Salmonella spp. These sequences also all carry a YARHG domain, pfam13308. 159 matched cddid_all.tbl CDD pfam14674 pfam14674 434117 FANCI_S1-cap FANCI solenoid 1 cap. This is the solenoid 1 cap (S1-cap) domain of the Fanconi anemia group I protein. 53 matched cddid_all.tbl CDD pfam14675 pfam14675 464254 FANCI_S1 FANCI solenoid 1. This is the solenoid 1 (S1) domain of the Fanconi anemia group I protein. 221 matched cddid_all.tbl CDD pfam14676 pfam14676 464255 FANCI_S2 FANCI solenoid 2. This is the solenoid 2 (S2) domain of the Fanconi anemia group I protein. 154 matched cddid_all.tbl CDD pfam14677 pfam14677 464256 FANCI_S3 FANCI solenoid 3. This is the solenoid 3 (S3) domain of the Fanconi anemia group I protein. 216 matched cddid_all.tbl CDD pfam14678 pfam14678 464257 FANCI_S4 FANCI solenoid 4. This is the solenoid 4 (S4) domain of the Fanconi anemia group I protein. 250 matched cddid_all.tbl CDD pfam14679 pfam14679 464258 FANCI_HD1 FANCI helical domain 1. This is the helical domain 1 (HD1) of the Fanconi anemia group I protein. 86 matched cddid_all.tbl CDD pfam14680 pfam14680 464259 FANCI_HD2 FANCI helical domain 2. This is the helical domain 2 (HD2) of the Fanconi anemia group I protein. 233 matched cddid_all.tbl CDD pfam14681 pfam14681 434124 UPRTase Uracil phosphoribosyltransferase. This family includes the enzyme uracil phosphoribosyltransferase (EC:2.4.2.9). This enzyme catalyzes the first step of UMP biosynthesis. 204 matched cddid_all.tbl CDD pfam14682 pfam14682 379667 SPOB_ab Sporulation initiation phospho-transferase B, C-terminal. Sporulation initiation phospho-transferase B or SpoOB is part of a phospho-relay that initiates sporulation in Bacillus subtilis. Spo0B is a two-domain protein consisting of an N-terminal alpha-helical hairpin domain and a C-terminal alpha/beta domain, represented by this family. Two subunits of Spo0B dimerize by a parallel association of helical hairpins to form a novel four-helix bundle from which the active histidine - involved in the auto-phosphorylation - protrudes. In the phospho-relay, the signal-receptor histidine kinases are dephosphorylated by a common response regulator, Spo0F. Spo0B then takes phosphorylated Spo0F as substrate hereby mediating the transfer of a phosphoryl group to Spo0A, the ultimate transcription factor. 113 matched cddid_all.tbl CDD pfam14683 pfam14683 464260 CBM-like Polysaccharide lyase family 4, domain III. CBM-like is domain III of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognizes and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain possesses a jelly roll beta-sandwich fold structurally homologous to carbohydrate binding modules (CBMs), and it carries two sulfate ions and a hexa-coordinated calcium ion. 158 matched cddid_all.tbl CDD pfam14684 pfam14684 434126 Tricorn_C1 Tricorn protease C1 domain. This domain is the C1 core domain of tricorn protease. This is a mixed alpha-beta domain. 70 matched cddid_all.tbl CDD pfam14685 pfam14685 405386 Tricorn_PDZ Tricorn protease PDZ domain. This domain is the PDZ domain of tricorn protease. 88 matched cddid_all.tbl CDD pfam14686 pfam14686 464261 fn3_3 Polysaccharide lyase family 4, domain II. FnIII-like is domain II of rhamnogalacturonan lyase (RG-lyase). The full-length protein specifically recognizes and cleaves alpha-1,4 glycosidic bonds between l-rhamnose and d-galacturonic acids in the backbone of rhamnogalacturonan-I, a major component of the plant cell wall polysaccharide, pectin. This domain displays an immunoglobulin-like or more specifically Fibronectin-III type fold and shows highest structural similarity to the C-terminal beta-sandwich subdomain of the pro-hormone/propeptide processing enzyme carboxypeptidase gp180 from duck. It serves to assist in producing the deep pocket, with domain III, into which the substrate fits. 74 matched cddid_all.tbl CDD pfam14687 pfam14687 464262 DUF4460 Domain of unknown function (DUF4460). This domain family is found in eukaryotes, and is typically between 103 and 119 amino acids in length. There is a conserved HPD sequence motif. There are two completely conserved residues (N and F) that may be functionally important. 111 matched cddid_all.tbl CDD pfam14688 pfam14688 464263 DUF4461 Domain of unknown function (DUF4461). This domain family is found in eukaryotes, and is approximately 310 amino acids in length. 304 matched cddid_all.tbl CDD pfam14689 pfam14689 434130 SPOB_a Sensor_kinase_SpoOB-type, alpha-helical domain. Sporulation initiation phospho-transferase B or SpoOB is part of a phospho-relay that initiates sporulation in Bacillus subtilis. Spo0B is a two-domain protein consisting of an N-terminal alpha-helical hairpin domain and a C-terminal alpha/beta domain. Two subunits of Spo0B dimerize by a parallel association of helical hairpins to form a novel four-helix bundle from which the active histidine - involved in the auto-phosphorylation - protrudes. In the phospho-relay, the signal-receptor histidine kinases are dephosphorylated by a common response regulator, Spo0F. Spo0B then takes phosphorylated Spo0F as substrate thereby mediating the transfer of a phosphoryl group to Spo0A, the ultimate transcription factor. The exact function of this alpha-helical domain is not known; it does not always occur just as the N-terminal domain of SPOB_ab, pfam14682. SCOP describes this domain as a histidine kinase-like fold lacking the kinase ATP-binding site. 62 matched cddid_all.tbl CDD pfam14690 pfam14690 464264 zf-ISL3 zinc-finger of transposase IS204/IS1001/IS1096/IS1165. 47 matched cddid_all.tbl CDD pfam14691 pfam14691 434132 Fer4_20 Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster. Domain II of the enzyme dihydroprymidine dehydrogenase binds FAD. Dihydroprymidine dehydrogenase catalyzes the first and rate-limiting step of pyrimidine degradation by converting pyrimidines to the corresponding 5,6- dihydro compounds. This domain carries two Fe4-S4 clusters. 113 matched cddid_all.tbl CDD pfam14692 pfam14692 405392 DUF4462 Domain of unknown function (DUF4462). This domain family is found in eukaryotes, and is approximately 30 amino acids in length. 28 matched cddid_all.tbl CDD pfam14693 pfam14693 464265 Ribosomal_TL5_C Ribosomal protein TL5, C-terminal domain. This family contains the C-terminal domain of ribosomal protein TL5. The N-terminal domain, which binds to 5S rRNA, is contained in family Ribosomal_L25p, pfam01386. Full length (N- and C-terminal domain) homologs of TL5 are also known as CTC proteins. TL5 or CTC are not found in Eukarya or Archaea. In some Bacteria, including E. coli, this ribosomal subunit occurs as a single domain protein (named Ribosomal subunit L25), where the only domain is homologous to TL5 N-terminal domain (hence included in family pfam01386). The function of the C-terminal domain of TLC is at present unknown. 84 matched cddid_all.tbl CDD pfam14694 pfam14694 464266 LINES_N Lines N-terminus. This family represents the N-terminus of protein lines. In Drosophila this protein is involved in embryonic segmentation and may function as a transcriptional regulator. 351 matched cddid_all.tbl CDD pfam14695 pfam14695 464267 LINES_C Lines C-terminus. This family represents the C-terminus of protein lines. In Drosophila this protein is involved in embryonic segmentation and may function as a transcriptional regulator. 37 matched cddid_all.tbl CDD pfam14696 pfam14696 434136 Glyoxalase_5 Hydroxyphenylpyruvate dioxygenase, HPPD, N-terminal. This domain is one of two barrel-shaped regions that together form the active enzyme, 4-hydroxyphenylpyruvic acid dioxygenase, EC:1.13.11.27. As can be deduced from the disposition of the various Glyoxalase families, _2, _3 and _4 in Pfam, pfam00903, pfam12681, pfam13468, pfam13669, these two regions are similar to be indicative of a gene-duplication event. At the individual sequence level slight differences in conformation have given rise to slightly different functions. In the case of UniProt:P80064, 4-hydroxyphenylpyruvic acid dioxygenase catalyzes the formation of homogentisate from 4-hydroxyphenylpyruvate, and the pyruvate part of the HPPD substrate (4-hydroxyphenylpyruvate), derived from L-tyrosine, and the O2 molecule occupy the three free coordination sites of the catalytic iron atom in the C-terminal domain. In plants and photosynthetic bacteria, the tyrosine degradation pathway is crucial because homogentisate, a tyrosine degradation product, is a precursor for the biosynthesis of photosynthetic pigments, such as quinones or tocopherols. 139 matched cddid_all.tbl CDD pfam14697 pfam14697 434137 Fer4_21 4Fe-4S dicluster domain. Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters. 59 matched cddid_all.tbl CDD pfam14698 pfam14698 464268 ASL_C2 Argininosuccinate lyase C-terminal. This domain is found at the C-terminus of argininosuccinate lyase. 68 matched cddid_all.tbl CDD pfam14699 pfam14699 464269 hGDE_N N-terminal domain from the human glycogen debranching enzyme. This domain is found on the very N-terminal of eukaryotic variants of the glycogen debranching enzyme (GDE), where it is immediately followed by the aldolase-like domain. The eukaryotic GDE performs two functions: 4-alpha-D-glucanotransferase, EC:2.4.1.25, and Amylo-alpha-1,6-glucosidase, EC:3.2.1.33, performed by the, respectively N- and C- terminal halves of eukaryotic GDE enzyme. The domain is involved in the glucosyltransferase activity, probably as a substrate-binding module (by analogy with other glucosyltransferases). 88 matched cddid_all.tbl CDD pfam14700 pfam14700 464270 RPOL_N DNA-directed RNA polymerase N-terminal. This is the N-terminal domain of DNA-directed RNA polymerase. This domain has a role in interaction with regions of upstream promoter DNA and the nascent RNA chain, leading to the processivity of the enzyme. In order to make mRNA transcripts the RNA polymerase undergoes a transition from the initiation phase (which only makes short fragments of RNA) to an elongation phase. This domain undergoes a structural change in the transition from initiation to elongation phase. The structural change results in abolition of the promoter binding site, creation of a channel accommodating the heteroduplex in the active site and formation of an exit tunnel which the RNA transcript passes through after peeling off the heteroduplex. 286 matched cddid_all.tbl CDD pfam14701 pfam14701 434141 hDGE_amylase Glycogen debranching enzyme, glucanotransferase domain. This is a glucanotransferase catalytic domain of the eukaryotic variant of the glycogen debranching enzyme (GDE). The eukaryotic GDEs performs two functions: 4-alpha-D-glucanotransferase, EC:2.4.1.25, and Amylo-alpha-1,6-glucosidase, EC:3.2.1.33, performed by the, respectively N- and C- terminal halves of eukaryotic GDE enzymes. The domain is a catalytic domain responsible for the glucanotransferase function. It belongs to the alpha-amylase clan and is predicted to have a structure of a 8-stranded alpha/beta barrel (TIM barrel) where strands are interrupted by long loops and additional mini-domains. In most other amylases, the catalytic domain is followed by a beta- barrel substrate binding domain, but presence of such a domain cannot be verified in the human (and other eukaryotic) GDE enzymes. 439 matched cddid_all.tbl CDD pfam14702 pfam14702 464271 hGDE_central Central domain of human glycogen debranching enzyme. This is a central domain of the eukaryotic variant of the glycogen debranching enzyme (GDE). The eukaryotic GDE performs two functions: 4-alpha-D-glucanotransferase, EC:2.4.1.25, and Amylo-alpha-1,6-glucosidase, EC:3.2.1.33, performed by the, respectively N- and C- terminal halves of eukaryotic GDE enzyme This central domain follows the glucanotransferase domain and precedes the glucosidase (GDE_N) domain. It is very likely that the current definition contains two or more domains, by analogy with bacterial GDEs, this domain should be involved in substrate- binding either for the N-terminal glucanotransferase and/or the the C-terminal glucosidase (or both). 242 matched cddid_all.tbl CDD pfam14703 pfam14703 464272 PHM7_cyt Cytosolic domain of 10TM putative phosphate transporter. PHM7_cyt is the predicted cytosolic domain of integral membrane proteins, such as yeast PHM7 and TM63A_HUMAN TRANSMEMBRANE PROTEIN 63A, SwissProt:O94886. This domain usually precedes the 7TM region, pfam02714, and follows a RSN1_TM, pfam13967. Fold recognition programs consistently and with high significance predict this domain to be distantly homologous to RNA binding proteins from the RRM clan. 164 matched cddid_all.tbl CDD pfam14704 pfam14704 464273 DERM Dermatopontin. Members of this family mediate cell adhesion via cell surface integrin binding. They also induce haemagglutination and aggregation of amebocytes. 151 matched cddid_all.tbl CDD pfam14705 pfam14705 464274 Costars Costars. This domain is found both alone and at the C-terminus of actin-binding Rho-activating protein (ABRA). It binds to actin, and in muscle regulates the actin cytoskeleton and cell motility. It has a winged helix-like fold consisting of three alpha-helices and four antiparallel beta strands. Unlike typical winged helix proteins it does not bind to DNA, but contains a hydrophobic groove which may be responsible for interaction with other proteins. 76 matched cddid_all.tbl CDD pfam14706 pfam14706 434146 Tnp_DNA_bind Transposase DNA-binding. This domain occurs at the C-terminus of transposases including E. coli tnpA. TnpA encodes a transposase and an inhibitor protein, the inhibitor only differs from the transposase by the absence of the N-terminal 55 amino acids, which includes most of this domain. This domain consists of alpha helices and turns, and functions as a DNA-binding domain. 57 matched cddid_all.tbl CDD pfam14707 pfam14707 405407 Sulfatase_C C-terminal region of aryl-sulfatase. 122 matched cddid_all.tbl CDD pfam14709 pfam14709 405408 DND1_DSRM double strand RNA binding domain from DEAD END PROTEIN 1. A C-terminal domain in human dead end protein 1 (DND1_HUMAN) homologous to double strand RNA binding domains (PF00035, PF00333) 80 matched cddid_all.tbl CDD pfam14710 pfam14710 434147 Nitr_red_alph_N Respiratory nitrate reductase alpha N-terminal. This is the N-terminal tail of the respiratory nitrate reductase alpha chain. The nitrate reductase complex is a dimer of heterotrimers each consisting of an alpha, beta and gamma chain. The N-terminal tail of the alpha chain interacts with the beta chain and contributes to the stability of the heterotrimer. 37 matched cddid_all.tbl CDD pfam14711 pfam14711 434148 Nitr_red_bet_C Respiratory nitrate reductase beta C-terminal. This domain occurs near the C-terminus of the respiratory nitrate reductase beta chain. The nitrate reductase complex is a dimer of heterotrimers each consisting of an alpha, beta and gamma chain. This domain plays a role in the interactions between subunits and shielding of the Fe-S clusters 81 matched cddid_all.tbl CDD pfam14712 pfam14712 464275 Snapin_Pallidin Snapin/Pallidin. This family of proteins includes Snapin, this protein is associated with the SNARE complex, which mediates synaptic vesicle docking and fusion. It also includes the yeast snapin-like protein SNN1, which is a part of a complex involved in endosomal cargo sorting. The family also includes pallidin, a component of a complex involved in biogenesis of lysosome-related organelles. 90 matched cddid_all.tbl CDD pfam14713 pfam14713 464276 DUF4464 Domain of unknown function (DUF4464). This family of proteins is found in eukaryotes. Proteins in this family are typically between 224 and 241 amino acids in length. There is a conserved YID sequence motif. 229 matched cddid_all.tbl CDD pfam14714 pfam14714 464277 KH_dom-like KH-domain-like of EngA bacterial GTPase enzymes, C-terminal. The KH-like domain at the C-terminus of the EngA subfamily of essential bacterial GTPases has a unique domain structure position. The two adjacent GTPase domains (GD1 and GD2), two domains of family MMR_HSR1, pfam01926, pack at either side of the C-terminal domain. This C-terminal domain resembles a KH domain but is missing the distinctive RNA recognition elements. Conserved motifs of the nucleotide binding site of GD1 are integral parts of the GD1-KH domain interface, suggesting the interactions between these two domains are directly influenced by the GTP/GDP cycling of the protein. In contrast, the GD2-KH domain interface is distal to the GDP binding site of GD2. This family has not been added to the KH clan since SCOP classifies it separately due to its missing the key KH motif/fold. 81 matched cddid_all.tbl CDD pfam14715 pfam14715 464278 FixP_N N-terminal domain of cytochrome oxidase-cbb3, FixP. This is the N-terminal domain of FixP, the cytochrome oxidase type-cbb3. the exact function is not known. 48 matched cddid_all.tbl CDD pfam14716 pfam14716 434152 HHH_8 Helix-hairpin-helix domain. 67 matched cddid_all.tbl CDD pfam14717 pfam14717 434153 DUF4465 Domain of unknown function (DUF4465). A large family of uncharacterized proteins mostly from human gut bacteroides, but also some environmental and water bacteria (Planctomycetes) as well as metagenomic samples Most proteins from this family are secreted or located on the outer surface and may participate in cell-cell interactions or cell-nutrient interactions This function is supported by a solved structure of a Bacteroides ovatus homolog, which adapts a galactose binding (jelly-roll) beta barrel structure 168 matched cddid_all.tbl CDD pfam14718 pfam14718 434154 SLT_L Soluble lytic murein transglycosylase L domain. Soluble lytic murein transglycosylase (SLT) consists of three domains, an N-terminal U domain, an L domain (linker domain) and a C-terminal domain (C). The L domain may be involved in the interaction of the enzyme with peptidoglycan. 68 matched cddid_all.tbl CDD pfam14719 pfam14719 405418 PID_2 Phosphotyrosine interaction domain (PTB/PID). 184 matched cddid_all.tbl CDD pfam14720 pfam14720 434155 NiFe_hyd_SSU_C NiFe/NiFeSe hydrogenase small subunit C-terminal. This domain is found at the C-terminus of hydrogenase small subunits including periplasmic [NiFeSe] hydrogenase small subunit, uptake hydrogenase small subunit and periplasmic [NiFe] hydrogenase small subunit. This C-terminal domain binds two of the three iron-sulfur clusters in this enzyme. 79 matched cddid_all.tbl CDD pfam14721 pfam14721 464279 AIF_C Apoptosis-inducing factor, mitochondrion-associated, C-term. This C-terminal domain appears to be a dimerization domain of the mitochondrial apoptosis-inducing factor 1. protein. The domain also appears at the C-terminus of FAD-dependent pyridine nucleotide-disulfide oxidoreductases. Apoptosis inducing factor (AIF) is a bifunctional mitochondrial flavoprotein critical for energy metabolism and induction of caspase-independent apoptosis. On reduction with NADH, AIF undergoes dimerization and forms tight, long-lived FADH2-NAD charge-transfer complexes proposed to be functionally important. 130 matched cddid_all.tbl CDD pfam14722 pfam14722 464280 KRAP_IP3R_bind Ki-ras-induced actin-interacting protein-IP3R-interacting domain. This family includes the N-terminus of the actin-interacting protein sperm-specific antigen 2, or KRAP (Ki-ras-induced actin-interacting protein). This region is found to be the residues that interact with inositol 1,4,5-trisphosphate receptor (IP3R). KRAP was first localized as a membrane-bound form with extracellular regions suggesting it might be involved in the regulation of filamentous actin and signals from the outside of the cells. It has now been shown to be critical for the proper subcellular localization and function of IP3R. Inositol 1,4,5-trisphosphate receptor functions as the Ca2+ release channel on specialized endoplasmic reticulum membranes, so the subcellular localization of IP3R is crucial for its proper function. 145 matched cddid_all.tbl CDD pfam14723 pfam14723 464281 SSFA2_C Sperm-specific antigen 2 C-terminus. This family includes the C-terminus of the actin-interacting protein sperm-specific antigen 2. 171 matched cddid_all.tbl CDD pfam14724 pfam14724 464282 mit_SMPDase Mitochondrial-associated sphingomyelin phosphodiesterase. The GO annotation for this family indicates that it is a single-pass membrane protein, and it appears to be found in mitochondrial membranes. Sphingolipids play important roles in regulating cellular responses, and although mitochondria contain sphingolipids, direct regulation of their levels in mitochondria or mitochondria-associated membranes is mostly unclear. Sphingomyelin phosphodiesterases catalyze the hydrolysis of sphingomyelin to ceramide and phosphocholine, and these metabolites are involved in signalling pathways. 816 matched cddid_all.tbl CDD pfam14725 pfam14725 434160 DUF4466 Domain of unknown function (DUF4466). 303 matched cddid_all.tbl CDD pfam14726 pfam14726 464283 RTTN_N Rotatin, an armadillo repeat protein, centriole functioning. Rotatin and its homologs such as Ana3 in Drosophila are found to be essential for centriole function. A deficiency of rotatin in mice leads to randomized heart tube looping, defects in embryonic turning, and abnormal expression of HNF3beta, lefty, and nodal. Thus it is required for left-right and axial patterning. Ana3 - the Drosophila homolog - is present in centrioles and basal bodies, is required for the structural integrity of both centrioles and basal bodies and for centriole cohesion. Rotatin also localizes to centrioles and basal bodies and appears to be essential for cilia function. This family represents the N-terminal domain. 97 matched cddid_all.tbl CDD pfam14727 pfam14727 464284 PHTB1_N PTHB1 N-terminus. This family includes the N-terminus of PTHB1 protein. This protein forms a part of the BBSome complex, which is required for ciliogenesis. 416 matched cddid_all.tbl CDD pfam14728 pfam14728 464285 PHTB1_C PTHB1 C-terminus. This family includes the C-terminus of PTHB1 protein. This protein forms a part of the BBSome complex, which is required for ciliogenesis. 376 matched cddid_all.tbl CDD pfam14729 pfam14729 291399 DUF4467 Domain of unknown function with cystatin-like fold (DUF4467). Large family of predicted lipoproteins from Gram-positive bacteria Experimentally determined structure shows a cystatitin-like fold, allowing us to classify this family in the NFT2 clan, despite lack of any detectable sequence similarity between members of this family and other families in this clan 94 matched cddid_all.tbl CDD pfam14730 pfam14730 434164 DUF4468 Domain of unknown function (DUF4468) with TBP-like fold. A large family of (predicted) secreted proteins with unknown functions from human gut and oral cavity. Typically forms a N-terminal domain with FMN binding domain at the C-terminus. Experimentaly determined 3D structure of this domain shows a variant of a TATA box binding - like fold, but no detectable sequence similarity to other proteins with this fold 89 matched cddid_all.tbl CDD pfam14731 pfam14731 291401 Staphopain_pro Staphopain proregion. This domain is the proregion of the cysteine protease staphopain. Like many papain type peptidases, staphopain is synthesized as an inactive precursor and cleavage of the proregion is required for activation. This proregion has a half-barrel or barrel-sandwich hybrid fold. The proregion blocks the active site cleft of the mature enzyme on one side of the nucleophilic cysteine 169 matched cddid_all.tbl CDD pfam14732 pfam14732 464286 UAE_UbL Ubiquitin/SUMO-activating enzyme ubiquitin-like domain. This is the C-terminal domain of ubiquitin-activating enzyme and SUMO-activating enzyme 2. It is structurally similar to ubiquitin. This domain is involved in E1-SUMO-thioester transfer to the SUMO E2 conjugating protein. 88 matched cddid_all.tbl CDD pfam14733 pfam14733 434166 ACDC AP2-coincident C-terminal. This family is found at the C-terminus of apicomplexan proteins containing the AP2 domain (pfam00847). 91 matched cddid_all.tbl CDD pfam14734 pfam14734 434167 DUF4469 Domain of unknown function (DUF4469) with IG-like fold. A C-terminal domain in a large family of (predicted) secreted proteins with uknown functions from human gut bacteroides 101 matched cddid_all.tbl CDD pfam14735 pfam14735 464287 HAUS4 HAUS augmin-like complex subunit 4. This family includes HAUS augmin-like complex subunit 4. The HAUS augmin-like complex contributes to mitotic spindle assembly, maintenance of chromosome integrity and completion of cytokinesis. 235 matched cddid_all.tbl CDD pfam14736 pfam14736 464288 N_Asn_amidohyd Protein N-terminal asparagine amidohydrolase. This family of enzymes catalyze the deamindation of N-terminal asparagines in peptides and proteins to aspartic acid. 270 matched cddid_all.tbl CDD pfam14737 pfam14737 464289 DUF4470 Domain of unknown function (DUF4470). This family is conserved from fungi to Metazoa and includes plants. The function is not known, but several members have zinc-finger domain, zf-MYND, pfam01753, at their very C-terminus. Others are also associated with DUF1279, pfam06916. 97 matched cddid_all.tbl CDD pfam14738 pfam14738 464290 CFAP91 Cilia- and flagella-associated protein 91. This entry represents a domain found in the CFAP91 protein. CFAP91 (also known as AMY-1-associating protein expressed in testis 1 or AAT-1) is a component of a spoke-associated complex, regulates flagellar dynein activity by mediating regulatory signals between the radial spokes and dynein arms. It binds to AMY1 and may play a role in spermatogenesis. 153 matched cddid_all.tbl CDD pfam14739 pfam14739 464291 DUF4472 Domain of unknown function (DUF4472). This family is specific to the Chordates. Some members also carry Kinesin-motor domains at their N-terminus, Kinesin, pfam00225. 107 matched cddid_all.tbl CDD pfam14740 pfam14740 464292 DUF4471 Domain of unknown function (DUF4471). This family is conserved from fungi to Metazoa and includes plants. The function is not known, but several members have zinc-finger domain, zf-MYND, pfam01753, at their very C-terminus. Others are also associated with DUF1279, pfam06916. This domain is more C-terminal in many members to DUF4470, pfam14737. 303 matched cddid_all.tbl CDD pfam14741 pfam14741 434174 GH114_assoc N-terminal glycosyl-hydrolase-114-associated domain. This short domain is also a very small family found at the N-terminus of GH114, glycosyl-hydrolases. 127 matched cddid_all.tbl CDD pfam14742 pfam14742 434175 GDE_N_bis N-terminal domain of (some) glycogen debranching enzymes. This domain is found on the N-terminal of some glycogen debranching enzymes and is usually followed by the GDE_C (PF06202) and in this sense it is analogous (but probably not homologous) to the GDE_N (PF12439). Its exact function is unknown 193 matched cddid_all.tbl CDD pfam14743 pfam14743 434176 DNA_ligase_OB_2 DNA ligase OB-like domain. This domain has an OB-like fold, but does not appear to be related to pfam03120. It is found at the C-terminus of the ATP dependent DNA ligase domain pfam01068. 60 matched cddid_all.tbl CDD pfam14744 pfam14744 434177 WASH-7_mid WASH complex subunit 7. This family is the central, conserved region of proteins that form subunit 7 of the WASH complex. In species such as Drosophila this protein is the only component of the 'complex'. This complex is a nucleation promoting factor necessary for the activation of Arp2/3 that nucleates and organizes actin filaments by associating with a pre-existing filament to induce the assembly of a branching filament. WASH thus effectively nucleates actin on endosomes. 346 matched cddid_all.tbl CDD pfam14745 pfam14745 434178 WASH-4_N WASH complex subunit 4, N-terminal. This entry is the conserved N-terminal region of proteins that form subunit 4 of the WASH complex, also known as subunit 7 or KIAA1033/SWIP. In species such as Drosophila this protein is the only component of the 'complex'. This complex is present at the surface of endosomes that recruits and activates the Arp2/3 complex to induce actin polymerization. This domain comprises the WAHD1 and the TBR (tubulin-binding region) domains. 566 matched cddid_all.tbl CDD pfam14746 pfam14746 464293 WASH-7_C WASH complex subunit 7, C-terminal. This family is the conserved C-terminal region of proteins that form subunit 7 of the WASH complex. In species such as Drosophila this protein is the only component of the 'complex'. This complex is a nucleation promoting factor necessary for the activation of Arp2/3 that nucleates and organizes actin filaments by associating with a pre-existing filament to induce the assembly of a branching filament. WASH thus effectively nucleates actin on endosomes. The C-terminus is predicted to include a transmembrane region. 175 matched cddid_all.tbl CDD pfam14747 pfam14747 373266 DUF4473 Domain of unknown function (DUF4473). This short family is largely confined to Caenorhabditis proteins. The function is not known. There are two well-conserved aspartate residues. 78 matched cddid_all.tbl CDD pfam14748 pfam14748 464294 P5CR_dimer Pyrroline-5-carboxylate reductase dimerization. Pyrroline-5-carboxylate reductase consists of two domains, an N-terminal catalytic domain (pfam03807) and a C-terminal dimerization domain. This is the dimerization domain. 104 matched cddid_all.tbl CDD pfam14749 pfam14749 464295 Acyl-CoA_ox_N Acyl-coenzyme A oxidase N-terminal. Acyl-coenzyme A oxidase consists of three domains. An N-terminal alpha-helical domain, a beta sheet domain (pfam02770) and a C-terminal catalytic domain (pfam01756). This entry represents the N-terminal alpha-helical domain. 120 matched cddid_all.tbl CDD pfam14750 pfam14750 464296 INTS2 Integrator complex subunit 2. This family of proteins are subunits of the integrator complex involved in snRNA transcription and processing. 1047 matched cddid_all.tbl CDD pfam14751 pfam14751 464297 DUF4474 Domain of unknown function (DUF4474). Domain found on N-termina of few families of uncharacterized Clostridia proteins. Typically followed by a proline-rich domain or other kinds of repeats 238 matched cddid_all.tbl CDD pfam14752 pfam14752 464298 RBP_receptor Retinol binding protein receptor. Proteins in this family function as retinol binding protein receptors. 603 matched cddid_all.tbl CDD pfam14753 pfam14753 464299 FAM221 Protein FAM221A/B. This family of proteins is found in eukaryotes. Proteins in this family are typically between 99 and 305 amino acids in length. 196 matched cddid_all.tbl CDD pfam14754 pfam14754 291424 IFR3_antag Papain-like auto-proteinase. The replicase polyproteins of the Nidoviruses such as, porcine arterivirus PRRSV, equine arterivirus EAV, human coronavirus 229E, and severe acute respiratory syndrome coronavirus (SARS-CoV), are predicted to be cleaved into 14 non-structural proteins (nsps) by the nsp4 main proteinase pfam05579 and three accessory proteinases residing in nsp1-alpha, nsp1-beta and nsp2. This family is the two nsp1 proteins that together act in a papain-like way to separate off the rest of the various functional domains of the polyprotein. Once inside the host cell, this nsp1 interferes with the regulation of interferon, thereby enabling the virus to replicate. 249 matched cddid_all.tbl CDD pfam14755 pfam14755 373271 Nsp2_AV Nsp2, transmembrane domain. This domain is found in Nsp2 protein of the RNA-arteriviruses, such as porcine arterivirus PRRSV and equine arterivirus EAV, which is a tetraspanning transmembrane protein. This domain resides adjacent to the peptidase C33 catalytic domain of Nsp2. 148 matched cddid_all.tbl CDD pfam14756 pfam14756 258893 Pdase_C33_assoc Peptidase_C33-associated domain. The nsps or non-structural protein subunits of the arteriviral polyproteins such as porcine arterivirus PRRSV and equine arterivirus EAV are auto-cleaved into functional units. the function of this particular domain is not known. 147 matched cddid_all.tbl CDD pfam14757 pfam14757 373272 NSP2-B_epitope Immunogenic region of nsp2 protein of arterivirus polyprotein. This domain is in a non-essential part of the nsp2 (non-structural protein) subunit section of the arterivirus polyprotein. This domain carries seven small sequence-regions that are predicted to be potential B-cell epitopes. 272 matched cddid_all.tbl CDD pfam14758 pfam14758 373273 NSP2_assoc Non-essential region of nsp2 of arterivirus polyprotein. This non-essential region of the nsp2 subunit of the arterivirus polyprotein of such as porcine arterivirus PRRSV and equine arterivirus EAV may offer immunogenic surfaces to B-cells. It is associated with Peptidase_C33, pfam05412. 198 matched cddid_all.tbl CDD pfam14759 pfam14759 434185 Reductase_C Reductase C-terminal. This domain occurs at the C-terminus of various reductase enzymes, including putidaredoxin reductase, ferredoxin reductase, 3-phenylpropionate/cinnamic acid dioxygenase ferredoxin--NAD(+) reductase component, benzene 1,2-dioxygenase system ferredoxin--NAD(+) reductase subunit, rhodocoxin reductase, biphenyl dioxygenase system ferredoxin--NAD(+) reductase component, rubredoxin-NAD(+) reductase and toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component. In putidaredoxin reductase this domain is involved in dimerization. In the FAD-containing NADH-ferredoxin reductase (BphA4) it is responsible for interaction with the Rieske-type [2Fe-2S] ferredoxin (BphA3). 83 matched cddid_all.tbl CDD pfam14760 pfam14760 434186 Rnk_N Rnk N-terminus. This domain occurs at the N-terminus of Rnk, an RNA polymerase-interacting protein of the GreA/GreB family (pfam01272). It has a coiled coil structure. 41 matched cddid_all.tbl CDD pfam14761 pfam14761 464300 HPS3_N Hermansky-Pudlak syndrome 3. This domain is at the N-terminus of these vertebrate proteins. This region carries the clathrin-binding motif LLDFE at residues 172-176 in SwissProt:Q969F9. There is also reference to a human Mendelian disease at MIM:614072. 211 matched cddid_all.tbl CDD pfam14762 pfam14762 464301 HPS3_Mid Hermansky-Pudlak syndrome 3, middle region. This domain is downstream of the N-terminus of these vertebrate proteins. This region carries a number of tyrosine sorting motifs and one of two di-leucine sorting boxes at residues 542-548 well as a peroxisomal matrix targetting motif at residues 614-623 in SwissProt:Q969F9. There is also reference to a human Mendelian disease at MIM:614072. 385 matched cddid_all.tbl CDD pfam14763 pfam14763 464302 HPS3_C Hermansky-Pudlak syndrome 3, C-terminal. This domain is downstream of the mid domain family, pfam14762, of these vertebrate proteins. This region carries a number of tyrosine sorting motifs and the second of two di-leucine sorting boxes at residues 711-717 well as the ER membrane-retention signal KKPL at residues 1000-1003 in SwissProt:Q969F9. There is also reference to a human Mendelian disease at MIM:614072. 352 matched cddid_all.tbl CDD pfam14764 pfam14764 464303 SPG48 AP-5 complex subunit, vesicle trafficking. This family would appear to be the second of the two larger subunits of the fifth Adaptor-Protein complex, AP-5. Adaptor protein (AP) complexes facilitate the trafficking of cargo from one membrane compartment of the cell to another by recruiting other proteins to particular types of vesicles. AP-5 is involved in trafficking proteins from endosomes towards other membranous compartments. There are genetic links between AP-5 and hereditary spastic paraplegia, a group of human genetic disorders characterized by progressive spasticity in the lower limbs. 118 matched cddid_all.tbl CDD pfam14765 pfam14765 434191 PS-DH Polyketide synthase dehydratase. This is the dehydratase domain of polyketide synthases. Structural analysis shows these DH domains are double hotdogs in which the active site contains a histidine from the N-terminal hotdog and an aspartate from the C-terminal hotdog. Studies have uncovered that a substrate tunnel formed between the DH domains may be essential for loading substrates and unloading products. 296 matched cddid_all.tbl CDD pfam14766 pfam14766 464304 RPA_interact_N Replication protein A interacting N-terminal. This family of proteins represents the N-terminal domain of replication protein A (RPA) interacting protein. RPA interacting protein is involved in the import of RPA into the nucleus. The N-terminal domain is responsible for interaction with importin beta. 39 matched cddid_all.tbl CDD pfam14767 pfam14767 434193 RPA_interact_M Replication protein A interacting middle. This family of proteins represents the middle domain of replication protein A (RPA) interacting protein. RPA interacting protein is involved in the import of RPA into the nucleus. This domain is responsible for interaction with RPA. 82 matched cddid_all.tbl CDD pfam14768 pfam14768 464305 RPA_interact_C Replication protein A interacting C-terminal. This family of proteins represents the C-terminal domain of replication protein A (RPA) interacting protein. RPA interacting protein is involved in the import of RPA into the nucleus. The C-terminal domain is a putative zinc finger. 80 matched cddid_all.tbl CDD pfam14769 pfam14769 464306 CLAMP Flagellar C1a complex subunit C1a-32. This family represents one small subunit, C1a-32, of the C1a projection (the seventh projection of flagellar). Numerous studies have indicated that each of the seven projections associated with the central pair of microtubules in flagellar plays a distinct role in regulating eukaryotic ciliary/flagellar motility. The C1a projection is a complex of proteins including PF6, C1a-86, C1a-34, C1a-32, C1a-18, and calmodulin. C1a projection is involved in modulating flagellar beat frequency and this is mediated via the C1a-34, C1a-32, and C1a-18 sub-complex by modulating the activity of both the inner and outer dynein arms. 99 matched cddid_all.tbl CDD pfam14770 pfam14770 405460 TMEM18 Transmembrane protein 18. The function of this family is not known, however it is predicted to be a three-pass membrane protein. 118 matched cddid_all.tbl CDD pfam14771 pfam14771 434196 DUF4476 Domain of unknown function (DUF4476). 91 matched cddid_all.tbl CDD pfam14772 pfam14772 464307 NYD-SP28 Sperm tail. NYD-SP28 is expressed in a development-dependent manner, localized in spermatogenic cell cytoplams and human spermatozoa tail. It is post-translationally modified during sperm capacitation and ultimately contributes to the success of fertilization. 102 matched cddid_all.tbl CDD pfam14773 pfam14773 464308 VIGSSK Helicase-associated putative binding domain, C-terminal. The function of this short, serine-rich C-terminal region is not known. However, as it is frequently found at the very C-terminus of P-loop containing nucleoside triphosphate hydrolases, it might possibly be a binding domain. 62 matched cddid_all.tbl CDD pfam14774 pfam14774 434199 FAM177 FAM177 family. This family of proteins is found in eukaryotes. Proteins in this family are typically between 134 and 205 amino acids in length. 117 matched cddid_all.tbl CDD pfam14775 pfam14775 464309 NYD-SP28_assoc Sperm tail C-terminal domain. NYD-SP28 is expressed in a development-dependent manner, localized in spermatogenic cell cytoplams and human spermatozoa tail. It is post-translationally modified during sperm capacitation and ultimately contributes to the success of fertilization. This short region is found at the very C-terminus of family members of family NYD-SP28, pfam14772. 60 matched cddid_all.tbl CDD pfam14776 pfam14776 434201 UNC-79 Cation-channel complex subunit UNC-79. This family is a component of a cation-channel complex. 524 matched cddid_all.tbl CDD pfam14777 pfam14777 464310 BBIP10 Cilia BBSome complex subunit 10. The BBSome (so-named after the association with Bardet-Biedl syndrome) is a complex of 8 subunits that lies at the base of the flagellar microtubule structure. The precise function of the all the individual components in cilia formation is unclear, however they function to promote loading of cargo to the ciliary axoneme. BBIP10 localizes to the primary cilium, and is present exclusively in ciliated organizms. It is required for cytoplasmic microtubule polymerization and acetylation, two functions not shared with any other BBSome subunits. BBIP10 physically interacts with HDAC6. BBSome-bound BBIP10 may therefore function to couple acetylation of axonemal microtubules and ciliary membrane growth. The primary cilium, a slim microtubule-based organelle that projects from the surface of vertebrate cells has crucial roles in vertebrate development and human genetic diseases. Cilia are required for the response to developmental signals, and evidence is accumulating that the primary cilium is specialized for Hedgehog (Hh) signal transduction. Formation of cilia, in turn, is regulated by other signalling pathways, possibly including the planar cell polarity pathway. The connections between cilia and developmental signalling have begun to clarify the basis of human diseases associated with ciliary dysfunction. 63 matched cddid_all.tbl CDD pfam14778 pfam14778 464311 ODR4-like Odorant response abnormal 4-like. In C.elegans, odr-4 and odr-8 are required for localising a subset of odorant GPCRs to the cilia of olfactory neurons. Olfactory receptors (ORs) are synthesized in endoplasmic reticulum of the olfactory neurons, trafficked to the cell surface membrane and transported to the tip of the olfactory cilium, where they bind with odorants. Various accessory proteins are required for proper targetting of different ORs to the cell membrane. ODR-4 was the first accessory protein to be described. 373 matched cddid_all.tbl CDD pfam14779 pfam14779 464312 BBS1 Ciliary BBSome complex subunit 1. The BBSome (so-named after the association with Bardet-Biedl syndrome) is a complex of 8 subunits that lies at the base of the flagellar microtubule structure. The precise function of the all the individual components in cilia formation is unclear, however they function to promote loading of cargo to the ciliary axoneme. The primary cilium, a slim microtubule-based organelle that projects from the surface of vertebrate cells has crucial roles in vertebrate development and human genetic diseases. Cilia are required for the response to developmental signals, and evidence is accumulating that the primary cilium is specialized for Hedgehog (Hh) signal transduction. Formation of cilia, in turn, is regulated by other signalling pathways, possibly including the planar cell polarity pathway. The connections between cilia and developmental signalling have begun to clarify the basis of human diseases associated with ciliary dysfunction. BBS1 predominantly localizes to the basal body and or transitional zone of ciliated cells. It has been found in a heptameric complex with BBS2, BBS5, BBS7, BBS8, and BBS9, termed the BBSome. Mutations in BBS1 can lead to retinal inadequacy. 254 matched cddid_all.tbl CDD pfam14780 pfam14780 464313 DUF4477 Domain of unknown function (DUF4477). 189 matched cddid_all.tbl CDD pfam14781 pfam14781 464314 BBS2_N Ciliary BBSome complex subunit 2, N-terminal. The BBSome (so-named after the association with Bardet-Biedl syndrome) is a complex of 8 subunits that lies at the base of the flagellar microtubule structure. The precise function of the all the individual components in cilia formation is unclear, however they function to promote loading of cargo to the ciliary axoneme. The primary cilium, a slim microtubule-based organelle that projects from the surface of vertebrate cells has crucial roles in vertebrate development and human genetic diseases. Cilia are required for the response to developmental signals, and evidence is accumulating that the primary cilium is specialized for Hedgehog (Hh) signal transduction. Formation of cilia, in turn, is regulated by other signalling pathways, possibly including the planar cell polarity pathway. The connections between cilia and developmental signalling have begun to clarify the basis of human diseases associated with ciliary dysfunction. BBS2 is one of the three Bardet-Biedl syndrome subunits that is required for leptin receptor signalling in the hypothalamus, and BBS2 and 4 are also required for the localization of somatostatin receptor 3 and melanin-concentrating hormone receptor 1 into neuronal cilia. 107 matched cddid_all.tbl CDD pfam14782 pfam14782 464315 BBS2_C Ciliary BBSome complex subunit 2, C-terminal. The BBSome (so-named after the association with Bardet-Biedl syndrome) is a complex of 8 subunits that lies at the base of the flagellar microtubule structure. The precise function of the all the individual components in cilia formation is unclear, however they function to promote loading of cargo to the ciliary axoneme. The primary cilium, a slim microtubule-based organelle that projects from the surface of vertebrate cells has crucial roles in vertebrate development and human genetic diseases. Cilia are required for the response to developmental signals, and evidence is accumulating that the primary cilium is specialized for Hedgehog (Hh) signal transduction. Formation of cilia, in turn, is regulated by other signalling pathways, possibly including the planar cell polarity pathway. The connections between cilia and developmental signalling have begun to clarify the basis of human diseases associated with ciliary dysfunction. BBS2 is one of the three Bardet-Biedl syndrome subunits that is required for leptin receptor signalling in the hypothalamus, and BBS2 and 4 are also required for the localization of somatostatin receptor 3 and melanin-concentrating hormone receptor 1 into neuronal cilia. 430 matched cddid_all.tbl CDD pfam14783 pfam14783 405473 BBS2_Mid Ciliary BBSome complex subunit 2, middle region. The BBSome (so-named after the association with Bardet-Biedl syndrome) is a complex of 8 subunits that lies at the base of the flagellar microtubule structure. The precise function of the all the individual components in cilia formation is unclear, however they function to promote loading of cargo to the ciliary axoneme. The primary cilium, a slim microtubule-based organelle that projects from the surface of vertebrate cells has crucial roles in vertebrate development and human genetic diseases. Cilia are required for the response to developmental signals, and evidence is accumulating that the primary cilium is specialized for Hedgehog (Hh) signal transduction. Formation of cilia, in turn, is regulated by other signalling pathways, possibly including the planar cell polarity pathway. The connections between cilia and developmental signalling have begun to clarify the basis of human diseases associated with ciliary dysfunction. BBS2 is one of the three Bardet-Biedl syndrome subunits that is required for leptin receptor signalling in the hypothalamus, and BBS2 and 4 are also required for the localization of somatostatin receptor 3 and melanin-concentrating hormone receptor 1 into neuronal cilia. 108 matched cddid_all.tbl CDD pfam14784 pfam14784 464316 ECSIT_C C-terminal domain of the ECSIT protein. This family represents the C-terminal domain of the evolutionarily conserved signaling intermediate in Toll pathway protein, an adapter protein of the Toll-like and IL-1 receptor signaling pathway, which is involved in the activation of NF-kappa-B via MAP3K1. This domain is missing in isoform 2. Fold recognition suggests that this domain may be distantly homologous to the pleckstrin homology domain 131 matched cddid_all.tbl CDD pfam14785 pfam14785 434209 MalF_P2 Maltose transport system permease protein MalF P2 domain. This is the second periplasmic domain (P2 domain) of the maltose transport system permease protein MalF. 164 matched cddid_all.tbl CDD pfam14786 pfam14786 434210 Death_2 Tube Death domain. This Tube-Death domain has an insertion between helices 2 and 3, and a C-terminal tail compared with the Death domain of Pelle proteins in Drosophila. The two N-terminal Death domains of the serine/threonine kinase Pelle and the adaptor protein Tube interact to form a six-helix bundle fold arranged in an open-ended linear array with plastic interfaces mediating their interactions. This interaction leads to the nuclear translocation of the transcription factor Dorsal and activation of zygotic patterning genes during Drosophila embryogenesis, and is assisted by the significant and indispensable contacts in the heterodimer contributed by the insertion and C-terminal tail described above. 146 matched cddid_all.tbl CDD pfam14787 pfam14787 373297 zf-CCHC_5 GAG-polyprotein viral zinc-finger. 36 matched cddid_all.tbl CDD pfam14788 pfam14788 405477 EF-hand_10 EF hand. 50 matched cddid_all.tbl CDD pfam14789 pfam14789 434211 THDPS_M Tetrahydrodipicolinate N-succinyltransferase middle. This is the middle domain of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase. 41 matched cddid_all.tbl CDD pfam14790 pfam14790 339376 THDPS_N Tetrahydrodipicolinate N-succinyltransferase N-terminal. This is the N-terminal domain of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase. 167 matched cddid_all.tbl CDD pfam14791 pfam14791 464317 DNA_pol_B_thumb DNA polymerase beta thumb. The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the thumb domain. 63 matched cddid_all.tbl CDD pfam14792 pfam14792 464318 DNA_pol_B_palm DNA polymerase beta palm. The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain. 110 matched cddid_all.tbl CDD pfam14793 pfam14793 434214 DUF4478 Pyrimidine/purine nucleotide 5'-monophosphate nucleosidases. This is an N-terminal domain found in pyrimidine/purine nucleotide 5'-monophosphate nucleosidases (PpnN) in bacteria. PpnN catalyzes the hydrolysis of the N-glycosidic bond of diverse pyrimidine and purine nucleotide 5'-monophosphates, to form ribose 5-phosphate and the corresponding free base. It can use AMP, GMP, IMP, CMP, dTMP and UMP as substrates. It is found in association with pfam03641 and pfam11892. 109 matched cddid_all.tbl CDD pfam14794 pfam14794 434215 DUF4479 Domain of unknown function (DUF4479). This domain family is found in bacteria, and is approximately 70 amino acids in length. The family is found in association with pfam01588. 71 matched cddid_all.tbl CDD pfam14795 pfam14795 434216 Leucyl-specific Leucine-tRNA synthetase-specific domain. This short region is found only in leucyl-tRNA synthetases. It is flexibly linked to the enzyme-core by beta-ribbons structures 56 matched cddid_all.tbl CDD pfam14796 pfam14796 464319 AP3B1_C Clathrin-adaptor complex-3 beta-1 subunit C-terminal. This domain lies at the C-terminus of the clathrin-adaptor protein complex-3 beta-1 subunit. The AP-3 complex is associated with the Golgi region of the cell as well as with more peripheral structures. The AP-3 complex may be directly involved in trafficking to lysosomes or alternatively it may be involved in another pathway, but that mis-sorting in that pathway may indirectly lead to defects in pigment granules. 148 matched cddid_all.tbl CDD pfam14797 pfam14797 434218 SEEEED Serine-rich region of AP3B1, clathrin-adaptor complex. This short low-complexity, highly serine-rich region lies on clathrin-adaptor complex 3 beta-1 subunit proteins, between family Adaptin_N, pfam01602 and a C-terminal domain, AP3B1_C,pfam14796. 111 matched cddid_all.tbl CDD pfam14798 pfam14798 464320 Ca_hom_mod Calcium homeostasis modulator. This family of proteins control cytosolic calcium concentration. They are transmembrane proteins which may be pore-forming ion channels. 248 matched cddid_all.tbl CDD pfam14799 pfam14799 464321 FAM195 FAM195 family. 98 matched cddid_all.tbl CDD pfam14800 pfam14800 464322 DUF4481 Domain of unknown function (DUF4481). 293 matched cddid_all.tbl CDD pfam14801 pfam14801 434222 GCD14_N tRNA methyltransferase complex GCD14 subunit N-term. This is the N-terminal domain of GCD14, itself a subunit of the tRNA methyltransferase complex that is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA. The exact function of the N-terminus is not known but it is necessary for maintaining the overall folding and for full enzymatic activity. 51 matched cddid_all.tbl CDD pfam14802 pfam14802 434223 TMEM192 TMEM192 family. The function of this family of transmembrane proteins is unknown. In vertebrates, proteins in this family are located in the lysosomal membrane and late endosome. In Arabidopsis, a member of this family has been found to weakly interact with FRIGIDA, a determinant of flowering time. 235 matched cddid_all.tbl CDD pfam14803 pfam14803 464323 Nudix_N_2 Nudix N-terminal. Ths domain occurs at the N-terminus of several Nudix (Nucleoside Diphosphate linked to X) hydrolases. 32 matched cddid_all.tbl CDD pfam14804 pfam14804 464324 Jag_N Jag N-terminus. This domain is found at the N-terminus of proteins containing pfam13083 and pfam01424, including the jag proteins. 50 matched cddid_all.tbl CDD pfam14805 pfam14805 464325 THDPS_N_2 Tetrahydrodipicolinate N-succinyltransferase N-terminal. This is the N-terminal domain of 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase. 67 matched cddid_all.tbl CDD pfam14806 pfam14806 434227 Coatomer_b_Cpla Coatomer beta subunit appendage platform. This family is found at the C-terminus of the coatamer beta subunit proteins (Beta-coat proteins). It is a platform domain on the appendage that carries a highly conserved tryptophan. 128 matched cddid_all.tbl CDD pfam14807 pfam14807 464326 AP4E_app_platf Adaptin AP4 complex epsilon appendage platform. This domain is found at the C terminal of clathrin-adaptor epsilon subunit, and at the C-terminus of the appendage on the platform domain. 100 matched cddid_all.tbl CDD pfam14808 pfam14808 464327 TMEM164 TMEM164 family. This family of proteins is found in eukaryotes. Proteins in this family are typically between 214 and 330 amino acids in length. There are two conserved sequence motifs: LNPCH and DPF. 250 matched cddid_all.tbl CDD pfam14809 pfam14809 373310 TGT_C1 C1 domain of tRNA-guanine transglycosylase dimerization. This short region of the tRNA-guanine transglycosylase enzyme acts as the dimerization domain of the whole protein. 70 matched cddid_all.tbl CDD pfam14810 pfam14810 434230 TGT_C2 Patch-forming domain C2 of tRNA-guanine transglycosylase. Domain C2 of tRNA-guanine transglycosylase is formed by a four-stranded anti-parallel beta-sheet lined with two alpha helices. It has conserved basic residues on the surface of the beta-sheets as does the C-terminal domain PUA, pfam01472. The catalytic domain, TGT has conserved basic residues on the outer surface of the N-terminal three-stranded beta sheet, which closes the barrel, and it is postulated that these basic residues from the three domains form a continuous, positively charged patch to which the tRNA binds. 70 matched cddid_all.tbl CDD pfam14811 pfam14811 464328 TPD Protein of unknown function TPD sequence-motif. This is a family of eukaryotic proteins of unknown function. A few members have an associated zinc-finger domain. All members carry a highly conserved TPD sequence-motif. 138 matched cddid_all.tbl CDD pfam14812 pfam14812 434232 PBP1_TM Transmembrane domain of transglycosylase PBP1 at N-terminal. This is the N-terminal, transmembrane, domain of the transglycosylases ()penicillin-binding proteins), the multi-domain membrane proteins essential for cell wall synthesis that are targeted by penicillin antibiotics. The TM domain is a single helix, several of whose residues lie in close proximity to hydrophobic residues in the TGT domain. The TM helix seems to be necessary for stabilizing the protein-membrane interaction, and the resulting orientation limits the interaction between PBPb1 and lipid II in the membrane in a 2D lateral diffusion fashion. 85 matched cddid_all.tbl CDD pfam14813 pfam14813 464329 NADH_B2 NADH dehydrogenase 1 beta subcomplex subunit 2. This family represents an accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. 69 matched cddid_all.tbl CDD pfam14814 pfam14814 434234 UB2H Bifunctional transglycosylase second domain. UB2H is the second domain of the transglycosylases, or penicillin-binding proteins PBP1bs)), the multi-domain membrane proteins essential for cell wall synthesis that are targeted by penicillin antibiotics. The exact function of the UB2H domain is uncertain, but it may act as the binding component of PBP1b with different binding partners, or it may participate in the regulation between DNA repair and/or synthesis and cell wall formation during the bacterial cell cycle. 85 matched cddid_all.tbl CDD pfam14815 pfam14815 464330 NUDIX_4 NUDIX domain. 114 matched cddid_all.tbl CDD pfam14816 pfam14816 464331 CANIN Coiled-coil and Nse Interacting (CANIN) domain. This domain is found at the C-terminal of the SMC5-SMC6 complex localization factor 2 (SFL2, also known as NSE6 and FAM178A)) which bridges the interaction between SMC6 and SFL1 (NSE5), being responsible for targeting the SMC5/6 complex to double-strand DNA breaks (DSBs) repair sites. It is suggested to be a regulatory element in SMC5/6 complex dynamics by locking its coiled-coiled arms together, thus being named as Coiled-coil And Nse INteracting (CANIN) domain. This domain is essential for the interaction with NSE5. It forms a U-shaped structure that seems to be structurally conserved in eukaryotes. 375 matched cddid_all.tbl CDD pfam14817 pfam14817 464332 HAUS5 HAUS augmin-like complex subunit 5. This family includes HAUS augmin-like complex subunit 5. The HAUS augmin-like complex contributes to mitotic spindle assembly, maintenance of chromosome integrity and completion of cytokinesis. 643 matched cddid_all.tbl CDD pfam14818 pfam14818 464333 DUF4482 Domain of unknown function (DUF4482). This family is found in eukaryotes, and is approximately 140 amino acids in length. The family is found in association with pfam11365. 138 matched cddid_all.tbl CDD pfam14819 pfam14819 464334 QueF_N Nitrile reductase, 7-cyano-7-deazaguanine-reductase N-term. The QueF monomer is made up of two ferredoxin-like domains aligned together with their beta-sheets that have additional embellishments. This subunit is composed of a three-stranded beta-sheet and two alpha-helices. QueF reduces a nitrile bond to a primary amine. The two monomer units together create suitable substrate-binding pockets. 111 matched cddid_all.tbl CDD pfam14820 pfam14820 434240 SPRR2 Small proline-rich 2. This family of small proteins is rich in proline, cysteine and glutamate. They contain a tandemly repeated nonamer, PKCPEPCPP. They are components of the cornified envelope of keratinocytes. 68 matched cddid_all.tbl CDD pfam14821 pfam14821 464335 Thr_synth_N Threonine synthase N terminus. This domain is found at the N-terminus of many threonine synthase enzymes. 79 matched cddid_all.tbl CDD pfam14822 pfam14822 434242 Vasohibin Vasohibin. This family of proteins function as angiogenesis inhibitors in animals. Reversible detyrosination of alpha-tubulin is crucial to microtubule dynamics and functions and defects have been implicated in cancer, brain disorganization, and cardiomyopathies. VASH1 and its homolog VASH2, when complexed with SVBP, exhibited robust and specific Tyr/Phe carboxypeptidase activity on microtubules. 245 matched cddid_all.tbl CDD pfam14823 pfam14823 434243 Sirohm_synth_C Sirohaem biosynthesis protein C-terminal. This domain is the C-terminus of a multifunctional enzyme which catalyzes the biosynthesis of sirohaem. Both of the catalytic activities of this enzyme (precorrin-2 dehydrogenase EC:1.3.1.76) and sirohydrochlorin ferrochelatase (EC:4.99.1.4) are located in the N-terminal domain of this enzyme, pfam13241. 66 matched cddid_all.tbl CDD pfam14824 pfam14824 464336 Sirohm_synth_M Sirohaem biosynthesis protein central. This is the central domain of a multifunctional enzyme which catalyzes the biosynthesis of sirohaem. Both of the catalytic activities of this enzyme (precorrin-2 dehydrogenase EC:1.3.1.76) and sirohydrochlorin ferrochelatase (EC:4.99.1.4) are located in the N-terminal domain of this enzyme, pfam13241. 25 matched cddid_all.tbl CDD pfam14825 pfam14825 464337 CFAP77 Cilia- and flagella-associated protein 77. This family of proteins is found in flagella. Proteins in this family are typically between 203 and 326 amino acids in length. There is a single completely conserved residue N that may be functionally important. 157 matched cddid_all.tbl CDD pfam14826 pfam14826 464338 FACT-Spt16_Nlob FACT complex subunit SPT16 N-terminal lobe domain. The FACT or facilitator of chromatin transcription complex binds to and alters the properties of nucleosomes. This family represents the N-terminal lobe of the NTD, or N-terminal domain, and acts as a protein-protein interaction domain presumably with partners outside of the FACT complex. Knockout of the whole NTD domain, 1-450 residues in UniProt:P32558, in yeast serves to tender the cells sensitive to DNA replication stress but is not lethal. The C-terminal half of NTD is structurally similar to aminopeptidases, and the most highly conserved surface residues line a cleft equivalent to the aminopeptidase substrate-binding site, family peptidase_M24, pfam00557. 160 matched cddid_all.tbl CDD pfam14827 pfam14827 464339 dCache_3 Double sensory domain of two-component sensor kinase. Cache_3 is the periplasmic sensor domains of sensor histidine kinase of E. coli DcuS. This domain forms one of the components of the two-component signalling system that allows bacteria to adapt to changing environments. The ability of bacteria to monitor and adapt to their environment is crucial to their survival, and two-component signal transduction systems mediate most of these adaptive responses. One component is a histidine kinase sensor - this domain - most commonly part of a homodimeric transmembrane sensor protein, and the second component is a cytoplasmic response regulator. The two components interact in tandem through a phospho-transfer cascade. 235 matched cddid_all.tbl CDD pfam14828 pfam14828 464340 Amnionless Amnionless. The amnionless protein forms a complex with cubilin. This complex is necessary for vitamin B12 uptake. 449 matched cddid_all.tbl CDD pfam14829 pfam14829 373324 GPAT_N Glycerol-3-phosphate acyltransferase N-terminal. GPAT_N is the N-terminal domain of glycerol-3-phosphate acyltransferases, and it forms a four-helix bundle. Glycerol-3-phosphate (1)-acyltransferase(G3PAT) catalyzes the incorporation of an acyl group from either acyl-acyl carrier proteins or acyl-CoAs into the sn-1 position of glycerol 3-phosphate to yield 1-acylglycerol-3-phosphate. G3PATs can either be selective, preferentially using the unsaturated fatty acid, oleate (C18:1), as the acyl donor, or non-selective, using either oleate or the saturated fatty acid, palmitate (C16:0), at comparable rates. The differential substrate-specificity for saturated versus unsaturated fatty acids seen within this enzyme family has been implicated in the sensitivity of plants to chilling temperatures. The exact function of this domain is not known. it lies upstream of family Acyltransferase, pfam01553. 76 matched cddid_all.tbl CDD pfam14830 pfam14830 434249 Haemocyan_bet_s Haemocyanin beta-sandwich. This antiparallel beta sandwich domain occurs in mollusc haemocyanins. Each mollusc haemocyanin contains several globular oxygen binding functional units. Each unit consists of an alpha-helical copper binding domain (pfam00264) and an antiparallel beta sandwich domain. 103 matched cddid_all.tbl CDD pfam14831 pfam14831 434250 DUF4484 Domain of unknown function (DUF4484). This domain is found, in a few members, a the the C-terminus of family Avl9, pfam09794. The function is not known. 184 matched cddid_all.tbl CDD pfam14832 pfam14832 434251 Tautomerase_3 Putative oxalocrotonate tautomerase enzyme. 4-oxalocrotonate tautomerase enzyme is involved in the anthranilate synthase pathway.1 136 matched cddid_all.tbl CDD pfam14833 pfam14833 434252 NAD_binding_11 NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase. 3-Hydroxyisobutyrate is a central metabolite in the valine catabolic pathway, and is reversibly oxidized to methylmalonate semi-aldehyde by a specific dehydrogenase belonging to the 3-hydroxyacid dehydrogenase family. The reaction is NADP-dependent and this region of the enzyme binds NAD. The NAD-binding domain of 6-phosphogluconate dehydrogenase adopts an alpha helical structure. 122 matched cddid_all.tbl CDD pfam14834 pfam14834 405516 GST_C_4 Glutathione S-transferase, C-terminal domain. GST conjugates reduced glutathione to a variety of targets including S-crystallin from squid, the eukaryotic elongation factor 1-gamma, the HSP26 family of stress-related proteins and auxin-regulated proteins in plants. Stringent starvation proteins in E. coli are also included in the alignment but are not known to have GST activity. The glutathione molecule binds in a cleft between N and C-terminal domains. The catalytically important residues are proposed to reside in the N-terminal domain. 117 matched cddid_all.tbl CDD pfam14835 pfam14835 434253 zf-RING_6 zf-RING of BARD1-type protein. The RING domain of the breast and ovarian cancer tumour-suppressor BRCA1 interacts with multiple cognate proteins, including the RING protein BARD1. Proper function of the BRCA1 RING domain is critical, as evidenced by the many cancer-predisposing mutations found within this domain. A dimer is formed between the RING domains of BRCA1 and BARD1. The BRCA1-BARD1 structure provides a model for its ubiquitin ligase activity, illustrates how the BRCA1 RING domain can be involved in associations with multiple protein partners and provides a framework for understanding cancer-causing mutations at the molecular level. The corresponding BRCA1-RING domain is on family zf-C3HC4_2, pfam13923. 65 matched cddid_all.tbl CDD pfam14836 pfam14836 405518 Ubiquitin_3 Ubiquitin-like domain. This ubiquitin-like domain is found in several ubiquitin carboxyl-terminal hydrolases and in gametogenetin-binding protein. 88 matched cddid_all.tbl CDD pfam14837 pfam14837 464341 INTS5_N Integrator complex subunit 5 N-terminus. This family of proteins represents the N-terminus of subunit 5 of the integrator complex involved in snRNA transcription and processing. 207 matched cddid_all.tbl CDD pfam14838 pfam14838 464342 INTS5_C Integrator complex subunit 5 C-terminus. This family of proteins represents the C-terminus of subunit 5 of the integrator complex involved in snRNA transcription and processing. 688 matched cddid_all.tbl CDD pfam14839 pfam14839 464343 DOR DOR family. This family of proteins regulate autophagy and gene transcription. 215 matched cddid_all.tbl CDD pfam14840 pfam14840 405522 DNA_pol3_delt_C Processivity clamp loader gamma complex DNA pol III C-term. This domain lies at the C-terminus of the delta subunit of the DNA polymerase III clamp loader gamma complex. Within the complex the several C-terminal domains, of gamma, delta and delta' form a helical scaffold, on which the rest of he subunits are hung. The gamma complex, an AAA+ ATPase, is the bacterial homolog of the eukaryotic replication factor C that loads the sliding clamp (beta, homologous to PCNA) onto DNA. 125 matched cddid_all.tbl CDD pfam14841 pfam14841 434257 FliG_M FliG middle domain. This is the middle domain of the flagellar rotor protein FliG. 76 matched cddid_all.tbl CDD pfam14842 pfam14842 434258 FliG_N FliG N-terminal domain. This is the N-terminal domain of the flagellar rotor protein FliG. 101 matched cddid_all.tbl CDD pfam14843 pfam14843 464344 GF_recep_IV Growth factor receptor domain IV. This is the fourth extracellular domain of receptor tyrosine protein kinases. Interaction between this domain and the furin-like domain (pfam00757) regulates the binding of ligands to the receptor L domains (pfam01030). 132 matched cddid_all.tbl CDD pfam14844 pfam14844 434260 PH_BEACH PH domain associated with Beige/BEACH. This PH domain is found in proteins containing the Beige/BEACH domain (pfam02138), it immediately precedes the Beige/BEACH domain. 99 matched cddid_all.tbl CDD pfam14845 pfam14845 434261 Glycohydro_20b2 beta-acetyl hexosaminidase like. 134 matched cddid_all.tbl CDD pfam14846 pfam14846 464345 DUF4485 Domain of unknown function (DUF4485). This family is found in eukaryotes, and is approximately 90 amino acids in length. 83 matched cddid_all.tbl CDD pfam14847 pfam14847 434263 Ras_bdg_2 Ras-binding domain of Byr2. This domain is the binding/interacting region of several protein kinases, such as the Schizosaccharomyces pombe Byr2. Byr2 is a Ser/Thr-specific protein kinase acting as mediator of signals for sexual differentiation in S. pombe by initiating a MAPK module, which is a highly conserved element in eukaryotes. Byr2 is activated by interacting with Ras, which then translocates the molecule to the plasma membrane. Ras proteins are key elements in intracellular signaling and are involved in a variety of vital processes such as DNA transcription, growth control, and differentiation. They function like molecular switches cycling between GTP-bound 'on' and GDP-bound 'off' states. 95 matched cddid_all.tbl CDD pfam14848 pfam14848 434264 HU-DNA_bdg DNA-binding domain. 123 matched cddid_all.tbl CDD pfam14849 pfam14849 464346 YidC_periplas YidC periplasmic domain. This is the periplasmic domain of YidC, a bacterial membrane protein which is required for the insertion and assembly of inner membrane proteins. 266 matched cddid_all.tbl CDD pfam14850 pfam14850 434266 Pro_dh-DNA_bdg DNA-binding domain of Proline dehydrogenase. This domain lies at the N-terminus of bifunctional proline-dehydrogenases and is found to bind DNA. 112 matched cddid_all.tbl CDD pfam14851 pfam14851 464347 FAM176 FAM176 family. Members of the FAM176 family regulate autophagy and apoptosis. 145 matched cddid_all.tbl CDD pfam14852 pfam14852 464348 Fis1_TPR_N Fis1 N-terminal tetratricopeptide repeat. The mitochondrial fission protein Fis1 consists of two tetratricopeptide repeats. This domain is the N-terminal tetratricopeptide repeat 33 matched cddid_all.tbl CDD pfam14853 pfam14853 434269 Fis1_TPR_C Fis1 C-terminal tetratricopeptide repeat. The mitochondrial fission protein Fis1 consists of two tetratricopeptide repeats. This domain is the C-terminal tetratricopeptide repeat 53 matched cddid_all.tbl CDD pfam14854 pfam14854 434270 LURAP Leucine rich adaptor protein. This family of proteins activate the canonical NF-kappa-B pathway, promote proinflammatory cytokine production and promote the antigen presenting and priming functions of dendritic cells. 117 matched cddid_all.tbl CDD pfam14855 pfam14855 405535 PapJ Pilus-assembly fibrillin subunit, chaperone. PapJ is part of the Pap pilus assembly complex that plays an auxiliary role by ensuring the proper integration of PapA into the fimbrial shaft. PapA is the major shaft protein of the pilus. 187 matched cddid_all.tbl CDD pfam14856 pfam14856 434271 Hce2 Pathogen effector; putative necrosis-inducing factor. The domain corresponds to the mature part of the Ecp2 effector protein from the tomato pathogen Cladopsorium fulvum. Effectors are low molecular weight proteins that are secreted by bacteria, oomycetes and fungi to manipulate their hosts and adapt to their environment. Ecp2 is a 165 amino acid secreted protein that was originally identified as a virulence factor in C. fulvum, since disruption reduces virulence of the fungus on tomato plants. We have recently determined that Ecp2 is a member of a novel, widely distributed and highly diversified within the fungal kingdom multigene superfamily, which we have designated Hce2, for Homologs of C. fulvum Ecp2 effector. Although Ecp2 is present in most organizms as a small secreted protein, the mature part of this protein can be found fused to other protein domains, including the fungal Glycoside Hydrolase family 18, Glyco_hydro_18 pfam00704 and other, unknown, protein domains. The intrinsic function of Ecp2 remains unknown but it is postulated by that it is a necrosis-inducing factor in plants that serves pathogenicity on the host. 103 matched cddid_all.tbl CDD pfam14857 pfam14857 464349 TMEM151 TMEM151 family. This family of proteins is found in eukaryotes. Proteins in this family are typically between 338 and 558 amino acids in length. 423 matched cddid_all.tbl CDD pfam14858 pfam14858 464350 CFAP54_N Cilia- and flagella-associated protein 54. This domain family is found in eukaryotes, and is typically between 542 and 565 amino acids in length. This entry represents the N-terminal region of the cilia- and flagella-associated protein 54 which is required for assembly and function of cilia and flagella. 542 matched cddid_all.tbl CDD pfam14859 pfam14859 258996 Colicin_M Colicin M. Colicin M is a toxin produced by, and active against, Escherichia coli. It catalyzes the hydrolysis of lipid I and lipid II peptidoglycan intermediates, therefore inhibiting peptidoglycan biosynthesis and leading to lysis of the bacterial cells. 269 matched cddid_all.tbl CDD pfam14860 pfam14860 434274 DrrA_P4M DrrA phosphatidylinositol 4-phosphate binding domain. This domain binds to phosphatidylinositol 4-phosphate. It is found in Legionella pneumophila DrrA, a protein involved in the redirection of endoplasmic reticulum-derived vesicles to the Legionella-containing vacuoles. 103 matched cddid_all.tbl CDD pfam14861 pfam14861 405540 Antimicrobial21 Plant antimicrobial peptide. This family includes plant antimicrobial peptides. They adopt an alpha-helical hairpin fold stabilized by two disulphide bonds. 30 matched cddid_all.tbl CDD pfam14862 pfam14862 373348 Defensin_big Big defensin. Big defensins are antimicrobial peptides. They consist of a hydrophobic N-terminal half, which is active against Gram-positive bacteria, and a cationic C-terminal half, which is active against Gram-negative bacteria. The C-terminal half adopts a beta-defensin-like structure. 55 matched cddid_all.tbl CDD pfam14863 pfam14863 464351 Alkyl_sulf_dimr Alkyl sulfatase dimerization. This domain is found in alkyl sulfatases such as the Pseudomonas aeruginosa SDS hydrolase, where it acts as a dimerization domain 136 matched cddid_all.tbl CDD pfam14864 pfam14864 405542 Alkyl_sulf_C Alkyl sulfatase C-terminal. This domain is found at the C-terminus of alkyl sulfatases. Together with the N-terminal catalytic domain, this domain forms a hydrophobic chute and may recruit hydrophobic substrates. 124 matched cddid_all.tbl CDD pfam14865 pfam14865 373349 Macin Macin. The macins are antimicrobial proteins. They form a disulphide-stabilized alpha-beta motif. 60 matched cddid_all.tbl CDD pfam14866 pfam14866 259003 Toxin_38 Potassium channel toxin. This family includes scorpion potassium channel toxins. 55 matched cddid_all.tbl CDD pfam14867 pfam14867 291529 Lantibiotic_a Lantibiotic alpha. Lantibiotics are two-component lanthionine-containing peptide antibiotics active on Gram-positive bacteria. 29 matched cddid_all.tbl CDD pfam14868 pfam14868 464352 DUF4487 Domain of unknown function (DUF4487). This family of proteins is found in eukaryotes. Proteins in this family are typically between 209 and 938 amino acids in length. There is a conserved WCF sequence motif. There is a single completely conserved residue W that may be functionally important. 579 matched cddid_all.tbl CDD pfam14869 pfam14869 405544 DUF4488 Domain of unknown function (DUF4488). In most members this domain covers almost the whole sequence, but a few member-sequences also carry a TonB_C domain, PF03544. This domain has a lipocalin fold. 122 matched cddid_all.tbl CDD pfam14870 pfam14870 405545 PSII_BNR Photosynthesis system II assembly factor YCF48. YCF48 is one of several assembly factors of the photosynthesis system II. The photosynthesis system II occurs in Cyanobacteria that are Gram-negative bacteria performing oxygenic photosynthesis. One of the three membranes surrounding these bacteria is the inner thylakoid membrane (TM) system that is localized within the cell and houses the large pigment-protein complexes of the photosynthetic electron transfer chain, i.e. Photosystem (PS) II, PSI, the cytochrome b6f complex, and the ATP synthase. YCF48 is necessary for efficient assembly and repair of the PSII. YCF48 is found predominantly in the thykaloid membrane. It is a BNR repeat protein. 304 matched cddid_all.tbl CDD pfam14871 pfam14871 405546 GHL6 Hypothetical glycosyl hydrolase 6. GHL6 is a family of hypothetical glycoside hydrolases. 135 matched cddid_all.tbl CDD pfam14872 pfam14872 434277 GHL5 Hypothetical glycoside hydrolase 5. GHL5 is a family of hypothetical glycoside hydrolases. 801 matched cddid_all.tbl CDD pfam14873 pfam14873 434278 BNR_assoc_N N-terminal domain of BNR-repeat neuraminidase. This domain is usually found at the N-terminus of the BNR-repeat neuraminidase protein family. 153 matched cddid_all.tbl CDD pfam14874 pfam14874 373355 PapD-like Flagellar-associated PapD-like. This domain is a putative PapD periplasmic pilus chaperone protein family. 102 matched cddid_all.tbl CDD pfam14875 pfam14875 464353 PIP49_N N-term cysteine-rich ER, FAM69. The FAM69 family of cysteine-rich type II transmembrane proteins localize to the endoplasmic reticulum (ER) in cultured cells, probably via N-terminal di-arginine motifs. These proteins carry at least 14 luminal cysteines which are conserved in all FAM69s. There are currently few indications of the involvement of FAM69 members in human diseases. It would appear that FAM69 proteins are predicted to be have a protein kinase structure and function. Analysis of three-dimensional structure models and conservation of the classic catalytic motifs of protein kinases in four of human FAM69 proteins suggests they might have retained catalytic phosphotransferase activity. An EF-hand Ca2+-binding domain, inserted within the structure of the kinase domain, suggests they function as Ca2+-dependent kinases (unpublished). 158 matched cddid_all.tbl CDD pfam14876 pfam14876 464354 RSF Respiratory growth transcriptional regulator. This is a family of transcriptional regulators that determine the transition from fermentative activity to growth on glycerol. 217 matched cddid_all.tbl CDD pfam14877 pfam14877 405550 mIF3 Mitochondrial translation initiation factor. This is a family of mitochondrial initiation factors IF3. 169 matched cddid_all.tbl CDD pfam14879 pfam14879 464355 DUF4489 Domain of unknown function (DUF4489). 142 matched cddid_all.tbl CDD pfam14880 pfam14880 434280 COX14 Cytochrome oxidase c assembly. COX14 plays an essential role in cytochrome oxidase assembly. The COX14 product is a low-molecular weight membrane protein of mitochondria, but it is not a subunit of cytochrome oxidase. Orthology-prediction methods have identified the vertebrate C12orf62 orthologues to be orthologues of the yeast COX14. 59 matched cddid_all.tbl CDD pfam14881 pfam14881 434281 Tubulin_3 Tubulin domain. This family includes the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. Misato from Drosophila and Dml1p from fungi are descendants of an ancestral tubulin-like protein, and exhibit regions with similarity to members of a GTPase family that includes eukaryotic tubulin and prokaryotic FtsZ. Dml1p and Misato have been co-opted into a role in mtDNA inheritance in yeast, and into a cell division-related mechanism in flies, respectively. Dml1p might additionally function in the partitioning of the mitochondrial organelle itself, or in the segregation of chromosomes, thereby explaining its essential requirement. This domain subject to extensive post-translational modifications. 180 matched cddid_all.tbl CDD pfam14882 pfam14882 434282 INT_rpt Integrase repeat unit. This repeat family is found on integrase proteins in up to 15 copies. The function is not known. 55 matched cddid_all.tbl CDD pfam14883 pfam14883 434283 GHL13 Hypothetical glycosyl hydrolase family 13. GHL13 is a family of hypothetical glycoside hydrolases. 325 matched cddid_all.tbl CDD pfam14884 pfam14884 464356 EFF-AFF Type I membrane glycoproteins cell-cell fusogen. EFF-AFF was first identified when EFF1 mutants were found to block cell fusion in all epidermal and vulval epithelia in the worm. However, fusion between the anchor cell and the utse syncytium that establishes a continuous uterine-vulval tube proceeds normally in eff-1 mutants and thus Aff1 was established as necessary for this and the fusion of heterologous cells in C. elegans. The transmembrane forms of FF proteins, like most viral fusogens, possess an N-terminal signal sequence followed by a long extracellular portion, a predicted transmembrane domain, and a short intracellular tail. A striking conservation in the position and number of all 16 cysteines in the extracellular portion of FF proteins from different nematode species suggests that these proteins are folded in a similar 3D structure that is essential for their fusogenic activity. C. elegans AFF-1 and EFF-1 proteins are essential for developmental cell-to-cell fusion and can merge insect cells. Thus FFs comprise an ancient family of cellular fusogens that can promote fusion when expressed on a viral particle. 471 matched cddid_all.tbl CDD pfam14885 pfam14885 434285 GHL15 Hypothetical glycosyl hydrolase family 15. GHL15 is a family of hypothetical glycoside hydrolases. 271 matched cddid_all.tbl CDD pfam14886 pfam14886 434286 FAM183 FAM183A and FAM183B related. The function of this family of metazoan sequences is not known. 107 matched cddid_all.tbl CDD pfam14887 pfam14887 434287 HMG_box_5 HMG (high mobility group) box 5. Nucleolar transcription factor/upstream binding factor contains six HMG box domains. This is the fifth HMG box domain in these proteins. This domain has lost DNA-binding ability. 84 matched cddid_all.tbl CDD pfam14888 pfam14888 434288 PBP-Tp47_c Penicillin-binding protein Tp47 domain C. Domain C is the largest domain in this unusual penicillin-binding protein PBP), Tp47. This domain is mainly characterized by an immunoglobulin fold with two opposing beta-sheets that form the typical barrel-like structure. In contrast to the classical immunoglobulin fold, however, this has an additional beta-strand inserted after strand 3. Also, the strands are connected by rather large loops. Helices are inserted between strands 2 and 3 and between strands 4 and 5. Domain C interacts with domain B via a surface that has a slightly concave, goblet-like shape. Tp47 is unusual in that it displays beta-lactamase activity, and thus it does not fit the classical structural and mechanistic paradigms for PBPs, and thus Tp47 appears to represent a new class of PBP. 159 matched cddid_all.tbl CDD pfam14889 pfam14889 434289 PBP-Tp47_a Penicillin-binding protein Tp47 domain a. This is the first domain in this unusual penicillin-binding protein PBP), Tp47 is mainly composed of beta-strands and is sequentially non-contiguous. The first three domains in Tp47 interact with each other through intimate domain-domain interfaces. Domain A contacts domain B through its N-terminal segment. Domain A also interacts tightly with domain C, Tp47 is unusual in that it displays beta-lactamase activity, and thus it does not fit the classical structural and mechanistic paradigms for PBPs, and thus Tp47 appears to represent a new class of PBP. 164 matched cddid_all.tbl CDD pfam14890 pfam14890 434290 Intein_splicing Intein splicing domain. Inteins are segments of protein which excise themselves from a precursor protein and mediate the rejoining of the remainder of the precursor (the extein). Most inteins consist of a splicing domain which is split into two segments by a homing endonuclease domain. This domain represents the splicing domain. 378 matched cddid_all.tbl CDD pfam14891 pfam14891 405561 Peptidase_M91 Effector protein. This family of proteins contains an HEXXH motif, typical of zinc metallopeptidases. The family includes the E. coli effector protein NleD, which cleaves and inactivates c-Jun N-terminal kinase (JNK). 173 matched cddid_all.tbl CDD pfam14892 pfam14892 434291 DUF4490 Domain of unknown function (DUF4490). This family of proteins is found in eukaryotes. Proteins in this family are typically between 101 and 220 amino acids in length. In mice, a member of this family whose expression is induced by p53 may play a role in DNA damage response. 99 matched cddid_all.tbl CDD pfam14893 pfam14893 464357 PNMA PNMA. The PNMA family includes paraneoplastic antigens Ma 1, 2 and 3, found in the serum of patients with paraneoplastic neurological disorders. The family also includes modulator of apoptosis 1, which has a role in death receptor-dependent apoptosis. 326 matched cddid_all.tbl CDD pfam14894 pfam14894 405564 Lsm_C Lsm C-terminal. This domain is found at the C-terminus of archaeal Lsm (like-Sm) proteins. 57 matched cddid_all.tbl CDD pfam14895 pfam14895 464358 PPPI_inhib Protein phosphatase 1 inhibitor. This family of proteins interacts with and inhibits the phosphatase activity of protein phosphatase 1 (PP1) complexes. 346 matched cddid_all.tbl CDD pfam14896 pfam14896 434294 Arabino_trans_C EmbC C-terminal domain. Arabinosyltransferase is involved in arabinogalactan (AG) biosynthesis pathway in mycobacteria. AG is a component of the macromolecular assembly of the mycolyl-AG-peptidoglycan complex of the cell wall. This enzyme has important clinical applications as it is believed to be the target of the antimycobacterial drug Ethambutol. This domain represents the C-terminal extracellular domain that is likely to bind to carbohydrate. 384 matched cddid_all.tbl CDD pfam14897 pfam14897 434295 EpsG EpsG family. This family of proteins are related to the EpsG protein from B. subtilis. These proteins are likely glycosyl transferases belonging to the membrane protein GT-C clan. 325 matched cddid_all.tbl CDD pfam14898 pfam14898 405568 DUF4491 Domain of unknown function (DUF4491). This family of proteins is found in bacteria. Proteins in this family are typically between 94 and 107 amino acids in length. There is a conserved EYY sequence motif. 90 matched cddid_all.tbl CDD pfam14899 pfam14899 434296 DUF4492 Domain of unknown function (DUF4492). This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. The function of these proteins is unknown. 63 matched cddid_all.tbl CDD pfam14900 pfam14900 464359 DUF4493 Domain of unknown function (DUF4493). This family of proteins is found in bacteria. Proteins in this family are typically between 264 and 710 amino acids in length. Many of these proteins have a lipid attachment site suggesting they are lipoproteins. 221 matched cddid_all.tbl CDD pfam14901 pfam14901 464360 Jiv90 Cleavage inducing molecular chaperone. Jiv90 is a fragment of the DnaJ protein in eukaryotes and in J-domain protein interacting with viral protein (Jiv) located in the N terminal region of the pestivirus viral polypeptide. The viral protein interacts stably with non structural (NS) protein NS2, causing a conformational change in NS2-NS3 and stimulates NS2-NS3 cleavage in trans. Cleavage of NS2-NS3 increases cytopathogenicity and consequently aids viral replication. Jiv therefore acts as a regulating cofactor for NS2 auto-protease. The efficient release of NS3 from the viral polypeptide by Jiv is considered crucial to the pestivirus cytopathogenicity. In eukaryotes, it usually lies 40 residues downstream of DnaJ family pfam00226. However, the function in eukaryotes is still unknown. 92 matched cddid_all.tbl CDD pfam14902 pfam14902 434298 DUF4494 Domain of unknown function (DUF4494). This family of proteins is found in bacteria. Proteins in this family are typically between 154 and 172 amino acids in length. There are two conserved sequence motifs: VDA and EAE. There is a single completely conserved residue E that may be functionally important. 139 matched cddid_all.tbl CDD pfam14903 pfam14903 464361 WG_beta_rep WG containing repeat. This repeat contains an N-terminal WG repeat motif. The extent of the repeat is poorly defined. This repeat may form a beta solenoid structure (Bateman A pers. obs.). 35 matched cddid_all.tbl CDD pfam14904 pfam14904 464362 FAM86 Family of unknown function. Function of this protein family is not known. 94 matched cddid_all.tbl CDD pfam14905 pfam14905 434300 OMP_b-brl_3 Outer membrane protein beta-barrel family. This family includes proteins annotated as TonB dependent receptors. But it is also likely to contain other membrane beta barrel proteins of other functions. 407 matched cddid_all.tbl CDD pfam14906 pfam14906 464363 DUF4495 Domain of unknown function (DUF4495). This domain family is found in eukaryotes, and is typically between 322 and 336 amino acids in length. There are two conserved sequence motifs: QMW and DLW. Proteins in this family vary in length from 793 to 1184 amino acids. 318 matched cddid_all.tbl CDD pfam14907 pfam14907 434302 NTP_transf_5 Uncharacterized nucleotidyltransferase. This family is likely to be an uncharacterized group of nucleotidyltransferases. 249 matched cddid_all.tbl CDD pfam14908 pfam14908 464364 HU-CCDC81_euk_1 CCDC81 eukaryotic HU domain 1. This is the first of two HU domains found in the CCDC81-like proteins. CCDC81 has been experimentally linked to the centrosome; eukaryotic CCDC81 HU domains are predicted to function in protein-protein interactions in centrosome organization and potentially contribute to cargo-binding in conjunction with Dynein-VII. A striking lineage-specific expansion of the domain is observed in birds, where the HU domains could function in recognition of non-self molecules. 89 matched cddid_all.tbl CDD pfam14909 pfam14909 464365 SPATA6 Spermatogenesis-assoc protein 6. This domain family is found in eukaryotes, and is approximately 140 amino acids in length. The family has similarity to the motor domain of kinesin related proteins and with the Caenorhabditis elegans neural calcium sensor protein (NCS-2). 139 matched cddid_all.tbl CDD pfam14910 pfam14910 464366 MMS22L_N S-phase genomic integrity recombination mediator, N-terminal. MMS22L (Methyl methanesulfonate-sensitivity protein 22-like) is found in yeast, plants and vertebrates, and is integrally concerned with DNA forking and repair mechanisms during replication. MMS22L complexes with TONSL and this complex accumulates at regions of ssDNA associated with distressed replication forks or at processed DNA breaks. Its depletion results in high levels of endogenous DNA double-strand breaks caused by an inability to complete DNA synthesis after replication fork collapse. Thus the complex mediates recovery from replication stress and homologous recombination in vertebrates, yeasts and plants. This family is the more N-terminal region of the proteins. 708 matched cddid_all.tbl CDD pfam14911 pfam14911 464367 MMS22L_C S-phase genomic integrity recombination mediator, C-terminal. MMS22L (Methyl methanesulfonate-sensitivity protein 22-like) is found in yeast, plants and vertebrates, and is integrally concerned with DNA forking and repair mechanisms during replication. MMS22L complexes with TONSL and this complex accumulates at regions of ssDNA associated with distressed replication forks or at processed DNA breaks. Its depletion results in high levels of endogenous DNA double-strand breaks caused by an inability to complete DNA synthesis after replication fork collapse. Thus the complex mediates recovery from replication stress and homologous recombination in vertebrates, yeasts and plants. This family is the more C-terminal region of the proteins. 375 matched cddid_all.tbl CDD pfam14912 pfam14912 464368 THEG Testicular haploid expressed repeat. This repeat is the only conserved part of the THEG proteins from vertebrate spermatids. Both human and mouse THEG are specifically expressed in the nucleus of haploid male germ cells and are involved in the regulation of nuclear functions. Although the differential gene expression of THEG in spermatid-Sertoli cell co-culture supports the relevance of germ cell-Sertoli cell interaction for gene regulation during spermatogenesis, THEG was not found to be essential for spermatogenesis in mice. 59 matched cddid_all.tbl CDD pfam14913 pfam14913 464369 DPCD DPCD protein family. This protein is a found in eukaryotes and a mutation in this protein is thought to cause Primary Ciliary Dyskinesia (PCD). This protein is 203 amino acids in length, 23 kDa in size and its function remains unknown. The gene that encodes this protein is a candidate gene for PCD and is expressed during ciliogenesis. PCD affects the airways and reproductive organs, and probing Northern blots show DPCD expression in humans is highest in the testes. Additionally, there is no indication of major splice variants. 190 matched cddid_all.tbl CDD pfam14914 pfam14914 464370 LRRC37AB_C LRRC37A/B like protein 1 C-terminal domain. This family represents the C-terminal domain of the putative Leucine Rich Repeat Containing protein 37A or protein 37B (LRRC37A/B) found in eukaryotes. The Leucine Rich Repeats (LRR) lies in the central region. The gene that encodes this protein is found in the chromosomal position 17q11.2, and its microdeletion results in the disease, neurofibromatosis type-1 (NF1). The function of the protein, LRRC37B is unknown, however experimental data shows expression in the aorta, heart, skeletal muscle, liver and brain during gestation. 147 matched cddid_all.tbl CDD pfam14915 pfam14915 464371 CCDC144C CCDC144C protein coiled-coil region. This family includes the human protein CCDC144C and the ankyrin repeat domain-containing protein 26-like 1 found in eukaryotes. Its function remains unknown, however, it is known to contain a coiled-coil domain which corresponds to this region. The ankyrin repeat which features in this protein is a common amino acid motif. 304 matched cddid_all.tbl CDD pfam14916 pfam14916 464372 CCDC92 Coiled-coil domain of unknown function. This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The function is not known and the proteins carry no other domains. 57 matched cddid_all.tbl CDD pfam14917 pfam14917 464373 CCDC74_C Coiled coil protein 74, C terminal. This is a C-terminal conserved domain of coiled-coil proteins from vertebrates. The function is not known. Expression levels in humans are elevated in breast cancer. 123 matched cddid_all.tbl CDD pfam14918 pfam14918 464374 MTBP_N MDM2-binding. MTBP, or MDM2-binding protein, binds to MDM2. The MDM2 protein, through its interaction with p53, plays an important role in the regulation of the G1 checkpoint of the cell cycle. MTBP promotes MDM2-mediated ubiquitination and degradation of p53 and also MDM2 stabilization in an MDM2 RING finger-dependent manner. MTBP differentially regulates the E3 ubiquitin ligase activity of MDM2 towards two of its most critical targets (itself and p53) and in doing so significantly contributes to MDM2-dependent p53 homeostasis in unstressed cells. MTBP inhibits cancer cell migration by interacting with a protein involved in cell motility. This motility protein is alpha-actinin-4 (ACTN4). It is unclear which regions of MTBP interact with which binding-partner. See PF14919, PF14920. 254 matched cddid_all.tbl CDD pfam14919 pfam14919 464375 MTBP_mid MDM2-binding. MTBP, or MDM2-binding protein, binds to MDM2. The MDM2 protein, through its interaction with p53, plays an important role in the regulation of the G1 checkpoint of the cell cycle. MTBP promotes MDM2-mediated ubiquitination and degradation of p53 and also MDM2 stabilization in an MDM2 RING finger-dependent manner. MTBP differentially regulates the E3 ubiquitin ligase activity of MDM2 towards two of its most critical targets (itself and p53) and in doing so significantly contributes to MDM2-dependent p53 homeostasis in unstressed cells. MTBP inhibits cancer cell migration by interacting with a protein involved in cell motility. This motility protein is alpha-actinin-4 (ACTN4). It is unclear which regions of MTBP interact with which binding-partner. See PF14918, PF14920. 336 matched cddid_all.tbl CDD pfam14920 pfam14920 464376 MTBP_C MDM2-binding. MTBP, or MDM2-binding protein, binds to MDM2. The MDM2 protein, through its interaction with p53, plays an important role in the regulation of the G1 checkpoint of the cell cycle. MTBP promotes MDM2-mediated ubiquitination and degradation of p53 and also MDM2 stabilization in an MDM2 RING finger-dependent manner. MTBP differentially regulates the E3 ubiquitin ligase activity of MDM2 towards two of its most critical targets (itself and p53) and in doing so significantly contributes to MDM2-dependent p53 homeostasis in unstressed cells. MTBP inhibits cancer cell migration by interacting with a protein involved in cell motility. This motility protein is alpha-actinin-4 (ACTN4). It is unclear which regions of MTBP interact with which binding-partner. See PF14918, PF14919. 257 matched cddid_all.tbl CDD pfam14921 pfam14921 464377 APCDDC Adenomatosis polyposis coli down-regulated 1. The domain is duplicated in most members of this family. APCDD is directly regulated by the beta-catenin/Tcf complex, and its elevated expression promotes proliferation of colonic epithelial cells in vitro and in vivo. APCDD1 has an N-terminal signal-peptide and a C-terminal transmembrane region. The domain is rich in cysteines, there being up to 12 such residues, a structural motif important for interaction between Wnt ligands and their receptors. APCDD1 is expressed in a broad repertoire of cell types, indicating that it may regulate a diverse range of biological processes controlled by Wnt signalling. 235 matched cddid_all.tbl CDD pfam14922 pfam14922 464378 FWWh Protein of unknown function. This is a family of eukaryotic proteins. Most members carry a highly distinctive, conserved sequence motif of FWWh, where h represents a hydrophobic residue. The function of the family is not known. 150 matched cddid_all.tbl CDD pfam14923 pfam14923 464379 CCDC142 Coiled-coil protein 142. The function of this coiled-coil domain-containing family is not known. It is found in eukaryotes. 455 matched cddid_all.tbl CDD pfam14924 pfam14924 464380 DUF4497 Protein of unknown function (DUF4497). This domain family is found in eukaryotes, and is typically between 107 and 123 amino acids in length. There are two completely conserved G residues that may be functionally important. 107 matched cddid_all.tbl CDD pfam14925 pfam14925 464381 HPHLAWLY Domain of unknown function. Members of this family carry two distinct, highly conserved sequence motifs, CPPPLYYTHL and HPHLAWLY. The family is found in eukaryotes, and the function is not known. This family lies at the C-terminus of members. 641 matched cddid_all.tbl CDD pfam14926 pfam14926 464382 CFAP300 Cilia- and flagella-associated protein 300. CFAP300 is a cilia- and flagella-associated protein that is essential for assembly of dynein arms. Mutations in the CFAP300 gene (C11orf70) cause defective cilia motility and primary ciliary dyskinesia. 246 matched cddid_all.tbl CDD pfam14927 pfam14927 434322 Neurensin Neurensin. The neurensin family includes the neuronal membrane proteins neurensin-1 and neurensin-2. Neurensin-1 plays a role in neurite extension. 132 matched cddid_all.tbl CDD pfam14928 pfam14928 405597 S_tail_recep_bd Short tail fibre protein receptor-binding domain. This domain is a receptor binding domain found on bacteriophage short tail fibre proteins. It contains a zinc-binding site and a potential lipopolysaccharide-binding site. 93 matched cddid_all.tbl CDD pfam14929 pfam14929 434323 TAF1_subA TAF RNA Polymerase I subunit A. TATA box binding protein associated factor RNA Polymerase I subunit A is found in eukaryotes and is encoded by the gene TAF1A in humans. Its function is to aid transcription of DNA into RNA by binding to the promoter at the -10 TATA box site. It is a component of the transcription factor SL1/TIF-IB complex, involved in PIC assembly (pre-initiation complex) during RNA polymerase I-dependent transcription. The rate of PIC formation depends on the rate of association of this protein. This protein also stabilizes nucleolar transcription factor 1/UBTF on rDNA. 365 matched cddid_all.tbl CDD pfam14930 pfam14930 434324 Qn_am_d_aII Quinohemoprotein amine dehydrogenase, alpha subunit domain II. This is the second domain of the alpha subunit of quinohemoprotein amine dehydrogenase 107 matched cddid_all.tbl CDD pfam14931 pfam14931 464383 IFT20 Intraflagellar transport complex B, subunit 20. IFT20 is subunit 20 of the intraflagellar transport complex B. The intraflagellar transport complex assembles and maintains eukaryotic cilia and flagella. IFT20 is localized to the Golgi complex and is anchored there by the Golgi polypeptide, GMAP210, whereas all other subunits except IFT172 localize to cilia and the peri-basal body or centrosomal region at the base of cilia. IFT20 accompanies Golgi-derived vesicles to the point of exocytosis near the basal bodies where the other IFT polypeptides are present, and where the intact IFT particle is assembled in association with the inner surface of the cell membrane. Passage of the IFT complex then follows, through the flagellar pore recognition site at the transition region, into the ciliary compartment. There also appears to be a role of intraflagellar transport (IFT) polypeptides in the formation of the immune synapse in non ciliated cells. The flagellum, in addition to being a sensory and motile organelle, is also a secretory organelle. A number of IFT components are expressed in haematopoietic cells, which have no cilia, indicating an unexpected role of IFT proteins in immune synapse-assembly and intracellular membrane trafficking in T lymphocytes; this suggests that the immune synapse could represent the functional homolog of the primary cilium in these cells. 109 matched cddid_all.tbl CDD pfam14932 pfam14932 464384 HAUS-augmin3 HAUS augmin-like complex subunit 3. This domain is subunit three of the augmin complex found from Drosophila to humans. The HAUS-augmin complex is made up of eight subunits. The augmin complex interacts with gamma-TuRC, and attenuation of this interaction severely impairs spindle MT generation. Furthermore, we provide evidence that human augmin plays critical and non-redundant roles in the kinetochore-MT attachment and also central spindle formation during anaphase in human cells.The HAUS complex is required for mitotic spindle assembly and for maintenance of centrosome integrity. 261 matched cddid_all.tbl CDD pfam14933 pfam14933 373400 CEP19 CEP19-like protein. This family includes the centrosomal protein of 19 kDa found in eukaryotes. In humans, it is encoded for by the gene CEP19 which is also known as C3orf34. These proteins localize in the centrosomes. Centrosomes are dynamic organelles that assemble around the centrioles. They organize the microtubule cytoskeleton and mitotic spindle apparatus and are required for cell division and cell migration. C3orf34 localizes near the centrosome in early interphase, to spindle poles during mitosis, and to distinct foci oriented towards the midbody at telophase. 150 matched cddid_all.tbl CDD pfam14934 pfam14934 464385 TMEM254 Transmembrane protein 254. This family contains proteins found in eukaryotes, including human Transmembrane protein TMEM254 (C10orf57). The exact function of this protein is still unknown, however it is thought to be an integral membrane protein. The protein sequence is 123 amino acids in length and has a mass of approximately 14.2 kDa. The family also includes some longer proteins that possess an N-terminal dehydrogenase domain, pfam01073. 91 matched cddid_all.tbl CDD pfam14935 pfam14935 434328 TMEM138 Transmembrane protein 138. This family of proteins is found in eukaryotes and members are approximately 160 amino acids in length. There are two conserved sequence motifs: YYY and DPR. This transmembrane protein belongs to a family found in eukaryotes and is involved in the biogenesis and degradation of ciliated cells. Mutations in this protein cause the disease Joubert syndrome(JBTS) where the cilia becomes non-motile. Ciliopathy can be severe since cilia provide the cell with large amounts of information through signals. Ciliopathy can affect cell behaviour as the appropriate signals between the cell and its environment are not made, which can affect cell survival. 119 matched cddid_all.tbl CDD pfam14936 pfam14936 464386 p53-inducible11 Tumour protein p53-inducible protein 11. TP53 is a tumour suppressor gene, when switched on it suppresses tumour development by inducing stable growth arrest or cell apoptosis. The tumour protein TP53 inducible protein 11 encoded for by the gene TP53I11, has a protein sequence of 189 amino acids in length and 21 kDa in mass. The role of this protein is thought to negatively regulate cell proliferation in response to stress, and therefore suppress tumour formation. 179 matched cddid_all.tbl CDD pfam14937 pfam14937 434330 DUF4500 Domain of unknown function (DUF4500). This family is found in eukaryotes. The function of this protein remains unknown. The gene which encodes for this protein is named chromosome 6 open reading frame 162 (C6orf162) and is found between the chromosomal positions 6q15-q16.1. It is thought that this protein may be an important part of membrane function. 81 matched cddid_all.tbl CDD pfam14938 pfam14938 405606 SNAP Soluble NSF attachment protein, SNAP. The soluble NSF attachment protein (SNAP) proteins are involved in vesicular transport between the endoplasmic reticulum and Golgi apparatus. They act as adaptors between SNARE (integral membrane SNAP receptor) proteins and NSF (N-ethylmaleimide-sensitive factor). They are structurally similar to TPR repeats. 273 matched cddid_all.tbl CDD pfam14939 pfam14939 464387 DCAF15_WD40 DDB1-and CUL4-substrate receptor 15, WD repeat. DCAFs, Ddb1- and Cul4-associated factors, are substrate receptors for the Cul4-Ddb1 Ubiquitin Ligase. There are 18 different factors, the majority of which are WD40-repeat-proteins. 206 matched cddid_all.tbl CDD pfam14940 pfam14940 464388 TMEM219 Transmembrane 219. This protein belongs to a family found in eukaryotes. Proteins in this family are typically between 240 and 315 amino acids in length. The domains in this family vary in length from 202 to 249 amino acids. Its exact function remains unknown, however, it is thought to have a role as a transmembrane protein. More specifically, it is possible that this transmembrane protein may have a role as an insulin-like growth factor binding protein 3-receptor (IGFBP-3R). This receptor binds to the ligand, insulin growth factor 3, which is a p53-induced, apoptosis factor important for cancer prevention. 236 matched cddid_all.tbl CDD pfam14941 pfam14941 464389 OAF Transcriptional regulator, Out at first. This family of proteins is found in eukaryotes. Proteins in this family are typically between 198 and 332 amino acids in length. The domains in this family vary in length from 239 to 242 amino acids. The gene, OAF (out at first), which encodes this protein, has a promoter which may help mediate regulation of neighbouring genes. An alternative name for this protein is HCV NS5A-transactivated protein 13 target protein 2, which stands for Hepatitis C virus nonstructural 5A-transactivated protein 13 target protein 2. NS5A inhibits double-stranded-RNA-activated protein kinase (PKR) activity, which is thought to allow Hepatitis C Virus replication to continue in the presence of an alpha interferon (IFN)induced antiviral response. 243 matched cddid_all.tbl CDD pfam14942 pfam14942 464390 Muted Organelle biogenesis, Muted-like protein. The protein is a coiled-coil protein and belongs to a family found in eukaryotes. It undergoes alternative splicing forming two isoforms. The larger isoform is 187 amino acids long in protein sequence length and 21 kDa in mass. The smaller isoform is 110 amino acids long in protein sequence length and 12 kDa in mass. This protein associates with other proteins in order to form biogenesis of lysosome-related organelles complex-1 BLOC1 complex. BLOC-1 is required for the normal biogenesis of specialized organelles of the endosomal-lysosomal system. 146 matched cddid_all.tbl CDD pfam14943 pfam14943 464391 MRP-S26 Mitochondrial ribosome subunit S26. This family of proteins corresponds to mitochondrial ribosomal subunit S26 in eukaryotes 168 matched cddid_all.tbl CDD pfam14944 pfam14944 434335 TCRP1 Tongue Cancer Chemotherapy Resistant Protein 1. This family of proteins are found in eukaryotes. Tongue Cancer Chemotherapy Resistant-associated Protein 1 (TCRP1) is resistant to the chemotherapy drug, cisplatin, which induces apoptosis in tumour cells. There is suggestion that TCRP1 can be targeted to reverse chemotherapy resistance. The precise mechanism of TCRP1 inducing resistance against chemotherapy is still not clear, but it is thought that TCRP1 alters cell signalling pathways affecting apoptosis or DNA repair capacity. Proteins in this family are typically between 194 and 235 amino acids in length. 237 matched cddid_all.tbl CDD pfam14945 pfam14945 464392 LLC1 Normal lung function maintenance, Low in Lung Cancer 1 protein. This protein is part of a family found in eukaryotes. It is 137 amino acids long in protein sequence length and mass is approximately 15.7 kDa. The protein is present in the normal lung epithelium, but absent or downregulated in most primary non-small lung cancers. The gene is known as Low in Lung Cancer 1 (LLC1). This protein is thought to have a role in the maintenance of normal lung function and its absence may lead to lung tumourigenesis. 118 matched cddid_all.tbl CDD pfam14946 pfam14946 464393 DUF4501 Domain of unknown function (DUF4501). This family of proteins is found in eukaryotes. Proteins in this family are typically between 167 and 308 amino acids in length. The exact function of this protein remains unknown, but it is thought to be a single-pass membrane protein. This family contains many highly conserved cysteine residues. 179 matched cddid_all.tbl CDD pfam14947 pfam14947 405615 HTH_45 Winged helix-turn-helix. This winged helix-turn-helix domain contains an extended C-terminal alpha helix which is responsible for dimerization of this domain. 77 matched cddid_all.tbl CDD pfam14948 pfam14948 464394 RESP18 RESP18 domain. This domain is found in the glucocorticoid-responsive protein regulated endocrine-specific protein 18 (RESP18) and in the N-terminal extracellular region of receptor-type tyrosine-protein phosphatases containing the protein-tyrosine phosphatase receptor IA-2 domain (pfam11548). 103 matched cddid_all.tbl CDD pfam14949 pfam14949 464395 ARF7EP_C ARF7 effector protein C-terminus. This family represents the C-terminus of the ARF7 effector protein (ARF7EP). ARF7EP interacts with ADP-ribosylation factor-like protein 14 and unconventional myosin-Ie and through this interaction controls movement of MHC-II-containing vesicles along the actin cytoskeleton in dendritic cells. It contains a conserved CXCXXXXCXXCXXXCXXCXXXXCXXXCXC motif in it's C-terminal half. 102 matched cddid_all.tbl CDD pfam14950 pfam14950 464396 DUF4502 Domain of unknown function (DUF4502). This family of proteins is found in eukaryotes. Proteins in this family are typically between 181 and 876 amino acids in length. 384 matched cddid_all.tbl CDD pfam14951 pfam14951 464397 DUF4503 Domain of unknown function (DUF4503). This family of proteins is found in eukaryotes. Proteins in this family are typically between 313 and 876 amino acids in length. 385 matched cddid_all.tbl CDD pfam14952 pfam14952 464398 zf-tcix Putative treble-clef, zinc-finger, Zn-binding. This domain resembles the zinc-binding domain of prokaryotic topoisomerases, family DNA_ligase_ZBD pfam03119. The function of the eukaryotic proteins it is carried on is not known. 42 matched cddid_all.tbl CDD pfam14953 pfam14953 464399 DUF4504 Domain of unknown function (DUF4504). This family of proteins is found in eukaryotes. Proteins in this family are typically between 253 and 329 amino acids in length. There are two conserved sequence motifs: LLGYP and SFS. 255 matched cddid_all.tbl CDD pfam14954 pfam14954 464400 LIX1 Limb expression 1. This entry represents the limb expression 1 (LIX1) family. 242 matched cddid_all.tbl CDD pfam14955 pfam14955 464401 MRP-S24 Mitochondrial ribosome subunit S24. This family of proteins corresponds to mitochondrial ribosomal subunit S24 in eukaryotes. 135 matched cddid_all.tbl CDD pfam14956 pfam14956 464402 DUF4505 Domain of unknown function (DUF4505). This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 166 and 225 amino acids in length. 177 matched cddid_all.tbl CDD pfam14957 pfam14957 464403 BORG_CEP Cdc42 effector. The Cdc42 effector (CEP) or binder of Rho GTPases (BORG) proteins are involved in the organization of the actin cytoskeleton. They may function as negative regulators of Rho GTPase signaling. 121 matched cddid_all.tbl CDD pfam14958 pfam14958 464404 PAAT-like ATPase PAAT-like. This family is found in eukaryotes. It represents the ATPase protein associated with ABC transporters (PAAT) and related proteins. PAAT is formed of a nucleotide-binding domain (NBD)-like domain and a signal for intramitochondrial sorting. PAAT interacts with the mitochondrial inner membrane ABC proteins: ABCB7, ABCB8 and ABCB10. It is involved in maintenance of mitochondrial homeostasis and cell survival. 141 matched cddid_all.tbl CDD pfam14959 pfam14959 464405 GSAP-16 gamma-Secretase-activating protein C-term. GSAP, or gamma-secretase-activating protein, also known as PION, regulates gamma-secretase activity. The holo-protein is a large, approx 850 residue protein that is rapidly cleaved to an active 16 kDa C-terminal fragment that is the stable, predominant form. GSAP is expressed in inclusion bodies and is important in brain function. It dramatically and selectively increases neurotoxic beta-Amyloid production in the brain through a mechanism involving its interactions with both gamma-secretase and its substrate, the amyloid precursor protein C-terminal fragment (APP-CTF). Accumulation of neurotoxic beta-Amyloid is a major hallmark of Alzheimer's disease. Formation of beta-Amyloid is catalyzed by gamma-secretase, a protease with numerous substrates that catalyzes the intra-membrane cleavage of integral membrane proteins such as Notch receptors and APP (beta-amyloid precursor protein). The secondary structure of GSAP is largely alpha-helical, lacking well-defined tertiary structure. GSAP represents a type of gamma-secretase regulator that directs enzyme specificity by interacting with a specific substrate. 108 matched cddid_all.tbl CDD pfam14960 pfam14960 434349 ATP_synth_reg ATP synthase regulation. Members of this family are subunits of mitochondrial ATP synthase (F-ATPase) and vacuolar ATPase (V-ATPase). In F-ATPase, this subunit regulates mitochondrial ATP synthase population. 50 matched cddid_all.tbl CDD pfam14961 pfam14961 464406 BROMI Broad-minded protein. Broad-minded protein (BROMI) interacts with cell cycle-related kinase (CCRK), together these proteins regulate ciliary membrane and axonemal growth. 1292 matched cddid_all.tbl CDD pfam14962 pfam14962 464407 AIF-MLS Mitochondria localization Sequence. This family contains a protein found in eukaryotes. Proteins in this family are typically between 240 and 613 amino acids in length. The family is found in association with pfam07992. This protein family is an N-terminal domain for the mitochondrial localization sequence for an apoptosis-inducing factor. The protein is also known as Corneal endothelium-specific protein 1 or as Ovary-specific acidic protein. It is thought to be important for membrane function and is expressed in the ovary and corneal endothelium. 192 matched cddid_all.tbl CDD pfam14963 pfam14963 464408 Get2_like Get2-like. Calcium signal-modulating cyclophilin ligand (CAML) was originally identified in a screen for cyclophilin B-interacting proteins. It is involved in calcium signalling and in other signalling pathways as it interacts with many other signalling molecules including proto-oncogene tyrosine-protein kinase LCK, tumor necrosis factor receptor superfamily member 13B and EGFR. It also mediates the membrane insertion of tail-anchored proteins (TA), acting as a TRC40 receptor (the homolog of yeast Get3). Although CAML shows no sequence similarity to yeast Get2, they share similar biochemical properties and topology, thus resulting in the Get2 homolog in mammals, playing the same essential role in the membrane insertion as that of Get2. It also shows similarity with ER membrane protein complex subunit 6 (EMC6). 270 matched cddid_all.tbl CDD pfam14964 pfam14964 464409 DUF4507 Domain of unknown function (DUF4507). This family of proteins is found in eukaryotes. Proteins in this family are typically between 346 and 434 amino acids in length. 359 matched cddid_all.tbl CDD pfam14965 pfam14965 464410 BRI3BP Negative regulator of p53/TP53. This family of transmembrane proteins is found in eukaryotes. Proteins in this family are typically between 213 and 245 amino acids in length. It is found in various tissues, including the brain, liver and kidneys. It was first discovered as a functional unknown gene, murine brain I3 (BRI3). This protein is also known as HCCRBP-1 and it plays a role in tumourigenesis, as it binds to an oncogene, HCCR-1, and acts as a negative regulator of p53/TP53 tumour suppressor. BRI3BP induces tumourigenesis by activating protein kinase C (PKC) activity but decreasing the pro-apoptotic PKC-alpha and PKC-delta isoform levels. BRI3BP is over-expressed in many tumours. 180 matched cddid_all.tbl CDD pfam14966 pfam14966 434355 DNA_repr_REX1B DNA repair REX1-B. This family of proteins includes Chlamydomonas reinhardtii REX1-B (Required for Excision 1-B) which is involved in a light-independent DNA repair pathway. 94 matched cddid_all.tbl CDD pfam14967 pfam14967 464411 FAM70 FAM70 protein. This family of proteins is found in eukaryotes. Proteins in this family are typically between 241 and 349 amino acids in length. The function of this family is unknown. 324 matched cddid_all.tbl CDD pfam14968 pfam14968 464412 CCDC84 Coiled coil protein 84. The function of this coiled-coil domain-containing family is not known. It is found in eukaryotes. 328 matched cddid_all.tbl CDD pfam14969 pfam14969 464413 DUF4508 Domain of unknown function (DUF4508). This family of proteins is found in eukaryotes. Proteins in this family are typically between 117 and 253 amino acids in length. 96 matched cddid_all.tbl CDD pfam14970 pfam14970 464414 TEDC1 Tubulin epsilon and delta complex protein 1. This family represents the tubulin epsilon and delta complex protein 1 (TEDC1). This complex is required for centriole maintenance and it is a component of several ciliary structures. It acts as a positive regulator of hedgehog signalling, which play key roles in embryonic development and in cancers. Additionally, this protein may play a role in counteracting perturbation of actin filaments, such as after treatment with the actin depolymerizing microbial metabolite Chivosazole F. 161 matched cddid_all.tbl CDD pfam14972 pfam14972 434360 Mito_morph_reg Mitochondrial morphogenesis regulator. This family of proteins regulate mitochondrial morphogenesis via a mechanism which is independent of mitofusins and dynamin-related protein 1. 159 matched cddid_all.tbl CDD pfam14973 pfam14973 464415 TINF2_N TERF1-interacting nuclear factor 2 N-terminus. This is the N-terminus of TERF1-interacting nuclear factor 2. It is required for the formation of the shelterin complex. The shelterin complex is involved in the protection and maintenance of telomeres. 148 matched cddid_all.tbl CDD pfam14974 pfam14974 464416 P_C10 Protein C10. The function of this protein family is unknown. Mutations in protein C (C12orf57) are implicated in the pathogenesis of colobomatous microphthalmia. 103 matched cddid_all.tbl CDD pfam14975 pfam14975 405640 DUF4512 Domain of unknown function (DUF4512). This family of proteins is found in eukaryotes. Proteins in this family are typically between 74 and 104 amino acids in length. There are two completely conserved residues (C and P) that may be functionally important. 103 matched cddid_all.tbl CDD pfam14976 pfam14976 405641 FAM72 FAM72 protein. This family of proteins is found in eukaryotes. Proteins in this family are typically between 145 and 264 amino acids in length. The function of this family is unknown. 145 matched cddid_all.tbl CDD pfam14977 pfam14977 464417 FAM194 FAM194 protein. This family is found in eukaryotes, and is approximately 210 amino acids in length. There is a conserved YPSG sequence motif. The function of this family is unknown. 203 matched cddid_all.tbl CDD pfam14978 pfam14978 434363 MRP-63 Mitochondrial ribosome protein 63. This family of proteins is present in the intact 55S subunit of the mitochondrial ribosome. It is not known if it belongs to the 28S or to the 39S subunit. 90 matched cddid_all.tbl CDD pfam14979 pfam14979 464418 TMEM52 Transmembrane 52. This family of transmembrane proteins is found in eukaryotes. Proteins in this family are typically between 160 and 236 amino acids in length. There is a conserved LLCG sequence motif. The function of this family is unknown. 148 matched cddid_all.tbl CDD pfam14980 pfam14980 434365 TIP39 TIP39 peptide. 51 matched cddid_all.tbl CDD pfam14981 pfam14981 464419 FAM165 FAM165 family. This family of proteins known as FAM165 are found in eukaryotes. Members of this family are as yet uncharacterized. Proteins in this family are typically short membrane proteins between 55 and 70 amino acids in length. 49 matched cddid_all.tbl CDD pfam14982 pfam14982 291643 UPF0731 UPF0731 family. The UPF0731 family of uncharacterized proteins is found in mammals. 78 matched cddid_all.tbl CDD pfam14983 pfam14983 464420 DUF4513 Domain of unknown function (DUF4513). This family of uncharacterized proteins is found in chordates. 138 matched cddid_all.tbl CDD pfam14984 pfam14984 434366 CD24 CD24 protein. 52 matched cddid_all.tbl CDD pfam14985 pfam14985 464421 TM140 TM140 protein family. This family of uncharacterized membrane proteins are called transmembrane protein 140. They are found in mammals. 180 matched cddid_all.tbl CDD pfam14986 pfam14986 464422 DUF4514 Domain of unknown function (DUF4514). This family of uncharacterized proteins are found in mammals. 60 matched cddid_all.tbl CDD pfam14987 pfam14987 464423 NADHdh_A3 NADH dehydrogenase 1 alpha subcomplex subunit 3. This family of proteins are accessory subunits of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I). This subunit is not believed to be catalytic. 78 matched cddid_all.tbl CDD pfam14988 pfam14988 405647 DUF4515 Domain of unknown function (DUF4515). This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 198 and 469 amino acids in length. There are two completely conserved L residues that may be functionally important. 206 matched cddid_all.tbl CDD pfam14989 pfam14989 464424 CCDC32 Coiled-coil domain containing 32. This family of proteins is found in eukaryotes. Proteins in this family are typically between 160 and 188 amino acids in length. The gene that encodes this protein is C15orf57 but its protein product is called Protein CCDC32 (Coiled-coil domain containing 32). The exact function of this protein is still unknown. 150 matched cddid_all.tbl CDD pfam14990 pfam14990 464425 DUF4516 Domain of unknown function (DUF4516). This family of proteins is found in eukaryotes. Proteins in this family are typically between 56 and 69 amino acids in length. 46 matched cddid_all.tbl CDD pfam14991 pfam14991 464426 MLANA Protein melan-A. 117 matched cddid_all.tbl CDD pfam14992 pfam14992 464427 TMCO5 TMCO5 family. The TMCO5 family includes human transmembrane and coiled-coil domain-containing proteins 5A and 5B. 278 matched cddid_all.tbl CDD pfam14993 pfam14993 464428 Neuropeptide_S Neuropeptide S precursor protein. 65 matched cddid_all.tbl CDD pfam14994 pfam14994 464429 TSGA13 Testis-specific gene 13 protein. This family of uncharacterized proteins are found in chordates. In humans this gene is found to be expressed specifically in the testes. 272 matched cddid_all.tbl CDD pfam14995 pfam14995 464430 TMEM107 Transmembrane protein. This family of proteins is found in eukaryotes. Proteins in this family are typically between 138 and 164 amino acids in length. There are two completely conserved residues (H and E) that may be functionally important and four transmembrane helices. The domains in this family vary in length from 124 to 126 amino acids. The precise function of the protein family is still unknown. 123 matched cddid_all.tbl CDD pfam14996 pfam14996 464431 RMP Retinal Maintenance. RMP is encoded for by a gene, C8orf37. Mutations in the gene cause two types of retinal dystrophies: cone-rod dystrophy type 16 (CORD16) and retinitis pigmentosa type 64 (RP64). CORD16 affects the cone receptors which detect red, green or blue wavelengths of light and RP64 affects the cone receptors first and then the rod receptors. Both of these affect the photo-receptors in the eye leading to colour blindness or blindness respectively. 154 matched cddid_all.tbl CDD pfam14997 pfam14997 464432 CECR6_TMEM121 CECR6/TMEM121 family. This family includes Cat eye syndrome critical region protein 6, a protein which has been identified in a screen for candidate genes for the developmental disorder Cat Eye Syndrome (CES). It also includes the TMEM121 transmembrane proteins. The function of this family is unknown. 194 matched cddid_all.tbl CDD pfam14998 pfam14998 464433 Ripply Transcription Regulator. The precise function of this family is not clear, but it is thought to play a role in somitogenesis, development and transcriptional repression. Ripply is also known by an alternative name, Bowline. Bowline, is an associate protein of the transcriptional co-repressor XGrg-4. This family contains two conserved sequence motifs: WRPW and FPVQATI. The WRPW motif is thought to be required for binding to tle/groucho proteins. Ripply3 is also known as Down Syndrome Critical Region Protein 6 homolog. This family of proteins is found in eukaryotes. Proteins in this family are typically between 109 and 154 amino acids in length. 85 matched cddid_all.tbl CDD pfam14999 pfam14999 373461 Shadoo Shadow of prion protein, neuroprotective. This protein family is a Prion-like protein and its function is neuroprotective and similar to PrP(C)-like. Shadoo is mainly expressed in the brain, and highly expressed in the hippocampus, the area of the brain which co-ordinates memory as well as spatial memory and navigation. This protein may also alter the biological actions of normal and abnormal Prion Protein (PrP) which lead to lethal neurodegenerative diseases. This family of proteins is found in eukaryotes. Proteins in this family are approximately 150 amino acids in length, of which the first 90 are alanine rich. 133 matched cddid_all.tbl CDD pfam15000 pfam15000 464434 TUSC2 Tumour suppressor candidate 2. This family of proteins are candidate tumour suppressors. 111 matched cddid_all.tbl CDD pfam15001 pfam15001 434380 AP-5_subunit_s1 AP-5 complex subunit sigma-1. This family of proteins are subunits of the adaptor protein complex AP-5. 192 matched cddid_all.tbl CDD pfam15002 pfam15002 464435 ERK-JNK_inhib ERK and JNK pathways, inhibitor. This coiled-coiled domain, CCDC134, is a secretory protein that inhibits Mitogen activated protein kinase (MAPK) pathways such as Raf-1/MEK/ERK and JNK/SAPK but not p38. CCDC134 is widely expressed in normal adult tissues, tumour tissues and cell lines, which shows its importance in cell signal transduction pathways, transcription regulation and therefore cell survival. Additionally, CCDC134 is known to bind to a transcription adaptor, hADA2a, which forms part of the general control nonderepressible 5 (GCN5) histone acetyltransferase complex. Acetylation usually 'switches genes on' for transcription. Moreover, knocking out CCDC134 suppressed hADA2a-induced cell apoptosis activity and G1/S cell cycle arrest suggesting its importance in cell survival. This family of proteins is found in eukaryotes. Proteins in this family are typically between 188 and 257 amino acids in length. This family is a coiled-coil domain containing protein 134 (CCDC134) whereby the coiled-coiled domain is a ubiquitous motif involved in oligomerization. 197 matched cddid_all.tbl CDD pfam15003 pfam15003 373465 HAUS2 HAUS augmin-like complex subunit 2. This family of proteins is found in eukaryotes. Proteins in this family are typically between 203 and 291 amino acids in length. HAUS augmin-like complex subunit 2 is alternatively called centrosomal protein of 27 kDa (CEP27). It localized in the microtubule organizing centre, the centrosome. These microtubules are part of the cytoskeleton and give the cell its shape, provides it with a platform for motility and are crucial for mitosis. This protein is part of the HAUS augmin-like complex. This interacts with the gamma-tubulin ring complex (gamma-TuRC) which is required for spindle generation. HAUS2 may also increase the tension between spindle and kinetochore allowing for chromosome segregation during mitosis. This protein is involved in mitotic spindle assembly, maintenance of centrosome integrity and completion of cytokinesis. 191 matched cddid_all.tbl CDD pfam15004 pfam15004 464436 MYEOV2 Myeloma-overexpressed-like. This family of proteins is found in eukaryotes. It includes human myeloma-overexpressed gene 2 protein. Proteins in this family are typically between 45 and 74 amino acids in length. There are two conserved sequence motifs: MKP and DEMF. The function of this family is unknown. 57 matched cddid_all.tbl CDD pfam15005 pfam15005 464437 IZUMO Izumo sperm-egg fusion, Ig domain-associated. This IZUMO family is a domain just upstream of the immunoglobulin domain on Izumo proteins in higher eukaryotes. The actual function of this region of the Izumo proteins is not known. The full-length protein is a molecule with a single immunoglobulin (Ig) domain. It is thought that Izumo proteins bind to putative Izumo receptors on the oocyte. Izumo is not detectable on the surface of fresh sperm but becomes exposed only after an exocytotic process, the acrosome reaction, has occurred. Studies have shown that knock-out mice (Izumo-/- males) were sterile despite normal mating behaviour and ejaculation, indicating the importance of the protein in fertilization. There are cysteine residues thought to form a disulphide bridge. Izumo is a typical type I membrane glycoprotein with one immunoglobulin-like domain and a putative N-glycoside link motif (Asn 204). There is a conserved GCL sequence motif. Izumo expression has been found to be testis-specific. 142 matched cddid_all.tbl CDD pfam15006 pfam15006 464438 DUF4517 Domain of unknown function (DUF4517). The function of this protein remains unknown. This family of proteins is found in eukaryotes and are typically between 160 and 182 amino acids in length. 152 matched cddid_all.tbl CDD pfam15007 pfam15007 464439 CEP44 Centrosomal spindle body, CEP44. CEP44 is a coiled coil domain found localized in the centrosome and spindle poles. 126 matched cddid_all.tbl CDD pfam15008 pfam15008 464440 DUF4518 Domain of unknown function (DUF4518). The precise function of this protein family is unknown but it is thought to be involved in apoptosis regulation. 263 matched cddid_all.tbl CDD pfam15009 pfam15009 464441 TMEM173 Transmembrane protein 173. Transmembrane protein 173, also known as stimulator of interferon genes protein (STING), is a transmembrane adaptor protein which is involved in innate immune signalling processes. It induces expression of type I interferons (IFN-alpha and IFN-beta) via the NF-kappa-B and IRF3, pathways in response to non-self cytosolic RNA and dsDNA. 293 matched cddid_all.tbl CDD pfam15010 pfam15010 464442 FAM131 Putative cell signalling. The precise function of this protein family is unknown, however studies have shown it undergoes Protein N-myristoylation; a type of lipid modification in eukaryotic and viral proteins. Protein N-myristoylation is usually an irreversible co-translational protein modification which is useful in cell signal transduction pathways. This indicates that FAM131 may have some sort of role in cell signalling due to its ability to be myristoylated. This family of proteins is found in eukaryotes and are typically between 257 and 361 amino acids in length. 292 matched cddid_all.tbl CDD pfam15011 pfam15011 464443 CK2S Casein Kinase 2 substrate. It is suggested that CK2S (C10orf109) is important in the regulation of cancer cell proliferation. Studies have indicated that CK2S is the downstream target of a protein kinase, casein kinase 2 (CK2), which is upregulated in cancer cells. CK2S has been found to be upregulated in cancer cells. The precise mechanism of CK2 targetting CK2S is not well characterized. It is found to be localized in the nucleus and cytoplasm. This family of proteins is found in eukaryotes. Proteins in this family are typically between 160 and 221 amino acids in length. There is a single completely conserved residue P that may be functionally important. 161 matched cddid_all.tbl CDD pfam15012 pfam15012 464444 DUF4519 Domain of unknown function (DUF4519). This family of proteins is found in eukaryotes. Proteins in this family are typically between and 59 amino acids in length. There are two conserved sequence motifs: KET and VLP. There is a single completely conserved residue P that may be functionally important. 55 matched cddid_all.tbl CDD pfam15013 pfam15013 464445 CCSMST1 CCSMST1 family. This family of proteins was discovered in a screen of Bos taurus placental ESTs. The B. taurus member of this family was named cattle cerebrum and skeletal muscle-specific transcript 1. This family of proteins is found in eukaryotes. Proteins in this family are typically between 97 and 157 amino acids in length. There is a single completely conserved residue D that may be functionally important. The function of this family is unknown. 74 matched cddid_all.tbl CDD pfam15014 pfam15014 464446 CLN5 Ceroid-lipofuscinosis neuronal protein 5. 296 matched cddid_all.tbl CDD pfam15015 pfam15015 464447 NYD-SP12_N Spermatogenesis-associated, N-terminal. NYD-SP12, also known as SPATA16, is a germ-cell specific participant in the Golgi apparatus, and its expression is confined to spermatogenic epithelium, not being found in interstitial cells. Computer analysis of the protein-sequence showed that NYD-SP12 contains a cluster of phosphorylation sites for protein kinase C as well as for cyclic nucleotide-dependent protein kinases. It is postulated that since the mutation of some Golgi apparatus' proteins are responsible for male infertility that NYD-SP12 might play a role in modification and sorting of acrosomal enzymes. OMIM:102530. 564 matched cddid_all.tbl CDD pfam15016 pfam15016 434393 DUF4520 Domain of unknown function (DUF4520). This family of proteins is found in eukaryotes. Proteins in this family are typically between 197 and 638 amino acids in length.This is the C-terminal domain of the member proteins. 89 matched cddid_all.tbl CDD pfam15017 pfam15017 464448 WRNPLPNID Putative WW-binding domain and destruction box. This short conserved region is a putative destruction-box, with its RxxLxxI sequence motif, though the homology is not absolute. The domain occurs on a number of tumourigenic proteins, on some RNA-binding proteins and serine-threonine regulatory proteins. The second less well-conserved motif, WITPS, is a potential WW domain ligand-binding motif for recruiting proteins to their substrates. WW domains bind tightly to short proline-containing peptides that are typically in regions of native disordered polypeptide, as this family is as it lies between a PIN domain and a zinc-binding domain. 56 matched cddid_all.tbl CDD pfam15018 pfam15018 464449 InaF-motif TRP-interacting helix. This highly conserved motif is thought to be a transmembrane helix that binds to transient receptor potential (TRP) calcium channel. It is known that proline-rich proteins inactivate tannins found in food compounds, and it is putatively thought that PRR24 does too. This is important since tannins often inhibit the uptake of iron. InaF is a protein required for TRP calcium channel function in Drosophila. TRP-related channels have been suggested to mediate store-operated calcium entry, important for Ca2+ homeostasis in a wide variety of cell types. The amino acid sequence of PRR-24 contains two completely conserved Y residues that may be functionally important. This domain family is found in eukaryotes, and is approximately 40 amino acids in length. 35 matched cddid_all.tbl CDD pfam15019 pfam15019 464450 C9orf72-like C9orf72-like protein family. The precise function of this family is unknown but members have been found to be localized in the cytoplasm of brain tissue. Defects in the gene, C9orf72, are the cause of frontotemporal dementia and/or amyotrophic lateral sclerosis (FTDALS) which is an autosomal dominant neurodegenerative disorder. The disorder is caused by a large expansion of a GGGGCC hexa-nucleotide within the first C9orf72 intron located between the first and the second non-coding exons. The expansion leads to the loss of transcription of one of the two transcripts encoding isoform 1 and to the formation of nuclear RNA foci. This domain family is found in eukaryotes, and is typically between 230 and 250 amino acids in length. There is a single completely conserved residue F that may be functionally important. 230 matched cddid_all.tbl CDD pfam15020 pfam15020 464451 CATSPERD Cation channel sperm-associated protein subunit delta. The CATSPER (cation channel of sperm) complex is a tetrameric complex consisting of CATSPER1, CATSPER2, CATSPER3 and CATSPER4, it functions as an alkalinization-activated calcium channel. This complex requires several auxiliary subunits, including CATSPERD. CATSPERD is essential for the cation channel function and may play a role in channel assembly or transport. 729 matched cddid_all.tbl CDD pfam15021 pfam15021 464452 DUF4521 Protein of unknown function (DUF4521). This family of vertebrate proteins is functionally uncharacterized. The family includes the Chromosome 20 protein C20orf196. 204 matched cddid_all.tbl CDD pfam15022 pfam15022 434399 DUF4522 Protein of unknown function (DUF4522). This family of proteins is functionally uncharacterized. This family of proteins is found in mammals. In human this protein is known as C4orf36. 117 matched cddid_all.tbl CDD pfam15023 pfam15023 464453 DUF4523 Protein of unknown function (DUF4523). This family of proteins is functionally uncharacterized. This family of proteins is found in mammals. 166 matched cddid_all.tbl CDD pfam15024 pfam15024 434401 Glyco_transf_18 Glycosyltransferase family 18. Enzymes belonging to glycosyltransferase family 18 (alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase) contribute to the creation of branches in complex-type N-glycans. This domain is responsible for the catalytic activity of the enzyme. 557 matched cddid_all.tbl CDD pfam15025 pfam15025 464454 DUF4524 Domain of unknown function (DUF4524). This family of proteins is found in eukaryotes. Proteins in this family are typically between 197 and 638 amino acids in length.This is the N-terminal domain of the member proteins. The human gene is from C5orf34. 146 matched cddid_all.tbl CDD pfam15027 pfam15027 373487 DUF4525 Domain of unknown function (DUF4525). This domain is found in eukaryotes. It is often found at the N-terminus of glycosyltransferase family 18 enzymes (pfam15024). It is also found in coiled-coil domain-containing protein 126. 137 matched cddid_all.tbl CDD pfam15028 pfam15028 464455 PTCRA Pre-T-cell antigen receptor. The pre-T-cell antigen receptor (pre-TCR), expressed by immature thymocytes, has a pivotal role in early T-cell development, including TCR beta-selection, survival and proliferation of CD4(-)CD8(-) double-negative thymocytes, and subsequent alpha/beta T-cell lineage differentiation. This protein contains an immunoglobulin domain. 127 matched cddid_all.tbl CDD pfam15029 pfam15029 434404 TMEM174 Transmembrane protein 174. This family of proteins is found in chordates and includes the human integral membrane protein TMEM174 protein. 235 matched cddid_all.tbl CDD pfam15030 pfam15030 464456 DUF4527 Protein of unknown function (DUF4527). This family of proteins is functionally uncharacterized. This family of proteins is found in vertebrates. 277 matched cddid_all.tbl CDD pfam15031 pfam15031 434406 DUF4528 Domain of unknown function (DUF4528). This family of proteins is found in eukaryotes. Proteins in this family are typically between 95 and 154 amino acids in length. This family includes Human C15orf61. 126 matched cddid_all.tbl CDD pfam15032 pfam15032 464457 DUF4529 Protein of unknown function (DUF4529). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. The proteins contain a conserved VLPPLK sequence motif. 406 matched cddid_all.tbl CDD pfam15033 pfam15033 464458 Kinocilin Kinocilin protein. This family of kinocilin proteins is found in vertebrate. In mouse it has been shown that this protein is expressed primarily in the kinocilium of sensory cells in the inner ear. 123 matched cddid_all.tbl CDD pfam15034 pfam15034 291693 KRTAP7 KRTAP type 7 family. This family of keratin associated proteins are found in vertebrate. 84 matched cddid_all.tbl CDD pfam15035 pfam15035 464459 Rootletin Ciliary rootlet component, centrosome cohesion. 190 matched cddid_all.tbl CDD pfam15036 pfam15036 434409 IL34 Interleukin 34. 157 matched cddid_all.tbl CDD pfam15037 pfam15037 464460 IL17_R_N Interleukin-17 receptor extracellular region. This domain is found at the N-terminus (extracellular region) of interleukin-17 receptor C and Interleukin-17 receptor E. This is the presumed ligand-binding domain. Human putative interleukin-17 receptor E-like consists only of this domain. 388 matched cddid_all.tbl CDD pfam15038 pfam15038 464461 Jiraiya Jiraiya. Jiraiya inhibits bone morphogenetic protein (BMP) signaling during embryogenesis. The human member of this family is TMEM221. 170 matched cddid_all.tbl CDD pfam15039 pfam15039 464462 DUF4530 Domain of unknown function (DUF4530). This family of proteins is found in eukaryotes. Proteins in this family are typically around 140 amino acids in length. The human member of this family is C19orf69. 113 matched cddid_all.tbl CDD pfam15040 pfam15040 373499 Humanin Humanin family. This family of proteins is found exclusively in humans. Humanin is a short anti-apoptotic peptide that interacts with Bax. 24 matched cddid_all.tbl CDD pfam15041 pfam15041 464463 DUF4531 Domain of unknown function (DUF4531). This family of uncharacterized proteins is found in mammals. This family includes the human protein C19orf71. 183 matched cddid_all.tbl CDD pfam15042 pfam15042 464464 LELP1 Late cornified envelope-like proline-rich protein 1. This family of uncharacterized proteins is found in mammals. 106 matched cddid_all.tbl CDD pfam15043 pfam15043 464465 CNRIP1 CB1 cannabinoid receptor-interacting protein 1. This family of proteins interacts with cannabinoid receptor 1 (CNR1) and attenuates CNR1-mediated tonic inhibition of voltage-gated calcium channels. 152 matched cddid_all.tbl CDD pfam15044 pfam15044 464466 CLU_N Mitochondrial function, CLU-N-term. CLU_N is the N-terminal domain of the Clueless protein, also known as TIF31-like in other organizms. The function of this domain is not known. It family is found in association with pfam13236. 79 matched cddid_all.tbl CDD pfam15045 pfam15045 464467 Clathrin_bdg Clathrin-binding box of Aftiphilin, vesicle trafficking. Aftiphilin forms a stable complex with p200 and gamma-synergin. This family contains a clathrin box, with two identified clathrin-binding motifs. This family of proteins is found in eukaryotes. 80 matched cddid_all.tbl CDD pfam15046 pfam15046 464468 DUF4532 Protein of unknown function (DUF4532). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. 279 matched cddid_all.tbl CDD pfam15047 pfam15047 464469 DUF4533 Protein of unknown function (DUF4533). This family of proteins is functionally uncharacterized. This family of proteins is found in mammals. This family includes two human proteins: C12orf60 and C12orf69. 225 matched cddid_all.tbl CDD pfam15048 pfam15048 405697 OSTbeta Organic solute transporter subunit beta protein. 122 matched cddid_all.tbl CDD pfam15049 pfam15049 464470 DUF4534 Protein of unknown function (DUF4534). This family of proteins is functionally uncharacterized. This family of proteins is found in mammals. Proteins in this family are typically between 170 and 190 amino acids in length. The protein includes the human integral membrane TMEM217 protein. 163 matched cddid_all.tbl CDD pfam15050 pfam15050 434419 SCIMP SCIMP protein. This family contains the SCIMP proteins which are a a transmembrane adaptor protein involved in major histocompatibility complex class II signaling. 132 matched cddid_all.tbl CDD pfam15051 pfam15051 373510 FAM198 FAM198 protein. This family of proteins is found in eukaryotes. The function of this family is unknown. Murine FAM198B is downregulated by FGFR signalling. 327 matched cddid_all.tbl CDD pfam15052 pfam15052 464471 TMEM169 TMEM169 protein family. This domain is thought to be structured transmembrane helices and includes the intermediary cytoplasmic domain. It is found in eukaryotes, and is approximately 130 amino acids in length. 131 matched cddid_all.tbl CDD pfam15053 pfam15053 464472 Njmu-R1 Mjmu-R1-like protein family. This protein family is thought to have a role in spermatogenesis. This family of proteins is found in eukaryotes. In humans, it is found in chromosome 17 open reading frame 75 (C17orf75). Proteins in this family are typically between 217 and 399 amino acids in length. 352 matched cddid_all.tbl CDD pfam15054 pfam15054 464473 DUF4535 Domain of unknown function (DUF4535). This family includes the uncharacterized protein C7orf73 that is found in eukaryotes. Members are generally less than 100 residues in length. Although the precise function of the domain is still unknown, members have a predicted N-terminal signal peptide sequence which suggests they are short secreted peptides. 45 matched cddid_all.tbl CDD pfam15055 pfam15055 464474 DUF4536 Domain of unknown function (DUF4536). This domain family is thought to be a transmembrane helix. It is found in eukaryotes, and is approximately 50 amino acids in length. In humans, it is located in the chromosomal position, C9orf123. The family contains the uncharacterized Sch. pombe protein TAM6 which is found in the mitochondrion. 47 matched cddid_all.tbl CDD pfam15056 pfam15056 434424 NRN1 Neuritin protein family. The domain family Neuritin1 (NRN1) is a GPI-anchored protein expressed in post-mitotic-differentiating neurons in the developing nervous system. NRN1 is a glutamate and neurotrophin receptor target encoding a neuronal protein that functions extracellularly to modulate neurite outgrowth (OMIM:607409). This family of proteins is found in eukaryotes. Proteins in this family are typically between and 158 amino acids in length. 89 matched cddid_all.tbl CDD pfam15057 pfam15057 464475 DUF4537 Domain of unknown function (DUF4537). The function of this domain family is unknown. It is found in eukaryotes, and is typically between 119 and 141 amino acids in length. In humans, it is found in the chromosomal position C11orf16. 124 matched cddid_all.tbl CDD pfam15058 pfam15058 434426 Speriolin_N Speriolin N terminus. This family represents the N-terminus of the sperm centrosome protein speriolin. 196 matched cddid_all.tbl CDD pfam15059 pfam15059 464476 Speriolin_C Speriolin C-terminus. This family represents the C-terminus of the sperm centrosome protein speriolin. 148 matched cddid_all.tbl CDD pfam15060 pfam15060 464477 PPDFL Differentiation and proliferation regulator. Pancreatic progenitor cell differentiation and proliferation factor-like protein (PPDFL) is alternatively named Exocrine differentiation and proliferation factor-like protein. PPDFL regulates exocrine cell fate. This protein is highly expressed in exocrine progenitor cells which eventually differentiate to form exocrine pancreatic cells. 110 matched cddid_all.tbl CDD pfam15061 pfam15061 405708 DUF4538 Domain of unknown function (DUF4538). This protein family is thought to be a transmembrane helix. Its function remains unknown. This family of proteins is found in eukaryotes. Proteins in this family are typically between 58 and 87 amino acids in length. 56 matched cddid_all.tbl CDD pfam15062 pfam15062 405709 ARL6IP6 Haemopoietic lineage transmembrane helix. ADP-ribosylation factor-like protein 6-interacting protein 6 (ARP6) is a transmembrane helix present in the J2E erythro-leukaemic cell line, but not its myeloid variants. In tissues, ARL-6 mRNA was most abundant in brain and kidney. While ARL-6 protein was predominantly cytosolic, it is known to bind to SEC61-beta subunit of a protein conducting channel SEC61p. 86 matched cddid_all.tbl CDD pfam15063 pfam15063 464478 TC1 Thyroid cancer protein 1. Thyroid cancer protein 1 (TC1) is thought to decrease in apoptosis and increase cell proliferation. It is found to be expressed in thyroid papillary carcinoma. This suggests its importance in thyroid cancer. The molecular mechanism of TC1, involves up-regulating cell signalling through ERK-1/2 signalling pathway and it positively regulates transition between the G1 and S phase in the cell cycle. It is thought to positively regulate Wnt/beta-catenin signalling pathway by interacting with its repressor. In humans, it is located in the chromosomal position, C8orf4. This family of proteins is found in eukaryotes and contains a conserved NIF sequence motif. 75 matched cddid_all.tbl CDD pfam15064 pfam15064 464479 CATSPERG Cation channel sperm-associated protein subunit gamma. This family represents the gamma subunit of the CATSPER, or cation channel sperm-associated protein complex. The complex appears only to be expressed in the flagellum of sperm. The complex is activated at alkaline intracellular pH, and being restricted to the flagellum is the mediating calcium channel. 971 matched cddid_all.tbl CDD pfam15065 pfam15065 464480 NCU-G1 Lysosomal transcription factor, NCU-G1. NCU-G1 is a set of highly conserved nuclear proteins rich in proline with a molecular weight of approximately 44 kDa. Especially high levels are detected in human prostate, liver and kidney. NCU-G1 is a dual-function family capable of functioning as a transcription factor as well as a nuclear receptor co-activator by stimulating the transcriptional activity of peroxisome proliferator-activated receptor-alpha (PPAR-alpha). 355 matched cddid_all.tbl CDD pfam15066 pfam15066 464481 CAGE1 Cancer-associated gene protein 1 family. CAGE-1 is a family of proteins overexpressed in tumour tissues compared with surrounding tissues. CAGE-1 gene showed testis-specific expression among normal tissues and displayed wide expression in a variety of cancer cell lines and cancer tissues. CAGE-1 is predominantly expressed during post-meiotic stages. It localizes to the acrosomal matrix and acrosomal granule showing it to be a component of the acrosome of mammalian spermatids and spermatozoa. 528 matched cddid_all.tbl CDD pfam15067 pfam15067 464482 FAM124 FAM124 family. The exact function of this protein family remains unknown. This family of proteins is found in eukaryotes. Proteins in this family are approximately 480 amino acids in length. There is a conserved LFL sequence motif. 235 matched cddid_all.tbl CDD pfam15068 pfam15068 464483 FAM101 FAM101 family. This protein family includes the actin regulators, Refilin A and B, however the exact function of this protein family remains unknown. Refilin is thought to stabilize peri-nuclear actin filament bundles, important in fibroblasts. Refilin is important as changes in localization and shape in the nucleus plays a role in cellular and developmental processes. 208 matched cddid_all.tbl CDD pfam15069 pfam15069 464484 FAM163 FAM163 family. This protein family is alternatively named Neuroblastoma-derived secretory proteins. Highly expressed in neuroblastoma compared to other tissues, suggesting that it may be used as a marker for metastasis in bone marrow. 164 matched cddid_all.tbl CDD pfam15070 pfam15070 464485 GOLGA2L5 Putative golgin subfamily A member 2-like protein 5. The function of the GOLGA2L5 protein family remains unknown. This family of proteins is thought to be found in the Golgi apparatus of eukaryotes. 521 matched cddid_all.tbl CDD pfam15071 pfam15071 434437 TMEM220 Transmembrane family 220, helix. Transmembrane 220 (TMEM220) is a domain of unknown function. It is thought to be a transmembrane helix. The length of this protein is typically between 150 and 160 amino acids. In humans, it is found in the chromosomal position 17p13.1. 100 matched cddid_all.tbl CDD pfam15072 pfam15072 464486 HROB Homologous recombination OB-fold protein. This family represents Homologous recombination OB-fold protein (HROB). During homologous recombination, HROB acts by recruiting the MCM8-MCM9 helicase complex to sites of DNA damage to promote DNA repair synthesis. 85 matched cddid_all.tbl CDD pfam15073 pfam15073 434439 SPATA48 Spermatogenesis-associated protein 48. Spermatogenesis-associated protein 48 is also known as post-meiotic spermatogenesis protein 1. Proteins in this family are typically between 109 and 302 amino acids in length. In humans, it is found in the chromosomal position, C7orf72. 128 matched cddid_all.tbl CDD pfam15074 pfam15074 405720 DUF4541 Domain of unknown function (DUF4541). This family of proteins is found in eukaryotes. Proteins in this family are typically between 100 and 163 amino acids in length. There is a conserved KLHRDDR sequence motif. There is a single completely conserved residue Y that may be functionally important. In humans, the gene is found in the chromosomal location, C5orf49. 92 matched cddid_all.tbl CDD pfam15075 pfam15075 464487 DUF4542 Domain of unknown function (DUF4542). This family of proteins is found in eukaryotes. Proteins in this family are typically between 123 and 173 amino acids in length. There is a conserved IPPYN sequence motif. The gene that encodes this protein in humans, is found in the chromosomal position, C17orf98. 134 matched cddid_all.tbl CDD pfam15076 pfam15076 373535 DUF4543 Domain of unknown function (DUF4543). This family of proteins is found in eukaryotes. Proteins in this family are typically between and 90 amino acids in length. The human member of this family is C17orf67. 74 matched cddid_all.tbl CDD pfam15077 pfam15077 464488 MAJIN Membrane-anchored junction protein. Membrane-anchored junction protein (MAJIN) is a meiosis-specific telomere-associated protein involved in meiotic telomere attachment to the nucleus inner membrane, a crucial step for homologous pairing and synapsis. It is a component of the MAJIN-TERB1-TERB2 complex, which promotes telomere cap exchange by mediating attachment of telomeric DNA to the inner nuclear membrane and replacement of the protective cap of telomeric chromosomes. 238 matched cddid_all.tbl CDD pfam15078 pfam15078 464489 DUF4545 Domain of unknown function (DUF4545). This family of proteins is found in eukaryotes. Proteins in this family are typically between and 417 amino acids in length. The human member of this family is C1orf141. 465 matched cddid_all.tbl CDD pfam15079 pfam15079 464490 Tsc35 Testis-specific protein 35. Tsc35 (also referred to in the literature as Tsc24) is essential for spermatogenesis in mammalian male reproduction. It is expressed in the testis from day 35 onwards in mice. 205 matched cddid_all.tbl CDD pfam15080 pfam15080 373539 DUF4547 Domain of unknown function (DUF4547). This family of proteins is found in eukaryotes. Proteins in this family are typically between 144 and 206 amino acids in length. The human member of this family is C3orf43. 196 matched cddid_all.tbl CDD pfam15081 pfam15081 373540 DUF4548 Domain of unknown function (DUF4548). This family of proteins is found in eukaryotes. Proteins in this family are typically between and 178 amino acids in length. The human member of this family is C1orf105. 167 matched cddid_all.tbl CDD pfam15082 pfam15082 464491 DUF4549 Domain of unknown function (DUF4549). This family of proteins is found in eukaryotes. Proteins in this family are typically between 143 and 1871 amino acids in length. The human member of this family is C6orf183. 142 matched cddid_all.tbl CDD pfam15083 pfam15083 464492 Colipase-like Colipase-like. This is a family of colipase-like proteins. 89 matched cddid_all.tbl CDD pfam15084 pfam15084 464493 DUF4550 Domain of unknown function (DUF4550). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is approximately 100 amino acids in length. This domain contains an N-terminal HXE motif. 95 matched cddid_all.tbl CDD pfam15085 pfam15085 405726 NPFF Neuropeptide FF. 109 matched cddid_all.tbl CDD pfam15086 pfam15086 405727 UPF0542 Uncharacterized protein family UPF0542. This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. There is a conserved LSWKL sequence motif. This family includes human protein C5orf43. 67 matched cddid_all.tbl CDD pfam15087 pfam15087 464494 DUF4551 Protein of unknown function (DUF4551). This family of proteins is functionally uncharacterized. This family of proteins is found in metazoa. This family includes human protein C12orf56. 544 matched cddid_all.tbl CDD pfam15088 pfam15088 434447 NADH_dh_m_C1 NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial. 49 matched cddid_all.tbl CDD pfam15089 pfam15089 464495 DUF4552 Domain of unknown function (DUF4552). This family of proteins is functionally uncharacterized. This family of proteins is found in vertebrates. Proteins in this family are typically between 425 and 649 amino acids in length. 425 matched cddid_all.tbl CDD pfam15090 pfam15090 464496 DUF4553 Domain of unknown function (DUF4553). This family of proteins is functionally uncharacterized. This family of proteins is found in vertebrates. This family includes the human protein C10orf12. 477 matched cddid_all.tbl CDD pfam15091 pfam15091 464497 DUF4554 Domain of unknown function (DUF4554). This family of proteins is functionally uncharacterized. This family of proteins is found in some vertebrates. This family includes human protein C11orf80. 456 matched cddid_all.tbl CDD pfam15092 pfam15092 405733 UPF0728 Uncharacterized protein family UPF0728. This family of proteins is functionally uncharacterized. This family of proteins is found in metazoa. There is a conserved GPY sequence motif. 88 matched cddid_all.tbl CDD pfam15093 pfam15093 464498 DUF4555 Domain of unknown function (DUF4555). This family of proteins is functionally uncharacterized. This family of proteins is found in metazoa.This family includes the human protein C7orf31. 284 matched cddid_all.tbl CDD pfam15094 pfam15094 464499 DUF4556 Domain of unknown function (DUF4556). This family of proteins is functionally uncharacterized. This family of proteins is found in vertebrates. This family includes human protein C1orf127. 215 matched cddid_all.tbl CDD pfam15095 pfam15095 434452 IL33 Interleukin 33. 266 matched cddid_all.tbl CDD pfam15096 pfam15096 464500 G6B G6B family. 224 matched cddid_all.tbl CDD pfam15097 pfam15097 464501 Ig_J_chain Immunoglobulin J chain. 134 matched cddid_all.tbl CDD pfam15098 pfam15098 434455 TMEM89 TMEM89 protein family. The function of this family of transmembrane proteins, TMEM89, has not, as yet, been determined. Members of this family are as yet uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are approximately 159 amino acids in length. 134 matched cddid_all.tbl CDD pfam15099 pfam15099 434456 PIRT Phosphoinositide-interacting protein family. The function of this family, PIRT, is not known, however it is predicted to be a multi-pass membrane protein. This family of proteins is thought to have a role in positively regulating TRPV1 channel activity via phosphatidylinositol 4,5-bisphosphate (PIP2). This family of proteins is found in eukaryotes. Proteins in this family are located in the cell membrane. Proteins in this family are approximately 140 amino acids in length. 128 matched cddid_all.tbl CDD pfam15100 pfam15100 464502 TMEM187 TMEM187 protein family. The function of this family, TMEM187, is not known, however it is predicted to be a multi-pass membrane protein. Members of this family are as yet uncharacterized. This protein family is also alternatively named ITBA1. This family of proteins are found in eukaryotes. Proteins in this family are typically between 239 and 267 amino acids in length. 240 matched cddid_all.tbl CDD pfam15101 pfam15101 464503 TERB2 Telomere-associated protein TERB2. TERB2 is a meiosis-specific telomere-associated protein involved in meiotic telomere attachment to the nucleus inner membrane, a crucial step for homologous pairing and synapsis. 207 matched cddid_all.tbl CDD pfam15102 pfam15102 434459 TMEM154 TMEM154 protein family. The function of this family of transmembrane proteins has not, as yet, been determined. However, it is thought to be a therapeutic target for ovine lentivirus infection. This family of proteins is found in eukaryotes and members are typically between 138 and 320 amino acids in length. 153 matched cddid_all.tbl CDD pfam15103 pfam15103 464504 G0-G1_switch_2 G0/G1 switch protein 2. This family of proteins regulate apoptosis by binding to Bcl-2 and preventing the formation of the anti-apoptotic BAX-BCL2 heterodimers. 105 matched cddid_all.tbl CDD pfam15104 pfam15104 464505 DUF4558 Domain of unknown function (DUF4558). This family of proteins is found in eukaryotes. Proteins in this family are typically between 78 and 121 amino acids in length. One member is annotated as being a flagellar associated protein. 86 matched cddid_all.tbl CDD pfam15105 pfam15105 464506 TMEM61 TMEM61 protein family. The function of this family of transmembrane proteins has not, as yet, been determined. Members of this family remain uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 150 and 211 amino acids in length. 182 matched cddid_all.tbl CDD pfam15106 pfam15106 464507 TMEM156 TMEM156 protein family. The function of this family of transmembrane proteins, TMEM 156, has not, as yet, been determined. Members of this family are as yet uncharacterized. This family of proteins are found in eukaryotes. Proteins in this family are approximately 310 amino acids in length. In humans, the gene encoding this protein is located in the chromosomal position, 4p14. 226 matched cddid_all.tbl CDD pfam15107 pfam15107 434464 FAM216B FAM216B protein family. The function of this family of proteins, FAM216B, has not, as yet, been determined. Members of this family are as yet uncharacterized. This family of proteins are found in eukaryotes. Proteins in this family are approximately 150 amino acids in length. In humans, the gene encoding this protein is located in the position, C13orf30. 111 matched cddid_all.tbl CDD pfam15108 pfam15108 434465 TMEM37 Voltage-dependent calcium channel gamma-like subunit protein family. This family of transmembrane proteins, TMEM37, has a role in stabilising the calcium channel in an inactivated (closed) state. It is a subunit of the L-type calcium channels. This family of proteins are found in eukaryotes. Proteins in this family are approximately 210 amino acids in length. 182 matched cddid_all.tbl CDD pfam15109 pfam15109 464508 TMEM125 TMEM125 protein family. The function of this family of transmembrane proteins, TMEM125, has not, as yet, been determined. Members of this family are as yet uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 55 and 232 amino acids in length. 111 matched cddid_all.tbl CDD pfam15110 pfam15110 464509 TMEM141 TMEM141 protein family. The function of this family of transmembrane proteins, TMEM141, has not, as yet, been determined. Members of this family remain uncharacterized. TMEM141 protein family is found in eukaryotes. Proteins in this family are typically between 103 and 124 amino acids in length. There are two completely conserved residues (C and W) that may be functionally important. 91 matched cddid_all.tbl CDD pfam15111 pfam15111 405750 TMEM101 TMEM101 protein family. The function of this family of transmembrane proteins, TMEM101, has not, as yet, been determined. Members of this family remain uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 127 and 257 amino acids in length. 249 matched cddid_all.tbl CDD pfam15112 pfam15112 464510 DUF4559 Domain of unknown function (DUF4559). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. This family includes human protein CXorf38. 311 matched cddid_all.tbl CDD pfam15113 pfam15113 434469 TMEM117 TMEM117 protein family. The function of this family of transmembrane proteins has not, as yet, been determined. Members of this family are as yet uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 181 and 504 amino acids in length. 410 matched cddid_all.tbl CDD pfam15114 pfam15114 464511 UPF0640 Uncharacterized protein family UPF0640. This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 70 and 80 amino acids in length. There are two conserved sequence motifs: PGK and YRFLP. 66 matched cddid_all.tbl CDD pfam15115 pfam15115 464512 HDNR Domain of unknown function with conserved HDNR motif. This family of proteins is found in eukaryotes. Proteins in this family are typically between 117 and 219 amino acids in length. There is a conserved HDNR sequence motif. The function is not known. 177 matched cddid_all.tbl CDD pfam15116 pfam15116 464513 CD52 CAMPATH-1 antigen. 41 matched cddid_all.tbl CDD pfam15117 pfam15117 373575 UPF0697 Uncharacterized protein family UPF0697. This family of uncharacterized proteins is found in vertebrates. Proteins in this family are typically around 100 amino acids in length. 98 matched cddid_all.tbl CDD pfam15118 pfam15118 434473 DUF4560 Domain of unknown function (DUF4560). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 66 and 78 amino acids in length. There are two conserved sequence motifs: FCK and RTL. 64 matched cddid_all.tbl CDD pfam15119 pfam15119 434474 APOC4 Apolipoprotein C4. 94 matched cddid_all.tbl CDD pfam15120 pfam15120 434475 SPACA9 Sperm acrosome-associated protein 9. This family of proteins found in eukaryotes represents sperm acrosome-associated protein 9 (SPACA9, previously known as C9orf9 or MAST). Sperm acrosome-associated protein 9 has been suggested to form a complex with calcium-binding proteins calreticulin and caldendrin localized to the acrosome. Despite this, no known protein interaction motifs have been identified in MAST/SPACA9. 164 matched cddid_all.tbl CDD pfam15121 pfam15121 464514 TMEM71 TMEM71 protein family. The function of this family, TMEM71, is not known, however it is predicted to be a transmembrane protein. This family of proteins is found in eukaryotes and located in the cell membrane. Proteins in this family vary between 41 and 291 amino acids in length. 150 matched cddid_all.tbl CDD pfam15122 pfam15122 434477 TMEM206 TMEM206 protein family. The function of this family of transmembrane proteins, TMEM206, has not, as yet, been determined. Members of this family are remain uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are approximately 350 amino acids in length. 296 matched cddid_all.tbl CDD pfam15123 pfam15123 464515 DUF4562 Domain of unknown function (DUF4562). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. There is a conserved HRYQNPW sequence motif. This family includes the human protein C4orf45. 112 matched cddid_all.tbl CDD pfam15124 pfam15124 434479 FANCD2OS FANCD2 opposite strand protein. This family of proteins of unknown function gets its name from its position in the mammalian genome: Fanconi anemia group D2 protein opposite strand transcript protein. 175 matched cddid_all.tbl CDD pfam15125 pfam15125 464516 TMEM238 TMEM238 protein family. The function of this family of transmembrane proteins, TMEM238; has not, as yet, been determined. Members of this family are as yet uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 61 and 153 amino acids in length. 64 matched cddid_all.tbl CDD pfam15127 pfam15127 464517 SmAKAP Small membrane A-kinase anchor protein. SmAKAP is a small membrane-bound PKA-RI-specific protein kinase A-anchoring protein, referred to as small membrane-AKAP. It is probably tethered to the plasma membrane most through a dual acylation of its N-terminal Met-Gly-Cys- motif (myristoylation and palmitoylation, respectively). It specifically targets PKA-RI isoforms to the plasma membrane. It localizes to plasma membranes, is enriched at cell-cell junctions and associates with filopodia. 97 matched cddid_all.tbl CDD pfam15128 pfam15128 464518 T_cell_tran_alt T-cell leukemia translocation-altered. This family of proteins is required for osteoclastogenesis. 92 matched cddid_all.tbl CDD pfam15129 pfam15129 464519 FAM150 FAM150 family. This family of proteins known as FAM150 is found in eukaryotes. Members of this family are as yet uncharacterized. Proteins in this family are approximately 143 amino acids in length. The function of this family has not, as yet, been determined, however it is predicted to be a secretory protein family. 124 matched cddid_all.tbl CDD pfam15130 pfam15130 405765 DUF4566 Domain of unknown function (DUF4566). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. This family includes human protein C6orf62. 226 matched cddid_all.tbl CDD pfam15131 pfam15131 434484 DUF4567 Domain of unknown function (DUF4567). This family of proteins is functionally uncharacterized. This family of proteins is found in some mammals. 75 matched cddid_all.tbl CDD pfam15132 pfam15132 434485 DUF4568 Domain of unknown function (DUF4568). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. 175 matched cddid_all.tbl CDD pfam15133 pfam15133 434486 TASL TLR adaptor interacting with SLC15A4 on the lysosome. In humans, TASL (TLR adaptor interacting with SLC15A4 on the lysosome) is encoded by CXorf21 that is associated with systemic lupus erythematosus. It is an immune adaptor that is required for recruitment and activation of IRF5 by TLR7, TLR8 and TLR9, in mechanistic analogy to IRF3 and its three adaptors STING, MAVS and TRIF. TASL interacts with the endolysosomal transporter SLC15A4 forming the SLC15A4-TASL complex, which is required for endolysosomal TLR signalling. TASL contains a pLxIS motif that is important for its function. 296 matched cddid_all.tbl CDD pfam15134 pfam15134 464520 DUF4570 Domain of unknown function (DUF4570). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. 110 matched cddid_all.tbl CDD pfam15135 pfam15135 464521 UPF0515 Uncharacterized protein UPF0515. This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. There are two conserved sequence motifs: PLT and HSC. 271 matched cddid_all.tbl CDD pfam15136 pfam15136 464522 UPF0449 Uncharacterized protein family UPF0449. This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. There is a conserved LPTRP sequence motif. 99 matched cddid_all.tbl CDD pfam15137 pfam15137 464523 DUF4571 Domain of unknown function (DUF4571). This family of proteins is functionally uncharacterized. This family of proteins is found in vertebrate. This family includes human protein C21orf62. 218 matched cddid_all.tbl CDD pfam15138 pfam15138 464524 Syncollin Syncollin. This family has a role in zymogen granule exocytosis. 112 matched cddid_all.tbl CDD pfam15139 pfam15139 464525 DUF4572 Domain of unknown function (DUF4572). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 160 and 220 amino acids in length. 195 matched cddid_all.tbl CDD pfam15140 pfam15140 434493 DUF4573 Domain of unknown function (DUF4573). This family of proteins is found in eukaryotes. Proteins in this family are typically approximately 360 amino acids in length. 176 matched cddid_all.tbl CDD pfam15141 pfam15141 464526 UQCC3 Ubiquinol-cytochrome-c reductase complex assembly factor 3. Complex III (cytochrome bc1) is a protein complex of the mitochondrial inner membrane that transfers electrons from ubiquinol to cytochrome c. UQCC3 functions in complex III assembly. The human UQCC3 is the ortholog of the fungal complex III assembly factor CBP4. It is also a potent antiviral protein independent of interferon production. 87 matched cddid_all.tbl CDD pfam15142 pfam15142 464527 INCA1 INCA1. This family of proteins inhibits cyclin-dependent kinase activity. 178 matched cddid_all.tbl CDD pfam15143 pfam15143 291801 DUF4575 Domain of unknown function (DUF4575). This family of uncharacterized proteins is found in eukaryotes. 129 matched cddid_all.tbl CDD pfam15144 pfam15144 464528 DUF4576 Domain of unknown function (DUF4576). This family of uncharacterized proteins is found in eukaryotes. 88 matched cddid_all.tbl CDD pfam15145 pfam15145 464529 DUF4577 Domain of unknown function (DUF4577). The function of this family of proteins, has not, as yet, been determined. Members of this family are as yet uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically 128 amino acids in length. 128 matched cddid_all.tbl CDD pfam15146 pfam15146 464530 FANCAA Fanconi anemia-associated. This family of proteins plays a role in the Fanconi anemia-associated DNA damage response. 441 matched cddid_all.tbl CDD pfam15147 pfam15147 464531 DUF4578 Domain of unknown function (DUF4578). This family of proteins is found in eukaryotes. Proteins in this family are typically between 44 and 137 amino acids in length. 126 matched cddid_all.tbl CDD pfam15148 pfam15148 464532 Apolipo_F Apolipoprotein F. 199 matched cddid_all.tbl CDD pfam15149 pfam15149 464533 CATSPERB Cation channel sperm-associated protein subunit beta protein family. The function of this family of transmembrane proteins, CATSPERB, has not, as yet, been determined. However, it is thought to play a role in sperm hyperactivation by associating with CATSPER1. This family of proteins is found in eukaryotes. Proteins in this family are typically between 220 and 1107 amino acids in length. 519 matched cddid_all.tbl CDD pfam15150 pfam15150 464534 PMAIP1 Phorbol-12-myristate-13-acetate-induced. This family carries a BH3 domain between residues 23 and 40. 54 matched cddid_all.tbl CDD pfam15151 pfam15151 464535 RGCC Response gene to complement 32 protein family. This family of proteins is found in eukaryotes. Proteins in this family are typically between 44 and 130 amino acids in length. There is a conserved KLGDT sequence motif. 128 matched cddid_all.tbl CDD pfam15152 pfam15152 434504 Kisspeptin Kisspeptin. 76 matched cddid_all.tbl CDD pfam15153 pfam15153 434505 CYTL1 Cytokine-like protein 1. The function of this family of proteins, CYTL1, has not, as yet, been determined. However it is thought to be a secretory protein expressed in CD34+ haemopoietic cells. This family of proteins is found in eukaryotes. Proteins in this family are typically between 134 and 145 amino acids in length. There are two conserved sequence motifs: PPTCYSR and DDC. 127 matched cddid_all.tbl CDD pfam15155 pfam15155 317559 MRFAP1 MORF4 family-associated protein1. This family of proteins is found in eukaryotes. Proteins in this family are typically between and 127 amino acids in length. 119 matched cddid_all.tbl CDD pfam15156 pfam15156 464536 CLN6 Ceroid-lipofuscinosis neuronal protein 6. This family of proteins is found in eukaryotes. Proteins in this family are typically between 190 and 310 amino acids in length. 280 matched cddid_all.tbl CDD pfam15157 pfam15157 434507 IQCJ-SCHIP1 Fusion protein IQCJ-SCHIP1 with IQ-like motif. This is a family of eukaryotic fusion proteins. It bridges two adjacent genes that encode distinct proteins, IQCJ, a novel IQ motif containing protein and SCHIP1, a schwannomin interacting protein. It contains a unique calmodulin-binding IQ motif at the N-terminus not shared with its shorter isoform SCHIP1, suggesting a distinctive function for this protein. It is localized to cytoplasm and actin-rich regions, and in differentiated PC12 cells is seen in neurite extensions. the exact physiological function is unclear. 153 matched cddid_all.tbl CDD pfam15158 pfam15158 405787 DUF4579 Domain of unknown function (DUF4579). This family of proteins is found in eukaryotes. Proteins in this family are typically between 192 and 239 amino acids in length. The human member of this family is C8orfK29. 184 matched cddid_all.tbl CDD pfam15159 pfam15159 464537 PIG-Y Phosphatidylinositol N-acetylglucosaminyltransferase subunit Y. This family of proteins represents subunit Y of the GPI-N-acetylglucosaminyltransferase (GPI-GnT) complex. It may regulate activity of the complex by binding the catalytic subunit, PIG-A. This family includes the ERI1 subunit found in yeast, such as Swiss:P62651. 70 matched cddid_all.tbl CDD pfam15160 pfam15160 373611 SASRP1 Spermatogenesis-associated serine-rich protein 1. Spermatogenesis-associated serine-rich protein 1 is a serine-rich protein differentially expressed during spermatogenesis. 236 matched cddid_all.tbl CDD pfam15161 pfam15161 317565 Neuropep_like Neuropeptide-like. This family contains putative neuropeptides. 61 matched cddid_all.tbl CDD pfam15162 pfam15162 464538 SCRE Protein SPO16 homolog. This entry represents the Protein SPO16 homolog (SPO16, also known as Synaptonemal complex reinforcing element SCRE), including the mammalian orthologue of budding yeast Spo16. It plays a key role in reinforcing the integrity of the central element of the synaptonemal complex (SC), resulting in the SC stabilization which ensures the progression of meiotic prophase I in male and female germ cells. It promotes homologous recombination and crossing-over in meiotic prophase I via its association with SHOC1. It is also required for the localization of TEX11 and MSH4 to recombination intermediates. 162 matched cddid_all.tbl CDD pfam15163 pfam15163 464539 Meiosis_expr Meiosis-expressed. This family of proteins is essential for spermiogenesis. 75 matched cddid_all.tbl CDD pfam15164 pfam15164 464540 WBS28 Williams-Beuren syndrome chromosomal region 28 protein homolog. WBS28 is an integral membrane family. These proteins have been identified as being linked to Williams-Beuren syndrome, OMIM:194050. This family of proteins is found in eukaryotes, and are typically 266 amino acids in length. 267 matched cddid_all.tbl CDD pfam15165 pfam15165 464541 REC114-like Meiotic recombination protein REC114-like. REC114-like members are necessary for meiotic DNA double-strand break formation. It functions in conjunction with Mei4. This family of proteins is found in eukaryotes. Proteins in this family are typically between 43 and 259 amino acids in length. 240 matched cddid_all.tbl CDD pfam15167 pfam15167 291823 DUF4581 Domain of unknown function (DUF4581). This family of proteins is found in eukaryotes. Proteins in this family are typically 131 amino acids in length. 131 matched cddid_all.tbl CDD pfam15168 pfam15168 464542 TRIQK Triple QxxK/R motif-containing protein family. TRIQK member-proteins share a characteriztic triple repeat of the sequence QXXK/R, as well as a hydrophobic C-terminal region. Xenopus and mouse triqk genes are broadly expressed throughout embryogenesis, and mtriqk is also generally expressed in mouse adult tissues. TRIQK proteins are localized to the endoplasmic reticulum membrane. This family is found in eukaryotes and members are typically between and 86 amino acids in length. 79 matched cddid_all.tbl CDD pfam15169 pfam15169 405793 Cybc1_Eros Cytochrome b-245 chaperone 1 / Eros. Cytochrome b-245 chaperone 1, also known as Eros (essential for reactive oxygen species) in mice, is a transmembrane protein that may play a central role as a chaperone critical for expression of gp91phox and p22phox and hence for the cytochrome b558 heterodimer. 184 matched cddid_all.tbl CDD pfam15170 pfam15170 373618 CaM-KIIN Calcium/calmodulin-dependent protein kinase II inhibitor. CaM-KIIN is the inhibitor of Calcium/calmodulin-dependent protein kinase II (CaMKII). CaMKII plays a central part in long-term potentiation, which underlies some forms of learning and memory. CaM-KIIN is a natural, specific inhibitor of CaMKII. This family is found in eukaryotes. 79 matched cddid_all.tbl CDD pfam15171 pfam15171 464543 Spexin Neuropeptide secretory protein family, NPQ, spexin. Spexin, alternatively named NPQ, is a peptide hormone and is derived from a pro-hormone. This family of proteins has a role in inducing stomach wall contraction and is expressed in the submucosal layer of the mouse oesophagus and stomach. Spexin, like most peptide hormones, is a ligand for G-protein coupled receptors. Spexin is also thought to have a role in controlling arterial blood pressure as well as salt and water balance. 90 matched cddid_all.tbl CDD pfam15172 pfam15172 434514 Prolactin_RP Prolactin-releasing peptide. 45 matched cddid_all.tbl CDD pfam15173 pfam15173 434515 FAM180 FAM180 family. This family of proteins is found in eukaryotes. Proteins in this family are typically between 117 and 182 amino acids in length. There are two conserved sequence motifs: ELAS and DFE. The function of this family is unknown. 137 matched cddid_all.tbl CDD pfam15174 pfam15174 291830 PRNT Prion-related protein testis-specific. PRNT is a family of prion-related proteins expressed in the testis. This family of proteins is found in eukaryotes. Proteins in this family are typically between 52 and 94 amino acids in length. 51 matched cddid_all.tbl CDD pfam15175 pfam15175 464544 SPATA24 Spermatogenesis-associated protein 24. This family of proteins bind to DNA and to TBP (TATA box binding protein), TATA-binding protein (TBP)-related protein 2 (TRF2) and several polycomb factors. It is likely to function as a transcription regulator. 170 matched cddid_all.tbl CDD pfam15176 pfam15176 464545 LRR19-TM Leucine-rich repeat family 19 TM domain. LRR19-TM is the single-span transmembrane region of LRRC19, a leucine-rich repeat protein family. LRRC19 functions as a transmembrane receptor inducing pro-inflammatory cytokines. This suggests its role in innate immunity. This family of proteins is found in eukaryotes. 115 matched cddid_all.tbl CDD pfam15177 pfam15177 464546 IL28A Interleukin-28A. The protein family, Interleukin-28A, plays an important role in modulating the immune system. This protein family is induced by viral infection and interacts with a class II receptor. This family of proteins is found in eukaryotes. Proteins in this family are typically between 145 and 195 amino acids in length. 157 matched cddid_all.tbl CDD pfam15179 pfam15179 434518 Myc_target_1 Myc target protein 1. This family of proteins is regulated by the c-Myc oncoprotein. It regulates the expression of several other c-Myc target genes. 193 matched cddid_all.tbl CDD pfam15180 pfam15180 464547 NPBW Neuropeptides B and W. The function of this family, NPBW, which includes Neuropeptides B and W, is thought to be involved in activating G-protein coupled receptors, GPR7 and GPR8. It is thought to play a regulatory role in the organization of neuroendocrine signals accessing the anterior pituitary gland. It is predicted that this effect will stimulate the increase in water-drinking and food-intake. This suggests it plays a role in the hypothalamic response to stress. This family of proteins is found in eukaryotes. 118 matched cddid_all.tbl CDD pfam15181 pfam15181 464548 SMRP1 Spermatid-specific manchette-related protein 1. This family of proteins, SMRP1, is thought to have a role in spermatogenesis and may be involved in differentiation or function of ciliated cells. This family of proteins is found in eukaryotes. Proteins in this family are typically approximately 260 amino acids in length. 262 matched cddid_all.tbl CDD pfam15182 pfam15182 464549 OTOS Otospiralin. This family of proteins, Otospiralin, has a role in maintaining the neurosensory epithelium of the inner ear. This family of proteins is found in eukaryotes. Proteins in this family are approximately 90 amino acids in length. 69 matched cddid_all.tbl CDD pfam15183 pfam15183 464550 MRAP Melanocortin-2 receptor accessory protein family. This family is thought to be involved in cell trafficking. It is required for MC2R expression in certain cell types, suggesting that it is involved in the processing, trafficking or function of MC2R. MRAP may be involved in the intracellular trafficking pathways in adipocyte cells. This family of proteins is found in eukaryotes. Proteins in this family are typically between 47 and 205 amino acids in length. 89 matched cddid_all.tbl CDD pfam15184 pfam15184 434523 TOM6p Mitochondrial import receptor subunit TOM6 homolog. TOMM6 forms part of the pre-protein translocase complex of the outer mitochondrial membrane (TOM complex). This family of proteins is found in eukaryotes. Proteins in this family are typically between 43 and 74 amino acids in length. 74 matched cddid_all.tbl CDD pfam15185 pfam15185 291841 BMF Bcl-2-modifying factor, apoptosis. BMF is thought to play a role in inducing apoptosis. It is thought to bind to Bcl-2 proteins. This family of proteins is found in eukaryotes. Proteins in this family are typically between 75 and 190 amino acids in length. There are two conserved sequence motifs: GNA and DQF. 224 matched cddid_all.tbl CDD pfam15186 pfam15186 464551 TEX13 Testis-expressed sequence 13 protein family. The function of this family of proteins has not, as yet, been determined. However, members are thought to be encoded for by spermatogonially-expressed, germ-cell-specific genes. This family of proteins is found in eukaryotes. Proteins in this family are typically between 177 and 384 amino acids in length. There are two conserved sequence motifs: FIN and LAL. 150 matched cddid_all.tbl CDD pfam15187 pfam15187 464552 Augurin Oesophageal cancer-related gene 4. Augurin is alternatively named oesophageal cancer-related gene 4 protein. The function of this family of transmembrane proteins, is to induce the senescence of oligodendrocyte and neural precursor cells, characterized by G1 arrest, RB1 dephosphorylation and accelerated CCND1 and CCND3 proteasomal degradation. Augurin has been found to stimulate the release of ACTH via the release of hypothalamic CRF. This family of proteins is found in eukaryotes. Proteins in this family are typically 145 amino acids in length. 115 matched cddid_all.tbl CDD pfam15188 pfam15188 464553 CCDC-167 Coiled-coil domain-containing protein 167. The function of this family of coiled-coil domains, has not, as yet, been determined. Members of this family remain uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between and 103 amino acids in length. 82 matched cddid_all.tbl CDD pfam15189 pfam15189 434527 MEIOC Meiosis-specific coiled-coil domain-containing protein MEIOC. This family of proteins is found in eukaryotes. In humans, it is encoded for on the chromosomal position C17orf104. 166 matched cddid_all.tbl CDD pfam15190 pfam15190 464554 TMEM251 Transmembrane protein 251. This family of proteins, also known as UPF0694, is found in eukaryotes. Proteins in this family are around 135 amino acids in length. In humans, it is found on the chromosomal position, C14orf109. 128 matched cddid_all.tbl CDD pfam15191 pfam15191 405806 Synaptonemal_3 Synaptonemal complex central element protein 3. 85 matched cddid_all.tbl CDD pfam15192 pfam15192 464555 TMEM213 TMEM213 family. This family of proteins is found in eukaryotes. Proteins in this family are typically between and 154 amino acids in length. The function of this family is unknown. 79 matched cddid_all.tbl CDD pfam15193 pfam15193 464556 FAM24 FAM24 family. This family of proteins is found in eukaryotes. Proteins in this family are typically between 87 and 101 amino acids in length. There are two conserved sequence motifs: FDLRT and CLY. The function of this family is unknown. 69 matched cddid_all.tbl CDD pfam15194 pfam15194 464557 TMEM191C TMEM191C family. This family of proteins is found in eukaryotes. Proteins in this family are typically between and 302 amino acids in length. There are two conserved sequence motifs: QDC and RLF. The function of this family is unknown. 121 matched cddid_all.tbl CDD pfam15195 pfam15195 464558 TMEM210 TMEM210 family. This family of proteins is found in eukaryotes. Proteins in this family are typically between and 149 amino acids in length. The function of this family is unknown. 114 matched cddid_all.tbl CDD pfam15196 pfam15196 259330 Harakiri Activator of apoptosis harakiri. 94 matched cddid_all.tbl CDD pfam15198 pfam15198 291852 Dexa_ind Dexamethasone-induced. 90 matched cddid_all.tbl CDD pfam15199 pfam15199 373639 DAOA D-amino acid oxidase activator. 82 matched cddid_all.tbl CDD pfam15200 pfam15200 464559 KRTDAP Keratinocyte differentiation-associated. 77 matched cddid_all.tbl CDD pfam15201 pfam15201 291855 Rod_cone_degen Progressive rod-cone degeneration. This family of proteins is involved in vision. 54 matched cddid_all.tbl CDD pfam15202 pfam15202 317593 Adipogenin Adipogenin. This family of proteins is involved in the stimulation of adipocyte differentiation and development. 79 matched cddid_all.tbl CDD pfam15203 pfam15203 464560 TMEM95 TMEM95 family. TMEM95 and its homologs can be found in eukaryotes. Proteins in this family are typically between 102 and 231 amino acids in length and they have a conserved LGG sequence motif. TMEM95 is a sperm membrane protein required for sperm-oocyte fusion and is essential for mammalian fertilization. 151 matched cddid_all.tbl CDD pfam15204 pfam15204 434535 KKLCAg1 Kita-kyushu lung cancer antigen 1. This is a family of cancer antigens. 87 matched cddid_all.tbl CDD pfam15205 pfam15205 434536 PLAC9 Placenta-specific protein 9. This family of proteins was identified as being enriched in placenta. 74 matched cddid_all.tbl CDD pfam15206 pfam15206 464561 FAM209 FAM209 family. This family of proteins is found in eukaryotes. Proteins in this family are typically between and 170 amino acids in length. The function of this family is unknown. 149 matched cddid_all.tbl CDD pfam15207 pfam15207 405814 TMEM240 TMEM240 family. This family of proteins is found in eukaryotes. Proteins in this family are typically between 54 and 175 amino acids in length. The function of this family is unknown. 174 matched cddid_all.tbl CDD pfam15208 pfam15208 464562 Rab15_effector Rab15 effector. This family of proteins has a role in receptor recycling from the endocytic recycling compartment. 240 matched cddid_all.tbl CDD pfam15209 pfam15209 464563 IL31 Interleukin 31. 125 matched cddid_all.tbl CDD pfam15210 pfam15210 464564 SFTA2 Surfactant-associated protein 2. 59 matched cddid_all.tbl CDD pfam15211 pfam15211 464565 CXCL17 VEGF co-regulated chemokine 1. 89 matched cddid_all.tbl CDD pfam15212 pfam15212 291866 SPATA19 Spermatogenesis-associated protein 19, mitochondrial. 130 matched cddid_all.tbl CDD pfam15213 pfam15213 434540 CDRT4 CMT1A duplicated region transcript 4 protein. 137 matched cddid_all.tbl CDD pfam15214 pfam15214 464566 PXT1 Peroxisomal testis-specific protein 1. This family of proteins is testis-specific. 51 matched cddid_all.tbl CDD pfam15215 pfam15215 434542 FDC-SP Follicular dendritic cell secreted peptide. 69 matched cddid_all.tbl CDD pfam15216 pfam15216 464567 TSLP Thymic stromal lymphopoietin. 125 matched cddid_all.tbl CDD pfam15217 pfam15217 464568 TSC21 TSC21 family. This family of proteins is testis-specific. 170 matched cddid_all.tbl CDD pfam15218 pfam15218 373654 SPATA25 Spermatogenesis-associated protein 25. This family of proteins may be involved in spermatogenesis. 222 matched cddid_all.tbl CDD pfam15219 pfam15219 434545 TEX12 Testis-expressed 12. 85 matched cddid_all.tbl CDD pfam15220 pfam15220 291874 HILPDA Hypoxia-inducible lipid droplet-associated. This family of proteins stimulate intracellular lipid accumulation, function as autocrine growth factors and enhance cell growth. 63 matched cddid_all.tbl CDD pfam15221 pfam15221 373655 LEP503 Lens epithelial cell protein LEP503. This protein may be involved in lens epithelial cell differentiation. 69 matched cddid_all.tbl CDD pfam15222 pfam15222 259356 KAR Kidney androgen-regulated. The function of this family is unknown. 105 matched cddid_all.tbl CDD pfam15223 pfam15223 434546 EPOP Elongin BC and Polycomb repressive complex 2-associated protein. This family of proteins is found in eukaryotes. Family members are approximately 835 amino acids in length and include the polycomb repressive complex 2-associated factor EPOP (Elongin BC and Polycomb Repressive Complex 2 (PRC2) Associated Protein, also termed C17orf96, esPRC2p48, E130012A19Rik), a scaffold protein expressed in the inner cell mass of the mouse blastocyst serving as a bridging partner between the PRC2/EED-EZH2 complex and the elongin BC complex, and fine-tuning the transcriptional status of Polycomb group (PcG) target genes in embryonic stem cells. Both EPOP and Elongin BC are required to maintain low levels of expression at PRC2 genomic targets. EPOP interacts with the H2B deubiquitinase USP7 to modulate transcriptional processes in mESCs similar to MYC. Functional studies found that the C-terminal region of EPOP directly interacts with PRC2 and that this region associates with the VEFS-box of the PRC2 core member SUZ12. Thus, suggesting that EPOP may directly affect PRC2 chromatin binding by altering the functionality of Suz12. This region is proposed to have evolved in early vertebrates and is also present in the paralog SKIDA1 (C10orf140) another novel PRC2-interacting protein, supporting the idea that proteins possessing this sequence are PRC2 regulators in the entire vertebrate branch. The family is found in association with pfam02437. 426 matched cddid_all.tbl CDD pfam15224 pfam15224 464569 SCRG1 Scrapie-responsive protein 1. This protein family has an important function in acting against the prion protein, Scrapie.This family of proteins is found in eukaryotes. Proteins in this family are approximately 98 amino acids in length. 76 matched cddid_all.tbl CDD pfam15225 pfam15225 434548 IL32 Interleukin 32. 100 matched cddid_all.tbl CDD pfam15226 pfam15226 373659 HPIP HCF-1 beta-propeller-interacting protein family. HPIP is a small cellular polypeptide that binds to the beta-propeller domain of HCF-1. HPIP regulates HCF-1 activity by modulating its subcellular localization. HCF-1 is a cellular protein required by VP16 to activate the herpes simplex virus- immediate-early genes. VP16 is a component of the viral tegument and, after release into the cell, binds to HCF-1 and translocates to the nucleus to form a complex with the POU domain protein Oct-1 and a VP16-responsive DNA sequence. HPIP-mediated export may provide the pool of cytoplasmic HCF-1 required for import of virion-derived VP16 into the nucleus. 133 matched cddid_all.tbl CDD pfam15227 pfam15227 464570 zf-C3HC4_4 zinc finger of C3HC4-type, RING. This is a family of primate-specific Ret finger protein-like (RFPL) zinc-fingers of the C3HC4 type. Ret finger protein-like proteins are primate-specific target genes of Pax6, a key transcription factor for pancreas, eye and neocortex development. This domain is likely to be DNA-binding. This zinc-finger domain together with the RDM domain, pfam11002, forms a large zinc-finger structure of the RING/U-Box superfamily. RING-containing proteins are known to exert an E3 ubiquitin protein ligase activity with the zinc-finger structure being mandatory for binding to the E2 ubiquitin-conjugating enzyme. 42 matched cddid_all.tbl CDD pfam15228 pfam15228 464571 DAP Death-associated protein. 97 matched cddid_all.tbl CDD pfam15229 pfam15229 464572 POM121 POM121 family. 226 matched cddid_all.tbl CDD pfam15230 pfam15230 464573 SRRM_C Serine/arginine repetitive matrix protein C-terminus. This domain is found near to the C-terminus of Serine/arginine repetitive matrix proteins 3 and 4. 67 matched cddid_all.tbl CDD pfam15231 pfam15231 434553 VCX_VCY Variable charge X/Y family. The variable charge X/Y (VCX/VCY) family of proteins has members on the Human X and Y chromosomes, is expressed in male germ calls and may play a role in spermatogenesis or in sex ratio distortion. 130 matched cddid_all.tbl CDD pfam15232 pfam15232 464574 DUF4585 Domain of unknown function (DUF4585). The function of this protein domain family is yet to be characterized. It is putatively thought to lie in the C-terminal domain of the DNA nucleotide repair protein, Xeroderma pigmentosa complementation group A (XPA). The function of XPA is to bind to DNA and repair any mismatched base pairs. This domain family is often found in eukaryotes, and is approximately 70 amino acids in length. There is a conserved DPE sequence motif. In humans, this protein is encoded for in the chromosomal position, Chromosome 5 open reading frame 65. Mutations in the gene lead to myelodysplastic syndromes, where there is inefficient stem cell production in the bone marrow. This suggests that the protein may have a role in forming blood cells. 73 matched cddid_all.tbl CDD pfam15233 pfam15233 464575 SYCE1 Synaptonemal complex central element protein 1. This family of proteins includes synaptonemal complex central element protein 1, a component of the synaptonemal complex involved in meiosis, and synaptonemal complex central element protein 1-like, which may be involved in meiosis. 152 matched cddid_all.tbl CDD pfam15234 pfam15234 464576 LAT Linker for activation of T-cells. 233 matched cddid_all.tbl CDD pfam15235 pfam15235 464577 GRIN_C G protein-regulated inducer of neurite outgrowth C-terminus. This represents the C-terminus of the G protein-regulated inducer of neurite outgrowth proteins. 130 matched cddid_all.tbl CDD pfam15236 pfam15236 434558 CCDC66 Coiled-coil domain-containing protein 66. This protein family, named Coiled-coil domain-containing protein 66 (CCDC) refers to a protein domain found in eukaryotes, and is approximately 160 amino acids in length. CCDC66 protein is detected mainly in the inner segments of photoreceptors in many vertebrates including mice and humans. It has been found in dogs, that a mutation in the CCDC66 gene causes generalized progressive retinal atrophy (gPRA). This shows that the protein encoded for by this gene is vital for healthy vision and guards against photoreceptor cell degeneration. The structure of CCDC66 proteins includes a heptad repeat pattern which contains at least one coiled-coil domain. There are at least two or more alpha-helices which form a cable-like structure. 154 matched cddid_all.tbl CDD pfam15237 pfam15237 464578 PTRF_SDPR PTRF/SDPR family. This family of proteins includes muscle-related coiled-coil protein (MURC), protein kinase C delta-binding protein (PRKCDBP), polymerase I and transcript release factor (PTRF) and serum deprivation-response protein (SDPR). MURC activates the Rho/ROCK pathway. PRKCDBP appears to act as an immune potentiator. PTRF is involved in caveolae formation and function. SDPR is involved in the targetting of protein kinase Calpha to caveolae. 250 matched cddid_all.tbl CDD pfam15238 pfam15238 434560 FAM181 FAM181. This family of proteins is found in eukaryotes. Proteins in this family are typically between 256 and 426 amino acids in length. 285 matched cddid_all.tbl CDD pfam15239 pfam15239 464579 DUF4586 Domain of unknown function (DUF4586). This protein family, refers to a domain of unknown function. The precise role of this protein domain remains to be elucidated. This family of proteins is found in eukaryotes and are typically between 256 and 320 amino acids in length. There is a single completely conserved residue, phenylalanine (F), that may be functionally important. In humans, the protein is found in the position, chromosome 4 open reading frame 47. 296 matched cddid_all.tbl CDD pfam15240 pfam15240 464580 Pro-rich Proline-rich protein. This family includes several eukaryotic proline-rich proteins. 167 matched cddid_all.tbl CDD pfam15241 pfam15241 464581 Cylicin_N Cylicin N-terminus. This is the N-terminus of cylicin proteins, which may play a role in spermatid differentiation. 107 matched cddid_all.tbl CDD pfam15242 pfam15242 464582 FAM53 Family of FAM53. The FAM53 protein family refers to a family of proteins, which bind to a transcriptional regulator that modulates cell proliferation. It is known to be highly important in neural tube development. It is found in eukaryotes and is typically between 303 and 413 amino acids in length. 304 matched cddid_all.tbl CDD pfam15243 pfam15243 464583 ANAPC15 Anaphase-promoting complex subunit 15. This is a component of the anaphase promoting complex/cyclosome. 89 matched cddid_all.tbl CDD pfam15244 pfam15244 464584 HSD3 Spermatogenesis-associated protein 7, or HSD3. Spermatogenesis-associated protein HSD3 also goes by the name of spermatogenesis-associated protein 7 or SPAT7. The family carries a single transmembrane domain. It functions in several tissues, and is expressed in the developing and mature mouse retina; it is expressed in multiple retinal layers in the adult mouse retina. Mutations lead to LCA disease, or Leber congenital amaurosis, which results in a number of retinal dystrophies. The disease- phenotype is characterized by severe visual loss at birth, nystagmus, a variety of fundus changes, and minimal or absent recordable responses on the electroretinogram (ERG). 414 matched cddid_all.tbl CDD pfam15245 pfam15245 464585 VGLL4 Transcription cofactor vestigial-like protein 4. These proteins act as transcriptional enhancer factor (TEF-1) cofactors. 216 matched cddid_all.tbl CDD pfam15246 pfam15246 464586 NCKAP5 Nck-associated protein 5, Peripheral clock protein. NCKAP5 is short for Nck-associated protein 5, which is also known as the Peripheral clock protein. NCKAP5 is a protein family, which interacts with the SH3-containing region of the adaptor protein Nck. Nck is a protein that interacts with receptor tyrosine kinases and guanine nucleotide exchange factor Sos. The role of Nck can be thought of as similar to Grb2. The role of NCKAP5 is to assist Nck with its adaptor protein role. 309 matched cddid_all.tbl CDD pfam15247 pfam15247 464587 SLBP_RNA_bind Histone RNA hairpin-binding protein RNA-binding domain. This family represents the RNA-binding domain of histone RNA hairpin-binding protein. 70 matched cddid_all.tbl CDD pfam15248 pfam15248 464588 DUF4587 Domain of unknown function (DUF4587). This protein family is a domain of unknown function. The precise function of this protein domain remains to be elucidated. This domain family is found in eukaryotes, and is typically between 64 and 79 amino acids in length. There are two conserved sequence motifs: QNAQ and HHH. In humans, it is found in the position, chromosome 21 open reading frame 58. 76 matched cddid_all.tbl CDD pfam15249 pfam15249 464589 GLTSCR1 Conserved region of unknown function on GLTSCR protein. This domain family is found in eukaryotes, and is typically between 105 and 124 amino acids in length. It is found on glioma tumour suppressor candidate region gene proteins. ** Forced reload 102 matched cddid_all.tbl CDD pfam15250 pfam15250 464590 Raftlin Raftlin. This family of proteins plays a role in the formation and/or maintenance of lipid rafts. 456 matched cddid_all.tbl CDD pfam15251 pfam15251 464591 DUF4588 Domain of unknown function (DUF4588). This family of proteins is found in eukaryotes. Proteins in this family are typically between 200 and 274 amino acids in length. There is a conserved LYK sequence motif. There is a single completely conserved residue A that may be functionally important. 238 matched cddid_all.tbl CDD pfam15252 pfam15252 464592 DUF4589 Domain of unknown function (DUF4589). This protein family is a domain of unknown function. The precise function of the protein domain remains to be elucidated. This family of proteins is found in eukaryotes and are typically between 215 and 293 amino acids in length. The protein contains two conserved sequence motifs: SSS and KST. 232 matched cddid_all.tbl CDD pfam15253 pfam15253 464593 STIL_N SCL-interrupting locus protein N-terminus. 404 matched cddid_all.tbl CDD pfam15254 pfam15254 464594 CCDC14 Coiled-coil domain-containing protein 14. This protein family, Coiled-coil domain-containing protein 14 (CCDC14) is a domain of unknown function. This family of proteins is found in eukaryotes. Proteins in this family are typically between 301 and 912 amino acids in length. 857 matched cddid_all.tbl CDD pfam15255 pfam15255 464595 CAP-ZIP_m WASH complex subunit CAP-Z interacting, central region. This domain is found on WASH complex subunits FAM21 and CAP-ZIP proteins, as well as on VPEF (vaccinia virus penetration factor). This family of proteins is found in eukaryotes. Proteins in this family are typically between 305 and 1321 amino acids in length. The exact function of this region is not known. 140 matched cddid_all.tbl CDD pfam15256 pfam15256 464596 SPATIAL SPATIAL. SPATIAL (stromal protein associated with thymii and lymph node) proteins may be involved in spermatid differentiation. 201 matched cddid_all.tbl CDD pfam15257 pfam15257 464597 DUF4590 Domain of unknown function (DUF4590). This family of proteins remains to be characterized and is a domain of unknown function. This domain family is found in eukaryotes, and is approximately 120 amino acids in length. There are two conserved sequence motifs: CCE and PCY. In humans, the gene encoding this protein lies in the position, chromosome 1 open reading frame 173. 114 matched cddid_all.tbl CDD pfam15258 pfam15258 464598 FAM222A Protein family of FAM222A. This protein family, FAM222A are a domain of unknown function. This family of proteins is found in eukaryotes and are typically between 411 and 562 amino acids in length. In humans, the gene encoding this protein domain lies in the position, chromosome 12 open reading frame 34. 524 matched cddid_all.tbl CDD pfam15259 pfam15259 464599 GTSE1_N G-2 and S-phase expressed 1. This family is the N-terminus of GTSE1 proteins. GTSE-1 (G2 and S phase-expressed-1) protein is specifically expressed during S and G2 phases of the cell cycle. It is mainly localized to the microtubules and when overexpressed delays the G2 to M transition. the full protein negatively regulates p53 transactivation function, protein levels, and p53-dependent apoptosis. This domain family is found in eukaryotes, and is approximately 140 amino acids in length. There is a conserved FDFD sequence motif. 144 matched cddid_all.tbl CDD pfam15260 pfam15260 464600 FAM219A Protein family FAM219A. This protein family, FAM219A is a domain of unknown function. This protein family has been found in eukaryotes. Proteins in this family are typically between 144 and 191 amino acids in length. There are two conserved sequence motifs: QLL and LDE. 124 matched cddid_all.tbl CDD pfam15261 pfam15261 464601 JHY Jhy protein. Jhy protein is the protein product of the gene Jhy (previously known as 4931429I11Rik). This protein family is found in eukaryotes, and is approximately 120 amino acids in length. In humans, the gene encoding this protein lies in the position chromosome 11 open reading frame 63. 126 matched cddid_all.tbl CDD pfam15262 pfam15262 464602 DUF4592 Domain of unknown function (DUF4592). This protein family is a domain of unknown function, which lies to the N-terminus of the protein. This domain family is found in eukaryotes, and is typically between 114 and 130 amino acids in length. There are two completely conserved residues (L and A) that may be functionally important. In humans, the gene that encodes this protein lies in the position, chromosome 2 open reading frame 55. 127 matched cddid_all.tbl CDD pfam15264 pfam15264 434584 TSSC4 Tumour suppressing sub-chromosomal transferable candidate 4. This family of proteins is expressed from a gene cluster where in humans the TSSC4 gene is not imprinted. This same cluster is associated with the Beckwith-Wiedermann syndrome. This domain family is found in eukaryotes, and is typically between 120 and 147 amino acids in length. There is a conserved YSL sequence motif. 126 matched cddid_all.tbl CDD pfam15265 pfam15265 464603 FAM196 FAM196 family. This protein family is a domain of unknown function. This family of proteins is found in eukaryotes and are typically between 441 and 534 amino acids in length. 491 matched cddid_all.tbl CDD pfam15266 pfam15266 464604 DUF4594 Domain of unknown function (DUF4594). This protein family is a domain of unknown function. The protein family is found in eukaryotes, and is typically between 170 and 183 amino acids in length.In humans, the gene encoding this protein lies in the position, chromosome 15 open reading frame 52. 177 matched cddid_all.tbl CDD pfam15268 pfam15268 464605 Dapper Dapper. This is a family of signalling proteins. They act in a diverse range of signaling pathways and have a range of binding partners. They act as homo- and heterodimers. 766 matched cddid_all.tbl CDD pfam15269 pfam15269 259402 zf-C2H2_7 Zinc-finger. this is a family of eukaryotic zinc-fingers. 54 matched cddid_all.tbl CDD pfam15270 pfam15270 405863 ACI44 Metallo-carboxypeptidase inhibitor. ACI44, a metallo-carboxypeptidase inhibitor, is one member of a battery of selective inhibitors protecting roundworms of the genus Ascaris, common parasites of the human gastrointestinal tract, from host enzymes and the immune system. 58 matched cddid_all.tbl CDD pfam15271 pfam15271 373701 BBP1_N Spindle pole body component BBP1, Mps2-binding protein. This N-terminal domain of BBP1, a spindle pole body component, interacts directly, though transiently, with the polo-box domain of Cdc5p. full length BBP1 localizes at the cytoplasmic side of the central plaque periphery of the spindle pole body (SPB) and plays an important role in inserting a duplication plaque into the nuclear envelope and assembling a functional inner plaque. Although not a membrane protein itself, BBP1 binds to Mps2 as well as to Spc29 and the half-bridge protein Kar1, thus providing a model for how the SPB core is tethered within the nuclear envelope and to the half-bridge. 151 matched cddid_all.tbl CDD pfam15272 pfam15272 405864 BBP1_C Spindle pole body component BBP1, C-terminal. This C-terminal domain of BBP1, a spindle pole body component, carries coiled-coils that are necessary for the localization of BBP1 to the spindle pole body (SPB). Although not a membrane protein itself, BBP1 binds to Mps2 as well as to Spc29 and the half-bridge protein Kar1, thus providing a model for how the SPB core is tethered within the nuclear envelope and to the half-bridge 183 matched cddid_all.tbl CDD pfam15273 pfam15273 464606 NHS NHS-like. This family of proteins includes Nance-Horan syndrome protein (NHS). 654 matched cddid_all.tbl CDD pfam15274 pfam15274 405866 MLIP Muscular LMNA-interacting protein. MLIP is a Muscle-enriched A-type Lamin-interacting Protein, an innovation of amniotes, and is expressed ubiquitously and most abundantly in heart, skeletal, and smooth muscle. MLIP interacts directly and co-localizes with lamin A and C in the nuclear envelope. MLIP also co-localizes with promyelocytic leukemia (PML) bodies within the nucleus. PML, like MLIP, is only found in amniotes, suggesting that a functional link between the nuclear envelope and PML bodies may exist through MLIP. 253 matched cddid_all.tbl CDD pfam15275 pfam15275 464607 PEHE PEHE domain. This domain was first identified in drosophila MSL1 (male-specific lethal 1). In drosophila it binds to the histone acetyltransferase males-absent on the first protein (MOF) and to protein male-specific lethal-3 (MSL3). 128 matched cddid_all.tbl CDD pfam15276 pfam15276 434590 PP1_bind Protein phosphatase 1 binding. This domain contains a protein phosphatase 1 (PP1) binding site. 62 matched cddid_all.tbl CDD pfam15277 pfam15277 464608 Sec3-PIP2_bind Exocyst complex component SEC3 N-terminal PIP2 binding PH. This is the N-terminal domain of fungal and eukaryotic Sec3 proteins. Sec3 is a component of the exocyst complex that is involved in the docking of exocytic vesicles with fusion sites on the plasma membrane.This N-terminal domain contains a cryptic pleckstrin homology (PH) fold, and all six positively charged lysine and arginine residues in the PH domain predicted to bind the PIP2 head group are conserved. The exocyst complex is essential for many exocytic events, by tethering vesicles at the plasma membrane for fusion. In fission yeast, polarised exocytosis for growth relies on the combined action of the exocyst at cell poles and myosin-driven transport along actin cables. 85 matched cddid_all.tbl CDD pfam15278 pfam15278 259411 Sec3_C_2 Sec3 exocyst complex subunit. This small Sec3 C-terminal domain family is based around the fission yeast protein, and is rather shorter than the budding yeast/vertebrate domain Sec3_C, family. pfam09763. In fact it is only this coiled-coil region that they carry in common. The full length fission yeast, UniProtKB:Q10324, protein Sec3 is redundant with Exo70 for viability and for the localization of other exocyst subunits, suggesting that these components act as exocyst tethers at the plasma membrane. Sec3, Exo70 and Sec5 are transported by the myosin V Myo52 along actin cables. The exocyst holo-complex, including Sec3 and Exo70, is present on exocytic vesicles, which can reach cell poles by either myosin-driven transport or random walk. 86 matched cddid_all.tbl CDD pfam15279 pfam15279 464609 SOBP Sine oculis-binding protein. SOBP is associated with syndromic and nonsyndromic intellectual disability. It carries a zinc-finger of the zf-C2H2 type at the N-terminus, and a highly characteriztic C-terminal PhPhPhPhPhPh motif. The deduced 873-amino acid protein contains an N-terminal nuclear localization signal (NLS), followed by 2 FCS-type zinc finger motifs, a proline-rich region (PR1), a putative RNA-binding motif region, and a C-terminal NLS embedded in a second proline-rich motif. SOBP is expressed in various human tissues, including developing mouse brain at embryonic day 14. In postnatal and adult mouse brain SOBP is expressed in all neurons, with intense staining in the limbic system. Highest expression is in layer V cortical neurons, hippocampus, pyriform cortex, dorsomedial nucleus of thalamus, amygdala, and hypothalamus. Postnatal expression of SOBP in the limbic system corresponds to a time of active synaptogenesis. the family is also referred to as Jackson circler, JXC1. In seven affected siblings from a consanguineous Israeli Arab family with mental retardation, anterior maxillary protrusion, and strabismus mutations were found in this protein. 325 matched cddid_all.tbl CDD pfam15280 pfam15280 464610 BORA_N Protein aurora borealis N-terminus. This family of proteins is required for the activation of the protein kinase Aurora-A. 207 matched cddid_all.tbl CDD pfam15281 pfam15281 464611 Consortin_C Consortin C-terminus. Consortin is a trans-Golgi network cargo receptor involved in targeting connexins to the plasma membrane. 113 matched cddid_all.tbl CDD pfam15282 pfam15282 464612 BMP2K_C BMP-2-inducible protein kinase C-terminus. This family represents the C-terminus of BMP2K and related proteins. 263 matched cddid_all.tbl CDD pfam15283 pfam15283 464613 DUF4595 Domain of unknown function (DUF4595) with porin-like fold. Large family of predicted secreted proteins mostly from CFG group, but also from Burkholderia, Pseudomonas and Streptomyces. Function of these proteins is not known. A 3D structure of a representative of this family from Bacteroides uniformis was solved by JCSG and deposited to PDB as 4ghb. There is some overlap with RHS-repeat (PF05593) family despite lack of obvious repeats in the structure. 207 matched cddid_all.tbl CDD pfam15284 pfam15284 317659 PAGK Phage-encoded virulence factor. PAGK represents a new of virulence factors that is translocated into the host cytoplasm via bacterial outer membrane vesicles (OMV). Members are small proteins composed of ~70 amino acids. In Salmonella they are secreted independently of the SPI-2 type-III secretion system, T3SS. The OMV functions as a vehicle for transferring virulence determinants to the cytoplasm of the infected host cell. OMVs are released from the cell envelopes of Gram-negative bacteria and comprise a variety of outer membrane and periplasmic constituents, including proteins, phospholipids, lipopolysaccharides, and DNA. 64 matched cddid_all.tbl CDD pfam15285 pfam15285 464614 BH3 Beclin-1 BH3 domain, Bcl-2-interacting. The BH3 domain is a short motif known to bind to Bcl-xLs. This interaction is important in apoptosis. 25 matched cddid_all.tbl CDD pfam15286 pfam15286 373714 Bcl-2_3 Apoptosis regulator M11, B cell 2 leukaemia/lymphoma like. pfam02180. Bcl-2_3 is a small family of eukaryotic proteins associated with autophagy. The family is found in association with pfam00452. 126 matched cddid_all.tbl CDD pfam15287 pfam15287 464615 KRBA1 KRBA1 family repeat. KRBA1 is a short repeating motif found in mammalian proteins. It is characterized by a highly conserved sequence of residues, SSPLxxLxxCLK. The function of the repeat, which can be present in up to seven copies, is unknown as is the function of the full length proteins. 44 matched cddid_all.tbl CDD pfam15288 pfam15288 464616 zf-CCHC_6 Zinc knuckle. This Zinc knuckle is found in FAM90A mammalian proteins. 42 matched cddid_all.tbl CDD pfam15289 pfam15289 434600 RFXA_RFXANK_bdg Regulatory factor X-associated C-terminal binding domain. This C-terminal domain of Regulatory factor X-associated protein binds to RFXANK, the Ankyrin-repeat regulatory factor X proteins. RFXA is part of the RFX complex, Mutants of either RFXAP or RFXANK protein fail to bind to each other. RFX5 binds only to the RFXANK-RFXAP scaffold and not to either protein alone, and neither the scaffold nor RFX5 alone can bind DNA. The binding of the RFXANK-RFXAP scaffold to RFX5 leads to a conformational change in the latter that exposes the DNA-binding domain of RFX5. The DNA-binding domain of RFX5 anchors the RFX complex to MHC class II X and S promoter boxes. 122 matched cddid_all.tbl CDD pfam15290 pfam15290 464617 Syntaphilin Golgi-localized syntaxin-1-binding clamp. Syntaphilin or Syntabulin is a family of eukaryotic proteins. Syntaphilin binds to syntaxin-1 thereby inhibiting SNARE complex formation by absorbing free syntaxin-1. So it is a syntaxin-1 clamp that controls SNARE assembly. 305 matched cddid_all.tbl CDD pfam15291 pfam15291 405879 Dermcidin Dermcidin, antibiotic peptide. Dermcidin is a family of peptides produced in the sweat to protect against pathogenic Gram-positive bacteria. 84 matched cddid_all.tbl CDD pfam15292 pfam15292 464618 Treslin_N Treslin N-terminus. This family represents the N-terminus of treslin, a checkpoint regulator which plays a role in DNA replication preinitiation complex formation. 793 matched cddid_all.tbl CDD pfam15293 pfam15293 464619 NUFIP2 Nuclear fragile X mental retardation-interacting protein 2. 596 matched cddid_all.tbl CDD pfam15294 pfam15294 464620 Leu_zip Leucine zipper. This family includes Leucine zipper transcription factor-like protein 1 (LZTFL1) and Leucine zipper protein 2 (LUZP2). 276 matched cddid_all.tbl CDD pfam15295 pfam15295 464621 CCDC50_N Coiled-coil domain-containing protein 50 N-terminus. 126 matched cddid_all.tbl CDD pfam15296 pfam15296 464622 Codanin-1_C Codanin-1 C-terminus. This domain is found near to the C-terminus of codanin-1. 120 matched cddid_all.tbl CDD pfam15297 pfam15297 464623 CKAP2_C Cytoskeleton-associated protein 2 C-terminus. This family includes the C-terminus of CKAP2 and CKAP2L. CKAP2 is a microtubule associated protein which stabilizes microtubules. 348 matched cddid_all.tbl CDD pfam15298 pfam15298 464624 AJAP1_PANP_C AJAP1/PANP C-terminus. This family includes the C-terminus of adherens junction-associated protein 1 (AJAP1) and of PILR-associating neural protein (PANP). AJAP1 inhibits cell adhesion and migration. PANP is a ligand for the immune inhibitory receptor paired immunoglobulin-like type 2 receptor alpha. 204 matched cddid_all.tbl CDD pfam15299 pfam15299 464625 ALS2CR8 Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8. This domain is found in amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8 protein. 227 matched cddid_all.tbl CDD pfam15300 pfam15300 464626 INT_SG_DDX_CT_C INTS6/SAGE1/DDX26B/CT45 C-terminus. This domain is found at the C-terminus of integrator complex subunit 6 (INTS6), sarcoma antigen 1 (SAGE1), protein DDX26B (DDX26B) and members of the cancer/testis antigen family 45. 62 matched cddid_all.tbl CDD pfam15301 pfam15301 464627 SLAIN SLAIN motif-containing family. The SLAIN motif containing family is named after the presence of a SLAIN motif in SLAIN1. They are a family of microtubule plus-end tracking proteins. 420 matched cddid_all.tbl CDD pfam15302 pfam15302 464628 P33MONOX P33 mono-oxygenase. This family of proteins contains a flavine-containing mono-oxygenase motif. It may have a role in the regulation of neuronal survival, differentiation and axonal outgrowth. 293 matched cddid_all.tbl CDD pfam15303 pfam15303 464629 RNF111_N E3 ubiquitin-protein ligase Arkadia N-terminus. This domain is found at the N-terminus of E3 ubiquitin-protein ligase Arkadia. 279 matched cddid_all.tbl CDD pfam15304 pfam15304 464630 AKAP2_C A-kinase anchor protein 2 C-terminus. This family includes the C-terminus of A-kinase anchor protein 2 (AKAP2). It includes the site where the regulatory subunits (RII) of protein kinase AII binds. 341 matched cddid_all.tbl CDD pfam15305 pfam15305 464631 IFT43 Intraflagellar transport protein 43. Intraflagellar transport protein 43 (IFT43) is a subunit of the IFT complex A (IFT-A) machinery of primary cilia. 136 matched cddid_all.tbl CDD pfam15306 pfam15306 464632 LIN37 LIN37. LIN37 is a component of the DREAM (or LINC) complex which represses cell cycle-dependent genes in quiescent cells and plays a role in the cell cycle-dependent activation of G2/M genes. 156 matched cddid_all.tbl CDD pfam15307 pfam15307 434617 SPACA7 Sperm acrosome-associated protein 7. SPACA7 is a family of eukaryotic proteins expressed in the testes. Proteins in this family are typically between 104 and 195 amino acids in length. There is a conserved DEIL sequence motif. The function is not known. 107 matched cddid_all.tbl CDD pfam15308 pfam15308 464633 CEP170_C CEP170 C-terminus. This family includes the C-terminus of centrosomal protein of 170 kDa (CEP170). 682 matched cddid_all.tbl CDD pfam15309 pfam15309 464634 ALMS_motif ALMS motif. This domain is found at the C-terminus of Alstrom syndrome protein 1 (ALMS1), KIAA1731 and C10orf90. 131 matched cddid_all.tbl CDD pfam15310 pfam15310 464635 VAD1-2 Vitamin A-deficiency (VAD) rat model signalling. VAD1-2 is a family of proteins found in eukaryotes. The family is expressed in testes and is involved in signalling during spermatogenesis. 249 matched cddid_all.tbl CDD pfam15311 pfam15311 464636 HYLS1_C Hydrolethalus syndrome protein 1 C-terminus. 89 matched cddid_all.tbl CDD pfam15312 pfam15312 464637 JSRP Junctional sarcoplasmic reticulum protein. JSRP, junctional sarcoplasmic reticulum protein 1, or junctional-face membrane protein of 45 kDa homolog, is a family of eukaryotic proteins. The family is to the junctional face membrane of the skeletal muscle sarcoplasmic reticulum (SR); it colocalizes with its Ca2+-release channel (the ryanodine receptor), and interacts with calsequestrin and the skeletal-muscle dihydro-pyridine receptor Cav1. It is key for the functional expression of voltage-dependent Ca2+ channels. 63 matched cddid_all.tbl CDD pfam15313 pfam15313 464638 HEXIM Hexamethylene bis-acetamide-inducible protein. HEXIM is a transcriptional regulator that functions as a general RNA polymerase II transcription inhibitor. In cooperation with 7SK snRNA it sequesters P-TEFb in a large inactive 7SK snRNP complex preventing RNA polymerase II phosphorylation and subsequent transcriptional elongation. HEXIM may also regulate NF-kappa-B, ESR1, NR3C1 and CIITA-dependent transcriptional activity. 136 matched cddid_all.tbl CDD pfam15314 pfam15314 464639 PRAP Proline-rich acidic protein 1, pregnancy-specific uterine. PRAP, or proline-rich acidic protein 1, is a family of eukaryotic proteins. PRAP is abundantly expressed in the epithelial cells of the human liver, kidney, gastrointestinal tract, and cervix. It is significantly down-regulated in hepatocellular carcinoma and right colon adenocarcinoma compared with the respective adjacent normal tissues. In the mouse it is expressed in the epithelial cells of the mouse and rat gastrointestinal tracts, and pregnant mouse uterus. This article describes the isolation, distribution, and functional characterization of the human homolog. PRAP was abundantly expressed in the epithelial cells of the human liver, kidney, gastrointestinal tract, and cervix. PRAP plays an important role in maintaining normal growth suppression. 45 matched cddid_all.tbl CDD pfam15315 pfam15315 464640 FRG2 Facioscapulohumeral muscular dystrophy candidate 2. This family of proteins is found in eukaryotes. The family is localized close to the D4Z4 repeats on chromosome 4 and 10 that are associated with the autosomal dominant facioscapulohumeral muscular dystrophy (FSHD). FRG2 are transcriptionally upregulated in FSHD myoblast cultures suggesting involvement in the pathogenesis of FSHD. 183 matched cddid_all.tbl CDD pfam15316 pfam15316 464641 MDFI MyoD family inhibitor. Members of this family inhibits the transactivation activity of the MyoD family of myogenic factors. They affect axin-mediated regulation of the Wnt and JNK signaling pathways, and regulate expression from viral promoters. 168 matched cddid_all.tbl CDD pfam15317 pfam15317 434627 Lbh Cardiac transcription factor regulator, Developmental protein. The family of proteins are cardiac transcription regulators, named Lbh, short for Limb, bud and heart. They regulate embryological development in the heart. More specifically, in humans, they may act as transcriptional activators in MAPK signaling pathway to mediate cellular functions. This family of proteins is found in eukaryotes. Proteins in this family are typically between 92 and 116 amino acids in length. 101 matched cddid_all.tbl CDD pfam15318 pfam15318 434628 Bclt Putative Bcl-2 like protein of testis. This family of proteins is found in eukaryotes. The family may represent a set of Bcl-2-like proteins involved in apoptosis, see UniProt:Q9BQM9. 175 matched cddid_all.tbl CDD pfam15319 pfam15319 464642 RHINO RAD9, RAD1, HUS1-interacting nuclear orphan protein. RHINO, or RAD9, RAD1, HUS1-interacting nuclear orphan, is a family of eukaryotic proteins. Under genotoxic stresses such as ionizing radiation during the S phase, RHINO plays a role in DNA damage response signalling. It is recruited to sites of DNA damage through interaction with the 9-1-1 cell-cycle checkpoint response complex and TOPBP1 in a ATR-dependent (ataxia telangiectasia and Rad3-related) manner. It is required for the progression of the G1 to S phase transition of breast cancer cells, and it is known to play a role in the stimulation of CHEK1 phosphorylation. It interacts with RAD9A, RAD18, TOPBP1 and UBE2N. 245 matched cddid_all.tbl CDD pfam15320 pfam15320 464643 RAM mRNA cap methylation, RNMT-activating mini protein. This family of proteins is found in eukaryotes. Proteins in this family are typically between 102 and 154 amino acids in length. There is a single completely conserved residue D that may be functionally important. RAM is a family of eukaryotic proteins that are an obligate component of the mammalian cap methyltransferase, RNMT (RNA guanine-7 methyltransferase). RAM consists of an N-terminal RNMT-activating domain and a C-terminal RNA-binding domain. Either RAM or RNMT independently have rather weak binding affinity for RNA, but together their RNA affinity is significantly increased. RAM is necessary for efficient cap methylation, maintaining mRNA expression levels, for mRNA translation and for cell viability. 83 matched cddid_all.tbl CDD pfam15321 pfam15321 464644 ATAD4 ATPase family AAA domain containing 4. ATAD4 is a family of proteins is found in eukaryotes. The family is also known as PRR15L, or proline-rich 15-like. ATAD4 is expressed almost exclusively in post-mitotic cells both during foetal development and in adult tissues, such as the intestinal epithelium and the testis. Its expression in mouse and human gastrointestinal tumours is linked, directly or indirectly, to the disruption of the Wnt signaling pathway. 95 matched cddid_all.tbl CDD pfam15322 pfam15322 464645 PMSI1 Protein missing in infertile sperm 1, putative. This family of proteins is found in eukaryotes. Proteins in this family are typically between 249 and 341 amino acids in length. 315 matched cddid_all.tbl CDD pfam15323 pfam15323 464646 Ashwin Developmental protein. This family of proteins are found in eukaryotes. These proteins have an important role to play in developmental biology, particularly embryogenesis. It plays an important role in cell survival and axial pattern. It is also thought to be a crucial subunit in the tRNA splicing ligase complex. Proteins in this family are typically between 141 and 232 amino acids in length. There are two conserved sequence motifs: HPE and PQR. 221 matched cddid_all.tbl CDD pfam15324 pfam15324 434634 TALPID3 Hedgehog signalling target. TALPID3 is a family of eukaryotic proteins that are targets for Hedgehog signalling. Mutations in this gene noticed first in chickens lead to multiple abnormalities of development. 1288 matched cddid_all.tbl CDD pfam15325 pfam15325 434635 MRI Modulator of retrovirus infection. MRI, or modulator of retrovirus infection, is a family of eukaryotic proteins that regulate the activity of the proteasome in the uncoating of retroviruses. 100 matched cddid_all.tbl CDD pfam15326 pfam15326 464647 TEX15 Testis expressed sequence 15. TEX15 is a family of eukaryotic proteins that is required for chromosomal synapsis and meiotic recombination. TEX15 regulates the loading of DNA repair proteins onto sites of double-stranded-breaks and, thus, its absence causes a failure in meiotic recombination. Two polymorphisms in the TEX15 gene could be considered the genetic risk factors for spermatogenic failure in the Chinese Han population. 234 matched cddid_all.tbl CDD pfam15327 pfam15327 464648 Tankyrase_bdg_C Tankyrase binding protein C terminal domain. This protein domain family is found at the C-terminal end of the Tankyrase binding protein in eukaryotes. The precise function of this protein is still unknown. However, it is known interacts with the enzyme tankyrase, a telomeric poly(ADP-ribose) polymerase, by binding to it. Tankyrin catalyzes poly(ADP-ribose) chain formation onto proteins. More specifically, it binds to the ankyrin domain in tankyrase. The protein domain is approximately 170 amino acids in length and contains two conserved sequence motifs: FPG and LKA. 169 matched cddid_all.tbl CDD pfam15328 pfam15328 464649 GCOM2 Putative GRINL1B complex locus protein 2. This protein family is named Putative GRINL1B complex locus protein 2. GRINL1B is short for: glutamate receptor, ionotropic, N-methyl D-aspartate-like 1B. The name indicates what sort of receptor it is thought to be, a ligand gated ion channel specific to the neurotransmitter Glutamate. This family of proteins is found in eukaryotes. Proteins in this family are typically between 325 and 463 amino acids in length. The protein is thought to be the product of a pseudogene with a role in helping assemble a gene transcription unit. 214 matched cddid_all.tbl CDD pfam15330 pfam15330 464650 SIT SHP2-interacting transmembrane adaptor protein, SIT. SIT, or SHP2-interacting transmembrane adaptor protein, is a disulfide-linked dimer that regulates human T Cell activation. 114 matched cddid_all.tbl CDD pfam15331 pfam15331 464651 TP53IP5 Cellular tumour antigen p53-inducible 5. TP53IP5 suppresses cell growth, and its intracellular location and expression change in a cell-cycle-dependent manner. 217 matched cddid_all.tbl CDD pfam15332 pfam15332 464652 LIME1 Lck-interacting transmembrane adapter 1. LIME1 is a family of eukaryotic transmembrane adaptors. It plays an important role in linking BCR stimulation to B-cell activation and is expressed in primary B cells. LIME localizes to lipid rafts in T cells in response to TCR stimulation, and is phosphorylated by Lck and recruits signalling molecules such as Lck, PI3K, Grb2, Gads, and SHP-2. LIME acts as the transmembrane adaptor linking BCR-induced membrane-proximal signalling to B-cell activation. 239 matched cddid_all.tbl CDD pfam15333 pfam15333 464653 TAF1D TATA box-binding protein-associated factor 1D. TAF1D is a family of eukaryotic proteins that are members of the SL1 complex The SL1 complex includes TBP and TAF1A, TAF1B and TAF1C, and plays a role in RNA polymerase I transcription. Alternatives names have included 'JOSD3, Josephin domain containing 3'. 217 matched cddid_all.tbl CDD pfam15334 pfam15334 464654 AIB Aurora kinase A and ninein interacting protein. AIB is a family of eukaryotic proteins necessary for the adequate functioning of Aurora-A, a protein involved in chromosome alignment, centrosome maturation, mitotic spindle assembly and aspects of tumourigenesis. AIB is likely to act as a regulator of Aurora-A activity. 326 matched cddid_all.tbl CDD pfam15335 pfam15335 464655 CAAP1 Caspase activity and apoptosis inhibitor 1. CAAP1, or caspase activity and apoptosis inhibitor 1, is a family of eukaryotic proteins involved in the regulation of apoptosis. It modulates a caspase-10 dependent mitochondrial caspase-3/9 feedback amplification loop. 63 matched cddid_all.tbl CDD pfam15336 pfam15336 464656 Auts2 Autism susceptibility gene 2 protein. Auts2, or FBRSL2, Fibrosin-1-like protein 2, is a family of eukaryotic proteins associated both with a susceptibility to autism and with influencing the number of corpora lutea produced by breeding sows. 217 matched cddid_all.tbl CDD pfam15337 pfam15337 464657 Vasculin Vascular protein family Vasculin-like 1. GC-rich promoter-binding protein 1-like 1 or Vasculin-like protein family 1, is likely to be a transcription factor. The domain family is found in eukaryotes, and is approximately 90 amino acids in length. 97 matched cddid_all.tbl CDD pfam15338 pfam15338 464658 TPIP1 p53-regulated apoptosis-inducing protein 1. TPIP1 is a family of eukaryotic proteins whose expression is induced by wild-type p53. Ectopically expressed TPIP1, which is localized within mitochondria, leads to apoptotic cell death through dissipation of mitochondrial A(psi)m. Phosphorylation of p53 Ser-46 regulates the transcriptional activation of TPIP1, thereby mediating p53-dependent apoptosis. 123 matched cddid_all.tbl CDD pfam15339 pfam15339 464659 Afaf Acrosome formation-associated factor. Afaf is a family of single pass type I membrane proteins. Afaf is a vesicle factor derived from the early endosome trafficking pathway that is involved in the biogenesis of the acrosome on the maturing spermatozoon head. 193 matched cddid_all.tbl CDD pfam15340 pfam15340 434649 COPR5 Cooperator of PRMT5 family. COPR5 is a family of histone H4-binding proteins expressed in the nucleus. It interacts with the N-terminus of histone H4 thereby mediating the association between histone H4 and PRMT5, PRMT5, the Janus kinase-binding protein 1 that catalyzes the formation of symmetric dimethyl-arginine residues in proteins. COPR5 is specifically required for histone H4 'Arg-3' methylation mediated by PRMT5, but not histone H3 'Arg-8' methylation, suggesting that it modulates the substrate specificity of PRMT5. This family of proteins is found in eukaryotes. 150 matched cddid_all.tbl CDD pfam15341 pfam15341 464660 SLX9 Ribosome biogenesis protein SLX9. SLX9 is present in pre-ribosomes from an early stage and is implicated in the processing events that remove the ITS1 spacer sequences. In eukaryotes, biogenesis of ribosomes starts in the nucleolus with transcription by RNA polymerase I of a large precursor RNA molecule, called 35S pre-rRNA in yeast, in which the 18S, 5.8S, and 25S mature rRNAs reside, while RNA polymerase III transcribes a 3'-extended pre-5S rRNA. The 35S precursor also contains external transcribed spacer elements (5' and 3'-ETS) at either end as well as internal transcribed spacers (ITS1 and ITS2) that separate the mature sequences. 118 matched cddid_all.tbl CDD pfam15342 pfam15342 434651 FAM212 FAM212 family. This domain family is found in eukaryotes, and is approximately 60 amino acids in length. 59 matched cddid_all.tbl CDD pfam15343 pfam15343 464661 DEPP Decidual protein induced by progesterone family. DEPP is a family of proteins expressed in various tissues, including pancreas, placenta, ovary, testis and kidney. High levels are found during the first trimester. Its expression is induced by progesterone, testosterone and, to a much lower extent, oestrogen. The family is alternatively known as fasting-induced gene protein, FIG. 188 matched cddid_all.tbl CDD pfam15344 pfam15344 464662 FAM217 FAM217 family. This family of proteins is found in eukaryotes. Proteins in this family are typically between 329 and 507 amino acids in length. There is a conserved YPDFLP sequence motif. 234 matched cddid_all.tbl CDD pfam15345 pfam15345 464663 TMEM51 Transmembrane protein 51. This family of proteins is found in eukaryotes. Proteins in this family are typically between 233 and 253 amino acids in length. 237 matched cddid_all.tbl CDD pfam15346 pfam15346 405931 ARGLU Arginine and glutamate-rich 1. ARGLU, arginine and glutamate-rich 1 protein family, is required for the oestrogen-dependent expression of ESR1 target genes. It functions in cooperation with MED1. The family of proteins is found in eukaryotes. 151 matched cddid_all.tbl CDD pfam15347 pfam15347 434654 PAG Phosphoprotein associated with glycosphingolipid-enriched. PAG, or Cbp/PAG (Csk binding protein/phospho-protein associated with glycosphingolipid-enriched microdomains) is a transmembrane family that has a negative regulatory role in T-cell activation through being an adapter for C-terminal Src kinase, Csk. This family of proteins is found in eukaryotes. 428 matched cddid_all.tbl CDD pfam15348 pfam15348 464664 GEMIN8 Gemini of Cajal bodies-associated protein 8. GEMIN8 proteins are found in the nuclear bodies called gems (Gemini of Cajal bodies) that are often in proximity to Cajal (coiled) bodies themselves. They are also found in the cytoplasm. The family is part of the SMN (survival motor neurone) complex that plays an essential role in spliceosomal snRNP assembly in the cytoplasm and is required for pre-mRNA splicing in the nucleus. GEMIN8 binds directly to SMN1 and mediates the interaction of the GEMIN6-GEMIN7 heterodimer. 230 matched cddid_all.tbl CDD pfam15349 pfam15349 434656 DCA16 DDB1- and CUL4-associated factor 16. DCA16 is a family of eukaryotic proteins that interacts with DDB1 and CUL4A. The family may function as a substrate receptor for the CUL4-DDB1 E3 ubiquitin-protein ligase complex. 216 matched cddid_all.tbl CDD pfam15350 pfam15350 464665 ETAA1 Ewing's tumour-associated antigen 1 homolog. This family of proteins is found in eukaryotes, where members are expressed at high levels in the brain, liver kidney and Ewing tumour cell lines. Proteins in this family are typically between 648 and 898 amino acids in length. 819 matched cddid_all.tbl CDD pfam15351 pfam15351 434658 JCAD Junctional protein associated with coronary artery disease. JCAD is a component of VE-cadherin-based cell-cell junctions in endothelial cells. The cell-cell or adherens junction is an adhesion complex that plays a crucial role in the organization and function of epithelial and endothelial cellular sheets. These junctions join the actin cytoskeleton to the plasma membrane to form adhesive contacts between cells or between cells and extracellular matrix. The junctions also mediate both cell adhesion and cell-signalling. JCAD localizes close to the apical membrane in epithelial cells. This family is found in eukaryotes. 1358 matched cddid_all.tbl CDD pfam15352 pfam15352 464666 K1377 Susceptibility to monomelic amyotrophy. This family of proteins is associated with a susceptibility to monomelic amyotrophy. 983 matched cddid_all.tbl CDD pfam15353 pfam15353 464667 HECA Headcase protein family homolog. HECA was characterized first in Drosophila where it regulates the proliferation and differentiation of cells during adult morphogenesis. In humans, HECA affects cell cycle progression and proliferation in head and neck cancer cells. It by slows down cell division of oral squamous cell carcinoma cells and may thereby act as a tumour-suppressor in head and neck cancers. 102 matched cddid_all.tbl CDD pfam15354 pfam15354 259486 KAAG1 Kidney-associated antigen 1. KAAG1, kidney-associated antigen 1, or RU2AS (RU2 antisense gene protein) has been found in mammals. It is expressed in testis and kidney, and, at lower levels, in urinary bladder and liver. It is expressed by a high proportion of tumours of various histologic origin, including melanomas, sarcomas and colorectal carcinomas. 84 matched cddid_all.tbl CDD pfam15355 pfam15355 405939 Chisel Stretch-responsive small skeletal muscle X protein, Chisel. The murine X-linked gene Chisel (Csl/Smpx) is selectively expressed in cardiac and skeletal muscle cells. It localizes to the costameric cytoskeleton of muscle cells through its association with focal adhesion proteins, where it may participate in regulating the dynamics of actin through the Rac1/p38 kinase pathway. Thus it is implicated in the maintenance of muscle integrity and in responses to biomechanical stress. 86 matched cddid_all.tbl CDD pfam15356 pfam15356 464668 SPR1 Psoriasis susceptibility locus 2. SPR1 is psoriasis susceptibility locus 2 protein family. 114 matched cddid_all.tbl CDD pfam15357 pfam15357 373780 SEEK1 Psoriasis susceptibility 1 candidate 1. This family is considered a candidate for susceptibility to psoriasis. 149 matched cddid_all.tbl CDD pfam15358 pfam15358 434661 TSKS Testis-specific serine kinase substrate. TSKS, testis-specific serine kinase substrate, is expressed in the testis and is downregulated in cancerous testicular tissue, in comparison with adjacent normal tissue. TSKS expression is very low to undetectable in seminoma, teratocarcinoma, embryonal, and Leydig cell tumours, while high in testicular tissue adjacent to tumours which contain pre-malignant carcinoma in situ. Recently it has been shown in human testis to be localized to the equatorial segment of ejaculated human sperm. The finding of a TSKS family member in mature sperm suggests that this family of kinases might play a role in sperm function. TSKS is localized during spermiogenesis to the centrioles of post-meiotic spermatids, where it reaches its greatest concentration during the period of flagellogenesis. 455 matched cddid_all.tbl CDD pfam15359 pfam15359 464669 CDV3 Carnitine deficiency-associated protein 3. This family of proteins is found in eukaryotes. Proteins in this family are typically between 128 and 251 amino acids in length. CDV3 is also known as TPP36 - tyrosine-phosphorylated protein 36. The function is not known. 128 matched cddid_all.tbl CDD pfam15360 pfam15360 464670 Apelin APJ endogenous ligand. Apelin is among the most potent stimulators of cardiac contractility known. The apelin-APJ signaling pathway is an important novel mediator of cardiovascular control. Apelin is an adipokine secreted by adipocytes where it is co-expressed with apelin receptor (APJ) in adipocytes. It suppresses adipogenesis through MAPK kinase/ERK dependent pathways and prevents lipid droplet fragmentation, thereby inhibiting basal lipolysis through AMP kinase dependent enhancement of perilipin expression. It also inhibits hormone-stimulated acute lipolysis through decreasing perilipin phosphorylation. Apelin induces a decrease of free fatty acid release via its dual inhibition on adipogenesis and lipolysis. As a vaso-active and vascular cell growth-regulating peptide Apelin is a target of the BMP pathway, the TGF-beta/bone morphogenic protein (BMP) system - a major pathway for angiogenesis. 55 matched cddid_all.tbl CDD pfam15361 pfam15361 464671 RIC3 Resistance to inhibitors of cholinesterase homolog 3. RIC3 is a protein associated with nicotinic acetylcholine receptors (nAChRs), neurotransmitter-gated ion channels expressed at the neuromuscular junction and within the central and peripheral nervous systems. It can enhance functional expression of multiple nAChR subtypes. RIC3 promotes functional expression of homomeric alpha-7 and alpha-8 nicotinic acetylcholine receptors at the cell surface. 142 matched cddid_all.tbl CDD pfam15362 pfam15362 464672 Enamelin Enamelin. ENAMELIN is involved in the mineralization and structural organization of enamel. It is necessary for the extension of enamel during the secretory stage of dental enamel formation. The proteins are expressed in teeth, particularly in odontoblasts, ameloblasts and cementoblasts. 907 matched cddid_all.tbl CDD pfam15363 pfam15363 464673 DUF4596 Domain of unknown function (DUF4596). This domain family is found in eukaryotes, and is approximately 50 amino acids in length. There is a conserved ELET sequence motif. There are two completely conserved residues (S and E) that may be functionally important. 46 matched cddid_all.tbl CDD pfam15364 pfam15364 464674 PAXIP1_C PAXIP1-associated-protein-1 C term PTIP binding protein. This protein domain family is the C-terminal domain of PAXIP1-associated-protein-1, which also goes by the name PTIP-associated protein 1. This family of proteins is found in eukaryotes. The function of this protein is to localize at the site of DNA damage and form foci with PTIP at the DNA break point. Furthermore, studies have shown that depletion of PA1 increases cellular sensitivity to ionizing radiation. Proteins in this family are typically between 122 and 254 amino acids in length. 134 matched cddid_all.tbl CDD pfam15365 pfam15365 464675 PNRC Proline-rich nuclear receptor coactivator motif. The PNRC family, proline-rich nuclear receptor coactivator, is found in eukaryotes. Studies in S. pombe show that the proteins carrying this motif are mRNA decapping proteins. In addition, this motif is found in Saccharomyces cerevisiae two intrinsically disordered decapping enhancers Edc1 and Edc2, which show limited sequence conservation with human PNRC2. This motif in the N-terminal domain serves two purposes: it enhances the activity of the catalytic domain by recognizing part of the mRNA cap structure (i.e. activation motif), and secondly, it directly interacts with the decapping activator Dcp1. Mutation in the (YAG) sequence led to los of activity of activate the decapping complex. Hence the activity of the family members involved in mRNA processing mechanisms depends on YAG activation motif that is 11-13 residues N-terminal of a conserved LPxP Dcp1 interaction motif. 19 matched cddid_all.tbl CDD pfam15366 pfam15366 464676 DUF4597 Domain of unknown function (DUF4597). This family of proteins is found in eukaryotes. Proteins in this family are typically between 63 and 76 amino acids in length. There is a conserved TPPTPT sequence motif. 63 matched cddid_all.tbl CDD pfam15367 pfam15367 464677 CABS1 Calcium-binding and spermatid-specific protein 1. CABS1 is a family of proteins found in eukaryotes. It is also known as NYD-SP26. It binds calcium and is specifically expressed in the elongate spermatids and then localized into the principal piece of flagella of matured spermatozoa. 397 matched cddid_all.tbl CDD pfam15368 pfam15368 464678 BioT2 Spermatogenesis family BioT2. BioT2 is a family of eukaryotic proteins expressed only in the testes. BioT2 is found abundantly in five types of murine cancer cell lines, suggesting it plays a role in testes development as well as tumourigenesis. 169 matched cddid_all.tbl CDD pfam15369 pfam15369 464679 KIAA1328 Uncharacterized protein KIAA1328. This function of this protein family remains uncharacterized. This family of proteins is found in eukaryotes. 327 matched cddid_all.tbl CDD pfam15370 pfam15370 405951 NOPCHAP1 NOP protein chaperone 1. This entry includes NOPCHAP1 from animals and New4 from fission yeast. NOPCHAP1 is a client-loading PAQosome/R2TP complex cofactor that selects NOP58 to promote box C/D small nucleolar ribonucleoprotein (snoRNP) assembly. The function of New4 is not clear. 111 matched cddid_all.tbl CDD pfam15371 pfam15371 464680 DUF4599 Domain of unknown function (DUF4599). The function of this family of eukaryotic proteins is not known. 88 matched cddid_all.tbl CDD pfam15372 pfam15372 434673 DUF4600 Domain of unknown function (DUF4600). 128 matched cddid_all.tbl CDD pfam15373 pfam15373 464681 DUF4601 Domain of unknown function (DUF4601). This protein family is a domain of unknown function, which is found in eukaryotes. In humans, the gene encoding this protein is found in the position, chromosome 19 open reading frame 45. 274 matched cddid_all.tbl CDD pfam15374 pfam15374 464682 CCDC71L Coiled-coil domain-containing protein 71L. The protein family, Coiled-coil domain-containing protein 71L, is a domain of unknown function, which is found in eukaryotes. 383 matched cddid_all.tbl CDD pfam15375 pfam15375 464683 DUF4602 Domain of unknown function (DUF4602). This family of proteins is found in eukaryotes. Proteins in this family are typically between 173 and 294 amino acids in length. This family includes Human C1orf131. 111 matched cddid_all.tbl CDD pfam15376 pfam15376 464684 DUF4603 Domain of unknown function (DUF4603). This protein family is a domain of unknown function. In particular, this domain lies at the C-terminal end of a protein found in eukaryotes. 1293 matched cddid_all.tbl CDD pfam15377 pfam15377 464685 DUF4604 Domain of unknown function (DUF4604). This protein family is a domain of unknown function, which is found in eukaryotes. Proteins in this family are typically between 141 and 174 amino acids in length and contain a conserved LSF sequence motif. 171 matched cddid_all.tbl CDD pfam15378 pfam15378 464686 DUF4605 Domain of unknown function (DUF4605). This protein family is a domain of unknown function, which is found in eukaryotes. Proteins in this family are typically between 82 and 137 amino acids in length. 59 matched cddid_all.tbl CDD pfam15379 pfam15379 464687 DUF4606 Domain of unknown function (DUF4606). This domain family is found in eukaryotes, and is approximately 100 amino acids in length. 103 matched cddid_all.tbl CDD pfam15380 pfam15380 464688 DUF4607 Domain of unknown function (DUF4607). This family of proteins is found in eukaryotes. Proteins in this family are typically between 207 and 359 amino acids in length. 264 matched cddid_all.tbl CDD pfam15382 pfam15382 464689 DUF4609 Domain of unknown function (DUF4609). This family of proteins is found in eukaryotes. Proteins in this family are typically between 70 and 139 amino acids in length. 68 matched cddid_all.tbl CDD pfam15383 pfam15383 464690 TMEM237 Transmembrane protein 237. This protein family is found in eukaryotes. The function of this protein is to aid the production of new cilia in ciliogenesis. Mutations in the protein cause a disease, named Joubert syndrome type 14 (JBTS14) and also affect cell signalling using the Wnt pathway. Proteins in this family are typically between 203 and 512 amino acids in length. There are two completely conserved G residues that may be functionally important. 247 matched cddid_all.tbl CDD pfam15384 pfam15384 464691 PAXX PAXX, PAralog of XRCC4 and XLF, also called C9orf142. PAXX is a set of eukaryotic proteins that belong to the XRCC4 superfamily of DNA-double-strand break-repair proteins. PAXX interacts directly with DSB-repair protein Ku and is recruited to DNA-damage sites in cells thus functioning with XRCC4 and XLF to bring about DSB repair and cell survival in response to DSB-inducing agents. 194 matched cddid_all.tbl CDD pfam15385 pfam15385 464692 SARG Specifically androgen-regulated gene protein. This family of proteins is found in eukaryotes, the function of this protein is still unknown but it is thought to be an androgen receptor. Protein expression is up-regulated in the presence of androgens, but not in the presence of glucocorticoids. SARG tends to be highly expressed in prostate tissue. Proteins in this family are typically between 340 and 587 amino acids in length. There is a conserved EETI sequence motif. 568 matched cddid_all.tbl CDD pfam15386 pfam15386 464693 Tantalus Drosophila Tantalus-like. An alpha+beta fold domain found in metazoan proteins such as Drosophila Tantalus. Drosophila Tantalus binds the chromatin protein Additional sex combs (Asx) and also binds DNA in vitro. 57 matched cddid_all.tbl CDD pfam15387 pfam15387 464694 DUF4611 Domain of unknown function (DUF4611). This family of proteins is found in eukaryotes. Proteins in this family are typically between 71 and 100 amino acids in length. There is a conserved AKR sequence motif. 96 matched cddid_all.tbl CDD pfam15388 pfam15388 464695 FAM117 Protein Family FAM117. This protein family is a domain of unknown function found in eukaryotes. Proteins in this family are typically between 269 and 453 amino acids in length. There are two conserved sequence motifs: RRT and TQT. 310 matched cddid_all.tbl CDD pfam15389 pfam15389 464696 DUF4612 Domain of unknown function (DUF4612). This protein family is a domain of unknown function, which is found in eukaryotes. Proteins in this family are typically between 109 and 323 amino acids in length. 110 matched cddid_all.tbl CDD pfam15390 pfam15390 464697 WDCP WD repeat and coiled-coil-containing protein family. This family includes WD repeat and coiled-coil-containing protein (WDCP, previously known as C2orf44), which is found in eukaryotes and consists of around 721 amino acids. The N-terminal contains two WD (tryptophan-aspartic acid) repeats (WD1 and WD2). WD repeats may be involved in a range of biological functions including apoptosis, transcriptional regulation and signal transduction. The C-terminal contains a proline-rich sequence (PPRLPQR), and is predicted to have leucine-rich coiled coil region (CC). WDCP was identified in a proteomic screen to find signalling components that interact with Hck (hematopoietic cell kinase), a non-receptor tyrosine kinase. WDCP was shown to bind tightly and specifically to the SH3 domain of Hck in U937 human monocytic cells. WDCP was also shown to exist as an oligomer when expressed in mammalian cells. While the function of WDCP is unknown, it has been identified in a gene fusion event with anaplastic lymphoma kinase (ALK) in colorectal cancer patients. 688 matched cddid_all.tbl CDD pfam15391 pfam15391 464698 DUF4614 Domain of unknown function (DUF4614). This domain family is found in eukaryotes, and is approximately 180 amino acids in length. There is a conserved EALT sequence motif. 174 matched cddid_all.tbl CDD pfam15392 pfam15392 464699 Joubert Joubert syndrome-associated. This family of proteins is domain of unknown function, which is found in eukaryotes. However, mutations in the gene lead to Joubert's Syndrome, indicating that the protein that the gene encodes for is vital for correct ciliogenesis. 339 matched cddid_all.tbl CDD pfam15393 pfam15393 464700 DUF4615 Domain of unknown function (DUF4615). This protein family is a domain of unknown function, which is found in eukaryotes. Proteins in this family are typically between 161 and 229 amino acids in length. There is a single completely conserved residue F that may be functionally important. 132 matched cddid_all.tbl CDD pfam15394 pfam15394 464701 DUF4616 Domain of unknown function (DUF4616). This protein family is a domain of unknown function found at the C-terminal domain of the proteins. This protein family is found in eukaryotes. Proteins in this family are typically between 166 and 538 amino acids in length. 505 matched cddid_all.tbl CDD pfam15395 pfam15395 464702 DUF4617 Domain of unknown function (DUF4617). This family of proteins is found in eukaryotes. Proteins in this family are typically between 702 and 1745 amino acids in length. 1086 matched cddid_all.tbl CDD pfam15396 pfam15396 464703 FAM60A Protein Family FAM60A. This protein family, FAM60A is a family of proteins is found in eukaryotes. It is known to be a cell cycle protein that binds to the promoter of a gene transcription repressor complex, named SIN4-HDAC complex. This means that FAM60A has an important role to play in 'switching on' gene expression. Proteins in this family are typically between 179 and 324 amino acids in length. 206 matched cddid_all.tbl CDD pfam15397 pfam15397 464704 DUF4618 Domain of unknown function (DUF4618). This family of proteins is found in eukaryotes. Proteins in this family are typically between 238 and 363 amino acids in length. There are two conserved sequence motifs: EYP and KCTPD. 258 matched cddid_all.tbl CDD pfam15398 pfam15398 464705 DUF4619 Domain of unknown function (DUF4619). This family of proteins is found in eukaryotes. Proteins in this family are typically between 128 and 299 amino acids in length. 296 matched cddid_all.tbl CDD pfam15399 pfam15399 405977 DUF4620 Domain of unknown function (DUF4620). 113 matched cddid_all.tbl CDD pfam15400 pfam15400 464706 TEX33 Testis-expressed sequence 33 protein family. This family of proteins is found in eukaryotes. Proteins in this family are typically between 147 and 280 amino acids in length. There are two conserved sequence motifs: NIRH and SYT. The function is not known. 138 matched cddid_all.tbl CDD pfam15401 pfam15401 405979 TAA-Trp-ring Tryptophan-ring motif of head of Trimeric autotransporter adhesin. TAA-head_Trp-ring is the tryptophan-ring motif of some Gram-negative Enterobacteriaceae. The Trp-ring folds into a beta-meander type on the top of the head domain of its trimeric autotransporter adhesin proteins. In conjunction with the GIN domain it is thought to be the region of the head that adheres to fibronectin. 65 matched cddid_all.tbl CDD pfam15402 pfam15402 434698 MELT_2 MELT motif. This entry represents MELT motifs found in the SPC7 and related proteins. 26 matched cddid_all.tbl CDD pfam15403 pfam15403 405980 HiaBD2 HiaBD2_N domain of Trimeric autotransporter adhesin (GIN). HiaBD2_N may represent the GIN domain of the Head region of TAAs - trimeric autotransporter adhesins. Not all TAAs carry this domain; however, in those that do, the GIN in combination with the Trp-ring domain is necessary for adhesion to fibronectin in the host cell. 52 matched cddid_all.tbl CDD pfam15404 pfam15404 434699 PH_4 Pleckstrin homology domain. This Pleckstrin homology domain is found in some fungal species. 184 matched cddid_all.tbl CDD pfam15405 pfam15405 405982 PH_5 Pleckstrin homology domain. This Pleckstrin homology domain is found in some fungal species. 135 matched cddid_all.tbl CDD pfam15406 pfam15406 373825 PH_6 Pleckstrin homology domain. This Pleckstrin homology domain is found in some fungal species. 112 matched cddid_all.tbl CDD pfam15407 pfam15407 434700 Spo7_2_N Sporulation protein family 7. Spo7_2 constitutes a different set of fungal and related species from those found in Spo7. This domain is found in general at the N-terminus. In many members the domain is associated with a Pleckstrin-homology - PH - domain. 64 matched cddid_all.tbl CDD pfam15409 pfam15409 405984 PH_8 Pleckstrin homology domain. This Pleckstrin homology domain is found in some fungal species. 89 matched cddid_all.tbl CDD pfam15410 pfam15410 434701 PH_9 Pleckstrin homology domain. This Pleckstrin homology domain is found in some fungal species. 118 matched cddid_all.tbl CDD pfam15411 pfam15411 464707 PH_10 Pleckstrin homology domain. This Pleckstrin homology domain is found in some fungal species. 120 matched cddid_all.tbl CDD pfam15412 pfam15412 464708 Nse4-Nse3_bdg Binding domain of Nse4/EID3 to Nse3-MAGE. This family includes Nse4 and EID3 members, that bind over this region to the Nse3 pocket, in MAGE family pfam01454. 56 matched cddid_all.tbl CDD pfam15413 pfam15413 405988 PH_11 Pleckstrin homology domain. This Pleckstrin homology domain is found in some fungal species. 105 matched cddid_all.tbl CDD pfam15414 pfam15414 405989 DUF4621 Protein of unknown function (DUF4621). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 350 amino acids in length. 329 matched cddid_all.tbl CDD pfam15415 pfam15415 405990 Mfa_like_2 Fimbrillin-like. This family of proteins is found in bacteria. Proteins in this family are typically between 348 and 360 amino acids in length. Analysis of structural comparisons shows this family to be part of the FimbA (CL0450) superfamily of adhesin components or fimbrillins. 312 matched cddid_all.tbl CDD pfam15416 pfam15416 405991 DUF4623 Domain of unknown function (DUF4623). This family of proteins is found in bacteria. Proteins in this family are approximately 470 amino acids in length. There are two conserved sequence motifs: HLL and RYL. 448 matched cddid_all.tbl CDD pfam15417 pfam15417 405992 DUF4624 Domain of unknown function (DUF4624). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 150 amino acids in length. 132 matched cddid_all.tbl CDD pfam15418 pfam15418 405993 DUF4625 Domain of unknown function (DUF4625). This family contains a likely bacterial Ig-like fold, suggesting it may be a family of lipoproteins. 131 matched cddid_all.tbl CDD pfam15419 pfam15419 464709 LNP1 Leukemia NUP98 fusion partner 1. This family of proteins includes leukemia NUP98 fusion partner 1, the gene encoding this protein is involved in a chromosomal translocation with the NUP98 locus in a form of T-cell acute lymphoblastic leukemia. 167 matched cddid_all.tbl CDD pfam15420 pfam15420 434705 Abhydrolase_9_N Alpha/beta-hydrolase family N-terminus. This is the N-terminal transmembrane domain of a family of alpha/beta hydrolases which may function as lipases. The C-terminal domain (pfam10081) is the catalytic domain. 208 matched cddid_all.tbl CDD pfam15421 pfam15421 405996 Polysacc_deac_3 Putative polysaccharide deacetylase. 423 matched cddid_all.tbl CDD pfam15423 pfam15423 405997 FLYWCH_N FLYWCH-type zinc finger-containing protein. This family is the N-terminus of some FLYWCH-zinc-finger proteins, found in eukaryotes. The family is found in association with pfam04500. There are two conserved sequence motifs: EQE and QEPS. 107 matched cddid_all.tbl CDD pfam15424 pfam15424 464710 ODAM Odontogenic ameloblast-associated family. 264 matched cddid_all.tbl CDD pfam15425 pfam15425 434707 DUF4627 Domain of unknown function (DUF4627). This family of proteins is found in bacteria. Proteins in this family are approximately 230 amino acids in length. There is a conserved WYK sequence motif. 202 matched cddid_all.tbl CDD pfam15427 pfam15427 464711 S100PBPR S100P-binding protein. S100PBPR is a family of proteins found in eukaryotes, and localized to cell nuclei where S100P is also present, and the two proteins co-immunoprecipitate. S100P is a member of the S100 family of calcium-binding proteins and there have been several recent reports of its over-expression in pancreatic ductal adenocarcinoma. In situ hybridization shows S100PBPR transcripts to be found in islet cells but not duct cells of the healthy pancreas. An interaction between S100P and S100PBPR may be involved in early pancreatic cancer. 389 matched cddid_all.tbl CDD pfam15428 pfam15428 434709 Imm26 Immunity protein 26. A predicted immunity protein with mostly all-beta fold and several conserved hydrophobic residues. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-URI1 or Tox-HNH family. The protein is also found heterogeneous poly-immunity loci. 107 matched cddid_all.tbl CDD pfam15429 pfam15429 464712 DUF4628 Domain of unknown function (DUF4628). This family of proteins is found in eukaryotes. Proteins in this family are typically between 152 and 673 amino acids in length. 273 matched cddid_all.tbl CDD pfam15430 pfam15430 464713 SVWC Single domain von Willebrand factor type C. SVWC is a family of single-domain von Willebrand factor type C proteins from lower eukaryotes. The canonical pattern of most von Willebrand factor type C (VWC) domains is of ten cysteines, however this family, largely but not exclusively of arthropod proteins, contains only eight. SVWC family proteins respond to environmental challenges, such as bacterial infection and nutritional status. They also are involved in anti-viral immunity, and all of these functions seem linked to SVWC expression being induced by Dicer2. 66 matched cddid_all.tbl CDD pfam15431 pfam15431 434712 TMEM190 Transmembrane protein 190. 128 matched cddid_all.tbl CDD pfam15432 pfam15432 434713 Sec-ASP3 Accessory Sec secretory system ASP3. Sec-ASP3 is family of bacterial proteins involved in the Sec secretory system. The family forms part of the accessory SecA2/SecY2 system specifically required to export GspB, a serine-rich repeat cell-wall glycoprotein adhesin encoded upstream in the same operon. 125 matched cddid_all.tbl CDD pfam15433 pfam15433 464714 MRP-S31 Mitochondrial 28S ribosomal protein S31. MRP-S31 is the mitochondrial 28S ribosomal subunit S31. This family of proteins is found in eukaryotes. Proteins in this family are typically between 246 and 395 amino acids in length. There are two conserved sequence motifs: RHFMELV and GLSKN. 303 matched cddid_all.tbl CDD pfam15434 pfam15434 464715 FAM104 Family 104. This family of proteins is found in eukaryotes. Proteins in this family are typically between 113 and 185 amino acids in length. There is a conserved SLQ sequence motif. 109 matched cddid_all.tbl CDD pfam15435 pfam15435 464716 UNC119_bdg UNC119-binding protein C5orf30 homolog. UNC119_bdg is a family of eukaryotic proteins that probably plays a role in trafficking of proteins, via interaction with unc119 family cargo adapters. The family may play a role in ciliary membrane localization. 198 matched cddid_all.tbl CDD pfam15436 pfam15436 434717 PGBA_N Plasminogen-binding protein pgbA N-terminal. PGBA_N is an N-terminal family of bacterial proteins that bind plasminogen. This activity was identified in In Helicobacter pylori where it is thought to contribute to the virulence of this bacterium. Both PgbA and PgbB are surface-exposed proteins that mediate binding to plasminogen such that it can be converted into plasmin in the presence of a Pg activator. 217 matched cddid_all.tbl CDD pfam15437 pfam15437 292077 PGBA_C Plasminogen-binding protein pgbA C-terminal. PGBA_C is an C-terminal family of bacterial proteins that bind plasminogen. This activity was identified in Helicobacter pylori where it is thought to contribute to the virulence of this bacterium. Both PgbA and PgbB are surface-exposed proteins that mediate binding to plasminogen such that it can be converted into plasmin in the presence of a plasminogen activator. 84 matched cddid_all.tbl CDD pfam15438 pfam15438 373844 Phyto-Amp Antigenic membrane protein of phytoplasma. Phyto-Amp is a family of phytopathogenic wall-less bacterial antigenic membrane proteins. The bacteria are limited to the phloem and pose a major threat to agriculture worldwide. They are transmitted in a persistent, propagative manner by phloem-sucking Hemipteran insects. Phytoplasma membrane proteins are in direct contact with hosts and are assumed to be involved in determining vector specificity. Phyto-Amp is thought to be one family of proteins that mediates such specificity. The proteins appear to be encoded by circular extrachromosomal elements, at least one of which is a plasmid. 147 matched cddid_all.tbl CDD pfam15439 pfam15439 464717 NYAP_N Neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adapter. NYAP_N is an N-terminal family of eukaryotic proteins that are substrates of tyrosine kinase in the brain. When first identified, the family members were referred to as unconventional myosin XVI, or Myr 8. However, proteins have now been identified as being integrally involved in neuronal function and morphogenesis. The family is involved in both the activation of phosphoinositide 3-kinase (PI3K) and the recruitment of the downstream effector WAVE complex to the close vicinity of PI3K; it also appears to regulate the brain size and neurite outgrowth in mice. 379 matched cddid_all.tbl CDD pfam15440 pfam15440 464718 THRAP3_BCLAF1 THRAP3/BCLAF1 family. This family includes thyroid hormone receptor-associated protein 3 (THRAP3), which is a spliceosome component and a subunit of the TRAP complex which plays a role in pre-mRNA splicing and in mRNA decay. It also includes the transcriptional repressor Bcl-2-associated transcription factor 1 (BCLAF1). 641 matched cddid_all.tbl CDD pfam15441 pfam15441 464719 ARHGEF5_35 RhoGEF 5/35 N-terminal disordered region. This entry includes Rho guanine nucleotide exchange factor 5 and Rho guanine nucleotide exchange factor 35. However, this region is disordered and the RhoGEF function resides in a different domain pfam00621. 488 matched cddid_all.tbl CDD pfam15442 pfam15442 434721 DUF4629 Domain of unknown function (DUF4629). This domain family is found in eukaryotes, and is approximately 150 amino acids in length. There are two conserved sequence motifs: MHML and LGKK. 150 matched cddid_all.tbl CDD pfam15443 pfam15443 464720 DUF4630 Domain of unknown function (DUF4630). This family of proteins is found in eukaryotes. Proteins in this family are typically between 124 and 286 amino acids in length. 156 matched cddid_all.tbl CDD pfam15444 pfam15444 464721 TMEM247 Transmembrane protein 247. This family of transmembrane proteins is found in eukaryotes. Proteins in this family are typically between 197 and 222 amino acids in length. The function of this family is unknown. 206 matched cddid_all.tbl CDD pfam15445 pfam15445 373851 ATS acidic terminal segments, variant surface antigen of PfEMP1. ATS is the intracellular and relatively conserved acidic terminal segment of the Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1). this domain appears to be present in all variants of the highly polymorphic PfEMP1 proteins. 446 matched cddid_all.tbl CDD pfam15446 pfam15446 434724 zf-PHD-like PHD/FYVE-zinc-finger like domain. This family appears to be a combination domain of several consecutive zinc-binding regions. 170 matched cddid_all.tbl CDD pfam15447 pfam15447 406013 NTS N-terminal segments of PfEMP1. This family, the N-terminal segment, is the most variable part of the variant surface antigen family of Plasmodium falciparum, the erythrocyte membrane protein-1 (PfEMP1) proteins. PfEMP1 is an important target for protective immunity and is implicated in the pathology of malaria through its ability to adhere to host endothelial receptors. A structural and functional study of the N-terminal domain of PfEMP1 from the VarO variant comprising the N-terminal segment (NTS) and the first DBL domain (DBL1alpha1), shows this region is directly implicated in rosetting. NTS, previously thought to be a structurally independent component of PfEMP1, forms an integral part of the DBL1alpha domain that is found to be the important heparin-binding site. This family is closely associated with PFEMP, pfam03011, and Duffy_binding, pfam05424. 36 matched cddid_all.tbl CDD pfam15448 pfam15448 406014 NTS_2 N-terminal segments of P. falciparum erythrocyte membrane protein. NTS_2 is a family of the most variable part of the variant surface antigen family of Plasmodium falciparum, the erythrocyte membrane protein-1 (PfEMP1). However, in this group of proteins conservation is high. PfEMP1 is an important target for protective immunity and is implicated in the pathology of malaria through its ability to adhere to host endothelial receptors. 50 matched cddid_all.tbl CDD pfam15449 pfam15449 464722 Retinal Retinal protein. This family of proteins is found in the photoreceptor cells of the retina. Mutations of the gene encoding this protein have been associated with retinal disorders such as retinitis pigmentosa and late-onset progressive retinal atrophy. The function of this family of proteins is unknown, but it is likely to be important in the development and function of the retina. 1293 matched cddid_all.tbl CDD pfam15450 pfam15450 464723 CCDC154 Coiled-coil domain-containing protein 154. CCDC154 is an osteopetrosis-related protein that suppresses cell proliferation by inducing G2/M arrest. 526 matched cddid_all.tbl CDD pfam15451 pfam15451 373857 DUF4632 Domain of unknown function (DUF4632). This family of proteins is found in eukaryotes. Proteins in this family are typically between 59 and 190 amino acids in length. 71 matched cddid_all.tbl CDD pfam15452 pfam15452 464724 NYAP_C Neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adapter. NYAP_C is a C-terminal family of eukaryotic proteins that are substrates of tyrosine kinase in the brain. When first identified, the family members were referred to as unconventional myosin XVI, or Myr 8. However, proteins have now been identified as being integrally involved in neuronal function and morphogenesis. The family is involved in both the activation of phosphoinositide 3-kinase (PI3K) and the recruitment of the downstream effector WAVE complex to the close vicinity of PI3K; it also appears to regulate the brain size and neurite outgrowth in mice. 259 matched cddid_all.tbl CDD pfam15453 pfam15453 464725 Pilt Protein incorporated later into Tight Junctions. Pilt is a family of eukaryotic tight junction-proteins that binds to guanylate-kinase. Pilt is a component of TJs (Tight junctions) rather than AJs (Adhesin junctions). The protein is incorporated into TJs after TJ strands are formed, thereby suggesting the name Pilt for 'protein incorporated later into TJs'. Pilt binds to the guanylate-kinase region of hDlg otherwise known as Disk large homolog. 362 matched cddid_all.tbl CDD pfam15454 pfam15454 464726 LAMTOR Late endosomal/lysosomal adaptor and MAPK and MTOR activator. LAMTOR is a family of eukaryotic proteins that have otherwise been referred to as Lipid raft adaptor protein p18, Late endosomal/lysosomal adaptor and MAPK and MTOR activator 1, and Protein associated with DRMs and endosomes. It is found to be one of three small proteins constituting the Rag complex or Ragulator that interact with each other, localize to endosomes and lysosomes, and play positive roles in the MAPK pathway. The complex does this by interacting with the Rag GTPases, recruiting them to lysosomes, and bringing about mTORC1 activation. 69 matched cddid_all.tbl CDD pfam15455 pfam15455 464727 Pro-rich_19 Proline-rich 19. This family includes proline-rich protein 19. 363 matched cddid_all.tbl CDD pfam15456 pfam15456 434730 Uds1 Up-regulated During Septation. Uds1 is a domain family is found mostly in fungi, and is typically between 120 and 138 amino acids in length. The GO annotation for the S.pombe protein describes the protein as barrier septum assembly involved in cell cycle cytokinesis, GO:0071937. Many of the uncharacterized members are listed as being involucrin repeat proteins, but this can not be substantiated. 119 matched cddid_all.tbl CDD pfam15457 pfam15457 406021 HopW1-1 Type III T3SS secreted effector HopW1-1/HopPmaA. HopW1-1 is a family of bacterial modular P. syringae Avr effectors that induce accumulation of the signal molecule salicylic acid (SA) and the transcripts of HWI1 (HOPW1-1-INDUCED GENE1) in Arabidopsis. Thus HopW1-1 elicits a resistance response in Arabidopsis. 321 matched cddid_all.tbl CDD pfam15458 pfam15458 464728 NTR2 Nineteen complex-related protein 2. Family members include the NTR2 or Nineteen complex-related protein 2 found in fungus and plants. NTR2 proteins form a complex with the DExD/H-box RNA helicase Prp43. Along with NTR1 it is an accessory factor of Prp43 in catalysing spliceosome disassembly. Disassembly of the spliceosome after completion of the splicing reaction is necessary for recycling of splicing factors to promote efficient splicing. NTR2 and NTR1 associate with a post-splicing complex containing the excised intron and the spliceosomal U2, U5, and U6 snRNAs, that supports a link with a late stage in the pre-mRNA splicing process. 214 matched cddid_all.tbl CDD pfam15459 pfam15459 464729 RRP14 60S ribosome biogenesis protein Rrp14. RRP14 is a family of nucleolar 60S ribosomal biogenesis proteins from eukaryotes. RRP14 functions in ribosome synthesis as it is required for the maturation of both small and large subunit rRNAs and it helps to prevent premature cleavage of the pre-rRNA at site C2. It also plays a role in cell polarity and/or spindle positioning 2], 62 matched cddid_all.tbl CDD pfam15460 pfam15460 464730 SAS4 Something about silencing, SAS, complex subunit 4. SAS4 is a family of largely fungal silencing regulators. This silencing is mediated by chromatin. SAS4 specifically silences the yeast mating-type genes HML and HMR. SAS4 is found to be one subunit of a complex, the SAS complex, that interacts with chromatin assembly factor Asf1p, and asf1 mutants show silencing defects similar to mutants in the SAS complex. Thus, ASF1-dependent chromatin-assembly may mediate the role of the SAS complex in silencing. Co-expression of Sas2, SAS4, and Sas5 in Escherichia coli leads to formation of a stable SAS complex that acetylates histones. SAS4 is essential for the acetyltransferase activity of Sas2, and Sas5 is also important. 99 matched cddid_all.tbl CDD pfam15461 pfam15461 434732 BCD Beta-carotene 15,15'-dioxygenase. This is a family of bacterial and archaeal proteins that catalyzes or regulates the conversion of beta-carotene to retinal. characterization of BCD proteins shows them to cleave beta-carotene at its central double bond (15,15') to yield two molecules of all-trans-retinal. However, the oxygen atom of retinal originated not from water but from molecular oxygen, suggesting that the enzyme was a beta-carotene 15,15'-dioxygenase, rather than a mono-oxygenase that catalyzes the same biochemical reaction. 267 matched cddid_all.tbl CDD pfam15462 pfam15462 464731 Barttin Bartter syndrome, infantile, with sensorineural deafness (Barttin). Barttin is a family of mammalian proteins that are chloride ion channel beta-subunits crucial for renal Cl-re-absorption and inner ear K+ secretion. Bartter syndrome is a term covering a heterogeneous group of autosomal recessive salt-losing nephropathies that are caused by disturbed transepithelial sodium chloride re-absorption in the distal nephron. Mutations in the BCD proteins lead to sensorial deafness. 223 matched cddid_all.tbl CDD pfam15463 pfam15463 434734 ECM11 Extracellular mutant protein 11. ECM11 is a family of largely fungal proteins. ECM11 interacts with Cdc6, an essential protein involved in the initiation of DNA replication, and is a nuclear protein involved in maintaining chromatin structure. It was previously identified as a protein involved in yeast cell wall biogenesis and organization, but is also found to be required in meiosis where its function is related to DNA replication and crossing-over. 133 matched cddid_all.tbl CDD pfam15464 pfam15464 434735 DUF4633 Domain of unknown function (DUF4633). This family of proteins is found in eukaryotes. Proteins in this family are typically between 94 and 123 amino acids in length. 112 matched cddid_all.tbl CDD pfam15465 pfam15465 434736 DUF4634 Domain of unknown function (DUF4634). This family of proteins is found in eukaryotes. Proteins in this family are typically between 98 and 133 amino acids in length. 131 matched cddid_all.tbl CDD pfam15466 pfam15466 406030 DUF4635 Domain of unknown function (DUF4635). This family of proteins is found in eukaryotes. Proteins in this family are typically between 120 and 154 amino acids in length. There are two conserved sequence motifs: LEQ and DLE. 134 matched cddid_all.tbl CDD pfam15467 pfam15467 464732 SGIII Secretogranin-3. Secretogranin_3 is a family of vertebrate proteins that is one of the granin family. Granins are rich in acidic amino acids, exhibit aggregation at low pH, and possess a high capacity for calcium binding. Because granins are restricted in their localization to secretory granules of neuroendocrine cells, two interesting characteriztics of their sorting mechanisms have been observed. These are, first, that they aggregate on low pH/high calcium concentrations and second that two of them carry an N-terminal disulfide loop, mutations in which lead to mis-sorting. Thus, granins are thought to be essential for the sorting of secretory proteins at the trans-Golgi network. Chromogranin A (CgA) binds to SGIII in secretory granules of endocrine cells. SGIII directly binds to cholesterol components of the secretory granule membrane and targets CgA to secretory granules in pituitary and pancreatic endocrine cells. Mutations in the SGIII gene may influence the risk of obesity through possible regulation of hypothalamic neuropeptide secretion. 449 matched cddid_all.tbl CDD pfam15468 pfam15468 373871 DUF4636 Domain of unknown function (DUF4636). This family of proteins is found in eukaryotes. Proteins in this family are typically between 196 and 244 amino acids in length. 243 matched cddid_all.tbl CDD pfam15469 pfam15469 464733 Sec5 Exocyst complex component Sec5. This entry represents the Sec5 component of the exocyst complex which is an octomeric complex that mediates the tethering of post-Golgi secretory vesicles to the plasma membrane during exocytosis. 810 matched cddid_all.tbl CDD pfam15470 pfam15470 406033 DUF4637 Domain of unknown function (DUF4637). This family of proteins is found in eukaryotes. Proteins in this family are typically between 142 and 178 amino acids in length. 164 matched cddid_all.tbl CDD pfam15471 pfam15471 464734 TMEM171 Transmembrane protein family 171. This family of proteins is found in eukaryotes. TMEM171 is also known as parturition-related protein 2. Proteins in this family are typically between 242 and 326 amino acids in length. 319 matched cddid_all.tbl CDD pfam15472 pfam15472 464735 DUF4638 Domain of unknown function (DUF4638). This family of proteins is found in eukaryotes. Proteins in this family are typically between 240 and 272 amino acids in length. 261 matched cddid_all.tbl CDD pfam15473 pfam15473 464736 PCNP PEST, proteolytic signal-containing nuclear protein family. PCNP is a PEST-containing nuclear protein that is ubiquitinated by NIRF, a Np95/ICBP90-like RING finger protein. PEST sequences, which are rich in proline (P), glutamic acid (E), serine (S) and threonine (T), are found in a number of short-lived proteins, such as transcription factors and cell cycle-associated proteins. Their function is generally controlled by proteolysis, mostly via ubiquitin-mediated degradation. Thus, NIRF and PCNP are a ubiquitin ligase and its substrate, respectively, that may constitute a novel signalling pathway with some relation to cell proliferation. 155 matched cddid_all.tbl CDD pfam15474 pfam15474 406036 MU117 Meiotically up-regulated gene family. This protein was identified as being up-regulated during meiosis in S.pombe. This family of proteins is found in largely in plants and fungi. Proteins in this family are typically between 128 and 920 amino acids in length. 104 matched cddid_all.tbl CDD pfam15475 pfam15475 464737 UPF0444 Transmembrane protein C12orf23, UPF0444. This family of proteins is found in eukaryotes. Proteins in this family are typically between 94 and 119 amino acids in length. 91 matched cddid_all.tbl CDD pfam15476 pfam15476 406038 SAP25 Histone deacetylase complex subunit SAP25. SAP25 is a family of proteins found in eukaryotes. SAP25 is a core component of the mSin3 co-repressor complex whose subcellular location is regulated by PML. mSin3, the transcriptional co-repressor, is associated with histone deacetylases (HDACs) and is utilized by many DNA-binding transcriptional repressors. SAP25 is a nucleo-cytoplasmic shuttling protein that is actively exported from the nucleus by a CRM1-dependent mechanism. It binds to the PAH1 domain of mSin3A, associates with the mSin3A-HDAC complex in vivo, and represses transcription when tethered to DNA. 202 matched cddid_all.tbl CDD pfam15477 pfam15477 464738 SMAP Small acidic protein family. This domain family is found in eukaryotes, and is approximately 70 amino acids in length. There is a single completely conserved residue G that may be functionally important. 73 matched cddid_all.tbl CDD pfam15478 pfam15478 434744 LKAAEAR Family of unknown function with LKAAEAR motif. This family of proteins is found in eukaryotes. Proteins in this family are typically between 119 and 235 amino acids in length. There is a conserved LKAAEAR sequence motif. 137 matched cddid_all.tbl CDD pfam15479 pfam15479 464739 DUF4639 Domain of unknown function (DUF4639). This family of proteins is found in eukaryotes. Proteins in this family are typically between 161 and 601 amino acids in length. 580 matched cddid_all.tbl CDD pfam15480 pfam15480 464740 DUF4640 Domain of unknown function (DUF4640). This family of proteins is found in eukaryotes. Proteins in this family are typically between 99 and 306 amino acids in length. 292 matched cddid_all.tbl CDD pfam15481 pfam15481 406043 CPG4 Chondroitin proteoglycan 4. CPG4 is a domain family found in nematodes of one of nine core chondroitin proteoglycans. Vertebrates produce multiple chondroitin sulfate proteoglycans that play important roles in development and tissue mechanics. In the nematode Caenorhabditis elegans, the chondroitin chains lack sulfate but nevertheless play essential roles in embryonic development and vulval morphogenesis. CPG4 has the largest predicted mass of the C. elegans CPGs at 84 kDa. The majority of its 35 predicted glycosaminoglycan attachment sites reside in the COOH-terminal half of the protein, of which four sites were confirmed by DTT modification. The family is rich in conserved cysteines. 94 matched cddid_all.tbl CDD pfam15482 pfam15482 406044 CCER1 Coiled-coil domain-containing glutamate-rich protein family 1. This is a family of coiled-coil family proteins found in eukaryotes. Proteins in this family are typically between 160 and 397 amino acids in length. 213 matched cddid_all.tbl CDD pfam15483 pfam15483 464741 DUF4641 Domain of unknown function (DUF4641). This family of proteins is found in eukaryotes. Proteins in this family are typically between 201 and 519 amino acids in length. 443 matched cddid_all.tbl CDD pfam15484 pfam15484 464742 DUF4642 Domain of unknown function (DUF4642). This family of proteins is found in eukaryotes. Proteins in this family are typically between 115 and 196 amino acids in length. 159 matched cddid_all.tbl CDD pfam15485 pfam15485 434748 DUF4643 Domain of unknown function (DUF4643). This family of proteins is found in eukaryotes. Proteins in this family are typically between 254 and 462 amino acids in length. 263 matched cddid_all.tbl CDD pfam15486 pfam15486 406048 DUF4644 Domain of unknown function (DUF4644). This family of proteins is found in eukaryotes. Proteins in this family are typically between 143 and 191 amino acids in length. 161 matched cddid_all.tbl CDD pfam15487 pfam15487 464743 FAM220 FAM220 family. This protein family is a domain of unknown function which is found in eukaryotes. Proteins in this family are typically between 217 and 277 amino acids in length. There are two completely conserved residues (S and L) that may be functionally important. 275 matched cddid_all.tbl CDD pfam15488 pfam15488 406050 DUF4645 Domain of unknown function (DUF4645). This family of proteins is found in eukaryotes. Proteins in this family are typically between 200 and 298 amino acids in length. 294 matched cddid_all.tbl CDD pfam15489 pfam15489 464744 CTC1 CST, telomere maintenance, complex subunit CTC1. CTC1 is one of the three components of the CST complex that assists Shelterin to protect the ends of telomeres from attack by DNA-repair mechanisms. Mutations in human CTC1 have been recognized as contributing to cerebroretinal microangiopathy. 1139 matched cddid_all.tbl CDD pfam15490 pfam15490 464745 Ten1_2 Telomere-capping, CST complex subunit. Ten1_2 is a family of primarily plant and vertebrate telomere-capping proteins that is evolutionarily related to the mostly fungal family of Ten1, pfam12658. 117 matched cddid_all.tbl CDD pfam15491 pfam15491 434752 CTC1_2 CST, telomere maintenance, complex subunit CTC1. CTC1 is one of the three components of the CST complex that assists Shelterin to protect the ends of telomeres from attack by DNA-repair mechanisms. This family largely represents sequences from plants species. 289 matched cddid_all.tbl CDD pfam15492 pfam15492 464746 Nbas_N Neuroblastoma-amplified sequence, N terminal. Nbas_N is an N-terminal family of metazoan sequences. This domain lies at the N-terminal of several WD40-containing proteins. The human protein is over-expressed in neuroblastoma cells. 281 matched cddid_all.tbl CDD pfam15493 pfam15493 406054 YrpD Domain of unknown function, YrpD. This family of proteins is found in bacteria. Proteins in this family are typically between 236 and 351 amino acids in length. The member from Bacillus subtilis, UniProtKB:O05411, is named YrpD. 203 matched cddid_all.tbl CDD pfam15494 pfam15494 464747 SRCR_2 Scavenger receptor cysteine-rich domain. SRCR_2 is a scavenger receptor cysteine-rich domain family found largely on vertebrate sequences up-stream of the trypsin-like transmembrane serine protease, Spinesin. 99 matched cddid_all.tbl CDD pfam15495 pfam15495 434755 Fimbrillin_C Major fimbrial subunit protein type IV, Fimbrillin, C-terminal. Fimbrillin_C is a C-terminal family of major fimbrial subunit protein type IV proteins largely from Bacillus species. The family is associated with family P_gingi_FimA, pfam06321. 84 matched cddid_all.tbl CDD pfam15496 pfam15496 434756 DUF4646 Domain of unknown function (DUF4646). This is a family of proteins largely from fungi. The function is not known. 121 matched cddid_all.tbl CDD pfam15497 pfam15497 464748 SNAPC5 snRNA-activating protein complex subunit 19, SNAPc subunit 19. SNAPc19 is a family of proteins found in eukaryotes. It is one of the five core components of the snRNA-activating protein complex or SNAPc that helps direct the nucleation of RNA polymerases II and III. The core RNA polymerase II snRNA promoters consist of a single essential element, the proximal sequence element (PSE), whereas the core RNA polymerase III snRNA promoters consist of both a PSE and a TATA box. The SNAPc binds to the PSE of both of these. SNAPc recognizes the PSE sequence common to all human snRNA genes, irrespective of polymerase specificity. SNAPc is also known as the PSE transcription factor (PTF) or PSE-binding protein (PBP). The human SNAP19 and SNAP45 subunits are dispensable for transcription in vitro and are not as widely conserved as the other three, SNAP190, SNAP43 and SNAP50, suggesting that these vertebrate-specific SNAPc subunits may have adapted specialized regulatory roles for snRNA gene transcription. 101 matched cddid_all.tbl CDD pfam15498 pfam15498 464749 Dendrin Nephrin and CD2AP-binding protein, Dendrin. Dendrin is a family of eukaryotic proteins found in the podocytes of the kidneys. Dendrin, originally identified in telencephalic dendrites, is a constituent of the slit diaphragm, SD, complex of podocytes, where it directly binds to nephrin and CD2AP. Kidney podocytes and their slit diaphragms (SDs) form the final barrier to urinary protein loss. SD proteins also participate in intracellular signalling pathways. Dendrin appears to prevent programmed cell death (apoptosis) through its binding to nephrin. The SD protein nephrin serves as a component of a signalling complex that directly links podocyte junctional integrity to actin cytoskeletal dynamics. Thus, dendrin is identified as an SD family with proapoptotic signalling properties that accumulates in the podocyte nucleus in response to glomerular injury. 656 matched cddid_all.tbl CDD pfam15499 pfam15499 464750 Peptidase_C98 Ubiquitin-specific peptidase-like, SUMO isopeptidase. Peptidase_C98 is a small family of SUMO - small ubiquitin-related modifier - isopeptidases found in eukaryotes. Reversible attachment of SUMO is an essential protein modification in all eukaryotic cells, The family neither binds nor cleaves ubiquitin, but is a potent SUMO isopeptidase, and the invariant residues required for SUMO binding and cleavage, in UniProtKB:Q5W0Q7, are Cys-236, His-456 and Asp-472, all of which are fully conserved in the family. Member proteins are low-abundance proteins that colocalize with coilin in Cajal bodies. Peptidase_C98 depletion does not affect global sumoylation, but causes striking coilin mis-localization and impairs cell proliferation, functions that are not dependent on the catalytic activity. Thus, Peptidase_C98 represents a third type of SUMO protease, with essential functions in Cajal body biology. 272 matched cddid_all.tbl CDD pfam15500 pfam15500 259631 Ntox1 Putative RNase-like toxin, toxin_1. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold and conserved cysteine, histidine and glutamate residues that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system. 96 matched cddid_all.tbl CDD pfam15501 pfam15501 464751 MDM1 Nuclear protein MDM1. This family of proteins is present in the nucleus. The function of MDM1 is not known. 557 matched cddid_all.tbl CDD pfam15502 pfam15502 434761 MPLKIP M-phase-specific PLK1-interacting protein. 64 matched cddid_all.tbl CDD pfam15503 pfam15503 434762 PPP1R35_C Protein phosphatase 1 regulatory subunit 35 C-terminus. This is the C-terminus of protein phosphatase 1 regulatory subunit 35. This protein interacts with and inhibits the serine/threonine-protein phosphatase PPP1CA. 144 matched cddid_all.tbl CDD pfam15504 pfam15504 464752 DUF4647 Domain of unknown function (DUF4647). This family of proteins is found in eukaryotes. Proteins in this family are typically between 282 and 480 amino acids in length. 467 matched cddid_all.tbl CDD pfam15505 pfam15505 464753 Vexin Vexin domain. Proteins containing this domain include Xenopus laevis Vexin and its human homolog, C8orf46. Vexin is transiently expressed in differentiating progenitors in the developing central nervous system (CNS) and is required for neurogenesis in the neural plate and retina. This entry corresponds to a presumed SH3 domain. 80 matched cddid_all.tbl CDD pfam15506 pfam15506 292144 OCC1 OCC1 family. The human member of this family, overexpressed in colon carcinoma 1 protein has been shown to be overexpressed in several colon carcinomas. 61 matched cddid_all.tbl CDD pfam15507 pfam15507 406064 DUF4649 Domain of unknown function (DUF4649). This family of Firmicute sequences has members that are annotated as ribose-phosphate pyrophosphokinase; however there is no evidence for this attribution. Member proteins are all shorter than 100 residues in length. 68 matched cddid_all.tbl CDD pfam15508 pfam15508 464754 NAAA-beta beta subunit of N-acylethanolamine-hydrolyzing acid amidase. NAAA-beta is a family of vertebral sequences that form the beta subunit of vertebral N-acylethanolamine-hydrolyzing acid amidase, a member of the choloylglycine hydrolase acid ceramidase family. The alpha subunit is represented by family CBAH, pfam02275. 63 matched cddid_all.tbl CDD pfam15509 pfam15509 464755 DUF4650 Domain of unknown function (DUF4650). This family of vertebrate proteins lies to the C-terminus of Ubiquitin-specific peptidase-like protein family peptidase_C98, pfam15499. It might be acting as the exosite for the peptidase. 519 matched cddid_all.tbl CDD pfam15510 pfam15510 434767 CENP-W CENP-W protein. CENP-W is a family of vertebral kinetochore proteins that associates directly with CENP-T. CENP-W members are histone-fold proteins. The histone fold region is critical for binding to centromeric DNA. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. 88 matched cddid_all.tbl CDD pfam15511 pfam15511 434768 CENP-T_C Centromere kinetochore component CENP-T histone fold. CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin. 108 matched cddid_all.tbl CDD pfam15512 pfam15512 464756 CAF-1_p60_C Chromatin assembly factor complex 1 subunit p60, C-terminal. CAF-1_p60_C is a family of vertebral proteins that is involved in chromatin assembly. CAF-1_p60 is one of the three subunits of the CAF-1 complex, and this domain binds to the C-terminal region of CAF-1_p150, family pfam12253. The N-terminal part of the CAF-1_p60 proteins is a WD-repeat structure, pfam00400. 171 matched cddid_all.tbl CDD pfam15513 pfam15513 434770 DUF4651 Domain of unknown function (DUF4651). family of short, secreted proteins specific to the Streptococcus genus, with distant homologs, not recognized by this HMM, found in other cocci. In all sequenced genomes, proteins from this family appear in a conserved genomic context with an thioredoxin, tRNA synthase and tRNA binding protein, but the functional implication of this is unclear 61 matched cddid_all.tbl CDD pfam15514 pfam15514 292152 ThaI Restriction endonuclease ThaI. This family of restriction endonucleases belongs to the PD-(D/E)XK superfamily. It cuts the recognition site CG^CG leaving blunt ends. 202 matched cddid_all.tbl CDD pfam15515 pfam15515 434771 MvaI_BcnI MvaI/BcnI restriction endonuclease family. This family of proteins includes the restriction endonucleases MvaI and BcnI. These enzymes both function as monomers. MvaI cleaves the sequence CC/WGG, where W is an A or a T nucleotide, leaving sticky ends. BcnI cleaves the sequence CC/SGG, where S is G or C, leaving sticky ends. 225 matched cddid_all.tbl CDD pfam15516 pfam15516 373914 BpuSI_N BpuSI N-terminal domain. This is the N-terminal (nuclease) domain of the BpuSI restriction endonuclease. 168 matched cddid_all.tbl CDD pfam15517 pfam15517 406070 TBPIP_N TBP-interacting protein N-terminus. This is the N-terminal restriction endonuclease-like domain found in several archaeal TATA-binding protein (TBP)-interacting proteins. 100 matched cddid_all.tbl CDD pfam15518 pfam15518 373916 L_protein_N L protein N-terminus. This endonuclease domain is found at the N-terminus of many bunyavirus L proteins. 93 matched cddid_all.tbl CDD pfam15519 pfam15519 464757 RBM39linker linker between RRM2 and RRM3 domains in RBM39 protein. A conserved linker between the second and the third RRM domain in human RBM39 (CAPER) protein, also present in other RNA binding proteins, especially those involved in RNA splicing. This linker was implicated in interactions with ESR1 and ESR2. Preliminary results from JCSG suggest that this is a structured domain with a well defined fold. 81 matched cddid_all.tbl CDD pfam15520 pfam15520 292158 Ntox10 Novel toxin 10. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold that is usually exported by the type 2 secretion system. 193 matched cddid_all.tbl CDD pfam15521 pfam15521 373918 Ntox11 Novel toxin 11. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin contains two structural domains, an N-terminal alpha/beta domain and a C-terminal all-beta domain. The domain contains conserved GxR, RxxxoH GxE and GxxH motifs and a conserved histidine residue. In bacterial polymorphic toxin systems, the toxin is usually exported by the Photorhabdus virulence cassette (PVC)-type export system. 256 matched cddid_all.tbl CDD pfam15522 pfam15522 259653 Ntox14 Novel toxin 14. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system. 218 matched cddid_all.tbl CDD pfam15523 pfam15523 406072 Ntox16 Novel toxin 16. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-alpha helical fold and conserved (DNE)xxH motif and arginine residue. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 6, or Photorhabdus virulence cassette (PVC)-type secretion system. 85 matched cddid_all.tbl CDD pfam15524 pfam15524 406073 Ntox17 Novel toxin 17. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses a mostly all-beta fold and a conserved ExD motif and a histidine residue. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 7 or TcdB/TcaC-type secretion system. 98 matched cddid_all.tbl CDD pfam15525 pfam15525 406074 DUF4652 Domain of unknown function (DUF4652). This family of uncharacterized proteins from Clostridia and Bacilli classes has an unusual structure of three beta propeller repeats that do not form a barrel, as in well known 6-, 7- etc beta propeller barrels, but instead are stacked in a three-layer beta-sheet sandwich. The function of all the proteins from this family is unknown. 193 matched cddid_all.tbl CDD pfam15526 pfam15526 434773 Ntox21 Novel toxin 21. Bacterial genomes and plasmids encode a variety of peptide and protein toxins that mediate inter-bacterial competition. Bacteriocins are diffusible proteins that parasitize cell-envelope proteins to enter and kill bacteria. Contact-dependent growth inhibition (CDI) is one mechanism of inter-bacterial competition. Novel Toxin 21 (alternatively 16S rRNA endonuclease CdiA) belongs to a family of prokaryotic polymorphic toxin systems implicated in intra-specific conflicts. This RNase toxin found in bacterial polymorphic toxin systems, is proposed to adopt the BECR (Barnase-EndoU-ColicinE5/D-RelE) fold, with two conserved lysine residues and [DS]xDxxxH, RxG[ST] and RxxD motifs. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2, type 4, type 5 or type 7 secretion systems. This is also referred to as the E. cloacae CdiAC. The CdiAC proteins carry a variety of sequence-diverse C-terminal domains, which represent a collection of distinct toxins. Many CdiA-CT toxins have nuclease activities. In accord with the structural homology, CdiA-CT cleaves 16S rRNA at the same site as colicin E3 and this nuclease activity is responsible for growth inhibition. 71 matched cddid_all.tbl CDD pfam15527 pfam15527 434774 Ntox22 Bacterial toxin 22. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses a mostly beta fold and two conserved histidines, two aspartates and a glutamate residue. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 5 secretion system. 129 matched cddid_all.tbl CDD pfam15528 pfam15528 373924 Ntox23 Bacterial toxin 23. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-beta fold and conserved ND and DxxR motifs and a histidine residue. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or TcdB/TcaC secretion system. 190 matched cddid_all.tbl CDD pfam15529 pfam15529 406077 Ntox24 Bacterial toxin 24. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-beta fold and conserved ND and DxxR motifs and a histidine residue. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or TcdB/TcaC secretion system. Interestingly, the toxin is also found in type-II toxin-antitoxin systems. 96 matched cddid_all.tbl CDD pfam15530 pfam15530 373925 Ntox25 Bacterial toxin 25. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses a mostly all-beta fold and conserved FGPY motif and a histidine residue. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 5 secretion system. 167 matched cddid_all.tbl CDD pfam15531 pfam15531 406078 Ntox27 Bacterial toxin 27. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold and conserved aspartate and glutamate residues, and an RxW motif. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 7 secretion systems. 130 matched cddid_all.tbl CDD pfam15532 pfam15532 434775 Ntox30 Bacterial toxin 30. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-beta fold and two conserved histidines present in an RxH and THIP motif. The domain additionally has a highly conserved arginine residue. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2, type 6 or type 7 secretion systems. 103 matched cddid_all.tbl CDD pfam15533 pfam15533 292170 Ntox33 Bacterial toxin 33. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold and [DN]xHxxK and DxxxD motifs. It is usually exported by the Type 2 secretory system. 65 matched cddid_all.tbl CDD pfam15534 pfam15534 406079 Ntox35 Bacterial toxin 35. A predicted RNase toxin found in bacterial polymorphic toxin systems that is proposed to adopt the BECR (Barnase-EndoU-ColicinE5/D-RelE) fold, and contains a conserved histidine residue and a KH motif. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2 secretion system. 77 matched cddid_all.tbl CDD pfam15535 pfam15535 434776 Ntox37 Bacterial toxin 37. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-beta fold and a conserved glutamate residue, and [KR] and Hx[DH] motifs. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 7 secretion systems. 64 matched cddid_all.tbl CDD pfam15536 pfam15536 292173 Ntox3 Bacterial toxin 3. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-beta fold and conserved aspartate, arginine, histidine and cysteine residues that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system. 133 matched cddid_all.tbl CDD pfam15537 pfam15537 292174 Ntox43 Bacterial toxin 43. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold with two conserved histidine residues. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2 or TcdB/TcaC-type secretion system. An example of this, the Pseudomonas RhsT-C, has been experimentally characterized. 127 matched cddid_all.tbl CDD pfam15538 pfam15538 406080 Ntox46 Bacterial toxin 46. A predicted toxin domain found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold with a conserved glutamine residue and a [KR]STxxPxxDxx[ST] motif. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 6 secretion system. 157 matched cddid_all.tbl CDD pfam15539 pfam15539 434777 CAF1-p150_C2 CAF1 complex subunit p150, region binding to CAF1-p60 at C-term. CAF1-p150_C2 is part of the binding region of the CAF1 complex p150 subunit to the p60 subunit. The CAF1 complex is essential in human cells for the de novo deposition of histones H3 and H4 at the DNA replication fork. 288 matched cddid_all.tbl CDD pfam15540 pfam15540 406082 Ntox47 Bacterial toxin 47. A predicted RNase toxin found in bacterial polymorphic toxin systems that is proposed to adopt the BECR (Barnase-EndoU-ColicinE5/D-RelE) fold, and contains two conserved aspartates, a glutamate, a histidine and an arginine residue and an RT motif. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2, type 6 or type 7 secretion system. 111 matched cddid_all.tbl CDD pfam15541 pfam15541 292178 Ntox4 Bacterial toxin 4. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system. 109 matched cddid_all.tbl CDD pfam15542 pfam15542 406083 Ntox50 Bacterial toxin 50. A predicted RNase toxin found in bacterial polymorphic toxin systems that is proposed to adopt the BECR (Barnase-EndoU-ColicinE5/D-RelE) fold, and contains two conserved histidine, a serine, two lysine, and a threonine residue and a HxVP motif. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2, type 6, type 7, and MuF-type secretion systems. 93 matched cddid_all.tbl CDD pfam15543 pfam15543 292180 Ntox5 Bacterial toxin 5. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system. 142 matched cddid_all.tbl CDD pfam15544 pfam15544 373932 Ntox6 Bacterial toxin 6. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold that is usually exported by the Photorhabdus virulence cassette (PVC)-type export system. 279 matched cddid_all.tbl CDD pfam15545 pfam15545 434778 Ntox8 Bacterial toxin 8. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an alpha+beta fold and HxR and HxxxH motifs and is usually exported by the type 2 and type 6 secretion system. 70 matched cddid_all.tbl CDD pfam15546 pfam15546 317880 DUF4653 Domain of unknown function (DUF4653). This family of proteins is found in eukaryotes. Proteins in this family are typically between 93 and 229 amino acids in length. 229 matched cddid_all.tbl CDD pfam15547 pfam15547 464758 C1ORF64 Steroid receptor-associated and regulated protein. Steroid receptor-associated and regulated protein is also known as ER-related factor, ERRF, or C1orf64. It is thought to regulate the transcriptional function of androgen and oestrogen receptors. Proteins in this family are typically between 145 and 169 amino acids in length, and have a conserved IDC sequence motif. 137 matched cddid_all.tbl CDD pfam15548 pfam15548 434779 DUF4655 Domain of unknown function (DUF4655). This family of proteins is found in eukaryotes. Proteins in this family are typically between 533 and 570 amino acids in length. 525 matched cddid_all.tbl CDD pfam15549 pfam15549 464759 PGC7_Stella PGC7/Stella/Dppa3 domain. The domain belongs to a fast evolving family known only from the placental mammals. The PGC7/Stella/Dppa3 protein protects imprinted regions from demethylation post-fertilization. This suggests that it might bind methylated DNA sequences directly. The conserved core includes a postively charged helical segment and a C-terminal CXCXXC motif that is predicted to chelate a metal ion. Most placental mammals contain 3-6 paralogs of this domain family. The CXCXXC motif is also conserved in a subset of fungal MBD4-like proteins. 166 matched cddid_all.tbl CDD pfam15550 pfam15550 464760 Draxin Draxin. This family of proteins inhibit Wnt signaling and act as chemorepulsive axon guidance molecules. 321 matched cddid_all.tbl CDD pfam15551 pfam15551 464761 DUF4656 Domain of unknown function (DUF4656). This family of proteins is found in eukaryotes. Proteins in this family are typically between 286 and 398 amino acids in length. 361 matched cddid_all.tbl CDD pfam15552 pfam15552 464762 DUF4657 Domain of unknown function (DUF4657). This family of proteins is found in eukaryotes. Proteins in this family are typically between 305 and 370 amino acids in length. 301 matched cddid_all.tbl CDD pfam15553 pfam15553 464763 TEX19 Testis-expressed protein 19. This family of proteins is expressed in testis. 159 matched cddid_all.tbl CDD pfam15554 pfam15554 464764 FSIP1 FSIP1 family. 395 matched cddid_all.tbl CDD pfam15555 pfam15555 464765 DUF4658 Domain of unknown function (DUF4658). This family of proteins is found in eukaryotes. Proteins in this family are typically between 129 and 161 amino acids in length. 123 matched cddid_all.tbl CDD pfam15556 pfam15556 464766 Zwint ZW10 interactor. This family of proteins is found in eukaryotes. Proteins in this family are typically between 127 and 281 amino acids in length. 252 matched cddid_all.tbl CDD pfam15557 pfam15557 464767 CAF1-p150_N CAF1 complex subunit p150, region binding to PCNA. CAF1-p150_N is part of the N-terminus of the CAF1 complex p150 subunit that binds to PCNA - proliferating cell nuclear antigen. The PCNA mediates the connection between CAF-1 and the DNA replication fork. The CAF1 complex is essential in human cells for the de novo deposition of histones H3 and H4 at the DNA replication fork. 230 matched cddid_all.tbl CDD pfam15558 pfam15558 464768 DUF4659 Domain of unknown function (DUF4659). This family of proteins is found in eukaryotes. Proteins in this family are typically between 427 and 674 amino acids in length. There are two completely conserved residues (D and I) that may be functionally important. 374 matched cddid_all.tbl CDD pfam15559 pfam15559 464769 DUF4660 Domain of unknown function (DUF4660). This family of proteins is found in eukaryotes. Proteins in this family are typically between 93 and 189 amino acids in length. 107 matched cddid_all.tbl CDD pfam15560 pfam15560 292197 Imm12 Immunity protein 12. A predicted immunity protein with an alpha+beta fold and several conserved charged and hydrophobic residues. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-URI2 family. The protein is also found in heterogeneous poly-immunity loci. 138 matched cddid_all.tbl CDD pfam15561 pfam15561 434791 Imm15 Immunity protein 15. A predicted immunity protein with an alpha+beta fold and several conserved polar and hydrophobic residues. Proteins containing this domain are present in heterogeneous poly-immunity loci in polymorphic toxin systems. 151 matched cddid_all.tbl CDD pfam15562 pfam15562 434792 Imm17 Immunity protein 17. A predicted immunity protein with two transmembrane helices, and a WxW motif and a conserved arginine between the two helices. Proteins containing this domain are present in heterogeneous poly-immunity loci in polymorphic toxin systems. 61 matched cddid_all.tbl CDD pfam15563 pfam15563 406098 Imm19 Immunity protein 19. A predicted immunity protein with an alpha+beta fold and a conserved HxxRN motif. Proteins containing this domain are present in heterogeneous poly-immunity loci in polymorphic toxin systems. 227 matched cddid_all.tbl CDD pfam15564 pfam15564 259695 Imm25 Immunity protein 25. A predicted immunity protein with an alpha+beta fold. Proteins containing this domain are present in heterogeneous poly-immunity loci of polymorphic toxin systems. 131 matched cddid_all.tbl CDD pfam15565 pfam15565 406099 Imm30 Immunity protein 30. A predicted immunity protein with a mostly alpha-helical fold and a conserved DxG motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-SHH family of HNH/Endonuclease VII fold nucleases. 96 matched cddid_all.tbl CDD pfam15566 pfam15566 292202 Imm32 Immunity protein 32. A predicted immunity protein with an alpha+beta fold and a conserved histidine residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Ntox12 or Ntox37 or Notx 7 families. 54 matched cddid_all.tbl CDD pfam15567 pfam15567 379730 Imm35 Immunity protein 35. A predicted immunity protein with an alpha+beta fold and a conserved tryptophan residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a protease domain such as Tox-PL1 and Ntox40. In some instances, it is also fused to a papain-like toxin, ADP-ribosyl glycohydrolase and a S8-like peptidase. Based on these associations the domain is likely to be a protease inhibitor. 84 matched cddid_all.tbl CDD pfam15568 pfam15568 259699 Imm39 Immunity protein 39. A predicted immunity protein with an alpha+beta fold and conserved GR, and GxK motifs. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-URI2 family of nucleases. 131 matched cddid_all.tbl CDD pfam15569 pfam15569 373946 Imm40 Immunity protein 40. A predicted immunity protein with an alpha+beta fold and conserved phenylalanine and tryptophan residues and a GGD motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Ntox19 family. 93 matched cddid_all.tbl CDD pfam15570 pfam15570 434793 Imm43 Immunity protein 43. A predicted immunity protein with an alpha+beta fold with conserved tryptophan, proline, aspartate, serine and arginine residues. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-AHH family of HNH/Endonuclease VII fold nucleases. The gene for this toxin is also found in heterogeneous poly-immunity loci. 124 matched cddid_all.tbl CDD pfam15571 pfam15571 292206 Imm44 Immunity protein 44. A predicted immunity protein with an alpha+beta fold. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-URI1, Tox-URI2 or Tox-ParBL1 families. The gene for this toxin is also found in heterogeneous poly-immunity loci that show variations in structure even between closely related strains. 126 matched cddid_all.tbl CDD pfam15572 pfam15572 406101 Imm45 Immunity protein 45. A predicted immunity protein with an alpha+beta fold and a conserved C-terminal tryptophan residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-ColE3 family. 95 matched cddid_all.tbl CDD pfam15573 pfam15573 406102 Imm47 Immunity protein 47. A predicted immunity protein with an alpha+beta fold and a conserved KxGDxxK motif. Proteins containing this domain are present in heterogeneous poly-immunity loci in polymorphic toxin systems. 258 matched cddid_all.tbl CDD pfam15574 pfam15574 317899 Imm48 Immunity protein 48. A predicted immunity protein with an all alpha-helical fold and a conserved HRG motif. Proteins containing this domain are present in heterogeneous poly-immunity loci in polymorphic toxin systems. 123 matched cddid_all.tbl CDD pfam15575 pfam15575 434794 Imm49 Immunity protein 49. A predicted immunity protein with an all alpha-helical fold and a conserved proline residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-REAse-1 or Tox-REase-6 families. 214 matched cddid_all.tbl CDD pfam15576 pfam15576 464770 DUF4661 Domain of unknown function (DUF4661). This family of proteins is found in eukaryotes. Proteins in this family are typically between 281 and 302 amino acids in length. 253 matched cddid_all.tbl CDD pfam15578 pfam15578 464771 DUF4662 Domain of unknown function (DUF4662). This family of proteins is found in eukaryotes. Proteins in this family are approximately 290 amino acids in length. 269 matched cddid_all.tbl CDD pfam15579 pfam15579 406106 Imm52 Immunity protein 52. A predicted immunity protein with an alpha+beta fold and conserved tryptophan and phenylalanine residues, and a GT motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-REase-5 family. 102 matched cddid_all.tbl CDD pfam15580 pfam15580 434796 Imm53 Immunity protein 53. A predicted immunity protein with an alpha+beta fold and a conserved tryptophan, and WE and PGW motifs. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Ntox24 or Ntox10 families. 91 matched cddid_all.tbl CDD pfam15581 pfam15581 434797 Imm58 Immunity protein 58. A predicted immunity protein with an alpha+beta fold and YxxxD, WxG, KxxxE motifs. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene. 109 matched cddid_all.tbl CDD pfam15582 pfam15582 292216 Imm65 Immunity protein 65. A predicted immunity protein with an alpha+beta fold and a conserved YxC motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Tox-JAB1 family. The immunity protein typically contains a signal peptide and a lipobox. 321 matched cddid_all.tbl CDD pfam15583 pfam15583 406107 Imm68 Immunity protein 68. A predicted immunity protein with an alpha+beta fold and a conserved glutamate residue. The domain is often fused to one or more immunity domains in poly-immunity proteins. 152 matched cddid_all.tbl CDD pfam15584 pfam15584 292218 Imm72 Immunity protein 72. A predicted immunity protein with a mostly all-beta fold and GxxE, WxDxRY motifs and a glutamate residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Ntox48 family. This domain is often fused to the Imm71 immunity domain. 81 matched cddid_all.tbl CDD pfam15585 pfam15585 406108 Imm7 Immunity protein 7. A predicted immunity protein with an alpha+beta fold and a conserved GxaG motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a Tox-REase-3 domain. 130 matched cddid_all.tbl CDD pfam15586 pfam15586 434798 Imm8 Immunity protein 8. A predicted immunity protein with an alpha+beta fold and a conserved WEa (a: aromatic) motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Ntox7 family. 114 matched cddid_all.tbl CDD pfam15587 pfam15587 434799 Imm9 Immunity protein 9. A predicted immunity protein with an alpha+beta fold and a conserved lysine residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-URI2 family. The protein is also found in heterogeneous poly-immunity loci. 149 matched cddid_all.tbl CDD pfam15588 pfam15588 379733 Imm10 Immunity protein 10. A predicted immunity protein with a mostly all-beta fold and a conserved arginine residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a Pput_2613 deaminase domain. The protein is also found in heterogeneous poly-immunity loci. 104 matched cddid_all.tbl CDD pfam15589 pfam15589 434800 Imm21 Immunity protein 21. A predicted immunity protein with an alpha+beta fold and conserved WxG and YxxxC motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the NGO1392-family of HNH/Endonuclease VII fold nucleases. 155 matched cddid_all.tbl CDD pfam15590 pfam15590 464772 Imm27 Immunity protein 27. A predicted immunity protein with an alpha+beta fold and a conserved aspartate and GGxP motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Ntox10 or Tox-ParB families. 67 matched cddid_all.tbl CDD pfam15591 pfam15591 292225 Imm31 Immunity protein 31. A predicted immunity protein with a mostly all-beta fold and a conserved GxS motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Ntox17 or Ntox7 families. 73 matched cddid_all.tbl CDD pfam15592 pfam15592 406112 Imm41 Immunity protein 41. A predicted immunity protein with an alpha+beta fold and a conserved SF motif and tryptophan residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Ntox21, Ntox29 or Tox-ART-RSE-like ADP-ribosyltransferase families. 108 matched cddid_all.tbl CDD pfam15593 pfam15593 406113 Imm42 Immunity protein 42. A predicted immunity protein with an alpha+beta fold. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Ntox18 family. 162 matched cddid_all.tbl CDD pfam15594 pfam15594 434802 Imm50 Immunity protein 50. A predicted immunity protein with an all-beta fold. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-HHH or Ntox24 families. 116 matched cddid_all.tbl CDD pfam15595 pfam15595 406115 Imm51 Immunity protein 51. A predicted immunity protein with an alpha+beta fold and a conserved tryptophan and Dx[DE] motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-RES or Tox-URI1 families. Proteins containing this domain are present in heterogeneous poly immunity loci in polymorphic toxin systems. 105 matched cddid_all.tbl CDD pfam15596 pfam15596 373959 Imm57 Immunity protein 57. A predicted immunity protein with a mostly alpha-helical fold and conserved aspartate and cysteine residues and an SE motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the LD-peptidase or Tox-Caspase families. 111 matched cddid_all.tbl CDD pfam15597 pfam15597 434803 Imm59 Immunity protein 59. A predicted immunity protein with an alpha+beta fold and a conserved [DE]R motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Ntox13 or Ntox40 families. In some proteins this domain is fused to the Imm38, pfam15599 immunity domain. 100 matched cddid_all.tbl CDD pfam15598 pfam15598 434804 Imm61 Immunity protein 61. A predicted immunity protein with an alpha+beta fold and a conserved arginine. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Ntox40 family. 157 matched cddid_all.tbl CDD pfam15599 pfam15599 434805 Imm63 Immunity protein 63. A predicted immunity protein with an alpha+beta fold and a conserved E+G and ExxY motifs. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Ntox40, Tox-CdiAC and Tox-ARC families. The protein is also found in poly-immunity loci in polymorphic toxin systems. 83 matched cddid_all.tbl CDD pfam15600 pfam15600 406119 Imm64 Immunity protein 64. A predicted immunity protein with an alpha+beta fold and a conserved DxEA motif and arginine residue. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Tox-ColD family. 207 matched cddid_all.tbl CDD pfam15601 pfam15601 434806 Imm70 Immunity protein 70. A predicted immunity protein with an alpha+beta fold and conserved tyrosine and tryptophan residues. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Tox-REase-10 family. 131 matched cddid_all.tbl CDD pfam15602 pfam15602 379737 Imm71 Immunity protein 71. A predicted immunity protein with a mostly alpha-helical fold and conserved arginine and phenylalanine residues. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Ntox48 family. This domain is often fused to the Imm72 immunity domain. 158 matched cddid_all.tbl CDD pfam15603 pfam15603 406121 Imm74 Immunity protein 74. A predicted immunity protein with an alpha+beta fold. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Tox-ARC family. This domain is also found in heterogeneous poly-immunity loci. 80 matched cddid_all.tbl CDD pfam15604 pfam15604 406122 Ntox15 Novel toxin 15. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses a most all-alpha helical fold and a conserved HxxD motif. In bacterial polymorphic toxin systems, the toxin is usually exported by the type 2, type 6, type 7 or Photorhabdus virulence cassette (PVC)-type secretion systems. This is shown to be a type IV secretion system protein that behaves as DNase. 154 matched cddid_all.tbl CDD pfam15605 pfam15605 373963 Ntox28 Bacterial toxin 28. This entry represents the C-terminal RNase toxin domain found in bacterial polymorphic toxin systems. The toxin possesses an all alpha-helical fold and conserved aspartate and glutamate residues, and K[DE] and [DN]HxxE motifs. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5 or type 7 secretion system. This C-terminal domain cleaves within tRNA anticodon loops, tRNase activity that is stimulated by CysK which stabilizes this domain and allows its binding to the tRNA substrate. 104 matched cddid_all.tbl CDD pfam15606 pfam15606 292240 Ntox34 Bacterial toxin 34. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-alpha helical fold and conserved lysine and cysteine residues, and GNxxD and WxCxH motifs. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 6 secretion system. 80 matched cddid_all.tbl CDD pfam15607 pfam15607 464773 Ntox44 Bacterial toxin 44. A predicted RNase toxin found in bacterial polymorphic toxin systems. The toxin possesses an all-alpha-helical fold with conserved DxK, GNxxxG, and DxxxD motifs. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 6 or type 7 secretion systems. 94 matched cddid_all.tbl CDD pfam15608 pfam15608 434808 PELOTA_1 PELOTA RNA binding domain. This RNA binding Pelota domain is at the C-terminus of a PRTase family. These PRTase+Pelota genes are found in the biosynthetic operon associated with the Ter stress-response operon and are predicted to be involved in the biosynthesis of a ribo-nucleoside involved in stress response. 79 matched cddid_all.tbl CDD pfam15609 pfam15609 434809 PRTase_2 Phosphoribosyl transferase. This PRTase family, and C-terminal TRSP domain, are related to OPRTases, and are predicted to use Orotate as substrate. These genes are found in the biosynthetic operon associated with the Ter stress-response operon and are predicted to be involved in the biosynthesis of a ribo-nucleoside involved in stress response. 189 matched cddid_all.tbl CDD pfam15610 pfam15610 434810 PRTase_3 PRTase ComF-like. This PRTase family is related to the ComF PRTases. These genes are found in the smaller biosynthetic operon associated with the Ter stress-response operon and are predicted to be involved in the biosynthesis of a ribo-nucleoside involved in stress-response. 264 matched cddid_all.tbl CDD pfam15611 pfam15611 434811 EH_Signature EH_Signature domain. This domain with a strongly conserved glutamate at the N-terminus and a histidine at the C-terminus, is found in a SWI2/SNF2 four gene operon. Its strict-neighbourhood association with SWI2/SNF2 ATPase strongly suggests a function in conjunction with it. The other genes in the operon are a OmpA protein and a TM protein. This has a DNA related function along with the TerY-P triad. 354 matched cddid_all.tbl CDD pfam15612 pfam15612 464774 WHIM1 WSTF, HB1, Itc1p, MBD9 motif 1. A conserved alpha helical motif that along with the WHIM2 and WHIM3 motifs, and the DDT domain comprise an alpha helical module found in diverse eukaryotic chromatin proteins.Based on the Ioc3 structure, this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The conserved basic residue in WHIM1 is involved in packing with the DDT motif. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognising and DNA binding domains, some of which discriminate methylated DNA. 46 matched cddid_all.tbl CDD pfam15613 pfam15613 464775 WSD Williams-Beuren syndrome DDT (WSD), D-TOX E motif. This family represents the combined alpha-helical module found in diverse eukaryotic chromatin proteins. Based on the Ioc3 structure, the N-terminus of this module is inferred to interact with nucleosomal linker DNA and the SLIDE domain of ISWI proteins. The resulting complex forms a protein ruler that measures out the spacing between two adjacent nucleosomes. The acidic residue from the GxD signature at the N-terminus is a major determinant of the interaction between the ISWI and WHIM motifs. The N-terminal portion also contacts the inter-nucleosomal linker DNA. The module shows a great domain architectural diversity and is often combined with other modified histone peptide recognizing and DNA binding domains, some of which discriminate methylated DNA. The WSD module constitutes the inter-nucleosomal linker DNA binding site in the major groove of DNA, and was first identified as WSD, the D-TOX E motif of plant homeodomains homologous with the mutant transcription factor causing Williams-Beuren syndrome in association with the DDT-domain. 69 matched cddid_all.tbl CDD pfam15615 pfam15615 434814 TerB_C TerB-C domain. TerB-C occurs C-terminal of TerB in TerB-N containing proteins. This domain displays multiple conserved acidic residues (TerBC). The presence of conserved acidic residues in both TerB-N and TerB-C suggests that they, like the TerB domain, might also chelate metals. These two domains may also occur together in the same protein independently of TerB. 143 matched cddid_all.tbl CDD pfam15616 pfam15616 406130 TerY_C TerY-C metal binding domain. TerY-C is found C-terminal to TerY-like vWA domains in some proteins. It has 8 conserved metal chelating cysteines or histidines. It occasionally occurs as solos. 129 matched cddid_all.tbl CDD pfam15617 pfam15617 406131 C-C_Bond_Lyase C-C_Bond_Lyase of the TIM-Barrel fold. This family of TIM-Barrel fold C-C bond lyase is related to citrate-lyase. These genes are found in the biosynthetic operon, with other enzymatic domains, associated with the Ter stress response operon and are predicted to be involved in the biosynthesis of a ribo-nucleoside involved in stress response. 320 matched cddid_all.tbl CDD pfam15619 pfam15619 464776 Lebercilin Ciliary protein causing Leber congenital amaurosis disease. Lebercilin is a family of eukaryotic ciliary proteins. Mutations in the gene, LCA5, are implicated in the disease Leber congenital amaurosis. In photoreceptors, lebercilin is uniquely localized at the cilium that bridges the inner and outer segments. Lebercilin functions as an integral element of selective protein transport through photoreceptor cilia. Lebercilin specifically interacts with the intraflagellar transport (IFT), and disruption of IFT can lead to Leber congenital amaurosis. 193 matched cddid_all.tbl CDD pfam15620 pfam15620 464777 CENP-C_mid Centromere assembly component CENP-C middle DNMT3B-binding region. CENP-C is a component of the centromere assembly complex in eukaryotes. CENP-C recruits the DNA methyltransferases DNMT3B, in order to establish the necessary epigenetic DNA-methylation essential for maintenance of chromatin structure and genomic stability. This middle region of CENP-C is the binding-domain for DNMT3B. Binding of CENP-C and DNMT3B to DNA occurs at both centromeric and peri-centromeric satellite repeats. CENP-C and DNMT3B regulate the histone code in these regions. 260 matched cddid_all.tbl CDD pfam15621 pfam15621 434817 PROL5-SMR Proline-rich submaxillary gland androgen-regulated family. SMR is a family of proteins found in eukaryotes. The family of SMR proteins is expressed in the submaxillary gland. SMR members may play a role in protection or detoxification. 103 matched cddid_all.tbl CDD pfam15622 pfam15622 464778 CENP_C_N Kinetochore assembly subunit CENP-C N-terminal. CENP-C is a vertebrate family that forms a core component of the centromeric chromatin. On depletion of CENP-C proper formation of both centromeres and kinetochores is prevented. The N-terminal of CENP-C is necessary for recruitment of some but not all components of the Mis12 complex of the kinetochore. 287 matched cddid_all.tbl CDD pfam15623 pfam15623 464779 CT47 Cancer/testis gene family 47. CT47 is a family of proteins found in eukaryotes. Proteins in this family are typically between 262 and 291 amino acids in length. There is a conserved HIL sequence motif. The function of this family is not known. 281 matched cddid_all.tbl CDD pfam15624 pfam15624 434820 Mif2_N Kinetochore CENP-C fungal homolog, Mif2, N-terminal. Mif2_N is a family of fungal proteins homologous to mammalian CENP-C. On depletion of CENP-C proper formation of both centromeres and kinetochores is prevented. The N-terminal of CENP-C is necessary for recruitment of some but not all components of the Mis12 complex of the kinetochore. 134 matched cddid_all.tbl CDD pfam15625 pfam15625 464780 CC2D2AN-C2 CC2D2A N-terminal C2 domain. Many ciliary proteins are involved in ciliogenesis and implicated for ciliophathies. A recent study has shown that many of them contain various new versions of C2 domains which are predicted to mediate membrane localizations for Y-shaped linkers of transition zone of cilia. This is the first C2 domain of ciliary CC2D2A proteins which also have another C2 domain (CC2D2AC-C2) and a new inactive transglutaminase-like peptidase domain (CC2D2A-TGL). 174 matched cddid_all.tbl CDD pfam15626 pfam15626 373975 mono-CXXC single CXXC unit. This is a solo version of the zf-CXXC domain with a conserved CXXCXXCX(n)C, zinc-binding motif. This is, thus far, only detected in the plant lineage in diverse chromatin proteins. Structural comparisons show that the mono-CXXC is homologous to the structural- zinc binding domain of medium chain dehydrogenases. The regular zf-CXXC domain binds nonmethyl-CpG dinucleotides. 53 matched cddid_all.tbl CDD pfam15627 pfam15627 464781 CEP76-C2 CEP76 C2 domain. Many ciliary proteins are involved in ciliogenesis and implicated for ciliophathies. A recent study has shown that many of them contain various new versions of C2 domains which are predicted to mediate membrane localizations for Y-shaped linkers of transition zone of cilia. This is the new C2 domain that is contained by ciliary CEP76 proteins. 157 matched cddid_all.tbl CDD pfam15628 pfam15628 373977 RRM_DME RRM in Demeter. This is a predicted RRM-fold domain present at the C-terminus of Demeter-like glycoslyases. These proteins are involved in DNA demethylation in plants where they catalyze removal of the 5mC base and subsequently cleave the backbone through lyase activity. Orthologs of Demeter are present in plants and stramenopiles. The RRM fold domain is predicted to facilitate interaction of the catalytic domain with ssDNA or regulatory RNA. 102 matched cddid_all.tbl CDD pfam15629 pfam15629 434822 Perm-CXXC Permuted single zf-CXXC unit. This is a permuted version of a single unit of the zf-CXXC domain that is detected in the Demeter-like proteins of land plants. Structural comparisons show that the mono-CXXC is homologous to the structural-zinc binding domain of medium chain dehydrogenases. The classical zf-CXXC domain binds nonmethyl-CpG dinucleotides. 32 matched cddid_all.tbl CDD pfam15630 pfam15630 464782 CENP-S CENP-S protein. CENP-S is a family of vertebral and fungal kinetochore component proteins. CENP-S complexes with CENP-X to form a stable CENP-T-W-S-X heterotetramer. 76 matched cddid_all.tbl CDD pfam15631 pfam15631 406142 Imm-NTF2-2 NTF2 fold immunity protein. A predicted immunity protein of the NTF2 fold. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, which usually contains toxin domains of the Tox-NucA family. This domain is also fused to ankyrin repeats and the pfam14025. 72 matched cddid_all.tbl CDD pfam15632 pfam15632 434824 ATPgrasp_Ter ATP-grasp in the biosynthetic pathway with Ter operon. This ATP-grasp family is related to carbamoyl phosphate synthetase. These genes are found in the biosynthetic operon associated with the Ter stress response operon and are predicted to be involved in the biosynthesis of a ribo-nucleoside involved in stress response. 131 matched cddid_all.tbl CDD pfam15633 pfam15633 406144 Tox-ART-HYD1 HYD1 signature containing ADP-ribosyltransferase. A predicted toxin of the ADP-ribosyltransferase superfamily present in bacterial polymorphic toxin systems. The domain has characteriztic histidine, tyrosine and aspartate residues that comprise the active site. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 6, or type 7 secretion system. ART-HYD1 domain toxin from Photorhabdus has been shown to have antibacterial activity and arrest translation by ADP-ribosylating specific position of 23S rRNA. 97 matched cddid_all.tbl CDD pfam15634 pfam15634 292267 Tox-ART-HYE1 HYE1 signature containing ADP-ribosyltransferase. A predicted toxin of the ADP-ribosyltransferase superfamily present in bacterial polymorphic toxin systems. The domain has characteriztic histidine, tyrosine and glutamate residues that comprise the active site. 282 matched cddid_all.tbl CDD pfam15635 pfam15635 434825 Tox-GHH2 GHH signature containing HNH/Endo VII superfamily nuclease toxin 2. A predicted toxin of the HNH/Endonuclease VII fold present in bacterial polymorphic toxin systems with a characteriztic s[AGP]HH signature motif. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type secretion system. 122 matched cddid_all.tbl CDD pfam15636 pfam15636 464783 Tox-GHH GHH signature containing HNH/Endo VII superfamily nuclease toxin. A predicted toxin of the HNH/Endonuclease VII fold present in bacterial polymorphic toxin systems with a characteriztic sG[HQ]H signature motif. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 6, type 7 or TcdB/TcaC-type secretion system. The metazoan teneurin proteins possess an inactive of this domain at their C-terminus. 78 matched cddid_all.tbl CDD pfam15637 pfam15637 434827 Tox-HNH-HHH HNH/Endo VII superfamily nuclease toxin with a HHH motif. A predicted toxin of the HNH/Endonuclease VII fold present in bacterial polymorphic toxin systems with characteriztic conserved s[GD]xxR and HHH motifs. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5, type 6, type 7 or Photorhabdus virulence cassette (PVC)-type secretion system. 103 matched cddid_all.tbl CDD pfam15638 pfam15638 406146 Tox-MPTase2 Metallopeptidase toxin 2. A zincin-like metallopeptidase domain found in bacterial polymorphic toxin systems. 196 matched cddid_all.tbl CDD pfam15639 pfam15639 406147 Tox-MPTase3 Metallopeptidase toxin 3. A zincin-like metallopeptidase domain found in bacterial polymorphic toxin systems. 137 matched cddid_all.tbl CDD pfam15640 pfam15640 406148 Tox-MPTase4 Metallopeptidase toxin 4. A zincin-like metallopeptidase domain found in bacterial polymorphic toxin systems. 132 matched cddid_all.tbl CDD pfam15641 pfam15641 464784 Tox-MPTase5 Metallopeptidase toxin 5. A zincin-like metallopeptidase domain found in bacterial polymorphic toxin systems. 110 matched cddid_all.tbl CDD pfam15642 pfam15642 292272 Tox-ODYAM1 Toxin in Odyssella and Amoebophilus. A predicted all-alpha fold toxin present in bacterial polymorphic toxin systems of the endosymbionts Odyssella and Amoebophilus. 385 matched cddid_all.tbl CDD pfam15643 pfam15643 434829 Tox-PL-2 Papain fold toxin 2. A papain fold toxin domain found in bacterial polymorphic toxin systems. 102 matched cddid_all.tbl CDD pfam15644 pfam15644 434830 Gln_amidase Papain fold toxin 1, glutamine deamidase. A papain fold toxin domain found in bacterial polymorphic toxin systems. In these systems they might function either as a releasing peptidase or toxin. In Shigella flexneri, UniProtKB:Q8VSD5, this protein is expressed from a plasmid, and delivered into the host via the type III secretion system where it deamidates the glutamine residue at position 100 in ubiquitin-activating enzyme E2, UBC13, to a glutamic acid residue. Invasion of host cells by pathogens normally invokes an acute inflammatory response through activating the TRAF6-mediated signalling pathway. UBC13 helps to activate TRAF6. Thus deamidation of UBC13 results in the dampening of the inflammatory response. The key glutaminase deamidase activity is mediated by a cys-his-glu triad, present in all members of the family. 113 matched cddid_all.tbl CDD pfam15645 pfam15645 406150 Tox-PLDMTX Dermonecrotoxin of the Papain-like fold. A papain fold toxin domain found in bacterial polymorphic toxin systems. 142 matched cddid_all.tbl CDD pfam15646 pfam15646 373987 Tox-REase-2 Restriction endonuclease fold toxin 2. A predicted toxin of the restriction endonuclease fold present in bacterial polymorphic toxin systems. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 7 or PrsW-peptidase dependent secretion system. 129 matched cddid_all.tbl CDD pfam15647 pfam15647 373988 Tox-REase-3 Restriction endonuclease fold toxin 3. A predicted toxin of the restriction endonuclease fold present in bacterial polymorphic toxin systems. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 6, type 7 or PrsW-peptidase dependent secretion system. 102 matched cddid_all.tbl CDD pfam15648 pfam15648 464785 Tox-REase-5 Restriction endonuclease fold toxin 5. A predicted toxin of the restriction endonuclease fold present in bacterial polymorphic toxin systems. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5, type 6, or PrsW-peptidase dependent secretion system. Versions of this domain are also found in caudoviruses. 95 matched cddid_all.tbl CDD pfam15649 pfam15649 434831 Tox-REase-7 Restriction endonuclease fold toxin 7. A predicted toxin of the restriction endonuclease fold present in bacterial polymorphic toxin systems. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5, type 6, or type 7 secretion system. 84 matched cddid_all.tbl CDD pfam15650 pfam15650 379747 Tox-REase-9 Restriction endonuclease fold toxin 9. A predicted toxin of the restriction endonuclease fold present in bacterial polymorphic toxin systems. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 7 secretion system. 87 matched cddid_all.tbl CDD pfam15651 pfam15651 434832 Tox-SGS Salivary glad secreted protein domain toxin. An alpha+beta fold domain with four conserved cysteine residues and a conserved [DE]xx[ND] motif. This domain is mainly present at the c-terminus of RHS repeats containing proteins in insects and crustaceans. Although no bacterial homologs have been identified, the domain architecture suggests an origin from bacterial polymorphic toxin systems. 97 matched cddid_all.tbl CDD pfam15652 pfam15652 379748 Tox-SHH HNH/Endo VII superfamily toxin with a SHH signature. A predicted toxin of the HNH/Endonuclease VII fold present in bacterial polymorphic toxin systems with two conserved histidine residues. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5, type 6 or type 7 secretion system. 97 matched cddid_all.tbl CDD pfam15653 pfam15653 434833 Tox-URI2 URI fold toxin 2. A predicted toxin of the URI nuclease fold present in bacterial polymorphic toxin systems. In bacterial polymorphic toxin systems, the toxin is exported by the type 2 or type 6 secretion system. 86 matched cddid_all.tbl CDD pfam15654 pfam15654 434834 Tox-WTIP Toxin with a conserved tryptophan and TIP tripeptide motif. A predicted toxin domain with two membrane spanning alpha helices and RxxR, Wx[ST]IP motifs. The domain is present in bacterial polymorphic toxin systems. The toxin is usually exported by the type 2 or Photorhabdus virulence cassette (PVC)-type secretion system. 67 matched cddid_all.tbl CDD pfam15655 pfam15655 406155 Imm-NTF2 NTF2 fold immunity protein. A predicted immunity protein of the NTF2 fold. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbor of the toxin gene, which usually contains toxin domains of the Tox-JAB-2 family. 129 matched cddid_all.tbl CDD pfam15656 pfam15656 317959 Tox-HDC Toxin with a H, D/N and C signature. A predicted alpha/beta fold peptidase domain with a strongly conserved triad of a histidine, aspartate/asparagine and cysteine residues that are predicted to comprise the active site of the predicted peptidase. Proteins bearing this predicted toxin domain are particularly common in both intracellular and extracellular pathogens. 130 matched cddid_all.tbl CDD pfam15657 pfam15657 373994 Tox-HNH-EHHH HNH/Endo VII superfamily nuclease toxins. A predicted toxin of the HNH/Endonuclease VII fold present in bacterial polymorphic toxin systems with a characteriztic conserved [ED]H motif and two histidine residues. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5, type 6, type 7 or Photorhabdus virulence cassette (PVC)-type secretion system. 69 matched cddid_all.tbl CDD pfam15658 pfam15658 317961 Latrotoxin_C Latrotoxin C-terminal domain. A toxin domain present in arthropod alphaproteobacterial, gammaproteobacterial endosymbionts and also at the C-termini of the latrotoxins of the black widow spider. The domain is characterized by a conserved, hydrophobic helix and is predicted to associate with the cell membrane. 137 matched cddid_all.tbl CDD pfam15659 pfam15659 434835 Toxin-JAB1 JAB-like toxin 1. 87 matched cddid_all.tbl CDD pfam15660 pfam15660 317963 Imm75 Putative Immunity protein 75. This family is highly conserved suggesting it might derive from a phage protein. Members are less than 90 residues in length, and the function is not known. 84 matched cddid_all.tbl CDD pfam15661 pfam15661 464786 CF222 C6orf222, uncharacterized family. This family of proteins is found in eukaryotes. Proteins in this family are typically between 618 and 652 amino acids in length. 608 matched cddid_all.tbl CDD pfam15662 pfam15662 434837 SPATA3 Spermatogenesis-associated protein 3 family. The SPATA3 family of proteins is expressed significantly in testis and faintly in epididymis in the ten tissues of testis, ovary, spleen, kidney, lung, heart, brain, epididymis, liver and skeletal muscle in mouse. Members are not expressed in the eight other tissues. This suggests that SPATA3 plays potential roles in spermatogenesis cell apoptosis or spermatogenesis. 190 matched cddid_all.tbl CDD pfam15663 pfam15663 464787 zf-CCCH_3 Zinc-finger containing family. zf-CCCH_3 family is found in eukaryotes, and is typically between 155 and 169 amino acids in length. 110 matched cddid_all.tbl CDD pfam15664 pfam15664 434839 TMEM252 Transmembrane protein 252 family. This family of proteins is found in eukaryotes. Proteins in this family are typically between 152 and 182 amino acids in length. The function is not known. 139 matched cddid_all.tbl CDD pfam15665 pfam15665 464788 FAM184 Family with sequence similarity 184, A and B. The function of FAM184 is not known. 211 matched cddid_all.tbl CDD pfam15666 pfam15666 464789 HGAL Germinal center-associated lymphoma. HGAL is a family of mammalian sequences typically between 104 and 179 amino acids in length. Members were discovered in a search for proteins precipitating diffuse large B-cell lymphomas. HGAL interacts with the cytoskeleton and aids the activity of interleukin-6 on cell migration. It also modulates the RhoA signalling pathway. 88 matched cddid_all.tbl CDD pfam15667 pfam15667 464790 GDWWSH Protein of unknown function with motif GDWWSH. This family of proteins is found in eukaryotes. Proteins in this family are typically between 135 and 289 amino acids in length. There are three conserved sequence motifs: GDWWSH, RSDF and KRHG. 249 matched cddid_all.tbl CDD pfam15668 pfam15668 464791 DUF4663 Domain of unknown function (DUF4663). This family of proteins is found in eukaryotes. Proteins in this family are typically between 289 and 334 amino acids in length. There are two completely conserved residues (W and G) that may be functionally important. 335 matched cddid_all.tbl CDD pfam15669 pfam15669 464792 CCDC24 Coiled-coil domain-containing protein 24 family. This family of proteins is found in eukaryotes. Proteins in this family are typically between 187 and 319 amino acids in length. There are two completely conserved residues (G and P) that may be functionally important. 195 matched cddid_all.tbl CDD pfam15670 pfam15670 464793 Spem1 Spermatid maturation protein 1. Spem1 is a family of mammalian proteins. Proteins are exclusively expressed in the cytoplasm of the last three steps of spermiogenesis in the mouse testis, and male mice deficient in Spem1 are completely infertile because of deformed sperm. 254 matched cddid_all.tbl CDD pfam15671 pfam15671 434846 PRR18 Proline-rich protein family 18. This family of proteins is found in eukaryotes. Proteins in this family are typically between 117 and 297 amino acids in length. The function is not known but there are many highly conserved proline residues. 266 matched cddid_all.tbl CDD pfam15672 pfam15672 406167 Mucin15 Cell-membrane associated Mucin15. Mucin15 is a family of vertebrate mucins associated with the cell-membrane. The function is not known. Members of the family are typically between 284 and 335 amino acids in length. 315 matched cddid_all.tbl CDD pfam15673 pfam15673 464794 Ciart Circadian-associated transcriptional repressor. Circadian-associated transcriptional repressor (Ciart or Chrono) is a negative regulatory component of the circadian clock. It functions as a transcriptional repressor, modulating BMAL1-CLOCK activity. It also regulates metabolic pathways such as the glucocorticoid response triggered by behavioral stress. 278 matched cddid_all.tbl CDD pfam15674 pfam15674 434848 CCDC23 Coiled-coil domain-containing protein 23. This family of proteins is found in eukaryotes. Proteins in this family are typically between 66 and 78 amino acids in length. There are two completely conserved residues (K and E) that may be functionally important. 57 matched cddid_all.tbl CDD pfam15675 pfam15675 434849 CLLAC CLLAC-motif containing domain. This short domain is found in chordates. It carries a highly conserved CLLAC sequence motif. The function is not known. 30 matched cddid_all.tbl CDD pfam15676 pfam15676 464795 S6OS1 Six6 opposite strand transcript 1 family. This family of proteins is found in eukaryotes. Proteins in this family are typically between 114 and 587 amino acids in length. The function is not known. 557 matched cddid_all.tbl CDD pfam15677 pfam15677 374010 CEND1 Cell cycle exit and neuronal differentiation protein 1. This family of neuron-specific proteins may have a role in the differentiation of neuroblastoma cells and neuronal precursors. It is involved in development of the cerebellum. 143 matched cddid_all.tbl CDD pfam15678 pfam15678 464796 SPICE Centriole duplication and mitotic chromosome congression. SPICE is a family of proteins found in chordates. It localizes to spindle microtubules in mitosis and to centrioles throughout the cell cycle. Deletion of SPICE compromises the architecture of spindles, the integrity of the spindle pole and the process of aligning chromosomes on the spindle (chromosome congression). 408 matched cddid_all.tbl CDD pfam15679 pfam15679 464797 DUF4665 Domain of unknown function (DUF4665). This family of proteins is found in eukaryotes. Proteins in this family are typically between 45 and 100 amino acids in length. 99 matched cddid_all.tbl CDD pfam15680 pfam15680 464798 OFCC1 Orofacial cleft 1 candidate gene 1 protein. This family of proteins is found in eukaryotes. Proteins in this family are typically between 125 and 276 amino acids in length. 109 matched cddid_all.tbl CDD pfam15681 pfam15681 464799 LAX Lymphocyte activation family X. LAX is a family of proteins is found in chordates. LAX is membrane-associates and expressed in B cells, T cells, and other lymphoid-specific cell types. It down-regulates antigen-receptor signalling in T cells by inhibiting TCR-mediated p38 MAPK activation. 350 matched cddid_all.tbl CDD pfam15682 pfam15682 464800 Mustang Musculoskeletal, temporally activated-embryonic nuclear protein 1. Mustang is a family of short, approx 80 residue, proteins found in chordates. It localizes to the nucleus and specifically, spatially in mesenchymal cells of the developing limbs and tail as well as in the fracture callus, especially in periosteal osteoprogenitor cells, proliferating chondrocytes, and young active osteoblasts. It is highly expressed during embryogenesis and inactivated in most adult tissues with the exception of skeletal muscle and tendon where is is acutely and differentially expressed during bone regeneration. 75 matched cddid_all.tbl CDD pfam15683 pfam15683 464801 TDRP Testis development-related protein. TDRP is a family of proteins found in chordates. It is predominantly expressed in the testis. distributed in both cytoplasm and the nuclei of spermatogenic cells. It may act as a nuclear factor with an important role in spermatogenesis. 147 matched cddid_all.tbl CDD pfam15684 pfam15684 464802 AROS Active regulator of SIRT1, or 40S ribosomal protein S19-binding 1. AROS is a family of chordate proteins active in the nucleolus. It has a stretch of polylysines at the N-terminus and in the middle regions and it localizes to the nucleus and especially the nucleolus in high concentrations. It binds to the 40S ribosomal protein RPS19, which is implicated in erythropoiesis. AROS is an active regulator of Sirtuin (SIRT1), an NAD+-dependent deacetylase protein that plays a role in cell survival and hormonal signalling, and AROS regulates the activity of SIRT1 by enhancing SIRT1-mediated de-acetylation of p53 and thus regulates growth of the cell. 125 matched cddid_all.tbl CDD pfam15685 pfam15685 434857 GGN Gametogenetin. GGN is a family of proteins largely found in mammals. It reacts with POG in the maturation of sperm and is expressed virtually only in the testis. It is found to be associated with the intracellular membrane, binds with GGNBP1 and may be involved in vesicular trafficking. 668 matched cddid_all.tbl CDD pfam15686 pfam15686 434858 LYRIC Lysine-rich CEACAM1 co-isolated protein family. LYRIC is a family of proteins found in eukaryotes. It is a type-1b membrane protein with a single transmembrane domain and localizes to the endoplasmic reticulum and the nuclear envelope. It is also found in the nucleolus, suggesting functional relationships between these two cellular compartments. It is found to be colocalized with tight junction proteins ZO-1 and occludin in polarised epithelial cells, suggesting that LYRIC is part of the tight junction complex. LYRIC has been shown to promote tumour cell migration and invasion by activating the transcription factor NF-kappaB. 423 matched cddid_all.tbl CDD pfam15687 pfam15687 434859 NRIP1_repr_1 Nuclear receptor-interacting protein 1 repression 1. This domain is the first (N-terminal) repression domain of nuclear receptor-interacting protein 1. 305 matched cddid_all.tbl CDD pfam15688 pfam15688 464803 NRIP1_repr_2 Nuclear receptor-interacting protein 1 repression 2. This domain is the second repression domain of nuclear receptor-interacting protein 1. 331 matched cddid_all.tbl CDD pfam15689 pfam15689 406181 NRIP1_repr_3 Nuclear receptor-interacting protein 1 repression 3. This domain is the third repression domain of nuclear receptor-interacting protein 1. 88 matched cddid_all.tbl CDD pfam15690 pfam15690 434861 NRIP1_repr_4 Nuclear receptor-interacting protein 1 repression 4. This domain is the fourth (C-terminal) repression domain of nuclear receptor-interacting protein 1. 312 matched cddid_all.tbl CDD pfam15691 pfam15691 464804 PPP1R32 Protein phosphatase 1 regulatory subunit 32. PPP1R32 is a family of eukaryotic proteins thought to be involved in the interactome of protein phosphatase-1. 418 matched cddid_all.tbl CDD pfam15692 pfam15692 464805 NKAP NF-kappa-B-activating protein. NKAP is a family of eukaryotic proteins that interacts with NF-kappa-B. It is a nuclear regulator of TNF- and IL-1-induced NF-kappa-B activation. NKAP does not interact with RIP in mammalian cells family is often found in association with pfam06047. 84 matched cddid_all.tbl CDD pfam15693 pfam15693 464806 Med26_C Mediator complex subunit 26 C-terminal. Med26_C is the C-terminal domain of subunit 26 of the Mediator complex in eukaryotes. Med19 and Med26 act synergistically to mediate the interaction between REST (a Kruppel-type zinc finger transcription factor that binds to a 21-bp RE1 silencing element present in over 900 human genes) and Mediator. The C-terminal domain is critical and sufficient for its assembly into Mediator and its interaction with Pol II. The most highly conserved C-terminal amino acids are critical for these interactions because deletion of the last eight amino acids from the Med26 C terminus disrupted binding to Mediator and Pol II. 182 matched cddid_all.tbl CDD pfam15694 pfam15694 464807 Med26_M Mediator complex subunit 26 middle domain. Med26_M is the middle domain of subunit 26 of Mediator. Med19 and Med26 act synergistically to mediate the interaction between REST (a Kruppel-type zinc finger transcription factor that binds to a 21-bp RE1 silencing element present in over 900 human genes) and Mediator. 255 matched cddid_all.tbl CDD pfam15695 pfam15695 292323 HERV-K_REC Rec (regulator of expression encoded by corf) of HERV-K-113. REC is a family of rec proteins from the HERV-K viral polyprotein family. Rec is a functional homolog of Rev and Rex, and binds to an RNA element, the Rec-responsive element (RcRE), in the 3'LTR of HTDV/HERV-K transcripts. Thus Rec mediates nuclear export of RNA by binding to its responsive element, RcRE, present in a transcript. The human small glutamine-rich tetratricopeptide repeat-containing protein (hSGT) that controls mitotic processes and is a checkpoint protein during pro-metaphase is found to be a Rec-interacting partner.interferes with its role as a negative regulator of the androgen receptor, leading to enhanced androgen receptor activity. HERV-K(HML-2) elements benefit from this enhanced activity, as this leads to a vicious cycle that can result in increased cell proliferation, an inhibition of apoptosis, and eventually tumourigenesis. 87 matched cddid_all.tbl CDD pfam15696 pfam15696 464808 RAD51_interact RAD51 interacting motif. This motif interacts with RAD51. 39 matched cddid_all.tbl CDD pfam15697 pfam15697 464809 DUF4666 Domain of unknown function (DUF4666). This family of proteins is found in plants. Proteins in this family are typically between 103 and 140 amino acids in length. There are two conserved sequence motifs: LQRS and FRR. 109 matched cddid_all.tbl CDD pfam15698 pfam15698 434867 Phosphatase Phosphatase. Members of this family have phosphatase activity. 256 matched cddid_all.tbl CDD pfam15699 pfam15699 464810 NPR1_interact NPR1 interacting. This family of proteins interacts via a motif at the C-terminus with the regulatory protein NPR1. 108 matched cddid_all.tbl CDD pfam15700 pfam15700 406191 DUF4667 Domain of unknown function (DUF4667). This family of proteins is found in fungi. Proteins in this family are typically between 172 and 313 amino acids in length. 231 matched cddid_all.tbl CDD pfam15701 pfam15701 406192 DUF4668 Domain of unknown function (DUF4668). This family of proteins is found in eukaryotes. Proteins in this family are typically between 142 and 211 amino acids in length. 162 matched cddid_all.tbl CDD pfam15702 pfam15702 464811 HPS6 Hermansky-Pudlak syndrome 6 protein N-terminal domain. This entry represents the N-terminal beta propeller domain of the HPS6 protein. 377 matched cddid_all.tbl CDD pfam15703 pfam15703 464812 LAT2 Linker for activation of T-cells family member 2. 177 matched cddid_all.tbl CDD pfam15704 pfam15704 406195 Mt_ATP_synt Mitochondrial ATP synthase subunit. This plant mitochondrial ATP synthase subunit may the the equivalent of the mitochondrial ATP synthase d subunit. 188 matched cddid_all.tbl CDD pfam15705 pfam15705 464813 TMEM132D_N Mature oligodendrocyte transmembrane protein, TMEM132D, N-term. TMEM132D_N is the N-terminal family of chordate proteins implicated in panic disorder. TMEM132D is a single-pass transmembrane protein that is highly expressed in the cortical regions of the human and mouse brain. The function is still unknown. It may act as a cell-surface marker for oligodendrocyte differentiation. Additionally, as it may be most strongly expressed in neurons and it colocalizes with actin filaments TMEM132D may be implicated in neuronal sprouting and connectivity in brain regions important for anxiety-related behaviour. 129 matched cddid_all.tbl CDD pfam15706 pfam15706 464814 TMEM132D_C Mature oligodendrocyte transmembrane protein, TMEM132D, C-term. TMEM132D_C is the C-terminal family of chordate proteins implicated in panic disorder. TMEM132D is a single-pass transmembrane protein that is highly expressed in the cortical regions of the human and mouse brain. The function is still unknown. It may act as a cell-surface marker for oligodendrocyte differentiation. Additionally, as it may be most strongly expressed in neurons and it colocalizes with actin filaments TMEM132D may be implicated in neuronal sprouting and connectivity in brain regions important for anxiety-related behaviour. 84 matched cddid_all.tbl CDD pfam15707 pfam15707 406198 MCCD1 Mitochondrial coiled-coil domain protein 1. This is a family of uncharacterized proteins known as mitochondrial coiled-coil domain protein 1. 90 matched cddid_all.tbl CDD pfam15708 pfam15708 406199 PRR20 Proline-rich protein family 20. This family of proteins is found in eukaryotes. Proteins in this family are typically between 73 and 221 amino acids in length. There is a conserved AYV sequence motif. 221 matched cddid_all.tbl CDD pfam15709 pfam15709 464815 DUF4670 Domain of unknown function (DUF4670). This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length. 522 matched cddid_all.tbl CDD pfam15710 pfam15710 464816 Brme1 Break repair meiotic recombinase recruitment factor 1. Brme1 (also known as Meiok21) is a component of meiotic recombination bridges involved in meiotic double-strand break repair. The C-terminal domain of Brme1 physically interacts with the N-terminal domain of HSF2BP. BRME1 facilitates the loading of RAD51 and DMC1 recombinases onto DSBs (DNA double-strand breaks) through interaction with MEILB2/HSF2BP and replacing ssDNA binding proteins. Brme1 is highly expressed in mice testes and fetal ovaries. Knockout of Brme1 results in male mice infertility. 667 matched cddid_all.tbl CDD pfam15711 pfam15711 464817 ILEI Interleukin-like EMT inducer. ILEI is a family of proteins found in vertebrates. It is heavily involved in the process of the transition from epithelial to mesenchymal tissue - EMT - during all of embryonic development, cancer progression, metastasis, and chronic inflammation/fibrosis. ILEI is upregulated exclusively at the level of translation, and abnormal ILEI expression, ie cytoplasmic over-expression instead of vesicular localization, is associated with EMT in human cancerous tissue. In order to induce and maintain the EMT of hepatocytes in a TGF-beta-independent fashion ILEI needs the cooperation of oncogenic Ras. 89 matched cddid_all.tbl CDD pfam15712 pfam15712 434876 NPAT_C NPAT C terminus. 680 matched cddid_all.tbl CDD pfam15713 pfam15713 434877 PTPRCAP Protein tyrosine phosphatase receptor type C-associated. 148 matched cddid_all.tbl CDD pfam15714 pfam15714 464818 SpoVT_C Stage V sporulation protein T C-terminal, transcription factor. SpoVT_C is the C-terminal part of the stage V sporulation protein T, a transcription factor involved in endospore formation in Gram-positive bacteria such as Bacillus subtilis. Sporulation is induced by conditions of environmental stress to protect the genome. SpoVT behaves as a tetramer that shows an overall significant distortion mediated by electrostatic interactions. Two monomers dimerize via the highly charged N-terminal AbrB-like domains, family pfam04014, to form swapped-hairpin beta-barrels. These asymmetric dimers then form tetramers through the formation of mixed helix bundles between their C-terminal domains. The C-termini themselves fold as GAF (cGMP-specific and cGMP-stimulated phosphodiesterases, Anabaena adenylate cyclases, and Escherichia coli FhlA) domains. 128 matched cddid_all.tbl CDD pfam15715 pfam15715 464819 PAF PCNA-associated factor histone like domain. This domain corresponds to a histone like fold in p15(PAF). 120 matched cddid_all.tbl CDD pfam15716 pfam15716 464820 DUF4672 Domain of unknown function (DUF4672). This family of proteins is found in eukaryotes. Proteins in this family are typically between 165 and 199 amino acids in length. 187 matched cddid_all.tbl CDD pfam15717 pfam15717 464821 PCM1_C Pericentriolar material 1 C terminus. 615 matched cddid_all.tbl CDD pfam15718 pfam15718 464822 MNR Protein moonraker. Protein moonraker is a centriolar satellite component involved in centriole duplication. It promotes centriole duplication by localizing WDR62 to the centrosome. 935 matched cddid_all.tbl CDD pfam15719 pfam15719 464823 DUF4674 Domain of unknown function (DUF4674). This family of proteins is found in eukaryotes. Proteins in this family are typically between 126 and 221 amino acids in length. 191 matched cddid_all.tbl CDD pfam15720 pfam15720 464824 DUF4675 Domain of unknown function (DUF4675). This family of proteins is found in eukaryotes. Proteins in this family are approximately 190 amino acids in length. 190 matched cddid_all.tbl CDD pfam15721 pfam15721 406212 ANXA2R Annexin-2 receptor. This family of proteins acts as annexin-2 receptors. 190 matched cddid_all.tbl CDD pfam15722 pfam15722 464825 FAM153 FAM153 family. This family of proteins is found in eukaryotes. Proteins in this family are typically between 109 and 289 amino acids in length. 114 matched cddid_all.tbl CDD pfam15723 pfam15723 434885 MqsR_toxin Motility quorum-sensing regulator, toxin of MqsA. MqsR_toxin is a family of bacterial toxins that act as an mRNA interferase. MqsR is the gene most highly upregulated in E. coli persister cells and it plays an essential role in biofilm regulation and cell signalling. It forms part of a bacterial toxin-antitoxin TA system, and as expected for a TA system, the expression of the MqsR toxin leads to growth arrest, while co-expression with its antitoxin, MqsA, rescues the growth arrest phenotype. In addition, MqsR associates with MqsA to form a tight, non-toxic complex and both MqsA alone and the MqsR:MqsA2:MqsR complex bind and regulate the mqsR promoter. The structure of MqsR shows that is is a member of the RelE/YoeB family of bacterial RNases that are structurally and functionally characterized bacterial toxins.y characterized bacterial toxins. 96 matched cddid_all.tbl CDD pfam15724 pfam15724 464826 TMEM119 TMEM119 family. This family of proteins is found in eukaryotes. Proteins in this family are typically between 217 and 283 amino acids in length. 252 matched cddid_all.tbl CDD pfam15725 pfam15725 292353 RCDG1 Renal cancer differentiation gene 1 protein. This family includes human protein C4orf46, also known as renal cancer differentiation gene 1 protein (RCDG1). 83 matched cddid_all.tbl CDD pfam15726 pfam15726 292354 DUF4677 Domain of unknown function (DUF4677). This family of proteins is found in eukaryotes. Proteins in this family are typically between 157 and 195 amino acids in length. 198 matched cddid_all.tbl CDD pfam15727 pfam15727 464827 DUF4678 Domain of unknown function (DUF4678). This family of proteins is found in eukaryotes. Proteins in this family are typically between 318 and 395 amino acids in length. 380 matched cddid_all.tbl CDD pfam15728 pfam15728 434888 DUF4679 Domain of unknown function (DUF4679). This family of proteins is found in eukaryotes. Proteins in this family are typically between 213 and 412 amino acids in length. 399 matched cddid_all.tbl CDD pfam15729 pfam15729 464828 ALS2CR11 Amyotrophic lateral sclerosis 2 candidate 11. This family of proteins is found in eukaryotes. Proteins in this family are typically between 286 and 727 amino acids in length. 417 matched cddid_all.tbl CDD pfam15730 pfam15730 406219 DUF4680 Domain of unknown function (DUF4680). This family of proteins is found in eukaryotes. Proteins in this family are typically between 65 and 178 amino acids in length. There are two conserved sequence motifs: VISRM and ENE. 144 matched cddid_all.tbl CDD pfam15731 pfam15731 292359 MqsA_antitoxin Antitoxin component of bacterial toxin-antitoxin system, MqsA. MqsA_antitoxin is a family of prokaryotic proteins that act as antidotes to the mRNA interferase MqsR. It has a zinc-binding at the very N-terminus indicating its DNA-binding capacity. MqsR is the gene most highly upregulated in E. Colo MqsR_toxin is a family of bacterial toxins that act as an mRNA interferase. MqsR is the gene most highly upregulated in E. coli persister cells and it plays an essential role in biofilm regulation and cell signalling. It forms part of a bacterial toxin-antitoxin TA system, and as expected for a TA system, the expression of the MqsR toxin leads to growth arrest, while co-expression with its antitoxin, MqsA, rescues the growth arrest phenotype. In addition, MqsR associates with MqsA to form a tight, non-toxic complex and both MqsA alone and the MqsR:MqsA2:MqsR complex bind and regulate the mqsR promoter. The structure of MqsR shows that is is a member of the RelE/YoeB family of bacterial RNases that are structurally and functionally characterized bacterial toxins. 131 matched cddid_all.tbl CDD pfam15732 pfam15732 464829 DUF4681 Domain of unknown function (DUF4681). This family of proteins is found in eukaryotes. Proteins in this family are typically between 101 and 127 amino acids in length. 125 matched cddid_all.tbl CDD pfam15733 pfam15733 464830 DUF4682 Domain of unknown function (DUF4682). This domain family is found in eukaryotes, and is typically between 152 and 183 amino acids in length. The family is found in association with pfam00566. There is a conserved NHLL sequence motif. 121 matched cddid_all.tbl CDD pfam15734 pfam15734 464831 MIIP Migration and invasion-inhibitory. This family of proteins binds to insulin-like growth factor binding protein 2 (IGFBP-2) and inhibits the invasion of glioma cells. 337 matched cddid_all.tbl CDD pfam15735 pfam15735 464832 DUF4683 Domain of unknown function (DUF4683). This domain family is found in eukaryotes, and is typically between 384 and 400 amino acids in length. 391 matched cddid_all.tbl CDD pfam15736 pfam15736 464833 DUF4684 Domain of unknown function (DUF4684). This family of proteins is found in eukaryotes. Proteins in this family are typically between 531 and 1277 amino acids in length. 435 matched cddid_all.tbl CDD pfam15737 pfam15737 464834 DUF4685 Domain of unknown function (DUF4685). This domain family is found in eukaryotes, and is typically between 106 and 131 amino acids in length. There are two conserved sequence motifs: SGE and VRF. 117 matched cddid_all.tbl CDD pfam15738 pfam15738 434896 YafQ_toxin Bacterial toxin of type II toxin-antitoxin system, YafQ. YafQ is a family of bacterial toxin ribonucleases of type II toxin-antitoxin systems. The E.coli gene is expressed from the dinB operon. The cognate antitoxin for the E. coli protein is DinJ, in family RelB_antitoxin, pfam02604. 88 matched cddid_all.tbl CDD pfam15739 pfam15739 464835 TSNAXIP1_N Translin-associated factor X-interacting N-terminus. This domain is found at the N-terminus of translin-associated factor X-interacting protein, a protein which may play a role in spermatogenesis. 111 matched cddid_all.tbl CDD pfam15740 pfam15740 464836 PPP1R26_N Protein phosphatase 1 regulatory subunit 26 N-terminus. This domain represents the N-terminus of protein phosphatase 1 regulatory subunit 26. 866 matched cddid_all.tbl CDD pfam15741 pfam15741 464837 LRIF1 Ligand-dependent nuclear receptor-interacting factor 1. This family of proteins interacts with the retinoic acid receptor RARalpha and inhibit it's ligand-dependent transcriptional activation. 739 matched cddid_all.tbl CDD pfam15742 pfam15742 464838 DUF4686 Domain of unknown function (DUF4686). This family of proteins is found in eukaryotes. Proteins in this family are typically between 498 and 775 amino acids in length. There is a conserved DLK sequence motif. 384 matched cddid_all.tbl CDD pfam15743 pfam15743 464839 SPATA1_C Spermatogenesis-associated C-terminus. This domain family is found in eukaryotes, and is approximately 150 amino acids in length. There is a single completely conserved residue E that may be functionally important. 150 matched cddid_all.tbl CDD pfam15744 pfam15744 464840 UPF0492 Uncharacterized protein family UPF0492. This family of proteins is found in eukaryotes. Proteins in this family are typically between 78 and 408 amino acids in length. 359 matched cddid_all.tbl CDD pfam15745 pfam15745 464841 AP1AR AP-1 complex-associated regulatory protein. 275 matched cddid_all.tbl CDD pfam15746 pfam15746 374072 TMEM215 TMEM215 family. This family of proteins is found in eukaryotes. Proteins in this family are approximately 230 amino acids in length. 225 matched cddid_all.tbl CDD pfam15747 pfam15747 374073 DUF4687 Domain of unknown function (DUF4687). This family of proteins is found in eukaryotes. Proteins in this family are typically between 76 and 140 amino acids in length. 120 matched cddid_all.tbl CDD pfam15748 pfam15748 464842 CCSAP Centriole, cilia and spindle-associated. This family of microtubule-binding proteins may play a role in embryonic brain development and cilia beating. 255 matched cddid_all.tbl CDD pfam15749 pfam15749 464843 MRNIP MRN-interacting protein. This family is found in eukaryotes. Family members include MRN complex-interacting protein (MRNIP), which plays a role in preventing the accumulation of damaged DNA in cells. It associates with the MRE11-RAD50-NBS1 (MRN) damage-sensing complex and is rapidly recruited to sites of DNA damage. Phosphorylation of a serine promotes nuclear localization of MRNIP. 100 matched cddid_all.tbl CDD pfam15750 pfam15750 464844 UBZ_FAAP20 Ubiquitin-binding zinc-finger. This domain is the ubiquitin-binding zinc-finger of the Fanconi anaemia-associated protein of 20 kDa. 35 matched cddid_all.tbl CDD pfam15751 pfam15751 464845 FANCA_interact FAAP20 FANCA interaction domain. This domain is found at the N-terminus of Fanconi anemia-associated protein of 20 kDa (FAAP20), where it is responsible for interaction with Fanconi anemia group A protein (FANCA). 108 matched cddid_all.tbl CDD pfam15752 pfam15752 464846 DUF4688 Domain of unknown function (DUF4688). This family of proteins is found in eukaryotes. Proteins in this family are typically between 331 and 596 amino acids in length. 400 matched cddid_all.tbl CDD pfam15753 pfam15753 464847 BLOC1S3 Biogenesis of lysosome-related organelles complex 1 subunit 3. This family of proteins are components of the biogenesis of lysosome-related organelles complex-1 (BLOC-1). 168 matched cddid_all.tbl CDD pfam15754 pfam15754 464848 SPESP1 Sperm equatorial segment protein 1. 322 matched cddid_all.tbl CDD pfam15755 pfam15755 406240 DUF4689 Domain of unknown function (DUF4689). This family of proteins is found in eukaryotes. Proteins in this family are typically between 202 and 224 amino acids in length. 223 matched cddid_all.tbl CDD pfam15756 pfam15756 464849 DUF4690 Small Novel Rich in Cartilage. This family of proteins is found in eukaryotes and include SNORC, a cartilage specific small membrane proteoglycan that plays a role in the regulation of chondrocyte maturation and postnatal endochondral ossification. There are two conserved sequence motifs: LGPGAI and LRKF. 96 matched cddid_all.tbl CDD pfam15757 pfam15757 464850 Amelotin Amelotin. This ameloblast-specific family of proteins may play a role in dental enamel formation. 195 matched cddid_all.tbl CDD pfam15758 pfam15758 434913 HRCT1 Histidine-rich carboxyl terminus protein 1. 78 matched cddid_all.tbl CDD pfam15759 pfam15759 464851 TMEM108 TMEM108 family. This family of proteins is found in eukaryotes. Proteins in this family are typically between 258 and 575 amino acids in length. 511 matched cddid_all.tbl CDD pfam15760 pfam15760 406245 DLEU7 Leukemia-associated protein 7. 194 matched cddid_all.tbl CDD pfam15761 pfam15761 464852 IMUP immortalization up-regulated protein. This family of proteins is found in eukaryotes. Proteins in this family are approximately 100 amino acids in length. There are two conserved sequence motifs: GDPK and KKPK. 101 matched cddid_all.tbl CDD pfam15762 pfam15762 464853 DUF4691 Domain of unknown function (DUF4691). This family of proteins is found in eukaryotes. Proteins in this family are typically between 71 and 317 amino acids in length. 170 matched cddid_all.tbl CDD pfam15763 pfam15763 434917 DUF4692 Regulator of human erythroid cell expansion (RHEX). This family of proteins is found in eukaryotes. Family members include human RHEX proteins which regulates erythroid progenitor cell expansion and erythroblast development. 166 matched cddid_all.tbl CDD pfam15764 pfam15764 464854 DUF4693 Domain of unknown function (DUF4693). This family of proteins is found in eukaryotes. Proteins in this family are typically between 238 and 436 amino acids in length. 285 matched cddid_all.tbl CDD pfam15765 pfam15765 434919 DUF4694 Domain of unknown function (DUF4694). This family of proteins is found in eukaryotes. Proteins in this family are typically between 154 and 217 amino acids in length. There is a conserved SSGY sequence motif. 155 matched cddid_all.tbl CDD pfam15766 pfam15766 374090 DUF4695 Domain of unknown function (DUF4695). This family of proteins is found in eukaryotes. Proteins in this family are typically between 109 and 206 amino acids in length. There is a conserved RFKTQP sequence motif. 107 matched cddid_all.tbl CDD pfam15767 pfam15767 464855 ARMH4 Armadillo-like helical domain-containing protein 4. This family represents the Armadillo-like helical domain-containing protein 4, whose function is not clear. 583 matched cddid_all.tbl CDD pfam15768 pfam15768 464856 CC190 Coiled-coil domain-containing protein 190. This family of proteins is found in eukaryotes. Proteins in this family are typically between 234 and 297 amino acids in length. 270 matched cddid_all.tbl CDD pfam15769 pfam15769 464857 DUF4698 Domain of unknown function (DUF4698). This family of proteins is found in eukaryotes. Proteins in this family are typically between 464 and 550 amino acids in length. 484 matched cddid_all.tbl CDD pfam15770 pfam15770 464858 DUF4699 Domain of unknown function (DUF4699). This family of proteins is found in eukaryotes. Proteins in this family are typically between 303 and 319 amino acids in length. 310 matched cddid_all.tbl CDD pfam15771 pfam15771 464859 IHO1 Interactor of HORMAD1 protein 1. Interactor of HORMAD1 protein 1 (IHO1, previously known as coiled-coil domain-containing protein 36 or DUF4700) is required for DNA double-strand breaks (DSBs) formation in unsynapsed regions during meiotic recombination. It is thought to function, in collaboration with SPO11-auxiliary proteins MEI4 and REC114, through the formation of DSB-promoting recombinosomes on chromatin at the onset of meiosis. 575 matched cddid_all.tbl CDD pfam15772 pfam15772 464860 UPF0688 UPF0688 family. This family of proteins is found in eukaryotes. Proteins in this family are typically between 176 and 243 amino acids in length. 233 matched cddid_all.tbl CDD pfam15773 pfam15773 464861 DAAP1 Dynein axonemal-associated protein 1. Daap1 is a axonemal dynein regulator that interacts with outer dynein arm (ODA) subunits and is required for deployment of ODA to the axoneme. 505 matched cddid_all.tbl CDD pfam15774 pfam15774 464862 DUF4702 Domain of unknown function (DUF4702). This family of proteins is found in eukaryotes. Proteins in this family are typically between 346 and 637 amino acids in length. 402 matched cddid_all.tbl CDD pfam15775 pfam15775 406259 DUF4703 Domain of unknown function (DUF4703). This family of proteins is found in eukaryotes. Proteins in this family are typically between 149 and 210 amino acids in length. 186 matched cddid_all.tbl CDD pfam15776 pfam15776 464863 PRR22 Proline-rich protein family 22. This family of proteins is found in eukaryotes. Proteins in this family are typically between 217 and 420 amino acids in length. 366 matched cddid_all.tbl CDD pfam15777 pfam15777 406260 Anti-TRAP Tryptophan RNA-binding attenuator protein inhibitory protein. 59 matched cddid_all.tbl CDD pfam15778 pfam15778 464864 UNC80_N UNC80 N-terminal. UNC80 is a family of proteins found in eukaryotes. This entry represents the N-terminal domain. NALCN and UNC80 form a complex in mouse brain, both being tyrosine-phosphorylated; this phosphorylation can be inhibited by PP1. NALCN as the cation channel activated by substance P receptor, and the coupling from receptor to channel is facilitated by UNC80 and Src kinases rather than by a G-protein. 187 matched cddid_all.tbl CDD pfam15779 pfam15779 434930 LRRC37 Leucine-rich repeat-containing protein 37 family. This domain family is found in eukaryotes, and is approximately 70 amino acids in length. The function of this protein is unknown but it is likely to be upregulated by androgen. 73 matched cddid_all.tbl CDD pfam15780 pfam15780 464865 ASH Abnormal spindle-like microcephaly-assoc'd, ASPM-SPD-2-Hydin. The ASH domain or N-terminal domain of abnormal spindle-like microcephaly-associated protein are found in proteins associated with cilia, flagella, the centrosome and the Golgi complex. The domain is also found in Hydin and OCRL whose deficiencies are associated with hydrocephalus and Lowe oculocerebrorenal syndrome (OCRL), respectively. The fact that Human ASPM protein carries an ASH domain indicates possible roles for ASPM in sperm flagellar or in ependymal cells' cilia. The presence of ASH in centrosomal and ciliary proteins indicates that ASPM may possess roles not only in mitotic spindle regulation, but also in ciliary and flagellar function. 98 matched cddid_all.tbl CDD pfam15781 pfam15781 434932 ParE-like_toxin ParE-like toxin of type II bacterial toxin-antitoxin system. 87 matched cddid_all.tbl CDD pfam15782 pfam15782 464866 GREB1 GREB1 N-terminal region. GREB1 (gene regulated by estrogen in breast cancer 1) was first identified as an oestrogen-regulated gene expressed in breast cancer. Its exact function is not known but its expression is regulated by the coordinated binding of oestrogen-receptors to distal sites interacting with Pol II to activate gene transcription from core promoters located at a considerable distance from the greb1 gene. 1102 matched cddid_all.tbl CDD pfam15783 pfam15783 464867 FSIP2 Fibrous sheath-interacting protein 2. FSIP2, fibrous sheath-interacting protein 2, is the C-terminal portion of a family of proteins found in mammals. The function is not known but the domain appears to be repeated up to 10 times in some members. 877 matched cddid_all.tbl CDD pfam15784 pfam15784 464868 GPS2_interact G-protein pathway suppressor 2-interacting domain. GPS2_interact is the more N-terminal domain of two co-repressor protein-families found in vertebrates. The domain is found in NCoR and SMRT proteins; N-CoR (nuclear receptor co-repressor) and SMRT (silencing mediator for retinoid and thyroid receptors) are related corepressors that mediate transcriptional repression by unliganded nuclear receptors and other classes of transcriptional repressors. GPS2 is a stoichiometric subunit of the N-CoR-HDAC3 complex. GPS2 links the complex to membrane receptor-related intracellular JNK (c-Jun amino-terminal kinase) signalling pathways. 89 matched cddid_all.tbl CDD pfam15785 pfam15785 464869 SMG1 Serine/threonine-protein kinase smg-1. SMG1 is a family of eukaryotic proteins. In humans this family acts as an mRNA-surveillance protein. In C.elegans, SMG1, a phosphatidylinositol kinase-related protein kinase, is a key regulator of growth. Loss of SMG1 leads to hyperactive responses to injury and subsequent growth that continues out of control. It has an antagonistic role to mTOR signalling in these worms and possibly also in higher eukaryotes. 602 matched cddid_all.tbl CDD pfam15786 pfam15786 434937 PET117 PET assembly of cytochrome c oxidase, mitochondrial. PET117 is a family of eukaryotic proteins found from fungi and plants to human. It is likely to be involved in the assembly of cytochrome C oxidase, and is found in the mitochondrion. 66 matched cddid_all.tbl CDD pfam15787 pfam15787 464870 DUF4704 Neurobeachin/BDCP, DUF4704 alpha solenoid region. This domain of unknown function is found in eukaryotes on neurobeachin and BEACH domain-containing proteins (BDCPs). Mutations in this proteins are associated with Lipopolysaccharide-responsive and beige-like anchor (LRBA) deficiency. According to structure prediction is adopts an alpha-helical solenoid structure. 486 matched cddid_all.tbl CDD pfam15788 pfam15788 406271 DUF4705 Domain of unknown function (DUF4705). DUF4705 is a family of repeated domains that is found in eukaryotes. It can occur up to 10 times in any one sequence. The repeat is rich in glycine and proline residues. 52 matched cddid_all.tbl CDD pfam15789 pfam15789 374113 Hyr1 Hyphally regulated cell wall GPI-anchored protein 1. Hyr1 family is a repeated domain found up to 39 times in a range of fungal and vertebral proteins. Hyr1 is a hypha-specific protein. 41 matched cddid_all.tbl CDD pfam15790 pfam15790 434938 EP400_N E1A-binding protein p400, N-terminal. EP400_N is a family of eukaryote proteins. the exact function of this domain is not known. This family is largely low-complexity residues. 489 matched cddid_all.tbl CDD pfam15791 pfam15791 464871 DMRT-like Doublesex-and mab-3-related transcription factor C1 and C2. DMRT-like is a C-terminal domain found on eukaryotic proteins for doublesex-and mab-3-related transcription factors C1 and C2. This is not the DM DNA-binding region. The family is all disorder and low-complexity. 119 matched cddid_all.tbl CDD pfam15792 pfam15792 464872 LAS2 Lung adenoma susceptibility protein 2. LAS2 is a family of eukaryotic proteins. Deletion of LAS2 is observed in approx. 40% of human lung adenocarcinomas, suggesting that loss of function of LAS2 may be a key step for promoting lung tumourigenesis. 75 matched cddid_all.tbl CDD pfam15793 pfam15793 464873 FAM35_C Protein family FAM35, C-terminal. FAM35_C is a family of proteins found in eukaryotes. the function is not known. 176 matched cddid_all.tbl CDD pfam15794 pfam15794 464874 CCDC106 Coiled-coil domain-containing protein 106. CCDC106, coiled-coil domain-containing protein 106, is a family of eukaryote proteins. Yeast two-hybrid screening has identified CCDC106 as a p53-interacting partner. CCDC106 is a negative regulator of p53 and may be involved in tumourigenesis in some cancers by promoting the degradation of p53 protein and inhibiting its transactivity. 220 matched cddid_all.tbl CDD pfam15795 pfam15795 464875 Spec3 Ectodermal ciliogenesis protein. Spec3 is a family of eukaryotic membrane proteins. In the sea urchin, Spec3 is expressed predominantly during ectodermal ciliogenesis. 85 matched cddid_all.tbl CDD pfam15796 pfam15796 464876 KELK KELK-motif containing domain of MRCK Ser/Thr protein kinase. KELK is a domain of eukaryotic proteins found in serine/threonine-protein kinase MRCK-type proteins. The region is low-complexity, but it is not a predicted disordered-binding domain. The name comes from a highly conserved sequence motif within the domain. The function is not known. 80 matched cddid_all.tbl CDD pfam15797 pfam15797 464877 DUF4706 Domain of unknown function (DUF4706). This domain family is found in eukaryotes, and is approximately 110 amino acids in length. 109 matched cddid_all.tbl CDD pfam15798 pfam15798 406279 PRAS Proline-rich AKT1 substrate 1. This domain family is found in eukaryotes, and is typically between 117 and 132 amino acids in length. PRAS domain family is found in eukaryotes, and is typically between 117 and 132 amino acids in length. It is a proline-rich family that can be phosphorylated by AKT, and in the phosphorylated state binds to 14-3-3. The AKT signalling pathway contributes to regulation of apoptosis after a variety of cell death stimuli, and PRAS is found to be a substrate. PRAS plays an important role in regulating cell survival downstream of the PI3-K/Akt pathway after re-perfusion injury after transient focal cerebral ischemia. Copper/zinc-SOD (SOD1), a cytosolic isoenzyme of superoxide dismutase, SOD, is highly protective against ischemia and re-perfusion injury after transient focal cerebral ischemia, and SOD1 thus contributes to the inhibition of direct oxidation of PRAS and the activation of its signalling pathway. PRAS is also a mTOR binding partner, and PRAS phosphorylation by AKT and its association with 14-3-3, a cytosolic anchor protein, are crucial for insulin to stimulate mTOR (mammalian target of rapamycin). 123 matched cddid_all.tbl CDD pfam15799 pfam15799 464878 CCD48 Coiled-coil domain-containing protein 48. This family of proteins is found in eukaryotes. Proteins in this family are typically between 161 and 575 amino acids in length. 577 matched cddid_all.tbl CDD pfam15800 pfam15800 464879 CiPC Clock interacting protein circadian. CiPC is a family of proteins found in eukaryotes. The protein was identified in sheep as a gene-orthologue involved in regulation of the circadian clock. Proteins in this family are typically between 220 and 400 amino acids in length. 338 matched cddid_all.tbl CDD pfam15801 pfam15801 464880 zf-C6H2 zf-MYND-like zinc finger, mRNA-binding. zf-C6H2 is an unusual zinc-finger similar to zf-MYND, pfam01753.This zinc-finger is found at the N-terminus of Pfam families Exo_endo_phos pfam03372 and Peptidase_M24 pfam00557. The domain is missing in prokaryotic methionine aminopeptidases, and is a unique type of zinc-finger domain. It consists of a C2-C2 zinc-finger motif similar to the RING finger family followed by a C2H2 motif similar to zinc-fingers involved in RNA-binding. In yeast the domain chelates zinc in a 2:1 ratio. The domain is found in yeast, plants and mammals. The domain is necessary for the association of the methionine aminopeptidase with the ribosome and the normal processing of the peptidase. 46 matched cddid_all.tbl CDD pfam15802 pfam15802 464881 DCAF17 DDB1- and CUL4-associated factor 17. DCAF17, DDB1- and CUL4-associated factor 17, is a family of proteins found in eukaryotes. It may function as a substrate-receptor for CUL4-DDB1 E3 ubiquitin-protein ligase complex. Mutations in the human protein, otherwise known as C2orf37, are responsible for Woodhouse-Sakati Syndrome. Woodhouse-Sakati Syndrome is a rare autosomal recessive multi-systemic disorder characterized by hypogonadism, alopecia, diabetes mellitus, mental retardation, and extrapyramidal syndrome. 474 matched cddid_all.tbl CDD pfam15803 pfam15803 464882 zf-SCNM1 Zinc-finger of sodium channel modifier 1. zf-SCNM1 is a C2H2 type zinc-finger conserved in eukaryotes found at the N-terminus of SCNM1, sodium channel modifier protein 1. Phylogenetic analysis of these zinc finger sequences places SCNM1 within the U1C subfamily of RNA binding proteins that is commonly found in RNA-processing proteins, suggesting that SCNM1 is involved in splicing activities. 27 matched cddid_all.tbl CDD pfam15804 pfam15804 464883 CCDC168_N Coiled-coil domain-containing protein 168. CCDC168_N is the N-terminal region of eukaryotic coiled-coil proteins 168 family. There are up to 17, on average 6, copies of this repeat in most members. 204 matched cddid_all.tbl CDD pfam15805 pfam15805 464884 SCNM1_acidic Acidic C-terminal region of sodium channel modifier 1 SCNM1. SCNM1_acidic is the C-terminal acidic region of eukaryotic sodium channel modifier protein 1. Deletion of this region affects the splicing and normal activity of the sodium channel Nav1.6 from gene Scn8a. SCNM1 sits within the U1C subfamily of RNA binding proteins that is commonly found in RNA-processing proteins, suggesting that SCNM1 is involved in splicing activities. SCNM1 and LUC7L2 associate with the mammalian spliceosomal subunit U1 snRNP. 46 matched cddid_all.tbl CDD pfam15806 pfam15806 464885 DUF4707 Domain of unknown function (DUF4707). This family of proteins is found in eukaryotes. The function is not known. 432 matched cddid_all.tbl CDD pfam15807 pfam15807 464886 MAP17 Membrane-associated protein 117 kDa, PDZK1-interacting protein 1. MAP17 is a family of proteins found in eukaryotes. It is a small non-glycosylated two-pass membrane protein, that is overexpressed in many tumours of different origins, including carcinomas. 121 matched cddid_all.tbl CDD pfam15808 pfam15808 434953 BCOR BCL-6 co-repressor, non-ankyrin-repeat region. BCOR is a domain family found in eukaryotes, and is approximately 220 amino acids in length. This domain lies just upstream of the ankyrin-repeat region at the C-terminus of BCL-6 co-repressor proteins. The function of this region is not known. 219 matched cddid_all.tbl CDD pfam15809 pfam15809 464887 STG Simian taste bud-specific gene product family. STG was first isolated from rhesus monkey taste buds. The exact function of STG is not known, but it has been implicated in follicular lymphomas, though not with psoriasis at least in a Swedish population despite lying close to the PSOR1 gene-locus. 240 matched cddid_all.tbl CDD pfam15810 pfam15810 434955 CCDC117 Coiled-coil domain-containing protein 117. CCDC117 is a family of coiled-coil proteins found in eukaryotes. Proteins in this family are typically between 203 and 279 amino acids in length. There is a conserved MELV sequence motif. The function is not known. 143 matched cddid_all.tbl CDD pfam15811 pfam15811 464888 SVIP Small VCP/p97-interacting protein. SVIP, small VCP/p97-interacting protein, is a family of proteins found in eukaryotes. SVIP was identified by yeast two-hybrid screening to be an interactive partner of VCP/p97. Mammalian VCP/p97 and its yeast counterpart Cdc48p participate in the formation of organelles, including the endoplasmic reticulum (ER), Golgi apparatus, and nuclear envelope. Over-expression of SVIP caused the formation of large vacuoles that seemed to be derived from the ER. The family has two putative coiled-coil regions and contains proteins of approximately 80 amino acids in length. 77 matched cddid_all.tbl CDD pfam15812 pfam15812 434956 MREG Melanoregulin. Melanoregulin is a family of proteins found in eukaryotes. It is a putative membrane fusion regulator. MREG forms a complex with peripherin-2. It is required for lysosome maturation and plays a role in intracellular trafficking. It is a negative regulator of melanosome intercellular transfer and it regulates intercellular melanosome transfer through palmitoylation. 148 matched cddid_all.tbl CDD pfam15813 pfam15813 464889 DUF4708 Domain of unknown function (DUF4708). This family of proteins is found in eukaryotes. 274 matched cddid_all.tbl CDD pfam15814 pfam15814 406293 FAM199X Protein family FAM199X. This family of proteins is found in eukaryotes. The function of FAM199X is not known. 320 matched cddid_all.tbl CDD pfam15815 pfam15815 464890 MKRN1_C E3 ubiquitin-protein ligase makorin, C-terminal. MKRN1_C is the very C-terminus of E3 ubiquitin-protein ligase makorin-1, or MKRN1, a family of eukaryotic putative ribonucleoproteins with a distinctive array of zinc-finger motifs. MKRN1 plays an important role in modulating the homeostasis of telomere-length through a dynamic balance involving the stability of the protein hTERT. MKRN1 has been shown to be a a transcriptional co-regulator and an E3 ligase. It functions simultaneously as a differentially negative regulator of p53 and p21, preferentially leading cells to p53-dependent apoptosis by suppressing p21. The exact function of the C-terminal region has not been determined. 87 matched cddid_all.tbl CDD pfam15816 pfam15816 464891 TMEM82 Transmembrane protein 82. TMEM82 is a family of proteins found in eukaryotes. The function is not known. 304 matched cddid_all.tbl CDD pfam15817 pfam15817 464892 TMEM40 Transmembrane protein 40 family. TMEM40 is a family of eukaryotic membrane proteins. 120 matched cddid_all.tbl CDD pfam15818 pfam15818 464893 CCDC73 Coiled-coil domain-containing protein 73 family. CCDC73 is a family of eukaryotic coiled-coil containing proteins. The function is not known. The alternative name is sarcoma antigen NY-SAR-79. 1048 matched cddid_all.tbl CDD pfam15819 pfam15819 406297 Fibin Fin bud initiation factor homolog. Fibin is a family of eukaryotic proteins expressed in the lateral plate mesoderm of presumptive pectoral fin bud regions. It acts as a signal molecule for the expression of Tbx5, a gene involved in the specification of fore-limb identity. Fibin is found to be expressed in cerebellum, skeletal muscle and many other embryonic as well as adult mouse tissues, suggesting roles in both embryogenesis and in adult life. Although Fibin is routed through the endoplasmic reticulum (ER) no significant evidence for secretion is found. Fibin is post-translationally modified and forms dimers when expressed heterologously and its expression is regulated by a number of cellular signalling pathways. 189 matched cddid_all.tbl CDD pfam15820 pfam15820 292448 ECSCR Endothelial cell-specific chemotaxis regulator. ECSCR, endothelial cell-specific chemotaxis regulator, is a family of proteins found in eukaryotes. It is also known as ARIA for apoptosis regulator through modulating IAP expression. It is a cell surface protein that regulates endothelial chemotaxis and tube formation, and interacts with filamin A. Filamin A anchors transmembrane proteins to the actin cytoskeleton becoming a scaffold for various signalling proteins. ECSCR is also known to interact with and regulate the function of several endothelial transmembrane molecules. It has been shown to play a role in angiogenesis, a complex process involving the migration, proliferation, and lumen formation of blood vessels by endothelial cells. ECSCR appears also to regulate endothelial apoptosis, probably through modulating proteasomal degradation of cIAP-1 and cIAP-2 in endothelial cells. 104 matched cddid_all.tbl CDD pfam15821 pfam15821 464894 DUF4709 Domain of unknown function (DUF4709). This domain family is found in eukaryotes, and is approximately 110 amino acids in length. There is a conserved QQL sequence motif. 110 matched cddid_all.tbl CDD pfam15822 pfam15822 318115 MISS MAPK-interacting and spindle-stabilising protein-like. MISS is a family of eukaryotic MAPK-interacting and spindle-stabilising protein-like proteins. MISS is rich in prolines and has four potential MAPK-phosphorylation sites, a MAPK-docking site, a PEST sequence (PEST motif) and a bipartite nuclear localization signal. The endogenous protein accumulates during mouse meiotic maturation and is found as discrete dots on the MII spindle. MISS is the first example of a physiological MAPK-substrate that is stabilized in MII that specifically regulates MII spindle integrity during the CSF arrest. 238 matched cddid_all.tbl CDD pfam15823 pfam15823 464895 UPF0524 UPF0524 of C3orf70. UPF0524 is a family of proteins found in eukaryotes. Proteins in this family are typically between 183 and 250 amino acids in length. The function is not known. 239 matched cddid_all.tbl CDD pfam15824 pfam15824 434963 SPATA9 Spermatogenesis-associated protein 9. SPATA9, spermatogenesis-associated protein 9, or testis development protein NYD-SP16, is a family of eukaryotic proteins associated with sperm production. It is highly expressed in human testis and contains one transmembrane domain. Its localization indicates it is likely to play an important role in testicular development and spermatogenesis and may be an important factor in male infertility. 253 matched cddid_all.tbl CDD pfam15825 pfam15825 464896 FAM25 FAM25 family. FAM25 is a family of proteins found in eukaryotes. Proteins in this family are typically between 54 and 95 amino acids in length. There is a conserved GEK sequence motif. The function is not known. 65 matched cddid_all.tbl CDD pfam15826 pfam15826 374148 PUMA Bcl-2-binding component 3, p53 upregulated modulator of apoptosis. PUMA (p53 upregulated modulator of apoptosis) is a family of eukaryotic proteins that are a target for activation by p53. The proteins contain BH3 domains and are induced in cells after p53 activation. They bind to Bcl-2, localize to the mitochondria to induce cytochrome c release, and activate the rapid induction of apoptosis. 189 matched cddid_all.tbl CDD pfam15827 pfam15827 406300 UPF0730 UPF0730 unknown protein family. UPF0730 is a family of proteins found in eukaryotes. Proteins in this family are typically between 51 and 156 amino acids in length. 46 matched cddid_all.tbl CDD pfam15828 pfam15828 464897 DUF4710 Domain of unknown function (DUF4710). This family of proteins is found in eukaryotes. Proteins in this family are typically between 60 and 150 amino acids in length. 77 matched cddid_all.tbl CDD pfam15829 pfam15829 464898 DUF4711 Domain of unknown function (DUF4711). This family of proteins is found in eukaryotes. Proteins in this family are typically between 130 and 288 amino acids in length. 217 matched cddid_all.tbl CDD pfam15830 pfam15830 464899 DUF4712 Domain of unknown function (DUF4712). This family of proteins is found in eukaryotes. Proteins in this family are typically between 133 and 267 amino acids in length. 250 matched cddid_all.tbl CDD pfam15831 pfam15831 464900 DUF4713 Domain of unknown function (DUF4713). This family of proteins is found in eukaryotes. Proteins in this family are typically between 68 and 91 amino acids in length. Members are single-pass membrane proteins. 56 matched cddid_all.tbl CDD pfam15832 pfam15832 406305 FAM27 FAM27 D and E protein family. FAM27 is a family of proteins found in eukaryotes. Proteins in this family are typically between 57 and 131 amino acids in length. 92 matched cddid_all.tbl CDD pfam15833 pfam15833 464901 DUF4714 Domain of unknown function (DUF4714). This family of proteins is found in eukaryotes. Proteins in this family are typically between 143 and 164 amino acids in length. 149 matched cddid_all.tbl CDD pfam15834 pfam15834 464902 THEG4 Testis highly expressed protein 4. THEG4, testis highly expressed protein 4, is a family of proteins found in eukaryotes. Proteins in this family are typically between 152 and 232 amino acids in length. 201 matched cddid_all.tbl CDD pfam15835 pfam15835 374157 DUF4715 Domain of unknown function (DUF4715). This family of proteins is found in eukaryotes. Proteins in this family are approximately 150 amino acids in length. The proteins are described as coiled-coil domain-containing protein ENSP00000299415-like. 139 matched cddid_all.tbl CDD pfam15836 pfam15836 406308 SSTK-IP SSTK-interacting protein, TSSK6-activating co-chaperone protein. SSTK-IP, SSTK-interacting protein or TSSK6-activating co-chaperone, is a family of proteins found in eukaryotes. SSTK-IP directly binds to HSP70, is found associated with HSP70 and HSP90 in cells, and facilitates HSP90-dependent enzymatic activation of SSTK. SSTK is a small serine/threonine kinase expressed post-meiotically and essential for male fertility along with two other serine threonine kinases. SSTK is one of the smallest protein kinases, consisting only of N- and C-lobes of a kinase catalytic domain, and forms stable associations with heat shock protein (HSP) 70 and 90. SSTK-IP, its interacting protein, thus represents the first germ cell-specific co-chaperone and protein kinase that requires the HSP90 machinery for catalytic activation. 125 matched cddid_all.tbl CDD pfam15837 pfam15837 406309 DUF4716 Domain of unknown function (DUF4716). This domain family is found in eukaryotes, and is approximately 60 amino acids in length. 60 matched cddid_all.tbl CDD pfam15838 pfam15838 464903 LLCFC1 LLLL and CFNLAS motif-containing protein 1. LLCFC1 (also known as SOF1) and its homologs can be found in eukaryotes. They have two conserved sequence motifs: LLLL and CFNLAS. LLCFC1 is a sperm protein required for sperm-oocyte fusion in mice. 72 matched cddid_all.tbl CDD pfam15839 pfam15839 464904 TEX29 Testis-expressed sequence 29 protein. TEX29, testis-expressed sequence 29 protein, is a family of proteins found in eukaryotes. Proteins in this family are typically between 39 and 150 amino acids in length. 76 matched cddid_all.tbl CDD pfam15840 pfam15840 464905 ARL17 ADP-ribosylation factor-like protein 17. ARL17 is a family of proteins found in primates. Proteins in this family are typically between 82 and 130 amino acids in length. Members of this family are also referred to as NBR2 or Neighbour of BRAC1 gene 2. 61 matched cddid_all.tbl CDD pfam15841 pfam15841 374162 TMEM239 Transmembrane protein 239 family. This family of proteins is found in primates. Proteins in this family are typically between 152 and 198 amino acids in length. 155 matched cddid_all.tbl CDD pfam15842 pfam15842 374163 DUF4718 Domain of unknown function (DUF4718). This family of proteins is found in eukaryotes. Proteins in this family are typically between 130 and 224 amino acids in length. 183 matched cddid_all.tbl CDD pfam15843 pfam15843 434972 DUF4719 Domain of unknown function (DUF4719). This family of proteins is found in eukaryotes. Proteins in this family are typically between 67 and 240 amino acids in length. 202 matched cddid_all.tbl CDD pfam15844 pfam15844 464906 TMCCDC2 Transmembrane and coiled-coil domain-containing protein 2. This family of proteins is found in primates. Proteins in this family are approximately 180 amino acids in length. 171 matched cddid_all.tbl CDD pfam15845 pfam15845 406313 NICE-1 Cysteine-rich C-terminal 1 family. NICE-1 is family of proteins found in primates. Proteins in this family are typically between 51 and 105 amino acids in length. 89 matched cddid_all.tbl CDD pfam15846 pfam15846 374167 DUF4720 Domain of unknown function (DUF4720). This family of proteins is found in vertebrates. Proteins in this family are typically between 101 and 117 amino acids in length. 94 matched cddid_all.tbl CDD pfam15847 pfam15847 406314 Loricrin Major keratinocyte cell envelope protein. Loricrin is a family of major keratinocyte cell envelope proteins found in primates. It acts as an important epidermal barrier, and is initially expressed in the granular layer comprising 70% of the total protein mass of the cornified layer. Expression of Loricrin is regulated by TNF-alpha via a c-Jun N-terminal kinase-dependent pathway. 312 matched cddid_all.tbl CDD pfam15848 pfam15848 464907 ODAPH Odontogenesis associated phosphoprotein. This family is found in mammals. It includes odontogenesis associated phosphoprotein (ODAPH or in human C4orf26) which is expressed in the enamel organ of the tooth and may promote nucleation of hydroxyapatite. 108 matched cddid_all.tbl CDD pfam15849 pfam15849 292477 DUF4722 Domain of unknown function (DUF4722). This family of proteins is found in vertebrates. Proteins in this family are typically between 86 and 203 amino acids in length. 167 matched cddid_all.tbl CDD pfam15851 pfam15851 434975 DUF4723 Domain of unknown function (DUF4723). This family of proteins is found in mammals. There are a number of conserved cysteines but it is unlikely to be a zinc-finger family. 82 matched cddid_all.tbl CDD pfam15852 pfam15852 406316 DUF4724 Domain of unknown function (DUF4724). This family of proteins is found in mammals. There is a conserved KVKPL sequence motif. 93 matched cddid_all.tbl CDD pfam15854 pfam15854 464908 GPR15L G-protein coupled receptor ligand 15. GPR15 is an orphan G protein-coupled receptor (GPCR) that is found in lymphocytes. It functions as a co-receptor of simian immunodeficiency virus and HIV-2 and plays a role in the trafficking of T cells to the lamina propria in the colon and to the skin. An activating ligand named GPR15L is shown to bind GPR15 and attract GPR15-expressing T cells including lymphocytes in colon-draining lymph nodes and thymic precursors of dermal epithelial T cell. This 9kDa CC-motif containing cationic polypeptide has been previously described as the 57 amino acid antimicrobial peptide AP-57, and as a Sushi Containing Domain-2 (SUSD2)-binding factor (CSBF), capable of inhibiting the growth of intestinal epithelial cancer cell lines. The chemokine is expressed by epithelial cells in gastrointestinal and genitourinary mucosae and in the skin. In humans GPR15L, is encoded by the gene C10ORF99 and has some features similar to the CC family of chemokines. However, it lacks significant homology to classic CC and CXC chemokines, yet shares many features with them, including a cationic domain predicted to comprise two disulfide bonds and a highly conserved GPCR-activating terminal peptide. Furthermore, the activating peptides of CC chemokines are typically located at the N-terminus, while that of GPR15L is C-terminal, a feature that it shares with some other GPCR ligands like chemerin and apela. 80 matched cddid_all.tbl CDD pfam15855 pfam15855 318139 DUF4726 Domain of unknown function (DUF4726). This family of proteins is found in vertebrates. Proteins in this family are typically between 40 and 110 amino acids in length. 101 matched cddid_all.tbl CDD pfam15856 pfam15856 434976 DUF4727 Domain of unknown function (DUF4727). This family of proteins is found in vertebrates. There are a number of conserved cysteines, but the domain is not a zinc-finger. 216 matched cddid_all.tbl CDD pfam15858 pfam15858 464909 LCE6A Late cornified envelope protein 6A family. LCE6A is a family of proteins is found in mammals. It was identified in a large-scale screening experiment as being involved in the barrier function of the epidermis. 81 matched cddid_all.tbl CDD pfam15859 pfam15859 434977 DEC1 Deleted in esophageal cancer 1 family. DEC1 is a family of proteins found in primates. The protein has been identified as being deleted in oesophageal cancers so is also referred to as candidate tumour suppressor CTS9. Proteins in this family are approximately 70 amino acids in length. 70 matched cddid_all.tbl CDD pfam15860 pfam15860 374176 DUF4728 Domain of unknown function (DUF4728). This family of arthropod proteins is functionally uncharacterized. 91 matched cddid_all.tbl CDD pfam15861 pfam15861 406321 partial_CstF Partial cleavage stimulation factor domain. Partial_CstF domain is a protein domain that occurs in proteins from apicomplexan parasites. Currently (as of 2012), little is known about the function of this domain. However, it is homologous to the amino-terminal part of the cleavage stimulation factor, which is thought to be involved with mRNA maturation in mammals. 62 matched cddid_all.tbl CDD pfam15862 pfam15862 464910 Coilin_N Coilin N-terminus. 138 matched cddid_all.tbl CDD pfam15863 pfam15863 406323 EELM2 Extended EGL-27 and MTA1 homology domain. EELM2, the extended EGL-27 and MTA1 homology domain is a protein domain that occurs in proteins from apicomplexan parasites. Part of the EELM2 domain is homologous to the ELM2 domain, but is 'extended' in that its boundaries (the region of conservation) are longer than in the ELM2 domain. Currently (as of 2012), little is known about the function of this domain. However, some proteins that contain an EELM2 domain also contain a PHD finger domain, which is thought to be involved in chromatin remodelling. This suggests an associated role for the EELM2 domain. 170 matched cddid_all.tbl CDD pfam15864 pfam15864 434979 PglL_A Protein glycosylation ligase. PglL_A is a pilin glycosylation ligase domain found in Gram negative bacteria. PglL protein O-oligosaccharyltransferases differ from the wider Wzy_C family, pfam04932, which contains both WaaL O-antigen ligases, in its substrate-specificity. PglL O-oligosaccharyltransferases (O-OTase) transfer oligosaccharide to serine or threonine in a protein. A further indication that the genes identified are PglL rather than WaaL homologs is that they are not located within lipopolysaccharide biosynthetic loci. The specific pilin glycosylation ligases are a subset of the more general bacterial protein o-oligosaccharyltransferases. 26 matched cddid_all.tbl CDD pfam15865 pfam15865 464911 Fanconi_A_N Fanconi anaemia group A protein N terminus. 355 matched cddid_all.tbl CDD pfam15866 pfam15866 434981 DUF4729 Domain of unknown function (DUF4729). This family of proteins is functionally uncharacterized. This family of proteins is found in insects. Proteins in this family are typically between 238 and 666 amino acids in length. 207 matched cddid_all.tbl CDD pfam15867 pfam15867 464912 Dynein_attach_N Dynein attachment factor N-terminus. This family represents the N-terminus of a dynein arm attachment factor which is required for dynein arm assembly and cilia motility. 68 matched cddid_all.tbl CDD pfam15868 pfam15868 464913 MBF2 Transcription activator MBF2. MBF2 activates transcription via its interaction with TFIIA. In Bombyx mori, it has been found to form a complex with MBF1 and the DNA-binding regulator FTZ-F1. 90 matched cddid_all.tbl CDD pfam15869 pfam15869 406329 TolB_like TolB-like 6-blade propeller-like. 295 matched cddid_all.tbl CDD pfam15870 pfam15870 464914 EloA-BP1 ElonginA binding-protein 1. This domain family is found in eukaryotes, and is typically between 144 and 167 amino acids in length. 163 matched cddid_all.tbl CDD pfam15871 pfam15871 464915 JMY Junction-mediating and -regulatory protein. JMY, Junction-mediating and -regulatory protein is also a WASP homolog-associated protein with actin, membranes and microtubules. This middle region is the coiled-coil region that putatively binds microtubules to the scaffold. This ability to interact with microtubules plays a role in membrane tubulation. 357 matched cddid_all.tbl CDD pfam15872 pfam15872 318153 SRTM1 Serine-rich and transmembrane domain-containing protein 1. This family of proteins is found in eukaryotes. Proteins in this family are approximately 100 amino acids in length. 103 matched cddid_all.tbl CDD pfam15873 pfam15873 292498 DUF4730 Domain of unknown function (DUF4730). This family of proteins is found in eukaryotes. Proteins in this family are approximately 60 amino acids in length. 55 matched cddid_all.tbl CDD pfam15874 pfam15874 464916 Il2rg Putative Interleukin 2 receptor, gamma chain. This family of proteins is found in eukaryotes. Proteins in this family are typically between 137 and 197 amino acids in length. 93 matched cddid_all.tbl CDD pfam15875 pfam15875 464917 DUF4731 Domain of unknown function (DUF4731). This family of proteins is found in eukaryotes. Proteins in this family are typically between 37 and 78 amino acids in length. 75 matched cddid_all.tbl CDD pfam15876 pfam15876 374189 DUF4732 Domain of unknown function (DUF4732). This family of proteins is found in eukaryotes. Proteins in this family are typically between 107 and 201 amino acids in length. 112 matched cddid_all.tbl CDD pfam15877 pfam15877 464918 TMEM232 Transmembrane protein family 232. This family of proteins is found in eukaryotes. The function is not known. 432 matched cddid_all.tbl CDD pfam15878 pfam15878 464919 DUF4733 Domain of unknown function (DUF4733). This family of proteins is found in eukaryotes. Proteins in this family are typically between 73 and 99 amino acids in length. 94 matched cddid_all.tbl CDD pfam15879 pfam15879 464920 MWFE NADH-ubiquinone oxidoreductase MWFE subunit. MWFE is a short subunit of NADH-ubiquinone oxidoreductase found in eukaryotes. It is necessary for the activity of NADH-ubiquinone oxidoreductase complex I in mitochondria. This subunit is essential for the assembly and function of the enzyme. MWFE is found to be phosphorylated, eg in rat heart mitochondria. The short family includes much of a signal peptide. 55 matched cddid_all.tbl CDD pfam15880 pfam15880 464921 NDUFV3 NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial. 35 matched cddid_all.tbl CDD pfam15881 pfam15881 434992 DUF4734 Domain of unknown function (DUF4734). This domain family is found in species of Drosophila, and is approximately 90 amino acids in length. The family is found in association with pfam07707. 91 matched cddid_all.tbl CDD pfam15882 pfam15882 464922 DUF4735 Domain of unknown function (DUF4735). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 288 and 410 amino acids in length. There are two completely conserved C residues that may be functionally important. In mammals this protein family is thyroid-specific. 283 matched cddid_all.tbl CDD pfam15883 pfam15883 434994 DUF4736 Domain of unknown function (DUF4736). This family of proteins is functionally uncharacterized. This family of proteins is found in insects. Proteins in this family are typically between 186 and 228 amino acids in length. 186 matched cddid_all.tbl CDD pfam15884 pfam15884 464923 QIL1 MICOS complex subunit MIC13, QIL1. Mic13 (also known as Qil1) is a component of the MICOS complex, a large protein complex of the mitochondrial inner membrane that plays crucial roles in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane. Mic13 is required for MICOS complex stability and cristae morphology. Family members such as C19orf70/QIL1 from human are orthologous to the yeast MIC12 pfam17050. 77 matched cddid_all.tbl CDD pfam15886 pfam15886 464924 CBM39 Carbohydrate binding domain (family 32). This domain is found at the N-terminus of beta-1,3-glucan-binding proteins involved in recognition of invading micro-organizms. It often co-occurs with pfam00722 (Glycosyl hydrolases family 16). It recognizes and binds to a triple-helical beta-1,3-glucan structure. 106 matched cddid_all.tbl CDD pfam15887 pfam15887 434997 Peptidase_Mx Putative zinc-binding metallo-peptidase. This family has a highly conserved HHExxH motif with a highly conserved ED pairing downstream. HExxH is indicative of a zinc-binding metallo-peptidase. 240 matched cddid_all.tbl CDD pfam15888 pfam15888 464925 FOG_N Folded gastrulation N-terminus. This is the N-terminal domain of the folded gastrulation protein. Folded gastrulation is required for morphogenic movements during gastrulation and nervous system development. It may act as a secreted signal and activate the G protein alpha subunit. This domain may be the G protein-coupled receptor ligand. 111 matched cddid_all.tbl CDD pfam15889 pfam15889 434999 DUF4738 Domain of unknown function (DUF4738). Family of uncharacterized proteins found in CFB group of bacteria, mostly from Bacteroides and Prevotella genera present in human gut and oral cavity, respectively. JCSG target SP13584B, the experimentally determined structure consists of two WD40-like beta sheet repeats forming a beta sandwich 134 matched cddid_all.tbl CDD pfam15890 pfam15890 435000 Peptidase_Mx1 Putative zinc-binding metallo-peptidase. This family is a putative zinc-binding metallo-peptidase. There are two highly conserved motifs, HHExxH and ED. HExxH with ED is indicative of zinc-binding metallo-peptidases. 238 matched cddid_all.tbl CDD pfam15891 pfam15891 464926 Nuc_deoxyri_tr2 Nucleoside 2-deoxyribosyltransferase like. 105 matched cddid_all.tbl CDD pfam15892 pfam15892 435002 BNR_4 BNR repeat-containing family member. BNR_4 is a family which carries the unique sequence motif SxDxGxTW which is so characteriztic of the repeats of the BNR family, pfam02012. It is unclear whether or not this unit is repeated throughout the sequences of this family, but if it is then the family is likely to be bacterial neuraminidase. 272 matched cddid_all.tbl CDD pfam15893 pfam15893 406347 DUF4739 Domain of unknown function (DUF4739). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 138 and 167 amino acids in length. 235 matched cddid_all.tbl CDD pfam15894 pfam15894 406348 SgrT Inhibitor of glucose uptake transporter SgrT. 53 matched cddid_all.tbl CDD pfam15895 pfam15895 374204 CAAX_1 CAAX box cerebral protein 1. CAAX_1 is a family of primate proteins. CAAX refers to the highly characteriztic C-terminal residues, a cysteine and two aliphatic residues followed by any residue, a C-terminal tetrapeptide recognition motif called the Ca1a2X box. This motif on substrates is recognized by prenyltransferases that then attach an isoprenoid lipid (a process termed prenylation), one of the many post-translational modifications that occur in cells. The function of the prenylated family is not known. 209 matched cddid_all.tbl CDD pfam15897 pfam15897 406349 DUF4741 Domain of unknown function (DUF4741). 169 matched cddid_all.tbl CDD pfam15898 pfam15898 464927 PRKG1_interact cGMP-dependent protein kinase interacting domain. This domain is found at the C-terminus of protein phosphatase 1 regulatory subunits 12A, 12B and 12C. In protein phosphatase 1 regulatory subunit 12A it has been found to bind to cGMP-dependent protein kinase 1 via a leucine zipper motif located at the C-terminus of this domain. 102 matched cddid_all.tbl CDD pfam15899 pfam15899 406351 BNR_6 BNR-Asp box repeat. This BNR repeat is found in proteins such as human sortilin. The model complements family BNR_5. 14 matched cddid_all.tbl CDD pfam15901 pfam15901 464928 Sortilin_C Sortilin, neurotensin receptor 3, C-terminal. Sortilin_C is the C-terminal cytoplasmic tail of sortilin, a Vps10p domain-containing family of proteins. Most sortilin is expressed within intracellular compartments, where it chaperones diverse ligands, including proBDNF and acid hydrolases. The sortilin cytoplasmic tail is homologous to mannose 6-phosphate receptor and is required for the intracellular trafficking of cargo proteins via interactions with distinct adaptor molecules. In addition to mediating lysosomal targeting of specific acid hydrolases, the sortilin cytoplasmic tail also directs trafficking of BDNF to the secretory pathway in neurons, where it can be released in response to depolarization to modulate cell survival and synaptic plasticity. 164 matched cddid_all.tbl CDD pfam15902 pfam15902 464929 Sortilin-Vps10 Sortilin, neurotensin receptor 3,. Sortilin, also known in mammals as neurotensin receptor-3, is the archetypical member of a Vps10-domain (Vps10-D) that binds neurotrophic factors and neuropeptides. This domain constitutes the entire luminal part of Sortilin and is activated in the trans-Golgi network by enzymatic propeptide cleavage. The structure of the domain has been determined as a ten-bladed propeller, with up to 9 BNR or beta-hairpin turns in it. The mature receptor binds various ligands, including its own propeptide (Sort-pro), neurotensin, the pro-forms of nerve growth factor-beta (NGF)6 and brain-derived neurotrophic factor (BDNF)7, lipoprotein lipase (LpL), apo lipoprotein AV14 and the receptor-associated protein (RAP)1. 444 matched cddid_all.tbl CDD pfam15903 pfam15903 464930 PL48 Filopodia upregulated, FAM65. PL48 is associated with cytotrophoblast and lineage-specific HL-60 cell differentiation. The N-terminal part of the family is found to induce the formation of filopodia. It is found in vertebrates. 297 matched cddid_all.tbl CDD pfam15904 pfam15904 464931 LIP1 LKB1 serine/threonine kinase interacting protein 1. LIP1 is a protein found in eukaryotes. It represents the N-terminus of a leucine-rich-repeat protein that is implicated in Peutz-Jeghers syndrome. LIP1 interacts with the TGF-beta-regulated transcription factor SMAD4 to form a LKB1-LIP1-SMAD4 ternary complex. Mutations in SMAD4 lead to juvenile polyposis, suggesting a mechanistic link between these two diseases. 90 matched cddid_all.tbl CDD pfam15905 pfam15905 464932 HMMR_N Hyaluronan mediated motility receptor N-terminal. HMMR_N is the N-terminal region of eukaryotic hyaluronan-mediated motility receptor proteins. The protein is functionally associated with BRCA1 and thus predicted to be a common, low-penetrance breast cancer candidate. 329 matched cddid_all.tbl CDD pfam15906 pfam15906 318178 zf-NOSIP Zinc-finger of nitric oxide synthase-interacting protein. 75 matched cddid_all.tbl CDD pfam15907 pfam15907 464933 Itfg2 Integrin-alpha FG-GAP repeat-containing protein 2. Members of this family are annotated as being integrin-alpha FG-GAP repeat-containing protein 2. 331 matched cddid_all.tbl CDD pfam15908 pfam15908 464934 HMMR_C Hyaluronan mediated motility receptor C-terminal. HMMR_C is the C-terminal region of eukaryotic hyaluronan-mediated motility receptor proteins. The protein is functionally associated with BRCA1 and thus predicted to be a common, low-penetrance breast cancer candidate. 157 matched cddid_all.tbl CDD pfam15909 pfam15909 464935 zf-C2H2_8 C2H2-type zinc ribbon. This family carries three zinc-fingers in tandem. 98 matched cddid_all.tbl CDD pfam15910 pfam15910 464936 V-set_2 ICOS V-set domain. This family contains divergent V-set ig domains found in the ICOS protein. 112 matched cddid_all.tbl CDD pfam15911 pfam15911 464937 WD40_3 WD domain, G-beta repeat. 57 matched cddid_all.tbl CDD pfam15912 pfam15912 464938 VIR_N Virilizer, N-terminal. VIR_N is the conserved N-terminus of the protein virilizer, necessary for male and female viability and required for the production of eggs capable of embryonic development. 265 matched cddid_all.tbl CDD pfam15913 pfam15913 464939 Furin-like_2 Furin-like repeat, cysteine-rich. The furin-like cysteine rich region has been found in a variety of proteins from eukaryotes that are involved in the mechanism of signal transduction by receptor tyrosine kinases, which involves receptor aggregation. 102 matched cddid_all.tbl CDD pfam15914 pfam15914 464940 FAM193_C FAM193 family C-terminal. This domain family is found in eukaryotes, and is approximately 60 amino acids in length. This C-terminal region of these proteins carries the most conserved residues. 57 matched cddid_all.tbl CDD pfam15915 pfam15915 435017 BAT GAF and HTH_10 associated domain. GAF-HTH_assoc domain is always found between GAF-2 and HTH_10 domains on bacterio-opsin activator proteins. The exact function is not known. 156 matched cddid_all.tbl CDD pfam15916 pfam15916 406365 DUF4743 Domain of unknown function (DUF4743). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and eukaryotes, and is approximately 150 amino acids in length. The family is found in association with pfam00293. 119 matched cddid_all.tbl CDD pfam15917 pfam15917 464941 PIEZO Piezo. This domain is found in proteins belonging to the piezo family. Piezo proteins are components of cation channels. This domain is found in association with pfam12166. 223 matched cddid_all.tbl CDD pfam15918 pfam15918 435019 DUF4744 Domain of unknown function (DUF4744). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 81 and 415 amino acids in length. 70 matched cddid_all.tbl CDD pfam15919 pfam15919 435020 HicB_lk_antitox HicB_like antitoxin of bacterial toxin-antitoxin system. This is a family of HicB-like antitoxins. 123 matched cddid_all.tbl CDD pfam15920 pfam15920 464942 WHAMM-JMY_N N-terminal of Junction-mediating and WASP homolog-associated. WHAMM-JMY_N is the very N-terminus of WHAMM and JMY proteins. The function of this conserved region is not known; there are two highly conserved tryptophan residues. 49 matched cddid_all.tbl CDD pfam15921 pfam15921 464943 CCDC158 Coiled-coil domain-containing protein 158. CCDC158 is a family of proteins found in eukaryotes. The function is not known. 1112 matched cddid_all.tbl CDD pfam15922 pfam15922 292544 YjeJ YjeJ-like. YjeJ is a family of bacterial proteins. The domains and proteins in this family vary in length from 283 to 284 amino acids. The function is not yet known. All proteins are Gammaproteobacteria. 283 matched cddid_all.tbl CDD pfam15923 pfam15923 374226 DUF4745 Domain of unknown function (DUF4745). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is approximately 180 amino acids in length. 133 matched cddid_all.tbl CDD pfam15924 pfam15924 464944 ALG11_N ALG11 mannosyltransferase N-terminus. 209 matched cddid_all.tbl CDD pfam15925 pfam15925 464945 SOSSC SOSS complex subunit C. SOSS complex subunit C is a component of the SOSS complex, a single-stranded DNA binding complex involved in genomic stability, double-stranded break repair and ataxia telangiectasia-mutated-dependent signaling pathways. 101 matched cddid_all.tbl CDD pfam15926 pfam15926 464946 RNF220 E3 ubiquitin-protein ligase RNF220. This family represents the central region of the E3 ubiquitin-protein ligase RNF220. 248 matched cddid_all.tbl CDD pfam15927 pfam15927 464947 Casc1_N Cancer susceptibility candidate 1 N-terminus. This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is approximately 200 amino acids in length. The family is found in association with pfam12366. There are two completely conserved residues (N and W) that may be functionally important. 201 matched cddid_all.tbl CDD pfam15928 pfam15928 435025 DUF4746 Domain of unknown function (DUF4746). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes, and is typically between 247 and 324 amino acids in length. The family is found in association with pfam00085. 292 matched cddid_all.tbl CDD pfam15929 pfam15929 374232 Myofilin Myofilin. Myofilin is an insect muscle protein found in thick muscle filaments. 146 matched cddid_all.tbl CDD pfam15930 pfam15930 318201 YdiH Domain of unknown function. YdiH is a family of proteins found in bacteria. Proteins in this family are typically between 62 and 80 amino acids in length. The function is not known. 62 matched cddid_all.tbl CDD pfam15931 pfam15931 435026 DUF4747 Domain of unknown function (DUF4747). This family of proteins is found in bacteria. Proteins in this family are typically between 263 and 305 amino acids in length. 257 matched cddid_all.tbl CDD pfam15932 pfam15932 435027 DUF4748 Domain of unknown function (DUF4748). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 114 and 139 amino acids in length. 52 matched cddid_all.tbl CDD pfam15933 pfam15933 406375 RnlB_antitoxin Antitoxin to bacterial toxin RNase LS or RnlA. RnlB_antitoxin, formerly known as yfjO, has been found to be the antidote protein to RNase LS or RnlA in E. coli. Bacterial toxin-antitoxin systems consist of a stable toxin and an unstable antitoxin. In this case, a novel type II system, RnlA is the stable toxin that causes inhibition of cell growth and rapidly degrades T4 late mRNAs to prevent their expression, and this is neutralized by the activity of the unstable antitoxin RnlB. 94 matched cddid_all.tbl CDD pfam15934 pfam15934 318204 Yuri_gagarin Yuri gagarin. The yuri gagarin protein found in Drosophila, it plays roles in spermatogenesis. 234 matched cddid_all.tbl CDD pfam15935 pfam15935 406376 RnlA_toxin RNase LS, bacterial toxin. RnlA_toxin is an RNase LS and a putative toxin of a bacterial toxin-antitoxin pair. Toxin-antitoxin systems consist of a stable toxin and an unstable antitoxin. In this case, a novel type II system, RnlA is the stable toxin that causes inhibition of cell growth and rapidly degrades T4 late mRNAs to prevent their expression, and this is neutralized by the activity of the unstable antitoxin RnlB. 87 matched cddid_all.tbl CDD pfam15936 pfam15936 464948 DUF4749 Domain of unknown function (DUF4749). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 121 and 170 amino acids in length. It is usually found in association with pfam00595 (PDZ) and pfam00412 (LIM), and often contains the conserved Zasp-like motif (IPR006643). 98 matched cddid_all.tbl CDD pfam15937 pfam15937 435029 PrlF_antitoxin prlF antitoxin for toxin YhaV_toxin. PrlF_antitoxin is a family of bacterial antitoxins that neutralizes the toxin YhaV. PrlF is labile and forms a homodimer that then binds to the YhaV toxin thereby neutralising its ribonuclease activity. Alone, it can also act as a transcription factor. The YhaV/PrlF complex binds the prlF-yhaV operon, probably regulating its expression negatively. Over-expression of PrlF leads to increased doubling time. 98 matched cddid_all.tbl CDD pfam15938 pfam15938 464949 DUF4750 Domain of unknown function (DUF4750). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 76 and 92 amino acids in length. There are two completely conserved W residues that may be functionally important. 52 matched cddid_all.tbl CDD pfam15939 pfam15939 292561 YmcE_antitoxin Putative antitoxin of bacterial toxin-antitoxin system. YmcE_antitoxin is the putative antitoxin for the supposed bacterial toxin GnsA, UniProtKB:P0AC92, family pfam08178. 76 matched cddid_all.tbl CDD pfam15940 pfam15940 435031 YjcB Family of unknown function. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. 88 matched cddid_all.tbl CDD pfam15941 pfam15941 435032 FidL_like FidL-like putative membrane protein. FidL-like is a family of bacterial proteins that are purported to be membrane proteins. 90 matched cddid_all.tbl CDD pfam15942 pfam15942 374242 DUF4751 Domain of unknown function (DUF4751). This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. 121 matched cddid_all.tbl CDD pfam15943 pfam15943 435033 YdaS_antitoxin Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT. YdaS_antitoxin is a family of putative bacterial antitoxins, neutralising the toxin YdaT, family pfam06254. 65 matched cddid_all.tbl CDD pfam15944 pfam15944 339554 DUF4752 Domain of unknown function (DUF4752). This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 90 and 105 amino acids in length. There is a conserved GLA sequence motif. 84 matched cddid_all.tbl CDD pfam15946 pfam15946 374244 DUF4754 Domain of unknown function (DUF4754). This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 80 matched cddid_all.tbl CDD pfam15947 pfam15947 318214 DUF4755 Domain of unknown function (DUF4755). This family of proteins is found in bacteria. Proteins in this family are approximately 160 amino acids in length. 129 matched cddid_all.tbl CDD pfam15948 pfam15948 406381 DUF4756 Domain of unknown function (DUF4756). This family of proteins is found in bacteria. Proteins in this family are approximately 160 amino acids in length. 158 matched cddid_all.tbl CDD pfam15949 pfam15949 464950 DUF4757 Domain of unknown function (DUF4757). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 145 and 166 amino acids in length. The family is found in association with pfam00412. There are two completely conserved residues (W and L) that may be functionally important. 170 matched cddid_all.tbl CDD pfam15950 pfam15950 464951 DUF4758 Putative sperm flagellar membrane protein. 129 matched cddid_all.tbl CDD pfam15951 pfam15951 464952 MITF_TFEB_C_3_N MITF/TFEB/TFEC/TFE3 N-terminus. This domain is found at the N-terminus of several transcription factors including microphthalmia-associated transcription factor, transcription factor EB, transcription factor EC and transcription factor E3. 151 matched cddid_all.tbl CDD pfam15952 pfam15952 464953 ESM4 Enhancer of split M4 family. This family of proteins includes enhancer of split M4, enhancer of split M2 and enhancer of split MAlpha. These proteins are part of the Notch signaling pathway. 172 matched cddid_all.tbl CDD pfam15953 pfam15953 435036 PDU_like Putative propanediol utilization. This family of proteins is found in bacteria. Proteins in this family are approximately 160 amino acids in length. 153 matched cddid_all.tbl CDD pfam15955 pfam15955 464954 Cuticle_4 Cuticle protein. 73 matched cddid_all.tbl CDD pfam15956 pfam15956 374251 DUF4760 Domain of unknown function (DUF4760). This family of proteins is found in bacteria, archaea and viruses. Proteins in this family are typically between 147 and 190 amino acids in length. There is a single completely conserved residue R that may be functionally important. 143 matched cddid_all.tbl CDD pfam15957 pfam15957 374252 Comm Commissureless. Commissureless regulates Roundabout (Robo) levels and as a result regulates controls axon guidance across the embryo midline. 110 matched cddid_all.tbl CDD pfam15958 pfam15958 318223 DUF4761 Domain of unknown function (DUF4761). This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. 105 matched cddid_all.tbl CDD pfam15959 pfam15959 406385 DUF4762 Domain of unknown function (DUF4762). This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved TTC sequence motif. 61 matched cddid_all.tbl CDD pfam15960 pfam15960 406386 DUF4763 Domain of unknown function (DUF4763). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 237 and 332 amino acids in length. There are two completely conserved residues (C and R) that may be functionally important. 236 matched cddid_all.tbl CDD pfam15961 pfam15961 464955 DUF4764 Domain of unknown function (DUF4764). 799 matched cddid_all.tbl CDD pfam15962 pfam15962 374256 DUF4765 Domain of unknown function (DUF4765). This domain family is found in bacteria, and is approximately 90 amino acids in length. 1128 matched cddid_all.tbl CDD pfam15963 pfam15963 464956 Myb_DNA-bind_7 Myb DNA-binding like. 85 matched cddid_all.tbl CDD pfam15964 pfam15964 435040 CCCAP Centrosomal colon cancer autoantigen protein family. CCCAP is a family of proteins found in eukaryotes. CCCAP is also known as SDCCAG8, serologically defined colon cancer antigen 8. It is associated with the centrosome. 703 matched cddid_all.tbl CDD pfam15965 pfam15965 464957 zf-TRAF_2 TRAF-like zinc-finger. 92 matched cddid_all.tbl CDD pfam15966 pfam15966 464958 F-box_4 F-box. 116 matched cddid_all.tbl CDD pfam15967 pfam15967 435043 Nucleoporin_FG2 Nucleoporin FG repeated region. Nucleoporin_FG2, or nucleoporin p58/p45, is a family of chordate nucleoporins. The proteins carry many repeats of the FG sequence motif. 586 matched cddid_all.tbl CDD pfam15968 pfam15968 292590 RexB Membrane-anchored ion channel, Abi component. RexB is a family of anti-lambda phage inner-membrane ion-channels with four transmembrane domains. On infection by phage, a phage protein-DNA complex is produced as a replication or recombination intermediate which activates RexA. RexA is an intracellular sensor that activates the membrane-anchored RexB. At least two RexA proteins are needed to activate one RexB protein. Activation opens the ion-channel leading to a drop in membrane potential, the outcome of which is the death of the host cell but also the cessation or abortion of the phage infection. RexA-RexB is one of the most well characterized bacterial abortive infection systems, or Abis. 139 matched cddid_all.tbl CDD pfam15969 pfam15969 374261 RexA Intracellular sensor of Lambda phage, Abi component. RexA is a family of bacterial anti-phage proteins. It forms one partner in the two-component abortive infection system, Abi, of E. coli in partnership with RexB, a membrane-anchored ion- channel. Two RexA are needed to activate one RexB, and activation causes opening of the channel, the efflux of cations, a drop in cellular levels of ATP and subsequent death of the host cell and abortion of the phage infecting process which requires ATP. 235 matched cddid_all.tbl CDD pfam15970 pfam15970 435044 HicB-like_2 HicB_like antitoxin of bacterial toxin-antitoxin system. This is a family of HicB-like antitoxins. 81 matched cddid_all.tbl CDD pfam15971 pfam15971 374262 Mannosyl_trans4 DolP-mannose mannosyltransferase. This family catalyzes the transfer of mannose from DolP-mannose to the N-linked tetrasaccharide bound to the S-layer glycoprotein to form a pentasaccharide. 163 matched cddid_all.tbl CDD pfam15972 pfam15972 374263 Unpaired Unpaired protein. Unpaired protein activates the JAK pathway. 177 matched cddid_all.tbl CDD pfam15973 pfam15973 435045 DUF4766 Domain of unknown function (DUF4766). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 106 and 128 amino acids in length. There is a conserved KVI sequence motif. 114 matched cddid_all.tbl CDD pfam15974 pfam15974 435046 Cadherin_tail Cadherin C-terminal cytoplasmic tail, catenin-binding region. Cadherin_tail is the cytoplasmic domain at the C-terminus of cadherin proteins. This domain binds p120 catenin, an action critical for the surface stability of cadherin-catenin cell-cell adhesion complexes. 134 matched cddid_all.tbl CDD pfam15975 pfam15975 435047 Flot Flotillin. Flotillin is a family of lipid-membrane-associated proteins found in bacteria, archaea and eukaryotes. The family is found in association with pfam01145, another integral membrane-associated domain. Flotillins in vertebrates are associated with sphingolipids and cholesterol-enriched membrane microdomains known as lipid-rafts. These rafts along with other membrane components are important in cell-signalling. Flotillins in other organizms have roles in viral pathogenesis, endocytosis, and membrane shaping. 121 matched cddid_all.tbl CDD pfam15976 pfam15976 435048 CooC_C CS1-pili formation C-terminal. CooC_C is a highly conserved C-terminal domain on fimbrial outer membrane usher proteins like TcfC. The protein is required for CS1 pilus formation. 93 matched cddid_all.tbl CDD pfam15977 pfam15977 435049 HTH_46 Winged helix-turn-helix DNA binding. 68 matched cddid_all.tbl CDD pfam15978 pfam15978 379756 TnsD Tn7-like transposition protein D. TnsD is a family of putative Tn7-like transposition proteins type D. 360 matched cddid_all.tbl CDD pfam15979 pfam15979 435050 Glyco_hydro_115 Glycosyl hydrolase family 115. Glyco_hydro_115 is a family of glycoside hydrolases likely to have the activity of xylan a-1,2-glucuronidase, EC:3.2.1.131, or a-(4-O-methyl)-glucuronidase EC:3.2.1.-. 335 matched cddid_all.tbl CDD pfam15980 pfam15980 435051 ComGF Putative Competence protein ComGF. ComGF is a family of putative bacterial competence proteins. 99 matched cddid_all.tbl CDD pfam15981 pfam15981 292603 EAV_GP5 Envelope glycoprotein GP 5 of equine arteritis virus. EAV_GP5 is a domain family found in equine arteritis virus envelope. It is approximately 80 amino acids in length and is found in association with pfam00951. 80 matched cddid_all.tbl CDD pfam15982 pfam15982 374269 TMEM135_C_rich N-terminal cysteine-rich region of Transmembrane protein 135. TMEM135_C_rich is a family of putative peroxisomal membrane proteins found in eukaryotes. This is the highly conserved N-terminal region that has several highly conserved cysteine residues. The domain is associated with family Tim17, pfam02466. 134 matched cddid_all.tbl CDD pfam15983 pfam15983 435052 DUF4767 Domain of unknown function (DUF4767). This domain family is found in bacteria, and is approximately 140 amino acids in length. There is a single completely conserved residue Q that may be functionally important. 137 matched cddid_all.tbl CDD pfam15984 pfam15984 435053 Collagen_mid Bacterial collagen, middle region. Collagen_mid is the conserved central region of bacterial collagen triple helix repeat proteins. 198 matched cddid_all.tbl CDD pfam15985 pfam15985 464959 KH_6 KH domain. KH motifs bind RNA in vitro. Auto-antibodies to Nova, a KH domain protein, cause para-neoplastic opsoclonus ataxia. 47 matched cddid_all.tbl CDD pfam15989 pfam15989 435055 DUF4768 Domain of unknown function (DUF4768). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 116 and 180 amino acids in length. There is a conserved FFFGQY sequence motif. 87 matched cddid_all.tbl CDD pfam15990 pfam15990 464960 UPF0767 UPF0767 family. This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between and 92 amino acids in length. There are two conserved sequence motifs: IGYN and SPSL. 83 matched cddid_all.tbl CDD pfam15991 pfam15991 464961 G_path_suppress G-protein pathway suppressor. This family of proteins inhibits G-protein- and mitogen-activated protein kinase-mediated signal transduction. 272 matched cddid_all.tbl CDD pfam15992 pfam15992 406403 DUF4769 Domain of unknown function (DUF4769). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 291 and 501 amino acids in length. 256 matched cddid_all.tbl CDD pfam15993 pfam15993 406404 Fuseless Fuseless. This family includes Drosophila fuseless protein and contains four WXGXW motifs. Fuseless is a transmembrane protein which regulates pre-synaptic calcium channels. 299 matched cddid_all.tbl CDD pfam15994 pfam15994 435057 DUF4770 Domain of unknown function (DUF4770). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 169 and 182 amino acids in length. There is a single completely conserved residue L that may be functionally important. 180 matched cddid_all.tbl CDD pfam15995 pfam15995 464962 DUF4771 Domain of unknown function (DUF4771). This domain family is found in eukaryotes, and is approximately 160 amino acids in length. There is a conserved RYGK sequence motif. 160 matched cddid_all.tbl CDD pfam15996 pfam15996 464963 PNISR Arginine/serine-rich protein PNISR. 179 matched cddid_all.tbl CDD pfam15997 pfam15997 464964 DUF4772 Domain of unknown function (DUF4772). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 107 and 124 amino acids in length. There is a single completely conserved residue V that may be functionally important. 112 matched cddid_all.tbl CDD pfam15998 pfam15998 464965 DUF4773 Domain of unknown function (DUF4773). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is approximately 120 amino acids in length. 117 matched cddid_all.tbl CDD pfam15999 pfam15999 406409 DUF4774 Domain of unknown function (DUF4774). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, eukaryotes and viruses, and is approximately 50 amino acids in length. 57 matched cddid_all.tbl CDD pfam16000 pfam16000 464966 CARMIL_C CARMIL C-terminus. This domain is found near to the C-terminus of leucine-rich repeat-containing proteins in the CARMIL family. In leucine-rich repeat-containing protein 16A (LRRC16A) it includes the region responsible for interaction with F-actin-capping protein subunit alpha-2 (CAPZA2). 299 matched cddid_all.tbl CDD pfam16001 pfam16001 406411 DUF4775 Domain of unknown function (DUF4775). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 308 and 484 amino acids in length. 456 matched cddid_all.tbl CDD pfam16002 pfam16002 464967 Headcase Headcase protein. This domain is found in Drosophila Headcase protein and the human Headcase protein homolog. In humans, it may have a role in some cancers. 197 matched cddid_all.tbl CDD pfam16003 pfam16003 406413 DUF4776 Domain of unknown function (DUF4776). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 444 and 485 amino acids in length. There is a conserved TLR sequence motif. 502 matched cddid_all.tbl CDD pfam16004 pfam16004 464968 EFTUD2 116 kDa U5 small nuclear ribonucleoprotein component N-terminus. 76 matched cddid_all.tbl CDD pfam16005 pfam16005 464969 MOEP19 KH-like RNA-binding domain. MOEP19 is a family of mammalian KH-like RNA-binding motifs. The family is expressed during early embryogenesis. It appears to effect an early form of molecular asymmetry within the murine oocyte cytoplasm. The family marks a defined cortical cytoplasmic domain in oocytes and provides evidence for mammalian oocyte polarity and a form of pre-patterning that persists in zygotes and early embryos through the morula stage. 85 matched cddid_all.tbl CDD pfam16006 pfam16006 464970 NUSAP Nucleolar and spindle-associated protein. This family of microtubule-associated proteins has a role in spindle microtubule organization 293 matched cddid_all.tbl CDD pfam16007 pfam16007 374290 DUF4777 Domain of unknown function (DUF4777). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is approximately 70 amino acids in length. 66 matched cddid_all.tbl CDD pfam16008 pfam16008 435064 DUF4778 Domain of unknown function (DUF4778). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 321 and 791 amino acids in length. There is a single completely conserved residue P that may be functionally important. 284 matched cddid_all.tbl CDD pfam16009 pfam16009 464971 DUF4779 Domain of unknown function (DUF4779). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 234 and 351 amino acids in length. 160 matched cddid_all.tbl CDD pfam16010 pfam16010 435066 CDH-cyt Cytochrome domain of cellobiose dehydrogenase. CDH-cyt is the cytochrome domain, at the N-terminus, of cellobiose dehydrogenase. CDH-cyt folds as a beta sandwich with the topology of the antibody Fab V(H) domain and binds iron. The haem iron is ligated by Met83 and His181 in UniProtKB:Q01738. 175 matched cddid_all.tbl CDD pfam16011 pfam16011 435067 CBM9_2 Carbohydrate-binding family 9. CBM9_2 is a family of putative endoxylanase-like proteins that belong to the Carbohydrate-binding family 9. 199 matched cddid_all.tbl CDD pfam16012 pfam16012 464972 DUF4780 Domain of unknown function (DUF4780). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 132 and 144 amino acids in length. There is a single completely conserved residue W that may be functionally important. 177 matched cddid_all.tbl CDD pfam16013 pfam16013 435069 DUF4781 Domain of unknown function (DUF4781). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and eukaryotes, and is typically between 288 and 306 amino acids in length. 308 matched cddid_all.tbl CDD pfam16014 pfam16014 464973 SAP130_C Histone deacetylase complex subunit SAP130 C-terminus. 371 matched cddid_all.tbl CDD pfam16015 pfam16015 464974 Promethin Promethin. 106 matched cddid_all.tbl CDD pfam16016 pfam16016 464975 VASt VAD1 Analog of StAR-related lipid transfer domain. The VASt (VAD1 Analog of StAR-related lipid transfer) domain is conserved across eukaryotes and is structurally related to Bet v1-like domains, including START lipid-binding domains. The 190-amino acid VASt domain is predominantly associated with lipid binding domains such as GRAM pfam02893, C2 and PH domains. The VASt domain is likely to have a function in binding large hydrophobic ligands and may be specific for sterol. The predicted structure of the VASt domain is a two-layer sandwich alpha beta fold, also called 'helix grip fold', containing three alpha helices (alpha1 to 3), six beta-sheets (beta1 to 6) and two loops (omega1 and 2) numbered from N to C terminus. Some proteins known to contain a VASt domain are : Plant vascular associated death1 (VAD1), a regulator of programmed cell death (PCD) harboring a GRAM putative lipid-binding domain. Yeast SNF1 Interacting Protein 3 (SIP3), may be involved in sterol transfer between intracellular membranes. Yeast Suicide Protein 1 (YSP1), a mitochondrial protein specifically required for the mitochondrial thread-grain transition, de-energization, and the cell death. May be involved in sterol transfer between intracellular membranes. Yeast Suicide Protein 2 (YSP2), a mitochondrial membrane protein involved in mitochondrial fragmentation and may be involved in sterol transfer between intracellular membranes.It is also found in human GramD1a-c. 147 matched cddid_all.tbl CDD pfam16017 pfam16017 464976 BTB_3 BTB/POZ domain. 106 matched cddid_all.tbl CDD pfam16018 pfam16018 435074 Anillin_N Anillin N-terminus. This domain is found towards the N-terminus of anillin. In mammalian anillin this domain is repeated. This domain overlaps with the region responsible for nuclear localization of anillin. 86 matched cddid_all.tbl CDD pfam16019 pfam16019 464977 CSRNP_N Cysteine/serine-rich nuclear protein N-terminus. This presumed domain is found at the N-terminus of cysteine/serine-rich nuclear proteins. These proteins act as transcriptional activators. 218 matched cddid_all.tbl CDD pfam16020 pfam16020 464978 Deltameth_res Deltamethrin resistance. This presumed domain is found in the deltamethrin-resistance protein prag01 from Culex pipiens pallens. 52 matched cddid_all.tbl CDD pfam16021 pfam16021 464979 PDCD7 Programmed cell death protein 7. 305 matched cddid_all.tbl CDD pfam16022 pfam16022 435078 DUF4783 Domain of unknown function (DUF4783). This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. There is a single completely conserved residue F that may be functionally important. Recent structures show this domain has an NTF2 fold. 102 matched cddid_all.tbl CDD pfam16023 pfam16023 464980 DUF4784 DUF4784 WD40-like domain. This is a family of uncharacterized proteins from Bacteroidetes. This entry adopts a 6-bladed beta propeller structure. 316 matched cddid_all.tbl CDD pfam16024 pfam16024 435080 DUF4785 Domain of unknown function (DUF4785). This family of proteins is found in bacteria. Proteins in this family are typically between 392 and 442 amino acids in length. 372 matched cddid_all.tbl CDD pfam16025 pfam16025 464981 CaM_bind Calcium-dependent calmodulin binding. This domain is found at the N-terminus of centriolar coiled-coil protein of 110 kDa (CCP110), where it binds calmodulin. Binding of calmodulin to this domain is calcium dependent. 78 matched cddid_all.tbl CDD pfam16026 pfam16026 464982 MIEAP Mitochondria-eating protein. This domain is found at the C-terminus of mitochondria-eating proteins. This family of proteins regulate mitochondrial quality. They have a role in the degradation of damaged mitochondrial proteins and in the degradation of damaged mitochondria. 198 matched cddid_all.tbl CDD pfam16027 pfam16027 406435 DUF4786 Domain of unknown function (DUF4786). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 209 and 353 amino acids in length. 162 matched cddid_all.tbl CDD pfam16028 pfam16028 464983 SLC3A2_N Solute carrier family 3 member 2 N-terminus. This domain is found at the N-terminus of solute carrier family 3 member 2 proteins (4F2 cell-surface antigen heavy chain). 77 matched cddid_all.tbl CDD pfam16029 pfam16029 464984 DUF4787 Domain of unknown function (DUF4787). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is approximately 70 amino acids in length. 62 matched cddid_all.tbl CDD pfam16030 pfam16030 464985 GD_N Serine protease gd N-terminus. This domain is found at the N-terminus of the serine protease gd (gastrulation defective) in insects. 108 matched cddid_all.tbl CDD pfam16031 pfam16031 435086 TonB_N TonB polyproline region. TonB from Escherichia coli and its homologs are critical for the uptake of siderophores through the outer membrane of Gram-negative bacteria using chemiosmotic energy. The proline-rich segment of TonB exists in a PPII-like conformation. The result implies that the proline-rich segment of TonB possesses a length of more than 15 nm, sufficient to span the periplasm of Gram-negative bacteria. 136 matched cddid_all.tbl CDD pfam16032 pfam16032 406440 DUF4788 Domain of unknown function (DUF4788). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is approximately 230 amino acids in length. There is a single completely conserved residue D that may be functionally important. 229 matched cddid_all.tbl CDD pfam16033 pfam16033 435087 DUF4789 Domain of unknown function (DUF4789). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 87 and 100 amino acids in length. There is a conserved GPC sequence motif. There are two completely conserved C residues that may be functionally important. 95 matched cddid_all.tbl CDD pfam16034 pfam16034 464986 JAKMIP_CC3 JAKMIP CC3 domain. This domain is found at the C-terminus of proteins belonging to the JAKMIP family (Janus kinase and microtubule-interacting proteins) and is predicted to be a coiled coil. It interacts with the Janus family kinases Tyk2 and Jak1. 199 matched cddid_all.tbl CDD pfam16035 pfam16035 435089 Chalcone_2 Chalcone isomerase like. 203 matched cddid_all.tbl CDD pfam16036 pfam16036 435090 Chalcone_3 Chalcone isomerase-like. Chalcone_3 is a family of largely bacterial members. 165 matched cddid_all.tbl CDD pfam16037 pfam16037 406445 DUF4790 Domain of unknown function (DUF4790). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 134 and 191 amino acids in length. There is a single completely conserved residue C that may be functionally important. 93 matched cddid_all.tbl CDD pfam16038 pfam16038 464987 TMIE TMIE protein. This family of proteins includes the mammalian transmembrane inner ear expressed protein. It's function is unknown. 85 matched cddid_all.tbl CDD pfam16039 pfam16039 406447 DUF4791 Domain of unknown function (DUF4791). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 189 and 203 amino acids in length. There are two conserved sequence motifs: PLPL and LGN. There is a single completely conserved residue N that may be functionally important. 162 matched cddid_all.tbl CDD pfam16040 pfam16040 464988 DUF4792 Domain of unknown function (DUF4792). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is approximately 70 amino acids in length. 71 matched cddid_all.tbl CDD pfam16041 pfam16041 464989 DUF4793 Domain of unknown function (DUF4793). This domain family is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. There are two completely conserved C residues that may be functionally important. 108 matched cddid_all.tbl CDD pfam16042 pfam16042 435094 DUF4794 Domain of unknown function (DUF4794). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 74 and 92 amino acids in length. 76 matched cddid_all.tbl CDD pfam16043 pfam16043 464990 DUF4795 Domain of unknown function (DUF4795). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 285 and 978 amino acids in length. 181 matched cddid_all.tbl CDD pfam16044 pfam16044 464991 DUF4796 Domain of unknown function (DUF4796). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 194 and 289 amino acids in length. There is a single completely conserved residue C that may be functionally important. 189 matched cddid_all.tbl CDD pfam16045 pfam16045 464992 LisH_2 LisH. 28 matched cddid_all.tbl CDD pfam16046 pfam16046 464993 FAM76 FAM76 protein. This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 233 and 341 amino acids in length. 303 matched cddid_all.tbl CDD pfam16047 pfam16047 292666 Antimicrobial22 Frog antimicrobial peptide. This family includes the antimicrobial peptides Grahamin and Nigrocin which are secreted from frog skin. 21 matched cddid_all.tbl CDD pfam16048 pfam16048 292667 Antimicrobial23 Frog antimicrobial peptide. This family includes antimicrobial peptides such as Ranacyclin which are secreted from frog skin. 17 matched cddid_all.tbl CDD pfam16049 pfam16049 292668 Antimicrobial24 Frog antimicrobial peptide. This family includes antimicrobial peptides such as Aurein-5 and Caerin 2 which are secreted from frog skin. 25 matched cddid_all.tbl CDD pfam16050 pfam16050 464994 CDC73_N Paf1 complex subunit CDC73 N-terminal. CDC73_N is the N-terminal region of the members of CDC73_C, pfam05179. CDC73 forms part of the Paf1 post-initiation complex. The exact function within the complex is not known. 301 matched cddid_all.tbl CDD pfam16051 pfam16051 435100 DUF4797 Domain of unknown function (DUF4797). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is approximately 40 amino acids in length. There is a conserved SGLPT sequence motif. There are two completely conserved residues (P and G) that may be functionally important. 44 matched cddid_all.tbl CDD pfam16053 pfam16053 464995 MRP-S34 Mitochondrial 28S ribosomal protein S34. 128 matched cddid_all.tbl CDD pfam16054 pfam16054 435102 TMEM72 Transmembrane protein family 72. This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 145 and 275 amino acids in length. 154 matched cddid_all.tbl CDD pfam16055 pfam16055 435103 DUF4798 Domain of unknown function (DUF4798). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 80 and 365 amino acids in length. There is a single completely conserved residue H that may be functionally important. 100 matched cddid_all.tbl CDD pfam16056 pfam16056 318308 DUF4799 Domain of unknown function (DUF4799). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 362 and 1493 amino acids in length. 375 matched cddid_all.tbl CDD pfam16057 pfam16057 464996 DUF4800 Domain of unknown function (DUF4800). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is approximately 310 amino acids in length. The family is found in association with pfam02138, pfam00400. There is a conserved RDN sequence motif. 254 matched cddid_all.tbl CDD pfam16058 pfam16058 464997 Mucin-like Mucin-like. This region is found repeated at the C-terminus (C-tail) of bile salt-activated lipase, where is O-glycosylated. This region is composed of biased amino acid composition that is likely to be disordered. The region contains many repeats of an approximately 11 residue degenerate repeat. 94 matched cddid_all.tbl CDD pfam16059 pfam16059 464998 MGA_dom MGA, conserved domain. This domain can be found in the MAX gene-associated protein (Mga), which is a dual-specificity transcription factor that contains both a bHLHZip domain and a T-box domain and is able to bind to and regulate transcriptional targets through both E-box sites as well as T-box-binding elements (TBEs). 51 matched cddid_all.tbl CDD pfam16060 pfam16060 464999 DUF4802 Domain of unknown function (DUF4802). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is approximately 70 amino acids in length. There are two conserved sequence motifs: CRC and YFDC. 64 matched cddid_all.tbl CDD pfam16061 pfam16061 465000 DUF4803 Domain of unknown function (DUF4803). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 351 and 686 amino acids in length. There is a conserved RRY sequence motif. 255 matched cddid_all.tbl CDD pfam16062 pfam16062 435109 DUF4804 Domain of unknown function (DUF4804). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 238 and 504 amino acids in length. 447 matched cddid_all.tbl CDD pfam16063 pfam16063 374340 DUF4805 Domain of unknown function (DUF4805). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 244 and 363 amino acids in length. There is a conserved WEL sequence motif. 265 matched cddid_all.tbl CDD pfam16064 pfam16064 465001 DUF4806 Domain of unknown function (DUF4806). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is approximately 80 amino acids in length. 87 matched cddid_all.tbl CDD pfam16065 pfam16065 465002 DUF4807 Domain of unknown function (DUF4807). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 171 and 270 amino acids in length. There is a conserved STLGG sequence motif. 126 matched cddid_all.tbl CDD pfam16066 pfam16066 374343 DUF4808 Domain of unknown function (DUF4808). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 106 and 135 amino acids in length. 121 matched cddid_all.tbl CDD pfam16067 pfam16067 435112 DUF4809 Domain of unknown function (DUF4809). This family of proteins is found in bacteria. Proteins in this family are typically between 120 and 137 amino acids in length. There is a conserved GGCNAC sequence motif. 129 matched cddid_all.tbl CDD pfam16068 pfam16068 435113 DUF4810 Domain of unknown function (DUF4810). This family of proteins is found in bacteria. Proteins in this family are typically between 117 and 134 amino acids in length. There is a conserved PES sequence motif. It is a putative lipoprotein. 84 matched cddid_all.tbl CDD pfam16069 pfam16069 435114 DUF4811 Domain of unknown function (DUF4811). This family of proteins is found in bacteria. Proteins in this family are typically between 188 and 241 amino acids in length. There is a single completely conserved residue Y that may be functionally important. 154 matched cddid_all.tbl CDD pfam16070 pfam16070 465003 TMEM132 Transmembrane protein family 132. This presumed domain is found in members of the TMEM132 family. TMEM132A may be involved in embryonic and postnatal brain development. TMEM132D may be a marker for oligodendrocyte differentiation. 344 matched cddid_all.tbl CDD pfam16071 pfam16071 465004 DUF4812 Domain of unknown function (DUF4812). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is approximately 100 amino acids in length. The family is found in association with pfam03791, pfam03790. There are two completely conserved residues (H and I) that may be functionally important. 65 matched cddid_all.tbl CDD pfam16072 pfam16072 435117 DUF4813 Domain of unknown function (DUF4813). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 345 and 672 amino acids in length. 288 matched cddid_all.tbl CDD pfam16073 pfam16073 465005 SAT Starter unit:ACP transacylase in aflatoxin biosynthesis. SAT is the N-terminal starter unit:ACP transacylase of the aflatoxin biosynthesis pathway. SAT selects the hexanoyl starter unit from a pair of specialized fungal fatty acid synthase subunits (HexA/HexB) and transfers it onto the polyketide synthase A acyl-carrier protein to prime polyketide chain elongation. The family is found in association with pfam02801, pfam00109, pfam00550, pfam00975, pfam00698. 239 matched cddid_all.tbl CDD pfam16074 pfam16074 435119 PilW Type IV Pilus-assembly protein W. PilW is a family of putative type IV pilus-assembly proteins. PilW is one of the component proteins of the pilus biogenesis process whereby pilus fibres are assembled in the periplasm, emerge onto the cell surface and are there stabilized, to allow bacterial attachment to host cells. PilW is an outer-membrane protein necessary for both the functionality of fibres and their stabilization. 126 matched cddid_all.tbl CDD pfam16075 pfam16075 374348 DUF4815 Domain of unknown function (DUF4815). 570 matched cddid_all.tbl CDD pfam16076 pfam16076 465006 Acyltransf_C Acyltransferase C-terminus. This domain is found at the C-terminus of several different acyltransferases including 1-acyl-sn-glycerol-3-phosphate acyltransferase, acyl-CoA:lysophosphatidylglycerol acyltransferase 1 and lysocardiolipin acyltransferase 1. 74 matched cddid_all.tbl CDD pfam16077 pfam16077 465007 Spaetzle Spaetzle. This family of proteins are nerve growth factor-like ligands required in the pathway that establishes the dorsal-ventral pattern of the embryo. They form a cystine knot structure. 93 matched cddid_all.tbl CDD pfam16078 pfam16078 465008 2-oxogl_dehyd_N 2-oxoglutarate dehydrogenase N-terminus. This domain is found at the N-terminus of 2-oxoglutarate dehydrogenases. 41 matched cddid_all.tbl CDD pfam16079 pfam16079 465009 Phage_holin_5_2 Phage holin family Hol44, in holin superfamily V. Phage_holin_V_2 is a family of small hydrophobic proteins with three transmembrane domains of the Hol44 family. These proteins are produced by double-stranded DNA bacteriophages that use an endolysin-holin strategy to achieve lysis of their hosts. The endolysins are peptidoglycan-degrading enzymes that are usually accumulated in the cytosol until access to the cell wall substrate is provided by the holin membrane lesion. Full activity of the endolysin Lys44 from oenophage fOg44 requires sudden ion-nonspecific dissipation of the proton motive force, undertaken by the fOg44 holin during phage-infection. 66 matched cddid_all.tbl CDD pfam16080 pfam16080 435124 Phage_holin_2_3 Bacteriophage holin family HP1. Phage_holin_2_3 is a family of small hydrophobic phage proteins called holins with one transmembrane domain. Holins are produced by double-stranded DNA bacteriophages that use an endolysin-holin strategy to achieve lysis of their hosts. The endolysins are peptidoglycan-degrading enzymes that are usually accumulated in the cytosol until access to the cell wall substrate is provided by the holin membrane lesion 1,2]. 56 matched cddid_all.tbl CDD pfam16081 pfam16081 435125 Phage_holin_7_1 Mycobacterial 2 TMS Phage Holin (M2 Hol) Family. Phage_holin_8_1 is a family of two transmembrane mycobacteriophage holins, small hydrophobic proteins that effect lysis of host mycobacterial cells in conjunction with a mycobacteria-specific lysin, lysB. The product of lysB gene targets the mycobacteria outer membrane, the last barrier to bacteriophage release. 121 matched cddid_all.tbl CDD pfam16082 pfam16082 406480 Phage_holin_2_4 Bacteriophage holin family, superfamily II-like. Phage_holin_2_4 is a family of small hydrophobic phage proteins called holins with one transmembrane domain. Holins are produced by double-stranded DNA bacteriophages that use an endolysin-holin strategy to achieve lysis of their hosts. The endolysins are peptidoglycan-degrading enzymes that are usually accumulated in the cytosol until access to the cell wall substrate is provided by the holin membrane lesion. 76 matched cddid_all.tbl CDD pfam16083 pfam16083 435126 Phage_holin_3_3 LydA holin phage, holin superfamily III. Phage_holin_3_3 is a family of small hydrophobic holin proteins with one or more transmembrane domains. Holins are encoded within the genomes of Gram-positive and Gram-negative bacteria as well as those of the bacteriophages of these organizms. Their primary function appears to be transport of murein hydrolases across the cytoplasmic membrane to the cell wall where these enzymes hydrolyse the cell wall polymer as a prelude to cell lysis. When chromosomally encoded, these enzymes are therefore autolysins. Holins may also facilitate leakage of electrolytes and nutrients from the cell cytoplasm, thereby promoting cell death. Some may catalyze export of nucleases. LydA and lydB are encoded on the dar operon. The phenotype of a rapid lysis in the absence of active LydB suggests that this protein might be an antagonist of the holin LydA. 78 matched cddid_all.tbl CDD pfam16084 pfam16084 292702 LydB LydA-holin antagonist. LydB is a family of proteins that are antagonistic to the lysing action of holin LydA. 147 matched cddid_all.tbl CDD pfam16085 pfam16085 318333 Phage_holin_3_5 Bacteriophage holin Hol, superfamily III. Phage_holin_6_2 is a family of holins classified as 1.E.20 in the TC database. The hol gene (PRF9) product (117 aas) of Pseudomonas aeruginosa PAO1 exhibits a hydrophobicity profile similar to holins of P2 and phiCTX phages with two peaks of hydrophobicity that might correspond to either one or two TMSs. Hol functions in conjunction with the lytic enzyme, Lys, a glycosyl hydrolase that breaks-up the murein in the bacterial cell-wall, causing lysis of the cell and hence entry of phage particles. Several members are annotated as pyocin R2_PP when encoded on the chromosome. 113 matched cddid_all.tbl CDD pfam16086 pfam16086 465010 DUF4816 Domain of unknown function (DUF4816). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 178 and 456 amino acids in length. There is a conserved WKP sequence motif. 41 matched cddid_all.tbl CDD pfam16087 pfam16087 465011 DUF4817 Helix-turn-helix domain (DUF4817). This family of proteins is functionally uncharacterized. This family of proteins is found primarily in insects, but also some other eukaryotes. Proteins in this family are typically between 109 and 322 amino acids in length. This domain may be involved in DNA-binding. 54 matched cddid_all.tbl CDD pfam16088 pfam16088 465012 BORCS7 BLOC-1-related complex sub-unit 7. This is a family of unknown function found in eukaryotes. Family members include BORCS7 (BLOC-1-related complex sub-unit 7) also known as Diaskedin (from the Ancient Greek 'diaskedazo', meaning 'to disperse') or C10orf32. It constitutes sub-unit 7 of the BORC complex (BLOC-one-related complex). BORC is a multisubunit complex that regulates the positioning of lysosomes at the cell periphery, and consequently affects cell migration. BORC associates with the lysosomal membrane, where it functions to recruit the small GTPase Arl8. This initiates a series of interactions that promote the microtubule-guided transport of lysosomes toward the cell periphery. 103 matched cddid_all.tbl CDD pfam16089 pfam16089 465013 DUF4818 Domain of unknown function (DUF4818). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 176 and 214 amino acids in length. There is a single completely conserved residue W that may be functionally important. 116 matched cddid_all.tbl CDD pfam16090 pfam16090 465014 DUF4819 Domain of unknown function (DUF4819). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically between 82 and 99 amino acids in length. 84 matched cddid_all.tbl CDD pfam16091 pfam16091 465015 DUF4820 Domain of unknown function (DUF4820). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 320 and 483 amino acids in length. There are two conserved sequence motifs: WSLP and RPLPW. 226 matched cddid_all.tbl CDD pfam16092 pfam16092 465016 CFAP61_N Cilia- and flagella-associated protein 61, N-terminal domain. This entry represents the N-terminal domain of proteins described as cilia- and flagella-associated protein. Proteins containing this domain includes FAP61 from Chlamydomonas reinhardtii. FAP61 is part of the calmodulin and spoke-associated complex (CSC) required for wild-type motility and for the stable assembly of a subset of radial spokes in motile cilia. 264 matched cddid_all.tbl CDD pfam16093 pfam16093 465017 PAC4 Proteasome assembly chaperone 4. PAC4 or proteasome assembly chaperone 4 protein promotes assembly of the 20S proteasome. It interacts with PSMG3. It associates with alpha subunits of the 20S proteasome. At the very C-terminal is a crucial HbYX or hydrophobic-tyrosine-X sequence motif that, in proteasome activators, opens the 20S proteasome entry pore. 72 matched cddid_all.tbl CDD pfam16094 pfam16094 465018 PAC1 Proteasome assembly chaperone 4. PAC1 is a family of eukaryotic proteasome assembly chaperone 1 proteins in eukaryotes that promotes assembly of the core 20S proteasome as part of a heterodimer with PAC2. 284 matched cddid_all.tbl CDD pfam16095 pfam16095 406489 COR C-terminal of Roc, COR, domain. The C-terminal of Roc domain, COR, along with Roc functions as the putative regulator of kinase activity. It functions as a proper GTP-binding protein with a low GTPase activity somehow stimulating the kinase activity. 196 matched cddid_all.tbl CDD pfam16096 pfam16096 465019 FXR_C1 Fragile X-related 1 protein C-terminal region 2. FXR_C1 is a small highly conserved region of the C-terminus of Fragile X-related proteins 1 and 2, FRX1, FRX2. The family is found in association with pfam05641, pfam00013. This family is immediately C-terminal to the core C terminal region, PF12235, and contains at least one block of RGG repeats that bind to G-quartet sequences in a wide variety of mRNAs. 76 matched cddid_all.tbl CDD pfam16097 pfam16097 435134 FXR_C3 Fragile X-related 1 protein C-terminal region 3. FXR_C1 is a small highly conserved region at the very C-terminus of Fragile X-related proteins 1 and 2, FRX1, FRX2. The family is found in association with pfam05641, pfam00013, PF16096. 68 matched cddid_all.tbl CDD pfam16098 pfam16098 465020 FXMR_C2 Fragile X-related mental retardation protein C-terminal region 2. FXMR_C2 is a small highly conserved region at the very C-terminus of Fragile X-related proteins FMR1. The family is found in association with pfam05641, pfam00013, PF16096. 86 matched cddid_all.tbl CDD pfam16099 pfam16099 465021 RMI1_C Recq-mediated genome instability protein 1, C-terminal OB-fold. RMI1_C is a C-terminal oligo-nucleotide binding domain of Recq-mediated genome instability proteins. This domain interacts with RMI2-OB folds to make up the RMI core complex. The RMI core interface is crucial for BLM, Bloom syndrome, dissolvasome assembly and may have additional cellular roles as a docking hub for other proteins. 138 matched cddid_all.tbl CDD pfam16100 pfam16100 465022 RMI2 RecQ-mediated genome instability protein 2. RMI2 is a eukaryotic family of an OB3, oligo-nucleotide-binding proteins. It is an essential component of the RMI complex that plays a vital role in the processing of homologous recombination intermediates in order to limit DNA-crossover-formation in cells. 128 matched cddid_all.tbl CDD pfam16101 pfam16101 406495 PRIMA1 Proline-rich membrane anchor 1. 122 matched cddid_all.tbl CDD pfam16102 pfam16102 406496 ACTH_assoc ACTH-associated domain. ACTH_assoc is the low-complexity regions immediately adjacent to the highly conserved binding motif of the ACTH_domain, pfam00976. the exact function is not known. 28 matched cddid_all.tbl CDD pfam16103 pfam16103 465023 DUF4822 Domain of unknown function (DUF4822). A lipocain-like domain found in functionally uncharacterized bacterial proteins, often as a repeat of two domains. Proteins with this domain are found in a wide range of bacteria and are often annotated as S-layer proteins, but the origin of this annotation is not clear 121 matched cddid_all.tbl CDD pfam16104 pfam16104 292722 FPRL1_inhibitor Formyl peptide receptor-like 1 inhibitory protein. This family consists of several formyl peptide receptor-like 1 inhibitory proteins from Staphylococcus aureus. These are secreted proteins that block the formyl peptide receptor-like 1 found in neutrophils, monocytes, B cells, and NK cells; and inhibit the binding of chemoattractants (such as formylated peptides) to FPRL1, which initiate phagocyte mobilization towards the infection site. 105 matched cddid_all.tbl CDD pfam16105 pfam16105 435138 DUF4823 Domain of unknown function (DUF4823). This family consists of hypothetical lipoproteins around 210 residues of length and is mainly found in various Pseudomonas species. The function of this family is unknown. 141 matched cddid_all.tbl CDD pfam16106 pfam16106 435139 DUF4824 Domain of unknown function (DUF4824). This family consists of several hypothetical lipoproteins around 270 residues in length and is mainly found in Pseudomonas species. The function of this family is unknown. 251 matched cddid_all.tbl CDD pfam16107 pfam16107 435140 DUF4825 Domain of unknown function (DUF4825). This domain forms the N-terminal, extracellular domain of some homologs of Staph BlaR1 proteases, where it replaces the penicillin-binding domain of BlaR1. It is also found in many uncharacterized proteins in a broad range of bacteria. Its association with BlaR1 homologs suggests it may be involved in substrate-, possibly antibiotic-binding, but this prediction has not been verified experimentally. 95 matched cddid_all.tbl CDD pfam16108 pfam16108 435141 DUF4826 Domain of unknown function (DUF4826). This family consists of uncharacterized proteins around 150 residues in length and is mainly found in various Shewanella species. The function of this protein is unknown. 125 matched cddid_all.tbl CDD pfam16109 pfam16109 435142 DUF4827 Domain of unknown function (DUF4827). This family consists of uncharacterized proteins around 200 residues in length and is mainly found in various Bacteroides species. Distant homology prediction algorithms consistently suggest a homology between this family and FKBP-type peptidyl-prolyl cis-trans isomerases (PF00254), but this relation is as yet not confirmed. The function of this family is unknown. 177 matched cddid_all.tbl CDD pfam16110 pfam16110 435143 DUF4828 Domain of unknown function (DUF4828). This family consists of uncharacterized proteins around 120 residues in length and is mainly found in various Enterococcus and Lactobacillus species. The function of this family is unknown. 79 matched cddid_all.tbl CDD pfam16111 pfam16111 379768 DUF4829 Domain of unknown function (DUF4829). This family consists of several uncharacterized proteins around 150 residues in length and is mainly found in various Clostridium species. The function of this family is unknown. 117 matched cddid_all.tbl CDD pfam16112 pfam16112 435144 DUF4830 Domain of unknown function (DUF4830). This family consists of several uncharacterized proteins around 150 residues in length and is mainly found in Clostridium, Eubacterium, and Ruminococcus species. The function of this family is unknown. 84 matched cddid_all.tbl CDD pfam16113 pfam16113 465024 ECH_2 Enoyl-CoA hydratase/isomerase. This family contains a diverse set of enzymes including: enoyl-CoA hydratase, napthoate synthase, carnitate racemase, 3-hydroxybutyryl-CoA dehydratase and dodecanoyl-CoA delta-isomerase. This family differs from pfam00378 in the structure of it's C-terminus. 331 matched cddid_all.tbl CDD pfam16114 pfam16114 465025 Citrate_bind ATP citrate lyase citrate-binding. This is the citrate-binding domain of ATP citrate lyase. This domain has a Rossmann fold. 178 matched cddid_all.tbl CDD pfam16115 pfam16115 435146 DUF4831 Domain of unknown function (DUF4831). This family consists of several uncharacterized proteins around 350 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 318 matched cddid_all.tbl CDD pfam16116 pfam16116 465026 DUF4832 Domain of unknown function (DUF4832). This family consists of uncharacterized proteins around 200 residues in length and is mainly found in various Bacteroides and Capnocytophaga species. The function of this family is unknown. Distant homology analysis suggests a possible similarity of proteins from this family to TIM barrel glycoside hydrolases and, subsequently its involvement in carbohydrate metabolism.The domain lies downstream of glycosyl hydrolases 42 suggesting that as a domain it might represent the carbohydrate-binding region of the enzyme. 213 matched cddid_all.tbl CDD pfam16117 pfam16117 465027 DUF4833 Domain of unknown function (DUF4833). This family consists of uncharacterized proteins around 170 residues in length and is mainly found in various Parabacteroides and Bacteroides species. The function of this family is unknown. 135 matched cddid_all.tbl CDD pfam16118 pfam16118 435149 DUF4834 Domain of unknown function (DUF4834). This family consists of uncharacterized proteins around 90 residues in length and is mainly found in various Parabacteroides and Bacteroides species. Protein in this family are characterized by a strongly conserved KDEGEYVD motif on the C-terminal and a very divergent N-terminal. The function of this family is unknown. 91 matched cddid_all.tbl CDD pfam16119 pfam16119 435150 DUF4835 Domain of unknown function (DUF4835). This family consists of uncharacterized proteins of around 300 residues in length and is mainly found in bacteria from the Cytophaga-Flavobacteria-Bacteroides (CFB) group, both environmental and from human microbiome. The function of this family is unknown. 276 matched cddid_all.tbl CDD pfam16120 pfam16120 435151 DUF4836 Domain of unknown function (DUF4836). This family consists of several uncharacterized proteins around 520 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 474 matched cddid_all.tbl CDD pfam16121 pfam16121 465028 40S_S4_C 40S ribosomal protein S4 C-terminus. This domain is found at the C-terminus of 40S ribosomal protein S4. 48 matched cddid_all.tbl CDD pfam16122 pfam16122 465029 40S_SA_C 40S ribosomal protein SA C-terminus. This domain is found at the C-terminus of 40S ribosomal protein SA. 98 matched cddid_all.tbl CDD pfam16123 pfam16123 465030 HAGH_C Hydroxyacylglutathione hydrolase C-terminus. This domain is found at the C-terminus of hydroxyacylglutathione hydrolase enzymes. Substrate binding occurs at the interface between this domain and the catalytic domain (pfam00753). 82 matched cddid_all.tbl CDD pfam16124 pfam16124 465031 RecQ_Zn_bind RecQ zinc-binding. This domain is the zinc-binding domain of ATP-dependent DNA helicase RecQ. 66 matched cddid_all.tbl CDD pfam16125 pfam16125 435156 DUF4837 Domain of unknown function (DUF4837). This family consists of uncharacterized proteins around 350 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 292 matched cddid_all.tbl CDD pfam16126 pfam16126 406516 DUF4838 Domain of unknown function (DUF4838). This family consists of several uncharacterized proteins found in various Bacteroides and Chloroflexus species. The function of this family is unknown. 263 matched cddid_all.tbl CDD pfam16127 pfam16127 406517 DUF4839 Domain of unknown function (DUF4839). This family consists of uncharacterized proteins around 300 residues in length and is mainly found in various Clostridium species. The function of this family is unknown. 122 matched cddid_all.tbl CDD pfam16128 pfam16128 435157 DUF4840 Domain of unknown function (DUF4840). This family consists of uncharacterized proteins around 220 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 143 matched cddid_all.tbl CDD pfam16129 pfam16129 435158 DUF4841 Domain of unknown function (DUF4841). this domain is found on the N-terminal of several uncharacterize proteins found in various Bacteroides species. Solved structure of one of them (BACOVA_00967) from Bacteroides ovatus shows a small beta barrel with an immunoglobulin-like fold. DUF4841 domain shows weak overlap with the DUF4114 family, suggesting a possible distant relation. Function of this domain is unknown. 69 matched cddid_all.tbl CDD pfam16130 pfam16130 435159 DUF4842 Domain of unknown function (DUF4842). This domain is found on the C-terminal of large number of uncharacterized proteins with broad phylogenetic distribution, which includes human gut Bacteroides, g-proteobacteria (Vibrio and Shewanella) and also spirochetes from Leptospira genus. Solved structure of Bacteroides ovatus protein BACOVA_00967 shows a large beta barrel with an immunoglobulin-like fold and significant structural similarity to collagen-binding domain of adhesin from S. aureus (1amx), but with several additional long loops and secondary structure elements. Function of this domain is unknown. 200 matched cddid_all.tbl CDD pfam16131 pfam16131 435160 Torus Torus domain. This domain is found in pre-mRNA-splicing factor CWC2. It includes a CCCH-type zinc finger. 109 matched cddid_all.tbl CDD pfam16132 pfam16132 374383 DUF4843 Domain of unknown function (DUF4843). This family consists of uncharacterized proteins around 220 residues in length and is mainly found in various Bacteroides species. Distant homology analysis suggest distant relation between this family and other families of proteins with immunoglobulin-like folds, which are often involved in substrate binding. However, specific function of this family is unknown. There is distant homology to the Calx-beta family pfam03160. 163 matched cddid_all.tbl CDD pfam16133 pfam16133 406522 DUF4844 Domain of unknown function (DUF4844). this family consists of short uncharacterized proteins found mostly in different strains of Acinetobacter bumanii, but also in several Shewanella species and in some bacteria from the CFB group. Solved structure of ABAYE3784 protein from Acinetobacter baumannii AYE shows a five helical bundle with a very strong structural similarity to a bromodomain domain. However, the specific function of proteins from the DUF4844 family is unknown 117 matched cddid_all.tbl CDD pfam16134 pfam16134 465032 THOC2_N THO complex subunit 2 N-terminus. This family represents the N-terminus of THO complex subunit 2. 614 matched cddid_all.tbl CDD pfam16135 pfam16135 465033 TDBD Tify domain binding domain. This entry contains a C-terminal presumed zinc binding domain from the NINJA protein which interacts with the Tify domain of JAZ1. 52 matched cddid_all.tbl CDD pfam16136 pfam16136 406525 NINJA_B Putative nuclear localization signal. NINJA proteins are Novel INteractor of JAZ proteins found in plants. NINJA proteins act as a transcriptional repressor, the activity of which is mediated by a functional TPL-binding EAR repression motif upstream from this domain. 114 matched cddid_all.tbl CDD pfam16137 pfam16137 435163 DUF4845 Domain of unknown function (DUF4845). This family consists of uncharacterized proteins around 120 residues in length and is mainly found in various Pseudomonas species. Distant homology analysis suggests that proteins from this family are related to pilin type IV proteins from the Bundlin (PF05307) family, this prediction is however not confirmed by any experimental evidence 85 matched cddid_all.tbl CDD pfam16138 pfam16138 435164 DUF4846 Domain of unknown function (4846). This family consists of uncharacterized proteins around 260 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 239 matched cddid_all.tbl CDD pfam16139 pfam16139 435165 DUF4847 Domain of unknown function (DUF4847). This uncharacterized domain has a lipocalin fold. 146 matched cddid_all.tbl CDD pfam16140 pfam16140 406529 DUF4848 Domain of unknown function (DUF4848). A small family of uncharacterized proteins around 310 residues in length and found in various Bacteroides species. The function of this family is unknown. 216 matched cddid_all.tbl CDD pfam16141 pfam16141 435166 DUF4849 Putative glycoside hydrolase Family 18, chitinase_18. This DUF is likely to be a form of glycosyl hydrolase from CAZy family 18, possibly chitinase 18. This would have the EC number of EC:3.2.1.14. 325 matched cddid_all.tbl CDD pfam16142 pfam16142 292760 DUF4850 Domain of unknown function (DUF4850). This family consists of several uncharacterized proteins around 250 residues in length and is mainly found in various Acinetobacter species. The function of this family is unknown. 184 matched cddid_all.tbl CDD pfam16143 pfam16143 374391 DUF4851 Domain of unknown function (DUF4851). This family consists of several uncharacterized proteins around 250 residues in length and is mainly found in various Desulfovibrio species. The function of this family is unknown. 195 matched cddid_all.tbl CDD pfam16144 pfam16144 406531 DUF4852 Domain of unknown function (DUF4852). This family consists of several uncharacterized proteins around 350 residues in length and is mainly found in various Parabacteroides, Bacteroides and Porphyromonas species. The function of this family is unknown. 121 matched cddid_all.tbl CDD pfam16145 pfam16145 435167 DUF4853 Domain of unknown function (DUF4853). This family consists of uncharacterized proteins around 220 residues in length and is mainly found in various Actinomyces species. The function of this family is unknown. 135 matched cddid_all.tbl CDD pfam16146 pfam16146 406533 DUF4854 Domain of unknown function (DUF4854). This family consists of uncharacterized proteins found in firmicutes and high GC Gram+ bacteria associated with human and animal guts. The function of this family is unknown. 105 matched cddid_all.tbl CDD pfam16147 pfam16147 435168 DUF4855 Domain of unknown function (DUF4855). This family consists of uncharacterized proteins around 400 residues in length and is mainly found in various Bacteroides species. Several proteins are annotated as glycerophosphodiester phosphodiesterases, but the origin of this annotation is not clear. 313 matched cddid_all.tbl CDD pfam16148 pfam16148 435169 DUF4856 Domain of unknown function (DUF4856). This family consists of uncharacterized proteins around 400 residues in length and is mainly found in various Bacteroides and Prevotella species. The function of this family is unknown. 362 matched cddid_all.tbl CDD pfam16149 pfam16149 435170 DUF4857 Domain of unknown function (DUF4857). This family consists of uncharacterized proteins around 340 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 270 matched cddid_all.tbl CDD pfam16150 pfam16150 435171 DUF4858 Domain of unknown function (DUF4858). This family consists of uncharacterized proteins around 190 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 187 matched cddid_all.tbl CDD pfam16151 pfam16151 406538 DUF4859 Domain of unknown function (DUF4859). This family consists of uncharacterized proteins around 340 residues in length and is mainly found in various Bacteroides and Prevotella species. The function of this family is unknown. 116 matched cddid_all.tbl CDD pfam16152 pfam16152 435172 DUF4860 Domain of unknown function (DUF4860). This family consists of uncharacterized proteins around 160 residues in length and is mainly found in various Eubacterium and Clostridium species. The function of this family is unknown. 98 matched cddid_all.tbl CDD pfam16153 pfam16153 435173 DUF4861 Domain of unknown function (DUF4861). This family consists of uncharacterized proteins around 400 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. However, in many instances the domain lies upstream of a glycosyl hydrolase family, usually family 88, so it might be involved in carbohydrate binding. 381 matched cddid_all.tbl CDD pfam16154 pfam16154 435174 DUF4862 Domain of unknown function (DUF4862). This family consists of uncharacterized proteins around 300 residues in length and is mainly found in various high GC Gram+ bacteria, but also in several pathogenic and non-pathogenic enterobacteria (Salmonella, E. coli). Distant homology analysis suggests this could be a branch of Xylose isomerase-like TIM barrel family, but this prediction is currently not confirmed by experiment 291 matched cddid_all.tbl CDD pfam16155 pfam16155 435175 DUF4863 Domain of unknown function (DUF4863). This family consists of uncharacterized proteins around 150 residues in length and is mainly found in various delta- proteobacteria, but also several fungal species. Distant homology analysis suggest proteins from this family have a cupin-like fold and may be related to a group of lyases involved in the metabolism of benzoate. Few proteins from this family are annotated as p-hydroxylaminobenzoate lyases, NbaB, and this proposed function matches well their phylogenetic distribution, but there seems to be no direct experimental verification of this function, therefore at this point we call it a DUF. 147 matched cddid_all.tbl CDD pfam16156 pfam16156 435176 DUF4864 Domain of unknown function (DUF4864). This family consists of uncharacterized proteins around 120 residues in length and is mainly found in various Anabaena and Nostoc species. Distant homology analysis suggests this family is related to NTF2-like proteins and specifically to proteins that bind small molecules. HMM partly overlaps with Tol_Tol_Ttg2 (PF05494) involved in Toluene tolerance and lumazine binding family (PF12870) and these families should form a clan. 101 matched cddid_all.tbl CDD pfam16157 pfam16157 465034 DUF4865 Domain of unknown function (DUF4865). This family consists of uncharacterized proteins around 180 residues in length and is mainly found in various Bacillus species. Distant homology and fold prediction suggests proteins from this family would have a ferrodoxin dimeric fold and specifically be related to the putative mono-oxygenase ydhR family PF08803, however this prediction has not been verified by experiment 181 matched cddid_all.tbl CDD pfam16158 pfam16158 465035 N_BRCA1_IG Ig-like domain from next to BRCA1 gene. Domain present between positions 365-485 in the human next to BRCA1 gene 1 protein Q14596 (NBR1_HUMAN) Distant homology and fold prediction analysis suggests this domain has an immunoglobulin like fold and is distantly homologous to domains involved in cell adhesion such as CARDB (PF07705). JCSG construct was crystalized confirming the domain boundaries 98 matched cddid_all.tbl CDD pfam16159 pfam16159 465036 FOXP-CC FOXP coiled-coil domain. This domain, approximately 60-70 residues in length, is mainly found in Forkhead box proteins in various Mammalia species. It is a coiled-coil domain, which modulates the dimeric associations of FOXP transcription factors. Several key disease mutations, for instance those found in the IPEX syndrome are located in this domain 68 matched cddid_all.tbl CDD pfam16160 pfam16160 465037 DUF4866 Domain of unknown function (DUF4866). This family consists of uncharacterized proteins around 250 residues in length and is mainly found in various human gut Firmicute species and abundant in human gut metagenomic datasets. The function of this family is unknown. 246 matched cddid_all.tbl CDD pfam16161 pfam16161 435181 DUF4867 Domain of unknown function (DUF4867). This family consists of uncharacterized proteins around 220 residues in length and is mainly found in various human gut Firmicutes and a few eubacteria species. It is also amply represented in human gut metagenomic datasets. Distant homology analysis and marginal HMM overlaps suggest this family is a distant homolog of Ureidoglycolate hydrolase pfam04115, but this prediction is not verified by experiment, therefore the function of this family is still unknown. 199 matched cddid_all.tbl CDD pfam16162 pfam16162 406549 DUF4868 Domain of unknown function (DUF4868). This family consists of uncharacterized proteins around 320 residues in length and is a phylogenetically broad range of bacteria associated with the human gut microbiome. A member of this family from Lactobacillus casei CRL 705 is part of the gene cluster involved in synthesis of bacteriocin toxin, but the specific function of this family is unknown. 186 matched cddid_all.tbl CDD pfam16163 pfam16163 435182 DUF4869 Domain of unknown function (DUF4869). This family consists of uncharacterized proteins around 150 residues in length. Its members are found in human gut Firmicutes and are also abundant in human gut metagenomics datasets. The function of this family is unknown. 128 matched cddid_all.tbl CDD pfam16164 pfam16164 465038 VWA_N2 VWA N-terminal. This domain is found in von Willebrand factor proteins, where it is found to the N-terminus of the first VWA domain (pfam00092). 79 matched cddid_all.tbl CDD pfam16165 pfam16165 435183 Ferlin_C Ferlin C-terminus. This domain is found at the C-terminus of proteins belonging to the ferlin family, including dysferlin, myoferlin, otoferlin and fer-1-like proteins. 154 matched cddid_all.tbl CDD pfam16166 pfam16166 374405 TIC20 Chloroplast import apparatus Tic20-like. Chloroplast function requires the import of nuclear encoded proteins from the cytoplasm across the chloroplast double membrane. This is accomplished by two protein complexes, the Toc complex located at the outer membrane and the Tic complex located at the inner membrane. The Toc complex recognizes specific proteins by a cleavable N-terminal sequence and is primarily responsible for translocation through the outer membrane, while the Tic complex translocates the protein through the inner membrane. This entry represents Tic20, a core member of the Tic complex. This protein is deeply embedded in the inner envelope membrane and is thought to function as a protein- conducting component of the Tic complex. 177 matched cddid_all.tbl CDD pfam16167 pfam16167 406553 DUF4871 Domain of unknown function (DUF4871). This family consists of uncharacterized proteins around 170 residues in length and is mainly found in various Bacillus species (B. cereus, B. thuringiensis and B. anthracis). The solved structure of B. anthracis homologs has a variant of the Greek-key beta barrel fold, making the DUF4870 family a member of a large group of bacterial immunoglobulin like domains, but the functional consequences of this classification remain unknown. 128 matched cddid_all.tbl CDD pfam16168 pfam16168 406554 AIDA Adhesin of bacterial autotransporter system, probable stalk. The AIDA repeat is found on bacterial autotransporter proteins. As the repeat is short and occurs multiple times, it is likely to be the region of the transporter that acts as the stalk between the beta-barrel inserted into the membrane and the N-terminal head domain. 57 matched cddid_all.tbl CDD pfam16169 pfam16169 435184 DUF4872 Domain of unknown function (DUF4872). Members of this family are often found in the gene neighbourhood, or fused to, non-ribosomal peptide synthetases. 173 matched cddid_all.tbl CDD pfam16170 pfam16170 435185 DUF4873 Domain of unknown function (DUF4873). This family consists mostly of short uncharacterized proteins found in various high GC Gram positive bacteria, primarily Mycobacterium species. However in some proteins, such as for instance Rv0943c proteins from Mycobacterium tuberculosis H37Rv, DUF4873 domain is found at the C-terminus, following the flavin-binding monooxygenase-like domain pfam00743, which is why probably many proteins with DUF4873 domains are annotated as monooxygenases. However these functions are not confirmed experimentally and the function of DUF4873 domain is still unknown. 91 matched cddid_all.tbl CDD pfam16171 pfam16171 465039 CENP-T_N Centromere kinetochore component CENP-T N-terminus. CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This family represents the N-terminus of CENP-T. 378 matched cddid_all.tbl CDD pfam16172 pfam16172 465040 DOCK_N DOCK N-terminus. This family is found near to the N-terminus of dedicator of cytokinesis (DOCK) proteins, between the variant SH3 domain (pfam07653) and the C2 domain (pfam14429). 317 matched cddid_all.tbl CDD pfam16173 pfam16173 435188 DUF4874 Domain of unknown function (DUF4874). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and eukaryotes, and is typically between 161 and 175 amino acids in length. There is a conserved WGE sequence motif. 162 matched cddid_all.tbl CDD pfam16174 pfam16174 465041 IHABP4_N Intracellular hyaluronan-binding protein 4 N-terminal. IHABP4_N is the N-terminal region of intracellular hyaluronan-binding protein 4-like and SERPINE1 mRNA binding protein 1-like proteins. This region carries nuclear localization sites, and may also be involved in the binding to some of the partners in the translational machinery. 140 matched cddid_all.tbl CDD pfam16175 pfam16175 292793 DUF4875 Domain of unknown function (DUF4875). Small protein family, with members present in few proteobacteria mostly Desulfovibrio species, but also a Vibrio phage vB, suggesting a possible phage origin Experimentally determined structure shows a fold reminiscent of a thioesterase/thiol ester dehydrase-isomerase fold, but a functional consequences of this similarity are not clear 127 matched cddid_all.tbl CDD pfam16176 pfam16176 465042 T-box_assoc T-box transcription factor-associated. This domain lies downstream of the T-box in many eukaryotic T-box proteins. The exact function is not known. 226 matched cddid_all.tbl CDD pfam16177 pfam16177 465043 ACAS_N Acetyl-coenzyme A synthetase N-terminus. This domain is found at the N-terminus of many acetyl-coenzyme A synthetase enzymes. 55 matched cddid_all.tbl CDD pfam16178 pfam16178 465044 Anoct_dimer dimerization domain of Ca+-activated chloride-channel, anoctamin. This family appears to be the cytoplasmic domain of the calcium-activated chloride-channel, anoctamin, protein. It is responsible for creating the homodimeric architecture of the chloride-channel proteins. 224 matched cddid_all.tbl CDD pfam16179 pfam16179 465045 RHD_dimer Rel homology dimerization domain. The Rel homology domain (RHD) is composed of two structural domains, an N-terminal DNA_binding domain (pfam00554) and a C-terminal dimerization domain. This is the dimerization domain. 102 matched cddid_all.tbl CDD pfam16180 pfam16180 374415 RelB_leu_zip RelB leucine zipper. This domain is a leucine zipper found in RelB transcription factors. 84 matched cddid_all.tbl CDD pfam16181 pfam16181 406565 RelB_transactiv RelB transactivation domain. This domain is the transactivation domain of the transcription factor RelB. 181 matched cddid_all.tbl CDD pfam16182 pfam16182 465046 AbLIM_anchor Putative adherens-junction anchoring region of AbLIM. AbLIM_anchor is a domain lying between the LIM actin-binding and the vilin-head domain of actin-binding LIM proteins. It is likely that this domain is involved in anchoring abLIMs to circumferential actin bundles in specific cell types. 319 matched cddid_all.tbl CDD pfam16183 pfam16183 465047 Kinesin_assoc Kinesin-associated. 177 matched cddid_all.tbl CDD pfam16184 pfam16184 465048 Cadherin_3 Cadherin-like. 111 matched cddid_all.tbl CDD pfam16185 pfam16185 465049 MTABC_N Mitochondrial ABC-transporter N-terminal five TM region. MTABC_N is the N-terminal five transmembrane helices of eukaryotic mitochondrial ABC-transporters. 244 matched cddid_all.tbl CDD pfam16186 pfam16186 465050 Arm_3 Atypical Arm repeat. This atypical Arm repeat appears at the very C-terminus of eukaryotic proteins such as importin subunit alpha-2, as the last of the repeating units. 49 matched cddid_all.tbl CDD pfam16187 pfam16187 465051 Peptidase_M16_M Middle or third domain of peptidase_M16. Peptidase_M16_M is the third domain of peptidase_M16 in eukaryotes of the insulin-degrading-enzyme type. Insulin-degrading enzymes - insulysin - are zinc metallopeptidases that metabolize several bioactive peptides, including insulin and the amyloid-beta-peptide. The tertiary structure of insulin-degrading enzymes resembles a clamshell composed of four structurally similar domains arranged to enclose a large central chamber. Substrates must enter the chamber, and it is likely that a hinge-like conformational change allows substrate binding and product release. Triphosphates are found to dock between the inner surfaces of the non-catalytic domains three and four. 284 matched cddid_all.tbl CDD pfam16188 pfam16188 465052 Peptidase_M24_C C-terminal region of peptidase_M24. This is a short region at the C-terminus of a number of metallo-peptidases of the M24 family. 63 matched cddid_all.tbl CDD pfam16189 pfam16189 465053 Creatinase_N_2 Creatinase/Prolidase N-terminal domain. 159 matched cddid_all.tbl CDD pfam16190 pfam16190 465054 E1_FCCH Ubiquitin-activating enzyme E1 FCCH domain. This domain is found in the ubiquitin-activating E1 family enzymes. 70 matched cddid_all.tbl CDD pfam16191 pfam16191 465055 E1_4HB Ubiquitin-activating enzyme E1 four-helix bundle. This domain is found in the ubiquitin-activating E1 family enzymes. 70 matched cddid_all.tbl CDD pfam16192 pfam16192 465056 PMT_4TMC C-terminal four TMM region of protein-O-mannosyltransferase. PMT_4TMC is the C-terminal four membrane-pass region of protein-O-mannosyltransferases and similar enzymes. 198 matched cddid_all.tbl CDD pfam16193 pfam16193 465057 AAA_assoc_2 AAA C-terminal domain. AAA_assoc_2 is found at the C-terminus of a relatively small set of AAA domains in proteins ranging from archaeal to fungi, plants and mammals. 81 matched cddid_all.tbl CDD pfam16195 pfam16195 465058 UBA2_C SUMO-activating enzyme subunit 2 C-terminus. 93 matched cddid_all.tbl CDD pfam16197 pfam16197 465059 KAsynt_C_assoc Ketoacyl-synthetase C-terminal extension. KAsynt_C_assoc represents the very C-terminus of a subset of proteins from the keto-acyl-synthetase 2 family. It is found in proteins ranging from bacteria to human. 111 matched cddid_all.tbl CDD pfam16198 pfam16198 465060 TruB_C_2 tRNA pseudouridylate synthase B C-terminal domain. This C-terminal region is found on a subset of TruB_B protein family members pfam01509. It is found from bacteria and archaea to fungi, plants and human. 65 matched cddid_all.tbl CDD pfam16199 pfam16199 465061 Radical_SAM_C Radical_SAM C-terminal domain. This domain is found as a C-terminal extension to a subset of Radical_SAM domains. It is found in archaeal, bacterial, fungal, plant and human proteins. 83 matched cddid_all.tbl CDD pfam16200 pfam16200 465062 Band_7_C C-terminal region of band_7. This domain is found on a subset of proteins as a C-terminal extension of the Band_7 family, pfam01145. It is found in proteins fro bacteria to fungi, plants and mammals. 63 matched cddid_all.tbl CDD pfam16201 pfam16201 465063 NopRA1 Nucleolar pre-ribosomal-associated protein 1. This family is found on the long vertebral and plant nucleolar proteins that also carry Npa1, pfam11707. 197 matched cddid_all.tbl CDD pfam16202 pfam16202 465064 BLM_N N-terminal region of Bloom syndrome protein. BLM_N is the very N-terminal region of chordate Bloom syndrome proteins. The exact function is not known. 370 matched cddid_all.tbl CDD pfam16203 pfam16203 406585 ERCC3_RAD25_C ERCC3/RAD25/XPB C-terminal helicase. This is the C-terminal helicase domain of ERCC3, RAD25 and XPB helicases. 248 matched cddid_all.tbl CDD pfam16204 pfam16204 465065 BDHCT_assoc BDHCT-box associated domain on Bloom syndrome protein. This family is found on Bloom syndrome-associated DEAD-box helicases in higher eukaryotes. It lies between the BDHCT, and DEAD-box families, pfam08072 and pfam00270. 223 matched cddid_all.tbl CDD pfam16205 pfam16205 435214 Ribosomal_S17_N Ribosomal_S17 N-terminal. This short N-terminal region is found in a number of higher eukaryotic ribosomal subunit 17 proteins. 67 matched cddid_all.tbl CDD pfam16206 pfam16206 465066 Mon2_C C-terminal region of Mon2 protein. Mon2 proteins are found from fungi to plants, to human and is a scaffold protein involved in multiple aspects of endo membrane trafficking. This C-terminal region is essential for Mon2 activity. 827 matched cddid_all.tbl CDD pfam16207 pfam16207 465067 RAWUL RAWUL domain RING finger- and WD40-associated ubiquitin-like. The RAWUL domain is found at the C-terminus of poly-comb group RING finger proteins. It is a ubiquitin-like domain. RAWUL binds directly to PUFD, a domain on BCOR proteins (BCL6 corepressor). BCOR has emerged as an important player in development and health. 66 matched cddid_all.tbl CDD pfam16208 pfam16208 465068 Keratin_2_head Keratin type II head. 156 matched cddid_all.tbl CDD pfam16209 pfam16209 465069 PhoLip_ATPase_N Phospholipid-translocating ATPase N-terminal. PhoLip_ATPase_N is found at the N-terminus of a number of phospholipid-translocating ATPases. It is found in higher eukaryotes. 67 matched cddid_all.tbl CDD pfam16210 pfam16210 406591 Keratin_2_tail Keratin type II cytoskeletal 1 tail. 135 matched cddid_all.tbl CDD pfam16211 pfam16211 465070 Histone_H2A_C C-terminus of histone H2A. 35 matched cddid_all.tbl CDD pfam16212 pfam16212 465071 PhoLip_ATPase_C Phospholipid-translocating P-type ATPase C-terminal. PhoLip_ATPase_C is found at the C-terminus of a number of phospholipid-translocating ATPases. It is found in higher eukaryotes. 250 matched cddid_all.tbl CDD pfam16213 pfam16213 465072 DCB dimerization and cyclophilin-binding domain of Mon2. DCB is the N-terminal domain of Mon2- and GIG1-like proteins from metazoa. Mon2 and BIG1 like proteins play an important role in the cytoplasm-to-vacuole transport pathway and are required for Golgi homeostasis. 172 matched cddid_all.tbl CDD pfam16214 pfam16214 318454 AC_N Adenylyl cyclase N-terminal extracellular and transmembrane region. This family covers the N-terminal extracellular region and the first transmembrane 5-6 pass region of adenylate cyclase. 415 matched cddid_all.tbl CDD pfam16215 pfam16215 435222 DUF4876 Protein of unknown function (DUF4876). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 392 and 433 amino acids in length. There is a conserved NNS sequence motif. 186 matched cddid_all.tbl CDD pfam16216 pfam16216 465073 GxGYxYP_N GxGYxY sequence motif in domain of unknown function N-terminal. This domain is found in bacteria, archaea and eukaryotes, and is typically between 213 and 231 amino acids in length. This domain is found in association with pfam14323. 215 matched cddid_all.tbl CDD pfam16217 pfam16217 465074 M64_N Peptidase M64 N-terminus. This domain is found at the N-terminus of IgA Peptidase M64. Its function is unknown. 115 matched cddid_all.tbl CDD pfam16218 pfam16218 465075 Peptidase_C101 Peptidase family C101. This is a family of cysteine-peptidases that is conserved in vertebrates. The key residues as found in SwissProt:Q96BN8 are Asp126, Cys129, His339 and Asn341. 265 matched cddid_all.tbl CDD pfam16219 pfam16219 435226 DUF4879 Domain of unknown function (DUF4879). family of short proteins of bacterial proteins of phage origin, exemplified by protein SPBc2p013 from Bacillus phage SPBc2, found in various Bacillus and Pseudomonas species. Structure show unexpected structural similarity to greek key beta barrels from the E-set domain, especially to domains involved in carbohydrate and protein- protein binding. However functional consequences of this similarity are not confirmed. 125 matched cddid_all.tbl CDD pfam16220 pfam16220 435227 DUF4880 Domain of unknown function (DUF4880). This domain can be found on the N-terminal of uncharacterized proteins from various Rhodopseudomonas and Pseudomonas species, often, but not always followed by the ron siderophore sensor protein family (FecR, PF04773). The function of this domain is unknown. 43 matched cddid_all.tbl CDD pfam16221 pfam16221 379798 HTH_47 winged helix-turn-helix. HTH_47 is an example of a circularly permuted winged helix-turn-helix domain. HTH_47 is found at the very C-terminus of DUF2172, which is structurally similar to M28-peptidases but lacking one of the key zinc-binding residues. 77 matched cddid_all.tbl CDD pfam16222 pfam16222 435228 DUF4881 Domain of unknown function (DUF4881). This small family consists of several uncharacterized proteins around 200 residues in length and is mainly found in various Desulfovibrio species. The function of this protein is unknown. 174 matched cddid_all.tbl CDD pfam16223 pfam16223 374442 DUF4882 Domain of unknown function (DUF4882). This small family consists of several uncharacterized proteins around 325 residues in length and is mainly found in various Acinetobacter species. The function of this family is unknown. 267 matched cddid_all.tbl CDD pfam16224 pfam16224 465076 DUF4883 DOmain of unknown function (DUF4883). This family consists of several uncharacterized proteins around 160 residues in length and is mainly found in various Clostridium species. The function of this family is unknown. 118 matched cddid_all.tbl CDD pfam16225 pfam16225 406602 DUF4884 Domain of unknown function (DUF4884). This family consists of several uncharacterized proteins around 90 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 49 matched cddid_all.tbl CDD pfam16226 pfam16226 292843 DUF4885 Domain of unknown function (DUF4885). This family consists of several uncharacterized proteins around 390 residues in length and is mainly found in various Bacillus subtillis species. This family is predicted to be functional in biosynthesis of rhizocticins and antifungal phosphonate oligopeptides, but the specific function of this family is still unknown. 325 matched cddid_all.tbl CDD pfam16227 pfam16227 435229 DUF4886 Domain of unknown function (DUF4886). This domain is mainly found in uncharacterized proteins around 290 residues in length and is mainly found in various Bacteroides species. It has a curved central beta sheet flanked by helices. Distant homolog analysis showed it has a similarity with GDSL-like Lipase/Acylhydrose family. The function of this domain is still unknown. 250 matched cddid_all.tbl CDD pfam16228 pfam16228 374444 DUF4887 Domain of unknown function (DUF4887). This family consists of uncharacterized proteins around 210 residues in length and is mainly found in various Staphylococcus species. The function of this family is unknown. 176 matched cddid_all.tbl CDD pfam16229 pfam16229 292846 DUF4888 Domain of unknown function (DUF4888). This family consists of uncharacterized proteins around 190 residues in length and is mainly found in various Staphylococcus species. The function of this family is unknown. 141 matched cddid_all.tbl CDD pfam16230 pfam16230 406604 DUF4889 Domain of unknown function (DUF4889). This family consists of uncharacterized proteins around 110 residues in length and is mainly found in various Staphylococcus aureus species. The function of this family is unknown. 71 matched cddid_all.tbl CDD pfam16231 pfam16231 435230 DUF4890 Domain of unknown function (DUF4890). This family consists of uncharacterized proteins around 200 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 109 matched cddid_all.tbl CDD pfam16232 pfam16232 435231 DUF4891 Domain of unknown function (DUF4891). This family consists of uncharacterized proteins around 140 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 92 matched cddid_all.tbl CDD pfam16233 pfam16233 406607 DUF4893 Domain of unknown function (DUF4893). This family consists of uncharacterized proteins around 200 residues in length and is mainly found in various Pseudomonas species. The function of this family is unknown. 171 matched cddid_all.tbl CDD pfam16234 pfam16234 435232 DUF4892 Domain of unknown function (DUF4892). This family consists of uncharacterized proteins around 270 residues in length and is mainly found in various Pseudomonas aeruginosa species. The function of this family is unknown. 182 matched cddid_all.tbl CDD pfam16235 pfam16235 406609 DUF4894 Domain of unknown function (DUF4894). A small family of uncharacterized proteins around 180 residues in length and found in various Thermotoga species. The function of this family is unknown. 122 matched cddid_all.tbl CDD pfam16236 pfam16236 406610 DUF4895 Domain of unknown function (DUF4895). A small family of uncharacterized proteins around 250 residues in length and found in various Thermotoga species. The function of this family is unknown. 218 matched cddid_all.tbl CDD pfam16237 pfam16237 406611 DUF4896 Domain of unknown function (DUF4896). A small family of uncharacterized proteins around 50 or 570 residues in length and found in various Thermotoga species. The function of this family is unknown. 44 matched cddid_all.tbl CDD pfam16238 pfam16238 406612 DUF4897 Domain of unknown function (DUF4897). A small family of uncharacterized proteins around 200 residues in length and found in various Thermotoga species. The function of this family is unknown. 152 matched cddid_all.tbl CDD pfam16239 pfam16239 406613 DUF4898 Domain of unknown function (DUF4898). A small family of uncharacterized proteins around 100 residues in length and found in various Sulfolobus species. The function of this family is unknown. 82 matched cddid_all.tbl CDD pfam16240 pfam16240 406614 DUF4899 Domain of unknown function (DUF4899). A small family of uncharacterized proteins around 340 residues in length and found in various Thermotoga and Thermosipho species. The function of this family is unknown. 283 matched cddid_all.tbl CDD pfam16241 pfam16241 435233 DUF4900 Domain of unknown function (DUF4900). This family consists of uncharacterized proteins around 600 residues in length and is mainly found in various Thermotoga and Fervidobaterium species. The function of this family is unknown. 88 matched cddid_all.tbl CDD pfam16242 pfam16242 435234 Pyrid_ox_like Pyridoxamine 5'-phosphate oxidase like. This domain, approximately 140 residues in length, is mainly found in general stress proteins in various Xanthomonas species. It is composed of a six-stranded antiparallel beta-barrel flanked by five alpha-helices and can bind to FMN and FAD, suggesting that it may help the bacteria to react against the oxidative stress induced by the defense mechanisms of the plant. 149 matched cddid_all.tbl CDD pfam16243 pfam16243 374451 Sm_like Sm_like domain. This domain, approximately 150 residues, is mainly found in several uncharacterized proteins in various Prochlorococcus and Synechococcus species. The crystal structure of ECX21941 reveals unexpected similarity to Sm/LSm proteins, which are important RNA-binding proteins, despite no detectable sequence similarity. The specific function of this family is unknown, but the structure analysis of ECX21941 indicates nucleic acid-binding capabilities and suggests a role in RNA and/or DNA processing. 85 matched cddid_all.tbl CDD pfam16244 pfam16244 406616 DUF4901 Domain of unknown function (DUF4901). This family consists of uncharacterized proteins around 470 residues in length and is mainly found in various Bacillus subtilis species. The function of this family is unknown. 228 matched cddid_all.tbl CDD pfam16245 pfam16245 406617 DUF4902 Domain of unknown function (DUF4902). A family of uncharacterized proteins around 140 residues in length and found in various Acidithiobacillacea and Acinetobacter species. It may be functional in extreme acidophile Acidithiobacillus ferrooxidans, but the specific function of this family is unknown. 118 matched cddid_all.tbl CDD pfam16246 pfam16246 406618 DUF4903 Domain of unknown function (DUF4903). A small family of uncharacterized proteins around 210 residues in length and found in various Bacteroides and Prevotella species. The function of this family is unknown. 190 matched cddid_all.tbl CDD pfam16247 pfam16247 292864 DUF4904 Domain of unknown function (DUF4904). This domain, approximately 130 residues in length, is mainly found in several uncharacterized proteins around 340 residues in Actinobacteria, Cyanobacteria and Metazoa species. It is mainly composed of antiparallel beta sheets and has a cystatin-like fold, but the specific function of this family is unknown. 127 matched cddid_all.tbl CDD pfam16248 pfam16248 435235 DUF4905 Domain of unknown function (DUF4905). A small family of uncharacterized proteins around 270 residues in length and found in various Cytophagales, Sphingobacteriaceae and Ignavibacteriaceae species. The function of this family is unknown. 83 matched cddid_all.tbl CDD pfam16249 pfam16249 406619 DUF4906 Domain of unknown function (DUF4906). A family of uncharacterized proteins around 300 residues in length and found in various Bacteroides species. The function of this family is unknown. 203 matched cddid_all.tbl CDD pfam16250 pfam16250 435236 DUF4907 Domain of unknown function (DUF4907). A family of uncharacterized proteins around 110 residues in length and found in various Bacteroides species. The function of this family is unknown. 65 matched cddid_all.tbl CDD pfam16251 pfam16251 406621 bCoV_NAB Betacoronavirus nucleic acid-binding (NAB). This is the nucleic acid-binding domain (NAB) from the multidomain nonstructural protein NSP3, and described as NSP3e domain. NSP3 is part of Orf1a polyproteins in SARS-CoV. It is an essential component of the replication/transcription complex. The global domain of the NAB represents a new fold, with a parallel four-strand beta-sheet holding two alpha-helices of three and four turns that are oriented antiparallel to the beta-strands and a group of residues form a positively charged patch on the protein surface as the binding site responsible for binding affinity for nucleic acids. When binding to ssRNA, the NAB prefers sequences with repeats of three consecutive Gs, such as (GGGA)5 and (GGGA)2. A positively charged surface patch (Lys75, Lys76, Lys99, and Arg106) is involved in RNA binding. 129 matched cddid_all.tbl CDD pfam16252 pfam16252 435237 DUF4908 Domain of unknown function (DUF4908). A small family of uncharacterized proteins around 260 residues in length and found in various Caulobacter and Brevundimonas species. The function of this family is unknown. 221 matched cddid_all.tbl CDD pfam16253 pfam16253 292870 DUF4909 Domain of unknown function (DUF4909). This family of proteins is found in bacteria. Proteins in this family are approximately 160 amino acids in length. Several members are associated with vancomycin virulence in Staph. aureus in some way. These proteins are all lipoproteins, carrying the characteriztic prokaryotic membrane-attachment site at their N-termini. 127 matched cddid_all.tbl CDD pfam16254 pfam16254 406622 DUF4910 Domain of unknown function (DUF4910). 339 matched cddid_all.tbl CDD pfam16255 pfam16255 435238 Lipase_GDSL_lke GDSL-like Lipase/Acylhydrolase. 203 matched cddid_all.tbl CDD pfam16256 pfam16256 435239 DUF4911 Domain of unknown function (DUF4911). This family consists of uncharacterized proteins around 75 residues in length and is mainly found in various Thermotogav species. The function of this family is unknown. 57 matched cddid_all.tbl CDD pfam16257 pfam16257 406624 UxaE tagaturonate epimerase. This family consists of uncharacterized proteins around 500 residues in length and is mainly found in various Bacteria species, such as Thermotoga, Paenibacillus and Rhodothermus. A newly recognized enzyme from the galacturonate utilization pathway in T. maritima with tagaturonate epimerase activity. 475 matched cddid_all.tbl CDD pfam16258 pfam16258 435240 DUF4912 Domain of unknown function (DUF4912). This family consists of uncharacterized proteins around 160 residues in length and is mainly found in various Clostridium species. The function of this family is unknown. 117 matched cddid_all.tbl CDD pfam16259 pfam16259 435241 DUF4913 Domain of unknown function (DUF4913). This family consists of uncharacterized proteins around 150 residues in length and is mainly found in various Arthrobacter species. The function of this family may be functional in enableing the growth of Arthrobacter sp. strain JBH1 with nitroglycerin as the sole source of carbon and nitrogen. 104 matched cddid_all.tbl CDD pfam16260 pfam16260 406627 DUF4914 Domain of unknown function (DUF4914). This family consists of uncharacterized proteins around 630 residues in length and is mainly found in various Thermotoga, Thermoanaerobacter and Carboxydibrachium species. The function of this family is unknown. 606 matched cddid_all.tbl CDD pfam16261 pfam16261 435242 DUF4915 Domain of unknown function (DUF4915). This family consists of uncharacterized proteins around 370 residues in length and is mainly found in various species, such as Shewanella, Rheinheimera, Saccharophagus, Leptolyngbya and so on. It contains serveral TPR repeat-containing proteins. The function of this family is unknown. 316 matched cddid_all.tbl CDD pfam16262 pfam16262 435243 DUF4916 Domain of unknown function (DUF4916). This domain family consists of uncharacterized proteins around 175 residues in length and is mainly found in various Streptomyces species. The function of this family is unknown. This family is related to the NUDIX hydrolases. 169 matched cddid_all.tbl CDD pfam16263 pfam16263 374458 DUF4917 Domain of unknown function (DUF4917). This family consists of uncharacterized proteins around 340 residues in length and is mainly found in various Burkholderia and Brucella species. The function of this family is unknown. 311 matched cddid_all.tbl CDD pfam16264 pfam16264 435244 SatD SatD family (SatD). This family consists of uncharacterized proteins around 220 residues in length and is mainly found in various Streptococcus species. The function of this family is involved in acid resistance. 211 matched cddid_all.tbl CDD pfam16265 pfam16265 406630 DUF4918 Domain of unknown function (DUF4918). This family consists of uncharacterized proteins around 230 residues in length and is mainly found in various Listeria species. The function of this family is unknown. 224 matched cddid_all.tbl CDD pfam16266 pfam16266 406631 DUF4919 Domain of unknown function (DUF4919). This family consists of uncharacterized proteins around 230 residues in length and is mainly found in various Bacteroides and Prevotella species. The function of this family is unknown. 184 matched cddid_all.tbl CDD pfam16267 pfam16267 435245 DUF4920 Domain of unknown function (DUF4920). This family consists of uncharacterized proteins around 190 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 87 matched cddid_all.tbl CDD pfam16268 pfam16268 435246 DUF4921 Domain of unknown function (DUF4921). This family consists of uncharacterized proteins around 450 residues in length and is mainly found in various Corynebacterium species. Several proteins are predicted as galactose-1-phosphate uridylytransferases. The function of this family is unknown. 425 matched cddid_all.tbl CDD pfam16269 pfam16269 465077 DUF4922 Domain of unknown function (DUF4922). This family consists of uncharacterized proteins around 310 residues in length and is mainly found in various Bacteroides and Parabacteroides species. Several members are annotated as putative glycosyltransferases, but the specific function of this family is still unknown. 146 matched cddid_all.tbl CDD pfam16270 pfam16270 435248 DUF4923 Lipocalin-like domain (DUF4923). This family consists of uncharacterized proteins around 200 residues in length and is mainly found in various Bacteroides and Parabacteroides species. The function of this family is unknown. This domain is distantly related to lipocalins. 175 matched cddid_all.tbl CDD pfam16271 pfam16271 435249 DUF4924 Domain of unknown function (DUF4924). This family consists of uncharacterized proteins around 180 residues in length and is mainly found in various Parabacteroides and Bacteroides species. The function of this family is unknown. 179 matched cddid_all.tbl CDD pfam16272 pfam16272 435250 DUF4925 Domain of unknown function (DUF4925). This family consists of uncharacterized proteins around 400 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 324 matched cddid_all.tbl CDD pfam16273 pfam16273 465078 NuDC Nuclear distribution C domain. This domain, approximately 40-50 residues in length, is mainly found in nuclear migration proteins in various Mammalia species. It may play a role not only in mitosis and cytokinesis, but also in interkinetic nuclear migration and neuronal migration during neocortical development. 66 matched cddid_all.tbl CDD pfam16274 pfam16274 465079 Qua1 Qua1 domain. This domain, approximately 40 residues in length, is mainly found in KH-domain containing, RNA-binding, signal transduction-associated protein 1 from yeast to human. It forms a homodimer composed of a perpendicular interaction of two helical hairpins, and the Qua1 domain is sufficient for homodimerization which is required for the regulation of alternative splicing. 52 matched cddid_all.tbl CDD pfam16275 pfam16275 465080 SF1-HH Splicing factor 1 helix-hairpin domain. This domain, approximately 100 residues in length, is mainly found in splicing factor 1 from yeast to human. It is a helix-hairpin domain, which forms a secondary, hydrophobic interface with U2AF65(UHM) to lock the orientation of the two subunits, which is essential for cooperative formation of the ternary SF1-U2AF65-RNA complex. In this domain, it contains a highly conserved SPSP motif in its C terminal and phophorylation of SPSP motif induces a disorder-to-order transition within a novel SF1/U2AF65 interface, indicating a phosphorylation-dependent control of pre-mRNA splicing factors. 114 matched cddid_all.tbl CDD pfam16276 pfam16276 465081 NPM1-C Nucleophosmin C-terminal domain. This domain, approximately 50 residues in length, is mainly found in Nucleophosmin proteins in mammalia species. Nucleophosmin, a nucleocytoplasmic shuttling protein, is related with cancer and involved in serveral cellluar functions, such as ribosome maturatation and export, centrosome duplication, and response to stress stimuli. This domain has a three-helix bundle which can bind G-quadruplex DNA and the interaction involves helices H1 and H2 of the NPM1-C domain mainly through electrostatic contacts with G-quadruplex phosphates, indicating a crucial role in rescuring its function in leukemia. 49 matched cddid_all.tbl CDD pfam16277 pfam16277 435253 DUF4926 Domain of unknown function (DUF4926). This family consists of uncharacterized proteins around 70 residues in length and is mainly found in various Caulobacter, Microcystis and Cyanothece species. The function of this family is unknown. 57 matched cddid_all.tbl CDD pfam16278 pfam16278 465082 zf-C2HE C2HE / C2H2 / C2HC zinc-binding finger. zf-C2HE is an unusual zinc-binding domain found in fungi, plants and metazoa. It is often found at the C-terminus of HIT-domain-containing proteins, pfam01230. In fungi the fourth ligand is a Glu, in plants it is Cys and in metazoans it is usually a His. The fourth ligand is often mutated in neurogenerative disease-states. 60 matched cddid_all.tbl CDD pfam16279 pfam16279 465083 DUF4927 Domain of unknown function (DUF4927). This family, around 80 residues, consists of uncharacterized and nuclear receptor coactivator 2 proteins and is mainly found in mammalia species. The specific function of this family is still unknown. 87 matched cddid_all.tbl CDD pfam16280 pfam16280 374468 DUF4928 Domain of unknown function (DUF4928). This family consists of uncharacterized proteins around 330 residues in length and is mainly found in various Bacteria species, such as Enterobacteriales, Clostridiales, Actinomycetales and so on. The function of this family is unknown. 306 matched cddid_all.tbl CDD pfam16282 pfam16282 465084 SANT_DAMP1_like SANT/Myb-like domain of DAMP1. This domain, approximately 90 residues, is mainly found in DNA methyltransferase 1-associated protein 1 (DAMP1) that plays an important role in development and maintenace of genome integrity in various mammalia species. It mainly consists of tandem repeats of three alpha-helices that are arranged in a helix-turn-helix motif and shows a structual similarity with SANT domain and Myb DNA-binding domain, indicating it contains a putative DNA binding site. 80 matched cddid_all.tbl CDD pfam16283 pfam16283 406646 DUF4929 Domain of unknown function (DUF4929). This family consists of uncharacterized proteins around 400 residues in length and is mainly found in various species, such as Bacteroides, Capnocytophaga and Prevotella. The function of this family is unknown. 366 matched cddid_all.tbl CDD pfam16284 pfam16284 374471 DUF4930 Domain of unknown function (DUF4930). A small family of uncharacterized proteins around 150 residues in length and found in various Staphylococcus aureus species. The function of this family is unknown. 144 matched cddid_all.tbl CDD pfam16285 pfam16285 406647 DUF4931 Domain of unknown function (DUF4931). This family consists of uncharacterized proteins around 270 residues in length and is mainly found in various Bacillus cereus species. Some members of this family are annotated as Galactose-1-phosphate uridylyltransferases, but the specific function of this family is unknown. 245 matched cddid_all.tbl CDD pfam16286 pfam16286 406648 DUF4932 Domain of unknown function (DUF4932). This family consists of uncharacterized proteins around 460 residues in length and is mainly found in various Bacteroides species, such as Bacteroides fragilis, Bacteroides sp. and so on. Several members are annotated as putative metalloproteases, but the specific function of this family is unknown. 330 matched cddid_all.tbl CDD pfam16287 pfam16287 406649 DUF4933 Domain of unknown function (DUF4933). This family consists of uncharacterized proteins around 450 residues in length and is mainly found in various species, such as Bacteroides and Parabacteroides. Several members are annotated as putative transmembrane proteins, but the specific function of this family is unknown. 386 matched cddid_all.tbl CDD pfam16288 pfam16288 435257 DUF4934 Domain of unknown function (DUF4934). This family consists of uncharacterized proteins around 400 residues in length and is mainly found in various Bacteroides species, such as Bacteroides fragilis and Bacteroides sp. The function of this family is unknown. 102 matched cddid_all.tbl CDD pfam16289 pfam16289 435258 PIN_12 PIN domain. This domain is found on the N-terminal region of uncharacterized proteins. It shows homology to other PIN-like families and contains several acidic residues critical for chelating metal ions that are conserved in other PIN-like domains. 171 matched cddid_all.tbl CDD pfam16290 pfam16290 406652 DUF4936 Domain of unknown function (DUF4936). This family consists of uncharacterized proteins around 100 residues in length and is mainly found in various Burkholderiales species, such as Herbaspirillum, Cupriavidus, Ralstonia and so on. The function of this family is unknown. 87 matched cddid_all.tbl CDD pfam16291 pfam16291 406653 DUF4937 Domain of unknown function (DUF4937. This family consists of uncharacterized proteins around 120 residues in length and is mainly found in various Bacillus species, such as Bacillus subtilis and Bacillus amyloliquefaciens. Several members are annotated as ydbC, but the specific function of this family is unknown. 89 matched cddid_all.tbl CDD pfam16292 pfam16292 292908 DUF4938 Domain of unknown function (DUF4938). A small family consists of several uncharacterized proteins around 300 residues in length and is mainly found in various Chloroflexus, Comamonas, Delfitia, Rubrivivax and Roseiflexus species. Several members are annotated as cyanophycin synthetases, but the function of this family is unknown. 302 matched cddid_all.tbl CDD pfam16293 pfam16293 406654 zf-C2H2_9 C2H2 type zinc-finger (1 copy). 57 matched cddid_all.tbl CDD pfam16294 pfam16294 465085 RSB_motif RNSP1-SAP18 binding (RSB) motif. The RSB motif on the Acinus protein is the core around which the ASAP complex is built. The apoptosis and splicing-associated protein complex, ASAP, is made up of three proteins, SAP18 (Sin3-associated protein of 18 kDa), RNA-binding protein S1 (RNPS1) and apoptotic chromatin inducer in the nucleus (Acinus). The ASAP complex appears to be an assembly of proteins at the interface between transcription, splicing and NMD, acting as a hub in the network of protein-interactions that regulate gene-expression. 91 matched cddid_all.tbl CDD pfam16295 pfam16295 292911 TetR_C_10 Tetracyclin repressor-like, C-terminal domain. This domain belongs to the TetR family of transcription factors. It is found in FadR, a fatty acyl-CoA dependent transcription factor that regulates genes encoding proteins involved in fatty-acid degradation and synthesis pathways. Structural and functional analysis indicate that B. subtilis FadR belongs to the TetR family of transcription factors, where it represses five fad operons involved in the fatty acid beta-oxidation cycle. FadR directly binds to upstream regions of the fadR, fadH, fadN, lcfB and fadF genes, and is deactivated by binding with long-chain acyl-CoAs in a similar manner as E. coli FadR. 132 matched cddid_all.tbl CDD pfam16296 pfam16296 435260 TM_PBP2_N N-terminal of TM subunit in PBP-dependent ABC transporters. This family mainly consists of Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs, such as Binding-protein-dependent transport systems inner membrane component and Maltose transport permease MalF. It is around 580 residues in length and is mainly found in various species, such as Thermotoga, Dictyoglomus, Thermosipho, Fervidobacterium, Mesotoga and so on. The function of this family is unknown. 79 matched cddid_all.tbl CDD pfam16297 pfam16297 465086 DUF4939 Domain of unknown function (DUF4939). This family consists of uncharacterized proteins around 110 residues in length and is mainly found in various mammalia species. LDOC1, a member of this family and a novel MZF-1-interacting protein, inhibits NF-kappaB activation and relates with cancer and some other diseases. But the specific function of this family is still unknown. 112 matched cddid_all.tbl CDD pfam16298 pfam16298 406658 DUF4940 Domain of unknown function (DUF4940). This family consists of several uncharacterized proteins around 250 residues in length and is mainly found in various Thermotoga species. The function of this family is unknown. 206 matched cddid_all.tbl CDD pfam16299 pfam16299 406659 DUF4941 Domain of unknown function (DUF4941). This family consists of several uncharacterized proteins around 300 residues in length and is mainly found in various Thermotoga species. The function of this family is unknown. 265 matched cddid_all.tbl CDD pfam16300 pfam16300 465087 WD40_4 Type of WD40 repeat. Most members of this family form part of the 7-bladed beta-propeller at the N-terminus of coronin proteins. 44 matched cddid_all.tbl CDD pfam16301 pfam16301 435262 DUF4943 Domain of unknown function (DUF4943). This small family consists of several uncharacterized proteins around 170 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 150 matched cddid_all.tbl CDD pfam16302 pfam16302 292918 DUF4944 Domain of unknown function (DUF4944). This family consists of uncharacterized proteins around 160 residues in length and is mainly found in various Bacillus species. The function of this family is unknown. 128 matched cddid_all.tbl CDD pfam16303 pfam16303 435263 DUF4945 Domain of unknown function (DUF4945). This small family consists of uncharacterized proteins around 140 residues in length and is mainly found in various Bacteroides species, such as Bacteroides fragilis and Bacteroides sp.. The function of this family is unknown. 120 matched cddid_all.tbl CDD pfam16304 pfam16304 435264 DUF4946 Domain of unknown function (DUF4946). This small family consists of uncharacterized proteins around 180 residues in length and is mainly found in various Pseudomonas species, especially in Pseudomonas aeruginosa. The function of this family is unknown. 152 matched cddid_all.tbl CDD pfam16305 pfam16305 406661 DUF4947 Domain of unknown function (DUF4947). This small family consists of uncharacterized proteins around 220 residues in length and is mainly found in various Streptococcus mutans species. The function of this family is unknown. 169 matched cddid_all.tbl CDD pfam16306 pfam16306 435265 DUF4948 Domain of unknown function (DUF4948). This small family consists of uncharacterized proteins around 200 residues in length and is mainly found in various Bacteroides, Paraprevotella, Parabacteroides and Alistipes species. The function of this family is unknown. 171 matched cddid_all.tbl CDD pfam16307 pfam16307 435266 DUF4949 Domain of unknown function (DUF4949). This small family consists of uncharacterized proteins around 140 residues in length and is mainly found in various Legionella pneumophila and longbeachae species. The function of this family is unknown. 110 matched cddid_all.tbl CDD pfam16308 pfam16308 292924 DUF4950 Domain of unknown function (DUF4950). This family consists of several uncharacterized proteins around 250 residues in length and is mainly found in various Enterococcus faecalis species. The function of this family is unknown. 191 matched cddid_all.tbl CDD pfam16309 pfam16309 339686 DUF4951 Domian of unknown function (DUF4951). This family consists of several uncharacterized proteins around 125 residues in length and is mainly found in various Acinetobacter baumannii species. The function of this family is unknown. 83 matched cddid_all.tbl CDD pfam16310 pfam16310 374481 DUF4952 Domian of unknown function (DUF4952). This family consists of several uncharacterized proteins around 150 residues in length and is mainly found in various Leptospira, Pseudomonas, Stenotrophomonas and Desulfovibrio species. The function of this family is unknown. 77 matched cddid_all.tbl CDD pfam16311 pfam16311 465088 TMEM100 Transmembrane protein 100. This family of proteins is found in eukaryotes. Proteins in this family are approximately 130 amino acids in length. There is some apparent similarity with family the phosphoinositide-interacting protein family PIRT, pfam15099, because those proteins are also transmembrane proteins. 133 matched cddid_all.tbl CDD pfam16312 pfam16312 465089 Oberon_cc Coiled-coil region of Oberon. Oberon_cc is the coiled-coil region of Oberon proteins from plants. Oberon is necessary for maintenance and/or establishment of both the shoot and root apical meristems in Arabidopsis. Most Oberon proteins carry a PHD finger domain, pfam07227 and this coiled-coil domain. Oberon proteins mediate the TMO7 (the direct target of MP) expression through modification of, or binding to, chromatin at the TMO7 locus. TMO7 stands for the target of Monopteros 7 (or Auxin response factor 7). 129 matched cddid_all.tbl CDD pfam16313 pfam16313 435269 DUF4953 Met-zincin. This is a family of uncharacterized proteins that carry the highly characteriztic met-zincin mmotif HExxHxxGxxH, the extended zinc-binding domain of metallopeptidases. 319 matched cddid_all.tbl CDD pfam16314 pfam16314 435270 DUF4954 Domain of unknown function (DUF4954). This family consists of uncharacterized proteins around 660 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown. 653 matched cddid_all.tbl CDD pfam16315 pfam16315 435271 DUF4955 Domain of unknown function (DUF4955). This family consists of uncharacterized proteins around 850 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown. 147 matched cddid_all.tbl CDD pfam16316 pfam16316 435272 DUF4956 Domain of unknown function (DUF4956). This family consists of uncharacterized proteins around 220 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown. 169 matched cddid_all.tbl CDD pfam16317 pfam16317 435273 Glyco_hydro_99 Glycosyl hydrolase family 99. This domain, around 350 residues, is mainly found in some uncharacterized proteins from bacteroides to human. Some proteins in this family, annotated as endo-alpha-mannosidases cleave mannoside linkages internally within an N-linked glycan chain, short circuiting the classical N-glycan biosynthetic pathway. This domain reveals a (beta-alpha)(8) barrel fold in which the catalytic centre is present in a long substrate-binding groove, consistent with cleavage within the N-glycan chain, providing a foundation upon which to develop new enzyme inhibitors targeting the hijacking of N-glycan synthesis in viral disease and cancer. 341 matched cddid_all.tbl CDD pfam16318 pfam16318 465090 DUF4957 Domain of unknown function (DUF4957). This family consists of uncharacterized proteins around 150 residues in length and is mainly found in various Bacteroides and Prevotella species. The function of this protein is unknown. 141 matched cddid_all.tbl CDD pfam16319 pfam16319 406670 DUF4958 Domain of unknown function (DUF4958). This family consists of uncharacterized proteins around 720 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown. 731 matched cddid_all.tbl CDD pfam16320 pfam16320 465091 Ribosomal_L12_N Ribosomal protein L7/L12 dimerization domain. This is the N-terminal dimerization domain of ribosomal protein L7/L12. 48 matched cddid_all.tbl CDD pfam16321 pfam16321 435275 Ribosom_S30AE_C Sigma 54 modulation/S30EA ribosomal protein C terminus. This domain often occurs at the C-terminus of proteins containing pfam02482. 54 matched cddid_all.tbl CDD pfam16322 pfam16322 465092 Tub_N Tubby N-terminal. Tub_N is the N-terminal region of Tubby proteins. It carries a nuclear localization signal and is able to activate transcription. 196 matched cddid_all.tbl CDD pfam16323 pfam16323 465093 DUF4959 Domain of unknown function (DUF4959). This family consists of uncharacterized proteins around 400 residues in length and is mainly found in various Bacteroides, Pedobacter and Parabacteroides species. Several proteins are annotated as Galactose-binding like proteins, but the specific function of this protein is unknown. 106 matched cddid_all.tbl CDD pfam16324 pfam16324 435277 DUF4960 Domain of unknown function (DUF4960). This family consists of uncharacterized proteins around 460 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown. 250 matched cddid_all.tbl CDD pfam16325 pfam16325 465094 Peptidase_U32_C Peptidase family U32 C-terminal domain. This domain is found at the C-terminus of many members of Peptidase family U32 (pfam01136). 79 matched cddid_all.tbl CDD pfam16326 pfam16326 465095 ABC_tran_CTD ABC transporter C-terminal domain. This domain is found at the C-terminus of ABC transporters. It has a coiled coil structure with an atypical 3(10)-helix in the alpha-hairpin region. It is involved in DNA_binding. 69 matched cddid_all.tbl CDD pfam16327 pfam16327 465096 CcmF_C Cytochrome c-type biogenesis protein CcmF C-terminal. This C-terminal region of CcmF, one of the cytochrome c-type biogenesis proteins, is associated at the C-terminal with Cytochrome_C_asm family pfam01578. It is possible that it is this domain which delivers reductant to haem on CcmE. 325 matched cddid_all.tbl CDD pfam16328 pfam16328 292944 DUF4961 Domain of unknown function (DUF4961). This small family consists of several uncharacterized proteins around 350 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown. 317 matched cddid_all.tbl CDD pfam16329 pfam16329 318535 Pestivirus_E2 Pestivirus envelope glycoprotein E2. 372 matched cddid_all.tbl CDD pfam16330 pfam16330 435281 MukB_hinge MukB hinge domain. The hinge domain of chromosome partition protein MukB is responsible for dimerization and is also involved in protein-DNA interactions and conformational flexibility. 167 matched cddid_all.tbl CDD pfam16331 pfam16331 435282 TolA_bind_tri TolA binding protein trimerization. This is the N-terminal domain of the YbgF protein. YbgF binds to TolA. This domain mediates trimerization. 72 matched cddid_all.tbl CDD pfam16332 pfam16332 435283 DUF4962 Domain of unknown function (DUF4962). This family consists of uncharacterized proteins around 870 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown. 474 matched cddid_all.tbl CDD pfam16334 pfam16334 435284 DUF4964 Domain of unknown function (DUF4964). This family consists of uncharacterized proteins around 840 residues in length and is mainly found in various Bacteroides species. Several proteins in this family are annotated as Glutaminases, but the function of this protein is unknown. 87 matched cddid_all.tbl CDD pfam16335 pfam16335 465097 DUF4965 Domain of unknown function (DUF4965). This family consists of uncharacterized proteins around 840 residues in length and is mainly found in various Bacteroides species. Several proteins in this family are annotated as Glutaminases, but the function of this protein is unknown. 174 matched cddid_all.tbl CDD pfam16338 pfam16338 465098 AGL_N Alpha-glucosidase, N-terminal. This domain is found in some members of the glycosyl hydrolase 31 family: alpha-glucosidase 2, alpha-xylosidase and alpha-glucosidase 31B. The function of this domain is unknown. It has a beta- sandwich fold and is adjacent the central catalytic unit. 90 matched cddid_all.tbl CDD pfam16339 pfam16339 318542 DUF4969 Domain of unknown function (DUF4969). This small family consists of several uncharacterized proteins around 540 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown. 79 matched cddid_all.tbl CDD pfam16341 pfam16341 406685 DUF4971 Domain of unknown function (DUF4971). This small family consists of uncharacterized proteins around 370 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown. 139 matched cddid_all.tbl CDD pfam16342 pfam16342 435287 DUF4972 Domain of unknown function (DUF4972). This family consists of uncharacterized proteins around 490 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown. 128 matched cddid_all.tbl CDD pfam16343 pfam16343 435288 DUF4973 Domain of unknown function (DUF4973). This family consists of uncharacterized proteins around 340 residues in length and is mainly found in various Bacteroides and Prevotella species. The function of this protein is unknown. 129 matched cddid_all.tbl CDD pfam16344 pfam16344 435289 DUF4974 Domain of unknown function (DUF4974). This family consists of uncharacterized proteins around 340 residues in length and is mainly found in various Bacteroides and Parabacterodies species. The function of this protein is unknown. 70 matched cddid_all.tbl CDD pfam16346 pfam16346 435290 DUF4975 Domain of unknown function (DUF4975). This family consists of uncharacterized proteins around 500 residues in length and is mainly found in various Bacteroides species. Several proteins in this family are annotated as Glycosyl hydrolases, but the function of this protein is unknown. 176 matched cddid_all.tbl CDD pfam16347 pfam16347 406689 DUF4976 Domain of unknown function (DUF4976). This family consists of uncharacterized proteins around 530 residues in length and is mainly found in various Bacteroides species. Several proteins in this family are annotated as Arylsulfatases, but the function of this protein is unknown. 103 matched cddid_all.tbl CDD pfam16348 pfam16348 465099 CoV_NSP4_C Coronavirus replicase NSP4, C-terminal. This is the C-terminal domain of the coronavirus nonstructural protein 4 (NSP4). NSP4 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. It is a membrane-spanning protein which is thought to anchor the viral replication-transcription complex (RTC) to modified endoplasmic reticulum membranes. This predominantly alpha-helical domain may be involved in protein-protein interactions. It has been shown that in Betacoronavirus, the coexpression of NSP3 and NSP4 results in a membrane rearrangement to induce double-membrane vesicles (DMVs) and convoluted membranes (CMs), playing a critical role in SARS-CoV replication. There are two well conserved amino acid residues (H120 and F121) in NSP4 among Betacoronavirus, essential for membrane rearrangements during interaction with NSP3. 92 matched cddid_all.tbl CDD pfam16349 pfam16349 406691 DUF4978 Domain of unknown function (DUF4978). This family consists of uncharacterized proteins around 540 residues in length and is mainly found in various Bacteroides and Prevotella species. Several proteins in this family are annotated as Glycoside hydrolases, but the function of this protein is unknown. 172 matched cddid_all.tbl CDD pfam16350 pfam16350 465100 FAO_M FAD dependent oxidoreductase central domain. This domain occurs in several FAD dependent oxidoreductases: Sarcosine dehydrogenase, Dimethylglycine dehydrogenase and Dimethylglycine dehydrogenase. It is situated between the DAO domain (pfam01266) and the GCV_T domain (pfam01571). 56 matched cddid_all.tbl CDD pfam16351 pfam16351 435292 DUF4979 Domain of unknown function (DUF4979). This family consists of uncharacterized proteins around 450 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown. 161 matched cddid_all.tbl CDD pfam16352 pfam16352 435293 DUF4980 Domain of unknown function (DUF4980). This family consists of uncharacterized proteins around 610 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown. 102 matched cddid_all.tbl CDD pfam16353 pfam16353 465101 LacZ_4 Beta-galactosidase, domain 4. This entry represents domain 4 found in beta-galactosidase and it is organized in a jelly-roll type barrel (Rutkiewicz-Krotewicz M. et al. Crystals 2018, 8(1), 13, https://doi.org/10.3390/cryst8010013). 88 matched cddid_all.tbl CDD pfam16355 pfam16355 465102 DUF4982 Domain of unknown function (DUF4982). This family is found in the C-terminal of uncharacterized proteins and beta-galactosidases around 680 residues in length from various Bacteroides species. The function of this protein is unknown. 62 matched cddid_all.tbl CDD pfam16356 pfam16356 374498 DUF4983 Domain of unknown function (DUF4983). This family consists of uncharacterized proteins around 600 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown. 93 matched cddid_all.tbl CDD pfam16357 pfam16357 374499 PepSY_TM_like_2 Putative PepSY_TM-like. This is a family of bacterial proteins with three PepSY-like TM regions. 197 matched cddid_all.tbl CDD pfam16358 pfam16358 435296 RcsF RcsF lipoprotein. The RcsF lipoprotein is a component of the Rcs signaling system. It activates the Rcs system by transmitting signals from the cell suface to the histidine kinase RcsC. 110 matched cddid_all.tbl CDD pfam16359 pfam16359 435297 RcsD_ABL RcsD-ABL domain. This domain is part of the RcsD histidine kinase. It recognizes the effector domain of RcsB. 103 matched cddid_all.tbl CDD pfam16360 pfam16360 465103 GTP-bdg_M GTP-binding GTPase Middle Region. This family locates between the N-terminal domain and MMR_HSR1 50S ribosome-binding GTPase of GTP-binding HflX-like proteins. The full-length members bind and interact with the 50S ribosome and are GTPases, hydrolysing GTP/GDP/ATP/ADP. This region is unknown for its function. 79 matched cddid_all.tbl CDD pfam16361 pfam16361 435299 Peptidase_S8_N N-terminal of Subtilase family. This is the N-terminal of Peptidase_S8 of subtilase family. It is around 100 residues in length from various Bacteroides species. The function of this family is unknown. 142 matched cddid_all.tbl CDD pfam16362 pfam16362 435300 YaiA YaiA protein. This family of proteins is found in Enterobacteriaceae, where they are immediately downstream of a Shikimate kinase. 62 matched cddid_all.tbl CDD pfam16363 pfam16363 465104 GDP_Man_Dehyd GDP-mannose 4,6 dehydratase. 327 matched cddid_all.tbl CDD pfam16364 pfam16364 435302 Antigen_C Cell surface antigen C-terminus. This repeated domain is found at the C-terminus of cell surface antigens. In the Streptococcus mutans antigen I/II there are three repeats of this domain, a cleft between the first two of these forms a binding site for the human salivary agglutinin (SAG). 171 matched cddid_all.tbl CDD pfam16365 pfam16365 292975 EutK_C Ethanolamine utilization protein EutK C-terminus. This is the C-terminal domain of the ethanolamine utilization protein EutK. It is a helix-turn-helix domain and is predicted to bind to nucleic acids. 55 matched cddid_all.tbl CDD pfam16366 pfam16366 465105 CEBP_ZZ Cytoplasmic polyadenylation element-binding protein ZZ domain. This ZZ-type zinc finger domain binds zinc via two conserved histidines in the C-terminal part of the domain. 56 matched cddid_all.tbl CDD pfam16367 pfam16367 465106 RRM_7 RNA recognition motif. 91 matched cddid_all.tbl CDD pfam16368 pfam16368 465107 CEBP1_N Cytoplasmic polyadenylation element-binding protein 1 N-terminus. This is the N-terminal domain of cytoplasmic polyadenylation element-binding protein 1. 307 matched cddid_all.tbl CDD pfam16369 pfam16369 465108 GH43_C C-terminal lipocalin-like domain. This is the C-terminal domain of Glycosyl hydrolases family 43. It is around 100 residues in length from various Bacteroides species. The function of this family is unknown. The domain is distantly related to lipocalins. 107 matched cddid_all.tbl CDD pfam16370 pfam16370 435306 MetallophosC C terminal of Calcineurin-like phosphoesterase. This is the C-terminal of Calcineurin-like phosphoesterases. It is around 150 residues in length from various Bacteroides species. The function of this family is unknown. 160 matched cddid_all.tbl CDD pfam16371 pfam16371 435307 MetallophosN N terminal of Calcineurin-like phosphoesterase. This is the N-terminal of Calcineurin-like phosphoesterases. It is around 150 residues in length from various Bacteroides species. The function of this family is unknown. 73 matched cddid_all.tbl CDD pfam16372 pfam16372 435308 DUF4984 Domain of unknown function (DUF4984). This domain is around 150 residues long and is located in the C-terminal of some uncharacterized proteins in various Bacteroides and Prevotella species. The function of this domain remains unknown. 161 matched cddid_all.tbl CDD pfam16373 pfam16373 435309 DUF4985 Domain of unknown function. This family around 100 residues locates in the C-terminal of some uncharacterized proteins in various Bacteroides, Prevotella and Prevotella species. The function of this family remains unknown. 114 matched cddid_all.tbl CDD pfam16374 pfam16374 406712 CIF Cycle inhibiting factor (CIF). Cycle inhibiting factors (Cif) are bacterial effectors that interfere with the eukarytoc cell cycle. CIF induce an irreversible cell cycle arrest upon injection into host cell. CIF blocks degradation of cyclin -dependent kinase inhibitors p21 and p27, inducing their accumulation in the cell. The x-ray crystal structure of Cif reveals it to be a divergent member of a superfamily of enzymes including cysteine proteases and acetyltransferases. 138 matched cddid_all.tbl CDD pfam16375 pfam16375 435310 DUF4986 Domain of unknown function. This family around 150 residues locates in the C-terminal of some uncharacterized proteins in various Bacteroides and Bacillus species. The function of this family remains unknown. 82 matched cddid_all.tbl CDD pfam16376 pfam16376 292986 fragilysinNterm N-terminal domain of fragilysin. N-terminal domain of fragilysin, an extracellular metalloprotease toxin, which is primary virulence factor of B. fragilis, an oportunistic pathogen of human gut. The N-terminal domain of fragilysin inhibits fragilysin and is cleaved in a mature, virulent form. 144 matched cddid_all.tbl CDD pfam16377 pfam16377 435311 DUF4987 Domain of unknown function. This family around 150 residues locates in the C-terminal of some uncharacterized proteins in various Bacteroides and Prevotella species. The function of this family remains unknown. 153 matched cddid_all.tbl CDD pfam16378 pfam16378 435312 DUF4988 Domain of unknown function. This family around 200 residues locates in the N-terminal of some uncharacterized proteins in various Bacteroides and Alistipes species. The function of this family remains unknown. The N-terminus of this model has been clipped by ~30 residues as it was capturing parts of collagen sequences, pfam01391. 182 matched cddid_all.tbl CDD pfam16379 pfam16379 339721 DUF4989 Domain of unknown function (DUF4989). This family around 300 residues locates in the N-terminal of some uncharacterized proteins in various Bacteroides and Alistipes species. The function of this family remains unknown. This entry contains a duplication of a DUF1735-like domain. 293 matched cddid_all.tbl CDD pfam16380 pfam16380 406716 DUF4990 Domain of unknown function. This family around 150 residues locates in the C-terminal of some uncharacterized proteins in various Bacteroides species. The function of this family remains unknown. 142 matched cddid_all.tbl CDD pfam16381 pfam16381 406717 Coatomer_g_Cpla Coatomer subunit gamma-1 C-terminal appendage platform. Coatomer_g_Cpla is the very C-terminal domain of the eukaryotic Coatomer subunit gamma-1 proteins. It acts as a platform domain to the C-terminal appendage. It carries one single protein/protein interaction site, which is the binding site for ARFGAP2 or ADP-ribosylation factor GTPase-activating protein. COPI-coated vesicles mediate retrograde transport from the Golgi back to the ER and intra-Golgi transport. The gamma-COPI is part of one of two subcomplexes that make up the heptameric coatomer complex along with the beta, delta and zeta subunits. 114 matched cddid_all.tbl CDD pfam16383 pfam16383 406718 DUF4992 Domain of unknown function. This family around 150 residues locates in the N-terminal of some uncharacterized proteins in various Bacteroides and Prevotella species. The function of this family remains unknown. 182 matched cddid_all.tbl CDD pfam16384 pfam16384 435313 DUF4993 Domain of unknown function. This family around 350 residues locates in the C-terminal of some uncharacterized proteins in various Bacteroides species. The function of this family remains unknown. 359 matched cddid_all.tbl CDD pfam16385 pfam16385 406720 DUF4994 Domain of unknown function. This family around 100 residues locates in the C-terminal of some uncharacterized proteins in various Bacteroides and Prevotella species. The function of this family remains unknown. 98 matched cddid_all.tbl CDD pfam16386 pfam16386 435314 DUF4995 Domain of unknown function. This family around 100 residues locates in the N-terminal of some uncharacterized proteins and glucuronyl hydrolases in various Bacteroides species. The function of this family remains unknown. 72 matched cddid_all.tbl CDD pfam16387 pfam16387 435315 DUF4996 Domain of unknown function. This family around 100 residues locates in the N-terminal of some glycerophosphoryl diester phosphodiesterases and uncharacterized proteins in various Bacteroides and Prevotella species. The function of this family remains unknown. 102 matched cddid_all.tbl CDD pfam16389 pfam16389 435316 DUF4998 Domain of unknown function. This family around 200 residues locates in the N-terminal of some uncharacterized proteins in various Bacteroides and Parabacteroides species. The function of this family remains unknown. 199 matched cddid_all.tbl CDD pfam16390 pfam16390 435317 DUF4999 Domain of unknown function. This family around 75 residues locates in the N-terminal of F5/8 type C domain proteins and some uncharacterized proteins in various Bacteroides species. The function of this family remains unknown. 76 matched cddid_all.tbl CDD pfam16391 pfam16391 406724 DUF5000 Domain of unknown function. This family around 200 residues locates in the C-terminal of some uncharacterized proteins in various Bacteroides and Parabacteroides species. The function of this family remains unknown. 149 matched cddid_all.tbl CDD pfam16392 pfam16392 406725 DUF5001 Ig-like domain. This family around 100 residues locates in the C-terminal of some uncharacterized proteins in various Bacteroides and Parabacteroides species. The function of this family remains unknown. It has an Ig like fold. 86 matched cddid_all.tbl CDD pfam16394 pfam16394 406726 DUF5003 Domain of unknown function (DUF5003). This small family of proteins is functionally uncharacterized. This family is found in bacteroides. Proteins in this family are typically between 500 and 650 amino acids in length. 316 matched cddid_all.tbl CDD pfam16395 pfam16395 406727 DUF5004 Domain of unknown function (DUF5004). This small family of proteins is functionally uncharacterized. This family is found in bacteroides. Proteins in this family are typically around 150 amino acids in length. 145 matched cddid_all.tbl CDD pfam16396 pfam16396 435318 DUF5005 Domain of unknown function (DUF5005). This small family of proteins is functionally uncharacterized. This family is found in bacteroides. Proteins in this family are typically around 440 amino acids in length. 443 matched cddid_all.tbl CDD pfam16397 pfam16397 406728 DUF5006 Domain of unknown function (DUF5006). This small family of proteins is functionally uncharacterized. This family is found in bacteroides. Proteins in this family are around 600 amino acids in length. 263 matched cddid_all.tbl CDD pfam16398 pfam16398 406729 DUF5007 Domain of unknown function (DUF5007). This small family of proteins is functionally uncharacterized. This family is found in Bacteroides and Sphingobacterium. The members in this family are around 350 residues in length. 287 matched cddid_all.tbl CDD pfam16399 pfam16399 435319 Aquarius_N Intron-binding protein aquarius N-terminus. This family represents the N-terminus of intron-binding protein aquarius, a splicing factor which links excision of introns from pre-mRNA with snoRP assembly. 791 matched cddid_all.tbl CDD pfam16400 pfam16400 374519 DUF5008 Domain of unknown function (DUF5008). This small family of proteins is functionally uncharacterized. This family is found in Bacteroides, Paraprevotella, and Sphingobacterium. The members in this family are around 550 residues in length. 101 matched cddid_all.tbl CDD pfam16401 pfam16401 293010 DUF5009 Domain of unknown function (DUF5009). This small family of proteins is functionally uncharacterized. This family is mainly found in various Bacteroides species. The members in this family are around 470 residues in length. 260 matched cddid_all.tbl CDD pfam16402 pfam16402 406731 DUF5010 Domain of unknown function (DUF5010). This small family of proteins is functionally uncharacterized. This family is found in bacteroides. Proteins in this family are around 600 amino acids in length. This family is related to glycosyl hydrolase family 99. 341 matched cddid_all.tbl CDD pfam16403 pfam16403 435320 DUF5011 Domain of unknown function (DUF5011). This entry represents a bacterial immunoglobulin-like domain. 71 matched cddid_all.tbl CDD pfam16404 pfam16404 374522 DUF5012 Domain of unknown function (DUF5012). This small family of proteins is functionally uncharacterized. This family is found in various Bacteroides species. Proteins in this family are around 230 amino acids in length. 125 matched cddid_all.tbl CDD pfam16405 pfam16405 435321 DUF5013 Domain of unknown function (DUF5013). This small family of proteins is functionally uncharacterized. This family is found in various Bacteroides and Parabacteroides species. Proteins in this family are around 400 amino acids in length. 149 matched cddid_all.tbl CDD pfam16406 pfam16406 435322 DUF5014 Domain of unknown function (DUF5014). This small family of proteins is functionally uncharacterized. This family is found in various Bacteroides species. Proteins in this family are around 630 amino acids in length. 90 matched cddid_all.tbl CDD pfam16407 pfam16407 406735 PKD_2 PKD-like family. This is a PKD-like family of proteins found in various Bacteroides species. 157 matched cddid_all.tbl CDD pfam16408 pfam16408 406736 DUF5016 Domain of unknown function (DUF5016). This family of proteins is functionally uncharacterized. This family is found in various Bacteroides species. Proteins in this family are around 660 amino acids in length. 125 matched cddid_all.tbl CDD pfam16409 pfam16409 406737 DUF5017 Domain of unknown function (DUF5017). This family of proteins is functionally uncharacterized. This family is found in various Bacteroides and Prevotella species. Proteins in this family are around 350 amino acids in length. 182 matched cddid_all.tbl CDD pfam16410 pfam16410 435323 DUF5018 Domain of unknown function (DUF5018). This family of proteins is functionally uncharacterized. This family is found in various Bacteroides and Alistipes species. Proteins in this family are around 600 amino acids in length. 351 matched cddid_all.tbl CDD pfam16411 pfam16411 435324 SusF_SusE Outer membrane protein SusF_SusE. SusE and SusF are two outer membrane proteins composed of tandem starch specific carbohydrate binding modules (CBMs) with no enzymatic activity. They are are likely to play an important role in starch metabolism in Bacteroides. It has been speculated that they could compete for starch in the human intestinal tract by sequestering starch at the bacterial surface and away from competitors. SusE has higher affinity for starch compared to SusF. 55 matched cddid_all.tbl CDD pfam16412 pfam16412 406740 DUF5020 Domain of unknown function (DUF5020). This family of proteins is functionally uncharacterized. This family is found in various Bacteroides species. Proteins in this family are around 235 amino acids in length. 212 matched cddid_all.tbl CDD pfam16413 pfam16413 465109 Mlh1_C DNA mismatch repair protein Mlh1 C-terminus. This is the C-terminal domain of DNA mismatch repair protein Mlh1, these proteins belong to the MutL family. This domain forms part of the endonuclease active site. 260 matched cddid_all.tbl CDD pfam16414 pfam16414 465110 NPC1_N Niemann-Pick C1 N terminus. This is the N-terminal domain of Niemann-Pick C1 family proteins. This family of proteins mediates transport of cholesterol from the intestinal lumen to enterocytes. This domain contains a cholesterol-binding pocket. 239 matched cddid_all.tbl CDD pfam16415 pfam16415 465111 CNOT1_CAF1_bind CCR4-NOT transcription complex subunit 1 CAF1-binding domain. This is the CAF1-binding domain of CCR4-NOT transcription complex. It adopts a MIF4G (middle portion of eIF4G) fold. 225 matched cddid_all.tbl CDD pfam16416 pfam16416 435328 GUN4_N ARM-like repeat domain, GUN4-N terminal. GUN4_N is the ARM-repeat like N-terminal domain of GUN4 proteins. It contains five helices arranged in an alternating antiparallel pattern that resembles ARM or HEAT repeats, though the functional importance of this poorly conserved domain in Gun4 is not currently known. 77 matched cddid_all.tbl CDD pfam16417 pfam16417 465112 CNOT1_TTP_bind CCR4-NOT transcription complex subunit 1 TTP binding domain. This is the TTP binding domain of CCR4-NOT transcription complex subunit 1. It adopts a MIF4G (middle portion of eIF4G) fold. 183 matched cddid_all.tbl CDD pfam16418 pfam16418 465113 CNOT1_HEAT CCR4-NOT transcription complex subunit 1 HEAT repeat. This domain is a HEAT repeat found in CCR4-NOT transcription complex subunit 1. 146 matched cddid_all.tbl CDD pfam16419 pfam16419 406747 CNOT1_HEAT_N CCR4-NOT transcription complex subunit 1 HEAT repeat. This domain is a HEAT repeat found in fungal CCR4-NOT transcription complex subunit 1 at the N-terminus of PF16418. 224 matched cddid_all.tbl CDD pfam16420 pfam16420 465114 ATG7_N Ubiquitin-like modifier-activating enzyme ATG7 N-terminus. This is the N-terminal domain of Ubiquitin-like modifier-activating enzyme ATG7. In Arabidopsis this domain binds the E2 enzymes ATG10 and ATG3. 308 matched cddid_all.tbl CDD pfam16421 pfam16421 465115 E2F_CC-MB E2F transcription factor CC-MB domain. This is the coiled coil (CC) - marked box (MB) domain of E2F transcription factors. This domain forms a heterodimer with the corresponding domain of the DP transcription factor, the heterodimer binds the C-terminus of retinoblastoma protein. 96 matched cddid_all.tbl CDD pfam16422 pfam16422 435333 COE1_DBD Transcription factor COE1 DNA-binding domain. 227 matched cddid_all.tbl CDD pfam16423 pfam16423 406751 COE1_HLH Transcription factor COE1 helix-loop-helix domain. This is the helix-loop-helix domain of transcription factor COE1. It is responsible for dimerization. 44 matched cddid_all.tbl CDD pfam16424 pfam16424 435334 DUF5021 Domain of unknown function (DUF5021). This family consists of Prepilin-type cleavage/methylation N-terminal domain proteins around 200 residues in length and is mainly found in various Eubacterium species. The function of this family is unknown. 157 matched cddid_all.tbl CDD pfam16425 pfam16425 293034 DUF5022 Domain of unknown function (DUF5022). This family consists of several uncharacterized proteins around 350 in length and is mainly found in various Firmicutes species. The function of this family is unknown. 287 matched cddid_all.tbl CDD pfam16426 pfam16426 406753 DUF5023 Domain of unknown function (DUF5023). This family consists of several uncharacterized proteins around 300 residues in length and is mainly found in various Eubacterium species. The function of this family is unknown. 197 matched cddid_all.tbl CDD pfam16427 pfam16427 406754 DUF5024 Domain of unknown function (DUF5024). This family consists of several uncharacterized proteins around 150 or 200 in length and is mainly found in various Bacteroides and Parabacteroides species. The function of this family is unknown. 104 matched cddid_all.tbl CDD pfam16428 pfam16428 435335 DUF5025 Domain of unknown function (DUF5025). This family consists of several uncharacterized proteins around 200 in length and is mainly found in various Parabacteroides species. The function of this family is unknown. 158 matched cddid_all.tbl CDD pfam16429 pfam16429 374540 DUF5026 Domain of unknown function (DUF5026). This family consists of several uncharacterized proteins around 100 residues in length and is mainly found in various Clostridiales species. The function of this family is unknown. 82 matched cddid_all.tbl CDD pfam16430 pfam16430 374541 DUF5027 Domain of unknown function (DUF5027). This family consists of several uncharacterized proteins around 180 in length and is mainly found in various Clostridiales species. The function of this family is unknown. 187 matched cddid_all.tbl CDD pfam16431 pfam16431 293040 DUF5028 Domain of unknown function (DUF5028). This family consists of several uncharacterized proteins around 200 in length and is mainly found in Eubacterium and Clostridium. The function of this family is unknown. 177 matched cddid_all.tbl CDD pfam16432 pfam16432 293041 DUF5029 Domain of unknown function (DUF5029). This family consists of several uncharacterized proteins around 550 in length and is mainly found in Bacteroides fragilis and sp. The function of this family is unknown. 210 matched cddid_all.tbl CDD pfam16433 pfam16433 406756 DUF5030 Domain of unknown function (DUF5030). This family consists of several uncharacterized proteins around 300 in length and is mainly found in various Bacteroides species. The function of this family is unknown. 307 matched cddid_all.tbl CDD pfam16434 pfam16434 406757 DUF5031 Domain of unknown function (DUF5031). This family consists of several uncharacterized proteins around 380 in length and is mainly found in Bacteroides fragilis and sp. The function of this family is unknown. 415 matched cddid_all.tbl CDD pfam16435 pfam16435 406758 DUF5032 Domain of unknown function (DUF5032). This family consists of several uncharacterized proteins around 270 in length and is mainly found in various Bacteroides and Parabacteroides species. The function of this family is unknown. 259 matched cddid_all.tbl CDD pfam16436 pfam16436 406759 DUF5033 Domain of unknown function (DUF5033). This family consists of several uncharacterized proteins around 200 in length and is mainly found in various Bacteroides species. The function of this family is unknown. 178 matched cddid_all.tbl CDD pfam16437 pfam16437 406760 DUF5034 Domain of unknown function (DUF5034). This family consists of several uncharacterized proteins around 190 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 169 matched cddid_all.tbl CDD pfam16438 pfam16438 435336 DUF5035 Domain of unknown function (DUF5035). This family consists of several uncharacterized proteins around 170 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 145 matched cddid_all.tbl CDD pfam16439 pfam16439 435337 DUF5036 Domain of unknown function (DUF5036). This family consists of several uncharacterized proteins around 240 residues in length and is mainly found in various Bacteroides and Parabacteroides species. The function of this family is unknown. 237 matched cddid_all.tbl CDD pfam16440 pfam16440 293049 DUF5037 Domain of unknown function (DUF5037). This family consists of several uncharacterized proteins around 270 residues in length and is mainly found in various Clostridiales species. The function of this family is unknown. 242 matched cddid_all.tbl CDD pfam16441 pfam16441 406763 DUF5038 Domain of unknown function (DUF5038). This family consists of several uncharacterized proteins around 200 residues in length and is mainly found in various Clostridiales species. The function of this family is unknown. 144 matched cddid_all.tbl CDD pfam16442 pfam16442 435338 DUF5039 Domain of unknown function (DUF5039). This family consists of several uncharacterized proteins around 240 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 203 matched cddid_all.tbl CDD pfam16443 pfam16443 465116 DUF5040 Domain of unknown function (DUF5040). This family consists of several uncharacterized proteins around 260 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 227 matched cddid_all.tbl CDD pfam16444 pfam16444 406766 DUF5041 Domain of unknown function (DUF5041). This family consists of several uncharacterized proteins around 230 residues in length and is mainly found in various Bacteroidales species. The function of this family is unknown. 192 matched cddid_all.tbl CDD pfam16445 pfam16445 406767 DUF5042 Domain of unknown function (DUF5042). This family consists of several uncharacterized proteins around 460 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 434 matched cddid_all.tbl CDD pfam16446 pfam16446 435340 DUF5043 Domain of unknown function (DUF5043). This family consists of several uncharacterized proteins around 200 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 155 matched cddid_all.tbl CDD pfam16447 pfam16447 374548 DUF5044 Domain of unknown function (DUF5044). This family consists of several uncharacterized proteins around 220 residues in length and is mainly found in various Clostridiales species. The function of this family is unknown. 178 matched cddid_all.tbl CDD pfam16448 pfam16448 465117 LapD_MoxY_N LapD/MoxY periplasmic domain. This domain is the N-terminal periplasmic domain of the LapD and MoxY receptor proteins. 124 matched cddid_all.tbl CDD pfam16449 pfam16449 435342 MatB Fimbrillin MatB. This is a family of fimbrial proteins. 168 matched cddid_all.tbl CDD pfam16450 pfam16450 465118 Prot_ATP_ID_OB Proteasomal ATPase OB C-terminal domain. This is the interdomain (ID) or oligonucleotide binding (OB) domain of proteasomal ATPase 56 matched cddid_all.tbl CDD pfam16451 pfam16451 465119 bCoV_S1_N Betacoronavirus-like spike glycoprotein S1, N-terminal. This entry represents the N-terminal domain of the betacoronavirus-like trimeric spike glycoprotein. The distal S1 subunit of the coronavirus spike protein is responsible for receptor binding. S1 contains two domains; an N-terminal galectin-like domain (NTD) and a receptor-binding domain (S1 RBD) also referred to as the S1 CTD or domain B. Either the S1 NTD or S1 RBD, or occasionally both, are involved in binding to host receptors. S1 NTD is located on the side of the spike trimer and mainly recognizes sugar receptors. For many betacoronaviruses (b-CoVs), for example mouse hepatitis virus (MHV), the RBD is located in the NTD. The structure of the MHV S1 NTD showed the same fold as human galectins (galactose-binding lectin), however it does not bind any sugar; instead, it binds to the carcinoembryonic antigen cell-adhesion molecule CEACAM1) through protein-protein interactions. All three CEACAM21a-binding sites in MHV spikes can be fully occupied by CEACAM1a. It has been shown that CEACAM1a binding to the MHV spike weakens the interactions between S1 and S2 and facilitates the proteolysis of the spike protein and dissociation of S1. The homologous bovine CoV (BCov) S1 NTD also possesses a galectin fold but binds to sialic acid-containing moieties on host cell membranes, as does the NTD of three other group A b-Covs, namely human CoV (HCoV) OC43, avian b-CoV, and infectious bronchitis virus (IBV). Despite the S1 NTD of human respiratory b-CoV HKU1 being highly homologous to the NTDs of MHV and bovine CoV, it does not bind to either sugar or human carcinoembryonic antigen-related cell adhesion molecules (CEACAMs) and the RBD is found instead in the S1 RBD domain. 296 matched cddid_all.tbl CDD pfam16452 pfam16452 435345 Phage_CI_C Bacteriophage CI repressor C-terminal domain. The C-terminal domain of the CI repressor functions in oligomer formation. 101 matched cddid_all.tbl CDD pfam16453 pfam16453 465120 IQ_SEC7_PH PH domain. This PH domain is found in IQ motif and SEC7 domain-containing proteins. 127 matched cddid_all.tbl CDD pfam16454 pfam16454 465121 PI3K_P85_iSH2 Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain. This domain is found between the two SH2 domains in phosphatidylinositol 3-kinase regulatory subunit P85. It forms a complex with the adaptor-binding domain of phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha. 161 matched cddid_all.tbl CDD pfam16455 pfam16455 465122 UBD Ubiquitin-binding domain. This ubiquitin-binding domain is found in ubiquitin domain-containing proteins. 101 matched cddid_all.tbl CDD pfam16456 pfam16456 435349 YmgD YmgD protein. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. 82 matched cddid_all.tbl CDD pfam16457 pfam16457 465123 PH_12 Pleckstrin homology domain. 128 matched cddid_all.tbl CDD pfam16458 pfam16458 435351 Beta-prism_lec Beta-prism lectin. This beta-prism fold lectin is the C-terminal domain of the Vibrio cholerae cytolytic pore-forming toxin hemolysin. It binds to N-glycans with a heptasaccharide GlcNAc4Man3 core (NGA2). 131 matched cddid_all.tbl CDD pfam16459 pfam16459 406779 Phage_TAC_13 Phage tail assembly chaperone, TAC. This family represents the phage-tail assembly chaperone proteins from a small set of Siphoviridae from Gammaproteobacteria. TACs are required for the morphogenesis of all long-tailed phages. The proposed function for the TAC is to coat the tape-measure protein to prevent it from forming unproductive complexes or precipitating before the tail tube protein has been incorporated. 98 matched cddid_all.tbl CDD pfam16460 pfam16460 293069 Phage_TTP_11 Phage tail tube, TTP, lambda-like. This family represents the phage-tail-tube protein from a set of Siphoviridae from Gammaproteobacteria. Tail tube proteins polymerize with the assistance of the Tail-tip complex, a tape measure protein and two chaperones. Infectivity of host is delivered through the tube. 137 matched cddid_all.tbl CDD pfam16461 pfam16461 406780 Phage_TTP_12 Lambda phage tail tube protein, TTP. This family represents the phage-tail-tube protein from a set of Siphoviridae from Gammaproteobacteria. Tail tube proteins polymerize with the assistance of the Tail-tip complex, a tape measure protein and two chaperones. Infectivity of host is delivered through the tube 134 matched cddid_all.tbl CDD pfam16462 pfam16462 465124 Phage_TAC_14 Phage tail assembly chaperone protein, TAC. This is a family of Siphoviridae phage tail assembly chaperone proteins. 113 matched cddid_all.tbl CDD pfam16463 pfam16463 435353 Phage_TTP_13 Phage tail tube protein family. This is a small family of Siphoviridae phage tail tube proteins. The tube protein polymerizes to form the shaft through which the infecting DNA passes into the host. 137 matched cddid_all.tbl CDD pfam16464 pfam16464 435354 DUF5045 Domain of unknown function (DUF5045). This family consists of N-terminal of several uncharacterized proteins around 260 residues in length and is mainly found in various Bacteroides and Parabacteroides species. The function of this family is unknown. 85 matched cddid_all.tbl CDD pfam16465 pfam16465 465125 DUF5046 Domain of unknown function (DUF5046). This small family consists of C-terminal of several uncharacterized proteins around 500 residues in length and is mainly found in various Faecalibacterium species. The function of this family is unknown. This family has distant similarity to WD40 repeats. 264 matched cddid_all.tbl CDD pfam16466 pfam16466 293075 DUF5047 Domain of unknown function (DUF5047). This family consists of N-terminal of several uncharacterized proteins and peptidases around 360 residues in length and is mainly found in various Streptomyces species. The function of this family is unknown. 135 matched cddid_all.tbl CDD pfam16467 pfam16467 435356 DUF5048 Domain of unknown function (DUF5048). This family consists of C-terminal of several uncharacterized proteins around 500 residues in length and is mainly found in various Faecalibacterium and Clostridium species. The function of this family is unknown. 102 matched cddid_all.tbl CDD pfam16468 pfam16468 379845 DUF5049 Domain of unknown function (DUF5049). This family consists of some uncharacterized proteins around 60 residues in length and is mainly found in various Lactobacillus and Selenomonas species. The function of this family is unknown. 57 matched cddid_all.tbl CDD pfam16469 pfam16469 406784 NPA Nematode polyprotein allergen ABA-1. The nematode polyprotein allergen ABA-1 is a lipid-binding protein comprising multiple tandem repeats of this domain. 116 matched cddid_all.tbl CDD pfam16470 pfam16470 465126 S8_pro-domain Peptidase S8 pro-domain. This domain is the pro-domain of several peptidases belonging to family S8. 77 matched cddid_all.tbl CDD pfam16471 pfam16471 465127 JIP_LZII JNK-interacting protein leucine zipper II. This is the second leucine zipper domain (LZII) of several JNK-interacting proteins (JIP). It interacts with the small GTP-binding protein ARF6. 69 matched cddid_all.tbl CDD pfam16472 pfam16472 465128 DUF5050 Domain of unknown function (DUF5050). 282 matched cddid_all.tbl CDD pfam16473 pfam16473 406788 Rv2179c-like 3'-5' exoribonuclease Rv2179c-like domain. This is a highly divergent 3' exoribonuclease family. The proteins constitute a typical RNase fold, where the active site residues form a magnesium catalytic centre. The protein of the solved structure readily cleaves 3' overhangs in a time-dependent manner. It is similar to DEDD-type RNases and is an unusual ATP-binding protein that binds ATP and dATP. It forms a dimer in solution and both protomers in the asymmetric unit bind a magnesium ion through Asp-6 in SwissProt:P9WJ73. Proteins containing this domain also include 3'-5' exonuclease dexA from bacteriophage T4. It may play a role in the final step of host DNA degradation, by scavenging DNA into mononucleotides. 177 matched cddid_all.tbl CDD pfam16474 pfam16474 465129 KIND Kinase non-catalytic C-lobe domain. The KIND domain (kinase non-catalytic C-lobe domain) evolved from a catalytic protein kinase fold and functions as an interaction domain. In SPIRE1 (protein spire homolog 1) this domain interacts with FMN2 (formin-2). 196 matched cddid_all.tbl CDD pfam16475 pfam16475 406790 DUF5052 Domain of unknown function (DUF5052). This family consists of uncharacterized proteins around 200 residues in length and is mainly found in various Firmicutes species. The function of this family is unknown. 199 matched cddid_all.tbl CDD pfam16476 pfam16476 435361 DUF5053 Domain of unknown function (DUF5053). This family consists of C-terminal of uncharacterized proteins around 100 residues in length and is mainly found in various Prevotella species. The function of this family is unknown. 59 matched cddid_all.tbl CDD pfam16477 pfam16477 406792 DUF5054 Domain of unknown function (DUF5054). This family consists of Glycosyl hydrolase family 38 proteins around 700 residues in length and is mainly found in various Clostridium and Rhizobium species. The function of this family is unknown. 287 matched cddid_all.tbl CDD pfam16478 pfam16478 374565 DUF5055 Domain of unknown function (DUF5055). This family consists of several uncharacterized proteins around 100 residues in length and is mainly found in butyrate-producing bacteriums. The function of this family is unknown. 105 matched cddid_all.tbl CDD pfam16479 pfam16479 435362 DUF5056 Domain of unknown function (DUF5056). This family consists of uncharacterized proteins around 360 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown. 93 matched cddid_all.tbl CDD pfam16480 pfam16480 435363 DUF5057 Domain of unknown function (DUF5057). This family consists of C-terminal of uncharacterized proteins and F5/8 type C domain proteins around 360 residues in length and is mainly found in various Firmicutes species. The function of this family is unknown. 355 matched cddid_all.tbl CDD pfam16481 pfam16481 465130 DUF5058 Domain of unknown function (DUF5058). This family consists of uncharacterized proteins around 250 residues in length and is mainly found in various Firmicutes species. The function of this family is unknown. 222 matched cddid_all.tbl CDD pfam16482 pfam16482 465131 Staufen_C Staufen C-terminal domain. This is the C-terminal domain of Staufen proteins. It consists of an N-terminal Staufen-swapping motif (SSM) comprising two alpha helices, connected by a linker region to a dsRNA-binding-like domain ('RBD'). The 'RBD' has the fold of a functional dsRNA-binding domain, but lacks the residues required to bind RNA. This domain is responsible for dimerization, the SSM from one molecule interacts with the 'RBD' of another. 110 matched cddid_all.tbl CDD pfam16483 pfam16483 435365 Glyco_hydro_64 Beta-1,3-glucanase. Family 64 glycoside hydrolases have beta-1,3-glucanase activity. 369 matched cddid_all.tbl CDD pfam16484 pfam16484 465132 CPT_N Carnitine O-palmitoyltransferase N-terminus. This domain is found at the N-terminus of carnitine O-palmitoyltransferases. It functions as a regulatory domain and is linked to the catalytic domain (pfam00755) via two transmembrane regions. 47 matched cddid_all.tbl CDD pfam16485 pfam16485 465133 PLN_propep Protealysin propeptide. This propeptide is cleaved during maturation of protealysin. Before cleavage it interacts with the catalytic domain, blocking the active site. 43 matched cddid_all.tbl CDD pfam16486 pfam16486 465134 ArgoN N-terminal domain of argonaute. ArgoN is the N-terminal domain of argonaute proteins in eukaryotes. ArgoN is composed of an antiparallel four-stranded beta sheet core that has two alpha helices positioned along one face of the sheet and an extended beta strand towards its N-terminus. The core fold of the N domain most closely resembles the catalytic domain of replication-initiator protein Rep. The N domain is linked to the PAZ domain via linker 1 region, and together these three regions are designated the PAZ-containing lobe of argonaute. 93 matched cddid_all.tbl CDD pfam16487 pfam16487 465135 ArgoMid Mid domain of argonaute. The ArgoMid domain is found to be part of the Piwi-lobe of the argonaute proteins. It is composed of a parallel four-stranded beta-sheet core surrounded by four alpha-helices and two additional short alpha-helices. It most closely resembles the amino terminal tryptic core of the E.coli lactose repressor. There is an extensive interface between the Mid and the Piwi domains. The conserved C-terminal half or the Mid has extensive interactions with Piwi, with a deep basic pocket on the surface of the `Mid adjacent to the interface with Piwi. The Mid carries a binding pocket for the 5' phosphate overhang of the guide strand of DNA. The N, Mid, and Piwi domains form a base upon which the PAZ domain sits, resembling a duck. The 5' phosphate and the U1 base are held in place by a conserved network of interactions from protein residues of the Mid and Piwi domains in order to place the guide uniquely in the proper position observed in all Argonaute-RNA complexes. 83 matched cddid_all.tbl CDD pfam16488 pfam16488 465136 ArgoL2 Argonaute linker 2 domain. ArgoL2 is the second linker domain in eukaryotic argonaute proteins. It starts with two alpha-helices aligned orthogonally to each other followed by a beta-strand involved in linking the two lobes, the PAZ lobe and the Piwi lobe of argonaute to each other. Linker 2 together with the N, PAZ and L1 domains form a compact global fold. Numerous residues from Piwi, L1 and L2 linkers direct the path of the phosphate backbone of nucleotides 7-9, thus allowing DNA-slicing. 47 matched cddid_all.tbl CDD pfam16489 pfam16489 465137 GAIN GPCR-Autoproteolysis INducing (GAIN) domain. The GAIN a domain of alpha-helices and beta-strands that is found in cell-adhesion GPCRs and precedes the GPS motif where the autoproteolysis occurs, family, pfam01825. The full GAIN domain, comprises the GPS and the GAIN, in cell-adhesion GPCRs, and is the functional unit for autoproteolysis. The GPS motif at the end of the GAIN domain is an ancient domain that exists in primitive ancestor organizms, and the full GAIN + GPS is conserved in all cell-adhesion GPCRs and all PKD1-related proteins. 205 matched cddid_all.tbl CDD pfam16490 pfam16490 435372 Oxidoreduct_C Putative oxidoreductase C terminal domain. This is the putative C-terminal domain of a bacterial oxidoreductase. It lies C-terminal to family GFO_IDH_MocA pfam01408 in some members. 278 matched cddid_all.tbl CDD pfam16491 pfam16491 465138 Peptidase_M48_N CAAX prenyl protease N-terminal, five membrane helices. The five N-terminal five transmembrane alpha-helices of peptidase_M48 family proteins including the CAAX prenyl proteases reside completely within the membrane of the endoplasmic reticulum. 179 matched cddid_all.tbl CDD pfam16492 pfam16492 465139 Cadherin_C_2 Cadherin cytoplasmic C-terminal. Cadherin_C_2 is the cytoplasmic C-terminal domain of some proto-cadherins. It is this region of the cadherins that allows cell-adhesion and the essential feature of metazoan multicellularity. Cadherins are cell-surface receptors that function in cell adhesion, cell polarity, and tissue morphogenesis. 84 matched cddid_all.tbl CDD pfam16493 pfam16493 465140 Meis_PKNOX_N N-terminal of Homeobox Meis and PKNOX1. Meis_PKNOX_N is a family found at the N-terminus of Meis, Myeloid ecotropic viral integration site, transcription regulators and PKNOX1 regulators, PBX/knotted 1 homeobox 1, homeobox proteins. 86 matched cddid_all.tbl CDD pfam16494 pfam16494 465141 Na_Ca_ex_C C-terminal extension of sodium/calcium exchanger domain. Na_Ca_ex_C is a region of the higher eukaryote sodium/calcium exchanger domain that extends toward the C-terminal, and is cytoplasmic. 136 matched cddid_all.tbl CDD pfam16495 pfam16495 465142 SWIRM-assoc_1 SWIRM-associated region 1. Much of the higher eukaryote SWI/SNF complex subunit SMARCC2 proteins is of low-complexity and or disordered. However, there are several short regions that are quite highly conserved. This is one of these regions. The function of the individual regions is not known. 84 matched cddid_all.tbl CDD pfam16496 pfam16496 465143 SWIRM-assoc_2 SWIRM-associated domain at the N-terminal. Much of the higher eukaryote SWI/SNF complex subunit SMARCC2 proteins is of low-complexity and or disordered. However, there are several short regions that are quite highly conserved. This is one of these regions. The function of the individual regions is not known. 412 matched cddid_all.tbl CDD pfam16497 pfam16497 465144 MHC_I_3 MHC-I family domain. 180 matched cddid_all.tbl CDD pfam16498 pfam16498 465145 SWIRM-assoc_3 SWIRM-associated domain at the C-terminal. Much of the higher eukaryote SWI/SNF complex subunit SMARCC2 proteins is of low-complexity and or disordered. However, there are several short regions that are quite highly conserved. This is one of these regions. The function of the individual regions is not known. 67 matched cddid_all.tbl CDD pfam16499 pfam16499 374582 Melibiase_2 Alpha galactosidase A. 284 matched cddid_all.tbl CDD pfam16500 pfam16500 465146 Cyclin_N2 Cyclin-A N-terminal APC/C binding region. This entry represents a disorder region found upstream of the family Cyclin_N, pfam00134. This region controls the stability of the region by recruiting the APC/C. This region includes the ABBA motif. 72 matched cddid_all.tbl CDD pfam16501 pfam16501 406813 SCAPER_N S phase cyclin A-associated protein in the endoplasmic reticulum. SCAPER_N is a short highly conserved region close to the N-terminus. SCAPER is localized to the endoplasmic reticulum and is a substrate for cyclin A/Cdk2. It associates with cyclin A and localizes to the ER. One theory suggests that SCAPER functions to create a local high concentration of cyclin A2 in the cytoplasm. Alternatively, SCAPER might be acting to sequester a portion of cellular cyclin A2 that could then be readily available for nuclear translocation, which may be needed for exit from G0 phase. 98 matched cddid_all.tbl CDD pfam16502 pfam16502 406814 DUF5059 Domain of unknown function (DUF5059). This domain is found fused to a copper-binding protein at the C-terminus, family Copper-bind, pfam00127. Its function is not known, and it is found in the Halobacteriaceae family in Archaea. 620 matched cddid_all.tbl CDD pfam16503 pfam16503 465147 zn-ribbon_14 Zinc-ribbon. This is a family of zinc-ribbons largely from eukaryotes that lie at the C-terminus of cytoplasmic tRNA adenylyltransferase 1 proteins. Most of these proteins carry an ATP-binding domain towards the N-terminus. 32 matched cddid_all.tbl CDD pfam16504 pfam16504 465148 SP24 Putative virion membrane protein of plant and insect virus. SP24, or structural protein of 24kD, is a family of putative virion membrane proteins of plant and insect viruses. These viruses are ssRNA positive-strand viruses, with no DNA stage. The family corresponds to the central region of the ORF3 of insect chroparaviruses and negeviruses and plant cileviruses, higreviruses and blunerviruses. It contains four transmembrane regions. Chronic bee paralysis virus (CBPV) is one of the more common member virions. SP24 is probably one of the major structural components of the virions. 147 matched cddid_all.tbl CDD pfam16505 pfam16505 293114 Emaravirus_P4 P4 movement protein of Emaravirus, and the 30K superfamily. Emaravirus_P4 is composed of movement proteins of the genus of negative-strand RNA viruses Emaravirus (related to the family Bunyaviridae), which infect plants. P4 is a movement protein of the 30K superfamily. 349 matched cddid_all.tbl CDD pfam16506 pfam16506 465149 DiSB-ORF2_chro Putative virion glycoprotein of insect viruses. This entry corresponds to putative glycoproteins from chroparaviruses. It carries two putative disulfide bridges. No similarity can be found with any other glycoproteins outside this region. 100 matched cddid_all.tbl CDD pfam16507 pfam16507 465150 BLM10_mid Proteasome-substrate-size regulator, mid region. The ordered regions of the yeast BLM10 or PA200 (human homolog), full-length protein encode 32 HEAT repeat (HR)-like modules, each comprising two helices joined by a turn, with adjacent repeats connected by a linker. Whereas a standard HEAT repeat is composed of ~50 residues, the BLM10 HEAT repeats are highly variable. The length of helices ranges from 8 to 35 residues, turns range from 2 to 87 residues, and linkers range from 1 to 88 residues, with the longest linker, between HR21 and HR22, containing additional secondary structures (two strands and three helices). BLM10_mid is the middle ordered region of the three in BLM10. BLM10 is found to surround the proteasome entry pore in the 1.2 MDa complex of proteasome and BLM10 to form a largely closed dome that is expected to restrict access of potential substrates. Thus Blm10 and PA200 are predominantly nuclear and stimulate the degradation of model peptides, although they do not appear to stimulate the degradation of proteins, recognize ubiquitin, or utilize ATP. 503 matched cddid_all.tbl CDD pfam16508 pfam16508 465151 NIBRIN_BRCT_II Second BRCT domain on Nijmegen syndrome breakage protein. 118 matched cddid_all.tbl CDD pfam16509 pfam16509 435386 KORA TrfB plasmid transcriptional repressor. KORA is a family of Gram-negative bacterial proteins that act as global repressors of genes involved in plasmid replication, conjugative transfer and stable inheritance in the IncP group of plasmids. KORA operates as a symmetric dimer, and contacts the DNA via the helix-turn-helix region at the N-terminus. 84 matched cddid_all.tbl CDD pfam16510 pfam16510 293119 P22_portal Phage P22-like portal protein. The portal protein of P22 and similar Podoviridae tail phages is a dodecameric structure consisting of a hip (2), a leg(1) and a barrel(3). DNA viruses such as bacteriophages and herpesviruses deliver their genome into and out of the capsid through large proteinaceous assemblies, known as portal proteins. Domains 1 and 3 are mostly helical and form the majority of the DNA-translocating channel. Domain 2 adopts an alpha-beta-fold characterized by two sheets of eight beta-strands, which cross each other to form a beta-barrel-like structure. 668 matched cddid_all.tbl CDD pfam16511 pfam16511 465152 FERM_f0 N-terminal or F0 domain of Talin-head FERM. FERM_f0 forms a stable globular structure. The fold is an ubiquitin-like fold joined to the f1 domain in a novel fixed orientation by an extensive charged interface. It is required for maximal integrin-activation, by interacting with other FA components, No binding partner has yet been found for it. 81 matched cddid_all.tbl CDD pfam16512 pfam16512 465153 RhoGAP-FF1 p190-A and -B Rho GAPs FF domain. RhoGAP-FF1 is the FF domain of the Rho GTPase activating proteins (GAPs). These are the key proteins that make the switch between the active guanosine-triphosphate-bound form of Rho guanosine triphosphatases (GTPases) and the inactive guanosine-diphosphate-bound form. Rho guanosine triphosphatases (GTPases) are a family of proteins with key roles in the regulation of actin cytoskeleton dynamics. The RhoGAP-FF1 region contains the FF domain that has been implicated in binding to the transcription factor TFII-I; and phosphorylation of Tyr308 within the first FF domain inhibits this interaction. The RhoGAPFF1 domain constitutes the first solved structure of an FF domain that lacks the first of the two highly conserved Phe residues, but the substitution of Phe by Tyr does not affect the domain fold. 80 matched cddid_all.tbl CDD pfam16514 pfam16514 435389 NADH-UOR_E putative NADH-ubiquinone oxidoreductase chain E. This putative NADH-ubiquinone oxidoreductase chain E family is found in Epsilonproteobacteria, chiefly in Helicobacter pylori. All proteins in the family are less than 100 residues in length. 74 matched cddid_all.tbl CDD pfam16515 pfam16515 465154 HIP1_clath_bdg Clathrin-binding domain of Huntingtin-interacting protein 1. HIP1_clath_bdg is the coiled-coil region of Huntington-interacting proteins 1. It carries a highly conserved HADLLRKN sequence motif at its N-terminus which effects the binding of HIP1R to clathrin light-chain EED regulatory site. this binding then stimulates clathrin lattice assembly. Huntingtin-interacting protein 1 (HIP1) is an obligate binding partner for Huntungtin, and loss of this interaction triggers the cascade of events that results in the apoptosis of neuronal cells and the onset of Hungtinton's disease. Clathrin light-chain binds to a flexible coiled-coil domain in HIP1 and induces a compact state that is refractory to actin binding. 99 matched cddid_all.tbl CDD pfam16516 pfam16516 465155 CC2-LZ Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator. CC2-LZ is a leucine-zipper domain associated with the CC2 coiled-coil region of NF-kappa-B essential modulator, NEMO. It plays a regulatory role, along with the very C-terminal zinc-finger; it contains a ubiquitin-binding domain (UBD) and represents one region that contributes to NEMO oligomerization. NEMO itself is an integral part of the IkappaB kinase complex and serves as a molecular switch via which the NF-kappaB signalling pathway is regulated. 100 matched cddid_all.tbl CDD pfam16517 pfam16517 435392 Nore1-SARAH Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain. The Nore1-SARAH, C-terminal, domain of Nore1, the tumour-suppressor, a novel Ras effector, has a characteriztic coiled-coil structure. It is a small helical module that is important in signal-transduction networks. The recombinant SARAH domain of Nore1 crystallizes as an anti-parallel homodimer with representative characteriztics of coiled coils. The central function of the SARAH domain seems to be the mediation of homo- and hetero-oligomerization between SARAH domain-containing proteins. Nore1 forms homo- and hetero complexes through its C-terminal SARAH (Sav/Rassf/Hpo) domain. 40 matched cddid_all.tbl CDD pfam16518 pfam16518 406825 GrlR T3SS negative regulator,GrlR. GrlR is a family of protobacterial type III secretion system negative regulators. Structurally, GrlR consists of a typical beta-barrel fold with eight beta-strands containing an internal hydrophobic cavity and a plug-like loop on one side of the barrel. Strong hydrophobic interactions between the two beta-barrels maintain its dimeric architecture. A unique surface-exposed EDED (Glu-Asp-Glu-Asp) motif is identified to be critical for GrlA-GrlR interaction and for the repressive activity of GrlR. The locus of enterocyte effacement (LEE) is essential for virulence of enterohaemorrhagic Escherichia coli (EHEC) and enteropathogenic E. coli (EPEC). It encodes some 20 genes including an overall regulator ler and two others, GrlR and GrlA, that form the type three secretion system for infection. GrlR comlexes with GrlA to repress expression of ler. GrlA is found in family pfam00462. 112 matched cddid_all.tbl CDD pfam16519 pfam16519 465156 TRPM_tetra tetramerization domain of TRPM. TRPM7_tetra is a short anti-parallel coiled-coil tetramerization domain of the transient receptor potential cation channel subfamily M member proteins 1-8. It is held together by extensive core packing and interstrand polar interactions. Transient receptor potential (TRP) channels comprise a large family of tetrameric cation-selective ion channels that respond to diverse forms of sensory input. The presence of cytoplasmic domains that direct channel assembly appears to be a feature of many voltage-gated ion channel superfamily members. 56 matched cddid_all.tbl CDD pfam16520 pfam16520 293128 BDV_M ssRNA-binding matrix protein of Bornaviridae. BDV_M is a family of matrix proteins from negative-strand Bornaviridae viruses. Its most stable oligomeric form is a tetramer, and it lies beneath the viral envelope where it associates with the inner layer of the viral membrane. It bridges the gap between the nucleocapsid and the viral envelope thereby imparting structural integrity and individual form to the virus particle. Borna disease virus (BDV) is a neurotropic enveloped RNA virus causing a noncytolytic, persistent infection of the central nervous system in mammals. The order to which this virus belongs, Mononegavirales, also contains the Ebola, mumps, rabies and measles viruses, amongst other highly infectious agents. 103 matched cddid_all.tbl CDD pfam16521 pfam16521 465157 Myosin-VI_CBD Myosin VI cargo binding domain. Myosin-VI_CBD is a C-terminal family that allows unconventional myosin-VI to recognize and select its binding cargoes. Several adaptor proteins have been reported to interact specifically with the CBD, thus defining the specific subcellular functions of myosin VI. The crystal structure determination of the myosin VI CBD/Dab2 (an endocytic adaptor protein Disabled-2 that is a cargo) complex shows that the Myosin-VI_CBD forms a cargo-induced dimer, suggesting that the motor undergoes monomer-to-dimer conversion that is dependent upon cargo binding. In the absence of cargo myosin VI exists as a stable monomer. This cargo binding-mediated monomer-to-dimer conversion mechanism adopted by myosin VI may be shared by other unconventional myosins, such as myosin VII and myosin X. 90 matched cddid_all.tbl CDD pfam16522 pfam16522 435395 FliS_cochap Flagellar FLiS export co-chaperone, HP1076. FliS_cochap is a family of largely Campylobacterales proteins that are co-chaperones for FliS, one of the type III secretion system flagellar chaperones. The HP1076 (Flis_cochap) and FliS complex together prevents premature polymerization of flagellins and is critical for flagellar assembly and bacterial colonization. The HP1076 shows co-chaperone activity that promotes protein folding of FliS with mutations in the flagellin binding pocket and enhances the chaperone activity of FliS. 146 matched cddid_all.tbl CDD pfam16523 pfam16523 465158 betaPIX_CC betaPIX coiled coil. betaPIX_CC is the very C-terminal coiled-coil region of betaPIX or p21-activated kinase interacting exchange factor proteins. The coiled-coil runs from residues 589-646 in UniProtKB:G31IU6, and the PDZ-binding site is the final eight residues immediately downstream. The coiled-coil trimerizes and thus exposes three potential PZD-binding surfaces, although only one of these is maximally used. One of the C-terminal ends of the coiled-coil forms an extensive beta-sheet interaction with the Shank PDZ, while the other two ends are not involved in ligand binding and form random coils. Thus the coiled-coil domain allows multimerization of betaPIX that is vital for its physiological functions. betaPIX and the Shank/ProSAP protein form a complex that acts as a protein scaffold for integrating signalling pathways and regulating postsynaptic structure.** Forced reload 84 matched cddid_all.tbl CDD pfam16524 pfam16524 435397 RisS_PPD Periplasmic domain of Sensor histidine kinase RisS. RisS_PPD is the periplasmic domain of the sensor histidine kinase RisS. It is purported to be the region of the kinase that senses the pH of the environs. 106 matched cddid_all.tbl CDD pfam16525 pfam16525 465159 MHB Haemophore, haem-binding. MHB is a coiled-coil molecule that binds free haem in mycobacterial cytoplasm to deliver it to membrane proteins for shuttling through the membrane. 76 matched cddid_all.tbl CDD pfam16526 pfam16526 465160 CLZ C-terminal leucine zipper domain of cyclic nucleotide-gated channels. The CLZ domain is the C-terminal leucine-zipper domain of of cyclic nucleotide-gated channel proteins. The CLZ domains form homotypic trimers in solution thus constraining the channel of the CNGs to contain three cyclic nucleotide-gated subunits, CNGA. The CLZ domains formed homotypic parallel 3-helix coiled-coil domains, consistent with their proposed role in regulating subunit assembly. 70 matched cddid_all.tbl CDD pfam16527 pfam16527 435400 CpxA_peri Two-component sensor protein CpxA, periplasmic domain. CpxA_peri is the periplasmic domain-family of the Gram-negative Gammaproteobacteria two-component signalling system, Cpx. It represents the recognition-site for sensing specific envelope stress signals. The fold that the domain-core of CpxA_peri conforms to is a PAS fold. The domain senses the environmental change and triggers a signal transduction to the cytoplasmic domain. As well as the PAS-core, there is a C-terminal tail that is necessary for ligand-sensing and binding to CpxP, a CpxA-associated and a regulatory protein. This domain recognizes KCl and RbCl (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 134 matched cddid_all.tbl CDD pfam16528 pfam16528 465161 Exo84_C Exocyst component 84 C-terminal. Exo84_C is the C-terminal helical region of the exocyst component Exo84. This region resembles a cullin-repeat, a multi-helical bundle. The exocyst is a large complex that is required for tethering vesicles at the final stages of the exocytic pathway in all eukaryotes. Exocyst subunits are composed of mostly helical modules strung together into long rods. 203 matched cddid_all.tbl CDD pfam16529 pfam16529 465162 Ge1_WD40 WD40 region of Ge1, enhancer of mRNA-decapping protein. Ge1_WD40 is the N-terminal region of Ge-1 or enhancer of mRNA-decapping proteins. WD40-repeat regions are involved in protein-protein interactions. 328 matched cddid_all.tbl CDD pfam16530 pfam16530 406834 IHHNV_capsid Infectious hypodermal and haematopoietic necrosis virus, capsid. IHHNV_capsid is the single capsid protein of infectious hypodermal and haematopoietic necrosis virus, found particularly in shrimp densovirus. Densoviruses are a subfamily of the parvoviruses. The capsid protein has an eight-stranded anti-parallel beta-barrel 'jelly roll' motif similar to that found in many icosahedral viruses, including other parvoviruses. The N-terminal portion of the IHHNV coat protein adopts a 'domain-swappe' conformation relative to its twofold-related neighbour. The loops connecting the strands of the structurally conserved jelly roll motif differ considerably in structure and length from those of other parvoviruses. IHHNV was first reported as a highly lethal disease of juvenile shrimp in 1983, and has only one type of capsid protein that lacks the phospholipase A2 activity that has been implicated as a requirement during parvoviral host cell infection. The structure of recombinant virus-like particles, composed of 60 copies of the 37.5-kDa coat protein is the smallest parvoviral capsid protein reported thus far. The small size of the PstDNV capsid protein makes the system attractive as a model for studying assembly mechanisms of icosahedral virus capsids. 323 matched cddid_all.tbl CDD pfam16531 pfam16531 465163 SAS-6_N Centriolar protein SAS N-terminal. SAS-6_N is the N-terminal domain of the SAS-6 centriolar protein, both in C.elegans and in humans. The N-terminal domain is the region through which the 9 rod-shaped homodimers that SAS-6 forms on oligomerization interact with each other. Proper functioning of the centriole requires this correct oligomerization. 88 matched cddid_all.tbl CDD pfam16532 pfam16532 406836 Phage_tail_NK Sf6-type phage tail needle knob or tip of some Caudovirales. Phage_tail_NK is the globular tip protein of some tailed bacteriophages. Tailed bacteriophage virions deliver DNA to susceptible cells after adsorbing to specific receptors on the surface of the bacteria. In the Gram-negative bacteria these receptors are surface proteins or polysaccharides. In the phage Sf6-type needle, this distal tip folds into a knob with a TNF-like fold, similar to the fibre knobs of bacteriophage PRD1 and Adenovirus. It contains three bound L-glutamate molecules that are bind tightly in the crevices between the trimers of this trimeric tip. 152 matched cddid_all.tbl CDD pfam16533 pfam16533 465164 SOAR STIM1 Orai1-activating region. SOAR is the Orai1-activating region of STIM1, where STIM1 are calcium sensors in the endoplasmic reticulum. As the store of calcium is depleted the calcium sensor in the ER activates Orai1, a Ca2+-release-activated Ca2+ (CRAC) channel, in the plasma membrane. The SOAR region, which runs from residues 340-443 on UniProtKB:Q13586, forms a dimer, and is essential for oligomerization of the whole of STIM1. 100 matched cddid_all.tbl CDD pfam16534 pfam16534 465165 ULD Ubiquitin-like oligomerization domain of SATB. ULD is an N-terminal oligomerization domain of SATB or special AT-rich sequence-binding proteins. SATBs are global chromatin organizers and regulators of gene expression that are essential for T-cell development, breast cancer tumour growth and metastasis. SATBs assemble into a tetramer via the ULD domain, and the tetramerization of SATBs are essential for recognising specific DNA sequences (such as multiple AT-rich DNA fragments). Thus, SATBs may regulate gene expression directly by binding to various promoters and upstream regions and thereby influencing promoter activity. 105 matched cddid_all.tbl CDD pfam16535 pfam16535 435406 T3SSipB Type III cell invasion protein SipB. T3SSipB is a family of pathogenic Gram-negative bacterial proteins that invade human intestinal cells via the type III secretion system translocators. T3SSipB represents the coiled -coil region of the proteins and is shown to be homologous in activity to the pore-forming toxins of other Gram-negative pathogens, such as colicin Ia. 155 matched cddid_all.tbl CDD pfam16536 pfam16536 406840 PNKP-ligase_C PNKP adenylyltransferase domain, C-terminal region. This is a short unique anti-parallel two-helical module with an extended tail peptide. It packs tightly against an extended peptide segment, residues 489-501 in UniProtKB:A3DJ38, near the N-terminus of the NTase domain, pfam16542. PNKP (polynucleotide 5'-kinase/3'-phosphatase) is the end-healing and end-sealing component of an RNA-repair system present in diverse bacteria from ten different phyla. RNA breakage by site-specific 'ribotoxins' is an ancient mechanism by which microbes respond to cellular stress and distinguish self from non-self. Ribotoxins are trans-esterifying endonucleases that generate 5'-OH and 2',3' cyclic phosphate termini. Repair of this type of RNA damage is feasible via sequential enzymatic end-healing and end-sealing steps. The exact function of this C-terminal region is unclear; however, the conformation of the bundles changes on transfer of a PO4 from ATP to AMP. 60 matched cddid_all.tbl CDD pfam16537 pfam16537 435407 T2SSB Type II secretion system protein B. This is the B protein from some operons of bacterial secretion systems of type II. The exact function of the B protein is not known, though in the case of Vibrio cholerae there is a fusion protein between proteins A and B that includes an AAA domain, a PG_binding domains well as this domain at the C-terminus. Many of the other species have no A or B domain genes in this operon. The type II secretion pathway is conserved in Gram-negative bacteria that are prevalent in bacterial pathogens of plants (Pseudomonas fluorescens, Erwinia or Xanthomonas species), animals (Aeromonas hydrophila) and humans (Klebsiella oxytoca, Pseudomonas aeruginosa, Vibrio cholerae or Legionella pneumophila). Typical type II secretion systems (T2SSs) are encoded by a set of 12 to 16 gsp (general secretion pathway) genes organized into large operons including the conserved 'core' genes denoted C to O and in some bacterial species, as indicated above, extra gsp genes such as gspAB, gspN or gspS. A different nomenclature is used for Pseudomonas T2SSs, so the B gene is referred to as the P protein. 60 matched cddid_all.tbl CDD pfam16538 pfam16538 435408 FlgT_C Flagellar assembly protein T, C-terminal domain. FlgT_C is the C-terminal domain of a family of flagellar proteins that make up part of the basal body of the flagellum. The flagellum is a large macromolecular assembly composed of three major parts: the basal body, the hook, and the filament. The basal body has two unique ring structures, the T ring and the H ring. FlgT is required to form and stabilize both ring structures. FlgT_C is not essential but stabilizes the H-ring structure.. 77 matched cddid_all.tbl CDD pfam16539 pfam16539 435409 FlgT_M Flagellar assembly protein T, middle domain. FlgT_M is the middle region of a family of flagellar proteins that make up part of the basal body of the flagellum. The flagellum is a large macromolecular assembly composed of three major parts: the basal body, the hook, and the filament. The basal body has two unique ring structures, the T ring and the H ring. FlgT is required to form and stabilize both ring structures. FlgT-N and FlgT-M are thought to be involved in the H-ring and the T-ring formation, respectively. and FlgT-M is also required for the stable association of FlgT with the basal body. 163 matched cddid_all.tbl CDD pfam16540 pfam16540 465166 MKLP1_Arf_bdg Arf6-interacting domain of mitotic kinesin-like protein 1. This family is a C-terminal region of mitotic kinesin-like proteins that is necessary for the interaction with the small GTPase Arf6. MKLP1 is a Flemming body-localising protein essential for cytokinesis, so its interaction with Arf6 shows how Arf6 is involved in cytokinesis. The Arf6-MKLP1 complex plays a crucial role in cytokinesis by connecting the microtubule bundle and membranes at the cleavage plane. 107 matched cddid_all.tbl CDD pfam16541 pfam16541 435411 AltA1 Alternaria alternata allergen 1. AltA1 is a family of fungal allergens. It shows a unique beta-barrel comprising 11 beta-strands. There is structural evidence for the location of IgE antibody-binding epitopes. The crystal structure will allow efforts to promote immunotherapy for patients allergic to Alternaria species. 107 matched cddid_all.tbl CDD pfam16542 pfam16542 435412 PNKP_ligase PNKP adenylyltransferase domain, ligase domain. PNKP_ligase is a classical ligase nucleotidyltransferase module of bacteria. PNKP (polynucleotide 5'-kinase/3'-phosphatase) is the end-healing and end-sealing component of an RNA-repair system present in diverse bacteria from ten different phyla. RNA breakage by site-specific 'ribotoxins' is an ancient mechanism by which microbes respond to cellular stress and distinguish self from non-self. Ribotoxins are trans-esterifying endonucleases that generate 5'-OH and 2',3' cyclic phosphate termini. Repair of this type of RNA damage is feasible via sequential enzymatic end-healing and end-sealing steps. 315 matched cddid_all.tbl CDD pfam16543 pfam16543 465167 DFRP_C DRG Family Regulatory Proteins, Tma46. DFRP_C is a family of eukaryotic translation machinery-associated protein 46 proteins that are the binding partner for the highly conserved Developmentally Regulated GTP-binding (DRG) GTPases. Thus this family is referred to as DRG Family Regulatory Proteins (DFRP). Binding of this DFRP modulates the function of the GTPase. 89 matched cddid_all.tbl CDD pfam16544 pfam16544 435414 STAR_dimer Homodimerization region of STAR domain protein. This family is the homodimerization domain of quaking proteins. Quaking-dimer is a helix-turn-helix dimer with an additional helix in the turn region. dimerization is required for adequate RNA-binding. Quaking is a prototypical member of the STAR (signal transducer and activator of RNA) protein family, which plays key roles in post-transcriptional gene regulation by controlling mRNA translation, stability and splicing. STAR_dimer is the homodimerization domain, Qua1 of the STAR domain of a series of proteins referred to as STAR/GSG, or Signal Transduction and Activation of RNA/GRP33, Sam68, GLD-1 family. These are conserved in higher eukaryotes and are RNA-binding transcriptional regulators. The STAR domain is a KH domain flanked by two homologous regions, Qua1 and Qua2. Qua1, this family, is the homodimerization domain, and the KH plus Qua2 is the RNA-binding region. 52 matched cddid_all.tbl CDD pfam16545 pfam16545 435415 CCM2_C Cerebral cavernous malformation protein, harmonin-homology. CCM2_HHD is a folded-helical region of a family of vertebral proteins, mutations in which cause cerebral cavernous malformations (CCMs). These malformations are congenital vascular anomalies of the central nervous system that can result in haemorrhagic stroke, seizures, recurrent headaches, and focal neurologic deficits. This domain is structurally homologous to the N-terminal domain of harmonin, so it is named the CCM2 harmonin-homology domain or CCM2_HHD. This protein is often called Malcavernin. 95 matched cddid_all.tbl CDD pfam16546 pfam16546 465168 SGTA_dimer Homodimerization domain of SGTA. SGTA_dimer is a short N-terminal domain at the start of SGTA or small glutamine-rich tetratricopeptide repeat-containing proteins. It is the homodimerization domain of the SGTA, a heat-shock protein (HSP) co-chaperone involved in the targeting of tail-anchor membrane proteins to the endoplasmic reticulum. This N-terminal homodimerization domain mediates the association with a single copy of Get4 or Get5 proteins, providing a link to the rest of the GET pathway. 64 matched cddid_all.tbl CDD pfam16547 pfam16547 435417 BLM10_N Proteasome-substrate-size regulator, N-terminal. The ordered regions of the yeast BLM10 or PA200 (human homolog), full-length protein encode 32 HEAT repeat (HR)-like modules, each comprising two helices joined by a turn, with adjacent repeats connected by a linker. Whereas a standard HEAT repeat is composed of ~50 residues, the BLM10 HEAT repeats are highly variable. The length of helices ranges from 8 to 35 residues, turns range from 2 to 87 residues, and linkers range from 1 to 88 residues, with the longest linker, between HR21 and HR22, containing additional secondary structures (two strands and three helices). BLM10_N is the N-terminal ordered region of the three in BLM10. BLM10 is found to surround the proteasome entry pore in the 1.2 MDa complex of proteasome and BLM10 to form a largely closed dome that is expected to restrict access of potential substrates. BLM10 and PA200 are predominantly nuclear and stimulate the degradation of model peptides, although they do not appear to stimulate the degradation of proteins, recognize ubiquitin, or utilize ATP. 81 matched cddid_all.tbl CDD pfam16548 pfam16548 465169 FlgT_N Flagellar assembly protein T, N-terminal domain. FlgT_N is the N-terminal domain of a family of flagellar proteins that make up part of the basal body of the flagellum. The flagellum is a large macromolecular assembly composed of three major parts: the basal body, the hook, and the filament. The basal body has two unique ring structures, the T ring and the H ring. FlgT is required to form and stabilize both ring structures. FlgT-N contributes to the construction of the H-ring structure, and adopts a two-layer alpha-beta sandwich architecture composed of a four-stranded anti-parallel beta-sheet and two alpha helices. 87 matched cddid_all.tbl CDD pfam16549 pfam16549 435419 T2SSS_2 Type II secretion system (T2SS) pilotin, S protein. T2S_S is the S protein or pilotin of the bacterial Gram-negative secretion system in Vibrio and some E.coli and Shigella. It is given the suffix _2 to distinguish it from the PulS_OutS family of pilotins from Klebsiella and Dickeya, etc. AspS is functionally equivalent and yet structurally unrelated to the pilotins found in Klebsiella and other bacteria. AspS binds to a specific targeting sequence in the Vibrio-type secretins, enhancing the kinetics of secretin assembly; homologs of AspS are found in all species of Vibrio as well those few strains of Escherichia and Shigella that have acquired a Vibrio-type T2SS. PulS is the Kelbsiella pilotin, found in PulS_OutS, pfam09691. Not all species with a type II secretion system have this pilotin or S protein. 104 matched cddid_all.tbl CDD pfam16550 pfam16550 465170 RPN13_C UCH-binding domain. RPN13_C is a family of all-helical domains that forms the binding-surface for the proteasome-ubiquitn-receptor protein Rpn13 to UCH37, one of the three de-ubiquitinating enzymes of the proteasome. 106 matched cddid_all.tbl CDD pfam16551 pfam16551 435421 Quaking_NLS Putative nuclear localization signal of quaking. Quaking_NLS is the very C-terminal region of quaking proteins that is purported to be the nuclear localization signal. 30 matched cddid_all.tbl CDD pfam16552 pfam16552 435422 OAM_alpha D-ornithine 4,5-aminomutase alpha-subunit. OAM_alpha is the 12.8kDa, alpha subunit of d-ornithine 4,5-aminomutase, or OAM, an enzyme that converts d-ornithine to 2,4-diaminopentanoic acid by way of radical propagation from an adenosylcobalamin to a pyridoxal 5'-phosphate cofactor. OAM is an alpha2-beta2 heterodimer comprising two strongly associating subunits. The packing of the alpha subunits against the beta helps to form the substrate and co-factor binding-regions. 115 matched cddid_all.tbl CDD pfam16553 pfam16553 465171 PUFD BCORL-PCGF1-binding domain. PUFD is the minimal domain at the C-terminus of BCORL (BCL6 corepressor) that is needed for binding and giving specificity to some of the PCGF proteins, polycomb-group RING finger homologs. PUFD binds to the RAWUL (RING finger- and WD40-associated ubiquitin-like) domain of the particular PCGF PCGF1, pfam16207. Polycomb group proteins form repressive complexes (PRC) that mediate epigenetic modifications of histones. In humans there are many different PCGF homologs whose functions all vary, but the direct binding partner of PCGF1 is BCOR. BCOR has emerged as an important player in development and health. 114 matched cddid_all.tbl CDD pfam16554 pfam16554 435424 OAM_dimer dimerization domain of d-ornithine 4,5-aminomutase. This family is the short dimerization domain of the enzyme D-ornithine 4,5-aminomutase. It sits between the TIM-barrel pfam09043 and pfam02310. The enzyme is an alpha2-beta2-heterodimer that converts D-ornithine to 2,4-diaminopentanoic acid by way of radical propagation from an adenosylcobalamin to a pyridoxal 5'-phosphate cofactor. 78 matched cddid_all.tbl CDD pfam16555 pfam16555 465172 GramPos_pilinD1 Gram-positive pilin subunit D1, N-terminal domain. GramPos_pilinD1 is the first subunit domain of Gram-positive pilins from Strep.pneumoniae. There are three major pilin subunits that form the polymeric backbone of the pilin from S. pneumoniae, constructed of three Ig-like, CnaB, domains along with a crucial N-terminal domain, D1. The three IG-like domains are stabilized by internal Lys-Asn isopeptide bonds, but this N-terminal domain makes few contact with the rest of the molecule due to the different orientation of its G beta-strand. Strand G of D1 also carries the YPKN motif that provides the essential Lys residue for the sortase-mediated intermolecular linkages along the pilus shaft. Gram-positive pili are formed from a single chain of covalently linked subunit proteins (pilins), usually comprising an adhesin at the distal tip, a major pilin that forms the polymer shaft and a minor pilin that mediates cell wall anchoring at the base. 161 matched cddid_all.tbl CDD pfam16556 pfam16556 435426 IL17R_fnIII_D1 Interleukin-17 receptor, fibronectin-III-like domain 1. IL17R_fnIII_D1 is the first of two fibronectin 3-like domains on interleukin-17 receptor proteins A and B. The tow fnIII domains are linked and together bind two molecules of IL-17 at one of its receptor-binding interfaces. This allows the other interface to bind to another receptor, thus allowing the IL-17 family of homodimeric cytokines to coordinate two different receptors. 154 matched cddid_all.tbl CDD pfam16557 pfam16557 435427 CUTL CUT1-like DNA-binding domain of SATB. CUTL is part of the N-terminal region of SATB proteins, special AT-rich sequence-binding proteins that are global chromatin organizers and gene expression regulators essential for T-cell development and breast cancer tumour growth and metastasis. CUTL carries a DNA-binding region just as CUT domains do. 72 matched cddid_all.tbl CDD pfam16558 pfam16558 465173 AZUL Amino-terminal Zinc-binding domain of ubiquitin ligase E3A. The AZUL or amino-terminal zinc-binding domain of ubiquitin E3a ligase is found in eukaryotes, and is an unusual zinc-finger domain. The final cysteine is usually mutated in Angelman syndrome patients. It is likely that AZUL plays a role in Ube3A substrate-recognition. 59 matched cddid_all.tbl CDD pfam16559 pfam16559 465174 GIT_CC GIT coiled-coil Rho guanine nucleotide exchange factor. GIT-CC is the coiled-coil region of GIT (G protein-coupled receptor kinase-interacting) proteins. This coiled-coil region is the surface that associates with the equivalent binding-region on beta-PIX, or p21-activated kinase-interacting exchange factor proteins. Both GIT and PIX complex together to form a scaffold for the formation of multi-protein assemblies. On its own the GIT-CC region assembles into a parallel two-stranded CC in the asymmetric unit. Similarly the PIX coiled-coil region assembles into a trimer. At least in vitro the two regions associate together into a stable heteropentameric complex that consists of one PIX trimer and one GIT dimer. 66 matched cddid_all.tbl CDD pfam16560 pfam16560 465175 SAPI Putative mobile pathogenicity island. SAPI is a family of putative Gram-positive mobile pathogenicity island proteins. SAPIs are responsible for many superantigen-related diseases in humans as they carry two or more superantigens. 213 matched cddid_all.tbl CDD pfam16561 pfam16561 465176 AMPK1_CBM Glycogen recognition site of AMP-activated protein kinase. AMPK1_CBM is a family found in close association with AMPKBI pfam04739. The surface of AMPK1_CBM reveals a carbohydrate-binding pocket. 85 matched cddid_all.tbl CDD pfam16562 pfam16562 465177 HECW_N N-terminal domain of E3 ubiquitin-protein ligase HECW1 and 2. HECW_N is a domain on E3 ubiquitin-protein ligases that lies upstream of the C2 domain; its function is not clearly understood, except perhaps to determine the substrate spectrum of the ligase. 118 matched cddid_all.tbl CDD pfam16563 pfam16563 465178 P66_CC Coiled-coil and interaction region of P66A and P66B with MBD2. This family is a short coiled-coil interaction region on the transcriptional repressors P66A and P66B. The P66A and B, or alpha and beta, complex with MBDs or methyl-binding domain-containing proteins via a coiled-coil region on each. This P66-MBD2 complex forms part of an assembly with NuRD, nucleosome remodelling and deacetylation protein. MBD2-NuRD binds methylated DNA and regulates transcription of eg, the foetal beta-globin gene during development. 40 matched cddid_all.tbl CDD pfam16564 pfam16564 465179 MBDa p55-binding region of Methyl-CpG-binding domain proteins MBD. MBDa is a second MBD domain of Methyl-CpG-binding domain proteins. region implicated in binding the RbAp46/48 (retinoblastoma protein-associated protein) homolog p55, which is one of the components of the MBD2-NuRD complex. The MBD2-NuRD complex is a nucleosome remodelling and deacetylation complex. 68 matched cddid_all.tbl CDD pfam16565 pfam16565 465180 MIT_C Phospholipase D-like domain at C-terminus of MIT. MIT_C is the C-terminal domain of MIT-containing proteins, pfam04212. It contains an unanticipated phospholipase d fold (PLD fold) that binds avidly to phosphoinositide-containing membranes. It is conserved in eukaryotes, though not fungi and plants, and some bacteria. 137 matched cddid_all.tbl CDD pfam16566 pfam16566 465181 CREPT Cell-cycle alteration and expression-elevated protein in tumour. CREPT (Cell-cycle alteration and expression-elevated protein in tumour) is a family of eukaryotic transcriptional regulators that ptromote the binding of RNA-polymerase to the CYCLIN D1, CCDN1, promoter and other genes involved in the cell-cycle. It promotes the formation of a chromatin loop in the CYCLIN D1 gene, and is preferentially expressed in a range of different human tumours. 147 matched cddid_all.tbl CDD pfam16567 pfam16567 293175 CagD Pathogenicity island component CagD. CagD is a tightly conserved family of proteins found in the pathogenic strains of Helicobacter species. It is one of some 30 proteins, produced from the genomic insert termed the pathogenicity island, required for the type IV secretion system - T4SS - that delivers CagA oncoprotein toxin into the host cell. CagD is a covalent dimer in which each monomer folds as a single domain composed of five beta-strands and three alpha-helices. CagD partially associates with the inner membrane, where it may be exposed to the periplasmic space; this may indicate that CagD is released into the supernatant during host cell infection in order then to bind to the host cell surface, or to be incorporated into the pilus structure. 205 matched cddid_all.tbl CDD pfam16568 pfam16568 465182 Sam68-YY Tyrosine-rich domain of Sam68. Sam68-YY is a short tyrosine-rich domain on Src-associated in mitosis, 68 kDa protein (Sam68), a protein that regulates TCF-1 alternative splicing. It is a crucial binding-partner of the APC-Arm domain that forms a superhelix with a positively charged groove, the surface-residues of which groove form numerous interactions with Sam68-YY to fix it in a bent conformation. APC-Arm is the armadillo repeat domain of the tumour-suppressor protein adenomatous polyposis coli or APC. APC plays plays important roles in Wnt signalling and other cellular processes. 55 matched cddid_all.tbl CDD pfam16569 pfam16569 435436 GramPos_pilinBB Gram-positive pilin backbone subunit 2, Cna-B-like domain. GramPos_pilinBB is one of the major backbone units of Gram-positive pili, such as those from S.pneumoniae. There are three major pilin subunits that form the polymeric backbone of the pilin from S. pneumoniae, constructed of three transthyretin-like, CnaB, domains along with a crucial N-terminal domain, D1. The three Cna-B like domains are stabilized by internal Lys-Asn isopeptdie bonds, Gram-positive pili are formed from a single chain of covalently linked subunit proteins (pilins), usually comprising an adhesin at the distal tip, a major pilin that forms the polymer shaft and a minor pilin that mediates cell wall anchoring at the base. 114 matched cddid_all.tbl CDD pfam16570 pfam16570 406873 GramPos_pilinD3 Gram-positive pilin backbone subunit 3, Cna-B-like domain. GramPos_pilinD3 is one of the major backbone units of Gram-positive pili, such as those from S.pneumoniae. There are three major pilin subunits that form the polymeric backbone of the pilin from S. pneumoniae, constructed of three transthyretin-like, CnaB, domains along with a crucial N-terminal domain, D1. The three Cna-B like domains are stabilized by internal Lys-Asn isopeptdie bonds, Gram-positive pili are formed from a single chain of covalently linked subunit proteins (pilins), usually comprising an adhesin at the distal tip, a major pilin that forms the polymer shaft and a minor pilin that mediates cell wall anchoring at the base. 141 matched cddid_all.tbl CDD pfam16571 pfam16571 435437 FBP_C FBP C-terminal treble-clef zinc-finger. FBP_C is a family from the C terminal end of fibronectin-binding proteins. It forms an extended four-cysteine zinc-finger with a unique structural fold. Fibronectin-binding proteins bind to elongation factor G - EF-G, which is mediated by the zinc-finger binding to the C-terminus of EF-G. FBPs release ribosomes by competing with them for EF-G. 155 matched cddid_all.tbl CDD pfam16572 pfam16572 406875 HlyD_D4 Long alpha hairpin domain of cation efflux system protein, CusB. HlyD_D4 is the long alpha-hairpin domain in the centre of CusB or HlyD proteins. CusB and HlyD proteins are membrane fusion proteins of the CusCFBA copper efflux system in E.coli and related bacteria. Efflux systems of this resistance-nodulation-division group - RND - have been developed to excrete poisonous metal ions, and in E.coli the only one that deals with silver and copper is the CusA transporter. The transporter CusA works in conjunction with a periplasmic component that is a membrane fusion protein, eg CusB, and an outer-membrane channel component CusC in a CusABC complex driven by import of protons. HlyD_D4 is thought to interact with the alpha-helical tunnels of the corresponding outer-membrane channels, ie the periplasmic domain of CusC. 54 matched cddid_all.tbl CDD pfam16573 pfam16573 465183 CLP1_N N-terminal beta-sandwich domain of polyadenylation factor. This family is the short N-terminal domain of the pre-mRNA cleavage complex II protein Clp1. Clp1 function involves some degree of adenine or guanine nucleotide-binding and participates in the 3'-end-processing of mRNAs in eukaryotes. 92 matched cddid_all.tbl CDD pfam16574 pfam16574 465184 CEP209_CC5 Coiled-coil region of centrosome protein CE290. CEP290 and similar centrosomal proteins carry a number of coiled-coil regions, and this is the fifth along the length of the protein. It is thought that the proteins are involved in cilia biosynthesis. 128 matched cddid_all.tbl CDD pfam16575 pfam16575 406878 CLP1_P mRNA cleavage and polyadenylation factor CLP1 P-loop. CLP1_P is the P-loop carrying domain of Clp1 mRNA cleavage and polyadenylation factor, Clp1, proteins in eukaryotes. Clp1 is essential for 3'-end processing of mRNAs. This region carries the P-loop suggesting it is the region that binds adenine or guanine nucleotide. 187 matched cddid_all.tbl CDD pfam16576 pfam16576 435440 HlyD_D23 Barrel-sandwich domain of CusB or HlyD membrane-fusion. HlyD_D23 is the combined domains 2 and 3 of the membrane-fusion proteins CusB and HlyD, which forms a barrel-sandwich. CusB and HlyD proteins are membrane fusion proteins of the CusCFBA copper efflux system in E.coli and related bacteria. The whole molecule hinges between D2 and D3. Efflux systems of this resistance-nodulation-division group - RND - have been developed to excrete poisonous metal ions, and in E.coli the only one that deals with silver and copper is the CusA transporter. The transporter CusA works in conjunction with a periplasmic component that is a membrane fusion protein, eg CusB, and an outer-membrane channel component CusC in a CusABC complex driven by import of protons. 214 matched cddid_all.tbl CDD pfam16577 pfam16577 318725 UBA_5 UBA domain. UBA_2 is a domain found on eukaryotic ubiquitin-interacting proteins. Sequestosome 1/p62 has recently been shown to interact with polyubiquitinated proteins through its UBA domain. This domain selectively binds K63-polyubiquitinated proteins. 62 matched cddid_all.tbl CDD pfam16578 pfam16578 465185 IL17R_fnIII_D2 Interleukin 17 receptor D. IL17R_fnIII_D2 is the second extracellular fibronectin III-like domain on interleukin17-receptor-D molecules. The exact ligands of IL17R-D are not known. 105 matched cddid_all.tbl CDD pfam16579 pfam16579 406881 AdenylateSensor Adenylate sensor of SNF1-like protein kinase. AdenylateSensor is a family found at the C-terminus of SNF1-like protein kinases snf other protein-kinases. 118 matched cddid_all.tbl CDD pfam16580 pfam16580 293188 Astro_capsid_p2 C-terminal tail of astrovirus capsid projection or spike. Astro_capsid_p2 is a family of turkey astroviral spike projections. These are globular domains on the surface of the viral capsid. Astroviruses cause diarrhoea in a variety of mammals and birds, and are small, non-enveloped, single-stranded RNA viruses. The spike carries three conserved patches on its surface which could be candidates for avian receptor-binding sites. 245 matched cddid_all.tbl CDD pfam16581 pfam16581 406882 HIGH_NTase1_ass Cytidyltransferase-related C-terminal region. This domain is found as the C-terminal portion of some HIGH_NTase1 proteins. The exact function is not known. 205 matched cddid_all.tbl CDD pfam16582 pfam16582 435442 TPP_enzyme_M_2 Middle domain of thiamine pyrophosphate. TPP_enzyme_M_2 is the middle domain of thiamine pyrophosphate in sequences not captured by pfam00205. This enzyme is necessary for the first step of the biosynthesis of menaquinone, or vitamin K2, an important cofactor in electron transport in bacteria. 207 matched cddid_all.tbl CDD pfam16583 pfam16583 406884 ZirS_C Zinc-regulated secreted antivirulence protein C-terminal domain. ZirS_C is the C-terminal domain of ZirS, zinc-regulated secreted protein, that is part of a type V-like secretion system. The domain adopts a bacterial Ig-like fold. This domain interacts with its transporter ZirT, and ZirS also interacts directly with ZirU, the third component of this antivirulence complex. ZirT is the zinc-regulated transporter through which ZirS is secreted. 141 matched cddid_all.tbl CDD pfam16584 pfam16584 293192 LolA_2 Outer membrane lipoprotein carrier protein LolA. LolA_2 is a family of Bacteroidetes outer membrane lipoprotein carrier protein LolA-like proteins. The exact function is not known. 152 matched cddid_all.tbl CDD pfam16585 pfam16585 406885 Lipocalin_8 Lipocalin-like domain. 135 matched cddid_all.tbl CDD pfam16586 pfam16586 435443 DUF5060 Domain of unknown function (DUF5060). This is the N-terminal domain of a putative glycoside hydrolase, DUF4038. It is found in a number of different bacterial orders. 69 matched cddid_all.tbl CDD pfam16587 pfam16587 406887 DUF5061 17 kDa common-antigen outer membrane protein. This is a family of bacterial lipoproteins related to the 17 kDa common-antigen proteins. 82 matched cddid_all.tbl CDD pfam16588 pfam16588 374649 zf-C2H2_10 C2H2 zinc-finger. 23 matched cddid_all.tbl CDD pfam16589 pfam16589 465186 BRCT_2 BRCT domain, a BRCA1 C-terminus domain. This BRCT domain, a BRCA1 C-terminus region, is found on many RAP1 proteins, usually at the very N-terminus. The function in human at least of a BRCT is to contribute to the heterogeneity of the telomere DNA length, but that may not be its general function, which remains unknown. 84 matched cddid_all.tbl CDD pfam16590 pfam16590 465187 ESP Exocrine gland-secreting peptide. ESP is a family of largely rodent exocrine gland-secreting peptides that are produced by the male extraorbital lacrimal gland to be secreted into the tear fluid. Other mice including females detect these peptides through receptors in the vomeronasal organ, and the receptors report information on mouse-strain, sex and species. The peptides are short, all carrying an N-terminal signal-peptide to indicate they are for secretion which accounts for much of the common conservation. 91 matched cddid_all.tbl CDD pfam16591 pfam16591 435446 HBM Helical bimodular sensor domain. The HBM sensor domain has been identified primarily in bacterial chemoreceptors but is also present on histidine kinases. characteriztic features of this domain are its size of approximately 250 amino acids and its location in the bacterial periplasm. The McpS chemoreceptor of Pseudomonas putida KT2440 was found to possess an HBM sensor domain and its 3D structure in complex with physiologically relevant ligands has been reported. This domain is composed of 2 long and 4 short helices that form two modules each composed of a 4-helix bundle. The McpS chemoreceptor mediates chemotaxis towards a number of organic acids. Both modules of the McpS HBM domain contain a ligand binding site. Chemo-attractants binds to each of these sites and their binding was shown to trigger a chemotactic response. This domain is primarily found in different proteobacteria but also in archaea. Interestingly, amino acids in both ligand binding sites showed a high degree of conservation suggesting that members of this family sense similar ligands. This domain recognizes Multiple TCA cycle intermediates, citrate and alpha-ketoglutarate (Matilla et.al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 246 matched cddid_all.tbl CDD pfam16592 pfam16592 435447 Cas9_REC REC lobe of CRISPR-associated endonuclease Cas9. The REC lobe of Cas9 - the CRISPR-associated endonuclease Cas9 - includes the REC1 and REC2 domains. REC1 forms an elongated, alpha-helical structure consisting of 25 alpha helices and two beta-sheets, whereas REC2 inserted within REC1 adopts a six-helix bundle structure. The REC lobe and the NUC lobe of Cas9 fold to present a positively charged groove at their interface which accommodates the negatively charged sgRNA:target DNA heteroduplex. CRISPR (clustered regularly interspaced short palindromic repeat)-Cas system occurs naturally in bacteria as a defence against invasion by phages or other mobile genetic elements. Cas9 is targeted to specific genomic locations by sgRNAs or single guide RNAs, in order to complex with invading DNA in order to cleave it and render it inactive. 539 matched cddid_all.tbl CDD pfam16593 pfam16593 435448 Cas9-BH Bridge helix of CRISPR-associated endonuclease Cas9. Cas9-BH is the bridge helix between the NUC and the REC lobes of Cas9 - the CRISPR-associated endonuclease Cas9. The REC lobe and the NUC lobe of Cas9 fold to present a positively charged groove at their interface which accommodates the negatively charged sgRNA:target DNA heteroduplex. CRISPR (clustered regularly interspaced short palindromic repeat)-Cas system occurs naturally in bacteria as a defence against invasion by phages or other mobile genetic elements. Cas9 is targeted to specific genomic locations by sgRNAs or single guide RNAs, in order to complex with invading DNA in order to cleave it and render it inactive. 33 matched cddid_all.tbl CDD pfam16594 pfam16594 406893 ATP-synt_Z Putative AtpZ or ATP-synthase-associated. This is a family of short highly conserved plant proteins that might be associated with ATP-synthase atp operon. 53 matched cddid_all.tbl CDD pfam16595 pfam16595 435449 Cas9_PI PAM-interacting domain of CRISPR-associated endonuclease Cas9. Cas9_PI is a family found at the C-terminal of bacterial type II CRISPR system Cas9 endonuclease. This domain adopts a novel protein fold that is unique to the Cas9 family. It is positioned in the structure-DNA-complex to recognize the PAM sequence on the non-complementary DNA strand of the crRNA. PAM sequence is protospacer-adjacent motifs on DNA. See family CRISPR-DR2, Rfam:RF01315. Cas9 carries two nuclease domains, HNH and RuvC, which cleave the DNA strands that are complementary and non-complementary to the 20 nucleotide guide sequence in crRNAs, respectively. 264 matched cddid_all.tbl CDD pfam16596 pfam16596 406895 MFMR_assoc Disordered region downstream of MFMR. This is a conserved region of disorder, identified with the MobiDB database, found in plants immediately to the C-terminus of the MFMR domain. 136 matched cddid_all.tbl CDD pfam16597 pfam16597 435450 Thyroglob_assoc Thyroglobulin_1 repeat associated disordered domain. This domain of conserved disorder lies almost invariably between the two repeated Thyroglobulin_1 domains, pfam00086. 61 matched cddid_all.tbl CDD pfam16598 pfam16598 465188 Edc3_linker Linker region of enhancer of mRNA-decapping protein 3. This region is located between the LSM14 pfam12701 (Lsm) and FDF pfam09532 domains of the enhancer of mRNA-decapping protein 3. This region is predicted to be natively unstructured. Its precise functional role is not known. 91 matched cddid_all.tbl CDD pfam16599 pfam16599 465189 PTN13_u3 Unstructured linker region on PTN13 protein between PDZ. This natively unstructured region lies between the first two PDZ domains on long eukaryotic tyrosine-protein phosphatase non-receptor type 13 proteins. The function is not known. However, since each of the PDZ domains binds with a different protein it is likely to be a linker region allowing flexibility between the PDZs. 191 matched cddid_all.tbl CDD pfam16600 pfam16600 465190 Caskin1-CID Caskin1 CASK-interaction domain. The Caskin1 protein interacts with the CASK protein via this region.CASK and Caskin1 are synaptic scaffolding proteins. The binding motif on human Caskin1 is EEIWVLRK. A similar motif is found on protein MINT1 and protein TIAM1, both shown to be able to bind to CASK though the motif. MINT1 and TIAM1 are not part of this family. This region is predicted to be natively unstructured. 55 matched cddid_all.tbl CDD pfam16601 pfam16601 406900 NPF Rabosyn-5 repeating NPF sequence-motif. NPF is a natively unstructured but well-conserved region found in eukaryotic proteins of the Rabenosyn-5 type, wherein the sequence motif arginine-proline-phenylalanine followed by several glutamates and aspartates is repeated up to four times along the sequence. NPF lies between the two Rab-binding domains, for Rab-4 and Rab-5, at the C-terminal end of these proteins. Rabosyn-5 (or rabenosyn) is also involved in cell-polarity determination in developing wing epithelia of Drosophila, when the NPF-motif may be implicated. These NPF motifs create a region of strong positive surface potential which appear to bind Eps15 homology, EH or EF-hand, domains on proteins involved in vesicle trafficking. 188 matched cddid_all.tbl CDD pfam16602 pfam16602 465191 USP19_linker Linker region of USP19 deubiquitinase. This region is generally located between a CS domain pfam04969 and the enzymatic UCH domain pfam00582 of USP19 deubiquitinases. This region is predicted to be natively unstructured. Its precise functional role is not known. 121 matched cddid_all.tbl CDD pfam16605 pfam16605 465192 LSM_int_assoc LSM-interacting associated unstructured. LSM_int_assoc is a family found largely on eukaryotic SART3 proteins just upstream of their C-terminal LSM-interacting domain. This region is natively unstructured. 61 matched cddid_all.tbl CDD pfam16606 pfam16606 465193 zf-C2H2_assoc Unstructured conserved, between two C2H2-type zinc-fingers. This domain is found on a set of eukaryotic Zinc finger protein 536 transcriptional regulator proteins sandwiched between zf-C2H2, pfam00096 and zf-H2C2_2 pfam13465. It is not conserved between other pairs of the zinc-fingers on these sequences. It is natively unstructured, and its function is not known. The proteins recognize and bind 2 copies of the core DNA sequence 5'-CCCCCA-3'. 80 matched cddid_all.tbl CDD pfam16607 pfam16607 465194 CYLD_phos_site Phosphorylation region of CYLD, unstructured. CYLD_phos_site is a natively unstructured region on a subset of tumour-suppressor and de-ubiquitinating enzyme CYLD proteins in eukaryotes. It lies between the second pair of CAP_GLY domains, pfam01302, on these proteins. This region of CYLD, being unstructured, carries a number of serine residues which, in response to cellular stimuli, become phosphorylated. This transient phosphorylation-state induces ubiquitination of TRAF2, a ubiquitin ligase that catalyzes both self-ubiquitination and the ubiquitination of specific target molecules involved in signal transduction. 157 matched cddid_all.tbl CDD pfam16608 pfam16608 465195 TNRC6-PABC_bdg TNRC6-PABC binding domain. TNRC6-PABC_bdg is a natively unstructured region on the higher eukaryote TNRC6 subset of GW182 proteins that carries the binding motif for the interaction with Polyadenylate-binding protein 1, PABC. TNRC6 are trinucleotide repeat-containing gene 6 proteins required for miRNA-mediated gene silencing that are localized to the P bodies (processing bodies). P bodies are cytoplasmic mRNP aggregates that are involved in general mRNA translation repression and decay, including nonsense-mediated decay. Thus GW182 proteins are essential for microRNA-mediated translational repression and deadenylation in animal cells being a major component of miRISCs. The interaction motif that binds to PABC is ShNWPPEFHPGVPWKGLQ. This region lies between a Q-rich region and the RRM, or RNA-recognition motif, pfam13893. 290 matched cddid_all.tbl CDD pfam16609 pfam16609 465196 SH3-RhoG_link SH3-RhoGEF linking unstructured region. This family of natively unstructured but conserved residues from higher eukaryotes is found to lie between an SH3 pfam00018 and the RhoGEF, pfam00621, domains. It is serine-rich and likely to be acidic and natively unstructured. 261 matched cddid_all.tbl CDD pfam16610 pfam16610 465197 dbPDZ_assoc Unstructured region between two PDZ domains on Dlg5. dbPDZ_assoc is found on higher eukaryote Dlg5, Disks large homolog 5, proteins, lying between the second pair of PDZ domains. The sequence is natively unstructured but may just be long extensions of the PDZs on these sequences in this position. The function is not known. 81 matched cddid_all.tbl CDD pfam16611 pfam16611 435461 RGS12_us2 Unstructured region between RBD and GoLoco. RGs12_us2 is a region of Regulator of G-protein signalling 12 proteins that is natively unstructured and lies between an RBD domain and a GoLoco motif, pfam02196 and pfam02188. The function is not known. 72 matched cddid_all.tbl CDD pfam16612 pfam16612 465198 RGS12_usC C-terminal unstructured region of RGS12. RGS12_usC is a region of Regulator of G-protein signalling 12 proteins that is natively unstructured and lies at the very C-terminus. It has a highly conserved central section. The function is not known. 146 matched cddid_all.tbl CDD pfam16613 pfam16613 465199 RGS12_us1 Unstructured region of RGS12. RGS12_us1 is a region of Regulator of G-protein signalling 12 proteins that is natively unstructured and lies N-terminal to other such regions in UniProt:E1BPP4. It is very glycine-rich, and the function is not known. 118 matched cddid_all.tbl CDD pfam16614 pfam16614 465200 RhoGEF67_u2 Unstructured region two on RhoGEF 6 and 7. RhoGEF67_u2 is a region of natively unstructured residues on Rho guanine nucleotide exchange factor 6 and 7 proteins. The function is not known. It lies after the PH domain and before the C-terminal coiled-coil. 99 matched cddid_all.tbl CDD pfam16615 pfam16615 465201 RhoGEF67_u1 Unstructured region one on RhoGEF 6 and 7. RhoGEF67_u1 is a region of natively unstructured residues on Rho guanine nucleotide exchange factor 6 and 7 proteins. The function is not known. It lies between the CH and the SH3 domains. 47 matched cddid_all.tbl CDD pfam16616 pfam16616 465202 PHC2_SAM_assoc Unstructured region on Polyhomeotic-like protein 1 and 2. PHC2_SAM_assoc is a natively unstructured region on Polyhomeotic-like proteins 1 and 2, that lies immediately upstream of the SAM domain, pfam00536. The function is not known. 123 matched cddid_all.tbl CDD pfam16617 pfam16617 435467 INTAP Intersectin and clathrin adaptor AP2 binding region. INTAP is a natively unstructured region of intersectin 1 proteins, lying between the first pair of SH3 domains, that binds to the clathrin adaptor AP2. This binding forms an intersectin-AP2 complex that functions as an important regulator of clathrin-mediated SV recycling in synapses. 115 matched cddid_all.tbl CDD pfam16618 pfam16618 435468 SH3-WW_linker Linker region between SH3 and WW domains on ARHGAP12. SH3-WW_linker is a natively unstructured region on Rho-GTPase activating factor 12 proteins that lies between the SH3 and the WW domains. it is found in higher eukaryotes, and the function is not known. 197 matched cddid_all.tbl CDD pfam16619 pfam16619 465203 SUIM_assoc Unstructured region C-term to UIM in Ataxin3. SUIM_assoc is a natively unstructured region on Ataxin 3 proteins that lies immediately C-terminal to the second UIM domain linking it to a third when present. The function is not known. It is rich in glutamine residues. 60 matched cddid_all.tbl CDD pfam16620 pfam16620 435470 23ISL Unstructured linker between I-set domains 2 and 3 on MYLCK. 23ISL is a natively unstructured region lying between the second and third I-set domains on higher eukaryotic myosin light chain kinase (MYLCK) proteins. The function is not known. It carries a highly conserved TSSTITLQ sequence motif which might be a binding domain. 162 matched cddid_all.tbl CDD pfam16621 pfam16621 465204 NECFESHC SH3 terminal domain of 2nd SH3 on Neutrophil cytosol factor 1. NECFESHC is the C-terminal domain of the second SH3 domain found on neutrophil cytosol factor 1 or p47phox proteins in higher eukaryotes. It is not unstructured as illustrated by the structure of PDB:1ng2. 50 matched cddid_all.tbl CDD pfam16622 pfam16622 465205 zf-C2H2_11 zinc-finger C2H2-type. Zinc-finger of C2H2 type found in higher eukaryotes. 27 matched cddid_all.tbl CDD pfam16623 pfam16623 465206 WW_FCH_linker Unstructured linker region between on GAS7 protein. WW_FCH_linker is a natively unstructured region on GAS7 or Growth arrest-specific protein 7 higher eukaryote proteins. It lies between the WW and the FCH domains. The function is not known but it carries a highly conserved TINCVTFP sequence motif which might be a binding domain. 92 matched cddid_all.tbl CDD pfam16624 pfam16624 465207 zf-C2H2_assoc2 Unstructured region upstream of a zinc-finger. zf-C2H2_assoc2 is a short region of natively unstructured sequence immediately upstream of a C2H2-type zinc-finger on eukaryotic Zinc-finger proteins 592 and 800. The function is not known. 95 matched cddid_all.tbl CDD pfam16625 pfam16625 435475 ISET-FN3_linker Unstructured linking region I-set and fnIII on Brother of CDO. ISET-FN3_linker is a short section of natively unstructured sequence on Biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding proteins or Brother of CDO. It is found in higher eukaryotes and lies between the second I-set and the first fnIII domains, pfam07679 and pfam00041. The function is not known. 65 matched cddid_all.tbl CDD pfam16626 pfam16626 374683 Papilin_u7 Linking region between Kunitz_BPTI and I-set on papilin. Papilin_u7 is a conserved region of natively unstructured residues on proteoglycan-like sulfated glycoprotein - papilin 0 in higher eukaryotes. It links the Kunitz_BPTI, pfam00014, and I-set domains pfam07679. The function is not known. 92 matched cddid_all.tbl CDD pfam16627 pfam16627 406921 BRX_assoc Unstructured region between BRX_N and BRX domain. BRX_assoc is a short stretch of plant transcription regulator proteins carrying the BRX domain that is natively unstructured. It connects the BRX_N and BRX domains in plant transcription regulators. The function is not known. 70 matched cddid_all.tbl CDD pfam16628 pfam16628 374685 Mac_assoc Unstructured region on maltose acetyltransferase. Mac_assoc is a region of natively unstructured residues on fungal maltose acetyltransferase proteins. It lies just upstream of the Mac, pfam12464, domain linking it with the upstream Zn_clus, pfam00172, the Zn(2)-Cys(6) binuclear cluster. the function of this region is not known. 185 matched cddid_all.tbl CDD pfam16629 pfam16629 435476 Arm_APC_u3 Armadillo-associated region on APC. Arm_APC_u3 is a semi-unstructured region lying immediately downstream of the armadillo fold before the beta-catenin binding motifs, APC_crr, pfam05923, on APC or adenomatous polyposis coli proteins in higher eukaryotes. The function is not known. 293 matched cddid_all.tbl CDD pfam16630 pfam16630 406923 APC_u5 Unstructured region on APC between 1st and 2nd catenin-bdg motifs. APC_u5 is a short region of natively unstructured sequence lying between the first and the second 15-residue beta-catenin binding motifs, APC_15aa, pfam05972, on APC or adenomatous polyposis coli proteins in higher eukaryotes. The function is not known. 100 matched cddid_all.tbl CDD pfam16631 pfam16631 465208 TUTF7_u4 Unstructured region 4 on terminal uridylyltransferase 7. TUTF7_u4 is the fourth natively unstructured region found on a set of higher eukaryote Terminal uridylyltransferase 7 proteins. The function is not known. The region is rich in arginine and lysine. 88 matched cddid_all.tbl CDD pfam16632 pfam16632 465209 Caskin-tail C-terminal region of Caskin. This region is found at the C-terminus of Caskin proteins. Caskins are CASK-binding synaptic scaffolding proteins. Part of this region is predicted to be in coiled-coil conformation. Its function is not known. 61 matched cddid_all.tbl CDD pfam16633 pfam16633 435478 APC_u9 Unstructured region on APC between 1st two creatine-rich regions. APC_u9 is a short region of natively unstructured sequence lying between the first and second APC_crr, pfam05923, domains on APC or adenomatous polyposis coli proteins in higher eukaryotes. The function is not known. 89 matched cddid_all.tbl CDD pfam16634 pfam16634 406927 APC_u13 Unstructured region on APC between APC_crr and SAMP. APC_u13 is a short region of natively unstructured sequence lying between the fourth creatine-rich region, APC_crr, pfam05923, and the SAMP pfam05924, domains on APC or adenomatous polyposis coli proteins in higher eukaryotes. The function is not known. 54 matched cddid_all.tbl CDD pfam16635 pfam16635 435479 APC_u14 Unstructured region on APC between SAMP and APC_crr. APC_u14 is a short region of natively unstructured sequence lying between the second SAMP pfam05924, and the fifth creatine-rich region, APC_crr, pfam05923, on APC or adenomatous polyposis coli proteins in higher eukaryotes. The function is not known. 94 matched cddid_all.tbl CDD pfam16636 pfam16636 435480 APC_u15 Unstructured region on APC between APC_crr regions 5 and 6. APC_u15 is a short region of natively unstructured sequence lying between the fifth and sixth creatine-rich, APC_crr, pfam05923, domains on APC or adenomatous polyposis coli proteins in higher eukaryotes. The function is not known. 81 matched cddid_all.tbl CDD pfam16637 pfam16637 465210 zf-C2H2_assoc3 Putative zinc-finger between two C2H2 zinc-fingers on Patz. zf-C2H2_assoc3 is a partially unstructured region on Patz or POZ-, AT hook-, and zinc finger-containing proteins of higher eukaryotes. It lies between the two C2H2-type zinc-fingers towards the C-terminus of these proteins and may well be an unusual zinc-finger itself. 75 matched cddid_all.tbl CDD pfam16638 pfam16638 465211 Tristanin_u2 Unstructured region on methyltransferase between zinc-fingers. Tristanin_u2 is a region of natively unstructured sequence on tristanin like or PR domain zinc finger protein 10s found in higher eukaryotes. It lies between two C2H2-type zinc-fingers. The function is not known. 130 matched cddid_all.tbl CDD pfam16639 pfam16639 435483 Apocytochr_F_N Apocytochrome F, N-terminal. This is the N-terminal domain of cytochrome f. It is a soluble lumen-side domain. 154 matched cddid_all.tbl CDD pfam16640 pfam16640 406933 Big_3_5 Bacterial Ig-like domain (group 3). This family consists of bacterial domains with an Ig-like fold. 90 matched cddid_all.tbl CDD pfam16641 pfam16641 465212 CLIP1_ZNF CLIP1 zinc knuckle. This zinc knuckle domain is found tandemly repeated at the C-terminal of the cytoplasmic linker protein CLIP1 (CLIP170). It forms a complex with the CAP-Gly domain of Dynactin. 17 matched cddid_all.tbl CDD pfam16642 pfam16642 465213 KCNQ2_u3 Unstructured region on Potassium channel subunit alpha KvLQT2. KCNQ2_u3 is a region of natively unstructured sequence on potassium voltage-gated channel subfamily KQT member 2 proteins from higher eukaryotes. It lies between families KCNQ_channel, pfam03520, and KCNQC3-Ank_bd, pfam11956. The function is not known. 98 matched cddid_all.tbl CDD pfam16643 pfam16643 406936 cNMPbd_u2 Unstructured region on cNMP-binding protein. cNMPbd_u2 is a natively unstructured region on a set of higher eukaryote cyclic nucleotide-binding domain-containing proteins. It lies between the second cNMP_binding, pfam00027, and the F-box, pfam00646, domains. The function is not known but there is a highly conserved DPDPFL sequence motif. 163 matched cddid_all.tbl CDD pfam16644 pfam16644 465214 NEXCaM_BD Regulatory region of Na+/H+ exchanger NHE binds to calmodulin. NEXCaM_BD is a coiled-coil domain found as part of the regulatory, C-terminal region of the 12-14 TM sodium/proton exchangers (NHEs)2 of the solute carrier 9 (SLC9) family in all animal kingdoms. The C- lobe of CaM binds the first alpha-helix of the NHE, or NEXCaM_BD region, and the N-lobe of CaM binds the second helix of NEXCaM_BD. 109 matched cddid_all.tbl CDD pfam16645 pfam16645 318786 PHtD_u1 Unstructured region on Pneumococcal histidine triad protein. PHtD_u1 is a natively unstructured region on Pneumococcal histidine triad proteins of higher eukaryotes lying between the first two Strep_his_triad domains so far identified, pfam04270. The function is not known but it does not carry the characteriztic histidine triad. 56 matched cddid_all.tbl CDD pfam16646 pfam16646 465215 AXIN1_TNKS_BD Axin-1 tankyrase binding domain. This is the N-terminal domain tankyrase binding domain of Axin-1. 75 matched cddid_all.tbl CDD pfam16647 pfam16647 406939 GCSF Granulocyte colony-stimulating factor. GCSF is a family of higher eukaryotic granulocyte colony-stimulating factor proteins. Granulocyte colony-stimulating factors are cytokines that are involved in haematopoeisis. They control the production, differentiation and function of white blood cell granulocytes. GCSF binds to the extracellular Ig-like and CRH domain of its receptor GCSFR, thereby triggering the receptor to homodimerize. Homodimerization result in activation of Janus tyrosine kinase-signal transducers and other activators of transcription (JAK-STAT)-type signalling cascades. 149 matched cddid_all.tbl CDD pfam16648 pfam16648 465216 Calpain_u2 Unstructured region on Calpain-3. Calpain_u2 is a region of natively unstructured sequence that lies between the Calpain_III, pfam01067 and the first EF-hand, Pfam;PF13833, domains on higher eukaryote calpain-3 proteins. The function is not known. 67 matched cddid_all.tbl CDD pfam16649 pfam16649 465217 IL23 Interleukin 23 subunit alpha. This family, interleukin 23 subunit alpha, is a heterodimer consisting of a 40 kDa subunit - p40 - that is shared with IL12 and a unique 19 kDa subunit - p19. IL23 is a pro-inflammatory cytokine that binds to adnectins and thus plays a key role in the pathogenesis of several autoimmune and inflammatory diseases. IL23 signalling on the cell membrane works through the interaction of four proteins, two of which are shared with the IL12-receptor complex; signalling through the cell membrane involves the combined aggregation of at least two receptor components and then the subsequent activation of the Jak/Tyk tyrosine kinases and the family of STAT transcription factors. 158 matched cddid_all.tbl CDD pfam16650 pfam16650 293256 SPEG_u2 Unstructured region on SPEG complex protein. SPEG_u2 is a region of natively unstructured but conserved sequence on Striated muscle-specific serine/threonine-protein kinase proteins in higher eukaryotes. It lies between two I-set immunoglobulin, pfam07679, domains. The function is not known. 57 matched cddid_all.tbl CDD pfam16652 pfam16652 465218 PH_13 Pleckstrin homology domain. 143 matched cddid_all.tbl CDD pfam16653 pfam16653 465219 Sacchrp_dh_C Saccharopine dehydrogenase C-terminal domain. This family comprises the C-terminal domain of saccharopine dehydrogenase. In some organizms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase. The saccharopine dehydrogenase can also function as a saccharopine reductase. 255 matched cddid_all.tbl CDD pfam16654 pfam16654 435491 DAPDH_C Diaminopimelic acid dehydrogenase C-terminal domain. This family comprises the C-terminal domain of diaminopimelic acid dehydrogenase. Diaminopimelate dehydrogenase is a NADPH-dependent enzyme that catalyzes the oxidative deamination of meso-2,6-diaminopimelate, which is the direct precursor of L-lysine in bacterial lysine biosynthesis. 154 matched cddid_all.tbl CDD pfam16655 pfam16655 379867 PhoD_N PhoD-like phosphatase, N-terminal domain. This domain is found at the N-terminus of proteins in the PhoD family pfam09423. 89 matched cddid_all.tbl CDD pfam16656 pfam16656 465220 Pur_ac_phosph_N Purple acid Phosphatase, N-terminal domain. This domain is found at the N-terminus of Purple acid phosphatase proteins. 93 matched cddid_all.tbl CDD pfam16657 pfam16657 435493 Malt_amylase_C Maltogenic Amylase, C-terminal domain. This is the C-terminal domain of Maltogenic amylase, an enzyme that hydrolyses starch material. Maltogenic amylases are central to carbohydrate metabolism. 75 matched cddid_all.tbl CDD pfam16658 pfam16658 465221 RF3_C Class II release factor RF3, C-terminal domain. 129 matched cddid_all.tbl CDD pfam16660 pfam16660 465222 PHD20L1_u1 PHD finger protein 20-like protein 1. PHD20L1_u1 is a region of natively unstructured but highly conserved sequence on a set of higher eukaryotic PHD finger protein 20-like protein 1 like proteins. The function is not known. 68 matched cddid_all.tbl CDD pfam16661 pfam16661 406948 Lactamase_B_6 Metallo-beta-lactamase superfamily domain. This family is part of the metallo-beta-lactamase superfamily. 192 matched cddid_all.tbl CDD pfam16662 pfam16662 406949 FLYWCH_u FLYWCH-type zinc finger-containing protein 1. FLYWCH_u is a region of natively unstructured but conserved sequence that lies between the FLYWCH zinc-finger domains on FLYWCH-type zinc finger-containing protein 1 proteins in higher eukaryotes. The function is not known but the N- and C-termini are likely to be part of the zinc-finger domains specific, to the eukaryotes. 62 matched cddid_all.tbl CDD pfam16663 pfam16663 435496 MAGI_u1 Unstructured region on MAGI. MAGI_u3 is a region of natively unstructured but highly conserved sequence on a subset, of higher eukaryote, membrane-associated guanylate kinase with WW and PDZ domain-containing proteins. The function is not known. 60 matched cddid_all.tbl CDD pfam16664 pfam16664 435497 STAC2_u1 Unstructured on SH3 and cysteine-rich domain-containing protein 2. STAC2_u1 is a region of natively unstructured but highly conserved sequence between C1_1 pfam00130, and an SH3 domain, eg pfam00018, on SH3 and cysteine-rich domain-containing proteins from higher eukaryotes. The function is not known. 125 matched cddid_all.tbl CDD pfam16665 pfam16665 465223 NCOA_u2 Unstructured region on nuclear receptor coactivator protein. NCOA_u2 is a region of natively unstructured but highly conserved sequence found on higher eukaryote nuclear receptor coactivator proteins. It lies between a PAS domain, pfam14598 and a steroid receptor coactivator domain, pfam08832. The function is not known. 119 matched cddid_all.tbl CDD pfam16666 pfam16666 465224 MAGI_u5 Unstructured region on MAGI. MAGI_u5 is a region of natively unstructured but highly conserved sequence on a subset, of higher eukaryote, membrane-associated guanylate kinase with WW and PDZ domain-containing proteins. The function is not known. This region lies between two PDZ, pfam00595 domains. 96 matched cddid_all.tbl CDD pfam16667 pfam16667 435500 MPDZ_u10 Unstructured region 10 on multiple PDZ protein. MPDZ_u10 is a region of natively unstructured but highly conserved sequence on multiple-PDZ-containing domain proteins in higher eukaryotes. It lies between two PDZ domains, pfam00595. The function is not known. 65 matched cddid_all.tbl CDD pfam16668 pfam16668 293273 JLPA Adhesin from Campylobacter. JLPA is a surface-exposed lipoprotein adhesin that promotes interaction with the host epithelial cells. It is found in the genus Campylobacter, and the structure is an unclosed half beta-barrel fold with a wide hydrophobic concave face; this represents a novel bacterial surface lipoprotein. 352 matched cddid_all.tbl CDD pfam16669 pfam16669 465225 TTC5_OB Tetratricopeptide repeat protein 5 OB fold domain. This OB fold domain is located at the C-terminus of Tetratricopeptide repeat protein 5 and is required for effective p53 response. 115 matched cddid_all.tbl CDD pfam16670 pfam16670 435502 PI-PLC-C1 Phosphoinositide phospholipase C, Ca2+-dependent. PI-PLC-C1 is a family of calcium 2+-dependent phosphatidylinositol-specific phospholipase C1 enzymes from bacteria and fungi. The enzyme classification number is EC:3.1.4.11. This enzyme is involved in part of the myo-inositol phosphate metabolic pathway. 330 matched cddid_all.tbl CDD pfam16671 pfam16671 293276 ACD Actin cross-linking domain. This domain is found in Vibrio cholerae RtxA toxin and VgrG1 protein. This domain cross-links to G-actin leading to cytoskeletal changes. 386 matched cddid_all.tbl CDD pfam16672 pfam16672 406957 LAMTOR5 Ragulator complex protein LAMTOR5. 88 matched cddid_all.tbl CDD pfam16673 pfam16673 465226 TRAF_BIRC3_bd TNF receptor-associated factor BIRC3 binding domain. This domain is found in TNF receptor-associated factor 1 and 2 (TRAF1 and TRAF2), where it binds to Baculoviral IAP repeat-containing protein 3 (BIRC3) (cIAP2). 64 matched cddid_all.tbl CDD pfam16674 pfam16674 465227 UCH_N N-terminal of ubiquitin carboxyl-terminal hydrolase 37. UCH_N is a domain found at the N-terminus of ubiquitin carboxyl-terminal hydrolase 37 or 26. The function is not known. 102 matched cddid_all.tbl CDD pfam16675 pfam16675 465228 FOXO_KIX_bdg KIX-binding domain of forkhead box O, CR2. FOXO_KIX_bd is the first part of the region of transcription factor forkhead box O family proteins that binds to the CREB-binding proteins via the KIX domain. Coactivator CBP/p300 is recruited by FOXO3 via the binding of this domain as well as the simultaneous binding of the more C-terminal TAD domain. 80 matched cddid_all.tbl CDD pfam16676 pfam16676 435506 FOXO-TAD Transactivation domain of FOXO protein family. TAD is a promiscuous binding domain that mediates the association of the transcription factor FOXO with the coactivator CBP/p300. Both this domain and the FOXO-KIX_bd family pfam16675 bind simultaneously the KIX domain of CBP/p300. Coactivator CBP/p300 is recruited by FOXO3 though binding to these two regions. The promiscuity of the TAD is further evidenced by that the finding that they also bind the TAZ1 and TAZ2 domains of CBP/p300. 40 matched cddid_all.tbl CDD pfam16677 pfam16677 435507 GP3_package DNA-packaging protein gp3. DNA-packaging protein gp3 (terminase small subunit) is involved in DNA packing in bacteriophage. it contains a channel where DNA is bound and passed to DNA-packaging protein gp2 (terminase large subunit). 106 matched cddid_all.tbl CDD pfam16678 pfam16678 465229 HOIP-UBA HOIP UBA domain pair. HOIP-UB is a binding domain on E3 ubiquitin-protein ligase RNF31 like proteins. E3 ubiquitin-protein ligase RNF31 is often referred to as HOIL-1L binding partner. The interaction of HOIL-1L and HOIP is thus via the UBL-UBA interaction. this interaction is important in E3 complex formation and the subsequent activation of NF-kappaB. This family contains two UBA-like domains. 150 matched cddid_all.tbl CDD pfam16679 pfam16679 465230 CDT1_C DNA replication factor Cdt1 C-terminal domain. This is the C-terminal domain of DNA replication factor Cdt1. This domain binds the MCM complex. 96 matched cddid_all.tbl CDD pfam16680 pfam16680 465231 Ig_4 T-cell surface glycoprotein CD3 delta chain. This is an immunoglobulin-like domain. It is found on the T-cell surface glycoprotein CD3 delta chain. CD3delta and CD3epsilon complex together as part of the T-cell receptor complex. 63 matched cddid_all.tbl CDD pfam16681 pfam16681 465232 Ig_5 Ig-like domain on T-cell surface glycoprotein CD3 epsilon chain. Ig_5 is an immunoglobulin domain found on T-cell surface glycoprotein CD3 epsilon chain. It forms a first-order complex with T-cell surface glycoprotein CD3 delta chain as part of the T-cell receptor complex. 75 matched cddid_all.tbl CDD pfam16682 pfam16682 435512 MSL2-CXC CXC domain of E3 ubiquitin-protein ligase MSL2. MSL2-CXC is an autonomously folded domain containing that binds three zinc ions. It lies on the E3 ubiquitin-protein ligase MSL2 in eukaryotes. The CXC domain critically contributes to the DNA-binding activity of MSL2. It carries 9 invariant cysteines within about a 50 residue region. 55 matched cddid_all.tbl CDD pfam16683 pfam16683 406967 TGase_elicitor Transglutaminase elicitor. TGase_elicitor is a family of largely oomycete sequences from plant pathogens that elicit transglutaminase/acyltransferase activity. The enzyme classification is E.C:2.3.2.13. From the presence of sequences from Vibrio spp one can propose a lateral gene transfer event having occurred between bacteria and oomycetes to the probable selective advantage of the pathogen. 361 matched cddid_all.tbl CDD pfam16684 pfam16684 406968 Telomere_res Telomere resolvase. Telomere resolvase (protelomerase) catalyzes the conversion of linear double-stranded DNA into hairpin telomeres. 272 matched cddid_all.tbl CDD pfam16685 pfam16685 435513 zf-RING_10 zinc RING finger of MSL2. zf-RING_10 is an N-terminal domain on E3 ubiquitin-protein ligase msl-2 proteins. The domain binds MSL1 and exhibits ubiquitin E3 ligase activity towards H2B K34, the histone proteins. 70 matched cddid_all.tbl CDD pfam16686 pfam16686 435514 POT1PC ssDNA-binding domain of telomere protection protein. POT1PC is the ssDNA-binding domain on a family of fungal telomere protection protein 1 proteins. POT1PC is able to accommodate heterogeneous ssDNA ligands. Pot1 proteins are the proteins responsible for binding to and protecting the 3' single-stranded DNA (ssDNA) overhang at most eukaryotic telomeres. 152 matched cddid_all.tbl CDD pfam16687 pfam16687 465233 ELYS-bb beta-propeller of ELYS nucleoporin. ELYS-bb is the N-terminal seven-bladed beta-propeller domain of ELYS nucleoporins in higher eukaryotes. It is required for anchorage of the nucleoporin to the nuclear envelope during cell-division. 488 matched cddid_all.tbl CDD pfam16688 pfam16688 465234 CNV-Replicase_N Replicase polyprotein N-term from Coronavirus nsp1. CNV-Replicase_N is the N-terminal domain of a family of ssRNA positive-stranded porcine transmissible gastroenteritis coronaviruses. the domain folds into a six-stranded beta-barrel fold with a long alpha helix on the rim of the barrel. This fold is shared with SARS-CoV nsp1. 108 matched cddid_all.tbl CDD pfam16689 pfam16689 435517 APC_N_CC Coiled-coil N-terminus of APC, dimerization domain. APC_N_CC is the N-terminal, coiled-coil dimerization domain of the adenomatosis polyposis coli (APC) tumour-repressor proteins. It plays a key role in the regulation of cellular levels of the oncogene product beta-catenin. Coiled-coil regions are binding repeats that in this case bind to the armadillo repeat region of beta-catenin. 52 matched cddid_all.tbl CDD pfam16690 pfam16690 465235 MMACHC Methylmalonic aciduria and homocystinuria type C family. 216 matched cddid_all.tbl CDD pfam16691 pfam16691 435519 DUF5062 Domain of unknown function (DUF5062). This family is found in Vibrio spp. The function is not known. 83 matched cddid_all.tbl CDD pfam16692 pfam16692 465236 Folliculin_C Folliculin C-terminal domain. This is the C-terminal domain of folliculin. It has guanine nucleotide exchange factor (GEF) activity. 226 matched cddid_all.tbl CDD pfam16693 pfam16693 293298 Yop-YscD_ppl Inner membrane component of T3SS, periplasmic domain. Yop-YscD-ppl is the periplasmic domain of Yop proteins like YscD from Proteobacteria. YscD forms part of the inner membrane component of the bacterial type III secretion injectosome apparatus. 254 matched cddid_all.tbl CDD pfam16694 pfam16694 435521 Cytochrome_P460 Cytochrome P460. 122 matched cddid_all.tbl CDD pfam16695 pfam16695 435522 Tai4 Type VI secretion system (T6SS), amidase immunity protein. Tai4 is a new form of autoimmunity protein for a type VI secretion system, T6SS. T6SS has roles in interspecies interactions, as well as higher order host-infection, by injecting effector proteins into the periplasmic compartment of the recipient cells of closely related species. Pseudomonas aeruginosa produces at least three effector proteins to other cells and thus has three specific cognate immunity proteins to protect itself. Tae4, or type VI amidase effector 4, in Enterobacter cloacae has a cognate Tai4 or type VI amidase immunity 4 protein. The effector is Tae4, pfam14113. 91 matched cddid_all.tbl CDD pfam16696 pfam16696 465237 ZFYVE21_C Zinc finger FYVE domain-containing protein 21 C-terminus. This is the C-terminal domain of Zinc finger FYVE domain-containing protein 21. It has a PH-like fold and is required for the regulation of focal adhesions and in cell migration. 126 matched cddid_all.tbl CDD pfam16697 pfam16697 465238 Yop-YscD_cpl Inner membrane component of T3SS, cytoplasmic domain. Yop-YscD-cpl is the cytoplasmic domain of Yop proteins like YscD from Proteobacteria. YscD forms part of the inner membrane component of the bacterial type III secretion injectosome apparatus. 94 matched cddid_all.tbl CDD pfam16698 pfam16698 465239 ADAM17_MPD Membrane-proximal domain, switch, for ADAM17. ADAM17_MPD is the membrane-proximal domain of a family of disintegrin and metalloproteinase domain-containing protein 17 found in metazoan species. ADAM17 is a major sheddase that is responsible for the regulation of a wide range of biological processes, such as cellular differentiation, regeneration, and cancer progression. This MPD region acts as the sheddase switch. PDI or protein-disulfide isomerase interacts with ADAM17 and to down-regulate its enzymatic activity. The interaction is directly with the MPD, the region of dimerization and substrate recognition, where it catalyzes an isomerization of disulfide bridges within the thioredoxin motif CXXC. this isomerization results in a major structural change between an active, open state and an inactive, closed state of the MPD. This change is thought to act as a molecular switch, allowing a global reorientation of the extracellular domains in ADAM17 and regulating its shedding activity. 62 matched cddid_all.tbl CDD pfam16699 pfam16699 465240 CSTF1_dimer Cleavage stimulation factor subunit 1, dimerization domain. This family is the dimerization domain, at the N-terminal, of a family of cleavage stimulation factor subunit 1 proteins from eukaryotes. This domain allows for homodimerization such that the functional state of CSTF1 is a heterohexamer. The cleavage stimulation factor (CstF) complex is composed of three subunits and is essential for pre-mRNA 3'-end processing. CstF recognizes U and G/U-rich cis-acting RNA sequence elements and helps to stabilize the cleavage and polyadenylation specificity factor (CPSF) at the polyadenylation site as required for productive RNA cleavage. 57 matched cddid_all.tbl CDD pfam16700 pfam16700 435527 SNCAIP_SNCA_bd Synphilin-1 alpha-Synuclein-binding domain. This coiled-coil domain found in Synphilin-1 is responsible for binding to alpha-Synuclein. 45 matched cddid_all.tbl CDD pfam16701 pfam16701 435528 Ad_Cy_reg Adenylate cyclase regulatory domain. This domain regulates the activity of Actinobacterial adenylate cyclase in a pH-dependent manner, allowing activation at acidic pH. 185 matched cddid_all.tbl CDD pfam16702 pfam16702 435529 DUF5063 Domain of unknown function (DUF5063). 167 matched cddid_all.tbl CDD pfam16703 pfam16703 435530 DUF5064 Domain of unknown function (DUF5064). This is found in Pseudomonas species. Several members are annotated as being acetyl-CoA carboxylase alpha subunit, but his could not be confirmed. 117 matched cddid_all.tbl CDD pfam16704 pfam16704 435531 Rab_bind Rab binding domain. This coiled-coil domain, found in GRIP and coiled-coil domain-containing protein 2 and RANBP2-like and GRIP domain-containing protein, has been shown to bind to Rab in GRIP and coiled-coil domain-containing protein 2. 65 matched cddid_all.tbl CDD pfam16705 pfam16705 465241 NUDIX_5 NUDIX, or N-terminal NPxY motif-rich, region of KRIT. NUDIX_5 is found in higher eukaryotes at the N-terminus of KRIT1 or Krev interaction trapped proteins. NUDIX_5 carries three NPxY-like motifs, and it is found to bind the integrin cytoplasmic-associated protein 1 ICAP1. In the absence of KRIT1 ICAP1 binds via its C-terminal PH/PTB fold domain to the integrin beta-1 cytoplasmic tail. Binding of KRIT1 to ICAP1 via NUDIX_5 out-competes the binding of ICAP1 to integrin cytoplasmic tails such that ICAP1 is sequestered in the nucleus. Integrin activation is thus prevented. 169 matched cddid_all.tbl CDD pfam16706 pfam16706 465242 Izumo-Ig Izumo-like Immunoglobulin domain. Izumo-Ig is the immunoglobulin domain on Izumo proteins from higher eukaryotes. Izumo is a typical type I membrane glycoprotein with one immunoglobulin-like domain and a putative N-glycoside link motif - glycosylation site. The full-length protein, eg Swiss:Q8IYV9, is a molecule with a single immunoglobulin (Ig) domain. It is thought that Izumo proteins bind to putative Izumo receptors on the oocyte. Izumo is not detectable on the surface of fresh sperm but becomes exposed only after an exocytotic process, the acrosome reaction, has occurred. Studies have shown that knock-out mice (Izumo-/- males) were sterile despite normal mating behaviour and ejaculation, indicating the importance of the protein in fertilization. There is a conserved GCL sequence motif. Izumo expression has been found to be testis-specific. 88 matched cddid_all.tbl CDD pfam16707 pfam16707 406984 CagS Cag pathogenicity island protein S of Helicobacter pylori. CagS is a family of proteins from the pathogenicity island of Helicobacter pylori. The gene lies just downstream of the cluster whose protein-products resemble those of the Vibrio proteins that form the structural core of T4SS. The exact function of CagS is not known. 196 matched cddid_all.tbl CDD pfam16708 pfam16708 406985 LppA Lipoprotein confined to pathogenic Mycobacterium. This is a family of lipoproteins found only in pathogenic mycobacteria. These pathogenic lipoproteins may play a role in host-pathogen interactions. Lipoproteins localized to the cell-envelope of pathogenic bacteria are major determinants of virulence. The proteins are localized to the cell-surface via an N-terminal lipidation carried out by a transferase - pro-lipoprotein diacylglyceryl transferase Lgt - which attaches a diacylglyceride molecule to a sulfur atom from a crucial cysteine, and a consecutively acting lipoprotein signal peptidase LspA that cleaves the signal peptide just before the modified cysteine. When the peptidase is inactivated the pathogen has difficulty in replicating inside macrophages. 153 matched cddid_all.tbl CDD pfam16709 pfam16709 465243 SCAB-Ig Ig domain of plant-specific actin-binding protein. This family is an Ig-like domain found on plant-specific actin-binding proteins or SCABs. SCAB proteins bind, bundle and stabilize actin filaments and regulate stomatal movement. The Ig-PH fusion domain is at the C-terminus. This domain is an Ig beta-sandwich fold consisting of two antiparallel beta-sheets built from strands beta1 and beta2 and strands beta3-beta6, respectively. 98 matched cddid_all.tbl CDD pfam16710 pfam16710 293315 CTXphi_pIII-N1 N-terminal N1 domain of Vibrio phage CTXphi pIII. CTXphi_pIII-N1 is the N-terminal domain, N1, of the pIII protein of the CTXphi bacteriophage of Vibrio cholerae. CTXphi is a ssDNA Inovirus. pIII is a minor coat protein. This domain interacts directly with the C-terminus of TolA, a periplasmic protein of Vibrio cholerae itself as part of the infection mechanism. 111 matched cddid_all.tbl CDD pfam16711 pfam16711 374744 SCAB-ABD Actin-binding domain of plant-specific actin-binding protein. SCAB-ABD is the actin-binding domain of plant-specific actin-binding proteins or SCABs. SCAB proteins bind, bundle and stabilize actin filaments and regulate stomatal movement. The Ig-PH fusion domain is at the C-terminus. The ABD is structurally independent from the first coiled-coil, CC1, domain which is also involved in binding; the CC1 is likely to function as a dimerization module, 41 matched cddid_all.tbl CDD pfam16712 pfam16712 465244 SCAB_CC Coiled-coil regions of plant-specific actin-binding protein. SCAB_CC is the two coiled-coil, dimerization domains of plant-specific actin-binding proteins or SCABs, CC1 and CC2, both of which contribute independently to dimerization. CC1 is also required for actin binding, indicating that SCAB1 is a bivalent actin cross-linker. since CC1 adopts an antiparallel helical hairpin that further dimerizes into a four-helix bundle. SCAB proteins bind, bundle and stabilize actin filaments and regulate stomatal movement, 168 matched cddid_all.tbl CDD pfam16713 pfam16713 293318 EAGR_box Enriched in aromatic and glycine Residues box. The Enriched in Aromatic and Glycine Residues (EAGR) box is found in proteins from Mycoplasma, often tandemly repeated, and may have a role in cell motility. 34 matched cddid_all.tbl CDD pfam16714 pfam16714 435535 TyrRSs_C Tyrosyl-tRNA synthetase C-terminal domain. This domain is found at the C-terminus of fungal tyrosyl-tRNA synthetases. It binds to group I introns. 120 matched cddid_all.tbl CDD pfam16715 pfam16715 435536 CDPS Cyclodipeptide synthase. This family of proteins includes enzymes involved in the synthesis of cyclodipeptides using aminoacyl-tRNAs as substrates, including cyclo(L-leucyl-L-leucyl) synthase, cyclo(L-tyrosyl-L-tyrosyl) synthase and cyclo(L-leucyl-L-phenylalanyl) synthase. They are structurally similar to class Ic aminoacyl-tRNA synthetases (aaRSs). 220 matched cddid_all.tbl CDD pfam16716 pfam16716 465245 BST2 Bone marrow stromal antigen 2. 91 matched cddid_all.tbl CDD pfam16717 pfam16717 435537 RAC_head Ribosome-associated complex head domain. The RAC head domain is involved in ribosome binding. 87 matched cddid_all.tbl CDD pfam16718 pfam16718 374750 IFS Immunity factor for SPN. Immunity factor for SPN (IFS) binds to and inhibits the SPN toxin. 164 matched cddid_all.tbl CDD pfam16719 pfam16719 465246 SAWADEE SAWADEE domain. The SAWADEE domain, found in plant homeobox proteins, has a pair of tandem tudor-like folds that bind chromatin. 126 matched cddid_all.tbl CDD pfam16720 pfam16720 374752 Albumin_I_a Albumin I chain a. The albumin I protein, a hormone-like peptide, stimulates kinase activity upon binding a membrane bound 43 kDa receptor. This domain represents the a chain. 48 matched cddid_all.tbl CDD pfam16721 pfam16721 293326 zf-H3C2 Zinc-finger like, probable DNA-binding. This is a family of probably DNA-binding zinc-fingers found on Gag-Pol polyproteins from mouse retroviruses. Added to clan to resolve overlaps with zf-H2C2, but neither are true members. 96 matched cddid_all.tbl CDD pfam16722 pfam16722 406993 SAPIS-gp6 Pathogenicity island protein gp6 in Staphylococcus. SAPIS-gp6 is a family of proteins produced from the pathogenicity island SAPI1 in pathogenic Staphylococcus aureus. This is a mobile genetic element that carries genes for several superantigen toxins. SAPIS-gp6 is a dimeric protein produced from the pathogenicity island with a helix-loop-helix motif similar to that of bacteriophage scaffolding proteins. It is thought to determine the size of the capsids of distribution of the SAPI1 genome as it acts as an internal scaffolding protein during capsid size determination. 72 matched cddid_all.tbl CDD pfam16723 pfam16723 374754 DUF5065 Domain of unknown function (DUF5065). This family is found in found in Bacillus species. The function is not known. 156 matched cddid_all.tbl CDD pfam16724 pfam16724 406994 T4-gp15_tss T4-like virus Myoviridae tail sheath stabilizer. T4-gp15_tss is the tail-sheath-stabilizer or tail-terminator protein of T4-like myoviridae phage. It forms a hexamer. It simultaneously forms the binding site for attachment of the capsid to the tail as gp15 binds to gp14 and gp13, the neck proteins, and completes the tail as it binds to the top of the tail via hexamer gp3 and the C-terminal domain of gp18 located in the last ring of the contractile tail sheath. 238 matched cddid_all.tbl CDD pfam16725 pfam16725 465247 Nucleolin_bd Nucleolin binding domain. This domain adopts a three helix fold resembling part of a winged helix motif. It binds nucleolin. 70 matched cddid_all.tbl CDD pfam16726 pfam16726 435540 OCRL_clath_bd Inositol polyphosphate 5-phosphatase clathrin binding domain. This domain is a clathrin binding domain found at the N-terminus of inositol polyphosphate 5-phosphatase OCRL. It has a PH domain-like fold. 101 matched cddid_all.tbl CDD pfam16727 pfam16727 465248 REV1_C DNA repair protein REV1 C-terminal domain. This is the C-terminal domain of DNA repair protein REV1. It interacts with REV7, POLN, POLK and POLI. 91 matched cddid_all.tbl CDD pfam16728 pfam16728 435542 DUF5066 Domain of unknown function (DUF5066). 221 matched cddid_all.tbl CDD pfam16729 pfam16729 435543 DUF5067 Domain of unknown function (DUF5067). 125 matched cddid_all.tbl CDD pfam16730 pfam16730 435544 DnaGprimase_HBD DnaG-primase C-terminal, helicase-binding domain. DnaG-primase_C is the C-terminal of a set of eubacterial DnaG primases that are a single-stranded DNA (ssDNA)-dependent RNA polymerase responsible for the synthesis of oligonucleotide primers needed for the replication of DNA. It interacts with helicase at the replication fork. 118 matched cddid_all.tbl CDD pfam16731 pfam16731 435545 GARP Glutamic acid/alanine-rich protein of Trypanosoma. GARP, or glutamic acid/alanine-rich protein, is one of a subset of major surface molecules on Trypanosoma species. They are all surface-orientated, immunodominant, and highly charged. GARP is interesting as ts expression coincides with the loss and gain of variant surface glycoprotein (VSG) molecules in the tsetse vector. It has an extended helical bundle structure that is homologous to the core surface structure of VSG, suggesting that it might replace the bloodstream VSG as the trypanosomes differentiate inside the tsetse vector after a blood-meal. 192 matched cddid_all.tbl CDD pfam16732 pfam16732 435546 ComP_DUS Type IV minor pilin ComP, DNA uptake sequence receptor. ComP-DUS is the DNA-uptake sequence receptor of pathogenic Proteobacteria. ComP is a type IV minor pilin -site on the minor type IV pilin, C one of three minor (low abundance) pilins in pathogenic Proteobacteria Neisseria species (with PilV and PilX). These modulate Tfp-mediated properties without affecting Tfp biogenesis. ComP plays a prominent role in competence at the level of DNA uptake. Comp is exposed on the surface of Neisseria filaments, and it is this that recognizes homotypic DNA through genus-specific DNA uptake sequence (DUS) motifs. 83 matched cddid_all.tbl CDD pfam16733 pfam16733 435547 NRho Rhomboid N-terminal domain. This is the N-terminal domain of rhomboid protease. 69 matched cddid_all.tbl CDD pfam16734 pfam16734 435548 Pilin_GH Type IV pilin-like G and H, putative. Pilin_GH is a family from Cyanobacteria. All the proteins are putatively annotated as being general secretion pathway proteins G and H, and are likely to be pilins of the type IV secretory pathway. 112 matched cddid_all.tbl CDD pfam16735 pfam16735 465249 MYO10_CC Unconventional myosin-X coiled coil domain. This coiled coil domain is found in unconventional myosin-X and is responsible for dimerization. 52 matched cddid_all.tbl CDD pfam16736 pfam16736 407005 sCache_like Single Cache-like. This entry represents the N-terminal Cache-like domain of the alkaline phosphatase synthesis sensor protein PhoR. It covers part of the PAS-like fold that share a central five-stranded beta- sheet of identical topology to other PAS domains. 114 matched cddid_all.tbl CDD pfam16737 pfam16737 465250 PHF12_MRG_bd PHD finger protein 12 MRG binding domain. This domain found in PHD finger protein 12 binds to the MRG domain of Mortality factor 4-like protein 1. 39 matched cddid_all.tbl CDD pfam16738 pfam16738 407007 CBM26 Starch-binding module 26. CBM26 is a carbohydrate-binding module that binds starch. 68 matched cddid_all.tbl CDD pfam16739 pfam16739 465251 CARD_2 Caspase recruitment domain. In the probable ATP-dependent RNA helicase DDX58 this CARD domain is found near the N-terminus and interacts with the C-terminal domain. 93 matched cddid_all.tbl CDD pfam16740 pfam16740 465252 SKA2 Spindle and kinetochore-associated protein 2. Spindle and kinetochore-associated protein 2 (SKA2) interacts with the N-termini of SKA1 and SKA3 and forms the Ska complex. This is a microtubule binding complex required for chromosome segregation. 110 matched cddid_all.tbl CDD pfam16741 pfam16741 465253 mRNA_decap_C mRNA-decapping enzyme C-terminus. The C-terminal domain of mRNA-decapping enzyme in Metazoa is responsible for trimerization. 43 matched cddid_all.tbl CDD pfam16742 pfam16742 465254 IL17R_D_N N-terminus of interleukin 17 receptor D. IL17R_D_N is found in higher eukaryotes. The function of this N-terminal domain is not known. 122 matched cddid_all.tbl CDD pfam16743 pfam16743 435554 PliI Periplasmic lysozyme inhibitor of I-type lysozyme. 121 matched cddid_all.tbl CDD pfam16744 pfam16744 407013 zf-RING_15 KIAA1045 RING finger. 72 matched cddid_all.tbl CDD pfam16745 pfam16745 465255 RsgA_N RsgA N-terminal domain. This domain is found at the N-terminus of RsgA domains. It has an OB fold. 54 matched cddid_all.tbl CDD pfam16746 pfam16746 465256 BAR_3 BAR domain of APPL family. BAR_12 is the BAR coiled-coil domain at the N-terminus of APPL or adaptor protein containing PH domain, PTB domain, and leucine zipper motif proteins in higher eukaryotes. This BAR domain contains four helices whereas the other classical BAR domains contain only three helices. The first three helices form an antiparallel coiled-coil, while the fourth helix, is unique to APPL1. BAR domains take part in many varied biological processes such as fission of synaptic vesicles, endocytosis, regulation of the actin cytoskeleton, transcriptional repression, cell-cell fusion, apoptosis, secretory vesicle fusion, and tissue differentiation. 235 matched cddid_all.tbl CDD pfam16747 pfam16747 407016 Adhesin_E Surface-adhesin protein E. Adhesin E plays a role in pathogenesis. It binds to host proteins including plasminogen, vitronectin and laminin. 125 matched cddid_all.tbl CDD pfam16748 pfam16748 465257 INSC_LBD Inscuteable LGN-binding domain. This is the LGN-binding domain (LBD) of the inscuteable homolog protein. It interacts with the TPR motifs of G-protein-signaling modulator 2 (GPSM2) (LGN) and stabilizes LGN. 47 matched cddid_all.tbl CDD pfam16749 pfam16749 374774 Arteri_nsp7a Arterivirus nonstructural protein 7 alpha. Nonstructural protein 7 alpha is likely to have a role in viral RNA synthesis. 128 matched cddid_all.tbl CDD pfam16750 pfam16750 435558 HK_sensor Sensor domain of 2-component histidine kinase. HK_sensor is the sensor domain found at the N-terminus of the integral membrane two-component system sensor histidine kinase proteins in bacteria. 110 matched cddid_all.tbl CDD pfam16751 pfam16751 435559 RsdA_SigD_bd Anti-sigma-D factor RsdA to sigma factor binding region. RsdA_SigD_bd is a domain at the N-terminus of anti-sigma-D factor RsdA proteins. It binds to the -35 promoter binding domain of sigma-D. The complex formed regulates the transcriptional expression of the bacterium. 46 matched cddid_all.tbl CDD pfam16752 pfam16752 465258 TBCC_N Tubulin-specific chaperone C N-terminal domain. This N-terminal domain of tubulin-specific chaperone C has a spectrin-like fold and binds to tubulin. 115 matched cddid_all.tbl CDD pfam16753 pfam16753 435561 Tipalpha TNF-alpha-Inducing protein of Helicobacter. Tipalpha is secreted from H. pylori as dimers and enters the gastric cells. It binds to DNA via the positively charged surface-patch formed between the two monomers of the crystal structure by the loop between helices alpha1 and alpha2. Each monomer consists of a helical domain and a mixed domain. 151 matched cddid_all.tbl CDD pfam16754 pfam16754 435562 Pesticin Bacterial toxin homolog of phage lysozyme, C-term. This the C-terminal activator domain of pesticin, a hydrolase enzyme secreted by Yersinia pestis and other Gammaproteobacteria to kill related bacteria occupying the same ecological niche. It is referred to as a bacteriocin and it leads to the hydrolysis of peptidoglycan. Its immunity protein is Pim. Pesticin carries an elongated N-terminal translocation domain, an intermediate receptor binding domain, and a C-terminal activity domain with structural analogy to lysozyme homologs. The full-length protein is toxic to bacteria when taken up to the target site via the outer or the inner membrane. The receptor domain is necessary for the close contact with the outer membrane; the N-terminal is a type of translocational, TonB box; the C-terminal domain is the death-delivering domain. 155 matched cddid_all.tbl CDD pfam16755 pfam16755 407023 NUP214 Nucleoporin or Nuclear pore complex subunit NUP214=Nup159. NUP214 is a family of nucleoporins or nuclear pore complex subunit 214 in vertebrates and 159 in yeast found in eukaryotes. It participates in allowing family 2 of DEAD-box ATPases Dbp5/DDX19 to localize to the nuclear pore complex where it takes part in mRNA export and re-modelling. NUP214 helps to regulate DEAD-box ATPase activity. 359 matched cddid_all.tbl CDD pfam16756 pfam16756 435563 PALB2_WD40 Partner and localizer of BRCA2 WD40 domain. This domain is found at the C-terminus of partner and localizer of BRCA2 (PALB2). It is a seven-bladed WD40-type beta-propeller. It binds to the N-terminus of BRCA2. 347 matched cddid_all.tbl CDD pfam16757 pfam16757 465259 Fucosidase_C Alpha-L-fucosidase C-terminal domain. The C-terminal domain of PDB:1hl8 is constructed of eight anti-parallel-strands packed into two-sheets of five and three strands, respectively, forming a two-layer-sandwich containing a Greek key motif. 90 matched cddid_all.tbl CDD pfam16758 pfam16758 407026 UL141 Herpes-like virus membrane glycoprotein UL141. UL141 is a family of glycoproteins from herpesvirus species. At it N-terminus it carries an Ig-like beta-sandwich domain, which binds to the cysteine-rich region of TRAIL-R2, a family of tumour necrosis factor receptor proteins. UL141 is both necessary and sufficient to retain TRAIL receptors in the ER, thereby preventing their cell surface expression and it is also necessary and sufficient to inhibit cell surface expression of CD155. 191 matched cddid_all.tbl CDD pfam16759 pfam16759 465260 LIG3_BRCT DNA ligase 3 BRCT domain. The BRCT domain of DNA ligase 3 (LIG3) binds to the C-terminal BRCT domain of the scaffolding protein X-ray repair cross-complementing protein 1 (XRCC1) and mediates homo- and heterodimerization. 77 matched cddid_all.tbl CDD pfam16760 pfam16760 465261 CBM53 Starch/carbohydrate-binding module (family 53). 76 matched cddid_all.tbl CDD pfam16761 pfam16761 435567 Clr2_transil Transcription-silencing protein, cryptic loci regulator Clr2. Clr2_transil is a domain carrying the first and second of three regions on Clr2 that are necessary for transcriptional silencing by the protein. Clr2 is a protein in the SHREC complex that is a crucial factor required for heterochromatin formation and it plays a major role in mating-type and rDNA silencing. The third region is family pfam10383. 68 matched cddid_all.tbl CDD pfam16762 pfam16762 407030 RHH_6 Ribbon-helix-helix domain. This ribbon-helix-helix domain binds to DNA and may be a part of a toxin-antitoxin system. 77 matched cddid_all.tbl CDD pfam16763 pfam16763 465262 Spidroin_N Major ampullate spidroin 1, spider silk protein 1, N-term. Spidroin is produced by a number of arachnids. Spidrions are made up of repetitive segments flanked by conserved non-repetitive domains, and this domain is the conserved non-repetitive region. Aggregation to form the rigid silk occurs due to association at the repetitive regions, and the N-terminal domain is necessary to prevent premature aggregation during storage before extrusion. This N_terminal region inhibits precocious aggregation and then accelerates and directs self-assembly as the pH is lowered along the extrusion duct. 125 matched cddid_all.tbl CDD pfam16764 pfam16764 465263 Sharpin_PH Sharpin PH domain. This PH domain is found at the N-terminus of sharpin and is involved in dimerization. 113 matched cddid_all.tbl CDD pfam16765 pfam16765 435570 Pim Pesticin immunity protein. Pim is the immunity protein produced by Yersinia pestis and other Gammaproteobacteria to protect themselves against the bacteriostatic activity of the toxin pesticin, pfam16754. 91 matched cddid_all.tbl CDD pfam16766 pfam16766 465264 CID_GANP Binding region of GANP to ENY2. CID is a domain on higher eukaryotic germinal-cent associated nuclear protein, or GANP, that binds to the transcription and mRNA export factor ENY2. The complex of these two proteins forms part of the TREX-2 complex that links transcription with nuclear messenger RNA export. 71 matched cddid_all.tbl CDD pfam16767 pfam16767 435571 KinB_sensor Sensor domain of alginate biosynthesis sensor protein KinB. KinB_sensor is the N-terminal sensor domain of histidine kinase from Pseudomonas species. The domain is the extracellular sensing domain, and is four helical bundle. It recognizes inorganic phosphate Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 121 matched cddid_all.tbl CDD pfam16768 pfam16768 435572 NupH_GANP Nucleoporin homology of Germinal-centre associated nuclear protein. NupH_GANP is the nucleoporin-homology domain at the N-terminus of human GANP or germinal-centre associated nuclear proteins. GANP is part of the TREX-2 complex that links transcription with nuclear messenger RNA export, and it associates with the mRNP particle through the interaction of the NupH_GANP with NXF1, the export factor. This attachment mediates efficient delivery of mRNPs to nuclear pore complexes. 292 matched cddid_all.tbl CDD pfam16769 pfam16769 465265 MCM3AP_GANP MCM3AP domain of GANP. MCM3AP_GANP is the C-terminal domain of germinal centre-associated proteins, GANPs in higher eukaryotes. GANP forms part of the TREX-2 complex which in higher eukaryotes requires the MCM3AP domain of GANP to facilitate its localization to the Nuclear pore complex and nuclear envelope. TREX-2 complex links transcription with nuclear messenger RNA export. 717 matched cddid_all.tbl CDD pfam16770 pfam16770 465266 RTT107_BRCT_5 Regulator of Ty1 transposition protein 107 BRCT domain. This is the fifth BRCT domain of regulator of Ty1 transposition protein 107 (RTT107). It is involved in binding phosphorylated histone H2A. 91 matched cddid_all.tbl CDD pfam16771 pfam16771 435575 RTT107_BRCT_6 Regulator of Ty1 transposition protein 107 BRCT domain. This is the sixth BRCT domain of regulator of Ty1 transposition protein 107 (RTT107). It is involved in binding phosphorylated histone H2A. 107 matched cddid_all.tbl CDD pfam16772 pfam16772 435576 TERF2_RBM Telomeric repeat-binding factor 2 Rap1-binding motif. This domain, found in telomeric repeat-binding factor 2, binds to the C-terminus of repressor activator protein 1 (RAP1) (telomeric repeat-binding factor 2-interacting protein 1). 41 matched cddid_all.tbl CDD pfam16773 pfam16773 374792 Phage_SSB Lactococcus phage single-stranded DNA binding protein. This single-stranded DNA binding protein is found in Lactococcus phage. It can stimulate RecA-mediated homologous recombination. Its structure is a variation of the typical oligonucleotide/oligosaccharide binding-fold of single-stranded DNA binding proteins. 117 matched cddid_all.tbl CDD pfam16774 pfam16774 465267 Baseplate Baseplate protein. This protein is a structural component of the phage baseplate in Siphoviridae. 166 matched cddid_all.tbl CDD pfam16775 pfam16775 407041 ZoocinA_TRD Target recognition domain of lytic exoenzyme. ZoocinA_TRD is domain found downstream of various lytic enzymes, such as peptidase M23 and phage lysins. The domain is composed of strands of antiparallel beta sheet with one short alpha helix at the C-terminal end. 106 matched cddid_all.tbl CDD pfam16776 pfam16776 465268 INPP5B_PH Type II inositol 1,4,5-trisphosphate 5-phosphatase PH domain. 142 matched cddid_all.tbl CDD pfam16777 pfam16777 435578 RHH_7 Transcriptional regulator, RHH-like, CopG. RHH_7 is a ribbon-helix-helix protein family expressed by Helicobacter species. These proteins bind to specific DNA sequences with high affinity and usually act as repressors. Many are putatively named CopG. 73 matched cddid_all.tbl CDD pfam16778 pfam16778 435579 Phage_tail_APC Phage tail assembly chaperone protein. Phage_tail_APC is a family of general phage tail assembly chaperone proteins from double-stranded DNA viruses with no RNA stage, many of which are unclassified. 60 matched cddid_all.tbl CDD pfam16779 pfam16779 407044 DMP12 DNA-mimic protein. This is a family of DNA-mimic proteins expressed by Neisseria species. In its monomeric form DMP12 interacts with the Neisseria dimeric form of the bacterial histone-like protein HU. HU proteins promote the assembly of higher-order DNA-protein structures, The interaction between DMP12 and HU protein may be instrumental in controlling the stability of the nucleoid in Neisseria as DMP12 prevents Neisseria HU protein from being digested by trypsin. 115 matched cddid_all.tbl CDD pfam16780 pfam16780 465269 AIMP2_LysRS_bd AIMP2 lysyl-tRNA synthetase binding domain. This is the lysyl-tRNA synthetase binding domain of aminoacyl tRNA synthase complex-interacting multifunctional protein 2 (AIMP2). 47 matched cddid_all.tbl CDD pfam16781 pfam16781 407046 DUF5068 Domain of unknown function (DUF5068). This family is expressed by Firmicutes. The function is not known. 185 matched cddid_all.tbl CDD pfam16782 pfam16782 407047 SIL1 Nucleotide exchange factor SIL1. This family consists of fungal SIL1 nucleotide-exchange factor proteins.It interacts with Hsp70 (heat-shock protein of 70 kDa) Bip. 289 matched cddid_all.tbl CDD pfam16783 pfam16783 465270 FANCM-MHF_bd FANCM to MHF binding domain. FANCM-MHF_bd is a structured region on Fanconi anaemia complementation group protein M that binds to a two-histone-fold-containing protein complex MHF. MHF binds double-strand DNA, stimulates the DNA-binding activity of FANCM, and contributes to the targeting of FANCM to chromatin. 116 matched cddid_all.tbl CDD pfam16784 pfam16784 293389 HNHc_6 Putative HNHc nuclease. This family is found in Gammaproteobacteria. It may be an HNH-like nucleases. The shorter matches are likely to be from phage proteins whereas the longer members are probably from the bacterial genomes. 203 matched cddid_all.tbl CDD pfam16785 pfam16785 407049 SMBP Small metal-binding protein. This histidine-rich protein binds metal ions. 111 matched cddid_all.tbl CDD pfam16786 pfam16786 407050 RecA_dep_nuc Recombination enhancement, RecA-dependent nuclease. REF is a family of P1-like phage RecA-dependent nucleases. It does not appear to act as a positive RecA regulator. It is a new kind of enzyme, a RecA-dependent nuclease. 102 matched cddid_all.tbl CDD pfam16787 pfam16787 407051 NDC10_II Centromere DNA-binding protein complex CBF3 subunit, domain 2. NDC10_II is a the second of five domains on the Kluyveromyces lactis Ndc10 protein. Each subunit of the Ndc10 dimer binds a separate fragment of DNA, suggesting that Ndc10 stabilizes a DNA loop at the centromere. 313 matched cddid_all.tbl CDD pfam16788 pfam16788 465271 ATF7IP_BD ATF-interacting protein binding domain. ATF7IP-BD is a short conserved region of activating transcription factor 7-interacting protein 1 found in higher eukaryotes. This domain appears to bind several key proteins such as TFIIE-alpha and TFIIE-beta as well the transcriptional regulator Sp1 which are part of the transcriptional machinery. 214 matched cddid_all.tbl CDD pfam16789 pfam16789 435583 YscO-like YscO-like protein. This family of proteins is similar to the type III secretion protein YscO. The family includes Chlamydia trachomatis CT670 which is found in a type III secretion gene cluster. CT670 interacts with CT671, a putative YscP homolog and CT670 and CT671 may form a chaperone-effector pair. 160 matched cddid_all.tbl CDD pfam16790 pfam16790 407053 Phage_clamp_A Bacteriophage clamp loader A subunit. This is the A subunit of bacteriophage DNA clamp loader required for loading of sliding clamps onto chromosomal DNA. These clamps are involved in processivity of DNA replication. 144 matched cddid_all.tbl CDD pfam16791 pfam16791 465272 Connexin40_C Connexin 40 C-terminal domain. This is the C-terminal domain of connexin 40. It interacts with the C-terminal and cytoplasmic loop domains of connexin 43 and with the cytoplasmic loop pf connexin 40. 106 matched cddid_all.tbl CDD pfam16792 pfam16792 407055 Caudo_bapla16 Phage tail base-plate attachment protein of Caudovirales ORF16. Caudo_bapla16 is a family of ORF16 tail-phage P2-like proteins that forms part of the base-plate at the tip of the phage tail. The whole base-plate complex is involved in host recognition and attachment, and consists of several proteins derived from consecutive open-reading-frames. This central domain is expressed from ORF16 in the lactococcal P2-phage and forms a trimer. 372 matched cddid_all.tbl CDD pfam16793 pfam16793 374806 RepB_primase RepB DNA-primase from phage plasmid. RepB_primase is a DNA-primase produced by P4-like phages. It is a zinc-independent primase unlike Pri-type primases. It takes up a dumbbell shaped consisting of an N-terminal catalytic domain separated by a long alpha-helix plus tether and a C-terminal helical-bundle domain. Primases are necessary for phage replication. RepBprime primases such as in this family recognize both ssiA and ssiB, ie only 1 single-stranded primase initiation site on each strand, independently of each other and then synthesize primers that are elongated by DNA polymerase III. The phage is thus replicated exclusively in leading strand mode. 230 matched cddid_all.tbl CDD pfam16794 pfam16794 465273 fn3_4 Fibronectin-III type domain. 101 matched cddid_all.tbl CDD pfam16795 pfam16795 407057 Phage_integr_3 Archaeal phage integrase. catalyzes cleavage and ligation of DNA. 162 matched cddid_all.tbl CDD pfam16796 pfam16796 465274 Microtub_bd Microtubule binding. This motor homology domain binds microtubules and lacks an ATP-binding site. 144 matched cddid_all.tbl CDD pfam16797 pfam16797 435587 Fungal_KA1 Fungal kinase associated-1 domain. This domain is found at the C-terminus of several fungal kinases. 115 matched cddid_all.tbl CDD pfam16798 pfam16798 435588 DUF5069 Domain of unknown function (DUF5069). 134 matched cddid_all.tbl CDD pfam16799 pfam16799 465275 VGPC1_C C-terminal membrane-localization domain of ion-channel, VCN1. VCN1_C is the short C-terminal region of voltage-gated proton channel 1 proteins in higher eukaryotes. The domain is necessary for achieving the dimeric architecture, two monomers form a dimer via parallel alpha-helical coiled-coil interaction. but it is also essential for localising the protein to an intracellular membrane. 48 matched cddid_all.tbl CDD pfam16800 pfam16800 374812 Endopep_inhib IseA DL-endopeptidase inhibitor. This domain functions as a DL-endopeptidase inhibitor. 150 matched cddid_all.tbl CDD pfam16801 pfam16801 435590 MSL1_dimer dimerization domain of Male-specific-Lethal 1. MSL1_dimer is the short coiled dimerization domain of higher eukaryotic MSL1, part of the MSL or Male-Specific Lethal complex. This complex regulates the dosage compensation of the male X chromosome in Drosophila and other eukaryotes. The structure of the MSL1/MSL2 core shows that two MSL2 subunits bind to a dimer formed by two molecules of MSL1. MSL11 is a substrate for MSL2 E3 ubiquitin ligase activity. 37 matched cddid_all.tbl CDD pfam16802 pfam16802 407062 DUF5070 Domain of unknown function (DUF5070). 154 matched cddid_all.tbl CDD pfam16803 pfam16803 435591 DRE2_N Fe-S cluster assembly protein DRE2 N-terminus. This is the N-terminal domain of the fungal Fe-S cluster assembly protein DRE2. 129 matched cddid_all.tbl CDD pfam16804 pfam16804 407064 DUF5071 Domain of unknown function (DUF5071). 119 matched cddid_all.tbl CDD pfam16805 pfam16805 435592 Trans_coact Phage late-transcription coactivator. This family of proteins is found in Caudovirales. It is a late-transcription coactivator which interacts with the host RNA polymerase forming a part of the initiation complex. 69 matched cddid_all.tbl CDD pfam16806 pfam16806 435593 ExsD Antiactivator protein ExsD. The antiactivator protein ExsD represses the transcriptional activator ExsA. ExsA activates expression of type III secretion system genes. Repression of ExsA by ExsD is relieved by the secretion chaperone ExsC. 234 matched cddid_all.tbl CDD pfam16807 pfam16807 407065 DUF5072 Domain of unknown function (DUF5072). 112 matched cddid_all.tbl CDD pfam16808 pfam16808 465276 PKcGMP_CC Coiled-coil N-terminus of cGMP-dependent protein kinase. PKcGMP_CC is the N-terminal coiled-coil, dimerization, domain of cGMP-protein kinases. 35 matched cddid_all.tbl CDD pfam16809 pfam16809 293414 NleF_casp_inhib NleF caspase inhibitor. Binds to and inhibits caspase-9, caspase-8 and caspase-4. therefore preventing caspase-induced apoptosis in the host cell. 145 matched cddid_all.tbl CDD pfam16810 pfam16810 465277 RXLR RXLR phytopathogen effector protein, Avirulence activity. RXLR is a family of phytopathogen avirulence or effector proteins. RXLR proteins are defined by a secretion signal peptide - not in this family - followed by a conserved N-terminal domain with the sequence motif RXLR (Arg-Xaa-Leu-Arg) consensus sequence. The RXLR part is required for translocation inside plant cells, although it appears to be dispensable for the biochemical activity of the effectors when expressed directly inside host cells. The effector activity resides in the C-terminal part of the family, which activate effector-triggered immunity in plants that carry a corresponding resistance (R) protein. The C-terminal region exhibits a fold appears to be able to evolve to outwit the host as the latter tries to acquire new immunity. 138 matched cddid_all.tbl CDD pfam16811 pfam16811 435596 TAtT TRAP transporter T-component. TAtT is a family of one component, the T-component, of a sub-set of TRAP-Ts or Tripartite ATP-independent periplasmic transporters. TRAP-Ts are bacterial transport systems implicated in the import of small molecules into the cytoplasm in bacteria. They are all periplasmic lipoproteins. TatT consists of a 13-alpha-helical fold containing cryptic tetratricopeptide repeat motifs (cTPRs) and encompassing a pore, ie is a water-soluble trimer whose protomers are each perforated by a pore. It forms a complex with a P component, and a putative ligand-binding cleft of TatPT aligns with the pore of TatT. Family TatPT is represented by some members of pfam03480. 263 matched cddid_all.tbl CDD pfam16812 pfam16812 318916 AdHead_fibreRBD C-terminal head domain of the fowl adenovirus type 1 long fibre. AdHead_fibreRBD is a C-terminal part of the head domain of the dsDNA viruses, no RNA stage, Adenovirus. This is a globular head domain with an anti-parallel beta-sandwich fold formed by two four-stranded beta-sheets with the same overall topology as human adenovirus fibre heads. This C-terminal domain is the receptor-binding domain of the avian adenovirus long fibre. 207 matched cddid_all.tbl CDD pfam16813 pfam16813 465278 Cas_St_Csn2 CRISPR-associated protein Csn2 subfamily St. Cas_St_Csn2 is a family of Csn2 CRISPR-associated (Cas) proteins found in Firmicutes, largely Streptococcus and Enterococcus. CRISPR-associated (Cas) proteins are the main executioners of the process whereby prokaryotes acquire immunity against foreign genetic material. Cas allow short segments of this DNA, called spacer, to become incorporated into chromosomal loci as clustered regularly interspaced short palindromic repeats or CRISPRs; the resulting encoded RNAs are then processed into small fragments that guide the silencing of the invading genetic elements. Thus Cas are involved in the acquisition of new spacers. This family of St_Csn2 is longer than the canonical Csn2, pfam09711 through the addition of a large C-terminal domain. The central domain present in both families appears to be a channel that selectively interacts with dsDNA. 335 matched cddid_all.tbl CDD pfam16814 pfam16814 293419 Read-through Read-through domain. The Enterobacteria phage minor coat protein A1 is a C-terminally extended version of the coat protein formed when ribosomes read-through a leaky stop codon. This is the C-terminal read-through domain of A1. 182 matched cddid_all.tbl CDD pfam16815 pfam16815 407068 HRI1 Protein HRI1. This fungal protein interacts with Sec72 and Hrr25, it's function is not yet known. 229 matched cddid_all.tbl CDD pfam16816 pfam16816 435597 DotD DotD protein. The DotD protein is a component of the Dot/Icm type IVB secretion system. It is involved in the outer membrane targeting of DotH. 120 matched cddid_all.tbl CDD pfam16817 pfam16817 407070 DUF5073 Domain of unknown function (DUF5073). This domain of unknown function is a membrane protein found in Mycobacterium. 121 matched cddid_all.tbl CDD pfam16818 pfam16818 407071 SLM4 Protein SLM4. The fungal protein SLM4 (EGO3, GSE1) is a component of the GSE complex and the EGO (TOR) complex. The GSE complex is required for trafficking GAP1 out of the endosome. The EGO complex is involved in the regulation of autophagy and cell growth. SLM4 is required for the integrity and function of the EGO complex. 157 matched cddid_all.tbl CDD pfam16819 pfam16819 435598 DUF5074 Domain of unknown function (DUF5074). This family of proteins from Bacteroidetes, is found with a PKD domain at the N-terminus. Several members are annotated as putative quinonprotein alcohol dehydrogenase-like proteins but this could not be confirmed. 113 matched cddid_all.tbl CDD pfam16820 pfam16820 407073 PKD_3 PKD-like domain. This PKD-like family is found in various Bacteroidetes species. 68 matched cddid_all.tbl CDD pfam16821 pfam16821 374824 C_Hendra C protein from hendra and measles viruses. This is a family of C proteins from a number of Morbillivirus species. 153 matched cddid_all.tbl CDD pfam16822 pfam16822 435599 ALGX SGNH hydrolase-like domain, acetyltransferase AlgX. ALGX is a family found in bacteria. The domain demonstrates catalytic activity similar to that of the SGNH hydrolase-like domain, with the typical Ser-His-Asp triad found in this enzyme. Alginate is an exopolysaccharide that contributes to biofilm formation. ALGX is secreted into the biofilm and is responsible for the acetylation of biofilm polymers that help protect them from host destruction. 267 matched cddid_all.tbl CDD pfam16823 pfam16823 374826 tPilZ Atypical PilZ domain, cyclic di-GMP receptor. Tetrameric PilZ (tPliZ, previously known as PilZ_2) is a family of cyclic di-GMP receptors found in Proteobacteria plant pathogens. tPilZ forms a tetramer that adopts a novel 'house-like' construct, with a central pillar domain of the four vertical alpha3 helices, a roof-top domain made up of the eight inclined alpha2 and alpha4 helices, and four corner-stone domains making up the PilZ domain. Cyclic-di-GMP is a universal secondary messenger molecule extensively involved in regulating bacterial pathogenicity which binds to cytoplasmic receptors containing PilZ domains. This domain is referred to as an atypical PilZ domain, it has the same structure as canonical PilZ domains with the exception of a short N-terminal alpha-helix and an insert that forms two additional alpha-helices. 136 matched cddid_all.tbl CDD pfam16824 pfam16824 435600 CBM_26 C-terminal carbohydrate-binding module. CBM_26 is a family of bacterial carbohydrate-binding modules frequently found at the C-terminus of enzymes. The combination is not unusual as the CBMs function to bring the relevant polysaccharide into close proximity to the active site. 125 matched cddid_all.tbl CDD pfam16825 pfam16825 407076 DUF5075 IGP family C-type lectin domain. This C-type lectin domain is present in the IGP 'invariant glycoprotein' family of proteins from Trypanosoma and Leishmania. 173 matched cddid_all.tbl CDD pfam16826 pfam16826 407077 DUF5076 Domain of unknown function (DUF5076). 84 matched cddid_all.tbl CDD pfam16827 pfam16827 374829 zf-HC3 zinc-finger. This is a family of putative zinc-fingers from Actinobacteriales. 67 matched cddid_all.tbl CDD pfam16828 pfam16828 407078 GAGBD GAG-binding domain on surface antigen. GAGBD is a domain on the surface antigen of the swine pathogen Streptococcus suis and related species. This domain expresses three clusters of basic residues, largely lysines, that are critical for heparin-binding and cell adhesion during bacterium-host cell adhesion. The GAGBD domain binds to the host cell surface glycosaminoglycans or GAGs of the Streptococcus. 152 matched cddid_all.tbl CDD pfam16829 pfam16829 293434 ATR13 Avirulence protein ATR13, RxLR effector. ATR13 is expressed by the plant pathogen oomycete Hyaloperonospora. Such phytopathogenic oomycetes like the one that infects Arabidopsis, Hyaloperonospora arabidopsidis (Hpa), grow intercellularly, forming parasitic structures called haustoria. Haustoria play a role in feeding and suppression of host defence systems. A whole range of pathogen proteins, called effectors, are secreted across this haustorial membrane, a subset of which are further translocated across the plant plasma membrane by an unknown mechanism that is present in both plants and animals. ATR13 is an RxLR effector from the downy mildew oomycete, and is a very dynamic protein. It contains two surface-exposed patches of polymorphism, one of which is involved in the specific recognition by host R-genes. The R-gene-products detect the presence of the infection by recognising the effector proteins. Once detected, the host R-genes trigger apoptosis of the host cell. The R-gene-products carry a specific motif, RxLR, that is recognizes the effector proteins. 101 matched cddid_all.tbl CDD pfam16830 pfam16830 407079 NBD94 Nucleotide-Binding Domain 94 of RH. NBD94 is a domain on one of the reticulocyte binding protein homolog family or RH proteins expressed by the malaria parasite merozoite. RH proteins recognize erythrocytes and are important in virulence. This domain has been shown to exhibit selective binding to ATP and ADP. Binding of ATP or ADP induces nucleotide-dependent structural changes in the C-terminal hinge-region of NBD94 that directly impact on the ability of the RH to bind to the red blood cells. 91 matched cddid_all.tbl CDD pfam16831 pfam16831 318930 CssAB CS6 fimbrial subunits A and B, Coli surface antigen 6. CssAB is a family of CS6 pilins from E.coli, including both subunits A and B. It acts as a colonization factor for the enterotoxigenic species pf E.coli to mediate bacterial attachment to the small intestinal epithelium. Both subunits in the fibre bind to receptors on epithelial cells, and that CssB, but not CssA, specifically recognizes the extracellular matrix protein fibronectin. 129 matched cddid_all.tbl CDD pfam16832 pfam16832 318931 EKLF_TAD1 Erythroid krueppel-like transcription factor, transactivation 1. This family is the first part of the minimal transactivation domain of erythroid-specific transcription factor EKFL in craniates. EKLF plays an important role in red blood cell development; it is posttranslationally modified by UBI on several lysine residues, and its turnover in the cell is regulated by ubiquitin-mediated degradation. In the first 90 residues at the N-terminus EKLF carries a minimal transactivation or TAD domain that is highly acidic. This minimal TAD of EKLF can be further subdivided into two independent domains EKLF_TAD1 (residues 1-40) and EKLF_TAD2 (residues 51-90), pfam16833, that are both capable of independently activating transcription. TAD1, is able to form a non-covalent interaction with ubiquitin. Both TAD1 and TAd2 are highly acidic and carry a PEST (sequence rich in proline, glutamic acid, serine, and threonine) region. Deletion of either PEST domain significantly slows down degradation of EKLF by ubiquitin. The minimal TAD has an overlapping activation/degradation function that is critical for the role of EKLF in red blood cell development. 27 matched cddid_all.tbl CDD pfam16833 pfam16833 407080 EKLF_TAD2 Erythroid krueppel-like transcription factor, transactivation 2. This family is the second part of the minimal transactivation domain of erythroid-specific transcription factor EKFL in craniates. EKLF plays an important role in red blood cell development; it is post-translationally modified by ubiquitin on several lysine residues, and its turnover in the cell is regulated by ubiquitin-mediated degradation. In the first 90 residues at the N-terminus EKLF carries a minimal transactivation or TAD domain that is highly acidic. This minimal TAD of EKLF can be further subdivided into two independent domains EKLF_TAD1 (residues 1-40), pfam16832, and EKLF_TAD2 (residues 51-90) that are both capable of independently activating transcription. Both TAD1 and TAD2 are highly acidic and carry a PEST (sequence rich in proline, glutamic acid, serine, and threonine) region. Deletion of either PEST domain significantly slows down degradation of EKLF by ubiquitin. The minimal TAD has an overlapping activation/degradation function that is critical for the role of EKLF in red blood cell development. 27 matched cddid_all.tbl CDD pfam16834 pfam16834 407081 CSM2 Shu complex component Csm2, DNA-binding. CSM2 is one of the components of the yeast Shu complex that maintains genomic stability during replication. CSM2 complexes first with Psy3, and their L2 loops confer the DNA-binding activity to the Shu complex. The Shu complex binds to recombination sites and is required for Rad51 assembly and function during meiosis. The heterodimer of Psy3-Csm2 stabilizes the Rad51-single-stranded DNA complex independently of nucleotide cofactor because Psy3-Csm2 is a structural mimic of the Rad51-dimer. 203 matched cddid_all.tbl CDD pfam16835 pfam16835 435601 SF3A2 Pre-mRNA-splicing factor SF3a complex subunit 2 (Prp11). SF3A2 is one of the components of the SF3a splicing factor complex of the mature U2 snRNP (small nuclear ribonucleoprotein particle). In yeast, SF3a shows a bifurcated assembly structure of three subunits, Prp9 (subunit 3), Prp11 (subunit 2) and Prp21 (subunit 1). with Prp21 wrapping around Prp11. 95 matched cddid_all.tbl CDD pfam16836 pfam16836 407083 PSY3 Shu complex component Psy3, DNA-binding description. PSY3 is one of the components of the yeast Shu complex that maintains genomic stability during replication. Psy3 complexes first with Cms2, and their L2 loops confer the DNA-binding activity to the Shu complex. The Shu complex binds to recombination sites and is required for Rad51 assembly and function during meiosis. The heterodimer of Psy3-Csm2 stabilizes the Rad51-single-stranded DNA complex independently of nucleotide cofactor because Psy3-Csm2 is a structural mimic of the Rad51-dimer. 216 matched cddid_all.tbl CDD pfam16837 pfam16837 465279 SF3A3 Pre-mRNA-splicing factor SF3A3, of SF3a complex, Prp9. SF3A3 is one of the components of the SF3a splicing factor complex of the mature U2 snRNP (small nuclear ribonucleoprotein particle). In yeast, SF3a shows a bifurcated assembly structure of three subunits, Prp9 (subunit 3), Prp11 (subunit 2) and Prp21 (subunit 1). Prp9 and Prp21 were not thought to interact with each other but the alpha1 helix of Prp9 does make important contacts with the SURP2 domain of Prp21, thus the two do interact via a bidentate-binding mode. Prp9 harbours a major binding site for stem-loop IIa of U2 snRNA. 50 matched cddid_all.tbl CDD pfam16838 pfam16838 407085 Caud_tail_N Caudoviral major tail protein N-terminus. This is the N-terminal domain of the major tail protein, or knob protein, from Caudovirales. 120 matched cddid_all.tbl CDD pfam16839 pfam16839 407086 Antimicrobial25 Nematode antimicrobial peptide. This family of antimicrobial peptides is found in nematodes. 54 matched cddid_all.tbl CDD pfam16840 pfam16840 465280 ACTL7A_N Actin-like protein 7A N-terminus. The N-terminus of actin-like protein 7A is required for interaction with testin (TES). 65 matched cddid_all.tbl CDD pfam16841 pfam16841 465281 CBM60 Ca-dependent carbohydrate-binding module xylan-binding. CBM60 is a family of xylan-binding modules found in conjunction with xylanase enzymes in many bacterial species that attack plant cell walls. Xylan is the major hemicellulose component of most plant cell walls, and is one of the most complex carbohydrates targeted by CBMs. CBM60 modules are evolutionarily related to CBM36 domains as both show circular permutation in the beta-barrel folds. CBM60 targets xylan but is also able to bind cellulose and galactan and thus contribute towards breakdown of the plant cell wall. Recognition of the ligand is conferred primarily through the polar interactions of O2 (oxygen) and O3 of a single sugar with a protein-bound calcium ion. 93 matched cddid_all.tbl CDD pfam16842 pfam16842 465282 RRM_occluded Occluded RNA-recognition motif. This family is an unusual, usually C-terminal, RNA-recognition motif found in fungi. In yeast it is the fourth RRM domain on the essential splicing factor Prp24. Structurally, it has a non-canonical RRM fold with the expected beta-aloha-beta-beta-alpha-beta RRM-fold is flanked by N- and C-terminal alpha-helices. These two additional flanking alpha-helices occlude the beta-sheet face. The electropositive surface thereby presented is an alternative RNA-binding surface that allows both binding and unwinding of the U6 small nuclear RNA's internal stem loop, at least in vitro. 79 matched cddid_all.tbl CDD pfam16843 pfam16843 407090 Get5_bdg Binding domain to Get4 on Get5, Golgi to ER traffic protein. Get5_bdg is the binding domain at the N-terminus of Get5, or Golgi to ER traffic protein 5, in yeast, that binds to Get4. Together with Get3, this tripartite complex is involved in the insertion of tail-anchored proteins in the ER membrane. 53 matched cddid_all.tbl CDD pfam16844 pfam16844 435604 DIMCO_N Dinitrogenase iron-molybdenum cofactor, N-terminal. DIMCO_N is the N-terminal domain of the gamma (Y) subunit of nitrogenase. An alternative name is NafY_N, for nitrogenase accessory factor Y N-terminal. This region is negatively charged and appears to be necessary for recognising and interacting with the apo state of dinitrogenase. The full-length NafY protein facilitates the transfer of iron-molybdenum cofactor, or FeMo-co, into apodinitrogenase by binding to both. The C-terminal region, family Nitro_FeMo-Co, pfam02579, is the part that binds to the cofactor, and the N-terminus binds to apodinitrogenase. Nitrogenase is the bacterial enzyme responsible for nitrogen fixation by catalysing the reduction of nitrogen gas (N2) to ammonium in an ATP-dependent manner. It has two components, dinitrogenase and dinitrogenase reductase. 91 matched cddid_all.tbl CDD pfam16845 pfam16845 407092 SQAPI Aspartic acid proteinase inhibitor. SQAPI, aspartic acid inhibitor first isolated from squash, inhibits a wide range of aspartic proteinases. This particular family of PAAPIs (proteinaceous aspartic acid inhibitors) seems to have evolved quite recently from an ancestral cystatin. Structurally it consists of a four-stranded anti-parallel beta-sheet gripping an alpha-helix in much the same manner that a hand grips a tennis racket. The unstructured N-terminus and the loop connecting beta-strands 1 and 2 are important for pepsin inhibition, but the loop connecting strands 3 and 4 is not. 83 matched cddid_all.tbl CDD pfam16846 pfam16846 407093 Cep3 Centromere DNA-binding protein complex CBF3 subunit B. Cep3 is one of the major components of the CBF3. It dimerizes and in so doing forms a large central channel that is large enough to accommodate duplex B-form DNA. The dimerization region is followed by a linker to the zinc-finger domain at the C-terminus. The CBF3 complex is an essential core component of the budding yeast kinetochore and is required for the centromeric localization of all other kinetochore proteins. Cep3 is the only component with DNA-binding properties. 507 matched cddid_all.tbl CDD pfam16847 pfam16847 293452 AvrPtoB_bdg Avirulence AvrPtoB, BAK1-binding domain. AvrPtoB_bdg is a binding region on a family of bacterial plant pathogenic proteins. Type III effector proteins are injected into plants by bacteria when they are under attack, eg Pseudomonas syringae when attacking tomato. AvrPtoB is one such effector that suppresses the plants' PAMP-triggered innate immunity. PAMPs are pathogen/microbe-associated molecular patterns that are detected as non-self by a host. AvrPtoB suppresses this response by binding to BAK1, a kinase that acts with several pattern recognition receptors to activate defence signalling. AvrPtoB_bdg is the region of AvrPtoB that binds to BAK1 thereby preventing its kinase activity after the perception of flagellin. 91 matched cddid_all.tbl CDD pfam16848 pfam16848 435605 SoDot-IcmSS Substrate of the Dot/Icm secretion system, putative. This is a family of putative substrates of the Dot/Icm type IVA secretion system from Legionella species. 177 matched cddid_all.tbl CDD pfam16849 pfam16849 293454 Glyco_transf_88 Glycosyltransferase family 88. This is a family of type A glycosyltransferases found in Legionella. It acts as a virulence factor by the glucosylation of EF1A (elongation factor 1A) thereby blocking protein synthesis in the host cell. 423 matched cddid_all.tbl CDD pfam16850 pfam16850 374843 Inhibitor_I66 Peptidase inhibitor I66. This family of serine protease inhibitors has a beta-trefoil fold and inhibits trypsin and chymotrypsin. 146 matched cddid_all.tbl CDD pfam16851 pfam16851 407095 Stomagen Stomagen. Stomagen (epidermal patterning factor-like protein 9) acts as a positive regulator of stomatal development. 50 matched cddid_all.tbl CDD pfam16852 pfam16852 293457 HHV-1_VABD Herpes viral adaptor-to-host cellular mRNA binding domain. HHV-1_VABD is the short region of the Herpes simplex 1 virus' specific signature adaptor protein that binds to the cellular mRNA export factor such as mouse REF. 42 matched cddid_all.tbl CDD pfam16853 pfam16853 407096 CDC13_N Cell division control protein 13 N-terminus. This domain is found at the N-terminus of fungal cell division control protein 13 (CDC13). It has an OB type fold. It is involved in dimerization of CDC13 and in interaction of CDC13 with the catalytic subunit of DNA polymerase alpha, Pol1. 208 matched cddid_all.tbl CDD pfam16854 pfam16854 407097 VPS53_C Vacuolar protein sorting-associated protein 53 C-terminus. This is the C-terminal domain of fungal vacuolar protein sorting-associated protein 53. 203 matched cddid_all.tbl CDD pfam16855 pfam16855 407098 Soc Small outer capsid protein. This protein attaches to and stabilizes the bacteriophage capsid. 74 matched cddid_all.tbl CDD pfam16856 pfam16856 407099 CDC4_D Cell division control protein 4 dimerization domain. This is the dimerization domain (D domain) of fungal cell division control protein 4. 51 matched cddid_all.tbl CDD pfam16857 pfam16857 435606 RNA_pol_inhib RNA polymerase inhibitor. This bacteriophage protein inhibits the bacterial host RNA polymerase by interacting with the RpoC subunit and inhibiting the formation of a promoter complex. 47 matched cddid_all.tbl CDD pfam16858 pfam16858 465283 CNDH2_C Condensin II complex subunit CAP-H2 or CNDH2, C-term. CNDH2_C is the C-terminal domain of the H2 subunit of the condensin II complex, found in eukaryotes but not fungi. Eukaryotes carry at least two condensin complexes, I and II, each made up of five subunits. The functions of the two complexes are collaborative but non-overlapping. CI appears to be functional in G2 phase in the cytoplasm beginning the process of chromosomal lateral compaction while the CII are concentrated in the nucleus, possibly to counteract the activity of cohesion at this stage. In prophase, CII contributes to axial shortening of chromatids while CI continues to bring about lateral chromatid compaction, during which time the sister chromatids are joined centrally by cohesins. There appears to be just one condensin complex in fungi. CI and CII each contain SMC2 and SMC4 (structural maintenance of chromosomes) subunits, then CI has non-SMC CAP-D2 (CND1), CAP-G (CND3), and CAP-H (CND2). CII has, in addition to the two SMCs, CAP-D3, CAPG2 and CAP-H2. All four of the CAP-D and CAP-G subunits have degenerate HEAT repeats, whereas the CAP-H are kleisins or SMC-interacting proteins (ie they bind directly to the SMC subunits in the complex). The SMC molecules are each long with a small hinge-like knob at the free end of a longish strand, articulating with each other at the hinge. Each strand ends in a knob-like head that binds to one or other end of the CAP-H subunit. The HEAT-repeat containing D and G subunits bind side-by-side between the ends of the H subunit. Activity of the various parts of the complex seem to be triggered by extensive phosphorylations, eg, entry of the complex, in Sch.pombe, into the nucleus during mitosis is promoted by Cdk1 phosphorylation of SMC4/Cut3; and it has been shown that Cdk1 phosphorylates CAP-D3 at Thr1415 in He-La cells thus promoting early stage chromosomal condensation by CII. 284 matched cddid_all.tbl CDD pfam16859 pfam16859 435608 TetR_C_11 Tetracyclin repressor-like, C-terminal domain. This family of bacterial transcriptional repressors is characterized by the short approximately 50 amino acid stretch of residues constituting the helix-turn-helix DNA binding motif, around the YRFhY motif. The target proteins that are repressed are involved in the transcriptional control of multi-drug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. 113 matched cddid_all.tbl CDD pfam16860 pfam16860 465284 CX9C CHCH-CHCH-like Cx9C, IMS import disulfide relay-system,. CX9C is the first half of a twin Cx9C motif in eukaryotic proteins. The function of this motif is to import nuclear-encoded mitochondrial intermembrane-space-proteins into the IMS (intermembrane space), as these latter lack a mitochondrial targeting sequence. The Cx9C proteins have a disulfide-bonded alpha-hairpin conformation. Cx9C-containing proteins are thus putative substrates for the Mia40-dependent thiol-disulfide exchange mechanism that carries out an oxidative folding process resulting in the proteins being trapped in the IMS. 42 matched cddid_all.tbl CDD pfam16861 pfam16861 435610 Carbam_trans_C Carbamoyltransferase C-terminus. This domain is found in NodU from Rhizobium, CmcH from Nocardia lactamdurans and the bifunctional carbamoyltransferase TobZ from Streptoalloteichus tenebrarius. NodU a Rhizobium nodulation protein involved in the synthesis of nodulation factors has 6-O-carbamoyltransferase-like activity. CmcH is involved in cephamycin (antibiotic) biosynthesis and has 3-hydroxymethylcephem carbamoyltransferase activity, EC:2.1.3.7 catalysing the reaction: Carbamoyl phosphate + 3-hydroxymethylceph-3-EM-4-carboxylate <=> phosphate + 3-carbamoyloxymethylcephem. TobZ functions as an ATP carbamoyltransferase and tobramycin carbamoyltransferase. These proteins contain two domains, this is the smaller, C-terminal, domain. 169 matched cddid_all.tbl CDD pfam16862 pfam16862 465285 Glyco_hydro_79C Glycosyl hydrolase family 79 C-terminal beta domain. This domain is found at the C-terminus of glycosyl hydrolase family 79 proteins. It's function is not yet known. 103 matched cddid_all.tbl CDD pfam16863 pfam16863 465286 NtCtMGAM_N N-terminal barrel of NtMGAM and CtMGAM, maltase-glucoamylase. NtCtMGAM_N is a beta-barrel-like structure just N-terminal to the catalytic domain of maltase-glucoamylase in eukaryotes. It contributes to the architecture of the substrate-binding site, by donating a loop that comes into close contact with two regions in the catalytic domain thereby creating the site. This family is frequently found at the N-terminus of Glycosyl hydrolase 31, pfam01055.to which it contributes as above. 113 matched cddid_all.tbl CDD pfam16864 pfam16864 465287 dimerization2 dimerization domain. This domain, found in methyltransferases, functions as a dimerization domain. 87 matched cddid_all.tbl CDD pfam16865 pfam16865 407107 GST_C_5 Glutathione S-transferase, C-terminal domain. Leishmania major and Trypanosoma cruzi glutathione-S-transferase (GST) has undergone gene duplication, diversification, and gene fusion leading to an four domain enzyme which contains two repeats of a GST N-terminal domain followed by a GST C-terminal domain. 108 matched cddid_all.tbl CDD pfam16866 pfam16866 465288 PHD_4 PHD-finger. 66 matched cddid_all.tbl CDD pfam16867 pfam16867 435615 DMSP_lyase Dimethlysulfonioproprionate lyase. Breaks down into dimethylsulfoniopropionate (DMSP) into acrylate and dimethyl sulfide. 162 matched cddid_all.tbl CDD pfam16868 pfam16868 435616 NMT1_3 NMT1-like family. 289 matched cddid_all.tbl CDD pfam16869 pfam16869 435617 CNDH2_M Condensin II complex subunit CAP-H2 or CNDH2, mid domain. CNDH2_M is the middle domain of the H2 subunit of the condensin II complex, found in eukaryotes but not fungi. Eukaryotes carry at least two condensin complexes, I and II, each made up of five subunits. The functions of the two complexes are collaborative but non-overlapping. CI appears to be functional in G2 phase in the cytoplasm beginning the process of chromosomal lateral compaction while the CII are concentrated in the nucleus, possibly to counteract the activity of cohesion at this stage. In prophase, CII contributes to axial shortening of chromatids while CI continues to bring about lateral chromatid compaction, during which time the sister chromatids are joined centrally by cohesins. There appears to be just one condensin complex in fungi. CI and CII each contain SMC2 and SMC4 (structural maintenance of chromosomes) subunits, then CI has non-SMC CAP-D2 (CND1), CAP-G (CND3), and CAP-H (CND2). CII has, in addition to the two SMCs, CAP-D3, CAPG2 and CAP-H2. All four of the CAP-D and CAP-G subunits have degenerate HEAT repeats, whereas the CAP-H are kleisins or SMC-interacting proteins (ie they bind directly to the SMC subunits in the complex). The SMC molecules are each long with a small hinge-like knob at the free end of a longish strand, articulating with each other at the hinge. Each strand ends in a knob-like head that binds to one or other end of the CAP-H subunit. The HEAT-repeat containing D and G subunits bind side-by-side between the ends of the H subunit. Activity of the various parts of the complex seem to be triggered by extensive phosphorylations, eg, entry of the complex, in Sch.pombe, into the nucleus during mitosis is promoted by Cdk1 phosphorylation of SMC4/Cut3; and it has been shown that Cdk1 phosphorylates CAP-D3 at Thr1415 in He-La cells thus promoting early stage chromosomal condensation by CII. This region represents the disordered section of CNDH2 between the N- and the C-termini. 126 matched cddid_all.tbl CDD pfam16870 pfam16870 465289 OxoGdeHyase_C 2-oxoglutarate dehydrogenase C-terminal. OxoGdeHyase_C is a family found immediately C-terminal to Transket_pyr, pfam02779. It is found at the C-terminus of 2-oxoglutarate dehydrogenase. 147 matched cddid_all.tbl CDD pfam16871 pfam16871 435619 DUF5077 Domain of unknown function (DUF5077). This family is found at the N-terminal of DUF3472, pfam00958. 189 matched cddid_all.tbl CDD pfam16872 pfam16872 407114 putAbiC Putative phage abortive infection protein. Several members are annotated as putative phage abortive infection proteins. 80 matched cddid_all.tbl CDD pfam16873 pfam16873 374859 AbiGii_2 Putative abortive phage resistance protein AbiGii toxin. AbiGii is a family of putative type IV toxin-antitoxin system toxins. The AbiG abortive phage resistance protein affects lactococcal bacteriophages phiP335 and phiQ30 but not the other P335 phage species. AbiGii toxin appears to confer resistance to phages by a mechanism of abortive infection that acts by interfering with phage RNA synthesis. The cognate anti-toxin is found in pfam10899. 397 matched cddid_all.tbl CDD pfam16874 pfam16874 465290 Glyco_hydro_36C Glycosyl hydrolase family 36 C-terminal domain. This domain is found at the C-terminus of many family 36 glycoside hydrolases. It has a beta-sandwich structure with a Greek key motif. 78 matched cddid_all.tbl CDD pfam16875 pfam16875 465291 Glyco_hydro_36N Glycosyl hydrolase family 36 N-terminal domain. This domain is found at the N-terminus of many family 36 glycoside hydrolases. It has a beta-supersandwich fold. 255 matched cddid_all.tbl CDD pfam16876 pfam16876 465292 Lipin_mid Lipin/Ned1/Smp2 multi-domain protein middle domain. This is a middle domain of lipins. Overall the enzyme acts as a magnesium-dependent phosphatidate phosphatase enzyme that catalyzes the conversion of phosphatidic acid to diacylglycerol during triglyceride, phosphatidylcholine and phosphatidylethanolamine biosynthesis. EC:5.2.1.8. 98 matched cddid_all.tbl CDD pfam16877 pfam16877 435623 DUF5078 Domain of unknown function (DUF5078). This family of unknown function is found in Mycobacterium spp. 119 matched cddid_all.tbl CDD pfam16878 pfam16878 465293 SIX1_SD Transcriptional regulator, SIX1, N-terminal SD domain. SIX1_SD is a family of eukaryotic proteins, and it is found N-terminal to the Homeobox domain. As a transcription factor it lacks intrinsic activation domains and thus needs to bind to the EYA family of co-factors in order to mediate transcriptional activation. It is the SD domain that is necessary for this protein-protein interaction, binding to the C-terminal region of EYA - Eyes absent homolog proteins. 110 matched cddid_all.tbl CDD pfam16879 pfam16879 465294 Sin3a_C C-terminal domain of Sin3a protein. Sin3a_C is a family of eukaryotic species. It is found at the C-terminus of the co-repressor Sin3a, and downstream of family Sin3_corepress, pfam08295. 281 matched cddid_all.tbl CDD pfam16880 pfam16880 465295 EHD_N N-terminal EH-domain containing protein. EHD_N is a short domain that lies at the very N-terminus of many dynamins and EF-hand domain-containing proteins. 33 matched cddid_all.tbl CDD pfam16881 pfam16881 465296 LIAS_N N-terminal domain of lipoyl synthase of Radical_SAM family. LIAS_N is found as the N-terminal domain of the Radical_SAM family in the members that are lipoyl synthase enzymes, particularly the mitochondrial ones in metazoa but also those in bacteria. 97 matched cddid_all.tbl CDD pfam16882 pfam16882 374866 DUF5079 Domain of unknown function (DUF5079). This protein is believed to be involved in the type VII secretion system. 241 matched cddid_all.tbl CDD pfam16883 pfam16883 293488 DUF5080 Domain of unknown function (DUF5080). This protein is believed to be involved in the type VII secretion system. 204 matched cddid_all.tbl CDD pfam16884 pfam16884 465297 ADH_N_2 N-terminal domain of oxidoreductase. N-terminal region of oxidoreductase and prostaglandin reductase and alcohol dehydrogenase. 108 matched cddid_all.tbl CDD pfam16885 pfam16885 465298 CAC1F_C Voltage-gated calcium channel subunit alpha, C-term. CAC1F_C is the C-terminal region of voltage-gated calcium channel subunit alpha in higher eukaryotes. The exact function of this domain is not known.This region lies immediately downstream from the CDB motif, pfam08673. 355 matched cddid_all.tbl CDD pfam16886 pfam16886 465299 ATP-synt_ab_Xtn ATPsynthase alpha/beta subunit N-term extension. ATP-synt_ab_Xtn is an extension of the alpha-beta catalytic subunit of VATA or V-type proton ATPase catalytic subunit at the N-terminal end. It is found from bacteria to humans, and was not modelled in family ATP-synt_ab, pfam00006. 120 matched cddid_all.tbl CDD pfam16887 pfam16887 318977 DUF5081 Domain of unknown function (DUF5081). This protein is believed to be involved in the type VII secretion system. 230 matched cddid_all.tbl CDD pfam16888 pfam16888 407125 DUF5082 Domain of unknown function (DUF5082). This entry contains proteins that are uncharacterized. 122 matched cddid_all.tbl CDD pfam16889 pfam16889 435631 Hepar_II_III_N Heparinase II/III N-terminus. This is the N-terminal domain of heparinase II/III proteins. It is a toroid-like domain. 343 matched cddid_all.tbl CDD pfam16890 pfam16890 435632 DUF5083 Domain of unknown function (DUF5083). This protein is believed to be involved in the type VII secretion system. 157 matched cddid_all.tbl CDD pfam16891 pfam16891 465300 STPPase_N Serine-threonine protein phosphatase N-terminal domain. This family is often found at the N-terminus of Metallophos family, in serine-threonine protein phosphatases. 48 matched cddid_all.tbl CDD pfam16892 pfam16892 407128 CHS5_N Chitin biosynthesis protein CHS5 N-terminus. This domain is found at the N-terminus of fungal chitin biosynthesis protein CHS5. It functions as a dimerization domain. 48 matched cddid_all.tbl CDD pfam16893 pfam16893 435634 fn3_2 Fibronectin type III domain. This fibronectin type III domain is found in fungal chitin biosynthesis protein CHS5 where, together with the neighbouring BRCT domain (pfam00533), it binds to the Arf1 GTPase. 89 matched cddid_all.tbl CDD pfam16894 pfam16894 318984 DUF5084 Domain of unknown function (DUF5084). This protein is believed to be involved in the type VII secretion system. 130 matched cddid_all.tbl CDD pfam16895 pfam16895 435635 DUF5085 Domain of unknown function (DUF5085). This protein is believed to be involved in the type VII secretion system. 141 matched cddid_all.tbl CDD pfam16896 pfam16896 435636 PGDH_C Phosphogluconate dehydrogenase (decarboxylating) C-term. PGDH_C is the C-terminal domain of putative bacterial phosphogluconate dehydrogenase proteins. 153 matched cddid_all.tbl CDD pfam16897 pfam16897 465301 MMR_HSR1_Xtn C-terminal region of MMR_HSR1 domain. MMR_HSR1_Xtn is the C-terminal region of some members of the MMR_HSR1 family. 105 matched cddid_all.tbl CDD pfam16898 pfam16898 465302 TOPRIM_C C-terminal associated domain of TOPRIM. TOPRIM_C is found as the C-terminal extension of the TOPRIM domain, pfam01751 in metazoa. 127 matched cddid_all.tbl CDD pfam16899 pfam16899 465303 Cyclin_C_2 Cyclin C-terminal domain. Cyclins contain two domains of similar all-alpha fold, this family corresponds with the C-terminal domain of some cyclins including cyclin C and cyclin H. 98 matched cddid_all.tbl CDD pfam16900 pfam16900 465304 REPA_OB_2 Replication protein A OB domain. Replication protein A contains two OB domains in it's DNA binding region. This is the second of the OB domains. 98 matched cddid_all.tbl CDD pfam16901 pfam16901 465305 DAO_C C-terminal domain of alpha-glycerophosphate oxidase. DAO_C is the C-terminal region of alpha-glycerophosphate oxidase. 126 matched cddid_all.tbl CDD pfam16902 pfam16902 407136 FokI_D3 FokI, D3 domain. Type IIS restriction endonuclease FokI is a member of an unusual class of bipartite restriction enzymes that recognizes the double- stranded DNA sequence 5'-GGATG-3' and cleave DNA phosphodiester groups 9 base pairs away on this strand and 13 base pairs away on the complementary strand. FokI contains amino- and carboxy- terminal domains corresponding to the DNA-recognition and cleavage functions, respectively. The recognition domain is made of three smaller subdomains (D1, D2 and D3) which are evolutionarily related to the helix-turn-helix-containing DNA-binding domain of the catabolite gene activator protein CAP. This is the D3 domain which is most similar to CAP and related proteins such as histone H5, HNF-3gamma and the biotin operon repressor (BirA). Despite its similarity, D3 barely touches the DNA. 69 matched cddid_all.tbl CDD pfam16903 pfam16903 407137 Capsid_N Major capsid protein N-terminus. This is the N-terminal domain of the major capsid protein in several dsDNA viruses. 196 matched cddid_all.tbl CDD pfam16904 pfam16904 407138 PurL_C Phosphoribosylformylglycinamidine synthase II C-terminus. This is the C-terminal domain of phosphoribosylformylglycinamidine synthase II in Thermatoga and related species. 94 matched cddid_all.tbl CDD pfam16905 pfam16905 465306 GPHH Voltage-dependent L-type calcium channel, IQ-associated. GPHH is a sequence motif found in this short domain on voltage-dependent L-type calcium channel proteins in eukaryotes. The domain is closely associated with the IQ-domain, pfam08763. 54 matched cddid_all.tbl CDD pfam16906 pfam16906 465307 Ribosomal_L26 Ribosomal proteins L26 eukaryotic, L24P archaeal. Ribosomal_L26 is a family of the 50S and the 60S ribosomal proteins from eukaryotes - L26 - and archaea - L25. 114 matched cddid_all.tbl CDD pfam16907 pfam16907 465308 Caskin-Pro-rich Proline rich region of Caskin proteins. This proline rich region is found in Caskin proteins. Caskins are CASK-binding synaptic scaffolding proteins. This region is predicted to be natively unstructured. Its function is not known. 91 matched cddid_all.tbl CDD pfam16908 pfam16908 465309 VPS13 Vacuolar sorting-associated protein 13, N-terminal. VPS13 is a family of eukaryotic vacuolar sorting-associated 13 proteins that lies just downstream from Chorein_N family, pfam12624. The exact function of this domain is not known. 234 matched cddid_all.tbl CDD pfam16909 pfam16909 465310 VPS13_C Vacuolar-sorting-associated 13 protein C-terminal. VPS13_C is a family of eukaryotic vacuolar sorting-associated 13 proteins that lies at the C-terminus of the members, The exact function of this domain is not known. 175 matched cddid_all.tbl CDD pfam16910 pfam16910 465311 VPS13_mid_rpt Repeating coiled region of VPS13. This repeat is a family of repeating regions of eukaryotic vacuolar sorting-associated 13 proteins. This repeating region shares a common core element that includes a well-conserved P-x4-P-x13-17-G sequence. The exact function of this repeat is not known. 236 matched cddid_all.tbl CDD pfam16911 pfam16911 435648 PapA_C Phthiocerol/phthiodiolone dimycocerosyl transferase C-terminus. 119 matched cddid_all.tbl CDD pfam16912 pfam16912 407146 Glu_dehyd_C Glucose dehydrogenase C-terminus. 211 matched cddid_all.tbl CDD pfam16913 pfam16913 293518 PUNUT Purine nucleobase transmembrane transport. PUNUT is a family of largely plant and fungal purine transporters. Most members are 10-pass transmembrane proteins, and they belong to the drug/metabolite transporter (dmt) superfamily. The plant vascular system transports nucloebases and their derivatives such as cytokinins and caffeine by a common H+-coupled high-affinity purine transport system; the PUNUT family members carry out this transport. 321 matched cddid_all.tbl CDD pfam16914 pfam16914 435649 TetR_C_12 Bacterial transcriptional repressor C-terminal. This domain is found at the C terminus of a small group of bacterial putative TetR transcriptional regulator proteins. 105 matched cddid_all.tbl CDD pfam16915 pfam16915 319001 Eryth_link_C Annelid erythrocruorin linker subunit C-terminus. This domain is found in linker subunits of the erythrocruorin respiratory complex in annelid worms. 120 matched cddid_all.tbl CDD pfam16916 pfam16916 465312 ZT_dimer dimerization domain of Zinc Transporter. ZT_dimer is the dimerization region of the whole molecule of zinc transporters since the full-length members form a homodimer during activity. The domain lies within the cytoplasm and exhibits an overall structural similarity with the copper metallochaperone Hah1 UniProtKB:O00244, exhibiting an open alpha-beta domain with two alpha helices (H1 and H2) aligned on one side and a three-stranded mixed beta-sheet (S1 to S3) on the other side. The N-terminal part of the members is the Cation_efflux family, pfam01545. 74 matched cddid_all.tbl CDD pfam16917 pfam16917 435651 BPL_LplA_LipB_2 Biotin/lipoate A/B protein ligase family. 182 matched cddid_all.tbl CDD pfam16918 pfam16918 435652 PknG_TPR Protein kinase G tetratricopeptide repeat. This domain is found at the C-terminus of protein kinase G and contains a tetratricopeptide repeat (TPR). 340 matched cddid_all.tbl CDD pfam16919 pfam16919 435653 PknG_rubred Protein kinase G rubredoxin domain. This rubredoxin domain is found at the N-terminus of protein kinase G, and is essential for kinase activity. 139 matched cddid_all.tbl CDD pfam16920 pfam16920 465313 LRRCT_2 Leucine rich repeat C-terminal motif. This entry represents the Leucine Rich Repeat C-terminal (LRRCT) capping motif from TRK receptors. 45 matched cddid_all.tbl CDD pfam16921 pfam16921 465314 Tex_YqgF Tex protein YqgF-like domain. This is the YqgF-like domain of the bacterial Tex protein, which is involved in transcriptional processes. 125 matched cddid_all.tbl CDD pfam16922 pfam16922 465315 SLD5_C DNA replication complex GINS protein SLD5 C-terminus. The C-terminal domain of DNA replication complex GINS protein SLD5 is important in the assembly of the GINS complex, a complex which is involved in initiation of DNA replication and progression of DNA replication forks. 57 matched cddid_all.tbl CDD pfam16923 pfam16923 465316 Glyco_hydro_63N Glycosyl hydrolase family 63 N-terminal domain. This is a family of eukaryotic enzymes belonging to glycosyl hydrolase family 63. They catalyze the specific cleavage of the non-reducing terminal glucose residue from Glc(3)Man(9)GlcNAc(2). Mannosyl oligosaccharide glucosidase EC:3.2.1.106 is the first enzyme in the N-linked oligosaccharide processing pathway. This family represents the N-terminal beta sandwich domain. 228 matched cddid_all.tbl CDD pfam16924 pfam16924 435658 DpaA_N Dipicolinate synthase subunit A N-terminal domain. 115 matched cddid_all.tbl CDD pfam16925 pfam16925 435659 TetR_C_13 Tetracyclin repressor-like, C-terminal domain. This domain is found in TetR-type regulators such as AcuR, acrylate-responsive repressor of acuR-acuI-dddL operons involved in acrylate catabolism. 113 matched cddid_all.tbl CDD pfam16926 pfam16926 465317 HisKA_4TM Archaeal 4TM region of histidine kinase. This N-terminal region of histidine-kinases consists of 4xTMs and is found in Archaea. 130 matched cddid_all.tbl CDD pfam16927 pfam16927 465318 HisKA_7TM N-terminal 7TM region of histidine kinase. HisKA_7TM is an N-terminal region consisting of seven transmembrane domains found in Archaea and some bacteria. It is always found associated with histidine kinase. 221 matched cddid_all.tbl CDD pfam16928 pfam16928 435660 Inj_translocase DNA/protein translocase of phage P22 injectosome. Inj_translocase is a family of putative phage translocases that are involved in the injectosome mechanism. Phage P22 of Salmonella typhimurium ejects four proteins, gp7, gp16, gp20 and gp26, which are ejected from the phage virion into the bacterial cell after absorption. These four proteins may play a role in DNA ejection. 217 matched cddid_all.tbl CDD pfam16929 pfam16929 435661 Asp2 Accessory Sec system GspB-transporter. Asp2 is a family of the SecA2/Y2 accessory Sec secretory system of Gram-positive bacteria. It is specific for large serine-rich repeat, cell-wall-anchored, glycoproteins such as GspB. Export of GspB requires the three Asp1-Asp3 proteins. Asp2, in conjunction with Asp3, probably acts as a chaperone in the early stage of GspB transport. Asp2 directly interacts with Aps1 and Asp3 to form a complex and stabilizes it; this complex is essential for substrate export. Moreover, Asp2 acetylates the GlcNAc residues on GspB. Asp1/2/3 complex stimulates the ATPase activity of SecA2 and also affects the export and glycosylation of pneumococcal serine-rich repeat proteins (PrsPs). 500 matched cddid_all.tbl CDD pfam16930 pfam16930 435662 Porin_5 Putative porin. 535 matched cddid_all.tbl CDD pfam16931 pfam16931 435663 Phage_holin_8 Putative phage holin. 123 matched cddid_all.tbl CDD pfam16932 pfam16932 435664 T4SS_TraI Type IV secretory system, conjugal DNA-protein transfer. T4SS_TraI is a family of putative Gram-negative, largely Proteobacterial, type IV conjugal DNA-Protein transfer or VirB secretory pathway (IVSP) proteins. 210 matched cddid_all.tbl CDD pfam16933 pfam16933 435665 PelG Putative exopolysaccharide Exporter (EPS-E). PelG is a family of putative exopolysaccharide transporters like PelG. Most members carry twelve transmembrane regions. The family also contains fusion proteins with glycosyl transferase group 1, which are putative flippase transporters. 452 matched cddid_all.tbl CDD pfam16934 pfam16934 293539 Mersacidin Two-component Enterococcus faecalis cytolysin (EFC). Mersacidin is a cytolysin, a lantibiotic produced by Gram-positive bacteria, The cytolysin is a 'pseudohaemolysin' which produces haemolysis on blood agar plates, but not in broth culture. Mersacidin is one of the type B lantibiotics (lanthionine-containing antibiotics) that contain post-translationally modified amino acids and cyclic ring structures. Mersacidin attacks the cell wall precursor lipid II, thereby inhibiting cell-wall synthesis. 68 matched cddid_all.tbl CDD pfam16935 pfam16935 435666 Hol_Tox Putative Holin-like Toxin (Hol-Tox). Hol_Tox is a family of small proteins (34-48aas) with a single TM region. Members can exhibit antibacterial activity against Gram-positive bacteria but not against Gram-negative bacteria. 34 matched cddid_all.tbl CDD pfam16936 pfam16936 435667 Holin_9 Putative holin. This is a family of putative holins from Actinobacteria with three TM regions. 78 matched cddid_all.tbl CDD pfam16937 pfam16937 465319 T3SS_HrpK1 Type III secretion system translocator protein, HrpF. T3SS_HrpK1 is a family of putative Type III secretion system pore-forming bacterial proteins. These allow transfer of pathogenic material from bacterial cytoplasm into the plant host cytoplasm. 256 matched cddid_all.tbl CDD pfam16938 pfam16938 435669 Phage_holin_Dp1 Putative phage holin Dp-1. Phage_holin_Dp1 is a family of putative phage-holins from Gram-positive bacteria, largely Firmicutes, with two probable TMSs. The family shows lytic activity. 62 matched cddid_all.tbl CDD pfam16939 pfam16939 293544 Porin_6 Putative porin. Porin_6 is a family of putative porins from Leptospira species. 282 matched cddid_all.tbl CDD pfam16940 pfam16940 374895 Tic110 Chloroplast envelope transporter. Tic110 is a family of chloroplast envelope proteins. Some are involved in protein translocation and others are neurotransmitter receptor, cys loop, ligand-gated ion channel or LIC proteins. 573 matched cddid_all.tbl CDD pfam16941 pfam16941 407166 CymA Putative cyclodextrin porin. 341 matched cddid_all.tbl CDD pfam16942 pfam16942 293547 CclA_1 Putative cyclic bacteriocin. This is a family of short proteins from Gram- putatively from the carnocylcin A family of bacteriocins. 103 matched cddid_all.tbl CDD pfam16943 pfam16943 374896 T4SS_CagC Cag pathogenicity island, type IV secretory system. T4SS_CagC is a family of putative pathogenicity island, type IV, conjugal DNA-protein transfer, secretory system proteins from Gram-negative bacteria. 119 matched cddid_all.tbl CDD pfam16944 pfam16944 435670 KCH Fungal potassium channel. KHC is a family of fungal proteins carrying three transmembrane domains. It is a member of the fungal potassium channel family of transporters, and includes a pair of homologous sequences that localize to distinct zones of the yeast plasma membrane and are induced during the response to mating pheromones. Together KCH1 and KCH2 promote low-affinity K+ uptake and are essential for K+-dependent activation of HACS - a high-affinity Ca2+ influx system that activates calcineurin and is essential for cell survival - in S. cerevisiae cells responding to mating pheromones. 251 matched cddid_all.tbl CDD pfam16945 pfam16945 407168 Phage_r1t_holin Putative lactococcus lactis phage r1t holin. Phage_r1t_holin is a family of putative phage r1t holins from lactococcus. these holins carry two hydrophobic putative TMs separated by a short beta-turn region. 70 matched cddid_all.tbl CDD pfam16946 pfam16946 319021 Porin_OmpG_1_2 OMPG-porin 1 family. Porin_OmpG_1_2 is a family of putative porins of the OmpG-type. these are channels without solute specificity. 294 matched cddid_all.tbl CDD pfam16947 pfam16947 407169 Ferredoxin_N N-terminal region of 4Fe-4S ferredoxin iron-sulfur binding. Ferredoxin_N is a short domain that is often found at the N-terminus of 4Fe-4S ferredoxin iron-sulfur binding domain proteins from Archaea and a few bacteria. 65 matched cddid_all.tbl CDD pfam16949 pfam16949 374899 ABC_tran_2 Putative ATP-binding cassette. This is a family of putative two component ABC exporters. This is the membrane protein of approximately 573 residues and twelve transmembrane domains. It is encoded adjacent to an ATPase. 542 matched cddid_all.tbl CDD pfam16951 pfam16951 293556 MaAIMP_sms Putative methionine and alanine importer, small subunit. MaAIMP_sms is a family of hypothetical proteins from Proteobacteria that purported to be small subunits of a methionine and alanine importer. 60 matched cddid_all.tbl CDD pfam16952 pfam16952 407170 Gln-synt_N_2 Glutamine synthetase N-terminal domain. 112 matched cddid_all.tbl CDD pfam16953 pfam16953 465320 PRORP Protein-only RNase P. PRORPs (protein-only RNase P) are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. Arabidopsis thaliana contains PRORP enzymes (PRORP1, PRORP2 and PRORP3) where PRORP1 localizes to mitochondria as well as chloroplasts, while PRORP2 and PRORP3 are found in the nucleus. In humans and most other metazoans, mt-RNase P is composed of three protein subunits (mitochondrial RNase P proteins 1-3; MRPP1-3), homologs to the Arabidopsis thaliana PRORP1-3. This domain corresponds to the metallonuclease domain of PRORPs. PRORP1 has 22% sequence identity to the human homolog MRPP3. PRORP1 crystal structure shows a V-shaped tripartite structure with a C-terminal metallonuclease domain of the NYN (N4BL1, YacP-like nuclease) family, with a typical and functional two-metal-ion catalytic site that has conserved aspartate residues. 242 matched cddid_all.tbl CDD pfam16954 pfam16954 465321 HRG Haem-transporter, endosomal/lysosomal, haem-responsive gene. HRG1 is a family of conserved, membrane-bound permeases that reside in distinct intracellular compartments and bind and transport haem in metazoa. These proteins carry four transmembrane domains, 4xTMs, modelled here in two pairs, the two N-terminal and the two more C-terminal. 51 matched cddid_all.tbl CDD pfam16955 pfam16955 374902 OFeT_1 Ferrous iron uptake permease, iron-lead transporter. OFeT_1 is a family of conserved archaeal membrane proteins that are putative oxidase-dependent Fe2+ transporters. 206 matched cddid_all.tbl CDD pfam16956 pfam16956 435673 Porin_7 Putative general bacterial porin. 287 matched cddid_all.tbl CDD pfam16957 pfam16957 435674 Mal_decarbox_Al Malonate decarboxylase, alpha subunit, transporter. Mal_decarbox_Al is a family of Na+-transporting carboxylic acid decarboxylases. 548 matched cddid_all.tbl CDD pfam16958 pfam16958 407174 PRP9_N Pre-mRNA-splicing factor PRP9 N-terminus. This is the N-terminal domain of pre-mRNA-splicing factor PRP9. 149 matched cddid_all.tbl CDD pfam16959 pfam16959 465322 Collectrin Renal amino acid transporter. Collectrin is a single-pass transmembrane protein that is homologous to the C-terminal region of human angiotensin-converting enzyme 2, ACE2, SwissProt:Q9BYF1, found in Peptidase_M2 pfam01401. Collectrin is critical for normal amino acid reabsorption in the kidney. 154 matched cddid_all.tbl CDD pfam16960 pfam16960 435676 HpuA Haemoglobin-haptoglobin utilization, porphyrin transporter. HpuA is a family of Neisseria spp proteins from the hpuAB operon, which are putative porphyrin transporters. 308 matched cddid_all.tbl CDD pfam16961 pfam16961 374905 OmpA_like Putative OmpA-OmpF-like porin family. This is a family of putative OmpA-OmpF-like porins from Bacteroidetes. 197 matched cddid_all.tbl CDD pfam16962 pfam16962 435677 ABC_export Putative ABC exporter. This is a family of putative ABC_exporters from Firmicutes. 530 matched cddid_all.tbl CDD pfam16963 pfam16963 435678 PelD_GGDEF PelD GGDEF domain. This degenerate GGDEF domain is found at the C-terminus of PelD, a membrane-bound c-di-GMP-specific receptor. It contains an RXXD motif resembling the allosteric inhibition site found in diguanylate cyclases. In PelD this RXXD motif binds to dimeric c-di-GMP. 123 matched cddid_all.tbl CDD pfam16964 pfam16964 435679 TadF Putative tight adherence pilin protein F. TadF is a family of proteins from the tad locus that is part of the type IV bacterial secretory system. 177 matched cddid_all.tbl CDD pfam16965 pfam16965 374907 CSG2 Ceramide synthase regulator. CSG2 is an integral membrane protein with up to 10 transmembrane segments that, when over-expressed, localizes to the endoplasmic reticulum. CSG2 is a family of fungal transmembrane proteins that regulate mannosyl phosphorylinositol ceramide synthase and are thereby implicated in calcium homoeostasis in the cell. 396 matched cddid_all.tbl CDD pfam16966 pfam16966 435680 Porin_8 Porin-like glycoporin RafY. This is a family of Gram-negative Gammaproteobacteria putative raffinose-like porins. 366 matched cddid_all.tbl CDD pfam16967 pfam16967 435681 TcfC E-set like domain. TcfC is a family of bacterial fimbrial proteins. These sit in the outer bacterial membrane surrounding the RcpA proteins of the fimbrial shaft. This family is from Gamma-proteobacteria. This domain represents an immunoglobulin like E-set domain. 68 matched cddid_all.tbl CDD pfam16968 pfam16968 407181 TadZ_N Pilus assembly protein TadZ N-terminal. TadZ_N is the N-terminal region of the Flp pilus assembly protein TadZ, which carries an AAA, ATPase domain immediately downstream, AAA_31, pfam13614. The domain is an example of a signal-transduction-response receiver. It is localized to the cytoplasmic side of the inner bacterial cell-membrane, contacting also with both tadA and RcpC. 129 matched cddid_all.tbl CDD pfam16969 pfam16969 465323 SRP68 RNA-binding signal recognition particle 68. SRP68 is a family that is part of the SRP or signal recognition particle complex. This complex, consisting of six proteins and a 7SL-RNA is necessary for guiding the emerging proteins designed for the membrane towards the translocation pore. SRP68 forms a stable heterodimer with SRP72, a protein with a TPR repeat. Specific RNA-binding of SRP68 is mediated by the N-terminal domain of approximately 200 residues of this family. 562 matched cddid_all.tbl CDD pfam16970 pfam16970 339870 FimA Type-1 fimbrial protein, A. FimA is a family of Gram-negative fimbrial component A proteins that form part of the pili. There are usually up to 1000 copies of this subunit in one pilus that form a helically wound rod onto which the tip fibrillum (FimF.FimG, FimH) is attached. Pilus subunits are translocated from the cytoplasm to the periplasm via the general secretory pathway SecYEG. 145 matched cddid_all.tbl CDD pfam16971 pfam16971 407183 RcpB Rough colony protein B, tight adherence - tad - subunit. RcpB is part of the Tad operon of proteins. The Tad (tight adherence) macromolecular transport system, present in many bacterial and archaeal species, represents an ancient and major new subtype of type II secretion. The three Rcp proteins (RcpA, RcpB, and RcpC) and TadD, a putative lipoprotein, are localized to the bacterial outer membrane. 168 matched cddid_all.tbl CDD pfam16972 pfam16972 374913 TipE Na+ channel auxiliary subunit TipE. TipE appears to be a family of insect Na+ channel auxiliary subunit proteins. 486 matched cddid_all.tbl CDD pfam16973 pfam16973 435683 FliN_N Flagellar motor switch protein FliN N-terminal. FliN is one of three proteins that form a switch-complex at the base of the basal body of the flagellum; the switch regulates the flagellum-motor. 50 matched cddid_all.tbl CDD pfam16974 pfam16974 465324 NAR2 High-affinity nitrate transporter accessory, Ig-like domain. NAR2 is a family of plant proteins with a C-terminal transmembrane region that is an essential accessory for high-affinity nitrate uptake. This family works together with NRT2, a 12xTM family of proteins that is part of family MFS_1, pfam07690. NAR2 is also involved in the repression of lateral root initiation in response to high ratios of sucrose to nitrogen in the medium. Therefore the two component-system of NAR2 and NRT2 itself is likely to be involved in the signalling pathway that integrates nutritional cues for the regulation of lateral root architecture. The functional unit of the high-affinity nitrate influx complex is likely to be a tetramer, in Arabidopsis, made up of two subunits each of NRT2.1 and NAR2.1. This entry corresponds to an immunoglobulin-like domain. 142 matched cddid_all.tbl CDD pfam16975 pfam16975 435685 UPAR_LY6_2 Ly6/PLAUR domain-containing protein 6, Lypd6. UPAR_LY6_2 is a family of higher eukaryotic proteins expressed in neurons. It modulates nicotinic acetylcholine receptors by selectively increasing Ca2+-influx through this ion channel. The family carries an LU protein domain - about 80 amino acids long characterized by a conserved pattern of 10 cysteine residues. The family is a positive feedback regulator of Wnt/beta-catenin signalling, eg for patterning of the mesoderm and neuroectoderm in zebrafish gastrulation, where Lypd6 is GPI-anchored to the plasma-membrane and interacts with the Wnt receptor Frizzled8 and the co-receptor Lrp6. 106 matched cddid_all.tbl CDD pfam16976 pfam16976 435686 RcpC Flp pilus assembly protein RcpC/CpaB. RcpC is a family of Gram-negative proteins expressed from the tight-adherence tad locus. RcpC is an auxillary protein that sits in the inner membrane and interacts with TadB and TadZ, an AAA ATPase. A recent study has identified two tandem beta-clip domains in RcpC95. beta-Clip domains are known to interact with carbohydrate moieties in other systems, such as SAF. 115 matched cddid_all.tbl CDD pfam16977 pfam16977 465325 ApeC C-terminal domain of apextrin. ApeC domain was first identified from two apextrin-like proteins (ALP) of the amphioxus Branchiostoma japonicum. Our functional studies show that amphioxus ALP1 and ALP2 are important anti-bacterial effectors, and that the apeC domain of the ALP1/2 mediates the bacterial recognition by binding to bacterial muramyl dipeptide (MDP). Further analysis shows that the apeC domain is present in various proteins from cnidarians, molluscs, arthropods, hemichordates, echinoderms and amphioxus. The apeC domain is also found to form different domain combinations with other domains (in press). 204 matched cddid_all.tbl CDD pfam16978 pfam16978 465326 CRIM SAPK-interacting protein 1 (Sin1), middle CRIM domain. CRIM is a domain in the middle of Sin1 that is important in the substrate recognition of TORC2. It is conserved from yeast to humans. TOR is a serine/threonine-specific protein kinase and forms functionally distinct protein complexes referred to as TORC1 and TORC2. 137 matched cddid_all.tbl CDD pfam16979 pfam16979 465327 SIN1_PH SAPK-interacting protein 1 (Sin1), Pleckstrin-homology. SIN1_PH is a pleckstrin-homology domain found at the C-terminus of SIN1. It is conserved from yeast to humans. PH-domains are involved in intracellular signalling or as constituents of the cytoskeleton. SIN1 (SAPK-interacting protein 1) plays an essential role in signal transduction, anf the PH domain is involved in lipid and membrane binding. 104 matched cddid_all.tbl CDD pfam16980 pfam16980 465328 CitMHS_2 Putative citrate transport. CitMHS is a family of putative citrate transporters, belonging to the Na+/H+ antiporter NhaD-like permease superfamily. 440 matched cddid_all.tbl CDD pfam16981 pfam16981 293586 Chi-conotoxin chi-Conotoxin or t superfamily. Chi-conotoxin is a family of Cone snail venom chi-conopeptide class bioactive peptides based. These conopeptides show a unique ability, highly selectively and non-competitively, to inhibit the noradrenaline transporter. They show an unusual cysteine-stabilized scaffold that presents a gamma-turn in an optimized conformation for high affinity interactions with the noradrenaline transporter. 60 matched cddid_all.tbl CDD pfam16982 pfam16982 465329 Flp1_like Putative Flagellin, Flp1-like, domain. 48 matched cddid_all.tbl CDD pfam16983 pfam16983 465330 MFS_MOT1 Molybdate transporter of MFS superfamily. MFS_MOT1 is a family of molybdenate transporters. Molybdenum is an essential element that is taken up into the cell in the oxyanion molybdate. Molybdenum is used in the form of molybdopterin-cofactor, which participates in the active site of enzymes involved in key reactions of carbon, nitrogen, and sulfur metabolism. 115 matched cddid_all.tbl CDD pfam16984 pfam16984 319052 Grp7_allergen Group 7 allergen. 180 matched cddid_all.tbl CDD pfam16985 pfam16985 435693 DUF5086 Domain of unknown function (DUF5086). 122 matched cddid_all.tbl CDD pfam16986 pfam16986 435694 CzcE Heavy-metal resistance protein CzcE. CzcE is involved in heavy-metal resistance. It binds copper, which induces a conformational change. 79 matched cddid_all.tbl CDD pfam16987 pfam16987 465331 KIX_2 KIX domain. This KIX domain is an activator-binding domain. 83 matched cddid_all.tbl CDD pfam16988 pfam16988 407195 Vps36-NZF-N Vacuolar protein sorting 36 NZF-N zinc-finger domain. The vacuolar protein sorting 36 NZF-N zinc-finger domain interacts with the C-terminus of vacuolar protein sorting 28. 65 matched cddid_all.tbl CDD pfam16989 pfam16989 435696 T6SS_VasJ Type VI secretion, EvfE, EvfF, ImpA, BimE, VC_A0119, VasJ. T6SS_VasJ is a family from Gram-negative bacteria that forms a component of the type VI pathogenic secretion system. In the case of the Escherichia coli RS218 strain UniProtKB:G8IRL4, EvfF,it represents expression of the full-length gene; whereas it is just the C-terminal part of EvfE, UniProtKB:G8IRL3. The N-terminal part of these sequences is in family ImpA_N, pfam06812. 254 matched cddid_all.tbl CDD pfam16990 pfam16990 293595 CBM_35 Carbohydrate binding module (family 35). This is a mannan-specific carbohydrate binding domain, previously known as the X4 module. Unlike other carbohydrate binding modules, binding to substrate causes a conformational change. 119 matched cddid_all.tbl CDD pfam16991 pfam16991 407197 SIR4_SID Sir4 SID domain. This is the Sir2 interaction domain (SID domain) of silent information regulator 4 (Sir4). 159 matched cddid_all.tbl CDD pfam16992 pfam16992 379914 RNA_pol_RpbG DNA-directed RNA polymerase, subunit G. RNA_pol_RpbG is a family of archaeal and fungal subunit G of DNA-directed RNA polymerase. 119 matched cddid_all.tbl CDD pfam16993 pfam16993 435697 Asp1 Accessory Sec system protein Asp1. Asp1, along with SecY2, SecA2, and other proteins forms part of the accessory secretory protein system. The system is involved in the export of serine-rich glycoproteins important for virulence in a number of Gram-positive species, including Streptococcus gordonii and Staphylococcus aureus. This protein family is assigned to transport rather than glycosylation function, but the specific molecular role is unknown. Asp1 is predicted to be cytosolic. 515 matched cddid_all.tbl CDD pfam16994 pfam16994 465332 Glyco_trans_4_5 Glycosyl-transferase family 4. 172 matched cddid_all.tbl CDD pfam16995 pfam16995 435699 tRNA-synt_2_TM Transmembrane region of lysyl-tRNA synthetase. tRNA-synt_2_TM is a family from the N-terminal region of tRNA-synthase-2, with 6xTMs. The presence of this region indicates that the protein is anchored in the membrane. The family is found in Actinobacteria. 215 matched cddid_all.tbl CDD pfam16996 pfam16996 435700 Asp4 Accessory secretory protein Sec Asp4. Asp4 and Asp5 are putative accessory components of the SecY2 channel of the SecA2-SecY2 mediated export system, but they are not present in all SecA2-SecY2 systems. This family of Asp4 is found in Firmicutes. 55 matched cddid_all.tbl CDD pfam16997 pfam16997 435701 Wap1 Wap1 domain. The Wap1 domain is found at the C-terminus of fungal Wpl1 proteins (also known as Rad61). These proteins are members of the cohesin complex. The Wap1 domain binds to the ATPase domain of Smc3. 373 matched cddid_all.tbl CDD pfam16998 pfam16998 435702 17kDa_Anti_2 17 kDa outer membrane surface antigen. 17kDa_Anti_2 is a surface protein that is found in several Proteobacteria species. 111 matched cddid_all.tbl CDD pfam16999 pfam16999 339878 V-ATPase_G_2 Vacuolar (H+)-ATPase G subunit. This family represents vacuolar (H+)-ATPase G subunit from several bacterial and archaeal species. Subunit G is a component of the peripheral stalk of the ATPase complex 104 matched cddid_all.tbl CDD pfam17000 pfam17000 465333 Asp5 Accessory secretory protein Sec, Asp5. Asp4 and Asp5 are putative accessory components of the SecY2 channel of the SecA2-SecY2 mediated export system, but they are not present in all SecA2-SecY2 systems. This family of Asp5 is found in Firmicutes. 71 matched cddid_all.tbl CDD pfam17001 pfam17001 407204 T3SS_basalb_I Type III secretion basal body protein I, YscI, HrpB, PscI. T3SS_basalb_I represents a family of Gram-negative type III secretion basal body proteins I. It is the inner rod protein of the secreted needle. YscI is suggested to form a rod that allows substrate passage across the inner membrane of the needle protein YscF through it. 94 matched cddid_all.tbl CDD pfam17002 pfam17002 374928 DUF5089 Domain of unknown function (DUF5089). This is a family of microsporidial-specific proteins of unknown function. There is distant homology to synaptosomal-associated 25 family proteins. 193 matched cddid_all.tbl CDD pfam17003 pfam17003 374929 Actin_micro Putative actin-like family. This is a family of microsporidial-specific proteins of unknown function. There is distant homology to the Actin family. 350 matched cddid_all.tbl CDD pfam17004 pfam17004 435703 SRP_TPR_like Putative TPR-like repeat. This is a family of microsporidial sequences that are likely to fold into a TPR-like structure. Many sequences are annotated as being signal recognition proteins. 109 matched cddid_all.tbl CDD pfam17005 pfam17005 407205 WD40_like WD40-like domain. This is a family of proteins which have weak homology to the WD40 repeat family. Members are largely from microsporidia and related species. 301 matched cddid_all.tbl CDD pfam17006 pfam17006 374931 DUF5087 Domain of unknown function (DUF5087). This is a family of microsporidial sequences of unknown function. 292 matched cddid_all.tbl CDD pfam17007 pfam17007 374932 HTH_micro HTH-like. This is a family of microsporidial sequences whose function is not known. It is possible that the proteins are DNA-binding as there is distant homology to helix-turn-helix families at the N-terminus. 454 matched cddid_all.tbl CDD pfam17008 pfam17008 374933 DUF5088 Domain of unknown function (DUF5088). This is a family of microsporidial sequences of unknown function. 184 matched cddid_all.tbl CDD pfam17009 pfam17009 374934 DUF5090 Domain of unknown function (DUF5090). This is a microsporidial-specific family of proteins of unknown function. The family is likely to be of four transmembrane domains. 187 matched cddid_all.tbl CDD pfam17010 pfam17010 374935 DUF5092 Domain of unknown function (DUF5092). his is a family of microsporidial-specific sequences of unknown function. There is one transmembrane domain towards the C-terminus. 145 matched cddid_all.tbl CDD pfam17011 pfam17011 374936 DUF5093 Domain of unknown function (DUF5093). This is a family of microsporidial sequences that may be distantly related to RRP7, pfam12923, ribosomal-RNA-processing protein 7. 131 matched cddid_all.tbl CDD pfam17012 pfam17012 374937 DUF5091 Domain of unknown function (DUF5091). This is a family of microsporidial-specific sequences of unknown function. 147 matched cddid_all.tbl CDD pfam17013 pfam17013 374938 Acetyltransf_15 Putative acetyl-transferase. This is a family of microsporidial proteins which may be distantly related to acetyl-transferase. 210 matched cddid_all.tbl CDD pfam17014 pfam17014 374939 Mad3_BUB1_I_2 Putative Mad3/BUB1 like region 1 protein. This family of microsporidial sequences may be related to the Mad3_BUB1_I family pfam08311. 128 matched cddid_all.tbl CDD pfam17015 pfam17015 374940 DUF5094 Domain of unknown function (DUF5094). This family of largely microsporidial-specific proteins is of unknown function. However there may be distant homology to family Csm1, pfam12539. 178 matched cddid_all.tbl CDD pfam17016 pfam17016 374941 DUF5095 Domain of unknown function (DUF5095). This is a family of microsporidial-specific sequences. The function is not known and there is no distant homology to any Pfam families so far. 229 matched cddid_all.tbl CDD pfam17017 pfam17017 374942 zf-C2H2_aberr Aberrant zinc-finger. This is a family of largely microsporidia-specific proteins with an aberrant zinc-finger motif of Cx(4)C2H repeated. 165 matched cddid_all.tbl CDD pfam17018 pfam17018 374943 MICSWaP Spore wall protein. This is a family of microsporidial spore-wall proteins. 193 matched cddid_all.tbl CDD pfam17019 pfam17019 374944 DUF5096 Domain of unknown function (DUF5096). This is a family of microsporidial sequences of unknown function. There is a well conserved Asp residue towards the C-terminus which may be functional. 192 matched cddid_all.tbl CDD pfam17020 pfam17020 407206 DUF5097 Domain of unknown function (DUF5097). This is a family of microsporidia-specific proteins of unknown function. There is the possibility of very distant homology to the WAC domain. 119 matched cddid_all.tbl CDD pfam17021 pfam17021 374945 Mei5_like Putative double-strand recombination repair-like. This is a family of microsporidia-specific sequences with homology to the double-strand recombination repair protein family, Mei5 pfam10376. 118 matched cddid_all.tbl CDD pfam17022 pfam17022 374946 PTP2 Polar tube protein 2 from Microsporidia. PTP2 is a family of microsporidial polar-tube protein 2 sequences. Humans can be infected with the unicellular eukaryote Microsporidia which are obligate intracellular parasites that produce resistant spores. To initiate entry into a new host cell a unique motile process is formed by a sudden extrusion of the polar tube protein from the spore. There are a series of conserved cysteine residues. 216 matched cddid_all.tbl CDD pfam17023 pfam17023 407207 DUF5098 Domain of unknown function (DUF5098). This is family of microsporidia-specific sequences with no known function. There is a very characteriztic NPW sequence motif at the very C-terminus. 461 matched cddid_all.tbl CDD pfam17024 pfam17024 374947 DMAP1_like Putative DMAP1-like. This is a family of microsporidia-specific sequences that may have distant homology to the family DMAP1, pfam05499. 113 matched cddid_all.tbl CDD pfam17025 pfam17025 374948 DUF5099 Domain of unknown function (DUF5099). This is a family of microsporidia-specific sequences of unknown function. 109 matched cddid_all.tbl CDD pfam17026 pfam17026 374949 zf-RRPl_C4 Putative ribonucleoprotein zinc-finger pf C4 type. This is a family of largely microsporidia-specific proteins. One member is annotated as being a ribonucleoprotein. The family carries two pairs of CxxC residues suggesting that there is DNA-binding. 108 matched cddid_all.tbl CDD pfam17027 pfam17027 374950 Bromo_TP_like Histone-fold protein. This is a family of microsporidia-specific sequences that have distant homology to the Bromo_TP family, pfam07524. 119 matched cddid_all.tbl CDD pfam17028 pfam17028 407208 8TM_micro 8TM Microsporidial transmembrane domain. This is a family of largely microsporidial-specific proteins that carry eight transmembrane regions, in two blocks of four. Such an arrangement of TMs suggests a transporter function of some kind. There is a highly conserved NFLNW sequence-motif at the C-terminus which might be of functional importance. 259 matched cddid_all.tbl CDD pfam17029 pfam17029 374951 DUF5100 Domain of unknown function (DUF5100). This is a family of microsporidia-specific sequences of unknown function. 126 matched cddid_all.tbl CDD pfam17030 pfam17030 374952 Beta_lactamase3 Putative beta-lactamase-like family. This is a family derived from microsporidia-specific proteins. There is homology to the beta-lactamase domain. 213 matched cddid_all.tbl CDD pfam17031 pfam17031 374953 DUF5101 Domain of unknown function (DUF5101). This is a family of short microsporidia-specific proteins of unknown function. 99 matched cddid_all.tbl CDD pfam17032 pfam17032 465334 zinc_ribbon_15 zinc-ribbon family. This zinc-ribbon region is found on a set of largely microsporidia-specific proteins. 73 matched cddid_all.tbl CDD pfam17033 pfam17033 407210 Peptidase_M99 Carboxypeptidase controlling helical cell shape catalytic. This is the peptidase domain of a D,L-carboxypeptidase. The active site residues are Arg86, Glu222 and the metal ligands, in the peptidase domain, are Gln46, Glu49 and His128 in UniProtKB:O25708. The protein binds many zinc ions and a calcium ion and there are other metal binding sites. The catalytic activity is the release of m-Dpm from the peptide muramyl-Ala-gamma-D-Glu-m-Dpm; this is probably the precursor of the cell wall cross-linking peptide. 227 matched cddid_all.tbl CDD pfam17034 pfam17034 374955 zinc_ribbon_16 Zinc-ribbon like family. This family is found at the C-terminus of WD40 repeat structures in eukaryotes. 125 matched cddid_all.tbl CDD pfam17035 pfam17035 435704 BET Bromodomain extra-terminal - transcription regulation. The BET, or bromodomain extra-terminal domain, is found on bromodomain proteins that play key roles in development, cancer progression and virus-host pathogenesis. It interacts with NSD3, JMJD6, CHD4, GLTSCR1, and ATAD5 all of which are shown to impart a pTEFb-independent transcriptional activation function on the bromodomain proteins. 64 matched cddid_all.tbl CDD pfam17036 pfam17036 465335 CBP_BcsS Cellulose biosynthesis protein BcsS. This is a family of bacterial cellulose biosynthesis proteins. Cellulose is necessary for biofilm formation in bacteria. Structural models show that this protein forms a membrane bound beta barrel structure. 207 matched cddid_all.tbl CDD pfam17037 pfam17037 374957 CBP_BcsO "Cellulose biosynthesis protein BcsO. This is a family of bacterial cellulose biosynthesis proteins. Cellulose is necessary for biofilm formation in bacteria. (Roemling U. and Galperin M.Y. ""Bacterial cellulose biosynthesis. Diversity of operons and subunits"" (manuscript in preparation))." 208 matched cddid_all.tbl CDD pfam17038 pfam17038 435706 CBP_BcsN "Cellulose biosynthesis protein BcsN. This is a family of bacterial cellulose biosynthesis proteins. Cellulose is necessary for biofilm formation in bacteria. (Roemling U. and Galperin M.Y. ""Bacterial cellulose biosynthesis. Diversity of operons and subunits"" (manuscript in preparation))." 186 matched cddid_all.tbl CDD pfam17039 pfam17039 465336 Glyco_tran_10_N Fucosyltransferase, N-terminal. This is the N-terminal domain of a family of fucosyltransferases. This enzyme transfers fucose from GDP-Fucose to GlcNAc in an alpha1,3 linkage. This family is known as glycosyltransferase family 10. The N-terminal domain is the likely binding-region for the fucose-like substrate (manuscript in publication). 109 matched cddid_all.tbl CDD pfam17040 pfam17040 407215 CBP_CCPA "Cellulose-complementing protein A. This is a family of bacterial cellulose-complementing protein A proteins necessary for cellulose biosynthesis. Cellulose is necessary for biofilm formation in bacteria. (Roemling U. and Galperin M.Y. ""Bacterial cellulose biosynthesis. Diversity of operons and subunits"" (manuscript in preparation))." 121 matched cddid_all.tbl CDD pfam17041 pfam17041 407216 SasG_E E domain. This short domain is about 50 amino acids in length. Its structure shows that it is composed of two beta sheets each of three strands. This domain is found associated with the pfam07501 domain and it has structural similarity with that domain although it is somewhat shorter. The E domain forms part of a rod like structure. 48 matched cddid_all.tbl CDD pfam17042 pfam17042 465337 NBD_C Nucleotide-binding C-terminal domain. This is the C-terminal domain found in proteins in a range of Proteobacteria as well as the Gram-positive Oceanobacillus iheyensis. Structural analysis of the whole protein indicates the N- and C-termini act together to produce a surface into which a threonate-ADP complex is bound, demonstrating that a sugar binding site is on the N-terminal domain, and a nucleotide binding site is in the C-terminal domain. There is a critical motif, DDXTG, at approximately residues 22-25. Proteins containing this domain have been predicted as kinases. Some members are associated with PdxA2 by physical clustering and gene fusion with PdxA2. Some members that are fused with PdxA2 have been shown to be involved in L-4-hydroxythreonine (4HT) phosphorylation, part of the alternative pathway to make PLP (pyridoxal 5'-phosphate) out of a toxic metabolite, 4HT. However, 4HT phosphorylation might not be the main function of this group of proteins. Moreover, some members that are not associated with pdxA2, and even one that is associated with pdxA2, have lost 4HT kinase activity. Functional analysis demonstrate that family members include D-Threonate kinases (DtnK), D-Erythronate kinases (DenK) and 3-Oxo-tetronate kinases (OtnK). 166 matched cddid_all.tbl CDD pfam17043 pfam17043 407218 MAT1-1-2 Mating type protein 1-1-2 of unknown function. MAT1-1-2 is a family of proteins present in Sordariomycetes. They are encoded by the MAT1-1-2 gene which is present in the mating types of Sordariomycetes. The most famous representative if this family is Neurospora crassa. MAT1-1-2 is the generic nomenclature of all mating-type genes encoding proteins with HPG (also termed PPF) domain. This gene and its domain was first identified in Podospora anserina (its name in this species is SMR1) and Neurospora crassa (its name in this species is mat A-2) by Debuchy et al (1993). HPG was the first name proposed for the domain found in MAT1-1-2 proteins see, based on the most conserved residues (histidine, proline and glycine). PPF was a second denomination proposed by Kanematsu et al (2007) for the same domain but these authors identified different conserved residues (proline, proline and phenylalanine). The function of this domain is not yet known. 147 matched cddid_all.tbl CDD pfam17044 pfam17044 319104 BPTA Borrelial persistence in ticks protein A. BPTA is a family of proteins that are found in Borrelia species. The function is not known. 196 matched cddid_all.tbl CDD pfam17045 pfam17045 465338 CEP63 Centrosomal protein of 63 kDa. CEP63 is a family of eukaryotic proteins involved in centriole activity. 264 matched cddid_all.tbl CDD pfam17046 pfam17046 407220 Ses_B SesB domain on fungal death-pathway protein. SesB is a short conserved domain found on fungal proteins that are part of the cell death or heterokaryon incompatibility pathway. 22 matched cddid_all.tbl CDD pfam17047 pfam17047 465339 SMP_LBD Synaptotagmin-like mitochondrial-lipid-binding domain. SMP is a proposed lipid-binding module, ie a synaptotagmin-like mitochondrial-lipid-binding domain found in eukaryotes. The SMP domain has a beta-barrel structure like protein modules in the tubular-lipid-binding (TULIP) superfamily. It dimerizes to form an approximately 90-Angstrom-long cylinder traversed by a channel lined entirely with hydrophobic residues. The following two C2 domains then form arched structures flexibly linked to the SMP domain. The SMP domain is a lipid-binding domain that links the ER with other lipid bilayer-membranes within the cell. 180 matched cddid_all.tbl CDD pfam17048 pfam17048 465340 Ceramidse_alk_C Neutral/alkaline non-lysosomal ceramidase, C-terminal. This family represents C-terminal domain of a group of neutral/alkaline ceramidases found in both bacteria and eukaryotes. The EC classification is EC:3.5.1.23. The enzyme hydrolyses ceramide to generate sphingosine and fatty acid. The enzyme plays a regulatory role in a variety of physiological events in eukaryotes and also functions as an exotoxin in particular bacteria. This C-terminal tail of the enzyme is highly conserved across all species and may play a role in the interaction of the enzyme with the plasma membranes. The tail is also vital for the stabilization of the enzyme as a whole. 165 matched cddid_all.tbl CDD pfam17049 pfam17049 407222 AEP1 ATPase expression protein 1. ATPase expression protein 1 (AEP1) is a yeast mitochondrial protein. It is essential for the expression of subunit 9 of mitochondrial ATP synthase. 396 matched cddid_all.tbl CDD pfam17050 pfam17050 435711 AIM5 Altered inheritance of mitochondria 5. AIM5 (also known as Mcs12 and Mic12) is a fungal mitochondrial inner membrane protein. It is a component of the mitochondrial inner membrane organizing system (MINOS/MitOS), which promotes normal mitochondrial morphology. 60 matched cddid_all.tbl CDD pfam17051 pfam17051 293656 COA2 Cytochrome C oxidase assembly factor 2. 86 matched cddid_all.tbl CDD pfam17052 pfam17052 407224 CAF20 Cap associated factor. In eukaryotes, the translation of mRNA is initiated by the binding of eIF4F complex, which is composed of eIF4E, eIF4A and eIF4G proteins. elF4E-binding proteins (4E-BPs) are involved in translational regulation through their interaction with eIF4E. There are two elF4E-binding proteins (4E-BPs) found in S. cerevisiae, Caf20 and Eap1. This entry represents Caf20 (also known as p20), which competes with elF4G for binding to elF4E and interferes with the formation of the elF4F complex, hence inhibiting translation. It is needed for the induction of pseudohyphal growth in response to nitrogen limitation. 151 matched cddid_all.tbl CDD pfam17053 pfam17053 407225 GEP5 Genetic interactor of prohibitin 5. Genetic interactor of prohibitin 5 (GEP5), also known as required for respiratory growth protein5 (RRG5), has been shown to interact with prohibitin ring complexes in the mitochondrial inner membrane that regulate cell proliferation as well as the dynamics and function of mitochondria. It is required for mitochondrial genome maintenance and is essential for respiratory growth. 214 matched cddid_all.tbl CDD pfam17054 pfam17054 293659 JUPITER Microtubule-Associated protein Jupiter. Is a microtubule-associated protein that binds to all microtubule populations in Drosophila. 208 matched cddid_all.tbl CDD pfam17055 pfam17055 293660 VMR2 Viral matrix protein M2. Is a viral transmembrane protein which forms a proton-selective ion channel that is needed for the efficient release of the viral genome during virus entry. Once is attached to the cell surface, the virion enters the cells by endocytosis. Acidification of the endosome triggers M2 ion channel activity. Also plays a role in viral proteins secretory pathways. Elevates the intravesicular pH of normally acidic compartments, such as trans-Golgi network. It seems that M2 protein ion channel activity can affect the status of the conformational form of cleaved HA during intracellular transport. 235 matched cddid_all.tbl CDD pfam17056 pfam17056 407226 KRE1 Killer toxin-resistance protein 1. The killer toxin-resistance protein 1 family are GPI-anchored plasma membrane proteins, found in yeast. They are involved in 1,6-beta-glucan formation and in the assembly and architecture of the cell wall. They also act as plasma membrane receptors for the yeast K1 viral toxin, and are involved in subsequent lethal channel formation. The family also includes Pga1 proteins, which have a role in oxidative stress response and in adhesion and biofilm formation. 66 matched cddid_all.tbl CDD pfam17057 pfam17057 293662 B3R Poxviridae B3 protein. This is a viral protein. Its function is unknown. 123 matched cddid_all.tbl CDD pfam17058 pfam17058 435712 MBR1 Mitochondrial biogenesis regulation protein 1. In yeast this protein participates in mitochondrial biogenesis and stress response. And also seems that may affect the NAM7 function, possibly at the level of mRNA turnover. 231 matched cddid_all.tbl CDD pfam17059 pfam17059 435713 MGTL MgtA leader peptide. MGTL is a bacterial protein that makes mgtA transcription sensitive to intracellular proline levels. When the levels of proline are low, this protein is not able to be translated and stem loop'C' forms in the mgt A 5'UTR which enables the transcription of the downstream mgtA gene. 17 matched cddid_all.tbl CDD pfam17060 pfam17060 407228 MPS2 Monopolar spindle protein 2. Is a fungal transmembrane protein which is part of the component of the spindle pole body (SPB) required for the insertion of the nascent SPB into the nuclear envelope and for the proper execution of spindle pole body (SPB) duplication. It seems that Mps2-Spc24 interaction may contribute to the localization of Spc24 and other kinetochore components to the inner plaque of the SPB. 340 matched cddid_all.tbl CDD pfam17061 pfam17061 465341 PARM PARM. Human PARM-1 is a mucin-like, androgen-regulated transmembrane protein that is present in most tissues, with high levels in the heart, kidney and placenta. It has been shown to be induced and expressed in prostate after castration and may have a role in cell proliferation and immortalization in prostate cancer. 296 matched cddid_all.tbl CDD pfam17062 pfam17062 407230 Osw5 Outer spore wall 5. In fungi the outermost cape of the spore wall is made up of a polymer that contains cross-linked amino acid dityrosine, which is important for the stress resistance of the spore. The OSW family of proteins have been implicated in assembly of this protective dityrosine coat. OSW5 null mutant spores show an enhanced spore wall permeability and vulnerability to beta glucanase digestion. The proteins are predicted to be integral membrane proteins. 70 matched cddid_all.tbl CDD pfam17063 pfam17063 435715 PSMalpha Phenol-soluble modulin alpha peptide family. This family includes various Phenol-soluble modulin proteins from S. Aureus. Psma4 is a methicillin-resistant Staphylococcus aureus (MRSA) protein that may recruit, activate and induce the lysis of human neutrophils. It stimulates the secretion of IL-8 and also has haemolytic activity during MRSA infection. 21 matched cddid_all.tbl CDD pfam17064 pfam17064 435716 QVR Sleepless protein. In Drosophila QUIVER (also known as SLEEPLESS protein) is required for homoeostatic regulation of sleep under normal conditions and following sleep deprivation. It is a novel potassium channel subunit that modulates the Shaker potassium channel which regulates the sleep. 85 matched cddid_all.tbl CDD pfam17065 pfam17065 293670 UPF0669 Putative cytokine, C6ORF120. C6orf120 is a secreted protein that promotes cell cycle progression of CD4(+) T-cells, not hepatocytes. In humans it has its main role in tunicamycin-induced CD4(+) T apoptosis that may be associated with endoplasmatic reticulum stress. This suggests that it might be a new cytokine with immununoregulatory function that is selective for CD4+ T cells. It is mainly expressed in hepatocytes and cells in germinal centre of lymph nodes. 185 matched cddid_all.tbl CDD pfam17066 pfam17066 465342 RITA RBPJ-interacting and tubulin associated protein. RITA is a highly conserved protein that binds to tubulin and shuttles between the cytoplasm and nucleus. It is responsible for export of RBP-J/CBF-1 from the nucleus, which modulates Notch-mediated transcription. 268 matched cddid_all.tbl CDD pfam17067 pfam17067 293672 RPS31 Ribosomal protein S31e. RPS31, Ubi3 precursor, which is part of mature 60S and 40S ribosomal subunits. It seems that linear ubiquitin fusion to Rps31 and its subsequent cleavage are required for the efficient production and functional integrity of 40S ribosomal subunits. 99 matched cddid_all.tbl CDD pfam17068 pfam17068 293673 RRG8 Required for respiratory growth protein 8 mitochondrial. RRG8 is a mitochondrial protein that plays an important role in maintenance of mtDNA due to is required for respiratory activity and maintenance and expression of the mitochondrial genome. 279 matched cddid_all.tbl CDD pfam17069 pfam17069 293674 RSRP Arginine/Serine-Rich protein 1. RSRP1 is an eukaryotic protein family. Its function is unknown. 299 matched cddid_all.tbl CDD pfam17070 pfam17070 319115 Thx 30S ribosomal protein Thx. Thx forms part of the 30S ribosomal subunit. It fits into a cavity between multiple RNA elements in the top of the 30S subunit head and stabilizes the organization of these elements. 27 matched cddid_all.tbl CDD pfam17071 pfam17071 293676 Capsid_VP7 Outer capsid protein VP7. Outer capsid protein VP7 is a reoviral protein that interacts with VP4 to form the outer icosahedral capsid. Outer capsids are involved directly in viral host interactions. 276 matched cddid_all.tbl CDD pfam17072 pfam17072 407233 Spike_torovirin Torovirinae spike glycoprotein. The spike glycoprotein is a corona viral transmembrane protein that mediates the binding of virions to the host cell receptor and is involved in membrane fusion. The torovirinae spike proteins appear distinct from other coronaviridae spike proteins, such as human SARS coronavirus. This entry also includes some alloherpesvirus fusion glycoproteins. 1271 matched cddid_all.tbl CDD pfam17073 pfam17073 319116 SafA Two-component-system connector protein. SafA is a bacterial transmembrane protein family that connects the signal transduction between the two component systems EvgS/EvgA and PhoQ/Phop. SafA interacts with PhoQ, leading to the PhoQ/PhoP system activation in response to acid stress conditions. 64 matched cddid_all.tbl CDD pfam17074 pfam17074 293679 Darcynin Darcynin, domain of unknown function. Darcynin is a bacterial protein family. Its function is unknown. 127 matched cddid_all.tbl CDD pfam17075 pfam17075 374974 RRT14 Regular of rDNA transcription protein 14. Regulator of rDNA transcription protein14 (RRT14) is a nucleolar protein that is involved in ribosome biogenensis. 196 matched cddid_all.tbl CDD pfam17076 pfam17076 293681 SBE2 SBE2, cell-wall formation. 820 matched cddid_all.tbl CDD pfam17077 pfam17077 293682 Msap1 Mitotic spindle associated protein SHE1. She1 seems to be related to the spindle integrity function of the Dam1 complex. She1 is a dynein regulator and limits dynein offloading by gating the recruitment of dynactin to the astral microtubule plus end. Aurora B phosphorylates She1, modulating its potency against dynein. 330 matched cddid_all.tbl CDD pfam17078 pfam17078 293683 SHE3 SWI5-dependent HO expression protein 3. SWI5-dependent HO expression protein 3 (She3) is an RNA-binding protein that binds specific mRNAs, including the mRNA of Ash1, which is invalid in cell-fate determination. She3 acts as an adapter protein that docks the myosin motor Myo4p onto an Ash1-She2p ribonucleoprotein complex. She3 seems to bind to Myo4p and Shep2p via different domains. 228 matched cddid_all.tbl CDD pfam17079 pfam17079 293684 SOTI Male-specific protein scotti. Soti is a post-meiotically transcribed gene that is required in late spermiogenesis for normal spermatid individualization. Besides, it is expressed in primary spermatocytes and round spermatids. 101 matched cddid_all.tbl CDD pfam17080 pfam17080 374975 SepA Multidrug Resistance efflux pump. SepA is a drug efflux protein that is involved in bacterial multidrug resistance. It is predicted to have four transmembrane domains. 144 matched cddid_all.tbl CDD pfam17081 pfam17081 407234 SOP4 Suppressor of PMA 1-7 protein. SOP4 is a family of fungal ER membrane proteins that regulate the quality control and intracellular transport of Pma1-7, a mutant plasma membrane ATPase. 209 matched cddid_all.tbl CDD pfam17082 pfam17082 293687 Spc29 Spindle Pole Component 29. Spc29 is a component of the Spc-110 subcomplex and is required for the SPB (Spindle pole body) duplication. Spc29 acts as a linker between the central plaque component Spc42 to the inner plaque component Spc110. 245 matched cddid_all.tbl CDD pfam17083 pfam17083 407235 Swm2 Nucleolar protein Swm2. The nucleolar protein SWM2 (Synthetic With MUD-2-delta protein2) constitutes a yeast protein family. SWM2 is a nonessential gene whose function is unknown, but it encodes a protein that binds Tgs1, an enzyme responsible for 2,2,7-trimethylguanosine (TMG) capping of small nuclear (sn) RNAs implicated in pre-mRNA splicing. 130 matched cddid_all.tbl CDD pfam17084 pfam17084 407236 TDA11 Topoisomerase I damage affected protein 11. Tda11 is a fungal protein family. The function is unknown. 465 matched cddid_all.tbl CDD pfam17085 pfam17085 293690 UCMA Unique cartilage matrix associated protein. UCMA is a secreted cartilage-specific protein located in chromosome 2 that is predominantly expressed in resting chondrocytes. It is secreted into the extracellular matrix as an uncleaved precursor and shows the same restricted distribution pattern in cartilage as UCMA mRNA. This protein is proteolytically processed and contains tyrosine sulfates. It seems to be to be involved in the negative control of osteogenic differentiation of osteochondrogenic precursor cells in peripheral zones of foetal cartilage. 134 matched cddid_all.tbl CDD pfam17086 pfam17086 435718 HV_small_capsid Small capsid protein of Herpesviridae. This is a family of herpes-type viral small capsid proteins. 75 matched cddid_all.tbl CDD pfam17087 pfam17087 293692 HHV-5_US34A Herpesvirus US34A protein family. Proteins in this human cytomegalovirus (HHV-5 )family contain a transmembrane domain. 64 matched cddid_all.tbl CDD pfam17088 pfam17088 407237 YCF90 Uncharacterized protein family. Ycf90 is an algal protein located in chloroplasts. Its function is unknown. 388 matched cddid_all.tbl CDD pfam17089 pfam17089 293694 YjbT Uncharacterized protein family. This is a family of bacterial proteins. The function is unknown. 92 matched cddid_all.tbl CDD pfam17090 pfam17090 374980 Ytca YtcA family. This is a family of bacterial transmembrane proteins. The function is unknown. 62 matched cddid_all.tbl CDD pfam17091 pfam17091 435719 Inovirus_G7P_1 Inovirus G7P protein. Tail virion protein 7P is a viral transmembrane protein that interacts with the packaging signal of the viral genome leading to the initiation the virion concomitant assembly-budding process in the host inner membrane. 38 matched cddid_all.tbl CDD pfam17092 pfam17092 465343 PCB_OB Penicillin-binding protein OB-like domain. 111 matched cddid_all.tbl CDD pfam17093 pfam17093 435721 PBP_N Penicillin-binding protein N-terminus. This domain occurs at the N-terminus of some penicillin-binding proteins in Caulobacter species. 138 matched cddid_all.tbl CDD pfam17094 pfam17094 293699 UPF0715 Uncharacterized protein family (UPF0715). This is a family of Bacilli transmembrane proteins. The function is unknown. 115 matched cddid_all.tbl CDD pfam17095 pfam17095 465344 CAMSAP_CC1 Spectrin-binding region of Ca2+-Calmodulin. CAMSAP_CC1 is the conserved region on calmodulin-regulated spectrin-associated proteins in eukaryotes that binds spectrin. CAMSAPs are vertebrate microtubule-binding proteins, representatives of a family of cytoskeletal proteins that arose in animals. This conserved CC1 region binds to both spectrin and Ca2+/calmodulin in vitro, although the binding of Ca2+/calmodulin inhibited the binding of spectrin. CC1 appears to be a functional region of CAMSAP1 that links spectrin-binding to neurite outgrowth. 59 matched cddid_all.tbl CDD pfam17096 pfam17096 407240 AIM3 Altered inheritance of mitochondria protein 3. AIM3 is a family of fungal proteins that are described as altered inheritance of mitochondria protein 3 proteins. 85 matched cddid_all.tbl CDD pfam17097 pfam17097 407241 Kre28 Spindle pole body component. In Saccharomyces cerevisae Kre28 and Spc105 form a kinetochore microtubule binding complex, which bridges between centromeric heterochromatin and kinetochore MAPs (microtubule associated protein, such as Bim1, Bik1 and SIk19) and motors (Cin8, Kar3). It may be regulated by sumoylation. 360 matched cddid_all.tbl CDD pfam17098 pfam17098 465345 Wtap WTAP/Mum2p family. The Wtap family includes female-lethal(2)D from Drosophila and pre-mRNA-splicing regulator WTAP from mammals. The former is required for female-specific splicing of Sex-lethal RNA, and the latter is a regulatory subunit of the RNA N6-methyladenosine methyltransferase. The family also includes the yeast Mum2p protein which is part of the Mis complex. 155 matched cddid_all.tbl CDD pfam17099 pfam17099 293704 TrpP Tryptophan transporter TrpP. TrpP is a bacterial transmembrane protein that is probably involved in tryptophan uptake. Its expression is regulated by tryptophan-activated RNA-binding regulatory protein (TRAP). 169 matched cddid_all.tbl CDD pfam17100 pfam17100 435723 NACHT_N N-terminal domain of NWD NACHT-NTPase. This is an N-terminal domain on putative NWD NACHT proteins, signal transducing ATPases which undergo ligand-induced oligomerization. 220 matched cddid_all.tbl CDD pfam17101 pfam17101 465346 Stealth_CR1 Stealth protein CR1, conserved region 1. Stealth_C1 is the first of several highly conserved regions on stealth proteins in metazoa and bacteria. There are up to four CR regions on all member proteins. CR1 carries a well-conserved IDVVYT sequence-motif. The domain is found in tandem with CR2, CR3 and CR4 on both potential metazoan hosts and pathogenic eubacterial species that are capsular polysaccharide phosphotransferases. The CR domains appear on eukaryotic proteins such as GNPTAB, N-acetylglucosamine-1-phosphotransferase subunits alpha/beta. Horizontal gene-transfer seems to have occurred between host and bacteria of these sequence-regions in order for the bacteria to evade detection by the host innate immune system. 29 matched cddid_all.tbl CDD pfam17102 pfam17102 465347 Stealth_CR3 Stealth protein CR3, conserved region 3. Stealth_CR3 is the third of several highly conserved regions on stealth proteins in metazoa and bacteria. There are up to four CR regions on all member proteins. The domain is found in tandem with CR1, CR2 and CR4 on both potential metazoan hosts and pathogenic eubacterial species that are capsular polysaccharide phosphotransferases. The CR domains appear on eukaryotic proteins such as GNPTAB, N-acetylglucosamine-1-phosphotransferase subunits alpha/beta. Horizontal gene-transfer seems to have occurred between host and bacteria of these sequence-regions in order for the bacteria to evade detection by the host innate immune system. 49 matched cddid_all.tbl CDD pfam17103 pfam17103 465348 Stealth_CR4 Stealth protein CR4, conserved region 4. Stealth_CR4 is the fourth highly conserved region on stealth proteins in metazoa and bacteria. There are four CR regions on mammalian members. CR4 carries a well-conserved CLND sequence-motif. The domain is found in tandem with CR1, CR2 and CR3 on both potential metazoan hosts and on pathogenic eubacterial species that are capsular polysaccharide phosphotransferases. The CR domains also appear on eukaryotic proteins such as GNPTAB, N-acetylglucosamine-1-phosphotransferase subunits alpha/beta. Horizontal gene-transfer seems to have occurred between host and bacteria of these sequence-regions in order for the bacteria to evade detection by the host innate immune system. 55 matched cddid_all.tbl CDD pfam17104 pfam17104 435727 DUF5102 Domain of unknown function (DUF5102). This is a family fungal sequences of no known function. 291 matched cddid_all.tbl CDD pfam17105 pfam17105 465349 BRD4_CDT C-terminal domain of bromodomain protein 4. BRD4_CDT is the short highly conserved C-terminal domain of certain bromodomain proteins, notably Brd4. The Brd4 CTD interacts with the cyclin T1 and Cdk9 subunits of positive transcription elongation factor b (pTEFb) complex. Brd4 displaces negative regulators, the HEXIM1 and 7SKsnRNA complex, from pTEFb, thereby transforming it into an active form that can phosphorylate RNA pol II. 44 matched cddid_all.tbl CDD pfam17106 pfam17106 465350 NACHT_sigma Sigma domain on NACHT-NTPases. NACHT_sigma is a short conserved region found on NACHT-NTPases. The function of this domain is not known. 42 matched cddid_all.tbl CDD pfam17107 pfam17107 465351 SesA N-terminal domain on NACHT_NTPase and P-loop NTPases. This is a family of fungal N-terminal domains that appear at the N-terminus of P-loop NTPases, NACHT-NTPases and Ankyrin or WD repeat proteins. The exact function is not known. 122 matched cddid_all.tbl CDD pfam17108 pfam17108 374992 HET-S N-terminal small S protein of HET, non-prionic. HET-S is an N-terminal domain on various fungal STAND proteins. The function is not known exactly. 23 matched cddid_all.tbl CDD pfam17109 pfam17109 465352 Goodbye fungal STAND N-terminal Goodbye domain. The Goodbye domain is an N-terminal domain on certain fungal STAND proteins. The exact function is not known. 120 matched cddid_all.tbl CDD pfam17110 pfam17110 465353 TFB6 Subunit 11 of the general transcription factor TFIIH. TFB6 is a family of fungal proteins that form the 11th subunit of the general transcription factor TFIIH. TFB6 facilitates the dissociation of Ssl2 helicase from TFIIH after the initiation of transcription. 170 matched cddid_all.tbl CDD pfam17111 pfam17111 374995 Helo_like_N Fungal N-terminal domain of STAND proteins. Helo_like is a family of predicted fungal STAND NTPases. The exact function is not known. 209 matched cddid_all.tbl CDD pfam17112 pfam17112 407252 Tom6 Mitochondrial import receptor subunit Tom6, fungal. Tom6 is the Tom6 subunit of the protein translocase complex TOM in fungi. This complex of the outer membrane of mitochondria is the entry gate for the vast majority of precursor proteins that are encoded by nuclear DNA, synthesized in the cytosol and imported into the mitochondria. Tom6 and Tom7 together play a role in the assembly, stability and dynamics of the TOM complex. 45 matched cddid_all.tbl CDD pfam17113 pfam17113 374997 AmpE Regulatory signalling modulator protein AmpE. AmpE is a family of bacterial regulatory proteins. AmpE in conjunction with AmpD sense the effect of beta-lactam on peptidoglycan synthesis and relay this signal to AmpR. AmpR regulates the production of beta-lactamase. 284 matched cddid_all.tbl CDD pfam17114 pfam17114 374998 Nod1 Gef2-related medial cortical node protein Nod1. This is a small family of fungal proteins that are involved in cytokinesis, the last stage of the cell-division cycle. Nod1 co-localizes with Gef2 - RhoGEF - in the contractile ring and its precursor cortical nodes. Nod1 and Gef2 interact through this C-terminal region of each, this interaction being important for their localization. 145 matched cddid_all.tbl CDD pfam17115 pfam17115 407253 Toast_rack_N N-terminal domain of toast_rack, DUF2154. This short domain lies at the N-terminus of DUF2154, pfam09922, hereafter named Toast_rack from its structural resemblance. The function of both domains is unknown though DUF2154 is proposed to be a cell-adhesion protein. 92 matched cddid_all.tbl CDD pfam17116 pfam17116 435731 DUF5103 Domain of unknown function (DUF5103). This is a family of Bacteroidetes proteins of unknown function. 288 matched cddid_all.tbl CDD pfam17117 pfam17117 465354 DUF5104 Domain of unknown function (DUF5104). This is a family of gut microbes of unknown function. 108 matched cddid_all.tbl CDD pfam17118 pfam17118 407256 DUF5105 Domain of unknown function (DUF5105). This is a family of Firmicutes proteins of unknown function. There is one structure, PDB:4r4g, a lipoprotein, whose N-terminus is represented by DUF4352, pfam11611. 189 matched cddid_all.tbl CDD pfam17119 pfam17119 407257 MMU163 Mitochondrial protein up-regulated during meiosis. This is a family of fungal mitochondrial proteins of unknown function. 253 matched cddid_all.tbl CDD pfam17120 pfam17120 375001 zf-RING_16 RING/Ubox like zinc-binding domain. 57 matched cddid_all.tbl CDD pfam17121 pfam17121 435732 zf-C3HC4_5 Zinc finger, C3HC4 type (RING finger). 51 matched cddid_all.tbl CDD pfam17122 pfam17122 293727 zf-C3H2C3 Zinc-finger. 35 matched cddid_all.tbl CDD pfam17123 pfam17123 465355 zf-RING_11 RING-like zinc finger. 29 matched cddid_all.tbl CDD pfam17124 pfam17124 435734 ThiJ_like ThiJ/PfpI family-like. This is a family of fungal and bacterial ThiJ/PfpI-like proteins. 186 matched cddid_all.tbl CDD pfam17125 pfam17125 465356 Methyltr_RsmF_N N-terminal domain of 16S rRNA methyltransferase RsmF. This is the N-terminal domain of the RsmF methyl transferase. RsmF is a multi-site-specific methyltransferase that is responsible for the synthesis of three modifications on cytidines in 16S ribosomal RNA. The N-terminus is critical for stabilising the catalytic core of the enzyme. 88 matched cddid_all.tbl CDD pfam17126 pfam17126 465357 RsmF_methylt_CI RsmF rRNA methyltransferase first C-terminal domain. This is the first of two distinct C-terminal domains of the 16S rRNA methyltransferase RsmF. It is necessary for stabilising the catalytic core, pfam01189. 61 matched cddid_all.tbl CDD pfam17127 pfam17127 435737 DUF5106 Domain of unknown function (DUF5106). This domain, found in Bacteroidetes proteins, is frequently associated with a putative thiol-disulfide oxidoreductase domain, pfam13905. The function of this domain is not known. 153 matched cddid_all.tbl CDD pfam17128 pfam17128 407262 DUF5107 Domain of unknown function (DUF5107). This family is found in range of different bacterial species. In many proteins it lies N-terminal to a TPR-repeat region at the C-terminus. 300 matched cddid_all.tbl CDD pfam17129 pfam17129 407263 Peptidase_M99_C C-terminal domain of metallo-carboxypeptidase. C-terminal immunoglobulin-like domain of helical cell shape-determining peptidoglycan hydrolases, a metallo-carboxypeptidase. The structural elements of this domain form a Ca2+ binding-channel, the Ca2+ being co-ordinated by six ligand-atoms. 100 matched cddid_all.tbl CDD pfam17130 pfam17130 407264 Peptidase_M99_m beta-barrel domain of carboxypeptidase M99. This is the central, beta-barrel, domain of the metallo-carboxypeptidase that maintains helical cell-shape in Helicobacter. It shows a novel fold. It has a highly positively charged surface which contributes to a high overall isoelectric point. A calcium-binding channel is formed from residues in the C-terminal Ig-like domain in conjunction with some of the long side-chains of residues from strands beta-14 and beta-18 of this domain. 73 matched cddid_all.tbl CDD pfam17131 pfam17131 435738 LolA_like Outer membrane lipoprotein-sorting protein. This is likely to be a family of outer-membrane lipoprotein-sorting proteins. 184 matched cddid_all.tbl CDD pfam17132 pfam17132 435739 Glyco_hydro_106 alpha-L-rhamnosidase. 875 matched cddid_all.tbl CDD pfam17133 pfam17133 435740 DUF5108 Domain of unknown function (DUF5108). This is a family of Bacteroidetes proteins. The domain lies upstream of a Fasciclin family, pfam02469. 218 matched cddid_all.tbl CDD pfam17134 pfam17134 407268 DUF5109 Domain of unknown function (DUF5109). This is a family of Gram-positive Bacteroidetes and Firmicutes proteins. It lies just C-terminal to a putative glycosyl-hydrolase family, DUF4434, pfam14488. It is likely to be some form of binding or recognition domain. 114 matched cddid_all.tbl CDD pfam17135 pfam17135 465358 Ribosomal_L18 Ribosomal protein 60S L18 and 50S L18e. This is a family of ribosomal proteins, 60S L18 from eukaryotes and 50S L18e from Archaea. 184 matched cddid_all.tbl CDD pfam17136 pfam17136 465359 ribosomal_L24 Ribosomal proteins 50S L24/mitochondrial 39S L24. This is the family of bacterial 50S ribosomal subunit proteins L24. It also carries some mitochondrial 39S L24 proteins. 60 matched cddid_all.tbl CDD pfam17137 pfam17137 465360 DUF5110 Domain of unknown function (DUF5110). This domain is likely to be a carbohydrate-binding domain of some description as it is found immediately C-terminal to the glycosyl-hydrolase family Glyco_hydro_31, pfam01055. 72 matched cddid_all.tbl CDD pfam17138 pfam17138 407272 DUF5111 Domain of unknown function (DUF5111). This family is found immediately downstream of SusE, a putative starch-processing family, pfam14292. It is possible that this domain represents a substrate-binding site. 121 matched cddid_all.tbl CDD pfam17139 pfam17139 435744 DUF5112 Domain of unknown function (DUF5112). This domain is frequently found upstream of family HATPase_c pfam000251. 266 matched cddid_all.tbl CDD pfam17140 pfam17140 435745 DUF5113 Domain of unknown function (DUF5113). This domain is frequently found downstream of family HATPase_c pfam000251 in duplicate. 162 matched cddid_all.tbl CDD pfam17141 pfam17141 407275 DUF5114 Domain of unknown function (DUF5114). This family lies further downstream of DUF5111, pfam17138, on proteins from Bacteroidetes that also carry a SusE family, pfam14292. 88 matched cddid_all.tbl CDD pfam17142 pfam17142 435746 DUF5115 Domain of unknown function (DUF5115). 275 matched cddid_all.tbl CDD pfam17144 pfam17144 465361 Ribosomal_L5e Ribosomal large subunit proteins 60S L5, and 50S L18. This family contains the large 60S ribosomal L5 proteins from Eukaryota and the 50S L18 proteins from Archaea. It has been shown that the amino terminal 93 amino acids of Swiss:P09895 are necessary and sufficient to bind 5S rRNA in vitro, suggesting that the entire family has a function in rRNA binding. 163 matched cddid_all.tbl CDD pfam17145 pfam17145 435748 DUF5119 Domain of unknown function (DUF5119). This is a family of uncharacterized Bacteroidia sequences. 197 matched cddid_all.tbl CDD pfam17146 pfam17146 465362 PIN_6 PIN domain of ribonuclease. This is a PIN domain found in eukaryotic ribonuclease Nob1 and archaeal ribonuclease VapC1. Budding yeast Nob1 is involved in proteasomal and 40S ribosomal subunit biogenesis. VapC1 is a toxic component and a ribonuclease of a toxin-antitoxin (TA) module. PIN domains are small protein domains identified by the presence of three strictly conserved acidic residues. Apart from these three residues, there is poor sequence conservation. PIN domains are found in eukaryotes, eubacteria and archaea. In eukaryotes they are ribonucleases involved in nonsense mediated mRNA decay and in processing of 18S ribosomal RNA. In prokaryotes, they are the toxic components of toxin-antitoxin (TA) systems, their toxicity arising by virtue of their ribonuclease activity. The PIN domain TA systems are now called VapBC TAs(virulence associated proteins), where VapB is the inhibitor and VapC, the PIN-domain ribonuclease toxin. 87 matched cddid_all.tbl CDD pfam17147 pfam17147 407280 PFOR_II Pyruvate:ferredoxin oxidoreductase core domain II. PFOR_II is a core domain of the anaerobic enzyme pyruvate:ferredoxin oxidoreductase and is necessary for inter subunit contacts in conjunction with domains I and IV. 102 matched cddid_all.tbl CDD pfam17148 pfam17148 465363 DUF5117 Domain of unknown function (DUF5117). This domain may fall upstream of a met-zincin domain. 189 matched cddid_all.tbl CDD pfam17149 pfam17149 319167 CHASE5 Periplasmic sensor domain found in signal transduction proteins. CHASE5 is a conserved periplasmic sensor domain found in histidine kinases, diguanylate cyclases/phosphodiesterases and methyl-accepting chemotaxis proteins. In Pseudomonas aeruginosa, CHASE5 is the sensor domain in the c-di-GMP phosphodiesterase BifA that regulates biofilm formation and in sensor kinase AruS that regulates arginine degradation pathways. These results suggest that CHASE5 might bind arginine or a related compound. 108 matched cddid_all.tbl CDD pfam17150 pfam17150 435751 CHASE6_C C-terminal domain of two-partite extracellular sensor domain. CHASE6 was originally described as a two-partite extracellular (periplasmic) sensor domain found in histidine kinases and HD-GYP-type c-di-GMP-specific phosphodiesterases and assigned to COG4250 in the COG database. Subsequently, its N-terminal part has been described as a separate DICT (DIguanylate Cyclases and Two-component systems) domain (PF10069) (Aravind L., Iyer LM, Anantharaman V. (2010) Natural history of sensor domains in the bacterial signalling systems. In: Sensory Mechanisms in Bacteria: Molecular Aspects of Signal Recognition ((Spiro S, Dixon R, eds)), pp. 1-38. Caister Academic Press, Norfolk, UK). The current entry contains only the C-terminal part of the original CHASE6 domain described in, which is found primarily in cyanobacteria. 80 matched cddid_all.tbl CDD pfam17151 pfam17151 407283 CHASE7 Periplasmic sensor domain. CHASE7 is a conserved periplasmic sensor domain found in histidine kinases and diguanylate cyclases/phosphodiesterases, including the diguanylate cyclase DgcQ (YedQ) that regulates biofilm formation and motility in Escherichia coli. 187 matched cddid_all.tbl CDD pfam17152 pfam17152 435752 CHASE8 Periplasmic sensor domain. CHASE8 is a conserved periplasmic sensor domain found in histidine kinases, diguanylate cyclases/phosphodiesterases and methyl-accepting chemotaxis proteins, including the diguanylate cyclase DgcN (YfiN) that regulates biofilm formation and motility in Escherichia coli. In Pseudomonas aeruginosa, CHASE8 is the sensor domain in the diguanylate cyclase TpbB that regulates biofilm formation by controlling the levels of extracellular DNA. 102 matched cddid_all.tbl CDD pfam17153 pfam17153 465364 CHASE9 Periplasmic sensor domain, extracellular. CHASE9 is a conserved extracellular (periplasmic) sensor domain found in histidine kinases, diguanylate cyclases/phosphodiesterases, methyl-accepting chemotaxis proteins, adenylate cyclases and protein serine phosphatases, including the c-di-GMP phosphodiesterases PdeI (YliE) of Escherichia coli. 116 matched cddid_all.tbl CDD pfam17154 pfam17154 435753 GAPES3 Gammaproteobacterial periplasmic sensor domain. GAPES3 (GAmmaproteobacterial PEriplasmic Sensor) domain is a periplasmic sensor domain found in diguanylate cyclases/phosphodiesterases, including the c-di-GMP phosphodiesterases PdeK (YhjK) of Escherichia coli and HmsP of Yersinia pestis. 121 matched cddid_all.tbl CDD pfam17155 pfam17155 319173 GAPES1 Gammaproteobacterial periplasmic sensor domain. GAPES1 (GAmmaproteobacterial PEriplasmic Sensor) domain is a periplasmic sensor domain found in diguanylate cyclases and methyl-accepting chemotaxis proteins, including the diguanylate cyclase DgcJ (YeaJ) that regulates biofilm formation and motility in Escherichia coli. 274 matched cddid_all.tbl CDD pfam17156 pfam17156 319174 GAPES2 Gammaproteobacterial periplasmic sensor domain. GAPES2 (GAmmaproteobacterial PEriplasmic Sensor) domain is a periplasmic sensor domain found in diguanylate cyclases, including the diguanylate cyclase DgcI (YliF) of Escherichia coli. It contains three conserved Cys residues that might participate in thiol-disulfide exchange. 204 matched cddid_all.tbl CDD pfam17157 pfam17157 435754 GAPES4 Gammaproteobacterial periplasmic sensor domain. GAPES4 (GAmmaproteobacterial PEriplasmic Sensor) domain is a periplasmic sensor domain found in various GGDEF- and EAL-containing proteins. In Escherichia coli, GAPES4 forms the N-terminal domain of the regulatory protein CsrD (YhdA), which contains enzymatically inactive GGDEF and EAL domains and controls CsrD) that controls the degradation of two non-coding RNAs, CsrB and CsrC. In Vibrio cholerae, GAPES4-containing protein MshH (Q9KUW1_VIBCH) inhibits biofilm formation, apparently acting through the glucose-specific enzyme IIA (Q9KTD8, pfam00358). 98 matched cddid_all.tbl CDD pfam17158 pfam17158 435755 MASE4 Membrane-associated sensor, integral membrane domain. MASE4 (Membrane-Associated SEnsor) is an integral membrane sensor domain found in various GGDEF domain proteins, including a functional diguanylate cyclase DgcT (YcdT) and the enzymatically inactive CdgI (YeaI) of Escherichia coli. In the Shiga toxin-producing enteroaggregative E. coli O104:H4, which caused the outbreak of the haemolytic uraemic syndrome in Germany in 2011, MASE4-containing diguanylate cyclase DgcX, UniProtKB:B7LBD9_ECO55, was highly expressed, ensuring strong biofilm formation. 239 matched cddid_all.tbl CDD pfam17159 pfam17159 435756 MASE3 Membrane-associated sensor domain. MASE3 (Membrane-Associated SEnsor) is an integral membrane sensor domain of unknown specificity found in histidine kinases, diguanylate cyclases and protein phosphatases in various bacteria and archaea. 226 matched cddid_all.tbl CDD pfam17160 pfam17160 319178 DUF5124 Domain of unknown function (DUF5124). 100 matched cddid_all.tbl CDD pfam17161 pfam17161 435757 DUF5123 Domain of unknown function (DUF5123). 116 matched cddid_all.tbl CDD pfam17162 pfam17162 435758 DUF5118 Domain of unknown function (DUF5118). This domain falls upstream of a met-zincin domain. 50 matched cddid_all.tbl CDD pfam17163 pfam17163 407291 DUF5125 Domain of unknown function (DUF5125). 193 matched cddid_all.tbl CDD pfam17164 pfam17164 435759 DUF5122 Domain of unknown function (DUF5122) beta-propeller. 36 matched cddid_all.tbl CDD pfam17165 pfam17165 435760 DUF5121 Domain of unknown function (DUF5121). 115 matched cddid_all.tbl CDD pfam17166 pfam17166 465365 DUF5126 Domain of unknown function (DUF5126). This domain lies C-terminal to DUF4959, pfam16323. 101 matched cddid_all.tbl CDD pfam17167 pfam17167 465366 Glyco_hydro_36 Glycosyl hydrolase 36 superfamily, catalytic domain. This is the catalytic region of the superfamily of enzymes referred to as GH36. UniProtKB:Q76IQ9 is a chitobiose phosphorylase that catalyzes the reversible phosphorolysis of chitobiose into alpha-GlcNAc-1-phosphate and GlcNAc with inversion of the anomeric configuration. The full-length enzyme comprises a beta sandwich domain and an (alpha/alpha)(6) barrel domain. The alpha-helical barrel component of the domain, this family, is the catalytic region. 425 matched cddid_all.tbl CDD pfam17168 pfam17168 465367 DUF5127 Domain of unknown function (DUF5127). 226 matched cddid_all.tbl CDD pfam17169 pfam17169 465368 NRBF2_MIT MIT domain of nuclear receptor-binding factor 2. This MIT domain is the microtubule interaction and trafficking of nuclear receptor-binding factor 2 - NRBF2 - in higher eukaryotes. It is a coiled-coil region at the N-terminus of pfam08961. NRBF2 plays an essential role in autophagy, the cellular pathway that degrades long-lived proteins and other cytoplasmic contents through lysosomes. NRBF2 binds Atg14L - a Beclin-binding protein - directly via the MIT domain and enhances Atg14L-linked Vps34 kinase (a class III phosphatidylinositol-3 kinase) activity and autophagy induction. 83 matched cddid_all.tbl CDD pfam17170 pfam17170 407298 DUF5128 6-bladed beta-propeller. This family is a 6-bladed beta-propeller structure of unknown function. There is a highly conserved FDxxG motif which might be important. 321 matched cddid_all.tbl CDD pfam17171 pfam17171 465369 GST_C_6 Glutathione S-transferase, C-terminal domain. This domain is closely related to PF00043. 64 matched cddid_all.tbl CDD pfam17172 pfam17172 465370 GST_N_4 Glutathione S-transferase N-terminal domain. This domain is homologous to pfam02798. 97 matched cddid_all.tbl CDD pfam17173 pfam17173 375028 DUF5129 Domain of unknown function (DUF5129). 337 matched cddid_all.tbl CDD pfam17174 pfam17174 435766 DUF5130 Domain of unknown function (DUF5130). 136 matched cddid_all.tbl CDD pfam17175 pfam17175 435767 MOLO1 Modulator of levamisole receptor-1. MOLO1 is a one-pass transmembrane protein that contains a single extracellular globular domain. It is a positive regulator of levamisole-sensitive acetylcholine receptors in Caenorhabditis elegans, UniProtKB:Q19280. These receptors are Cys-loop ligand-gated ion channels, and the MOLO1 domain is an auxiliary subunit of the gated channel. The proteins carry a Rossmann fold. 122 matched cddid_all.tbl CDD pfam17176 pfam17176 465371 tRNA_bind_3 tRNA-binding domain. This domain, found at the C-terminus of tRNA(Met) cytidine acyltransferase, may be involved in tRNA-binding. This family represents the tRNA-binding domain proteins not captured by pfam13725. 119 matched cddid_all.tbl CDD pfam17177 pfam17177 407303 PPR_long Pentacotripeptide-repeat region of PRORP. Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. PPR_long is the region of Arabidopsis protein-only RNase P (PRORP) enzyme that consists of up to eleven alpha-helices. PRORPs are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. All PPR proteins contain tandemly repeated sequence motifs (the PPR motifs) which can vary in number. The series of helix-turn-helix motifs formed by PPR motifs throughout the protein produces a superheros with a central groove that allows the protein to bind RNA. Proteins containing PPR motifs are known to have roles in transcription, RNA processing, splicing, stability, editing, and translation. Over a decade after the discovery of PPR proteins, the super-helical structure was confirmed. The protein-only mitochondrial RNase P crystal structure from Arabidopsis thaliana (PRORP1) confirmed the role of its PPR motifs in pre-tRNA binding and suggest it has evolved independently from other RNase P proteins that rely on catalytic RNA. 212 matched cddid_all.tbl CDD pfam17178 pfam17178 435769 MASE5 Membrane-associated sensor. MASE5 is a family of bacterial membrane-associated sensor domains. It is an integral membrane sensor domain found in various GGDEF domain proteins, including a diguanylate cyclase DgcY (EcSMS35_1716) from multidrug-resistant environmental isolate Escherichia coli SMS-3-5 (Hengge R. et al. (2015): A systematic naming system for GGDEF- and EAL-containing c-di-GMP turnover proteins in Escherichia coli K-12. J.Bacteriol., in preparation). 192 matched cddid_all.tbl CDD pfam17179 pfam17179 465372 Fer4_22 4Fe-4S dicluster domain. 95 matched cddid_all.tbl CDD pfam17180 pfam17180 407306 zf-3CxxC_2 Zinc-binding domain. 74 matched cddid_all.tbl CDD pfam17181 pfam17181 407307 EPF Epidermal patterning factor proteins. EPF is a family of plant epidermal cell growth factors. It is a signalling peptide that determines the spacing and separation of the development of stomatal cells in the upper epidermis of plant leaf cells. 45 matched cddid_all.tbl CDD pfam17182 pfam17182 465373 OSK OSK domain. This entry represents the OSK domain defined by Jeske and colleagues. The domain is related to SGNH hydrolases but lacks the active site residues. The domain binds to RNA. 202 matched cddid_all.tbl CDD pfam17183 pfam17183 375036 Blt1_C Get5 carboxyl domain. During size-dependent cell cycle transitions controlled by the ubiquitous cyclin-dependent kinase Cdk1, Blt1 has been shown to co-localize with Cdr2 in the medial interphase nodes, as well as with Mid1 which was previously shown to localize to similar interphase structures. Physical interactions between Blt1-Mid1, Blt1-Cdr2 and Cdr2-Mid1 were detected, indicating that medial cortical nodes are formed by the ordered, Cdr2-dependent assembly of multiple interacting proteins during interphase. This entry corresponds to the C-terminal dimerization domain. 51 matched cddid_all.tbl CDD pfam17184 pfam17184 435771 Rit1_C Rit1 N-terminal domain. This domain is the N-terminal domain from the enzyme (EC:2.4.2.-) which modifies exclusively the initiator tRNA in position 64 using 5'-phosphoribosyl-1'-pyrophosphate as the modification donor. As the initiator tRNA participates both in the initiation and elongation of translation, the 2'-O-ribosyl phosphate modification discriminates the initiator tRNAs from the elongator tRNAs. The N-terminal domain is the most conserved region of the protein. 273 matched cddid_all.tbl CDD pfam17185 pfam17185 465374 NlpE_C NlpE C-terminal OB domain. This family represents a bacterial outer membrane lipoprotein that is necessary for signalling by the Cpx pathway. This pathway responds to cell envelope disturbances and increases the expression of periplasmic protein folding and degradation factors. While the molecular function of the NlpE protein is unknown, it may be involved in detecting bacterial adhesion to abiotic surfaces. In Escherichia coli and Salmonella typhi, NlpE is also known to confer copper tolerance in copper-sensitive strains of Escherichia coli, and may be involved in copper efflux and delivery of copper to copper-dependent enzymes. This domain is found at the C-terminus of the NlpE protein. 90 matched cddid_all.tbl CDD pfam17186 pfam17186 435773 Lipocalin_9 Lipocalin-like domain. This family contains the members of the old Pfam family DUF2006. Structural characterization of family member Swiss:Q82US3 (from DUF2006 now merged into this family) has revealed a lipocalin-like fold with domain duplication. This entry represents the C-terminal domain of the pair. 129 matched cddid_all.tbl CDD pfam17187 pfam17187 465375 Svf1_C Svf1-like C-terminal lipocalin-like domain. Family of proteins that are involved in survival during oxidative stress. This entry corresponds to the the C-terminal domain of a pair of lipocalin domains. 163 matched cddid_all.tbl CDD pfam17188 pfam17188 435775 MucB_RseB_C MucB/RseB C-terminal domain. Members of this family are regulators of the anti-sigma E protein RseD. 98 matched cddid_all.tbl CDD pfam17189 pfam17189 465376 Glyco_hydro_30C Glycosyl hydrolase family 30 beta sandwich domain. 63 matched cddid_all.tbl CDD pfam17190 pfam17190 407315 RecG_N RecG N-terminal helical domain. This four helical bundle domain is found at the N-terminus of bacterial RecG proteins. 89 matched cddid_all.tbl CDD pfam17191 pfam17191 407316 RecG_wedge RecG wedge domain. This DNA-binding domain has an OB-fold with large elaborations. 162 matched cddid_all.tbl CDD pfam17192 pfam17192 407317 MukF_M MukF middle domain. The kicA and kicB genes are found upstream of mukB. It has been suggested that the kicB gene encodes a killing factor and the kicA gene codes for a protein that suppresses the killing function of the kicB gene product. It was also demonstrated that KicA and KicB can function as a post-segregational killing system, when the genes are transferred from the E. coli chromosome onto a plasmid. 161 matched cddid_all.tbl CDD pfam17193 pfam17193 407318 MukF_C MukF C-terminal domain. This presumed domain is found at the C-terminus of the MukF protein. 158 matched cddid_all.tbl CDD pfam17194 pfam17194 465377 AbiEi_3_N Transcriptional regulator, AbiEi antitoxin N-terminal domain. AbiEi_3 is the cognate antitoxin of the type IV toxin-antitoxin 'innate immunity' bacterial abortive infection (Abi) system that protects bacteria from the spread of a phage infection. The Abi system is activated upon infection with phage to abort the cell thus preventing the spread of phage through viral replication. There are some 20 or more Abis, and they are predominantly plasmid-encoded lactococcal systems. TA, toxin-antitoxin, systems on plasmids function by killing cells that lose the plasmid upon division. AbiE phage resistance systems function as novel Type IV TAs and are widespread in bacteria and archaea. The cognate antitoxin is pfam13338. 93 matched cddid_all.tbl CDD pfam17195 pfam17195 407320 DUF5132 Protein of unknown function (DUF5132). Proteins in this family are uncharacterized, but have been identified as members of a gene cluster for the synthesis of Ansamitocin. 47 matched cddid_all.tbl CDD pfam17196 pfam17196 407321 DUF5133 Protein of unknown function (DUF5133). This protein of unknown function is part of the Borrelidin synthesis genomic cluster. Borrelidin is a polyketide antibiotic. 65 matched cddid_all.tbl CDD pfam17197 pfam17197 435778 DUF5134 Domain of unknown function (DUF5134). Proteins in this family are uncharacterized, but have been identified as members of a gene cluster for the synthesis of the tetramic-acid antibiotic streptolydigin, which inhibits bacterial RNA polymerase (RNAP). 157 matched cddid_all.tbl CDD pfam17198 pfam17198 435779 AveC_like Spirocyclase AveC-like. AveC catalyzes the stereospecific spiroketalization of a dihydroxy-ketone polyketide intermediate in the biosynthetic pathway of Avermectin, a potent antiparasitic agent. Additionally, it has a unique dehydration activity that serves to determine the regiospecific saturation pattern for spiroketal diversity. MeiC, the counterpart in the biosynthesis of AVE-like meilingmycin, also has spirocyclase activity, but lacks the dehydratase activity. 229 matched cddid_all.tbl CDD pfam17199 pfam17199 407323 DUF5136 Protein of unknown function (DUF5136). Sequences in this family have been identified in Micromonospora as part of the genomic cluster for the synthesis of dynemicin, an enediyne antitumor antibiotic. 28 matched cddid_all.tbl CDD pfam17200 pfam17200 435780 sCache_2 Single Cache domain 2. This entry represents the single Cache domain 2 (sCache_2), which contains the long N-terminal helix domain. This domain recognizes pyruvate, acetate, propionate, glycolate, L-lactate, acetoacetate, urea and hydroxyurea, acetamide, formamide, L-malate and citromalate, malonate, methyl and bromosuccinate and citraconic acid (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 153 matched cddid_all.tbl CDD pfam17201 pfam17201 465378 Cache_3-Cache_2 Cache 3/Cache 2 fusion domain. The Cache_3-Cache_2 domain likely originated as a fusion of sCache_3 and sCache_2 domains. 298 matched cddid_all.tbl CDD pfam17202 pfam17202 465379 sCache_3_3 Single cache domain 3. 104 matched cddid_all.tbl CDD pfam17203 pfam17203 435783 sCache_3_2 Single cache domain 3. This domain is associated to sensor histidine kinases and recognizes citrate and TCA cycle intermediates, Ag(II), Zn(II), Mg(II) (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 140 matched cddid_all.tbl CDD pfam17204 pfam17204 375047 Sid-5 Sid-5 family. SID-5 is a C. elegans endosome-associated protein that is required for efficient systemic RNA. 76 matched cddid_all.tbl CDD pfam17205 pfam17205 465380 PSI_integrin Integrin plexin domain. This short disulphide rich domain is found at the N-terminus of integrin beta chains. 47 matched cddid_all.tbl CDD pfam17206 pfam17206 435785 SeqA_N SeqA protein N-terminal domain. The binding of SeqA protein to hemimethylated GATC sequences is important in the negative modulation of chromosomal initiation at oriC, and in the formation of SeqA foci necessary for Escherichia coli chromosome segregation. SeqA tetramers are able to aggregate or multimerize in a reversible, concentration-dependent manner. Apart from its function in the control of DNA replication, SeqA may also be a specific transcription factor. This short domain mediates dimerization. 36 matched cddid_all.tbl CDD pfam17207 pfam17207 465381 MCM_OB MCM OB domain. This family contains an OB-fold found within MCM proteins. This domain contains an insertion at the zinc binding motif. 126 matched cddid_all.tbl CDD pfam17208 pfam17208 465382 RBR RNA binding Region. 56 matched cddid_all.tbl CDD pfam17209 pfam17209 435788 Hfq Hfq protein. 64 matched cddid_all.tbl CDD pfam17210 pfam17210 435789 SdrD_B SdrD B-like domain. This family corresponds to the B-like domain from the SdrD protein. This domain has three calcium binding sites within a greek key beta sandwich fold. 112 matched cddid_all.tbl CDD pfam17211 pfam17211 407332 VHL_C VHL box domain. This domain represents the short C-terminal alpha helical domain from the VHL protein. 49 matched cddid_all.tbl CDD pfam17212 pfam17212 407333 Tube Tail tubular protein. This family includes the tail tubular gp11 protein from bacteriophage T7. 169 matched cddid_all.tbl CDD pfam17213 pfam17213 465383 Hydin_ADK Hydin Adenylate kinase-like domain. This domain found in the Hydin protein is homologous to adenylate kinases. 199 matched cddid_all.tbl CDD pfam17214 pfam17214 435791 KH_7 KH domain. 68 matched cddid_all.tbl CDD pfam17215 pfam17215 435792 Rrp44_S1 S1 domain. This domain corresponds to the S1 domain found at the C-terminus of ribonucleases such as yeast Rrp44. 87 matched cddid_all.tbl CDD pfam17216 pfam17216 375054 Rrp44_CSD1 Rrp44-like cold shock domain. 148 matched cddid_all.tbl CDD pfam17217 pfam17217 465384 UPA UPA domain. The UPA domain is conserved in UNC5, PIDD, and Ankyrins. It has a beta sandwich structure. 140 matched cddid_all.tbl CDD pfam17218 pfam17218 465385 CBX7_C CBX family C-terminal motif. This motif is found at the C-terminus of CBX family proteins. It is bound by the RAWUL domain of the RING1B protein. 33 matched cddid_all.tbl CDD pfam17219 pfam17219 465386 YAF2_RYBP Yaf2/RYBP C-terminal binding motif. This motif is found in the Yaf2 and RYBP proteins that are homologous parts of the PRC1 complex. This motif forms a beta hairpin structure when it binds to the RAWUL domain pfam16207. 33 matched cddid_all.tbl CDD pfam17220 pfam17220 375058 DUF5137 Protein of unknown function (DUF5137). This is a family of uncharacterized yeast proteins. 78 matched cddid_all.tbl CDD pfam17221 pfam17221 465387 COMMD1_N COMMD1 N-terminal domain. This helical domain is found at the N-terminus of COMMD1. 102 matched cddid_all.tbl CDD pfam17222 pfam17222 407341 Peptidase_C107 Viral cysteine endopeptidase C107. This is a family of viral cysteine endopeptidases that process RNA polyproteins. Site directed mutagenesis suggest that H1434 and C1539 form the catalytic dyad. 314 matched cddid_all.tbl CDD pfam17223 pfam17223 375060 CPCFC Cuticle protein CPCFC. This entry contains cuticle proteins with a CX(5)C motif, although some members have a CX(7)C motif. In Anopheles gambiae, mRNA for this protein is most abundant immediately following ecdysis in larvae, pupae and adults, and is localized primarily in epidermis that secretes hard cuticle, sclerites, setae, head capsules, appendages and spermatheca. EM immunolocalization studies have shown that the protein is present in the endocuticle of legs and antennae. CPCFC is found throughout the Hexapoda and in several classes of Crustacea. 17 matched cddid_all.tbl CDD pfam17224 pfam17224 407342 DUF5300 Domain of unknown function (DUF5300). This small family of proteins found in Clostridiales is functionally uncharacterized. Proteins in this family are around 130 amino acids in length. Based on NMR structure 2MCA, it forms a beta-sandwich structure consisting of two 4-stranded antiparallel b-strands. The structure is very similar to glutamine glutamyltransferases (1l9n) and peptide transporters (5a9h). 98 matched cddid_all.tbl CDD pfam17225 pfam17225 435795 DUF5301 Domain of unknown function (DUF5300). This small family of proteins is functionally uncharacterized. It is found mainly in Firmicutes. Proteins in this family are around 130 amino acids in length. Based on NMR structure 2MCT, it forms an alpha/beta structure with a 6 stranded antiparallel b-sheet planked by a single alpha helix. The only protein with similar structures is a putative lipoprotein (PDB code 4R7R). 97 matched cddid_all.tbl CDD pfam17226 pfam17226 465388 MTA_R1 MTA R1 domain. The R1 domain is found in the MTA1 protein and its homologs. The domain is composed of 4 alpha helices. It has been shown to bind to the RBBP4 protein. The MTA proteins contain a second partial copy of this domain called R2. The R2 domain is matched by this model for some proteins. 78 matched cddid_all.tbl CDD pfam17227 pfam17227 435797 DUF5302 Family of unknown function (DUF5302). Family of unknown function found in Actinobacteria with highly conserved motif of FRRKSG found at the C-terminus. 52 matched cddid_all.tbl CDD pfam17228 pfam17228 435798 SGP Sulphur globule protein. Sulphur globules are membrane-bounded intracellular globules, used by purple sulphur bacteria to transiently store sulphur during the oxidization of reduced sulphur compounds. This proteobacterial family contains structural proteins of these sulphur globules, and includes sulphur globule protein CV1 (SgpA) and sulphur globule protein CV2 (SgpB). 97 matched cddid_all.tbl CDD pfam17229 pfam17229 435799 SMG1_N Serine/threonine-protein kinase SMG1 N-terminal. This entry represents the N-terminal disordered region of SMG1, which is a member of the phosphoinositide 3 kinase-like kinase (PIKK) family. SMG1 associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay. It also plays an important role in genotoxic stress responses to DNA damage. 106 matched cddid_all.tbl CDD pfam17230 pfam17230 435800 DUF5304 Family of unknown function (DUF5304). This family of unknown function is found in Actinobacteria. 148 matched cddid_all.tbl CDD pfam17231 pfam17231 407348 DUF5305 Family of unknown function (DUF5305). This family consists of several hypothetical proteins of unknown function. 215 matched cddid_all.tbl CDD pfam17232 pfam17232 407349 Pep1_7 Elicitor peptide 1-7. This entry include a group of elicitor peptides from plants, including Arabidopsis AtPEP1-7. AtPEP1 activates transcription of the defensive gene defensin (PDF1.2) and activates the synthesis of H(2)O(2), both being components of the innate immune response. 82 matched cddid_all.tbl CDD pfam17233 pfam17233 407350 DUF5308 Family of unknown function (DUF5308). This family of uncharacterized fungal proteins are primarily found in ascomycota. 162 matched cddid_all.tbl CDD pfam17234 pfam17234 435801 MPM1 Mitochondrial peculiar membrane protein 1. This family contains mitochondrial peculiar membrane proteins, found predominantly in Saccharomycetales. 172 matched cddid_all.tbl CDD pfam17235 pfam17235 435802 STD1 STD1/MTH1. This family of proteins includes the known homologs STD1 (also known as MSN3) and MTH1. Both STD1 and MTH1 are involved in modulating the expression of glucose-regulated genes in yeast, but have been shown to function by slightly different methods. It has been suggested that both STD1 and MTH1 are required to repress the hexose transporter genes in low glucose conditions. STD1 has also been shown to stimulate SNF1 kinase through interaction with the catalytic domain of SNF1, antagonising auto-inhibition and promoting an active conformation of the kinase. 213 matched cddid_all.tbl CDD pfam17236 pfam17236 435803 DUF5309 Family of unknown function (DUF5309). This is a family of uncharacterized proteins found in viruses and bacteria. 280 matched cddid_all.tbl CDD pfam17237 pfam17237 435804 Emr1 ERMES regulator 1. The endoplasmic reticulum-mitochondria encounter structure (ERMES) complex creates contact sites between the endoplasmic reticulum and mitochondria, playing crucial roles in interorganelle communication, mitochondrial fission, mtDNA inheritance, lipid transfer, and autophagy. Emr1, also known as Mco6 in budding yeasts, mediates the formation ERMES foci, thereby contributing to the formation of ER-mitochondrial contact sites. 44 matched cddid_all.tbl CDD pfam17238 pfam17238 407355 DUF5311 Family of unknown function (DUF5311). This domain can be found in Streptophyta. On the N terminal of this family, the Nucleoporin Nup120/160 family pfam11715 is often present. 194 matched cddid_all.tbl CDD pfam17239 pfam17239 375073 DUF5312 Family of unknown function (DUF5312). This is a family of unknown function, mostly found in Spirochaeta. 553 matched cddid_all.tbl CDD pfam17240 pfam17240 435805 DUF5313 Family of unknown function (DUF5313). This is a family of unknown function, found mostly in Actinobacteria and composed of trans-membrane proteins. 123 matched cddid_all.tbl CDD pfam17241 pfam17241 407356 Retrotran_gag_4 Ty5 Gag N-terminal region. This entry corresponds to part of the Gag protein found in a variety of retrotransposons. It is not clear whether this covers the matrix or capsid proteins partially or entirely. 154 matched cddid_all.tbl CDD pfam17242 pfam17242 435806 DUF5315 Disordered region of unknown function (DUF5315). This is a family of unknown function found mostly in Saccharomycetales. 77 matched cddid_all.tbl CDD pfam17243 pfam17243 435807 POTRA_TamA_1 POTRA domain TamA domain 1. This family represents the POTRA domain found in the membrane insertase TamA. 74 matched cddid_all.tbl CDD pfam17244 pfam17244 465389 CDC24_OB3 Cell division control protein 24, OB domain 3. This family contains OB-fold domains that bind to nucleic acids. The family includes a domain found in Cell division control protein 24 (Cdc24). Cdc24 plays an essential role in the progression of normal DNA replication and is required to maintain genomic integrity. Cdc24 has been reported to interact with replication factor C (RFC) as well as proliferating cell nuclear antigen (PCNA), and has been suggested to act as a target for the regulation of damage repair DNA synthesis. 206 matched cddid_all.tbl CDD pfam17245 pfam17245 465390 CDC24_OB2 Cell division control protein 24, OB domain 2. This family contains OB-fold domains that bind to nucleic acids. The family includes a domain found in Cell division control protein 24 (Cdc24). Cdc24 plays an essential role in the progression of normal DNA replication and is required to maintain genomic integrity. Cdc24 has been reported to interact with replication factor C (RFC) as well as proliferating cell nuclear antigen (PCNA), and has been suggested to act as a target for the regulation of damage repair DNA synthesis. 128 matched cddid_all.tbl CDD pfam17246 pfam17246 465391 CDC24_OB1 Cell division control protein 24, OB domain 1. This family contains OB-fold domains that bind to nucleic acids. The family includes a domain found in Cell division control protein 24 (Cdc24). Cdc24 plays an essential role in the progression of normal DNA replication and is required to maintain genomic integrity. Cdc24 has been reported to interact with replication factor C (RFC) as well as proliferating cell nuclear antigen (PCNA), and has been suggested to act as a target for the regulation of damage repair DNA synthesis. 122 matched cddid_all.tbl CDD pfam17247 pfam17247 465392 DUF5316 Family of unknown function (DUF5316). This is a family of unknown function mainly found in Firmicutes. Might contain multiple trans-membrane sequences. 74 matched cddid_all.tbl CDD pfam17248 pfam17248 435811 DUF5317 Family of unknown function (DUF5317). This is a family of unknown function found mainly in Bacteria. Members of this family have multiple trans-membrane domains with the majority typically constituted of 4 trans-membrane regions. 150 matched cddid_all.tbl CDD pfam17249 pfam17249 407364 DUF5318 Family of unknown function (DUF5318). This family of unknown function is mostly found in Actinobacteria. 131 matched cddid_all.tbl CDD pfam17250 pfam17250 435812 NDUFB11 NADH-ubiquinone oxidoreductase 11 kDa subunit. Complex I of the respiratory chain is a proton-pumping, NADH ubiquinone oxidoreductase that oxidizes NADH in the electron transport pathway. Plants contain the series of 14 highly conserved complex I subunits found in other eukaryotic and related prokaryotic enzymes. 86 matched cddid_all.tbl CDD pfam17251 pfam17251 435813 Pom Protochlamydia outer membrane protein. This family represents an outer membrane protein found in environmental chlamydia. The protein shows porin function. 282 matched cddid_all.tbl CDD pfam17252 pfam17252 465393 DUF5319 Family of unknown function (DUF5319). This is a family of unknown function mostly found in Actinobacteria. 121 matched cddid_all.tbl CDD pfam17253 pfam17253 435815 DUF5320 Family of unknown function (DUF5320). A number of this family members have a coiled coil domain at the C terminal. 99 matched cddid_all.tbl CDD pfam17254 pfam17254 407369 DUF5321 Family of unknown function (DUF5321). This is a family of unknown function. Most of the members seem to carry one trans-membrane region. 160 matched cddid_all.tbl CDD pfam17255 pfam17255 435816 EbsA EbsA-like protein. This is a family of unknown function which contains the EbsA protein from Enterococcus faecalis. The uncharacterized family is mainly found in lactobacilli and consists of two N-terminal transmembrane helices followed by a bacterial PH domain. 133 matched cddid_all.tbl CDD pfam17256 pfam17256 435817 ANAPC16 Anaphase-promoting complex, subunit 16. The Anaphase-promoting complex/cyclosome (APC/C) is a 1.5 megaDaltons assembly ubiquitin ligase complex comprising 19 subunits. This multifunctional ubiquitin-protein ligase targets different substrates for ubiquitylation and therefore regulates a variety of cellular processes such as cell division, differentiation, genome stability, energy metabolism, cell death, autophagy as well as carcinogenesis. The APC/C complex contains two sub-complexes,the Platform and the Arc Lamp. The Arc Lamp, which mediates transient association with regulators and ubiquitination substrates, contains the small subunits APC16, CDC26, APC13, and tetratricopeptide repeat (TPR) proteins. APC16 is a conserved subunit of the APC/C. APC16 was found in association with tandem-affinity-purified mitotic checkpoint complex protein complexes. APC16 is a bona fide subunit of human APC/C. It is present in APC/C complexes throughout the cell cycle. The phenotype of APC16-depleted cells copies depletion of other APC/C subunits, and APC16 is important for APC/C activity towards mitotic substrates. APC16 sequence homologs can be identified in metazoans, but not fungi, by four conserved primary sequence stretches. 80 matched cddid_all.tbl CDD pfam17257 pfam17257 375084 DUF5323 Family of unknown function (DUF5323). This family of proteins found in Eukaryota, has no known function. 62 matched cddid_all.tbl CDD pfam17258 pfam17258 407372 DUF5324 Family of unknown function (DUF5324). This is a family of unknown function, mostly found in Actinobacteria. Most of the family members contain one trans-membrane domain. 220 matched cddid_all.tbl CDD pfam17259 pfam17259 407373 DUF5325 Family of unknown function (DUF5325). This is a family of unknown function mainly found in Bacilli. Family members of this family are predicted to have trans-membrane domains. 61 matched cddid_all.tbl CDD pfam17260 pfam17260 435818 DUF5326 Family of unknown function (DUF5326). This is a family of unknown function mostly found in Actinobacteria. Many of the family members are predicted to contain two trans-membrane domains. 70 matched cddid_all.tbl CDD pfam17261 pfam17261 435819 DUF5327 Family of unknown function (DUF5327). This bacterial family of proteins has no known function and is mostly found in Bacilli. 96 matched cddid_all.tbl CDD pfam17262 pfam17262 435820 Cas6b_C Cas6b C-terminal domain. Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation. Four Cas proteins (Cas5, Cas6b, Cas7 and Cas8b) are proposed to form a Type I-B Cascade complex that mediates the antiviral defense. This is the C-terminal domain found in Cas6b proteins. Cas6b is a member of Cas6 RNA processing endoribonucleases found in bacteria and archaea whose RNA substrates have a wide range of structural features. Cocrystal structures of Cas6 from Methanococcus maripaludis (MmCas6b) bound with its repeat RNA revealed a dual-site binding structure and a cleavage site conformation poised for phosphodiester bond breakage. 114 matched cddid_all.tbl CDD pfam17263 pfam17263 465394 DUF5329 Family of unknown function (DUF5329). This is a bacterial family of proteins with unknown function. 95 matched cddid_all.tbl CDD pfam17264 pfam17264 435822 DUF5330 Family of unknown function (DUF5330). This is a family of unknown function which is mostly found in Bacteria. 65 matched cddid_all.tbl CDD pfam17265 pfam17265 435823 DUF5331 Family of unknown function (DUF5331). This bacterial family of unknown function can be found in Cyanobacteria. 113 matched cddid_all.tbl CDD pfam17266 pfam17266 465395 DUF5332 Family of unknown function (DUF5332). This family of uncharacterized proteins is mostly found in Chromadorea. Family members include dct-5 proteins. Dct-5 is a target of DAF-16, a forkhead transcription factor, which is a key regulator of longevity, metabolism and dauer diapause in Caenorhabditis elegans. 150 matched cddid_all.tbl CDD pfam17267 pfam17267 435825 DUF5333 Family of unknown function (DUF5333). This family of uncharacterized proteins is mostly found in Alphaproteobacteria. 110 matched cddid_all.tbl CDD pfam17268 pfam17268 339984 DUF5334 Family of unknown function (DUF5334). This is a family of unknown function which can is found mainly in Proteobacteria. 71 matched cddid_all.tbl CDD pfam17269 pfam17269 435826 DUF5335 Family of unknown function (DUF5335). This bacterial family of proteins has no known function. 110 matched cddid_all.tbl CDD pfam17270 pfam17270 465396 DUF5336 Family of unknown function (DUF5336). This Actinobacterial family of proteins has no known function. Most of the family members are predicted to have have 4 trans-membrane regions. 113 matched cddid_all.tbl CDD pfam17271 pfam17271 435828 Usher_TcfC TcfC Usher-like barrel domain. This is the presumed beta barrel domain from the usher-like TcfC family of proteins. 420 matched cddid_all.tbl CDD pfam17272 pfam17272 435829 DUF5337 Family of unknown function (DUF5337). This family of unknown function is found in Rhodobacterales. Most members are predicted to have 2 trans-membrane regions. 74 matched cddid_all.tbl CDD pfam17273 pfam17273 435830 DUF5338 Family of unknown function (DUF5338). This is a family of unknown function which can be found mostly in Proteobacteria. 69 matched cddid_all.tbl CDD pfam17274 pfam17274 435831 DUF5339 Family of unknown function (DUF5339). This is a family of unknown function that can be found mostly in Proteobacteria. Some of the family members are predicted to contain a coiled coil region. 70 matched cddid_all.tbl CDD pfam17275 pfam17275 435832 DUF5340 Family of unknown function (DUF5340). This family of unknown function can be found in Cyanobacteria. 70 matched cddid_all.tbl CDD pfam17276 pfam17276 407389 DUF5341 Family of unknown function (DUF5341). This is a family of unknown function, which can be found mostly in Ascomycota. 161 matched cddid_all.tbl CDD pfam17277 pfam17277 435833 DUF5342 Family of unknown function (DUF5342). This family of no known function is found in Bacilli. 69 matched cddid_all.tbl CDD pfam17278 pfam17278 435834 DUF5343 Family of unknown function (DUF5343). This is a family of unknown function which is found in Bacteria and Archaea. 138 matched cddid_all.tbl CDD pfam17279 pfam17279 435835 DUF5344 Family of unknown function (DUF5344). This is a Bacterial family of unknown function. Family members are predicted to belong to Type VII secretion (T7S) system. There is a conserved YxxxD/E sequence. It is a general secretion signal that is present in all known mycobacterial T7S substrates or substrate complexes. 87 matched cddid_all.tbl CDD pfam17280 pfam17280 435836 DUF5345 Family of unknown function (DUF5345). This is a family of unknown function. It is found mostly in Bacteria. Members of this family are predicted to contain 2 trans-membrane regions. 77 matched cddid_all.tbl CDD pfam17281 pfam17281 465397 DUF5346 Family of unknown function (DUF5346). This family of unknown function is found in Nematoda. 102 matched cddid_all.tbl CDD pfam17282 pfam17282 435838 DUF5347 Family of unknown function (DUF5347). This family of unknown function is found in Bacteria, mainly in Proteobacteria. 101 matched cddid_all.tbl CDD pfam17283 pfam17283 465398 Zn_ribbon_SprT SprT-like zinc ribbon domain. This family represents a domain found in eukaryotes and prokaryotes. The domain contains a characteriztic motif of the zinc ribbon. This family includes the bacterial SprT protein. 38 matched cddid_all.tbl CDD pfam17284 pfam17284 407397 Spermine_synt_N Spermidine synthase tetramerization domain. This domain represents the N-terminal tetramerization domain from spermidine synthase. 53 matched cddid_all.tbl CDD pfam17285 pfam17285 435840 PRMT5_TIM PRMT5 TIM barrel domain. This domain corresponds to the N-terminal TIM barrel domain from PRMT5 proteins.. 248 matched cddid_all.tbl CDD pfam17286 pfam17286 435841 PRMT5_C PRMT5 oligomerization domain. 173 matched cddid_all.tbl CDD pfam17287 pfam17287 465399 POTRA_3 POTRA domain. This POTRA domain is found in ShlB-like proteins. 56 matched cddid_all.tbl CDD pfam17288 pfam17288 375107 Terminase_3C Terminase RNAseH like domain. 154 matched cddid_all.tbl CDD pfam17289 pfam17289 435843 Terminase_6C Terminase RNaseH-like domain. 154 matched cddid_all.tbl CDD pfam17290 pfam17290 407402 Arena_ncap_C Arenavirus nucleocapsid C-terminal domain. This domain represents the the C-terminal domain that contains 3'-5' exoribonuclease activity involved in suppressing interferon induction. This domain has an RNaseH-like fold. 177 matched cddid_all.tbl CDD pfam17291 pfam17291 435844 M60-like_N N-terminal domain of M60-like peptidases. This accessory domain has a jelly roll topology. 106 matched cddid_all.tbl CDD pfam17292 pfam17292 465400 POB3_N POB3-like N-terminal PH domain. This domain is found at the N-terminus of POB3 and related proteins. 93 matched cddid_all.tbl CDD pfam17293 pfam17293 465401 Arm-DNA-bind_5 Arm DNA-binding domain. This domain is the N-terminal Arm DNA-binding domain found in various tyrosine recombinases. 87 matched cddid_all.tbl CDD pfam17294 pfam17294 407406 Lipoprotein_22 Uncharacterized lipoprotein family. The proteins in this family all have an N-terminal lipoprotein attachment motif. No member of this family has been functionally characterized. 166 matched cddid_all.tbl CDD pfam17295 pfam17295 435847 DUF5348 Domain of unknown function (DUF5348). 69 matched cddid_all.tbl CDD pfam17296 pfam17296 340012 ArenaCapSnatch Arenavirus cap snatching domain. This domain represents the N-terminal domain of the Arenavirus polymerase that is involved in cap snatching during transcription initiation. 171 matched cddid_all.tbl CDD pfam17297 pfam17297 465402 PEPCK_N Phosphoenolpyruvate carboxykinase N-terminal domain. catalyzes the formation of phosphoenolpyruvate by decarboxylation of oxaloacetate. 218 matched cddid_all.tbl CDD pfam17298 pfam17298 407409 DUF5349 Family of unknown function (DUF5349). This is a family of unknown function found in Saccharomycetaceae. 362 matched cddid_all.tbl CDD pfam17299 pfam17299 435849 DUF5350 Family of unknown function (DUF5350). This family is found in Euryarchaeota, predominantly in Methanomicrobia and Archaeoglobi. No known function for this family has been demonstrated. 57 matched cddid_all.tbl CDD pfam17300 pfam17300 407411 FIN1 Filaments in between nuclei protein-1. Fin1 is a kinetochore protein, predicted to contain two putative coiled-coil regions at its C terminus. It is present in a filamentous structure associated with the spindle and spindle pole in dividing cells during anaphase. Fin1 is a substrate of S-phase cyclin-dependent kinase (CDK). It binds to PP1 creating the Fin1- PPI complex which is recruited onto kinetochores promoting spindle assembly checkpoint (SAC) dis-assembly during anaphase. This is an important step in cell division since the kinetochore is the docking site for the spindle assembly checkpoint that monitors the defects in chromosome attachment and blocks anaphase onset. Fin1 has two RXXS/T sequences: S377 (RVTS), S526 (RKVS) that can be phosphorylated. Upon phosphorylation, interactions with other proteins such as Bmh1 and Bmh2 is promoted. However, de-phosphorylation during anaphase promotes the kinetochore recruitment of Fin1-PP1. 240 matched cddid_all.tbl CDD pfam17301 pfam17301 465403 LpqV Putative lipoprotein LpqV. This is a family of cell surface proteins found in Mycobacterium with no known function. 114 matched cddid_all.tbl CDD pfam17302 pfam17302 435851 DUF5351 Family of unknown function (DUF5351). This family of unknown function is found in Bacillales. 29 matched cddid_all.tbl CDD pfam17303 pfam17303 407414 DUF5352 Family of unknown function (DUF5352). This is a family of unknown function found mostly in Eukaryota. 165 matched cddid_all.tbl CDD pfam17304 pfam17304 407415 DUF5353 Family of unknown function (DUF5353). This is a family of unknown function found mostly in Fungi. Members of this family are predicted to contain 2 trans-membrane regions. 68 matched cddid_all.tbl CDD pfam17305 pfam17305 375117 DUF5354 Family of unknown function (DUF5354). This family of unknown function is found mostly in Metazoa. 124 matched cddid_all.tbl CDD pfam17306 pfam17306 435852 DUF5355 Family of unknown function (DUF5355). This family of unknown function is found in Saccharomycetales. 332 matched cddid_all.tbl CDD pfam17307 pfam17307 407417 Smim3 Small integral membrane protein 3. This domain family can be found in Smim3 proteins (Small integral membrane protein 3) also known as NID67 (NGF-induced differentiation clone 67). It is a primary response gene, hypothesized to be involved in forming or regulating ion channels in neuronal differentiation. It is strongly induced by NGF (Nerve Growth Factor) and FGF (Fibroblast Growth Factor), both of which cause these cells to differentiate. The amino acid sequence of NID67 is strongly conserved among rat, mouse and human. This family of small membrane proteins is only 60 amino acids long and analysis of the predicted peptide sequence reveals a stretch of 29 hydrophobic and uncharged residues which very likely comprise a trans-membrane region. 60 matched cddid_all.tbl CDD pfam17308 pfam17308 375119 Corazonin Pro-corazonin. This domain family is found in Corazonin proteins in Drosophila and other Anthropods. Corazonin (Crz)is a neuropeptide with a wide spectrum of biological functions in diverse insect groups. It was first discovered due to its myostimulatory activities on the heart muscle of Periplaneta Americana and the hyper-neural muscle of Carausius morosus. In Drosophila melanogaster, Crz plays diverse roles ranging from a regulator of insulin producing cells in the brain to roles specific to tissues, life stages, and gender. 134 matched cddid_all.tbl CDD pfam17309 pfam17309 407418 DUF5356 Family of unknown function (DUF5356). This is a family of unknown function found in Chromadorea. 135 matched cddid_all.tbl CDD pfam17310 pfam17310 435853 DUF5357 Family of unknown function (DUF5357). This is a family of unknown function found in Cyanobacteria. Most of the family members are predicted to have several trans-membrane regions. 322 matched cddid_all.tbl CDD pfam17311 pfam17311 435854 DUF5358 Family of unknown function (DUF5358). This family of unknown function is found in Proteobacteria. 161 matched cddid_all.tbl CDD pfam17312 pfam17312 465404 Helveticin_J Bacteriocin helveticin-J. Bacteriocins are biologically active proteins or protein complexes that display a bactericidal mode of action towards closely related species. Bacteriocins produced by lactic acid bacteria are grouped into different classes. Class III of bacteriocins includes large heat liable proteins. Lactobacillus helveticus 481 produces a 37-kDa bacteriocin called helveticin J which is a representative for Class III bacteriocins. 317 matched cddid_all.tbl CDD pfam17313 pfam17313 435856 DUF5359 Family of unknown function (DUF5359). This is a family of unknown function found in Bacillales. Most of the family members are predicted to have one trans-membrane region. 56 matched cddid_all.tbl CDD pfam17314 pfam17314 435857 DUF5360 Family of unknown function (DUF5360). This is a family of unknown function. It is present in Bacteria and most of the family members are predicted to have 4 trans-membrane regions. 127 matched cddid_all.tbl CDD pfam17315 pfam17315 435858 FMP23 Found in mitochondrial proteome. FMP23 gene encodes a putative mitochondrial protein involved in iron-copper homoeostasis. It was observed to be induced in response to ATX1 deletion and high copper conditions. 118 matched cddid_all.tbl CDD pfam17316 pfam17316 465405 Perilipin_2 Perilipin protein. This family includes Pet10p and Sps4p which are yeast perilipin proteins. 253 matched cddid_all.tbl CDD pfam17317 pfam17317 407425 MFA1_2 Mating hormone A-factor 1&2. The polypeptides encoded by the MFa1 and MFa2 genes are precursors of 36 and 38 amino acids, respectively. These mating pheromones secreted by S. cerevisiae a-cells, exhibit a single amino acid residue difference (the MFa1 gene product contains a valine instead of the leucine coded for by MFa2 at position 6 of the mature a-factor). The most significant feature of the primary a-factor gene products is the presence of a specific C-terminal motif, found in all known farnesylated proteins, representing a signal for modification of polypeptides with an isoprenoid group. In the case of both a-factor precursors, this specific sequence of amino acids is -CVIA. However, the general motif is referred to as a CAAX box, since the consensus sequence of amino acids present at the C terminus of isoprenylated proteins consists of an invariable cysteine (C) residue followed by two aliphatic (A) amino acids and ending in a carboxyl-terminal residue of almost any (X) type The specific CAAX sequence has also been shown to target the peptide for either farnesylation or geranylgeranylation. 34 matched cddid_all.tbl CDD pfam17318 pfam17318 465406 DUF5361 Family of unknown function (DUF5361). This is a family of unknown function found in Bacteria. 36 matched cddid_all.tbl CDD pfam17319 pfam17319 435861 DUF5362 Family of unknown function (DUF5362). This is a family of unknown function found in Bacteria. Most of the family members are predicted to have 2 trans-membrane regions. 94 matched cddid_all.tbl CDD pfam17320 pfam17320 435862 DUF5363 Family of unknown function (DUF5363). This is a family of unknown function found in Gammaproteobacteri. 54 matched cddid_all.tbl CDD pfam17321 pfam17321 435863 Vac17 Vacuole-related protein 17. Vac17 serves as an adaptor protein recruiting vacuole vesicles to the actin cable tracks by its dual interaction with Vac8 and the Myo2 motor protein. It is directly phosphorylated by Cdk1. Vac17 plays an important role in vacuole inheritance and segregation in cell division. 408 matched cddid_all.tbl CDD pfam17322 pfam17322 435864 DUF5364 Family of unknown function (DUF5364). This family of unknown function is found in Saccharomycetales. 185 matched cddid_all.tbl CDD pfam17323 pfam17323 435865 ToxS Trans-membrane regulatory protein ToxS. Gram negative bacteria such as Vibrio cholera require the production of a number of virulence factors during infection. ToxS, a member of this domain family, is required for ToxR activity. The ToxR and ToxS regulatory proteins are considered to be at the root of the V. cholera virulence regulon, called the ToxR regulon. ToxS serves as a mediator of ToxR function, perhaps by influencing its stability and/or capacity to dimerize, hence ToxS plays an important function in transcriptional activation of Vibrio cholerae virulence genes. 147 matched cddid_all.tbl CDD pfam17324 pfam17324 340040 BLI1 BLOC-1 interactor 1. In yeast BLOC-1 consists of six subunits localized to the endosomes. In the absence of BLOC-1 subunits, the balance between recycling and degradation of selected cargoes is impaired. This family contains BLI1 (BlOC-1 interactor 1) protein, a subunit of the BLOC-1 complex which mediates endosomal maturation. 111 matched cddid_all.tbl CDD pfam17325 pfam17325 407431 SPG4 Stationary phase protein 4. Saccharomyces cerevisiae respond and cope to starvation by ceasing growth and entering a non-proliferating state referred to as stationary phase. Expression of SPG4 has been shown to be higher in stressed cells, and stationary phase cells compared to active cells. It is not required for growth on non-fermentable carbon sources. 109 matched cddid_all.tbl CDD pfam17326 pfam17326 435866 DUF5365 Family of unknown function (DUF5365). This is a family of unknown function found in Bacillaceae. 116 matched cddid_all.tbl CDD pfam17327 pfam17327 407433 AHL_synthase Acyl homoserine lactone synthase. Members of this family are involved in quorum sensing processes. In gram negative bacteria, N-acylhomoserine lactones (AHLs) act as signals. As the bacterial density increases, AHLs accumulate, and once they reach a critical level (quorum), they interact with cognate receptor proteins, which then affect target gene expression. Some AHLs are synthesized by LuxM (AHL synthase) and homologs (VanM and opaM). LuxM enzymes use S-adenosyl-methionine (SAM) as one of its two substrates and are capable of using either acyl-acyl-carrier-protein (acyl-ACP) or acyl-coenzyme A (acyl-CoA) as the other substrate. VanM, the LuxM homolog, produces two auto-inducers C6HSL and 3OC6HSL. Both autoinducers are detected by the VanN receptor. The autoinducers HAI-1, is synthesized by the cytoplasmic enzymes LuxM. 376 matched cddid_all.tbl CDD pfam17328 pfam17328 435867 DUF5366 Family of unknown function (DUF5366). This is a family of unknown function, found in Bacillales. Members of the family are predicted to have between 4 and 5 trans-membrane regions. 158 matched cddid_all.tbl CDD pfam17329 pfam17329 435868 DUF5367 Family of unknown function (DUF5367). This bacterial family of proteins of unknown function is predicted to contain 3 or 4 trans-membrane regions. 98 matched cddid_all.tbl CDD pfam17330 pfam17330 435869 SWC7 SWR1 chromatin-remodelling complex, sub-unit Swc7. The SWR1 complex is involved in chromatin-remodeling by promoting the the ATP-dependent exchange of histone H2A for the H2A variant HZT1 in Saccharomyces cerevisiae or H2AZ in mammals. The SWR1 chromatin-remodeling complex is composed of at least 14 subunits and has a molecular mass of about 1.2 to 1.5 MDa. In S. cerevisiae there are core conserved subunits (ATPase; Swr1,RuvB-like; Rvb1 and Rvb2, Actin; Act1, Actin-related: Arp4 and Arp6, YEATS protein) and non-conserved subunits (Vps71 (Swc6), Vps72 (Swc2), Swc3, Swc4, Swc5, Swc7, Bdf1). Seven of the SWR1 subunits are involved in maintaining complex integrity and H2AZ histone replacement activity: Swr1, Swc2, Swc3, Arp6, Swc5, Yaf9 and Swc6. Arp4 is required for the association of Bdf1, Yaf9, and Swc4 and Arp4 is also required for SWR1 H2AZ histone replacement activity in vitro. Furthermore the N-terminal region of the ATPase Swr1 provides the platform upon which Bdf1, Swc7, Arp4, Act1, Yaf9 and Swc4 associate. It also contains an additional H2AZ-H2B specific binding site, distinct from the binding site of the Swc2 subunit. In eukaryotes the deposition of variant histones into nucleosomes by the chromatin-remodeling complexes such as the SWR1 and INO80 complexes have many crucial functions including the control of gene regulation and expression, checkpoint regulation, DNA replication and repair, telomere maintenance and chromosomal segregation and as such represent critical components of pathways that maintain genomic integrity. This entry represents the subunit Swc7; the smallest subunit of the SWR1 complex. Swc7 is not required for H2AZ binding. It associates with the N terminus of Swr1, and the association of Bdf1 requires Swc7, Yaf9, and Arp4. 98 matched cddid_all.tbl CDD pfam17331 pfam17331 435870 GFD1 GFD1 mRNA transport factor. Following transcription, mRNA is processed, packaged into messenger ribonucleoprotein (mRNP) particles, and transported through nuclear pores (NPCs) to the cytoplasm. Gfd1 is one of several factors that, although not essential for mRNA export, enhances the efficiency of the process, either by facilitating integration of different steps in the gene expression pathway or by increasing the rate of key steps. Gfd1 localizes to the cytoplasm and nuclear rim. It interacts with a number of components of the mRNA export machinery in yeast. Most notably, Gfd1 interacts with the Dbp5-activating protein, Gle1, the cytoplasmic nucleoporin Nup42/Rip1, the putative RNA helicase, Dbp5, and a protein implicated in mRNA export, Zds1. Gfd1 forms a complex with Nab2 both in vitro and in vivo in which Gfd1 binds to the N-terminal domain of Nab2. The crystal structure, together with complementary NMR data, indicated that residues 126-150 of Gfd1 form a single alpha-helix that binds primarily to helix 2 of Nab2-N. Gfd1 functions to co-ordinate Dbp5 and Gle1 to facilitate the removal of Nab2 from mRNPs at the cytoplasmic face of nuclear pores. 44 matched cddid_all.tbl CDD pfam17332 pfam17332 407438 DUF5592 Family of unknown function (DUF5592). This is a family of unknown function found in Bacilli.Family members contain two predicted trans-membrane regions. 89 matched cddid_all.tbl CDD pfam17333 pfam17333 375136 DEFB136 Beta defensin 136. Beta-defensins are small cationic peptides that have triple-stranded beta-sheet structure. They are characterized by the presence of multiple cysteine residues (forming three distinctive intramolecular disulfide bridges) and a highly similar tertiary structure known as the defensin motif. All beta-defensin genes encode a precursor peptide that consists of a hydrophobic, leucine-rich signal sequence, a pro-sequence, and a mature six-cysteine defensin motif at the carboxy terminus. They exhibit broad-spectrum antimicrobial properties and contribute to mucosal immune responses at epithelial sites. Several beta-defensins family members have been shown to play essential roles in sperm maturation and fertility in rats, mice and humans. In addition to the wide spectrum of antimicrobial activity, mammalian beta-defensins have been reported to have other roles in the immune system, such as the chemotactic ability for immature dendritic cells and memory T-cells via chemokine receptor-6 demonstrated by human beta-defensin-2. This entry contains beta-defensins such as DEFB136, the mouse homolog Defb42 and Ostricacin-3. 51 matched cddid_all.tbl CDD pfam17334 pfam17334 407439 CsgA Minor curli fiber component A. Curli are extracellular functional amyloids that are assembled by enteric bacteria during biofilm formation and host colonization. The csg (curli specific gene) operon encodes major structural and accessory proteins that are required for curli production. The csgBAC operon encodes the major and minor curli fiber components, CsgA and CsgB, respectively. CsgA is secreted to the extracellular milieu as an unfolded protein and forms amyloid polymers upon interacting with the CsgB nucleator. CsgA is comprised of five imperfect repeating units with highly conserved glutamine and asparagine residues that are important for amyloid formation. Each repeating unit is predicted to form a strand-loop-strand motif. In vitro, CsgC inhibits CsgA amyloid formation at substoichiometric concentrations and maintains CsgA in a non-beta-sheet rich conformation, making CsgC an efficient and selective amyloid inhibitor. 83 matched cddid_all.tbl CDD pfam17335 pfam17335 407440 IES5 Ino80 complex subunit 5. The INO80 chromatin remodeling complex is known to be related to DNA repair in yeast, mammals, and plants. In yeast, the INO80 complex is recruited to the DSBs (DNA double-strand breaks) through the direct interaction of its Nhp10 (non-histone protein 10) or Arp4 (Actin-Related Protein) subunits with phosphorylated histone H2A. However, the ortholog of yeast Nhp10 does not exist in mammals. The Nhp10 module consists of Nhp10, Ies1, Ies3, and Ies5. These yeast-specific subunits cross-link to the N terminus of Ino80 and form a stable complex in-vitro, which helps high-affinity targeting of INO80 to nucleosome-binding. 110 matched cddid_all.tbl CDD pfam17336 pfam17336 435871 DUF5368 Family of unknown function (DUF5368). This is a family of unknown function found in Proteobacteria and predicted to contain 2 trans-membrane regions. 111 matched cddid_all.tbl CDD pfam17337 pfam17337 407442 Gal_GalNac_35kD Galactose-inhibitable lectin 35 kDa subunit. The role of the cell surface D-galactose (Gal)/N-Acetyl-D-galactosamine (GalNAc), lectin in the adhesion process has been demonstrated in Entamoeba histolytica, a protozoan parasite that causes amebiasis in humans. The Gal/GalNAc lectin is a heterotrimeric protein complex. It is composed of a 260 kDa heterodimer of trans-membrane disulphide-linked heavy 170 kDa subunit and glycosylphosphatidylinositol (GPI)-anchored light 31 kDa/35 kDa subunits. The light subunits are non-covalently associated with an intermediate subunit of 150 kDa. Inhibition of expression of 35 kDa subunit of Gal/GalNAc lectin inhibits the cytotoxic and cytopathic activity of E. histolytica, but no decrease in adherence capacity to mammalian cells was evident. Interestingly, a carbohydrate-binding activity has been reported for the 35 kDa light subunit of the lectin molecules of the closely related Entamoeba invadens. This entry is related to the light subunit where this domain of unknown function is present. The light subunit consists of several polypeptide chains with considerable antigenic homology. The two light (31/35 kDa) subunits of the lectin are present in two isoforms: the 31 kDa isoform is glycerolphosphatidylinositol (GPI) anchored; and the 35 kDa isoform is more highly glycosylated. 225 matched cddid_all.tbl CDD pfam17338 pfam17338 435872 GP88 Gene product 88. This family of unknown function is found in Bacteria. 231 matched cddid_all.tbl CDD pfam17339 pfam17339 407443 PH_15 PH domain. This entry contains a PH domain. 107 matched cddid_all.tbl CDD pfam17340 pfam17340 407444 DUF5370 Family of unknown function (DUF5370). This is a family of unknown function found in Bacillaceae. 63 matched cddid_all.tbl CDD pfam17341 pfam17341 340057 DUF5371 Family of unknown function (DUF5371). This is a family of unknown function found in Euryarchaeota. 65 matched cddid_all.tbl CDD pfam17342 pfam17342 435873 DUF5372 Family of unknown function (DUF5372). This family of unknown function is found in Bacteria. 78 matched cddid_all.tbl CDD pfam17343 pfam17343 407446 DUF5373 Family of unknown function (DUF5373). This family of unknown function is found in Caenorhabditis. Members of this family are predicted to contain 4 trans-membrane regions. 182 matched cddid_all.tbl CDD pfam17344 pfam17344 435874 DUF5374 Family of unknown function (DUF5374). This is a family of unknown function found in Pasteurellaceae. 40 matched cddid_all.tbl CDD pfam17345 pfam17345 435875 DUF5375 Family of unknown function (DUF5375). This is a family of unknown function found in Enterobacteriaceae. 106 matched cddid_all.tbl CDD pfam17346 pfam17346 435876 DUF5376 Family of unknown function (DUF5376). This is a family of unknown function found in Bacteria. 134 matched cddid_all.tbl CDD pfam17347 pfam17347 407448 DUF5377 Family of unknown function (DUF5377). This is a family of unknown function found in Pasteurellaceae. 96 matched cddid_all.tbl CDD pfam17349 pfam17349 407449 DUF5378 Family of unknown function (DUF5378). This is a family of unknown function which is found in Mycoplasmataceae.Family members are predicted to contain 7 trans-membrane regions 282 matched cddid_all.tbl CDD pfam17351 pfam17351 375145 DUF5380 Family of unknown function (DUF5380). This is a family of unknown function found in Rhabditida. 85 matched cddid_all.tbl CDD pfam17352 pfam17352 340067 MFS18 Male Flower Specific protein 18. This domain family is found on MFS18 protein from Maize. MFS18 mRNA accumulates in the glumes and in anther walls, paleas and lemmas of mature florets. It is particularly associated with the vascular bundle in the glumes and encodes a polypeptide of 12 kDa, rich in glycine, proline and serine that has similarities with other plant structural proteins. There is no known function of this family in Maize or other Poaceae. 97 matched cddid_all.tbl CDD pfam17353 pfam17353 407450 DUF5381 Family of unknown function (DUF5381). This is a family of unknown function found in Bacillales. 169 matched cddid_all.tbl CDD pfam17354 pfam17354 375147 DUF5382 Family of unknown function (DUF5382). This is a family of unknown function found in Caenorhabditis. 418 matched cddid_all.tbl CDD pfam17355 pfam17355 407451 DUF5383 Family of unknown function (DUF5383). This is a family of unknown function found in Bacillales. Members of this family are predicted to contain one trans-membrane region. 124 matched cddid_all.tbl CDD pfam17356 pfam17356 407452 PBSX_XtrA Phage-like element PBSX protein XtrA. This is a family of unknown function found in Bacilli. 64 matched cddid_all.tbl CDD pfam17357 pfam17357 375150 FIT1_2 Facilitor Of iron transport 1 and 2. Fit proteins (facilitor of iron transport) found on Saccharomyces cerevisiae cell wall are mannoproteins implicated in the siderophore-iron bound transport. This domain family can be found in FIT1 and FIT2 proteins in Saccharomycetaceae. The FIT1-3 cell wall mannoproteins are attached to the beta-glucan layer through a GPI (glycosylphosphatidylinoisitol) anchor. They are very rich in serine and threonine residues (40-50 % serine and threonine) and bear several short repeat of 6-7 amino acids sequence. The exact domain function is unknown. 86 matched cddid_all.tbl CDD pfam17358 pfam17358 407453 DUF5384 Family of unknown function (DUF5384). This is a family of unknown function found in Proteobacteria. 145 matched cddid_all.tbl CDD pfam17359 pfam17359 407454 DUF5385 Family of unknown function (DUF5385). This is a family of unknown function found in Mycoplasmataceae. Family members are predicted to have one trans-membrane region. 217 matched cddid_all.tbl CDD pfam17360 pfam17360 375152 DUF5386 Family of unknown function (DUF5386). This is a family of unknown function found in Chromadorea. 170 matched cddid_all.tbl CDD pfam17361 pfam17361 435877 DUF5387 Family of unknown function (DUF5387). This is a family of unknown function found in Strongyloides. 222 matched cddid_all.tbl CDD pfam17362 pfam17362 435878 pXO2-34 Family of unknown function. This is a family of unknown function found in Bacilli. 79 matched cddid_all.tbl CDD pfam17363 pfam17363 375154 DUF5388 Family of unknown function (DUF5388). This is a family of unknown function found in Lactobacillales. 70 matched cddid_all.tbl CDD pfam17364 pfam17364 435879 DUF5389 Family of unknown function (DUF5389). This is a family of unknown function found in Pasteurellaceae. Family members are predicted to have 3 trans-membrane regions. 104 matched cddid_all.tbl CDD pfam17365 pfam17365 375156 DUF5390 Family of unknown function (DUF5390). This is a family of unknown function found in Caenorhabditis. 141 matched cddid_all.tbl CDD pfam17366 pfam17366 375157 AGA2 A-agglutinin-binding subunit Aga2. The wall of Saccharomyces cerevisiae consists of mannoproteins, beta-glucans, and a small amount of chitin. Mannoproteins include Aga2p where this domain family is found. There are two main display systems for yeast, the agglutinin system and the flocculin system. The S. cerevisiae sexual agglutinins facilitate the mating between two types of cells, a and alpha. A-Agglutinin consists of two subunits, encoded by two unlinked genes, AGA1 and AGA2. The cell surface adhesion protein (Aga2), enhances agglutination between a and alpha cells. Optimal binding includes interactions of the alpha-agglutinin binding pocket with the Aga2p terminal carboxyl group. This O-mannosylated glycopeptide is doubly disulfide linked to Aga1p. The Aga2p half-cystines near the ends of the peptide are linked to two Aga1p Cys residues separated by only two residues. This closeness of the disulfide bonds stabilizes the alpha/beta structure in Aga2p. 58 matched cddid_all.tbl CDD pfam17367 pfam17367 407456 NiFe_hyd_3_EhaA NiFe-hydrogenase-type-3 Eha complex subunit A. Energy-converting [NiFe] hydrogenases are membrane-bound enzymes with a six-subunit core: the large and small hydrogenase subunits, plus two hydrophilic proteins and two integral membrane proteins. Their large and small subunits show little sequence similarity to other [NiFe] hydrogenases, except for key conserved residues coordinating the active site and [FeS] cluster. Energy-converting [NiFe] hydrogenases function as ion pumps, catalyzing the reduction of ferredoxin with H2 driven by the proton-motive force or the sodium-ion-motive force. Eha and Ehb hydrogenases contain extra subunits in addition to those shared by other energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type). Eha contains a 6[4Fe-4S] polyferredoxin, a 10[4Fe-4S] polyferredoxin, ten other predicted integral membrane proteins (EhaA, EhaB, EhaC, EhaD, EhaE, EhaF, EhaG, EhaI, EhaK, EhaL) and four hydrophobic subunits (EhaM, EhaR, EhS, EhT). Eha and Ehb catalyze the reduction of low-potential redox carriers (e.g. ferredoxins or polyferredoxins), which then might function as electron donors to oxidoreductases. Based on sequence similarity and genome context analysis, other organizms such as Methanopyrus kandleri, Methanocaldococcus jannaschii, and Methanothermobacter marburgensis also encode Eha-like [NiFe]-hydrogenase-3-type complexes and have very similar eha operon structure. This domain family can be found on the small membrane proteins that are predicted to be the EhaA trans-membrane subunits of multisubunit membrane-bound [NiFe]-hydrogenase Eha complexes. 94 matched cddid_all.tbl CDD pfam17368 pfam17368 407457 YwcE Spore morphogenesis and germination YwcE. The ywcE gene codes for a holin-like protein that localizes to the cell and spore membranes. It is expressed at the onset of sporulation and transcription is repressed during growth by the transition-state regulator AbrB. YwcE is an 83-residue protein with three trans-membrane regions and a highly charged C-terminal tail. Moreover, YwcE has a dual start motif, which plays a role in the regulation of class I or class II holins. It is likely to have the N terminus on the outside of the membrane and the C terminus in the cytoplasm. This family is found in YwcE proteins in Bacilli. 85 matched cddid_all.tbl CDD pfam17369 pfam17369 435880 DUF5391 Family of unknown function (DUF5391). This is a family of unknown function found in Bacilli. Family members are predicted to have 4 trans-membrane regions. 135 matched cddid_all.tbl CDD pfam17370 pfam17370 375160 DUF5392 Family of unknown function (DUF5392). This is a family of unknown function found in Bacilli. Family members are predicted to have 2 trans-membrane regions. 139 matched cddid_all.tbl CDD pfam17371 pfam17371 407459 DUF5393 Family of unknown function (DUF5393). This is a family of unknown function found in Trypanosomatidae. 666 matched cddid_all.tbl CDD pfam17372 pfam17372 407460 DUF5394 Family of unknown function (DUF5394). This is a family of unknown function found in Rickettsiales. 205 matched cddid_all.tbl CDD pfam17373 pfam17373 407461 DUF5395 Family of unknown function (DUF5395). This is a family of unknown function found in Archaea and Bacteria. 81 matched cddid_all.tbl CDD pfam17374 pfam17374 340089 DUF5396 Family of unknown function (DUF5396). This is a family of unknown function found in Mycoplasma. 947 matched cddid_all.tbl CDD pfam17375 pfam17375 435881 DUF5397 Family of unknown function (DUF5397). This is a family of unknown function found in Proteobacteria. 59 matched cddid_all.tbl CDD pfam17376 pfam17376 435882 DUF5398 Family of unknown function (DUF5398). This is a family of unknown function found in Chlamydiales. 80 matched cddid_all.tbl CDD pfam17377 pfam17377 435883 DUF5399 Family of unknown function (DUF5399). This is a family of unknown function found in Chlamydiales. 140 matched cddid_all.tbl CDD pfam17378 pfam17378 465407 REC104 Meiotic recombination protein REC104. REC104 is one of several meiosis specific genes required for generating meiotic DSBs (double strand breaks). It is suggested that Rec102 and Rec104 directly promote DSB formation as part of a multiprotein complex with Spo11. Rec102 and Rec104 are mutually dependent for proper sub-cellular localization, and share a requirement for Spo11 and Ski8 for their recruitment to meiotic chromosomes. Moreover, Rec102 is required for Rec104 to accumulate to normal steady-state levels and to be properly phosphorylated. It is likely that Rec102 and Rec104 move freely in and out of the nucleus but are most stably sequestered there only when they can form a complex on chromosomes. This domain family is found on Rec104 proteins in yeast. 182 matched cddid_all.tbl CDD pfam17379 pfam17379 435885 DUF5400 Family of unknown function (DUF5400). This is a family of unknown function found in Methanobacteria and Methanococci. Members of this family are predicted to contain 4 trans-membrane regions. 100 matched cddid_all.tbl CDD pfam17380 pfam17380 375164 DUF5401 Family of unknown function (DUF5401). This is a family of unknown function found in Chromadorea. 722 matched cddid_all.tbl CDD pfam17381 pfam17381 375165 Svs_4_5_6 Seminal vesicle secretory proteins 4/5/6. There are seven major proteins involved in murine seminal vesicle secretion (SVS1-7). Mouse Svs2-Svs6 genes evolved by gene duplication and belong to the same gene family. This domain family is found in SVS4/5 and 6. SVS4 is a basic, thermostable, secretory protein synthesized by rat seminal vesicle epithelium under strict androgen transcriptional control. This protein has potent nonspecies-specific immunomodulatory, anti-inflammatory, and pro-coagulant activities that have been shown to be located in the N-terminal region of Svs4 (fragment 1-70). The N-terminal segment has a high amino-acid sequence similarity with the C-terminal segment 34-66 of uteroglobin, a rabbit steroid-inducible, cytokine-like, multifunctional, secreted protein. Furthermore, SVS4 acts as a sperm capacitation inhibitor, by interacting with SVS3 and SVS2. 91 matched cddid_all.tbl CDD pfam17382 pfam17382 340097 Ycf70 Uncharacterized Ycf70-like. This is a family of unknown function found in Poaceae. 89 matched cddid_all.tbl CDD pfam17383 pfam17383 375166 kleA_kleC Uncharacterized KorC regulated protein A. This is a family of unknown function found in Proteobacteria. 76 matched cddid_all.tbl CDD pfam17384 pfam17384 465408 DUF150_C RimP C-terminal SH3 domain. This family represents the C-terminal domain from RimP. 67 matched cddid_all.tbl CDD pfam17385 pfam17385 465409 LBP_M Lacto-N-biose phosphorylase central domain. The gene which codes for this protein in gut-bacteria is located in a novel putative operon for galactose metabolism. The protein appears to be a carbohydrate-processing phosphorolytic enzyme (EC:2.4.1.211), unlike either glycoside hydrolases or glycoside lyase. Intestinal colonization by bifidobacteria is important for human health, especially in pediatrics, because colonization seems to prevent infection by some pathogenic bacteria that cause diarrhoea or other illnesses. The operon seems to be involved in intestinal colonization by bifidobacteria mediated by metabolism of mucin sugars. In addition, it may also resolve the question of the nature of the bifidus factor in human milk as the lacto-N-biose structure found in milk oligosaccharides. 221 matched cddid_all.tbl CDD pfam17386 pfam17386 465410 LBP_C Lacto-N-biose phosphorylase C-terminal domain. The gene which codes for this protein in gut-bacteria is located in a novel putative operon for galactose metabolism. The protein appears to be a carbohydrate-processing phosphorolytic enzyme (EC:2.4.1.211), unlike either glycoside hydrolases or glycoside lyase. Intestinal colonization by bifidobacteria is important for human health, especially in pediatrics, because colonization seems to prevent infection by some pathogenic bacteria that cause diarrhoea or other illnesses. The operon seems to be involved in intestinal colonization by bifidobacteria mediated by metabolism of mucin sugars. In addition, it may also resolve the question of the nature of the bifidus factor in human milk as the lacto-N-biose structure found in milk oligosaccharides. 53 matched cddid_all.tbl CDD pfam17387 pfam17387 465411 Glyco_hydro_59M Glycosyl hydrolase family 59 central domain. 116 matched cddid_all.tbl CDD pfam17388 pfam17388 465412 GP24_25 Mycobacteriophage tail assembly protein. Bacteriophages (viruses of bacteria) use a specialized organelle called a tail to deliver their genetic material and proteins across the cell envelope during infection. This family represents tail assembly proteins found in phages from Siphoviridae family, which includes Mycobacteriophage L5, D29 and Lamina13. This phages have long non-contractile tails. This proteins are likely to interact with the tape measure protein. 123 matched cddid_all.tbl CDD pfam17389 pfam17389 407469 Bac_rhamnosid6H Bacterial alpha-L-rhamnosidase 6 hairpin glycosidase domain. This family consists of bacterial rhamnosidase A and B enzymes. L-Rhamnose is abundant in biomass as a common constituent of glycolipids and glycosides, such as plant pigments, pectic polysaccharides, gums or biosurfactants. Some rhamnosides are important bioactive compounds. For example, terpenyl glycosides, the glycosidic precursor of aromatic terpenoids, act as important flavouring substances in grapes. Other rhamnosides act as cytotoxic rhamnosylated terpenoids, as signal substances in plants or play a role in the antigenicity of pathogenic bacteria. 340 matched cddid_all.tbl CDD pfam17390 pfam17390 379972 Bac_rhamnosid_C Bacterial alpha-L-rhamnosidase C-terminal domain. This family consists of bacterial rhamnosidase A and B enzymes. L-Rhamnose is abundant in biomass as a common constituent of glycolipids and glycosides, such as plant pigments, pectic polysaccharides, gums or biosurfactants. Some rhamnosides are important bioactive compounds. For example, terpenyl glycosides, the glycosidic precursor of aromatic terpenoids, act as important flavouring substances in grapes. Other rhamnosides act as cytotoxic rhamnosylated terpenoids, as signal substances in plants or play a role in the antigenicity of pathogenic bacteria. 78 matched cddid_all.tbl CDD pfam17391 pfam17391 465413 Urocanase_N Urocanase N-terminal domain. 127 matched cddid_all.tbl CDD pfam17392 pfam17392 465414 Urocanase_C Urocanase C-terminal domain. 196 matched cddid_all.tbl CDD pfam17393 pfam17393 435892 DUF5402 Family of unknown function (DUF5402). This is a family of unknown function found in Methanobacteria and Methanococci. 120 matched cddid_all.tbl CDD pfam17394 pfam17394 340109 KleE Uncharacterized KleE stable inheritance protein. This is a family of unknown function found in Proteobacteria. Family Members are predicted to contain two trans-membrane regions. 108 matched cddid_all.tbl CDD pfam17395 pfam17395 407472 DUF5403 Family of unknown function (DUF5403). This is a family of unknown function found in Actinobacteria. 96 matched cddid_all.tbl CDD pfam17396 pfam17396 435893 DUF1611_N Domain of unknown function (DUF1611_N) Rossmann-like domain. 94 matched cddid_all.tbl CDD pfam17397 pfam17397 340112 DUF5404 Family of unknown function (DUF5404). This is a family of unknown function found in Chordata. This domain is located downstream the N-terminal of Fip1 pfam05182. Family members such as Swiss:P70537 and Swiss:P70675 contain this domain. The Tsx gene resides at the X-inactivation centre and once thought to encode a protein expressed in testis. However, this was disputed upon further analysis. ORF and immunostaining analysis concluded that Tsx may be non-coding. Tsx long transcript is abundantly expressed in meiotic germ cells, embryonic stem cells, and brain. In vertebrates, Fip1 is the evolutionary precursor of eutherian Tsx, hence its location upstream from the Tsx gene. 145 matched cddid_all.tbl CDD pfam17398 pfam17398 435894 NolB Nodulation protein NolB. This domain family of unknown function is found in Rhizobiales. Family members are involved in Nodulation (nodule development in plants). 149 matched cddid_all.tbl CDD pfam17399 pfam17399 435895 DUF5405 Domain of unknown function (DUF5405). This domain family is found in Enterobacteriaceae. This protein may have a phage origin being found in bacteriophage P2 Swiss:Q06425. The majority of proteins have a conserved cysteine residue close to their C-terminus which may have functional significance. 88 matched cddid_all.tbl CDD pfam17400 pfam17400 465415 DUF5406 Family of unknown function (DUF5406). This is a family of unknown function found in Bacteria. 116 matched cddid_all.tbl CDD pfam17401 pfam17401 435897 DUF5407 Family of unknown function (DUF5407). This is a family of unknown function found in Chlamydiales. 74 matched cddid_all.tbl CDD pfam17402 pfam17402 340117 DUF5408 Family of unknown function (DUF5408). This is a family of unknown function found in Helicobacteraceae. Family members are predicted to contain one trans-membrane region. 63 matched cddid_all.tbl CDD pfam17403 pfam17403 465416 Nrap_D2 Nrap protein PAP/OAS-like domain. Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localized in the nucleolus. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript. 148 matched cddid_all.tbl CDD pfam17404 pfam17404 465417 Nrap_D3 Nrap protein domain 3. Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localized in the nucleolus. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript. 159 matched cddid_all.tbl CDD pfam17405 pfam17405 465418 Nrap_D4 Nrap protein nucleotidyltransferase domain 4. Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localized in the nucleolus. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript. 201 matched cddid_all.tbl CDD pfam17406 pfam17406 465419 Nrap_D5 Nrap protein PAP/OAS1-like domain 5. Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localized in the nucleolus. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript. 157 matched cddid_all.tbl CDD pfam17407 pfam17407 465420 Nrap_D6 Nrap protein domain 6. Members of this family are nucleolar RNA-associated proteins (Nrap) which are highly conserved from yeast (Saccharomyces cerevisiae) to human. In the mouse, Nrap is ubiquitously expressed and is specifically localized in the nucleolus. Nrap is a large nucleolar protein (of more than 1000 amino acids). Nrap appears to be associated with ribosome biogenesis by interacting with pre-rRNA primary transcript. 128 matched cddid_all.tbl CDD pfam17408 pfam17408 465421 MCD_N Malonyl-CoA decarboxylase N-terminal domain. This family consists of several eukaryotic malonyl-CoA decarboxylase (MLYCD) proteins. Malonyl-CoA, in addition to being an intermediate in the de novo synthesis of fatty acids, is an inhibitor of carnitine palmitoyltransferase I, the enzyme that regulates the transfer of long-chain fatty acyl-CoA into mitochondria, where they are oxidized. After exercise, malonyl-CoA decarboxylase participates with acetyl-CoA carboxylase in regulating the concentration of malonyl-CoA in liver and adipose tissue, as well as in muscle. Malonyl-CoA decarboxylase is regulated by AMP-activated protein kinase (AMPK). 85 matched cddid_all.tbl CDD pfam17409 pfam17409 435904 MoaF_C MoaF C-terminal domain. MoaF protein is essential for the production of the monoamine-inducible 30kDa protein in Klebsiella. It is necessary for reconstituting organoautotrophic growth in Ralstonia eutropha. It is conserved in Proteobacteria and some lower eukaryotes. The operon regulating the Moa genes is responsible for molybdenum cofactor biosynthesis. This entry corresponds to the C-terminal domain. 113 matched cddid_all.tbl CDD pfam17410 pfam17410 407484 Stevor Subtelomeric Variable Open Reading frame. The parasite protein STEVOR (Subtelomeric Variable Open Reading frame) is an erythrocyte-binding protein recognizing Glycophorin C on the red blood cell (RBC) surface. The cytoplasmic domain of STEVOR is shown to interact with ankyrin complex at the erythrocyte skeleton. It is phosphorylated by protein kinase A (PKA) at a specific serine residue (S324). The N-terminal semi-conserved region of Stevor that is present in this domain is shown to specifically bind to to a chymotrypsin-resistant RBC receptor. The expression of STEVOR in multiple parasite stages including merozoites suggests that STEVOR mediates multiple distinct functions in parasitic infectious cycle. 275 matched cddid_all.tbl CDD pfam17411 pfam17411 465422 SmaI Type II site-specific deoxyribonuclease. Family members of this domain are Type II site-specific deoxyribonuclease EC=3.1.21.4. The endonuclease SmaI recognizes and cleaves the sequence CCCGGGG on DNA, yielding a blunt end scission. It has been used for the diagnosis of neurogenic muscle weakness, ataxia and retinitis pigmentosa disease or Leigh's disease. Due to its specificity in recognizing the cleavage site, it is used in Leigh's disease to specifically eliminate the mutant mitochondrial DNA (mtDNA), which coexists with the wild-type mtDNA (heteroplasmy). Only the mutant mtDNA, but not the wild-type mtDNA, is selectively restricted by the enzyme. By delivering the SmaI gene fused to a mitochondrial targeting sequence, specific elimination of the mutant mtDNA was demonstrated, resulting in restoration of both the normal intracellular ATP level and normal mitochondrial membrane potential. The same strategy has also been demonstrated retinitis pigmentosa (NARP), where a mutant mitochondrial DNA carrying a T8993G transversion has been targeted by using SmaI enzymes. 241 matched cddid_all.tbl CDD pfam17412 pfam17412 407486 VraX Family of unknown function. This domain family is found in VraX proteins from Staphylococcus aureus. The vraX gene belongs to the vra operon together with the vraA gene encoding for a long chain fatty acid-CoA ligase, which is up-regulated in the VISA (vancomycin-intermediate S. aureus). The gene product, a 55-amino acids protein,is upregulated in the stress response to cell wall-active antibiotics and other surface-interactive molecules. VraX harbors a putative phosphorylation site, and could therefore be involved in regulatory processes within the cell. However, no exact function has been demonstrated. 55 matched cddid_all.tbl CDD pfam17413 pfam17413 340128 VirB7 Outer membrane lipoprotein virB7. The type IV secretion systems (T4SSs) are ancestrally related to bacterial conjugation machines and are able to translocate proteins and/or protein-DNA complexes to the extracellular milieu or the host interior, in many cases contributing to the ability of the bacterial pathogen to colonize the host and evade its immune system. In the pathogenic plant pathogen Agrobacterium tumefaciens T4SS allows the bacterium to transfer a segment of its tumor inducing (Ti-) plasmid DNA into plant cells causing crown gall tumor disease. Proteins in the virB and virD operons catalyze processing of the T-DNA and its transfer to plants. The VirB proteins assemble a secretion apparatus spanning both bacterial membranes to allow transfer of DNA and protein substrates into plant cells. VirB7 and VirB8, along with VirB6, VirB9 and VirB10, are the core components of the Agrobacterium DNA translocation apparatus. Structural studies with the Escherichia coli plasmid pKM101 VirB homologs showed that three proteins, TraN (VirB7 homolog), TraO (VirB9) and TraF (VirB10), form a hetero-tetradecameric structure with 14-fold symmetry forming an outer membrane channel through which the substrates pass. VirB7 stabilizes VirB9 and in its absence bacteria do not accumulate VirB9 preventing assembly of the secretion machine. Members of the VirB7 family are typically 45-65 residues long, becoming 15-20 residues shorter after removal of the N-terminal signal sequence and covalent attachment to lipid molecules. 35 matched cddid_all.tbl CDD pfam17414 pfam17414 435905 MatP_C MatP C-terminal ribbon-helix-helix domain. This family, many of whose members are YcbG, organizes the macrodomain Ter of the chromosome of bacteria such as E coli. In these bacteria, insulated macrodomains influence the segregation of sister chromatids and the mobility of chromosomal DNA. organization of the Terminus region (Ter) into a macrodomain relies on the presence of a 13 bp motif called matS repeated 23 times in the 800-kb-long domain. MatS sites are the main targets in the E. coli chromosome of YcbG or MatP (macrodomain Ter protein). MatP accumulates in the cell as a discrete focus that co-localizes with the Ter macrodomain. The effects of MatP inactivation reveal its role as the main organizer of the Ter macrodomain: in the absence of MatP, DNA is less compacted, the mobility of markers is increased, and segregation of the Ter macrodomain occurs early in the cell cycle. A specific organizational system is required in the Terminus region for bacterial chromosome management during the cell cycle. This entry represents the C-terminal ribbon-helix-helix domain. 60 matched cddid_all.tbl CDD pfam17415 pfam17415 435906 NigD_C NigD-like C-terminal beta sandwich domain. This family of proteins is functionally uncharacterized. This family of proteins is found in Bacteroides species. Proteins in this family are typically between 234 and 260 amino acids in length. These proteins possess an N-terminal lipoprotein attachment site. The family includes NigD a protein found in the Nig operon that encodes a bacteriocin called nigrescin. It has been suggested that NigD may be the immunity protein for nigrescin (NigC) because it is directly downstream. This entry represents the C-terminal beta-sandwich domain of NigD. 120 matched cddid_all.tbl CDD pfam17416 pfam17416 435907 Glycoprot_B_PH1 Herpesvirus Glycoprotein B. This domain has a PH-like fold. 210 matched cddid_all.tbl CDD pfam17417 pfam17417 407490 Glycoprot_B_PH2 Herpesvirus Glycoprotein B PH-like domain. This domain corresponds to the second PH-like domain in herpesvirus glycoprotein B. 97 matched cddid_all.tbl CDD pfam17418 pfam17418 435908 SdpA Sporulation delaying protein SdpA. Spore formation by the bacterium Bacillus subtilis is an elaborate developmental process that is triggered by nutrient limitation. Cells that have entered the pathway to sporulate produce and export a killing factor and a signaling protein that act cooperatively to block sister cells from sporulating and to cause them to lyse. The sporulating cells feed on the nutrients thereby released, which allows them to keep growing rather than to complete morphogenesis. Entry into sporulation is governed by the regulatory protein Spo0A (master regulator of sporulation). Upon Spo0A phosphorylation, it represses the expression of abrB, a negative regulator of skfABCEFGH and sdpAB, leading to the transcriptional activation of sdpAB operon. The production of SdpAB is essential for the SDP toxin. SDP is a 42-amino-acid, ribosomally synthesized AMP which contains a disulfide bond between two cysteine residues located at the N terminus. SDP acts by rapidly collapsing the proton motive force thereby inducing autolysin mediated lysis on neighboring species and non-biofilm producing B. subtilis cells (which do not produce SdpI) to respond by moving away, while autolysis would release nutrients that can be readily used to promote biofilm growth. SdpAB proteins are required to produce SDP from SdpC33-203. This domain family is found in SdpA proteins which are predicted to be a 158-amino-acid proteins suggest to be primarily cytoplasmic. 142 matched cddid_all.tbl CDD pfam17419 pfam17419 407492 MauJ Methylamine utilization protein MauJ. This domain family is found in MauJ proteins. The exact function of the MauJ proteins is unknown but thought to be involved in methylamine utilization. MauJ is predicted to be a cytoplasmic protein. 282 matched cddid_all.tbl CDD pfam17420 pfam17420 340135 GP17 Superinfection exclusion gene product 17. Bacteriophages infect host cells by injecting their genome through the cell wall. To this end, tailed bacteriophages have evolved complex tail machines that extend from a unique capsid vertex, providing both an attachment point to the host surface, and a channel for genome-ejection through the cell envelope. Family members of this domain are putative gp17 proteins involved in genome delivery tail machine in Entereobacteria phage p22 and Salmonella phage ViI. Gp17 found in other bacteriophages such as SPP1 (siphophage SPP1, a lytic Bacillus subtilis phage) has been identified as a tail completion protein adopting an alpha/beta fold, and found to be located at the interface between the head-to-tail connector and the tail of bacteriophage SPP1. 98 matched cddid_all.tbl CDD pfam17421 pfam17421 340136 DUF5409 Family of unknown function (DUF5409). This domain of unknown function is found in Poxviridae. 88 matched cddid_all.tbl CDD pfam17422 pfam17422 465423 DUF5410 Family of unknown function (DUF5410). This is a family of unknown function found in Rickettsia. 350 matched cddid_all.tbl CDD pfam17423 pfam17423 407493 SwrA Swarming motility protein. This domain family is found in Bacillus. Members of this family are Swra proteins involved in swarming motility (a multicellular movement of hyper-flagellated cells on a surface). SwrA is a key transcription factor facilitating this cascade. It acts synergistically with DegU to drive the fla/che operon encoding flagella components, chemotaxis constituents and the alternative sigma factor sigmaD, which is regarded as the primary event in the development of motility. LonA protease of Bacillus subtilis inhibits SwrA by proteolytically restricting its accumulation. SwrA does not contain any known DNA binding domain, and it has been shown to interact with the N-terminal domain of DegU. Anecdotally, in most laboratory strains, e.g. 168, the swrA coding sequence contains a nucleotide insertion that prematurely interrupts its reading frame, causing a non-swarming phenotype strain. 116 matched cddid_all.tbl CDD pfam17424 pfam17424 407494 DUF5411 Family of unknown function (DUF5411). This is a family of unknown function found in Bacteria. 134 matched cddid_all.tbl CDD pfam17425 pfam17425 407495 Arylsulfotran_N Arylsulfotransferase Ig-like domain. This family consists of several bacterial Arylsulfotransferase proteins. Arylsulfotransferase (ASST) transfers a sulfate group from phenolic sulfate esters to a phenolic acceptor substrate. This domain has an Ig-like fold. 89 matched cddid_all.tbl CDD pfam17426 pfam17426 435909 Putative_G5P Putative Gamma DNA binding protein G5P. This domain family is found in Gammaproteobacterial proteins. Members of the family are predicted to be G5P DNA binding proteins. Homologous proteins are found in pfam02303 108 matched cddid_all.tbl CDD pfam17427 pfam17427 340142 Phi29_Phage_SSB Phage Single-stranded DNA-binding protein. DNA replication of phi29 and related phages takes place via a strand displacement mechanism, a process that generates large amounts of single-stranded DNA (ssDNA). Consequently, phage-encoded ssDNA-binding proteins (SSBs) are essential proteins during phage phi29-like DNA replication. Single-stranded DNA-binding proteins (SSBs) destabilize double-stranded DNA (dsDNA) and bind without sequence specificity, but selectively and cooperatively, to single-stranded DNA (ssDNA) conferring a regular structure to it, which is recognized and exploited by a variety of enzymes involved in DNA replication, repair and recombination. Phage phi29 protein p5 is the SSB protein active during phi29 DNA replication. It protects ssDNA against nuclease degradation and greatly stimulates dNTP incorporation during phi29 DNA replication process. Binding of the SSB to ssDNA prevents non-productive binding of the viral DNA polymerase to ssDNA, and allows the release DNA polymerase molecules that are already titrated by the ssDNA. This effect would be of particular importance in phi29-like DNA replication systems, where large amounts of ssDNA are generated and SSB binding to ssDNA could favor efficient re-usage of templates. This domain family is found in SSB proteins in phage phi-29, homologs are found in pfam00436. 123 matched cddid_all.tbl CDD pfam17428 pfam17428 435910 DUF5412 Family of unknown function (DUF5412). This is a family of unknown function found in Bacteria. Members of this family have one or two predicted trans-membrane regions. 118 matched cddid_all.tbl CDD pfam17429 pfam17429 435911 GP70 Gene product 70. This family of unknown function is found in Mycobcterium phage and Actinobacteria. 54 matched cddid_all.tbl CDD pfam17430 pfam17430 340145 YqgC Uncharacterized YqgC-like. This is a family of unknown function found in Enterobacteriaceae such as E.coli and Shigella. 51 matched cddid_all.tbl CDD pfam17431 pfam17431 407499 YpmT Uncharacterized YmpT-like. This is a family of unknown function found in Bacillus. 62 matched cddid_all.tbl CDD pfam17432 pfam17432 465424 DUF3458_C Domain of unknown function (DUF3458_C) ARM repeats. This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. 324 matched cddid_all.tbl CDD pfam17433 pfam17433 407501 Glyco_hydro_49N Glycosyl hydrolase family 49 N-terminal Ig-like domain. Family of dextranase (EC 3.2.1.11) and isopullulanase (EC 3.2.1.57). Dextranase hydrolyses alpha-1,6-glycosidic bonds in dextran polymers. This domain corresponds to the N-terminal Ig-like fold. 186 matched cddid_all.tbl CDD pfam17434 pfam17434 340149 DUF5413 Family of unknown function (DUF5413). This is a family of unknown function found in Bradyrhizobiaceae. Family members contain 3 or 4 predicted trans-membrane regions. 133 matched cddid_all.tbl CDD pfam17435 pfam17435 407502 DUF5414 Family of unknown function (DUF5414). This is a family of unknown function found in Chlamydiales. Family members have a known structure such as Swiss:Q9Z7A3. 183 matched cddid_all.tbl CDD pfam17436 pfam17436 435913 DUF5415 Family of unknown function (DUF5415). This is a family of unknown function found in Enterococcus. 66 matched cddid_all.tbl CDD pfam17437 pfam17437 407503 DUF5416 Family of unknown function (DUF5416). This is a family of unknown function found in Campylobacteria. 173 matched cddid_all.tbl CDD pfam17438 pfam17438 465425 DUF5417 Family of unknown function (DUF5417). This is a family of unknown function found in Proteobacteria. 91 matched cddid_all.tbl CDD pfam17439 pfam17439 340154 DUF5418 Family of unknown function (DUF5418). This is a family of unknown function found in Methanocaldococcus jannaschii. Family members have three predicted trans-membrane regions. 151 matched cddid_all.tbl CDD pfam17440 pfam17440 435915 Thiol_cytolys_C Thiol-activated cytolysin beta sandwich domain. This domain has an immunoglobulin like fold. It is found at the C-terminus of the thiol-activated cytolsin protein. 102 matched cddid_all.tbl CDD pfam17441 pfam17441 375192 DUF5419 Family of unknown function (DUF5419). This is a family of unknown function found in Mycobacterium phages and bacteria. 54 matched cddid_all.tbl CDD pfam17442 pfam17442 340157 U62_UL91 Functional domain of U62 and UL91 proteins. Human herpesvirus 6A (HHV-6A) and HHV-6B are classified as roseoloviruses and are highly prevalent in the human population. Roseolovirus reactivation in an immunocompromised host can cause severe pathologies. Human cytomegalovirus (HCMV) is responsible for significant diseases in developing fetus as well as in an immunocompromised host. During their productive cycle, herpesviruses have a regulated temporal cascade of gene expression that can be divided into three general stages: immediate-early (IE), early (E), and late (L). Following viral DNA replication, late viral genes that mainly encode structural proteins start to be transcribed, ultimately leading to the assembly and release of infectious particles. This domain family is found in Human herpesvirus 6A and 6B (HHV-6A/B) as well as HCMV. Family members are shown to be involved in late gene expression such as UL91 in Human Cytomegalovirus. This functional domain is located on the N-terminal (1-71 amino acids) of full-length UL91. It has been found to suffice for transcriptional activation of true-late genes within the nucleus of infected cells. In other words, UL91 is fully functional as a 71-aa N-terminal polypeptide and This small 71-aa polypeptide contains all protein-protein interaction motifs crucial to mediate transcriptional activation. 65 matched cddid_all.tbl CDD pfam17443 pfam17443 340158 pXO2-72 Uncharacterized protein pXO2-72. This is a family of unknown function found in Bacilli. 62 matched cddid_all.tbl CDD pfam17444 pfam17444 340159 YhdX Uncharacterized YhdX-like. This is a family of unknown function found in Bacillus. 33 matched cddid_all.tbl CDD pfam17445 pfam17445 340160 Mfa1 Mating factor A1. Many pathogenic fungi undergo morphological changes in order to infect their hosts. The Ustilago maydis pathogenic cycle starts when two mating compatible haploid yeast cells recognize each other via a pheromone-receptor system which is encoded by two sets of genes a and b. The a locus (a1 and a2) controls the cell fusion by encoding intercellular recognition system consisting of precursors (mfa1 and mfa2) and receptors (pra1 and pra2) of lipopeptide pheromones. The open reading frame codes for a 42-amino acid precursor, which is processed to a shorter peptide of 13 amino acids. The terminal CAAX motif is typical of farnesylated fungal pheromones, in which the last three amino acids are removed during farnesylation of the cysteine residue. This terminal cysteine is known to be Omethylated in several fungal pheromones. Mating leads to the formation of a dikaryon filament, whose apical tip differentiates into a specialized structure for plant penetration known as the appressorium. Once inside the plant, U. maydis proliferates, inducing the formation of tumours and eventually develops into diploid spores. This mating process requires cross-talk between cAMP and mitogen-activated protein kinase (MAPK) signaling. Upstream regulation of a locus has been demonstrated where Hos2 (Histone deacetylases (HDACs) plant homolog) directly regulates the expression of U. maydis mating-type genes downstream of the cAMP-PKA pathway. Furthermore, pheromone recognition blocks cell cycle progression in U. maydis cells in order to prepare mating partners for conjugation where cells undergo arrest in G2 phase. This entry relates to the domain found in Mfa1 proteins in Ustilgo maydis and U. hordei. 43 matched cddid_all.tbl CDD pfam17446 pfam17446 407506 LtuA Late transcription unit A. This is a family of unknown function found in Chlamydia. 46 matched cddid_all.tbl CDD pfam17447 pfam17447 407507 YkpC Uncharacterized YkpC-like. This is a family of unknown function found in Bacillus. 42 matched cddid_all.tbl CDD pfam17448 pfam17448 340163 YqaH Uncharacterized YqaH-like. This is a family of unknown function found in Bacillus. 88 matched cddid_all.tbl CDD pfam17449 pfam17449 340164 YrzK Uncharacterized YrzK-like. This is a family of unknown function found in Bacillus. 54 matched cddid_all.tbl CDD pfam17450 pfam17450 407508 Melibiase_2_C Alpha galactosidase A C-terminal beta sandwich domain. 86 matched cddid_all.tbl CDD pfam17451 pfam17451 435916 Glyco_hyd_101C Glycosyl hydrolase 101 beta sandwich domain. Virulence of pathogenic organizms such as the Gram-positive Streptococcus pneumoniae is largely determined by the ability to degrade host glycoproteins and to metabolize the resultant carbohydrates. This family is the enzymatic region, EC:3.2.1.97, of the cell surface proteins that specifically cleave Gal-beta-1,3-GalNAc-alpha-Ser/Thr (T-antigen, galacto-N-biose), the core 1 type O-linked glycan common to mucin glycoproteins. This reaction is exemplified by the S. pneumoniae protein Swiss:B2DRU5, where Asp764 is the catalytic nucleophile-base and Glu796 the catalytic proton donor. This domain represents C-terminal the beta sandwich domain. 117 matched cddid_all.tbl CDD pfam17452 pfam17452 340167 YnfE Uncharacterized YnfE-like. This is a family of unknown function found in Bacillus. 78 matched cddid_all.tbl CDD pfam17453 pfam17453 340168 Sigma_M_inh Sigma-M inhibitor. This family includes members such as Sigma M inhibitor proteins YhdK. In Bacillus subtilis, sigM (yhdM) gene, is required for growth and survival after salt stress. Expression of sigM is positively autoregulated and is controlled by growth phase and medium composition. SigM-dependent transcription is regulated by the products of both the yhdL and the yhdK genes, which are co-transcribed with the sigM gene. The small hydrophobic protein YhdK, appears to interact with the trans-membrane domain of YhdL, suggesting some specific role for YhdK in the anti-sigma function of YhdL. 96 matched cddid_all.tbl CDD pfam17454 pfam17454 465426 Bee_toxin Honey bee toxin. Bee venom contains a variety of peptides such as melittin, apamin, adolapin and mast cell degranulating peptide. Bee venom has been used in the treatment of major neurodegenerative disorders, including Alzheimer's Disease, Parkinson's Disease, Epilepsy, Multiple Sclerosis and Amyotrophic Lateral Sclerosis. Secondary structure analysis of apamin, mast cell degranulating peptide, tertiapin and secapin have been studied. The predicted structure for mast cell degranulating peptide is almost spherical with the eight positive centres evenly distributed over the surface. It has also been suggested that these four peptides share a common folding pattern, which is centred on a beta-turn covalently linked to an alpha-helical segment by two disulphide links. It is further suggested that apamin, mast cell degranulating peptide and tertiapin form a single molecular class. This domain family is found in apamin, mast cell degranulating peptide and tertiapin. Apamin, the most widely studied member of this family has been shown to be a selective blocker of small-conductance Ca2+-activated K+ (KCa2.X or SK) channels. 50 matched cddid_all.tbl CDD pfam17455 pfam17455 407510 LtuB Late transcription unit B. This is a family of unknown function. Family members include the Chlamydia late transcription unit B protein. 79 matched cddid_all.tbl CDD pfam17456 pfam17456 340171 TcpS Toxin-coregulated pilus protein S. The toxin-coregulated pilus (TCP) and cholera toxin (CT) are two main virulence factors produced by V. cholerae, which allows the bacterium to colonize and establish an infection in a host and to cause the physical symptoms of the disease, respectively. Increased expression of the TCP, a type IV pilus expressed by the tcp operon (tcpABQCRDSTEF) located on the Vibrio pathogenicity island (VPI), has been associated with enhanced attachment and is essential for colonization of the intestinal epithelium. This domain of unknown function is found in TcpS proteins in Vibrionaceae such as Vibrio choleae. 152 matched cddid_all.tbl CDD pfam17457 pfam17457 407511 DUF5420 Family of unknown function (DUF5420). This is a domain of unknown function found in Gammaproteobacteria such as Haemophilus influenzae. 185 matched cddid_all.tbl CDD pfam17458 pfam17458 465427 DUF5421 Family of unknown function (DUF5421). This is a domain of unknown function found in Chlamydia. 283 matched cddid_all.tbl CDD pfam17459 pfam17459 340174 DUF5422 Family of unknown function (DUF5422). This is a family of unknown function found in Chlamydia. Members of this family have 1-4 predicted trans-membrane regions. 153 matched cddid_all.tbl CDD pfam17460 pfam17460 465428 RP854 Uncharacterized protein RP854. This is a family of unknown function found in Rickettsia. Members of this family are predicted to have one trans-membrane region. 212 matched cddid_all.tbl CDD pfam17461 pfam17461 375197 DUF5423 Family of unknown function (DUF5423). This is a domain of unknown function found in Chlamydia. Family members have 4 predicted trans-membrane regions. 348 matched cddid_all.tbl CDD pfam17462 pfam17462 340177 DUF5424 Family of unknown function (DUF5424). This is a family of unknown function specific to Rickettsia amblyommii. 175 matched cddid_all.tbl CDD pfam17463 pfam17463 340178 GP79 Gene product 79. This is a domain of unknown function found in Mycobacterium phage. Family members include the full Gp79 protein found in Mycobacteriophage L5. Mycobacteriophage L5, is a phage isolated from Mycobacterium smegmatis. It forms stable lysogens in M. smegmatis and has a broad host range among the pathogenic mycobacteria. L5 encodes gene products (gp) toxic to the host M. smegmatis. Expression of gp79 interferes with the cell membrane or cell-wall synthesis of M. smegmatis, leading to altered cell morphology. It also has a bactericidal effect on E. coli. The N-terminal segment of gp79 (amino acids 1-41) shares sequence similarity with the signal peptide of the D-alanylD-alanine carboxypeptidase of Bacillus licheniformis. This enzyme removes C-terminal D-alanyl residues from sugarpeptide cell-wall precursors and is also a penicillin-binding protein (PBP). The homology of the hydrophobic N-terminal part of gp79 to a PBP (penicillin-binding protein) signal peptide may indicate an interaction of gp79 with proteins or metabolites involved in the peptidoglycan synthesis of M. smegmatis. 51 matched cddid_all.tbl CDD pfam17464 pfam17464 340179 Pns11_12 Non-structural protein 11 and 12. This is a domain of unknown function found in Phytoreovirus. Family members include the Rice dwarf virus Pns11 and Pns12. Rice dwarf virus (RDV) is an icosahedral, double-layered particle. The viral genome consists of 12 segmented dsRNAs that encode seven structural (P1, P2, P3, P5, P7, P8 and P9) and five non-structural (Pns4, Pns6, Pns10, Pns11 and Pns12) proteins. Pns11 is known to bind nucleic acids and Pns12 is a phosphorylated protein. The non-structural proteins Pns6, Pns11 and Pns12 of RDV are the major constituents of the matrix of viral inclusions in which the assembly of progeny virions and the synthesis of viral RNA are thought to occur. 205 matched cddid_all.tbl CDD pfam17465 pfam17465 340180 U83 Chemokine-like protein, HHV-6 U83 gene product. Human herpesvirus 6A (HHV-6A) and HHV-6B are classified as roseoloviruses and are highly prevalent in the human population. Roseolovirus reactivation in an immunocompromised host can cause severe pathologies. HHV6 A/B encode two putative chemokine receptors and a chemokine-like protein. The HHV6 U83 gene encodes a CC chemokine, which functions as a highly selective and efficacious agonist for the human CCR2 receptor both in respect of signal transduction and the ability to induce chemotaxis. homologs of the U83 gene products are found in Human cytomegalovirus encoded chemokines vCXC1 and vCXC2. HHV-6 CCL4 contains a region with the CC/CX3C chemokine motif and a glycosaminoglycan (GAG)-binding epitope, BBXB (B being a basic residue), found right before the third Cys residue, which very likely forms a disulfide bridge back to the first Cys of the protein. This gene is the only HHV-6A/B divergent gene that is specific for these viruses. The U83 chemokine gene is distinct between HHV-6A and HHV-6B strains, encoding up to 13 % amino acid differences. The HHV-6A (U83A) and HHV-6B (U83B) chemokines have distinct specificities which determine chemoattraction or diversion of different leukocyte subsets for infection or immune evasion, thus an early component of cellular tropism as well as mediator of innate immunity. U83 also has a varied gene structure, with N-terminal length variation determining production of the encoded mature secreted chemokine, coupled with control by cell-directed splicing which truncates the chemokine gene early in replication to encode an antagonist. The 'long' active form of U83A has a unique broad specificity for receptors CCR1, CCR4, CCR5, CCR6 and CCR8 present on plasmacytoid and myeloid dendritic and monocyte/macrophage antigen presenting cells, as well as both TH1 and TH2 skin homing lymphocytes and NK cells; it is also amongst the highest affinity ligands for CCR5 and inhibits HIV-1 binding at this coreceptor. U83A can both block and divert human chemokine action while occupying the human chemokine receptors. 97 matched cddid_all.tbl CDD pfam17466 pfam17466 340181 NinD Family of unknown function. This is a family of unknown function found in Enterobacteria phage P22 and Enterobacteria phage lambda. 57 matched cddid_all.tbl CDD pfam17467 pfam17467 340182 E7R Viral Protein E7. This domain family is found in Vaccinia and Variola viruses. Family members include E7R gene product. Vaccinia virus (VV) is a large double-stranded DNA virus that replicates in the cytoplasm of infected cells. Many viruses express proteins that are modified by myristic acid. Myristic acid is a 14-carbon fatty acid that is cotranslationally transferred to the penultimate glycine residue found within the consensus sequence MGXXX(S/T/A/C/N) (where X is any amino acid) at the amino terminus of target proteins. E7R proteins in Vaccina virus have been shown to be myristylated. The expressed E7R protein has also been found to reside within mature infectious virions. 60 matched cddid_all.tbl CDD pfam17468 pfam17468 340183 GP52 Phage gene product 52. This is a family of unknown function found in Mycobacterium phage. 61 matched cddid_all.tbl CDD pfam17469 pfam17469 340184 GP68 Gp68-like predicted RNA polymerase component. This is family represents a protein that purifies with the non-virion RNA polymerase in group 1/PhiKZ-like phages that is predicted to be composed of a series of alpha helical hairpins. 78 matched cddid_all.tbl CDD pfam17470 pfam17470 340185 Gp45_2 Phage gene product 45.2. This is a family of unknown function found in Myoviridae. 58 matched cddid_all.tbl CDD pfam17471 pfam17471 340186 GP63 Gene product 63. This is a family of unknown function found in Mycobacterium. 73 matched cddid_all.tbl CDD pfam17472 pfam17472 340187 DUF5425 Family of unknown function (DUF5425). This is a family of unknown function found in Borreliella burgdorferi. 76 matched cddid_all.tbl CDD pfam17473 pfam17473 340188 DUF5426 Family of unknown function (DUF5426). This is a family of unknown function found in Mycoplasma. 137 matched cddid_all.tbl CDD pfam17474 pfam17474 340189 U71 Tegument protein UL11 homolog. Human herpesvirus 6A (HHV-6A) and HHV-6B are classified as roseoloviruses and are highly prevalent in the human population. Roseolovirus reactivation in an immunocompromised host can cause severe pathologies. During their productive cycle, herpesviruses have a regulated temporal cascade of gene expression that can be divided into three general stages: immediate-early (IE), early (E), and late (L). Following viral DNA replication, late viral genes that mainly encode structural proteins start to be transcribed, ultimately leading to the assembly and release of infectious particles. This domain family is found in tegument protein UL11 homolog (U71) in HHV-6A/B. It is a myristylated virion protein which is expressed at the early stage of the lytic cycle. 52 matched cddid_all.tbl CDD pfam17475 pfam17475 435917 Binary_toxB_2 Clostridial binary toxin B/anthrax toxin PA domain 2. This domain forms the middle beta sandwish domain in anthrax toxin. 198 matched cddid_all.tbl CDD pfam17476 pfam17476 375198 Binary_toxB_3 Clostridial binary toxin B/anthrax toxin PA domain 3. This entry represents the beta-grasp domain in anthrax protective antigen. 102 matched cddid_all.tbl CDD pfam17477 pfam17477 407512 Rota_VP4_MID Rotavirus VP4 membrane interaction domain. This entry represents the VP4 membrane interaction domain. 225 matched cddid_all.tbl CDD pfam17478 pfam17478 465429 VP4_helical Rotavirus VP4 helical domain. 291 matched cddid_all.tbl CDD pfam17479 pfam17479 435919 DUF3048_C Protein of unknown function (DUF3048) C-terminal domain. Some members in this bacterial family of proteins are annotated as YerB. However currently no function is known. This entry represents the C-terminal domain. 114 matched cddid_all.tbl CDD pfam17480 pfam17480 435920 AlphaC_N2 AlphaC N-terminal domain 2. This is the second domain on the N-terminal region found on the alpha C protein (ACP). ACP is found in Streptococcus and acts as an invasin which plays a role in the internalization and translocation of the organizm across human epithelial surfaces. Group B Streptococcus is the leading cause of diseases including bacterial pneumonia, sepsis and meningitis. ACP consists of an N-terminal domain (NtACP; 170 amino acids) followed by a variable number of tandem repeats (82 amino acids each) and a C-terminal domain (45 amino acids) containing an LPXTG peptidoglycan-anchoring motif. The NtACP, contains two structural domains, D1 and D2. D1, the more distal (amino-terminal) portion pfam08829 and consists of a beta sandwich with strong structural homology to fibronectin's integrin-binding region (FnIII10). This entry, D2 (connects distally to Domain 1 and proximally to the repeat region) consists of three antiparallel alpha helix coils. It is suggested that the GAG-binding region of ACP may extend from Domain 2 into the repeat region. 71 matched cddid_all.tbl CDD pfam17481 pfam17481 435921 Phage_sheath_1N Phage tail sheath protein beta-sandwich domain. This entry represents the N-terminal beta sandwich domain found in a variety of phage tail sheath proteins. 100 matched cddid_all.tbl CDD pfam17482 pfam17482 435922 Phage_sheath_1C Phage tail sheath C-terminal domain. This entry represents the C-terminal domain in a variety of phage tail sheath proteins. 104 matched cddid_all.tbl CDD pfam17483 pfam17483 435923 TbpB_C C-lobe handle domain of Tf-binding protein B. Bacterial lipoproteins represent a large group of specialized membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis, and cell adherence. Pathogenic Gram-negative bacteria within the Neisseriaceae and Pasteurellaceae families rely on a specialized uptake system, characterized by an essential surface receptor complex that acquires iron from host transferrin (Tf) and transports the iron across the outer membrane. They have an iron uptake system composed of surface exposed lipoprotein, Tf-binding protein B (TbpB), and an integral outer-membrane protein, Tf-binding protein A (TbpA), that together function to extract iron from the host iron binding glycoprotein (Tf). TbpB is a bilobed (N and C lobe) lipid-anchored protein with each lobe consisting of an eight-stranded beta barrel flanked by a 'handle' domain made up of four (N lobe) or eight (C lobe) beta strands. TbpB extends from the outer membrane surface by virtue of an N-terminal peptide region that is anchored to the outer membrane by fatty acyl chains on the N-terminal cysteine and is involved in the initial capture of iron-loaded Tf. This domain family is found in the handle domain of the C lobe (domain C) of TbpB proteins. It consists of a squashed six-stranded beta sheet flanked by two antiparallel beta strands and has no supporting alpha helix as in the N lobe. 100 matched cddid_all.tbl CDD pfam17484 pfam17484 435924 TbpB_A N-Lobe handle Tf-binding protein B. Bacterial lipoproteins represent a large group of specialized membrane proteins that perform a variety of functions including maintenance and stabilization of the cell envelope, protein targeting and transit to the outer membrane, membrane biogenesis, and cell adherence. Pathogenic Gram-negative bacteria within the Neisseriaceae and Pasteurellaceae families rely on a specialized uptake system, characterized by an essential surface receptor complex that acquires iron from host transferrin (Tf) and transports the iron across the outer membrane. They have an iron uptake system composed of surface exposed lipoprotein, Tf-binding protein B (TbpB), and an integral outer-membrane protein, Tf-binding protein A (TbpA), that together function to extract iron from the host iron binding glycoprotein (Tf). TbpB is a bilobed (N and C lobe) lipid-anchored protein with each lobe consisting of an eight-stranded beta barrel flanked by a 'handle' domain made up of four (N lobe) or eight (C lobe) beta strands. TbpB extends from the outer membrane surface by virtue of an N-terminal peptide region that is anchored to the outer membrane by fatty acyl chains on the N-terminal cysteine and is involved in the initial capture of iron-loaded Tf. The 4-residue conserved LSAC motif found at the amino terminus of TbpB represents a prototypical lipobox, with the cysteine residue serving as the first amino acid in the mature protein which is subsequently modified by the addition of a diacyl glycerol. A second conserved motif of interest is located two amino acids downstream of the LSAC site. This region consists of four glycine residues in tandem. Deletion of the conserved polyglycine motif has significant negative effects on growth in certain conditions, while mutational analysis revealed that the LSAC motif constituting the lipobox of TbpB is necessary for lipidation and hence tethering of TbpB to the bacterial surface. This domain family is found on the N-terminal region of TbpB proteins, which comprises the N lobe handle consisting of a four-stranded antiparallel beta sheets held together by a short surface-exposed alpha helix. Tf-binding activity primarily resides in the TbpB N lobe. 135 matched cddid_all.tbl CDD pfam17485 pfam17485 340200 SatRNA_48 Satellite RNA 48 kDa protein. Satellite RNAs (satRNAs) are short RNA molecules, usually <1,500 nt, that depend on cognate helper viruses for replication, encapsidation, movement, and transmission, but most share little or no sequence homology to the helper viruses. In contrast, satellite viruses are satRNAs that encode and are encapsidated in their own capsid proteins (CPs). Members of this family are nonstructural proteins of 48kDa in size which been shown to be involved in the replication of the sat-RNA. They are found in tomato black ring virus (TBRV). 299 matched cddid_all.tbl CDD pfam17486 pfam17486 340201 Cys_Knot_tox Cystine knot toxins. This family is found in Araneaea (spiders) and family members are venomus peptides with 4 disulfide bonds. Cystine knot toxins (CKTs) are small, compact molecules cross-linked by three to five disulfide bonds and are often the key contributors to the activity and potency of the venom. While these disulfide-rich peptides can adopt a number of different structural motifs, three of the most observed structural scaffold motifs are the inhibitor cystine knot (ICK) and the disulfide-directed beta-hairpin (DDH) and Kunitz motif. These venomus peptides mainly act on membrane proteins in electro-excitable cell membranes by modulating voltage-activated sodium (NaV), calcium (CaV), and potassium (KV) channels, acid-sensing ion channels (ASICs), transient receptor potential (TRP) channels, and mechanosensitive channels (MSCs). 70 matched cddid_all.tbl CDD pfam17487 pfam17487 407518 Ribosomal_S12 Ribosomal protein S12. This is a family of unknown function. Family members are ribosomal proteins found in the mitochondria (RPS12). Homologus RPS12 proteins in bacterial ribosoms participate in stabilizing the second base pair of the codon-anticodon duplex in the A site and is likely to be critical for the fidelity of decoding process. A similar role can be anticipated for this protein in mitochondrial ribosomes. This has been shown where the product of edited RPS12 mRNA translation represented a component of the mitoribosome's small subunit. 87 matched cddid_all.tbl CDD pfam17488 pfam17488 407519 Herpes_glycoH_C Herpesvirus glycoprotein H C-terminal domain. Herpesvirus glycoprotein H (gH) is a virion associated envelope glycoprotein. Complex formation between gH and gL has been demonstrated in both virions and infected cells. This entry represents the C-terminal domain. 135 matched cddid_all.tbl CDD pfam17489 pfam17489 407520 Tnp_22_trimer L1 transposable element trimerization domain. This entry represents the trimerization domain. 43 matched cddid_all.tbl CDD pfam17490 pfam17490 407521 Tnp_22_dsRBD L1 transposable element dsRBD-like domain. This entry represents the double stranded RNA-binding-like domain. 65 matched cddid_all.tbl CDD pfam17491 pfam17491 340206 m_DGTX_Dc1a_b_c Spider Toxins mu-diguetoxin-1 a, b and c. This family has members that are 56-59 residue mu-diguetoxin-1 toxins, which have been isolated from the weaving spider, Diguetia canities. These toxins were isolated as a result of their potent insect paralytic activities, designated mu-DGTX-Dc1a to -Dc1c (formerly DTX9.2, DTX11 and DTX12). Family members such as beta-Diguetoxin-Dc1a (Dc1a) has been structurally characterized and shown to have disulfide bonds which form a classical inhibitor cysteine knot (ICK) motif in which the Cys13-Cys26 and Cys20-Cys40 disulfide bonds and the intervening sections of the polypeptide backbone forming a 23-residue ring that is pierced by the Cys25-Cys54 disulfide bond. This ICK motif is commonly found in spider toxins, and this particular scaffold provides these peptides (so-called knottins) with an unusually high degree of chemical, thermal and biological stability. Dc1a contains an additional disulfide bond (Cys42-Cys52) that appears to serve as a molecular staple which limits the flexibility of a disordered serine-rich hairpin loop. The extended N-terminus of Dc1a along with an unusually large loop between Cys26 and Cys40 enables the formation of an N-terminal three-stranded antiparallel beta-sheet that is not found in any other knottin.The molecular surface of Dc1a contains a relatively uniform distribution of charged residues; moreover, there are no distinct clusters of hydrophobic residues that might mediate an interaction with lipid bilayers. 55 matched cddid_all.tbl CDD pfam17492 pfam17492 340207 D_CNTX Delta Ctenitoxins. This family includes peptides isolated from Phoneutria such as delta-ctenitoxins. Members of the CNTX-Pn1a family and its paralogs (delta-CNTX-Pn1b through delta-CNTX-Pn1e) of Phoneutria toxins have complex effects on sodium channels but their primary effect appears to be an inhibition of channel inactivation, a pharmacology similar to that of the delta-atracotoxins and delta-conotoxins. Orthologous toxins such as delta-CNTX-Pr1/PK1 and Pn2 are also family members, some of which act by blocking the calcium channels. Delta-CNTX-Pn1a and delta-CNTX-PN2a are 48-amino-acid polypeptides, with 5 disulfide bridges. The later has a complex pharmacology that results in inhibition of NaV channel inactivation and a hyperpolarizing shift in the channel activation potential. 48 matched cddid_all.tbl CDD pfam17493 pfam17493 340208 DUF5428 Family of unknown function (DUF5428). This is a family of unknown function found in Betanecrovirus. 63 matched cddid_all.tbl CDD pfam17494 pfam17494 340209 DUF5429 Family of unknown function (DUF5429). This is a family of unknown function. 76 matched cddid_all.tbl CDD pfam17495 pfam17495 375203 OrfA Vpr-like OrfA. Family members include OrfA protein, a multifunctional accessory protein found in Feline immunodeficiency virus (FIV), a lentivirus that causes AIDS in domestic cats. Multiple potential functions have been ascribed to OrfA, including transactivation of viral protein expression, effects on virion formation and infectivity, host cell cycle arrest and downregulation of cell surface expression of the primary FIV receptor, CD134. 106 matched cddid_all.tbl CDD pfam17496 pfam17496 435925 DUF5431 Family of unknown function (DUF5431). This is a family of unknown function found in Enterobacteriaceae. 70 matched cddid_all.tbl CDD pfam17497 pfam17497 340212 DUF5432 Family of unknown function (DUF5432). This is a family of unknown function found in Orthopoxvirus. 74 matched cddid_all.tbl CDD pfam17498 pfam17498 435926 DUF5433 Family of unknown function (DUF5433). This is a family of unknown function found in Orthopoxviruses. 67 matched cddid_all.tbl CDD pfam17499 pfam17499 375204 Pilosulin Ant venom peptides. Members of this family are found in Myrmecia pilosula and represent a group of peptides that display cytotoxic, hypotensive, histamine-releasing and antimicrobial activities. Pilosulins constitute the major allergens of the venom of Myrmecia pilosula (Myrmeciinae). Pilosulin 1 is a long linear peptide (57 amino acids) and displays haemolytic and cytolytic activities. Pilosulins 3, 4, and 5 are a group of homo- and heterodimeric peptides. Pilosulin 1 is expressed in the venom sac of ants in the form of a propeptide (112 kDa) which undergoes extensive post-translational modification. It is proposed to give rise to a family of six homologous C-terminal peptide sub-sequences containing between 27 and 56 amino acid residues in the final venom. Furthermore, it is found to form random coils and have minimal secondary structure. However, in increasingly hydrophobic conditions, approximately one-third of the peptide forms alpha-helix secondary structures. Studies on human erythrocytes and lymphocytes, show that Pilosulin 1 is highly lytic towards leukocytes and that the NH2-terminus (20 N-terminal residues) of Pilosulin 1 is critical for its cytotoxic activity and antimicrobial activities. Another family member Pilosulin 3, is a heterodimer of Pilosulin 3a and Pilosulin 3b linked in anti-parallel fashion through 2 disulfide bridges. This peptide is the most abundant peptide found in native venom. 74 matched cddid_all.tbl CDD pfam17500 pfam17500 340215 CKI Colicin-K immunity. Colicins are bacterial toxins produced by Escherichia coli strains and are active against E. coli or related strains. These bacterial antibiotic toxins play an important role in the E. coli colonization of environmental niches. Colicin K uses the Tsx nucleoside-specific receptor for binding at the cell surface, the OmpA protein for translocation through the outer membrane, and the TolABQR proteins for the transit through the periplasm. The N-terminal domain interacts with components of its import machinery, including the TolB and TolQ proteins. Members of this family are colicin K immunity proteins. These proteins are able to protect a cell against colicin K. 96 matched cddid_all.tbl CDD pfam17501 pfam17501 340216 Viral_RdRp_C Viral RNA-directed RNA polymerase. This is the C-terminal of RNA-directed RNA polymerase (Protein A) found in Alphanodaviruses such as Flock House Virus (FHV). FHV is a positive-stranded RNA virus with a bipartite genome of RNAs, RNA1 and RNA2. RNA1 encodes protein A, which is the catalytic subunit of the RNA-dependent RNA polymerase (RdRp) and functions as the sole viral replicase protein responsible for RNA replication. FHV protein A also possesses a terminal nucleotidyl transferase (TNTase) activity, which is able to restore the nucleotide loss at the 3'-end initiation site of RNA template to rescue RNA synthesis initiation. It has also been reported that FHV protein A replicates viral RNA in concert with the mitochondrial outer membrane and other viral or cellular factors and mediates the formation of viral RNA replication complexes and small spherules by inducing membrane rearrangement.This domain is also found in B1 proteins which are encoded by the subgenomic RNA3 during FHV replication. The function of translated B1 protein is poorly defined, but may be important for maintenance of RNA replication. 101 matched cddid_all.tbl CDD pfam17502 pfam17502 340217 DUF5434 Family of unknown function (DUF5434). This is a family of unknown function found in Varicellovirus. 189 matched cddid_all.tbl CDD pfam17503 pfam17503 435927 DUF5435 Family of unknown function (DUF5435). This is a family of unknown function found in Varicellovirus. 205 matched cddid_all.tbl CDD pfam17504 pfam17504 340219 DUF5436 Family of unknown function (DUF5436). This is a family of unknown function found in Orthopoxvirus. 79 matched cddid_all.tbl CDD pfam17505 pfam17505 375205 DUF5437 Family of unknown function (DUF5437). This is a family of unknown function found in Alphabaculovirus. 60 matched cddid_all.tbl CDD pfam17506 pfam17506 340221 DUF5438 Family of unknown function (DUF5438). This is a family of unknown function found in Orthopoxvirus. 71 matched cddid_all.tbl CDD pfam17507 pfam17507 340222 DUF5439 Family of unknown function (DUF5439). This is a family of unknown function found in Orthopoxvirus. 75 matched cddid_all.tbl CDD pfam17508 pfam17508 340223 MccV Microcin V bacteriocin. Family members are bacterial microcin-V peptides MccV, also known as colicin V. MccV was the first antibiotic substance reported to be produced by E. coli. This antibacterial agent was initially named colicin V (ColV). However, on account of several characteriztics (low molecular mass, non-inducible production, and dedicated export system), it became classified within the microcins. The structural gene cvaC, encodes the 103-aa MccV precursor. The dedicated export system of MccV has been well characterized and involves two genes that form the second operon. The MccV protein has an N-terminal double glycine motif which precedes the cleavage site for the precursor protein. 104 matched cddid_all.tbl CDD pfam17509 pfam17509 375206 DUF5440 Family of unknown function (DUF5440). This is a family of unknown function found in bacteria. 93 matched cddid_all.tbl CDD pfam17510 pfam17510 375207 GP44 Gene product 44. This is a family with unknown function. Family members are hypothetical proteins found in Mycobacterium phages. 107 matched cddid_all.tbl CDD pfam17511 pfam17511 340226 Mobilization_B Mobilization protein B. This is a family of unknown function found in Bacteria. Family members include Mobilization protein B (MobB). MobB contains a putative membrane-spanning domain, and might be involved in anchoring or presenting MobA, and the covalently-linked plasmid DNA, to the conjugative pore for subsequent export. In agreement with this, MobB has been shown to be associated with the membrane. Deletion of the membrane-spanning domain disrupts this association and decreases the frequency of both type IV transport and plasmid mobilization. MobB is one out of three proteins encoded by RSF1010 that are required for its mobilization along with MobA and MobC. MobB encoded by the broad-host-range plasmid R1162 is required for its efficient transfer by conjugation. The C-terminal half of the protein contains a membrane domain essential for transfer, while the other, functionally active region of MobB, identified by mutagenesis, is at the N-terminal end. One mutation affecting this region inhibits replication, suggesting that this part of the protein is contacting and sequestering the relaxase-linked primase. A model that represents MobB molecules as anchored in the membrane at one end and engaging the relaxase at the other. This arrangement is suggested to increase the transfer frequency by raising the probability of contact between the relaxase and the membrane-embedded, coupling protein for type IV secretion. 136 matched cddid_all.tbl CDD pfam17512 pfam17512 340227 Sh_2 Metapneumovirus Small hydrophobic protein. This family is found in SH (small hydrophobic) proteins present in Metapneumovirus such as the Avian metapneumovirus (AMPV), a paramyxovirus that has three membrane proteins (G, F, and SH). Among them, the SH protein is a small type II integral membrane protein. It is located in both the plasma membrane as well as within intracellular compartments. AMPV type C- SH protein localizes in the endoplasmic reticulum (ER), Golgi, and cell surface, and is transported through ER-Golgi secretory pathway. AMPV SH protein is modified by N-linked glycans and can be released into the extracellular environment. Furthermore, it has been shown that glycosylated AMPV SH proteins form homodimers through cysteine-mediated disulfide bonds. 174 matched cddid_all.tbl CDD pfam17513 pfam17513 375208 DUF5441 Family of unknown function (DUF5441). This is a family of unknown function found in Mastadenoviruses. 189 matched cddid_all.tbl CDD pfam17514 pfam17514 340229 DUF5442 Family of unknown function (DUF5442). This is a family of unknown function found in Chironomus. 107 matched cddid_all.tbl CDD pfam17515 pfam17515 340230 CPV_Polyhedrin Cypovirus polyhedrin. This family is found in polyhedrin proteins of Cypoviruses. These viruses possess a single capsid layer with turrets and are commonly embedded in crystalline occlusion bodies called polyhedra, which are formed in the cell cytoplasm and mainly composed of a single virus-encoded protein, polyhedron. Cypoviruses have been classified into 21 distinct types. Within each type the amino acid sequence of polyhedrins are highly conserved, whilst between types there is little conservation. Structural analysis and comparison of the different polyhedrins reveals five variable regions: the N-terminal loop, connections between secondary structures (H2 and H3, beta-E and beta-F, beta-F and beta-G, beta-G and beta-H), and the C-terminal loop, which is designate V1-V5 respectively. V2 forms a cap at one end of the protein and is subdivided across two sections of the polypeptide, V2n and V2c. Differences in these regions give each polyhedrin its characteriztic appearance. The base domain (residues 74-110) is a region that is neither required for proper folding of the protein, nor for crystal assembly, but fine-tunes the crystal, locking-down the structure, often in conjunction with NTPs. This region is also implicated in virion recognition and packaging. 241 matched cddid_all.tbl CDD pfam17516 pfam17516 435928 ProQ_C ProQ C-terminal domain. This domain is found at the C-terminus of many ProQ proteins. 51 matched cddid_all.tbl CDD pfam17517 pfam17517 465430 IgGFc_binding IgGFc binding protein. This domain is found at the N terminal of Swiss:Q9Y6R7 and has been shown to confer IgG Fc binding activity. It may play a role in immune protection and inflammation in the intestines of primates. 292 matched cddid_all.tbl CDD pfam17518 pfam17518 340233 DUF5443 Family of unknown function (DUF5443). This is a family of unknown function found in Mycoplasma. 344 matched cddid_all.tbl CDD pfam17519 pfam17519 407526 DUF5444 Family of unknown function (DUF5444). This is a family of unknown function found in Enterobacterales. 62 matched cddid_all.tbl CDD pfam17520 pfam17520 340235 DUF5445 Family of unknown function (DUF5445). This is a family of unknown function found in Enterobacteriaceae. 52 matched cddid_all.tbl CDD pfam17521 pfam17521 465431 Secapin Honey bee peptides. Family members are bee venom peptides such as Secapin. Mature secapin is composed of 25 amino acid residues that contain a disulfide link. Secapin has been demonstrated to act as a potent neurotoxin. In Apis mellifera secapin exhibits anti-bacterial activity and induces inflammation and pain with anti-fibrinolytic, anti-elastolytic, and anti-microbial activities. Secapin shares a common folding pattern with apamin, mast cell degranulating peptide and tertiapin; it is centred on a beta-turn covalently linked to an alpha-helical segment by one disulphide link (two disulphide links in the other peptides). 45 matched cddid_all.tbl CDD pfam17522 pfam17522 340237 DUF5446 Family of unknown function (DUF5446). This is a family of unknown function found in Bacillales. 72 matched cddid_all.tbl CDD pfam17523 pfam17523 340238 MPS-4 MinK-related peptide, potassium channel accessory sub-unit protein 4. MinK-related peptides (MiRPs or KCNEs) are single-transmembrane proteins that associate with pore-forming ion-channel sub-units to form stable complexes with channel properties markedly distinct from those of the isolated pore-forming sub-units. MPS-4 is expressed exclusively in the C. elegans nervous system and is essential for neuronal excitability. 78 matched cddid_all.tbl CDD pfam17524 pfam17524 407527 CnrY Anti-sigma factor CnrY. This family is found in alpha and beta proteobacteria. Family members include anti-sigma factor CnrY from Cupriavidus metallidurans. Sigma factors are multi-domain sub-units of bacterial RNA polymerase (RNAP) that play critical roles in transcription initiation, including the recognition and opening of promoters as well as the initial steps in RNA synthesis. They also control a wide variety of adaptive responses such as morphological development and the management of stress. A recurring theme in sigma factor control is their sequestration by anti-sigma factors that occlude their RNAP-binding determinants. CnrH, controls cobalt and nickel resistance in Cupriavidus metallidurans. CnrH is regulated by a complex of two transmembrane proteins: the periplasmic sensor CnrX and the anti-sigma CnrY. At rest, CnrH is sequestered by CnrY whose 45-residue-long cytosolic domain is one of the shortest anti-sigma domains. Upon Ni(II) or Co(II) ions detection by CnrX in the periplasm, CnrH is released between CnrH and the cytosolic domain of CnrY (CnrYc). The CnrH/CnrYC complex displays an unexpected structural similarity to the anti-sigma NepR in complex with its antagonist PhyR, whereas NepR shares no sequence similarity with CnrY. Crystal structure of CnrH/CnrY shows that CnrYC residues 3-19 are folded as a well-defined alpha-helix. The peptide further extends along the hydrophobic groove of sigma 2 with no canonical structure except for a short helical turn spanning residues 24-28. CnrY has a hydrophobic knob made of V4, W7 and L8 side chains protruding into sigma 4 hydrophobic pocket and contributing to the interface. In vivo investigation of CnrY function pinpoints part of the hydrophobic knob as a hotspot in CnrH inhibitory binding. 98 matched cddid_all.tbl CDD pfam17525 pfam17525 340240 DUF5447 Family of unknown function (DUF5447). This is a family of unknown function found in Pseudomonas. 92 matched cddid_all.tbl CDD pfam17526 pfam17526 435930 DUF5448 Family of unknown function (DUF5448). This is a family of unknown function found in Gammaproteobacteria. 118 matched cddid_all.tbl CDD pfam17527 pfam17527 340242 ALC Phage ALC protein. During the course of infection of Escherichia coil by bacteriophage T4, transcription of viral late genes does not take place unless template DNA contains hydroxymethyl cytosine (hmCyt), a modification normally effected by virus-encoded enzymes. Bacteriophage T4 Alc protein acts as a site-specific termination factor participating in shutting off host transcription after infection of E. coli, while the bacteriophage T4 transcription is protected from the action of Alc by overall substitution of cytosine with 5-hydroxymethyl cytosine in T4 DNA. Based on genetic studies, Alc is thought to bind directly to the beta sub-unit dispensable region 1 (bDR1) of E.coli RNAP. However, immune-isolation experiments show that Alc binds both core and sigma 70-holoenzyme of RNAP. 177 matched cddid_all.tbl CDD pfam17528 pfam17528 407528 HdcB Histidine decarboxylase maturation protein HdcB. This family represents histidine decarboxylase maturation protein HdcB, mainly found in Lactobacillus. HdcB performs a cleavage and modification of the pyruvoyl-dependent histidine decarboxylase HdcA, generating the pyruvoyl prosthetic group. 174 matched cddid_all.tbl CDD pfam17529 pfam17529 465432 DUF5450 Family of unknown function (DUF5450). This is a family of unknown function found in Giardia intestinalis. 161 matched cddid_all.tbl CDD pfam17530 pfam17530 340245 NS3 Non-structural protein NS3. This is a family of proteins found in Densoviruses. Members of this family such as NS3 found in Junonia coenia have been shown to be involved in viral DNA replication. Generation of deletion mutants and replicative cycle analysis show that NS3 is required for viral DNA replication. Bioinformatics analysis of Bombyx mori densovirus protein NS3, show that it has two putative zinc-finger motifs, 6 putative N glycosylation sites, and 4 putative phosphorylation sites. 245 matched cddid_all.tbl CDD pfam17531 pfam17531 465433 O_Spanin_T7 Spanin, outer lipoprotein subunit T7-like virus. This family contains members of the outer membrane spanin subunit protein (o-spanin), found in Bacteriophage T7. Spanins are lytic proteins that act on bacterial outer membrane by disrupting it, allowing progeny virions to spread. O-spanin acts together with inner membrane spanin subunit (i-spanin) to form the spanin complex necessary for function. The gene encoding this protein (Rz1-like o-spanin) is completely embedded in the longer gene for the Rz-like i-spanin subunit. 60 matched cddid_all.tbl CDD pfam17532 pfam17532 340247 DUF5451 Family of unknown function (DUF5451). This is a family of unknown function found in Epstein-Barr virus. 148 matched cddid_all.tbl CDD pfam17533 pfam17533 340248 DUF5452 Family of unknown function (DUF5452). This is a family of unknown function found in Mycoplasmataceae. 169 matched cddid_all.tbl CDD pfam17534 pfam17534 340249 DUF5453 Family of unknown function (DUF5453). This is a family of unknown function found in Mycoplasma. Family members have 4 predicted trans-membrane regions. 186 matched cddid_all.tbl CDD pfam17535 pfam17535 340250 DUF5454 Family of unknown function (DUF5454). This is a family of unknown function found in Mycoplasma. 221 matched cddid_all.tbl CDD pfam17536 pfam17536 340251 Mx_ML Matrix and Matrix long proteins N-terminal. This entry represents the N-terminal fragment of family members such as the Matrix (Mx) and Matrix protein long (ML) proteins. They are found in Thogoto virus (THOV), a tick-transmitted orthomyxovirus with a genome consisting of six single-stranded RNA segments that encode seven structural proteins. Matrix proteins of the family Orthomyxoviridae are major structural components of the viral capsid, located below the viral lipid membrane and provide protection for viral ribonucleoproteins (vRNPs). They serve as a major participant during the processes of virus invasion and budding. Furthermore, they play specific roles throughout the viral life cycle, usually by interacting with other viral components or host cellular proteins. ML protein, an extended version of the viral M protein, is a viral IFN antagonist. ML is essential for virus growth and pathogenesis in an IFN-competent host. In the presence of ML the activation and/or action of the interferon regulatory factor-3 (IRF-3) is severely affected. This effect depends on direct interaction of ML with the transcription factor IIB (TFIIB). ML suppresses IRF-7 in a similar manner as it suppresses IRF-3. Studies have revealed that ML associates with IRF-7 and prevents IRF-7 dimerization and interaction with TRAF6. Structural analysis revealed that N-terminal fragment of M protein (MN) undergoes conformational changes that result in specific, pH-dependent inter-molecular interactions. Comparison of THOV MN and influenza A virus (IAV) MN region, showed low sequence identity. However, superimposition of the two structures in neutral condition, showed that both matrix proteins contain nine helices connected with same topology. Since the matrix layer of IAV disassembles in acidic endosome at the beginning of infection and repacks in the neutral cytoplasm, a change of pH might be a key regulator for the capsid assembly/disassembly transition during these processes. Hence, pH-dependent conformational transition model was studied in THOV MN, where interactions such as hydrogen bonds and hydrophobic interactions are suggested to be involved in THOV matrix assembly. 149 matched cddid_all.tbl CDD pfam17537 pfam17537 435932 DUF5455 Family of unknown function (DUF5455). This is a family of unknown function found in Proteobacteria. Family members contain three predicted trans-membrane regions. 102 matched cddid_all.tbl CDD pfam17538 pfam17538 407531 C_LFY_FLO DNA Binding Domain (C-terminal) Leafy/Floricaula. This family consists of various plant development proteins which are homologs of floricaula (FLO) and Leafy (LFY) proteins which are floral meristem identity proteins. Mutations in the sequences of these proteins affect flower and leaf development. LFY is a plant-specific transcription factor (TF) essential for flower development. It is one of the few master regulators of flower development, as it integrates environmental and endogenous signals to orchestrate the whole floral network. Transcription factors such as LFY, recognize short DNA motifs primarily through their DNA-binding domain. Upon binding to short stretches of DNA called cis-elements or TF binding sites (TFBS), they regulate gene expression. This entry represents the DNA binding domain found in C-terminal of LFY proteins in plants. Structure-function studies have demonstrated that LFY binds semi-palindromic 19-bp DNA elements through its highly conserved C-terminal DBD, a unique helix-turn-helix fold that by itself dimerizes on DNA. 169 matched cddid_all.tbl CDD pfam17539 pfam17539 340254 DUF5456 Family of unknown function (DUF5456). This is a family of unknown function found in Bacteroides. 152 matched cddid_all.tbl CDD pfam17540 pfam17540 375213 DUF5457 Family of unknown function (DUF5457). This is a family of unknown function found in Bacteria. Family members have one predicted trans-membrane region. 89 matched cddid_all.tbl CDD pfam17541 pfam17541 435933 TssC Type VI secretion system, TssC, VipB. T6SSs are toxin delivery systems. It is a multiprotein complex requiring numerous core proteins (Tss proteins) including cytoplasmic, transmembrane, and outer membrane components. The needle or tube apparatus is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex. VipB is a family of Gram-negative type VI secretion system components of the tail sheath. They have been known as COG3517. These sheath-components, of which there are many copies in the sheath, are also variously referred to as TssC. On contact with another bacterial cell the sheath contracts and pushes the puncturing device and tube through the cell envelope and punches the target bacterial cell. VipA and VipB (TssB and TssC) proteins were shown to form a cog-wheel like tubular structure in V. cholerae that was noticed to resemble T4 phage gp18 polysheath. Two beta-strands of VipA and four beta-strands of VipB intertwine forming the middle layer of the sheath. The sheath assembles around an inner Hcp tube and is attached to a structure called a baseplate that spans the bacterial membranes. Importantly, VipA/VipB sheath was shown to form a long contractile organelle in V. cholerae and in E. coli, suggesting that sheath contraction powers the secretion. 430 matched cddid_all.tbl CDD pfam17542 pfam17542 340257 RP853 Uncharacterized RP853. This is a family of unknown function found in Rickettsia. Family members are predicted to contain one trans-membrane region. 317 matched cddid_all.tbl CDD pfam17544 pfam17544 340259 DUF5460 Family of unknown function (DUF5460). This is a family of unknown function found in Rickettsia. Family members are predicted to contain one trans-membrane region. 375 matched cddid_all.tbl CDD pfam17545 pfam17545 340260 DUF5461 Family of unknown function (DUF5461). This is a family of unknown function found in viruses. 93 matched cddid_all.tbl CDD pfam17546 pfam17546 340261 Defb50 Beta defensin 50. Beta-defensin are small cationic antimicrobial peptides. Family members such as beta-defensin 50 (Defb50) has poor antimicrobial activity in its oxidized form, but this improves under reduced conditions. 50 matched cddid_all.tbl CDD pfam17547 pfam17547 407533 DUF5462 Family of unknown function (DUF5462). This is a family of unknown function found in Gammaproteobacteria. 157 matched cddid_all.tbl CDD pfam17548 pfam17548 340263 p6 Histone-like Protein p6. Family members such as protein p6 from Bacillus subtilis phage phi29 bind double-stranded DNA, forming a large nucleoprotein complex all along the viral genome, and have been proposed to be an architectural protein with a global role in genome organization. P6 is also involved in viral transcriptional control, repressing the C2 early promoter located at the right DNA end,and together with the viral regulatory protein p4, repressing early promoters A2b/A2c and activating late promoter A3. 76 matched cddid_all.tbl CDD pfam17549 pfam17549 340264 Phage_Gp17 Gene Product 17. Family members such as protein 17 (gene product 17/gp17) found in Bacillus phage phi29, is involved in DNA replication and in pulling the phage DNA into the cell during the injection process. 140 matched cddid_all.tbl CDD pfam17550 pfam17550 340265 PsaF Family of unknown function. This is a family of unknown function found in Yersinia pestis. 162 matched cddid_all.tbl CDD pfam17551 pfam17551 340266 DUF5463 Family of unknown function (DUF5463). This is a family of unknown function found in Yersinia pestis. 32 matched cddid_all.tbl CDD pfam17552 pfam17552 340267 DUF5464 Family of unknown function (DUF5464). This is a family of unknown function found in Bacteriophages. 51 matched cddid_all.tbl CDD pfam17553 pfam17553 340268 DUF5465 Family of unknown function (DUF5465). This is a family of unknown function found in Enterobacteria phage T7. 19 matched cddid_all.tbl CDD pfam17554 pfam17554 340269 DUF5466 Family of unknown function (DUF5466). This is a family of unknown function found in Enterobacteria phage T7. 57 matched cddid_all.tbl CDD pfam17555 pfam17555 435934 TssN Type VI secretion system, TssN. T6SSs are toxin delivery systems. It is a multiprotein complex requiring numerous core proteins (Tss proteins) including cytoplasmic, transmembrane, and outer membrane components. The needle or tube apparatus is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex. TssN proteins have multiple predicted transmembrane (TM) regions. In Flavobacterium johnsoniae, three specific components (TssN, TssO and TssP) are absent in the other sub-types of T6SS. 274 matched cddid_all.tbl CDD pfam17556 pfam17556 340271 MIT_LIKE_ACTX MIT-like atracotoxin family. This family includes peptides such as the Atracotoxin-Hvf17. It is a a non-toxic peptide isolated from the venom of Blue Mountains funnel-web spider Hadronyche versuta. It does not function like classical funnel-web spider atracotoxins to modulate mammalian or insect voltage-gated ion channel function since it lacks insecticidal activity and fails to affect vas deferens smooth muscle or skeletal muscle contractility. This peptide has ten conserved cysteine residues similar to AVIT family members such as MIT1. Due to the lack of the AVIT N-terminal four residues and lack of functional similarity to the AVIT family, the Atracotoxin-Hvf17 is classified as MIT-like atracotoxin. 68 matched cddid_all.tbl CDD pfam17557 pfam17557 375216 Conotoxin_I2 I2-superfamily conotoxins. Conotoxins (or conopeptides) are the peptidic components of the venoms of marine cone snails (genus Conus). They are classified in one of three ways: gene superfamily, cysteine framework or pharmacological family. Several distinct cysteine frameworks have been described in conotoxins. Members of this family display a XI cysteine pattern (C-C-CC-CC-C-C) and belong to the I2- superfamily conotoxins. Family members such as Kappa-conotoxin ViTx and Kappa-conotoxin SrXIA inhibit voltage gated potassium channels (Kv). 38 matched cddid_all.tbl CDD pfam17558 pfam17558 375217 AGH Androgenic gland hormone. This family contains members such as the Androgenic gland hormone (AGH) of the woodlouse, Armadillidium vulgare. AGH is a heterodimeric glycopeptide synthesized and secreted from androgenic glands. It is responsible for sex differentiation in crustaceans and contains 4 disulfide bonds. 121 matched cddid_all.tbl CDD pfam17560 pfam17560 340275 Megourin Aphid Megourins. This family is fond in the vetch aphid Megoura viciae with members such as Megourin 1, 2 and 3. Megourins are antimicrobial peptides that act against Gram-positive bacteria and fungi. 63 matched cddid_all.tbl CDD pfam17561 pfam17561 435935 TssO Type VI secretion system, TssO. T6SSs are toxin delivery systems. It is a multiprotein complex requiring numerous core proteins (Tss proteins) including cytoplasmic, transmembrane, and outer membrane components. The needle or tube apparatus is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex. TssO proteins have one predicted TM region near their N-termini. In Flavobacterium johnsoniae, three specific components (TssN, TssO and TssP) are absent in the other sub-types of T6SS. 148 matched cddid_all.tbl CDD pfam17562 pfam17562 340277 Styelin Styelin. This is a family of antimicrobial peptides found in Stela clava (Sea squirt). Family members are alpha-helical phenylalanine-rich antimicrobial peptides effective against a panel of Gram-negative and Gram-positive bacteria. Styelin contains unusual amino acids such as dihydroxyarginine, dihydroxylysine, 6-bromotryptophan, and 3,4-dihydroxyphenylalanine which are important for the antimicrobial activity at high salt concentrations. 59 matched cddid_all.tbl CDD pfam17563 pfam17563 340278 Cu Cupiennin. Cupiennin are small cationic alpha-helical peptides from the venom of the ctenid spider Cupiennius salei which are characterized by high bactericidal as well as hemolytic activities. Family members such as cupiennin 1a exert both cytolytic and antibacterial effects. The cytolytic activity of the cupiennin peptides depends primarily on the amphipathic N-terminus, which is capable of inserting into the membrane, and is modulated by the C-terminus via electrostatic interactions with the cell surface. 27 matched cddid_all.tbl CDD pfam17564 pfam17564 340279 DUF5470 Family of unknown function (DUF5470). This is a family of unknown function found in viruses. 73 matched cddid_all.tbl CDD pfam17565 pfam17565 340280 DUF5471 Family of unknown function (DUF5471). This is a family of unknown function found in Enterobacteria phage T7. 70 matched cddid_all.tbl CDD pfam17566 pfam17566 340281 DUF5472 Family of unknown function (DUF5472). This is a family of unknown function found in Human papillomavirus. 73 matched cddid_all.tbl CDD pfam17567 pfam17567 340282 DUF5473 Family of unknown function (DUF5473). This is a family of unknown function found in Human adenovirus. 106 matched cddid_all.tbl CDD pfam17568 pfam17568 340283 DUF5474 Family of unknown function (DUF5474). This is a family of unknown function found in Saccharomycetales. 77 matched cddid_all.tbl CDD pfam17569 pfam17569 340284 DUF5475 Family of unknown function (DUF5475). This is a family of unknown function found in Alphabaculovirus. 81 matched cddid_all.tbl CDD pfam17570 pfam17570 375218 T7-like_gp67 Bacteriophage T7-like, protein 6.7. Protein 6.7 is ejected from the infecting virion. It is found in tail-less particles and has been defined as a head protein. 61 matched cddid_all.tbl CDD pfam17571 pfam17571 340286 DUF5477 Family of unknown function (DUF5477). This is a family of unknown function found in Podoviridae. 77 matched cddid_all.tbl CDD pfam17572 pfam17572 340287 DUF5478 Family of unknown function (DUF5478). This is a family of unknown function found in Alphabaculovirus. 86 matched cddid_all.tbl CDD pfam17573 pfam17573 435936 GA-like GA-like domain. This domain is found in bacterial cell surface proteins. It is related to the GA domain that forms a three helix bundle. 50 matched cddid_all.tbl CDD pfam17574 pfam17574 340289 TA_inhibitor Inhibitor of toxin/antitoxin system (Gp4.5). This is a family of prokaryotic toxin-antitoxin (TA) systems inhibitors, found in Podoviridae such as Enterobacteria phage T7. Family members such as Gene product 4.5 have been shown to neutralize TA-system-mediated abortive infection by inhibiting the Lon protease activity, thus preventing antitoxin degradation and toxin activation. 89 matched cddid_all.tbl CDD pfam17575 pfam17575 340290 DUF5479 Family of unknown function (DUF5479). This is a family of unknown function found in Kappa-papillomavirus. 101 matched cddid_all.tbl CDD pfam17576 pfam17576 340291 DUF5480 Family of unknown function (DUF5480). This is a family of unknown function found in Podoviridae. 71 matched cddid_all.tbl CDD pfam17577 pfam17577 340292 ETM ECORI-T site. This is a family of unknown function found in Alphabaculovirus. 109 matched cddid_all.tbl CDD pfam17578 pfam17578 340293 DUF5481 Family of unknown function (DUF5481). This is a family of unknown function found in Myoviridae. 103 matched cddid_all.tbl CDD pfam17579 pfam17579 340294 DUF5482 Family of unknown function (DUF5482). This is a family of unknown function found in Saccharomycetales. 159 matched cddid_all.tbl CDD pfam17580 pfam17580 340295 GBR_NSP5 Group B Rotavirus Non-structural protein 5. Family members such as non-structural protein 5 (NSP5), are found in Group B rotaviruses (GBR). Group B rotavirus (GBR) is genetically and antigenically distinct from Group A rotavirus (GAR). Hence phylogneetic studies have been carried out and show that the C-terminal region of NSP5, which is conserved among GAR and critical for its function for viroplasm-like structure formation in cells, was also conserved in GBR NSP5. 176 matched cddid_all.tbl CDD pfam17581 pfam17581 340296 DUF5483 Family of unknown function (DUF5483). This is a family of unknown function found in Saccharomycetaceae. 441 matched cddid_all.tbl CDD pfam17582 pfam17582 340297 UL20 Cytomegalovirus UL20. This family has members such as the human cytomegalovirus glycoprotein UL20. UL20 is a type I trans-membrane glycoprotein with an immunoglobulin-like ectodomain that is highly polymorphic among HCMV strains. 304 matched cddid_all.tbl CDD pfam17583 pfam17583 340298 DUF5484 Family of unknown function (DUF5484). This is a family of unknown function found in Myoviridae. 43 matched cddid_all.tbl CDD pfam17584 pfam17584 340299 ComS Bacillus competence protein S. ComS is crucial for competence development as it prevents proteolytic degradation of ComK, the key transcriptional activator of all genes required for the uptake and integration of DNA. This family includes members of the Bacillus comS proteins such as Swiss:P80355. 44 matched cddid_all.tbl CDD pfam17585 pfam17585 340300 Phage_Arf Accessory recombination function protein. Family members are found in Caudovirales such as Salmonella virus P22. Family members have a recombination accessory function. 47 matched cddid_all.tbl CDD pfam17586 pfam17586 340301 DUF5485 Family of unknown function (DUF5485). This is a family of unknown function found in Alphabaculovirus. 56 matched cddid_all.tbl CDD pfam17587 pfam17587 340302 Dmd Discriminator of mRNA degradation. This family includes Dmd peptides from T4 phages. Dmd can suppress the toxicities of toxins such as LsoA (an endoribonucleases toxin expressed by E.coli). Crystal structure analysis show that Dmd is inserted into the deep groove between the N-terminal repeated domain (NRD) and the Dmd-binding domain (DBD) of LsoA. Site-directed mutagenesis of Dmd revealed the conserved residues (W31 and N40) are necessary for LsoA binding and the toxicity suppression. 60 matched cddid_all.tbl CDD pfam17588 pfam17588 340303 DUF5486 Family of unknown function (DUF5486). This is a family of unknown function found in Myoviridae. 53 matched cddid_all.tbl CDD pfam17589 pfam17589 407536 DUF5487 Family of unknown function (DUF5487). This is a family of unknown function found in Myoviridae. 66 matched cddid_all.tbl CDD pfam17590 pfam17590 340305 DUF5488 Family of unknown function (DUF5488). This is a family of unknown function found in Orthopoxvirus. 70 matched cddid_all.tbl CDD pfam17591 pfam17591 340306 UL41A Herpesvirus UL41A. Members of this family are found in Human cytomegalovirus. No known function has been reported. 78 matched cddid_all.tbl CDD pfam17592 pfam17592 340307 DUF5489 Family of unknown function (DUF5489). This is a family of unknown function found in Alphafusellovirus. 78 matched cddid_all.tbl CDD pfam17593 pfam17593 340308 DUF5490 Family of unknown function (DUF5490). This is a family of unknown function found in Myoviridae. 62 matched cddid_all.tbl CDD pfam17594 pfam17594 340309 GP57 Phage Tail fiber assembly helper gene product 57. Gene product 57 (Gp57) is a chaperone protein for short tail fiberphage protein that acts as a molecular chaperone of gp12, increasing the folding efficacy and production efficiency. 75 matched cddid_all.tbl CDD pfam17595 pfam17595 340310 DUF5491 Family of unknown function (DUF5491). This is a family of unknown function found in Myoviridae. 68 matched cddid_all.tbl CDD pfam17596 pfam17596 340311 DUF5492 Family of unknown function (DUF5492). This is a family of unknown function found in Alphabaculovirus. 80 matched cddid_all.tbl CDD pfam17597 pfam17597 340312 DUF5493 Family of unknown function (DUF5493). This is a family of unknown function found in viruses. 82 matched cddid_all.tbl CDD pfam17598 pfam17598 340313 DUF5494 Family of unknown function (DUF5494). This is a family of unknown function found in viruses. 84 matched cddid_all.tbl CDD pfam17599 pfam17599 340314 DUF5495 Family of unknown function (DUF5495). This is a family of unknown function found in Myoviridae. 87 matched cddid_all.tbl CDD pfam17600 pfam17600 340315 DUF5496 Family of unknown function (DUF5496). This is a family of unknown function found in Myoviridae. 87 matched cddid_all.tbl CDD pfam17601 pfam17601 340316 DUF5497 Family of unknown function (DUF5497). This is a family of unknown function found in Alphabaculovirus. 89 matched cddid_all.tbl CDD pfam17602 pfam17602 340317 DUF5498 Family of unknown function (DUF5498). This is a family of unknown function found in Myoviridae. 96 matched cddid_all.tbl CDD pfam17603 pfam17603 340318 DUF5499 Family of unknown function (DUF5499). This is a family of unknown function found in Myoviridae. 97 matched cddid_all.tbl CDD pfam17604 pfam17604 340319 DUF5500 Family of unknown function (DUF5500). This is a family of unknown function found in Herpesvirus. 98 matched cddid_all.tbl CDD pfam17605 pfam17605 340320 DUF5501 Family of unknown function (DUF5501). This is a family of unknown function found in Alphabaculovirus. 107 matched cddid_all.tbl CDD pfam17606 pfam17606 340321 DUF5502 Family of unknown function (DUF5502). This is a family of unknown function found in Listeria. 87 matched cddid_all.tbl CDD pfam17607 pfam17607 340322 DUF5503 Family of unknown function (DUF5503). This is a family of unknown function found in Enterobacteriaceae. 116 matched cddid_all.tbl CDD pfam17608 pfam17608 340323 DUF5504 Family of unknown function (DUF5504). This is a family of unknown function found in Lactobacillus. Family members have 4 predicted trans-membrane regions. 124 matched cddid_all.tbl CDD pfam17609 pfam17609 340324 HCMV_UL124 Family of unknown function. This is a family of unknown function found in beta-herpesvirus. Family members such as UL124 is a predicted membrane glycoprotein with one predicted trans-membrane region. 126 matched cddid_all.tbl CDD pfam17610 pfam17610 340325 DUF5505 Family of unknown function (DUF5505). This is a family of unknown function found in Alphabaculovirus. 156 matched cddid_all.tbl CDD pfam17611 pfam17611 340326 DUF5506 Family of unknown function (DUF5506). This is a family of unknown function found in Fowl aviadenovirus. 161 matched cddid_all.tbl CDD pfam17612 pfam17612 340327 DUF5507 Family of unknown function (DUF5507). This is a family of unknown function found in Escherichia. 160 matched cddid_all.tbl CDD pfam17613 pfam17613 340328 motB Modifier of transcription. Family members are transcription regulation-related proteins found in Myoviridae such as Enterobacteria phage T4. 162 matched cddid_all.tbl CDD pfam17614 pfam17614 340329 FPV060 Viral CC-type chemokine. Family members found in Fowlpox virus are CC chemokine-like proteins. Fpv060 contains the conserved pattern of four cysteine residues similar to the CC chemokine family. Fpv060 also contains more cysteines in the mature protein, than cellular chemokines and one predicted trans-membrane region. In vitro studies show N-terminal glycosylation and show that Fpv060 from Fowl pox virus is much larger and has many more cysteine residues than host chemokines and viral homologs. 188 matched cddid_all.tbl CDD pfam17615 pfam17615 375219 C166 Family of unknown function. Family members found in Fuselloviridae are predicted to play a role in virus function. 171 matched cddid_all.tbl CDD pfam17616 pfam17616 340331 US6 Viral unique short region 6. This family has members such as US6 found in HCMV (Human cytomegalovirus). US6 is a unique short region glycoprotein found in the ER. It blocks the binding of ATP by TAP1 (Transporter associated with Antigen Processing 1) through a conformational change and subsequently inhibits TAP-mediated peptide translocation to the ER. It also down regulates only MHC class I. Inhibition of US6 of TAP has been shown to require residues 89 to 108 of the HCMV US6 luminal domain, whereas sequences that flank this region stabilize the binding of the viral protein to TAP. Residues 81 to 90 and the C-terminal 39 residues of HCMV US6 may also contribute to the stabilization of the interaction between US6 and TAP. 161 matched cddid_all.tbl CDD pfam17617 pfam17617 340332 US10 Viral unique short region 10. This family contains US10 proteins found in HCMV Human cytomegalovirus. US10 is a unique short region trans-membrane glycoprotein found in the endoplasmic reticulum (ER). It down-regulates cell surface expression of HLA-G, but not that of classical class I MHC molecules. Despite of binding to classical class I MHC molecules and delaying their trafficking, it does not affect their steady-state cell surface levels. US10 contains a tri-leucine motif in the cytoplasmic tail which is responsible for down-regulation of HLA-G. 161 matched cddid_all.tbl CDD pfam17618 pfam17618 465434 SL4P Uncharacterized Strongylid L4 protein. Family members are predicted non-classically secreted proteins found in Ancylostoma ceylaniucum. Homologs are found in strongylids A. ceylanicum, N. americanus, H. contortus and Angiostrongylus cantonensis, where the corresponding genes in A. cantonensis are expressed in L4 larvae. Thus this family members found in A, ceylaniucum have been named strongylid L4 proteins (SL4Ps). Although SL4Ps do not resemble any domains of known function, they do have a conspicuous number of charged residues (both acidic and basic) in their N-terminal, most highly conserved regions. 88 matched cddid_all.tbl CDD pfam17619 pfam17619 465435 SCVP Secreted clade V proteins. Family members are found in strongylid parasites (A. ceylanicum, N. americanus, H. contortus and Heterorhabditis bacteriophora) and in related non-parasitic clade V species (C. elegans, Caenorhabditis briggsae and P. pacificus), hence the name secreted clade V proteins (SCVPs). In A. ceylanicum, the encoded 150 residue proteins are predicted to be classically secreted. 96 matched cddid_all.tbl CDD pfam17620 pfam17620 340335 ORF45 Family of unknown function. Family members found in alphabaculoviruses such as orf45 have been implicated in late gene expression when linked to orf41. 191 matched cddid_all.tbl CDD pfam17621 pfam17621 340336 DUF5508 Family of unknown function (DUF5508). This is a family of unknown function found in Enterobacteriaceae. 263 matched cddid_all.tbl CDD pfam17622 pfam17622 340337 UL16 Viral unique long protein 16. This family contains members such as UL16 found in the human cytomegalovirus (HCMV). It is an immunoevasin which subverts NKG2D-mediated immune responses by retaining a select group of diverse NKG2D ligands inside the cell. UL16 is a heavily glycosylated 50 kDa type I trans-membrane glycoprotein. The ectodomain folds into a modified version of the a variable (V-type) (immunoglobulin Ig)-like domain. The N-terminal plug region (amino acids 27-50) is covalently linked to the Ig-like core with a disulfide bond. UL16 protein utilizes a three-stranded beta-sheet to engage the alpha-helical surface of the MHC class I-like MICB platform domain. Residues at the center of this beta-sheet mimic a central binding motif employed by the structurally unrelated C-type lectin-like NKG2D to facilitate engagement of diverse NKG2D ligands. 204 matched cddid_all.tbl CDD pfam17623 pfam17623 340338 B277 Domain of unknown function. This is a family of unknown function, however family members such as B277 have been suggested to play a role in viral function. 277 matched cddid_all.tbl CDD pfam17624 pfam17624 340339 US30 Family of unknown function. This is a family of unknown function found in Cytomegalovirus. One of the family members US30 is a putative membrane glycoprotein with one predicted trans-membrane region. 282 matched cddid_all.tbl CDD pfam17625 pfam17625 340340 DUF5509 Family of unknown function (DUF5509). This is a family of unknown function found in Baculoviridae. 362 matched cddid_all.tbl CDD pfam17626 pfam17626 340341 IncF Inclusion membrane protein F. The chlamydial inclusion membrane is extensively modified by the insertion of type III secreted effector proteins. These inclusion membrane proteins (Incs) are exposed to the cytosol and share a common structural feature of a long, bi-lobed hydrophobic domain but little or no primary amino acid sequence similarity. This family has members such as the IncF proteins found in Chlamydia trachomatis. IncF, is enriched at the point of contact of RBs (reticulate bodies) with the inclusion membrane. It is expressed early in the developmental cycle and interacts with many other Inc proteins, like Ct058 or Ct850, which are expressed later during the cycle. Thus, IncF could act as an interaction node for Inc proteins. IncF consists of 104 amino acids of which 38 N-terminal amino acids encoding the signal sequence for the type III system and 12 C-terminal amino acids may be localized in the host cell cytoplasm. Suggesting that IncF or other small Incs interact with other Inc proteins by their trans-membrane domain. It has been identified to be capable of homo-oligomerization and also displayed self-interacting properties. 104 matched cddid_all.tbl CDD pfam17627 pfam17627 340342 IncE Inclusion membrane protein E. The chlamydial inclusion membrane is extensively modified by the insertion of type III secreted effector proteins. These inclusion membrane proteins (Incs) have two major characteriztics: an N-terminal type III secretion signal that is necessary for their secretion out of the bacterium and a hydrophobic region consisting of at least two trans-membrane helices that allows insertion into the inclusion membrane. Generally, both the N- and C-terminal regions of the Inc are exposed to the host cell cytosol. This family has members such as the IncE (also known as CT116) proteins found in Chlamydia trachomatis. IncE Interacts with Retromer-Associated Sorting Nexins (SNXs) directly binding the PX-domains of SNX5/6. It is expressed within the first 2 hours of C. trachomatis infection. IncE region 101-132 is the binding site for SNX5/6 causing re-localization of SNX5/6 from endosomes to the inclusion membrane. IncE101-132 expression was shown to be sufficient to maintain CI-MPR (Cation-Independent Mannose-6-Phosphate Receptor) in retromer-containing compartments, thereby disrupting efficient CI-MPR trafficking to the trans-Golgi. It has been suggested that SNX5/6 bind directly to IncE independently of phosphoinositides and that the predicted IncE C-terminal beta-hairpin is required. IncE-mediated sequestration of retromer SNX-BAR proteins may promote Golgi fragmentation, a process that facilitates lipid acquisition by C. trachomatis and enhances progeny production. 132 matched cddid_all.tbl CDD pfam17628 pfam17628 340343 IncD Inclusion membrane protein D. The chlamydial inclusion membrane is extensively modified by the insertion of type III secreted effector proteins. These inclusion membrane proteins (Incs) have two major characteriztics: an N-terminal type III secretion signal that is necessary for their secretion out of the bacterium and a hydrophobic region consisting of at least two trans-membrane helices that allows insertion into the inclusion membrane. Generally, both the N- and C-terminal regions of the Inc are exposed to the host cell cytosol. This family has members such as the IncD proteins found in Chlamydia trachomatis. This C. trachomatis effector protein IncD has been shown to recruit the lipid transfer protein CERT to the inclusion membrane by directly interacting with CERT PH domain, which mediates the FFAT motif-dependent recruitment of the ER-resident protein VAPB (vesicle-associated membrane protein-associated protein) to the inclusion. 141 matched cddid_all.tbl CDD pfam17629 pfam17629 340344 DUF5510 Family of unknown function (DUF5510). This is a family of unknown function found in Rickettsia. Family members are predicted to have 2 or 3 trans-membrane regions. 62 matched cddid_all.tbl CDD pfam17630 pfam17630 340345 DUF5511 Family of unknown function (DUF5511). This is a family of unknown function found in Bacillus. 69 matched cddid_all.tbl CDD pfam17631 pfam17631 340346 DUF5512 Family of unknown function (DUF5512). This is a family of unknown function found in Bacillus. 139 matched cddid_all.tbl CDD pfam17632 pfam17632 340347 DUF5513 Family of unknown function (DUF5513). This is a family of unknown function found in Bacillus. 91 matched cddid_all.tbl CDD pfam17633 pfam17633 340348 DUF5514 Family of unknown function (DUF5514). This is a family of unknown function found in Bacillus. 142 matched cddid_all.tbl CDD pfam17634 pfam17634 340349 GP67 Gene product 67. This is a family of unknown function found in Myoviridae such as Enterobacteria phages. Family members such as Gp67, is a prohead core (scaffold) protein. 80 matched cddid_all.tbl CDD pfam17635 pfam17635 465436 bCoV_Orf14 Betacoronavirus uncharacterized protein 14 (SARS-CoV-2 like). This family contains proteins found in SARS and SARS-like coronaviruses. It includes uncharacterized protein 14 from SARS coronavirus 2 (SARS-CoV-2), human SARS coronavirus (SARS-CoV) and bat coronavirus Rp3/2004 (SARS-like coronavirus Rp3). In SARS-CoV, orf14 is completely contained within the ORF encoding the nucleocapsid protein (N). In SARS-CoV-2 uncharacterized protein 14 is predicted to contain one transmembrane helix. 70 matched cddid_all.tbl CDD pfam17636 pfam17636 340351 UL21a Viral Unique Long protein 21a. Members of this family such as UL21a found in Human cytomegalovirus (HCMV) is required for HCMV to establish efficient productive infection. It is a short-lived cytoplasmic protein that facilitates HCMV replication. It has also been shown to be responsible for APC1, APC4 and APC5 degradation. 123 matched cddid_all.tbl CDD pfam17637 pfam17637 375222 DUF5516 Family of unknown function (DUF5516). This is a family of unknown function found in T7 viruses. 37 matched cddid_all.tbl CDD pfam17638 pfam17638 340353 UL42 HCMV UL42. Family members include UL42 proteins found in Human cytomegalovirus (HCMV). UL42 has two Pro-Pro-X-Tyr (PPxY) sequences, a hydrophobic region at the C terminus and no N-terminal signal peptide. These features are shared with herpes simplex virus (HSV) UL56. UL42 has a putative C-terminal trans-membrane region. HCMV UL42 interacts with Itch, a member of the Nedd4 family of ubiquitin E3 ligases, through its PY motifs as observed in HSV UL56, suggestive of a regulatory function. 125 matched cddid_all.tbl CDD pfam17639 pfam17639 340354 DUF5517 Family of unknown function (DUF5517). This is a family of unknown function found in Fuselloviridae. Structure analysis suggest a role in viral assembly. 100 matched cddid_all.tbl CDD pfam17640 pfam17640 340355 UL17 Uncharacterized UL17. This is a family of unknown function found in beta-herpesviruses such as Human cytomegalovirus (HCMV). 102 matched cddid_all.tbl CDD pfam17641 pfam17641 407540 ASPRs Ancylostoma-associated secreted protein related. This family includes members encoded by ASP-related genes which are distant homologs to ASPs (Ancylostoma-associated secreted proteins). ASPs are a diverse set of secreted cysteine-rich proteins pfam00188. ASPRs, on the other hand are predicted to be secreted with one ASPR in Heligmosomoides bakeri shown to be secreted by parasitic adults. Thus, like ASPs, ASPRs are suggested to comprise an important element of hookworm infection in vivo. 118 matched cddid_all.tbl CDD pfam17642 pfam17642 435939 TssD Hemolysin coregulated protein Hcp (TssD). T6SSs are toxin delivery systems. It is a multiprotein complex requiring numerous core proteins (Tss proteins) including cytoplasmic, transmembrane, and outer membrane components. The needle or tube apparatus is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex. These tube and trans-envelope sub-assemblies are linked via TssK. This entry comprises family members such as the inner tube protein Hcp (TssD). Hcp proteins form hexamers that stack to form the inner tube/needle structure of the puncturing device. Other functions have also been described for Hcp proteins, for example, some Hcp proteins have been shown to have a chaperone function in that they bind to and stabilize effectors. In addition, there are 'evolved' Hcp proteins that have the Hcp domain at the N-terminal half of the protein and a toxic effector function present in the C-terminal portion of the protein. 127 matched cddid_all.tbl CDD pfam17643 pfam17643 435940 TssR Type VI secretion system, TssR. T6SSs are toxin delivery systems. It is a multiprotein complex requiring numerous core proteins (Tss proteins) including cytoplasmic, transmembrane, and outer membrane components. The needle or tube apparatus is comprised of a phage-like complex, similar to the T4 contractile bacteriophage tail, which is thought to be anchored to the membrane by a trans-envelope complex. This entry relates to TssR family members. TssR proteins have no predicted TM regions. 745 matched cddid_all.tbl CDD pfam17644 pfam17644 375225 30K_MP_core Core domain of 30K viral movement proteins. This entry represents the core domain found in viral movement proteins (MP) of the 30K type. The core domain is conserved among MPs of 30K sharing the same predicted secondary structure which consists of 1 alpha-helix and 7 predicted beta-strands. The only sequence feature common to all 30K MPs is a short region between beta-strands 1 and 2, which contains several conserved hydrophobic positions, and a nearly-invariant aspartate which constitutes the sequence signature of the superfamily. This signature aspartate has a conserved role in essential for viral cell-to-cell movement. 138 matched cddid_all.tbl CDD pfam17645 pfam17645 375226 Amdase Arylmalonate decarboxylase. This entry contains members such as the arylmalonate decarboxylases (AMDase; EC 4.1.1.76), which belong to the family of carboxy-lyases (EC 4.1). Amdases are capable of decarboxylating a range of alpha-disubstituted malonic acid derivates to enantiopure products without the need for any cofactor. AMDases are members of the widespread Asp/Glu racemase family pfam01177 together with aspartate (EC 5.1.1.13) and glutamate racemases (EC 5.1.1.3), hydantoin racemases (EC 5.1.99.5) and maleate isomerases (EC 5.2.1.1). 217 matched cddid_all.tbl CDD pfam17646 pfam17646 375227 Zemlya Closterovirus 1a polyprotein central region. This family represents an alignment of the Zemlya region of closteroviruses. The alignment of the 1a polyprotein of the Closteroviridae family members revealed that this region was not conserved in other genera. The homologs of the Zemlya region are not found in other viral or cellular proteins. This region is named the Zemlya region (zemlya is the Russian word for Earth), meaning that its conserved amino acid sequence represents a 'solid ground' within the highly variable central region of 1a polyporotein. It is composed of four predicted alpha-helices, alphaA to alphaD, and contains three conserved positions: i) a strictly conserved glutamate (E) in helix alphaA (E1291 in Beet yellows closterovirus (BYV)); ii) a strictly conserved proline (P1380) in alphaD; and iii) a conserved basic position (arginine or lysine; R1384 in BYV). The presence of a conserved proline in helix alphaD is noteworthy because prolines are strongly disfavoured in helices; this proline most probably induces a kink in the helix. Functional studies have suggested that most part of the Zemlya region, targets the ER and remodels the ER membranes. More specifically, deletion analysis and substitutions of the conserved hydrophobic amino acid residues suggest a role of the putative amphipathic helix (alphaD) in the formation of globules. Hence it was proposed that this specific region in 1a protein protein may be involved in the biogenesis of closterovirus. 106 matched cddid_all.tbl CDD pfam17647 pfam17647 435941 DUF5518 Family of unknown function (DUF5518). This is a family of unknown function found in Archaea. Family members have multiple predicted trans-membrane regions. 118 matched cddid_all.tbl CDD pfam17648 pfam17648 435942 DUF5519 Family of unknown function (DUF5519). This is a family of unknown function. 96 matched cddid_all.tbl CDD pfam17649 pfam17649 435943 VPS38 Vacuolar protein sorting 38. The class III phosphatidylinositol-3-kinase (PI3K) known as Vps34 (vacuolar protein sorting 34, encoded by PIK3C3) regulate intracellular membrane trafficking in endocytic sorting, cytokinesis and autophagy. Vps34 forms complexes with other proteins: Vps15 (encoded by PIK3R4, known as p150 in mammalian cells), Vps30 (encoded by VPS30/ATG6 in yeast, equivalent to mammalian Beclin 1, encoded by BECN1) and either Vps38 (UVRAG) or Atg14 (ATG14L). This family includes members such as Vps38 found in Saccharomyces cerevisiae. Vps38 is characteriztic of complex II and essential for vacuolar protein sorting. In mammalian cells, complex II is also involved in autophagy, receptor degradation and cytokinesis as well as signaling, recycling and lysosomal tubulation. Independently from complex I and II, Beclin 1 and UVRAG also play separate roles in endosome function and neuron viability. In complex I, Vps38/UVRAG is substituted with Atg14/ATG14L. Although the N-terminal domains of Vps30, Vps38 and Atg14 differ, the overall similarity of their domain organizations suggests that these proteins may have evolved from a common ancestor. 425 matched cddid_all.tbl CDD pfam17650 pfam17650 465437 RACo_linker RACo linker region. This family includes reductive activator of CoFeSP (RACo) proteins, Swiss:Q3ACS2. Structure analysis of RACo indicate that it contains 4 regions: N-terminal region pfam00111 (residues 3-94) binding the [2Fe-2S] cluster, a linker region (residues 95-125), the middle region (residues 126-206), and the large C-terminal domain pfam14574 (residues 207-630). This entry pertains to the linker region. The linker region is only present in RACE (reductive activases for corrinoid enzymes) protein sequences with the N-terminal [2Fe-2S] cluster family pfam00111 and is absent in the RamA-like RACE proteins, suggesting that the linker domain and the N-terminal domain form one functional unit. 86 matched cddid_all.tbl CDD pfam17651 pfam17651 435945 Raco_middle RACo middle region. This family includes reductive activator of CoFeSP (RACo) proteins, Swiss:Q3ACS2. Structure analysis of RACo indicate that it contains 4 regions: N-terminal region pfam00111 (residues 3-94) binding the [2Fe-2S] cluster, a linker region (residues 95-125), the middle region (residues 126-206), and the large C-terminal domain pfam14574 (residues 207-630). This entry pertains to the middle region. This region contains residues in their alpha-helices (H6 and H7) that mediate dimerization with subdomain I of the C-terminal domain. 163 matched cddid_all.tbl CDD pfam17652 pfam17652 435946 Glyco_hydro81C Glycosyl hydrolase family 81 C-terminal domain. Family of eukaryotic beta-1,3-glucanases. Within the Aspergillus fumigatus protein Swiss:Q9UVV0 two perfectly conserved Glu residues (E550 or E554) have been proposed as putative nucleophiles of the active site of the Engl1 endoglucanase, while the proton donor would be D475. The endo-beta-1,3-glucanase activity is essential for efficient spore release. This entry represents the helical C-terminal domain. 349 matched cddid_all.tbl CDD pfam17653 pfam17653 435947 DUF5522 Family of unknown function (DUF5522). This is a family of unknown function. Family members are found in Bacteria and Eukaryotes. In algae, this family is found on the N-terminal of diphthamide synthase family pfam01902 and is predicted to be a membrane transporter belonging to The ATP-binding Cassette (ABC) family. In nematoda, it is found on the N-terminal side of ribosomal protein family L14 pfam00238. It is also found on the N-terminal of Cob(I)alamin adenosyltransferase pfam01923 in other eukaryotes. Family members found in homo sapiens such as Swiss:Q5VUE5, have been shown to be highly expressed in 15 high-grade neuroendocrine tumor cell lines and YAP1-positive small-cell lung cancer cell lines as well as being up-regulated in two human Multiple Myloma cell lines in response to selective nuclear export inhibitor KPT-276. The HMM profile of this family reveals 4 highly conserved cysteines. 48 matched cddid_all.tbl CDD pfam17654 pfam17654 465438 Trnau1ap Selenocysteine tRNA 1 associated proteins. This entry represents the C-terminal region of Selenocysteine tRNA 1 associated proteins (Trnau1ap also known as Secp43). Family members found in Eukaryotes have been shown to serve an essential role in the synthesis of selenoproteins, which have critical functions in numerous biological processes. Selenium deficiency results in a variety of diseases, including cardiac disease. Trnau1ap proteins harbor RNA recognition motifs (RRM) pfam00076 and Tyr-rich region found in the C-terminal. The Tyr-rich region (amino acids 185-225) is conserved among several mammals, including human, chimp, dog, cattle, mouse and rat. Furthermore, constitutive deletion of exons corresponding to the Tyr-rich region in mouse resulted in embryonic lethality. 101 matched cddid_all.tbl CDD pfam17655 pfam17655 465439 IRK_C Inward rectifier potassium channel C-terminal domain. This cytoplasmic C-terminal domain has an Ig fold. 174 matched cddid_all.tbl CDD pfam17656 pfam17656 435950 ChapFlgA_N FlgA N-terminal domain. Presumed domain found to N-terminus of SAF-like domain in FlgA proteins. 76 matched cddid_all.tbl CDD pfam17657 pfam17657 407553 DNA_pol3_finger Bacterial DNA polymerase III alpha subunit finger domain. 166 matched cddid_all.tbl CDD pfam17658 pfam17658 465440 DUF5520 Family of unknown function (DUF5520). This is a family of unknown function found in Mammalia. 337 matched cddid_all.tbl CDD pfam17659 pfam17659 465441 DUF5521 Family of unknown function (DUF5521). This is a family of unknown function found in Eukaryota. Family members include the human CXorf57. High-throughput sequencing used to identify genes driving tumorigenesis in Avian leukosis virus (ALV)-induced B-cell lymphomas, showed CXorf57 as the 10th most frequently targeted common integration site by ALV. ALV induces B-cell lymphoma and other neoplasms in chickens by integrating within or near cancer genes and perturbing their expression. CXorf57 encodes a protein that has a conserved putative replication factor A protein 1 domain. Several proteins with this domain have been shown to be involved in recognition of DNA damage for nucleotide excision repair. CXorf57 contains 24 unique integration sites that are spaced throughout the gene and in no preferred orientation. 848 matched cddid_all.tbl CDD pfam17660 pfam17660 465442 BTRD1 Bacterial tandem repeat domain 1. This short domain is found in a wide variety of bacterial proteins. 50 matched cddid_all.tbl CDD pfam17661 pfam17661 465443 DUF5523 Family of unknown function (DUF5523). This is a family of unknown function found in Eukaryotes. Family members such as the human CC1D2A protein carry the domain architecture where pfam15625 and pfam00168 are found at the C-terminal region of this family. However, other family members such as Swiss:D6R9V3, do not carry either of the above mentioned Pfam families. 255 matched cddid_all.tbl CDD pfam17662 pfam17662 465444 DUF5524 Family of unknown function (DUF5524). This is a family of unknown function found in Metazoa. 290 matched cddid_all.tbl CDD pfam17663 pfam17663 435956 DUF5525 Family of unknown function (DUF5525). This is a family of unknown function found in Chordata. 1023 matched cddid_all.tbl CDD pfam17664 pfam17664 465445 HOATZ-like Cilia- and flagella-associated protein HOATZ-like. This entry represents cilia- and flagella-associated protein, HOATZ, and related proteins, found in metazoa. In mice HOATZ is encoded by the gene designated 4833427G06Rik (C11orf88). Mouse Hoatz mRNA is specifically expressed in tissues with motile cilia and flagella. Hoatz knockout mice developed hydrocephalus and male infertility, and the ependymal cilia frequently showed disorganized axonemes. 168 matched cddid_all.tbl CDD pfam17665 pfam17665 465446 DUF5527 Family of unknown function (DUF5527). This is a family of unknown function found in Chordata. 139 matched cddid_all.tbl CDD pfam17666 pfam17666 465447 DUF5528 Family of unknown function (DUF5528). This is a family of unknown function found in Chordata. 152 matched cddid_all.tbl CDD pfam17667 pfam17667 435959 Pkinase_fungal Fungal protein kinase. This domain appears to be a variant of the protein kinase domain that is found in a variety of fungal species. 387 matched cddid_all.tbl CDD pfam17668 pfam17668 435960 Acetyltransf_17 Acetyltransferase (GNAT) domain. 112 matched cddid_all.tbl CDD pfam17669 pfam17669 435961 DUF5529 Family of unknown function (DUF5529). This is a family of unknown function found in Chordata. 185 matched cddid_all.tbl CDD pfam17670 pfam17670 465448 DUF5530 Family of unknown function (DUF5530). This is a family of unknown function found in Chordata. 141 matched cddid_all.tbl CDD pfam17671 pfam17671 407566 DUF5531 Family of unknown function (DUF5531). This is a family of unknown function found in Mammalia. Family members have one or several predicted trans-membrane regions. 151 matched cddid_all.tbl CDD pfam17672 pfam17672 465449 FIMP fertilization-influencing membrane protein. In mice, 4930451I11Rik encodes two isoforms: a transmembrane (TM) form and a secreted form. FIMP is the TM form. It is a sperm-specific transmembrane protein that is essential for the sperm-oocyte fusion process. 89 matched cddid_all.tbl CDD pfam17673 pfam17673 465450 DUF5532 Family of unknown function (DUF5532). This is a family of unknown function found in mammals. 92 matched cddid_all.tbl CDD pfam17674 pfam17674 465451 HHH_9 HHH domain. 70 matched cddid_all.tbl CDD pfam17675 pfam17675 465452 APG6_N Apg6 coiled-coil region. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. Autophagy is a bulk degradation process induced by starvation in eukaryotic cells. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway. 127 matched cddid_all.tbl CDD pfam17676 pfam17676 465453 Peptidase_S66C LD-carboxypeptidase C-terminal domain. Muramoyl-tetrapeptide carboxypeptidase hydrolyses a peptide bond between a di-basic amino acid and the C-terminal D-alanine in the tetrapeptide moiety in peptidoglycan. This cleaves the bond between an L- and a D-amino acid. The function of this activity is in murein recycling. This family also includes the microcin c7 self-immunity protein Swiss:Q47511. This family corresponds to Merops family S66. 120 matched cddid_all.tbl CDD pfam17677 pfam17677 465454 Glyco_hydro38C2 Glycosyl hydrolases family 38 C-terminal beta sandwich domain. This domain is found at the C-terminal end of various glycosyl hydrolases belonging to family 38. The domain has a beta sandwich fold. 71 matched cddid_all.tbl CDD pfam17678 pfam17678 465455 Glyco_hydro_92N Glycosyl hydrolase family 92 N-terminal domain. This domain is found at the N-terminus of family 92 glycosyl hydrolase proteins. 231 matched cddid_all.tbl CDD pfam17679 pfam17679 375249 Dip gp37/Dip protein. This protein is found in the giant phage phi KZ. This protein has been shown to bind to RNAse E of the host P. aeruginosa and to inhibit the RNA degradation machinery of the bacterium. 273 matched cddid_all.tbl CDD pfam17680 pfam17680 435970 FlgO FlgO protein. This entry represents the FlgO protein. Mutation of this protein in Vibrio cholerae has been shown to reduce motility. FlgO is an outer membrane protein that localizes throughout the membrane and not at the flagellar pole. Although FlgO and FlgP do not specifically localize to the flagellum, they are required for flagellar stability. Proteins in this family mostly contain an N-terminal lipoprotein attachment motif. 130 matched cddid_all.tbl CDD pfam17681 pfam17681 465456 GCP_N_terminal Gamma tubulin complex component N-terminal. This is the N-terminal domain found in components of the gamma-tubulin complex proteins (GCPs). Family members include spindle pole body (SBP) components such as Spc97 and Spc98 which function as the microtubule-organizing center in yeast. Furthermore, family members such as human GCP4 (Gamma-tubulin complex component 4) have been structurally elucidated. Functional studies have shown that the N-terminal domain defines the functional identity of GCPs, suggesting that all GCPs are incorporated into the helix of gamma-tubulin small complexes (gTURCs) via lateral interactions between their N-terminal domains. Thereby, they define the direct neighbors and position the GCPs within the helical wall of gTuRC. Sequence alignment of human GCPs based on the GCP4 structure helped delineate conserved regions in the N- and C-terminal domains. In addition to the conserved sequences, the N-terminal domains carry specific insertions of various sizes depending on the GCP, i.e. internal insertions or N-terminal extensions. These insertions may equally contribute to the function of individual GCPs as they have been implied in specific interactions with regulatory or structural proteins. For instance, GCP6 carries a large internal insertion phosphorylated by Plk4 and containing a domain of interaction with keratins, whereas the N-terminal extension of GCP3 interacts with the recruitment protein MOZART1. 298 matched cddid_all.tbl CDD pfam17682 pfam17682 465457 Tau95_N Tau95 Triple barrel domain. TFIIIC1 is a multisubunit DNA binding factor that serves as a dynamic platform for assembly of pre-initiation complexes on class III genes. This entry represents the tau 95 subunit which holds a key position in TFIIIC, exerting both upstream and downstream influence on the TFIIIC-DNA complex by rendering the complex more stable. Once bound to tDNA-intragenic promoter elements, TFIIIC directs the assembly of TFIIIB on the DNA, which in turn recruits the RNA polymerase III (pol III) and activates multiple rounds of transcription. 115 matched cddid_all.tbl CDD pfam17683 pfam17683 465458 TFIIF_beta_N TFIIF, beta subunit N-terminus. Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter. 104 matched cddid_all.tbl CDD pfam17684 pfam17684 407577 SCAB-PH PH domain of plant-specific actin-binding protein. This family is a PH domain found on plant-specific actin-binding proteins or SCABs. SCAB proteins bind, bundle and stabilize actin filaments and regulate stomatal movement. The Ig-PH fusion domain is at the C-terminus. This domain adopts the PH fold, of seven beta-strands, beta7-beta13 and two alpha-helices, alpha1 and alpha2 arranged into a beta-barrel. The canonical phosphoinositide-binding pocket of the classic PH domain is degenerate in this fused one, and the charge on the pocket suggest that the Ig-PH domain contains a non-canonical binding site for inositol phosphates. 108 matched cddid_all.tbl CDD pfam17685 pfam17685 375254 DUF5533 Family of unknown function (DUF5533). This is a family of unknown function found in chordata. Family members have multiple predicted transmembrane regions. 139 matched cddid_all.tbl CDD pfam17686 pfam17686 435974 DUF5534 Family of unknown function (DUF5534). This is a family of unknown function found in mammals. Family members have one or several predicted trans-membrane regions. 183 matched cddid_all.tbl CDD pfam17687 pfam17687 375256 DUF5535 Family of unknown function (DUF5535). This is a family of unknown function found in mammals. 105 matched cddid_all.tbl CDD pfam17688 pfam17688 435975 DUF5536 Family of unknown function (DUF5536). This is a family of unknown function found in mammals. 214 matched cddid_all.tbl CDD pfam17689 pfam17689 435976 Arabino_trans_N Arabinosyltransferase concanavalin like domain. Arabinosyltransferase is involved in arabinogalactan (AG) biosynthesis pathway in mycobacteria. AG is a component of the macromolecular assembly of the mycolyl-AG-peptidoglycan complex of the cell wall. This enzyme has important clinical applications as it is believed to be the target of the antimycobacterial drug Ethambutol. 155 matched cddid_all.tbl CDD pfam17690 pfam17690 375258 DUF5537 Family of unknown function (DUF5537). This is a family of unknown function found in chordata. 160 matched cddid_all.tbl CDD pfam17691 pfam17691 465459 Croc_4 Contingent replication of cDNA 4. Family members are 18-kDa serine/threonine-rich polypeptides containing a P-loop motif and an SH3-binding region with phosphorylation sites for a variety of protein kinases (cdc2, CDK2, MAPK, CDK5, protein kinase C, Ca(2+)/calmodulin protein kinase 2, casein kinase 2) involved in cell proliferation and differentiation. Functional studies revealed that expression is associated with proliferating and migrating cells in developing brain. Furthermore, it has been suggested that CROC-4 participates in brain-specific c-fos signaling pathways involved in cellular remodeling of brain architecture. C1orf61 expression was also found associated with the progression of liver disease as well as human embryogenesis. It was shown to be up-regulated in hepatic cirrhosis tissues and further up-regulated in primary hepatocellular carcinoma tumors where it was suggested to play a role as a tumor activator. 79 matched cddid_all.tbl CDD pfam17692 pfam17692 407582 DUF5538 Family of unknown function (DUF5538). This is a family of unknown function found in primates. 130 matched cddid_all.tbl CDD pfam17693 pfam17693 465460 DUF5539 Family of unknown function (DUF5539). This is a family of unknown function found in primates. 201 matched cddid_all.tbl CDD pfam17694 pfam17694 465461 DUF5540 Family of unknown function (DUF5540). This is a family of unknown function found in primates. 77 matched cddid_all.tbl CDD pfam17695 pfam17695 407583 DUF5541 Family of unknown function (DUF5541). This is a family of unknown function found in primates. 116 matched cddid_all.tbl CDD pfam17696 pfam17696 465462 DUF5542 Family of unknown function (DUF5542). This is a family of unknown function. The C-terminal has a strongly conserved WxxxW motif. 68 matched cddid_all.tbl CDD pfam17697 pfam17697 375265 DUF5543 Family of unknown function (DUF5543). This is a family of unknown function found in primates. 118 matched cddid_all.tbl CDD pfam17698 pfam17698 375266 DUF5544 Family of unknown function (DUF5544). This is a family of unknown function found in primates. 125 matched cddid_all.tbl CDD pfam17699 pfam17699 375267 DUF5545 Family of unknown function (DUF5545). This is a family of unknown function found in primates. 221 matched cddid_all.tbl CDD pfam17700 pfam17700 407585 DUF5546 Family of unknown function (DUF5546). This is a family of unknown function found in primates. 135 matched cddid_all.tbl CDD pfam17701 pfam17701 435981 DUF5547 Family of unknown function (DUF5547). This is a family of unknown function found in mammals. 122 matched cddid_all.tbl CDD pfam17702 pfam17702 465463 DUF5548 Family of unknown function (DUF5548). This is a family of unknown function found in primates. 177 matched cddid_all.tbl CDD pfam17703 pfam17703 407588 DUF5549 Family of unknown function (DUF5549). This is a family of unknown function found in mammals. 200 matched cddid_all.tbl CDD pfam17704 pfam17704 465464 DUF5550 Family of unknown function (DUF5550). This is a family of unknown function found in primates. 123 matched cddid_all.tbl CDD pfam17705 pfam17705 465465 DUF5551 Family of unknown function (DUF5551). This is a family of unknown function found in primates. 156 matched cddid_all.tbl CDD pfam17706 pfam17706 375274 DUF5552 Family of unknown function (DUF5552). This is a family of unknown function found in primates. 217 matched cddid_all.tbl CDD pfam17707 pfam17707 465466 DUF5553 Family of unknown function (DUF5553). This is a family of unknown function found in primates. 223 matched cddid_all.tbl CDD pfam17708 pfam17708 407590 Gasdermin_C Gasdermin PUB domain. The precise function of this protein is unknown. A deletion/insertion mutation is associated with an autosomal dominant non-syndromic hearing impairment form. In addition, this protein has also been found to contribute to acquired etoposide resistance in melanoma cells. This family also includes the gasdermin protein 174 matched cddid_all.tbl CDD pfam17709 pfam17709 375277 DUF5554 Family of unknown function (DUF5554). This is a family of unknown function found in primates. 75 matched cddid_all.tbl CDD pfam17710 pfam17710 407591 DUF5555 Family of unknown function (DUF5555). This is a family of unknown function found in mammals. 295 matched cddid_all.tbl CDD pfam17711 pfam17711 465467 DUF5556 Family of unknown function (DUF5556). This is a family of unknown function found in primates. 179 matched cddid_all.tbl CDD pfam17712 pfam17712 375280 DUF5557 Family of unknown function (DUF5557). This is a family of unknown function found in primates. 90 matched cddid_all.tbl CDD pfam17713 pfam17713 407592 DUF5558 Family of unknown function (DUF5558). This is a family of unknown function found in Homo sapiens. 129 matched cddid_all.tbl CDD pfam17714 pfam17714 375282 DUF5559 Family of unknown function (DUF5559). This is a family of unknown function found in primates. 194 matched cddid_all.tbl CDD pfam17715 pfam17715 375283 DUF5560 Family of unknown function (DUF5560). This is a family of unknown function found in primates. 165 matched cddid_all.tbl CDD pfam17716 pfam17716 407593 DUF5561 Family of unknown function (DUF5561). This is a family of unknown function found in eukaryota. 255 matched cddid_all.tbl CDD pfam17717 pfam17717 435987 DUF5562 Family of unknown function (DUF5562). This is a family of unknown function found in mammals. Family members have one or several predicted transmembrane regions. 168 matched cddid_all.tbl CDD pfam17718 pfam17718 375286 DUF5563 Family of unknown function (DUF5563). This is a family of unknown function found in chordata. 192 matched cddid_all.tbl CDD pfam17719 pfam17719 465468 DUF5564 Family of unknown function (DUF5564). This is a family of unknown function found in chordata. 98 matched cddid_all.tbl CDD pfam17720 pfam17720 407596 DUF5565 Family of unknown function (DUF5565). This is a family of unknown function found in bacteria and eukaryotes. 324 matched cddid_all.tbl CDD pfam17721 pfam17721 465469 DUF5566 Family of unknown function (DUF5566). This is a family of unknown function found in chordata. 233 matched cddid_all.tbl CDD pfam17722 pfam17722 465470 IFTAP Intraflagellar transport-associated protein. Intraflagellar transport-associated protein (IFTAP, C11ORF74) interacts with the IFT-A complex and is accumulated at the distal tip in the absence of an IFT-A subunit IFT139. In IFTAP-knockout (KO) cells, the BBSome components cannot enter cilia. However, IFTAP-KO mice demonstrated no obvious anatomical abnormalities associated with ciliary dysfunctions. 234 matched cddid_all.tbl CDD pfam17723 pfam17723 435991 RHH_8 Ribbon-Helix-Helix transcriptional regulator family. This family of proteins are likely to be transcriptional regulators that have an N-terminal ribbon-helix-helix domain. Although some members of the family are annotated as CopG, this family does not include that protein. 119 matched cddid_all.tbl CDD pfam17724 pfam17724 465471 DUF5568 Family of unknown function (DUF5568). This is a family of unknown function found in chordata. 203 matched cddid_all.tbl CDD pfam17725 pfam17725 435993 YBD YAP binding domain. TEA domain transcription factors contain an N-terminal TEA domain pfam01285 and a C-terminal YAP binding domain (YBD). This entry corresponds to the YBD that binds to the oncoproteins YAP and TAZ. The structure of the YBD shows that it has an Ig-like beta sandwich fold. 202 matched cddid_all.tbl CDD pfam17726 pfam17726 435994 DpnI_C Dam-replacing HTH domain. Dam-replacing protein (DRP) is an restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis. This domain represents the C-terminal HTH domain. 70 matched cddid_all.tbl CDD pfam17727 pfam17727 435995 CtsR_C CtsR C-terminal dimerization domain. This family consists of several Firmicute transcriptional repressor of class III stress genes (CtsR) proteins. CtsR of L. monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon. This entry corresponds to the C-terminal dimerization domain. 72 matched cddid_all.tbl CDD pfam17728 pfam17728 435996 BsuBI_PstI_RE_N BsuBI/PstI restriction endonuclease HTH domain. This family represents the C-terminus of bacterial enzymes similar to type II restriction endonucleases BsuBI and PstI (EC:3.1.21.4). The enzymes of the BsuBI restriction/modification (R/M) system recognize the target sequence 5'CTGCAG and are functionally identical with those of the PstI R/M system. 140 matched cddid_all.tbl CDD pfam17729 pfam17729 465472 DUF5569 Family of unknown function (DUF5569). This is a family of unknown function found in mammals. 225 matched cddid_all.tbl CDD pfam17730 pfam17730 465473 Centro_C10orf90 Centrosomal C10orf90. This is the N-terminal region found on proteins encoded by C10orf90. Most of the family members carry ALMS motif on their C-terminal pfam15309.SiRNA mediated functional analysis suggest that the C10orf90 encoded proteins have a role in centrosomal functions. 511 matched cddid_all.tbl CDD pfam17731 pfam17731 465474 DUF5570 Family of unknown function (DUF5570). This is a family of unknown function found in chordata. Family members contain a transmembrane region in the C-terminal and have been shown to be localized to the Golgi apparatus. 123 matched cddid_all.tbl CDD pfam17732 pfam17732 465475 DUF5571 Family of unknown function (DUF5571). This is a family of unknown function found in chordata. Family members carry a zinc finger family on the N-terminal pfam15663. 352 matched cddid_all.tbl CDD pfam17733 pfam17733 436001 DUF5572 Family of unknown function (DUF5572). This is a family of unknown function found in eukaryotes. Family members carry a highly conserved KPWE sequence at the C-terminal. 48 matched cddid_all.tbl CDD pfam17734 pfam17734 375300 Spt46 Spermatogenesis-associated protein 46. This family is found in chordata. Functional characterization studies showed that the deletion of Spata46 in mice resulted in subfertility with abnormal sperm head shape and a failure of sperm-egg fusion. Spata46 has also been shown to localize to the nuclear membrane by a transmembrane region in the N-terminal. 228 matched cddid_all.tbl CDD pfam17735 pfam17735 407610 BslA Biofilm surface layer A. This family includes members such as BslA (previously called YuaB). Secreted BslA from Bacillus subtillis has been shown to form surface layers around the biofilm self-assembling at interfaces of B. subtilis biofilms, forming an elastic film. structural analysis revealed that BslA consists of an Ig-type fold with the addition of an unusual, extremely hydrophobic cap region. The hydrophobic cap exhibits physiochemical properties similar to the hydrophobic surface found in fungal hydrophobins; thus, BslA is defined as member of a class of bacterially produced hydrophobins. 121 matched cddid_all.tbl CDD pfam17736 pfam17736 465476 Ig_C17orf99 C17orf99 Ig domain. This Ig domain is found in tandem in the uncharacterized human protein C17orf99, which is found across mammalian species. 95 matched cddid_all.tbl CDD pfam17737 pfam17737 436003 Ig_C19orf38 Ig domain in C19orf38 (HIDE1). This entry represents an Ig domain found in the uncharacterized human protein C19orf38, which is found across mammals. Family members have one predicted transmembrane region which is not included in this entry. The C19orf38 protein is also known as HIDE1 after Highly expressed in Immature DEndritic cell transcript 1 protein. 91 matched cddid_all.tbl CDD pfam17738 pfam17738 436004 DUF5575 Family of unknown function (DUF5575). This is a family of unknown function found in chordates. 309 matched cddid_all.tbl CDD pfam17739 pfam17739 465477 DUF5576 Family of unknown function (DUF5576). This is a family of unknown function found in Hominidae. 134 matched cddid_all.tbl CDD pfam17740 pfam17740 407613 DUF5577 Family of unknown function (DUF5577). This is a family of unknown function found in Metazoa. 334 matched cddid_all.tbl CDD pfam17741 pfam17741 436006 DUF5578 Family of unknown function (DUF5578). This is a family of unknown function found in Eukaryotes. 268 matched cddid_all.tbl CDD pfam17742 pfam17742 375307 DUF5579 Family of unknown function (DUF5579). This is a family of unknown function found in chordates. Family members carry one predicted transmembrane region. 202 matched cddid_all.tbl CDD pfam17743 pfam17743 465478 DUF5580 Family of unknown function (DUF5580). This is a family of unknown function found in metazoa. 547 matched cddid_all.tbl CDD pfam17744 pfam17744 465479 DUF5581 Family of unknown function (DUF5581). This is a family of unknown function found in chordates. 312 matched cddid_all.tbl CDD pfam17745 pfam17745 465480 Ydr279_N Ydr279p protein triple barrel domain. RNases H are enzymes that specifically hydrolyse RNA when annealed to a complementary DNA and are present in all living organizms. In yeast RNase H2 is composed of a complex of three proteins (Rnh2Ap, Ydr279p and Ylr154p), this family represents the homologs of Ydr279p. It is not known whether non yeast proteins in this family fulfil the same function. This domain corresponds to the N-terminal triple barrel domain. 66 matched cddid_all.tbl CDD pfam17746 pfam17746 436009 SfsA_N SfsA N-terminal OB domain. This family contains Sugar fermentation stimulation proteins. Which is probably a regulatory factor involved in maltose metabolism. This domain corresponds to the N-terminal OB fold. 66 matched cddid_all.tbl CDD pfam17747 pfam17747 436010 VID27_PH VID27 PH-like domain. This region has been predicted to contain a PH-like domain. 109 matched cddid_all.tbl CDD pfam17748 pfam17748 436011 VID27_N VID27 N-terminal region. This region may contain a PH domain. 173 matched cddid_all.tbl CDD pfam17749 pfam17749 465481 MIP-T3_C Microtubule-binding protein MIP-T3 C-terminal region. This protein, which interacts with both microtubules and TRAF3 (tumour necrosis factor receptor-associated factor 3), is conserved from worms to humans. The N-terminal region is the microtubule binding domain and is well-conserved; the C-terminal 100 residues, also well-conserved, constitute the coiled-coil region which binds to TRAF3. The central region of the protein is rich in lysine and glutamic acid and carries KKE motifs which may also be necessary for tubulin-binding, but this region is the least well-conserved. 154 matched cddid_all.tbl CDD pfam17750 pfam17750 407622 Reo_sigmaC_M Reovirus sigma C capsid protein triple beta spiral. This short region forms a triple beta spiral structural motif. 40 matched cddid_all.tbl CDD pfam17751 pfam17751 465482 SKICH SKICH domain. The SKICH domains of SKIP and PIPP mediate plasma membrane localization. The functions of the SKICH domains of NDP52 and CALCOCO1 are not known. 102 matched cddid_all.tbl CDD pfam17752 pfam17752 407624 BLF1 Burkholderia lethal factor 1. This family includes members such as BLF1 (Burkholderia lethal factor 1) also known as BPSL1549. BLF1 is a potent toxin from Burkholderia pseudomallei causing melioidosis. BLF1 interacts with the human translation factor eIF4A causing deamidation of Gln339 to Glu. Thereby, reducing endogenous host cell protein synthesis and triggering increased stress granule formation, which is associated with translational blocks. Structural analysis of BLF1 revealed an alpha/beta fold comprising a sandwich of two mixed beta-sheets surrounded by loops and alpha-helices, where the beta-sheet core of the catalytic pocket is structurally similar to that of the deamidase domain of CNF1 pfam05785. 213 matched cddid_all.tbl CDD pfam17753 pfam17753 465483 Ig_mannosidase Ig-fold domain. This Ig-like fold domain is found in mannosidase enzymes. 78 matched cddid_all.tbl CDD pfam17754 pfam17754 436014 TetR_C_14 MftR C-terminal domain. This domain is found at the C-terminus of TetR like transcription factors including the Mycofactin biosynthesis transcription factor. 112 matched cddid_all.tbl CDD pfam17755 pfam17755 465484 UvrA_DNA-bind UvrA DNA-binding domain. 110 matched cddid_all.tbl CDD pfam17756 pfam17756 465485 RET_CLD1 RET Cadherin like domain 1. RET is a single transmembrane-spanning receptor tyrosine kinase (RTK) that plays critical roles in the development of vertebrates. Structural analysis indicate that RET contains four consecutive cadherin-like domains (CLD). This entry relates to the first CLD at the N-terminal. Several regions within RET-CLD1 have been shown to be important for ligand-coreceptor binding. CLD1 and CLD2 have a distinctive clamshell shape and CLD1 is essential for CLD2 folding. CLD1 contains 2 sites for GDNF receptor alpha 1 binding. 124 matched cddid_all.tbl CDD pfam17757 pfam17757 465486 UvrB_inter UvrB interaction domain. This domain is found in the UvrB protein where it interacts with the UvrA protein. 91 matched cddid_all.tbl CDD pfam17758 pfam17758 436018 Prot_ATP_OB_N Proteasomal ATPase OB N-terminal domain. This is N-terminal oligonucleotide binding (OB) domain of proteasomal ATPase 62 matched cddid_all.tbl CDD pfam17759 pfam17759 465487 tRNA_synthFbeta Phenylalanyl tRNA synthetase beta chain CLM domain. This domain corresponds to the catalytic like domain (CLM) in the beta chain of phe tRNA synthetase. 214 matched cddid_all.tbl CDD pfam17760 pfam17760 436020 UvrA_inter UvrA interaction domain. This domain found in UvrA proteins interacts with the UvrB protein. 109 matched cddid_all.tbl CDD pfam17761 pfam17761 465488 DUF1016_N DUF1016 N-terminal domain. This family may include an HTH domain. 137 matched cddid_all.tbl CDD pfam17762 pfam17762 465489 HTH_ParB HTH domain found in ParB protein. 50 matched cddid_all.tbl CDD pfam17763 pfam17763 465490 Asparaginase_C Glutaminase/Asparaginase C-terminal domain. This domain is found at the C-terminus of asparaginase enzymes. 114 matched cddid_all.tbl CDD pfam17764 pfam17764 465491 PriA_3primeBD 3'DNA-binding domain (3'BD). This domain represents the N-terminal DNA-binding domain found in the PriA protein. The 3'BD, which has been shown to bind the 3' end of the leading-strand arm of replication fork structures. 96 matched cddid_all.tbl CDD pfam17765 pfam17765 465492 MLTR_LBD MmyB-like transcription regulator ligand binding domain. This domain is found in a family of actinobacterial transcription factors. The structure shows it has a PAS domain like fold and it is bound to Myristic acid. 168 matched cddid_all.tbl CDD pfam17766 pfam17766 465493 fn3_6 Fibronectin type-III domain. This FN3 like domain is found at the C-terminus of cucumisin proteins. 98 matched cddid_all.tbl CDD pfam17767 pfam17767 465494 NAPRTase_N Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain. Nicotinate phosphoribosyltransferase (EC:2.4.2.11) is the rate limiting enzyme that catalyzes the first reaction in the NAD salvage synthesis. This is the N-terminal domain of the enzyme. 125 matched cddid_all.tbl CDD pfam17768 pfam17768 465495 RecJ_OB RecJ OB domain. This OB-fold is found in RecJ proteins where is binds to ssDNA. 107 matched cddid_all.tbl CDD pfam17769 pfam17769 436029 PurK_C Phosphoribosylaminoimidazole carboxylase C-terminal domain. This entry represents the C-terminal domain of the PurK enzyme. 56 matched cddid_all.tbl CDD pfam17770 pfam17770 436030 RNase_J_C Ribonuclease J C-terminal domain. This domain is found at the C-terminus of Ribonuclease J proteins. Its function is unknown, but deletion of this domain causes dissociation to monomers. 102 matched cddid_all.tbl CDD pfam17771 pfam17771 465496 ADAMTS_CR_2 ADAMTS cysteine-rich domain 2. This cysteine rich domain is found in a variety of ADAMTS peptidases (A Disintegrin and Metalloproteinase with Thrombospondin Motifs) which is closely related to the ADAM family (pfam08516). Members of the ADAM-TS family have been implicated in a range of diseases. For instance, members of this family have been found to participate directly in processes in the central nervous system (CNS) such as the regulation of brain plasticity. 68 matched cddid_all.tbl CDD pfam17772 pfam17772 407644 zf-MYST MYST family zinc finger domain. This zinc finger domain is found in the MYST family of histone acetyltransferases. 55 matched cddid_all.tbl CDD pfam17773 pfam17773 465497 UPF0176_N UPF0176 acylphosphatase like domain. This domain is found at the N-terminus of UPF0176 family proteins. It adopts a fold similar to the pfam00708 family. 92 matched cddid_all.tbl CDD pfam17774 pfam17774 436033 YlmH_RBD Putative RNA-binding domain in YlmH. This domain adopts an RRM like fold and is found in the B. subtilis YlmH cell division protein. 84 matched cddid_all.tbl CDD pfam17775 pfam17775 465498 UPF0225 UPF0225 domain. This entry represents an NTF2-like domain found in bacterial proteins. 99 matched cddid_all.tbl CDD pfam17776 pfam17776 465499 NLRC4_HD2 NLRC4 helical domain HD2. This entry represents a helical domain found in the NLRC4 protein and NOD2 protein. 122 matched cddid_all.tbl CDD pfam17777 pfam17777 465500 RL10P_insert Insertion domain in 60S ribosomal protein L10P. This domain is found in prokaryotic and archaeal ribosomal L10 protein. 71 matched cddid_all.tbl CDD pfam17778 pfam17778 407650 BLACT_WH Beta-lactamase associated winged helix domain. This winged helix domain is found at the C-terminus of some beta lactamase enzymes. 46 matched cddid_all.tbl CDD pfam17779 pfam17779 465501 NOD2_WH NOD2 winged helix domain. This winged helix domain is found in the NOD2 protein. Its molecular function is not known. 57 matched cddid_all.tbl CDD pfam17780 pfam17780 465502 OCRE OCRE domain. The OCtamer REpeat (OCRE) has been annotated as a 42-residue sequence motif with 12 tyrosine residues in the spliceosome trans-regulatory elements RBM5 and RBM10 (RBM [RNA-binding motif]), which are known to regulate alternative splicing of Fas and Bcl-x pre-mRNA transcripts. The structure of the domain consists of an anti-parallel arrangement of six beta strands. 51 matched cddid_all.tbl CDD pfam17781 pfam17781 465503 RPN1_RPN2_N RPN1 N-terminal domain. This domain is found at the N-terminus of the 26S proteasome regulatory subunits RPN1 (also known as 26S proteasome non-ATPase regulatory subunit 2 (PMSD2). The domain is formed by an array of alpha helices. 301 matched cddid_all.tbl CDD pfam17782 pfam17782 436040 DprA_WH DprA winged helix domain. This winged helix domain is found in the DprA protein. 61 matched cddid_all.tbl CDD pfam17783 pfam17783 436041 CvfB_WH CvfB-like winged helix domain. This winged helix domain is found in RNA-binding proteins such as CvfB. 58 matched cddid_all.tbl CDD pfam17784 pfam17784 465504 Sulfotransfer_4 Sulfotransferase domain. This family of proteins are distantly related to sulfotransferase enzymes. This protein in S. mansonii has been shown to be involved in resistance to oxamniquine and to have sulfotransferase activity. 215 matched cddid_all.tbl CDD pfam17785 pfam17785 436043 PUA_3 PUA-like domain. This PUA-like domain is found at the N-terminus of SAM-dependent methyltransferases. 64 matched cddid_all.tbl CDD pfam17786 pfam17786 465505 Mannosidase_ig Mannosidase Ig/CBM-like domain. This domain corresponds to domain 4 in the structure of Bacteroides thetaiotaomicron beta-mannosidase, BtMan2A. This domain has an Ig-like fold. 90 matched cddid_all.tbl CDD pfam17787 pfam17787 465506 PH_14 PH domain. This entry corresponds to the PH domain found at the N-terminus of phospholipase C enzymes. 131 matched cddid_all.tbl CDD pfam17788 pfam17788 436045 HypF_C HypF Kae1-like domain. This domain is found in the HypF protein. In the structure it is one of the two subdomains of the Kae1 domain. 99 matched cddid_all.tbl CDD pfam17789 pfam17789 465507 MG4 Macroglobulin domain MG4. This domain is MG4 found in complement C3 and C5 proteins. 95 matched cddid_all.tbl CDD pfam17790 pfam17790 465508 MG1 Macroglobulin domain MG1. This entry represents the N-terminal macroglobulin domain found in complement proteins C3, C4 and C5. 101 matched cddid_all.tbl CDD pfam17791 pfam17791 465509 MG3 Macroglobulin domain MG3. This entry corresponds to the MG3 domain found in complement components C3, C4 and C5. 83 matched cddid_all.tbl CDD pfam17792 pfam17792 436049 ThiD2 ThiD2 family. This domain functions as a ThiD protein and is called the ThiD2 family. The domain is associated with the ThiE domain in some proteins. 124 matched cddid_all.tbl CDD pfam17793 pfam17793 436050 AHD ANC1 homology domain (AHD). This entry corresponds to the ANC1 homology domain (AHD) found in AF-9. 61 matched cddid_all.tbl CDD pfam17794 pfam17794 407666 Vault_2 Major Vault Protein repeat domain. This short domain is found repeated numerous times in the Major Vault Protein. This entry is related to pfam01505. 60 matched cddid_all.tbl CDD pfam17795 pfam17795 407667 Vault_3 Major Vault Protein Repeat domain. This domain is found in the Major Vault Protein. 62 matched cddid_all.tbl CDD pfam17796 pfam17796 407668 Vault_4 Major Vault Protein repeat domain. 61 matched cddid_all.tbl CDD pfam17797 pfam17797 465510 RL RL domain. The RRM-like (RL) domain is found in the N-terminal region of the polyA polymerase PAPD1. It contributes to PAPD1 dimerization and has a fold similar to RNP-type RBDs. 71 matched cddid_all.tbl CDD pfam17798 pfam17798 436052 TRIF-NTD TRIF N-terminal domain. The N-terminal domain of TRIF/TICAM-1 has a structure that consists of eight antiparallel helices. This domain believed to be involved in self-regulation of TRIF by interacting with its TIR domain. 157 matched cddid_all.tbl CDD pfam17799 pfam17799 436053 RRM_Rrp7 Rrp7 RRM-like N-terminal domain. This domain corresponds to the N-terminal RNA-binding domain found in the Rrp7 protein. It has an RRM-like fold with a circular permutation. 162 matched cddid_all.tbl CDD pfam17800 pfam17800 465511 NPL Nucleoplasmin-like domain. 90 matched cddid_all.tbl CDD pfam17801 pfam17801 465512 Melibiase_C Alpha galactosidase C-terminal beta sandwich domain. This domain is found at the C-terminus of alpha galactosidase enzymes. 74 matched cddid_all.tbl CDD pfam17802 pfam17802 465513 SpaA Prealbumin-like fold domain. This entry contains a prealbumin-like domain from a wide variety of bacterial surface proteins. This entry corresponds to domain 1 and domain 3 of SpaA from Corynebacterium diphtheriae. Some members of this family contain an isopeptide bond. 72 matched cddid_all.tbl CDD pfam17803 pfam17803 465514 Cadherin_4 Bacterial cadherin-like domain. This entry contains numerous bacterial cadherin-like domains found in extracelullar proteins. 71 matched cddid_all.tbl CDD pfam17804 pfam17804 436058 TSP_NTD Tail specific protease N-terminal domain. The N-terminal domain of tail specific proteases has a novel fold composed of 10 alpha helices. 188 matched cddid_all.tbl CDD pfam17805 pfam17805 436059 AsnC_trans_reg2 AsnC-like ligand binding domain. This entry contains an AsnC-like ligand binding domain. 82 matched cddid_all.tbl CDD pfam17806 pfam17806 375343 SO_alpha_A3 Sarcosine oxidase A3 domain. This short domain is found in Heterotetrameric Sarcosine Oxidase's alpha A3 domain. This domain binds to FMN in sarcosine oxidase. This domain is related to pfam04324 but lacks its iron binding cysteine residues. 87 matched cddid_all.tbl CDD pfam17807 pfam17807 407678 zf-UBP_var Variant UBP zinc finger. This domain is found in ubiquitin C-terminal hydrolase enzymes and is related to the pfam02148 domain. However, it has an altered pattern of zinc binding residues. 64 matched cddid_all.tbl CDD pfam17808 pfam17808 375345 fn3_PAP Fn3-like domain from Purple Acid Phosphatase. This entry represents an N-terminal Fn3-like domain found at the N-terminus of purple acid phosphatase enzymes. 118 matched cddid_all.tbl CDD pfam17809 pfam17809 375346 UPA_2 UPA domain. The UPA domain is conserved in UNC5, PIDD, and Ankyrins. It has a beta sandwich structure. 131 matched cddid_all.tbl CDD pfam17810 pfam17810 436060 Arg_decarb_HB Arginine decarboxylase helical bundle domain. This entry represents a helical bundle domain that is found between the two enzymatic domains of the arginine decarboxylases. 84 matched cddid_all.tbl CDD pfam17811 pfam17811 465515 JHD Jumonji helical domain. This 4-helix bundle domain is associated with the Jumonji domain pfam02373. 104 matched cddid_all.tbl CDD pfam17812 pfam17812 465516 RET_CLD3 RET Cadherin like domain 3. RET is a single transmembrane-spanning receptor tyrosine kinase (RTK) that plays critical roles in the development of vertebrates. Structural analysis indicate that RET contains four consecutive cadherin-like domains (CLD). This entry relates to CLD3. Classical cadherin calcium-coordinating motifs can be found between CLD2 and CLD3. 114 matched cddid_all.tbl CDD pfam17813 pfam17813 465517 RET_CLD4 RET Cadherin like domain 4. RET is a single transmembrane-spanning receptor tyrosine kinase (RTK) that plays critical roles in the development of vertebrates. Structural analysis indicate that the ligand-binding RET ectodomain (RET-ECD) contains four consecutive cadherin-like domains (CLD1-CLD4) followed by a membrane-proximal cysteine-rich domain (CRD). This entry relates to CLD4 which is required for CRD folding. 104 matched cddid_all.tbl CDD pfam17814 pfam17814 375350 LisH_TPL LisH-like dimerization domain. TOPLESS (TPL) proteins have a highly conserved N-terminal domain containing a lissencephaly homologous (LisH) dimerization motif. 30 matched cddid_all.tbl CDD pfam17815 pfam17815 436064 PDZ_3 PDZ domain. This entry contains the second PDZ domain from plant peptidases such as Deg2. This domain is involved in cage assembly. 145 matched cddid_all.tbl CDD pfam17816 pfam17816 407684 PDZ_4 PDZ domain. This entry represents a PDZ domain that is found in the CPAF protein from chlamydia trachomatis. 114 matched cddid_all.tbl CDD pfam17817 pfam17817 465518 PDZ_5 PDZ domain. This entry corresponds to PDZ domains found in neurabin and spinophilin proteins. The PDZ domain in spinophilin mediates its interaction with protein phosphatase PP1. 71 matched cddid_all.tbl CDD pfam17818 pfam17818 407686 KCT2 Keratinocyte-associated gene product. This entry includes Keratinocyte-associated transmembrane protein 2 found in humans. Functional studies show that KCP2 localizes to the endoplasmic reticulum, consistent with a role in protein biosynthesis, and has a functional KKxx retrieval signal at its cytosolic C-terminus. 187 matched cddid_all.tbl CDD pfam17819 pfam17819 465519 DUF5582 Family of unknown function (DUF5582). This is a family of unknown function found in chordata. 146 matched cddid_all.tbl CDD pfam17820 pfam17820 436067 PDZ_6 PDZ domain. This entry represents the PDZ domain from a wide variety of proteins. 54 matched cddid_all.tbl CDD pfam17821 pfam17821 436068 DUF5583 Family of unknown function (DUF5583). This is a family of unknown function found in chordata. 130 matched cddid_all.tbl CDD pfam17822 pfam17822 465520 ARMH2 Armadillo-like helical domain-containing protein 2. The function of this Armadillo-like helical domain-containing protein is not known. 229 matched cddid_all.tbl CDD pfam17823 pfam17823 465521 DUF5585 Family of unknown function (DUF5585). This is a family of unknown function found in chordata. 506 matched cddid_all.tbl CDD pfam17824 pfam17824 465522 DUF5586 Family of unknown function (DUF5586). This is a family of unknown function found in chordata. 402 matched cddid_all.tbl CDD pfam17825 pfam17825 465523 DUF5587 Family of unknown function (DUF5587). This is a family of unknown function found in chordata. 1442 matched cddid_all.tbl CDD pfam17826 pfam17826 465524 DUF5588 Family of unknown function (DUF5588). This is a family of unknown function found in chordata. 362 matched cddid_all.tbl CDD pfam17827 pfam17827 436073 PrmC_N PrmC N-terminal domain. This entry corresponds to the N-terminal alpha helical domain of the HemK protein. HemK is a methyltransferase enzyme that carries out the methylation of the N5 nitrogen of the glutamine found in the conserved GGQ motif of class-1 release factors. 71 matched cddid_all.tbl CDD pfam17828 pfam17828 407694 FAS_N N-terminal domain in fatty acid synthase subunit beta. This entry represents the N-terminal domain found in fatty acid synthase proteins such as Swiss:P07149. 127 matched cddid_all.tbl CDD pfam17829 pfam17829 436074 GH115_C Gylcosyl hydrolase family 115 C-terminal domain. This domain is found at the C-terminus of glycosyl hydrolase family 115 proteins. This domain has a beta-sandwich fold. 172 matched cddid_all.tbl CDD pfam17830 pfam17830 436075 STI1 STI1 domain. This entry corresponds to the STI1 domain that is found in two copies in the Sti1 protein. 55 matched cddid_all.tbl CDD pfam17831 pfam17831 465525 PDH_E1_M Pyruvate dehydrogenase E1 component middle domain. This entry represents one of the thiamin diphosphate-binding domains found in pyruvate dehydrogenase E1 component. 229 matched cddid_all.tbl CDD pfam17832 pfam17832 436077 Pre-PUA Pre-PUA-like domain. This Pre-PUA-like domain is found in a wide variety of proteins including the eukaryotic translation initiation factor 2D, where it is found at the N-terminus. 86 matched cddid_all.tbl CDD pfam17833 pfam17833 436078 UPF0113_N UPF0113 Pre-PUA domain. 77 matched cddid_all.tbl CDD pfam17834 pfam17834 436079 GHD Beta-sandwich domain in beta galactosidase. This entry corresponds to a beta sandwich like domain found in glycosyl hydrolase family 35 beta galactosidase enzymes. 72 matched cddid_all.tbl CDD pfam17835 pfam17835 436080 NOG1_N NOG1 N-terminal helical domain. This domain is found at the N-terminus of NOG1 GTPase proteins. 160 matched cddid_all.tbl CDD pfam17836 pfam17836 436081 PglD_N PglD N-terminal domain. This alpha/beta domain is found at the N-terminus of proteins such as PglD. This domain binds a UDP-sugar substrate. 78 matched cddid_all.tbl CDD pfam17837 pfam17837 465526 4PPT_N 4'-phosphopantetheinyl transferase N-terminal domain. This entry represents the N-terminal domain from 4'- phosphopantetheinyl transferase enzymes. This domain is structurally related to the pfam01648 domain with which it forms a pseudodimeric arrangement. 68 matched cddid_all.tbl CDD pfam17838 pfam17838 436083 PH_16 PH domain. 127 matched cddid_all.tbl CDD pfam17839 pfam17839 465527 CNP_C_terminal C-terminal domain of cyclic nucleotide phosphodiesterase. This is the C-temrinal domain found in Listeria monocytogenes, Lmo2642 cyclic nucleotide phosphodiesterase. The auxiliary C-terminal domain, consists of five alpha-helices forming a long helical bundle, and is connected to the catalytic domain pfam00149 by two loop segments. It is suggested that this auxiliary domain of Lmo2642 might confer functional specificity to the protein through the interactions with unknown factors or involving the substrate recognition. 108 matched cddid_all.tbl CDD pfam17840 pfam17840 465528 Tugs Tethering Ubl4a to BAGS domain. This is the C-terminal domain of Ubiquitin-like protein 4A an ortholog of yeast Get5. In budding yeast, GET proteins directly mediate the insertion of newly synthesized TA proteins into endoplasmic reticulum membranes. Similarly, mammalian BAG6, Ubl4a, and SGTA make up a trimeric complex that binds TA proteins post-translationally and then loads them onto the cytosolic ATPase TRC40, which in turn targets them to the endoplasmic reticulum. Structural studies show that this C-terminal TUGS domain of Ubl4a is essential for BAG6 tethering. Given that BAG6 mediates oligomeric complex formation of Ubl4a, TRC35, and TRC40 (mammalian counterparts of Get5, Get4, and Get3, respectively), the C-terminal TUGS domain might be crucial for supporting BAG6-mediated Ubl4a-TRC35 complex formation in humans as an alternative to the direct Get5-Get4 interaction in yeast. 47 matched cddid_all.tbl CDD pfam17841 pfam17841 436086 Bep_C_terminal BID domain of Bartonella effector protein (Bep). This entry is the BID (Bep intracellular delivery) domain located at the C-terminal of Bartonella effector proteins (Beps). It functions as a secretion signal in a subfamily of protein substrates of bacterial type IV secretion (T4S) systems. It mediates transfer of (1) relaxases and the attached DNA during bacterial conjugation, and (2) numerous Beps during protein transfer into host cells infected by pathogenic Bartonella species. Crystal structure of several representative BID domains show a conserved fold characterized by a compact, antiparallel four-helix bundle topped with a hook. 97 matched cddid_all.tbl CDD pfam17842 pfam17842 465529 dsRBD2 Double-stranded RNA binding domain 2. This domain is found in HEN1 proteins from Arabidopsis. Structural characterization reveal that small RNA substrate bind to two double-stranded RNA (dsRNA)-specific binding domains, dsRBD1 and dsRBD2. This entry relates to dsRBD2 which together with dsRBD1 forms a strong grip on the duplex region of the small RNA substrate, and these interactions help position the other duplex terminus towards the MTase domain pfam13847. 147 matched cddid_all.tbl CDD pfam17843 pfam17843 436088 MycE_N MycE methyltransferase N-terminal. This is the N-terminal domain found in MycE from the mycinamicin biosynthetic pathway. MycE is a tetramer of a two-domain polypeptide, comprising a C-terminal catalytic MT domain and an N-terminal auxiliary domain, which is important for quaternary assembly and for substrate binding. 111 matched cddid_all.tbl CDD pfam17844 pfam17844 465530 SCP_3 Bacterial SCP ortholog. This domain is found in MSMEG_5817 gene product from M. smegmatis. It has been shown to be vital for mycobacterial survival within host macrophages. Crystal structure revealed a Rossmann-like fold alpha/beta two-layer sandwich forming a highly hydrophobic interface cavity and with high structural homology to the SCP family. Hence, it has been suggested that this domain may be involved in the interaction of apolar ligands through its hydrophobic cavity. Alanine-scanning mutagenesis of the hydrophobic cavity of MSMEG_5817 protein demonstrated that the conserved Val82 residue plays an important role in ligand binding. 93 matched cddid_all.tbl CDD pfam17845 pfam17845 407710 FbpC_C_terminal FbpC C-terminal regulatory nucleotide binding domain. Most functional ABC transporters are composed of at least four sub-units: two trans-membrane (TM) domains where the transport process takes place and two cytoplasmic nucleotide binding domains (NBDs) providing the energy required for active transport. This entry is one of the two NBDs found at the the C-terminal domain of FbpC, ferric iron uptake transporter, from the Neisseria gonorrhoeae. The C-terminal regulatory domain adopts two OB-folds per monomer. These are similar in topology to those seen in the NBD (nucleotide binding domain) from the maltose uptake ABC transporter, MalK. However, FbpC does not open as far as MalK when ATP is removed from their respective closed structures. This difference was suggested to be due to the substantial domain swap in the regulatory domain of FbpC. 55 matched cddid_all.tbl CDD pfam17846 pfam17846 375377 XRN_M Xrn1 helical domain. This helical domain is part of the Xrn1 catalytic core. Xrn1 is a cytoplasmic 5'-3' exonuclease that degrades decapped mRNAs. 442 matched cddid_all.tbl CDD pfam17847 pfam17847 375378 GlcV_C_terminal Glucose ABC transporter C-terminal domain. This is the C-terminal domain found at the ATPase subunit of the glucose ABC transporter from Sulfolobus solfataricus. Overall, the C-terminal domain (residues 243-353) contains only beta-strands, which form an elongated barrel-shaped structure composed of two parts. This entry represents the upper part which includes a three-stranded anti-parallel beta-sheets and two small anti-parallel beta-strands. The overall structure of this domain is very similar to that of the C-terminal domain of MalK from T. litoralis however, the function of the C-terminal domain in GlcV is not clear. 61 matched cddid_all.tbl CDD pfam17848 pfam17848 436090 zf-ACC Acetyl-coA carboxylase zinc finger domain. Acetyl-coA carboxylase (ACC) is a central metabolic enzyme that catalyzes the committed step in fatty acid biosynthesis: biotin- dependent conversion of acetyl-coA to malonyl-coA. In bacteria this protein contains a small zinc finger domain. 26 matched cddid_all.tbl CDD pfam17849 pfam17849 436091 OB_Dis3 Dis3-like cold-shock domain 2 (CSD2). This domain has an OB fold and is found in the Dis3l2 protein. This domain along with CSD1 binds to RNA. 77 matched cddid_all.tbl CDD pfam17850 pfam17850 465531 CysA_C_terminal CysA C-terminal regulatory domain. ABC (ATP-binding cassette) transporters share a common architecture comprising two variable hydrophobic transmembrane domains (TMDs) that form the translocation pathway and two conserved hydrophilic ABC-ATPases that hydrolyze ATP. This is the C-terminal regulatory domain found at the ATPase subunit of CysA, a putative sulfate ABC transporter from Alicyclobacillus acidocaldarius. The regulatory domain of CysA is built up of an elongated beta-barrel composed of two beta-sandwiches that form a common hydrophobic core. 43 matched cddid_all.tbl CDD pfam17851 pfam17851 436093 GH43_C2 Beta xylosidase C-terminal Concanavalin A-like domain. This domain is found to the C-terminus of the pfam04616 domain. This domain adopts a concanavalin A-like fold. 203 matched cddid_all.tbl CDD pfam17852 pfam17852 465532 Dynein_AAA_lid Dynein heavy chain AAA lid domain. This entry corresponds to the extension domain of AAA domain 5 in the dynein heavy chain. This domain is composed of 8 alpha helices. 126 matched cddid_all.tbl CDD pfam17853 pfam17853 465533 GGDEF_2 GGDEF-like domain. This domain is distantly related to the GGDEF domain, suggesting these may by diguanylate cyclase enzymes. 116 matched cddid_all.tbl CDD pfam17854 pfam17854 436096 FtsK_alpha FtsK alpha domain. FtsK is a DNA translocase that coordinates chromosome segregation and cell division in bacteria. In addition to its role as activator of XerCD site-specific recombination, FtsK can translocate double-stranded DNA (dsDNA) rapidly and directionally and reverse direction. FtsK can be split into three domains called alpha (this entry), beta and gamma. The alpha and beta domains contain the core ATPase machinery of the DNA translocase. 101 matched cddid_all.tbl CDD pfam17855 pfam17855 465534 MCM_lid MCM AAA-lid domain. This entry represents the AAA-lid domain found in MCM proteins. 86 matched cddid_all.tbl CDD pfam17856 pfam17856 436097 TIP49_C TIP49 AAA-lid domain. This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases. 66 matched cddid_all.tbl CDD pfam17857 pfam17857 465535 AAA_lid_1 AAA+ lid domain. This domain represents the AAA lid domain from dynein heavy chain D3. 100 matched cddid_all.tbl CDD pfam17858 pfam17858 375386 Defensin_int Platypus intermediate defensin-like peptide. This entry represents a defensin like peptide identified in the platypus genome. Structurally it resembles the beta defensins. The peptide was found to display potent antimicrobial activity against Staphylococcus aureus and Pseudomonas aeruginosa. 44 matched cddid_all.tbl CDD pfam17859 pfam17859 375387 Pelovaterin Pelovaterin. The pelovaterin peptide is a major intracrystalline peptide found in turtle eggshell. The global fold of pelovaterin is similar to that of human beta-defensins. Pelovaterin exhibits strong antimicrobial activity against two pathogenic gram-negative bacteria, Pseudomonas aeruginosa and Proteus vulgaris. 42 matched cddid_all.tbl CDD pfam17860 pfam17860 375388 Defensin_RK-1 RK-1-like defensin. This family includes RK-1 a defensin like peptide from rabbit kidney. The family also includes some rat alpha defensins. 34 matched cddid_all.tbl CDD pfam17861 pfam17861 465536 Laterosporulin Laterosporulin defensin-like peptide. This entry corresponds to a bacteriocin from the bacterium Brevibacillus laterosporus called laterosporulin. This peptide has a defensin-like structure. 49 matched cddid_all.tbl CDD pfam17862 pfam17862 465537 AAA_lid_3 AAA+ lid domain. This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains. 45 matched cddid_all.tbl CDD pfam17863 pfam17863 465538 AAA_lid_2 AAA lid domain. This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains. 73 matched cddid_all.tbl CDD pfam17864 pfam17864 380039 AAA_lid_4 RuvB AAA lid domain. The RuvB protein makes up part of the RuvABC revolvasome which catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalyzed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This entry contains the AAA lid domain that is found to the C-terminus of the AAA domain. 74 matched cddid_all.tbl CDD pfam17865 pfam17865 407722 AAA_lid_5 Midasin AAA lid domain. This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains. This lid domain is found in midasin proteins. 104 matched cddid_all.tbl CDD pfam17866 pfam17866 465539 AAA_lid_6 AAA lid domain. This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains. 60 matched cddid_all.tbl CDD pfam17867 pfam17867 465540 AAA_lid_7 Midasin AAA lid domain. This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains. This lid domain is found in midasin proteins. 106 matched cddid_all.tbl CDD pfam17868 pfam17868 465541 AAA_lid_8 AAA lid domain. This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains. 72 matched cddid_all.tbl CDD pfam17869 pfam17869 465542 Cys_box Anosmin cysteine rich domain. This is the Cys-box (cysteine-rich) domain found on the N-terminal of anosmin-1 proteins. It is suggested that the Cys-box domain may resemble the cysteine-rich region of the insulin-like growth factor receptor. Family members are found in chordates. 82 matched cddid_all.tbl CDD pfam17870 pfam17870 465543 Insulin_TMD Insulin receptor trans-membrane segment. This entry represents the trans-membrane domain (TMD) found in insulin receptor proteins. The TMD of the insulin receptor is within the beta-subunit and contains 23 amino acids. Mutations in the TMD were shown to have effects on receptor biosynthetic processing and kinase activation. Substitution of the entire TMD of the insulin receptor (IR) resulted in constitutive kinase activation in vitro, while replacing the TMD with that of glycophorin A inhibited insulin action. Structural studies show that TMD contains a helix and a kink when it is purified in dodecylphosphocholine (DPC) micelles. The residues 942-948 preceding the TMD have a propensity to be a short helix and may interact with membrane. 47 matched cddid_all.tbl CDD pfam17871 pfam17871 465544 AAA_lid_9 AAA lid domain. This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains. 104 matched cddid_all.tbl CDD pfam17872 pfam17872 407729 AAA_lid_10 AAA lid domain. This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains. 99 matched cddid_all.tbl CDD pfam17873 pfam17873 375396 Rep_1B Replicase polyprotein 1ab. This entry relates to a regulatory domain found in replicase polyprotein 1ab found in Arterivirus. Structural studies of arterivirus helicase (nsp10), indicate that this domain undergoes conformational changes on substrate binding. Besides the large conformational change, it is suggested that the regions at the surface of domain 1B not directly involved in DNA binding may become flexible. For example, domain 1B residues Arg95, Gly125 and Ala131 become disordered after DNA binding. Together with domains 1A and 2A it forms a nucleic acid-binding channel where the single-stranded part of the DNA substrate is bound to. 53 matched cddid_all.tbl CDD pfam17874 pfam17874 436107 TPR_MalT MalT-like TPR region. This entry contains a series of TPR repeats. 336 matched cddid_all.tbl CDD pfam17875 pfam17875 465545 RPA43_OB RPA43 OB domain in RNA Pol I. This is OB domain found in RPA43 proteins (DNA-directed RNA polymerase I subunit RPA43, also known as A43) in yeast. Functional analysis of RNA polymerase I show that, subunits A14 and A43 form the heterodimer A14/43, which is distantly related to Rpb4/7 in Pol II and C17/25 in Pol III. Crystal structure analysis show that A43-A14 heterodimer forms the stalk that provides a platform for initiation factors and interacts with newly synthesized RNA. 114 matched cddid_all.tbl CDD pfam17876 pfam17876 465546 CSD2 Cold shock domain. Crystallographic structure analysis of E. coli wild-type RNase II revealed that the amino-terminal region starts with an alpha-helix followed by two consecutive five-stranded anti-parallel beta-barrels, identified as cold-shock domains (CSD1 and CSD2). This entry relates to CSD2 which lacks the typical sequence motifs RNPI and RNPII but contributes to RNA binding. 74 matched cddid_all.tbl CDD pfam17877 pfam17877 465547 Dis3l2_C_term DIS3-like exonuclease 2 C terminal. This is the C-terminal S1 domain found in Dis3L2 proteins. Dis3L2 belongs to the RNase II/R 3-5 exonuclease superfamily, which includes the catalytic subunit of the RNA exosome in yeast and in humans. 87 matched cddid_all.tbl CDD pfam17878 pfam17878 465548 ssDBP Single-stranded DNA-binding protein. Family members include single-stranded DNA binding protein encoded by the filamentous Pseudomonas bacteriophage Pf3. 72 matched cddid_all.tbl CDD pfam17879 pfam17879 375400 DNA_ligase_C DNA ligase C-terminal domain. This is the C-terminal domain found in ATP-Dependent DNA Ligase from Bacteriophage T7. This domain has no ligase activity, however together with the N-terminal domain they bind to double-stranded DNA consistent with the idea that the DNA-binding site is between the domains in the intact protein. Furthermore, although the fold of domain 2 is very similar to a number of other proteins that bind single-stranded DNA, this domain does not bind to single-stranded DNA but instead has a high affinity for double-stranded DNA. 109 matched cddid_all.tbl CDD pfam17880 pfam17880 407735 Yos9_DD Yos9 dimerzation domain. This is the dimerization domain (DD) found in Yos9 proteins in yeast. Structural analysis revealed that this domain contributes to self association of Yos9. The overall fold of the domain can be classified as an alpha-beta-roll architecture, comprising two alpha-helices and seven beta-strands. 128 matched cddid_all.tbl CDD pfam17881 pfam17881 465549 DUF5590 Domain of unknown function (DUF5590). This is a domain of unknown function found in bacterial proteins. 45 matched cddid_all.tbl CDD pfam17882 pfam17882 465550 SBD OAA-family lectin sugar binding domain. This domain is found in agglutinin family of lectins. Oscillatoria agardhii agglutinin (OAA)- family lectins comprise either one or two homologous domains, with a single domain possessing two glycan binding sites. OAA is one of the lectins with anti-HIV activity. This sugar binding domain is also found in Pseudomonas fluorescens agglutinin (PFA) and myxobacterial hemagglutinin (MBHA), where MBHA contains two sugar-binding domains (i.e. 4 sugar binding sites), whereas OAA and PFA are single-domain proteins (i.e. 2 sugar binding sites). 76 matched cddid_all.tbl CDD pfam17883 pfam17883 465551 MBG MBG domain. This domain is found in a variety of bacterial extracellular proteins. Although initially described as having a divergent Ig fold this domain has a novel topology that is like a mirror image of the beta grasp fold. Hence the name of Mirror Beta Grasp (MBG) domain. 98 matched cddid_all.tbl CDD pfam17884 pfam17884 436115 DUF5591 Domain of unknown function (DUF5591). This is a domain of unknown function found in archaeal tRNA-guanine transglycosylase (EC:2.4.2.48) and in archaeosine synthase (EC:2.6.1.97) proteins. 150 matched cddid_all.tbl CDD pfam17885 pfam17885 436116 Smoa_sbd Styrene monooxygenase A putative substrate binding domain. This domain is found in the 46 kDa FAD-specific styrene epoxidase (SMOA) protein, comprises a part of the styrene monooxygenase (SMO) two-component flavoprotein monooxygenase enzyme. Structural analysis indicates that SMOA monomer comprises two globular domains spanned by a long alpha-helix. This domain contains a putative substrate binding site. 108 matched cddid_all.tbl CDD pfam17886 pfam17886 436117 ArsA_HSP20 HSP20-like domain found in ArsA. This domain is found at the C-terminus of ArsA like proteins. This domain is related to HSP20. 63 matched cddid_all.tbl CDD pfam17887 pfam17887 465552 Jak1_Phl Jak1 pleckstrin homology-like domain. This entry is for the pleckstrin homology-like (PHL) subdomain found in Jak1 proteins. JAK1 is a member of the Janus kinase (JAK) family of non-receptor tyrosine kinases that are activated in response to cytokines and interferons. PHL (residues 283-419) together with the N-terminal ubiquitin-like subdomain (residues 36-111) and an acyl-coenzyme A binding protein-like subdomain (residues 148-282), associate into a canonical tri-lobed FERM domain. 140 matched cddid_all.tbl CDD pfam17888 pfam17888 436119 Carm_PH Carmil pleckstrin homology domain. This is a non-canonical pleckstrin homology (PH) domain connected to a 16-leucine-rich repeat domain found in CARMIL (CP Arp2/3 complex myosin-I linker) proteins. The PH domain is interconnected with an N-terminal helix (N-helix), residues 10-20 and a C-terminal linker (Linker), residues 129-147 in Swiss:Q6EDY6. Structural and functional studies indicate that the PH domain involved in direct binding to the PM (plasma membrane) and a HD (helical domain) responsible for antiparallel dimerization and enhancement of CARMIL's membrane-binding activity. Furthermore, it appears that CARMIL's PH domain mediates non-specific binding to the membrane, in contrast to other PH domains that bind polyphosphorylated phosphatidylinositides, which are thought to function as signalling lipids. 94 matched cddid_all.tbl CDD pfam17889 pfam17889 436120 NLRC4_HD NLRC4 helical domain. This is a helical domain found in NLRC4, Nucleotide-binding and oligomerization domain-like receptor (NLR) proteins. Structural and functional studies indicate that the helical domain HD2 repressively contacted a conserved and functionally important alpha-helix of the NBD (nucleotide binding domain) in Swiss:Q3UP24. Furthermore, the HD2 domain was shown to cap the N-terminal side of the LRR (leucine-rich repeat) domain via extensive interactions. Other family members carrying this domain include baculoviral IAP repeat-containing protein 1 (Birc1) also known as neuronal apoptosis inhibitory protein (Naip). 106 matched cddid_all.tbl CDD pfam17890 pfam17890 436121 WW_like Peptidoglycan hydrolase LytB WW-like domain. Structural analysis revealed that the catalytic domain of LytB consists of three structurally independent modules: SH3b, WW domain-like, and the glycoside hydrolase family 73 (GH73). This entry is the WW like domain found in endo-beta-N-acetylglucosaminidase LytB from Streptococcus pneumoniae. Functional analysis show that the deletion of both SH3b and WW modules almost completely abolished the activity of LytB. Furthermore, it was shown that the SH3b and WW modules are indispensable for LytB in cell separation. 53 matched cddid_all.tbl CDD pfam17891 pfam17891 436122 FluMu_N Mu-like prophage FluMu N-terminal domain. Structural analysis of HI1506 (also known as Mu-like prophage FluMu protein gp35) from Haemophilus influenzae show that HI1506 consists of two structured domains connected by an unstructured 30 amino acid loop. This entry is the N-terminal domain which comprises a three-stranded antiparallel beta-sheet packed against an alpha-helix. 49 matched cddid_all.tbl CDD pfam17892 pfam17892 436123 Cadherin_5 Cadherin-like domain. 98 matched cddid_all.tbl CDD pfam17893 pfam17893 465553 Cas9_b_hairpin CRISPR-associated endonuclease Cas9 beta-hairpin domain. This is beta-hairpin domain found in Cas9 proteins from Actinobacteria. The beta-hairpin domain is not conserved in all type II-C Cas9 proteins. The beta-hairpin in Cas 9 from Streptococcus pyogenes blocks the HNH domain active site. 90 matched cddid_all.tbl CDD pfam17894 pfam17894 465554 Cas9_Topo Topo homolgy domain in CRISPR-associated endonuclease Cas9. This is the Topo-homology domain found in Cas9 proteins from Actinobacteria. This domain bears structural similarity to a domain found in topoisomerase II. 71 matched cddid_all.tbl CDD pfam17895 pfam17895 407749 Dicer_N Giardia Dicer N-terminal domain. This is the N-terminal domain found in dicer proteins from Giardia intestinalis. The N-terminal region (i.e. the platform domain) forms a flat surface composed of antiparallel beta sheet and three alpha helices. This surface contains a large positively charged region that could interact directly with the negatively charged phosphodiester backbone of the modeled dsRNA helix. 144 matched cddid_all.tbl CDD pfam17896 pfam17896 465555 NSP2_gammaCoV Non-structural protein 2, gammacoronavirus. Avian infectious bronchitis virus (IBV) is a gammacoronavirus that belongs to Group III of coronaviruses. They have a large genome containing the replicase gene consisting of two large ORFs, ORF1a and 1b that encode two replicase polyproteins ppa1a/1ab, which are then auto-proteolytically processed into 15 or 16 matured nonstructural proteins to achieve viral genomic replication, assembly and maturation. This group contains avian viruses and differs from the other groups in that they do not encode the essential pathogenic factor non-structural protein 1 (NSP1) and instead start with NSP2. IBV NSP2 is one of the first replicase proteins to be translated and processed in the viral life cycle. NSP2 is a weak protein kinase R (PKR) antagonist, which may suggest that it plays a role in interfering with intracellular immunity. 358 matched cddid_all.tbl CDD pfam17897 pfam17897 436126 VCPO_N Vanadium chloroperoxidase N-terminal domain. This is the N-terminal domain found in Vanadium chloroperoxidase proteins found in fungi. 215 matched cddid_all.tbl CDD pfam17898 pfam17898 436127 GerD Spore germination GerD central core domain. This is the central core domain found in GerD from a thermophilic Bacillus. GerD plays a critical role in nutrient receptor-mediated spore germination in Bacillus species. The crystal structure of GerD reveals this domain as a trimeric superhelical rope fold. Alterations in GerD structure have profound effects on spores' nutrient germination. 114 matched cddid_all.tbl CDD pfam17899 pfam17899 465556 Peptidase_M61_N Peptidase M61 N-terminal domain. This domain is found at the N-terminus of pfam05299 and has a beta sandwich-like fold with similarity to the baculovirus p35 protein. 168 matched cddid_all.tbl CDD pfam17900 pfam17900 465557 Peptidase_M1_N Peptidase M1 N-terminal domain. This domain is found at the N-terminus of aminopeptidases from the M1 family. 186 matched cddid_all.tbl CDD pfam17901 pfam17901 375414 EF-hand_12 EF-hand fold domain. This domain is found in Dd-STATa, a STAT protein (Signal transducer and activator of transcription A) which transcriptionally regulates cellular differentiation in Dictyostelium discoideum. The EF-hand domains predicted to contain several basic residues that lie close to the DNA backbone. 93 matched cddid_all.tbl CDD pfam17902 pfam17902 407754 SH3_10 SH3 domain. This entry represents an SH3 domain. 65 matched cddid_all.tbl CDD pfam17903 pfam17903 407755 KH_8 Krr1 KH1 domain. This entry represents the first KH domain in the KRR1 protein. Krr1 is a ribosomal assembly factor. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif and is involved in binding another assembly factor, Kri1. 81 matched cddid_all.tbl CDD pfam17904 pfam17904 436130 KH_9 FMRP KH0 domain. This entry corresponds to the KH0 domain from the FMRP protein. This is a divergent KH domain that was discovered through solving the structure of an N-terminal fragment of the FMRP protein. KH0 does not have the canonical G-X-X-G motif between helices A and B. It has been suggested that this domain may be involved in RNA binding. 85 matched cddid_all.tbl CDD pfam17905 pfam17905 407757 KH_10 GLD-3 KH domain 5. This entry corresponds to KH5 of the GLD-3 protein. The 4 KH domains KH2 to KH5 form a proteolytically stable structure. 95 matched cddid_all.tbl CDD pfam17906 pfam17906 465558 HTH_48 HTH domain in Mos1 transposase. The N-terminal domain of the Mos1 Mariner transposase comprises two HTH domains. This HTH domain binds in the DNA major groove to the transposons inverted repeats. 50 matched cddid_all.tbl CDD pfam17907 pfam17907 465559 AWS AWS domain. This entry represents the AWS (associated with SET domain) domain. This is a zinc binding domain. The full AWS domain contains 8 cysteines. This entry represents the N-terminal part of the domain, with the C-terminal part interwoven with the SET domain. 39 matched cddid_all.tbl CDD pfam17908 pfam17908 465560 APAF1_C APAF-1 helical domain. This domain represents the C-terminal alpha helical domain of the apoptotic Apaf-1 protein. 135 matched cddid_all.tbl CDD pfam17909 pfam17909 375422 Htr2 Htr2 transmembrane domain. Archaebacterial photoreceptors mediate phototaxis by regulating cell motility through two-component signaling cascades like those found in chemotaxis signaling chains of enteric bacteria. The photoreceptor sensory rhodopsin II from N. pharaonis (NpSRII) in complex with its cognate transducer NpHtrII serves as a system for transmembrane signal transfer. This entry is for the transmembrane domain of the transducer HtrII. Studies suggest that conformation changes of the NpSRII/NpHtrII complex may be crucial for the mechanism of signal propagation spanning the membrane domain and feeding into the HAMP domain. Furthermore, HtrII in H. salinarum not only transmits the signal from the photoreceptor SRII but also operates as a chemoreceptor. 61 matched cddid_all.tbl CDD pfam17910 pfam17910 465561 FeoB_Cyto FeoB cytosolic helical domain. FeoB is a G-protein coupled membrane protein essential for Fe(II) uptake in prokaryotes. In the structures, a canonical G-protein domain (G domain) is followed by a helical bundle domain (S-domain) which is represented by this entry. 90 matched cddid_all.tbl CDD pfam17911 pfam17911 465562 Ski2_N Ski2 N-terminal region. This region is the N-terminal extended region found in the Ski2 protein. The Ski complex is a conserved multiprotein assembly required for the cytoplasmic functions of the exosome, including RNA turnover, surveillance, and interference. Ski2, Ski3, and Ski8 assemble in a tetramer with 1:1:2 stoichiometry. 134 matched cddid_all.tbl CDD pfam17912 pfam17912 465563 OB_MalK MalK OB fold domain. This entry corresponds to one of two OB-fold domains found in the MalK transport protein. 53 matched cddid_all.tbl CDD pfam17913 pfam17913 436135 FHA_2 FHA domain. This entry represents a divergent FHA domain which in PNK binds to phosphorylated segment of XRCC1. 97 matched cddid_all.tbl CDD pfam17914 pfam17914 436136 HopA1 HopA1 effector protein family. This family includes the HopA1 effector protein from Pseudomonas syringae. Structurally this protein has an alpha + beta fold. The effector protein HopA1 was shown to affect the EDS1 complex by binding EDS1 directly and activating the immune response signaling pathway. 170 matched cddid_all.tbl CDD pfam17915 pfam17915 436137 zf_Rg Reverse gyrase zinc finger. This is the N-terminal zinc finger domain present in reverse gyrase proteins. Most reverse gyrases conserve the N-terminal zinc finger of the zinc ribbon type, pointing to a crucial function of this domain. Structure of Thermotoga maritima reverse gyrase elucidates that the N-terminal zinc finger firmly attaches the H1 (helicase 1) domain to the topoisomerase domain contributing to double-strand DNA (dsDNA) binding. 49 matched cddid_all.tbl CDD pfam17916 pfam17916 465564 LID LIM interaction domain (LID). LIM-homeodomain (LIM-HD) proteins are transcription factors that are critical in the development of many cell types and tissues. The activity of LIM-HD proteins is dependent on the essential cofactor LIM domain-binding protein 1 (Ldb1). This entry represents a 30-residue LIM interaction domain (LID) that binds to the LIM domains of all LIM-HD and closely related LIM-only (LMO) proteins. Isl1 (Insulin gene enhancer protein 1) and Isl2 each contain a LID-like sequence in their C-terminal regions, the Lhx3-binding domain (LBD), which binds the LIM domains Lhx3 and Lhx4. 29 matched cddid_all.tbl CDD pfam17917 pfam17917 465565 RT_RNaseH RNase H-like domain found in reverse transcriptase. DNA polymerase and ribonuclease H (RNase H) activities allow reverse transcriptases to convert the single-stranded retroviral RNA genome into double-stranded DNA, which is integrated into the host chromosome during infection. This entry represents the RNase H like domain. 104 matched cddid_all.tbl CDD pfam17918 pfam17918 465566 TetR_C_15 Tetracyclin repressor-like, C-terminal domain. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. This entry represents the C-terminal domain found in a number of different TetR transcription regulator proteins including SlmA proteins found in E. coli. Unlike other TetR proteins, SlmA functions not as a transcription regulator but rather as an NO (nucleoid occlusion) factor. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. 108 matched cddid_all.tbl CDD pfam17919 pfam17919 465567 RT_RNaseH_2 RNase H-like domain found in reverse transcriptase. 100 matched cddid_all.tbl CDD pfam17920 pfam17920 465568 TetR_C_16 Tetracyclin repressor-like, C-terminal domain. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. This entry represents the C-terminal domain found in a number of different TetR transcription regulator proteins found in Actinobacteria. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. 107 matched cddid_all.tbl CDD pfam17921 pfam17921 465569 Integrase_H2C2 Integrase zinc binding domain. This zinc binding domain is found in a wide variety of integrase proteins. 58 matched cddid_all.tbl CDD pfam17922 pfam17922 436144 TetR_C_17 Tetracyclin repressor-like, C-terminal domain. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. This entry represents the C-terminal domain present in Yfir transcription regulator proteins found in Bacillus subtilus. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. 100 matched cddid_all.tbl CDD pfam17923 pfam17923 436145 TetR_C_18 Tetracyclin repressor-like, C-terminal domain. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. This entry represents the C-terminal domain present in TetR transcriptional regulations found in proteobacteria. 113 matched cddid_all.tbl CDD pfam17924 pfam17924 436146 TetR_C_19 Tetracyclin repressor-like, C-terminal domain. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. This entry represents the C-terminal domain present the transcriptional regulator heme-regulated transporter regulator (HrtR), which senses and binds a heme molecule as its physiological effector to regulate the expression of the heme-efflux system responsible for heme homeostasis in L. lactis. 117 matched cddid_all.tbl CDD pfam17925 pfam17925 465570 TetR_C_20 Tetracyclin repressor-like, C-terminal domain. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. This entry represents the C-terminal domain present the transcriptional regulator KstR that regulates a large set of genes responsible for cholesterol catabolism. This is important for Mycobacterium tuberculosis during infection, both at an early stage in the macrophage phagosome and later within the necrotic granuloma. 107 matched cddid_all.tbl CDD pfam17926 pfam17926 436148 TetR_C_21 Tetracyclin repressor-like, C-terminal domain. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. This entry represents the C-terminal domain present the TetR Transcriptional Repressor found in Streptomyces coelicolor A3. Family members include HTH-type transcriptional repressor sco4008, which is suggested to be a transcriptional repressor of sco4007 responsible for the multidrug resistance system in S. coelicolor A3. 111 matched cddid_all.tbl CDD pfam17927 pfam17927 407776 Ins134_P3_kin_N Inositol 1,3,4-trisphosphate 5/6-kinase pre-ATP-grasp domain. This family consists of several inositol 1, 3, 4-trisphosphate 5/6-kinase proteins. Inositol 1,3,4-trisphosphate is at a branch point in inositol phosphate metabolism. It is dephosphorylated by specific phosphatases to either inositol 3,4-bisphosphate or inositol 1,3-bisphosphate. Alternatively, it is phosphorylated to inositol 1,3,4,6-tetrakisphosphate or inositol 1,3,4,5-tetrakisphosphate by inositol trisphosphate 5/6-kinase. This entry represents the N-terminal pre-ATP-grasp domain. 80 matched cddid_all.tbl CDD pfam17928 pfam17928 465571 TetR_C_22 Tetracyclin repressor-like, C-terminal domain. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. This entry represents the C-terminal domain present the TetR Transcriptional Repressor present in sco1712 proteins from Streptomyces coelicolo which act as a regulator of antibiotic production. 113 matched cddid_all.tbl CDD pfam17929 pfam17929 465572 TetR_C_34 Tetracyclin repressor-like, C-terminal domain. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. This entry represents the C-terminal domain present in putative TetR family transcriptional regulators found in bacteria. 120 matched cddid_all.tbl CDD pfam17930 pfam17930 436151 LpxI_N LpxI N-terminal domain. This entry represents the N-terminal domain of the LpxI enzyme that is involved in biosynthesis of lipid A. Specifically it carried out the hydrolysis of UDP-2,3-diacyl- glucosamine. This step is either carried out by LpxI or LpxH. This domain has a Rossmann fold. 129 matched cddid_all.tbl CDD pfam17931 pfam17931 465573 TetR_C_23 Tetracyclin repressor-like, C-terminal domain. This is a C-terminal domain present in putative TetR family transcriptional regulators found in bacteria. 127 matched cddid_all.tbl CDD pfam17932 pfam17932 465574 TetR_C_24 Tetracyclin repressor-like, C-terminal domain. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. This entry represents the C-terminal domain present in family members such as HTH-type transcriptional repressor KstR2 as well as fatty acid metabolism regulator proteins. In Mycobacterium smegmatis, KstR2 is involved in involved in cholesterol catabolism, while YsiA in Bacillus subtilis is involved in fatty acid degradation. 114 matched cddid_all.tbl CDD pfam17933 pfam17933 465575 TetR_C_25 Tetracyclin repressor-like, C-terminal domain. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. This entry represents the C-terminal domain present in Rv1219c of Mycobacterium tuberculosis. Structural studies indicate that the helix alpha 10 of the C-terminal end of Rv1219c forms a long arm feature, a feature which is unique in Rv1219c compared to some other members of the TetR family. Furthermore, it has been shown that substrate binding occurs in the C-terminal regulatory domain of Rv1219c. 106 matched cddid_all.tbl CDD pfam17934 pfam17934 407783 TetR_C_26 Tetracyclin repressor-like, C-terminal domain. This entry represents the C-terminal domain present in putative HTH-type transcriptional regulator. Family members are found in bacilli. 109 matched cddid_all.tbl CDD pfam17935 pfam17935 436155 TetR_C_27 Tetracyclin repressor-like, C-terminal domain. This is the C-terminal domain present in putative TetR transcriptional regulators. 106 matched cddid_all.tbl CDD pfam17936 pfam17936 465576 Big_6 Bacterial Ig domain. This domain is found in a wide variety of extracellular bacterial proteins often in multiple tandem copies. 83 matched cddid_all.tbl CDD pfam17937 pfam17937 436157 TetR_C_28 Tetracyclin repressor-like, C-terminal domain. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. This entry represents the C-terminal domain present in CgmR (C. glutamicum multidrug-responsive transcriptional repressor), previously called CGL2612 protein. CgmR (CGL2612) from Corynebacterium glutamicum is a multidrug-resistance-related transcription factor belonging to the TetR family. It regulates expression of the immediately upstream gene cgmA (cgl2611) by binding to the operator cgmO in the cgmA promoter. The cgmA gene encodes a permease belonging to the major facilitator superfamily, a protein family composed of bacterial multidrug exporters, and the pair of CgmR and CgmA confers multidrug resistance on C. glutamicum. 97 matched cddid_all.tbl CDD pfam17938 pfam17938 436158 TetR_C_29 Tetracyclin repressor-like, C-terminal domain. This domain is found in the C-terminal region of putative TetR-family regulatory proteins. 119 matched cddid_all.tbl CDD pfam17939 pfam17939 465577 TetR_C_30 Tetracyclin repressor-like, C-terminal domain. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. This entry represents the C-terminal domain present in the Pseudomonas aeruginosa PsrA which regulates the fadBA5 beta-oxidation operon. Functional analysis of PsrA indicated its importance in regulating b-oxidative enzymes. It has also been suggested that PsrA, a member of the TetR family of repressors, could affect global gene expression including activation of rpoS. 113 matched cddid_all.tbl CDD pfam17940 pfam17940 436160 TetR_C_31 Tetracyclin repressor-like, C-terminal domain. This is the C-terminal domain found in putative transcriptional regulator, TetR family proteins. 107 matched cddid_all.tbl CDD pfam17941 pfam17941 465578 PP_kinase_C_1 Polyphosphate kinase C-terminal domain 1. Polyphosphate kinase (Ppk) catalyzes the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. This C1-terminal domain has a structure similar to phospholipase D. It is one of two closely related carboxy-terminal domains (C1 and C2 domains). Both the C1 and C2 domains (residues 322-502 and 503-687, respectively) consist of a sevenstranded mixed beta-sheet flanked by five alpha-helices. However, the structural topology and relative orientations of the helices to the beta-sheet in these two domains are different. The C1 and C2 domains are highly conserved in the PPK family. Some of the residues previously shown to be crucial for the enzyme catalytic activity are located in these two domains. 167 matched cddid_all.tbl CDD pfam17942 pfam17942 465579 Morc6_S5 Morc6 ribosomal protein S5 domain 2-like. This domain is found in MORC6 proteins in eukaryotes. Arabidopsis microrchidia (MORC) ATPase family proteins are conserved among plants and animals and are involved in transcriptional silencing. In Arabidopsis, MORC6/DMS11 was reported to function in the condensation of pericentromeric heterochromatin, thereby facilitating transcriptional silencing. Further studies demonstrate that MORC6 and its homologs MORC1 and MORC2 form a complex which associates with SUVH9, required for Pol V occupancy in the RdDM (RNA-directed DNA methylation) pathway. 139 matched cddid_all.tbl CDD pfam17943 pfam17943 407792 HOCHOB Homeobox-cysteine loop-homeobox. This domain is considered a double homeodomain, termed HOCHOB, present in the C. elegans genome. Family members include CEH-91 and CEH-93 that share extended sequence similarity with each other upstream of their typical HDs (Homeodomains). CEH-92, another family member, has three copies of this domain. The domain consists of two divergent HDs that are separated by a linker of about 17 residues. The linker has a number of conserved positions, two of which are cysteine residues suggesting that they could be involved in metal binding. Hence, the name HOCHOB (Homeobox-cysteine loop-homeobox). Furthermore, there are two conserved histidine residues, one in each HD (in CEH-91 displaced by two positions), and there is also a conserved aspartic acid. It is speculated that the HOCHOB domain is an evolutionary novelty that is derived from two HDs and may have gained metal-binding capacity. 120 matched cddid_all.tbl CDD pfam17944 pfam17944 436163 Arg_decarbox_C Arginine decarboxylase C-terminal helical extension. This small three helical domain is found at the C-terminus of the arginine decarboxylase enzyme. 50 matched cddid_all.tbl CDD pfam17945 pfam17945 436164 Crystall_4 Beta/Gamma crystallin. This is the C-terminal domain found in mucin glycoproteins such as secreted protease of C1 esterase inhibitor from EHEC (StcE). This domain adopts a beta/gamma crystallin fold and has been shown to be dispensable for substrate binding. Furthermore, deletion analysis suggest that lack of the C-terminal resulted in impaired association with the cell surface. 90 matched cddid_all.tbl CDD pfam17946 pfam17946 436165 RecC_C RecC C-terminal domain. This entry corresponds to the C-terminal domain of the RecC protein. This domain has a PD(D/E)XK like fold. Deleting this domain eliminates RecD assembly within the RecBCD complex. 223 matched cddid_all.tbl CDD pfam17947 pfam17947 407796 4HB Four helical bundle domain. This domain is found in elongation factor 3A where it packs against the bottom of the concave face of the HEAT domain. 78 matched cddid_all.tbl CDD pfam17948 pfam17948 465580 DnaT DnaT DNA-binding domain. This domain is found in E.coli primosomal protein 1 (Pp1). PP1 domain (residues 84-153) in Swiss:P0A8J2 can bind to different types of ssDNA, which is fundamental for its physiological substrate bindings. Functional analysis indicate that both N- and C- terminals are essential to having the cooperative effect in binding ssDNA. The ssDNA bound complex displays a spiral filament assembly that is adopted by many proteins that are involved in DNA replication, such as DnaA, RecA and PriB. This domain is similar to pfam08585 except that it contains an extra loop at the N-terminus (84-99). Structural analysis indicate that this extra loop might be essential for the stabilization of the three-helix bundle. 69 matched cddid_all.tbl CDD pfam17949 pfam17949 375443 PND FANCM pseudonuclease domain. This entry represents the pseudonuclease domain (PND) from the FANCM protein. This domain is part of the PD(D/E)XK superfamily but does not appear to have a full set of catalytic residues. 125 matched cddid_all.tbl CDD pfam17950 pfam17950 465581 SpmSyn_N S-adenosylmethionine decarboxylase N -terminal. This is the N-terminal domain found in human spermine synthase (EC 2.5.1.22). The N-terminal domain, which forms the major part of the dimerization interface, shows a considerable structural similarity to the AdoMetDC-like fold (S-adenosylmethionine decarboxylase, the enzyme that forms the aminopropyl donor substrate), pfam02675. Deletion of the N-terminal domain led to a complete loss of spermine synthase activity, suggesting that dimerization may be required for activity. The N-terminal domain (amino acids 1-117) includes seven beta-strands and two alpha-helices. 96 matched cddid_all.tbl CDD pfam17951 pfam17951 407799 FAS_meander Fatty acid synthase meander beta sheet domain. This domain is found in fungal fatty acid synthase beta chain proteins. 146 matched cddid_all.tbl CDD pfam17952 pfam17952 407800 Cas6_N Cas6 N-terminal domain. The CRISPR-Cas system is a prokaryotic defense mechanism against foreign genetic elements. The key elements of this defense system are the Cas proteins and the CRISPR RNA.Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes. CRISPRs appear to provide acquired resistance against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA).The defense reaction is divided into three stages. In the adaptation stage, the invader DNA is cleaved, and a piece of it is selected to be integrated as a new spacer into the CRISPR locus, where it is stored as an identity tag for future attacks by this invader. During the second stage (the expression stage), the CRISPR RNA (pre-crRNA) is transcribed and subsequently processed into the mature crRNAs. In the third stage (the interference stage), Cas proteins, together with crRNAs, identify and degrade the invader.The CRISPR-Cas systems have been sorted into three major classes. In CRISPR-Cas types I and III, the mature crRNA is generally generated by a member of the Cas6 protein family. Whereas in system III the Cas6 protein acts alone, in some class I systems it is part of a complex of Cas proteins known as Cascade (CRISPR-associated complex for antiviral defense). This entry represents the N-terminal domain of Cas 6 proteins. The Cas6 protein is an endoribonuclease necessary for crRNA production whereas the additional Cas proteins that form the Cascade complex are needed for crRNA stability. Structural analysis of Sulfolobus sulfotaricus P2 Cas6 (SsCas6) proteins indicate that SsCas6 is able to bind and cleave the nonstructured RNA by stabilizing an otherwise unstable duplex of two base pairs near the cleavage site, leading to an inline conformation around the scissile phosphate necessary for its breakage. 115 matched cddid_all.tbl CDD pfam17953 pfam17953 465582 Csm4_C CRISPR Csm4 C-terminal domain. Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation. The interference complex of the type III-A CRISPR-Cas system is composed of five Cas proteins (Csm1-Csm5) and a crRNA, and targets invading DNA. This entry represents the C-terminal domain found in Csm4. Csm4 structurally resembles Cmr3, a component of the type III-B CRISPR-Cas interference complex. Studies indicate that Csm3-Csm4 complex binds single-stranded RNA in a non-sequence-specific manner. Structural analysis show, Csm3 and Csm4 have one and two ferredoxin-like folds (also known as an RRM-like fold), respectively. The long beta-hairpin inserted into the C-terminal ferredoxin-like fold of Csm4, is well-conserved in the Cmr3 structure. The corresponding beta-hairpin of Cmr3 binds the D1 domain of Cmr2, as observed in the Cmr2-Cmr3 complex structure. Furthermore, it is suggested that the hairpin of Csm4 is responsible for the interaction with Csm1 (ortholog of Cmr2). 91 matched cddid_all.tbl CDD pfam17954 pfam17954 465583 Pirin_C_2 Quercetinase C-terminal cupin domain. Experiments on the YhhW protein show that is has quercetinase activity. This entry represents the C-terminal cupin domain from the two cupin domains that make up the protein. This domain is usually associated with pfam02678. 86 matched cddid_all.tbl CDD pfam17955 pfam17955 465584 Cas6b_N Cas6b N-terminal domain. Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation. Four Cas proteins (Cas5, Cas6b, Cas7 and Cas8b) are proposed to form a Type I-B Cascade complex that mediates the antiviral defense. This is the N-terminal domain found in Cas6b proteins. Cas6b is a member of Cas6 RNA processing endoribonucleases found in bacteria and archaea whose RNA substrates have a wide range of structural features. Cocrystal structures of Cas6 from Methanococcus maripaludis (MmCas6b) bound with its repeat RNA revealed a dual-site binding structure and a cleavage site conformation poised for phosphodiester bond breakage. 105 matched cddid_all.tbl CDD pfam17956 pfam17956 465585 NAPRTase_C Nicotinate phosphoribosyltransferase C-terminal domain. This domain is found at the C-terminus of some Nicotinate phosphoribosyltransferase enzymes. The function of this domain is uncertain. 111 matched cddid_all.tbl CDD pfam17957 pfam17957 436171 Big_7 Bacterial Ig domain. This entry represents a bacterial ig-like domain that is found in glycosyl hydrolase enzymes. 67 matched cddid_all.tbl CDD pfam17958 pfam17958 465586 EF-hand_13 EF-hand domain. This entry represents an EF-hand domain found in one of the regulatory B subunits of PP2A. 90 matched cddid_all.tbl CDD pfam17959 pfam17959 465587 EF-hand_14 EF-hand domain. This EF-hand domain is found at the N-terminus of the human glutaminase enzyme. 90 matched cddid_all.tbl CDD pfam17960 pfam17960 465588 TIG_plexin TIG domain. This entry represents an TIG or IPT domain (Ig domain shared by Plexins and Transcription factors) found in plexins. 89 matched cddid_all.tbl CDD pfam17961 pfam17961 465589 Big_8 Bacterial Ig domain. This entry represents a bacterial Ig-fold domain that is found in a wide range of bacterial cell surface adherence proteins. 102 matched cddid_all.tbl CDD pfam17962 pfam17962 436175 bMG6 Bacterial macroglobulin domain 6. This macroglobulin domain is found in bacterial alpha 2 macroglobulin proteins. It adopts an Ig-like beta sandwich fold. 112 matched cddid_all.tbl CDD pfam17963 pfam17963 465590 Big_9 Bacterial Ig domain. This entry represents a wide variety of bacterial Ig domains. 90 matched cddid_all.tbl CDD pfam17964 pfam17964 465591 Big_10 Bacterial Ig domain. This entry represents a bacterial Ig-like domain found associated with transpeptidase domains. 182 matched cddid_all.tbl CDD pfam17965 pfam17965 465592 MucBP_2 Mucin binding domain. This domain is found in bacterial cell surface proteins that interact with mucins. The archetypal member of this family is the Mub-R5 B1 domain. This domain has a beta-grasp fold. 75 matched cddid_all.tbl CDD pfam17966 pfam17966 465593 Muc_B2 Muc B2-like domain. This entry corresponds to the Muc B2 domain. This domain is related to the Muc B1 domain pfam17965. This domain may be involved in mucin binding. This domain is often found associated with the related pfam17965 in bacterial cell surface proteins. 68 matched cddid_all.tbl CDD pfam17967 pfam17967 465594 Pullulanase_N2 Pullulanase N2 domain. This domain is found close to the N-terminus of the Klebsiella starch debranching pullulanase enzyme. The structure of the domain is a beta sandwich fold. 112 matched cddid_all.tbl CDD pfam17968 pfam17968 465595 Tlr3_TMD Toll-like receptor 3 trans-membrane domain. Toll-like receptor (TLR) 3 is an endosomal TLR that mediates immune responses against viral infections upon activation by its ligand double-stranded RNA, a replication intermediate of most viruses. TLR3 is expressed widely in the body and activates both the innate and adaptive immune systems. This entry represents the Toll-like receptor 3 trans-membrane domain which has been shown to form dimers and trimers with different surfaces for helix-helix interaction. 33 matched cddid_all.tbl CDD pfam17969 pfam17969 465596 Ldt_C L,D-transpeptidase C-terminal domain. This is the C-terminal domain found in d-transpeptidases (Ldt) homologs from E.coli. Three of these enzymes (YbiS, ErfK, YcfS) have been shown to cross-link Braun's lipoprotein to the peptidoglycan (PG), while the other two (YnhG, YcbB) form direct meso-diaminopimelate (DAP-DAP, or 3-3) cross-links within the PG. Family members include erfK (ldtA), ybiS (ldtB), ycfS (ldtC), and ynhG (ldtE). 67 matched cddid_all.tbl CDD pfam17970 pfam17970 465597 bMG1 Bacterial Alpha-2-macroglobulin MG1 domain. Alpha-2-macroglobulins (A2Ms) are plasma proteins that trap and inhibit a broad range of proteases and are major components of the eukaryotic innate immune system. However, A2M-like proteins were identified in pathogenically invasive bacteria and species that colonize higher eukaryotes. Bacterial A2Ms are located in the periplasm where they are believed to provide protection to the cell by trapping external proteases through a covalent interaction with an activated thioester. This domain is found on the N-terminal region in A2Ms in bacteria. Structure analysis of Salmonella enterica ser A2Ms (SA-A2Ms) show that they are composed of 13 domains, all of which fold as variants of beta sandwiches with the exception of the TED, which consists of 14 alpha helices. Most of the beta sandwich domains appear to serve a structural role and are referred to as the macroglobulin-like (MG) domains. This is the MG1 domain which is the farthest from the body of the structure. It is normally anchored to the inner membrane in vivo and connected to MG2 by a flexible linker. 105 matched cddid_all.tbl CDD pfam17971 pfam17971 375455 LIFR_D2 Leukemia inhibitory factor receptor D2 domain. This is the D2 domain in cytokine-binding module 1 (CBM1) found in Leukemia inhibitory factor receptor (LIFR) and OSM receptors (OSMR). LIFR has an extracellular region with a modular structure containing two cytokine-binding modules (CBM) separated by an Ig-like domain and followed by three membrane-proximal fibronectin type-III (FNIII) domains. The D2 domain in CBM1 shows structural similarity to the corresponding CBM domains of both gp130 and IL-6Ralpha because it contains conserved structural features like the WSXWS motif. The WSXWS motif in cytokine receptors is a molecular switch involved in receptor activation. 114 matched cddid_all.tbl CDD pfam17972 pfam17972 436183 bMG5 Bacterial Alpha-2-macroglobulin MG5 domain. Alpha-2-macroglobulins (A2Ms) are plasma proteins that trap and inhibit a broad range of proteases and are major components of the eukaryotic innate immune system. However, A2M-like proteins were identified in pathogenically invasive bacteria and species that colonize higher eukaryotes. Bacterial A2Ms are located in the periplasm where they are believed to provide protection to the cell by trapping external proteases through a covalent interaction with an activated thioester. This domain is found on the N-terminal region in A2Ms in bacteria. Structure analysis of Salmonella enterica ser A2Ms (SA-A2Ms) show that they are composed of 13 domains, all of which fold as variants of beta sandwiches with the exception of the TED, which consists of 14 alpha helices. Most of the beta sandwich domains appear to serve a structural role and are referred to as the macroglobulin-like (MG) domains. This is the MG5 domain. 127 matched cddid_all.tbl CDD pfam17973 pfam17973 465598 bMG10 Bacterial Alpha-2-macroglobulin MG10 domain. Alpha-2-macroglobulins (A2Ms) are plasma proteins that trap and inhibit a broad range of proteases and are major components of the eukaryotic innate immune system. However, A2M-like proteins were identified in pathogenically invasive bacteria and species that colonize higher eukaryotes. Bacterial A2Ms are located in the periplasm where they are believed to provide protection to the cell by trapping external proteases through a covalent interaction with an activated thioester. This domain is found on the C-terminal region in A2Ms in bacteria. Structure analysis of Salmonella enterica ser A2Ms (SA-A2Ms) show that they are composed of 13 domains, all of which fold as variants of beta sandwiches with the exception of the TED, which consists of 14 alpha helices. Most of the beta sandwich domains appear to serve a structural role and are referred to as the macroglobulin-like (MG) domains. This is the MG10 domain. MG10 is markedly different from the other MG domains in that it has more beta strands and an alpha helix. The position of MG10 is stabilized by, in addition to other hydrogen bonds, the formation of a beta sheet with MG9. 128 matched cddid_all.tbl CDD pfam17974 pfam17974 407821 GalBD_like Galactose-binding domain-like. Proteins containing a galactose-binding domain-like fold can be found in several different protein families, in both eukaryotes and prokaryotes. The common function of these domains is to bind to specific ligands, such as cell-surface-attached carbohydrate substrates for galactose oxidase and sialidase, phospholipids on the outer side of the mammalian cell membrane for coagulation factor Va, membrane-anchored ephrin for the Eph family of receptor tyrosine kinases, and a complex of broken single-stranded DNA and DNA polymerase beta for XRCC1. The structure of the galactose-binding domain-like members consists of a beta-sandwich, in which the strands making up the sheets exhibit a jellyroll fold. 190 matched cddid_all.tbl CDD pfam17975 pfam17975 465599 RNR_Alpha Ribonucleotide reductase alpha domain. This is the alpha helical domain of ribonucleotide reductases. Family members include Ribonucleotide reductase (RNR, EC:1.17.4.1), which catalyze the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs divide into three classes on the basis of their metallocofactor usage. This domain is found in Class II. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Many organizms have more than one class of RNR present in their genomes. Ribonucleotide reductase is an oligomeric enzyme composed of a large sub-unit (700 to 1000 residues) and a small sub-unit (300 to 400 residues) - class II RNRs are less complex, using the small molecule B12 in place of the small chain. Some family members carry ATP cone domain which acts as a functional regulator. Competitive binding of ATP and dATP to an N-terminal ATP-cone domain determines enzyme activity. As the ratio of dATP to ATP increases above a certain threshold, the enzyme activity is turned off. Substrate nucleotides are recognized by relatively simple H-bonding interactions at the N-terminus of one or more alpha helices. In the monomeric class II RNR, the effector binds in a pocket formed by helices in a 130 amino acid insertion which constitutes this domain. 101 matched cddid_all.tbl CDD pfam17976 pfam17976 465600 zf-RING_12 RING/Ubox like zinc-binding domain. This is a RING zinc finger domain found in parkin proteins. Parkin consists of a ubiquitin-like (Ubl) domain and a 60-amino acid linker followed by this domain RING0 and three additional zinc finger domains characteriztic of the RBR family. RING0 binds two coordinated zinc atoms at each extremity of the domain with a hairpin. Deletion of RING0 massively derepressed parkin activity supporting the role of RING0 in autoinhibition, point mutations in RING0 (Phe146 to Ala) or RING2 (Phe463 to Ala) both increased parkin activity. The REP (repressor element of parkin) and RING0 domains play a preeminent role in repressing parkin ligase activity through their interactions with RING1 and RING2, respectively. 73 matched cddid_all.tbl CDD pfam17977 pfam17977 375459 zf-RING_13 RING/Ubox like zinc-binding domain. This is a zinc binding domain found in nidovirus helicase. It includes includes 12 or 13 conserved Cys/His residues. Amino acid substitutions in ZBD or the adjacent spacer that connects it to the downstream domain can profoundly affect EAV (equine arteritis virus) helicase activity and RNA synthesis, with most replacements of conserved Cys or His residues yielding replication-negative virus phenotypes. 68 matched cddid_all.tbl CDD pfam17978 pfam17978 465601 zf-RING_14 RING/Ubox like zinc-binding domain. This is a RING zinc finger domain found in parkin proteins. Parkin consists of a ubiquitin-like (Ubl) domain and a 60-amino acid linker followed by RING0 and three additional zinc finger domains characteriztic of the RBR family. This entry relates to RING1 zinc binding domain. The RING1 domain displays the C3HC4 cross-brace motif characteriztic of RING domains. The N-terminal Ubl domain binds to RING1. 89 matched cddid_all.tbl CDD pfam17979 pfam17979 465602 zf-CRD Cysteine rich domain with multizinc binding regions. This is a cysteine rich domain which contains four zinc-binding regions (binding five zinc ions). Family members include human CHFR which interacts with Poly(ADP-ribose) (PAR) through a 20-amino acid PAR binding zinc finger region (PBZ) found at the C-terminal end of this cysteine-rich domain (i.e. the 4th region towards the C-terminal). CHFR lacking PBZ does not co-localize with nuclear PAR foci in interphase cells and cannot rescue antephase checkpoint function despite retaining autoubiquitination activity. Hence it has been suggested that the CHFR-PAR interaction is an important part of the antephase checkpoint and could form part of the checkpoint sensor for cellular stress and microtubule poisons or be required for proper localization of CHFR. The PBZ region of CHFR contains two adenine binding sites. 158 matched cddid_all.tbl CDD pfam17980 pfam17980 465603 ADD_DNMT3 Cysteine rich ADD domain in DNMT3. This is a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, AD-DATRX) found in DNMT3A proteins. The ADD domains of the DNMT3 family have a decisive role in blocking DNMT activity in the areas of the genome with chromatin containing methylated H3K4. Furthermore, the ADD domain of DNMMT3A (ADD-3A) competes with the chromodomain (CD) of heterochromatin protein 1 alpha (HP1alpha, CDHP1alpha) for binding to the H3 tail. The DNA methyltransferase (DNMT) 3 family members DNMT3A and DNMT3B and the DNMT3-like non-enzymatic regulatory factor DNMT3L, are involved in de-novo establishment of DNA methylation patterns in early mammalian development. 56 matched cddid_all.tbl CDD pfam17981 pfam17981 465604 ADD_ATRX Cysteine Rich ADD domain. This is a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, AD-DATRX) found in ATRX proteins. Chromatin-associated human protein ATRX was originally identified because mutations in the ATRX gene cause a severe form of syndromal X-linked mental retardation called ATR-X syndrome. Mutations or knockdown of ATRX expression cause diverse effects, including altered patterns of DNA methylation, a telomere-dysfunction phenotype, aberrant chromosome segregation, premature sister chromatid separation and changes in gene expression. ATRX localizes predominantly to large, tandemly repeated regions (such as telomeres, centromeres and ribosomal DNA) associated with heterochromatin, and studies show that it directs H3.3 deposition to pericentric and telomeric heterochromatin. The ADD domain of ATRX, in which most syndrome-causing mutations occur, engages the N-terminal tail of histone H3 through two rigidly oriented binding pockets, one for unmodified Lys4 and the other for di- or trimethylated Lys9. Mutations in the ATRX ADD domain cause mislocalization of ATRX protein to heterochromatin, and this may contribute to understanding the underlying etiology of ATRX syndrome. Structure analysis of the ADD domain of ATRX revealed that it contains a PHD zinc-finger domain packed against a GATA-like zinc finger. Same structure is also found in the DNMT3 DNA methyltransferases and DNMT3L. 56 matched cddid_all.tbl CDD pfam17982 pfam17982 465605 C5HCH NSD Cys-His rich domain. This is an NSD-specific Cys-His rich region (C5HCH) domain. Family members include NSD3 (nuclear receptor SET domain-containing) proteins. This domain is located on the C-terminal of NSD1, 2 and 3 proteins. C5HCH domain lies adjacent to the fifth plant homeodomain (PHD5). The PHD5-C5HCH module of NSD3 (PHD5-C5HCHNSD3) recognizes the H3 N-terminal peptide containing unmodified K4 and trimethylated K9. Moreover, it has been reported that the PHD5-C5HCH module of NSD1 (PHD5-C5HCH) was the sole region required for tight binding of the NUP98-NSD1 fusion protein to the HoxA9 gene promoter, implicating that PHD5-C5HCH might have chromatin targeting ability. 50 matched cddid_all.tbl CDD pfam17983 pfam17983 375465 Tryp_inh Trypsin inhibitors 1,2 and 3. This is domain is found in trypsin inhibitor 1, 2 and 3 found in Chenopodiaceae. Structure analysis of S. oleracea trypsin inhibitor III (SOTI-III), in complex with bovine pancreatic trypsin, shows a knottin-like cystine-bridge topology. 33 matched cddid_all.tbl CDD pfam17984 pfam17984 375466 TERT_thumb Telomerase reverse transcriptase thumb DNA binding domain. The catalytic subunit of telomerase is structurally similar to retroviral reverse transcriptases, viral RNA polymerases and, to a lesser extent, the bacteriophage B-family DNA polymerases. Like its structural homologs, the core catalytic subunit of telomerase, TERT, contains the fingers, palm and thumb domains required for nucleic acid and nucleotide associations as well as catalysis. The four major TERT domains: the RNA binding domain (TRBD); the fingers domain, implicated in nucleotide binding and processivity; the palm domain, which contains the active site of the enzyme; and the thumb domain, implicated in DNA binding and processivity are organized into a ring configuration similar to that observed for the substrate-free enzyme. This is the thumb domain found in Tribolium castaneum telomerase catalytic subunit, TERT. Contacts between TERT and the DNA substrate are mostly mediated via backbone interactions with the thumb loop and helix. The thumb helix sits in the minor groove of the RNA-DNA heteroduplex, making extensive contacts with the phosphodiester backbone and the ribose groups of the RNA-DNA hybrid. 191 matched cddid_all.tbl CDD pfam17985 pfam17985 407829 SipA_VBS SipA vinculin binding site. This motif family includes the three vinculin binding sites found in the Shigella SipA/IpaA protein. The family also includes some proteins from Chlamydia species. 22 matched cddid_all.tbl CDD pfam17986 pfam17986 407830 EKAL EMP3-KAHRP-like N-terminal domain. This is the N-terminal domain which is found at the N terminus of the erythrocyte cytoskeleton-associated protein (EMP3) and the knob-associated histidine-rich protein (KAHRP). KAHRP found in protozoan parasites such as Plasmodium falciparum, is involved in both rigidifying the host cell and the formation of cytoadherent knob structures. 53 matched cddid_all.tbl CDD pfam17987 pfam17987 436190 PMT2_N Phosphoethanolamine N-methyltransferase 2 N-terminal. This is the N-terminal vestigial domain found in Haemonchus contortus phosphoethanolamine N-methyltransferases 2 (PMT2). Structural analysis reveal changes leading to loss of function in the vestigial domains of the nematode PMT. 124 matched cddid_all.tbl CDD pfam17988 pfam17988 375470 VEGFR-2_TMD VEGFR-2 Transmembrane domain. This is a transmembrane domain (TMD) of vascular endothelial growth factor receptor 2 which regulates blood vessel homeostasis. Transmembrane signalling by receptor tyrosine kinases (RTKs) requires specific orientation of the intracellular kinase domains in active receptor dimers. Two mutants in VEGFR-2 TMD showed constitutive kinase activity, suggesting that precise TMD orientation is mandatory for kinase activation. Scanning mutagenesis and structural analysis indicated that introducing two polar amino acids in distinct positions of the TMD (G770E/F777E and I771E/L778E mutations) reorients transmembrane helices and leads to stable dimer formation. Therefore, it has been suggested that the transition between the inactive and the active dimeric state of VEGFR-2 implicates alternative dimeric TMD conformations. 35 matched cddid_all.tbl CDD pfam17989 pfam17989 465606 ALP_N Actin like proteins N terminal domain. This is the N-terminal domain found in archaeal actin homolog Ta0583 found in thermophilic archaeon Thermoplasma acidophilum. Structural analysis indicate that the fold of Ta0583 contains the core structure of actin indicating that it belongs to the actin/Hsp70 superfamily of ATPases. Furthermore,Ta0583 co-crystallized with ADP shows that the nucleotide binds at the interface between the subdomains of Ta0583 in a manner similar to that of actin. It has been suggested that Ta0583 might function in the cellular organization of T. acidophilum. Other family members include ParM another actin-like protein found in Staphylococcus aureus. Crystal structure co-ordinates revealed that this protein is most structurally related to the chromosomally encoded Actin-like proteins (Alp) Ta0583 from the archaea Thermoplasma acidophilum. Furthermore, biophysical analyses have suggested that ParM filaments undergo a treadmilling-like mechanism of motion in vitro similar to that of F-actin. The recruitment of ParM to the segrosome complex, was shown to be required for the conversion of static ParM filaments to a dynamic form proficient for active segregation and facilitated by the C-terminus of ParR 149 matched cddid_all.tbl CDD pfam17990 pfam17990 436192 LodA_N L-Lysine epsilon oxidase N-terminal. This is the N-terminal domain found in antimicrobial protein (LodA) with lysine-epsilon oxidase activity (EC 1.4.3.20) which is produced by gram-negative marine bacteria such as Marinomonas mediterranea. The enzyme, previously named marinocine, catalyzes the oxidative deamination of l-lysine into 6-semialdehyde 2-aminoadipic acid, ammonia, and hydrogen peroxide (H2O2). Orthologous proteins have been detected in other bacterial genera, where they participate in biofilm development and dispersal. It has been shown that M. mediterranea LodA and its homologs induce cell death in the microcolonies formed in the process of biofilm development due to the hydrogen peroxide generated by their enzymatic activity. Moreover, cells dispersed from the biofilm by means of this mechanism show a phenotypic variation in growth and biofilm formation. The active form of LodA containing the quinonic cofactor is generated intracellularly only in the presence of LodB, suggesting that the latter protein is involved in this process. 215 matched cddid_all.tbl CDD pfam17991 pfam17991 465607 Thioredoxin_10 Thioredoxin like C-terminal domain. This is the C-terminal thioredoxin like domain found in Rv2874 in the pathogenic bacterium Mycobacterium tuberculosis. Structure analysis of Rv2874-C shows the presence of a C-terminal domain formed by the 128 residues Thr568-Gly695. These residues form a jelly-roll structure in which two antiparallel beta-sheets sandwich a hydrophobic core. This domain is combined with a second domain with a carbohydrate-binding module (CBM) fold. 142 matched cddid_all.tbl CDD pfam17992 pfam17992 436194 Agarase_CBM Agarase CBM like domain. This is the N-terminal CBM-like domain in exo-beta-agarase proteins (EC:3.2.1.81) found in the marine microbe Saccharophagus degradans. This enzyme catalyzes a critical step in the metabolism of agarose by S. degradans through cleaving agarose oligomers into neoagarobiose products that can be further processed into monomers. The CBM-like domain is structurally very similar to some CBM families. A loop in the CBM-like domain is involved in forming the roof of the active site channel. The contribution of the CBM-like domain to formation of the active site of the enzyme supports a role in substrate recognition explaining the exo-mode of beta-agarase action. 182 matched cddid_all.tbl CDD pfam17993 pfam17993 407836 HA70_C Haemagglutinin 70 C-terminal domain. This is the C-terminal domain found in hemagglutinin component such as HA70 found in Clostridium botulinum. HA is a component of the large botulinum neurotoxin complex and is critical for its oral toxicity. HA plays multiple roles in toxin penetration in the gastrointestinal tract, including protection from the digestive environment, binding to the intestinal mucosal surface, and disruption of the epithelial barrier. HA consists of three different proteins, designated HA70 (also known as HA3), HA33 (HA1), and HA17 (HA2) based on molecular mass. HA70 consists of three domains (D1-3). The D1 and D2 domains, which adopt similar structures, mediate the trimerization of HA70 with each protomer. The D3 domain, sitting at the tip of the trimer, is composed of two similar jelly-roll-like beta-sandwich structures. Furthermore, crystal structures of HA70 in a complex with alpha2,3- or alpha2,6-SiaLac (alpha2,6-sialyllactose), show that alpha2,3- and alpha2,6-SiaLac bound to the same region in the D3 domain of HA70. This domain is the D3 domain found in HA3/HA70 which has been shown to be involved in binding to carbohydrate of glycoproteins from epithelial cells in the infection process. 135 matched cddid_all.tbl CDD pfam17994 pfam17994 436195 Glft2_N Galactofuranosyltransferase 2 N-terminal. This is the N-terminal beta-barrel domain found in the polymerizing galactofuranosyltransferase GlfT2 (Rv3808c). This enzyme synthesizes the bulk of the galactan portion of the mycolyl-arabinogalactan complex, which is the largest component of the mycobacterial cell wall such as in Mycobacterium tuberculosis. The N-terminal domain contains two short helices preceding a 10-stranded beta-sandwich with jelly roll topology. 140 matched cddid_all.tbl CDD pfam17995 pfam17995 407838 GH101_N Endo-alpha-N-acetylgalactosaminidase N-terminal. This is the N-terminal domain found in Streptococcus pneumoniae endo-alpha-N-acetylgalactosaminidase (EC:3.2.1.97), a cell surface-anchored glycoside hydrolase from family GH101 involved in the breakdown of mucin type O-linked glycans. This is a twisted beta-sandwich domain composed of two sheets of six and seven antiparallel beta-strands. The domain appears to be missing the extended metal and carbohydrate-binding loops. 180 matched cddid_all.tbl CDD pfam17996 pfam17996 465608 CE2_N Carbohydrate esterase 2 N-terminal. This is the N-terminal beta-sheet domain with jelly roll topology found in CE2 acetyl-esterase from the bacterium Clostridium thermocellum. This enzyme displays dual activities, it catalyzes the deacetylation of plant polysaccharides and also potentiates the activity of its appended cellulase catalytic module through its noncatalytic cellulose binding function. This N-terminal jelly-roll domain appears to extend the substrate/cellulose binding cleft of the catalytic domain in C.thermocellum. 108 matched cddid_all.tbl CDD pfam17997 pfam17997 375474 Cry1Ac_D5 Insecticidal delta-endotoxin CryIA(c) domain 5. This domain is found in the protoxins portion of insecticidal proteins (parasporins, or Cry proteins) such as those from Bacillus thuringiensis (Bt) Cry1Ac. The protoxin portion comprise a proteolytically labile C-terminal segment (sometimes referred to as the protoxin domain). This is domain V in Cry1Ac from B. thuringiensis. One of the four protoxin domains (D-IV through D-VII). Domains V and VII are beta-rolls (similar to D-II or D-III) that closely resemble carbohydrate-binding modules (CBM) found in sugar hydrolases, however, it is difficult to guess which particular carbohydrates (if any) may serve as their ligands because residues on the putative sugar-binding interfaces are conserved neither in sequence nor in local structure. Structural analysis indicate that there are putative disulfide crosslinking at the dimer interface mediated by cysteines within 783-823 region of this domain which together with other cysteines creates a three-dimensional network of cross-links across the crystal which may play a role in stabilizing mature Bt Cry1Ac. 173 matched cddid_all.tbl CDD pfam17998 pfam17998 465609 AgI_II_C2 Cell surface antigen I/II C2 terminal domain. This is the second domain (C2) located in the C-terminal region found in antigen I/II type adhesin protein AspA from S. pyogenes. Together with C3, these two domains form an elongated structure, each domain adopts the DEv-IgG fold. Similar to the classical IgG folds, it is comprised of two major antiparallel beta-sheets, designated ABED and CFG. For the C2-domain, there are two additional strands on the CFG sheet. Furthermore, sheets ABED and CFG are interconnected by several cross-connecting loops and one alpha-helix (DH1). The side chains of D982 and N996 in the C2-domain are involved in hydrogen bonding with the side chains of R1264 and N1295 in the C3 domain. Main chain hydrogen bonding can also be observed between S992 in C2 and N1189/G1191 in C3, furthermore stabilizing the interaction between the domains. The C2 domain contains one bound metal ion, modeled as Ca2+, and both the C2- and C3-domains are stabilized by conserved isopeptide bonds, which connect the beta-sheets of the central DEv-IgG motifs.Other members of this family include Major cell-surface adhesin PAc from Streptococcus mutans and SspB from Streptococcus gordonii. 180 matched cddid_all.tbl CDD pfam17999 pfam17999 436198 PulA_N1 Pullulanase N1-terminal domain. This is the N-terminal domain found in debranching enzyme such as Pullulanase (PulA)from Anoxybacillus sp. LM18-11. The PulA structure comprises four domains (N1, N2, A, and C). This is the N1 domain which has been identified as a carbohydrate-binding motif. Two maltotriose or maltotetraose molecules were found between the N1 domain and a loop of the A domain in the PulA-maltotriose or PulA-maltotetraose structures. These carbohydrates are bound in a parallel binding mode close to each other and form hydrogen bonds. The sugar moieties bound to the N1 domain are not immediately adjacent to the active site, but the enzyme might use N1 binding to attract and grab the substrate. Functional analysis indicate that N1 is important for catalytic activity and thermostability in addition to assisting substrate binding. The structure of the N1 domain reveals a classic distorted beta-jelly roll fold consisting of two anti-parallel beta-sheets, forming a concave and a convex surface. On the concave side of N1 domain there is a cleft to accommodate two molecules of maltotriose or maltotetraose. 85 matched cddid_all.tbl CDD pfam18000 pfam18000 465610 Top6b_C Type 2 DNA topoisomerase 6 subunit B C-terminal domain. This is the C-terminal domain found in archaeal type 2 DNA topoisomerase 6 subunit B (EC:5.99.1.3). This region is a small helix-two turns-helix (H2TH) domain inserted between the GHKL and transducer domains which adopts an immunoglobulin-like fold. Mutation analysis of this C-terminal domain showed that the overall activity of the mutant mesophilic methanogen M. mazei Top6B (MmT6) is modestly reduced but its relative activity on different substrates is not affected. Due to the similarity of the B subunit's CTD to known protein- and carbohydrate-binding modules, it has been suggested that it could regulate topo VI spatially, perhaps by localizing the enzyme to a specific subcellular region or functional partner. 112 matched cddid_all.tbl CDD pfam18001 pfam18001 465611 Il13Ra_Ig Interleukin-13 receptor subunit alpha Ig-like domain. This is the N-terminal Ig-like domain found in IL-13Ralpha1 type two cytokine complex. The IL-13Ralpha1 contains an extra N-terminal Ig-like domain not found in other receptors of the the common gamma-chain subfamily. The extra N-terminal IL-13Ralpha1 Ig-like domain contacts the dorsal surfaces of both IL-4 and IL-13. Mutational studies show that the deletion of this domain affects the binding of IL-13 to IL-13Ralpha1. 95 matched cddid_all.tbl CDD pfam18002 pfam18002 436201 T6_Ig_like T6 antigen Ig like domain. This is the N-terminal immunoglobulin-like domain. Family members carrying this domain include Trypsin-resistant surface T6 protein found in Streptococcus pyogenes. 145 matched cddid_all.tbl CDD pfam18003 pfam18003 465612 DUF3823_C Domain of unknown function (DUF3823_C). This is a family of uncharacterized proteins from Bacteroidetes. This domain has an Ig-like fold. 103 matched cddid_all.tbl CDD pfam18004 pfam18004 465613 RPN2_C 26S proteasome regulatory subunit RPN2 C-terminal domain. This is the C-terminal domain found in S. cerevisiae Rpn2 (26S proteasome regulatory subunit RPN2) as well as other eukaryotic species. A study revealed that the C-terminal 52 residues of the Rpn2 C-terminal domain are responsible for mediating interactions with the ubiquitin-binding subunit Rpn13. Futhermore, the extreme C-terminal 20 or 21 residues of Rpn2 (926-945 or 925-945) of S. cerevisiae, were shown to be equally effective at binding Rpn13. Multiple sequence alignments indicate that Rpn2 orthologs are highly conserved in this C-terminal region and share characteriztic acidic, aromatic, and proline residues, suggesting a common function. In the structure of Rpn2 from S. cerevisiae, this region is exposed and disordered, and is thus accessible for associating with Rpn13. The Rpn2 binding surface of human Rpn13 has been mapped by nuclear magnetic resonance titration to one surface of its Pru domain. 159 matched cddid_all.tbl CDD pfam18005 pfam18005 465614 eIF3m_C_helix eIF3 subunit M, C-terminal helix. This is the C-terminal helix domain found in Eukaryotic translation initiation factor 3 subunit M (eIF3m). In mammalian eIF3a, the C-terminal helix following the PCI domain is involved in interactions with other core subunits. 29 matched cddid_all.tbl CDD pfam18006 pfam18006 436205 SepRS_C O-phosphoseryl-tRNA synthetase C-terminal domain. The SSHS domain is mainly found in Archaea. The domain makes up part of the anticodon binding domain at the C-terminal of O-phosphoserine--tRNA(Cys) ligase. 31 matched cddid_all.tbl CDD pfam18007 pfam18007 465615 DUF5593 Domain of unknown function (DUF5593). This is a domain of unknown function found in Corynebacteriales. 93 matched cddid_all.tbl CDD pfam18008 pfam18008 436207 Bac_RepA_C Replication initiator protein A C-terminal domain. This is the C-terminal domain (CTD) that can be found in the conserved replication initiator, RepA,essential for staphylococcal propagation. RepA CTD shared the strongest structural homology to the Enterococcus faecalis DnaD CTD, yet perform distinct functions. RepA CTD shows strong sequence homology between RepA_N plasmids in genus-specific clusters, suggesting that it may perform host-specific functions necessary for replication. The RepA CTD interacts with the host DnaG primase, which binds the replicative helicase. Structural data indicate that the RepA CTD exists as a monomeric entity, flexibly tethered to the DNA-bound NTD. 95 matched cddid_all.tbl CDD pfam18009 pfam18009 375484 Fer4_23 4Fe-4S iron-sulfur cluster binding domain. This is the C-terminal domain found in Deinococcus radiodurans protein DR2241 (a Ribosomal protein S2-related protein). This domain has been shown to harbour the sequence motifs CxxC and CxxxC which bind a [4Fe-4S] iron-sulphur cluster. Together with the preceding domain, it is heavily involved in the tetramer formation. 82 matched cddid_all.tbl CDD pfam18010 pfam18010 436208 HTH_49 Cry35Ab1 HTH C-terminal domain. This is the C-terminal domain found in Bacillus thuringiensis protein Cry35Ab1 (an insecticidal protein). The domain has three helices held in a hydrophobic core, the first two form a typical helix-loop-helix whilst the third helix is perpendicular. The domain is structurally homologous to BinB and proteins containing similar beta-trefoil lectin-like domains. The domain is not required for insecticidal activity or for immuno-reactivity and its function is likely to be to bind to WCR brush border membrane vesicles. 29 matched cddid_all.tbl CDD pfam18011 pfam18011 436209 Catalase_C C-terminal domain found in long catalases. This domain is found at the C-terminus of a variety of large catalase enzymes from bacteria. Structurally it is related to class I glutamine amidotransferase domains. The precise molecular function of this domain is uncertain. 150 matched cddid_all.tbl CDD pfam18012 pfam18012 465616 PH_17 PH domain. This entry represents the C-terminal part of the split PH domain from syntrophin proteins. 59 matched cddid_all.tbl CDD pfam18013 pfam18013 465617 Phage_lysozyme2 Phage tail lysozyme. This domain has a lysozyme like fold. It is found in the tail protein of various phages probably giving them the ability to degrade the host cell wall peptidoglycan layer. 139 matched cddid_all.tbl CDD pfam18014 pfam18014 436212 Acetyltransf_18 Acetyltransferase (GNAT) domain. This entry represents a likely acetyltransferase enzyme that is related to pfam06852. 123 matched cddid_all.tbl CDD pfam18015 pfam18015 465618 Acetyltransf_19 Acetyltransferase (GNAT) domain. This entry represents a likely acetyltransferase enzyme that is related to pfam13302. 113 matched cddid_all.tbl CDD pfam18016 pfam18016 436214 SAM_3 SAM domain (Sterile alpha motif). 65 matched cddid_all.tbl CDD pfam18017 pfam18017 407856 SAM_4 SAM domain (Sterile alpha motif). This entry corresponds to a SAM domain that is found at the N-terminus of the human C19orf47 protein. 84 matched cddid_all.tbl CDD pfam18018 pfam18018 436215 DNA_pol_D_N DNA polymerase delta subunit OB-fold domain. The eukaryotic DNA polymerase delta (Pol delta) participates in genome replication, homologous recombination, DNA repair and damage tolerance. Human Pol delta consists of four subunits: p125, p50, p66 and p12. The first three subunits correspond to the three subunits of S. cerevisiae Pol delta. p50 serves as a scaffold for the assembly of Pol delta by interacting simultaneously with all of the other three subunits. This entry corresponds to the OB fold domain found in the p50 subunit. 129 matched cddid_all.tbl CDD pfam18019 pfam18019 436216 HD_6 HD domain. This HD domain is found at the N-terminus of Cas3 enzymes fused to a helicase domain. This domain is sometimes found as a separate protein. It acts as a nuclease that cleaves ssDNA. 212 matched cddid_all.tbl CDD pfam18020 pfam18020 465619 TIG_2 TIG domain found in plexin. This entry represents a TIG domain found in plexin proteins. TIG domains have an Ig-like fold. 94 matched cddid_all.tbl CDD pfam18021 pfam18021 407860 Agglutinin_C Agglutinin C-terminal. This is the C-terminal domain of the alpha chain found in Marasmius Oreades lectin protein (MOA) which binds specifically with Gal.alpha(1,3)Gal-containing sugar epitopes. The enzymatic activity of the MOA may be associated with this domain. The domain has an alpha/beta-fold, which features a central six-stranded, mostly anti-parallel, beta-sheet flanked by three alpha-helices, and a short two-stranded beta-sheet. 93 matched cddid_all.tbl CDD pfam18022 pfam18022 407861 Lectin_C_term Ricin-type beta-trefoil lectin C-terminal domain. This is the C-terminal domain of the beta chain found in Polyporus squamosus lectin protein (PSL). PSL binds specifically to glycans terminating with the sequence: Neu5Ac.alpha2-6Gal.beta. The C-terminal domain is not involved in the binding to the Neu5Ac.alpha2-6Gal.beta. The C-terminal domain is characterized by a central five-stranded beta-sheet that is flanked by three alpha-helices and topped by a short strand. It shows high fold similarity to its closest relative, the Gal.alpha1-3Gal-binding agglutinin from the mushroom Marasmius oreades agglutinin (MOA). 102 matched cddid_all.tbl CDD pfam18023 pfam18023 375495 FKBP_N_2 BDBT FKBP like N-terminal. This is the N-terminal domain of the beta chain found in Drosophila melanogaster protein BDBT (a FK506-Binding Protein) which stimulates the DBT circadian function. The domain contains the DBT-binding site. The domain is structurally homologous to the peptidyl prolyl isomerase (PPIase) regions of FK506-binding proteins despite low sequence homology. BDBT is structurally related to the immunophilin FKBP51 and it shares a common domain organization consisting of PPIase-like and TPR domains with noncanonical immunophilins such as FKBP38 or FKBPL. 113 matched cddid_all.tbl CDD pfam18024 pfam18024 407862 HTH_50 Helix-turn-helix domain. The TyrR protein of Haemophilus influenzae is a 36-kD transcription factor whose major function is to control the expression of genes important in the biosynthesis and transport of aromatic amino acids. This entry represents the C-terminal helix-turn-helix DNA-binding domain of TyrR and related proteins. 50 matched cddid_all.tbl CDD pfam18025 pfam18025 436218 FucT_N Alpha-(1,3)-fucosyltransferase FucT N-terminal domain. This is the N-terminal domain of the alpha chain found in Helicobacter pylori Fucosyltransferase protein which is involved in the production of Lewis x trisaccharide, a major component of lipopolysaccharide. The N-terminal domain contains the catalyst base, Glu-95 which is equivalent to the Asp-100 of other members of the glycosyltransferases-B family. The domain contains the pocket where LacNAc binds. The domain is composed of 2-10 heptad repeats and a conserved N-terminal alpha-beta-alpha motif which has little sequence similarity to the conserved N-terminal motif in other glycosyltransferases. 92 matched cddid_all.tbl CDD pfam18026 pfam18026 465620 Exog_C Endo/exonuclease (EXOG) C-terminal domain. This is the C-terminal domain found in EndoG-like mitochondrial endo/exonuclease (EXOG) proteins in higher eukaryotes. Evolutionary conserved mitochondrial nucleases are involved in programmed cell death and normal cell proliferation in lower and higher eukaryotes. It has been proposed that during metazoan evolution duplication of an ancestral nuclease gene could have generated the paralogous EndoG- and EXOG-protein subfamilies in higher eukaryotes, thereby maintaining the full endo/exonuclease activity found in mitochondria of lower eukaryotes. Family members include the human EXOG, a dimeric mitochondrial enzyme that displays 5'-3' exonuclease activity and further differs from EndoG in substrate specificity. This C-terminal domain is predicted to fold into a coiled-coil structure. Deletion of the domain led to a pronounced reduction in EXOG activity, revealing that the presence and most likely the proper positioning of this domain in EXOG proteins is crucial for its enzymatic activity. 49 matched cddid_all.tbl CDD pfam18027 pfam18027 407865 Pepdidase_M14_N Cytosolic carboxypeptidase N-terminal domain. This entry corresponds to the N-terminal domain of cytosolic carboxypeptidases. The N-terminal domain folds into a nine-stranded antiparallel beta sandwich. This domain is specific to CCP proteins and is absent in other carboxypeptidases. It has been hypothesized that the N-terminal domain might contribute to folding, might have a regulatory function and/or might be involved in binding other proteins. 107 matched cddid_all.tbl CDD pfam18028 pfam18028 375500 Zmiz1_N Zmiz1 N-terminal tetratricopeptide repeat domain. This is the N-terminal domain found in Zmiz1 proteins (Zinc finger MIZ domain-containing protein 1). Zmiz1 is a direct Notch1 cofactor that heterogeneously regulates Notch target genes. Zmiz1 directly interacts with the RAM1 domain of Notch1 through this N-terminal tetratricopeptide repeat (TPR) domain. Furthermore, it has been shown that Zmiz1 and Notch1 cooperatively recruit each other to chromatin through direct interaction via the N-terminal TPR domain resulting in a slight increase in activating histone marks and decrease of repressive histone marks. Functional analysis indicate that the N-Terminal Domain of Zmiz1 is important for driving Myc transcription and proliferation indirectly. 93 matched cddid_all.tbl CDD pfam18029 pfam18029 436220 Glyoxalase_6 Glyoxalase-like domain. This entry comprises a diverse set of domains related to the Glyoxalase domain. The exact specificity of these proteins is uncertain. 110 matched cddid_all.tbl CDD pfam18030 pfam18030 465621 Rimk_N RimK PreATP-grasp domain. This is the N-terminal domain found in Escherichia coli RimK proteins (Ribosomal protein S6-L-glutamate ligase). This domain precedes the ATP-grasp domain pfam08443. 94 matched cddid_all.tbl CDD pfam18031 pfam18031 465622 UCH_C Ubiquitin carboxyl-terminal hydrolases. This is the C-terminal domain found in eukaryotic UCH37 proteins (also known as Ubiquitin carboxyl-terminal hydrolase isozyme L5, UCHL5). UCH37 is a subunit of two complexes: INO80, which performs ATP-dependent sliding of nucleosomes for transcriptional regulation and DNA repair, and the 26S proteasome, which performs ATP-dependent proteolysis of polyubiquitylated proteins in the cytosol and nucleus. Recruitment to the proteasome is mediated by the C-terminal domain of RPN13 (also known as ADRM1). Recruitment to INO80 is mediated by the N-terminal domain of NFRKB. Structural and biochemical analysis reveal that RPN13 and NFRKB make similar interactions with the UCH37 C-terminal domain but have very different interactions with the catalytic UCH domain that are activating in the case of RPN13 and highly inhibitory in the case of NFRKB. 46 matched cddid_all.tbl CDD pfam18032 pfam18032 436223 FRP Photoprotection regulator fluorescence recovery protein. This family includes fluorescence recovery protein (FRP) domain, which is found in Synechocystis sp. PCC 6803 substr. Kazusa. FRP causes the dissociation of the orange carotenoid protein (OCP) from the phycobilisomes by interacting with the C-terminal domain of OCP, accelerating the conversion of the active red OCP to the inactive orange form. A patch of residues (W50, D54, H53, and R60), contributed by both chains of the FRP dimer cause the acceleration of the OCPr to OCPo conversion. Mutation of the absolutely conserved amino acids (R60) affect the activity of FRP. 99 matched cddid_all.tbl CDD pfam18033 pfam18033 436224 SpuA_C SpuA C-terminal. This is the C-terminal beta sandwich domain found in Streptococcus pneumoniae Spu4 proteins. Spu4 is a large multimodular cell wall-attached enzyme involved in the degradation of glycogen. 93 matched cddid_all.tbl CDD pfam18034 pfam18034 436225 Bac_GH3_C Bacterial Glycosyl hydrolase family 3 C-terminal domain. This is the C-terminal domain of the glycoside hydrolase family (pfam00933) 137 matched cddid_all.tbl CDD pfam18035 pfam18035 465623 Bap31_Bap29_C Bap31/Bap29 cytoplasmic coiled-coil domain. Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31. This entry represents the cytoplasmic domain which forms a heterodimeric coiled-coil with Bap29. This Bap29 and Bap31 are homologous to each other and this entry includes both proteins. 52 matched cddid_all.tbl CDD pfam18036 pfam18036 465624 Ubiquitin_4 Ubiquitin-like domain. This domain has a ubiquitin-like fold. It is found in a diverse range of proteins including the 25KDa U11/U12 component. 89 matched cddid_all.tbl CDD pfam18037 pfam18037 436228 Ubiquitin_5 Ubiquitin-like domain. This entry includes N-terminal ubiquitin-like domain from proteins such as NEDD8 ultimate buster protein. 96 matched cddid_all.tbl CDD pfam18038 pfam18038 436229 FERM_N_2 FERM N-terminal domain. This entry represents the FERM N-terminal domain found in focal adhesion kinases. 99 matched cddid_all.tbl CDD pfam18039 pfam18039 407876 UBA_6 UBA-like domain. This entry represents a UBA-like domain found at the N-terminus of ribonuclease ZC3 proteins. 42 matched cddid_all.tbl CDD pfam18040 pfam18040 436230 BPA_C beta porphyranase A C-terminal. This is the C-terminal domain found in Bacteroides plebeius of proteins such as beta-porphyranase A (BPA), a beta-galactanase that cleaves the beta-1,4 glycosidic bond. Porphyranase degrade red seaweed glycans. This domain adopts a beta sandwich shape. 95 matched cddid_all.tbl CDD pfam18041 pfam18041 465625 MapZ_EC1 MapZ extracellular domain 1. This is the extracellular domain 1 (MapZextra1) found in Streptococcus pneumoniae cell division site positioning protein MapZ. MapZ ensures accurate placement of the bacterial division site. The domain is a rigid four alpha-helices with two flexible linkers. The N-terminal end of MapZextra1 is connected to the trans-membrane segment of MapZ whilst the C-terminal is linked to MapZextra2 via a serine rich linker (SRL).The highly conserved residues are not accessible at the surface but are directly involved in many inter-helices interactions allowing for rigidity. 129 matched cddid_all.tbl CDD pfam18042 pfam18042 407879 ORF_12_N ORF 12 gene product N-terminal. This is the N-terminal domain of Streptomyces clavuligerus ORF 12 gene product, which is directly involved in biosynthesis of Clavulanic acid (CA). The N-terminal domain consists of one four-stranded antiparallel beta-sheet surrounded by four alpha-helices and folds similarly to steroid isomerases and polyketide cyclases (PKTC). However, the N-terminal domain has no apparent polar-lined active-site pocket or conserved catalytic residues analogous to those of either the steroid isomerases or PKTCs. ORF 12 has 2 binding sites, CA is able to bind both to an active site and between the two domains. The active site pocket is lined by residues from both the N- and the C-terminal domains (His88, Ser173, Thr209, Ser234, Ser278, Met383, Phe374, Ala376 and Phe385). The C-2 carboxylate of CA is positioned deep in the pocket, making electrostatic interactions with Lys375, Arg418 and Lys89. Lys89 is located in strand beta-2 of the N-terminal domain and may also be involved in the beta-lactam core-binding region, including the residues Lys89 as well as Arg418. 92 matched cddid_all.tbl CDD pfam18043 pfam18043 436232 T4_Rnl2_C T4 RNA ligase 2 C-terminal. This is the C-terminal domain of Enterobacteria phage T4 RNA ligase 2 (Rnl2). The C-terminal domain consists of a four-helix bundle. The C-terminal domain is thought to be critical for binding the Rnl2 to adenylylated nicked duplex. This is known as step 2 of the ligation pathway. 82 matched cddid_all.tbl CDD pfam18044 pfam18044 465626 zf-CCCH_4 CCCH-type zinc finger. This short zinc binding domain has the pattern of three cysteines and one histidine to coordinate the zinc ion. This domain is found in a wide variety of proteins such as E3 ligases. 22 matched cddid_all.tbl CDD pfam18045 pfam18045 407882 ISP3_C ISP3 C-terminal. This is the C-terminal domain of ISP3 protein, which plays a role in asexual daughter cell formation, for example in T.gondii. The domain consists of a seven-stranded antiparallel beta-sandwich bordered on one end by a interstrand loop (open end) and capped at the other end by an amphipathic C-terminal helix (closed end). The loop between beta 5 and beta 6 is extended and variable. The domain adopts a pleckstrin homology (PH) fold, despite having neglible sequence similarity. PH domains are often found in proteins that support protein-lipid and play a role in mediating membrane localization through IP binding. However, the Phospholipid Binding Properties of PH domains is not conserved in the ISP3. Unlike PH domains, ISP3 is cysteine rich. The cysteine-rich nature of the ISP3s and the number of surface-exposed cysteines may result in redox instability and may also facilitate higher order multimerization. There are no disulfide bonds in ISP3 unlike in ISP1. It is worth noting that ISP1 and ISP3 share low sequence identity but contain the same secondary core elements. 110 matched cddid_all.tbl CDD pfam18046 pfam18046 407883 FKBP26_C FKBP26_C-terminal. This is the C-terminal domain (CTD) of Methanocaldococcus jannaschii peptidyl-prolyl cis/trans isomerase FKBP26. FKBP26 mediates protein folding. CTD has an alpha/beta-sandwich structure composed of three alpha-helices and a three-stranded, mixed-orientation beta-sheet. The CTD domain is responsible for dimerization of FKBP26 by through inter-subunit antiparallel pairing of the third beta-strands of the two CTDs. The CTD dimer forms a continuous, six-stranded mixed beta-sheet. A CTD-like structure is also found in the phylogenetically conserved NifU proteins (HIRIP5 in mouse and humans). 72 matched cddid_all.tbl CDD pfam18047 pfam18047 436234 PatG_D PatG Domain. This is a domain found in PatG proteins, these proteins are involved in prfocessing the precursor peptide to yield the cyclic Patellamide. PatG can be found in Prochloron sp. 111 matched cddid_all.tbl CDD pfam18048 pfam18048 436235 TRAF6_Z2 TNF receptor-associated factor 6 zinc finger 2. This domain is the second of three zinc fingers of Homo sapiens TNF receptor associated factor 6 (TRAF6). TRAF6 mediates Lys63 (K63)-linked polyubiquitination for Necrosis Factor-kappaB activation. The first three residues and the last Cys of finger 1 form a classical type I beta-turn. 27 matched cddid_all.tbl CDD pfam18049 pfam18049 465627 DNA_pol_P_Exo DNA polymerase nu pseudo-exo. This domain, known as the Pseudo-exo domain, is found DNA polymerase Nu protein in species such as Homo sapiens. Residues 192-416 of Pol nu formed a degenerate 3'-5'-exonuclease domain, which deviates from the equivalent. 216 matched cddid_all.tbl CDD pfam18050 pfam18050 465628 Cyclophil_like2 Cyclophilin-like family. This entry represents a family of cyclophilin-like proteins found in a range of bacterial species. 113 matched cddid_all.tbl CDD pfam18051 pfam18051 436238 RPN1_C 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal. This is the C-terminal domain found in RPN1 proteins (26S proteasome non-ATPase regulatory subunit 2). The 26S proteasome holocomplex consists of a 28-subunit barrel-shaped core particle (CP) in the center capped at the top and bottom by 19-subunit regulatory particles (RPs). The CP forms the catalytic chamber and the RP is formed from two subcomplexes known as the lid and the base. The lid comprises nine Rpn subunits in yeast (Rpn3/5/6/7/8/9/11/12/15) and the base comprises three Rpn subunits (Rpn1/2/13) and six ATPases (Rpt1-6). 54 matched cddid_all.tbl CDD pfam18052 pfam18052 436239 Rx_N Rx N-terminal domain. This entry represents the N-terminal domain found in many plant resistance proteins. This domain has been predicted to be a coiled-coil, however the structure shows that it adopts a four helical bundle fold. 93 matched cddid_all.tbl CDD pfam18053 pfam18053 465629 GyrB_insert DNA gyrase B subunit insert domain. This is the insert domain found in DNA gyrase B subunit proteins. Studies indicate that the insert has two functions, acting as a steric buttress to pre-configure the primary DNA-binding site, and serving as a relay that may help coordinate communication between different functional domains. 167 matched cddid_all.tbl CDD pfam18054 pfam18054 407891 CEL_III_C CEL-III C-terminal. This is the C-terminal domain found in Cucumaria echinata CEL-III protein which is a lectin that exhibits both hemolytic and hemagglutinating activity. The domain is responsible for oligomerization and insertion of CEL-III into the erythrocyte membrane. The domain is composed of eight stranded beta sandwich and two alpha helices, the latter changes conformation upon binding to the cell surface carbohydrates. 154 matched cddid_all.tbl CDD pfam18055 pfam18055 465630 RPN6_N 26S proteasome regulatory subunit RPN6 N-terminal domain. This is the N-terminal domain found in RPN6 proteins (26S proteasome regulatory subunit). The 26S proteasome holocomplex consists of a 28-subunit barrel-shaped core particle (CP) in the center capped at the top and bottom by 19-subunit regulatory particles (RPs). The CP forms the catalytic chamber and the RP is formed from two subcomplexes known as the lid and the base. The lid comprises nine Rpn subunits in yeast (Rpn3/5/6/7/8/9/11/12/15) and the base comprises three Rpn subunits (Rpn1/2/13) and six ATPases (Rpt1-6). Phosphorylation of Rpn6 enhances proteasome ATPase activity and promotes the formation of doubly capped (30S) proteasome, hence accelerating the degradation of short-lived proteins. 117 matched cddid_all.tbl CDD pfam18056 pfam18056 407893 PBP3 Penicillin Binding Protein 3 Domain. This domain belongs to peptidoglycan synthesis regulatory factor 3 (PBP3) from streptococcus pneumoniae. Peptidoglycan synthesis regulatory factor are known as Penicillin binding proteins (PBP) and are membrane-associated enzymes that perform critical functions in the bacterial cell division process. The domain contributes residues to the active site such as Arg 278. 110 matched cddid_all.tbl CDD pfam18057 pfam18057 465631 DUF5594 Domain of unknown function (DUF5594). This domain was first discovered in BPSL1050, a highly immunoreactive protein found in Burkholderia pseudomallei. The domain's structure consists of three helical regions which pack onto an antiparallel beta sheet, formed by four strands. The beta sheet is solvent exposed on one side and packs tightly against the three helices on the other side, generating a network of hydrophobic and aromatic interactions that contribute to tight packing of the protein. Is is thought that the small loop L1, the main loop L2, and part of helix alpha-3 extending until Leu120 are the three main immunogenic sequences. 115 matched cddid_all.tbl CDD pfam18058 pfam18058 407895 SbsC_C SbsC C-terminal domain. This is the C-terminal domain found in Bacterial Cell Surface Layer Protein SbsC which can be found in species such as Geobacillus stearothermophilus. The C-terminal domain is the third and last triple-helical bundle and adopts a canonical coiled-coil structure. A similar overall arrangement of antiparallel triple-helical bundles has been found in the cytoskeletal protein spectrin (2SPC). 132 matched cddid_all.tbl CDD pfam18059 pfam18059 436243 Csd3_N Csd3 N-terminal. Csd3 (also known as HdpA) is a bi-functional enzyme with delta,delta-endopeptidase activity and delta,delta-carboxypeptidase activity. The N-terminal domain is also known as domain 1 and is composed of an alpha/beta fold consisting of a five-stranded antiparallel beta-sheet and three short alpha-helices. Domain 1 blocks the active-site cleft of the LytM domain, with the protruding helix alpha-3 contributing to the Zn2+ coordination sphere. The fold of domain 1 is very remotely related to monellin/cystatin superfamily proteins, some of which act as inhibitors of cysteine peptidases. 83 matched cddid_all.tbl CDD pfam18060 pfam18060 407897 F_actin_bund_C F actin bundling C terminal. This is the C-terminal domain found in 34 kDa F actin bundling protein. ABP34 is a calcium regulated actin binding protein that cross links actin filaments into bundles. Residues 216-244 in the C-domain are part of the strongest actin-binding sites (residue 193 residue 254) and have conserved sequences with the actin-binding regions of alpha-actinin and ABP120. 87 matched cddid_all.tbl CDD pfam18061 pfam18061 407898 CRISPR_Cas9_WED CRISPR-Cas9 WED domain. This domain, known as the wedge (WED) domain, is found in Cas9 proteins which are present in Staphylococcus aureus. Cas9 cleaves double-stranded DNA targets with a protospacer adjacent motif (PAM) and complementarity to the guide RNA. The Cas9 WED domain has a fold comprising a twisted five-stranded beta sheet flanked by four alpha helices, and is responsible for the recognition of the distorted repeat: anti-repeat duplex. WED domains are responsible for the recognition of single-guide RNA scaffolds. 126 matched cddid_all.tbl CDD pfam18062 pfam18062 407899 RE_AspBHI_N Restriction endonuclease AspBHI N-terminal. This is the N-terminal domain found in modification-dependent restriction endonuclease proteins such as AspBHI, which can be found in Azoarcus sp. AspBHI is a homo-tetrameric protein that recognizes 5-methylcytosine in the double-strand DNA sequence context of (C/T) (C/G) (5mC) nucleotide (C/G) and cleaves the two strands at a fixed distance (N12/N16) 3 to the modified cytosine. The N-terminal domain is responsible for DNA-recognition and resembles an SRA-like 5-methylcytosine binding domain in structure and function. 185 matched cddid_all.tbl CDD pfam18063 pfam18063 407900 BB_PF Beta barrel Pore-forming domain. This domain is found in Monalysin Pore-forming Toxin which is a type of beta-barrel pore-forming toxin protein found in Pseudomonas entomophila. Monalysin forms a stable doughnut-like 18-mer complex composed of two disk-shaped nonamers to form a pore. The domain is composed of a central twisted beta -sheet composed of three antiparallel beta-strands (beta 3, beta 6, and beta 8/9) and flanked by the pore-forming segment and the C-terminal region on either side. The pore-forming domain (residues 102-170) is located between strands beta 3 and beta 6, and is formed from two antiparallel beta-strands connected by three alpha-helices, alpha 3, alpha 4, and alpha 5. The C-terminal region forms a long alpha-helix followed by a small hairpin and a short alpha-helix. 204 matched cddid_all.tbl CDD pfam18064 pfam18064 436244 ParB_C Centromere-binding protein ParB C-terminal. This is the C-terminal domain found in centromere-binding protein ParB, which is used for stable segregation. The C-terminal domain has a ribbon-helix helix (RHH) motif with a C-terminal loop (residues 119-128) following helix alpha-2. The domain forms a dimer with the C-terminal of the beta chain. The function of the C-terminal domain is to bind to DNA. 47 matched cddid_all.tbl CDD pfam18065 pfam18065 436245 PatG_C PatG C-terminal. This is the C-terminal domain of Prochloron sp. PatG, which process the precursor peptide to yield the cyclic Patellamide. The C-terminal domain of PatG is 56% structurally homologous to the C-terminal domain of PatA. 115 matched cddid_all.tbl CDD pfam18066 pfam18066 407902 Phage_ABA_S Phage ABA sandwich domain. This domain is found in a prophage protein BC1872 found in B. cereus. The domain forms a three-layer beta/alpha/beta sandwich. Three alpha-helices, alpha1, alpha2, and alpha3, are sandwiched on one side by three-stranded antiparallel beta-sheet (beta3, beta4, and beta5) and on the other by a beta-hairpin (beta1 and beta2). 89 matched cddid_all.tbl CDD pfam18067 pfam18067 407903 Lipase_C Lipase C-terminal domain. This domain is found in Archaeoglobus fulgidus lipase (AFL). The domain consists of a layer of seven beta-sheet. When the domain is combined with the proximal domain, which is also a layer of seven beta-sheet, they form a beta sandwich. The combination of these two domains is known as the C-terminal domain. It is likely that the C-terminal domain plays an important role in substrate specificity, catalytic efficiency but also attributes partly to AFLs stability. 96 matched cddid_all.tbl CDD pfam18068 pfam18068 407904 Npun_R1517 Npun R1517. This domain belongs to NPun R1517 which is found in Nostoc punctiforme. Studies indicate that Npun R1517 is encoded by orphan gene 29. Npun R1517 adopts a sleigh-shaped structure with a two-stranded antiparallel beta-sheet forming the floor of the sleigh, a HTH forming the seat and a HTH forming the front of the sleigh. 74 matched cddid_all.tbl CDD pfam18069 pfam18069 436246 DR2241 DR2241 stabilising domain. This is the middle domain found in DR2241, a multi-domain protein with an N-terminal cobalamin (vitamin B12) chelatase domain. DR2241 is found in D. radiodurans. The middle domain has four alpha-helices (alpha7-alpha10) in contact with the N-terminal domains and C-terminal domain and five anti-parallel beta-strands with strand order 12354 at the outer side of one monomer. The middle domain, as well as the C-terminal domain, are heavily involved in the tetramer stabilization. 111 matched cddid_all.tbl CDD pfam18070 pfam18070 407906 Cas9_PI2 CRISPR-Cas9 PI domain. This domain is found in Cas9 proteins which can be Staphylococcus aureus. Cas9 cleaves double-stranded DNA targets with a protospacer adjacent motif (PAM) and complementarity to the guide RNA. When this domain is combined with the C-terminal domain it is called the Pam-interacting (PI) domain. The Cas9 orthologs from different microbes have highly divergent sequences but their PI domains share a conserved core fold and recognize distinct PAM sequences. 59 matched cddid_all.tbl CDD pfam18071 pfam18071 407907 HMW1C_N HMW1C N-terminal. This is the N-terminal domain found in Actinobacillus pleuropneumoniae HMW1C (ApHMW1C). HMW1 adhesin is an N-linked glycoprotein that mediates adherence to respiratory epithelium through N-glycosylation of protein acceptor sites an O-glycosylation of sugar acceptor sites. The N-terminal domain forms an all alpha domain (AAD) when combined with the domain spanning from residue 154 to residue 245. The AAD interacts extensively with the C-terminal GT-B fold in order to create unique groove with potential to accommodate the acceptor protein. 143 matched cddid_all.tbl CDD pfam18072 pfam18072 465632 FGAR-AT_linker Formylglycinamide ribonucleotide amidotransferase linker domain. This is the linker domain found in Formylglycinamide ribonucleotide amidotransferase (FGAR-AT), also known as Phosphoribosylformylglycinamidine synthase (EC:6.3.5.3), PurL and formylglycinamidine ribonucleotide (FGAM) synthase. This enzyme catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP, Pi, and glutamate in the fourth step of the purine biosynthetic pathway. The structure analysis of Salmonella typhimurium FGAR-AT reveals that this linker domain is made up of a long hydrophilic belt with an extended conformation. 50 matched cddid_all.tbl CDD pfam18073 pfam18073 436248 Rubredoxin_2 Rubredoxin metal binding domain. This is the C-terminal rubredoxin metal binding domain found in Interest in lipopolysaccharide (LPS) assembly protein B (LapB). Rubredoxin proteins form small non-heme iron binding sites that use four cysteine residues to coordinate a single metal ion in a tetrahedral environment. Rubredoxins are most commonly found in bacterial systems, but have also been found in eukaryotes. The key features of these rubredoxin-like domains are the extended loops or 'knuckles' and the tetracysteine mode of iron binding. Structural analysis of LapB from Escherichia coli show that the rubredoxin metal binding domain is intimately bound to the TPR motifs and that this association to the TPR motifs is essential to LPS regulation and growth in vivo. Other family members include RadA proteins which play a role in DNA damage repair. In E. coli, a protein known as RadA (or Sms) participates in the recombinational repair of radiation-damaged DNA in a process that uses an undamaged DNA strand in one DNA duplex to fill a DNA strand gap in a homologous sister DNA duplex. RadA carries a zinc finger at the N-terminal domain. 28 matched cddid_all.tbl CDD pfam18074 pfam18074 465633 PriA_C Primosomal protein N C-terminal domain. This is the C-terminal domain found in PriA DNA helicase, a multifunctional enzyme that mediates the process of restarting prematurely terminated DNA replication reactions in bacteria. The C-terminal domain (CTD) bears similarity to the S10 subunit which binds branched rRNA within the bacterial ribosome. The C-terminal domain is part of the helicase domain of PriA proteins. It acts together with the 3' DNA-binding domain to form a site for binding ssDNA-binding protein (SSB). 96 matched cddid_all.tbl CDD pfam18075 pfam18075 465634 FtsX_ECD FtsX extracellular domain. This is the extracellular domain (ECD) found in FtsX enzyme, a homolog of the transmembrane PG-hydrolase regulator. The FtsX extracellular domain binds the PG peptidase Rv2190c/RipC N-terminal segment, causing a conformational change that activates the enzyme ileading to PG hydrolysis in Mycobacterium tuberculosis. Structural analysis of FtsX ECD reveals fold containing two lobes connected by a flexible hinge. Mutations in the hydrophobic cleft between the lobes showed reduction in RipC binding in vitro and inhibition of FtsX function in Mycobacterium smegmatis. 94 matched cddid_all.tbl CDD pfam18076 pfam18076 465635 FGAR-AT_N Formylglycinamide ribonucleotide amidotransferase N-terminal. This is the N-terminal domain found in Formylglycinamide ribonucleotide amidotransferase (FGAR-AT), also known as Phosphoribosylformylglycinamidine synthase (EC:6.3.5.3), PurL and formylglycinamidine ribonucleotide (FGAM) synthase. This enzyme catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide and glutamine to formylglycinamidine ribonucleotide, ADP, Pi, and glutamate in the fourth step of the purine biosynthetic pathway. 115 matched cddid_all.tbl CDD pfam18077 pfam18077 465636 DUF5595 Domain of unknown function (DUF5595). This domain is found in Nude C 80 (Ndc80) proteins which can be found in species such as Homo sapiens. Ndc80 protein complexes are a core component of the end-on attachment sites for kinetochore microtubules. Ndc80 is also known as Hec1, for highly expressed in cancer 1. 73 matched cddid_all.tbl CDD pfam18078 pfam18078 465637 Thioredoxin_11 Thioredoxin-like SNTX domain. This domain is found in pore-forming toxin stonustoxin (SNTX), a lethal venom found in Synanceia horrida. Because of the thioredoxin-like nature of the domain, it is referred to as the THX domain. The THX domain is comprised of a five-stranded beta-sheet and shares greatest structural similarity with Saccharomyces cerevisiae mitochondrial THX3. It is thought that THX domain plays a purely structural role. 126 matched cddid_all.tbl CDD pfam18079 pfam18079 436254 AglB_L1 Archaeal glycosylation protein B long peripheral domain. This domain is found in Archaeal Glycosylation B protein (AglB-Long) in A. fulgidus. When the domain, known as peripheral l (Pl), is combined with the central core (CC) and insertion (IS) sub-units, they form the C-terminal domain. It is thought that the C-terminal domain may contribute toward the increased thermal stability of the AglB proteins in the hyper-thermophilic. 87 matched cddid_all.tbl CDD pfam18080 pfam18080 465638 Gal_mutarotas_3 Galactose mutarotase-like fold domain. This domain is found in endo-alpha-N-acetylgalactosaminidase present in Streptococcus pneumoniae. Endo-alpha-N-acetylgalactosaminidase is a cell surface-anchored glycoside hydrolase involved in the breakdown of mucin type O-linked glycans. The domain, known as domain 2, exhibits strong structural similarlity to the galactose mutarotase-like fold but lacks the active site residues. Domains, found in a number of glycoside hydrolases, structurally similar to domain 2 confer stability to the multidomain architectures. 241 matched cddid_all.tbl CDD pfam18081 pfam18081 465639 FANC_SAP Fanconi anemia-associated nuclease SAP domain. This domain is found in Fanconi-anemia-associated nuclease 1 (FAN1) present in Pseudomonas aeruginosa. FAN1 is a nuclease associated with Fanconi anemia (FA), an autosomal recessive genetic disorder caused by defects in FA genes responsible for processing DNA inter-strand cross-links (ICLs). The domain, known as the SAP domain, helps to augment the overall protein DNA interaction by interacting with the 3' and 5' ends of the template strand. Support of the pre-nick segment binding is crucial as multiple mutations in this domain resulted in hypersensitivity to a cross-linking agent in the SAP domain of Caenorhabditis elegans' FAN1. The helix-hairpin-helix of the SAP recognize three consecutive phosphate groups (C19, A20 and A21) at the 3' end of the template via the basic residues K116, K135 and K117. 51 matched cddid_all.tbl CDD pfam18082 pfam18082 465640 NAT_N N-acyltransferase N-terminal domain. This is the N-terminal all helix domain found in N-acyltransferases (NATs), the gene products orf11 and dbv8. The all-helix domain is composed of eight helices with two helix-turn-helix motifs in tandem. It is structurally akin to the AAA+ protein family (ATPases associated with diverse cellular activities). 129 matched cddid_all.tbl CDD pfam18083 pfam18083 436258 PutA_N Proline utilization A N-terminal domain. This domain is found in Proline utilization A (PutA) proteins present in Geobacter sulfurreducens. PutA are bifunctional peripheral membrane flavoenzymes that catalyze the oxidation of l-proline to l-glutamate and couple the oxidation of imported proline imported to the reduction of membrane-associated quinones. This domain is located at the N-terminus and is referred to as the alpha domain. The hydrocarbon tail of Zwittergent 3-12 binds to an exposed hydrophobic patch of the alpha domain which contains aromatic and nonpolar residues. The domain may be involved in membrane association. 113 matched cddid_all.tbl CDD pfam18084 pfam18084 465641 ARTD15_N ARTD15 N-terminal domain. This is the N-terminal domain of poly ADP-ribose polymerase (PARP16 also known as ARTD15) present in homo sapiens. ARTDs catalyze the formation of branched or unbranched chains of ADP-ribose units on protein side chains. The N-terminal domain of ARTD15 does not share any obvious sequence similarity with the regulatory domains of ARTD1-4. The N-terminal domain arrangement in both ARTD15 and ARTD1-3 suggests a regulatory role through different mechanisms. 81 matched cddid_all.tbl CDD pfam18085 pfam18085 465642 Mak_N_cap Maltokinase N-terminal cap domain. Glycogen is a central energy storage molecule in bacteria and the metabolic pathways associated with its biosynthesis and degradation are crucial for maintaining cellular energy homeostasis. In mycobacteria, the GlgE pathway involves the combined action of trehalose synthase (TreS), maltokinase (Mak) and maltosyltransferase (GlgE). The N-terminal lobe can be divided into two subdomains: a cap N-terminal subdomain comprising the first 88 amino acid residues. This entry is for the cap N-terminal domain found in mycobacterial maltokinase (Mak), (EC:2.7.1.175). The N-terminal cap subdomain and the C-terminal lobe are predominantly acidic, the intermediate subdomain is enriched in positively charged residues. A structural search with only the first 88 amino acid residues of Mak, corresponding to the N-terminal cap subdomain of maltokinases, unveiled a resemblance with proteins displaying the cystatin fold and a remote similarity with the N-terminal domain of the serine/threonine protein kinase GCN2. Conservation of the cap subdomain in maltokinases (including the bifunctional TreS-Mak enzymes), in particular of the residues in the proximity of the P-loop, together with the potential flexibility of this region, are compatible with regulatory functions for this subdomain. Hence it is hypothesized that the N-terminal cap subdomain plays a central role in modulation of Mak enzymatic activity. 88 matched cddid_all.tbl CDD pfam18086 pfam18086 465643 PPIP5K2_N Diphosphoinositol pentakisphosphate kinase 2 N-terminal domain. This is the N-terminal domain found in the Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 (PPIP5K2), EC:2.7.4.24. Structure analysis of human PPIP5K2 indicate that this region forms alpha-beta-alpha domain.PPIP5K2 is one of the mammalian PPIP5K isoforms responsible for synthesis of diphosphoinositol polyphosphates (inositol pyrophosphates; PP-InsPs), regulatory molecules that function at the interface of cell signaling and organizmic homeostasis. 90 matched cddid_all.tbl CDD pfam18087 pfam18087 436262 RuBisCo_chap_C Rubisco Assembly chaperone C-terminal domain. This is the C-terminal domain, also known as the beta domain, of Rubsico Assembly Chaperone protein (Raf1). Raf1 is necessary for rubisco to catalyze the rate-limiting step of carbon fixation through carboxylating the five-carbon sugar substrate ribulose-1,5-bisphosphate. The beta domains primary function is dimerization, which is critical for Raf1 to achieve the necessary avidity for complex formation with RbcL (the large complex sub-unbit of Rubsico) assembly intermediates. The beta domain is also involved, to a small extent, in binding to RbcL with use of the lustiness near the beta domain's conserved top surface. 138 matched cddid_all.tbl CDD pfam18088 pfam18088 465644 Glyco_H_20C_C Glycoside Hydrolase 20C C-terminal domain. This is the C-terminal domain of Glycoside hydrolase 20 C (GH20C) present in S. pneumoniae. GH20C possesses the ability to hydrolyze the beta-linkages joining either N-acetylglucosamine or N-acetylgalactosamine to a wide variety of aglycon residues. The C-terminal domain is commonly known as Domain III is important in dimerization as it forms the primary interface of the dimer. However, there is presently no evidence supporting dimerization as being necessary for catalysis. Domain III is unusual among structurally characterized GH20 enzymes but in GH20 enzymes possessing domain III, dimerization seems to be a conserved feature. 194 matched cddid_all.tbl CDD pfam18089 pfam18089 465645 DAPG_hydrolase DAPG hydrolase PhiG domain. This domain is found in 2,4-diacetylphloroglucinol hydrolase PhiG present in Pseudomonas fluorescens. 2,4-diacetylphloroglucinol hydrolase is the gene product of PhiG that is responsible for cleaving toxic 2,4-diacetylphloroglucinol (DAPG). The small N-terminal region of the domain is involved in dimerization through hydrogen bonding of the dimer interface. The C-terminal catalytic region resembles the tetracenomycin aromatase/cyclase and has a Bet v1-like fold. DAPG PhiG is the first discovered hydrolase whose catalytic domain belongs to the Bet v1-like fold, rather than the classical alpha/beta-fold hydrolases. 224 matched cddid_all.tbl CDD pfam18090 pfam18090 375543 SoPB_HTH Centromere-binding protein HTH domain. This domain is found in centromere-binding protein (SopB). SopB displays an intriguing range of DNA-binding properties essential for partition; it binds the centromere to form a partition complex, which recruits NTPase (SopA), and it also inhibits SopA polymerization. The domain has a helix-turn-helix (HTH) structure and is thought to be the specific DNA-binding domain mainly through residues from the recognition helix, alpha 3, of the HTH. The domain has show structural similarity to the DNA-binding domains of P1 ParB and KorB. 75 matched cddid_all.tbl CDD pfam18091 pfam18091 436265 E3_UbLigase_RBR E3 Ubiquitin Ligase RBR C-terminal domain. This is the C-terminal domain of HOIP present in Homo sapiens. HOIP synthesize the linear ubiquitin chains that help control innate immunity and inflammation. This region has an RBR domain which catalyzes the transfer of ubiquitin onto a substrate. 92 matched cddid_all.tbl CDD pfam18092 pfam18092 436266 DraK_HK_N DraK Histidine Kinase N-terminal domain. This is the N-terminal domain found in DraK Histidine Kinase (HK) present in Streptomyces coelicolor. Activation of the DraK HK leads to autophosphorylation of its kinase domain in the cytoplasm and subsequent transphosphorylation of DraR promoting blue-pigmented polyketide actinorhodin (ACT) production. The N-terminal domain is known as the sensor (or input) domain and undergoes a conformational change resulting in phosphorylation of a conserved histidine in its cytoplasmic kinase domain. 85 matched cddid_all.tbl CDD pfam18093 pfam18093 436267 Trm5_N tRNA methyltransferase 5 N-terminal domain. This is the N-terminal domain of tRNA methyltransferase 5 (Trm5) present in Methanocaldococcus jannaschii. Trm5 catalyzes the methyl transfer from S-adenosyl methionine (AdoMet) to N1 of G37. This domain, also known as the D1 domain, contacts the tertiary core (elbow) region of the tRNA L shape in a ternary complex of the enzyme with tRNA and AdoMet. 47 matched cddid_all.tbl CDD pfam18094 pfam18094 436268 DNA_pol_B_N DNA polymerase beta N-terminal domain. This is the N-terminal domain of DNA polymerase beta present in Homo sapiens. DNA polymerase beta is a repair enzyme that has a key role in the base excision repair of simple DNA lesions. 104 matched cddid_all.tbl CDD pfam18095 pfam18095 436269 PAS_12 UPF0242 C-terminal PAS-like domain. This domain is found at the C-terminus of proteins of the UPF0242 family. This domain is related to the PAS domain pfam13426. 153 matched cddid_all.tbl CDD pfam18096 pfam18096 465646 Thump_like THUMP domain-like. This is a domain of unknown function found in bacteria. 76 matched cddid_all.tbl CDD pfam18097 pfam18097 465647 Vta1_C Vta1 C-terminal domain. This is the C-terminal domain of Vta1 proteins pfam04652. Structural and functional analysis indicate that this C-terminal domain promotes the ATP-dependent double ring assembly of Vps4. Furthermore, it has been shown that it is necessary and sufficient for protein dimerization. Mutations in Lys-299 and Lys-302 completely abolished the ability of Vta1 to stimulate the ATPase activity of Vps4 while mutation in Lys-322 had no effect. 38 matched cddid_all.tbl CDD pfam18098 pfam18098 436272 RPN5_C 26S proteasome regulatory subunit RPN5 C-terminal domain. This is the C-terminal domain of the 26S proteasome regulatory subunit RPN5 proteins.This helical domain can be found adjacent to pfam01399. The 26S proteasome is the major ATP-dependent protease in eukaryotes. Three subcomplexes form this degradation machine: the lid, the base, and the core. The helices found at the C terminus of each lid subunit form a helical bundle that directs the ordered self-assembly of the lid subcomplex. This domain which comprises the tail of RPN5 along with the tail of Rpn9, are important for Rpn12 binding to the lid. 32 matched cddid_all.tbl CDD pfam18099 pfam18099 407934 DUF5010_C DUF5010 C-terminal domain. This domain is found at the end of a family of putative glycosyl hydrolases pfam16402. This domain is likely to function as a carbohydrate binding domain due to its similarity with pfam03422. 112 matched cddid_all.tbl CDD pfam18100 pfam18100 465648 PDE4_UCR Phosphodiesterase 4 upstream conserved regions (UCR). This is the upstream conserved region (UCR) found in Phosphodiesterase 4 (PDE4) enzymes. PDE4 is a contributor to intracellular signalling and an important drug target. The four members of this enzyme family (PDE4A to -D) are functional dimers in which each subunit contains two upstream conserved regions (UCR), UCR1 and -2, which precede the C-terminal catalytic domain pfam00233. Due to alternative promoters/start sites and variable mRNA splicing, transcription from the four PDE4 genes results in the expression of more than 25 different isoforms of PDE4. Each isoform has a unique N-terminal region that determines its specific subcellular localization by mediating interactions with scaffolding proteins. The isoforms are further classified into long, short, and supershort forms based on the presence or absence of two upstream conserved regions (UCRs, known as UCR1 and UCR2). Long splice variants contain both UCR1 and UCR2, short variants lack UCR1, and the supershort forms of PDE4 additionally lack part of UCR2. The extent to which UCRs are present determines critical functional differences between the isoforms. Phosphorylation by protein kinase A (PKA) at a conserved site on UCR1 activates all long PDE4 isoforms. Mutation and deletion studies have shown that long forms of PDE4 are dimeric, with key dimerization interactions mediated by UCR1 and UCR2, and that the C-terminal half of UCR2 could play a negative regulatory role. 119 matched cddid_all.tbl CDD pfam18101 pfam18101 465649 Pan3_PK Pan3 Pseudokinase domain. This is a pseudokinase (PK) domain found in PAB-dependent poly(A)-specific ribonuclease subunit pan3. PAN3 proteins contain three prominent regions: an unstructured N-terminal region (N-term), a central PK domain, and a highly conserved C-terminal domain (C-term). The PAN3 PK domain has retained its ATP binding capacity, and this function is required for mRNA degradation in vivo. Analysis of Pan3 amino acids sequences show that, despite of retaining the general structural characteriztics of protein kinases, the PK domain has substitutions in all the conserved motifs that are critical for kinase activity, such as in the catalytic VAIK and HRD motifs and in the Mg2+ binding DFG motif. However, the PAN3 PK domain has been shown to bind ATP. Furthermore, similar to other kinases, the ATP-binding site is located in the cleft between the N- and C-lobes of the kinase fold, however, the ATP-binding pocket is wider than that of typical kinases. 138 matched cddid_all.tbl CDD pfam18102 pfam18102 465650 DTC Deltex C-terminal domain. This is the C-terminal domains found in members of the Deltex family of proteins which comprises five members (DTX1, 2, 3, 4, and 3L). This conserved C-terminal region of about 150 residues of the Deltex family, is preceded by a RING E3 ligase domain in four of the members. Crystal structure of the Deltex C-terminal (DTC) domain reveals a fold composed of a central beta-sheet lined with two long parallel alpha-helices. 133 matched cddid_all.tbl CDD pfam18103 pfam18103 375552 SH3_11 Retroviral integrase C-terminal SH3 domain. This is the carboxy-terminal domain (CTD) found in retroviral integrase, an essential retroviral enzyme that binds both termini of linear viral DNA and inserts them into a host cell chromosome. The CTD adopts an SH3-like fold. Each CTD makes contact with the phosphodiester backbone of both viral DNA molecules, essentially crosslinking the structure. 63 matched cddid_all.tbl CDD pfam18104 pfam18104 465651 Tudor_2 Jumonji domain-containing protein 2A Tudor domain. This is the tudor domain found in histone demethylase Jumonji domain-containing protein 2A (JMJD2A). Structure and function analysis indicate that this domain can recognize equally well two unrelated histone peptides, H3K4me3 and H4K20me3, by means of two very different binding mechanisms. JMJD2 also known as KDM4, is a conserved iron (II)-dependent jumonji-domain demethylase subfamily that is essential during development. Vertebrate KDM4A-C proteins contain a conserved double tudor domain (DTD). 35 matched cddid_all.tbl CDD pfam18105 pfam18105 436277 PGM1_C PGM1 C-terminal domain. This is the C-terminal domain found in PGM1 present in Streptomyces cirratus. PGM1 is a gene product that links precursor peptides together to form the antibiotic Pheganomycin. 53 matched cddid_all.tbl CDD pfam18106 pfam18106 465652 Rol_Rep_N Rolling Circle replication initiation protein N-terminal domain. This is the N-terminal domain of the Rolling Circle Replication Initiator Protein (Rep) from Geobacillus stearothermophilus. This protein acts on plasmids from family pT181 to initiate replication, recruit a helicase to the site of initiation and terminate replication after DNA synthesis. These proteins possess a unique active site and a catalytically essential metal ion is bound in a distinct manner from other rolling circle Reps. 92 matched cddid_all.tbl CDD pfam18107 pfam18107 407941 HTH_ABP1_N Fission yeast centromere protein N-terminal domain. This domain is found in the fission yeast centromere protein (Abp1) in species such as Shizosaccharomyces pombe. The domain, referred to as Domain 1, is DNA-binding and makes up half of the N-terminal region. 61 matched cddid_all.tbl CDD pfam18108 pfam18108 465653 QSOX_Trx1 QSOX Trx-like domain. This domain is found in Quiescin sulfhydryl oxidase (QSOX), an oxidoreductase present in Homo sapiens capable of both generating and transferring disulfide modules within a single polypeptide. The domain is thioredoxin-like, hence referred to as Trx1 domain. Trx1 domain has a di-cysteine motif (Cys-X-X-Cys) which is related to the redox-active domains of protein disulfide isomerase. The Trx1 domain is responsible for intramolecular disulfide transfer through the di-cysteine motif. 108 matched cddid_all.tbl CDD pfam18109 pfam18109 436280 Fer4_24 Ferredoxin I 4Fe-4S cluster domain. This is domain is found in Ferredoxin I (FdI), an Iron-sulfur ([Fe-S]) cluster-containing protein, present in species such as Azotobacter vinelandii. [Fe-S] proteins participate in electron transfer, catalytic, regulatory, and structural function. The FdI cluster exhibits a pH-dependent reduction potential and reversible protonation in the reduced state. 35 matched cddid_all.tbl CDD pfam18110 pfam18110 465654 BRCC36_C BRCC36 C-terminal helical domain. This is the C-terminal domain of BRCC36, a Zn2+ dependent deubiquitinating enzyme, present in Camponotus floridanus. BRCC36 hydrolyzes lysine linked ubiquitin chains as part of macromolecular complexes that participate in either interferon signalling or DNA-damage recognition. The domain consists of 2 non canonical helices. The domain interacts hydrophobically with helices alpha 4 and alpha 5 of KIAA0157 in the form of a coiled coil helical bundle. This interaction helps establish the association of BRCC36 with KIAA0157, a pseudo-DUB MPN- protein that is essential for the activity of BRCC36. 81 matched cddid_all.tbl CDD pfam18111 pfam18111 465655 RPGR1_C Retinitis pigmentosa G-protein regulator interacting C-terminal. This is the C-terminal domain of retinitis pigmentosa G-protein regulator (RPGR) interacting protein-1 present in Homo sapiens. A mutation in RPGR interacting protein-1 can be observed in the eye disease Leber congenital amaurosis. The domain is commonly known as the RPGR-interacting domain (RID) and is thought to have a C2-like fold. 166 matched cddid_all.tbl CDD pfam18112 pfam18112 407946 Zn-C2H2_12 Autophagy receptor zinc finger-C2H2 domain. This domain is found in calcium-binding and coiled-coil domain 2/NDP25 (CALCOCO2/NDP25) found in Homo sapiens. CALCOCO2/NDP25 is an ubiquitin-binding autophagy receptor involved in the selective autophagic degradation of invading pathogens. This domain is a typical C2H2-type zinc finger which specifically recognizes mono-ubiquitin or poly-ubiquitin chain. The overall ubiquitin-binding mode utilizes the C-terminal alpha-helix to interact with the solvent-exposed surface of the central beta-sheet of ubiquitin, similar to that observed in the RABGEF1/Rabex-5 or POLN/Pol-eta zinc finger. 27 matched cddid_all.tbl CDD pfam18113 pfam18113 436282 Rbx_binding Rubredoxin binding C-terminal domain. This is the C-terminal domain found in rubredoxin reductase (RdxR) present in Pseudomonas aeruginosa. RdxR are important in prokaryotes as they allow for the metabolism of inert n-alkanes and RdxR is also crucial for archaea and anaerobic bacteria in the response to oxidative stress. This domain is known to recognize and bind to rubredoxin. 71 matched cddid_all.tbl CDD pfam18114 pfam18114 436283 Suv3_N Suv3 helical N-terminal domain. This is the N-terminal domain of Suv3 present in Homo sapiens. Suv3 is an NTP-dependent RNA/DNA helicase that is necessary for the degradation of mature mtRNAs. Suv3 has been found to interact in vitro with polynucleotide phosphorylase. 116 matched cddid_all.tbl CDD pfam18115 pfam18115 436284 Tudor_3 DNA repair protein Crb2 Tudor domain. This is the tudor domain found in DNA repair protein crb2. Structural and functional studies of Crb2 and its mammalian homolog 53BP1 indicate that the conserved tandem-Tudor domain of 53BP1 and Crb2 preferentially interacts with H4K20me2, though it also binds to H4K20me1. Furthermore, despite low amino acid sequence similarity, Crb2 is structurally related to 53BP1 in having two tudor domains and a conserved dimethyllysine-binding pocket, and that, like 53BP1, it directly binds H4-K20me2. 50 matched cddid_all.tbl CDD pfam18116 pfam18116 436285 SNX17_FERM_C Sorting Nexin 17 FERM C-terminal domain. This is the C-terminal domain of sorting nexin 17 (SNX17) present in Homo sapiens. SNX17 localizes to early endosomes where it directly binds NPX(Y/F) motifs in the target receptors to mediate their rates of endocytic internalization, recycling, or degradation. The domain is known as terminal band 4.1/ezrin/radixin/moesin (FERM) domain. The FERM domain binds directly to the common motif, NPX(Y/F), in the cytoplasmic region of its target proteins. 109 matched cddid_all.tbl CDD pfam18117 pfam18117 407951 EDS1_EP Enhanced disease susceptibility 1 protein EP domain. The plant specific protein family, which comprises EDS1 (Enhanced disease susceptibility 1), PAD4 (Phytoalexin deficient4) and SAG101 (Senescence-associated gene 101), is involved in innate immunity. Signaling by intracellular immune receptors with NB-ARC domain (pfam00931) relies on this protein family. C-terminus of Arabidopsis EDS1 and PAD4 proteins did not have recognizable sequence homology to other domains and therefore named EP domain (EDS1-PAD4). A combination of an N-terminal lipase_3 domain (pfam01764) and the C-terminal EP-domain is the defining feature of this family. Structurally, EP domain comprises exclusively of alpha-helices (PDB:4NFU). Structure-function analysis of Arabidopsis proteins showed that EDS1 forms heterodimers with PAD4 or SAG101, chiefly through the N-terminal lipase_3 domain. These heterodimers are essential for plant defense signaling. The EP domain is not stable without the lipase_3 domain, but is required for immunity. Mutations of conserved residues in the EP domain of EDS1 strongly affect its immune signaling function. 214 matched cddid_all.tbl CDD pfam18118 pfam18118 436286 PRC2_HTH_1 Polycomb repressive complex 2 tri-helical domain. This domain can be found in the Polycomb repressive complex 2 (PRC2) present in Homo sapiens. Polycomb complexes maintain repressive chromatin states by silencing gene expression. PRC2 does this by methylating lysine 27 of histone H3. This domain makes up part of the N-lobe which is involved in regulation. 101 matched cddid_all.tbl CDD pfam18119 pfam18119 465656 RIG-I_C RIG-I receptor C-terminal domain. This is the C-terminal domain of Innate Immune Pattern-Recognition Receptor RIG-I present in homo sapiens. RIG-I is a key cytosolic pattern-recognition receptors of the vertebrate innate immune system that form the first line of defense against RNA viral infection. RNA binding to RIG-I is mediated both by the C-terminal domain and by the helicase domain. The C-terminal domain specifically binds the 5'triphosphate end with a 10-fold higher affinity compared to 5'OH-dsRNA. 139 matched cddid_all.tbl CDD pfam18120 pfam18120 465657 DUF5597 Domain of unknown function (DUF5597). This is the C-terminal domain of xyloglucan utilization locus (XyGUL) present in Cellvibrio japonicas. XyGUL is required for xyloglucan utilization. It is also the C-terminal domain of PF02449 and PF01301. 119 matched cddid_all.tbl CDD pfam18121 pfam18121 465658 TFA2_Winged_2 TFA2 Winged helix domain 2. This is the second winged helix domain can be found in TFA2 proteins present in Saccharomyces cerevisiae. In form 2, the domain interacts directly with Rad3, a DNA helicase. 61 matched cddid_all.tbl CDD pfam18122 pfam18122 465659 APC1_C Anaphase-promoting complex sub unit 1 C-terminal domain. This is the C-terminal domain of chain A, also known as sub-unit 1, found in anaphase-promoting complex (APC/C) present in Homo sapiens. APC/C is an ubiquitin ligase that controls chromosome segregation and mitotic exit. 159 matched cddid_all.tbl CDD pfam18124 pfam18124 465660 Kindlin_2_N Kindlin-2 N-terminal domain. This is the N-terminal domain (K2-N) of Kindlin-2 protein present in Homo sapiens. Kindlin-2 is a regulator for heterodimeric integrin adhesion receptors promotes integrin activation. Activation depends on binding of the N-terminal domain to the integrin beta cytoplasmic tail (CT), which disrupts the receptors association with alpha-CT and triggers the conformational transitions in the receptor. K2-N contains a conserved positively charged surface that binds to membrane enriched with negatively charged phosphatidylinositol-(4,5)-bisphosphate (PIP2). K2-N is also very similar to the homologous kindlin-1 F0. 89 matched cddid_all.tbl CDD pfam18125 pfam18125 436291 RlmM_FDX RlmM ferredoxin-like domain. This domain is found in Ribosomal methyltransferase RlmM (YdgE) present in E. coli. RlmM catalyzes the S-adenosyl methionine (AdoMet)-dependent 2'O methylation of C2498 in 23S ribosomal RNA. The domain is ferredoxin-like and forms part of the THUMP domain which binds RNA. THUMP domains typically have low sequence similarity. 71 matched cddid_all.tbl CDD pfam18126 pfam18126 436292 Mitoc_mL59 Mitochondrial ribosomal protein mL59. This domain is a protein found in mitochondrial ribosome 54S large sub unit present in species such as Saccharomyces cerevisiae. The domain used to be referred to as MRP25 but is now called mL59 protein. mL59 is known to partially stabilize a change in the rRNA path prior to helix 82-ES1 ultimately leading to the stabilization of the phosphate backbone of the tRNA acceptor stem. It is worth noting that the domain is encoded in the nucleus and imported from the cytoplasm. 129 matched cddid_all.tbl CDD pfam18127 pfam18127 436293 NAMPT_N Nicotinamide phosphoribosyltransferase, N-terminal domain. This is the N-terminal domain found in Nicotinamide phosphoribosyltransferase (NAMPT) present in Homo sapiens. NAMPT captures nicotinamide (NAM) and replenish the nicotinamide adenine dinucleotide (NAD+) pool during ADP-ribosylation and transferase reactions. 97 matched cddid_all.tbl CDD pfam18128 pfam18128 375576 HydF_dimer Hydrogen maturase F dimerization domain. This domain is found in Hydrogen maturase F (HydF) present in Thermotoga neapolitana. HydF is a GTPase, containing an FeS cluster-binding motif, that is able to are able to activate HydA produced so that HydA can drive the reversible reduction of protons to molecular H2. This domain, referred to as domain II, is responsible for HydF dimerization through the formation of a continuous beta-sheet comprising eight beta-strands from two monomers. 99 matched cddid_all.tbl CDD pfam18129 pfam18129 465661 SH3_12 Xrn1 SH3-like domain. This is the C-terminal SH3-like domain which can be found in the exoribonuclease Xrn1. Xrn1 is a 175 kDa processive exoribonuclease that is conserved from yeast to mammals which targets cytoplasmic RNA substrates marked by a 5' monophosphate for processive 5'-to-3' degradation. The Sh3-like domain in Xrn1 lacks the canonical SH3 residues normally involved in binding proline-rich peptide motifs and instead engages in non-canonical interactions with the catalytic domain. Additionally it is essential in maintaining the structural integrity of Xrn1, since partial truncation of this domain in yeast Xrn1 yields an inactive protein. There is a long loop projecting from the SH3-like domain that contacts the PAZ/Tudor domain, occluding the functional surface that binds RNA or peptide motifs containing methylated arginines, respectively, in canonical PAZ and Tudor domain. 68 matched cddid_all.tbl CDD pfam18130 pfam18130 407962 ATPgrasp_N ATP-grasp N-terminal domain. This is the N-terminal domain found in BL00235 present in Bacillus licheniformis. BL00235 is a ATP-grasp superfamily protein that catalyzes the formation of an alpha-peptide bond between two L-amino acids in an ATP-dependent manner. BL00235 has a highly restricted substrate specificity: the N-terminal substrate is confined to L-methionine an L-leucine, while the C-terminal substrates include small residues such as L-alanine, L-serine, L-threonine and L-cysteine. 81 matched cddid_all.tbl CDD pfam18131 pfam18131 407963 KN17_SH3 KN17 SH3-like C-terminal domain. This domain can be found at the C terminus of the human KIN17 protein and its homologs. In human cells, over-expression of KIN17 modifies the nuclear morphology and inhibits S-phase progression, thus blocking cell growth as part of the response to genotoxics. The C-terminal domain exhibits an all-beta structure consisting of two tightly packed SH3-like subdomains. It binds to RNA and is generally well conserved. This domain has structural similarity with various SH3-like domains, although it lacks similarities in both primary sequence and charge distribution. 53 matched cddid_all.tbl CDD pfam18132 pfam18132 465662 Tyosinase_C Tyosinase C-terminal domain. This is the C-terminal domain of Tyosinase present in Aspergillus oryzae. Tyosinase is a dinuclear copper monooxygenase/oxidase that plays a crucial role in the melanin pigment biosynthesis. The C-terminal domain is referred to as the shielding domain as it prohibits substrate access to the enzyme-active site and blocks the oxidase/oxygenase activity to avoid undesirable intracellular reactions of highly reactive quinonoid products. This means the domain may play an important role in regulating the enzyme activity. Two of the three cysteines (Cys522, and Cys525) that play a significant role in the copper incorporation process belong to the C-terminal domain. 124 matched cddid_all.tbl CDD pfam18133 pfam18133 436296 HydF_tetramer Hydrogen maturase F tetramerization domain. This is the C-terminal domain found in Hydrogen maturase F (HydF) present in Thermotoga neapolitana. HydF is a GTPase, containing an FeS cluster-binding motif, that is able to are able to activate HydA produced so that HydA can drive the reversible reduction of protons to molecular H2. This domain is known as domain III, and is primarily responsible for homotetramer formation. Interactions between the two FeS cluster-binding domains worth noting are the interactions between beta-2 strands, the initial part of the long loop that connects strand beta-2 to strand beta-3, and the loop that connects strand beta-1 to helix alpha-3. There are three highly conserved cysteine residues (Cys-302, Cys-353, and Cys-356) that represent the FeS cluster-binding site which form a superficial pocket. 118 matched cddid_all.tbl CDD pfam18134 pfam18134 436297 AGS_C Adenylyl/Guanylyl and SMODS C-terminal sensor domain. Predicted to function as a sensor domain, sensing nucleotides or nucleotide derivatives generated by bacterial adenylyl/guanylyl cyclase domains. The sensing of ligands by AGS-C is predicted to activate effectors deployed by a class of conflict systems which are reliant on the on the production and sensing of the nucleotide second messengers. 129 matched cddid_all.tbl CDD pfam18135 pfam18135 465663 Type_ISP_C Type ISP C-terminal specificity domain. This is the C-terminal domain of Type ISP restriction-modification enzyme LLaBIII present in Lactococcus lactis subsp. cremoris. Type ISP restriction-modification (RM) enzymes provide a potent defence against infection by foreign and bacteriophage DNA. This domain interacts extensively with DNA and is known as the target recognition domain (TRD). TRD works by recognising 6/7 base pairs of asymmetric sequence. 342 matched cddid_all.tbl CDD pfam18136 pfam18136 465664 DNApol_Exo DNA mitochondrial polymerase exonuclease domain. This domain belongs to human mitochondrial DNA polymerase (Pol-gamma). Pol-gamma has a catalytic subunit, Pol gamma-A, which possesses both polymerase and proofreading exonuclease activities and an accessory subunit, Pol gamma-B, which accelerates polymerization rate and suppresses exonuclease activity. This domain is the exonuclease domain of the catalytic subunit, Pol gamma-A. 282 matched cddid_all.tbl CDD pfam18137 pfam18137 436299 ORC_WH_C Origin recognition complex winged helix C-terminal. This is the C-terminal winged-helix (WH) DNA-binding domain of the origin recognition complex present in Drosophila melanogaster. The WH domain is responsible for recognizing origin sequences. 131 matched cddid_all.tbl CDD pfam18138 pfam18138 436300 bacHORMA_1 Bacterial HORMA domain family 1. Family of bacterial HORMA domains found in conserved genome contexts with Pch2/TRIP13 P-loop NTPases. Acts as a 'third component' in broad class of conflict systems reliant on the production of second messenger nucleotide or nucleotide derivatives. Together with Pch2/TRIP13, could act as co-effectors or in regulation of other effectors of the systems. It is found in proteins from the CBASS (cyclic oligonucleotide-based antiphage signaling system), a system that provides immunity against bacteriophage. This domain is found in CD-NTase-associated protein 7 (Cap7) from E.coli, that acts as a sensor protein of CBSS and binds to a closure peptide allowing it to activate the CD-NTase CdnC for second messenger synthesis and, therefore, it activates a diverse range of effectors. 169 matched cddid_all.tbl CDD pfam18139 pfam18139 465665 LSDAT_euk SLOG in TRPM. Family in the SLOG superfamily, found in several eukaryotic channels including diverse ciliate channels and the TRPM class of animal ion channels. Positioned near the N-terminus of all TRPM channels, it is predicted to play a regulatory role for the channel in potentially recognizing a universal nucleotide or nucleotide-derived ligand. 266 matched cddid_all.tbl CDD pfam18140 pfam18140 465666 PCC_BT Propionyl-coenzyme A carboxylase BT domain. This domain is found in Propionyl-coenzyme A carboxylase (PCC), present in Roseobacter denitrificans. PCC is a mitochondrial biotin-dependent enzyme that is essential for the catabolism of certain amino acids, cholesterol, and fatty acids with an odd number of carbon atoms. Since this domain mediates biotin carboxylase-carboxyltransferase interactions it is referred to as the BT domain. The BT domain is located between biotin carboxylase and the biotin carboxyl carrier protein domains. The BT domain shares some structural similarity with the pyruvate carboxylase tetramerization domain of pyruvate carboxylase. 126 matched cddid_all.tbl CDD pfam18141 pfam18141 407973 UPF1_1B_dom RNA helicase UPF1, 1B domain. UPF1 (or regulator of nonsense transcripts 1 homolog) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. Together with UPF2 and UPF3, forms a surveillance complex, in which UPF2 acts as a bridge between UPF1 and UPF3. UPF2 and UPF3 are non-enzymatic components of the complex that stimulate the activity of UPF1. UPF1 has a N-terminal cysteine/histidine-rich zinc-binding domain (CH/ZBD), a regulatory 1B domain, followed by a helicase core that belongs to superfamily 1 (SF1). This entry represents 1B domain of UPF1 which has a regulatory role. It suffers conformational changes from an inhibitory state to a transition-state complex that modulate RNA binding. 93 matched cddid_all.tbl CDD pfam18142 pfam18142 436303 SLATT_fungal SMODS and SLOG-associating 2TM effector domain. The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function in bacteria as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. The role of this fungal family is not yet understood, although the expansion of the family in many fungal lineages points to a potential role in conflict. 121 matched cddid_all.tbl CDD pfam18143 pfam18143 436304 HAD_SAK_2 HAD domain in Swiss Army Knife RNA repair proteins. Family of HAD domain phophoesterases observed in large eukaryotic proteins with predicted role in RNA repair, the so-called 'Swiss Army Knife' repair proteins. May be involved in phosphate group removal during RNA re-ligation. 143 matched cddid_all.tbl CDD pfam18144 pfam18144 436305 SMODS Second Messenger Oligonucleotide or Dinucleotide Synthetase domain. Nucleotide synthetase enzyme of the DNA polymerase beta superfamily. Experimental studies have demonstrated cGAMP synthetase activity in the Vibrio cholerae DncV protein, a member of the SMODS family. The diversity inherent to the SMODS family suggests members of the family could generate a range of nucleotides, cyclic and/or linear. The nucleotide second messengers generated by the SMODS domains are predicted to activate effectors in a class of conflict systems reliant on the production and sensing of the nucleotide second messengers. 164 matched cddid_all.tbl CDD pfam18145 pfam18145 436306 SAVED SMODS-associated and fused to various effectors sensor domain. Predicted to function as a sensor domain, sensing nucleotides or nucleotide derivatives generated by SMODS and other nucleotide synthetase domains. This domain has been characterized in CD-NTase-associated protein 4 (Cap4), the founding member of a major family of downstream receptors that specifically respond to nucleotide second messenger signals in CBASS immunity, a bacterial system that provides immunity against bacteriophage. SAVED exhibits divergence in its nucleotide binding pocket which enables the recognition of a wide range of CD-NTase products such as bacterial second messengers with alternative ring size, nucleobase, and 3'-5' or 2'-5' phosphodiester linkages. The sensing of ligands by SAVED activates effectors that are essential for CBASS-mediated protection of bacteria from phage infection. 190 matched cddid_all.tbl CDD pfam18146 pfam18146 436307 CinA_KH Damage-inducible protein CinA KH domain. This domain is found in competence-induced protein A (CinA) present in Thermus thermophiles. CinA is important in the horizontal transfer of genes via competence and may also participate in the pyridine nucleotide cycle, which recycles products formed by non-redox uses of NAD. This domain has a KH-type fold and contains the absolutely conserved Glu-187, which stabilizes the binding of Mg2+ and hence polarizes the P=O bond for hydrolysis. A major feature of the CinA in T. thermophiles structure is the asymmetry in the dimer, which is caused by contact between a KH-type domain on the opposite chain and the bound ADP-ribose. This has the effect of closing the active site, allowing additional recognition of ADP-ribose by residues from the KH-type domain. 73 matched cddid_all.tbl CDD pfam18147 pfam18147 436308 Suv3_C_1 Suv3 C-terminal domain 1. This domain is found in Suv3 present in Homo sapiens. Suv3 is an NTP-dependent RNA/DNA helicase that is necessary for the degradation of mature mtRNAs. Suv3 has been found to interact in vitro with polynucleotide phosphorylase. This domain makes up part of the C-terminal domain. 41 matched cddid_all.tbl CDD pfam18148 pfam18148 375589 RGS_DHEX Regulator of G-protein signalling DHEX domain. This domain is found in RGS9 (Class C) regulator of G-protein signalling (RGS) protein present in Mus musculus. RGS proteins attenuate heterotrimeric G-protein signalling by enhancing the intrinsic GTPase activity of G-alpha subunits and are vital for proper signal transduction kinetics. The domain is referred to as DEP helical extension (DHEX) because it is located next to N-terminal Dishevelled/Egl-10/Pleckstrin homology (DEP) domain. Both the DEP and DHEX domains are necessary, but not sufficient, to bind anchoring proteins such as RGS9 anchor protein. DHEX has no close structural homologs. This domain is also found in regulator of G-protein signaling 7 (RGS7), the crystal structure of which has been solved. 100 matched cddid_all.tbl CDD pfam18149 pfam18149 436309 Helicase_PWI N-terminal helicase PWI domain. This domain is found in spliceosomal RNA helicase Brr2. Brr2 is required for the assembly of a catalytically active spliceosome on a messenger RNA precursor. The domain is found in the N-terminal region and is non-canonically PWI-like. The PWI-like domain is thought to be involved in protein-protein interactions. 111 matched cddid_all.tbl CDD pfam18150 pfam18150 465667 DUF5600 Domain of unknown function (DUF5600). This domain can be found in EH-domain-containing ATPase 2 (EHD2) present in Mus musculus. The domain is helical in nature and has extensive contacts with the G-domain. 107 matched cddid_all.tbl CDD pfam18151 pfam18151 465668 DUF5601 Domain of unknown function (DUF5601). This domain is found in the catalytic core RABEX-5 present in Homo sapiens. RABEX, also known as Rab GTPase exchange factors, regulate endocytic trafficking through activation of the Rab families RAB5, RAB21 and RAB22. The domain is helical in nature. 65 matched cddid_all.tbl CDD pfam18152 pfam18152 436312 DAHP_snth_FXD DAHP synthase ferredoxin-like domain. This domain is found in 3-Deoxy-d-arabino-heptulosonate-7-phosphate synthase (DAHPS) present in Thermotoga maritime. DAHPS catalyzes the first reaction of the aromatic biosynthetic pathway in bacteria, fungi, and plants, the condensation of PEP and E4P with the formation of DAHP. The domain is ferredoxin-like and is thought to play a critical role in feedback regulation of the enzyme. 67 matched cddid_all.tbl CDD pfam18153 pfam18153 407984 S_2TMBeta SMODS-associating 2TM, beta-strand rich effector domain. Predicted sensor/effector coupled domain which occurs in conserved genome contexts with the SMODS nucleotide synthetase. In addition to the predicted pore-forming 2TM region, the domain contains seven predicted beta-strands, suggestive of a lipocalin-like beta-barrel structure which could act as the sensor which activates the pore-forming effector response. 180 matched cddid_all.tbl CDD pfam18154 pfam18154 436313 pPIWI_RE_REase REase associating with pPIWI_RE. Restriction endonuclease (REase) domain family, found in a conserved three-gene island that also contains a DinG-type helicase and the pPIWI_RE module. This three gene island is predicted to form a conflict system which targets R-loop formation of invasive plasmids during plasmid replication. 118 matched cddid_all.tbl CDD pfam18155 pfam18155 436314 pPIWI_RE_Z pPIWI RE three-gene island domain Z. Poorly-understood domain observed N-terminal to DinG-type helicase, which is part of a conserved three-gene island also containing a REase domain and the pPIWI_RE module. This three gene island is predicted to form a conflict system which targets R-loop formation of invasive plasmids during plasmid replication. 167 matched cddid_all.tbl CDD pfam18156 pfam18156 436315 pPIWI_RE_Y pPIWI_RE three-gene island domain Y. Poorly-understood domain observed N-terminal to restriction endonuclease (REase) domain, which is part of a conserved three-gene island also containing a DinG-type helicase and the pPIWI_RE module. This three gene island is predicted to form a conflict system which targets R-loop formation of invasive plasmids during plasmid replication. 144 matched cddid_all.tbl CDD pfam18157 pfam18157 436316 MID_pPIWI_RE MID domain of pPIWI_RE. MID domain of the pPIWI_RE PIWI/Argonaute module. pPIWI_RE is found in a conserved three-gene island that also contains a DinG-type helicase and an REase nuclease. This three gene island is predicted to form a conflict system which targets R-loop formation of invasive plasmids during plasmid replication. 141 matched cddid_all.tbl CDD pfam18158 pfam18158 436317 AidB_N Adaptive response protein AidB N-terminal domain. This is the N-terminal domain of Adaptive response protein AidB present in E. coli. AidB is upregulated in response to small doses of DNA-methylating agents initiates a response that mitigates the mutagenic and cytotoxic effects of DNA methylation. Tetramer formation is thought to be carried out by the N-terminal domain. 156 matched cddid_all.tbl CDD pfam18159 pfam18159 465669 S_4TM SMODS-associating 4TM effector domain. Predicted pore-forming effector domain found in conserved genome contexts with diverse nucleotide synthetases including the SMODS synthetases. Predicted to function as a pore-forming effector in a class of conflict systems reliant on the production of second messenger nucleotide or nucleotide derivatives. S-4TM domains are predicted to initiate cell suicide responses upon their activation. 290 matched cddid_all.tbl CDD pfam18160 pfam18160 436319 SLATT_5 SMODS and SLOG-associating 2TM effector domain family 5. The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family contains an additional C-terminal alpha-helix, and strictly associates with a reverse transcriptase domain, part of a predicted retroelement with diversity-generating potential. 191 matched cddid_all.tbl CDD pfam18161 pfam18161 436320 ISP1_C ISP1 C-terminal. This is the C-terminal domain of ISP1 protein, which plays a role in asexual daughter cell formation, such as in Toxi. gondii. The domain consists of a seven-stranded antiparallel beta-sandwich bordered on one end by an inter-strand loop (open end) and capped at the other end by an amphipathic C-terminal helix (closed end). The domain adopts a pleckstrin homology (PH) fold, despite having negligible sequence similarity. PH domains are often found in proteins that support protein-lipid and play a role in mediating membrane localization through IP binding. However, the Phospholipid Binding Properties of PH domains is not conserved in the TgISP1. Unlike PH domains, ISP1 is cysteine rich. The cysteine-rich nature of the ISPs and the number of surface-exposed cysteines may result in redox instability and may also facilitate higher order multimerization. A disulfide bond between beta 2 and beta 3 is likely a structural feature of the ISP1, as both cysteines appear broadly conserved. 107 matched cddid_all.tbl CDD pfam18162 pfam18162 465670 Arc_C Arc C-lobe. This is the C-terminal domain of Arc protein present in found in Rattus norvegicus. The Arc protein modulates the trafficking of AMPA-type glutamate receptors. This domains tertiary structure is similar to the capsid domain of HIV gag protein. The domain is thought to have evolved from the capsid domain of Ty3/Gypsy retrotransposon. 83 matched cddid_all.tbl CDD pfam18163 pfam18163 436321 LD_cluster2 SLOG cluster2. Family in the SLOG superfamily, observed associating with distinct effector domains including the patatin lipase or a protein containing one enzymatically active and one inactive copy of the TIR domain. 261 matched cddid_all.tbl CDD pfam18164 pfam18164 436322 GNAT_C GNAT-like C-terminal domain. This is the C-terminal domain found in N-acyltransferase (NAT) proteins present in Actinoplanes teichomyceticus. In this organizm, NAT proteins are responsible for N-acylation in the synthesis of the antibiotic teicoplanin. The C-terminal domain undergoes a substantial conformational change upon binding to Acyl-CoA. The C-terminal domain is considered Gcn5-related N-acetyltransferase like (GNAT-like) but differs from the canonical GNAT fold in that it lacks the first beta strand and has an additional four alpha helices. 141 matched cddid_all.tbl CDD pfam18165 pfam18165 436323 pP_pnuc_1 Predicted pPIWI-associating nuclease. Predicted nuclease effector domain associating with prokaryotic PIWI-centered conflict systems. 133 matched cddid_all.tbl CDD pfam18166 pfam18166 436324 pP_pnuc_2 Predicted pPIWI-associating nuclease. Predicted nuclease effector domain associating with prokaryotic PIWI-centered conflict systems. 122 matched cddid_all.tbl CDD pfam18167 pfam18167 436325 Sa_NUDIX SMODS-associated NUDIX domain. NUDIX domain with distinctive features in the substrate-interacting region observed associating with SMODS domain synthetases. Predicted to cleave nucleotide diphosphate bonds, potentially to regulate flux through the pore formed by fused 2TM module. 199 matched cddid_all.tbl CDD pfam18168 pfam18168 407999 PPL5 Prim-pol family 5. Family of prim-pol enzymes currently known only in kinetoplastids. 321 matched cddid_all.tbl CDD pfam18169 pfam18169 408000 SLATT_6 SMODS and SLOG-associating 2TM effector domain 6. The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family associates with a SMODS nucleotide synthetase domain fused to the predicted AGS-C sensor domain. It is sometimes further coupled to R-M systems. 176 matched cddid_all.tbl CDD pfam18171 pfam18171 408001 LSDAT_prok SLOG in TRPM, prokaryote. Family in the SLOG superfamily, fused to or operonically associating with SLATT domain in diverse prokaryotes. Predicted to function as ligand sensor in conjunction with the SLATT transmembrane domain. 194 matched cddid_all.tbl CDD pfam18172 pfam18172 436326 LepB_GAP_N LepB GAP domain N-terminal subdomain. This is a subdomain of a Rab GTPase-activating protein (GAP) effector from Legionella pneumophilia. This GAP modulates Rab enzymes that act as molecular switches in regulating vesicular transport in eukaryotic cells. This N-terminal subdomain belongs to the the GAP domain of the protein. The catalytic arginine finger (Arg444) is located within this sub-domain and it is the only arginine residue required for GAP activity. 188 matched cddid_all.tbl CDD pfam18173 pfam18173 375605 bacHORMA_2 Bacterial HORMA domain 2. Family of bacterial HORMA domains found in conserved genome contexts with Pch2/TRIP13 P-loop NTPases. Acts as a 'third component' in broad class of conflict systems reliant on the production of second messenger nucleotide or nucleotide derivatives. Together with Pch2/TRIP13, could act as co-effectors or in regulation of other effectors of the systems. This domain found in bacterial proteins from the cyclic-oligonucleotide-based anti-phage signalling system (CBASS), such us CD-NTase-associated protein 7 from P. aeruginosa (Cap7), which is part of the type III-CBASS. CBSSs are a family of defence systems against bacteriophages. 166 matched cddid_all.tbl CDD pfam18174 pfam18174 436327 HU-CCDC81_bac_1 CCDC81-like prokaryotic HU domain 1. First of two HU domains found in bacterial proteins typically fused to a C-terminal transmembrane helix and an extracellular peptidoglycan-binding domain. The HU domains in many of these proteins are predicted to function in tethering the nucleoid to the cell envelope. 59 matched cddid_all.tbl CDD pfam18175 pfam18175 465671 HU-CCDC81_bac_2 CCDC81-like prokaryotic HU domain 2. Second of two HU domains found in bacterial proteins typically fused to a C-terminal transmembrane helix and an extracellular peptidoglycan-binding domain. The HU domains in many of these proteins are predicted to function in tethering the nucleoid to the cell envelope. 70 matched cddid_all.tbl CDD pfam18176 pfam18176 408005 KptA_kDCL KptA in kinetoplastid DICER domain. KptA ADP-ribosyltransferase domain observed in kinetoplastid DICER-like (DCL) enzymes. Appears to have lost most residues required for catalyzing phospho-transfer to NAD; however, several positively-charged residues implicated in RNA end recognition remain well-conserved. 158 matched cddid_all.tbl CDD pfam18177 pfam18177 408006 La_HTH_kDCL La HTH in kinetoplastid DICER domain. Winged HTH domain family observed in kinetoplastid DICER-like (DCL) enzymes, situated N-terminal to the KptA_kDCL domain pfam18176. 89 matched cddid_all.tbl CDD pfam18178 pfam18178 436329 TPALS TIR- and PNP-associating SLOG family. Family in the SLOG superfamily associating with predicted TIR- and PNP-like effector domains. Members of this family are predicted to function as sensors of nucleotide or nucleotide-derived ligands, which are likely processed or modified by the associating effectors. Often co-occur genomically with the bacterial HORMA and Pch2/TRIP13 domains. 232 matched cddid_all.tbl CDD pfam18179 pfam18179 408008 SUa-2TM SMODS- and Ubiquitin system-associated 2TM effector domain. Predicted pore-forming effector domain observed exclusively in conserved genome contexts with the SMODS nucleotide synthetases and the bacterial Ubiquitin conjugation systems. 278 matched cddid_all.tbl CDD pfam18180 pfam18180 436330 LD_cluster3 SLOG cluster3 family. Family in the SLOG superfamily, observed to associate with a predicted effector protein containing one enzymatically active and inactive copy of the TIR domain. 170 matched cddid_all.tbl CDD pfam18181 pfam18181 436331 SLATT_1 SMODS and SLOG-associating 2TM effector domain 1. The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family is often C-terminally fused to the SLATT_3 family, and is typically operonically linked to either inactive TIR domains or SLOG domains which could act as regulators of the SLATT channels. In relatively rare instances, it is genomically linked as a standalone domain to the RelA/SpoT nucleotide synthetase and the predicted NA37/YejK sensor domain. 122 matched cddid_all.tbl CDD pfam18182 pfam18182 408011 mCpol minimal CRISPR polymerase domain. Minimal version of the CRISPR polymerase domain. Predicted to generate cyclic nucleotides, potentially sensed by CARF domains which in turn activate various effector domain including HEPN RNases, CARF sensor and effectors are found in conserved genome contexts. Part of a broader class of conflict systems reliant on the production of second messenger nucleotide or nucleotide derivatives. Implicates CRISPR polymerase of the Type III CRISPR/Cas systems in a nucleotide synthetase functional role. 114 matched cddid_all.tbl CDD pfam18183 pfam18183 436332 SLATT_2 SMODS and SLOG-associating 2TM effector domain 2. The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family is the only prokaryotic SLATT family to exist as a standalone domain, with no as-yet discernable genome associations. 192 matched cddid_all.tbl CDD pfam18184 pfam18184 436333 SLATT_3 SMODS and SLOG-associating 2TM effector domain 3. The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family is always N-terminally fused to the SLATT_1 family, and is typically operonically linked to either inactive TIR domains or SLOG domains which could act as regulators of the SLATT channels. 156 matched cddid_all.tbl CDD pfam18185 pfam18185 436334 STALD Sir2- and TIR-associating SLOG family. Family in the SLOG superfamily, associating with predicted Sir2- and TIR-like effector domains. Members of this family are predicted to functions as sensors of nucleotide or nucleotide-derived ligands, which are likely processed or modified by the associating effectors. 207 matched cddid_all.tbl CDD pfam18186 pfam18186 436335 SLATT_4 SMODS and SLOG-associating 2TM effector domain family 4. The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family is often coupled to the SMODS nucleotide synthetase and is sometimes further embedded in other conflict systems like CRISPR/Cas or R-M systems. 165 matched cddid_all.tbl CDD pfam18187 pfam18187 408016 RIF5_SNase_1 TbRIF5 SNase domain 1. Staphylococcus nuclease (SNase) domain family found in the Trypanosoma brucei TbRIF5 protein, which could contribute to the processing of dsRNA targets. 166 matched cddid_all.tbl CDD pfam18188 pfam18188 408017 PPL4 Prim-pol 4. Family of prim-pol enzymes with predicted roles in RNA processing and repair, potentially acting independently of a DNA template. One member of the family is fused to kinetoplastid DICER-like protein 1 (DCL1). 159 matched cddid_all.tbl CDD pfam18189 pfam18189 408018 RIF5_SNase_2 TbRIF5 SNase domain 2. Staphylococcus nuclease (SNase) domain family found in the Trypanosoma brucei TbRIF5 protein, which could contribute to the processing of dsRNA targets. 179 matched cddid_all.tbl CDD pfam18190 pfam18190 465672 Plk4_PB1 Polo-like Kinase 4 Polo Box 1. This domain is found in Polo-like kinase 4 (Plk4) present in Drosophila melanogaster. Plk4 is a conserved component in the duplication pathway of centrioles which is needed to prevent chromosomal instability. The domain is Polo Box 1 (PB1) and has a pseudo-symmetric dimerization interface across PB1-PB1. 107 matched cddid_all.tbl CDD pfam18191 pfam18191 465673 PnpCD_PnpD_N Hydroquinone 1,2-dioxygenase large subunit N-terminal. This is the N-terminal domain of the alpha subunit, known as PnpD, of Hydroquinone 1,2-dioxygenase (PnpCD) present in Pseudomonas sp. strain WBC-3. PnpCD is the key enzyme in the degradation pathway of pollutant para-nitrophenol (PNP). The N-terminal domain residues Trp-76 and Phe-79 are indispensable in the formation of the active site pocket. The N-terminal domain also plays a vital role in formation of the heterotetrameric structure. Structural homologs of the N-terminal domain exhibit the nature to bind nucleic acids but due to the steric effect of the C-terminal domain, this N-terminal domain cannot bind nucleic acids. 151 matched cddid_all.tbl CDD pfam18192 pfam18192 408020 DNTTIP1_dimer DNTTIP1 dimerization domain. This is the N-terminal domain of DNTTIP1, a protein that forms part of a novel histone deacetylase complex present in Homo sapiens. Histone deacetylase complexes comprise DNTTIP1, histone deacetylase (HDAC) and the repressor protein MIDEAS. The acetylation of histone tails plays a critical role in determining the accessibility of chromatin to transcriptional regulators and RNA polymerase complexes. This N-terminal domain is responsible for dimerization of histone deacetylase 1(HDAC1). The N-terminal domain also interacts and mediates the assembly of the HDAC1- MIDEAS complex. 69 matched cddid_all.tbl CDD pfam18193 pfam18193 436338 Fibrillin_U_N Fibrillin 1 unique N-terminal domain. This is the N-terminal domain of human fibrillin-1. Fibrillin is a primary constituent of microfibrils in the extracellular matrix of many elastic and non-elastic connective tissues. This domain, known as the fibrillin unique N-terminal (FUN) domain, constitutes the minimal interaction site for the fibrillin C terminus. The FUN domain has homologs in the human proteins LTBP-1L/2 and VWCE, which are also associated with a C-terminal EGF-like domain. 37 matched cddid_all.tbl CDD pfam18194 pfam18194 465674 Xrn1_D3 Exoribonuclease 1 Domain-3. This domain is found in 5' to 3' exoribonuclease 1 (XRN1) present in Kluyveromyces lactis. XRN1 is involved in transcription, RNA metabolism, and RNA interference. This domain, known as D3, is the third of four domains located far from the active site. These four domains may help to stabilize the N-terminal segment of Xrn1 for catalysis. 71 matched cddid_all.tbl CDD pfam18195 pfam18195 465675 GatD_N GatD N-terminal domain. This is the N-terminal domain of GatD protein present in Pyrococcus abyssi. Two GatD and two GatE associate to form a tetramer complex. The tetramer complex is able to mature Glutamic acid-tRNA Glutamine into Glutamine-tRNA Glutamine, a necessary step in the translation of proteins. The N-terminal domain is involved in anchoring GatD to GatE in order to form the tetramer. 54 matched cddid_all.tbl CDD pfam18196 pfam18196 408024 Cdh1_DBD_1 Chromodomain helicase DNA-binding domain 1. This domain can be found in chromodomain helicase DNA-binding protein 1 (Chd1) present in Saccharomyces cerevisiae. Cdh1 proteins have been associated with the efficient assembly and spacing of nucleosomes. The domain consists of four helices, alpha helix 1-4, and can be divided into regions SANT, HL1 and the beta-linker. The HL1 region comprises of some 40 residues specific to budding yeast that are unlikely to form such a prominent feature or perform a conserved function in other species. The domain itself forms part of the DNA-binding domain. Basic residues on the alpha-1 helix are thought to be important for DNA interaction. 120 matched cddid_all.tbl CDD pfam18197 pfam18197 380135 DUF5602 Domain of unknown function (DUF5602). This domain is found in TTHB210 protein present in Thermus thermophilus. TTHB210 is a Sigma-E factor regulated gene product that forms a homodecamer. This domain is chain G and can be classified with chains A, C, E and I based on its folds. 50 matched cddid_all.tbl CDD pfam18198 pfam18198 465676 AAA_lid_11 Dynein heavy chain AAA lid domain. This family represents the AAA lid domain found neat the C-terminal region of dynein heavy chain. 139 matched cddid_all.tbl CDD pfam18199 pfam18199 465677 Dynein_C Dynein heavy chain C-terminal domain. This family represents the C-terminal domain of dynein heavy chain. This domain is a complex structure comprising six alpha-helices and an incomplete six-stranded antiparallel beta-barrel. The shape of this domain is distinctively flat, spreading over the AAA1, AAA5 and AAA6 domain. 301 matched cddid_all.tbl CDD pfam18200 pfam18200 436343 Big_11 Bacterial Ig-like domain. This presumed domain is found repeat in bacterial cell surface proteins. 80 matched cddid_all.tbl CDD pfam18201 pfam18201 408028 PIH1_CS PIH1 CS-like domain. This domain is found in yeast PIH1 and its homologs. This domain consists of a seven-stranded beta sandwich with the topology of a CS domain, a structural motif also found in Hsp90 co-chaperones such as p23/Sba1 and Sgt1. 100 matched cddid_all.tbl CDD pfam18202 pfam18202 465678 TQ T-Q ester bond containing domain. This domain is found in gram positive bacterial surface proteins. It contains a very unusual isopeptide bond between a conserved N-terminal threonine residue on the first beta strand of the Ig-like fold and and a glutamine residue in the final strand of the domain. 125 matched cddid_all.tbl CDD pfam18203 pfam18203 408030 IPTL-CTERM IPTL-CTERM motif. This entry represents a predicted C-terminal sorting motif. 28 matched cddid_all.tbl CDD pfam18204 pfam18204 465679 PGF-CTERM PGF-CTERM motif. 23 matched cddid_all.tbl CDD pfam18205 pfam18205 408032 VPDSG-CTERM VPDSG-CTERM motif. The PEP-CTERM/exosortase system has been previously identified through in silico analysis. This entry describes a PEP-CTERM-like variant C-terminal protein sorting signal, as found at the C terminus of twenty otherwise unrelated proteins in Verrucomicrobiae bacterium DG1235. The variant motif, VPDSG, seems an intermediate between the VPEP motif of typical exosortase systems and the classical LPXTG of sortase in Gram-positive bacteria. 26 matched cddid_all.tbl CDD pfam18206 pfam18206 436346 Porphyrn_cat_1 Porphyranase catalytic subdomain 1. This domain is found in porphyranase protein present in Bacteroides plebeius. Porphyranase breaks down porphyran during digestion of red seaweed glycans. It is worth noting that red seaweed glycans contain sulfate esters that are absent in terrestrial plants. This domain makes up part of the catalytic domain of the porphyranase protein. 104 matched cddid_all.tbl CDD pfam18207 pfam18207 436347 LIFR_N Leukemia inhibitory factor receptor N-terminal domain. This domain can be found in leukemia inhibitory factor receptor (LIFR). LIFR is a cell surface receptor that mediates the actions of LIF and other interleukin-6 type cytokines through the formation of signalling complexes with gp130. This is the N-terminal domain, referred to as domain 1, which contains conserved disulfide bonds between Cys-10 to Cys-20 and Cys-37 to Cys-45. 78 matched cddid_all.tbl CDD pfam18208 pfam18208 408035 NES_C_h Nicking enzyme C-terminal middle helical domain. This domain is found in nicking enzyme in S. aureus. NES initiates and terminates the transfer of plasmids that variously confer resistance to a range of drugs, including vancomycin and gentamicin. This domain is found in the C-terminal region of NES. The C-terminal region is required for conjugation and significantly impacts the catalytic activity of the N-terminal relaxase. 109 matched cddid_all.tbl CDD pfam18209 pfam18209 408036 ESF1 Embryo surrounding factor 1. This domain is Embryo surrounding factor 1 (ESF1) protein present in Arabidopsis thaliana. Maternally contributed central cell ESF1 peptides play an important role in suspensor formation and pro-embryo development. The biological activity of ESF1 depends on structural topology, which is stabilized by disulfide bonds. 56 matched cddid_all.tbl CDD pfam18210 pfam18210 465680 Knl1_RWD_C Knl1 RWD C-terminal domain. This domain is found in Knl1, a sub-unit of the KMN network, present in Homo sapiens. The KMN network is the core of the outer kinetochore which is responsible for microtubule binding/stabilization and controls the spindle assembly checkpoint. This domain is the second of two RING finger, WD repeat, DEAD-like helicase (RWD) domains. The tandem RWD domains mediate kinetochore targeting of the microtubule-binding subunits by interacting with the Mis12 complex. The Mis12 complex is a KMN sub-complex that tethers directly onto the underlying chromatin layer. 152 matched cddid_all.tbl CDD pfam18211 pfam18211 465681 Csm1_B Csm1 subunit domain B. This domain is found in the Csm1 subunit of the Csm complex found in Thermococcus onnurineus. Csm is a type III-A CRISPR-Cas system, which is an RNA-guided immune defense mechanism that detects and destroys foreign DNA or RNA. This domain is known as domain A and is positioned side by side with domain C. Both domain A and domain C adopt the BABBA topology. Domain A interacts primarily with domain B. 94 matched cddid_all.tbl CDD pfam18212 pfam18212 408039 ZNRF_3_ecto ZNRF-3 Ectodomain. This domain is found in ZNRF-3 protein present in Danio rerio. ZNRF-3 is a transmembrane E3 ubiquitin ligase that antagonizes Wnt signalling, the signalling system used to mediate Rspo protein actions. ZNFR3 and RNF43, alongside the Rspo proteins, have emerged as a system with therapeutic potential for a number of pathological processes. This domain is known as the ectodomain. 104 matched cddid_all.tbl CDD pfam18213 pfam18213 408040 SUB1_ProdP9 SUB1 protease Prodomain ProdP9. This domain is the bound prodomain fragment ProdP9 of the SUB1 protein present in Plasmodium falciparum. SUB1 is a serine protease that processes a subset of parasite proteins that play indispensable roles in egress and invasion. The C-terminal stalk of ProdP9 binds in the active site groove in a substrate-like manner and is truncated at the N terminus as a result of the chymotrypsin digestion step used during purification. ProdP9 is structural similar to MIC5 from Toxoplasma gondii, despite low sequence identity. 80 matched cddid_all.tbl CDD pfam18214 pfam18214 408041 STATa_Ig STATa Immunoglobulin-like domain. This domain is found in signal transducer and activator of transcription A protein (STATa) present in Dictyostelium discoideum (dd). STATa is responsible for transcriptionally regulating cellular differentiation in Dictyostelium discoideum. ddSTATa is the only non-metazoan known to employ SH2 domain signaling. This domain adopts an Immunoglobulin-like fold. 122 matched cddid_all.tbl CDD pfam18215 pfam18215 436350 Rtt106_N Histone chaperone Rtt106 N-terminal domain. This is the N-terminal domain of Rtt106 in Saccharomyces cerevisiae. Rtt106 is a histone chaperone that contributes to the deposition of newly synthesized acetylated Histone 3 Lysine 56 (H3K56ac) carrying H3-H4 complex on replicating DNA. The N-terminal domain of Rtt106 homodimerizes and interacts with H3-H4 independently of acetylation. 45 matched cddid_all.tbl CDD pfam18216 pfam18216 436351 N_formyltrans_C N-formyltransferase dimerization C-terminal domain. This is the C-terminal domain of N-formyltransferase found in Francisella tularensis. N-formylated sugars are observed on O-antigens of pathogenic Gram-negative bacteria. This C-terminal domain is responsible for dimerization. In particular, the beta hairpin motif present in the domain helps create a subunit-subunit interface. The dimeric interface is characterized by a hydrophobic patch formed by Ile 195, Leu 197, Val 201, Met 203, Ile 207, Phe 223, Val 231, Val 233, Leu 235, and Leu 237 from both monomers. 52 matched cddid_all.tbl CDD pfam18217 pfam18217 436352 Zap1_zf2 Zap1 zinc finger 2. This domain can be found in Zap1 present in Saccharomyces cerevisiae. Zap1 regulates S. cerevisiae which mediates the transcription of genes encoding uptake vacuolar transporters. This domain corresponds to zinc finger 2 (zf2) which has been shown to be a constitutive transcriptional activator. The two zinc fingers interactions stabilizes Zn(II)-binding. 24 matched cddid_all.tbl CDD pfam18218 pfam18218 436353 Spa1_C Lantibiotic immunity protein Spa1 C-terminal domain. This is the C-terminal domain found in SpaI present in Bacillus subtilis. SpaI is an immunity lipoprotein that protects the Gram-positive bacteria against their own lantibiotics, in this case subtilin. SpaI together with the ABC transporter SpaFEG protects the membrane from subtilin insertion. 99 matched cddid_all.tbl CDD pfam18219 pfam18219 436354 SidC_N SidC N-terminal domain. This is the N-terminal domain of SidC present in Legionella pneumophilia. SidC appears to be involved in modulating mammalian trafficking by promoting the communication between ER-derived vesicles and the Legionella containing vacuole. The N-terminal domain (SidC-N) has a novel fold with 4 potential subdomains. SidC-N does not show structural similarity to any known protein domain in the protein data bank. 465 matched cddid_all.tbl CDD pfam18220 pfam18220 465682 BspA_v Adhesin BspA variable domain. This domain is found in BspA protein present in Streptococcus agalactiae. BspA is an antigen I/II family polypeptide that confers adhesion linked to pathogenesis in group B Streptococcus. This domain is referred to as the variable domain (BspA-V). BspA-V is responsible for binding to scavenger receptor gp340. BspA-V adopts a fold that is distinct from those of other AgI/II family polypeptide variable domains. 150 matched cddid_all.tbl CDD pfam18221 pfam18221 375648 MU2_FHA Mutator 2 Fork head associated domain. This is the N-terminal forkhead-associated (FHA) domain found in Drosophila mutator 2 (MU2) protein. FHA domains are generally phosphothreonine (pThr) specific-binding domains and are present in DNA repair and checkpoint proteins. However, phosphothreonine binding is not conserved in the MU2 active site pocket due to the absence of three key residues needed for pThr binding. Dimerization, is conserved between FHA domains of Drosophila MU2 and human MDC1 albeit through different interfaces. The MU2 FHA domain dimerizes via the beta-sheet 2, the MDC1 FHA domain dimerizes via the opposite beta-sheet 1. 94 matched cddid_all.tbl CDD pfam18222 pfam18222 408047 PilN_bio_d PilN biogenesis protein dimerization domain. This domain is found in PilN type IV pilus biogenesis protein present in Thermus thermophiles. PilN is an integral inner membrane protein needed for the formation of type IV pilus. This domain forms a dimer which is mediated by symmetric contacts between residues in alpha-1, beta-1, beta-3 and alpha-3. 102 matched cddid_all.tbl CDD pfam18223 pfam18223 408048 PilJ_C Pili PilJ C-terminal domain. This is the C-terminal domain of PilJ, a Type IV pilin found in gram-positive Clostridium difficile. Incorporation of PilJ into pili exposes the C-terminal domain of PilJ to create a novel interaction surface. This C-terminal domain is not observed in other Type IV pilin proteins. 95 matched cddid_all.tbl CDD pfam18224 pfam18224 465683 ToxB_N ToxB N-terminal domain. This is the N-terminal domain of ToxB found in Pyrenophora tritici-repentis. This domain is crucial for toxin activity. There are only two amino acid differences between ToxB and toxb, an inactive homolog of ToxB. These two differences are a Val at position 3 in ToxB compared to a Thr in toxb, and an Ala at position 12 in ToxB compared to a Val in toxb. AvrPiz-t, a secreted avirulence protein produced by the rice blast fungus, is a structural homolog to ToxB. 61 matched cddid_all.tbl CDD pfam18225 pfam18225 408050 AbfS_sensor Sensor histidine kinase (AbfS) sensor domain. This is the sensor domain of sensor histidine kinase (AbfS) present in Cellvibrio japonicus. AbfS forms part of the AbfR/S two-component system which is needed to to activate the expression of the suite of enzymes that remove the numerous side chains from xylan. The overall fold of the sensor domain is that of a classical Per Arndt Sim domain. This domain binds xylotriose and xylobiose (Matilla et.al, FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 65 matched cddid_all.tbl CDD pfam18226 pfam18226 436356 QslA_E LasR-specific antiactivator QslA chain E. This domain is chain E of QslA present in Pseudomonas aeruginosa. QslA is an antiactivator which binds to the transcription factor LasR, disrupting its dimerization and preventing LasR from binding to target DNA. Chain E interacts with chain F of QslA and forms the dimerization interface. Chain E also interacts with chain A of ligand-binding domain in LasR. 71 matched cddid_all.tbl CDD pfam18227 pfam18227 436357 LepB_GAP_C LepB GAP domain C-terminal subdomain. This subdomain is found in the Rab1 GTPase-activating protein (GAP) domain of GAP LepB present in Legionella pneumophilia. LepB inactivates Rab1, a key regulator of the secretory vesicular trafficking machinery, by acting as a GTPase-activating protein. LepB is also an antagonist of DrrA, which promotes Rab1. LepB acts by an atypical RabGAP mechanism that is reminiscent of classical GAPs. This is the C-terminal subdomain of the GAP domain and consists of an unusual fold. 80 matched cddid_all.tbl CDD pfam18228 pfam18228 375655 CdiI_N CdiI N-terminal domain. This is the N-terminal domain of Contact-dependent growth inhibition immunity (CdiI) proteins present in Enterobacter cloacae. CdiI proteins neutralize CdiA-CT toxins to protect toxin-producing cells from auto-inhibition. Structural homology searches reveal that Enterobacter cloacae's CdiI is most similar to the Whirly family of single-stranded DNA-binding protein. 108 matched cddid_all.tbl CDD pfam18229 pfam18229 408053 GcnA_N N-acetyl-beta-D-glucosaminidase N-terminal domain. This is the N-terminal domain found in N-acetyl-beta-D-glucosaminidase (GcnA) present in Streptococcus gordonii. GcnA is a family 20 glycosidase that cleaves N-acetyl-beta-D-glucosamine and N-acetyl-beta-D-galactosamine from 4-methylumbelliferylated substrates. Similar N-terminal domains have been observed in all family 20 glycosidases although the number of beta-sheet strands may vary from five. 78 matched cddid_all.tbl CDD pfam18230 pfam18230 408054 Glyc_hyd_38C_2 Glycosyl hydrolases family 38 C-terminal sub-domain. This is a subdomain found in the C-terminal region of golgi alpha-mannosidase II present in Drosophila melanogaster. These proteins are important in glycoprotein processing and are thought to cleave mannosidic bonds through a double displacement mechanism involving a reaction intermediate.This subdomain is found at the C-terminal of Glycosyl hydrolases family 38 C-terminal domain. 89 matched cddid_all.tbl CDD pfam18231 pfam18231 375658 DUF5603 Domain of unknown function (DUF5603). This domain is found in the C-terminal region of free serine kinase (SerK) in the hyperthermophilic archaeon Thermococcus kodakarensis. SerK converts ADP and l-serine (Ser) into AMP and O-phospho-l-serine (Sep), which is a precursor of l-cysteine. The domain is not conserved in the ParB/Srx family. The differences between SerK and the other members of the ParB/Srx family is concentrated in the C-terminal region, which may include residues involved in the Sep binding. 105 matched cddid_all.tbl CDD pfam18232 pfam18232 375659 Chalcone_N Chalcone isomerase N-terminal domain. This is the N-terminal domain of chalcone isomerase present in Eubacterium ramulus. Chalcone isomerase is involved in the degradation pathway of flavone naringenin. 102 matched cddid_all.tbl CDD pfam18233 pfam18233 436358 Cdc13_OB4_dimer Cdc13 OB4 dimerization domain. This domain is found in Cdc13 proteins in several Candida species. The Cdc13-Stn1-Ten1 complex is crucial for telomere protection. This domain is the C-terminal OB4 domain and is responsible for dimerization. Dimerization of Cdc13 is important for high-affinity DNA binding. 115 matched cddid_all.tbl CDD pfam18234 pfam18234 436359 VioE Violacein biosynthetic enzyme VioE. This domain is VioE present in Chromobacterium violaceum. VioE plays a key role in the biosynthesis of violacein. Violacein has potential medical applications as an antibacterial, anti-tryptanocidal, anti-ulcerogenic and as an anti-cancer drug. VioE forms a homodimer with a chiefly hydrophobic interface between the two VioE monomers.The fact that VioE adopts a fold normally associated with lipoprotein carrier proteins may be due to VioE for binding the hydrophobic polyethylene glycol. 182 matched cddid_all.tbl CDD pfam18235 pfam18235 465684 OST_P2 Oligosaccharyltransferase Peripheral 2 domain. This is a domain found in the C-terminal region of STT3 present in P. furiosus. STT3 is an Oligosaccharyltransferase which catalyzes the transfer of a heptasaccharide, containing one hexouronate and two pentose residues, onto peptides in an Asn-X-Thr/Ser-motif-dependent manner. This domain, known as the Peripheral 2 (P2) domain, encircles the central core domain. 133 matched cddid_all.tbl CDD pfam18236 pfam18236 408058 AGO_N Argonaute N domain. This is the N domain often found in the N-terminal region of Argonaute (AGO) present in Kluyveromyces polyspora. AGO forms part of the RNA-induced silencing complex that mediates the gene silencing pathway, RNA interference. The N domain blocks the nucleic acid-binding channel and prevents propagation of guide-target pairing beyond position 16. 122 matched cddid_all.tbl CDD pfam18237 pfam18237 436361 Tk-SP_N-pro Tk-SP N-propeptide domain. This is the N-propeptide domain found in Tk-SP, a subtilisin-like serine protease from Thermococcus kodakaraensis. The beta sheet of this domain packs tightly to the two nearly parallel alpha helices 2 and 3 located at the surface of the subtilisin domain. Gln105 and Asp107 of the N-propeptide domain also bind to the N-termini of these two alpha-helices to form helix caps. 67 matched cddid_all.tbl CDD pfam18238 pfam18238 436362 LnmK_N_HDF LnmK N-terminal Hot Dog Fold domain. This domain is found in LnmK and is present in Streptomyces atroolivaceus. LnmK is a bifunctional acyltransferase/decarboxylase (AT/DC) that catalyzes first self-acylation using methylmalonyl-CoA as a substrate and subsequently trans-acylation of the methylmalonyl group to the phosphopantetheinyl group of the LnmL acyl carrier protein. LnmK is a homodimer composed of two monomeric double-hot-dog folds (DHDF). This domain is the N-terminal hot dog fold. 176 matched cddid_all.tbl CDD pfam18239 pfam18239 465685 HA1 Hemagglutinin I. This domain is hemagglutinin I (HA1) present in Physarum polycephalum. Although the physiological function of the secreted HA1 remains to be established, HA1 recognizes cell wall polysaccharides of E. coli. The beta-sandwich fold of HA1, composed of two up and down beta-sheets, is conserved among other legume lectin-like proteins. The up and down beta-sheet region is a minimal carbohydrate recognition domain. 90 matched cddid_all.tbl CDD pfam18240 pfam18240 408061 PSII_Pbs31 Photosystem II Psb31 protein. This domain is Psb31, an extrinsic protein found in photosystem II (PSII) present in Chaetoceros gracilis. Photosystem II (PSII) is a multisubunit, membrane protein complex located in the thylakoid membranes of oxygenic photosynthetic organizms from cyanobacteria to higher plants. The four helices in the N-terminal domain are arranged in an up-down-up-down fold and are similar in structure to PsbQ protein in Spinach, despite low sequence homology. 93 matched cddid_all.tbl CDD pfam18241 pfam18241 408062 AvrM-A Flax-rust effector AvrM-A. This domain is found in AvrM-A present in Melampsora lini. AvrM-A is a natural variant of AvrM which is a secreted effector protein that can internalize into plant cells in the absence of the pathogen and bind to phosphoinositides. AvrM results in effector-triggered immunity. This domain makes up part of the C-terminal region, which is highly conserved in AvrM. The domain is required for M-dependent effector-triggered immunity. 147 matched cddid_all.tbl CDD pfam18242 pfam18242 375669 LupA Legionella ubiquitin-specific protease A domain. This domain is found in Legionella ubiquitin-specific protease A (LupA). LupA removes a ubiquitin modification from LegC3 which inactivates the cognate effector. This domain is typical of eukaryotic ubiquitin proteases involved in deconjugation of ubiquitin or ubiquitin-like proteins from their targets. 178 matched cddid_all.tbl CDD pfam18243 pfam18243 436364 BfiI_DBD Metal-independent restriction enzyme BfiI DNA binding domain. This domain is found in the metal-independent restriction enzyme BfiI present in Bacillus firmus. This domain is found in the C-terminal of the protein and is responsible for DNA binding. The domain exhibits a beta-barrel-like structure similar to the effector DNA-binding domain of the Mg2+ dependent restriction enzyme EcoRII and to the B3-like DNA-binding domain of plant transcription factors. 165 matched cddid_all.tbl CDD pfam18244 pfam18244 408064 CttA_N Cellulose-binding protein CttA N-terminal domain. This is the N-terminal domain of cellulose-binding protein CttA present in Ruminococcus flavefaciens. CttA mediates attachment of the bacterial substrate via two carbohydrate-binding modules. The domain is known as the X-module and lacks a true hydrophobic core. Unlike the X-modules in other types of CohE-XDoc complexes it does not contribute to the binding surface. This X-module appears to serve as an extended spacer, which separates the cellulose-binding modules at the N terminus of CttA and the bacterial cell wall. The domain does not share structural similarity with other known X-modules from cellulolytic bacteria but does show similarity to G5-1 module of StrH from S. pneumoniae. 71 matched cddid_all.tbl CDD pfam18245 pfam18245 408065 XRN1_DBM 5-3 exonuclease XRN1 DCP1-binding motif. This domain is found in the 5'-3' exonuclease (XRN1) present in Drosophila melanogaster. XRN1 degrades deadenylated mRNA that has recently been decapped by decapping enzyme 2 (DCP2). DCP2 associates with decapping activators DCP1 and EDC4. The direct interaction between DCP1 and XRN1 couples mRNA decapping to 5' exonucleolytic degradation. This domain is responsible for binding to DCP1. In particular, the helical C-terminal region of the domain contributes to the binding affinity and the specificity of the interaction. 26 matched cddid_all.tbl CDD pfam18246 pfam18246 465686 OST_IS Oligosaccharyltransferase Insert domain. This is a domain found in STT3 present in P. furiosus. In P. furiousus, STT3 is an Oligosaccharyltransferase which catalyzes the transfer of a heptasaccharide, containing one hexouronate and two pentose residues, onto peptides in an Asn-X-Thr/Ser-motif-dependent manner. This domain is inserted into the central core (CC) domain and hence is referred to as the Insert (IS) domain. This IS domain contains a disulphide bond. 91 matched cddid_all.tbl CDD pfam18247 pfam18247 375674 AvrM_N Flax-rust effector AvrM N-terminal domain. This is the N-terminal domain found in AvrM present in Melampsora lini. AvrM is a secreted effector protein that can internalize into plant cells in the absence of pathogens, binds to phosphoinositides and results in effector-triggered immunity. This domain is related to the WY domain core in oomycete effectors. 65 matched cddid_all.tbl CDD pfam18248 pfam18248 375675 RalF_SCD RalF C-terminal Sec-7 capping domain. This is the C-terminal domain of RalF protein present in Legionella pneumophilia. RalF is secreted into host cytosol via the Dot/Icm type IV transporter where it acts to recruit ADP-ribosylation factor (Arf) to pathogen-containing phagosomes in the establishment of a replicative organelle. This domain forms a cap over the active site in the Sec7 domain and so is referred to as the Sec7-capping domain. 147 matched cddid_all.tbl CDD pfam18249 pfam18249 375676 Ca_bind_SSO6904 Calcium binding protein SSO6904. This domain is SSO6904 present in Sulfolobus solfataricus. SSO6904 is a calcium binding protein thought to have a weak affinity for other cations such as Mg2+ and Zn2+. The structure of SSO6904 is similar to that of saposin-fold proteins. Saposin proteins are membrane-interacting glycoproteins required for the hydrolysis of certain sphingolipids by specific lysosomal hydrolases. 90 matched cddid_all.tbl CDD pfam18250 pfam18250 436365 Tgi2PP Effector immunity protein Tgi2PP. This domain is Tgi2PP found in Pseudomonas protegens. Tgi2PP is part of the Tge2PP- Tgi2PP Effector-immunity pair secreted by the type VI secretion system (T6SS). Tgi2PP interacts predominantly by hydrogen bonding and hydrophobic interactions with Tge2PP via the insertion of the beta-sheet core of Tgi2PP into the substrate-binding groove of Tge2PP. Tgi2PP contains a similar topology to the periplasmic E. coli colicin M immunity protein. 43 matched cddid_all.tbl CDD pfam18251 pfam18251 375678 Defensin_5 Fungal defensin Copsin. This domain is Copsin present in Coprinopsis cinerea. Copsin is a defensin that interferes with peptidoglycan synthesis and has a CS-alpha-beta fold. Copsin is stabilized by a unique connectivity of six cysteine bonds in contrast to most other CS-alpha-beta defensins which are linked by three or four disulfide bonds. 39 matched cddid_all.tbl CDD pfam18252 pfam18252 408068 Cu_bind_CorA Copper(I)-binding protein CorA. This domain is found in CorA present in Methylomicrobium album. CorA is a copper repressible surface associated copper(I)-binding protein. CorA can bind one copper ion per protein molecule. The overall fold of CorA is similar to M. capsulatus protein MopE, including the unique copper(I)-binding site and most of the secondary structure elements. 175 matched cddid_all.tbl CDD pfam18253 pfam18253 408069 HipN Hsp70-interacting protein N N-terminal domain. This is the N-terminal domain, known as HipN, found in Hsp70-interacting protein (Hip) present in Rattus norvegicus. Hip cooperates with the chaperone Hsp70 in protein folding and prevention of aggregation and may delay substrate release by slowing ADP dissociation from Hsp70. HipN is responsible for N-terminal homo-dimerization which is necessary so that the Hip dimer can interact with Hsp70 molecules. 42 matched cddid_all.tbl CDD pfam18254 pfam18254 436366 HMw1_D2 HMW1 domain 2. This domain is found in Actinobacillus pleuropneumoniae HMW1C (ApHMW1C). HMW1 adhesin is an N-linked glycoprotein that mediates adherence to respiratory epithelium through N-glycosylation of protein acceptor sites and O-glycosylation of sugar acceptor sites. This domain forms an all alpha domain (AAD) when combined with the N-terminal domain. The AAD interacts extensively with the C-terminal GT-B fold in order to create a unique groove with the potential to accommodate the acceptor protein. 88 matched cddid_all.tbl CDD pfam18255 pfam18255 436367 SAM_DrpA DNA processing protein A sterile alpha motif domain. This is the N-terminal domain found in DNA processing protein A (DprA) present in Streptococcus pneumoniae. DprA has recently been discovered to be a transformation-dedicated RecA loader. Transformation is believed to play a major role in genetic plasticity. This domain is known as the sterile alpha motif (SAM) domain. DprAs are able to form a type of dimer through SAM-SAM interactions, also known as N/N interactions. 62 matched cddid_all.tbl CDD pfam18256 pfam18256 375683 HscB_4_cys Co-chaperone HscB tetracysteine metal binding motif. This is the N-terminal domain of human co-chaperone protein HscB (hHscB). This domain is capable of binding a metal ion through its tetracysteine metal binding motif. The metal atom is coordinated by a set of four cysteine residues (Cys41, Cys44, Cys58 and Cys61) on opposed beta-hairpins. Although the N-domain lacks any recognizable secondary structure elements, it has several distant structural homologs including C-4 zinc finger domains and rubredoxin. 27 matched cddid_all.tbl CDD pfam18257 pfam18257 436368 DsbG_N Disulfide isomerase DsbG N-terminal. This is the N-terminal domain found in DsbG, a protein disulfide isomerase present in the periplasm of Helicobacter pylori. The formation of correct disulfide bonds is critical in the folding process of many secretory and membrane proteins in bacteria. Non-native disulfides are corrected by the isomerase DsbC, and, to a lesser extent, by DsbG. The N-terminal domain is involved in dimerization. The dimer interface of Helicobacter pylori's DsbG is stabilized by hydrophobic interactions and hydrogen bonds involving alpha 1, beta-3 to beta-4 loop, beta-4 and beta-4 to alpha-2 loop. This pattern of dimerization is similar to that of E. coli's DsbG. 90 matched cddid_all.tbl CDD pfam18258 pfam18258 408073 IL4_i_Ig Interleukin-4 inducing immunoglobulin-binding domain. This domain is found in Interleukin-4 inducing protein alpha-1 (IPSE/alpha-1) present in Schistosoma mansoni, a parasite of humans. IPSE/alpha-1 triggers the release of IL-4 from basophils in the liver which is a major site of egg deposition during S. mansoni infection. This domain adopts a beta gamma-crystallin fold that is stabilized by three disulfide bonds within the domain (23/26, 59/93, and 111/121). The domain is involved in immunoglobulin binding. 89 matched cddid_all.tbl CDD pfam18259 pfam18259 465687 CBM65_1 Carbohydrate binding module 65 domain 1. This domain is found in the non-catalytic carbohydrate binding module 65B (CMB65B) present in Eubacterium cellulosolvens. CBMs are present in plant cell wall degrading enzymes and are responsible for targeting, which enhances catalysis. CBM65s display higher affinity for oligosaccharides, such as cellohexaose, and particularly polysaccharides than cellotetraose, which fully occupies the core component of the substrate binding cleft. The concave surface presented by beta-sheet 2 comprises the beta-glucan binding site in CBM65s. C6 of all the backbone glucose moieties makes extensive hydrophobic interactions with the surface tryptophans of CBM65s. Three out of the four surface Trp are highly conserved. The conserved metal ion site typical of CBMs is absent in this CBM65 family. 111 matched cddid_all.tbl CDD pfam18260 pfam18260 436370 Nab2p_Zf1 Nuclear polyadenylated RNA-binding 2 protein CCCH zinc finger 1. This domain is found in nuclear polyadenylated RNA-binding 2 protein (Nab2p) present in Saccharomyces cerevisiae. Nab2p is a major family of Poly A-binding proteins whose interactions are thought to be crucial for the control of poly(A) tail length. This domain is the first of seven CCCH zinc fingers which are responsible for polyadenosine RNA binding. When combined with the next three zinc fingers (Zf1-4), these four zinc fingers together may bind RNA in the 3' to 5' direction. 26 matched cddid_all.tbl CDD pfam18261 pfam18261 436371 Rpn9_C Rpn9 C-terminal helix. The 26S proteasome is the major ATP-dependent protease in eukaryotes which plays a key role in intracellular protein degradation. The lid of the 26S proteasome contains six PCI-domain-containing proteins (Rpn3/5/6/7/9/12), two MPN-domain-containing proteins (Rpn8/11), and one peptide, Sem1. The only catalytically active member of the lid is Rpn11, which serves as the essential deubiquitinase of the proteasome. The C terminus of each subunit in the lid is predicted to form one or more helices. These C-terminal helices are highly conserved and have been predicted to form a helical bundle structure. In yeast, Rpn9 was found to be necessary for the integrity and efficiency of the 26S proteasome. This entry represents a helix domain C-terminal to the PCI domain found in Rpn9, a subunit of the 26S proteasome. C-terminal truncations of Rpn5 or Rpn9 have been shown not to cause any major lid assembly defects but to prevent the association of Rpn12. 33 matched cddid_all.tbl CDD pfam18262 pfam18262 408077 PhetRS_B1 Phe-tRNA synthetase beta subunit B1 domain. This is the N-terminal domain found in human cytosolic phenylalanyl tRNA synthetase beta subunit. 83 matched cddid_all.tbl CDD pfam18263 pfam18263 465688 MCM6_C MCM6 C-terminal winged-helix domain. The minichromosome maintenance (Mcm) complex is the replicative helicase in eukaryotic species, that plays essential roles in the initiation and elongation phases of DNA replication. During late M and early G(1), the Mcm complex is loaded onto chromatin to form prereplicative complex in a Cdt1-dependent manner. This entry represents the C-terminal domain of human Mcm6 which is the Cdt1 binding domain (CBD). The structure of CBD exhibits a typical winged helix fold that is generally involved in protein-nucleic acid interaction. The CBD failed to interact with DNA in experiments. The CBD-Cdt1 interaction involves the helix-turn-helix motif of CBD. 107 matched cddid_all.tbl CDD pfam18264 pfam18264 408079 preSET_CXC CXC domain. This domain is found to the N-terminus of the SET domain in the EZH2 protein. It is a zinc binding domain.ED L9LD52.1/505-536; 32 matched cddid_all.tbl CDD pfam18265 pfam18265 465689 Nas2_N Nas2 N_terminal domain. Nas2 is a proteosome assembly chaperone. Nas2 bivalently binds the proteasome Rpt5 subunit. The Nas2 N-terminal helical domain masks the Rpt1-interacting surface of Rpt5. 79 matched cddid_all.tbl CDD pfam18266 pfam18266 465690 Ncstrn_small Nicastrin small lobe. This domain is part of the protein Nicastrin, a component of gamma secretase present in Homo sapiens. Gamma-secretase is thought to contribute to Alzheimer's disease development by generating beta-amyloid peptides. This domain is the known as the small lobe which forms the 'lid'. The lid is an extended surface loop that covers the hydrophilic pocket that is thought to be responsible for substrate recruitment. On substrate binding, the large lobe is thought to rotate relative to the small lobe. 167 matched cddid_all.tbl CDD pfam18267 pfam18267 408082 Rubredoxin_C Rubredoxin NAD+ reductase C-terminal domain. This is the C-terminal domain of NADH rubredoxin oxidoreductase present in Clostridium acetobutylicum. The majority of obligatory anaerobes detoxify micro-aerobic environments by consuming O2 via H2O-forming NADH oxidase. This enzyme offers an alternate reaction pathway for scavenging of O2 and reactive oxygen species, wherein the reducing equivalent is obtained from NADH. 70 matched cddid_all.tbl CDD pfam18268 pfam18268 408083 Hit1_C Hit1 C-terminal. This domain is found in Hit1 protein (Hit1p) present in Saccharomyces cerevisiae. Hit1p contributes to C/D small nucleolar RNPs (snoRNPs) stability and pre-RNA maturation kinetics by associating with U3 snoRNA precursors and influencing its 3'-end processing. Snu13p-Rsa1p-Hit1p heterotrimer binds C/D snoRNAs. C/D snoRNAs are essential for the biogenesis of ribosomes and spliceosomes. The domain adopts a Pac-Hit fold that forms a claw which locks the alpha-1 helix of Rsa1p, while the Rsa1p alpha-2 helix packs against the exposed surface of the Hit1p Pac-Hit domain alpha-3 helix. 82 matched cddid_all.tbl CDD pfam18269 pfam18269 465691 T3SS_ATPase_C T3SS EscN ATPase C-terminal domain. This is the C-terminal domain of the EscN protein family of ATPases that form part of the Type III secretion system (T3SS) present in Escherichia coli. T3SS is a macromolecular complex that creates a syringe-like apparatus extending from the bacterial cytosol across three membranes to the eukaryotic cytosol. This process is essential for pathogenicity. EscN is a functionally unique ATPase that provides an inner-membrane recognition gate for the T3SS chaperone-virulence effector complexes as well as a potential source of energy for their subsequent secretion.The C-terminal domain of T3SS ATPases mediates binding with multiple contact points along the chaperone. 70 matched cddid_all.tbl CDD pfam18270 pfam18270 436376 Evf Virulence factor Evf. This domain is found in Erwinia virulence factor (Evf) present in the Drosophila Pathogen, Erwinia carotovora. Evf is able to bind to model membranes containing negatively charged phospholipids and to promote their aggregation. Palmitoic acid covalently binds to the completely conserved Cys209. The structure of Evf is unlike any virulence factors known to date. 235 matched cddid_all.tbl CDD pfam18271 pfam18271 465692 GH131_N Glycoside hydrolase 131 catalytic N-terminal domain. This is the N-terminal domain found in glycoside hydrolase family 131 (GH131A) protein observed in Coprinopsis cinerea. GH131A exhibits bifunctional exo-beta-1,3-/-1,6- and endo-beta-1,4 activity toward beta-glucan. This domain is catalytic in nature though the catalytic mechanism of C. cinerea GH131A is different from that of typical glycosidases that use a pair of carboxylic acid residues as the catalytic residues. In the case of GH131A, Glu98 and His218 may form a catalytic dyad and Glu98 may activate His218 during catalysis. 250 matched cddid_all.tbl CDD pfam18272 pfam18272 408086 ssDNA_TraI_N single-stranded DNA binding TraI N-terminal subdomain. This is a subdomain found in TraI present in E. coli. Tra1 is a conjugative relaxase that forms part of the Type IV secretion system. This subdomain, referred to as 2A, is located in N-terminal region of the translocation signal (TSA) domain. TSA is known to reside in a larger ssDNA-binding domain. 53 matched cddid_all.tbl CDD pfam18273 pfam18273 436377 T3RM_EcoP15I_C Type III R-M EcoP15I C-terminal domain. This domain is found in the Type III restriction-modification EcoP15I complex, present in E. coli. The Mod subunits function as a dimer with ModA recognizing the DNA and ModB methylating the target adenine base. This domain is found in the C-terminal of the ModB subunit. 97 matched cddid_all.tbl CDD pfam18274 pfam18274 375701 V_ATPase_prox Vacuolar ATPase Subunit I N-terminal proximal lobe. This domain is found in the cytoplasmic N-terminal domain of vacuolar ATP synthase subunit I present in Meiothermus ruber. Subunit I is a homolog of subunit A which associates with the membrane-bound complex of eukaryotic vacuolar H+-ATPase (V-ATPase) acidification machinery. The domain forms the proximal lobe that caps one end of the alpha helix bundle, with the distal lobe capping the other end. Although the two lobes exhibit a similar motif, the molecular nature of the coupling with the identical stalks is thought to be dissimilar. 52 matched cddid_all.tbl CDD pfam18275 pfam18275 436378 His_Me_b4a2 His-Me finger endonuclease beta4-alpha2 domain. This domain is found in Hpy991 present in Helicobacter pylori. Hpy991 is a beta-beta-alpha-Me restriction endonuclease that recognizes the CGWCG target sequence and cleaves both DNA strands with a stagger that leads to 5'-recessed ends in the cleavage products. This domain is the first of two beta4-alpha2 repeats found after the N-terminal domain. The two repeats have low overall sequence similarity but readily identified by a structural comparison. Both repeats contain contains two CXXC motifs that map to the first beta-hairpin and the first alpha-helix. The four cysteine residues coordinate a structurally bound Zn2+ ion tetrahedrally. The major groove is in contact with the first repeat, with the beta-hairpin 2 inserting deeply into the groove. 52 matched cddid_all.tbl CDD pfam18276 pfam18276 465693 TcA_TcB_BD Tc toxin complex TcA C-terminal TcB-binding domain. This domain is found in the C-terminal region of the Tc toxin TcA, present in Photorhabdus luminescens. Tc Toxin complexes bind to the cell surface, are endocytosed and perforate the host endosomal membrane by forming channels that translocate toxic enzymes into the host. This domain is responsible for binding to toxin TcB. Binding of TcA to TcB/TcC opens the beta-propeller gate. 287 matched cddid_all.tbl CDD pfam18277 pfam18277 436380 AbrB_C AbrB C-terminal domain. This is the C-terminal domain of AbrB protein from Bacillus subtilis. AbrB is a transition state regulator. Functions of AbrB include biofilm formation, antibiotic production, competence development, extracellular enzyme production, motility, and sporulation. The C-terminal domain is responsible for multimerization and, to a lesser extent than the N-terminal domain, also contributes in DNA binding. 37 matched cddid_all.tbl CDD pfam18278 pfam18278 436381 RANK_CRD_2 Receptor activator of the NF-KB cysteine-rich repeat domain 2. This domain is found in the receptor activator of the NF-KB (RANK) present in Mus musculus. RANK and its cognate ligand RANKL play a role in bone remodelling, immune function and mammary gland development in conjunction with various cytokines and hormones. The binding of RANKL to RANK causes trimerization of the receptor, which activates the signalling pathway and results in osteoclastogenesis from progenitor cells and the activation of mature osteoclasts receptor activator of the NF-KB. This domain is the second of four cysteine rich pseudo-repeat domains (CRDs) and so is known as CRD2. RANK moves via a hinge region between CRD2 and CRD3 to make close contact with RANKL. 41 matched cddid_all.tbl CDD pfam18279 pfam18279 375706 zf-WRNIP1_ubi Werner helicase-interacting protein 1 ubiquitin-binding domain. This domain is found in the Werner helicase-interacting protein 1 present in Homo sapiens. The domain is a zinc finger responsible and has a zinc-coordinating B-B-A fold. WRNIP1 UBZ binds ubiquitin in a similar manner to Rad18 UBZ. 21 matched cddid_all.tbl CDD pfam18280 pfam18280 375707 AadA_C Aminoglycoside adenyltransferase C-terminal domain. This is the C-terminal domain of aminoglycoside (3'')(9) adenyltransferase (AadA) present in Salmonella enterica. AadA acts as a monomer to catalyze the magnesium-dependent transfer of adenosine monophosphate from ATP to the two chemically dissimilar drugs streptomycin and spectinomycin. 104 matched cddid_all.tbl CDD pfam18281 pfam18281 408092 BILBO1_N BILBO1 N-terminal domain. This is the N-terminal domain of BIBLO1 present in Trypanosoma brucei. BILBO1 is a flagella pocket collar component. Depletion of BIBLO1 prevents flagella pocket and flagella pocket collar biogenesis and leads to cell death. This domain has a ubiquitin-like fold and has a conserved patch of four aromatic residues (Phe-12, Trp-71, Tyr-87, and Phe-89) and three basic residues (Lys-15, Lys-60, and Lys-62). 92 matched cddid_all.tbl CDD pfam18282 pfam18282 436382 RAP80_UIM RAP80 N-terminal ubiquitin interaction motif. This is the N-terminal domain found in RAP80 protein present in Homo sapiens. RAP80 is fundamental for protein recruitment in the DNA damage response. The N-terminal domain is a ubiquitin-interacting motif (UIM). RAP80 is involved in multivalent recognition of polyUb chains through N-terminal domain. 57 matched cddid_all.tbl CDD pfam18283 pfam18283 436383 CBM77 Carbohydrate binding module 77. This domain is the non-catalytic carbohydrate binding module 77 (CBM77) present in Ruminococcus flavefaciens. CBMs fulfil a critical targeting function in plant cell wall depolymerization. In CBM77, a cluster of conserved basic residues (Lys1092, Lys1107 and Lys1162) confer calcium-independent recognition of homogalacturonan. 108 matched cddid_all.tbl CDD pfam18284 pfam18284 465694 DNA_meth_N DNA methylase N-terminal domain. This is the N-terminal domain of DNA methylase (pfam00145). Family members include Modification methylase EcoRII (EC:2.1.1.37) and DNA-cytosine methyltransferase. 57 matched cddid_all.tbl CDD pfam18285 pfam18285 408095 LuxT_C Tetracycline repressor LuxT C-terminal domain. This is the C-terminal domain of LuxT. LuxT is a tetracycline repressor family regulator identified in Vibrio alginolyticus which may play a role in the fine-tuning of the virulence via quorum sensing (QS). 87 matched cddid_all.tbl CDD pfam18286 pfam18286 408096 T3SS_ExsE Type III secretion system ExsE. This domain is found in ExsE present in Pseudomonas aeruginosa. ExsE forms part of the ExsACDE signaling cascade which acts as an important regulatory switch that ensures timely expression of the Type III secretion system (T3SS) and so plays a critical role in facilitating infection. Prior to host-cell contact, the T3SS is inactive and ExsE and Type III Secretion Chaperone (ExsC) form a stable complex. ExsC forms a compact homodimer and ExsE wraps around one face of this dimer. 46 matched cddid_all.tbl CDD pfam18287 pfam18287 465695 Hfx_Cass5 Integron Cassette Protein Hfx_Cass5. This domain forms part of the integron cassette protein Hfx_CASS5 present in Vibrio cholerae. The structure of Hfx is a tetramer built from two domain-swapped dimers. 59 matched cddid_all.tbl CDD pfam18288 pfam18288 436386 FAA_hydro_N_2 Fumarylacetoacetase N-terminal domain 2. This is domain is found in the N-terminal region of Fumarylacetoacetate (FAA) hydrolase (pfam01557). Family members of this domain include Pseudogulbenkiania ferrooxidans and Cupriavidus gilardii. 78 matched cddid_all.tbl CDD pfam18289 pfam18289 465696 HU-CCDC81_euk_2 CCDC81 eukaryotic HU domain 2. This is the second of two HU domains found in the CCDC81-like proteins. CCDC81 has been experimentally linked to the centrosome; eukaryotic CCDC81 HU domains are predicted to function in protein-protein interactions in centrosome organization and potentially contribute to cargo-binding in conjunction with Dynein-VII. A striking lineage-specific expansion of the domain is observed in birds, where the HU domains could function in recognition of non-self molecules. 75 matched cddid_all.tbl CDD pfam18290 pfam18290 465697 Nudix_hydro Nudix hydrolase domain. This domain is found just before the N-terminal region of nucleoside diphosphate-linked moiety (Nudix) hydrolases (pfam00293). Nudix hydrolases catalyze the hydrolysis of nucleoside diphosphates which are often toxic metabolic intermediates and signalling molecules. 80 matched cddid_all.tbl CDD pfam18291 pfam18291 436389 HU-HIG HU domain fused to wHTH, Ig, or Glycine-rich motif. Rapidly-diverging family of HU domains predominantly observed in the bacteroidetes lineage with a predicted role in recognition and possible interception of the DNA of parasitic elements, a counter-conflict strategy preventing incorporation of these elements into the host genome. 125 matched cddid_all.tbl CDD pfam18292 pfam18292 465698 ZIP4_domain Zinc transporter ZIP4 domain. This domain is found in ZRT1-IRT1-like protein 4 (ZIP4) present in Homo sapiens and Mus musculus. ZIP4 is a zinc transporter that allows uptake of the essential nutrient zinc. The domain is found before the N-terminal of ZIP Zinc transporter domain (Pfam: PF02535). 170 matched cddid_all.tbl CDD pfam18293 pfam18293 436391 Caprin-1_dimer Caprin-1 dimerization domain. This domain is found in human Caprin-1 protein. Caprin-1 plays a role in many important biological processes, including cellular proliferation, innate immune response and synaptic plasticity. This domain is found in the highly conserved homologous region 1(HR1) and is responsible for the tight homodimerization of Caprin-1. 116 matched cddid_all.tbl CDD pfam18294 pfam18294 436392 Pept_S41_N Peptidase S41 N-terminal domain. This domain is found in the N-terminal region of proteins carrying the peptidase S41 domain (Pfam: PF03572) in Bacteroidetes. 49 matched cddid_all.tbl CDD pfam18295 pfam18295 408104 Pdase_M17_N2 M17 aminopeptidase N-terminal domain 2. This domain is found in the N-terminal region of M17 aminopeptidase (pfam00883) present in Homo sapiens and Mus musculus. M17 aminopeptidases are Zn-dependent exopeptidases that catalyze the removal of unsubstituted amino acid residues from the N-terminus of peptides. 121 matched cddid_all.tbl CDD pfam18296 pfam18296 465699 MID_MedPIWI MID domain of medPIWI. MID domain of the medPIWI PIWI/Argonaute module. medPIWI is the core globular domain of the Med13 protein. Med13 is one member of the CDK8 subcomplex of the Mediator transcriptional coactivator complex. The medPIWI module in Med13 is predicted to bind double-stranded nucleic acids, triggering the experimentally-observed conformational switch in the CDK8 subcomplex which regulates the Mediator complex. 192 matched cddid_all.tbl CDD pfam18297 pfam18297 465700 NFACT-R_2 NFACT protein RNA binding domain. NFACT-R RNA binding family found found in bacteria fused to the ThiI domain as a variant of the canonical tRNA 4-thiouridylation pathway. 105 matched cddid_all.tbl CDD pfam18298 pfam18298 408107 NusG_add NusG additional domain. This domain is found in Thermotoga maritima NusG, which interacts with RNA polymerase and other proteins to form multi-component complexes that modulate transcription. This domain is referred to as Domain II and is an additional domain inserted into the N-terminal domain. 109 matched cddid_all.tbl CDD pfam18299 pfam18299 436395 R2K_2 ATP-grasp domain, R2K clade family 2. Family of ATP-grasp enzymes belonging to the R2K clade, wherein one of the absolutely-conserved lysine residues has migrated to the RAGYNA domain which is a part of the core ATP-grasp module. This family is predicted to catalyze peptide ligation reactions on protein substrates in biological conflict contexts, probably between bacteriophages and their hosts. 147 matched cddid_all.tbl CDD pfam18300 pfam18300 408109 DUF5604 Domain of unknown function (DUF5604). This domain is often found in the N-terminal region of proteins carrying the SET domain (pfam00856), such as the SETDB1 protein present in Homo sapiens. SETDB1 is a histone methyltransferase that suppresses gene expression and modulates heterochromatin formation through H3K9me2/3. 58 matched cddid_all.tbl CDD pfam18301 pfam18301 408110 preATP-grasp_3 pre ATP-grasp 3 domain. This domain is found just before the N-terminal of the ATP grasp 3 domain (pfam02655). The domain is carried by species such as Azospirillum brasilense and Methylobacter tundripaludum. 76 matched cddid_all.tbl CDD pfam18303 pfam18303 408111 Saf_2TM SAVED-fused 2TM effector domain. Predicted pore-forming effector domain directly fused to predicted SAVED sensor domain. Binding of a ligand via the SAVED sensor is predicted to activate the Saf-2TM and initiate a cell suicide response. Component of a class of conflict systems reliant on the production of second messenger nucleotide or nucleotide derivative. 152 matched cddid_all.tbl CDD pfam18304 pfam18304 375731 SabA_adhesion SabA N-terminal extracellular adhesion domain. This is the N-terminal extracellular adhesion domain of Sialic acid binding adhesin (SabA) present in Helicobacter pylori. The N-terminal domain of SabA functions as a sugar-binding adhesion domain with conserved disulfide bonds. Notably, these amino acid residues are not only conserved among SabA orthologs but also between SabA and BabA. 299 matched cddid_all.tbl CDD pfam18305 pfam18305 436396 DNA_pol_A_exoN 3' to 5' exonuclease C-terminal domain. This domain is found just after the C-terminal region of the HRDC domain (pfam00570) in 3'-5' exonuclease proteins (pfam01612). The domain is carried by species such as Streptomyces griseoaurantiacus and Streptomyces albulus. 87 matched cddid_all.tbl CDD pfam18306 pfam18306 436397 LDcluster4 SLOG cluster4 family. Family in the SLOG superfamily, observed as a standalone domain with little informative genome context, although related families in the SLOG superfamily are predicted to function in diverse conflict contexts. 152 matched cddid_all.tbl CDD pfam18307 pfam18307 465701 Tfb2_C Transcription factor Tfb2 (p52) C-terminal domain. This is the C-terminal domain of Transcription factor Tfb2 present in Saccharomyces cerevisiae. Tfb2 is referred to as p52 in humans. The interaction between p8-Tfb5 and p52-Tfb2 has a key role in the maintenance of the transcription factor TFIIH architecture and TFIIHs function in nucleotide-excision repair (NER) pathway. The C-terminal domain of Tfb2 is thought to have a crucial role in DNA repair. 68 matched cddid_all.tbl CDD pfam18308 pfam18308 465702 GGA_N-GAT N-terminal extension of GAT domain. This region is found in the N-terminal region of the GGA and Tom1 (GAT) domain in Golgi-localizing gamma-adaptin ARF-binding protein 1 (GGA1) present in Homo sapiens. The GAT domain is the key region in GGA that interacts with ARF. ARF plays a crucial role in docking adaptor proteins to membranes. This region is referred to as N-GAT and it interacts extensively with ARF. 39 matched cddid_all.tbl CDD pfam18309 pfam18309 436399 PAZ_3 Argonaute PAZ domain. This is a PAZ domain is found in argonaute present in Thermus thermophiles. Argonaute has a central role in the RNA interference pathway by mediating the maturation of small interfering RNA (siRNA) through initial degradation of the passenger strand, followed by guide-strand-mediated sequence-specific cleavage of target mRNA. The nucleic-acid-binding channel is thought to be positioned between the PAZ and PIWI domain. 87 matched cddid_all.tbl CDD pfam18310 pfam18310 465703 DUF5605 Domain of unknown function (DUF5605). This domain is found in the C-terminal region of proteins carrying pfam16586 and pfam13204. The C-terminal domain is carried by species such as Bacteroides vulgatus. 73 matched cddid_all.tbl CDD pfam18311 pfam18311 436400 Rrp40_N Exosome complex exonuclease Rrp40 N-terminal domain. This is the N-terminal domain of Rrp40 of the exosome complex present in Saccharomyces cerevisiae. The RNA exosome complex is responsible for degrading RNA molecules in the 3' to 5' direction. Rrp40 is a 'cap' protein and binds the RNase PH barrel on the opposite side from the S1/KH ring. The N-terminal domain of Rrp44 forms a long beta-hairpin that is wedged in between Rrp41-Rrp42 and approaches the N terminus of the cap protein Rrp4. 47 matched cddid_all.tbl CDD pfam18312 pfam18312 465704 ScsC_N Copper resistance protein ScsC N-terminal domain. This is the N-terminal domain found in Copper resistance protein ScsS present in Proteus mirabilis. ScsC is a powerful disulfide isomerase that is able to refold and reactivate the scrambled disulfide form of the model substrate RNase A. The protein has a thioredoxin 4 domain (pfam13462) but, unlike other characterized proteins in this family, it is trimeric. The N-terminal domain is responsible for trimerization of ScsC which is needed for isomerase activity. 34 matched cddid_all.tbl CDD pfam18313 pfam18313 436402 TLP1_add_C Thiolase-like protein type 1 additional C-terminal domain. This domain is found in thiolase-like protein type 1 (TLP1) present in Mycobacterium smegmatis. Thiolase enzymes are acetyl-coenzyme A acetyltransferases which convert two units of acetyl-CoA to acetoacetyl CoA in the mevalonate pathway. This domain is deemed an additional C-terminal region, much like the SPC2-thiolase present in mammals which has an additional C-terminal domain termed the sterol carrier protein-2 (SPC2). However, the additional C-terminal domain in TLP1 folds differently to the traditional SCP2-fold observed in mammalian SPC2-thiolase. The topology of the C-terminal domain of TLP1 is reminiscent of single strand nucleic acid binding proteins. 83 matched cddid_all.tbl CDD pfam18314 pfam18314 465705 FAS_I_H Fatty acid synthase type I helical domain. This domain is found in the fatty acid synthase (FAS) complex present in species such as Mycobacterium smegmatis and Thermomyces lanuginosus. FAS is a homo-hexameric enzyme that catalyzes synthesis of fatty acid precursors of mycolic acids. This domain is composed of dimerization module 1 (DM1) and four-helix bundle (4HB), both of which are conserved parts of the acetyl transferase. 203 matched cddid_all.tbl CDD pfam18315 pfam18315 408122 VCH_CASS14 Integron cassette protein VCH_CASS1 chain. This domain is a chain that forms part of the integron cassette protein VCH_CASS14 present in Vibrio cholerae. In each monomer lies a deep binding pocket for small molecule substrates formed by helices alpha-1 and alpha-2 and residues from the central four strands of the beta-sheet. The pocket is extensively lined with hydrophobic side chains. 97 matched cddid_all.tbl CDD pfam18316 pfam18316 465706 S-l_SbsC_C S-layer protein SbsC C-terminal domain. This domain is found in the crystalline bacterial cell-surface layer (S-layer) protein SbsC present in Geobacillus stearothermophilus. S-layers are a common feature of archaeal cell envelopes. SbsC is an oblique lattice forming protein. This domain, termed Domain 9, is located at the C-terminal region of SbsC. The C-terminal region comprises the self-assembly domain responsible for the formation of the crystalline array. 85 matched cddid_all.tbl CDD pfam18317 pfam18317 436404 SDH_C Shikimate 5'-dehydrogenase C-terminal domain. This domain is found in the C-terminal region of Shikimate 5'-dehydrogenase (SDH) present in Methanocaldococcus jannaschii. SDH catalyzes the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway. The domain is found just after the C-terminal domain (pfam01488) which is responsible for NADP binding. 31 matched cddid_all.tbl CDD pfam18318 pfam18318 465707 Gln-synt_C-ter Glutamine synthetase C-terminal domain. This domain is found in type III glutamine synthetase present in Bacteroides fragilis. Glutamine synthetase (GS) are large oligomeric enzymes that catalyze the condensation of ammonium and glutamate to form glutamine, the principal source of nitrogen for protein and nucleic acid synthesis. This domain is located in the C-terminal end of the protein. 118 matched cddid_all.tbl CDD pfam18319 pfam18319 465708 PriA_CRR PriA DNA helicase Cys-rich region (CRR) domain. This is a cys-rich region (CRR) domain found in PriA DNA helicases. In bacteria, the replication restart process is orchestrated by the PriA DNA helicase, which identifies replication forks via structure-specific DNA binding and interactions with fork-associated ssDNA-binding proteins (SSBs). The CRR region which is embedded within the C-terminal helicase lobe has been identified to bind two Zn2+ ions. This 50-residue insertion forms a structure on the surface of the helicase core in which two Zn2+ ions are coordinated by invariant Cys residues. Biochemical experiments have shown that sequence changes to Zn2+-binding Cys residues in the PriA CRR can eliminate helicase, but not ATPase, activity and can block assembly of PriB onto DNA-bound PriA, implicating the CRR in multiple functions in PriA. 27 matched cddid_all.tbl CDD pfam18320 pfam18320 436407 Csc2 Csc2 Crispr. The Csc2 Crispr family of proteins forms a core RNA recognition motif-like domain, flanked by three peripheral insertion domains: a lid domain, a Zinc-binding domain and a helical domain. The CRISPR-Cas system is possibly a mechanism of defence against invading pathogens and plasmids that functions analogously to the RNA interference (RNAi) systems in eukaryotes. 298 matched cddid_all.tbl CDD pfam18321 pfam18321 436408 3HCDH_RFF 3-hydroxybutyryl-CoA dehydrogenase reduced Rossmann-fold domain. This domain is found in 3-hydroxybutyryl-CoA dehydrogenase present in E. coli. 3-hydroxybutyryl-CoA dehydrogenase catalyzes the second step in the biosynthesis of n-butanol from acetyl-CoA, in which acetoacetyl-CoA is reduced to 3-hydroxybutyryl-CoA. This domain is a reduced Rossmann-fold domain and, unlike the first Rossmann-fold domain, it is missing the catalytic residues and an NAD(H) binding cleft. 69 matched cddid_all.tbl CDD pfam18322 pfam18322 465709 CLIP_1 Serine protease Clip domain PPAF-2. This domain is found in Prophenoloxidase-activating factor (PPAF)-II present in the beetle Holotrichia diomphalia. PPAF-II is indispensable for the generation of the active phenoloxidase leading to melanization, a major defense mechanism of insects. This domain is the clip domain and it is thought to tightly associate with regions I-III of the serine protease-like (SPL) domain. The clip domain is a protein-interaction module that plays an essential role in the binding and activation of PO76s via its central cleft. 52 matched cddid_all.tbl CDD pfam18323 pfam18323 465710 CSN5_C Cop9 signalosome subunit 5 C-terminal domain. The COP9 (Constitutive photomorphogenesis 9) signalosome (CSN), a large multiprotein complex that resembles the 19S lid of the 26S proteasome, plays a central role in the regulation of the E3-cullin RING ubiquitin ligases (CRLs). The catalytic activity of the CSN complex is carried by subunit 5 (CSN5), also known as c-Jun activation domain-binding protein-1 (Jab1). This entry is the C-terminal domain found in CSN5 proteins. CSN5, whose two C-terminal helices form an antiparallel hairpin, inserts its final C-terminal helix (helix II) into the central CSN6 framework at the core of the bundle. Deletion of the C-terminal helices has a pronounced effect on CSN integrity. 81 matched cddid_all.tbl CDD pfam18324 pfam18324 436411 TT1725 Hypothetical protein TT1725. This is the hypothetical protein TT1725 found in Thermus thermophilus HB8. The sequence is conserved in three predicted prokaryotic proteins with unknown functions, including Deinococcus radiodurans, Stigmatella aurantiaca, and Mycobacterium leprae. The presence of positively-charged residues in the alpha-1 helix suggests this region binds to a protein with a negatively charged region or to nucleic acids. 110 matched cddid_all.tbl CDD pfam18325 pfam18325 465711 Fas_alpha_ACP Fatty acid synthase subunit alpha Acyl carrier domain. This is the acyl carrier domain (ACP) found in fatty acid synthase subunit alpha (FAS2) EC:2.3.1.86.The fungal type I fatty acid synthase (FAS) is a 2.6 MDa multienzyme complex, catalyzing all necessary steps for the synthesis of long acyl chains. To be catalytically competent, the FAS must be activated by a posttranslational modification of the central acyl carrier domain (ACP) by an intrinsic phosphopantetheine transferase (PPT). 162 matched cddid_all.tbl CDD pfam18326 pfam18326 375753 RFX5_N RFX5 N-terminal domain. This is the N-terminal domain of regulatory factor X (RFX)-5 protein of the RFX complex present in Homo sapiens. The RFX complex is made up of RFX5, RFXAP and RFXB. The complex is involved in the regulation of the expression of the major histocompatibility complex class II (MHCII) gene products. These gene products are essential for the initiation and regulation of the mammalian immune response. The N-terminal domain of RFX5 is responsible for homodimerization of RFX5 which promotes folding of the C-terminal domain of RFXAP. The folding of RFXAP results in the formation of a potential binding site for RFXB to bind to the MHCII promoter. 59 matched cddid_all.tbl CDD pfam18327 pfam18327 465712 PRODH Proline utilization A proline dehydrogenase N-terminal domain. This is the N-terminal domain found in Proline utilization A (PutA) proteins. Proline utilization A (PutA) is a flavoprotein that has mutually exclusive roles as a transcriptional repressor of the put regulon and a membrane-associated enzyme that catalyzes the oxidation of proline to glutamate. The N-terminal region carries the flavoenzyme proline dehydrogenase (PRODH) domain which catalyzes the 2-electron oxidation of proline with the concomitant reduction of a flavin cofactor. 48 matched cddid_all.tbl CDD pfam18328 pfam18328 436414 PfaD_N Fatty acid synthase subunit PfaD N-terminal domain. This domain is found in N-terminal region of PfaD, an enoyl reductase enzyme present in Bacillus subtilis. PfaD plays a role in the biosynthesis of polyunsaturated fatty acids. The domain is typically found just before the N-terminal region of a nitronate monooxygenase domain (pfam03060). 62 matched cddid_all.tbl CDD pfam18329 pfam18329 465713 SGBP_B_XBD Surface glycan-binding protein B xyloglucan binding domain. This is the C-terminal domain found in the surface glycan-binding protein-B (SGBP-B) protein found in Bacteroides ovatus. SGBP-B is a cell-surface-localized, xyloglucan-specific binding protein. The C-terminal domain mediates xyloglucan binding. The domain display similarity to the C-terminal beta-sandwich domain of many GH13 enzyme. 184 matched cddid_all.tbl CDD pfam18330 pfam18330 436416 Lig_C Ligase Pab1020 C-terminal region. This is the C-terminal region of RNA ligase Pab1020 present in Pyrococcus abyssi. Pab1020 catalyzes the nucleotidylation of oligo-ribonucleotides in an ATP-dependent reaction. This region contains both a dimerization domain and a C-terminal domain. 125 matched cddid_all.tbl CDD pfam18331 pfam18331 436417 PKHD_C PKHD-type hydroxylase C-terminal domain. This is the C-terminal domain found in PKHD-type hydroxylase enzymes. Family members are found mostly in Bacteria and carry the 2OG-Fe(II) oxygenase superfamily pfam13640. 43 matched cddid_all.tbl CDD pfam18332 pfam18332 436418 XRN1_D1 Exoribonuclease Xrn1 D1 domain. This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic and is involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This domain (D1) along with 3 other domains, make up a 510-residue segment following the conserved regions found in XRNs but they are only present in XRN1 and are absent in Rat1/XRN2. The amino acid sequences of these four domains contain an excess of basic residues, suggesting that these domains might help in binding the RNA substrate. Mutational studies carried out in D1 domain show that the mutant forms had dramatically reduced nuclease activity towards ssDNA substrate indicating that domain D1 is required for Xrn1 nuclease activity. 192 matched cddid_all.tbl CDD pfam18333 pfam18333 465714 ssDNA_DBD Non-canonical single-stranded DNA-binding domain. This domain is found in ThermoDBP, a non-canonical single-stranded DNA-binding protein in Thermoproteales. Single-stranded DNA-binding proteins are needed for DNA metabolism, sequestering and protecting transiently formed ssDNA during DNA replication and recombination, detecting DNA damage and recruiting repair proteins. The outer edge of the ssDNA-binding cleft, formed by this domain, has a strongly positive electrostatic surface potential because of the conserved basic residues R49, K54, R65, R80, R86, R90, K97, and R112. 106 matched cddid_all.tbl CDD pfam18334 pfam18334 436419 XRN1_D2_D3 Exoribonuclease Xrn1 D2/D3 domain. This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic, involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This entry relates to domain 2 and 3 combined which can be found in the 510-residue C-terminal extension found in XRN1 and not in XRN2/Rat1. Domain D2 is formed by two stretches of Xrn1, residues 915-960 and 1134-1151. The presence of domain (D3) is suggested based on structure. This domain is formed by residues 979-1109, in the insert of domain D2. It is suggested that domains D2-D4 may help maintain domain D1 pfam18332 in the correct conformation, thereby indirectly stabilising the conformation of the N-terminal segment pfam03159. 87 matched cddid_all.tbl CDD pfam18335 pfam18335 465715 SH3_13 ATP-dependent RecD-like DNA helicase SH3 domain. This is an SH3 (SRC homology domain 3) domain found in RecD helicases (EC 3.6.4.12) that belong to the bacterial Superfamily 1B (SF1B). This superfamily of helicases translocate in a 5'-3' direction and are required for a range of cellular activities across all domains of life. Structural analysis indicate that the extension of the 5'-tail of the unwound DNA duplex induces a large conformational change in the RecD subunit, that is transferred through the RecC subunit to activate the nuclease domain of the RecB subunit. The process involves this SH3 domain that binds to a region of the RecB subunit. Studies of RecD in E. coli also revealed that the SH3 domain interacts with the ssDNA tail in a location different to that normally occupied by a peptide in canonical eukaryotic SH3 domains, thus retaining the potential to bind peptide at the same time as the ssDNA tail. 65 matched cddid_all.tbl CDD pfam18336 pfam18336 408142 Tudor_FRX1 Fragile X mental retardation Tudor domain. This is the N-terminal Tudor domain (Tud1) found in Fragile X mental retardation syndrome-related protein 1 (Fxr1). The Tud1 domain forms a canonical Tudor barrel. It is usually found in tandem with Agenet domain pfam05641. 49 matched cddid_all.tbl CDD pfam18337 pfam18337 465716 Tudor_RapA RapA N-terminal Tudor like domain. This is one of two Tudor-like domains found in the N-terminal region of RapA proteins. RapA is an abundant RNAP-associated protein of 110-kDa molecular weight with ATPase activity. It forms a stable complex with the RNAP core enzyme, but not with the holoenzyme. The ATPase activity of RapA increases upon its binding to RNAP. The N-terminal region of RapA contains two copies of a Tudor-like domains, both folded as a highly bent antiparallel beta-sheet. This fold is also found in transcription factor NusG, ribosomal protein L24, human SMN (survival of motor neuron) protein, mammalian DNA repair factor 53BP1, putative fission yeast DNA repair factor Crb2 and bacterial transcription-repair coupling factor known as Mfd. The functional roles of the N-terminal region homologs in these proteins suggest that the Tudor-like domains of RapA may interact with both nucleic acids and RNAP. 62 matched cddid_all.tbl CDD pfam18338 pfam18338 465717 BppL_N Lower baseplate protein N-terminal domain. This domain is found in the N-terminal region of the receptor-binding protein of bacteriophage TP901-1, which infects Lactococcus lactis. The receptor-binding protein of phage TP901-1 is termed the lower baseplate protein (BppL) and is trimeric in nature. The N-terminal domain of BppL plugs into the upper baseplate protein (BppU). 25 matched cddid_all.tbl CDD pfam18339 pfam18339 436422 Tudor_1_RapA RapA N-terminal Tudor like domain 1. This is one of two Tudor-like domains found in the N-terminal region of RapA proteins. RapA is an abundant RNAP-associated protein of 110-kDa molecular weight with ATPase activity. It forms a stable complex with the RNAP core enzyme, but not with the holoenzyme. The ATPase activity of RapA increases upon its binding to RNAP. The N-terminal region of RapA contains two copies of a Tudor-like domains, both folded as a highly bent antiparallel beta-sheet. This fold is also found in transcription factor NusG, ribosomal protein L24, human SMN (survival of motor neuron) protein, mammalian DNA repair factor 53BP1, putative fission yeast DNA repair factor Crb2 and bacterial transcription-repair coupling factor known as Mfd. The functional roles of the N-terminal region homologs in these proteins suggest that the Tudor-like domains of RapA may interact with both nucleic acids and RNAP. 51 matched cddid_all.tbl CDD pfam18340 pfam18340 465718 TraI_2B DNA relaxase TraI 2B/2B-like domain. This is the 2B and 2B-like sub-domain found in TraI (EC:5.99.1.2) a relaxase of F-family plasmids. It contains four domains; a trans-esterase domain that executes the nicking and covalent attachment of the T-strand to the relaxase, a vestigial helicase domain (carrying the 2B/2B-like sub-domain) that operates as an ssDNA-binding domain, an active 5' to 3' helicase domain, and a C-terminal domain that functions as a recruitment platform for relaxosome components. The 2B sub-domains in TraI are formed by residues 625-773 in the vestigial helicase domain and residues 1255-1397 in the active helicase domain. The 2B/2B-like sub-domain interacts with ssDNA where it contributes to the surface area where ssDNA bind. In other words the ssDNA-binding site is located in a groove between the 2B and 2B-like parts of the sub-domain. The sub-domain parts appear to act as clamps holding the ssDNA in place, resulting in the ssDNA being completely surrounded by protein. In previous studies, the 2B/2B-like sub-domain of the TraI vestigial helicase domain has been identified as translocation signal A (TSA) since it contains sequences essential for the recruitment of TraI to the T4S system. Thus, the 2B/2B-like sub-domain plays two major roles in relaxase function: (1) interacting with the DNA and possibly promoting high processivity and (2) mediating recruitment of the relaxosome to the T4S system. 79 matched cddid_all.tbl CDD pfam18341 pfam18341 436424 PSA_CBD PSA endolysin C-terminal cell wall binding domain. This is the C-terminal domain of bacteriophage PSA endolysin. The C-terminal domain is the cell wall-binding domain (CBD) which is composed of two structurally homologous subdomains. CBD comprises two copies of a beta-barrel-like folds, which are held together by means of swapped beta-strands. The observed structure of the CBD sub-domains from Listeriaphage endolysin (N-acetyl-muramoyl-l-alanine amidase), could be the result of either a gene duplication during evolution of the CBD or the pick-up of another functionally equivalent coding sequence, followed by swapping of the respective ancestral leading beta-strands. 61 matched cddid_all.tbl CDD pfam18342 pfam18342 408148 LytB_WW Endo-beta-N-acetylglucosaminidase LytB WW domain. This domain has can be found in endo-beta-N-acetylglucosaminidase LytB (EC 3.2.1.96) of S. pneumoniae and other gram positive bacteria. Comparative analysis revealed that the second all-beta module derived from the WW-like segments is structurally similar to the chitin binding domain of S. marcescens chitinase ChiB, implying a peptide binding function for this module. 66 matched cddid_all.tbl CDD pfam18343 pfam18343 408149 SH3_14 Dda helicase SH3 domain. This is a Src homology-3 (SH3) like beta-barrel domain which can be found in Dda enzyme. Dda is a phage T4 SF1B helicase. The Dda SH3 domain contains two insertions (compared to RecD2), a second beta-ribbon that is referred to as the hook and a beta-ribbon/two-helix substructure that is referred to as the tower. The tower region within the domain is rigidly connected to domain 2A in Dda and appears to be specifically designed for the task of supporting the extended pin. Hence, it is suggested that 2A and this SH3 domain move as one unit during the ATP-driven translocation of ssDNA while maintaining contact with the pin. In this scenario, the pin-tower interaction can be considered as an additional transmission site that serves to more efficiently couple the energy from ATP binding and hydrolysis to the unwinding of dsDNA. 134 matched cddid_all.tbl CDD pfam18344 pfam18344 436425 CBM32 Carbohydrate binding module family 32. This domain is found in GH84C present in Clostridium perfringens. GH84C is a beta-N-acetylglucosaminidase. This domain is a family 32 carbohydrate binding module (CBM) which preferentially recognizes the non-reducing terminus of N-acetyllactosamine. 64 matched cddid_all.tbl CDD pfam18345 pfam18345 465719 zf_CCCH_4 Zinc finger domain. This is a zinc finger domain found in Zinc finger CCCH-type with G patch domain-containing proteins such as ZIP. Functional studies indicate that ZIP specifically targets EGFR and represses its transcription, and that the zinc finger and the coiled-coil domains are central to that process. 19 matched cddid_all.tbl CDD pfam18346 pfam18346 465720 SH3_15 Mind bomb SH3 repeat domain. The REP domain of Mind bomb which serves as the substrate recognition domain for a second, membrane-distal epitope of the Notch ligand (C-box). Although the first Mib repeat of REP may play a dominant role in ligand binding, the two repeats appear to cooperate in the engagement of the Jag1 tail. Mind bomb (Mib) proteins are large, multi-domain E3 ligases that promote ubiquitination of the cytoplasmic tails of Notch ligands. The structure and functional analysis, show that Mib1 contains two independent substrate recognition domains that engage two distinct epitopes from the cytoplasmic tail of the ligand Jagged1, one in the intracellular membrane proximal region and the other near the C terminus. REP domains have a five-stranded anti-parallel twisted beta sheet topology similar to that of SH3 domains. 67 matched cddid_all.tbl CDD pfam18347 pfam18347 465721 DUF5606 Domain of unknown function (DUF5606). This is a domain of unknown function found at the N-terminal region of bacterial proteins. 46 matched cddid_all.tbl CDD pfam18348 pfam18348 436429 SH3_16 Bacterial dipeptidyl-peptidase Sh3 domain. This is the first of two N-terminal bacterial SH3 (SH3b) domains found in bacterial dipeptidyl-peptidases VI such as gamma-D-glutamyl-L-diamino acid endopeptidases. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed. 49 matched cddid_all.tbl CDD pfam18349 pfam18349 375776 PAZ_4 PAZ domain. This is a Paz domain found in Argonaute proteins from Aquifex aeolicus bacteria. The PAZ core fold in Aquifex aeolicus bacteria Ago (Aa-Ago) proteins is closely related to the human hAgo1 PAZ domain. Structural and functional studies of Aa-Ago indicate that conformational rearrangement of the PAZ domain may be critical for the catalytic cycle of Argonaute and the RNA-induced silencing complex. 93 matched cddid_all.tbl CDD pfam18350 pfam18350 436430 SH3_17 Restriction endonuclease SH3 domain. This is an N-terminal beta-barrel domain found in the Hpy99I protomer region. Hpy99I is a type II restriction endonuclease (REase) found in the gastric pathogen Helicobacter pylori. The beta-barrel domain has the SH3-domain fold. Deletion of the beta-barrel domain drastically reduced the activity of Hpy99I. 53 matched cddid_all.tbl CDD pfam18351 pfam18351 408155 Ago_N_1 Fungal Argonaute N-terminal domain. The AGO (Argonaute) proteins have four domains: an N-terminal domain, the PAZ domain, the MID domain and the PIWI domain. This entry is for the N-terminal domain. The N-terminal domain of AGOs is the most variable domain. Compared with prokaryotic Argonautes, KpAGO (Kluyveromyces polysporus Argonaute) has numerous surface-exposed insertion segments, with a cluster of conserved insertions re-positioning the N domain, contributing to the formation of nucleic-acid-binding channel to enable full propagation of the 3' end of the guide RNA guide-target pairing. The guide strand is used by the RISC complex to specify interactions with target RNAs. If sequence complementarity between guide and target is extensive, AGO catalyzes cleavage, resulting in slicing of the target RNA. 95 matched cddid_all.tbl CDD pfam18352 pfam18352 465722 Gp138_N Phage protein Gp138 N-terminal domain. This domain is found in the N-terminal domain of gene product 138 (gp138) in an unidentified bacteriophage. Gp138 is thought to be involved in the process of opening the host cell membrane during infection. The domain has an OB-fold with an intramolecular disulfide bond between C114 and C120. 98 matched cddid_all.tbl CDD pfam18353 pfam18353 436432 PG_isomerase_N Phosphoglucose isomerase N-terminal domain. This domain is found in the N-terminal region of glucose-6-phosphate isomerase-like protein, just before the phospho-glucose isomerase C-terminal SIS domain (pfam10432). 112 matched cddid_all.tbl CDD pfam18354 pfam18354 436433 SH3_18 CarS bacterial SH3 domain. This is an SH3 domain found in antirepressor proteins such as CarS from Myxococcus xanthus. CarS antirepressor recognizes and neutralizes its cognate repressors to turn on a photo-inducible promoter. CarS physically interacts with the MerR-type winged-helix DNA-binding domain of these repressors leading to activation of carB operon. Structural studies of CarS from M. Xanthus reveals a beta-barrel fold akin to that in SH3 domains. However, it diverges from the typical SH3 domain fold in the lengths and conformations of the connecting loops. Functional analysis reveal that SH3 domain-like fold in the antirepressor CasS, mimics operator DNA in sequestering the repressor DNA recognition helix to activate transcription. 85 matched cddid_all.tbl CDD pfam18355 pfam18355 375782 DUF5607 Domain of unknown function (DUF5607). 65 matched cddid_all.tbl CDD pfam18356 pfam18356 408157 DUF5608 Domain of unknown function (DUF5608). 56 matched cddid_all.tbl CDD pfam18357 pfam18357 436434 DtxR Diphteria toxin repressor SH3 domain. This is an SH3 domain which can be found in diphtheria toxin repressor (DtxR) proteins. DtxR) from Corynebacterium diphtheriae regulates the expression of the gene on corynebacteriophages that encodes diphtheria toxin (DT). Other genes regulated by DtxR include those that encode proteins involved in siderophore-mediated iron uptake. 78 matched cddid_all.tbl CDD pfam18358 pfam18358 408159 Tudor_4 Histone methyltransferase Tudor domain. This is a Tudor domain found in histone-lysine N-methyltransferase SETDB1 proteins (EC:2.1.1.43), also known as Eggless in Drosophila. In Drosophila, SetdB1 (Egg) is important for oogenesis and the silencing of chromosome 4. 50 matched cddid_all.tbl CDD pfam18359 pfam18359 465723 Tudor_5 Histone methyltransferase Tudor domain 1. This is the first TUDOR domain found in SETDB1 enzymes (EC:2.1.1.43) in homosapiens, also known as Eggless in Drosophila. In Drosophila, SetdB1 (Egg) is important for oogenesis and the silencing of chromosome 4. SET domain, bifurcated 1 (SETDB1) is a histone methyltransferase (HMT) that methylates lysine 9 on histone H3 (H3K9). The enzymatic activity of SETDB1, in association with MBD1-containing chromatin-associated factor 1 (MCAF1), converts H3K9me2 to H3K9me3 and represses subsequent transcription. SETDB1 is amplified in cancers such as melanoma and lung cancer, and increased expression of SETDB1 promotes tumorigenesis in a zebrafish melanoma model. In addition, SETDB1 is required for endogenous retrovirus silencing during early embryogenesis, inhibition of adipocyte differentiation, and differentiation of mesenchymal cells into osteoblasts. The tandem Tudor domains in the N-terminal region are involved in protein-protein interactions. The second tudor domain is pfam18385. 53 matched cddid_all.tbl CDD pfam18360 pfam18360 465724 hnRNP_Q_AcD Heterogeneous nuclear ribonucleoprotein Q acidic domain. This is an acidic sequence segment domain found in the splicing factor SYNCRIP (hnRNP Q) which is involved in viral replication, neural morphogenesis, modulation of circadian oscillation and the regulation of the cytidine deaminase APOBEC1. This domain is a self-folding globular domain with an all alpha-helix architecture with negatively charged surface areas. Additionally it contains a large hydrophobic cavity and a positively charged surface area as potential epitopes for inter-molecular interactions. 70 matched cddid_all.tbl CDD pfam18361 pfam18361 375787 ssDBP_DBD Single stranded DNA-binding protein ss DNA binding domain. This domain is found in the N-terminal of ThermoDBP, a single stranded DNA binding protein found in Thermoproteus tenax. ThermoDBP binds specifically to ssDNA with low sequence specificity. This domain is responsible for ssDNA binding. Conserved motif 'LIYWIRSDR' is located at the C-terminal end of the domain and is thought to participate in ssDNA binding. 136 matched cddid_all.tbl CDD pfam18362 pfam18362 465725 THB Tri-helix bundle domain. This domain can be found in the myosin-binding motif (m-domain) region present in myosin-binding protein C (MyBP-C). MyBP-C is a sarcomeric assembly protein necessary for the regulation of sarcomere structure and function. The MyBP-C family of proteins consists mainly of modules with immunoglobulin (Ig) or fibronectin folds. This domain exhibits a three-helix bundle fold and there is a known actin-binding motif, LK(R/K)XK positioned in the third helix (alpha3), similar to that found in villin and related proteins. 34 matched cddid_all.tbl CDD pfam18363 pfam18363 436438 PI_PP_I Phosphoinositide phosphatase insertion domain. This domain is found in the effector protein SidP present in Legionella longbeachae. SidP functions as a Phosphoinositide-3-phosphatase specifically hydrolyzing Phosphoinositide(3)P, referred to as PI(3)P, and PI(3,5)P2. The domain is inserted into the N-terminal portion of the catalytic domain and is referred to as the appendage or insertion (I) domain. 94 matched cddid_all.tbl CDD pfam18364 pfam18364 465726 Molybdopterin_N Molybdopterin oxidoreductase N-terminal domain. This is the N-terminal domain of pfam00384 found in a number of molybdopterin-containing oxidoreductases such as dimethyl sulfoxide/trimethylamine N-oxide reductase, also known as DMSO reductase (EC:1.7.2.3, EC:1.8.5.3). 41 matched cddid_all.tbl CDD pfam18365 pfam18365 436440 PI_PP_C Phosphoinositide phosphatase C-terminal domain. This domain is found in the C-terminal region of effector protein SidP present in Legionella longbeachae. SidP functions as a PI-3-phosphatase specifically hydrolyzing PI(3)P and PI(3,5)P2. This C-terminal domain is rich with glutamate residues. 125 matched cddid_all.tbl CDD pfam18366 pfam18366 436441 zf_ZIC Zic proteins zinc finger domain. This is the ZF1 (Zinc Finger 1) domain found in Zic family proteins found in Eukaryotes. In humans, there are five members of the Zic family that are involved in human congenital anomalies. One of them, ZIC3, causes X-linked heterotaxy (HTX1), which is a left-right axis disturbance that manifests as variable combinations of heart malformation, altered lung lobation, splenic abnormality and gastrointestinal malrotation. Zic faily proteins contain multiple zinc finger domains (ZFD), which are generally composed of five tandemly repeated C2H2 zinc finger (ZF) motifs. Sequence comparison analysis reveal that this N-terminal ZF (ZF1) domain of the Zic zinc finger domains is unique in that it possesses more amino acid residues (6-38 amino acids) between the two cysteine residues of the C2H2 motif compared to Gli and Glis ZF1s or any of the other ZFs (ZF2-5) in the Gli/Glis/Zic superfamily of proteins. Mutations in cysteine 253 (C253S) or histidine 286 (H286R) in ZIC3 ZF1, which are found in heterotaxy patients, result in extranuclear localization of the mutant ZIC3 protein. Furthermore, mutations in the evolutionarily conserved amino acid residues (C253, W255, C268, H281 and H286) of ZF1 generally impair nuclear localization. 45 matched cddid_all.tbl CDD pfam18367 pfam18367 436442 Rv2175c_C Rv2175c C-terminal domain of unknown function. This is the C-terminal domain of unknown function found in actinomycetes such as M. tuberculosis Rv2175c. Rv2175c has a DNA binding activity and possesses a winged helix-turn-helix fold, furthermore it is identified as a substrate of the PknL kinase. 56 matched cddid_all.tbl CDD pfam18368 pfam18368 465727 Ig_GlcNase Exo-beta-D-glucosaminidase Ig-fold domain. This domain can be found in 2 glycoside hydrolase subfamily of beta-glucosaminidases (EC:3.2.1.165) such as CsxA, from Amycolatopsis orientalis that has exo-beta-D-glucosaminidase (exo-chitosanase) activity. It has an immunoglobulin-like topology. 102 matched cddid_all.tbl CDD pfam18369 pfam18369 436444 PKS_DE Polyketide synthase dimerization element domain. This is the dimerization element domain found in bacterial modular polyketide synthase ketoreductases. The dimerization element (DE) domain is N-terminal to the KR domain pfam08659. DE domain is necessary for KR function, presumably because the dimeric DE orients the KR domains for optimal activity within a module. 45 matched cddid_all.tbl CDD pfam18370 pfam18370 408170 RGI_lyase Rhamnogalacturonan I lyases beta-sheet domain. This is the beta-sheet domain found in rhamnogalacturonan (RG) lyases, which are responsible for an initial cleavage of the RG type I (RG-I) region of plant cell wall pectin. Polysaccharide lyase family 11 carrying this domain, such as YesW (EC:4.2.2.23) and YesX (EC:4.2.2.24), cleave glycoside bonds between rhamnose and galacturonic acid residues in RG-I through a beta-elimination reaction. Other family members carrying this domain are hemagglutinin A, lysine gingipain (Kgp) and Chitinase C (EC:3.2.1.14). 86 matched cddid_all.tbl CDD pfam18371 pfam18371 465728 FAD_SOX Flavin adenine dinucleotide (FAD)-dependent sulfhydryl oxidase. This is a flavin adenine dinucleotide (FAD) binding domain found in Quiescin sulfhydryl oxidases (QSOX) (EC:1.8.3.2). QSOX is a multi-domain disulfide catalyst that is localized primarily to the Golgi apparatus and secreted fluids and has attracted attention due to its over-production in tumors. Structural studies indicate that the closure of the Trx1 domain over the FAD-binding site may enhance the active-site chemistry for disulfide formation. 104 matched cddid_all.tbl CDD pfam18372 pfam18372 465729 I-EGF_1 Integrin beta epidermal growth factor like domain 1. This is the I-EGF 1 domain found in several integrin betas such as integrin beta 1-7. Structural analysis reveal an epidermal growth factor-like (I-EGF) domains 1 and 2. EGF1 lacks one disulfide (C2-C4) relative to the integrin EGF 2, 3, and 4 domains, this allows the C-terminal end of EGF1 to flex remarkably relative to its N-terminal end. 29 matched cddid_all.tbl CDD pfam18373 pfam18373 465730 Spectrin_like Spectrin like domain. Desmoplakin (DP) is an integral part of desmosomes, where it links desmosomal cadherins to the intermediate filaments. The N-terminal region of DP contains a plakin domain common to members of the plakin family. Plakin domains contain multiple copies of spectrin repeats (SRs) pfam00435. Spectrin repeats (SRs) consist of three alpha-helices (A, B, and C) that form an antiparallel triple-helical bundle. This entry describes SR6 which has a divergent structure relative to the other SRs. SR6 shows significant deviations in helices A and B where they are significantly shorter than in other repeats. Structural comparison revealed that SR6 is more similar to other three-helix-bundle proteins, including target of Myb1 and the syntaxin Habc domain, than to other SR proteins. Due to these differences with other spectrin repeats, this region is termed spectrin-like repeat. 78 matched cddid_all.tbl CDD pfam18374 pfam18374 436448 Enolase_like_N Enolase N-terminal domain-like. This is the N-terminal domain found in o-succinylbenzoate synthase (OSBS) enzymes (EC:4.2.1.113). Like other members of the enolase superfamily, OSBS enzymes are composed of a C-terminal catalytic (beta/alpha)7beta-barrel domain pfam00113 and an N-terminal capping domain with an alpha+beta fold that is found in the enolase superfamily. This domain is different from other enolase super family N-terminal domains such as pfam03952. This actino-bacterial N-terminal domain lacks the prototypical first two helices of the enolase capping domains. Structural analysis of T. fusca OSBS reveals that this is compensated for with an extra helix appended to the C-terminus. 51 matched cddid_all.tbl CDD pfam18375 pfam18375 465731 CDH1_2_SANT_HL1 CDH1/2 SANT-Helical linker 1. CDH1 is an ATP-dependent chromatin-remodelling factor and plays an important role in regulating nucleosome assembly and mobilization. CHD1 consists of double chromodomain, SNF2-related ATPase domain, and a C-terminal DNA-binding domain. The DNA-binding domain contains SANT (Swi3, Ada2, N-CoR, TFIIIB) and SLIDE (SANT-like ISWI) domains in its C-terminal region. SANT domains are structurally related to Myb-like domains are common motifs found in chromatin interacting proteins. Deletion of individual SANT or SLIDE domains in CDH1 does not significantly affect nucleosome binding, but combined deletion of both domains severely compromise binding, suggesting that the SANT-SLIDE motif recognizes DNA/nucleosomes as a single cooperative unit. SANT sequences of Chd1 proteins are the most distantly relation group of sequences relation to other SANT/Myb sequences, and are more diverse than other SANT proteins. The SANT and SLIDE regions are well conserved in both Chd1 and ISWI (imitation switch) remodelling enzymes. This domain comprises the SANT region and the helical linker region 1 (HL1). 90 matched cddid_all.tbl CDD pfam18376 pfam18376 465732 MDD_C Mevalonate 5-diphosphate decarboxylase C-terminal domain. Mevalonate diphosphate decarboxylase (EC:4.1.1.33) catalyzes the ATP dependent decarboxylation of mevalonate 5-diphosphate (MVAPP) to form isopentenyl 5-diphosphate. The reaction is required for production of polyisoprenoids and sterols from acetyl-CoA. This entry represents the C-terminal domain of the mevalonate 5-diphosphate decarboxylase enzyme which is a member of the GHMP kinase superfamily. 186 matched cddid_all.tbl CDD pfam18377 pfam18377 436450 FERM_F2 FERM F2 acyl-CoA binding protein-like domain. This is an F2 lobe domain consisting of an acyl-CoA binding protein fold found in FERM region of Jak-family tyrosine kinases. Multidomain JAK molecules interact with receptors through their FERM and SH2-like domains, triggering a series of phosphorylation events, resulting in the activation of their kinase domains. Overall, the FERM region maintains the typical three-lobed architecture, with an F1 lobe consisting of a ubiquitin-like fold, an F2 lobe consisting of an acyl-CoA binding protein fold, and an F3 lobe consisting of a pleckstrin-homology (PH) fold. JAK1 FERM-F2 domain has been shown to act as the interaction site for the IFNLR1 box1 motif (PxxLxF) of class II cytokine receptors which is essential for kinase activation. 131 matched cddid_all.tbl CDD pfam18378 pfam18378 436451 Nup188_C Nuclear pore protein NUP188 C-terminal domain. This is C-terminal domain of Nup188. It is a right-handed arc-shaped superhelical structure built from 19 helices that form 6 helical repeats, which are stacked in regular order. The first helical pair (alpha1 and alpha2) forms a HEAT repeat followed by 5 ARM repeats. 370 matched cddid_all.tbl CDD pfam18379 pfam18379 465733 FERM_F1 FERM F1 ubiquitin-like domain. This is an F1 lobe domain consisting of a ubiquitin like fold found in FERM region of Jak-family tyrosine kinases. Multidomain JAK molecules interact with receptors through their FERM and SH2-like domains, triggering a series of phosphorylation events, resulting in the activation of their kinase domains. Overall, the FERM region maintains the typical three-lobed architecture, with an F1 lobe consisting of a ubiquitin-like fold, an F2 lobe consisting of an acyl-CoA binding protein fold, and an F3 lobe consisting of a pleckstrin-homology (PH) fold. 96 matched cddid_all.tbl CDD pfam18380 pfam18380 408180 GEN1_C Holliday junction resolvase Gen1 C-terminal domain. This is the C-terminal domain found in GEN1 resolvase. It is composed of three-strand antiparallel beta sheets and four alpha helices. GEN1 protein, a member of the XPG/Rad2 family of structure-selective endonucleases, is specialized for the cleavage of Holliday junction recombination intermediates. Structural comparison indicates that the C-terminal domain is similar to a series of chromobox homology proteins. Functional analysis indicates that the chromodomain provides an additional DNA binding site necessary for efficient HJ cleavage, and its truncation severely hampers GEN1's catalytic activity. 104 matched cddid_all.tbl CDD pfam18381 pfam18381 465734 YcaO_C YcaO cyclodehydratase C-terminal domain. This is the proline-rich C-terminal domain found in ribosomal protein S12 methylthiotransferase accessory factor YcaO. It has been shown to be involved in both C protein recognition and cyclodehydration. The C-terminal domain resembles a tetratricopeptide repeat that mediates dimerization. 172 matched cddid_all.tbl CDD pfam18382 pfam18382 465735 Formin_GBD_N Formin N-terminal GTPase-binding domain. This is the N-terminal GTPase-binding domain (GBD) of formins also known as formin homology domain-containing proteins (FHOD) pfam02181. This GBD is recruited by Rac and Ras GTPases in cells and plays an essential role for FHOD1-mediated actin remodelling and transcriptional activation, localizes to specific GTPases in cells, and binds to GTPases in vitro. It exhibits structural similarity to the ubiquitin superfold as found, for example, in the Ras-binding domains of c-Raf1 or PI3 kinase, but contains an unusual loop that inserts into the first FH3 repeat. 119 matched cddid_all.tbl CDD pfam18383 pfam18383 465736 IFT81_CH Intraflagellar transport 81 calponin homology domain. This is the N-terminal domain found in IFT81 proteins. Crystal structure analysis revealed that IFT81-N adopts the fold of a calponin homology (CH) domain with structural similarity to the kinetochore complex component NDC80 with microtubule (MT)-binding properties. Functional analysis show that IFT74 and IFT81 form a tubulin-binding module required for ciliogenesis. It is suggested that IFT81-N binds the globular domain of tubulin to provide specificity, and IFT74-N recognizes the beta-tubulin tail to increase affinity. 124 matched cddid_all.tbl CDD pfam18384 pfam18384 375810 zf_CCCH_5 Unkempt Zinc finger domain 1 (Znf1). This is CCCH zinc finger 1 domain found in Unkempt N-terminal region. Unkempt is an evolutionary conserved RNA-binding protein that regulates translation of its target genes and is required for the establishment of the early bipolar neuronal morphology. It carries six CCCH zinc fingers (ZnFs) forming two compact clusters, ZnF1-3 and ZnF4-6, that recognize distinct trinucleotide RNA substrates. These clusters, recognize an unexpectedly short stretch of RNA sequence-only three consecutive ribonucleotides-with a varying degree of specificity. ZnF1-3 binds to the UUA motif of RNA substrates. 40 matched cddid_all.tbl CDD pfam18385 pfam18385 408184 Tiam_CC_Ex T-lymphoma invasion and metastasis CC-Ex domain. This is the CC and Ex subdomains found in PH-CC-Ex globular domain from Tiam1 and Tiam2 proteins (T-lymphoma invasion and metastasis). The CC subdomain forms an antiparallel coiled coil with two long alpha-helices, together with the C-terminal Ex subdomain they form a small globular domain comprising three alpha-helices. The CC subdomain of the Tiam2 PHCCEx domain follows the C-terminal alpha1 helix of the PH pfam00169 subdomain through a four-residue linker. 98 matched cddid_all.tbl CDD pfam18386 pfam18386 436456 ROQ_II Roquin II domain. The ROQ domain is composed of three subdomains, I, II and III. This entry describes the second domain, ROQ II. Structural analysis reveals similarity of domain II to the helix-turn-helix (HTH) fold. Mutagenesis and biochemical studies show that that the HTH fold in domain II contributes to binding dsRNA at the 5'arm. 56 matched cddid_all.tbl CDD pfam18387 pfam18387 465737 zf_C2H2_ZHX Zinc-fingers and homeoboxes C2H2 finger domain. This is a C2H2 zinc-finger domain found in ZHX proteins such as ZHX1. ZHXs are multidomain proteins comprising two C2H2 zinc finger motifs and five homeodomains. Both homeodomains and zinc fingers are short protein modules involved in protein-DNA and/or protein-protein interactions; they are frequently associated with roles in transcriptional regulation. All members of the ZHX family are reported to be able to form both homo- and heterodimers via the region containing homeodomain 1. ZHX1 is a transcriptional repressor which is ubiquitously expressed. It interacts with nuclear factor Y subunit A (NFYA) and DNA methyl transferase 3B (DNMT3B) for its repression activity. Changes in expression profiles of rat ZHX1 ortholog have been associated with glomerular disease. In addition to the five homeodomains, ZHX1, which also contains of two N terminal C2H2 zincfingers forms homodimers via homeodomain and can also form heterodimers with ZHX3. 53 matched cddid_all.tbl CDD pfam18388 pfam18388 436458 ATG29_N Atg29 N-terminal domain. This is the N-terminal domain found in fungal Atg proteins such as Atg29. In yeast, the induction of autophagy begins at a single perivacuolar site that is proximal to the vacuole, called the phagophore assembly site (PAS). Atg17-Atg29-Atg31 complex (Atg1 complex) formation is a prerequisite for PAS assembly. Functional analysis indicate that the N-terminal half Atg29 can bind Atg31. 54 matched cddid_all.tbl CDD pfam18389 pfam18389 465738 TrmO_C TrmO C-terminal domain. This domain is found at the C-terminus of TrmO tRNA methyltransferase proteins. This domain has a RelE fold. 65 matched cddid_all.tbl CDD pfam18390 pfam18390 465739 GlgX_C Glycogen debranching enzyme C-terminal domain. This is the C-terminal domain of the glycogen debranching enzyme GlgX. GlgX hydrolyzes alpha-1,6-glycosidic linkages of phosphorylase-limit dextrin containing only three or four glucose subunits produced by glycogen phosphorylase. Sequence analysis suggests that GlgX is a debranching enzyme belonging to the glycoside hydrolase GH-13 family in the CAZy database. 85 matched cddid_all.tbl CDD pfam18391 pfam18391 436460 CHIP_TPR_N CHIP N-terminal tetratricopeptide repeat domain. This is N-terminal tetratricopeptide repeat (TPR) domain found in C terminus of Hsp70 interacting proteins (CHIP). The TPR domain of CHIP binds directly to EEVD motifs located at the C termini of Hsc/Hsp70 and Hsp90. 83 matched cddid_all.tbl CDD pfam18392 pfam18392 465740 CSN7a_helixI COP9 signalosome complex subunit 7a helix I domain. This is The C-terminal helix I domain found in COP9 signalosome complex subunit 7a. The helix from CSN7 (helix I) contacts CSN6 helices I and II at the base of the bundle, nearest the PCI ring. 50 matched cddid_all.tbl CDD pfam18393 pfam18393 465741 MotY_N MotY N-terminal domain. The bacterial flagellar motor is a rotary motor complex composed of various proteins. MotX and MotY are essential for the Na+-driven flagellar motor motility of Vibrio, Shewanella and Aeromonas species. MotY is main component for T-ring formation and absence of MotY completely disrupt the T-ring formation. This is the N-terminal domain of MotY which is shown to be essential for motility and responsible for the interaction with both MotX and the basal body. Functional analysis suggests that MotY-N connects the basal body to MotX and that the PomA/PomB complex associates with MotX to form the functional stator complex around the rotor. MotY-N alone does not associate strongly with the basal body, but the partial T-ring structure made of the MotY-N/MotX complex is sufficient to allow at least a few PomA/PomB stator complexes to be incorporated into the motor. 146 matched cddid_all.tbl CDD pfam18394 pfam18394 465742 TBK1_CCD1 TANK-binding kinase 1 coiled-coil domain 1. This is a coiled-coil domain found in TANK-binding kinase 1 (TBK1), it comprises one of two coiled-coil domains found in the scaffold dimerization region. TBK1 is a serine/threonine kinase and a noncanonical member of the IKK family implicated in diverse cellular functions, including innate immune response as well as tumorigenesis and development. Deletion of the coiled-coil 1 region in TBK1 lead to a severe impairment in TBK1 function even upon over-expression. 256 matched cddid_all.tbl CDD pfam18395 pfam18395 465743 Cas3_C Cas3 C-terminal domain. This is the C-temrinal domain of Cas3 proteins. The C-terminal domain (CTD) is shown to completely wrap ssDNA inside the helicase. Deletion of the CTD (aa 819-924) reduced CRISPR interference. It is suggested that the CTD regulates the N-terminal HD nuclease activity by functioning as a substrate filter. 108 matched cddid_all.tbl CDD pfam18396 pfam18396 465744 TBK1_ULD TANK binding kinase 1 ubiquitin-like domain. This is the ubiquitin-like domain (ULD) found in TANK-binding kinase 1 (TBK1). TBK1 is a serine/threonine kinase and a noncanonical member of the IKK family implicated in diverse cellular functions, including innate immune response as well as tumorigenesis and development. It has been reported that the ULD of TBK1 regulates kinase activity, playing an important role in signaling and mediating interactions with other molecules in the IFN pathway. Deletion of ULD indicates that it is required for the kinase domain to form an enzymatically active conformation. TBK1 ULD has a ubiquitin-like structure and an Ile44 hydrophobic patch, which is conserved among ULDs and IKK and IKK-related proteins. This hydrophobic patch is involved in ULD-SDD interactions in TBK1 and other IKK and IKK-related proteins. 88 matched cddid_all.tbl CDD pfam18397 pfam18397 465745 IKBKB_SDD IQBAL scaffold dimerization domain. This is the C-terminal scaffold dimerization domain (SDD) found in inhibitor of nuclear factor kappa-B kinase subunit beta IKBKB (EC:2.7.11.10). IKK2 also known as IKBKB is one of the core component of IKB kinases (IKK). IKB kinase (IKK) is an enzyme that quickly becomes active in response to diverse stresses on a cell. The SDD consists primarily of two long alpha-helices. 275 matched cddid_all.tbl CDD pfam18398 pfam18398 465746 CLIP_SPH_mas Clip-domain serine protease homolog masquerade. The clip domain is a structural/regulatory unit in many arthropod serine proteases. The clip domain super-family also includes serine protease homologs (SPHs). This entry describes clip domains in the SPHs (CLIP subfamily A), which belong to group-3. SPHs usually carry between 1 to 5 clip domains. One of the most prominent family members is masquerade (mas). Deletion in drosophila models lead to defects in somatic muscle attachment and in the formation of the nervous system during embryogenesis. 32 matched cddid_all.tbl CDD pfam18399 pfam18399 465747 CLIP_SPH_Scar Clip-domain serine protease homolog Scarface. The clip domain is a structural/regulatory unit in many arthropod serine proteases. The clip domain super-family also includes serine protease homologs (SPHs). This entry describes clip domains in the SPHs (CLIP subfamily A), which belong to group-3. SPHs usually carry between 1 to 5 clip domains. The most prominent family member of carrying this clip domain is Scarface proteins in drosophila, which bear an inactive catalytic site, representing a subgroup of serine protease homologs (SPH). Loss-of-function induces defects in JNK-controlled morphogenetic events such as embryonic dorsal closure and adult male terminalia rotation. 66 matched cddid_all.tbl CDD pfam18400 pfam18400 465748 Thioredoxin_12 Thioredoxin-like domain. This is one of four TRXL(thioredoxin-like) domains found in UDP-glucose:glycoprotein glucosyltransferase (UGGT). 187 matched cddid_all.tbl CDD pfam18401 pfam18401 465749 Thioredoxin_13 Thioredoxin-like domain. This is the second out of four TRXL(thioredoxin-like) domains found in UDP-glucose:glycoprotein glucosyltransferase (UGGT). 136 matched cddid_all.tbl CDD pfam18402 pfam18402 465750 Thioredoxin_14 Thioredoxin-like domain. This is the third out of four TRXL(thioredoxin-like) domains found in UDP-glucose:glycoprotein glucosyltransferase (UGGT). 248 matched cddid_all.tbl CDD pfam18403 pfam18403 465751 Thioredoxin_15 Thioredoxin-like domain. This is the fourth TRXL(thioredoxin-like) domain found in UDP-glucose:glycoprotein glucosyltransferase (UGGT). 205 matched cddid_all.tbl CDD pfam18404 pfam18404 436473 Glyco_transf_24 Glucosyltransferase 24. This is the catalytic domain found in UDP-glucose:glycoprotein glucosyltransferase (UGGT). This domain belongs to glucosyltransferase 24 family (GT24) A-type domain. The GT domain displays the expected glycosyltransferase type A (GT-A) fold. 268 matched cddid_all.tbl CDD pfam18405 pfam18405 436474 SLC25_like Mitochondrial SLC25 homolog. This family includes distant homologs of mitochondrial carrier proteins (MCs, also known in mammals as solute carrier family 25, SLC25). Sequence analysis suggest that it is likely that Lpg1137 forms a standard MC structure with a pseudo-threefold symmetry with six transmembrane helices. Furthermore, sequence logos of the repeats in homologs of Lpg1137, compared to sequence logo of the eukaryotic mitochondrial carriers support the structural similarity by highlighting the conservation of structurally important Pro and Gly residues (e.g., Pro at positions 15 and 239 in the logos or the YxG motif at positions 45-47. It was previously thought that members of this family are serine proteases that target the mitochondria-associated ER membrane (MAM) and degrades STX17 (syntaxin 17), a SNARE implicated in macroautophagy/autophagy as well as mitochondria dynamics and membrane trafficking in fed cells. 285 matched cddid_all.tbl CDD pfam18406 pfam18406 436475 DUF1281_C Ferredoxin-like domain in Api92-like protein. This domain has a ferredoxin like fold. It is often found to the C terminus of pfam06924. 88 matched cddid_all.tbl CDD pfam18407 pfam18407 465752 GNAT_like GCN5-related N-acetyltransferase like domain. This is a domain with a GCN5-related N-acetyltransferase (GNAT) fold which can be found in Rv1692 phophatases. Crystal structure of Rv1692 indicates that this C-temrinal extension, which is absent in other characterized HADSF members, resembles a small GCN5-related N-acetyltransferase (GNAT) fold. Furthermore, it is fused to the HADSF catalytic domain pfam13242. Functional studies indicate that this GNAT region is not likely to be involved in acetyl group transfer using AcCoA and SucCoA, it could nonetheless be a regulatory domain. Furthermore, it is suggested that this GNAT domain is required for the solubility of the HADSF fold of Rv1692 and is potentially needed for the structural integrity of this enzyme. 60 matched cddid_all.tbl CDD pfam18408 pfam18408 465753 zf_Hakai C2H2 Hakai zinc finger domain. This is the C2H2 zinc finger domain found in E3 ubiquitin ligase Hakai. Hakai targets tyrosine-phosphorylated E-cadherin. It carries a Tyr(P)-binding domain, coined the HYB domain for Hakai phosphotyrosine (Tyr(P)) binding. HYB domain structure illustrates that it forms a zinc-coordinated homodimer in an antiparallel, intertwined configuration, utilizing residues from the Tyr(P)-binding region of two Hakai monomers. The C-terminal region of the HYB domain, which harbors the atypical zinc-coordination motif and key residues involved in the Tyr(P) interaction, plays an important role in the dimerization observed in the HYB domain. 32 matched cddid_all.tbl CDD pfam18409 pfam18409 465754 Plk4_PB2 Polo-like Kinase 4 Polo Box 2. This Polo box (PB) domain is found in Polo-like kinase 4 (Plk4) present in Drosophila melanogaster. Plk4 is a conserved component in the duplication pathway of centrioles which is needed to prevent chromosomal instability. Plk4 localizes to centrioles in M/G1. Structural analysis reveals two tandem, homodimerized polo boxes, PB1-PB2, that form a winged architecture. This domain is PB2, together with PB1 pfam18190, they are required for binding the centriolar protein Asterless (Asl) as well as robust centriole targeting. In other words, PB1-PB2 cassette collectively binds Asl and affords robust centriole localization, optimally positioning the kinase domain for trans-autophosphorylation. 110 matched cddid_all.tbl CDD pfam18410 pfam18410 465755 BTHB Basic tilted helix bundle domain. This domain is found on the N-terminal region of FKBPs such as FKBP25 and in the core region of E3 ubiquitin ligase HectD1. It adopts a compact 5-helix bundle, hence termed BTHB (Basic Tilted Helix Bundle) domain. In FKBP25, it has been suggested to have a role in regulating the association state of nucleosomes by interacting with nucleolin. Moreover, this basic domain in FKBP25 forms alternative complexes with other chromatin-related proteins, such as the HDAC1, HDAC2, and the transcriptional regulator YY1, the DNA binding activity of which is enhanced on binding FKBP25. Structural analysis of this fold suggests that the DNA binding properties of FKBP25 and HectD1 are presented by the conserved basic region. 72 matched cddid_all.tbl CDD pfam18411 pfam18411 465756 Annexin_like Annexin-like domain. This annexin-like domain can be found in astrotactin 2 (Astn-2), an integral membrane perforin-like protein linked to the planar cell polarity pathway in hair cells. The annexin-like domain is closest in fold to repeat three of human annexin V and similarly binds calcium, yet shares no sequence homology with it. Notably, this ASTN-2 annexin-like domain is closer in structure to human annexin repeat 3 than human annexin repeat 3 is to repeat 1. Annexin-like domains are known for their capacity to remodel membranes, triggered by calcium binding, and have also been suggested to be involved in the formation of pores in membranes both are possible biological roles of the ASTN-2 annexin-like domain. 93 matched cddid_all.tbl CDD pfam18412 pfam18412 465757 Wza_C Outer-membrane lipoprotein Wza C-terminal domain. This is the C-terminal domain found in Wza, an integral outer membrane lipoprotein, which is essential for group 1 capsule export in Escherichia coli. The domain is exposed on the cell surface and is suggested to mimic antimicrobial peptide pore formation. 30 matched cddid_all.tbl CDD pfam18413 pfam18413 465758 Neuraminidase Neuraminidase-like domain. This is a neuraminidase-like domain, which is structurally homologous to neuraminidases. It can be found in TcA subunit in tripartite Tc toxin complexes of bacterial pathogens. Functional analysis suggest that the neuraminidase-like domain acts as an electrostatic lock that opens at high or low pH values. 170 matched cddid_all.tbl CDD pfam18414 pfam18414 436483 zf_C2H2_10 C2H2 type zinc-finger. This is a zinc finger domain C2H2 which can be found in optineurin (optic neuropathy inducing protein) and NF-kappa-B essential modulator (NEMO) furthermore, it can be found in kinase TBK1, a member of the IKK (inhibitor of nuclear factor kappa-B kinase) family. The C-terminal region, which carries the zinc finger domain, constitutes the regulatory domain of NEMO, as it receives the activation signal from upstream molecules, and subsequently transmits this activation to the kinases bound to the N-terminal domain. The isolated NEMO zinc finger is thought to be involved in protein-protein rather than protein-DNA interaction. 26 matched cddid_all.tbl CDD pfam18415 pfam18415 436484 HKR_ArcB_TM Histidine kinase receptor ArcB trans-membrane domain. Histidine kinase receptors (HKRs) are part of a two-component system, in which an HKR in the bacterial inner membrane transmits a signal to a response regulator located in the cytoplasm. This is a trans-membrane domain (TM) found in ArcB (class 2, aerobic respiratory control sensor). ArcB has two TM helices connected by a short periplasmic loop. TM domain structures suggests a loose helical packing which provides an inherent flexibility in the TM domains and that this is perhaps essential to the mechanism of signal transduction across the membrane. 75 matched cddid_all.tbl CDD pfam18416 pfam18416 465759 GbpA_2 N-acetylglucosamine binding protein domain 2. This domain can be found in N-acetylglucosamine binding protein (GbpA) from Vibrio cholerae, a bacterial pathogen that colonizes the chitinous exoskeleton of zooplankton as well as the human gastrointestinal tract. GbpA binds to GlcNAc oligosaccharides. Structural comparison show that there are distant structural similarities between domain 2 of GbpA and the beta-domain of the flagellin protein p5. It is suggested that this domain interacts with the bacterial surface, and functions to project an alginate binding domain of the protein from the cell surface. 102 matched cddid_all.tbl CDD pfam18417 pfam18417 436486 LodA_C L-lysine epsilon oxidase C-terminal domain. This is the C-terminal domain of L-Lysine epsilon-oxidase (LodA, EC 1.4.3.20), an enzyme which catalyzes the oxidative deamination of free L-lysine into L-2-aminoadipate 6-semialdehyde, ammonia and hydrogen peroxide. 144 matched cddid_all.tbl CDD pfam18418 pfam18418 408216 AnkUBD Ankyrin ubiquitin-binding domain. This is an Ankyrin repeat domain found in TRABID (also known as Ubiquitin thioesterase ZRANB1) (EC:3.4.19.12). In TRABID, the first ankyrin repeat spans residues 260-290 and is connected to the second repeat residues 313-340 by a long linker that packs against what would correspond to the concave surface in an extended ankyrin-repeat structure. Ankyrin-repeat domains mediate protein interactions through a variety of surfaces. The ankyrin domain of TRABID interacts with ubiquitin, hence it is referred to as the ankyrin ubiquitin-binding domain, or AnkUBD. 96 matched cddid_all.tbl CDD pfam18419 pfam18419 436487 ATP-grasp_6 ATP-grasp-like domain. Glutathione biosynthesis is achieved in most organizms via a conserved two-step approach relying on the capacity of two independent and unrelated ligases to perform peptide synthesis coupled to ATP hydrolysis. In a first and rate-limiting step, gamma-glutamylcysteine ligase (gamma-ECL) (or GshA; EC:6.3.2.2) uses l-glutamate and l-cysteine to form gamma-glutamylcysteine (gamma-EC), which, in a second step, is condensed with glycine to glutathione by glutathione synthetase (GS) (or GshB; EC:6.3.2.3). However, several pathogenic and free-living bacteria carry out glutathione biosynthesis based on a single enzyme that catalyzes both the gamma-ECL and the GS reactions. Such bifunctional glutathione-synthesizing enzymes have been termed gamma-GCS-GS or GshF. Hybrid GshF contains a typical gamma-proteobacterial gamma-ECL fused to an ATP-grasp-like domain. The ATP-grasp-like module is responsible for the ensuing formation of glutathione from gamma-glutamylcysteine and glycine. The ATP-grasp-like domain has an antiparallel beta-sheet in the GshF structures in contrast to all structurally characterized members of the ATP-grasp superfamily. 54 matched cddid_all.tbl CDD pfam18420 pfam18420 375846 CSN4_RPN5_eIF3a CSN4/RPN5/eIF3a helix turn helix domain. Cullin-RING E3 ubiquitin ligases (CRLs) are regulated by the eight-subunit COP9 signalosome (CSN). Enzymatically, CSN functions as an isopeptidase that removes the ubiquitin-like activator NEDD8 from CRLs, but it can also bind deneddylated CRLs and maintain them in an inactive state. The CSN subunits CSN1, CSN2, CSN3, CSN4, CSN7 and CSN8, share a common domain composition: an N-terminal array of tandem alpha-helical tetratricopeptide/-like repeats, a 34 residue motif, followed by a PCI domain, which encompasses a WH subdomain, a linker, and one or two alpha-helices at the C-terminus. This entry describes the C-terminal helices found on CSN4. The two helices from CSN4 (helices I and II) form a brace roughly perpendicular to the bundle axis in contact with the three C-terminal helices of CSN6. CSN5, whose two C-terminal helices form an antiparallel hairpin, inserts its final C-terminal helix (helix II) into the central CSN6 framework at the core of the bundle. Both CSN1 and CSN4 are dependent on the presence of their C-terminal helix (CSN1 isoform-2 residues: 466-527; and CSN4: 364-406) for integration into CSN. COP9 signalosome shares common architecture with the 26S proteasome lid and eIF3 where the 19S lid subunit RPN5 and the eIF3 core subunit eIF3a share significant structural similarity with CSN4. 42 matched cddid_all.tbl CDD pfam18421 pfam18421 436488 Peptidase_M23_N Peptidase family M23 N-terminal domain. This is the N-terminal domain of Peptidase M23 pfam01551 mostly found in proteobacteria. 73 matched cddid_all.tbl CDD pfam18422 pfam18422 436489 TNFR_16_TM Tumor necrosis factor receptor member 16 trans-membrane domain. This is the helical trans-membrane domain found in tumor necrosis factor receptor superfamily member 16 (also known as p75 neurotrophin receptor, and nerve growth factor receptor-NGFR). p75 plays prominent biological functions such the induction of cell death, and it demonstrates several other activities, like survival, axonal growth, and cell migration. The trans-membrane (TM) domain of p75 stabilizes the receptor dimers through a disulfide bond, essential for the NGF signalling Structural and mutational analysis indicate that Cys257 plays the key role in this stabilization process. Furthermore, although the p75-C257A mutant is still capable to form dimers and bind to NGF, it is unable to transduce the signals triggered by NGF binding in some cell signalling paradigms. 38 matched cddid_all.tbl CDD pfam18423 pfam18423 465760 zf_CopZ Zinc binding domain. This is N-terminal domain containing a mononuclear metal center for zinc binding found in copper chaperone CopZ proteins. 62 matched cddid_all.tbl CDD pfam18424 pfam18424 465761 a_DG1_N2 Alpha-Dystroglycan N-terminal domain 2. This is the second N-terminal domain found in alpha-Dystroglycan (DG). The murine skeletal muscle N-terminal alpha-DG region, contains two autonomous domains; the first identified as an Ig-like and the second resembling ribosomal RNA-binding proteins. This domain is similar to the small subunit ribosomal protein S6 of Thermus thermophilus (S6 domain). It is suggested that the S6 domain may be of functional relevance for LARGE (like-acetylglucosaminyltransferase) recognition along the alpha-DG maturation pathway. 123 matched cddid_all.tbl CDD pfam18425 pfam18425 465762 CspB_prodomain Csp protease B prodomain. Csp proteases (Csps) and the subtilase protease family Subtilases are serine proteases that contain a catalytic triad in the order of Asp, His and Ser. Structure analysis reveals that Csps are subtilisin-like proteases with two distinctive functional features: a central jellyroll domain and a retained prodomain. The prodomain adopts a similar fold to the prodomains of related subtilisin-like proteases with the C-terminal region extending deep into the catalytic cleft. However, unlike the majority of subtilisin-like proteases, the prodomain stays bound to the subtilase domain via a network of interactions that result in tighter prodomain binding relative to other subtilases. Finally the prodomain acts as both an intramolecular chaperone and an inhibitor of CspB protease activity. 89 matched cddid_all.tbl CDD pfam18426 pfam18426 436493 Tli4_C Tle cognate immunity protein 4 C-terminal domain. T6SS bacteria employ toxic effectors to inhibit rival cells and concurrently use effector cognate immunity proteins to protect their sibling cells. The effector and immunity pairs (E-I pairs) endow the bacteria with a great advantage in niche competition. This is the C-terminal domain of Tli4. The Tle cognate immunity proteins (Tlis) can directly disable the transported Tle protein and thereby mediate the self-protection process. The Tle-Tli effector-immunity (E-I) pairs confer substantial advantage to the donor cell during interbacterial competition. Tli4 displays a two-domain structure, in which a large lobe and a small lobe form a crab claw-like conformation. Tli4 uses this crab claw to grasp the cap domain of Tle4, especially the lid2 region, which prevents the interfacial activation of Tle4 and thus causes enzymatic dysfunction of Tle4. Structural comparison indicates similarity between this C-terminal domain of Tli4 and Tsi3, which is the cognate immunity protein of the effector protein Tse3 in P. aeruginosa PDB:4n7s. 161 matched cddid_all.tbl CDD pfam18427 pfam18427 465763 DDR_swiveling DD-reactivating factor swiveling domain. AdoCbl-dependent diol dehydratase (DD) (EC 4.2.1.28) is one of the enzymes that catalyzes the conversion of 1,2-propanediol, 1,2-ethanediol, and glycerol to the corresponding aldehydes. A DD-reactivating factor (DDR) is responsible for the rapid reactivation of the inactivated holoDD in the presence of AdoCbl, ATP, and Mg2+. DDR exists as a dimer of heterodimer (alpha-beta)2. The alpha subunit has four domains: ATPase domain, swiveling domain, linker domain, and insert domain. The beta subunit, composed of a single domain, has a similar fold to the beta subunit of diol dehydratase (DD). This entry describes the swiveling domain of DDR, which structurally connects the beta subunit and the ATPase domain of the other alpha subunit. Furthermore, the beta subunit moves with the swiveling domain while the linker domain acts as a flat spring or a hinge for the domain movement of the swiveling domain. 162 matched cddid_all.tbl CDD pfam18428 pfam18428 465764 BRCT_3 BRCA1 C Terminus (BRCT) domain. Brca1 C-terminal (BRCT) domains are a common protein-protein interaction regions in proteins involved in the DNA damage response and DNA repair. For example 53BP1 which plays multiple roles in mammalian DNA damage repair, has a C-terminal tandem BRCT domain (BRCT2), which in its orthologs, Saccharomyces cerevisiae Rad9p and Schizosaccharomyces pombe Crb2, mediates binding to the equivalents of gammaH2AX. Structural and functional studies indicate that the 53BP1-BRCT2 domain is a competent binding module for phosphorylated peptides with a clear specificity for the DNA-damage marker gammaH2AX, and in isolation from other parts of 53BP1 is sufficient for localization to sites of DNA damage in cells associated with gammaH2AX. 100 matched cddid_all.tbl CDD pfam18429 pfam18429 436496 DUF5609 Domain of unknown function (DUF5609). This is a probable HAD-like (haloalkanoate dehalogenase) domain found in bacterial phosphoserine phosphatases. 65 matched cddid_all.tbl CDD pfam18430 pfam18430 408227 DBD_HTH Putative DNA-binding domain. This is a putative DNA-binding protein dimerization domain found bacterial proteins such as CD3330, (a transposon-related DNA-binding protein from Clostridium difficile). Crystal structure analysis suggests that CD3330 N-terminus is involved in dimer formation and also in crystal packing but the C-terminus is open to solvent. 35 matched cddid_all.tbl CDD pfam18431 pfam18431 436497 RNAse_A_bac Bacterial CdiA-CT RNAse A domain. Contact-dependent growth inhibition (CDI) is an important mechanism of inter-bacterial competition found in many Gram-negative pathogens. CDI+ cells express cell-surface CdiA proteins that bind neighboring bacteria and deliver C-terminal toxin domains (CdiA-CT) to inhibit target-cell growth. Structure analysis of CdiA-CT shows that it adopts the same fold (with two beta-sheets forming an overall kidney shape) as angiogenin and other RNase A paralogs, but the toxin does not share sequence similarity with these nucleases and lacks the characteriztic disulfide bonds of the superfamily. Furthermore, structural comparison analysis identified human angiogenin, Rana pipiens protein P-30 (onconase) and mouse pancreatic ribonuclease (RNase 1) as the closest structural homologs of CdiA-CT. 113 matched cddid_all.tbl CDD pfam18432 pfam18432 408229 ECD Extracellular Cadherin domain. This is an extracellular cadherin (EC) domain which can be found at the N-terminal region of Protocadherin 15 (Pcdh15). Pcdh15 features exceptionally long extracellular domains containing 11 ECs. These repeats are structurally similar, but not identical in sequence, often featuring linkers with conserved calcium-binding sites that confer mechanical strength to them. 110 matched cddid_all.tbl CDD pfam18433 pfam18433 436498 DUF5610 Domain of unknown function (DUF5610). This is a domain of unknown function found in bacterial proteins. 113 matched cddid_all.tbl CDD pfam18434 pfam18434 436499 Kazal_3 Kazal-type serine protease inhibitor domain. Kazal domain found in factor I-like modules (FIMs) region on the carboxyl-terminal of complement component C7 proteins. Complement component C7 is a subunit of the membrane attack complex (MAC), a fundamental machinery in the mammalian innate immunity. KAZAL domains are common in serine protease inhibitors. 50 matched cddid_all.tbl CDD pfam18435 pfam18435 465765 EstA_Ig_like Esterase Ig-like N-terminal domain. This is an N-terminal immunoglobulin (Ig)-like domain found in esterases such as EstA. Analysis of the EstA structure confirms that it is a member of the alpha/beta hydrolase family, with a conserved Ser-Asp-His catalytic triad. The Ig-like domain presumably plays a role in the multimerization of EstA into an unusual hexameric structure. Additionally, it may also participate in the catalysis of EstA by guiding the substrate to the active site. 120 matched cddid_all.tbl CDD pfam18436 pfam18436 465766 HECW1_helix Helical box domain of E3 ubiquitin-protein ligase HECW1. This is a region of 109 amino acids found in HECW1 proteins in Eukaryotes.Polymorphisms in the same region in the C.elegans homolog affects C. elegans behavioural avoidance of a lawn of Pseudomonas aeruginosa. 67 matched cddid_all.tbl CDD pfam18437 pfam18437 465767 Nup54_C Nup54 C-terminal interacting domain. The mammalian nuclear pore complex (NPC) conducts nucleocytoplasmic transport and contains multiple copies of nucleoporins (nups). This is the C-terminal interacting domain found on Nup54. Nup45 is a splice variant of Nup58 with an identical alpha-helical region. Nup54 along with Nup62 and Nup58 are essential for nuclear transport. The C-terminal part of the alpha-helical region of Nup54 interacts with a C-terminal part of the alpha-helical region of Nup58. Interestingly, this region appears in two distinct conformations: a single helix and a helix-loop-helix, termed 'straight' and 'bent'. Whereas the straight conformer consists of a 34 residues long alpha helix (residues 460-493), the bent conformer is composed of two alpha helices, each 13 residues long, connected by a central loop (N helix, residues 460-472; C helix, residues 477-489). 39 matched cddid_all.tbl CDD pfam18438 pfam18438 465768 Glyco_hydro_38 Glycosyl hydrolases family 38 C-terminal domain 1. The enzymatic hydrolysis of alpha-mannosides is catalyzed by glycoside hydrolases (GH), termed alpha-mannosidases. Streptococcal (Sp) GH38 alpha-mannosidase active on N-glycans and possibly O-glycans. SpGH38 structure can be considered as five domains: an N-terminal alpha/beta-domain, a three-helix bundle and three predominantly beta-sheet domains. This is the first of the three beta-sheet domains found in GH38, termed Beta-1. Structural analysis indicate that the beta-1 domain bows outward from the protein core, is involved in dimer interactions whilst also forming a lid 'above' and somewhat into the active centre of its dimer. 111 matched cddid_all.tbl CDD pfam18439 pfam18439 465769 zf_UBZ Ubiquitin-Binding Zinc Finger. This is ubiquitin-binding zinc finger (UBZ) domain found in DNA polymerase eta (EC:2.7.7.7). It is important in the recruitment of the polymerase to the stalled replication machinery in translesion synthesis. The UBZ domain adopts a classical C2H2 zinc-finger structure characterized by a beta-beta-alpha fold. 32 matched cddid_all.tbl CDD pfam18440 pfam18440 408237 GlcNAc-1_reg Putative GlcNAc-1 phosphotransferase regulatory domain. The Golgi enzyme UDP-GlcNAc-lysosomal enzyme N-acetylglucosamine-1-phosphotransferase (GlcNAc-1-phosphotransferase), an alpha2beta2gamma2 hexamer, mediates the initial step in the addition of the mannose 6-phosphate targeting signal on newly synthesized lysosomal enzymes. GNPTAB encodes the alpha and beta subunits of GlcNAc-1-phosphotransferase, and mutations in this gene cause the lysosomal storage disorders mucolipidosis II and III alpha-beta The alpha-beta subunits contain three identifiable domains separated by so-called spacer regions. This domain is part of the first spacer region, Spacer-1. Studies indicate that GlcNAc-1 lacking spacer-1 exhibits enhanced phosphorylation of several non-lysosomal glycoproteins, while the phosphorylation of lysosomal acid hydrolases is not altered. In view of these effects on the maturation and function of GlcNAc-1, it is suggested to rename 'spacer-1' the 'regulatory-1' domain. 88 matched cddid_all.tbl CDD pfam18441 pfam18441 465770 Hen1_Lam_C Hen1 La-motif C-terminal domain. RNA silencing is a conserved regulatory mechanism in fungi, plants and animals that regulates gene expression and defence against viruses and transgenes. A conserved S-adenosyl-l-methionine-dependent RNA methyltransferase, HUA ENHANCER 1 (HEN1), and its homologs are responsible for 2'-O-methylation on the 3' terminal nucleotide of microRNAs and small interfering RNAs (siRNAs). The 2'-O-methylation protects miRNAs and siRNAs from 3'-end uridylation and 3'-to-5' exonuclease-mediated degradation. This domain lies on the C-terminal region of the La-motif domain found in HEN1. 136 matched cddid_all.tbl CDD pfam18442 pfam18442 375868 G2BR E3 gp78 Ube2g2-binding region (G2BR). The activity of RING finger ubiquitin ligases (E3) is dependent on their ability to facilitate transfer of ubiquitin from ubiquitin-conjugating enzymes (E2) to substrates. The G2BR domain within the E3 gp78 binds selectively and with high affinity to the E2 Ube2g2. Binding to the G2BR results in conformational changes in Ube2g2 that affect ubiquitin loading. The Ube2g2-G2BR interaction also causes a 50-fold increase in affinity between the E2 and RING finger. Hence, the Ube2g2-binding region (G2BR) is required for the function of gp78. In yeast, Ubc7p, the ortholog of Ube2g2, is recruited by Cue1p to the ER membrane. Cue1p directly binds Ubc7p through a stretch of 50 aa domain analogous to G2BR, i.e. suggesting that this domain which activates ERAD and Hrd1p stimulating ubiquitylation, might be the yeast equivalent of the G2BR domain. 26 matched cddid_all.tbl CDD pfam18443 pfam18443 436506 Tli4_N Tle cognate immunity protein 4 N-terminal domain. T6SS bacteria employ toxic effectors to inhibit rival cells and concurrently use effector cognate immunity proteins to protect their sibling cells. The effector and immunity pairs (E-I pairs) endow the bacteria with a great advantage in niche competition. This is the C-terminal domain of Tli4. The Tle cognate immunity proteins (Tlis) can directly disable the transported Tle protein and thereby mediate the self-protection process. The Tle-Tli effector-immunity (E-I) pairs confer substantial advantage to the donor cell during interbacterial competition. Tli4 displays a two-domain conformation (domains I and II) and contains 17 beta-strands and four helices. These two domains pack into a crab claw-like conformation functioning as an inhibitor of Tle4. Both domains adopt an alpha+beta architecture. Domain I features a central antiparallel beta-sheet sandwiched by two helices and a short antiparallel beta-sheet. This entry comprises the N-terminal domain I found in Tli4 proteins. 138 matched cddid_all.tbl CDD pfam18444 pfam18444 408240 RRM_9 RNA recognition motif. The Mex67-Mtr2 complex (TAP-p15 or NXF1-NXT1 in metazoans) is the principal mRNA export factor in Saccharomyces cerevisiae. Mex67 is a member of the NXF family of proteins and has conserved homologs through eukaryotes from yeast to humans. Although sequence conservation is poor between S. cerevisiae Mex67 and Homo sapiens NXF1, they do show functional complementarity. Mex67 and TAP/NXF1 are modular proteins that contain four structural domains: an N-terminal RNA recognition motif (RRM), a leucine rich repeat (LRR) domain, a nuclear transport factor 2-like domain (NTF2L) and an ubiquitin-associated domain (UBA). This entry describes the N-terminal RNA recognition motif (RRM) found in Mex67 proteins. 70 matched cddid_all.tbl CDD pfam18445 pfam18445 375871 zf_PR_Knuckle PR zinc knuckle motif. This is a zinc knuckle motif found in PRDM4 (Schwann cell factor 1, SC-1), a member of the PR protein family. PRDM4 is a transcriptional regulator that has been implied in transduction of nerve growth factor signals via the p75 neurotrophin receptor and in cell growth arrest. The short motif is also present in several other PR proteins including human PRDM6 (PRISM), PRDM7, PRDM9 (meisetz), PRDM10 (tristanin), PRDM11, and PRDM15. The conservation of cysteine and histidine residues suggested that this 20 amino acid motif binds zinc, hence the name 'PR zinc knuckle' to distinguish it from the longer (30 amino acid) C2H2-like zinc fingers that are located C-terminally of the PR domain. The PR zinc knuckle fold is similar to that of Gag-knuckles (a beta-hairpin providing two zinc ligands followed by a short helix or a loop providing the other two zinc ligands) and zinc ribbons (two beta-hairpins, each providing two zinc ligands). 38 matched cddid_all.tbl CDD pfam18446 pfam18446 465771 DUF5611 Domain of unknown function (DUF5611). This is a domain of unknown function. Studies of the TA0095 gene product indicate that this 96-residue hypothetical protein from Thermoplasma acidophilum is a member of the COG4004 orthologous group of unknown function found in Archaea bacteria. The structure displays an alpha/beta two-layer sandwich architecture formed by three alpha-helices and five beta-strands. Furthermore, structural homologs indicate that the TA0095 structure belongs to the TBP-like fold. 102 matched cddid_all.tbl CDD pfam18447 pfam18447 465772 FN3_7 Fibronectin type III domain. This domain is found in Interleukin-7 receptor subunit alpha (IL-7Ralpha), which together IL-7 form a complex crucial to several signalling cascades leading to the development and homeostasis of T and B cells. IL-7Ralpha carries a 219 residue ectodomain on the N-terminal region which is crucial for T and B-cell development. Mutations in the IL-7Ralpha ectodomain inhibits T and B cell development, resulting in patients with a form of severe combined immunodeficiency (SCID). The ectodomain folds into two fibronectin type III (FNIII) domains connected by a 310-helical linker. This entry comprises the first of the two FNIII domains, D1 while D2 domain is pfam00041. In the D1 domain of IL-7Ralpha, a disulfide bond (C22R-C37R) conserved among cytokine receptor class I (CRH I) family members bridges two beta strands. 97 matched cddid_all.tbl CDD pfam18448 pfam18448 436509 CBM46 Carbohydrate binding domain. Carbohydrate active enzymes (CAZYmes) that target recalcitrant polysaccharides are modular enzymes containing noncatalytic carbohydrate-binding modules (CBMs) that direct enzymes to their cognate substrate, thus potentiating catalysis. The structure of Bacillus halodurans endo-beta-1,4-glucanase B (Cel5B) reveals that CBM46 is tightly associated with the catalytic module and, dependent on the glucan presented to the enzyme, can contribute directly to substrate binding or play a targeting role in directing the enzyme to regions of the plant cell wall rich in the polysaccharide hydrolyzed by the enzyme. The CBM46 domain displays a classic beta-sandwich jelly roll fold. Against beta-1,3-1,4-glucans CBM46 domain participates in productive substrate binding and thus plays a direct role in the hydrolytic activity of the enzyme. 105 matched cddid_all.tbl CDD pfam18449 pfam18449 436510 Endotoxin_C2 Delta endotoxin. This is domain (D-VI) can be found in Bacillus thuringiensis (Bt) insecticidal protein Cry1Ac. Full length structural analysis reveal that Cry1Ac contains seven distinct domains (DI-DVII): the three canonical toxin core domains (D-I through D-III) and four protoxin domains (D-IV through D-VII). Cry1Ac is sickle-shaped with the toxic core as handle and the protoxin domains as the blade. Domains IV and VI are alpha-bundles that resemble structural/interaction domains such as spectrin [PDB ID: 1CUN] or bacterial fibrinogen-binding complement inhibitor. 63 matched cddid_all.tbl CDD pfam18450 pfam18450 408245 zf_C2H2_6 Zinc Finger domain. This is a C2H2 type zinc finger domain which can be found in Zinc finger and BTB domain-containing protein 21 (ZBTB21). 28 matched cddid_all.tbl CDD pfam18451 pfam18451 436511 CdiA_C Contact-dependent growth inhibition CdiA C-terminal domain. Contact-dependent growth inhibition (CDI) systems encode polymorphic toxin/immunity proteins that mediate competition between neighboring bacterial cells. CDI is mediated by the CdiB/CdiA family of two-partner secretion proteins. This domain represents the C-terminal of CdiA proteins (CdiA-CT), which contains the CDI toxin activity. The C-terminal nuclease domain forms a stable complex with its cognate immunity protein. It is also sufficient to inhibit growth when expressed in E. coli cells, consolidating the idea that they constitute the functional CDI toxin. The CdiA-CT C-terminal domains are structurally similar to type IIS restriction endonucleases suggesting that the toxins have metal-dependent DNase activity. 81 matched cddid_all.tbl CDD pfam18452 pfam18452 465773 Ig_6 Immunoglobulin domain. This is an immunoglobulin domain which can be found in Interleukin-18 receptor alpha (IL-18Ra). IL-18Ra ectodomain folds into three immunoglobulin (Ig)-like domains, similar to IL-1 receptors. Each domain comprises a two-layer sandwich of six to nine beta-strands and contains at least one intra-domain disulfide bond. 128 matched cddid_all.tbl CDD pfam18453 pfam18453 436513 C4bp_oligo Oligomerization domain of C4b-binding protein alpha. This is the C-terminal oligomerization domain found in C4b-binding protein (C4BP), which contains 14 cysteines that form 7 intermolecular disulfide bridges. C4BP is a plasma glycoprotein complex of 570 kDa, which is mainly produced in the liver. C4BP is the major inhibitor of complement activation, the major isoform consists of 7alpha and one beta-chain where each alpha-chain comprises eight complement control domain proteins (CCPs) and a C-terminal oligomerization domain. This domain carries a stretch of 42-45 amino acids that has been shown to be required for ring formation. 49 matched cddid_all.tbl CDD pfam18454 pfam18454 436514 Mtd_N Major tropism determinant N-terminal domain. This is the N-terminal domain of major tropism determinant (Mtd), a retroelement-encoded receptor-binding protein. Mtd-N forms a three-fold symmetric beta-prism. This resembles the pseudo three-fold-symmetric beta-prisms of monocot lectins, but lacks residues in these lectins identified as binding carbohydrates. The beta-prism and beta-sandwich domains reinforce overall trimeric assembly and therefore may have indirect roles in stabilizing the backbone of the variable region. 37 matched cddid_all.tbl CDD pfam18455 pfam18455 465774 GBR2_CC Gamma-aminobutyric acid type B receptor subunit 2 coiled-coil domain. This is the intracellular coiled-coil domain found in Gamma-aminobutyric acid type B receptor subunit 2 (GBR2). The coiled-coil complex between the GABAB receptor subunits GBR1 and GBR2 is responsible for facilitating the surface transport of the intact receptor. Disruption of the hydrophobic coiled-coil interface with single mutations in either subunit impairs surface expression of GBR1, confirming that the coiled-coil interaction is required to inactivate the adjacent ER retention signal of GBR1. 39 matched cddid_all.tbl CDD pfam18456 pfam18456 465775 CmlA_N Diiron non-heme beta-hydroxylase N-terminal domain. This is the N-terminal domain found in Diiron non-heme beta-hydroxylase (CmlA). CmlA catalyzes beta-hydroxylation of the precursor molecule l-p-aminophenylalanine (l-PAPA) to form l-p-aminophenylserine. Structural analysis indicate that the N-terminal domain facilitates dimerization and has a mixed alpha-beta topology. Furthermore, a projecting 'dimerization arm' (residues 108-146) from the N-terminal domain of CmlA mediates the interaction between the monomers. 232 matched cddid_all.tbl CDD pfam18457 pfam18457 408250 PUD1_2 Up-Regulated in long-lived daf-2. This entry includes C. elegans PUD-1 and PUD-2, two proteins up-regulated in daf-2(loss-of-function) (PUD), are homologous 17-kD proteins with similar beta-sandwich folds that further associate with each other into a V-shaped heterodimer. 172 matched cddid_all.tbl CDD pfam18458 pfam18458 465776 XPB_DRD Xeroderma pigmentosum group B helicase damage recognition domain. This domain is found in the N-terminal region of xeroderma pigmentosum group B (XPB) helicase present in Archaeoglobus fulgidus. XPB is essential for transcription, nucleotide excision repair, and TFIIH functional assembly. The domain is a damage recognition domain (DRD) which allows XPB to unwind damaged DNA as needed for nucleotide excision repair. 57 matched cddid_all.tbl CDD pfam18459 pfam18459 408252 PCSK9_C1 Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain. This entry represents a subdomain found in the C-terminal cysteine/histidine-rich domain (CRD) of PCSK9 (also known as neural apoptosis-regulated convertase, NARC-1). PCSK9 has been shown to regulate circulating LDL-R levels by controlling LDL-R degradation. Furthermore, numerous mutations in the PCSK9 gene have been identified and associated with hypercholesterolemia (gain of function) or hypocholesterolemia (loss of function). The fully folded CRD, shows structural similarity to the resistin homotrimer, a small cytokine associated with obesity and diabetes. The C-terminal domain from PCSK9 consists of three, three-stranded beta-subdomains arranged in a pseudothreefold, and each of the subdomains in the CRD of PCSK9 consists of three structurally conserved disulfide bonds. 83 matched cddid_all.tbl CDD pfam18460 pfam18460 436518 HetR_C Heterocyst differentiation regulator C-terminal Hood domain. This is the C-terminal hood domain found in Heterocyst differentiation control protein (HetR). HetR-C binds to PatS peptide. Two PatS6 peptides bind to the lateral clefts of HetR-Hood domain, and trigger significant conformational changes of the flap domain, resulting in dissociation of the auxiliary alpha-helix and eventually release of HetR from the DNA major grove and termination of transcription. 79 matched cddid_all.tbl CDD pfam18461 pfam18461 436519 Atypical_Card Atypical caspase recruitment domain. The N-terminal effector domain found in NLRC5. It adopts a six alpha-helix bundle with a general death fold. Structure and sequence analysis of the NLRC5-N indicate that it possesses a fold similar to the one of the death-fold domains; however, it displays significant differences in the number of core alpha-helices and their relative orientation. Hence, it is suggested that NLRC5 belongs to the caspase recruitment domain (CARD) subfamily as an atypical CARD. 95 matched cddid_all.tbl CDD pfam18462 pfam18462 408255 DUF5612 Domain of unknown function (DUF5612). This is a domain of unknown function which is mostly found at the C-terminal of ACT domains such as pfam01842. 143 matched cddid_all.tbl CDD pfam18463 pfam18463 465777 PCSK9_C3 Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain. This entry represents a subdomain found in the C-terminal cysteine/histidine-rich domain (CRD) of PCSK9 (also known as neural apoptosis-regulated convertase, NARC-1). PCSK9 has been shown to regulate circulating LDL-R levels by controlling LDL-R degradation. Furthermore, numerous mutations in the PCSK9 gene have been identified and associated with hypercholesterolemia (gain of function) or hypocholesterolemia (loss of function). The fully folded CRD, shows structural similarity to the resistin homotrimer, a small cytokine associated with obesity and diabetes. The C-terminal domain from PCSK9 consists of three, three-stranded beta-subdomains arranged in a pseudothreefold, and each of the subdomains in the CRD of PCSK9 consists of three structurally conserved disulfide bonds. 74 matched cddid_all.tbl CDD pfam18464 pfam18464 465778 PCSK9_C2 Proprotein convertase subtilisin-like/kexin type 9 C-terminal domain. This entry represents a subdomain found in the C-terminal cysteine/histidine-rich domain (CRD) of PCSK9 (also known as neural apoptosis-regulated convertase, NARC-1). PCSK9 has been shown to regulate circulating LDL-R levels by controlling LDL-R degradation. Furthermore, numerous mutations in the PCSK9 gene have been identified and associated with hypercholesterolemia (gain of function) or hypocholesterolemia (loss of function). The fully folded CRD, shows structural similarity to the resistin homotrimer, a small cytokine associated with obesity and diabetes. The C-terminal domain from PCSK9 consists of three, three-stranded beta-subdomains arranged in a pseudothreefold, and each of the subdomains in the CRD of PCSK9 consists of three structurally conserved disulfide bonds. 66 matched cddid_all.tbl CDD pfam18465 pfam18465 465779 Rieske_3 Rieske 3Fe-4S. This domain is comprised of the iron-sulphur cluster and Rieske subunit found in the large subunit of arsenite oxidase. Arsenite oxidase is a 100 kDa molybdenum- and iron-sulfur-containing protein located on the outer surface of the inner membrane of Gram-negative organizms. The large subunit of arsenite oxidase is similar to other members of the dimethylsulfoxide (DMSO) reductase family of molybdenum enzymes. The large subunit of arsenite oxidase is divided into four domains, with domain I binding the [3Fe-4S] cluster. Domain I, consists of three antiparallel beta sheets and six helices. The [3Fe-4S] cluster is coordinated by the motif Cys21-X2-Cys24-X3-Cys28 near the interface with domains III and IV. A large, flattened funnel-like cavity bounded by domains I, II, and III leads to the molybdenum center pfam00384 located near the center of the molecule. 96 matched cddid_all.tbl CDD pfam18466 pfam18466 408259 GluRS_N Glutamate--tRNA ligase N-terminal domain. This is an N-terminal domain of Glutamate--tRNA ligase (GluRS, EC:6.1.1.17). The domain adopts a classical glutathione S-transferase (GST)-like fold and it interacts with tRNA-aminoacylation cofactor ARC1 (Arc1p) N-terminal domain for the formation of aminoacyl-tRNA synthetase (aaRS) complex in yeast. 55 matched cddid_all.tbl CDD pfam18467 pfam18467 436523 DUF5613 Domain of unknown function (DUF5613). This is a domain of unknown function found in bacteria. 97 matched cddid_all.tbl CDD pfam18468 pfam18468 408261 Pfk_N Phosphofructokinase N-terminal domain yeast. This is a phosphofructokinase (Pfk) N-terminal domain found in yeast ATP-dependent 6-phosphofructokinase subunit alpha. ATP-dependent 6-phosphofructokinases (Pfks, EC 2.7.1.11) catalyze the phosphorylation of fructose 6-phosphate (F-6-P) to fructose 1,6-bisphosphate, a key control step of glycolysis in most organizms. The N-terminal domain contains the active site and is related to glyoxalase I (E.C. 4.4.1.5). 98 matched cddid_all.tbl CDD pfam18469 pfam18469 436524 PH_18 Pleckstrin homology domain. This is a Pleckstrin Homology (PH) domain found on the N-terminal region of the histone chaperone Rtt106 in yeast. Rtt106 binds histone H3 acetylated at lysine 56 (H3K56ac) and facilitates nucleosome assembly during several molecular processes and this N-PH domain is shown to mediate histone binding. 140 matched cddid_all.tbl CDD pfam18470 pfam18470 465780 Cas9_a Cas9 alpha-helical lobe domain. This is an alpha-helical lobe domain found in Cas9 proteins. Cas9 enzymes adopt a bilobed architecture composed of a nuclease lobe containing juxtaposed RuvC and HNH nuclease domains and a variable alpha-helical lobe likely to be involved in nucleic acid binding. Amino acid residues located in both the nuclease and alpha-helical lobe clefts are highly conserved within type II-A Cas9 proteins. 220 matched cddid_all.tbl CDD pfam18471 pfam18471 408264 Ribosomal_L27_C Ribosomal L27 protein C-terminal domain. This is the C-terminal domain of 54S ribosomal protein L2 (also known as Mitochondrial large ribosomal subunit protein bL27m). bL27 C-terminal region interacts with an expansion segment of 21S rRNA to form part of the central protuberance. 240 matched cddid_all.tbl CDD pfam18472 pfam18472 465781 HP1451_C HP1451 C-terminal domain. HP1451 modulates the ATPase activity of HP0525 H. pylori. It is suggested that HP1451 acts as an inhibitory factor of HP0525 to regulate Cag-mediated secretion. It consists of two domains. The two HP1451 domains (referred to as the KH-domain and S8-domain) interact with each other via two salt bridges. The second domain is structurally homologous to other nucleic acid-binding proteins such as the NTD of ribosomal protein S8 and DNaseI. 67 matched cddid_all.tbl CDD pfam18473 pfam18473 408266 Urease_linker Urease subunit beta-alpha linker domain. This domain is present in bacterial ureases and corresponds to the gap region between the C-terminus of the beta-chain Urease beta subunit pfam00699 and the N-terminus of the alpha-chain Urease alpha-subunit, N-terminal domain pfam00449. It is suggested that this region is required for the stability of the putative transmembrane beta-barrel, and might be the reason for bacterial urease (B. pasteurii) not being lethal to insects. 34 matched cddid_all.tbl CDD pfam18474 pfam18474 436527 DUF5614 Family of unknown function (DUF5614). This is an N-terminal domain found in C7orf25 protein UPF0415. It is distantly related to the PD-(D/E)XK nucleases. 221 matched cddid_all.tbl CDD pfam18475 pfam18475 436528 PIN7 PIN domain. This is a bacterial PIN-like domain of unknown function. 103 matched cddid_all.tbl CDD pfam18476 pfam18476 436529 PIN_8 PIN like domain. This is a domain of unknown function, suggested to be a member of PIN like domains clan. 228 matched cddid_all.tbl CDD pfam18477 pfam18477 436530 PIN_9 PIN like domain. This is a domain of unknown function that resembles the PIN like domains. Family members include Ribonuclease VapC9. 116 matched cddid_all.tbl CDD pfam18478 pfam18478 436531 PIN_10 PIN like domain. This is a bacterial domain of unknown function suggested to resemble PIN like domains. 83 matched cddid_all.tbl CDD pfam18479 pfam18479 436532 PIN_11 PIN like domain. This is a eukaryotic/eumetazoan PIN like domain found in the C-terminal region of bilateral ZNF451 proteins such as isoform 1 of human ZNF451. ZNF451 was shown to interact with p300 by the PIN-like domain and to negatively regulate TGF-beta signalling in a p300-dependent and sumoylation-independent manner. This domain is suggested to posses a potential active nuclease due to the presence of at least four conserved Asp residues in the predicted active site. Furthermore, it contains several conserved Cys and His residues, which may suggest stabilization of the domain structure with an embedded short zinc-binding loop. 118 matched cddid_all.tbl CDD pfam18480 pfam18480 465782 DUF5615 Domain of unknown function (DUF5615). This is a domain of unknown function found in potential toxin-antitoxin system component. 77 matched cddid_all.tbl CDD pfam18481 pfam18481 465783 DUF5616 Domain of unknown function (DUF5616). This domain is found in a number of prokaryotic proteins. It is mostly found fused with the N-terminal domain pfam04256. This C-terminal domain is suggested to be a PIN like domain. 140 matched cddid_all.tbl CDD pfam18482 pfam18482 436535 Pih1_fungal_CS Fungal Pih1 CS domain. The Pih1 protein is part of the R2TP complex. The CS domain of Pih1 binds to the unstructured region of Tah1. The C-terminal domain of Pih1 consists of a seven-stranded beta sandwich with the topology of a CS domain, a structural motif also found in Hsp90 cochaperones such as p23/Sba1 and Sgt1. 90 matched cddid_all.tbl CDD pfam18483 pfam18483 465784 Bact_lectin Bacterial lectin. This entry primarily matches to legume-like lectin domains found in prokaryotes. 211 matched cddid_all.tbl CDD pfam18484 pfam18484 408277 CDCA Cadmium carbonic anhydrase repeat. This domain is the cadmium carbonic anhydrase repeat unit of the beta-carbonic anhydrase of a marine diatom, that uses both zinc and cadmium for catalysis of the reversible hydration of carbon dioxide for use in inorganic carbon acquisition for photosynthesis (thus being a cambialistic enzyme). Compared with alpha- and gamma-carbonic anhydrases that use three histidines to coordinate the zinc-atom, this beta-carbonic anhydrase has two cysteines and one histidine, and rapidly binds cadmium. 184 matched cddid_all.tbl CDD pfam18485 pfam18485 436537 GST_N_5 Glutathione S-transferase, N-terminal domain. This is the N-terminal (GST-N) domain containing a thioredoxin fold. This domain found in methionyl-tRNA synthetase (MRS), a multi-tRNA synthetase complex (MSC) component. 74 matched cddid_all.tbl CDD pfam18486 pfam18486 465785 PUB_1 PNGase/UBA- or UBX-containing domain. This is a PUB domain (PNGase/UBA- or UBX-containing domain), found in E3 ubiquitin-protein ligase RNF31, also known as Ring finger protein 31 and HOIL-1-interacting protein (HOIP) (EC:2.3.2.27). RNF31/HOIP is observed to contribute to inborn human immunity disorders, in which RNF31/HOIP missense mutation at PUB domain gives rise to the de-stabilized LUBAC complex (linear ubiquitin chain assembly complex) and subsequently causes the auto-inflammation and immunodeficiency. In addition, RNF31 is reported to modify ERK and JNK pathways leading to cisplatin resistance. Functional studies indicate that HOIP and OTULIN interact and act as a bimolecular editing pair for linear ubiquitin signals where the HOIP-PUB domain binds to the PUB interacting motif (PIM) of OTULIN and the chaperone VCP/p9. This interaction plays an important role where the HOIP binding to OTULIN is required for the recruitment of OTULIN to the TNF receptor complex and to counteract HOIP-dependent activation of the NF-KB pathway. 64 matched cddid_all.tbl CDD pfam18487 pfam18487 408280 TSR Thrombospondin type 1 repeat. This is a thrombospondin type I repeat (TSR) found in properdin. Properdin, also known as factor P (fP), is a glycoprotein constructed from a common pool of structure units or modules, which are homologous to the thrombospondin type 1 repeat, TSR. It is positive regulator of the complement system that stabilizes the alternative pathway C3-convertase C3bBb. Properdin also inhibits the factor H-mediated cleavage of C3b by factor I. In addition, properdin acts as a pattern recognition molecule capable of identifying and interacting with microbial surfaces, apoptotic cells, and necrotic cells. However this role of pattern recognition is controversial. Studies indicate that this domain is a TSR variants. It is present at the N-terminal of properdin and has been denoted as TSR-0. It is suggested that the TSR-0 domain of properdin which possesses only the six Cys residues and no CWR-layered motif (which is usually found in other TSR domains) may constitute a truncated TSR domain. 50 matched cddid_all.tbl CDD pfam18488 pfam18488 408281 WYL_3 WYL domain. Many phytopathogens secrete and/or inject 'effector' proteins inside host cells to modulate cellular processes. Phytopathogens deliver effector proteins inside host plant cells to promote infection. Crystal structures of the effector domains from two oomycete RXLR proteins, Phytophthora capsici AVR3a11 and Phytophthora infestans PexRD2 reveal a core alpha-helical fold (termed the 'WY-domain') which enables functional adaptation of these fast evolving effectors through (i) insertion/deletions in loop regions between alpha-helices, (ii) extensions to the N and C termini, (iii) amino acid replacements in surface residues, (iv) tandem domain duplications, and (v) oligomerization. It is proposed that the core fold provides both a degree of molecular stability and plasticity that enables development/maintenance of effector virulence activities while allowing evasion of recognition by the plant innate immune system during rapid 'arms race' co-evolution. 63 matched cddid_all.tbl CDD pfam18489 pfam18489 408282 Alpha_Helical Alpha helical domain. This is the N-terminal domain found in putative tRNA-binding proteins found in archaea. Structural analysis from Pyrococcus horikoshii indicate that it is a helical domain where many conserved residues are found in the first three helices and are mainly located on the inverse side of the putative tRNA-binding site. A structural homology search suggested that this fold prefers to bind proteins/peptides. 127 matched cddid_all.tbl CDD pfam18490 pfam18490 465786 tRNA_bind_4 tRNA-binding domain. This is the N-terminal domain found in archeal type-2 serine-tRNA ligase (SerRS) (EC:6.1.1.11). The SerRS N-terminal domain interacts with the extra-arm stem and the outer corner of tRNA specific to Selenocysteine (tRNA-Sec). 160 matched cddid_all.tbl CDD pfam18491 pfam18491 436540 SRA SET and RING associated domain. This is the C-terminal domain found in PvuRts1I, a modification-dependent restriction endonuclease that recognizes 5-hydroxymethylcytosine (5hmC) as well as 5-glucosylhydroxymethylcytosine (5ghmC) in double-stranded DNA in bacteria. Structural analysis indicates that it has the typical SRA (SET and RING associated) domain fold (pfam02182). 144 matched cddid_all.tbl CDD pfam18492 pfam18492 408285 ORF_2_N Open reading frame 2 N-terminal domain. This is the N-terminal domain found in ORF 2 (open reading frame 2), a protein encoded just downstream of asp (A. sobria serine protease). The ORF 2 N-terminal domain is essential for proper ASP folding. This domain is intrinsically disordered but forms some degree of secondary structure upon binding ASP. 121 matched cddid_all.tbl CDD pfam18493 pfam18493 436541 DUF5617 Domain of unknown function (DUF5617). This is a C-terminal domain of unknown function found in gammaproteobacteria. 90 matched cddid_all.tbl CDD pfam18494 pfam18494 465787 Pullulanase_Ins Pullulanase Ins domain. Pullulanases (pullulan 6-glucanohydrolase, EC 3.2.1.41) are debranching enzymes that are able to hydrolyze the alpha-1,6-glycosidic linkage in pullulan, starch, amylopectin, and related oligosaccharides. Type I pullulanases specifically cleave the alpha-1,6-glycosidic linkages in pullulan and branched oligosaccharides to produce maltotriose and linear oligosaccharides, respectively. Structural analysis of Klebsiella lipoprotein pullulanase (PulA) illustrates that the catalytic core is composed of two major regions: the TIM-barrel domain A and beta-sandwich fold domain C. PulA contains an extra domain, a highly mobile Ins subdomain of unknown function which is inserted into the catalytic TIM-barrel domain A of Klebsiella pullulanases. The Ins subdomain is rich in helical and loop secondary structure. A disulfide bond between Cys491 and Cys506 and two Ca2+ ions presumably stabilizes this domain.This insertion is also found in pullulanases from other Gram-negative genera that have a functional T2SS, such as Vibrio, Aeromonas, and Photorhabdus. Functional analysis indicate that this domain is required for PulA secretion via the T2SS. 74 matched cddid_all.tbl CDD pfam18495 pfam18495 436543 VbhA Antitoxin VbhA. VbhT is a bacterial Fic protein of the mammalian pathogen B. schoenbuchensis7,8. It is composed of an N-terminal FIC domain and a C-terminal BID domain. FIC domains are known to catalyze adenylylation (also called AMPylation). This entry represents VbhA, an antitoxin that binds FIC domain (filamentation induced by cyclic AMP) of VbhT and inhibits its activity. It inhibits the adenylylation activity of VbhT by positioning close to the putative ATP-binding site, hence competing with ATP binding. 47 matched cddid_all.tbl CDD pfam18496 pfam18496 436544 ColG_sub Collagenase G catalytic helper subdomain. This is the catalytic helper subdomain found in collagenase G from Clostridium histolyticum. This domain is indispensable for proper folding and full peptidase activity. 116 matched cddid_all.tbl CDD pfam18497 pfam18497 436545 RNase_3_N Ribonuclease III N-terminal domain. This is the N-terminal domain of eukaryotic ribonuclease 3 (RNase III, EC:3.1.26.3). Structure analysis of Saccharomyces cerevisiaeRNase III (Rnt1p) :RNA revealed specific contacts between the N-terminal domain (NTD) dimer and the 5' end region of the tetraloop. Deletion of the NTD led to cleavage at alternative site(s), suggesting that this region increases the precision of the cleavage site selectivity. 95 matched cddid_all.tbl CDD pfam18498 pfam18498 436546 DUF5618 Domain of unknown function (DUF5618). This is a domain of unknown function found in bacteria. 121 matched cddid_all.tbl CDD pfam18499 pfam18499 408292 Cue1_U7BR Ubc7p-binding region of Cue1. Cue1p (coupling of ubiquitin conjugation to ER degradation protein 1) is an integral component of yeast endoplasmic reticulum (ER)-associated degradation (ERAD) ubiquitin ligase (E3) complexes. It tethers the ERAD ubiquitin-conjugating enzyme (E2), Ubc7p, to the ER and prevents its degradation, and also activates Ubc7p. This domain represents the Ubc7p-binding region (U7BR) of Cue1p with Ubc7p. The U7BR is as E2-binding domain that includes three alpha-helices that interact extensively with the 'backside' of Ubc7p. U7BR stimulates both RING-independent and RING-dependent ubiquitin transfer from Ubc7p. Moreover, the U7BR enhances ubiquitin-activating enzyme (E1)-mediated charging of Ubc7p with ubiquitin. 52 matched cddid_all.tbl CDD pfam18500 pfam18500 436547 CadC_C1 CadC C-terminal domain 1. CadC is an integral membrane protein of 512 amino acids comprising an N-terminal cytoplasmic DNA-binding domain, a transmembrane helix, and a C-terminal periplasmic domain. CadC belongs to the ToxR-like regulators that encompass biochemically non-modified one-component systems with similar gross topology, including several low pH-induced transcription regulators. Structural analysis of the C-terminal periplasmic domain indicates that it resembles the sensory domain of a (pH-activated) ToxR-like regulator. Furthermore, it is composed of two subdomains with a cavity at their interface that is suited to accommodate cadaverine, the feedback inhibitor of the Cad system. This is the N-terminal subdomain of the C-terminal periplasmic domain. It is composed of five-stranded beta-sheets. 134 matched cddid_all.tbl CDD pfam18501 pfam18501 408294 REC1 Alpha helical recognition lobe domain. Cpf1 is an RNA-guided endonuclease of a type V CRISPR-Cas system. Cpf1 adopts a bilobed architecture consisting of an alpha-helical recognition (REC) lobe and a nuclease (NUC) lobe, with the small CRISPR RNAs (crRNAs)-target DNA heteroduplex bound to the positively charged, central channel between the two lobes. The REC lobe consists of the REC1 and REC2 domains where REC1 comprises 13 alpha helices, and REC2 comprises ten alpha helices and two beta strands that form a small antiparallel sheet. This entry represents REC1 domain. 245 matched cddid_all.tbl CDD pfam18502 pfam18502 436548 Mrpl_C 54S ribosomal protein L8 C-terminal domain. This is the C-terminal domain of mitochondrial 54S ribosomal protein L8. 111 matched cddid_all.tbl CDD pfam18503 pfam18503 465788 RPN6_C_helix 26S proteasome subunit RPN6 C-terminal helix domain. This is the C-terminal helix domain found in RPN6, a component of the 26S proteasome. The C-terminal helices are essential for lid assembly. 27 matched cddid_all.tbl CDD pfam18504 pfam18504 375930 Csm1_N Csm1 N-terminal domain. In the budding yeast Saccharomyces cerevisiae, sister chromatid co-orientation in meiosis I depends on the four-protein monopolin complex (Mam1, Csm1, Lrs4, and Hrr25/casein kinase 1), which localizes to centromeres from meiotic prophase through metaphase I. Csm1 and Lrs4, form a complex that resides in the nucleolus during interphase and relocalizes to centromeres during meiotic prophase, accompanied by phosphorylation of Lrs4. This is the N-terminal domain of Csm1 which forms a coiled-coil. 70 matched cddid_all.tbl CDD pfam18505 pfam18505 436550 DUF5619 Domain of unknown function (DUF5619). This is a domain of unknown function found in bacteria and archaea. 85 matched cddid_all.tbl CDD pfam18506 pfam18506 436551 RelB_N RelB Antitoxin alpha helical domain. This is an alpha helix domain found in the N-terminal region of antitoxin RelB. RelE-RelB (RelBE) is a toxin-antitoxin (TA) protein complex. It is suggested that the toxic action of RelE is counteracted by antitoxin RelB, which wraps around RelE, blocks its active site and prevents sterically the binding to the ribosomal A-site.The long N-terminal alpha-helix of the tightly bound antitoxin RelB covers the presumed active site of the toxin RelE that is formed by a central beta-sheet. 46 matched cddid_all.tbl CDD pfam18507 pfam18507 375933 WW_1 WW domain. This is a WW domain found in histone-lysine N-methyltransferase, H3 lysine-36 specific (EC:2.1.1.43) in Saccharomyces cerevisiae. The WW domain is the simplest natural beta-sheet structure. It is a 35-residue protein module found in signaling and regulatory proteins with two highly conserved tryptophans and a strictly conserved proline. 27 matched cddid_all.tbl CDD pfam18508 pfam18508 436552 zf_C2H2_13 Zinc finger domain. The SAGA (Spt-Ada-Gcn5-acetyltransferase) complex performs multiple functions in transcription activation including deubiquitinating histone H2B, which is mediated by a subcomplex called the deubiquitinating module (DUBm). The yeast DUBm comprises a catalytic subunit, Ubp8, and three additional subunits, Sgf11, Sus1 and Sgf73, all of which are required for DUBm activity. A portion of the non-globular Sgf73 subunit lies between the Ubp8 catalytic domain and the zinc finger (ZnF)-UBP domain and has been proposed to contribute to deubiquitinating activity by maintaining the catalytic domain in an active conformation. Sgf73 contributes to maintaining both the organization and ubiquitin-binding conformation of Ubp8, thereby contributing to overall DUBm activity. This domain is a Sgf73 fragment in the DUB module. It is a zinc finger (ZnF) domain whose integrity is essential for the incorporation of this subunit into DUBm as well as for the catalytic activity of Ubp8, as either a short deletion or point mutations in Sgf73 zinc-coordinating residues disrupt the association of Sgf73 with the rest of the DUBm. 42 matched cddid_all.tbl CDD pfam18509 pfam18509 375935 MCR Magnetochrome domain. Magnetotactic bacteria (MTB) align along the Earth's magnetic field using an organelle called the magnetosome. The magnetosome-associated protein MamP is conserved in all MTB and has a PDZ domain, a small c-type cytochrome domain (the first magnetochrome domain, MCR1), a 17-residue linker and a second magnetochrome domain (MCR2). This entry describes the two tandem magnetochrome domains carrying c-type cytochrome motifs CX2CH. 30 matched cddid_all.tbl CDD pfam18510 pfam18510 408300 NUC Nuclease domain. This is a nuclease (NUC) domain found in Cpf1, an RNA-guided endonuclease of a type V CRISPR-Cas system. Structural and functional analysis indicate that this domain is involved in DNA cleavage. 158 matched cddid_all.tbl CDD pfam18511 pfam18511 436553 F-box_5 F-box. Jasmonates are a family of plant hormones that regulate plant growth, development and responses to stress. COI1 is an F-box protein that functions as the substrate-recruiting module of the Skp1-Cul1-F-box protein (SCF) ubiquitin E3 ligase complex. The role of COI1-mediated JAZ degradation in jasmonate (JA) signaling is analogous to auxin signaling through the receptor F-box protein transport inhibitor response 1 (TIR1), which promotes hormone-dependent turnover of the AUX/IAA transcriptional repressors. The crystal structure of COI1 reveals a TIR1-like overall architecture, with an N-terminal tri-helical F-box motif bound to ASK1 and a C-terminal horseshoe-shaped solenoid domain formed by 18 tandem leucine-rich repeats. This entry represents the N-terminal F-box domain which is also found in other auxin signaling f-box proteins such as AFB1, AFB2 and AFB3. 42 matched cddid_all.tbl CDD pfam18512 pfam18512 375938 BssB_TutG Benzylsuccinate synthase beta subunit. Members of this family include benzylsuccinate synthase beta subunit found in bacteria. BssB acts as a regulator of activation and may additionally be involved in regulating access to the enzyme's active site. It adopts a fold similar to that of a high potential iron-sulfur protein (HiPIP) and resembles the single small subunit of HPAD, which is known as the HpdC or HPADgamma in that system. 66 matched cddid_all.tbl CDD pfam18513 pfam18513 408302 Pro_sub2 Prodomain subtilisin 2. Plasmodium subtilisin 2 (Sub2) is a multidomain protein that plays an important role in malaria infection. This domain is a conserved region of the inhibitory prodomain of Sub2 from Plasmodium falciparum, termed prosub2 which has structural similarity to bacterial and mammalian subtilisin-like prodomains. 88 matched cddid_all.tbl CDD pfam18514 pfam18514 408303 Get5_C Get5 C-terminal domain. Tail-anchored trans-membrane proteins are targeted to membranes post-translationally. The proteins Get4 and Get5 form an obligate complex that catalyzes the transfer of tail-anchored proteins destined to the endoplasmic reticulum from Sgt2 to the cytosolic targeting factor Get3. This is the carboxyl domain of Get5 (Get5-C), a homodimerization domain, resulting in a heterotetrameric Get4/Get5 complex. 38 matched cddid_all.tbl CDD pfam18515 pfam18515 436554 Rh5 Rh5 coiled-coil domain. This is a helical coiled-coil domain found in reticulocyte-binding protein homolog 5 (RH5), a Plasmodium falciparum protein essential for erythrocyte invasion. 255 matched cddid_all.tbl CDD pfam18516 pfam18516 408305 RuvC_1 RuvC nuclease domain. This is a RuvC nuclease domain found in type V CRISPR-associated protein Cas12a (Cpf1), used for genome editing applications. These proteins carry out endoribonuclease activity for processing its own guide RNAs and RNA-guided DNase activity for target DNA cleavage. The C-terminal region of Cas12a carries the RUVC domain, NUC domain pfam18510 and the arginine-rich bridge helix (BH). Both the NUC and BH domains are nested in the RuvC domain. Mutations in the RuvC domain impair cleavage of both strands in a target DNA duplex, while a mutation in the Nuc domain impaired target strand cleavage only. This indicates that the DNA nuclease active sites are located at the interface of the RuvC and Nuc domains and that cleavage of the non-target DNA strand by the RuvC domain is a prerequisite for target strand cleavage by the Nuc domain. 412 matched cddid_all.tbl CDD pfam18517 pfam18517 465789 LZ3wCH Leucine zipper with capping helix domain. This domain is found at the C-terminal region of Hop2 and Mnd1 proteins. In meiotic DNA recombination, the Hop2-Mnd1 complex promotes Dmc1-mediated single-stranded DNA (ssDNA) invasion into homologous chromosomes to form a synaptic complex. Hop2 (for homologous pairing; also known as TBPIP) is expressed specifically during meiosis, same as Mnd1 (for meiotic nuclear divisions 1). The C-terminal region of both Hop2 and Mnd1, folds into three alpha-helices that are interrupted by two short non-helical regions. These alpha-helices of the two proteins together form a parallel coiled coil that provides the major interface for heterodimer formation. The non-helical regions form substantially kinked junctions between adjacent leucine zippers: the LZ1-LZ2 and LZ2-LZ3 junctions.This domain is the C-terminal segment of Hop2 and Mnd1 which folds back onto the C-terminal leucine zipper (LZ3) to form a helical bundle-like structure, hence designated LZ3wCH (for LZ3 with capping helices). The LZ3wCH region plays a role in interacting with the Dmc1 nucleofilament. 55 matched cddid_all.tbl CDD pfam18518 pfam18518 436556 TcA_RBD TcA receptor binding domain. Tc toxin complexes are virulence factors of many bacteria such as the plague pathogen Yersinia pestis. Tc toxins are composed of TcA, TcB and TcC subunits. TcA forms a large bell-shaped pentameric structure and enters the membrane like a syringe, forming a translocation channel through which the cytotoxic domain is probably transported into the cytoplasm. TcA has four receptor-binding domains. This domain is one of 4 receptor binding domains found in TcA. All four domains have an immunoglobulin (Ig)-like beta-sandwich fold of two sheets with antiparallel beta-strands. The domains are structurally reminiscent of the receptor-binding domains of the diphtheria and anthrax toxins. 130 matched cddid_all.tbl CDD pfam18519 pfam18519 408308 Sgf11_N SAGA-associated factor 11 N-terminal domain. The SAGA (Spt-Ada-Gcn5-Acetyltransferase) transcriptional co-activator is a protein complex that regulates inducible yeast genes by performing multiple functions including acetylating core histones, recruiting the RNA polymerase II preinitiation complex, and deubiquitinating histone H2B. The deubiquitinating activity of SAGA resides in a distinct sub-complex called the deubiquitinating module (DUBm), which consists of four proteins that are conserved across eukaryotes: Ubp8, Sgf11, Sus1 and Sgf73. The DUBm proteins are organized into two lobes around the globular domains of Ubp8. In SAGA, Sus1 binds to Sgf11 by wrapping around this N-terminal domain of Sgf11, forming a stable dimer. 39 matched cddid_all.tbl CDD pfam18520 pfam18520 375946 Spc110_C Spindle pole body component 110 C-terminal domain. This is the C-terminal domain found in Spc110 proteins. Spc110 is a spindle pole body component (SPB) protein. The N-terminus is shown to bind to gamma-tubulin small complex (g-TuSC) while this C-terminal domain is essential for calmodulin-binding. The C-terminus of Spc110 is anchored to the SPB via a conserved PACT domain. 52 matched cddid_all.tbl CDD pfam18521 pfam18521 375947 TAD2 Transactivation domain 2. This is a N-terminal transactivation domain (TAD) domain 2 found in p53 proteins. In p53 two TAD domains are found termed TAD1 (residues 1-39) and TAD2 (residues 40-61), both of which have been shown to be able to independently activate gene transcription and are intrinsically disordered protein domains that adopt a helical conformation for at least part of their length when bound. This inherent flexibility allows the TADs to adapt to and bind a broad range of proteins. This entry describes TAD2 which can independently interact with Taz2 domain of the histone acetyltransferase p300. It has also been shown to bind to OB-fold domain of replication protein 70 A (RPA) as well as the pleckstrin homology (PH) domain of the p62 and Tfb1 subunits of human and yeast TFIIH. 25 matched cddid_all.tbl CDD pfam18522 pfam18522 408309 DUF5620 Domain of unknown function (DUF5620). This is a domain of unknown function predicted to be a carbohydrate binding module. 119 matched cddid_all.tbl CDD pfam18523 pfam18523 408310 Sld3_N Sld3 N-terminal domain. Sld3 is conserved in yeast and fungi, and treslin, also known as Ticrr, has been identified as the functional counterpart of Sld3 in metazoans. Yeast Sld3 and its metazoan counterpart treslin are the hub proteins mediating protein associations critical for formation of the helicase. This entry represents the N-terminal domain of Sld3 which is shown to bind to the N-terminal domain of Sld7. 116 matched cddid_all.tbl CDD pfam18524 pfam18524 408311 HPIP_like High potential iron-sulfur protein like. This is a C-terminal domain found in 4-hydroxyphenylacetate decarboxylase small subunit (EC:4.1.1.83), which catalyzes the last reaction in the fermentative production of p-cresol from tyrosine. The C-terminal domain [4Fe-4S] cluster bears structural similarity to high-potential iron-sulfur proteins (HiPIPs). HiPIPs have an N-terminal extension of 20-40 residues, so the structural similarity is limited to their Fe/S cluster-binding scaffold. Furthermore, despite of the weak amino acid sequence identity, the cluster binding motifs are remarkably similar to H/CX2CX12-13CX16-17C for the gamma-subunit and CX2CX13-19CX14-19C for HiPIPs. 40 matched cddid_all.tbl CDD pfam18525 pfam18525 465790 Cas9_C Cas9 C-terminal domain. This is the C-terminal domain of Cas9 enzymes found in actinobacteria. 108 matched cddid_all.tbl CDD pfam18526 pfam18526 408313 DB_JBP1 Thymine dioxygenase JBP1 DNA-binding domain. The J-binding protein 1 (JBP1) is essential for biosynthesis and maintenance of DNA base-J (beta-d-glucosyl-hydroxymethyluracil). Base-J and JBP1 are confined to some pathogenic protozoa and are absent from higher eukaryotes, prokaryotes and viruses. JBP1 recognizes J-containing DNA (J-DNA) through the DNA-Binding JBP1 domain (DB-JBP1), which binds to J-DNA with approximately the same affinity and specificity as full-length JBP1. Structure analysis of DB-JBP1 revealed a helix-turn-helix variant fold, a 'helical bouquet' with a 'ribbon' helix encompassing the amino acids responsible for DNA binding. Mutation of a single residue (Asp525) in the ribbon helix abrogates specificity toward J-DNA. 164 matched cddid_all.tbl CDD pfam18527 pfam18527 465791 STT3_PglB_C STT3/PglB C-terminal beta-barrel domain. Asparagine-linked glycosylation is a post-translational modification of proteins containing the conserved sequence motif Asn-X-Ser/Thr. The attachment of oligosaccharides is implicated in diverse processes such as protein folding and quality control, organizm development or host-pathogen interactions. The reaction is catalyzed by oligosaccharyltransferase (OST), a membrane protein complex located in the endoplasmic reticulum. The central, catalytic enzyme of OST is the STT3 subunit, which has homologs in bacteria and archaea. Structural analysis of a bacterial OST, undecaprenyl-diphosphooligosaccharide protein glycotransferase EC:2.4.99.19 (PglB) protein, revealed two domains: a transmembrane domain and a periplasmic domain. This entry represents the C-terminal periplasmic beta-barrel domain. 79 matched cddid_all.tbl CDD pfam18528 pfam18528 408315 Ret2_MD RNA editing 3' terminal uridylyl transferase 2 middle domain. Post-transcriptional RNA editing in Trypanosomatids (pathogenic protozoa) is catalyzed by a large multiprotein complex, the editosome. A key editosome enzyme, RNA editing terminal uridylyl transferase 2 (TUTase 2; RET2) catalyzes the uridylate addition reaction. RET2 structure consists of three domains: the N-terminal domain (NTD), the middle domain (MD) and the C-terminal domain (CTD). This MD domain is mainly composed of six helices and a four-stranded antiparallel beta-sheet. structural comparison reveals that the fold of this MD is topologically similar to the binding domains of several RNA-binding proteins such as the RNA-binding domain of the U1A spliceosomal protein, the RRM domain of the human La protein and the CTD of an archaeal CCA-adding enzyme. The CTD of the archaeal CCA-adding enzyme has been shown to bind double-stranded tRNA stem substrate through the alpha-helices regions. Hence it is suggested that this domain might be an RNA-binding domain. 93 matched cddid_all.tbl CDD pfam18529 pfam18529 408316 MIX Mitochondrial membrane-anchored proteins. MIX forms an all alpha-helical fold comprising seven alpha-helices that fold into a single domain. The distribution of helices is similar to a number of scaffold proteins, namely HEAT repeats, 14-3-3, and tetratricopeptide repeat proteins, suggesting that MIX mediates protein-protein interactions. 151 matched cddid_all.tbl CDD pfam18530 pfam18530 408317 Swi6_N Swi6 N-terminal domain. This is a putative DNA binding domain, it comprises four alpha helices and five beta strands arranged in a mixed alpha/beta fold. 108 matched cddid_all.tbl CDD pfam18531 pfam18531 408318 Polo_box_2 Polo box domain. In metazoans, Plk4 kinases control daughter centriole assembly. Plk4 homologs have an N-terminal kinase domain, a C-terminal polo box, and a central domain termed the 'cryptic polo box' (CPB) that has been shown to dimerize, to be sufficient for centriole localization and to be required for Plk4 to promote centriole assembly. Probable serine/threonine-protein kinase zyg-1 (EC:2.7.11.1) (ZYG-1) is a Plk4 homlog found in C. elegans. Crystal structure for the CPB of C. elegans ZYG-1, reveals that it forms a Z-shaped dimer containing an intermolecular beta-sheet with an extended basic surface patch. Electrostatic interactions between the basic patch on the ZYG-1 CPB dimer and the SPD-2 acidic region dock ZYG-1 onto centrioles to promote new centriole assembly. ZYG-1 CPB contains two tandem polo boxes (PB1 and PB2), each containing a six-stranded beta-sheet with an alpha-helix packed against one side. 112 matched cddid_all.tbl CDD pfam18532 pfam18532 436559 DUF5621 Domain of unknown function (DUF5621). This is a domain of unknown function found in gammaproteobacteria. 139 matched cddid_all.tbl CDD pfam18533 pfam18533 408320 DUF5622 Domain of unknown function (DUF5622). This is a domain of unknown function found in archaea-specific ribosomal proteins such as L46a which is suggested to directly bind to rRNA in the ribosome. 66 matched cddid_all.tbl CDD pfam18534 pfam18534 408321 HBD Helical bundle domain. Lpg0393 is a Legionella pneumophila effector protein. Structure analysis reveals that it has two domains, the N-terminal domain is a Vps9-like domain, which is structurally most similar to the catalytic core of human Rabex-5 that activates the endosomal Rab proteins Rab5, Rab21 and Rab22. The C-terminal domain is a helical bundle domain. The C-terminal helical bundle of Lpg0393 corresponds to the N-terminal helical bundle of Rabex-5, it lacks an obvious region that corresponds to the membrane-binding motif of Rabex-5. One possibility may be that Lpg0393 localization to endosomes depends on an unknown Legionella effector. 84 matched cddid_all.tbl CDD pfam18535 pfam18535 408322 Gal11_ABD1 Gal11 activator-binding domain (ABD1). This is activator-binding domain (ABD1) found in Gal11/med15 proteins. Structural analysis indicate that it binds to the central activator domain (cAD) of Gcn4. Mutations in Gal11-ABD1 W196 residue abolishes the binding to Gcn4 cAD. 81 matched cddid_all.tbl CDD pfam18536 pfam18536 465792 DUF5623 Domain of unknown function (DUF5623). This is a domain of unknown function found in proteobacteria. 125 matched cddid_all.tbl CDD pfam18537 pfam18537 465793 CODH_A_N Carbon monoxide dehydrogenase subunit alpha N-terminal domain. Acetyl-coenzyme A (CoA) synthase/carbon monoxide dehydrogenase (ACS/CODH) is a bifunctional enzyme that catalyzes the reversible reduction of CO2 to CO (CODH activity). This entry is for the N-terminal domain found in ACS/CODH subunit alpha. 83 matched cddid_all.tbl CDD pfam18538 pfam18538 436562 DUF5624 Domain of unknown function (DUF5624). This is a domain of unknown function found mainly in bacteria. 130 matched cddid_all.tbl CDD pfam18539 pfam18539 436563 DUF5625 Domain of unknown function (DUF5625). This is a domain of unknown function found in proteobacteria. 130 matched cddid_all.tbl CDD pfam18540 pfam18540 436564 DUF5626 Domain of unknown function (DUF5626). This is a domain of unknown function mostly found in firmicutes. 120 matched cddid_all.tbl CDD pfam18541 pfam18541 436565 RuvC_III RuvC endonuclease subdomain 3. Cas9 proteins are abundant across the bacterial kingdom, but vary widely in both sequence and size. All known Cas9 enzymes contain an HNH domain that cleaves the DNA strand complementary to the guide RNA sequence (target strand), and a RuvC nuclease domain required for cleaving the noncomplementary strand (non-target strand), yielding double-strand DNA breaks (DSBs). The crystal structures of type II-A and II-C Cas9 proteins highlight the features in Cas9 enzymes that support their function as RNA-guided endonucleases. Cas9 enzymes adopt a bilobed architecture composed of a nuclease lobe containing juxtaposed RuvC and HNH nuclease domains and a variable alpha-helical lobe likely to be involved in nucleic acid binding. The RuvC domain forms the structural core of the nuclease lobe, a six-stranded beta sheet surrounded by four alpha helices, with all three conserved subdomains (I, II, III) contributing catalytic residues to the active site. 160 matched cddid_all.tbl CDD pfam18542 pfam18542 408329 TFIIB_C_1 Transcription factor IIB C-terminal module 1. In the pathogenic trypanosome, Trypanosoma brucei, transcription factor IIB (tTFIIB) is essential for spliced leader (SL) RNA gene transcription and cell viability, but has a highly divergent primary sequence in comparison to TFIIB in other eukaryotes. Structure analysis of the C-terminal region of trypanosome TFIIB, reveals 2, closely packed helical modules followed by a C-terminal extension of 32 aa. The trypanosome-specific region comprises the second helical module and the C-terminal extension. Both helical modules contain the canonical 5-helix cyclin fold characteriztic of TFIIB proteins. This domain is mostly found in Trypanosomatidae. 98 matched cddid_all.tbl CDD pfam18543 pfam18543 465794 ID Intracellular delivery domain. This is a C-terminal domain found in BepA proteins from Bartonella henselae. It is a type IV secretion system (T4SS) effector protein. BepA from Bartonella henselae is composed of an N-terminal Fic domain and a C-terminal Bartonella intracellular delivery (ID) domain, the latter being responsible for T4SS-mediated translocation into host cells. The ID domain of BepA mediates inhibition of apoptosis and exhibits an OB (oligonucleotide/oligosaccharide binding)-fold. 53 matched cddid_all.tbl CDD pfam18544 pfam18544 408331 Polo_box_3 Polo box domain. In metazoans, Plk4 kinases control daughter centriole assembly. Plk4 homologs have an N-terminal kinase domain, a C-terminal polo box, and a central domain termed the 'cryptic polo box' (CPB) that has been shown to dimerize, to be sufficient for centriole localization and to be required for Plk4 to promote centriole assembly. Probable serine/threonine-protein kinase zyg-1 (EC:2.7.11.1) (ZYG-1) is a Plk4 homlog found in C. elegans. Crystal structure for the CPB of C. elegans ZYG-1, reveals that it forms a Z-shaped dimer containing an intermolecular beta-sheet with an extended basic surface patch. Electrostatic interactions between the basic patch on the ZYG-1 CPB dimer and the SPD-2 acidic region dock ZYG-1 onto centrioles to promote new centriole assembly. ZYG-1 CPB contains two tandem polo boxes (PB1 and PB2), each containing a six-stranded beta-sheet with an alpha-helix packed against one side. This entry represents PB2. 97 matched cddid_all.tbl CDD pfam18545 pfam18545 408332 HalOD1 Halobacterial output domain 1. HalOD1 (Halobacterial output domain 1) is a protein domain that is specific for haloarchaea and their viruses. It is found in a stand-alone version and also in combination with Response_reg pfam00072 and other domains (Galperin et al., 2018, Phyletic distribution and lineage-specific domain architectures of archaeal two-component signal transduction systems). 75 matched cddid_all.tbl CDD pfam18546 pfam18546 465795 MetOD1 Methanogen output domain 1. MetOD1 (Methanogen output domain 1) is a protein domain that is found in euryarchaeal classes Methanobacteria and Methanomicrobia, either in stand-alone form or in combination with the Response_reg pfam00072 domain (Galperin et al., 2018, Phyletic distribution and lineage-specific domain architectures of archaeal two-component signal transduction systems). This domain is distantly related to the HNOB and V4R domains. 142 matched cddid_all.tbl CDD pfam18547 pfam18547 375973 HalOD2 Halobacterial output domain 2. HalOD2 (Halobacterial output domain 2) is a protein domain that is found in haloarchaea in combination with the Response_reg pfam00072 domain (Galperin et al., 2018, Phyletic distribution and lineage-specific domain architectures of archaeal two-component signal transduction systems). 52 matched cddid_all.tbl CDD pfam18548 pfam18548 436568 MetOD2 Metanogen output domain 2. MetOD2 (Metanogen output domain 2) is found in euryarchaeal class Methanomicrobia, usually in combination with the Response_reg pfam00072 domain (Galperin et al., 2018, Phyletic distribution and lineage-specific domain architectures of archaeal two-component signal transduction systems). 88 matched cddid_all.tbl CDD pfam18549 pfam18549 408334 NitrOD1 Nitrosopumilus output domain 1. NitrOD1 (Nitrosopumilus output domain 1) is found in thaumarchaea, either in stand-alone form or in combination with the Response_reg pfam00072 domain (Galperin et al., 2018, Phyletic distribution and lineage-specific domain architectures of archaeal two-component signal transduction systems). 68 matched cddid_all.tbl CDD pfam18550 pfam18550 375976 NitrOD2 Nitrososphaera output domain 2. NitrOD2 (Nitrososphaera output domain 2) is found in thaumarchaea, either in stand-alone form or in combination with the Response_reg pfam00072 domain (Galperin et al., 2018, Phyletic distribution and lineage-specific domain architectures of archaeal two-component signal transduction systems). 104 matched cddid_all.tbl CDD pfam18551 pfam18551 436569 TackOD1 Thaumarchaeal output domain 1. TackOD1 (Thaumarchaeal output domain 1) is a predicted metal-binding domain found in archaea and in some bacteria. It contains 11 highly conserved Cys residues, which form 5 CxxC motifs and an HxxC motif. In several instances, it is found in combination with the Response_reg pfam00072 domain (Galperin et al., 2018, Phyletic distribution and lineage-specific domain architectures of archaeal two-component signal transduction systems). 188 matched cddid_all.tbl CDD pfam18552 pfam18552 465796 PheRS_DBD1 PheRS DNA binding domain 1. This is a DNA-binding fold domain found in Phenylalanyl-tRNA Synthetase (EC:6.1.1.20) N-terminal region. This domain belongs to a superfamily of 'winged helix' DNA-biding domains. The topology of DBD-1 and DBD-3 closely resembles the topology of the Z-DNA-binding domain Zalpha of double-stranded RNA (dsRNA) adenosine deaminase and other domains from DNA-binding proteins. Mutational analysis indicate that DBD-1, 2 and 3 play critical roles in tRNA-Phe binding and recognition, i.e., from the drastic reduction of aminoacylation activity seen upon removal of the N-terminal domains. 59 matched cddid_all.tbl CDD pfam18553 pfam18553 465797 PheRS_DBD3 PheRS DNA binding domain 3. This is a DNA-binding fold domain found in Phenylalanyl-tRNA Synthetase N-terminal region. This domain belongs to a superfamily of 'winged helix' DNA-biding domains. The topology of DBD-1 and DBD-3 closely resembles the topology of the Z-DNA-binding domain Zalpha of double-stranded RNA (dsRNA) adenosine deaminase and other domains from DNA-binding proteins. Mutational analysis indicate that DBD-1, 2 and 3 play critical roles in tRNAPhe binding and recognition, i.e., from the drastic reduction of aminoacylation activity seen upon removal of the N-terminal domains. 57 matched cddid_all.tbl CDD pfam18554 pfam18554 465798 PheRS_DBD2 PheRS DNA binding domain 2. This is a DNA-binding fold domain found in Phenylalanyl-tRNA Synthetase N-terminal region. Mutational analysis indicate that DBD-1, 2 and 3 play critical roles in tRNA- Phe binding and recognition, i.e., from the drastic reduction of aminoacylation activity seen upon removal of the N-terminal domains. DBD-2 and DBD-3 constitute large insertions sequentially included between two neighboring antiparallel strands of the DBD-1 domain. Moreover, the DBD-3 pfam18553 is the domain insertion into DBD-2. 33 matched cddid_all.tbl CDD pfam18555 pfam18555 436573 MobL MobL relaxases. This family includes members of relaxase enzymes. These enzymes initiate bacterial conjugation contributing to the spread of antibiotic resistance. These MobL relaxases are found mainly in Firmicutes. It is suggested that MobL type relaxases play a prominent role in horizontal gene transfer in Firmicutes bacteria. Family members carry a stretch of relaxase motif III 'HUH' sequence that is characteriztic of the HUH endonuclease superfamily essential for enzymatic activity. 387 matched cddid_all.tbl CDD pfam18556 pfam18556 465799 TetR_C_35 Bacterial Tetracyclin repressor, C-terminal domain. This is the C-terminal tetracyclin repressor domain found in bacteria. Family members include TetR family transcriptional regulators Rv3249c and Rv1816 found in Mycobacterium tuberculosis. Palmitic acid (a fatty acid) and isopropyl laurate (a fatty acid ester), were identified as binding ligands to Rv3249c and Rv1816 respectively. Similar to other TetR family regulators, these proteins are alpha-helical dimeric proteins consisting of a smaller N-terminal DNA-binding domain and a larger C-terminal regulatory domain. 105 matched cddid_all.tbl CDD pfam18557 pfam18557 465800 NepR Anti-sigma factor NepR. The general stress response sigma factor in alphaproteobacteria, sigma EcfG is inactivated by the anti-sigma factor NepR, which is itself regulated by the response regulator PhyR. NepR forms two helices that extend over the surface of the PhyR subdomains. Homology modeling and comparative analysis of NepR, PhyR and sigmaEcfG mutants indicate that NepR contacts both proteins with the same determinants, showing sigma factor mimicry at the atomic level. This entry represents NepR domains found in alphaproteobacteria. 33 matched cddid_all.tbl CDD pfam18558 pfam18558 465801 HTH_51 Helix-turn-helix domain. This is helix turn helix domain found in polyketide synthases (PKSs) in fungi. They are multidomain enzymes that biosynthesize a wide range of natural products. Family members include citrinin polyketide synthases which contain a C-methyltransferase (CMeT) domain pfam08242 that adds one or more S-adenosylmethionine (SAM)-derived methyl groups to the carbon framework. 90 matched cddid_all.tbl CDD pfam18559 pfam18559 436577 Exop_C Galactose-binding domain-like. This is the C-terminal domain found in ExoP (exo-1,3/1,4-beta-glucanase) from Pseudoalteromonas. This domain contains a beta-sandwich fold which is common in glycosyl hydrolases (GH7, 11, 12 and 16) and in some 23 carbohydrate-binding modules. It is suggested that the main role of this domain is to provide structural stability necessary for ExoP activity, however no substrate-binding role has been shown. 155 matched cddid_all.tbl CDD pfam18560 pfam18560 465802 Lectin_like Lectin like domain. This is a lectin like domain found in Cwp84, a surface-located cysteine protease (a member of the C1A cysteine protease family, also known as papain proteases) responsible for the maturation of the SlpA precursor protein which has been implicated in the degradation of extracellular matrix proteins such as fibronectin, laminin and vitronectin. Structural comparison indicates that this domain is similar to carbohydrate-binding domains. 156 matched cddid_all.tbl CDD pfam18561 pfam18561 465803 Regnase_1_C Endoribonuclease Regnase 1/ ZC3H12 C-terminal domain. This is the C-terminal domain found in regnase-1, an RNase that directly cleaves mRNAs of inflammatory genes such as IL-6 and IL-12p40, and negatively regulates cellular inflammatory responses. The C-terminal domain is composed of three alpha helices and resembles ubiquitin associated protein 1 in structure. 44 matched cddid_all.tbl CDD pfam18562 pfam18562 408346 CIDR1_gamma Cysteine-Rich Interdomain Region 1 gamma. Rosetting is the capacity of infected RBCs to bind uninfected RBCs, which is consistently associated with severe malaria in African children. The rosette-forming PfEMP1 adhesins, namely IT4/R29, Palo Alto 89F5 VarO, 3D7/PF13_0003 and IT4/var60, belong to a specific sub-group called groupA/UpsA var genes and all four present a specific Duffy Binding-Like and and Cysteine-Rich Interdomain Region (DBL1alpha1-CIDR1gamma) double domain Head region found at the extracellular region of PfEMP1. This entry represents the CIDR1gamma domain which increases the binding affinity to VarO (Palo Alto VarO parasites). 52 matched cddid_all.tbl CDD pfam18563 pfam18563 436580 TubC_N TubC N-terminal docking domain. This is the N-terminal docking domain found in TubC proteins from the tubulysin polyketide synthase and nonribosomal polypeptide synthetase (PKS-NRPS) system, which binds to C-terminal docking domain of TubB. 52 matched cddid_all.tbl CDD pfam18564 pfam18564 436581 Glyco_hydro_5_C Glycoside hydrolase family 5 C-terminal domain. This is the C-terminal domain of endo-glycoceramidase II (EGC), a membrane-associated family 5 glycosidase pfam00150. The C-terminal domain assumes a beta-sandwich fold, which resembles that of many carbohydrate-binding modules. 86 matched cddid_all.tbl CDD pfam18565 pfam18565 436582 Glyco_hydro2_C5 Glycoside hydrolase family 2 C-terminal domain 5. Domain 5 is found in dimeric beta-D-galactosidase from Paracoccus sp. 32d, which contributes to stabilization of the functional dimer. It is suggested that the location of this domain 5, may be one of the factors responsible for the creation of a functional dimer and cold-adaptation of this enzyme. 103 matched cddid_all.tbl CDD pfam18566 pfam18566 465804 Ldi Linalool dehydratase/isomerase. This (alpha,alpha)6 barrel fold domain is found in linalool dehydratase/isomerase (Ldi) EC:4.2.1.127. An enzyme found in the betaproteobacterium Castellaniella defragrans 65Phen that mineralizes monoterpenes coupled to anaerobic denitrification. The periplasmic enzyme reversibly catalyzes the isomerization from the primary alkenol geraniol into the tertiary alkenol (S)-linalool and its dehydration to beta-myrcene. Each monomer is built up of a classical (alpha,alpha)6 barrel fold composed of six inner helices. Structural data of Ldi revealed the terpene binding site between two monomers inside a hydrophobic channel, and three catalytic clusters involved in catalysis. 316 matched cddid_all.tbl CDD pfam18567 pfam18567 436583 TIR_3 Toll/interleukin-1 receptor domain. This is a Toll/interleukin-1 receptor (TIR) domain found in the N-terminal region of B-cell adaptor for phosphoinositide 3-kinase (BCAP). BCAP functions in linking the B-cell receptor (BCR) and the co-receptor CD19 to the activation of PI3K via interaction with the SH2 domains on the regulatory p85 subunit. BCAP TIR associates with the MAL/TIRAP adaptor and the TIR domains of Toll-like receptors (TLRs). 128 matched cddid_all.tbl CDD pfam18568 pfam18568 465805 COS TRIM C-terminal subgroup One Signature domain. This domain is found in the C-terminal region of the TRIM subgroup C-1 proteins such as E3 ubiquitin-protein ligase Midline-1 protein which is required for the proper development during embryogenesis. Mutations of MID1 are associated with X-linked Opitz G syndrome, characterized by midline anomalies. This domain is also found in MURF1-3 proteins that do not contain the FNIII and B30.2 domains. MUF1-3 proteins are also associated with microtubules. Deletion of the COS domain does not affect MID1 dimerization but disrupts the localization to the microtubules. 52 matched cddid_all.tbl CDD pfam18569 pfam18569 436585 Thioredoxin_16 Thioredoxin-like domain. This is a thioredoxin like domain found in AIMP2 proteins (Aminoacyl tRNA synthetase complex interacting multifunctional protein 2). Aimp2 is a component of human multi-tRNA synthetase complex (MSC). MSC is a macromolecular protein complex consisting of nine different ARSs and three ARS-interacting multifunctional proteins (AIMPs). 93 matched cddid_all.tbl CDD pfam18570 pfam18570 408354 Nup54_57_C NUP57/Nup54 C-terminal domain. The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. NPCs are formed by multiple copies of 34 distinct proteins, termed nucleoporins (nups). In yeast, the channel nups Nsp1, Nup49, and Nup57 constitute part of the central transport channel and form the diffusion barrier with their disordered phenylalanine-glycine (FG) repeats. Structural studies of yeast Nup57 indicate that it contains left-handed coiled-coil domains (CCD1-3). This entry represents the third CCD located at the C-terminal region of Nup57 which is composed of five heptad repeats. Nup57 in yeast is the equivalent to human Nup54 pfam13874. 29 matched cddid_all.tbl CDD pfam18571 pfam18571 408355 VWA_3_C von Willebrand factor type A C-terminal domain. This is the C-terminal domain of von Willebrand factor type A pfam13768. 47 matched cddid_all.tbl CDD pfam18572 pfam18572 465806 T6PP_N Trehalose-6-phosphate phosphatase N-terminal helical bundle domain. This is the N-terminal domain found in trehalose-6-phosphate phosphatase (T6PP, EC 3.1.3.12) from parasitic nematodes such as Brugia malayi. In the model nematode Caenorhabditis elegans, T6PP is essential for survival due to the toxic effect(s) of the accumulation of trehalose 6-phosphate. T6PP has also been shown to be essential in Mycobacterium tuberculosis. The N-terminal domain composed of a three-helix bundle is similar in topology to the Microtubule Interacting and Transport (MIT) domains of the Vps4-like ATPases from Sulfolobus acidocaldarius. MIT domains are protein-interacting domains typically associated with multivesicular body formation, cytokinetic abscission, or viral budding. Mutational analysis indicate that deletion or mutation of the MIT-like domain is highly destabilizing to the enzyme. 98 matched cddid_all.tbl CDD pfam18573 pfam18573 436587 BclA_C BclA C-terminal domain. This is the C-terminal domain of BclA (Bacillus collagen-like protein of anthracis) which is expressed on spores of Bacillus species. Trimers of the C-terminal domain (CTD) form the tips of the spore's hair-like nap and are the immunodominant target of vertebrate antibodies and drive trimerization. Structure analysis indicate the C-terminal region of the peptide folding into an all-beta structure with a jelly-fold topology, similar to the first human complement C1q, a member of the tumor necrosis factor (TNF)-like family. The C-terminal globular domain has been shown to be located on the exterior of the exosporium, and therefore is critical in determining the immunogenicity of the spore in a mammalian host. 127 matched cddid_all.tbl CDD pfam18574 pfam18574 465807 zf_C2HC_14 C2HC Zing finger domain. This is a zinc finger domain together with a linker region found in RNF125, a small protein (25kD) that contains a RING domain, three zinc fingers (ZnFs) and a ubiquitin interacting motif (UIM). The C2HC ZnF plays an essential role in the interaction of RNF125 with the E2 UbcH5a, which originates from the requirement of the C2HC-ZnF for the structural stability of the RING domain. A mutation at one of the contact residues in the C2HC-ZnF, a highly conserved M112, resulted in the loss of ubiquitin ligase activity. Furthermore, mutations at the Zn2+ chelating cysteine residues, C100 and C103 of this domain resulted in a loss of activity. 33 matched cddid_all.tbl CDD pfam18575 pfam18575 465808 HAMP_N3 HAMP N-terminal domain 3. Aer2 soluble receptor from Pseudomonas aeruginosa contains three successive HAMP domains in the N-terminal region. HAMP domains are widespread prokaryotic signaling modules. This entry is the third N-terminal HAMP domain (HAMP3). HAMP3 adopt a conformation resembling Af1503, with only minor differences in helical tilt and orientation. The basic construction of each HAMP domain consists of a monomeric unit of two parallel alpha helices (AS1 and AS2) joined by an elongated connector of 12-14 residues form a parallel four-helix bundle. 43 matched cddid_all.tbl CDD pfam18576 pfam18576 436590 HTH_52 Helix-turn-helix domain. This is a helix turn helix domain found in bacilli. 64 matched cddid_all.tbl CDD pfam18577 pfam18577 436591 ASTN_2_hairpin Astrotactin-2 C-terminal beta-hairpin domain. This is a beta-hairpin domain found at the C-terminal region of astrotactin 2 proteins (ASTN-2). ASTN-2 is an integral membrane perforin-like protein linked to the planar cell polarity pathway in hair cells. it consists of multiple polypeptide folds: a perforin-like domain, a minimal epidermal growth factor-like module, a fibronectin type III domain Fn (III) and an annexin-like domain as well as the beta hairpin domain which packs across the fibronectin domain. 47 matched cddid_all.tbl CDD pfam18578 pfam18578 436592 Raf1_N Rubisco accumulation factor 1 alpha helical domain. This is the N-terminal alpha helical domain found in Rubisco accumulation factor1 (Raf1). Raf1 from Arabidopsis thaliana consists of an N-terminal alpha-domain, a flexible linker segment and a C-terminal beta-sheet domain that mediates dimerization. The alpha-domains mediate the majority of functionally important contacts with RbcL (Rubisco large subunits) by bracketing each RbcL dimer at the top and bottom. The alpha-domain alone is essentially inactive. 106 matched cddid_all.tbl CDD pfam18579 pfam18579 436593 Raf1_HTH Rubisco accumulation factor 1 helix turn helix domain. This is helix turn helix domain found in alpha helical region of Rubisco accumulation factor1 (Raf1). Raf1 from Arabidopsis thaliana consists of an N-terminal alpha-domain, a flexible linker segment and a C-terminal beta-sheet domain that mediates dimerization. The alpha-domains mediate the majority of functionally important contacts with RbcL (Rubisco large subunits) by bracketing each RbcL dimer at the top and bottom. The alpha-domain alone is essentially inactive. 61 matched cddid_all.tbl CDD pfam18580 pfam18580 436594 HTH_SUN2 SUN2 helix-turn-helix domain. LINC complexes are formed by coupling of KASH (Klarsicht, ANC-1, and Syne/Nesprin Homology) and SUN (Sad1 and UNC-84) proteins from the inner and outer nuclear membranes (INM and ONM, respectively). the formation of LINC complexes by KASH and SUN proteins at the nuclear envelope (NE) establishes the physical linkage between the cytoskeleton and nuclear lamina, which is instrumental for the mechanical force transmission from the cytoplasm to the nuclear interior, and is essential for cellular processes such as nuclear positioning and migration, centrosome-nucleus anchorage, and chromosome dynamics. This entry represents an HTH domain found in SUN2 that forms a three-helix bundle to lock the SUN domain in an inactive conformation acting as an inhibitory component. 58 matched cddid_all.tbl CDD pfam18581 pfam18581 465809 SYCP2_ARLD Synaptonemal complex 2 armadillo-repeat-like domain. Synaptonemal complex protein 2 (SYCP2) N-terminal region contains two separate subdomains an ARLD (armadillo-repeat-like domain) and an SLD (Spt16M-like domain). The ARLD domain belongs to the armadillo-repeat protein family. Armadillo-repeat units often form a superhelix, which typically provides a platform for many protein partners that transduce Wnt signaling, such as beta-catenin. The ARLD of mouse SYCP2 was found to associate with different protein partners, including CENP J and CENP F. ARLD structure is highly similar to that of the 'required for cell differentiation (RCD-1)' protein. 175 matched cddid_all.tbl CDD pfam18582 pfam18582 408366 HZS_alpha Hydrazine synthase alpha subunit middle domain. The crystal structure of hydrazine synthase multiprotein complex isolated from the anammox organizm Kuenenia stuttgartiensis implies a two-step mechanism for hydrazine synthesis: a three-electron reduction of nitric oxide to hydroxylamine at the active site of the gamma-subunit and its subsequent condensation with ammonia, yielding hydrazine in the active centre of the alpha-subunit. The alpha-subunit consists of three domains: an N-terminal domain which includes a six-bladed beta-propeller, a middle domain binding a pentacoordinated c-type haem (haem alphaI) and a C-terminal domain which harbours a bis-histidine-coordinated c-type haem (haem alphaII). This entry represents the middle domain of subunit alpha of hydrazine synthase (HZS). 98 matched cddid_all.tbl CDD pfam18583 pfam18583 465810 Arnt_C Aminoarabinose transferase C-terminal domain. ArnT is a member of the GT-C family of glycosyltransferases, and it has a similar fold to a bacterial oligosaccharyltransferase (OST) from Campylobacter lari (PglB) and to an archaeal OST from Archaeoglobus fulgidus (AglB). This entry represents the C-terminal periplasmic domain of Arnt proteins. 103 matched cddid_all.tbl CDD pfam18584 pfam18584 465811 SYCP2_SLD Synaptonemal complex 2 Spt16M-like domain. Synaptonemal complex protein 2 (SYCP2) N-terminal region contains two separate subdomains an ARLD (armadillo-repeat-like domain) and an SLD (Spt16M-like domain). The SLD structure is highly similar to the middle domain of the histone chaperone FACT. It consists of a twisted ten-stranded beta-sheet flanked by two helices. Since the SLD domain structurally resembles Spt16M, which is known as the well-recognized histone protein H2A-H2B; it is speculated that the SLD may be involved in chromatin binding. 111 matched cddid_all.tbl CDD pfam18585 pfam18585 436598 zf-CCCH_6 Chromatin remodeling factor Mit1 C-terminal Zn finger 2. The Snf2/Hdac Repressive Complex (SHREC) is the fission yeast nucleosome remodeling and deacetylation (NuRD) equivalent and plays a major role in transcriptional gene silencing (TGS) within S. pombe heterochromatin. SHREC consists of the chromatin remodeler Mit1, the HDAC Clr3, and Clr1 and Clr2 proteins. The Mit1 C terminus contains two zinc binding motifs (CCHC zinc fingers) at the C-terminus onto which the alpha helices from both Clr1 and Mit1 pack. The Mit1 chromatin remodeler uses its C-terminal domain to intimately bind to the N-terminal half of Clr1 to integrate into the SHREC complex. This is entry represents the second C-terminal zinc-binding domain found on Mit-1. 53 matched cddid_all.tbl CDD pfam18586 pfam18586 376012 zf-CCCH_7 Chromatin remodeling factor Mit1 C-terminal Zn finger 1. The Snf2/Hdac Repressive Complex (SHREC) is the fission yeast nucleosome remodeling and deacetylation (NuRD) equivalent and plays a major role in transcriptional gene silencing (TGS) within S. pombe heterochromatin. SHREC consists of the chromatin remodeler Mit1, the HDAC Clr3, and Clr1 and Clr2 proteins. The Mit1 C terminus contains two zinc binding motifs (CCHC zinc fingers) at the C-terminus onto which the alpha helices from both Clr1 and Mit1 pack. The Mit1 chromatin remodeler uses its C-terminal domain to intimately bind to the N-terminal half of Clr1 to integrate into the SHREC complex. This is entry represents the first C-terminal zinc-binding domain found on Mit-1. 90 matched cddid_all.tbl CDD pfam18587 pfam18587 436599 PLL PTX/LNS-Like (PLL) domain. Adhesion G protein-coupled receptors (aGPCRs) play critical roles in diverse neurobiological processes including brain development, synaptogenesis, and myelination. The aGPCR GPR56/ADGRG1 regulates both oligodendrocyte and cortical development. The N-terminal domain of GPR56 has low sequence identity and a fold that likely diverged from the PTX and LNS domains. It also has a conserved motif (HphiC91xxWxxxxG) that was identified among canonical PTX domains. Thus, it is termed the Pentraxin/Laminin/neurexin/sex-hormone-binding-globulin-Like (PLL) domain. Truncation-based analyses suggest that the regions of GPR56 responsible for binding TG2 and collagen III are within the PLL domain, most likely in the surface-exposed conserved patch. Furthermore, it is suggested that the conserved patch of the PLL domain mediates an essential function in CNS myelination. 134 matched cddid_all.tbl CDD pfam18588 pfam18588 436600 WcbI Polysaccharide biosynthesis enzyme WcbI. Capsular polysaccharides (CPSs) are protective structures on the surfaces of many Gram-negative bacteria. wcbI is one of several genes in the CPS biosynthetic cluster whose deletion leads to significant attenuation of the pathogen. Structural analysis and biophysical assays suggest that WcbI functions as an acetyltransferase enzyme but it requires another functional module to carry out this function. WcbI adopts a predominantly helical fold where the N-terminal 100 amino acids form a ligand-binding domain and binds tightly to coenzyme A and its derivative acetyl-CoA. 207 matched cddid_all.tbl CDD pfam18589 pfam18589 465812 ObR_Ig Obesity receptor immunoglobulin like domain. This is the immunoglobulin-like domain (IGD) found in obesity receptors (ObR). ObR is a single membrane-spanning receptor belonging to the class I cytokine receptor family. All isoforms have an identical extracellular part consisting of six domains: an N-terminal domain (NTD), two CRH domains (CRH1 and CRH2), an immunoglobulin-like domain (IGD), and two additional membrane-proximal fibronectin type III (FN III) domains. ObR activation depends on the CRH2, IGD, and FN III domains, however the CRH2 domain is the major leptin-binding determinant in the receptor. The IGD and membrane-proximal domains have no detectable affinity for the ligand, but are nonetheless indispensable for receptor activation. Deletion of the IGD results in a receptor with wild-type affinity for leptin, but completely devoid of biological activity. 105 matched cddid_all.tbl CDD pfam18590 pfam18590 436602 IMP2_N Immune Mapped Protein 2 (IMP2) N-terminal domain. Immune Mapped Protein 2 (IMP2) N-terminal domain which is conserved across both IMP1 and IMP2 families. It is suggested that the globular domain likely contributes to a shared function, hence it is termed 'IMP1-like domain'. 90 matched cddid_all.tbl CDD pfam18591 pfam18591 436603 IMP2_C Immune Mapped Protein 2 (IMP2) C-terminal domain. Immune Mapped Protein 2 (IMP2) C-terminal domain. 63 matched cddid_all.tbl CDD pfam18592 pfam18592 465813 Tho1_MOS11_C Tho1/MOS11 C-terminal domain. THO is a multi-protein complex involved in the formation of messenger ribonuclear particles (mRNPs) by coupling transcription with mRNA processing and export. Some studies show that Tho1, like Sub2, can assemble onto the nascent mRNA during transcription and that Tho1 and Sub2 can provide alternative pathways for mRNP biogenesis in the absence of a functional THO complex. This is the C-terminal domain found in Tho1 and MOS11 proteins. The C-terminal region of Tho1 from Saccharomyces cerevisiae, adopts a helical fold similar to that of the WHEP RNA-binding domains of metazoan aminoacyl-tRNA synthetases. 37 matched cddid_all.tbl CDD pfam18593 pfam18593 436605 CdiI_2 CdiI immunity protein. Contact-dependent growth inhibition (CDI) is an important mechanism of inter-bacterial competition found in many Gram-negative pathogens. CDI+ cells express cell-surface CdiA proteins that bind neighboring bacteria and deliver C-terminal toxin domains (CdiA-CT) to inhibit target-cell growth. CDI+ bacteria also produce CdiI immunity proteins, which specifically neutralize cognate CdiA-CT toxins to prevent self-inhibition. Structure analysis of CdiI immunity protein from Yersinia kristensenii shows that it is composed of eight alpha-helices packed together to form a nearly spherical structure with weak structural homology to a putative TetR family transcriptional repressor. The CdiI protein fits into the curved cavity of the CdiA-CTYkris toxin domain where it most likely neutralizes toxin activity by blocking access to RNA substrates. This domain is mostly found in gammaproteobacteria. 91 matched cddid_all.tbl CDD pfam18594 pfam18594 408377 Sas6_CC Sas6/XLF/XRCC4 coiled-coil domain. This is a coiled-coil domain found at the C-terminal of spindle assembly abnormal protein 6 (Sas6). The highly conserved protein SAS-6 constitutes the center of the cartwheel assembly that scaffolds centrioles early in their biogenesis.Structural analysis of Sas6 show that similar to XLF, and XRCC4 it forms a parallel coiled-coil dimer. 30 matched cddid_all.tbl CDD pfam18595 pfam18595 465814 Nuf2_DHR10-like Nuf2, DHR10-like domain. This domain is found at the C-terminal region of Nuf2 proteins. This domain was identified as MazG related domain also designated as Designed helical repeat protein 10 (DHR10) that actually adopts a coiled-coil structure. Nuf2 is part of the Ndc80 complex, which binds to the spindle and is required for chromosome segregation and spindle checkpoint activity. 117 matched cddid_all.tbl CDD pfam18596 pfam18596 436607 Sld7_C Sld7 C-terminal domain. This is an alpha helical domain found at the C-terminal region of Sld7 proteins. Yeast Sld3 and its metazoan counterpart treslin are the hub proteins mediating protein associations critical for formation of the replicative helicase at the replication origins of chromosomes. Sld7 forms a complex with Sld3 throughout the cell cycle, and associates with and dissociates from origins in an Sld3- dependent manner and is thought to regulate the function of Sld3. Structural analysis of S. cerevisiae Sld7 indicates that two Sld7 molecules form a homodimer using their C-terminal domains. 77 matched cddid_all.tbl CDD pfam18597 pfam18597 465815 SH3_19 Myosin X N-terminal SH3 domain. This is the N-terminal Sh3 domain found in myosin X. Myosin X is essential for neuritogenesis, wound healing, cancer metastasis and some pathogenic infections. Myosin X is required for filopodia formation and extension. 52 matched cddid_all.tbl CDD pfam18598 pfam18598 465816 TetR_C_36 Tetracyclin repressor-like, C-terminal domain. This is a C-terminal TetR regulatory domain found in QsdR proteins (quorum-sensing degradation regulation). 111 matched cddid_all.tbl CDD pfam18599 pfam18599 436610 LCIB_C_CA Limiting CO2-inducible proteins B/C beta carbonyic anhydrases. Limiting CO2-inducible B protein (LCIB)-LCIC complex plays an important role in the microalgal CO2-concentrating mechanisms (CCMs).LCIB and homologs (LCIB1-4 and LCIC) structurally resemble beta carbonyic anhydrases (b-CAs) with striking similarities in overall fold, zinc-binding motif, and especially putative active site architecture. 222 matched cddid_all.tbl CDD pfam18600 pfam18600 465817 Ezh2_MCSS MCSS domain. Polycomb repressive complex 2 (PRC2) carries out the methylation of lysine 27 of histone H3, a hallmark of repressive chromatin. Three core subunits make up the catalytic core of PRC2; the SET domain containing EZH2, the zinc-finger containing SUZ12 and the WD40 repeat protein EED. The complex forms a compact arrangement of three lobes. The middle lobe largely comprises two domains that mark the beginning of the carboxy (C)-terminal region of EZH2 (MCSS and SANT2) and the helical, C-terminal, component of the Suz12 Vefs domain. This entry describes the MCSS (also known as SANT2L) domain. There is one zinc binding (Zn1Cys3His1) which is formed solely by MCSS. 53 matched cddid_all.tbl CDD pfam18601 pfam18601 436611 EZH2_N EZH2 N-terminal domain. Polycomb repressive complex 2 (PRC2) carries out the methylation of lysine 27 of histone H3, a hallmark of repressive chromatin. Three core subunits make up the catalytic core of PRC2; the SET domain containing EZH2, the zinc-finger containing SUZ12 and the WD40 repeat protein EED. The complex forms a compact arrangement of three lobes. This is the N-terminal domain of EZH2. 79 matched cddid_all.tbl CDD pfam18602 pfam18602 465818 Rap1a Rap1a immunity proteins. The structures of the immunity proteins, Rap1a, responsible for the inhibition and neutralization of Ssp1 endopeptidase, revealed two distinct folds. The structure of the Ssp1-Rap1a complex revealed a tightly bound heteromeric assembly with two effector molecules flanking a Rap1a dimer. The Rap1a subunit displays a compact globular structure constructed from five alpha-helices that assemble to form the highly stable symmetric dimer. 91 matched cddid_all.tbl CDD pfam18603 pfam18603 436613 LAL_C2 L-amino acid ligase C-terminal domain 2. l-amino-acid ligases (LALs; EC 6.3.2.28) were discovered to be ATP-grasp superfamily enzymes that catalyze the formation of an alpha-peptide bond between two l-amino acids in an ATP-dependent manner. The members of this family share a common structural architecture that consists of three domains referred to as the A-domain, B-domain and C-domain. The C domain can be further divided into the C1-subdomain and the C2-subdomain. This entry represents the C2 subdomain. 78 matched cddid_all.tbl CDD pfam18604 pfam18604 436614 PreAtp-grasp Pre ATP-grasp domain. This is a preATP grasp domain region found inon the N-terminal of pfam02222 in Pheganomycin (PGM1). 94 matched cddid_all.tbl CDD pfam18606 pfam18606 465819 HTH_53 Zap helix turn helix N-terminal domain. Zinc-finger antiviral protein (ZAP) is a host factor that specifically inhibits the replication of certain viruses, such as HIV-1, by targeting viral mRNA for degradation. This domain is a helix turn helix domain found at the N-terminal region constituting the top cockpit layer of the protein. 62 matched cddid_all.tbl CDD pfam18607 pfam18607 436616 HTH_54 ParA helix turn helix domain. The accurate segregation of DNA is essential for the faithful inheritance of genetic information. Segregation of the prototypical P1 plasmid par system requires two proteins, ParA and ParB, and a centromere. When bound to ATP, ParA mediates segregation by interacting with centromere-bound ParB, but when bound to ADP, ParA fulfills a different function: DNA-binding transcription autoregulation. ParA consists of an elongated N-terminal alpha-helix which mediates dimerization, a winged-HTH and a Walker-box containing C-domain. This entry describes the N-terminal alpha helix domain combined with the winged HTH region. 92 matched cddid_all.tbl CDD pfam18608 pfam18608 465820 XAF1_C XIAP-associated factor 1 C-terminal domain. XIAP-associated factor 1 (XAF1) is a 301-amino acids interferon (INF)-inducible pro-apoptotic protein. The XIAP binding region within XAF1, XIAP RING binding site, is located at the C-terminal portion of XAF1. This entry represents the C-terminal region which is functionally identified as XIAP RING-binding domain of XAF1. 51 matched cddid_all.tbl CDD pfam18609 pfam18609 408391 SAM_Exu Exuperantia SAM-like domain. Exuperantia (Exu) is associated with localization of bicoid (bcd) mRNA and required for its localization at the anterior pole of the oocyte. Crystal structure of Exu reveals a dimeric assembly with each monomer consisting of a 3'-5' EXO-like domain and a sterile alpha motif (SAM)-like domain. The SAM-like domain interacts with its target RNA as a homodimer and is required for RNA binding activity. 73 matched cddid_all.tbl CDD pfam18610 pfam18610 408392 Peripla_BP_7 Periplasmic binding protein domain. Treponema pallidum, the bacterium that causes syphilis, is an obligate human parasite. T. pallidum lacks the machinery for the de novo synthesis of many key nutrients therefore it acquires these nutrients from its human host. MglB-2 from T. pallidum has been shown to act as the ligand-binding element of an ABC transporter for D-glucose. The overall fold of MglB-2 resembles those of LBPs (Ligand-binding proteins sometimes called 'Periplasmic Binding Proteins') that serve as receptors for nutrients and cofactors in bacterial ABC transporters. Furthermore, structural analysis of MglB-2 i found in Treponema pallidum shows it to be one of the founding member of a family of proteins related to the 'Type I' or 'Cluster B' LBPs. This domain can also be found on the C-terminal region of pfam13407. 71 matched cddid_all.tbl CDD pfam18611 pfam18611 436618 IL3Ra_N IL-3 receptor alpha chain N-terminal domain. Interleukin-3 (IL-3) is an activated T cell product that bridges innate and adaptive immunity and contributes to several immunopathologies. Structure of IL-3 receptor alpha chain (IL3Ra) in complex with the anti-leukemia antibody CSL362 reveals that the N-terminal domain (NTD), a domain also present in the granulocyte-macrophage colony-stimulating factor (GM-CSF), contains the CSL362 binding epitope. Furthermore, NTD of IL3Ra adopts a typical fibronectin type III (FnIII) fold. 76 matched cddid_all.tbl CDD pfam18612 pfam18612 436619 Bac_A_amyl_C Bacterial Alpha amylase C-terminal domain. This is a bacterial alpha amaylase C-terminal domain found mostly in bacilli. 69 matched cddid_all.tbl CDD pfam18613 pfam18613 465821 TrkA_TMD Tyrosine kinase receptor A trans-membrane domain. This receptor consists of 796 amino acids and can be divided in the extracellular ligand-binding domain, the trans-membrane domain, and the intracellular tyrosine kinase domain.This domain is the TMD of TrkA which has shown to be involved in the interaction with amyloid precursor protein (APP). 22 matched cddid_all.tbl CDD pfam18614 pfam18614 436621 RNase_II_C_S1 RNase II-type exonuclease C-terminal S1 domain. This entry describes the C-terminal S1 domain found in type 2 RNase exonucleases. DrR63 proteins from Deinococcus radiodurans are an RNase II-type enzymes (DrII). Structure analysis of DrII indicates that it has an N-terminal HTH domain which interacts with a flexible loop that connects two beta-strands from the conserved C-terminal S1 domain, forming a beta-wing fold common in wHTH domains. 59 matched cddid_all.tbl CDD pfam18615 pfam18615 465822 SMYLE_N Short myomegalin-like EB1 binding proteins, N-terminal domain. This N-terminal region is found in SMYLE (for short myomegalin-like EB1 binding protein). It includes the SMYLE homology (SmyH) domain found in the first 100 residues at the N terminus. This conserved SmyH domain is required and sufficient for PKA scaffolding protein AKAP9, and the pericentrosomal protein CDK5RAP2 binding. 387 matched cddid_all.tbl CDD pfam18616 pfam18616 465823 CdiI_3 CDI immunity proteins. Contact-dependent growth inhibition (CDI) is a widespread mechanism of bacterial competition. CDI+ bacteria deliver the toxic C-terminal region of contact-dependent inhibition A proteins (CdiA-CT) into neighboring target bacteria and produce CDI immunity proteins (CdiI) which bind CdiA-CT domains and neutralize their toxic activity to protect against self-inhibition. CdiI immunity proteins are also variable and only neutralize their cognate CdiA-CT toxins. Structure analysis of CdiI from Escherichia coli 536 (EC536) shows that is composed of a single domain and that it blocks the interaction with substrate, strongly suggesting that the immunity protein occludes the nuclease active site. 95 matched cddid_all.tbl CDD pfam18617 pfam18617 408399 Nup214_FG Nucleoporin Nup214 phenylalanine-glycine (FG) domain. CRM1 is the major nuclear export receptor. During translocation through the nuclear pore, transport complexes transiently interact with phenylalanine-glycine (FG) repeats of multiple nucleoporins. On the cytoplasmic side of the nuclear pore, CRM1 tightly interacts with the nucleoporin Nup214. Nup214 binds to N- and C-terminal regions of CRM1, thereby clamping CRM1 in a closed conformation and stabilizing the export complex. This entry represents an FG repeat region within the C terminus of Nup214 which is required for its interaction with CRM1. 62 matched cddid_all.tbl CDD pfam18618 pfam18618 465824 HP0268 HP0268. HP0268 is a small, characterized protein that is conserved in H. pylori strains and consists of 80 amino acid residues with a molecular weight of approximately 9.5 kDa. HP0268 has nicking endonuclease and RNase activities, both of which are specific for a single-strand of nucleotides. It is structurally similar to small MutS-related (SMR) domains, that can be categorized roughly into three subfamilies according to their arrangement in the domain architecture.HP0268 falls into subfamily 3 that is found as stand-alone type proteins. It is proposed that HP0268 has become an evolutionary intermediate between RNases and nicking endonucleases during H. pylori adaptation to the extremely acidic environment of the stomach. 80 matched cddid_all.tbl CDD pfam18619 pfam18619 436625 GAIN_A GPCR-Autoproteolysis-INducing (GAIN) subdomain A. GPR56 is a a cell-surface G protein-coupled receptor (GPCR) which belongs to the adhesion G protein-coupled receptor (aGPCR) family, a large family of chimeric proteins that have both adhesion and signaling functions and play critical roles in diverse neurobiological processes including brain development, synaptogenesis, and myelination. This entry represents GPCR-Autoproteolysis-INducing (GAIN) subdomain A, including PLL-GAIN linker (F161-D175) region. 48 matched cddid_all.tbl CDD pfam18620 pfam18620 465825 DUF5627 Family of unknown function (DUF5627). This is a domain of unknown function found in bacteria. 133 matched cddid_all.tbl CDD pfam18621 pfam18621 465826 DUF5628 Family of unknown function (DUF5628). This is a domain of unknown function found in Actinobacteria. 110 matched cddid_all.tbl CDD pfam18622 pfam18622 408404 HTH_55 RctB helix turn helix domain. RctB is a highly conserved 75.3 kD protein (658 residues), which is unique to the Vibrionaceae. The first 500 amino acids of RctB are sufficient to mediate oriCII-based replication and its C-terminal 165 residues may mediate regulatory processes. RctB contains at least three DNA binding winged-helix-turn-helix motifs, and mutations within any of these severely compromise biological activity. This entry describes domain 1 located at the N-terminal region of RctB proteins. Mutational analysis show that it binds oriCII DNA, and that this function is critical for the capacity of RctB to mediate oriCII-based replication. 107 matched cddid_all.tbl CDD pfam18623 pfam18623 436628 TnsE_C TnsE C-terminal domain. The bacterial transposon Tn7 facilitates horizontal transfer by directing transposition into actively replicating DNA with the element-encoded protein TnsE. Structural analysis of the C-terminal domain of TnsE identified a central V-shaped loop that toggles between two distinct conformations. It is suggested that a conformational change within the C-terminal domain of TnsE underlies target site selection by regulating stable engagement of the target DNA while providing a signal for activating transposition. 145 matched cddid_all.tbl CDD pfam18624 pfam18624 436629 CdiI_4 CDI immunity protein. Contact-dependent growth inhibition (CDI) is a mechanism of inter-cellular competition in which Gram-negative bacteria exchange polymorphic toxins using type V secretion systems. Structure analysis of the CDI toxin from Escherichia coli NC101 reveals that it has moderate structural homology to Whirly-like proteins found in plastids, but appears to lack the characteriztic Whirly RNA-binding site. 101 matched cddid_all.tbl CDD pfam18625 pfam18625 465827 EspB_PE ESX-1 secreted protein B PE domain. The ESX-1 secretion system is an important virulence determinant in Mycobacterium tuberculosis. ESX-1 secreted protein B (EspB) contains putative PE (Pro-Glu) and PPE (Pro-Pro-Glu) domains, and a C-terminal domain, which is processed by MycP1 protease during secretion. This domain represents the PE domain located at the N-terminal region of EspB which carries the conserved YxxxD/E secretion motif. 78 matched cddid_all.tbl CDD pfam18626 pfam18626 436631 Gln_deamidase_2 Glutaminase. Protein glutaminase (PG, EC 3.5.1.44) can deamidate glutamine residues in proteins to glutamate residues. This entry represents the mature PG enzyme which bears partial homology to factor XIII-like Transglutaminase (TG), especially its Cys-His-Asp catalytic triad. A similar triad (Cys-His-Asn) is also shared by some cysteine proteases such as papain and actinidin. The mature PG is a monomer enzyme consisting of 185 amino acid residues. 106 matched cddid_all.tbl CDD pfam18627 pfam18627 436632 PgdA_N Peptidoglycan GlcNAc deacetylase N-terminal domain. This is the N-terminal and middle domain found in Streptococcus pneumoniae peptidoglycan GlcNAc deacetylase (SpPgdA). PgdA protects the Gram-positive bacterial cell wall from host lysozymes by deacetylating peptidoglycan GlcNAc residues. It is a member of the family 4 carbohydrate esterases (CE-4). 218 matched cddid_all.tbl CDD pfam18628 pfam18628 436633 P2_N Viral coat protein P2 N-terminal domain. P2 (30.2 kDa) is the major outer-coat protein of the marine lipid-containing bacteriophage PM2. Each sub-unit of P2 is composed of two beta barrel jelly rolls, disposed normal to the surface of the capsid, which lend pseudo-6-fold symmetry to the molecules, facilitating their close packing within the capsid. There is a Ca2+ ion located between the two beta barrels of P2 that helps PM2 molecular organizations stabilization. This entry represents the N-terminal jelly roll domain of P2. 127 matched cddid_all.tbl CDD pfam18629 pfam18629 436634 DUF5629 Family of unknown function (DUF5629). This is a domain of unknown function found in hypothetical proteins from Pseudomonas aeruginosa. 98 matched cddid_all.tbl CDD pfam18630 pfam18630 408412 Peptidase_M60_C Peptidase M60 C-terminal domain. This is C-terminal domain (CTD) of M60-peptidases pfam13402. It Can also be found at the C-terminal region of gingipain B (RgpB) from P. gingivalis. It was found to possess a typical Ig-like fold encompassing seven antiparallel beta-strands organized in two beta-sheets, packed into a beta-sandwich structure that can spontaneously dimerize through C-terminal strand swapping. Translocation of gingipains from the periplasm across the OM is dependent on the conserved CTD, which appears to be important for secretion of the proteins and in particular, truncation of the last few C-terminal residues of this domain leads to accumulation of gingipains in the periplasm. Subsequently, the T9SS targeting signal was demonstrated to reside within the last 22 residues at the C-terminus of the CTD. During gingipain translocation across the OM, the CTD is cleaved off by PorU. 65 matched cddid_all.tbl CDD pfam18631 pfam18631 408413 Cucumopine_C Cucumopine synthase C-terminal helical bundle domain. McbB from Marinactinospora thermotolerans is an enzyme that catalyzes the Pictet-Spengler (PS) reaction of L-tryptophan and oxaloacetaldehyde to produce the betaC scaffold of marinacarbolines. This is the C-terminal domain composed of 5 bundled alpha helices. It is weakly similar to the signal transduction histidine-protein kinase BarA from E. coli and the DNA endonuclease I-MsoI from Monomastix sp. 141 matched cddid_all.tbl CDD pfam18632 pfam18632 436635 DUF5630 Family of unknown function (DUF5630). This is a domain of unknown function mostly found in Legionella. 218 matched cddid_all.tbl CDD pfam18633 pfam18633 436636 zf-CCCH_8 Zinc-finger antiviral protein (ZAP) zinc finger domain 3. Zinc-finger antiviral protein (ZAP) is a host factor that specifically inhibits the replication of certain viruses, such as HIV-1, by targeting viral mRNA for degradation. N-terminal domain of ZAP is the major functional domain which contains four zinc-finger motifs. This entry represents the third zinc finger type CCCH. 28 matched cddid_all.tbl CDD pfam18634 pfam18634 408416 RXLR_WY RXLR phytopathogen effector protein WY-domain. Filamentous plant pathogens cause devastating diseases of crops. Phytophthora infestans, the Irish potato famine pathogen, facilitates disease on its hosts by delivering effector proteins that modulate host cell processes to the benefit of the parasite, a strategy used by many biotrophic plant pathogens. The Phytophthora infestans RXLR-type effector PexRD54 binds potato ATG8 via its ATG8 family-interacting motif (AIM) and perturbs host-selective autophagy. The N-terminal region of PexRD54 contains 5 tandem WY domains. The WY domain is a conserved structural unit consisting of three alpha-helices and two characteriztic hydrophobic amino acids, frequently W (Trp) and Y (Tyr), which contribute to a stable hydrophobic core. Deletion analysis show that the WY domains of PexRD54 are dispensable for ATG8CL binding suggesting an alternative function for these domains. 51 matched cddid_all.tbl CDD pfam18635 pfam18635 465828 EpCAM_N Epithelial cell adhesion molecule N-terminal domain. EpCAM (epithelial cell adhesion molecule), a stem and carcinoma cell marker, is a cell surface protein involved in homotypic cell-cell adhesion via intercellular oligomerization and proliferative signalling via proteolytic cleavage. Structure analysis indicate that it is composed of three domains: N-domain, Thyroglobulin type-1A (TY) domain and the C-terminal domain. This entry represents the small and compact disulphide-rich N-terminal domain of 39 amino-acid residues. 33 matched cddid_all.tbl CDD pfam18636 pfam18636 436638 Sld7_N Mitochondrial morphogenesis protein SLD7 N-terminal domain. The initiation of eukaryotic chromosomal DNA replication requires the formation of an active replicative helicase at the replication origins of chromosomes. Yeast Sld3 and its metazoan counterpart treslin are the hub proteins mediating protein associations critical for formation of the helicase. The Sld7 protein interacts with Sld3, and the complex formed is thought to regulate the function of Sld3. Although Sld7 is a non-essential DNA replication protein that is found in only a limited range of yeasts, its depletion slowed the growth of cells and caused a delay in the S phase. Structure analysis indicates that the N-terminal domain of Sld7 binds to the N-terminal region of Sld3. 122 matched cddid_all.tbl CDD pfam18637 pfam18637 408419 AUDH_Cupin Aldos-2-ulose dehydratase/isomerase (AUDH) Cupin domain. The enzyme aldos-2-ulose dehydratase/isomerase (AUDH) participates in carbohydrate secondary metabolism, catalyzing the conversion of glucosone and 1,5-d-anhydrofructose to the secondary metabolites cortalcerone and microthecin, respectively. Crystal structure analysis revealed that the enzyme subunit is built up of three domains, an N-terminal seven-bladed propeller, a bicupin and a C-terminal lectin domain. This entry describes the second Cupin domain (residues 574-739) composed of two antiparallel sheets that build up the jellyroll sandwich fold formed from four and five beta-strands. This cupin domain in AUDH is found to contain a zinc binding site where the metal site is located at the bottom of the cleft formed by the beta-sandwich, as observed in many cupins. 156 matched cddid_all.tbl CDD pfam18638 pfam18638 408420 CyRPA Cysteine-Rich Protective Antigen 6 bladed domain. Plasmodium falciparum Cysteine-Rich Protective Antigen (PfCyRPA) is a 42.8 kDa protein of 362 residues with a predicted N-terminal secretion signal. It is part of a multi-protein complex including the PfRH5-interacting protein PfRipr and the reticulocyte binding-like homologous protein PfRH5, which binds to the erythrocyte receptor basigin. PfRH5, PfCyRPA, and PfRipr colocalize during parasite invasion at the junction between merozoites and erythrocytes. The complex seems to be required both for triggering Ca2+ release and establishment of tight junctions. PfCyRPA adopts a 6-bladed beta-propeller structure with similarity to the classic sialidase fold, but it has no sialidase activity and fulfills a purely non-enzymatic function. Each blade of the propeller is constructed by a four-stranded anti-parallel beta-sheet. 315 matched cddid_all.tbl CDD pfam18639 pfam18639 436639 Longin_2 Yeast longin domain. This is a longin domain which is found in the N-terminal region of Lst4 proteins in yeast. Lst4 is the Fnip1/2 orthologue found in mammals. Lst4 forms a complex with Lst7 and are targeted to the vacuole when the cells are starved of carbon, and to a lesser extent nitrogen. Lst4 and Fnip1/2 belong to the DENN family of proteins which comprise an N-terminal longin domain, commonly found in a variety of trafficking proteins, and a C-terminal DENN domain. This domain is made up of a core five-strand beta-sheet, with one short alpha-helix. 158 matched cddid_all.tbl CDD pfam18640 pfam18640 436640 LepB_N LepB N-terminal domain. Rab GTPases constitute the largest family of small GTP-binding proteins that act as molecular switches in regulating vesicular transport in eukaryotic cells. LepB is a Rab GTPase-activating protein (GAP) effector found in Legionella pneumophila. This entry represents the N-terminal domain which is followed by a GAP domain. 183 matched cddid_all.tbl CDD pfam18641 pfam18641 436641 LidA_Long_CC LidA long coiled-coil domain. LidA, another Rab1-interacting bacterial effector protein, is translocated by Legionella into the host cytosol at the beginning of infection, and it localized to the Legionella-containing vacuole (LCV) at the cytosolic surface. It has been shown that tight interaction with Rab1 allows LidA to facilitate the Legionella targeting factor (DrrA/SidM)-catalyzed release of Rab1 from GDP dissociation inhibitors (GDI). The base of the protein is formed by two antiparallel coiled-coil structures forming a long coiled-coil domain. This region of LidA interacts with switch and interswitch regions of Rab1 the nucleotide binding pocket of Rab8a, hence blocking access to the GDP/GTP-binding site to a great extent. 177 matched cddid_all.tbl CDD pfam18642 pfam18642 436642 IMPa_helical Immunomodulating metalloprotease helical domain. IMPa is an immunomodulator metalloprotease that belongs to the peptidase M60 family pfam13402. This entry represents the helical domain found at the N-terminal of the Ig domain. 108 matched cddid_all.tbl CDD pfam18643 pfam18643 436643 RE_BsaWI BsaWI restriction endonuclease type 2. Type II restriction endonucleases recognize short 4-8 bp nucleotide sequences and cleave phosphodiester bonds within or close to their target site. BsaWI restriction endonuclease from the thermophilic bacterium Bacillus stearothermophilus W1718 belongs to a group of restriction endonucleases that share CCGG motif within their target sites, termed 'CCGG-family'. However, the R-(D/E)R motif residues, which are supposed to recognize CCGG from the major groove side, are poorly ordered and located far away from the DNA bases. BsaWI contacts with the CCGG tetranucleotide from the minor groove side. It is folded into two domains an N-terminal helical domain and a C-terminal catalytic domain. Furthermore, it carries a PDXKXE motif at the putative active site. 105 matched cddid_all.tbl CDD pfam18644 pfam18644 436644 Phage_int_SAM_6 Phage integrase SAM-like domain. Xer recombinases are members of the tyrosine site-specific recombinase superfamily, a large group of enzymes that catalyze DNA breakage and rejoining using a conserved tyrosine nucleophile. Tyrosine recombinases promote various programmed DNA rearrangements including the monomerization of phage, plasmid and chromosome multimers, resolution of hairpin telomeres, and the movement of virulence and antibiotic resistance carrying integrative mobile genetic elements. Structural analysis of Helicobacter pylori XerH indicates that this N-terminal domain consisting of six alpha-helices contacts the DNA using a four-helix bundle. 132 matched cddid_all.tbl CDD pfam18645 pfam18645 436645 DUF5631 Family of unknown function (DUF5631). This is an alpha helical domain found at the C-terminal region of the hypothetical protein Rv3899c from Mycobacterium tuberculosis which is conserved across mycobacteria. 96 matched cddid_all.tbl CDD pfam18646 pfam18646 408428 DUF5632 Family of unknown function (DUF5632). This an alpha-beta-alpha domain found at the N-terminal region of Rv3899c, a hypothetical protein from Mycobacterium tuberculosis which is conserved across mycobacteria. 80 matched cddid_all.tbl CDD pfam18647 pfam18647 408429 Fungal_lectin_2 Alpha-galactosyl-binding fungal lectin. This domain can be found in alpha-galactosyl binding Lyophyllum decastes lectin (LDL). It is composed of five-stranded anti-parallel beta-sheet and two alpha-helices and contain conserved cysteines responsible for disulfide bridges. The protein with the highest similarity is ginkbilobin-2, a protein with apparent anti-fungal properties isolated from the seeds of the ginkgo biloba tree. Homologous sequences can be divided into two groups, where the proteins in the group with closest homology to LDL only consist of a single LDL-like domain. In the second group of sequences, the LDL-like domain is found at the C-terminal end of a larger domain with homology to members of the Ser, Gly, Asn, His consensus sequence (SGNH)-hydrolase family, which is part of the Gly, Asp, Ser, Leu motif-esterase/lipase superfamily. 102 matched cddid_all.tbl CDD pfam18648 pfam18648 408430 ADPRTs_Tse2 Tse2 ADP-ribosyltransferase toxins. Tse2 from P. aeruginosa has structural features similar to ADP-ribosylating toxins. It is a cytoactive toxin secreted by a type six secretion apparatus of Pseudomonas aeruginosa and found mostly in gamma proteobacteria. It naturally attacks a target in the cytoplasm of bacterial cells. Structural analysis shows similarity between Tse2 and nicotinamide adenine dinucleotide (NAD)-dependent enzymes from bacteria, notably the mono-ADP-ribosyltransferase toxins (ADPRTs). Furthermore, it revealed that the Tse2 active site is occluded upon binding the cognate immunity protein Tsi2. The abrogation of toxicity for the R14A, S80A, and H122A mutant Tse2 proteins indicates the importance of these amino acids in the mechanism of Tse2 toxicity and, given their conservation with NAD-reactive enzymes, also supports their assignment as being involved in a catalytic reaction. 155 matched cddid_all.tbl CDD pfam18649 pfam18649 436646 EcpB_C EcpB C-terminal domain. This is an immunoglobulin like domain found at the C-terminal region of EcpB. It is a periplasmic chaperone which along with EcpE help assemble the E. coli common pilus (ECP) EcpA and EcpD subunits. The C-terminal domain is predicted to contain residues that might be involved in binding a C-terminal carboxylate anchor. 72 matched cddid_all.tbl CDD pfam18650 pfam18650 436647 IMPa_N_2 Immunomodulating metalloprotease N-terminal domain. PA0572 of P. aeruginosa is an inhibitor of PSGL-1, also known as an immunomodulating metalloprotease of P. aeruginosa (IMPa). IMPa prevents neutrophil extravasation and thereby protects P. aeruginosa from neutrophil attack. It belongs to the peptidase M60 family pfam13402. This entry represents the N-terminal alpha/beta-fold domain. 200 matched cddid_all.tbl CDD pfam18651 pfam18651 436648 CshA_NR2 Surface adhesin CshA non-repetitive domain 2. The multifunctional fibrillar adhesin CshA, which mediates binding to both host molecules and other microorganizms, is an important determinant of colonization by Streptococcus gordonii, an oral commensal and opportunistic pathogen of animals and humans. CshA binds the high-molecular-weight glycoprotein fibronectin (Fn) via an N-terminal non-repetitive region, and this protein-protein interaction has been proposed to promote S. gordonii colonization at multiple sites within the host. This 259-kDa polypeptide is organized in the form of a leader peptide (residues 1-41), a non-repetitive region (residues 42-778), 17 repeat domains (R1-R17, each about 101-aa residues), and a C-terminal cell wall anchor. The non-repetitive Fn-binding region of CshA in turn is composed of three distinct domains, designated as non-repetitive domain 1 (NR1, CshA(42-222)), non-repetitive domain 2 (NR2, CshA(223-540)), and non-repetitive domain 3 (NR3, CshA(582-814)). The NR2 domain of CshA is shown to adopt a globular structure with a lectin-like fold and a ligand-binding site on its surface with structural homologs identified as those involved in binding carbohydrates or glycoproteins. 259 matched cddid_all.tbl CDD pfam18652 pfam18652 465829 Adhesin_P1_N Adhesin P1 N-terminal domain. The cariogenic bacterium Streptococcus mutans uses adhesin P1 to adhere to tooth surfaces, extracellular matrix components, and other bacteria. The N terminus forms a stabilizing scaffold by wrapping behind the base of P1's elongated stalk and physically 'locking' it into place. It is suggested that the N-terminal has such a pronounced impact on P1 immunogenicity, antigenicity, folding, stability, and adherent function. 106 matched cddid_all.tbl CDD pfam18653 pfam18653 408435 Arcadin_1 Arcadin 1. Arcadin-1 is encoded by arcade gene cluster which also encodes cernactin. Crenactin is a filament-forming protein from the crenarchaeon Pyrobaculum calidifontis which shows exceptional similarity to eukaryotic F-actin. Arcadin-1 on the other hand does not seem to be related to any known eukaryotic actin binding proteins nor does it affect crenactin polymerization. 111 matched cddid_all.tbl CDD pfam18654 pfam18654 408436 LegC3_N LegC3 N-terminal coiled-coil domain. LegC3 is an effector protein secreted by Legionella pneumophila which is believed to act by inhibiting vacuolar fusion. The N-terminal domain of LegC3 is composed of a long discontinuous coiled-coil capped by an antiparallel four-helix bundle that is rigidly connected to the coiled-coil segment. The features responsible for fusion inhibition are located mainly within the N-terminal domain, as this domain alone was sufficient to inhibit vacuole fusion, and that this domain remains associated with vacuoles. 296 matched cddid_all.tbl CDD pfam18655 pfam18655 465830 SHIRT SHIRT domain. The SHIRT domain is found in a range of presumed bacterial adhesin proteins. 82 matched cddid_all.tbl CDD pfam18656 pfam18656 408438 DUF5633 Family of unknown function (DUF5633). This entry represents a 40 residue repeat that is often found in tandem in a small set of bacterial cell surface proteins. The function of this region is not known. 41 matched cddid_all.tbl CDD pfam18657 pfam18657 436651 YDG YDG domain. This presumed domain is found in a wide variety of bacterial cell surface proteins. This domain has a highly conserved YDG motif near its N-terminus. This domain is likely related to the pfam17883 domain. 85 matched cddid_all.tbl CDD pfam18658 pfam18658 465831 zf-C2H2_12 Spin-doc zinc-finger. This is a zinc finger domain C2H2 type which can be found in SPIN1 docking protein (SPIN-DOC) and Epm2a-interacting protein 1 (Epm2aip1). SPIN-DOC is a Spindlin1 (SPIN1) regulator that directly binds and strongly disrupts its histone methylation reading ability, causing it to disassociate from chromatin. Epm2aip1 is a glycogen synthase (GS)-associated protein. In the absence of Epm2aip1, the sensitivity of the liver to insulin, in which GS is a principal actor, is impaired. 64 matched cddid_all.tbl CDD pfam18659 pfam18659 408441 CelTOS Cell-traversal protein for ookinetes and sporozoites. Cell-traversal protein for ookinetes and sporozoites (CelTOS) is a conserved protein that is essential for traversal of malaria parasites in both the mosquito vector and human host and is therefore critical for malaria transmission and disease pathogenesis. It specifically binds phosphatidic acid commonly present within the inner leaflet of plasma membranes, and potently disrupts liposomes composed of phosphatidic acid by forming pores. CelTOS resembles class I viral membrane fusion glycoproteins and a bacterial pore-forming toxin with roles in membrane binding and disruption. CelTOS forms an alpha helical dimer that resembles a tuning fork. Structure analysis indicate that it has a distinct structural architecture with two subdomains that independently resemble membrane binding and/or disrupting proteins and could simultaneously act during disruption. 116 matched cddid_all.tbl CDD pfam18660 pfam18660 408442 Tsi6 Tsi6. Tsi6 inhibits the NADase activity of Tse6, an integral membrane toxin from Pseudomonas aeruginosa. The Tsi6 immunity protein adopts an all-alpha-helical fold that binds to a surface of Tse6. 83 matched cddid_all.tbl CDD pfam18661 pfam18661 408443 AvrLm4-7 Avirulence Effector AvrLm4-7. AvrLm4-7 is found in Leptosphaeria maculans, an ascomycete fungus in the dothideomycete group which is responsible for stem canker (blackleg) of Brassica napus (oilseed rape, OSR) and other crucifers. AvrLm4-7 is one of six avirulence genes which encodes a small secreted protein strongly over-expressed at the onset of plant infection. This gene confers a dual recognition specificity by two distinct resistance genes of OSR, Rlm4 and Rlm7 and loss of AvrLm4 avirulence was demonstrated to be associated with a strong fitness cost. Structure and functional analysis of AvrLm4-7 protein show that it contains the motifs RAWG and RYRE, part of a well-structured protein region held together by disulfide bridges. Mutations in the RAWG motif or in the RYRE motif (especially mutations in both motifs) almost abolished the translocation of AvrLm4-7 into cells. Furthermore, loss of recognition of AvrLm4-7 by Rlm4 is caused by the mutation of a single glycine to an arginine residue located in a loop of the protein. 86 matched cddid_all.tbl CDD pfam18662 pfam18662 436653 HTH_56 Cch helix turn helix domain. Staphylococcal Cassette Chromosome, or SCC elements, are a family of genomic islands found in S. aureus and closely related species. SCC elements that carry the mecA gene are called SCCmec and render S. aureus methicillin-resistant, creating the MRSA strains. Cch, the self-loading helicase encoded by SCCmec type IV, belongs to the pre-sensor II insert clade of AAA+ ATPases, as do the archaeal and eukaryotic MCM-family replicative helicases. The N-terminal domain carries pfam06048. The central domain (residues 157-438) contains an AAA+ ATPase fold. This domain is found at the C-terminal region, it is a winged helix-turn-helix (WH) domain typical of many dsDNA-binding proteins. 110 matched cddid_all.tbl CDD pfam18663 pfam18663 376087 Pallilysin Pallilysin beta barrel domain. The Treponema pallidum protein, Tp0751 (also known as pallilysin), possesses adhesive properties and has been previously reported to mediate attachment to the host extracellular matrix components laminin, fibronectin, and fibrinogen. Tp0751 adopts an eight-stranded beta-barrel with a profile of short conserved regions consistent with a non-canonical lipocalin fold. Lipocalins, along with fatty acid-binding proteins and avidins, are members of the calycin superfamily, which is defined by the distinct features of a central beta-barrel and a key structural signature consisting of three short conserved regions (SCR1, SCR2, and SCR3). However, Tp0751 does not contain all three conserved regions, hence it is considered an outlier to canonical lipocalins. In SCR1, there is a GxW motif. 118 matched cddid_all.tbl CDD pfam18664 pfam18664 436654 CdiA_C_tRNase CdiA C-terminal tRNase domain. This entry represents the C-terminal tRNase domain of CdiA a type II toxin/immunity protein complex which can be found in B. pseudomallei isolate E479. The C-terminal tRNase domain has an alpha/beta-fold characteriztic of PD(D/E)XK nucleases. The PD(D/E)XK superfamily includes most restriction endonucleases and other enzymes involved in DNA recombination and repair. 116 matched cddid_all.tbl CDD pfam18665 pfam18665 408446 TetR_C_37 Tetracyclin repressor-like, C-terminal domain. IcaR belongs to the tetracycline repressor (TetR) family of proteins, which are involved in a wide variety of gene regulations. It binds to a 42 bp region immediately upstream of the icaA gene. This entry represents the C-terminal domain which is involved in dimerization. 117 matched cddid_all.tbl CDD pfam18666 pfam18666 408447 CBM64 Carbohydrate-binding module 64. Spirochaeta thermophila secretes seven glycoside hydrolases for plant biomass degradation that carry a carbohydrate-binding module 64 (CBM64) appended at the C-terminus. CBM64 adsorbs to various beta1-4-linked pyranose substrates and shows high affinity for cellulose. Structure analysis indicates a jelly-roll-like fold corresponding to a surface-binding type A CBM. 74 matched cddid_all.tbl CDD pfam18667 pfam18667 408448 BppU_IgG Baseplate upper protein immunoglobulin like domain. This is a beta-sandwich immunoglobulin fold domain, which resembles the plexin-A2 C-terminal domain in structure. In baseplate upper protein (BppU, also known as ORF48) trimer, this domain plays part in surrounding the Dit hexameric core. 96 matched cddid_all.tbl CDD pfam18668 pfam18668 408449 Tail_spike_N Tail spike TSP1/Gp66 receptor binding N-terminal domain. Bacteriophages recognize and bind to their hosts with the help of receptor-binding proteins (RBPs) that emanate from the phage particle in the form of fibers or tailspikes. RBPs of podovirus G7C tailspikes gp63.1 and gp66 are essential for infection of its natural host bacterium E. coli 4s. Gp63.1 and gp66 form a stable complex, in which the N-terminal part of gp66 serves as an attachment site for gp63.1 and anchors the gp63.1-gp66 complex to the G7C tail. The two N-terminal domains show 70% sequence identity to the N-terminal region of the CBA120 phage tailspike 1 (orf210, TSP1). The N-terminal domain of TSP1 is the virion head binding domain that interfaces with the phage baseplate. The N-terminal domain can be further divided into two subdomains, each beginning with a alpha-helix followed by an anti-parallel beta-sandwich. Subdomain two folds similarly to the chitin binding domain of Chitinase from Bacillus circulans. 70 matched cddid_all.tbl CDD pfam18669 pfam18669 436655 Trp_ring Trimeric autotransporter adhesin Trp ring domain. Autotransporters are synthesized as precursor proteins with three functional domains, namely, an N-terminal signal peptide, an internal passenger domain, and a C-terminal pore-forming translocator domain. The C-terminal translocator domain is embedded in the outer membrane and facilitates delivery of the internal passenger domain to the bacterial surface. In conventional autotransporters, the C-terminal translocator domain contains approximately 300 amino acids and is monomeric. In contrast, in trimeric autotransporters, the translocator domain contains 60 to 70 amino acids and forms trimers in the outer membrane. This entry represents a Trp-ring domain which is found in the translocator region of H. influenzae Hia autotransporter, an adhesive protein that promotes adherence to respiratory epithelial cells. Trp-ring domains appear to be crucial repeated modular units in Hia, both in the general architecture of the passenger domain and in the structure of the binding domains. 50 matched cddid_all.tbl CDD pfam18670 pfam18670 436656 V_ATPase_I_N V-type ATPase subunit I, N-terminal domain. Vacuolar H+-ATPase (V-ATPase) is a ubiquitous multi-subunit proton pump that acidifies a wide variety of intracellular compartments, which in turn affects many biological processes, including membrane trafficking, protein degradation and coupled transport of small molecules and pH homeostasis. Subunit 'a' of V0 (the functional domain responsible for proton transport) sector is highly conserved across eukaryotic species and exists in multiple isoforms. It is the largest subunit of V-ATPases and partitioned almost equally into an N-terminal cytosolic domain and a C-terminal integral membrane. Structure analysis of the N-terminal cytosolic domain from the Meiothermus ruber subunit 'I' homolog of subunit a shows that it is composed of a curved long central alpha-helix bundle capped on both ends by two lobes with similar alpha/beta architecture. 90 matched cddid_all.tbl CDD pfam18671 pfam18671 408452 4HPAD_g_N 4-Hydroxyphenylacetate decarboxylase subunit gamma N-terminal. 4-Hydroxyphenylacetate decarboxylase (4-HPAD) is a heterotetramer consisting of catalytic beta-subunit harboring the putative glycyl/thiyl dyad and a distinct small gamma-subunit with two [4Fe-4S] clusters (EC:4.1.1.83). The gamma-subunit is proposed to be involved in the regulation of the oligomeric state and catalytic activity of the enzyme and it comprises two domains with some amino acid sequence identity that are structurally related by a pseudo-2-fold symmetry indicating a gene duplication origin. This entry represents the N-terminal domain which binds one [4Fe-4S] cluster through His3, Cys6, Cys19, and Cys36. 31 matched cddid_all.tbl CDD pfam18672 pfam18672 376096 PilZN1 N-terminal PilZ-like domain PilZN1. This domain is found in PilZ domain-containing proteins from Deltaproteobacteria, such as swiss:Q748G9 from Geobacter sulfurreducens. This domain is located N-terminal to a canonical PilZ domain, with a PilZ-related structure comprising the beta-barrel fold, lacking the C-terminal alpha-helix and both c-d-GMP-binding motifs. This domain also has a N-terminal loop that forms a short alpha-helix (3 residues). 93 matched cddid_all.tbl CDD pfam18673 pfam18673 436657 IrmA interleukin receptor mimic protein A. The E. coli interleukin [IL] receptor mimic protein A (IrmA), is a small (13 kDa) Uropathogenic E. coli (UPEC) protein that was originally identified in a large reverse genetic screen as a broadly protective vaccine antigen. It has a fibronectin III (FNIII)-like fold that forms a domain-swapped dimer with structural mimicry to the binding domain of the IL-2 receptor (IL-2R), the IL-4 receptor (IL-4R) and, to a lesser extent, the IL-10 receptor (IL-10R). IrmA binds to all three cytokines, with the greatest affinity observed for IL-4. It is suggested that IrmA may contribute to manipulation of the innate immune response during UPEC infection. 109 matched cddid_all.tbl CDD pfam18674 pfam18674 408454 TarS_C1 TarS beta-glycosyltransferase C-terminal domain 1. Beta-glycosyltransferase TarS is an enzyme responsible for the glycosylation of wall teichoic acid polymers of the S. aureus cell wall, a process that has been shown to be specifically responsible for methicillin resistance in MRSA. It contains a trimerization domain composed of tandem carbohydrate binding motifs.The two C-terminally localized regions composed of a series of beta-sheets participate in an extensive trimerization interface and they assume an immunoglobulin-like fold. It is suggested that both carbohydrate binding domains may be involved in polyRboP binding, however unlike pullulanase, the CBMs of TarS are involved in the formation of an extensive trimerization interface. 148 matched cddid_all.tbl CDD pfam18675 pfam18675 408455 HepII_C Heparinase II C-terminal domain. Heparinase II (HepII) is an 85-kDa dimeric enzyme that depolymerizes both heparin and heparan sulfate glycosaminoglycans. The protein is composed of three domains: an N-terminal alpha-helical domain, a central two-layered beta-sheet domain, and a C-terminal domain forming a two-layered beta-sheet. The C-terminal domain contains nine beta-strands packed together in a manner resembling a beta-barrel. 88 matched cddid_all.tbl CDD pfam18676 pfam18676 436658 MBG_2 MBG domain (YGX type). This domain is found in a variety of bacterial extracellular proteins. This domain is related to the MBG domain (pfam17883). But it replaces the characteriztic YDG motif close the N-terminus with a YGX motif. 73 matched cddid_all.tbl CDD pfam18677 pfam18677 408457 ArnB_C Archaellum regulatory network B, C-terminal domain. This is the C-terminal domain found in archeal proteins that carry a von Willebrand factor type A domain such as ArnB from Sulfolobus acidocaldarius. ArnB is involved in negative regulation of the archaellum (former: archaeal flagellum), and the C-terminal domain is phosphorylated by ArnC and ArnD on serine and threonine residues affecting docking of ArnA. 72 matched cddid_all.tbl CDD pfam18678 pfam18678 436659 AOC_like Allene oxide cyclase barrel like domain. This is an allene oxide cyclase barrel like domain found in spirotetronate cyclases such as AbyU, a Diels-Alderase enzyme. It is comprised of two eight-stranded antiparallel beta-barrels. 122 matched cddid_all.tbl CDD pfam18679 pfam18679 436660 HTH_57 ThcOx helix turn helix domain. This is a winged helix turn helix domain which is found in cyanobactin oxidase ThcOx N-terminal region. The oxidase converts thiazolines to thiazoles. 112 matched cddid_all.tbl CDD pfam18680 pfam18680 408460 SPECT1 Plasmodium host cell traversal SPECT1. This domain is found in SPECT1 (sporozoite microneme protein essential for cell traversal). It is formed of a four alpha-helix bundle with a 'hook'-like feature at one end. These helices in parallel or antiparallel alignment. 180 matched cddid_all.tbl CDD pfam18681 pfam18681 408461 DUF5634 Family of unknown function (DUF5634). This is a domain of unknown function mostly found in bacilli. 95 matched cddid_all.tbl CDD pfam18682 pfam18682 436661 PilA4 Pilin A4. This domain is found in the major pilin protein PilA. PilA4 binds to PilMNO forming a complex with a well-defined platform linking the cytoplasmic PilM protein to pilus subunits in the periplasm. Structure analysis indicate that it is comprised of one alpha-helix and 4 beta-sheets. 83 matched cddid_all.tbl CDD pfam18683 pfam18683 408463 ChiW_Ig_like Chitinase W immunoglobulin-like domain. This is an immunoglobulin like domain found in ChiW, a chitinase with high activity towards various chitins. ChiW has a multi-modular architecture composed of six domains to function efficiently on the cell surface: a right-handed beta-helix domain (carbohydrate-binding module family 54, CBM-54), a Gly-Ser-rich loop, 1st immunoglobulin-like (Ig-like) fold domain, 1st beta/alpha-barrel catalytic domain (glycoside hydrolase family 18, GH-18), 2nd Ig-like fold domain and 2nd beta/alpha-barrel catalytic domain (GH-18). 106 matched cddid_all.tbl CDD pfam18684 pfam18684 408464 PlyB_C Pleurotolysin B C-terminal domain. This a trefoil C-terminal beta-rich domain found in PlyB, one of the components of pleurotolysin (Ply) pore-forming protein. Ply is a membrane attack complex/perforin-like family (MACPF) protein consisting of two components, PlyA and PlyB. PlyB and PlyA act together to form relatively small and regular pores in liposomes. The PlyB C-terminal trefoil sits on top of the PlyA dimer. 173 matched cddid_all.tbl CDD pfam18685 pfam18685 436662 DUF5635 Family of unknown function (DUF5635). This is a domain of unknown function which is found at the C-terminal region of pfam13749 in actinobacteria. 86 matched cddid_all.tbl CDD pfam18686 pfam18686 436663 DUF5636 Family of unknown function (DUF5636). This is a domain of unknown function mostly found in gammaproteobacteria. 194 matched cddid_all.tbl CDD pfam18687 pfam18687 376111 DUF5637 Family of unknown function (DUF5637). This is a domain of unknown function found in predicted cysteine knot peptides. 33 matched cddid_all.tbl CDD pfam18688 pfam18688 436664 DUF5638 Family of unknown function (DUF5638). This is a domain of unknown function found in Legionella. 104 matched cddid_all.tbl CDD pfam18689 pfam18689 436665 PriX Primase X. This domain is found in non-catalytic subunit of the archaeal eukaryotic-type primase, PriX. Detailed sequence analysis combined with structural analysis of a truncated PriX protein from the hyperthermophilic archaeon Sulfolobus solfataricus shows that, PriX is essential for the survival of the organizm and that it is homologous to the C-terminal domain of archaeal and eukaryotic large primase subunits PriL. Highly conserved PriX homologs are present in many members of the phylum Crenarchaeota. 95 matched cddid_all.tbl CDD pfam18690 pfam18690 436666 DUF5639 Family of unknown function (DUF5639). This is a domain of unknown function which is mainly found in Deinococcus-Thermus. Some family members can be found in the C-terminal region of pfam01565. 82 matched cddid_all.tbl CDD pfam18691 pfam18691 408468 Cdc13_OB2 Cell division control protein 13, OB2 domain. Cdc13 is an essential yeast protein required for telomere length regulation and genome stability. Cdc13, like a number of single-stranded telomere binding proteins, consists of several oligonucleotide-oligosaccharide binding (OB) folds. These folds potentially arise from evolutionary gene duplication and are involved in multiple functions, including nucleic acid and protein binding and Cdc13 dimerization. This entry represents the OB2 domain, second OB-fold counting from the N terminus of Cdc13. Biochemical assays indicate OB2 is not involved in telomeric DNA or Stn1 binding. However, disruption of the OB2 dimer in full-length Cdc13 affects Cdc13-Stn1 association, leading to telomere length deregulation, increased temperature sensitivity, and Stn1 binding defects. Hence it is suggested that the dimerization of the OB2 domain of Cdc13 is required for proper Cdc13, Stn1, Ten1 (CST) assembly and productive telomere capping. 111 matched cddid_all.tbl CDD pfam18692 pfam18692 408469 DUF5640 Family of unknown function (DUF5640). This domain is found in proteins of unknown function. It has composed of eight antiparallel beta strands and carries a G-X-W motif in the N-terminal region. The conserved glycine-X-tryptophan (G-X-W) motif is characteriztic for the lipocalin family. 83 matched cddid_all.tbl CDD pfam18693 pfam18693 465832 TRAM_2 TRAM domain. This is a C-terminal TRAM (after TRM2, a family of uridine methylases, and MiaB) domain found in the methylthiotransferases RimO enzymes that catalyze the conversion of aspartate to 2-methylthio-aspartate (msD) in the S12 protein near the decoding center in prokaryotic ribosomes. The TRAM domain in RimO, contains five anti-parallel beta-strands and docks on the surface of the Radical-SAM domain at the distal edge of its open TIM-barrel from its conserved [4Fe-4S] cluster. 63 matched cddid_all.tbl CDD pfam18694 pfam18694 465833 TDP43_N Transactive response DNA-binding protein N-terminal domain. This domain can be found at the N-terminal region of transactive response DNA-binding protein 43 kDa (TDP-43), an RNA transporting and processing protein whose aberrant aggregates are implicated in neurodegenerative diseases. TDP-43 N-terminal domain has been shown to play an important role in the aggregation of TDP-43 monomers and its loss of function affects the RNA metabolic levels. Secondary structure of the N-terminal domain consists of six beta-strands and it resembles axin 1. 74 matched cddid_all.tbl CDD pfam18695 pfam18695 465834 cPLA2_C2 Cytosolic phospholipases A2 C2-domain. Cytosolic phospholipases A2 (cPLA2s) consist of a family of calcium-sensitive enzymes that function to generate lipid second messengers through hydrolysis of membrane-associated glycerophospholipids. In humans, the cPLA2 family contains six isoforms. Structural information of full length cPLA2alpha apo form, shows that it is composed of two domains; an N-terminal Ca2 + binding C2 domain and a C-terminal alpha/beta hydrolase core. This entry describes the N-terminal Ca2+ binding C2 domain which is composed of an eight-stranded antiparallel beta-sandwich consisting of two four-stranded beta-sheets. C2 domains are present in many lipid-binding proteins including Copines, CAPRI and Rabphilin-3A all of which are involved in membrane trafficking. 111 matched cddid_all.tbl CDD pfam18696 pfam18696 465835 SMP_C2CD2L Synaptotagmin-like, mitochondrial and lipid-binding domain. This is a lipid transport domain found in phospholipid transfer proteins such as C2CD2L-like (also known as TMEM24). The TMEM24-SMP domain is shown to bind glycerolipids with a preference for phosphatidylinositol (PI).The bound PI is then transferred to the plasma membrane (PM) where it is converted to phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2] to replenish pools of this lipid hydrolyzed during glucose-stimulated signaling. PI(4,5)P2 is required for Ca2+-dependent exocytosis hence, the SMP domain of TMEM24 is essential for sustaining the intracellular Ca2+ oscillations that trigger bursts of insulin granule release and hence insulin secretion. The SMP domain belongs to a superfamily of lipid/hydrophobic ligand-binding domains called TULIP for (tubular lipid-binding proteins) it adopts TULIP fold with two alpha helices and a highly curved antiparallel beta sheet forming a cornucopia-like structure. 152 matched cddid_all.tbl CDD pfam18697 pfam18697 436671 MLVIN_C Murine leukemia virus (MLV) integrase (IN) C-terminal domain. This is the C-terminal domain (CTD) which can be found in murine leukemia virus (MLV) integrase (IN) proteins. The MLV IN C-terminal domain interacts with the bromo and extraterminal (BET) proteins through the ET domain. This interaction provides a structural basis for global in vivo integration-site preferences andt disruption of this interaction through truncation mutations affects the global targeting profile of MLV. The CTD consists an SH3 fold followed by a long unstructured tail. 83 matched cddid_all.tbl CDD pfam18698 pfam18698 436672 HisK_sensor Histidine kinase sensor domain. The Bacillus subtilis ResD-ResE two-component (TC) regulatory system activates genes involved in nitrate respiration in response to oxygen limitation or nitric oxide (NO). The sensor kinase ResE activates the response regulator ResD through phosphorylation, which then binds to the regulatory region of genes involved in anaerobiosis to activate their transcription. In other words, ResE is involved in sensing signals related to the redox state of the cells. ResE is composed of an N-terminal signal input domain and a C-terminal catalytic domain. The N-terminal domain contains two transmembrane subdomains and a large extra-cytoplasmic loop. Mutational analysis indicate that cytoplasmic ResE lacking the transmembrane segments and the extra-cytoplasmic loop retains the ability to sense oxygen limitation and NO, which leads to transcriptional activation of ResDE-dependent genes. Having said that, it is also proposed that the extra-cytoplasmic region may serve as a second signal-sensing subdomain. This suggests that the extracytoplasmic region could contribute to amplification of ResE activity leading to the robust activation of genes required for anaerobic metabolism in B. subtilis. This entry represents the extracytoplasmic subdomain. Family members also include SrrB found in S. aureus that is similar to ResE of B. subtilis. 126 matched cddid_all.tbl CDD pfam18699 pfam18699 465836 MRPL52 Mitoribosomal protein mL52. Members of this family include the mamalian mitoribosomal proteins mL52 which is found in the 39S subunit. The mL52 has no homologs in yeast. 91 matched cddid_all.tbl CDD pfam18700 pfam18700 465837 Castor1_N Cytosolic arginine sensor for mTORC1 subunit 1 N-terminal domain. CASTOR1 (Cytosolic arginine sensor for mTORC1 subunit 1) has been identified as the cytosolic arginine sensor for the mTORC1 pathway. In the absence of arginine, CASTOR1 binds to GATOR2 and inhibits mTORC1 signaling; whereas in the presence of arginine, CASTOR1 interacts with arginine and no longer associates with GATOR2. The arginine sits in a pocket between the N-terminal domain (NTD) and the C-terminal domain (CTD) of CASTOR1. The CASTOR1-NTD on the opposite side of the arginine-binding site was identified to mediate direct physical interaction with its downstream effector GATOR2, via GATOR2 subunit Mios. 61 matched cddid_all.tbl CDD pfam18701 pfam18701 465838 DUF5641 Family of unknown function (DUF5641). This presumed domain is found in a range of retrotransposon polyproteins. 94 matched cddid_all.tbl CDD pfam18702 pfam18702 465839 DUF5642 Domain of unknown function (DUF5642). This is a domain of unknown function found in actinobacteria. 186 matched cddid_all.tbl CDD pfam18703 pfam18703 465840 MALT1_Ig MALT1 Ig-like domain. This is an Immunoglobulin like domain which can be found in the mucosa-associated lymphoid tissue lymphoma translocation 1 (MALT1) paracaspase. Malt1 is a key component of the Carma1/Bcl10/MALT1 signalosome and is critical for NF-kB signaling in multiple contexts. The MALT1 C-terminal Ig domain is suggested to recruit key factors to promote NF-kB activation. The It is also proposed to undergo Lys63-linked ubiquitylation via TRAF6 in potentially nine different lysines to recruit the IKK complex. 138 matched cddid_all.tbl CDD pfam18704 pfam18704 465841 Chromo_2 Chromatin organization modifier domain 2. Chromodomains serve as chromatin-targeting modules, general protein interaction elements as well as dimerization sites. They are found in many chromatin-associated proteins that bind modified histone tails for chromatin targeting. Chromodomains often recognize modified lysines through their aromatic cage thus targeting proteins to chromatin. Family members such as GEN1 carry a chomodomain which directly contacts DNA and its truncation severely hampers GEN1's catalytic activity. The chromodomain allows GEN1 to correctly position itself against DNA molecules, and without the chromodomain, GEN1's ability to cut DNA was severely impaired. The GEN1 chromodomain was found to be distantly related to the CDY chromodomains and chromobox proteins, particularly to the chromo-shadow domains of CBX1, CBX3 and CBX5. Furthermore, it is conserved from yeast (Yen1) to humans with the only exception being the Caenorhabditis elegans GEN1, which has a much smaller protein size of 443 amino acids compared to yeast Yen1 (759 aa) or human GEN1 (908 aa). 63 matched cddid_all.tbl CDD pfam18705 pfam18705 465842 DUF5643 Family of unknown function (DUF5643). This is an immunoglobulin-like domain found in bacteria. 117 matched cddid_all.tbl CDD pfam18706 pfam18706 465843 ISPD_C D-ribitol-5-phosphate cytidylyltransferase C-terminal domain. This domain is located at the C-terminal region of ISPD (isoprenoid synthase domain containing protein, EC:2.7.7.40), pfam01128. Structural homologs can be found in two distinct alpha/beta protein families including the seven-stranded NAD(P) (H)-dependent short-chain dehydrogenases/reductases and five-stranded response regulator proteins involved in bacterial sensing systems. 169 matched cddid_all.tbl CDD pfam18707 pfam18707 465844 IL2RB_N1 Interleukin-2 receptor subunit beta N-terminal domain 1. IL-2Rbeta is a member of the class I cytokine receptor superfamily. It carries a cytokine-binding homology region, which is divided in two fibronectin type-III (FN-III) domains termed D1 and D2. Each domain contains seven beta-strands that form a sandwich of two antiparallel beta-sheets. The N-terminal D1 domain of IL-2Rbeta includes two highly conserved disulfide bridges. This entry describes D1 of the N-terminal region of IL2Rbeta. 92 matched cddid_all.tbl CDD pfam18708 pfam18708 436682 MapZ_C2 MapZ extracellular C-terminal domain 2. In the pneumococcus cell division, MapZ (Midcell Anchored Protein Z) locates at the division site before FtsZ and guides septum positioning. MapZ forms ring structures at the cell equator and moves apart as the cell elongates, therefore behaving as a permanent beacon of division sites. MapZ then positions the FtsZ-ring through direct protein-protein interactions. Structural analysis indicate that it displays a bi-modular structure composed of two subdomains separated by a flexible serine-rich linker. The extracellular C-terminal domain carries a conserved patch of amino acids which plays a crucial function in binding peptidoglycan and positioning MapZ at the cell equator. 94 matched cddid_all.tbl CDD pfam18709 pfam18709 408486 DLP_helical Dynamin-like helical domain. This helical domain is found in bacterial proteins such as labile enterotoxin output A (LeoA), a large GTPase (64.2 kDa) with a putative involvement in membrane vesicle (MV) secretion in Escherichia coli. The crystal structure of LeoA reveals a fold with all the hallmarks of a dynamin-like protein (DLP). 344 matched cddid_all.tbl CDD pfam18710 pfam18710 436683 ComR_TPR ComR tetratricopeptide. In Gram-positive bacteria, cell-to-cell communication mainly relies on extracellular signaling peptides. ComR is a member of the RNPP family, which positively controls competence for natural DNA transformation in streptococci. It is directly activated by the binding of its associated pheromone XIP. The crystal structure analysis of ComR shows that it contains an N-terminal helix-turn-helix (HTH), DNA binding domain (DBD) and a C-terminal tetratricopeptide repeat (TPR) domain. The TPR domain is composed of 11 alpha-helices forming 5 TPR motifs followed by an additional C-terminal alpha-helix 16 called CAP. The pheromone XIP binding site is found in the TPR region. Biochemical and mutational analysis indicate that, if the interacting XIP is accepted it can then trigger the conformational change of the TPR domain to open the DBD-TPR interface to allow dimer formation that is required to bind DNA. 222 matched cddid_all.tbl CDD pfam18711 pfam18711 436684 TxDE Toxoflavin-degrading enzyme. This domain is found in toxoflavin-degrading enzymes such as toxoflavin lyase (TflA) also known as toxoflavin-degrading enzyme (TxDE). TflA/TxDE is structurally similar to the vicinal oxygen chelate superfamily of metalloenzymes, despite the lack of apparent sequence identity. 55 matched cddid_all.tbl CDD pfam18712 pfam18712 436685 DUF5644 Family of unknown function (DUF5644). This is a domain of unknown function found at the C-terminal region of Helicobacterial proteins of unknown function. 109 matched cddid_all.tbl CDD pfam18713 pfam18713 436686 DUF5645 Domain of unknown function (DUF5645). This is a domain of unknown function found in Diptera. Some family members carry pfam08445 on their C-terminal. 125 matched cddid_all.tbl CDD pfam18714 pfam18714 436687 PI-TkoII_IV DNA polymerase II intein Domain IV. This domain can be found in the hyperthermophilic archaeon Thermococcus kodakaraensis Pol-2 intein. It is suggested to be a potential DNA binding domain. 150 matched cddid_all.tbl CDD pfam18715 pfam18715 465845 Phage_spike Phage spike trimer. Bacteriophages penetrate the host cell membrane using their tail to inject genetic material into the host. In this penetration process, they use central spike domain located beneath their baseplate. The spike domain folds as a trimeric iron-binding structure. This entry contains three copies of the repeat unit. 52 matched cddid_all.tbl CDD pfam18716 pfam18716 465846 VATC Vms1-associating treble clef domain. Treble clef fold domain found at C-terminus of many, but not all, Vms1/ANKZF1-like proteins. 43 matched cddid_all.tbl CDD pfam18717 pfam18717 408494 CxC4 CxC4 like cysteine cluster associated with KDZ transposases. A predicted Zinc chelating domain present N-terminal to the KDZ transposase domain. 129 matched cddid_all.tbl CDD pfam18718 pfam18718 408495 CxC5 CxC5 like cysteine cluster associated with KDZ transposases. A predicted Zinc chelating domain present N-terminal to the KDZ transposase domain. 117 matched cddid_all.tbl CDD pfam18719 pfam18719 465847 ArlS_N ArlS sensor domain. This entry represents the N-terminal extracellular sensor domain of the ArlS protein from S. aureus. It recognizes LL-37 antimicrobial peptide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043). 127 matched cddid_all.tbl CDD pfam18720 pfam18720 376143 EGF_Tenascin Tenascin EGF domain. This entry represents the EGF-like domains found in tenascin proteins. 29 matched cddid_all.tbl CDD pfam18721 pfam18721 408497 CxC6 CxC6 like cysteine cluster associated with KDZ transposases. A predicted Zinc chelating domain inserted into the core of the KDZ transposase domain. 66 matched cddid_all.tbl CDD pfam18722 pfam18722 436691 MazG_C MazG C-terminal domain. An alpha+beta fold domain found C-terminal to the MazG superfamily pyrophosphatase domain. The domain has a conserved DxYRxHDxxH motif indicative of catalytic activity. Based on its broader context in DNA modification, it is proposed to function as a nucleotide kinase. 190 matched cddid_all.tbl CDD pfam18723 pfam18723 436692 aGPT-Pplase1 alpha-glutamyl/putrescinyl thymine pyrophosphorylase clade 1. An alpha helical domain related to the alpha-helical DNA glycosylases, predicted to catalyze the in situ synthesis of hypermodified bases such as alpha-glutamyl, putrescinyl thymine, 5-(2-aminoethoxy)methyluridine or 5-(2-aminoethyl)uridine. The enzyme is predicted to utilize a high-energy pyrophosphate DNA base intermediate which is subject to a nucleophilic attack by the modifying moiety. Members of this clade are found in phages with hypermodified bases and eukaryotes such as fungi and stramenopiles. 281 matched cddid_all.tbl CDD pfam18724 pfam18724 436693 aGPT-Pplase2 Alpha-glutamyl/putrescinyl thymine pyrophosphorylase clade 2. An alpha helical domain related to the alpha-helical DNA glycosylases, predicted to catalyze the in situ synthesis of hypermodified bases such as alpha-glutamyl, putrescinyl thymine, 5-(2-aminoethoxy)methyluridine or 5-(2-aminoethyl)uridine. The enzyme is predicted to utilize a high-energy pyrophosphate DNA base intermediate which is subject to a nucleophilic attack by the modifying moiety. Mainly found in caudoviruses and prophages. 230 matched cddid_all.tbl CDD pfam18725 pfam18725 408501 HEPN_SAV2148 SAV2148-like HEPN. SAV2148-like HEPN nuclease domain. 216 matched cddid_all.tbl CDD pfam18726 pfam18726 436694 HEPN_SAV_6107 SAV_6107-like HEPN. SAV_6107-like HEPN. 98 matched cddid_all.tbl CDD pfam18727 pfam18727 376150 ALMS_repeat Alstrom syndrome repeat. This entry contains a single repeat unit of approximately 47 AA. It is found in Alstrom syndrome protein 1 (ALMS1) and homologs. 47 matched cddid_all.tbl CDD pfam18728 pfam18728 465848 HEPN_AbiV AbiV. AbiV-like HEPN 157 matched cddid_all.tbl CDD pfam18729 pfam18729 436696 HEPN_STY4199 STY4199-like HEPN. STY4199-like HEPN nuclease domain. 282 matched cddid_all.tbl CDD pfam18730 pfam18730 436697 HEPN_Cthe2314 Cthe_2314-like HEPN. Cthe_2314-like HEPN. 174 matched cddid_all.tbl CDD pfam18731 pfam18731 465849 HEPN_Swt1 Swt1-like HEPN. Swt1-like HEPN. This HEPN domain might have a role in binding and sensing unspliced pre-mRNAs that are specifically targeted by the Swt1 nuclease at the nuclear envelope. 115 matched cddid_all.tbl CDD pfam18732 pfam18732 376155 HEPN_AbiA_CTD HEPN like, Abia C-terminal domain. AbiA-CTD-like HEPN nuclease. Fused to Reverse Transcriptase; in operon with R-M system. 132 matched cddid_all.tbl CDD pfam18733 pfam18733 436699 HEPN_LA2681 LA2681-like HEPN. LA2681-like HEPN nuclease. 207 matched cddid_all.tbl CDD pfam18734 pfam18734 465850 HEPN_AbiU2 AbiU2. AbiU2-like HEPN 197 matched cddid_all.tbl CDD pfam18735 pfam18735 465851 HEPN_RiboL-PSP RiboL-PSP-HEPN. RiboL-PSP-HEPN. Fused to endoRNase L-PSP; in operon with ParB. 191 matched cddid_all.tbl CDD pfam18736 pfam18736 408510 pEK499_p136 HEPN pEK499 p136. pEK499_p136-like HEPN. 150 matched cddid_all.tbl CDD pfam18737 pfam18737 436702 HEPN_MAE_28990 MAE_28990/MAE_18760-like HEPN. HEPN-like nuclease. MAE_28990 In operon with a ParB nuclease and DNA methylase genes. MAE_18760-like HEPN found fused to HEPN/RES-NTD1, HEPN/Toprim-NTD1, Schlafen and a novel beta rich domain. In operon with ParA/Soj ATPase of SIMIBI-type GTPase fold. 210 matched cddid_all.tbl CDD pfam18738 pfam18738 436703 HEPN_DZIP3 DZIP3/ hRUL138-like HEPN. DZIP3/ hRUL138-like HEPN nuclease. Fusion to TPR, Zn-ribbon, RING, Ankyrin, CARD, NACHT ATPase, DEATH and LRR in various animal lineages. 144 matched cddid_all.tbl CDD pfam18739 pfam18739 436704 HEPN_Apea Apea-like HEPN. Apea-like HEPN nuclease. In epsilonproteobacteria embedded in R-M operons. 100 matched cddid_all.tbl CDD pfam18740 pfam18740 465852 EC042_2821 EC042_2821-lke REase. REase Fold Fused to HEPN (EC042_2821) and an N-terminal wHTH in some. 188 matched cddid_all.tbl CDD pfam18741 pfam18741 465853 MTES_1575 REase_MTES_1575. Vsr REase Fold. Fused to HEPN (SWT1/Abi2 family), along with Transglutaminase and wHTH. 96 matched cddid_all.tbl CDD pfam18742 pfam18742 436706 DpnII-MboI REase_DpnII-MboI. REase Fold fused to DpnII/MboI-NTD. 150 matched cddid_all.tbl CDD pfam18743 pfam18743 436707 AHJR-like REase_AHJR-like. REase Fold fused to HEPN(DUF86) pfam01934. 123 matched cddid_all.tbl CDD pfam18744 pfam18744 436708 SNAD1 Secreted Novel AID/APOBEC-like Deaminase 1. A family of secreted AID/APOBEC like deaminases found sporadically across vertebrates. 211 matched cddid_all.tbl CDD pfam18745 pfam18745 436709 SNAD2 Secreted Novel AID/APOBEC-like Deaminase 2. A family of secreted AID/APOBEC like deaminases found in ray-finned fishes. 200 matched cddid_all.tbl CDD pfam18746 pfam18746 436710 aGPT-Pplase3 Alpha-glutamyl/putrescinyl thymine pyrophosphorylase clade 3. An alpha helical domain related to the alpha-helical DNA glycosylases, predicted to catalyze the in situ synthesis of hypermodified bases such as alpha-glutamyl, putrescinyl thymine, 5-(2-aminoethoxy)methyluridine or 5-(2-aminoethyl)uridine. The enzyme is predicted to utilize a high-energy pyrophosphate DNA base intermediate which is subject to a nucleophilic attack by the modifying moiety. Mainly found in bacterial mobile operons. 274 matched cddid_all.tbl CDD pfam18747 pfam18747 408520 Ploopntkinase2 P-loop Nucleotide Kinase2. A P-loop Nucleotide Kinase predicted to be involved in modified base biosynthesis. 298 matched cddid_all.tbl CDD pfam18748 pfam18748 408521 Ploopntkinase1 P-loop Nucleotide Kinase1. A P-loop Nucleotide Kinase predicted to be involved in modified base biosynthesis. 196 matched cddid_all.tbl CDD pfam18749 pfam18749 376171 SNAD3 Secreted Novel AID/APOBEC-like Deaminase 3. A family of AID/APOBEC like deaminases found in vertebrates that were derived from secreted versions of the family. 379 matched cddid_all.tbl CDD pfam18750 pfam18750 465854 SNAD4 Secreted Novel AID/APOBEC-like Deaminase 4. A family of secreted AID/APOBEC like deaminases found only in sponges that often shows lineage-specific expansions. 116 matched cddid_all.tbl CDD pfam18751 pfam18751 436712 Ploopntkinase3 P-loop Nucleotide Kinase3. A P-loop Nucleotide Kinase predicted to be involved in modified base biosynthesis. 184 matched cddid_all.tbl CDD pfam18752 pfam18752 376174 DAAD Dictyosteliid AID/APOBEC-like Deaminase. A family of secreted AID/APOBEC-like deaminases found in dictyostellids that often shows lineage-specific expansions. 291 matched cddid_all.tbl CDD pfam18753 pfam18753 436713 Nmad2 Nucleotide modification associated domain 2. A beta-strand rich domain containing a conserved cysteine and charged residues predicted to play a role in modified DNA base biosynthesis. 201 matched cddid_all.tbl CDD pfam18754 pfam18754 465855 Nmad3 Nucleotide modification associated domain 3. An alpha+beta fold domain with a high conserved HxD and D motifs suggestive of enzymatic function and predicted to be involved in modifed nucleotide biosynthesis. 244 matched cddid_all.tbl CDD pfam18755 pfam18755 465856 RAMA Restriction Enzyme Adenine Methylase Associated. An alpha+beta fold domain associated with restriction enzymes across prokaryotes and fused to JAB deubiquitinases, and chromatin proteins in a wide range of eukaryotes. The domain is predicted to function as a modified-DNA reader domain. 108 matched cddid_all.tbl CDD pfam18756 pfam18756 408527 Nmad4 Nucleotide modification associated domain 4. An alpha+beta fold domain typically associated with DNA methylases and likely to be involved in modified nucleotide biosynthesis. 87 matched cddid_all.tbl CDD pfam18757 pfam18757 436716 Nmad5 Nucleotide modification associated domain 5. An alpha+beta fold domain associated with DNA base modifying genes in prokaryotes, and likely to be involved in modified DNA base biosynthesis. 205 matched cddid_all.tbl CDD pfam18758 pfam18758 465857 KDZ Kyakuja-Dileera-Zisupton transposase. A transposase family with an RNaseH catalytic domain, often fused to DNA binding domains such as SAP or cysteine cluster domains. KDZ transposases are widely present in fungi, metazoa, chlorophytes and haotpohytes. Fungal versions are often associated with a TET/JBP family of dioxygenases. 219 matched cddid_all.tbl CDD pfam18759 pfam18759 408530 Plavaka Plavaka transposase. A transposase with an RNaseH catalytic domain that often has a histone binding BAM/BAH domain at the C-terminus and is sometimes associated with TET/JBP family of dioxygenases in fungi. 320 matched cddid_all.tbl CDD pfam18760 pfam18760 408531 ART-PolyVal ADP-Ribosyltransferase in polyvalent proteins. A family of ADP-Ribosyltransferases found in polyvalent proteins of phages and conjugative elements. These are in turn related to the Tox-ART-HYD2 group of ADP-Ribosyltransferases that are seen in polymorphic toxin systems and in toxin-antitoxin systems. These are predicted to modify host proteins. 136 matched cddid_all.tbl CDD pfam18761 pfam18761 436717 Heliorhodopsin Heliorhodopsin. Heliorhodopsins, distantly related to type-1 rhodopsins, are embedded in the membrane with their N termini facing the cell cytoplasm, an orientation that is opposite to that of type-1 or type-2 rhodopsins. Heliorhodopsins show photocycles that are longer than one second, which is suggestive of light-sensory activity. Heliorhodopsin photocycles accompany retinal isomerization and proton transfer, as in type-1 and type-2 rhodopsins, but protons are never released from the protein.The structures of several heliorhodopsins have been solved displaying seven transmembrane helices (TM), six loops and short N and C termini. Heliorhodopsins share a common fold with the type-1 rhodopsins, however there are clear structural differences, particularly within the loop regions and the large cavity in the cytoplasmic part of heliorhodpsin. Heliorhodpsins are present in Archaea, Bacteria, Eukarya, and viruses. 242 matched cddid_all.tbl CDD pfam18762 pfam18762 465858 Kinase-PolyVal Serine/Threonine/Tyrosine Kinase found in polyvalent proteins. A family of protein kinases found in polyvalent proteins of phages and prophages that although preserving their active site residues for ATP-binding and phosphotransfer appear to have lost the C-terminal subdomain characteriztic of this superfamily. 160 matched cddid_all.tbl CDD pfam18763 pfam18763 436719 ddrB-ParB ddrB-like ParB superfamily domain. A member of the ParB/sulfiredoxin superfamily of proteins found in polyvalent proteins prototyped by the version in the phage P1 ddRB protein. These proteins are predicted to function as nucleases. 122 matched cddid_all.tbl CDD pfam18764 pfam18764 436720 nos_propeller Nitrous oxide reductase propeller repeat. Nitrous oxide reductases usually contain a seven-bladed beta-propeller domain with external short alpha-helices. This entry represents a single blade of the propeller, with imperfect alpha-helix, usually at the C-terminus of the repeat region. 71 matched cddid_all.tbl CDD pfam18765 pfam18765 465859 Polbeta Polymerase beta, Nucleotidyltransferase. A member of the nucleotidyltransferase fold found in polymorphic toxins (NTox45) and polyvalent proteins. 93 matched cddid_all.tbl CDD pfam18766 pfam18766 465860 SWI2_SNF2 SWI2/SNF2 ATPase. A SWi2/SNF2 ATPase found in polyvalent proteins. 222 matched cddid_all.tbl CDD pfam18767 pfam18767 408538 AID Activation induced deaminase. The activation induced deaminase is a vertebrate-specific member of the classical AID/APOBEC cytosine deaminases that is involved in antibody diversification. 90 matched cddid_all.tbl CDD pfam18768 pfam18768 436723 RNPP_C RNPP family C-terminal domain. The bacterial PIcR helix-turn-helix transcription factor includes five TPR units of different lengths. This entry represents the TPR containing domain as a whole. This family is called RNPP after (Rapm NprR, PrgX, and PlcR). 213 matched cddid_all.tbl CDD pfam18769 pfam18769 408540 APOBEC1 APOBEC1. APOBEC1 deaminates cytosine both in RNA and ssDNA and has roles in both mRNA editing and ssDNA mutagenesis as part of the defense against retroviruses and genomic retrotransposons. 101 matched cddid_all.tbl CDD pfam18770 pfam18770 465861 Arm_vescicular Armadillo tether-repeat of vescicular transport factor. Armadillo-like tether-repeat of general vescicular transport factor. This entry contains a single copy of the repeat unit. 60 matched cddid_all.tbl CDD pfam18771 pfam18771 465862 APOBEC3 APOBEC3. APOBEC3 deaminases act as restriction factors in the innate response to retroviruses and various retroelements. 135 matched cddid_all.tbl CDD pfam18772 pfam18772 465863 APOBEC2 APOBEC2. APOBEC2 is a highly conserved (slow-evolving) family of AID/APOBECs found in most vertebrates including cartilaginous fishes. APOBEC2 is poorly understood in terms of their molecular functions and substrate specificity. 174 matched cddid_all.tbl CDD pfam18773 pfam18773 436727 Importin_rep Importin 13 repeat. Importin 13 has a spiralic structure containing repeats structurally similar to HEAT repeats. It serves as receptor for nuclear localization signals (NLS) in cargo substrates, mediating docking of the importin/substrate complex to the nuclear pore complex (NPC). It contains several repeats structurally similar to the HEAT repeat. This Pfam entry represents a single repeat unit. 40 matched cddid_all.tbl CDD pfam18774 pfam18774 408545 APOBEC4_like APOBEC4-like -AID/APOBEC-deaminase. Cnidarian and Algal homologs of the APOBEC4-like AID/APOBEC-like deaminases characterized by a distinct Zn chelating site involving residues from the conserved loops 1 and 3. 131 matched cddid_all.tbl CDD pfam18775 pfam18775 436728 APOBEC4 APOBEC4. A member of the AID/APOBEC family of cytosine deaminases. The biological function of APOBEC4 is poorly understood. However, it is widely conserved across vertebrates. 74 matched cddid_all.tbl CDD pfam18776 pfam18776 408547 Hexapep_loop Hexapeptide repeat including loop. This entry contains a single hexapeptide repeat unit including a loop between two strands. 24 matched cddid_all.tbl CDD pfam18777 pfam18777 465864 CRM1_repeat Chromosome region maintenance or exportin repeat. Chromosome region maintenance 1 or exportin 1 mediates the nuclear transport of proteins bearing a leucin-rich nuclear export signal (NES). It contains helical repeats that are structurally similar to HEAT repeats, but share little sequence similarity with them. N-terminal, C-terminal and central repeats show slightly different structural arrangements, with N- and C- termini repeats interacting with each other. This entry represents the central repeats of CRM1. 37 matched cddid_all.tbl CDD pfam18778 pfam18778 465865 NAD1 Novel AID APOBEC clade 1. A distinct family of AID/APOBEC-like deaminases found in ray-finned fishes, the coelacanth, amphibians, lizards, and marsupials. 175 matched cddid_all.tbl CDD pfam18779 pfam18779 436731 LRR_RI_capping Capping Ribonuclease inhibitor Leucine Rich Repeat. Leucine-rich repeats are composed of a beta-alpha unit. This repeat unit is found as capping unit (N- or C- terminal of the repeat region) of Ribonuclease Inhibitors. 30 matched cddid_all.tbl CDD pfam18780 pfam18780 465866 HNH_repeat Homing endonuclease associated repeat. This entry represents a 60 residue repeat of unknown function found associated with homing endonuclease domains. 54 matched cddid_all.tbl CDD pfam18781 pfam18781 408552 Phage_spike_2 Phage spike trimer. This Pfam entry includes some phage spike repeats that fail to be detected with the pfam18715 model. 78 matched cddid_all.tbl CDD pfam18782 pfam18782 436733 NAD2 Novel AID APOBEC clade 2. A distnct family of AID/APOBEC deaminases found only in Amphibians. 176 matched cddid_all.tbl CDD pfam18783 pfam18783 436734 IPU_b_solenoid Isopullulanase beta-solenoid repeat. IPU and dextranase repeat unit includes three (or one long and one short) parallel beta-strands. The repeat region as a whole folds into a beta-helix, known as beta-solenoid. 33 matched cddid_all.tbl CDD pfam18784 pfam18784 436735 CRM1_repeat_2 CRM1 / Exportin repeat 2. Chromosome region maintenance 1 / Exportin 1 mediates the nuclear transport of proteins bearing a leucin-rich nuclear export signal (NES). It contains helical repeats that are structurally similar to HEAT repeats, but share little sequence similarity with them. N-, C-terminal and central repeats show slightly different structural arrangements, with N- and C- terminal repeats interacting with each other. This Pfam entry includes some CRM1 repeats that fail to be detected with the pfam18777 model. 68 matched cddid_all.tbl CDD pfam18785 pfam18785 408556 Inv-AAD Invertebrate-AID/APOBEC-deaminase. A classical AID/APOBEC-like deaminases found in lophotrochozoans, echinoderms and cnidarians. 129 matched cddid_all.tbl CDD pfam18786 pfam18786 408557 Importin_rep_2 Importin 13 repeat. Importin 13 serves as receptor for nuclear localization signals (NLS) in cargo substrates. It mediates docking of the importin/substrate complex to the nuclear pore complex (NPC). It contains several repeats structurally similar to the HEAT repeat. This Pfam entry represents a single repeat unit. 44 matched cddid_all.tbl CDD pfam18787 pfam18787 436736 CRM1_repeat_3 CRM1 / Exportin repeat 3. Chromosome region maintenance 1 / Exportin 1 mediates the nuclear transport of proteins bearing a leucin-rich nuclear export signal (NES). It contains helical repeats that are structurally similar to HEAT repeats, but share little sequence similarity with them. N-, C-terminal and central repeats show slightly different structural arrangements, with N- and C- terminal repeats interacting with each other. This Pfam entry includes some CRM1 repeats that fail to be detected with the PF18777 model. 51 matched cddid_all.tbl CDD pfam18788 pfam18788 436737 DarA_N Defence against restriction A N-terminal. This is an alpha and beta fold domain. It has a conserved aspartate, and an asparagine residue followed by a basic residue in a Nx+ motif. This predicted structural domain is mainly found in polyvalent proteins of phages/prophages. The P1 hdf protein, a solo version of the domain, and the Phage P1 DarA protein that contains this domain are components of the phage P1 head. The domain might be involved in a counter-restriction activity. 101 matched cddid_all.tbl CDD pfam18789 pfam18789 436738 DarA_C Defence against restriction A C-terminal. This is a mostly alpha-helical domain found in polyvalent proteins of phages and prophages. In Phage P1, the DarA protein is a component of the phage P1 head. 70 matched cddid_all.tbl CDD pfam18790 pfam18790 436739 KfrB KfrB protein. This is an alpha and beta domain found in polyvalent proteins of conjugative element or often in the neighbourhood of one. The KfrB domain has been speculated to play a role in discrimination of self from non-self in plasmid conjugation systems. 61 matched cddid_all.tbl CDD pfam18791 pfam18791 465867 Transp_inhibit Transport inhibitor response 1 protein domain. The F-box protein Transport inhibitor response 1 (TIR1) is a receptor for auxin, triggering an auxin-enhanced and ubiquitin-mediated degradation of substrates. The targets are recruited via interaction with the leucine-rich repeat region of the protein. This Pfam entry represents a specific unit of the LRR region, including an insertion of one short alpha-helix in the loop between the beta-strand and the following helix. It shares some sequence homology with a unit with similar structure of Coronatine-insensitive protein 1. 47 matched cddid_all.tbl CDD pfam18792 pfam18792 408563 UspA1_rep Ubiquitous surface protein adhesin repeat. The UspA1 head domain is globally similar to other structures of TAA head domains and comprises a trimeric left-handed parallel beta-roll, which is formed from 14 repeating 14-16 residue segments that form a ladder of beta-strand coils. This Pfam entry represents a single repeat unit of the beta-ladder. 13 matched cddid_all.tbl CDD pfam18793 pfam18793 436741 nos_propeller_2 Nitrous oxide reductase propeller repeat 2. Nitrous oxide reductases usually contain a seven-bladed beta-propeller domain with external short alpha-helices. This entry represents a single blade of the propeller, without alpha- helical insertion. 70 matched cddid_all.tbl CDD pfam18794 pfam18794 408565 HSM3_C DNA mismatch repair protein HSM3, C terminal domain. Hsm3 is a proteasome-dedicated chaperone that forms a base precursor, Hsm3-Rpt1-Rpt2-Rpn1. Hsm3 consists of 23 alpha-helices forming 11 repeats similar to HEAT repeats. This entry include the last 5 repeats at the C terminal. 177 matched cddid_all.tbl CDD pfam18795 pfam18795 465868 HSM3_N DNA mismatch repair protein HSM3, N terminal domain. Hsm3 is a proteasome-dedicated chaperone that forms a base precursor, Hsm3-Rpt1-Rpt2-Rpn1. Hsm3 consists of 23 alpha-helices forming 11 repeats similar to the HEAT repeats. This entry includes the first 5 repeats at the N-terminal. 237 matched cddid_all.tbl CDD pfam18796 pfam18796 465869 LPD1 Large polyvalent protein-associated domain 1. This is an alpha helical domain with a conserved ExxARxxE motif that is found in polyvalent proteins of both conjugative elements and phages and prophages. 78 matched cddid_all.tbl CDD pfam18797 pfam18797 465870 APC_rep Adenomatous polyposis coli (APC) repeat. Adenomatous polyposis coli contains an armadillo repeat and uses its highly conserved surface groove to recognize the APC-binding region (ABR) of Asef. This entry represents a single repeat unit of the Armadillo region. 74 matched cddid_all.tbl CDD pfam18798 pfam18798 436745 LPD3 Large polyvalent protein-associated domain 3. This domain is predicted to adopt an alpha and beta fold. The secondary structure arrangement suggests it to be a member of the BECR fold. The domain is found in polyvalent proteins of both conjugative elements and phages/prophages. 110 matched cddid_all.tbl CDD pfam18799 pfam18799 436746 LPD5 Large polyvalent protein-associated domain 5. This domain is predicted to be an enzymatic alpha beta domain. It often found N-terminal to a metallopeptidase domain in polyvalent proteins. The domain contains a conserved aspartate, lysine, and two arginine residues. 146 matched cddid_all.tbl CDD pfam18800 pfam18800 436747 Atthog Attenuator of Hedgehog. Attenuator of Hedgehog is a integral membrane protein of the tetraspan family that functions as a negative regulator of Hedgehog signaling. 141 matched cddid_all.tbl CDD pfam18801 pfam18801 436748 RapH_N response regulator aspartate phosphatase H, N terminal. Rap proteins consist of a N-terminal 3-helix bundle and a tetratricopeptide domain. This entry represents the conserved region of the C-terminal bundle. 62 matched cddid_all.tbl CDD pfam18802 pfam18802 465871 CxC1 CxC1 like cysteine cluster associated with KDZ transposases. A predicted Zinc chelating domain present N-terminal to the KDZ transposase domain. 105 matched cddid_all.tbl CDD pfam18803 pfam18803 465872 CxC2 CxC2 like cysteine cluster associated with KDZ transposases. A predicted Zinc chelating domain present N-terminal to the KDZ transposase domain. 107 matched cddid_all.tbl CDD pfam18804 pfam18804 408575 CxC3 CxC3 like cysteine cluster associated with KDZ transposases. A predicted Zinc chelating domain present N-terminal to the KDZ transposase domain. 113 matched cddid_all.tbl CDD pfam18805 pfam18805 436750 LRR_10 Leucine-rich repeat. This Pfam entry includes some LRRs that fail to be detected with the pfam00560 model. This entry represents two repeat units. 67 matched cddid_all.tbl CDD pfam18806 pfam18806 465873 Importin_rep_3 Importin 13 repeat. Importin 13 serves as receptor for nuclear localization signals (NLS) in cargo substrates. It mediates docking of the importin/substrate complex to the nuclear pore complex (NPC). It contains several repeats structurally similar to the HEAT repeat. This Pfam entry represents a single repeat unit. 75 matched cddid_all.tbl CDD pfam18807 pfam18807 465874 TTc_toxin_rep Tripartite Tc toxins repeat. Tripartite Tc toxin complexes of bacterial pathogens perforate the host membrane and translocate toxic enzymes into the host cell. These structures undergo a transition between a prepore to a pore state and they are mainly constituted by closed beta-layer repeats. This Pfam entry includes a single repeat unit. 45 matched cddid_all.tbl CDD pfam18808 pfam18808 408579 Importin_rep_4 Importin repeat. The importin subunit beta-3 has a superhelical structure composed of tandem repeats structurally similar to HEAT repeats. This Pfam entry includes a single repeat unit. 90 matched cddid_all.tbl CDD pfam18809 pfam18809 436753 PBECR1 phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease1. A predicted endoRNase of the Barnase-EndoU-ColicinE5/D-RelE like nuclease fold found in polyvalent proteins of phages and conjugative elements. The predicted active site contains a conserved histidine and threonine residues. 109 matched cddid_all.tbl CDD pfam18810 pfam18810 436754 PBECR2 phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease2. A predicted endoRNase of the Barnase-EndoU-ColicinE5/D-RelE like nuclease fold found in polyvalent proteins of phages. The predicted active site contains a conserved arginine and threonine residues. 121 matched cddid_all.tbl CDD pfam18811 pfam18811 465875 DPPIV_rep Dipeptidyl peptidase IV (DPP IV) low complexity region. Dipeptidyl peptidase IV includes an helical N-terminal region, the pfam00930 domain and the pfam00326 domain, comprising the active site. This Pfam entry represents a sequence that can be repeated in the low complexity region between the helical N-terminus and the DPPIV_N domain. 21 matched cddid_all.tbl CDD pfam18812 pfam18812 465876 PBECR3 phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease3. A predicted endoRNase of the Barnase-EndoU-ColicinE5/D-RelE like nuclease fold found in polyvalent proteins of phages and conjugative elements. The predicted active site contains a conserved histidine and threonine residues. 116 matched cddid_all.tbl CDD pfam18813 pfam18813 436757 PBECR4 phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease4. A predicted endoRNase of the Barnase-EndoU-ColicinE5/D-RelE like nuclease fold found in polyvalent proteins of phages and conjugative elements. The predicted active site contains a conserved histidine residue. 185 matched cddid_all.tbl CDD pfam18814 pfam18814 436758 PBECR5 phage-Barnase-EndoU-ColicinE5/D-RelE like nuclease5. A predicted endoRNase of the Barnase-EndoU-ColicinE5/D-RelE like nuclease fold found in polyvalent proteins of phages and conjugative elements. The predicted active site contains a conserved histidine and threonine residues. 241 matched cddid_all.tbl CDD pfam18815 pfam18815 436759 AFP_2 Bacterial antifreeze protein repeat. This family of proteins is involved in stopping the formation of ice crystals at low temperatures. The structure folds as a Ca(2+)-bound parallel beta-helix with an extensive array of ice-like surface waters that are anchored via hydrogen bonds directly to the polypeptide backbone and adjacent side chains. 52 matched cddid_all.tbl CDD pfam18816 pfam18816 465877 Importin_rep_5 Importin repeat. The importin subunit beta-3 has a superhelical structure composed of tandem repeats structurally similar to HEAT repeats. This Pfam entry includes a single repeat unit and includes sequences not captured by pfam18808. 52 matched cddid_all.tbl CDD pfam18817 pfam18817 408588 HEAT_UF Repeat of uncharacterized protein PH0542. Repeat found in PH0542 showing some sequence similarity to HEAT repeat. 45 matched cddid_all.tbl CDD pfam18818 pfam18818 465878 MPTase-PolyVal Zincin-like metallopeptidase. Zincin-like Metallopeptidase frequently found in polyvalent proteins of phages and conjugative elements. The active site is comprised of a HEXXH motif and a C-terminal glutamate. 126 matched cddid_all.tbl CDD pfam18819 pfam18819 436762 MuF_C Phage MuF-C-terminal domain. A predicted endoRNase of the Barnase-EndoU-ColicinE5/D-RelE like nuclease fold found in polyvalent proteins of phages and conjugative elements and also fused to the MuF domain, a structural component of the phage head. The predicted active site contains a conserved histidine and serine residues. 103 matched cddid_all.tbl CDD pfam18820 pfam18820 376239 BD_b_sandwich Bdellovibrio Beta-sandwich. A beta-sandwich domain exclusively found at the N-terminal of CHROMO domains in many Bdellovibrio proteins. 131 matched cddid_all.tbl CDD pfam18821 pfam18821 465879 LPD7 Large polyvalent protein-associated domain 7. This domain contains conserved aspartate and phenylalanine residues. It is widely present in polyvalent proteins and gene neighbourhoods of conjugative elements. This domain is also known as PTox1. 92 matched cddid_all.tbl CDD pfam18822 pfam18822 436764 CdvA CdvA-like coiled-coil domain. A coiled coil region domain related to the CdvA-like proteins. 123 matched cddid_all.tbl CDD pfam18823 pfam18823 436765 InPase Inorganic Pyrophosphatase. A type I Inorganic Pyrophosphatase family domain that is found in polyvalent proteins. 135 matched cddid_all.tbl CDD pfam18824 pfam18824 436766 LPD11 Large polyvalent protein-associated domain 11. This is an alpha-helical domain with conserved hydrophobic residues. It is found in polyvalent proteins of conjugative elements. 69 matched cddid_all.tbl CDD pfam18825 pfam18825 408595 LPD13 Large polyvalent protein-associated domain 13. This is an alpha and beta domain that is found in polyvalent proteins of both conjugative elements and phages/prophages. 139 matched cddid_all.tbl CDD pfam18826 pfam18826 465880 bVLRF1 Bacteroidetes VLRF1 release factor. Archaeo-eukaryotic release factor domain family belonging to the VLRF1 clade observed primarily in the bacteroidetes bacterial lineage. Contains a conserved glutamine residue in the release factor catalytic loop, suggesting it functions as an active peptidyl-tRNA hydrolase at the ribosome. 143 matched cddid_all.tbl CDD pfam18827 pfam18827 408597 LPD14 Large polyvalent protein-associated domain 14. This is an alpha-helical domain with a conserved glutamate residue that is mainly found in polyvalent proteins of prophages. 136 matched cddid_all.tbl CDD pfam18828 pfam18828 408598 LPD15 Large polyvalent-protein-associated domain 15. This is a predicted enzymatic alpha and beta domain. It is found at the N-terminus of polyvalent proteins of conjugative elements. 99 matched cddid_all.tbl CDD pfam18829 pfam18829 465881 Importin_rep_6 Importin repeat 6. The importin subunit beta-3 has a superhelical structure composed of tandem repeats structurally similar to HEAT repeats. This Pfam entry represents two consecutive repeat units and includes sequences captured by pfam18808. 110 matched cddid_all.tbl CDD pfam18830 pfam18830 436769 LPD16 Large polyvalent protein-associated domain 16. This is an alpha and beta fold domain that is mainly found in polyvalent proteins of conjugative elements. 82 matched cddid_all.tbl CDD pfam18831 pfam18831 408601 LRR_11 Leucine-rich repeat. This Pfam entry includes some LRRs that fail to be detected with the pfam00560 model. This entry represents one repeat unit. 29 matched cddid_all.tbl CDD pfam18832 pfam18832 436770 LPD18 Large polyvalent protein-associated domain 18. This is a mostly all beta domain which contains conserved acidic residues. It is mainly found in polyvalent proteins of conjugative elements. 86 matched cddid_all.tbl CDD pfam18833 pfam18833 436771 TPR_22 Tetratricopeptide repeat. This Pfam entry includes outlying Tetratricopeptide-like repeats (two repeat units) that are not matched by pfam00515. 92 matched cddid_all.tbl CDD pfam18834 pfam18834 465882 LPD22 Large polyvalent protein associated domain 22. This is a predicted enzymatic alpha-helical domain with highly conserved aspartate residues. The domain is found in polyvalent proteins of phage and prophage genes and is often the immediate neighbour of a lysozyme gene. 98 matched cddid_all.tbl CDD pfam18835 pfam18835 465883 Beta_helix_2 Beta helix repeat of Inulin fructotransferase. This region contains a right-handed parallel beta helix repeat unit found in Inulin fructotransferase. This Pfam entry includes sequences not found by pfam13229. 68 matched cddid_all.tbl CDD pfam18836 pfam18836 465884 B_solenoid_ydck YdcK Beta solenoid repeat. The crystal structure of YdcK from Salmonella cholerae includes a beta-solenoid repeat. This Pfam entry includes a single repeat unit of YDCK repeat. 16 matched cddid_all.tbl CDD pfam18837 pfam18837 408607 LRR_12 Leucine-rich repeat. This Pfam entry includes some LRRs that fail to be detected with the pfam00560 model. This entry represents one repeat unit. 30 matched cddid_all.tbl CDD pfam18838 pfam18838 465885 LPD23 Large polyvalent protein associated domain 23. This is an alpha-helical domain that is usually N-terminal to a metallopeptidase domain. The domain is found in both in polyvalent proteins of conjugative elements and phages/prophages. 58 matched cddid_all.tbl CDD pfam18839 pfam18839 408609 LPD24 Large polyvalent protein associated domain 24. This is an all-beta domain that is mostly seen in polyvalent proteins of conjugative elements. 70 matched cddid_all.tbl CDD pfam18840 pfam18840 436774 LPD25 Large polyvalent protein associated domain 25. This is an alpha and beta fold domain found in polyvalent proteins of conjugative elements. 99 matched cddid_all.tbl CDD pfam18841 pfam18841 408611 B_solenoid_dext Beta solenoid repeat from Dextranase. The crystal structures of Dex49A from Penicillium minioluteum and of ATCC9642 isopullulanase from Aspergillus niger include beta-solenoid repeats, sharing structural similarities. This Pfam entry includes a single repeat unit of the repeat regions. 33 matched cddid_all.tbl CDD pfam18842 pfam18842 408612 LPD26 Large polyvalent protein associated domain 26. This is a small alpha-helical domain with two acidic residues conserved in a predicted loop between two of its helices. The domain is mainly found in polyvalent proteins of conjugative elements. 57 matched cddid_all.tbl CDD pfam18843 pfam18843 436775 LPD28 Large polyvalent protein associated domain 28. This is a beta strand rich domain that lacks strongly conserved polar residues. It is fast diverging and is found in polyvalent proteins of conjugative elements. 96 matched cddid_all.tbl CDD pfam18844 pfam18844 465886 baeRF_family2 Bacterial archaeo-eukaryotic release factor family 2. Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome. This family contains a well-conserved 'FP' motif in the catalytic loop. 149 matched cddid_all.tbl CDD pfam18845 pfam18845 465887 baeRF_family3 Bacterial archaeo-eukaryotic release factor family 3. Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome. 168 matched cddid_all.tbl CDD pfam18846 pfam18846 436778 baeRF_family5 Bacterial archaeo-eukaryotic release factor family 5. Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome. This family unusually lacks the fusion to the C-terminal Pelota domain. 132 matched cddid_all.tbl CDD pfam18847 pfam18847 436779 LPD29 Large polyvalent protein associated domain 29. This is an alpha and beta fold domain with conserved polar residues that is found in polyvalent proteins of conjugative elements. 91 matched cddid_all.tbl CDD pfam18848 pfam18848 436780 baeRF_family6 Bacterial archaeo-eukaryotic release factor family 6. Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome. 149 matched cddid_all.tbl CDD pfam18849 pfam18849 436781 baeRF_family7 Bacterial archaeo-eukaryotic release factor family 7. Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome. Consistent with this, many members of the family associate on the genome with HPF-like ribosome hibernation factor. 144 matched cddid_all.tbl CDD pfam18850 pfam18850 436782 LPD30 Large polyvalent protein associated domain 30. This is an alpha and beta fold domain that is found in polyvalent proteins of conjugative elements. 121 matched cddid_all.tbl CDD pfam18851 pfam18851 436783 baeRF_family8 Bacterial archaeo-eukaryotic release factor family 8. Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome. 141 matched cddid_all.tbl CDD pfam18852 pfam18852 408622 LPD34 Large polyvalent protein associated domain 34. This is a predicted enzymatic alpha and beta fold domain with a large, prominent helix with conserved glutamate residue and several additional conserved residues including the motifs HTxN and SN. The domain is associated with polyvalent proteins of firmicute conjugative elements. 213 matched cddid_all.tbl CDD pfam18853 pfam18853 408623 LPD37 Large polyvalent protein associated domain 37. This is and alpha and beta fold domain that is found in polyvalent proteins that are likely to be phage/prophage-derived. 244 matched cddid_all.tbl CDD pfam18854 pfam18854 436784 baeRF_family10 Bacterial archaeo-eukaryotic release factor family 10. Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome. 143 matched cddid_all.tbl CDD pfam18855 pfam18855 408625 baeRF_family11 Bacterial archaeo-eukaryotic release factor family 11. Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome. 139 matched cddid_all.tbl CDD pfam18856 pfam18856 436785 baeRF_family12 Bacterial archaeo-eukaryotic release factor family 12. Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome. 138 matched cddid_all.tbl CDD pfam18857 pfam18857 465888 LPD38 Large polyvalent protein associated domain 38. This is an alpha and beta fold domain found in polyvalent proteins of phages and prophages. 190 matched cddid_all.tbl CDD pfam18858 pfam18858 436787 LPD39 Large polyvalent protein associated domain 39. This is a predicted enzymatic alpha-helical domain that is associated with polyvalent proteins of phages and prophages. 196 matched cddid_all.tbl CDD pfam18859 pfam18859 436788 acVLRF1 Actinobacteria/chloroflexi VLRF1 release factor. Archaeo-eukaryotic release factor domain family belonging to the VLRF1 clade, observed primarily in the actinbacteria and chloroflexi bacterial lineages. Contains a conserved glutamine residue in the release factor catalytic loop, suggesting it functions as an active peptidyl-tRNA hydrolase at the ribosome. 130 matched cddid_all.tbl CDD pfam18860 pfam18860 436789 AbiJ_NTD3 AbiJ N-terminal domain 3. Alpha + beta domain. Found fused to AbiJ-like HEPN. Fused to other domains presumably involved in defense. 167 matched cddid_all.tbl CDD pfam18861 pfam18861 465889 PTP_tm TM proximal of protein tyrosine phosphatase, receptor type J. Protein tyrosine phosphatases (PTPs) are known to be signaling molecules that regulate a variety of cellular processes, including cell growth, differentiation, mitotic cycle, and oncogenic transformation. PTP receptor type J possesses an extracellular region containing five fibronectin type III repeats, the transmembrane region included in this Pfam entry, and a intracytoplasmic catalytic domain. This entry probably contains part of a Fn3 domain at the N-terminus. 126 matched cddid_all.tbl CDD pfam18862 pfam18862 436791 ApeA_NTD1 ApeA N-terminal domain 1. Mostly beta strands. Fused to HEPN (Apea). Several conserved aromatic residues, abundant but poorly conserved. 420 matched cddid_all.tbl CDD pfam18863 pfam18863 465890 AbiJ_NTD4 AbiJ N-terminal domain 4. Alpha + beta. Found fused to AbiJ-like HEPN and heat repeats. 153 matched cddid_all.tbl CDD pfam18864 pfam18864 465891 AbiTii AbiTii. Alpha + beta domain. Found fused to the N-terminus of the c2405 family of HEPN domains and in few cases to Ymh. 186 matched cddid_all.tbl CDD pfam18865 pfam18865 408635 AbiJ_NTD5 AbiJ N-terminal domain 5. Mostly alpha helical. Found fused to AbiJ-lke HEPN, and to other domains presumably involved in defense. 93 matched cddid_all.tbl CDD pfam18866 pfam18866 465892 CxC7 CxC7 like cysteine cluster associated with KDZ transposases. A predicted Zinc chelating domain present N-terminal to the KDZ transposase domain. 64 matched cddid_all.tbl CDD pfam18867 pfam18867 408637 HEPN-like_int HEPN-like integron domain. This is a HEPN-like nuclease. Part of mobile integron element. The integron cassettes are known to be activated by stress conditions, thereby allowing swapping of genetic material that might be of adaptive value. Hence it is hypothesized that the HEPN domains present in some integron cassettes contribute to the stress response by functioning as RNases that induce dormancy by probably inhibiting translation and thus enabling survival of harsh conditions. 151 matched cddid_all.tbl CDD pfam18868 pfam18868 408638 zf-C2H2_3rep Zinc finger C2H2-type, 3 repeats. This Pfam entry includes three instances of the Zinc finger C2H2-type. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. 126 matched cddid_all.tbl CDD pfam18869 pfam18869 408639 HEPN_RnaseLS RnaseLS-like HEPN. RnaseLS-like HEPN. 124 matched cddid_all.tbl CDD pfam18870 pfam18870 436794 HEPN_RES_NTD1 HEPN/RES N-terminal domain 1. Mostly alpha helical. Fused to HEPN (MAE_28990 superfamily), RES domain, a potential RNase found in various toxin systems. 131 matched cddid_all.tbl CDD pfam18871 pfam18871 436795 HEPN_Toprim_N HEPN/Toprim N-terminal domain 1. Alpha + beta domain. Fused to two distinct HEPN families: MAE_28990 and ERFG_01251 families, TOPRIM and a Mrr-like REase domain. 223 matched cddid_all.tbl CDD pfam18872 pfam18872 465893 Daz Daz repeat. This short repeat is found in the Daz proteins is a varying number of copies. The molecular function of these repeats in unknown. 21 matched cddid_all.tbl CDD pfam18873 pfam18873 436796 Sgo0707_N1 Sgo0707 N-terminal domain. This domain found at the N-terminus of the cell surface Sgo0707 protein. This domain is called the N1 domain and is involved in host colonization.The largest domain, N1, comprises a putative binding cleft with a single cysteine located in its centre and exhibits an unexpected structural similarity to the variable domains of the streptococcal Antigen I/II adhesins. 268 matched cddid_all.tbl CDD pfam18874 pfam18874 436797 QPE QPE domain. This sort presumed domain is found in a small set of gram positive organizms in cell surface proteins with an N-terminal collagen binding domain. We have named this domain QPE after the most conserved sequence motif. 44 matched cddid_all.tbl CDD pfam18875 pfam18875 436798 AF4_int AF4 interaction motif. This short motif found in the AF4 protein interacts with AF9. 15 matched cddid_all.tbl CDD pfam18876 pfam18876 465894 AF-4_C AF-4 proto-oncoprotein C-terminal region. This family consists of AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental retardation syndrome) nuclear proteins. These proteins have been linked to human diseases such as acute lymphoblastic leukaemia and mental retardation. The family also contains a Drosophila AF4 protein homolog Lilliputian which contains an AT-hook domain. Lilliputian represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila. 262 matched cddid_all.tbl CDD pfam18877 pfam18877 465895 SSSPR-51 SSSPR-51 domain. This repeat domain is designated SSSPR-51, Streptococcal and Staphylococcal Surface Protein Repeat of size 51. These repeats are homologous to the listerial repeats of pfam06458, but shorter on average by about 8 amino acids. 48 matched cddid_all.tbl CDD pfam18878 pfam18878 465896 PPE-PPW PPE-PPW subfamily C-terminal region. This entry represents the C-terminal region of a subfamily of PPE proteins known as the PPW subfamily. The PPW refers to three conserved residues found in the sequence alignment. The region also contains a second conserved motif GFGT. 48 matched cddid_all.tbl CDD pfam18879 pfam18879 465897 EspA_EspE EspA/EspE family. This family of proteins includes Mycobacterium tuberculosis EspA and EspE proteins. 84 matched cddid_all.tbl CDD pfam18880 pfam18880 408650 UDI Uracil-DNA glycosylase inhibitor. Uracil-DNA glycosylase inhibitor (UGI) found in Bacillus subtilis phage, is an inhibitor that inactivates the host uracil-DNA glycosylase (UDG), also known as (UNG) uracil-DNA N-glycosylase. UDG is a highly conserved enzyme responsible for the initiation of uracil-base excision repair (1). UGI forms a tight non-covalent bond to UDG, completely inhibiting it from binding to DNA by inserting its beta-1 strand into the conserved DNA-binding groove of the enzyme (2). In complex with UDG, UGI folds into an alpha-beta-alpha sandwich structure formed by five-stranded antiparallel beta-strands and two helices (3). 82 matched cddid_all.tbl CDD pfam18881 pfam18881 408651 DUF5646 Family of unknown function (DUF5646). This is a family of unknown function. Family members include the archaeal homolog the bacterial RelB, a toxin-antitoxin system which is activated during amino acid starvation. This family is mostly found in thermococcus archaea. 69 matched cddid_all.tbl CDD pfam18882 pfam18882 436803 DUF5647 Family of unknown function (DUF5647). This is a family of unknown function. Family members include the hypothetical protein TTHC002 from Thermus thermophilus. Its has an alpha-beta-alpha-beta(3) structure and forms a dimer with a single beta-sheet, folded in a barrel-like shape. 79 matched cddid_all.tbl CDD pfam18883 pfam18883 465898 AC_1 Autochaperone Domain Type 1. This entry represents the autochaperone domain of type 1 (AC-1) in the Type Va Secretion System (T5aSS). Autotransporters (ATs) belong to a family of modular proteins secreted by the Type V, subtype a, secretion system (T5aSS) and considered as an important source of virulence factors in lipopolysaccharidic diderm bacteria (archetypical Gram-negative bacteria). The AC of type 1 with beta-fold appears as a prevalent and conserved structural element exclusively associated to beta-helical AT passenger. 114 matched cddid_all.tbl CDD pfam18884 pfam18884 465899 TSP3_bac Bacterial TSP3 repeat. This entry contains a novel bacterial thrombospondin type 3 repeat which differs from the typical consensus by containing a glutamate in place of one of the calcium binding aspartate residues. 22 matched cddid_all.tbl CDD pfam18885 pfam18885 436806 DUF5648 Repeat of unknown function (DUF5648). This entry represents a repeat of approximately 40 residues in length. It is often associated with enzymatic domains in bacterial cell surface proteins. This entry may represent a beta-propeller repeat, although most proteins only possess three repeats rather than the expected 6-8 copies. 39 matched cddid_all.tbl CDD pfam18886 pfam18886 436807 DUF5649 Repeats of unknown function (DUF5649). This entry represents a series of potential beta-helix repeats found in a variety of putative bacterial adhesin proteins. 68 matched cddid_all.tbl CDD pfam18887 pfam18887 436808 MBG_3 MBG domain. This entry corresponds to an MBG (mirror beta grasp) domain. It is found in a variety of bacterial cell surface proteins. 72 matched cddid_all.tbl CDD pfam18888 pfam18888 408658 DUF5650 Repeat of unknown function (DUF5650). This entry represents a repeating region found in filamentous hemagglutinin proteins from various bacteria. This entry may contain a beta helix structure. 55 matched cddid_all.tbl CDD pfam18889 pfam18889 436809 Beta_helix_3 Beta helix repeat. This entry contains a 30 residue repeat found in a variety of bacterial cell surface proteins. This repeat is related to pfam14262, meaning that it has a beta-helix structure. The sequence repeat is quite glycine rich. 20 matched cddid_all.tbl CDD pfam18890 pfam18890 465900 FANCL_d2 FANCL UBC-like domain 2. This entry represents the second of three UBC-like domain found in the FANCL protein, which is the catalytic E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits of the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2. 91 matched cddid_all.tbl CDD pfam18891 pfam18891 465901 FANCL_d3 FANCL UBC-like domain 3. This entry represents the third of three UBC-like domain found in the FANCL protein, which is the catalytic E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits of the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2. 97 matched cddid_all.tbl CDD pfam18892 pfam18892 408662 DUF5651 Family of unknown function (DUF5651). This entry represents a probable zinc binding domain found at the C-terminus of some Firmicute bacteria. The function of these proteins is unknown. 54 matched cddid_all.tbl CDD pfam18893 pfam18893 436812 DUF5652 Family of unknown function (DUF5652). This entry represents a protein containing two transmembrane helices. Many of these proteins are found in organizms in the Candidate Phyla Radiation. 71 matched cddid_all.tbl CDD pfam18894 pfam18894 465902 PhageMetallopep Putative phage metallopeptidase. This entry represents a probable metallopeptidase found in a variety of phage and bacterial proteomes. 138 matched cddid_all.tbl CDD pfam18895 pfam18895 436814 T4SS_pilin Type IV secretion system pilin. This entry represents likely Type IV secretion system pilins. 71 matched cddid_all.tbl CDD pfam18896 pfam18896 436815 SLT_3 Lysozyme like domain. This entry represents a lysozyme like domain found in candidate phyla radiation bacteria. The domain contains several conserved cysteine and histidine residues suggesting that it may bind to zinc. 89 matched cddid_all.tbl CDD pfam18897 pfam18897 408667 Gp3-like Recombination directionality factor-like. This entry includes Gp3 from Streptomyces phage phiC31. Gp3 is a recombination directionality factor that interacts directly with the integrase tetramer to activate excision and inhibit integration. The characteriztics of the protein distribution suggest prophage matches in addition to the phage matches. 194 matched cddid_all.tbl CDD pfam18898 pfam18898 436816 DUF5654 Family of unknown function (DUF5654). This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 79 and 98 amino acids in length. The region contains two predicted transmembrane helices. The Eukaryotic examples are found in the Foraminiferan Reticulomyxa filosa that contains several proteins with this family.s 71 matched cddid_all.tbl CDD pfam18899 pfam18899 465903 DUF5655 Domain of unknown function (DUF5655). This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 122 and 304 amino acids in length. 110 matched cddid_all.tbl CDD pfam18900 pfam18900 436818 DUF5656 Protein of unknown function (DUF5656). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 237 and 274 amino acids in length. These proteins are likely to be integral membrane proteins. 242 matched cddid_all.tbl CDD pfam18901 pfam18901 408671 DUF5657 Family of unknown function (DUF5657). This family of small integral membrane proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 61 matched cddid_all.tbl CDD pfam18902 pfam18902 465904 DUF5658 Domain of unknown function (DUF5658). This family of proteins is found in bacteria, archaea and viruses. Proteins in this family are typically between 101 and 135 amino acids in length. There is a completely conserved aspartate and a conserved EXNP motif that may be functionally important. 82 matched cddid_all.tbl CDD pfam18903 pfam18903 408673 DUF5659 Domain of unknown function (DUF5659). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 78 and 90 amino acids in length. 75 matched cddid_all.tbl CDD pfam18904 pfam18904 408674 DUF5660 Domain of unknown function (DUF5660). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and fungi, and is approximately 110 amino acids in length. 109 matched cddid_all.tbl CDD pfam18905 pfam18905 408675 DUF5661 Protein of unknown function (DUF5661). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea and viruses. Proteins in this family are typically between 89 and 148 amino acids in length. 71 matched cddid_all.tbl CDD pfam18906 pfam18906 436820 Phage_tube_2 Phage tail tube protein. This family of proteins are tube proteins which polymerize to form the phage tails. 287 matched cddid_all.tbl CDD pfam18907 pfam18907 436821 DUF5662 Family of unknown function (DUF5662). This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 175 and 193 amino acids in length. Many proteins in this family are annotated as catalase, but this could not be verified. 157 matched cddid_all.tbl CDD pfam18908 pfam18908 408678 DUF5663 Protein of unknown function (DUF5663). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 102 and 113 amino acids in length. 86 matched cddid_all.tbl CDD pfam18909 pfam18909 465905 dGTP_diPhyd_N dATP/dGTP diphosphohydrolase, N-terminal. This entry represent the N-terminal region of SHab15497_00040, an Acinetobacter phage protein that catalyzes the hydrolysis of dGTP into dGMP, which is needed among others for the first step of biosynthesis of dZTP (2-amino-2'-deoxyadenosine-5'- triphosphate). 99 matched cddid_all.tbl CDD pfam18910 pfam18910 436823 DUF5665 Domain of unknown function (DUF5665). This entry represents a functionally uncharacterized family of integral membrane proteins. This protein family is found in bacteria, and is approximately 60 amino acids in length. There are several conserved glycines in the first transmembrane helix that may be functionally important. 56 matched cddid_all.tbl CDD pfam18911 pfam18911 436824 PKD_4 PKD domain. This entry is composed of PKD domains found in bacterial surface proteins. 85 matched cddid_all.tbl CDD pfam18912 pfam18912 465906 DZR_2 Double zinc ribbon domain. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 60 amino acids in length. The family is found in association with pfam00156. This entry corresponds to two zinc ribbon motifs. This domain is found at the N-terminus of the ComF operon protein 3. 56 matched cddid_all.tbl CDD pfam18913 pfam18913 436826 FBPase_C Fructose-1-6-bisphosphatase, C-terminal domain. This entry represents the C-terminal domain of Fructose-1-6-bisphosphatase enzymes. According to ECOD this domain has a Rossmann-like fold. 125 matched cddid_all.tbl CDD pfam18914 pfam18914 465907 DUF5666 Domain of unknown function (DUF5666). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and archaea, and is approximately 60 amino acids in length. This domain is likely to adopt an OB-fold based on similarity to other families. 60 matched cddid_all.tbl CDD pfam18915 pfam18915 436828 DUF5667 Domain of unknown function (DUF5667). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and archaea, and is typically between 95 and 113 amino acids in length. 102 matched cddid_all.tbl CDD pfam18916 pfam18916 465908 Lycopene_cyc Lycopene cyclase. 92 matched cddid_all.tbl CDD pfam18917 pfam18917 465909 DUF5668 Domain of unknown function (DUF5668). This entry is composed of two transmembrane helices that are often found in 2 or three copies in a protein. The members of this family are functionally uncharacterized. This domain family is found in bacteria and archaea, and is approximately 40 amino acids in length. This entry is often associated with pfam09922 a putative adhesive domain that adopts a beta helix fold. 42 matched cddid_all.tbl CDD pfam18918 pfam18918 465910 DUF5669 Family of unknown function (DUF5669). This is a family of unknown function. Family members are mostly found in gammaproteobacteria. 76 matched cddid_all.tbl CDD pfam18919 pfam18919 465911 DUF5670 Family of unknown function (DUF5670). This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 50 amino acids in length. There is a single completely conserved residue W that may be functionally important. These proteins contain two transmembrane helices. 43 matched cddid_all.tbl CDD pfam18920 pfam18920 436833 DUF5671 Domain of unknown function (DUF5671). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 168 and 339 amino acids in length. These proteins are likely to be integral membrane proteins. 132 matched cddid_all.tbl CDD pfam18921 pfam18921 465912 Cyanophycin_syn Cyanophycin synthase-like N-terminal domain. This domain is found at the N-terminus of cyanophycin synthase proteins and related enzymes from bacteria and archaea. It is approximately 120 amino acids in length. The family is found in association with pfam08245, pfam02875. This domain is found in isolation in some proteins. 115 matched cddid_all.tbl CDD pfam18922 pfam18922 465913 DUF5672 Protein of unknown function (DUF5672). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 260 and 408 amino acids in length. This entry corresponds to a region of about 200 amino acids in length with multiple conserved motifs. There are two conserved sequence motifs: GAP and NGG. In some proteins this domain is found associated with various glycosyl transferase enzyme domains, suggesting this domain has a related role in glycan biosynthesis. 164 matched cddid_all.tbl CDD pfam18923 pfam18923 465914 DUF5673 Domain of unknown function (DUF5673). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and archaea, and is approximately 90 amino acids in length. The domain is usually found C-terminal to a pair of transmembrane helices. 66 matched cddid_all.tbl CDD pfam18924 pfam18924 408694 DUF5674 Protein of unknown function (DUF5674). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 110 amino acids in length. 109 matched cddid_all.tbl CDD pfam18925 pfam18925 465915 DUF5675 Family of unknown function (DUF5675). This presumed domain is found in bacteria, archaea, alveolata and caudoviruses. Proteins in this family are typically between 133 and 179 amino acids in length. 113 matched cddid_all.tbl CDD pfam18926 pfam18926 436837 DUF5676 2TM family of unknown function (DUF5676). This family of presumed integral membrane proteins is found in bacteria and archaea. Proteins in this family are approximately 90 amino acids in length and contain two predicted transmembrane helices. 82 matched cddid_all.tbl CDD pfam18927 pfam18927 436838 CrtO Glycosyl-4,4'-diaponeurosporenoate acyltransferase. This family of proteins is found in certain bacterial lineages. In staphylococcus this protein is known to be Glycosyl-4,4'-diaponeurosporenoate acyltransferase an enzyme involved in the final step of synthesis of staphyloxanthin, an orange pigment found in most S. aureus strains. Proteins in this family are typically between 157 and 184 amino acids in length. Members of the family contain and EXXH motif that may be functionally important. 120 matched cddid_all.tbl CDD pfam18928 pfam18928 465916 DUF5677 Family of unknown function (DUF5677). This family of proteins is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 250 and 347 amino acids in length. These proteins contain a conserved RXXXE motif an invariant Histidine that may be functionally important. 163 matched cddid_all.tbl CDD pfam18929 pfam18929 408699 DUF5678 Family of unknown function (DUF5678). This presumed domain family is found in bacteria and archaea. Proteins in this family are typically between 64 and 76 amino acids in length. 50 matched cddid_all.tbl CDD pfam18930 pfam18930 408700 DUF5679 Domain of unknown function (DUF5679). This family of domains is found in bacteria, archaea, eukaryotes and viruses. Proteins in this family are typically between 48 and 68 amino acids in length. These domains contain four conserved cysteines suggesting that this domain is zinc binding 40 matched cddid_all.tbl CDD pfam18931 pfam18931 408701 DUF5680 Domain of unknown function (DUF5680). This family of presumed domains is found in bacteria and archaea. Proteins in this family are typically between 152 and 220 amino acids in length. In some of the proteins this domain is associated with an N-terminal HTH domain, suggesting that they are transcriptional regulators. This suggests that this may be a previously unidentified ligand binding domain. 104 matched cddid_all.tbl CDD pfam18932 pfam18932 465917 DUF5681 Family of unknown function (DUF5681). This domain family is found in bacteria, archaea and viruses, and is typically between 75 and 86 amino acids in length. There is a conserved SGNP sequence motif. There are two completely conserved G residues that may be functionally important. 77 matched cddid_all.tbl CDD pfam18933 pfam18933 408703 PsbP_2 PsbP-like protein. This family is related to the PsbP family. 184 matched cddid_all.tbl CDD pfam18934 pfam18934 436841 DUF5682 Family of unknown function (DUF5682). This is a family of unknown function, mostly found in bacteria. 728 matched cddid_all.tbl CDD pfam18935 pfam18935 465918 DUF5683 Family of unknown function (DUF5683). This is a domain of unknown function found mostly in bacteria. 151 matched cddid_all.tbl CDD pfam18936 pfam18936 465919 DUF5684 Family of unknown function (DUF5684). This is a family of unknown function mostly found in bacteria. Some family members can be found at the N-terminal region of pfam00717. 80 matched cddid_all.tbl CDD pfam18937 pfam18937 465920 DUF5685 Family of unknown function (DUF5685). This is a family of unknown function mostly found in bacteria. 271 matched cddid_all.tbl CDD pfam18938 pfam18938 465921 aRib Atypical Rib domain. This entry contains atypical Rib (aRib) domains. These are found in a variety of bacterial cell surface proteins. These proteins share a conserved motif with the Rib domain (YPDXXD). The structure of the aRib domain has been solved from two proteins, the SrpA adhesin and the GspB adhesin. In these proteins this domain has been termed the unique domain due to its lack of similarity to any other known structures at the time. The aRib domain from SrpA has been shown to mediate a dimer interaction. This family has been added to the E-set clan based on its similarity to the Rib domain, although it does not contain the Ig fold. 71 matched cddid_all.tbl CDD pfam18939 pfam18939 465922 DUF5686 Family of unknown function (DUF5686). This is a family of unknown function, mostly found in bacteria. Family members can be found at the C-terminal region of pfam13715. 667 matched cddid_all.tbl CDD pfam18940 pfam18940 465923 DUF5687 Family of unknown function (DUF5687). This is a family of unknown function mainly found in bacteria. 484 matched cddid_all.tbl CDD pfam18941 pfam18941 436848 DUF5688 Family of unknown function (DUF5688). This is a family of unknown function found in bacteria. 290 matched cddid_all.tbl CDD pfam18942 pfam18942 465924 DUF5689 Family of unknown function (DUF5689). This is a domain of unknown function. It is mostly found in bacteria and can be present in multiple copies. 219 matched cddid_all.tbl CDD pfam18943 pfam18943 465925 DUF5690 Family of unknown function (DUF5690). This is a family of unknown function mostly found in bacteria. 382 matched cddid_all.tbl CDD pfam18944 pfam18944 465926 DUF5691 Family of unknown function (DUF5691). This is a family of unknown function. Some family members overlap with pfam13646. 208 matched cddid_all.tbl CDD pfam18945 pfam18945 436852 VipB_2 EvpB/VC_A0108, tail sheath gpW/gp25-like domain. EvpB is a family of Gram-negative probable type VI secretion system components of the tail sheath. They have been known as COG:COG3517. These sheath-components, of which there are many copies in the sheath, are also variously referred to as VipA/VipB and TssB/TssC. On contact with another bacterial cell the sheath contracts and pushes the puncturing device and tube through the cell envelope and punches the target bacterial cell. This entry represents the gpW/gp25-like domain. 111 matched cddid_all.tbl CDD pfam18946 pfam18946 436853 Apex GpV Apex motif. This entry represents a short motif found at the C-terminus of Phage gpV proteins. These proteins act as a spike for piercing the host membrane. The apex motif contains a conserved HXH motif that coordinates an iron ion. 23 matched cddid_all.tbl CDD pfam18947 pfam18947 465927 HAMP_2 HAMP domain. 67 matched cddid_all.tbl CDD pfam18948 pfam18948 436855 DUF5692 Family of unknown function (DUF5692). This is a family of unknown function mostly found in bacteria. 304 matched cddid_all.tbl CDD pfam18949 pfam18949 465928 DUF5693 Family of unknown function (DUF5693). This is a family of unknown function found in bacteria. 611 matched cddid_all.tbl CDD pfam18950 pfam18950 465929 DUF5694 Family of unknown function (DUF5694). This is a family of unknown function, mostly found in bacteria. 185 matched cddid_all.tbl CDD pfam18951 pfam18951 465930 DUF5695 Family of unknown function (DUF5695). This is a family of unknown function mainly found in fungi and bacteria. 858 matched cddid_all.tbl CDD pfam18952 pfam18952 436859 DUF5696 Family of unknown function (DUF5696). This is a family of unknown function with some overlap with clan family members of CL0058. 613 matched cddid_all.tbl CDD pfam18953 pfam18953 465931 SAP_new25 SAP domain-containing new25. This family includes Schizosaccharomyces specific SAP domain containing proteins such as gene product new25. SAP ( SAF-A/B, Acinus and PIAS) motif is a DNA/RNA binding domain found in diverse nuclear and cytoplasmic proteins. For instance, the SAP domain of SUMO E3 ligase PIAS1 from human is shown to bind an A/T-rich DNA. 51 matched cddid_all.tbl CDD pfam18954 pfam18954 436861 DUF5697 Family of unknown function (DUF5697). This entry likely contains an N-terminal Helix-tun-helix motif and is therefore likely to be a transcriptional regulator. 161 matched cddid_all.tbl CDD pfam18955 pfam18955 436862 DUF5698 Domain of unknown function (DUF5698). This family is functionally uncharacterized. This family family is found in bacteria and archaea, and is approximately 60 amino acids in length and contains two probable transmembrane helices. This entry is found in association with pfam10035. The C-terminal transmembrane helix contains a GXXXGXXXG motif that is characteriztic of transmembrane helices that dimerize. 58 matched cddid_all.tbl CDD pfam18956 pfam18956 436863 DUF5699 Family of unknown function (DUF5699). 61 matched cddid_all.tbl CDD pfam18957 pfam18957 436864 RibLong Long Rib domain. This entry represents the Long Rib domain that is closely related to the pfam08428 Rib domain but has a conserved insertion. These domains are found in bacterial cell surface proteins. 92 matched cddid_all.tbl CDD pfam18958 pfam18958 436865 DUF5700 Putative zinc dependent peptidase (DUF5700). This entry represents a group of putative zinc dependent peptidases that have the characteriztic HEXXH motif. This family is most related to pfam10026. 279 matched cddid_all.tbl CDD pfam18959 pfam18959 465932 DUF5701 Family of unknown function (DUF5701). This is a family of unknown function mostly found in bacteria. 192 matched cddid_all.tbl CDD pfam18960 pfam18960 436867 DUF5702 Family of unknown function (DUF5702). This family is mostly found in bacteria. 278 matched cddid_all.tbl CDD pfam18961 pfam18961 465933 DUF5703_N Domain of unknown function (DUF5703). This is an N-terminal domain of unknown function mostly found in bacteria. It is possible that this domain might be a putative glycoside hydrolase. This family belongs to the Galactose Mutarotase-like superfamily. 287 matched cddid_all.tbl CDD pfam18962 pfam18962 436869 Por_Secre_tail Secretion system C-terminal sorting domain. Species that include Porphyromonas gingivalis, Fibrobacter succinogenes, Flavobacterium johnsoniae, Cytophaga hutchinsonii, Gramella forsetii, Prevotella intermedia, and Salinibacter ruber have on average twenty or more copies of this C-terminal domain, associated with sorting to the outer membrane and covalent modification. This domain targets proteins to type IX secretion systems and is secreted then cleaved off by a C-terminal signal peptidease. Based on similarity to other families it is likely that this domain adopts an immunoglobulin like fold. 75 matched cddid_all.tbl CDD pfam18963 pfam18963 436870 DUF5703 Family of unknown function (DUF5703). This family includes members mostly found in Actinobacteria. Some family members are thought to be dihydroorotate dehydrogenases, however there is no evidence to support the relationship to pfam01180. 51 matched cddid_all.tbl CDD pfam18964 pfam18964 436871 DUF5704 Family of unknown function (DUF5704). This entry is mainly found in Firmicutes and has a notable number of highly conserved aromatic amino acids. The entry is found towards the C-terminus of pfam02368 in some of the members and there are members that present two copies. 185 matched cddid_all.tbl CDD pfam18965 pfam18965 408735 VP3-like Outer capsid protein VP3-like. This entry represents a group of Reoviridae proteins, including outer capsid protein VP3 from Cryphonectria parasitica mycoreovirus 1. 1052 matched cddid_all.tbl CDD pfam18966 pfam18966 436872 Lipoprotein_23 Uncharacterized lipoprotein. This entry includes members found in Actinobacteria (mostly streptomycetaceae, micromonosporales and pseudonocardiales). Some members are annotated as lipoproteins. 179 matched cddid_all.tbl CDD pfam18967 pfam18967 465934 DUF5706 Family of unknown function (DUF5706). 107 matched cddid_all.tbl CDD pfam18968 pfam18968 436874 DUF5707 Family of unknown function (DUF5707). 98 matched cddid_all.tbl CDD pfam18969 pfam18969 436875 DUF5708 Family of unknown function (DUF5708). This family includes members in Actinobacteria. All family members present double transmembrane. 60 matched cddid_all.tbl CDD pfam18970 pfam18970 465935 DUF5709 Family of unknown function (DUF5709). 49 matched cddid_all.tbl CDD pfam18971 pfam18971 408741 CagA_N CagA protein. The Helicobacter pylori type IV secretion effector CagA is a major bacterial virulence determinant and critical for gastric carcinogenesis. X-ray crystallographic analysis of the N-terminal CagA fragment (residues 1-876) revealed that the region has a structure comprised of three discrete domains. Domain I constitutes a mobile CagA N terminus, while Domain II tethers CagA to the plasma membrane by interacting with membrane phosphatidylserine. Domain III interacts intramolecularly with the intrinsically disordered C-terminal region, and this interaction potentiates the pathogenic scaffold/hub function of CagA. 876 matched cddid_all.tbl CDD pfam18972 pfam18972 436877 Wheel Cns1/TTC4 Wheel domain. The wheel domain is found at the C-terminus of yeast Cns1 and human TTC4 proteins. The structure of the domain shows an overall fold consisting of a twisted five-stranded beta sheet surrounded by several alpha helices. The Hsp90 chaperone machinery in eukaryotes comprises a number of distinct accessory factors. Cns1 is one of the few essential co-chaperones in yeast. Cns1 is important for maintaining translation elongation, specifically chaperoning the elongation factor eEF2. In this context, Cns1 interacts with the novel co-factor Hgh1 and forms a quaternary complex together with eEF2 and Hsp90. 114 matched cddid_all.tbl CDD pfam18973 pfam18973 408743 CBL Putative Chitin binding like. This family includes host-selective toxins such as SnTox1 found in S. nodorum. SnTox1 is a necrotrophic effector contains 6 cysteine residues, a common feature for some fungal avirulence effectors such as the Avr and ECP effectors from Cladosporium fulvum. The high content of cysteine residues and high stability suggest that SnTox1 may function in the plant apoplastic space which is abundant in plant defense components. Protein sequence analysis indicate that SnTox1 contains a C-terminal chitin binding (CB) like motif. Three-dimensional (3D) structure-based sequence alignment suggested that the putative CB motif in SnTox1 was more similar to those of plant-specific ChtBDs than to Avr4 proteins, which are related to invertebrate ChtBDs. Furthermore, SnTox1 contained all secondary-structure-related residues including the strictly conserved b-strand-forming 'CCS' motif found only in plant-specific ChtBD1 proteins. 48 matched cddid_all.tbl CDD pfam18974 pfam18974 436878 DUF5710 Domain of unknown function (DUF5710). This is a domain of unknown function which can be found in DNA primases such as TraC. 44 matched cddid_all.tbl CDD pfam18975 pfam18975 465936 DUF5711 Family of unknown function (DUF5711). This is a family of unknown function mostly found in bacteria and archea. Some members contain WD repeats. 344 matched cddid_all.tbl CDD pfam18976 pfam18976 465937 DUF5712 Family of unknown function (DUF5712). This is a family of unknown function mainly found in Bacteroidetes. 292 matched cddid_all.tbl CDD pfam18977 pfam18977 436881 DUF5713 Family of unknown function (DUF5713). This is a family of unknown function, mainly found in bacteria. 107 matched cddid_all.tbl CDD pfam18978 pfam18978 465938 DUF5714 Family of unknown function (DUF5714). This is a family of unknown function, mainly found in bacteria. It is distantly related to Pfam family pfam09719, which is a heme binding cytochrome. This domain is found associated with other domains such as the Radical SAM domain and a methyltransferase. 173 matched cddid_all.tbl CDD pfam18979 pfam18979 436883 DUF5715 Family of unknown function (DUF5715). This is a family of unknown function, mainly found in bacteria. 170 matched cddid_all.tbl CDD pfam18980 pfam18980 465939 DUF5716_C Family of unknown function (DUF5716) C-terminal. This is a C-terminal domain found in bacterial sequences of unknown function. 295 matched cddid_all.tbl CDD pfam18981 pfam18981 408751 InlK_D3 Internalin K domain (D3/D4). This domain is found at the elbow of internalin surface proteins, used by the bacteria to invade mammalian cells. This domain has an Ig-like fold. 75 matched cddid_all.tbl CDD pfam18982 pfam18982 465940 DUF5716 Family of unknown function (DUF5716). This is a family of unknown function, mostly found in bacteria. 433 matched cddid_all.tbl CDD pfam18983 pfam18983 436886 DUF5717 Family of unknown function (DUF5717)C-terminal. This is a C-terminal domain of a family of unknown function found in bacteria. 306 matched cddid_all.tbl CDD pfam18984 pfam18984 436887 DUF5717_N Family of unknown function (DUF5717)N-terminal. This is the N-terminal domain found in sequences of unknown function in bacteria. 875 matched cddid_all.tbl CDD pfam18985 pfam18985 465941 DUF5718 Family of unknown function (DUF5718). This is a family of unknown function, mostly found in bacteria. 250 matched cddid_all.tbl CDD pfam18986 pfam18986 465942 DUF5719 Family of unknown function (DUF5719). This is a family of unknown function, mostly found in bacteria. 319 matched cddid_all.tbl CDD pfam18987 pfam18987 408757 DUF5720 Family of unknown function (DUF5720). This is a family of unknown function, mostly found in bacteria. 100 matched cddid_all.tbl CDD pfam18988 pfam18988 436890 DUF5721 Family of unknown function (DUF5721). This is a family of unknown function, mostly found in Firmicutes. 149 matched cddid_all.tbl CDD pfam18989 pfam18989 436891 DUF5722 Family of unknown function (DUF5722). This is a family of unknown function mainly found in bacteria. 394 matched cddid_all.tbl CDD pfam18990 pfam18990 465943 DUF5723 Family of unknown function (DUF5723). This is a family of unknown function mainly found in bacteria. 378 matched cddid_all.tbl CDD pfam18991 pfam18991 436893 DUF5724 Family of unknown function (DUF5724). This is a family of unknown function mainly found in bacteria. 342 matched cddid_all.tbl CDD pfam18992 pfam18992 436894 DUF5725 Family of unknown function (DUF5725). A highly conserved domain of unknown function found in Platyhelminthes. 158 matched cddid_all.tbl CDD pfam18993 pfam18993 436895 Rv0078B Rv0078B-related antitoxin. Putative antitoxin protein according to TASmania database. 63 matched cddid_all.tbl CDD pfam18994 pfam18994 436896 Prophage_tailD1 Prophage endopeptidase tail N-terminal domain. This domain represents the N-terminal domain of prophage tail proteins that are probably acting as endopeptidases. This domain has a RIFT related fold. 84 matched cddid_all.tbl CDD pfam18995 pfam18995 465944 PRT6_C Proteolysis_6 C-terminal. This is the C-terminal domain mainly found in E3 ubiquitin ligases. Proteolysis 6 (PRT6) encodes a ubiquitin E3 ligase belonging to the N-end rule pathway of targeted protein degradation, which is a specialized subset of the ubiquitin proteasome system. In Arabidopsis, at least two N-recognins (E3 ubiquitin ligases) with different substrate specificities exist, namely PROTEOLYSIS1 (PRT1) and PRT6. 444 matched cddid_all.tbl CDD pfam18996 pfam18996 408766 DUF5726 Family of unknown function (DUF5726). This family is found in various Platyhelminthes, with many of the sequences annotated as being the polyprotein of the transposon Ty3-I Gag-Pol. However, the genomic location of other members suggests that this region is not always found in a transposon. The family members are characterized by a highly conserved DxDxDxCC motif. The function of this family is currently unknown. 90 matched cddid_all.tbl CDD pfam18997 pfam18997 408767 DUF5727 Family of unknown function (DUF5727). A conserved domain of unknown function found in Platyhelminthes, closely related to glycosylphosphatidylinositol (GPI)-anchored protein GP50, known as Diagnostic antigen GP50. GP50 is a family of highly expressed antigens exclusive to tapeworms. 192 matched cddid_all.tbl CDD pfam18998 pfam18998 436898 Flg_new_2 Divergent InlB B-repeat domain. This family of domains are found in bacterial cell surface proteins. They are often found in tandem array. This domain is closely related to pfam09479. 74 matched cddid_all.tbl CDD pfam18999 pfam18999 408769 DUF5728 Family of unknown function (DUF5728). This is a highly conserved domain of unknown function found in Platyhelminthes, with many of the sequences annotated as being the small conductance calcium-activated potassium channel protein. However, the location suggests that this domain belongs to the intracellular amino terminus of these transmembrane proteins, immediately next to the calcium-activated SK potassium channel. 188 matched cddid_all.tbl CDD pfam19000 pfam19000 408770 DUF5729 Family of unknown function (DUF5729). This is a highly conserved domain of unknown function found in Platyhelminthes, with many of the sequences annotated as being the small conductance calcium-activated potassium channel protein. However, the location suggests that this domain belongs to the intracellular amino terminus of these transmembrane proteins, near the calcium-activated SK potassium channel. 141 matched cddid_all.tbl CDD pfam19001 pfam19001 408771 DUF5730 Family of unknown function (DUF5730). A highly conserved domain of unknown function found in Platyhelminthes, in which the first 21 residues correspond to a transmembrane domain. 182 matched cddid_all.tbl CDD pfam19002 pfam19002 408772 DUF5731 Family of unknown function (DUF5731). A highly conserved domain of unknown function found in Platyhelminthes. 108 matched cddid_all.tbl CDD pfam19003 pfam19003 436899 DUF5732 Family of unknown function (DUF5732). This family is found in various Platyhelminthes, with many of the sequences annotated as being the STARP-like antigen. This highly conserved domain is located next to the basic helix-loop-helix motif found in this antigen. The function of this family is currently unknown. 85 matched cddid_all.tbl CDD pfam19004 pfam19004 408774 DUF5733 Family of unknown function (DUF5733). A highly conserved domain of unknown function found in Platyhelminthes. 115 matched cddid_all.tbl CDD pfam19005 pfam19005 408775 DUF5734 Family of unknown function (DUF5734). This is a conserved domain found in various Platyhelminthes. The function of this family is still unknown. 83 matched cddid_all.tbl CDD pfam19006 pfam19006 408776 DUF5735 Family of unknown function (DUF5735). A highly conserved domain of unknown function found in different Platyhelminthes. 138 matched cddid_all.tbl CDD pfam19007 pfam19007 408777 DUF5736 Family of unknown function (DUF5736). A highly conserved domain of unknown function found in various Platyhelminthes. 111 matched cddid_all.tbl CDD pfam19008 pfam19008 408778 DUF5737 Family of unknown function (DUF5737). A highly conserved domain of unknown function found in various Platyhelminthes. 99 matched cddid_all.tbl CDD pfam19009 pfam19009 408779 DUF5738 Family of unknown function (DUF5738). A highly conserved domain of unknown function found in various Platyhelminthes. 104 matched cddid_all.tbl CDD pfam19010 pfam19010 408780 DUF5739 Family of unknown function (DUF5739). A highly conserved domain of unknown function found in various Platyhelminthes. 114 matched cddid_all.tbl CDD pfam19011 pfam19011 408781 DUF5740 Family of unknown function (DUF5740). This family is found in various Platyhelminthes, with many of the sequences annotated as being part of death domain-containing proteins. This highly conserved domain is located at the amino terminus. The function of this family is currently unknown. 94 matched cddid_all.tbl CDD pfam19012 pfam19012 408782 DUF5741 Family of unknown function (DUF5741). This coiled-coil is found in various Platyhelminthes, with many of the sequences annotated as being uveal autoantigen with coiled-coil. This region is one of the numerous coiled-coil regions which constitutes this antigen. The function is currently unknown. 82 matched cddid_all.tbl CDD pfam19013 pfam19013 408783 DUF5742 Family of unknown function (DUF5742). A highly conserved domain of unknown function found in various Platyhelminthes. 111 matched cddid_all.tbl CDD pfam19014 pfam19014 408784 DUF5743 Family of unknown function (DUF5743). A highly conserved domain of unknown function found in various Platyhelminthes. 186 matched cddid_all.tbl CDD pfam19015 pfam19015 408785 DUF5744 Family of unknown function (DUF5744). This is a highly conserved domain found in various Platyhelminthes. Its function is currently unknown. 81 matched cddid_all.tbl CDD pfam19016 pfam19016 465945 DUF5745 Domain of unknown function (DUF5745). This is a domain of unknown function found in Platyhelminthes. It shows homology with the calponin homology (CH) domain. 59 matched cddid_all.tbl CDD pfam19017 pfam19017 436901 DUF5746 Domain of unknown function (DUF5746). This is a highly conserved domain found in various Platyhelminthes. Its function is currently unknown, with some of the sequences annotated as being Palmitoyltransferase. This highly conserved domain is located at the amino terminus, next to a DHHC domain (named for its signature tetrapeptide Asp-His-His-Cys). 175 matched cddid_all.tbl CDD pfam19018 pfam19018 465946 Vanin_C Vanin C-terminal domain. This domain is found at the C terminus of Vanin 1 and related proteins. 165 matched cddid_all.tbl CDD pfam19019 pfam19019 408789 Phlebo_G2_C Phlebovirus glycoprotein G2 C-terminal domain. This family consists of several Phlebovirus glycoprotein G2 C-terminal Ig-like domains. 171 matched cddid_all.tbl CDD pfam19020 pfam19020 436903 Ta1207 Ta1207 family. The function of this family is unknown. The protein forms a homopentameric complex in T. acidophilum. Each protein is composed of two structurally similar domains. 277 matched cddid_all.tbl CDD pfam19021 pfam19021 408791 Cmr7A "CRISPR system CMR subunit Cmr7 1. The CRISPR-Cas system is a prokaryotic defense mechanism against foreign genetic elements. The key elements of this defense system are the Cas proteins and the CRISPR RNA. In the CRISPR-Cas system, RNA is targeted by the CMR complex. In Sulfolobus solfataricus this complex is composed of seven CAS protein subunits (Cmr1-7) and carries a diverse ""payload"" of targeting crRNA. This entry represent the Cmr7 subunit of the CMR complex." 197 matched cddid_all.tbl CDD pfam19022 pfam19022 465947 DUF5748 Family of unknown function (DUF5748). The function of this family of euryarchaeal proteins is unknown. 101 matched cddid_all.tbl CDD pfam19023 pfam19023 408793 DUF5749 Family of unknown function (DUF5749). The function of this family of euryarchaeal proteins is unknown. The structure of this protein forms a beta barrel. 78 matched cddid_all.tbl CDD pfam19024 pfam19024 436905 DUF5750 Family of unknown function (DUF5750). The function of this family of proteins is unknown. 91 matched cddid_all.tbl CDD pfam19025 pfam19025 436906 DUF5751 Family of unknown function (DUF5751). The function of this archaeal family is unknown. 116 matched cddid_all.tbl CDD pfam19026 pfam19026 436907 HYPK_UBA HYPK UBA domain. This entry represents the UBA domain found at the C-terminus of the HYPK protein and its homologs. This domain in HYPK mediates a protein interaction with the Naa15 C-terminus. 41 matched cddid_all.tbl CDD pfam19027 pfam19027 436908 DUF5752 Family of unknown function (DUF5752). This family includes the OrfY protein from the hyperthermophilic archaeum Thermoproteus tenax. This protein co-occurs with the treS/P protein in an operon regulating the synthesis of trehalose. The structure of this protein shows it contains an internal duplication. 208 matched cddid_all.tbl CDD pfam19028 pfam19028 465948 TSP1_spondin Spondin-like TSP1 domain. This entry represents a sub-type of TSP1 domains that have an alternative disulphide binding pattern compared to the canonical TSP1 domain. 52 matched cddid_all.tbl CDD pfam19029 pfam19029 465949 DUF883_C DUF883 C-terminal glycine zipper region. This family corresponds to the C-terminal presumed transmembrane helix found in DUF883 proteins. The helix contains a glycine zipper motif suggestive of dimerization. 30 matched cddid_all.tbl CDD pfam19030 pfam19030 465950 TSP1_ADAMTS Thrombospondin type 1 domain. This subfamily of thrombospondin type 1 repeats are mainly found in ADAMTS proteins. 55 matched cddid_all.tbl CDD pfam19031 pfam19031 436911 Intu_longin_1 First Longin domain of INTU, CCZ1 and HPS4. This entry is specific to the first Longin domain of the HerMon (Hermansky-Pudlak syndrome and MON1/CCZ1) family, including protein sequences of INTU, CCZ1 and HPS4 families. The Mon1/Ccz1 complex (MC1) is the GDP/GTP exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 during vesicular trafficking. The Hps1/Hps4 complex (BLOC-3) is a Rab32 and Rab38 GEF and is required for biogenesis of melanosomes and platelet dense granules. Inturned (INTU) and Fuzzy (FUZ) proteins interact as members of the ciliogenesis and planar polarity effector (CPLANE) complex that controls recruitment of intraflagellar transport machinery to the basal body of primary cilia. 112 matched cddid_all.tbl CDD pfam19032 pfam19032 465951 Intu_longin_2 Intu longin-like domain 2. This entry represents a longin-like domain found in Intu and related proteins. 120 matched cddid_all.tbl CDD pfam19033 pfam19033 436913 Intu_longin_3 Intu longin-like domain 3. This entry represents a longin-like domain found in Intu and related proteins. 98 matched cddid_all.tbl CDD pfam19034 pfam19034 408804 RnlA-toxin_DBD RNase LS, bacterial toxin DBD domain. RnlA toxin is an RNase LS and a putative toxin of a bacterial toxin-antitoxin pair. Toxin-antitoxin systems consist of a stable toxin and an unstable antitoxin. In this case, a novel type II system, RnlA is the stable toxin that causes inhibition of cell growth and rapidly degrades T4 late mRNAs to prevent their expression, and this is neutralized by the activity of the unstable antitoxin RnlB. This entry represents the C-terminal DBD domain, responsible for the RNA cleavage activity and toxicity. Through interaction between DBDs, RnlA dimerizes in solution. T4 Dmd binds to DBD for inhibition of RnlA toxicity and RnlB also inhibits the toxicity of DBD. 125 matched cddid_all.tbl CDD pfam19035 pfam19035 465952 TSP1_CCN CCN3 Nov like TSP1 domain. This entry represents a sub-type of TSP1 domains found in matricellular CCN proteins that have an alternative disulphide binding pattern compared to the canonical TSP1 domains. 44 matched cddid_all.tbl CDD pfam19036 pfam19036 465953 Fuz_longin_1 First Longin domain of FUZ, MON1 and HPS1. This entry is specific to the first Longin domain of the HerMon (Hermansky-Pudlak syndrome and MON1-CCZ1) family, including protein sequences of FUZ, MON1 and HPS1 families. The Mon1/Ccz1 complex (MC1) is the GDP/GTP exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 during vesicular trafficking. The Hps1/Hps4 complex (BLOC-3) is a Rab32 and Rab38 GEF and is required for biogenesis of melanosomes and platelet dense granules. Inturned (INTU) and Fuzzy (FUZ) proteins interact as members of the ciliogenesis and planar polarity effector (CPLANE) complex that controls recruitment of intraflagellar transport machinery to the basal body of primary cilia. 125 matched cddid_all.tbl CDD pfam19037 pfam19037 465954 Fuz_longin_2 Second Longin domain of FUZ, MON1 and HPS1. This entry represents a longin-like domain found in Fuz and related proteins. This entry is specific to the second Longin domain of the HerMon (Hermansky-Pudlak syndrome and MON1-CCZ1) family, including protein sequences of FUZ, MON1 and HPS1 families. The Mon1/Ccz1 complex (MC1) is the GDP/GTP exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 during vesicular trafficking. The Hps1/Hps4 complex (BLOC-3) is a Rab32 and Rab38 GEF and is required for biogenesis of melanosomes and platelet dense granules. Inturned (INTU) and Fuzzy (FUZ) proteins interact as members of the ciliogenesis and planar polarity effector (CPLANE) complex that controls recruitment of intraflagellar transport machinery to the basal body of primary cilia. 98 matched cddid_all.tbl CDD pfam19038 pfam19038 465955 Fuz_longin_3 Third Longin domain of FUZ, MON1 and HPS1. This entry represents a longin-like domain found in Fuz and related proteins. This entry is specific to the third Longin domain of the HerMon (Hermansky-Pudlak syndrome and MON1-CCZ1) family, including protein sequences of FUZ, MON1 and HPS1 families. The Mon1/Ccz1 complex (MC1) is the GDP/GTP exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 during vesicular trafficking. The Hps1/Hps4 complex (BLOC-3) is a Rab32 and Rab38 GEF and is required for biogenesis of melanosomes and platelet dense granules. Inturned (INTU) and Fuzzy (FUZ) proteins interact as members of the ciliogenesis and planar polarity effector (CPLANE) complex that controls recruitment of intraflagellar transport machinery to the basal body of primary cilia. 103 matched cddid_all.tbl CDD pfam19039 pfam19039 465956 ASK_PH ASK kinase PH domain. This PH-like domain is found in the regulatory region of ASK1 and related kinase proteins. This domain is found adjacent to the kinase domain. 101 matched cddid_all.tbl CDD pfam19040 pfam19040 436916 SGNH SGNH domain (fused to AT3 domains). This entry include SGNH domains that are found fused to membrane domains from the AT3 families pfam01757. 245 matched cddid_all.tbl CDD pfam19041 pfam19041 408811 CBP30 Nuclear cap binding complex subunit CBP30. This entry represents the CBP30 component of the trypanasome nuclear cap binding complex. Trypanosomes have a different cap 4 structure for mRNAs. CBP30 is part of the complex that recognizes this cap. 299 matched cddid_all.tbl CDD pfam19042 pfam19042 408812 CBP110 Nuclear cap binding complex subunit CBP110. This entry represents the CBP110 component of the trypanasome nuclear cap binding complex. Trypanosomes have a different cap 4 structure for mRNAs. CBP110 is part of the complex that recognizes this cap. 987 matched cddid_all.tbl CDD pfam19043 pfam19043 408813 CBP66 Nuclear cap binding complex subunit CBP66. This entry represents the CBP66 component of the trypanasome nuclear cap binding complex. Trypanosomes have a different cap 4 structure for mRNAs. CBP66 is part of the complex that recognizes this cap. 583 matched cddid_all.tbl CDD pfam19044 pfam19044 436917 P-loop_TraG TraG P-loop domain. This entry represents the P-loop domain found in the TraG conjugation protein. 413 matched cddid_all.tbl CDD pfam19045 pfam19045 408815 Ligase_CoA_2 Ligase-CoA domain. This domain is related to pfam00549 and adopts a flavodoxin fold. 162 matched cddid_all.tbl CDD pfam19046 pfam19046 465957 GM130_C GM130 C-terminal binding motif. This entry represents the C-terminal motif from the GM130 protein that is bound by the GRASP65 PDZ domain pfam04495. 46 matched cddid_all.tbl CDD pfam19047 pfam19047 465958 HOOK_N HOOK domain. This domain is found at the N-terminus of HOOK proteins. 151 matched cddid_all.tbl CDD pfam19048 pfam19048 465959 SidE_mART SidE mono-ADP-ribosyltransferase domain. This domain found in the SidE bacterial effector protein mediates the mono-ADP-ribosylation of ubiquitin, which is then ligated to host proteins by the pfam12252 domain. 337 matched cddid_all.tbl CDD pfam19049 pfam19049 465960 SidE_DUB SidE DUB domain. This entry represents the N-terminal deubiquitinating domain from the SidE protein. The SidE protein is a bacterial effector protein that can ubiquitinate and presumably deubiquitinate host proteins. 173 matched cddid_all.tbl CDD pfam19050 pfam19050 408820 PhoD_2 PhoD related phosphatase. This entry contains a domain that is presumed to be a phosphatase enzyme based on its similarity to pfam09423. 543 matched cddid_all.tbl CDD pfam19051 pfam19051 436922 GFO_IDH_MocA_C2 Oxidoreductase family, C-terminal alpha/beta domain. This entry represents a domain found at the C-terminus of a variety of oxidoreductase enzymes. The domain is related to pfam02894. 254 matched cddid_all.tbl CDD pfam19052 pfam19052 465961 BRINP BMP/retinoic acid-inducible neural-specific protein. This entry represents the BMP/retinoic acid-inducible neural-specific protein (BRINP) family, including BRINP1/2/3. They are predominantly and widely expressed in both the central nervous system (CNS) and peripheral nervous system (PNS). They inhibit neuronal cell proliferation by negative regulation of the cell cycle G1/S transition. 448 matched cddid_all.tbl CDD pfam19053 pfam19053 436924 EccD EccD-like transmembrane domain. This entry represents an integral membrane component of the ESX type VII secretion systems, EccD. This region includes 11 predicted transmembrane alpha helices. 392 matched cddid_all.tbl CDD pfam19054 pfam19054 465962 DUF5753 Domain of unknown function (DUF5753). This entry represents a putative ligand binding domain found in bacterial transcription regulators that have an N-terminal HTH domain pfam13560. 178 matched cddid_all.tbl CDD pfam19055 pfam19055 465963 ABC2_membrane_7 ABC-2 type transporter. 409 matched cddid_all.tbl CDD pfam19056 pfam19056 465964 WD40_2 WD40 repeated domain. This entry contains an array of WD40 repeats found in RhoGEF proteins. 487 matched cddid_all.tbl CDD pfam19057 pfam19057 465965 PH_19 PH domain. This entry contains a PH domain found in RhoGEF proteins. 151 matched cddid_all.tbl CDD pfam19058 pfam19058 436929 DUF5754 Family of unknown function (DUF5754). This is a family of uncharacterized proteins of unknown function found in viruses. 49 matched cddid_all.tbl CDD pfam19059 pfam19059 408829 DUF5755 Family of unknown function (DUF5755). This family of unknown function appears to be primarily restricted to mimiviridae and phycodnaviridae. This entry may be found at the N terminus of longer proteins, which contain a C-terminal DNA polymerase family domain and a DNA polymerase family B exonuclease domain. 92 matched cddid_all.tbl CDD pfam19060 pfam19060 436930 DVNP DVNP family. Dinoflagellate viral nucleoprotein (DVNPs) are known to function in DNA packaging in Dinoflagellate as a histone replacement. It displaces nucleosomes when expressed in yeast. This family is predominantly found in Phycodnaviridae. 77 matched cddid_all.tbl CDD pfam19061 pfam19061 465966 DUF5757 Family of unknown function (DUF5757). This is a family of uncharacterized proteins of unknown function found in viruses. It is thought to be part of the early transcription factor large subunit. 96 matched cddid_all.tbl CDD pfam19062 pfam19062 436932 DUF5758 Family of unknown function (DUF5758). This is a family of uncharacterized proteins of unknown function found in viruses, as well as in bacteria. It is predicted to be a pentapeptide repeat-containing protein. 105 matched cddid_all.tbl CDD pfam19063 pfam19063 436933 DUF5759 Family of unknown function (DUF5759). This is a family of uncharacterized proteins of unknown function found in viruses. 71 matched cddid_all.tbl CDD pfam19064 pfam19064 436934 DUF5760 Family of unknown function (DUF5760). This is a family of uncharacterized proteins of unknown function found in Phycodnaviridae and Mimiviridae. 86 matched cddid_all.tbl CDD pfam19065 pfam19065 436935 DUF5761 Family of unknown function (DUF5761). This is a family of uncharacterized proteins of unknown function found in viruses. 62 matched cddid_all.tbl CDD pfam19066 pfam19066 436936 DUF5762 Family of unknown function (DUF5762). This is a family of uncharacterized proteins of unknown function found in viruses. It is inferred from homology to be a membrane-component. 69 matched cddid_all.tbl CDD pfam19067 pfam19067 436937 DUF5763 Family of unknown function (DUF5763). This is a family of uncharacterized proteins of unknown function found predominantly in viruses. However, some matches with predicted proteins from Archaea and Eukaryotes were also found. 39 matched cddid_all.tbl CDD pfam19068 pfam19068 436938 DUF5764 Family of unknown function (DUF5764). This is a family of uncharacterized proteins of known function found in viruses, particularly in Conferred and Mummified. 134 matched cddid_all.tbl CDD pfam19069 pfam19069 436939 DUF5765 Family of unknown function (DUF5765). This is a family of proteins of unknown function found in viruses, which are thought to be membrane proteins. 91 matched cddid_all.tbl CDD pfam19070 pfam19070 408840 DUF5766 Family of unknown function (DUF5766). This is a family of uncharacterized proteins of unknown function found in viruses. 77 matched cddid_all.tbl CDD pfam19071 pfam19071 436940 DUF5767 Family of unknown function (DUF5767). This is a family uncharacterized proteins of unknown function found in viruses. 84 matched cddid_all.tbl CDD pfam19072 pfam19072 408842 DUF5768 Family of unknown function (DUF5768). This is a family of uncharacterized proteins of unknown function found in viruses. 123 matched cddid_all.tbl CDD pfam19073 pfam19073 436941 DUF5769 Family of unknown function (DUF5769). This is a family of uncharacterized proteins of unknown function found in Mimiviridae. 191 matched cddid_all.tbl CDD pfam19074 pfam19074 465967 DUF5770 Family of unknown function (DUF5770). This is a family of uncharacterized proteins of unknown function found in Iridoviridae. 131 matched cddid_all.tbl CDD pfam19075 pfam19075 436943 DUF5771 Family of unknown function (DUF5771). This is a family of uncharacterized proteins of unknown function found in viruses which apparently has N-acetyltransferase activity. 69 matched cddid_all.tbl CDD pfam19076 pfam19076 436944 CshA_repeat Surface adhesin CshA repetitive domain. Repeat domain from surface fibrillar adhesin CshA. This domain forms several tandem repeats with high sequence identity. CshA is found primarily in streptococci species, but also in other Gram+ bacteria. 99 matched cddid_all.tbl CDD pfam19077 pfam19077 465968 Big_13 Bacterial Ig-like domain. Presumed domain found as tandem repeats of high sequence identity in bacterial cell surface proteins. 102 matched cddid_all.tbl CDD pfam19078 pfam19078 436946 Big_12 Bacterial Ig-like domain. Presumed domain found as tandem repeats of high sequence identity in bacterial cell surface proteins. 102 matched cddid_all.tbl CDD pfam19079 pfam19079 465969 CFSR Collagen-flanked surface repeat. Repeat flanked by collagen-like CXX motifs found in bacterial cell surface proteins. 49 matched cddid_all.tbl CDD pfam19080 pfam19080 408850 DUF5772 Family of unknown function (DUF5772). This is a family of proteins of unknown function found in viruses which appears to contain transmembrane proteins inferred from homology. 84 matched cddid_all.tbl CDD pfam19081 pfam19081 465970 Ig_7 Ig-like domain CHU_C associated. Presumed Ig-like domain found as tandem repeats in proteins with the gliding motility-associated C-terminal domain CHU_C 84 matched cddid_all.tbl CDD pfam19082 pfam19082 436948 DUF5773 Family of unknown function (DUF5773). This is a family of uncharacterized proteins of unknown function found in Phycodnaviridae. 177 matched cddid_all.tbl CDD pfam19083 pfam19083 465971 DUF5774 Family of unknown function (DUF5774). This is a family of uncharacterized proteins of unknown function found in viruses. 123 matched cddid_all.tbl CDD pfam19084 pfam19084 436950 DUF5775 Family of unknown function (DUF5775). This is a family of uncharacterized proteins of unknown function, found in phycodnaviruses. The protein contains a predicted N-terminal transmembrane helix. 81 matched cddid_all.tbl CDD pfam19085 pfam19085 436951 Choline_bind_2 Choline-binding repeat. this entry contains a pair of presumed choline-binding repeats that are often found adjacent to pfam01473. 38 matched cddid_all.tbl CDD pfam19086 pfam19086 465972 Terpene_syn_C_2 Terpene synthase family 2, C-terminal metal binding. 199 matched cddid_all.tbl CDD pfam19087 pfam19087 465973 DUF5776 Domain of unknown function (DUF5776). Presumed stalk domain found in bacterial surface proteins forming tandem repeats with high sequence identity. This domain is also associated with other known bacterial surface protein stalks and adhesive domains. 67 matched cddid_all.tbl CDD pfam19088 pfam19088 465974 TUTase TUTase nucleotidyltransferase domain. This nucleotidyltransferase domain is found in TUTase enzymes. Terminal uridyltransferases (TUTases) execute 3' RNA uridylation across protists, fungi, metazoan and plant species. 218 matched cddid_all.tbl CDD pfam19089 pfam19089 436955 DUF5777 Membrane bound beta barrel domain (DUF5777). This entry contains integral membrane beta barrel proteins. 244 matched cddid_all.tbl CDD pfam19090 pfam19090 436956 DUF5778 Family of unknown function (DUF5778). Family of unknown function predominantly found in Halobacteria. 126 matched cddid_all.tbl CDD pfam19091 pfam19091 436957 DUF5779 Family of unknown function (DUF5779). Family of unknown function predominantly found in Halobacteria. 96 matched cddid_all.tbl CDD pfam19092 pfam19092 436958 DUF5780 Family of unknown function (DUF5780). This entry adopts a Greek-key beta sandwich topology, with long loops in some of the members. While a structure is known, the function of this domain is yet to be determined. 109 matched cddid_all.tbl CDD pfam19093 pfam19093 436959 DUF5781 Family of unknown function (DUF5781). Family of unknown function predominantly found in Halobacteria. 243 matched cddid_all.tbl CDD pfam19094 pfam19094 465975 EMC6_arch EMC6-arch. This family represents the ER membrane protein complex subunit 6 (EMC6) homolog from archaea. They contain three transmembrane regions. 87 matched cddid_all.tbl CDD pfam19095 pfam19095 436961 DUF5783 Family of unknown function (DUF5783). Family of unknown function predominantly found in Halobacteria. 105 matched cddid_all.tbl CDD pfam19096 pfam19096 436962 DUF5784 Family of unknown function (DUF5784). Family of unknown function predominantly found in Halobacteria. 328 matched cddid_all.tbl CDD pfam19097 pfam19097 436963 Snu56_snRNP Snu56-like U1 small nuclear ribonucleoprotein component. This family is a component of the U1 snRNP particle, which recognizes and binds the 5'-splice site of pre-mRNA. Together with other non-snRNP factors, U1 snRNP forms the spliceosomal commitment complex, which targets pre-mRNA to the splicing pathway. 436 matched cddid_all.tbl CDD pfam19098 pfam19098 436964 DUF5785 Family of unknown function (DUF5785). Family of unknown function predominantly found in Halobacteria. 98 matched cddid_all.tbl CDD pfam19099 pfam19099 436965 DUF5786 Family of unknown function (DUF5786). Family of unknown function predominantly found in Halobacteria. 55 matched cddid_all.tbl CDD pfam19100 pfam19100 436966 DUF5787 Family of unknown function (DUF5787). Family of unknown function predominantly found in Halobacteria. 264 matched cddid_all.tbl CDD pfam19101 pfam19101 436967 DUF5788 Family of unknown function (DUF5788). This is a family of proteins of unknown function predominantly found in Halobacteria. 132 matched cddid_all.tbl CDD pfam19102 pfam19102 436968 DUF5789 Family of unknown function (DUF5789). This is a family of proteins of unknown function predominantly found in Halobacteria. 74 matched cddid_all.tbl CDD pfam19103 pfam19103 436969 DUF5790 Family of unknown function (DUF5790). This is a family of proteins of unknown function found predominantly in Halobacteria. 126 matched cddid_all.tbl CDD pfam19104 pfam19104 436970 DUF5791 Family of unknown function (DUF5791). This is a family of proteins of unknown function predominantly found in Halobacteria. 124 matched cddid_all.tbl CDD pfam19105 pfam19105 436971 DUF5792 Family of unknown function (DUF5792). This family contains a domain of unknown function found in prasinoviruses. 157 matched cddid_all.tbl CDD pfam19106 pfam19106 436972 DUF5793 Family of unknown function (DUF5793). This is a family of proteins of unknown function predominantly found in Halobacteria. 157 matched cddid_all.tbl CDD pfam19107 pfam19107 436973 DUF5794 Family of unknown function (DUF5794). This is a family of proteins of unknown function predominantly found in Halobacteria. 128 matched cddid_all.tbl CDD pfam19108 pfam19108 436974 DUF5795 Family of unknown function (DUF5795). Family of unknown function predominantly found in Halobacteria. 74 matched cddid_all.tbl CDD pfam19109 pfam19109 436975 DUF5796 Family of unknown function (DUF5796). Family of proteins of unknown function predominantly found in Halobacteria. 139 matched cddid_all.tbl CDD pfam19110 pfam19110 436976 DUF5797 Family of unknown function (DUF5797). This is a family of proteins of unknown function predominantly found in Halobacteria. 163 matched cddid_all.tbl CDD pfam19111 pfam19111 436977 DUF5798 Family of unknown function (DUF5798). Family of unknown function predominantly found in Halobacteria. 89 matched cddid_all.tbl CDD pfam19112 pfam19112 436978 VanA_C Vanillate O-demethylase oxygenase C-terminal domain. This domain is found in a wide variety of oxygenases such as Vanillate O-demethylase oxygenase and Toluene-4-sulfonate monooxygenase. 195 matched cddid_all.tbl CDD pfam19113 pfam19113 436979 DUF5799 Family of unknown function (DUF5799). This is a family of proteins of unknown function predominantly found in Halobacteria. 148 matched cddid_all.tbl CDD pfam19114 pfam19114 436980 EsV_1_7_cys "EsV-1-7 cysteine-rich motif. The EsV-1-7 repeat is a cysteine-rich motif of unknown function. The motif was originally identified in the Ectocarpus ""immediate upright"" protein, which has an EsV-1-7 domain that contains five EsV-1-7 repeats. The name is derived from the Ectocarpus virus EsV-1 protein EsV-1-7, which possesses six EsV-1-7 repeats. Ectocarpus has a large family of EsV-1-7 domain proteins with between one and 19 copies of the motif (C-X4-C-X16-C-X2-H-X12). In addition to brown algae, EsV-1-7 domain proteins have been found in eustigmatophytes, oomycetes, cryptophytes, two families of green algae (Coccomyxaceae and Selenastraceae) and also in viral genomes, such as Emiliania huxleyi virus PS401 and Pithovirus sibericum. Based on this unusual distribution, it has been proposed that EsV-1-7 domain genes have been exchanged between lineages by horizontal gene transfer during evolution." 35 matched cddid_all.tbl CDD pfam19115 pfam19115 408885 DUF5800 Family of unknown function (DUF5800). This is a family of proteins of unknown function predominantly found in Halobacteria. 64 matched cddid_all.tbl CDD pfam19116 pfam19116 465976 DUF5801 Domain of unknown function (DUF5801). This entry contains a presumed domain that is found as tandem repeats in a number of bacterial proteins. 152 matched cddid_all.tbl CDD pfam19117 pfam19117 436982 Mim2 Mitochondrial import 2. This entry, together with pfam08219 form the Mim1/Mim2 complex, which is specific to fungi. This complex is responsible for the assembly and/or insertion of a subset of mitochondrial outer membrane proteins, including subunits of the main mitochondrial outer membrane translocase. 45 matched cddid_all.tbl CDD pfam19118 pfam19118 436983 DUF5802 Family of unknown function (DUF5802). Family of unknown function predominantly found in Halobacteria. 113 matched cddid_all.tbl CDD pfam19119 pfam19119 436984 DUF5803 Family of unknown function (DUF5803). Family of unknown function predominantly found in Halobacteria. 196 matched cddid_all.tbl CDD pfam19120 pfam19120 436985 DUF5804 Family of unknown function (DUF5804). Family of unknown function predominantly found in Halobacteria and Methanomicrobia. 108 matched cddid_all.tbl CDD pfam19121 pfam19121 436986 DUF5805 Family of unknown function (DUF5805). This is a family of proteins of unknown function predominantly found in Halobacteria. 67 matched cddid_all.tbl CDD pfam19122 pfam19122 408892 DUF5806 Family of unknown function (DUF5806). This is a family of proteins of unknown function predominantly found in Halobacteria and Methanomicrobia. 148 matched cddid_all.tbl CDD pfam19123 pfam19123 436987 DUF5807 Family of unknown function (DUF5807). This is a family of proteins of unknown function found in Halobacteria. 106 matched cddid_all.tbl CDD pfam19124 pfam19124 465977 DUF5808 Family of unknown function (DUF5808). This is a family of proteins of unknown function predominantly found in Firmicutes but also in Actinobacteria and Halobacteria. Members of this family are thought to be DUF1648 domain-containing proteins as they are membrane-components. 26 matched cddid_all.tbl CDD pfam19125 pfam19125 436989 DUF5809 Family of unknown function (DUF5809). This is a family of proteins of unknown function predominantly found in Halobacteria. 130 matched cddid_all.tbl CDD pfam19126 pfam19126 436990 DUF5810 Family of unknown function (DUF5810). This is a family of proteins of unknown function predominantly found in Halobacteria, but also in Eukaryotes. This family contains some members that are predicted as C2H2-type domain-containing proteins. 66 matched cddid_all.tbl CDD pfam19127 pfam19127 465978 Choline_bind_3 Choline-binding repeat. Pair of presumed choline-binding repeats often found adjacent to pfam01473. 47 matched cddid_all.tbl CDD pfam19128 pfam19128 436992 DUF5811 Family of unknown function (DUF5811). This is a family of proteins of unknown function predominantly found in Halobacteria. 103 matched cddid_all.tbl CDD pfam19129 pfam19129 436993 DUF5812 Family of unknown function (DUF5812). This is a family of unknown function predominantly found in Halobacteria. 140 matched cddid_all.tbl CDD pfam19130 pfam19130 436994 DUF5813 Family of unknown function (DUF5813). This is a family of unknown function found predominantly in Halobacteria. 143 matched cddid_all.tbl CDD pfam19131 pfam19131 465979 DUF5814 Family of unknown function (DUF5814). This is a family of proteins that are thought to have helicase activity, predominantly found in Halobacteria and Methanomicrobia. 148 matched cddid_all.tbl CDD pfam19132 pfam19132 436996 DUF5815 Family of unknown function (DUF5815). This is a family of unknown function predominantly found in Halobacteria. 155 matched cddid_all.tbl CDD pfam19133 pfam19133 436997 DUF5816 Family of unknown function (DUF5816). This is a family of proteins predominantly found in Halobacteria. They are thought to be GNAT (Gcn5-related N-acetyltransferases) family acetyltransferases. 72 matched cddid_all.tbl CDD pfam19134 pfam19134 436998 DUF5817 Domain of unknown function (DUF5817). This domain is present in a family of proteins predominantly found in Halobacteria. These proteins are thought to be the replication protein H. 51 matched cddid_all.tbl CDD pfam19135 pfam19135 436999 DUF5818 Protein of unknown function (DUF5818). This is a family of uncharacterized proteins. 57 matched cddid_all.tbl CDD pfam19136 pfam19136 465980 DUF5819 Family of unknown function (DUF5819). This is a family of uncharacterized proteins. 168 matched cddid_all.tbl CDD pfam19137 pfam19137 437001 DUF5820 Family of unknown function (DUF5820). This is a family of unknown function predominantly found in Halobacteria. 117 matched cddid_all.tbl CDD pfam19138 pfam19138 437002 DUF5821 Family of unknown function (DUF5821). This is a family of proteins of unknown function predominantly found in Halobacteria. 217 matched cddid_all.tbl CDD pfam19139 pfam19139 437003 DUF5822 Family of unknown function (DUF5822). This is a family of proteins of unknown function predominantly found in Halobacteria. This family includes some members which are thought to be peptidoglycan binding proteins. 38 matched cddid_all.tbl CDD pfam19140 pfam19140 408910 DUF5823 Family of unknown function (DUF5823). This is a family of uncharacterized proteins. 178 matched cddid_all.tbl CDD pfam19141 pfam19141 408911 DUF5824 Family of unknown function (DUF5824). This family contains a domain of unknown function, which is predominantly found in Phycodnaviridae and Caudovirale viruses. 127 matched cddid_all.tbl CDD pfam19142 pfam19142 408912 DUF5825 Family of unknown function (DUF5825). This is a family of uncharacterized proteins. 180 matched cddid_all.tbl CDD pfam19143 pfam19143 465981 Omp85_2 OMP85 superfamily. This entry represents the membrane spanning beta barrel domain of various Omp85 superfamily related proteins that have often have POTRA and Patatin domains. This family contains mainly flavobacterial proteins. 351 matched cddid_all.tbl CDD pfam19144 pfam19144 408914 DUF5826 Family of unknown function (DUF5826). This family of unknown function is mostly found in prasinoviruses and is likely to represent membrane proteins with two transmembrane regions. 68 matched cddid_all.tbl CDD pfam19145 pfam19145 437005 DUF5827 Family of unknown function (DUF5827). This is a family of proteins of unknown function predominantly found in Halobacteria. 87 matched cddid_all.tbl CDD pfam19146 pfam19146 437006 DUF5828 Family of unknown function (DUF5828). This is a family of proteins of unknown function predominantly found in Halobacteria. 175 matched cddid_all.tbl CDD pfam19147 pfam19147 437007 DUF5829 Family of unknown function (DUF5829). This is a family of uncharacterized proteins. 265 matched cddid_all.tbl CDD pfam19148 pfam19148 437008 DUF5830 Family of unknown function (DUF5830). This is a family of proteins predominantly found in Halobacteria. Some members includes the MarR family transcriptional regulator. 114 matched cddid_all.tbl CDD pfam19149 pfam19149 437009 DUF5831 Family of unknown function (DUF5831). This family of unknown function is found mostly in prasinoviruses. 72 matched cddid_all.tbl CDD pfam19150 pfam19150 465982 DUF5832 Family of unknown function (DUF5832). This entry contains proteins of unknown function found predominantly in the Phycodnaviridae, Mimiviridae, Marseilleviridae and Iridoviridae virus families. 81 matched cddid_all.tbl CDD pfam19151 pfam19151 408921 Sublancin Sublancin. This family represents sublancin, a small bacteriocin active against Gram-positive bacteria. This family appears to be restricted to Bacilli. Sublancin was thought to be a lantibiotic but was later shown to be an S-linked glycopeptide. Glycosylation is essential for its antimicrobial activity. Sublancin is biosynthesized as a precursor peptide bearing an N-terminal leader peptide, and a C-terminal core peptide that is converted into the mature peptide. Sublancin comprises two alpha helices and a well-defined inter-helical loop. Sublancin inhibits B.cereus spore outgrowth, after the germination stage, approximately 1000-fold better than it inhibits exponential growth of the same cells and inhibits B.subtilis strain ATCC6633 and B. megaterium strain 14581. 57 matched cddid_all.tbl CDD pfam19152 pfam19152 408922 DUF5834 Family of unknown function (DUF5834). This family represents an uncharacterized protein that is associated with the thiocillin biosynthetic gene cluster. 159 matched cddid_all.tbl CDD pfam19153 pfam19153 408923 DUF5835 Family of unknown function (DUF5835). 53 matched cddid_all.tbl CDD pfam19154 pfam19154 408924 DUF5836 Family of unknown function (DUF5836). This family represents the induction peptide AbpIP, which regulates the biosynthesis of the bacteriocin ABP-118 in Lactobacillus salivarius subsp. salivarius UCC118. 38 matched cddid_all.tbl CDD pfam19155 pfam19155 437011 DUF5837 Family of unknown function (DUF5837). This family of unknown function is associated with the tenuecyclamide A biosynthetic gene cluster. 61 matched cddid_all.tbl CDD pfam19156 pfam19156 437012 DUF5838 Family of unknown function (DUF5838). This family of unknown function is associated with the biosynthetic gene cluster for anacyclamide A10. The family appears to be restricted to Cyanobacteria. Some matches also contain a methyltransferase domain at the N terminus. 289 matched cddid_all.tbl CDD pfam19157 pfam19157 465983 DUF5839 Family of unknown function (DUF5839). This family of unknown function is associated with the biosynthetic gene cluster for glycocin F. The family appears to be restricted to Firmicutes. 83 matched cddid_all.tbl CDD pfam19158 pfam19158 408928 DUF5840 Family of unknown function (DUF5840). This family contains uncharacterized proteins. It also contains the anacyclamide synthesis protein AcyE. Cyanobactins are small, cyclic peptides found in cyanobacteria. They are ribosomally synthesized and post-translationally modified. Cyanobactin biosynthesis clusters contain 7-12 genes. Anaclyclamides are a type of cyanobactin produced in strains of the cyanobacteria Anabaena. AcyE is a 49-amino-acid protein with N-terminal homology to the peptide precursor proteins in the other cyanobactin pathways. The core peptide of AcyE is cleaved during post-translational processing of the precursor peptide. 49 matched cddid_all.tbl CDD pfam19159 pfam19159 408929 DUF5841 Family of unknown function (DUF5841). This family of unknown function is associated with the biosynthetic gene cluster for enterocin A. 48 matched cddid_all.tbl CDD pfam19160 pfam19160 465984 SPARK SPARK. This entry is typically found as an extracellular domain of plant receptor-like kinases, many of which play a role in signalling during plant-fungal symbiosis. The precise function of this entry is unknown (Montero H et.al. PNAS June 22, 2021 118 (25) e2105281118). 158 matched cddid_all.tbl CDD pfam19161 pfam19161 408931 DUF5843 Family of unknown function (DUF5843). This is a family of uncharacterized proteins of unknown function predominantly found in viruses. 196 matched cddid_all.tbl CDD pfam19162 pfam19162 437015 DUF5844 Family of unknown function (DUF5844). This is a family of uncharacterized proteins of unknown function found in Iridoviridae. 109 matched cddid_all.tbl CDD pfam19163 pfam19163 437016 DUF5845 Family of unknown function (DUF5845). This is a family of uncharacterized proteins of unknown function found in viruses. 80 matched cddid_all.tbl CDD pfam19164 pfam19164 437017 DUF5846 Family of unknown function (DUF5846). This is a family of uncharacterized proteins of unknown function predominantly found in Mimiviridae. 116 matched cddid_all.tbl CDD pfam19165 pfam19165 437018 DUF5847 Family of unknown function (DUF5847). This is a family of uncharacterized proteins of unknown function predominantly found in Mimiviridae. 409 matched cddid_all.tbl CDD pfam19166 pfam19166 408936 DUF5848 Family of unknown function (DUF5848). This is a family of uncharacterized proteins of unknown function predominantly found in viruses. This family is also found in Bacteria and Fungi. 64 matched cddid_all.tbl CDD pfam19167 pfam19167 408937 DUF5849 Family of unknown function (DUF5849). This is a family of uncharacterized proteins of unknown function predominantly found in viruses. 200 matched cddid_all.tbl CDD pfam19168 pfam19168 465985 DUF5850 Family of unknown function (DUF5850). This is a family of uncharacterized proteins of unknown function predominantly found in Iridoviridae. The family contains a conserved motif towards the C-terminus of these proteins. This motif contains a central RGD sequence which suggests these viral proteins may bind to integrins. 156 matched cddid_all.tbl CDD pfam19169 pfam19169 408939 DUF5851 Family of unknown function (DUF5851). This is a family of uncharacterized proteins of unknown function predominantly found in Mimiviridae. 353 matched cddid_all.tbl CDD pfam19170 pfam19170 437020 DUF5852 Family of unknown function (DUF5852). This is a family of uncharacterized proteins of unknown function predominantly found in Iridoviridae. 187 matched cddid_all.tbl CDD pfam19171 pfam19171 408941 DUF5853 Family of unknown function (DUF5853). This is a family of uncharacterized proteins of unknown function predominantly found in Phycodnaviridae. 136 matched cddid_all.tbl CDD pfam19172 pfam19172 437021 DUF5854 Family of unknown function (DUF5854). This is a family of uncharacterized proteins of unknown function predominantly found in Mimiviridae. 159 matched cddid_all.tbl CDD pfam19173 pfam19173 437022 DUF5855 Family of unknown function (DUF5855). This is a family of uncharacterized proteins of unknown function predominantly found in Phycodnaviridae. 182 matched cddid_all.tbl CDD pfam19174 pfam19174 465986 DUF5856 Family of unknown function (DUF5856). This is a family of uncharacterized proteins of unknown function predominantly found in viruses. This family was also found in Bacteria. 94 matched cddid_all.tbl CDD pfam19175 pfam19175 437024 DUF5857 Family of unknown function (DUF5857). This is a family of uncharacterized proteins of unknown function predominantly found in viruses. 287 matched cddid_all.tbl CDD pfam19176 pfam19176 465987 DUF5858 Family of unknown function (DUF5858). This is a family of uncharacterized proteins of unknown function predominantly found in Marseillevirus. 61 matched cddid_all.tbl CDD pfam19177 pfam19177 408947 DUF5859 Family of unknown function (DUF5859). This is a family of uncharacterized proteins of unknown function predominantly found in viruses. 162 matched cddid_all.tbl CDD pfam19178 pfam19178 408948 DUF5860 Family of unknown function (DUF5860). This is a family of uncharacterized proteins of unknown function predominantly found in viruses. 167 matched cddid_all.tbl CDD pfam19179 pfam19179 465988 TTC3_DZIP3_dom E3 ubiquitin-protein ligase TTC3/DZIP3 domain. This domain is found in E3 ubiquitin-protein ligases TTC3 and DZIP3 and its function is unknown. TTC3 mediates ubiquitination and degradation of phosphorylated Akt, apparently its preferable target. DZIP3 is also able to bind RNA through a Lys-rich region which enhances is ubiquitination activity. It is suggested that RNA-binding proteins or ribonucleoprotein particles might be physiological targets for this enzyme, which could be important during viral infections, especially for those replicating through RNA intermediates. This domain is also found in uncharacterized proteins found in viruses. 116 matched cddid_all.tbl CDD pfam19180 pfam19180 437027 DUF5862 Family of unknown function (DUF5862). This is a family of uncharacterized proteins of unknown function predominantly found in Ascoviridae. This family also includes uncharacterized proteins found in Bacteria. 68 matched cddid_all.tbl CDD pfam19181 pfam19181 465989 DUF5863 Family of unknown function (DUF5863). This is a family of uncharacterized proteins of unknown function predominantly found in viruses. 169 matched cddid_all.tbl CDD pfam19182 pfam19182 437029 DUF5864 Family of unknown function (DUF5864). This is a family of uncharacterized proteins of unknown function predominantly found in Mimiviridae. 136 matched cddid_all.tbl CDD pfam19183 pfam19183 408953 DUF5865 Family of unknown function (DUF5865). This is a family of uncharacterized proteins of unknown function predominantly found in viruses. 210 matched cddid_all.tbl CDD pfam19184 pfam19184 437030 DUF5866 Family of unknown function (DUF5866). This is a family of uncharacterized proteins of unknown function predominantly found in Mimiviridae. 74 matched cddid_all.tbl CDD pfam19185 pfam19185 408955 DUF5867 Family of unknown function (DUF5867). This is a family of uncharacterized proteins of unknown function predominantly found in viruses. 274 matched cddid_all.tbl CDD pfam19186 pfam19186 437031 DUF5868 Family of unknown function (DUF5868). This is a family of uncharacterized proteins of unknown function predominantly found in Mimiviridae. 195 matched cddid_all.tbl CDD pfam19187 pfam19187 465990 HTH_PafC PafC helix-turn-helix domain. This entry is an N-terminal HTH domain found in the PafC protein. Transcriptional activator PafBC is responsible for upregulating the majority of genes induced by DNA damage. 115 matched cddid_all.tbl CDD pfam19188 pfam19188 465991 AGRB_N Adhesion GPCR B N-terminal region. This region is found at the N-terminus of various adhesion G-protein coupled receptor B proteins. This region contains 10 cysteine residues that probably form disulphide bonds. 177 matched cddid_all.tbl CDD pfam19189 pfam19189 437034 Mtf2 Mtf2 family. This family appears to be distantly related to PPR repeats. 195 matched cddid_all.tbl CDD pfam19190 pfam19190 408960 BACON_2 Viral BACON domain. This family represents a distinct class of BACON domains found in crAss-like phages, the most common viral family in the human gut, in which they are found in tail fiber genes. This suggests they may play a role in phage-host interactions. 91 matched cddid_all.tbl CDD pfam19191 pfam19191 437035 HEF_HK HEF_HK domain. This is a dimerization and histidine phosphotransfer (DHp) domain found in Histidine Kinases (HK). This domain is belongs to the His_Kinase_A (CL0025) clan. HK domain architectures typically contain DHp domains adjacent to GHKL domains, such as HATPase_c (pfam02518) and HATPase_c_3 (pfam13589) which comprise the ATP-binding regions. 67 matched cddid_all.tbl CDD pfam19192 pfam19192 437036 Response_reg_2 Response receiver domain. This is a receiver domain (REC) commonly found in the same gene-neighbourhood of its cognate HK. Together they comprise a Two-Component System (TCS). There is a high degree of specificity among REC and DHp domains in a cognate pair. This domain is related to the Response_reg (pfam00072) domain. We found that pfam19191 and this domain show high degree of linkage in the same gene-neighbourhoods across several bacterial lineages. This implies that they comprise a TCS. 178 matched cddid_all.tbl CDD pfam19193 pfam19193 465992 Tectonin Tectonin domain. This entry represents proteins homologous to tectonin. This protein adopts a 6 bladed beta propeller structure. 215 matched cddid_all.tbl CDD pfam19194 pfam19194 437038 DUF5869 Family of unknown function (DUF5869). This is a family of uncharacterized proteins of unknown function found in Marseillevirus. 159 matched cddid_all.tbl CDD pfam19195 pfam19195 408965 DUF5870 Family of unknown function (DUF5870). This is a family of uncharacterized proteins of unknown function predominantly found in viruses. 488 matched cddid_all.tbl CDD pfam19196 pfam19196 437039 DUF5871 Family of unknown function (DUF5871). This is a family of uncharacterized proteins of unknown function predominantly found in Phycodnaviridae. 136 matched cddid_all.tbl CDD pfam19197 pfam19197 437040 DUF5872 Family of unknown function (DUF5872). This is a family of uncharacterized proteins of unknown function predominantly found in viruses and Bacteria. 116 matched cddid_all.tbl CDD pfam19198 pfam19198 437041 RsaA_NTD RsaA N-terminal domain. This entry represents the N-terminal domain of the RsaA S-layer protein from Caulobacter crescentus. This domain binds to lipopolysaccharide. 180 matched cddid_all.tbl CDD pfam19199 pfam19199 437042 Phage_coatGP8 Phage major coat protein, Gp8. Class I phage major coat protein Gp8 or B. The coat protein is largely alpha-helix with a slight curve. 69 matched cddid_all.tbl CDD pfam19200 pfam19200 465993 MupG_N 6-phospho-N-acetylmuramidase, N-terminal. This domain represents the N-terminal domain of 6-phospho-N-acetylmuramidase (MupG) from Staphylococcus aureus, also found in putative phospho sugar glycosidases from Gram-negative and -positive species, but mainly firmicutes. MupG, specifically cleaves MurNAc 6P-GlcNAc, a product of cell wall turnover, into the sugars MurNAc 6P and GlcNAc, involved in cell wall turnover and recycling. Since some species, for example Lactobacillus plantarum, possess several putative paralogs, the substrate specificity of the proteins containing this domain may not be limited to cell wall sugars, but may include phosphorylated disaccharides in general. Most of these proteins appear to consist of two structural subdomains, as it can be seen in the two available crystal structures of Enterococcus faecalis (PDB:2p0o) and Bacillus cereus (PDB:1X7F). This entry is the larger N-terminal domain that constitutes a TIM-barrel like structure and the C-terminal domain is similar to the cyclophilin family. It should be noted that some proteins lack the C-terminal domain. 235 matched cddid_all.tbl CDD pfam19201 pfam19201 408971 DUF5873 Family of unknown function (DUF5873). This is a family of uncharacterized proteins of unknown function predominantly found in Phyconaviridae. 109 matched cddid_all.tbl CDD pfam19202 pfam19202 408972 DUF5874 Family of unknown function (DUF5874). This is a family of uncharacterized proteins of unknown function predominantly found in Phycodnaviridae. This entry includes proteins that are also found in Fungi. 74 matched cddid_all.tbl CDD pfam19203 pfam19203 408973 DUF5875 Family of unknown function (DUF5875). This is a family of uncharacterized proteins of unknown function predominantly found in Iridoviridae. 228 matched cddid_all.tbl CDD pfam19204 pfam19204 437044 DUF5876 Family of unknown function (DUF5876). This is a family of uncharacterized proteins of unknown function predominantly found in Iridoviridae. 561 matched cddid_all.tbl CDD pfam19205 pfam19205 465994 DUF5877 Family of unknown function (DUF5877). This is a family of uncharacterized proteins of unknown functions predominantly found in Iridoviridae. 609 matched cddid_all.tbl CDD pfam19206 pfam19206 408976 DUF5878 Family of unknown function (DUF5878). This is a family of uncharacterized proteins of unknown function found in viruses. 148 matched cddid_all.tbl CDD pfam19207 pfam19207 408977 DUF5879 Family of unknown function (DUF5879). This is a family of uncharacterized proteins of unknown function predominantly found in viruses. 273 matched cddid_all.tbl CDD pfam19208 pfam19208 437046 DUF5880 Family of unknown function (DUF5880). This is a family of uncharacterized proteins of unknown function predominantly found in Phycodnaviridae. This family also includes uncharacterized proteins found in Archaea and Eukaryotes. 97 matched cddid_all.tbl CDD pfam19209 pfam19209 437047 CoV_S1_C Coronavirus spike glycoprotein S1, C-terminal. This entry represents a domain found at the C-terminus of the Coronavirus S1 protein. It is found across a range of alpha, beta and gamma coronaviruses. This small all beta stranded domain is known as subdomain 2 in the structure of the porcine epidemic diarrhea virus spike protein. 57 matched cddid_all.tbl CDD pfam19211 pfam19211 465995 CoV_NSP2_N Coronavirus replicase NSP2, N-terminal. This entry corresponds to the N-terminal region of coronavirus non-structural protein 2. NSP2 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. The function of this protein is uncertain. This region contains numerous conserved and semi-conserved cysteine residues. 204 matched cddid_all.tbl CDD pfam19212 pfam19212 465996 CoV_NSP2_C Coronavirus replicase NSP2, C-terminal. This entry corresponds to a presumed domain found at the C-terminus of Coronavirus non-structural protein 2 (NSP2). NSP2 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. The function of NSP2 is uncertain. This presumed domain is found in two copies in some viral NSP2 proteins. This domain is found in both alpha and betacoronaviruses. 156 matched cddid_all.tbl CDD pfam19213 pfam19213 465997 CoV_NSP6 Coronavirus replicase NSP6. This entry represents proteins found in Coronaviruses and includes the Non-structural Protein 6 (NSP6). Coronaviruses encode large replicase polyproteins which are proteolytically processed by viral proteases to generate mature Nonstructural Proteins (NSPs). NSP6 is a membrane protein containing 6 transmembrane domains with a large C-terminal tail. NSP6 from the avian coronavirus, infectious bronchitis virus (IBV) and the mouse hepatitis virus (MHV) have been shown to localize to the ER and to generate autophagosomes. Coronavirus NSP6 proteins have also been shown to limit autophagosome expansion. This may favour coronavirus infection by reducing the ability of autophagosomes to deliver viral components to lysosomes for degradation. NSP6 from IBV, MHV and severe acute respiratory syndrome coronavirus (SARS-CoV) have also been found to activate autophagy. 260 matched cddid_all.tbl CDD pfam19214 pfam19214 465998 CoV_S2_C Coronavirus spike glycoprotein S2, intravirion. This entry represents the cysteine rich intravirion region found at the C-terminus of coronavirus spike proteins (S). These cysteine residues are targets for palmitoylation, necessary for efficiently S incorporation into virions and S-mediated membrane fusions. 42 matched cddid_all.tbl CDD pfam19215 pfam19215 465999 CoV_NSP15_C Coronavirus replicase NSP15, uridylate-specific endoribonuclease. This entry represents the C-terminal domain of coronavirus non-structural protein 15 (NSP15 or nsp15). NSP15 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. This domain exhibits endoribonuclease activity designated EndoU, highly conserved in all known CoVs and is part of the replicase-transcriptase complex that plays important roles in virus replication and transcription. NSP15 is a Uridylate-specific endoribonuclease that cleaves the 5'-polyuridines from negative-sense viral RNA, termed PUN RNA either upstream or downstream of uridylates, at GUU or GU to produce molecules with 2',3'-cyclic phosphate ends. PUN RNA is a CoV MDA5-dependent pathogen-associated molecular pattern (PAMP). 155 matched cddid_all.tbl CDD pfam19216 pfam19216 466000 CoV_NSP15_M Coronavirus replicase NSP15, middle domain. This entry represents the non-catalytic middle domain from coronavirus non-structural protein 15 (NSP15). NSP15 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. This domain is formed by ten beta strands organized into three beta hairpins. 118 matched cddid_all.tbl CDD pfam19217 pfam19217 466001 CoV_NSP4_N Coronavirus replicase NSP4, N-terminal. This is the N-terminal domain of the coronavirus nonstructural protein 4 (NSP4). NSP4 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. NSP4 is a membrane-spanning protein which is thought to anchor the viral replication-transcription complex to modified endoplasmic reticulum membranes. This N-terminal region represents the membrane spanning region, covering four transmembrane regions. 351 matched cddid_all.tbl CDD pfam19218 pfam19218 466002 CoV_NSP3_C Coronavirus replicase NSP3, C-terminal. This family represents the C-terminal region of non-structural protein NSP3 (also known as nsp3). NSP3 is the product of ORF1a. It is found in human SARS coronavirus polyprotein 1a and 1ab, and in related coronavirus polyproteins. It is a multifunctional protein comprising up to 16 different domains and regions. NSP3 binds to viral RNA, nucleocapsid protein, as well as other viral proteins and participates in polyprotein processing. 463 matched cddid_all.tbl CDD pfam19219 pfam19219 466003 CoV_NSP15_N Coronavirus replicase NSP15, N-terminal oligomerization. This is the N-terminal domain of the coronavirus nonstructural protein 15 (NSP15), which is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. NSP15, is a nidoviral RNA uridylate-specific endoribonuclease (NendoU) carrying C-terminal catalytic domain belonging to the EndoU family. The SARS-CoV-2 NendoU monomers assemble into a double-ring hexamer, generated by a dimer of trimers. The hexamer is stabilized by the interactions of N-terminal oligomerization domain. 61 matched cddid_all.tbl CDD pfam19220 pfam19220 437057 Crescentin Crescentin protein. This entry represents a bacterial equivalent to Intermediate Filament proteins, named crescentin, whose cytoskeletal function is required for the vibrioid and helical shapes of Caulobacter crescentus. Without crescentin, the cells adopt a straight-rod morphology. Crescentin has characteriztic features of IF proteins including the ability to assemble into filaments in vitro without energy or cofactor requirements. In vivo, crescentin forms a helical structure that colocalizes with the inner cell curvatures beneath the cytoplasmic membrane. 401 matched cddid_all.tbl CDD pfam19221 pfam19221 466004 MELT MELT motif. The outer kinetochore protein scaffold KNL1 is essential for error-free chromosome segregation during mitosis and meiosis. A critical feature of KNL1 is an array of repeats containing MELT-like motifs. When phosphorylated, these motifs form docking sites for the BUB1-BUB3 dimer that regulates chromosome biorientation and the spindle assembly checkpoint. This entry mainly represents vertebrate proteins although MELT motifs are found much more widely. 25 matched cddid_all.tbl CDD pfam19222 pfam19222 408991 Noda_Vmethyltr Nodavirus Vmethyltransferase. This entry represents a family of nodavirus proteins that is homologous to pfam01660. These proteins are likely methytransferases involved in mRNA capping. 148 matched cddid_all.tbl CDD pfam19223 pfam19223 408992 Chropara_Vmeth Chroparavirus methyltransferase. This entry represents a family of chroparavirus proteins that is homologous to pfam01660. These proteins are likely methytransferases involved in mRNA capping. 319 matched cddid_all.tbl CDD pfam19224 pfam19224 408993 pATOM36 pATOM36 family. This entry represents the trypanosome Peripherally associated ATOM36 protein which has been shown to complement a deletion of the Mim1/Mim2 complex in yeast. The integral MOM protein, peripheral archaic translocase of the outer membrane 36 (pATOM36), in analogy to the MIM complex, is involved in the assembly and/or membrane insertion of a small subset of MOM proteins including subunits of the main trypanosomal outer membrane protein translocase (ATOM complex). 270 matched cddid_all.tbl CDD pfam19225 pfam19225 437059 Spo16 Spo16 protein. This entry represents proteins related to yeast Spo16. Spo16 forms a complex with Zip2 and Zip4. Zip2 and Spo16, form a meiosis-specific XPF-ERCC1-like complex. The recombinant Zip2 XPF domain together with Spo16 preferentially binds branched DNA structures, such as D loops and HJs. The Spo16 protein contains a C-terminal HHH motif. 167 matched cddid_all.tbl CDD pfam19226 pfam19226 466005 DisA DisA glycoprotein. This entry corresponds to a putative viral glycoprotein. 360 matched cddid_all.tbl CDD pfam19227 pfam19227 408996 Salyut Salyut domain. This entry represents the Salyut domain found in the replicase of all viruses of the viral family Tymoviridae, composed of viruses that infect plants and insects. it is located within a long, hypervariable, Proline-rich hinge region located between the Alphavirus-like methyltransferase (pfam01660) and the pfam01443. It is located 150-20aa downstream the Iceberg region that forms the C-terminus of Vmethyltransf. The function of this family is unknown. 51 matched cddid_all.tbl CDD pfam19228 pfam19228 437060 DUF5881 Family of unknown function (DUF5881). This is a family of uncharacterized proteins of unknown function predominantly found in viruses. 163 matched cddid_all.tbl CDD pfam19229 pfam19229 466006 DUF5882 Family of unknown function (DUF5882). This is a family of uncharacterized proteins of unknown function predominantly found in Marseillevirus. 198 matched cddid_all.tbl CDD pfam19230 pfam19230 437062 DUF5883 Family of unknown function (DUF5883). This is a family of uncharacterized proteins of unknown function predominantly found in Phycodnavirus. 120 matched cddid_all.tbl CDD pfam19231 pfam19231 437063 DUF5884 Family of unknown function (DUF5884). This is a family of uncharacterized proteins of unknown function predominantly found in Mimivirus. 161 matched cddid_all.tbl CDD pfam19232 pfam19232 437064 DUF5885 Family of unknown function (DUF5885). This is a family of uncharacterized proteins of unknown function found in viruses. 265 matched cddid_all.tbl CDD pfam19233 pfam19233 437065 DUF5886 Family of unknown function (DUF5886). This is a family of uncharacterized proteins of unknown function predominantly found in Mimiviridae. 135 matched cddid_all.tbl CDD pfam19234 pfam19234 466007 DUF5887 Family of unknown function (DUF5887). This is a family of uncharacterized proteins of unknown function predominantly found in viruses. This family includes proteins that are thought to have acetyltransferase activity. 130 matched cddid_all.tbl CDD pfam19235 pfam19235 437067 DUF5888 Family of unknown function (DUF5888). This is a family of uncharacterized proteins of unknown function found in viruses. This family also includes proteins found in Bacteria and Fungi that are thought to contain WD40 repeats. 140 matched cddid_all.tbl CDD pfam19236 pfam19236 437068 ADAMTS_CR_3 ADAMTS cysteine-rich domain. This cysteine rich domain is found in a variety of ADAMTS and ADAMTS-like endopeptidases widely spread in animals. It is a well-conserved cysteine-rich sequence containing 10 cysteine residues. ADAM-TS (A Disintegrin and Metalloproteinase with Thrombospondin Motifs) is closely related to the ADAM family (A Disintegrin and Metalloproteinase, pfam08516) and consists of at least 20 members sharing a high degree of sequence similarity and conserved domain organization. Members of the ADAMTS family have been implicated in a range of diseases. 115 matched cddid_all.tbl CDD pfam19237 pfam19237 437069 DUF5889 Family of unknown function (DUF5889). This is a family of uncharacterized proteins of unknown function predominantly found in Mimiviridae. 115 matched cddid_all.tbl CDD pfam19238 pfam19238 437070 Radical_SAM_2 Radical SAM-like domain. This family represents a set of radical SAM like domains that are often found associated with pfam04459. 151 matched cddid_all.tbl CDD pfam19239 pfam19239 466008 GIY_YIG_domain GIY-YIG domain-containing protein. This is a family of proteins that contain the GIY-YIG domain, predominantly found in Bacteria, Fungi and plants (i.e. in Protein EFFECTOR OF TRANSCRIPTION 1,2 and 3 from Arabidopsis) but also in viruses. This is a well characterized domain among the members of the GYI-YIG endonuclease family, which is involved in several cellular processes such as DNA repair and recombination and transfer of mobile genetic elements. 164 matched cddid_all.tbl CDD pfam19240 pfam19240 437072 DUF5890 Family of unknown function (DUF5890). This is a family of uncharacterized proteins found in viruses, which presumably contain a Host Targeting (HT) motif. This motif is involved in targeting host proteins as part of the infection process in several organizms. 75 matched cddid_all.tbl CDD pfam19241 pfam19241 437073 DUF5891 Family of unknown function (DUF5891). This is a family of uncharacterized proteins predominantly found in viruses which is apparently a Putative RNA methyltransferase. 198 matched cddid_all.tbl CDD pfam19242 pfam19242 437074 Zn_finger_prot Putative zinc finger protein. This is a family of proteins predominantly found in Iridoviridae, which contains a zinc finger domain. 268 matched cddid_all.tbl CDD pfam19243 pfam19243 437075 DUF5892 Family of unknown function (DUF5892). This is a family of uncharacterized proteins of unknown function predominantly found in Iridoviridae. 327 matched cddid_all.tbl CDD pfam19244 pfam19244 437076 Poly_A_pol_cat Poly(A) polymerase catalytic subunit. This family represents the Poly(A) polymerase catalytic subunit found in viruses. 131 matched cddid_all.tbl CDD pfam19245 pfam19245 466009 DUF5893 Family of unknown function (DUF5893). This is a family of uncharacterized proteins of unknown function predominantly found in Marseillevirus. 147 matched cddid_all.tbl CDD pfam19246 pfam19246 437078 DUF5894 Family of unknown function (DUF5894). This is a family of uncharacterized proteins of unknown function predominantly found in Mimiviridae. 57 matched cddid_all.tbl CDD pfam19247 pfam19247 437079 DUF5895 Family of unknown function (DUF5895). This is a family of uncharacterized proteins of unknown function found in viruses and Bacteria. 153 matched cddid_all.tbl CDD pfam19248 pfam19248 466010 DUF5896 Family of unknown function (DUF5896). This is a family of uncharacterized proteins of unknown function predominantly found in Marseillevirus. 191 matched cddid_all.tbl CDD pfam19249 pfam19249 437081 DUF5897 Family of unknown function (DUF5897). This is a family of uncharacterized proteins of unknown function found in viruses. 200 matched cddid_all.tbl CDD pfam19250 pfam19250 437082 DUF5898 Family of unknown function (DUF5898). This is a family of uncharacterized proteins of unknown function found in viruses. This family is also found in eukaryotes and Bacteria. 109 matched cddid_all.tbl CDD pfam19251 pfam19251 437083 DUF5899 Family of unknown function (DUF5899). This is a family of uncharacterized proteins of unknown function predominantly found in Mimiviridae and Phycodnaviridae. 139 matched cddid_all.tbl CDD pfam19252 pfam19252 466011 HIND HIND motif. The Hub1 interacting motif (HIND) is a short motif found in 1 to 3 copies in spliceosomal proteins such as Snu66. The motif is bound by the Hub1 protein. 22 matched cddid_all.tbl CDD pfam19253 pfam19253 437085 DUF5900 Family of unknown function (DUF5900). This is a family of uncharacterized proteins of unknown function found in viruses. These proteins are thought to include F-box domain containing proteins, a conserved domain present in numerous proteins, involved in protein- protein interaction. 100 matched cddid_all.tbl CDD pfam19254 pfam19254 437086 DUF5901 Family of unknown function (DUF5901). This is a family of uncharacterized proteins of unknown function predominantly found in Phycodnaviridae. This family also includes proteins found in plants. 47 matched cddid_all.tbl CDD pfam19255 pfam19255 437087 DUF5902 Family of unknown function (DUF5902). This is a family of uncharacterized proteins of unknown function predominantly found in viruses. 104 matched cddid_all.tbl CDD pfam19256 pfam19256 466012 LAIKA LAIKA domain. This presumed domain is found exclusively in the CCAR1 protein. 68 matched cddid_all.tbl CDD pfam19257 pfam19257 466013 BURAN BURAN domain. This presumed domain is found exclusively in the CCAR1 protein. 82 matched cddid_all.tbl CDD pfam19258 pfam19258 466014 KxYKxGKxW_sig KxYKxGKxW signal peptide. This entry represents a novel form of signal peptide that occurs as an N-terminal domain with a recognizable motif, reminiscent of the YSIRK signal peptide. 41 matched cddid_all.tbl CDD pfam19259 pfam19259 437091 Ty3_capsid Ty3 transposon capsid-like protein. This entry corresponds to the capsid protein found in the Ty3 transposons of yeast as well as other transposable elements. 197 matched cddid_all.tbl CDD pfam19260 pfam19260 437092 DUF5903 Family of unknown function (DUF5903). This is a family of uncharacterized proteins of unknown function mostly found in Prasinoviruses. 129 matched cddid_all.tbl CDD pfam19261 pfam19261 437093 DUF5904 Domain of unknown function (DUF5904). This family represents a domain of unknown function that is found in Phycodnaviridae. This entry is likely to represent membrane proteins with four transmembrane regions. 133 matched cddid_all.tbl CDD pfam19262 pfam19262 466015 DUF5905 Family of unknown function (DUF5905). This is a family of uncharacterized proteins of unknown function predominantly found in Marseilleviridae. 105 matched cddid_all.tbl CDD pfam19263 pfam19263 466016 DUF5906 Family of unknown function (DUF5906). This is a family of proteins of unknown function found in viruses. This family is a P-loop member whose proteins are thought to be SF3 helicases, which are involved in replication initiation. 114 matched cddid_all.tbl CDD pfam19264 pfam19264 437096 DUF5907 Repeat of unknown function (DUF5907). This entry represents a protein repeats whose length varies between 50 and 80 residues. It is found in a variety of iridoviruses. It may be distantly related to minor tail protein found in phages. 80 matched cddid_all.tbl CDD pfam19265 pfam19265 466017 DUF5908 Family of unknown function (DUF5908). This short protein of unknown function is found within the operon of a contractile injection system of Photorhabdus asymbiotica. 55 matched cddid_all.tbl CDD pfam19266 pfam19266 466018 CIS_tube Contractile injection system tube protein. This protein is part of a contractile injection system. This family includes the Pvc7 protein from the Photorhabdus asymbiotica virulence cassette (PVC). Pvc7 is made of a tube protein (this entry) and an additional LysM domain. The equivalents of these two parts in T4 phage are gp48 and gp53, respectively. 158 matched cddid_all.tbl CDD pfam19267 pfam19267 437099 CIS_spike_tip Contractile injection system spike tip protein. This entry represents the spike tip protein from a contractile injection system. This entry includes Pvc10 (the homolog of T4 gp5.4). This protein was part of a CryoEM structure and although not resolved at atomic resolution in the map, it forms the sharp conical tip on the Pvc8 spike. 141 matched cddid_all.tbl CDD pfam19268 pfam19268 466019 CIS_TMP Contractile injection system tape measure protein. This protein is found as part of contractile injection systems. It is the tape measure protein which dictates the length of the syringe tail. It is found in low copy number. This protein is most likely not present in the mature syringes. Deletion of the tape measure protein Pvc14 resulted in large variations in the length of the syringes. The N and C-termini of these proteins are well conserved, but they have a wide length variation in the central region. 470 matched cddid_all.tbl CDD pfam19269 pfam19269 466020 Anticodon_2 Anticodon binding domain. This entry represents the anticodon binding domain found at the C-terminus of the class-I glutamyl tRNA synthetase enzyme. 148 matched cddid_all.tbl CDD pfam19270 pfam19270 466021 FBO_C F-box only protein C-terminal region. This entry represents the C-terminal region of several F-box only proteins. These proteins are the substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins. This family includes yeast HRT3 protein as well as human F-box only 9 protein. 211 matched cddid_all.tbl CDD pfam19271 pfam19271 437103 Nis1 Nis1 family. Necrosis-inducing secreted protein 1 (Nis1) is a fungal secreted effector that induces necrotic lesions in plants it infects (2). This protein interacts with the host receptor-like kinases and inhibits their kinase activity. 114 matched cddid_all.tbl CDD pfam19272 pfam19272 466022 ASMase_C Acid sphingomyelin phosphodiesterase C-terminal region. This entry corresponds to the C-terminal region of the phosphodiesterase domain found in acid sphingomyelin phosphodiesterases. It contains two disulphide bridges. 143 matched cddid_all.tbl CDD pfam19273 pfam19273 437105 Exportin-5 Exportin-5 family. Exportin-5 mediates the nuclear export of proteins bearing a double-stranded RNA binding domain (dsRBD) and double-stranded RNAs (cargos). Exportin-5 yeast homolog, also known as Msn5, is involved in nuclear import of replication protein A and export of Far1 and transcription factors Swi5, Swi6, Msn2, and Pho4. Its Arabidopsis homolog, HASTY 1, is involved in the nuclear export of microRNAs (miRNAs). 811 matched cddid_all.tbl CDD pfam19274 pfam19274 437106 PI4K_N PI4-kinase N-terminal region. This entry represents the long non-catalytic N-terminal region in PI4K proteins. This region forms a large alpha solenoid structure. 1179 matched cddid_all.tbl CDD pfam19275 pfam19275 437107 HflX_C HflX C-terminal domain. This entry represents the C-terminal domain of the HflX protein. HflX binds to the intersubunit face of the 50S subunit. Its C-terminal domain (CTD) predominantly interacts with the NTD of uL11 at the bL12 stalk base. Truncation of the CTD rendered HflX inactive in 70S splitting. 102 matched cddid_all.tbl CDD pfam19276 pfam19276 466023 HD_assoc_2 HD associated region. This entry represents a region that forms part of a larger HD domain.According to the original paper describing the HD domain this family represents cluster 1. 222 matched cddid_all.tbl CDD pfam19277 pfam19277 466024 GPAT_C Glycerol-3-phosphate acyltransferase C-terminal region. This entry represents the C-terminal region of Glycerol-3-phosphate acyltransferase. 370 matched cddid_all.tbl CDD pfam19278 pfam19278 437110 Hydant_A_C Hydantoinase/oxoprolinase C-terminal domain. This domain is found at the C-terminus of acetophenone carboxylase alpha subunit. According to ECOD this domain adopts a reverse ferredoxin fold. This domain is found at the C-terminus of a wide range of related enzymes subunits. 193 matched cddid_all.tbl CDD pfam19279 pfam19279 437111 YegS_C YegS C-terminal NAD kinase beta sandwich-like domain. This entry represents the C-terminal domain found in the YegS protein. It is related to the beta sandwich domain of NAD kinases. The structure of YegS reveals a two-domain protein with the active site crevice found between the two domains. The C-terminal domain contains 13 beta-strands and two alpha-helices. The likely substrate for YegS is phosphatidylglycerol. 158 matched cddid_all.tbl CDD pfam19280 pfam19280 466025 CERK_C Ceramide kinase C-terminal domain. This domain is found at the C-terminus of ceramide kinase enzymes. It is related to the beta sandwich domain of NAD kinases. Along with the N-terminal domain it catalyzes specifically the phosphorylation of ceramide to form ceramide 1-phosphate. This family contains ceramide kinase like proteins that lack the ceramide kinase activity. It also contains ore distantly related proteins this may have different functions. 222 matched cddid_all.tbl CDD pfam19281 pfam19281 437113 PHYHIP_C Phytanoyl-CoA hydroxylase-interacting protein C-terminus. This entry includes PHYHIP and PHYHIPL from humans. PHYHIP interacts with DYRK1A and may contribute to new cellular functions of DYRK1A. 221 matched cddid_all.tbl CDD pfam19282 pfam19282 437114 Exportin-T Exportin-T. Exportin-T mediates the nuclear export of aminoacylated tRNAs. Its budding yeast homolog, known as Los1, is involved in nuclear export of pre-tRNA and in re-export of mature tRNAs. It binds to RanGTP and mature tRNAs cooperatively to form a nuclear export complex. 687 matched cddid_all.tbl CDD pfam19283 pfam19283 466026 APEH_N Acylamino-acid-releasing enzyme, N-terminal domain. This entry represents the N-terminal region from the Acylamino-acid-releasing enzyme (EC:3.4.19.1). The protein is involved in removing the N-acetyl or N-formyl amino acid from the N-terminus of a polypeptide. This domain does not represent the catalytic domain which is found at the C-terminus of these proteins. 274 matched cddid_all.tbl CDD pfam19284 pfam19284 437116 Arc_MA Arc MA domain. This is the N-terminal matrix-like domain (MA) of Activity-Regulated Cytoskeleton-Associated protein (Arc). This domain might be involved in stabilising the relative domain orientations of the capside-like domain (CA) upon capsid assembly. Arc is a regulator of synaptic scaling and dendrite remodelling. 108 matched cddid_all.tbl CDD pfam19285 pfam19285 466027 NmU-R2_C_term Neuromedin-U receptor 2, C-terminal. This domain represents the C-terminal region of the Neuromedin-U receptor 2, a rhodopsin-like GPCR member. It contains two potential casein kinase II phosphorylation sites at threonines residues and one protein kinase C phosphorylation site at a serine residue, which are important to regulate the receptor functionality. This receptor is predominantly expressed in the central nervous system, particularly in the medulla oblongata, pontine reticular formation, spinal cord and thalamus, as its physiological roles are related to modulation of sensory function, neuroendocrine control, food intake as well as with circadian rhythm. However, peripheral expression of this receptor has been determined and includes kidney (medulla), lung and trachea. 67 matched cddid_all.tbl CDD pfam19286 pfam19286 466028 DUF5909 Domain of unknown function (DUF5909). This is the C-terminal region of the Zinc finger SWIM domain-containing protein 1, whose function is currently unknown. 84 matched cddid_all.tbl CDD pfam19287 pfam19287 466029 DUF5910 Family of unknown function (DUF5910). This entry corresponds to a protein precursor of a peptide from the edible fungi Cordyceps militaris is said to induce apoptosis in mammalian cell lines in vitro. 129 matched cddid_all.tbl CDD pfam19288 pfam19288 437120 CofH_C CofH/MqnC C-terminal region. This entry represents the C-terminal half of the CofH and MqnC enzymes. This entry is found to the C-terminus of pfam04055. 125 matched cddid_all.tbl CDD pfam19289 pfam19289 437121 PmbA_TldD_C PmbA/TldA metallopeptidase C-terminal domain. This entry represents a group of metalloproteases. The tertiary structure of the Escherichia coli TdlD/TdlE complex has been solved, and shows that the TdlD subunit is the active peptidase, binding a single zinc ion at an HEXXXH motif in which the glutamic acid is a substrate-binding residue and the two histidines are zinc ligands. The third zinc ligand is a cysteine, C-terminal to the HEXXXH motif. The TldE (also known as PmbA) by itself has no catalytic activity, does not bind zinc, and does not carry the HEXXXH motif. TldD and TldE were originally identified as regulators of DNA gyrase. Later, they are shown to be metalloproteases involved in CcdA degradation. 221 matched cddid_all.tbl CDD pfam19290 pfam19290 437122 PmbA_TldD_M PmbA/TldA metallopeptidase central domain. This entry represents a group of metalloproteases. The tertiary structure of the Escherichia coli TdlD/TdlE complex has been solved, and shows that the TdlD subunit is the active peptidase, binding a single zinc ion at an HEXXXH motif in which the glutamic acid is a substrate-binding residue and the two histidines are zinc ligands. The third zinc ligand is a cysteine, C-terminal to the HEXXXH motif. The TldE (also known as PmbA) by itself has no catalytic activity, does not bind zinc, and does not carry the HEXXXH motif. TldD and TldE were originally identified as regulators of DNA gyrase. Later, they are shown to be metalloproteases involved in CcdA degradation. 106 matched cddid_all.tbl CDD pfam19291 pfam19291 437123 TREH_N Trehalase-like, N-terminal. This presumed domain is found at the N-terminal region of bacterial and archaeal trehalases which catalyze the hydrolysis of alpha,alpha-trehalose into two molecules of D-glucose, followed by the glycoside hydrolase domain (pfam00723). This domain is also found in the uncharacterized protein C4H3.03c from S. pombe. The function of this domain is not clear. 212 matched cddid_all.tbl CDD pfam19292 pfam19292 437124 KPBB_C Phosphorylase b kinase C-terminal domain. This entry represents the C-terminal domain found in Phosphorylase b kinase regulatory alpha and beta subunits, which control the catalytic activity of the Phosphorylase kinase catalytic gamma subunit. this domain has been proposed as the second calcineurin B-like (CBL-2) domain containing a gamma subunit-binding site. 238 matched cddid_all.tbl CDD pfam19293 pfam19293 437125 CdaA_N CdaA N-terminal transmembrane domain. This entry represents the amino terminal three helical transmembrane region found in the CdaA diadenylate cyclase enzyme. 81 matched cddid_all.tbl CDD pfam19294 pfam19294 437126 DACZ_N Diadenylate cyclase, N-terminal. This domain is found at the N-terminus of the DacZ diadenylate cyclase enzyme from euryarchaea. This domain appears to be distantly related to the C-terminal domain of pyruvate kinase pfam02887. 125 matched cddid_all.tbl CDD pfam19295 pfam19295 437127 SufBD_N SufBD protein N-terminal region. This entry represents the N-terminal part of the SufB and SufD proteins. It has a right handed beta helix structure. This family is associated with the C-terminal region pfam01458 172 matched cddid_all.tbl CDD pfam19296 pfam19296 437128 RelA_AH_RIS RelA/SpoT, AH and RIS domains. This entry represents the alpha helical (AH) and Ribosome-InterSubunit (RIS) domains found in RelA/SpoT proteins, adjacent to the ACT domain. AH domain interacts with A/R tRNA and links the very C-terminal subdomains with TGS domain. The RIS domain is part of the binding interface between the C-terminal region and the ribosome, bridging the large and the small ribosomal subunits. RIS contains a four-stranded beta-sheet and a short alpha-helix. RelA/SpoT-homolog proteins (RHS) mediate the stringent response in bacteria which enables its metabolic adaptation under stress conditions. These enzymes synthesize the second messenger (p)ppGpp, which is a regulatory metabolite of the stringent response characterized by growth arrest and the modulation of gene expression in response to various nutritional stresses. 185 matched cddid_all.tbl CDD pfam19297 pfam19297 466030 QcrA_N QcrA subunit N-terminal region. This entry describes the N-terminal region of the QcrA subunit which is part of respiratory complex III. This region includes anchoring transmembrane helical regions. 221 matched cddid_all.tbl CDD pfam19298 pfam19298 466031 KshA_C 3-Ketosteroid 9alpha-hydroxylase C-terminal domain. KshAB is a complex of KshA and KshB that catalyzes the 3-Ketosteroid 9alpha-hydroxylase reaction. This entry represents the C-terminal domain catalytic domain of KshA. This domain The catalytic domain shares the TBP-like fold found in other Rieske oxygenases. 203 matched cddid_all.tbl CDD pfam19299 pfam19299 466032 DUF5914 Domain of unknown function (DUF5914). This presumed domain is found to the C-terminus of pfam00355. This family includes a protein called CrtV that may be a methyltransferase or demethylase. 185 matched cddid_all.tbl CDD pfam19300 pfam19300 437132 BPD_transp_1_N Binding-prot-dependent transport system membrane comp, N-term. This is the N-terminal transmembrane domain of the Binding-protein-dependent transport system inner membrane component. 114 matched cddid_all.tbl CDD pfam19301 pfam19301 437133 LigXa_C LigXa C-terminal domain like. This entry represents the C-terminal domain of a Rieske oxygenase enzyme. This entry includes the 5,5'-dehydrodivanillate O-demethylase three-component monooxygenase which is composed of an oxygenase (LigXa) in this entry, a ferredoxin (LigXc) and a ferredoxin reductase (LigXd). 303 matched cddid_all.tbl CDD pfam19302 pfam19302 437134 DUF5915 Domain of unknown function (DUF5915). This presumed domain is found at the C-terminus of isoleucyl tRNA ligase enzymes. 195 matched cddid_all.tbl CDD pfam19303 pfam19303 437135 Anticodon_3 Anticodon binding domain of methionyl tRNA ligase. This domain is found in methionyl tRNA ligase. The domain binds to the anticodon of the tRNA ligase. 152 matched cddid_all.tbl CDD pfam19304 pfam19304 437136 PGDH_inter D-3-phosphoglycerate dehydrogenase intervening domain. This domain is found in the D-3-phosphoglycerate dehydrogenase enzyme. In the structure of the Mycobacterium tuberculosis enzyme this domain was described as the intervening domain, also known as the allosteric substrate binding domain (ASB). The intervening domain between the substrate-binding and regulatory domains is not present in E. coli PGDH. This domain is closely related to pfam03315. It serves as an anion-binding site and may function as an allosteric site for the control of enzyme activity. 119 matched cddid_all.tbl CDD pfam19305 pfam19305 466033 MmgE_PrpD_C MmgE/PrpD C-terminal domain. This entry represents the C-terminal domain of 2-methylcitrate dehydratase EC:4.2.1.79 (PrpD) that is required for propionate catabolism. It catalyzes the third step of the 2-methylcitric acid cycle. This domain is related to the serine dehydratase beta chain. 173 matched cddid_all.tbl CDD pfam19306 pfam19306 437138 Lhr_WH Helicase Lhr winged helix domain. Mycobacterial Lhr is a DNA damage-inducible superfamily 2 helicase that uses adenosine triphosphate (ATP) hydrolysis to drive unidirectional 3' to 5' translocation along single-stranded DNA (ssDNA). This entry represents the third domain which has a winged helix domain fold. 147 matched cddid_all.tbl CDD pfam19307 pfam19307 437139 PCLP Phage capsid-like protein. This entry includes the immunodominant 35 kDa protein of Mycobacterium leprae. This protein is functionally uncharacterized, but it forms a large 950 kDa complex with itself. This protein was shown not to be exported from the bacterium. Some members of this family contain an N-terminal cyclic nucleotide binding domain pfam00027. This family includes proteins annotated as phage capsid proteins, such as UniProt:A0A1X9IAH4 suggesting that in bacteria this protein is a co-opted phage protein. 254 matched cddid_all.tbl CDD pfam19308 pfam19308 437140 CRISPR_Cas6_N CRISPR Cas6 N-terminal domain. In Type I and III CRISPR/Cas systems, the Cas6 family of endoribonucleases generates functional CRISPR-derived RNAs by site-specific cleavage of repeat sequences in precursor transcripts. The structure of Cas6 showed it adopts a tandem ferredoxin/RRM fold. This entry represents the N-terminal domain. 147 matched cddid_all.tbl CDD pfam19309 pfam19309 466034 Frem_N Frem protein N-terminal domain. This entry represents a presumed domain found at the N-terminus of Frem related proteins. 202 matched cddid_all.tbl CDD pfam19310 pfam19310 437142 TOP_N Neurolysin/Thimet oligopeptidase, N-terminal domain. Thimet oligopeptidase and neurolysin are closely related zinc-dependent metallopeptidases that metabolize small bioactive peptides. They cleave many substrates at the same sites, but they recognize different positions on others. This entry represents the up-down alpha bundle domain found at the N terminus of these and related M3 peptidases. 123 matched cddid_all.tbl CDD pfam19311 pfam19311 466035 KELAA KELAA motif. This short motif is found at the C-terminus of FHIP proteins, FAM160B proteins and UPF0518 family proteins. It has a conserved KELAA sequence for which it is named. 32 matched cddid_all.tbl CDD pfam19312 pfam19312 437144 NtrY_N NtrY N-terminal region. This entry represents the probable sensor region of the two component regulator protein NtrY. This region includes four probable transmembrane helices. 291 matched cddid_all.tbl CDD pfam19313 pfam19313 466036 DUF5916 Domain of unknown function (DUF5916). This entry represents a long region of similarity found to the C-terminus of a CBM9 domain. According to BOCTOPUS prediction this region has a membrane barrel topology suggesting this entry may represent a novel carbohydrate channel. 572 matched cddid_all.tbl CDD pfam19314 pfam19314 466037 DUF5917 Family of unknown function (DUF5917). This short presumed domain is found close to the C-terminus of FHIP proteins, FAM160B proteins and UPF0518 family proteins. 94 matched cddid_all.tbl CDD pfam19315 pfam19315 437147 MC_hydratase Mesaconyl-CoA hydratase. UniProt:G0HQ35 (HAH_1340) has been characterized as a mesaconyl-CoA hydratase. This enzyme belongs to the HotDog superfamily and contains two HotDog domains. This enzyme is most closely related to pfam01575. 352 matched cddid_all.tbl CDD pfam19316 pfam19316 437148 PIGO_PIGG GPI ethanolamine phosphate transferase membrane region. This entry corresponds to the transmembrane region of the GPI ethanolamine phosphate transferase enzymes. The family includes the PIGO and PIGG proteins from human. These proteins are involved in the pathway glycosylphosphatidylinositol-anchor biosynthesis. 423 matched cddid_all.tbl CDD pfam19317 pfam19317 466038 Gag_p24_C Gag protein p24 C-terminal domain. p24 forms inner protein layer of the nucleocapsid. ELISA tests for p24 is the most commonly used method to demonstrate virus replication both in vivo and in vitro. 74 matched cddid_all.tbl CDD pfam19318 pfam19318 466039 DUF5918 Family of unknown function (DUF5918). This family represents the N-terminal domain of the RING finger protein 37 (RNF37), an U-box domain-containing protein. This is a variable region that probably has a role in function regulation. 211 matched cddid_all.tbl CDD pfam19319 pfam19319 437151 DUF5919 Domain of unknown function (DUF5919). This is the C-terminal domain of pfam18725 domain-containing proteins, whose function is unknown. 161 matched cddid_all.tbl CDD pfam19320 pfam19320 437152 GlfT2_domain3 Galactofuranosyltransferase-2, domain 3. This entry represents the third domain of GlfT2 (Rv3808c), a polymerizing galactofuranosyltransferase that synthesizes the galactan portion of the peptidoglycan complex of the mycobacteria cell wall. It consists of eight alpha-helices, five of which immediately follow the glycosyltransferase (GT) domain and form the central portion of domain 3. Three helices at the C terminus of the polypeptide chain wrap around these core helices to complete the domain. The first helix in domain 3 anchors loop 1 and is conserved in many GT-A proteins. The flanking domains and many hydrophobic residues found at the interface between domains 2 and 3 of this protein are conserved among many proteins of mycobacteria, related Actinobacteria and more distantly related species, suggesting conserved structure structure and function relationships. The alpha2- and alpha6-helices from domain 3 and alpha1 from domain 4 contribute with a patch of exposed hydrophobic residues which probably generate a binding site for the hydrophobic acyl chains of membrane phospholipids. These surface-exposed hydrophobic residues may also contribute to the specificity and affinity binding of UDP donors. 197 matched cddid_all.tbl CDD pfam19321 pfam19321 466040 KCTD18_C BTB/POZ domain-containing protein KCTD18 C-terminus. This entry represents the C-terminal region of BTB/POZ domain-containing protein KCTD18. This domain is highly variable among the BTB domain-containing KCTD proteins and it has been proposed that it could be used to bind and recruit diverse cellular proteins destined for different processes such as ubiquitination and degradation or regulation of G-protein coupled receptors. 309 matched cddid_all.tbl CDD pfam19322 pfam19322 466041 RKP_N E3 ubiquitin-protein ligase RKP N-terminus. This domain represents the N-terminal region of the E3 ubiquitin-protein ligase RKP from plants. It was demonstrated that RKP is a functional ubiquitin E3 ligase and is able to interact with cell-cycle inhibitor ICK/KRP proteins. 137 matched cddid_all.tbl CDD pfam19323 pfam19323 437155 KCTD4_C BTB/POZ domain-containing protein KCTD4 C-terminus. This entry represents the C-terminal region of BTB/POZ domain-containing protein KCTD4. This domain is highly variable among the BTB domain-containing KCTD proteins and it has been proposed that it could play a role in binding or recruiting diverse protein targets involved in different cellular processes, such us ubiquitination, cell proliferation or control of G-protein coupled receptors, among others. 122 matched cddid_all.tbl CDD pfam19324 pfam19324 466042 LETM2_N LETM1 domain-containing protein LETM2 N-terminus. This family represents the N-terminal region of the LETM1-domain- containing protein LETM2, a mitochondrial protein that is expressed preferentially in spermatocytes and spermatozoa during developmental stages from spermatocyte to spermatozoon. LETM2 might contribute to the reorganization of the inner and cristae membranes during spermatogenesis. Despite its name, it does not contain an EF-hand domain as LETM1, but it contains a putative leucine zipper coiled coil domain. 111 matched cddid_all.tbl CDD pfam19325 pfam19325 437157 RNF152_C E3 ubiquitin-protein ligase RNF152 C-terminus. This family represents the C-terminal region of the E3 ubiquitin ligase RNF152 containing the hydrophobic transmembrane domain, responsible for the lysosomal localization of the protein as well as its ubiquitination activity. This protein polyubiquitinates several proteins and itself, which leads to proteasome degradation. It has been shown that RNF152 has also pro-apoptotic activity, dependent on its RING finger and transmembrane domains. In addition, the transmembrane domain of RNF152 is necessary for negative regulation of the mTORC1 pathway in an amino-acid-sensitive manner, as it mediates RNF152-RagA interaction and RagA ubiquitination. 136 matched cddid_all.tbl CDD pfam19326 pfam19326 437158 AMP_deaminase AMP deaminase. 622 matched cddid_all.tbl CDD pfam19327 pfam19327 437159 Ap4A_phos_N Ap4A phosphorylase N-terminal domain. This entry represents the N-terminal HIT-like domain from the Ap4A phosphorylase enzyme. 179 matched cddid_all.tbl CDD pfam19328 pfam19328 437160 DAP_DH_C 2,4-diaminopentanoate dehydrogenase C-terminal domain. This entry represents the C-terminal presumed domain from the 2,4-diaminopentanoic acid C 4 dehydrogenase enzyme. This enzyme is involved in the ornithine fermentation pathway. It catalyzes the oxidative deamination of (2R,4S)-2,4-diaminopentanoate (DAP) to yield 2-amino-4-ketopentanoate (AKP). The N-terminal domain has a Rossmann fold. 206 matched cddid_all.tbl CDD pfam19329 pfam19329 466043 KCTD11_21_C BTB/POZ domain-containing protein KCTD11/21 C-terminus. This family represents the C-terminal region of BTB/POZ domain-containing protein KCTD11 (known as REN: EGF-, NGF- and retinoic acid-responsive gene) and one homolog, a member of KCTD containing, Cullin3 adaptor, suppressor of Hedgehog (KCASH) family, KCASH2-KCTD21 protein. They share high similarity and a BTB domain responsible for oligomerization and formation of a Cullin3 ubiquitin ligase complex, specific expression in brain and cerebellum where they have a role in neuronal differentiation, and suppressor activity on acetylation-dependent Hedgehog/Gli signalling through ubiquitination and degradation of histone deacetylase 1. These proteins have been described as tumor suppressors that inhibit medulloblastoma growth by antagonizing Hedgehog signalling. 154 matched cddid_all.tbl CDD pfam19330 pfam19330 437162 DNER_C Delta and Notch-like EGF-related receptor C-terminus. This family represents the C-terminal region of the Delta and Notch-like epidermal growth factor-related receptor (DNER) containing the transmembrane domain and the short cytoplasmic region including AP-1-binding site required for its somatodendritic distribution. This receptor is highly expressed in Purkinje cells taking part in the differentiation and maturation of Bergmann glia via physical contact with Purkinje cells and granular cells. Recently, it has been demonstrated that DNER is induced in lung recruited macrophages after chronic inflammation in which induces IFNgamma expression via a non-canonical Notch NFkappaB pathway. 112 matched cddid_all.tbl CDD pfam19331 pfam19331 437163 MCCA_BT Methylcrotonoyl-CoA carboxylase subunit alpha BT domain. This family represents the BT domain in the methylcrotonoyl-CoA carboxylase subunit alpha, located between the biotin carboxylase (BC) and biotin carboxyl carrier protein (BCCP) domains. This domain mediates crucial interactions between the BC domain in the the alpha subunit and the carboxyltransferase (CT) domain in the beta subunit of this enzyme which are based on ion-pair, hydrogen-bonding and hydrophobic interactions. This domain has a backbone fold with a long helix surrounded by an eight-stranded anti-parallel beta barrel. There is a hook comprising the C-terminal part of the helix and the loop connecting it to the first strand of the beta barrel, which appears to have a central role in alpha and beta subunits interactions. 165 matched cddid_all.tbl CDD pfam19332 pfam19332 437164 RNF180_C E3 ubiquitin-protein ligase RNF180 C-terminus. This family represents the C-terminal region of the E3 ubiquitin-protein ligase RNF180 (Also known as Rines: RING finger protein in neural stem cells) which comprises its transmembrane domain. This is an integral membrane protein located mainly on the cytoplasmic side of the endoplasmic reticulum and functions as an E3 ubiquitin ligase. It is thought that it is involved in modulation of neuronal function, such as regulation of synaptic structure and synaptic plasticity due to its high expression in mature brain. 101 matched cddid_all.tbl CDD pfam19333 pfam19333 466044 FAXC_N Failed axon connections homolog N-terminus. This family represents the N-terminal domain of the failed axon connections homolog (FAXC). This protein is localized to the cellular membranes, thus it is likely that this region anchors it to the plasma membrane. It is thought to play a role in axonal development, being involved in cell-cell interactions. 104 matched cddid_all.tbl CDD pfam19334 pfam19334 466045 DUF5920 Domain of unknown function (DUF5920). This domain is found in the Telomerase protein component 1 (TEP1) and it contains an homology region to the telomerase associated protein from Tetrahymena p80. TEP1 is a component of the telomerase ribonucleoprotein complex and is thought to be responsible for catalysing the addition of new telomeres to chromosomes. TEP1 is also a component of the vault particle, a cytoplasmic ribonucleoprotein complex, in which it is required for vault RNA stability and its association with the vault particle. This domain is localized between the TROVE (pfam05731) and DUF4062 (pfam13271) domains. 203 matched cddid_all.tbl CDD pfam19335 pfam19335 437167 HMBD Heavy metal binding domain. This domain is a copper-binding domain found in single or multiple copies at the N-terminus of a wide variety of copper or other heavy metal binding transporters and other proteins. 28 matched cddid_all.tbl CDD pfam19336 pfam19336 466046 DUF5921 Domain of unknown function (DUF5921). This family represents a domain of unknown function located between the Transcription factor IIIC subunit delta N-term (pfam12657) and the Putative zinc-finger of transcription factor IIIC complex (pfam12660) within the transcription Factor IIIC 90 kDa subunit (TFIIIC-delta/TFIIIC90, also known as general transcription factor 3C polypeptide 4). TFIIIC is a multisubunit complex that directly recognizes promoter elements and recruits TFIIIB and RNA polymerase III, being absolutely required for RNA polymerase III transcription. TFIIIC90 has an intrinsic histone acetyltransferase activity with a substrate specificity for histone H3. This domain is likely to be involved in the interaction with other components of the TFIIIC complex. 431 matched cddid_all.tbl CDD pfam19337 pfam19337 437169 BAMBI_C BMP and activin membrane-bound inhibitor homolog C-terminus. This family represents the C-terminal domain of BMP and activin membrane-bound inhibitor homolog (BAMBI) which contains the transmembrane domain and a short intracellular domain that, unlike all other known TGF-beta type I or type II receptors, does not encode a serine/threonine-kinase domain. However, it shares sequence homology with the E6 and catalytic loops of receptor serine/threonine kinases. BAMBI is an essential regulator of cell proliferation and differentiation that represses transforming growth factor-beta and enhances Wnt/beta-catenin signalling in various cell types. It stably associates with TGF-beta-family receptors and inhibits BMP and activin as well as TGF-beta signalling. 138 matched cddid_all.tbl CDD pfam19338 pfam19338 437170 NTF3_N Neutrophin-3 N-terminus. This family represents the N-terminal region of neutrophin-3 (NTF3) which contains two precursor homology regions located upstream of the mature NTF3 sequence. These regions play important and specific roles in the folding, processing and transport of neurotrophic factors. 114 matched cddid_all.tbl CDD pfam19339 pfam19339 466047 ANGEL2_N Protein angel homolog 2 N-terminal. This family represents the N-terminal unstructured domain of the protein angel homolog 2 (ANGEL2). This protein is a member of the CCR4 nocturin family and 2',3'-cyclic phosphatase activity involved in RNA processing and modification. 172 matched cddid_all.tbl CDD pfam19340 pfam19340 466048 GCP6_N Gamma-tubulin complex component 6 N-terminus. This family represents the N-terminal alpha-helical region of Gamma-tubulin complex component 6 (GCP6), a protein indispensable for assembly of the gamma-tubulin complex and for microtubule nucleation. It is located at the centrioles and the pericentriolar material, being required for centriole formation and reduplication. It has been shown that the N-terminal domains define the functional identity of gamma-tubulin complex proteins. GCP6 carries a large internal insertion phosphorylated by Plk4 and contains a domain of interaction with keratins. 315 matched cddid_all.tbl CDD pfam19341 pfam19341 437173 B3GALT2_N Beta-1,3-galactosyltransferase 2 N-terminus. This family represents the N-terminal region of the beta-1,3- galactosyltransferase 2 which contains a short cytosolic region, a transmembrane region which indicates that this protein has a type II transmembrane topology, typical for all mammalian glycosyltransferases and a stem region with two putative N-glycosylation sites. This enzyme catalyzes the synthesis of type 1 carbohydrate chains, which contain the Gal(beta 1-3) GlcNAc linkage. 81 matched cddid_all.tbl CDD pfam19342 pfam19342 437174 MGP3_C MGP3 C-terminal domain. This entry represents the C-terminal domain from the Mycoplasma genitalium p110 adhesin protein. This domain has an Ig fold. It is adjacent to the membrane. This domain contains a bound potassium ion. 113 matched cddid_all.tbl CDD pfam19343 pfam19343 466049 DUF5923 Family of unknown function (DUF5923). This entry represents a family of uncharacterized fungal proteins. These proteins often also contain a C-terminal pfam14613 domain. 630 matched cddid_all.tbl CDD pfam19344 pfam19344 437176 TetR_C_32 Tetracyclin repressor-like, C-terminal domain. This is the C-terminal domain found in putative transcriptional regulator, TetR family proteins. 139 matched cddid_all.tbl CDD pfam19345 pfam19345 437177 MTHFR_2 Mycobacterial methylenetetrahydrofolate reductase. This family includes the 5,10-methylenetetrahydrofolate reductase EC:1.7.99.5 from mycobacteria. The structure for this domain is known to be a TIM barrel. Both MTHFR1 and MTHFR2 found in Mycobacterium smegmatis are involved in de novo methionine biosynthesis and required for antifolate resistance in mycobacteria. Both of these MTHFRs are monomeric and lack flavin coenzymes. 295 matched cddid_all.tbl CDD pfam19346 pfam19346 437178 DUF5924 Family of unknown function (DUF5924). This family of uncharacterized proteins is found in bacteria. This entry represents a likely integral membrane region with six transmembrane helices. The family is found in association with pfam11141. 259 matched cddid_all.tbl CDD pfam19347 pfam19347 437179 DUF5925 Domain of unknown function (DUF5925). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and viruses, and is approximately 180 amino acids in length. The family is found to the N-terminus of pfam00004. There are three conserved sequence motifs: GWT, ELA and MGFW. Proteins in this family vary in length from 364 to 384 amino acids. The domains in this family vary in length from 177 to 180 amino acids. 178 matched cddid_all.tbl CDD pfam19348 pfam19348 437180 DUF5926 Family of unknown function (DUF5926). This entry represents a presumed domain that is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 294 and 327 amino acids in length. Many proteins in this family are annotated at Topoisomerase II, but the source of this annotation is unclear. 266 matched cddid_all.tbl CDD pfam19349 pfam19349 437181 DUF5927 Family of unknown function (DUF5927). This entry represents a presumed domain that is functionally uncharacterized. This domain family is primarily found in Rhodobacteria, and is approximately 300 amino acids in length. The family is found to the C-terminus of pfam02485 and so is likely to have a role in carbohydrate modification. 300 matched cddid_all.tbl CDD pfam19350 pfam19350 437182 DUF5928 Family of unknown function (DUF5928). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 260 amino acids in length. The family is found to the C-terminus of pfam02485 and so is likely to have a role in carbohydrate modification. 256 matched cddid_all.tbl CDD pfam19351 pfam19351 466050 DUF5929 Domain of unknown function (DUF5929). This presumed domain is functionally uncharacterized. This domain family is found in flavobacteria, and is approximately 220 amino acids in length. The family is found to the C-terminus of pfam04326. Proteins in this family vary in length from 377 to 380 amino acids. 222 matched cddid_all.tbl CDD pfam19352 pfam19352 466051 TetR_C_38 Tetracyclin repressor-like, C-terminal domain. This presumed domain belongs to the tetracycline repressor (TetR) C-terminal domain family of proteins, which are involved in a wide variety of gene regulations. This domain family is found in bacteria, and is approximately 140 amino acids in length. The family is found to the C-terminus of pfam00440. 135 matched cddid_all.tbl CDD pfam19353 pfam19353 466052 DUF5930 Family of unknown function (DUF5930). This family of proteins is functionally uncharacterized. This family of proteins is found in rhodobacteria. Proteins in this family are typically between 411 and 445 amino acids in length. The family is found to the N-terminus of pfam01551. 320 matched cddid_all.tbl CDD pfam19354 pfam19354 437186 DUF5931 Family of unknown function (DUF5931). This presumed domain is functionally uncharacterized. This domain family is found in actinobacteria, and is approximately 170 amino acids in length. This domain is found at the N-terminus of 2 component signalling proteins which also contain pfam07730, and pfam02518. This domain presumably binds an as yet unknown ligand. 175 matched cddid_all.tbl CDD pfam19355 pfam19355 437187 DUF5932 Family of unknown function (DUF5932). This presumed domain is functionally uncharacterized. This domain family is found in Bacteroidetes, and is approximately 110 amino acids in length. The family is found in association with pfam00072. There is a conserved PIL sequence motif. 111 matched cddid_all.tbl CDD pfam19356 pfam19356 466053 DUF5933 Domain of unknown function (DUF5933). This presumed domain is functionally uncharacterized. This domain family is found in Actinobacteria, and is approximately 140 amino acids in length. The family is found in association with pfam14378. 144 matched cddid_all.tbl CDD pfam19357 pfam19357 437189 DUF5934 Family of unknown function (DUF5934). This presumed domain found in type IV secretion system proteins is functionally uncharacterized. This domain family is found in proteobacteria, and is approximately 170 amino acids in length. The family is found in association with pfam11130. There are two conserved sequence motifs: GWDL and QGEY. 172 matched cddid_all.tbl CDD pfam19358 pfam19358 437190 DUF5935 Family of unknown function (DUF5935). This presumed domain is functionally uncharacterized, but is is found in O-antigen polymerase proteins. This domain family is mainly found in proteobacteria, and is approximately 190 amino acids in length. The family is found in association with pfam04932. 193 matched cddid_all.tbl CDD pfam19359 pfam19359 437191 DUF5936 Family of unknown function (DUF5936). This presumed domain is functionally uncharacterized although it is found in the Type 2 secretion protein F. This domain family is found in Actinobacteria, and is approximately 140 amino acids in length. The family is found in association with pfam00482. 141 matched cddid_all.tbl CDD pfam19360 pfam19360 437192 TadB_TadC_N TadB/TadC N-terminal domain. This presumed domain is functionally uncharacterized but is found at the N-terminus of type II secretion protein TadB or TadC. This domain family is mainly found in alpha proteobacteria, and is approximately 140 amino acids in length. The family is found in association with pfam00482. 143 matched cddid_all.tbl CDD pfam19361 pfam19361 466054 DUF5937 Family of unknown function (DUF5937). This family of proteins is functionally uncharacterized but contains a C-terminal DNA-binding HTH domain. This family is distantly related to pfam02624 suggesting it is likely to be a ligand binding domain. This family of proteins is found in actinobacteria and firmicutes. Proteins in this family are typically between 326 and 366 amino acids in length. 267 matched cddid_all.tbl CDD pfam19362 pfam19362 466055 DUF5938 Family of unknown function (DUF5938). This presumed domain is functionally uncharacterized. This domain family is found in proteobacteria and actinobacteria, and is approximately 240 amino acids in length. The family is found in association with pfam03435. 234 matched cddid_all.tbl CDD pfam19363 pfam19363 437195 DUF5939 Family of unknown function (DUF5939). This presumed domain is functionally uncharacterized. This domain family is found in a wide variety of bacteria such as proteobacteria, spirochaetes, firmicutes and actinobacteria, and is approximately 280 amino acids in length. The family is found in to the N-terminus of pfam00211. 281 matched cddid_all.tbl CDD pfam19364 pfam19364 437196 DUF5940 Family of unknown function (DUF5940). This presumed domain is functionally uncharacterized. This domain family is found mainly in firmicutes, and is approximately 170 amino acids in length. The family is found in association with pfam08545. 166 matched cddid_all.tbl CDD pfam19365 pfam19365 466056 DUF5941 Family of unknown function (DUF5941). This family of proteins is functionally uncharacterized. This family of proteins is found in actinobacteria. The family is found in association with pfam01066. This entry contains several transmembrane helices. 207 matched cddid_all.tbl CDD pfam19366 pfam19366 437198 DUF5942 Domain of unknown function (DUF5942). This presumed integral membrane domain is functionally uncharacterized. This domain family is found mainly in cyanobacteria, and is approximately 190 amino acids in length. The family is found to the C-terminus of pfam00082. 191 matched cddid_all.tbl CDD pfam19367 pfam19367 437199 DUF5943 Domain of unknown function (DUF5943). This presumed domain is functionally uncharacterized. This domain family is found in proteobacteria and sporadically in archaea, and is approximately 100 amino acids in length. There are two conserved sequence motifs: NNH and RLS. This domain is often found to the N-terminus of pfam02830. 96 matched cddid_all.tbl CDD pfam19368 pfam19368 437200 AraR_C AraR C-terminal winged HTH domain. This entry represents the C-terminal DNA-binding domain of AraR proteins which are involved in regulating Arabinose utilization. This domain has a winged helix-turn-helix structure. 82 matched cddid_all.tbl CDD pfam19369 pfam19369 437201 DUF5944 Family of unknown function (DUF5944). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001797) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 243 matched cddid_all.tbl CDD pfam19370 pfam19370 437202 DUF5945 Family of unknown function (DUF5945). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000561) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 130 matched cddid_all.tbl CDD pfam19371 pfam19371 466057 DUF5946 Family of unknown function (DUF5946). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001707) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 141 matched cddid_all.tbl CDD pfam19372 pfam19372 466058 DUF5947 Family of unknown function (DUF5947). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001065) is described by MIBiG as an example of the following biosynthetic class, polyketide. 179 matched cddid_all.tbl CDD pfam19373 pfam19373 437205 DUF5948 Family of unknown function (DUF5948). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001281) is described by MIBiG as an example of the following biosynthetic class, polyketide. 70 matched cddid_all.tbl CDD pfam19374 pfam19374 466059 DUF5949 Family of unknown function (DUF5949). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide. 167 matched cddid_all.tbl CDD pfam19375 pfam19375 466060 DUF5950 Family of unknown function (DUF5950). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001576) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 103 matched cddid_all.tbl CDD pfam19376 pfam19376 437208 DUF5951 Family of unknown function (DUF5951). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001805) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). 59 matched cddid_all.tbl CDD pfam19377 pfam19377 437209 DUF5952 Family of unknown function (DUF5952). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000178) is described by MIBiG as an example of the following biosynthetic class, polyketide. 93 matched cddid_all.tbl CDD pfam19378 pfam19378 437210 DUF5953 Family of unknown function (DUF5953). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001431) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. 233 matched cddid_all.tbl CDD pfam19379 pfam19379 466061 DUF5954 Family of unknown function (DUF5954). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001973) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). 295 matched cddid_all.tbl CDD pfam19380 pfam19380 437212 DUF5955 Family of unknown function (DUF5955). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001731) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). 88 matched cddid_all.tbl CDD pfam19381 pfam19381 437213 DUF5956 Family of unknown function (DUF5956). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001073) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. 100 matched cddid_all.tbl CDD pfam19382 pfam19382 437214 DUF5957 Family of unknown function (DUF5957). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001062) is described by MIBiG as an example of the following biosynthetic class, polyketide. 59 matched cddid_all.tbl CDD pfam19383 pfam19383 466062 DUF5958 Family of unknown function (DUF5958). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001920) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 125 matched cddid_all.tbl CDD pfam19384 pfam19384 466063 DUF5959 Family of unknown function (DUF5959). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001707) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 134 matched cddid_all.tbl CDD pfam19385 pfam19385 466064 DUF5960 Family of unknown function (DUF5960). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000561) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 83 matched cddid_all.tbl CDD pfam19386 pfam19386 437218 DUF5961 Family of unknown function (DUF5961). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000573) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 72 matched cddid_all.tbl CDD pfam19387 pfam19387 437219 DUF5962 Family of unknown function (DUF5962). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000498) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 99 matched cddid_all.tbl CDD pfam19388 pfam19388 437220 DUF5963 Family of unknown function (DUF5963). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001171) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 83 matched cddid_all.tbl CDD pfam19389 pfam19389 466065 DUF5964 Family of unknown function (DUF5964). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000523) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 60 matched cddid_all.tbl CDD pfam19390 pfam19390 437222 DUF5965 Family of unknown function (DUF5965). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000561) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 74 matched cddid_all.tbl CDD pfam19391 pfam19391 437223 DUF5966 Family of unknown function (DUF5966). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000498) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 95 matched cddid_all.tbl CDD pfam19392 pfam19392 437224 DUF5967 Family of unknown function (DUF5967). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000571) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 43 matched cddid_all.tbl CDD pfam19393 pfam19393 437225 DUF5968 Family of unknown function (DUF5968). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000566) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 150 matched cddid_all.tbl CDD pfam19394 pfam19394 437226 DUF5969 Family of unknown function (DUF5969). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000604) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 93 matched cddid_all.tbl CDD pfam19395 pfam19395 437227 DUF5970 Family of unknown function (DUF5970). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000616) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 77 matched cddid_all.tbl CDD pfam19396 pfam19396 437228 DUF5971 Family of unknown function (DUF5971). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001555) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 97 matched cddid_all.tbl CDD pfam19397 pfam19397 437229 DUF5972 Family of unknown function (DUF5972). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001634) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 28 matched cddid_all.tbl CDD pfam19398 pfam19398 466066 DUF5973 Family of unknown function (DUF5973). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001577) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 79 matched cddid_all.tbl CDD pfam19399 pfam19399 437231 DUF5974 Family of unknown function (DUF5974). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000576) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 38 matched cddid_all.tbl CDD pfam19400 pfam19400 437232 DUF5975 Family of unknown function (DUF5975). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000486) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 125 matched cddid_all.tbl CDD pfam19401 pfam19401 437233 DUF5976 Family of unknown function (DUF5976). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000624) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post-translationally modified peptide). 50 matched cddid_all.tbl CDD pfam19402 pfam19402 437234 RamS Lanthionine-containing peptide SapB precursor RamS. This entry represents a member of a biosynthetic gene cluster (BGC). The BGC (BGC0000551) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesized and post- translationally modified peptide). This family includes RamS, the precursor of lanthionine-containing peptide SapB (also known as ProSapB). SapB, which does not appear to exhibit antibiotic activity, is formed from RamS through proteolytic cleavage and subsequent creation of lanthionine bridges. 42 matched cddid_all.tbl CDD pfam19403 pfam19403 437235 SpaA_2 Prealbumin-like fold domain. Domain related to SpaA found as tandem repeats in bacterial surface proteins, associated with VWA and PA14 adhesins 97 matched cddid_all.tbl CDD pfam19404 pfam19404 437236 DUF5977 Family of unknown function (DUF5977). Domain found as tandem repeats in bacterial surface proteins, commonly associated with PA14 adhesive domain. 64 matched cddid_all.tbl CDD pfam19405 pfam19405 437237 DUF5978 Family of unknown function (DUF5978). This presumed domain is found as highly identical tandem repeats in bacterial cell surface proteins associated with Bact_lectin. 73 matched cddid_all.tbl CDD pfam19406 pfam19406 437238 PKD_5 PKD-like domain. Presumed PKD-like domain found as tandem repeats in bacterial cell surface proteins, commonly associated with Bact_lectin adhesive domain. 95 matched cddid_all.tbl CDD pfam19407 pfam19407 466067 DUF5979 Domain of unknown function (DUF5979). This domain is found as tandem repeats in bacterial cell surface proteins, associated with TED adhesive domains. This domain contains a conserved lysine, glutamic acid and asparagine diagnostic of an intradomain thioester bond. 103 matched cddid_all.tbl CDD pfam19408 pfam19408 466068 PKD_6 PKD-like domain. Presumed PKD-like domain found as tandem repeats in bacterial cell surface proteins, commonly associated with PA14 and DUF11 domains. 85 matched cddid_all.tbl CDD pfam19409 pfam19409 437241 Thiopep_pre Thiopeptide-type bacteriocin precursor. This entry represents a member of a biosynthetic gene cluster (BGC). The BGC (BGC0001753) is described by MIBiG as an example of a RiPP (ribosomally synthesized and post-translationally modified peptide) BGC. Members of this protein family are the precursors of a family of small bacteriocins (i.e. microcins) with thiopeptide type modifications, a highly modified subclass of heterocycle- containing peptide antibiotics. 36 matched cddid_all.tbl CDD pfam19410 pfam19410 466069 DUF5980 Family of unknown function (DUF5980). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000666) is described by MIBiG as an example of the following biosynthetic class, terpene. 97 matched cddid_all.tbl CDD pfam19411 pfam19411 437243 Clink Cell cycle link protein Clink. This entry represents the cell cycle link protein Clink from Banana bunchy top virus (BBTV) which was identified as a suppressor of RNA silencing. It interacts with retinoblastoma-related proteins (pRB) and S-phase kinase-associated protein 1 (SKP1). Clink contains LxCxE and F-box motifs that mediate the interactions with the respective proteins and the capacity of Clink to bind pRB correlates with its ability to stimulate viral replication. pRB is a key cell cycle regulator, which represses onset and progression into S-phase by interacting with a wide range of cell cycle-related proteins. 141 matched cddid_all.tbl CDD pfam19412 pfam19412 437244 DUF5982 Domain of unknown function (DUF5982). This short domain of unknown function is found at the N-terminus of pfam01103. 64 matched cddid_all.tbl CDD pfam19413 pfam19413 466070 YaiO YaiO membrane beta barrel domain. This entry represents a domain of bacterial outer membrane beta barrel fro the YaiO protein. YaiO was experimentally shown to be localized to the outer membrane. 173 matched cddid_all.tbl CDD pfam19414 pfam19414 437246 Astro_p19 Astrovirus p19 protein. This entry represents the p19 protein found in human astrovirus. 174 matched cddid_all.tbl CDD pfam19415 pfam19415 437247 Astro_1A Astrovirus transmembrane protein 1A. This entry represents the transmembrane protein 1A from human astrovirus. This protein is part of the non-structural 1a polyprotein. 244 matched cddid_all.tbl CDD pfam19416 pfam19416 437248 Astro_VPg Astrovirus VPg protein. This entry represents the presumed VPg protein from human astrovirus. Viral genome-linked proteins (VPgs) are virus-encoded small proteins that are covalently linked to the 5' terminus of many RNA viral genomes through a phosphodiester bond. Viral genome-linked proteins (VPgs) have been identified in several single-stranded positive-sense RNA virus families. The protein resulting from this putative VPg coding region is a highly disordered protein. A common feature of VPgs is that they are rich in basic amino acids (mostly Lys (K), Gly (G), Thr (T), and Arg (R)), which favors the interaction with the negatively charged RNA. Tyr-693 at the conserved TEEEY-like motif has been postulated to be the residue responsible for the covalent linkage to viral RNA. Mutagenesis of Tyr-693 in the VPg protein is lethal for HAstV replication. 104 matched cddid_all.tbl CDD pfam19417 pfam19417 437249 RnlA_toxin_N RNase LS, bacterial toxin N-terminal. RnlA_toxin is an RNase LS and a putative toxin of a bacterial toxin-antitoxin pair. Toxin-antitoxin systems consist of a stable toxin and an unstable antitoxin. In this case, a novel type II system, RnlA is the stable toxin that causes inhibition of cell growth and rapidly degrades T4 late mRNAs to prevent their expression, and this is neutralized by the activity of the unstable antitoxin RnlB. This entry represents the N-terminal domain composed of four-stranded twisted antiparallel beta-sheet and two alpha-helices. 82 matched cddid_all.tbl CDD pfam19418 pfam19418 466071 DEPDC5_CTD DEPDC5 protein C-terminal region. This entry represents the C-terminal domain (CTD) (residues 1,291-1,603) of the DEPDC5 protein. It contains two structurally similar lobes and has a pseudo-2-fold rotational symmetry. Each half consists of a five-stranded beta-sheet, with an alpha-helix covering one side. The CTD is located in the core of DEPDC5 and contacts all the other domains of DEPDC5 except the NTD, making it the central organizer of this multi-domain protein. 303 matched cddid_all.tbl CDD pfam19419 pfam19419 437251 DUF5983 Family of unknown function (DUF5983). This family of proteins are likely to be phage derived. 162 matched cddid_all.tbl CDD pfam19420 pfam19420 437252 DDAH_eukar N,N dimethylarginine dimethylhydrolase, eukaryotic. This family contains N(G),N(G)-dimethylarginine dimethylaminohydrolases (DDAH) from eukaryotes. It also includes arginine deiminases and DDAH from prokaryotes. These enzymes are involved in arginine metabolism and belong to the amidinotransferase (AT) superfamily as they share the alpha/beta propeller fold, which includes structurally important residues (buried hydrophobic residues, buried hydrophilic residues hydrogen-bonded with mainchain groups and the hallmark of three consecutive buried Gly residues near the C-terminus, conserved among its members. 288 matched cddid_all.tbl CDD pfam19421 pfam19421 466072 Fry_C Furry protein C-terminal. This is the C-terminal domain of Furry (Fry) protein. Fry plays a crucial role in the structural integrity of mitotic centrosomes and in the maintenance of spindle bipolarity. This domain binds to polo-like kinase 1 (Plk1) through the polo-box domain (PBD) of Plk1 in a manner dependent on the cyclin-dependent kinase 1-mediated Fry phosphorylation, promoting Plk1 activity during early mitosis. Fry also binds to Aurora A and may function as a scaffold promoting the interaction between AURKA and PLK1, thereby enhancing AURKA-mediated PLK1 phosphorylation. 633 matched cddid_all.tbl CDD pfam19422 pfam19422 466073 Ariadne Ariadne domain. This entry represents the Ariadne domain found in the Ariadne subfamily E3 ubiquitin ligase proteins. The C-terminal Ariadne domain adopts an elongated four-helix bundle consisting of an antiparallel arrangement of seven-to-ten-turn long helices. The Ariadne domain is straddled on one side by the IBR domain, and on the other by the RING2 domain. Notably, the Ariadne domain embraces the surface of RING2 containing the catalytic Cys357. The ariadne Domain Masks the HHARI Catalytic Cys357 and Inhibits Intrinsic E3 Activity. 261 matched cddid_all.tbl CDD pfam19423 pfam19423 466074 E3_UBR4_N E3 ubiquitin-protein ligase UBR4 N-terminal. This entry represents the N-terminal of E3 ubiquitin-protein ligases UBR4 (POE or PUSHOVER in Drosophila), which are components of the N-rule pathway, identified as noncanonical N-recognins implicated in bulk lysosomal degradation and autophagy. These are extraordinarily large proteins that recognize and bind to proteins with N-terminal destabilising residues according to the N-end rule leading them to their ubiquitination and degradation. These proteins share a UBR box (pfam02207) with others E3-ligases UBR box proteins but UBR4 lacks the ubiquitylation domain, suggesting that it may interact with other catalytic proteins. 1598 matched cddid_all.tbl CDD pfam19424 pfam19424 466075 UNC80 Protein UNC80 central region. This family represents the protein UNC80 found in eukaryotes, a component of the NALCN sodium channel complex. NALC is a cation voltage-independent channel activated by substance P, neurotensin, acetylcholine and noradrenaline that controls neuronal excitability. UNC80 forms a complex with UNC79 and both are key regulators of the channel and required for the proper expression and axonal localization of NALCN. UNC80 is required for NALCN control by GPCRs and essential for its sensitivity to extracellular calcium. This protein acts as a scaffold for Src family of tyrosine kinases (SFK) and UNC-79 to mediate interaction with NALCN. 704 matched cddid_all.tbl CDD pfam19425 pfam19425 437257 Csd3_N2 Csd3 second domain. This entry represents the second domain from the Csd3 peptidase. This domain has a similar structure to pfam18059 despite low sequence similarity. 122 matched cddid_all.tbl CDD pfam19426 pfam19426 437258 MIER1_3_C Mesoderm induction early response protein 1/3 C-terminal. This domain is found at the C-terminal of MIER1 and MIER3. MIER1 is a transcriptional repressor that regulates the expression of a number of genes including SP1 target genes, recruiting histone deacetylase 1 (HDAC1) through its ELM2 domain. It has two isoforms, alpha and beta, which differ in their C-terminal domains, both of them being able to interact with HDAC1. The gene encoding MIER3 has been identified as a candidate cancer susceptibility gene. MIER1 and 3 share two regions of high homology, one at the N-terminal and the second at the C-terminal, represented in this entry, which includes a short region located immediately downstream of the SANT extension that is 84% identical. 217 matched cddid_all.tbl CDD pfam19427 pfam19427 466076 Insc_C Protein inscuteable C-terminal. This entry represents the C-terminal region of protein Inscuteable (Insc) containing four putative armadillo repeats and the conserved extreme C-terminal tetrapeptide Glu-Ser-Phe-Val which is in agreement with the class I PDZ-binding motif X-Ser/Thr-X-/ (X and /are unspecified and hydrophobic residues, respectively). Insc functions as an adaptor protein that binds simultaneously with Partner of Insc (Pins, consisting of alpha subunit (Ga) of heterotrimeric G proteins and its guanine nucleotide dissociation inhibitor) and Par3 (PDZ-containing proteins) to regulate their apical localization in neuroblasts, which is required for the correct execution of the asymmetric division. 394 matched cddid_all.tbl CDD pfam19428 pfam19428 437260 Sema4F_C Semaphorin 4F C-terminal. Semaphorins are a large and diverse family of proteins, widely expressed across divergent animal phyla. They are secreted and membrane-associated proteins, conserved both structurally and functionally, and they are divided in eight classes (1-7 and V). They are involved in axon guidance and influence the migration of neurons and glial cells. This entry represents the C-terminal domain of Semaphorin 4F (also known as Semaphorin-W) which plays a role in visual system development and in oligodendrocyte precursor migration and differentiation. Like other Semaphorin 4 members, it includes a Ig-like domain, adjacent the PSI domain (plexin-semaphorin-integrin domain, conserved across all semaphorins), a transmembrane region and a short intracellular tail. The latter is rich in proline residues similar to other transmembrane semaphorins suggesting that it may interact with cytoskeletal or signalling proteins. It also contains a cyclic nucleotide-dependent protein kinase phosphorylation site, involved in signal transduction into the cell. Sema4F is found in glutamatergic synapses, preferentially in postsynaptic dendrites, attached to SAP90/PSD-95-scaffolding protein. Sema4F interacts with SAP90/PSD-95 PDZ domains through the critical last last three C-terminal amino acids. 197 matched cddid_all.tbl CDD pfam19429 pfam19429 437261 EVA_Class_A Evasins Class A. This family represents evasins proteins from ticks, secreted glycoproteins that enhance host blood flow and have anti-inflammatory activity as they bind to chemokines and prevent leukocyte recruitment. Evasins can be divided in two classes based on their chemokine selectivity. Class A binds CC chemokines and includes Evasin-1 (EVA-1) and Evasin-4, being EVA-1 more selective. Class B Evasins include Evasin-3 which binds and inhibits several CXC chemokines but not CC chemokines. This family contains eight conserved Cys residues that define four intramolecular disulfide bonds. The N- and C-terminal regions are flexible, extend from either side of the core and form a concave surface with the first beta-sheet suitable for binding another EVA-1 molecule or to a chemokine. There are two Gly residues strictly conserved. Predicted glycosylation sites were identified on the exterior surface of the structure. These proteins are interesting therapeutic anti-inflammatory agents. 73 matched cddid_all.tbl CDD pfam19430 pfam19430 437262 TBC1D23_C TBC1 domain family member 23 C-terminal. TBC1 domain family member 23 (TBC1D23) belongs to a family of TBC domain-containing Rab-specific GTPase-activating proteins, which plays a role in endosome-to-Golgi trafficking. It acts as a bridging factor in which the TBC domain binds to Golgi adaptor proteins golgin-97 and golgin-245 and its C-terminal to FAM21 subunit of the WASH complex, which regulates multiple endosomal trafficking routes. TBC1D23 is important for normal brain development, especially in axonal and dendritic growth. This entry represents the C-terminal domain that contains residues for specific FAM21 binding and for the cargo of endosome-derived carriers. It adopts a fold similar to the Pleckstrin homology (PH) domain. Mutations in this protein, and particularly in this domain, are linked with Pontocerebellar hypoplasia (PCH), suggesting that the TBC1D23 C-terminal domain is required for neuronal growth and brain development. 225 matched cddid_all.tbl CDD pfam19431 pfam19431 466077 MEKK4_N MEKK4 N-terminal. This domain represents the regulatory N-terminal non-catalytic region of Mitogen-activated protein kinase kinase kinase 4 (MEKK4) which contains a putative PH-domain. This N-terminal region acts as an autoinhibitory domain that must be dissociated from the catalytic domain to allow the activation of these kinases. 974 matched cddid_all.tbl CDD pfam19432 pfam19432 466078 RME-8_N DNAJ protein RME-8 N-terminal. DNAJ protein RME-8 (receptor-mediated endocytosis-8; Gvr2 in Arabidopsis) is involved in membrane trafficking through early endosomes and in the regulation of endosomal membrane tubulation. It regulates the dynamics of SNX1 (sorting nexin 1) on the endosomal membrane. It coordinates the function of the WASH complex and the retromer SNX dimer through its interaction with FAM21 subunit in WASH complex. This is the N-terminal domain of RME-8, which is required for membrane association and interaction with FAM21 tail domain. It contains critical residues mediating phosphatidylinositol 3-phosphate (PI(3)P) binding, required for its association with endosomes. 819 matched cddid_all.tbl CDD pfam19433 pfam19433 466079 NDNF_C Neuron-derived Neurotrophic Factor C-terminal. This is the C-terminal domain of Neuron-derived Neurotrophic Factor (NDNF). NDNF is a glycosylated and disulfide-bonded secreted protein expressed in brain and spinal cord that promotes migration and neurite growth of hippocampal neurons. It also promotes endothelial cell survival, vessel formation and plays an important role in the process of revascularization. This domain contains the second fibronectin type III domain (FnIII) present in NDNF and one of the two potential consensus sites for N-linked glycosylation. 174 matched cddid_all.tbl CDD pfam19434 pfam19434 466080 OPA1_C Dynamin-like GTPase OPA1 C-terminal. This entry represents the C-terminal domain of Dynamin-like GTPase OPA1. This protein is involved in mitochondrial fusion and inner membrane remodelling, essential for normal mitochondrial morphology by regulating the equilibrium between mitochondrial fusion and mitochondrial fission. Mutations in human OPA1 cause optic atrophy. This domain includes the helix bundle (HB) domains HB1 (C-terminal) and HB2 (equivalent to extreme C-terminal bundle signaling element (BSE) and to the stalk domain of dynamin-1, respectively) and the lipid-interacting stalk (LIS, equivalent to the PH domain of dynamin-1). 345 matched cddid_all.tbl CDD pfam19435 pfam19435 466081 IntS14_b-barrel Integrator complex subunit 14, beta-barrel domain. This entry represents the central beta-barrel domain of Integrator complex subunit 14 (IntS14), a component of the integrator complex which is involved in the transcription of small nuclear RNAs (snRNA) and their 3'-box-dependent processing. This complex is also involved in the 3'-end processing of the U7 snRNA, and the spliceosomal snRNAs U1 and U5. IntS14 interacts with IntS13, both of them consist of an N-terminal von-Willebrand type A like domain (VWA), followed by a central beta-barrel domain and a C-terminal alpha-helical domain connected through a linker. The interface involves all domains of both proteins, both beta-barrel domains form the centre of the complex and contribute to the major contact between Ints13-IntS14. 147 matched cddid_all.tbl CDD pfam19436 pfam19436 466082 ACS_CODH_B_C ACS/CODH beta subunit C-terminal. Acetyl-CoA synthase/CO dehydrogenase (ACS/CODH) is a bifunctional enzyme that catalyzes the reversible reduction of CO2 to CO (CODH activity, the beta subunit) and the synthesis or degradation of acetyl-CoA (catalyzed by ACS, the alpha subunit). CODH contains the B-, C-, and D-clusters. This domain represents the middle and C-terminal regions of CODH which have an alpha/beta Rossmann-like fold and are the contribute ligands to the active site C-cluster. The C-cluster generates CO from CO2 and contains one Ni atom, four Fe atoms, and five labile sulfur atoms, arranged as an asymmetrical heteronuclear [Ni-4Fe-5S] cluster. 245 matched cddid_all.tbl CDD pfam19437 pfam19437 437269 VCIP135_N VCIP135 N-terminal. Deubiquitinating protein VCIP135 is required for the p97/p47 and p97/p37 pathways during Golgi biogenesis. It reverses ubiquitination events that occurs during mitotic disassembly, regulating Golgi membrane dynamics during mitosis. This entry represents the N-terminal domain of VCIP135 that interacts with the WW domain-containing adaptor with coiled coil (WAC) and increases its deubiquitinating activity, necessary only for p97/p47-mediated Golgi membrane fusion. 168 matched cddid_all.tbl CDD pfam19438 pfam19438 437270 LIN9_C LIN9 C-terminal. MuvB transcriptional regulatory complex interacts with B-Myb to form the MMB complex during S-phase of the cell cycle to activate genes required for the G2 and M phases. This is a domain found at the C-terminal of LIN9, one of the core members of the MuvB complex that functions as a scaffold protein and forms a subcomplex with the C-terminal of LIN152. This subcomplex forms a binding interface that recruits B-Myb to the MuvB complex which is arranged as a three-stranded antiparallel coiled-coil as the core of the structure. LIN9 contributes two helices (alpha1 and alpha2) that run antiparallel and are connected through a short linker. 272 matched cddid_all.tbl CDD pfam19439 pfam19439 466083 CLEC16A_C CLEC16A C-terminal. This is the C-terminal domain of C-type lectin domain family 16, member A (CLEC16A, the Drosophila orthologue Ema and GOP-1 in C. elegans), an evolutionarily conserved endosomal membrane protein required for trafficking of fluid-phase and receptor-mediated endocytic cargos. It is required for mitophagy, autophagy and endosome maturation. This protein has been identified as a susceptibility gene for autoimmune diseases like type 1 diabetes, multiple sclerosis and adrenal dysfunction. This domain is also present in GFS9/TT9 (TRANSPARENT TESTA 9) a protein from Arabidopsis required for vacuolar development through membrane fusion at vacuoles and for membrane trafficking machinery and accumulation of flavonoids in the seed coat. 762 matched cddid_all.tbl CDD pfam19440 pfam19440 466084 TTC7_N Tetratricopeptide repeat protein 7 N-terminal. This is the N-terminal domain of TTC7, a protein that forms the regulatory subunit of the PI4KIIIalpha complex (also known as PI4KA). This complex is composed of PI4KIIIalpha, TTC7 and FAM126A and catalyzes the first step in plasma membrane phosphoinositide synthesis. This TTC7 N-terminal domain contains basic residues suitable for interaction with the acidic inner leaflet of the plasma membrane and is required for localising the active site near its substrate. TTC7 acts as a bridge between PI4KA and EFR3B-FAM126A, via direct interactions. ERF3B is not part of the complex but contributes to its recruitment to the membrane. 386 matched cddid_all.tbl CDD pfam19441 pfam19441 437273 ASTN_1_2_N Astrotactin 1/2 N-terminal. This entry represents the N-terminal domain of Astrotactin (ASTN) proteins 1 and 2, which includes the transmembrane and cytosolic regions. These are vertebrate-specific proteins involved in neuronal migration during neurodevelopment. ASTN1 is a neuronal receptor required for neuroblasts migration along glial fibers, especially in the cerebellum. ASTN2 is an endosome membrane protein that binds ASTN1 and mediates its recycling by promoting ASTN1 internalization and transport during its endocytosis. 555 matched cddid_all.tbl CDD pfam19442 pfam19442 437274 CRIM1_C Cysteine-rich motor neuron 1 protein C-terminal. Cysteine-rich motor neuron 1 protein (CRIM1) interacts with growth factors implicated in motor neuron differentiation and survival, playing a role in central nervous system development. It is upregulated in endothelial cells during tube formation. CRIM1 also modulates BMP activity, which affects its processing and delivery to the cell surface. This is CRIM1 C-terminal domain containing the transmembrane region. 130 matched cddid_all.tbl CDD pfam19443 pfam19443 466085 DAHL DAHL domain. The DAHL (Double All-Helical Ligand-binding) domain is a novel periplasmic sensory domain, which is found in major types of bacterial signal transduction proteins: histidine kinases and diguanylate cyclases/phosphodiesterases, and, occasionally in chemoreceptors. The majority of the DAHL domain-containing proteins were found in alpha-, beta-, gamma- and epsilonproteobacteria. It is also present in some cyanobacterial species. Secondary structure prediction suggested that DAHL consists predominantly of alpha-helical regions. The DAHL domain was identified in the Tlp10 chemoreceptor from the human pathogen Campylobacter jejuni and in the VirA sensor histidine kinase from a plant pathogen Agrobacterium tumefaciens. This domain recognizes Asp, Ile, purine, fumarate, malate, alpha-ketoglutarate, mannose, rhamnose, fucose, sialic acid, Arg, thiamine and galactose (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1 https://doi.org/10.1093/femsre/fuab043). 222 matched cddid_all.tbl CDD pfam19444 pfam19444 466086 MTP_lip_bd MTP large subunit, lipid-binding domain. Microsomal triglyceride transfer protein (MTP) is essential in lipid metabolism, especially in the biogenesis of very low-density lipoproteins and chylomicrons via the transfer of neutral lipids and the assembly of apoB-containing lipoproteins. It is a heterodimer consisting of a large MTP alpha-subunit and a protein disulfide isomerase (PDI) beta-subunit. The MTP large subunit has and N-terminal beta-barrel domain, a central alpha-helical domain and a C-terminal 2-beta-sheet domain. This is the highly conserved MTP C-terminal domain involved in lipid-binding and transfer activity, with preference of neutral 3 chain-containing lipids. The beta-sheets are named A and C and form a sandwich comprising the lipid-binding site between them. Half of the A-sheet interacts with the beta-barrel. This domain also interacts with a' and b' domains of PDI. 258 matched cddid_all.tbl CDD pfam19445 pfam19445 466087 eIF3h_C C-terminal region of eIF3h. This entry represents a C-terminal helical region present in eukaryotic initiation factor 3 chain H. This protein is part of the eIF3 complex that is involved in eukaryotic translation initiation. eIF3 is a large and structurally complex molecular assembly that, in the majority of eukaryotes, consists of 11-13 subunits (eIF3a-IF3m) with a molecular weight of 600-800 kDa. 196 matched cddid_all.tbl CDD pfam19446 pfam19446 437278 DUF5984 Family of unknown function (DUF5984). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000838) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the flexirubin biosynthetic gene cluster from Flavobacterium johnsoniae. This protein has no known function. It is found in Actinobacteria, Proteobacteria and Bacteroidetes. Proteins in this family are typically between 234 and 271 amino acids in length. 243 matched cddid_all.tbl CDD pfam19447 pfam19447 466088 DUF5985 Family of unknown function (DUF5985). This family of uncharacterized proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length and contain three transmembrane helices. 86 matched cddid_all.tbl CDD pfam19448 pfam19448 437280 DUF5986 Family of unknown function (DUF5986). This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 235 and 254 amino acids in length. There is a single completely conserved residue R that may be functionally important. 239 matched cddid_all.tbl CDD pfam19449 pfam19449 437281 DUF5987 Family of unknown function (DUF5987). This family of uncharacterized proteins is found in actinobacteria. Proteins in this family are approximately 190 amino acids in length. Many protein in this family are annotated as regulator, but the source of this annotation is uncertain. 180 matched cddid_all.tbl CDD pfam19450 pfam19450 466089 DUF5988 Family of unknown function (DUF5988). This family of proteins is found in bacteria. Proteins in this family are typically between 68 and 82 amino acids in length. There are two conserved sequence motifs: GGP and YEHF. 70 matched cddid_all.tbl CDD pfam19451 pfam19451 466090 DUF5989 Family of unknown function (DUF5989). This family of proteins is primarily found in bacteria. Proteins in this family are integral membrane proteins that are approximately 50 amino acids in length. There is a C-terminal conserved APFIY sequence motif. This family may have distant partial similarity to pfam02694 suggesting this may be a transporter protein. 49 matched cddid_all.tbl CDD pfam19452 pfam19452 466091 DUF5990 Family of unknown function (DUF5990). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001048) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide), polyketide, and saccharide. This family includes a protein in the tallysomycin A biosynthetic gene cluster from Streptoalloteichus hindustanus. Some members of this family have been annotated as monooxygenase, but this could not be confirmed. 139 matched cddid_all.tbl CDD pfam19453 pfam19453 437285 DUF5991 Family of unknown function (DUF5991). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001890) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). The exemplar is the amphi-enterobactin 1 biosynthetic gene cluster from Vibrio campbellii. 123 matched cddid_all.tbl CDD pfam19454 pfam19454 437286 DUF5992 Family of unknown function (DUF5992). This family of proteins is found in bacteria. Proteins in this family are typically between 105 and 116 amino acids in length. 106 matched cddid_all.tbl CDD pfam19455 pfam19455 466092 DUF5993 Family of unknown function (DUF5993). This family of integral membrane proteins is found primarily in proteobacteria. Proteins in this family are approximately 50 amino acids in length. 50 matched cddid_all.tbl CDD pfam19456 pfam19456 466093 MobI MobI protein. MobI is conserved across conjugative plasmids of incompatibility group C (IncC), integrative conjugative elements of the SXT/R391 family and numerous genomic islands mobilized by IncC plasmids. Alongside a relaxase of the MOBH1 family, this protein is essential to conjugative transfer of these elements and is likely a relaxosome component involved in recognition of the origin of transfer. 116 matched cddid_all.tbl CDD pfam19457 pfam19457 466094 DUF5994 Family of unknown function (DUF5994). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000202) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family contains a protein found in the azicemicin B biosynthetic gene cluster from Kibdelosporangium sp. MJ126-NF4. The function of this protein is unknown. 111 matched cddid_all.tbl CDD pfam19458 pfam19458 466095 DUF5995 Family of unknown function (DUF5995). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000354) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This includes a protein from the friulimicin A biosynthetic gene cluster from Actinoplanes friuliensis. 224 matched cddid_all.tbl CDD pfam19459 pfam19459 466096 DUF5996 Family of unknown function (DUF5996). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000434) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This family includes a protein from the SW-163C biosynthetic gene cluster from Streptomyces sp. SNA15896. 296 matched cddid_all.tbl CDD pfam19460 pfam19460 466097 DUF5997 Family of unknown function (DUF5997). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001814) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This family includes a protein from the ulleungmycin biosynthetic gene cluster from Streptomyces sp. KCB13F003. 108 matched cddid_all.tbl CDD pfam19461 pfam19461 437293 DUF5998 Family of unknown function (DUF5998). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001522) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the auroramycin biosynthetic gene cluster from Streptomyces filamentosus. Some members of this family have been identified as putative phosphodiesterases. 179 matched cddid_all.tbl CDD pfam19462 pfam19462 466098 DUF5999 Family of unknown function (DUF5999). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a protein from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus. This family appears to be predominantly found in Actinobacteria. 57 matched cddid_all.tbl CDD pfam19463 pfam19463 466099 DUF6000 Family of unknown function (DUF6000). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000026) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a protein from the avilamycin A biosynthetic gene cluster from Streptomyces viridochromogenes Tue57 and appears to be predominantly found in bacteria. 185 matched cddid_all.tbl CDD pfam19464 pfam19464 437296 DUF6001 Family of unknown function (DUF6001). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000919) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). This family includes a protein from the phaseolotoxin biosynthetic gene cluster from Pseudomonas syringae. 359 matched cddid_all.tbl CDD pfam19465 pfam19465 437297 DUF6002 Family of unknown function (DUF6002). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000833) is described by MIBiG as an example of the following biosynthetic classes, saccharide and other (unspecified). This family includes a protein from the coumermycin A1 biosynthetic gene cluster from Streptomyces rishiriensis. 447 matched cddid_all.tbl CDD pfam19466 pfam19466 466100 DUF6003 Family of unknown function (DUF6003). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000100) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from monensin biosynthetic gene cluster from Streptomyces cinnamonensis. 140 matched cddid_all.tbl CDD pfam19467 pfam19467 437299 DUF6004 Family of unknown function (DUF6004). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000033) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the calicheamicin biosynthetic gene cluster from Micromonospora echinospora. 400 matched cddid_all.tbl CDD pfam19468 pfam19468 437300 DUF6005 Family of unknown function (DUF6005). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000942) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). This family includes a protein from the petrobactin biosynthetic gene cluster from Bacillus anthracis str. Ames. 327 matched cddid_all.tbl CDD pfam19469 pfam19469 437301 DUF6006 Family of unknown function (DUF6006). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001016) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. This family includes a protein from then microcystin biosynthetic gene cluster from Anabaena sp. 90. 140 matched cddid_all.tbl CDD pfam19470 pfam19470 437302 DUF6007 Family of unknown function (DUF6007). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000758) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a protein from the capsular polysaccharide biosynthetic gene cluster from Staphylococcus aureus 65 matched cddid_all.tbl CDD pfam19471 pfam19471 437303 DUF6008 Family of unknown function (DUF6008). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000112) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the neocarzinostatin biosynthetic gene cluster from Streptomyces carzinostaticus subsp. neocarzinostaticus and appears to be restricted to Actinobacteria. 236 matched cddid_all.tbl CDD pfam19472 pfam19472 466101 DUF6009 Family of unknown function (DUF6009). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000965) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the C-1027 biosynthetic gene cluster from Streptomyces globisporus. 127 matched cddid_all.tbl CDD pfam19473 pfam19473 466102 DUF6010 Family of unknown function (DUF6010). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001011) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. This family includes a protein from the meridamycin biosynthetic gene cluster from Streptomyces sp. NRRL 30748. 120 matched cddid_all.tbl CDD pfam19474 pfam19474 466103 DUF6011 Family of unknown function (DUF6011). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000413) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This family includes a protein encoded by the pyoverdin biosynthetic gene cluster from Pseudomonas protegens Pf-5. 37 matched cddid_all.tbl CDD pfam19475 pfam19475 437307 DUF6012 Family of unknown function (DUF6012). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000128) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein encoded by the pyoluteorin biosynthetic gene cluster from Pseudomonas sp. M18 203 matched cddid_all.tbl CDD pfam19476 pfam19476 466104 DUF6013 Family of unknown function (DUF6013). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001120) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. This family includes a protein from the burkholderic acid biosynthetic gene cluster from Burkholderia thailandensis E264 and appears to be predominantly found in Burkholderiaceae 184 matched cddid_all.tbl CDD pfam19477 pfam19477 437309 DUF6014 Family of unknown function (DUF6014). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000332) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This family includes a protein from the cyanopeptolin biosynthetic gene cluster from Microcystis sp. NIVA-CYA 172/5 and appears to be predominantly found in Cyanobacteria. 172 matched cddid_all.tbl CDD pfam19478 pfam19478 437310 TrbL_2 TrbL/VirB6 plasmid conjugal transfer like protein. Although members of this family are uncharacterized it appears to be related to pfam04610 which is a conjugal transfer protein TrbL/VirB6 found in proteobacteria. This protein family is found in Firmicute bacteria, and is approximately 170 amino acids in length. 174 matched cddid_all.tbl CDD pfam19479 pfam19479 466105 DUF6015 Family of unknown function (DUF6015). This family of proteins is functionally uncharacterized. This family of proteins is found in archaea. Proteins in this family are typically between 119 and 142 amino acids in length. 140 matched cddid_all.tbl CDD pfam19480 pfam19480 437312 DUF6016 Domain of unknown function (DUF6016). This presumed domain is related to proteins in the Cupin superfamily. These proteins contain 1 or 2 copies of the domain. This family of proteins is found in Proteobacteria and Bacteroidetes. Proteins in this family are typically between 132 and 162 amino acids in length. 141 matched cddid_all.tbl CDD pfam19481 pfam19481 437313 DUF6017 Family of unknown function (DUF6017). This presumed domain is functionally uncharacterized. It is found to the C-terminus of a helix-turn-helix domain which strongly suggests that it is a transcriptional regulatory protein. These domains associated with HTH domains often bind to a ligand. This domain family is found in firmicutes, and is approximately 150 amino acids in length. 148 matched cddid_all.tbl CDD pfam19482 pfam19482 437314 DUF6018 Family of unknown function (DUF6018). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000320) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This family includes a protein from the cereulide biosynthetic gene cluster from Bacillus cereus and appears to be predominantly found in Bacilli. 115 matched cddid_all.tbl CDD pfam19483 pfam19483 437315 DUF6019 Family of unknown function (DUF6019). This family of proteins is functionally uncharacterized. This family of proteins is found in Clostridia. Proteins in this family are typically between 51 and 67 amino acids in length and have a single transmembrane helix. 63 matched cddid_all.tbl CDD pfam19484 pfam19484 466106 DUF6020 Family of unknown function (DUF6020). This family of integral membrane proteins is functionally uncharacterized. This family of proteins is found in Firmicutes and Actinobacteria. Proteins in this family are typically between 587 and 710 amino acids in length. 614 matched cddid_all.tbl CDD pfam19485 pfam19485 437317 DUF6021 Family of unknown function (DUF6021). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000399) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This family includes a protein from the orfamide A biosynthetic gene cluster from Pseudomonas protegens Pf-5 and appears to be predominantly found in Pseudomonadaceae. 65 matched cddid_all.tbl CDD pfam19486 pfam19486 437318 DUF6022 Family of unknown function (DUF6022). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000693) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a protein from the butirosin A biosynthetic gene cluster from Bacillus circulans and appears to be predominantly found in Bacilli. 155 matched cddid_all.tbl CDD pfam19487 pfam19487 437319 DUF6023 Family of unknown function (DUF6023). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001077) is described by MIBiG as an example of the following biosynthetic classes, polyketide and terpene. This family includes a protein from the alkyl-O-dihydrogeranyl- methoxyhydroquinones biosynthetic gene cluster from Actinoplanes missouriensis 431 and appears to be predominantly found in Actinobacteria. 150 matched cddid_all.tbl CDD pfam19488 pfam19488 437320 DUF6024 Family of unknown function (DUF6024). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001992) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). This family includes a protein from the thioguanine biosynthetic gene cluster from Erwinia amylovora CFBP1430. 290 matched cddid_all.tbl CDD pfam19489 pfam19489 466107 SLT_4 Transglycosylase SLT domain. This entry represents a set of SLT like domains found in proteobacteria. SLT domains are enzymes that degrade murein. 184 matched cddid_all.tbl CDD pfam19490 pfam19490 437322 DUF6025 Family of unknown function (DUF6025). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000938) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). This family includes a protein from the fosfomycin biosynthetic gene cluster from Streptomyces fradiae. 458 matched cddid_all.tbl CDD pfam19491 pfam19491 437323 DUF6026 Family of unknown function (DUF6026). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001285) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). This family includes a protein from the pseudopyronine A biosynthetic gene cluster from Pseudomonas putida and appears to be predominantly found in Pseudomonas. 51 matched cddid_all.tbl CDD pfam19492 pfam19492 437324 DUF6027 Family of unknown function (DUF6027). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001387) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). This family includes a protein from the nucleocidin biosynthetic gene cluster from Streptomyces calvus and appear to be predominantly found in Actinobacteria. 134 matched cddid_all.tbl CDD pfam19493 pfam19493 466108 Trypco1 Trypsin-co-occurring domain 1. Trypsin-like peptidase effector in the classical NTP-dependent ternary system (vWA-MoxR-VMAP) frequently co-occurs with one of two proteins (Trypco1 or Trypco2) which are mostly mutually exclusively. This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus. 97 matched cddid_all.tbl CDD pfam19494 pfam19494 437326 DUF6029 Family of unknown function (DUF6029). This family of proteins is functionally uncharacterized. This family of proteins is found primarily in Bacteroidetes. Proteins in this family are typically between 531 and 570 amino acids in length. There is a conserved GGVCR sequence motif. 533 matched cddid_all.tbl CDD pfam19495 pfam19495 437327 DUF6030 Family of unknown function (DUF6030). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000762) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a protein from the exopolysaccharide biosynthetic gene cluster from Rhizobium leguminosarum bv. viciae and appears to be predominantly found in proteobacteria. 251 matched cddid_all.tbl CDD pfam19496 pfam19496 437328 DUF6031 Family of unknown function (DUF6031). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000919) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). This family includes a protein from the phaseolotoxin biosynthetic gene cluster from Pseudomonas syringae and appears to be predominantly found in bacteria. 175 matched cddid_all.tbl CDD pfam19497 pfam19497 437329 DUF6032 Family of unknown function (DUF6032). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001410) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a protein from the polysaccharide A biosynthetic gene cluster from Bacteroides fragilis. 493 matched cddid_all.tbl CDD pfam19498 pfam19498 437330 DUF6033 Protein of unknown function (DUF6033). This family of proteins is functionally uncharacterized. This family of proteins is primarily found in Clostridia. Proteins in this family are typically between 212 and 271 amino acids in length. 204 matched cddid_all.tbl CDD pfam19499 pfam19499 437331 DUF6034 Family of unknown function (DUF6034). This family of proteins is functionally uncharacterized. This family of proteins is mainly found in Clostridia. Proteins in this family are typically between 466 and 533 amino acids in length. 491 matched cddid_all.tbl CDD pfam19500 pfam19500 437332 DUF6035 Family of unknown function (DUF6035). This family of proteins is functionally uncharacterized. This family of proteins is found in Proteobacteria and Bacteroidetes. Proteins in this family are typically between 425 and 520 amino acids in length. There is a conserved GVD sequence motif. This family contains a PD-(D/E)XK nuclease domain. 498 matched cddid_all.tbl CDD pfam19501 pfam19501 437333 YetA YetA-like protein. This family of proteins which includes YetA from B. subtilis is functionally uncharacterized. This family of proteins is found in Actinobacteria, Firmicutes, Proteobacteria and fungi. Proteins in this family are typically between 863 and 928 amino acids in length. 866 matched cddid_all.tbl CDD pfam19502 pfam19502 466109 DUF6036 Nucleotidyltransferase of unknown function (DUF6036). This family of proteins is functionally uncharacterized. It belongs to the nucleotidyltransferase superfamily. This family of proteins is found in bacteria, archaea and viruses. Proteins in this family are typically between 172 and 232 amino acids in length. 163 matched cddid_all.tbl CDD pfam19503 pfam19503 466110 DUF6037 Family of unknown function (DUF6037). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000758) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a protein from the capsular polysaccharide biosynthetic gene cluster from Staphylococcus aureus. 200 matched cddid_all.tbl CDD pfam19504 pfam19504 437336 DUF6038 Family of unknown function (DUF6038). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000758) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a protein from the capsular polysaccharide biosynthetic gene cluster from Staphylococcus aureus. 544 matched cddid_all.tbl CDD pfam19505 pfam19505 437337 DUF6039 Family of unknown function (DUF6039). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001101) is described by MIBiG as an example of the following biosynthetic classes, NRP and Polyketide (Macrolide). This family includes a protein from the leinamycin biosynthetic gene cluster from Streptomyces atroolivaceus and appears to be predominantly found in Actinobacteria. 298 matched cddid_all.tbl CDD pfam19506 pfam19506 437338 DUF6040 Family of unknown function (DUF6040). This family of proteins is functionally uncharacterized. This family of proteins is found in Clostridia. Proteins in this family are typically between 203 and 265 amino acids in length. 233 matched cddid_all.tbl CDD pfam19507 pfam19507 437339 DUF6041 Family of unknown function (DUF6041). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000260) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the prodigiosin biosynthetic gene cluster from Hahella chejuensis KCTC 2396 140 matched cddid_all.tbl CDD pfam19508 pfam19508 437340 DUF6042 Family of unknown function (DUF6042). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000291) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). This family includes a protein from the A54145 biosynthetic gene cluster from Streptomyces fradiae. 227 matched cddid_all.tbl CDD pfam19509 pfam19509 437341 DUF6043 Family of unknown function (DUF6043). This family of proteins is functionally uncharacterized. This family of proteins is found in Bacteroidetes. Proteins in this family are typically between 293 and 398 amino acids in length. 314 matched cddid_all.tbl CDD pfam19510 pfam19510 437342 DUF6044 Protein of unknown function (DUF6044). This family of integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 557 and 582 amino acids in length. There is a conserved YNG sequence motif. 564 matched cddid_all.tbl CDD pfam19511 pfam19511 437343 DUF6045 Family of unknown function (DUF6045). This family of proteins is functionally uncharacterized. This family of proteins is found primarily in Firmicute bacteria. Proteins in this family are typically between 286 and 301 amino acids in length. 285 matched cddid_all.tbl CDD pfam19512 pfam19512 437344 DUF6046 Domain of unknown function (DUF6046). This family of presumed domains is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 196 and 222 amino acids in length. 122 matched cddid_all.tbl CDD pfam19513 pfam19513 437345 DUF6047 Family of unknown function (DUF6047). This family of proteins is functionally uncharacterized. This family of proteins is found in Bacteroidetes bacteria. Proteins in this family are typically between 238 and 400 amino acids in length. 189 matched cddid_all.tbl CDD pfam19514 pfam19514 437346 MobC_2 MobC-like protein. This family consists of several bacterial MobC-like, mobilization proteins. MobC proteins belong to the group of relaxases. Together with MobA and MobB they bind to a single cis-active site of a mobilising plasmid, the origin of transfer (oriT) region. 140 matched cddid_all.tbl CDD pfam19515 pfam19515 437347 DUF6048 Domain of unknown function (DUF6048). This entry represents a family of uncharacterized membrane spanning beta barrel proteins. This family of proteins is primarily found in Bacteroidetes bacteria. Proteins in this family are typically between 228 and 255 amino acids in length. 232 matched cddid_all.tbl CDD pfam19516 pfam19516 437348 DUF6049 Family of unknown function (DUF6049). This family of proteins is functionally uncharacterized. This family of proteins is found primarily in Actinobacteria. Proteins in this family are typically between 695 and 823 amino acids in length. 690 matched cddid_all.tbl CDD pfam19517 pfam19517 437349 DUF6050 Family of unknown function (DUF6050). This family of proteins is functionally uncharacterized. This family of proteins is found mainly in Clostridia. Proteins in this family are typically between 103 and 122 amino acids in length. 116 matched cddid_all.tbl CDD pfam19518 pfam19518 466111 RhoGAP_pG1_pG2 p190RhoGAP, pG1 and pG2 domains. The p190RhoGAP (GTPase-activating protein) proteins, p190RhoGAP-A (ARHGAP35) and p190RhoGAP-B (ARHGAP5)4-6, regulates Rho GTP hydrolysis and are important for proper Rho signalling. They share a domain organization containing a GTP-binding GTPase domain, four FF domains, two GTPase-like folds (pG1 and pG2) in the middle domain and a C-terminal GAP domain. This entry represents pG1 and pG2 which are important for GAP activity toward RhoA and were classified as pseudoGTPases as they lack nucleotide-binding activity. Crystal structures revealed a small GTPase fold in both cases with a central 6-stranded beta-sheet surrounded by four alpha-helices. 699 matched cddid_all.tbl CDD pfam19519 pfam19519 437351 DUF6051 Family of unknown function (DUF6051). This family of proteins is functionally uncharacterized. This family of proteins is found in Bacteroidetes bacteria. Proteins in this family are typically between 377 and 403 amino acids in length. 406 matched cddid_all.tbl CDD pfam19520 pfam19520 466112 Dpp_8_9_N Dipeptidyl peptidase 8 and 9 N-terminal. Dipeptidyl peptidase (DPP) family members 8 and 9 are similar to DPP4, consisting of one N-terminal beta-propeller and a C-terminal alpha/beta hydrolase domain, which form a functional homodimer. This entry represents the N-terminal beta-propeller of DPP8 and 9 which consists of eight blades and enlaces a central round pore. It provides the key arginine residue fundamental for substrate fixation which is located in the R-segment, at the interconnecting loop between blades 1 and 2. Ligand binding to DPP8/9 induces a rearrangement at the active site through a disorder-order transition in a loop segment which includes the key arginine residue and partially folds in an alpha-helix (R-helix). DPP8 and DPP9 play a role in the immune system and in preadipocyte differentiation. DPP9 is also essential for neonatal survival and plays a role in antigen maturation, cell migration, and cell adhesion. 155 matched cddid_all.tbl CDD pfam19521 pfam19521 437353 Apc1_N Anaphase-promoting complex subunit 1 N-terminal. The anaphase-promoting complex subunit 1 (Apc1) is the largest scaffolding subunit that constitutes anaphase-promoting complex/cyclosome (APC/C), the crucial RING E3 ubiquitin ligase that controls cell cycle processes like sister chromatid segregation, cytokinesis and the initiation of chromosome replication. This domain represents the Apc1 N-terminal region that is rich in beta-strands and regulatory phosphorylation sites. It contains WD40 repeats and is essential for APC/C catalytic activity as it mediates the coactivator-induced conformational change of the APC/C which promotes UbcH10 binding. 136 matched cddid_all.tbl CDD pfam19522 pfam19522 437354 DUF6052 Family of unknown function (DUF6052). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001397) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. This family includes a protein from the lidamycin biosynthetic gene cluster from Streptomyces globisporus C-1027 and appears to be predominantly present in bacteria. 61 matched cddid_all.tbl CDD pfam19523 pfam19523 437355 DUF6053 Family of unknown function (DUF6053). 34 matched cddid_all.tbl CDD pfam19524 pfam19524 437356 DUF6054 Family of unknown function (DUF6054). This family of proteins is functionally uncharacterized. This family of proteins is found primarily in Firmicute bacteria. Proteins in this family are approximately 110 amino acids in length. 111 matched cddid_all.tbl CDD pfam19525 pfam19525 466113 Ets1_N_flank Ets1 N-terminal flanking region of Ets domain. Ets1 is a member of the Ets family of transcription factors in which the DNA-binding activity is in an autoinhibited state. The autoinhibition of Ets1 is mediated by structural coupling of the regions flanking the Ets domain. The inhibitory regions are folded as helices HI1 and HI2 N-terminal to the ETS domain and as H4 C-terminal to the ETS domain, which are packed together to form an inhibitory module. This domain represents the N-terminal flanking region of Ets domain which contains the residues forming HI1 and HI2 helices and additional residues(244-301) N-terminal to HI1. HI1 and HI2 exert the autoinhibitory function by directing the inhibitory residues N-terminal to HI1 to mask the Ets domain DNA-binding surface. These residues are flexible and function by masking the DNA-binding surface of the Ets domain. Phosphorylation of serine residues present in this region enhances autoinhibition dramatically. These inhibitory sequences are required for cooperative DNA binding. 188 matched cddid_all.tbl CDD pfam19526 pfam19526 466114 Slr4 S-layer protein Slr4. This family represents a novel S-layer protein widely distributed in Gammaproteobacteria including species of Pseudoalteromonas and Vibrio, and are found exclusively in marine metagenomes. These proteins assemble into paracrystalline sheets with a unique square lattice symmetry. 369 matched cddid_all.tbl CDD pfam19527 pfam19527 437359 DUF6055 Family of unknown function (DUF6055). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and fungi. Proteins in this family are typically between 431 and 744 amino acids in length. Protein in this family often contain a C-terminal pfam16151 domain. These proteins are likely to be cell surface proteins. 421 matched cddid_all.tbl CDD pfam19528 pfam19528 437360 DUF6056 Family of unknown function (DUF6056). This family of integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 448 and 528 amino acids in length. There is a conserved NYL sequence motif. 444 matched cddid_all.tbl CDD pfam19529 pfam19529 437361 DUF6057 Family of unknown function (DUF6057). This family of integral membrane proteins is functionally uncharacterized. This family of proteins is found primarily in Bacteroidetes bacteria. Proteins in this family are typically between 379 and 586 amino acids in length. 544 matched cddid_all.tbl CDD pfam19530 pfam19530 437362 Ndh2_N NAD(P)H-quinone oxidoreductase subunit 2 N-terminal. This domain represents the N-terminal of NAD(P)H-quinone oxidoreductase subunit 2 (or subunit B), part of the P-module (pumping) of the photosynthetic complex I from plants and cyanobacteria, which is structurally and functionally related to the respiratory complex I from mitochondria and bacteria. It is involved in the electron transfer between photosynthetic complex I and photosystem I. 100 matched cddid_all.tbl CDD pfam19531 pfam19531 437363 DUF6058 Family of unknown function (DUF6058). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001590) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the formicamycins A-M biosynthetic gene cluster from Streptomyces sp. KY5. 126 matched cddid_all.tbl CDD pfam19532 pfam19532 437364 TMEM131_like Transmembrane protein 131-like. Transmembrane protein 131-like (TMEM131L) was identified as a negative regulator of thymocyte proliferation that acts through mixed Wnt-dependent and independent mechanisms. It has two isoforms, L and S, which have different subcellular localization. L isoform, the membrane-associated form, inhibits canonical Wnt/beta-catenin signalling through the induction of lysosome-dependent degradation of the active phosphorylated form of the LRP6 coreceptor. This protein contains three conserved homology domains (CHD1, 2 and 3), a transmembrane region and a C-terminal serine-rich region. This family is related to pfam12371. 1429 matched cddid_all.tbl CDD pfam19533 pfam19533 466115 Rab3-GAP_cat_C Rab3 GTPase-activating protein catalytic subunit C-terminal. This domain corresponds to the C-terminal region of the catalytic subunit of the GTPase activating protein that has specificity for Rab3 subfamily and converts active Rab3-GTP to the inactive form Rab3-GDP. Rab3 proteins are involved in regulated exocytosis of neurotransmitters and hormones. 204 matched cddid_all.tbl CDD pfam19534 pfam19534 466116 DUF6059 Family of unknown function (DUF6059). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001922) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the isoindolinomycin biosynthetic gene cluster from Streptomyces sp. SoC090715LN-16 and appears to be predominantly found in Actinobacteria. 57 matched cddid_all.tbl CDD pfam19535 pfam19535 437367 DUF6060 Family of unknown function (DUF6060). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001035) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide), polyketide and other (Aminocoumarin). This family includes a protein from the pneumocandin B0 biosynthetic gene cluster from Glarea lozoyensis ATCC 20868 and appear to be predominantly found in fungi. 170 matched cddid_all.tbl CDD pfam19536 pfam19536 437368 POU2F1_C POU domain, class 2, transcription factor 1 C-terminal. This domain represents the C-terminal region of the POU domain, class 2 subfamily, transcription factor 1, which is localized adjacent to the homeobox domain. This transcription factor activates the promoters of the genes for some small nuclear RNAs (snRNA) and of genes such as those for histone H2B and immunoglobulins. 284 matched cddid_all.tbl CDD pfam19537 pfam19537 437369 DUF6061 Family of unknown function (DUF6061). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. Several proteins in this family are annotated as toxin-antitoxin system proteins. 81 matched cddid_all.tbl CDD pfam19538 pfam19538 437370 DUF6062 Family of unknown function (DUF6062). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 234 and 254 amino acids in length. This family contains two repeated domains that each contain a conserved CXXC and GXCXXH sequence motif. This suggests that these proteins are likely to be metal binding. 243 matched cddid_all.tbl CDD pfam19539 pfam19539 437371 DUF6063 Family of unknown function (DUF6063). This family of proteins is functionally uncharacterized. This family of proteins is found primarily in bacteria. Proteins in this family are typically between 237 and 249 amino acids in length. They contain a central predicted transmembrane helix. 244 matched cddid_all.tbl CDD pfam19540 pfam19540 437372 DUF6064 Family of unknown function (DUF6064). This family of integral membrane proteins is functionally uncharacterized. This family of proteins is found in Proteobacteria and Bacteroidetes. Proteins in this family are typically between 215 and 242 amino acids in length. 210 matched cddid_all.tbl CDD pfam19541 pfam19541 437373 DUF6065 Family of unknown function (DUF6065). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001418) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. This family includes a protein from the myxochromide D biosynthetic gene cluster from Hyalangium minutum. 236 matched cddid_all.tbl CDD pfam19542 pfam19542 466117 DUF6066 Family of unknown function (DUF6066). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001418) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. This family includes a protein from the myxochromide D biosynthetic gene cluster from Hyalangium minutum and appears to be predominantly found in Cystobacterineae. 211 matched cddid_all.tbl CDD pfam19543 pfam19543 437375 DUF6067 Family of unknown function (DUF6067). This family of proteins is functionally uncharacterized. This family of proteins is mainly found in bacteria. 967 matched cddid_all.tbl CDD pfam19544 pfam19544 437376 DUF6068 Family of unknown function (DUF6068). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001902) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. This family includes a protein from the bengamide biosynthetic gene cluster from Myxococcus virescens and appears to be predominantly found in cystobacterineae. 392 matched cddid_all.tbl CDD pfam19545 pfam19545 437377 DUF6069 Family of unknown function (DUF6069). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001769) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the family saquayamycin A biosynthetic gene cluster from Streptomyces sp. and appears to be predominantly found in Actinobacteria. 129 matched cddid_all.tbl CDD pfam19546 pfam19546 437378 DUF6070 Family of unknown function (DUF6070). This family of proteins is functionally uncharacterized. This family of proteins is found in Firmicute bacteria. Proteins in this family are typically between 388 and 427 amino acids in length. There are two conserved sequence motifs: PEV and DGT. 344 matched cddid_all.tbl CDD pfam19547 pfam19547 437379 DUF6071 Family of unknown function (DUF6071). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001065) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family contains a protein from the herboxidiene biosynthetic gene cluster from Streptomyces chromofuscus. 220 matched cddid_all.tbl CDD pfam19548 pfam19548 437380 CHRDL_1_2_C Chordin-like protein 1/2 C-terminal. This is the C-terminal domain of Chordin-like proteins 1 and 2. These proteins can bind BMPs family ligands and inhibit its activity by blocking their interaction with their receptors. They are involved in myoblast and osteoblast differentiation and maturation. 120 matched cddid_all.tbl CDD pfam19549 pfam19549 437381 DUF6072 Family of unknown function (DUF6072). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000967) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. This family includes a protein from the calyculin A biosynthetic gene cluster from uncultured Candidatus Entotheonella sp. and appears to be predominantly found in bacteria. 129 matched cddid_all.tbl CDD pfam19550 pfam19550 437382 DUF6073 Family of unknown function (DUF6073). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001804) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the tiancimycin biosynthetic gene cluster from Streptomyces sp. CB03234 and appears to be predominantly found in bacteria. 219 matched cddid_all.tbl CDD pfam19551 pfam19551 437383 DUF6074 Family of unknown function (DUF6074). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001765) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a protein from the salecan biosynthetic gene cluster from Agrobacterium tumefaciens and appears to be predominantly found in Rhizobiales. 83 matched cddid_all.tbl CDD pfam19552 pfam19552 437384 DUF6075 Family of unknown function (DUF6075). This family of proteins is functionally uncharacterized. This family of proteins is found primarily in Firmicute bacteria. Proteins in this family are typically between 130 and 155 amino acids in length. There is a conserved AFNL sequence motif. 129 matched cddid_all.tbl CDD pfam19553 pfam19553 437385 DUF6076 Family of unknown function (DUF6076). This family of proteins is functionally uncharacterized. This family of proteins is primarily found in Firmicute bacteria. Proteins in this family are typically between 251 and 390 amino acids in length. These proteins contain 4 conserved cysteines suggestive of a zinc-binding motif. 168 matched cddid_all.tbl CDD pfam19554 pfam19554 437386 DUF6077 Family of unknown function (DUF6077). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 347 and 622 amino acids in length. 354 matched cddid_all.tbl CDD pfam19555 pfam19555 437387 DUF6078 Family of unknown function (DUF6078). This family of proteins is functionally uncharacterized. This family of proteins is found in Bacteroidetes bacteria. Proteins in this family are approximately 150 amino acids in length. This family contains 4 conserved cysteines towards the N-terminus which may form a zinc-binding motif. 145 matched cddid_all.tbl CDD pfam19556 pfam19556 437388 PRTRC_E PRTRC system protein E. A novel genetic system characterized by six or seven major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family averages about 150 amino acids in length, but the last third contains low-complexity sequence that complicates sequence comparisons. 175 matched cddid_all.tbl CDD pfam19557 pfam19557 437389 DUF6079 Family of unknown function (DUF6079). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically around 1200 amino acids in length. This family includes a P-loop domain at the N-terminus. 1240 matched cddid_all.tbl CDD pfam19558 pfam19558 437390 DUF6080 Family of unknown function (DUF6080). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 439 and 479 amino acids in length. 447 matched cddid_all.tbl CDD pfam19559 pfam19559 437391 DUF6081 Family of unknown function (DUF6081). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001964) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the alkylpyrone-407 biosynthetic gene cluster from Cystobacterineae bacterium. 274 matched cddid_all.tbl CDD pfam19560 pfam19560 466118 DUF6082 Family of unknown function (DUF6082). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a protein from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus and appears to be predominantly found in actinobacteria. 163 matched cddid_all.tbl CDD pfam19561 pfam19561 466119 DUF6083 Family of unknown function (DUF6083). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC00001735) is described by MIBiG as an example of the following biosynthetic class, other. This family includes a protein from the pentostatine biosynthetic gene cluster from Streptomyces antibioticus and appears to be predominantly found in Streptomyces. 112 matched cddid_all.tbl CDD pfam19562 pfam19562 437394 DUF6084 Family of unknown function (DUF6084). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001065) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the herboxidiene biosynthetic gene cluster from Streptomyces chromofuscus and appears to be predominantly found in Actinobacteria. 213 matched cddid_all.tbl CDD pfam19563 pfam19563 466120 DUF6085 Family of unknown function (DUF6085). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001905) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the violapyrone B biosynthetic gene cluster from Streptomyces somaliensis and appears to be predominantly found in Actinobacteria and Caudovirale bacteriophages. 115 matched cddid_all.tbl CDD pfam19564 pfam19564 466121 DUF6086 Family of unknown function (DUF6086). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000721) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a protein from the tobramycin biosynthetic gene cluster from Streptoalloteichus tenebrarius and appears to be predominantly found in Actinobacteria. 119 matched cddid_all.tbl CDD pfam19565 pfam19565 437397 DUF6087 Family of unknown function (DUF6087). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a protein from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus. 99 matched cddid_all.tbl CDD pfam19566 pfam19566 437398 Snx8_BAR_dom Sorting nexin 8/Mvp1 BAR domain. This is the BAR (Bin/amphiphysin/Rvs) domain of Sortin nexin 8 (Snx8), which can sense, stabilize and induce membrane curvature. These proteins are involved in intracellular protein transport from early endosomes to the trans-Golgi network. Its yeast counterpart, Mvp1 is required for sorting proteins to the vacuole. 258 matched cddid_all.tbl CDD pfam19567 pfam19567 437399 CpsB_CapC Capsular polysaccharide synthesis, CpsB/CapC. 234 matched cddid_all.tbl CDD pfam19568 pfam19568 437400 Spore_III_AA Sporulation stage III, protein AA. 306 matched cddid_all.tbl CDD pfam19569 pfam19569 437401 START_2 START-like superfamily domain. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. This family appears to be distantly related to the START domain. 126 matched cddid_all.tbl CDD pfam19570 pfam19570 437402 DUF6088 Family of unknown function (DUF6088). This family of proteins is functionally uncharacterized. This family of proteins is found primarily in bacteria. Proteins in this family are typically between 197 and 228 amino acids in length. This family appears to be distantly related to pfam13338 suggesting proteins in this family may be an antitoxin component of a toxin/antitoxin system. 172 matched cddid_all.tbl CDD pfam19571 pfam19571 437403 ACT_8 ACT domain pair. This entry represents a pair of ACT domains. These domains bind to amino acids and often form regulatory subunits of enzymes. Proteins in this family are found in bacteria and archaea. Proteins in this family are approximately 140 amino acids in length. 141 matched cddid_all.tbl CDD pfam19572 pfam19572 437404 PorV Type IX secretion system protein PorV. This entry represents the PorV protein. The Bacteroidete T9SS contains at least 15 proteins. PorQ, PorU, PorV and PorZ form a cell surface-exposed attachment complex that proteolytically removes the substrate CTD following transport and covalently links some substrate proteins to a lipopolysaccharide anchor. A pool of PorV proteins in the outer membrane is thought to shuttle substrate proteins from the translocon to the attachment complex. The PorV protein has a membrane beta barrel topology. 243 matched cddid_all.tbl CDD pfam19573 pfam19573 437405 DUF6089 Domain of unknown function (DUF6089). This family of membrane bound beta barrel proteins is functionally uncharacterized. This family of proteins is found in Bacteroidetes bacteria. Proteins in this family are typically between 227 and 265 amino acids in length. 226 matched cddid_all.tbl CDD pfam19574 pfam19574 437406 LolA_3 Outer membrane lipoprotein carrier protein LolA-like. This family of proteins is related to the pfam03548 and found in proteobacteria. 192 matched cddid_all.tbl CDD pfam19575 pfam19575 437407 HTH_58 Helix-turn-helix domain. This family of proteins is functionally uncharacterized. However, it contains a helix-turn-helix domain which strongly suggests these proteins are transcriptional regulators. This family of proteins is primarily found in actinobacteria. Proteins in this family are typically between 69 and 86 amino acids in length. 73 matched cddid_all.tbl CDD pfam19576 pfam19576 437408 Acyltransf_2 Acyltransferase. This family of proteins are likely to function as acyltransferases. Proteins in this family are found in Bacteria. 266 matched cddid_all.tbl CDD pfam19577 pfam19577 437409 DcaP DcaP outer membrane protein. This entry includes DcaP which is the most abundant outer membrane channel protein in Acinetobacter baumannii. X-ray crystallography reveals a trimeric porin-like structure and suggests dicarboxylic acids as potential substrates. 410 matched cddid_all.tbl CDD pfam19578 pfam19578 437410 DUF6090 Family of unknown function (DUF6090). This family of proteins is functionally uncharacterized. Proteins in this family are primarily found in Bacteroidetes. Proteins in this family are typically between 241 and 255 amino acids in length. 182 matched cddid_all.tbl CDD pfam19579 pfam19579 466122 FtsL_2 Bacteriodetes cell division protein (FtsL-like). This family of share similarity to pfam04977 and pfam04999 suggesting it is a cell division protein. Proteins in this family are primarily found in Bacteroidetes. Proteins in this family are typically between 105 and 129 amino acids in length. 100 matched cddid_all.tbl CDD pfam19580 pfam19580 437412 Exo_endo_phos_3 Endonuclease/Exonuclease/phosphatase family. This domain appears to be related to pfam03372. 311 matched cddid_all.tbl CDD pfam19581 pfam19581 437413 Glyoxalase_7 Glyoxalase superfamily protein. 133 matched cddid_all.tbl CDD pfam19582 pfam19582 437414 AdeT1_2 Solute-binding protein AdeT 1/2. This entry represents the Probable solute-binding protein AdeT1/2 from Acinetobacter baumannii. These proteins are involved in resistance to antibiotics by active efflux. 392 matched cddid_all.tbl CDD pfam19583 pfam19583 437415 ODP ODP family beta lactamase. The ODP (Oxygen-binding Di-iron Protein) domain is a distinct member of the metallo-beta-lactamase superfamily recruited to various bacterial and archaeal signal transduction pathways, including chemotaxis, to function as oxygen and iron sensors (1). ODP was shown to act as a sensor for chemotactic responses to both iron and oxygen in the human pathogen Treponema denticola (Td). The ODP di-iron site binds oxygen at high affinity to reversibly form an unusually stable peroxo adduct. 194 matched cddid_all.tbl CDD pfam19584 pfam19584 437416 MCAfunc MCAfunc domain. MCAfunc domain (MCAfunc) is located in the N-terminal region of a mechanosensitive channel protein MID1-COMPLEMENTING ACTIVITY (MCA). MCAfunc represents the provisionally advocated ARPK domain (Amino-terminal domain of Rice putative Protein Kinases), overlapping with the EF hand-like region at the N-terminus. In MCA proteins, MCAfunc has Ca2+ influx activity and is proposed to be a functional domain of MCAs. MCAfunc is exclusively observed in streptophytes and exists not only in MCA but also in E3 ubiquitin ligase-like proteins, ARO3 like proteins and and protein kinases. In the most basal plant lineage, charophytes, MCAfunc is only found in E3 ubiquitin ligase-like proteins and protein of presently unknown function, while MCA proteins are exclusively found in land plants, from bryophytes to angiosperms. 143 matched cddid_all.tbl CDD pfam19585 pfam19585 437417 DUF6092 Family of unknown function (DUF6092). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001986) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). This family includes a member from the purincyclamide biosynthetic gene cluster from Streptomyces chrestomyceticus and appears to be predominantly found in bacteria. 86 matched cddid_all.tbl CDD pfam19586 pfam19586 466123 DUF6093 Family of unknown function (DUF6093). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. This family includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus and appears to be predominantly found in Actinobacteria. 117 matched cddid_all.tbl CDD pfam19587 pfam19587 437419 DUF6094 Uncharacterized methyltransferase family (DUF6094). This family of proteins is functionally uncharacterized, but The C-terminus appears to be related to methyltransferases. This family of proteins is found in bacteria. Proteins in this family are typically between 362 and 396 amino acids in length. 339 matched cddid_all.tbl CDD pfam19588 pfam19588 437420 SxtJ Saxitoxin biosynthesis operon protein SxtJ. This family of integral membrane proteins is functionally uncharacterized. It is found in cyanobacterial Saxitoxin biosynthesis operon. This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. 99 matched cddid_all.tbl CDD pfam19589 pfam19589 466124 DUF6095 Family of unknown function (DUF6095). This family of predicted integral membrane proteins is functionally uncharacterized. This family of proteins is found in Bacteroidetes. Proteins in this family are approximately 70 amino acids in length. 73 matched cddid_all.tbl CDD pfam19590 pfam19590 437422 TrbL_3 TrbL/VirB6 plasmid conjugal transfer like protein. This family of proteins are related to the Type IV secretion system protein TrbL. This family of proteins is found in archaea. Proteins in this family are typically between 353 and 403 amino acids in length. 377 matched cddid_all.tbl CDD pfam19591 pfam19591 437423 DUF6096 Family of unknown function (DUF6096). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and phage. Proteins in this family are typically between 124 and 138 amino acids in length. 130 matched cddid_all.tbl CDD pfam19592 pfam19592 437424 DUF6097 Family of unknown function (DUF6097). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001796) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the tauramamide biosynthetic gene cluster from Brevibacillus laterosporus DSM 25 and appears to be predominantly found in bacteria. 146 matched cddid_all.tbl CDD pfam19593 pfam19593 437425 DUF6098 Family of unknown function (DUF6098). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000847) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the thienamycin biosynthetic gene cluster from Streptomyces cattleya and it appears to be predominantly found in actinobacteria. 141 matched cddid_all.tbl CDD pfam19594 pfam19594 437426 DUF6099 Family of unknown function (DUF6099). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000222) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the FD-594 biosynthetic gene cluster from Streptomyces sp. TA-0256 and it appears to be predominantly found in actinobacteria. 142 matched cddid_all.tbl CDD pfam19595 pfam19595 437427 DUF6100 Family of unknown function (DUF6100). This family of proteins is functionally uncharacterized. This family of proteins is found in Firmicute bacteria. Proteins in this family are approximately 220 amino acids in length. 222 matched cddid_all.tbl CDD pfam19596 pfam19596 437428 DUF6101 Family of unknown function (DUF6101). This family of proteins is functionally uncharacterized. This family of proteins is found primarily in Alphaproteobacteria. Proteins in this family are typically between 173 and 189 amino acids in length. 184 matched cddid_all.tbl CDD pfam19597 pfam19597 437429 DUF6102 Family of unknown function (DUF6102). This family of putative integral membrane proteins is functionally uncharacterized. This family of proteins is found in Firmicute bacteria. Proteins in this family are typically between 198 and 292 amino acids in length. 278 matched cddid_all.tbl CDD pfam19598 pfam19598 466125 DUF6103 Family of unknown function (DUF6103). This family of proteins is functionally uncharacterized. This family of proteins is found in Firmicute bacteria. Proteins in this family are typically between 83 and 94 amino acids in length. 89 matched cddid_all.tbl CDD pfam19599 pfam19599 437431 DUF6104 Family of unknown function (DUF6104). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. 58 matched cddid_all.tbl CDD pfam19600 pfam19600 437432 DUF6105 Family of unknown function (DUF6105). This family of putative integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. 110 matched cddid_all.tbl CDD pfam19601 pfam19601 437433 DUF6106 Family of unknown function (DUF6106). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 170 amino acids in length. This protein is distantly related to pfam14256. 173 matched cddid_all.tbl CDD pfam19602 pfam19602 437434 DUF6107 Family of unknown function (DUF6107). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 105 and 125 amino acids in length. 106 matched cddid_all.tbl CDD pfam19603 pfam19603 437435 DUF6108 Family of unknown function (DUF6108). This family of proteins is functionally uncharacterized. This family of proteins is found in Bacteroidetes. Proteins in this family are typically between 148 and 173 amino acids in length. 138 matched cddid_all.tbl CDD pfam19604 pfam19604 437436 DUF6109 Family of unknown function (DUF6109). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000069) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the gephyronic acid biosynthetic gene cluster from Archangium violaceum Cb vi76 and appears to be predominantly found in bacteria. 671 matched cddid_all.tbl CDD pfam19605 pfam19605 437437 DUF6110 Family of unknown function (DUF6110). This family of proteins is functionally uncharacterized. This family of proteins is found primarily in Firmicute bacteria. Proteins in this family are typically between 88 and 109 amino acids in length. 85 matched cddid_all.tbl CDD pfam19606 pfam19606 437438 DUF6111 Family of unknown function (DUF6111). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 86 and 106 amino acids in length. 87 matched cddid_all.tbl CDD pfam19607 pfam19607 437439 DUF6112 Family of unknown function (DUF6112). This family of putative integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 88 and 112 amino acids in length. 88 matched cddid_all.tbl CDD pfam19608 pfam19608 437440 DUF6113 Family of unknown function (DUF6113). This family of putative integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 136 and 154 amino acids in length. 129 matched cddid_all.tbl CDD pfam19609 pfam19609 466126 DUF6114 Family of unknown function (DUF6114). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000696) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the gentamicin biosynthetic gene cluster from Micromonospora echinospora and appears to be predominantly found in actinobacteria and firmicutes. 106 matched cddid_all.tbl CDD pfam19610 pfam19610 466127 DUF6115 Family of unknown function (DUF6115). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 237 and 288 amino acids in length. 167 matched cddid_all.tbl CDD pfam19611 pfam19611 437443 DUF6116 Family of unknown function (DUF6116). This family of putative integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. 50 matched cddid_all.tbl CDD pfam19612 pfam19612 437444 DUF6117 Family of unknown function (DUF6117). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 71 and 116 amino acids in length. 87 matched cddid_all.tbl CDD pfam19613 pfam19613 437445 DUF6118 Family of unknown function (DUF6118). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 222 and 245 amino acids in length. 245 matched cddid_all.tbl CDD pfam19614 pfam19614 466128 DUF6119 Family of unknown function (DUF6119). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 523 and 552 amino acids in length. 532 matched cddid_all.tbl CDD pfam19615 pfam19615 437447 DUF6120 Family of unknown function (DUF6120). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 125 and 138 amino acids in length. There is a conserved MGK sequence motif. 92 matched cddid_all.tbl CDD pfam19616 pfam19616 437448 DUF6121 Family of unknown function (DUF6121). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 133 and 164 amino acids in length. 146 matched cddid_all.tbl CDD pfam19617 pfam19617 466129 DUF6122 Family of unknown function (DUF6122). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 104 and 120 amino acids in length. There are two conserved sequence motifs: HYG and RCSI. 102 matched cddid_all.tbl CDD pfam19618 pfam19618 437450 DUF6123 Family of unknown function (DUF6123). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. 89 matched cddid_all.tbl CDD pfam19619 pfam19619 437451 DUF6124 Family of unknown function (DUF6124). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 85 and 119 amino acids in length. 75 matched cddid_all.tbl CDD pfam19620 pfam19620 437452 DUF6125 Family of unknown function (DUF6125). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 170 and 247 amino acids in length. 164 matched cddid_all.tbl CDD pfam19621 pfam19621 466130 DUF6126 Family of unknown function (DUF6126). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000663) is described by MIBiG as an example of the following biosynthetic class, terpene. It includes a member from the hopene biosynthetic gene cluster from Streptomyces coelicolor A3(2) and appears to be predominantly found in actinobacteria. 40 matched cddid_all.tbl CDD pfam19622 pfam19622 466131 DUF6127 Family of unknown function (DUF6127). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 100 amino acids in length. 79 matched cddid_all.tbl CDD pfam19623 pfam19623 437455 DUF6128 Family of unknown function (DUF6128). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 110 amino acids in length. 113 matched cddid_all.tbl CDD pfam19624 pfam19624 437456 DUF6129 Family of unknown function (DUF6129). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 50 amino acids in length. 53 matched cddid_all.tbl CDD pfam19625 pfam19625 437457 DUF6130 Family of unknown function (DUF6130). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 137 and 161 amino acids in length. There are two conserved sequence motifs: NLRI and HVTVDD. 139 matched cddid_all.tbl CDD pfam19626 pfam19626 437458 DUF6131 Family of unknown function (DUF6131). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 50 amino acids in length. 59 matched cddid_all.tbl CDD pfam19627 pfam19627 466132 ADNP_N Activity-dependent neuroprotector homeobox protein N-terminal. This entry represent the N-terminal domain of Activity-dependent neuroprotector homeobox protein (ADNP, also known as Activity- dependent neuroprotective protein), which contains zinc finger motifs. It is involved in transcriptional regulation and it is vital for mammalian brain formation. In humans, de novo mutations result in a syndromic form of autism-like spectrum disorder (ASD), including cognitive and motor deficits, the ADNP syndrome. This protein is also related to autophagy and the pathophysiology of schizophrenia. 744 matched cddid_all.tbl CDD pfam19628 pfam19628 437460 DUF6132 Family of unknown function (DUF6132). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 74 amino acids in length. 60 matched cddid_all.tbl CDD pfam19629 pfam19629 437461 DUF6133 Family of unknown function (DUF6133). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 73 and 87 amino acids in length. There are two conserved sequence motifs: KIL and LLLAGLY. 63 matched cddid_all.tbl CDD pfam19630 pfam19630 466133 DUF6134 Domain of unknown function (DUF6134). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 210 and 241 amino acids in length. 181 matched cddid_all.tbl CDD pfam19631 pfam19631 466134 Trypco2 Trypsin-co-occurring domain 2. Trypsin-like peptidase effector in the classical NTP-dependent ternary system (vWA-MoxR-VMAP) frequently co-occurs with one of two proteins (Trypco1 or Trypco2) which are mostly mutually exclusively. This entry also includes a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000949) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the A-500359 A biosynthetic gene cluster from Streptomyces griseus and appears to be predominantly found in bacteria. 78 matched cddid_all.tbl CDD pfam19632 pfam19632 437464 DUF6136 Family of unknown function (DUF6136). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000299) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the alterochromide A biosynthetic gene cluster from Pseudoalteromonas piscicida JCM 20779 and appears to be predominantly found in gammaproteobacteria. 356 matched cddid_all.tbl CDD pfam19633 pfam19633 437465 SDG2_C Protein SET DOMAIN GROUP 2 C-terminal. Histone-lysine N-methyltransferase ATXR3, also known as protein SET DOMAIN GROUP 2 (SDG2), is a histone methyltransferase specifically required for trimethylation of Lys-4 of histone H3 (H3K4me3) and is crucial for both sporophyte and gametophyte development. This is the POST_SET domain located at the C-terminal of SDG2, although there is no significant sequence homology with other Arabidopsis SDGs outside of the SET domain. 420 matched cddid_all.tbl CDD pfam19634 pfam19634 437466 DUF6137 Family of unknown function (DUF6137). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000709) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the neomycin biosynthetic gene cluster from Streptomyces fradiae ATCC 10745 = DSM 40063 and appears to be predominantly found in bacteria. 82 matched cddid_all.tbl CDD pfam19635 pfam19635 437467 DUF6138 Family of unknown function (DUF6138). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000452) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the tyrocidine biosynthetic gene cluster from Brevibacillus brevis NBRC 100599 and appears to be predominantly found in bacteria. 545 matched cddid_all.tbl CDD pfam19636 pfam19636 437468 DUF6139 Family of unknown function (DUF6139). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. There are two conserved sequence motifs: EATN and KGYAI. 77 matched cddid_all.tbl CDD pfam19637 pfam19637 437469 DUF6140 Family of unknown function (DUF6140). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. 69 matched cddid_all.tbl CDD pfam19638 pfam19638 437470 DUF6141 Family of unknown function (DUF6141). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 159 and 175 amino acids in length. 164 matched cddid_all.tbl CDD pfam19639 pfam19639 437471 DUF6142 Family of unknown function (DUF6142). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 105 and 121 amino acids in length. 103 matched cddid_all.tbl CDD pfam19640 pfam19640 466135 DUF6143 Family of unknown function (DUF6143). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 173 and 198 amino acids in length. 182 matched cddid_all.tbl CDD pfam19641 pfam19641 437473 DUF6144 Family of unknown function (DUF6144). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 190 amino acids in length. 181 matched cddid_all.tbl CDD pfam19642 pfam19642 437474 DUF6145 Family of unknown function (DUF6145). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 110 and 124 amino acids in length. 119 matched cddid_all.tbl CDD pfam19643 pfam19643 437475 DUF6146 Family of unknown function (DUF6146). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 138 and 158 amino acids in length. 133 matched cddid_all.tbl CDD pfam19644 pfam19644 437476 DUF6147 Family of unknown function (DUF6147). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 155 and 173 amino acids in length. 139 matched cddid_all.tbl CDD pfam19645 pfam19645 466136 DUF6148 Family of unknown function (DUF6148). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 74 matched cddid_all.tbl CDD pfam19646 pfam19646 437478 DUF6149 Family of unknown function (DUF6149). This family of proteins is functionally uncharacterized. This family of proteins is found in archaea. Proteins in this family are typically between 191 and 204 amino acids in length. 200 matched cddid_all.tbl CDD pfam19647 pfam19647 437479 DUF6150 Family of unknown function (DUF6150). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 93 and 116 amino acids in length. 98 matched cddid_all.tbl CDD pfam19648 pfam19648 437480 DUF6151 Family of unknown function (DUF6151). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 185 and 201 amino acids in length. 188 matched cddid_all.tbl CDD pfam19649 pfam19649 437481 DUF6152 Family of unknown function (DUF6152). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 122 and 152 amino acids in length. There are two conserved sequence motifs: AHH and NPH. 98 matched cddid_all.tbl CDD pfam19650 pfam19650 466137 DUF6153 Family of unknown function (DUF6153). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001435) is described by MIBiG as an example of the following biosynthetic classes, polyketide and NRP (non-ribosomal peptide). It includes a member from the ikarugamycin biosynthetic gene cluster from Streptomyces sp. ZJ306 and appears to be predominantly found in Actinobacteria. 116 matched cddid_all.tbl CDD pfam19651 pfam19651 437483 DUF6154 Family of unknown function (DUF6154). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 79 matched cddid_all.tbl CDD pfam19652 pfam19652 437484 DUF6155 Family of unknown function (DUF6155). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 169 and 185 amino acids in length. 170 matched cddid_all.tbl CDD pfam19653 pfam19653 437485 DUF6156 Family of unknown function (DUF6156). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 96 and 117 amino acids in length. There are two conserved sequence motifs: RNT and VYGE. 96 matched cddid_all.tbl CDD pfam19654 pfam19654 437486 DUF6157 Family of unknown function (DUF6157). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. 136 matched cddid_all.tbl CDD pfam19655 pfam19655 466138 DUF6158 Family of unknown function (DUF6158). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus and appears to be predominantly found in actinobacteria. 66 matched cddid_all.tbl CDD pfam19656 pfam19656 437488 DUF6159 Family of unknown function (DUF6159). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 277 and 315 amino acids in length. 204 matched cddid_all.tbl CDD pfam19657 pfam19657 437489 DUF6160 Family of unknown function (DUF6160). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 153 and 460 amino acids in length. 320 matched cddid_all.tbl CDD pfam19658 pfam19658 437490 DUF6161 Family of unknown function (DUF6161). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is typically between 206 and 231 amino acids in length. There are two conserved sequence motifs: HLA and LFSR. 215 matched cddid_all.tbl CDD pfam19659 pfam19659 437491 DUF6162 Family of unknown function (DUF6162). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 190 amino acids in length. 240 matched cddid_all.tbl CDD pfam19660 pfam19660 437492 DUF6163 Family of unknown function (DUF6163). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 141 and 157 amino acids in length. 145 matched cddid_all.tbl CDD pfam19661 pfam19661 437493 DUF6164 Family of unknown function (DUF6164). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. 116 matched cddid_all.tbl CDD pfam19662 pfam19662 437494 DUF6165 Family of unknown function (DUF6165). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 129 and 147 amino acids in length. 134 matched cddid_all.tbl CDD pfam19663 pfam19663 437495 DUF6166 Family of unknown function (DUF6166). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 104 and 215 amino acids in length. There are two conserved sequence motifs: GDRTIDG and VVANF. 96 matched cddid_all.tbl CDD pfam19664 pfam19664 437496 DUF6167 Family of unknown function (DUF6167). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 86 and 118 amino acids in length. 96 matched cddid_all.tbl CDD pfam19665 pfam19665 437497 DUF6168 Family of unknown function (DUF6168). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. 128 matched cddid_all.tbl CDD pfam19666 pfam19666 437498 DUF6169 Family of unknown function (DUF6169). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 137 and 167 amino acids in length. 92 matched cddid_all.tbl CDD pfam19667 pfam19667 437499 DUF6170 Family of unknown function (DUF6170). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 84 and 107 amino acids in length. 100 matched cddid_all.tbl CDD pfam19668 pfam19668 437500 DUF6171 Family of unknown function (DUF6171). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 90 amino acids in length. 80 matched cddid_all.tbl CDD pfam19669 pfam19669 437501 DUF6172 Family of unknown function (DUF6172). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 98 and 116 amino acids in length. There is a conserved KRER sequence motif. 95 matched cddid_all.tbl CDD pfam19670 pfam19670 437502 DUF6173 Family of unknown function (DUF6173). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 139 and 154 amino acids in length. 102 matched cddid_all.tbl CDD pfam19671 pfam19671 437503 DUF6174 Family of unknown function (DUF6174). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 151 and 236 amino acids in length. 122 matched cddid_all.tbl CDD pfam19672 pfam19672 437504 DUF6175 Family of unknown function (DUF6175). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 316 and 421 amino acids in length. 289 matched cddid_all.tbl CDD pfam19673 pfam19673 437505 DUF6176 Family of unknown function (DUF6176). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000198) is described by MIBiG as an example of the following biosynthetic classes, polyketide and saccharide. It includes a member from the arenimycin A biosynthetic gene cluster from Salinispora arenicola CNB527. 109 matched cddid_all.tbl CDD pfam19674 pfam19674 466139 DUF6177 Family of unknown function (DUF6177). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000360) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the GE81112 biosynthetic gene cluster from Streptomyces sp. L-49973 and appears to be predominantly found in Actinobacteria. 329 matched cddid_all.tbl CDD pfam19675 pfam19675 466140 ORC3_ins Origin recognition complex subunit 3 insertion domain. This is the large domain insertion of ORC subunit 3 (ORC3) located between the N-terminal AAA+-like subunit and the C-terminal winged- helix (WH) DNA-binding domain. ORC3 is a component of the origin recognition complex (ORC) that binds origins of replication, required to assemble the pre-replication complex necessary to initiate DNA replication. This domain insertion forms a bi-lobed alpha-helical protuberance that engages a short alpha-helix formed at the ORC6 C-terminal, allowing its binding to ORC1-5 subunits, which constitute the ORC core. 233 matched cddid_all.tbl CDD pfam19676 pfam19676 466141 DUF6178 Family of unknown function (DUF6178). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001091) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the corallopyronin biosynthetic gene cluster from Corallococcus coralloides. This family appears to be predominantly found in proteobacteria. 561 matched cddid_all.tbl CDD pfam19677 pfam19677 466142 DUF6179 Family of unknown function (DUF6179). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001520) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the aurantinin B biosynthetic gene cluster from Bacillus subtilis. This family appears to be predominantly found in firmicutes. 272 matched cddid_all.tbl CDD pfam19678 pfam19678 437510 DUF6180 Family of unknown function (DUF6180). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000385) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the lysobactin biosynthetic gene cluster from Lysobacter sp. ATCC 53042. 102 matched cddid_all.tbl CDD pfam19679 pfam19679 437511 DUF6181 Family of unknown function (DUF6181). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus. 134 matched cddid_all.tbl CDD pfam19680 pfam19680 437512 DUF6182 Family of unknown function (DUF6182). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001774) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the spicamycin biosynthetic gene cluster from Streptomyces fimbriatus. This family appears to be predominantly found in Actinobacteria. 242 matched cddid_all.tbl CDD pfam19681 pfam19681 466143 DUF6183 Family of unknown function (DUF6183). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001726) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the pactamides biosynthetic gene cluster from Streptomyces pactum. This family appears to be predominantly found in Actinobacteria. 358 matched cddid_all.tbl CDD pfam19682 pfam19682 437514 DUF6184 Family of unknown function (DUF6184). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000990) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the epothilone biosynthetic gene cluster from Sorangium cellulosum. This family appears to be predominantly found in Proteobacteria. 81 matched cddid_all.tbl CDD pfam19683 pfam19683 437515 DUF6185 Family of unknown function (DUF6185). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001485) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the 3-demethylchuangxinmycin biosynthetic gene cluster from Actinoplanes tsinanensis. This family appears to be predominantly found in Actinobacteria. 811 matched cddid_all.tbl CDD pfam19684 pfam19684 437516 DUF6186 Family of unknown function (DUF6186). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001215) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the conglobatin biosynthetic gene cluster from Streptomyces conglobatus. This family appears to be predominantly found in Actinobacteria. 37 matched cddid_all.tbl CDD pfam19685 pfam19685 437517 DUF6187 Family of unknown function (DUF6187). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001503) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the amycolamycin A biosynthetic gene cluster from Amycolatopsis sp.. This family appears to be predominantly found in Actinobacteria. 141 matched cddid_all.tbl CDD pfam19686 pfam19686 466144 DUF6188 Family of unknown function (DUF6188). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus. This family appears to be predominantly found in bacteria. 121 matched cddid_all.tbl CDD pfam19687 pfam19687 437519 MARF1_LOTUS MARF1 LOTUS domain. This is the LOTUS domain which is repeated in the C-terminal of of Meiosis regulator and mRNA stability factor 1 (MARF1) protein, an essential regulator of oogenesis required for completion of meiosis and retrotransposon silencing, key to maintain germline integrity. This domain provides RNA-binding properties to this protein, acting as an adapter to recruit targets for the effector domain NYN (pfam01936) at the N-terminal (RNase activity). 211 matched cddid_all.tbl CDD pfam19688 pfam19688 437520 DUF6189 Family of unknown function (DUF6189). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000807) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member of the phosphonoglycans biosynthetic gene cluster from Stackebrandtia nassauensis DSM 44728. 102 matched cddid_all.tbl CDD pfam19689 pfam19689 437521 DUF6190 Family of unknown function (DUF6190). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0002018) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the azomycin biosynthetic gene cluster from Streptomyces cattleya NRRL 8057 = DSM 46488. This family appears to be predominantly found in bacteria. 165 matched cddid_all.tbl CDD pfam19690 pfam19690 466145 DUF6191 Family of unknown function (DUF6191). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0002014) is described by MIBiG as an example of the following biosynthetic classes, polyketide and NRP (non-ribosomal peptide). It includes a member of the pepticinnamin E biosynthetic gene cluster from Actinobacteria bacterium OK006. This family appears to be predominantly found in Actinobacteria. 42 matched cddid_all.tbl CDD pfam19691 pfam19691 466146 DUF6192 Family of unknown function (DUF6192). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000713) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from from the ribostamycin biosynthetic gene cluster from Streptomyces ribosidificus. This family appears to be predominantly found in bacteria. 212 matched cddid_all.tbl CDD pfam19692 pfam19692 466147 DUF6193 Family of unknown function (DUF6193). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000087) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the lasalocid biosynthetic gene cluster from Streptomyces lasaliensis. This family appears to be predominantly found in Actinobacteria. 112 matched cddid_all.tbl CDD pfam19693 pfam19693 437525 PSMdelta Phenol-soluble modulin delta protein. This entry represents the phenol-soluble modulin delta peptide found in staphylococcal species. 22 matched cddid_all.tbl CDD pfam19694 pfam19694 466148 DUF6194 Family of unknown function (DUF6194). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001597) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the fluvirucin B2 biosynthetic gene cluster from Actinomadura fulva subsp. indica. This family appears to be predominantly found in bacteria. 156 matched cddid_all.tbl CDD pfam19695 pfam19695 437527 DUF6195 Family of unknown function (DUF6195). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus. 139 matched cddid_all.tbl CDD pfam19696 pfam19696 466149 DUF6196 Family of unknown function (DUF6196). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001381) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the brasilinolide A biosynthetic gene cluster from Nocardia terpenica. This family appears to be predominantly found in bacteria. 144 matched cddid_all.tbl CDD pfam19697 pfam19697 437529 Atg11_middle Atg11 middle domain. This domain represents the region comprised between residues 522 and 583 from fission yeast protein Atg11, which is necessary and sufficient for Atg11 autophagy function and for supporting Atg1 kinase activity as it harbours an Atg1-binding domain at the N-terminal and a homodimerization domain at the C-terminal. The N-terminal part contains the conserved aromatic residues Phe and Tyr necessary for the direct and specific interaction with the tMIT domain of Atg1. This interaction is required for the autophagy function of Atg11. The C-terminal part of this domain, residues 546-583, is predicted to adopt a coiled-coil conformation which mediates Atg11 homodimerization. It seems to be conserved among Schizosaccharomyces. 79 matched cddid_all.tbl CDD pfam19698 pfam19698 437530 DUF6197 Family of unknown function (DUF6197). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus. 143 matched cddid_all.tbl CDD pfam19699 pfam19699 466150 CLSTN_C Calsyntenin C-terminal. This is the cytoplasmic C-terminal domain of clasyntenin (CLSTN) proteins 1, 2 and 3 (also known as Alcadein-alpha, gamma and beta). These are postsynaptic Ca2-binding proteins, evolutionarily conserved type I membrane proteins. CLSTN forms a complex with APP and X11-like that stabilizes both APP and CLSTN proteins metabolically. CLSTN strongly associates with kinesin-1 light chains (KLC1) that induce kinesin-1 association with vesicles and functions as a novel cargo in axonal anterograde transport. This domain includes the WD motifs required for KLC1 interaction (although one WD motif is sufficient), and the NP motif. 354 matched cddid_all.tbl CDD pfam19700 pfam19700 466151 DUF6198 Family of unknown function (DUF6198). This family represents a putative integral membrane protein that is likely to be the membrane component of an ABC transport system. 217 matched cddid_all.tbl CDD pfam19701 pfam19701 437533 DUF6199 Family of unknown function (DUF6199). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000087) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the lasalocid biosynthetic gene cluster from Streptomyces lasaliensis. 50 matched cddid_all.tbl CDD pfam19702 pfam19702 466152 DUF6200 Family of unknown function (DUF6200). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001943) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the vioprolides A biosynthetic gene cluster from Cystobacter sp.. This family appears to be predominantly found in bacteria. 76 matched cddid_all.tbl CDD pfam19703 pfam19703 437535 DUF6201 Family of unknown function (DUF6201). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001133) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the taxlllaid A biosynthetic gene cluster from Xenorhabdus bovienii SS-2004. This family appears to be predominantly found in Proteobacteria. 129 matched cddid_all.tbl CDD pfam19704 pfam19704 466153 DNAPKcs_CC5 DNA-PKcs, CC5. This entry represents the C-terminal region of the circular cradle segment (CC, also known as M-HEAT repeats) from DNA-dependent protein kinase catalytic subunit (DNA-PKcs), containing most of the supersecondary structure CC4 and the complete CC5. DNA-PKcs is involved in DNA nonhomologous end joining (NHEJ), required for double-strand break (DSB) repair. It interacts with the C-terminal peptide of Ku80 which presents the DNA ends for repair. The structures in this entry contain Ku-binding site B and one of the caspase-3 cleavage sites. 641 matched cddid_all.tbl CDD pfam19705 pfam19705 437537 DUF6202 Family of unknown function (DUF6202). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000877) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the polyoxin A biosynthetic gene cluster from Streptomyces cacaoi subsp. asoensis. 274 matched cddid_all.tbl CDD pfam19706 pfam19706 437538 DUF6203 Family of unknown function (DUF6203). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001944) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the funisamine biosynthetic gene cluster from Streptosporangium sp.. 54 matched cddid_all.tbl CDD pfam19707 pfam19707 466154 DUF6204 Family of unknown function (DUF6204). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001070) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the kirromycin biosynthetic gene cluster from Streptomyces collinus Tu 365. This family appears to be predominantly found in Actinobacteria. 114 matched cddid_all.tbl CDD pfam19708 pfam19708 437540 DUF6205 Family of unknown function (DUF6205). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000078) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the incednine biosynthetic gene cluster from Streptomyces sp. ML694-90F3. 143 matched cddid_all.tbl CDD pfam19709 pfam19709 437541 DUF6206 Family of unknown function (DUF6206). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001063) is described by MIBiG as an example of the following biosynthetic classes, polyketide and NRP (non-ribosomal peptide). It includes a member from the undecylprodigiosin biosynthetic gene cluster from Streptomyces coelicolor A3(2). This family appears to be predominantly present in bacteria. 264 matched cddid_all.tbl CDD pfam19710 pfam19710 466155 PIK3CG_ABD PIK3 catalytic subunit gamma adaptor-binding domain. This is the N-terminal domain from PI3-kinase catalytic subunit gamma (PIK3CG, also known as p110 catalytic subunit gamma) which contains the adaptor-binding domain (ABD). This is a globular domain with an alpha/beta sandwich topology, common to all catalytic subunits of PIK3s, and it is similar to ubiquitin-like domains. This domain interacts with the regulatory subunit of the p101 type. 195 matched cddid_all.tbl CDD pfam19711 pfam19711 437543 DUF6207 Family of unknown function (DUF6207). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001709) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the nystatin biosynthetic gene cluster from Streptomyces albulus. This family appears to be predominantly found in Actinobacteria. 67 matched cddid_all.tbl CDD pfam19712 pfam19712 466156 AGK_C Acylglycerol kinase C-terminal. This domain corresponds to the C-terminal of mitochondrial Acylglycerol kinase (AGK, also known as MuLK). AGK is a metazoan-specific protein integrated into the mitochondrial inner membrane through a short N-terminal transmembrane domain. This large C-terminal domain is adjacent the kinase domain and it is oriented to the intermembrane space. AGK is a subunit of the human TIM22 complex which stabilizes the complex and regulates the import and assembly of mitochondrial carrier proteins, a function independent of its kinase activity. Disturbances in both functions of AGK (phospholipid metabolism and mitochondrial protein biogenesis) contribute to the pathogenesis of Sengers syndrome. 215 matched cddid_all.tbl CDD pfam19713 pfam19713 437545 DUF6208 Family of unknown function (DUF6208). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000976) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the curacin A biosynthetic gene cluster from Moorea producens 3L. This family appears to be predominantly found in Cyanobacteria. 306 matched cddid_all.tbl CDD pfam19714 pfam19714 437546 DUF6209 Family of unknown function (DUF6209). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC00001940) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the pyxidicycline A biosynthetic gene cluster from Pyxidicoccus fallax. This family appears to be predominantly found in bacteria. 237 matched cddid_all.tbl CDD pfam19715 pfam19715 466157 DUF6210 Family of unknown function (DUF6210). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001448) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the malacidin A biosynthetic gene cluster from uncultured bacterium. This family appears to be predominantly found in bacteria. 114 matched cddid_all.tbl CDD pfam19716 pfam19716 437548 DUF6211 Family of unknown function (DUF6211). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus. 92 matched cddid_all.tbl CDD pfam19717 pfam19717 437549 DUF6212 Family of unknown function (DUF6212). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000801) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the galactoglucan biosynthetic gene cluster from Sinorhizobium meliloti. This family appears to be predominantly found in proteobacteria. 388 matched cddid_all.tbl CDD pfam19718 pfam19718 466158 USP47_C Ubiquitin carboxyl-terminal hydrolase 47 C-terminal. This is the C-terminal domain of Ubiquitin carboxyl-terminal hydrolase 47 (USP47), a ubiquitin-specific protease involved in deubiquitinating of monoubiquitinated DNA polymerase beta (Polbeta), being required for its stability and, therefore, plays a role in DNA base excision repair (BER). The C-terminal domains in USPs mediate protein- protein interactions. 240 matched cddid_all.tbl CDD pfam19719 pfam19719 437551 DUF6213 Family of unknown function (DUF6213). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001916) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the lavendiol biosynthetic gene cluster from Streptomyces lavendulae. This family appears to be predominantly found in Actinobacteria. 66 matched cddid_all.tbl CDD pfam19720 pfam19720 466159 DUF6214 Family of unknown function (DUF6214). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001782) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the spiroindimicin A biosynthetic gene cluster from Streptomyces sp. SCSIO 03032. This family appears to be predominantly found in Actinobacteria. 155 matched cddid_all.tbl CDD pfam19721 pfam19721 437553 DUF6215 Family of unknown function (DUF6215). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001856) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the caniferolide A biosynthetic gene cluster from Streptomyces caniferus. This family appears to be predominantly found in Actinobacteria. 135 matched cddid_all.tbl CDD pfam19722 pfam19722 466160 SENP3_5_N Sentrin-specific protease 3/5 N-terminal. Sentrin/SUMO-specific proteases (SENPs) reversibly regulate the covalent modification of proteins by SUMO. SENP3 and 5 share considerable sequence homology and exhibit similar substrate specificity, as they are active against SUMO-2 and SUMO-3 but less so for SUMO-1. They are more closely related than to SENP1/2. This entry covers the N-terminal domain of SENP5, which contains a conserved region directly preceding the catalytic domain, which is shared with SENP3. This domain is responsible for the subcellular localization. SENP3 and 5 colocalize in the nucleolus and their depletion causes defects in ribosome biogenesis. 570 matched cddid_all.tbl CDD pfam19723 pfam19723 437555 DUF6216 Family of unknown function (DUF6216). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001055) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the yersiniabactin biosynthetic gene cluster from Escherichia coli. This family appears to be predominantly found in Proteobacteria. 270 matched cddid_all.tbl CDD pfam19724 pfam19724 437556 DUF6217 Family of unknown function (DUF6217). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001142) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member of the tryptoquialanine biosynthetic gene cluster from Penicillium aethiopicum. This family appears to be predominantly found in fungi. 132 matched cddid_all.tbl CDD pfam19725 pfam19725 466161 RPC5_C DNA-directed RNA polymerase III subunit RPC5 C-terminal. This is the C-terminal domain of DNA-directed RNA polymerase III subunit RPC5 (POLR3E). PolIII is a complex consisting of 17 subunits and transcribes small RNAs, such as 5S rRNA and tRNA, that is involved in innate immune system as it senses viral DNA to produce non-self RNA polymerase III transcripts, which induce type I interferon and NF-Kappa-B. RPC5 forms a subcomplex with RPC4 which is close to the polymerase active centre that enables open promoter complex formation and facilitates termination and reinitiation. Mutations in this subunit are associated with impaired induction of type I IFN and increased susceptibility to viral infections. 252 matched cddid_all.tbl CDD pfam19726 pfam19726 437558 DUF6218 Family of unknown function (DUF6218). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000696) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the gentamicin biosynthetic gene cluster from Micromonospora echinospora. 229 matched cddid_all.tbl CDD pfam19727 pfam19727 437559 DUF6219 Family of unknown function (DUF6219). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001575) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the dipeptide aldehydes biosynthetic gene cluster from Ruminococcus sp. 5_1_39BFAA. This family appears to be predominantly found in bacteria. 69 matched cddid_all.tbl CDD pfam19728 pfam19728 466162 DUF6220 Family of unknown function (DUF6220). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001612) is described by MIBiG as an example of the following biosynthetic class, alkaloid. It includes a member from the ambiguine H isonitrile biosynthetic gene cluster from Fischerella ambigua UTEX 1903. This family appears to be predominantly found in bacteria. 65 matched cddid_all.tbl CDD pfam19729 pfam19729 466163 FBXL18_LRR F-box/LRR-repeat protein 18, LRR. This entry represents the leucine-rich repeats (LRR) from F-box/LRR repeat protein 18 (also known as F-box and leucine-rich repeat protein 18, FBXL18), associated with F-box domains. This protein is the substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex through its F-box and the LRR motifs mediate the protein-protein interactions required for the binding of the specific substrates by SCFs complexes. 594 matched cddid_all.tbl CDD pfam19730 pfam19730 466164 DUF6221 Family of unknown function (DUF6221). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001065) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the herboxidiene biosynthetic gene cluster from Streptomyces chromofuscus. This family appears to be predominantly found in Actinobacteria. 110 matched cddid_all.tbl CDD pfam19731 pfam19731 437563 DUF6222 Family of unknown function (DUF6222). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001503) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the amycolamycin A biosynthetic gene cluster from Amycolatopsis sp.. 67 matched cddid_all.tbl CDD pfam19732 pfam19732 437564 SpoIIE_N Stage II sporulation protein E N-terminal. This is the N-terminal domain found in Stage II sporulation protein E which includes the 10 transmembrane domains and the regulatory domain, the latter located adjacent the PP2C phosphatase domain. The regulatory domain mediates the formation of dimers between SpoIIE molecules, required for phosphatase activation. An N-terminal 45-residue long alpha-helix makes intramolecular contacts with the switch helices (alpha1 and alpha2) of the phosphatase domain. 605 matched cddid_all.tbl CDD pfam19733 pfam19733 437565 DUF6223 Family of unknown function (DUF6223). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001848) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the diazaquinomycin H biosynthetic gene cluster from Micromonospora sp. B006. This family appears to be predominantly found in bacteria. 99 matched cddid_all.tbl CDD pfam19734 pfam19734 437566 DUF6224 Family of unknown function (DUF6224). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000084) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the laidlomycin biosynthetic gene cluster from Streptomyces sp. CS684. 146 matched cddid_all.tbl CDD pfam19735 pfam19735 437567 DUF6225 Family of unknown function (DUF6225). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000896) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the cycloserine biosynthetic gene cluster from Streptomyces lavendulae subsp. lavendulae. 87 matched cddid_all.tbl CDD pfam19736 pfam19736 466165 DUF6226 Family of unknown function (DUF6226). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000223) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the rabelomycin biosynthetic gene cluster from uncultured bacterium BAC AB649/1850. This family appears to be predominantly found in Actinobacteria. 200 matched cddid_all.tbl CDD pfam19737 pfam19737 466166 FKTN_N Fukutin N-terminal. This is the N-terminal domain of fukutin, which contains the transmembrane domain required for its localization to the Golgi and participates in the interaction with POMGnT1 for normal POMGnT1 location and activity. Fukutin is a ribitol-phosphate transferase that forms a complex with FKRP and TMEM5 which may contribute to specific biosynthesis of glycans required for dystroglycan function. 278 matched cddid_all.tbl CDD pfam19738 pfam19738 437570 DUF6227 Family of unknown function (DUF6227). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000118) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the pactamycin biosynthetic gene cluster from Streptomyces pactum. This family appears to be predominantly found in Actinobacteria. 229 matched cddid_all.tbl CDD pfam19739 pfam19739 466167 DUF6228 Family of unknown function (DUF6228). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001042) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the sanglifehrin A biosynthetic gene cluster from Streptomyces flaveolus. This family appears to be predominantly found in Actinobacteria. 133 matched cddid_all.tbl CDD pfam19740 pfam19740 437572 DUF6229 Family of unknown function (DUF6229). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000385) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the lysobactin biosynthetic gene cluster from Lysobacter sp. ATCC 53042. This family appears to be predominantly found in bacteria. 62 matched cddid_all.tbl CDD pfam19741 pfam19741 466168 DUF6230 Family of unknown function (DUF6230). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001774) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the MS-271 biosynthetic gene cluster from Streptomyces sp. This family appears to be predominantly found in Actinobacteria. Some members of this family have been identified as putative cholesterol esterases. 157 matched cddid_all.tbl CDD pfam19742 pfam19742 437574 DUF6231 Family of unknown function (DUF6231). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000387) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the mangotoxin biosynthetic gene cluster from Pseudomonas syringae pv. syringae. This family appears to be predominantly found in Proteobacteria. 156 matched cddid_all.tbl CDD pfam19743 pfam19743 437575 ASTN1_2_EGF_Fn ASTN1/2 EGF-like and Fn(III) domains. Astrotactin-1 and 2 (ASTN1/2) are integral membrane proteins with a large C-terminal domain, extracellular for ASTN1 and endosome luminal for ASTN-2. They play critical roles in neurodevelopment, and ASTN-2 is also involved in the planar cell polarity pathway in hair cells. This is a domain found in the middle of the C-terminal of ASTN-1 and 2, which comprises a EGF- like domain (EGF4) and a fibronectin type III (Fn(III)) domain. These subdomains are located between the MACPF and annexin- like domains. The structure of Fn(III) from ASTN2 revealed an unexpected feature which has two additional beta strands folded across the core. The junction between EGF-4 and Fn(III) domains in ASTN2 (but not in ASTN1) is thought to be an inositol triphosphate binding site. 216 matched cddid_all.tbl CDD pfam19744 pfam19744 466169 DUF6232 Family of unknown function (DUF6232). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000223) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the rabelomycin biosynthetic gene cluster from uncultured bacterium BAC AB649/1850. This family appears to be predominantly found in bacteria. 123 matched cddid_all.tbl CDD pfam19745 pfam19745 466170 FUT8_N_cat Alpha-(1,6)-fucosyltransferase N- and catalytic domains. This entry represents the N-terminal coiled-coil and the catalytic domains of the Alpha-(1,6)-fucosyltransferase (FUT8), an enzyme that catalyzes the transfer of a fucose residue in alpha 1-6 linkage to the N-Acetylglucosamine (GlcNAc) residue in N-glycans. The catalytic domain comprises two structures, an open sheet alpha/beta structure, which contains five helices and three beta- strands at the N-terminal, and a Rossmann fold that contains five helices and five beta-strands at the C-terminal. The latter is conserved among the alpha1,2-, alpha1,6-, and protein O-fucosyltransferases and is similar to GT-B group glycosyltransferases. 431 matched cddid_all.tbl CDD pfam19746 pfam19746 466171 DUF6233 Family of unknown function (DUF6233). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001973) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the fervenulin biosynthetic gene cluster from Streptomyces hiroshimensis. This family appears to be predominantly found in Actinoabacteria. 58 matched cddid_all.tbl CDD pfam19747 pfam19747 437579 DUF6234 Family of unknown function (DUF6234). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000709) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the neomycin biosynthetic gene cluster from Streptomyces fradiae ATCC 10745 = DSM 40063. This family appears to be predominantly found in Actinobacteria. 126 matched cddid_all.tbl CDD pfam19748 pfam19748 437580 DUF6235 Family of unknown function (DUF6235). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001503) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the amycolamycin A biosynthetic gene cluster from Amycolatopsis sp.. This family appears to be predominantly found in Actinobacteria. 96 matched cddid_all.tbl CDD pfam19749 pfam19749 437581 DUF6236 Family of unknown function (DUF6236). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001432) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the myxochromide D biosynthetic gene cluster from Stigmatella erecta. 328 matched cddid_all.tbl CDD pfam19750 pfam19750 437582 DUF6237 Family of unknown function (DUF6237). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001214) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the marformycin A biosynthetic gene cluster from Streptomyces drozdowiczii. 90 matched cddid_all.tbl CDD pfam19751 pfam19751 466172 DUF6238 Family of unknown function (DUF6238). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus. This family appears to be predominantly found in bacteria. 152 matched cddid_all.tbl CDD pfam19752 pfam19752 437584 DUF6239 Family of unknown function (DUF6239). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000081) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the kedarcidin biosynthetic gene cluster from Streptoalloteichus sp. ATCC 53650. 188 matched cddid_all.tbl CDD pfam19753 pfam19753 466173 DUF6240 Family of unknown function (DUF6240). This family of bacterial proteins is functionally uncharacterized. Proteins in this family are typically between 969 and 1090 amino acids in length. Some members of this family are thought to be related to the Flagellar hook-length control protein FliK. 272 matched cddid_all.tbl CDD pfam19754 pfam19754 437586 DUF6241 Family of unknown function (DUF6241). This family of proteins is functionally uncharacterized and it is found in bacteria and viruses. Proteins in this family are typically between 161 and 200 amino acids in length. There are some conserved sequences: HQK and KWG at the N-terminal, and HNxxW near the C-terminal. 90 matched cddid_all.tbl CDD pfam19755 pfam19755 437587 DUF6242 Domain of unknown function (DUF6242). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 290 amino acids in length. It contains a BNR/Asp box motif at the C-terminal, which contains the characteriztic sequence motif SxDxGxT/xW of the BNR family, present as repeats in sialidases and others glycosyl hydrolases. 218 matched cddid_all.tbl CDD pfam19756 pfam19756 466174 DUF6243 Family of unknown function (DUF6243). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001931) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the carrimycin biosynthetic gene cluster from unidentified unclassified sequences. This family appears to be predominantly found in Actinobacteria. 67 matched cddid_all.tbl CDD pfam19757 pfam19757 437589 DUF6244 Family of unknown function (DUF6244). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000267) is described by MIBiG as an example of the following biosynthetic classes, polyketide and saccharide. This entry includes a member from the saquayamycin Z biosynthetic gene cluster from Micromonospora sp. Tu 6368. This family appears to be predominantly found in Actinobacteria. 87 matched cddid_all.tbl CDD pfam19758 pfam19758 437590 DUF6245 Family of unknown function (DUF6245). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the istamycin biosynthetic gene cluster from Streptomyces tenjimariensis. 168 matched cddid_all.tbl CDD pfam19759 pfam19759 437591 DUF6246 Family of unknown function (DUF6246). This family of proteins found in bacteria and viruses is functionally uncharacterized. Proteins in this family are typically between 205 and 235 amino acids in length. 185 matched cddid_all.tbl CDD pfam19760 pfam19760 437592 DUF6247 Family of unknown function (DUF6247). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000345) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the eponemycin biosynthetic gene cluster from Streptomyces hygroscopicus. This family appears to be predominantly found in Actinobacteria. 99 matched cddid_all.tbl CDD pfam19761 pfam19761 437593 DUF6248 Family of unknown function (DUF6248). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus. 155 matched cddid_all.tbl CDD pfam19762 pfam19762 466175 DUF6249 Domain of unknown function (DUF6249). This domain family is found in bacterial proteins, functionally uncharacterized. Proteins in this family are typically between 174 and 239 amino acids in length. This domain is thought to contain transmembrane regions. This family is distantly related to pfam11239. 106 matched cddid_all.tbl CDD pfam19763 pfam19763 466176 DUF6250 Domain of unknown function (DUF6250). This domain is found in bacterial proteins which are functionally uncharacterized. Proteins in this family are typically between 225 and 1025 amino acids in length. There is a conserved Tryptophan residue at the N-terminal and a highly conserved SDLN sequence. 164 matched cddid_all.tbl CDD pfam19764 pfam19764 466177 DUF6251 Family of unknown function (DUF6251). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the istamycin biosynthetic gene cluster from Streptomyces tenjimariensis. 116 matched cddid_all.tbl CDD pfam19765 pfam19765 466178 DUF6252 Family of unknown function (DUF6252). This family of proteins found in bacteria is functionally uncharacterized. Proteins in this family are typically between 166 and 277 amino acids in length. A conserved glycine residue and the conserved sequences GTF and GxF can be found at the C-terminal. 125 matched cddid_all.tbl CDD pfam19766 pfam19766 437598 DUF6253 Family of unknown function (DUF6253). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001778) is described by MIBiG as an example of the following biosynthetic class, other (unspecified). It includes a member from the showdomycin biosynthetic gene cluster from Streptomyces showdoensis. 81 matched cddid_all.tbl CDD pfam19767 pfam19767 437599 DUF6254 Family of unknown function (DUF6254). This family of bacterial proteins is functionally uncharacterized. Proteins in this family are typically between 39 and 59 amino acids in length. This family contains a highly conserved sequence HGKV/IKS/T. 36 matched cddid_all.tbl CDD pfam19768 pfam19768 437600 DUF6255 Family of unknown function (DUF6255). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001662) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the mediomycin A biosynthetic gene cluster from Kitasatospora mediocidica. 69 matched cddid_all.tbl CDD pfam19769 pfam19769 466179 CPxCG_zf CPxCG-related zinc finger. This family includes small CPxCG-related zinc finger archaeal proteins, which are typically between 200 and 221 amino acids in length. They are likely to bind DNA and to be potential transcriptional regulators. These zinc fingers are characterized by the specific CPxCG pattern (variants CPxCx and CxxCG) and a second Cys/His pattern potentially more general, being 7-40 residues apart, forming a zinc finger motif. This family contains the specific CxxCG motif and the Cys motif (CPxCx) at the N-terminal. A member of this family, the Nif-regulating protein A, contains the patterns CxxCG and HxxxH (the latter unique to this protein, located 24 residues away from the CxxCG pattern) to form the zinc finger motif. It is a DNA-binding protein that enhances the transcription of the nitrogen fixation (nif) operon under nitrogen-limited conditions. 184 matched cddid_all.tbl CDD pfam19770 pfam19770 437602 DUF6256 Family of unknown function (DUF6256). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001215) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the conglobatin biosynthetic gene cluster from Streptomyces conglobatus. 110 matched cddid_all.tbl CDD pfam19771 pfam19771 437603 DUF6257 Family of unknown function (DUF6257). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the istamycin biosynthetic gene cluster from Streptomyces tenjimariensis. 61 matched cddid_all.tbl CDD pfam19772 pfam19772 437604 DUF6258 Family of unknown function (DUF6258). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000974) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the crocacin biosynthetic gene cluster from Chondromyces crocatus. 136 matched cddid_all.tbl CDD pfam19773 pfam19773 437605 DUF6259 Domain of unknown function (DUF6259). This domain is found in bacterial proteins and it is functionally uncharacterized. However, some proteins are putative glycoside hydrolases and this domain has some overlaps with clan family members of CL0058. Proteins containing this domain are typically between 678 and 749 amino acids in length. 300 matched cddid_all.tbl CDD pfam19774 pfam19774 437606 DUF6260 Family of unknown function (DUF6260). This family of proteins, functionally uncharacterized, is found in bacteria and viruses. Proteins in this family are typically between 341 and 365 amino acids in length. Some members are thought to be coat proteins. 305 matched cddid_all.tbl CDD pfam19775 pfam19775 437607 DUF6261 Family of unknown function (DUF6261). This family of bacterial proteins is functionally uncharacterized. Proteins in this family are typically between 246 and 334 amino acids in length. Some members are thought to be hemagglutinin-related proteins. 154 matched cddid_all.tbl CDD pfam19776 pfam19776 466180 DUF6262 Family of unknown function (DUF6262). This family of proteins, functionally uncharacterized, is found in bacteria. Proteins in this family are typically between 124 and 143 amino acids in length. Some members included in this family are hypothetical transposases, associated with transposon Tn554. There is a conserved sequence GV/LSR/K and a highly conserved tyrosine residue. 110 matched cddid_all.tbl CDD pfam19777 pfam19777 466181 DUF6263 Family of unknown function (DUF6263). This family of proteins found in bacteria is functionally uncharacterized. Proteins in this family are typically between 298 and 349 amino acids in length. There is a conserved sequence pattern PxxxI/VxxGxxW. 196 matched cddid_all.tbl CDD pfam19778 pfam19778 437610 RE_endonuc Endonuclease domain. This represents the C-terminal endonuclease domain found in a variety of class III restriction endonuclease proteins. 109 matched cddid_all.tbl CDD pfam19779 pfam19779 466182 DUF6264 Family of unknown function (DUF6264). This family of putative integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 179 and 218 amino acids in length. 182 matched cddid_all.tbl CDD pfam19780 pfam19780 466183 DUF6265 Domain of unknown function (DUF6265). This family of domains is functionally uncharacterized. This family of proteins is primarily found in bacteria. Proteins in this family are typically between 159 and 170 amino acids in length. The domain is found in some proteins associated with carbohydrate binding domains. The domain has some conserved aromatic residues that may suggest a carbohydrate binding function. 116 matched cddid_all.tbl CDD pfam19781 pfam19781 437613 DUF6266 Family of unknown function (DUF6266). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 210 amino acids in length. There are two conserved sequence motifs: AMSY and DNS. 198 matched cddid_all.tbl CDD pfam19782 pfam19782 437614 DUF6267 Family of unknown function (DUF6267). This family of proteins is functionally uncharacterized. This family of proteins is primarily found in myoviruses. Proteins in this family are typically between 298 and 400 amino acids in length. 313 matched cddid_all.tbl CDD pfam19783 pfam19783 437615 DUF6268 Domain of unknown function (DUF6268). This family of integral membrane beta-barrel proteins is functionally uncharacterized. This family of proteins is found in Bacteroidetes bacteria. Proteins in this family are typically between 300 and 313 amino acids in length. 280 matched cddid_all.tbl CDD pfam19784 pfam19784 466184 DUF6269 Family of unknown function (DUF6269). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001975) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It includes a member from the atratumycin biosynthetic gene cluster from Streptomyces atratus. 77 matched cddid_all.tbl CDD pfam19785 pfam19785 437617 UPF0738 Family of unknown function (UPF0738). This family of proteins is functionally uncharacterized. This family of proteins is found in Firmicute bacteria. Proteins in this family are approximately 120 amino acids in length. 117 matched cddid_all.tbl CDD pfam19786 pfam19786 466185 DUF6270 Family of unknown function (DUF6270). This family of bacterial proteins is functionally uncharacterized. Proteins in this family are typically between 258 and 528 amino acids in length. There is a conserved GSC sequence motif. 222 matched cddid_all.tbl CDD pfam19787 pfam19787 466186 DUF6271 Family of unknown function (DUF6271). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000093) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the meilingmycin biosynthetic gene cluster from Streptomyces nanchangensis. This family appears to be predominantly found in bacteria. 435 matched cddid_all.tbl CDD pfam19788 pfam19788 466187 DUF6272 Family of unknown function (DUF6272). This family of proteins found in bacteria is functionally uncharacterized. Proteins in this family are approximately 180 amino acids in length. There are two conserved sequence motifs, ExxQN and GAGLG. 135 matched cddid_all.tbl CDD pfam19789 pfam19789 466188 DUF6273 Family of unknown function (DUF6273). This family of proteins is functionally uncharacterized. This family of proteins is found in Firmicute bacteria. Proteins in this family are typically between 204 and 573 amino acids in length. This region is found in proteins that are likely to be surface exposed. 175 matched cddid_all.tbl CDD pfam19790 pfam19790 466189 DUF6274 Family of unknown function (DUF6274). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000119) is described by MIBiG as an example of the following biosynthetic classes, polyketide and saccharide, in particular the 7-deoxypactamycin biosynthetic gene cluster from Streptomyces pactum. This family appears to be predominantly found in Actinobacteria. 74 matched cddid_all.tbl CDD pfam19791 pfam19791 437623 DUF6275 Family of unknown function (DUF6275). This family of proteins is functionally uncharacterized. This family of proteins is found in Firmicute bacteria and their phage. Proteins in this family are approximately 90 amino acids in length. 80 matched cddid_all.tbl CDD pfam19792 pfam19792 437624 DUF6276 Family of unknown function (DUF6276). This family of proteins is functionally uncharacterized. This family of proteins is found in archaea. Proteins in this family are approximately 130 amino acids in length. They contain an N-terminal zinc binding domain. 129 matched cddid_all.tbl CDD pfam19793 pfam19793 437625 DUF6277 Family of unknown function (DUF6277). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001096) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the FR901464 biosynthetic gene cluster from Pseudomonas sp. 2663. 117 matched cddid_all.tbl CDD pfam19794 pfam19794 466190 DUF6278 Family of unknown function (DUF6278). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001590) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the formicamycins A-M biosynthetic gene cluster from Streptomyces sp. KY5. This family appears to be predominantly found in Actinobacteria. 146 matched cddid_all.tbl CDD pfam19795 pfam19795 437627 DUF6279 Family of unknown function (DUF6279). This family of proteins, found in bacteria, is functionally uncharacterized. Proteins in this family are typically between 280 and 295 amino acids in length. There is a conserved WHxxxxLP sequence motif and a conserved Q residue. 195 matched cddid_all.tbl CDD pfam19796 pfam19796 437628 DUF6280 Family of unknown function (DUF6280). This family of proteins is functionally uncharacterized. This family of proteins is found in Alphaproteobacteria. Proteins in this family are approximately 110 amino acids in length. 86 matched cddid_all.tbl CDD pfam19797 pfam19797 466191 DUF6281 Family of unknown function (DUF6281). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus. 100 matched cddid_all.tbl CDD pfam19798 pfam19798 437630 Sulfotransfer_5 Sulfotransferase domain. This entry represents a family of sulfotransferase enzymes. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 238 and 379 amino acids in length. 226 matched cddid_all.tbl CDD pfam19799 pfam19799 437631 DUF6282 Family of unknown function (DUF6282). This family of proteins is functionally uncharacterized and it is found in bacteria and archaea. Proteins in this family are typically between 280 and 313 amino acids in length. This family has some overlaps with families from the clan CL0034. 201 matched cddid_all.tbl CDD pfam19800 pfam19800 437632 DUF6283 Family of unknown function (DUF6283). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001735) is described by MIBiG as an example of the following biosynthetic class, other (unspecified), in particular the pentostatine biosynthetic gene cluster from Streptomyces antibioticus. This family appears to be predominantly found in bacteria. 115 matched cddid_all.tbl CDD pfam19801 pfam19801 466192 DUF6284 Family of unknown function (DUF6284). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the istamycin biosynthetic gene cluster from Streptomyces tenjimariensis. This family appears to be predominantly found in Actinoabactteria. 86 matched cddid_all.tbl CDD pfam19802 pfam19802 466193 DUF6285 Domain of unknown function (DUF6285). This domain family is found in bacterial proteins and it is functionally uncharacterized. In some members of this family, thought to be aminoglycoside phosphotransferases, it is located at the C-terminal. 91 matched cddid_all.tbl CDD pfam19803 pfam19803 466194 DUF6286 Family of unknown function (DUF6286). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 181 and 228 amino acids in length. There is a conserved GV motif. 103 matched cddid_all.tbl CDD pfam19804 pfam19804 466195 DUF6287 Domain of unknown function (DUF6287). This presumed domain, found in bacteria, is functionally uncharacterized. It is around 50 amino acids in length and contains a conserved GTW sequence motif. 34 matched cddid_all.tbl CDD pfam19805 pfam19805 437637 DUF6288 Family of unknown function (DUF6288). This family of bacterial proteins is functionally uncharacterized. Proteins in this family are approximately 800 amino acids in length and they presumably contain PDZ domains. 401 matched cddid_all.tbl CDD pfam19806 pfam19806 437638 DUF6289 Family of unknown function (DUF6289). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000385) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the lysobactin biosynthetic gene cluster from Lysobacter sp. ATCC 53042. 43 matched cddid_all.tbl CDD pfam19807 pfam19807 437639 DUF6290 Family of unknown function (DUF6290). This family of proteins is functionally uncharacterized, they are predominantly found in bacteria but also in viruses. Proteins in this family are approximately 80 amino acids in length and presumably contain a ribbon-helix-helix DNA-binding motif. 72 matched cddid_all.tbl CDD pfam19808 pfam19808 437640 DUF6291 Family of unknown function (DUF6291). This family of proteins, found in bacteria and viruses, is functionally uncharacterized. Proteins in this family are typically between 179 and 275 amino acids in length. There are two conserved residues, a leucine and a tyrosine. 79 matched cddid_all.tbl CDD pfam19809 pfam19809 466196 DUF6292 Family of unknown function (DUF6292). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001203) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the clarexpoxcin biosynthetic gene cluster from uncultured bacterium AR_456. This family appears to be predominantly found in Actinobacteria. 89 matched cddid_all.tbl CDD pfam19810 pfam19810 437642 DUF6293 Family of unknown function (DUF6293). This family of archaeal proteins is functionally uncharacterized. Proteins in this family are typically between 252 and 307 amino acids in length. There is a conserved sequence motif HxxPxxG and a conserved Asparagine residue. 210 matched cddid_all.tbl CDD pfam19811 pfam19811 437643 DUF6294 Family of unknown function (DUF6294). This BGC (BGC0000081) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the kedarcidin biosynthetic gene cluster from Streptoalloteichus sp. ATCC 53650CC. This family appears to be predominantly found in bacteria. 89 matched cddid_all.tbl CDD pfam19812 pfam19812 437644 DUF6295 Family of unknown function (DUF6295). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001922) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the isoindolinomycin biosynthetic gene cluster from Streptomyces sp. SoC090715LN-16. This family appears to be predominantly found in bacteria. 87 matched cddid_all.tbl CDD pfam19813 pfam19813 437645 DUF6296 Family of unknown function (DUF6296). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000187) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the asukamycin biosynthetic gene cluster from Streptomyces nodosus subsp. asukaensis. This family appears to be predominantly found in actinobacteria. 78 matched cddid_all.tbl CDD pfam19814 pfam19814 437646 DUF6297 Family of unknown function (DUF6297). This family of bacterial proteins is functionally uncharacterized. Proteins in this family are typically between 139 and 579 amino acids in length. There is a conserved sequence motif GPV. Some members of this family are hypothetical ABC transporter permeases. 372 matched cddid_all.tbl CDD pfam19815 pfam19815 466197 DUF6298 Family of unknown function (DUF6298). This family of bacterial proteins is functionally uncharacterized. Proteins in this family are typically between 664 and 1043 amino acids in length. Some members of this family are thought to be pectin/pectate lyases. 487 matched cddid_all.tbl CDD pfam19816 pfam19816 437648 DUF6299 Family of unknown function (DUF6299). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000376) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular JBIR-34 biosynthetic gene cluster from Streptomyces sp. Sp080513GE-23. This family appears to be predominantly found in actinobacteria. 114 matched cddid_all.tbl CDD pfam19817 pfam19817 437649 DUF6300 Family of unknown function (DUF6300). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0002024) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular, the nargenicin biosynthetic gene cluster from Nocardia argentinensis. This family appears to be predominantly found in bacteria and unclassified phages. 110 matched cddid_all.tbl CDD pfam19818 pfam19818 437650 DUF6301 Family of unknown function (DUF6301). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001381) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the brasilinolide A biosynthetic gene cluster from Nocardia terpenica. This family appears to be predominantly found in actinobacteria. 139 matched cddid_all.tbl CDD pfam19819 pfam19819 466198 DUF6302 Family of unknown function (DUF6302). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus. 135 matched cddid_all.tbl CDD pfam19820 pfam19820 466199 DUF6303 Family of unknown function (DUF6303). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the istamycin biosynthetic gene cluster from Streptomyces tenjimariensis. This family appears to be predominantly found in actinobacteria. 93 matched cddid_all.tbl CDD pfam19821 pfam19821 437653 Phage_capsid_2 Phage capsid protein. This entry represents a family of phage capsid protein. This family of proteins is found in bacteria and phage. Proteins in this family are approximately 280 amino acids in length. 292 matched cddid_all.tbl CDD pfam19822 pfam19822 437654 DUF6304 Family of unknown function (DUF6304). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000262) is described by MIBiG as an example of the following biosynthetic classes, polyketide and saccharide, in particular the prejadomycin biosynthetic gene cluster from Streptomyces sp. PGA64. This family appears to be predominantly found in bacteria. 157 matched cddid_all.tbl CDD pfam19823 pfam19823 437655 DUF6305 Domain of unknown function (DUF6305). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 183 and 215 amino acids in length. This family may be distantly related to pfam09370 suggesting these proteins may function as an enzyme of unknown activity. 154 matched cddid_all.tbl CDD pfam19824 pfam19824 437656 Tlp Small, acid-soluble spore protein Tlp. 70 matched cddid_all.tbl CDD pfam19825 pfam19825 437657 DUF6306 Domain of unknown function (DUF6306). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 137 and 172 amino acids in length. Protein in this family belong to the ferritin clan. 129 matched cddid_all.tbl CDD pfam19826 pfam19826 437658 DUF6307 Family of unknown function (DUF6307). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000202) is described by MIBiG as an example of the following biosynthetic class, polyketide. 43 matched cddid_all.tbl CDD pfam19827 pfam19827 437659 DUF6308 Family of unknown function (DUF6308). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000699) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the hygromycin A biosynthetic gene cluster from Streptomyces hygroscopicus subsp. hygroscopicus. This family appears to be predominantly found in Actinobacteria. 189 matched cddid_all.tbl CDD pfam19828 pfam19828 466200 DUF6309 Family of unknown function (DUF6309). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000078) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the incednine biosynthetic gene cluster from Streptomyces sp. ML694-90F3. 186 matched cddid_all.tbl CDD pfam19829 pfam19829 437661 DUF6310 Family of unknown function (DUF6310). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001417) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the myxochromide D biosynthetic gene cluster from Cystobacterineae bacterium. This family appears to be predominantly found in Cystobacterineae. 126 matched cddid_all.tbl CDD pfam19830 pfam19830 437662 DUF6311 Family of unknown function (DUF6311). This presumed integral membrane domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 300 amino acids in length. 303 matched cddid_all.tbl CDD pfam19831 pfam19831 466201 DUF6312 Family of unknown function (DUF6312). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001772) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the scytophycin biosynthetic gene cluster from Anabaena sp. UHCC 0451. 98 matched cddid_all.tbl CDD pfam19832 pfam19832 437664 DUF6313 Family of unknown function (DUF6313). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus. 183 matched cddid_all.tbl CDD pfam19833 pfam19833 437665 RecG_dom3_C ATP-dependent DNA helicase RecG, domain 3, C-terminal. This domain is found in ATP-dependent DNA helicase RecG from bacteria the homolog from Arabidopsis, which has a critical role in recombination and DNA repair. This protein comprises three structural domains, the largest N-terminal Domain 1 which interacts with DNA junctions, and Domains 2 and 3 at the C-terminal which contain the characteriztic motifs that identify RecG as an SF2 helicase. This domain represents the C-terminal of Domain 3. Around 50 residues that extend from its end cross back to Domain 1 forming a hook that wraps around the extended alpha-helix. This interaction provides a link between Domain 1 and 3 and it is likely that these residues are involved in conformational changes associated with domain movements arising from ATP binding and hydrolysis. 87 matched cddid_all.tbl CDD pfam19834 pfam19834 437666 DUF6314 Family of unknown function (DUF6314). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 138 and 177 amino acids in length. 132 matched cddid_all.tbl CDD pfam19835 pfam19835 437667 SegE_GIY-YIG Putative endonuclease segE, GIY-YIG domain. This domain family is found in viruses. Proteins containing this domain are typically between 147 and 298 amino acids in length. They have a GIY-YIG domain at the N-terminal, which suggests they are likely to be endonucleases. Included in this family is the Putative endonuclease segE from Bacteriophage T4. 118 matched cddid_all.tbl CDD pfam19836 pfam19836 437668 DUF6315 Family of unknown function (DUF6315). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000081) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the kedarcidin biosynthetic gene cluster from Streptoalloteichus sp. ATCC 53650. 174 matched cddid_all.tbl CDD pfam19837 pfam19837 466202 DUF6316 Domain of unknown function (DUF6316). This domain is found in bacterial proteins, functionally uncharacterized. It is approximately 50-70 amino acids in length and it has the conserved sequence TRExxxxGPF/Y. 55 matched cddid_all.tbl CDD pfam19838 pfam19838 466203 LptD_2 LptD protein. This entry likely represents the LptD homolog of Bacteriodetes bacteria. LptD is an essential outer membrane protein that mediates the final transport of lipopolysaccharide (LPS) to outer leaflet. 474 matched cddid_all.tbl CDD pfam19839 pfam19839 437671 RHH_9 Ribbon-helix-helix protein. This entry represents a family of Ribbon-helix-helix proteins. 65 matched cddid_all.tbl CDD pfam19840 pfam19840 437672 DUF6317 Family of unknown function (DUF6317). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001740) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the phthoxazolin biosynthetic gene cluster from Streptomyces avermitilis. 100 matched cddid_all.tbl CDD pfam19841 pfam19841 466204 GldN Gliding motility associated protein GldN. 219 matched cddid_all.tbl CDD pfam19842 pfam19842 466205 YqeC YqeC protein. This entry includes the E. coli YqeC protein. This protein belongs to the P-loop superfamily. 135 matched cddid_all.tbl CDD pfam19843 pfam19843 437675 DUF6318 Family of unknown function (DUF6318). This family of proteins is functionally uncharacterized. This family of proteins is found in Actinobacteria. 158 matched cddid_all.tbl CDD pfam19844 pfam19844 437676 DUF6319 Family of unknown function (DUF6319). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 146 and 251 amino acids in length. 116 matched cddid_all.tbl CDD pfam19845 pfam19845 466206 DUF6320 Family of unknown function (DUF6320). This family of proteins is functionally uncharacterized. This family of proteins is mainly found in Firmicute bacteria. Proteins in this family are typically between 220 and 604 amino acids in length. 186 matched cddid_all.tbl CDD pfam19846 pfam19846 437678 DUF6321 Domain of unknown function (DUF6321). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and viruses, and is approximately 80 amino acids in length. It has a conserved sequence GGLxxxGRxxY and a conserved tryptophan residue at the C-terminal. 72 matched cddid_all.tbl CDD pfam19847 pfam19847 437679 DUF6322 Family of unknown function (DUF6322). This family of proteins, predominantly found in Caudovirales, is functionally uncharacterized. Proteins in this family are approximately 150 amino acids in length. There are conserved sequences: ETINSMDYNTGY at the N-terminal, WTG in the centre and TDTTS at the C-terminal. 100 matched cddid_all.tbl CDD pfam19848 pfam19848 466207 DUF6323 Family of unknown function (DUF6323). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001520) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the aurantinin B biosynthetic gene cluster from Bacillus subtilis. This family appears to be predominantly present in Firmicutes. 127 matched cddid_all.tbl CDD pfam19849 pfam19849 437681 DUF6324 Family of unknown function (DUF6324). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There are two conserved sequence motifs: QIGPT and GMVR. 60 matched cddid_all.tbl CDD pfam19850 pfam19850 437682 DUF6325 Family of unknown function (DUF6325). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 142 and 156 amino acids in length. 141 matched cddid_all.tbl CDD pfam19851 pfam19851 437683 DUF6326 Family of unknown function (DUF6326). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 137 and 159 amino acids in length. 135 matched cddid_all.tbl CDD pfam19852 pfam19852 437684 DUF6327 Family of unknown function (DUF6327). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 71 and 82 amino acids in length. There are two conserved sequence motifs: KKY and YQK. 83 matched cddid_all.tbl CDD pfam19853 pfam19853 466208 DUF6328 Family of unknown function (DUF6328). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000219) is described by MIBiG as an example of the following biosynthetic classes, polyketide and saccharide, in particular the elloramycin biosynthetic gene cluster from Streptomyces olivaceus. This family appears to be predominantly found in Actinobacteria. 141 matched cddid_all.tbl CDD pfam19854 pfam19854 437686 DUF6329 Family of unknown function (DUF6329). This domain is predominantly found in uncharacterized bacterial proteins and its function is unknown. This domain is approximately 60 amino acids in length and it contains three conserved residues, a cysteine, a leucine and a tryptophan. 39 matched cddid_all.tbl CDD pfam19855 pfam19855 437687 DUF6330 Family of unknown function (DUF6330). This family of bacterial proteins is functionally uncharacterized. Proteins in this family are approximately 70 amino acids in length. 69 matched cddid_all.tbl CDD pfam19856 pfam19856 437688 DUF6331 Family of unknown function (DUF6331). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001060) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the dynemicin A biosynthetic gene cluster from Micromonospora chersina. 103 matched cddid_all.tbl CDD pfam19857 pfam19857 466209 DUF6332 Family of unknown function (DUF6332). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001598) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the foxicins A-D biosynthetic gene cluster from Streptomyces diastatochromogenes. This family appears to be predominantly found in Actinobacteria. 85 matched cddid_all.tbl CDD pfam19858 pfam19858 437690 OxRdtase_C Bacterial oxidoreductases, C-terminal. This is the C-terminal domain of predicted bacterial oxidoreductases. This domain is related to pfam02894, and it is likely to be an alpha/beta-domain involved in substrate binding and oligomerization. 163 matched cddid_all.tbl CDD pfam19859 pfam19859 437691 DUF6333 Family of unknown function (DUF6333). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000274) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the tetarimycin A biosynthetic gene cluster from uncultured bacterium. 234 matched cddid_all.tbl CDD pfam19860 pfam19860 466210 DUF6334 Family of unknown function (DUF6334). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001543) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the chejuenolide A biosynthetic gene cluster from Hahella chejuensis. 125 matched cddid_all.tbl CDD pfam19861 pfam19861 437693 DUF6335 Family of unknown function (DUF6335). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001615) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular hexose-palythine-serine biosynthetic gene cluster from Heteroscytonema crispum UCFS10. 124 matched cddid_all.tbl CDD pfam19862 pfam19862 437694 DUF6336 Family of unknown function (DUF6336). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001593) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the ficellomycin biosynthetic gene cluster from Streptomyces ficellus. 128 matched cddid_all.tbl CDD pfam19863 pfam19863 437695 DUF6337 Family of unknown function (DUF6337). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000791) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the O-antigen biosynthetic gene cluster from Cronobacter sakazakii. 358 matched cddid_all.tbl CDD pfam19864 pfam19864 466211 Radical_SAM_N2 Radical SAM proteins, N-terminal. This domain is found at the N-terminal of radical SAM proteins from bacteria and archaea. Proteins containing this domain are thought to catalyze diverse reactions, including methylations, isomerization, ring formation, anaerobic oxidation and protein radical formation. The function of this domain is unknown. 151 matched cddid_all.tbl CDD pfam19865 pfam19865 466212 DUF6338 Family of unknown function (DUF6338). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001593) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the ficellomycin biosynthetic gene cluster from Streptomyces ficellus. 207 matched cddid_all.tbl CDD pfam19866 pfam19866 466213 DUF6339 Family of unknown function (DUF6339). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 247 and 267 amino acids in length. 175 matched cddid_all.tbl CDD pfam19867 pfam19867 466214 DUF6340 Family of unknown function (DUF6340). This family of proteins is found in bacteria and it is functionally uncharacterized. Members in this family are about 350 amino acids in length and are likely to contain TRP repeats. 260 matched cddid_all.tbl CDD pfam19868 pfam19868 466215 DUF6341 Family of unknown function (DUF6341). This family of uncharacterized proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There are two conserved sequence motifs, WIF and YW. Probably, they are Uracil phosphoribosyltransferases. 50 matched cddid_all.tbl CDD pfam19869 pfam19869 437701 DUF6342 Family of unknown function (DUF6342). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001877) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the cyphomycin biosynthetic gene cluster from Streptomyces sp. ISID311. 99 matched cddid_all.tbl CDD pfam19870 pfam19870 466216 DUF6343 Family of unknown function (DUF6343). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001558) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the cosmomycin C biosynthetic gene cluster from Streptomyces sp. CNT302. This family appears to be predominantly found in Actinobacteria. 82 matched cddid_all.tbl CDD pfam19871 pfam19871 466217 DUF6344 Family of unknown function (DUF6344). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000843) is described by MIBiG as an example of the following biosynthetic class, other (unspecified), in particular the alanylclavam biosynthetic gene cluster from Streptomyces clavuligerus ATCC 27064. This family appears to be predominantly found in Actinobacteria. 34 matched cddid_all.tbl CDD pfam19872 pfam19872 437704 DUF6345 Family of unknown function (DUF6345). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus. This family appears to be predominantly found in bacteria and archaea. 224 matched cddid_all.tbl CDD pfam19873 pfam19873 437705 DUF6346 Family of unknown function (DUF6346). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000223) is described by MIBiG as an example of the following biosynthetic class, polyketide, rabelomycin biosynthetic gene cluster from uncultured bacterium BAC AB649/1850. This family appears to be predominantly found in Actinobacteria. 144 matched cddid_all.tbl CDD pfam19874 pfam19874 466218 DUF6347 Family of unknown function (DUF6347). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001130) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the fabclavine Ia biosynthetic gene cluster from Xenorhabdus budapestensis. 124 matched cddid_all.tbl CDD pfam19875 pfam19875 466219 DUF6348 Family of unknown function (DUF6348). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0002011) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the ansacarbamitocin A biosynthetic gene cluster from Amycolatopsis alba DSM 44262. This family appears to be predominantly found in bacteria. 193 matched cddid_all.tbl CDD pfam19876 pfam19876 437708 DUF6349 Family of unknown function (DUF6349). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus. 187 matched cddid_all.tbl CDD pfam19877 pfam19877 466220 DUF6350 Family of unknown function (DUF6350). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 414 and 529 amino acids in length. 333 matched cddid_all.tbl CDD pfam19878 pfam19878 437710 DUF6351 Tannase-like family of unknown function (DUF6351). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 717 and 769 amino acids in length. This family appears to be related to pfam07519. 638 matched cddid_all.tbl CDD pfam19879 pfam19879 437711 DUF6352 Family of unknown function (DUF6352). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 340 amino acids in length. 290 matched cddid_all.tbl CDD pfam19880 pfam19880 466221 DUF6353 Family of unknown function (DUF6353). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 255 and 305 amino acids in length. 255 matched cddid_all.tbl CDD pfam19881 pfam19881 437713 DUF6354 Family of unknown function (DUF6354). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001735) is described by MIBiG as an example of the following biosynthetic class, other (unspecified), in particular the pentostatine biosynthetic gene cluster from Streptomyces antibioticus. 121 matched cddid_all.tbl CDD pfam19882 pfam19882 437714 DUF6355 Family of unknown function (DUF6355). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001807) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the totopotensamide A biosynthetic gene cluster from Streptomyces pactum. This family appears to be predominantly present in Actinobacteria. 61 matched cddid_all.tbl CDD pfam19883 pfam19883 437715 DUF6356 Family of unknown function (DUF6356). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 71 and 88 amino acids in length. There are two conserved sequence motifs: KTGS and RMV. 64 matched cddid_all.tbl CDD pfam19884 pfam19884 437716 DUF6357 Family of unknown function (DUF6357). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000368) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the streptobactin biosynthetic gene cluster from Streptomyces sp. ATCC 700974. 417 matched cddid_all.tbl CDD pfam19885 pfam19885 437717 DUF6358 Family of unknown function (DUF6358). This family of integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 62 and 77 amino acids in length. There are two conserved sequence motifs: FILN and VVLIYLK. This family is related to pfam17259. 61 matched cddid_all.tbl CDD pfam19886 pfam19886 437718 DUF6359 Domain of unknown function (DUF6359). This family of proteins is functionally uncharacterized. This family of proteins is primarily found in bacteria. This entry may represent an Ig-like fold. 111 matched cddid_all.tbl CDD pfam19887 pfam19887 437719 DUF6360 Family of unknown function (DUF6360). This family of proteins is functionally uncharacterized. This family of proteins is found in archaea. Proteins in this family are approximately 100 amino acids in length. 91 matched cddid_all.tbl CDD pfam19888 pfam19888 466222 DUF6361 Family of unknown function (DUF6361). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 388 and 411 amino acids in length. 388 matched cddid_all.tbl CDD pfam19889 pfam19889 437721 DUF6362 Domain of unknown function (DUF6362). This domain of unknown function is found in uncharacterized bacterial proteins. It has a conserved WP motif and it may contain a helix-turn-helix motif as it overlaps with members in clan CL0123. 98 matched cddid_all.tbl CDD pfam19890 pfam19890 466223 DUF6363 Domain of unknown function (DUF6363). This presumed domain is functionally uncharacterized. This domain is found at the C-terminal of patatin-like proteins from bacteria. There is a conserved tyrosine residue and a conserved FxxxPP sequence motif. 75 matched cddid_all.tbl CDD pfam19891 pfam19891 466224 DUF6364 Family of unknown function (DUF6364). This family of uncharacterized proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length and they seem to belong to the toxin-antitoxin system. They are likely to contain a ribbon-helix-helix DNA-binding motif. 78 matched cddid_all.tbl CDD pfam19892 pfam19892 437724 DUF6365 Family of unknown function (DUF6365). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001960) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the hiroshidine biosynthetic gene cluster from Streptomyces hiroshimensis. 397 matched cddid_all.tbl CDD pfam19893 pfam19893 437725 DUF6366 Family of unknown function (DUF6366). This family of proteins is functionally uncharacterized. Proteins in this family are found in bacteria and they are approximately 70 amino acids in length. It contains the RE/K and GW conserved motifs. 69 matched cddid_all.tbl CDD pfam19894 pfam19894 437726 DUF6367 Family of unknown function (DUF6367). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001053) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the tubulysin A biosynthetic gene cluster from Archangium disciforme. 143 matched cddid_all.tbl CDD pfam19895 pfam19895 437727 DUF6368 Family of unknown function (DUF6368). This BGC (BGC0001740) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the phthoxazolin biosynthetic gene cluster from Streptomyces avermitilis. 179 matched cddid_all.tbl CDD pfam19896 pfam19896 437728 DUF6369 Family of unknown function (DUF6369). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000728) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the capsular polysaccharide biosynthetic gene cluster from Klebsiella pneumoniae subsp. ozaenae. 412 matched cddid_all.tbl CDD pfam19897 pfam19897 466225 DUF6370 Family of unknown function (DUF6370). This family of proteins is found in bacteria and it is functionally uncharacterized. Proteins in this family are approximately 110 amino acids in length. Some of the members included in this family are thought to be glutaminyl-tRNA synthetases. There are some conserved sequence motifs: CGxC, YFVD/EG and GDAH. 75 matched cddid_all.tbl CDD pfam19898 pfam19898 466226 DUF6371 Domain of unknown function (DUF6371). This domain of unknown function is found in uncharacterized bacterial proteins. This domain is about 150 amino acids in length. 150 matched cddid_all.tbl CDD pfam19899 pfam19899 437731 DUF6372 Family of unknown function (DUF6372). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the istamycin biosynthetic gene cluster from Streptomyces tenjimariensis. 59 matched cddid_all.tbl CDD pfam19900 pfam19900 437732 DUF6373 Family of unknown function (DUF6373). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001517) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the asperphenamate biosynthetic gene cluster from Aspergillus terreus NIH2624. 49 matched cddid_all.tbl CDD pfam19901 pfam19901 437733 DUF6374 Family of unknown function (DUF6374). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0002024) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the nargenicin biosynthetic gene cluster from Nocardia argentinensis. 59 matched cddid_all.tbl CDD pfam19902 pfam19902 437734 DUF6375 Family of unknown function (DUF6375). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001020) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the muraymycin C1 biosynthetic gene cluster from Streptomyces sp. NRRL 30471. 134 matched cddid_all.tbl CDD pfam19903 pfam19903 437735 DUF6376 Family of unknown function (DUF6376). This family of bacterial proteins is functionally uncharacterized. Proteins in this family are approximately 150 amino acids in length. Probably, this family correspond to lipoproteins. 116 matched cddid_all.tbl CDD pfam19904 pfam19904 466227 DUF6377 Domain of unknown function (DUF6377). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 250 amino acids in length. This domain is likely to be present in transcriptional regulators. 247 matched cddid_all.tbl CDD pfam19905 pfam19905 466228 DUF6378 Domain of unknown function (DUF6378). This domain of unknown function is found in proteins from bacteria and phages which are functionally uncharacterized. This domain is about 100 amino acids in length. It contains two conserved sequence motifs, KxxR and DxxxDxxGY. 81 matched cddid_all.tbl CDD pfam19906 pfam19906 437738 DUF6379 Domain of unknown function (DUF6379). This domain of unknown function is found in uncharacterized proteins from bacteria and eukaryotes. It is about 100 amino acids in length and contains a DG conserved motif. 112 matched cddid_all.tbl CDD pfam19907 pfam19907 437739 DUF6380 Family of unknown function (DUF6380). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000663) is described by MIBiG as an example of the following biosynthetic class, terpene, in particular the hopene biosynthetic gene cluster from Streptomyces coelicolor A3(2). 46 matched cddid_all.tbl CDD pfam19908 pfam19908 466229 DUF6381 Family of unknown function (DUF6381). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001558) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the cosmomycin C biosynthetic gene cluster from Streptomyces sp. CNT302. This family appears to be predominantly found in actinobacteria. 62 matched cddid_all.tbl CDD pfam19909 pfam19909 466230 DUF6382 Domain of unknown function (DUF6382). This domain of unknown function is present at the N-terminal of uncharacterized proteins predominantly found in Firmicutes, which also contain a FHA (Forkhead-associated) domain. It is approximately 160 amino acids in length and contains a conserved sequence YxI/V motif and a Proline conserved residue. 163 matched cddid_all.tbl CDD pfam19910 pfam19910 437742 DUF6383 Domain of unknown function (DUF6383). This presumed domain is functionally uncharacterized. This domain is mainly found at the C-terminal of uncharacterized proteins, predominantly from Bacteriodetes. It is about 74 amino acids in length and it contains the GQ and GxxV/IV conserved sequence motifs. This domain has similarity to the Type IX secretion system targeting domain. 74 matched cddid_all.tbl CDD pfam19911 pfam19911 437743 DUF6384 Family of unknown function (DUF6384). This family of proteins is functionally uncharacterized. Proteins in this family are typically between 306 and 346 amino acids in length and they are predominantly found in Proteobacteria. There is a conserved sequence MDXXdTLRH at the N-terminal and a conserved sequence YxxVEA at the C-terminal. 308 matched cddid_all.tbl CDD pfam19912 pfam19912 437744 DUF6385 Domain of unknown function (DUF6385). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 80 amino acids in length. There is a conserved sequence motif SG. 82 matched cddid_all.tbl CDD pfam19913 pfam19913 437745 WCOB Wolframin C-terminal OB-fold domain. OB fold domain found at the C-terminus of the wolframin protein. Localizes to the ER lumen and lacks the conserved polar residues typical of OB-fold domain-mediated nucleic acid-binding. Predicted to mediate protein-protein interactions. 120 matched cddid_all.tbl CDD pfam19914 pfam19914 466231 WEF-hand Wolframin EF-hand domain. Contains two characteriztic copies of the bihelical repeat forming the basic EF-hand unit. The absence of the characteriztic calcium-binding motif, suggesting it could self-dimerize or dimerize with other EF-hand-containing proteins. 80 matched cddid_all.tbl CDD pfam19915 pfam19915 466232 bpX0 MoxR-vWA-beta-propeller ternary system domain bpX0. Uncharacterized domain found in the MoxR-vWA-beta-propeller ternary system, a class of NTP-dependent biological conflict systems. 162 matched cddid_all.tbl CDD pfam19916 pfam19916 437748 VMAP-M0 vWA-MoxR associated protein middle region 0. Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities. 104 matched cddid_all.tbl CDD pfam19917 pfam19917 466233 bpX1 MoxR-vWA-beta-propeller ternary system domain bpX1. Uncharacterized domain found in the MoxR-vWA-beta-propeller ternary system, a class of NTP-dependent biological conflict systems. 84 matched cddid_all.tbl CDD pfam19918 pfam19918 466234 bpX2 MoxR-vWA-beta-propeller ternary system domain bpX2. Uncharacterized domain found in the MoxR-vWA-beta-propeller ternary system, a class of NTP-dependent biological conflict systems. 227 matched cddid_all.tbl CDD pfam19919 pfam19919 437751 bpX3 MoxR-vWA-beta-propeller ternary system domain bpX3. Uncharacterized domain found in the MoxR-vWA-beta-propeller ternary system, a class of NTP-dependent biological conflict systems. 175 matched cddid_all.tbl CDD pfam19920 pfam19920 437752 bpX4 MoxR-vWA-beta-propeller ternary system domain bpX4. Uncharacterized domain found in the MoxR-vWA-beta-propeller ternary system, a class of NTP-dependent biological conflict systems. 202 matched cddid_all.tbl CDD pfam19921 pfam19921 437753 bpX5 MoxR-vWA-beta-propeller ternary system domain bpX5. Uncharacterized domain found in the MoxR-vWA-beta-propeller ternary system, a class of NTP-dependent biological conflict systems. 135 matched cddid_all.tbl CDD pfam19922 pfam19922 437754 bpX6 MoxR-vWA-beta-propeller ternary system domain bpX6. Uncharacterized domain found in the MoxR-vWA-beta-propeller ternary system, a class of NTP-dependent biological conflict systems. 170 matched cddid_all.tbl CDD pfam19923 pfam19923 437755 DUF6386 Family of unknown function (DUF6386). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001796) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the tauramamide biosynthetic gene cluster from Brevibacillus laterosporus DSM 25. 145 matched cddid_all.tbl CDD pfam19924 pfam19924 437756 DUF6387 Family of unknown function (DUF6387). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001055) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the yersiniabactin biosynthetic gene cluster from Escherichia coli. This family appears to be predominantly found in proteobacteria. 212 matched cddid_all.tbl CDD pfam19925 pfam19925 437757 DUF6388 Family of unknown function (DUF6388). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001859) is described by MIBiG as an example of the following biosynthetic class, other (unspecified), in particular fosfomycin biosynthetic gene cluster from Pseudomonas syringae. This family is predominantly found in proteobacteria. Some members of this family have been putatively identified as DNA repair proteins. 107 matched cddid_all.tbl CDD pfam19926 pfam19926 437758 DUF6389 Family of unknown function (DUF6389). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000081) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the kedarcidin biosynthetic gene cluster from Streptoalloteichus sp. ATCC 53650. 149 matched cddid_all.tbl CDD pfam19927 pfam19927 466235 DUF6390 Family of unknown function (DUF6390). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001065) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the herboxidiene biosynthetic gene cluster from Streptomyces chromofuscus. This family appears to be predominantly found in actinobacteria. 244 matched cddid_all.tbl CDD pfam19928 pfam19928 437760 DUF6391 Domain of unknown function (DUF6391). This domain of unknown function is found in uncharacterized proteins from bacteria, mainly from Cyanobacteria. It contains the conserved sequence motifs LEHAT, GF, CGTN and QxxxTT. 137 matched cddid_all.tbl CDD pfam19929 pfam19929 437761 DUF6392 Family of unknown function (DUF6392). This family of proteins is functionally uncharacterized and it is predominantly found in Proteobacteria. Proteins in this family are typically between 55 and 170 amino acids in length. Proteins in this family are likely to be related to pyocin immunity protein. 151 matched cddid_all.tbl CDD pfam19930 pfam19930 437762 DUF6393 Family of unknown function (DUF6393). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000385) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the lysobactin biosynthetic gene cluster from Lysobacter sp. ATCC 53042. 96 matched cddid_all.tbl CDD pfam19931 pfam19931 437763 DUF6394 Family of unknown function (DUF6394). This family of proteins found in bacteria is functionally uncharacterized. Proteins in this family are typically between 113 and 127 amino acids in length. 89 matched cddid_all.tbl CDD pfam19932 pfam19932 437764 DUF6395 Family of unknown function (DUF6395). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000755) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the capsular polysaccharide biosynthetic gene cluster from Avibacterium paragallinarum 221. This family appears to be predominantly found in Actinobacteria and Firmicutes. 174 matched cddid_all.tbl CDD pfam19933 pfam19933 437765 DUF6396 Domain of unknown function (DUF6396). This presumed domain of unknown function is found in uncharacterized proteins mainly from Proteobacteria, and is about 100 amino acids in length. It has the conserved sequences RxxRY and PLPPAxLPxWDG. 108 matched cddid_all.tbl CDD pfam19934 pfam19934 466236 DUF6397 Family of unknown function (DUF6397). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000406) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the phosphinothricintripeptide biosynthetic gene cluster from Streptomyces viridochromogenes. This family appears to be predominantly found in Actinobacteria. 243 matched cddid_all.tbl CDD pfam19935 pfam19935 437767 DUF6398 Domain of unknown function (DUF6398). This domain is functionally uncharacterized, it is present in proteins from bacteria and archaea. This domain is approximately typically 100 amino acids in length and contains a conserved WA sequence motif. 106 matched cddid_all.tbl CDD pfam19936 pfam19936 437768 DUF6399 Family of unknown function (DUF6399). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000967) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the calyculin A biosynthetic gene cluster from uncultured Candidatus Entotheonella sp.. This family appears to be predominantly found in proteobacteria and cyanobacteria. 146 matched cddid_all.tbl CDD pfam19937 pfam19937 466237 GldC-like Gliding motility-associated protein GldC-like. This family of uncharacterized proteins is found in Bacteroidetes. Proteins is these family are likely to be related to the Gliding motility-associated protein GldC, a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes such as Cytophaga johnsonae (Flavobacterium johnsoniae) and Cytophaga hutchinsonii. Gliding motility appears closely linked to chitin utilization in the model species C. johnsonae. 90 matched cddid_all.tbl CDD pfam19938 pfam19938 437770 DUF6400 Family of unknown function (DUF6400). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000144) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the salinomycin biosynthetic gene cluster from Streptomyces albus. This family appears to be predominantly found in Actinobacteria. 69 matched cddid_all.tbl CDD pfam19939 pfam19939 437771 DUF6401 Family of unknown function (DUF6401). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001580) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the ebelactone biosynthetic gene cluster from Kitasatospora aburaviensis. This family appears to be predominantly found in actinobacteria. 77 matched cddid_all.tbl CDD pfam19940 pfam19940 437772 DUF6402 Family of unknown function (DUF6402). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000464) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the xenoamicin A biosynthetic gene cluster from Xenorhabdus doucetiae. This family appears to be predominantly found in proteobacteria. 275 matched cddid_all.tbl CDD pfam19941 pfam19941 437773 DUF6403 Family of unknown function (DUF6403). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001447) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the primycin biosynthetic gene cluster from Saccharomonospora azurea SZMC 14600. 77 matched cddid_all.tbl CDD pfam19942 pfam19942 437774 DUF6404 Family of unknown function (DUF6404). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001055) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the yersiniabactin biosynthetic gene cluster from Escherichia coli. This family appears to be predominantly found in Proteobacteria. 115 matched cddid_all.tbl CDD pfam19943 pfam19943 437775 DUF6405 Family of unknown function (DUF6405). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000434) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the SW-163C biosynthetic gene cluster from Streptomyces sp. SNA15896. 37 matched cddid_all.tbl CDD pfam19944 pfam19944 466238 DUF6406 Family of unknown function (DUF6406). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001916) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the lavendiol biosynthetic gene cluster from Streptomyces lavendulae. 84 matched cddid_all.tbl CDD pfam19945 pfam19945 437777 DUF6407 Family of unknown function (DUF6407). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000926) is described by MIBiG as an example of the following biosynthetic class, other (unspecified), in particular the rhizocticin A biosynthetic gene cluster from Bacillus subtilis subsp. spizizenii ATCC 6633. 96 matched cddid_all.tbl CDD pfam19946 pfam19946 437778 DUF6408 Family of unknown function (DUF6408). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000106) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the naphthomycin A biosynthetic gene cluster from Streptomyces sp. CS. 42 matched cddid_all.tbl CDD pfam19947 pfam19947 437779 DUF6409 Family of unknown function (DUF6409). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus. 122 matched cddid_all.tbl CDD pfam19948 pfam19948 437780 DUF6410 Family of unknown function (DUF6410). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001062) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the TLN-05220 biosynthetic gene cluster from Micromonospora echinospora subsp. challisensis. 198 matched cddid_all.tbl CDD pfam19949 pfam19949 466239 DUF6411 Family of unknown function (DUF6411). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001740) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the phthoxazolin biosynthetic gene cluster from Streptomyces avermitilis. 63 matched cddid_all.tbl CDD pfam19950 pfam19950 466240 DUF6412 Family of unknown function (DUF6412). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001514) is described by MIBiG as an example of the following biosynthetic class, other (unspecified), in particular the aristeromycin biosynthetic gene cluster from Streptomyces citricolor. This family appears to be predominantly found in Actinobacteria. 30 matched cddid_all.tbl CDD pfam19951 pfam19951 437783 DUF6413 Family of unknown function (DUF6413). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001749) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the epipyriculol biosynthetic gene cluster from Pyricularia oryzae 70-15. This family appears to be predominantly found in fungi. 74 matched cddid_all.tbl CDD pfam19952 pfam19952 437784 DUF6414 Family of unknown function (DUF6414). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, mainly Firmicutes. Proteins in this family are typically between 231 and 275 amino acids in length. It has two conserved sequences motifs, GYY and RFN. 246 matched cddid_all.tbl CDD pfam19953 pfam19953 437785 EACC1 Effector Associated Constant Component 1. Effector Associated Constant Component 1 (EACC1) is a component of a membrane-associated two-gene conflict system, a class of NTP-dependent biological conflict systems. It is found either a standalone domain or fused to EAD1 or EAD2. It is comprised of a single conserved TM helix with short, N- and C-terminal extensions. Predicted to insert into the membrane and protrude beyond both the outer and inner layers of the bilayer. 107 matched cddid_all.tbl CDD pfam19954 pfam19954 437786 EAD10 Effector-associated domain 10. Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteriztic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP, iSTAND, or GAP1. Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling attenuates collinear transcription requirements. 77 matched cddid_all.tbl CDD pfam19955 pfam19955 466241 EAD1 Effector-associated domain 1. Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteriztic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP, iSTAND, or GAP1. Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating the EAD-EAD coupling approximates the advantages of collinear transcription. 91 matched cddid_all.tbl CDD pfam19956 pfam19956 437788 EAD2 Effector-associated domain 2. Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteriztic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP, iSTAND, or GAP1. Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating the EAD-EAD coupling approximates the advantages of collinear transcription. 82 matched cddid_all.tbl CDD pfam19957 pfam19957 437789 EAD5 Effector-associated domain 5. Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteriztic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP, iSTAND, or GAP1. Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling attenuates collinear transcription requirements. 133 matched cddid_all.tbl CDD pfam19958 pfam19958 437790 EAD6 Effector-associated domain 6. Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteriztic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP, iSTAND, or GAP1. Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling attenuates collinear transcription requirements. 76 matched cddid_all.tbl CDD pfam19959 pfam19959 437791 EAD4 Effector-associated domain 4. Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteriztic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP, iSTAND, or GAP1. Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling attenuates collinear transcription requirements. 122 matched cddid_all.tbl CDD pfam19960 pfam19960 437792 EAD7 Effector-associated domain 7. Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteriztic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP, iSTAND, or GAP1. Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling attenuates collinear transcription requirements. 62 matched cddid_all.tbl CDD pfam19961 pfam19961 437793 EAD8 Effector-associated domain 8. Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteriztic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP, iSTAND, or GAP1. Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling attenuates collinear transcription requirements. 96 matched cddid_all.tbl CDD pfam19962 pfam19962 437794 EAD9 Effector-associated domain 9. Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteriztic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP, iSTAND, or GAP1. Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling attenuates collinear transcription requirements. 62 matched cddid_all.tbl CDD pfam19963 pfam19963 437795 VMAP-M1 vWA-MoxR associated protein middle region (VMAP-M) 1. Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities. 114 matched cddid_all.tbl CDD pfam19964 pfam19964 437796 EAD11 Effector-associated domain 11. Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteriztic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP, iSTAND, or GAP1. Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling attenuates collinear transcription requirements. 80 matched cddid_all.tbl CDD pfam19965 pfam19965 437797 VMAP-M2 vWA-MoxR associated protein middle region (VMAP-M) 2. Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities. 215 matched cddid_all.tbl CDD pfam19966 pfam19966 437798 VMAP-M4 vWA-MoxR associated protein middle region (VMAP-M) 4. Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities. 107 matched cddid_all.tbl CDD pfam19967 pfam19967 437799 VMAP-M5 vWA-MoxR associated protein middle region (VMAP-M) 5. Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities. 136 matched cddid_all.tbl CDD pfam19968 pfam19968 437800 VMAP-M7 vWA-MoxR associated protein middle region (VMAP-M) 7. Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities. 160 matched cddid_all.tbl CDD pfam19969 pfam19969 466242 VMAP-M8 vWA-MoxR associated protein middle region (VMAP-M) 8. Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities. 97 matched cddid_all.tbl CDD pfam19970 pfam19970 466243 VMAP-M9 vWA-MoxR associated protein middle region (VMAP-M) 9. Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities. 135 matched cddid_all.tbl CDD pfam19971 pfam19971 437803 TCAD2 Ternary complex associated domain 2. Novel uncharacterized protein domain found associated with the vWA-MoxR-VMAP ternary systems. 90 matched cddid_all.tbl CDD pfam19972 pfam19972 437804 TCAD3 Ternary complex associated domain 3. Novel uncharacterized protein domain found associated with the vWA-MoxR-VMAP ternary systems 48 matched cddid_all.tbl CDD pfam19973 pfam19973 437805 TCAD7 Ternary complex associated domain 7. Novel uncharacterized protein domain found associated with the vWA-MoxR-VMAP ternary systems 101 matched cddid_all.tbl CDD pfam19974 pfam19974 466244 TCAD9 Ternary complex associated domain 9. Novel uncharacterized protein domain found associated with the vWA-MoxR-VMAP ternary systems. This domain is likely a phosphotransferase enzyme. 428 matched cddid_all.tbl CDD pfam19975 pfam19975 466245 DO-GTPase1 Double-GTPase 1. GTPase of a GTPase-centric, NTP-dependent ternary systems. The domain belongs to a previously unrecognized family of the TRAFAC clade with a conserved glutamate in its Walker B motif. 271 matched cddid_all.tbl CDD pfam19976 pfam19976 437808 GAAD GTPase-associated adaptor domain. Adaptor domain in the GTPase-centric systems of NTP-dependent conflict systems that directly couples the effector to the GAP1 component. 62 matched cddid_all.tbl CDD pfam19977 pfam19977 466246 xRRM xRRM domain. This entry represents the xRRM domain, which is an atypical RRM domain. 118 matched cddid_all.tbl CDD pfam19978 pfam19978 437810 Inovirus_G7P_2 Tail virion protein G7P. Tail virion protein 7P is a viral transmembrane protein that interacts with the packaging signal of the viral genome leading to the initiation the virion concomitant assembly-budding process in the host inner membrane. 33 matched cddid_all.tbl CDD pfam19979 pfam19979 437811 DUF6415 Family of unknown function (DUF6415). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus. This family appears to be predominantly found in Actinobacteria. 95 matched cddid_all.tbl CDD pfam19980 pfam19980 437812 DUF6416 Family of unknown function (DUF6416). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001300) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the anthracimycin biosynthetic gene cluster from Streptomyces sp. CNH365. 100 matched cddid_all.tbl CDD pfam19981 pfam19981 437813 DUF6417 Family of unknown function (DUF6417). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000087) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the lasalocid biosynthetic gene cluster from Streptomyces lasaliensis. This family appears to be predominantly found in Actinobacteria. 68 matched cddid_all.tbl CDD pfam19982 pfam19982 437814 DUF6418 Family of unknown function (DUF6418). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001589) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the exopolysaccharides biosynthetic gene cluster from Burkholderia cenocepacia J2315. This family appears to be predominantly found in Proteobacteria. 109 matched cddid_all.tbl CDD pfam19983 pfam19983 437815 DUF6419 Family of unknown function (DUF6419). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000299) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the alterochromide A biosynthetic gene cluster from Pseudoalteromonas piscicida JCM 20779. 71 matched cddid_all.tbl CDD pfam19984 pfam19984 437816 DUF6420 Family of unknown function (DUF6420). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the istamycin biosynthetic gene cluster from Streptomyces tenjimariensis. 158 matched cddid_all.tbl CDD pfam19985 pfam19985 437817 DUF6421 Family of unknown function (DUF6421). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000877) is described by MIBiG as an example of the following biosynthetic class, other (unspecified), in particular the polyoxin A biosynthetic gene cluster from Streptomyces cacaoi subsp. asoensis. This family appears to be predominantly found in Actinobacteria. 437 matched cddid_all.tbl CDD pfam19986 pfam19986 437818 DUF6422 Family of unknown function (DUF6422). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001916) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the lavendiol biosynthetic gene cluster from Streptomyces lavendulae. 94 matched cddid_all.tbl CDD pfam19987 pfam19987 437819 DUF6423 Family of unknown function (DUF6423). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001503) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the amycolamycin A biosynthetic gene cluster from Amycolatopsis sp.. 161 matched cddid_all.tbl CDD pfam19988 pfam19988 437820 DUF6424 Family of unknown function (DUF6424). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000379) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in particular the glycinocin A biosynthetic gene cluster from streptomyces viridochromogenes. 277 matched cddid_all.tbl CDD pfam19989 pfam19989 437821 DUF6425 Family of unknown function (DUF6425). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001281) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the ustilagic acid biosynthetic gene cluster from Ustilago maydis 521. This family appears to be predominantly found in fungi. 227 matched cddid_all.tbl CDD pfam19990 pfam19990 437822 DUF6426 Family of unknown function (DUF6426). This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001396) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the aldgamycin J biosynthetic gene cluster from Streptomyces sp. A1(2016). 206 matched cddid_all.tbl CDD pfam19991 pfam19991 437823 HMA_2 Heavy metal associated domain 2. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 180 and 190 amino acids in length. These proteins are distantly related to the HMA domain pfam00403 particularly in the N-terminal half of the family. This family lacks the conserved pair of cysteines found in the HMA domain but does have an N-terminal conserved histidine that may fulfil a similar role. 154 matched cddid_all.tbl CDD pfam19992 pfam19992 437824 DUF6427 Family of unknown function (DUF6427). This entry represents a set of uncharacterized bacterial proteins that are likely integral membrane proteins. 301 matched cddid_all.tbl CDD pfam19993 pfam19993 466247 DO-GTPase2 Double-GTPase 2. GTPase of a GTPase-centric, NTP-dependent ternary systems. The domain belongs to a previously unrecognized family of the TRAFAC clade with a conserved glutamate in its Walker B motif. 227 matched cddid_all.tbl CDD pfam19994 pfam19994 437826 GASH GTPase-associated system helical domain. This entry represents a Helical domain observed in the GAP1-N1 type of GTPase-centric ternary systems, a class of NTP-dependent biological conflict systems. GASH is one component of the GTPase-activated complex in these systems, potentially involved in the sensing of invasive elements. 368 matched cddid_all.tbl CDD pfam19995 pfam19995 437827 iSTAND inactive STAND. An inactive P-loop NTPase domain of the STAND subfamily of AAA+ NTPases. iSTAND is a component of the MoxR-vWA-iSTAND ternary systems of NTP-dependent conflict systems. The iSTAND component shows clear architectural parallels to the VMAP of the vWA-MoxR-VMAP systems. 161 matched cddid_all.tbl CDD pfam19996 pfam19996 466248 ivWA-helical_N N-terminal helical region fused to the FtsH ternary system vWA domain. Functionally Uncharacterized helical domain fused a the N-terminus of the ivWA domain, a core component of the FtsH ternary systems, a class of NTP-dependent biological conflict systems. 270 matched cddid_all.tbl CDD pfam19997 pfam19997 466249 ivWA vWA domain found in the FtsH ternary systems. Highly-divergent vWA domain lacking metal-chelating aspartates of typical vWA domains. Core component of the FtsH ternary systems, a class of NTP-dependent biological conflict systems. 253 matched cddid_all.tbl CDD pfam19998 pfam19998 437830 fvmX1 FtsH ternary system domain X1. Uncharacterized domain found in the FtsH ternary system, a class of NTP-dependent biological conflict systems. 269 matched cddid_all.tbl CDD pfam19999 pfam19999 437831 fvmX3 FtsH ternary system domain X3. Uncharacterized domain found in the FtsH ternary system, a class of NTP-dependent biological conflict systems. 85 matched cddid_all.tbl CDD pfam20000 pfam20000 437832 fvmX2 FtsH ternary system domain X2. Uncharacterized domain found in the FtsH ternary system, a class of NTP-dependent biological conflict systems. 261 matched cddid_all.tbl CDD pfam20001 pfam20001 466250 DUF6428 Family of unknown function (DUF6428). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 155 and 220 amino acids in length. There are two conserved sequence motif, DCGG and QLW, and conserved cysteine residues at the C-terminal. 143 matched cddid_all.tbl CDD pfam20002 pfam20002 466251 fvmX3-analog FtsH ternary system domain X3-analog. Uncharacterized domain found in the FtsH ternary system, a class of NTP-dependent biological conflict systems. This domain is positionally-equivalent and mutually-exclusive to the fvmX3 domain in gene neighborhoods. 89 matched cddid_all.tbl CDD pfam20003 pfam20003 466252 fvmX5 FtsH ternary system domain X5. Uncharacterized domain found in the FtsH ternary system, a class of NTP-dependent biological conflict systems. 187 matched cddid_all.tbl CDD pfam20004 pfam20004 466253 fvmX6 FtsH ternary system domain X6. Uncharacterized domain found in the FtsH ternary system, a class of NTP-dependent biological conflict systems. 349 matched cddid_all.tbl CDD pfam20005 pfam20005 466254 fvmX7 FtsH ternary system domain X7. Uncharacterized domain found in the FtsH ternary system, a class of NTP-dependent biological conflict systems. 422 matched cddid_all.tbl CDD pfam20006 pfam20006 437838 fvmYukDl_N YukD-like N-terminal domain. Uncharacterized domain found N-terminal to YukD-like Ubiquitin domain in FtsH ternary systems, a class of NTP-dependent biological conflict systems. 85 matched cddid_all.tbl CDD pfam20007 pfam20007 437839 fvmRadSAM-pep FtsH ternary system-associated peptide. Predicted peptide-effector encoded as standalone domain in some FtsH ternary system neighborhoods. Likely modified by the Radical SAM domain also found in these neighborhoods. The FtsH ternary systems are a class of NTP-dependent biological conflict systems. 73 matched cddid_all.tbl CDD pfam20008 pfam20008 466255 DUF6429 Domain of unknown function (DUF6429). This domain of unknown function is found in uncharacterized bacterial proteins. This domain is about 70 amino acids in length and contains the conserved sequence motifs WK, RS and TxxG. 48 matched cddid_all.tbl CDD pfam20009 pfam20009 466256 GEVED GEVED domain. Ths presumed domain is found in the CshA protein from Streptococcus gordonii. The domain is named after the sequence found in CshA in the conserved C-terminal region. The conserved negatively charged residues suggests that this domain may bind to calcium ions. This domain is part of the non-repetitive region NR3. 43 matched cddid_all.tbl CDD pfam20010 pfam20010 466257 Collagen_trimer Collagen trimerization domain. This small domain mediate trimerization in various collagen proteins. 49 matched cddid_all.tbl CDD pfam20011 pfam20011 437843 fvmJAB_N JAB N-terminal domain. Domain observed N-terminal to JAB deubiquitinase in the Ub system component of the FtsH ternary systems, a class of NTP-dependent biological conflict systems. 158 matched cddid_all.tbl CDD pfam20012 pfam20012 466258 GAP1-N1 GTPase-associated protein 1, N-terminal domain type 1. One of two types of domain found at the N-terminus of the GTPase-associated protein 1 (GAP1) of the GTPase-centric ternary systems, a class of NTP-dependent biological conflict systems. This domain is predicted to mediate effector-GAP1 interactions. 102 matched cddid_all.tbl CDD pfam20013 pfam20013 466259 GAP1-N2 GTPase-associated protein 1, N-terminal domain type 2. One of two types of domain found at the N-terminus of the GTPase-associated protein 1 (GAP1) of the GTPase-centric ternary systems, a class of NTP-dependent biological conflict systems. This domain is predicted to mediate effector-GAP1 interactions. 139 matched cddid_all.tbl CDD pfam20014 pfam20014 466260 GAP1-M GTPase-associated protein 1, middle domain. Middle domain found in the multidomain GTPase-associated protein 1 (GAP1) of the GTPase-centric systems, a class of NTP-dependent biological conflict systems. 101 matched cddid_all.tbl CDD pfam20015 pfam20015 437847 VMAP-M12 vWA-MoxR associated protein middle region (VMAP-M) 12. Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities. 136 matched cddid_all.tbl CDD pfam20016 pfam20016 466261 DUF6430 Domain of unknown function (DUF6430). This domain is found in bacterial proteins and is functionally uncharacterized. It contains the conserved sequences GDxF, SxxG and PxxGxG. Some proteins containing this domain also have the Bacterial transcriptional activator domain pfam03704. It is likely that proteins containing this domain function as a transcriptional regulator. 183 matched cddid_all.tbl CDD pfam20017 pfam20017 437849 VMAP-M15 vWA-MoxR associated protein middle region (VMAP-M) 15. Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities. 81 matched cddid_all.tbl CDD pfam20018 pfam20018 437850 VMAP-M14 vWA-MoxR associated protein middle region (VMAP-M) 14. Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities. 132 matched cddid_all.tbl CDD pfam20019 pfam20019 437851 VMAP-M20 vWA-MoxR associated protein middle region 20. Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities. 129 matched cddid_all.tbl CDD pfam20020 pfam20020 437852 DUF6431 Domain of unknown function (DUF6431). This domain of unknown function is found in uncharacterized proteins from bacteria. This domain is about 90 amino acids in length. It contains the conserved sequences CxxC, RxxCxxxxC and a conserved LP motif. 82 matched cddid_all.tbl CDD pfam20021 pfam20021 437853 VMAP-M18 vWA-MoxR associated protein middle region (VMAP-M) 18. Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities. 109 matched cddid_all.tbl CDD pfam20022 pfam20022 437854 VMAP-M19 vWA-MoxR associated protein middle region 19. Highly variable central region of the vWA-MoxR associated protein (VMAP) of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. VMAP-Ms may be involved in sensing of invasive entities. 115 matched cddid_all.tbl CDD pfam20023 pfam20023 466262 WSLR Wolframin Sel1-like repeat. N-terminal Sel1-like repeats found in the wolframin protein. This region has been linked to calmodulin-binding, suggesting these repeats may mediate a protein interaction. 39 matched cddid_all.tbl CDD pfam20024 pfam20024 437856 DUF6432 Family of unknown function (DUF6432). This family of proteins is functionally uncharacterized. This family of proteins is found in archaea. Proteins in this family are approximately 100 amino acids in length. Members in this family are thought to belong to the MarR family of transcriptional regulators. 97 matched cddid_all.tbl CDD pfam20025 pfam20025 437857 DUF6433 Family of unknown function (DUF6433). This family of proteins is functionally uncharacterized. This family of proteins is found in phages. Proteins in this family are typically between 144 and 156 amino acids in length. Proteins in this family contain the conserved motifs NFD and LEGL. 115 matched cddid_all.tbl CDD pfam20026 pfam20026 466263 DUF6434 Domain of unknown function (DUF6434). This domain of unknown function is found in uncharacterized proteins mainly from bacteria, but it is also found in eukaryotes. Some proteins containing this domain also contain zinc finger C2H2-type domains. There are three conserved motifs: TxI/V, RxFF and FxF, and a conserved W/Y residue at the C-terminal. 64 matched cddid_all.tbl CDD pfam20027 pfam20027 437859 DUF6435 Family of unknown function (DUF6435). This family of proteins found in bacteria is functionally uncharacterized. Proteins in this family are approximately 60 amino acids in length and they are predicted to have a coiled-coil structure. There are two conserved motifs: KxLxxxY and EA. 53 matched cddid_all.tbl CDD pfam20028 pfam20028 437860 VMAP-C vWA-MoxR associated protein C-terminal domain. C-terminal region of the VMAP protein of the classical ternary system (vWA-MoxR-VMAP) in NTP-dependent conflict systems. Mixed alpha+beta domain with no apparent structural similarity to known protein folds. Contains several, nearly universally polar residues, suggesting a conserved interaction interface. Enzymatic function for VMAP-C though possible appears unlikely. Sensing of invasive elements by VMAP-Ms are predicted to trigger a sequence of conformational changes, which is communicated to the switch-component (MoxR) of the system via the more constant VMAP-C. 237 matched cddid_all.tbl CDD pfam20029 pfam20029 437861 DUF6436 Domain of unknown function (DUF6436). This domain of unknown function is found in uncharacterized bacterial proteins. This domain is about 60 amino acids in length and contains the conserved motifs GPY, GxxC and GCxC. These conserved cysteine residues and the fact that this domain has overlaps with families in clan CL0172 suggest that it is related to thioredoxins and it is likely in thiol-disulfide isomerases. 59 matched cddid_all.tbl CDD pfam20030 pfam20030 437862 bpMoxR MoxR domain in the MoxR-vWA-beta-propeller ternary systems. Core MoxR component domain of the MoxR-vWA-beta-propeller ternary systems, a class of NTP-dependent biological conflict systems. 205 matched cddid_all.tbl CDD pfam20031 pfam20031 466264 DUF6437 Family of unknown function (DUF6437). This family of proteins is functionally uncharacterized. This family of proteins is found in Alphaproteobacteria. Proteins in this family are typically between 76 and 122 amino acids in length. 76 matched cddid_all.tbl CDD pfam20032 pfam20032 466265 ADYC ADYC domain. This domain is named ADYC after the most conserved motif. This family of proteins is functionally uncharacterized. This family of proteins is found in proteobacteria and cyanobacteria. Proteins in this family are typically between 280 and 416 amino acids in length. This family has 7 conserved cysteine and one conserved histidine which might indicate a zinc-binding function. 179 matched cddid_all.tbl CDD pfam20033 pfam20033 466266 DUF6438 Domain of unknown function (DUF6438). This domain of unknown function is found in uncharacterized proteins from bacteria and archaea. This domain is about 75 amino acids in length and it contains the conserved motif CxxxGxCP. Towards the C-terminal there are two conserved residues, a Glycine and an Aspartate. Some of the proteins containing this domain also have an ankyrin repeat-containing region. 76 matched cddid_all.tbl CDD pfam20034 pfam20034 437866 Peptidase_S80 Peptidase S80 family. This family represents the protease responsible for the proteolysis of head proteins, a critical step in the morphogenesis of many tailed phages, Cleavage facilitates the conversion of the prohead to the mature capsid. All these cleavages are carried out by action at consensus S/A/G-X-E recognition sequences at 39 cleavage sites. Evidence of multiple processing sites in nine phiKZ proteins appears to represent a built-in mechanism by which the phage ensures that the majority of the propeptide regions are removed, and emphasizes the essential nature of processing in phiKZ-head morphogenesis. The family is classified by MEROPS as a serine peptidase. 229 matched cddid_all.tbl CDD pfam20035 pfam20035 437867 DUF6439 Family of unknown function (DUF6439). This family of proteins is functionally uncharacterized. This family of proteins is found in cyanobacteria. Proteins in this family are typically between 87 and 98 amino acids in length. 92 matched cddid_all.tbl CDD pfam20036 pfam20036 466267 Gp13-like Major capsid protein 13-like. This family represents phage capsid/coat proteins found in phages but also in bacteria. Included in this family is the Major capsid protein 13 from Bacillus phage SPP1 which is part of the icosahedral capsid together with the auxiliary protein gp12, which are organized in a T=7 lattice. This family contains some conserved motifs: GD, GxxxxV/IxxD and NW. 310 matched cddid_all.tbl CDD pfam20037 pfam20037 466268 DUF6440 Family of unknown function (DUF6440). This family of proteins is functionally uncharacterized. This family of proteins is mainly found in Firmicutes but also in viruses. Proteins in this family are approximately 60 amino acids in length and they contain three conserved motifs: RF, TGxxY and TPLLD. Some members of this family are probably Xylan 1,4-beta-xylosidases. 53 matched cddid_all.tbl CDD pfam20038 pfam20038 437870 HTH_59 Helix-turn-helix domain. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 63 and 82 amino acids in length. This domain is a helix-turn-helix suggesting it is likely a DNA-binding transcriptional regulator. 66 matched cddid_all.tbl CDD pfam20039 pfam20039 437871 DUF6441 Family of unknown function (DUF6441). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 210 amino acids in length. 216 matched cddid_all.tbl CDD pfam20040 pfam20040 437872 DUF6442 Family of unknown function (DUF6442). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. 102 matched cddid_all.tbl CDD pfam20041 pfam20041 466269 DUF6443 Domain of unknown function (DUF6443). This presumed domain is functionally uncharacterized. This domain family is predominantly found in Bacteroidetes, and is about 100 amino acids in length. This domain contains a highly conserved YDxxGR motif which suggests that it is related the RHS repeats, that appear to be involved in ligand binding. RHS repeats share structural similarity with the eukaryotic tyrosine-aspartate (YD) repeat. 101 matched cddid_all.tbl CDD pfam20042 pfam20042 466270 DUF6444 Family of unknown function (DUF6444). This entry represents a region that is sometimes found a the N-terminus of transposon proteins. It is also sometimes found as part of a shorter protein, presumably involved in transposition. 76 matched cddid_all.tbl CDD pfam20043 pfam20043 466271 DUF6445 Family of unknown function (DUF6445). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 229 and 242 amino acids in length. 224 matched cddid_all.tbl CDD pfam20044 pfam20044 466272 DUF6446 Family of unknown function (DUF6446). This family of proteins is functionally uncharacterized. This family of proteins is predominantly found in Rhodobacterales. Proteins in this family are typically between 160 and 175 amino acids in length. There are some conserved motifs: IDA/S, SSPxRxRACF and DG. Many members in this family are thought to be histidine kinases. 129 matched cddid_all.tbl CDD pfam20045 pfam20045 437877 DUF6447 Family of unknown function (DUF6447). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 75 matched cddid_all.tbl CDD pfam20046 pfam20046 437878 DUF6448 Family of unknown function (DUF6448). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 187 and 219 amino acids in length and may contain a LysM domain. 147 matched cddid_all.tbl CDD pfam20047 pfam20047 437879 DUF6449 Domain of unknown function (DUF6449). This presumed domain is functionally uncharacterized found in ABC transporter permeases. This domain family is found in bacteria and is approximately 300 amino acids in length. 152 matched cddid_all.tbl CDD pfam20048 pfam20048 437880 DUF6450 Domain of unknown function (DUF6450). This presumed domain is functionally uncharacterized. This domain family is found in phages, and is approximately 60 amino acids in length. It contains the conserved sequences WSxxxLTxY and DPTFIASVFTG. 68 matched cddid_all.tbl CDD pfam20049 pfam20049 437881 DUF6451 Domain of unknown function (DUF6451). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, predominantly in Platyhelminthes, and is approximately 40 amino acids in length. It contains the conserved sequences QLxNIWNSK and KxRIFN. Many sequences containing this domain also contain a reverse transcriptase domain (pfam00078). 33 matched cddid_all.tbl CDD pfam20050 pfam20050 437882 DUF6452 Family of unknown function (DUF6452). This family of proteins is functionally uncharacterized. This family of proteins is found in Bacteroidetes. Proteins in this family are typically between 159 and 189 amino acids in length. This proteins contain the conserved motifs PL and SxxCG. 107 matched cddid_all.tbl CDD pfam20051 pfam20051 466273 DUF6453 Family of unknown function (DUF6453). This family of uncharacterized proteins is mainly found in phages. It may represent structural phage proteins. There are several conserved motifs: FxxI, GxxxxP and FSxxxxP, and also 7 additional conserved Glycine residues. 291 matched cddid_all.tbl CDD pfam20052 pfam20052 466274 GAP1-C GTPase-associated protein 1, C-terminal domain. C-terminal domain found in the multidomain GTPase-associated protein 1 (GAP1) of the GTPase-centric systems, a class of NTP-dependent biological conflict systems. This domain is predicted to mediate effector deployment in the GTPase-centric systems. 514 matched cddid_all.tbl CDD pfam20053 pfam20053 466275 WC-rich Wolframin cysteine-rich domain. Located N-terminal to the wolframin OB-fold domain, this region could represent an extension to the core of the OB fold domain. The observed conserved cysteine residues could contribute to disulfide-bond-mediated cross-linking in calcium-stores regulation. 106 matched cddid_all.tbl CDD pfam20054 pfam20054 437886 Tc-38 Trypanosoma Tc-38 (p38) protein. Domain found in multiple copies in kinetoplastid-specific minicircle binding proteins that evolved from a prokaryotic ArdCN domain 69 matched cddid_all.tbl CDD pfam20055 pfam20055 437887 DUF6454 Family of unknown function (DUF6454). This family of proteins is functionally uncharacterized. This family of proteins is found primarily in bacteria. Proteins in this family are typically between 294 and 372 amino acids in length. 292 matched cddid_all.tbl CDD pfam20056 pfam20056 466276 DUF6455 Family of unknown function (DUF6455). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. This presumed domain contains a conserved histidine and four conserved cysteines suggestive of zinc binding. 85 matched cddid_all.tbl CDD pfam20057 pfam20057 437889 DUF6456 Domain of unknown function (DUF6456). This presumed domain is sometimes associated with a helix-turn-helix domain suggesting that it may be a small molecule ligand binding domain. This family of proteins is found in bacteria. 137 matched cddid_all.tbl CDD pfam20058 pfam20058 437890 DUF6457 Domain of unknown function (DUF6457). This presumed domain is functionally uncharacterized. This family of proteins is found in bacteria. This domain is found C-terminal to an MobA-like guanyltransferase domain. 81 matched cddid_all.tbl CDD pfam20059 pfam20059 437891 DUF6458 Domain of unknown function (DUF6458). This family of proteins is functionally uncharacterized. This family of proteins is primarily found in actinobacteria. Proteins in this family are typically between 74 and 95 amino acids in length. This domain is related to pfam18969. 78 matched cddid_all.tbl CDD pfam20060 pfam20060 466277 DUF6459 Family of unknown function (DUF6459). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 143 and 204 amino acids in length. 104 matched cddid_all.tbl CDD pfam20061 pfam20061 466278 DUF6460 Domain of unknown function (DUF6460). This domain on unknown function is found at the C-terminal of uncharacterized proteins, found in Alphaproteobacteria. Proteins containing this domain are typically between 88 and 109 amino acids in length. There is a conserved motif GAxI/VVxP. Some members of this entry are likely integrases. 36 matched cddid_all.tbl CDD pfam20062 pfam20062 437894 DUF6461 Family of unknown function (DUF6461). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 198 and 278 amino acids in length. 208 matched cddid_all.tbl CDD pfam20063 pfam20063 437895 DUF6462 Family of unknown function (DUF6462). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, mainly in Firmicutes. Proteins in this family are typically between 62 and 78 amino acids in length. Some of the members are probably transcriptional regulators. This family has overlaps with families in clan CL0123, which suggests that they share the helix-turn-helix motif. 51 matched cddid_all.tbl CDD pfam20064 pfam20064 437896 DUF6463 Family of unknown function (DUF6463). This family of integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. This family appears to be related to pfam03729. 119 matched cddid_all.tbl CDD pfam20065 pfam20065 437897 DUF6464 Family of unknown function (DUF6464). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 101 and 122 amino acids in length. 101 matched cddid_all.tbl CDD pfam20066 pfam20066 437898 Glyoxalase_8 Glyoxalase superfamily protein. This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 80 amino acids in length. This domain is part of the Glyoxalase superfamily. 143 matched cddid_all.tbl CDD pfam20067 pfam20067 437899 SSL_N Strictosidine synthase-like, N-terminal. This domain is found at the N-terminal of strictosidine synthase-like (SSL) proteins including Adipocyte plasma membrane- associated proteins (APMAPs) from animals, Protein STRICTOSIDINE SYNTHASE-LIKE (SSLs) from Arabidopsis and SGL proteins, being also present in bacterial sequences. It is about 50 amino acids in length. It contains residues involved in metal coordination in the active site. This domain is also found in Gluconolactonase and Sugar lactone lactonase. These proteins share a six-bladed beta-propeller fold structure and have similar structural and mechanistic features to SS (strictosidine synthase) that involve nucleophilic attack on an electrophilic substrate, although they do not catalyze the SS reaction as they lack the catalytic glutamate required for SS activity; they catalyze hydrolytic reactions instead. APMAPs shows similarity with paraoxonases (PON) and has a strong arylesterase activity with beta-naphthyl acetate and phenyl acetate. They are involved in adipocyte differentiation. 46 matched cddid_all.tbl CDD pfam20068 pfam20068 437900 Amphi-Trp Amphi-Trp domain. 93 matched cddid_all.tbl CDD pfam20069 pfam20069 466279 DUF6465 Family of unknown function (DUF6465). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 117 and 173 amino acids in length. These proteins have a highly charged N-terminus. 130 matched cddid_all.tbl CDD pfam20070 pfam20070 466280 DUF6466 Family of unknown function (DUF6466). This family of proteins is functionally uncharacterized. This family of proteins is mainly found in Bifidobacteria. Proteins in this family are approximately 190 amino acids in length. They contain the conserved motifs QQQQ, SxxLT and KPW. Members in this family are probably cell surface proteins, some of them are likely elastin binding proteins. 146 matched cddid_all.tbl CDD pfam20072 pfam20072 437904 DUF6468 Domain of unknown function (DUF6468). This domain of unknown function is found in uncharacterized proteins predominantly from Alphaproteobacteria but it is also present in some sequences from eukaryotes. This domain is approximately 75 amino acids in length. 76 matched cddid_all.tbl CDD pfam20073 pfam20073 437905 DUF6469 Domain of unknown function (DUF6469). This presumed domain is functionally uncharacterized. This domain family is found in plants, and is approximately 120 amino acids in length. It is found in hypothetical UvrD-like Helicases and related sequences, all containing a P-loop motif that is characteriztic of the AAA superfamily. This domain is located towards the N-terminal, adjacent the AAA domain (pfam13086). There are two conserved motifs, GD and RIW. There is also a highly conserved D residue. 130 matched cddid_all.tbl CDD pfam20074 pfam20074 437906 DUF6470 Family of unknown function (DUF6470). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, predominantly in Firmicutes, but also in eukaryotes. Proteins in this family are typically between 185 and 202 amino acids in length. There is a conserved motif ID. 177 matched cddid_all.tbl CDD pfam20075 pfam20075 437907 DUF6471 Domain of unknown function (DUF6471). This domain of unknown function is found in uncharacterized proteins from bacteria (predominantly Proteobacteria) and eukaryotes. This domain is approximately 60 amino acids in length. There is a conserved motif KxxRG and a highly conserved L residue. It may be a DNA-binding domain. 65 matched cddid_all.tbl CDD pfam20076 pfam20076 437908 DUF6472 Domain of unknown function (DUF6472). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. The proteins contain 4 conserved cysteines. 57 matched cddid_all.tbl CDD pfam20077 pfam20077 466281 CcmD_alt CcmD family protein. 61 matched cddid_all.tbl CDD pfam20078 pfam20078 466282 DUF6473 Domain of unknown function (DUF6473). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is typically between 141 and 178 amino acids in length. 274 matched cddid_all.tbl CDD pfam20079 pfam20079 466283 DUF6474 Family of unknown function (DUF6474). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 208 and 230 amino acids in length. 217 matched cddid_all.tbl CDD pfam20080 pfam20080 437912 ALTTAQ_rpt ALTTAQ repeat. This repeat is called after the short repeat ALTTAQ found in uncharacterized proteins from Proteobacteria, some eukaryotes and viruses, and it is functionally uncharacterized. 38 matched cddid_all.tbl CDD pfam20081 pfam20081 437913 DUF6475 Domain of unknown function (DUF6475). This presumed domain is functionally uncharacterized. This domain family is found in Proteobacteria and viruses, and is approximately 90 amino acids in length. It contains the conserved motifs FDD and MGGW. 90 matched cddid_all.tbl CDD pfam20082 pfam20082 466284 DUF6476 Family of unknown function (DUF6476). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. 91 matched cddid_all.tbl CDD pfam20083 pfam20083 466285 DUF6477 Family of unknown function (DUF6477). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 96 and 116 amino acids in length. 97 matched cddid_all.tbl CDD pfam20084 pfam20084 437916 TrbK Conjugative transfer region protein TrbK. 109 matched cddid_all.tbl CDD pfam20085 pfam20085 437917 TGL Protein-glutamine gamma-glutamyltransferase. 247 matched cddid_all.tbl CDD pfam20086 pfam20086 437918 DUF6478 Family of unknown function (DUF6478). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 260 amino acids in length. 257 matched cddid_all.tbl CDD pfam20087 pfam20087 466286 DUF6479 Family of unknown function (DUF6479). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is typically between 39 and 51 amino acids in length. 120 matched cddid_all.tbl CDD pfam20088 pfam20088 437920 DUF6480 Family of unknown function (DUF6480). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 75 and 88 amino acids in length. 78 matched cddid_all.tbl CDD pfam20089 pfam20089 437921 DUF6481 Family of unknown function (DUF6481). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. 119 matched cddid_all.tbl CDD pfam20090 pfam20090 437922 DUF6482 Family of unknown function (DUF6482). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. 101 matched cddid_all.tbl CDD pfam20091 pfam20091 437923 Abhydrolase_10 Alpha/beta hydrolase domain. This entry represents a protein that belongs to the alpha/beta hydrolase superfamily. Although proteins in this family are uncharacterized they are likely to have an enzymatic activity. 386 matched cddid_all.tbl CDD pfam20092 pfam20092 437924 DUF6483 Family of unknown function (DUF6483). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 119 and 132 amino acids in length. 119 matched cddid_all.tbl CDD pfam20093 pfam20093 466287 DUF6484 Domain of unknown function (DUF6484). This domain of unknown function is found in uncharacterized proteins from Proteobacteria. This domain is approximately 80 amino acids in length and exhibits overlaps with pfam04717, which suggests that it has an OB fold and, thus, it belongs to the same clan. Many proteins containing this domain are related to the Type VI secretion system and to Phage-related baseplate proteins. 61 matched cddid_all.tbl CDD pfam20094 pfam20094 466288 GWxTD_dom GWxTD domain. This domain is found in uncharacterized proteins from bacteria, mainly in Bacteroidetes. This domain is approximately 180 amino acids in length and it is rich in aromatic residues, with Trp, Tyr, or Phe as the majority amino acids in the most-conserved residue positions. 172 matched cddid_all.tbl CDD pfam20095 pfam20095 437927 DUF6485 Domain of unknown function (DUF6485). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 70 matched cddid_all.tbl CDD pfam20096 pfam20096 437928 DUF6486 Family of unknown function (DUF6486). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 30 amino acids in length. There is a conserved IAVASA sequence motif. 31 matched cddid_all.tbl CDD pfam20097 pfam20097 437929 DUF6487 Domain of unknown function (DUF6487). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. This domain is likely to be a zinc-binding domain. 68 matched cddid_all.tbl CDD pfam20098 pfam20098 466289 DUF6488 Family of unknown function (DUF6488). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. 110 matched cddid_all.tbl CDD pfam20099 pfam20099 437931 DUF6489 Family of unknown function (DUF6489). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. 80 matched cddid_all.tbl CDD pfam20100 pfam20100 437932 DUF6490 Family of unknown function (DUF6490). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 119 and 168 amino acids in length. 127 matched cddid_all.tbl CDD pfam20101 pfam20101 437933 DUF6491 Family of unknown function (DUF6491). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 139 and 155 amino acids in length. 138 matched cddid_all.tbl CDD pfam20102 pfam20102 437934 DUF6492 Family of unknown function (DUF6492). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 305 and 329 amino acids in length. 289 matched cddid_all.tbl CDD pfam20103 pfam20103 437935 DUF6493 Family of unknown function (DUF6493). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 470 amino acids in length. 938 matched cddid_all.tbl CDD pfam20104 pfam20104 437936 DUF6494 Family of unknown function (DUF6494). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. There is a conserved SQREIE sequence motif. 68 matched cddid_all.tbl CDD pfam20105 pfam20105 466290 DUF6495 Family of unknown function (DUF6495). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 160 amino acids in length. 156 matched cddid_all.tbl CDD pfam20106 pfam20106 437938 DUF6496 Family of unknown function (DUF6496). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 64 and 166 amino acids in length. 58 matched cddid_all.tbl CDD pfam20107 pfam20107 437939 DUF6497 Family of unknown function (DUF6497). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 121 and 153 amino acids in length. 119 matched cddid_all.tbl CDD pfam20108 pfam20108 437940 DUF6498 Family of unknown function (DUF6498). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 229 and 247 amino acids in length. 210 matched cddid_all.tbl CDD pfam20109 pfam20109 437941 DUF6499 Family of unknown function (DUF6499). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 73 and 100 amino acids in length. There is a conserved PDTPGR sequence motif. 68 matched cddid_all.tbl CDD pfam20110 pfam20110 437942 DUF6500 Family of unknown function (DUF6500). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. 53 matched cddid_all.tbl CDD pfam20111 pfam20111 437943 DUF6501 Family of unknown function (DUF6501). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. 67 matched cddid_all.tbl CDD pfam20112 pfam20112 437944 DUF6502 Family of unknown function (DUF6502). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 269 and 295 amino acids in length. 268 matched cddid_all.tbl CDD pfam20113 pfam20113 466291 DUF6503 Family of unknown function (DUF6503). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 238 and 271 amino acids in length. 235 matched cddid_all.tbl CDD pfam20114 pfam20114 437946 DUF6504 Family of unknown function (DUF6504). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 111 and 361 amino acids in length. 102 matched cddid_all.tbl CDD pfam20115 pfam20115 437947 DUF6505 Family of unknown function (DUF6505). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 100 amino acids in length. 159 matched cddid_all.tbl CDD pfam20116 pfam20116 437948 DUF6506 Family of unknown function (DUF6506). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 100 amino acids in length. 96 matched cddid_all.tbl CDD pfam20117 pfam20117 466292 DUF6507 Family of unknown function (DUF6507). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 115 and 135 amino acids in length. 124 matched cddid_all.tbl CDD pfam20118 pfam20118 437950 DUF6508 Family of unknown function (DUF6508). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 131 and 449 amino acids in length. 129 matched cddid_all.tbl CDD pfam20119 pfam20119 437951 DUF6509 Family of unknown function (DUF6509). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. There are two conserved sequence motifs: DPTGI and ILA. 95 matched cddid_all.tbl CDD pfam20120 pfam20120 437952 DUF6510 Family of unknown function (DUF6510). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There is a conserved RCP sequence motif. 86 matched cddid_all.tbl CDD pfam20121 pfam20121 437953 DUF6511 Family of unknown function (DUF6511). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 87 and 141 amino acids in length. 69 matched cddid_all.tbl CDD pfam20122 pfam20122 437954 DUF6512 Family of unknown function (DUF6512). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is typically between 35 and 59 amino acids in length. 181 matched cddid_all.tbl CDD pfam20123 pfam20123 437955 DUF6513 Family of unknown function (DUF6513). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and archaea, and is typically between 75 and 86 amino acids in length. 86 matched cddid_all.tbl CDD pfam20124 pfam20124 437956 DUF6514 Family of unknown function (DUF6514). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. 94 matched cddid_all.tbl CDD pfam20125 pfam20125 466293 DUF6515 Family of unknown function (DUF6515). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 194 and 339 amino acids in length. 179 matched cddid_all.tbl CDD pfam20126 pfam20126 466294 DUF6516 Family of unknown function (DUF6516). This presumed domain is functionally uncharacterized. This domain family is found in archaea, and is approximately 60 amino acids in length. 85 matched cddid_all.tbl CDD pfam20127 pfam20127 466295 DUF6517 Family of unknown function (DUF6517). This family of proteins is functionally uncharacterized. This family of proteins is found in archaea. Proteins in this family are typically between 210 and 252 amino acids in length. These proteins contain an N-terminal TAT signal. 186 matched cddid_all.tbl CDD pfam20128 pfam20128 466296 DUF6518 Family of unknown function (DUF6518). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 205 and 220 amino acids in length. 201 matched cddid_all.tbl CDD pfam20129 pfam20129 437961 DUF6519 Family of unknown function (DUF6519). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 523 and 1105 amino acids in length. 593 matched cddid_all.tbl CDD pfam20130 pfam20130 466297 DUF6520 Family of unknown function (DUF6520). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 89 and 103 amino acids in length. 83 matched cddid_all.tbl CDD pfam20131 pfam20131 466298 MC3 ABC-three component (ABC-3C) system Middle Component 3. Middle Components (MCs) of the ABC-3C biological conflict systems occupy the central position between the catalytic effector and ABC ATPases of the systems. MCs are defined by distinctive patterns of conserved charged residues. As some MCs are HTH domains, they are predicted to function akin to kleisins as DNA-binding partners for the ABC ATPases, assisting in recognition and responding to invasive elements such as DNA viruses. 159 matched cddid_all.tbl CDD pfam20132 pfam20132 466299 DUF6522 Family of unknown function (DUF6522). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 88 and 99 amino acids in length. 88 matched cddid_all.tbl CDD pfam20133 pfam20133 437965 HHL1-like Protein HHL1-like. This entry represents a group of proteins from plants and Cyanobacteria, including HHL1 from Arabidopsis. HHL1 functions in protecting photosystem II against photodamage. 143 matched cddid_all.tbl CDD pfam20134 pfam20134 437966 DUF6524 Family of unknown function (DUF6524). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 131 and 142 amino acids in length. 131 matched cddid_all.tbl CDD pfam20135 pfam20135 466300 DUF6525 Family of unknown function (DUF6525). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 69 and 100 amino acids in length. There are two conserved sequence motifs: AALPWSP and RAE. 78 matched cddid_all.tbl CDD pfam20136 pfam20136 466301 DUF6526 Family of unknown function (DUF6526). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. 148 matched cddid_all.tbl CDD pfam20137 pfam20137 466302 DUF6527 Family of unknown function (DUF6527). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 118 and 131 amino acids in length. 63 matched cddid_all.tbl CDD pfam20138 pfam20138 437970 DUF6528 Family of unknown function (DUF6528). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 311 and 340 amino acids in length. 327 matched cddid_all.tbl CDD pfam20139 pfam20139 437971 DUF6529 Family of unknown function (DUF6529). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 183 and 197 amino acids in length. Based on similarity to pfam03188 these proteins may be cytochromes. 171 matched cddid_all.tbl CDD pfam20140 pfam20140 437972 DUF6530 Family of unknown function (DUF6530). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 160 amino acids in length. 159 matched cddid_all.tbl CDD pfam20141 pfam20141 466303 Island Brassinosteroid receptor island domain. The island domain in BRI1 corresponds to a large insertion in the regular repeat-structure between LRRs 21 and 22. The resulting 70-residue segment forms a small domain that folds back into the interior of the LRR superhelix, where it makes extensive polar and hydrophobic interactions with LRRs 13-25. The domain fold is characterized by an anti-parallel beta-sheet, which is sandwiched between the LRR core and a 3-10 helix and stabilized by a disulphide bridge. The insertion of a folded domain into the LRR repeat has not been observed in other LRR receptor structures, and is probably an adaptation to the challenge of sensing a small steroid ligand (rather than larger ligands, such as proteins, nucleic acids, or lipids. 65 matched cddid_all.tbl CDD pfam20142 pfam20142 466304 Scaffold Scaffold domain. This entry represents the scaffolding domain from the L,D-transpeptidases. 140 matched cddid_all.tbl CDD pfam20143 pfam20143 437975 NAD_kinase_C ATP-NAD kinase C-terminal domain. Members of this family include ATP-NAD kinases EC:2.7.1.23, which catalyzes the phosphorylation of NAD to NADP utilizing ATP and other nucleoside triphosphates as well as inorganic polyphosphate as a source of phosphorus. Also includes NADH kinases EC:2.7.1.86. This entry represents the C-terminal beta sandwich domain. 125 matched cddid_all.tbl CDD pfam20144 pfam20144 466305 TIG_SUH TIG domain. This entry represents a TIG-like domain found in the suppressor of hairless protein. 92 matched cddid_all.tbl CDD pfam20145 pfam20145 466306 ARMET_N "ARMET, N-terminal. This is the N-terminal domain of ARMET proteins (also known as mesencephalic astrocyte-derived neurotrophic factor (MANF) or arginine-rich protein), a saposin-like domain consisting of five alpha-helices with three cystein bridges that stabilizes the globular ""closed leaf"" conformation. ARMET is a small protein of approximately 170 residues which contain four di-sulfide bridges that are highly conserved from nematodes to humans. It is a soluble protein resident in the endoplasmic reticulum and induced by ER stress. It appears to be involved with dealing with mis-folded proteins in the ER, thus in quality control of ER stress." 97 matched cddid_all.tbl CDD pfam20146 pfam20146 466307 NRF Nose resistant-to-fluoxetine protein, N-terminal domain. 118 matched cddid_all.tbl CDD pfam20147 pfam20147 466308 Crinkler Crinkler effector protein N-terminal domain. Phytophthora sojae encodes hundreds of putative host cytoplasmic effectors with conserved FLAK motifs following signal peptides, termed crinkling- and necrosis-inducing proteins (CRN) or Crinkler. Their functions and mechanisms in pathogenesis are mostly unknown. This N-terminal domain contains a ubiquitin-like fold. 103 matched cddid_all.tbl CDD pfam20148 pfam20148 466309 DUF6531 Domain of unknown function (DUF6531). This putative domain is found in a range of RHS proteins. 74 matched cddid_all.tbl CDD pfam20149 pfam20149 437981 DUF6532 Domain of unknown function (DUF6532). This entry represents a large family of uncharacterized fungal proteins. 196 matched cddid_all.tbl CDD pfam20150 pfam20150 466310 2EXR 2EXR family. This entry contains proteins with two conserved ExR motifs that may be functionally important. This entry represents a large and diverse family of proteins found in fungi. 92 matched cddid_all.tbl CDD pfam20151 pfam20151 437983 DUF6533 Family of unknown function (DUF6533). This entry represents a short conserved region found in a large family of fungal integral membrane proteins. 46 matched cddid_all.tbl CDD pfam20152 pfam20152 437984 DUF6534 Family of unknown function (DUF6534). This entry represents a large family of fungal integral membrane proteins. 80 matched cddid_all.tbl CDD pfam20153 pfam20153 437985 DUF6535 Family of unknown function (DUF6535). This entry represents an integral membrane region of a large family of fungal proteins. This region likely contains three transmembrane helices. Some proteins contain two copies of this region. The function of these proteins is unknown. 177 matched cddid_all.tbl CDD pfam20154 pfam20154 466311 LNT_N Apolipoprotein N-acyltransferase N-terminal domain. This domain represents the N-terminal transmembrane region of the apolipoprotein N-acyltransferase enzyme. The enzyme catalyzes the phospholipid dependent N-acylation of the N-terminal cysteine of apolipoprotein, the last step in lipoprotein maturation. This entry does not represent the enzymatic domain found at the C-terminus of the protein. 159 matched cddid_all.tbl CDD pfam20155 pfam20155 466312 TMP_3 Tape measure protein. This entry represents phage tape measure proteins that are required to assemble the page tail. The protein serves as a base for tail tube protein polymerization and acts as a template for tail length determination. 192 matched cddid_all.tbl CDD pfam20156 pfam20156 437988 Maf_C Flagellin glycosyltransferase Maf helical bundle domain. This entry represents the Flagellin glycosyltransferase Maf helical bundle domain. 122 matched cddid_all.tbl CDD pfam20157 pfam20157 437989 Maf_flag10_N Glycosyltransferase Maf N-terminal domain. This entry represents the N-terminal Rossmann like domain from the flagellin glycosyltransferase Maf. 230 matched cddid_all.tbl CDD pfam20158 pfam20158 437990 Cas5fv_helical Cas5fv helical domain. This entry represents the Cas5fv helical domain. 158 matched cddid_all.tbl CDD pfam20159 pfam20159 437991 YidB YidB-like protein. This entry includes the uncharacterized protein YidB from E. coli. This entry was previously a subset of the DUF937 family. 138 matched cddid_all.tbl CDD pfam20160 pfam20160 466313 C-JID C-JID domain. C-terminal jelly roll/Ig-like domain (C-JID) was defined in cryogenic electron microscopy (cryoEM) structures of plant intracellular immune receptors containing Toll/interleukin-1 receptor (TIR, PF01582), nucleotide-binding (NB-ARC, PF00931) and leucine-rich repeat (LRR) domains (TIR-NLRs). Structurally, the C-JID core is represented by a beta-sandwich made up of 8 to 9 beta-strands. C-JID matches the so-called post LRR domain originally detected via a set of MEME motifs. The domain showed a strong distribution bias towards TIR-NLRs of dicotyledonous plant species despite broader taxonomic distribution of TIR-NLR in plant groups. Structure-function analyses of cryoEM structures suggest that C-JID domains play a role in substrate-recognition, such as binding to effector proteins from pathogens, and thus are involved in the initiation of signaling by TIR-NLR receptors. Presence of C-JID (or post-LRR) and its importance for the function of Arabidopsis TIR-NLR RPS4 that partners with RRS1 for effector recognition suggest that C-JID has additional functions. 108 matched cddid_all.tbl CDD pfam20161 pfam20161 437993 VpsR VpsR domain. VpsR appears superficially to be a response regulator, based on extension of its alignment to response regulators AlgB and NrtC all the way to the N-terminus. Instead of being a response regulator with a histidine kinase partner, the sigma-54-dependent transcription factor VpsR directly binds to cyclic-di-GMP. Its regulon includes genes for the biosynthesis of the biofilm matrix component called Vibrio polysaccharide (VPS). 121 matched cddid_all.tbl CDD pfam20162 pfam20162 437994 Etd1 Septation protein etd1. This family includes the Septation protein etd1 from Schizosaccharomyces pombe, which activates the GTPase Spg1 to trigger signaling through the septum initiation network (SIN) pathway and onset of cytokinesis. The proper regulation of Etd1 is crucial for both activation of Spg1 in anaphase and inactivation of Spg1 when cytokinesis is complete. It was suggested that Etd1 is the functional homolog of budding yeast Lte1 as they have the same function but a very low sequence similarity. 98 matched cddid_all.tbl CDD pfam20163 pfam20163 466314 DUF6536 Family of unknown function (DUF6536). Proteins in this family are found in Fungi. 154 matched cddid_all.tbl CDD pfam20164 pfam20164 466315 GspA_SrpA_N GspA/SrpA SigLec-like domain. This domain is an adhesive domain that binds to sialoglycan. A Thr-Arg motif conserved across homologous carbohydrate-binding adhesins that may orient the sialic acid moiety of carbohydrate ligands. 111 matched cddid_all.tbl CDD pfam20165 pfam20165 466316 KBTB_W-LIR KBTB, W-type LIR motif. LC3 Interacting Regions (LIRs), also known as ATG8-interacting motifs (AIMs), are short-linear motifs (SLiMs) of autophagy receptors and adaptor proteins that facilitates the selective recruitment of autophagy substrates to the autophagosome. ATG8 proteins are highly conserved in eukaryotes and play a key role in selective autophagy as they recognize and bind different autophagy receptors and adaptors containing a specific class of SLiMs. LIRs are characterized by degenerated sequences with a four-residue core central sequence involved in ATG8-binding, with the W/Y/FxxL/I/V pattern. Based on the aromatic amino acid in position 1 they can be classified into W-type, Y-type and F-type. This is the W-type LIR motif from Kelch repeat and BTB domain-containing proteins (KBTBs), characterized by the core LIR sequence WVxV. 12 matched cddid_all.tbl CDD pfam20166 pfam20166 466317 ATG4_LIR ATG4, F-type LIR motif. LC3 Interacting Regions (LIRs), also known as ATG8-interacting motifs (AIMs), are short-linear motifs (SLiMs) of autophagy receptors and adaptor proteins that facilitates the selective recruitment of autophagy substrates to the autophagosome. ATG8 proteins are highly conserved in eukaryotes and play a key role in selective autophagy as they recognize and bind different autophagy receptors and adaptors containing a specific class of SLiMs. LIRs are characterized by degenerated sequences with a four-residue core central sequence involved in ATG8-binding, with the W/Y/FxxL/I/V pattern. Based on the aromatic amino acid in position 1 they can be classified into W-type, Y-type and F-type. This entry is the F-type LIR motif from ATG4, which contains the seqeunce FEI/VL. There are acidic residues at the N-terminal of this motif (Asp and Glu), which may contribute to stabilize the binding or may provide specificity toward a certain class of ATG8 proteins. 29 matched cddid_all.tbl CDD pfam20167 pfam20167 466318 Transposase_32 Putative plant transposon protein. This entry represents a likely transposon related protein from plants. This entry appears related to ORF1 from the ATHILA group of Arabidopsis thaliana retrotransposons pfam03078. 177 matched cddid_all.tbl CDD pfam20168 pfam20168 466319 PDS5 Sister chromatid cohesion protein PDS5 protein. This entry represents the Sister chromatid cohesion protein PDS5. The large PDS5 molecule is exclusively alpha helical, composed of a large number of HEAT-like repeats and helical extensions/additions that deviate from the HEAT repeat pattern. 1051 matched cddid_all.tbl CDD pfam20169 pfam20169 466320 DUF6537 Family of unknown function (DUF6537). This entry represents a presumed domain that is found associated with a variety of enzyme domains. The function of this domain is unknown. 201 matched cddid_all.tbl CDD pfam20170 pfam20170 466321 Plexin_RBD Plexin cytoplasmic RhoGTPase-binding domain. This entry represents the RhoGTPase-binding domain found in the cytoplasmic domain of plexins. 113 matched cddid_all.tbl CDD pfam20171 pfam20171 466322 OpcA_G6PD_C Glucose-6-phosphate dehydrogenase subunit C-terminal domain. Members of this family are found in various prokaryotic OpcA and glucose-6-phosphate dehydrogenase proteins. This entry represents the C-terminal domain. 136 matched cddid_all.tbl CDD pfam20172 pfam20172 466323 DUF6538 Domain of unknown function (DUF6538). This short presumed domain is found at the N-terminus of a variety of phage integrase proteins. 60 matched cddid_all.tbl CDD pfam20173 pfam20173 466324 DUF6539 Family of unknown function (DUF6539). This presumed domain contains 6 conserved cysteines and histidines that presumably form a zinc binding site. The function of this domain is unknown. 54 matched cddid_all.tbl CDD pfam20174 pfam20174 466325 DUF6540 Family of unknown function (DUF6540). This entry contains a large diverse family of fungal proteins of unknown function. 121 matched cddid_all.tbl CDD pfam20175 pfam20175 466326 Tra1_central Tra1 HEAT repeat central region. This entry represents part of the Tra1 protein composed of alpha solenoid repeats that forms the central region. This is named as central due to its position relative to the ring region. 593 matched cddid_all.tbl CDD pfam20176 pfam20176 466327 DUF6541 Family of unknown function (DUF6541). This family is composed of a group of large bacterial integral membrane proteins that likely have a transporter function. 646 matched cddid_all.tbl CDD pfam20177 pfam20177 466328 DUF6542 Domain of unknown function (DUF6542). This entry represents an integral membrane domain composed of four predicted transmembrane helices. The function of this region is unknown. 123 matched cddid_all.tbl CDD pfam20178 pfam20178 466329 DUF6543 Family of unknown function (DUF6543). This entry represents a region of unknown function found in a variety of bacterial proteins. 589 matched cddid_all.tbl CDD pfam20179 pfam20179 466330 MSS51_C MSS51 C-terminal domain. This presumed domain is found at the C-terminus of the MSS51 protein. 184 matched cddid_all.tbl CDD pfam20180 pfam20180 466331 UQCC2_CBP6 Complex III assembly factor UQCC2/CBP6. This family represents mitochondrial respiratory chain complex III (or cytochrome b-c1 complex) assembly factors, including Cbp6 from yeast and its human orthologue UQCC2 (Ubiquinol-Cytochrome c Reductase Complex Assembly Factor 2). These proteins have diverged significantly among eukaryotes and UQCC2/Cbp6 have an overall low amino acid conservation. UQCC2 interacts with UQCC1, the human orthologue of the Cbp6 binding partner Cbp3, to form a complex necessary for cytochrome b biogenesis. Cbp3-Cbp6 complex interacts with mitochondrial ribosomes for efficient translation of cytochrome b transcript and it also interacts with newly synthesized cytochrome b to assist its correct assembly. These proteins contain a LRY-like N-terminal sequence being related to the LYR superfamily of proteins, which function as subunits or assembly factors for respiratory complexes I, II, III, and V. 89 matched cddid_all.tbl CDD pfam20181 pfam20181 466332 DUF6544 Family of unknown function (DUF6544). This entry represents a set of uncharacterized protein found in bacteria. 221 matched cddid_all.tbl CDD pfam20182 pfam20182 466333 DUF6545 Family of unknown function (DUF6545). This entry represents an integral membrane protein of unknown function. Proteins in this family are found in a range of bacterial species. 134 matched cddid_all.tbl CDD pfam20183 pfam20183 466334 DUF6546 Family of unknown function (DUF6546). This entry represents a family of uncharacterized proteins. Some of these contain an N-terminal F-box domain pfam00646. 203 matched cddid_all.tbl CDD pfam20184 pfam20184 466335 DUF6547 Family of unknown function (DUF6547). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 116 and 127 amino acids in length. 117 matched cddid_all.tbl CDD pfam20185 pfam20185 466336 DUF6548 Family of unknown function (DUF6548). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are around 180 amino acids in length. They contain highly conserved motifs, YKxLD and I/LC at the N-terminal and LKxxRxxRN in the middle. 165 matched cddid_all.tbl CDD pfam20186 pfam20186 466337 DUF6549 Family of unknown function (DUF6549). This presumed domain is functionally uncharacterized. This domain family is mainly found in bacteria, and is typically between 120 and 180 amino acids in length. There are two highly conserved residues, an aspartate and a tryptophan, and a NP conserved motif. 167 matched cddid_all.tbl CDD pfam20187 pfam20187 466338 DUF6550 Family of unknown function (DUF6550). This family of proteins is functionally uncharacterized. This family of proteins is found in Firmicutes. Proteins in this family are approximately 180 amino acids in length. There are two conserved sequence motifs at the C-terminal: FGW/I and I/VGxM. 190 matched cddid_all.tbl CDD pfam20188 pfam20188 466339 DUF6551 Family of unknown function (DUF6551). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 200 amino acids in length. Many sequences are related to ParB proteins, annotated as ParB-like or ParB domain-containing proteins. It contains the conserved motifs YQR, DGQH and EAxxF. 241 matched cddid_all.tbl CDD pfam20189 pfam20189 466340 DUF6552 Family of unknown function (DUF6552). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, mainly Proteobacteria. Proteins in this family are approximately 90 amino acids in length and some members are associated with Ubiquinone biosynthesis methyltransferases. 78 matched cddid_all.tbl CDD pfam20190 pfam20190 466341 DUF6553 Family of unknown function (DUF6553). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, mainly Firmicutes and Actinobacteria. Proteins in this family are approximately 200 amino acids in length and contain the conserved motifs RY and DxF/Y 188 matched cddid_all.tbl CDD pfam20191 pfam20191 466342 DUF6554 Family of unknown function (DUF6554). This family of proteins is functionally uncharacterized. This family of proteins is found in Cyanobacteria. Proteins in this family are typically between 131 and 150 amino acids in length. 102 matched cddid_all.tbl CDD pfam20192 pfam20192 466343 DUF6555 Family of unknown function (DUF6555). This family of proteins is functionally uncharacterized. This family of proteins is found in Proteobacteria. Proteins in this family are typically between 76 and 94 amino acids in length. 74 matched cddid_all.tbl CDD pfam20193 pfam20193 466344 DUF6556 Family of unknown function (DUF6556). This family of proteins is functionally uncharacterized. This family of proteins is found in Firmicutes. Proteins in this family are typically between 130 and 155 amino acids in length. Some members are predicted histone acetyltransferases. 113 matched cddid_all.tbl CDD pfam20194 pfam20194 466345 DUF6557 Family of unknown function (DUF6557). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 140 and 200 amino acids in length. There is a quite conserved EMTFxxG motif. 144 matched cddid_all.tbl CDD pfam20195 pfam20195 466346 DUF6558 Family of unknown function (DUF6558). This family includes uncharacterized proteins from Firmicutes and phages, some members are phage tail-related proteins. Included in this entry is the prophage-derived protein YomH from Bacillus subtilis (swiss:O31977). 260 matched cddid_all.tbl CDD pfam20196 pfam20196 466347 DUF6559 Family of unknown function (DUF6559). This family of proteins is functionally uncharacterized. This family of proteins is found in Gammaproteobacteria. Proteins in this family are approximately 120 amino acids in length. There are two conserved motifs, LxxxYG and Y/FT/SxxQI/V. 125 matched cddid_all.tbl CDD pfam20197 pfam20197 466348 DUF6560 Family of unknown function (DUF6560). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, mainly Firmicutes. Proteins in this family are typically between 157 and 193 amino acids in length. There are three highly conserved residues, tryptophan, phenylalanine/ tyrosine and lysine. 174 matched cddid_all.tbl CDD pfam20198 pfam20198 466349 DUF6561 Family of unknown function (DUF6561). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteriophages, mainly in Myovirus. Proteins in this family are approximately 80 amino acids in length. There are two conserved sequence motifs: EP and PxxxxxxxY. 84 matched cddid_all.tbl CDD pfam20199 pfam20199 466350 RepSA Replication initiator protein, pSAM2. This entry represents a family of protein that can be found in (and are an essential part of) actinomycete integrative and conjugative elements (AICEs). 436 matched cddid_all.tbl CDD pfam20200 pfam20200 466351 DUF6562 Family of unknown function (DUF6562). This family of proteins is functionally uncharacterized. This family of proteins is found in Bacteroidetes. Proteins in this family are typically between 340 and 430 amino acids in length and have the conserved motifs WAD, RP and TxxG. Some members are hypothetical Fimbrillin-A associated anchor protein Mfa1/Mfa2 and related to pfam08842. 296 matched cddid_all.tbl CDD pfam20201 pfam20201 466352 DUF6563 Family of unknown function (DUF6563). This family of proteins is functionally uncharacterized. This family of proteins is found in Bacteroidetes. Proteins in this family are around 230 amino acids in length. They contain the conserved motifs GGxDY and LYxNC in addition to three Y/F conserved residues. 191 matched cddid_all.tbl CDD pfam20202 pfam20202 466353 DUF6564 Domain of unknown function (DUF6564). This domain is functionally uncharacterized and is found in proteins from bacteria and archaea. This domain is found in Protein LicC (swiss:P14183), a CTP:phosphocholine cytidylyltransferase involved in LPS biosynthesis. Members containing this domain are annotated as nucleotidyltransferases. It is probable that this domain has a Rossmann like fold. 230 matched cddid_all.tbl CDD pfam20203 pfam20203 466354 DUF6565 Domain of unknown function (DUF6565). This domain is found in uncharacterized proteins from Bacteroidetes and its function is unknown. It is approximately 60 amino acids in length. It contains a conserved motif DxxxW and a highly conserved tyrosine residue. 77 matched cddid_all.tbl CDD pfam20204 pfam20204 466355 DUF6566 Domain of unknown function (DUF6566). This domain is found in functionally uncharacterized proteins from Burkholderiaceae. This domain is approximately 60 amino acids in length and it has a conserved tryptophan residue at the N-terminal, the conserved motifs PxW and AxRxxxE and an aspartate conserved residue at the C-terminal. Some members containing this domain are hypothetical transposases. 78 matched cddid_all.tbl CDD pfam20205 pfam20205 466356 DUF6567 Family of unknown function (DUF6567). This family of proteins is functionally uncharacterized. This family of proteins is found mainly in Bacteroidetes. Proteins in this family are approximately 120 amino acids in length. There is a conserved motif NF/Y and two conserved residues, a Cys and an Asn. 123 matched cddid_all.tbl CDD pfam20206 pfam20206 466357 Tra1_ring Tra1 HEAT repeat ring region. This entry represents part of the Tra1 protein composed of alpha solenoid repeats that form a ring region. 1678 matched cddid_all.tbl CDD pfam20207 pfam20207 466358 DUF6568 Family of unknown function (DUF6568). This family of proteins is functionally uncharacterized. This family of proteins is mainly found in Firmicutes. Proteins in this family are approximately 170 amino acids in length. There are two conserved motifs, CxxF and YxN, and two conserved residues, Tyr at the N-terminal and a Gly at the C-terminal. Many members of this family are thought to belong to the Thioredoxin superfamily. 161 matched cddid_all.tbl CDD pfam20208 pfam20208 466359 DUF6569 Family of unknown function (DUF6569). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 311 and 364 amino acids in length. There are two conserved sequences GxxxxGxxQ and CxxxGRW. 302 matched cddid_all.tbl CDD pfam20209 pfam20209 466360 DUF6570 Domain of unknown function (DUF6570). This entry represents a presumed domain of unknown function that is found in a wide range of proteins that includes eukaryotic transposon protein. 134 matched cddid_all.tbl CDD pfam20210 pfam20210 466361 Laa1_Sip1_HTR5 Laa1/Sip1/HEATR5 HEAT repeat region. 179 matched cddid_all.tbl CDD pfam20211 pfam20211 466362 DUF6571 Family of unknown function (DUF6571). This family of proteins is functionally uncharacterized. This family of proteins is found in Actinobacteria. Proteins in this family are typically between 547 and 730 amino acids in length. 685 matched cddid_all.tbl CDD pfam20212 pfam20212 466363 DUF6572 Family of unknown function (DUF6572). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 107 and 214 amino acids in length. These proteins may have a threefold symmetric beta-trefoil fold, a symmetric protein structure thought to be conserved in protein evolution. 106 matched cddid_all.tbl CDD pfam20213 pfam20213 466364 DUF6573 Family of unknown function (DUF6573). This family of proteins is functionally uncharacterized. This family of proteins is mainly found in Proteobacteria. Proteins in this family are approximately 130 amino acids in length. 138 matched cddid_all.tbl CDD pfam20214 pfam20214 466365 DUF6574 Family of unknown function (DUF6574). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, mainly Firmicutes. Proteins in this family are typically between 116 and 320 amino acids in length. Many members are thought to contain a zinc ribbon domain. 258 matched cddid_all.tbl CDD pfam20215 pfam20215 466366 DUF6575 Family of unknown function (DUF6575). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 101 and 403 amino acids in length. There some conserved motifs, Y/FL, WL and LP. 218 matched cddid_all.tbl CDD pfam20216 pfam20216 466367 DUF6576 Family of unknown function (DUF6576). This presumed domain is functionally uncharacterized. This domain family corresponds to the C-terminal domain of proteins that are thought to belong to the rhomboid family. It is approximately 40 amino acids in length and it is found mainly in Bacteroidetes. It contains the conserved sequences DxILDKI, GYxxL and EKxxL. 47 matched cddid_all.tbl CDD pfam20217 pfam20217 466368 DUF6577 Family of unknown function (DUF6577). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, mainly Bacteroidetes and Firmicutes. Proteins in this family are typically between 239 and 255 amino acids in length. There are some conserved sequences, GxY, EKxxVD and YAxxRR and a conserved His. 204 matched cddid_all.tbl CDD pfam20218 pfam20218 466369 DUF6578 Family of unknown function (DUF6578). This family of proteins is functionally uncharacterized. This family of proteins is mainly found in Actinobacteria. Proteins in this family are typically between 132 and 185 amino acids in length. There are three conserved motifs, WQ, CCG and GxV. 124 matched cddid_all.tbl CDD pfam20219 pfam20219 466370 DUF6579 Family of unknown function (DUF6579). This family of proteins is functionally uncharacterized. This family of proteins is found in Fungi. Proteins in this family are approximately 300 amino acids in length. There are some conserved motifs, HxFF, HPD and FHLLI. 210 matched cddid_all.tbl CDD pfam20220 pfam20220 466371 ABC_toxin_N ABC toxin N-terminal region. This entry represents the region found N-terminal to the neuraminidase domain in the pore forming ABC toxins. 124 matched cddid_all.tbl CDD pfam20221 pfam20221 466372 DUF6580 Family of unknown function (DUF6580). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 200 amino acids in length. Some members are hypothetical ECF transporters related to the Gx transporter superfamily (CL0315). 167 matched cddid_all.tbl CDD pfam20222 pfam20222 466373 DUF6581 Family of unknown function (DUF6581). This entry represents a putative domain found in the yeast Transcription factor tau 138 kDa subunit. 404 matched cddid_all.tbl CDD pfam20223 pfam20223 466374 DUF6582 Family of unknown function (DUF6582). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically around 100 amino acids in length. It includes two conserved motifs, FA and HVRxA. 83 matched cddid_all.tbl CDD pfam20224 pfam20224 466375 DUF6583 Family of unknown function (DUF6583). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, mainly in Firmicutes. Proteins in this family are typically between 454 and 596 amino acids in length. There are two highly conserved residues, a Tyr and an Asp. 446 matched cddid_all.tbl CDD pfam20225 pfam20225 466376 DUF6584 Family of unknown function (DUF6584). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, mainly Actinobacteria and Firmicutes. Many members are thought to contain TPR regions There are two conserved motifs, AxRL and LxxY. 171 matched cddid_all.tbl CDD pfam20226 pfam20226 466377 DUF6585 Family of unknown function (DUF6585). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 246 and 268 amino acids in length. There are seven highly conserved Gly residues. 249 matched cddid_all.tbl CDD pfam20227 pfam20227 466378 DUF6586 Family of unknown function (DUF6586). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, mainly in Proteobacteria. Proteins in this family are approximately 150 amino acids in length. There is a conserved motif NQ and a highly conserved Tryptophan residue. 153 matched cddid_all.tbl CDD pfam20228 pfam20228 466379 DUF6587 Family of unknown function (DUF6587). This family of proteins is functionally uncharacterized. This family of proteins is found in Proteobacteria. Proteins in this family are typically between 80 and 101 amino acids in length and contain four conserved cysteine residues at the C-terminal. 82 matched cddid_all.tbl CDD pfam20229 pfam20229 466380 ChrB_N Protein ChrB, N-terminal. This is the N-terminal domain found in Chromate resistance protein ChrB, a protein involved in the reduction of chromate accumulation and are essential for chromate resistance. This domain may be involved in DNA binding and contains two highly conserved arginine residues important for its function. 159 matched cddid_all.tbl CDD pfam20230 pfam20230 466381 DUF6588 Family of unknown function (DUF6588). This family of proteins is functionally uncharacterized. This family of proteins is found in Bacteroidetes. Proteins in this family are typically between 332 and 351 amino acids in length. There are several conserved Gly residues and two conserved motifs, AQ and GW. 335 matched cddid_all.tbl CDD pfam20231 pfam20231 466382 DUF6589 Family of unknown function (DUF6589). This entry represents a fungal protein family of unknown function. 417 matched cddid_all.tbl CDD pfam20232 pfam20232 466383 T6SS_FHA_C C-terminal domain of Type VI secretion system FHA protein. This presumed domain is found at the C-terminus of a group of proteins thought to be expressed in a Type VI secretion system locus. These proteins contain an N-terminal FHA domain. The function of this domain is unknown. 180 matched cddid_all.tbl CDD pfam20233 pfam20233 466384 DUF6590 Family of unknown function (DUF6590). This presumed domain found in Fungi is functionally uncharacterized. 152 matched cddid_all.tbl CDD pfam20234 pfam20234 466385 DUF6591 Family of unknown function (DUF6591). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, mainly Firmicutes and Actinobacteria, and is approximately 80 amino acids in length. It contains a highly conserved tryptophan residue and the conserved sequence YxxxxxxY. 227 matched cddid_all.tbl CDD pfam20235 pfam20235 466386 DUF6592 Family of unknown function (DUF6592). This putative domain is found in plant E3-ligase proteins. The function of this domain is unknown. The domain is about 120 amino acids in length. 116 matched cddid_all.tbl CDD pfam20236 pfam20236 466387 DUF6593 Family of unknown function (DUF6593). This entry represents a large family of Uncharacterized fungal proteins. 150 matched cddid_all.tbl CDD pfam20237 pfam20237 466388 DUF6594 Family of unknown function (DUF6594). This entry represents a group of uncharacterized proteins that contain a set of C-terminal transmembrane helices. The family may be related to pfam10267. 233 matched cddid_all.tbl CDD pfam20238 pfam20238 466389 DUF6595 Family of unknown function (DUF6595). This uncharacterized domain found in fungi is related to pfam03067. 144 matched cddid_all.tbl CDD pfam20239 pfam20239 466390 DUF6596 Family of unknown function (DUF6596). This presumed domain is found at the C-terminus of bacterial RNA polymerase ECF sigma factor proteins. 102 matched cddid_all.tbl CDD pfam20240 pfam20240 466391 DUF6597 Domain of unknown function (DUF6597). This presumed domain is found at the N-terminus of bacterial transcription factor proteins, suggesting that this may be a regulatory domain that binds to some as yet unknown ligand. 104 matched cddid_all.tbl CDD pfam20241 pfam20241 466392 DUF6598 Domain of unknown function (DUF6598). This putative domain is found in one or more copies in several plant proteins. The function of the domain is unknown. 241 matched cddid_all.tbl CDD pfam20242 pfam20242 466393 Emfourin Emfourin. This family represents a protealysin inhibitor called Emfourin, after M4 family inhibitor (M4in), as protealysin is a metallo- endopeptidase from MEROPS peptidase family M4. Emfourin is a potent inhibitor that forms a 1:1 stoichiometry complex with protealysin. 91 matched cddid_all.tbl CDD pfam20243 pfam20243 466394 MbnP MbnP. This entry represents a group of uncharacterized proteins that include methanobactin biosynthesis operon protein MbnP. The respective proteins, MbnP and MbnH, are referred to in the TIGRFAM database as the metallo-mystery pair. 191 matched cddid_all.tbl CDD pfam20244 pfam20244 466395 DUF6599 Family of unknown function (DUF6599). This entry represents a family of uncharacterized bacterial proteins. 185 matched cddid_all.tbl CDD pfam20245 pfam20245 466396 DUF6600 Family of unknown function (DUF6600). This entry represents a bacterial protein of unknown function. It is rich in conserved tryptophan residues and contains a central HYGRW motif that may be of functional importance. 102 matched cddid_all.tbl CDD pfam20246 pfam20246 466397 DUF6601 Family of unknown function (DUF6601). This entry represents a family found in fungi. The function of this region is unknown. It appears to contain a pair of C-terminal transmembrane helices. 239 matched cddid_all.tbl CDD pfam20247 pfam20247 466398 DUF6602 Domain of unknown function (DUF6602). This entry represents a bacterial domain of unknown function. This domain is sometimes associated with a pfam14464 domain. This could suggest this domain has a role in a bacterial cognate of a Ubiquitin-like pathway. 104 matched cddid_all.tbl CDD pfam20248 pfam20248 466399 DUF6603 Family of unknown function (DUF6603). This entry represents a large potential domain found in a wide range of uncharacterized fungal proteins. 502 matched cddid_all.tbl CDD pfam20249 pfam20249 466400 VasX_N VasX toxin N-terminal region. This entry represents the N-terminal region of the VasX toxin from Vibrio cholerae. 156 matched cddid_all.tbl CDD pfam20250 pfam20250 466401 FapA_N Flagellar Assembly Protein A N-terminal region. This entry represents an N-terminal region of the FapA protein and its homologs. This region is found in multiple copies in some proteins. Members of this family include FapA (flagellar assembly protein A) found in Vibrio vulnificus. The synthesis of flagella allows bacteria to respond to chemotaxis by facilitating motility. Studies examining the role of FapA show that the loss or delocalization of FapA results in a complete failure of the flagellar biosynthesis and motility in response to glucose mediated chemotaxis. The polar localization of FapA is required for flagellar synthesis, and dephosphorylated EIIAGlc (Glucose-permease IIA component) inhibited the polar localization of FapA through direct interaction. 174 matched cddid_all.tbl CDD pfam20251 pfam20251 466402 Big_14 Bacterial Ig-like domain. This bacterial Ig-like domain shows some similarity to pfam12690 suggesting it may act as a protease inhibitor similar to B. subtilis BsuPI. 108 matched cddid_all.tbl CDD pfam20252 pfam20252 466403 BIG2_C BIG2 C-terminal domain. This presumed domain is found at the C-terminus of BIG2 the brefeldin A-inhibited guanine nucleotide-exchange protein. The function of this region is unknown. 178 matched cddid_all.tbl CDD pfam20253 pfam20253 466404 DUF6604 Family of unknown function (DUF6604). This entry represents a putative domain found at the N-terminus of a wide range of fungal proteins of unknown function. 247 matched cddid_all.tbl CDD pfam20254 pfam20254 466405 DUF6605 Domain of unknown function (DUF6605). This entry represents a bacterial domain of unknown function often found associated with bacterial Ig-like domains. 370 matched cddid_all.tbl CDD pfam20255 pfam20255 466406 DUF6606 Family of unknown function (DUF6606). This entry represents a domain of unknown function found at the N-terminus of a variety of proteins that contain pfam12340. 267 matched cddid_all.tbl CDD pfam20256 pfam20256 466407 MoCoBD_2 Molybdopterin cofactor-binding domain. 282 matched cddid_all.tbl CDD pfam20257 pfam20257 466408 SAM_HAT_C SAM hydroxide adenosyltransferase C-terminal domain. This is a family of proteins, previously known as DUF62, found in archaebacteria and bacteria. The structure of proteins in this family is similar to that of a bacterial fluorinating enzyme. S-adenosyl-l-methionine hydroxide adenosyltransferases utilizes a rigorously conserved amino acid side chain triad (Asp-Arg-His) which may have a role in activating water to hydroxide ion. This family used to be known as DUF62. This entry represents the C-terminal domain of these enzymes. 84 matched cddid_all.tbl CDD pfam20258 pfam20258 466409 tRNA_Me_trans_C Aminomethyltransferase beta-barrel domain. This domain is found at the C-terminus of tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs. 77 matched cddid_all.tbl CDD pfam20259 pfam20259 466410 tRNA_Me_trans_M tRNA methyl transferase PRC-barrel domain. This family represents a central PRC-barrel domain in tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs. 66 matched cddid_all.tbl CDD pfam20260 pfam20260 466411 PUA_4 RNA methyltransferase PUA domain. RNA methyltransferases modify nucleotides during ribosomal RNA maturation in a site-specific manner. The Escherichia coli member is specific for U1498 methylation. 48 matched cddid_all.tbl CDD pfam20262 pfam20262 466412 UNC80_C Protein UNC80 C-terminal region. This family represents the protein UNC80 found in eukaryotes, a component of the NALCN sodium channel complex. NALC is a cation voltage-independent channel activated by substance P, neurotensin, acetylcholine and noradrenaline that controls neuronal excitability. UNC80 forms a complex with UNC79 and both are key regulators of the channel and required for the proper expression and axonal localization of NALCN. UNC80 is required for NALCN control by GPCRs and essential for its sensitivity to extracellular calcium. This protein acts as a scaffold for Src family of tyrosine kinases (SFK) and UNC-79 to mediate interaction with NALCN. 1079 matched cddid_all.tbl CDD pfam20263 pfam20263 466413 LYRM2-like LYR motif-containing protein 2-like. This entry represents LYR motif-containing proteins, including LYR motif-containing protein 2 from animals, whose function is not clear, and Cup1 (caffeine unstable phenotype 1, previously known as uncharacterized protein C17G9.13c) from S. pombe. Cup1 has been characterized; it is a mitochondrial protein whose silencing by heterochromatin island formation results in caffeine resistance. LYR-motif containing proteins are basic polypeptides carrying a conserved tripeptide L-Y-R (leucine/tyrosine/arginine) sequence close to the N-terminus in addition to some basic arginine/lysine residues and a highly-conserved phenylalanine downstream of the LYR motif. 86 matched cddid_all.tbl CDD pfam20264 pfam20264 466414 DUF4784_N DUF4784 N-terminal Ig-like domain. This is a family of uncharacterized proteins from Bacteroidetes. This domain is found to the N-terminus of a WD40-like domain in DUF4784 family protein. 107 matched cddid_all.tbl CDD pfam20265 pfam20265 466415 LARA_dom ATPase, RavA, LARA domain. This is the LARA (LdcI Associating domain of RavA) domain of bacterial regulatory ATPase RavA (Regulatory ATPase variant A). It adopts an unique fold which consists of a compact antiparallel beta-barrel- like structure formed by six beta-strands and one alpha-helix. This domain mediates the interaction between RavA and LdcI (inducible lysine decarboxylase) which form a cage-like complex proposed to assist assembly of specific respiratory complexes in E. coli. 104 matched cddid_all.tbl CDD pfam20266 pfam20266 466416 Mab-21_C Mab-21 protein HhH/H2TH-like domain. This family contains Mab-21 and Mab-21 like proteins. In C. elegans these proteins are required for several aspects of embryonic development. 102 matched cddid_all.tbl CDD pfam20267 pfam20267 466417 GREB1_C GREB1 C-terminal region. GREB1 (gene regulated by estrogen in breast cancer 1) was first identified as an oestrogen-regulated gene expressed in breast cancer. Its exact function is not known but its expression is regulated by the coordinated binding of oestrogen-receptors to distal sites interacting with Pol II to activate gene transcription from core promoters located at a considerable distance from the greb1 gene. 688 matched cddid_all.tbl CDD pfam20268 pfam20268 466418 SBDS_C SBDS protein, C-terminal domain. Members containing this domain are highly conserved in species ranging from archaea to vertebrates and plants, including several Shwachman-Bodian-Diamond syndrome (SBDS) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. These proteins play a role in RNA metabolism. In yeast Sdo1 is involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes. The SBDS protein is composed of three domains. The N-terminal (pfam01172) (FYSH) domain (domain I) is the most frequent target for disease mutations and contains a novel mixed alpha/beta-fold, the central domain (domain II, pfam09377) consists of a three-helical bundle and this C-terminal domain which has a ferredoxin-like fold. 67 matched cddid_all.tbl CDD pfam20269 pfam20269 466419 CATRA-N CASPASE and TPR Repeat-Associated N-terminal domain. One of two constant domains forming the CATRA module which is in turn C-terminally fused to a diverse range of conflict effector domains. This gene, along with a gene encoding the CATASP domain and a gene encoding a TPR repeat region fused to a CASPASE domain, forms the three gene island making up the CATRA conflict systems. This alpha/beta domain is predicted to be involved in recognition of invasive molecules or in the transmitting of a signal through conformational change, enabling CASPASE-mediated proteolysis to free the fused effector domains. 204 matched cddid_all.tbl CDD pfam20270 pfam20270 466420 CATRA-C CASPASE and TPR Repeat-Associated C-terminal domain. One of two constant domains forming the CATRA module which is in turn C-terminally fused to a diverse range of conflict effector domains. This gene, along with a gene encoding the CATASP domain and a gene encoding a TPR repeat region fused to a CASPASE domain, forms the three gene island making up the CATRA conflict systems. This all alpha-helical domain is predicted to be involved in recognition of invasive molecules or in the transmitting of a signal through conformational change, enabling CASPASE-mediated proteolysis to free the fused effector domains. 137 matched cddid_all.tbl CDD pfam20271 pfam20271 466421 CATASP CATRA-Associated Small Protein. Small, rapidly-evolving domain predicted to possess a compact, four-helix structure. Along with a gene encoding a TPR repeat region fused to a CASPASE domain and a gene encoding the CATRA module (CATRA-N+CATRA-C) C-terminally fused to a diverse range of conflict effector domains, forms the three gene island making up the CATRA conflict systems. Plays a possible inhibitory role in the CATRA system which is relieved upon sensing of an invasive molecule or is directly cleaved by the CASPASE domain. 86 matched cddid_all.tbl CDD pfam20272 pfam20272 466422 E2-Crich Cysteine-rich domain, C-terminal to E2 domain. Cysteine-rich domain observed C-terminal to certain E2 domains which are part of prokaryotic Ubiquitin systems found as secondary effector modules in nucleotide-activated effector conflict systems. 128 matched cddid_all.tbl CDD pfam20273 pfam20273 466423 E2-E1mid Domain observed between E2 and E1 domains. Certain prokaryotic Ubiquitin systems contain this domain between E2 and E1 fusion proteins. Many of these systems are secondary effector modules associating with nucleotide-activated effector systems. 118 matched cddid_all.tbl CDD pfam20274 pfam20274 466424 cREC_REC Cyclic-phosphate processing Receiver domain. This is a divergent version of the Receiver (Rec) domain linked to different NAD+/ADPr-processing enzymes. Unlike conventional Rec domains, cREC is never found in two-component Histidine Kinase signalling systems. Instead, it is found in association with NAD+-processing systems that generate or recognize cyclic nucleotides. Known Rec domains process phosphoester linkages by means of catalytic aspartate residues that are also conserved in cREC. Accordingly, it is predicted that these are cADPr or 2_-3_ cyclic nucleotide-processing enzymes. 88 matched cddid_all.tbl CDD pfam20275 pfam20275 466425 CTD10 C-terminal domain 10 of the ABC-three component (ABC-3C) systems. C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector. 132 matched cddid_all.tbl CDD pfam20276 pfam20276 466426 CTD1 C-terminal domain 1 of the ABC-three component (ABC-3C) systems. C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector. 247 matched cddid_all.tbl CDD pfam20277 pfam20277 466427 CTD11 C-terminal domain 11 of the ABC-three component (ABC-3C) systems. C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector. 140 matched cddid_all.tbl CDD pfam20278 pfam20278 466428 CTD2 C-terminal domain 2 of the ABC-three component (ABC-3C) systems. C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector. 333 matched cddid_all.tbl CDD pfam20279 pfam20279 466429 CTD12 C-terminal domain 12 of the ABC-three component (ABC-3C) systems. C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector. 144 matched cddid_all.tbl CDD pfam20280 pfam20280 466430 CTD4 C-terminal domain 4 of the ABC-three component (ABC-3C) systems. C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector. 218 matched cddid_all.tbl CDD pfam20281 pfam20281 466431 CTD5 C-terminal domain 5 of the ABC-three component (ABC-3C) systems. C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector. 207 matched cddid_all.tbl CDD pfam20282 pfam20282 466432 CTD6 C-terminal domain 6 of the ABC-three component (ABC-3C) systems. C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector. 130 matched cddid_all.tbl CDD pfam20283 pfam20283 466433 CTD7 C-terminal domain 7 of the ABC-three component (ABC-3C) systems. C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector. 126 matched cddid_all.tbl CDD pfam20284 pfam20284 466434 CTD8 C-terminal domain 8 of the ABC-three component (ABC-3C) systems. C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector. 127 matched cddid_all.tbl CDD pfam20285 pfam20285 466435 CTD9 C-terminal domain 9 of the ABC-three component (ABC-3C) systems. C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serves as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector. 113 matched cddid_all.tbl CDD pfam20286 pfam20286 466436 divDNApol Divergent Family B DNA polymerase. This family represents a Divergent Family B DNA polymerase found in PhiKZ/ group 1 phages. 705 matched cddid_all.tbl CDD pfam20287 pfam20287 466437 SH3DP SH3 fold domain associated with phage DNA polymerases. This is an SH3 fold domain related to nucleic acid binding toxins of uncharacterized function usually associated with a divergent Family B DNA polymerase in group 1/PhiKZ-like phages. 122 matched cddid_all.tbl CDD pfam20288 pfam20288 466438 MC2 ABC-three component (ABC-3C) system Middle Component 2. Middle Components (MCs) of the ABC-3C biological conflict systems occupy the central position between the catalytic effector and ABC ATPases of the systems. MCs are defined by distinctive patterns of conserved charged residues. As some MCs are HTH domains, they are predicted to function akin to kleisins as DNA-binding partners for the ABC ATPases, assisting in recognition and responding to invasive elements such as DNA viruses. 145 matched cddid_all.tbl CDD pfam20289 pfam20289 466439 MComp1 ABC-three component (ABC-3C) system Middle Component 1. Middle Components (MCs) of the ABC-3C biological conflict systems occupy the central position between the catalytic effector and ABC ATPases of the systems. MCs are defined by distinctive patterns of conserved charged residues. As some MCs are HTH domains, they are predicted to function akin to kleisins as DNA-binding partners for the ABC ATPases, assisting in recognition and responding to invasive elements such as DNA viruses. 99 matched cddid_all.tbl CDD pfam20290 pfam20290 466440 MC4 ABC-three component (ABC-3C) system Middle Component 4. Middle Components (MCs) of the ABC-3C biological conflict systems occupy the central position between the catalytic effector and ABC ATPases of the systems. MCs are defined by distinctive patterns of conserved charged residues. As some MCs are HTH domains, they are predicted to function akin to kleisins as DNA-binding partners for the ABC ATPases, assisting in recognition and responding to invasive elements such as DNA viruses. 133 matched cddid_all.tbl CDD pfam20291 pfam20291 466441 MC5 ABC-three component (ABC-3C) system Middle Component 5. Middle Components (MCs) of the ABC-3C biological conflict systems occupy the central position between the catalytic effector and ABC ATPases of the systems. MCs are defined by distinctive patterns of conserved charged residues. As some MCs are HTH domains, they are predicted to function akin to kleisins as DNA-binding partners for the ABC ATPases, assisting in recognition and responding to invasive elements such as DNA viruses. 167 matched cddid_all.tbl CDD pfam20292 pfam20292 466442 MC7 ABC-three component (ABC-3C) system Middle Component 7. Middle Components (MCs) of the ABC-3C biological conflict systems occupy the central position between the catalytic effector and ABC ATPases of the systems. MCs are defined by distinctive patterns of conserved charged residues. As some MCs are HTH domains, they are predicted to function akin to kleisins as DNA-binding partners for the ABC ATPases, assisting in recognition and responding to invasive elements such as DNA viruses. MC7 is a MC unifiable with the HTH fold. 69 matched cddid_all.tbl CDD pfam20293 pfam20293 466443 MC6 ABC-three component (ABC-3C) system Middle Component 6. Middle Components (MCs) of the ABC-3C biological conflict systems occupy the central position between the catalytic effector and ABC ATPases of the systems. MCs are defined by distinctive patterns of conserved charged residues. As some MCs are HTH domains, they are predicted to function akin to kleisins as DNA-binding partners for the ABC ATPases, assisting in recognition and responding to invasive elements such as DNA viruses. MC6 is a MC unifiable with the HTH fold. 76 matched cddid_all.tbl CDD pfam20294 pfam20294 466444 KMPT-N KTSC and Metallopeptidase N-terminal fusion domain. Uncharacterized alpha/beta domain N-terminally fused to diverse Metallopeptidase (MPTase) and the lysyl tRNA synthetase KTSC RNA-binding domain protein. Currently observed in only the jumbo phages. 66 matched cddid_all.tbl CDD pfam20295 pfam20295 466445 MC8 ABC-three component (ABC-3C) system Middle Component 8. Middle Components (MCs) of the ABC-3C biological conflict systems occupy the central position between the catalytic effector and ABC ATPases of the systems. MCs are defined by distinctive patterns of conserved charged residues. As some MCs are HTH domains, they are predicted to function akin to kleisins as DNA-binding partners for the ABC ATPases, assisting in recognition and responding to invasive elements such as DNA viruses. MC8 is a MC unifiable with the HTH fold. 48 matched cddid_all.tbl CDD pfam20296 pfam20296 466446 MTaX1 Methylase-associated X1. This is a globular domain found across several restriction- modification systems. 110 matched cddid_all.tbl CDD pfam20297 pfam20297 466447 MSSS MutS2 and Smr-associated SH3 domain. This is a SH3-like domain associated with the MutS-like ABC ATPase and Smr domains. It has been predicted to play a role in lesion recognition or alternatively in mediating contacts with RNA primers or misincorporated ribonucleotides during DNA repair or interacting with the ribosome at the intersection between DNA repair and ribosome rescue. 42 matched cddid_all.tbl CDD pfam20298 pfam20298 466448 E2-ntca Prokaryotic E2 domain. This is an E2 domain observed in certain prokaryotic Ubiquitin systems found as secondary effectors in nucleotide-activated effector conflict systems. 109 matched cddid_all.tbl CDD pfam20299 pfam20299 466449 NARF Nucleotidyltransferase-Associated Rossmannoid Fold. This family represents an inactive member of the Receiver superfamily of the Rossmonnoid fold, predicted to function as a sensor domain in certain nucleotide-activated effector conflict systems. It is thought to bind nucleotides synthesized by both the SMODS domain and the CRISPR polymerase (Cpol) domain of the Cas10-like proteins, depending on genome context. N-terminal transmembrane segments are observed, suggesting that nucleotide binding initiates a membrane-perforating and cell-suicide response in conflict. 112 matched cddid_all.tbl CDD pfam20300 pfam20300 466450 prok_STING Prokaryotic STING domain. This is a STING sensor domain found in certain prokaryotic nucleotide-activated effector conflict systems. Binding to a nucleotide activates fused effector proteins in conflict response against invasive elements. Certain versions in prokaryotes may additionally regulate bacterial ion channels. Transferred to eukaryotes on multiple occasions, representatives observed are in animal-choanoflagellate, haptophyte/stramenopile, and fungal lineages. 137 matched cddid_all.tbl CDD pfam20301 pfam20301 466451 pNTSase1 Predicted novel nucleotide synthetase. Conserved genome contexts in NAD+-derived nucleotide-activated effector systems predict a function as a previously-uncharacterized nucleotide synthetase. 163 matched cddid_all.tbl CDD pfam20302 pfam20302 466452 HisK-N-like HisK-N-like globin domain of the ASK signalosome. Predicted non-heme-binding version of the Globin domain identified in ASK signalosome. Displays strongest affinities to the HisK-N family of sensor domains, which inhibit histidine kinase activation required for sporulation in bacteria of the firmicutes lineage. This globin domain is predicted to represent an independent sensory element recognizing a fatty acid or a related membrane-derived molecule which regulates activity of the ASK signalosome in apoptosis. 133 matched cddid_all.tbl CDD pfam20303 pfam20303 466453 YLATT YEATS-Like-Associating Three TM. This is a conserved, three transmembrane helix-containing domain found fused to certain prokaryotic YEATS domain. Genome context displacement patterns predict an effector role for this domain, as a membrane-perforating, cell-suicide response-enacting domain. 107 matched cddid_all.tbl CDD pfam20304 pfam20304 466454 Sp-CxC Small protein from certain CxC ATPase-based DNA modification systems. Analogous to an antitoxin, this small protein potentially acts as a negative regulatory component that might sense the presence of invaders by acting as a binding factor or substrate for invader-encoded enzymes like viral peptidases in certain CxC ABC ATPase-based DNA modification systems. 63 matched cddid_all.tbl CDD pfam20305 pfam20305 466455 pYEATS prokaryotic YEATS domain. This entry represents a prokaryotic YEATS domain. pYEATS is fused to diverse effector domains, suggesting that the binding to a ligand activates an effector-based response against an invasive threat. It has been predicted to specifically recognize invader-induced modifications of macromolecules by acyl moieties (e.g. phage-encoded acylations of surface polysaccharides) to unleash the fused effectors through a conformational change. 73 matched cddid_all.tbl CDD pfam20306 pfam20306 466456 Sp-DndD Small protein found in certain Dnd DNA modification systems. Analogous to an antitoxin, this small protein potentially acts as a negative regulatory component that might sense the presence of invaders by acting as a binding factor or substrate for invader-encoded enzymes like viral peptidases in certain Dnd systems. 51 matched cddid_all.tbl CDD pfam20307 pfam20307 466457 divDNAB Divergent DnaB-like ATPase. This domain is found in a divergent DnaB-like helicase of the RecA-ATP-synthetase superfamily of P-loop NTPases found in phages, which is characterized by a modified ATP-binding Walker B motif. 356 matched cddid_all.tbl CDD pfam20308 pfam20308 466458 TPR-S Tetratricopeptide Repeats-Sensor. This entry represents a sensor domain consisting of 7 TPR repeats forming a tightly-wound solenoid structure harbouring a deep central pocket. The TPR-S binding pocket is lined with several conserved aromatic and polar residues predicted to bind a NAD+-derived nucleotide in prokaryotic NAD+-derived nucleotide-activated effector conflict systems. It has been acquired at the base of the choanoflagellate-animal lineage as a core component of the ASK signalosome. 105 matched cddid_all.tbl CDD pfam20309 pfam20309 466459 DRHyd-ASK Deoxyribohydrolase (DRHyd) domain of the ASK signalosome. This is an uncharacterized DRHyd domain observed in ASK signalosome proteins ASK1, ASK2, and ASK3. Potentially generates nucleotide-derived signal recognized by the TPR-S domain found in the same proteins. 36 matched cddid_all.tbl CDD pfam20310 pfam20310 466460 HTH_Tnp_2 Transposon related HTH domain protein. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 103 and 265 amino acids in length. This protein contains a helix-turn-helix motif that is likely to be DNA-binding. 131 matched cddid_all.tbl CDD pfam20311 pfam20311 466461 DUF6607 Family of unknown function (DUF6607). This family of proteins is functionally uncharacterized. This family of proteins is found in primarily found in Bacteroidetes and proteobacteria. Proteins in this family are typically between 300 and 331 amino acids in length. 296 matched cddid_all.tbl CDD pfam20312 pfam20312 466462 DUF6608 Family of unknown function (DUF6608). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. 131 matched cddid_all.tbl CDD pfam20313 pfam20313 466463 DUF6609 Family of unknown function (DUF6609). This family of integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 180 amino acids in length. 176 matched cddid_all.tbl CDD pfam20314 pfam20314 466464 DUF6610 Family of unknown function (DUF6610). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea and viruses. Proteins in this family are typically between 304 and 335 amino acids in length. 198 matched cddid_all.tbl CDD pfam20315 pfam20315 466465 DUF6611 Family of unknown function (DUF6611). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 165 and 185 amino acids in length. 168 matched cddid_all.tbl CDD pfam20316 pfam20316 466466 DUF6612 Family of unknown function (DUF6612). This family of proteins is functionally uncharacterized. However, based on similarity to other families it is likely to be involved in lipoprotein biosynthesis. This family of proteins is found in bacteria. Proteins in this family are typically between 263 and 293 amino acids in length. 237 matched cddid_all.tbl CDD pfam20317 pfam20317 466467 HTH_60 Helix-turn-helix domain. This family of proteins contains a likely DNA-binding helix-turn-helix but is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 128 and 151 amino acids in length. 140 matched cddid_all.tbl CDD pfam20318 pfam20318 466468 DUF6613 Family of unknown function (DUF6613). This family of proteins is functionally uncharacterized. However, the contain an N-terminal pfam07963 suggesting these may be pilin proteins. This family of proteins is found in bacteria. Proteins in this family are typically between 203 and 237 amino acids in length. 191 matched cddid_all.tbl CDD pfam20319 pfam20319 466469 DUF6614 Family of unknown function (DUF6614). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. 116 matched cddid_all.tbl CDD pfam20320 pfam20320 466470 DUF6615 Family of unknown function (DUF6615). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 301 and 317 amino acids in length. These proteins contain a conserved sequence motif FREE that may be functionally important. 289 matched cddid_all.tbl CDD pfam20321 pfam20321 466471 DUF6616 Family of unknown function (DUF6616). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 120 amino acids in length. 111 matched cddid_all.tbl CDD pfam20322 pfam20322 466472 DUF6617 Family of unknown function (DUF6617). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 315 and 341 amino acids in length. 316 matched cddid_all.tbl CDD pfam20323 pfam20323 466473 DUF6618 Family of unknown function (DUF6618). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 98 and 116 amino acids in length. 92 matched cddid_all.tbl CDD pfam20324 pfam20324 466474 DUF6619 Family of unknown function (DUF6619). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 100 amino acids in length. 100 matched cddid_all.tbl CDD pfam20325 pfam20325 466475 DUF6620 Family of unknown function (DUF6620). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 188 and 366 amino acids in length. 450 matched cddid_all.tbl CDD pfam20326 pfam20326 466476 DUF6621 Family of unknown function (DUF6621). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 200 amino acids in length. 190 matched cddid_all.tbl CDD pfam20327 pfam20327 466477 DUF6622 Family of unknown function (DUF6622). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are approximately 170 amino acids in length. 183 matched cddid_all.tbl CDD pfam20328 pfam20328 466478 DUF6623 Family of unknown function (DUF6623). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 147 and 199 amino acids in length. 149 matched cddid_all.tbl CDD pfam20329 pfam20329 466479 DUF6624 Family of unknown function (DUF6624). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 188 and 316 amino acids in length. 173 matched cddid_all.tbl CDD pfam20330 pfam20330 466480 DUF6625 Family of unknown function (DUF6625). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 292 and 338 amino acids in length. 267 matched cddid_all.tbl CDD pfam20331 pfam20331 466481 DUF6626 Family of unknown function (DUF6626). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. 96 matched cddid_all.tbl CDD pfam20332 pfam20332 466482 DUF6627 Family of unknown function (DUF6627). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. 125 matched cddid_all.tbl CDD pfam20333 pfam20333 466483 DUF6628 Family of unknown function (DUF6628). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. 137 matched cddid_all.tbl CDD pfam20334 pfam20334 466484 DUF6629 Family of unknown function (DUF6629). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 212 and 228 amino acids in length. 209 matched cddid_all.tbl CDD pfam20335 pfam20335 466485 DUF6630 Family of unknown function (DUF6630). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 168 and 270 amino acids in length. 172 matched cddid_all.tbl CDD pfam20336 pfam20336 466486 DUF6631 Family of unknown function (DUF6631). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 132 and 168 amino acids in length. 160 matched cddid_all.tbl CDD pfam20337 pfam20337 466487 DUF6632 Family of unknown function (DUF6632). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 127 and 139 amino acids in length. 136 matched cddid_all.tbl CDD pfam20338 pfam20338 466488 DUF6633 Family of unknown function (DUF6633). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 148 and 213 amino acids in length. 105 matched cddid_all.tbl CDD pfam20339 pfam20339 466489 DUF6634 Family of unknown function (DUF6634). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 106 and 169 amino acids in length. 157 matched cddid_all.tbl CDD pfam20340 pfam20340 466490 DUF6635 Family of unknown function (DUF6635). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 273 and 325 amino acids in length. 273 matched cddid_all.tbl CDD pfam20341 pfam20341 466491 DUF6636 Family of unknown function (DUF6636). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 136 and 200 amino acids in length. 140 matched cddid_all.tbl CDD pfam20342 pfam20342 466492 DUF6637 Family of unknown function (DUF6637). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. 103 matched cddid_all.tbl CDD pfam20343 pfam20343 466493 DUF6638 Family of unknown function (DUF6638). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 412 and 454 amino acids in length. 439 matched cddid_all.tbl CDD pfam20344 pfam20344 466494 DUF6639 Family of unknown function (DUF6639). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 218 and 231 amino acids in length. 231 matched cddid_all.tbl CDD pfam20345 pfam20345 466495 DUF6640 Family of unknown function (DUF6640). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 133 and 156 amino acids in length. 129 matched cddid_all.tbl CDD pfam20346 pfam20346 466496 DUF6641 Family of unknown function (DUF6641). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 150 amino acids in length. 143 matched cddid_all.tbl CDD pfam20347 pfam20347 466497 DUF6642 Family of unknown function (DUF6642). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 186 and 200 amino acids in length. 188 matched cddid_all.tbl CDD pfam20348 pfam20348 466498 DUF6643 Family of unknown function (DUF6643). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 144 and 171 amino acids in length. 150 matched cddid_all.tbl CDD pfam20349 pfam20349 466499 DUF6644 Family of unknown function (DUF6644). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 156 and 167 amino acids in length. 154 matched cddid_all.tbl CDD pfam20350 pfam20350 466500 DUF6645 Family of unknown function (DUF6645). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and viruses, and is approximately 120 amino acids in length. The family is found in association with pfam03629, pfam08410. 119 matched cddid_all.tbl CDD pfam20351 pfam20351 466501 DUF6646 Family of unknown function (DUF6646). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 170 amino acids in length. 158 matched cddid_all.tbl CDD pfam20352 pfam20352 466502 DUF6647 Family of unknown function (DUF6647). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 158 and 180 amino acids in length. 175 matched cddid_all.tbl CDD pfam20353 pfam20353 466503 DUF6648 Family of unknown function (DUF6648). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 180 amino acids in length. 182 matched cddid_all.tbl CDD pfam20354 pfam20354 466504 DUF6649 Family of unknown function (DUF6649). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically between 197 and 268 amino acids in length. 227 matched cddid_all.tbl CDD pfam20355 pfam20355 466505 DUF6650 Family of unknown function (DUF6650). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 150 and 175 amino acids in length. 150 matched cddid_all.tbl CDD pfam20356 pfam20356 466506 DUF6651 Family of unknown function (DUF6651). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, eukaryotes and viruses, and is approximately 110 amino acids in length. 113 matched cddid_all.tbl CDD pfam20357 pfam20357 466507 DUF6652 Family of unknown function (DUF6652). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 189 and 210 amino acids in length. 183 matched cddid_all.tbl CDD pfam20358 pfam20358 466508 DUF6653 Family of unknown function (DUF6653). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 149 and 172 amino acids in length. 170 matched cddid_all.tbl CDD pfam20360 pfam20360 466509 DUF6655 Family of unknown function (DUF6655). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 205 and 301 amino acids in length. 259 matched cddid_all.tbl CDD pfam20361 pfam20361 466510 DUF6656 Family of unknown function (DUF6656). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 200 amino acids in length. 182 matched cddid_all.tbl CDD pfam20362 pfam20362 466511 DUF6657 Family of unknown function (DUF6657). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 200 amino acids in length. 141 matched cddid_all.tbl CDD pfam20363 pfam20363 466512 DUF6658 Family of unknown function (DUF6658). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 177 and 198 amino acids in length. 178 matched cddid_all.tbl CDD pfam20364 pfam20364 466513 DUF6659 Family of unknown function (DUF6659). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 121 and 132 amino acids in length. 131 matched cddid_all.tbl CDD pfam20365 pfam20365 466514 DUF6660 Family of unknown function (DUF6660). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are approximately 110 amino acids in length. 102 matched cddid_all.tbl CDD pfam20366 pfam20366 466515 DUF6661 Family of unknown function (DUF6661). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 200 amino acids in length. 174 matched cddid_all.tbl CDD pfam20367 pfam20367 466516 DUF6662 Family of unknown function (DUF6662). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 296 and 311 amino acids in length. 308 matched cddid_all.tbl CDD pfam20368 pfam20368 466517 DUF6663 Family of unknown function (DUF6663). This family of proteins is functionally uncharacterized. This family of proteins is found in archaea. Proteins in this family are typically between 194 and 253 amino acids in length. 243 matched cddid_all.tbl CDD pfam20369 pfam20369 466518 DUF6664 Family of unknown function (DUF6664). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. 107 matched cddid_all.tbl CDD pfam20370 pfam20370 466519 DUF6665 Family of unknown function (DUF6665). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. 106 matched cddid_all.tbl CDD pfam20371 pfam20371 466520 DUF6666 Family of unknown function (DUF6666). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 357 and 490 amino acids in length. 340 matched cddid_all.tbl CDD pfam20372 pfam20372 466521 DUF6667 Family of unknown function (DUF6667). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 358 and 460 amino acids in length. 252 matched cddid_all.tbl CDD pfam20373 pfam20373 466522 DUF6668 Family of unknown function (DUF6668). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 168 and 208 amino acids in length. 130 matched cddid_all.tbl CDD pfam20374 pfam20374 466523 DUF6669 Family of unknown function (DUF6669). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 150 and 161 amino acids in length. 156 matched cddid_all.tbl CDD pfam20375 pfam20375 466524 DUF6670 Family of unknown function (DUF6670). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 345 and 372 amino acids in length. 294 matched cddid_all.tbl CDD pfam20376 pfam20376 466525 DUF6671 Domain of unknown function (DUF6671). This family of proteins is functionally uncharacterized. It belongs to the PD-(D/E)XK nuclease superfamily suggesting it has a nuclease function. This family of proteins is found in bacteria. Proteins in this family are typically between 278 and 290 amino acids in length. 217 matched cddid_all.tbl CDD pfam20377 pfam20377 466526 DUF6672 Family of unknown function (DUF6672). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 134 and 164 amino acids in length. This family contains an N-terminal predicted transmembrane helix and a negatively charged C-terminus. 153 matched cddid_all.tbl CDD pfam20378 pfam20378 466527 DUF6673 Family of unknown function (DUF6673). This presumed domain is functionally uncharacterized. This domain family is found in bacteria and viruses, and is typically between 47 and 65 amino acids in length. 114 matched cddid_all.tbl CDD pfam20379 pfam20379 466528 DUF6674 Family of unknown function (DUF6674). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 259 and 297 amino acids in length. There are two conserved sequence motifs: AMKIP and SMN. 251 matched cddid_all.tbl CDD pfam20380 pfam20380 466529 DUF6675 Family of unknown function (DUF6675). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 242 and 267 amino acids in length. 254 matched cddid_all.tbl CDD pfam20381 pfam20381 466530 DUF6676 Family of unknown function (DUF6676). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 172 and 197 amino acids in length. 157 matched cddid_all.tbl CDD pfam20382 pfam20382 466531 DUF6677 Family of unknown function (DUF6677). This family of integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 135 and 210 amino acids in length. 117 matched cddid_all.tbl CDD pfam20383 pfam20383 466532 DUF6678 Family of unknown function (DUF6678). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 112 and 148 amino acids in length. 122 matched cddid_all.tbl CDD pfam20384 pfam20384 466533 DUF6679 Family of unknown function (DUF6679). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. There is a conserved DQQRWIE sequence motif. 103 matched cddid_all.tbl CDD pfam20385 pfam20385 466534 DUF6680 Family of unknown function (DUF6680). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 120 amino acids in length. 170 matched cddid_all.tbl CDD pfam20386 pfam20386 466535 DUF6681 Family of unknown function (DUF6681). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 258 and 288 amino acids in length. 267 matched cddid_all.tbl CDD pfam20387 pfam20387 466536 DUF6682 Family of unknown function (DUF6682). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 216 and 235 amino acids in length. 224 matched cddid_all.tbl CDD pfam20388 pfam20388 466537 DUF6683 Family of unknown function (DUF6683). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 228 and 260 amino acids in length. 237 matched cddid_all.tbl CDD pfam20389 pfam20389 466538 DUF6684 Family of unknown function (DUF6684). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 77 and 127 amino acids in length. 79 matched cddid_all.tbl CDD pfam20390 pfam20390 466539 DUF6685 Family of unknown function (DUF6685). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 188 and 325 amino acids in length. 206 matched cddid_all.tbl CDD pfam20391 pfam20391 466540 DUF6686 Family of unknown function (DUF6686). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 102 and 118 amino acids in length. 57 matched cddid_all.tbl CDD pfam20392 pfam20392 466541 DUF6687 Family of unknown function (DUF6687). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 342 and 363 amino acids in length. 339 matched cddid_all.tbl CDD pfam20393 pfam20393 466542 Pro_CA_2 Putative carbonic anhydrase. This family of proteins are likely to be prokaryotic carbonic anhydrase enzymes related to pfam00484.. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 130 amino acids in length. 125 matched cddid_all.tbl CDD pfam20394 pfam20394 466543 DUF6688 Family of unknown function (DUF6688). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 360 and 412 amino acids in length. 367 matched cddid_all.tbl CDD pfam20395 pfam20395 466544 CTD3 C-terminal domain 3 of the ABC-three component (ABC-3C) systems. C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serves as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector. 162 matched cddid_all.tbl CDD pfam20396 pfam20396 466545 DUF6689 Family of unknown function (DUF6689). This family of proteins is functionally uncharacterized. This family of proteins is found in gamma proteobacteria. Proteins in this family are typically between 273 and 287 amino acids in length. 275 matched cddid_all.tbl CDD pfam20397 pfam20397 466546 DUF6690 Family of unknown function (DUF6690). This presumed domain is functionally uncharacterized. This domain family is found in Planctomycete bacteria, and is approximately 170 amino acids in length. 244 matched cddid_all.tbl CDD pfam20398 pfam20398 466547 DUF6691 Family of unknown function (DUF6691). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 137 and 165 amino acids in length. Proteins in this family are related to the thiosulfate transporter, but appear to be about half the length. Suggesting this family may operate as a dimer to make a functional transporter. 142 matched cddid_all.tbl CDD pfam20399 pfam20399 466548 PH_20 PH domain. This entry represents a PH domain found in a variety of fungal proteins. 84 matched cddid_all.tbl CDD pfam20400 pfam20400 466549 BAR_4 BAR-like domain. This entry represents a BAR-like domain found in a variety of fungal proteins. 192 matched cddid_all.tbl CDD pfam20401 pfam20401 466550 Rhomboid_2 Rhomboid-like protein. This family of proteins is related to the Rhomboid proteins and thus is likely to be an intramembrane proteomes. This family of proteins is found primarily in actinobacteria. Proteins in this family are typically between 221 and 283 amino acids in length. 194 matched cddid_all.tbl CDD pfam20402 pfam20402 466551 DUF6692 Domain of unknown function (DUF6692). This family of proteins is functionally uncharacterized. This family of proteins is found in Alphaproteobacteria. Proteins in this family are typically between 161 and 194 amino acids in length. This family is related to pfam03713 and is therefore part of the ferritin superfamily. 162 matched cddid_all.tbl CDD pfam20403 pfam20403 466552 DUF6693 Family of unknown function (DUF6693). This family of small integral membrane proteins is functionally uncharacterized. This family may be distantly related to pfam05987. This family of proteins is found in proteobacteria. Proteins in this family are typically between 104 and 121 amino acids in length. 109 matched cddid_all.tbl CDD pfam20404 pfam20404 466553 DUF6694 Family of unknown function (DUF6694). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 109 and 273 amino acids in length. 106 matched cddid_all.tbl CDD pfam20405 pfam20405 466554 DUF6695 Family of unknown function (DUF6695). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 329 and 354 amino acids in length. 325 matched cddid_all.tbl CDD pfam20406 pfam20406 466555 SAM_KSR1_N Kinase suppressor RAS 1 N-terminal helical hairpin. 54 matched cddid_all.tbl CDD pfam20407 pfam20407 466556 DUF1583_N Domain of unknown function (DUF1583_N). Most of these Rhodopirellula baltica hypothetical proteins also match pfam07619. 150 matched cddid_all.tbl CDD pfam20408 pfam20408 466557 Abhydrolase_11 Alpha/beta hydrolase domain. This entry represents a protein that belongs to the alpha/beta hydrolase superfamily. Although proteins in this family are uncharacterized they are likely to have an enzymatic activity. 193 matched cddid_all.tbl CDD pfam20409 pfam20409 466558 SnoaL_5 SnoaL-like domain. This family contains a large number of proteins that share the SnoaL fold. 118 matched cddid_all.tbl CDD pfam20410 pfam20410 466559 DUF6696 Domain of unknown function (DUF6696). This entry represents an uncharacterized domain that is found associated with pfam01471, but also a range of lipase and glycosyl hydrolase enzyme domains This suggests this domain may be a regulatory domain. 101 matched cddid_all.tbl CDD pfam20411 pfam20411 466560 DUF6697 Domain of unknown function (DUF6697). This entry represents a fungal domain of unknown function. 180 matched cddid_all.tbl CDD pfam20412 pfam20412 466561 RALGAPB_N RALGAPB N-terminal domain. This putative domain is found at the N-terminus of the Ral GTPase-activating protein beta subunit. The function of this region is not known. 125 matched cddid_all.tbl CDD pfam20413 pfam20413 466562 Kiaa1109_N Kiaa1109 N-terminal region. This entry represents a long uncharacterized region found at the N-terminus of a group of very long eukaryotic proteins. It is found in the human protein Kiaa1109. 976 matched cddid_all.tbl CDD pfam20414 pfam20414 466563 DUF6698 Family of unknown function (DUF6698). This entry represents an uncharacterized family of fungal proteins. 206 matched cddid_all.tbl CDD pfam20415 pfam20415 466564 DUF6699 Family of unknown function (DUF6699). This entry represents a family of uncharacterized fungal proteins 131 matched cddid_all.tbl CDD pfam20416 pfam20416 466565 DUF6700 Domain of unknown function (DUF6700). This putative domain is found in the UTP20 protein which associated with the U3 snRNA. 221 matched cddid_all.tbl CDD pfam20417 pfam20417 466566 Gemin6_C Gemin6 C-terminal domain. This entry corresponds to a putative domain found at the C-terminus of several mammalian Gemin6 proteins. This domain appears to be distantly related to pfam09793 suggesting it may have an RNA-binding function. The exact function of Gemin6 is unknown but it has been found to form part of the pfam06003 complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles. 80 matched cddid_all.tbl CDD pfam20418 pfam20418 466567 Herpes_gE_N Alphaherpesvirus glycoprotein E N-terminal. Glycoprotein E (gE) of Alphaherpesvirus forms a complex with glycoprotein I (gI) (pfam01688), functioning as an immunoglobulin G (IgG) Fc binding protein. gE is involved in virus spread but is not essential for propagation. This entry represents the N-terminal domain of gE, which interacts with gI. 127 matched cddid_all.tbl CDD pfam20419 pfam20419 466568 DUF6701 Family of unknown function (DUF6701). This entry represents an uncharacterized region found in a wide range of bacterial cell surface proteins. 575 matched cddid_all.tbl CDD pfam20420 pfam20420 466569 DUF6702 Domain of unknown function (DUF6702). This entry represents an uncharacterized family of proteins. Some members of the family are annotated as Peptidase E, but the does not appear to be any evidence to support that assertion. 141 matched cddid_all.tbl CDD pfam20421 pfam20421 466570 DHR-2_Lobe_C DHR-2, Lobe C. DOCK (dedicator of cytokinesis) proteins are guanine nucleotide exchange factors (GEFs) that activate some small GTPases, such as Rac or Cdc42, by exchanging bound GDP for free GTP to control cell migration, morphogenesis, and phagocytosis. These proteins share a DOCK-type C2 domain (also termed the DOCK-homology region (DHR)-1) at the N-terminal, and the DHR-2 domain (also termed the DOCKER domain) at the C-terminal. DHR-2 is the GEF catalytic domain organized into three lobes A, B and C, with the Rho-family binding site and catalytic centre generated entirely from lobes B and C. This entry represents Lobe C which form an antiparallel four alpha-helical bundle and contains a loop known as the nucleotide sensor characterized by a conserved valine residue essential for catalytic activity. 103 matched cddid_all.tbl CDD pfam20422 pfam20422 466571 DHR-2_Lobe_B DHR-2, Lobe B. DOCK (dedicator of cytokinesis) proteins are guanine nucleotide exchange factors (GEFs) that activate some small GTPases, such as Rac or Cdc42, by exchanging bound GDP for free GTP to control cell migration, morphogenesis, and phagocytosis. These proteins share a DOCK-type C2 domain (also termed the DOCK-homology region (DHR)-1) at the N-terminal, and the DHR-2 domain (also termed the DOCKER domain) at the C-terminal. DHR-2 is the GEF catalytic domain organized into three lobes A, B and C, with the Rho-family binding site and catalytic centre generated entirely from lobes B and C. This entry represents Lobe B which adopts an unusual architecture of two antiparallel beta sheets disposed in a loosely packed orthogonal arrangement. This lobe changes its position relative to lobe C and the bound GTPase, which suggests that lobe B distinguishes between the switch 1 conformations of Rac1 and Cdc42. 77 matched cddid_all.tbl CDD pfam20423 pfam20423 466572 AceK_regulatory Isocitrate dehydrogenase kinase/phosphatase (AceK), regulatory domain. This is the N-terminal regulatory domain of bacterial isocitrate dehydrogenase kinase/phosphatase (AceK) proteins (EC:2.7.1.116). It has an alpha-helical fold, with two long, parallel alpha-helices that form a large hairpin structure followed by two short, parallel alpha-helices forming a small hairpin segment. This domain is linked to the C-terminal kinase domain by a short (27 residues) alpha-helix. 302 matched cddid_all.tbl CDD pfam20424 pfam20424 466573 PilZN3 PilZN3 domain. This is a noncanonical PilZ domain found in spirochaetes, such as B. burgdorferi BB0733 and Treponema denticola TDE0214 proteins. They have a PilZN3-PilZ domain architecture and affect the motility and virulence of these organizms. Secondary structure predictions suggest that this domain retains the C-terminal alpha-helix of PilZ and three additional alpha helices. 135 matched cddid_all.tbl CDD pfam20425 pfam20425 466574 Neurobeachin Neurobeachin alpha solenoid region. This region is found in any neurobeachin homologs. It forms an extended alpha solenoid structure. 423 matched cddid_all.tbl CDD pfam20426 pfam20426 466575 NBCH_WD40 Neurobeachin beta propeller domain. This entry represents the beta propeller domain found at the C-terminus of neurobeachin-like proteins. 350 matched cddid_all.tbl CDD pfam20427 pfam20427 466576 NRP1_C Nuclear speckle splicing regulatory protein 1, RS-like domain. This domain found at the C-terminal of Nuclear speckle splicing regulatory protein 1 (NRP1, also known as Nuclear speckle-related protein 70 and Coiled-coil domain-containing protein 55). This is the RS-like domain, that resembles the arginine/serine-rich (RS) domain in other SR proteins, interacts with two SR proteins and with target mRNA, being essential for NRP1 activity. NRP1 is a RNA-binding protein that mediates pre-mRNA alternative splicing regulation. 174 matched cddid_all.tbl CDD pfam20428 pfam20428 466577 Sey1_3HB Sey1 three-helix bundle domain. This is the three-helix bundle (3HB) domain found at the C-terminal of Sey1 from yeast and RHD3 from Arabidopsis, GTP-binding proteins involved in homotypic membrane fusion of the endoplasmic reticulum. This is a stalk-like domain composed of four 3HBs that interacts with its own GTPase domain and that of a neighbouring molecule, to undergo major conformational changes during the GTP cycle to drive membrane fusion. 419 matched cddid_all.tbl CDD pfam20429 pfam20429 466578 Tab2-like_C RNA-binding protein Tab2/Atab2, C terminal. This is the C-terminal domain of Tab2 from plant and cyanobacteria. Tab2 was first identified in Chlamydomonas reinhardtii as a RNA binding protein required for translation of the chloroplast PsaB photosystem I subunit. Later, the Tab2 homolog from Arabidopsis (Atab2) was found involved in the signalling pathway of light-controlled synthesis of photosystem proteins during early plant development, presumably functioning as an activator of translation with targets at PSI and PSII. Directed mutagenesis experiments carried out in Chlamydomonas reinhardtii, Tab2, indicated the importance of a highly conserved C-terminal tripeptide WLL for normal psaB translation. 211 matched cddid_all.tbl CDD pfam20430 pfam20430 466579 Eplus_motif E+ motif. This is the E+ motif found in some plant pentatricopeptide repeat (PPR) proteins which contain a C-terminal DYW deaminase domain. The DYW domain is required for RNA editing, a process that deaminates specific cytidines to uridines. This motif, together with the E motif, precedes the DYW domain and, although their role is not clear, they are essential in th RNA editing reaction. The E/E+ motifs may contain two degenerate PPR motifs that could be involved in RNA or protein binding. 28 matched cddid_all.tbl CDD pfam20431 pfam20431 466580 E_motif E motif. This entry represents the E motif found in plant pentatricopeptide repeat (PPR) proteins which contain a DYW deaminase domain. The DYW domain is required for RNA editing, a process that deaminates specific cytidines to uridines. This motif, together with the E+ motif, precedes the DYW domain and, although their role is not clear, they are essential in the RNA editing reaction. The E/E+ motifs may contain two degenerate PPR motifs that could be involved in RNA or protein binding. 63 matched cddid_all.tbl CDD pfam20432 pfam20432 466581 Xre-like-HTH Antitoxin Xre-like helix-turn-helix domain. This entry represents the N-terminal domain of the antitoxin component Xre of a type II toxin-antitoxin (TA) system, which is the helix-turn-helix (HTH) DNA binding domain, structurally similar to the Cro repressor, therefore, also referred to as HTH/Cro-like DNA-binding domain. This domain is also found in other antitoxin components, associated with a C-terminal toxin-binding domain pfam09722. 57 matched cddid_all.tbl CDD pfam20433 pfam20433 466582 PKAT_KLD PKAT, KLD domain. This is the Kringle-like domain (KLD) found in Melanocyte protein PMEL, Transmembrane glycoprotein NMB (GPNMB) and TMEM130, which is downstream the PKD domain. It contains six highly conserved cysteine residues that form the disulphide bonds of mature PMEL dimers. (Chrystal et. al., Molecules 2021, 26(12), 3529; https://doi.org/10.3390/molecules26123529). This domain is perfectly conserved in PMEL and GPNMB which suggests that GPNMB also forms dimers. PMEL and GPNMB, together with TMEM130 (its most ancient paralogue), have a conserved domain architecture and have been recently described as the PKAT (PKD- and KLD-Associated Transmembrane) protein family (Chrystal et. al., Molecules 2021, 26(12), 3529; https://doi.org/10.3390/molecules26123529). PMEL and GPNMB share overlapping phenotypes and disease associations, such as melanin-based pigmentation, cancer, neurodegenerative disease and glaucoma. 51 matched cddid_all.tbl CDD pfam20434 pfam20434 466583 BD-FAE BD-FAE. This family represents a novel bifunctional feruloyl and acetyl xylan esterase (BD-FAE, previously known as bifunctional carbohydrate esterase (CE)), which is active on complex natural xylans and was identified as the basis of a monophyletic clade gathering all homologs identified in PULs (polysaccharide utilization loci) predicted to act on xylan. It adopts an alpha-beta-hydrolase fold with the catalytic triad Ser-Asp-His. This new family of proteins is a new candidate for biomass processing due to its capacity to remove ferulic acid and acetic acid from natural corn and birchwood xylan substrates. 215 matched cddid_all.tbl CDD pfam20435 pfam20435 466584 ASY3-like Meiosis-specific protein ASY3-like. This entry represents a group of plant meiosis-specific proteins, such as AtASY3 from Arabidopsis and PAIR3 from rice. They are coiled-coil domain proteins required for normal meiosis. PAIR3 is an axial element and part of the synaptonemal complex (SC) that forms between homologous chromosomes during meiosis. Members of this family are homologs of SCYP2 from vertebrates and fungal Red1/Rec10. 793 matched cddid_all.tbl CDD pfam20436 pfam20436 466585 LonB_AAA-LID Archaeal LonB, AAA+ ATPase LID domain. The species-specific Lon-insertion domain (LID) is characteriztic of Lon proteases (also known as endopeptidase La) and is fused to the AAA+ module. Bacterial and eukaryotic Lons (LonA) have a LID at the N-terminal of AAA+ module; in archaeal Lons (LonB) the LID, represented in this entry, is inserted within the AAA+ module in a series of transmembrane segments known as the membrane-anchoring region (MA). In the Lon-like protease LonC, which does not have ATPase activity, the LID is also within the AAA-like module similar to LonBs; in this case, it is predicted to contain coiled-coil regions rather than transmembrane segments. 65 matched cddid_all.tbl CDD pfam20437 pfam20437 466586 LonC_helical Lon-like LonC helical domain. This domain represents the helical domain found in the Lon-like LonC protease from Meiothermus taiwanensis, a Lon-like protease with no ATPase activity. 34 matched cddid_all.tbl CDD pfam20438 pfam20438 466587 SpoIVA_middle Stage IV sporulation protein A, middle domain. This is the structural middle domain of Stage IV sporulation protein A (SpoIVA) which follows the ATPase domain and the predicted secondary structure suggests that it is composed of two symmetrical units containing alpha-helices and beta-strands. SpoIVA acts in the mother cell compartment and plays a role in spore coat morphogenesis. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. 179 matched cddid_all.tbl CDD pfam20439 pfam20439 466588 SpoIVA_C Sporulation stage IV protein A, C-terminal. SpoIVA (Sporulation stage IV protein A) acts in the mother cell compartment and plays a role in spore coat morphogenesis. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. This entry represents the C-terminal domain of SpoIVA, which plays a key role in targeting the protein to the outer forespore membrane, in particular the five hydrophobic residues at the extreme C-terminal are essential for this function. Structure predictions suggest that it has three conserved alpha helices followed by a beta-hairpin. 76 matched cddid_all.tbl CDD pfam20440 pfam20440 466589 GvpD_bR2 GvpD basic region 2. GvpD is a regulator of gas vesicle formation acting as a repressor through the interaction and breakdown induction of the transcriptional activator GvpE. This entry represents the C-terminal domain of GvpD, which contains the second basic region (bR2, arginine-rich) that may be important for its function. 254 matched cddid_all.tbl CDD pfam20441 pfam20441 466590 TerL_nuclease Terminase large subunit, endonuclease domain. This is the endonuclease domain of Terminase large subunit TerL, a key component of the DNA packing machinery in tailed bacteriophages and related viruses. TerL comprises a N-terminal ATPase domain (pfam03354) which powers the DNA translocation and this C-terminal endonuclease domain that cuts concatemeric DNA first in the initiation phase in a sequence specific site and later in the completion stage of the DNA packaging process when the capsid is full. Cryo-EM studies indicate that TerL forms a pentamer that binds to a dodecameric assembly called portal and attaches to the capsid. It has been proposed that nuclease domains form a radially arranged ring that is proximal to portal, playing a key role in pentamer assembly. This nuclease domain has a RNAse H-like fold and it has been proposed to utilize a two-metal catalysis mechanism like in other RNAse H-like endonucleases such as RNase H, transposases, retroviral integrases and RuvC Holliday junction resolvases. 284 matched cddid_all.tbl CDD pfam20442 pfam20442 466591 BrxL_N BREX system Lon protease-like protein BrxL N-terminal. This entry represents the N-terminal domain of BREX system Lon protease-like protein BrxL from Bacillus cereus and similar proteins. BrxL is part of a type 1 BREX system, which contains a C-terminal Lon-like protease domain (pfam05362). BREX systems (bacteriophage exclusion) provide immunity against bacteriophage, a system that allows phage adsorption but prevents phage DNA replication, without degradation of the phage DNA. 132 matched cddid_all.tbl CDD pfam20443 pfam20443 466592 LAP1_N Lamina-associated polypeptide 1, N-terminal. Torsin-1A-interacting proteins 1 and 2 (TOIP 1/2) also known as LAP1 proteins (Lamina-associated polypeptide 1) are type 2 integral membrane proteins with a single membrane-spanning region of the inner nuclear membrane. These proteins interact with and activate Torsin A, an AAA+ ATPase localized to the endoplasmic reticulum (ER) through a perinuclear domain, and forms a heterohexameric (LAP1-Torsin)3 ring that targets Torsin to the nuclear envelope. LAP1 has an atypical AAA+ fold and provides an arginine finger to the Torsin A active site to promote its ATPase activity. A single mutation in Torsin A causes early onset primary dystonia, a painful and severely disabling neuromuscular disease. This entry represents the N-terminal domain of LAP1 which contains transmembrane helices. 238 matched cddid_all.tbl CDD pfam20444 pfam20444 466593 DUF6703 Family of unknown function (DUF6703). This family of putative integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 85 and 118 amino acids in length. 122 matched cddid_all.tbl CDD pfam20445 pfam20445 466594 RHS_N Retrotransposon hot spot proteins N-terminal. Members of this entry are retrotransposon hot spot (RHS) proteins. They are associated with polymorphic subtelomeric regions in Trypanosoma. These proteins contain a conserved box 1 with a P-loop motif and a retrotransposon insertion site at the C-terminal (pfam07999). This domain represents the N-terminal region of the conserved box 1 from RHSPs. 127 matched cddid_all.tbl CDD pfam20446 pfam20446 466595 ABC_N ATPase of the ABC class N-terminal. This is the N-terminal domain of various bacterial predicted ABC class ATPases which shows sequence and structural similarities to the N-terminal domain of MRB1590 (swiss:Q57ZF2) from kinetoplastids, a core protein of the multiprotein mitochondrial RNA binding complex 1 (MRB1) involved in kinetoplastid RNA (kRNA) editing. MRB1590 is a dimer and contains a central ABC ATPase fold (pfam09818) between novel N- and C-terminal regions. The N-terminal domains combine and form a RNA-binding basic pore which involves an arginine patch that has been suggested to act as a chaperone to bind and stabilize ssRNA during kRNA editing processes. N-terminal MRB1590 shows structural similarity to chaperones. 162 matched cddid_all.tbl CDD pfam20447 pfam20447 466596 DUF6704 Family of unknown function (DUF6704). This family of presumed integral membrane proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 76 and 89 amino acids in length. 68 matched cddid_all.tbl CDD pfam20448 pfam20448 466597 DUF6705 Family of unknown function (DUF6705). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 170-200 amino acids in length. 198 matched cddid_all.tbl CDD pfam20449 pfam20449 466598 DUF6706 Family of unknown function (DUF6706). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 100 amino acids in length. 108 matched cddid_all.tbl CDD pfam20450 pfam20450 466599 PPV_E1_DBD Papillomavirus E1, DNA-binding domain. This is the DNA-binding domain (DBD) of Papillomavirus E1 protein, a DNA helicase that is required for initiation of viral DNA replication. This protein forms a complex with the E2 protein pfam00508 at the origin of replication (ori). This domain is found in the central region of E1 and binds DNA at specific sites of viral origin, and also binds cooperatively with E2-DBD. This domain comprises a five-stranded antiparallel beta-sheet flanked by alpha helices on each side. This domain binds originally as a dimer in which each monomer binds to one half-site of the palindromic E1 binding site, and promotes the assembly of the hexameric helicase on the ori. E1 has a domain architecture and function similar to SV40 T-antigen. 139 matched cddid_all.tbl CDD pfam20451 pfam20451 466600 Calmod_bind_M Calmodulin binding protein central domain. The members of this family are putative or actual calmodulin binding proteins expressed by various plant species. Some members are known to be involved in the induction of plant defence responses. However, their precise function in this regards is as yet unknown. 67 matched cddid_all.tbl CDD pfam20452 pfam20452 466601 Calmod_bind_C Calmodulin binding protein C-terminal domain. The members of this family are putative or actual calmodulin binding proteins expressed by various plant species. Some members are known to be involved in the induction of plant defence responses. However, their precise function in this regards is as yet unknown. 62 matched cddid_all.tbl CDD pfam20453 pfam20453 466602 DUF6707 Family of unknown function (DUF6707). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 190 and 350 amino acids in length. 195 matched cddid_all.tbl CDD pfam20454 pfam20454 466603 GpA_nuclease Terminase large subunit gpA, endonuclease domain. Terminase enzymes mediate the packaging viral DNA into an empty procapsid in a process called DNA packaging and are composed of a heterotrimeric complex of a large subunit (TerL, gpA) and the small subunit (TerS, gpNu1) (TerL-TerS2). TerL contains all the catalytic activities required for for DNA maturation and packaging. At the N-terminal reside the DNA translocase (packaging) and ATPase activities, while at the C-terminal resides the DNA maturation (nuclease/helicase) catalytic activity. This entry represents the endonuclease domain found at the C-terminal of Terminase large subunit (GpA) from Bacteriophage lambda, which excises an individual genome from the concatemer at the cos site. 293 matched cddid_all.tbl CDD pfam20455 pfam20455 466604 DUF6708 Family of unknown function (DUF6708). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 200 amino acids in length. 171 matched cddid_all.tbl CDD pfam20456 pfam20456 466605 DUF6709 Family of unknown function (DUF6709). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 340 and 435 amino acids in length. 331 matched cddid_all.tbl CDD pfam20457 pfam20457 466606 DUF6710 Family of unknown function (DUF6710). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 220 and 300 amino acids in length. 193 matched cddid_all.tbl CDD pfam20458 pfam20458 466607 DUF6711 Family of unknown function (DUF6711). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 115 and 155 amino acids in length. 134 matched cddid_all.tbl CDD pfam20459 pfam20459 466608 DUF6712 Family of unknown function (DUF6712). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 270 and 340 amino acids in length. 275 matched cddid_all.tbl CDD pfam20460 pfam20460 466609 DUF6713 Family of unknown function (DUF6713). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 117 and 141 amino acids in length. 117 matched cddid_all.tbl CDD pfam20461 pfam20461 466610 DUF6714 Family of unknown function (DUF6714). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 150 and 185 amino acids in length. 159 matched cddid_all.tbl CDD pfam20462 pfam20462 466611 DUF6715 Domain of unknown function (DUF6715). This putative domain is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 200 amino acids in length. This domain appears to belong to the NTF2 superfamily. 192 matched cddid_all.tbl CDD pfam20463 pfam20463 466612 PDH_C Prephenate dehydrogenase, dimerization domain. Members of this family are prephenate dehydrogenases EC:1.3.1.12 (PDHs) involved in tyrosine biosynthesis. This is the C-terminal, helical dimerization domain of PDHs. 102 matched cddid_all.tbl CDD pfam20464 pfam20464 466613 MmeI_N MmeI, N-terminal domain. Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues 301-320) via a multi-helical spacer (residues 156-300). These are followed by the target recognition domain (TRD, residues 621-825), and a final C-terminal helical bundle (residues 826-919). This domain corresponds to the N-terminal endonuclease, it cuts the two DNA strands at one site simultaneously with enzyme bound at two sites interacting to accomplish the cleavage. 138 matched cddid_all.tbl CDD pfam20465 pfam20465 466614 MmeI_hel MmeI, helicase spacer domain. Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues 301-320) via a multi-helical spacer (residues 156-300). These are followed by the target recognition domain (TRD, residues 621-825), and a final C-terminal helical bundle (residues 826-919). The endonuclease cuts the two DNA strands at one site simultaneously with enzyme bound at two sites interacting to accomplish the cleavage. This domain corresponds to the multi-helical spacer. It is thought to play a key role in positioning the endonuclease cleavage domain correctly. 153 matched cddid_all.tbl CDD pfam20466 pfam20466 466615 MmeI_TRD MmeI, target recognition domain. Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues 301-320) via a multi-helical spacer (residues 156-300). These are followed by the target recognition domain (TRD, residues 621-825), and a final C-terminal helical bundle (residues 826-919). The DNA is embedded between the TRD and the MTase domain. The TRD makes contacts to the DNA bases primarily in the major groove, while the MTase domain makes several contacts to the DNA in the minor groove. This domain corresponds to the TRD. It consists of two alpha/beta subdomains. 206 matched cddid_all.tbl CDD pfam20467 pfam20467 466616 MmeI_C MmeI, C-terminal domain. Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues 301-320) via a multi-helical spacer (residues 156-300). These are followed by the target recognition domain (TRD, residues 621-825), and a final C-terminal helical bundle (residues 826-919). The DNA is embedded between the TRD and the MTase domain. The TRD makes contacts to the DNA bases primarily in the major groove, while the MTase domain makes several contacts to the DNA in the minor groove. This domain corresponds to the C-terminal region. 83 matched cddid_all.tbl CDD pfam20468 pfam20468 466617 HPS6_C Hermansky-Pudlak syndrome 6 protein C-terminal domain. This entry represents the C-terminal alpha solenoid domain of the HPS6 protein. 387 matched cddid_all.tbl CDD pfam20469 pfam20469 466618 OLD-like_TOPRIM Overcoming lysogenization defect protein-like, TOPRIM domain. This entry represents the topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as RNase activity consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain. The nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. The TOPRIM domain has two conserved motifs, one of which centres at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. 67 matched cddid_all.tbl CDD pfam20470 pfam20470 466619 HTH_61 Helix-turn-helix domain. This entry represents a presumed helix-turn-helix domain found in DNA polymerase theta. 92 matched cddid_all.tbl CDD pfam20471 pfam20471 466620 DUF6716 Putative glycosyltransferase (DUF6716). This entry represents a group of uncharacterized proteins that belong to the GT- superfamily of glycosyltransferases. 341 matched cddid_all.tbl CDD pfam20472 pfam20472 466621 PDDEXK_11 PD-(D/E)XK nuclease superfamily domain. This family contains many hypothetical bacterial proteins. It has been identified as a member of the PD-(D/E)XK nuclease superfamily. 144 matched cddid_all.tbl CDD pfam20473 pfam20473 466622 MmeI_Mtase MmeI, DNA-methyltransferase domain. Type IIL Restriction-Modification Enzyme MmeI is a large enzyme that integrates DNA recognition and methyltransferase and endonuclease activities within the same polypeptide. MmeI is composed of five domains. An N-terminal endonuclease domain (residues 1-155), connects to a DNA-methyltransferase domain (MTase, residues 301-320) via a multi-helical spacer (residues 156-300). These are followed by the target recognition domain (TRD, residues 621-825), and a final C-terminal helical bundle (residues 826-919). The DNA is embedded between the TRD and the MTase domain. The TRD makes contacts to the DNA bases primarily in the major groove, while the MTase domain makes several contacts to the DNA in the minor groove. This domain corresponds to the DNA-methyltransferase. Structurally, it consists of a twisted beta-sheet flanked by alpha-helices on both sides. 258 matched cddid_all.tbl CDD pfam20474 pfam20474 466623 PHL PHL domain. This presumed domain is found in the PHL protein. 155 matched cddid_all.tbl CDD pfam20475 pfam20475 466624 DUF6717 Family of unknown function (DUF6717). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 115 amino acids in length. 115 matched cddid_all.tbl CDD pfam20476 pfam20476 466625 DUF6718 Family of unknown function (DUF6718). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 74 matched cddid_all.tbl CDD pfam20477 pfam20477 466626 DUF6719 Family of unknown function (DUF6719). This family is functionally uncharacterized. This family of proteins is found in proteobacteria. Proteins in this family are typically 74 amino acids in length. 78 matched cddid_all.tbl CDD pfam20478 pfam20478 466627 P2RX7_C P2X purinoreceptor 7 intracellular domain. This entry represents the intracellular domain found at the the C-terminus of P2X purinoreceptor 7 protein. 185 matched cddid_all.tbl CDD pfam20479 pfam20479 466628 TMEM128 TMEM128 protein. This entry represents the uncharacterized TMEM128 protein which contains four transmembrane helices. This protein is resident in the endoplasmic reticulum. 124 matched cddid_all.tbl CDD pfam20480 pfam20480 466629 DUF6720 Family of unknown function (DUF6720). This family of proteins is functionally uncharacterized. This family of proteins is found in fungi. Proteins in this family are typically between 305 and 340 amino acids in length. 306 matched cddid_all.tbl CDD pfam20481 pfam20481 466630 DUF6721 Domain of unknown function (DUF6721). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is typically a 100 amino acids in length. 96 matched cddid_all.tbl CDD pfam20482 pfam20482 466631 DUF6722 Family of unknown function (DUF6722). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 65 amino acids in length. 49 matched cddid_all.tbl CDD pfam20483 pfam20483 466632 Flavi_NS5_thumb Flavivirus RNA-directed RNA polymerase, thumb domain. Flaviviruses produce a large polyprotein from the ssRNA genome, encoding structural proteins required for virus assembly and non-structural (NS1-5) proteins involved in replication of the viral genome. This polyprotein is cleaved by viral and cellular proteases to produce mature viral proteins. NS5 is the largest mature viral protein and contains a N-terminal methyltransferase (MTase) domain separated by a short linker from the C-terminal RNA-directed RNA polymerase domain (RdRp) that adopts a characteriztic right-handed fingers-palm-thumb fold and possesses a number of short regions and motifs homologous to other RNA-directed RNA polymerases. This entry represents the thumb domain of NS5 RdRp. NS5 binds to a the stem loop A (SLA) at the 5' extremity of Flavivirus genome and regulates translation of the viral genome. 164 matched cddid_all.tbl CDD pfam20484 pfam20484 466633 DUF6723 Family of unknown function (DUF6723). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 81 and 125 amino acids in length. 73 matched cddid_all.tbl CDD pfam20485 pfam20485 466634 DUF6724 Family of unknown function (DUF6724). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 62 and 74 amino acids in length. 64 matched cddid_all.tbl CDD pfam20486 pfam20486 466635 DUF6725 Family of unknown function (DUF6725). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. 83 matched cddid_all.tbl CDD pfam20487 pfam20487 466636 DUF6726 Family of unknown function (DUF6726). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There is a conserved LTKVV sequence motif. 58 matched cddid_all.tbl CDD pfam20488 pfam20488 466637 Birna_VP1_thumb "Birnavirus RNA dependent RNA polymerase (VP1), thumb domain. Birnaviruses are dsRNA viruses. The RNA dependent RNA polymerase, also known as VP1, contains the conserved RdRp motifs that reside in the catalytic ""palm"" domain of all classes of polymerases but in a characteriztic permuted order, thus, it adopts a unique active site topology. Additionally, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. This entry covers the thumb domain of RdRP from Birnaviruses." 167 matched cddid_all.tbl CDD pfam20489 pfam20489 466638 Birna_RdRp_C "Birnavirus RNA dependent RNA polymerase (VP1), C-terminal. Birnaviruses are dsRNA viruses. This entry corresponds to the C-terminal domain of RNA dependent RNA polymerase also known as VP1. All of the birnavirus VP1 proteins contain conserved RdRp motifs that reside in the catalytic ""palm"" domain of all classes of polymerases. However, the birnavirus RdRps lack the highly conserved Gly-Asp-Asp (GDD) sequence, a component of the proposed catalytic site of this enzyme family that exists in the conserved motif VI of the palm domain of other RdRps. This RdRp has the five essential RNA polymerase motifs in a permuted order of C-A-B-D-E to form a conserved catalytic active site. This domain is mostly alpha-helical that runs across the canyon in the front of the palm, and wraps around the fingers subdomain, which may function to prevent back-primed RNA synthesis during protein priming." 103 matched cddid_all.tbl CDD pfam20490 pfam20490 466639 SCGB3A Secretoglobin 3A. This family includes secretoglobin family 3A member 1 (SCGB3A1) and member 2 (SCGB3A2), also known as uteroglobin-related proteins. They are a small secreted proteins expressed in airway epithelial cells. SCGB3A2, also known as UGRP1, has an important anti-inflammatory activity and is involved in asthma. SCGB3A2 mediates its anti-inflammatory action through inhibition of ERK and JNK activation. It is also involved in lung development and has anti-fibrotic activity in lung. 68 matched cddid_all.tbl CDD pfam20491 pfam20491 466640 Ermin Ermin. This is a cytoskeletal protein exclusively expressed in oligodendrocytes that plays a role in cytoskeletal rearrangements during the late wrapping and/or compaction phases of myelinogenesis and in maintenance and stability of myelin sheath in the adult. It may also play an important role in late-stage oligodendroglia maturation, myelin/Ranvier node formation during CNS development, and in the maintenance and plasticity of related structures in the mature CNS. Ermin associates with the myosin phosphatase Rho interacting protein protein (Mprip/p116RIP) and inactivates RhoA, a GTPase that controls cytoskeletal rearrangement in differentiating cells, thus contributing to oligodendrocyte morphogenesis. It has a C-terminal actin-binding domain similar to those of members of the ERM family but lacks the conserved N-terminal FERM domain. 284 matched cddid_all.tbl CDD pfam20492 pfam20492 466641 ERM_helical Ezrin/radixin/moesin, alpha-helical domain. The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins. 120 matched cddid_all.tbl CDD pfam20493 pfam20493 466642 WD-like_fungi Fungal WD-like. This is an uncharacterized family of proteins found in Fungi, present in S. japonicus but seems to be absent in S. pombe and S. cerevisiae. It may be a divergent WD repeat-like family of proteins. There are eight conserved cysteine residues. 199 matched cddid_all.tbl CDD pfam20494 pfam20494 466643 YfjS_YafY Lipoprotein YfjS/YafY domain. This entry is based on the E. coli YfjS and YafY lipoproteins. 113 matched cddid_all.tbl CDD pfam20495 pfam20495 466644 DUF6727 Family of unknown function (DUF6727). This is a family of uncharacterized proteins exclusively found in S. japonicus. It contains a highly conserved PLLLP motif at the C-terminal. 152 matched cddid_all.tbl CDD pfam20496 pfam20496 466645 Dbl7 Double strand break localizing Dbl7. This family represents the Schizosaccharomyces specific protein double strand break localizing Dbl7. Dbls localize to DNA double-strand breaks (DSBs) and are involved in DSB repair. 274 matched cddid_all.tbl CDD pfam20497 pfam20497 466646 SWI-SNF_Ssr4_C SWI/SNF and RSC complexes subunit Ssr4 C-terminal. This entry represents the C-temrinal domain of Ssr4 (SWI/SNF and RSC complexes subunit ssr4), an essential component of the chromatin-remodelling SWI/SNF and RSC (remodelling the structure of chromatin) complexes only found in S. pombe. This domain contains a conserved RYxxxHEWMEEI/V motif. RSC is involved in transcription regulation and nucleosome positioning which controls, particularly, membrane and organelle development genes. The ATP-dependent chromatin remodelling complex SWI/SNF is required for the positive and negative regulation of gene expression of a large number of genes through the regulation of nucleosome remodelling. 458 matched cddid_all.tbl CDD pfam20498 pfam20498 466647 DUF6728 Family of unknown function (DUF6728). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 45 and 78 amino acids in length. 55 matched cddid_all.tbl CDD pfam20499 pfam20499 466648 DUF6729 Domain of unknown function (DUF6729). This presumed domain is functionally uncharacterized. This domain family is found in eukaryotes, and is approximately 220 amino acids in length. 232 matched cddid_all.tbl CDD pfam20500 pfam20500 466649 DNA-PKcs_N DNA-PKcs, N-terminal. This entry represents the N-terminal domain of DNA-dependent protein kinase catalytic subunit (DNA-PKcs), which is arranged in four supersecondary alpha-helical structures, N1 to N4, that resemble HEAT repeats. Therefore, this domain is also known as N-HEAT. This domain likely mediates DNA binding and, together with the Circular Cradle, forms a ring through which Ku70/80 may present DNA for repair. DNA-PKcs is involved in DNA nonhomologous end joining (NHEJ), required for double-strand break (DSB) repair. It is recruited by Ku70/80 heterodimer to DNA ends. 810 matched cddid_all.tbl CDD pfam20501 pfam20501 466650 MbhE MBH, subunit E. Hydrogen gas-evolving membrane-bound hydrogenase (MBH) is a respiratory complex homologous to the quinone-reducing Complex I. Like Complex I, MBH has peripheral and membrane arms. MBH is made of 14 subunits (MbhA-N). MbhJ, K, L, N and M form the Membrane-anchored hydrogenase module. MbhJ, K, L, N are predicted to be exposed to the cytoplasm and form the peripheral arm. The remaining 10 subunits are predicted to be integral membrane proteins forming the membrane arm, made of 44 transmembrane helices (TMH). MbhA, B, C and F form the Sodium translocation module. MbhD, E, G and H form the Proton translocation module. MbhI is the linker between the hydrogenase module and the proton-translocating membrane module. It anchors the discontinuous TMH7 of MbhH via its middle lateral helix and the C-terminal of TMH2, found in MbhE. MbhD and MbhE together are equivalent to Nqo10 of Complex I. MbhE has two transmembrane helices: TMH1 and TMH2. 98 matched cddid_all.tbl CDD pfam20502 pfam20502 466651 DNAPKcs_CC1-2 DNA-dependent protein kinase catalytic subunit, CC1/2. DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is involved in DNA nonhomologous end joining (NHEJ) which is recruited by Ku70/80 heterodimer to DNA ends and required for double-strand break (DSB) repair. It folds into three well-defined large structural units, consisting of a N-terminal region, the Circular Cradle (consisting of five supersecondary alpha-helical structures CC1 to CC5), and the C-terminal Head (comprising FAT, FRB, kinase, and FATC). The N-terminal and CCs regions resemble HEAT repeats, and thus, they are also referred to as N-HEAT and M-HEAT ('middle'), respectively. The CCs form a curved elliptical ring that serves as a scaffold to maintain the integrity of the whole complex. This entry represents CC1 and CC2, which contain the Highly conserved region I (HCR-I). 810 matched cddid_all.tbl CDD pfam20503 pfam20503 466652 DUF6730 Family of unknown function (DUF6730). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 105 and 155 amino acids in length. 82 matched cddid_all.tbl CDD pfam20504 pfam20504 466653 IntS14_C Integrator complex subunit 14, alpha-helical domain. This entry represents the C-terminal alpha-helical domain of Integrator complex subunit 14 (IntS14), a component of the integrator complex which is involved in the transcription of small nuclear RNAs (snRNA) and their 3'-box dependent processing. This complex is also involved in the 3'-end processing of the U7 snRNA, and the spliceosomal snRNAs U1 and U5. IntS14 interacts with IntS13; both of them consist of an N-terminal VWA domain followed by a central beta-barrel domain and a C-terminal alpha-helical domain, which are connected through a linker devoid of secondary structure elements. This domain contribute to binding by packing against the beta-barrel of IntS13. 103 matched cddid_all.tbl CDD pfam20505 pfam20505 466654 DUF6731 Family of unknown function (DUF6731). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 297 and 311 amino acids in length. 294 matched cddid_all.tbl CDD pfam20506 pfam20506 466655 DUF6732 Family of unknown function (DUF6732). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 73 amino acids in length. 72 matched cddid_all.tbl CDD pfam20507 pfam20507 466656 DUF6733 Family of unknown function (DUF6733). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 240 and 250 amino acids in length. 243 matched cddid_all.tbl CDD pfam20508 pfam20508 466657 DUF6734 Family of unknown function (DUF6734). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 430 and 555 amino acids in length. 288 matched cddid_all.tbl CDD pfam20509 pfam20509 466658 DUF6735 Family of unknown function (DUF6735). This family of proteins is functionally uncharacterized. This family of proteins is found in archaea. Proteins in this family are typically between 178 and 220 amino acids in length. 204 matched cddid_all.tbl CDD pfam20510 pfam20510 466659 HgmA_N Homogentisate 1,2-dioxygenase N-terminal. Homogentisate dioxygenase cleaves the aromatic ring during the metabolic degradation of Phe and Tyr. Homogentisate dioxygenase deficiency causes alkaptonuria. The structure of homogentisate dioxygenase shows that the enzyme forms a hexamer arrangement comprised of a dimer of trimers. The active site iron ion is coordinated near the interface between the trimers. This entry represents the N-terminal domain which forms a jelly roll of beta-strands. 271 matched cddid_all.tbl CDD pfam20511 pfam20511 466660 PMI_typeI_cat Phosphomannose isomerase type I, catalytic domain. This entry represents the catalytic domain of Phosphomannose isomerase type I enzymes (EC 5.3.1.8) which contains a zinc-binding site. It is composed of beta-strands connected by long loops in a jelly roll conformation. 143 matched cddid_all.tbl CDD pfam20512 pfam20512 466661 PMI_typeI_hel Phosphomannose isomerase type I, helical insertion domain. This entry represents the alpha-helical insertion domain of Phosphomannose isomerase type I enzymes (EC 5.3.1.8), in which the helices are packed closely, connected by short turns and loops. This domain packs closely against the catalytic domain, interrupting it. 88 matched cddid_all.tbl CDD pfam20513 pfam20513 466662 UBact Prokaryotic ubiquitin-like protein UBact. UBact is a ubiquitin-like protein found in Gram-negative bacteria. It differs from ubiquitin and most ubiquitin-like proteins (including the mycobacterial Pup) in that it lacks the characteriztic C-terminal di-glycine motif. UBact conjugation-degradation system appears to be homologous to the pupylation system for proteasomal degradation in bacteria. 43 matched cddid_all.tbl CDD pfam20514 pfam20514 466663 ROXA-like_wH ROXA-like winged helix. This entry represents the winged helix domain of ribosomal oxygenases, including ROXA from E.coli, which is reminiscent of WH-domains involved in protein-protein and protein-nucleic acid interactions. However, this domain has an overall negative charge suggesting they do not directly bind nucleic acids. 115 matched cddid_all.tbl CDD pfam20515 pfam20515 466664 2OG-FeII_Oxy_6 Tet-like 2OG-Fe(II) oxygenase superfamily. This entry represents an uncharacterized family of fungal proteins. The AlphaFold prediction for an example protein shows that it is most closely related to Tet-like dioxygenases. This strongly suggests that this family of proteins are DNA modification enzymes. 206 matched cddid_all.tbl CDD pfam20516 pfam20516 466665 PDDEXK_12 PD-(D/E)XK nuclease superfamily. This entry contains a large family of uncharacterized fungal proteins. Structure prediction suggests it is likely to be an endonuclease enzyme related to the PD-(D/E)XK nuclease superfamily. 247 matched cddid_all.tbl CDD pfam20517 pfam20517 466666 TMEM127 Transmembrane protein 127. TMEM127 modulates mTOR function in the endolysosome. Its interaction with early endosomal GTPase Rab5 to inhibit mTOR signalling seems to be related with its tumour-suppressing properties. 113 matched cddid_all.tbl CDD pfam20518 pfam20518 466667 Apc1_MidN Anaphase-promoting complex subunit 1 middle domain. Apc1 is the largest of the subunits of the anaphase-promoting complex or cyclosome. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes. Apc1 consists of a N-terminal WD40 beta-propeller domain, followed by the middle domain (Mid-N), a PC domain and the C-terminal domain (MidC). This entry represents the middle domain of Apc1, MidN (also referred to as the first helical domain), that coaleses with the C-terminal domain to form Apc1Mid that connects Apc1WD40 with Apc1PC. Apc1Mid consists of an alpha-solenoid capped by a beta-sandwich. 371 matched cddid_all.tbl CDD pfam20519 pfam20519 466668 Polycystin_dom Polycystin domain. This domain represents the polycystin domain from group II of Transient receptor potential (TRP) channels (TRPP) including PKD1, PKD2, PKD2L and mucolipins. The polycystin domain display a sandwich-like shape with five beta-sheets in the tilted middle layer, three alpha-helices on one side and a large loop with two short antiparallel beta-sheets on the other. 199 matched cddid_all.tbl CDD pfam20520 pfam20520 466669 Ac45-VOA1_TM V0 complex accessory subunit Ac45/VOA1 transmembrane domain. This entry represents the transmembrane domain from ER/Golgi membrane proteins including V0 complex accessory subunit Ac45 (ATP6AP1, also known as V-type proton ATPase subunit S1) from animals and the yeast homolog V0 assembly protein 1 (VOA1) which are essential for V0 ATPase assembly, stability and function. In humans, mutations of ATP6AP1 cause immunodeficiency with hypogammaglobulinemia, hepatopathy and neurocognitive abnormalities. This entry also includes ER membrane BIG1 proteins from yeast, involved in cell wall biogenesis. 39 matched cddid_all.tbl CDD pfam20521 pfam20521 466670 DUF6736 Family of unknown function (DUF6736). This presumed domain is functionally uncharacterized. This domain family is found in fungi, and is approximately 130 amino acids in length. 129 matched cddid_all.tbl CDD pfam20522 pfam20522 466671 DUF6737 Domain of unknown function (DUF6737). This presumed domain is functionally uncharacterized. This domain is approximately 57 amino acids in length. 57 matched cddid_all.tbl CDD pfam20523 pfam20523 466672 DUF6738 Domain of unknown function (DUF6738). This presumed domain is functionally uncharacterized. This domain family is found in plants, and is approximately 70 amino acids in length. 85 matched cddid_all.tbl CDD pfam20524 pfam20524 466673 DUF6739 Family of unknown function (DUF6739). This protein family is functionally uncharacterized. It is found in eukaryotes. 691 matched cddid_all.tbl CDD pfam20525 pfam20525 466674 DUF6740 Family of unknown function (DUF6740). This family of proteins is functionally uncharacterized. This family of proteins is found in eukaryotes. Proteins in this family are typically around 520 amino acids in length. 532 matched cddid_all.tbl CDD pfam20526 pfam20526 466675 DUF6741 Domain of unknown function (DUF6741). This presumed domain is functionally uncharacterized. This domain family is found in fungi, and is approximately 130 amino acids in length. 129 matched cddid_all.tbl CDD pfam20527 pfam20527 466676 DUF6742 Domain of unknown function (DUF6742). This presumed domain family is functionally uncharacterized. This domain is found in eukaryotes and is around 40 amino acids in length. 43 matched cddid_all.tbl CDD pfam20528 pfam20528 466677 DUF6743 Domain of unknown function (DUF6743). This presumed domain family is functionally uncharacterized. This domain is found in Sar and is typically 80 amino acids in length. 78 matched cddid_all.tbl CDD pfam20529 pfam20529 466678 DUF6744 Family of unknown function (DUF6744). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 290 and 350 amino acids in length. 316 matched cddid_all.tbl CDD pfam20530 pfam20530 466679 DUF6745 Domain of unknown function (DUF6745). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is typically 200 amino acids in length. 206 matched cddid_all.tbl CDD pfam20531 pfam20531 466680 DUF6746 Family of unknown function (DUF6746). This family of proteins is functionally uncharacterized. This family of proteins is found in proteobacteria. Proteins in this family are approximately 130 amino acids in length. 124 matched cddid_all.tbl CDD pfam20532 pfam20532 466681 DUF6747 Family of unknown function (DUF6747). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length. There are two conserved sequence motifs: YFKAF and FRVSTG. 55 matched cddid_all.tbl CDD pfam20533 pfam20533 466682 DUF6748 Domain of unknown function (DUF6748). This presumed domain family is functionally uncharacterized. This domain is found in bacterial and eukaryotic proteins. It is around 100 amino acids in length. 199 matched cddid_all.tbl CDD pfam20534 pfam20534 466683 DUF6749 Domain of unknown function (DUF6749). This presumed domain is functionally uncharacterized. This domain family is found in proteobacteria, and is approximately 40 amino acids in length. There is a conserved FTS sequence motif. 137 matched cddid_all.tbl CDD pfam20535 pfam20535 466684 DUF6750 Family of unknown function (DUF6750). This family of proteins is functionally uncharacterized. This family of proteins is found in proteobacteria. Proteins in this family are approximately 130 amino acids in length. 129 matched cddid_all.tbl CDD pfam20536 pfam20536 466685 DUF6751 Family of unknown function (DUF6751). This family of proteins is functionally uncharacterized. This family of proteins is found in Firmicutes bacteria. Proteins in this family are typically 115 amino acids in length. 113 matched cddid_all.tbl CDD pfam20537 pfam20537 466686 DUF6752 Domain of unknown function (DUF6752). This presumed domain family is functionally uncharacterized. It is found in bacterial proteins and is typically 54 amino acids in length. 55 matched cddid_all.tbl CDD pfam20538 pfam20538 466687 DUF6753 Family of unknown function (DUF6753). This family of proteins is functionally uncharacterized. This family of proteins is found in cyanobacteria. Proteins in this family are typically between 225 and 243 amino acids in length. 217 matched cddid_all.tbl CDD pfam20539 pfam20539 466688 DUF6754 Domain of unknown function (DUF6754). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 250 amino acids in length. 257 matched cddid_all.tbl CDD pfam20540 pfam20540 466689 DUF6755 Family of unknown function (DUF6755). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 80 amino acids in length. 75 matched cddid_all.tbl CDD pfam20541 pfam20541 466690 DUF6756 Family of unknown function (DUF6756). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 159 and 191 amino acids in length. 160 matched cddid_all.tbl CDD pfam20542 pfam20542 466691 DUF6757 Family of unknown function (DUF6757). This family of proteins is functionally uncharacterized. This family of proteins is found in archaea. Proteins in this family are approximately 50 amino acids in length. 54 matched cddid_all.tbl CDD pfam20543 pfam20543 466692 CowN N2-fixation sustaining protein CowN. N2-fixation sustaining protein CowN is required to maintain N2-dependent growth in the presence of low levels of carbon monoxide. It is thought to act by protecting the N2 fixation ability of the nitrogenase complex. 94 matched cddid_all.tbl CDD pfam20544 pfam20544 466693 DUF6758 Family of unknown function (DUF6758). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 215 amino acids in length. 207 matched cddid_all.tbl CDD pfam20545 pfam20545 466694 DUF6759 Domain of unknown function (DUF6759). This presumed domain family is functionally uncharacterized. This domain is found in bacteria and is typically 100 amino acids in length. 94 matched cddid_all.tbl CDD pfam20546 pfam20546 466695 DUF6760 Family of unknown function (DUF6760). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically 89 amino acids in length. 89 matched cddid_all.tbl CDD pfam20547 pfam20547 466696 DUF6761 Family of unknown function (DUF6761). This family of proteins is functionally uncharacterized. This family of proteins is found in cyanobacteria. Proteins in this family are approximately 80 amino acids in length. 81 matched cddid_all.tbl CDD pfam20548 pfam20548 466697 DUF6762 Family of unknown function (DUF6762). This family of proteins is functionally uncharacterized. This family of proteins is found in Firmicutes bacteria. Proteins in this family are approximately 135 amino acids in length. 132 matched cddid_all.tbl CDD pfam20549 pfam20549 466698 DUF6763 Family of unknown function (DUF6763). This family of proteins is functionally uncharacterized. This family of proteins is found in proteobacteria. Proteins in this family are tipically between 95 and 160 amino acids in length. 97 matched cddid_all.tbl CDD pfam20550 pfam20550 466699 DUF6764 Family of unknown function (DUF6764). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically 165 and 195 amino acids in length. 164 matched cddid_all.tbl CDD pfam20551 pfam20551 466700 DUF6765 Family of unknown function (DUF6765). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 352 and 375 amino acids in length. It contains the conserved motifs FHFxxxP, GH and PD, and a conserved Phe residue at the C-terminal. 304 matched cddid_all.tbl CDD pfam20552 pfam20552 466701 HTH_62 Recombinase-like helix-turn-helix domain. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 73 and 103 amino acids in length. This family of proteins show similarity to the HTH domain of recombinases pfam07508. 72 matched cddid_all.tbl CDD pfam20553 pfam20553 466702 Methyltransf_35 Putative O-methyltransferase. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 312 and 330 amino acids in length. An AlphaFold model shows this family are similar to known O-methyltransferases. 310 matched cddid_all.tbl CDD pfam20554 pfam20554 466703 DUF6766 Domain of unknown function (DUF6766). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 215 and 226 amino acids in length. Structure prediction shows this family contains 4 alpha helices. 221 matched cddid_all.tbl CDD pfam20555 pfam20555 466704 DUF6767 Domain of unknown function (DUF6767). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 59 and 74 amino acids in length. There are two conserved sequence motifs: VTGP and DPE. The proteins contain four conserved cysteines. Proteins in this family are found in actinobacteria. 57 matched cddid_all.tbl CDD pfam20556 pfam20556 466705 DUF6768 Family of unknown function (DUF6768). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 130 amino acids in length. 123 matched cddid_all.tbl CDD pfam20557 pfam20557 466706 DnaT_2 Putative DnaT-like ssDNA binding protein. This presumed domain is functionally uncharacterized. This domain family is found in bacteria and viruses, and is approximately 110 amino acids in length. This domain is predicted to contain a complex four helical bundle structure. The structure shows similarity to the single stranded binding protein DnaT. 166 matched cddid_all.tbl CDD pfam20558 pfam20558 466707 DUF6769 Family of unknown function (DUF6769). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically 136 amino acids in length. 130 matched cddid_all.tbl CDD pfam20559 pfam20559 466708 DUF6770 Family of unknown function (DUF6770). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 514 and 521 amino acids in length. 520 matched cddid_all.tbl CDD pfam20560 pfam20560 466709 MotA_N Motility protein A N-terminal. This entry represents the N-terminal domain of Motility protein A (MotA). MotA is a membrane protein that forms the stator element of the flagellar motor complex together with MotB with 5:2 stoichiometry, which couples ion flow across the cytoplasmic membrane to generate torque, and thus, it is required for rotation of the flagellar motor. This domain contains conserved torque-generating charged residues at the C-terminal and is adjacent pfam01618, which represents MotA TMH3 and TMH4. 91 matched cddid_all.tbl CDD pfam20561 pfam20561 466710 DUF6771 Domain of unknown function (DUF6771). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length. 63 matched cddid_all.tbl CDD pfam20562 pfam20562 466711 DUF6772 Domain of unknown function (DUF6772). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 292 and 316 amino acids in length. An AlphaFold prediction show similarity to the concanavalin superfamily suggesting that this family may be involved in carbohydrate binding. 284 matched cddid_all.tbl CDD pfam20563 pfam20563 466712 DUF6773 Family of unknown function (DUF6773). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 151 and 172 amino acids in length. This family has a conserved sequence motif DER and two conserved residues, a Tyr and a Gly. 162 matched cddid_all.tbl CDD pfam20564 pfam20564 466713 DUF6774 Family of unknown function (DUF6774). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 57 and 70 amino acids in length. There is a conserved sequence motif QLGDTL. 28 matched cddid_all.tbl CDD pfam20565 pfam20565 466714 DUF6775 Probable metallopeptidase family (DUF6775). This family is functionally uncharacterized. This domain family is found in archaea. An AlphaFold prediction shows close similarity to zinc dependent peptidases. 256 matched cddid_all.tbl CDD pfam20566 pfam20566 466715 Eap1 eIF4E-associated protein. This fungal family includes eIF4E-associated protein (Eap1) from yeast, which plays a role in cell growth and is implicated in the TOR signaling cascade. Eap1 binds to eIF4E and regulates translation. It competes with eIF4G (the large subunit of the cap-binding complex, eukaryotic initiation factor 4F (eIF4F)) for binding to eIF4E and accelerates mRNA degradation by promoting decapping. It associates with Puf5p and Dhh1p, being essential for Puf5p mediated repression. This family also includes the uncharacterized protein from S. pombe SPCC14G10.04, which has been shown to interact with eIF4E, 4F complex subunits. 152 matched cddid_all.tbl CDD pfam20567 pfam20567 466716 DUF6776 Family of unknown function (DUF6776). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 234 and 251 amino acids in length. 149 matched cddid_all.tbl CDD pfam20568 pfam20568 466717 DUF6777 Domain of unknown function (DUF6777). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 160 amino acids in length. 163 matched cddid_all.tbl CDD pfam20569 pfam20569 466718 DUF6778 Family of unknown function (DUF6778). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria, predominantly in Rhodobacteria. Proteins in this family are typically between 203 and 225 amino acids in length. This family contains the conserved sequence motifs DIVW, RFH and GGxH. 164 matched cddid_all.tbl CDD pfam20570 pfam20570 466719 DUF6779 Domain of unknown function (DUF6779). This presumed domain is functionally uncharacterized. This domain family is mainly found in bacteria, and is approximately 100 amino acids in length. 108 matched cddid_all.tbl CDD pfam20571 pfam20571 466720 DUF6780 Domain of unknown function (DUF6780). This presumed domain is functionally uncharacterized. This domain family is found at the C-terminal of fungal sequences, and is typically between 48 and 62 amino acids in length. The domain is found in association with pfam00735. There is a conserved sequence motif WxRHxAAxK that may be functionally important. 62 matched cddid_all.tbl CDD pfam20572 pfam20572 466721 DUF6781 Family of unknown function (DUF6781). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 223 and 298 amino acids in length. 213 matched cddid_all.tbl CDD pfam20573 pfam20573 466722 DUF6782 Putative metallopeptidase family (DUF6782). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 256 and 362 amino acids in length. There is a conserved HEXRH sequence motif which is characteriztic of metallopeptidase enzymes. 241 matched cddid_all.tbl CDD pfam20574 pfam20574 466723 DUF6783 Family of unknown function (DUF6783). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 61 and 97 amino acids in length. 60 matched cddid_all.tbl CDD pfam20575 pfam20575 466724 HTH_63 Helix-turn-helix domain. This family of proteins is functionally uncharacterized. This family of proteins is found in archaea. Proteins in this family are typically between 161 and 201 amino acids in length. This family shares similarity with pfam01638 suggesting it is a transcriptional regulatory protein. 148 matched cddid_all.tbl CDD pfam20576 pfam20576 466725 HEWD HEWD domain. This small domain is functionally uncharacterized. This family of proteins is found in archaea. Proteins in this family are approximately 60 amino acids in length. There is a conserved HEWD sequence after which the domain is named. 61 matched cddid_all.tbl CDD pfam20577 pfam20577 466726 Phage_ORF5 Phage ORF5 protein. This family of proteins is found in bacteriophage such as Bacteriophage phiMH2K and Bacteriophage Chp1. Proteins in this family are typically between 81 and 96 amino acids in length. These proteins appear to have a role in phage packaging. 75 matched cddid_all.tbl CDD pfam20578 pfam20578 466727 aBig_2 Atrophied bacterial Ig domain. This domain is related to pfam02368 a bacterial immunoglobulin-like domain. According to structure predictions members of this domain family have lost several beta strands found on one sheet of the Ig domain. This domain is found in a wide range of bacterial cell surface proteins. 89 matched cddid_all.tbl CDD pfam20579 pfam20579 466728 LapA LapA domain. This Ig-like domain is found repeated in the LapA adhesin found in pseudomonas species. This domain is likely calcium binding and distantly related to the CalX-beta domain pfam03160. 99 matched cddid_all.tbl CDD pfam20580 pfam20580 466729 DUF6784 Domain of unknown function (DUF6784). This presumed domain is found at the C-terminal of uncharacterized proteins from bacteria. It contains the conserved sequence motifs WW/FPLHPLGY and RxGG. 102 matched cddid_all.tbl CDD pfam20581 pfam20581 466730 DUF6785 Family of unknown function (DUF6785). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. There are highly conserved sequence motifs: FSxWFF and ExxxFP. There are eleven conserved tryptophan residues, which may suggest to play an important role. 499 matched cddid_all.tbl CDD pfam20582 pfam20582 466731 UPF0758_N UPF0758 N-terminal. This domain is functionally uncharacterized, found at the N-terminal of the uncharacterized UPF0758 proteins from bacteria and archaea, and is approximately 90 amino acids in length. UPF0758 was previously known as the radC family, a name that was assigned according to the radC102 mutant of E. coli which was later demonstrated to be an allele of the transcription-repair-coupling factor recG. UPF0758 has been described as a putative JAMM-family deubiquitinating enzyme, but its function remains to be determined. Structure prediction using Colab notebook from AlphaFold DB suggests that it has an alpha bundle fold. It may contain two helix-hairpin-helix (HhH) motifs. This domain is found in association with pfam04002. 71 matched cddid_all.tbl CDD pfam20583 pfam20583 466732 DUF6786 Family of unknown function (DUF6786). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 397 and 433 amino acids in length. 376 matched cddid_all.tbl CDD pfam20584 pfam20584 466733 DUF6787 Family of unknown function (DUF6787). This family of proteins found in bacteria is functionally uncharacterized and is approximately 100 amino acids in length. Some members of this family are putative diacylglyceryl transferases. 79 matched cddid_all.tbl CDD pfam20585 pfam20585 466734 Pectate_lyase_5 Putative pectate lyase-like adhesive domain. This putative domain is found at the N-terminus of a large number of bacterial proteins. Its adhesive function was described in Lactobacillus reuteri serine-rich repeat proteins. Structure predictions show it is composed of a beta solenoid repeat related to Pectate lyase. 126 matched cddid_all.tbl CDD pfam20586 pfam20586 466735 DUF6788 Family of unknown function (DUF6788). This family of proteins is functionally uncharacterized. This family of proteins is mainly found in bacteria and archaea. Proteins in this family are around 100 amino acids in length. There are two conserved sequence motifs, CGxxxCxC containing three conserved Cys residues and HGP. 103 matched cddid_all.tbl CDD pfam20587 pfam20587 466736 DUF6789 Family of unknown function (DUF6789). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. These are likely membrane proteins. 144 matched cddid_all.tbl CDD pfam20588 pfam20588 466737 DMTF1_N Cyclin-D-binding Myb-like transcription factor 1 N-terminal. This domain is found at the N-terminal of Cyclin-D-binding Myb-like transcription factor 1 (DMTF1), which is rich in acidic residues, adjacent pfam00249. DMTF1 is a tumour suppressor that interacts with and activates CDKN2A/ARF in response to Ras-Raf signalling, thus inducing p53-dependent cell cycle arrest. 72 matched cddid_all.tbl CDD pfam20589 pfam20589 466738 DUF6790 Family of unknown function (DUF6790). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 159 and 176 amino acids in length. 158 matched cddid_all.tbl CDD pfam20590 pfam20590 466739 DUF6791 Domain of unknown function (DUF6791). This presumed domain is functionally uncharacterized. This domain family is found, and is approximately 160 amino acids in length. The domain is found in sequences that belong to the Thif family and is in association with pfam00899, located at its N-terminal. 149 matched cddid_all.tbl CDD pfam20591 pfam20591 466740 DUF6792 Domain of unknown function (DUF6792). This presumed domain is functionally uncharacterized. This domain is found in bacteria, and is around 250 amino acids in length. There is a conserved sequence motif GHSLGG. It may have an alpha/beta hydrolase fold suggesting a catalytic role. 218 matched cddid_all.tbl CDD pfam20592 pfam20592 466741 pAdhesive_10 Putative adhesin domain (group 10). This domain is found N-terminal to repeating stalk domains in bacterial surface proteins. The structure model of this domain consists out of seven beta-strands within two beta-sheets, similar to the RrgB pilus backbone, which was again described to correspond to the collagen binding domain. The position of this domain at the tip of bacterial surface proteins suggests an adhesive function. 167 matched cddid_all.tbl CDD pfam20593 pfam20593 466742 DUF6793 Family of unknown function (DUF6793). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 110 amino acids in length. Proteins in this family might have an RNA polymerase activity. 107 matched cddid_all.tbl CDD pfam20594 pfam20594 466743 DUF6794 Domain of unknown function (DUF6794). This domain is functionally uncharacterized, found in bacteria. It is around 120 amino acids in length. There is a conserved sequence motif GxxxRN. 83 matched cddid_all.tbl CDD pfam20595 pfam20595 466744 pAdhesive_6 Putative adhesive domain (group 6). This domain resembles the SdrG_C_C adhesive domain, known to bind within a supra-domain with the Big_8 domain (pfam17961) to fibrinogen. It is found N-terminal to repeating stalk domains in bacterial surface proteins. 165 matched cddid_all.tbl CDD pfam20596 pfam20596 466745 pAdhesive_11 Putative adhesive domain (group 11). This domain is found N-terminal to repeating stalk domains in Firmicutes and Actinobacteria surface proteins. The structure model resembles a receptor binding domain in cattle suggesting protein binding function. The structure model also resembles partly a galactose binding Yersinia pestis antigen. 112 matched cddid_all.tbl CDD pfam20597 pfam20597 466746 pAdhesive_15 Putative Ice-binding-like adhesive domain. This domain is found N-terminal to repeating stalk domains in bacterial surface proteins. The structure model of this domain is highly similar to the Ice_binding adhesive domain (pfam11999). However, the bacterial species in which this domain can be found, are less likely to be water-based and thus the function seems unlikely to be ice-binding. This domain is found in a Bacillus anthracis protein with the gene name BA_0871 or BASH2_04951, which was described to be collagen binding and to be involved in the bacterial pathogenicity. 253 matched cddid_all.tbl CDD pfam20598 pfam20598 466747 DUF6795 Domain of unknown function (DUF6795). This domain, mainly found in bacteria and eukaryotes, is functionally uncharacterized. This domain is approximately 100 amino acids in length and, based on structure prediction and overlaps with other families, belongs to the transthyretin superfamily. It is likely to have a seven stranded beta sandwich fold. 103 matched cddid_all.tbl CDD pfam20599 pfam20599 466748 DUF6796 Family of unknown function (DUF6796). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and fungi. Proteins in this family are typically between 220 and 250 amino acids in length. 225 matched cddid_all.tbl CDD pfam20600 pfam20600 466749 ExoX-like_C Exodeoxyribonuclease X-like C-terminal. This short domain is found at the C-terminal of Exodeoxyribonuclease 10 (ExoX) from Escherichia coli (strain K12) and it is functionally uncharacterized. This domain is found in bacteria and eukaryotes There is a conserved FGKY/H sequence motif. 28 matched cddid_all.tbl CDD pfam20601 pfam20601 466750 DUF6797 Domain of unknown function (DUF6797). This presumed domain is functionally uncharacterized. This domain is found in bacteria, and is around 100 amino acids in length. This domain is found in association with pfam13442. There is a conserved sequence motif GPLP. 96 matched cddid_all.tbl CDD pfam20602 pfam20602 466751 pAdhesive_8 Putative adhesive domain (group 8). The structure model of this domain resembles the C-terminal domains of the Streptococcus intermedius antigen I/II (AgI/II). The N-terminal domain of AgI/II (also called adhesin P1, antigen B or PAc) folds towards the stalk, where it gets locked in place. Given that this domain is found N-terminal to repeating stalk domains in bacterial surface proteins, the domain is suggested to have a potential protein binding function. 141 matched cddid_all.tbl CDD pfam20603 pfam20603 466752 Bact_hydrolase Bacterial hydrolase. This family of proteins, found in bacteria, is thought to have a hydrolase activity. 160 matched cddid_all.tbl CDD pfam20604 pfam20604 466753 DUF6798 Domain of unknown function (DUF6798). This presumed domain is functionally uncharacterized. This domain family is mainly found in bacteria and archaea, and is approximately 60 amino acids in length. There is a conserved WxxR sequence motif and a conserved Lys residue. Members of this entry may be transmembrane proteins. 60 matched cddid_all.tbl CDD pfam20605 pfam20605 466754 Antitox_RHH Antitoxin-like ribbon-helix-helix. This presumed domain is found in bacteria, and is approximately 60 amino acids in length. Structure prediction suggests that it has a ribbon-helix-helix motif, a DNA-binding motif commonly found in antitoxin families. Members containing this domain may be related to CopG antitoxin family. 50 matched cddid_all.tbl CDD pfam20606 pfam20606 466755 DUF6799 Domain of unknown function (DUF6799). This domain is functionally uncharacterized. This domain is found in bacteria and eukaryotes and it is approximately 50 amino acids in length. 63 matched cddid_all.tbl CDD pfam20607 pfam20607 466756 DUF6800 Family of unknown function (DUF6800). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length and have conserved Arginine residues. This family may have an alpha-helical structure. 43 matched cddid_all.tbl CDD pfam20608 pfam20608 466757 Phage_tube_C Phage tail tube protein C-terminal domain. This short all beta domain is found at the C-terminus of some phage tube proteins 82 matched cddid_all.tbl CDD pfam20609 pfam20609 466758 pAdhesive_17 Putative adhesive domain (group 17). The structure model of this domain folds into 10 beta strands arranged in two beta sheets as well as 4-5 elongated alpha helices. The beta sheets distantly resemble the Collagen_bind (pfam05737) domain. It is annotated N-terminal to repeating stalk domains in bacterial surface proteins. This domain can be found on a E. faecalis protein encoded by the EF3314 gene, which was proposed to contribute to the interaction of E. faecalis with the host and to the bacterial virulence. 289 matched cddid_all.tbl CDD pfam20610 pfam20610 466759 TED_2 Thioester domain. This domain is related to the TED domain pfam08341. 130 matched cddid_all.tbl CDD pfam20611 pfam20611 466760 DUF6801 Family of unknown function (DUF6801). This domain is found in a variety of bacterial extracellular proteins. It contains a beta barrel structure. 159 matched cddid_all.tbl CDD pfam20612 pfam20612 466761 SHOCT_2 SHOCT domain. This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 53 and 72 amino acids in length. This family of proteins is related to the SHOCT domain. 53 matched cddid_all.tbl CDD pfam20613 pfam20613 466762 HipA_2 HipA-like kinase. This family of proteins is distantly related to the HipA protein. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 254 and 265 amino acids in length. 240 matched cddid_all.tbl CDD pfam20614 pfam20614 466763 Mycovirus_RNAse homologs of viral RNAse III, found in viruses infecting fungi. This domain is found in viruses infecting fungi (mycoviruses), either as a standalone domain in short proteins (e.g. in deltaflexiviruses), or in polyproteins (e.g. endornaviruses or hypoviruses). It is homologous to RNAse III domains (pfam14622, pfam00636, pfam11469) as seen using sequence-based searches. Its function is unknown. 77 matched cddid_all.tbl CDD pfam20615 pfam20615 466764 DUF6802 Family of unknown function (DUF6802). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 101 and 135 amino acids in length. 102 matched cddid_all.tbl CDD pfam20616 pfam20616 466765 Caps_syn_GfcC_N Capsule biosynthesis GfcC, N-terminal. Many bacteria are covered in a layer of surface-associated polysaccharide called the capsule. These capsules can be divided into four groups depending upon the organization of genes responsible for capsule assembly, the assembly pathway and regulation. This family plays a role in group 4 capsule biosynthesis. These proteins have a beta-grasp fold. Two beta-grasp domains, D2 and D3, are arranged in tandem. There is a C-terminal amphipathic helix which packs against D3. A helical hairpin insert in D2 binds to D3 and constrains its position, a conserved arginine residue at the end of this hairpin is essential for structural integrity. This entry represents D2 domain found at the N-terminal. 129 matched cddid_all.tbl CDD pfam20617 pfam20617 466766 DUF6803 Family of unknown function (DUF6803). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 162 and 222 amino acids in length. Structurally, proteins in this family are made of a Four Helix Bundle. 162 matched cddid_all.tbl CDD pfam20618 pfam20618 466767 GPD_NAD_C_bact Bacterial GPD, NAD-dependent C-terminal. This is the C-terminal domain of NAD-dependent glycerol-3-phosphate dehydrogenase (GPD) from bacteria and archaea. GPD catalyzes the reversible reduction of dihydroxyacetone phosphate to glycerol-3-phosphate. 66 matched cddid_all.tbl CDD pfam20619 pfam20619 466768 DUF6804 Family of unknown function (DUF6804). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are typically between 98 and 195 amino acids in length and adopt a helix-rich bundle structure and share a similar fold with a flagellin homolog, hook-associated protein. 91 matched cddid_all.tbl CDD pfam20620 pfam20620 466769 DUF6805 Family of unknown function (DUF6805). This presumed domain is functionally uncharacterized. This domain family is found in bacteria, and is approximately 130 amino acids in length. The family is found in association with pfam07944, pfam16375. 133 matched cddid_all.tbl CDD pfam20621 pfam20621 466770 DUF6806 Family of unknown function (DUF6806). This family of proteins is functionally uncharacterized. This family of proteins is found in bacteria. Proteins in this family are approximately 210 amino acids in length and their N-terminal share a similar structure with the Crispr-associated endoribonuclease Cas2. 159 matched cddid_all.tbl CDD pfam20622 pfam20622 466771 Big_15 Bacterial Ig domain (Big_16). This bacterial Ig-like domain is found in the stalk regions of bacterial cell surface adhesins. 82 matched cddid_all.tbl CDD pfam20623 pfam20623 466772 Sgo0707_N2 Sgo0707 N2 domain. This domain represents the N2 domain found in the Sgo0707 adhesin protein. This domain is closely related to pfam16569. 141 matched cddid_all.tbl CDD pfam20624 pfam20624 466773 DMRT5_DMB DMRT5, DMB domain. This is the DMB domain found at the C-terminal of DMRT5 proteins (doublesex and mab-3 related transcription factor, also known as Doublesex- and mab-3-related transcription factor A2). These proteins are involved in sexual development although not restricted to the developing gonads in vertebrates. DMRT5, together with DMRT4, has been identified as an important regulator of neurogenesis. This domain is adjacent the DMA domain (pfam03474), both of which are required for neuronal differentiation. 88 matched cddid_all.tbl CDD sd00001 sd00001 275365 TSP3 Calcium-binding Thrombospondin type 3 (TSP3) repeat. TSP3 repeats of the vertebrate thrombospondin (TSP)-1,-2,-3,-4 and TSP-5/also known as COMP (cartilage oligomeric matrix protein), and related proteins. These short aspartate-rich repeats are a continuous series of calcium binding sites that can be divided into two sequence motifs: N-type and C-type. N-type and C-type motifs are distinguished by their sequence length, calcium ion binding, and their interactions with water molecules. C-type motifs are higher affinity binding sites compared to N-type motifs. 59 matched cddid_all.tbl CDD sd00002 sd00002 275366 TSP3 Calcium-binding Thrombospondin type 3 (TSP3) repeat. TSP3 repeats of the vertebrate thrombospondin (TSP)-1,-2,-3,-4 and TSP-5/also known as COMP (cartilage oligomeric matrix protein), and related proteins. These short aspartate-rich repeats are a continuous series of calcium binding sites that can be divided into two sequence motifs: N-type and C-type. N-type and C-type motifs are distinguished by their sequence length, calcium ion binding, and their interactions with water molecules. C-type motifs are higher affinity binding sites compared to N-type motifs. 59 matched cddid_all.tbl CDD sd00003 sd00003 275367 TSP3_1C Calcium-binding Thrombospondin type 3 (TSP3) repeat; C-type motif 1C. TSP3 repeats of the vertebrate thrombospondin (TSP)-1,-2,-3,-4 and TSP-5/also known as COMP (cartilage oligomeric matrix protein), and related proteins. These short aspartate-rich repeats are a continuous series of calcium binding sites that can be divided into two sequence motifs: N-type and C-type. N-type and C-type motifs are distinguished by their sequence length, calcium ion binding, and their interactions with water molecules. C-type motifs are higher affinity binding sites compared to N-type motifs. The first TSP3 repeat 1C deviates from the canonical C-type calcium binding repeat in containing an insert relative to the other C-type repeats, however, the residues of the interrupted halves are positioned identically to C-type repeats without the insert. 35 matched cddid_all.tbl CDD sd00004 sd00004 276811 PPR Pentatricopeptide repeat, an RNA-binding module. The Pentatricopeptide repeat (PPR) is a 35-residue repeat motif that forms two anti-parallel alpha helices and binds single-stranded RNA in a sequence-specific and modular manner. It is present in a large family of RNA-binding proteins that are found in protists, fungi, and metazoan, but are most abundant in the mitochondria and chloroplasts of terrestrial plants. PPR proteins function in many aspects of RNA metabolism, including splicing, editing, degradation, and translation. They contain between 2 to 30 PPR repeats, organized into a hairpin of alpha helices. Proteins containing only arrays of PPR repeats that are 35-amino acid in length are called P class proteins. The second type of PPR proteins, called PLS class, contain additional C-terminal endonuclease or RNA editing domains and a distinct PPR architecture of triplet repeats alternating between a typical PPR, a longer PPR and a short PPR of 31 residues. 100 matched cddid_all.tbl CDD sd00005 sd00005 276810 TPR Tetratricopeptide repeat. The Tetratricopeptide repeat (TPR) typically contains 34 amino acids and is found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans. It is present in a variety of proteins including those involved in chaperone, cell-cycle, transcription, and protein transport complexes. The number of TPR motifs varies among proteins. Those containing 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accommodate an alpha-helix of a target protein. It has been proposed that TPR proteins preferentially interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes. 60 matched cddid_all.tbl CDD sd00006 sd00006 276809 TPR Tetratricopeptide repeat. The Tetratricopeptide repeat (TPR) typically contains 34 amino acids and is found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans. It is present in a variety of proteins including those involved in chaperone, cell-cycle, transcription, and protein transport complexes. The number of TPR motifs varies among proteins. Those containing 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accommodate an alpha-helix of a target protein. It has been proposed that TPR proteins preferentially interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes. 97 matched cddid_all.tbl CDD sd00008 sd00008 276808 TPR_YbbN C-terminal Tetratricopeptide repeat (TPR) region of YbbN and similar motifs. The Tetratricopeptide repeat (TPR) typically contains 34 amino acids and is found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans. It is present in a variety of proteins including those involved in chaperone, cell-cycle, transcription, and protein transport complexes. YbbN is a thioredoxin-like protein containing two tandem TPR repeats at the C-terminus, separated by two alpha helices. Its N-terminal thioredoxin-like domain is not a functional oxidoreductase. It functions in heat stress response and DNA synthesis as a chaperone or co-chaperone. 171 matched cddid_all.tbl CDD sd00010 sd00010 276807 SLR Sel1-like repeat. Sel1-like repeats (SLRs) share similar alpha-helical conformations with Tetratricopeptide repeats (TPRs), but with different consensus sequence lengths and superhelical topologies. SLRs contain 36 to 44 amino acids and are present in bacteria and eukaryotes but not in archaea. SLR proteins are involved in a variety of functions, and many serve as adaptor proteins for the assembly of macromolecular complexes. The SLR family was named after the Caenorhabditis elegans Sel1 protein which is predicted to fold into 11 SLRs, a transmembrane domain, and an N-terminal signal sequence. The human Sel1L protein contains an additional fibronectin type-II domain and an N-terminal PEST sequence. Its downregulation is associated with the development of breast and pancreatic carcinomas. 133 matched cddid_all.tbl CDD sd00016 sd00016 276806 Apc5 Tetratricopeptide repeat (TPR)-like motif of Apc5 and similar motifs. Apc5 is a subunit of the anaphase-promoting complex/cyclosome (APC/C) which is a multi-subunit ubiquitin ligase that mediates the proteolysis of cell cycle proteins in mitosis and G1. Apc5 binds the poly(A) binding protein (PABP), which directly binds the internal ribosome entry site (IRES) of growth factor 2 mRNA. PABP was found to enhance IRES-mediated translation, whereas Apc5 over-expression counteracted this effect. In addition to its association with the APC/C complex, Apc5 binds much heavier complexes and co-sediments with the ribosomal fraction. The N-terminus of Afi1 serves to stabilize the union between Apc4 and Apc5, both of which lie towards the bottom-front of the APC. This model represents the Tetratricopeptide repeat (TPR)-like motif region of Apc5. 98 matched cddid_all.tbl CDD sd00017 sd00017 275368 ZF_C2H2 Zinc finger, C2H2 type. The C2H2 zinc finger is a classical zinc finger domain. C2H2-type zinc fingers are ubiquitous; more than 1% of all mammalian proteins are predicted to contain at least one zinc finger. They often function as DNA or protein binding structural motifs, such as in eukaryotic transcription factors, and therefore they play important roles in cellular processes such as development, differentiation, and oncosuppression. C2H2 zinc finger proteins contain from 1 to more than 30 zinc finger repeats. 78 matched cddid_all.tbl CDD sd00018 sd00018 275369 ZF_C2H2 Zinc finger, C2H2 type. The C2H2 zinc finger is a classical zinc finger domain. C2H2-type zinc fingers are ubiquitous; more than 1% of all mammalian proteins are predicted to contain at least one zinc finger. They often function as DNA or protein binding structural motifs, such as in eukaryotic transcription factors, and therefore they play important roles in cellular processes such as development, differentiation, and oncosuppression. C2H2 zinc finger proteins contain from 1 to more than 30 zinc finger repeats. 24 matched cddid_all.tbl CDD sd00019 sd00019 275370 ZF_C2H2 Zinc finger, C2H2 type. The C2H2 zinc finger is a classical zinc finger domain. C2H2-type zinc fingers are ubiquitous; more than 1% of all mammalian proteins are predicted to contain at least one zinc finger. They often function as DNA or protein binding structural motifs, such as in eukaryotic transcription factors, and therefore they play important roles in cellular processes such as development, differentiation, and oncosuppression. C2H2 zinc finger proteins contain from 1 to more than 30 zinc finger repeats. 49 matched cddid_all.tbl CDD sd00020 sd00020 275371 ZF_C2H2 Zinc finger, C2H2 type. The C2H2 zinc finger is a classical zinc finger domain. C2H2-type zinc fingers are ubiquitous; more than 1% of all mammalian proteins are predicted to contain at least one zinc finger. They often function as DNA or protein binding structural motifs, such as in eukaryotic transcription factors, and therefore they play important roles in cellular processes such as development, differentiation, and oncosuppression. C2H2 zinc finger proteins contain from 1 to more than 30 zinc finger repeats. 46 matched cddid_all.tbl CDD sd00025 sd00025 275375 zf-RanBP2 RanBP2-type zinc finger. The zf-RanBP2 domain represents a new superfamily of C2C2-type zinc finger motif, which is characterized by the conserved sequence pattern W-X-C-X(2,4)-C-X(3)-N-X(6)-C-X(2)-C. They fold into a structure composed of two orthogonal beta-hairpin strands that sandwich a single Zn2+ ion coordinated with four cysteine residues. zf-RanBP2 domains are mainly found in eukaryotic proteins and some exist in bacteria and archaea. According to different binding partners, the superfamily can be classified into several families. For instance, the E3 SUMO-protein ligase RanBP2-like family binds Ran, the nuclear protein localization protein 4 homolog (NPL4)-like family binds ubiquitin, and the zinc finger Ran-binding domain-containing protein 2 (ZRANB2)-like family binds single-stranded RNA (ssRNA). Most of superfamily members contain one copy of zf-RanBP2, but some contain several zf-RanBP2 domains. 293 matched cddid_all.tbl CDD sd00029 sd00029 275376 zf-RanBP2 RanBP2-type zinc finger. The zf-RanBP2 domain represents a new superfamily of C2C2-type zinc finger motif, which is characterized by the conserved sequence pattern W-X-C-X(2,4)-C-X(3)-N-X(6)-C-X(2)-C. They fold into a structure composed of two orthogonal beta-hairpin strands that sandwich a single Zn2+ ion coordinated with four cysteine residues. zf-RanBP2 domains are mainly found in eukaryotic proteins and some exist in bacteria and archaea. According to different binding partners, the superfamily can be classified into several families. For instance, the E3 SUMO-protein ligase RanBP2-like family binds Ran, the nuclear protein localization protein 4 homolog (NPL4)-like family binds ubiquitin, and the zinc finger Ran-binding domain-containing protein 2 (ZRANB2)-like family binds single-stranded RNA (ssRNA). Most of superfamily members contain one copy of zf-RanBP2, but some contain several zf-RanBP2 domains. 74 matched cddid_all.tbl CDD sd00030 sd00030 275377 zf-RanBP2 RanBP2-type zinc finger. The zf-RanBP2 domain represents a new superfamily of C2C2-type zinc finger motif, which is characterized by the conserved sequence pattern W-X-C-X(2,4)-C-X(3)-N-X(6)-C-X(2)-C. They fold into a structure composed of two orthogonal beta-hairpin strands that sandwich a single Zn2+ ion coordinated with four cysteine residues. zf-RanBP2 domains are mainly found in eukaryotic proteins and some exist in bacteria and archaea. According to different binding partners, the superfamily can be classified into several families. For instance, the E3 SUMO-protein ligase RanBP2-like family binds Ran, the nuclear protein localization protein 4 homolog (NPL4)-like family binds ubiquitin, and the zinc finger Ran-binding domain-containing protein 2 (ZRANB2)-like family binds single-stranded RNA (ssRNA). Most of superfamily members contain one copy of zf-RanBP2, but some contain several zf-RanBP2 domains. 60 matched cddid_all.tbl CDD sd00031 sd00031 275378 LRR_1 leucine-rich repeats. A leucine-rich repeat (LRR) is a structural protein motif of 20-30 amino acids that is unusually rich in the hydrophobic amino acid leucine. The conserved eleven-residue sequence motif (LxxLxLxxN/CxL) within the LRRs corresponds to the beta-strand and adjacent loop regions, whereas the remaining parts of the repeats are variable. LRRs fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Leucine-rich repeats are usually involved in protein-protein interactions. 110 matched cddid_all.tbl CDD sd00032 sd00032 275379 LRR_2 leucine rich repeats. A leucine-rich repeat (LRR) is a structural protein motif of 20-30 amino acids that is unusually rich in the hydrophobic amino acid leucine. The conserved eleven-residue sequence motif (LxxLxLxxN/CxL) within the LRRs corresponds to the beta-strand and adjacent loop regions, whereas the remaining parts of the repeats are variable. LRRs fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Leucine-rich repeats are usually involved in protein-protein interactions. 205 matched cddid_all.tbl CDD sd00033 sd00033 275380 LRR_RI leucine-rich repeats, ribonuclease inhibitor (RI)-like subfamily. A leucine-rich repeat (LRR) is a structural protein motif of 20-30 amino acids that is unusually rich in the hydrophobic amino acid leucine. The conserved eleven-residue sequence motif (LxxLxLxxN/CxL) within the LRRs corresponds to the beta-strand and adjacent loop regions, whereas the remaining parts of the repeats are variable. LRRs fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Leucine-rich repeats are usually involved in protein-protein interactions. 238 matched cddid_all.tbl CDD sd00034 sd00034 275381 LRR_AMN1 leucine-rich repeats, antagonist of mitotic exit network protein 1-like subfamily. A leucine-rich repeat (LRR) is a structural protein motif of 20-30 amino acids that is unusually rich in the hydrophobic amino acid leucine. The conserved eleven-residue sequence motif (LxxLxLxxN/CxL) within the LRRs corresponds to the beta-strand and adjacent loop regions, whereas the remaining parts of the repeats are variable. LRRs fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Leucine-rich repeats are usually involved in protein-protein interactions. 212 matched cddid_all.tbl CDD sd00035 sd00035 275382 LRR_NTF leucine-rich repeats, nuclear transport factor-like subfamily. A leucine-rich repeat (LRR) is a structural protein motif of 20-30 amino acids that is unusually rich in the hydrophobic amino acid leucine. The conserved eleven-residue sequence motif (LxxLxLxxN/CxL) within the LRRs corresponds to the beta-strand and adjacent loop regions, whereas the remaining parts of the repeats are variable. LRRs fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Leucine-rich repeats are usually involved in protein-protein interactions. 144 matched cddid_all.tbl CDD sd00036 sd00036 275383 LRR_3 leucine-rich repeats. A leucine-rich repeat (LRR) is a structural protein motif of 20-30 amino acids that is unusually rich in the hydrophobic amino acid leucine. The conserved eleven-residue sequence motif (LxxLxLxxN/CxL) within the LRRs corresponds to the beta-strand and adjacent loop regions, whereas the remaining parts of the repeats are variable. LRRs fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Leucine-rich repeats are usually involved in protein-protein interactions. 142 matched cddid_all.tbl CDD sd00037 sd00037 275384 PASTA PASTA domain. PASTA domain is found at the C-termini of several penicillin-binding proteins (PBPs) and bacterial serine/threonine kinases. It is a small globular domain consisting of 3 beta-sheets and an alpha-helix. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain. 126 matched cddid_all.tbl CDD sd00038 sd00038 276965 Kelch Kelch repeat. Kelch repeats are 44 to 56 amino acids in length and form a four-stranded beta-sheet corresponding to a single blade of five to seven bladed beta propellers. The Kelch superfamily is a large evolutionary conserved protein family whose members are present throughout the cell and extracellularly, and have diverse activities. Kelch repeats are often in combination with other domains, like BTB and BACK or F-box domains. 140 matched cddid_all.tbl CDD sd00039 sd00039 293791 7WD40 WD40 repeats in seven bladed beta propellers. The WD40 repeat is found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing, and cytoskeleton assembly. It typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40. Between the GH and WD dipeptides lies a conserved core. It forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel beta-sheet. The WD40 sequence repeat originally described in literature forms the first three strands of one blade and the last strand in the next blade. The C-terminal WD40 repeat completes the blade structure of the N-terminal WD40 repeat to create the closed ring propeller-structure. The residues on the top and bottom surface of the propeller are proposed to coordinate interactions with other proteins and/or small ligands, allowing them to bind either stably or reversibly. 293 matched cddid_all.tbl CDD sd00041 sd00041 293790 GyrA-ParC_C beta-pinwheel repeat found at the C-terminus of GyrA, ParC, and similar proteins. Beta-pinwheel repeats are found at the C-terminus of both DNA gyrase subunit A and ParC, a subunit of topoisomerase IV (topo IV). DNA gyrase, a type IIA topoisomerase is a GyrA2GyrB2 heterotetramer which introduces negative supercoiling into the circular bacterial chromosome. Topo IV, a type IIB topoisomerase, is a ParC2ParE2 tetramer, which primarily relaxes positive supercoils and mediates topological unlinking of entangled DNA segments such as catenanes. The GyrA C-terminal repeat region, referred to as the C-terminal domain or CTD, binds DNA nonspecifically; it is thought to constrain a positive supercoil by wrapping a DNA duplex around its surface, upon strand passage, this wrap is converted into two negative supercoils. All known gyrase CTDs have 6 bladed beta-pinwheels, the topo IV CTD in various organisms is more variable and includes both 3-bladed and 8-bladed pinwheels. 253 matched cddid_all.tbl CDD sd00042 sd00042 293789 LVIVD LVIVD repeat. LVIVD repeats are mainly found in bacterial and archaeal cell surface proteins, many of them hypothetical. Structurally, LVIVD repeats have been predicted to form a beta-propeller, with each repeat forming one four-stranded anti-parallel beta-sheet blade. 120 matched cddid_all.tbl CDD sd00043 sd00043 293788 ARM armadillo repeat. Armadillo (ARM)/beta-catenin-like repeats are approximately 40 amino acid long, tandemly repeated sequence motif, first identified in the Drosophila segment polarity gene armadillo. These repeats were also found in the mammalian armadillo homolog beta-catenin, the junctional plaque protein plakoglobin, the adenomatous polyposis coli (APC) tumor suppressor protein, and a number of other proteins. ARM has been implicated in mediating protein-protein interactions, but no common features among the target proteins recognized by the ARM repeats have been identified. ARM repeats are related to HEAT repeats. 117 matched cddid_all.tbl CDD sd00044 sd00044 293787 HEAT HEAT repeats. The canonical HEAT repeat consists of two helices forming a helical hairpin. HEAT repeats are found in a diverse family of proteins, including the four proteins from which its name is based: Huntingtin, Elongation factor 3, the PR65/A subunit of protein phosphatase 2A (PP2A), and the lipid kinase TOR (target of rapamycin). The HEAT repeat family is related to armadillo (ARM)/beta-catenin-like repeats. 181 matched cddid_all.tbl CDD sd00045 sd00045 293786 ANK ankyrin repeats. Ankyrin repeats are one of the most abundant repeat motifs, and generally function as scaffolds for protein-protein interactions in processes including cell cycle, transcriptional regulation, signal transduction, vesicular trafficking, and inflammatory response. Although predominantly found in eukaryotic proteins, they are also found in some bacterial and viral proteins. Less is known of their physiological roles in prokaryotes. Some bacterial ANK proteins play key roles in microbial pathogenesis by mimicking or manipulating host function(s). The pathogen Providencia alcalifaciens N-formyltransferase ankyrin repeats function in small molecule binding and allosteric control. Ankyrin-repeat proteins have been associated with a number of human diseases. 98 matched cddid_all.tbl CDD sd00046 sd00046 293785 FHA_bHelix beta-helical repeat found in filamentous hemagglutinin and related adhesins and CdiA family proteins. This model contains ten copies of an approximately 20-residue repeat found in two-partner secretion (TPS) proteins, including the filamentous hemagglutinin (FHA) family of adhesins and CdiA family proteins. These repeats form a right-handed beta-helical structure, and are found in large secreted proteins from a number of plant and animal pathogens. FHA family adhesins bind to various types of cells and may contribute to attachment, aggregation, and pathogenesis. CdiA proteins are involved in contact-dependent growth inhibition (CDI). 209 matched cddid_all.tbl CDD smart00002 smart00002 128322 PLP Myelin proteolipid protein (PLP or lipophilin). 60 matched cddid_all.tbl CDD smart00003 smart00003 128323 NH Neurohypophysial hormones. Vasopressin/oxytocin gene family. 78 matched cddid_all.tbl CDD smart00004 smart00004 197463 NL Domain found in Notch and Lin-12. The Notch protein is essential for the proper differentiation of the Drosophila ectoderm. This protein contains 3 NL domains. 38 matched cddid_all.tbl CDD smart00005 smart00005 214467 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers. 88 matched cddid_all.tbl CDD smart00006 smart00006 128326 A4_EXTRA amyloid A4. amyloid A4 precursor of Alzheimers disease 165 matched cddid_all.tbl CDD smart00008 smart00008 214468 HormR Domain present in hormone receptors. 70 matched cddid_all.tbl CDD smart00010 smart00010 197466 small_GTPase Small GTPase of the Ras superfamily; ill-defined subfamily. SMART predicts Ras-like small GTPases of the ARF, RAB, RAN, RAS, and SAR subfamilies. Others that could not be classified in this way are predicted to be members of the small GTPase superfamily without predictions of the subfamily. 166 matched cddid_all.tbl CDD smart00012 smart00012 214469 PTPc_DSPc "Protein tyrosine phosphatase, catalytic domain, undefined specificity. Protein tyrosine phosphatases. Homologues detected by this profile and not by those of ""PTPc"" or ""DSPc"" are predicted to be protein phosphatases with a similar fold to DSPs and PTPs, yet with unpredicted specificities." 105 matched cddid_all.tbl CDD smart00013 smart00013 214470 LRRNT Leucine rich repeat N-terminal domain. 33 matched cddid_all.tbl CDD smart00014 smart00014 214471 acidPPc Acid phosphatase homologues. 116 matched cddid_all.tbl CDD smart00015 smart00015 197470 IQ Calmodulin-binding motif. Short calmodulin-binding motif containing conserved Ile and Gln residues. 23 matched cddid_all.tbl CDD smart00017 smart00017 214472 OSTEO Osteopontin. Osteopontin is an acidic phosphorylated glycoprotein of about 40 Kd which is abundant in the mineral matrix of bones and which binds tightly to hydroxyapatite. It is suggested that osteopontin might function as a cell attachment factor and could play a key role in the adhesion of osteoclasts to the mineral matrix of bone 287 matched cddid_all.tbl CDD smart00018 smart00018 197472 PD P or trefoil or TFF domain. Proposed role in renewal and pathology of mucous epithelia. 46 matched cddid_all.tbl CDD smart00019 smart00019 128335 SF_P Pulmonary surfactant proteins. Pulmonary surfactant associated proteins promote alveolar stability by lowering the surface tension at the air-liquid interface in the peripheral air spaces. SP-C, a component of surfactant, is a highly hydrophobic peptide of 35 amino acid residues which is processed from a larger precursor protein. SP-C is post-translationally modified by the covalent attachment of two palmitoyl groups on two adjacent cysteines 191 matched cddid_all.tbl CDD smart00020 smart00020 214473 Tryp_SPc Trypsin-like serine protease. Many of these are synthesised as inactive precursor zymogens that are cleaved during limited proteolysis to generate their active forms. A few, however, are active as single chain molecules, and others are inactive due to substitutions of the catalytic triad residues. 229 matched cddid_all.tbl CDD smart00021 smart00021 197474 DAX Domain present in Dishevelled and axin. Domain of unknown function. 83 matched cddid_all.tbl CDD smart00022 smart00022 214474 PLAc Cytoplasmic phospholipase A2, catalytic subunit. Cytosolic phospholipases A2 hydrolyse arachidonyl phospholipids. Family includes phospholipases B isoforms. 549 matched cddid_all.tbl CDD smart00023 smart00023 128339 COLIPASE Colipase. Colipase is a protein that functions as a cofactor for pancreatic lipase, with which it forms a stoichiometric complex. It also binds to the bile-salt covered triacylglycerol interface thus allowing the enzyme to anchor itself to the water-lipid interface. Colipase is a small protein of approximately 100 amino-acid residues with five conserved disulfide bonds. 95 matched cddid_all.tbl CDD smart00025 smart00025 214475 Pumilio Pumilio-like repeats. Pumilio-like repeats that bind RNA. 36 matched cddid_all.tbl CDD smart00026 smart00026 128341 EPEND Ependymins. Ependymins are the predominant proteins in the cerebrospinal fluid (CSF) of teleost fish. They have been implicated in the neurochemistry of memory and neuronal regeneration. They are glycoproteins of about 200 amino acids that can bind calcium. Four cysteines are conserved that probably form disulfide bonds. 191 matched cddid_all.tbl CDD smart00027 smart00027 197477 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences. 96 matched cddid_all.tbl CDD smart00028 smart00028 197478 TPR "Tetratricopeptide repeats. Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a ""knobs and holes"" mechanism." 34 matched cddid_all.tbl CDD smart00029 smart00029 214476 GASTRIN gastrin / cholecystokinin / caerulein family. This family gathers small proteins of about 100 130 amino acids that act as hormones, among them gastrin, cholecystokinin and preprocaerulein which stimulate gastric, biliary, and pancreatic secretion and smooth muscle contraction. 14 matched cddid_all.tbl CDD smart00030 smart00030 128345 CLb CLUSTERIN Beta chain. 206 matched cddid_all.tbl CDD smart00031 smart00031 214477 DED Death effector domain. 79 matched cddid_all.tbl CDD smart00032 smart00032 214478 CCP Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR). The complement control protein (CCP) modules (also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been identified in several proteins of the complement system. A missense mutation in seventh CCP domain causes deficiency of the b subunit of factor XIII. 56 matched cddid_all.tbl CDD smart00033 smart00033 214479 CH Calponin homology domain. Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). These domains cross-link actin filaments into bundles and networks. A calponin homology domain is predicted in yeasst Cdc24p. 101 matched cddid_all.tbl CDD smart00034 smart00034 214480 CLECT C-type lectin (CTL) or carbohydrate-recognition domain (CRD). Many of these domains function as calcium-dependent carbohydrate binding modules. 124 matched cddid_all.tbl CDD smart00035 smart00035 128350 CLa CLUSTERIN alpha chain. 216 matched cddid_all.tbl CDD smart00036 smart00036 214481 CNH Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2. 302 matched cddid_all.tbl CDD smart00037 smart00037 128352 CNX Connexin homologues. Connexin channels participate in the regulation of signaling between developing and differentiated cell types. 34 matched cddid_all.tbl CDD smart00038 smart00038 197483 COLFI Fibrillar collagens C-terminal domain. Found at C-termini of fibrillar collagens: Ephydatia muelleri procollagen EMF1alpha, vertebrate collagens alpha(1)III, alpha(1)II, alpha(2)V etc. 232 matched cddid_all.tbl CDD smart00039 smart00039 128354 CRF corticotropin-releasing factor. 40 matched cddid_all.tbl CDD smart00040 smart00040 128355 CSF2 Granulocyte-macrophage colony-simulating factor (GM-CSF). GM-CSF stimulates the development of and the cytotoxic activity of white blood cells. 121 matched cddid_all.tbl CDD smart00041 smart00041 214482 CT C-terminal cystine knot-like domain (CTCK). The structures of transforming growth factor-beta (TGFbeta), nerve growth factor (NGF), platelet-derived growth factor (PDGF) and gonadotropin all form 2 highly twisted antiparallel pairs of beta-strands and contain three disulphide bonds. The domain is non-globular and little is conserved among these presumed homologues except for their cysteine residues. CT domains are predicted to form homodimers. 82 matched cddid_all.tbl CDD smart00042 smart00042 214483 CUB Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. This domain is found mostly among developmentally-regulated proteins. Spermadhesins contain only this domain. 102 matched cddid_all.tbl CDD smart00043 smart00043 214484 CY Cystatin-like domain. Cystatins are a family of cysteine protease inhibitors that occur mainly as single domain proteins. However some extracellular proteins such as kininogen, His-rich glycoprotein and fetuin also contain these domains. 107 matched cddid_all.tbl CDD smart00044 smart00044 214485 CYCc Adenylyl- / guanylyl cyclase, catalytic domain. Present in two copies in mammalian adenylyl cyclases. Eubacterial homologues are known. Two residues (Asn, Arg) are thought to be involved in catalysis. These cyclases have important roles in a diverse range of cellular processes. 194 matched cddid_all.tbl CDD smart00045 smart00045 214486 DAGKa Diacylglycerol kinase accessory domain (presumed). Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. DAG can be produced from the hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2) by a phosphoinositide-specific phospholipase C and by the degradation of phosphatidylcholine (PC) by a phospholipase C or the concerted actions of phospholipase D and phosphatidate phosphohydrolase. This domain might either be an accessory domain or else contribute to the catalytic domain. Bacterial homologues are known. 160 matched cddid_all.tbl CDD smart00046 smart00046 214487 DAGKc Diacylglycerol kinase catalytic domain (presumed). Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. DAG can be produced from the hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2) by a phosphoinositide-specific phospholipase C and by the degradation of phosphatidylcholine (PC) by a phospholipase C or the concerted actions of phospholipase D and phosphatidate phosphohydrolase. This domain is presumed to be the catalytic domain. Bacterial homologues areknown. 124 matched cddid_all.tbl CDD smart00047 smart00047 214488 LYZ2 Lysozyme subfamily 2. Eubacterial enzymes distantly related to eukaryotic lysozymes. 147 matched cddid_all.tbl CDD smart00048 smart00048 128363 DEFSN Defensin/corticostatin family. Cysteine-rich domains that lyse bacteria, fungi and enveloped viruses by forming multimeric membrane-spanning channels. 29 matched cddid_all.tbl CDD smart00049 smart00049 214489 DEP Domain found in Dishevelled, Egl-10, and Pleckstrin. Domain of unknown function present in signalling proteins that contain PH, rasGEF, rhoGEF, rhoGAP, RGS, PDZ domains. DEP domain in Drosophila dishevelled is essential to rescue planar polarity defects and induce JNK signalling (Cell 94, 109-118). 77 matched cddid_all.tbl CDD smart00050 smart00050 214490 DISIN Homologues of snake disintegrins. Snake disintegrins inhibit the binding of ligands to integrin receptors. They contain a 'RGD' sequence, identical to the recognition site of many adhesion proteins. Molecules containing both disintegrin and metalloprotease domains are known as ADAMs. 75 matched cddid_all.tbl CDD smart00051 smart00051 128366 DSL delta serrate ligand. 63 matched cddid_all.tbl CDD smart00052 smart00052 214491 EAL Putative diguanylate phosphodiesterase. Putative diguanylate phosphodiesterase, present in a variety of bacteria. 242 matched cddid_all.tbl CDD smart00053 smart00053 197491 DYNc Dynamin, GTPase. Large GTPases that mediate vesicle trafficking. Dynamin participates in the endocytic uptake of receptors, associated ligands, and plasma membrane following an exocytic event. 240 matched cddid_all.tbl CDD smart00054 smart00054 197492 EFh EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions. 29 matched cddid_all.tbl CDD smart00055 smart00055 214492 FCH Fes/CIP4 homology domain. Alignment extended from original report. Highly alpha-helical. Also known as the RAEYL motif or the S. pombe Cdc15 N-terminal domain. 87 matched cddid_all.tbl CDD smart00057 smart00057 214493 FIMAC factor I membrane attack complex. 68 matched cddid_all.tbl CDD smart00058 smart00058 214494 FN1 Fibronectin type 1 domain. One of three types of internal repeat within the plasma protein, fibronectin. Found also in coagulation factor XII, HGF activator and tissue-type plasminogen activator. In t-PA and fibronectin, this domain type contributes to fibrin-binding. 45 matched cddid_all.tbl CDD smart00059 smart00059 128373 FN2 Fibronectin type 2 domain. One of three types of internal repeat within the plasma protein, fibronectin. Also occurs in coagulation factor XII, 2 type IV collagenases, PDC-109, and cation-independent mannose-6-phosphate and secretory phospholipase A2 receptors. In fibronectin, PDC-109, and the collagenases, this domain contributes to collagen-binding function. 49 matched cddid_all.tbl CDD smart00060 smart00060 214495 FN3 Fibronectin type 3 domain. One of three types of internal repeat within the plasma protein, fibronectin. The tenth fibronectin type III repeat contains a RGD cell recognition sequence in a flexible loop between 2 strands. Type III modules are present in both extracellular and intracellular proteins. 83 matched cddid_all.tbl CDD smart00061 smart00061 214496 MATH meprin and TRAF homology. 95 matched cddid_all.tbl CDD smart00062 smart00062 214497 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe 219 matched cddid_all.tbl CDD smart00063 smart00063 214498 FRI Frizzled. Drosophila melanogaster frizzled mediates signalling that polarises a precursor cell along the anteroposterior axis. Homologues of the N-terminal region of frizzled exist either as transmembrane or secreted molecules. Frizzled homologues are reported to be receptors for the Wnt growth factors. (Not yet in MEDLINE: the FRI domain occurs in several receptor tyrosine kinases [Xu, Y.K. and Nusse, Curr. Biol. 8 R405-R406 (1998); Masiakowski, P. and Yanopoulos, G.D., Curr. Biol. 8, R407 (1998)]. 113 matched cddid_all.tbl CDD smart00064 smart00064 214499 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PHD finger and the RING finger. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. The FYVE finger functions in the membrane recruitment of cytosolic proteins by binding to phosphatidylinositol 3-phosphate (PI3P), which is prominent on endosomes. The R+HHC+XCG motif is critical for PI3P binding. 68 matched cddid_all.tbl CDD smart00065 smart00065 214500 GAF Domain present in phytochromes and cGMP-specific phosphodiesterases. Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa. 149 matched cddid_all.tbl CDD smart00066 smart00066 214501 GAL4 GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain. Gal4 is a positive regulator for the gene expression of the galactose- induced genes of S. cerevisiae. Is present only in fungi. 43 matched cddid_all.tbl CDD smart00067 smart00067 128381 GHA Glycoprotein hormone alpha chain homologues. Also called gonadotropins. Glycoprotein hormones consist of two glycosylated chains (alpha and beta) of similar topology. 87 matched cddid_all.tbl CDD smart00068 smart00068 214502 GHB Glycoprotein hormone beta chain homologues. Also called gonadotropins. Glycoprotein hormones consist of two glycosylated chains (alpha and beta) of similar topology. 107 matched cddid_all.tbl CDD smart00069 smart00069 214503 GLA Domain containing Gla (gamma-carboxyglutamate) residues. A hyaluronan-binding domain found in proteins associated with the extracellular matrix, cell adhesion and cell migration. 65 matched cddid_all.tbl CDD smart00070 smart00070 128384 GLUCA Glucagon like hormones. 27 matched cddid_all.tbl CDD smart00071 smart00071 128385 Galanin Galanin. Galanin is a neuropeptide that controls various biological activities: it regulates the release growth hormone, inhibits the release of insulin and somatostatin, contracts smooth muscle of the gastrointestinal and genitourinary tract and may be involved in the control of adrenal secretion 103 matched cddid_all.tbl CDD smart00072 smart00072 214504 GuKc Guanylate kinase homologues. Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions. 174 matched cddid_all.tbl CDD smart00073 smart00073 197502 HPT Histidine Phosphotransfer domain. Contains an active histidine residue that mediates phosphotransfer reactions. Domain detected only in eubacteria. This alignment is an extension to that shown in the Cell structure paper. 92 matched cddid_all.tbl CDD smart00075 smart00075 214505 HYDRO Hydrophobins. 76 matched cddid_all.tbl CDD smart00076 smart00076 197503 IFabd Interferon alpha, beta and delta. Interferons produce antiviral and antiproliferative responses in cells. They are classified into five groups, all of them related but gamma-interferon. 117 matched cddid_all.tbl CDD smart00077 smart00077 128390 ITAM Immunoreceptor tyrosine-based activation motif. Motif that may be dually phosphorylated on tyrosine that links antigen receptors to downstream signalling machinery. 21 matched cddid_all.tbl CDD smart00078 smart00078 214506 IlGF Insulin / insulin-like growth factor / relaxin family. Family of proteins including insulin, relaxin, and IGFs. Insulin decreases blood glucose concentration. 66 matched cddid_all.tbl CDD smart00079 smart00079 197504 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb 133 matched cddid_all.tbl CDD smart00080 smart00080 197505 LIF_OSM leukemia inhibitory factor. OSM, Oncostatin M 157 matched cddid_all.tbl CDD smart00082 smart00082 214507 LRRCT Leucine rich repeat C-terminal domain. 51 matched cddid_all.tbl CDD smart00084 smart00084 197507 NMU Neuromedin U. Neuromedin U (NmU) is a vertebrate peptide which stimulates uterine smooth muscle contraction and causes selective vasoconstriction. Like most other active peptides, it is proteolytically processed from a larger precursor protein. The mature peptides are 8 (NmU-8) to 25 (NmU-25) residues long and C- terminally amidated. The sequence of the C-terminal extremity of NmU is extremely well conserved in mammals, birds and amphibians. 25 matched cddid_all.tbl CDD smart00085 smart00085 214508 PA2c Phospholipase A2. 117 matched cddid_all.tbl CDD smart00086 smart00086 197509 PAC Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain). PAC motif occurs C-terminal to a subset of all known PAS motifs. It is proposed to contribute to the PAS domain fold. 43 matched cddid_all.tbl CDD smart00087 smart00087 128398 PTH Parathyroid hormone. 36 matched cddid_all.tbl CDD smart00088 smart00088 214509 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function. 88 matched cddid_all.tbl CDD smart00089 smart00089 214510 PKD Repeats in polycystic kidney disease 1 (PKD1) and other proteins. Polycystic kidney disease 1 protein contains 14 repeats, present elsewhere such as in microbial collagenases. 79 matched cddid_all.tbl CDD smart00090 smart00090 214511 RIO RIO-like kinase. 237 matched cddid_all.tbl CDD smart00091 smart00091 214512 PAS PAS domain. PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. 67 matched cddid_all.tbl CDD smart00092 smart00092 128403 RNAse_Pc Pancreatic ribonuclease. 123 matched cddid_all.tbl CDD smart00093 smart00093 214513 SERPIN SERine Proteinase INhibitors. 359 matched cddid_all.tbl CDD smart00094 smart00094 214514 TR_FER Transferrin. 332 matched cddid_all.tbl CDD smart00095 smart00095 128406 TR_THY Transthyretin. 121 matched cddid_all.tbl CDD smart00096 smart00096 128407 UTG Uteroglobin. 69 matched cddid_all.tbl CDD smart00097 smart00097 128408 WNT1 found in Wnt-1. 305 matched cddid_all.tbl CDD smart00098 smart00098 214515 alkPPc Alkaline phosphatase homologues. 419 matched cddid_all.tbl CDD smart00099 smart00099 128410 btg1 tob/btg1 family. The tob/btg1 is a family of proteins that inhibit cell proliferation. 108 matched cddid_all.tbl CDD smart00100 smart00100 197516 cNMP Cyclic nucleotide-monophosphate binding domain. Catabolite gene activator protein (CAP) is a prokaryotic homologue of eukaryotic cNMP-binding domains, present in ion channels, and cNMP-dependent kinases. 120 matched cddid_all.tbl CDD smart00101 smart00101 128412 14_3_3 14-3-3 homologues. 14-3-3 homologues mediates signal transduction by binding to phosphoserine-containing proteins. They are involved in growth factor signalling and also interact with MEK kinases. 244 matched cddid_all.tbl CDD smart00102 smart00102 214516 ADF Actin depolymerisation factor/cofilin -like domains. Severs actin filaments and binds to actin monomers. 127 matched cddid_all.tbl CDD smart00103 smart00103 214517 ALBUMIN serum albumin. 187 matched cddid_all.tbl CDD smart00104 smart00104 197517 ANATO Anaphylatoxin homologous domain. C3a, C4a and C5a anaphylatoxins are protein fragments generated enzymatically in serum during activation of complement molecules C3, C4, and C5. They induce smooth muscle contraction. These fragments are homologous to a three-fold repeat in fibulins. 35 matched cddid_all.tbl CDD smart00105 smart00105 214518 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs. 119 matched cddid_all.tbl CDD smart00107 smart00107 128417 BTK Bruton's tyrosine kinase Cys-rich motif. Zinc-binding motif containing conserved cysteines and a histidine. Always found C-terminal to PH domains (but not all PH domains are followed by BTK motifs). The crystal structure shows this motif packs against the PH domain. The PH+Btk module pair has been called the Tec homology (TH) region. 36 matched cddid_all.tbl CDD smart00108 smart00108 214519 B_lectin Bulb-type mannose-specific lectin. 114 matched cddid_all.tbl CDD smart00109 smart00109 197519 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains. 50 matched cddid_all.tbl CDD smart00110 smart00110 128420 C1Q Complement component C1q domain. Globular domain found in many collagens and eponymously in complement C1q. When part of full length proteins these domains form a 'bouquet' due to the multimerization of heterotrimers. The C1q fold is similar to that of tumour necrosis factor. 135 matched cddid_all.tbl CDD smart00111 smart00111 128421 C4 C-terminal tandem repeated domain in type 4 procollagens. Duplicated domain in C-terminus of type 4 collagens. Mutations in alpha-5 collagen IV are associated with X-linked Alport syndrome. 114 matched cddid_all.tbl CDD smart00112 smart00112 214520 CA Cadherin repeats. Cadherins are glycoproteins involved in Ca2+-mediated cell-cell adhesion. Cadherin domains occur as repeats in the extracellular regions which are thought to mediate cell-cell contact when bound to calcium. 81 matched cddid_all.tbl CDD smart00113 smart00113 128423 CALCITONIN calcitonin. This family is formed by calcitonin, the calcitonin gene-related peptide, and amylin. They are short polypeptide hormones. 38 matched cddid_all.tbl CDD smart00114 smart00114 128424 CARD Caspase recruitment domain. Motif contained in proteins involved in apoptotic signalling. Mediates homodimerisation. Structure consists of six antiparallel helices arranged in a topology homologue to the DEATH and the DED domain. 88 matched cddid_all.tbl CDD smart00115 smart00115 214521 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues. 241 matched cddid_all.tbl CDD smart00116 smart00116 214522 CBS Domain in cystathionine beta-synthase and other proteins. Domain present in all 3 forms of cellular life. Present in two copies in inosine monophosphate dehydrogenase, of which one is disordered in the crystal structure. A number of disease states are associated with CBS-containing proteins including homocystinuria, Becker's and Thomsen disease. 49 matched cddid_all.tbl CDD smart00119 smart00119 214523 HECTc Domain Homologous to E6-AP Carboxyl Terminus with. E3 ubiquitin-protein ligases. Can bind to E2 enzymes. 328 matched cddid_all.tbl CDD smart00120 smart00120 214524 HX Hemopexin-like repeats. Hemopexin is a heme-binding protein that transports heme to the liver. Hemopexin-like repeats occur in vitronectin and some matrix metalloproteinases family (matrixins). The HX repeats of some matrixins bind tissue inhibitor of metalloproteinases (TIMPs). 45 matched cddid_all.tbl CDD smart00121 smart00121 197525 IB Insulin growth factor-binding protein homologues. High affinity binding partners of insulin-like growth factors. 75 matched cddid_all.tbl CDD smart00125 smart00125 128430 IL1 Interleukin-1 homologues. Cytokines with various biological functions. Interluekin 1 alpha and beta are also known as hematopoietin and catabolin. 147 matched cddid_all.tbl CDD smart00126 smart00126 128431 IL6 Interleukin-6 homologues. Family includes granulocyte colony-stimulating factor (G-CSF) and myelomonocytic growth factor (MGF). IL-6 is also known as B-cell stimulatory factor 2. 154 matched cddid_all.tbl CDD smart00127 smart00127 128432 IL7 Interleukin-7 and interleukin-9 family. IL-7 is a cytokine that acts as a growth factor for early lymphoid cells of both B- and T-cell lineages. IL-9 is a multifunctional cytokine that, although originally described as a T-cell growth factor, its function in T-cell response remains unclear. 146 matched cddid_all.tbl CDD smart00128 smart00128 214525 IPPc Inositol polyphosphate phosphatase, catalytic domain homologues. Mg(2+)-dependent/Li(+)-sensitive enzymes. 306 matched cddid_all.tbl CDD smart00129 smart00129 214526 KISc Kinesin motor, catalytic domain. ATPase. Microtubule-dependent molecular motors that play important roles in intracellular transport of organelles and in cell division. 335 matched cddid_all.tbl CDD smart00130 smart00130 214527 KR Kringle domain. Named after a Danish pastry. Found in several serine proteases and in ROR-like receptors. Can occur in up to 38 copies (in apolipoprotein(a)). Plasminogen-like kringles possess affinity for free lysine and lysine- containing peptides. 83 matched cddid_all.tbl CDD smart00131 smart00131 197529 KU BPTI/Kunitz family of serine protease inhibitors. Serine protease inhibitors. One member of the family is encoded by an alternatively-spliced form of Alzheimer's amyloid beta-protein. 53 matched cddid_all.tbl CDD smart00132 smart00132 214528 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways. 54 matched cddid_all.tbl CDD smart00133 smart00133 214529 S_TK_X Extension to Ser/Thr-type protein kinases. 64 matched cddid_all.tbl CDD smart00134 smart00134 214530 LU Ly-6 antigen / uPA receptor -like domain. Three-fold repeated domain in urokinase-type plasminogen activator receptor; occurs singly in other GPI-linked cell-surface glycoproteins (Ly-6 family, CD59, thymocyte B cell antigen, Sgp-2). Topology of these domains is similar to that of snake venom neurotoxins. 85 matched cddid_all.tbl CDD smart00135 smart00135 214531 LY "Low-density lipoprotein-receptor YWTD domain. Type ""B"" repeats in low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. Also present in a variety of molecules similar to gp300/megalin." 43 matched cddid_all.tbl CDD smart00136 smart00136 214532 LamNT Laminin N-terminal domain (domain VI). N-terminal domain of laminins and laminin-related protein such as Unc-6/ netrins. 238 matched cddid_all.tbl CDD smart00137 smart00137 214533 MAM Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others). Likely to have an adhesive function. Mutations in the meprin MAM domain affect noncovalent associations within meprin oligomers. In receptor tyrosine phosphatase mu-like molecules the MAM domain is important for homophilic cell-cell interactions. 161 matched cddid_all.tbl CDD smart00138 smart00138 214534 MeTrc Methyltransferase, chemotaxis proteins. Methylates methyl-accepting chemotaxis proteins to form gamma-glutamyl methyl ester residues. 264 matched cddid_all.tbl CDD smart00139 smart00139 214535 MyTH4 Domain in Myosin and Kinesin Tails. Domain present twice in myosin-VIIa, and also present in 3 other myosins. 152 matched cddid_all.tbl CDD smart00140 smart00140 128445 NGF Nerve growth factor (NGF or beta-NGF). NGF is important for the development and maintenance of the sympathetic and sensory nervous systems. 106 matched cddid_all.tbl CDD smart00141 smart00141 197537 PDGF Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family. Platelet-derived growth factor is a potent activator for cells of mesenchymal origin. PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer. Members of the VEGF family are homologues of PDGF. 83 matched cddid_all.tbl CDD smart00142 smart00142 214536 PI3K_C2 Phosphoinositide 3-kinase, region postulated to contain C2 domain. Outlier of C2 family. 100 matched cddid_all.tbl CDD smart00143 smart00143 197539 PI3K_p85B PI3-kinase family, p85-binding domain. Region of p110 PI3K that binds the p85 subunit. 78 matched cddid_all.tbl CDD smart00144 smart00144 197540 PI3K_rbd PI3-kinase family, Ras-binding domain. Certain members of the PI3K family possess Ras-binding domains in their N-termini. These regions show some similarity (although not highly significant similarity) to Ras-binding RA domains (unpublished observation). 108 matched cddid_all.tbl CDD smart00145 smart00145 214537 PI3Ka Phosphoinositide 3-kinase family, accessory domain (PIK domain). PIK domain is conserved in all PI3 and PI4-kinases. Its role is unclear but it has been suggested to be involved in substrate presentation. 184 matched cddid_all.tbl CDD smart00146 smart00146 214538 PI3Kc Phosphoinositide 3-kinase, catalytic domain. Phosphoinositide 3-kinase isoforms participate in a variety of processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, and apoptosis. These homologues may be either lipid kinases and/or protein kinases: the former phosphorylate the 3-position in the inositol ring of inositol phospholipids. The ataxia telangiectesia-mutated gene produced, the targets of rapamycin (TOR) and the DNA-dependent kinase have not been found to possess lipid kinase activity. Some of this family possess PI-4 kinase activities. 240 matched cddid_all.tbl CDD smart00147 smart00147 214539 RasGEF Guanine nucleotide exchange factor for Ras-like small GTPases. 242 matched cddid_all.tbl CDD smart00148 smart00148 197543 PLCXc Phospholipase C, catalytic domain (part); domain X. Phosphoinositide-specific phospholipases C. These enzymes contain 2 regions (X and Y) which together form a TIM barrel-like structure containing the active site residues. Phospholipase C enzymes (PI-PLC) act as signal transducers that generate two second messengers, inositol-1,4,5-trisphosphate and diacylglycerol. The bacterial enzyme appears to be a homologue of the mammalian PLCs. 143 matched cddid_all.tbl CDD smart00149 smart00149 128454 PLCYc Phospholipase C, catalytic domain (part); domain Y. Phosphoinositide-specific phospholipases C. These enzymes contain 2 regions (X and Y) which together form a TIM barrel-like structure containing the active site residues. Phospholipase C enzymes (PI-PLC) act as signal transducers that generate two second messengers, inositol-1,4,5-trisphosphate and diacylglycerol. The bacterial enzyme appears to be a homologue of the mammalian PLCs. 115 matched cddid_all.tbl CDD smart00150 smart00150 197544 SPEC Spectrin repeats. 101 matched cddid_all.tbl CDD smart00151 smart00151 128456 SWIB SWI complex, BAF60b domains. 77 matched cddid_all.tbl CDD smart00152 smart00152 128457 THY Thymosin beta actin-binding motif. 37 matched cddid_all.tbl CDD smart00153 smart00153 128458 VHP Villin headpiece domain. 36 matched cddid_all.tbl CDD smart00154 smart00154 197545 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis. 39 matched cddid_all.tbl CDD smart00155 smart00155 197546 PLDc Phospholipase D. Active site motifs. Phosphatidylcholine-hydrolyzing phospholipase D (PLD) isoforms are activated by ADP-ribosylation factors (ARFs). PLD produces phosphatidic acid from phosphatidylcholine, which may be essential for the formation of certain types of transport vesicles or may be constitutive vesicular transport to signal transduction pathways. PC-hydrolysing PLD is a homologue of cardiolipin synthase, phosphatidylserine synthase, bacterial PLDs, and viral proteins. Each of these appears to possess a domain duplication which is apparent by the presence of two motifs containing well-conserved histidine, lysine, aspartic acid, and/or asparagine residues which may contribute to the active site. An E. coli endonuclease (nuc) and similar proteins appear to be PLD homologues but possess only one of these motifs. The profile contained here represents only the putative active site regions, since an accurate multiple alignment of the repeat units has not been achieved. 28 matched cddid_all.tbl CDD smart00156 smart00156 197547 PP2Ac Protein phosphatase 2A homologues, catalytic domain. Large family of serine/threonine phosphatases, that includes PP1, PP2A and PP2B (calcineurin) family members. 271 matched cddid_all.tbl CDD smart00157 smart00157 197548 PRP Major prion protein. The prion protein is a major component of scrapie-associated fibrils in Creutzfeldt-Jakob disease, kuru, Gerstmann-Straussler syndrome and bovine spongiform encephalopathy. 218 matched cddid_all.tbl CDD smart00159 smart00159 128463 PTX Pentraxin / C-reactive protein / pentaxin family. This family form a doscoid pentameric structure. Human serum amyloid P demonstrates calcium-mediated ligand-binding. 206 matched cddid_all.tbl CDD smart00160 smart00160 197549 RanBD Ran-binding domain. Domain of apporximately 150 residues that stabilises the GTP-bound form of Ran (the Ras-like nuclear small GTPase). 130 matched cddid_all.tbl CDD smart00162 smart00162 128465 SAPA Saposin/surfactant protein-B A-type DOMAIN. Present as four and three degenerate copies, respectively, in prosaposin and surfactant protein B. Single copies in acid sphingomyelinase, NK-lysin amoebapores and granulysin. Putative phospholipid membrane binding domains. 34 matched cddid_all.tbl CDD smart00164 smart00164 214540 TBC Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. Widespread domain present in Gyp6 and Gyp7, thereby giving rise to the notion that it performs a GTP-activator activity on Rab-like GTPases. 216 matched cddid_all.tbl CDD smart00165 smart00165 197551 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin. 37 matched cddid_all.tbl CDD smart00166 smart00166 197552 UBX Domain present in ubiquitin-regulatory proteins. Present in FAF1 and Shp1p. 77 matched cddid_all.tbl CDD smart00167 smart00167 128469 VPS9 Domain present in VPS9. Domain present in yeast vacuolar sorting protein 9 and other proteins. 117 matched cddid_all.tbl CDD smart00173 smart00173 214541 RAS Ras subfamily of RAS small GTPases. Similar in fold and function to the bacterial EF-Tu GTPase. p21Ras couples receptor Tyr kinases and G protein receptors to protein kinase cascades 164 matched cddid_all.tbl CDD smart00174 smart00174 197554 RHO Rho (Ras homology) subfamily of Ras-like small GTPases. Members of this subfamily of Ras-like small GTPases include Cdc42 and Rac, as well as Rho isoforms. 174 matched cddid_all.tbl CDD smart00175 smart00175 197555 RAB Rab subfamily of small GTPases. Rab GTPases are implicated in vesicle trafficking. 164 matched cddid_all.tbl CDD smart00176 smart00176 128473 RAN Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases. Ran is involved in the active transport of proteins through nuclear pores. 200 matched cddid_all.tbl CDD smart00177 smart00177 128474 ARF ARF-like small GTPases; ARF, ADP-ribosylation factor. Ras homologues involved in vesicular transport. Activator of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. ARFs are N-terminally myristoylated. Contains ATP/GTP-binding motif (P-loop). 175 matched cddid_all.tbl CDD smart00178 smart00178 197556 SAR Sar1p-like members of the Ras-family of small GTPases. Yeast SAR1 is an essential gene required for transport of secretory proteins from the endoplasmic reticulum to the Golgi apparatus. 184 matched cddid_all.tbl CDD smart00179 smart00179 214542 EGF_CA Calcium-binding EGF-like domain. 39 matched cddid_all.tbl CDD smart00180 smart00180 214543 EGF_Lam Laminin-type epidermal growth factor-like domai. 46 matched cddid_all.tbl CDD smart00181 smart00181 214544 EGF Epidermal growth factor-like domain. 35 matched cddid_all.tbl CDD smart00182 smart00182 214545 CULLIN Cullin. 143 matched cddid_all.tbl CDD smart00183 smart00183 128480 NAT_PEP Natriuretic peptide. Atrial natriuretic peptides are vertebrate hormones important in the overall control of cardiovascular homeostasis and sodium and water balance in general. 24 matched cddid_all.tbl CDD smart00184 smart00184 214546 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s) 40 matched cddid_all.tbl CDD smart00185 smart00185 214547 ARM Armadillo/beta-catenin-like repeats. Approx. 40 amino acid repeat. Tandem repeats form superhelix of helices that is proposed to mediate interaction of beta-catenin with its ligands. Involved in transducing the Wingless/Wnt signal. In plakoglobin arm repeats bind alpha-catenin and N-cadherin. 41 matched cddid_all.tbl CDD smart00186 smart00186 214548 FBG Fibrinogen-related domains (FReDs). Domain present at the C-termini of fibrinogen beta and gamma chains, and a variety of fibrinogen-related proteins, including tenascin and Drosophila scabrous. 212 matched cddid_all.tbl CDD smart00187 smart00187 197563 INB "Integrin beta subunits (N-terminal portion of extracellular region). Portion of beta integrins that lies N-terminal to their EGF-like repeats. Integrins are cell adhesion molecules that mediate cell-extracellular matrix and cell-cell interactions. They contain both alpha and beta subunits. Beta integrins are proposed to have a von Willebrand factor type-A ""insert"" or ""I"" -like domain (although this remains to be confirmed)." 423 matched cddid_all.tbl CDD smart00188 smart00188 128485 IL10 Interleukin-10 family. Interleukin-10 inhibits the synthesis of a number of cytokines, including IFN-gamma, IL-2, IL-3, TNF and GM-CSF produced by activated macrophages and by helper T cells. 137 matched cddid_all.tbl CDD smart00189 smart00189 128486 IL2 Interleukin-2 family. Interleukin-2 is a cytokine produced by T-helper cells in response to antigenic or mitogenic stimulation. This protein is required for T-cell proliferation and other activities crucial to the regulation of the immune response. 154 matched cddid_all.tbl CDD smart00190 smart00190 197564 IL4_13 Interleukins 4 and 13. Interleukins-4 and -13 are cytokines involved in inflammatory and immune responses. IL-4 stimulates B and T cells. 138 matched cddid_all.tbl CDD smart00191 smart00191 214549 Int_alpha Integrin alpha (beta-propellor repeats). Integrins are cell adhesion molecules that mediate cell-extracellular matrix and cell-cell interactions. They contain both alpha and beta subunits. Alpha integrins are proposed to contain a domain containing a 7-fold repeat that adopts a beta-propellor fold. Some of these domains contain an inserted von Willebrand factor type-A domain. Some repeats contain putative calcium-binding sites. The 7-fold repeat domain is homologous to a similar domain in phosphatidylinositol-glycan-specific phospholipase D. 57 matched cddid_all.tbl CDD smart00192 smart00192 197566 LDLa Low-density lipoprotein receptor domain class A. Cysteine-rich repeat in the low-density lipoprotein (LDL) receptor that plays a central role in mammalian cholesterol metabolism. The N-terminal type A repeats in LDL receptor bind the lipoproteins. Other homologous domains occur in related receptors, including the very low-density lipoprotein receptor and the LDL receptor-related protein/alpha 2-macroglobulin receptor, and in proteins which are functionally unrelated, such as the C9 component of complement. Mutations in the LDL receptor gene cause familial hypercholesterolemia. 33 matched cddid_all.tbl CDD smart00193 smart00193 128490 PTN Pleiotrophin / midkine family. Heparin-binding domain family. 80 matched cddid_all.tbl CDD smart00194 smart00194 214550 PTPc Protein tyrosine phosphatase, catalytic domain. 259 matched cddid_all.tbl CDD smart00195 smart00195 214551 DSPc Dual specificity phosphatase, catalytic domain. 138 matched cddid_all.tbl CDD smart00197 smart00197 214552 SAA Serum amyloid A proteins. Serum amyloid A proteins are induced during the acute-phase response. Secondary amyloidosis is characterised by the extracellular accumulation in tissues of SAA proteins. SAA proteins are apolipoproteins. 103 matched cddid_all.tbl CDD smart00198 smart00198 214553 SCP SCP / Tpx-1 / Ag5 / PR-1 / Sc7 family of extracellular domains. Human glioma pathogenesis-related protein GliPR and the plant pathogenesis-related protein represent functional links between plant defense systems and human immune system. This family has no known function. 144 matched cddid_all.tbl CDD smart00199 smart00199 197570 SCY Intercrine alpha family (small cytokine C-X-C) (chemokine CXC). Family of cytokines involved in cell-specific chemotaxis, mediation of cell growth, and the inflammatory response. 59 matched cddid_all.tbl CDD smart00200 smart00200 214554 SEA Domain found in sea urchin sperm protein, enterokinase, agrin. Proposed function of regulating or binding carbohydrate sidechains. 121 matched cddid_all.tbl CDD smart00201 smart00201 197571 SO Somatomedin B -like domains. Somatomedin-B is a peptide, proteolytically excised from vitronectin, that is a growth hormone-dependent serum factor with protease-inhibiting activity. 43 matched cddid_all.tbl CDD smart00202 smart00202 214555 SR Scavenger receptor Cys-rich. The sea urchin egg peptide speract contains 4 repeats of SR domains that contain 6 conserved cysteines. May bind bacterial antigens in the protein MARCO. 101 matched cddid_all.tbl CDD smart00203 smart00203 197573 TK Tachykinin family. Tachykinins are a group of biologically active peptides which excite neurons, evoke behavioral responses, are potent vasodilatators and contract (directly or indirectly) many smooth muscles. These peptides are synthesized as longer precursors and then processed to peptides from ten to twelve residues long. 11 matched cddid_all.tbl CDD smart00204 smart00204 214556 TGFB Transforming growth factor-beta (TGF-beta) family. Family members are active as disulphide-linked homo- or heterodimers. TGFB is a multifunctional peptide that controls proliferation, differentiation, and other functions in many cell types. 102 matched cddid_all.tbl CDD smart00205 smart00205 128501 THN Thaumatin family. The thaumatin family gathers proteins related to plant pathogenesis. The thaumatin family includes very basic members with extracellular and vacuolar localization. Thaumatin itsel is a potent sweet-tasting protein. Several members of this family display significant in vitro activity of inhibiting hyphal growth or spore germination of various fungi probably by a membrane permeabilizing mechanism. 218 matched cddid_all.tbl CDD smart00206 smart00206 128502 NTR Tissue inhibitor of metalloproteinase family. Form complexes with metalloproteinases, such as collagenases, and irreversibly inactivate them. 172 matched cddid_all.tbl CDD smart00207 smart00207 214557 TNF Tumour necrosis factor family. Family of cytokines that form homotrimeric or heterotrimeric complexes. TNF mediates mature T-cell receptor-induced apoptosis through the p75 TNF receptor. 125 matched cddid_all.tbl CDD smart00208 smart00208 214558 TNFR Tumor necrosis factor receptor / nerve growth factor receptor repeats. Repeats in growth factor receptors that are involved in growth factor binding. TNF/TNFR 39 matched cddid_all.tbl CDD smart00209 smart00209 214559 TSP1 Thrombospondin type 1 repeats. Type 1 repeats in thrombospondin-1 bind and activate TGF-beta. 53 matched cddid_all.tbl CDD smart00210 smart00210 214560 TSPN Thrombospondin N-terminal -like domains. Heparin-binding and cell adhesion domain of thrombospondin 184 matched cddid_all.tbl CDD smart00211 smart00211 214561 TY Thyroglobulin type I repeats. The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases and binding partners of heparin. 46 matched cddid_all.tbl CDD smart00212 smart00212 214562 UBCc Ubiquitin-conjugating enzyme E2, catalytic domain homologues. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. This pathway functions in regulating many fundamental processes required for cell viability.TSG101 is one of several UBC homologues that lacks this active site cysteine. 145 matched cddid_all.tbl CDD smart00213 smart00213 214563 UBQ Ubiquitin homologues. Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression 72 matched cddid_all.tbl CDD smart00214 smart00214 214564 VWC von Willebrand factor (vWF) type C domain. 59 matched cddid_all.tbl CDD smart00215 smart00215 214565 VWC_out von Willebrand factor (vWF) type C domain. 67 matched cddid_all.tbl CDD smart00216 smart00216 214566 VWD von Willebrand factor (vWF) type D domain. Von Willebrand factor contains several type D domains: D1 and D2 are present within the N-terminal propeptide whereas the remaining D domains are required for multimerisation. 163 matched cddid_all.tbl CDD smart00217 smart00217 197580 WAP Four-disulfide core domains. 47 matched cddid_all.tbl CDD smart00218 smart00218 128514 ZU5 Domain present in ZO-1 and Unc5-like netrin receptors. Domain of unknown function. 104 matched cddid_all.tbl CDD smart00219 smart00219 197581 TyrKc Tyrosine kinase, catalytic domain. Phosphotransferases. Tyrosine-specific kinase subfamily. 257 matched cddid_all.tbl CDD smart00220 smart00220 214567 S_TKc Serine/Threonine protein kinases, catalytic domain. Phosphotransferases. Serine or threonine-specific kinase subfamily. 254 matched cddid_all.tbl CDD smart00221 smart00221 214568 STYKc Protein kinase; unclassified specificity. Phosphotransferases. The specificity of this class of kinases can not be predicted. Possible dual-specificity Ser/Thr/Tyr kinase. 258 matched cddid_all.tbl CDD smart00222 smart00222 214569 Sec7 Sec7 domain. Domain named after the S. cerevisiae SEC7 gene product, which is required for proper protein transport through the Golgi. The domain facilitates guanine nucleotide exchange on the small GTPases, ARFs (ADP ribosylation factors). 189 matched cddid_all.tbl CDD smart00223 smart00223 128519 APPLE APPLE domain. Four-fold repeat in plasma kallikrein and coagulation factor XI. Factor XI apple 3 mediates binding to platelets. Factor XI apple 1 binds high-molecular-mass kininogen. Apple 4 in factor XI mediates dimer formation and binds to factor XIIa. Mutations in apple 4 cause factor XI deficiency, an inherited bleeding disorder. 79 matched cddid_all.tbl CDD smart00224 smart00224 128520 GGL G protein gamma subunit-like motifs. 63 matched cddid_all.tbl CDD smart00225 smart00225 197585 BTB Broad-Complex, Tramtrack and Bric a brac. Domain in Broad-Complex, Tramtrack and Bric a brac. Also known as POZ (poxvirus and zinc finger) domain. Known to be a protein-protein interaction motif found at the N-termini of several C2H2-type transcription factors as well as Shaw-type potassium channels. Known structure reveals a tightly intertwined dimer formed via interactions between N-terminal strand and helix structures. However in a subset of BTB/POZ domains, these two secondary structures appear to be missing. Be aware SMART predicts BTB/POZ domains without the beta1- and alpha1-secondary structures. 97 matched cddid_all.tbl CDD smart00226 smart00226 197586 LMWPc Low molecular weight phosphatase family. 134 matched cddid_all.tbl CDD smart00227 smart00227 128523 NEBU The Nebulin repeat is present also in Las1. Tandem arrays of these repeats are known to bind actin. 31 matched cddid_all.tbl CDD smart00228 smart00228 214570 PDZ Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities. 85 matched cddid_all.tbl CDD smart00229 smart00229 214571 RasGEFN "Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif. A subset of guanine nucleotide exchange factor for Ras-like small GTPases appear to possess this domain N-terminal to the RasGef (Cdc25-like) domain. The recent crystal structureof Sos shows that this domain is alpha-helical and plays a ""purely structural role"" (Nature 394, 337-343)." 127 matched cddid_all.tbl CDD smart00230 smart00230 128526 CysPc Calpain-like thiol protease family. Calpain-like thiol protease family (peptidase family C2). Calcium activated neutral protease (large subunit). 318 matched cddid_all.tbl CDD smart00231 smart00231 214572 FA58C Coagulation factor 5/8 C-terminal domain, discoidin domain. Cell surface-attached carbohydrate-binding domain, present in eukaryotes and assumed to have horizontally transferred to eubacterial genomes. 139 matched cddid_all.tbl CDD smart00232 smart00232 214573 JAB_MPN JAB/MPN domain. Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function. 135 matched cddid_all.tbl CDD smart00233 smart00233 214574 PH Pleckstrin homology domain. Domain commonly found in eukaryotic signalling proteins. The domain family possesses multiple functions including the abilities to bind inositol phosphates, and various proteins. PH domains have been found to possess inserted domains (such as in PLC gamma, syntrophins) and to be inserted within other domains. Mutations in Brutons tyrosine kinase (Btk) within its PH domain cause X-linked agammaglobulinaemia (XLA) in patients. Point mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids. 102 matched cddid_all.tbl CDD smart00234 smart00234 214575 START in StAR and phosphatidylcholine transfer protein. putative lipid-binding domain in StAR and phosphatidylcholine transfer protein 205 matched cddid_all.tbl CDD smart00235 smart00235 214576 ZnMc Zinc-dependent metalloprotease. Neutral zinc metallopeptidases. This alignment represents a subset of known subfamilies. Highest similarity occurs in the HExxH zinc-binding site/ active site. 139 matched cddid_all.tbl CDD smart00236 smart00236 197593 fCBD Fungal-type cellulose-binding domain. Small four-cysteine cellulose-binding domain of fungi 34 matched cddid_all.tbl CDD smart00237 smart00237 197594 Calx_beta Domains in Na-Ca exchangers and integrin-beta4. Domain in Na-Ca exchangers and integrin subunit beta4 (and some cyanobacterial proteins) 90 matched cddid_all.tbl CDD smart00238 smart00238 197595 BIR Baculoviral inhibition of apoptosis protein repeat. Domain found in inhibitor of apoptosis proteins (IAPs) and other proteins. Acts as a direct inhibitor of caspase enzymes. 71 matched cddid_all.tbl CDD smart00239 smart00239 214577 C2 Protein kinase C conserved region 2 (CalB). Ca2+-binding motif present in phospholipases, protein kinases C, and synaptotagmins (among others). Some do not appear to contain Ca2+-binding sites. Particular C2s appear to bind phospholipids, inositol polyphosphates, and intracellular proteins. Unusual occurrence in perforin. Synaptotagmin and PLC C2s are permuted in sequence with respect to N- and C-terminal beta strands. SMART detects C2 domains using one or both of two profiles. 101 matched cddid_all.tbl CDD smart00240 smart00240 214578 FHA Forkhead associated domain. Found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. 52 matched cddid_all.tbl CDD smart00241 smart00241 214579 ZP Zona pellucida (ZP) domain. ZP proteins are responsible for sperm-adhesion fo the zona pellucida. ZP domains are also present in multidomain transmembrane proteins such as glycoprotein GP2, uromodulin and TGF-beta receptor type III (betaglycan). 252 matched cddid_all.tbl CDD smart00242 smart00242 214580 MYSc Myosin. Large ATPases. ATPase; molecular motor. Muscle contraction consists of a cyclical interaction between myosin and actin. The core of the myosin structure is similar in fold to that of kinesin. 677 matched cddid_all.tbl CDD smart00243 smart00243 128539 GAS2 Growth-Arrest-Specific Protein 2 Domain. GROWTH-ARREST-SPECIFIC PROTEIN 2 Domain 73 matched cddid_all.tbl CDD smart00244 smart00244 214581 PHB prohibitin homologues. prohibitin homologues 160 matched cddid_all.tbl CDD smart00245 smart00245 214582 TSPc tail specific protease. tail specific protease 192 matched cddid_all.tbl CDD smart00246 smart00246 128542 WH2 Wiskott Aldrich syndrome homology region 2. Wiskott Aldrich syndrome homology region 2 / actin-binding motif 18 matched cddid_all.tbl CDD smart00247 smart00247 214583 XTALbg Beta/gamma crystallins. Beta/gamma crystallins 82 matched cddid_all.tbl CDD smart00248 smart00248 197603 ANK ankyrin repeats. Ankyrin repeats are about 33 amino acids long and occur in at least four consecutive copies. They are involved in protein-protein interactions. The core of the repeat seems to be an helix-loop-helix structure. 30 matched cddid_all.tbl CDD smart00249 smart00249 214584 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers. 47 matched cddid_all.tbl CDD smart00250 smart00250 197605 PLEC Plectin repeat. 38 matched cddid_all.tbl CDD smart00251 smart00251 128547 SAM_PNT SAM / Pointed domain. A subfamily of the SAM domain 82 matched cddid_all.tbl CDD smart00252 smart00252 214585 SH2 Src homology 2 domains. Src homology 2 domains bind phosphotyrosine-containing polypeptides via 2 surface pockets. Specificity is provided via interaction with residues that are distinct from the phosphotyrosine. Only a single occurrence of a SH2 domain has been found in S. cerevisiae. 84 matched cddid_all.tbl CDD smart00253 smart00253 128549 SOCS suppressors of cytokine signalling. suppressors of cytokine signalling 43 matched cddid_all.tbl CDD smart00254 smart00254 214586 ShKT ShK toxin domain. ShK toxin domain 33 matched cddid_all.tbl CDD smart00255 smart00255 214587 TIR Toll - interleukin 1 - resistance. 140 matched cddid_all.tbl CDD smart00256 smart00256 197608 FBOX A Receptor for Ubiquitination Targets. 41 matched cddid_all.tbl CDD smart00257 smart00257 197609 LysM Lysin motif. 44 matched cddid_all.tbl CDD smart00258 smart00258 128554 SAND SAND domain. 73 matched cddid_all.tbl CDD smart00259 smart00259 128555 ZnF_A20 A20-like zinc fingers. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappaB activation. 26 matched cddid_all.tbl CDD smart00260 smart00260 214588 CheW Two component signalling adaptor domain. 138 matched cddid_all.tbl CDD smart00261 smart00261 214589 FU Furin-like repeats. 45 matched cddid_all.tbl CDD smart00262 smart00262 214590 GEL Gelsolin homology domain. Gelsolin/severin/villin homology domain. Calcium-binding and actin-binding. Both intra- and extracellular domains. 90 matched cddid_all.tbl CDD smart00263 smart00263 197612 LYZ1 Alpha-lactalbumin / lysozyme C. 127 matched cddid_all.tbl CDD smart00264 smart00264 214591 BAG BAG domains, present in regulator of Hsp70 proteins. BAG domains, present in Bcl-2-associated athanogene 1 and silencer of death domains 79 matched cddid_all.tbl CDD smart00265 smart00265 128561 BH4 BH4 Bcl-2 homology region 4. 27 matched cddid_all.tbl CDD smart00266 smart00266 128562 CAD Domains present in proteins implicated in post-mortem DNA fragmentation. 74 matched cddid_all.tbl CDD smart00267 smart00267 128563 GGDEF diguanylate cyclase. Diguanylate cyclase, present in a variety of bacteria. 163 matched cddid_all.tbl CDD smart00268 smart00268 214592 ACTIN Actin. ACTIN subfamily of ACTIN/mreB/sugarkinase/Hsp70 superfamily 373 matched cddid_all.tbl CDD smart00269 smart00269 197615 BowB Bowman-Birk type proteinase inhibitor. 55 matched cddid_all.tbl CDD smart00270 smart00270 214593 ChtBD1 Chitin binding domain. 38 matched cddid_all.tbl CDD smart00271 smart00271 197617 DnaJ DnaJ molecular chaperone homology domain. 60 matched cddid_all.tbl CDD smart00272 smart00272 197618 END Endothelin. 22 matched cddid_all.tbl CDD smart00273 smart00273 214594 ENTH Epsin N-terminal homology (ENTH) domain. 127 matched cddid_all.tbl CDD smart00274 smart00274 128570 FOLN Follistatin-N-terminal domain-like. Follistatin-N-terminal domain-like, EGF-like. Region distinct from the kazal-like sequence 24 matched cddid_all.tbl CDD smart00275 smart00275 214595 G_alpha G protein alpha subunit. Subunit of G proteins that contains the guanine nucleotide binding site 342 matched cddid_all.tbl CDD smart00276 smart00276 214596 GLECT Galectin. Galectin - galactose-binding lectin 128 matched cddid_all.tbl CDD smart00277 smart00277 197621 GRAN Granulin. 51 matched cddid_all.tbl CDD smart00278 smart00278 197622 HhH1 Helix-hairpin-helix DNA-binding motif class 1. 20 matched cddid_all.tbl CDD smart00279 smart00279 197623 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs. 36 matched cddid_all.tbl CDD smart00280 smart00280 197624 KAZAL Kazal type serine protease inhibitors. Kazal type serine protease inhibitors and follistatin-like domains. 46 matched cddid_all.tbl CDD smart00281 smart00281 214597 LamB Laminin B domain. 127 matched cddid_all.tbl CDD smart00282 smart00282 214598 LamG Laminin G domain. 132 matched cddid_all.tbl CDD smart00283 smart00283 214599 MA Methyl-accepting chemotaxis-like domains (chemotaxis sensory transducer). Thought to undergo reversible methylation in response to attractants or repellants during bacterial chemotaxis. 262 matched cddid_all.tbl CDD smart00284 smart00284 128580 OLF Olfactomedin-like domains. 255 matched cddid_all.tbl CDD smart00285 smart00285 197628 PBD P21-Rho-binding domain. Small domains that bind Cdc42p- and/or Rho-like small GTPases. Also known as the Cdc42/Rac interactive binding (CRIB). 36 matched cddid_all.tbl CDD smart00286 smart00286 128582 PTI Plant trypsin inhibitors. 29 matched cddid_all.tbl CDD smart00287 smart00287 214600 SH3b Bacterial SH3 domain homologues. 63 matched cddid_all.tbl CDD smart00288 smart00288 197630 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function. 133 matched cddid_all.tbl CDD smart00289 smart00289 214601 WR1 Worm-specific repeat type 1. Worm-specific repeat type 1. Cysteine-rich domain apparently unique (so far) to C. elegans. Often appears with KU domains. About 3 dozen worm proteins contain this domain. 38 matched cddid_all.tbl CDD smart00290 smart00290 197632 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger. 50 matched cddid_all.tbl CDD smart00291 smart00291 197633 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy. 44 matched cddid_all.tbl CDD smart00292 smart00292 214602 BRCT breast cancer carboxy-terminal domain. 78 matched cddid_all.tbl CDD smart00293 smart00293 214603 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues 63 matched cddid_all.tbl CDD smart00294 smart00294 128590 4.1m putative band 4.1 homologues' binding motif. 19 matched cddid_all.tbl CDD smart00295 smart00295 214604 B41 Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs. 201 matched cddid_all.tbl CDD smart00297 smart00297 197636 BROMO bromo domain. 107 matched cddid_all.tbl CDD smart00298 smart00298 214605 CHROMO Chromatin organization modifier domain. 55 matched cddid_all.tbl CDD smart00299 smart00299 128594 CLH Clathrin heavy chain repeat homology. 140 matched cddid_all.tbl CDD smart00300 smart00300 197638 ChSh Chromo Shadow Domain. 61 matched cddid_all.tbl CDD smart00301 smart00301 214606 DM Doublesex DNA-binding motif. 54 matched cddid_all.tbl CDD smart00302 smart00302 128597 GED Dynamin GTPase effector domain. 92 matched cddid_all.tbl CDD smart00303 smart00303 197639 GPS G-protein-coupled receptor proteolytic site domain. Present in latrophilin/CL-1, sea urchin REJ and polycystin. 49 matched cddid_all.tbl CDD smart00304 smart00304 197640 HAMP HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain. 53 matched cddid_all.tbl CDD smart00305 smart00305 197641 HintC Hint (Hedgehog/Intein) domain C-terminal region. Hedgehog/Intein domain, C-terminal region. Domain has been split to accommodate large insertions of endonucleases. 46 matched cddid_all.tbl CDD smart00306 smart00306 197642 HintN Hint (Hedgehog/Intein) domain N-terminal region. Hedgehog/Intein domain, N-terminal region. Domain has been split to accommodate large insertions of endonucleases. 100 matched cddid_all.tbl CDD smart00307 smart00307 214607 ILWEQ I/LWEQ domain. Thought to possess an F-actin binding function. 200 matched cddid_all.tbl CDD smart00308 smart00308 214608 LH2 Lipoxygenase homology 2 (beta barrel) domain. 105 matched cddid_all.tbl CDD smart00309 smart00309 197643 PAH Pancreatic hormones / neuropeptide F / peptide YY family. Pancreatic hormone is a regulator of pancreatic and gastrointestinal functions. 36 matched cddid_all.tbl CDD smart00310 smart00310 197644 PTBI Phosphotyrosine-binding domain (IRS1-like). 99 matched cddid_all.tbl CDD smart00311 smart00311 214609 PWI PWI, domain in splicing factors. 74 matched cddid_all.tbl CDD smart00312 smart00312 214610 PX PhoX homologous domain, present in p47phox and p40phox. Eukaryotic domain of unknown function present in phox proteins, PLD isoforms, a PI3K isoform. 105 matched cddid_all.tbl CDD smart00313 smart00313 214611 PXA Domain associated with PX domains. unpubl. observations 176 matched cddid_all.tbl CDD smart00314 smart00314 214612 RA Ras association (RalGDS/AF-6) domain. RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Kalhammer et al. have shown that not all RA domains bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase. Predicted RA domains in PLC210 and nore1 found to bind RasGTP. Included outliers (Grb7, Grb14, adenylyl cyclases etc.) 90 matched cddid_all.tbl CDD smart00315 smart00315 214613 RGS Regulator of G protein signalling domain. RGS family members are GTPase-activating proteins for heterotrimeric G-protein alpha-subunits. 118 matched cddid_all.tbl CDD smart00316 smart00316 197648 S1 Ribosomal protein S1-like RNA-binding domain. 72 matched cddid_all.tbl CDD smart00317 smart00317 214614 SET SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain. Putative methyl transferase, based on outlier plant homologues 124 matched cddid_all.tbl CDD smart00318 smart00318 214615 SNc Staphylococcal nuclease homologues. 137 matched cddid_all.tbl CDD smart00319 smart00319 128614 TarH Homologues of the ligand binding domain of Tar. Homologues of the ligand binding domain of the wild-type bacterial aspartate receptor, Tar. 135 matched cddid_all.tbl CDD smart00320 smart00320 197651 WD40 WD40 repeats. Note that these repeats are permuted with respect to the structural repeats (blades) of the beta propeller domain. 40 matched cddid_all.tbl CDD smart00321 smart00321 214616 WSC present in yeast cell wall integrity and stress response component proteins. Domain present in WSC proteins, polycystin and fungal exoglucanase 95 matched cddid_all.tbl CDD smart00322 smart00322 197652 KH K homology RNA-binding domain. 68 matched cddid_all.tbl CDD smart00323 smart00323 214617 RasGAP "GTPase-activator protein for Ras-like GTPases. All alpha-helical domain that accelerates the GTPase activity of Ras, thereby ""switching"" it into an ""off"" position. Improved domain limits from structure." 344 matched cddid_all.tbl CDD smart00324 smart00324 214618 RhoGAP GTPase-activator protein for Rho-like GTPases. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases. etter domain limits and outliers. 174 matched cddid_all.tbl CDD smart00325 smart00325 214619 RhoGEF Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases. Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains. Improved coverage. 180 matched cddid_all.tbl CDD smart00326 smart00326 214620 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations. 56 matched cddid_all.tbl CDD smart00327 smart00327 214621 VWA von Willebrand factor (vWF) type A domain. VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods. 175 matched cddid_all.tbl CDD smart00328 smart00328 214622 BPI1 BPI/LBP/CETP N-terminal domain. Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) N-terminal domain 225 matched cddid_all.tbl CDD smart00329 smart00329 128624 BPI2 BPI/LBP/CETP C-terminal domain. Bactericidal permeability-increasing protein (BPI) / Lipopolysaccharide-binding protein (LBP) / Cholesteryl ester transfer protein (CETP) C-terminal domain 202 matched cddid_all.tbl CDD smart00330 smart00330 214623 PIPKc Phosphatidylinositol phosphate kinases. 342 matched cddid_all.tbl CDD smart00331 smart00331 214624 PP2C_SIG Sigma factor PP2C-like phosphatases. 193 matched cddid_all.tbl CDD smart00332 smart00332 214625 PP2Cc Serine/threonine phosphatases, family 2C, catalytic domain. The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence similarity. 252 matched cddid_all.tbl CDD smart00333 smart00333 197660 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished). 57 matched cddid_all.tbl CDD smart00335 smart00335 197661 ANX Annexin repeats. 53 matched cddid_all.tbl CDD smart00336 smart00336 197662 BBOX B-Box-type zinc finger. 42 matched cddid_all.tbl CDD smart00337 smart00337 214626 BCL BCL (B-Cell lymphoma); contains BH1, BH2 regions. (BH1, BH2, (BH3 (one helix only)) and not BH4(one helix only)). Involved in apoptosis regulation 100 matched cddid_all.tbl CDD smart00338 smart00338 197664 BRLZ basic region leucin zipper. 65 matched cddid_all.tbl CDD smart00339 smart00339 214627 FH "FORKHEAD. FORKHEAD, also known as a ""winged helix""" 89 matched cddid_all.tbl CDD smart00340 smart00340 128634 HALZ homeobox associated leucin zipper. 44 matched cddid_all.tbl CDD smart00341 smart00341 128635 HRDC Helicase and RNase D C-terminal. Hypothetical role in nucleic acid binding. Mutations in the HRDC domain cause human disease. 81 matched cddid_all.tbl CDD smart00342 smart00342 197666 HTH_ARAC helix_turn_helix, arabinose operon control protein. 84 matched cddid_all.tbl CDD smart00343 smart00343 197667 ZnF_C2HC zinc finger. 17 matched cddid_all.tbl CDD smart00344 smart00344 214628 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli) 108 matched cddid_all.tbl CDD smart00345 smart00345 197669 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor. 60 matched cddid_all.tbl CDD smart00346 smart00346 214629 HTH_ICLR helix_turn_helix isocitrate lyase regulation. 91 matched cddid_all.tbl CDD smart00347 smart00347 197670 HTH_MARR helix_turn_helix multiple antibiotic resistance protein. 101 matched cddid_all.tbl CDD smart00348 smart00348 128642 IRF interferon regulatory factor. interferon regulatory factor, also known as trytophan pentad repeat 107 matched cddid_all.tbl CDD smart00349 smart00349 214630 KRAB krueppel associated box. 61 matched cddid_all.tbl CDD smart00350 smart00350 214631 MCM minichromosome maintenance proteins. 509 matched cddid_all.tbl CDD smart00351 smart00351 128645 PAX Paired Box domain. 125 matched cddid_all.tbl CDD smart00352 smart00352 197673 POU Found in Pit-Oct-Unc transcription factors. 75 matched cddid_all.tbl CDD smart00353 smart00353 197674 HLH helix loop helix domain. 53 matched cddid_all.tbl CDD smart00354 smart00354 197675 HTH_LACI helix_turn _helix lactose operon repressor. 70 matched cddid_all.tbl CDD smart00355 smart00355 197676 ZnF_C2H2 zinc finger. 23 matched cddid_all.tbl CDD smart00356 smart00356 214632 ZnF_C3H1 zinc finger. 27 matched cddid_all.tbl CDD smart00357 smart00357 214633 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor. 64 matched cddid_all.tbl CDD smart00358 smart00358 214634 DSRM Double-stranded RNA binding motif. 67 matched cddid_all.tbl CDD smart00359 smart00359 214635 PUA Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase. 76 matched cddid_all.tbl CDD smart00360 smart00360 214636 RRM RNA recognition motif. 73 matched cddid_all.tbl CDD smart00361 smart00361 214637 RRM_1 RNA recognition motif. 70 matched cddid_all.tbl CDD smart00363 smart00363 214638 S4 S4 RNA-binding domain. 60 matched cddid_all.tbl CDD smart00364 smart00364 214639 LRR_BAC Leucine-rich repeats, bacterial type. 20 matched cddid_all.tbl CDD smart00365 smart00365 197684 LRR_SD22 Leucine-rich repeat, SDS22-like subfamily. 22 matched cddid_all.tbl CDD smart00367 smart00367 197685 LRR_CC Leucine-rich repeat - CC (cysteine-containing) subfamily. 26 matched cddid_all.tbl CDD smart00368 smart00368 197686 LRR_RI Leucine rich repeat, ribonuclease inhibitor type. 28 matched cddid_all.tbl CDD smart00369 smart00369 197687 LRR_TYP Leucine-rich repeats, typical (most populated) subfamily. 24 matched cddid_all.tbl CDD smart00370 smart00370 197688 LRR Leucine-rich repeats, outliers. 24 matched cddid_all.tbl CDD smart00380 smart00380 197689 AP2 DNA-binding domain in plant proteins such as APETALA2 and EREBPs. 64 matched cddid_all.tbl CDD smart00382 smart00382 214640 AAA ATPases associated with a variety of cellular activities. AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment. 148 matched cddid_all.tbl CDD smart00384 smart00384 197691 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y). 13 matched cddid_all.tbl CDD smart00385 smart00385 214641 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control. 83 matched cddid_all.tbl CDD smart00386 smart00386 214642 HAT HAT (Half-A-TPR) repeats. Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs. 33 matched cddid_all.tbl CDD smart00387 smart00387 214643 HATPase_c Histidine kinase-like ATPases. Histidine kinase-, DNA gyrase B-, phytochrome-like ATPases. 111 matched cddid_all.tbl CDD smart00388 smart00388 214644 HisKA His Kinase A (phosphoacceptor) domain. Dimerisation and phosphoacceptor domain of histidine kinases. 66 matched cddid_all.tbl CDD smart00389 smart00389 197696 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes 57 matched cddid_all.tbl CDD smart00390 smart00390 214645 GoLoco LGN motif, putative GEFs specific for G-alpha GTPases. GEF specific for Galpha_i proteins 23 matched cddid_all.tbl CDD smart00391 smart00391 128673 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain 77 matched cddid_all.tbl CDD smart00392 smart00392 214646 PROF Profilin. Binds actin monomers, membrane polyphosphoinositides and poly-L-proline. 129 matched cddid_all.tbl CDD smart00393 smart00393 214647 R3H Putative single-stranded nucleic acids-binding domain. 79 matched cddid_all.tbl CDD smart00394 smart00394 197697 RIIa RIIalpha, Regulatory subunit portion of type II PKA R-subunit. RIIalpha, Regulatory subunit portion of type II PKA R-subunit. Contains dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs). 38 matched cddid_all.tbl CDD smart00396 smart00396 197698 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p 71 matched cddid_all.tbl CDD smart00397 smart00397 197699 t_SNARE "Helical region found in SNAREs. All alpha-helical motifs that form twisted and parallel four-helix bundles in target soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptor proteins. This motif found in ""Q-SNAREs""." 66 matched cddid_all.tbl CDD smart00398 smart00398 197700 HMG high mobility group. 70 matched cddid_all.tbl CDD smart00399 smart00399 197701 ZnF_C4 c4 zinc finger in nuclear hormone receptors. 70 matched cddid_all.tbl CDD smart00400 smart00400 128681 ZnF_CHCC zinc finger. 55 matched cddid_all.tbl CDD smart00401 smart00401 214648 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG]. 52 matched cddid_all.tbl CDD smart00404 smart00404 214649 PTPc_motif Protein tyrosine phosphatase, catalytic domain motif. 105 matched cddid_all.tbl CDD smart00406 smart00406 214650 IGv Immunoglobulin V-Type. 81 matched cddid_all.tbl CDD smart00407 smart00407 214651 IGc1 Immunoglobulin C-Type. 75 matched cddid_all.tbl CDD smart00410 smart00410 214653 IG_like Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG. 85 matched cddid_all.tbl CDD smart00411 smart00411 197709 BHL bacterial (prokaryotic) histone like domain. 90 matched cddid_all.tbl CDD smart00412 smart00412 128690 Cu_FIST Copper-Fist. binds DNA only in present of copper or silver 39 matched cddid_all.tbl CDD smart00413 smart00413 197710 ETS erythroblast transformation specific domain. variation of the helix-turn-helix motif 87 matched cddid_all.tbl CDD smart00414 smart00414 197711 H2A Histone 2A. 106 matched cddid_all.tbl CDD smart00415 smart00415 214654 HSF heat shock factor. 105 matched cddid_all.tbl CDD smart00417 smart00417 128694 H4 Histone H4. 74 matched cddid_all.tbl CDD smart00418 smart00418 197713 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor. 66 matched cddid_all.tbl CDD smart00419 smart00419 128696 HTH_CRP helix_turn_helix, cAMP Regulatory protein. 48 matched cddid_all.tbl CDD smart00420 smart00420 197714 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor. 53 matched cddid_all.tbl CDD smart00421 smart00421 197715 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon 58 matched cddid_all.tbl CDD smart00422 smart00422 197716 HTH_MERR helix_turn_helix, mercury resistance. 70 matched cddid_all.tbl CDD smart00423 smart00423 214655 PSI domain found in Plexins, Semaphorins and Integrins. 47 matched cddid_all.tbl CDD smart00424 smart00424 128701 STE STE like transcription factors. 111 matched cddid_all.tbl CDD smart00425 smart00425 214656 TBOX Domain first found in the mice T locus (Brachyury) protein. 190 matched cddid_all.tbl CDD smart00426 smart00426 128703 TEA TEA domain. 68 matched cddid_all.tbl CDD smart00427 smart00427 197718 H2B Histone H2B. 97 matched cddid_all.tbl CDD smart00428 smart00428 128705 H3 Histone H3. 105 matched cddid_all.tbl CDD smart00429 smart00429 214657 IPT ig-like, plexins, transcription factors. 90 matched cddid_all.tbl CDD smart00430 smart00430 214658 HOLI Ligand binding domain of hormone receptors. 163 matched cddid_all.tbl CDD smart00431 smart00431 128708 SCAN leucine rich region. 113 matched cddid_all.tbl CDD smart00432 smart00432 197721 MADS MADS domain. 59 matched cddid_all.tbl CDD smart00433 smart00433 214659 TOP2c TopoisomeraseII. Eukaryotic DNA topoisomerase II, GyrB, ParE 594 matched cddid_all.tbl CDD smart00434 smart00434 214660 TOP4c DNA Topoisomerase IV. Bacterial DNA topoisomerase IV, GyrA, ParC 444 matched cddid_all.tbl CDD smart00435 smart00435 214661 TOPEUc DNA Topoisomerase I (eukaryota). DNA Topoisomerase I (eukaryota), DNA topoisomerase V, Vaccina virus topoisomerase, Variola virus topoisomerase, Shope fibroma virus topoisomeras 391 matched cddid_all.tbl CDD smart00436 smart00436 214662 TOP1Bc Bacterial DNA topoisomeraes I ATP-binding domain. Extension of TOPRIM in Bacterial DNA topoisomeraes I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase beta subunit 89 matched cddid_all.tbl CDD smart00437 smart00437 214663 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain. Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit 259 matched cddid_all.tbl CDD smart00438 smart00438 128715 ZnF_NFX Repressor of transcription. 20 matched cddid_all.tbl CDD smart00439 smart00439 214664 BAH Bromo adjacent homology domain. 121 matched cddid_all.tbl CDD smart00440 smart00440 128717 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases. 40 matched cddid_all.tbl CDD smart00441 smart00441 128718 FF Contains two conserved F residues. A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues. 55 matched cddid_all.tbl CDD smart00442 smart00442 214665 FGF Acidic and basic fibroblast growth factor family. Mitogens that stimulate growth or differentiation of cells of mesodermal or neuroectodermal origin. The family play essential roles in patterning and differentiation during vertebrate embryogenesis, and have neurotrophic activities. 126 matched cddid_all.tbl CDD smart00443 smart00443 197727 G_patch glycine rich nucleic binding domain. A predicted glycine rich nucleic binding domain found in the splicing factor 45, SON DNA binding protein and D-type Retrovirus- polyproteins. 47 matched cddid_all.tbl CDD smart00444 smart00444 214666 GYF Contains conserved Gly-Tyr-Phe residues. Proline-binding domain in CD2-binding protein. Contains conserved Gly-Tyr-Phe residues. 56 matched cddid_all.tbl CDD smart00445 smart00445 214667 LINK Link (Hyaluronan-binding). 94 matched cddid_all.tbl CDD smart00446 smart00446 197729 LRRcap "occurring C-terminal to leucine-rich repeats. A motif occurring C-terminal to leucine-rich repeats in ""sds22-like"" and ""typical"" LRR-containing proteins." 19 matched cddid_all.tbl CDD smart00448 smart00448 214668 REC cheY-homologous receiver domain. CheY regulates the clockwise rotation of E. coli flagellar motors. This domain contains a phosphoacceptor site that is phosphorylated by histidine kinase homologues. 55 matched cddid_all.tbl CDD smart00449 smart00449 214669 SPRY Domain in SPla and the RYanodine Receptor. Domain of unknown function. Distant homologues are domains in butyrophilin/marenostrin/pyrin homologues. 122 matched cddid_all.tbl CDD smart00450 smart00450 197731 RHOD Rhodanese Homology Domain. An alpha beta fold found duplicated in the Rhodanese protein. The the Cysteine containing enzymatically active version of the domain is also found in the CDC25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and stress proteins such as Senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions with a loss of the cysteine are also seen in Dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases. These are likely to play a role in protein interactions. 100 matched cddid_all.tbl CDD smart00451 smart00451 197732 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins. 35 matched cddid_all.tbl CDD smart00452 smart00452 214670 STI Soybean trypsin inhibitor (Kunitz) family of protease inhibitors. 172 matched cddid_all.tbl CDD smart00453 smart00453 197734 WSN Worm-specific (usually) N-terminal domain. 69 matched cddid_all.tbl CDD smart00454 smart00454 197735 SAM Sterile alpha motif. Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation. 68 matched cddid_all.tbl CDD smart00455 smart00455 128731 RBD Raf-like Ras-binding domain. 70 matched cddid_all.tbl CDD smart00456 smart00456 197736 WW Domain with 2 conserved Trp (W) residues. Also known as the WWP or rsp5 domain. Binds proline-rich polypeptides. 33 matched cddid_all.tbl CDD smart00457 smart00457 214671 MACPF membrane-attack complex / perforin. 195 matched cddid_all.tbl CDD smart00458 smart00458 214672 RICIN Ricin-type beta-trefoil. Carbohydrate-binding domain formed from presumed gene triplication. 118 matched cddid_all.tbl CDD smart00459 smart00459 128735 Sorb Sorbin homologous domain. First found in the peptide hormone sorbin and later in the ponsin/ArgBP2/vinexin family of proteins. 50 matched cddid_all.tbl CDD smart00460 smart00460 214673 TGc Transglutaminase/protease-like homologues. Transglutaminases are enzymes that establish covalent links between proteins. A subset of transglutaminase homologues appear to catalyse the reverse reaction, the hydrolysis of peptide bonds. Proteins with this domain are both extracellular and intracellular, and it is likely that the eukaryotic intracellular proteins are involved in signalling events. 68 matched cddid_all.tbl CDD smart00461 smart00461 214674 WH1 WASP homology region 1. Region of the Wiskott-Aldrich syndrome protein (WASp) that contains point mutations in the majority of patients with WAS. Unknown function. Ena-like WH1 domains bind polyproline-containing peptides, and that Homer contains a WH1 domain. 106 matched cddid_all.tbl CDD smart00462 smart00462 214675 PTB Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain. PTB/PI domain structure similar to those of pleckstrin homology (PH) and IRS-1-like PTB domains. 134 matched cddid_all.tbl CDD smart00463 smart00463 214676 SMR Small MutS-related domain. 80 matched cddid_all.tbl CDD smart00464 smart00464 197740 LON Found in ATP-dependent protease La (LON). N-terminal domain of the ATP-dependent protease La (LON), present also in other bacterial ORFs. 92 matched cddid_all.tbl CDD smart00465 smart00465 214677 GIYc GIY-YIG type nucleases (URI domain). 84 matched cddid_all.tbl CDD smart00466 smart00466 197742 SRA SET and RING finger associated domain. Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533. 155 matched cddid_all.tbl CDD smart00467 smart00467 197743 GS GS motif. Aa approx. 30 amino acid motif that precedes the kinase domain in types I and II TGF beta receptors. Mutation of two or more of the serines or threonines in the TTSGSGSG of TGF-beta type I receptor impairs phosphorylation and signaling activity. 30 matched cddid_all.tbl CDD smart00468 smart00468 128744 PreSET N-terminal to some SET domains. A Cys-rich putative Zn2+-binding domain that occurs N-terminal to some SET domains. Function is unknown. Unpublished. 98 matched cddid_all.tbl CDD smart00469 smart00469 128745 WIF Wnt-inhibitory factor-1 like domain. Occurs as extracellular domain in metazoan Ryk receptor tyrosine kinases. C. elegans Ryk is required for cell-cuticle recognition. WIF-1 binds to Wnt and inhibits its activity. 136 matched cddid_all.tbl CDD smart00470 smart00470 214678 ParB ParB-like nuclease domain. Plasmid RK2 ParB preferentially cleaves single-stranded DNA. ParB also nicks supercoiled plasmid DNA preferably at sites with potential single-stranded character, like AT-rich regions and sequences that can form cruciform structures. ParB also exhibits 5-->3 exonuclease activity. 89 matched cddid_all.tbl CDD smart00471 smart00471 214679 HDc Metal dependent phosphohydrolases with conserved 'HD' motif. Includes eukaryotic cyclic nucleotide phosphodiesterases (PDEc). This profile/HMM does not detect HD homologues in bacterial glycine aminoacyl-tRNA synthetases (beta subunit). 124 matched cddid_all.tbl CDD smart00472 smart00472 197746 MIR Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases. 57 matched cddid_all.tbl CDD smart00473 smart00473 214680 PAN_AP divergent subfamily of APPLE domains. Apple-like domains present in Plasminogen, C. elegans hypothetical ORFs and the extracellular portion of plant receptor-like protein kinases. Predicted to possess protein- and/or carbohydrate-binding functions. 78 matched cddid_all.tbl CDD smart00474 smart00474 214681 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes 172 matched cddid_all.tbl CDD smart00475 smart00475 214682 53EXOc 5'-3' exonuclease. 259 matched cddid_all.tbl CDD smart00476 smart00476 128752 DNaseIc deoxyribonuclease I. Deoxyribonuclease I catalyzes the endonucleolytic cleavage of double-stranded DNA. The enzyme is secreted outside the cell and also involved in apoptosis in the nucleus. 276 matched cddid_all.tbl CDD smart00477 smart00477 214683 NUC DNA/RNA non-specific endonuclease. prokaryotic and eukaryotic double- and single-stranded DNA and RNA endonucleases also present in phosphodiesterases 210 matched cddid_all.tbl CDD smart00478 smart00478 214684 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases 149 matched cddid_all.tbl CDD smart00479 smart00479 214685 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases. 169 matched cddid_all.tbl CDD smart00480 smart00480 214686 POL3Bc DNA polymerase III beta subunit. 345 matched cddid_all.tbl CDD smart00481 smart00481 197753 POLIIIAc DNA polymerase alpha chain like domain. DNA polymerase alpha chain like domain, incl. family of hypothetical proteins 67 matched cddid_all.tbl CDD smart00482 smart00482 214687 POLAc DNA polymerase A domain. 207 matched cddid_all.tbl CDD smart00483 smart00483 214688 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases 334 matched cddid_all.tbl CDD smart00484 smart00484 214689 XPGI Xeroderma pigmentosum G I-region. domain in nucleases 73 matched cddid_all.tbl CDD smart00485 smart00485 214690 XPGN Xeroderma pigmentosum G N-region. domain in nucleases 99 matched cddid_all.tbl CDD smart00486 smart00486 214691 POLBc DNA polymerase type-B family. DNA polymerase alpha, delta, epsilon and zeta chain (eukaryota), DNA polymerases in archaea, DNA polymerase II in e. coli, mitochondrial DNA polymerases and and virus DNA polymerases 474 matched cddid_all.tbl CDD smart00487 smart00487 214692 DEXDc DEAD-like helicases superfamily. 201 matched cddid_all.tbl CDD smart00488 smart00488 214693 DEXDc2 DEAD-like helicases superfamily. 289 matched cddid_all.tbl CDD smart00490 smart00490 197757 HELICc helicase superfamily c-terminal domain. 82 matched cddid_all.tbl CDD smart00491 smart00491 214694 HELICc2 helicase superfamily c-terminal domain. 142 matched cddid_all.tbl CDD smart00493 smart00493 214695 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins. 75 matched cddid_all.tbl CDD smart00494 smart00494 214696 ChtBD2 Chitin-binding domain type 2. 49 matched cddid_all.tbl CDD smart00495 smart00495 197760 ChtBD3 Chitin-binding domain type 3. 41 matched cddid_all.tbl CDD smart00496 smart00496 128772 IENR2 Intron-encoded nuclease repeat 2. Short helical motif of unknown function (unpublished results). 17 matched cddid_all.tbl CDD smart00497 smart00497 197761 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished). 53 matched cddid_all.tbl CDD smart00498 smart00498 214697 FH2 Formin Homology 2 Domain. FH proteins control rearrangements of the actin cytoskeleton, especially in the context of cytokinesis and cell polarisation. Members of this family have been found to interact with Rho-GTPases, profilin and other actin-assoziated proteins. These interactions are mediated by the proline-rich FH1 domain, usually located in front of FH2 (but not listed in SMART). Despite this cytosolic function, vertebrate formins have been assigned functions within the nucleus. A set of Formin-Binding Proteins (FBPs) has been shown to bind FH1 with their WW domain. 392 matched cddid_all.tbl CDD smart00499 smart00499 214698 AAI Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family. 79 matched cddid_all.tbl CDD smart00500 smart00500 128776 SFM Splicing Factor Motif, present in Prp18 and Pr04. 44 matched cddid_all.tbl CDD smart00501 smart00501 128777 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure 93 matched cddid_all.tbl CDD smart00502 smart00502 128778 BBC B-Box C-terminal domain. Coiled coil region C-terminal to (some) B-Box domains 127 matched cddid_all.tbl CDD smart00503 smart00503 214699 SynN Syntaxin N-terminal domain. Three-helix domain that (in Sso1p) slows the rate of its reaction with the SNAP-25 homologue Sec9p 117 matched cddid_all.tbl CDD smart00504 smart00504 128780 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination. 63 matched cddid_all.tbl CDD smart00505 smart00505 214700 Knot1 Knottins. Knottins, representing plant lectins/antimicrobial peptides, plant proteinase/amylase inhibitors, plant gamma-thionins and arthropod defensins. 45 matched cddid_all.tbl CDD smart00506 smart00506 214701 A1pp "Appr-1""-p processing enzyme. Function determined by Martzen et al. Extended family detected by reciprocal PSI-BLAST searches (unpublished results, and Pehrson & Fuji)." 133 matched cddid_all.tbl CDD smart00507 smart00507 214702 HNHc HNH nucleases. 52 matched cddid_all.tbl CDD smart00508 smart00508 214703 PostSET Cysteine-rich motif following a subset of SET domains. 17 matched cddid_all.tbl CDD smart00509 smart00509 197766 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere). 75 matched cddid_all.tbl CDD smart00510 smart00510 128786 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere). 102 matched cddid_all.tbl CDD smart00511 smart00511 128787 ORANGE Orange domain. This domain confers specificity among members of the Hairy/E(SPL) family. 45 matched cddid_all.tbl CDD smart00512 smart00512 214704 Skp1 Found in Skp1 protein family. Family of Skp1 (kinetochore protein required for cell cycle progression) and elongin C (subunit of RNA polymerase II transcription factor SIII) homologues. 104 matched cddid_all.tbl CDD smart00513 smart00513 128789 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation. 35 matched cddid_all.tbl CDD smart00515 smart00515 214705 eIF5C Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5. 83 matched cddid_all.tbl CDD smart00516 smart00516 214706 SEC14 Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p). Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) and in RhoGAPs, RhoGEFs and the RasGAP, neurofibromin (NF1). Lipid-binding domain. The SEC14 domain of Dbl is known to associate with G protein beta/gamma subunits. 158 matched cddid_all.tbl CDD smart00517 smart00517 197769 PolyA C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. Involved in homodimerisation (either directly or indirectly) 64 matched cddid_all.tbl CDD smart00518 smart00518 214707 AP2Ec AP endonuclease family 2. These endonucleases play a role in DNA repair. Cleave phosphodiester bonds at apurinic or apyrimidinic sites 273 matched cddid_all.tbl CDD smart00520 smart00520 128794 BASIC Basic domain in HLH proteins of MYOD family. 91 matched cddid_all.tbl CDD smart00521 smart00521 128795 CBF CCAAT-Binding transcription Factor. 62 matched cddid_all.tbl CDD smart00523 smart00523 214708 DWA Domain A in dwarfin family proteins. 109 matched cddid_all.tbl CDD smart00524 smart00524 197770 DWB Domain B in dwarfin family proteins. 171 matched cddid_all.tbl CDD smart00525 smart00525 197771 FES iron-sulpphur binding domain in DNA-(apurinic or apyrimidinic site) lyase (subfamily of ENDO3). 21 matched cddid_all.tbl CDD smart00526 smart00526 197772 H15 Domain in histone families 1 and 5. 66 matched cddid_all.tbl CDD smart00527 smart00527 197773 HMG17 domain in high mobilty group proteins HMG14 and HMG 17. 88 matched cddid_all.tbl CDD smart00528 smart00528 128801 HNS Domain in histone-like proteins of HNS family. 46 matched cddid_all.tbl CDD smart00529 smart00529 197774 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor 95 matched cddid_all.tbl CDD smart00530 smart00530 197775 HTH_XRE Helix-turn-helix XRE-family like proteins. 56 matched cddid_all.tbl CDD smart00531 smart00531 128804 TFIIE Transcription initiation factor IIE. 147 matched cddid_all.tbl CDD smart00532 smart00532 214709 LIGANc Ligase N family. 441 matched cddid_all.tbl CDD smart00533 smart00533 214710 MUTSd DNA-binding domain of DNA mismatch repair MUTS family. 308 matched cddid_all.tbl CDD smart00534 smart00534 197777 MUTSac ATPase domain of DNA mismatch repair MUTS family. 185 matched cddid_all.tbl CDD smart00535 smart00535 197778 RIBOc Ribonuclease III family. 129 matched cddid_all.tbl CDD smart00536 smart00536 197779 AXH domain in Ataxins and HMG containing proteins. unknown function 116 matched cddid_all.tbl CDD smart00537 smart00537 214711 DCX Domain in the Doublecortin (DCX) gene product. Tandemly-repeated domain in doublin, the Doublecortin gene product. Proposed to bind tubulin. Doublecortin (DCX) is mutated in human X-linked neuronal migration defects. 89 matched cddid_all.tbl CDD smart00538 smart00538 197780 POP4 A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins. 92 matched cddid_all.tbl CDD smart00539 smart00539 214712 NIDO Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins. 152 matched cddid_all.tbl CDD smart00540 smart00540 128813 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin. 44 matched cddid_all.tbl CDD smart00541 smart00541 128814 FYRN FY-rich domain, N-terminal region. is sometimes closely juxtaposed with the C-terminal region (FYRC), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins. 44 matched cddid_all.tbl CDD smart00542 smart00542 197781 FYRC FY-rich domain, C-terminal region. is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins. 86 matched cddid_all.tbl CDD smart00543 smart00543 214713 MIF4G "Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) ""Novel eIF4G domain homologues (in press)" 200 matched cddid_all.tbl CDD smart00544 smart00544 214714 MA3 "Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) ""Novel eIF4G domain homologues"" in press" 113 matched cddid_all.tbl CDD smart00545 smart00545 128818 JmjN Small domain found in the jumonji family of transcription factors. To date, this domain always co-occurs with the JmjC domain (although the reverse is not true). 42 matched cddid_all.tbl CDD smart00546 smart00546 214715 CUE "Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) ""Proteins of the Endoplasmic reticulum"" (in press)" 43 matched cddid_all.tbl CDD smart00547 smart00547 197784 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP. 25 matched cddid_all.tbl CDD smart00548 smart00548 214716 IRO Motif in Iroquois-class homeodomain proteins (only). Unknown function. 18 matched cddid_all.tbl CDD smart00549 smart00549 197785 TAFH TAF homology. Domain in Drosophila nervy, CBFA2T1, human TAF105, human TAF130, and Drosophila TAF110. Also known as nervy homology region 1 (NHR1). 92 matched cddid_all.tbl CDD smart00550 smart00550 128823 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab. 68 matched cddid_all.tbl CDD smart00551 smart00551 214717 ZnF_TAZ TAZ zinc finger, present in p300 and CBP. 79 matched cddid_all.tbl CDD smart00552 smart00552 214718 ADEAMc tRNA-specific and double-stranded RNA adenosine deaminase (RNA-specific editase). 374 matched cddid_all.tbl CDD smart00553 smart00553 197786 SEP Domain present in Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47. 93 matched cddid_all.tbl CDD smart00554 smart00554 214719 FAS1 Four repeated domains in the Fasciclin I family of proteins, present in many other contexts. 97 matched cddid_all.tbl CDD smart00555 smart00555 128828 GIT Helical motif in the GIT family of ADP-ribosylation factor GTPase-activating proteins. Helical motif in the GIT family of ADP-ribosylation factor GTPase-activating proteins, and in yeast Spa2p and Sph1p (CPP; unpublished results). In p95-APP1 the N-terminal GIT motif might be involved in binding PIX. 31 matched cddid_all.tbl CDD smart00557 smart00557 214720 IG_FLMN Filamin-type immunoglobulin domains. These form a rod-like structure in the actin-binding cytoskeleton protein, filamin. The C-terminal repeats of filamin bind beta1-integrin (CD29). 93 matched cddid_all.tbl CDD smart00558 smart00558 214721 JmjC A domain family that is part of the cupin metalloenzyme superfamily. Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press). 58 matched cddid_all.tbl CDD smart00559 smart00559 128831 Ku78 Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen. This is a single stranded DNA- and ATP-depedent helicase that has a role in chromosome translocation. This is a domain of unknown function C-terminal to its von Willebrand factor A domain, that also occurs in bacterial hypothetical proteins. 140 matched cddid_all.tbl CDD smart00560 smart00560 214722 LamGL LamG-like jellyroll fold domain. 133 matched cddid_all.tbl CDD smart00561 smart00561 214723 MBT Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. These proteins are involved in transcriptional regulation. 96 matched cddid_all.tbl CDD smart00562 smart00562 197791 NDK Enzymes that catalyze nonsubstrate specific conversions of nucleoside diphosphates to nucleoside triphosphates. These enzymes play important roles in bacterial growth, signal transduction and pathogenicity. 135 matched cddid_all.tbl CDD smart00563 smart00563 214724 PlsC Phosphate acyltransferases. Function in phospholipid biosynthesis and have either glycerolphosphate, 1-acylglycerolphosphate, or 2-acylglycerolphosphoethanolamine acyltransferase activities. Tafazzin, the product of the gene mutated in patients with Barth syndrome, is a member of this family. 118 matched cddid_all.tbl CDD smart00564 smart00564 128836 PQQ beta-propeller repeat. Beta-propeller repeat occurring in enzymes with pyrrolo-quinoline quinone (PQQ) as cofactor, in Ire1p-like Ser/Thr kinases, and in prokaryotic dehydrogenases. 33 matched cddid_all.tbl CDD smart00567 smart00567 128837 EZ_HEAT E-Z type HEAT repeats. Present in subunits of cyanobacterial phycocyanin lyase, and other proteins. Probable scaffolding role. 30 matched cddid_all.tbl CDD smart00568 smart00568 214725 GRAM domain in glucosyltransferases, myotubularins and other putative membrane-associated proteins. 60 matched cddid_all.tbl CDD smart00569 smart00569 197794 L27 domain in receptor targeting proteins Lin-2 and Lin-7. 53 matched cddid_all.tbl CDD smart00570 smart00570 197795 AWS associated with SET domains. subdomain of PRESET 50 matched cddid_all.tbl CDD smart00571 smart00571 214726 DDT domain in different transcription and chromosome remodeling factors. 63 matched cddid_all.tbl CDD smart00572 smart00572 128842 DZF domain in DSRM or ZnF_C2H2 domain containing proteins. 246 matched cddid_all.tbl CDD smart00573 smart00573 214727 HSA domain in helicases and associated with SANT domains. 73 matched cddid_all.tbl CDD smart00574 smart00574 214728 POX domain associated with HOX domains. 140 matched cddid_all.tbl CDD smart00575 smart00575 128845 ZnF_PMZ plant mutator transposase zinc finger. 28 matched cddid_all.tbl CDD smart00576 smart00576 128846 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors 77 matched cddid_all.tbl CDD smart00577 smart00577 214729 CPDc catalytic domain of ctd-like phosphatases. 148 matched cddid_all.tbl CDD smart00579 smart00579 214730 FBD domain in FBox and BRCT domain containing plant proteins. 72 matched cddid_all.tbl CDD smart00580 smart00580 197798 PUG domain in protein kinases, N-glycanases and other nuclear proteins. 57 matched cddid_all.tbl CDD smart00581 smart00581 128850 PSP proline-rich domain in spliceosome associated proteins. 54 matched cddid_all.tbl CDD smart00582 smart00582 214731 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA. 124 matched cddid_all.tbl CDD smart00583 smart00583 214732 SPK domain in SET and PHD domain containing proteins and protein kinases. 114 matched cddid_all.tbl CDD smart00584 smart00584 214733 TLDc domain in TBC and LysM domain containing proteins. 165 matched cddid_all.tbl CDD smart00586 smart00586 128854 ZnF_DBF Zinc finger in DBF-like proteins. 49 matched cddid_all.tbl CDD smart00587 smart00587 214734 CHK ZnF_C4 abd HLH domain containing kinases domain. subfamily of choline kinases 196 matched cddid_all.tbl CDD smart00588 smart00588 128856 NEUZ domain in neuralized proteins. 123 matched cddid_all.tbl CDD smart00589 smart00589 128857 PRY associated with SPRY domains. 52 matched cddid_all.tbl CDD smart00591 smart00591 214735 RWD domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain. 107 matched cddid_all.tbl CDD smart00592 smart00592 197800 BRK domain in transcription and CHROMO domain helicases. 45 matched cddid_all.tbl CDD smart00593 smart00593 214736 RUN domain involved in Ras-like GTPase signaling. 64 matched cddid_all.tbl CDD smart00594 smart00594 214737 UAS UAS domain. 122 matched cddid_all.tbl CDD smart00595 smart00595 214738 MADF subfamily of SANT domain. 89 matched cddid_all.tbl CDD smart00596 smart00596 128863 PRE_C2HC PRE_C2HC domain. 69 matched cddid_all.tbl CDD smart00597 smart00597 214739 ZnF_TTF zinc finger in transposases and transcription factors. 91 matched cddid_all.tbl CDD smart00602 smart00602 214740 VPS10 VPS10 domain. 612 matched cddid_all.tbl CDD smart00603 smart00603 128866 LCCL LCCL domain. 85 matched cddid_all.tbl CDD smart00604 smart00604 214741 MD MD domain. 145 matched cddid_all.tbl CDD smart00605 smart00605 214742 CW CW domain. 94 matched cddid_all.tbl CDD smart00606 smart00606 128869 CBD_IV Cellulose Binding Domain Type IV. 129 matched cddid_all.tbl CDD smart00607 smart00607 128870 FTP eel-Fucolectin Tachylectin-4 Pentaxrin-1 Domain. 151 matched cddid_all.tbl CDD smart00608 smart00608 214743 ACR ADAM Cysteine-Rich Domain. 137 matched cddid_all.tbl CDD smart00609 smart00609 197803 VIT Vault protein Inter-alpha-Trypsin domain. 130 matched cddid_all.tbl CDD smart00611 smart00611 214744 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins. 312 matched cddid_all.tbl CDD smart00612 smart00612 128874 Kelch Kelch domain. 47 matched cddid_all.tbl CDD smart00613 smart00613 214745 PAW domain present in PNGases and other hypothetical proteins. present in several copies in proteins with unknown function in C. elegans 89 matched cddid_all.tbl CDD smart00614 smart00614 214746 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases 50 matched cddid_all.tbl CDD smart00615 smart00615 128877 EPH_lbd Ephrin receptor ligand binding domain. 177 matched cddid_all.tbl CDD smart00630 smart00630 214747 Sema semaphorin domain. 390 matched cddid_all.tbl CDD smart00631 smart00631 214748 Zn_pept Zn_pept domain. 277 matched cddid_all.tbl CDD smart00632 smart00632 214749 Aamy_C Aamy_C domain. 81 matched cddid_all.tbl CDD smart00633 smart00633 214750 Glyco_10 Glycosyl hydrolase family 10. 263 matched cddid_all.tbl CDD smart00634 smart00634 214751 BID_1 Bacterial Ig-like domain (group 1). 92 matched cddid_all.tbl CDD smart00635 smart00635 214752 BID_2 Bacterial Ig-like domain 2. 81 matched cddid_all.tbl CDD smart00636 smart00636 214753 Glyco_18 Glyco_18 domain. 334 matched cddid_all.tbl CDD smart00637 smart00637 214754 CBD_II CBD_II domain. 92 matched cddid_all.tbl CDD smart00638 smart00638 214755 LPD_N Lipoprotein N-terminal Domain. 574 matched cddid_all.tbl CDD smart00639 smart00639 214756 PSA Paramecium Surface Antigen Repeat. 62 matched cddid_all.tbl CDD smart00640 smart00640 214757 Glyco_32 Glycosyl hydrolases family 32. 437 matched cddid_all.tbl CDD smart00641 smart00641 128889 Glyco_25 Glycosyl hydrolases family 25. 109 matched cddid_all.tbl CDD smart00642 smart00642 214758 Aamy Alpha-amylase domain. 166 matched cddid_all.tbl CDD smart00643 smart00643 214759 C345C Netrin C-terminal Domain. 114 matched cddid_all.tbl CDD smart00644 smart00644 214760 Ami_2 Ami_2 domain. 126 matched cddid_all.tbl CDD smart00645 smart00645 214761 Pept_C1 Papain family cysteine protease. 175 matched cddid_all.tbl CDD smart00646 smart00646 214762 Ami_3 Ami_3 domain. 113 matched cddid_all.tbl CDD smart00647 smart00647 214763 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers 64 matched cddid_all.tbl CDD smart00648 smart00648 197818 SWAP Suppressor-of-White-APricot splicing regulator. domain present in regulators which are responsible for pre-mRNA splicing processes 54 matched cddid_all.tbl CDD smart00649 smart00649 197819 RL11 Ribosomal protein L11/L12. 132 matched cddid_all.tbl CDD smart00650 smart00650 128898 rADc Ribosomal RNA adenine dimethylases. 169 matched cddid_all.tbl CDD smart00651 smart00651 197820 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing 67 matched cddid_all.tbl CDD smart00652 smart00652 128900 eIF1a eukaryotic translation initiation factor 1A. 83 matched cddid_all.tbl CDD smart00653 smart00653 214764 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5. 110 matched cddid_all.tbl CDD smart00654 smart00654 128902 eIF6 translation initiation factor 6. 200 matched cddid_all.tbl CDD smart00656 smart00656 214765 Amb_all Amb_all domain. 190 matched cddid_all.tbl CDD smart00657 smart00657 128904 RPOL4c DNA-directed RNA-polymerase II subunit. 118 matched cddid_all.tbl CDD smart00658 smart00658 197821 RPOL8c RNA polymerase subunit 8. subunit of RNA polymerase I, II and III 143 matched cddid_all.tbl CDD smart00659 smart00659 128906 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III 44 matched cddid_all.tbl CDD smart00661 smart00661 197822 RPOL9 RNA polymerase subunit 9. 52 matched cddid_all.tbl CDD smart00662 smart00662 214766 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain 224 matched cddid_all.tbl CDD smart00663 smart00663 214767 RPOLA_N RNA polymerase I subunit A N-terminus. 295 matched cddid_all.tbl CDD smart00664 smart00664 214768 DoH Possible catecholamine-binding domain present in a variety of eukaryotic proteins. A predominantly beta-sheet domain present as a regulatory N-terminal domain in dopamine beta-hydroxylase, mono-oxygenase X and SDR2. Its function remains unknown at present (Ponting, Human Molecular Genetics, in press). 148 matched cddid_all.tbl CDD smart00665 smart00665 214769 B561 Cytochrome b-561 / ferric reductase transmembrane domain. Cytochrome b-561 recycles ascorbate for the generation of norepinephrine by dopamine-beta-hydroxylase in the chromaffin vesicles of the adrenal gland. It is a transmembrane heme protein with the two heme groups being bound to conserved histidine residues. A cytochrome b-561 homologue, termed Dcytb, is an iron-regulated ferric reductase in the duodenal mucosa. Other homologues of these are also likely to be ferric reductases. SDR2 is proposed to be important in regulating the metabolism of iron in the onset of neurodegenerative disorders. 129 matched cddid_all.tbl CDD smart00666 smart00666 214770 PB1 PB1 domain. Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate. 81 matched cddid_all.tbl CDD smart00667 smart00667 128913 LisH Lissencephaly type-1-like homology motif. Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly. 34 matched cddid_all.tbl CDD smart00668 smart00668 128914 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function. 58 matched cddid_all.tbl CDD smart00670 smart00670 214771 PINc Large family of predicted nucleotide-binding domains. From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi. 111 matched cddid_all.tbl CDD smart00671 smart00671 214772 SEL1 Sel1-like repeats. These represent a subfamily of TPR (tetratricopeptide repeat) sequences. 36 matched cddid_all.tbl CDD smart00672 smart00672 214773 CAP10 Putative lipopolysaccharide-modifying enzyme. 256 matched cddid_all.tbl CDD smart00673 smart00673 197827 CARP Domain in CAPs (cyclase-associated proteins) and X-linked retinitis pigmentosa 2 gene product. 38 matched cddid_all.tbl CDD smart00674 smart00674 197828 CENPB Putative DNA-binding domain in centromere protein B, mouse jerky and transposases. 66 matched cddid_all.tbl CDD smart00675 smart00675 128920 DM11 Domains in hypothetical proteins in Drosophila including 2 in CG15241 and CG9329. 164 matched cddid_all.tbl CDD smart00676 smart00676 128921 DM10 Domains in hypothetical proteins in Drosophila, C. elegans and mammals. Occurs singly in some nucleoside diphosphate kinases. 104 matched cddid_all.tbl CDD smart00678 smart00678 128922 WWE Domain in Deltex and TRIP12 homologues. Possibly involved in regulation of ubiquitin-mediated proteolysis. 73 matched cddid_all.tbl CDD smart00679 smart00679 128923 CTNS Repeated motif present between transmembrane helices in cystinosin, yeast ERS1p, mannose-P-dolichol utilization defect 1, and other hypothetical proteins. Function unknown, but likely to be associated with the glycosylation machinery. 32 matched cddid_all.tbl CDD smart00680 smart00680 197829 CLIP Clip or disulphide knot domain. Present in horseshoe crab proclotting enzyme N-terminal domain, Drosophila Easter and silkworm prophenoloxidase-activating enzyme. 52 matched cddid_all.tbl CDD smart00682 smart00682 214774 G2F G2 nidogen domain and fibulin. 227 matched cddid_all.tbl CDD smart00683 smart00683 128926 DM16 Repeats in sea squirt COS41.4, worm R01H10.6, fly CG1126 etc. 55 matched cddid_all.tbl CDD smart00684 smart00684 128927 DM15 Tandem repeat in fly CG14066 (La related protein), human KIAA0731 and worm R144.7. Unknown function. 39 matched cddid_all.tbl CDD smart00685 smart00685 128928 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241. 59 matched cddid_all.tbl CDD smart00686 smart00686 128929 DM13 Domain present in fly proteins (CG14681, CG12492, CG6217), worm H06A10.1 and Arabidopsis thaliana MBG8.9. 108 matched cddid_all.tbl CDD smart00688 smart00688 128930 DM7 Domain of unknown function in Drosophila CG15332, CG15333 and CG18293. 95 matched cddid_all.tbl CDD smart00689 smart00689 214775 DM6 Cysteine-rich domain currently specific to Drosophila. 157 matched cddid_all.tbl CDD smart00690 smart00690 214776 DM5 Domain of unknown function, currently peculiar to Drosophila. 102 matched cddid_all.tbl CDD smart00692 smart00692 128933 DM3 Zinc finger domain in CG10631, C. elegans LIN-15B and human P52rIPK. 59 matched cddid_all.tbl CDD smart00693 smart00693 214777 DysFN Dysferlin domain, N-terminal region. Domain of unknown function present in yeast peroxisomal proteins, dysferlin, myoferlin and hypothetical proteins. Due to an insertion of a dysferlin domain within a second dysferlin domain we have chosen to predict these domains in two parts: the N-terminal region and the C-terminal region. 62 matched cddid_all.tbl CDD smart00694 smart00694 128935 DysFC Dysferlin domain, C-terminal region. Domain of unknown function present in yeast peroxisomal proteins, dysferlin, myoferlin and hypothetical proteins. Due to an insertion of a dysferlin domain within a second dysferlin domain we have chosen to predict these domains in two parts: the N-terminal region and the C-terminal region. 34 matched cddid_all.tbl CDD smart00695 smart00695 197831 DUSP Domain in ubiquitin-specific proteases. 88 matched cddid_all.tbl CDD smart00696 smart00696 128937 DM9 Repeats found in Drosophila proteins. 71 matched cddid_all.tbl CDD smart00697 smart00697 214778 DM8 Repeats found in several Drosophila proteins. 93 matched cddid_all.tbl CDD smart00698 smart00698 197832 MORN Possible plasma membrane-binding motif in junctophilins, PIP-5-kinases and protein kinases. 22 matched cddid_all.tbl CDD smart00700 smart00700 214779 JHBP Juvenile hormone binding protein domains in insects. The juvenile hormone exerts pleiotropic functions during insect life cycles and its binding proteins regulate these functions. 224 matched cddid_all.tbl CDD smart00701 smart00701 128941 PGRP Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme. The bacteriophage molecule, but not its moth homologue, has been shown to have N-acetylmuramoyl-L-alanine amidase activity. One member of this family, Tag7, is a cytokine. 142 matched cddid_all.tbl CDD smart00702 smart00702 214780 P4Hc Prolyl 4-hydroxylase alpha subunit homologues. Mammalian enzymes catalyse hydroxylation of collagen, for example. Prokaryotic enzymes might catalyse hydroxylation of antibiotic peptides. These are 2-oxoglutarate-dependent dioxygenases, requiring 2-oxoglutarate and dioxygen as cosubstrates and ferrous iron as a cofactor. 165 matched cddid_all.tbl CDD smart00703 smart00703 214781 NRF N-terminal domain in C. elegans NRF-6 (Nose Resistant to Fluoxetine-4) and NDG-4 (resistant to nordihydroguaiaretic acid-4). Also present in several other worm and fly proteins. 110 matched cddid_all.tbl CDD smart00704 smart00704 197836 ZnF_CDGSH CDGSH-type zinc finger. Function unknown. 38 matched cddid_all.tbl CDD smart00705 smart00705 128945 THEG Repeats in THEG (testicular haploid expressed gene) and several fly proteins. 20 matched cddid_all.tbl CDD smart00706 smart00706 214782 TECPR Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins. 35 matched cddid_all.tbl CDD smart00707 smart00707 128947 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2. 26 matched cddid_all.tbl CDD smart00708 smart00708 214783 PhBP Insect pheromone/odorant binding protein domains. 103 matched cddid_all.tbl CDD smart00709 smart00709 128949 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins. 160 matched cddid_all.tbl CDD smart00710 smart00710 214784 PbH1 Parallel beta-helix repeats. The tertiary structures of pectate lyases and rhamnogalacturonase A show a stack of parallel beta strands that are coiled into a large helix. Each coil of the helix represents a structural repeat that, in some homologues, can be recognised from sequence information alone. Conservation of asparagines might be connected with asparagine-ladders that contribute to the stability of the fold. Proteins containing these repeats most often are enzymes with polysaccharide substrates. 23 matched cddid_all.tbl CDD smart00711 smart00711 197839 TDU Short repeats in human TONDU, fly vestigial and other proteins. Unknown function. 16 matched cddid_all.tbl CDD smart00712 smart00712 197840 PUR DNA/RNA-binding repeats in PUR-alpha/beta/gamma and in hypothetical proteins from spirochetes and the Bacteroides-Cytophaga-Flexibacter bacteria. 63 matched cddid_all.tbl CDD smart00713 smart00713 128953 GYR Motif of unknown function with conserved Gly, Tyr, Arg tripeptide in Drosophila proteins. 18 matched cddid_all.tbl CDD smart00714 smart00714 197841 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins. 67 matched cddid_all.tbl CDD smart00715 smart00715 128955 LA Domain in the RNA-binding Lupus La protein; unknown function. 80 matched cddid_all.tbl CDD smart00717 smart00717 197842 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains. 49 matched cddid_all.tbl CDD smart00718 smart00718 214785 DM4_12 DM4/DM12 family of domains in Drosophila melanogaster proteins of unknown function. 95 matched cddid_all.tbl CDD smart00719 smart00719 197843 Plus3 Short conserved domain in transcriptional regulators. Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1. 109 matched cddid_all.tbl CDD smart00720 smart00720 214786 calpain_III calpain_III domain. 143 matched cddid_all.tbl CDD smart00721 smart00721 214787 BAR BAR domain. 239 matched cddid_all.tbl CDD smart00722 smart00722 214788 CASH Domain present in carbohydrate binding proteins and sugar hydrolses. 153 matched cddid_all.tbl CDD smart00723 smart00723 128962 AMOP Adhesion-associated domain present in MUC4 and other proteins. 154 matched cddid_all.tbl CDD smart00724 smart00724 214789 TLC TRAM, LAG1 and CLN8 homology domains. Protein domain with at least 5 transmembrane alpha-helices. Lag1p and Lac1p are essential for acyl-CoA-dependent ceramide synthesis, TRAM is a subunit of the translocon and the CLN8 gene is mutated in Northern epilepsy syndrome. The family may possess multiple functions such as lipid trafficking, metabolism, or sensing. Trh homologues possess additional homeobox domains. 205 matched cddid_all.tbl CDD smart00725 smart00725 214790 NEAT NEAr Transporter domain. 123 matched cddid_all.tbl CDD smart00726 smart00726 197845 UIM Ubiquitin-interacting motif. Present in proteasome subunit S5a and other ubiquitin-associated proteins. 20 matched cddid_all.tbl CDD smart00727 smart00727 128966 STI1 Heat shock chaperonin-binding motif. 41 matched cddid_all.tbl CDD smart00728 smart00728 214791 ChW Clostridial hydrophobic, with a conserved W residue, domain. 46 matched cddid_all.tbl CDD smart00729 smart00729 214792 Elp3 Elongator protein 3, MiaB family, Radical SAM. This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases. 216 matched cddid_all.tbl CDD smart00730 smart00730 214793 PSN Presenilin, signal peptide peptidase, family. Presenilin 1 and presenilin 2 are polytopic membrane proteins, whose genes are mutated in some individuals with Alzheimer's disease. Distant homologues, present in eukaryotes and archaea, also contain conserved aspartic acid residues which are predicted to contribute to catalysis. At least one member of this family has been shown to possess signal peptide peptidase activity. 249 matched cddid_all.tbl CDD smart00731 smart00731 214794 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function. 146 matched cddid_all.tbl CDD smart00732 smart00732 128971 YqgFc Likely ribonuclease with RNase H fold. YqgF proteins are likely to function as an alternative to RuvC in most bacteria, and could be the principal holliday junction resolvases in low-GC Gram-positive bacteria. In Spt6p orthologues, the catalytic residues are substituted indicating that they lack enzymatic functions. 99 matched cddid_all.tbl CDD smart00733 smart00733 197848 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins. 31 matched cddid_all.tbl CDD smart00734 smart00734 128973 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids. 24 matched cddid_all.tbl CDD smart00735 smart00735 128974 ZM ZASP-like motif. Short motif (26 amino acids) present in an alpha-actinin-binding protein, ZASP, and similar molecules. 26 matched cddid_all.tbl CDD smart00736 smart00736 214795 CADG Dystroglycan-type cadherin-like domains. Cadherin-homologous domains present in metazoan dystroglycans and alpha/epsilon sarcoglycans, yeast Axl2p and in a very large protein from magnetotactic bacteria. Likely to bind calcium ions. 97 matched cddid_all.tbl CDD smart00737 smart00737 214796 ML Domain involved in innate immunity and lipid metabolism. ML (MD-2-related lipid-recognition) is a novel domain identified in MD-1, MD-2, GM2A, Npc2 and multiple proteins of unknown function in plants, animals and fungi. These single-domain proteins were predicted to form a beta-rich fold containing multiple strands, and to mediate diverse biological functions through interacting with specific lipids. 119 matched cddid_all.tbl CDD smart00738 smart00738 197850 NGN In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. In Spt5p, this domain may confer affinity for Spt4p.Spt4p 106 matched cddid_all.tbl CDD smart00739 smart00739 128978 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54. 28 matched cddid_all.tbl CDD smart00740 smart00740 197851 PASTA PASTA domain. 67 matched cddid_all.tbl CDD smart00741 smart00741 214797 SapB Saposin (B) Domains. Present in multiple copies in prosaposin and in pulmonary surfactant-associated protein B. In plant aspartic proteinases, a saposin domain is circularly permuted. This causes the prediction algorithm to predict two such domains, where only one is truly present. 76 matched cddid_all.tbl CDD smart00742 smart00742 128981 Hr1 Rho effector or protein kinase C-related kinase homology region 1 homologues. Alpha-helical domain found in vertebrate PRK1 and yeast PKC1 protein kinases C. The HR1 in rhophilin bind RhoGTP; those in PRK1 bind RhoA and RhoB. Also called RBD - Rho-binding domain 57 matched cddid_all.tbl CDD smart00743 smart00743 214798 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions. 59 matched cddid_all.tbl CDD smart00744 smart00744 128983 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Classical RING domain: C-x (2) -C-x (9-39)-C-x(1-3)-H-x(2-3)-C-x(2)-C-x(4-48) -C-x(2)-C 49 matched cddid_all.tbl CDD smart00745 smart00745 197854 MIT Microtubule Interacting and Trafficking molecule domain. 77 matched cddid_all.tbl CDD smart00746 smart00746 214799 TRASH metallochaperone-like domain. 39 matched cddid_all.tbl CDD smart00747 smart00747 128986 CFEM eight cysteine-containing domain present in fungal extracellular membrane proteins. 65 matched cddid_all.tbl CDD smart00748 smart00748 214800 HEPN Higher Eukarytoes and Prokaryotes Nucleotide-binding domain. 113 matched cddid_all.tbl CDD smart00749 smart00749 197856 BON bacterial OsmY and nodulation domain. 61 matched cddid_all.tbl CDD smart00750 smart00750 214801 KIND kinase non-catalytic C-lobe domain. It is an interaction domain identified as being similar to the C-terminal protein kinase catalytic fold (C lobe). Its presence at the N terminus of signalling proteins and the absence of the active-site residues in the catalytic and activation loops suggest that it folds independently and is likely to be non-catalytic. The occurrence of KIND only in metazoa implies that it has evolved from the catalytic protein kinase domain into an interaction domain possibly by keeping the substrate-binding features 176 matched cddid_all.tbl CDD smart00751 smart00751 128990 BSD domain in transcription factors and synapse-associated proteins. 51 matched cddid_all.tbl CDD smart00752 smart00752 214802 HTTM Horizontally Transferred TransMembrane Domain. Sequence analysis of vitamin K dependent gamma-carboxylases (VKGC) revealed the presence of a novel domain, HTTM (Horizontally Transferred TransMembrane) in its N-terminus. In contrast to most known domains, HTTM contains four transmembrane regions. Its occurrence in eukaryotes, bacteria and archaea is more likely caused by horizontal gene transfer than by early invention. The conservation of VKGC catalytic sites indicates an enzymatic function also for the other family members. 271 matched cddid_all.tbl CDD smart00754 smart00754 214804 CHRD A domain in the BMP inhibitor chordin and in microbial proteins. 118 matched cddid_all.tbl CDD smart00755 smart00755 197860 Grip golgin-97, RanBP2alpha,Imh1p and p230/golgin-245. 46 matched cddid_all.tbl CDD smart00756 smart00756 214805 VKc Family of likely enzymes that includes the catalytic subunit of vitamin K epoxide reductase. Bacterial homologues are fused to members of the thioredoxin family of oxidoreductases. 142 matched cddid_all.tbl CDD smart00757 smart00757 214806 CRA CT11-RanBPM. protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) 99 matched cddid_all.tbl CDD smart00758 smart00758 214807 PA14 domain in bacterial beta-glucosidases other glycosidases, glycosyltransferases, proteases, amidases, yeast adhesins, and bacterial toxins. 136 matched cddid_all.tbl CDD smart00759 smart00759 128998 Flu_M1_C Influenza Matrix protein (M1) C-terminal domain. This region is thought to be a second domain of the M1 matrix protein. 95 matched cddid_all.tbl CDD smart00760 smart00760 197863 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding. 69 matched cddid_all.tbl CDD smart00761 smart00761 214808 HDAC_interact Histone deacetylase (HDAC) interacting. This domain is found on transcriptional regulators. It forms interactions with histone deacetylases. 102 matched cddid_all.tbl CDD smart00762 smart00762 214809 Cog4 COG4 transport protein. This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport. 324 matched cddid_all.tbl CDD smart00763 smart00763 214810 AAA_PrkA PrkA AAA domain. This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain. 361 matched cddid_all.tbl CDD smart00764 smart00764 129003 Citrate_ly_lig Citrate lyase ligase C-terminal domain. Proteins of this family contain the C-terminal domain of citrate lyase ligase EC:6.2.1.22. 182 matched cddid_all.tbl CDD smart00765 smart00765 129004 MANEC The MANEC domain, formerly called MANSC. This domain, comprising 8 conserved cysteines, is found in the N terminus of higher multicellular animal membrane and extracellular proteins. It is postulated that this domain may play a role in the formation of protein complexes involving various protease activators and inhibitors. It is possible that some of the cysteine residues in the MANSC domain form structurally important disulfide bridges. All of the MANSC-containing proteins contain predicted transmembrane regions and signal peptides. It has been proposed that the MANSC domain in HAI-1 might function through binding with hepatocyte growth factor activator and matriptase. 93 matched cddid_all.tbl CDD smart00766 smart00766 197866 DnaG_DnaB_bind DNA primase DnaG DnaB-binding. DnaG_DnaB_bind defines a domain of primase required for functional interaction with DnaB that attracts primase to the replication fork. DnaG_DnaB_bind is responsible for the interaction between DnaG and DnaB. 125 matched cddid_all.tbl CDD smart00767 smart00767 214811 DCD DCD is a plant specific domain in proteins involved in development and programmed cell death. The domain is shared by several proteins in the Arabidopsis and the rice genomes, which otherwise show a different protein architecture. Biological studies indicate a role of these proteins in phytohormone response, embryo development and programmed cell death by pathogens or ozone. 132 matched cddid_all.tbl CDD smart00768 smart00768 197867 X8 Possibly involved in carbohydrate binding. The X8 domain, which may be involved in carbohydrate binding, is found in an Olive pollen antigen as well as at the C terminus of family 17 glycosyl hydrolases. It contains 6 conserved cysteine residues which presumably form three disulfide bridges. 85 matched cddid_all.tbl CDD smart00769 smart00769 214812 WHy Water Stress and Hypersensitive response. 100 matched cddid_all.tbl CDD smart00770 smart00770 214813 Zn_dep_PLPC Zinc dependent phospholipase C (alpha toxin). This domain conveys a zinc dependent phospholipase C activity (EC 3.1.4.3). It is found in a monomeric phospholipase C of Bacillus cereus as well as in the alpha toxin of Clostridium perfringens and Clostridium bifermentans, which is involved in haemolysis and cell rupture. It is also found in a lecithinase of Listeria monocytogenes, which is involved in breaking the 2-membrane vacuoles that surround the bacterium. Structure information: PDB 1ca1. 241 matched cddid_all.tbl CDD smart00771 smart00771 129010 ZipA_C ZipA, C-terminal domain (FtsZ-binding). C-terminal domain of ZipA, a component of cell division in E.coli. It interacts with the FtsZ protein in one of the initial steps of septum formation. The structure of this domain is composed of three alpha-helices and a beta-sheet consisting of six antiparallel beta-strands. 131 matched cddid_all.tbl CDD smart00773 smart00773 214814 WGR Proposed nucleic acid binding domain. This domain is named after its most conserved central motif. It is found in a variety of polyA polymerases as well as in molybdate metabolism regulators (e.g. in E.coli) and other proteins of unknown function. The domain is found in isolation in some proteins and is between 70 and 80 residues in length. It is proposed that it may be a nucleic acid binding domain. 84 matched cddid_all.tbl CDD smart00774 smart00774 214815 WRKY DNA binding domain. The WRKY domain is a DNA binding domain found in one or two copies in a superfamily of plant transcription factors. These transcription factors are involved in the regulation of various physiological programs that are unique to plants, including pathogen defense, senescence and trichome development. The domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger-like motif. It binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core is essential for function and WRKY binding. 59 matched cddid_all.tbl CDD smart00775 smart00775 197870 LNS2 This domain is found in Saccharomyces cerevisiae protein SMP2, proteins with an N-terminal lipin domain and phosphatidylinositol transfer proteins. SMP2 is involved in plasmid maintenance and respiration. Lipin proteins are involved in adipose tissue development and insulin resistance. 157 matched cddid_all.tbl CDD smart00776 smart00776 214816 NPCBM This novel putative carbohydrate binding module (NPCBM) domain is found at the N-terminus of glycosyl hydrolase family 98 proteins. 145 matched cddid_all.tbl CDD smart00777 smart00777 214817 Mad3_BUB1_I Mad3/BUB1 hoMad3/BUB1 homology region 1. Proteins containing this domain are checkpoint proteins involved in cell division. This region has been shown to be essential for the binding of the binding of BUB1 and MAD3 to CDC20p. 124 matched cddid_all.tbl CDD smart00778 smart00778 129016 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities. 37 matched cddid_all.tbl CDD smart00780 smart00780 197872 PIG-X PIG-X / PBN1. Mammalian PIG-X and yeast PBN1 are essential components of glycosylphosphatidylinositol-mannosyltransferase I. These enzymes are involved in the transfer of sugar molecules. 203 matched cddid_all.tbl CDD smart00782 smart00782 129018 PhnA_Zn_Ribbon PhnA Zinc-Ribbon. This protein family includes an uncharacterised member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterised phosphonoacetate hydrolase designated PhnA. 47 matched cddid_all.tbl CDD smart00783 smart00783 129019 A_amylase_inhib Alpha amylase inhibitor. Alpha amylase inhibitor inhibits mammalian alpha-amylases specifically, by forming a tight stoichiometric 1:1 complex with alpha-amylase. The inhibitor has no action on plant and microbial alpha amylases. 69 matched cddid_all.tbl CDD smart00784 smart00784 214818 SPT2 SPT2 chromatin protein. This entry includes the Saccharomyces cerevisiae protein SPT2 which is a chromatin protein involved in transcriptional regulation. 106 matched cddid_all.tbl CDD smart00785 smart00785 129021 AARP2CN AARP2CN (NUC121) domain. This domain is the central domain of AARP2. It is weakly similar to the GTP-binding domain of elongation factor TU. 83 matched cddid_all.tbl CDD smart00786 smart00786 129022 SHR3_chaperone ER membrane protein SH3. This family of proteins are membrane localised chaperones that are required for correct plasma membrane localisation of amino acid permeases (AAPs). Shr3 prevents AAPs proteins from aggregating and assists in their correct folding. In the absence of Shr3, AAPs are retained in the ER. 196 matched cddid_all.tbl CDD smart00787 smart00787 197874 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association. 312 matched cddid_all.tbl CDD smart00788 smart00788 197875 Adenylsucc_synt Adenylosuccinate synthetase. Adenylosuccinate synthetase plays an important role in purine biosynthesis, by catalyzing the GTP-dependent conversion of IMP and aspartic acid to AMP. Adenylosuccinate synthetase has been characterized from various sources ranging from Escherichia coli (gene purA) to vertebrate tissues. In vertebrates, two isozymes are present - one involved in purine biosynthesis and the other in the purine nucleotide cycle. The crystal structure of adenylosuccinate synthetase from E. coli reveals that the dominant structural element of each monomer of the homodimer is a central beta-sheet of 10 strands. The first nine strands of the sheet are mutually parallel with right-handed crossover connections between the strands. The 10th strand is antiparallel with respect to the first nine strands. In addition, the enzyme has two antiparallel beta-sheets, comprised of two strands and three strands each, 11 alpha-helices and two short 3/10-helices. Further, it has been suggested that the similarities in the GTP-binding domains of the synthetase and the p21ras protein are an example of convergent evolution of two distinct families of GTP-binding proteins. Structures of adenylosuccinate synthetase from Triticum aestivum and Arabidopsis thaliana when compared with the known structures from E. coli reveals that the overall fold is very similar to that of the E. coli protein. 417 matched cddid_all.tbl CDD smart00789 smart00789 129025 Ad_cyc_g-alpha Adenylate cyclase G-alpha binding domain. This fungal domain is found in adenylate cyclase and interacts with the alpha subunit of heterotrimeric G proteins. 51 matched cddid_all.tbl CDD smart00790 smart00790 129026 AFOR_N Aldehyde ferredoxin oxidoreductase, N-terminal domain. Enzymes of the aldehyde ferredoxin oxidoreductase (AOR) family contain a tungsten cofactor and an 4Fe4S cluster and catalyse the interconversion of aldehydes to carboxylates. This family includes AOR, formaldehyde ferredoxin oxidoreductase (FOR), glyceraldehyde-3-phosphate ferredoxin oxidoreductase (GAPOR), all isolated from hyperthermophilic archea. carboxylic acid reductase found in clostridia. and hydroxycarboxylate viologen oxidoreductase from Proteus vulgaris, the sole member of the AOR family containing molybdenum. GAPOR may be involved in glycolysis. but the functions of the other proteins are not yet clear. AOR has been proposed to be the primary enzyme responsible for oxidising the aldehydes that are produced by the 2-keto acid oxidoreductases. 199 matched cddid_all.tbl CDD smart00791 smart00791 129027 Agglutinin Amaranthus caudatus agglutinin or amaranthin is a lectin from the ancient South American crop, amaranth grain. Although its biological function is unknown, it has a high binding specificity for the methyl-glycoside of the T-antigen, found linked to serine or threonine residues of cell surface glycoproteins. The protein is comprised of a homodimer, with each homodimer consisting of two beta-trefoil domains. 139 matched cddid_all.tbl CDD smart00792 smart00792 197876 Agouti Agouti protein. The agouti protein regulates pigmentation in the mouse hair follicle producing a black hair with a subapical yellow band. A highly homologous protein agouti signal protein (ASIP) is present in humans and is expressed at highest levels in adipose tissue where it may play a role in energy homeostasis and possibly human pigmentation. 124 matched cddid_all.tbl CDD smart00793 smart00793 214819 AgrB Accessory gene regulator B. The accessory gene regulator (agr) of Staphylococcus aureus is the central regulatory system that controls the gene expression for a large set of virulence factors. The arg locus consists of two transcripts: RNAII and RNAIII. RNAII encodes four genes (agrA, B, C, and D) whose gene products assemble a quorum sensing system. At low cell density, the agr genes are continuously expressed at basal levels. A signal molecule, autoinducing peptide (AIP), produced and secreted by the bacteria, accumulates outside of the cells. When the cell density increases and the AIP concentration reaches a threshold, it activates the agr response, i.e. activation of secreted protein gene expression and subsequent repression of cell wall-associated protein genes. AgrB and AgrD are essential for the production of the autoinducing peptide which functions as a signal for quorum sensing. AgrB is a transmembrane protein. AgrB is involved in the proteolytic processing of AgrD and may have both proteolytic enzyme activity and a transporter facilitating the export of the processed AgrD peptide. 184 matched cddid_all.tbl CDD smart00794 smart00794 129030 AgrD Staphylococcal AgrD protein. This family consists of several AgrD proteins from many Staphylococcus species. The agr locus was initially described in Staphylococcus aureus as an element controlling the production of exoproteins implicated in virulence. Its pattern of action has been shown to be complex, upregulating certain extracellular toxins and enzymes expressed post-exponentially and repressing some exponential-phase surface components. AgrD encodes the precursor of the autoinducing peptide (AIP).The AIP derived from AgrD by the action of AgrB interacts with AgrC in the membrane to activate AgrA, which upregulates transcription both from promoter P2, amplifying the response, and from P3, initiating the production of a novel effector: RNAIII. In S. aureus, delta-hemolysin is the only translation product of RNA III and is not involved in the regulatory functions of the transcript, which is therefore the primary agent for modulating the expression of other operons controlled by agr. 45 matched cddid_all.tbl CDD smart00795 smart00795 129031 Agro_virD5 Agrobacterium VirD5 protein. The virD operon in Agrobacterium encodes a site-specific endonuclease, and a number of other poorly characterised products. This family represents the VirD5 protein. 780 matched cddid_all.tbl CDD smart00796 smart00796 214820 AHS1 Allophanate hydrolase subunit 1. This domain represents subunit 1 of allophanate hydrolase (AHS1). 201 matched cddid_all.tbl CDD smart00797 smart00797 214821 AHS2 Allophanate hydrolase subunit 2. This domain represents subunit 2 of allophanate hydrolase (AHS2). 280 matched cddid_all.tbl CDD smart00798 smart00798 214822 AICARFT_IMPCHas AICARFT/IMPCHase bienzyme. This is a family of bifunctional enzymes catalysing the last two steps in de novo purine biosynthesis. The bifunctional enzyme is found in both prokaryotes and eukaryotes. The second last step is catalysed by 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase (AICARFT), this enzyme catalyses the formylation of AICAR with 10-formyl-tetrahydrofolate to yield FAICAR and tetrahydrofolate. The last step is catalysed by IMP (Inosine monophosphate) cyclohydrolase (IMPCHase), cyclizing FAICAR (5-formylaminoimidazole-4-carboxamide ribonucleotide) to IMP. 311 matched cddid_all.tbl CDD smart00799 smart00799 214823 DENN Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN. The DENN domain is found in a variety of signalling proteins involved in Rab-mediated processes or regulation of MAPKs signalling pathways. The DENN domain is always encircled on both sides by more divergent domains, called uDENN (for upstream DENN) and dDENN (for downstream DENN). The function of the DENN domain remains to date unclear, although it appears to represent a good candidate for a GTP/GDP exchange activity. 183 matched cddid_all.tbl CDD smart00800 smart00800 214824 uDENN Domain always found upstream of DENN domain, found in a variety of signalling proteins. The uDENN domain is part of the tripartite DENN domain. It is always found upstream of the DENN domain itself, which is found in a variety of signalling proteins involved in Rab-mediated processes or regulation of MAPKs signalling pathways. The DENN domain is always encircled on both sides by more divergent domains, called uDENN (for upstream DENN) and dDENN (for downstream DENN). The function of the DENN domain remains to date unclear, although it appears to represent a good candidate for a GTP/GDP exchange activity. 89 matched cddid_all.tbl CDD smart00801 smart00801 129037 dDENN Domain always found downstream of DENN domain, found in a variety of signalling proteins. The dDENN domain is part of the tripartite DENN domain. It is always found downstream of the DENN domain itself, which is found in a variety of signalling proteins involved in Rab-mediated processes or regulation of MAPKs signalling pathways. The DENN domain is always encircled on both sides by more divergent domains, called uDENN (for upstream DENN) and dDENN (for downstream DENN). The function of the DENN domain remains to date unclear, although it appears to represent a good candidate for a GTP/GDP exchange activity. 69 matched cddid_all.tbl CDD smart00802 smart00802 214825 UME Domain in UVSB PI-3 kinase, MEI-41 and ESR-1. Characteristic domain in UVSP PI-3 kinase, MEI-41 and ESR-1. Found in nucleolar proteins. Associated with FAT, FATC, PI3_PI4_kinase modules. 107 matched cddid_all.tbl CDD smart00803 smart00803 129039 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold. 65 matched cddid_all.tbl CDD smart00804 smart00804 197882 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain. 63 matched cddid_all.tbl CDD smart00805 smart00805 197883 AGTRAP Angiotensin II, type I receptor-associated protein. This family consists of several angiotensin II, type I receptor-associated protein (AGTRAP) sequences. AGTRAP is known to interact specifically with the C-terminal cytoplasmic region of the angiotensin II type 1 (AT(1)) receptor to regulate different aspects of AT(1) receptor physiology. The function of this family is unclear. 159 matched cddid_all.tbl CDD smart00806 smart00806 214826 AIP3 Actin interacting protein 3. Aip3p/Bud6p is a regulator of cell and cytoskeletal polarity in Saccharomyces cerevisiae that was previously identified as an actin-interacting protein. Actin-interacting protein 3 (Aip3p) localizes at the cell cortex where cytoskeleton assembly must be achieved to execute polarized cell growth, and deletion of AIP3 causes gross defects in cell and cytoskeletal polarity. Aip3p localization is mediated by the secretory pathway, mutations in early- or late-acting components of the secretory apparatus lead to Aip3p mislocalization. 426 matched cddid_all.tbl CDD smart00807 smart00807 214827 AKAP_110 A-kinase anchor protein 110 kDa. This family consists of several mammalian protein kinase A anchoring protein 3 (PRKA3) or A-kinase anchor protein 110 kDa (AKAP 110) sequences. Agents that increase intracellular cAMP are potent stimulators of sperm motility. Anchoring inhibitor peptides, designed to disrupt the interaction of the cAMP-dependent protein kinase A (PKA) with A kinase-anchoring proteins (AKAPs), are potent inhibitors of sperm motility. PKA anchoring is a key biochemical mechanism controlling motility. AKAP110 shares compartments with both RI and RII isoforms of PKA and may function as a regulator of both motility- and head-associated functions such as capacitation and the acrosome reaction. 851 matched cddid_all.tbl CDD smart00808 smart00808 197885 FABD F-actin binding domain (FABD). FABD is the F-actin binding domain of Bcr-Abl and its cellular counterpart c-Abl. The Bcr-Abl tyrosine kinase causes different forms of leukemia in humans. Depending on its position within the cell, Bcr-Abl differentially affects cellular growth. The FABD forms a compact left-handed four-helix bundle in solution. 126 matched cddid_all.tbl CDD smart00809 smart00809 197886 Alpha_adaptinC2 Adaptin C-terminal domain. Adaptins are components of the adaptor complexes which link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. Gamma-adaptin is a subunit of the golgi adaptor. Alpha adaptin is a heterotetramer that regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This Ig-fold domain is found in alpha, beta and gamma adaptins and consists of a beta-sandwich containing 7 strands in 2 beta-sheets in a greek-key topology.. The adaptor appendage contains an additional N-terminal strand. 104 matched cddid_all.tbl CDD smart00810 smart00810 129046 Alpha-amyl_C2 Alpha-amylase C-terminal beta-sheet domain. This entry represents the beta-sheet domain that is found in several alpha-amylases, usually at the C-terminus. This domain is organised as a five-stranded anti-parallel beta-sheet. 61 matched cddid_all.tbl CDD smart00811 smart00811 214828 Alpha_kinase Alpha-kinase family. This family is a novel family of eukaryotic protein kinase catalytic domains, which have no detectable similarity to conventional kinases. The family contains myosin heavy chain kinases and Elongation Factor-2 kinase and a bifunctional ion channel. This family is known as the alpha-kinase family. The structure of the kinase domain revealed unexpected similarity to eukaryotic protein kinases in the catalytic core as well as to metabolic enzymes with ATP-grasp domains. 198 matched cddid_all.tbl CDD smart00812 smart00812 214829 Alpha_L_fucos Alpha-L-fucosidase. O-Glycosyl hydrolases (EC 3.2.1.-) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Because the fold of proteins is better conserved than their sequences, some of the families can be grouped in 'clans'. Family 29 encompasses alpha-L-fucosidases, which is a lysosomal enzyme responsible for hydrolyzing the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins. Deficiency of alpha-L-fucosidase results in the lysosomal storage disease fucosidosis. 384 matched cddid_all.tbl CDD smart00813 smart00813 214830 Alpha-L-AF_C Alpha-L-arabinofuranosidase C-terminus. This entry represents the C terminus (approximately 200 residues) of bacterial and eukaryotic alpha-L-arabinofuranosidase. This catalyses the hydrolysis of non-reducing terminal alpha-L-arabinofuranosidic linkages in L-arabinose-containing polysaccharides. 189 matched cddid_all.tbl CDD smart00814 smart00814 129050 Alpha_TIF Alpha trans-inducing protein (Alpha-TIF). Alpha-TIF (VP16) from Herpes Simplex virus is an essential tegument protein involved in the transcriptional activation of viral immediate early (IE) promoters (alpha genes) during the lytic phase of viral infection. VP16 associates with cellular transcription factors to enhance transcription rates, including the general transcription factor TFIIB and the transcriptional coactivator PC4. The N-terminal residues of VP16 confer specificity for the IE genes, while the C-terminal residues are responsible for transcriptional activation. Within the C-terminal region are two activation regions that can independently and cooperatively activate transcription. VP16 forms a transcriptional regulatory complex with two cellular proteins, the POU-domain transcription factor Oct-1 and the cell-proliferation factor HCF-1. VP16 is an alpha/beta protein with an unusual fold. Other transcription factors may have a similar topology. 356 matched cddid_all.tbl CDD smart00815 smart00815 214831 AMA-1 Apical membrane antigen 1. Apical membrane antigen 1 (AMA-1) is a Plasmodium asexual blood-stage antigen. It has been suggested that positive selection operates on the AMA-1 gene in regions coding for antigenic sites. 239 matched cddid_all.tbl CDD smart00816 smart00816 129052 Amb_V_allergen Amb V Allergen. Amb V is an Ambrosia sp (ragweed) pollen allergen. Amb t V has been shown to contain a C-terminal helix as the major T cell epitope. Free sulphhydryl groups also play a major role in the T cell recognition of cross-reactivity T cell epitopes within these related allergens. 45 matched cddid_all.tbl CDD smart00817 smart00817 214832 Amelin Ameloblastin precursor (Amelin). This family consists of several mammalian Ameloblastin precursor (Amelin) proteins. Matrix proteins of tooth enamel consist mainly of amelogenin but also of non-amelogenin proteins, which, although their volumetric percentage is low, have an important role in enamel mineralisation. One of the non-amelogenin proteins is ameloblastin, also known as amelin and sheathlin. Ameloblastin (AMBN) is one of the enamel sheath proteins which is though to have a role in determining the prismatic structure of growing enamel crystals. 411 matched cddid_all.tbl CDD smart00818 smart00818 197891 Amelogenin "Amelogenins, cell adhesion proteins, play a role in the biomineralisation of teeth. They seem to regulate formation of crystallites during the secretory stage of tooth enamel development and are thought to play a major role in the structural organisation and mineralisation of developing enamel. The extracellular matrix of the developing enamel comprises two major classes of protein: the hydrophobic amelogenins and the acidic enamelins. Circular dichroism studies of porcine amelogenin have shown that the protein consists of 3 discrete folding units: the N-terminal region appears to contain beta-strand structures, while the C-terminal region displays characteristics of a random coil conformation. Subsequent studies on the bovine protein have indicated the amelogenin structure to contain a repetitive beta-turn segment and a ""beta-spiral"" between Gln112 and Leu138, which sequester a (Pro, Leu, Gln) rich region. The beta-spiral offers a probable site for interactions with Ca2+ ions. Muatations in the human amelogenin gene (AMGX) cause X-linked hypoplastic amelogenesis imperfecta, a disease characterised by defective enamel. A 9bp deletion in exon 2 of AMGX results in the loss of codons for Ile5, Leu6, Phe7 and Ala8, and replacement by a new threonine codon, disrupting the 16-residue (Met1-Ala16) amelogenin signal peptide." 165 matched cddid_all.tbl CDD smart00822 smart00822 214833 PKS_KR This enzymatic domain is part of bacterial polyketide synthases. It catalyses the first step in the reductive modification of the beta-carbonyl centres in the growing polyketide chain. It uses NADPH to reduce the keto group to a hydroxy group. 180 matched cddid_all.tbl CDD smart00823 smart00823 214834 PKS_PP Phosphopantetheine attachment site. Phosphopantetheine (or pantetheine 4' phosphate) is the prosthetic group of acyl carrier proteins (ACP) in some multienzyme complexes where it serves as a 'swinging arm' for the attachment of activated fatty acid and amino-acid groups. 86 matched cddid_all.tbl CDD smart00824 smart00824 214835 PKS_TE Thioesterase. Peptide synthetases are involved in the non-ribosomal synthesis of peptide antibiotics. Next to the operons encoding these enzymes, in almost all cases, are genes that encode proteins that have similarity to the type II fatty acid thioesterases of vertebrates. There are also modules within the peptide synthetases that also share this similarity. With respect to antibiotic production, thioesterases are required for the addition of the last amino acid to the peptide antibiotic, thereby forming a cyclic antibiotic. Thioesterases (non-integrated) have molecular masses of 25-29 kDa. 212 matched cddid_all.tbl CDD smart00825 smart00825 214836 PKS_KS Beta-ketoacyl synthase. The structure of beta-ketoacyl synthase is similar to that of the thiolase family and also chalcone synthase. The active site of beta-ketoacyl synthase is located between the N and C-terminal domains. 298 matched cddid_all.tbl CDD smart00826 smart00826 214837 PKS_DH Dehydratase domain in polyketide synthase (PKS) enzymes. 167 matched cddid_all.tbl CDD smart00827 smart00827 214838 PKS_AT Acyl transferase domain in polyketide synthase (PKS) enzymes. 298 matched cddid_all.tbl CDD smart00828 smart00828 214839 PKS_MT Methyltransferase in polyketide synthase (PKS) enzymes. 224 matched cddid_all.tbl CDD smart00829 smart00829 214840 PKS_ER Enoylreductase. Enoylreductase in Polyketide synthases. 287 matched cddid_all.tbl CDD smart00830 smart00830 214841 CM_2 Chorismate mutase type II. Chorismate mutase, catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine.. 79 matched cddid_all.tbl CDD smart00831 smart00831 214842 Cation_ATPase_N Cation transporter/ATPase, N-terminus. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+, Na+, Ca2+, Na+/K+, and H+/K+. In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases. 75 matched cddid_all.tbl CDD smart00832 smart00832 214843 C8 This domain contains 8 conserved cysteine residues. Not all of the conserved cysteines have been included in the alignment model. It is found in disease-related proteins including von Willebrand factor, Alpha tectorin, Zonadhesin and Mucin. 76 matched cddid_all.tbl CDD smart00833 smart00833 214844 CobW_C Cobalamin synthesis protein cobW C-terminal domain. CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis. They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids. This entry represents the C-terminal domain found in CobW, as well as in P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression. 92 matched cddid_all.tbl CDD smart00834 smart00834 197903 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence. 41 matched cddid_all.tbl CDD smart00835 smart00835 214845 Cupin_1 Cupin. This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant. 146 matched cddid_all.tbl CDD smart00836 smart00836 214846 DALR_1 DALR anticodon binding domain. This all alpha helical domain is the anticodon binding domain of Arginyl tRNA synthetase. This domain is known as the DALR domain after characteristic conserved amino acids. 122 matched cddid_all.tbl CDD smart00837 smart00837 129070 DPBB_1 Rare lipoprotein A (RlpA)-like double-psi beta-barrel. Rare lipoprotein A (RlpA) contains a conserved region that has the double-psi beta-barrel (DPBB) fold. The function of RlpA is not well understood, but it has been shown to act as a prc mutant suppressor in Escherichia coli. The DPBB fold is often an enzymatic domain. The members of this family are quite diverse, and if catalytic this family may contain several different functions. Another example of this domain is found in the N terminus of pollen allergen. 87 matched cddid_all.tbl CDD smart00838 smart00838 197906 EFG_C Elongation factor G C-terminus. This domain includes the carboxyl terminal regions of Elongation factor G, elongation factor 2 and some tetracycline resistance proteins and adopt a ferredoxin-like fold. 85 matched cddid_all.tbl CDD smart00839 smart00839 214847 ELFV_dehydrog Glutamate/Leucine/Phenylalanine/Valine dehydrogenase. Glutamate, leucine, phenylalanine and valine dehydrogenases are structurally and functionally related. They contain a Gly-rich region containing a conserved Lys residue, which has been implicated in the catalytic activity, in each case a reversible oxidative deamination reaction. 102 matched cddid_all.tbl CDD smart00840 smart00840 214848 DALR_2 This DALR domain is found in cysteinyl-tRNA-synthetases. 56 matched cddid_all.tbl CDD smart00841 smart00841 214849 Elong-fact-P_C Elongation factor P, C-terminal. These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology. 57 matched cddid_all.tbl CDD smart00842 smart00842 214850 FtsA Cell division protein FtsA. FtsA is essential for bacterial cell division, and co-localizes to the septal ring with FtsZ. It has been suggested that the interaction of FtsA-FtsZ has arisen through coevolution in different bacterial strains. 187 matched cddid_all.tbl CDD smart00843 smart00843 197911 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding. 63 matched cddid_all.tbl CDD smart00844 smart00844 197912 GA GA module. The protein G-related albumin-binding (GA) module is composed of three alpha helices. This module is found in a range of bacterial cell surface proteins. The GA module from the Peptostreptococcus magnus albumin-binding protein (PAB) shows a strong affinity for albumin. 60 matched cddid_all.tbl CDD smart00845 smart00845 197913 GatB_Yqey GatB domain. This domain is found in GatB and proteins related to bacterial Yqey. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB which transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain. It does however suggest that Yqey and its relatives have a role in tRNA metabolism. 147 matched cddid_all.tbl CDD smart00846 smart00846 214851 Gp_dh_N Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain. GAPDH is a tetrameric NAD-binding enzyme involved in glycolysis and glyconeogenesis. N-terminal domain is a Rossmann NAD(P) binding fold. 149 matched cddid_all.tbl CDD smart00847 smart00847 214852 HA2 Helicase associated domain (HA2) Add an annotation. This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding. 82 matched cddid_all.tbl CDD smart00848 smart00848 214853 Inhibitor_I29 Cathepsin propeptide inhibitor domain (I29). This domain is found at the N-terminus of some C1 peptidases such as Cathepsin L where it acts as a propeptide. There are also a number of proteins that are composed solely of multiple copies of this domain such as the peptidase inhibitor salarin. This family is classified as I29 by MEROPS. Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. 57 matched cddid_all.tbl CDD smart00849 smart00849 214854 Lactamase_B Metallo-beta-lactamase superfamily. Apart from the beta-lactamases a number of other proteins contain this domain. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake. Except for the competence protein these proteins bind two zinc ions per molecule as cofactor. 177 matched cddid_all.tbl CDD smart00850 smart00850 197918 LytTR LytTr DNA-binding domain. This domain is found in a variety of bacterial transcriptional regulators. The domain binds to a specific DNA sequence pattern. 96 matched cddid_all.tbl CDD smart00851 smart00851 214855 MGS MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes inosicase. The known structures in this family show a common phosphate binding site. 91 matched cddid_all.tbl CDD smart00852 smart00852 214856 MoCF_biosynth Probable molybdopterin binding domain. This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor. The domain is presumed to bind molybdopterin. The structure of this domain is known, and it forms an alpha/beta structure. In the known structure of Gephyrin this domain mediates trimerisation. 138 matched cddid_all.tbl CDD smart00853 smart00853 214857 MutL_C MutL C terminal dimerisation domain. MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation. 140 matched cddid_all.tbl CDD smart00854 smart00854 214858 PGA_cap Bacterial capsule synthesis protein PGA_cap. This protein is a putative poly-gamma-glutamate capsule biosynthesis protein found in bacteria. Poly-gamma-glutamate is a natural polymer that may be involved in virulence and may help bacteria survive in high salt concentrations. It is a surface-associated protein. 239 matched cddid_all.tbl CDD smart00855 smart00855 214859 PGAM Phosphoglycerate mutase family. Phosphoglycerate mutase (PGAM) and bisphosphoglycerate mutase (BPGM) are structurally related enzymes that catalyse reactions involving the transfer of phospho groups between the three carbon atoms of phosphoglycerate... Both enzymes can catalyse three different reactions with different specificities, the isomerization of 2-phosphoglycerate (2-PGA) to 3-phosphoglycerate (3-PGA) with 2,3-diphosphoglycerate (2,3-DPG) as the primer of the reaction, the synthesis of 2,3-DPG from 1,3-DPG with 3-PGA as a primer and the degradation of 2,3-DPG to 3-PGA (phosphatase activity). In mammals, PGAM is a dimeric protein with two isoforms, the M (muscle) and B (brain) forms. In yeast, PGAM is a tetrameric protein. 158 matched cddid_all.tbl CDD smart00856 smart00856 214860 PMEI Plant invertase/pectin methylesterase inhibitor. This domain inhibits pectin methylesterases (PMEs) and invertases through formation of a non-covalent 1:1 complex. It has been implicated in the regulation of fruit development, carbohydrate metabolism and cell wall extension. It may also be involved in inhibiting microbial pathogen PMEs. It has been observed that it is often expressed as a large inactive preprotein. It is also found at the N-termini of PMEs predicted from DNA sequences, suggesting that both PMEs and their inhibitors are expressed as a single polyprotein and subsequently processed. It has two disulphide bridges and is mainly alpha-helical. 148 matched cddid_all.tbl CDD smart00857 smart00857 214861 Resolvase Resolvase, N terminal domain. The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase. 148 matched cddid_all.tbl CDD smart00858 smart00858 214862 SAF This domain family includes a range of different proteins. Such as antifreeze proteins and flagellar FlgA proteins, and CpaB pilus proteins. 63 matched cddid_all.tbl CDD smart00859 smart00859 214863 Semialdhyde_dh Semialdehyde dehydrogenase, NAD binding domain. The semialdehyde dehydrogenase family is found in N-acetyl-glutamine semialdehyde dehydrogenase (AgrC), which is involved in arginine biosynthesis, and aspartate-semialdehyde dehydrogenase, an enzyme involved in the biosynthesis of various amino acids from aspartate. This family is also found in yeast and fungal Arg5,6 protein, which is cleaved into the enzymes N-acety-gamma-glutamyl-phosphate reductase and acetylglutamate kinase. These are also involved in arginine biosynthesis. All proteins in this entry contain a NAD binding region of semialdehyde dehydrogenase. 123 matched cddid_all.tbl CDD smart00860 smart00860 214864 SMI1_KNR4 SMI1 / KNR4 family. Proteins in this family are involved in the regulation of 1,3-beta-glucan synthase activity and cell-wall formation. 127 matched cddid_all.tbl CDD smart00861 smart00861 214865 Transket_pyr Transketolase, pyrimidine binding domain. Transketolase (TK) catalyzes the reversible transfer of a two-carbon ketol unit from xylulose 5-phosphate to an aldose receptor, such as ribose 5-phosphate, to form sedoheptulose 7-phosphate and glyceraldehyde 3- phosphate. This enzyme, together with transaldolase, provides a link between the glycolytic and pentose-phosphate pathways. TK requires thiamine pyrophosphate as a cofactor. In most sources where TK has been purified, it is a homodimer of approximately 70 Kd subunits. TK sequences from a variety of eukaryotic and prokaryotic sources show that the enzyme has been evolutionarily conserved. In the peroxisomes of methylotrophic yeast Hansenula polymorpha, there is a highly related enzyme, dihydroxy-acetone synthase (DHAS) (also known as formaldehyde transketolase), which exhibits a very unusual specificity by including formaldehyde amongst its substrates. 136 matched cddid_all.tbl CDD smart00862 smart00862 214866 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding. 76 matched cddid_all.tbl CDD smart00863 smart00863 197931 tRNA_SAD Threonyl and Alanyl tRNA synthetase second additional domain. The catalytically active form of threonyl/alanyl tRNA synthetase is a dimer. Within the tRNA synthetase class II dimer, the bound tRNA interacts with both monomers making specific interactions with the catalytic domain, the C-terminal domain, and this SAD domain (the second additional domain). The second additional domain is comprised of a pair of perpendicularly orientated antiparallel beta sheets, of four and three strands, respectively, that surround a central alpha helix that forms the core of the domain. 43 matched cddid_all.tbl CDD smart00864 smart00864 214867 Tubulin Tubulin/FtsZ family, GTPase domain. This domain is found in all tubulin chains, as well as the bacterial FtsZ family of proteins. These proteins are involved in polymer formation. Tubulin is the major component of microtubules, while FtsZ is the polymer-forming protein of bacterial cell division, it is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ and tubulin are GTPases, this entry is the GTPase domain. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in bacteria and archaea. 192 matched cddid_all.tbl CDD smart00865 smart00865 214868 Tubulin_C Tubulin/FtsZ family, C-terminal domain. This domain is found in the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. These proteins are GTPases and are involved in polymer formation. Tubulin is the major component of microtubules, while FtsZ is the polymer-forming protein of bacterial cell division, it is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in bacteria and archaea. This is the C-terminal domain. 120 matched cddid_all.tbl CDD smart00866 smart00866 214869 UTRA The UbiC transcription regulator-associated (UTRA) domain is a conserved ligand-binding domain. It has a similar fold to HutC/FarR-like bacterial transcription factors of the GntR family. It is believed to modulate activity of bacterial transcription factors in response to binding small molecules. 143 matched cddid_all.tbl CDD smart00867 smart00867 214870 YceI YceI-like domain. E. coli YceI is a base-induced periplasmic protein. The recent structure of a member of this family shows that it binds to polyisoprenoid. The structure consists of an extended, eight-stranded, antiparallel beta-barrel that resembles the lipocalin fold. 166 matched cddid_all.tbl CDD smart00868 smart00868 214871 zf-AD Zinc-finger associated domain (zf-AD). The zf-AD domain, also known as ZAD, forms an atypical treble-cleft-like zinc co-ordinating fold. The zf-AD domain is thought to be involved in mediating dimer formation, but does not bind to DNA. 73 matched cddid_all.tbl CDD smart00869 smart00869 214872 Autotransporter Autotransporter beta-domain. Secretion of protein products occurs by a number of different pathways in bacteria. One of these pathways known as the type IV pathway was first described for the IgA1 protease. The protein component that mediates secretion through the outer membrane is contained within the secreted protein itself, hence the proteins secreted in this way are called autotransporters. This family corresponds to the presumed integral membrane beta-barrel domain that transports the protein. This domain is found at the C-terminus of the proteins it occurs in. The N-terminus contains the variable passenger domain that is translocated across the membrane. Once the passenger domain is exported it is cleaved auto-catalytically in some proteins, in others a different peptidase is used and in some cases no cleavage occurs. 268 matched cddid_all.tbl CDD smart00870 smart00870 214873 Asparaginase Asparaginase, found in various plant, animal and bacterial cells. Asparaginase catalyses the deamination of asparagine to yield aspartic acid and an ammonium ion, resulting in a depletion of free circulatory asparagine in plasma. The enzyme is effective in the treatment of human malignant lymphomas, which have a diminished capacity to produce asparagine synthetase: in order to survive, such cells absorb asparagine from blood plasma..- if Asn levels have been depleted by injection of asparaginase, the lymphoma cells die. 323 matched cddid_all.tbl CDD smart00871 smart00871 214874 AraC_E_bind Bacterial transcription activator, effector binding domain. This domain is found in the probable effector binding domain of a number of different bacterial transcription activators.and is also present in some DNA gyrase inhibitors. The absence of a HTH motif in the DNA gyrase inhibitors is thought to indicate the fact that these do not bind DNA. 158 matched cddid_all.tbl CDD smart00872 smart00872 214875 Alpha-mann_mid Alpha mannosidase, middle domain. Members of this entry belong to the glycosyl hydrolase family 38, This domain, which is found in the central region adopts a structure consisting of three alpha helices, in an immunoglobulin/albumin-binding domain-like fold. The domain is predominantly found in the enzyme alpha-mannosidase. 79 matched cddid_all.tbl CDD smart00873 smart00873 214876 B3_4 B3/4 domain. This domain is found in tRNA synthetase beta subunits as well as in some non tRNA synthetase proteins. 174 matched cddid_all.tbl CDD smart00874 smart00874 197942 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits. 68 matched cddid_all.tbl CDD smart00875 smart00875 197943 BACK BTB And C-terminal Kelch. The BACK domain is found juxtaposed to the BTB domain; they are separated by as little as two residues. 101 matched cddid_all.tbl CDD smart00876 smart00876 214877 BATS Biotin and Thiamin Synthesis associated domain. Biotin synthase (BioB), , catalyses the last step of the biotin biosynthetic pathway. The reaction consists in the introduction of a sulphur atom into dethiobiotin. BioB functions as a homodimer. Thiamin synthesis if a complex process involving at least six gene products (ThiFSGH, ThiI and ThiJ). Two of the proteins required for the biosynthesis of the thiazole moiety of thiamine (vitamin B(1)) are ThiG and ThiH (this entry) and form a heterodimer. Both of these reactions are thought of involve the binding of co-factors, and both function as dimers.. This domain therefore may be involved in co-factor binding or dimerisation. 94 matched cddid_all.tbl CDD smart00877 smart00877 197945 BMC Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure. 75 matched cddid_all.tbl CDD smart00878 smart00878 214878 Biotin_carb_C Biotin carboxylase C-terminal domain. Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyses the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference are in this C-terminal domain. 107 matched cddid_all.tbl CDD smart00879 smart00879 214879 Brix The Brix domain is found in a number of eukaryotic proteins. Members include SSF proteins from yeast and humans, Arabidopsis thaliana Peter Pan-like protein and several hypothetical proteins. 180 matched cddid_all.tbl CDD smart00880 smart00880 214880 CHAD The CHAD domain is an alpha-helical domain functionally associated with some members of the adenylate cyclase family. It has conserved histidines that may chelate metals. 262 matched cddid_all.tbl CDD smart00881 smart00881 214881 CoA_binding CoA binding domain. This domain has a Rossmann fold and is found in a number of proteins including succinyl CoA synthetases, malate and ATP-citrate ligases. 100 matched cddid_all.tbl CDD smart00882 smart00882 214882 CoA_trans Coenzyme A transferase. Coenzyme A (CoA) transferases belong to an evolutionary conserved family of enzymes catalyzing the reversible transfer of CoA from one carboxylic acid to another. They have been identified in many prokaryotes and in mammalian tissues. The bacterial enzymes are heterodimer of two subunits (A and B) of about 25 Kd each while eukaryotic SCOT consist of a single chain which is colinear with the two bacterial subunits. 212 matched cddid_all.tbl CDD smart00883 smart00883 197951 Cpn10 Chaperonin 10 Kd subunit. The chaperonins are 'helper' molecules required for correct folding and subsequent assembly of some proteins. These are required for normal cell growth, and are stress-induced, acting to stabilise or protect disassembled polypeptides under heat-shock conditions. Type I chaperonins present in eubacteria, mitochondria and chloroplasts require the concerted action of 2 proteins, chaperonin 60 (cpn60) and chaperonin 10 (cpn10). The 10 kDa chaperonin (cpn10 - or groES in bacteria) exists as a ring-shaped oligomer of between six to eight identical subunits, while the 60 kDa chaperonin (cpn60 - or groEL in bacteria) forms a structure comprising 2 stacked rings, each ring containing 7 identical subunits. These ring structures assemble by self-stimulation in the presence of Mg2+-ATP. The central cavity of the cylindrical cpn60 tetradecamer provides as isolated environment for protein folding whilst cpn-10 binds to cpn-60 and synchronizes the release of the folded protein in an Mg2+-ATP dependent manner. The binding of cpn10 to cpn60 inhibits the weak ATPase activity of cpn60. 93 matched cddid_all.tbl CDD smart00884 smart00884 214883 Cullin_Nedd8 Cullin protein neddylation domain. This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae, and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue. 68 matched cddid_all.tbl CDD smart00885 smart00885 197953 D5_N D5 N terminal like. This domain is found in D5 proteins of DNA viruses and bacteriophage P4 DNA primases phages. 141 matched cddid_all.tbl CDD smart00886 smart00886 214884 Dabb Stress responsive A/B Barrel Domain. The function of this domain is unknown, but it is upregulated in response to salt stress in Populus balsamifera (balsam poplar). It is also found at the C-terminus of a fructose 1,6-bisphosphate aldolase from Hydrogenophilus thermoluteolus.It is found in the pA01 plasmid, which encodes genes for molybdopterin uptake and degradation of plant alkaloid nicotine. The structure of one has been solved and the domain forms an alpha-beta barrel dimer. Although there is a clear duplication within the domain it is not obviously detectable in the sequence. 97 matched cddid_all.tbl CDD smart00887 smart00887 214885 EB_dh Ethylbenzene dehydrogenase. Eythylbenzene dehydrogenase is a heterotrimer of three subunits that catalyses the anaerobic degradation of hydrocarbons. The alpha subunit contains the catalytic centre as a Molybdenum cofactor-complex. This removes an electron-pair from the hydrocarbon and passes it along an electron transport system involving iron-sulphur complexes held in the beta subunit and a Haem b molecule contained in the gamma subunit. The electron-pair is then subsequently passed to an as yet unknown receiver. The enzyme is found in a variety of different bacteria. 209 matched cddid_all.tbl CDD smart00888 smart00888 214886 EF1_GNE EF-1 guanine nucleotide exchange domain. Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta). This entry represents the guanine nucleotide exchange domain of the beta (EF-1beta, also known as EF1B-alpha) and delta (EF-1delta, also known as EF1B-beta) chains of EF1B proteins from eukaryotes and archaea. The beta and delta chains have exchange activity, which mainly resides in their homologous guanine nucleotide exchange domains, found in the C-terminal region of the peptides. Their N-terminal regions may be involved in interactions with the gamma chain (EF-1gamma). 88 matched cddid_all.tbl CDD smart00889 smart00889 214887 EFG_IV Elongation factor G, domain IV. Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF2 (EF-G) is a G-protein. It brings about the translocation of peptidyl-tRNA and mRNA through a ratchet-like mechanism: the binding of GTP-EF2 to the ribosome causes a counter-clockwise rotation in the small ribosomal subunit; the hydrolysis of GTP to GDP by EF2 and the subsequent release of EF2 causes a clockwise rotation of the small subunit back to the starting position. This twisting action destabilises tRNA-ribosome interactions, freeing the tRNA to translocate along the ribosome upon GTP-hydrolysis by EF2. EF2 binding also affects the entry and exit channel openings for the mRNA, widening it when bound to enable the mRNA to translocate along the ribosome. EF2 has five domains. This entry represents domain IV found in EF2 (or EF-G) of both prokaryotes and eukaryotes. The EF2-GTP-ribosome complex undergoes extensive structural rearrangement for tRNA-mRNA movement to occur. Domain IV, which extends from the 'body' of the EF2 molecule much like a lever arm, appears to be essential for the structural transition to take place. 120 matched cddid_all.tbl CDD smart00890 smart00890 197958 EKR Domain of unknown function. EKR is a short, 33 residue, domain found in bacterial and some lower eukaryotic species which lies between a POR (pyruvate ferredoxin/flavodoxin oxidoreductase) and the 4Fe-4S binding domain Fer4. It contains a characteristic EKR sequence motif. The exact function of this domain is not known. 57 matched cddid_all.tbl CDD smart00891 smart00891 214888 ERCC4 ERCC4 domain. This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases, and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases. 98 matched cddid_all.tbl CDD smart00892 smart00892 214889 Endonuclease_NS DNA/RNA non-specific endonuclease. A family of bacterial and eukaryotic endonucleases share the following characteristics: they act on both DNA and RNA, cleave double-stranded and single-stranded nucleic acids and require a divalent ion such as magnesium for their activity. An histidine has been shown to be essential for the activity of the Serratia marcescens nuclease. This residue is located in a conserved region which also contains an aspartic acid residue that could be implicated in the binding of the divalent ion. 198 matched cddid_all.tbl CDD smart00893 smart00893 214890 ETF "Electron transfer flavoprotein domain. Electron transfer flavoproteins (ETFs) serve as specific electron acceptors for primary dehydrogenases, transferring the electrons to terminal respiratory systems. They can be functionally classified into constitutive, ""housekeeping"" ETFs, mainly involved in the oxidation of fatty acids (Group I), and ETFs produced by some prokaryotes under specific growth conditions, receiving electrons only from the oxidation of specific substrates (Group II). ETFs are heterodimeric proteins composed of an alpha and beta subunit, and contain an FAD cofactor and AMP. ETF consists of three domains: domains I and II are formed by the N- and C-terminal portions of the alpha subunit, respectively, while domain III is formed by the beta subunit. Domains I and III share an almost identical alpha-beta-alpha sandwich fold, while domain II forms an alpha-beta-alpha sandwich similar to that of bacterial flavodoxins. FAD is bound in a cleft between domains II and III, while domain III binds the AMP molecule. Interactions between domains I and III stabilise the protein, forming a shallow bowl where domain II resides. This entry represents the N-terminal domain of both the alpha and beta subunits from Group I and Group II ETFs." 185 matched cddid_all.tbl CDD smart00894 smart00894 214891 Excalibur Excalibur calcium-binding domain. Extracellular Ca2+-dependent nuclease YokF from Bacillus subtilis and several other surface-exposed proteins from diverse bacteria are encoded in the genomes in two paralogous forms that differ by a ~45 amino acid fragment, which comprises a novel conserved domain. Sequence analysis of this domain revealed a conserved DxDxDGxxCE motif, which is strikingly similar to the Ca2+-binding loop of the calmodulin-like EF-hand domains, suggesting an evolutionary relationship between them. Functions of many of the other proteins in which the novel domain, named Excalibur (extracellular calcium-binding region), is found, as well as a structural model of its conserved motif are consistent with the notion that the Excalibur domain binds calcium. This domain is but one more example of the diversity of structural contexts surrounding the EF-hand-like calcium-binding loop in bacteria. This loop is thus more widespread than hitherto recognised and the evolution of EF-hand-like domains is probably more complex than previously appreciated. 37 matched cddid_all.tbl CDD smart00895 smart00895 214892 FCD This entry represents the C-terminal ligand binding domain of many members of the GntR family. This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in and that are regulators of sugar biosynthesis operons. Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family, and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR, HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA. 123 matched cddid_all.tbl CDD smart00896 smart00896 214893 FDX-ACB Ferredoxin-fold anticodon binding domain. This is the anticodon binding domain found in some phenylalanyl tRNA synthetases. The domain has a ferredoxin fold, consisting of an alpha+beta sandwich with anti-parallel beta-sheets (beta-alpha-beta x2). 93 matched cddid_all.tbl CDD smart00897 smart00897 214894 FIST FIST N domain. The FIST N domain is a novel sensory domain, which is present in signal transduction proteins from Bacteria, Archaea and Eukarya. Chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids. 196 matched cddid_all.tbl CDD smart00898 smart00898 214895 Fapy_DNA_glyco Formamidopyrimidine-DNA glycosylase N-terminal domain. This entry represents the catalytic domain of DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway. These enzymes are primarily from bacteria, and have both DNA glycosylase activity and AP lyase activity. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; ) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; ). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes. Fpg binds one ion of zinc at the C-terminus, which contains four conserved and essential cysteines.. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine. These protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger (see PDB:1K82). The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a beta-hairpin loop formed by the zinc finger. 115 matched cddid_all.tbl CDD smart00899 smart00899 214896 FeoA This entry represents the core domain of the ferrous iron (Fe2+) transport protein FeoA found in bacteria. This domain also occurs at the C-terminus in related proteins. The transporter Feo is composed of three proteins: FeoA a small, soluble SH3-domain protein probably located in the cytosol; FeoB, a large protein with a cytosolic N-terminal G-protein domain and a C-terminal integral inner-membrane domain containing two 'Gate' motifs which likely functions as the Fe2+ permease; and FeoC, a small protein apparently functioning as an [Fe-S]-dependent transcriptional repressor. Feo allows the bacterial cell to acquire iron from its environment. 72 matched cddid_all.tbl CDD smart00900 smart00900 214897 FMN_bind This conserved region includes the FMN-binding site of the NqrC protein as well as the NosR and NirI regulatory proteins. 86 matched cddid_all.tbl CDD smart00901 smart00901 214898 FRG This domain contains a conserved N-terminal (F/Y)RG motif. It is functionally uncharacterised. 103 matched cddid_all.tbl CDD smart00902 smart00902 214899 Fe_hyd_SSU Iron hydrogenase small subunit. Many microorganisms, such as methanogenic, acetogenic, nitrogen-fixing, photosynthetic, or sulphate-reducing bacteria, metabolise hydrogen. Hydrogen activation is mediated by a family of enzymes, termed hydrogenases, which either provide these organisms with reducing power from hydrogen oxidation, or act as electron sinks. There are two hydrogenases families that differ functionally from each other: NiFe hydrogenases tend to be more involved in hydrogen oxidation, while Iron-only FeFe (Fe only) hydrogenases in hydrogen production. Fe only hydrogenases show a common core structure, which contains a moiety, deeply buried inside the protein, with an Fe-Fe dinuclear centre, nonproteic bridging, terminal CO and CN- ligands attached to each of the iron atoms, and a dithio moiety, which also bridges the two iron atoms and has been tentatively assigned as a di(thiomethyl)amine. This common core also harbours three [4Fe-4S] iron-sulphur clusters. In FeFe hydrogenases, as in NiFe hydrogenases, the set of iron-sulphur clusters is dispersed regularly between the dinuclear Fe-Fe centre and the molecular surface. These clusters are distant by about 1.2 nm from each other but the [4Fe-4S] cluster closest to the dinuclear centre is covalently bound to one of the iron atoms though a thiolate bridging ligand. The moiety including the dinuclear centre, the thiolate bridging ligand, and the proximal [4Fe-4S] cluster is known as the H-cluster. A channel, lined with hydrophobic amino acid side chains, nearly connects the dinuclear centre and the molecular surface. Furthermore hydrogen-bonded water molecule sites have been identified at the interior and at the surface of the protein. The small subunit is comprised of alternating random coil and alpha helical structures that encompass the large subunit in a novel protein fold. 52 matched cddid_all.tbl CDD smart00903 smart00903 214900 Flavin_Reduct Flavin reductase like domain. This entry represents the FMN-binding domain found in NAD(P)H-flavin oxidoreductases (flavin reductases), a class of enzymes capable of producing reduced flavin for bacterial bioluminescence and other biological processes. This domain is also found in various other oxidoreductase and monooxygenase enzymes... This domain consists of a beta-barrel with Greek key topology, and is related to the ferredoxin reductase-like FAD-binding domain. The flavin reductases have a different dimerisation mode than that found in the PNP oxidase-like family, which also carries an FMN-binding domain with a similar topology. 147 matched cddid_all.tbl CDD smart00904 smart00904 214901 Flavokinase Riboflavin kinase. Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase, which converts it into FMN, and FAD synthetase, which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme. the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases. This entry represents riboflavin kinase, which occurs as part of a bifunctional enzyme or a stand-alone enzyme. 124 matched cddid_all.tbl CDD smart00905 smart00905 214902 FolB Dihydroneopterin aldolase. Dihydroneopterin aldolase catalyses the conversion of 7,8-dihydroneopterin to 6-hydroxymethyl-7,8-dihydropterin in the biosynthetic pathway of tetrahydrofolate. In the opportunistic pathogen Pneumocystis carinii, dihydroneopterin aldolase function is expressed as the N-terminal portion of the multifunctional folic acid synthesis protein (Fas). This region encompasses two domains, FasA and FasB, which are 27% amino acid identical. FasA and FasB also share significant amino acid sequence similarity with bacterial dihydroneopterin aldolases. This region consists of two tandem sequences each homologous to folB and which form tetramers. 113 matched cddid_all.tbl CDD smart00906 smart00906 214903 Fungal_trans Fungal specific transcription factor domain. This domain is found in a number of fungal transcription factors including transcriptional activator xlnR, yeast regulatory protein GAL4, and other transcription proteins regulating a variety of cellular and metabolic processes. 93 matched cddid_all.tbl CDD smart00907 smart00907 197975 GDNF GDNF/GAS1 domain. This cysteine rich domain is found in multiple copies in GNDF and GAS1 proteins. GDNF and neurturin (NTN) receptors are potent survival factors for sympathetic, sensory and central nervous system neurons.. GDNF and neurturin promote neuronal survival by signaling through similar multicomponent receptors that consist of a common receptor tyrosine kinase and a member of a GPI-linked family of receptors that determines ligand specificity. 86 matched cddid_all.tbl CDD smart00908 smart00908 214904 Gal-bind_lectin Galactoside-binding lectin. Animal lectins display a wide variety of architectures. They are classified according to the carbohydrate-recognition domain (CRD) of which there are two main types, S-type and C-type. Galectins (previously S-lectins) bind exclusively beta-galactosides like lactose. They do not require metal ions for activity. Galectins are found predominantly, but not exclusively in mammals. Their function is unclear. They are developmentally regulated and may be involved in differentiation, cellular regulation and tissue construction. 122 matched cddid_all.tbl CDD smart00909 smart00909 214905 Germane Sporulation and spore germination. The GerMN domain is a region of approximately 100 residues that is found, duplicated, in the Bacillus GerM protein and is implicated in both sporulation and spore germination. The domain is found in a number of different bacterial species both alone and in association with other domains such as Amidase_3 pfam01520 Gmad1 and Gmad2. It is predicted to have a novel alpha-beta fold. 84 matched cddid_all.tbl CDD smart00910 smart00910 214906 HIRAN The HIRAN protein (HIP116, Rad5p N-terminal) is found in the N-terminal regions of the SWI2/SNF2 proteins typified by HIP116 and Rad5p. HIRAN is found as a standalone protein in several bacteria and prophages, or fused to other catalytic domains, such as a nuclease of the restriction endonuclease fold and TDP1-like DNA phosphoesterases, in the eukaryotes. It has been predicted that this protein functions as a DNA-binding domain that probably recognises features associated with damaged DNA or stalled replication forks. 90 matched cddid_all.tbl CDD smart00911 smart00911 214907 HWE_HK HWE histidine kinase. The HWE domain is found in a subset of two-component system kinases, belonging to the same superfamily as. In. the HWE family was defined by the presence of conserved a H residue and a WXE motifs and was limited to members of the proteobacteria. However, many homologues of this domain are lack the WXE motif. Furthermore, homologues are found in a wide range of Gram-positive and Gram-negative bacteria as well as in several archaea. 84 matched cddid_all.tbl CDD smart00912 smart00912 214908 Haemagg_act haemagglutination activity domain. This domain is suggested to be a carbohydrate- dependent haemagglutination activity site. It is found in a range of haemagglutinins and haemolysins. 119 matched cddid_all.tbl CDD smart00913 smart00913 197981 IBN_N Importin-beta N-terminal domain. Members of the importin-beta (karyopherin-beta) family can bind and transport cargo by themselves, or can form heterodimers with importin-alpha. As part of a heterodimer, importin-beta mediates interactions with the pore complex, while importin-alpha acts as an adaptor protein to bind the nuclear localisation signal (NLS) on the cargo through the classical NLS import of proteins. Importin-beta is a helicoidal molecule constructed from 19 HEAT repeats. Many nuclear pore proteins contain FG sequence repeats that can bind to HEAT repeats within importins.. which is important for importin-beta mediated transport. 67 matched cddid_all.tbl CDD smart00914 smart00914 197982 IDEAL A short protein domain of unknown function. It is found at the C-terminus of proteins in the UPF0302 family. It is named after the sequence of the most conserved region in some members. 37 matched cddid_all.tbl CDD smart00915 smart00915 214909 Jacalin Jacalin-like lectin domain. This entry represents a mannose-binding lectin domain with a beta-prism fold consisting of three 4-stranded beta-sheets, with an internal pseudo 3-fold symmetry. Some lectins in this group stimulate distinct T- and B- cell functions, such as Jacalin, which binds to the T-antigen and acts as an agglutinin. This domain is found in 1 to 6 copies in lectins. The domain is also found in the salt-stress induced protein from rice and an animal prostatic spermine-binding protein. 128 matched cddid_all.tbl CDD smart00916 smart00916 197984 L51_S25_CI-B8 Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain. Proteins containing this domain are located in the mitochondrion and include ribosomal protein L51, and S25. This domain is also found in mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) . It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins. 70 matched cddid_all.tbl CDD smart00917 smart00917 214910 LeuA_dimer LeuA allosteric (dimerisation) domain. This is the C-terminal regulatory (R) domain of alpha-isopropylmalate synthase, which catalyses the first committed step in the leucine biosynthetic pathway. This domain, is an internally duplicated structure with a novel fold. It comprises two similar units that are arranged such that the two -helices pack together in the centre, crossing at an angle of 34 degrees, sandwiched between the two three-stranded, antiparallel beta-sheets. The overall domain is thus constructed as a beta-alpha-beta three-layer sandwich. 131 matched cddid_all.tbl CDD smart00918 smart00918 214911 Lig_chan-Glu_bd Ligated ion channel L-glutamate- and glycine-binding site. This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine. It is found in association with Lig_chan. 62 matched cddid_all.tbl CDD smart00919 smart00919 214912 Malic_M Malic enzyme, NAD binding domain. Malic enzymes (malate oxidoreductases) catalyse the oxidative decarboxylation of malate to form pyruvate. 231 matched cddid_all.tbl CDD smart00920 smart00920 214913 MHC_II_alpha Class II histocompatibility antigen, alpha domain. Class II MHC glycoproteins are expressed on the surface of antigen-presenting cells (APC), including macrophages, dendritic cells and B cells. MHC II proteins present peptide antigens that originate extracellularly from foreign bodies such as bacteria. Proteins from the pathogen are degraded into peptide fragments within the APC, which sequesters these fragments into the endosome so they can bind to MHC class II proteins, before being transported to the cell surface. MHC class II receptors display antigens for recognition by helper T cells (stimulate development of B cell clones) and inflammatory T cells (cause the release of lymphokines that attract other cells to site of infection). 81 matched cddid_all.tbl CDD smart00921 smart00921 197989 MHC_II_beta Class II histocompatibility antigen, beta domain. Class II MHC glycoproteins are expressed on the surface of antigen-presenting cells (APC), including macrophages, dendritic cells and B cells. MHC II proteins present peptide antigens that originate extracellularly from foreign bodies such as bacteria. Proteins from the pathogen are degraded into peptide fragments within the APC, which sequesters these fragments into the endosome so they can bind to MHC class II proteins, before being transported to the cell surface. MHC class II receptors display antigens for recognition by helper T cells (stimulate development of B cell clones) and inflammatory T cells (cause the release of lymphokines that attract other cells to site of infection). 72 matched cddid_all.tbl CDD smart00922 smart00922 214914 MR_MLE Mandelate racemase / muconate lactonizing enzyme, C-terminal domain. Mandelate racemase (MR) and muconate lactonizing enzyme (MLE) are two bacterial enzymes involved in aromatic acid catabolism. They catalyze mechanistically distinct reactions yet they are related at the level of their primary, quaternary (homooctamer) and tertiary structures.. This entry represents the C-terminal region of these proteins. 97 matched cddid_all.tbl CDD smart00923 smart00923 197991 MbtH MbtH-like protein. This domain is found in the MbtH protein as well as at the N-terminus of the antibiotic synthesis protein NIKP1. This domain is about 70 amino acids long and contains 3 fully conserved tryptophan residues. Many of the members of this family are found in known antibiotic synthesis gene clusters. 49 matched cddid_all.tbl CDD smart00924 smart00924 214915 MgtE_N MgtE intracellular N domain. This region is the integral membrane part of the eubacterial MgtE family of magnesium transporters. It is presumed to be an intracellular domain, that may be involved in magnesium binding. 105 matched cddid_all.tbl CDD smart00925 smart00925 214916 MltA MltA specific insert domain. This beta barrel domain is found inserted in the MltA a murein degrading transglycosylase enzyme. This domain may be involved in peptidoglycan binding. 153 matched cddid_all.tbl CDD smart00926 smart00926 197994 Molybdop_Fe4S4 Molybdopterin oxidoreductase Fe4S4 domain. The molybdopterin oxidoreductase Fe4S4 domain is found in a number of reductase/dehydrogenase families, which include the periplasmic nitrate reductase precursor and the formate dehydrogenase alpha chain. 55 matched cddid_all.tbl CDD smart00927 smart00927 214917 MutH DNA mismatch repair enzyme MutH. MutS, MutL and MutH are the three essential proteins for initiation of methyl-directed DNA mismatch repair to correct mistakes made during DNA replication in Escherichia coli. MutH cleaves a newly synthesized and unmethylated daughter strand 5' to the sequence d(GATC) in a hemi-methylated duplex. Activation of MutH requires the recognition of a DNA mismatch by MutS and MutL. 100 matched cddid_all.tbl CDD smart00928 smart00928 197996 NADH_4Fe-4S NADH-ubiquinone oxidoreductase-F iron-sulfur binding region. 46 matched cddid_all.tbl CDD smart00929 smart00929 214918 NADH-G_4Fe-4S_3 NADH-ubiquinone oxidoreductase-G iron-sulfur binding region. 41 matched cddid_all.tbl CDD smart00930 smart00930 197998 NIL This domain is found at the C-terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family. 76 matched cddid_all.tbl CDD smart00931 smart00931 197999 NOSIC NOSIC (NUC001) domain. This is the central domain in Nop56/SIK1-like proteins. 52 matched cddid_all.tbl CDD smart00932 smart00932 214919 Nfu_N Scaffold protein Nfu/NifU N terminal. This domain is found at the N terminus of NifU and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the the assembly of iron-sulphur clusters. 88 matched cddid_all.tbl CDD smart00933 smart00933 214920 NurA NurA nuclease. This family includes NurA a nuclease exhibiting both single-stranded endonuclease activity and 5'-3' exonuclease activity on single-stranded and double-stranded DNA from the hyperthermophilic archaeon Sulfolobus acidocaldarius. 262 matched cddid_all.tbl CDD smart00934 smart00934 214921 OMPdecase Orotidine 5'-phosphate decarboxylase / HUMPS family. Orotidine 5'-phosphate decarboxylase (OMPdecase) catalyzes the last step in the de novo biosynthesis of pyrimidines, the decarboxylation of OMP into UMP. In higher eukaryotes OMPdecase is part, with orotate phosphoribosyltransferase, of a bifunctional enzyme, while the prokaryotic and fungal OMPdecases are monofunctional protein. 212 matched cddid_all.tbl CDD smart00935 smart00935 214922 OmpH Outer membrane protein (OmpH-like). This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterized as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery. 140 matched cddid_all.tbl CDD smart00936 smart00936 198004 PBP5_C Penicillin-binding protein 5, C-terminal domain. Penicillin-binding protein 5 expressed by E. coli functions as a D-alanyl-D-alanine carboxypeptidase. It is composed of two domains that are oriented at approximately right angles to each other. The N-terminal domain (pfam00768) is the catalytic domain. The C-terminal domain featured in this family is organized into a sandwich of two anti-parallel beta-sheets, and has a relatively hydrophobic surface as compared to the N-terminal domain. Its precise function is unknown; it may mediate interactions with other cell wall-synthesising enzymes, thus allowing the protein to be recruited to areas of active cell wall synthesis. It may also function as a linker domain that positions the active site in the catalytic domain closer to the peptidoglycan layer, to allow it to interact with cell wall peptides. 92 matched cddid_all.tbl CDD smart00937 smart00937 214923 PCRF This domain is found in peptide chain release factors. 116 matched cddid_all.tbl CDD smart00938 smart00938 198006 P-II Nitrogen regulatory protein P-II. P-II modulates the activity of glutamine synthetase. 102 matched cddid_all.tbl CDD smart00939 smart00939 214924 PepX_C X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain. This domain is found at the C-terminus of cocaine esterase CocE, several glutaryl-7-ACA acylases, and the putative diester hydrolase NonD of Streptomyces griseus (all hydrolases). The domain, which is a beta sandwich, is also found in serine peptidases belonging to MEROPS peptidase family S15: Xaa-Pro dipeptidyl-peptidases. Members of this entry, that are not characterised as peptidases, show extensive low-level similarity to the Xaa-Pro dipeptidyl-peptidases. 214 matched cddid_all.tbl CDD smart00940 smart00940 198008 PepX_N X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal. This N-terminal domain adopts a secondary structure consisting of a helical bundle of eight alpha helices and three beta strands, with the last alpha helix connecting to the first strand of the catalytic domain. The first strand of the N-terminus also forms a small parallel beta sheet with strand five of the catalytic domain. This domain mediates dimerisation of the protein, with two proline residues present in the domain being critical for interaction. 156 matched cddid_all.tbl CDD smart00941 smart00941 214925 PYNP_C Pyrimidine nucleoside phosphorylase C-terminal domain. This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP) there is an added three-stranded anti-parallel beta sheet as compared to other members of the family, such as E. coli thymidine phosphorylase (TP). The domain contains an alpha/ beta hammerhead fold and residues in this domain seem to be important in formation of the homodimer. 75 matched cddid_all.tbl CDD smart00942 smart00942 214926 PriCT_1 Primase C terminal 1 (PriCT-1). This alpha helical domain is found at the C terminal of primases. 66 matched cddid_all.tbl CDD smart00943 smart00943 214927 Prim-Pol Bifunctional DNA primase/polymerase, N-terminal. Members of this family adopt a structure consisting of a core of antiparallel beta sheets. They are found in various bacterial hypothetical proteins, and have been shown to harbour both primase and polymerase activities. 154 matched cddid_all.tbl CDD smart00944 smart00944 214928 Pro-kuma_activ Pro-kumamolisin, activation domain. This domain is found at the N-terminus of peptidases belonging to MEROPS peptidase family S53 (sedolisin, clan SB). The domain adopts a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptidase. 136 matched cddid_all.tbl CDD smart00945 smart00945 198013 ProQ ProQ/FINO family. This family includes ProQ, which is required for full activation of the osmoprotectant transporter, ProQ, in Escherichia coli. 113 matched cddid_all.tbl CDD smart00946 smart00946 198014 ProRS-C_1 Prolyl-tRNA synthetase, C-terminal. Members of this family are predominantly found in prokaryotic prolyl-tRNA synthetase. They contain a zinc binding site, and adopt a structure consisting of alpha helices and antiparallel beta sheets arranged in 2 layers, in a beta-alpha-beta-alpha-beta motif. 67 matched cddid_all.tbl CDD smart00947 smart00947 214929 Pro_CA Carbonic anhydrase. Carbonic anhydrases (CA) are zinc metalloenzymes which catalyze the reversible hydration of carbon dioxide. In Escherichia coli, CA (gene cynT) is involved in recycling carbon dioxide formed in the bicarbonate-dependent decomposition of cyanate by cyanase (gene cynS). By this action, it prevents the depletion of cellular bicarbonate. In photosynthetic bacteria and plant chloroplast, CA is essential to inorganic carbon fixation. Prokaryotic and plant chloroplast CA are structurally and evolutionary related and form a family distinct from the one which groups the many different forms of eukaryotic CA's. 154 matched cddid_all.tbl CDD smart00948 smart00948 198016 Proteasome_A_N Proteasome subunit A N-terminal signature Add an annotation. This domain is conserved in the A subunits of the proteasome complex proteins. 23 matched cddid_all.tbl CDD smart00949 smart00949 198017 PAZ This domain is named PAZ after the proteins Piwi Argonaut and Zwille. This domain is found in two families of proteins that are involved in post-transcriptional gene silencing. These are the Piwi family and the Dicer family, that includes the Carpel factory protein. The function of the domains is unknown but has been suggested to mediate complex formation between proteins of the Piwi and Dicer families by hetero-dimerisation. The three-dimensional structure of this domain has been solved. The PAZ domain is composed of two subdomains. One subdomain is similar to the OB fold, albeit with a different topology. The OB-fold is well known as a single-stranded nucleic acid binding fold. The second subdomain is composed of a beta-hairpin followed by an alpha-helix. The PAZ domains shows low-affinity nucleic acid binding and appears to interact with the 3' ends of single-stranded regions of RNA in the cleft between the two subdomains. PAZ can bind the characteristic two-base 3' overhangs of siRNAs, indicating that although PAZ may not be a primary nucleic acid binding site in Dicer or RISC, it may contribute to the specific and productive incorporation of siRNAs and miRNAs into the RNAi pathway. 138 matched cddid_all.tbl CDD smart00950 smart00950 214930 Piwi This domain is found in the protein Piwi and its relatives. The function of this domain is the dsRNA guided hydrolysis of ssRNA. Determination of the crystal structure of Argonaute reveals that PIWI is an RNase H domain, and identifies Argonaute as Slicer, the enzyme that cleaves mRNA in the RNAi RISC complex.. In addition, Mg+2 dependence and production of 3'-OH and 5' phosphate products are shared characteristics of RNaseH and RISC. The PIWI domain core has a tertiary structure belonging to the RNase H family of enzymes. RNase H fold proteins all have a five-stranded mixed beta-sheet surrounded by helices. By analogy to RNase H enzymes which cleave single-stranded RNA guided by the DNA strand in an RNA/DNA hybrid, the PIWI domain can be inferred to cleave single-stranded RNA, for example mRNA, guided by double stranded siRNA. 301 matched cddid_all.tbl CDD smart00951 smart00951 214931 QLQ QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N-terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions. 36 matched cddid_all.tbl CDD smart00952 smart00952 214932 RAP This domain is found in various eukaryotic species, particularly in apicomplexans. In Plasmodium falciparum, the domain is found in proteins that are important in various parasite-host cell interactions. It is thought to be an RNA-binding domain. 58 matched cddid_all.tbl CDD smart00953 smart00953 214933 RES RES domain. This presumed protein contains 3 highly conserved polar groups that could form an active site. These are an arginine, glutamate and serine, hence the RES domain. RES is found widely distributed in bacteria, it has about 150 residues in length. 121 matched cddid_all.tbl CDD smart00954 smart00954 214934 RelA_SpoT Region found in RelA / SpoT proteins. The functions of Escherichia coli RelA and SpoT differ somewhat. RelA produces pppGpp (or ppGpp) from ATP and GTP (or GDP). SpoT degrades ppGpp, but may also act as a secondary ppGpp synthetase. The two proteins are strongly similar. In many species, a single homolog to SpoT and RelA appears reponsible for both ppGpp synthesis and ppGpp degradation. (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species. 111 matched cddid_all.tbl CDD smart00955 smart00955 214935 RNB This domain is the catalytic domain of ribonuclease II. 286 matched cddid_all.tbl CDD smart00956 smart00956 214936 RQC This DNA-binding domain is found in the RecQ helicase among others and has a helix-turn-helix structure. The RQC domain, found only in RecQ family enzymes, is a high affinity G4 DNA binding domain. 92 matched cddid_all.tbl CDD smart00957 smart00957 214937 SecA_DEAD SecA DEAD-like domain. SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP dependent manner. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the. 380 matched cddid_all.tbl CDD smart00958 smart00958 214938 SecA_PP_bind SecA preprotein cross-linking domain. The SecA ATPase is involved in the insertion and retraction of preproteins through the plasma membrane. This domain has been found to cross-link to preproteins, thought to indicate a role in preprotein binding. The pre-protein cross-linking domain is comprised of two sub domains that are inserted within the ATPase domain. 114 matched cddid_all.tbl CDD smart00959 smart00959 198027 Rho_N Rho termination factor, N-terminal domain. The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers. This domain is found to the N-terminus of the RNA binding domain. 43 matched cddid_all.tbl CDD smart00960 smart00960 214939 Robl_LC7 Roadblock/LC7 domain. This family includes proteins that are about 100 amino acids long and have been shown to be related. Members of this family of proteins are associated with both flagellar outer arm dynein and Drosophila and rat brain cytoplasmic dynein. It is proposed that roadblock/LC7 family members may modulate specific dynein functions. This family also includes Golgi-associated MP1 adapter protein and MglB from Myxococcus xanthus, a protein involved in gliding motility. However the family also includes members from non-motile bacteria such as Streptomyces coelicolor, suggesting that the protein may play a structural or regulatory role. 88 matched cddid_all.tbl CDD smart00961 smart00961 198029 RuBisCO_small Ribulose bisphosphate carboxylase, small chain. RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP), thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome. which results in RuBisCO being more abundant during the day when it is required. 96 matched cddid_all.tbl CDD smart00962 smart00962 214940 SRP54 SRP54-type protein, GTPase domain. This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins. 197 matched cddid_all.tbl CDD smart00963 smart00963 214941 SRP54_N SRP54-type protein, helical bundle domain. This entry represents the N-terminal helical bundle domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. 77 matched cddid_all.tbl CDD smart00964 smart00964 214942 STAT_int STAT protein, protein interaction domain. STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. STAT proteins also include an SH2 domain. 120 matched cddid_all.tbl CDD smart00965 smart00965 198033 STN Secretin and TonB N terminus short domain. This is a short domain found at the N-terminus of the Secretins of the bacterial type II/III secretory system as well as the TonB-dependent receptor proteins. These proteins are involved in TonB-dependent active uptake of selective substrates. 52 matched cddid_all.tbl CDD smart00966 smart00966 198034 SpoVT_AbrB SpoVT / AbrB like domain. This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation. AbrB is thought to interact directly with the transcription initiation regions of genes under its control. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator. DNA-binding activity in this AbrB homologue requires hexamerisation. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins. 45 matched cddid_all.tbl CDD smart00967 smart00967 214943 SpoU_sub_bind RNA 2'-O ribose methyltransferase substrate binding. This domain is a RNA 2'-O ribose methyltransferase substrate binding domain. 70 matched cddid_all.tbl CDD smart00968 smart00968 214944 SMC_hinge SMC proteins Flexible Hinge Domain. This entry represents the hinge region of the SMC (Structural Maintenance of Chromosomes) family of proteins. The hinge region is responsible for formation of the DNA interacting dimer. It is also possible that the precise structure of it is an essential determinant of the specificity of the DNA-protein interaction. 120 matched cddid_all.tbl CDD smart00969 smart00969 198037 SOCS_box The SOCS box acts as a bridge between specific substrate- binding domains and more generic proteins that comprise a large family of E3 ubiquitin protein ligases. 34 matched cddid_all.tbl CDD smart00970 smart00970 214945 s48_45 Sexual stage antigen s48/45 domain. This family contains sexual stage s48/45 antigens from Plasmodium (approximately 450 residues long). These are surface proteins expressed by Plasmodium male and female gametes that have been shown to play a conserved and important role in fertilisation. 116 matched cddid_all.tbl CDD smart00971 smart00971 198039 SATase_N Serine acetyltransferase, N-terminal. The N-terminal domain of serine acetyltransferase has a sequence that is conserved in plants.and bacteria. 105 matched cddid_all.tbl CDD smart00972 smart00972 198040 SCPU Spore Coat Protein U domain. This domain is found in a bacterial family of spore coat proteins.as well as a family of secreted pili proteins involved in motility and biofilm formation. 59 matched cddid_all.tbl CDD smart00973 smart00973 214946 Sec63 Sec63 Brl domain. This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases. 314 matched cddid_all.tbl CDD smart00974 smart00974 214947 T5orf172 This entry represents the putative helicase A859L. 80 matched cddid_all.tbl CDD smart00975 smart00975 214948 Telomerase_RBD Telomerase ribonucleoprotein complex - RNA binding domain. Telomeres in most organisms are comprised of tandem simple sequence repeats. The total length of telomeric repeat sequence at each chromosome end is determined in a balance of sequence loss and sequence addition. One major influence on telomere length is the enzyme telomerase. It is a reverse transcriptase that adds these simple sequence repeats to chromosome ends by copying a template sequence within the RNA component of the enzyme. The RNA binding domain of telomerase - TRBD - is made up of twelve alpha helices and two short beta sheets. How telomerase and associated regulatory factors physically interact and function with each other to maintain appropriate telomere length is poorly understood. It is known however that TRBD is involved in formation of the holoenzyme (which performs the telomere extension) in addition to recognition and binding of RNA. 136 matched cddid_all.tbl CDD smart00976 smart00976 214949 Telo_bind Telomeric single stranded DNA binding POT1/CDC13. The telomere-binding protein forms a heterodimer in ciliates consisting of an alpha and a beta subunit. This complex may function as a protective cap for the single-stranded telomeric overhang. Alpha subunit consists of 3 structural domains, all with the same beta-barrel OB fold. 137 matched cddid_all.tbl CDD smart00977 smart00977 198045 TilS_C TilS substrate C-terminal domain. This domain is found in the tRNA(Ile) lysidine synthetase (TilS) protein. 69 matched cddid_all.tbl CDD smart00978 smart00978 214950 Tim44 Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane. Tim44 is thought to bind phospholipids of the mitochondrial inner membrane both by electrostatic interactions and by penetrating the polar head group region. 147 matched cddid_all.tbl CDD smart00979 smart00979 198047 TIFY This short possible domain is found in a variety of plant transcription factors that contain GATA domains as well as other motifs. Although previously known as the Zim domain this is now called the tify domain after its most conserved amino acids. TIFY proteins can be further classified into two groups depending on the presence (group I) or absence (group II) of a C2C2-GATA domain. Functional annotation of these proteins is still poor, but several screens revealed a link between TIFY proteins of group II and jasmonic acid-related stress response. 36 matched cddid_all.tbl CDD smart00980 smart00980 214951 THAP The THAP domain is a putative DNA-binding domain (DBD) and probably also binds a zinc ion. It features the conserved C2CH architecture (consensus sequence: Cys - 2-4 residues - Cys - 35-50 residues - Cys - 2 residues - His). Other universal features include the location of the domain at the N-termini of proteins, its size of about 90 residues, a C-terminal AVPTIF box and several other conserved residues. Orthologues of the human THAP domain have been identified in other vertebrates and probably worms and flies, but not in other eukaryotes or any prokaryotes. 80 matched cddid_all.tbl CDD smart00981 smart00981 214952 THUMP The THUMP domain is named after after thiouridine synthases, methylases and PSUSs. The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterised RNA-binding domains. It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets. 83 matched cddid_all.tbl CDD smart00982 smart00982 198050 TRCF This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli. A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by the transcription-repair-coupling factor (TRCF) which releases RNAP and the truncated transcript. 100 matched cddid_all.tbl CDD smart00983 smart00983 214953 TPK_B1_binding Thiamin pyrophosphokinase, vitamin B1 binding domain. Thiamin pyrophosphokinase (TPK) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamin) to form the coenzyme thiamin pyrophosphate (TPP). Thus, TPK is important for the formation of a coenzyme required for central metabolic functions. The structure of thiamin pyrophosphokinase suggest that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis. 66 matched cddid_all.tbl CDD smart00984 smart00984 214954 UDPG_MGDP_dh_C UDP binding domain. The UDP-glucose/GDP-mannose dehydrogenases are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate. 99 matched cddid_all.tbl CDD smart00985 smart00985 214955 UBA_e1_C Ubiquitin-activating enzyme e1 C-terminal domain. This presumed domain found at the C terminus of Ubiquitin-activating enzyme e1 proteins is functionally uncharacterised. 128 matched cddid_all.tbl CDD smart00986 smart00986 214956 UDG Uracil DNA glycosylase superfamily. 156 matched cddid_all.tbl CDD smart00988 smart00988 214958 UreE_N UreE urease accessory protein, N-terminal domain. UreE is a urease accessory protein. Urease hydrolyses urea into ammonia and carbamic acid. 65 matched cddid_all.tbl CDD smart00989 smart00989 198057 V4R The V4R (vinyl 4 reductase) domain is a predicted small molecular binding domain, that may bind to hydrocarbons. 61 matched cddid_all.tbl CDD smart00990 smart00990 214959 VRR_NUC This model contains proteins with the VRR-NUC domain. It is associated with members of the PD-(D/E)XK nuclease superfamily, which include the type III restriction modification enzymes, for example StyLTI. 108 matched cddid_all.tbl CDD smart00991 smart00991 214960 WHEP-TRS A conserved domain of 46 amino acids, called WHEP-TRS has been shown.to exist in a number of higher eukaryote aminoacyl-transfer RNA synthetases. This domain is present one to six times in the several enzymes. There are three copies in mammalian multifunctional aminoacyl-tRNA synthetase in a region that separates the N-terminal glutamyl-tRNA synthetase domain from the C-terminal prolyl-tRNA synthetase domain, and six copies in the intercatalytic region of the Drosophila enzyme. The domain is found at the N-terminal extremity of the mammalian tryptophanyl- tRNA synthetase and histidyl-tRNA synthetase, and the mammalian, insect, nematode and plant glycyl- tRNA synthetases. This domain could contain a central alpha-helical region and may play a role in the association of tRNA-synthetases into multienzyme complexes. 56 matched cddid_all.tbl CDD smart00992 smart00992 214961 YccV-like Hemimethylated DNA-binding protein YccV like. YccV is a hemimethylated DNA binding protein which has been shown to regulate dnaA gene expression. The structure of one of the hypothetical proteins in this family has been solved and it forms a beta sheet structure with a terminating alpha helix. 98 matched cddid_all.tbl CDD smart00993 smart00993 198061 YL1_C YL1 nuclear protein C-terminal domain. This domain is found in proteins of the YL1 family. These proteins have been shown to be DNA-binding and may be a transcription factor. This domain is found in proteins that are not YL1 proteins. 30 matched cddid_all.tbl CDD smart00994 smart00994 198062 zf-C4_ClpX ClpX C4-type zinc finger. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type. This presumed zinc binding domain is found at the N-terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. The molecular function of this domain is now known. 39 matched cddid_all.tbl CDD smart00995 smart00995 214962 AD Anticodon-binding domain. This domain of approximately 100 residues is conserved from plants to humans. It is frequently found in association with Lsm domain-containing proteins. 90 matched cddid_all.tbl CDD smart00996 smart00996 214963 AdoHcyase S-adenosyl-L-homocysteine hydrolase. 426 matched cddid_all.tbl CDD smart00997 smart00997 198065 AdoHcyase_NAD S-adenosyl-L-homocysteine hydrolase, NAD binding domain. 162 matched cddid_all.tbl CDD smart00998 smart00998 198066 ADSL_C Adenylosuccinate lyase C-terminus. Adenylosuccinate lyase catalyses two steps in the synthesis of purine nucleotides: the conversion of succinylaminoimidazole-carboxamide ribotide into aminoimidazole-carboxamide ribotide (the fifth step of de novo IMP biosynthesis); the formation of adenosine monophosphate (AMP) from adenylosuccinate (the final step in the synthesis of AMP from IMP). This entry represents the C-terminal, seven alpha-helical, domain of adenylosuccinate lyase. 81 matched cddid_all.tbl CDD smart00999 smart00999 198067 Aerolysin Aerolysin toxin. This family represents the pore forming lobe of aerolysin. 368 matched cddid_all.tbl CDD smart01000 smart01000 214964 Aha1_N Activator of Hsp90 ATPase, N-terminal. This domain is predominantly found in the protein 'Activator of Hsp90 ATPase', it adopts a secondary structure consisting of an N-terminal alpha-helix leading into a four-stranded meandering antiparallel beta-sheet, followed by a C-terminal alpha-helix. The two helices are packed together, with the beta-sheet curving around them. They bind to the molecular chaperone HSP82 and stimulate its ATPase activity. 134 matched cddid_all.tbl CDD smart01001 smart01001 214965 AIRC AIR carboxylase. Members of this family catalyse the decarboxylation of 1-(5-phosphoribosyl)-5-amino-4-imidazole-carboxylate (AIR). This family catalyse the sixth step of de novo purine biosynthesis. Some members of this family contain two copies of this domain. 152 matched cddid_all.tbl CDD smart01002 smart01002 214966 AlaDh_PNT_C Alanine dehydrogenase/PNT, C-terminal domain. Alanine dehydrogenase catalyzes the NAD-dependent reversible reductive amination of pyruvate into alanine. 149 matched cddid_all.tbl CDD smart01003 smart01003 214967 AlaDh_PNT_N Alanine dehydrogenase/PNT, N-terminal domain. Alanine dehydrogenase catalyzes the NAD-dependent reversible reductive amination of pyruvate into alanine. 133 matched cddid_all.tbl CDD smart01004 smart01004 214968 ALAD Delta-aminolevulinic acid dehydratase. This entry represents porphobilinogen (PBG) synthase (PBGS, or 5-aminoaevulinic acid dehydratase, or ALAD, ), which functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses a Knorr-type condensation reaction between two molecules of ALA to generate porphobilinogen, the pyrrolic building block used in later steps. The structure of the enzyme is based on a TIM barrel topology made up of eight identical subunits, where each subunit binds to a metal ion that is essential for activity, usually zinc (in yeast, mammals and certain bacteria) or magnesium (in plants and other bacteria). A lysine has been implicated in the catalytic mechanism. The lack of PBGS enzyme causes a rare porphyric disorder known as ALAD porphyria, which appears to involve conformational changes in the enzyme. 321 matched cddid_all.tbl CDD smart01005 smart01005 214969 Ala_racemase_C Alanine racemase, C-terminal domain. Alanine racemase plays a role in providing the D-alanine required for cell wall biosynthesis by isomerising L-alanine to D-alanine. Proteins contains this domain are found in both prokaryotic and eukaryotic proteins. 124 matched cddid_all.tbl CDD smart01006 smart01006 198074 AlcB Siderophore biosynthesis protein domain. AlcB is the conserved 45 residue region of one of the proteins of a complex which mediates alcaligin biosynthesis in Bordetella and aerobactin biosynthesis in E. coli and other bacteria. The protein appears to catalyse N-acylation of the hydroxylamine group in N-hydroxyputrescine with succinyl CoA - an activated mono-thioester derivative of succinic acid that is an intermediate in the Krebs cycle. 48 matched cddid_all.tbl CDD smart01007 smart01007 214970 Aldolase_II Class II Aldolase and Adducin N-terminal domain. This family includes class II aldolases and adducins which have not been ascribed any enzymatic function. 185 matched cddid_all.tbl CDD smart01008 smart01008 214971 Ald_Xan_dh_C Aldehyde oxidase and xanthine dehydrogenase, a/b hammerhead domain. Aldehyde oxidase catalyses the conversion of an aldehyde in the presence of oxygen and water to an acid and hydrogen peroxide. The enzyme is a homodimer, and requires FAD, molybdenum and two 2FE-2S clusters as cofactors. Xanthine dehydrogenase catalyses the hydrogenation of xanthine to urate, and also requires FAD, molybdenum and two 2FE-2S clusters as cofactors. This activity is often found in a bifunctional enzyme with xanthine oxidase activity too. The enzyme can be converted from the dehydrogenase form to the oxidase form irreversibly by proteolysis or reversibly through oxidation of sulphydryl groups. 107 matched cddid_all.tbl CDD smart01009 smart01009 214972 AlkA_N AlkA N-terminal domain. This domain is found at the N terminus of bacterial AlkA . AlkA (3-methyladenine-DNA glycosylase II) is a base excision repair glycosylase from Escherichia coli. It removes a variety of alkylated bases from DNA, primarily by removing alkylation damage from duplex and single stranded DNA. AlkA flips a 1-azaribose abasic nucleotide out of DNA. This produces a 66 degrees bend in the DNA and a marked widening of the minor groove. 113 matched cddid_all.tbl CDD smart01010 smart01010 214973 AMPKBI 5'-AMP-activated protein kinase beta subunit, interation domain. This region is found in the beta subunit of the 5'-AMP-activated protein kinase complex, and its yeast homologues Sip1, Sip2 and Gal83, which are found in the SNF1 kinase complex. This region is sufficient for interaction of this subunit with the kinase complex, but is not solely responsible for the interaction, and the interaction partner is not known. The isoamylase N-terminal domain is sometimes found in proteins belonging to this family. 100 matched cddid_all.tbl CDD smart01011 smart01011 198079 AMP_N Aminopeptidase P, N-terminal domain. This domain is structurally very similar to the creatinase N-terminal domain. However, little or no sequence similarity exists between the two families. 135 matched cddid_all.tbl CDD smart01012 smart01012 198080 ANTAR ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins. The majority of the domain consists of a coiled-coil. 55 matched cddid_all.tbl CDD smart01013 smart01013 198081 APC2 Anaphase promoting complex (APC) subunit 2. The anaphase promoting complex or cyclosome (APC2) is an E3 ubiquitin ligase which is part of the SCF family of ubiquitin ligases. Ubiquitin ligases catalyse the transfer of ubiquitin from the ubiquitin conjugating enzyme (E2), to the substrate protein. 60 matched cddid_all.tbl CDD smart01014 smart01014 198082 ARID ARID/BRIGHT DNA binding domain. Members of the recently discovered ARID (AT-rich interaction domain) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. 88 matched cddid_all.tbl CDD smart01015 smart01015 214974 Arfaptin Arfaptin-like domain. Arfaptin interacts with ARF1, a small GTPase involved in vesicle budding at the Golgi complex and immature secretory granules. The structure of arfaptin shows that upon binding to a small GTPase, arfaptin forms an elongated, crescent-shaped dimer of three-helix coiled-coils. The N-terminal region of ICA69 is similar to arfaptin. 217 matched cddid_all.tbl CDD smart01016 smart01016 214975 Arg_tRNA_synt_N Arginyl tRNA synthetase N terminal dom. This domain is found at the amino terminus of Arginyl tRNA synthetase, also called additional domain 1 (Add-1). It is about 140 residues long and it has been suggested that this domain will be involved in tRNA recognition. 85 matched cddid_all.tbl CDD smart01017 smart01017 214976 Arrestin_C Arrestin (or S-antigen), C-terminal domain. Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain. Arrestins comprise a family of closely-related proteins that includes beta-arrestin-1 and -2, which regulate the function of beta-adrenergic receptors by binding to their phosphorylated forms, impairing their capacity to activate G(S) proteins; Cone photoreceptors C-arrestin (arrestin-X). which could bind to phosphorylated red/green opsins; and Drosophila phosrestins I and II, which undergo light-induced phosphorylation, and probably play a role in photoreceptor transduction. 142 matched cddid_all.tbl CDD smart01018 smart01018 198086 B12-binding_2 B12 binding domain. Cobalamin-dependent methionine synthase is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain. The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases. 84 matched cddid_all.tbl CDD smart01019 smart01019 214977 B3 B3 DNA binding domain. Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see ) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations. 96 matched cddid_all.tbl CDD smart01020 smart01020 198088 B2-adapt-app_C Beta2-adaptin appendage, C-terminal sub-domain. Members of this family adopt a structure consisting of a 5 stranded beta-sheet, flanked by one alpha helix on the outer side, and by two alpha helices on the inner side. This domain is required for binding to clathrin, and its subsequent polymerisation. Furthermore, a hydrophobic patch present in the domain also binds to a subset of D-phi-F/W motif-containing proteins that are bound by the alpha-adaptin appendage domain (epsin, AP180, eps15). 111 matched cddid_all.tbl CDD smart01021 smart01021 214978 Bac_rhodopsin Bacteriorhodopsin-like protein. The bacterial opsins are retinal-binding proteins that provide light- dependent ion transport and sensory functions to a family of halophilic bacteria.. They are integral membrane proteins believed to contain seven transmembrane (TM) domains, the last of which contains the attachment point for retinal (a conserved lysine). 233 matched cddid_all.tbl CDD smart01022 smart01022 214979 ASCH The ASCH domain adopts a beta-barrel fold similar to that of the PUA domain. It is thought to function as an RNA-binding domain during coactivation, RNA-processing and possibly during prokaryotic translation regulation. 99 matched cddid_all.tbl CDD smart01023 smart01023 198091 BAF Barrier to autointegration factor. Barrier-to-autointegration factor (BAF) is an essential protein that is highly conserved in metazoan evolution, and which may act as a DNA-bridging protein. BAF binds directly to double-stranded DNA, to transcription activators, and to inner nuclear membrane proteins, including lamin A filament proteins that anchor nuclear-pore complexes in place, and nuclear LEM-domain proteins that bind to laminins filaments and chromatin. New findings suggest that BAF has structural roles in nuclear assembly and chromatin organization, represses gene expression and might interlink chromatin structure, nuclear architecture and gene regulation in metazoans. BAF can be exploited by retroviruses to act as a host component of pre-integration complexes, which promote the integration of the retroviral DNA into the host chromosome by preventing autointegration of retroviral DNA. BAF might contribute to the assembly or activity of retroviral pre-integration complexes through direct binding to the retroviral proteins p55 Gag and matrix, as well as to DNA. 87 matched cddid_all.tbl CDD smart01024 smart01024 214980 BCS1_N This domain is found at the N terminal of the mitochondrial ATPase BCS1. It encodes the import and intramitochondrial sorting for the protein. 170 matched cddid_all.tbl CDD smart01025 smart01025 214981 BEN The BEN domain is found in diverse animal proteins. Proteins containing BEN domains are BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, the chordopoxvirus virosomal protein E5R and several proteins of polydnaviruses. Computational analysis suggests that the BEN domain mediates protein-DNA and protein-protein interactions during chromatin organisation and transcription. 80 matched cddid_all.tbl CDD smart01026 smart01026 214982 Beach Beige/BEACH domain. The BEACH domain was described in the BEIGE protein (D1035670) and in the highly homologous CHS protein. The BEACH domain is usually followed by a series of WD repeats. The function of the BEACH domain is unknown. 280 matched cddid_all.tbl CDD smart01027 smart01027 214983 Beta-Casp Beta-Casp domain. The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease. The active site of this enzyme is located at the interface of these two domains. 126 matched cddid_all.tbl CDD smart01028 smart01028 198096 Beta-TrCP_D D domain of beta-TrCP. This domain is found in eukaryotes, and is approximately 40 amino acids in length. It is found associated with F-box domain, WD domain. The protein that contains this domain functions as a ubiquitin ligase. Ubiquitination is required to direct proteins towards the proteasome for degradation. This protein is part of the WD40 class of F box proteins. The D domain of these F box proteins is involved in mediating the dimerisation of the protein. Dimerisation is necessary to polyubiquitinate substrates so this D domain is vital in directing substrates towards the proteasome for degradation. 40 matched cddid_all.tbl CDD smart01029 smart01029 198097 BetaGal_dom2 Beta-galactosidase, domain 2. This is the second domain of the five-domain beta-galactosidase enzyme that altogether catalyses the hydrolysis of beta(1-3) and beta(1-4) galactosyl bonds in oligosaccharides as well as the inverse reaction of enzymatic condensation and trans-glycosylation. This domain is made up of 16 antiparallel beta-strands and an alpha-helix at its C terminus. The fold of this domain appears to be unique. In addition, the last seven strands of the domain form a subdomain with an immunoglobulin-like (I-type Ig) fold in which the first strand is divided between the two beta-sheets. In penicillin spp this strand is interrupted by a 12-residue insertion which forms an additional edge-strand to the second beta-sheet of the sub-domain. The remainder of the second domain forms a series of beta-hairpins at its N terminus, four strands of which are contiguous with part of the Ig-like sub-domain, forming in total a seven-stranded antiparallel beta-sheet. This domain is associated with family Glyco_hydro_35, which is N-terminal to it, but itself has no metazoan members. 182 matched cddid_all.tbl CDD smart01030 smart01030 214984 BHD_1 Rad4 beta-hairpin domain 1. This short domain is found in the Rad4 protein. This domain binds to DNA. 54 matched cddid_all.tbl CDD smart01031 smart01031 214985 BHD_2 Rad4 beta-hairpin domain 2. This short domain is found in the Rad4 protein. This domain binds to DNA. 56 matched cddid_all.tbl CDD smart01032 smart01032 198100 BHD_3 Rad4 beta-hairpin domain 3. This short domain is found in the Rad4 protein. This domain binds to DNA. 75 matched cddid_all.tbl CDD smart01033 smart01033 198101 BING4CT BING4CT (NUC141) domain. This C terminal domain is found in the BING4 family of nucleolar WD40 repeat proteins. 80 matched cddid_all.tbl CDD smart01034 smart01034 198102 BLUF Sensors of blue-light using FAD. The BLUF domain has been shown to bind FAD in the AppA protein. AppA is involved in the repression of photosynthesis genes in response to blue-light. 92 matched cddid_all.tbl CDD smart01035 smart01035 214986 BOP1NT BOP1NT (NUC169) domain. This N terminal domain is found in BOP1-like WD40 proteins. 264 matched cddid_all.tbl CDD smart01036 smart01036 214987 BP28CT BP28CT (NUC211) domain. This C-terminal domain is found in BAP28-like nucleolar proteins. 151 matched cddid_all.tbl CDD smart01037 smart01037 198105 Bet_v_1 Pathogenesis-related protein Bet v I family. This family is named after Bet v 1, the major birch pollen allergen. This protein belongs to family 10 of plant pathogenesis-related proteins (PR-10), cytoplasmic proteins of 15-17 kd that are wide-spread among dicotyledonous plants. In recent years, a number of diverse plant proteins with low sequence similarity to Bet v 1 was identified. A classification by sequence similarity yielded several subfamilies related to PR-10.- Pathogenesis-related proteins PR-10: These proteins were identified as major tree pollen allergens in birch and related species (hazel, alder), as plant food allergens expressed in high levels in fruits, vegetables and seeds (apple, celery, hazelnut), and as pathogenesis-related proteins whose expression is induced by pathogen infection, wounding, or abiotic stress. Hyp-1, an enzyme involved in the synthesis of the bioactive naphthodianthrone hypericin in St. John's wort (Hypericum perforatum) also belongs to this family. Most of these proteins were found in dicotyledonous plants. In addition, related sequences were identified in monocots and conifers. - Cytokinin-specific binding proteins: These legume proteins bind cytokinin plant hormones. - (S)-Norcoclaurine synthases are enzymes catalysing the condensation of dopamine and 4-hydroxyphenylacetaldehyde to (S)-norcoclaurine, the first committed step in the biosynthesis of benzylisoquinoline alkaloids such as morphine. -Major latex proteins and ripening-related proteins are proteins of unknown biological function that were first discovered in the latex of opium poppy (Papaver somniferum) and later found to be upregulated during ripening of fruits such as strawberry and cucumber. The occurrence of Bet v 1-related proteins is confined to seed plants with the exception of a cytokinin-binding protein from the moss Physcomitrella patens. 151 matched cddid_all.tbl CDD smart01038 smart01038 214988 Bgal_small_N Beta galactosidase small chain. This domain comprises the small chain of dimeric beta-galactosidases EC:3.2.1.23. This domain is also found in single chain beta-galactosidase. 272 matched cddid_all.tbl CDD smart01039 smart01039 198107 BRICHOS The BRICHOS domain is found in a variety of proteins implicated in dementia, respiratory distress and cancer. Its exact function is unknown; roles that have been proposed for the domain, which is about 100 amino acids long, include (a) targeting of the protein to the secretory pathway, (b) intramolecular chaperone-like function, and (c) assisting the specialised intracellular protease processing system. This C-terminal domain is embedded in the endoplasmic reticulum lumen, and binds to the N-terminal, transmembrane, SP_C, pfam08999 provided that it is in non-helical conformation. Thus the Brichos domain of proSP-C is a chaperone that induces alpha-helix formation of an aggregation-prone TM region. 96 matched cddid_all.tbl CDD smart01040 smart01040 214989 Bro-N BRO family, N-terminal domain. This family includes the N-terminus of baculovirus BRO and ALI motif proteins. The function of BRO proteins is unknown. It has been suggested that BRO-A and BRO-C are DNA binding proteins that influence host DNA replication and/or transcription. This Pfam domain does not include the characteristic invariant alanine, leucine, isoleucine motif of the ALI proteins. 89 matched cddid_all.tbl CDD smart01041 smart01041 214990 BRO1 BRO1-like domain. This domain is found in a number proteins including Rhophilin and BRO1. It is known to have a role in endosomal targeting. ESCRT-III subunit Snf7 binds to a conserved hydrophobic patch in the BRO1 domain that is required for protein complex formation and for the protein-sorting function of BRO1. 381 matched cddid_all.tbl CDD smart01042 smart01042 198110 Brr6_like_C_C Di-sulfide bridge nucleocytoplasmic transport domain. Brr6_like_C_C is the highly conserved C-terminal region of a group of proteins found in fungi. It carries four highly conserved cysteine residues. It is suggested that members of the family interact with each other via di-sulfide bridges to form a complex which is involved in nucleocytoplasmic transport. 134 matched cddid_all.tbl CDD smart01043 smart01043 198111 BTAD Bacterial transcriptional activator domain. Found in the DNRI/REDD/AFSR family of regulators. This region of AFSR along with the C terminal region is capable of independently directing actinorhodin production. This family contains TPR repeats. 145 matched cddid_all.tbl CDD smart01044 smart01044 214991 Btz CASC3/Barentsz eIF4AIII binding. This domain is found on CASC3 (cancer susceptibility candidate gene 3 protein) which is also known as Barentsz (Btz). CASC3 is a component of the EJC (exon junction complex) which is a complex that is involved in post-transcriptional regulation of mRNA in metazoa. The complex is formed by the association of four proteins (eIF4AIII, Barentsz, Mago, and Y14), mRNA, and ATP. This domain wraps around eIF4AIII and stacks against the 5' nucleotide. 106 matched cddid_all.tbl CDD smart01045 smart01045 214992 BURP The BURP domain is found at the C-terminus of several different plant proteins. It was named after the proteins in which it was first identified: the BNM2 clone-derived protein from Brassica napus; USPs and USP-like proteins; RD22 from Arabidopsis thaliana; and PG1beta from Lycopersicon esculentum. This domain is around 230 amino acid residues long. It possesses the following conserved features: two phenylalanine residues at its N-terminus; two cysteine residues; and four repeated cysteine-histidine motifs, arranged as: CH-X(10)-CH-X(25-27)-CH-X(25-26)-CH, where X can be any amino acid. The function of this domain is unknown. 222 matched cddid_all.tbl CDD smart01046 smart01046 198114 c-SKI_SMAD_bind c-SKI Smad4 binding domain. c-SKI is an oncoprotein that inhibits TGF-beta signaling through interaction with Smad proteins. This domain binds to Smad4. 95 matched cddid_all.tbl CDD smart01047 smart01047 214993 C1_4 TFIIH C1-like domain. The carboxyl-terminal region of TFIIH is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C. 49 matched cddid_all.tbl CDD smart01048 smart01048 214994 C6 This domain of unknown function is found in a C. elegans protein. It is presumed to be an extracellular domain. The C6 domain contains six conserved cysteine residues in most copies of the domain. However some copies of the domain are missing cysteine residues 1 and 3 suggesting that these form a disulphide bridge. 98 matched cddid_all.tbl CDD smart01049 smart01049 214995 Cache_2 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins. Members include the animal dihydropyridine-sensitive voltage-gated Ca2+ channel; alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria, with Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions. 91 matched cddid_all.tbl CDD smart01050 smart01050 214996 CactinC_cactus Cactus-binding C-terminus of cactin protein. CactinC_cactus is the C-terminal 200 residues of the cactin protein which are necessary for the association of cactin with IkappaB-cactus as one of the intracellular members of the Rel complex. The Rel (NF-kappaB) pathway is conserved in invertebrates and vertebrates. In mammals, it controls the activities of the immune and inflammatory response genes as well as viral genes, and is critical for cell growth and survival. In Drosophila, the Rel pathway functions in the innate cellular and humoral immune response, in muscle development, and in the establishment of dorsal-ventral polarity in the early embryo. Most members of the family also have a Cactin_mid domain further upstream. 129 matched cddid_all.tbl CDD smart01051 smart01051 198119 CAMSAP_CKK Microtubule-binding calmodulin-regulated spectrin-associated. This is the C-terminal domain of a family of eumetazoan proteins collectively defined as calmodulin-regulated spectrin-associated, or CAMSAP, proteins. CAMSAP proteins carry an N-terminal region that includes the CH domain, a central region including a predicted coiled-coil and this C-terminal, or CKK, domain - defined as being present in CAMSAP, KIAA1078 and KIAA1543, The C-terminal domain is the part of the CAMSAP proteins that binds to microtubules. The domain appears to act by producing inhibition of neurite extension, probably by blocking microtubule function. CKK represents a domain that has evolved with the metazoa. The structure of a murine hypothetical protein from RIKEN cDNA has shown the domain to adopt a mainly beta barrel structure with an associated alpha-helical hairpin. 129 matched cddid_all.tbl CDD smart01052 smart01052 214997 CAP_GLY Cytoskeleton-associated proteins (CAPs) are involved in the organisation of microtubules and transportation of vesicles and organelles along the cytoskeletal network. A conserved motif, CAP-Gly, has been identified in a number of CAPs, including CLIP-170 and dynactins. The crystal structure of Caenorhabditis elegans F53F4.3 protein CAP-Gly domain was recently solved. The domain contains three beta-strands. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove. 68 matched cddid_all.tbl CDD smart01053 smart01053 198121 CaMBD Calmodulin binding domain. Small-conductance Ca2+-activated K+ channels (SK channels) are independent of voltage and gated solely by intracellular Ca2+. These membrane channels are heteromeric complexes that comprise pore-forming alpha-subunits and the Ca2+-binding protein calmodulin (CaM). CaM binds to the SK channel through this the CaM-binding domain (CaMBD), which is located in an intracellular region of the alpha-subunit immediately carboxy-terminal to the pore. Channel opening is triggered when Ca2+ binds the EF hands in the N-lobe of CaM. The structure of this domain complexed with CaM is known. This domain forms an elongated dimer with a CaM molecule bound at each end; each CaM wraps around three alpha-helices, two from one CaMBD subunit and one from the other. 76 matched cddid_all.tbl CDD smart01054 smart01054 214998 CaM_binding Plant calmodulin-binding domain. The sequences featured in this family are found repeated in a number of plant calmodulin-binding proteins, and are thought to constitute the calmodulin-binding domains.. Binding of the proteins to calmodulin depends on the presence of calcium ions.. These proteins are thought to be involved in various processes, such as plant defence responses.and stolonisation or tuberization. 115 matched cddid_all.tbl CDD smart01055 smart01055 214999 Cadherin_pro Cadherin prodomain like. Cadherins are a family of proteins that mediate calcium dependent cell-cell adhesion. They are activated through cleavage of a prosequence in the late Golgi. This domain corresponds to the folded region of the prosequence, and is termed the prodomain. The prodomain shows structural resemblance to the cadherin domain, but lacks all the features known to be important for cadherin-cadherin interactions. 87 matched cddid_all.tbl CDD smart01056 smart01056 198124 Candida_ALS_N Cell-wall agglutinin N-terminal ligand-sugar binding. This is likely to be the sugar or ligand binding domain of the yeast alpha-agglutinins. 245 matched cddid_all.tbl CDD smart01057 smart01057 215000 Carb_anhydrase Eukaryotic-type carbonic anhydrase. Carbonic anhydrases are zinc metalloenzymes which catalyse the reversible hydration of carbon dioxide to bicarbonate.. CAs have essential roles in facilitating the transport of carbon dioxide and protons in the intracellular space, across biological membranes and in the layers of the extracellular space; they are also involved in many other processes, from respiration and photosynthesis in eukaryotes to cyanate degradation in prokaryotes. There are five known evolutionarily distinct CA families (alpha, beta, gamma, delta and epsilon) that have no significant sequence identity and have structurally distinct overall folds. Some CAs are membrane-bound, while others act in the cytosol; there are several related proteins that lack enzymatic activity. The active site of alpha-CAs is well described, consisting of a zinc ion coordinated through 3 histidine residues and a water molecule/hydroxide ion that acts as a potent nucleophile. The enzyme employs a two-step mechanism: in the first step, there is a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide; in the second step, the active site is regenerated by the ionisation of the zinc-bound water molecule and the removal of a proton from the active site. Beta- and gamma-CAs also employ a zinc hydroxide mechanism, although at least some beta-class enzymes do not have water directly coordinated to the metal ion. 247 matched cddid_all.tbl CDD smart01058 smart01058 215001 CarD_TRCF CarD-like/TRCF domain. CarD is a Myxococcus xanthus protein required for the activation of light- and starvation-inducible genes. This family includes the presumed N-terminal domain. CarD interacts with the zinc-binding protein CarG, to form a complex that regulates multiple processes in Myxococcus xanthus. This family also includes a domain to the N-terminal side of the DEAD helicase of TRCF proteins. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription. This domain is involved in binding to the stalled RNA polymerase. 99 matched cddid_all.tbl CDD smart01059 smart01059 215002 CAT Chloramphenicol acetyltransferase. Chloramphenicol acetyltransferase (CAT).catalyzes the acetyl-CoA dependent acetylation of chloramphenicol (Cm), an antibiotic which inhibits prokaryotic peptidyltransferase activity. Acetylation of Cm by CAT inactivates the antibiotic. A histidine residue, located in the C-terminal section of the enzyme, plays a central role in its catalytic mechanism. There is a second family of CAT. evolutionary unrelated to the main family described above. These CAT belong to the bacterial hexapeptide-repeat containing-transferases family (see ). The crystal structure of the type III enzyme from Escherichia coli with chloramphenicol bound has been determined. CAT is a trimer of identical subunits (monomer Mr 25,000) and the trimeric structure is stabilised by a number of hydrogen bonds, some of which result in the extension of a beta-sheet across the subunit interface. Chloramphenicol binds in a deep pocket located at the boundary between adjacent subunits of the trimer, such that the majority of residues forming the binding pocket belong to one subunit while the catalytically essential histidine belongs to the adjacent subunit. His195 is appropriately positioned to act as a general base catalyst in the reaction, and the required tautomeric stabilisation is provided by an unusual interaction with a main-chain carbonyl oxygen. 202 matched cddid_all.tbl CDD smart01060 smart01060 215003 Catalase Catalases are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen, serving to protect cells from its toxic effects. Hydrogen peroxide is produced as a consequence of oxidative cellular metabolism and can be converted to the highly reactive hydroxyl radical via transition metals, this radical being able to damage a wide variety of molecules within a cell, leading to oxidative stress and cell death. Catalases act to neutralise hydrogen peroxide toxicity, and are produced by all aerobic organisms ranging from bacteria to man. Most catalases are mono-functional, haem-containing enzymes, although there are also bifunctional haem-containing peroxidase/catalases that are closely related to plant peroxidases, and non-haem, manganese-containing catalases that are found in bacteria. 373 matched cddid_all.tbl CDD smart01061 smart01061 215004 CAT_RBD CAT RNA binding domain. This RNA binding domain is found at the amino terminus of transcriptional antitermination proteins such as BglG, SacY and LicT. These proteins control the expression of sugar metabolising operons in Gram+ and Gram- bacteria. This domain has been called the CAT (Co-AntiTerminator) domain. It binds as a dimer.to short Ribonucleotidic Anti-Terminator (RAT) hairpin, each monomer interacting symmetrically with both strands of the RAT hairpin. In the full-length protein, CAT is followed by two phosphorylatable PTS regulation domains that modulate the RNA binding activity of CAT. Upon activation, the dimeric proteins bind to RAT targets in the nascent mRNA, thereby preventing abortive dissociation of the RNA polymerase from the DNA template. 55 matched cddid_all.tbl CDD smart01062 smart01062 198130 Ca_chan_IQ Voltage gated calcium channel IQ domain. Voltage gated calcium channels control cellular calcium entry in response to changes in membrane potential. The isoleucine-glutamine (IQ) motif in the voltage gated calcium channel IQ domain interacts with hydrophobic pockets of Ca2+/calmodulin. The interaction regulates two self-regulatory calcium dependent feedback mechanism, calcium dependent inactivation (CDI), and calcium-dependent facilitation (CDF). 31 matched cddid_all.tbl CDD smart01063 smart01063 215005 CBM49 Carbohydrate binding domain CBM49. This domain is found at the C terminal of cellulases and in vitro binding studies have shown it to binds to crystalline cellulose. 84 matched cddid_all.tbl CDD smart01064 smart01064 198132 CBM_10 Cellulose or protein binding domain. This domain is found in two distinct sets of proteins with different functions. Those found in aerobic bacteria bind cellulose (or other carbohydrates); but in anaerobic fungi they are protein binding domains, referred to as dockerin domains or docking domains. They are believed to be responsible for the assembly of a multiprotein cellulase/hemicellulase complex, similar to the cellulosome found in certain anaerobic bacteria. 29 matched cddid_all.tbl CDD smart01065 smart01065 215006 CBM_2 Starch binding domain. 88 matched cddid_all.tbl CDD smart01066 smart01066 198134 CBM_25 Carbohydrate binding domain. 83 matched cddid_all.tbl CDD smart01067 smart01067 215007 CBM_3 Cellulose binding domain. 83 matched cddid_all.tbl CDD smart01068 smart01068 215008 CBM_X Putative carbohydrate binding domain. 62 matched cddid_all.tbl CDD smart01069 smart01069 215009 CDC37_C Cdc37 C terminal domain. Cdc37 is a protein required for the activity of numerous eukaryotic protein kinases. This domains corresponds to the C terminal domain whose function is unclear. It is found C terminal to the Hsp90 chaperone (Heat shocked protein 90) binding domain pfam08565 and the N terminal kinase binding domain of Cdc37. 93 matched cddid_all.tbl CDD smart01070 smart01070 215010 CDC37_M Cdc37 Hsp90 binding domain. Cdc37 is a molecular chaperone required for the activity of numerous eukaryotic protein kinases. This domains corresponds to the Hsp90 chaperone (Heat shocked protein 90) binding domain of Cdc37. It is found between the N terminal Cdc37 domain which is predominantly involved in kinase binding, and the C terminal domain of Cdc37 whose function is unclear. 155 matched cddid_all.tbl CDD smart01071 smart01071 198139 CDC37_N Cdc37 N terminal kinase binding. Cdc37 is a molecular chaperone required for the activity of numerous eukaryotic protein kinases. This domain corresponds to the N terminal domain which binds predominantly to protein kinases.and is found N terminal to the Hsp (Heat shocked protein) 90-binding domain. Expression of a construct consisting of only the N-terminal domain of Saccharomyces pombe Cdc37 results in cellular viability. This indicates that interactions with the cochaperone Hsp90 may not be essential for Cdc37 function. 154 matched cddid_all.tbl CDD smart01072 smart01072 215011 CDC48_2 Cell division protein 48 (CDC48) domain 2. This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the C-terminus. The VAT-N domain found in AAA ATPases is a substrate 185-residue recognition domain. 64 matched cddid_all.tbl CDD smart01073 smart01073 215012 CDC48_N Cell division protein 48 (CDC48) N-terminal domain. This domain has a double psi-beta barrel fold and includes VCP-like ATPase and N-ethylmaleimide sensitive fusion protein N-terminal domains. Both the VAT and NSF N-terminal functional domains consist of two structural domains of which this is at the N-terminus. The VAT-N domain found in AAA ATPases is a substrate 185-residue recognition domain. 82 matched cddid_all.tbl CDD smart01074 smart01074 215013 Cdc6_C CDC6, C terminal. The C terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity. 84 matched cddid_all.tbl CDD smart01075 smart01075 215014 CDT1 DNA replication factor CDT1 like. CDT1 is a component of the replication licensing system and promotes the loading of the mini-chromosome maintenance complex onto chromatin. Geminin is an inhibitor of CDT1 and prevents inappropriate re-initiation of replication on an already fired origin. This region of CDT1 binds to Geminin. 164 matched cddid_all.tbl CDD smart01076 smart01076 198144 CG-1 CG-1 domains are highly conserved domains of about 130 amino-acid residues. The domains contain a predicted bipartite NLS and are named after a partial cDNA clone isolated from parsley encoding a sequence-specific DNA-binding protein. CG-1 domains are associated with CAMTA proteins (for CAlModulin -binding Transcription Activator) that are transcription factors containing a calmodulin -binding domain and ankyrins (ANK) motifs. 118 matched cddid_all.tbl CDD smart01077 smart01077 198145 Cg6151-P Uncharacterized conserved protein CG6151-P. This is a family of small, less than 200 residue long, proteins which are named as CG6151-P proteins that are conserved from fungi to humans. The function is unknown. The fungal members have a characteristic ICP sequence motif. Some members are annotated as putative clathrin-coated vesicle protein but this could not be defined. 111 matched cddid_all.tbl CDD smart01078 smart01078 198146 CGGC This putative domain contains a quite highly conserved sequence of CGGC in its central region. The domain has many conserved cysteines and histidines suggestive of a zinc binding function. 106 matched cddid_all.tbl CDD smart01079 smart01079 215015 CHASE This domain is found in the extracellular portion of receptor-like proteins - such as serine/threonine kinases and adenylyl cyclases. Predicted to be a ligand binding domain. 176 matched cddid_all.tbl CDD smart01080 smart01080 215016 CHASE2 CHASE2 is an extracellular sensory domain, which is present in various classes of transmembrane receptors that are parts of signal transduction pathways in bacteria. Specifically, CHASE2 domains are found in histidine kinases, adenylate cyclases, serine/threonine kinases and predicted diguanylate cyclases/phosphodiesterases. Environmental factors that are recognised by CHASE2 domains are not known at this time. 303 matched cddid_all.tbl CDD smart01081 smart01081 215017 CHB_HEX Putative carbohydrate binding domain. This domain represents the N terminal domain in chitobiases and beta-hexosaminidases EC:3.2.1.52. It is composed of a beta sandwich structure that is similar in structure to the cellulose binding domain of cellulase from Cellulomonas fimi. This suggests that this may be a carbohydrate binding domain. 160 matched cddid_all.tbl CDD smart01082 smart01082 198150 CHZ Histone chaperone domain CHZ. This domain is highly conserved from yeasts to humans and is part of the chaperone protein HIRIP3 in vertebrates which interacts with the H3.3 chaperone HIRA, implicated in histone replacement during transcription. N- and C- termini of Chz family members are relatively divergent but do contain similar acidic stretches rich in Glu/Asp residues, characteristic of all histone chaperones. 38 matched cddid_all.tbl CDD smart01083 smart01083 198151 Cir_N N-terminal domain of CBF1 interacting co-repressor CIR. This is a 45 residue conserved region at the N-terminal end of a family of proteins referred to as CIRs (CBF1-interacting co-repressors). CBF1 (centromere-binding factor 1) acts as a transcription factor that causes repression by binding specifically to GTGGGAA motifs in responsive promoters, and it requires CIR as a co-repressor. CIR binds to histone deacetylase and to SAP30 and serves as a linker between CBF1 and the histone deacetylase complex. 37 matched cddid_all.tbl CDD smart01084 smart01084 198152 CKS Cyclin-dependent kinase regulatory subunit. Cyclin-dependent kinase regulatory subunit. 70 matched cddid_all.tbl CDD smart01085 smart01085 198153 CK_II_beta Casein kinase II regulatory subunit. 184 matched cddid_all.tbl CDD smart01086 smart01086 198154 ClpB_D2-small C-terminal, D2-small domain, of ClpB protein. This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit and thereby providing enough binding energy to stabilise the functional assembly. The domain is associated with two Clp_N at the N-terminus as well as AAA and AAA_2. 90 matched cddid_all.tbl CDD smart01087 smart01087 215018 COG6 Conserved oligomeric complex COG6. COG6 is a component of the conserved oligomeric golgi complex, which is composed of eight different subunits and is required for normal golgi morphology and localisation. 598 matched cddid_all.tbl CDD smart01088 smart01088 198156 Col_cuticle_N Nematode cuticle collagen N-terminal domain. The function of this domain is unknown. It is found in the N-terminal region of nematode cuticle collagens. Cuticle is a tough elastic structure secreted by hypodermal cells and is primarily composed of collagen proteins. 53 matched cddid_all.tbl CDD smart01089 smart01089 198157 Connexin_CCC Gap junction channel protein cysteine-rich domain. 67 matched cddid_all.tbl CDD smart01090 smart01090 215019 Copper-fist Copper fist is an N-terminal domain involved in copper-dependent DNA binding. The domain is named for its resemblance to a fist. It can be found in some fungal transcription factors. These proteins activate the transcription of the metallothionein gene in response to copper. Metallothionein maintains copper levels in yeast. The copper fist domain is similar in structure to metallothionein itself, and on copper binding undergoes a large conformational change, which allows DNA binding. 38 matched cddid_all.tbl CDD smart01091 smart01091 215020 CorC_HlyC Transporter associated domain. This small domain is found in a family of proteins with the DUF21 domain and two CBS domains with this domain found at the C-terminus of the proteins, the domain is also found at the C terminus of some Na+/H+ antiporters. This domain is also found in CorC that is involved in Magnesium and cobalt efflux. The function of this domain is uncertain but might be involved in modulating transport of ion substrates. 78 matched cddid_all.tbl CDD smart01092 smart01092 215021 CO_deh_flav_C CO dehydrogenase flavoprotein C-terminal domain. 102 matched cddid_all.tbl CDD smart01093 smart01093 198161 CP12 CP12 domain. 72 matched cddid_all.tbl CDD smart01094 smart01094 215022 CpcD CpcD/allophycocyanin linker domain. 51 matched cddid_all.tbl CDD smart01095 smart01095 198163 Cpl-7 Cpl-7 lysozyme C-terminal domain. This domain was originally found in the C-terminal moiety of the Cpl-7 lysozyme encoded by the Streptococcus pneumoniae bacteriophage Cp-7. It is assumed that these repeats represent cell wall binding motifs although no direct evidence has been obtained so far. 42 matched cddid_all.tbl CDD smart01096 smart01096 198164 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. 124 matched cddid_all.tbl CDD smart01097 smart01097 198165 CPSase_sm_chain Carbamoyl-phosphate synthase small chain, CPSase domain. The carbamoyl-phosphate synthase domain is in the amino terminus of protein. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesise carbamoyl phosphate. The small chain has a GATase domain in the carboxyl terminus. 130 matched cddid_all.tbl CDD smart01098 smart01098 215023 CPSF73-100_C This is the C-terminal conserved region of the pre-mRNA 3'-end-processing of the polyadenylation factor CPSF-73/CPSF-100 proteins. The exact function of this domain is not known. 212 matched cddid_all.tbl CDD smart01099 smart01099 198167 CPW_WPC This group of sequences is defined by a domain of about 61 residues in length with six well-conserved cysteine residues and six well-conserved aromatic sites. The domain can be found in tandem repeats, and is known so far only in Plasmodium falciparum. It is named for motifs of CPxxW and (less well conserved) WPC. Its function is unknown. 60 matched cddid_all.tbl CDD smart01100 smart01100 215024 CRAL_TRIO_N CRAL/TRIO, N-terminal domain. 48 matched cddid_all.tbl CDD smart01101 smart01101 215025 CRISPR_assoc This domain forms an anti-parallel beta strand structure with flanking alpha helical regions. 215 matched cddid_all.tbl CDD smart01102 smart01102 198170 CRM1_C CRM1 C terminal. CRM1 (also known as Exportin1) mediates the nuclear export of proteins bearing a leucine-rich nuclear export signal (NES). CRM1 forms a complex with the NES containing protein and the small GTPase Ran. This region forms an alpha helical structure formed by six helical hairpin motifs that are structurally similar to the HEAT repeat, but share little sequence similarity to the HEAT repeat. 321 matched cddid_all.tbl CDD smart01103 smart01103 198171 CRS1_YhbY Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome. 84 matched cddid_all.tbl CDD smart01104 smart01104 215026 CTD Spt5 C-terminal nonapeptide repeat binding Spt4. The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif. 121 matched cddid_all.tbl